Multiple sequence alignment - TraesCS1B01G392600

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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 TraesCS1B01G392600 chr1B 100.000 3347 0 0 1 3347 625807906 625811252 0.000000e+00 6181.0
1 TraesCS1B01G392600 chr1B 92.308 221 15 2 1020 1239 625775078 625775297 2.510000e-81 313.0
2 TraesCS1B01G392600 chr1B 91.667 192 14 1 1460 1651 625777314 625777503 7.120000e-67 265.0
3 TraesCS1B01G392600 chr1B 90.446 157 14 1 110 265 625774916 625775072 4.380000e-49 206.0
4 TraesCS1B01G392600 chr1D 90.989 1709 107 20 1661 3337 455115155 455116848 0.000000e+00 2259.0
5 TraesCS1B01G392600 chr1D 90.530 1584 91 31 110 1651 455112831 455114397 0.000000e+00 2039.0
6 TraesCS1B01G392600 chr1D 88.000 75 8 1 3115 3188 481338435 481338361 1.650000e-13 87.9
7 TraesCS1B01G392600 chr1A 89.388 1112 60 15 1913 2972 549054072 549055177 0.000000e+00 1347.0
8 TraesCS1B01G392600 chr1A 91.249 857 41 5 834 1665 549047451 549048298 0.000000e+00 1136.0
9 TraesCS1B01G392600 chr1A 91.081 740 58 2 110 841 549045770 549046509 0.000000e+00 994.0
10 TraesCS1B01G392600 chr1A 91.085 258 22 1 1661 1918 549049014 549049270 6.870000e-92 348.0
11 TraesCS1B01G392600 chr1A 88.235 102 12 0 1 102 549045631 549045732 4.530000e-24 122.0
12 TraesCS1B01G392600 chr7A 83.825 915 110 22 1661 2562 78510782 78511671 0.000000e+00 835.0
13 TraesCS1B01G392600 chr7A 77.419 930 165 30 766 1662 78509022 78509939 2.300000e-141 512.0
14 TraesCS1B01G392600 chr7D 86.269 772 92 8 1661 2422 74599570 74600337 0.000000e+00 826.0
15 TraesCS1B01G392600 chr7D 77.553 940 164 29 766 1662 74597796 74598731 1.060000e-144 523.0
16 TraesCS1B01G392600 chr7B 85.751 772 96 8 1661 2422 18207646 18208413 0.000000e+00 804.0
17 TraesCS1B01G392600 chr7B 77.046 941 160 37 766 1662 18205889 18206817 1.080000e-134 490.0
18 TraesCS1B01G392600 chr2B 81.818 121 14 8 3109 3225 23272225 23272341 9.890000e-16 95.3
19 TraesCS1B01G392600 chr3A 84.884 86 11 2 3104 3188 28890894 28890978 5.950000e-13 86.1
20 TraesCS1B01G392600 chr5D 83.529 85 12 2 3113 3196 217741502 217741585 9.960000e-11 78.7
21 TraesCS1B01G392600 chr3D 83.529 85 11 3 3109 3191 578069572 578069655 3.580000e-10 76.8
22 TraesCS1B01G392600 chr5B 93.182 44 2 1 3104 3147 706311477 706311435 2.790000e-06 63.9
23 TraesCS1B01G392600 chr3B 89.362 47 3 2 479 525 188441492 188441536 1.300000e-04 58.4


