Multiple sequence alignment - TraesCS2D01G020000

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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 TraesCS2D01G020000 chr2D 100.000 3482 0 0 1 3482 9603748 9607229 0.000000e+00 6431.0
1 TraesCS2D01G020000 chr2D 84.960 1895 261 15 623 2509 19586638 19588516 0.000000e+00 1899.0
2 TraesCS2D01G020000 chr2D 83.607 1885 280 28 640 2508 8695302 8697173 0.000000e+00 1742.0
3 TraesCS2D01G020000 chr2D 83.676 1850 268 21 678 2520 85929901 85928079 0.000000e+00 1712.0
4 TraesCS2D01G020000 chr2D 82.276 1529 241 17 998 2520 8670687 8672191 0.000000e+00 1295.0
5 TraesCS2D01G020000 chr2B 90.107 2901 256 20 578 3462 11518742 11515857 0.000000e+00 3738.0
6 TraesCS2D01G020000 chr2B 89.793 2900 236 32 578 3462 12421889 12424743 0.000000e+00 3661.0
7 TraesCS2D01G020000 chr2B 85.380 1710 237 11 814 2520 768807185 768805486 0.000000e+00 1760.0
8 TraesCS2D01G020000 chr2B 83.784 1850 270 19 678 2520 138993610 138991784 0.000000e+00 1727.0
9 TraesCS2D01G020000 chr2B 82.866 321 43 6 3146 3460 12945690 12946004 9.520000e-71 278.0
10 TraesCS2D01G020000 chr2B 87.333 150 18 1 713 862 11540986 11540838 1.660000e-38 171.0
11 TraesCS2D01G020000 chr2B 86.395 147 19 1 640 786 768807328 768807183 3.600000e-35 159.0
12 TraesCS2D01G020000 chr2A 91.337 2251 155 17 578 2825 8706990 8709203 0.000000e+00 3040.0
13 TraesCS2D01G020000 chr2A 82.512 1704 260 27 823 2520 8736990 8735319 0.000000e+00 1461.0
14 TraesCS2D01G020000 chr2A 91.738 581 26 3 1 581 8705182 8705740 0.000000e+00 787.0
15 TraesCS2D01G020000 chr2A 87.342 79 8 2 484 561 9086269 9086346 4.790000e-14 89.8
16 TraesCS2D01G020000 chr5B 86.364 88 6 4 479 565 576217394 576217476 1.330000e-14 91.6
17 TraesCS2D01G020000 chr5B 87.342 79 10 0 484 562 643914707 643914629 1.330000e-14 91.6
18 TraesCS2D01G020000 chr5B 100.000 32 0 0 421 452 121001421 121001390 3.750000e-05 60.2
19 TraesCS2D01G020000 chr1B 86.250 80 11 0 483 562 12917669 12917748 1.720000e-13 87.9
20 TraesCS2D01G020000 chr6A 100.000 32 0 0 421 452 255186919 255186888 3.750000e-05 60.2
21 TraesCS2D01G020000 chr3D 100.000 32 0 0 421 452 307935853 307935884 3.750000e-05 60.2
22 TraesCS2D01G020000 chr1D 100.000 32 0 0 421 452 50709220 50709189 3.750000e-05 60.2
23 TraesCS2D01G020000 chr7D 94.737 38 0 2 415 452 547491162 547491127 1.350000e-04 58.4
24 TraesCS2D01G020000 chr7A 94.737 38 0 2 415 452 631254255 631254290 1.350000e-04 58.4
25 TraesCS2D01G020000 chr6D 89.130 46 5 0 407 452 26404888 26404933 1.350000e-04 58.4
26 TraesCS2D01G020000 chr4A 94.737 38 0 2 417 452 164517496 164517533 1.350000e-04 58.4


