Multiple sequence alignment - TraesCS5A01G010400

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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 TraesCS5A01G010400 chr5A 100.000 2993 0 0 1 2993 6775222 6772230 0.000000e+00 5528.0
1 TraesCS5A01G010400 chr5A 91.135 925 82 0 1197 2121 14864455 14863531 0.000000e+00 1254.0
2 TraesCS5A01G010400 chr5A 94.751 724 32 4 2116 2835 14854808 14854087 0.000000e+00 1122.0
3 TraesCS5A01G010400 chr5A 91.360 544 45 2 658 1200 14895631 14895089 0.000000e+00 743.0
4 TraesCS5A01G010400 chr5D 93.457 2262 142 4 658 2915 8594083 8591824 0.000000e+00 3352.0
5 TraesCS5A01G010400 chr5D 100.000 45 0 0 2949 2993 305244196 305244152 1.910000e-12 84.2
6 TraesCS5A01G010400 chr5B 91.054 1006 75 6 658 1662 8937341 8936350 0.000000e+00 1345.0
7 TraesCS5A01G010400 chr5B 93.274 565 38 0 1212 1776 8943539 8942975 0.000000e+00 833.0
8 TraesCS5A01G010400 chr5B 90.554 307 29 0 1850 2156 8936387 8936081 9.990000e-110 407.0
9 TraesCS5A01G010400 chr3D 80.142 1828 292 39 664 2453 555531757 555533551 0.000000e+00 1299.0
10 TraesCS5A01G010400 chr3D 95.122 41 2 0 2304 2344 555536846 555536886 6.930000e-07 65.8
11 TraesCS5A01G010400 chr3D 80.220 91 13 3 2203 2288 597673193 597673283 2.490000e-06 63.9
12 TraesCS5A01G010400 chr3B 79.357 1836 298 44 664 2464 738716565 738718354 0.000000e+00 1216.0
13 TraesCS5A01G010400 chr3B 98.483 659 10 0 1 659 167060767 167060109 0.000000e+00 1162.0
14 TraesCS5A01G010400 chr3B 79.191 1038 186 14 994 2013 617439293 617438268 0.000000e+00 693.0
15 TraesCS5A01G010400 chr1A 97.879 660 13 1 1 659 593998734 593999393 0.000000e+00 1140.0
16 TraesCS5A01G010400 chr1A 96.741 675 6 2 1 659 82683665 82684339 0.000000e+00 1110.0
17 TraesCS5A01G010400 chr1A 100.000 45 0 0 2949 2993 8243601 8243645 1.910000e-12 84.2
18 TraesCS5A01G010400 chr4A 97.724 659 9 2 1 658 309246252 309246905 0.000000e+00 1129.0
19 TraesCS5A01G010400 chr7B 97.727 660 6 3 1 659 557441870 557441219 0.000000e+00 1127.0
20 TraesCS5A01G010400 chr7B 96.450 676 8 2 1 660 673689045 673689720 0.000000e+00 1101.0
21 TraesCS5A01G010400 chr2A 96.893 676 5 2 1 660 100651914 100651239 0.000000e+00 1118.0
22 TraesCS5A01G010400 chr4B 96.741 675 6 2 1 659 416490077 416490751 0.000000e+00 1110.0
23 TraesCS5A01G010400 chr4B 100.000 45 0 0 2949 2993 23713557 23713513 1.910000e-12 84.2
24 TraesCS5A01G010400 chr6B 96.593 675 7 2 1 659 560985953 560985279 0.000000e+00 1105.0
25 TraesCS5A01G010400 chr3A 79.485 1516 268 23 664 2157 692677282 692678776 0.000000e+00 1037.0
