Multiple sequence alignment - TraesCS2D01G503000

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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 TraesCS2D01G503000 chr2D 100.000 7035 0 0 736 7770 596917719 596910685 0.000000e+00 12992
1 TraesCS2D01G503000 chr2D 100.000 460 0 0 1 460 596918454 596917995 0.000000e+00 850
2 TraesCS2D01G503000 chr2A 94.089 7105 251 65 736 7770 731162990 731155985 0.000000e+00 10637
3 TraesCS2D01G503000 chr2A 91.350 474 23 9 1 460 731163540 731163071 3.960000e-177 632
4 TraesCS2D01G503000 chr2B 96.946 3995 86 12 3239 7212 725963955 725959976 0.000000e+00 6669
5 TraesCS2D01G503000 chr2B 91.382 2170 116 24 878 3029 725966383 725964267 0.000000e+00 2905
6 TraesCS2D01G503000 chr2B 93.576 467 16 7 1 460 725967253 725966794 0.000000e+00 684
7 TraesCS2D01G503000 chr2B 91.781 365 15 10 7410 7770 725959863 725959510 1.950000e-135 494
8 TraesCS2D01G503000 chr2B 93.671 158 9 1 3028 3185 725964107 725963951 1.300000e-57 235
9 TraesCS2D01G503000 chr6A 77.405 447 81 10 6425 6864 614862483 614862050 1.670000e-61 248


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 TraesCS2D01G503000 chr2D 596910685 596918454 7769 True 6921.0 12992 100.0000 1 7770 2 chr2D.!!$R1 7769
1 TraesCS2D01G503000 chr2A 731155985 731163540 7555 True 5634.5 10637 92.7195 1 7770 2 chr2A.!!$R1 7769
2 TraesCS2D01G503000 chr2B 725959510 725967253 7743 True 2197.4 6669 93.4712 1 7770 5 chr2B.!!$R1 7769

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
85 90 0.250510 GAGCGGAATGGAATCTCCCC 60.251 60.000 0.00 0.00 35.03 4.81 F
1510 1575 0.465705 CCTCTGATTTGCTCCCGCTA 59.534 55.000 0.00 0.00 36.97 4.26 F
1514 1579 0.546122 TGATTTGCTCCCGCTATGGT 59.454 50.000 0.00 0.00 36.97 3.55 F
3394 3644 0.388520 TCAAGCTCGGTGACATCGTG 60.389 55.000 8.18 6.92 0.00 4.35 F
3781 4031 0.546122 TTCCGATTGCCATGCCTACT 59.454 50.000 0.00 0.00 0.00 2.57 F
4765 5017 0.032615 AGGAGACTGGTAGGAGGCTG 60.033 60.000 0.00 0.00 41.13 4.85 F
6367 6621 2.167662 CACACATTGGGGTTTACCTCC 58.832 52.381 0.00 0.00 40.03 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1640 1719 0.674534 GATTCGGTGCTCGTATCCCT 59.325 55.000 7.85 0.00 38.97 4.20 R
3394 3644 1.882167 GAGACGAGCATCAGCAGGC 60.882 63.158 0.00 0.00 45.49 4.85 R
3688 3938 0.107703 GCTGGATCGGGAACATGACA 60.108 55.000 0.00 0.00 0.00 3.58 R
4765 5017 0.904394 ACATGTTTGTGCCCATCCCC 60.904 55.000 0.00 0.00 33.85 4.81 R
5296 5549 1.837439 TGGAAACGGCATAGATCTGGT 59.163 47.619 5.18 0.00 0.00 4.00 R
6624 6878 0.102120 GGCCTGACTCGTCTGATCTG 59.898 60.000 0.00 0.00 0.00 2.90 R
