Multiple sequence alignment - TraesCS3D01G090600

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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 TraesCS3D01G090600 chr3D 100.000 2177 0 0 1 2177 45955850 45953674 0.000000e+00 4021.0
1 TraesCS3D01G090600 chr3D 95.840 601 22 3 1 601 274344556 274345153 0.000000e+00 968.0
2 TraesCS3D01G090600 chr3D 87.935 489 33 12 1278 1760 45922822 45923290 8.780000e-154 553.0
3 TraesCS3D01G090600 chr3D 91.120 259 16 4 987 1245 45922215 45922466 5.750000e-91 344.0
4 TraesCS3D01G090600 chr3D 94.089 203 4 4 609 811 45921650 45921844 3.510000e-78 302.0
5 TraesCS3D01G090600 chr3D 100.000 51 0 0 917 967 45922026 45922076 6.400000e-16 95.3
6 TraesCS3D01G090600 chr5D 95.797 571 24 0 1 571 367421728 367422298 0.000000e+00 922.0
7 TraesCS3D01G090600 chr5D 94.921 571 26 1 1 571 15557650 15558217 0.000000e+00 891.0
8 TraesCS3D01G090600 chr5A 95.096 571 28 0 1 571 605094953 605095523 0.000000e+00 900.0
9 TraesCS3D01G090600 chrUn 95.238 567 27 0 1 567 42662648 42662082 0.000000e+00 898.0
10 TraesCS3D01G090600 chrUn 95.062 567 28 0 1 567 325821886 325822452 0.000000e+00 893.0
11 TraesCS3D01G090600 chrUn 95.062 567 28 0 1 567 325855799 325856365 0.000000e+00 893.0
12 TraesCS3D01G090600 chrUn 95.062 567 28 0 1 567 392948190 392948756 0.000000e+00 893.0
13 TraesCS3D01G090600 chrUn 95.062 567 28 0 1 567 466777440 466776874 0.000000e+00 893.0
14 TraesCS3D01G090600 chr3A 85.968 506 37 17 1267 1761 57717267 57716785 5.360000e-141 510.0
15 TraesCS3D01G090600 chr3A 85.575 513 38 19 1260 1761 57482024 57482511 2.490000e-139 505.0
16 TraesCS3D01G090600 chr3A 93.204 309 11 5 609 915 57481164 57481464 1.530000e-121 446.0
17 TraesCS3D01G090600 chr3A 92.038 314 15 5 604 915 57718137 57717832 1.190000e-117 433.0
18 TraesCS3D01G090600 chr3A 96.016 251 10 0 975 1225 57481539 57481789 2.010000e-110 409.0
19 TraesCS3D01G090600 chr3A 96.016 251 10 0 975 1225 57717757 57717507 2.010000e-110 409.0
20 TraesCS3D01G090600 chr3A 79.948 384 30 19 1818 2177 57716037 57715677 2.790000e-59 239.0
21 TraesCS3D01G090600 chr3A 78.832 137 6 13 1762 1888 57483157 57483280 1.080000e-08 71.3
22 TraesCS3D01G090600 chr3B 86.179 492 37 8 1267 1756 71554904 71554442 8.970000e-139 503.0
23 TraesCS3D01G090600 chr3B 93.307 254 15 1 975 1228 71555318 71555067 7.340000e-100 374.0
24 TraesCS3D01G090600 chr3B 88.737 293 20 8 1893 2177 71547231 71546944 1.600000e-91 346.0
25 TraesCS3D01G090600 chr3B 90.640 203 11 5 609 811 71555931 71555737 1.660000e-66 263.0
26 TraesCS3D01G090600 chr3B 94.937 79 4 0 1761 1839 71553746 71553668 8.160000e-25 124.0
27 TraesCS3D01G090600 chr3B 95.455 66 3 0 912 977 71555555 71555490 2.960000e-19 106.0
28 TraesCS3D01G090600 chr7B 86.813 91 11 1 1762 1852 642271979 642272068 1.380000e-17 100.0
29 TraesCS3D01G090600 chr7A 86.813 91 11 1 1762 1852 670568361 670568450 1.380000e-17 100.0
30 TraesCS3D01G090600 chr7D 89.610 77 8 0 1762 1838 578485560 578485636 4.950000e-17 99.0
31 TraesCS3D01G090600 chr1B 82.692 104 18 0 1018 1121 677273985 677273882 2.300000e-15 93.5


