Multiple sequence alignment - TraesCS4D01G256400

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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 TraesCS4D01G256400 chr4D 100.000 3488 0 0 1 3488 425972229 425975716 0.000000e+00 6442
1 TraesCS4D01G256400 chr4A 88.955 3522 189 70 1 3429 39053991 39050577 0.000000e+00 4165
2 TraesCS4D01G256400 chr4B 94.058 1481 53 10 1412 2882 522083564 522085019 0.000000e+00 2215
3 TraesCS4D01G256400 chr4B 89.785 1439 70 33 1 1416 522076924 522078308 0.000000e+00 1772
4 TraesCS4D01G256400 chr4B 89.971 339 15 8 2893 3231 522085068 522085387 1.500000e-113 420
5 TraesCS4D01G256400 chr4B 86.792 265 19 9 3224 3488 522086641 522086889 7.370000e-72 281


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 TraesCS4D01G256400 chr4D 425972229 425975716 3487 False 6442 6442 100.000000 1 3488 1 chr4D.!!$F1 3487
1 TraesCS4D01G256400 chr4A 39050577 39053991 3414 True 4165 4165 88.955000 1 3429 1 chr4A.!!$R1 3428
2 TraesCS4D01G256400 chr4B 522076924 522078308 1384 False 1772 1772 89.785000 1 1416 1 chr4B.!!$F1 1415
3 TraesCS4D01G256400 chr4B 522083564 522086889 3325 False 972 2215 90.273667 1412 3488 3 chr4B.!!$F2 2076

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
199 205 0.249322 AATATTCCGGTCCACTCGCG 60.249 55.0 0.00 0.00 0.00 5.87 F
440 453 0.315251 TGTGCTCCACTCTTGAGACG 59.685 55.0 4.49 0.00 35.11 4.18 F
630 650 0.383949 TCTTTTTGGTTCAGCACGCC 59.616 50.0 0.00 0.00 0.00 5.68 F
1008 1040 0.659957 GATTGAGCGCCATGGAAGAC 59.340 55.0 18.40 4.17 0.00 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1029 1061 0.318762 GGCTGTACTCCCGGATGATC 59.681 60.000 0.73 0.0 0.00 2.92 R
1734 1817 1.373999 GAAGAGCTGCACAGACGCT 60.374 57.895 1.02 0.0 36.57 5.07 R
2257 2340 1.845568 GTTCACGAACGACACGTACAA 59.154 47.619 0.14 0.0 39.99 2.41 R
2735 2823 0.397675 TCCGAGATGAGATGGCTGGT 60.398 55.000 0.00 0.0 0.00 4.00 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
29 30 1.289160 TGAATCACCTGGGAAGGGAG 58.711 55.000 0.00 0.00 0.00 4.30
30 31 0.548510 GAATCACCTGGGAAGGGAGG 59.451 60.000 0.00 0.00 35.26 4.30
31 32 0.921256 AATCACCTGGGAAGGGAGGG 60.921 60.000 0.00 0.00 33.16 4.30
32 33 2.865183 ATCACCTGGGAAGGGAGGGG 62.865 65.000 0.00 0.00 33.57 4.79
105 106 4.099881 TCGCCGGATAACCTTAACTATTGT 59.900 41.667 5.05 0.00 0.00 2.71
135 136 0.491823 TTCAGGTTCAGGGGGAGAGA 59.508 55.000 0.00 0.00 0.00 3.10
136 137 0.719015 TCAGGTTCAGGGGGAGAGAT 59.281 55.000 0.00 0.00 0.00 2.75
