Multiple sequence alignment - TraesCS1D01G312200

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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 TraesCS1D01G312200 chr1D 100.000 2684 0 0 1 2684 407879584 407876901 0.000000e+00 4957.0
1 TraesCS1D01G312200 chr1A 93.541 1378 62 12 966 2332 503377200 503375839 0.000000e+00 2026.0
2 TraesCS1D01G312200 chr1A 91.066 985 53 15 4 967 503378201 503377231 0.000000e+00 1299.0
3 TraesCS1D01G312200 chr1A 87.162 148 15 3 966 1110 243607597 243607743 5.940000e-37 165.0
4 TraesCS1D01G312200 chr1B 88.556 1704 94 30 966 2585 548541418 548539732 0.000000e+00 1973.0
5 TraesCS1D01G312200 chr1B 85.529 1002 59 25 4 961 548542410 548541451 0.000000e+00 968.0
6 TraesCS1D01G312200 chr1B 98.039 51 1 0 2634 2684 548539505 548539455 3.680000e-14 89.8
7 TraesCS1D01G312200 chr7B 89.623 742 53 12 1385 2113 639551495 639552225 0.000000e+00 922.0
8 TraesCS1D01G312200 chr7B 89.084 742 63 12 1385 2113 682603433 682602697 0.000000e+00 905.0
9 TraesCS1D01G312200 chr7B 88.814 742 58 12 1386 2113 66447167 66446437 0.000000e+00 887.0
10 TraesCS1D01G312200 chr7B 75.107 233 51 6 1226 1456 711000857 711001084 4.730000e-18 102.0
11 TraesCS1D01G312200 chr6B 89.623 742 52 12 1385 2113 116214974 116215703 0.000000e+00 920.0
12 TraesCS1D01G312200 chr6B 89.084 742 64 10 1385 2113 160516949 160516212 0.000000e+00 905.0
13 TraesCS1D01G312200 chr4A 87.682 755 63 10 1385 2113 657047674 657048424 0.000000e+00 852.0
14 TraesCS1D01G312200 chr3D 86.235 247 32 2 1231 1476 437475833 437476078 1.580000e-67 267.0
15 TraesCS1D01G312200 chr3A 85.366 246 36 0 1231 1476 575484865 575485110 3.430000e-64 255.0
16 TraesCS1D01G312200 chr3B 84.553 246 38 0 1231 1476 572679518 572679763 7.420000e-61 244.0
17 TraesCS1D01G312200 chr7D 76.106 226 47 6 1226 1449 616908430 616908650 7.850000e-21 111.0
18 TraesCS1D01G312200 chr5D 91.892 74 5 1 895 967 35590542 35590615 4.730000e-18 102.0
19 TraesCS1D01G312200 chr5A 95.312 64 3 0 904 967 219924500 219924563 4.730000e-18 102.0


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 TraesCS1D01G312200 chr1D 407876901 407879584 2683 True 4957.000000 4957 100.0000 1 2684 1 chr1D.!!$R1 2683
1 TraesCS1D01G312200 chr1A 503375839 503378201 2362 True 1662.500000 2026 92.3035 4 2332 2 chr1A.!!$R1 2328
