Multiple sequence alignment - TraesCS1D01G014800

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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 TraesCS1D01G014800 chr1D 100.000 2972 0 0 1 2972 7069049 7066078 0 5489
1 TraesCS1D01G014800 chr1D 84.913 2353 281 35 665 2961 7059326 7056992 0 2311
2 TraesCS1D01G014800 chr1D 86.921 1965 239 12 998 2959 7422679 7420730 0 2189
3 TraesCS1D01G014800 chr1D 85.396 1972 260 14 998 2958 7868620 7870574 0 2021
4 TraesCS1D01G014800 chr1D 84.365 1970 287 15 998 2961 7384629 7382675 0 1912
5 TraesCS1D01G014800 chr1A 86.207 2320 277 28 679 2961 8633507 8631194 0 2471
6 TraesCS1D01G014800 chr1A 83.688 1974 287 20 998 2961 9340925 9342873 0 1829
7 TraesCS1D01G014800 chr1A 91.408 547 39 6 1 544 8634547 8634006 0 743
8 TraesCS1D01G014800 chr1B 83.111 2321 328 40 667 2959 9550928 9548644 0 2056
9 TraesCS1D01G014800 chr1B 83.747 2178 306 26 803 2970 10014552 10016691 0 2017
10 TraesCS1D01G014800 chr1B 84.705 1968 272 18 998 2961 10060089 10062031 0 1940
11 TraesCS1D01G014800 chr1B 84.152 1975 273 23 998 2961 9693116 9691171 0 1877
12 TraesCS1D01G014800 chr4B 83.585 1986 290 18 994 2970 4990775 4992733 0 1829


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 TraesCS1D01G014800 chr1D 7066078 7069049 2971 True 5489 5489 100.0000 1 2972 1 chr1D.!!$R2 2971
1 TraesCS1D01G014800 chr1D 7056992 7059326 2334 True 2311 2311 84.9130 665 2961 1 chr1D.!!$R1 2296
2 TraesCS1D01G014800 chr1D 7420730 7422679 1949 True 2189 2189 86.9210 998 2959 1 chr1D.!!$R4 1961
3 TraesCS1D01G014800 chr1D 7868620 7870574 1954 False 2021 2021 85.3960 998 2958 1 chr1D.!!$F1 1960
4 TraesCS1D01G014800 chr1D 7382675 7384629 1954 True 1912 1912 84.3650 998 2961 1 chr1D.!!$R3 1963
5 TraesCS1D01G014800 chr1A 9340925 9342873 1948 False 1829 1829 83.6880 998 2961 1 chr1A.!!$F1 1963
6 TraesCS1D01G014800 chr1A 8631194 8634547 3353 True 1607 2471 88.8075 1 2961 2 chr1A.!!$R1 2960
7 TraesCS1D01G014800 chr1B 9548644 9550928 2284 True 2056 2056 83.1110 667 2959 1 chr1B.!!$R1 2292
8 TraesCS1D01G014800 chr1B 10014552 10016691 2139 False 2017 2017 83.7470 803 2970 1 chr1B.!!$F1 2167
9 TraesCS1D01G014800 chr1B 10060089 10062031 1942 False 1940 1940 84.7050 998 2961 1 chr1B.!!$F2 1963
10 TraesCS1D01G014800 chr1B 9691171 9693116 1945 True 1877 1877 84.1520 998 2961 1 chr1B.!!$R2 1963
11 TraesCS1D01G014800 chr4B 4990775 4992733 1958 False 1829 1829 83.5850 994 2970 1 chr4B.!!$F1 1976

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
568 594 0.107831 ACCCTAAACGCTGCAGAACA 59.892 50.0 20.43 0.0 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2415 2878 0.179 CAAGCTCGGCCAAGTATCCT 59.821 55.0 2.24 0.0 0.0 3.24 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
117 118 0.506932 CGACGCGTTCACATTGAAGT 59.493 50.000 15.53 0.00 37.00 3.01
146 147 3.186047 GCCGTTCGGTCACATCGG 61.186 66.667 12.81 0.00 43.37 4.18
164 165 0.179145 GGTCCGATCGACACGAATGT 60.179 55.000 18.66 0.00 43.95 2.71
