Multiple sequence alignment - TraesCS4A01G432000

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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 TraesCS4A01G432000 chr4A 100.000 2757 0 0 1 2757 702504246 702507002 0.000000e+00 5092
1 TraesCS4A01G432000 chr4A 86.728 1085 114 6 678 1757 702339673 702340732 0.000000e+00 1179
2 TraesCS4A01G432000 chr4A 91.008 645 53 3 1 643 702339030 702339671 0.000000e+00 865
3 TraesCS4A01G432000 chr4A 85.159 849 116 8 913 1755 701312310 701311466 0.000000e+00 861
4 TraesCS4A01G432000 chr4A 81.850 865 114 14 909 1754 702381047 702381887 0.000000e+00 688
5 TraesCS4A01G432000 chr4A 80.976 820 124 22 1 804 702380003 702380806 3.020000e-174 621
6 TraesCS4A01G432000 chr4A 82.564 585 88 14 233 809 701313071 701312493 1.140000e-138 503
7 TraesCS4A01G432000 chr1B 99.600 1001 4 0 1757 2757 639015672 639014672 0.000000e+00 1827
8 TraesCS4A01G432000 chr1B 94.810 1002 51 1 1757 2757 129135555 129134554 0.000000e+00 1561
9 TraesCS4A01G432000 chr2B 99.300 1000 7 0 1758 2757 18682629 18683628 0.000000e+00 1808
10 TraesCS4A01G432000 chr2B 99.201 1001 8 0 1757 2757 642828111 642827111 0.000000e+00 1805
11 TraesCS4A01G432000 chr7A 99.101 1001 8 1 1757 2757 529274223 529275222 0.000000e+00 1797
12 TraesCS4A01G432000 chr7A 84.970 845 115 5 913 1755 29110573 29111407 0.000000e+00 846
13 TraesCS4A01G432000 chr7A 85.623 779 107 3 912 1688 29033262 29034037 0.000000e+00 813
14 TraesCS4A01G432000 chr7A 83.333 822 113 20 1 807 29109576 29110388 0.000000e+00 737
15 TraesCS4A01G432000 chr6B 99.001 1001 7 1 1757 2757 356868169 356869166 0.000000e+00 1790
16 TraesCS4A01G432000 chr6B 98.996 996 10 0 1757 2752 401431865 401430870 0.000000e+00 1784
17 TraesCS4A01G432000 chr3A 98.902 1002 9 2 1757 2757 31839043 31838043 0.000000e+00 1788
18 TraesCS4A01G432000 chr5B 97.502 1001 25 0 1757 2757 39717615 39718615 0.000000e+00 1711
19 TraesCS4A01G432000 chr7D 86.187 847 110 5 913 1755 28696827 28697670 0.000000e+00 909
20 TraesCS4A01G432000 chr7D 85.884 843 99 6 915 1754 28674868 28675693 0.000000e+00 880
21 TraesCS4A01G432000 chr7D 83.883 819 111 18 1 807 28695833 28696642 0.000000e+00 761
22 TraesCS4A01G432000 chr7D 82.843 816 124 13 1 804 28673856 28674667 0.000000e+00 717


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 TraesCS4A01G432000 chr4A 702504246 702507002 2756 False 5092.0 5092 100.0000 1 2757 1 chr4A.!!$F1 2756
