Multiple sequence alignment - TraesCS2D01G399500

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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 TraesCS2D01G399500 chr2D 100.000 4018 0 0 1 4018 512684772 512688789 0.000000e+00 7420.0
1 TraesCS2D01G399500 chr2A 93.076 3914 135 57 175 4018 656239010 656242857 0.000000e+00 5602.0
2 TraesCS2D01G399500 chr2B 94.298 3367 108 33 692 4018 602762070 602765392 0.000000e+00 5077.0
3 TraesCS2D01G399500 chr2B 88.491 643 36 16 87 701 602761415 602762047 0.000000e+00 743.0
4 TraesCS2D01G399500 chr1B 93.972 1742 49 11 2277 3975 332586679 332584951 0.000000e+00 2584.0
5 TraesCS2D01G399500 chr6A 95.219 1255 31 4 2296 3525 441441550 441442800 0.000000e+00 1958.0
6 TraesCS2D01G399500 chr6A 79.201 601 93 23 2099 2682 473575567 473574982 4.870000e-104 388.0
7 TraesCS2D01G399500 chr6A 91.051 257 14 1 2299 2555 441443045 441442798 4.970000e-89 339.0
8 TraesCS2D01G399500 chr6A 87.500 200 25 0 2093 2292 500083817 500083618 8.680000e-57 231.0
9 TraesCS2D01G399500 chr6A 86.486 185 20 4 2129 2309 520355715 520355532 8.810000e-47 198.0
10 TraesCS2D01G399500 chr6A 81.915 94 12 3 3890 3982 473573758 473573669 1.550000e-09 75.0
11 TraesCS2D01G399500 chr6D 79.035 601 94 23 2099 2682 334227663 334227078 2.270000e-102 383.0
12 TraesCS2D01G399500 chr6D 87.179 195 25 0 2098 2292 358326193 358325999 5.230000e-54 222.0
13 TraesCS2D01G399500 chr6D 96.774 31 1 0 3952 3982 334225776 334225746 7.000000e-03 52.8
14 TraesCS2D01G399500 chr6B 78.798 599 87 25 2099 2676 486224664 486225243 2.280000e-97 366.0
15 TraesCS2D01G399500 chr6B 87.000 200 26 0 2093 2292 539727742 539727543 4.040000e-55 226.0
16 TraesCS2D01G399500 chr6B 81.915 94 12 3 3890 3982 486226492 486226581 1.550000e-09 75.0


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 TraesCS2D01G399500 chr2D 512684772 512688789 4017 False 7420.0 7420 100.0000 1 4018 1 chr2D.!!$F1 4017
1 TraesCS2D01G399500 chr2A 656239010 656242857 3847 False 5602.0 5602 93.0760 175 4018 1 chr2A.!!$F1 3843
2 TraesCS2D01G399500 chr2B 602761415 602765392 3977 False 2910.0 5077 91.3945 87 4018 2 chr2B.!!$F1 3931
3 TraesCS2D01G399500 chr1B 332584951 332586679 1728 True 2584.0 2584 93.9720 2277 3975 1 chr1B.!!$R1 1698
4 TraesCS2D01G399500 chr6A 441441550 441442800 1250 False 1958.0 1958 95.2190 2296 3525 1 chr6A.!!$F1 1229
5 TraesCS2D01G399500 chr6A 473573669 473575567 1898 True 231.5 388 80.5580 2099 3982 2 chr6A.!!$R4 1883
6 TraesCS2D01G399500 chr6D 334225746 334227663 1917 True 217.9 383 87.9045 2099 3982 2 chr6D.!!$R2 1883
7 TraesCS2D01G399500 chr6B 486224664 486226581 1917 False 220.5 366 80.3565 2099 3982 2 chr6B.!!$F1 1883

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
124 125 0.313987 CGTATCCCAGCGTATCTGCA 59.686 55.000 0.00 0.0 41.50 4.41 F
636 663 1.134367 CCGATCGAGCAAGAACACCTA 59.866 52.381 18.66 0.0 0.00 3.08 F
1169 1277 0.035458 GTGTGGGTGTCCTCTTGGAG 59.965 60.000 0.00 0.0 44.16 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1117 1219 0.107945 GCTCCCATCAGAGAAAGCGT 60.108 55.000 0.0 0.0 35.82 5.07 R
1827 1945 2.337583 ACGATGATCAACACAAGACCG 58.662 47.619 0.0 0.0 0.00 4.79 R