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 TraesCS2D01G020000 chr2D 9603748 9607229 3481 False 6431.0 6431 100.0000 1 3482 1 chr2D.!!$F3 3481
1 TraesCS2D01G020000 chr2D 19586638 19588516 1878 False 1899.0 1899 84.9600 623 2509 1 chr2D.!!$F4 1886
2 TraesCS2D01G020000 chr2D 8695302 8697173 1871 False 1742.0 1742 83.6070 640 2508 1 chr2D.!!$F2 1868
3 TraesCS2D01G020000 chr2D 85928079 85929901 1822 True 1712.0 1712 83.6760 678 2520 1 chr2D.!!$R1 1842
4 TraesCS2D01G020000 chr2D 8670687 8672191 1504 False 1295.0 1295 82.2760 998 2520 1 chr2D.!!$F1 1522
5 TraesCS2D01G020000 chr2B 11515857 11518742 2885 True 3738.0 3738 90.1070 578 3462 1 chr2B.!!$R1 2884
6 TraesCS2D01G020000 chr2B 12421889 12424743 2854 False 3661.0 3661 89.7930 578 3462 1 chr2B.!!$F1 2884
7 TraesCS2D01G020000 chr2B 138991784 138993610 1826 True 1727.0 1727 83.7840 678 2520 1 chr2B.!!$R3 1842
8 TraesCS2D01G020000 chr2B 768805486 768807328 1842 True 959.5 1760 85.8875 640 2520 2 chr2B.!!$R4 1880
9 TraesCS2D01G020000 chr2A 8705182 8709203 4021 False 1913.5 3040 91.5375 1 2825 2 chr2A.!!$F2 2824
10 TraesCS2D01G020000 chr2A 8735319 8736990 1671 True 1461.0 1461 82.5120 823 2520 1 chr2A.!!$R1 1697

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
914 2181 0.027455 TTGTGCGACAAAACTCAGCG 59.973 50.0 0.0 0.0 34.76 5.18 F
930 2197 0.033991 AGCGAGACTTGGAGAGGCTA 60.034 55.0 0.0 0.0 46.50 3.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2029 3305 0.613260 ATAGCGTGCAACTCCTTGGA 59.387 50.0 0.0 0.0 31.75 3.53 R
2777 4073 1.073964 CATCCACACGACAGCAGAAG 58.926 55.0 0.0 0.0 0.00 2.85 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
45 46 0.881796 TCGTGACGCTGATGAGAAGT 59.118 50.000 0.00 0.00 0.00 3.01
85 86 0.693049 AGGAAAGAATCAGGCGGTGT 59.307 50.000 0.00 0.00 0.00 4.16
87 88 2.007608 GGAAAGAATCAGGCGGTGTAC 58.992 52.381 0.00 0.00 0.00 2.90
196 197 2.340210 TGCAGCACAAGAAAGGTACA 57.660 45.000 0.00 0.00 0.00 2.90
204 205 4.703897 CACAAGAAAGGTACAGGAGTTGA 58.296 43.478 0.00 0.00 0.00 3.18
205 206 5.123227 CACAAGAAAGGTACAGGAGTTGAA 58.877 41.667 0.00 0.00 0.00 2.69
208 209 4.962155 AGAAAGGTACAGGAGTTGAACTG 58.038 43.478 0.90 0.00 40.48 3.16
210 211 3.753294 AGGTACAGGAGTTGAACTGTG 57.247 47.619 0.90 2.48 46.58 3.66
241 242 6.478512 TTTTTAATTGACTTGTTGCCTCCT 57.521 33.333 0.00 0.00 0.00 3.69
242 243 7.589958 TTTTTAATTGACTTGTTGCCTCCTA 57.410 32.000 0.00 0.00 0.00 2.94
243 244 6.817765 TTTAATTGACTTGTTGCCTCCTAG 57.182 37.500 0.00 0.00 0.00 3.02
244 245 2.859165 TTGACTTGTTGCCTCCTAGG 57.141 50.000 0.82 0.82 38.80 3.02
279 280 0.460987 CCGCTTGAAAGAGCCGAGAT 60.461 55.000 0.00 0.00 39.51 2.75
280 281 1.202417 CCGCTTGAAAGAGCCGAGATA 60.202 52.381 0.00 0.00 39.51 1.98
