Multiple sequence alignment - TraesCS4A01G067900

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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 TraesCS4A01G067900 chr4A 100.000 3880 0 0 1 3880 66337206 66341085 0.000000e+00 7166.0
1 TraesCS4A01G067900 chr4A 77.255 255 31 20 286 517 7336906 7336656 1.460000e-24 124.0
2 TraesCS4A01G067900 chr4A 75.758 264 40 16 283 527 172893148 172892890 1.140000e-20 111.0
3 TraesCS4A01G067900 chr4A 75.191 262 42 18 284 527 211586431 211586175 6.860000e-18 102.0
4 TraesCS4A01G067900 chr4A 90.323 62 6 0 1615 1676 573326969 573326908 8.930000e-12 82.4
5 TraesCS4A01G067900 chr4B 90.980 3326 170 54 1 3266 471651436 471654691 0.000000e+00 4361.0
6 TraesCS4A01G067900 chr4B 84.043 94 13 2 435 527 603763999 603763907 5.340000e-14 89.8
7 TraesCS4A01G067900 chr4B 86.957 69 9 0 1606 1674 42395475 42395543 1.160000e-10 78.7
8 TraesCS4A01G067900 chr4D 93.306 2898 103 40 531 3378 384669620 384672476 0.000000e+00 4193.0
9 TraesCS4A01G067900 chr4D 81.298 262 28 13 285 527 293136713 293136972 3.960000e-45 193.0
10 TraesCS4A01G067900 chr4D 72.696 293 63 16 1386 1674 29828330 29828609 8.930000e-12 82.4
11 TraesCS4A01G067900 chr1A 95.833 504 18 3 3378 3880 476976978 476977479 0.000000e+00 811.0
12 TraesCS4A01G067900 chr1A 95.618 502 19 3 3378 3878 579825487 579825986 0.000000e+00 802.0
13 TraesCS4A01G067900 chr7A 94.455 523 23 6 3361 3880 16067293 16067812 0.000000e+00 800.0
14 TraesCS4A01G067900 chr7A 85.981 107 13 2 284 389 204178427 204178322 3.170000e-21 113.0
15 TraesCS4A01G067900 chr2A 95.079 508 20 5 3375 3880 687137038 687137542 0.000000e+00 795.0
16 TraesCS4A01G067900 chr2A 94.444 504 24 4 3378 3880 724114075 724113575 0.000000e+00 773.0
17 TraesCS4A01G067900 chr2A 82.468 154 20 7 283 432 657525936 657525786 1.130000e-25 128.0
18 TraesCS4A01G067900 chr2A 76.866 134 24 7 398 527 239765373 239765243 6.960000e-08 69.4
19 TraesCS4A01G067900 chr6A 94.488 508 24 4 3375 3880 32608038 32608543 0.000000e+00 780.0
20 TraesCS4A01G067900 chr5A 94.643 504 24 3 3378 3880 300371722 300371221 0.000000e+00 778.0
21 TraesCS4A01G067900 chr5A 94.477 507 25 3 3374 3879 673519158 673519662 0.000000e+00 778.0
22 TraesCS4A01G067900 chr5A 85.542 83 10 2 446 527 287442959 287443040 6.910000e-13 86.1
23 TraesCS4A01G067900 chr3A 94.466 506 24 4 3376 3880 642706677 642707179 0.000000e+00 776.0
24 TraesCS4A01G067900 chr3A 78.968 252 49 4 1838 2087 623777529 623777778 6.670000e-38 169.0
25 TraesCS4A01G067900 chr3A 85.882 85 11 1 283 366 117294899 117294815 5.340000e-14 89.8
26 TraesCS4A01G067900 chr3A 73.864 264 48 17 283 528 745383986 745384246 6.910000e-13 86.1
