Multiple sequence alignment - TraesCS2A01G229200

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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 TraesCS2A01G229200 chr2A 100.000 2699 0 0 1 2699 257852862 257855560 0.000000e+00 4985.0
1 TraesCS2A01G229200 chr2A 92.308 117 9 0 1 117 744299665 744299549 1.660000e-37 167.0
2 TraesCS2A01G229200 chr2B 91.648 1353 76 21 998 2327 260638797 260640135 0.000000e+00 1838.0
3 TraesCS2A01G229200 chr2B 97.416 387 9 1 2313 2699 260640219 260640604 0.000000e+00 658.0
4 TraesCS2A01G229200 chr2D 97.358 795 21 0 1905 2699 207250792 207249998 0.000000e+00 1352.0
5 TraesCS2A01G229200 chr2D 90.774 1008 30 13 943 1902 207251819 207250827 0.000000e+00 1288.0
6 TraesCS2A01G229200 chr3D 89.067 750 44 9 228 945 433539444 433540187 0.000000e+00 896.0
7 TraesCS2A01G229200 chr3D 91.707 410 29 5 539 945 588823245 588822838 5.040000e-157 564.0
8 TraesCS2A01G229200 chr3D 91.848 368 25 3 228 594 588823584 588823221 2.400000e-140 508.0
9 TraesCS2A01G229200 chr3D 91.946 149 11 1 112 259 433539294 433539442 9.790000e-50 207.0
10 TraesCS2A01G229200 chr3D 91.275 149 12 1 112 259 588823766 588823618 4.560000e-48 202.0
11 TraesCS2A01G229200 chr1D 92.195 410 27 5 539 945 78112367 78112774 2.330000e-160 575.0
12 TraesCS2A01G229200 chr1D 91.667 372 26 3 228 598 78112028 78112395 6.670000e-141 510.0
13 TraesCS2A01G229200 chr1D 89.933 149 14 1 112 259 78111846 78111994 9.860000e-45 191.0
14 TraesCS2A01G229200 chr7D 86.558 491 34 18 112 601 458358912 458358453 1.850000e-141 512.0
15 TraesCS2A01G229200 chr7D 93.143 350 16 3 596 945 458358404 458358063 8.620000e-140 507.0
16 TraesCS2A01G229200 chr3B 91.781 365 29 1 228 592 125828604 125828967 8.620000e-140 507.0
17 TraesCS2A01G229200 chr3B 93.970 199 12 0 747 945 125847046 125847244 4.370000e-78 302.0
18 TraesCS2A01G229200 chr3B 94.737 152 7 1 600 751 125829026 125829176 4.490000e-58 235.0
19 TraesCS2A01G229200 chr3B 95.690 116 5 0 1 116 736676228 736676343 1.280000e-43 187.0
20 TraesCS2A01G229200 chr6B 82.515 509 55 16 1193 1683 703147084 703147576 1.490000e-112 416.0
21 TraesCS2A01G229200 chr6B 95.161 124 6 0 998 1121 703146356 703146479 2.120000e-46 196.0
22 TraesCS2A01G229200 chr6B 88.172 93 10 1 853 945 685563943 685564034 2.840000e-20 110.0
23 TraesCS2A01G229200 chr6A 81.096 529 61 17 1185 1683 608073815 608074334 1.170000e-103 387.0
24 TraesCS2A01G229200 chr6A 95.082 122 6 0 998 1119 608073353 608073474 2.740000e-45 193.0
25 TraesCS2A01G229200 chr6A 89.130 92 10 0 855 946 570841019 570840928 6.110000e-22 115.0
26 TraesCS2A01G229200 chr6D 80.943 530 54 20 1185 1683 461387683 461388196 2.540000e-100 375.0
27 TraesCS2A01G229200 chr6D 95.082 122 6 0 998 1119 461387199 461387320 2.740000e-45 193.0