335 336 6.928492 ACCACCAACTGCAAACTTTATAATTG 59.072 34.615 0.00 0.00 0.00 2.32
494 495 9.790389 ATAAGATCTTAAATTATACTCGCTCCG 57.210 33.333 18.79 0.00 0.00 4.63
497 498 7.808856 AGATCTTAAATTATACTCGCTCCGTTC 59.191 37.037 0.00 0.00 0.00 3.95
505 506 5.779529 ATACTCGCTCCGTTCCTTTATAA 57.220 39.130 0.00 0.00 0.00 0.98
508 509 4.868734 ACTCGCTCCGTTCCTTTATAAAAG 59.131 41.667 0.00 0.00 0.00 2.27
513 514 5.876460 GCTCCGTTCCTTTATAAAAGGTGTA 59.124 40.000 16.04 3.40 38.55 2.90
679 1936 9.636789 AACAATATTTATTTGGACCTACCTACC 57.363 33.333 0.00 0.00 39.86 3.18
701 1958 4.457949 CCGTGAATACTAAAAACCCAAGCT 59.542 41.667 0.00 0.00 0.00 3.74
758 2015 7.806690 TGTCATTCTCACATGTTTTTACTAGC 58.193 34.615 0.00 0.00 0.00 3.42
900 2167 6.072112 TGTTTGGAGACTTTTCTATTGTGC 57.928 37.500 0.00 0.00 29.47 4.57
911 2178 5.743026 TTTCTATTGTGCGACAAAACTCA 57.257 34.783 5.94 0.00 41.96 3.41
914 2181 0.027455 TTGTGCGACAAAACTCAGCG 59.973 50.000 0.00 0.00 34.76 5.18
923 2190 2.158957 ACAAAACTCAGCGAGACTTGGA 60.159 45.455 11.64 0.00 33.01 3.53
924 2191 2.447244 AAACTCAGCGAGACTTGGAG 57.553 50.000 11.64 0.00 33.32 3.86
925 2192 1.621992 AACTCAGCGAGACTTGGAGA 58.378 50.000 11.64 0.00 33.32 3.71
926 2193 1.173043 ACTCAGCGAGACTTGGAGAG 58.827 55.000 11.64 0.00 33.32 3.20
928 2195 1.153667 CAGCGAGACTTGGAGAGGC 60.154 63.158 0.00 0.00 0.00 4.70
930 2197 0.033991 AGCGAGACTTGGAGAGGCTA 60.034 55.000 0.00 0.00 46.50 3.93
960 2228 4.256983 TGTCCAGACTCCATAGACATCT 57.743 45.455 0.00 0.00 32.75 2.90
993 2263 2.158986 CCTCATCGATTGTCTTCCTGCT 60.159 50.000 0.00 0.00 0.00 4.24
994 2264 3.529533 CTCATCGATTGTCTTCCTGCTT 58.470 45.455 0.00 0.00 0.00 3.91
1114 2384 1.617947 ATCCGAGGAGAAGGTGGTGC 61.618 60.000 0.00 0.00 0.00 5.01
1143 2413 1.134759 CAGCACCTCCTGATGAGAGTG 60.135 57.143 0.00 0.00 44.42 3.51
1150 2420 2.036217 CTCCTGATGAGAGTGAGCATCC 59.964 54.545 0.00 0.00 44.42 3.51
1224 2494 1.758280 CTCAAGATGCTCTCAGAGGCT 59.242 52.381 3.18 0.00 29.94 4.58
1281 2551 2.887151 ACAAATCCCTCCAAGACAGG 57.113 50.000 0.00 0.00 0.00 4.00
1390 2661 1.918262 AGAAGGATGACAAGGCCATGA 59.082 47.619 16.33 0.00 0.00 3.07
1434 2705 6.642540 CCTTGGAAAGCTTAGAAATTGTTGTC 59.357 38.462 0.00 0.00 44.44 3.18
1479 2750 0.684535 TTCTTGGTGGATGTGAGCGA 59.315 50.000 0.00 0.00 0.00 4.93
1588 2859 2.023673 TGTTGGAGCAGAACAACCTTG 58.976 47.619 0.00 0.00 44.72 3.61
1589 2860 2.024414 GTTGGAGCAGAACAACCTTGT 58.976 47.619 0.00 0.00 44.72 3.16
1590 2861 3.211045 GTTGGAGCAGAACAACCTTGTA 58.789 45.455 0.00 0.00 41.31 2.41
1641 2914 0.109723 TAGGTGGTGTTGGAGTTGGC 59.890 55.000 0.00 0.00 0.00 4.52
1669 2942 2.294233 ACATTGGTTGCTCATGTGTGTC 59.706 45.455 0.00 0.00 0.00 3.67
1685 2958 2.670592 TCGCGACGAGAGGGTTCA 60.671 61.111 3.71 0.00 0.00 3.18