137 138 1.127343 CAGGTTCAGGGGGAGAGATC 58.873 60.000 0.00 0.00 0.00 2.75
138 139 0.397816 AGGTTCAGGGGGAGAGATCG 60.398 60.000 0.00 0.00 0.00 3.69
139 140 1.403687 GGTTCAGGGGGAGAGATCGG 61.404 65.000 0.00 0.00 0.00 4.18
140 141 0.688087 GTTCAGGGGGAGAGATCGGT 60.688 60.000 0.00 0.00 0.00 4.69
141 142 0.397254 TTCAGGGGGAGAGATCGGTC 60.397 60.000 0.00 0.00 0.00 4.79
142 143 1.075970 CAGGGGGAGAGATCGGTCA 60.076 63.158 0.00 0.00 0.00 4.02
181 184 0.882927 CGGCCGACTCAGAAAACCAA 60.883 55.000 24.07 0.00 0.00 3.67
182 185 1.534729 GGCCGACTCAGAAAACCAAT 58.465 50.000 0.00 0.00 0.00 3.16
183 186 2.706890 GGCCGACTCAGAAAACCAATA 58.293 47.619 0.00 0.00 0.00 1.90
189 195 4.034048 CGACTCAGAAAACCAATATTCCGG 59.966 45.833 0.00 0.00 0.00 5.14
198 204 1.217882 CAATATTCCGGTCCACTCGC 58.782 55.000 0.00 0.00 0.00 5.03
199 205 0.249322 AATATTCCGGTCCACTCGCG 60.249 55.000 0.00 0.00 0.00 5.87
200 206 2.694829 ATATTCCGGTCCACTCGCGC 62.695 60.000 0.00 0.00 0.00 6.86
245 251 2.388106 GGTAAAACCGACCGTTGTTG 57.612 50.000 0.00 0.00 33.93 3.33
313 319 3.574445 GCGAGCCAGAGCATGCAG 61.574 66.667 21.98 9.16 43.56 4.41
315 321 1.883544 CGAGCCAGAGCATGCAGAG 60.884 63.158 21.98 8.39 43.56 3.35
371 383 6.316390 CCACTATCCAAAGACCTTAATGTCAC 59.684 42.308 12.61 0.00 37.73 3.67
403 415 4.476410 GCCTTAAACGCCGCTGCC 62.476 66.667 0.00 0.00 0.00 4.85
405 417 3.419759 CTTAAACGCCGCTGCCGT 61.420 61.111 0.00 0.00 41.24 5.68
406 418 2.048409 TTAAACGCCGCTGCCGTA 60.048 55.556 4.45 0.00 38.06 4.02
407 419 1.628447 CTTAAACGCCGCTGCCGTAA 61.628 55.000 4.45 0.00 38.06 3.18
408 420 1.226686 TTAAACGCCGCTGCCGTAAA 61.227 50.000 4.45 0.92 38.06 2.01
409 421 1.899521 TAAACGCCGCTGCCGTAAAC 61.900 55.000 4.45 0.00 38.06 2.01
434 447 2.619849 CCCAATCATGTGCTCCACTCTT 60.620 50.000 0.00 0.00 35.11 2.85
435 448 2.422479 CCAATCATGTGCTCCACTCTTG 59.578 50.000 0.00 0.00 35.11 3.02
436 449 3.340928 CAATCATGTGCTCCACTCTTGA 58.659 45.455 0.00 0.00 35.11 3.02
437 450 2.756840 TCATGTGCTCCACTCTTGAG 57.243 50.000 0.00 0.00 35.11 3.02
438 451 2.250924 TCATGTGCTCCACTCTTGAGA 58.749 47.619 4.49 0.00 35.11 3.27
439 452 2.028658 TCATGTGCTCCACTCTTGAGAC 60.029 50.000 4.49 0.00 35.11 3.36
440 453 0.315251 TGTGCTCCACTCTTGAGACG 59.685 55.000 4.49 0.00 35.11 4.18
441 454 0.598562 GTGCTCCACTCTTGAGACGA 59.401 55.000 4.49 0.00 31.26 4.20
554 574 3.494048 CCCTCTGTCAGTCATATGCTTCC 60.494 52.174 0.00 0.00 0.00 3.46
624 644 5.868801 TCTGCAGTTTTTCTTTTTGGTTCAG 59.131 36.000 14.67 0.00 0.00 3.02
