Multiple sequence alignment - TraesCS1D01G175900

Loading Multiple Alignment...

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 TraesCS1D01G175900 chr1D 100.000 3450 0 0 1 3450 250142338 250138889 0.000000e+00 6372.0
1 TraesCS1D01G175900 chr1A 91.796 2121 142 15 1 2112 320225433 320223336 0.000000e+00 2924.0
2 TraesCS1D01G175900 chr1A 92.188 640 35 9 2107 2737 320223299 320222666 0.000000e+00 891.0
3 TraesCS1D01G175900 chr1A 95.484 310 8 1 3147 3450 320156160 320155851 1.110000e-134 490.0
4 TraesCS1D01G175900 chr1A 93.050 259 12 3 2824 3082 320156428 320156176 1.170000e-99 374.0
5 TraesCS1D01G175900 chr1A 100.000 28 0 0 166 193 12121214 12121187 6.000000e-03 52.8
6 TraesCS1D01G175900 chr1B 91.200 2125 124 23 3 2112 364418055 364420131 0.000000e+00 2830.0
7 TraesCS1D01G175900 chr1B 88.120 665 49 14 2096 2753 364420157 364420798 0.000000e+00 763.0
8 TraesCS1D01G175900 chr1B 90.000 420 22 6 3041 3450 364422851 364423260 3.050000e-145 525.0
9 TraesCS1D01G175900 chr1B 95.545 202 3 2 2783 2978 364422326 364422527 5.560000e-83 318.0
10 TraesCS1D01G175900 chr1B 100.000 31 0 0 2764 2794 364420831 364420861 1.340000e-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 TraesCS1D01G175900 chr1D 250138889 250142338 3449 True 6372.00 6372 100.000 1 3450 1 chr1D.!!$R1 3449
1 TraesCS1D01G175900 chr1A 320222666 320225433 2767 True 1907.50 2924 91.992 1 2737 2 chr1A.!!$R3 2736
2 TraesCS1D01G175900 chr1A 320155851 320156428 577 True 432.00 490 94.267 2824 3450 2 chr1A.!!$R2 626
3 TraesCS1D01G175900 chr1B 364418055 364423260 5205 False 898.88 2830 92.973 3 3450 5 chr1B.!!$F1 3447

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
346 368 0.034756 GCCGCAAACTTCCCCAAAAT 59.965 50.0 0.0 0.0 0.00 1.82 F
368 392 0.250234 CCACCCAAGCTCGAATCTGA 59.750 55.0 0.0 0.0 0.00 3.27 F
558 583 0.312416 CCCTCTAGCTTCGTGGATCG 59.688 60.0 0.0 0.0 41.41 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1203 1231 0.096628 GCAGCTCTGACAAGCAATCG 59.903 55.0 0.29 0.0 45.00 3.34 R
1360 1388 0.323178 AGCAACTGCCCTTGATCCAG 60.323 55.0 0.00 0.0 43.38 3.86 R
2476 2552 0.029834 GCAGCCCAAGATTATGCACG 59.970 55.0 0.00 0.0 36.88 5.34 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
26 27 7.812191 GCATAAAAATGACATAGGTTGACACAA 59.188 33.333 0.00 0.00 32.88 3.33
37 42 8.020819 ACATAGGTTGACACAAAATAAATCGTG 58.979 33.333 0.00 0.00 35.48 4.35
106 120 3.901222 AGGTAAAATCCCACCCAACTTTG 59.099 43.478 0.00 0.00 35.25 2.77
