Multiple sequence alignment - TraesCS3A01G167900

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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 TraesCS3A01G167900 chr3A 100.000 3446 0 0 1 3446 174541796 174545241 0.000000e+00 6364.0
1 TraesCS3A01G167900 chr3A 75.849 1031 203 32 707 1714 164611031 164612038 1.860000e-132 483.0
2 TraesCS3A01G167900 chr3A 76.940 902 139 36 2249 3114 175239689 175240557 1.890000e-122 449.0
3 TraesCS3A01G167900 chr3A 75.684 987 185 39 709 1666 65480648 65479688 3.160000e-120 442.0
4 TraesCS3A01G167900 chr3A 76.000 225 25 17 1831 2032 709450632 709450850 4.740000e-14 89.8
5 TraesCS3A01G167900 chr3A 75.132 189 23 19 694 869 164928992 164929169 2.220000e-07 67.6
6 TraesCS3A01G167900 chr3B 96.625 1600 28 5 209 1797 226005206 226003622 0.000000e+00 2632.0
7 TraesCS3A01G167900 chr3B 95.822 742 26 5 2235 2973 226003162 226002423 0.000000e+00 1194.0
8 TraesCS3A01G167900 chr3B 79.098 1086 190 24 653 1712 260842258 260843332 0.000000e+00 713.0
9 TraesCS3A01G167900 chr3B 91.982 449 8 7 1830 2253 226003635 226003190 3.800000e-169 604.0
10 TraesCS3A01G167900 chr3B 89.865 444 21 8 3004 3446 226001160 226000740 1.810000e-152 549.0
11 TraesCS3A01G167900 chr3B 75.573 1048 192 46 650 1659 205775415 205776436 3.130000e-125 459.0
12 TraesCS3A01G167900 chr3B 78.871 691 107 20 2252 2908 225798023 225797338 6.830000e-117 431.0
13 TraesCS3A01G167900 chr3B 94.472 199 9 2 1 199 226006855 226006659 4.320000e-79 305.0
14 TraesCS3A01G167900 chr3B 82.787 244 27 9 8 236 90855598 90855355 1.620000e-48 204.0
15 TraesCS3A01G167900 chr3B 80.625 160 28 3 3287 3445 252398855 252398698 1.680000e-23 121.0
16 TraesCS3A01G167900 chr3B 86.458 96 12 1 2992 3086 225797282 225797187 1.690000e-18 104.0
17 TraesCS3A01G167900 chr3B 75.806 186 27 13 694 869 213723522 213723699 1.030000e-10 78.7
18 TraesCS3A01G167900 chr3D 95.533 985 38 6 2235 3215 155685132 155686114 0.000000e+00 1570.0
19 TraesCS3A01G167900 chr3D 95.626 846 27 2 667 1503 155675005 155675849 0.000000e+00 1349.0
20 TraesCS3A01G167900 chr3D 78.698 1075 192 20 651 1702 182320192 182321252 0.000000e+00 682.0
21 TraesCS3A01G167900 chr3D 92.225 463 24 8 213 674 155674294 155674745 0.000000e+00 645.0
22 TraesCS3A01G167900 chr3D 78.891 938 167 20 801 1712 182334363 182335295 1.060000e-169 606.0
23 TraesCS3A01G167900 chr3D 98.371 307 5 0 1491 1797 155683898 155684204 1.090000e-149 540.0
24 TraesCS3A01G167900 chr3D 78.667 900 124 42 2249 3114 155953001 155953866 1.410000e-148 536.0