1733 3006 5.610132 ACCTGAATGGAGATAACCTCATGAT 59.390 40.000 0.00 0.00 43.76 2.45
1833 3109 5.301805 TGACTGGAAAAGGTTTCATTCCTTC 59.698 40.000 5.48 3.18 43.50 3.46
1850 3126 5.901413 TCCTTCCTCATAAGAATCAGCAT 57.099 39.130 0.00 0.00 0.00 3.79
1851 3127 5.862845 TCCTTCCTCATAAGAATCAGCATC 58.137 41.667 0.00 0.00 0.00 3.91
1857 3133 5.282055 TCATAAGAATCAGCATCGGAAGT 57.718 39.130 0.00 0.00 0.00 3.01
1958 3234 9.255304 GTCTTATGATGAGTTGAGGTATCTTTC 57.745 37.037 0.00 0.00 0.00 2.62
2029 3305 7.402862 ACTAGTACAAATAGCAGATGGGTTTT 58.597 34.615 0.00 0.00 0.00 2.43
2050 3326 0.729116 CAAGGAGTTGCACGCTATGG 59.271 55.000 0.00 0.00 0.00 2.74
2346 3631 5.129485 TCCTAGCATTAGACCCAAAGAAGAG 59.871 44.000 0.00 0.00 0.00 2.85
2432 3717 0.520404 CATGCTGAGGACACAAGTGC 59.480 55.000 0.00 0.00 36.16 4.40
2476 3767 3.569049 AAACGACGAGGAGTGCCCG 62.569 63.158 0.00 0.00 40.87 6.13
2585 3877 9.702726 CGGAGTACAATTGAACTAAATGTATTG 57.297 33.333 13.59 0.00 31.75 1.90
2601 3893 5.276461 TGTATTGCGGATCTCATGTAACT 57.724 39.130 0.00 0.00 0.00 2.24
2604 3896 7.269316 TGTATTGCGGATCTCATGTAACTTAA 58.731 34.615 0.00 0.00 0.00 1.85
2658 3950 3.708451 TCCACCACATGCTCTTCTAGTA 58.292 45.455 0.00 0.00 0.00 1.82
2727 4019 7.497909 GGTACATGCATCATCATCATCATCATA 59.502 37.037 0.00 0.00 0.00 2.15
2734 4026 8.840321 GCATCATCATCATCATCATAATCATCA 58.160 33.333 0.00 0.00 0.00 3.07
2777 4073 3.525537 ACCGATGATGAAGTGTGATGTC 58.474 45.455 0.00 0.00 0.00 3.06
2780 4076 4.269603 CCGATGATGAAGTGTGATGTCTTC 59.730 45.833 0.00 0.00 40.02 2.87
2815 4111 7.103641 GTGGATGTGGATTCTACAAAGAACTA 58.896 38.462 6.96 0.00 44.40 2.24
2884 4180 4.143333 CCGACTAGGTGCCCGGTG 62.143 72.222 0.00 0.00 37.40 4.94
2920 4216 4.762251 AGCTTCTCCCACAAAATCAGTAAC 59.238 41.667 0.00 0.00 0.00 2.50
2962 4258 5.762045 ACTGAAACCAGTTCGATTTCAATG 58.238 37.500 11.18 4.96 41.83 2.82
2967 4263 4.007659 ACCAGTTCGATTTCAATGTACCC 58.992 43.478 0.00 0.00 0.00 3.69
2970 4266 4.454161 CAGTTCGATTTCAATGTACCCACA 59.546 41.667 0.00 0.00 39.52 4.17
3010 4306 1.378882 GATGAGATTGCCTTGCGCCA 61.379 55.000 4.18 0.00 36.24 5.69
3025 4326 4.023137 CCACAAGGCTTGGGATGG 57.977 61.111 30.41 23.34 35.62 3.51
3027 4328 1.383799 CACAAGGCTTGGGATGGGA 59.616 57.895 29.26 0.00 35.62 4.37
3028 4329 0.682209 CACAAGGCTTGGGATGGGAG 60.682 60.000 29.26 3.08 35.62 4.30
3031 4332 1.867595 AAGGCTTGGGATGGGAGGTG 61.868 60.000 0.00 0.00 0.00 4.00
3033 4334 1.384191 GCTTGGGATGGGAGGTGTT 59.616 57.895 0.00 0.00 0.00 3.32
3034 4335 0.967380 GCTTGGGATGGGAGGTGTTG 60.967 60.000 0.00 0.00 0.00 3.33
3035 4336 0.323725 CTTGGGATGGGAGGTGTTGG 60.324 60.000 0.00 0.00 0.00 3.77
3036 4337 2.043953 GGGATGGGAGGTGTTGGC 60.044 66.667 0.00 0.00 0.00 4.52
