Multiple sequence alignment - TraesCS3D01G490400

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 TraesCS3D01G490400 chr3D 100.000 3089 0 0 1 3089 584449339 584446251 0.000000e+00 5705
1 TraesCS3D01G490400 chr3D 77.184 767 125 33 1032 1754 584456828 584456068 4.800000e-108 401
2 TraesCS3D01G490400 chr3D 78.974 585 92 21 1103 1664 584130001 584130577 1.350000e-98 370
3 TraesCS3D01G490400 chrUn 93.605 2236 101 20 861 3089 45489206 45487006 0.000000e+00 3299
4 TraesCS3D01G490400 chrUn 96.284 619 19 1 1 615 45490120 45489502 0.000000e+00 1013
5 TraesCS3D01G490400 chrUn 80.880 523 93 5 1234 1754 45482937 45482420 3.710000e-109 405
6 TraesCS3D01G490400 chrUn 96.392 194 7 0 630 823 45489404 45489211 1.380000e-83 320
7 TraesCS3D01G490400 chr3B 86.910 1398 123 23 1022 2368 781483449 781482061 0.000000e+00 1513
8 TraesCS3D01G490400 chr3B 95.238 336 14 2 630 963 781483790 781483455 5.870000e-147 531
9 TraesCS3D01G490400 chr3B 79.059 659 116 19 1103 1754 781494671 781494028 1.700000e-117 433
10 TraesCS3D01G490400 chr3B 76.757 740 126 25 1032 1730 781356275 781357009 3.760000e-99 372
11 TraesCS3D01G490400 chr3B 89.825 285 24 3 1905 2187 781475452 781475171 8.140000e-96 361
12 TraesCS3D01G490400 chr3B 97.531 162 4 0 1 162 781484261 781484100 8.440000e-71 278


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 TraesCS3D01G490400 chr3D 584446251 584449339 3088 True 5705 5705 100.000000 1 3089 1 chr3D.!!$R1 3088
1 TraesCS3D01G490400 chr3D 584456068 584456828 760 True 401 401 77.184000 1032 1754 1 chr3D.!!$R2 722
2 TraesCS3D01G490400 chr3D 584130001 584130577 576 False 370 370 78.974000 1103 1664 1 chr3D.!!$F1 561
3 TraesCS3D01G490400 chrUn 45487006 45490120 3114 True 1544 3299 95.427000 1 3089 3 chrUn.!!$R2 3088
4 TraesCS3D01G490400 chrUn 45482420 45482937 517 True 405 405 80.880000 1234 1754 1 chrUn.!!$R1 520
5 TraesCS3D01G490400 chr3B 781482061 781484261 2200 True 774 1513 93.226333 1 2368 3 chr3B.!!$R3 2367
6 TraesCS3D01G490400 chr3B 781494028 781494671 643 True 433 433 79.059000 1103 1754 1 chr3B.!!$R2 651
7 TraesCS3D01G490400 chr3B 781356275 781357009 734 False 372 372 76.757000 1032 1730 1 chr3B.!!$F1 698

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
546 754 1.202770 ACTTCAGCCACCACTGGTAAC 60.203 52.381 0.0 0.0 40.17 2.50 F
1514 1865 0.530744 CTCCCTCGACGTTGGATTCA 59.469 55.000 2.2 0.0 0.00 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1668 2019 0.035056 AGTGTACAATGCCTCAGCCC 60.035 55.0 0.0 0.0 38.69 5.19 R
