Multiple sequence alignment - TraesCS2D01G226700

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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 TraesCS2D01G226700 chr2D 100.000 2204 0 0 405 2608 194764515 194762312 0.000000e+00 4071.0
1 TraesCS2D01G226700 chr2D 100.000 229 0 0 1 229 194764919 194764691 8.630000e-115 424.0
2 TraesCS2D01G226700 chr2B 93.217 1784 73 19 863 2607 250744472 250742698 0.000000e+00 2580.0
3 TraesCS2D01G226700 chr2B 84.211 475 42 16 419 864 250771238 250770768 5.160000e-117 431.0
4 TraesCS2D01G226700 chr2B 96.330 109 3 1 1 108 623511577 623511685 7.420000e-41 178.0
5 TraesCS2D01G226700 chr2A 92.171 1852 79 23 797 2608 209396491 209394666 0.000000e+00 2556.0
6 TraesCS2D01G226700 chr2A 87.887 355 24 9 405 749 209397191 209396846 1.450000e-107 399.0
7 TraesCS2D01G226700 chr2A 91.803 122 8 2 109 229 209397378 209397258 4.460000e-38 169.0
8 TraesCS2D01G226700 chr2A 89.796 98 8 2 109 205 357487590 357487686 9.800000e-25 124.0
9 TraesCS2D01G226700 chr2A 89.394 66 5 2 109 173 187505872 187505808 5.980000e-12 82.4
10 TraesCS2D01G226700 chr4D 97.248 109 2 1 1 108 372423755 372423863 1.590000e-42 183.0
11 TraesCS2D01G226700 chr4D 96.364 110 3 1 1 109 304641056 304640947 2.060000e-41 180.0
12 TraesCS2D01G226700 chr4D 94.737 114 4 2 1 112 461592429 461592316 2.670000e-40 176.0
13 TraesCS2D01G226700 chrUn 96.364 110 2 2 1 108 243517116 243517225 2.060000e-41 180.0
14 TraesCS2D01G226700 chr1B 96.364 110 2 2 1 108 45477568 45477677 2.060000e-41 180.0
15 TraesCS2D01G226700 chr6D 94.783 115 3 3 1 113 353764584 353764697 2.670000e-40 176.0
16 TraesCS2D01G226700 chr6D 94.017 117 4 3 1 115 378373734 378373849 9.590000e-40 174.0
17 TraesCS2D01G226700 chr4A 93.277 119 6 2 1 117 550916183 550916301 9.590000e-40 174.0
18 TraesCS2D01G226700 chr7D 79.200 125 15 9 109 228 209572045 209572163 2.780000e-10 76.8


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 TraesCS2D01G226700 chr2D 194762312 194764919 2607 True 2247.500000 4071 100.000000 1 2608 2 chr2D.!!$R1 2607
1 TraesCS2D01G226700 chr2B 250742698 250744472 1774 True 2580.000000 2580 93.217000 863 2607 1 chr2B.!!$R1 1744
2 TraesCS2D01G226700 chr2A 209394666 209397378 2712 True 1041.333333 2556 90.620333 109 2608 3 chr2A.!!$R2 2499

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
33 34 0.040499 AGACACACTCTCCCCCTCTC 59.96 60.0 0.0 0.0 0.0 3.2 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1668 1993 1.103803 CGGCTAAGCTCACTCTACCA 58.896 55.0 0.0 0.0 0.0 3.25 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
20 21 2.760634 TACGAGGGTACGTAGACACA 57.239 50.000 0.00 0.00 44.72 3.72
21 22 1.160137 ACGAGGGTACGTAGACACAC 58.840 55.000 0.00 0.00 44.72 3.82
22 23 1.271054 ACGAGGGTACGTAGACACACT 60.271 52.381 0.00 0.00 44.72 3.55
23 24 1.396301 CGAGGGTACGTAGACACACTC 59.604 57.143 8.17 8.17 40.93 3.51