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 TraesCS3D01G090600 chr3D 45953674 45955850 2176 True 4021.000 4021 100.00000 1 2177 1 chr3D.!!$R1 2176
1 TraesCS3D01G090600 chr3D 274344556 274345153 597 False 968.000 968 95.84000 1 601 1 chr3D.!!$F1 600
2 TraesCS3D01G090600 chr3D 45921650 45923290 1640 False 323.575 553 93.28600 609 1760 4 chr3D.!!$F2 1151
3 TraesCS3D01G090600 chr5D 367421728 367422298 570 False 922.000 922 95.79700 1 571 1 chr5D.!!$F2 570
4 TraesCS3D01G090600 chr5D 15557650 15558217 567 False 891.000 891 94.92100 1 571 1 chr5D.!!$F1 570
5 TraesCS3D01G090600 chr5A 605094953 605095523 570 False 900.000 900 95.09600 1 571 1 chr5A.!!$F1 570
6 TraesCS3D01G090600 chrUn 42662082 42662648 566 True 898.000 898 95.23800 1 567 1 chrUn.!!$R1 566
7 TraesCS3D01G090600 chrUn 325821886 325822452 566 False 893.000 893 95.06200 1 567 1 chrUn.!!$F1 566
8 TraesCS3D01G090600 chrUn 325855799 325856365 566 False 893.000 893 95.06200 1 567 1 chrUn.!!$F2 566
9 TraesCS3D01G090600 chrUn 392948190 392948756 566 False 893.000 893 95.06200 1 567 1 chrUn.!!$F3 566
10 TraesCS3D01G090600 chrUn 466776874 466777440 566 True 893.000 893 95.06200 1 567 1 chrUn.!!$R2 566
11 TraesCS3D01G090600 chr3A 57715677 57718137 2460 True 397.750 510 88.49250 604 2177 4 chr3A.!!$R1 1573
12 TraesCS3D01G090600 chr3A 57481164 57483280 2116 False 357.825 505 88.40675 609 1888 4 chr3A.!!$F1 1279
13 TraesCS3D01G090600 chr3B 71553668 71555931 2263 True 274.000 503 92.10360 609 1839 5 chr3B.!!$R2 1230

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
909 1013 0.030297 AGGCCATCACCAGAGGAGAT 60.03 55.0 5.01 0.0 33.47 2.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2150 3683 0.109827 TGCGCATCGAATTTGGTGTG 60.11 50.0 5.66 14.2 0.0 3.82 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
143 144 2.289072 CGCAGAGGAAGGAGAAGAACAA 60.289 50.000 0.00 0.00 0.00 2.83
240 241 2.731571 GCCAGTGCCGATGGACCTA 61.732 63.158 3.28 0.00 40.51 3.08
316 317 1.346395 TCCTAGACGAAGGCAAAAGCA 59.654 47.619 0.00 0.00 36.51 3.91
354 355 2.170817 GGAGGCCGGAGAAACTTATTCT 59.829 50.000 5.05 0.00 0.00 2.40
394 395 4.504916 CTCGGCAGCGTCTCCCTG 62.505 72.222 0.00 0.00 0.00 4.45
417 418 1.652947 CCTAACCCTACCACACACCT 58.347 55.000 0.00 0.00 0.00 4.00
778 785 1.364626 GATCGGTGACTGGCTTGCTG 61.365 60.000 0.00 0.00 0.00 4.41
779 786 3.730761 CGGTGACTGGCTTGCTGC 61.731 66.667 0.00 0.00 41.94 5.25
780 787 2.282040 GGTGACTGGCTTGCTGCT 60.282 61.111 0.00 0.00 42.39 4.24
781 788 1.900498 GGTGACTGGCTTGCTGCTT 60.900 57.895 0.00 0.00 42.39 3.91
782 789 1.458639 GGTGACTGGCTTGCTGCTTT 61.459 55.000 0.00 0.00 42.39 3.51
783 790 0.039708 GTGACTGGCTTGCTGCTTTC 60.040 55.000 0.00 0.00 42.39 2.62
784 791 1.174712 TGACTGGCTTGCTGCTTTCC 61.175 55.000 0.00 0.00 42.39 3.13
785 792 2.192608 GACTGGCTTGCTGCTTTCCG 62.193 60.000 0.00 0.00 42.39 4.30
786 793 2.985282 TGGCTTGCTGCTTTCCGG 60.985 61.111 0.00 0.00 42.39 5.14
787 794 2.985847 GGCTTGCTGCTTTCCGGT 60.986 61.111 0.00 0.00 42.39 5.28
817 824 3.524648 GACGGGCGGACCTTTCACA 62.525 63.158 0.00 0.00 36.97 3.58
903 1007 4.100084 CCGCAGGCCATCACCAGA 62.100 66.667 5.01 0.00 46.14 3.86
904 1008 2.513204 CGCAGGCCATCACCAGAG 60.513 66.667 5.01 0.00 0.00 3.35