2502 2868 0.249238 GAGGCGGTCTATGCTGTCAG 60.249 60.0 0.0 0.0 0.00 3.51 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
33 34 5.253330 TCCTTTACCTGCCAGAAATAAGTG 58.747 41.667 0.00 0.00 0.00 3.16
105 110 2.768527 GAGGTGGATGAATCTCCAGTGA 59.231 50.000 0.00 0.00 45.87 3.41
145 249 7.042797 ACATGAAAATTGTCAAACTGTAGCT 57.957 32.000 1.55 0.00 0.00 3.32
251 459 7.995289 TGACAAAGACAACATTATTGTGAGTT 58.005 30.769 0.00 0.00 35.83 3.01
283 491 6.038985 CACACATCGATGTTAGTCAAGAGAT 58.961 40.000 28.04 0.00 39.39 2.75
345 553 4.051922 CGCCCATTACACTATTCTCAGTC 58.948 47.826 0.00 0.00 0.00 3.51
357 565 2.814280 TCTCAGTCGGTTTCTTGGTC 57.186 50.000 0.00 0.00 0.00 4.02
389 597 4.989168 GCCTTCTCTTTGTTCTCGTCTTTA 59.011 41.667 0.00 0.00 0.00 1.85
391 599 6.147985 GCCTTCTCTTTGTTCTCGTCTTTATT 59.852 38.462 0.00 0.00 0.00 1.40
392 600 7.308049 GCCTTCTCTTTGTTCTCGTCTTTATTT 60.308 37.037 0.00 0.00 0.00 1.40
481 689 8.186163 ACAATGCAAAATGTGATGTATACTCTG 58.814 33.333 4.17 0.00 0.00 3.35
499 707 8.970859 ATACTCTGCAGTAAAAGAGCATTTAT 57.029 30.769 14.67 0.00 43.13 1.40
546 754 1.202770 ACTTCAGCCACCACTGGTAAC 60.203 52.381 0.00 0.00 40.17 2.50
599 807 5.503031 CGATTGCCACAATCATAAGTCACTC 60.503 44.000 17.73 0.00 0.00 3.51
615 823 3.056322 GTCACTCCACTTACGGGTACATT 60.056 47.826 0.00 0.00 0.00 2.71
617 825 2.277084 CTCCACTTACGGGTACATTGC 58.723 52.381 0.00 0.00 0.00 3.56
619 827 1.339247 CCACTTACGGGTACATTGCCA 60.339 52.381 0.00 0.00 0.00 4.92
620 828 1.735571 CACTTACGGGTACATTGCCAC 59.264 52.381 0.00 0.00 0.00 5.01
621 829 1.348366 ACTTACGGGTACATTGCCACA 59.652 47.619 0.00 0.00 0.00 4.17
622 830 2.224572 ACTTACGGGTACATTGCCACAA 60.225 45.455 0.00 0.00 0.00 3.33
624 832 1.459450 ACGGGTACATTGCCACAATC 58.541 50.000 0.00 0.00 0.00 2.67
625 833 1.271652 ACGGGTACATTGCCACAATCA 60.272 47.619 0.00 0.00 0.00 2.57
626 834 2.023673 CGGGTACATTGCCACAATCAT 58.976 47.619 0.00 0.00 0.00 2.45
627 835 3.210227 CGGGTACATTGCCACAATCATA 58.790 45.455 0.00 0.00 0.00 2.15
628 836 3.629855 CGGGTACATTGCCACAATCATAA 59.370 43.478 0.00 0.00 0.00 1.90
753 1045 5.776517 ACATGCATGTTATCGTTCGTACGG 61.777 45.833 26.61 0.00 42.33 4.02
853 1145 3.434299 CGAAGCCACATTAAAACCGTACT 59.566 43.478 0.00 0.00 0.00 2.73
854 1146 4.435121 CGAAGCCACATTAAAACCGTACTC 60.435 45.833 0.00 0.00 0.00 2.59
855 1147 3.340928 AGCCACATTAAAACCGTACTCC 58.659 45.455 0.00 0.00 0.00 3.85
856 1148 3.075884 GCCACATTAAAACCGTACTCCA 58.924 45.455 0.00 0.00 0.00 3.86
872 1166 3.671716 ACTCCACGTCCAACTAATTTCC 58.328 45.455 0.00 0.00 0.00 3.13