7500 7786 1.142748 CTAGCTCTCCTTGCACGGG 59.857 63.158 9.71 3.87 0.00 5.28 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
63 68 4.451652 GCTCGCAGGCAGAAACGC 62.452 66.667 0.00 0.00 0.00 4.84
85 90 0.250510 GAGCGGAATGGAATCTCCCC 60.251 60.000 0.00 0.00 35.03 4.81
86 91 1.228276 GCGGAATGGAATCTCCCCC 60.228 63.158 0.00 0.00 35.03 5.40
806 839 2.844839 GGAGACCTCCCCCATCGG 60.845 72.222 4.72 0.00 43.94 4.18
883 923 4.567385 GCGGAGGAGAGAGCAGCG 62.567 72.222 0.00 0.00 0.00 5.18
955 996 4.459089 GTGGACTCCGCCTGCTCC 62.459 72.222 0.00 0.00 0.00 4.70
1048 1089 1.064946 GCCGTCGATCTGGTGAGAG 59.935 63.158 0.00 0.00 0.00 3.20
1086 1136 1.878656 CTCTCTTCCGACGCCCTGTT 61.879 60.000 0.00 0.00 0.00 3.16
1097 1147 2.742372 CCCTGTTTCTCGCGGTGG 60.742 66.667 6.13 0.00 0.00 4.61
1140 1190 1.873355 GCGACGCTCGTTTCGAACTT 61.873 55.000 13.73 0.00 42.81 2.66
1164 1214 1.591059 CCCTGCTGCTTCGATCTCG 60.591 63.158 0.00 0.00 41.45 4.04
1165 1215 1.591059 CCTGCTGCTTCGATCTCGG 60.591 63.158 0.00 0.00 40.29 4.63
1174 1224 1.950216 CTTCGATCTCGGGACAGATGA 59.050 52.381 0.00 0.00 40.29 2.92
1175 1225 2.278332 TCGATCTCGGGACAGATGAT 57.722 50.000 0.00 0.00 40.29 2.45
1176 1226 3.418684 TCGATCTCGGGACAGATGATA 57.581 47.619 0.00 0.00 40.29 2.15
1177 1227 3.339141 TCGATCTCGGGACAGATGATAG 58.661 50.000 0.00 0.00 40.29 2.08
1178 1228 3.008049 TCGATCTCGGGACAGATGATAGA 59.992 47.826 0.00 0.00 40.29 1.98
1179 1229 3.944650 CGATCTCGGGACAGATGATAGAT 59.055 47.826 0.00 0.00 32.94 1.98
1180 1230 4.201901 CGATCTCGGGACAGATGATAGATG 60.202 50.000 0.00 0.00 32.94 2.90
1181 1231 4.105754 TCTCGGGACAGATGATAGATGT 57.894 45.455 0.00 0.00 0.00 3.06
1182 1232 3.823304 TCTCGGGACAGATGATAGATGTG 59.177 47.826 0.00 0.00 0.00 3.21
1183 1233 2.297315 TCGGGACAGATGATAGATGTGC 59.703 50.000 0.00 0.00 34.86 4.57
1202 1252 1.841450 CGGAGAATCGCAGGAACTAC 58.159 55.000 0.00 0.00 31.88 2.73
1204 1254 1.134560 GGAGAATCGCAGGAACTACGT 59.865 52.381 0.00 0.00 46.69 3.57
1510 1575 0.465705 CCTCTGATTTGCTCCCGCTA 59.534 55.000 0.00 0.00 36.97 4.26
1511 1576 1.071385 CCTCTGATTTGCTCCCGCTAT 59.929 52.381 0.00 0.00 36.97 2.97
1512 1577 2.141517 CTCTGATTTGCTCCCGCTATG 58.858 52.381 0.00 0.00 36.97 2.23
1513 1578 1.202687 TCTGATTTGCTCCCGCTATGG 60.203 52.381 0.00 0.00 36.97 2.74
1514 1579 0.546122 TGATTTGCTCCCGCTATGGT 59.454 50.000 0.00 0.00 36.97 3.55
1515 1580 1.064758 TGATTTGCTCCCGCTATGGTT 60.065 47.619 0.00 0.00 36.97 3.67
1516 1581 1.604278 GATTTGCTCCCGCTATGGTTC 59.396 52.381 0.00 0.00 36.97 3.62
1603 1679 2.633488 GATCCTACCCAGCTGTTTCAC 58.367 52.381 13.81 0.00 0.00 3.18
1640 1719 2.564062 ACGTAAATCTCCTCCGTGGAAA 59.436 45.455 0.00 0.00 45.63 3.13