28 TraesCS2A01G229200 chrUn 92.810 153 11 0 747 899 39380802 39380650 3.500000e-54 222.0
29 TraesCS2A01G229200 chr1B 98.230 113 2 0 1 113 659686774 659686886 5.890000e-47 198.0
30 TraesCS2A01G229200 chr1B 93.860 114 7 0 1 114 645102076 645102189 3.570000e-39 172.0
31 TraesCS2A01G229200 chr1B 93.750 112 7 0 1 112 473497173 473497062 4.620000e-38 169.0
32 TraesCS2A01G229200 chr5A 97.321 112 3 0 1 112 355114540 355114429 9.860000e-45 191.0
33 TraesCS2A01G229200 chr5B 96.460 113 4 0 1 113 515191595 515191707 1.280000e-43 187.0
34 TraesCS2A01G229200 chr5B 97.170 106 3 0 1 106 522394114 522394219 2.130000e-41 180.0
35 TraesCS2A01G229200 chr7A 93.966 116 6 1 1 116 646955512 646955626 9.930000e-40 174.0
36 TraesCS2A01G229200 chr7B 90.385 52 5 0 395 446 686662174 686662225 4.820000e-08 69.4
37 TraesCS2A01G229200 chr4D 97.222 36 1 0 912 947 22008288 22008323 8.070000e-06 62.1


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 TraesCS2A01G229200 chr2A 257852862 257855560 2698 False 4985.000000 4985 100.0000 1 2699 1 chr2A.!!$F1 2698
1 TraesCS2A01G229200 chr2B 260638797 260640604 1807 False 1248.000000 1838 94.5320 998 2699 2 chr2B.!!$F1 1701
2 TraesCS2A01G229200 chr2D 207249998 207251819 1821 True 1320.000000 1352 94.0660 943 2699 2 chr2D.!!$R1 1756
3 TraesCS2A01G229200 chr3D 433539294 433540187 893 False 551.500000 896 90.5065 112 945 2 chr3D.!!$F1 833
4 TraesCS2A01G229200 chr3D 588822838 588823766 928 True 424.666667 564 91.6100 112 945 3 chr3D.!!$R1 833
5 TraesCS2A01G229200 chr1D 78111846 78112774 928 False 425.333333 575 91.2650 112 945 3 chr1D.!!$F1 833
6 TraesCS2A01G229200 chr7D 458358063 458358912 849 True 509.500000 512 89.8505 112 945 2 chr7D.!!$R1 833
7 TraesCS2A01G229200 chr3B 125828604 125829176 572 False 371.000000 507 93.2590 228 751 2 chr3B.!!$F3 523
8 TraesCS2A01G229200 chr6B 703146356 703147576 1220 False 306.000000 416 88.8380 998 1683 2 chr6B.!!$F2 685
9 TraesCS2A01G229200 chr6A 608073353 608074334 981 False 290.000000 387 88.0890 998 1683 2 chr6A.!!$F1 685
10 TraesCS2A01G229200 chr6D 461387199 461388196 997 False 284.000000 375 88.0125 998 1683 2 chr6D.!!$F1 685

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
38 39 0.036294 GCCCCAGACTTGGTACTGAC 60.036 60.0 0.00 0.0 43.40 3.51 F
967 1094 0.162294 GCGTAAAGAAACGTCCACGG 59.838 55.0 3.81 0.0 44.64 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1694 2579 0.326264 GTTGGCCACTGAGGATCACT 59.674 55.0 3.88 0.0 42.56 3.41 R
2109 3033 0.038892 AAGCTCGCCACATTTGCTTG 60.039 50.0 0.00 0.0 41.61 4.01 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
22 23 4.978186 GACCTTTTTGTAACGATTAGCCC 58.022 43.478 0.00 0.00 0.00 5.19
23 24 3.760151 ACCTTTTTGTAACGATTAGCCCC 59.240 43.478 0.00 0.00 0.00 5.80