1 TraesCS4A01G432000 chr4A 702339030 702340732 1702 False 1022.0 1179 88.8680 1 1757 2 chr4A.!!$F2 1756
2 TraesCS4A01G432000 chr4A 701311466 701313071 1605 True 682.0 861 83.8615 233 1755 2 chr4A.!!$R1 1522
3 TraesCS4A01G432000 chr4A 702380003 702381887 1884 False 654.5 688 81.4130 1 1754 2 chr4A.!!$F3 1753
4 TraesCS4A01G432000 chr1B 639014672 639015672 1000 True 1827.0 1827 99.6000 1757 2757 1 chr1B.!!$R2 1000
5 TraesCS4A01G432000 chr1B 129134554 129135555 1001 True 1561.0 1561 94.8100 1757 2757 1 chr1B.!!$R1 1000
6 TraesCS4A01G432000 chr2B 18682629 18683628 999 False 1808.0 1808 99.3000 1758 2757 1 chr2B.!!$F1 999
7 TraesCS4A01G432000 chr2B 642827111 642828111 1000 True 1805.0 1805 99.2010 1757 2757 1 chr2B.!!$R1 1000
8 TraesCS4A01G432000 chr7A 529274223 529275222 999 False 1797.0 1797 99.1010 1757 2757 1 chr7A.!!$F2 1000
9 TraesCS4A01G432000 chr7A 29033262 29034037 775 False 813.0 813 85.6230 912 1688 1 chr7A.!!$F1 776
10 TraesCS4A01G432000 chr7A 29109576 29111407 1831 False 791.5 846 84.1515 1 1755 2 chr7A.!!$F3 1754
11 TraesCS4A01G432000 chr6B 356868169 356869166 997 False 1790.0 1790 99.0010 1757 2757 1 chr6B.!!$F1 1000
12 TraesCS4A01G432000 chr6B 401430870 401431865 995 True 1784.0 1784 98.9960 1757 2752 1 chr6B.!!$R1 995
13 TraesCS4A01G432000 chr3A 31838043 31839043 1000 True 1788.0 1788 98.9020 1757 2757 1 chr3A.!!$R1 1000
14 TraesCS4A01G432000 chr5B 39717615 39718615 1000 False 1711.0 1711 97.5020 1757 2757 1 chr5B.!!$F1 1000
15 TraesCS4A01G432000 chr7D 28695833 28697670 1837 False 835.0 909 85.0350 1 1755 2 chr7D.!!$F2 1754
16 TraesCS4A01G432000 chr7D 28673856 28675693 1837 False 798.5 880 84.3635 1 1754 2 chr7D.!!$F1 1753

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
63 64 0.958822 GCAGGATTTGGTTGGTTCGT 59.041 50.0 0.0 0.0 0.00 3.85 F
1302 1523 0.179045 ATTCCGACCAGCCATACTGC 60.179 55.0 0.0 0.0 45.78 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1528 1755 0.107456 CTCTTGCACACCACCTCACT 59.893 55.000 0.0 0.0 0.0 3.41 R
2232 2476 5.741011 TGATACCTTTTGCCCTAACTGTAG 58.259 41.667 0.0 0.0 0.0 2.74 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
40 41 4.463070 ACGGGGTTTGTGTTTTACTACAT 58.537 39.130 0.00 0.00 0.00 2.29
63 64 0.958822 GCAGGATTTGGTTGGTTCGT 59.041 50.000 0.00 0.00 0.00 3.85
231 238 5.746990 TTGAAGAAGAAGTAGAGAAGGGG 57.253 43.478 0.00 0.00 0.00 4.79
252 259 6.016555 GGGGGTGAATATATTTAGTTGGCAT 58.983 40.000 0.00 0.00 0.00 4.40