886 1180 2.951229 ATTTCCCCATACGTCCATCC 57.049 50.000 0.00 0.00 0.00 3.51
1396 1747 4.717313 GTCCCGGGGCTCAACACC 62.717 72.222 20.78 0.00 0.00 4.16
1418 1769 2.432456 GCGTGTCCATGTCTCGCA 60.432 61.111 20.95 0.51 43.81 5.10
1420 1771 1.361668 GCGTGTCCATGTCTCGCATT 61.362 55.000 20.95 0.00 43.81 3.56
1432 1783 0.735978 CTCGCATTGACTACGCACCA 60.736 55.000 0.00 0.00 0.00 4.17
1510 1861 3.379445 GGCTCCCTCGACGTTGGA 61.379 66.667 2.20 8.98 0.00 3.53
1514 1865 0.530744 CTCCCTCGACGTTGGATTCA 59.469 55.000 2.20 0.00 0.00 2.57
1609 1960 3.945285 TCCACTTTCAGAGGAACAACAAC 59.055 43.478 0.00 0.00 31.92 3.32
1668 2019 4.680237 TCCGGGCACGCAGAAGTG 62.680 66.667 0.58 0.00 44.47 3.16
1717 2068 2.260434 GTTCCAGCCGACGTGCTA 59.740 61.111 9.94 0.00 40.32 3.49
1736 2087 4.147449 CCAGGGCGCTCGATGTCA 62.147 66.667 7.64 0.00 0.00 3.58
1765 2116 1.064621 GGTCGAGCCGTGCGTAATA 59.935 57.895 2.39 0.00 0.00 0.98
1769 2120 3.240069 GTCGAGCCGTGCGTAATATAAT 58.760 45.455 0.00 0.00 0.00 1.28
1770 2121 3.300066 GTCGAGCCGTGCGTAATATAATC 59.700 47.826 0.00 0.00 0.00 1.75
1773 2124 4.432503 CGAGCCGTGCGTAATATAATCAAC 60.433 45.833 0.00 0.00 0.00 3.18
1776 2127 6.395629 AGCCGTGCGTAATATAATCAACTAT 58.604 36.000 0.00 0.00 0.00 2.12
1778 2129 8.030692 AGCCGTGCGTAATATAATCAACTATTA 58.969 33.333 0.00 0.00 34.56 0.98
1779 2130 8.649841 GCCGTGCGTAATATAATCAACTATTAA 58.350 33.333 0.00 0.00 33.76 1.40
1803 2154 1.276989 CCATGCCCAGCACTTGAATTT 59.723 47.619 0.00 0.00 43.04 1.82
1804 2155 2.496871 CCATGCCCAGCACTTGAATTTA 59.503 45.455 0.00 0.00 43.04 1.40
1809 2160 3.334691 CCCAGCACTTGAATTTACTCGA 58.665 45.455 0.00 0.00 0.00 4.04
1824 2176 9.148104 GAATTTACTCGACACCTTTTGTATACT 57.852 33.333 4.17 0.00 39.17 2.12
1825 2177 9.498176 AATTTACTCGACACCTTTTGTATACTT 57.502 29.630 4.17 0.00 39.17 2.24
1826 2178 8.891671 TTTACTCGACACCTTTTGTATACTTT 57.108 30.769 4.17 0.00 39.17 2.66
1827 2179 9.979578 TTTACTCGACACCTTTTGTATACTTTA 57.020 29.630 4.17 0.00 39.17 1.85
1883 2238 5.109210 GCTGTTTACTGTTGCTTTTTCCTT 58.891 37.500 0.00 0.00 0.00 3.36
1889 2244 3.006859 ACTGTTGCTTTTTCCTTATGGCC 59.993 43.478 0.00 0.00 0.00 5.36
1987 2343 5.845985 TGAAATGATTGTGTCGAGAGTTC 57.154 39.130 0.00 0.00 0.00 3.01
2038 2396 6.294473 AGGTAGCATGGAAAATCATAGAGTG 58.706 40.000 0.00 0.00 0.00 3.51
2118 2477 0.666913 AACAGACGTACACTCACGCT 59.333 50.000 0.00 0.00 45.77 5.07
2158 2517 8.456940 CACACATCCTATCCCTATATCCCTATA 58.543 40.741 0.00 0.00 0.00 1.31
2198 2557 8.907222 ACTAAACCGGTAAATCTTTAGTTCAA 57.093 30.769 17.49 0.00 36.47 2.69