24 25 3.759618 CCTTTTTGTAACGATTAGCCCCA 59.240 43.478 0.00 0.00 0.00 4.96
25 26 4.142469 CCTTTTTGTAACGATTAGCCCCAG 60.142 45.833 0.00 0.00 0.00 4.45
26 27 3.985019 TTTGTAACGATTAGCCCCAGA 57.015 42.857 0.00 0.00 0.00 3.86
27 28 2.973694 TGTAACGATTAGCCCCAGAC 57.026 50.000 0.00 0.00 0.00 3.51
28 29 2.463752 TGTAACGATTAGCCCCAGACT 58.536 47.619 0.00 0.00 0.00 3.24
29 30 2.835764 TGTAACGATTAGCCCCAGACTT 59.164 45.455 0.00 0.00 0.00 3.01
30 31 2.403252 AACGATTAGCCCCAGACTTG 57.597 50.000 0.00 0.00 0.00 3.16
31 32 0.541863 ACGATTAGCCCCAGACTTGG 59.458 55.000 0.00 0.00 44.60 3.61
32 33 0.541863 CGATTAGCCCCAGACTTGGT 59.458 55.000 0.00 0.00 43.40 3.67
33 34 1.760613 CGATTAGCCCCAGACTTGGTA 59.239 52.381 0.00 0.00 43.40 3.25
34 35 2.483188 CGATTAGCCCCAGACTTGGTAC 60.483 54.545 0.00 0.00 43.40 3.34
35 36 2.337359 TTAGCCCCAGACTTGGTACT 57.663 50.000 0.00 0.00 43.40 2.73
36 37 1.568504 TAGCCCCAGACTTGGTACTG 58.431 55.000 0.00 0.00 43.40 2.74
37 38 0.178903 AGCCCCAGACTTGGTACTGA 60.179 55.000 0.00 0.00 43.40 3.41
38 39 0.036294 GCCCCAGACTTGGTACTGAC 60.036 60.000 0.00 0.00 43.40 3.51
39 40 1.348064 CCCCAGACTTGGTACTGACA 58.652 55.000 0.00 0.00 43.40 3.58
40 41 1.909302 CCCCAGACTTGGTACTGACAT 59.091 52.381 0.00 0.00 43.40 3.06
41 42 2.355108 CCCCAGACTTGGTACTGACATG 60.355 54.545 0.00 0.00 43.40 3.21
42 43 2.303022 CCCAGACTTGGTACTGACATGT 59.697 50.000 0.00 0.00 43.40 3.21
43 44 3.513912 CCCAGACTTGGTACTGACATGTA 59.486 47.826 0.00 0.00 43.40 2.29
44 45 4.020573 CCCAGACTTGGTACTGACATGTAA 60.021 45.833 0.00 0.00 43.40 2.41
45 46 5.512404 CCCAGACTTGGTACTGACATGTAAA 60.512 44.000 0.00 0.00 43.40 2.01
46 47 5.995282 CCAGACTTGGTACTGACATGTAAAA 59.005 40.000 0.00 0.00 39.79 1.52
47 48 6.485313 CCAGACTTGGTACTGACATGTAAAAA 59.515 38.462 0.00 0.00 39.79 1.94
48 49 7.174946 CCAGACTTGGTACTGACATGTAAAAAT 59.825 37.037 0.00 0.00 39.79 1.82
49 50 8.567948 CAGACTTGGTACTGACATGTAAAAATT 58.432 33.333 0.00 0.00 36.38 1.82
50 51 9.787435 AGACTTGGTACTGACATGTAAAAATTA 57.213 29.630 0.00 0.00 0.00 1.40
69 70 9.719355 AAAAATTATCAAAAGTGGTACCAATCC 57.281 29.630 18.31 4.26 0.00 3.01
70 71 6.693315 ATTATCAAAAGTGGTACCAATCCG 57.307 37.500 18.31 7.71 0.00 4.18
71 72 2.156098 TCAAAAGTGGTACCAATCCGC 58.844 47.619 18.31 3.40 35.90 5.54
72 73 1.883275 CAAAAGTGGTACCAATCCGCA 59.117 47.619 18.31 0.00 37.86 5.69
73 74 2.491693 CAAAAGTGGTACCAATCCGCAT 59.508 45.455 18.31 0.00 37.86 4.73
74 75 1.750193 AAGTGGTACCAATCCGCATG 58.250 50.000 18.31 0.00 37.86 4.06
75 76 0.618458 AGTGGTACCAATCCGCATGT 59.382 50.000 18.31 0.00 37.86 3.21
76 77 1.834896 AGTGGTACCAATCCGCATGTA 59.165 47.619 18.31 0.00 37.86 2.29
77 78 2.237643 AGTGGTACCAATCCGCATGTAA 59.762 45.455 18.31 0.00 37.86 2.41
78 79 3.118038 AGTGGTACCAATCCGCATGTAAT 60.118 43.478 18.31 0.00 37.86 1.89