3356 3689 2.674796 AGCTAACTAACTCCAAGCCG 57.325 50.000 0.0 0.0 33.63 5.52 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
30 31 7.817418 TTTAATACAAAGGATATCTGGGTGC 57.183 36.000 2.05 0.00 0.00 5.01
31 32 5.387113 AATACAAAGGATATCTGGGTGCA 57.613 39.130 2.05 0.00 0.00 4.57
32 33 3.004752 ACAAAGGATATCTGGGTGCAC 57.995 47.619 8.80 8.80 0.00 4.57
33 34 2.578021 ACAAAGGATATCTGGGTGCACT 59.422 45.455 17.98 0.00 0.00 4.40
34 35 3.010584 ACAAAGGATATCTGGGTGCACTT 59.989 43.478 17.98 0.00 0.00 3.16
35 36 4.227300 ACAAAGGATATCTGGGTGCACTTA 59.773 41.667 17.98 5.08 0.00 2.24
36 37 5.103940 ACAAAGGATATCTGGGTGCACTTAT 60.104 40.000 17.98 7.77 0.00 1.73
37 38 6.101150 ACAAAGGATATCTGGGTGCACTTATA 59.899 38.462 17.98 9.67 0.00 0.98
38 39 6.959606 AAGGATATCTGGGTGCACTTATAT 57.040 37.500 17.98 13.64 0.00 0.86
39 40 6.959606 AGGATATCTGGGTGCACTTATATT 57.040 37.500 17.98 0.54 0.00 1.28
40 41 6.951971 AGGATATCTGGGTGCACTTATATTC 58.048 40.000 17.98 12.58 0.00 1.75
41 42 6.501805 AGGATATCTGGGTGCACTTATATTCA 59.498 38.462 17.98 3.63 0.00 2.57
42 43 6.820656 GGATATCTGGGTGCACTTATATTCAG 59.179 42.308 17.98 12.27 0.00 3.02
43 44 5.894298 ATCTGGGTGCACTTATATTCAGA 57.106 39.130 17.98 16.40 35.01 3.27
44 45 5.023533 TCTGGGTGCACTTATATTCAGAC 57.976 43.478 17.98 0.00 0.00 3.51
45 46 4.130118 CTGGGTGCACTTATATTCAGACC 58.870 47.826 17.98 5.10 0.00 3.85
46 47 3.131396 GGGTGCACTTATATTCAGACCG 58.869 50.000 17.98 0.00 0.00 4.79
47 48 3.431766 GGGTGCACTTATATTCAGACCGT 60.432 47.826 17.98 0.00 0.00 4.83
48 49 4.189231 GGTGCACTTATATTCAGACCGTT 58.811 43.478 17.98 0.00 0.00 4.44
49 50 4.034048 GGTGCACTTATATTCAGACCGTTG 59.966 45.833 17.98 0.00 0.00 4.10
50 51 4.868171 GTGCACTTATATTCAGACCGTTGA 59.132 41.667 10.32 0.00 0.00 3.18
51 52 5.523916 GTGCACTTATATTCAGACCGTTGAT 59.476 40.000 10.32 0.00 0.00 2.57
52 53 6.037172 GTGCACTTATATTCAGACCGTTGATT 59.963 38.462 10.32 0.00 0.00 2.57
53 54 6.597672 TGCACTTATATTCAGACCGTTGATTT 59.402 34.615 0.00 0.00 0.00 2.17
54 55 7.120579 TGCACTTATATTCAGACCGTTGATTTT 59.879 33.333 0.00 0.00 0.00 1.82
55 56 7.429340 GCACTTATATTCAGACCGTTGATTTTG 59.571 37.037 0.00 0.00 0.00 2.44
56 57 8.664798 CACTTATATTCAGACCGTTGATTTTGA 58.335 33.333 0.00 0.00 0.00 2.69
57 58 8.665685 ACTTATATTCAGACCGTTGATTTTGAC 58.334 33.333 0.00 0.00 0.00 3.18
58 59 8.786826 TTATATTCAGACCGTTGATTTTGACT 57.213 30.769 0.00 0.00 0.00 3.41
59 60 9.878667 TTATATTCAGACCGTTGATTTTGACTA 57.121 29.630 0.00 0.00 0.00 2.59
60 61 8.964476 ATATTCAGACCGTTGATTTTGACTAT 57.036 30.769 0.00 0.00 0.00 2.12
61 62 6.480524 TTCAGACCGTTGATTTTGACTATG 57.519 37.500 0.00 0.00 0.00 2.23
62 63 5.547465 TCAGACCGTTGATTTTGACTATGT 58.453 37.500 0.00 0.00 0.00 2.29
63 64 5.408299 TCAGACCGTTGATTTTGACTATGTG 59.592 40.000 0.00 0.00 0.00 3.21
64 65 4.154195 AGACCGTTGATTTTGACTATGTGC 59.846 41.667 0.00 0.00 0.00 4.57
65 66 3.818210 ACCGTTGATTTTGACTATGTGCA 59.182 39.130 0.00 0.00 0.00 4.57
66 67 4.458989 ACCGTTGATTTTGACTATGTGCAT 59.541 37.500 0.00 0.00 0.00 3.96
67 68 5.030295 CCGTTGATTTTGACTATGTGCATC 58.970 41.667 0.00 0.00 0.00 3.91
68 69 5.391843 CCGTTGATTTTGACTATGTGCATCA 60.392 40.000 0.00 0.00 0.00 3.07
69 70 6.260377 CGTTGATTTTGACTATGTGCATCAT 58.740 36.000 0.00 0.00 40.25 2.45
70 71 7.408910 CGTTGATTTTGACTATGTGCATCATA 58.591 34.615 0.00 0.00 37.91 2.15