24 25 2.709213 GAGGGTACGTAGACACACTCT 58.291 52.381 10.55 0.00 41.06 3.24
25 26 2.677337 GAGGGTACGTAGACACACTCTC 59.323 54.545 10.55 4.79 41.06 3.20
26 27 1.742268 GGGTACGTAGACACACTCTCC 59.258 57.143 0.00 0.00 0.00 3.71
27 28 1.742268 GGTACGTAGACACACTCTCCC 59.258 57.143 0.00 0.00 0.00 4.30
28 29 1.742268 GTACGTAGACACACTCTCCCC 59.258 57.143 0.00 0.00 0.00 4.81
29 30 0.611340 ACGTAGACACACTCTCCCCC 60.611 60.000 0.00 0.00 0.00 5.40
30 31 0.323542 CGTAGACACACTCTCCCCCT 60.324 60.000 0.00 0.00 0.00 4.79
31 32 1.476477 GTAGACACACTCTCCCCCTC 58.524 60.000 0.00 0.00 0.00 4.30
32 33 1.006162 GTAGACACACTCTCCCCCTCT 59.994 57.143 0.00 0.00 0.00 3.69
33 34 0.040499 AGACACACTCTCCCCCTCTC 59.960 60.000 0.00 0.00 0.00 3.20
34 35 1.304547 ACACACTCTCCCCCTCTCG 60.305 63.158 0.00 0.00 0.00 4.04
35 36 1.304547 CACACTCTCCCCCTCTCGT 60.305 63.158 0.00 0.00 0.00 4.18
36 37 0.900647 CACACTCTCCCCCTCTCGTT 60.901 60.000 0.00 0.00 0.00 3.85
37 38 0.900647 ACACTCTCCCCCTCTCGTTG 60.901 60.000 0.00 0.00 0.00 4.10
38 39 1.985116 ACTCTCCCCCTCTCGTTGC 60.985 63.158 0.00 0.00 0.00 4.17
39 40 1.684049 CTCTCCCCCTCTCGTTGCT 60.684 63.158 0.00 0.00 0.00 3.91
40 41 0.395862 CTCTCCCCCTCTCGTTGCTA 60.396 60.000 0.00 0.00 0.00 3.49
41 42 0.261991 TCTCCCCCTCTCGTTGCTAT 59.738 55.000 0.00 0.00 0.00 2.97
42 43 0.390860 CTCCCCCTCTCGTTGCTATG 59.609 60.000 0.00 0.00 0.00 2.23
43 44 1.227674 CCCCCTCTCGTTGCTATGC 60.228 63.158 0.00 0.00 0.00 3.14
44 45 1.522092 CCCCTCTCGTTGCTATGCA 59.478 57.895 0.00 0.00 36.47 3.96
45 46 0.107456 CCCCTCTCGTTGCTATGCAT 59.893 55.000 3.79 3.79 38.76 3.96
46 47 1.506493 CCCTCTCGTTGCTATGCATC 58.494 55.000 0.19 0.00 38.76 3.91
47 48 1.069823 CCCTCTCGTTGCTATGCATCT 59.930 52.381 0.19 0.00 38.76 2.90
48 49 2.297315 CCCTCTCGTTGCTATGCATCTA 59.703 50.000 0.19 0.00 38.76 1.98
49 50 3.056250 CCCTCTCGTTGCTATGCATCTAT 60.056 47.826 0.19 0.00 38.76 1.98
50 51 4.158579 CCCTCTCGTTGCTATGCATCTATA 59.841 45.833 0.19 0.00 38.76 1.31
51 52 5.339177 CCTCTCGTTGCTATGCATCTATAG 58.661 45.833 0.19 0.00 38.76 1.31
52 53 5.124617 CCTCTCGTTGCTATGCATCTATAGA 59.875 44.000 0.19 4.57 38.76 1.98
53 54 6.183360 CCTCTCGTTGCTATGCATCTATAGAT 60.183 42.308 9.57 9.57 38.76 1.98
54 55 7.012799 CCTCTCGTTGCTATGCATCTATAGATA 59.987 40.741 14.92 1.25 38.76 1.98
55 56 7.924940 TCTCGTTGCTATGCATCTATAGATAG 58.075 38.462 14.92 9.92 38.76 2.08
56 57 7.770897 TCTCGTTGCTATGCATCTATAGATAGA 59.229 37.037 14.92 7.05 43.00 1.98
58 59 8.563732 TCGTTGCTATGCATCTATAGATAGATC 58.436 37.037 14.92 5.88 45.70 2.75
59 60 8.567104 CGTTGCTATGCATCTATAGATAGATCT 58.433 37.037 14.92 0.00 45.70 2.75
62 63 8.358895 TGCTATGCATCTATAGATAGATCTTGC 58.641 37.037 14.92 13.85 45.70 4.01
63 64 7.538334 GCTATGCATCTATAGATAGATCTTGCG 59.462 40.741 14.92 3.72 45.70 4.85
64 65 6.765915 TGCATCTATAGATAGATCTTGCGT 57.234 37.500 14.92 0.00 45.70 5.24
65 66 6.558909 TGCATCTATAGATAGATCTTGCGTG 58.441 40.000 14.92 1.46 45.70 5.34