1674 1753 2.411069 CCGAATCTTAGATCTGCGCATG 59.589 50.000 12.24 5.41 0.00 4.06
1757 1836 2.893637 TGGAGATTTTCGAGCAGTAGC 58.106 47.619 0.00 0.00 42.56 3.58
1758 1837 2.233676 TGGAGATTTTCGAGCAGTAGCA 59.766 45.455 0.00 0.00 45.49 3.49
1771 1851 5.738225 CGAGCAGTAGCAGTAGTTTTAGTAC 59.262 44.000 0.00 0.00 45.49 2.73
1785 1865 9.662947 GTAGTTTTAGTACAATTAGTGGGATGT 57.337 33.333 0.00 0.00 0.00 3.06
1804 1884 2.568062 TGTGAGTACGGATTTGGGCTTA 59.432 45.455 0.00 0.00 0.00 3.09
1999 2079 5.332656 CGCTCTCGCTTATCCTATTGTTTTC 60.333 44.000 0.00 0.00 0.00 2.29
2339 2421 3.299340 AGCTACTGTTCTGTACAACGG 57.701 47.619 5.18 5.18 38.44 4.44
2414 2496 2.019249 ACACCTCAAATCATCGCATGG 58.981 47.619 0.00 0.00 0.00 3.66
2434 2517 3.019564 GGTCTTGGTTCTCATCAATGGG 58.980 50.000 0.00 0.00 0.00 4.00
2452 2535 1.923864 GGGTTGTTTCGCTTGTGTTTG 59.076 47.619 0.00 0.00 0.00 2.93
2630 2713 4.252878 CAAGTTTGGTGCCTGTTTTCTTT 58.747 39.130 0.00 0.00 0.00 2.52
2634 2717 2.031120 TGGTGCCTGTTTTCTTTCCTG 58.969 47.619 0.00 0.00 0.00 3.86
2910 2996 1.244019 GCGCCCAAGACAAAGGTGAT 61.244 55.000 0.00 0.00 32.75 3.06
2943 3029 1.073763 TGCTGTCCTGTTAGGTTGCAT 59.926 47.619 0.00 0.00 36.53 3.96
3007 3094 9.036671 GTCTGCTTCCAATATACTTTTCTAGTC 57.963 37.037 0.00 0.00 38.33 2.59
3246 3493 6.648725 GGTGGAAACTTGCTGCATTTATTTTA 59.351 34.615 1.84 0.00 0.00 1.52
3247 3494 7.334171 GGTGGAAACTTGCTGCATTTATTTTAT 59.666 33.333 1.84 0.00 0.00 1.40
3249 3496 8.719648 TGGAAACTTGCTGCATTTATTTTATTG 58.280 29.630 1.84 0.00 0.00 1.90
3250 3497 8.934825 GGAAACTTGCTGCATTTATTTTATTGA 58.065 29.630 1.84 0.00 0.00 2.57
3251 3498 9.962759 GAAACTTGCTGCATTTATTTTATTGAG 57.037 29.630 1.84 0.00 0.00 3.02
3252 3499 9.492973 AAACTTGCTGCATTTATTTTATTGAGT 57.507 25.926 1.84 0.00 0.00 3.41
3394 3644 0.388520 TCAAGCTCGGTGACATCGTG 60.389 55.000 8.18 6.92 0.00 4.35
3688 3938 4.818546 GTGGGAATCGTCATTGAGATCATT 59.181 41.667 0.00 0.00 0.00 2.57
3781 4031 0.546122 TTCCGATTGCCATGCCTACT 59.454 50.000 0.00 0.00 0.00 2.57
4114 4364 2.298729 GCACTTCTTGCCATTTAACCCA 59.701 45.455 0.00 0.00 46.63 4.51
4218 4468 2.409948 AGAACCATAGAAGCACAGCC 57.590 50.000 0.00 0.00 0.00 4.85
4426 4678 7.894753 AGACAGGTACCTTAACTTCTATACC 57.105 40.000 13.15 0.00 33.65 2.73
4452 4704 1.553248 TGCTATTTCGGCTGTAGTGGT 59.447 47.619 0.00 0.00 0.00 4.16
4500 4752 5.194473 TGAGACTATCACAGGAAGTACCT 57.806 43.478 0.00 0.00 40.79 3.08
4572 4824 0.704076 CCCTGTTTGATCCCCCAAGA 59.296 55.000 0.00 0.00 0.00 3.02
4681 4933 4.019919 TCTCGCTTAGAATTTTGCATGC 57.980 40.909 11.82 11.82 0.00 4.06
4688 4940 3.756933 AGAATTTTGCATGCTTGGTGT 57.243 38.095 20.33 0.00 0.00 4.16