25 TraesCS3A01G167900 chr3D 92.287 376 7 4 1897 2253 155684732 155685104 6.590000e-142 514.0
26 TraesCS3A01G167900 chr3D 76.292 987 184 36 707 1668 148700169 148699208 6.690000e-132 481.0
27 TraesCS3A01G167900 chr3D 75.988 987 180 44 709 1665 55084843 55083884 1.130000e-124 457.0
28 TraesCS3A01G167900 chr3D 85.915 213 20 9 9 214 26208802 26208593 5.790000e-53 219.0
29 TraesCS3A01G167900 chr3D 96.053 76 3 0 1829 1904 155684190 155684265 1.300000e-24 124.0
30 TraesCS3A01G167900 chr3D 89.231 65 2 4 805 869 148252447 148252388 3.690000e-10 76.8
31 TraesCS3A01G167900 chr3D 95.238 42 2 0 3405 3446 155687142 155687183 2.220000e-07 67.6
32 TraesCS3A01G167900 chr4B 78.071 1099 184 31 656 1712 397010503 397009420 2.900000e-180 641.0
33 TraesCS3A01G167900 chr4B 83.333 246 25 10 8 237 168565400 168565645 2.690000e-51 213.0
34 TraesCS3A01G167900 chr4B 83.051 236 32 5 8 235 99578015 99577780 1.250000e-49 207.0
35 TraesCS3A01G167900 chr4A 77.657 1101 191 31 653 1712 154354622 154355708 1.360000e-173 619.0
36 TraesCS3A01G167900 chr4A 82.927 164 24 4 3286 3446 533195397 533195559 9.970000e-31 145.0
37 TraesCS3A01G167900 chr4A 80.108 186 27 7 3268 3446 533442200 533442018 2.790000e-26 130.0
38 TraesCS3A01G167900 chr4D 77.627 1104 186 30 656 1712 319328542 319327453 6.320000e-172 614.0
39 TraesCS3A01G167900 chr4D 85.227 88 11 1 3272 3359 62881975 62882060 4.740000e-14 89.8
40 TraesCS3A01G167900 chr4D 97.222 36 0 1 3287 3321 62883938 62883973 3.710000e-05 60.2
41 TraesCS3A01G167900 chr2D 83.613 238 30 6 8 238 420565252 420565487 7.490000e-52 215.0
42 TraesCS3A01G167900 chr5A 82.883 222 27 7 25 237 673922166 673921947 4.540000e-44 189.0
43 TraesCS3A01G167900 chr5A 79.828 233 39 8 8 235 408846586 408846357 2.750000e-36 163.0
44 TraesCS3A01G167900 chr6D 80.162 247 34 12 4 238 451758909 451759152 1.640000e-38 171.0
45 TraesCS3A01G167900 chr7B 80.488 164 23 7 3287 3446 714674423 714674265 2.170000e-22 117.0
46 TraesCS3A01G167900 chr7B 78.313 166 27 5 3285 3446 714681910 714681750 7.870000e-17 99.0
47 TraesCS3A01G167900 chr6A 92.593 54 3 1 3285 3338 39194977 39195029 3.690000e-10 76.8


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 TraesCS3A01G167900 chr3A 174541796 174545241 3445 False 6364.00 6364 100.0000 1 3446 1 chr3A.!!$F3 3445
1 TraesCS3A01G167900 chr3A 164611031 164612038 1007 False 483.00 483 75.8490 707 1714 1 chr3A.!!$F1 1007