71 72 7.374228 CGTTGATTTTGACTATGTGCATCATAC 59.626 37.037 0.00 0.00 37.91 2.39
72 73 7.263100 TGATTTTGACTATGTGCATCATACC 57.737 36.000 0.00 0.00 37.91 2.73
73 74 7.056006 TGATTTTGACTATGTGCATCATACCT 58.944 34.615 0.00 0.00 37.91 3.08
74 75 6.682423 TTTTGACTATGTGCATCATACCTG 57.318 37.500 0.00 0.00 37.91 4.00
75 76 5.357742 TTGACTATGTGCATCATACCTGT 57.642 39.130 0.00 0.00 37.91 4.00
76 77 4.696455 TGACTATGTGCATCATACCTGTG 58.304 43.478 0.00 0.00 37.91 3.66
77 78 3.470709 ACTATGTGCATCATACCTGTGC 58.529 45.455 0.00 0.00 37.91 4.57
78 79 2.423446 ATGTGCATCATACCTGTGCA 57.577 45.000 0.00 0.00 45.69 4.57
81 82 2.320745 TGCATCATACCTGTGCAGAG 57.679 50.000 3.32 3.32 43.30 3.35
82 83 1.134310 TGCATCATACCTGTGCAGAGG 60.134 52.381 27.52 27.52 43.30 3.69
83 84 1.590932 CATCATACCTGTGCAGAGGC 58.409 55.000 28.90 0.00 36.46 4.70
84 85 0.471617 ATCATACCTGTGCAGAGGCC 59.528 55.000 28.90 0.00 40.13 5.19
85 86 0.909133 TCATACCTGTGCAGAGGCCA 60.909 55.000 28.90 17.68 40.13 5.36
86 87 0.463295 CATACCTGTGCAGAGGCCAG 60.463 60.000 28.90 14.86 40.13 4.85
88 89 3.644606 CCTGTGCAGAGGCCAGGT 61.645 66.667 18.17 0.00 45.64 4.00
89 90 2.359602 CTGTGCAGAGGCCAGGTG 60.360 66.667 5.01 0.00 40.13 4.00
90 91 4.648626 TGTGCAGAGGCCAGGTGC 62.649 66.667 15.18 15.18 40.13 5.01
100 101 2.404995 GCCAGGTGCTGCTCATCAC 61.405 63.158 0.00 0.00 36.87 3.06
110 111 3.557185 TGCTGCTCATCACATTTCGTATC 59.443 43.478 0.00 0.00 0.00 2.24
114 115 3.496130 GCTCATCACATTTCGTATCCCAG 59.504 47.826 0.00 0.00 0.00 4.45
121 122 3.321111 ACATTTCGTATCCCAGCGTATCT 59.679 43.478 0.00 0.00 0.00 1.98
124 125 0.313987 CGTATCCCAGCGTATCTGCA 59.686 55.000 0.00 0.00 41.50 4.41
132 133 2.611224 CCAGCGTATCTGCATGATGCTA 60.611 50.000 19.19 7.23 45.31 3.49
137 138 4.435253 GCGTATCTGCATGATGCTACATTC 60.435 45.833 19.19 4.97 45.31 2.67
145 146 5.065602 TGCATGATGCTACATTCTGAGTTTC 59.934 40.000 19.19 0.00 45.31 2.78
154 155 5.035784 ACATTCTGAGTTTCTAAAAGCGC 57.964 39.130 0.00 0.00 0.00 5.92
156 157 3.402628 TCTGAGTTTCTAAAAGCGCCT 57.597 42.857 2.29 0.00 0.00 5.52
157 158 3.326747 TCTGAGTTTCTAAAAGCGCCTC 58.673 45.455 2.29 0.00 0.00 4.70
158 159 3.006967 TCTGAGTTTCTAAAAGCGCCTCT 59.993 43.478 2.29 0.00 0.00 3.69
159 160 4.219944 TCTGAGTTTCTAAAAGCGCCTCTA 59.780 41.667 2.29 0.00 0.00 2.43
160 161 5.086104 TGAGTTTCTAAAAGCGCCTCTAT 57.914 39.130 2.29 0.00 0.00 1.98
161 162 5.109903 TGAGTTTCTAAAAGCGCCTCTATC 58.890 41.667 2.29 0.00 0.00 2.08
162 163 4.443621 AGTTTCTAAAAGCGCCTCTATCC 58.556 43.478 2.29 0.00 0.00 2.59
163 164 4.081087 AGTTTCTAAAAGCGCCTCTATCCA 60.081 41.667 2.29 0.00 0.00 3.41
211 212 7.201626 GCCATGCATTATGTTTTGAAGCAATAA 60.202 33.333 0.00 0.00 34.87 1.40
294 299 5.383130 CACGCCTTAAAAGCTAAAACTCTC 58.617 41.667 0.00 0.00 0.00 3.20
313 318 1.730064 TCGACGAATTTTGTAGCCAGC 59.270 47.619 0.00 0.00 0.00 4.85
418 430 2.281762 GCACTGTCGCGTAATAGAAAGG 59.718 50.000 5.77 0.00 0.00 3.11
419 431 3.766151 CACTGTCGCGTAATAGAAAGGA 58.234 45.455 5.77 0.00 0.00 3.36
420 432 4.171005 CACTGTCGCGTAATAGAAAGGAA 58.829 43.478 5.77 0.00 0.00 3.36
421 433 4.624024 CACTGTCGCGTAATAGAAAGGAAA 59.376 41.667 5.77 0.00 0.00 3.13
422 434 5.119588 CACTGTCGCGTAATAGAAAGGAAAA 59.880 40.000 5.77 0.00 0.00 2.29