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 TraesCS1B01G392600 chr1B 625807906 625811252 3346 False 6181.000000 6181 100.000000 1 3347 1 chr1B.!!$F1 3346
1 TraesCS1B01G392600 chr1B 625774916 625777503 2587 False 261.333333 313 91.473667 110 1651 3 chr1B.!!$F2 1541
2 TraesCS1B01G392600 chr1D 455112831 455116848 4017 False 2149.000000 2259 90.759500 110 3337 2 chr1D.!!$F1 3227
3 TraesCS1B01G392600 chr1A 549054072 549055177 1105 False 1347.000000 1347 89.388000 1913 2972 1 chr1A.!!$F1 1059
4 TraesCS1B01G392600 chr1A 549045631 549049270 3639 False 650.000000 1136 90.412500 1 1918 4 chr1A.!!$F2 1917
5 TraesCS1B01G392600 chr7A 78509022 78511671 2649 False 673.500000 835 80.622000 766 2562 2 chr7A.!!$F1 1796
6 TraesCS1B01G392600 chr7D 74597796 74600337 2541 False 674.500000 826 81.911000 766 2422 2 chr7D.!!$F1 1656
7 TraesCS1B01G392600 chr7B 18205889 18208413 2524 False 647.000000 804 81.398500 766 2422 2 chr7B.!!$F1 1656

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
412 444 0.678048 AAGTTCGCTGGGCAGGAATC 60.678 55.0 0.0 0.0 0.0 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2367 6499 0.033228 TTTTGATTTGTGCTGGGCCG 59.967 50.0 0.0 0.0 0.0 6.13 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 9.871238 AATACGGATGTAACATCTACATAATCC 57.129 33.333 5.66 3.89 38.18 3.01
45 46 2.039418 ACATAATCCAGCGGCTCAGTA 58.961 47.619 0.00 0.00 0.00 2.74
47 48 1.480789 TAATCCAGCGGCTCAGTACA 58.519 50.000 0.00 0.00 0.00 2.90
79 80 6.878923 AGTGTTGTGCAGTTTAGCTATCAATA 59.121 34.615 0.00 0.00 34.99 1.90
89 90 9.847706 CAGTTTAGCTATCAATATGATACTCGT 57.152 33.333 0.00 0.00 38.26 4.18
117 148 9.526713 CCTCATATATATCTGATACAAGTGCAC 57.473 37.037 9.40 9.40 0.00 4.57
145 176 3.759086 TCTAGCACGATCTGAGACAAGTT 59.241 43.478 0.00 0.00 0.00 2.66
159 190 8.593679 TCTGAGACAAGTTATGTATTTCCTGAA 58.406 33.333 0.00 0.00 44.12 3.02
209 240 1.688735 CTCCTCAAGATGGCGATGGTA 59.311 52.381 0.00 0.00 0.00 3.25
221 252 1.414158 CGATGGTAGATGTCAGGGGT 58.586 55.000 0.00 0.00 0.00 4.95
224 255 2.568546 TGGTAGATGTCAGGGGTGAT 57.431 50.000 0.00 0.00 0.00 3.06
315 347 2.361104 GTCCCTTTCATGCCCGCA 60.361 61.111 0.00 0.00 0.00 5.69
330 362 3.966215 GCAAGAGCTTGTGCGGTA 58.034 55.556 11.47 0.00 45.42 4.02
410 442 1.600636 CAAGTTCGCTGGGCAGGAA 60.601 57.895 0.00 0.00 0.00 3.36
412 444 0.678048 AAGTTCGCTGGGCAGGAATC 60.678 55.000 0.00 0.00 0.00 2.52
468 500 3.902881 ATGATCGTCTTCCTGCTTCTT 57.097 42.857 0.00 0.00 0.00 2.52