2 TraesCS3A01G167900 chr3A 175239689 175240557 868 False 449.00 449 76.9400 2249 3114 1 chr3A.!!$F4 865
3 TraesCS3A01G167900 chr3A 65479688 65480648 960 True 442.00 442 75.6840 709 1666 1 chr3A.!!$R1 957
4 TraesCS3A01G167900 chr3B 226000740 226006855 6115 True 1056.80 2632 93.7532 1 3446 5 chr3B.!!$R4 3445
5 TraesCS3A01G167900 chr3B 260842258 260843332 1074 False 713.00 713 79.0980 653 1712 1 chr3B.!!$F3 1059
6 TraesCS3A01G167900 chr3B 205775415 205776436 1021 False 459.00 459 75.5730 650 1659 1 chr3B.!!$F1 1009
7 TraesCS3A01G167900 chr3B 225797187 225798023 836 True 267.50 431 82.6645 2252 3086 2 chr3B.!!$R3 834
8 TraesCS3A01G167900 chr3D 155674294 155675849 1555 False 997.00 1349 93.9255 213 1503 2 chr3D.!!$F4 1290
9 TraesCS3A01G167900 chr3D 182320192 182321252 1060 False 682.00 682 78.6980 651 1702 1 chr3D.!!$F2 1051
10 TraesCS3A01G167900 chr3D 182334363 182335295 932 False 606.00 606 78.8910 801 1712 1 chr3D.!!$F3 911
11 TraesCS3A01G167900 chr3D 155683898 155687183 3285 False 563.12 1570 95.4964 1491 3446 5 chr3D.!!$F5 1955
12 TraesCS3A01G167900 chr3D 155953001 155953866 865 False 536.00 536 78.6670 2249 3114 1 chr3D.!!$F1 865
13 TraesCS3A01G167900 chr3D 148699208 148700169 961 True 481.00 481 76.2920 707 1668 1 chr3D.!!$R4 961
14 TraesCS3A01G167900 chr3D 55083884 55084843 959 True 457.00 457 75.9880 709 1665 1 chr3D.!!$R2 956
15 TraesCS3A01G167900 chr4B 397009420 397010503 1083 True 641.00 641 78.0710 656 1712 1 chr4B.!!$R2 1056
16 TraesCS3A01G167900 chr4A 154354622 154355708 1086 False 619.00 619 77.6570 653 1712 1 chr4A.!!$F1 1059
17 TraesCS3A01G167900 chr4D 319327453 319328542 1089 True 614.00 614 77.6270 656 1712 1 chr4D.!!$R1 1056

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
209 219 0.252835 ATTGCAAAAGGAGGCCCCAT 60.253 50.000 1.71 0.0 37.41 4.00 F
213 223 0.685458 CAAAAGGAGGCCCCATGGAG 60.685 60.000 15.22 0.0 37.41 3.86 F
1797 3582 3.339253 TCTGCATATGTCTGCACAAGT 57.661 42.857 4.29 0.0 46.76 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1801 3586 0.466124 GAAAGGAGGATCAGTCCCCG 59.534 60.0 9.26 0.0 46.34 5.73 R
1802 3587 0.840617 GGAAAGGAGGATCAGTCCCC 59.159 60.0 9.26 1.7 46.34 4.81 R
3121 6787 0.175531 GGGAAATGGCAATCCGTTGG 59.824 55.0 14.33 0.0 40.62 3.77 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
60 61 7.761409 TGAATAGTATCATGTGTTGAAAAGCC 58.239 34.615 0.00 0.00 38.03 4.35
63 64 5.316167 AGTATCATGTGTTGAAAAGCCTCA 58.684 37.500 0.00 0.00 38.03 3.86