905 1009 2.124403 GCAGGCCATCACCAGAGG 60.124 66.667 5.01 0.00 0.00 3.69
906 1010 2.673200 GCAGGCCATCACCAGAGGA 61.673 63.158 5.01 0.00 0.00 3.71
907 1011 1.525923 CAGGCCATCACCAGAGGAG 59.474 63.158 5.01 0.00 0.00 3.69
908 1012 0.979709 CAGGCCATCACCAGAGGAGA 60.980 60.000 5.01 0.00 0.00 3.71
909 1013 0.030297 AGGCCATCACCAGAGGAGAT 60.030 55.000 5.01 0.00 33.47 2.75
910 1014 0.108207 GGCCATCACCAGAGGAGATG 59.892 60.000 14.17 14.17 45.76 2.90
915 1019 2.450867 TCACCAGAGGAGATGAGAGG 57.549 55.000 0.00 0.00 0.00 3.69
967 1076 6.092122 CACAGTTTCAGTCTCAGTTGTTACAA 59.908 38.462 0.00 0.00 0.00 2.41
968 1077 6.653320 ACAGTTTCAGTCTCAGTTGTTACAAA 59.347 34.615 0.00 0.00 0.00 2.83
972 1081 8.662141 GTTTCAGTCTCAGTTGTTACAAACTTA 58.338 33.333 0.00 0.00 38.34 2.24
982 1309 0.390209 TACAAACTTAGCCCCGCGTC 60.390 55.000 4.92 0.00 0.00 5.19
1176 1503 1.078759 CCGGCAAGCTGTTCGACTAG 61.079 60.000 0.00 0.00 0.00 2.57
1225 1552 2.801996 CGTTCCGTCACGCGCTAA 60.802 61.111 5.73 0.00 39.71 3.09
1226 1553 2.767697 GTTCCGTCACGCGCTAAC 59.232 61.111 5.73 0.14 39.71 2.34
1228 1555 3.919973 TTCCGTCACGCGCTAACCC 62.920 63.158 5.73 0.00 39.71 4.11
1240 1567 2.539476 CGCTAACCCATTTGGATTTGC 58.461 47.619 0.53 0.53 37.39 3.68
1245 1572 4.980339 AACCCATTTGGATTTGCTTCTT 57.020 36.364 0.00 0.00 37.39 2.52
1246 1573 4.541973 ACCCATTTGGATTTGCTTCTTC 57.458 40.909 0.00 0.00 37.39 2.87
1247 1574 3.056607 ACCCATTTGGATTTGCTTCTTCG 60.057 43.478 0.00 0.00 37.39 3.79
1250 1577 5.095490 CCATTTGGATTTGCTTCTTCGTAC 58.905 41.667 0.00 0.00 37.39 3.67
1251 1578 4.398549 TTTGGATTTGCTTCTTCGTACG 57.601 40.909 9.53 9.53 0.00 3.67
1253 1580 4.177165 TGGATTTGCTTCTTCGTACGTA 57.823 40.909 16.05 4.53 0.00 3.57
1254 1581 3.922240 TGGATTTGCTTCTTCGTACGTAC 59.078 43.478 15.90 15.90 0.00 3.67
1270 1940 3.683802 ACGTACGCCCTATCTAGCTATT 58.316 45.455 16.72 0.00 0.00 1.73
1282 1952 8.367911 CCCTATCTAGCTATTGTTGTGACATAA 58.632 37.037 0.00 0.00 35.29 1.90
1297 1967 9.490663 GTTGTGACATAATTATACTTGACTTGC 57.509 33.333 0.00 0.00 0.00 4.01
1438 2127 7.791029 TCCAGTCATGTACAACATACATACAT 58.209 34.615 0.00 0.00 36.53 2.29
1461 2150 9.371136 ACATACATACATTTGTACACTCAAGAG 57.629 33.333 0.00 0.00 35.04 2.85
1462 2151 9.371136 CATACATACATTTGTACACTCAAGAGT 57.629 33.333 0.00 0.00 36.69 3.24
1530 2234 4.347453 CAGCAGCAACCGTTGGCC 62.347 66.667 13.12 0.00 0.00 5.36
1552 2256 0.760567 TATCATCGCAGGGCTGAGGT 60.761 55.000 0.00 0.00 0.00 3.85
1569 2273 0.320771 GGTGTGAGCATGACCGTCTT 60.321 55.000 0.00 0.00 0.00 3.01
1579 2283 3.240134 GACCGTCTTGAGGCCAGCA 62.240 63.158 5.01 0.00 0.00 4.41
1613 2317 1.330655 GGAGAAGACCTGCCATCCGA 61.331 60.000 0.00 0.00 0.00 4.55
1666 2370 1.078918 CGGCTGGAGTTCATGCTGA 60.079 57.895 0.00 0.00 34.02 4.26
1684 2388 1.266718 TGAGCAAAGTCCGTGAAATGC 59.733 47.619 0.00 0.00 0.00 3.56
1793 3248 8.223177 TCTAGCTTAAACTTACTAGTAGCAGG 57.777 38.462 12.73 6.08 36.42 4.85
1794 3249 5.662456 AGCTTAAACTTACTAGTAGCAGGC 58.338 41.667 12.73 8.13 36.42 4.85
1795 3250 4.809958 GCTTAAACTTACTAGTAGCAGGCC 59.190 45.833 2.23 0.00 34.85 5.19
1796 3251 5.626116 GCTTAAACTTACTAGTAGCAGGCCA 60.626 44.000 5.01 0.00 34.85 5.36
