Multiple sequence alignment - TraesCS6D01G220700

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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 TraesCS6D01G220700 chr6D 100.000 2714 0 0 1 2714 311299657 311302370 0.000000e+00 5012
1 TraesCS6D01G220700 chr6B 88.341 2333 114 65 1 2255 515186853 515184601 0.000000e+00 2656
2 TraesCS6D01G220700 chr6B 87.500 320 17 6 2397 2714 515184060 515183762 5.560000e-92 348
3 TraesCS6D01G220700 chr6A 88.387 1550 63 58 757 2243 448060720 448062215 0.000000e+00 1757
4 TraesCS6D01G220700 chr6A 81.501 773 74 41 1 749 448059690 448060417 3.030000e-159 571
5 TraesCS6D01G220700 chr6A 85.389 527 53 10 2190 2714 448063276 448063780 2.390000e-145 525
6 TraesCS6D01G220700 chr6A 92.377 223 16 1 2035 2256 448063058 448063280 1.570000e-82 316
7 TraesCS6D01G220700 chr6A 83.046 348 37 14 2365 2709 448062653 448062981 2.040000e-76 296
8 TraesCS6D01G220700 chr2B 87.678 211 23 2 1392 1602 572156612 572156819 2.700000e-60 243
9 TraesCS6D01G220700 chr7B 82.895 228 25 7 2489 2714 143178975 143178760 2.760000e-45 193
10 TraesCS6D01G220700 chr7B 88.406 138 13 3 2578 2714 143246099 143245964 2.160000e-36 163


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 TraesCS6D01G220700 chr6D 311299657 311302370 2713 False 5012 5012 100.0000 1 2714 1 chr6D.!!$F1 2713
1 TraesCS6D01G220700 chr6B 515183762 515186853 3091 True 1502 2656 87.9205 1 2714 2 chr6B.!!$R1 2713
2 TraesCS6D01G220700 chr6A 448059690 448063780 4090 False 693 1757 86.1400 1 2714 5 chr6A.!!$F1 2713

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
668 711 0.042731 ACCGAATCCCTCTCTTCCCA 59.957 55.0 0.0 0.0 0.0 4.37 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2201 2652 0.310854 AGCAGCGCACTGTTTTTACC 59.689 50.0 11.47 0.0 46.3 2.85 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
51 55 6.101332 TGCTTTGGATGTTAATTCTTGCATC 58.899 36.000 0.00 0.00 37.56 3.91
135 140 0.401738 CCCCTTTTGTCTGGAGCAGA 59.598 55.000 0.00 0.00 38.25 4.26
144 155 1.137872 GTCTGGAGCAGATTGGATCGT 59.862 52.381 0.00 0.00 42.73 3.73
193 204 4.510571 GTCTTAGAATTAGACCGGCCAAA 58.489 43.478 0.00 0.00 36.79 3.28
194 205 4.939439 GTCTTAGAATTAGACCGGCCAAAA 59.061 41.667 0.00 0.00 36.79 2.44
262 273 1.227089 GACGGTCGATCTGCATGCT 60.227 57.895 20.33 0.00 0.00 3.79
263 274 1.485838 GACGGTCGATCTGCATGCTG 61.486 60.000 20.33 18.97 0.00 4.41
266 277 0.460811 GGTCGATCTGCATGCTGTCA 60.461 55.000 20.33 3.70 0.00 3.58
273 284 3.429141 GCATGCTGTCACGCTGCT 61.429 61.111 11.37 0.00 41.79 4.24
336 364 1.534729 GAAAAGAGATGCAACCCGGT 58.465 50.000 0.00 0.00 0.00 5.28
337 365 1.468914 GAAAAGAGATGCAACCCGGTC 59.531 52.381 0.00 0.00 0.00 4.79
338 366 0.673644 AAAGAGATGCAACCCGGTCG 60.674 55.000 0.00 0.00 0.00 4.79