636 663 1.134367 CCGATCGAGCAAGAACACCTA 59.866 52.381 18.66 0.00 0.00 3.08
640 667 1.134367 TCGAGCAAGAACACCTATCGG 59.866 52.381 0.00 0.00 0.00 4.18
663 703 1.268283 CCTTCCTCCCCCTCACAGTC 61.268 65.000 0.00 0.00 0.00 3.51
664 704 1.608717 CTTCCTCCCCCTCACAGTCG 61.609 65.000 0.00 0.00 0.00 4.18
665 705 3.775654 CCTCCCCCTCACAGTCGC 61.776 72.222 0.00 0.00 0.00 5.19
666 706 4.135153 CTCCCCCTCACAGTCGCG 62.135 72.222 0.00 0.00 0.00 5.87
669 709 4.457496 CCCCTCACAGTCGCGCAT 62.457 66.667 8.75 0.00 0.00 4.73
670 710 2.887568 CCCTCACAGTCGCGCATC 60.888 66.667 8.75 0.00 0.00 3.91
671 711 3.250323 CCTCACAGTCGCGCATCG 61.250 66.667 8.75 0.00 40.15 3.84
703 776 2.040884 TCCAATCCCCTCCCCTCG 60.041 66.667 0.00 0.00 0.00 4.63
902 978 3.369471 CCTCCGCTCAAGAAATCTACCAA 60.369 47.826 0.00 0.00 0.00 3.67
903 979 3.861840 TCCGCTCAAGAAATCTACCAAG 58.138 45.455 0.00 0.00 0.00 3.61
905 981 4.020573 TCCGCTCAAGAAATCTACCAAGAA 60.021 41.667 0.00 0.00 34.73 2.52
997 1087 2.084596 GGGGGTAGCCAAAGTCCTT 58.915 57.895 14.06 0.00 0.00 3.36
1109 1211 3.244353 CCTCTCTGTGACATGGTTCTTGT 60.244 47.826 0.00 0.00 0.00 3.16
1114 1216 3.351740 TGTGACATGGTTCTTGTTGTGT 58.648 40.909 0.00 0.00 0.00 3.72
1117 1219 2.098614 ACATGGTTCTTGTTGTGTGCA 58.901 42.857 0.00 0.00 0.00 4.57
1145 1247 2.901192 CTCTGATGGGAGCATGATCTCT 59.099 50.000 12.89 0.00 33.70 3.10
1162 1270 0.188587 TCTCTCTGTGTGGGTGTCCT 59.811 55.000 0.00 0.00 0.00 3.85
1163 1271 0.605589 CTCTCTGTGTGGGTGTCCTC 59.394 60.000 0.00 0.00 0.00 3.71
1164 1272 0.188587 TCTCTGTGTGGGTGTCCTCT 59.811 55.000 0.00 0.00 0.00 3.69
1165 1273 1.051812 CTCTGTGTGGGTGTCCTCTT 58.948 55.000 0.00 0.00 0.00 2.85
1166 1274 0.758734 TCTGTGTGGGTGTCCTCTTG 59.241 55.000 0.00 0.00 0.00 3.02
1167 1275 0.250467 CTGTGTGGGTGTCCTCTTGG 60.250 60.000 0.00 0.00 0.00 3.61
1168 1276 0.692756 TGTGTGGGTGTCCTCTTGGA 60.693 55.000 0.00 0.00 40.69 3.53
1169 1277 0.035458 GTGTGGGTGTCCTCTTGGAG 59.965 60.000 0.00 0.00 44.16 3.86
1179 1287 1.150135 TCCTCTTGGAGTCTTGGGTCT 59.850 52.381 0.00 0.00 37.46 3.85
1241 1349 0.386352 CTGCAACACAATCAGCACCG 60.386 55.000 0.00 0.00 32.87 4.94
1254 1362 1.140804 GCACCGCTCTCTCTTCTCC 59.859 63.158 0.00 0.00 0.00 3.71
1255 1363 1.599606 GCACCGCTCTCTCTTCTCCA 61.600 60.000 0.00 0.00 0.00 3.86
1256 1364 1.110442 CACCGCTCTCTCTTCTCCAT 58.890 55.000 0.00 0.00 0.00 3.41
1257 1365 2.302260 CACCGCTCTCTCTTCTCCATA 58.698 52.381 0.00 0.00 0.00 2.74
1258 1366 2.293122 CACCGCTCTCTCTTCTCCATAG 59.707 54.545 0.00 0.00 0.00 2.23
1259 1367 1.885887 CCGCTCTCTCTTCTCCATAGG 59.114 57.143 0.00 0.00 0.00 2.57
1313 1427 1.139058 TGCGGCTTTAATCCTCTCTCC 59.861 52.381 0.00 0.00 0.00 3.71
1325 1439 3.535962 CTCTCCGCTGCCCTCCTC 61.536 72.222 0.00 0.00 0.00 3.71
1430 1544 2.055042 CCCTCCTCACCTCACCTCG 61.055 68.421 0.00 0.00 0.00 4.63
1450 1564 0.396278 CCCCTTCCTTTCTCATGGCC 60.396 60.000 0.00 0.00 0.00 5.36
1613 1731 0.551396 CTTCTTCCCCGGCCCTTATT 59.449 55.000 0.00 0.00 0.00 1.40
1643 1761 3.369892 CCTTTGCCTTTCTCTGCTAGCTA 60.370 47.826 17.23 3.10 0.00 3.32
1712 1830 0.462759 GAGATTCTTGACGCCCCCAG 60.463 60.000 0.00 0.00 0.00 4.45
1745 1863 1.687493 CTCCCCACCTCCACCTCTC 60.687 68.421 0.00 0.00 0.00 3.20