175 176 0.874607 CACGAATGTAGGTAGGCGGC 60.875 60.000 0.00 0.00 0.00 6.53
202 203 3.270027 TGTCACATTCATTCTAAGCGGG 58.730 45.455 0.00 0.00 0.00 6.13
213 214 1.009829 CTAAGCGGGAGTGAATGTGC 58.990 55.000 0.00 0.00 0.00 4.57
225 226 1.005037 AATGTGCGACGAGGCTTCA 60.005 52.632 0.00 0.00 0.00 3.02
237 238 3.567473 GCTTCAGGAGCGGAACAC 58.433 61.111 0.00 0.00 42.46 3.32
269 270 3.474570 AGATGGGGCCGCTCAGAC 61.475 66.667 21.80 7.62 0.00 3.51
297 298 2.281484 GTGACAGAGGCCCGCAAA 60.281 61.111 0.00 0.00 0.00 3.68
316 317 2.651382 ACCTCCTACCGTTTTGCTTT 57.349 45.000 0.00 0.00 0.00 3.51
337 338 3.330126 TGGTTTATGGGGTTTTGGACA 57.670 42.857 0.00 0.00 0.00 4.02
359 360 1.004200 AAACCGGTCCATGGACGTC 60.004 57.895 33.24 21.74 45.41 4.34
415 416 4.953269 GACGCTGATCAAATTAAACGTCA 58.047 39.130 15.86 0.00 45.73 4.35
440 441 0.698818 GGGCCCTCCTCTCTTTGAAA 59.301 55.000 17.04 0.00 0.00 2.69
446 447 4.401925 CCCTCCTCTCTTTGAAACAACAT 58.598 43.478 0.00 0.00 0.00 2.71
467 468 9.616634 CAACATGCGCTTGATAGAAATAATAAT 57.383 29.630 27.85 0.00 0.00 1.28
550 576 9.713713 TTTTAGGGGCAAAATAGAAAATAACAC 57.286 29.630 0.00 0.00 0.00 3.32
551 577 6.294361 AGGGGCAAAATAGAAAATAACACC 57.706 37.500 0.00 0.00 0.00 4.16
552 578 5.188948 AGGGGCAAAATAGAAAATAACACCC 59.811 40.000 0.00 0.00 0.00 4.61
553 579 5.188948 GGGGCAAAATAGAAAATAACACCCT 59.811 40.000 0.00 0.00 32.86 4.34
554 580 6.381707 GGGGCAAAATAGAAAATAACACCCTA 59.618 38.462 0.00 0.00 32.86 3.53
555 581 7.093245 GGGGCAAAATAGAAAATAACACCCTAA 60.093 37.037 0.00 0.00 32.86 2.69
556 582 8.315482 GGGCAAAATAGAAAATAACACCCTAAA 58.685 33.333 0.00 0.00 0.00 1.85
557 583 9.146984 GGCAAAATAGAAAATAACACCCTAAAC 57.853 33.333 0.00 0.00 0.00 2.01
567 593 0.517316 CACCCTAAACGCTGCAGAAC 59.483 55.000 20.43 0.00 0.00 3.01
568 594 0.107831 ACCCTAAACGCTGCAGAACA 59.892 50.000 20.43 0.00 0.00 3.18
581 607 1.957113 GCAGAACAGAATGGGGGAAGG 60.957 57.143 0.00 0.00 43.62 3.46
595 621 1.415200 GGAAGGCCGAAGAGGAGTAT 58.585 55.000 0.00 0.00 45.00 2.12
612 642 3.393800 AGTATCCAAATCGAATCTGGCG 58.606 45.455 6.03 0.00 0.00 5.69
614 644 0.392327 TCCAAATCGAATCTGGCGCA 60.392 50.000 10.83 0.00 0.00 6.09
615 645 0.664761 CCAAATCGAATCTGGCGCAT 59.335 50.000 10.83 0.00 0.00 4.73
617 647 0.583438 AAATCGAATCTGGCGCATCG 59.417 50.000 10.83 10.93 36.67 3.84
647 711 2.352032 CCCCTTCTTCCTCGCTCGT 61.352 63.158 0.00 0.00 0.00 4.18
677 749 4.656041 CGCTTGTTGATGAGGAGAAATTC 58.344 43.478 0.00 0.00 0.00 2.17
729 1107 2.103771 TGCTATTGTCCCTGATGCTCTC 59.896 50.000 0.00 0.00 0.00 3.20
733 1111 0.532573 TGTCCCTGATGCTCTCGTTC 59.467 55.000 0.00 0.00 0.00 3.95
736 1114 0.526524 CCCTGATGCTCTCGTTCGTC 60.527 60.000 0.00 0.00 0.00 4.20
760 1138 5.869579 TCTACTGATTTTGCAGGTTCTTCT 58.130 37.500 0.00 0.00 40.20 2.85
762 1140 5.444663 ACTGATTTTGCAGGTTCTTCTTC 57.555 39.130 0.00 0.00 40.20 2.87
763 1141 4.889409 ACTGATTTTGCAGGTTCTTCTTCA 59.111 37.500 0.00 0.00 40.20 3.02
764 1142 5.537674 ACTGATTTTGCAGGTTCTTCTTCAT 59.462 36.000 0.00 0.00 40.20 2.57
765 1143 6.017400 TGATTTTGCAGGTTCTTCTTCATC 57.983 37.500 0.00 0.00 0.00 2.92