339 367 1.541310 AAGAGATGCAACCCGGTCGA 61.541 55.000 0.00 0.00 0.00 4.20
385 413 1.017177 TGTGCACGCTATTTCGTCCC 61.017 55.000 13.13 0.00 41.21 4.46
395 423 0.957395 ATTTCGTCCCACTGCAGCAG 60.957 55.000 21.54 21.54 37.52 4.24
438 466 4.202050 ACTCAAATCACAAACAGCTTGGAC 60.202 41.667 0.00 0.00 39.56 4.02
444 472 3.953612 TCACAAACAGCTTGGACTGAAAT 59.046 39.130 0.00 0.00 40.25 2.17
494 523 2.507407 TTCTCCCGGGATTTCTTTGG 57.493 50.000 27.07 10.02 0.00 3.28
500 529 0.168128 CGGGATTTCTTTGGACGCAC 59.832 55.000 0.00 0.00 0.00 5.34
526 559 0.179132 TGAACGTGTACGCTGTGTGT 60.179 50.000 3.71 0.00 44.43 3.72
530 563 0.868177 CGTGTACGCTGTGTGTGTGA 60.868 55.000 3.71 0.00 40.02 3.58
531 564 0.852777 GTGTACGCTGTGTGTGTGAG 59.147 55.000 3.71 0.00 40.02 3.51
532 565 0.458260 TGTACGCTGTGTGTGTGAGT 59.542 50.000 3.71 0.00 40.02 3.41
533 566 1.677052 TGTACGCTGTGTGTGTGAGTA 59.323 47.619 3.71 0.00 40.02 2.59
549 582 0.606604 AGTACCGCGGACATGTTCTT 59.393 50.000 35.90 8.50 0.00 2.52
551 584 1.017177 TACCGCGGACATGTTCTTGC 61.017 55.000 35.90 0.00 0.00 4.01
552 585 2.480555 CGCGGACATGTTCTTGCC 59.519 61.111 0.00 0.00 0.00 4.52
553 586 2.480555 GCGGACATGTTCTTGCCG 59.519 61.111 16.35 16.35 44.47 5.69
555 588 1.671054 CGGACATGTTCTTGCCGGT 60.671 57.895 13.61 0.00 38.40 5.28
560 593 0.802494 CATGTTCTTGCCGGTGTACC 59.198 55.000 1.90 0.00 0.00 3.34
577 613 5.279106 GGTGTACCGTATAGATAACATGCCA 60.279 44.000 0.00 0.00 0.00 4.92
579 615 6.702723 GTGTACCGTATAGATAACATGCCAAA 59.297 38.462 0.00 0.00 0.00 3.28
580 616 6.926826 TGTACCGTATAGATAACATGCCAAAG 59.073 38.462 0.00 0.00 0.00 2.77
582 618 6.223852 ACCGTATAGATAACATGCCAAAGAG 58.776 40.000 0.00 0.00 0.00 2.85
586 622 8.826710 CGTATAGATAACATGCCAAAGAGAAAA 58.173 33.333 0.00 0.00 0.00 2.29
589 625 7.765695 AGATAACATGCCAAAGAGAAAAGAA 57.234 32.000 0.00 0.00 0.00 2.52
591 627 8.641541 AGATAACATGCCAAAGAGAAAAGAAAA 58.358 29.630 0.00 0.00 0.00 2.29
592 628 8.822652 ATAACATGCCAAAGAGAAAAGAAAAG 57.177 30.769 0.00 0.00 0.00 2.27
594 637 6.877236 ACATGCCAAAGAGAAAAGAAAAGAA 58.123 32.000 0.00 0.00 0.00 2.52
595 638 7.330262 ACATGCCAAAGAGAAAAGAAAAGAAA 58.670 30.769 0.00 0.00 0.00 2.52
599 642 6.818644 GCCAAAGAGAAAAGAAAAGAAAAGGT 59.181 34.615 0.00 0.00 0.00 3.50
600 643 7.979537 GCCAAAGAGAAAAGAAAAGAAAAGGTA 59.020 33.333 0.00 0.00 0.00 3.08
601 644 9.521503 CCAAAGAGAAAAGAAAAGAAAAGGTAG 57.478 33.333 0.00 0.00 0.00 3.18
602 645 9.521503 CAAAGAGAAAAGAAAAGAAAAGGTAGG 57.478 33.333 0.00 0.00 0.00 3.18
605 648 8.275758 AGAGAAAAGAAAAGAAAAGGTAGGAGT 58.724 33.333 0.00 0.00 0.00 3.85
606 649 9.557061 GAGAAAAGAAAAGAAAAGGTAGGAGTA 57.443 33.333 0.00 0.00 0.00 2.59
634 677 7.055667 ACTAGGATATATGATGGCATTACCG 57.944 40.000 0.00 0.00 43.94 4.02
654 697 2.889578 CGGAAACTCAACGACCGAA 58.110 52.632 0.00 0.00 45.31 4.30