1746 1864 2.174876 CTCCCCACCTCCACCTCTCT 62.175 65.000 0.00 0.00 0.00 3.10
1827 1945 2.533266 TAGCTAGCTTGGCATGTAGC 57.467 50.000 24.88 18.43 44.65 3.58
1880 1998 0.441533 GTGACTGATCAAGTGCTGCG 59.558 55.000 0.00 0.00 40.07 5.18
2297 2418 0.871057 GCAAGAACAAGCGCTCTTCT 59.129 50.000 19.67 19.67 29.29 2.85
3356 3689 1.037579 AGCTTCATTTTAGGCCGGCC 61.038 55.000 39.29 39.29 0.00 6.13
3357 3690 1.727467 CTTCATTTTAGGCCGGCCG 59.273 57.895 38.88 23.96 41.95 6.13
3358 3691 1.724582 CTTCATTTTAGGCCGGCCGG 61.725 60.000 40.26 40.26 41.95 6.13
3370 3703 2.669240 GGCCGGCTTGGAGTTAGT 59.331 61.111 28.56 0.00 42.00 2.24
3380 3713 3.707793 CTTGGAGTTAGTTAGCTAGGCG 58.292 50.000 0.00 0.00 0.00 5.52
3485 3818 0.632294 GTAGGAGTGGGGAGAGGACT 59.368 60.000 0.00 0.00 0.00 3.85
3670 4069 7.764443 ACATACAATGAGTACAAGTACCATCAC 59.236 37.037 6.74 0.00 36.75 3.06
3722 4133 6.589523 TCATTATTGTGCTTGTTGGTTTATGC 59.410 34.615 0.00 0.00 0.00 3.14
3723 4134 3.808466 TTGTGCTTGTTGGTTTATGCA 57.192 38.095 0.00 0.00 0.00 3.96
3724 4135 4.333913 TTGTGCTTGTTGGTTTATGCAT 57.666 36.364 3.79 3.79 32.98 3.96
3754 4165 1.541588 GGCTCACCCAAAGTTGATCAC 59.458 52.381 0.00 0.00 0.00 3.06
3791 4202 8.613060 AGAGCATGTAATAATATGTGTCCTTG 57.387 34.615 0.00 0.00 0.00 3.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 8.691797 GCACCCAGATATCCTTTGTATTAAAAA 58.308 33.333 0.00 0.00 0.00 1.94
5 6 7.836685 TGCACCCAGATATCCTTTGTATTAAAA 59.163 33.333 0.00 0.00 0.00 1.52
7 8 6.770785 GTGCACCCAGATATCCTTTGTATTAA 59.229 38.462 5.22 0.00 0.00 1.40
8 9 6.101150 AGTGCACCCAGATATCCTTTGTATTA 59.899 38.462 14.63 0.00 0.00 0.98
9 10 5.103940 AGTGCACCCAGATATCCTTTGTATT 60.104 40.000 14.63 0.00 0.00 1.89
10 11 4.413520 AGTGCACCCAGATATCCTTTGTAT 59.586 41.667 14.63 0.00 0.00 2.29
11 12 3.780294 AGTGCACCCAGATATCCTTTGTA 59.220 43.478 14.63 0.00 0.00 2.41
12 13 2.578021 AGTGCACCCAGATATCCTTTGT 59.422 45.455 14.63 0.00 0.00 2.83
13 14 3.287867 AGTGCACCCAGATATCCTTTG 57.712 47.619 14.63 0.00 0.00 2.77
14 15 5.653255 ATAAGTGCACCCAGATATCCTTT 57.347 39.130 14.63 0.00 0.00 3.11
15 16 6.959606 ATATAAGTGCACCCAGATATCCTT 57.040 37.500 14.63 0.00 0.00 3.36
16 17 6.501805 TGAATATAAGTGCACCCAGATATCCT 59.498 38.462 14.63 0.00 0.00 3.24
17 18 6.711277 TGAATATAAGTGCACCCAGATATCC 58.289 40.000 14.63 0.53 0.00 2.59
18 19 7.547370 GTCTGAATATAAGTGCACCCAGATATC 59.453 40.741 14.63 5.22 32.90 1.63
19 20 7.390027 GTCTGAATATAAGTGCACCCAGATAT 58.610 38.462 14.63 8.67 32.90 1.63
20 21 6.239600 GGTCTGAATATAAGTGCACCCAGATA 60.240 42.308 14.63 6.64 32.90 1.98
21 22 5.455326 GGTCTGAATATAAGTGCACCCAGAT 60.455 44.000 14.63 0.97 32.90 2.90
22 23 4.141711 GGTCTGAATATAAGTGCACCCAGA 60.142 45.833 14.63 11.57 0.00 3.86
23 24 4.130118 GGTCTGAATATAAGTGCACCCAG 58.870 47.826 14.63 9.54 0.00 4.45
24 25 3.431626 CGGTCTGAATATAAGTGCACCCA 60.432 47.826 14.63 1.03 0.00 4.51
25 26 3.131396 CGGTCTGAATATAAGTGCACCC 58.869 50.000 14.63 1.51 0.00 4.61
26 27 3.793559 ACGGTCTGAATATAAGTGCACC 58.206 45.455 14.63 0.00 0.00 5.01
27 28 4.868171 TCAACGGTCTGAATATAAGTGCAC 59.132 41.667 9.40 9.40 0.00 4.57
28 29 5.079689 TCAACGGTCTGAATATAAGTGCA 57.920 39.130 0.00 0.00 0.00 4.57
29 30 6.604735 AATCAACGGTCTGAATATAAGTGC 57.395 37.500 0.00 0.00 0.00 4.40