272 279 4.627035 GCATTTTGAGTTAATGAGGGCAAC 59.373 41.667 0.00 0.00 35.49 4.17
286 293 4.469586 TGAGGGCAACTGAATAGTATGTGA 59.530 41.667 0.00 0.00 35.69 3.58
288 295 5.371526 AGGGCAACTGAATAGTATGTGATG 58.628 41.667 0.00 0.00 35.69 3.07
336 346 6.721208 AGGCATGTGATTCTTAAGAGGAAAAA 59.279 34.615 5.12 0.00 0.00 1.94
374 384 9.273016 CACAAATAGAAATATACACAGTAGGGG 57.727 37.037 0.00 0.00 0.00 4.79
375 385 8.437575 ACAAATAGAAATATACACAGTAGGGGG 58.562 37.037 0.00 0.00 0.00 5.40
395 405 3.398318 GGGGGACTCCATATTGGTTTT 57.602 47.619 0.00 0.00 39.03 2.43
554 570 7.649533 TCATCCAAATTAACTTGCTCATGAT 57.350 32.000 0.00 0.00 0.00 2.45
570 586 9.481340 TTGCTCATGATACAATCTAGATGTAAC 57.519 33.333 5.86 9.95 36.88 2.50
643 660 7.596749 AAGTACTCTTCAAAATACCACATCG 57.403 36.000 0.00 0.00 0.00 3.84
644 661 6.698380 AGTACTCTTCAAAATACCACATCGT 58.302 36.000 0.00 0.00 0.00 3.73
645 662 5.862924 ACTCTTCAAAATACCACATCGTG 57.137 39.130 0.00 0.00 0.00 4.35
646 663 5.305585 ACTCTTCAAAATACCACATCGTGT 58.694 37.500 0.00 0.00 0.00 4.49
647 664 5.763204 ACTCTTCAAAATACCACATCGTGTT 59.237 36.000 0.00 0.00 0.00 3.32
648 665 6.932400 ACTCTTCAAAATACCACATCGTGTTA 59.068 34.615 0.00 0.00 0.00 2.41
649 666 7.442969 ACTCTTCAAAATACCACATCGTGTTAA 59.557 33.333 0.00 0.00 0.00 2.01
650 667 7.577979 TCTTCAAAATACCACATCGTGTTAAC 58.422 34.615 0.00 0.00 0.00 2.01
669 686 9.026074 GTGTTAACGAGAATTTTGAAAAATGGA 57.974 29.630 0.26 0.00 38.53 3.41
670 687 9.757227 TGTTAACGAGAATTTTGAAAAATGGAT 57.243 25.926 0.26 0.00 38.53 3.41
672 689 7.889589 AACGAGAATTTTGAAAAATGGATCC 57.110 32.000 4.20 4.20 38.53 3.36
673 690 6.991938 ACGAGAATTTTGAAAAATGGATCCA 58.008 32.000 18.88 18.88 38.53 3.41
674 691 7.441017 ACGAGAATTTTGAAAAATGGATCCAA 58.559 30.769 20.67 1.96 38.53 3.53
675 692 7.930865 ACGAGAATTTTGAAAAATGGATCCAAA 59.069 29.630 20.67 6.08 38.53 3.28
676 693 8.437742 CGAGAATTTTGAAAAATGGATCCAAAG 58.562 33.333 20.67 0.00 38.53 2.77
721 771 2.674357 TGTAATTTCGAACTAAGGCCGC 59.326 45.455 0.00 0.00 0.00 6.53
774 824 8.924511 AATTTGAGAGGAAACAGTTCAATCTA 57.075 30.769 0.00 0.00 33.68 1.98
809 859 2.107366 TGCATGGAGGAGATGACGTTA 58.893 47.619 0.00 0.00 0.00 3.18
810 860 2.499693 TGCATGGAGGAGATGACGTTAA 59.500 45.455 0.00 0.00 0.00 2.01
811 861 3.134623 TGCATGGAGGAGATGACGTTAAT 59.865 43.478 0.00 0.00 0.00 1.40
812 862 3.496130 GCATGGAGGAGATGACGTTAATG 59.504 47.826 0.00 0.00 0.00 1.90