2 TraesCS1D01G312200 chr1B 548539455 548542410 2955 True 1010.266667 1973 90.7080 4 2684 3 chr1B.!!$R1 2680
3 TraesCS1D01G312200 chr7B 639551495 639552225 730 False 922.000000 922 89.6230 1385 2113 1 chr7B.!!$F1 728
4 TraesCS1D01G312200 chr7B 682602697 682603433 736 True 905.000000 905 89.0840 1385 2113 1 chr7B.!!$R2 728
5 TraesCS1D01G312200 chr7B 66446437 66447167 730 True 887.000000 887 88.8140 1386 2113 1 chr7B.!!$R1 727
6 TraesCS1D01G312200 chr6B 116214974 116215703 729 False 920.000000 920 89.6230 1385 2113 1 chr6B.!!$F1 728
7 TraesCS1D01G312200 chr6B 160516212 160516949 737 True 905.000000 905 89.0840 1385 2113 1 chr6B.!!$R1 728
8 TraesCS1D01G312200 chr4A 657047674 657048424 750 False 852.000000 852 87.6820 1385 2113 1 chr4A.!!$F1 728

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
705 759 0.106719 TTTGATGCCGGATTCTCCCC 60.107 55.0 5.05 0.0 31.13 4.81 F
809 867 0.758685 ATAGAGGCTTCGCTCCTGCT 60.759 55.0 0.00 0.0 36.97 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1648 1752 0.107508 AGCTCAACGACATCCATGGG 60.108 55.0 13.02 0.0 0.0 4.0 R
2383 2602 0.107654 ACTAACCTGAATGCCGCCTC 60.108 55.0 0.00 0.0 0.0 4.7 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
111 112 5.699097 ATTACAGCAAAGACGGCTTTTTA 57.301 34.783 15.19 0.12 42.27 1.52
113 114 4.160736 ACAGCAAAGACGGCTTTTTATC 57.839 40.909 15.19 3.75 42.27 1.75
144 149 5.705609 AAGCCATACACTTAAACCAGTTG 57.294 39.130 0.00 0.00 0.00 3.16
152 157 8.873830 CATACACTTAAACCAGTTGATAGACTG 58.126 37.037 0.00 0.00 45.19 3.51
203 210 3.040147 AGTGTTTATCCACCGTCAGTG 57.960 47.619 0.00 0.00 46.83 3.66
315 322 1.975660 AGCGCAAAAGGTCCAACTAA 58.024 45.000 11.47 0.00 0.00 2.24
316 323 1.880027 AGCGCAAAAGGTCCAACTAAG 59.120 47.619 11.47 0.00 0.00 2.18
322 329 4.278419 GCAAAAGGTCCAACTAAGTGACAT 59.722 41.667 0.00 0.00 0.00 3.06
451 463 2.695970 CGTCCCTCCCTCCCTCTCT 61.696 68.421 0.00 0.00 0.00 3.10
471 483 2.763902 CCACCCTCCTTTCCCACC 59.236 66.667 0.00 0.00 0.00 4.61
490 502 1.612991 CCCCAATCCAATCACGTCACA 60.613 52.381 0.00 0.00 0.00 3.58
635 689 3.462678 GAGGAGAGGCCGGTCCAC 61.463 72.222 23.94 16.22 43.43 4.02
702 756 2.294512 GGGATTTTGATGCCGGATTCTC 59.705 50.000 5.05 0.00 0.00 2.87
705 759 0.106719 TTTGATGCCGGATTCTCCCC 60.107 55.000 5.05 0.00 31.13 4.81