626 646 4.391523 GCAGTTTTTCTTTTTGGTTCAGCA 59.608 37.500 0.00 0.00 0.00 4.41
628 648 4.625311 AGTTTTTCTTTTTGGTTCAGCACG 59.375 37.500 0.00 0.00 0.00 5.34
629 649 2.202295 TTCTTTTTGGTTCAGCACGC 57.798 45.000 0.00 0.00 0.00 5.34
630 650 0.383949 TCTTTTTGGTTCAGCACGCC 59.616 50.000 0.00 0.00 0.00 5.68
631 651 0.934436 CTTTTTGGTTCAGCACGCCG 60.934 55.000 0.00 0.00 0.00 6.46
632 652 1.658686 TTTTTGGTTCAGCACGCCGT 61.659 50.000 0.00 0.00 0.00 5.68
633 653 1.658686 TTTTGGTTCAGCACGCCGTT 61.659 50.000 0.00 0.00 0.00 4.44
634 654 1.658686 TTTGGTTCAGCACGCCGTTT 61.659 50.000 0.00 0.00 0.00 3.60
720 740 3.006003 GGTTTTTAATTCCGGTCTGCCAA 59.994 43.478 0.00 0.00 34.09 4.52
875 897 2.435059 GCGCCGCTTTCTCCTCTT 60.435 61.111 0.00 0.00 0.00 2.85
891 923 4.798682 TTCTCCTCCCCGCTCCCC 62.799 72.222 0.00 0.00 0.00 4.81
963 995 2.093288 TGAGTGAGTCGTAGGGATACGT 60.093 50.000 7.59 0.00 43.31 3.57
973 1005 4.842139 GTAGGGATACGTACGGTATACG 57.158 50.000 21.06 5.00 46.67 3.06
974 1006 2.699954 AGGGATACGTACGGTATACGG 58.300 52.381 21.06 8.76 42.52 4.02
975 1007 2.038557 AGGGATACGTACGGTATACGGT 59.961 50.000 21.06 18.67 42.52 4.83
976 1008 2.812011 GGGATACGTACGGTATACGGTT 59.188 50.000 21.06 6.46 42.52 4.44
977 1009 3.998341 GGGATACGTACGGTATACGGTTA 59.002 47.826 21.06 8.31 42.52 2.85
978 1010 4.142966 GGGATACGTACGGTATACGGTTAC 60.143 50.000 21.06 14.13 42.52 2.50
979 1011 7.350327 GGGATACGTACGGTATACGGTTACG 62.350 52.000 25.51 25.51 42.52 3.18
990 1022 2.170738 CGGTTACGTACAGTCGGGA 58.829 57.895 0.00 0.00 34.81 5.14
1008 1040 0.659957 GATTGAGCGCCATGGAAGAC 59.340 55.000 18.40 4.17 0.00 3.01
1029 1061 2.234296 AGAGGGGAAGCCAAGGGTG 61.234 63.158 0.00 0.00 0.00 4.61
1206 1238 1.416401 GTAAGTGCCTGCTGCCCTATA 59.584 52.381 0.00 0.00 40.16 1.31
1250 1306 0.937304 CTGCTGCACAGTTACACGTT 59.063 50.000 0.00 0.00 41.86 3.99
1495 1555 2.119495 GTCTCACCATCCCACAGGTAT 58.881 52.381 0.00 0.00 36.07 2.73
1512 1572 7.754924 CCACAGGTATAACACAATTGAATTGAC 59.245 37.037 23.37 10.17 42.83 3.18
1517 1577 9.341899 GGTATAACACAATTGAATTGACTTGAC 57.658 33.333 23.37 12.87 42.83 3.18
1734 1817 1.673626 GCCACGGATAAGTCCAACGAA 60.674 52.381 0.00 0.00 45.37 3.85
1998 2081 1.869132 GACGAAGGTTTTAAGTGGCGT 59.131 47.619 0.00 0.00 0.00 5.68
2596 2679 4.098196 AGTCGAGATTTTGTAGGAGCCTAC 59.902 45.833 17.74 17.74 46.56 3.18
2597 2680 4.098196 GTCGAGATTTTGTAGGAGCCTACT 59.902 45.833 23.17 6.99 46.53 2.57
2598 2681 5.298777 GTCGAGATTTTGTAGGAGCCTACTA 59.701 44.000 23.17 15.45 46.53 1.82