766 1144 5.535783 TGATTTTGCAGGTTCTTCTTCATCA 59.464 36.000 0.00 0.00 0.00 3.07
767 1145 4.836125 TTTGCAGGTTCTTCTTCATCAC 57.164 40.909 0.00 0.00 0.00 3.06
768 1146 3.490439 TGCAGGTTCTTCTTCATCACA 57.510 42.857 0.00 0.00 0.00 3.58
769 1147 4.025040 TGCAGGTTCTTCTTCATCACAT 57.975 40.909 0.00 0.00 0.00 3.21
787 1171 0.813184 ATTCACAGCCAAATGAGCCG 59.187 50.000 0.00 0.00 0.00 5.52
793 1177 2.032634 GCCAAATGAGCCGTCGACA 61.033 57.895 17.16 0.00 0.00 4.35
794 1178 1.970917 GCCAAATGAGCCGTCGACAG 61.971 60.000 17.16 5.18 0.00 3.51
807 1202 1.098129 TCGACAGATGCGGAGAGAGG 61.098 60.000 0.00 0.00 0.00 3.69
822 1217 1.206849 GAGAGGCAGAGAGAGGTTTGG 59.793 57.143 0.00 0.00 0.00 3.28
841 1236 6.294731 GGTTTGGTGGCTATATGGAATCAATC 60.295 42.308 0.00 0.00 0.00 2.67
846 1241 6.541641 GGTGGCTATATGGAATCAATCAGATC 59.458 42.308 0.00 0.00 35.39 2.75
856 1252 7.719483 TGGAATCAATCAGATCAAATTTAGGC 58.281 34.615 0.00 0.00 35.39 3.93
859 1255 8.450578 AATCAATCAGATCAAATTTAGGCGTA 57.549 30.769 0.00 0.00 35.39 4.42
873 1269 1.202463 AGGCGTATGACATCTGCTGAC 60.202 52.381 10.57 0.00 0.00 3.51
942 1362 3.553511 GGTGCTCGAATGAGTATTCAGTG 59.446 47.826 0.00 0.00 44.48 3.66
943 1363 4.424626 GTGCTCGAATGAGTATTCAGTGA 58.575 43.478 0.00 0.00 44.48 3.41
961 1381 3.007398 AGTGAGAGTGAGATTTGGTCACC 59.993 47.826 0.00 0.00 44.65 4.02
963 1383 3.259374 TGAGAGTGAGATTTGGTCACCTC 59.741 47.826 0.00 11.60 44.65 3.85
964 1384 3.513515 GAGAGTGAGATTTGGTCACCTCT 59.486 47.826 0.00 0.00 44.65 3.69
965 1385 3.513515 AGAGTGAGATTTGGTCACCTCTC 59.486 47.826 4.86 4.86 44.65 3.20
978 1415 2.093288 TCACCTCTCAGCAACCATCATC 60.093 50.000 0.00 0.00 0.00 2.92
1143 1582 3.077556 ATCCGCGACTCCAAGGCT 61.078 61.111 8.23 0.00 0.00 4.58
1149 1588 1.294780 CGACTCCAAGGCTGAGCTT 59.705 57.895 3.72 0.00 32.98 3.74
1194 1633 1.078143 GGCAGAGCGGTTCAAGGAT 60.078 57.895 0.00 0.00 0.00 3.24
1198 1637 1.207089 CAGAGCGGTTCAAGGATACCA 59.793 52.381 0.00 0.00 33.94 3.25
1224 1663 1.079819 CACAGCCATCTTCGTCGGT 60.080 57.895 0.00 0.00 0.00 4.69
1305 1744 1.377202 GGATTGCAAGCACGGAGGA 60.377 57.895 17.68 0.00 0.00 3.71
1328 1767 2.079158 CGCTGCCAAGATGAAGAAGAA 58.921 47.619 0.00 0.00 0.00 2.52
1427 1866 0.462759 AGGAAGCAGGATTACGCAGC 60.463 55.000 0.00 0.00 0.00 5.25
1485 1924 2.828933 GACAAGTCGAGGTCAAGCC 58.171 57.895 6.87 0.00 34.22 4.35
1557 1996 0.108804 AGTTGATACGGTGGCTGACG 60.109 55.000 0.00 0.00 0.00 4.35
1558 1997 1.082117 GTTGATACGGTGGCTGACGG 61.082 60.000 0.00 0.00 0.00 4.79
1559 1998 2.106332 GATACGGTGGCTGACGGG 59.894 66.667 0.00 0.00 0.00 5.28
1560 1999 4.157120 ATACGGTGGCTGACGGGC 62.157 66.667 0.00 0.00 41.27 6.13
1576 2027 2.672996 GCAGTGGCGGTGGTGATT 60.673 61.111 0.00 0.00 0.00 2.57
1688 2139 2.294791 TGAAATTGGATTTTGACGCCGT 59.705 40.909 0.00 0.00 31.47 5.68
1701 2152 4.992511 GCCGTGGCGTGGGTAACA 62.993 66.667 0.00 0.00 39.74 2.41
1717 2168 4.280174 GGGTAACAGTGTCAGAGAGTTACA 59.720 45.833 13.61 0.00 43.71 2.41
1743 2194 5.825151 TCTCGAAGATCTGCTGAAGAAGATA 59.175 40.000 0.49 0.00 40.48 1.98