27 TraesCS4A01G067900 chr3B 79.608 255 42 9 1838 2087 641805196 641805445 1.430000e-39 174.0
28 TraesCS4A01G067900 chr3B 76.050 238 38 19 295 528 747751382 747751160 5.300000e-19 106.0
29 TraesCS4A01G067900 chr3D 77.778 252 52 4 1838 2087 480969939 480970188 6.710000e-33 152.0
30 TraesCS4A01G067900 chr3D 74.886 219 35 18 326 527 269731917 269732132 8.930000e-12 82.4
31 TraesCS4A01G067900 chr6D 90.361 83 7 1 282 363 360056775 360056693 1.470000e-19 108.0
32 TraesCS4A01G067900 chr6D 81.022 137 17 7 283 411 11083664 11083529 2.470000e-17 100.0
33 TraesCS4A01G067900 chr7D 83.333 108 14 4 283 387 426171936 426172042 3.190000e-16 97.1
34 TraesCS4A01G067900 chr7B 73.705 251 46 18 283 516 533100997 533100750 3.210000e-11 80.5


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 TraesCS4A01G067900 chr4A 66337206 66341085 3879 False 7166 7166 100.000 1 3880 1 chr4A.!!$F1 3879
1 TraesCS4A01G067900 chr4B 471651436 471654691 3255 False 4361 4361 90.980 1 3266 1 chr4B.!!$F2 3265
2 TraesCS4A01G067900 chr4D 384669620 384672476 2856 False 4193 4193 93.306 531 3378 1 chr4D.!!$F3 2847
3 TraesCS4A01G067900 chr1A 476976978 476977479 501 False 811 811 95.833 3378 3880 1 chr1A.!!$F1 502
4 TraesCS4A01G067900 chr7A 16067293 16067812 519 False 800 800 94.455 3361 3880 1 chr7A.!!$F1 519
5 TraesCS4A01G067900 chr2A 687137038 687137542 504 False 795 795 95.079 3375 3880 1 chr2A.!!$F1 505
6 TraesCS4A01G067900 chr2A 724113575 724114075 500 True 773 773 94.444 3378 3880 1 chr2A.!!$R3 502
7 TraesCS4A01G067900 chr6A 32608038 32608543 505 False 780 780 94.488 3375 3880 1 chr6A.!!$F1 505
8 TraesCS4A01G067900 chr5A 300371221 300371722 501 True 778 778 94.643 3378 3880 1 chr5A.!!$R1 502
9 TraesCS4A01G067900 chr5A 673519158 673519662 504 False 778 778 94.477 3374 3879 1 chr5A.!!$F2 505
10 TraesCS4A01G067900 chr3A 642706677 642707179 502 False 776 776 94.466 3376 3880 1 chr3A.!!$F2 504

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
909 979 0.120377 TCCTTCCCACATACCCACCT 59.880 55.0 0.0 0.0 0.0 4.00 F
912 982 0.178858 TTCCCACATACCCACCTCCA 60.179 55.0 0.0 0.0 0.0 3.86 F
2252 2332 0.323629 TAGGGGTTTGTCTGCGGAAG 59.676 55.0 0.0 0.0 0.0 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2147 2225 0.040246 GGCCGAGATGTCGTAGTAGC 60.040 60.0 11.66 6.7 45.30 3.58 R
2756 2860 0.957395 ACGCCACATGAGGAAAGCAG 60.957 55.0 13.99 0.0 0.00 4.24 R
3395 3515 0.691078 GGCCAGACAGGATAGGGTCA 60.691 60.0 0.00 0.0 41.22 4.02 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
77 78 0.462937 TTCACGTGTCAAGGGTGTGG 60.463 55.000 16.51 0.00 33.51 4.17
115 140 1.630126 ATCATTCTGGCGCTGACCCT 61.630 55.000 7.64 0.00 0.00 4.34
123 148 1.675641 GCGCTGACCCTGGTTTCAT 60.676 57.895 0.00 0.00 0.00 2.57