226 248 1.715993 GTCTCGAACTTTCTGCCTCC 58.284 55.000 0.00 0.00 0.00 4.30
263 285 3.719121 CCTCTCTGGGTGACTGGG 58.281 66.667 0.00 0.00 0.00 4.45
264 286 1.229336 CCTCTCTGGGTGACTGGGT 60.229 63.158 0.00 0.00 0.00 4.51
265 287 0.041238 CCTCTCTGGGTGACTGGGTA 59.959 60.000 0.00 0.00 0.00 3.69
280 302 1.669440 GGTAACCACTCTCGCACCA 59.331 57.895 0.00 0.00 0.00 4.17
311 333 0.179018 ACAGAGCACACAACTTCCCC 60.179 55.000 0.00 0.00 0.00 4.81
312 334 0.890996 CAGAGCACACAACTTCCCCC 60.891 60.000 0.00 0.00 0.00 5.40
313 335 1.150536 GAGCACACAACTTCCCCCA 59.849 57.895 0.00 0.00 0.00 4.96
314 336 1.152756 AGCACACAACTTCCCCCAC 60.153 57.895 0.00 0.00 0.00 4.61
315 337 2.200337 GCACACAACTTCCCCCACC 61.200 63.158 0.00 0.00 0.00 4.61
316 338 1.896660 CACACAACTTCCCCCACCG 60.897 63.158 0.00 0.00 0.00 4.94
317 339 2.282180 CACAACTTCCCCCACCGG 60.282 66.667 0.00 0.00 0.00 5.28
342 364 4.572571 ACGCCGCAAACTTCCCCA 62.573 61.111 0.00 0.00 0.00 4.96
346 368 0.034756 GCCGCAAACTTCCCCAAAAT 59.965 50.000 0.00 0.00 0.00 1.82
350 374 1.003118 GCAAACTTCCCCAAAATCCCC 59.997 52.381 0.00 0.00 0.00 4.81
366 390 1.604378 CCCACCCAAGCTCGAATCT 59.396 57.895 0.00 0.00 0.00 2.40
368 392 0.250234 CCACCCAAGCTCGAATCTGA 59.750 55.000 0.00 0.00 0.00 3.27
412 436 1.089920 AGGTGCAGCATGATTCGTTC 58.910 50.000 19.63 0.00 39.69 3.95
470 494 4.263209 CGCTGCGTGTGCCCAAAA 62.263 61.111 14.93 0.00 41.78 2.44
489 513 6.183361 CCCAAAATTTAGGGGAAAGTTTCAGT 60.183 38.462 18.71 3.74 41.96 3.41
558 583 0.312416 CCCTCTAGCTTCGTGGATCG 59.688 60.000 0.00 0.00 41.41 3.69
610 635 1.203300 TGATCTCTCACAGGGTTCCCA 60.203 52.381 10.73 0.00 0.00 4.37
668 695 3.554960 GGCGCCATAGTATGACTCATGAA 60.555 47.826 24.80 0.00 0.00 2.57
716 743 2.048597 TGTCGCGGTTACTGCTGG 60.049 61.111 14.59 0.00 0.00 4.85
774 801 2.943033 GGTTTGTAGCTGTGACACAAGT 59.057 45.455 10.02 2.24 33.96 3.16
790 818 6.479990 TGACACAAGTTTATCTGTGAAGTCAG 59.520 38.462 9.06 0.00 36.28 3.51
867 895 3.393800 CCAAGTGACAAGTACTGACAGG 58.606 50.000 7.51 0.00 30.09 4.00
922 950 9.221775 GAGCACGTTTCCTAATTTTTATGTATG 57.778 33.333 0.00 0.00 0.00 2.39
943 971 3.444742 TGGCTTGGATGCTTATGTTCTTG 59.555 43.478 0.00 0.00 0.00 3.02
947 975 2.424601 TGGATGCTTATGTTCTTGCTGC 59.575 45.455 0.00 0.00 0.00 5.25
956 984 1.610038 TGTTCTTGCTGCTTGTGATGG 59.390 47.619 0.00 0.00 0.00 3.51
976 1004 2.492088 GGGGTGTGCTAATTGAAGGTTC 59.508 50.000 0.00 0.00 0.00 3.62
1065 1093 3.741325 CCCTTCCGGGTCATCCTT 58.259 61.111 0.00 0.00 46.12 3.36