1797 3252 4.473477 AAACTTACTAGTAGCAGGCCAG 57.527 45.455 5.01 0.00 33.17 4.85
1798 3253 3.103080 ACTTACTAGTAGCAGGCCAGT 57.897 47.619 5.01 0.00 31.21 4.00
1799 3254 4.246712 ACTTACTAGTAGCAGGCCAGTA 57.753 45.455 5.01 0.00 31.21 2.74
1800 3255 4.208746 ACTTACTAGTAGCAGGCCAGTAG 58.791 47.826 5.01 3.07 31.21 2.57
1801 3256 2.830651 ACTAGTAGCAGGCCAGTAGT 57.169 50.000 5.01 3.79 0.00 2.73
1802 3257 2.379972 ACTAGTAGCAGGCCAGTAGTG 58.620 52.381 5.01 0.00 31.26 2.74
1803 3258 2.025226 ACTAGTAGCAGGCCAGTAGTGA 60.025 50.000 5.01 0.00 31.26 3.41
1804 3259 1.479709 AGTAGCAGGCCAGTAGTGAG 58.520 55.000 5.01 0.00 0.00 3.51
1805 3260 0.461961 GTAGCAGGCCAGTAGTGAGG 59.538 60.000 5.01 0.00 0.00 3.86
1806 3261 0.687757 TAGCAGGCCAGTAGTGAGGG 60.688 60.000 5.01 0.00 0.00 4.30
1809 3264 4.375406 GGCCAGTAGTGAGGGCTA 57.625 61.111 0.00 0.00 46.87 3.93
1810 3265 2.604118 GGCCAGTAGTGAGGGCTAA 58.396 57.895 0.00 0.00 46.87 3.09
1811 3266 0.466124 GGCCAGTAGTGAGGGCTAAG 59.534 60.000 0.00 0.00 46.87 2.18
1812 3267 0.466124 GCCAGTAGTGAGGGCTAAGG 59.534 60.000 0.00 0.00 44.32 2.69
1813 3268 1.965318 GCCAGTAGTGAGGGCTAAGGA 60.965 57.143 0.00 0.00 44.32 3.36
1814 3269 1.757699 CCAGTAGTGAGGGCTAAGGAC 59.242 57.143 0.00 0.00 0.00 3.85
1815 3270 1.757699 CAGTAGTGAGGGCTAAGGACC 59.242 57.143 0.00 0.00 42.21 4.46
1857 3356 6.266323 ACATATACGTCAACAAGTAGCAGAG 58.734 40.000 0.00 0.00 0.00 3.35
1874 3377 1.064389 AGAGGCCAGTATTTTGCTCCC 60.064 52.381 5.01 0.00 0.00 4.30
1888 3391 0.890683 GCTCCCCACAATTTCCTGTG 59.109 55.000 0.00 0.00 45.24 3.66
1915 3437 9.492973 TGACATATAGTATCATGTTGGTTCATG 57.507 33.333 0.00 0.00 44.36 3.07
1928 3450 5.068329 TGTTGGTTCATGTGAATTTACTGCA 59.932 36.000 1.75 0.00 36.33 4.41
1935 3458 6.437928 TCATGTGAATTTACTGCAGTGTTTC 58.562 36.000 29.57 24.72 0.00 2.78
1965 3488 3.520290 AGTGTTGAAACTCTGACGTGA 57.480 42.857 0.00 0.00 32.09 4.35
1968 3491 4.271049 AGTGTTGAAACTCTGACGTGAATG 59.729 41.667 0.00 0.00 32.09 2.67
1969 3492 3.559655 TGTTGAAACTCTGACGTGAATGG 59.440 43.478 0.00 0.00 0.00 3.16
1970 3493 3.744238 TGAAACTCTGACGTGAATGGA 57.256 42.857 0.00 0.00 0.00 3.41
1971 3494 4.271696 TGAAACTCTGACGTGAATGGAT 57.728 40.909 0.00 0.00 0.00 3.41
1972 3495 4.641396 TGAAACTCTGACGTGAATGGATT 58.359 39.130 0.00 0.00 0.00 3.01
1973 3496 4.452114 TGAAACTCTGACGTGAATGGATTG 59.548 41.667 0.00 0.00 0.00 2.67
1974 3497 3.961480 ACTCTGACGTGAATGGATTGA 57.039 42.857 0.00 0.00 0.00 2.57
1975 3498 4.478206 ACTCTGACGTGAATGGATTGAT 57.522 40.909 0.00 0.00 0.00 2.57
1976 3499 4.437239 ACTCTGACGTGAATGGATTGATC 58.563 43.478 0.00 0.00 0.00 2.92
1977 3500 4.081476 ACTCTGACGTGAATGGATTGATCA 60.081 41.667 0.00 0.00 0.00 2.92
1978 3501 4.831107 TCTGACGTGAATGGATTGATCAA 58.169 39.130 11.26 11.26 0.00 2.57
1989 3512 5.913137 TGGATTGATCAAAACATGGGTAC 57.087 39.130 13.09 0.00 0.00 3.34
1991 3514 5.418524 TGGATTGATCAAAACATGGGTACTG 59.581 40.000 13.09 0.00 0.00 2.74
1992 3515 4.782019 TTGATCAAAACATGGGTACTGC 57.218 40.909 5.45 0.00 0.00 4.40
1999 3522 5.012251 TCAAAACATGGGTACTGCACTACTA 59.988 40.000 0.00 0.00 0.00 1.82
2000 3523 5.693769 AAACATGGGTACTGCACTACTAT 57.306 39.130 0.00 0.00 0.00 2.12