723 777 2.356741 CCCCCGCTTTCTTTATCTCCAA 60.357 50.000 0.00 0.00 0.00 3.53
727 781 5.105351 CCCCGCTTTCTTTATCTCCAATTTT 60.105 40.000 0.00 0.00 0.00 1.82
745 799 8.084073 TCCAATTTTGTTCTTCTTCTTGCTATG 58.916 33.333 0.00 0.00 0.00 2.23
771 825 1.934410 TGGGGTTTCCAGCTTCCAA 59.066 52.632 0.00 0.00 41.46 3.53
774 828 0.961753 GGGTTTCCAGCTTCCAACTG 59.038 55.000 0.00 0.00 34.82 3.16
804 862 2.652795 GTCGTTATAGAGGCTTCGCTC 58.347 52.381 0.00 0.00 0.00 5.03
809 867 0.758685 ATAGAGGCTTCGCTCCTGCT 60.759 55.000 0.00 0.00 36.97 4.24
821 879 4.785453 CCTGCTGTCCTTCCGCCC 62.785 72.222 0.00 0.00 0.00 6.13
852 910 2.214920 ACTCCAACCTCCGGTGGTC 61.215 63.158 27.59 0.00 39.83 4.02
853 911 3.296709 CTCCAACCTCCGGTGGTCG 62.297 68.421 27.59 17.60 39.83 4.79
863 925 2.426023 GGTGGTCGGCTGTGTTCT 59.574 61.111 0.00 0.00 0.00 3.01
993 1091 6.245408 AGTGGTTGTTCTTGGCATAATTCTA 58.755 36.000 0.00 0.00 0.00 2.10
1526 1624 1.068055 CAACAATGGCAACTCTGAGGC 60.068 52.381 9.85 3.51 37.61 4.70
1547 1645 3.579302 TGGTGCCTGTTGGGAGGG 61.579 66.667 0.00 0.00 37.23 4.30
1595 1699 1.938577 CAGGTTCGATGAAGATGGCAG 59.061 52.381 0.00 0.00 0.00 4.85
1674 1781 2.072298 GATGTCGTTGAGCTCTGCTTT 58.928 47.619 16.19 0.00 39.88 3.51
1697 1804 5.545588 TCCTAGCTGAATCTATGAATGTGC 58.454 41.667 0.00 0.00 0.00 4.57
1719 1842 3.025287 CAAGGATTGTTTGGGGTTTCG 57.975 47.619 0.00 0.00 42.34 3.46
1720 1843 2.364002 CAAGGATTGTTTGGGGTTTCGT 59.636 45.455 0.00 0.00 42.34 3.85
1721 1844 2.673258 AGGATTGTTTGGGGTTTCGTT 58.327 42.857 0.00 0.00 0.00 3.85
1722 1845 3.035363 AGGATTGTTTGGGGTTTCGTTT 58.965 40.909 0.00 0.00 0.00 3.60
1723 1846 3.452990 AGGATTGTTTGGGGTTTCGTTTT 59.547 39.130 0.00 0.00 0.00 2.43
1724 1847 3.558006 GGATTGTTTGGGGTTTCGTTTTG 59.442 43.478 0.00 0.00 0.00 2.44
1725 1848 2.674796 TGTTTGGGGTTTCGTTTTGG 57.325 45.000 0.00 0.00 0.00 3.28
1799 1922 3.511146 GGAATGAAAGGGCAATCAGTGAA 59.489 43.478 0.00 0.00 0.00 3.18
1918 2058 6.451393 TCTGGTACAAAATTGTAATGCCAAC 58.549 36.000 7.53 0.00 44.46 3.77
1927 2067 1.135431 TGTAATGCCAACATGCGCTTC 60.135 47.619 9.73 0.00 36.36 3.86
1964 2118 7.335627 TCTGGTTTGGATTCGTTAGTATTCAT 58.664 34.615 0.00 0.00 0.00 2.57
1996 2150 6.656693 GGATGGGACCATGATACTGATAAAAG 59.343 42.308 8.88 0.00 36.70 2.27
2048 2228 9.003112 CGCTGTTCAATATCAATTTCTTAGTTG 57.997 33.333 0.00 0.00 0.00 3.16