1203 1231 0.747283 CCTGGATGAGGCTTGCTGTC 60.747 60.000 0.00 0.00 34.01 3.51
1302 1330 5.308497 TGAGAAGTGGGTGGACATTTACTTA 59.692 40.000 0.00 0.00 0.00 2.24
1341 1369 1.300156 GGACATCTGCATCGCGCTA 60.300 57.895 5.56 0.00 43.06 4.26
1408 1436 0.537143 TGTCCTGCATGTGTTGGACC 60.537 55.000 15.67 1.93 45.98 4.46
1414 1442 0.318120 GCATGTGTTGGACCCCAAAG 59.682 55.000 0.00 0.00 45.73 2.77
1457 1485 2.593346 CTCAAGCGAGCTGAGGTATT 57.407 50.000 0.00 0.00 31.00 1.89
1466 1494 4.299978 CGAGCTGAGGTATTACTTAAGGC 58.700 47.826 7.53 0.00 0.00 4.35
1488 1516 1.156736 GGATGGACAAAGTGGACACG 58.843 55.000 0.00 0.00 36.20 4.49
1489 1517 1.270625 GGATGGACAAAGTGGACACGA 60.271 52.381 0.00 0.00 36.20 4.35
1517 1545 1.449246 GGCTCGACAGCTGCTCAAT 60.449 57.895 15.27 0.00 46.03 2.57
1653 1681 1.227999 GCGTCTTTGTGGCTGCACTA 61.228 55.000 0.50 0.00 0.00 2.74
1695 1723 0.036732 TGGAGTTGCATGTCCCTCAC 59.963 55.000 11.41 0.00 31.04 3.51
1743 1771 1.607628 GATCTTCATGCCACCATCAGC 59.392 52.381 0.00 0.00 0.00 4.26
1821 1849 1.881973 GAAGTTGAAGCATGTGCCAGA 59.118 47.619 0.57 0.00 43.38 3.86
1848 1876 1.596260 CATGCATTGACTAGGACTGCG 59.404 52.381 0.00 0.00 35.63 5.18
1873 1901 6.349426 CAGCTTGAAAATGAAAATGACAACG 58.651 36.000 0.00 0.00 0.00 4.10
1893 1921 2.331132 GGCTTGTGCTGTCAGCCTC 61.331 63.158 21.99 14.88 41.51 4.70
1916 1944 0.899717 AAGCAAATGGTGATGCCGGT 60.900 50.000 1.90 0.00 43.57 5.28
1919 1947 0.452987 CAAATGGTGATGCCGGTCAG 59.547 55.000 1.90 0.00 41.21 3.51
1934 1962 1.517242 GTCAGCACTGGACAGAAAGG 58.483 55.000 6.29 0.00 35.36 3.11
1936 1964 1.345741 TCAGCACTGGACAGAAAGGAG 59.654 52.381 6.29 0.00 0.00 3.69
1938 1966 1.346068 AGCACTGGACAGAAAGGAGAC 59.654 52.381 6.29 0.00 0.00 3.36
1942 1970 0.104672 TGGACAGAAAGGAGACCCCA 60.105 55.000 0.00 0.00 37.41 4.96
1943 1971 0.615850 GGACAGAAAGGAGACCCCAG 59.384 60.000 0.00 0.00 37.41 4.45
1976 2004 0.179062 CCAGCTGATGACAGTAGCCC 60.179 60.000 17.39 0.00 45.04 5.19
1988 2016 1.448013 GTAGCCCGGAGTGTGAAGC 60.448 63.158 0.73 0.00 0.00 3.86
2003 2031 2.857152 GTGAAGCGATCATGACAGAGAC 59.143 50.000 0.00 0.00 40.97 3.36
2010 2038 4.273724 GCGATCATGACAGAGACTAGTACA 59.726 45.833 0.00 0.00 0.00 2.90
2025 2053 6.207810 AGACTAGTACAGAAGAAGGAACACAG 59.792 42.308 0.00 0.00 0.00 3.66
2028 2056 3.760580 ACAGAAGAAGGAACACAGGAG 57.239 47.619 0.00 0.00 0.00 3.69
2032 2060 2.327325 AGAAGGAACACAGGAGGCTA 57.673 50.000 0.00 0.00 0.00 3.93
2037 2065 3.690460 AGGAACACAGGAGGCTAAAATG 58.310 45.455 0.00 0.00 0.00 2.32