3037 4338 2.616458 GGGATGGGAGGTGTTGGCT 61.616 63.158 0.00 0.00 0.00 4.75
3038 4339 1.077429 GGATGGGAGGTGTTGGCTC 60.077 63.158 0.00 0.00 0.00 4.70
3039 4340 1.077429 GATGGGAGGTGTTGGCTCC 60.077 63.158 0.00 0.00 36.58 4.70
3040 4341 2.876368 GATGGGAGGTGTTGGCTCCG 62.876 65.000 0.00 0.00 38.11 4.63
3050 4351 0.034896 GTTGGCTCCGTCCTTCAAGA 59.965 55.000 0.00 0.00 0.00 3.02
3085 4386 6.161855 AGGTGGAAACAAAGAGGAAAATTC 57.838 37.500 0.00 0.00 46.06 2.17
3086 4387 4.982295 GGTGGAAACAAAGAGGAAAATTCG 59.018 41.667 0.00 0.00 46.06 3.34
3091 4392 3.486383 ACAAAGAGGAAAATTCGAGGCA 58.514 40.909 0.00 0.00 0.00 4.75
3127 4428 5.169836 ACGAAAACATGAAGTTCTTCCAC 57.830 39.130 0.00 0.00 40.26 4.02
3128 4429 4.036380 ACGAAAACATGAAGTTCTTCCACC 59.964 41.667 0.00 0.00 40.26 4.61
3139 4441 0.830648 TCTTCCACCCTATTGCCTCG 59.169 55.000 0.00 0.00 0.00 4.63
3141 4443 1.271840 TTCCACCCTATTGCCTCGCT 61.272 55.000 0.00 0.00 0.00 4.93
3149 4451 1.945394 CTATTGCCTCGCTGCATTTCT 59.055 47.619 0.00 0.00 41.70 2.52
3151 4453 1.372582 TTGCCTCGCTGCATTTCTAG 58.627 50.000 0.00 0.00 41.70 2.43
3170 4472 8.789767 TTTCTAGAGAAATATGATCCACTCCT 57.210 34.615 0.46 0.00 38.94 3.69
3183 4485 0.738975 CACTCCTTCGATGTCGGCTA 59.261 55.000 2.25 0.00 40.29 3.93
3199 4501 1.067142 GGCTACGACTTCATGGTCACA 60.067 52.381 0.00 0.00 36.12 3.58
3200 4502 1.993370 GCTACGACTTCATGGTCACAC 59.007 52.381 0.00 0.00 36.12 3.82
3236 4538 1.516603 GCGCTCCACGTCTTCTACC 60.517 63.158 0.00 0.00 46.11 3.18
3299 4601 2.046411 TGGCCGCACGTCAATCAT 60.046 55.556 0.00 0.00 0.00 2.45
3329 4631 6.406370 TGAGACCTACATTCGATGTTTCATT 58.594 36.000 5.94 0.00 41.63 2.57
3354 4656 0.108756 GTACCCGAGCAAGTGGAGTC 60.109 60.000 0.00 0.00 0.00 3.36
3366 4668 4.439700 GCAAGTGGAGTCAATGGATTCATG 60.440 45.833 0.00 0.00 31.80 3.07
3403 4705 4.778213 ACAGTATATCATGCCACTTGGT 57.222 40.909 0.00 0.00 37.57 3.67
3450 4758 0.621082 TCACCAACCACACCACTTCA 59.379 50.000 0.00 0.00 0.00 3.02
3462 4770 1.364626 CCACTTCAGCATCTCCACGC 61.365 60.000 0.00 0.00 0.00 5.34
3463 4771 1.446792 ACTTCAGCATCTCCACGCG 60.447 57.895 3.53 3.53 0.00 6.01
3464 4772 2.806856 CTTCAGCATCTCCACGCGC 61.807 63.158 5.73 0.00 0.00 6.86
3469 4777 2.586079 CATCTCCACGCGCGGAAT 60.586 61.111 35.22 16.04 33.65 3.01
3470 4778 2.279517 ATCTCCACGCGCGGAATC 60.280 61.111 35.22 0.00 33.65 2.52
3471 4779 3.076258 ATCTCCACGCGCGGAATCA 62.076 57.895 35.22 15.20 33.65 2.57
3472 4780 2.960957 ATCTCCACGCGCGGAATCAG 62.961 60.000 35.22 20.61 33.65 2.90
3473 4781 4.812476 TCCACGCGCGGAATCAGG 62.812 66.667 35.22 23.12 29.93 3.86
3475 4783 3.853330 CACGCGCGGAATCAGGTG 61.853 66.667 35.22 16.67 0.00 4.00
3476 4784 4.373116 ACGCGCGGAATCAGGTGT 62.373 61.111 35.22 5.42 0.00 4.16