2599 2682 5.531659 TCGAGATTTTGTAGGAGCCTACTAG 59.468 44.000 23.17 7.18 46.53 2.57
2600 2683 5.299782 CGAGATTTTGTAGGAGCCTACTAGT 59.700 44.000 23.17 0.00 46.53 2.57
2601 2684 6.485984 CGAGATTTTGTAGGAGCCTACTAGTA 59.514 42.308 23.17 1.89 46.53 1.82
2622 2705 7.476540 AGTAGTTTGTTTTCCTTTTTCTGGT 57.523 32.000 0.00 0.00 0.00 4.00
2735 2823 2.027605 GCGGATGGCGATCGAGAA 59.972 61.111 21.57 2.95 0.00 2.87
2742 2830 2.184322 GCGATCGAGAACCAGCCA 59.816 61.111 21.57 0.00 0.00 4.75
2748 2836 1.489481 TCGAGAACCAGCCATCTCAT 58.511 50.000 3.95 0.00 41.73 2.90
2749 2837 1.410517 TCGAGAACCAGCCATCTCATC 59.589 52.381 3.95 0.00 41.73 2.92
2750 2838 1.411977 CGAGAACCAGCCATCTCATCT 59.588 52.381 3.95 0.00 41.73 2.90
2751 2839 2.545532 CGAGAACCAGCCATCTCATCTC 60.546 54.545 3.95 0.00 41.73 2.75
2752 2840 1.411977 AGAACCAGCCATCTCATCTCG 59.588 52.381 0.00 0.00 0.00 4.04
2790 2878 4.330894 CACATGCAGTTACTACCAGATGTG 59.669 45.833 0.00 0.00 35.07 3.21
2791 2879 4.020218 ACATGCAGTTACTACCAGATGTGT 60.020 41.667 0.00 0.00 0.00 3.72
2836 2937 0.474660 ACCCTGGATATCTCCCCTGC 60.475 60.000 2.05 0.00 41.29 4.85
2855 2956 1.877443 GCTTTTCGTCCCTGTAAGCAA 59.123 47.619 0.00 0.00 40.58 3.91
2991 3133 3.807538 TGTCGCTCGCCGTACCTC 61.808 66.667 0.00 0.00 38.35 3.85
3023 3165 4.406173 ACTGTGCGAGCTCGACGG 62.406 66.667 38.74 33.07 43.02 4.79
3066 3209 4.100084 CAGATGGGGCGCCTGACA 62.100 66.667 28.56 22.63 0.00 3.58
3095 3238 1.522580 CCCAGCTTAGCTTCGCTCC 60.523 63.158 3.00 0.00 40.44 4.70
3106 3249 1.784525 CTTCGCTCCTTCGTTTGACT 58.215 50.000 0.00 0.00 0.00 3.41
3113 3256 0.250295 CCTTCGTTTGACTGGGCAGA 60.250 55.000 0.00 0.00 0.00 4.26
3117 3260 1.227853 GTTTGACTGGGCAGACCGT 60.228 57.895 0.00 0.00 44.64 4.83
3127 3278 1.485943 GCAGACCGTTCGTTCGTTC 59.514 57.895 0.00 0.00 0.00 3.95
3130 3281 0.658536 AGACCGTTCGTTCGTTCGTC 60.659 55.000 2.67 0.00 0.00 4.20
3140 3291 0.810823 TTCGTTCGTCCGTTTGGCTT 60.811 50.000 0.00 0.00 34.14 4.35
3189 3340 1.143305 GCACTGCTGATATGCTACGG 58.857 55.000 0.00 0.00 36.40 4.02
3191 3342 1.043816 ACTGCTGATATGCTACGGCT 58.956 50.000 0.00 0.00 38.93 5.52
3233 4645 0.961019 TACTGCGACCACCTAACGTT 59.039 50.000 5.88 5.88 0.00 3.99
3302 4714 1.003851 TCGCGAAATAGGAAAAGGCG 58.996 50.000 6.20 0.00 43.12 5.52
3307 4719 2.290641 CGAAATAGGAAAAGGCGATGGG 59.709 50.000 0.00 0.00 0.00 4.00
3391 4803 0.875728 CATTGGGTTTTGTCGCCGTA 59.124 50.000 0.00 0.00 0.00 4.02
3392 4804 0.876399 ATTGGGTTTTGTCGCCGTAC 59.124 50.000 0.00 0.00 0.00 3.67