1766 2217 3.257561 CGAGTTCGGCATCGCAGG 61.258 66.667 0.00 0.00 36.13 4.85
1767 2218 2.184322 GAGTTCGGCATCGCAGGA 59.816 61.111 0.00 0.00 36.13 3.86
1768 2219 1.447838 GAGTTCGGCATCGCAGGAA 60.448 57.895 0.00 0.00 36.13 3.36
1791 2242 6.401047 AATATTGCCAATGTTGAGATGAGG 57.599 37.500 0.00 0.00 0.00 3.86
1792 2243 1.466856 TGCCAATGTTGAGATGAGGC 58.533 50.000 0.00 0.00 40.93 4.70
1810 2261 2.119009 CGCCTAGCAGAGTCCATCA 58.881 57.895 0.00 0.00 0.00 3.07
1816 2267 2.936919 AGCAGAGTCCATCAACAACA 57.063 45.000 0.00 0.00 0.00 3.33
1818 2269 3.759581 AGCAGAGTCCATCAACAACAAT 58.240 40.909 0.00 0.00 0.00 2.71
1892 2343 2.158957 TGTGGTCGGAGATAAGGAATGC 60.159 50.000 0.00 0.00 40.67 3.56
1923 2374 1.406539 TCTAACTGTACCGGCCGATTC 59.593 52.381 30.73 8.40 0.00 2.52
1924 2375 1.135527 CTAACTGTACCGGCCGATTCA 59.864 52.381 30.73 14.07 0.00 2.57
1969 2420 2.884639 GTGTCATTGTTGGCAACTAGGT 59.115 45.455 28.71 10.97 39.65 3.08
1980 2437 3.198872 GGCAACTAGGTAGTCTGCAATC 58.801 50.000 18.01 5.64 39.66 2.67
2004 2461 1.282875 GGAACCGCTGCAAGAACAC 59.717 57.895 0.00 0.00 34.07 3.32
2087 2544 0.679002 GAGCTGCAGGAATTGGCTCA 60.679 55.000 17.12 0.00 45.79 4.26
2125 2582 1.133790 GTCAAGGCTTGCCTATTGCTG 59.866 52.381 22.31 9.08 42.00 4.41
2151 2608 4.845580 ATTGGCCGCCTGCTCTCG 62.846 66.667 11.61 0.00 40.92 4.04
2160 2617 1.597854 CCTGCTCTCGTGCAAACCA 60.598 57.895 0.00 0.00 42.83 3.67
2173 2630 0.310854 CAAACCACCAACTTCCGCTC 59.689 55.000 0.00 0.00 0.00 5.03
2194 2651 2.505407 CAATGGGAGGATGTGTACAGGA 59.495 50.000 0.00 0.00 0.00 3.86
2195 2652 2.335681 TGGGAGGATGTGTACAGGAA 57.664 50.000 0.00 0.00 0.00 3.36
2229 2686 1.203237 TGGCGAAAGATCTGATCCCA 58.797 50.000 13.83 10.62 0.00 4.37
2257 2714 6.126796 TGTTCATATGATCCTAAAGGTCAGCA 60.127 38.462 6.17 0.00 36.34 4.41
2269 2726 2.206576 GGTCAGCATGGAAGACCTTT 57.793 50.000 0.00 0.00 46.45 3.11
2325 2782 7.560991 TGTGCATTATCCCAAGAAGATTATGTT 59.439 33.333 0.00 0.00 34.68 2.71
2326 2783 7.864379 GTGCATTATCCCAAGAAGATTATGTTG 59.136 37.037 0.00 0.00 34.68 3.33
2384 2844 3.563479 GCAGGGTTTATCAGGGAAAAGGA 60.563 47.826 0.00 0.00 0.00 3.36
2385 2845 4.672899 CAGGGTTTATCAGGGAAAAGGAA 58.327 43.478 0.00 0.00 0.00 3.36
2386 2846 4.706962 CAGGGTTTATCAGGGAAAAGGAAG 59.293 45.833 0.00 0.00 0.00 3.46
2415 2878 1.425066 ACATTGGAGGAAGTGGCAGAA 59.575 47.619 0.00 0.00 0.00 3.02
2473 2936 4.225942 TGCAGGTAGTGAAGAGGAATCATT 59.774 41.667 0.00 0.00 0.00 2.57
2474 2937 5.189180 GCAGGTAGTGAAGAGGAATCATTT 58.811 41.667 0.00 0.00 0.00 2.32
2577 3043 2.092538 AGTTTATGATGGCTCTGCTGCT 60.093 45.455 0.00 0.00 0.00 4.24
2610 3079 2.279918 GTTGAGGGTGCACGTCGT 60.280 61.111 11.45 0.00 36.79 4.34
2619 3088 1.264020 GGTGCACGTCGTATATCGGTA 59.736 52.381 11.45 0.00 40.32 4.02
2649 3118 0.591170 ACGTTGAACAATTGAGCCGG 59.409 50.000 13.59 0.00 0.00 6.13
2678 3147 2.919856 ACAGCTCCGTGCACTCCT 60.920 61.111 16.19 2.50 45.94 3.69
2679 3148 2.125753 CAGCTCCGTGCACTCCTC 60.126 66.667 16.19 1.62 45.94 3.71
2745 3214 3.883830 ACATCTTCGAATCTGCTGTCT 57.116 42.857 0.00 0.00 0.00 3.41