2005 3528 5.950544 TGGGTACTGCACTACTATGATTT 57.049 39.130 3.91 0.00 0.00 2.17
2042 3565 3.689649 CGCCAAGCTTTATTAGTCAACCT 59.310 43.478 0.00 0.00 0.00 3.50
2043 3566 4.437390 CGCCAAGCTTTATTAGTCAACCTG 60.437 45.833 0.00 0.00 0.00 4.00
2044 3567 4.459337 GCCAAGCTTTATTAGTCAACCTGT 59.541 41.667 0.00 0.00 0.00 4.00
2045 3568 5.392057 GCCAAGCTTTATTAGTCAACCTGTC 60.392 44.000 0.00 0.00 0.00 3.51
2046 3569 5.705441 CCAAGCTTTATTAGTCAACCTGTCA 59.295 40.000 0.00 0.00 0.00 3.58
2047 3570 6.206634 CCAAGCTTTATTAGTCAACCTGTCAA 59.793 38.462 0.00 0.00 0.00 3.18
2048 3571 6.803154 AGCTTTATTAGTCAACCTGTCAAC 57.197 37.500 0.00 0.00 0.00 3.18
2049 3572 5.705905 AGCTTTATTAGTCAACCTGTCAACC 59.294 40.000 0.00 0.00 0.00 3.77
2052 3575 7.309194 GCTTTATTAGTCAACCTGTCAACCATT 60.309 37.037 0.00 0.00 0.00 3.16
2069 3592 3.160269 CCATTGCTTCCTTCTTCCTTGT 58.840 45.455 0.00 0.00 0.00 3.16
2077 3600 1.479389 CCTTCTTCCTTGTGGCCTTGT 60.479 52.381 3.32 0.00 0.00 3.16
2090 3623 0.166814 GCCTTGTCGAGCATTGTGTC 59.833 55.000 0.00 0.00 0.00 3.67
2091 3624 0.798776 CCTTGTCGAGCATTGTGTCC 59.201 55.000 0.00 0.00 0.00 4.02
2092 3625 0.798776 CTTGTCGAGCATTGTGTCCC 59.201 55.000 0.00 0.00 0.00 4.46
2093 3626 0.948623 TTGTCGAGCATTGTGTCCCG 60.949 55.000 0.00 0.00 0.00 5.14
2094 3627 2.100631 GTCGAGCATTGTGTCCCGG 61.101 63.158 0.00 0.00 0.00 5.73
2095 3628 2.819595 CGAGCATTGTGTCCCGGG 60.820 66.667 16.85 16.85 0.00 5.73
2096 3629 3.134127 GAGCATTGTGTCCCGGGC 61.134 66.667 18.49 12.24 0.00 6.13
2097 3630 3.628646 GAGCATTGTGTCCCGGGCT 62.629 63.158 18.49 6.42 0.00 5.19
2138 3671 2.557317 ACCAAAACAGGTGTCGTACAG 58.443 47.619 0.00 0.00 41.30 2.74
2150 3683 0.320421 TCGTACAGGCCTTGCAAGTC 60.320 55.000 24.35 12.71 0.00 3.01
2161 3694 3.383761 CCTTGCAAGTCACACCAAATTC 58.616 45.455 24.35 0.00 0.00 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
143 144 3.156293 TGTTGGTATGATTTGCTGCTGT 58.844 40.909 0.00 0.00 0.00 4.40
337 338 2.603560 CGTCAGAATAAGTTTCTCCGGC 59.396 50.000 0.00 0.00 0.00 6.13
394 395 1.980036 TGTGTGGTAGGGTTAGGGTTC 59.020 52.381 0.00 0.00 0.00 3.62
417 418 0.035152 TCGGGTCTGTTCGCTAGGTA 60.035 55.000 0.00 0.00 0.00 3.08
475 476 2.441532 CCGCCGGTTCCCTCTCTA 60.442 66.667 1.90 0.00 0.00 2.43
601 605 3.393800 GTGAGTGACCCCGATCATATTG 58.606 50.000 0.00 0.00 0.00 1.90
602 606 2.035961 CGTGAGTGACCCCGATCATATT 59.964 50.000 0.00 0.00 0.00 1.28
817 824 4.073549 GGCGACTAGTGATGGATAGTACT 58.926 47.826 0.00 0.00 32.43 2.73
885 989 4.100084 CTGGTGATGGCCTGCGGA 62.100 66.667 3.32 0.00 0.00 5.54
886 990 4.100084 TCTGGTGATGGCCTGCGG 62.100 66.667 3.32 0.00 0.00 5.69
887 991 2.513204 CTCTGGTGATGGCCTGCG 60.513 66.667 3.32 0.00 0.00 5.18
888 992 2.124403 CCTCTGGTGATGGCCTGC 60.124 66.667 3.32 0.00 0.00 4.85
890 994 0.030297 ATCTCCTCTGGTGATGGCCT 60.030 55.000 3.32 0.00 35.04 5.19
891 995 0.108207 CATCTCCTCTGGTGATGGCC 59.892 60.000 16.48 0.00 44.88 5.36
892 996 3.702147 CATCTCCTCTGGTGATGGC 57.298 57.895 16.48 0.00 44.88 4.40
895 999 2.517553 TCCTCTCATCTCCTCTGGTGAT 59.482 50.000 0.00 0.00 36.51 3.06
897 1001 2.091939 TCTCCTCTCATCTCCTCTGGTG 60.092 54.545 0.00 0.00 0.00 4.17
898 1002 2.175499 CTCTCCTCTCATCTCCTCTGGT 59.825 54.545 0.00 0.00 0.00 4.00