2046 2074 3.053395 AGGAGGCTAAAATGATGCAGGAA 60.053 43.478 0.00 0.00 0.00 3.36
2047 2075 3.317430 GGAGGCTAAAATGATGCAGGAAG 59.683 47.826 0.00 0.00 0.00 3.46
2048 2076 4.202441 GAGGCTAAAATGATGCAGGAAGA 58.798 43.478 0.00 0.00 0.00 2.87
2049 2077 4.801164 AGGCTAAAATGATGCAGGAAGAT 58.199 39.130 0.00 0.00 0.00 2.40
2050 2078 5.945310 AGGCTAAAATGATGCAGGAAGATA 58.055 37.500 0.00 0.00 0.00 1.98
2077 2105 4.568359 CCCACTGTGAGAATAAGTTGATCG 59.432 45.833 9.86 0.00 0.00 3.69
2078 2106 5.410924 CCACTGTGAGAATAAGTTGATCGA 58.589 41.667 9.86 0.00 0.00 3.59
2151 2221 0.179113 CGGAAGGCAGAGAAGAGCTC 60.179 60.000 5.27 5.27 44.29 4.09
2181 2251 2.839486 TCTCCAGCATGTCGAAAAGT 57.161 45.000 0.00 0.00 0.00 2.66
2211 2281 2.513897 CGGCTCGGGTTGGATTCC 60.514 66.667 0.00 0.00 0.00 3.01
2327 2397 2.496070 TCACCGAGGTTAGGTCTTGATG 59.504 50.000 0.00 0.00 40.59 3.07
2329 2399 1.482593 CCGAGGTTAGGTCTTGATGCT 59.517 52.381 0.00 0.00 0.00 3.79
2330 2400 2.093447 CCGAGGTTAGGTCTTGATGCTT 60.093 50.000 0.00 0.00 0.00 3.91
2339 2409 4.642429 AGGTCTTGATGCTTTACGTTTCT 58.358 39.130 0.00 0.00 0.00 2.52
2371 2444 6.767524 TGTTCTCTGTTGGTGTAAAACATT 57.232 33.333 0.00 0.00 36.95 2.71
2372 2445 6.791303 TGTTCTCTGTTGGTGTAAAACATTC 58.209 36.000 0.00 0.00 36.95 2.67
2423 2496 0.671781 ACCGCTCTTCTGACATGTGC 60.672 55.000 1.15 0.00 0.00 4.57
2476 2552 2.887568 CCACATCTCAGCGGCGAC 60.888 66.667 12.98 1.23 0.00 5.19
2547 2623 4.863131 CGTAGGTTTGATAGTCCTTGTGTC 59.137 45.833 0.00 0.00 33.34 3.67
2548 2624 5.336531 CGTAGGTTTGATAGTCCTTGTGTCT 60.337 44.000 0.00 0.00 33.34 3.41
2697 2778 8.502387 GCAATGTTAGAGATGAAAGATGTATCC 58.498 37.037 0.00 0.00 0.00 2.59
2738 2819 6.240894 AGTCTTTGAGGTATCTTGCATTTCA 58.759 36.000 0.00 0.00 0.00 2.69
2744 2825 8.750515 TTGAGGTATCTTGCATTTCATATGAA 57.249 30.769 14.23 14.23 0.00 2.57
2745 2826 8.158169 TGAGGTATCTTGCATTTCATATGAAC 57.842 34.615 17.76 7.54 33.13 3.18
2747 2828 7.934457 AGGTATCTTGCATTTCATATGAACAC 58.066 34.615 17.76 10.47 33.13 3.32
2748 2829 7.776969 AGGTATCTTGCATTTCATATGAACACT 59.223 33.333 17.76 3.35 33.13 3.55
2749 2830 8.408601 GGTATCTTGCATTTCATATGAACACTT 58.591 33.333 17.76 1.09 33.13 3.16
2750 2831 9.229784 GTATCTTGCATTTCATATGAACACTTG 57.770 33.333 17.76 13.25 33.13 3.16
2760 2865 0.461870 TGAACACTTGTGCTCGTGCT 60.462 50.000 11.19 0.00 40.48 4.40
2762 2867 1.439353 AACACTTGTGCTCGTGCTGG 61.439 55.000 11.19 1.24 40.48 4.85
2982 4569 6.166984 ACACTACGGCTACTCTACTATACA 57.833 41.667 0.00 0.00 0.00 2.29
3003 4712 4.231890 ACAATTATCCCTCCCCTTGCTTTA 59.768 41.667 0.00 0.00 0.00 1.85