26 TraesCS5A01G010400 chr3A 83.209 268 40 4 2201 2464 692693834 692694100 1.070000e-59 241.0
27 TraesCS5A01G010400 chr3A 75.309 162 33 6 2304 2462 692697133 692697290 1.490000e-08 71.3
28 TraesCS5A01G010400 chr7A 96.364 55 2 0 605 659 712113181 712113235 1.140000e-14 91.6
29 TraesCS5A01G010400 chr7A 93.103 58 2 2 603 659 479575976 479575920 1.910000e-12 84.2
30 TraesCS5A01G010400 chrUn 100.000 45 0 0 2949 2993 403876338 403876382 1.910000e-12 84.2
31 TraesCS5A01G010400 chr6D 100.000 45 0 0 2949 2993 374127311 374127267 1.910000e-12 84.2
32 TraesCS5A01G010400 chr6D 100.000 45 0 0 2949 2993 430878405 430878449 1.910000e-12 84.2
33 TraesCS5A01G010400 chr4D 100.000 45 0 0 2949 2993 61158702 61158746 1.910000e-12 84.2
34 TraesCS5A01G010400 chr4D 100.000 45 0 0 2949 2993 237472045 237472089 1.910000e-12 84.2
35 TraesCS5A01G010400 chr1D 100.000 45 0 0 2949 2993 205483113 205483069 1.910000e-12 84.2


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 TraesCS5A01G010400 chr5A 6772230 6775222 2992 True 5528.0 5528 100.000 1 2993 1 chr5A.!!$R1 2992
1 TraesCS5A01G010400 chr5A 14863531 14864455 924 True 1254.0 1254 91.135 1197 2121 1 chr5A.!!$R3 924
2 TraesCS5A01G010400 chr5A 14854087 14854808 721 True 1122.0 1122 94.751 2116 2835 1 chr5A.!!$R2 719
3 TraesCS5A01G010400 chr5A 14895089 14895631 542 True 743.0 743 91.360 658 1200 1 chr5A.!!$R4 542
4 TraesCS5A01G010400 chr5D 8591824 8594083 2259 True 3352.0 3352 93.457 658 2915 1 chr5D.!!$R1 2257
5 TraesCS5A01G010400 chr5B 8936081 8937341 1260 True 876.0 1345 90.804 658 2156 2 chr5B.!!$R2 1498
6 TraesCS5A01G010400 chr5B 8942975 8943539 564 True 833.0 833 93.274 1212 1776 1 chr5B.!!$R1 564
7 TraesCS5A01G010400 chr3D 555531757 555536886 5129 False 682.4 1299 87.632 664 2453 2 chr3D.!!$F2 1789
8 TraesCS5A01G010400 chr3B 738716565 738718354 1789 False 1216.0 1216 79.357 664 2464 1 chr3B.!!$F1 1800
9 TraesCS5A01G010400 chr3B 167060109 167060767 658 True 1162.0 1162 98.483 1 659 1 chr3B.!!$R1 658
10 TraesCS5A01G010400 chr3B 617438268 617439293 1025 True 693.0 693 79.191 994 2013 1 chr3B.!!$R2 1019
11 TraesCS5A01G010400 chr1A 593998734 593999393 659 False 1140.0 1140 97.879 1 659 1 chr1A.!!$F3 658
12 TraesCS5A01G010400 chr1A 82683665 82684339 674 False 1110.0 1110 96.741 1 659 1 chr1A.!!$F2 658
13 TraesCS5A01G010400 chr4A 309246252 309246905 653 False 1129.0 1129 97.724 1 658 1 chr4A.!!$F1 657
14 TraesCS5A01G010400 chr7B 557441219 557441870 651 True 1127.0 1127 97.727 1 659 1 chr7B.!!$R1 658