4695 4947 5.921004 TTTGCATGCTTGGTGTAAATTTC 57.079 34.783 20.33 0.00 0.00 2.17
4703 4955 4.619760 GCTTGGTGTAAATTTCGCTAAACC 59.380 41.667 0.00 0.00 0.00 3.27
4707 4959 5.122711 TGGTGTAAATTTCGCTAAACCTAGC 59.877 40.000 0.00 0.00 46.14 3.42
4765 5017 0.032615 AGGAGACTGGTAGGAGGCTG 60.033 60.000 0.00 0.00 41.13 4.85
4901 5153 2.972713 GTCTTCCCTGGTATGCTCCATA 59.027 50.000 0.00 0.00 36.84 2.74
5203 5456 4.398358 CAGAGGATGAAGAACTACACGGTA 59.602 45.833 0.00 0.00 0.00 4.02
5239 5492 9.906660 TTGCAAACTTGATAATTAGTAACCTTG 57.093 29.630 0.00 0.00 0.00 3.61
5289 5542 7.118825 CAGACTCATTGCTCTTTTTCTGTCATA 59.881 37.037 0.00 0.00 0.00 2.15
5295 5548 9.282247 CATTGCTCTTTTTCTGTCATATGTTAC 57.718 33.333 1.90 0.00 0.00 2.50
5296 5549 7.977789 TGCTCTTTTTCTGTCATATGTTACA 57.022 32.000 1.90 0.00 0.00 2.41
5309 5562 6.591834 GTCATATGTTACACCAGATCTATGCC 59.408 42.308 1.90 0.00 0.00 4.40
5538 5792 6.467677 CATTAGTAGCCAATGCAGGTACTAT 58.532 40.000 18.59 10.08 45.31 2.12
5773 6027 9.787532 CTTCTTCACAGTGAGTTTTCAAATTTA 57.212 29.630 2.82 0.00 34.49 1.40
6047 6301 2.210961 TCGCACAATTGGTACGTGAAA 58.789 42.857 10.83 0.00 37.53 2.69
6056 6310 6.528774 ACAATTGGTACGTGAAAAACAGTTTC 59.471 34.615 10.83 0.00 0.00 2.78
6260 6514 4.074970 AGTTCTTCATCCGATTTGTGCTT 58.925 39.130 0.00 0.00 0.00 3.91
6349 6603 7.040961 TCAGCACCTTTATTTTTAGGTACACAC 60.041 37.037 0.00 0.00 42.81 3.82
6366 6620 2.556622 CACACACATTGGGGTTTACCTC 59.443 50.000 0.00 0.00 40.03 3.85
6367 6621 2.167662 CACACATTGGGGTTTACCTCC 58.832 52.381 0.00 0.00 40.03 4.30
6369 6623 2.449345 ACACATTGGGGTTTACCTCCTT 59.551 45.455 0.00 0.00 40.03 3.36
6622 6876 5.813513 ATCTTTCCACTTCCAAATTGCTT 57.186 34.783 0.00 0.00 0.00 3.91
6624 6878 6.084326 TCTTTCCACTTCCAAATTGCTTAC 57.916 37.500 0.00 0.00 0.00 2.34
6643 6898 0.102120 CAGATCAGACGAGTCAGGCC 59.898 60.000 0.00 0.00 0.00 5.19
6773 7043 1.887198 AGAACTACACCGTGTGAGGAG 59.113 52.381 14.66 6.05 36.96 3.69
6774 7044 1.612463 GAACTACACCGTGTGAGGAGT 59.388 52.381 14.66 6.70 38.59 3.85
6775 7045 2.574006 ACTACACCGTGTGAGGAGTA 57.426 50.000 14.66 0.00 36.51 2.59
7012 7282 4.204775 GGTTGTAATCGTTTTCGCGTTTTT 59.795 37.500 5.77 0.00 43.73 1.94
7104 7374 1.542492 CCATGCTTGCTATCCCATCC 58.458 55.000 0.00 0.00 0.00 3.51
7173 7443 4.301628 CCTTTTCTGCAATGGAGTTTCAC 58.698 43.478 0.85 0.00 32.27 3.18
7236 7507 1.312815 GCTATCATTGCCAGTGGACC 58.687 55.000 15.20 0.00 0.00 4.46
7286 7567 7.403312 TGATTGGAATGTTTATGTGGTTAGG 57.597 36.000 0.00 0.00 0.00 2.69
7299 7580 3.146066 GTGGTTAGGCACACATTTGAGA 58.854 45.455 0.00 0.00 37.54 3.27