2216 2577 9.621629 TTAGTTCAATGAGTTGGTAAGAGAAAA 57.378 29.630 0.00 0.00 35.99 2.29
2301 2662 6.356186 TGGACTAAACTTTAGAGAACCCTC 57.644 41.667 14.37 1.27 39.72 4.30
2319 2680 8.817876 AGAACCCTCTAATAAATACAGGCTATC 58.182 37.037 0.00 0.00 0.00 2.08
2411 2777 1.270252 TGCACAGCTCATTCAACTCGA 60.270 47.619 0.00 0.00 0.00 4.04
2430 2796 5.419155 ACTCGAGTGAATAGGTGATTTGAGA 59.581 40.000 19.30 0.00 0.00 3.27
2502 2868 6.640518 TGACCCACACATTCTCTTTCTATAC 58.359 40.000 0.00 0.00 0.00 1.47
2510 2876 7.038048 CACATTCTCTTTCTATACTGACAGCA 58.962 38.462 1.25 0.00 0.00 4.41
2526 2892 0.912486 AGCATAGACCGCCTCCTTTT 59.088 50.000 0.00 0.00 0.00 2.27
2558 2924 2.108250 CTGTTTTCCCCTTCTCCCTTCA 59.892 50.000 0.00 0.00 0.00 3.02
2564 2930 0.914644 CCCTTCTCCCTTCATGCTCA 59.085 55.000 0.00 0.00 0.00 4.26
2576 2942 3.717400 TCATGCTCATAGAACGACTCC 57.283 47.619 0.00 0.00 0.00 3.85
2596 2962 1.359475 CTACGGTTCTAGCCTCCGC 59.641 63.158 15.98 0.00 46.92 5.54
2640 3006 2.583520 CTCTGCAGGCTCACCCTC 59.416 66.667 15.13 0.00 44.09 4.30
2642 3008 3.324930 CTGCAGGCTCACCCTCCA 61.325 66.667 5.57 0.00 44.09 3.86
2649 3015 1.003233 GCTCACCCTCCACCTTGTC 60.003 63.158 0.00 0.00 0.00 3.18
2707 3073 9.518906 AAAATTGAGAAAAATTGAATTTGGCAC 57.481 25.926 3.62 0.00 31.77 5.01
2708 3074 5.903764 TGAGAAAAATTGAATTTGGCACG 57.096 34.783 3.62 0.00 31.77 5.34
2709 3075 4.210955 TGAGAAAAATTGAATTTGGCACGC 59.789 37.500 3.62 0.08 31.77 5.34
2710 3076 3.498018 AGAAAAATTGAATTTGGCACGCC 59.502 39.130 3.62 0.00 31.77 5.68
2711 3077 1.427435 AAATTGAATTTGGCACGCCG 58.573 45.000 1.78 0.00 39.42 6.46
2742 3108 3.360533 ACGCGTCTGAGTTAACATATCG 58.639 45.455 5.58 7.05 0.00 2.92
2873 3239 1.629043 TAGAGACTCCACGCCTTTGT 58.371 50.000 0.00 0.00 0.00 2.83
2874 3240 0.759346 AGAGACTCCACGCCTTTGTT 59.241 50.000 0.00 0.00 0.00 2.83
2875 3241 0.868406 GAGACTCCACGCCTTTGTTG 59.132 55.000 0.00 0.00 0.00 3.33
2876 3242 1.166531 AGACTCCACGCCTTTGTTGC 61.167 55.000 0.00 0.00 0.00 4.17
2965 3331 2.664424 GCGCGCAATTGTTCTCAGTTTA 60.664 45.455 29.10 0.00 0.00 2.01
2966 3332 3.550561 CGCGCAATTGTTCTCAGTTTAA 58.449 40.909 8.75 0.00 0.00 1.52
2967 3333 3.971871 CGCGCAATTGTTCTCAGTTTAAA 59.028 39.130 8.75 0.00 0.00 1.52
2968 3334 4.439449 CGCGCAATTGTTCTCAGTTTAAAA 59.561 37.500 8.75 0.00 0.00 1.52
2969 3335 5.052040 CGCGCAATTGTTCTCAGTTTAAAAA 60.052 36.000 8.75 0.00 0.00 1.94
3027 3397 9.612066 AAATAAAGCTTTTGGATTGAACTTCAA 57.388 25.926 18.47 6.67 41.09 2.69
3083 3453 7.415541 GCATCAAGTACATAGATTTGCTCCAAA 60.416 37.037 0.00 0.00 37.75 3.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