15 TraesCS5A01G010400 chr7B 673689045 673689720 675 False 1101.0 1101 96.450 1 660 1 chr7B.!!$F1 659
16 TraesCS5A01G010400 chr2A 100651239 100651914 675 True 1118.0 1118 96.893 1 660 1 chr2A.!!$R1 659
17 TraesCS5A01G010400 chr4B 416490077 416490751 674 False 1110.0 1110 96.741 1 659 1 chr4B.!!$F1 658
18 TraesCS5A01G010400 chr6B 560985279 560985953 674 True 1105.0 1105 96.593 1 659 1 chr6B.!!$R1 658
19 TraesCS5A01G010400 chr3A 692677282 692678776 1494 False 1037.0 1037 79.485 664 2157 1 chr3A.!!$F1 1493

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
783 803 1.138859 TGGATCATACTGGCCGAGTTG 59.861 52.381 12.22 10.43 35.96 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2702 5331 0.179067 TGACCGTCCAAGCGAAAACT 60.179 50.0 0.0 0.0 0.0 2.66 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
265 267 2.476821 CTTACTTTGACGGTGGTTCGT 58.523 47.619 0.00 0.00 46.83 3.85
569 571 5.551305 ACGTGAGGATATGATGATGGAAA 57.449 39.130 0.00 0.00 0.00 3.13
675 693 8.862325 AGTAGAGATAGACACATGATAGGAAG 57.138 38.462 0.00 0.00 0.00 3.46
746 766 9.169592 CAATGAAATGGAAGGAAGCAATAAAAT 57.830 29.630 0.00 0.00 0.00 1.82
783 803 1.138859 TGGATCATACTGGCCGAGTTG 59.861 52.381 12.22 10.43 35.96 3.16
868 888 2.866762 GTTGCCAATTGTTTTAACGCCA 59.133 40.909 4.43 0.00 0.00 5.69
952 972 4.005650 ACATACGACCTTGAGACGTAGAA 58.994 43.478 0.00 0.00 43.66 2.10
972 992 8.932791 CGTAGAAAAACACAAATCTATACCTGT 58.067 33.333 0.00 0.00 0.00 4.00
991 1023 5.020132 CCTGTTCTCCTCTTCCTTTCTCTA 58.980 45.833 0.00 0.00 0.00 2.43
1162 1194 2.189521 CCGAGGTAGCCGCCATTT 59.810 61.111 0.00 0.00 0.00 2.32
1176 1208 1.200519 CCATTTCCTACTCACCCGGA 58.799 55.000 0.73 0.00 0.00 5.14
1287 1319 5.003804 ACCGACAATAACAAGCTGAAGAAT 58.996 37.500 0.00 0.00 0.00 2.40
1311 1343 4.801624 CTGCAGCACGGCGAGCTA 62.802 66.667 30.06 15.86 41.14 3.32
1374 1406 0.114954 AGGAGGCCATGGCAAAGAAA 59.885 50.000 36.56 0.00 44.11 2.52
1375 1407 1.197812 GGAGGCCATGGCAAAGAAAT 58.802 50.000 36.56 13.65 44.11 2.17
1377 1409 1.551883 GAGGCCATGGCAAAGAAATGT 59.448 47.619 36.56 9.95 44.11 2.71
1379 1411 1.002315 GGCCATGGCAAAGAAATGTGT 59.998 47.619 36.56 0.00 44.11 3.72
1413 1445 2.058125 TTGCGGTCTGGCTTAACCCA 62.058 55.000 0.00 0.00 37.83 4.51
1429 1461 4.447138 AACCCAAAACTAGGTGACATGA 57.553 40.909 0.00 0.00 36.19 3.07
1578 1610 4.034258 CCACTGCCGCAACAGCTG 62.034 66.667 13.48 13.48 41.60 4.24
1579 1611 2.974148 CACTGCCGCAACAGCTGA 60.974 61.111 23.35 0.00 41.60 4.26
1624 1665 1.052617 TAGCACCAGCACCAACACTA 58.947 50.000 0.00 0.00 45.49 2.74