94 95 5.890334 CATGTAATGTCCCAATTGTGGTAC 58.110 41.667 4.43 5.02 40.72 3.34
95 96 5.249780 TGTAATGTCCCAATTGTGGTACT 57.750 39.130 4.43 0.00 44.30 2.73
96 97 5.636123 TGTAATGTCCCAATTGTGGTACTT 58.364 37.500 4.43 4.11 44.30 2.24
97 98 6.071984 TGTAATGTCCCAATTGTGGTACTTT 58.928 36.000 4.43 11.03 44.30 2.66
98 99 6.551601 TGTAATGTCCCAATTGTGGTACTTTT 59.448 34.615 4.43 6.94 44.30 2.27
99 100 4.927978 TGTCCCAATTGTGGTACTTTTG 57.072 40.909 4.43 0.00 44.30 2.44
100 101 4.282496 TGTCCCAATTGTGGTACTTTTGT 58.718 39.130 4.43 0.00 44.30 2.83
101 102 4.098654 TGTCCCAATTGTGGTACTTTTGTG 59.901 41.667 4.43 0.00 44.30 3.33
102 103 3.068873 TCCCAATTGTGGTACTTTTGTGC 59.931 43.478 4.43 0.00 44.30 4.57
103 104 3.181471 CCCAATTGTGGTACTTTTGTGCA 60.181 43.478 4.43 0.00 44.30 4.57
104 105 4.437239 CCAATTGTGGTACTTTTGTGCAA 58.563 39.130 4.43 0.00 40.42 4.08
105 106 5.055812 CCAATTGTGGTACTTTTGTGCAAT 58.944 37.500 4.43 0.00 40.42 3.56
106 107 5.526846 CCAATTGTGGTACTTTTGTGCAATT 59.473 36.000 4.43 0.00 40.42 2.32
107 108 6.703607 CCAATTGTGGTACTTTTGTGCAATTA 59.296 34.615 4.43 0.00 40.42 1.40
108 109 7.225538 CCAATTGTGGTACTTTTGTGCAATTAA 59.774 33.333 4.43 0.00 40.42 1.40
109 110 7.707774 ATTGTGGTACTTTTGTGCAATTAAC 57.292 32.000 0.00 0.00 36.74 2.01
110 111 6.458232 TGTGGTACTTTTGTGCAATTAACT 57.542 33.333 0.00 0.00 36.74 2.24
133 134 2.359850 GTCACCCATTGCCGCTGA 60.360 61.111 0.00 0.00 0.00 4.26
134 135 1.750399 GTCACCCATTGCCGCTGAT 60.750 57.895 0.00 0.00 0.00 2.90
182 183 4.435436 TCGCCGTCGAGCTGCATT 62.435 61.111 1.02 0.00 40.21 3.56
299 365 2.425592 CACCTGTCTCCGGCAACA 59.574 61.111 0.00 2.06 0.00 3.33
362 428 4.617486 TTCGCTGTCGTCACGCGT 62.617 61.111 5.58 5.58 46.31 6.01
393 459 2.125147 CCGCCATGGACGATGTGT 60.125 61.111 24.22 0.00 42.00 3.72
405 471 3.964729 GATGTGTTGCGTCGCAGCG 62.965 63.158 25.67 9.06 42.53 5.18
473 540 6.512415 GCGCTGCATATTAGATTCTCAACTTT 60.512 38.462 0.00 0.00 0.00 2.66
475 542 7.254556 CGCTGCATATTAGATTCTCAACTTTCA 60.255 37.037 0.00 0.00 0.00 2.69
528 595 2.042259 CGCTGCCAATGGAGCTTCA 61.042 57.895 17.22 0.00 32.70 3.02
561 628 0.961019 GGTGTTGCAATGAAGCTCCA 59.039 50.000 0.59 0.00 34.99 3.86
571 638 4.537433 AAGCTCCATCGAGGCCGC 62.537 66.667 0.00 0.00 36.55 6.53
589 689 1.986575 GCCGAGTGCTTCAATGGAGC 61.987 60.000 6.57 6.57 36.87 4.70
647 768 2.609610 TTACAAGGGGCCGGCTCT 60.610 61.111 28.78 21.01 0.00 4.09
730 851 3.560251 ACTGCGAGCCTGGTTGGT 61.560 61.111 0.00 0.00 38.35 3.67
743 864 1.029947 GGTTGGTATGTCTTGCCGGG 61.030 60.000 2.18 0.00 31.55 5.73
788 909 0.670546 CGTGTGCGTGGAAGAGGATT 60.671 55.000 0.00 0.00 0.00 3.01
808 929 1.073125 TGAGAGCGTGGGGAATTTTCA 59.927 47.619 0.00 0.00 0.00 2.69
967 1094 0.162294 GCGTAAAGAAACGTCCACGG 59.838 55.000 3.81 0.00 44.64 4.94
