Multiple sequence alignment - TraesCS2A01G352000

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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 TraesCS2A01G352000 chr2A 100.000 2578 0 0 1 2578 592689858 592692435 0.000000e+00 4761
1 TraesCS2A01G352000 chr2A 100.000 1312 0 0 2863 4174 592692720 592694031 0.000000e+00 2423
2 TraesCS2A01G352000 chr2B 90.802 2555 115 59 89 2578 527872328 527874827 0.000000e+00 3306
3 TraesCS2A01G352000 chr2B 92.751 676 35 7 2870 3541 527874838 527875503 0.000000e+00 965
4 TraesCS2A01G352000 chr2B 85.346 621 36 19 3570 4174 527875502 527876083 3.590000e-165 592
5 TraesCS2A01G352000 chr2B 93.684 95 1 2 1 95 527872211 527872300 2.020000e-28 137
6 TraesCS2A01G352000 chr2D 93.050 2259 80 34 344 2578 448120323 448122528 0.000000e+00 3230
7 TraesCS2A01G352000 chr2D 92.679 1325 58 18 2870 4169 448122539 448123849 0.000000e+00 1873
8 TraesCS2A01G352000 chr2D 87.197 289 8 9 93 352 448119686 448119974 6.780000e-78 302
9 TraesCS2A01G352000 chr2D 93.684 95 2 1 1 95 448119562 448119652 5.630000e-29 139
10 TraesCS2A01G352000 chr7A 92.522 682 42 5 1788 2468 10809169 10809842 0.000000e+00 968
11 TraesCS2A01G352000 chr7A 94.595 185 6 1 1565 1749 10808980 10809160 2.460000e-72 283
12 TraesCS2A01G352000 chr3B 89.826 403 29 3 1370 1772 275910389 275910779 1.340000e-139 507
13 TraesCS2A01G352000 chr4A 90.685 365 25 4 2009 2372 196611477 196611121 1.050000e-130 477
14 TraesCS2A01G352000 chr4A 91.608 143 12 0 1370 1512 196613216 196613074 9.150000e-47 198


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 TraesCS2A01G352000 chr2A 592689858 592694031 4173 False 3592.0 4761 100.00000 1 4174 2 chr2A.!!$F1 4173
1 TraesCS2A01G352000 chr2B 527872211 527876083 3872 False 1250.0 3306 90.64575 1 4174 4 chr2B.!!$F1 4173
2 TraesCS2A01G352000 chr2D 448119562 448123849 4287 False 1386.0 3230 91.65250 1 4169 4 chr2D.!!$F1 4168
3 TraesCS2A01G352000 chr7A 10808980 10809842 862 False 625.5 968 93.55850 1565 2468 2 chr7A.!!$F1 903
4 TraesCS2A01G352000 chr4A 196611121 196613216 2095 True 337.5 477 91.14650 1370 2372 2 chr4A.!!$R1 1002

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
940 1404 0.178953 ACCCAAGAAAGGCACAGCAT 60.179 50.0 0.0 0.0 0.0 3.79 F
943 1407 0.455633 CAAGAAAGGCACAGCATCGC 60.456 55.0 0.0 0.0 0.0 4.58 F
2522 4189 0.530744 TCCATTCGTTGACTCCTCCG 59.469 55.0 0.0 0.0 0.0 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2278 3941 0.179034 GTATCCAGCCAGCCAAGGAG 60.179 60.0 0.00 0.0 32.91 3.69 R
2556 4223 0.756294 TTCTGCCGTCCTCAAGAACA 59.244 50.0 0.00 0.0 0.00 3.18 R
3864 5562 0.249280 GTTGGTGCCCGAAACCTTTG 60.249 55.0 3.34 0.0 38.60 2.77 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
57 58 3.415087 ATCTGGACCAGCCTGCCC 61.415 66.667 17.33 0.00 37.63 5.36