2088 2278 6.375736 TCAGAAAAGTTGTTCCACACATAACA 59.624 34.615 0.00 0.00 34.43 2.41
2090 2285 7.220683 CAGAAAAGTTGTTCCACACATAACAAG 59.779 37.037 0.00 0.00 43.99 3.16
2195 2390 4.870636 ACCAATGGGATTAAGAATGCTCA 58.129 39.130 3.55 0.00 38.05 4.26
2199 2394 6.016777 CCAATGGGATTAAGAATGCTCAGTAC 60.017 42.308 0.00 0.00 35.59 2.73
2205 2400 7.224949 GGGATTAAGAATGCTCAGTACAAGTAC 59.775 40.741 2.18 2.18 36.35 2.73
2233 2428 2.429250 GCCGGGCTTAATATTTTGTGGT 59.571 45.455 12.87 0.00 0.00 4.16
2261 2456 1.603802 TCAAGAGGCGCACTTTTCAAG 59.396 47.619 10.83 2.39 0.00 3.02
2342 2537 3.252974 AGCTTCACTAGTACCACATGC 57.747 47.619 0.00 0.00 0.00 4.06
2344 2539 4.023980 AGCTTCACTAGTACCACATGCTA 58.976 43.478 0.00 0.00 0.00 3.49
2346 2541 5.129485 AGCTTCACTAGTACCACATGCTATT 59.871 40.000 0.00 0.00 0.00 1.73
2347 2542 6.323996 AGCTTCACTAGTACCACATGCTATTA 59.676 38.462 0.00 0.00 0.00 0.98
2368 2587 0.179156 TCTTTCCGACGGCGATGTAC 60.179 55.000 15.16 0.00 40.82 2.90
2383 2602 3.056962 CGATGTACTGGATCATCTGGGAG 60.057 52.174 0.00 0.00 38.47 4.30
2387 2606 0.686224 CTGGATCATCTGGGAGAGGC 59.314 60.000 0.00 0.00 0.00 4.70
2389 2608 1.670590 GATCATCTGGGAGAGGCGG 59.329 63.158 0.00 0.00 0.00 6.13
2402 2621 0.107654 GAGGCGGCATTCAGGTTAGT 60.108 55.000 13.08 0.00 0.00 2.24
2405 2624 1.873591 GGCGGCATTCAGGTTAGTATG 59.126 52.381 3.07 0.00 0.00 2.39
2407 2626 2.560504 CGGCATTCAGGTTAGTATGCA 58.439 47.619 0.00 0.00 42.07 3.96
2424 2643 1.450312 CAGACAATCAGACGGGGCC 60.450 63.158 0.00 0.00 0.00 5.80
2465 2684 3.395941 ACTGTCTCTGGTTCATTTTCCCT 59.604 43.478 0.00 0.00 0.00 4.20
2466 2685 4.141158 ACTGTCTCTGGTTCATTTTCCCTT 60.141 41.667 0.00 0.00 0.00 3.95
2496 2715 4.437682 TTGAAAGAAAAGAGAGCTCCCA 57.562 40.909 10.93 0.00 0.00 4.37
2504 2723 2.416680 AGAGAGCTCCCAGCATTTTC 57.583 50.000 10.93 0.00 45.56 2.29
2505 2724 1.914798 AGAGAGCTCCCAGCATTTTCT 59.085 47.619 10.93 0.00 45.56 2.52
2506 2725 2.015587 GAGAGCTCCCAGCATTTTCTG 58.984 52.381 10.93 0.00 45.56 3.02
2509 2728 1.074405 AGCTCCCAGCATTTTCTGTGA 59.926 47.619 0.00 0.00 45.56 3.58
2510 2729 1.888512 GCTCCCAGCATTTTCTGTGAA 59.111 47.619 0.00 0.00 41.89 3.18
2511 2730 2.494870 GCTCCCAGCATTTTCTGTGAAT 59.505 45.455 0.00 0.00 41.89 2.57
2512 2731 3.675228 GCTCCCAGCATTTTCTGTGAATG 60.675 47.826 0.00 0.00 41.89 2.67