3004 4713 4.731313 ATTATCCCTCCCCTTGCTTTAG 57.269 45.455 0.00 0.00 0.00 1.85
3012 4721 1.959282 CCCCTTGCTTTAGGATGCATC 59.041 52.381 18.81 18.81 39.07 3.91
3024 4733 3.740128 ATGCATCGGGTCGCTCACC 62.740 63.158 0.00 0.00 45.97 4.02
3090 4938 5.107913 CGTGTTGTTATCGTCGTTTCCTTTA 60.108 40.000 0.00 0.00 0.00 1.85
3091 4939 6.400303 CGTGTTGTTATCGTCGTTTCCTTTAT 60.400 38.462 0.00 0.00 0.00 1.40
3092 4940 6.952083 GTGTTGTTATCGTCGTTTCCTTTATC 59.048 38.462 0.00 0.00 0.00 1.75
3093 4941 6.091169 TGTTGTTATCGTCGTTTCCTTTATCC 59.909 38.462 0.00 0.00 0.00 2.59
3094 4942 5.722263 TGTTATCGTCGTTTCCTTTATCCA 58.278 37.500 0.00 0.00 0.00 3.41
3119 4967 0.902984 ACCAGCAGTATCCGTCACCA 60.903 55.000 0.00 0.00 0.00 4.17
3123 4971 1.899814 AGCAGTATCCGTCACCAGAAA 59.100 47.619 0.00 0.00 0.00 2.52
3124 4972 2.000447 GCAGTATCCGTCACCAGAAAC 59.000 52.381 0.00 0.00 0.00 2.78
3125 4973 2.353803 GCAGTATCCGTCACCAGAAACT 60.354 50.000 0.00 0.00 0.00 2.66
3126 4974 3.512680 CAGTATCCGTCACCAGAAACTC 58.487 50.000 0.00 0.00 0.00 3.01
3193 5041 4.013728 AGAGCTAAGATGAACTGACGAGT 58.986 43.478 0.00 0.00 0.00 4.18
3195 5043 3.129638 AGCTAAGATGAACTGACGAGTCC 59.870 47.826 0.34 0.00 0.00 3.85
3205 5053 1.170290 TGACGAGTCCGAGCAGAACA 61.170 55.000 0.34 0.00 39.50 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 8.020819 CACGATTTATTTTGTGTCAACCTATGT 58.979 33.333 0.00 0.00 0.00 2.29
17 18 5.387342 GCAGCACGATTTATTTTGTGTCAAC 60.387 40.000 0.00 0.00 34.86 3.18
26 27 2.661195 GCGTTTGCAGCACGATTTATTT 59.339 40.909 21.08 0.00 40.20 1.40
28 29 1.895051 GCGTTTGCAGCACGATTTAT 58.105 45.000 21.08 0.00 40.20 1.40
29 30 3.376347 GCGTTTGCAGCACGATTTA 57.624 47.368 21.08 0.00 40.20 1.40
106 120 2.094700 GCTCCGATTTTCCTTTTCCACC 60.095 50.000 0.00 0.00 0.00 4.61
168 190 2.098376 TAGGGCTAGGGCTAGGGCT 61.098 63.158 0.00 0.00 38.73 5.19
169 191 1.610967 CTAGGGCTAGGGCTAGGGC 60.611 68.421 0.00 0.00 38.73 5.19
173 195 0.778881 TAGGGCTAGGGCTAGGGCTA 60.779 60.000 0.00 0.00 38.73 3.93
202 224 2.081212 AGAAAGTTCGAGACGCGCG 61.081 57.895 30.96 30.96 40.61 6.86
226 248 3.727391 AGGGGATAGGTTAGAAAATGGGG 59.273 47.826 0.00 0.00 0.00 4.96
260 282 1.669440 GTGCGAGAGTGGTTACCCA 59.331 57.895 0.00 0.00 38.87 4.51
261 283 1.079336 GGTGCGAGAGTGGTTACCC 60.079 63.158 0.00 0.00 0.00 3.69
262 284 0.034337 TTGGTGCGAGAGTGGTTACC 59.966 55.000 0.00 0.00 0.00 2.85
263 285 1.529865 GTTTGGTGCGAGAGTGGTTAC 59.470 52.381 0.00 0.00 0.00 2.50