899 1003 2.489619 CCTCTCCTCTCATCTCCTCTGG 60.490 59.091 0.00 0.00 0.00 3.86
900 1004 2.442878 TCCTCTCCTCTCATCTCCTCTG 59.557 54.545 0.00 0.00 0.00 3.35
901 1005 2.713167 CTCCTCTCCTCTCATCTCCTCT 59.287 54.545 0.00 0.00 0.00 3.69
902 1006 2.711009 TCTCCTCTCCTCTCATCTCCTC 59.289 54.545 0.00 0.00 0.00 3.71
903 1007 2.713167 CTCTCCTCTCCTCTCATCTCCT 59.287 54.545 0.00 0.00 0.00 3.69
904 1008 2.224867 CCTCTCCTCTCCTCTCATCTCC 60.225 59.091 0.00 0.00 0.00 3.71
905 1009 2.711009 TCCTCTCCTCTCCTCTCATCTC 59.289 54.545 0.00 0.00 0.00 2.75
906 1010 2.713167 CTCCTCTCCTCTCCTCTCATCT 59.287 54.545 0.00 0.00 0.00 2.90
907 1011 2.711009 TCTCCTCTCCTCTCCTCTCATC 59.289 54.545 0.00 0.00 0.00 2.92
908 1012 2.713167 CTCTCCTCTCCTCTCCTCTCAT 59.287 54.545 0.00 0.00 0.00 2.90
909 1013 2.126882 CTCTCCTCTCCTCTCCTCTCA 58.873 57.143 0.00 0.00 0.00 3.27
910 1014 1.202818 GCTCTCCTCTCCTCTCCTCTC 60.203 61.905 0.00 0.00 0.00 3.20
911 1015 0.846693 GCTCTCCTCTCCTCTCCTCT 59.153 60.000 0.00 0.00 0.00 3.69
912 1016 0.550914 TGCTCTCCTCTCCTCTCCTC 59.449 60.000 0.00 0.00 0.00 3.71
913 1017 0.258774 GTGCTCTCCTCTCCTCTCCT 59.741 60.000 0.00 0.00 0.00 3.69
914 1018 0.033601 TGTGCTCTCCTCTCCTCTCC 60.034 60.000 0.00 0.00 0.00 3.71
915 1019 1.102978 GTGTGCTCTCCTCTCCTCTC 58.897 60.000 0.00 0.00 0.00 3.20
967 1076 4.091939 GGGACGCGGGGCTAAGTT 62.092 66.667 12.47 0.00 0.00 2.66
982 1309 2.641305 CATCTTCTCTCTTGGCTTGGG 58.359 52.381 0.00 0.00 0.00 4.12
985 1312 1.064832 GCCCATCTTCTCTCTTGGCTT 60.065 52.381 0.00 0.00 34.61 4.35
1127 1454 3.441290 CGAAGACGAGGAGGCCGT 61.441 66.667 0.00 0.00 43.56 5.68
1176 1503 3.977244 CTTGTGTTGGGGGCGCAC 61.977 66.667 10.83 4.83 0.00 5.34
1225 1552 3.056607 CGAAGAAGCAAATCCAAATGGGT 60.057 43.478 0.00 0.00 38.11 4.51
1226 1553 3.056607 ACGAAGAAGCAAATCCAAATGGG 60.057 43.478 0.00 0.00 35.41 4.00
1228 1555 4.788100 CGTACGAAGAAGCAAATCCAAATG 59.212 41.667 10.44 0.00 0.00 2.32
1247 1574 2.421619 AGCTAGATAGGGCGTACGTAC 58.578 52.381 17.90 15.90 0.00 3.67
1250 1577 3.439476 ACAATAGCTAGATAGGGCGTACG 59.561 47.826 11.84 11.84 0.00 3.67
1251 1578 5.162075 CAACAATAGCTAGATAGGGCGTAC 58.838 45.833 0.00 0.00 0.00 3.67
1253 1580 3.641906 ACAACAATAGCTAGATAGGGCGT 59.358 43.478 0.00 0.00 0.00 5.68
1254 1581 3.990469 CACAACAATAGCTAGATAGGGCG 59.010 47.826 0.00 0.00 0.00 6.13
1255 1582 4.991687 GTCACAACAATAGCTAGATAGGGC 59.008 45.833 0.00 0.00 0.00 5.19
1256 1583 6.161855 TGTCACAACAATAGCTAGATAGGG 57.838 41.667 0.00 0.00 30.70 3.53
1257 1584 9.935241 ATTATGTCACAACAATAGCTAGATAGG 57.065 33.333 0.00 0.00 39.30 2.57
1282 1952 8.190784 GCTTAACAATGGCAAGTCAAGTATAAT 58.809 33.333 7.80 0.00 0.00 1.28
1297 1967 1.667724 CTCGCTCCAGCTTAACAATGG 59.332 52.381 0.00 0.00 39.32 3.16
1443 2132 9.826574 TTAACTAACTCTTGAGTGTACAAATGT 57.173 29.630 0.00 0.00 0.00 2.71
1446 2135 9.309516 CAGTTAACTAACTCTTGAGTGTACAAA 57.690 33.333 8.04 0.00 44.19 2.83
1447 2136 7.437267 GCAGTTAACTAACTCTTGAGTGTACAA 59.563 37.037 8.04 0.00 44.19 2.41
1448 2137 6.921857 GCAGTTAACTAACTCTTGAGTGTACA 59.078 38.462 8.04 0.00 44.19 2.90
1449 2138 6.921857 TGCAGTTAACTAACTCTTGAGTGTAC 59.078 38.462 8.04 0.00 44.19 2.90