2513 2732 3.760151 CTCCCAGCATTTTCTGTGAATGA 59.240 43.478 8.98 0.00 36.78 2.57
2514 2733 3.760151 TCCCAGCATTTTCTGTGAATGAG 59.240 43.478 8.98 2.79 36.78 2.90
2515 2734 3.760151 CCCAGCATTTTCTGTGAATGAGA 59.240 43.478 8.98 0.00 36.78 3.27
2520 2747 4.155462 GCATTTTCTGTGAATGAGAGCTGA 59.845 41.667 0.00 0.00 36.78 4.26
2540 2767 7.553334 AGCTGATAATGATGCAGAAATGTTTT 58.447 30.769 0.00 0.00 0.00 2.43
2556 2783 2.954989 TGTTTTGCACTTGACATGGCTA 59.045 40.909 0.00 0.00 0.00 3.93
2586 2813 4.488126 GCACTATCTGCTTGTTGTTCAA 57.512 40.909 0.00 0.00 43.33 2.69
2610 2998 0.317799 GTGTGCACCAATTGATGCCA 59.682 50.000 22.17 15.87 41.33 4.92
2611 2999 0.317799 TGTGCACCAATTGATGCCAC 59.682 50.000 22.17 18.61 41.33 5.01
2618 3006 4.142093 GCACCAATTGATGCCACTAAGAAT 60.142 41.667 14.35 0.00 35.73 2.40
2624 3012 4.200838 TGATGCCACTAAGAATGTTCGA 57.799 40.909 0.00 0.00 0.00 3.71
2630 3018 3.684305 CCACTAAGAATGTTCGATGCACA 59.316 43.478 0.00 0.00 0.00 4.57
2632 3020 5.496387 CACTAAGAATGTTCGATGCACATC 58.504 41.667 1.85 0.31 33.54 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.054878 CTGCAAATGACCAAAGCAAGTC 58.945 45.455 0.00 0.00 34.45 3.01
1 2 2.694628 TCTGCAAATGACCAAAGCAAGT 59.305 40.909 0.00 0.00 34.45 3.16
2 3 3.374220 TCTGCAAATGACCAAAGCAAG 57.626 42.857 0.00 0.00 34.45 4.01
33 34 4.202010 ACATCCGTGGAAGTTGTTTTTGAG 60.202 41.667 0.00 0.00 0.00 3.02
35 36 4.040445 ACATCCGTGGAAGTTGTTTTTG 57.960 40.909 0.00 0.00 0.00 2.44
36 37 3.242936 CGACATCCGTGGAAGTTGTTTTT 60.243 43.478 0.00 0.00 0.00 1.94
37 38 2.289547 CGACATCCGTGGAAGTTGTTTT 59.710 45.455 0.00 0.00 0.00 2.43
111 112 1.922447 TGTATGGCTTTGGTCAGGGAT 59.078 47.619 0.00 0.00 0.00 3.85
113 114 1.004745 AGTGTATGGCTTTGGTCAGGG 59.995 52.381 0.00 0.00 0.00 4.45
144 149 5.786401 AAAATCGCACAGTTCAGTCTATC 57.214 39.130 0.00 0.00 0.00 2.08
203 210 6.257193 CCATAAACTAACGGTGGATGAACTAC 59.743 42.308 0.00 0.00 31.59 2.73
243 250 1.754226 CTCCTCCCTCTCTAACAGTGC 59.246 57.143 0.00 0.00 0.00 4.40
315 322 0.613260 TTGGCCGAGCTTATGTCACT 59.387 50.000 0.00 0.00 0.00 3.41
316 323 1.009829 CTTGGCCGAGCTTATGTCAC 58.990 55.000 7.18 0.00 0.00 3.67
400 407 1.830847 GCCGGTGTGGGAGGTTTTT 60.831 57.895 1.90 0.00 38.63 1.94
451 463 2.204244 GGGAAAGGAGGGTGGGGA 60.204 66.667 0.00 0.00 0.00 4.81
471 483 1.468520 GTGTGACGTGATTGGATTGGG 59.531 52.381 0.00 0.00 0.00 4.12