2772 3241 3.704566 TGGATCTGCAAGGTACTCGTATT 59.295 43.478 0.00 0.00 38.49 1.89
2827 3296 4.965119 AATCTGCGTTATTTGGGTCTTC 57.035 40.909 0.00 0.00 0.00 2.87
2835 3304 2.667473 ATTTGGGTCTTCGAGGTACG 57.333 50.000 0.00 0.00 44.09 3.67
2925 3394 6.434028 ACTCTAAGCTGACATATTTGCCAAAA 59.566 34.615 0.00 0.00 0.00 2.44
2971 3440 9.026121 AGTTGAGATACCTGTACATATATGTCC 57.974 37.037 21.49 11.47 41.97 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 3.118298 TCCGCCTACCCTGGTTATTTAAC 60.118 47.826 0.00 0.00 35.50 2.01
70 71 2.659897 CTACTCCAGCCGATGCGC 60.660 66.667 0.00 0.00 44.33 6.09
91 92 1.225936 GTGAACGCGTCGATCGAGA 60.226 57.895 20.09 0.00 41.61 4.04
146 147 2.373269 CTACATTCGTGTCGATCGGAC 58.627 52.381 16.41 12.44 46.27 4.79
164 165 4.133373 AGGACGGCCGCCTACCTA 62.133 66.667 31.37 0.00 39.96 3.08
175 176 2.977914 AGAATGAATGTGACAGGACGG 58.022 47.619 0.00 0.00 0.00 4.79
187 188 4.487714 TTCACTCCCGCTTAGAATGAAT 57.512 40.909 0.00 0.00 0.00 2.57
202 203 1.687494 GCCTCGTCGCACATTCACTC 61.687 60.000 0.00 0.00 0.00 3.51
213 214 2.202676 GCTCCTGAAGCCTCGTCG 60.203 66.667 0.00 0.00 45.92 5.12
237 238 2.230940 ATCTGAAATCGTCGCCGCG 61.231 57.895 6.39 6.39 0.00 6.46
241 242 1.776034 GCCCCATCTGAAATCGTCGC 61.776 60.000 0.00 0.00 0.00 5.19
252 253 3.474570 GTCTGAGCGGCCCCATCT 61.475 66.667 0.00 0.00 0.00 2.90
269 270 1.202348 CCTCTGTCACATAGGTGCTCG 60.202 57.143 1.79 0.00 44.87 5.03
289 290 2.437895 GGTAGGAGGTTTGCGGGC 60.438 66.667 0.00 0.00 0.00 6.13
297 298 2.621526 CAAAAGCAAAACGGTAGGAGGT 59.378 45.455 0.00 0.00 0.00 3.85
302 303 5.404066 CCATAAACCAAAAGCAAAACGGTAG 59.596 40.000 0.00 0.00 0.00 3.18
316 317 3.654273 TGTCCAAAACCCCATAAACCAA 58.346 40.909 0.00 0.00 0.00 3.67
337 338 0.034477 GTCCATGGACCGGTTTGGAT 60.034 55.000 31.37 9.63 40.22 3.41
351 352 2.158856 ACATCATGCATCAGACGTCCAT 60.159 45.455 13.01 5.13 0.00 3.41
359 360 1.886542 CCATCCCACATCATGCATCAG 59.113 52.381 0.00 0.00 0.00 2.90
390 391 4.142902 ACGTTTAATTTGATCAGCGTCCTG 60.143 41.667 0.00 0.00 40.54 3.86
391 392 4.000988 ACGTTTAATTTGATCAGCGTCCT 58.999 39.130 0.00 0.00 0.00 3.85
415 416 0.031010 AGAGAGGAGGGCCCGTTATT 60.031 55.000 18.44 3.02 40.87 1.40
424 425 3.820557 TGTTGTTTCAAAGAGAGGAGGG 58.179 45.455 0.00 0.00 0.00 4.30
440 441 4.970662 ATTTCTATCAAGCGCATGTTGT 57.029 36.364 11.47 1.56 0.00 3.32
446 447 9.056005 ACAGAATTATTATTTCTATCAAGCGCA 57.944 29.630 11.47 0.00 32.27 6.09
526 527 7.093245 GGGTGTTATTTTCTATTTTGCCCCTAA 60.093 37.037 0.00 0.00 0.00 2.69
536 562 7.627726 GCAGCGTTTAGGGTGTTATTTTCTATT 60.628 37.037 3.94 0.00 37.71 1.73
549 575 0.107831 TGTTCTGCAGCGTTTAGGGT 59.892 50.000 9.47 0.00 0.00 4.34
550 576 0.798776 CTGTTCTGCAGCGTTTAGGG 59.201 55.000 9.47 0.00 38.52 3.53
551 577 1.795768 TCTGTTCTGCAGCGTTTAGG 58.204 50.000 9.47 0.00 44.66 2.69
552 578 3.425359 CCATTCTGTTCTGCAGCGTTTAG 60.425 47.826 9.47 3.03 44.66 1.85
553 579 2.483877 CCATTCTGTTCTGCAGCGTTTA 59.516 45.455 9.47 0.00 44.66 2.01
554 580 1.267806 CCATTCTGTTCTGCAGCGTTT 59.732 47.619 9.47 0.00 44.66 3.60