1450 2139 7.046292 TGCAGTTAACTAACTCTTGAGTGTA 57.954 36.000 8.04 0.00 44.19 2.90
1451 2140 5.914033 TGCAGTTAACTAACTCTTGAGTGT 58.086 37.500 8.04 0.00 44.19 3.55
1452 2141 6.619446 GCATGCAGTTAACTAACTCTTGAGTG 60.619 42.308 14.21 0.00 44.19 3.51
1453 2142 5.409826 GCATGCAGTTAACTAACTCTTGAGT 59.590 40.000 14.21 0.00 44.19 3.41
1454 2143 5.641209 AGCATGCAGTTAACTAACTCTTGAG 59.359 40.000 21.98 0.00 44.19 3.02
1455 2144 5.551233 AGCATGCAGTTAACTAACTCTTGA 58.449 37.500 21.98 0.00 44.19 3.02
1456 2145 5.869753 AGCATGCAGTTAACTAACTCTTG 57.130 39.130 21.98 7.58 44.19 3.02
1457 2146 6.246420 CAAGCATGCAGTTAACTAACTCTT 57.754 37.500 21.98 5.77 44.19 2.85
1458 2147 5.869753 CAAGCATGCAGTTAACTAACTCT 57.130 39.130 21.98 0.00 44.19 3.24
1552 2256 0.678950 TCAAGACGGTCATGCTCACA 59.321 50.000 11.27 0.00 0.00 3.58
1569 2273 2.372890 CCTCCTCATGCTGGCCTCA 61.373 63.158 3.32 1.86 0.00 3.86
1579 2283 1.760086 CTCCGGTCTGCCTCCTCAT 60.760 63.158 0.00 0.00 0.00 2.90
1623 2327 1.934956 CAGATCGTCGAGTTCCGCG 60.935 63.158 0.00 0.00 38.47 6.46
1660 2364 0.035317 TCACGGACTTTGCTCAGCAT 59.965 50.000 0.00 0.00 38.76 3.79
1666 2370 1.267806 CTGCATTTCACGGACTTTGCT 59.732 47.619 0.00 0.00 0.00 3.91
1684 2388 1.560004 CTGCAGCACGTGTGTACCTG 61.560 60.000 18.38 15.67 32.64 4.00
1707 2413 1.130955 GCACCACAGAATTTTGTGCG 58.869 50.000 20.74 16.30 45.52 5.34
1753 2459 7.946655 TTAAGCTAGATTCGTTATGTCATGG 57.053 36.000 0.00 0.00 0.00 3.66
1792 3247 0.466124 CTTAGCCCTCACTACTGGCC 59.534 60.000 0.00 0.00 46.55 5.36
1793 3248 0.466124 CCTTAGCCCTCACTACTGGC 59.534 60.000 0.00 0.00 45.70 4.85
1794 3249 1.757699 GTCCTTAGCCCTCACTACTGG 59.242 57.143 0.00 0.00 0.00 4.00
1795 3250 1.757699 GGTCCTTAGCCCTCACTACTG 59.242 57.143 0.00 0.00 0.00 2.74
1796 3251 1.343176 GGGTCCTTAGCCCTCACTACT 60.343 57.143 0.00 0.00 42.81 2.57
1797 3252 1.121378 GGGTCCTTAGCCCTCACTAC 58.879 60.000 0.00 0.00 42.81 2.73
1798 3253 0.396695 CGGGTCCTTAGCCCTCACTA 60.397 60.000 0.00 0.00 43.92 2.74
1799 3254 1.686110 CGGGTCCTTAGCCCTCACT 60.686 63.158 0.00 0.00 43.92 3.41
1800 3255 2.732619 CCGGGTCCTTAGCCCTCAC 61.733 68.421 0.00 0.00 43.92 3.51
1801 3256 2.365105 CCGGGTCCTTAGCCCTCA 60.365 66.667 0.00 0.00 43.92 3.86
1802 3257 3.862991 GCCGGGTCCTTAGCCCTC 61.863 72.222 2.18 0.00 43.92 4.30
1805 3260 1.842010 ATAGGCCGGGTCCTTAGCC 60.842 63.158 13.96 8.76 46.13 3.93
1806 3261 1.371558 CATAGGCCGGGTCCTTAGC 59.628 63.158 13.96 0.00 37.66 3.09
1807 3262 1.070289 GAACATAGGCCGGGTCCTTAG 59.930 57.143 13.96 10.03 37.66 2.18
1808 3263 1.125633 GAACATAGGCCGGGTCCTTA 58.874 55.000 13.96 0.00 37.66 2.69
1809 3264 0.912487 TGAACATAGGCCGGGTCCTT 60.912 55.000 13.96 0.00 37.66 3.36
1810 3265 1.306654 TGAACATAGGCCGGGTCCT 60.307 57.895 2.18 13.39 40.21 3.85
1811 3266 1.146263 CTGAACATAGGCCGGGTCC 59.854 63.158 2.18 0.00 0.00 4.46
1812 3267 0.179081 GTCTGAACATAGGCCGGGTC 60.179 60.000 2.18 0.00 0.00 4.46
1813 3268 1.905512 GTCTGAACATAGGCCGGGT 59.094 57.895 2.18 0.00 0.00 5.28
1814 3269 1.227263 CGTCTGAACATAGGCCGGG 60.227 63.158 2.18 0.00 0.00 5.73
1815 3270 0.527817 GTCGTCTGAACATAGGCCGG 60.528 60.000 0.00 0.00 0.00 6.13