105 110 6.636454 TTTCATGTACCCTGAATCCTAGTT 57.364 37.500 8.33 0.00 32.94 2.24
145 249 8.650143 TTATAGTGATGTGTGCAGAGGATATA 57.350 34.615 0.00 0.00 0.00 0.86
261 469 7.196331 TGTATCTCTTGACTAACATCGATGTG 58.804 38.462 30.57 21.02 41.61 3.21
345 553 1.508632 ACGACATGACCAAGAAACCG 58.491 50.000 0.00 0.00 0.00 4.44
357 565 2.549754 ACAAAGAGAAGGCAACGACATG 59.450 45.455 0.00 0.00 46.39 3.21
389 597 7.517320 TGATATAGGCATGTGTCCACTTAAAT 58.483 34.615 0.00 0.00 0.00 1.40
391 599 6.493189 TGATATAGGCATGTGTCCACTTAA 57.507 37.500 0.00 0.00 0.00 1.85
392 600 6.126911 TGTTGATATAGGCATGTGTCCACTTA 60.127 38.462 0.00 0.00 0.00 2.24
439 647 4.582240 TGCATTGTAACCATGTTCTGTTGA 59.418 37.500 0.00 0.00 0.00 3.18
499 707 7.936496 TTGTTGCCTATCAGTCATAATTTGA 57.064 32.000 0.00 0.00 0.00 2.69
546 754 3.311106 GCACACATCATCAGTGGTTTTG 58.689 45.455 0.00 0.00 41.21 2.44
599 807 1.339247 TGGCAATGTACCCGTAAGTGG 60.339 52.381 0.00 0.00 0.00 4.00
615 823 6.186957 AGAATGGTTACTTATGATTGTGGCA 58.813 36.000 0.00 0.00 0.00 4.92
617 825 7.339212 TGGAAGAATGGTTACTTATGATTGTGG 59.661 37.037 0.00 0.00 0.00 4.17
619 827 7.888021 TGTGGAAGAATGGTTACTTATGATTGT 59.112 33.333 0.00 0.00 0.00 2.71
620 828 8.279970 TGTGGAAGAATGGTTACTTATGATTG 57.720 34.615 0.00 0.00 0.00 2.67
621 829 8.877864 TTGTGGAAGAATGGTTACTTATGATT 57.122 30.769 0.00 0.00 0.00 2.57
622 830 8.739972 GTTTGTGGAAGAATGGTTACTTATGAT 58.260 33.333 0.00 0.00 0.00 2.45
624 832 7.312899 GGTTTGTGGAAGAATGGTTACTTATG 58.687 38.462 0.00 0.00 0.00 1.90
625 833 6.436218 GGGTTTGTGGAAGAATGGTTACTTAT 59.564 38.462 0.00 0.00 0.00 1.73
626 834 5.771165 GGGTTTGTGGAAGAATGGTTACTTA 59.229 40.000 0.00 0.00 0.00 2.24
627 835 4.587262 GGGTTTGTGGAAGAATGGTTACTT 59.413 41.667 0.00 0.00 0.00 2.24
628 836 4.141018 AGGGTTTGTGGAAGAATGGTTACT 60.141 41.667 0.00 0.00 0.00 2.24
753 1045 3.789756 CCATCGTGTCAGTGTAATACGAC 59.210 47.826 6.05 0.00 45.03 4.34
756 1048 4.201685 GCAACCATCGTGTCAGTGTAATAC 60.202 45.833 0.00 0.00 0.00 1.89
825 1117 4.097892 GGTTTTAATGTGGCTTCGATCCAT 59.902 41.667 9.72 0.00 35.81 3.41
853 1145 2.290450 GGGGAAATTAGTTGGACGTGGA 60.290 50.000 0.00 0.00 0.00 4.02
854 1146 2.089201 GGGGAAATTAGTTGGACGTGG 58.911 52.381 0.00 0.00 0.00 4.94
855 1147 2.785562 TGGGGAAATTAGTTGGACGTG 58.214 47.619 0.00 0.00 0.00 4.49
856 1148 3.732048 ATGGGGAAATTAGTTGGACGT 57.268 42.857 0.00 0.00 0.00 4.34
859 1153 4.384427 GGACGTATGGGGAAATTAGTTGGA 60.384 45.833 0.00 0.00 0.00 3.53