30 31 8.664798 TCAAAATCAACGGTCTGAATATAAGTG 58.335 33.333 0.00 0.00 0.00 3.16
31 32 8.665685 GTCAAAATCAACGGTCTGAATATAAGT 58.334 33.333 0.00 0.00 0.00 2.24
32 33 8.883731 AGTCAAAATCAACGGTCTGAATATAAG 58.116 33.333 0.00 0.00 0.00 1.73
33 34 8.786826 AGTCAAAATCAACGGTCTGAATATAA 57.213 30.769 0.00 0.00 0.00 0.98
35 36 8.830580 CATAGTCAAAATCAACGGTCTGAATAT 58.169 33.333 0.00 0.00 0.00 1.28
36 37 7.822334 ACATAGTCAAAATCAACGGTCTGAATA 59.178 33.333 0.00 0.00 0.00 1.75
37 38 6.655003 ACATAGTCAAAATCAACGGTCTGAAT 59.345 34.615 0.00 0.00 0.00 2.57
38 39 5.995282 ACATAGTCAAAATCAACGGTCTGAA 59.005 36.000 0.00 0.00 0.00 3.02
39 40 5.408299 CACATAGTCAAAATCAACGGTCTGA 59.592 40.000 0.00 0.00 0.00 3.27
40 41 5.621422 CACATAGTCAAAATCAACGGTCTG 58.379 41.667 0.00 0.00 0.00 3.51
41 42 4.154195 GCACATAGTCAAAATCAACGGTCT 59.846 41.667 0.00 0.00 0.00 3.85
42 43 4.083537 TGCACATAGTCAAAATCAACGGTC 60.084 41.667 0.00 0.00 0.00 4.79
43 44 3.818210 TGCACATAGTCAAAATCAACGGT 59.182 39.130 0.00 0.00 0.00 4.83
44 45 4.418013 TGCACATAGTCAAAATCAACGG 57.582 40.909 0.00 0.00 0.00 4.44
45 46 5.630061 TGATGCACATAGTCAAAATCAACG 58.370 37.500 0.00 0.00 0.00 4.10
46 47 7.645340 GGTATGATGCACATAGTCAAAATCAAC 59.355 37.037 8.62 0.00 41.41 3.18
47 48 7.557358 AGGTATGATGCACATAGTCAAAATCAA 59.443 33.333 8.62 0.00 41.41 2.57
48 49 7.012610 CAGGTATGATGCACATAGTCAAAATCA 59.987 37.037 8.62 0.00 41.41 2.57
49 50 7.012704 ACAGGTATGATGCACATAGTCAAAATC 59.987 37.037 8.62 0.00 41.41 2.17
50 51 6.830324 ACAGGTATGATGCACATAGTCAAAAT 59.170 34.615 8.62 0.00 41.41 1.82
51 52 6.093909 CACAGGTATGATGCACATAGTCAAAA 59.906 38.462 8.62 0.00 41.41 2.44
52 53 5.585844 CACAGGTATGATGCACATAGTCAAA 59.414 40.000 8.62 0.00 41.41 2.69
53 54 5.118286 CACAGGTATGATGCACATAGTCAA 58.882 41.667 8.62 0.00 41.41 3.18
54 55 4.696455 CACAGGTATGATGCACATAGTCA 58.304 43.478 8.62 0.00 41.41 3.41
55 56 3.496130 GCACAGGTATGATGCACATAGTC 59.504 47.826 8.62 5.77 41.41 2.59
56 57 3.118298 TGCACAGGTATGATGCACATAGT 60.118 43.478 8.62 3.02 44.17 2.12
57 58 3.469739 TGCACAGGTATGATGCACATAG 58.530 45.455 8.62 2.55 44.17 2.23
58 59 3.134442 TCTGCACAGGTATGATGCACATA 59.866 43.478 0.00 0.00 44.17 2.29
59 60 2.092807 TCTGCACAGGTATGATGCACAT 60.093 45.455 0.00 0.00 44.17 3.21
60 61 1.278699 TCTGCACAGGTATGATGCACA 59.721 47.619 0.00 0.00 44.17 4.57
61 62 1.938577 CTCTGCACAGGTATGATGCAC 59.061 52.381 0.00 0.00 44.17 4.57
62 63 1.134310 CCTCTGCACAGGTATGATGCA 60.134 52.381 0.00 0.00 46.73 3.96
63 64 1.590932 CCTCTGCACAGGTATGATGC 58.409 55.000 0.00 0.00 39.88 3.91
64 65 1.590932 GCCTCTGCACAGGTATGATG 58.409 55.000 9.97 0.00 35.72 3.07
65 66 0.471617 GGCCTCTGCACAGGTATGAT 59.528 55.000 9.97 0.00 40.13 2.45
66 67 0.909133 TGGCCTCTGCACAGGTATGA 60.909 55.000 9.97 0.00 40.13 2.15
67 68 0.463295 CTGGCCTCTGCACAGGTATG 60.463 60.000 9.97 0.00 40.13 2.39
68 69 1.630126 CCTGGCCTCTGCACAGGTAT 61.630 60.000 9.97 0.00 44.43 2.73
69 70 2.293318 CCTGGCCTCTGCACAGGTA 61.293 63.158 9.97 0.00 44.43 3.08
70 71 3.644606 CCTGGCCTCTGCACAGGT 61.645 66.667 9.97 0.00 44.43 4.00
72 73 2.359602 CACCTGGCCTCTGCACAG 60.360 66.667 3.32 0.00 40.13 3.66
73 74 4.648626 GCACCTGGCCTCTGCACA 62.649 66.667 3.32 0.00 40.13 4.57
74 75 4.341783 AGCACCTGGCCTCTGCAC 62.342 66.667 18.36 0.00 46.50 4.57