661 704 0.818296 CTCAACGACCGAATCCCTCT 59.182 55.000 0.00 0.00 0.00 3.69
662 705 0.815734 TCAACGACCGAATCCCTCTC 59.184 55.000 0.00 0.00 0.00 3.20
663 706 0.818296 CAACGACCGAATCCCTCTCT 59.182 55.000 0.00 0.00 0.00 3.10
664 707 1.204941 CAACGACCGAATCCCTCTCTT 59.795 52.381 0.00 0.00 0.00 2.85
665 708 1.104630 ACGACCGAATCCCTCTCTTC 58.895 55.000 0.00 0.00 0.00 2.87
666 709 0.386113 CGACCGAATCCCTCTCTTCC 59.614 60.000 0.00 0.00 0.00 3.46
667 710 0.753867 GACCGAATCCCTCTCTTCCC 59.246 60.000 0.00 0.00 0.00 3.97
668 711 0.042731 ACCGAATCCCTCTCTTCCCA 59.957 55.000 0.00 0.00 0.00 4.37
669 712 1.344496 ACCGAATCCCTCTCTTCCCAT 60.344 52.381 0.00 0.00 0.00 4.00
670 713 1.071385 CCGAATCCCTCTCTTCCCATG 59.929 57.143 0.00 0.00 0.00 3.66
671 714 1.071385 CGAATCCCTCTCTTCCCATGG 59.929 57.143 4.14 4.14 0.00 3.66
672 715 2.412591 GAATCCCTCTCTTCCCATGGA 58.587 52.381 15.22 0.00 0.00 3.41
673 716 2.594536 ATCCCTCTCTTCCCATGGAA 57.405 50.000 15.22 4.85 39.66 3.53
674 717 2.359376 TCCCTCTCTTCCCATGGAAA 57.641 50.000 15.22 0.00 41.54 3.13
675 718 2.642982 TCCCTCTCTTCCCATGGAAAA 58.357 47.619 15.22 6.33 41.54 2.29
676 719 2.993146 TCCCTCTCTTCCCATGGAAAAA 59.007 45.455 15.22 3.60 41.54 1.94
752 795 8.443953 AGCTAGCGAATCTTTTCATTCTTAAT 57.556 30.769 9.55 0.00 31.48 1.40
771 1108 8.721133 TCTTAATTTTTCTAGGGCCTTTTCTT 57.279 30.769 13.45 0.00 0.00 2.52
772 1109 8.585018 TCTTAATTTTTCTAGGGCCTTTTCTTG 58.415 33.333 13.45 0.00 0.00 3.02
773 1110 4.600692 TTTTTCTAGGGCCTTTTCTTGC 57.399 40.909 13.45 0.00 0.00 4.01
774 1111 3.525800 TTTCTAGGGCCTTTTCTTGCT 57.474 42.857 13.45 0.00 0.00 3.91
778 1115 2.086610 AGGGCCTTTTCTTGCTTTGA 57.913 45.000 0.00 0.00 0.00 2.69
789 1126 8.919661 CCTTTTCTTGCTTTGATTTGAATACTC 58.080 33.333 0.00 0.00 0.00 2.59
805 1142 4.902443 ATACTCACGTACATCACCTGAG 57.098 45.455 0.00 0.00 42.63 3.35
814 1151 5.123502 ACGTACATCACCTGAGTTACTACTG 59.876 44.000 0.00 0.00 33.84 2.74
816 1153 3.832490 ACATCACCTGAGTTACTACTGCA 59.168 43.478 0.00 0.00 33.84 4.41
867 1214 4.236935 CAAGGCTAAAATGACGCACAAAT 58.763 39.130 0.00 0.00 0.00 2.32
869 1216 3.505680 AGGCTAAAATGACGCACAAATCA 59.494 39.130 0.00 0.00 0.00 2.57
875 1222 0.534877 TGACGCACAAATCACTGGCT 60.535 50.000 0.00 0.00 0.00 4.75
876 1223 0.166814 GACGCACAAATCACTGGCTC 59.833 55.000 0.00 0.00 0.00 4.70
941 1304 1.000612 GAGTCTTCCCTCCCCGTCT 59.999 63.158 0.00 0.00 0.00 4.18
945 1308 3.959329 CTTCCCTCCCCGTCTCGGT 62.959 68.421 7.40 0.00 46.80 4.69
946 1309 3.534704 TTCCCTCCCCGTCTCGGTT 62.535 63.158 7.40 0.00 46.80 4.44
948 1311 2.577593 CCTCCCCGTCTCGGTTTC 59.422 66.667 7.40 0.00 46.80 2.78
950 1313 1.511768 CTCCCCGTCTCGGTTTCTC 59.488 63.158 7.40 0.00 46.80 2.87
951 1314 2.181021 CCCCGTCTCGGTTTCTCG 59.819 66.667 7.40 0.00 46.80 4.04
952 1315 2.506438 CCCGTCTCGGTTTCTCGC 60.506 66.667 7.40 0.00 46.80 5.03
