Multiple sequence alignment - TraesCS5D01G410500

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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 TraesCS5D01G410500 chr5D 100.000 3233 0 0 1 3233 473847355 473850587 0.000000e+00 5971.0
1 TraesCS5D01G410500 chr5B 91.088 2738 147 50 107 2801 580842657 580845340 0.000000e+00 3615.0
2 TraesCS5D01G410500 chr5B 89.556 450 27 6 2793 3233 580845514 580845952 1.310000e-153 553.0
3 TraesCS5D01G410500 chr5B 76.642 137 28 4 1081 1215 580849414 580849548 4.470000e-09 73.1
4 TraesCS5D01G410500 chr5A 90.684 2136 124 44 376 2487 593339408 593341492 0.000000e+00 2772.0
5 TraesCS5D01G410500 chr5A 88.778 401 25 7 2835 3233 593349442 593349824 1.050000e-129 473.0
6 TraesCS5D01G410500 chr5A 88.520 392 25 11 1 378 593338920 593339305 1.060000e-124 457.0
7 TraesCS5D01G410500 chr7D 76.774 155 29 7 1081 1231 540369771 540369620 2.670000e-11 80.5
8 TraesCS5D01G410500 chr7A 76.821 151 30 5 1081 1228 621564651 621564799 2.670000e-11 80.5
9 TraesCS5D01G410500 chr7B 76.159 151 31 5 1081 1228 583382323 583382471 1.240000e-09 75.0
10 TraesCS5D01G410500 chr2D 90.385 52 5 0 1165 1216 316328612 316328561 5.790000e-08 69.4
11 TraesCS5D01G410500 chr2D 96.774 31 1 0 1298 1328 382128649 382128619 6.000000e-03 52.8
12 TraesCS5D01G410500 chr2A 90.385 52 5 0 1165 1216 418794834 418794885 5.790000e-08 69.4
13 TraesCS5D01G410500 chr2A 96.774 31 1 0 1298 1328 516308672 516308642 6.000000e-03 52.8
14 TraesCS5D01G410500 chr6A 89.091 55 5 1 1171 1225 109135828 109135881 2.080000e-07 67.6
15 TraesCS5D01G410500 chr1A 97.143 35 1 0 1291 1325 60955941 60955907 3.480000e-05 60.2
16 TraesCS5D01G410500 chr1B 75.510 147 21 13 1182 1325 100308717 100308851 1.250000e-04 58.4
17 TraesCS5D01G410500 chr3D 100.000 28 0 0 1297 1324 600529368 600529341 6.000000e-03 52.8
18 TraesCS5D01G410500 chr2B 96.774 31 1 0 1298 1328 452912518 452912488 6.000000e-03 52.8


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 TraesCS5D01G410500 chr5D 473847355 473850587 3232 False 5971.0 5971 100.000 1 3233 1 chr5D.!!$F1 3232
1 TraesCS5D01G410500 chr5B 580842657 580849548 6891 False 1413.7 3615 85.762 107 3233 3 chr5B.!!$F1 3126
2 TraesCS5D01G410500 chr5A 593338920 593341492 2572 False 1614.5 2772 89.602 1 2487 2 chr5A.!!$F2 2486

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
555 680 0.028242 AGTGAGAGCGTCGCTATTCG 59.972 55.000 21.77 0.0 44.64 3.34 F
714 846 1.000843 CCAGACACCGTCACATCAAGA 59.999 52.381 0.00 0.0 34.60 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1501 1647 0.249868 TAGAGGTGTGCTGTGTGTGC 60.250 55.0 0.00 0.00 0.0 4.57 R