86 87 0.851332 CTTCCTTTCCCCCTCCCCTT 60.851 60.000 0.00 0.00 0.00 3.95
170 212 3.061848 GCCCGCTTTGCTTGGCTA 61.062 61.111 11.07 0.00 39.74 3.93
171 213 2.877691 CCCGCTTTGCTTGGCTAC 59.122 61.111 0.00 0.00 0.00 3.58
172 214 1.675641 CCCGCTTTGCTTGGCTACT 60.676 57.895 0.00 0.00 0.00 2.57
174 216 1.503542 CGCTTTGCTTGGCTACTGG 59.496 57.895 0.00 0.00 0.00 4.00
270 335 1.529865 GTTTGTCCCTGCTCGTGTAAC 59.470 52.381 0.00 0.00 0.00 2.50
331 396 2.765699 TGGATTGGCTTCTATTTTGGCC 59.234 45.455 0.00 0.00 44.31 5.36
348 413 2.288702 TGGCCGTTTTTCATCATTGGTG 60.289 45.455 0.00 0.00 0.00 4.17
349 414 1.726248 GCCGTTTTTCATCATTGGTGC 59.274 47.619 0.00 0.00 0.00 5.01
439 875 3.550436 GCCATGCTCGACTTACTACTACC 60.550 52.174 0.00 0.00 0.00 3.18
460 896 3.141398 CACTGCAGAACTGTGTACCAAT 58.859 45.455 23.35 0.00 41.81 3.16
484 926 2.742116 TACGGGAGATGGGCCAAGC 61.742 63.158 11.89 5.89 0.00 4.01
496 938 2.825532 TGGGCCAAGCAAAGACTTTATC 59.174 45.455 2.13 0.00 0.00 1.75
530 972 3.757745 CGTAGCTTTGGTGGTAATTGG 57.242 47.619 0.00 0.00 0.00 3.16
531 973 3.078837 CGTAGCTTTGGTGGTAATTGGT 58.921 45.455 0.00 0.00 0.00 3.67
532 974 4.255301 CGTAGCTTTGGTGGTAATTGGTA 58.745 43.478 0.00 0.00 0.00 3.25
534 976 5.181622 CGTAGCTTTGGTGGTAATTGGTAAA 59.818 40.000 0.00 0.00 0.00 2.01
535 977 5.462530 AGCTTTGGTGGTAATTGGTAAAC 57.537 39.130 0.00 0.00 0.00 2.01
536 978 4.022676 AGCTTTGGTGGTAATTGGTAAACG 60.023 41.667 0.00 0.00 0.00 3.60
572 1015 4.740268 TCATTTCTGCAATCACATCAAGC 58.260 39.130 0.00 0.00 0.00 4.01
580 1023 3.244976 CAATCACATCAAGCGGAAAACC 58.755 45.455 0.00 0.00 0.00 3.27
592 1035 1.660264 GAAAACCCCGCTGCAAACG 60.660 57.895 0.00 1.91 0.00 3.60
617 1060 1.820581 CAAGGATTGGCTGCCATGG 59.179 57.895 24.03 7.63 43.94 3.66
621 1064 0.903942 GGATTGGCTGCCATGGAAAA 59.096 50.000 24.03 6.57 31.53 2.29
622 1065 1.278699 GGATTGGCTGCCATGGAAAAA 59.721 47.619 24.03 5.72 31.53 1.94
635 1078 1.360931 GGAAAAATGCATGTGCGCCC 61.361 55.000 4.18 0.00 45.83 6.13
753 1200 1.075600 GGAGTCAGGGAGGGAGGAG 60.076 68.421 0.00 0.00 0.00 3.69
754 1201 1.075600 GAGTCAGGGAGGGAGGAGG 60.076 68.421 0.00 0.00 0.00 4.30
755 1202 1.547755 AGTCAGGGAGGGAGGAGGA 60.548 63.158 0.00 0.00 0.00 3.71
776 1223 7.147655 GGAGGATATATGTACATACTGGCACAT 60.148 40.741 17.69 3.42 38.20 3.21
932 1396 0.392706 GGTGCCAAACCCAAGAAAGG 59.607 55.000 0.00 0.00 44.02 3.11
940 1404 0.178953 ACCCAAGAAAGGCACAGCAT 60.179 50.000 0.00 0.00 0.00 3.79
941 1405 0.529378 CCCAAGAAAGGCACAGCATC 59.471 55.000 0.00 0.00 0.00 3.91
943 1407 0.455633 CAAGAAAGGCACAGCATCGC 60.456 55.000 0.00 0.00 0.00 4.58
949 1413 3.506108 GCACAGCATCGCCAATCT 58.494 55.556 0.00 0.00 0.00 2.40
950 1414 1.063649 GCACAGCATCGCCAATCTG 59.936 57.895 0.00 0.00 0.00 2.90
951 1415 1.651240 GCACAGCATCGCCAATCTGT 61.651 55.000 0.00 0.00 40.08 3.41