953 1316 2.874780 CCGTCTCGGTTTCTCGCG 60.875 66.667 0.00 0.00 42.73 5.87
954 1317 2.126965 CGTCTCGGTTTCTCGCGT 60.127 61.111 5.77 0.00 0.00 6.01
955 1318 2.144680 CGTCTCGGTTTCTCGCGTC 61.145 63.158 5.77 0.00 0.00 5.19
956 1319 1.800713 GTCTCGGTTTCTCGCGTCC 60.801 63.158 5.77 1.58 0.00 4.79
957 1320 1.970114 TCTCGGTTTCTCGCGTCCT 60.970 57.895 5.77 0.00 0.00 3.85
958 1321 1.514443 CTCGGTTTCTCGCGTCCTC 60.514 63.158 5.77 0.00 0.00 3.71
959 1322 2.874780 CGGTTTCTCGCGTCCTCG 60.875 66.667 5.77 0.31 40.37 4.63
1041 1407 2.317609 CCTTCCTTCCACACACGCG 61.318 63.158 3.53 3.53 0.00 6.01
1044 1410 2.280524 CCTTCCACACACGCGGAA 60.281 61.111 12.47 1.61 38.99 4.30
1085 1463 3.602513 CTTCGACCTGCCAGCTGCT 62.603 63.158 8.66 0.00 42.00 4.24
1086 1464 3.889134 TTCGACCTGCCAGCTGCTG 62.889 63.158 22.44 22.44 42.00 4.41
1703 2102 3.060098 GCGTGCTCGATTGAATAGATAGC 59.940 47.826 13.13 0.00 39.71 2.97
1873 2293 2.237143 TCTAGCTCAACATGTTCCCCAG 59.763 50.000 8.48 3.74 0.00 4.45
1883 2303 1.607467 GTTCCCCAGCTTGCATGGT 60.607 57.895 4.19 1.05 35.96 3.55
1884 2304 1.607178 TTCCCCAGCTTGCATGGTG 60.607 57.895 21.32 21.32 35.96 4.17
1885 2305 2.036098 CCCCAGCTTGCATGGTGA 59.964 61.111 27.66 0.00 37.61 4.02
1921 2348 2.562738 CTGTATGATCTGGTGGCCGATA 59.437 50.000 0.00 0.00 0.00 2.92
1922 2349 2.562738 TGTATGATCTGGTGGCCGATAG 59.437 50.000 0.00 0.00 0.00 2.08
1924 2351 2.015456 TGATCTGGTGGCCGATAGAT 57.985 50.000 13.39 13.39 39.76 1.98
1925 2352 1.895798 TGATCTGGTGGCCGATAGATC 59.104 52.381 24.80 24.80 43.57 2.75
1979 2408 5.888161 GGATCATGGTTGTCAATTAACCTCT 59.112 40.000 9.48 0.00 46.11 3.69
1992 2421 6.318648 TCAATTAACCTCTCCGATTGAAATGG 59.681 38.462 0.00 0.00 34.75 3.16
2038 2483 3.111853 TCTTGTGTTGAGCGAGTCATT 57.888 42.857 0.00 0.00 34.17 2.57
2039 2484 3.059884 TCTTGTGTTGAGCGAGTCATTC 58.940 45.455 0.00 0.00 34.17 2.67
2040 2485 2.820059 TGTGTTGAGCGAGTCATTCT 57.180 45.000 0.00 0.00 34.17 2.40
2041 2486 2.407090 TGTGTTGAGCGAGTCATTCTG 58.593 47.619 0.00 0.00 34.17 3.02
2042 2487 1.127582 GTGTTGAGCGAGTCATTCTGC 59.872 52.381 0.00 0.00 34.17 4.26
2053 2498 0.610174 TCATTCTGCTCTGCTTCCGT 59.390 50.000 0.00 0.00 0.00 4.69
2110 2558 2.074230 AAAGCGACGTCCGTGGTGTA 62.074 55.000 10.58 0.00 41.15 2.90
2172 2623 1.136611 GCAAGCTACTTCGTGTTGTCG 60.137 52.381 0.00 0.00 0.00 4.35
2187 2638 1.887242 GTCGAGTGTTGTGCTGGCA 60.887 57.895 0.00 0.00 0.00 4.92
2201 2652 0.174845 CTGGCATCCAATGGTGCTTG 59.825 55.000 20.32 12.62 41.04 4.01
2233 2684 1.214589 GCTGCTTTGTCTGCCATGG 59.785 57.895 7.63 7.63 0.00 3.66
2263 2781 0.318120 AGGGCGTCCAATTTTTGCTG 59.682 50.000 9.71 0.00 34.83 4.41
2271 2789 4.432712 GTCCAATTTTTGCTGTGACAACT 58.567 39.130 0.00 0.00 0.00 3.16
2276 2794 6.237915 CCAATTTTTGCTGTGACAACTCTTTC 60.238 38.462 0.00 0.00 0.00 2.62