1235 2078 7.663905 TCCGGTATCAAATATAAATCCACCAAG 59.336 37.037 0.00 0.00 0.00 3.61
1271 2114 0.546267 AGCTCACCCTGTCCATCACT 60.546 55.000 0.00 0.00 0.00 3.41
1350 2225 5.359292 CACTCTACTCTGATGAACATCTCCA 59.641 44.000 14.50 0.00 38.60 3.86
1351 2226 5.593909 ACTCTACTCTGATGAACATCTCCAG 59.406 44.000 14.50 10.07 38.60 3.86
1360 2235 2.690497 TGAACATCTCCAGTCGATCTCC 59.310 50.000 0.00 0.00 0.00 3.71
1402 2281 9.647797 CCTTTGGGGTTTTACTTTCATTATTAC 57.352 33.333 0.00 0.00 0.00 1.89
1477 2356 0.978907 TGCAGAGTTCAGCATCCTCA 59.021 50.000 0.00 0.00 33.35 3.86
1630 2514 2.486982 CAGAACATTGTCCTCAAGCTGG 59.513 50.000 0.00 0.00 36.97 4.85
1645 2529 2.768769 TGGGGAACACCGACACCA 60.769 61.111 0.00 0.00 41.60 4.17
1691 2576 0.322187 GTTAACATCCCAGGCACGGT 60.322 55.000 0.00 0.00 0.00 4.83
1702 2587 2.046892 GCACGGTGCAGTGATCCT 60.047 61.111 27.10 0.00 44.26 3.24
1730 2615 2.759114 CCATGGTGGTCAGGCAGT 59.241 61.111 2.57 0.00 31.35 4.40
1785 2673 6.286758 TGCTTCCTCTGAGCTATGAAAATAG 58.713 40.000 0.00 0.00 40.75 1.73
1805 2693 0.247736 GCAACGTCCTGGTGAGATCT 59.752 55.000 0.00 0.00 0.00 2.75
1902 2794 7.859325 AGTTTTGGTTCTGCATATACGTAAT 57.141 32.000 0.00 0.00 0.00 1.89
1903 2795 7.916552 AGTTTTGGTTCTGCATATACGTAATC 58.083 34.615 0.00 0.00 0.00 1.75
1930 2854 9.163894 TCAACTAGAAATAGGATGATCTGGATT 57.836 33.333 0.00 0.00 0.00 3.01
1964 2888 4.246458 GACAATACTCCCTGACTGAACAC 58.754 47.826 0.00 0.00 0.00 3.32
2083 3007 0.793861 GACGCACAACCGAAATAGCA 59.206 50.000 0.00 0.00 0.00 3.49
2109 3033 0.529992 ATCGCGGCAAGTAACTAGGC 60.530 55.000 6.13 0.00 0.00 3.93
2182 3106 3.443045 CGGTGGTGCTTGCCCATC 61.443 66.667 6.20 5.14 33.76 3.51
2221 3145 4.781934 ACTGGGTCCTTGATTTAGCATAC 58.218 43.478 0.00 0.00 0.00 2.39
2356 3378 5.006746 CAGCTAATTTCTGACCACGGATAAC 59.993 44.000 0.00 0.00 33.54 1.89
2584 3606 4.973168 AGACAAACAGGAACTCTAATGCA 58.027 39.130 0.00 0.00 34.60 3.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.142534 GGGGCTAATCGTTACAAAAAGGTC 60.143 45.833 0.00 0.00 0.00 3.85
1 2 3.760151 GGGGCTAATCGTTACAAAAAGGT 59.240 43.478 0.00 0.00 0.00 3.50
3 4 4.698304 TCTGGGGCTAATCGTTACAAAAAG 59.302 41.667 0.00 0.00 0.00 2.27
4 5 4.456566 GTCTGGGGCTAATCGTTACAAAAA 59.543 41.667 0.00 0.00 0.00 1.94
6 7 3.262405 AGTCTGGGGCTAATCGTTACAAA 59.738 43.478 0.00 0.00 0.00 2.83
7 8 2.835764 AGTCTGGGGCTAATCGTTACAA 59.164 45.455 0.00 0.00 0.00 2.41
8 9 2.463752 AGTCTGGGGCTAATCGTTACA 58.536 47.619 0.00 0.00 0.00 2.41
9 10 3.195661 CAAGTCTGGGGCTAATCGTTAC 58.804 50.000 0.00 0.00 0.00 2.50
10 11 2.169769 CCAAGTCTGGGGCTAATCGTTA 59.830 50.000 0.00 0.00 39.30 3.18
11 12 1.065418 CCAAGTCTGGGGCTAATCGTT 60.065 52.381 0.00 0.00 39.30 3.85
12 13 0.541863 CCAAGTCTGGGGCTAATCGT 59.458 55.000 0.00 0.00 39.30 3.73