953 1417 1.063649 CAGCATCGCCAATCTGTGC 59.936 57.895 0.00 0.00 36.11 4.57
973 1445 3.839432 CGGGAAGCTCGGGGAGAC 61.839 72.222 0.00 0.00 0.00 3.36
974 1446 2.683933 GGGAAGCTCGGGGAGACA 60.684 66.667 0.00 0.00 0.00 3.41
975 1447 2.726351 GGGAAGCTCGGGGAGACAG 61.726 68.421 0.00 0.00 0.00 3.51
976 1448 1.682684 GGAAGCTCGGGGAGACAGA 60.683 63.158 0.00 0.00 0.00 3.41
1017 1489 1.000866 AATGGGGGCTTCCTCTTGC 59.999 57.895 0.00 0.00 35.33 4.01
1095 1567 1.213013 CCACCAGAAGTCGGACTCG 59.787 63.158 11.71 3.33 37.82 4.18
1233 1705 0.674895 GCTGCGGATTTCTGGTCTGT 60.675 55.000 0.00 0.00 0.00 3.41
1234 1706 1.081892 CTGCGGATTTCTGGTCTGTG 58.918 55.000 0.00 0.00 0.00 3.66
1249 1721 3.068024 GGTCTGTGTTTTCCAGCAATCAA 59.932 43.478 0.00 0.00 0.00 2.57
1250 1722 4.293415 GTCTGTGTTTTCCAGCAATCAAG 58.707 43.478 0.00 0.00 0.00 3.02
1251 1723 3.054878 CTGTGTTTTCCAGCAATCAAGC 58.945 45.455 0.00 0.00 0.00 4.01
1252 1724 2.224018 TGTGTTTTCCAGCAATCAAGCC 60.224 45.455 0.00 0.00 34.23 4.35
1255 1727 0.597568 TTTCCAGCAATCAAGCCGTG 59.402 50.000 0.00 0.00 34.23 4.94
1373 1848 1.065928 GAGATCCTACGTGGCGGTG 59.934 63.158 0.00 0.00 35.26 4.94
1550 2025 4.309950 GCCGTGTCCAAGTCCGGT 62.310 66.667 0.00 0.00 42.36 5.28
1752 2537 4.154918 CACCGCTAATTCTCTTTTCTGCTT 59.845 41.667 0.00 0.00 0.00 3.91
1769 2554 2.887337 GCTTGAGAGAGCAGTAGTTCC 58.113 52.381 0.00 0.00 42.25 3.62
1770 2555 2.733858 GCTTGAGAGAGCAGTAGTTCCG 60.734 54.545 0.00 0.00 42.25 4.30
1771 2556 2.201921 TGAGAGAGCAGTAGTTCCGT 57.798 50.000 0.00 0.00 0.00 4.69
1774 2559 3.690139 TGAGAGAGCAGTAGTTCCGTAAG 59.310 47.826 0.00 0.00 0.00 2.34
1776 2561 4.333690 AGAGAGCAGTAGTTCCGTAAGAA 58.666 43.478 0.00 0.00 43.02 2.52
1778 2563 5.243283 AGAGAGCAGTAGTTCCGTAAGAAAA 59.757 40.000 0.00 0.00 43.02 2.29
1789 2574 3.444618 CGTAAGAAAAACGGCCAGTAC 57.555 47.619 2.24 0.00 43.02 2.73
1790 2575 2.801679 CGTAAGAAAAACGGCCAGTACA 59.198 45.455 2.24 0.00 43.02 2.90
1791 2576 3.363280 CGTAAGAAAAACGGCCAGTACAC 60.363 47.826 2.24 0.00 43.02 2.90
2087 3744 0.670546 ACGGGCTCAAGAACATCGTG 60.671 55.000 0.00 0.00 0.00 4.35
2146 3803 4.814294 CCTCCAGGTACGCACGCC 62.814 72.222 0.00 0.00 0.00 5.68
2157 3814 2.202349 GCACGCCGCACAGAATTC 60.202 61.111 0.00 0.00 41.79 2.17
2167 3828 4.245660 CCGCACAGAATTCTTCTTGAGTA 58.754 43.478 4.86 0.00 38.11 2.59
2256 3919 1.411977 TGGTTGTGTGGAAATTGCTGG 59.588 47.619 0.00 0.00 0.00 4.85
2278 3941 3.127721 GCTAATCTGAGTCCACTTTTGGC 59.872 47.826 0.00 0.00 43.56 4.52
2398 4061 9.294030 CAGCAAGAAATTTTACCAGCTTATTAG 57.706 33.333 0.00 0.00 0.00 1.73
2479 4142 0.964860 TTTCCACATGCCCCGTGATG 60.965 55.000 0.00 0.00 36.43 3.07
2482 4145 1.656818 CCACATGCCCCGTGATGTTC 61.657 60.000 0.00 0.00 36.43 3.18
2496 4163 4.142534 CGTGATGTTCTTGCCATCAGAATT 60.143 41.667 3.48 0.00 46.80 2.17
2519 4186 1.347707 TGCTTCCATTCGTTGACTCCT 59.652 47.619 0.00 0.00 0.00 3.69