520 552 8.855110 TGTAGTTGATTGTTGGTATTTGATTGT 58.145 29.630 0.00 0.00 0.00 2.71
598 632 7.466725 GCAATTAGTTGATCCTACGTGCAAATA 60.467 37.037 0.00 0.00 37.53 1.40
733 772 1.202710 TCGCAATGGGTAGTGTGTGTT 60.203 47.619 0.00 0.00 34.30 3.32
759 798 3.731867 CGTTTGGGAGTAATGCATGCTTC 60.732 47.826 20.33 8.47 0.00 3.86
785 827 8.886719 CATTAGTTCTCTTGCATGAAGTAATCA 58.113 33.333 21.68 8.47 42.28 2.57
919 1916 1.403814 CGCCAATGTCTCCTCCTCTA 58.596 55.000 0.00 0.00 0.00 2.43
953 1961 4.313020 AAAGAGGAAGCATCATCCAGTT 57.687 40.909 0.00 0.00 37.06 3.16
964 1973 3.031417 ATCCAGTTTCTCGCCCCCG 62.031 63.158 0.00 0.00 0.00 5.73
989 2009 3.260884 CCCCTAGCTAGTTTCTGAACACA 59.739 47.826 19.31 0.00 38.26 3.72
991 2011 4.262463 CCCTAGCTAGTTTCTGAACACACA 60.262 45.833 19.31 0.00 38.26 3.72
1102 2129 6.463472 CCACTATGAGCTCCATTCTGTTGATA 60.463 42.308 12.15 0.00 36.71 2.15
1157 2184 3.181497 CCGTTTGCAACCTTCTATCATGG 60.181 47.826 0.00 0.00 0.00 3.66
1207 2258 2.355837 TCGCTGACGGTGCTTCAC 60.356 61.111 0.00 0.00 40.63 3.18
1249 2300 0.318441 TCACTTGCCTCTCTTGTCGG 59.682 55.000 0.00 0.00 0.00 4.79
1277 3387 4.895889 ACCGGAGATTTCACATCTCATAGA 59.104 41.667 9.46 0.00 44.70 1.98
1294 3404 4.103153 TCATAGAAGGTGGAATGGGATCAC 59.897 45.833 0.00 0.00 0.00 3.06
1429 4259 3.591196 TTGGAACAGTTTATGCATGCC 57.409 42.857 16.68 0.00 42.39 4.40
1455 4285 6.459923 TGTTAAATATTGCCTCCACCAAAAC 58.540 36.000 0.00 0.00 0.00 2.43
1457 4287 7.451877 TGTTAAATATTGCCTCCACCAAAACTA 59.548 33.333 0.00 0.00 0.00 2.24
1682 5773 6.741992 TTCTGTGTACTATTCATGCTTTGG 57.258 37.500 0.00 0.00 0.00 3.28
1893 5989 3.141488 CGGACCCGCAGTAGAGCT 61.141 66.667 0.00 0.00 0.00 4.09
1967 6066 1.630369 TGGCTCTAGCAAGGTCATTGT 59.370 47.619 4.07 0.00 44.36 2.71
2014 6113 1.202794 TGTCAGCATCTTCACCAGCAA 60.203 47.619 0.00 0.00 0.00 3.91
2080 6179 3.030291 TCCAACCCATCCAACATAATGC 58.970 45.455 0.00 0.00 0.00 3.56
2107 6206 5.132648 ACCCAAGGAATATTCAGCACAGATA 59.867 40.000 17.07 0.00 0.00 1.98
2109 6208 6.206243 CCCAAGGAATATTCAGCACAGATAAG 59.794 42.308 17.07 0.00 0.00 1.73
2169 6268 5.646793 CACATCTGATGACTTTTCTGTGGAT 59.353 40.000 23.59 0.00 31.47 3.41
2236 6338 7.443575 AGGCTTACAACATAGATGATGATGTTC 59.556 37.037 6.76 0.00 46.30 3.18
2254 6356 8.198807 TGATGTTCACATGGACTATATCATCT 57.801 34.615 0.00 0.00 36.57 2.90
2326 6458 1.126488 ATGGGATGACGATGCACTCT 58.874 50.000 0.00 0.00 0.00 3.24
2356 6488 4.538738 TGAATCTGGATGATTGCCATTGA 58.461 39.130 0.00 0.00 44.70 2.57