1626 1667 0.250295 GCACCAGCACCAACACTAGA 60.250 55.000 0.00 0.00 41.58 2.43
1667 1708 2.892425 GGCGATGCCTCCAACTCG 60.892 66.667 0.00 0.00 46.69 4.18
1839 1892 2.031919 ATGTCGCCGCAACCAGAA 59.968 55.556 0.00 0.00 0.00 3.02
1843 1896 1.302112 TCGCCGCAACCAGAATTCA 60.302 52.632 8.44 0.00 0.00 2.57
1844 1897 0.676466 TCGCCGCAACCAGAATTCAT 60.676 50.000 8.44 0.00 0.00 2.57
1903 1962 2.284331 TGCCGGAGTTCCCTGCTA 60.284 61.111 5.05 0.00 44.45 3.49
1906 1965 0.815615 GCCGGAGTTCCCTGCTAATG 60.816 60.000 5.05 0.00 41.37 1.90
2013 2072 4.221703 TGAGGAGAAGAAGACAAGATCCAC 59.778 45.833 0.00 0.00 0.00 4.02
2034 2093 3.752222 ACATCGAGTTCTGAGTACGAGTT 59.248 43.478 0.00 0.00 36.49 3.01
2035 2094 4.215827 ACATCGAGTTCTGAGTACGAGTTT 59.784 41.667 0.00 0.00 36.49 2.66
2042 2101 3.483421 TCTGAGTACGAGTTTGAGTCCA 58.517 45.455 0.00 0.00 0.00 4.02
2043 2102 3.502595 TCTGAGTACGAGTTTGAGTCCAG 59.497 47.826 0.00 0.00 0.00 3.86
2054 2113 1.081481 TGAGTCCAGGAGTGAGGGTA 58.919 55.000 0.00 0.00 0.00 3.69
2061 2120 2.035632 CAGGAGTGAGGGTATGAGTCC 58.964 57.143 0.00 0.00 0.00 3.85
2065 2124 1.285373 AGTGAGGGTATGAGTCCGTCT 59.715 52.381 0.00 0.00 39.62 4.18
2091 2150 6.112734 AGTTAAACTATCCATTGACGCATCA 58.887 36.000 0.00 0.00 0.00 3.07
2126 2185 5.059833 GGATGCCGATCTCTTAGTTCATTT 58.940 41.667 0.00 0.00 0.00 2.32
2127 2186 5.049818 GGATGCCGATCTCTTAGTTCATTTG 60.050 44.000 0.00 0.00 0.00 2.32
2168 2227 2.294979 TCATGCTTGCAGGTGATGATC 58.705 47.619 7.14 0.00 0.00 2.92
2173 2233 2.228059 CTTGCAGGTGATGATCCATCC 58.772 52.381 4.69 0.00 39.87 3.51
2176 2236 1.142465 GCAGGTGATGATCCATCCACT 59.858 52.381 4.69 0.81 39.87 4.00
2197 2257 7.621428 CACTTGTGTGGAAGATTCATTATCT 57.379 36.000 0.00 0.00 41.54 1.98
2291 2361 4.711846 AGCCTTTTCTTTGGTTCTCTTTGT 59.288 37.500 0.00 0.00 0.00 2.83
2532 5017 1.876799 TGCCTATGTTGTGTTGGTTCG 59.123 47.619 0.00 0.00 0.00 3.95
2559 5044 9.866655 TTATAGAAATCCTAATTGTGCCATTCT 57.133 29.630 0.00 0.00 0.00 2.40
2640 5125 4.220602 AGAAAAGGGCACTCGCAAAAATAT 59.779 37.500 0.00 0.00 41.24 1.28
2641 5126 3.508744 AAGGGCACTCGCAAAAATATG 57.491 42.857 0.00 0.00 41.24 1.78
2642 5127 1.750778 AGGGCACTCGCAAAAATATGG 59.249 47.619 0.00 0.00 41.24 2.74
2643 5128 1.559831 GGCACTCGCAAAAATATGGC 58.440 50.000 0.00 0.00 41.24 4.40
2644 5129 1.135141 GGCACTCGCAAAAATATGGCA 60.135 47.619 0.00 0.00 41.24 4.92
2645 5130 2.481795 GGCACTCGCAAAAATATGGCAT 60.482 45.455 4.88 4.88 41.24 4.40
2647 5132 3.772932 CACTCGCAAAAATATGGCATGT 58.227 40.909 10.98 0.00 0.00 3.21
2702 5331 5.082633 TCTACATAGTTAGGGTGGCCATA 57.917 43.478 9.72 0.00 0.00 2.74