2306 2476 0.521867 CTTTGACGCATGCACCGATG 60.522 55.0 19.57 2.13 0.0 3.84 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 52 4.214971 GGCAAAGATGACAGCATACATAGG 59.785 45.833 0.00 0.00 34.11 2.57
52 53 4.214971 GCAAAGATGACAGCATACATAGGG 59.785 45.833 0.00 0.00 34.11 3.53
53 54 4.630644 AAGATGACAGCATACATAGGGG 57.369 45.455 0.00 0.00 34.11 4.79
131 132 2.549754 GTGCGATCGGAAAATGATCCAT 59.450 45.455 18.30 0.00 39.23 3.41
230 237 3.012934 TCCATCTGACACCTCATCGTA 57.987 47.619 0.00 0.00 0.00 3.43
438 558 8.258007 TCACTCGATGGAAACTTACTGATTAAT 58.742 33.333 0.00 0.00 0.00 1.40
446 566 9.146984 TGGAAACTTACTGATTAATTAGTCACG 57.853 33.333 15.52 8.51 0.00 4.35
447 567 9.362539 GGAAACTTACTGATTAATTAGTCACGA 57.637 33.333 15.52 0.00 0.00 4.35
449 569 8.699283 AACTTACTGATTAATTAGTCACGACC 57.301 34.615 15.52 0.00 0.00 4.79
450 570 7.833786 ACTTACTGATTAATTAGTCACGACCA 58.166 34.615 15.52 0.00 0.00 4.02
452 572 8.697846 TTACTGATTAATTAGTCACGACCAAG 57.302 34.615 15.52 0.00 0.00 3.61
453 573 5.581085 ACTGATTAATTAGTCACGACCAAGC 59.419 40.000 7.05 0.00 0.00 4.01
454 574 5.483811 TGATTAATTAGTCACGACCAAGCA 58.516 37.500 6.58 0.00 0.00 3.91
455 575 5.350365 TGATTAATTAGTCACGACCAAGCAC 59.650 40.000 6.58 0.00 0.00 4.40
457 577 2.148916 TTAGTCACGACCAAGCACTG 57.851 50.000 0.00 0.00 0.00 3.66
458 578 1.037493 TAGTCACGACCAAGCACTGT 58.963 50.000 0.00 0.00 0.00 3.55
459 579 1.037493 AGTCACGACCAAGCACTGTA 58.963 50.000 0.00 0.00 0.00 2.74
460 580 1.618837 AGTCACGACCAAGCACTGTAT 59.381 47.619 0.00 0.00 0.00 2.29
461 581 2.823747 AGTCACGACCAAGCACTGTATA 59.176 45.455 0.00 0.00 0.00 1.47
462 582 3.447586 AGTCACGACCAAGCACTGTATAT 59.552 43.478 0.00 0.00 0.00 0.86
463 583 4.643334 AGTCACGACCAAGCACTGTATATA 59.357 41.667 0.00 0.00 0.00 0.86
464 584 5.302059 AGTCACGACCAAGCACTGTATATAT 59.698 40.000 0.00 0.00 0.00 0.86
465 585 6.489022 AGTCACGACCAAGCACTGTATATATA 59.511 38.462 0.00 0.00 0.00 0.86
499 620 5.365619 ACGAAGGTCACAGTAAAATTCAGT 58.634 37.500 0.00 0.00 0.00 3.41
502 623 6.564125 CGAAGGTCACAGTAAAATTCAGTGTC 60.564 42.308 0.00 0.00 0.00 3.67
509 632 8.783093 TCACAGTAAAATTCAGTGTCCAATTAG 58.217 33.333 0.00 0.00 0.00 1.73
520 645 5.934625 CAGTGTCCAATTAGTTCTACTTGCT 59.065 40.000 4.96 0.00 0.00 3.91
522 647 5.062308 GTGTCCAATTAGTTCTACTTGCTCG 59.938 44.000 4.96 0.00 0.00 5.03
555 680 0.028242 AGTGAGAGCGTCGCTATTCG 59.972 55.000 21.77 0.00 44.64 3.34
608 734 3.944055 TTTAGCCAGAGACTGACACTC 57.056 47.619 0.00 0.00 32.44 3.51
609 737 1.454201 TAGCCAGAGACTGACACTCG 58.546 55.000 0.00 0.00 39.12 4.18