1418 1769 0.107214 CCCCATGGTGCGTAGTCAAT 60.107 55.000 11.73 0.00 0.00 2.57
1420 1771 2.986290 CCCCATGGTGCGTAGTCA 59.014 61.111 11.73 0.00 0.00 3.41
1507 1858 0.035534 CGGTGGTGGTGATGAATCCA 60.036 55.000 0.00 0.00 0.00 3.41
1510 1861 1.378514 GCCGGTGGTGGTGATGAAT 60.379 57.895 1.90 0.00 0.00 2.57
1514 1865 2.034066 CTTGCCGGTGGTGGTGAT 59.966 61.111 1.90 0.00 0.00 3.06
1668 2019 0.035056 AGTGTACAATGCCTCAGCCC 60.035 55.000 0.00 0.00 38.69 5.19
1765 2116 7.949565 TGGGCATGGACATTAATAGTTGATTAT 59.050 33.333 0.00 0.00 29.93 1.28
1769 2120 5.122707 TGGGCATGGACATTAATAGTTGA 57.877 39.130 0.00 0.00 0.00 3.18
1770 2121 4.261741 GCTGGGCATGGACATTAATAGTTG 60.262 45.833 0.00 0.00 0.00 3.16
1773 2124 3.254166 GTGCTGGGCATGGACATTAATAG 59.746 47.826 0.00 0.00 41.91 1.73
1776 2127 1.005805 AGTGCTGGGCATGGACATTAA 59.994 47.619 0.00 0.00 41.91 1.40
1778 2129 0.251922 AAGTGCTGGGCATGGACATT 60.252 50.000 0.00 0.00 41.91 2.71
1779 2130 0.968901 CAAGTGCTGGGCATGGACAT 60.969 55.000 0.00 0.00 41.91 3.06
1780 2131 1.604308 CAAGTGCTGGGCATGGACA 60.604 57.895 0.00 0.00 41.91 4.02
1784 2135 2.754946 AAATTCAAGTGCTGGGCATG 57.245 45.000 0.00 0.00 41.91 4.06
1787 2138 2.159517 CGAGTAAATTCAAGTGCTGGGC 60.160 50.000 0.00 0.00 0.00 5.36
1788 2139 3.125316 GTCGAGTAAATTCAAGTGCTGGG 59.875 47.826 0.00 0.00 0.00 4.45
1789 2140 3.745975 TGTCGAGTAAATTCAAGTGCTGG 59.254 43.478 0.00 0.00 0.00 4.85
1804 2155 9.498176 AAATAAAGTATACAAAAGGTGTCGAGT 57.502 29.630 5.50 0.00 41.98 4.18
1883 2238 5.667172 ACATATATATCACCAGCAGGCCATA 59.333 40.000 5.01 0.00 39.06 2.74
1889 2244 7.172703 CCATGCATACATATATATCACCAGCAG 59.827 40.741 0.00 0.00 33.67 4.24
1987 2343 8.789881 TGTTTCATAAAGTTACATTTTGGTCG 57.210 30.769 0.00 0.00 0.00 4.79
2118 2477 2.091852 TGTGTGAGCATGCGTTCATA 57.908 45.000 13.01 7.17 34.63 2.15
2158 2517 4.390264 GGTTTAGTCTCTTGAAGGTGCTT 58.610 43.478 0.00 0.00 0.00 3.91
2216 2577 7.639113 TCCAGTTCAAACACATTTAGAGTTT 57.361 32.000 0.00 0.00 40.89 2.66
2301 2662 9.776158 CACGAGTAGATAGCCTGTATTTATTAG 57.224 37.037 0.00 0.00 0.00 1.73
2319 2680 3.126831 GCCATTGGATCTTCACGAGTAG 58.873 50.000 6.95 0.00 0.00 2.57
2398 2764 5.518128 CACCTATTCACTCGAGTTGAATGAG 59.482 44.000 31.51 26.69 33.78 2.90
2411 2777 5.046014 ACTGCTCTCAAATCACCTATTCACT 60.046 40.000 0.00 0.00 0.00 3.41
2430 2796 5.690464 ACATAAGATCTTCCAAGACTGCT 57.310 39.130 12.24 0.00 37.98 4.24
2478 2844 5.762179 ATAGAAAGAGAATGTGTGGGTCA 57.238 39.130 0.00 0.00 0.00 4.02
2502 2868 0.249238 GAGGCGGTCTATGCTGTCAG 60.249 60.000 0.00 0.00 0.00 3.51