131 156 1.844497 ACCCTGGTTTCATACTAGCCC 59.156 52.381 0.00 0.00 34.23 5.19
161 186 0.598065 GAAAATTGACGGGCTGCACT 59.402 50.000 0.00 0.00 0.00 4.40
188 213 5.105554 TCAGCAGTTTGGCTAAAAAGAACAA 60.106 36.000 0.00 0.00 43.68 2.83
241 266 4.346734 CACTCTGTGCCACATTATTGAC 57.653 45.455 0.00 0.00 0.00 3.18
242 267 4.005650 CACTCTGTGCCACATTATTGACT 58.994 43.478 0.00 0.00 0.00 3.41
246 271 4.218200 TCTGTGCCACATTATTGACTTTGG 59.782 41.667 0.00 0.00 0.00 3.28
305 330 6.679638 GCACTCCCTCCGTTTTTATTTATTCC 60.680 42.308 0.00 0.00 0.00 3.01
306 331 6.376018 CACTCCCTCCGTTTTTATTTATTCCA 59.624 38.462 0.00 0.00 0.00 3.53
307 332 6.376299 ACTCCCTCCGTTTTTATTTATTCCAC 59.624 38.462 0.00 0.00 0.00 4.02
308 333 6.246919 TCCCTCCGTTTTTATTTATTCCACA 58.753 36.000 0.00 0.00 0.00 4.17
309 334 6.893005 TCCCTCCGTTTTTATTTATTCCACAT 59.107 34.615 0.00 0.00 0.00 3.21
310 335 8.053963 TCCCTCCGTTTTTATTTATTCCACATA 58.946 33.333 0.00 0.00 0.00 2.29
311 336 8.856103 CCCTCCGTTTTTATTTATTCCACATAT 58.144 33.333 0.00 0.00 0.00 1.78
329 354 9.967451 TCCACATATTAGTTTTAATTGGAGTCA 57.033 29.630 0.00 0.00 32.54 3.41
502 540 9.456147 TTTAAGCTTAGACAAACCTAATATGCA 57.544 29.630 6.24 0.00 0.00 3.96
503 541 7.938140 AAGCTTAGACAAACCTAATATGCAA 57.062 32.000 0.00 0.00 0.00 4.08
561 600 2.298300 CTTTTGCAACGTCTACTTGCG 58.702 47.619 0.00 0.00 45.92 4.85
609 648 0.249280 TCACGTGTGTGCCACAGTAG 60.249 55.000 16.51 0.00 45.43 2.57
698 742 2.490217 CCTACGGGCACAGTCTCG 59.510 66.667 0.00 0.00 38.12 4.04
729 779 1.227556 CGGATCCCATTCCACGGAC 60.228 63.158 6.06 0.00 35.34 4.79
778 835 4.065281 GTCTCCGGGTCCCACGTG 62.065 72.222 9.08 9.08 0.00 4.49
785 842 2.426023 GGTCCCACGTGCAGAACT 59.574 61.111 10.91 0.00 0.00 3.01
793 850 2.946762 GTGCAGAACTCCCAACGC 59.053 61.111 0.00 0.00 0.00 4.84
884 954 2.483889 CGCCTTCTACTCCCCAAATCTC 60.484 54.545 0.00 0.00 0.00 2.75
889 959 4.338795 TCTACTCCCCAAATCTCACTCT 57.661 45.455 0.00 0.00 0.00 3.24
890 960 4.689062 TCTACTCCCCAAATCTCACTCTT 58.311 43.478 0.00 0.00 0.00 2.85
892 962 2.573915 ACTCCCCAAATCTCACTCTTCC 59.426 50.000 0.00 0.00 0.00 3.46
893 963 2.843113 CTCCCCAAATCTCACTCTTCCT 59.157 50.000 0.00 0.00 0.00 3.36
894 964 3.260205 TCCCCAAATCTCACTCTTCCTT 58.740 45.455 0.00 0.00 0.00 3.36
896 966 3.615155 CCCAAATCTCACTCTTCCTTCC 58.385 50.000 0.00 0.00 0.00 3.46
897 967 3.615155 CCAAATCTCACTCTTCCTTCCC 58.385 50.000 0.00 0.00 0.00 3.97
898 968 3.009473 CCAAATCTCACTCTTCCTTCCCA 59.991 47.826 0.00 0.00 0.00 4.37
899 969 3.990959 AATCTCACTCTTCCTTCCCAC 57.009 47.619 0.00 0.00 0.00 4.61
900 970 2.398754 TCTCACTCTTCCTTCCCACA 57.601 50.000 0.00 0.00 0.00 4.17
901 971 2.907892 TCTCACTCTTCCTTCCCACAT 58.092 47.619 0.00 0.00 0.00 3.21