3477 4785 3.853330 CGCGCGGAATCAGGTGTG 61.853 66.667 24.84 0.00 0.00 3.82
3478 4786 2.434185 GCGCGGAATCAGGTGTGA 60.434 61.111 8.83 0.00 37.02 3.58
3479 4787 2.456119 GCGCGGAATCAGGTGTGAG 61.456 63.158 8.83 0.00 35.66 3.51
3480 4788 1.079819 CGCGGAATCAGGTGTGAGT 60.080 57.895 0.00 0.00 35.66 3.41
3481 4789 1.354337 CGCGGAATCAGGTGTGAGTG 61.354 60.000 0.00 0.00 35.66 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 46 9.513906 TTTCCTGATCATTTTCATTGTACTGTA 57.486 29.630 0.00 0.00 0.00 2.74
85 86 1.262417 TCACATGCCAAGTCTCGGTA 58.738 50.000 0.00 0.00 0.00 4.02
87 88 1.742761 ATTCACATGCCAAGTCTCGG 58.257 50.000 0.00 0.00 0.00 4.63
163 164 2.615912 GTGCTGCATACTTCCCTCAATC 59.384 50.000 5.27 0.00 0.00 2.67
196 197 4.963318 TTCATCTCACAGTTCAACTCCT 57.037 40.909 0.00 0.00 0.00 3.69
241 242 2.301870 CGGGCCATGCTATAGAAACCTA 59.698 50.000 4.39 0.00 0.00 3.08
242 243 1.072331 CGGGCCATGCTATAGAAACCT 59.928 52.381 4.39 0.00 0.00 3.50
243 244 1.523758 CGGGCCATGCTATAGAAACC 58.476 55.000 4.39 0.00 0.00 3.27
244 245 0.875059 GCGGGCCATGCTATAGAAAC 59.125 55.000 4.39 0.00 0.00 2.78
279 280 1.128809 TCCCGTGCCCCAACTCTTTA 61.129 55.000 0.00 0.00 0.00 1.85
280 281 2.115266 CCCGTGCCCCAACTCTTT 59.885 61.111 0.00 0.00 0.00 2.52
335 336 5.069914 GGGAAGGGAGTATCTTCTCTTTCTC 59.930 48.000 0.00 0.00 38.01 2.87
493 494 9.902196 AACAAATACACCTTTTATAAAGGAACG 57.098 29.630 21.62 12.84 39.81 3.95
553 554 8.110860 TGAAGGGCTAACAAGAAAATTAGAAG 57.889 34.615 0.00 0.00 31.20 2.85
679 1936 5.622770 AGCTTGGGTTTTTAGTATTCACG 57.377 39.130 0.00 0.00 0.00 4.35
701 1958 2.224549 CCAAGCGACACGGAAAACATTA 59.775 45.455 0.00 0.00 0.00 1.90
758 2015 3.111853 TGGAGTACACAAGTTGCTCTG 57.888 47.619 1.81 0.00 32.59 3.35
900 2167 1.772182 AGTCTCGCTGAGTTTTGTCG 58.228 50.000 5.66 0.00 0.00 4.35
911 2178 0.033991 TAGCCTCTCCAAGTCTCGCT 60.034 55.000 0.00 0.00 0.00 4.93
914 2181 5.662674 TTAACTTAGCCTCTCCAAGTCTC 57.337 43.478 0.00 0.00 31.43 3.36
923 2190 6.013293 AGTCTGGACAAATTAACTTAGCCTCT 60.013 38.462 3.51 0.00 0.00 3.69
924 2191 6.174049 AGTCTGGACAAATTAACTTAGCCTC 58.826 40.000 3.51 0.00 0.00 4.70
925 2192 6.128138 AGTCTGGACAAATTAACTTAGCCT 57.872 37.500 3.51 0.00 0.00 4.58
926 2193 5.354513 GGAGTCTGGACAAATTAACTTAGCC 59.645 44.000 3.51 0.00 0.00 3.93
928 2195 9.319143 CTATGGAGTCTGGACAAATTAACTTAG 57.681 37.037 3.51 0.00 0.00 2.18
930 2197 7.824779 GTCTATGGAGTCTGGACAAATTAACTT 59.175 37.037 3.51 0.00 0.00 2.66
960 2228 0.461548 CGATGAGGAAGCTGCTGGTA 59.538 55.000 1.35 0.00 0.00 3.25
993 2263 0.039472 TGGCAGCCTCCATAGCAAAA 59.961 50.000 14.15 0.00 0.00 2.44
994 2264 0.259647 ATGGCAGCCTCCATAGCAAA 59.740 50.000 14.15 0.00 44.60 3.68
1033 2303 2.832129 AGGAGATGAAACGGCTCACTAA 59.168 45.455 0.00 0.00 0.00 2.24