2510 2876 1.209747 GGACAAAAGGAGGCGGTCTAT 59.790 52.381 0.00 0.00 0.00 1.98
2526 2892 1.523154 GGAAAACAGGCATGCGGACA 61.523 55.000 12.44 0.00 0.00 4.02
2558 2924 3.027412 AGTGGAGTCGTTCTATGAGCAT 58.973 45.455 0.00 0.00 0.00 3.79
2564 2930 2.996631 ACCGTAGTGGAGTCGTTCTAT 58.003 47.619 0.00 0.00 42.00 1.98
2576 2942 0.381089 CGGAGGCTAGAACCGTAGTG 59.619 60.000 12.33 0.00 41.47 2.74
2608 2974 1.985116 AGAGGAAGAGGACGTGGGC 60.985 63.158 0.00 0.00 0.00 5.36
2615 2981 0.975040 GAGCCTGCAGAGGAAGAGGA 60.975 60.000 17.39 0.00 42.93 3.71
2649 3015 5.467735 TCAGTCAACTTCAAGTCATGACATG 59.532 40.000 27.02 24.45 38.04 3.21
2695 3061 1.454201 TATCGGCGTGCCAAATTCAA 58.546 45.000 12.06 0.00 35.37 2.69
2696 3062 1.454201 TTATCGGCGTGCCAAATTCA 58.546 45.000 12.06 0.00 35.37 2.57
2697 3063 2.032799 TCATTATCGGCGTGCCAAATTC 59.967 45.455 12.06 0.00 35.37 2.17
2698 3064 2.020720 TCATTATCGGCGTGCCAAATT 58.979 42.857 12.06 0.00 35.37 1.82
2699 3065 1.674359 TCATTATCGGCGTGCCAAAT 58.326 45.000 12.06 6.36 35.37 2.32
2700 3066 1.454201 TTCATTATCGGCGTGCCAAA 58.546 45.000 12.06 2.33 35.37 3.28
2701 3067 1.674359 ATTCATTATCGGCGTGCCAA 58.326 45.000 12.06 0.00 35.37 4.52
2702 3068 2.139917 GTATTCATTATCGGCGTGCCA 58.860 47.619 12.06 0.00 35.37 4.92
2703 3069 1.126113 CGTATTCATTATCGGCGTGCC 59.874 52.381 6.85 0.00 0.00 5.01
2704 3070 1.461888 GCGTATTCATTATCGGCGTGC 60.462 52.381 6.85 0.00 0.00 5.34
2705 3071 1.201661 CGCGTATTCATTATCGGCGTG 60.202 52.381 6.85 0.00 34.94 5.34
2706 3072 1.057636 CGCGTATTCATTATCGGCGT 58.942 50.000 6.85 0.00 34.94 5.68
2707 3073 1.057285 GACGCGTATTCATTATCGGCG 59.943 52.381 13.97 0.00 41.26 6.46
2708 3074 2.090658 CAGACGCGTATTCATTATCGGC 59.909 50.000 13.97 0.00 0.00 5.54
2709 3075 3.561503 TCAGACGCGTATTCATTATCGG 58.438 45.455 13.97 0.00 0.00 4.18
2710 3076 4.219802 ACTCAGACGCGTATTCATTATCG 58.780 43.478 13.97 0.00 0.00 2.92
2711 3077 7.166970 TGTTAACTCAGACGCGTATTCATTATC 59.833 37.037 13.97 8.66 0.00 1.75
2873 3239 5.950758 TTCTTATAACAAGCTTTCCGCAA 57.049 34.783 0.00 0.00 42.61 4.85
2874 3240 5.950758 TTTCTTATAACAAGCTTTCCGCA 57.049 34.783 0.00 0.00 42.61 5.69
2875 3241 5.230097 GCATTTCTTATAACAAGCTTTCCGC 59.770 40.000 0.00 0.00 39.57 5.54
2876 3242 6.321717 TGCATTTCTTATAACAAGCTTTCCG 58.678 36.000 0.00 0.00 0.00 4.30
2877 3243 9.801873 TTATGCATTTCTTATAACAAGCTTTCC 57.198 29.630 3.54 0.00 0.00 3.13
3062 3432 7.448469 ACAAGTTTGGAGCAAATCTATGTACTT 59.552 33.333 0.00 0.00 35.74 2.24


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

AutoCloner maintained by Alex Coulton.