902 972 4.061131 TCTCACTCTTCCTTCCCACATA 57.939 45.455 0.00 0.00 0.00 2.29
903 973 3.769844 TCTCACTCTTCCTTCCCACATAC 59.230 47.826 0.00 0.00 0.00 2.39
904 974 2.838202 TCACTCTTCCTTCCCACATACC 59.162 50.000 0.00 0.00 0.00 2.73
905 975 2.092914 CACTCTTCCTTCCCACATACCC 60.093 54.545 0.00 0.00 0.00 3.69
906 976 2.196595 CTCTTCCTTCCCACATACCCA 58.803 52.381 0.00 0.00 0.00 4.51
907 977 1.913419 TCTTCCTTCCCACATACCCAC 59.087 52.381 0.00 0.00 0.00 4.61
908 978 0.996583 TTCCTTCCCACATACCCACC 59.003 55.000 0.00 0.00 0.00 4.61
909 979 0.120377 TCCTTCCCACATACCCACCT 59.880 55.000 0.00 0.00 0.00 4.00
910 980 0.546598 CCTTCCCACATACCCACCTC 59.453 60.000 0.00 0.00 0.00 3.85
911 981 0.546598 CTTCCCACATACCCACCTCC 59.453 60.000 0.00 0.00 0.00 4.30
912 982 0.178858 TTCCCACATACCCACCTCCA 60.179 55.000 0.00 0.00 0.00 3.86
953 1023 2.622962 CCCCAAAACCTTCGTCCGC 61.623 63.158 0.00 0.00 0.00 5.54
975 1045 0.827368 AAATCTCACCTCGCTCTCCC 59.173 55.000 0.00 0.00 0.00 4.30
977 1047 1.943730 ATCTCACCTCGCTCTCCCCT 61.944 60.000 0.00 0.00 0.00 4.79
978 1048 1.227664 CTCACCTCGCTCTCCCCTA 59.772 63.158 0.00 0.00 0.00 3.53
1701 1779 1.681538 TCCATCTGGACTACGCTCTC 58.318 55.000 0.00 0.00 39.78 3.20
2001 2079 1.225827 CGTCTACGTGTTCGCGCTA 60.226 57.895 5.56 0.00 41.18 4.26
2097 2175 2.813908 CCGCTCACGTACAAGCCC 60.814 66.667 10.18 0.00 37.70 5.19
2195 2273 2.055042 AGCCCACGGTGAGCTCTAG 61.055 63.158 11.67 8.59 28.40 2.43
2199 2277 1.408405 CCCACGGTGAGCTCTAGTCTA 60.408 57.143 16.19 0.00 0.00 2.59
2200 2278 2.577700 CCACGGTGAGCTCTAGTCTAT 58.422 52.381 16.19 0.00 0.00 1.98
2205 2285 4.577283 ACGGTGAGCTCTAGTCTATTTCTC 59.423 45.833 16.19 0.00 0.00 2.87
2252 2332 0.323629 TAGGGGTTTGTCTGCGGAAG 59.676 55.000 0.00 0.00 0.00 3.46
2267 2347 1.557832 CGGAAGGGGGATGACACTTTA 59.442 52.381 0.00 0.00 0.00 1.85
2336 2416 2.807631 CCGTAGGTTGACCACGGTCG 62.808 65.000 23.85 12.41 46.17 4.79
2347 2427 2.081212 CACGGTCGACTCTCAACGC 61.081 63.158 16.46 0.00 0.00 4.84
2349 2429 1.797933 CGGTCGACTCTCAACGCAG 60.798 63.158 16.46 0.00 0.00 5.18
2372 2452 7.148853 GCAGTTCAGATTGTGCAATTAGAAAAG 60.149 37.037 11.63 9.49 35.91 2.27
2378 2458 7.652909 CAGATTGTGCAATTAGAAAAGTTTCCA 59.347 33.333 0.00 0.00 37.92 3.53
2387 2467 7.681939 ATTAGAAAAGTTTCCAGCGTAATCA 57.318 32.000 0.13 0.00 37.92 2.57
2396 2476 2.670905 TCCAGCGTAATCAACATCAACG 59.329 45.455 0.00 0.00 36.67 4.10
2443 2523 3.493877 CAGATTCTGGCAATCGTCATCTC 59.506 47.826 5.73 0.00 0.00 2.75
2487 2567 2.932614 GTCACCATCGACCAGATTCTTG 59.067 50.000 0.00 0.00 37.52 3.02
2493 2573 3.053831 TCGACCAGATTCTTGTTTCCC 57.946 47.619 0.00 0.00 0.00 3.97
2533 2613 6.262049 TCGACATCATTCTCAGGTTTCAAAAA 59.738 34.615 0.00 0.00 0.00 1.94