490 502 2.444895 GGGCGGAGGAGATGGAGT 60.445 66.667 0.00 0.00 0.00 3.85
615 669 3.213402 GACCGGCCTCTCCTCTCG 61.213 72.222 0.00 0.00 0.00 4.04
702 756 1.211949 TGGAGATAAAGAAAGCGGGGG 59.788 52.381 0.00 0.00 0.00 5.40
705 759 6.389906 ACAAAATTGGAGATAAAGAAAGCGG 58.610 36.000 0.00 0.00 0.00 5.52
723 777 7.309438 GGGACATAGCAAGAAGAAGAACAAAAT 60.309 37.037 0.00 0.00 0.00 1.82
727 781 4.287067 AGGGACATAGCAAGAAGAAGAACA 59.713 41.667 0.00 0.00 0.00 3.18
771 825 6.017400 TCTATAACGACGAAAAGTTCCAGT 57.983 37.500 0.00 0.00 0.00 4.00
774 828 4.267214 GCCTCTATAACGACGAAAAGTTCC 59.733 45.833 0.00 0.00 0.00 3.62
804 862 4.785453 GGGCGGAAGGACAGCAGG 62.785 72.222 0.00 0.00 41.24 4.85
809 867 1.497309 ATTGAAGGGGCGGAAGGACA 61.497 55.000 0.00 0.00 0.00 4.02
821 879 1.734465 GTTGGAGTGCGAGATTGAAGG 59.266 52.381 0.00 0.00 0.00 3.46
863 925 1.737029 CGAGCTGCTCTGAAATCGGAA 60.737 52.381 25.59 0.00 0.00 4.30
993 1091 1.671054 CCCGTCGTCCATTTGTGCT 60.671 57.895 0.00 0.00 0.00 4.40
1062 1160 4.452733 CCCAGGAGGTCGCCGAAC 62.453 72.222 0.00 0.00 0.00 3.95
1488 1586 3.003763 AAGCAGAGGGTCGGGTCC 61.004 66.667 0.00 0.00 0.00 4.46
1568 1666 2.027285 TCTTCATCGAACCTGCAATCCA 60.027 45.455 0.00 0.00 0.00 3.41
1647 1751 1.097547 GCTCAACGACATCCATGGGG 61.098 60.000 13.02 7.37 0.00 4.96
1648 1752 0.107508 AGCTCAACGACATCCATGGG 60.108 55.000 13.02 0.00 0.00 4.00
1674 1781 5.306419 AGCACATTCATAGATTCAGCTAGGA 59.694 40.000 0.00 0.00 30.16 2.94
1697 1804 3.305335 CGAAACCCCAAACAATCCTTGAG 60.305 47.826 0.00 0.00 0.00 3.02
1711 1834 0.462375 AACTGCCAAAACGAAACCCC 59.538 50.000 0.00 0.00 0.00 4.95
1714 1837 2.222707 GCAACAACTGCCAAAACGAAAC 60.223 45.455 0.00 0.00 46.13 2.78
1715 1838 1.996191 GCAACAACTGCCAAAACGAAA 59.004 42.857 0.00 0.00 46.13 3.46
1716 1839 1.634702 GCAACAACTGCCAAAACGAA 58.365 45.000 0.00 0.00 46.13 3.85
1717 1840 3.337398 GCAACAACTGCCAAAACGA 57.663 47.368 0.00 0.00 46.13 3.85
1768 1891 3.523157 TGCCCTTTCATTCCATGAGAGTA 59.477 43.478 0.00 0.00 39.22 2.59
1851 1974 4.532521 ACTGTAACCTCCTTCTATTGCTGT 59.467 41.667 0.00 0.00 0.00 4.40
1852 1975 5.091261 ACTGTAACCTCCTTCTATTGCTG 57.909 43.478 0.00 0.00 0.00 4.41
1918 2058 3.132160 AGATTCAGAGATGAAGCGCATG 58.868 45.455 11.47 0.00 39.00 4.06
1927 2067 5.095145 TCCAAACCAGAGATTCAGAGATG 57.905 43.478 0.00 0.00 0.00 2.90