264 286 1.870580 CGTTTGGTGCGAGAGTGGTTA 60.871 52.381 0.00 0.00 0.00 2.85
265 287 1.157870 CGTTTGGTGCGAGAGTGGTT 61.158 55.000 0.00 0.00 0.00 3.67
280 302 1.065551 GTGCTCTGTTTTCTGCCGTTT 59.934 47.619 0.00 0.00 0.00 3.60
342 364 0.611896 CGAGCTTGGGTGGGGATTTT 60.612 55.000 0.00 0.00 0.00 1.82
346 368 1.910580 GATTCGAGCTTGGGTGGGGA 61.911 60.000 0.00 0.00 0.00 4.81
350 374 2.208431 GATCAGATTCGAGCTTGGGTG 58.792 52.381 0.00 0.00 0.00 4.61
368 392 2.016704 GATTCGATGCGCGTCGGAT 61.017 57.895 41.66 40.27 42.31 4.18
412 436 4.872691 ACAAGCAGGAAATCGAGATTAGTG 59.127 41.667 0.00 0.00 0.00 2.74
470 494 7.241628 AGATTCACTGAAACTTTCCCCTAAAT 58.758 34.615 0.00 0.00 0.00 1.40
489 513 2.092753 GGCCTGATTGACCTCAGATTCA 60.093 50.000 0.00 0.00 44.48 2.57
574 599 7.384660 GTGAGAGATCATGAATGGCTAAGTAAG 59.615 40.741 0.00 0.00 0.00 2.34
610 635 7.115414 AGAAACAAGCTAGGCTATCAAAATCT 58.885 34.615 0.00 0.00 38.25 2.40
668 695 8.770010 AGAACATATTACTACTACAGAAGCCT 57.230 34.615 0.00 0.00 0.00 4.58
716 743 1.004440 GCTCACTGGACCTCACCAC 60.004 63.158 0.00 0.00 35.91 4.16
774 801 5.447624 TCGTGACTGACTTCACAGATAAA 57.552 39.130 0.00 0.00 45.38 1.40
790 818 7.561556 TCGTTTTAGAATCTCTTTTTCGTGAC 58.438 34.615 0.00 0.00 0.00 3.67
867 895 0.520404 CCAAGCGATGCATATGGAGC 59.480 55.000 12.59 1.89 33.15 4.70
913 941 6.777091 ACATAAGCATCCAAGCCATACATAAA 59.223 34.615 0.00 0.00 34.23 1.40
922 950 3.736126 GCAAGAACATAAGCATCCAAGCC 60.736 47.826 0.00 0.00 34.23 4.35
943 971 1.604593 ACACCCCATCACAAGCAGC 60.605 57.895 0.00 0.00 0.00 5.25
947 975 2.198827 TTAGCACACCCCATCACAAG 57.801 50.000 0.00 0.00 0.00 3.16
956 984 3.191371 CAGAACCTTCAATTAGCACACCC 59.809 47.826 0.00 0.00 0.00 4.61
976 1004 0.514255 CTGCACCACAATCGACACAG 59.486 55.000 0.00 0.00 0.00 3.66
1065 1093 3.208592 AGGTGAGGTCCCCCTGGA 61.209 66.667 0.00 0.00 42.86 3.86
1087 1115 4.093291 CAGCGCCTGGAGCTTCCT 62.093 66.667 22.82 0.00 44.06 3.36
1155 1183 0.915364 GGACCTCCAAGGCATTCTCT 59.085 55.000 0.00 0.00 39.63 3.10
1203 1231 0.096628 GCAGCTCTGACAAGCAATCG 59.903 55.000 0.29 0.00 45.00 3.34
1353 1381 2.586245 CCTTGATCCAGCCGAGCA 59.414 61.111 0.00 0.00 34.30 4.26
1360 1388 0.323178 AGCAACTGCCCTTGATCCAG 60.323 55.000 0.00 0.00 43.38 3.86
1414 1442 2.625823 CCAATGACGGCACACCACC 61.626 63.158 0.00 0.00 34.57 4.61
1457 1485 2.181125 TGTCCATCCACGCCTTAAGTA 58.819 47.619 0.97 0.00 0.00 2.24
1466 1494 1.156736 GTCCACTTTGTCCATCCACG 58.843 55.000 0.00 0.00 0.00 4.94
1653 1681 1.898863 ATGGCTTGGGACTACCTGAT 58.101 50.000 0.00 0.00 41.11 2.90