64 65 5.948162 AGTATCATGTGTTGAAAAGCCTCAT 59.052 36.000 0.00 0.00 38.03 2.90
65 66 7.112122 AGTATCATGTGTTGAAAAGCCTCATA 58.888 34.615 0.00 0.00 38.03 2.15
91 92 2.626780 GCACGGCCCTCCTTTCAAC 61.627 63.158 0.00 0.00 0.00 3.18
155 156 9.716507 GTGTCCATGTATATGTGTATTTTTCAC 57.283 33.333 0.00 0.00 36.48 3.18
204 214 3.598019 TGATGAATTGCAAAAGGAGGC 57.402 42.857 1.71 0.00 0.00 4.70
205 215 2.234414 TGATGAATTGCAAAAGGAGGCC 59.766 45.455 1.71 0.00 0.00 5.19
206 216 0.975887 TGAATTGCAAAAGGAGGCCC 59.024 50.000 1.71 0.00 0.00 5.80
209 219 0.252835 ATTGCAAAAGGAGGCCCCAT 60.253 50.000 1.71 0.00 37.41 4.00
210 220 1.193462 TTGCAAAAGGAGGCCCCATG 61.193 55.000 12.24 8.94 37.41 3.66
211 221 2.361567 GCAAAAGGAGGCCCCATGG 61.362 63.158 4.14 4.14 37.41 3.66
213 223 0.685458 CAAAAGGAGGCCCCATGGAG 60.685 60.000 15.22 0.00 37.41 3.86
216 226 3.883549 GGAGGCCCCATGGAGCTC 61.884 72.222 18.67 12.80 34.14 4.09
217 227 4.247380 GAGGCCCCATGGAGCTCG 62.247 72.222 18.67 0.00 0.00 5.03
1753 3538 3.625649 TCCCATCACATTCATCACGAA 57.374 42.857 0.00 0.00 38.22 3.85
1757 3542 3.439825 CCATCACATTCATCACGAACCAA 59.560 43.478 0.00 0.00 36.12 3.67
1797 3582 3.339253 TCTGCATATGTCTGCACAAGT 57.661 42.857 4.29 0.00 46.76 3.16
1798 3583 3.678289 TCTGCATATGTCTGCACAAGTT 58.322 40.909 4.29 0.00 46.76 2.66
1799 3584 3.437741 TCTGCATATGTCTGCACAAGTTG 59.562 43.478 4.29 0.00 46.76 3.16
1807 3592 3.670377 GCACAAGTTGCCGGGGAC 61.670 66.667 2.18 0.00 46.63 4.46
1808 3593 2.113139 CACAAGTTGCCGGGGACT 59.887 61.111 2.18 0.00 0.00 3.85
1809 3594 2.113139 ACAAGTTGCCGGGGACTG 59.887 61.111 2.18 0.00 0.00 3.51
1810 3595 2.429930 CAAGTTGCCGGGGACTGA 59.570 61.111 2.18 0.00 36.31 3.41
1811 3596 1.002134 CAAGTTGCCGGGGACTGAT 60.002 57.895 2.18 0.00 36.31 2.90
1812 3597 1.026718 CAAGTTGCCGGGGACTGATC 61.027 60.000 2.18 0.00 36.31 2.92
1813 3598 2.124695 GTTGCCGGGGACTGATCC 60.125 66.667 2.18 0.00 45.42 3.36
1814 3599 2.285368 TTGCCGGGGACTGATCCT 60.285 61.111 2.18 0.00 45.46 3.24
1815 3600 2.367202 TTGCCGGGGACTGATCCTC 61.367 63.158 2.18 0.00 45.46 3.71
1816 3601 3.551407 GCCGGGGACTGATCCTCC 61.551 72.222 2.18 0.00 43.61 4.30
1817 3602 2.283809 CCGGGGACTGATCCTCCT 59.716 66.667 0.00 0.00 43.61 3.69
1818 3603 1.383248 CCGGGGACTGATCCTCCTT 60.383 63.158 0.00 0.00 43.61 3.36
1819 3604 0.983378 CCGGGGACTGATCCTCCTTT 60.983 60.000 0.00 0.00 43.61 3.11
1820 3605 0.466124 CGGGGACTGATCCTCCTTTC 59.534 60.000 6.51 0.00 43.61 2.62
1821 3606 0.840617 GGGGACTGATCCTCCTTTCC 59.159 60.000 6.51 0.00 45.46 3.13