2357 6489 4.340097 TGAATCTGGATGATTGCCATTGAC 59.660 41.667 0.00 0.00 44.70 3.18
2367 6499 3.585990 CCATTGACGATGCCGGCC 61.586 66.667 26.77 8.57 44.97 6.13
2407 6542 0.325933 TGTGCATGTGAAGGAGGAGG 59.674 55.000 0.00 0.00 0.00 4.30
2408 6543 0.615331 GTGCATGTGAAGGAGGAGGA 59.385 55.000 0.00 0.00 0.00 3.71
2412 6553 2.485124 GCATGTGAAGGAGGAGGAGATG 60.485 54.545 0.00 0.00 0.00 2.90
2415 6556 2.022625 TGTGAAGGAGGAGGAGATGGAT 60.023 50.000 0.00 0.00 0.00 3.41
2418 6559 3.729524 TGAAGGAGGAGGAGATGGATCTA 59.270 47.826 0.00 0.00 37.25 1.98
2421 6562 3.732204 AGGAGGAGGAGATGGATCTAGTT 59.268 47.826 0.00 0.00 37.25 2.24
2446 6587 2.928801 TCCACAAACTTGCAGCTAGA 57.071 45.000 11.12 0.00 0.00 2.43
2516 6657 4.320870 ACGGAATATGACGAACTTTTGGT 58.679 39.130 6.34 0.00 0.00 3.67
2578 6720 3.988976 TCTGAATGCTTTCTACAGGCT 57.011 42.857 12.96 0.00 32.78 4.58
2641 6784 5.721232 AGAACAGACGGTGGTAAATAAGAG 58.279 41.667 0.00 0.00 0.00 2.85
2681 6828 7.278875 TGGGCTAAAAATGAAGTGTTTGATTT 58.721 30.769 0.00 0.00 32.50 2.17
2702 6849 8.291740 TGATTTACATGTTGAATCAGTGTTCTG 58.708 33.333 22.99 0.00 42.54 3.02
2703 6850 7.566760 TTTACATGTTGAATCAGTGTTCTGT 57.433 32.000 2.30 0.00 41.91 3.41
2705 6852 8.669946 TTACATGTTGAATCAGTGTTCTGTAA 57.330 30.769 2.30 10.46 41.91 2.41
2976 7137 5.357878 CAGGCTTCCTGCTATTTCATTACAA 59.642 40.000 0.00 0.00 45.13 2.41
2983 7144 7.546358 TCCTGCTATTTCATTACAAACCAATG 58.454 34.615 0.00 0.00 35.19 2.82
2993 7154 3.192541 ACAAACCAATGGCTTCCAAAC 57.807 42.857 0.00 0.00 36.95 2.93
3034 7195 2.309613 GTTTTAAGGAAACACCGGGGT 58.690 47.619 1.51 1.51 45.57 4.95
3056 7217 2.358195 GGAACAGCCCCACCTGAATATT 60.358 50.000 0.00 0.00 36.67 1.28
3085 7246 0.109132 AAGCTGCAAAATACAGGCGC 60.109 50.000 0.00 0.00 35.62 6.53
3093 7254 1.248101 AAATACAGGCGCACCAACCC 61.248 55.000 10.83 0.00 39.06 4.11
3119 7280 0.460811 GGATGACACTGATGCTCGCA 60.461 55.000 0.00 0.00 0.00 5.10
3128 7289 2.163010 ACTGATGCTCGCATTTTTCTGG 59.837 45.455 5.79 0.00 36.70 3.86
3134 7295 4.732784 TGCTCGCATTTTTCTGGATTTAC 58.267 39.130 0.00 0.00 0.00 2.01
3145 7306 6.976934 TTTCTGGATTTACTTCAAGCCTTT 57.023 33.333 0.00 0.00 0.00 3.11
3169 7330 0.456824 GATGCGCGTTCAGTGAGAGA 60.457 55.000 8.43 0.00 0.00 3.10
3174 7335 1.332178 GCGTTCAGTGAGAGAAGACG 58.668 55.000 8.13 8.13 0.00 4.18
3178 7339 3.422546 CGTTCAGTGAGAGAAGACGTTTC 59.577 47.826 4.92 0.00 0.00 2.78
3198 7359 1.990563 CCGTCTACTACAAAGGCGTTG 59.009 52.381 11.68 11.68 40.38 4.10