7300 7581 3.568007 GTGGTTAGGCACACATTTGAGAA 59.432 43.478 0.00 0.00 37.54 2.87
7304 7585 5.634859 GGTTAGGCACACATTTGAGAAAATG 59.365 40.000 9.12 9.12 43.77 2.32
7309 7590 5.049167 GCACACATTTGAGAAAATGGTGAA 58.951 37.500 22.70 0.00 42.78 3.18
7310 7591 5.176223 GCACACATTTGAGAAAATGGTGAAG 59.824 40.000 22.70 14.30 42.78 3.02
7314 7595 5.299279 ACATTTGAGAAAATGGTGAAGACGT 59.701 36.000 13.94 0.00 42.78 4.34
7315 7596 6.485313 ACATTTGAGAAAATGGTGAAGACGTA 59.515 34.615 13.94 0.00 42.78 3.57
7316 7597 6.539649 TTTGAGAAAATGGTGAAGACGTAG 57.460 37.500 0.00 0.00 0.00 3.51
7317 7598 7.307989 CATTTGAGAAAATGGTGAAGACGTAGT 60.308 37.037 0.00 0.00 38.95 2.73
7334 7615 6.097915 ACGTAGTTGAAGAAATCCAAGAGA 57.902 37.500 0.00 0.00 37.78 3.10
7335 7616 6.702329 ACGTAGTTGAAGAAATCCAAGAGAT 58.298 36.000 0.00 0.00 37.78 2.75
7336 7617 6.814146 ACGTAGTTGAAGAAATCCAAGAGATC 59.186 38.462 0.00 0.00 37.78 2.75
7337 7618 7.038659 CGTAGTTGAAGAAATCCAAGAGATCT 58.961 38.462 0.00 0.00 32.47 2.75
7338 7619 8.191446 CGTAGTTGAAGAAATCCAAGAGATCTA 58.809 37.037 0.00 0.00 32.47 1.98
7366 7651 4.196971 GTGTAAAGGTAGCTGGTTATGGG 58.803 47.826 0.00 0.00 0.00 4.00
7367 7652 3.847780 TGTAAAGGTAGCTGGTTATGGGT 59.152 43.478 0.00 0.00 0.00 4.51
7369 7654 5.488203 TGTAAAGGTAGCTGGTTATGGGTAA 59.512 40.000 0.00 0.00 0.00 2.85
7383 7668 2.933573 TGGGTAACACGTTGGTTGAAT 58.066 42.857 1.76 0.00 39.74 2.57
7393 7678 6.574350 ACACGTTGGTTGAATAAATCCAAAA 58.426 32.000 0.00 0.00 40.82 2.44
7500 7786 5.975410 AGCGAGCTGTAGATAAATTGTTC 57.025 39.130 0.00 0.00 0.00 3.18
7503 7789 4.209288 CGAGCTGTAGATAAATTGTTCCCG 59.791 45.833 0.00 0.00 0.00 5.14
7515 7801 2.035442 GTTCCCGTGCAAGGAGAGC 61.035 63.158 21.23 13.24 34.08 4.09
7580 7866 0.179145 ACCGACTATTCTTCCACGCG 60.179 55.000 3.53 3.53 0.00 6.01
7614 7904 4.415150 CTGCCCTCCGCCACACAT 62.415 66.667 0.00 0.00 36.24 3.21
7765 8058 4.023536 GCATTCCACCTTTCGTTGTCTTTA 60.024 41.667 0.00 0.00 0.00 1.85
7769 8062 2.551032 CACCTTTCGTTGTCTTTACCCC 59.449 50.000 0.00 0.00 0.00 4.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
63 68 1.542108 GGAGATTCCATTCCGCTCCAG 60.542 57.143 0.00 0.00 43.55 3.86
102 123 4.388499 CTGGGTCGGGTCGGGTTG 62.388 72.222 0.00 0.00 0.00 3.77
154 175 3.125573 GGCGCCTTCCGTTCCTTC 61.126 66.667 22.15 0.00 39.71 3.46
228 256 3.150903 ATGCCAGCCACTTGTGGGT 62.151 57.895 17.56 17.56 40.82 4.51
754 787 0.626916 TGCTTTATACCCACCCACCC 59.373 55.000 0.00 0.00 0.00 4.61
806 839 1.518302 GGAGGAGAGAAACCGGAGC 59.482 63.158 9.46 0.00 0.00 4.70
955 996 2.742372 CGAACCAGCACGGGAAGG 60.742 66.667 0.00 0.00 40.22 3.46
1063 1104 2.047443 GGCGTCGGAAGAGAGAGGT 61.047 63.158 0.00 0.00 43.49 3.85