3393 4805 1.497223 TTGGGTTTTGTCGCCGTACG 61.497 55.000 8.69 8.69 45.62 3.67
3394 4806 1.955663 GGGTTTTGTCGCCGTACGT 60.956 57.895 15.21 0.00 44.19 3.57
3404 4816 0.927083 CGCCGTACGTGTAAGGATCG 60.927 60.000 15.21 6.84 36.93 3.69
3414 4826 0.531974 GTAAGGATCGCATTCGCCCA 60.532 55.000 0.02 0.00 35.26 5.36
3415 4827 0.531974 TAAGGATCGCATTCGCCCAC 60.532 55.000 0.02 0.00 35.26 4.61
3418 4830 3.173390 GATCGCATTCGCCCACTGC 62.173 63.158 0.00 0.00 35.26 4.40
3439 4851 4.472286 GCGTTGTGCATTATTGTTACTGT 58.528 39.130 0.00 0.00 45.45 3.55
3441 4853 5.506832 GCGTTGTGCATTATTGTTACTGTAC 59.493 40.000 0.00 0.00 45.45 2.90
3442 4854 6.619874 GCGTTGTGCATTATTGTTACTGTACT 60.620 38.462 0.00 0.00 45.45 2.73
3443 4855 7.412129 GCGTTGTGCATTATTGTTACTGTACTA 60.412 37.037 0.00 0.00 45.45 1.82
3444 4856 8.600625 CGTTGTGCATTATTGTTACTGTACTAT 58.399 33.333 0.00 0.00 29.08 2.12
3456 4868 8.246908 TGTTACTGTACTATTTTGAATCACGG 57.753 34.615 0.00 0.00 0.00 4.94
3457 4869 5.796350 ACTGTACTATTTTGAATCACGGC 57.204 39.130 0.00 0.00 0.00 5.68
3464 4876 1.695813 TTTGAATCACGGCGCATTTG 58.304 45.000 10.83 2.23 0.00 2.32
3471 4883 0.248580 CACGGCGCATTTGCATATGT 60.249 50.000 16.96 0.00 42.21 2.29
3472 4884 0.248580 ACGGCGCATTTGCATATGTG 60.249 50.000 21.83 21.83 42.21 3.21
3483 4895 1.016627 GCATATGTGCGTGGTGTCAT 58.983 50.000 4.29 0.00 42.28 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 1.134068 GGCCAACTTGTAGATCTCCCC 60.134 57.143 0.00 0.00 0.00 4.81
30 31 1.473434 CGGCCAACTTGTAGATCTCCC 60.473 57.143 2.24 0.00 0.00 4.30
31 32 1.941325 CGGCCAACTTGTAGATCTCC 58.059 55.000 2.24 0.00 0.00 3.71
32 33 1.134670 AGCGGCCAACTTGTAGATCTC 60.135 52.381 2.24 0.00 0.00 2.75
105 106 0.534203 GAACCTGAACCCAACTCGCA 60.534 55.000 0.00 0.00 0.00 5.10
135 136 0.038166 AGGCCAACATTGTGACCGAT 59.962 50.000 5.01 0.00 0.00 4.18
136 137 0.179004 AAGGCCAACATTGTGACCGA 60.179 50.000 5.01 0.00 0.00 4.69
137 138 0.039256 CAAGGCCAACATTGTGACCG 60.039 55.000 5.01 0.00 0.00 4.79
138 139 0.319813 GCAAGGCCAACATTGTGACC 60.320 55.000 5.01 0.00 0.00 4.02
139 140 3.199764 GCAAGGCCAACATTGTGAC 57.800 52.632 5.01 0.00 0.00 3.67
164 167 4.201920 GGAATATTGGTTTTCTGAGTCGGC 60.202 45.833 0.00 0.00 0.00 5.54
181 184 1.362717 CGCGAGTGGACCGGAATAT 59.637 57.895 9.46 0.00 0.00 1.28
182 185 2.802792 CGCGAGTGGACCGGAATA 59.197 61.111 9.46 0.00 0.00 1.75
183 186 4.814294 GCGCGAGTGGACCGGAAT 62.814 66.667 12.10 0.00 0.00 3.01