813 863 3.819564 TGGAGGAGATGACGTTAATGG 57.180 47.619 0.00 0.00 0.00 3.16
814 864 3.104512 TGGAGGAGATGACGTTAATGGT 58.895 45.455 0.00 0.00 0.00 3.55
815 865 3.118775 TGGAGGAGATGACGTTAATGGTG 60.119 47.826 0.00 0.00 0.00 4.17
816 866 3.118738 GGAGGAGATGACGTTAATGGTGT 60.119 47.826 0.00 0.00 0.00 4.16
817 867 4.504858 GAGGAGATGACGTTAATGGTGTT 58.495 43.478 0.00 0.00 0.00 3.32
818 868 4.906618 AGGAGATGACGTTAATGGTGTTT 58.093 39.130 0.00 0.00 0.00 2.83
819 869 4.695455 AGGAGATGACGTTAATGGTGTTTG 59.305 41.667 0.00 0.00 0.00 2.93
820 870 4.693566 GGAGATGACGTTAATGGTGTTTGA 59.306 41.667 0.00 0.00 0.00 2.69
821 871 5.163854 GGAGATGACGTTAATGGTGTTTGAG 60.164 44.000 0.00 0.00 0.00 3.02
822 872 5.547465 AGATGACGTTAATGGTGTTTGAGA 58.453 37.500 0.00 0.00 0.00 3.27
823 873 5.639506 AGATGACGTTAATGGTGTTTGAGAG 59.360 40.000 0.00 0.00 0.00 3.20
824 874 4.062293 TGACGTTAATGGTGTTTGAGAGG 58.938 43.478 0.00 0.00 0.00 3.69
825 875 4.202274 TGACGTTAATGGTGTTTGAGAGGA 60.202 41.667 0.00 0.00 0.00 3.71
826 876 4.710324 ACGTTAATGGTGTTTGAGAGGAA 58.290 39.130 0.00 0.00 0.00 3.36
827 877 5.127491 ACGTTAATGGTGTTTGAGAGGAAA 58.873 37.500 0.00 0.00 0.00 3.13
828 878 5.008316 ACGTTAATGGTGTTTGAGAGGAAAC 59.992 40.000 0.00 0.00 36.53 2.78
829 879 5.008217 CGTTAATGGTGTTTGAGAGGAAACA 59.992 40.000 0.00 0.00 42.26 2.83
830 880 6.438763 GTTAATGGTGTTTGAGAGGAAACAG 58.561 40.000 0.00 0.00 44.47 3.16
831 881 3.644966 TGGTGTTTGAGAGGAAACAGT 57.355 42.857 0.00 0.00 44.47 3.55
832 882 3.963129 TGGTGTTTGAGAGGAAACAGTT 58.037 40.909 0.00 0.00 44.47 3.16
882 936 9.978044 CATACCAAGGTACTAAGTAGGATAAAC 57.022 37.037 0.14 0.00 38.49 2.01
889 943 9.336171 AGGTACTAAGTAGGATAAACTCTTACG 57.664 37.037 0.00 0.00 38.03 3.18
948 1160 6.612049 CACTATATAAACCCTATCCTCCTCCC 59.388 46.154 0.00 0.00 0.00 4.30
991 1211 6.666417 CAGTTGAATCCTCTCAAAGACAAAG 58.334 40.000 0.00 0.00 37.08 2.77
999 1220 4.133078 CTCTCAAAGACAAAGGAGCAAGT 58.867 43.478 0.00 0.00 0.00 3.16
1005 1226 2.706190 AGACAAAGGAGCAAGTACCACT 59.294 45.455 0.00 0.00 0.00 4.00
1019 1240 6.289064 CAAGTACCACTTTTTCTACCAGACT 58.711 40.000 0.00 0.00 36.03 3.24
1064 1285 1.879372 GCATCATCTTGGCGCTCCATA 60.879 52.381 7.64 0.00 43.05 2.74
1075 1296 1.888215 CGCTCCATAGCCATGTCATT 58.112 50.000 0.00 0.00 46.68 2.57
1091 1312 2.819608 GTCATTGGCCTCACTGCTAAAA 59.180 45.455 3.32 0.00 35.26 1.52
1092 1313 3.255642 GTCATTGGCCTCACTGCTAAAAA 59.744 43.478 3.32 0.00 35.26 1.94