1086 1136 2.664851 CAAGCACCACCGCGAGAA 60.665 61.111 8.23 0.00 36.85 2.87
1097 1147 1.135972 CATACAGCGTGAACCAAGCAC 60.136 52.381 7.52 0.00 41.02 4.40
1140 1190 2.947532 CGAAGCAGCAGGGGACAGA 61.948 63.158 0.00 0.00 0.00 3.41
1164 1214 2.611473 CCGCACATCTATCATCTGTCCC 60.611 54.545 0.00 0.00 0.00 4.46
1165 1215 2.297315 TCCGCACATCTATCATCTGTCC 59.703 50.000 0.00 0.00 0.00 4.02
1183 1233 1.841450 GTAGTTCCTGCGATTCTCCG 58.159 55.000 0.00 0.00 0.00 4.63
1201 1251 2.480845 GCCAGCGGATTAATCTAACGT 58.519 47.619 14.95 0.00 0.00 3.99
1202 1252 1.798813 GGCCAGCGGATTAATCTAACG 59.201 52.381 14.95 11.07 0.00 3.18
1204 1254 1.414919 ACGGCCAGCGGATTAATCTAA 59.585 47.619 14.95 0.00 0.00 2.10
1310 1373 9.403583 AGTAACCAGTTAAACTTTTGATGAAGA 57.596 29.630 0.00 0.00 0.00 2.87
1427 1491 2.486907 GCCCTCTCCATCATTGAAGAGG 60.487 54.545 19.66 19.66 41.72 3.69
1510 1575 2.749044 CGGCAGCAGCAGAACCAT 60.749 61.111 2.65 0.00 44.61 3.55
1561 1637 1.165270 AAAATTCCTCCGCCGAACAG 58.835 50.000 0.00 0.00 0.00 3.16
1630 1706 1.067212 CTCGTATCCCTTTCCACGGAG 59.933 57.143 0.00 0.00 35.21 4.63
1640 1719 0.674534 GATTCGGTGCTCGTATCCCT 59.325 55.000 7.85 0.00 38.97 4.20
1674 1753 7.375834 ACGAAATAAAAACTGGGGAAGAAATC 58.624 34.615 0.00 0.00 0.00 2.17
1757 1836 9.886132 ATCCCACTAATTGTACTAAAACTACTG 57.114 33.333 0.00 0.00 0.00 2.74
1758 1837 9.886132 CATCCCACTAATTGTACTAAAACTACT 57.114 33.333 0.00 0.00 0.00 2.57
1771 1851 4.119862 CCGTACTCACATCCCACTAATTG 58.880 47.826 0.00 0.00 0.00 2.32
1785 1865 3.985019 TTAAGCCCAAATCCGTACTCA 57.015 42.857 0.00 0.00 0.00 3.41
1804 1884 6.072673 CCCGTGCTTAACTATCTTTTGACTTT 60.073 38.462 0.00 0.00 0.00 2.66
2066 2146 2.506438 GCTCGTACGCACTCACCC 60.506 66.667 11.24 0.00 0.00 4.61
2129 2209 1.909781 GGGTGTCCTGGACCGTACA 60.910 63.158 23.42 2.56 33.89 2.90
2311 2393 2.102588 ACAGAACAGTAGCTTCCACGTT 59.897 45.455 0.00 0.00 0.00 3.99
2414 2496 3.690460 ACCCATTGATGAGAACCAAGAC 58.310 45.455 0.00 0.00 0.00 3.01
2434 2517 5.942325 AATACAAACACAAGCGAAACAAC 57.058 34.783 0.00 0.00 0.00 3.32
2452 2535 2.952310 GGGGATGTTCTCCTGCAAATAC 59.048 50.000 0.00 0.00 44.28 1.89
2630 2713 3.330701 ACAAGGAGCAATTAAGACCAGGA 59.669 43.478 0.00 0.00 0.00 3.86
2634 2717 2.755103 CCCACAAGGAGCAATTAAGACC 59.245 50.000 0.00 0.00 38.24 3.85
2710 2796 4.816109 TCCATGACCCAGGAGAGG 57.184 61.111 0.00 0.00 0.00 3.69
3007 3094 5.674525 TCTATATCACAGTTGAAAGCAGGG 58.325 41.667 0.00 0.00 34.61 4.45
3085 3332 1.953686 TGCTAAGCCAGGTTCAACAAC 59.046 47.619 0.00 0.00 0.00 3.32
3136 3383 5.757886 TGCAGAACAAAAGTACAATACAGC 58.242 37.500 0.00 0.00 0.00 4.40