245 251 1.515081 TTTAGTGGCGTTACAGCACC 58.485 50.000 0.00 0.00 39.27 5.01
249 255 3.197434 GCCTTTTTAGTGGCGTTACAG 57.803 47.619 0.00 0.00 39.71 2.74
313 319 2.027100 CCCCTTTACACCTGGTTCTCTC 60.027 54.545 0.00 0.00 0.00 3.20
315 321 1.613520 GCCCCTTTACACCTGGTTCTC 60.614 57.143 0.00 0.00 0.00 2.87
371 383 0.808755 AAGGCGCCGTGAAATTAAGG 59.191 50.000 23.20 0.00 0.00 2.69
434 447 7.172875 TCGTAAAAATAAAAATGGGTCGTCTCA 59.827 33.333 0.00 0.00 0.00 3.27
435 448 7.479603 GTCGTAAAAATAAAAATGGGTCGTCTC 59.520 37.037 0.00 0.00 0.00 3.36
436 449 7.300320 GTCGTAAAAATAAAAATGGGTCGTCT 58.700 34.615 0.00 0.00 0.00 4.18
437 450 6.246956 CGTCGTAAAAATAAAAATGGGTCGTC 59.753 38.462 0.00 0.00 0.00 4.20
438 451 6.079120 CGTCGTAAAAATAAAAATGGGTCGT 58.921 36.000 0.00 0.00 0.00 4.34
439 452 5.508922 CCGTCGTAAAAATAAAAATGGGTCG 59.491 40.000 0.00 0.00 0.00 4.79
440 453 5.286797 GCCGTCGTAAAAATAAAAATGGGTC 59.713 40.000 0.00 0.00 0.00 4.46
441 454 5.162794 GCCGTCGTAAAAATAAAAATGGGT 58.837 37.500 0.00 0.00 0.00 4.51
624 644 1.810030 CTCCTCCTAAACGGCGTGC 60.810 63.158 15.70 0.00 0.00 5.34
626 646 2.577593 GCTCCTCCTAAACGGCGT 59.422 61.111 6.77 6.77 0.00 5.68
628 648 0.597898 GATCGCTCCTCCTAAACGGC 60.598 60.000 0.00 0.00 0.00 5.68
629 649 0.744874 TGATCGCTCCTCCTAAACGG 59.255 55.000 0.00 0.00 0.00 4.44
630 650 1.866063 GCTGATCGCTCCTCCTAAACG 60.866 57.143 2.84 0.00 35.14 3.60
631 651 1.859383 GCTGATCGCTCCTCCTAAAC 58.141 55.000 2.84 0.00 35.14 2.01
632 652 0.385751 CGCTGATCGCTCCTCCTAAA 59.614 55.000 7.71 0.00 36.13 1.85
633 653 2.033793 CGCTGATCGCTCCTCCTAA 58.966 57.895 7.71 0.00 36.13 2.69
634 654 3.751342 CGCTGATCGCTCCTCCTA 58.249 61.111 7.71 0.00 36.13 2.94
735 755 9.726438 ACCCATAATCTCTAAAAATTCCTATCG 57.274 33.333 0.00 0.00 0.00 2.92
808 830 3.966844 CAGTTAGCGCGCGTATATATAGG 59.033 47.826 32.35 9.19 0.00 2.57
891 923 3.592814 TCGTCGATAGGCCGGCTG 61.593 66.667 28.56 11.45 37.48 4.85
892 924 3.593794 GTCGTCGATAGGCCGGCT 61.594 66.667 28.56 15.07 37.48 5.52
905 937 1.226688 CGATCTGCGGTCATGTCGT 60.227 57.895 11.42 0.00 36.03 4.34
972 1004 0.734889 ATCCCGACTGTACGTAACCG 59.265 55.000 0.00 0.00 40.83 4.44
973 1005 2.164219 TCAATCCCGACTGTACGTAACC 59.836 50.000 0.00 0.00 0.00 2.85
974 1006 3.432782 CTCAATCCCGACTGTACGTAAC 58.567 50.000 0.00 0.00 0.00 2.50
975 1007 2.159338 GCTCAATCCCGACTGTACGTAA 60.159 50.000 0.00 0.00 0.00 3.18
976 1008 1.402968 GCTCAATCCCGACTGTACGTA 59.597 52.381 0.00 0.00 0.00 3.57
977 1009 0.172803 GCTCAATCCCGACTGTACGT 59.827 55.000 0.00 0.00 0.00 3.57