2724 5393 0.034198 TTTCGCTTGGACGGTCATGA 59.966 50.000 10.76 0.00 0.00 3.07
2832 5501 0.666913 AGTGTAGCGTGTGTTCGAGT 59.333 50.000 0.00 0.00 0.00 4.18
2840 5509 0.861837 GTGTGTTCGAGTCTTGGCTG 59.138 55.000 0.00 0.00 0.00 4.85
2850 5519 1.542030 AGTCTTGGCTGACGACTAGTG 59.458 52.381 0.00 0.00 41.47 2.74
2881 5550 8.109560 AGGTTAAAAATATGCCTCTAAGGGTA 57.890 34.615 0.00 0.00 35.37 3.69
2915 5584 2.038426 TCTCGTCCACAACACCATCATT 59.962 45.455 0.00 0.00 0.00 2.57
2916 5585 2.813754 CTCGTCCACAACACCATCATTT 59.186 45.455 0.00 0.00 0.00 2.32
2917 5586 4.000325 CTCGTCCACAACACCATCATTTA 59.000 43.478 0.00 0.00 0.00 1.40
2919 5588 3.751175 CGTCCACAACACCATCATTTACT 59.249 43.478 0.00 0.00 0.00 2.24
2920 5589 4.932799 CGTCCACAACACCATCATTTACTA 59.067 41.667 0.00 0.00 0.00 1.82
2921 5590 5.410132 CGTCCACAACACCATCATTTACTAA 59.590 40.000 0.00 0.00 0.00 2.24
2923 5592 5.943416 TCCACAACACCATCATTTACTAAGG 59.057 40.000 0.00 0.00 0.00 2.69
2925 5594 6.208599 CCACAACACCATCATTTACTAAGGTT 59.791 38.462 0.00 0.00 0.00 3.50
2926 5595 7.083858 CACAACACCATCATTTACTAAGGTTG 58.916 38.462 0.00 0.00 38.21 3.77
2927 5596 6.775629 ACAACACCATCATTTACTAAGGTTGT 59.224 34.615 0.00 0.00 39.92 3.32
2928 5597 7.286775 ACAACACCATCATTTACTAAGGTTGTT 59.713 33.333 0.00 0.00 41.37 2.83
2929 5598 7.214467 ACACCATCATTTACTAAGGTTGTTG 57.786 36.000 0.00 0.00 0.00 3.33
2930 5599 6.775629 ACACCATCATTTACTAAGGTTGTTGT 59.224 34.615 0.00 0.00 0.00 3.32
2931 5600 7.040686 ACACCATCATTTACTAAGGTTGTTGTC 60.041 37.037 0.00 0.00 0.00 3.18
2932 5601 6.433093 ACCATCATTTACTAAGGTTGTTGTCC 59.567 38.462 0.00 0.00 0.00 4.02
2933 5602 6.127730 CCATCATTTACTAAGGTTGTTGTCCC 60.128 42.308 0.00 0.00 0.00 4.46
2934 5603 5.942961 TCATTTACTAAGGTTGTTGTCCCA 58.057 37.500 0.00 0.00 0.00 4.37
2935 5604 6.366340 TCATTTACTAAGGTTGTTGTCCCAA 58.634 36.000 0.00 0.00 0.00 4.12
2936 5605 6.834451 TCATTTACTAAGGTTGTTGTCCCAAA 59.166 34.615 0.00 0.00 0.00 3.28
2937 5606 6.453926 TTTACTAAGGTTGTTGTCCCAAAC 57.546 37.500 0.00 0.00 32.03 2.93
2938 5607 3.970842 ACTAAGGTTGTTGTCCCAAACA 58.029 40.909 0.00 0.00 38.26 2.83
2939 5608 4.345854 ACTAAGGTTGTTGTCCCAAACAA 58.654 39.130 0.00 0.00 45.38 2.83
2953 5622 1.873591 CAAACAAGTTGGGGTCTCTCG 59.126 52.381 7.96 0.00 33.18 4.04
2954 5623 0.250338 AACAAGTTGGGGTCTCTCGC 60.250 55.000 7.96 0.00 0.00 5.03
2956 5625 2.593956 AAGTTGGGGTCTCTCGCCC 61.594 63.158 0.00 0.00 46.91 6.13
2962 5631 1.452108 GGGTCTCTCGCCCAAATGG 60.452 63.158 0.00 0.00 45.40 3.16
2984 5653 2.492088 GTTTCATACCCAAAGGACTGGC 59.508 50.000 0.00 0.00 34.88 4.85