1695 1723 2.482864 GCCTGTGACCAACCAAATTTG 58.517 47.619 11.40 11.40 0.00 2.32
1743 1771 0.676782 ATCGCCTTTTGACTTCCCCG 60.677 55.000 0.00 0.00 0.00 5.73
1821 1849 4.081406 TCCTAGTCAATGCATGCAGTTTT 58.919 39.130 26.69 12.94 0.00 2.43
1848 1876 5.910637 TGTCATTTTCATTTTCAAGCTGC 57.089 34.783 0.00 0.00 0.00 5.25
1858 1886 4.050553 CAAGCCACGTTGTCATTTTCATT 58.949 39.130 0.00 0.00 0.00 2.57
1860 1888 2.425312 ACAAGCCACGTTGTCATTTTCA 59.575 40.909 0.00 0.00 35.71 2.69
1873 1901 2.641559 GCTGACAGCACAAGCCAC 59.358 61.111 22.62 0.00 41.89 5.01
1893 1921 2.613691 GGCATCACCATTTGCTTTGAG 58.386 47.619 0.00 0.00 38.88 3.02
1916 1944 1.345741 CTCCTTTCTGTCCAGTGCTGA 59.654 52.381 0.02 0.00 0.00 4.26
1919 1947 1.609320 GGTCTCCTTTCTGTCCAGTGC 60.609 57.143 0.00 0.00 0.00 4.40
1925 1953 0.615850 CCTGGGGTCTCCTTTCTGTC 59.384 60.000 0.00 0.00 36.20 3.51
1934 1962 4.683671 GCTTAAGATTACACCTGGGGTCTC 60.684 50.000 3.99 3.95 31.02 3.36
1936 1964 3.542648 GCTTAAGATTACACCTGGGGTC 58.457 50.000 3.99 0.00 31.02 4.46
1938 1966 2.241176 TGGCTTAAGATTACACCTGGGG 59.759 50.000 6.67 0.00 0.00 4.96
1942 1970 3.519510 TCAGCTGGCTTAAGATTACACCT 59.480 43.478 15.13 0.00 0.00 4.00
1943 1971 3.873910 TCAGCTGGCTTAAGATTACACC 58.126 45.455 15.13 0.00 0.00 4.16
1976 2004 0.926155 CATGATCGCTTCACACTCCG 59.074 55.000 0.00 0.00 37.11 4.63
1988 2016 5.755861 TCTGTACTAGTCTCTGTCATGATCG 59.244 44.000 0.00 0.00 0.00 3.69
2003 2031 5.477291 TCCTGTGTTCCTTCTTCTGTACTAG 59.523 44.000 0.00 0.00 0.00 2.57
2010 2038 1.349357 GCCTCCTGTGTTCCTTCTTCT 59.651 52.381 0.00 0.00 0.00 2.85
2025 2053 2.936202 TCCTGCATCATTTTAGCCTCC 58.064 47.619 0.00 0.00 0.00 4.30
2028 2056 6.039717 TGTTATCTTCCTGCATCATTTTAGCC 59.960 38.462 0.00 0.00 0.00 3.93
2032 2060 5.127682 GGGTGTTATCTTCCTGCATCATTTT 59.872 40.000 0.00 0.00 0.00 1.82
2037 2065 2.945668 GTGGGTGTTATCTTCCTGCATC 59.054 50.000 0.00 0.00 0.00 3.91
2071 2099 4.642437 ACTGATACTCTCAAGCTCGATCAA 59.358 41.667 0.00 0.00 32.14 2.57
2077 2105 5.574891 TCTTCACTGATACTCTCAAGCTC 57.425 43.478 0.00 0.00 32.14 4.09
2078 2106 7.123397 TGTTATCTTCACTGATACTCTCAAGCT 59.877 37.037 0.00 0.00 32.14 3.74
2211 2281 1.007336 CCCCGACTCGTTTCGACAAG 61.007 60.000 9.52 0.00 41.78 3.16
2280 2350 1.941294 CTTGCTGCATCTGACATCCTC 59.059 52.381 1.84 0.00 0.00 3.71
2327 2397 4.084013 ACATACACAGCAGAAACGTAAAGC 60.084 41.667 0.00 0.00 0.00 3.51
2329 2399 5.756347 AGAACATACACAGCAGAAACGTAAA 59.244 36.000 0.00 0.00 0.00 2.01