13 14 3.386543 CCAAGTCTGGGGCTAATCG 57.613 57.895 0.00 0.00 39.30 3.34
23 24 7.490962 TTTTTACATGTCAGTACCAAGTCTG 57.509 36.000 0.00 0.00 0.00 3.51
24 25 8.691661 AATTTTTACATGTCAGTACCAAGTCT 57.308 30.769 0.00 0.00 0.00 3.24
43 44 9.719355 GGATTGGTACCACTTTTGATAATTTTT 57.281 29.630 16.04 0.00 0.00 1.94
44 45 8.032451 CGGATTGGTACCACTTTTGATAATTTT 58.968 33.333 16.04 0.00 0.00 1.82
45 46 7.543756 CGGATTGGTACCACTTTTGATAATTT 58.456 34.615 16.04 0.00 0.00 1.82
46 47 6.405397 GCGGATTGGTACCACTTTTGATAATT 60.405 38.462 16.04 0.00 0.00 1.40
47 48 5.067283 GCGGATTGGTACCACTTTTGATAAT 59.933 40.000 16.04 1.24 0.00 1.28
48 49 4.396790 GCGGATTGGTACCACTTTTGATAA 59.603 41.667 16.04 0.00 0.00 1.75
49 50 3.942748 GCGGATTGGTACCACTTTTGATA 59.057 43.478 16.04 0.00 0.00 2.15
50 51 2.752903 GCGGATTGGTACCACTTTTGAT 59.247 45.455 16.04 3.80 0.00 2.57
51 52 2.156098 GCGGATTGGTACCACTTTTGA 58.844 47.619 16.04 0.00 0.00 2.69
52 53 1.883275 TGCGGATTGGTACCACTTTTG 59.117 47.619 16.04 5.02 0.00 2.44
53 54 2.279935 TGCGGATTGGTACCACTTTT 57.720 45.000 16.04 0.00 0.00 2.27
54 55 2.091541 CATGCGGATTGGTACCACTTT 58.908 47.619 16.04 1.98 0.00 2.66
55 56 1.004277 ACATGCGGATTGGTACCACTT 59.996 47.619 16.04 4.97 0.00 3.16
56 57 0.618458 ACATGCGGATTGGTACCACT 59.382 50.000 16.04 9.86 0.00 4.00
57 58 2.319136 TACATGCGGATTGGTACCAC 57.681 50.000 16.04 3.66 0.00 4.16
58 59 3.210227 CATTACATGCGGATTGGTACCA 58.790 45.455 11.60 11.60 0.00 3.25
59 60 3.211045 ACATTACATGCGGATTGGTACC 58.789 45.455 4.43 4.43 0.00 3.34
60 61 3.250040 GGACATTACATGCGGATTGGTAC 59.750 47.826 0.00 0.00 0.00 3.34
61 62 3.472652 GGACATTACATGCGGATTGGTA 58.527 45.455 0.00 0.00 0.00 3.25
62 63 2.297701 GGACATTACATGCGGATTGGT 58.702 47.619 0.00 0.00 0.00 3.67
63 64 1.608590 GGGACATTACATGCGGATTGG 59.391 52.381 0.00 0.00 0.00 3.16
64 65 2.296792 TGGGACATTACATGCGGATTG 58.703 47.619 0.00 0.00 0.00 2.67
65 66 2.727123 TGGGACATTACATGCGGATT 57.273 45.000 0.00 0.00 0.00 3.01
66 67 2.727123 TTGGGACATTACATGCGGAT 57.273 45.000 0.00 0.00 39.30 4.18
67 68 2.687425 CAATTGGGACATTACATGCGGA 59.313 45.455 0.00 0.00 39.30 5.54
68 69 2.426738 ACAATTGGGACATTACATGCGG 59.573 45.455 10.83 0.00 39.30 5.69
69 70 3.437428 CACAATTGGGACATTACATGCG 58.563 45.455 10.83 0.00 39.30 4.73
70 71 3.784338 CCACAATTGGGACATTACATGC 58.216 45.455 9.95 0.00 39.57 4.06
83 84 6.601741 AATTGCACAAAAGTACCACAATTG 57.398 33.333 3.24 3.24 35.55 2.32
84 85 7.984617 AGTTAATTGCACAAAAGTACCACAATT 59.015 29.630 0.00 0.00 39.06 2.32
85 86 7.496747 AGTTAATTGCACAAAAGTACCACAAT 58.503 30.769 0.00 0.00 0.00 2.71
86 87 6.868622 AGTTAATTGCACAAAAGTACCACAA 58.131 32.000 0.00 0.00 0.00 3.33
87 88 6.458232 AGTTAATTGCACAAAAGTACCACA 57.542 33.333 0.00 0.00 0.00 4.17
88 89 5.918576 GGAGTTAATTGCACAAAAGTACCAC 59.081 40.000 0.00 0.00 0.00 4.16