66 67 6.375455 TGCATCTATAGATAGATCTTGCGTGA 59.625 38.462 14.92 0.00 45.70 4.35
67 68 6.912051 GCATCTATAGATAGATCTTGCGTGAG 59.088 42.308 14.92 0.00 45.70 3.51
102 103 6.698359 TTTAAAATTGCATGCTACGTTTCC 57.302 33.333 20.33 0.00 0.00 3.13
103 104 2.939460 AATTGCATGCTACGTTTCCC 57.061 45.000 20.33 0.00 0.00 3.97
104 105 1.832883 ATTGCATGCTACGTTTCCCA 58.167 45.000 20.33 0.00 0.00 4.37
105 106 1.610363 TTGCATGCTACGTTTCCCAA 58.390 45.000 20.33 0.00 0.00 4.12
106 107 0.878416 TGCATGCTACGTTTCCCAAC 59.122 50.000 20.33 0.00 0.00 3.77
107 108 0.878416 GCATGCTACGTTTCCCAACA 59.122 50.000 11.37 0.00 32.54 3.33
136 137 3.181475 CCTTTTCCGCTGCTCATACTCTA 60.181 47.826 0.00 0.00 0.00 2.43
160 162 2.161855 TGCTTGTGTAGAATGCCTTGG 58.838 47.619 0.00 0.00 0.00 3.61
163 165 2.198827 TGTGTAGAATGCCTTGGGTG 57.801 50.000 0.00 0.00 0.00 4.61
170 172 0.178924 AATGCCTTGGGTGCCTCTTT 60.179 50.000 0.00 0.00 0.00 2.52
174 176 1.165270 CCTTGGGTGCCTCTTTAACG 58.835 55.000 0.00 0.00 0.00 3.18
179 181 0.872388 GGTGCCTCTTTAACGTGTGG 59.128 55.000 0.00 0.00 0.00 4.17
183 185 3.185797 GTGCCTCTTTAACGTGTGGTAAG 59.814 47.826 0.00 0.00 0.00 2.34
201 203 6.038936 GTGGTAAGCTCAACCTTAACTTGAAA 59.961 38.462 16.76 0.00 36.27 2.69
491 493 7.269937 CGAAATCTAGTGCAAATGAAACTCAAG 59.730 37.037 0.00 0.00 0.00 3.02
511 525 5.652014 TCAAGGAAAAATGCCTATGACGAAT 59.348 36.000 0.00 0.00 33.76 3.34
514 528 5.652014 AGGAAAAATGCCTATGACGAATCAA 59.348 36.000 0.00 0.00 38.69 2.57
522 536 6.345298 TGCCTATGACGAATCAAACAATCTA 58.655 36.000 0.00 0.00 38.69 1.98
523 537 6.479990 TGCCTATGACGAATCAAACAATCTAG 59.520 38.462 0.00 0.00 38.69 2.43
525 539 7.306866 GCCTATGACGAATCAAACAATCTAGAC 60.307 40.741 0.00 0.00 38.69 2.59
528 542 6.687604 TGACGAATCAAACAATCTAGACAGA 58.312 36.000 0.00 0.00 34.56 3.41
595 609 4.737855 TCCTTCAAATAAGAGTCCCTCG 57.262 45.455 0.00 0.00 35.36 4.63
616 630 1.007607 ATTCTGGGGTACAAAGGGGG 58.992 55.000 0.00 0.00 0.00 5.40
619 633 1.132135 TCTGGGGTACAAAGGGGGTAA 60.132 52.381 0.00 0.00 0.00 2.85
620 634 1.927371 CTGGGGTACAAAGGGGGTAAT 59.073 52.381 0.00 0.00 0.00 1.89
621 635 1.641714 TGGGGTACAAAGGGGGTAATG 59.358 52.381 0.00 0.00 0.00 1.90
622 636 1.063492 GGGGTACAAAGGGGGTAATGG 60.063 57.143 0.00 0.00 0.00 3.16
623 637 1.924552 GGGTACAAAGGGGGTAATGGA 59.075 52.381 0.00 0.00 0.00 3.41
624 638 2.516702 GGGTACAAAGGGGGTAATGGAT 59.483 50.000 0.00 0.00 0.00 3.41
625 639 3.723154 GGGTACAAAGGGGGTAATGGATA 59.277 47.826 0.00 0.00 0.00 2.59
649 663 5.819901 AGGTTAGCTGCTCAAAAGATGATAC 59.180 40.000 4.91 0.00 37.44 2.24
651 665 3.201290 AGCTGCTCAAAAGATGATACCG 58.799 45.455 0.00 0.00 37.44 4.02
653 667 2.288666 TGCTCAAAAGATGATACCGGC 58.711 47.619 0.00 0.00 37.44 6.13
670 684 2.288763 CCGGCTGCCTTACAAACAAAAT 60.289 45.455 17.92 0.00 0.00 1.82
674 688 4.501400 GGCTGCCTTACAAACAAAATGACT 60.501 41.667 12.43 0.00 0.00 3.41