75 76 4.340246 CAGCACCTGGCCTCTGCA 62.340 66.667 18.36 0.00 46.50 4.41
77 78 3.972971 GAGCAGCACCTGGCCTCTG 62.973 68.421 3.32 4.80 46.50 3.35
78 79 3.715097 GAGCAGCACCTGGCCTCT 61.715 66.667 3.32 0.00 46.50 3.69
79 80 3.341202 ATGAGCAGCACCTGGCCTC 62.341 63.158 3.32 0.00 46.50 4.70
80 81 3.336568 ATGAGCAGCACCTGGCCT 61.337 61.111 3.32 0.00 46.50 5.19
81 82 2.827642 GATGAGCAGCACCTGGCC 60.828 66.667 0.00 0.00 46.50 5.36
82 83 2.045634 TGATGAGCAGCACCTGGC 60.046 61.111 0.00 0.00 45.30 4.85
83 84 0.393944 ATGTGATGAGCAGCACCTGG 60.394 55.000 15.30 0.00 46.28 4.45
84 85 1.460504 AATGTGATGAGCAGCACCTG 58.539 50.000 15.30 0.00 46.28 4.00
85 86 2.089980 GAAATGTGATGAGCAGCACCT 58.910 47.619 15.30 3.78 46.28 4.00
86 87 1.202110 CGAAATGTGATGAGCAGCACC 60.202 52.381 15.30 0.43 46.28 5.01
87 88 1.466167 ACGAAATGTGATGAGCAGCAC 59.534 47.619 11.59 11.59 46.94 4.40
88 89 1.812235 ACGAAATGTGATGAGCAGCA 58.188 45.000 0.00 0.00 0.00 4.41
89 90 3.059325 GGATACGAAATGTGATGAGCAGC 60.059 47.826 0.00 0.00 0.00 5.25
90 91 3.496130 GGGATACGAAATGTGATGAGCAG 59.504 47.826 0.00 0.00 37.60 4.24
100 101 3.675225 CAGATACGCTGGGATACGAAATG 59.325 47.826 0.00 0.00 41.07 2.32
110 111 1.154197 CATCATGCAGATACGCTGGG 58.846 55.000 0.00 0.00 45.03 4.45
121 122 4.146745 ACTCAGAATGTAGCATCATGCA 57.853 40.909 13.38 0.00 41.55 3.96
124 125 9.453572 TTTTAGAAACTCAGAATGTAGCATCAT 57.546 29.630 0.00 0.00 37.40 2.45
132 133 4.083271 GGCGCTTTTAGAAACTCAGAATGT 60.083 41.667 7.64 0.00 37.40 2.71
137 138 3.330267 AGAGGCGCTTTTAGAAACTCAG 58.670 45.455 7.64 0.00 0.00 3.35
145 146 5.560966 TTTTTGGATAGAGGCGCTTTTAG 57.439 39.130 7.64 0.00 0.00 1.85
180 181 7.201626 GCTTCAAAACATAATGCATGGCAATAA 60.202 33.333 0.00 0.00 43.62 1.40
247 248 6.090763 TGCTCGTGTACAGTTCAAAATATGAG 59.909 38.462 0.00 0.00 39.77 2.90
248 249 5.929415 TGCTCGTGTACAGTTCAAAATATGA 59.071 36.000 0.00 0.00 35.85 2.15
294 299 1.526986 CGCTGGCTACAAAATTCGTCG 60.527 52.381 0.00 0.00 0.00 5.12
313 318 1.122501 CAAGTCATGTTGTCGTCGACG 59.877 52.381 31.30 31.30 41.45 5.12
419 431 8.721478 GCAACCTTTTCTCTTTTCTTTTCTTTT 58.279 29.630 0.00 0.00 0.00 2.27
420 432 7.877612 TGCAACCTTTTCTCTTTTCTTTTCTTT 59.122 29.630 0.00 0.00 0.00 2.52
421 433 7.331934 GTGCAACCTTTTCTCTTTTCTTTTCTT 59.668 33.333 0.00 0.00 0.00 2.52
422 434 6.813649 GTGCAACCTTTTCTCTTTTCTTTTCT 59.186 34.615 0.00 0.00 0.00 2.52
547 563 1.094785 CATTGTAAGGGAAGGCACCG 58.905 55.000 0.00 0.00 0.00 4.94
663 703 3.287408 CAGATCTATCTATCGATGCGCG 58.713 50.000 8.54 0.00 36.99 6.86
664 704 3.042189 GCAGATCTATCTATCGATGCGC 58.958 50.000 8.54 0.00 34.85 6.09
665 705 4.526625 GAGCAGATCTATCTATCGATGCG 58.473 47.826 8.54 0.00 34.14 4.73
666 706 4.337836 TGGAGCAGATCTATCTATCGATGC 59.662 45.833 8.54 0.00 34.85 3.91
668 708 6.265196 GGATTGGAGCAGATCTATCTATCGAT 59.735 42.308 2.16 2.16 34.85 3.59
669 709 5.592282 GGATTGGAGCAGATCTATCTATCGA 59.408 44.000 0.00 0.00 34.85 3.59
670 710 5.221224 GGGATTGGAGCAGATCTATCTATCG 60.221 48.000 0.00 0.00 34.85 2.92
671 711 5.070313 GGGGATTGGAGCAGATCTATCTATC 59.930 48.000 0.00 4.96 34.85 2.08
674 714 3.180507 GGGGATTGGAGCAGATCTATCT 58.819 50.000 0.00 0.00 37.72 1.98
678 718 1.433121 GAGGGGATTGGAGCAGATCT 58.567 55.000 0.00 0.00 0.00 2.75