2330 2400 5.294356 AGAACATACACAGCAGAAACGTAA 58.706 37.500 0.00 0.00 0.00 3.18
2339 2409 3.181455 ACCAACAGAGAACATACACAGCA 60.181 43.478 0.00 0.00 0.00 4.41
2394 2467 1.071605 GAAGAGCGGTGTACAAGCAG 58.928 55.000 21.74 3.75 0.00 4.24
2423 2496 4.106925 GTGAGGCTGAGCAGGGGG 62.107 72.222 6.82 0.00 0.00 5.40
2476 2552 0.029834 GCAGCCCAAGATTATGCACG 59.970 55.000 0.00 0.00 36.88 5.34
2574 2653 9.295214 CACACTAATGACTCAGTATTTGTCTAG 57.705 37.037 0.00 0.00 0.00 2.43
2586 2665 5.185828 ACTGATACTGCACACTAATGACTCA 59.814 40.000 0.00 0.00 0.00 3.41
2738 2819 2.416547 GCACGAGCACAAGTGTTCATAT 59.583 45.455 15.61 0.07 40.25 1.78
2744 2825 1.889105 CCAGCACGAGCACAAGTGT 60.889 57.895 7.77 0.00 45.49 3.55
2745 2826 1.563435 CTCCAGCACGAGCACAAGTG 61.563 60.000 7.77 0.00 45.49 3.16
2747 2828 1.301244 ACTCCAGCACGAGCACAAG 60.301 57.895 7.77 3.37 45.49 3.16
2748 2829 1.595109 CACTCCAGCACGAGCACAA 60.595 57.895 7.77 0.00 45.49 3.33
2749 2830 2.029518 CACTCCAGCACGAGCACA 59.970 61.111 7.77 0.00 45.49 4.57
2750 2831 0.319555 TAACACTCCAGCACGAGCAC 60.320 55.000 7.77 0.00 45.49 4.40
2760 2865 5.047590 TGCTAAAGATTCGAGTAACACTCCA 60.048 40.000 0.89 0.00 42.12 3.86
2762 2867 6.365247 TGTTGCTAAAGATTCGAGTAACACTC 59.635 38.462 12.40 0.00 39.75 3.51
2982 4569 4.140924 CCTAAAGCAAGGGGAGGGATAATT 60.141 45.833 0.00 0.00 32.55 1.40
3003 4712 3.157217 GAGCGACCCGATGCATCCT 62.157 63.158 20.87 10.63 0.00 3.24
3004 4713 2.663188 GAGCGACCCGATGCATCC 60.663 66.667 20.87 5.88 0.00 3.51
3012 4721 4.907034 CGATCGGTGAGCGACCCG 62.907 72.222 9.56 12.41 44.55 5.28
3090 4938 3.435601 GGATACTGCTGGTTGGATTGGAT 60.436 47.826 0.00 0.00 0.00 3.41
3091 4939 2.092429 GGATACTGCTGGTTGGATTGGA 60.092 50.000 0.00 0.00 0.00 3.53
3092 4940 2.301346 GGATACTGCTGGTTGGATTGG 58.699 52.381 0.00 0.00 0.00 3.16
3093 4941 1.942657 CGGATACTGCTGGTTGGATTG 59.057 52.381 0.00 0.00 0.00 2.67
3094 4942 1.559682 ACGGATACTGCTGGTTGGATT 59.440 47.619 0.00 0.00 0.00 3.01
3119 4967 2.953020 CTGCTGAAGCTACGAGTTTCT 58.047 47.619 3.61 0.00 42.66 2.52
3193 5041 1.674359 TTTGCTTTGTTCTGCTCGGA 58.326 45.000 0.00 0.00 0.00 4.55
3195 5043 1.783140 GCTTTTGCTTTGTTCTGCTCG 59.217 47.619 0.00 0.00 43.35 5.03
3205 5053 5.117592 CGATTGATTTCTTCGCTTTTGCTTT 59.882 36.000 0.00 0.00 44.80 3.51
3274 5129 1.809869 CGAGCAGGACGATGAGGAA 59.190 57.895 0.00 0.00 0.00 3.36
3383 5247 4.056125 CGTCGGCTGAGGAGTGCA 62.056 66.667 9.71 0.00 31.63 4.57


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

AutoCloner maintained by Alex Coulton.