978 1010 0.866061 CGCTCAATCCCGACTGTACG 60.866 60.000 0.00 0.00 0.00 3.67
979 1011 1.146358 GCGCTCAATCCCGACTGTAC 61.146 60.000 0.00 0.00 0.00 2.90
988 1020 0.464373 TCTTCCATGGCGCTCAATCC 60.464 55.000 6.96 0.00 0.00 3.01
990 1022 1.091771 CGTCTTCCATGGCGCTCAAT 61.092 55.000 6.96 0.00 0.00 2.57
1008 1040 2.437359 CTTGGCTTCCCCTCTGCG 60.437 66.667 0.00 0.00 0.00 5.18
1029 1061 0.318762 GGCTGTACTCCCGGATGATC 59.681 60.000 0.73 0.00 0.00 2.92
1167 1199 3.164269 AGCATGAGGTAGGCCGGG 61.164 66.667 2.18 0.00 36.57 5.73
1206 1238 1.202302 CGACGATGCACAGAGGTACAT 60.202 52.381 0.00 0.00 33.66 2.29
1271 1331 3.732774 GCTGCAATCGATTGAAATCAGCA 60.733 43.478 36.82 27.26 43.42 4.41
1281 1341 2.283298 CACTACCAGCTGCAATCGATT 58.717 47.619 8.66 4.39 0.00 3.34
1483 1543 6.073447 TCAATTGTGTTATACCTGTGGGAT 57.927 37.500 5.13 0.00 36.25 3.85
1495 1555 8.681806 TCAAGTCAAGTCAATTCAATTGTGTTA 58.318 29.630 9.98 0.00 41.02 2.41
1734 1817 1.373999 GAAGAGCTGCACAGACGCT 60.374 57.895 1.02 0.00 36.57 5.07
1845 1928 2.597510 GCGTCCAGGGGCAAAACT 60.598 61.111 0.00 0.00 0.00 2.66
1962 2045 3.691342 TCCACGACGGCCAGGAAG 61.691 66.667 2.24 0.00 33.14 3.46
2257 2340 1.845568 GTTCACGAACGACACGTACAA 59.154 47.619 0.14 0.00 39.99 2.41
2596 2679 8.683615 ACCAGAAAAAGGAAAACAAACTACTAG 58.316 33.333 0.00 0.00 0.00 2.57
2597 2680 8.584063 ACCAGAAAAAGGAAAACAAACTACTA 57.416 30.769 0.00 0.00 0.00 1.82
2598 2681 7.476540 ACCAGAAAAAGGAAAACAAACTACT 57.523 32.000 0.00 0.00 0.00 2.57
2599 2682 8.680001 TCTACCAGAAAAAGGAAAACAAACTAC 58.320 33.333 0.00 0.00 0.00 2.73
2600 2683 8.810990 TCTACCAGAAAAAGGAAAACAAACTA 57.189 30.769 0.00 0.00 0.00 2.24
2601 2684 7.614192 TCTCTACCAGAAAAAGGAAAACAAACT 59.386 33.333 0.00 0.00 0.00 2.66
2622 2705 9.277783 CACCATTTTCTCTTCTTTTCTTCTCTA 57.722 33.333 0.00 0.00 0.00 2.43
2637 2720 1.678970 AGCCGCCCACCATTTTCTC 60.679 57.895 0.00 0.00 0.00 2.87
2735 2823 0.397675 TCCGAGATGAGATGGCTGGT 60.398 55.000 0.00 0.00 0.00 4.00
2742 2830 7.147776 TGTGCATGATAATATCCGAGATGAGAT 60.148 37.037 0.00 0.00 0.00 2.75
2748 2836 5.467035 TGTGTGCATGATAATATCCGAGA 57.533 39.130 0.00 0.00 0.00 4.04
2791 2879 9.959721 TGAGTAGCATCTAGACATACATACATA 57.040 33.333 0.00 0.00 0.00 2.29
2836 2937 4.766404 AATTGCTTACAGGGACGAAAAG 57.234 40.909 0.00 0.00 0.00 2.27
2970 3112 4.746951 TACGGCGAGCGACACACG 62.747 66.667 16.62 0.00 45.66 4.49
2991 3133 3.382832 AGTGGCGGAACTCGGGAG 61.383 66.667 0.00 0.00 39.69 4.30