694 826 2.421424 AGCGCCAAGAGTTCATTCAATC 59.579 45.455 2.29 0.00 0.00 2.67
714 846 1.000843 CCAGACACCGTCACATCAAGA 59.999 52.381 0.00 0.00 34.60 3.02
789 925 6.930667 AAACTAGACCAAAACACACGTATT 57.069 33.333 0.00 0.00 0.00 1.89
796 932 4.641094 ACCAAAACACACGTATTTCTCCAA 59.359 37.500 0.00 0.00 0.00 3.53
803 939 5.995282 ACACACGTATTTCTCCAAAGATCAA 59.005 36.000 0.00 0.00 0.00 2.57
804 940 6.485313 ACACACGTATTTCTCCAAAGATCAAA 59.515 34.615 0.00 0.00 0.00 2.69
805 941 7.174946 ACACACGTATTTCTCCAAAGATCAAAT 59.825 33.333 0.00 0.00 0.00 2.32
806 942 8.023128 CACACGTATTTCTCCAAAGATCAAATT 58.977 33.333 0.00 0.00 0.00 1.82
884 1026 2.159627 CGAGCGCCTGTCAAATTAACTT 59.840 45.455 2.29 0.00 0.00 2.66
886 1028 3.412386 AGCGCCTGTCAAATTAACTTCT 58.588 40.909 2.29 0.00 0.00 2.85
971 1114 5.421056 ACCACATATACTGATATACCACGGG 59.579 44.000 0.00 0.00 0.00 5.28
1040 1186 4.521062 GGCGCTGCTCGTCCTCAT 62.521 66.667 7.64 0.00 41.07 2.90
1041 1187 2.959071 GCGCTGCTCGTCCTCATC 60.959 66.667 0.00 0.00 41.07 2.92
1042 1188 2.279120 CGCTGCTCGTCCTCATCC 60.279 66.667 0.00 0.00 0.00 3.51
1043 1189 2.780094 CGCTGCTCGTCCTCATCCT 61.780 63.158 0.00 0.00 0.00 3.24
1044 1190 1.067250 GCTGCTCGTCCTCATCCTC 59.933 63.158 0.00 0.00 0.00 3.71
1048 1194 2.833582 TCGTCCTCATCCTCGCCC 60.834 66.667 0.00 0.00 0.00 6.13
1051 1197 1.456705 GTCCTCATCCTCGCCCTCT 60.457 63.158 0.00 0.00 0.00 3.69
1237 1383 4.485834 CGCCGCATGCAGCAACAT 62.486 61.111 24.73 0.00 46.13 2.71
1270 1416 7.465173 GCTGATGCTTATGAGTTATGATCATG 58.535 38.462 18.72 0.00 36.19 3.07
1409 1555 4.436998 GCCACGAGACGGTGAGGG 62.437 72.222 0.00 0.00 40.38 4.30
1508 1658 4.927782 TCGCCCTGGTGCACACAC 62.928 66.667 20.43 1.36 46.66 3.82
1517 1667 2.271821 TGCACACACAGCACACCT 59.728 55.556 0.00 0.00 37.02 4.00
1518 1668 1.819208 TGCACACACAGCACACCTC 60.819 57.895 0.00 0.00 37.02 3.85
1519 1669 1.524621 GCACACACAGCACACCTCT 60.525 57.895 0.00 0.00 0.00 3.69
1527 1686 3.193691 ACACAGCACACCTCTATCTGTAC 59.806 47.826 0.00 0.00 36.37 2.90
1533 1692 5.877012 AGCACACCTCTATCTGTACATTTTG 59.123 40.000 0.00 0.00 0.00 2.44
1535 1694 5.643348 CACACCTCTATCTGTACATTTTGCA 59.357 40.000 0.00 0.00 0.00 4.08
1545 1704 0.038343 ACATTTTGCACCGGACATGC 60.038 50.000 9.46 8.89 43.68 4.06
1547 1706 1.887344 ATTTTGCACCGGACATGCCC 61.887 55.000 9.46 0.00 42.69 5.36
1555 1714 4.864334 GGACATGCCCGGAGCCTG 62.864 72.222 0.73 10.81 42.71 4.85
1556 1715 3.785859 GACATGCCCGGAGCCTGA 61.786 66.667 20.93 2.46 39.28 3.86
1557 1716 3.329542 GACATGCCCGGAGCCTGAA 62.330 63.158 20.93 2.15 39.28 3.02