3208 7369 2.650608 CAAAGGCGTTGTAGCAACTTC 58.349 47.619 4.92 2.94 39.27 3.01
3209 7370 1.961793 AAGGCGTTGTAGCAACTTCA 58.038 45.000 9.82 0.00 39.27 3.02
3210 7371 2.185004 AGGCGTTGTAGCAACTTCAT 57.815 45.000 9.82 0.00 39.27 2.57
3227 7389 8.325997 GCAACTTCATTAATCTCAAAATGATGC 58.674 33.333 9.53 7.98 40.71 3.91
3230 7392 7.977853 ACTTCATTAATCTCAAAATGATGCACC 59.022 33.333 0.00 0.00 40.71 5.01
3232 7394 6.318396 TCATTAATCTCAAAATGATGCACCGA 59.682 34.615 0.00 0.00 37.23 4.69
3234 7396 3.057969 TCTCAAAATGATGCACCGACT 57.942 42.857 0.00 0.00 0.00 4.18
3235 7397 3.002791 TCTCAAAATGATGCACCGACTC 58.997 45.455 0.00 0.00 0.00 3.36
3237 7399 3.145286 TCAAAATGATGCACCGACTCAA 58.855 40.909 0.00 0.00 0.00 3.02
3241 7403 2.014335 TGATGCACCGACTCAATCTG 57.986 50.000 0.00 0.00 0.00 2.90
3271 7433 5.050490 GTGTGCGTTCATAAGGATGAGTAT 58.950 41.667 0.00 0.00 43.03 2.12
3296 7458 6.043327 TGTGCGTATGTATAAACATTCTGC 57.957 37.500 0.00 0.47 44.07 4.26
3297 7459 5.130519 GTGCGTATGTATAAACATTCTGCG 58.869 41.667 0.00 0.00 44.07 5.18
3298 7460 4.210328 TGCGTATGTATAAACATTCTGCGG 59.790 41.667 0.00 0.00 44.07 5.69
3313 7475 2.139917 CTGCGGCTGTACTGTGTTTAA 58.860 47.619 0.00 0.00 0.00 1.52
3337 7499 5.452078 AAAGTAGCAAAATACAGCAAGCA 57.548 34.783 0.00 0.00 0.00 3.91
3338 7500 4.425577 AGTAGCAAAATACAGCAAGCAC 57.574 40.909 0.00 0.00 0.00 4.40
3339 7501 3.820467 AGTAGCAAAATACAGCAAGCACA 59.180 39.130 0.00 0.00 0.00 4.57
3340 7502 3.293311 AGCAAAATACAGCAAGCACAG 57.707 42.857 0.00 0.00 0.00 3.66
3341 7503 2.029649 AGCAAAATACAGCAAGCACAGG 60.030 45.455 0.00 0.00 0.00 4.00
3342 7504 2.927871 GCAAAATACAGCAAGCACAGGG 60.928 50.000 0.00 0.00 0.00 4.45
3343 7505 2.557924 CAAAATACAGCAAGCACAGGGA 59.442 45.455 0.00 0.00 0.00 4.20
3344 7506 2.119801 AATACAGCAAGCACAGGGAG 57.880 50.000 0.00 0.00 0.00 4.30
3345 7507 1.279496 ATACAGCAAGCACAGGGAGA 58.721 50.000 0.00 0.00 0.00 3.71
3346 7508 1.279496 TACAGCAAGCACAGGGAGAT 58.721 50.000 0.00 0.00 0.00 2.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 9.031537 TGGATTATGTAGATGTTACATCCGTAT 57.968 33.333 20.28 14.08 38.84 3.06
12 13 6.311445 CGCTGGATTATGTAGATGTTACATCC 59.689 42.308 20.28 8.00 38.84 3.51
17 18 4.283467 AGCCGCTGGATTATGTAGATGTTA 59.717 41.667 0.00 0.00 0.00 2.41
19 20 2.634940 AGCCGCTGGATTATGTAGATGT 59.365 45.455 0.00 0.00 0.00 3.06
22 23 2.297315 CTGAGCCGCTGGATTATGTAGA 59.703 50.000 0.00 0.00 0.00 2.59