3023 3165 1.898574 ATCCGCCCCATCAATTCGC 60.899 57.895 0.00 0.00 0.00 4.70
3066 3209 1.127567 TAAGCTGGGCACAGTGAGGT 61.128 55.000 19.18 0.00 46.62 3.85
3095 3238 0.868406 GTCTGCCCAGTCAAACGAAG 59.132 55.000 0.00 0.00 0.00 3.79
3106 3249 2.029964 GAACGAACGGTCTGCCCA 59.970 61.111 0.00 0.00 0.00 5.36
3113 3256 1.658409 GGACGAACGAACGAACGGT 60.658 57.895 11.97 3.91 37.61 4.83
3117 3260 0.571661 CAAACGGACGAACGAACGAA 59.428 50.000 17.35 0.00 37.61 3.85
3127 3278 1.489824 CGTACAAGCCAAACGGACG 59.510 57.895 0.00 0.00 33.13 4.79
3140 3291 0.107081 CAATATTCCCCGGGCGTACA 59.893 55.000 17.73 0.00 0.00 2.90
3149 3300 2.218603 CGGTACAGTGCAATATTCCCC 58.781 52.381 0.00 0.00 0.00 4.81
3191 3342 2.672651 CCCATGACAACCAGCGCA 60.673 61.111 11.47 0.00 0.00 6.09
3233 4645 0.459899 ATTCATCTCGCACCTACGCA 59.540 50.000 0.00 0.00 0.00 5.24
3391 4803 1.556564 CGAATGCGATCCTTACACGT 58.443 50.000 0.00 0.00 40.82 4.49
3392 4804 0.229753 GCGAATGCGATCCTTACACG 59.770 55.000 0.00 0.00 40.82 4.49
3393 4805 0.582005 GGCGAATGCGATCCTTACAC 59.418 55.000 0.00 0.00 44.10 2.90
3394 4806 0.531974 GGGCGAATGCGATCCTTACA 60.532 55.000 0.00 0.00 44.10 2.41
3418 4830 6.827641 AGTACAGTAACAATAATGCACAACG 58.172 36.000 0.00 0.00 28.13 4.10
3432 4844 7.178074 GCCGTGATTCAAAATAGTACAGTAAC 58.822 38.462 0.00 0.00 0.00 2.50
3435 4847 4.328983 CGCCGTGATTCAAAATAGTACAGT 59.671 41.667 0.00 0.00 0.00 3.55
3436 4848 4.782195 GCGCCGTGATTCAAAATAGTACAG 60.782 45.833 0.00 0.00 0.00 2.74
3437 4849 3.062909 GCGCCGTGATTCAAAATAGTACA 59.937 43.478 0.00 0.00 0.00 2.90
3438 4850 3.062909 TGCGCCGTGATTCAAAATAGTAC 59.937 43.478 4.18 0.00 0.00 2.73
3439 4851 3.263261 TGCGCCGTGATTCAAAATAGTA 58.737 40.909 4.18 0.00 0.00 1.82
3441 4853 2.823196 TGCGCCGTGATTCAAAATAG 57.177 45.000 4.18 0.00 0.00 1.73
3442 4854 3.773860 AATGCGCCGTGATTCAAAATA 57.226 38.095 4.18 0.00 0.00 1.40
3443 4855 2.652941 AATGCGCCGTGATTCAAAAT 57.347 40.000 4.18 0.00 0.00 1.82
3444 4856 2.057316 CAAATGCGCCGTGATTCAAAA 58.943 42.857 4.18 0.00 0.00 2.44
3445 4857 1.695813 CAAATGCGCCGTGATTCAAA 58.304 45.000 4.18 0.00 0.00 2.69
3446 4858 0.732196 GCAAATGCGCCGTGATTCAA 60.732 50.000 4.18 0.00 0.00 2.69
3447 4859 1.154054 GCAAATGCGCCGTGATTCA 60.154 52.632 4.18 0.00 0.00 2.57
3448 4860 0.526096 ATGCAAATGCGCCGTGATTC 60.526 50.000 4.18 0.00 45.83 2.52
3449 4861 0.737804 TATGCAAATGCGCCGTGATT 59.262 45.000 4.18 0.00 45.83 2.57


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

AutoCloner maintained by Alex Coulton.