684 698 7.363205 ACAAACAAAATGACTCAAAAACCAG 57.637 32.000 0.00 0.00 0.00 4.00
686 700 7.117667 ACAAACAAAATGACTCAAAAACCAGAC 59.882 33.333 0.00 0.00 0.00 3.51
707 721 5.239306 AGACATGTTCACACCAGTACAAATG 59.761 40.000 0.00 0.00 0.00 2.32
715 729 5.238432 TCACACCAGTACAAATGTCACATTC 59.762 40.000 2.74 0.00 0.00 2.67
737 751 5.918608 TCACTCTCACAAACTTCTAAAGCT 58.081 37.500 0.00 0.00 0.00 3.74
755 1056 4.405116 AGCTCCATTCTGTCAATCTCTC 57.595 45.455 0.00 0.00 0.00 3.20
768 1069 0.898320 ATCTCTCCCGTGTTGTCCAG 59.102 55.000 0.00 0.00 0.00 3.86
770 1071 2.099652 CTCTCCCGTGTTGTCCAGCA 62.100 60.000 0.00 0.00 0.00 4.41
782 1083 3.769739 TGTCCAGCAGTACAAGACATT 57.230 42.857 0.00 0.00 32.75 2.71
787 1088 2.095567 CAGCAGTACAAGACATTGCACC 60.096 50.000 0.00 0.00 40.27 5.01
795 1096 1.210155 GACATTGCACCGCTCCAAC 59.790 57.895 0.00 0.00 0.00 3.77
829 1150 5.765182 GTGTCCAATATATCTCCAAACAGGG 59.235 44.000 0.00 0.00 38.24 4.45
883 1204 2.697751 AGCTCTTCAGTCTTCACACACT 59.302 45.455 0.00 0.00 0.00 3.55
914 1235 4.968259 ACATACCAAACAGTTCAGTGCTA 58.032 39.130 0.00 0.00 0.00 3.49
933 1254 3.879892 GCTACTTATCCTTTCCCTTGCAG 59.120 47.826 0.00 0.00 0.00 4.41
1236 1557 2.124736 GGCATCTACGGCAGCCAA 60.125 61.111 13.30 0.00 46.26 4.52
1322 1647 0.750546 ATCTCCATTGCTGCATGCGT 60.751 50.000 14.09 0.00 46.63 5.24
1748 2073 2.551459 CTGACCTTGCTTTGTGAAGGAG 59.449 50.000 5.33 0.00 41.26 3.69
1837 2162 7.667043 TGAACCGAGGCAATTGATATATAAC 57.333 36.000 10.34 0.00 0.00 1.89
1867 2195 1.902938 AGAAGAACCTTGCTTCAGCC 58.097 50.000 0.00 0.00 43.19 4.85
1885 2213 2.689983 AGCCTGCTAATGTTATGCAACC 59.310 45.455 0.00 0.00 36.22 3.77
1905 2241 5.054390 ACCATGTAAAATTTGTAGGTGCG 57.946 39.130 0.00 0.00 0.00 5.34
2052 2406 1.021968 GTGCCGGTCAACAGTTCTTT 58.978 50.000 1.90 0.00 0.00 2.52
2058 2412 3.194861 CGGTCAACAGTTCTTTCTGACA 58.805 45.455 3.75 0.00 38.50 3.58
2084 2438 4.010667 TCTACACCAAAACGCCTACAAT 57.989 40.909 0.00 0.00 0.00 2.71
2088 2442 1.616374 ACCAAAACGCCTACAATTGGG 59.384 47.619 10.83 3.27 43.77 4.12
2102 2456 6.817140 CCTACAATTGGGTCTAGTTTCTACAC 59.183 42.308 10.83 0.00 0.00 2.90
2103 2457 6.182507 ACAATTGGGTCTAGTTTCTACACA 57.817 37.500 10.83 0.00 0.00 3.72
2107 2461 4.220724 TGGGTCTAGTTTCTACACACACT 58.779 43.478 0.00 0.00 0.00 3.55
2138 2493 7.327214 TCTGCTAAACCAAAAACACAAGATTT 58.673 30.769 0.00 0.00 0.00 2.17
2142 2499 9.914923 GCTAAACCAAAAACACAAGATTTAAAG 57.085 29.630 0.00 0.00 0.00 1.85
2243 2605 6.987403 ACCCAAAATACAACAATAACACCT 57.013 33.333 0.00 0.00 0.00 4.00
2267 2629 4.070716 AGGCACTTGAATCTCAACAGAAG 58.929 43.478 0.00 0.00 27.25 2.85
2269 2631 3.666374 GCACTTGAATCTCAACAGAAGCG 60.666 47.826 0.00 0.00 32.21 4.68
2274 2636 3.056536 TGAATCTCAACAGAAGCGCTACT 60.057 43.478 12.05 0.00 30.24 2.57
2275 2637 4.157840 TGAATCTCAACAGAAGCGCTACTA 59.842 41.667 12.05 0.00 30.24 1.82
2296 2658 2.949644 ACACAGTACAAAGCCTTCAACC 59.050 45.455 0.00 0.00 0.00 3.77