1964 2118 0.466007 CATGGTCCCATCCGATTGCA 60.466 55.000 0.00 0.00 33.90 4.08
2048 2228 5.121454 ACTTTTCTGAATCGATGCTCAAGTC 59.879 40.000 4.68 0.00 0.00 3.01
2088 2278 3.191371 CCGTTTTGCTTGAGGCTTATCTT 59.809 43.478 0.00 0.00 42.39 2.40
2090 2285 2.747446 TCCGTTTTGCTTGAGGCTTATC 59.253 45.455 0.00 0.00 42.39 1.75
2122 2317 5.109903 AGATACGAAAGCAGACAATGTACC 58.890 41.667 0.00 0.00 0.00 3.34
2195 2390 1.730064 CGGCATTTGCGTACTTGTACT 59.270 47.619 8.94 0.00 43.26 2.73
2199 2394 1.136565 CCCGGCATTTGCGTACTTG 59.863 57.895 0.00 0.00 43.26 3.16
2205 2400 0.665835 TATTAAGCCCGGCATTTGCG 59.334 50.000 13.15 0.00 43.26 4.85
2233 2428 2.028112 AGTGCGCCTCTTGAATTCTACA 60.028 45.455 4.18 0.00 0.00 2.74
2261 2456 5.521906 ACAAGAAAAAGAAAAGGGAGAGC 57.478 39.130 0.00 0.00 0.00 4.09
2332 2527 6.704493 TCGGAAAGAATAATAGCATGTGGTAC 59.296 38.462 0.00 0.00 0.00 3.34
2333 2528 6.704493 GTCGGAAAGAATAATAGCATGTGGTA 59.296 38.462 0.00 0.00 0.00 3.25
2334 2529 5.527582 GTCGGAAAGAATAATAGCATGTGGT 59.472 40.000 0.00 0.00 0.00 4.16
2335 2530 5.333339 CGTCGGAAAGAATAATAGCATGTGG 60.333 44.000 0.00 0.00 0.00 4.17
2336 2531 5.333339 CCGTCGGAAAGAATAATAGCATGTG 60.333 44.000 4.91 0.00 0.00 3.21
2337 2532 4.750098 CCGTCGGAAAGAATAATAGCATGT 59.250 41.667 4.91 0.00 0.00 3.21
2338 2533 4.377431 GCCGTCGGAAAGAATAATAGCATG 60.377 45.833 17.49 0.00 0.00 4.06
2339 2534 3.746492 GCCGTCGGAAAGAATAATAGCAT 59.254 43.478 17.49 0.00 0.00 3.79
2340 2535 3.128349 GCCGTCGGAAAGAATAATAGCA 58.872 45.455 17.49 0.00 0.00 3.49
2341 2536 2.155155 CGCCGTCGGAAAGAATAATAGC 59.845 50.000 17.49 0.00 0.00 2.97
2342 2537 3.635331 TCGCCGTCGGAAAGAATAATAG 58.365 45.455 17.49 0.00 36.13 1.73
2344 2539 2.589798 TCGCCGTCGGAAAGAATAAT 57.410 45.000 17.49 0.00 36.13 1.28
2346 2541 1.135527 ACATCGCCGTCGGAAAGAATA 59.864 47.619 17.49 0.00 36.13 1.75
2347 2542 0.108329 ACATCGCCGTCGGAAAGAAT 60.108 50.000 17.49 1.22 36.13 2.40
2368 2587 0.686224 GCCTCTCCCAGATGATCCAG 59.314 60.000 0.00 0.00 0.00 3.86
2383 2602 0.107654 ACTAACCTGAATGCCGCCTC 60.108 55.000 0.00 0.00 0.00 4.70
2387 2606 2.545526 CTGCATACTAACCTGAATGCCG 59.454 50.000 3.91 0.00 43.19 5.69
2389 2608 4.191544 TGTCTGCATACTAACCTGAATGC 58.808 43.478 3.71 0.00 43.92 3.56
2402 2621 1.138859 CCCCGTCTGATTGTCTGCATA 59.861 52.381 0.00 0.00 0.00 3.14