2634 2738 4.059773 AGATCTGGAGTTCTCACTTCCT 57.940 45.455 0.00 0.00 31.22 3.36
2680 2784 1.064952 TGCGCGTCTAGAATCGAATGA 59.935 47.619 8.43 0.00 0.00 2.57
2811 2915 3.037549 TGGCTTGTGATTCAAAAGGGTT 58.962 40.909 16.56 0.00 35.48 4.11
2813 2917 2.802247 GCTTGTGATTCAAAAGGGTTGC 59.198 45.455 16.56 1.14 35.48 4.17
2827 2931 3.575247 TTGCCGGTGGACATGGGT 61.575 61.111 1.90 0.00 0.00 4.51
2870 2974 2.827642 GCTGCTGCCCTCATGGTC 60.828 66.667 3.85 0.00 36.04 4.02
2936 3047 0.842635 ATGGCTGAGATTCAGGGGTC 59.157 55.000 8.06 0.00 44.43 4.46
2958 3070 3.510360 CGGTGGATAGGACGGAATAGAAT 59.490 47.826 0.00 0.00 0.00 2.40
2984 3096 2.189594 CTCTGGAGCAATGGTGTTGA 57.810 50.000 0.00 0.00 0.00 3.18
2985 3097 2.719739 CTCTGGAGCAATGGTGTTGAT 58.280 47.619 0.00 0.00 0.00 2.57
2986 3098 2.422479 CTCTGGAGCAATGGTGTTGATG 59.578 50.000 0.00 0.00 0.00 3.07
2987 3099 2.040145 TCTGGAGCAATGGTGTTGATGA 59.960 45.455 0.00 0.00 0.00 2.92
3097 3209 7.973944 GGGTAAGCTGATGAAACGATTAATTTT 59.026 33.333 0.00 0.00 0.00 1.82
3237 3349 4.107473 TGGTACCCCAGTACTGCTATCTAT 59.893 45.833 17.86 0.89 46.81 1.98
3244 3356 8.982723 ACCCCAGTACTGCTATCTATAAATATG 58.017 37.037 17.86 0.00 0.00 1.78
3325 3445 6.473397 AGTTCATCTGAATTCGTCAACTTC 57.527 37.500 0.04 0.00 35.22 3.01
3337 3457 2.219216 CGTCAACTTCGAGCGGTTAAAA 59.781 45.455 0.00 0.00 0.00 1.52
3340 3460 5.548250 GTCAACTTCGAGCGGTTAAAATAG 58.452 41.667 0.00 0.00 0.00 1.73
3410 3530 0.824759 GCGTTGACCCTATCCTGTCT 59.175 55.000 0.00 0.00 32.67 3.41
3451 3571 4.394712 CGGACAAAGGAGGCGGCT 62.395 66.667 13.09 13.09 0.00 5.52
3628 3748 2.992273 GCCCACATCAATGCGCACA 61.992 57.895 14.90 0.00 0.00 4.57
3692 3812 3.751518 GTCCTTCTTTAAGTGGGAAGCA 58.248 45.455 9.28 0.00 36.21 3.91
3787 3910 0.630134 AACCCTAGCCTAGACCTCGT 59.370 55.000 0.00 0.00 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
77 78 1.011968 TGCTATTGGTCGACGCACAC 61.012 55.000 9.92 0.00 0.00 3.82
115 140 2.174639 CCCATGGGCTAGTATGAAACCA 59.825 50.000 20.41 0.00 0.00 3.67
131 156 2.674747 CGTCAATTTTCTTGGGCCCATG 60.675 50.000 29.23 28.54 0.00 3.66
161 186 4.826733 TCTTTTTAGCCAAACTGCTGATGA 59.173 37.500 0.00 0.00 42.77 2.92
188 213 7.730364 AAGAAGATGAATACAACAAACTCGT 57.270 32.000 0.00 0.00 0.00 4.18
230 255 9.642327 TTGATTTCATCCAAAGTCAATAATGTG 57.358 29.630 0.00 0.00 0.00 3.21
241 266 6.167685 TGCAAGGAATTGATTTCATCCAAAG 58.832 36.000 3.67 0.00 35.94 2.77
242 267 6.111669 TGCAAGGAATTGATTTCATCCAAA 57.888 33.333 3.67 0.00 35.94 3.28
246 271 4.751060 TGCTGCAAGGAATTGATTTCATC 58.249 39.130 0.00 0.00 35.94 2.92
481 519 7.762382 ACTTTGCATATTAGGTTTGTCTAAGC 58.238 34.615 0.00 0.00 33.36 3.09
499 537 9.660180 ACTCCTTTTGTTTTTATTTACTTTGCA 57.340 25.926 0.00 0.00 0.00 4.08