2314 2676 8.839343 CCTTCAACCTTTATTTCATTTGCTTTT 58.161 29.630 0.00 0.00 0.00 2.27
2338 2700 6.314917 TCTATTAGCCTCCATCAGTACATGA 58.685 40.000 0.00 0.00 43.70 3.07
2398 2760 5.336102 AGATTCAATTGGGGAACATTCACT 58.664 37.500 5.42 0.00 0.00 3.41
2400 2762 5.885449 TTCAATTGGGGAACATTCACTTT 57.115 34.783 5.42 0.00 0.00 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.028112 AGTGTGTCTACGTACCCTCGTA 60.028 50.000 0.00 0.00 43.80 3.43
2 3 1.160137 GTGTGTCTACGTACCCTCGT 58.840 55.000 0.00 0.00 45.97 4.18
3 4 1.396301 GAGTGTGTCTACGTACCCTCG 59.604 57.143 0.00 0.00 0.00 4.63
4 5 2.677337 GAGAGTGTGTCTACGTACCCTC 59.323 54.545 0.00 0.00 34.71 4.30
5 6 2.617532 GGAGAGTGTGTCTACGTACCCT 60.618 54.545 0.00 0.00 34.71 4.34
6 7 1.742268 GGAGAGTGTGTCTACGTACCC 59.258 57.143 0.00 0.00 34.71 3.69
7 8 1.742268 GGGAGAGTGTGTCTACGTACC 59.258 57.143 0.00 0.00 36.91 3.34
8 9 1.742268 GGGGAGAGTGTGTCTACGTAC 59.258 57.143 0.00 0.00 36.91 3.67
9 10 1.340405 GGGGGAGAGTGTGTCTACGTA 60.340 57.143 0.00 0.00 36.91 3.57
10 11 0.611340 GGGGGAGAGTGTGTCTACGT 60.611 60.000 0.00 0.00 36.91 3.57
11 12 0.323542 AGGGGGAGAGTGTGTCTACG 60.324 60.000 0.00 0.00 36.91 3.51
12 13 1.006162 AGAGGGGGAGAGTGTGTCTAC 59.994 57.143 0.00 0.00 34.71 2.59
13 14 1.285373 GAGAGGGGGAGAGTGTGTCTA 59.715 57.143 0.00 0.00 34.71 2.59
14 15 0.040499 GAGAGGGGGAGAGTGTGTCT 59.960 60.000 0.00 0.00 38.71 3.41
15 16 1.316706 CGAGAGGGGGAGAGTGTGTC 61.317 65.000 0.00 0.00 0.00 3.67
16 17 1.304547 CGAGAGGGGGAGAGTGTGT 60.305 63.158 0.00 0.00 0.00 3.72
17 18 0.900647 AACGAGAGGGGGAGAGTGTG 60.901 60.000 0.00 0.00 0.00 3.82
18 19 0.900647 CAACGAGAGGGGGAGAGTGT 60.901 60.000 0.00 0.00 0.00 3.55
19 20 1.893786 CAACGAGAGGGGGAGAGTG 59.106 63.158 0.00 0.00 0.00 3.51
20 21 1.985116 GCAACGAGAGGGGGAGAGT 60.985 63.158 0.00 0.00 0.00 3.24
21 22 0.395862 TAGCAACGAGAGGGGGAGAG 60.396 60.000 0.00 0.00 0.00 3.20
22 23 0.261991 ATAGCAACGAGAGGGGGAGA 59.738 55.000 0.00 0.00 0.00 3.71
23 24 0.390860 CATAGCAACGAGAGGGGGAG 59.609 60.000 0.00 0.00 0.00 4.30
24 25 1.686325 GCATAGCAACGAGAGGGGGA 61.686 60.000 0.00 0.00 0.00 4.81
25 26 1.227674 GCATAGCAACGAGAGGGGG 60.228 63.158 0.00 0.00 0.00 5.40
26 27 0.107456 ATGCATAGCAACGAGAGGGG 59.893 55.000 0.00 0.00 43.62 4.79
27 28 1.069823 AGATGCATAGCAACGAGAGGG 59.930 52.381 0.00 0.00 43.62 4.30
28 29 2.522836 AGATGCATAGCAACGAGAGG 57.477 50.000 0.00 0.00 43.62 3.69
29 30 6.188400 TCTATAGATGCATAGCAACGAGAG 57.812 41.667 0.00 0.00 43.62 3.20
30 31 6.765915 ATCTATAGATGCATAGCAACGAGA 57.234 37.500 14.60 0.00 43.62 4.04
31 32 7.924940 TCTATCTATAGATGCATAGCAACGAG 58.075 38.462 23.03 9.34 43.62 4.18
32 33 7.865706 TCTATCTATAGATGCATAGCAACGA 57.134 36.000 23.03 0.09 43.62 3.85
33 34 8.567104 AGATCTATCTATAGATGCATAGCAACG 58.433 37.037 23.03 1.83 46.98 4.10
36 37 8.358895 GCAAGATCTATCTATAGATGCATAGCA 58.641 37.037 23.03 2.62 46.98 3.49