2277 2795 5.384063 TTTTTGCTGTGACAACTCTTTCA 57.616 34.783 0.00 0.00 0.00 2.69
2358 2876 8.378172 TCACTATCAAAACAAAGGTGAAGTAG 57.622 34.615 0.00 0.00 30.81 2.57
2360 2878 9.268268 CACTATCAAAACAAAGGTGAAGTAGTA 57.732 33.333 0.00 0.00 0.00 1.82
2361 2879 9.269453 ACTATCAAAACAAAGGTGAAGTAGTAC 57.731 33.333 0.00 0.00 0.00 2.73
2363 2881 5.824097 TCAAAACAAAGGTGAAGTAGTACCC 59.176 40.000 0.00 0.00 37.70 3.69
2391 4131 2.599408 AGATGGTACGTATCGGGGAT 57.401 50.000 0.00 0.00 0.00 3.85
2403 4143 2.592308 GGGGATCGCTTGGCTCTT 59.408 61.111 9.90 0.00 0.00 2.85
2427 4167 1.407258 TGCTGGTGCACCTTTTAACAC 59.593 47.619 34.75 15.69 45.31 3.32
2429 4169 2.159170 GCTGGTGCACCTTTTAACACAA 60.159 45.455 34.75 11.10 39.41 3.33
2430 4170 3.443976 CTGGTGCACCTTTTAACACAAC 58.556 45.455 34.75 5.70 34.69 3.32
2466 4207 2.668144 AATGGTCGAAAAACCCTGGA 57.332 45.000 0.00 0.00 38.65 3.86
2467 4208 2.668144 ATGGTCGAAAAACCCTGGAA 57.332 45.000 0.00 0.00 38.65 3.53
2468 4209 2.438800 TGGTCGAAAAACCCTGGAAA 57.561 45.000 0.00 0.00 38.65 3.13
2469 4210 2.952116 TGGTCGAAAAACCCTGGAAAT 58.048 42.857 0.00 0.00 38.65 2.17
2470 4211 3.301274 TGGTCGAAAAACCCTGGAAATT 58.699 40.909 0.00 0.00 38.65 1.82
2471 4212 3.068873 TGGTCGAAAAACCCTGGAAATTG 59.931 43.478 0.00 0.00 38.65 2.32
2472 4213 3.069016 GGTCGAAAAACCCTGGAAATTGT 59.931 43.478 0.00 0.00 32.82 2.71
2475 4216 3.807071 CGAAAAACCCTGGAAATTGTTGG 59.193 43.478 0.00 0.00 0.00 3.77
2550 4291 3.270027 CTTTCGTGATATGGTCCAGCAA 58.730 45.455 0.00 0.00 0.00 3.91
2607 4348 9.165035 ACTAGGCGTACTATTCACTCTATATTC 57.835 37.037 0.00 0.00 0.00 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
135 140 0.248289 AACGGACCGAACGATCCAAT 59.752 50.000 23.38 0.00 34.35 3.16
144 155 4.893601 TGCACGCAACGGACCGAA 62.894 61.111 23.38 0.00 0.00 4.30
199 210 2.013400 CAACCACCATGCGCATACTTA 58.987 47.619 24.84 0.00 0.00 2.24
209 220 2.872557 CGAGCAGCAACCACCATG 59.127 61.111 0.00 0.00 0.00 3.66
262 273 0.800683 GCGTGTATAGCAGCGTGACA 60.801 55.000 0.00 0.00 34.19 3.58
263 274 0.800683 TGCGTGTATAGCAGCGTGAC 60.801 55.000 0.00 0.00 40.01 3.67
266 277 4.088421 GTGCGTGTATAGCAGCGT 57.912 55.556 0.00 0.00 46.10 5.07
307 318 0.902531 ATCTCTTTTCGCGGGAAGGA 59.097 50.000 14.94 15.11 32.80 3.36
308 319 1.009829 CATCTCTTTTCGCGGGAAGG 58.990 55.000 14.94 11.94 32.80 3.46
309 320 0.375106 GCATCTCTTTTCGCGGGAAG 59.625 55.000 14.94 11.12 32.80 3.46
310 321 0.321210 TGCATCTCTTTTCGCGGGAA 60.321 50.000 11.32 11.32 0.00 3.97
336 364 2.844946 TGCCAGTTGAAAATGACTCGA 58.155 42.857 0.00 0.00 0.00 4.04
337 365 3.058016 ACATGCCAGTTGAAAATGACTCG 60.058 43.478 0.00 0.00 0.00 4.18
338 366 4.232221 CACATGCCAGTTGAAAATGACTC 58.768 43.478 0.00 0.00 0.00 3.36
339 367 3.638160 ACACATGCCAGTTGAAAATGACT 59.362 39.130 0.00 0.00 0.00 3.41