555 581 0.877071 CCATTCTGTTCTGCAGCGTT 59.123 50.000 9.47 0.00 44.66 4.84
556 582 0.957395 CCCATTCTGTTCTGCAGCGT 60.957 55.000 9.47 0.00 44.66 5.07
557 583 1.651240 CCCCATTCTGTTCTGCAGCG 61.651 60.000 9.47 0.00 44.66 5.18
567 593 2.124151 CGGCCTTCCCCCATTCTG 60.124 66.667 0.00 0.00 0.00 3.02
568 594 1.926426 CTTCGGCCTTCCCCCATTCT 61.926 60.000 0.00 0.00 0.00 2.40
569 595 1.453928 CTTCGGCCTTCCCCCATTC 60.454 63.158 0.00 0.00 0.00 2.67
570 596 1.926426 CTCTTCGGCCTTCCCCCATT 61.926 60.000 0.00 0.00 0.00 3.16
571 597 2.286121 TCTTCGGCCTTCCCCCAT 60.286 61.111 0.00 0.00 0.00 4.00
572 598 3.009115 CTCTTCGGCCTTCCCCCA 61.009 66.667 0.00 0.00 0.00 4.96
573 599 3.798511 CCTCTTCGGCCTTCCCCC 61.799 72.222 0.00 0.00 0.00 5.40
581 607 2.981859 TTTGGATACTCCTCTTCGGC 57.018 50.000 0.00 0.00 37.46 5.54
595 621 0.392327 TGCGCCAGATTCGATTTGGA 60.392 50.000 4.18 0.00 33.76 3.53
597 623 1.658373 CGATGCGCCAGATTCGATTTG 60.658 52.381 4.18 0.00 33.59 2.32
622 652 1.307430 AGGAAGAAGGGGAGGCTCC 60.307 63.158 25.80 25.80 35.23 4.70
623 653 1.681486 CGAGGAAGAAGGGGAGGCTC 61.681 65.000 5.78 5.78 0.00 4.70
624 654 1.687493 CGAGGAAGAAGGGGAGGCT 60.687 63.158 0.00 0.00 0.00 4.58
625 655 2.904131 CGAGGAAGAAGGGGAGGC 59.096 66.667 0.00 0.00 0.00 4.70
658 730 7.629866 GCATCATGAATTTCTCCTCATCAACAA 60.630 37.037 0.00 0.00 29.69 2.83
659 731 6.183360 GCATCATGAATTTCTCCTCATCAACA 60.183 38.462 0.00 0.00 29.69 3.33
660 732 6.039493 AGCATCATGAATTTCTCCTCATCAAC 59.961 38.462 0.00 0.00 29.69 3.18
661 733 6.039382 CAGCATCATGAATTTCTCCTCATCAA 59.961 38.462 0.00 0.00 29.69 2.57
662 734 5.531287 CAGCATCATGAATTTCTCCTCATCA 59.469 40.000 0.00 0.00 29.69 3.07
663 735 5.563085 GCAGCATCATGAATTTCTCCTCATC 60.563 44.000 0.00 0.00 29.69 2.92
677 749 4.493708 CGAAACAAGTAGAGCAGCATCATG 60.494 45.833 0.00 0.00 0.00 3.07
729 1107 3.673338 TGCAAAATCAGTAGAGACGAACG 59.327 43.478 0.00 0.00 0.00 3.95
733 1111 3.589988 ACCTGCAAAATCAGTAGAGACG 58.410 45.455 0.00 0.00 32.32 4.18
736 1114 5.936956 AGAAGAACCTGCAAAATCAGTAGAG 59.063 40.000 0.00 0.00 32.32 2.43
760 1138 4.523558 TCATTTGGCTGTGAATGTGATGAA 59.476 37.500 0.00 0.00 35.35 2.57
762 1140 4.421058 CTCATTTGGCTGTGAATGTGATG 58.579 43.478 0.00 0.00 35.35 3.07
763 1141 3.119245 GCTCATTTGGCTGTGAATGTGAT 60.119 43.478 0.00 0.00 35.35 3.06
764 1142 2.229543 GCTCATTTGGCTGTGAATGTGA 59.770 45.455 0.00 0.00 35.35 3.58
765 1143 2.602878 GCTCATTTGGCTGTGAATGTG 58.397 47.619 0.00 0.00 35.35 3.21
766 1144 1.547372 GGCTCATTTGGCTGTGAATGT 59.453 47.619 0.00 0.00 35.35 2.71
767 1145 1.468565 CGGCTCATTTGGCTGTGAATG 60.469 52.381 0.00 0.00 35.18 2.67
768 1146 0.813184 CGGCTCATTTGGCTGTGAAT 59.187 50.000 0.00 0.00 0.00 2.57
769 1147 0.537143 ACGGCTCATTTGGCTGTGAA 60.537 50.000 0.00 0.00 46.03 3.18
787 1171 0.028770 CTCTCTCCGCATCTGTCGAC 59.971 60.000 9.11 9.11 0.00 4.20
793 1177 1.076412 TCTGCCTCTCTCCGCATCT 60.076 57.895 0.00 0.00 33.78 2.90
794 1178 1.106351 TCTCTGCCTCTCTCCGCATC 61.106 60.000 0.00 0.00 33.78 3.91