30 31 1.704641 TATGTACTGAGCCGCTGGAT 58.295 50.000 0.00 0.00 0.00 3.41
33 34 2.515926 ACATATGTACTGAGCCGCTG 57.484 50.000 6.56 0.00 0.00 5.18
45 46 6.633500 AAACTGCACAACACTAACATATGT 57.367 33.333 1.41 1.41 0.00 2.29
47 48 6.655003 AGCTAAACTGCACAACACTAACATAT 59.345 34.615 0.00 0.00 34.99 1.78
102 103 2.899900 ACCTCTGTGCACTTGTATCAGA 59.100 45.455 19.41 9.47 34.62 3.27
103 104 3.056250 AGACCTCTGTGCACTTGTATCAG 60.056 47.826 19.41 5.09 0.00 2.90
104 105 2.899900 AGACCTCTGTGCACTTGTATCA 59.100 45.455 19.41 0.00 0.00 2.15
107 108 2.231478 GCTAGACCTCTGTGCACTTGTA 59.769 50.000 19.41 0.00 0.00 2.41
108 109 1.001406 GCTAGACCTCTGTGCACTTGT 59.999 52.381 19.41 9.47 0.00 3.16
117 148 2.290367 CTCAGATCGTGCTAGACCTCTG 59.710 54.545 0.00 4.10 34.36 3.35
145 176 7.558161 CTGCAACAGATTCAGGAAATACATA 57.442 36.000 0.00 0.00 32.44 2.29
209 240 2.485659 ACATCATCACCCCTGACATCT 58.514 47.619 0.00 0.00 0.00 2.90
297 329 2.361104 GCGGGCATGAAAGGGACA 60.361 61.111 0.00 0.00 0.00 4.02
301 333 1.805254 CTCTTGCGGGCATGAAAGG 59.195 57.895 10.00 0.00 31.27 3.11
315 347 1.361668 CGCATACCGCACAAGCTCTT 61.362 55.000 0.00 0.00 42.60 2.85
362 394 1.591594 CGACCTCACTGTGCGTGTT 60.592 57.895 2.12 0.00 44.16 3.32
410 442 1.277557 AGCTCGAAGCAAACAGAGGAT 59.722 47.619 9.09 0.00 45.56 3.24
412 444 0.795085 CAGCTCGAAGCAAACAGAGG 59.205 55.000 9.09 0.00 45.56 3.69
468 500 6.552008 AGGTTCAGATTATTCAACTGGGAAA 58.448 36.000 0.00 0.00 33.19 3.13
579 613 5.734855 ATGTATTTGCACGTAGGATCAAC 57.265 39.130 0.00 0.00 0.00 3.18
759 798 8.886719 TGATTACTTCATGCAAGAGAACTAATG 58.113 33.333 10.61 0.00 35.82 1.90
896 1893 1.375908 GAGGAGACATTGGCGCACA 60.376 57.895 10.83 1.22 0.00 4.57
897 1894 2.109126 GGAGGAGACATTGGCGCAC 61.109 63.158 10.83 0.00 0.00 5.34
919 1916 3.121929 TCCTCTTTACCTGCATCTCCT 57.878 47.619 0.00 0.00 0.00 3.69
978 1998 1.133915 GGAGGGGTGTGTGTTCAGAAA 60.134 52.381 0.00 0.00 0.00 2.52
1157 2184 2.418368 TGTGCCTTGTGGATATGACC 57.582 50.000 0.00 0.00 34.57 4.02
1207 2258 4.019860 AGGTCCAGGATTATGAATGATCGG 60.020 45.833 0.00 0.00 0.00 4.18
1249 2300 3.191371 AGATGTGAAATCTCCGGTTTTGC 59.809 43.478 0.00 0.00 0.00 3.68
1257 2308 6.705381 CACCTTCTATGAGATGTGAAATCTCC 59.295 42.308 10.03 0.00 42.83 3.71
1277 3387 1.710244 TGTGTGATCCCATTCCACCTT 59.290 47.619 0.00 0.00 0.00 3.50
1294 3404 1.326852 GCTCATCTCATGCGTCTTGTG 59.673 52.381 0.00 0.00 0.00 3.33
1356 4174 4.319549 CCTTTGACAACGTTAGCCTTCTTC 60.320 45.833 0.00 0.00 0.00 2.87