515 553 7.013369 GGTCTCATTTTTCACTACTCCTTTTGT 59.987 37.037 0.00 0.00 0.00 2.83
517 555 7.290813 AGGTCTCATTTTTCACTACTCCTTTT 58.709 34.615 0.00 0.00 0.00 2.27
518 556 6.842676 AGGTCTCATTTTTCACTACTCCTTT 58.157 36.000 0.00 0.00 0.00 3.11
520 558 6.441088 AAGGTCTCATTTTTCACTACTCCT 57.559 37.500 0.00 0.00 0.00 3.69
584 623 3.636043 GCACACACGTGACGGTGG 61.636 66.667 25.01 15.81 46.80 4.61
609 648 1.288752 CATGGGAAACGTTGGTGCC 59.711 57.895 0.00 1.93 0.00 5.01
729 779 2.354403 CGGGGGTTGTTTACTGGAGTAG 60.354 54.545 0.00 0.00 0.00 2.57
778 835 1.869690 GAAGCGTTGGGAGTTCTGC 59.130 57.895 0.00 0.00 0.00 4.26
785 842 2.355363 CGACACGAAGCGTTGGGA 60.355 61.111 0.00 0.00 38.32 4.37
813 870 2.225963 ACGGCGATAGTAGCACAGTATC 59.774 50.000 16.62 0.00 36.55 2.24
814 871 2.228059 ACGGCGATAGTAGCACAGTAT 58.772 47.619 16.62 0.00 36.08 2.12
815 872 1.671979 ACGGCGATAGTAGCACAGTA 58.328 50.000 16.62 0.00 36.08 2.74
817 874 1.852895 GAAACGGCGATAGTAGCACAG 59.147 52.381 16.62 0.00 36.08 3.66
818 875 1.202817 TGAAACGGCGATAGTAGCACA 59.797 47.619 16.62 0.00 36.08 4.57
819 876 1.852895 CTGAAACGGCGATAGTAGCAC 59.147 52.381 16.62 0.00 36.08 4.40
820 877 1.475280 ACTGAAACGGCGATAGTAGCA 59.525 47.619 16.62 0.49 36.08 3.49
821 878 2.205307 ACTGAAACGGCGATAGTAGC 57.795 50.000 16.62 0.00 39.35 3.58
822 879 3.791887 CAGAACTGAAACGGCGATAGTAG 59.208 47.826 16.62 7.63 39.35 2.57
823 880 3.192001 ACAGAACTGAAACGGCGATAGTA 59.808 43.478 16.62 0.00 39.35 1.82
824 881 2.029290 ACAGAACTGAAACGGCGATAGT 60.029 45.455 16.62 9.07 39.35 2.12
825 882 2.599082 GACAGAACTGAAACGGCGATAG 59.401 50.000 16.62 8.38 0.00 2.08
884 954 2.092914 GGGTATGTGGGAAGGAAGAGTG 60.093 54.545 0.00 0.00 0.00 3.51
889 959 0.996583 GGTGGGTATGTGGGAAGGAA 59.003 55.000 0.00 0.00 0.00 3.36
890 960 0.120377 AGGTGGGTATGTGGGAAGGA 59.880 55.000 0.00 0.00 0.00 3.36
892 962 0.546598 GGAGGTGGGTATGTGGGAAG 59.453 60.000 0.00 0.00 0.00 3.46
893 963 0.178858 TGGAGGTGGGTATGTGGGAA 60.179 55.000 0.00 0.00 0.00 3.97
894 964 0.178858 TTGGAGGTGGGTATGTGGGA 60.179 55.000 0.00 0.00 0.00 4.37
896 966 0.034477 GGTTGGAGGTGGGTATGTGG 60.034 60.000 0.00 0.00 0.00 4.17
897 967 0.991920 AGGTTGGAGGTGGGTATGTG 59.008 55.000 0.00 0.00 0.00 3.21
898 968 1.286248 GAGGTTGGAGGTGGGTATGT 58.714 55.000 0.00 0.00 0.00 2.29
899 969 0.546598 GGAGGTTGGAGGTGGGTATG 59.453 60.000 0.00 0.00 0.00 2.39
900 970 0.120377 TGGAGGTTGGAGGTGGGTAT 59.880 55.000 0.00 0.00 0.00 2.73
901 971 0.104356 TTGGAGGTTGGAGGTGGGTA 60.104 55.000 0.00 0.00 0.00 3.69
902 972 0.776080 ATTGGAGGTTGGAGGTGGGT 60.776 55.000 0.00 0.00 0.00 4.51
903 973 0.034089 GATTGGAGGTTGGAGGTGGG 60.034 60.000 0.00 0.00 0.00 4.61
904 974 0.698238 TGATTGGAGGTTGGAGGTGG 59.302 55.000 0.00 0.00 0.00 4.61