3143 3390 6.765989 ACTATCAGTTGCAGAACAAAAGTACA 59.234 34.615 0.00 0.00 40.82 2.90
3246 3493 4.394610 GGGCAAACAAACAAACAACTCAAT 59.605 37.500 0.00 0.00 0.00 2.57
3247 3494 3.748568 GGGCAAACAAACAAACAACTCAA 59.251 39.130 0.00 0.00 0.00 3.02
3249 3496 3.330267 TGGGCAAACAAACAAACAACTC 58.670 40.909 0.00 0.00 0.00 3.01
3250 3497 3.409026 TGGGCAAACAAACAAACAACT 57.591 38.095 0.00 0.00 0.00 3.16
3251 3498 4.394610 AGAATGGGCAAACAAACAAACAAC 59.605 37.500 0.00 0.00 0.00 3.32
3252 3499 4.583871 AGAATGGGCAAACAAACAAACAA 58.416 34.783 0.00 0.00 0.00 2.83
3394 3644 1.882167 GAGACGAGCATCAGCAGGC 60.882 63.158 0.00 0.00 45.49 4.85
3688 3938 0.107703 GCTGGATCGGGAACATGACA 60.108 55.000 0.00 0.00 0.00 3.58
3781 4031 1.313772 CCATGGTGACCGACAAAACA 58.686 50.000 2.57 0.00 0.00 2.83
4108 4358 3.071023 CAGTCCTCTTGTCAGTTGGGTTA 59.929 47.826 0.00 0.00 0.00 2.85
4114 4364 2.829741 GAGCAGTCCTCTTGTCAGTT 57.170 50.000 0.00 0.00 37.60 3.16
4200 4450 2.113860 TGGCTGTGCTTCTATGGTTC 57.886 50.000 0.00 0.00 0.00 3.62
4212 4462 5.252969 ACATGTAATAAAGCATGGCTGTG 57.747 39.130 0.00 0.00 44.74 3.66
4213 4463 5.920193 AACATGTAATAAAGCATGGCTGT 57.080 34.783 0.00 0.00 44.74 4.40
4426 4678 4.572389 ACTACAGCCGAAATAGCATTTGAG 59.428 41.667 0.00 0.00 0.00 3.02
4452 4704 5.076182 TGGCATTAGAAATTGACTCACCAA 58.924 37.500 0.00 0.00 0.00 3.67
4572 4824 1.051008 TGGTCTCAGCACTGTCATGT 58.949 50.000 0.00 0.00 0.00 3.21
4663 4915 3.305094 CCAAGCATGCAAAATTCTAAGCG 59.695 43.478 21.98 0.00 0.00 4.68
4681 4933 6.009115 AGGTTTAGCGAAATTTACACCAAG 57.991 37.500 0.00 0.00 0.00 3.61
4703 4955 7.436673 GTCACCTGAAGTAAATCACATAGCTAG 59.563 40.741 0.00 0.00 0.00 3.42
4707 4959 6.406370 TGGTCACCTGAAGTAAATCACATAG 58.594 40.000 0.00 0.00 0.00 2.23
4719 4971 1.972872 AGCAAGTTGGTCACCTGAAG 58.027 50.000 0.63 0.00 0.00 3.02
4765 5017 0.904394 ACATGTTTGTGCCCATCCCC 60.904 55.000 0.00 0.00 33.85 4.81
4901 5153 6.543465 TGCATAACTAAACAGATAAGCATGCT 59.457 34.615 16.30 16.30 35.03 3.79
5289 5542 3.388024 ACGGCATAGATCTGGTGTAACAT 59.612 43.478 5.18 0.00 39.98 2.71
5295 5548 2.213499 GGAAACGGCATAGATCTGGTG 58.787 52.381 5.18 5.54 0.00 4.17
5296 5549 1.837439 TGGAAACGGCATAGATCTGGT 59.163 47.619 5.18 0.00 0.00 4.00
5309 5562 2.303163 TACGGATGGTGATGGAAACG 57.697 50.000 0.00 0.00 0.00 3.60
6056 6310 6.205464 TGTCCTGAATTTCTTACTTTGCAGAG 59.795 38.462 2.03 2.03 0.00 3.35
6260 6514 1.615424 GTCCCAGGCCCTTCCACTA 60.615 63.158 0.00 0.00 37.29 2.74
6349 6603 2.825532 CAAGGAGGTAAACCCCAATGTG 59.174 50.000 8.73 0.25 36.42 3.21
6366 6620 2.686915 GAGGGTCATCATTTGCTCAAGG 59.313 50.000 0.00 0.00 0.00 3.61
6367 6621 3.377485 CAGAGGGTCATCATTTGCTCAAG 59.623 47.826 0.00 0.00 0.00 3.02