2520 4187 2.003301 GCTTCCATTCGTTGACTCCTC 58.997 52.381 0.00 0.00 0.00 3.71
2521 4188 2.622436 CTTCCATTCGTTGACTCCTCC 58.378 52.381 0.00 0.00 0.00 4.30
2522 4189 0.530744 TCCATTCGTTGACTCCTCCG 59.469 55.000 0.00 0.00 0.00 4.63
2554 4221 3.071459 CTGTCGGTCGCGTTCATGC 62.071 63.158 5.77 0.00 0.00 4.06
2555 4222 3.109547 GTCGGTCGCGTTCATGCA 61.110 61.111 5.77 0.00 34.15 3.96
2556 4223 2.125713 TCGGTCGCGTTCATGCAT 60.126 55.556 5.77 0.00 34.15 3.96
2557 4224 2.021793 CGGTCGCGTTCATGCATG 59.978 61.111 21.07 21.07 34.15 4.06
2902 4572 2.996249 ACCACGATGATGATCTGCTT 57.004 45.000 0.00 0.00 0.00 3.91
2905 4575 2.728318 CCACGATGATGATCTGCTTACG 59.272 50.000 0.00 0.00 0.00 3.18
2930 4600 1.680735 TGCTTGTGTTGGTTGATGGAC 59.319 47.619 0.00 0.00 0.00 4.02
2931 4601 1.680735 GCTTGTGTTGGTTGATGGACA 59.319 47.619 0.00 0.00 0.00 4.02
2932 4602 2.543653 GCTTGTGTTGGTTGATGGACAC 60.544 50.000 0.00 0.00 41.97 3.67
2933 4603 1.304254 TGTGTTGGTTGATGGACACG 58.696 50.000 0.00 0.00 43.93 4.49
3183 4857 0.741326 CGACGACTGATGACCCATCT 59.259 55.000 8.22 0.00 41.06 2.90
3184 4858 1.947456 CGACGACTGATGACCCATCTA 59.053 52.381 8.22 0.00 41.06 1.98
3185 4859 2.554462 CGACGACTGATGACCCATCTAT 59.446 50.000 8.22 0.00 41.06 1.98
3195 4869 4.485653 TGACCCATCTATCATCACCCTA 57.514 45.455 0.00 0.00 0.00 3.53
3261 4935 2.278401 GGCTACTACCGAACGGCG 60.278 66.667 13.32 4.80 39.32 6.46
3288 4962 2.580867 GTAGCTCACCTCGCAGCG 60.581 66.667 9.06 9.06 40.84 5.18
3352 5030 3.006110 TCTTTTGCGGTATAGGATACGGG 59.994 47.826 6.38 0.00 46.39 5.28
3363 5041 1.218196 AGGATACGGGACAGGAGTGAT 59.782 52.381 0.00 0.00 46.39 3.06
3390 5069 1.002544 GCTGAGCCTAATTAGCCGGAT 59.997 52.381 5.05 0.00 0.00 4.18
3441 5120 5.475564 ACATGGTGTTGTTATTCTTGTACCC 59.524 40.000 0.00 0.00 0.00 3.69
3446 5125 4.263594 TGTTGTTATTCTTGTACCCTCCCC 60.264 45.833 0.00 0.00 0.00 4.81
3488 5167 2.457366 TGCTCGAGTTTTCTTCCTCC 57.543 50.000 15.13 0.00 0.00 4.30
3493 5172 4.995487 GCTCGAGTTTTCTTCCTCCTTTTA 59.005 41.667 15.13 0.00 0.00 1.52
3494 5173 5.107026 GCTCGAGTTTTCTTCCTCCTTTTAC 60.107 44.000 15.13 0.00 0.00 2.01
3496 5175 6.531021 TCGAGTTTTCTTCCTCCTTTTACAT 58.469 36.000 0.00 0.00 0.00 2.29
3497 5176 6.426937 TCGAGTTTTCTTCCTCCTTTTACATG 59.573 38.462 0.00 0.00 0.00 3.21
3498 5177 6.204882 CGAGTTTTCTTCCTCCTTTTACATGT 59.795 38.462 2.69 2.69 0.00 3.21
3499 5178 7.386848 CGAGTTTTCTTCCTCCTTTTACATGTA 59.613 37.037 0.08 0.08 0.00 2.29
3522 5201 9.908152 TGTATGTACATCGATCGATTTTATTCT 57.092 29.630 27.45 11.65 31.62 2.40
3545 5229 2.905075 TCCATGATGGATTCACGACAC 58.095 47.619 10.75 0.00 42.67 3.67
3547 5231 1.594397 CATGATGGATTCACGACACCG 59.406 52.381 0.00 0.00 37.11 4.94
3549 5233 0.174845 GATGGATTCACGACACCGGA 59.825 55.000 9.46 0.00 40.78 5.14
3550 5234 0.175760 ATGGATTCACGACACCGGAG 59.824 55.000 9.46 1.26 40.78 4.63