2985 5654 1.668826 TCATACCCAAAGGACTGGCT 58.331 50.000 0.00 0.00 34.88 4.75
2986 5655 2.840511 TCATACCCAAAGGACTGGCTA 58.159 47.619 0.00 0.00 34.88 3.93
2987 5656 2.771943 TCATACCCAAAGGACTGGCTAG 59.228 50.000 0.00 0.00 34.88 3.42
2988 5657 2.337359 TACCCAAAGGACTGGCTAGT 57.663 50.000 0.69 0.69 40.66 2.57
2990 5659 1.780919 ACCCAAAGGACTGGCTAGTTT 59.219 47.619 3.47 0.00 37.25 2.66
2992 5661 3.230976 CCCAAAGGACTGGCTAGTTTTT 58.769 45.455 3.47 6.04 37.25 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
569 571 7.654022 TTGTTTGGTTTAATTTGGTCTCTCT 57.346 32.000 0.00 0.00 0.00 3.10
675 693 1.155042 GAATGAGCGCCATGAGATCC 58.845 55.000 2.29 0.00 35.24 3.36
769 789 0.324943 AAGCACAACTCGGCCAGTAT 59.675 50.000 2.24 0.00 32.30 2.12
783 803 0.921347 CCTGTCACGCGTATAAGCAC 59.079 55.000 13.44 2.49 36.85 4.40
806 826 9.469807 GAGGTATTGTTCAGTATTCTCTGTATG 57.530 37.037 0.00 0.00 36.85 2.39
808 828 8.824756 AGAGGTATTGTTCAGTATTCTCTGTA 57.175 34.615 0.00 0.00 36.85 2.74
842 862 5.050431 GCGTTAAAACAATTGGCAACTCATT 60.050 36.000 10.83 0.00 37.61 2.57
952 972 8.164070 AGGAGAACAGGTATAGATTTGTGTTTT 58.836 33.333 0.00 0.00 0.00 2.43
972 992 4.158764 CGCTTAGAGAAAGGAAGAGGAGAA 59.841 45.833 0.00 0.00 35.58 2.87
991 1023 3.434319 CGGTGCCATTGCTCGCTT 61.434 61.111 0.00 0.00 38.71 4.68
1162 1194 2.043248 GCCTCCGGGTGAGTAGGA 60.043 66.667 8.76 0.00 39.65 2.94
1353 1385 1.210204 TCTTTGCCATGGCCTCCTCT 61.210 55.000 33.44 0.00 41.09 3.69
1374 1406 2.528127 TGGTCCCCCACGACACAT 60.528 61.111 0.00 0.00 35.17 3.21
1375 1407 3.238497 CTGGTCCCCCACGACACA 61.238 66.667 0.00 0.00 35.17 3.72
1377 1409 1.537889 AATCTGGTCCCCCACGACA 60.538 57.895 0.00 0.00 35.17 4.35
1379 1411 2.966732 GCAATCTGGTCCCCCACGA 61.967 63.158 0.00 0.00 35.17 4.35
1413 1445 3.264450 CCTCCCTCATGTCACCTAGTTTT 59.736 47.826 0.00 0.00 0.00 2.43
1429 1461 0.473501 GCCATCATCTCCTCCTCCCT 60.474 60.000 0.00 0.00 0.00 4.20
1513 1545 1.141858 GATGTTCTCCATCCCCAGGTC 59.858 57.143 0.00 0.00 43.59 3.85
1624 1665 2.852449 CATCTGCTGCATCTCCATTCT 58.148 47.619 1.31 0.00 0.00 2.40
1667 1708 1.065854 CCATCCCTATGGCGAATCCTC 60.066 57.143 0.00 0.00 46.17 3.71
1903 1962 2.676608 TGGCGGCATCTCCACATT 59.323 55.556 7.97 0.00 34.01 2.71
1932 1991 2.685017 ATCTCTGTCCCAGCGGCA 60.685 61.111 1.45 0.00 0.00 5.69
2013 2072 4.343811 AACTCGTACTCAGAACTCGATG 57.656 45.455 0.00 0.00 0.00 3.84
2034 2093 0.191064 ACCCTCACTCCTGGACTCAA 59.809 55.000 0.00 0.00 0.00 3.02
2035 2094 1.081481 TACCCTCACTCCTGGACTCA 58.919 55.000 0.00 0.00 0.00 3.41
2042 2101 1.410365 CGGACTCATACCCTCACTCCT 60.410 57.143 0.00 0.00 0.00 3.69