1368 4186 0.958091 TCCATTGCCCTTTGACAACG 59.042 50.000 0.00 0.00 0.00 4.10
1429 4259 5.913137 TGGTGGAGGCAATATTTAACAAG 57.087 39.130 0.00 0.00 0.00 3.16
1455 4285 7.905031 GCAGAAAGCAACTAATAGCATTTAG 57.095 36.000 4.62 4.62 44.79 1.85
1486 4342 6.607735 AATTTGCAAGAACAAACTCATTGG 57.392 33.333 0.00 0.00 42.01 3.16
1967 6066 4.611367 AGGTTCTTTCGGATCTAGAGGAA 58.389 43.478 0.00 0.00 0.00 3.36
2014 6113 1.468506 GCCCGATTTTGTGTTGGGGT 61.469 55.000 0.83 0.00 40.21 4.95
2080 6179 3.629398 GTGCTGAATATTCCTTGGGTGAG 59.371 47.826 12.90 2.34 0.00 3.51
2169 6268 7.334671 TCTGCGTTAAATAAACCATCACACATA 59.665 33.333 0.00 0.00 34.33 2.29
2283 6415 9.425577 CATGTCATATCCATATCTATCTCATGC 57.574 37.037 0.00 0.00 0.00 4.06
2326 6458 7.093421 TGGCAATCATCCAGATTCAATGTTTAA 60.093 33.333 0.00 0.00 45.06 1.52
2367 6499 0.033228 TTTTGATTTGTGCTGGGCCG 59.967 50.000 0.00 0.00 0.00 6.13
2377 6509 5.050634 CCTTCACATGCACAGTTTTGATTTG 60.051 40.000 0.00 0.00 0.00 2.32
2407 6542 6.656632 TGGATGTGTAACTAGATCCATCTC 57.343 41.667 0.00 0.00 43.30 2.75
2412 6553 6.407202 AGTTTGTGGATGTGTAACTAGATCC 58.593 40.000 0.00 0.00 40.08 3.36
2415 6556 5.468746 GCAAGTTTGTGGATGTGTAACTAGA 59.531 40.000 0.00 0.00 38.04 2.43
2418 6559 3.951037 TGCAAGTTTGTGGATGTGTAACT 59.049 39.130 0.00 0.00 38.04 2.24
2421 6562 2.293122 GCTGCAAGTTTGTGGATGTGTA 59.707 45.455 0.00 0.00 35.30 2.90
2603 6746 5.400782 CGTCTGTTCTCAATATGGATTCTCG 59.599 44.000 0.00 0.00 0.00 4.04
2681 6828 8.846943 ATTACAGAACACTGATTCAACATGTA 57.153 30.769 0.00 0.00 35.80 2.29
2731 6891 8.925700 GCACAAAATTGAAATAGGAAGTAAAGG 58.074 33.333 0.00 0.00 0.00 3.11
2735 6895 8.637986 ACAAGCACAAAATTGAAATAGGAAGTA 58.362 29.630 0.00 0.00 0.00 2.24
2819 6980 9.857957 TGTTTTCCTTTTAACTCAATTTTACGT 57.142 25.926 0.00 0.00 0.00 3.57
2976 7137 2.676748 TCTGTTTGGAAGCCATTGGTT 58.323 42.857 4.26 0.00 31.53 3.67
2983 7144 5.904362 AACTGATATTCTGTTTGGAAGCC 57.096 39.130 0.00 0.00 35.44 4.35
3019 7180 1.647334 TTCCACCCCGGTGTTTCCTT 61.647 55.000 12.77 0.00 44.02 3.36
3021 7182 1.900016 GTTCCACCCCGGTGTTTCC 60.900 63.158 12.77 0.00 44.02 3.13
3034 7195 1.434513 ATTCAGGTGGGGCTGTTCCA 61.435 55.000 0.00 0.00 36.21 3.53
3036 7197 2.736670 ATATTCAGGTGGGGCTGTTC 57.263 50.000 0.00 0.00 0.00 3.18
3037 7198 3.473113 AAATATTCAGGTGGGGCTGTT 57.527 42.857 0.00 0.00 0.00 3.16
3038 7199 4.814224 ATAAATATTCAGGTGGGGCTGT 57.186 40.909 0.00 0.00 0.00 4.40