1107 1328 4.644685 TGCTAAAAAGATTCAGGGGCATAC 59.355 41.667 0.00 0.00 0.00 2.39
1140 1361 1.765074 GGGTGCCTCTACAACCCAA 59.235 57.895 5.22 0.00 41.96 4.12
1184 1405 3.709653 TCTCGGCTATTATGGAACCAACT 59.290 43.478 0.00 0.00 0.00 3.16
1191 1412 2.512692 TATGGAACCAACTGCTGCAT 57.487 45.000 1.31 0.00 0.00 3.96
1195 1416 0.953727 GAACCAACTGCTGCATGTCA 59.046 50.000 1.31 0.00 0.00 3.58
1197 1418 1.624336 ACCAACTGCTGCATGTCAAT 58.376 45.000 1.31 0.00 0.00 2.57
1226 1447 0.250901 GGCCTCATATCCACGCCAAT 60.251 55.000 0.00 0.00 39.50 3.16
1276 1497 4.407296 ACCAAACCTTTGTTGGAGCAATAA 59.593 37.500 10.07 0.00 36.45 1.40
1290 1511 1.604278 GCAATAAGAGGCCATTCCGAC 59.396 52.381 5.01 0.00 40.77 4.79
1302 1523 0.179045 ATTCCGACCAGCCATACTGC 60.179 55.000 0.00 0.00 45.78 4.40
1326 1547 2.590007 GTCTATGCCGCTGCTGGG 60.590 66.667 0.70 0.25 38.71 4.45
1364 1585 7.066284 ACCATCTACATGTTCAAGTAAGCAATC 59.934 37.037 2.30 0.00 0.00 2.67
1371 1592 5.688823 TGTTCAAGTAAGCAATCGATTGTG 58.311 37.500 32.52 23.25 39.88 3.33
1377 1598 3.729526 AAGCAATCGATTGTGAAGTCG 57.270 42.857 32.52 11.03 39.88 4.18
1475 1702 5.488919 AGAGGTGAGATGGGATTCTGTAAAA 59.511 40.000 0.00 0.00 0.00 1.52
1525 1752 5.280654 AGCAATTGGAAAAACAGACACAT 57.719 34.783 7.72 0.00 0.00 3.21
1527 1754 6.215845 AGCAATTGGAAAAACAGACACATAC 58.784 36.000 7.72 0.00 0.00 2.39
1528 1755 5.982516 GCAATTGGAAAAACAGACACATACA 59.017 36.000 7.72 0.00 0.00 2.29
1542 1769 1.270839 ACATACAGTGAGGTGGTGTGC 60.271 52.381 0.00 0.00 0.00 4.57
1688 1928 6.314917 AGGACTGGAACCTATTTTTCACAAT 58.685 36.000 0.00 0.00 35.84 2.71
1727 1969 8.332777 GCTTTTGCAAGTAATAGAACATGATC 57.667 34.615 0.00 0.00 46.58 2.92
2232 2476 2.225255 GGAGTTTCTTCTGCTTGCTGAC 59.775 50.000 1.73 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 0.105760 ACCAACCAAATCCTGCACCA 60.106 50.000 0.00 0.00 0.00 4.17
110 114 6.809976 ACTTAAGGGATAGTTCCTTAGTGG 57.190 41.667 7.53 0.00 44.68 4.00
162 166 5.801947 GTGTTTCTTTCGTTCGGTATAGCTA 59.198 40.000 0.00 0.00 0.00 3.32
252 259 5.136828 TCAGTTGCCCTCATTAACTCAAAA 58.863 37.500 0.00 0.00 32.69 2.44
272 279 5.463392 CGGTCCAACATCACATACTATTCAG 59.537 44.000 0.00 0.00 0.00 3.02
286 293 0.392461 CATTCGTCCCGGTCCAACAT 60.392 55.000 0.00 0.00 0.00 2.71
288 295 0.320946 TTCATTCGTCCCGGTCCAAC 60.321 55.000 0.00 0.00 0.00 3.77
340 350 9.884465 GTGTATATTTCTATTTGTGAATCTGGC 57.116 33.333 0.00 0.00 0.00 4.85
349 359 8.437575 CCCCCTACTGTGTATATTTCTATTTGT 58.562 37.037 0.00 0.00 0.00 2.83