3552 5236 1.215647 GATTCACGACACCGGAGCT 59.784 57.895 9.46 0.00 40.78 4.09
3566 5250 1.743252 GAGCTGCCCTTTGGTCGAG 60.743 63.158 0.00 0.00 0.00 4.04
3569 5253 1.371183 CTGCCCTTTGGTCGAGTGA 59.629 57.895 0.00 0.00 0.00 3.41
3629 5314 5.412594 TGAGAGAGCAATGAAAACATGTACC 59.587 40.000 0.00 0.00 0.00 3.34
3662 5347 4.460948 AATGTTGGTCAGCAATCATTCC 57.539 40.909 9.99 0.00 0.00 3.01
3688 5373 7.609097 TCTTGCTGAAAGAGATATACTCCAT 57.391 36.000 0.00 0.00 45.96 3.41
3690 5375 8.489489 TCTTGCTGAAAGAGATATACTCCATTT 58.511 33.333 0.00 0.00 45.96 2.32
3691 5376 8.442632 TTGCTGAAAGAGATATACTCCATTTG 57.557 34.615 0.00 0.00 45.96 2.32
3696 5381 6.753913 AAGAGATATACTCCATTTGCAGGA 57.246 37.500 0.00 0.00 45.96 3.86
3704 5389 4.666512 ACTCCATTTGCAGGACATTAACT 58.333 39.130 0.00 0.00 0.00 2.24
3708 5393 4.418392 CATTTGCAGGACATTAACTCAGC 58.582 43.478 0.00 0.00 0.00 4.26
3728 5413 2.791004 GCAGCAAAATTTAGGCTATGCG 59.209 45.455 14.71 7.59 38.74 4.73
3732 5417 3.796717 GCAAAATTTAGGCTATGCGTTCC 59.203 43.478 0.00 0.00 0.00 3.62
3855 5553 4.101942 GCTTCAACTATCAGTCTCTCACG 58.898 47.826 0.00 0.00 0.00 4.35
3864 5562 4.797693 TCAGTCTCTCACGATATTCGAC 57.202 45.455 3.62 0.00 43.74 4.20
3967 5665 3.979495 GCTTTCATCAGTTCTGCAACAAG 59.021 43.478 0.00 0.00 34.60 3.16
4056 5754 0.319728 ACTAGCCTATGCATGAGCCG 59.680 55.000 10.16 8.50 41.13 5.52
4075 5773 1.135731 CTCGACTCGACTCAGGCAC 59.864 63.158 0.00 0.00 0.00 5.01
4089 5787 0.531090 AGGCACGAGTACAACGCAAA 60.531 50.000 11.31 0.00 0.00 3.68
4131 5829 4.886121 GTACCCTACCTGCGCCGC 62.886 72.222 4.18 0.00 0.00 6.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
119 156 2.272471 GAGGAAGGGGAAAGCGGG 59.728 66.667 0.00 0.00 0.00 6.13
121 158 2.820037 GCGAGGAAGGGGAAAGCG 60.820 66.667 0.00 0.00 0.00 4.68
164 206 1.907739 CTAGCCAGCCAGTAGCCAA 59.092 57.895 0.00 0.00 45.47 4.52
270 335 0.250513 GCTTGTCCTGTAGAGGTGGG 59.749 60.000 5.71 0.00 40.76 4.61
306 371 4.339247 CCAAAATAGAAGCCAATCCATCGT 59.661 41.667 0.00 0.00 0.00 3.73
331 396 1.984990 CGGCACCAATGATGAAAAACG 59.015 47.619 0.00 0.00 0.00 3.60
348 413 4.683334 GTTGCTTGTGACCGCGGC 62.683 66.667 28.58 19.01 0.00 6.53
349 414 4.368808 CGTTGCTTGTGACCGCGG 62.369 66.667 26.86 26.86 0.00 6.46
439 875 2.238942 TGGTACACAGTTCTGCAGTG 57.761 50.000 14.67 7.47 40.01 3.66
460 896 1.327690 GCCCATCTCCCGTACTGTCA 61.328 60.000 0.00 0.00 0.00 3.58
484 926 4.633565 GGCTCCACTCTGATAAAGTCTTTG 59.366 45.833 8.14 0.00 0.00 2.77
496 938 1.140589 CTACGCTGGCTCCACTCTG 59.859 63.158 0.00 0.00 0.00 3.35
527 969 3.564053 AAGAAGACCCACGTTTACCAA 57.436 42.857 0.00 0.00 0.00 3.67
528 970 3.135167 AGAAAGAAGACCCACGTTTACCA 59.865 43.478 0.00 0.00 0.00 3.25
529 971 3.736720 AGAAAGAAGACCCACGTTTACC 58.263 45.455 0.00 0.00 0.00 2.85