2405 2624 2.109126 GCCCCGTCTGATTGTCTGC 61.109 63.158 0.00 0.00 0.00 4.26
2407 2626 1.274703 ATGGCCCCGTCTGATTGTCT 61.275 55.000 0.00 0.00 0.00 3.41
2424 2643 6.317140 AGACAGTGCATTTTATCAGTACCATG 59.683 38.462 0.00 0.00 0.00 3.66
2476 2695 3.808618 GCTGGGAGCTCTCTTTTCTTTCA 60.809 47.826 16.21 0.00 38.45 2.69
2477 2696 2.746904 GCTGGGAGCTCTCTTTTCTTTC 59.253 50.000 16.21 0.00 38.45 2.62
2478 2697 2.107204 TGCTGGGAGCTCTCTTTTCTTT 59.893 45.455 16.21 0.00 42.97 2.52
2479 2698 1.701847 TGCTGGGAGCTCTCTTTTCTT 59.298 47.619 16.21 0.00 42.97 2.52
2480 2699 1.356124 TGCTGGGAGCTCTCTTTTCT 58.644 50.000 16.21 0.00 42.97 2.52
2481 2700 2.416680 ATGCTGGGAGCTCTCTTTTC 57.583 50.000 16.21 1.71 42.97 2.29
2482 2701 2.895242 AATGCTGGGAGCTCTCTTTT 57.105 45.000 16.21 0.15 42.97 2.27
2496 2715 4.156190 CAGCTCTCATTCACAGAAAATGCT 59.844 41.667 0.00 0.00 34.73 3.79
2504 2723 6.347806 GCATCATTATCAGCTCTCATTCACAG 60.348 42.308 0.00 0.00 0.00 3.66
2505 2724 5.469084 GCATCATTATCAGCTCTCATTCACA 59.531 40.000 0.00 0.00 0.00 3.58
2506 2725 5.469084 TGCATCATTATCAGCTCTCATTCAC 59.531 40.000 0.00 0.00 0.00 3.18
2509 2728 5.866207 TCTGCATCATTATCAGCTCTCATT 58.134 37.500 0.00 0.00 0.00 2.57
2510 2729 5.485209 TCTGCATCATTATCAGCTCTCAT 57.515 39.130 0.00 0.00 0.00 2.90
2511 2730 4.950205 TCTGCATCATTATCAGCTCTCA 57.050 40.909 0.00 0.00 0.00 3.27
2512 2731 6.205076 ACATTTCTGCATCATTATCAGCTCTC 59.795 38.462 0.00 0.00 0.00 3.20
2513 2732 6.062749 ACATTTCTGCATCATTATCAGCTCT 58.937 36.000 0.00 0.00 0.00 4.09
2514 2733 6.315091 ACATTTCTGCATCATTATCAGCTC 57.685 37.500 0.00 0.00 0.00 4.09
2515 2734 6.710597 AACATTTCTGCATCATTATCAGCT 57.289 33.333 0.00 0.00 0.00 4.24
2520 2747 7.101054 AGTGCAAAACATTTCTGCATCATTAT 58.899 30.769 13.49 0.00 46.90 1.28
2540 2767 2.785540 TCATAGCCATGTCAAGTGCA 57.214 45.000 0.00 0.00 33.57 4.57
2610 2998 5.725110 GATGTGCATCGAACATTCTTAGT 57.275 39.130 2.89 0.00 38.37 2.24
2624 3012 4.799564 AAATTACAAACCCGATGTGCAT 57.200 36.364 0.00 0.00 32.27 3.96
2630 3018 7.551617 CCTACTCTACAAAATTACAAACCCGAT 59.448 37.037 0.00 0.00 0.00 4.18
2632 3020 6.875195 TCCTACTCTACAAAATTACAAACCCG 59.125 38.462 0.00 0.00 0.00 5.28
2633 3021 8.803397 ATCCTACTCTACAAAATTACAAACCC 57.197 34.615 0.00 0.00 0.00 4.11


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

AutoCloner maintained by Alex Coulton.