2043 2102 1.033574 CGGACTCATACCCTCACTCC 58.966 60.000 0.00 0.00 0.00 3.85
2054 2113 6.183360 GGATAGTTTAACTCAGACGGACTCAT 60.183 42.308 0.00 0.00 0.00 2.90
2061 2120 6.020599 CGTCAATGGATAGTTTAACTCAGACG 60.021 42.308 0.00 6.75 37.01 4.18
2065 2124 5.483811 TGCGTCAATGGATAGTTTAACTCA 58.516 37.500 0.00 0.00 0.00 3.41
2091 2150 0.737367 CGGCATCCATCGACGCATAT 60.737 55.000 0.00 0.00 0.00 1.78
2097 2156 0.600557 AGAGATCGGCATCCATCGAC 59.399 55.000 0.00 0.00 38.25 4.20
2099 2158 2.230025 ACTAAGAGATCGGCATCCATCG 59.770 50.000 0.00 0.00 0.00 3.84
2150 2209 1.064240 TGGATCATCACCTGCAAGCAT 60.064 47.619 0.00 0.00 0.00 3.79
2173 2233 7.621428 AGATAATGAATCTTCCACACAAGTG 57.379 36.000 0.00 0.00 42.62 3.16
2197 2257 8.748412 ACAAAGATTGCAAGCCATTAATACTAA 58.252 29.630 11.83 0.00 0.00 2.24
2291 2361 4.081752 AGTTCATTCTTGTGTTGTTGCCAA 60.082 37.500 0.00 0.00 0.00 4.52
2399 2471 7.879677 TCGAAATATATGCAATTCTCATGTCCT 59.120 33.333 0.00 0.00 0.00 3.85
2674 5303 6.462628 GGCCACCCTAACTATGTAGAAGTAAG 60.463 46.154 0.00 0.00 0.00 2.34
2702 5331 0.179067 TGACCGTCCAAGCGAAAACT 60.179 50.000 0.00 0.00 0.00 2.66
2821 5490 0.861837 CAGCCAAGACTCGAACACAC 59.138 55.000 0.00 0.00 0.00 3.82
2832 5501 0.243907 GCACTAGTCGTCAGCCAAGA 59.756 55.000 0.00 0.00 0.00 3.02
2840 5509 7.412137 TTTTAACCTTTAAGCACTAGTCGTC 57.588 36.000 0.00 0.00 0.00 4.20
2881 5550 3.941483 GTGGACGAGACCATTCATGATTT 59.059 43.478 0.00 0.00 42.17 2.17
2933 5602 1.873591 CGAGAGACCCCAACTTGTTTG 59.126 52.381 0.00 0.00 34.63 2.93
2934 5603 1.814248 GCGAGAGACCCCAACTTGTTT 60.814 52.381 0.00 0.00 0.00 2.83
2935 5604 0.250338 GCGAGAGACCCCAACTTGTT 60.250 55.000 0.00 0.00 0.00 2.83
2936 5605 1.371558 GCGAGAGACCCCAACTTGT 59.628 57.895 0.00 0.00 0.00 3.16
2937 5606 1.376037 GGCGAGAGACCCCAACTTG 60.376 63.158 0.00 0.00 0.00 3.16
2938 5607 3.069778 GGCGAGAGACCCCAACTT 58.930 61.111 0.00 0.00 0.00 2.66
2962 5631 6.882412 AGCCAGTCCTTTGGGTATGAAACC 62.882 50.000 0.00 0.00 46.57 3.27
2963 5632 2.492088 GCCAGTCCTTTGGGTATGAAAC 59.508 50.000 0.00 0.00 38.72 2.78
2964 5633 2.378547 AGCCAGTCCTTTGGGTATGAAA 59.621 45.455 0.00 0.00 46.57 2.69
2966 5635 1.668826 AGCCAGTCCTTTGGGTATGA 58.331 50.000 0.00 0.00 46.57 2.15
2967 5636 2.505819 ACTAGCCAGTCCTTTGGGTATG 59.494 50.000 4.61 2.96 46.74 2.39
2969 5638 2.337359 ACTAGCCAGTCCTTTGGGTA 57.663 50.000 4.17 4.17 46.57 3.69
2971 5640 2.586648 AAACTAGCCAGTCCTTTGGG 57.413 50.000 0.00 0.00 38.72 4.12


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

AutoCloner maintained by Alex Coulton.