1114 2384 0.252479 AGGAGGTGCTGCAATCTCTG 59.748 55.000 23.92 0.00 0.00 3.35
1150 2420 0.745845 CCATCCGCCTCCTCAACAAG 60.746 60.000 0.00 0.00 0.00 3.16
1224 2494 3.708890 CACGCGGTATCCTTTGTACATA 58.291 45.455 12.47 0.00 0.00 2.29
1281 2551 1.541588 CTAACCTTGTCAAAGCCTGCC 59.458 52.381 0.00 0.00 31.51 4.85
1390 2661 1.954362 GCACCATCTGACTCGAGGCT 61.954 60.000 21.24 0.00 0.00 4.58
1434 2705 1.200716 ACAAATTCTGCCATGTGAGCG 59.799 47.619 0.00 0.00 0.00 5.03
1588 2859 3.459232 TGCTAGTGCATGATCACCTAC 57.541 47.619 0.00 0.00 45.31 3.18
1641 2914 5.050634 CACATGAGCAACCAATGTTTTCTTG 60.051 40.000 0.00 0.00 32.52 3.02
1669 2942 2.504244 GTGAACCCTCTCGTCGCG 60.504 66.667 0.00 0.00 0.00 5.87
1685 2958 5.221722 TGCAAAATAGAGGAGAAGTGTGAGT 60.222 40.000 0.00 0.00 0.00 3.41
1733 3006 3.199946 GGTCCTTCCATGGTCAAGTATCA 59.800 47.826 12.58 0.00 35.97 2.15
1833 3109 4.263018 TCCGATGCTGATTCTTATGAGG 57.737 45.455 0.00 0.00 0.00 3.86
1850 3126 6.721668 ACTTATGATGATGATCCTACTTCCGA 59.278 38.462 0.00 0.00 0.00 4.55
1851 3127 6.929625 ACTTATGATGATGATCCTACTTCCG 58.070 40.000 0.00 0.00 0.00 4.30
1958 3234 1.308069 CCCGAATGCCAGTGTCTTGG 61.308 60.000 0.00 0.00 41.35 3.61
2029 3305 0.613260 ATAGCGTGCAACTCCTTGGA 59.387 50.000 0.00 0.00 31.75 3.53
2346 3631 9.525409 CTTGATTCCCATGAAATTAGAATGAAC 57.475 33.333 0.00 0.00 33.32 3.18
2432 3717 2.550978 CGGGATGTAAAGCACTACCTG 58.449 52.381 0.00 0.00 0.00 4.00
2546 3838 8.201464 TCAATTGTACTCCGTATACATGAACAT 58.799 33.333 5.13 0.00 32.70 2.71
2585 3877 7.766219 TTACTTTAAGTTACATGAGATCCGC 57.234 36.000 1.94 0.00 0.00 5.54
2670 3962 6.785488 TGTAAAGCAACATTACTGAGACAG 57.215 37.500 0.00 0.00 34.94 3.51
2734 4026 9.226606 TCGGTATCAACTTTAGAAAAATGTGAT 57.773 29.630 0.00 0.00 34.67 3.06
2735 4027 8.610248 TCGGTATCAACTTTAGAAAAATGTGA 57.390 30.769 0.00 0.00 0.00 3.58
2736 4028 9.277565 CATCGGTATCAACTTTAGAAAAATGTG 57.722 33.333 0.00 0.00 0.00 3.21
2744 4036 7.706607 CACTTCATCATCGGTATCAACTTTAGA 59.293 37.037 0.00 0.00 0.00 2.10
2777 4073 1.073964 CATCCACACGACAGCAGAAG 58.926 55.000 0.00 0.00 0.00 2.85
2780 4076 1.293963 CCACATCCACACGACAGCAG 61.294 60.000 0.00 0.00 0.00 4.24
2851 4147 6.150809 ACCTAGTCGGTTTCTTAGTCTAACTG 59.849 42.308 0.00 0.00 46.37 3.16
2853 4149 6.320944 CACCTAGTCGGTTTCTTAGTCTAAC 58.679 44.000 0.00 0.00 46.37 2.34
2859 4155 2.889852 GGCACCTAGTCGGTTTCTTAG 58.110 52.381 0.00 0.00 46.37 2.18
2890 4186 1.973812 GTGGGAGAAGCTGGCCAAC 60.974 63.158 7.01 0.92 0.00 3.77
2892 4188 2.005606 TTTGTGGGAGAAGCTGGCCA 62.006 55.000 4.71 4.71 0.00 5.36
2900 4196 7.040686 GCTAAAGTTACTGATTTTGTGGGAGAA 60.041 37.037 0.00 0.00 0.00 2.87
2901 4197 6.430000 GCTAAAGTTACTGATTTTGTGGGAGA 59.570 38.462 0.00 0.00 0.00 3.71