1822 3607 1.584724 GGGACTGATCCTCCTTTCCA 58.415 55.000 6.51 0.00 45.46 3.53
1823 3608 1.916181 GGGACTGATCCTCCTTTCCAA 59.084 52.381 6.51 0.00 45.46 3.53
1824 3609 2.308866 GGGACTGATCCTCCTTTCCAAA 59.691 50.000 6.51 0.00 45.46 3.28
1825 3610 3.348119 GGACTGATCCTCCTTTCCAAAC 58.652 50.000 0.00 0.00 42.45 2.93
1826 3611 3.244911 GGACTGATCCTCCTTTCCAAACA 60.245 47.826 0.00 0.00 42.45 2.83
1827 3612 4.398319 GACTGATCCTCCTTTCCAAACAA 58.602 43.478 0.00 0.00 0.00 2.83
1828 3613 4.803452 ACTGATCCTCCTTTCCAAACAAA 58.197 39.130 0.00 0.00 0.00 2.83
1829 3614 5.397360 ACTGATCCTCCTTTCCAAACAAAT 58.603 37.500 0.00 0.00 0.00 2.32
1830 3615 6.552008 ACTGATCCTCCTTTCCAAACAAATA 58.448 36.000 0.00 0.00 0.00 1.40
1831 3616 7.184862 ACTGATCCTCCTTTCCAAACAAATAT 58.815 34.615 0.00 0.00 0.00 1.28
1832 3617 7.123247 ACTGATCCTCCTTTCCAAACAAATATG 59.877 37.037 0.00 0.00 0.00 1.78
1833 3618 6.953520 TGATCCTCCTTTCCAAACAAATATGT 59.046 34.615 0.00 0.00 43.14 2.29
1834 3619 6.834168 TCCTCCTTTCCAAACAAATATGTC 57.166 37.500 0.00 0.00 39.40 3.06
1835 3620 6.552008 TCCTCCTTTCCAAACAAATATGTCT 58.448 36.000 0.00 0.00 39.40 3.41
1836 3621 6.434028 TCCTCCTTTCCAAACAAATATGTCTG 59.566 38.462 0.00 0.00 39.40 3.51
1837 3622 6.024552 TCCTTTCCAAACAAATATGTCTGC 57.975 37.500 0.00 0.00 39.40 4.26
1838 3623 5.538053 TCCTTTCCAAACAAATATGTCTGCA 59.462 36.000 0.00 0.00 39.40 4.41
1839 3624 5.634859 CCTTTCCAAACAAATATGTCTGCAC 59.365 40.000 0.00 0.00 39.40 4.57
1840 3625 5.781210 TTCCAAACAAATATGTCTGCACA 57.219 34.783 0.00 0.00 39.40 4.57
1841 3626 5.375417 TCCAAACAAATATGTCTGCACAG 57.625 39.130 0.00 0.00 39.40 3.66
1842 3627 4.218200 TCCAAACAAATATGTCTGCACAGG 59.782 41.667 0.00 0.00 39.40 4.00
1976 4238 7.996644 ACGAGGGTTTGTGGTTAATGATTATAT 59.003 33.333 0.00 0.00 0.00 0.86
2152 4432 7.658525 TGTATTCCTTGATGGTAAAATGCAT 57.341 32.000 0.00 0.00 37.07 3.96
2267 4640 7.545265 GCTCTGTTTTGTGCCATCATAATTTTA 59.455 33.333 0.00 0.00 0.00 1.52
2389 4777 5.987347 CCAATCTTGACTGCAAAAGACAAAT 59.013 36.000 7.98 0.00 39.53 2.32
2427 4815 1.908483 CCTGGAGGGACTTACCAGC 59.092 63.158 0.00 0.00 45.76 4.85
2428 4816 0.909610 CCTGGAGGGACTTACCAGCA 60.910 60.000 0.00 0.00 45.76 4.41
2537 4926 5.591877 GGATCTGTTATGATTTGGTGCTCTT 59.408 40.000 0.00 0.00 0.00 2.85
2864 5284 3.557228 AGTGATCCCTTGAATCTGCTC 57.443 47.619 0.00 0.00 0.00 4.26
2930 5351 6.277605 TCACTCGAGTTTTTAGTGTTGATCA 58.722 36.000 17.26 0.00 41.12 2.92
2946 5367 2.290260 TGATCATCGGTTTGAGCCTTGT 60.290 45.455 0.00 0.00 31.02 3.16