375 385 3.296854 GAAAACCAATATGGAGTCCCCC 58.703 50.000 6.74 0.00 40.96 5.40
376 386 3.052869 AGGAAAACCAATATGGAGTCCCC 60.053 47.826 6.74 0.00 40.96 4.81
377 387 4.251103 AGGAAAACCAATATGGAGTCCC 57.749 45.455 6.74 0.00 40.96 4.46
379 389 8.981724 GTTTTTAGGAAAACCAATATGGAGTC 57.018 34.615 2.85 0.00 45.64 3.36
395 405 8.098286 TGGAGAAACTCATAATCGTTTTTAGGA 58.902 33.333 0.00 0.00 33.82 2.94
506 521 4.392138 AGATGGCTAGTTTTAACTCGCAAC 59.608 41.667 17.43 9.81 46.15 4.17
531 547 8.407832 TGTATCATGAGCAAGTTAATTTGGATG 58.592 33.333 12.08 0.00 0.00 3.51
643 660 9.026074 TCCATTTTTCAAAATTCTCGTTAACAC 57.974 29.630 6.39 0.00 36.52 3.32
644 661 9.757227 ATCCATTTTTCAAAATTCTCGTTAACA 57.243 25.926 6.39 0.00 36.52 2.41
646 663 9.418045 GGATCCATTTTTCAAAATTCTCGTTAA 57.582 29.630 6.95 0.00 36.52 2.01
647 664 8.580720 TGGATCCATTTTTCAAAATTCTCGTTA 58.419 29.630 11.44 0.00 36.52 3.18
648 665 7.441017 TGGATCCATTTTTCAAAATTCTCGTT 58.559 30.769 11.44 0.00 36.52 3.85
649 666 6.991938 TGGATCCATTTTTCAAAATTCTCGT 58.008 32.000 11.44 0.00 36.52 4.18
650 667 7.887996 TTGGATCCATTTTTCAAAATTCTCG 57.112 32.000 17.06 0.00 36.52 4.04
651 668 9.276590 ACTTTGGATCCATTTTTCAAAATTCTC 57.723 29.630 17.06 0.00 36.52 2.87
652 669 9.276590 GACTTTGGATCCATTTTTCAAAATTCT 57.723 29.630 17.06 0.00 36.52 2.40
653 670 8.506437 GGACTTTGGATCCATTTTTCAAAATTC 58.494 33.333 17.06 7.70 36.52 2.17
654 671 7.997803 TGGACTTTGGATCCATTTTTCAAAATT 59.002 29.630 17.06 0.00 41.47 1.82
655 672 7.516452 TGGACTTTGGATCCATTTTTCAAAAT 58.484 30.769 17.06 0.00 41.47 1.82
656 673 6.893583 TGGACTTTGGATCCATTTTTCAAAA 58.106 32.000 17.06 2.99 41.47 2.44
657 674 6.491714 TGGACTTTGGATCCATTTTTCAAA 57.508 33.333 17.06 3.79 41.47 2.69
658 675 6.287525 GTTGGACTTTGGATCCATTTTTCAA 58.712 36.000 17.06 14.48 45.71 2.69
659 676 5.508825 CGTTGGACTTTGGATCCATTTTTCA 60.509 40.000 17.06 9.22 45.71 2.69
660 677 4.923281 CGTTGGACTTTGGATCCATTTTTC 59.077 41.667 17.06 9.70 45.71 2.29
661 678 4.799255 GCGTTGGACTTTGGATCCATTTTT 60.799 41.667 17.06 0.00 45.71 1.94
662 679 3.306019 GCGTTGGACTTTGGATCCATTTT 60.306 43.478 17.06 1.79 45.71 1.82
663 680 2.231235 GCGTTGGACTTTGGATCCATTT 59.769 45.455 17.06 2.20 45.71 2.32
664 681 1.818674 GCGTTGGACTTTGGATCCATT 59.181 47.619 17.06 2.62 45.71 3.16
665 682 1.271871 TGCGTTGGACTTTGGATCCAT 60.272 47.619 17.06 0.00 45.71 3.41
666 683 0.109532 TGCGTTGGACTTTGGATCCA 59.890 50.000 11.44 11.44 44.74 3.41