530 972 4.374399 TGAGAAAGAAGACCCACGTTTAC 58.626 43.478 0.00 0.00 0.00 2.01
531 973 4.675976 TGAGAAAGAAGACCCACGTTTA 57.324 40.909 0.00 0.00 0.00 2.01
532 974 3.553828 TGAGAAAGAAGACCCACGTTT 57.446 42.857 0.00 0.00 0.00 3.60
534 976 3.771577 AATGAGAAAGAAGACCCACGT 57.228 42.857 0.00 0.00 0.00 4.49
535 977 4.153117 CAGAAATGAGAAAGAAGACCCACG 59.847 45.833 0.00 0.00 0.00 4.94
536 978 4.083057 GCAGAAATGAGAAAGAAGACCCAC 60.083 45.833 0.00 0.00 0.00 4.61
592 1035 4.133796 GCCAATCCTTGCACCGCC 62.134 66.667 0.00 0.00 0.00 6.13
617 1060 1.360931 GGGGCGCACATGCATTTTTC 61.361 55.000 13.89 0.00 42.21 2.29
621 1064 4.764771 AGGGGGCGCACATGCATT 62.765 61.111 13.89 0.00 42.21 3.56
635 1078 1.207329 GGTTCACCTACAGCTACAGGG 59.793 57.143 15.38 5.43 36.15 4.45
753 1200 6.697455 CGATGTGCCAGTATGTACATATATCC 59.303 42.308 18.27 6.03 40.53 2.59
754 1201 6.199154 GCGATGTGCCAGTATGTACATATATC 59.801 42.308 18.27 9.21 40.53 1.63
755 1202 6.042777 GCGATGTGCCAGTATGTACATATAT 58.957 40.000 18.27 8.10 40.53 0.86
776 1223 0.874175 CCAATCGAATGCCGTAGCGA 60.874 55.000 0.00 0.00 44.31 4.93
919 1383 0.752658 GCTGTGCCTTTCTTGGGTTT 59.247 50.000 0.00 0.00 0.00 3.27
932 1396 1.063649 CAGATTGGCGATGCTGTGC 59.936 57.895 0.00 0.00 0.00 4.57
941 1405 4.170062 CCGCTGCACAGATTGGCG 62.170 66.667 7.22 7.22 44.48 5.69
943 1407 1.651240 CTTCCCGCTGCACAGATTGG 61.651 60.000 0.81 0.00 0.00 3.16
944 1408 1.798735 CTTCCCGCTGCACAGATTG 59.201 57.895 0.81 0.00 0.00 2.67
945 1409 2.042831 GCTTCCCGCTGCACAGATT 61.043 57.895 0.81 0.00 35.14 2.40
946 1410 2.437359 GCTTCCCGCTGCACAGAT 60.437 61.111 0.81 0.00 35.14 2.90
973 1445 3.488384 GCGTCAGTCAGTCTAATCCTCTG 60.488 52.174 0.00 0.00 0.00 3.35
974 1446 2.685897 GCGTCAGTCAGTCTAATCCTCT 59.314 50.000 0.00 0.00 0.00 3.69
975 1447 2.539953 CGCGTCAGTCAGTCTAATCCTC 60.540 54.545 0.00 0.00 0.00 3.71
976 1448 1.402259 CGCGTCAGTCAGTCTAATCCT 59.598 52.381 0.00 0.00 0.00 3.24
1233 1705 1.000385 CGGCTTGATTGCTGGAAAACA 60.000 47.619 0.00 0.00 35.80 2.83
1234 1706 1.000274 ACGGCTTGATTGCTGGAAAAC 60.000 47.619 0.00 0.00 43.17 2.43
1252 1724 3.451556 ATCAGATCAGGCGGCCACG 62.452 63.158 23.09 12.09 44.63 4.94
1255 1727 2.031768 GGATCAGATCAGGCGGCC 59.968 66.667 12.11 12.11 0.00 6.13
1373 1848 4.426313 CCCTTGCCCGAGAACCCC 62.426 72.222 0.00 0.00 0.00 4.95
1444 1919 0.460284 CAGGTAGTACTGCTTGGCGG 60.460 60.000 14.18 0.00 41.29 6.13
1711 2209 4.764823 GCGGTGGAATTAATAATGGATGGA 59.235 41.667 0.00 0.00 0.00 3.41
1712 2210 4.766891 AGCGGTGGAATTAATAATGGATGG 59.233 41.667 0.00 0.00 0.00 3.51
1714 2212 8.650143 AATTAGCGGTGGAATTAATAATGGAT 57.350 30.769 0.00 0.00 0.00 3.41
1752 2537 2.201921 ACGGAACTACTGCTCTCTCA 57.798 50.000 0.00 0.00 0.00 3.27
1769 2554 2.801679 TGTACTGGCCGTTTTTCTTACG 59.198 45.455 0.00 0.00 38.67 3.18
1770 2555 3.560896 TGTGTACTGGCCGTTTTTCTTAC 59.439 43.478 0.00 0.00 0.00 2.34