2973 5394 3.940209 TTTGCATTGTTGACCATCCTC 57.060 42.857 0.00 0.00 0.00 3.71
2977 5398 3.640498 TGCATTGTTGACCATCCTCAAAA 59.360 39.130 0.00 0.00 31.90 2.44
2987 5408 5.003096 ACCATCCTCAAAATTGGTTCTCT 57.997 39.130 0.00 0.00 39.41 3.10
3116 6782 2.869192 CGAAGGAGCTGGAAATTAGAGC 59.131 50.000 0.00 0.00 0.00 4.09
3117 6783 3.679917 CGAAGGAGCTGGAAATTAGAGCA 60.680 47.826 0.00 0.00 35.03 4.26
3173 6839 5.615289 CTGATATTGGAGGAGTTGGGTTAG 58.385 45.833 0.00 0.00 0.00 2.34
3222 7786 6.639563 ACGCAAAATAATATGGGAAAAGCTT 58.360 32.000 0.00 0.00 34.03 3.74
3356 7921 3.122297 TGTTGCAAAAGAAATGAAGCCG 58.878 40.909 0.00 0.00 0.00 5.52
3397 7962 4.541973 TCTGCAGTATCATCTGTGTTGT 57.458 40.909 14.67 0.00 37.70 3.32
3401 7966 5.247862 TGCAGTATCATCTGTGTTGTGAAT 58.752 37.500 0.00 0.00 37.70 2.57
3402 7967 5.706833 TGCAGTATCATCTGTGTTGTGAATT 59.293 36.000 0.00 0.00 37.70 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
91 92 7.267600 GTGTGTAAATTTTCAGGACGAAATACG 59.732 37.037 0.00 0.00 43.12 3.06
772 2497 1.984570 TGACGGGCTCAGGGAAGAG 60.985 63.158 0.00 0.00 38.68 2.85
780 2505 2.525629 TTGGGAGTGACGGGCTCA 60.526 61.111 5.71 0.00 34.83 4.26
915 2643 4.695231 CGCGGTTCGGAGTCGTGT 62.695 66.667 0.00 0.00 37.69 4.49
1692 3477 4.821589 GGAAGCCTCCACGCTCGG 62.822 72.222 0.00 0.00 41.96 4.63
1753 3538 6.139679 TGGAATTCAGTTCTCCTAATTGGT 57.860 37.500 7.93 0.00 37.01 3.67
1757 3542 6.060788 GCAGATGGAATTCAGTTCTCCTAAT 58.939 40.000 7.93 0.00 37.01 1.73
1797 3582 2.285368 AGGATCAGTCCCCGGCAA 60.285 61.111 0.00 0.00 46.34 4.52
1798 3583 2.764128 GAGGATCAGTCCCCGGCA 60.764 66.667 0.00 0.00 46.34 5.69
1799 3584 3.551407 GGAGGATCAGTCCCCGGC 61.551 72.222 0.00 0.00 46.34 6.13
1800 3585 0.983378 AAAGGAGGATCAGTCCCCGG 60.983 60.000 9.26 0.00 46.34 5.73
1801 3586 0.466124 GAAAGGAGGATCAGTCCCCG 59.534 60.000 9.26 0.00 46.34 5.73
1802 3587 0.840617 GGAAAGGAGGATCAGTCCCC 59.159 60.000 9.26 1.70 46.34 4.81
1803 3588 1.584724 TGGAAAGGAGGATCAGTCCC 58.415 55.000 9.26 0.00 46.34 4.46
1804 3589 3.244911 TGTTTGGAAAGGAGGATCAGTCC 60.245 47.826 5.38 5.38 45.45 3.85
1805 3590 4.021102 TGTTTGGAAAGGAGGATCAGTC 57.979 45.455 0.00 0.00 36.25 3.51
1806 3591 4.453480 TTGTTTGGAAAGGAGGATCAGT 57.547 40.909 0.00 0.00 36.25 3.41
1807 3592 5.990120 ATTTGTTTGGAAAGGAGGATCAG 57.010 39.130 0.00 0.00 36.25 2.90
1808 3593 6.953520 ACATATTTGTTTGGAAAGGAGGATCA 59.046 34.615 0.00 0.00 30.09 2.92
1809 3594 7.340487 AGACATATTTGTTTGGAAAGGAGGATC 59.660 37.037 0.00 0.00 35.79 3.36