667 684 1.243902 TTGCGTTGGACTTTGGATCC 58.756 50.000 4.20 4.20 36.70 3.36
668 685 3.049912 GTTTTGCGTTGGACTTTGGATC 58.950 45.455 0.00 0.00 0.00 3.36
669 686 2.223947 GGTTTTGCGTTGGACTTTGGAT 60.224 45.455 0.00 0.00 0.00 3.41
670 687 1.135333 GGTTTTGCGTTGGACTTTGGA 59.865 47.619 0.00 0.00 0.00 3.53
671 688 1.136110 AGGTTTTGCGTTGGACTTTGG 59.864 47.619 0.00 0.00 0.00 3.28
672 689 2.577449 AGGTTTTGCGTTGGACTTTG 57.423 45.000 0.00 0.00 0.00 2.77
673 690 3.056465 TGAAAGGTTTTGCGTTGGACTTT 60.056 39.130 0.00 0.00 0.00 2.66
674 691 2.494073 TGAAAGGTTTTGCGTTGGACTT 59.506 40.909 0.00 0.00 0.00 3.01
675 692 2.096248 TGAAAGGTTTTGCGTTGGACT 58.904 42.857 0.00 0.00 0.00 3.85
676 693 2.570442 TGAAAGGTTTTGCGTTGGAC 57.430 45.000 0.00 0.00 0.00 4.02
721 771 6.647895 TGTGATACTGCTGCATTACATAGATG 59.352 38.462 1.31 0.00 0.00 2.90
739 789 6.655003 TGTTTCCTCTCAAATTCCTGTGATAC 59.345 38.462 0.00 0.00 0.00 2.24
774 824 5.068198 CCTCCATGCAATTTACTACAAGCAT 59.932 40.000 0.00 0.00 42.82 3.79
809 859 4.536765 ACTGTTTCCTCTCAAACACCATT 58.463 39.130 0.00 0.00 40.57 3.16
810 860 4.170468 ACTGTTTCCTCTCAAACACCAT 57.830 40.909 0.00 0.00 40.57 3.55
811 861 3.644966 ACTGTTTCCTCTCAAACACCA 57.355 42.857 0.00 0.00 40.57 4.17
812 862 3.002348 CGAACTGTTTCCTCTCAAACACC 59.998 47.826 0.00 0.00 40.57 4.16
813 863 3.869246 TCGAACTGTTTCCTCTCAAACAC 59.131 43.478 0.00 0.00 40.57 3.32
814 864 3.869246 GTCGAACTGTTTCCTCTCAAACA 59.131 43.478 0.00 0.00 42.68 2.83
815 865 3.247886 GGTCGAACTGTTTCCTCTCAAAC 59.752 47.826 0.00 0.00 36.87 2.93
816 866 3.134081 AGGTCGAACTGTTTCCTCTCAAA 59.866 43.478 0.00 0.00 0.00 2.69
817 867 2.698797 AGGTCGAACTGTTTCCTCTCAA 59.301 45.455 0.00 0.00 0.00 3.02
818 868 2.317040 AGGTCGAACTGTTTCCTCTCA 58.683 47.619 0.00 0.00 0.00 3.27
819 869 4.516365 TTAGGTCGAACTGTTTCCTCTC 57.484 45.455 14.77 0.00 0.00 3.20
820 870 4.322801 CCATTAGGTCGAACTGTTTCCTCT 60.323 45.833 14.77 5.01 0.00 3.69
821 871 3.933332 CCATTAGGTCGAACTGTTTCCTC 59.067 47.826 14.77 0.00 0.00 3.71
822 872 3.939066 CCATTAGGTCGAACTGTTTCCT 58.061 45.455 14.77 3.17 0.00 3.36
831 881 8.174737 TGGAAACATTAACACCATTAGGTCGAA 61.175 37.037 0.00 0.00 40.85 3.71
832 882 6.744622 TGGAAACATTAACACCATTAGGTCGA 60.745 38.462 0.00 0.00 40.85 4.20
851 901 7.124750 TCCTACTTAGTACCTTGGTATGGAAAC 59.875 40.741 2.59 0.00 0.00 2.78
856 910 9.978044 GTTTATCCTACTTAGTACCTTGGTATG 57.022 37.037 2.59 0.00 0.00 2.39