1771 2556 3.806380 TGTGTACTGGCCGTTTTTCTTA 58.194 40.909 0.00 0.00 0.00 2.10
1774 2559 3.636282 AATGTGTACTGGCCGTTTTTC 57.364 42.857 0.00 0.00 0.00 2.29
1776 2561 4.394439 AAAAATGTGTACTGGCCGTTTT 57.606 36.364 0.00 0.00 0.00 2.43
2087 3744 2.690778 GCCGATGACCTTGTGCACC 61.691 63.158 15.69 0.00 0.00 5.01
2157 3814 7.048629 TCTAATGAGGCTCATACTCAAGAAG 57.951 40.000 29.02 15.43 46.89 2.85
2167 3828 3.249752 AGGCTGATCTAATGAGGCTCAT 58.750 45.455 24.01 24.01 38.13 2.90
2278 3941 0.179034 GTATCCAGCCAGCCAAGGAG 60.179 60.000 0.00 0.00 32.91 3.69
2404 4067 9.598517 GTCAACATCTACTACAGTACTACTACT 57.401 37.037 0.00 0.00 33.01 2.57
2405 4068 9.598517 AGTCAACATCTACTACAGTACTACTAC 57.401 37.037 0.00 0.00 0.00 2.73
2496 4163 3.002791 GAGTCAACGAATGGAAGCATCA 58.997 45.455 0.00 0.00 0.00 3.07
2506 4173 1.835494 TCTCGGAGGAGTCAACGAAT 58.165 50.000 4.96 0.00 41.26 3.34
2519 4186 3.373130 CGACAGTGTGTACTATTCTCGGA 59.627 47.826 0.00 0.00 34.74 4.55
2520 4187 3.487042 CCGACAGTGTGTACTATTCTCGG 60.487 52.174 0.00 0.00 34.74 4.63
2521 4188 3.126514 ACCGACAGTGTGTACTATTCTCG 59.873 47.826 0.00 0.00 34.74 4.04
2522 4189 4.660105 GACCGACAGTGTGTACTATTCTC 58.340 47.826 0.00 0.00 34.74 2.87
2554 4221 1.081892 CTGCCGTCCTCAAGAACATG 58.918 55.000 0.00 0.00 0.00 3.21
2555 4222 0.976641 TCTGCCGTCCTCAAGAACAT 59.023 50.000 0.00 0.00 0.00 2.71
2556 4223 0.756294 TTCTGCCGTCCTCAAGAACA 59.244 50.000 0.00 0.00 0.00 3.18
2557 4224 1.000955 TCTTCTGCCGTCCTCAAGAAC 59.999 52.381 0.00 0.00 0.00 3.01
2862 4529 4.567747 GGTTTCACCTCTCTCTCTCTCTCT 60.568 50.000 0.00 0.00 34.73 3.10
2863 4530 3.694566 GGTTTCACCTCTCTCTCTCTCTC 59.305 52.174 0.00 0.00 34.73 3.20
2864 4531 3.075283 TGGTTTCACCTCTCTCTCTCTCT 59.925 47.826 0.00 0.00 39.58 3.10
2865 4532 3.192633 GTGGTTTCACCTCTCTCTCTCTC 59.807 52.174 0.00 0.00 39.58 3.20
2866 4533 3.161866 GTGGTTTCACCTCTCTCTCTCT 58.838 50.000 0.00 0.00 39.58 3.10
2867 4534 2.094957 CGTGGTTTCACCTCTCTCTCTC 60.095 54.545 0.00 0.00 39.58 3.20
2868 4535 1.889829 CGTGGTTTCACCTCTCTCTCT 59.110 52.381 0.00 0.00 39.58 3.10
2878 4545 3.242543 GCAGATCATCATCGTGGTTTCAC 60.243 47.826 0.00 0.00 40.36 3.18
2905 4575 0.872881 CAACCAACACAAGCAGCAGC 60.873 55.000 0.00 0.00 42.56 5.25
3183 4857 5.721480 CCATGTAGGATGTAGGGTGATGATA 59.279 44.000 0.00 0.00 41.22 2.15
3184 4858 4.533707 CCATGTAGGATGTAGGGTGATGAT 59.466 45.833 0.00 0.00 41.22 2.45
3185 4859 3.903714 CCATGTAGGATGTAGGGTGATGA 59.096 47.826 0.00 0.00 41.22 2.92
3234 4908 1.583054 GGTAGTAGCCGCTCCAAATG 58.417 55.000 0.00 0.00 0.00 2.32
3254 4928 0.656785 TACCACAAACAACGCCGTTC 59.343 50.000 0.00 0.00 0.00 3.95
3288 4962 2.414785 AAATTCGCCATCCGCCCAC 61.415 57.895 0.00 0.00 36.73 4.61
3352 5030 3.119291 CAGCGACATAATCACTCCTGTC 58.881 50.000 0.00 0.00 35.72 3.51
3363 5041 4.307432 GCTAATTAGGCTCAGCGACATAA 58.693 43.478 14.28 0.00 0.00 1.90