1810 3595 7.123247 CAGACATATTTGTTTGGAAAGGAGGAT 59.877 37.037 0.00 0.00 35.01 3.24
1811 3596 6.434028 CAGACATATTTGTTTGGAAAGGAGGA 59.566 38.462 0.00 0.00 35.01 3.71
1812 3597 6.624423 CAGACATATTTGTTTGGAAAGGAGG 58.376 40.000 0.00 0.00 35.01 4.30
1813 3598 6.095377 GCAGACATATTTGTTTGGAAAGGAG 58.905 40.000 8.53 0.00 38.17 3.69
1814 3599 5.538053 TGCAGACATATTTGTTTGGAAAGGA 59.462 36.000 8.53 0.00 35.75 3.36
1815 3600 5.634859 GTGCAGACATATTTGTTTGGAAAGG 59.365 40.000 8.53 0.00 39.45 3.11
1816 3601 6.215121 TGTGCAGACATATTTGTTTGGAAAG 58.785 36.000 8.53 0.00 39.45 2.62
1817 3602 6.154203 TGTGCAGACATATTTGTTTGGAAA 57.846 33.333 8.53 0.00 39.45 3.13
1818 3603 5.278907 CCTGTGCAGACATATTTGTTTGGAA 60.279 40.000 8.53 0.00 39.45 3.53
1819 3604 4.218200 CCTGTGCAGACATATTTGTTTGGA 59.782 41.667 8.53 3.40 38.17 3.53
1820 3605 4.487948 CCTGTGCAGACATATTTGTTTGG 58.512 43.478 8.53 0.00 38.17 3.28
1821 3606 3.922240 GCCTGTGCAGACATATTTGTTTG 59.078 43.478 0.02 2.94 40.13 2.93
1822 3607 3.573538 TGCCTGTGCAGACATATTTGTTT 59.426 39.130 0.02 0.00 44.23 2.83
1823 3608 3.156293 TGCCTGTGCAGACATATTTGTT 58.844 40.909 0.02 0.00 44.23 2.83
1824 3609 2.794103 TGCCTGTGCAGACATATTTGT 58.206 42.857 0.02 0.00 44.23 2.83
1836 3621 1.247567 ACCACTTAACATGCCTGTGC 58.752 50.000 0.00 0.00 35.22 4.57
1837 3622 5.401550 CATTTACCACTTAACATGCCTGTG 58.598 41.667 0.00 0.00 35.22 3.66
1838 3623 4.082245 GCATTTACCACTTAACATGCCTGT 60.082 41.667 0.00 0.00 37.12 4.00
1839 3624 4.082300 TGCATTTACCACTTAACATGCCTG 60.082 41.667 0.00 0.00 35.49 4.85
1840 3625 4.082245 GTGCATTTACCACTTAACATGCCT 60.082 41.667 0.00 0.00 35.49 4.75
1841 3626 4.173256 GTGCATTTACCACTTAACATGCC 58.827 43.478 0.00 0.00 35.49 4.40
1842 3627 3.851403 CGTGCATTTACCACTTAACATGC 59.149 43.478 0.00 0.00 36.15 4.06
1978 4240 9.323985 AGCACAACAAAGATAGAGATTTAGATC 57.676 33.333 0.00 0.00 0.00 2.75
1979 4241 9.678260 AAGCACAACAAAGATAGAGATTTAGAT 57.322 29.630 0.00 0.00 0.00 1.98
1983 4245 8.239998 GCTTAAGCACAACAAAGATAGAGATTT 58.760 33.333 22.59 0.00 41.59 2.17
2152 4432 5.981088 ATCAATTAAGCACCACAATGACA 57.019 34.783 0.00 0.00 0.00 3.58
2513 4902 5.128919 AGAGCACCAAATCATAACAGATCC 58.871 41.667 0.00 0.00 0.00 3.36
2537 4926 2.475111 GAGTTGCGTGATGTTCGAAGAA 59.525 45.455 0.00 0.00 45.90 2.52
2930 5351 2.017049 GCATACAAGGCTCAAACCGAT 58.983 47.619 0.00 0.00 33.69 4.18
2966 5387 5.990120 AAGAGAACCAATTTTGAGGATGG 57.010 39.130 0.00 0.00 38.91 3.51
2973 5394 9.538508 AATCAAGAGAAAAGAGAACCAATTTTG 57.461 29.630 0.00 0.00 0.00 2.44