395 423 3.755378 AGTTCCACAGTTGATTCATCTGC 59.245 43.478 19.88 7.56 35.36 4.26
500 529 0.111266 GCGTACACGTTCACTGCAAG 60.111 55.000 3.44 0.00 42.22 4.01
526 559 1.214325 CATGTCCGCGGTACTCACA 59.786 57.895 27.15 21.84 0.00 3.58
530 563 0.606604 AAGAACATGTCCGCGGTACT 59.393 50.000 27.15 7.72 0.00 2.73
531 564 0.719465 CAAGAACATGTCCGCGGTAC 59.281 55.000 27.15 21.38 0.00 3.34
532 565 1.017177 GCAAGAACATGTCCGCGGTA 61.017 55.000 27.15 16.34 0.00 4.02
533 566 2.325082 GCAAGAACATGTCCGCGGT 61.325 57.895 27.15 3.60 0.00 5.68
553 586 5.166398 GGCATGTTATCTATACGGTACACC 58.834 45.833 0.00 0.00 0.00 4.16
555 588 6.408107 TTGGCATGTTATCTATACGGTACA 57.592 37.500 0.00 0.00 0.00 2.90
560 593 7.946655 TTCTCTTTGGCATGTTATCTATACG 57.053 36.000 0.00 0.00 0.00 3.06
563 599 9.466497 TTCTTTTCTCTTTGGCATGTTATCTAT 57.534 29.630 0.00 0.00 0.00 1.98
564 600 8.862325 TTCTTTTCTCTTTGGCATGTTATCTA 57.138 30.769 0.00 0.00 0.00 1.98
575 611 9.521503 CTACCTTTTCTTTTCTTTTCTCTTTGG 57.478 33.333 0.00 0.00 0.00 3.28
577 613 9.475620 TCCTACCTTTTCTTTTCTTTTCTCTTT 57.524 29.630 0.00 0.00 0.00 2.52
579 615 8.275758 ACTCCTACCTTTTCTTTTCTTTTCTCT 58.724 33.333 0.00 0.00 0.00 3.10
580 616 8.453238 ACTCCTACCTTTTCTTTTCTTTTCTC 57.547 34.615 0.00 0.00 0.00 2.87
611 654 7.055667 ACGGTAATGCCATCATATATCCTAG 57.944 40.000 0.00 0.00 36.97 3.02
612 655 6.238925 CGACGGTAATGCCATCATATATCCTA 60.239 42.308 0.00 0.00 36.97 2.94
613 656 5.451937 CGACGGTAATGCCATCATATATCCT 60.452 44.000 0.00 0.00 36.97 3.24
614 657 4.745125 CGACGGTAATGCCATCATATATCC 59.255 45.833 0.00 0.00 36.97 2.59
615 658 4.745125 CCGACGGTAATGCCATCATATATC 59.255 45.833 5.48 0.00 36.97 1.63
616 659 4.404394 TCCGACGGTAATGCCATCATATAT 59.596 41.667 14.79 0.00 36.97 0.86
617 660 3.764972 TCCGACGGTAATGCCATCATATA 59.235 43.478 14.79 0.00 36.97 0.86
618 661 2.565391 TCCGACGGTAATGCCATCATAT 59.435 45.455 14.79 0.00 36.97 1.78
619 662 1.964933 TCCGACGGTAATGCCATCATA 59.035 47.619 14.79 0.00 36.97 2.15
620 663 0.756294 TCCGACGGTAATGCCATCAT 59.244 50.000 14.79 0.00 36.97 2.45
621 664 0.537653 TTCCGACGGTAATGCCATCA 59.462 50.000 14.79 0.00 36.97 3.07
622 665 1.329599 GTTTCCGACGGTAATGCCATC 59.670 52.381 14.79 0.00 36.97 3.51
631 674 0.595825 GTCGTTGAGTTTCCGACGGT 60.596 55.000 14.79 0.00 42.53 4.83
637 680 1.730612 GGATTCGGTCGTTGAGTTTCC 59.269 52.381 0.00 0.00 0.00 3.13
654 697 2.594536 TTCCATGGGAAGAGAGGGAT 57.405 50.000 13.02 0.00 36.71 3.85
674 717 1.318576 CCGGTGGTTGAGCTCTTTTT 58.681 50.000 16.19 0.00 0.00 1.94
675 718 0.537371 CCCGGTGGTTGAGCTCTTTT 60.537 55.000 16.19 0.00 0.00 2.27
676 719 1.073199 CCCGGTGGTTGAGCTCTTT 59.927 57.895 16.19 0.00 0.00 2.52
679 722 1.671379 GTTCCCGGTGGTTGAGCTC 60.671 63.158 6.82 6.82 0.00 4.09
752 795 4.223144 AGCAAGAAAAGGCCCTAGAAAAA 58.777 39.130 0.00 0.00 0.00 1.94