807 1202 0.957888 GCCACCAAACCTCTCTCTGC 60.958 60.000 0.00 0.00 0.00 4.26
822 1217 7.108194 TGATCTGATTGATTCCATATAGCCAC 58.892 38.462 0.00 0.00 35.14 5.01
841 1236 6.603237 TGTCATACGCCTAAATTTGATCTG 57.397 37.500 0.00 0.00 0.00 2.90
846 1241 5.008019 AGCAGATGTCATACGCCTAAATTTG 59.992 40.000 0.00 0.00 0.00 2.32
851 1247 2.693074 TCAGCAGATGTCATACGCCTAA 59.307 45.455 2.98 0.00 0.00 2.69
856 1252 3.181492 ACTCAGTCAGCAGATGTCATACG 60.181 47.826 0.00 0.00 0.00 3.06
859 1255 3.597255 CAACTCAGTCAGCAGATGTCAT 58.403 45.455 0.00 0.00 0.00 3.06
873 1269 2.564771 TCTTTGTGCAGTCCAACTCAG 58.435 47.619 0.00 0.00 0.00 3.35
942 1362 3.513515 AGAGGTGACCAAATCTCACTCTC 59.486 47.826 3.63 0.00 38.50 3.20
943 1363 3.513515 GAGAGGTGACCAAATCTCACTCT 59.486 47.826 12.86 0.00 38.50 3.24
961 1381 2.562635 CCAGATGATGGTTGCTGAGAG 58.437 52.381 0.00 0.00 44.91 3.20
978 1415 7.040409 GCCATGGTAGGTTATCTATTTTTCCAG 60.040 40.741 14.67 0.00 0.00 3.86
989 1426 1.002087 CCTCCGCCATGGTAGGTTATC 59.998 57.143 22.26 0.68 39.52 1.75
991 1428 1.692173 GCCTCCGCCATGGTAGGTTA 61.692 60.000 23.00 9.54 37.37 2.85
1066 1505 2.564721 GCAGTGCCCCACCAAAGAC 61.565 63.158 2.85 0.00 34.49 3.01
1149 1588 1.524002 GTAGGCCTGCATGCTCTCA 59.476 57.895 17.99 0.00 0.00 3.27
1194 1633 0.840617 TGGCTGTGGTCTTGTTGGTA 59.159 50.000 0.00 0.00 0.00 3.25
1198 1637 2.508526 GAAGATGGCTGTGGTCTTGTT 58.491 47.619 0.00 0.00 32.67 2.83
1290 1729 1.298157 CGAATCCTCCGTGCTTGCAA 61.298 55.000 0.00 0.00 0.00 4.08
1305 1744 2.408271 TCTTCATCTTGGCAGCGAAT 57.592 45.000 0.00 0.00 0.00 3.34
1328 1767 3.698040 CCAGGTTTTGATATGCTTGAGCT 59.302 43.478 4.44 0.00 42.66 4.09
1434 1873 2.666526 GCAGATCCGCCGATTCCC 60.667 66.667 0.00 0.00 0.00 3.97
1485 1924 0.679002 CATCCCTGGTGAAGTGCAGG 60.679 60.000 0.00 0.00 34.74 4.85
1558 1997 2.813226 TAATCACCACCGCCACTGCC 62.813 60.000 0.00 0.00 0.00 4.85
1559 1998 0.748005 ATAATCACCACCGCCACTGC 60.748 55.000 0.00 0.00 0.00 4.40
1560 1999 1.134401 AGATAATCACCACCGCCACTG 60.134 52.381 0.00 0.00 0.00 3.66
1561 2000 1.134401 CAGATAATCACCACCGCCACT 60.134 52.381 0.00 0.00 0.00 4.00
1562 2001 1.299541 CAGATAATCACCACCGCCAC 58.700 55.000 0.00 0.00 0.00 5.01
1563 2002 0.180171 CCAGATAATCACCACCGCCA 59.820 55.000 0.00 0.00 0.00 5.69
1576 2027 1.134580 GCTGTTGCTCTGCTCCAGATA 60.135 52.381 11.19 0.00 39.92 1.98
1665 2116 2.993220 GGCGTCAAAATCCAATTTCACC 59.007 45.455 0.00 0.00 0.00 4.02
1688 2139 1.070105 GACACTGTTACCCACGCCA 59.930 57.895 0.00 0.00 0.00 5.69
1701 2152 5.004448 TCGAGATTGTAACTCTCTGACACT 58.996 41.667 0.00 0.00 37.57 3.55
1717 2168 4.998671 TCTTCAGCAGATCTTCGAGATT 57.001 40.909 0.00 0.00 34.53 2.40
1766 2217 6.921857 CCTCATCTCAACATTGGCAATATTTC 59.078 38.462 13.23 0.00 0.00 2.17
1767 2218 6.684613 GCCTCATCTCAACATTGGCAATATTT 60.685 38.462 13.23 6.42 38.79 1.40
1768 2219 5.221382 GCCTCATCTCAACATTGGCAATATT 60.221 40.000 13.23 4.91 38.79 1.28
1791 2242 1.300542 GATGGACTCTGCTAGGCGC 60.301 63.158 0.00 0.00 31.76 6.53
1792 2243 0.461548 TTGATGGACTCTGCTAGGCG 59.538 55.000 0.00 0.00 31.76 5.52