679 719 0.399833 GGAGGGGATTGGAGCAGATC 59.600 60.000 0.00 0.00 0.00 2.75
981 1071 0.251165 TGCAAGGACTTTGGCTACCC 60.251 55.000 0.00 0.00 37.26 3.69
1049 1147 3.126000 CGGCAAGATCAAGGAGAAGAAAC 59.874 47.826 0.00 0.00 0.00 2.78
1109 1211 0.657312 CAGAGAAAGCGTGCACACAA 59.343 50.000 18.64 0.00 0.00 3.33
1114 1216 0.674581 CCCATCAGAGAAAGCGTGCA 60.675 55.000 0.00 0.00 0.00 4.57
1117 1219 0.107945 GCTCCCATCAGAGAAAGCGT 60.108 55.000 0.00 0.00 35.82 5.07
1145 1247 0.188587 AGAGGACACCCACACAGAGA 59.811 55.000 0.00 0.00 33.88 3.10
1162 1270 2.408565 ACAAGACCCAAGACTCCAAGA 58.591 47.619 0.00 0.00 0.00 3.02
1163 1271 2.938956 ACAAGACCCAAGACTCCAAG 57.061 50.000 0.00 0.00 0.00 3.61
1164 1272 2.777692 AGAACAAGACCCAAGACTCCAA 59.222 45.455 0.00 0.00 0.00 3.53
1165 1273 2.408565 AGAACAAGACCCAAGACTCCA 58.591 47.619 0.00 0.00 0.00 3.86
1166 1274 3.403968 GAAGAACAAGACCCAAGACTCC 58.596 50.000 0.00 0.00 0.00 3.85
1167 1275 3.071747 AGGAAGAACAAGACCCAAGACTC 59.928 47.826 0.00 0.00 0.00 3.36
1168 1276 3.049344 AGGAAGAACAAGACCCAAGACT 58.951 45.455 0.00 0.00 0.00 3.24
1169 1277 3.493767 AGGAAGAACAAGACCCAAGAC 57.506 47.619 0.00 0.00 0.00 3.01
1241 1349 2.315176 TGCCTATGGAGAAGAGAGAGC 58.685 52.381 0.00 0.00 0.00 4.09
1254 1362 4.973168 TCACCTTAAAGCCTATGCCTATG 58.027 43.478 0.00 0.00 38.69 2.23
1255 1363 5.456763 CCTTCACCTTAAAGCCTATGCCTAT 60.457 44.000 0.00 0.00 38.69 2.57
1256 1364 4.141482 CCTTCACCTTAAAGCCTATGCCTA 60.141 45.833 0.00 0.00 38.69 3.93
1257 1365 3.372025 CCTTCACCTTAAAGCCTATGCCT 60.372 47.826 0.00 0.00 38.69 4.75
1258 1366 2.952310 CCTTCACCTTAAAGCCTATGCC 59.048 50.000 0.00 0.00 38.69 4.40
1259 1367 3.378427 CACCTTCACCTTAAAGCCTATGC 59.622 47.826 0.00 0.00 37.95 3.14
1325 1439 2.169144 GCTTTCATGGATCAAAAGGGGG 59.831 50.000 0.00 0.00 32.01 5.40
1430 1544 1.039785 GCCATGAGAAAGGAAGGGGC 61.040 60.000 0.00 0.00 0.00 5.80
1450 1564 3.510719 CGAGGCAAGAGAGAGAAGAAAG 58.489 50.000 0.00 0.00 0.00 2.62
1613 1731 4.827284 CAGAGAAAGGCAAAGGAAAAGGTA 59.173 41.667 0.00 0.00 0.00 3.08
1643 1761 5.793967 AGGATACAAAGGGAGATTAGAGGT 58.206 41.667 0.00 0.00 41.41 3.85
1723 1841 3.403558 GTGGAGGTGGGGAGGCTC 61.404 72.222 5.78 5.78 0.00 4.70
1827 1945 2.337583 ACGATGATCAACACAAGACCG 58.662 47.619 0.00 0.00 0.00 4.79
1880 1998 4.142160 TGAGGACACAGATACACACATAGC 60.142 45.833 0.00 0.00 0.00 2.97
3356 3689 2.674796 AGCTAACTAACTCCAAGCCG 57.325 50.000 0.00 0.00 33.63 5.52
3357 3690 3.741700 GCCTAGCTAACTAACTCCAAGCC 60.742 52.174 0.00 0.00 33.63 4.35
3358 3691 3.459145 GCCTAGCTAACTAACTCCAAGC 58.541 50.000 0.00 0.00 0.00 4.01
3359 3692 3.130693 ACGCCTAGCTAACTAACTCCAAG 59.869 47.826 0.00 0.00 0.00 3.61
3370 3703 1.683943 ATGTACCGACGCCTAGCTAA 58.316 50.000 0.00 0.00 0.00 3.09
3485 3818 2.560504 CACCAAACACACTGTAGCTCA 58.439 47.619 0.00 0.00 0.00 4.26
3582 3980 4.017177 ACTACTACAAACTTGGAAGCCC 57.983 45.455 0.00 0.00 0.00 5.19
3722 4133 7.624549 ACTTTGGGTGAGCCTATATATGTATG 58.375 38.462 1.06 0.00 34.45 2.39
3723 4134 7.814693 ACTTTGGGTGAGCCTATATATGTAT 57.185 36.000 1.06 0.00 34.45 2.29
3724 4135 7.291416 TCAACTTTGGGTGAGCCTATATATGTA 59.709 37.037 1.06 0.00 34.45 2.29


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

AutoCloner maintained by Alex Coulton.