3042 6696 1.826720 TCGGGTAATAAAGCTCGTGGT 59.173 47.619 0.00 0.00 0.00 4.16
3089 6743 4.399395 CCAGCTCCTTCGGCAGCA 62.399 66.667 0.00 0.00 38.18 4.41
3116 6782 1.683943 ATGGCAATCCGTTGGAGATG 58.316 50.000 0.00 0.00 34.05 2.90
3117 6783 2.442236 AATGGCAATCCGTTGGAGAT 57.558 45.000 0.00 0.00 40.02 2.75
3120 6786 1.181786 GGAAATGGCAATCCGTTGGA 58.818 50.000 6.90 0.00 40.62 3.53
3121 6787 0.175531 GGGAAATGGCAATCCGTTGG 59.824 55.000 14.33 0.00 40.62 3.77
3122 6788 0.894141 TGGGAAATGGCAATCCGTTG 59.106 50.000 14.33 0.00 40.62 4.10
3123 6789 1.638529 TTGGGAAATGGCAATCCGTT 58.361 45.000 14.33 0.00 43.26 4.44
3124 6790 1.864669 ATTGGGAAATGGCAATCCGT 58.135 45.000 14.33 3.35 36.54 4.69
3125 6791 4.399004 TTTATTGGGAAATGGCAATCCG 57.601 40.909 14.33 0.00 36.54 4.18
3126 6792 5.066375 GCTTTTTATTGGGAAATGGCAATCC 59.934 40.000 12.86 12.86 34.85 3.01
3127 6793 5.882000 AGCTTTTTATTGGGAAATGGCAATC 59.118 36.000 0.00 0.00 0.00 2.67
3128 6794 5.648960 CAGCTTTTTATTGGGAAATGGCAAT 59.351 36.000 0.00 0.00 0.00 3.56
3129 6795 5.002516 CAGCTTTTTATTGGGAAATGGCAA 58.997 37.500 0.00 0.00 0.00 4.52
3130 6796 4.285517 TCAGCTTTTTATTGGGAAATGGCA 59.714 37.500 0.00 0.00 0.00 4.92
3131 6797 4.831107 TCAGCTTTTTATTGGGAAATGGC 58.169 39.130 0.00 0.00 0.00 4.40
3173 6839 2.550180 GAGACCTGTTGGAGCTGTTTTC 59.450 50.000 0.00 0.00 37.04 2.29
3238 7802 3.114616 CGCCACGCAGAGAAGGTG 61.115 66.667 0.00 0.00 0.00 4.00
3326 7891 3.902881 TCTTTTGCAACATGGGTGTTT 57.097 38.095 0.00 0.00 46.07 2.83
3367 7932 7.864379 CACAGATGATACTGCAGAAAAAGTTTT 59.136 33.333 23.35 0.00 41.06 2.43
3368 7933 7.013655 ACACAGATGATACTGCAGAAAAAGTTT 59.986 33.333 23.35 0.00 41.06 2.66
3369 7934 6.488006 ACACAGATGATACTGCAGAAAAAGTT 59.512 34.615 23.35 0.00 41.06 2.66
3370 7935 6.000219 ACACAGATGATACTGCAGAAAAAGT 59.000 36.000 23.35 0.00 41.06 2.66
3371 7936 6.492007 ACACAGATGATACTGCAGAAAAAG 57.508 37.500 23.35 4.75 41.06 2.27
3372 7937 6.262944 ACAACACAGATGATACTGCAGAAAAA 59.737 34.615 23.35 3.38 41.06 1.94
3373 7938 5.764686 ACAACACAGATGATACTGCAGAAAA 59.235 36.000 23.35 5.62 41.06 2.29
3374 7939 5.179929 CACAACACAGATGATACTGCAGAAA 59.820 40.000 23.35 8.48 41.06 2.52
3375 7940 4.692155 CACAACACAGATGATACTGCAGAA 59.308 41.667 23.35 2.98 41.06 3.02
3406 7971 1.115467 AACATGGGTGTTGCGGAAAA 58.885 45.000 0.00 0.00 46.43 2.29
3407 7972 2.814023 AACATGGGTGTTGCGGAAA 58.186 47.368 0.00 0.00 46.43 3.13


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

AutoCloner maintained by Alex Coulton.