37 38 7.538334 CGCAAGATCTATCTATAGATGCATAGC 59.462 40.741 23.03 16.06 46.98 2.97
38 39 8.567104 ACGCAAGATCTATCTATAGATGCATAG 58.433 37.037 23.03 13.32 46.98 2.23
39 40 8.348507 CACGCAAGATCTATCTATAGATGCATA 58.651 37.037 23.03 4.34 46.98 3.14
40 41 7.067981 TCACGCAAGATCTATCTATAGATGCAT 59.932 37.037 23.03 14.71 46.98 3.96
41 42 6.375455 TCACGCAAGATCTATCTATAGATGCA 59.625 38.462 23.03 10.91 46.98 3.96
42 43 6.790282 TCACGCAAGATCTATCTATAGATGC 58.210 40.000 23.03 16.46 46.98 3.91
43 44 6.912051 GCTCACGCAAGATCTATCTATAGATG 59.088 42.308 23.03 13.69 43.73 2.90
44 45 6.601217 TGCTCACGCAAGATCTATCTATAGAT 59.399 38.462 18.99 18.99 46.10 1.98
45 46 5.940470 TGCTCACGCAAGATCTATCTATAGA 59.060 40.000 4.57 4.57 44.62 1.98
46 47 6.188400 TGCTCACGCAAGATCTATCTATAG 57.812 41.667 0.00 0.00 44.62 1.31
77 78 7.307455 GGGAAACGTAGCATGCAATTTTAAAAA 60.307 33.333 21.98 0.00 0.00 1.94
78 79 6.146347 GGGAAACGTAGCATGCAATTTTAAAA 59.854 34.615 21.98 2.51 0.00 1.52
79 80 5.635700 GGGAAACGTAGCATGCAATTTTAAA 59.364 36.000 21.98 0.00 0.00 1.52
80 81 5.164954 GGGAAACGTAGCATGCAATTTTAA 58.835 37.500 21.98 0.00 0.00 1.52
81 82 4.218635 TGGGAAACGTAGCATGCAATTTTA 59.781 37.500 21.98 0.00 0.00 1.52
82 83 3.006323 TGGGAAACGTAGCATGCAATTTT 59.994 39.130 21.98 12.86 0.00 1.82
83 84 2.560542 TGGGAAACGTAGCATGCAATTT 59.439 40.909 21.98 13.67 0.00 1.82
84 85 2.166829 TGGGAAACGTAGCATGCAATT 58.833 42.857 21.98 6.80 0.00 2.32
85 86 1.832883 TGGGAAACGTAGCATGCAAT 58.167 45.000 21.98 1.90 0.00 3.56
86 87 1.268352 GTTGGGAAACGTAGCATGCAA 59.732 47.619 21.98 0.00 0.00 4.08
87 88 0.878416 GTTGGGAAACGTAGCATGCA 59.122 50.000 21.98 2.77 0.00 3.96
88 89 0.878416 TGTTGGGAAACGTAGCATGC 59.122 50.000 10.51 10.51 0.00 4.06
89 90 1.135689 GCTGTTGGGAAACGTAGCATG 60.136 52.381 0.00 0.00 0.00 4.06
90 91 1.165270 GCTGTTGGGAAACGTAGCAT 58.835 50.000 0.00 0.00 0.00 3.79
91 92 0.107831 AGCTGTTGGGAAACGTAGCA 59.892 50.000 5.57 0.00 33.81 3.49
92 93 1.235724 AAGCTGTTGGGAAACGTAGC 58.764 50.000 0.00 0.00 0.00 3.58
93 94 3.187842 GGTAAAGCTGTTGGGAAACGTAG 59.812 47.826 0.00 0.00 0.00 3.51
94 95 3.140623 GGTAAAGCTGTTGGGAAACGTA 58.859 45.455 0.00 0.00 0.00 3.57
95 96 1.951602 GGTAAAGCTGTTGGGAAACGT 59.048 47.619 0.00 0.00 0.00 3.99
96 97 2.227194 AGGTAAAGCTGTTGGGAAACG 58.773 47.619 0.00 0.00 0.00 3.60
97 98 4.665833 AAAGGTAAAGCTGTTGGGAAAC 57.334 40.909 0.00 0.00 0.00 2.78
98 99 4.100344 GGAAAAGGTAAAGCTGTTGGGAAA 59.900 41.667 0.00 0.00 0.00 3.13
99 100 3.639561 GGAAAAGGTAAAGCTGTTGGGAA 59.360 43.478 0.00 0.00 0.00 3.97
100 101 3.227614 GGAAAAGGTAAAGCTGTTGGGA 58.772 45.455 0.00 0.00 0.00 4.37
101 102 2.030274 CGGAAAAGGTAAAGCTGTTGGG 60.030 50.000 0.00 0.00 0.00 4.12
102 103 2.607038 GCGGAAAAGGTAAAGCTGTTGG 60.607 50.000 0.00 0.00 0.00 3.77
103 104 2.293399 AGCGGAAAAGGTAAAGCTGTTG 59.707 45.455 0.00 0.00 33.31 3.33
104 105 2.293399 CAGCGGAAAAGGTAAAGCTGTT 59.707 45.455 7.04 0.00 44.75 3.16