3056 7217 7.814107 CCTGTATTTTGCAGCTTTGAGAAATAA 59.186 33.333 0.00 0.00 32.93 1.40
3093 7254 1.733912 CATCAGTGTCATCCAACCACG 59.266 52.381 0.00 0.00 34.34 4.94
3119 7280 7.544804 AGGCTTGAAGTAAATCCAGAAAAAT 57.455 32.000 0.00 0.00 0.00 1.82
3152 7313 0.664466 CTTCTCTCACTGAACGCGCA 60.664 55.000 5.73 0.00 0.00 6.09
3154 7315 1.332178 GTCTTCTCTCACTGAACGCG 58.668 55.000 3.53 3.53 0.00 6.01
3155 7316 1.332178 CGTCTTCTCTCACTGAACGC 58.668 55.000 0.00 0.00 0.00 4.84
3174 7335 2.665052 CGCCTTTGTAGTAGACGGAAAC 59.335 50.000 0.00 0.00 0.00 2.78
3178 7339 1.990563 CAACGCCTTTGTAGTAGACGG 59.009 52.381 0.00 0.00 0.00 4.79
3189 7350 2.294074 TGAAGTTGCTACAACGCCTTT 58.706 42.857 0.13 0.00 0.00 3.11
3192 7353 2.989422 AATGAAGTTGCTACAACGCC 57.011 45.000 0.13 2.38 0.00 5.68
3200 7361 9.582431 CATCATTTTGAGATTAATGAAGTTGCT 57.418 29.630 0.00 0.00 42.25 3.91
3202 7363 9.361315 TGCATCATTTTGAGATTAATGAAGTTG 57.639 29.630 0.00 0.00 42.25 3.16
3203 7364 9.362539 GTGCATCATTTTGAGATTAATGAAGTT 57.637 29.630 0.00 0.00 42.25 2.66
3205 7366 7.166970 CGGTGCATCATTTTGAGATTAATGAAG 59.833 37.037 0.00 0.00 42.25 3.02
3208 7369 6.415867 GTCGGTGCATCATTTTGAGATTAATG 59.584 38.462 0.00 0.00 33.96 1.90
3209 7370 6.319658 AGTCGGTGCATCATTTTGAGATTAAT 59.680 34.615 0.00 0.00 0.00 1.40
3210 7371 5.647658 AGTCGGTGCATCATTTTGAGATTAA 59.352 36.000 0.00 0.00 0.00 1.40
3227 7389 4.152402 CACCTTTAACAGATTGAGTCGGTG 59.848 45.833 0.00 0.00 35.35 4.94
3230 7392 4.377431 GCACACCTTTAACAGATTGAGTCG 60.377 45.833 0.00 0.00 0.00 4.18
3232 7394 3.498397 CGCACACCTTTAACAGATTGAGT 59.502 43.478 0.00 0.00 0.00 3.41
3234 7396 3.472652 ACGCACACCTTTAACAGATTGA 58.527 40.909 0.00 0.00 0.00 2.57
3235 7397 3.896648 ACGCACACCTTTAACAGATTG 57.103 42.857 0.00 0.00 0.00 2.67
3237 7399 3.472652 TGAACGCACACCTTTAACAGAT 58.527 40.909 0.00 0.00 0.00 2.90
3241 7403 4.453136 TCCTTATGAACGCACACCTTTAAC 59.547 41.667 0.00 0.00 0.00 2.01
3271 7433 7.358848 CGCAGAATGTTTATACATACGCACATA 60.359 37.037 0.00 0.00 44.14 2.29
3293 7455 1.790755 TAAACACAGTACAGCCGCAG 58.209 50.000 0.00 0.00 0.00 5.18
3294 7456 2.242047 TTAAACACAGTACAGCCGCA 57.758 45.000 0.00 0.00 0.00 5.69
3295 7457 3.612472 TTTTAAACACAGTACAGCCGC 57.388 42.857 0.00 0.00 0.00 6.53
3313 7475 6.200854 GTGCTTGCTGTATTTTGCTACTTTTT 59.799 34.615 0.00 0.00 0.00 1.94
3318 7480 4.159377 TGTGCTTGCTGTATTTTGCTAC 57.841 40.909 0.00 0.00 0.00 3.58


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

AutoCloner maintained by Alex Coulton.