3373 5052 1.443802 GCATCCGGCTAATTAGGCTC 58.556 55.000 29.79 13.98 45.70 4.70
3390 5069 7.557358 ACCAATGTACAAATATGAATCAGAGCA 59.443 33.333 0.00 0.00 0.00 4.26
3427 5106 2.744166 GCGGGGAGGGTACAAGAATAAC 60.744 54.545 0.00 0.00 0.00 1.89
3441 5120 2.931068 GCAACCAAAAGGCGGGGAG 61.931 63.158 0.00 0.00 0.00 4.30
3446 5125 0.671251 TACCAAGCAACCAAAAGGCG 59.329 50.000 0.00 0.00 0.00 5.52
3488 5167 8.502161 TCGATCGATGTACATACATGTAAAAG 57.498 34.615 15.15 5.78 46.20 2.27
3493 5172 7.946655 AAAATCGATCGATGTACATACATGT 57.053 32.000 29.99 7.98 46.20 3.21
3496 5175 9.908152 AGAATAAAATCGATCGATGTACATACA 57.092 29.630 29.99 10.75 40.98 2.29
3545 5229 4.351054 ACCAAAGGGCAGCTCCGG 62.351 66.667 0.00 0.00 37.90 5.14
3547 5231 2.747855 CGACCAAAGGGCAGCTCC 60.748 66.667 0.00 0.00 37.90 4.70
3549 5233 2.348998 CTCGACCAAAGGGCAGCT 59.651 61.111 0.00 0.00 37.90 4.24
3550 5234 2.032681 ACTCGACCAAAGGGCAGC 59.967 61.111 0.00 0.00 37.90 5.25
3552 5236 1.070786 GTCACTCGACCAAAGGGCA 59.929 57.895 0.00 0.00 37.90 5.36
3566 5250 2.094894 CGTGAAGATGAAGGCATGTCAC 59.905 50.000 0.00 0.00 39.98 3.67
3569 5253 1.089920 GCGTGAAGATGAAGGCATGT 58.910 50.000 0.00 0.00 34.11 3.21
3629 5314 0.388907 CCAACATTTGCAGCCTTCCG 60.389 55.000 0.00 0.00 0.00 4.30
3662 5347 7.440198 TGGAGTATATCTCTTTCAGCAAGATG 58.560 38.462 0.00 0.00 40.95 2.90
3683 5368 4.701651 TGAGTTAATGTCCTGCAAATGGAG 59.298 41.667 0.00 0.00 33.78 3.86
3684 5369 4.661222 TGAGTTAATGTCCTGCAAATGGA 58.339 39.130 0.00 0.00 0.00 3.41
3688 5373 3.485394 TGCTGAGTTAATGTCCTGCAAA 58.515 40.909 0.00 0.00 0.00 3.68
3690 5375 2.703416 CTGCTGAGTTAATGTCCTGCA 58.297 47.619 0.00 0.00 0.00 4.41
3691 5376 1.399791 GCTGCTGAGTTAATGTCCTGC 59.600 52.381 0.00 0.00 0.00 4.85
3696 5381 7.092716 CCTAAATTTTGCTGCTGAGTTAATGT 58.907 34.615 0.00 0.00 0.00 2.71
3704 5389 4.440525 GCATAGCCTAAATTTTGCTGCTGA 60.441 41.667 19.53 5.50 36.57 4.26
3708 5393 4.032703 ACGCATAGCCTAAATTTTGCTG 57.967 40.909 19.53 10.82 36.57 4.41
3823 5508 4.264253 TGATAGTTGAAGCTGAACCATGG 58.736 43.478 11.19 11.19 0.00 3.66
3855 5553 3.242641 GCCCGAAACCTTTGTCGAATATC 60.243 47.826 0.00 0.00 39.64 1.63
3864 5562 0.249280 GTTGGTGCCCGAAACCTTTG 60.249 55.000 3.34 0.00 38.60 2.77
3921 5619 4.767928 AGAGTGTGAGTACTTCTTACCAGG 59.232 45.833 0.00 0.00 32.58 4.45
3967 5665 1.648467 GACCCCATTCAGTCGCAAGC 61.648 60.000 0.00 0.00 37.18 4.01
4056 5754 2.101380 GCCTGAGTCGAGTCGAGC 59.899 66.667 17.12 11.78 36.23 5.03
4075 5773 8.965172 AGTAATAATAGATTTGCGTTGTACTCG 58.035 33.333 0.00 0.40 0.00 4.18
4089 5787 8.213679 ACATGTCAGTTGCCAGTAATAATAGAT 58.786 33.333 0.00 0.00 0.00 1.98
4131 5829 2.202676 GGAGCGAGCCGTGAGAAG 60.203 66.667 0.00 0.00 0.00 2.85


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

AutoCloner maintained by Alex Coulton.