105 106 1.880027 CAGCGGAAAAGGTAAAGCTGT 59.120 47.619 7.04 0.00 44.75 4.40
106 107 2.619013 CAGCGGAAAAGGTAAAGCTG 57.381 50.000 0.80 0.80 44.51 4.24
107 108 0.881796 GCAGCGGAAAAGGTAAAGCT 59.118 50.000 0.00 0.00 35.06 3.74
136 137 5.068198 CCAAGGCATTCTACACAAGCATATT 59.932 40.000 0.00 0.00 0.00 1.28
160 162 0.872388 CCACACGTTAAAGAGGCACC 59.128 55.000 0.00 0.00 0.00 5.01
163 165 2.159037 GCTTACCACACGTTAAAGAGGC 59.841 50.000 0.00 0.00 0.00 4.70
170 172 2.366266 AGGTTGAGCTTACCACACGTTA 59.634 45.455 18.06 0.00 38.16 3.18
174 176 4.386711 AGTTAAGGTTGAGCTTACCACAC 58.613 43.478 18.06 11.95 38.16 3.82
491 493 5.499139 TGATTCGTCATAGGCATTTTTCC 57.501 39.130 0.00 0.00 0.00 3.13
566 580 9.408648 GGGACTCTTATTTGAAGGATTTTCATA 57.591 33.333 0.00 0.00 0.00 2.15
567 581 8.118600 AGGGACTCTTATTTGAAGGATTTTCAT 58.881 33.333 0.00 0.00 0.00 2.57
595 609 2.623239 CCCCCTTTGTACCCCAGAATTC 60.623 54.545 0.00 0.00 0.00 2.17
616 630 5.215252 TGAGCAGCTAACCTATCCATTAC 57.785 43.478 0.00 0.00 0.00 1.89
619 633 4.778213 TTTGAGCAGCTAACCTATCCAT 57.222 40.909 0.00 0.00 0.00 3.41
620 634 4.225042 TCTTTTGAGCAGCTAACCTATCCA 59.775 41.667 0.00 0.00 0.00 3.41
621 635 4.770795 TCTTTTGAGCAGCTAACCTATCC 58.229 43.478 0.00 0.00 0.00 2.59
622 636 6.051717 TCATCTTTTGAGCAGCTAACCTATC 58.948 40.000 0.00 0.00 0.00 2.08
623 637 5.994250 TCATCTTTTGAGCAGCTAACCTAT 58.006 37.500 0.00 0.00 0.00 2.57
624 638 5.420725 TCATCTTTTGAGCAGCTAACCTA 57.579 39.130 0.00 0.00 0.00 3.08
625 639 4.292186 TCATCTTTTGAGCAGCTAACCT 57.708 40.909 0.00 0.00 0.00 3.50
649 663 0.671251 TTTGTTTGTAAGGCAGCCGG 59.329 50.000 5.55 0.00 0.00 6.13
651 665 3.740832 GTCATTTTGTTTGTAAGGCAGCC 59.259 43.478 1.84 1.84 0.00 4.85
653 667 5.830912 TGAGTCATTTTGTTTGTAAGGCAG 58.169 37.500 0.00 0.00 0.00 4.85
670 684 4.946772 TGAACATGTCTGGTTTTTGAGTCA 59.053 37.500 0.00 0.00 0.00 3.41
674 688 4.142271 GGTGTGAACATGTCTGGTTTTTGA 60.142 41.667 0.00 0.00 0.00 2.69
684 698 5.008613 ACATTTGTACTGGTGTGAACATGTC 59.991 40.000 0.00 0.00 0.00 3.06
686 700 5.008514 TGACATTTGTACTGGTGTGAACATG 59.991 40.000 0.00 0.00 0.00 3.21
707 721 5.525378 AGAAGTTTGTGAGAGTGAATGTGAC 59.475 40.000 0.00 0.00 0.00 3.67
715 729 5.178438 GGAGCTTTAGAAGTTTGTGAGAGTG 59.822 44.000 0.00 0.00 0.00 3.51
737 751 2.432146 CGGGAGAGATTGACAGAATGGA 59.568 50.000 0.00 0.00 43.62 3.41
755 1056 0.949105 GTACTGCTGGACAACACGGG 60.949 60.000 0.22 0.00 0.00 5.28
768 1069 1.135972 CGGTGCAATGTCTTGTACTGC 60.136 52.381 6.54 0.00 44.04 4.40
770 1071 1.156736 GCGGTGCAATGTCTTGTACT 58.843 50.000 6.54 0.00 44.54 2.73
782 1083 0.541392 AGATATGTTGGAGCGGTGCA 59.459 50.000 4.13 4.13 0.00 4.57
787 1088 4.541779 GACACTAGAGATATGTTGGAGCG 58.458 47.826 0.00 0.00 0.00 5.03
829 1150 2.440409 TCTGAATCTTTTGCCTGCCTC 58.560 47.619 0.00 0.00 0.00 4.70
883 1204 4.465886 ACTGTTTGGTATGTACTTTGGCA 58.534 39.130 0.00 0.00 0.00 4.92
914 1235 3.330701 TGTCTGCAAGGGAAAGGATAAGT 59.669 43.478 0.00 0.00 0.00 2.24