757 1094 3.157087 TCAAAGCAAGAAAAGGCCCTAG 58.843 45.455 0.00 0.00 0.00 3.02
758 1095 3.237268 TCAAAGCAAGAAAAGGCCCTA 57.763 42.857 0.00 0.00 0.00 3.53
759 1096 2.086610 TCAAAGCAAGAAAAGGCCCT 57.913 45.000 0.00 0.00 0.00 5.19
760 1097 3.407424 AATCAAAGCAAGAAAAGGCCC 57.593 42.857 0.00 0.00 0.00 5.80
763 1100 8.822652 AGTATTCAAATCAAAGCAAGAAAAGG 57.177 30.769 0.00 0.00 0.00 3.11
771 1108 5.940192 ACGTGAGTATTCAAATCAAAGCA 57.060 34.783 0.00 0.00 46.88 3.91
789 1126 4.436242 AGTAACTCAGGTGATGTACGTG 57.564 45.455 0.00 0.00 44.46 4.49
805 1142 4.537015 CACAAAGGCTTTGCAGTAGTAAC 58.463 43.478 33.69 0.00 44.39 2.50
814 1151 2.010817 CGTCGCACAAAGGCTTTGC 61.011 57.895 33.69 23.49 44.39 3.68
816 1153 2.331451 GCGTCGCACAAAGGCTTT 59.669 55.556 13.44 6.68 0.00 3.51
867 1214 2.523168 TGTGGGACGAGCCAGTGA 60.523 61.111 0.00 0.00 38.95 3.41
912 1272 2.529389 AAGACTCCGGGCAAGGGT 60.529 61.111 0.00 0.00 0.00 4.34
941 1304 2.564975 GAGGACGCGAGAAACCGA 59.435 61.111 15.93 0.00 0.00 4.69
952 1315 5.333111 GGCTTGTTTTTATATAGCGAGGACG 60.333 44.000 0.00 0.00 42.93 4.79
953 1316 5.526111 TGGCTTGTTTTTATATAGCGAGGAC 59.474 40.000 0.00 0.00 32.74 3.85
954 1317 5.676552 TGGCTTGTTTTTATATAGCGAGGA 58.323 37.500 0.00 0.00 32.74 3.71
955 1318 6.560253 ATGGCTTGTTTTTATATAGCGAGG 57.440 37.500 0.00 0.00 32.74 4.63
956 1319 7.417612 ACAATGGCTTGTTTTTATATAGCGAG 58.582 34.615 0.00 0.00 43.05 5.03
957 1320 7.066404 TGACAATGGCTTGTTTTTATATAGCGA 59.934 33.333 4.29 0.00 45.57 4.93
958 1321 7.192913 TGACAATGGCTTGTTTTTATATAGCG 58.807 34.615 4.29 0.00 45.57 4.26
959 1322 8.925161 TTGACAATGGCTTGTTTTTATATAGC 57.075 30.769 4.29 0.00 45.57 2.97
960 1323 9.023967 GCTTGACAATGGCTTGTTTTTATATAG 57.976 33.333 4.29 0.00 45.57 1.31
961 1324 8.748412 AGCTTGACAATGGCTTGTTTTTATATA 58.252 29.630 0.00 0.00 45.57 0.86
962 1325 7.614494 AGCTTGACAATGGCTTGTTTTTATAT 58.386 30.769 0.00 0.00 45.57 0.86
963 1326 6.991938 AGCTTGACAATGGCTTGTTTTTATA 58.008 32.000 0.00 0.00 45.57 0.98
964 1327 5.857268 AGCTTGACAATGGCTTGTTTTTAT 58.143 33.333 0.00 0.00 45.57 1.40
965 1328 5.275067 AGCTTGACAATGGCTTGTTTTTA 57.725 34.783 0.00 0.00 45.57 1.52
966 1329 4.122046 GAGCTTGACAATGGCTTGTTTTT 58.878 39.130 3.68 0.00 45.57 1.94
1041 1407 0.312102 GCTTTCCTGTGCTGTGTTCC 59.688 55.000 0.00 0.00 0.00 3.62
1044 1410 1.893808 CCGCTTTCCTGTGCTGTGT 60.894 57.895 0.00 0.00 0.00 3.72
1085 1463 3.142162 CCGCCTTGCCATCATGCA 61.142 61.111 0.00 0.00 40.07 3.96
1086 1464 4.580551 GCCGCCTTGCCATCATGC 62.581 66.667 0.00 0.00 0.00 4.06
1087 1465 3.133767 CTGCCGCCTTGCCATCATG 62.134 63.158 0.00 0.00 0.00 3.07
1765 2174 1.154282 GCATGATCGCATCGCATGG 60.154 57.895 0.00 0.00 39.71 3.66
1802 2212 2.735772 GGCCGCTCCTCCATCTTCA 61.736 63.158 0.00 0.00 0.00 3.02