905 975 1.352352 AGTGATTGGAGGTTGGAGGTG 59.648 52.381 0.00 0.00 0.00 4.00
906 976 1.630878 GAGTGATTGGAGGTTGGAGGT 59.369 52.381 0.00 0.00 0.00 3.85
907 977 1.912043 AGAGTGATTGGAGGTTGGAGG 59.088 52.381 0.00 0.00 0.00 4.30
908 978 2.093235 GGAGAGTGATTGGAGGTTGGAG 60.093 54.545 0.00 0.00 0.00 3.86
909 979 1.909302 GGAGAGTGATTGGAGGTTGGA 59.091 52.381 0.00 0.00 0.00 3.53
910 980 1.065126 GGGAGAGTGATTGGAGGTTGG 60.065 57.143 0.00 0.00 0.00 3.77
911 981 1.065126 GGGGAGAGTGATTGGAGGTTG 60.065 57.143 0.00 0.00 0.00 3.77
912 982 1.290134 GGGGAGAGTGATTGGAGGTT 58.710 55.000 0.00 0.00 0.00 3.50
953 1023 0.459237 AGAGCGAGGTGAGATTTGCG 60.459 55.000 0.00 0.00 0.00 4.85
975 1045 1.152440 AGGAGTGGAGCGGGATAGG 60.152 63.158 0.00 0.00 0.00 2.57
977 1047 1.152525 GGAGGAGTGGAGCGGGATA 60.153 63.158 0.00 0.00 0.00 2.59
978 1048 2.444895 GGAGGAGTGGAGCGGGAT 60.445 66.667 0.00 0.00 0.00 3.85
1482 1560 1.714794 CGATCTGCTTGTCGAGGTTT 58.285 50.000 0.00 0.00 40.11 3.27
1825 1903 3.823369 AGATCCGTATCTCCACCGT 57.177 52.632 0.00 0.00 38.04 4.83
1875 1953 3.479269 GTCGCGGCCTTCTCGTTG 61.479 66.667 6.13 0.00 0.00 4.10
2001 2079 2.749621 GGGCTTCATGTTCTCGTTGAAT 59.250 45.455 0.00 0.00 36.99 2.57
2147 2225 0.040246 GGCCGAGATGTCGTAGTAGC 60.040 60.000 11.66 6.70 45.30 3.58
2195 2273 6.593382 AGCATGAACAACTGAGAGAAATAGAC 59.407 38.462 0.00 0.00 0.00 2.59
2199 2277 6.712095 TGTAAGCATGAACAACTGAGAGAAAT 59.288 34.615 0.00 0.00 0.00 2.17
2200 2278 6.054941 TGTAAGCATGAACAACTGAGAGAAA 58.945 36.000 0.00 0.00 0.00 2.52
2205 2285 6.082338 GTCAATGTAAGCATGAACAACTGAG 58.918 40.000 0.00 0.00 35.15 3.35
2252 2332 2.420058 CACCTAAAGTGTCATCCCCC 57.580 55.000 0.00 0.00 41.93 5.40
2267 2347 2.569059 CGAGAAATGATGCCATCACCT 58.431 47.619 10.06 7.59 43.01 4.00
2336 2416 2.423926 TCTGAACTGCGTTGAGAGTC 57.576 50.000 6.52 0.00 31.46 3.36
2337 2417 3.062763 CAATCTGAACTGCGTTGAGAGT 58.937 45.455 13.56 9.68 38.92 3.24
2338 2418 3.062763 ACAATCTGAACTGCGTTGAGAG 58.937 45.455 13.56 6.32 38.92 3.20
2339 2419 2.802247 CACAATCTGAACTGCGTTGAGA 59.198 45.455 11.40 11.40 39.74 3.27
2340 2420 2.663879 GCACAATCTGAACTGCGTTGAG 60.664 50.000 0.00 0.81 0.00 3.02
2347 2427 7.864379 ACTTTTCTAATTGCACAATCTGAACTG 59.136 33.333 0.00 3.52 0.00 3.16
2349 2429 8.579682 AACTTTTCTAATTGCACAATCTGAAC 57.420 30.769 0.00 0.00 0.00 3.18
2372 2452 4.678509 TGATGTTGATTACGCTGGAAAC 57.321 40.909 0.00 0.00 0.00 2.78
2378 2458 3.322369 TGACGTTGATGTTGATTACGCT 58.678 40.909 0.00 0.00 35.77 5.07
2396 2476 6.348540 GGATCTGTGTGGAATAAACAACTGAC 60.349 42.308 0.00 0.00 0.00 3.51
2443 2523 3.007635 GAGGGGTCACACCTAATTTTCG 58.992 50.000 0.00 0.00 38.79 3.46
2509 2589 5.611796 TTTGAAACCTGAGAATGATGTCG 57.388 39.130 0.00 0.00 0.00 4.35