933 1254 1.134551 GTGGAGAAGGGCAGAGATGTC 60.135 57.143 0.00 0.00 0.00 3.06
1080 1401 2.284995 GTCCTCAGCCCTCCCTGT 60.285 66.667 0.00 0.00 34.47 4.00
1082 1403 4.423209 GGGTCCTCAGCCCTCCCT 62.423 72.222 0.00 0.00 42.81 4.20
1236 1557 2.359602 TCGAAGTCGTCCCTCGCT 60.360 61.111 0.00 0.00 40.80 4.93
1322 1647 2.358957 CCATTCTTGTCAGATGCCGAA 58.641 47.619 0.00 0.00 0.00 4.30
1668 1993 1.103803 CGGCTAAGCTCACTCTACCA 58.896 55.000 0.00 0.00 0.00 3.25
1719 2044 1.299541 AAGCAAGGTCAGTCGTTGTG 58.700 50.000 2.73 0.00 41.97 3.33
1720 2045 1.670811 CAAAGCAAGGTCAGTCGTTGT 59.329 47.619 2.73 0.00 41.97 3.32
1748 2073 5.182760 ACTCAAACTTTCAATGGAGATCAGC 59.817 40.000 0.00 0.00 0.00 4.26
1760 2085 5.065988 GGTTCAGCAACTACTCAAACTTTCA 59.934 40.000 0.00 0.00 32.50 2.69
1837 2162 4.435651 GCAAGGTTCTTCTTCCGAATAACG 60.436 45.833 0.00 0.00 37.20 3.18
1867 2195 5.252969 ACATGGTTGCATAACATTAGCAG 57.747 39.130 0.00 0.00 39.72 4.24
1885 2213 9.944663 AATATACGCACCTACAAATTTTACATG 57.055 29.630 0.00 0.00 0.00 3.21
2052 2406 4.350368 TTTGGTGTAGATGCTTGTCAGA 57.650 40.909 0.00 0.00 0.00 3.27
2058 2412 1.539827 GGCGTTTTGGTGTAGATGCTT 59.460 47.619 0.00 0.00 0.00 3.91
2084 2438 4.652421 AGTGTGTGTAGAAACTAGACCCAA 59.348 41.667 0.00 0.00 0.00 4.12
2088 2442 5.755813 TCGAAGTGTGTGTAGAAACTAGAC 58.244 41.667 0.00 0.00 0.00 2.59
2102 2456 3.745975 TGGTTTAGCAGATTCGAAGTGTG 59.254 43.478 3.35 1.89 0.00 3.82
2103 2457 4.002906 TGGTTTAGCAGATTCGAAGTGT 57.997 40.909 3.35 0.00 0.00 3.55
2107 2461 5.974751 GTGTTTTTGGTTTAGCAGATTCGAA 59.025 36.000 0.00 0.00 0.00 3.71
2185 2547 7.365741 TGTGATTTCTTTCTTCTCAGCAAATC 58.634 34.615 0.00 0.00 32.00 2.17
2198 2560 9.157104 TGGGTTTTAGTTTTTGTGATTTCTTTC 57.843 29.630 0.00 0.00 0.00 2.62
2199 2561 9.508642 TTGGGTTTTAGTTTTTGTGATTTCTTT 57.491 25.926 0.00 0.00 0.00 2.52
2229 2591 2.884639 GTGCCTGAGGTGTTATTGTTGT 59.115 45.455 0.00 0.00 0.00 3.32
2243 2605 3.071457 TCTGTTGAGATTCAAGTGCCTGA 59.929 43.478 0.00 0.00 37.00 3.86
2267 2629 2.344741 GCTTTGTACTGTGTAGTAGCGC 59.655 50.000 0.00 0.00 39.96 5.92
2269 2631 4.189639 AGGCTTTGTACTGTGTAGTAGC 57.810 45.455 0.00 0.00 39.96 3.58
2274 2636 4.131596 GGTTGAAGGCTTTGTACTGTGTA 58.868 43.478 0.00 0.00 0.00 2.90
2275 2637 2.949644 GGTTGAAGGCTTTGTACTGTGT 59.050 45.455 0.00 0.00 0.00 3.72
2314 2676 6.314917 TCATGTACTGATGGAGGCTAATAGA 58.685 40.000 0.00 0.00 0.00 1.98
2322 2684 6.602410 ACATAGATCATGTACTGATGGAGG 57.398 41.667 11.12 5.10 46.34 4.30
2338 2700 7.490402 GCCGTTGTAAAACTGTAGTACATAGAT 59.510 37.037 2.82 0.00 0.00 1.98
2384 2746 2.225017 GGAGGAAAGTGAATGTTCCCCA 60.225 50.000 0.00 0.00 43.78 4.96
2398 2760 1.074775 ATTGTGCAGGCGGAGGAAA 59.925 52.632 0.00 0.00 0.00 3.13
2400 2762 2.046023 CATTGTGCAGGCGGAGGA 60.046 61.111 0.00 0.00 0.00 3.71


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

AutoCloner maintained by Alex Coulton.