6369 6623 2.573009 TCAGAGGGTCATCATTTGCTCA 59.427 45.455 0.00 0.00 0.00 4.26
6569 6823 3.597255 TGCAATCTCAGCTCTTCTCTTG 58.403 45.455 0.00 0.00 0.00 3.02
6622 6876 2.017782 GCCTGACTCGTCTGATCTGTA 58.982 52.381 5.63 0.00 0.00 2.74
6624 6878 0.102120 GGCCTGACTCGTCTGATCTG 59.898 60.000 0.00 0.00 0.00 2.90
6643 6898 4.611310 AATCATCAGCAATCAACGACTG 57.389 40.909 0.00 0.00 0.00 3.51
6773 7043 5.753744 TGTTTGTTGGTTCAATGTCGATAC 58.246 37.500 0.00 0.00 0.00 2.24
6774 7044 6.205658 TCATGTTTGTTGGTTCAATGTCGATA 59.794 34.615 0.00 0.00 0.00 2.92
6775 7045 4.909696 TGTTTGTTGGTTCAATGTCGAT 57.090 36.364 0.00 0.00 0.00 3.59
7012 7282 4.356436 GACTAGTTAGGGGAAACTGGGTA 58.644 47.826 0.00 0.00 40.98 3.69
7104 7374 8.122472 AGAATTGTCTTTGTATAAACCCAAGG 57.878 34.615 0.00 0.00 0.00 3.61
7236 7507 4.994471 TGTGCTGCACAGGAGCCG 62.994 66.667 29.99 0.00 39.62 5.52
7286 7567 4.619973 TCACCATTTTCTCAAATGTGTGC 58.380 39.130 16.44 0.00 45.57 4.57
7299 7580 6.053005 TCTTCAACTACGTCTTCACCATTTT 58.947 36.000 0.00 0.00 0.00 1.82
7300 7581 5.607477 TCTTCAACTACGTCTTCACCATTT 58.393 37.500 0.00 0.00 0.00 2.32
7304 7585 5.120363 GGATTTCTTCAACTACGTCTTCACC 59.880 44.000 0.00 0.00 0.00 4.02
7309 7590 6.015350 TCTCTTGGATTTCTTCAACTACGTCT 60.015 38.462 0.00 0.00 0.00 4.18
7310 7591 6.157211 TCTCTTGGATTTCTTCAACTACGTC 58.843 40.000 0.00 0.00 0.00 4.34
7327 7608 9.838339 ACCTTTACACAATTATAGATCTCTTGG 57.162 33.333 0.00 0.00 0.00 3.61
7332 7613 9.988815 CAGCTACCTTTACACAATTATAGATCT 57.011 33.333 0.00 0.00 0.00 2.75
7333 7614 9.209175 CCAGCTACCTTTACACAATTATAGATC 57.791 37.037 0.00 0.00 0.00 2.75
7334 7615 8.714906 ACCAGCTACCTTTACACAATTATAGAT 58.285 33.333 0.00 0.00 0.00 1.98
7335 7616 8.086143 ACCAGCTACCTTTACACAATTATAGA 57.914 34.615 0.00 0.00 0.00 1.98
7336 7617 8.732746 AACCAGCTACCTTTACACAATTATAG 57.267 34.615 0.00 0.00 0.00 1.31
7338 7619 9.120538 CATAACCAGCTACCTTTACACAATTAT 57.879 33.333 0.00 0.00 0.00 1.28
7366 7651 6.670233 TGGATTTATTCAACCAACGTGTTAC 58.330 36.000 0.00 0.00 0.00 2.50
7367 7652 6.879276 TGGATTTATTCAACCAACGTGTTA 57.121 33.333 0.00 0.00 0.00 2.41
7369 7654 5.776173 TTGGATTTATTCAACCAACGTGT 57.224 34.783 0.00 0.00 37.46 4.49
7383 7668 4.219507 TGCTGCCGAATTCTTTTGGATTTA 59.780 37.500 3.52 0.00 38.53 1.40
7393 7678 3.550437 AGAATACTGCTGCCGAATTCT 57.450 42.857 12.09 12.09 33.23 2.40
7500 7786 1.142748 CTAGCTCTCCTTGCACGGG 59.857 63.158 9.71 3.87 0.00 5.28
7503 7789 1.520342 CGGCTAGCTCTCCTTGCAC 60.520 63.158 15.72 0.00 42.96 4.57


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

AutoCloner maintained by Alex Coulton.