1816 3271 0.172578 TGTCGTCTGAACATAGGCCG 59.827 55.000 0.00 0.00 0.00 6.13
1857 3356 0.324275 TGGGGAGCAAAATACTGGCC 60.324 55.000 0.00 0.00 0.00 5.36
1888 3391 8.887036 TGAACCAACATGATACTATATGTCAC 57.113 34.615 0.00 0.00 36.56 3.67
1904 3426 5.068329 TGCAGTAAATTCACATGAACCAACA 59.932 36.000 0.00 0.00 36.80 3.33
1915 3437 8.743099 GTTAAAGAAACACTGCAGTAAATTCAC 58.257 33.333 26.83 17.95 38.05 3.18
1945 3468 3.520290 TCACGTCAGAGTTTCAACACT 57.480 42.857 0.00 0.00 0.00 3.55
1960 3483 5.703978 TGTTTTGATCAATCCATTCACGT 57.296 34.783 9.40 0.00 0.00 4.49
1962 3485 5.813672 CCCATGTTTTGATCAATCCATTCAC 59.186 40.000 9.40 0.00 0.00 3.18
1964 3487 5.981174 ACCCATGTTTTGATCAATCCATTC 58.019 37.500 9.40 0.00 0.00 2.67
1965 3488 6.669154 AGTACCCATGTTTTGATCAATCCATT 59.331 34.615 9.40 3.06 0.00 3.16
1968 3491 5.679638 GCAGTACCCATGTTTTGATCAATCC 60.680 44.000 9.40 3.51 0.00 3.01
1969 3492 5.105797 TGCAGTACCCATGTTTTGATCAATC 60.106 40.000 9.40 6.59 0.00 2.67
1970 3493 4.771577 TGCAGTACCCATGTTTTGATCAAT 59.228 37.500 9.40 0.00 0.00 2.57
1971 3494 4.022416 GTGCAGTACCCATGTTTTGATCAA 60.022 41.667 3.38 3.38 0.00 2.57
1972 3495 3.505680 GTGCAGTACCCATGTTTTGATCA 59.494 43.478 0.00 0.00 0.00 2.92
1973 3496 3.758554 AGTGCAGTACCCATGTTTTGATC 59.241 43.478 0.00 0.00 0.00 2.92
1974 3497 3.766545 AGTGCAGTACCCATGTTTTGAT 58.233 40.909 0.00 0.00 0.00 2.57
1975 3498 3.222173 AGTGCAGTACCCATGTTTTGA 57.778 42.857 0.00 0.00 0.00 2.69
1976 3499 4.072131 AGTAGTGCAGTACCCATGTTTTG 58.928 43.478 24.85 0.00 0.00 2.44
1977 3500 4.367039 AGTAGTGCAGTACCCATGTTTT 57.633 40.909 24.85 4.28 0.00 2.43
1978 3501 5.188948 TCATAGTAGTGCAGTACCCATGTTT 59.811 40.000 27.13 14.33 0.00 2.83
2016 3539 6.204882 GGTTGACTAATAAAGCTTGGCGATAT 59.795 38.462 0.00 0.00 0.00 1.63
2017 3540 5.526111 GGTTGACTAATAAAGCTTGGCGATA 59.474 40.000 0.00 0.00 0.00 2.92
2018 3541 4.335594 GGTTGACTAATAAAGCTTGGCGAT 59.664 41.667 0.00 0.00 0.00 4.58
2019 3542 3.687698 GGTTGACTAATAAAGCTTGGCGA 59.312 43.478 0.00 0.00 0.00 5.54
2020 3543 3.689649 AGGTTGACTAATAAAGCTTGGCG 59.310 43.478 0.00 0.00 30.18 5.69
2042 3565 3.228188 AGAAGGAAGCAATGGTTGACA 57.772 42.857 1.11 0.00 0.00 3.58
2043 3566 3.057245 GGAAGAAGGAAGCAATGGTTGAC 60.057 47.826 1.11 0.00 0.00 3.18
2044 3567 3.157087 GGAAGAAGGAAGCAATGGTTGA 58.843 45.455 1.11 0.00 0.00 3.18
2045 3568 3.160269 AGGAAGAAGGAAGCAATGGTTG 58.840 45.455 1.11 0.00 0.00 3.77
2046 3569 3.532641 AGGAAGAAGGAAGCAATGGTT 57.467 42.857 0.00 0.00 0.00 3.67
2047 3570 3.160269 CAAGGAAGAAGGAAGCAATGGT 58.840 45.455 0.00 0.00 0.00 3.55
2048 3571 3.057033 CACAAGGAAGAAGGAAGCAATGG 60.057 47.826 0.00 0.00 0.00 3.16
2049 3572 3.057033 CCACAAGGAAGAAGGAAGCAATG 60.057 47.826 0.00 0.00 36.89 2.82
2052 3575 1.819305 GCCACAAGGAAGAAGGAAGCA 60.819 52.381 0.00 0.00 36.89 3.91
2069 3592 1.073025 ACAATGCTCGACAAGGCCA 59.927 52.632 5.01 0.00 0.00 5.36
2077 3600 2.264480 CCGGGACACAATGCTCGA 59.736 61.111 0.00 0.00 0.00 4.04
2138 3671 1.391157 TTGGTGTGACTTGCAAGGCC 61.391 55.000 29.26 20.01 31.13 5.19
2150 3683 0.109827 TGCGCATCGAATTTGGTGTG 60.110 50.000 5.66 14.20 0.00 3.82


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

AutoCloner maintained by Alex Coulton.