1810 2261 9.797556 GTACTTTTTACCTTGAAGATTGTTGTT 57.202 29.630 0.00 0.00 0.00 2.83
1818 2269 7.996644 ACCAAGATGTACTTTTTACCTTGAAGA 59.003 33.333 0.00 0.00 36.61 2.87
1892 2343 4.097589 CGGTACAGTTAGAAGTAGGGAAGG 59.902 50.000 0.00 0.00 0.00 3.46
1899 2350 1.745087 CGGCCGGTACAGTTAGAAGTA 59.255 52.381 20.10 0.00 0.00 2.24
1923 2374 8.188799 ACTTCATGCTTTCTTGATGTGATAATG 58.811 33.333 0.00 0.00 35.16 1.90
1924 2375 8.188799 CACTTCATGCTTTCTTGATGTGATAAT 58.811 33.333 15.60 0.00 45.26 1.28
1969 2420 3.559171 GGTTCCAAGTGGATTGCAGACTA 60.559 47.826 0.00 0.00 44.98 2.59
1980 2437 2.133742 CTTGCAGCGGTTCCAAGTGG 62.134 60.000 13.74 0.00 33.17 4.00
2087 2544 6.507023 CCTTGACACTTTGCTATGAACTTTT 58.493 36.000 0.00 0.00 0.00 2.27
2125 2582 3.190160 GCGGCCAATGCATGCAAC 61.190 61.111 26.68 14.18 39.42 4.17
2151 2608 0.248866 CGGAAGTTGGTGGTTTGCAC 60.249 55.000 0.00 0.00 0.00 4.57
2160 2617 0.609131 CCCATTGAGCGGAAGTTGGT 60.609 55.000 0.00 0.00 0.00 3.67
2173 2630 2.505407 TCCTGTACACATCCTCCCATTG 59.495 50.000 0.00 0.00 0.00 2.82
2194 2651 2.036992 TCGCCAACTGCAAATCCAAATT 59.963 40.909 0.00 0.00 41.33 1.82
2195 2652 1.617850 TCGCCAACTGCAAATCCAAAT 59.382 42.857 0.00 0.00 41.33 2.32
2221 2678 6.070136 AGGATCATATGAACATCTGGGATCAG 60.070 42.308 9.99 0.00 42.21 2.90
2229 2686 8.267620 TGACCTTTAGGATCATATGAACATCT 57.732 34.615 9.99 7.46 38.94 2.90
2257 2714 6.414732 TCAAATCATACGAAAGGTCTTCCAT 58.585 36.000 0.00 0.00 35.89 3.41
2325 2782 5.454755 CCTCACTGTCCTTTTCCTCTTTACA 60.455 44.000 0.00 0.00 0.00 2.41
2326 2783 4.998033 CCTCACTGTCCTTTTCCTCTTTAC 59.002 45.833 0.00 0.00 0.00 2.01
2384 2844 4.982241 TCCTCCAATGTTCTGTTCTCTT 57.018 40.909 0.00 0.00 0.00 2.85
2385 2845 4.349342 ACTTCCTCCAATGTTCTGTTCTCT 59.651 41.667 0.00 0.00 0.00 3.10
2386 2846 4.453819 CACTTCCTCCAATGTTCTGTTCTC 59.546 45.833 0.00 0.00 0.00 2.87
2415 2878 0.179000 CAAGCTCGGCCAAGTATCCT 59.821 55.000 2.24 0.00 0.00 3.24
2473 2936 2.798283 GACAATGTTTCAGTCGTCCGAA 59.202 45.455 0.00 0.00 0.00 4.30
2474 2937 2.400399 GACAATGTTTCAGTCGTCCGA 58.600 47.619 0.00 0.00 0.00 4.55
2577 3043 2.237143 CTCAACAGAGAATGCCCCAGTA 59.763 50.000 0.00 0.00 0.00 2.74
2632 3101 1.880027 AGACCGGCTCAATTGTTCAAC 59.120 47.619 0.00 0.00 0.00 3.18
2649 3118 1.510480 GGAGCTGTGTTGCACCAGAC 61.510 60.000 10.55 0.00 42.09 3.51
2678 3147 7.683437 ATATCGATACACCTCTCAAATACGA 57.317 36.000 7.41 0.00 0.00 3.43
2679 3148 8.021396 TCAATATCGATACACCTCTCAAATACG 58.979 37.037 7.41 0.00 0.00 3.06
2693 3162 6.148480 AGGCTTCAGCAAATCAATATCGATAC 59.852 38.462 7.41 0.00 44.36 2.24
2745 3214 4.441495 CGAGTACCTTGCAGATCCAACATA 60.441 45.833 0.00 0.00 0.00 2.29
2772 3241 1.064758 ACCTCATCGGGCAGCATTTTA 60.065 47.619 0.00 0.00 36.97 1.52
2827 3296 1.597445 GCTTTCGATCTCCGTACCTCG 60.597 57.143 0.00 0.00 39.75 4.63
2835 3304 0.813210 CAGGCAGGCTTTCGATCTCC 60.813 60.000 0.00 0.00 0.00 3.71
2925 3394 8.062065 TCAACTTCTGAGGTTTTACAACATTT 57.938 30.769 2.04 0.00 34.15 2.32


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

AutoCloner maintained by Alex Coulton.