991 1211 4.454847 GGTAGAAAAAGTGGTACTTGCTCC 59.545 45.833 0.00 0.00 38.66 4.70
999 1220 5.607477 CACAGTCTGGTAGAAAAAGTGGTA 58.393 41.667 4.53 0.00 0.00 3.25
1005 1226 3.315191 GCAAGCACAGTCTGGTAGAAAAA 59.685 43.478 4.53 0.00 0.00 1.94
1019 1240 2.367894 TGGAATTTCCATTGCAAGCACA 59.632 40.909 14.24 0.00 42.67 4.57
1075 1296 2.949177 TCTTTTTAGCAGTGAGGCCA 57.051 45.000 5.01 0.00 0.00 5.36
1091 1312 1.922447 TGTGGTATGCCCCTGAATCTT 59.078 47.619 0.00 0.00 0.00 2.40
1092 1313 1.492176 CTGTGGTATGCCCCTGAATCT 59.508 52.381 0.00 0.00 0.00 2.40
1107 1328 1.528309 ACCCTTTTGGCGACTGTGG 60.528 57.895 0.00 0.00 37.83 4.17
1129 1350 2.564062 CCGGTACTCTTTGGGTTGTAGA 59.436 50.000 0.00 0.00 0.00 2.59
1191 1412 0.321021 GGCCCAACAATGCATTGACA 59.679 50.000 38.99 0.00 40.14 3.58
1195 1416 1.575419 ATGAGGCCCAACAATGCATT 58.425 45.000 5.99 5.99 0.00 3.56
1197 1418 2.309613 GATATGAGGCCCAACAATGCA 58.690 47.619 0.00 0.00 0.00 3.96
1205 1426 2.818169 GGCGTGGATATGAGGCCCA 61.818 63.158 0.00 0.00 38.24 5.36
1226 1447 1.448119 CCTCTAGGATCTCACGCGCA 61.448 60.000 5.73 0.00 37.39 6.09
1276 1497 3.036429 GCTGGTCGGAATGGCCTCT 62.036 63.158 3.32 0.00 0.00 3.69
1320 1541 3.702048 GCCACTACCGACCCAGCA 61.702 66.667 0.00 0.00 0.00 4.41
1326 1547 1.108776 TAGATGGTGCCACTACCGAC 58.891 55.000 0.00 0.00 43.87 4.79
1364 1585 1.148310 AAGTGCCGACTTCACAATCG 58.852 50.000 0.00 0.00 38.01 3.34
1377 1598 0.466372 GGATGCTAAGGGGAAGTGCC 60.466 60.000 0.00 0.00 0.00 5.01
1500 1727 3.960102 TGTCTGTTTTTCCAATTGCTCCT 59.040 39.130 0.00 0.00 0.00 3.69
1525 1752 0.833949 TTGCACACCACCTCACTGTA 59.166 50.000 0.00 0.00 0.00 2.74
1527 1754 0.179048 TCTTGCACACCACCTCACTG 60.179 55.000 0.00 0.00 0.00 3.66
1528 1755 0.107456 CTCTTGCACACCACCTCACT 59.893 55.000 0.00 0.00 0.00 3.41
1542 1769 1.691196 TGGTGGCACCTTTTCTCTTG 58.309 50.000 34.69 0.00 39.58 3.02
1570 1797 2.035632 CTCTGGTCGCCTTCCTTATCT 58.964 52.381 0.00 0.00 0.00 1.98
1648 1888 4.141390 CCAGTCCTTCTAAGCCCATACAAT 60.141 45.833 0.00 0.00 0.00 2.71
1649 1889 3.199946 CCAGTCCTTCTAAGCCCATACAA 59.800 47.826 0.00 0.00 0.00 2.41
1688 1928 5.521906 TGCAAAAGCACCAAGTTATACAA 57.478 34.783 0.00 0.00 0.00 2.41
1709 1949 8.352752 TGCTAACGATCATGTTCTATTACTTG 57.647 34.615 2.44 0.00 33.32 3.16
1727 1969 7.748683 TCAAAAGTGTATTGCTATTTGCTAACG 59.251 33.333 0.00 0.00 43.37 3.18
2232 2476 5.741011 TGATACCTTTTGCCCTAACTGTAG 58.259 41.667 0.00 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.