2953 4249 5.619086 CGGAGTTTGTGGGTACATTGAAATC 60.619 44.000 0.00 0.00 36.53 2.17
2967 4263 2.802816 CTGAAAGAGGACGGAGTTTGTG 59.197 50.000 0.00 0.00 36.96 3.33
2970 4266 2.047830 ACCTGAAAGAGGACGGAGTTT 58.952 47.619 0.00 0.00 46.33 2.66
3010 4306 1.693640 CTCCCATCCCAAGCCTTGT 59.306 57.895 3.37 0.00 0.00 3.16
3023 4324 3.636231 CGGAGCCAACACCTCCCA 61.636 66.667 2.13 0.00 44.86 4.37
3025 4326 2.047179 GACGGAGCCAACACCTCC 60.047 66.667 0.00 0.00 44.35 4.30
3027 4328 2.113243 GAAGGACGGAGCCAACACCT 62.113 60.000 0.00 0.00 0.00 4.00
3028 4329 1.671379 GAAGGACGGAGCCAACACC 60.671 63.158 0.00 0.00 0.00 4.16
3031 4332 0.034896 TCTTGAAGGACGGAGCCAAC 59.965 55.000 0.00 0.00 0.00 3.77
3033 4334 0.762418 TTTCTTGAAGGACGGAGCCA 59.238 50.000 0.00 0.00 0.00 4.75
3034 4335 1.443802 CTTTCTTGAAGGACGGAGCC 58.556 55.000 0.00 0.00 0.00 4.70
3035 4336 0.799393 GCTTTCTTGAAGGACGGAGC 59.201 55.000 0.00 0.00 35.82 4.70
3036 4337 1.270839 TGGCTTTCTTGAAGGACGGAG 60.271 52.381 0.00 0.00 35.82 4.63
3037 4338 0.762418 TGGCTTTCTTGAAGGACGGA 59.238 50.000 0.00 0.00 35.82 4.69
3038 4339 1.470098 CATGGCTTTCTTGAAGGACGG 59.530 52.381 0.00 0.00 35.82 4.79
3039 4340 1.470098 CCATGGCTTTCTTGAAGGACG 59.530 52.381 0.00 0.00 35.82 4.79
3040 4341 1.821136 CCCATGGCTTTCTTGAAGGAC 59.179 52.381 6.09 0.00 35.82 3.85
3050 4351 1.442886 TTCCACCTCCCCATGGCTTT 61.443 55.000 6.09 0.00 35.81 3.51
3086 4387 2.869503 TTTCCCTCGCGGATTGCCTC 62.870 60.000 6.13 0.00 41.63 4.70
3091 4392 0.320946 TTTCGTTTCCCTCGCGGATT 60.321 50.000 6.13 0.00 41.63 3.01
3127 4428 2.190313 TGCAGCGAGGCAATAGGG 59.810 61.111 0.00 0.00 41.65 3.53
3149 4451 7.004691 TCGAAGGAGTGGATCATATTTCTCTA 58.995 38.462 0.00 0.00 0.00 2.43
3151 4453 6.090483 TCGAAGGAGTGGATCATATTTCTC 57.910 41.667 0.00 0.00 0.00 2.87
3157 4459 3.253432 CGACATCGAAGGAGTGGATCATA 59.747 47.826 0.00 0.00 43.02 2.15
3183 4485 2.037121 TCATGTGTGACCATGAAGTCGT 59.963 45.455 12.30 0.00 46.12 4.34
3299 4601 6.464222 ACATCGAATGTAGGTCTCAAAGAAA 58.536 36.000 0.00 0.00 42.78 2.52
3354 4656 5.184479 AGAACTCAACCACATGAATCCATTG 59.816 40.000 0.00 0.00 0.00 2.82
3366 4668 3.470645 ACTGTACCAGAACTCAACCAC 57.529 47.619 0.00 0.00 35.18 4.16
3385 4687 7.744087 TTGATAACCAAGTGGCATGATATAC 57.256 36.000 0.00 0.00 39.32 1.47
3403 4705 6.537301 ACAGAGAAACAACGTTGTCTTGATAA 59.463 34.615 32.36 0.00 41.31 1.75
3440 4748 1.059098 TGGAGATGCTGAAGTGGTGT 58.941 50.000 0.00 0.00 0.00 4.16
3462 4770 1.079819 ACTCACACCTGATTCCGCG 60.080 57.895 0.00 0.00 0.00 6.46
3463 4771 2.460330 CACTCACACCTGATTCCGC 58.540 57.895 0.00 0.00 0.00 5.54


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

AutoCloner maintained by Alex Coulton.