89 90 5.830991 AGGAGTTAATTGCACAAAAGTACCA 59.169 36.000 0.00 0.00 0.00 3.25
90 91 6.327279 AGGAGTTAATTGCACAAAAGTACC 57.673 37.500 0.00 0.00 0.00 3.34
91 92 6.577427 CGAAGGAGTTAATTGCACAAAAGTAC 59.423 38.462 0.00 0.00 0.00 2.73
92 93 6.261381 ACGAAGGAGTTAATTGCACAAAAGTA 59.739 34.615 0.00 0.00 0.00 2.24
93 94 5.067283 ACGAAGGAGTTAATTGCACAAAAGT 59.933 36.000 0.00 0.00 0.00 2.66
94 95 5.519722 ACGAAGGAGTTAATTGCACAAAAG 58.480 37.500 0.00 0.00 0.00 2.27
95 96 5.066634 TGACGAAGGAGTTAATTGCACAAAA 59.933 36.000 0.00 0.00 0.00 2.44
96 97 4.576873 TGACGAAGGAGTTAATTGCACAAA 59.423 37.500 0.00 0.00 0.00 2.83
97 98 4.024387 GTGACGAAGGAGTTAATTGCACAA 60.024 41.667 0.00 0.00 0.00 3.33
98 99 3.496884 GTGACGAAGGAGTTAATTGCACA 59.503 43.478 0.00 0.00 0.00 4.57
99 100 3.120304 GGTGACGAAGGAGTTAATTGCAC 60.120 47.826 0.00 0.00 0.00 4.57
100 101 3.071479 GGTGACGAAGGAGTTAATTGCA 58.929 45.455 0.00 0.00 0.00 4.08
101 102 2.418976 GGGTGACGAAGGAGTTAATTGC 59.581 50.000 0.00 0.00 0.00 3.56
102 103 3.670625 TGGGTGACGAAGGAGTTAATTG 58.329 45.455 0.00 0.00 0.00 2.32
103 104 4.569719 ATGGGTGACGAAGGAGTTAATT 57.430 40.909 0.00 0.00 0.00 1.40
104 105 4.261801 CAATGGGTGACGAAGGAGTTAAT 58.738 43.478 0.00 0.00 0.00 1.40
105 106 3.670625 CAATGGGTGACGAAGGAGTTAA 58.329 45.455 0.00 0.00 0.00 2.01
106 107 2.614481 GCAATGGGTGACGAAGGAGTTA 60.614 50.000 0.00 0.00 0.00 2.24
107 108 1.882352 GCAATGGGTGACGAAGGAGTT 60.882 52.381 0.00 0.00 0.00 3.01
108 109 0.321653 GCAATGGGTGACGAAGGAGT 60.322 55.000 0.00 0.00 0.00 3.85
109 110 1.026718 GGCAATGGGTGACGAAGGAG 61.027 60.000 0.00 0.00 0.00 3.69
110 111 1.002624 GGCAATGGGTGACGAAGGA 60.003 57.895 0.00 0.00 0.00 3.36
133 134 2.029073 CAAGGCGACGGCGGATAT 59.971 61.111 15.06 0.00 41.24 1.63
134 135 4.884257 GCAAGGCGACGGCGGATA 62.884 66.667 15.06 0.00 41.24 2.59
220 222 2.825387 TGCGATGCAGCATGGGAC 60.825 61.111 14.22 0.02 42.92 4.46
277 343 3.625897 CCGGAGACAGGTGGTGCA 61.626 66.667 0.00 0.00 0.00 4.57
299 365 1.839994 TGGAGGATGCTCCGAAGAAAT 59.160 47.619 26.19 0.00 46.18 2.17
362 428 0.181587 TGGCGGAAACTCCAAGACAA 59.818 50.000 0.00 0.00 35.91 3.18
388 454 4.075910 CGCTGCGACGCAACACAT 62.076 61.111 24.51 0.00 38.41 3.21
473 540 1.374125 CGCATGGTGAAGACGGTGA 60.374 57.895 0.00 0.00 0.00 4.02
475 542 2.742372 GCGCATGGTGAAGACGGT 60.742 61.111 0.30 0.00 0.00 4.83
571 638 0.392193 AGCTCCATTGAAGCACTCGG 60.392 55.000 0.00 0.00 0.00 4.63
730 851 1.823295 GAGCTCCCGGCAAGACATA 59.177 57.895 0.87 0.00 44.79 2.29
788 909 1.073125 TGAAAATTCCCCACGCTCTCA 59.927 47.619 0.00 0.00 0.00 3.27
808 929 0.900647 CTTCGTCCTCCTCCTGTGGT 60.901 60.000 0.00 0.00 0.00 4.16
844 965 3.694566 GCCGTTGGATTGGTCTTTCTTAT 59.305 43.478 0.00 0.00 0.00 1.73