1873 2293 1.019673 ACGATCATCACCATGCAAGC 58.980 50.000 0.00 0.00 0.00 4.01
1883 2303 0.458370 CAGGACGCACACGATCATCA 60.458 55.000 0.00 0.00 43.93 3.07
1884 2304 0.458543 ACAGGACGCACACGATCATC 60.459 55.000 0.00 0.00 43.93 2.92
1885 2305 0.815095 TACAGGACGCACACGATCAT 59.185 50.000 0.00 0.00 43.93 2.45
1921 2348 1.064060 GCAAATTAACGGCTGCGATCT 59.936 47.619 0.00 0.00 0.00 2.75
1922 2349 1.064060 AGCAAATTAACGGCTGCGATC 59.936 47.619 0.00 0.00 39.80 3.69
1924 2351 2.550487 AGCAAATTAACGGCTGCGA 58.450 47.368 0.00 0.00 39.80 5.10
1932 2361 5.174398 CCATTGATCGATGCAGCAAATTAAC 59.826 40.000 16.49 0.00 0.00 2.01
1979 2408 1.604915 TCCGCCCATTTCAATCGGA 59.395 52.632 0.00 0.00 45.70 4.55
1992 2421 2.218603 ACCACGAATATTTCATCCGCC 58.781 47.619 0.00 0.00 0.00 6.13
2038 2483 0.610174 AATCACGGAAGCAGAGCAGA 59.390 50.000 0.00 0.00 0.00 4.26
2039 2484 1.396301 GAAATCACGGAAGCAGAGCAG 59.604 52.381 0.00 0.00 0.00 4.24
2040 2485 1.442769 GAAATCACGGAAGCAGAGCA 58.557 50.000 0.00 0.00 0.00 4.26
2041 2486 0.371645 CGAAATCACGGAAGCAGAGC 59.628 55.000 0.00 0.00 0.00 4.09
2053 2498 4.875536 CCAGTAACACATGATCCGAAATCA 59.124 41.667 0.00 3.39 0.00 2.57
2110 2558 6.038356 CGGTTGTACGGACTATTTTCAGTAT 58.962 40.000 0.00 0.00 30.35 2.12
2172 2623 0.890542 TGGATGCCAGCACAACACTC 60.891 55.000 0.00 0.00 0.00 3.51
2201 2652 0.310854 AGCAGCGCACTGTTTTTACC 59.689 50.000 11.47 0.00 46.30 2.85
2271 2789 3.125656 ATGGACCCATGGATCTGAAAGA 58.874 45.455 15.22 0.00 40.89 2.52
2294 2812 1.024579 ACGATCAACATCCAACGGCC 61.025 55.000 0.00 0.00 0.00 6.13
2358 2876 5.767168 ACGTACCATCTATTCTACTGGGTAC 59.233 44.000 0.00 0.00 43.52 3.34
2360 2878 4.801164 ACGTACCATCTATTCTACTGGGT 58.199 43.478 0.00 0.00 32.89 4.51
2361 2879 6.183360 CGATACGTACCATCTATTCTACTGGG 60.183 46.154 0.00 0.00 32.89 4.45
2363 2881 6.183360 CCCGATACGTACCATCTATTCTACTG 60.183 46.154 0.00 0.00 0.00 2.74
2391 4131 2.260869 GCAACCAAGAGCCAAGCGA 61.261 57.895 0.00 0.00 0.00 4.93
2460 4201 4.414337 TTGTTTCCAACAATTTCCAGGG 57.586 40.909 0.00 0.00 45.79 4.45
2513 4254 2.286772 CGAAAGTCGTTTTGTCCCCAAG 60.287 50.000 0.00 0.00 34.72 3.61
2561 4302 8.145122 GCCTAGTATAGTGCTGATTTAGACTTT 58.855 37.037 0.00 0.00 36.82 2.66
2562 4303 7.522399 CGCCTAGTATAGTGCTGATTTAGACTT 60.522 40.741 0.00 0.00 36.82 3.01
2563 4304 6.072397 CGCCTAGTATAGTGCTGATTTAGACT 60.072 42.308 0.00 0.00 36.82 3.24
2564 4305 6.087522 CGCCTAGTATAGTGCTGATTTAGAC 58.912 44.000 0.00 0.00 36.82 2.59
2565 4306 5.768662 ACGCCTAGTATAGTGCTGATTTAGA 59.231 40.000 0.00 0.00 36.82 2.10
2566 4307 6.015027 ACGCCTAGTATAGTGCTGATTTAG 57.985 41.667 0.00 0.00 36.82 1.85
2567 4308 6.713903 AGTACGCCTAGTATAGTGCTGATTTA 59.286 38.462 0.00 0.00 36.82 1.40
2607 4348 7.652909 TGAGCATAAAAACAAATTGTCCAAGAG 59.347 33.333 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.