2533 2613 2.689983 CCACAAGGAAAGTGAGCAGTTT 59.310 45.455 3.11 3.11 39.30 2.66
2535 2615 1.490490 TCCACAAGGAAAGTGAGCAGT 59.510 47.619 0.00 0.00 42.23 4.40
2536 2616 2.260844 TCCACAAGGAAAGTGAGCAG 57.739 50.000 0.00 0.00 42.23 4.24
2575 2655 6.440647 TGGAGTCACCAGATCTACTTGTTTAT 59.559 38.462 0.00 0.00 44.64 1.40
2634 2738 5.252547 TGGCATTTTGACTATCAAGTAGCA 58.747 37.500 10.95 0.00 37.70 3.49
2680 2784 1.122019 AGAACACCTGCCGGAGACTT 61.122 55.000 5.05 0.00 0.00 3.01
2756 2860 0.957395 ACGCCACATGAGGAAAGCAG 60.957 55.000 13.99 0.00 0.00 4.24
2811 2915 4.343323 CACCCATGTCCACCGGCA 62.343 66.667 0.00 0.00 0.00 5.69
2813 2917 3.859118 TTGCACCCATGTCCACCGG 62.859 63.158 0.00 0.00 0.00 5.28
2858 2962 4.783621 GCTGCGACCATGAGGGCA 62.784 66.667 0.00 0.00 46.60 5.36
2870 2974 1.140589 CTCAGTACCTCAGGCTGCG 59.859 63.158 10.34 2.87 0.00 5.18
2936 3047 2.511659 TCTATTCCGTCCTATCCACCG 58.488 52.381 0.00 0.00 0.00 4.94
2982 3094 5.726793 AGGATCAGGATCATCATCATCATCA 59.273 40.000 11.12 0.00 39.54 3.07
2983 3095 6.241882 AGGATCAGGATCATCATCATCATC 57.758 41.667 11.12 0.00 39.54 2.92
2984 3096 6.241882 GAGGATCAGGATCATCATCATCAT 57.758 41.667 16.53 0.00 45.11 2.45
2985 3097 5.678955 GAGGATCAGGATCATCATCATCA 57.321 43.478 16.53 0.00 45.11 3.07
3097 3209 6.463360 TGAAATACATAGCTTCGATGCCATA 58.537 36.000 18.70 7.14 0.00 2.74
3237 3349 8.955388 TCAGCTTTTGTACTTCATGCATATTTA 58.045 29.630 0.00 0.00 0.00 1.40
3244 3356 3.916776 GCTTCAGCTTTTGTACTTCATGC 59.083 43.478 0.00 0.00 38.21 4.06
3250 3362 2.508526 CTGGGCTTCAGCTTTTGTACT 58.491 47.619 0.00 0.00 41.70 2.73
3298 3410 8.553459 AGTTGACGAATTCAGATGAACTTAAT 57.447 30.769 6.22 0.00 36.80 1.40
3299 3411 7.962964 AGTTGACGAATTCAGATGAACTTAA 57.037 32.000 6.22 0.00 36.80 1.85
3300 3412 7.148804 CGAAGTTGACGAATTCAGATGAACTTA 60.149 37.037 14.56 0.00 32.66 2.24
3303 3423 5.118664 TCGAAGTTGACGAATTCAGATGAAC 59.881 40.000 6.22 1.37 36.84 3.18
3325 3445 6.578020 TTATCACACTATTTTAACCGCTCG 57.422 37.500 0.00 0.00 0.00 5.03
3337 3457 5.528690 AGCAATCGCAACATTATCACACTAT 59.471 36.000 0.00 0.00 42.27 2.12
3340 3460 4.019919 AGCAATCGCAACATTATCACAC 57.980 40.909 0.00 0.00 42.27 3.82
3394 3514 1.204146 GCCAGACAGGATAGGGTCAA 58.796 55.000 0.00 0.00 41.22 3.18
3395 3515 0.691078 GGCCAGACAGGATAGGGTCA 60.691 60.000 0.00 0.00 41.22 4.02
3427 3547 2.501261 GCCTCCTTTGTCCGTTTTACT 58.499 47.619 0.00 0.00 0.00 2.24
3472 3592 2.875933 GGACACAAAACGGACAAGATGA 59.124 45.455 0.00 0.00 0.00 2.92
3728 3848 4.388499 GGTTTGAGGAGGCCGCGA 62.388 66.667 8.23 0.00 0.00 5.87
3819 3942 3.663202 CCTTTGCGGCCGTAGTTT 58.337 55.556 28.70 0.00 0.00 2.66


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

AutoCloner maintained by Alex Coulton.