898 1019 6.537355 ACTGATTTCAGGAGAAAATCAGTCA 58.463 36.000 26.59 11.49 45.91 3.41
945 1072 1.123756 GTGGACGTTTCTTTACGCGAG 59.876 52.381 15.93 0.00 45.06 5.03
946 1073 1.130955 GTGGACGTTTCTTTACGCGA 58.869 50.000 15.93 0.00 45.06 5.87
952 1079 0.601841 ATCGCCGTGGACGTTTCTTT 60.602 50.000 0.00 0.00 37.74 2.52
967 1094 3.305110 GGAGAAGAAGAAGATCGATCGC 58.695 50.000 19.33 15.17 0.00 4.58
1235 2078 1.521681 CTCCTCGTTCCATTCCGGC 60.522 63.158 0.00 0.00 33.14 6.13
1271 2114 0.611618 TAACGGGGAGCGTCCAGTTA 60.612 55.000 15.66 15.66 38.90 2.24
1350 2225 2.516227 TCAGGAACAGGAGATCGACT 57.484 50.000 0.00 0.00 0.00 4.18
1351 2226 3.254892 GTTTCAGGAACAGGAGATCGAC 58.745 50.000 0.00 0.00 38.18 4.20
1360 2235 3.181476 CCAAAGGTTGGTTTCAGGAACAG 60.181 47.826 0.00 0.00 45.93 3.16
1402 2281 6.486657 TCATGGTCAAAGACTTCCTGTAAAAG 59.513 38.462 0.00 0.00 32.47 2.27
1403 2282 6.361433 TCATGGTCAAAGACTTCCTGTAAAA 58.639 36.000 0.00 0.00 32.47 1.52
1404 2283 5.935945 TCATGGTCAAAGACTTCCTGTAAA 58.064 37.500 0.00 0.00 32.47 2.01
1630 2514 2.668550 GCTGGTGTCGGTGTTCCC 60.669 66.667 0.00 0.00 0.00 3.97
1645 2529 1.047596 AGGTGCAGGATGATCTCGCT 61.048 55.000 7.83 0.00 39.69 4.93
1691 2576 1.297689 GCCACTGAGGATCACTGCA 59.702 57.895 0.00 0.00 42.56 4.41
1694 2579 0.326264 GTTGGCCACTGAGGATCACT 59.674 55.000 3.88 0.00 42.56 3.41
1727 2612 2.740981 CAGAAAGCAGCCAGTAGAACTG 59.259 50.000 0.00 0.00 45.53 3.16
1728 2613 2.370189 ACAGAAAGCAGCCAGTAGAACT 59.630 45.455 0.00 0.00 0.00 3.01
1729 2614 2.481952 CACAGAAAGCAGCCAGTAGAAC 59.518 50.000 0.00 0.00 0.00 3.01
1730 2615 2.368548 TCACAGAAAGCAGCCAGTAGAA 59.631 45.455 0.00 0.00 0.00 2.10
1785 2673 0.741221 GATCTCACCAGGACGTTGCC 60.741 60.000 0.00 0.00 0.00 4.52
1805 2693 5.755409 AACACCCACTGTAATGATCTGTA 57.245 39.130 0.00 0.00 30.51 2.74
1865 2753 7.538678 GCAGAACCAAAACTATAAACAGACATG 59.461 37.037 0.00 0.00 0.00 3.21
1902 2794 8.007153 TCCAGATCATCCTATTTCTAGTTGAGA 58.993 37.037 0.00 0.00 0.00 3.27
1903 2795 8.187913 TCCAGATCATCCTATTTCTAGTTGAG 57.812 38.462 0.00 0.00 0.00 3.02
1930 2854 5.491078 AGGGAGTATTGTCAACTGGGAAATA 59.509 40.000 0.00 0.00 0.00 1.40
2064 2988 0.793861 TGCTATTTCGGTTGTGCGTC 59.206 50.000 0.00 0.00 0.00 5.19
2083 3007 2.319136 TACTTGCCGCGATTGGTAAT 57.681 45.000 8.23 0.00 32.95 1.89
2109 3033 0.038892 AAGCTCGCCACATTTGCTTG 60.039 50.000 0.00 0.00 41.61 4.01
2221 3145 3.130160 GCAGCAAGGGAAGCTCCG 61.130 66.667 0.00 0.00 41.14 4.63
2356 3378 1.269569 GGTGGAAAAGGAGGCAAAACG 60.270 52.381 0.00 0.00 0.00 3.60
2472 3494 4.141287 CTGTGTGGAATTCCTGGTTTACA 58.859 43.478 24.73 16.18 36.82 2.41
2578 3600 5.387113 AACCCCAATCTAGATGTGCATTA 57.613 39.130 5.86 0.00 0.00 1.90
2584 3606 5.456763 GGAGCATAAACCCCAATCTAGATGT 60.457 44.000 5.86 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.