1558 1717 2.194056 CATGCCCGGAGCCTGAAT 59.806 61.111 0.73 0.00 39.28 2.57
1559 1718 1.454479 CATGCCCGGAGCCTGAATT 60.454 57.895 0.73 0.00 39.28 2.17
1560 1719 1.039233 CATGCCCGGAGCCTGAATTT 61.039 55.000 0.73 0.00 39.28 1.82
1561 1720 0.324645 ATGCCCGGAGCCTGAATTTT 60.325 50.000 0.73 0.00 42.71 1.82
1576 1735 6.293516 GCCTGAATTTTCATGTTTGATTTGCA 60.294 34.615 0.00 0.00 36.46 4.08
1578 1737 7.748683 CCTGAATTTTCATGTTTGATTTGCATG 59.251 33.333 0.00 0.00 40.76 4.06
1638 1797 4.459089 GACGGCCTGAGCTCCACC 62.459 72.222 12.15 8.95 39.73 4.61
1755 1914 2.671682 GCCCTCTCAGGTGAACCC 59.328 66.667 0.00 0.00 36.42 4.11
1757 1916 1.538876 CCCTCTCAGGTGAACCCCA 60.539 63.158 0.00 0.00 36.42 4.96
1777 1936 4.462280 CGCCTCCCAACCGTACCC 62.462 72.222 0.00 0.00 0.00 3.69
1800 1965 2.954868 CGCCGCATGGACGTACTC 60.955 66.667 0.00 0.00 37.49 2.59
1802 1967 3.077519 GCCGCATGGACGTACTCCT 62.078 63.158 0.00 0.00 40.26 3.69
1803 1968 1.226974 CCGCATGGACGTACTCCTG 60.227 63.158 0.00 0.00 40.26 3.86
1823 1988 4.201950 CCTGCTAACATAACAGTTCATGGC 60.202 45.833 0.00 0.00 33.07 4.40
1824 1989 4.588899 TGCTAACATAACAGTTCATGGCT 58.411 39.130 0.00 0.00 33.07 4.75
1825 1990 4.395854 TGCTAACATAACAGTTCATGGCTG 59.604 41.667 13.98 13.98 39.67 4.85
1826 1991 4.201950 GCTAACATAACAGTTCATGGCTGG 60.202 45.833 17.95 6.81 38.22 4.85
1827 1992 3.439857 ACATAACAGTTCATGGCTGGT 57.560 42.857 17.95 15.19 38.22 4.00
1828 1993 3.347216 ACATAACAGTTCATGGCTGGTC 58.653 45.455 17.95 0.00 38.22 4.02
2073 2238 2.442272 GCCTCCGACCAGCTCCTA 60.442 66.667 0.00 0.00 0.00 2.94
2169 2334 2.184322 GCCATCGTCAAGCTCGGA 59.816 61.111 0.00 0.00 0.00 4.55
2282 2452 4.374399 GTTGATATACACCGGGGTTACTG 58.626 47.826 18.35 0.00 0.00 2.74
2301 2471 1.630244 GCGCTGGCTGAGTTAGTGTG 61.630 60.000 0.00 0.00 35.83 3.82
2303 2473 1.630244 GCTGGCTGAGTTAGTGTGCG 61.630 60.000 0.00 0.00 0.00 5.34
2304 2474 0.319900 CTGGCTGAGTTAGTGTGCGT 60.320 55.000 0.00 0.00 0.00 5.24
2305 2475 0.599991 TGGCTGAGTTAGTGTGCGTG 60.600 55.000 0.00 0.00 0.00 5.34
2306 2476 1.493311 GCTGAGTTAGTGTGCGTGC 59.507 57.895 0.00 0.00 0.00 5.34
2307 2477 1.221466 GCTGAGTTAGTGTGCGTGCA 61.221 55.000 0.00 0.00 0.00 4.57
2308 2478 1.432514 CTGAGTTAGTGTGCGTGCAT 58.567 50.000 0.00 0.00 0.00 3.96
2309 2479 1.391485 CTGAGTTAGTGTGCGTGCATC 59.609 52.381 0.00 0.00 0.00 3.91
2310 2480 0.366871 GAGTTAGTGTGCGTGCATCG 59.633 55.000 0.00 0.00 43.12 3.84
2383 2555 3.139077 AGATTCGTTGGGTTTCACAGTC 58.861 45.455 0.00 0.00 0.00 3.51
2388 2560 2.375146 GTTGGGTTTCACAGTCCTGTT 58.625 47.619 0.00 0.00 42.83 3.16
2506 2678 1.502690 ATGGGGGACGTATAACTGCA 58.497 50.000 0.00 0.00 0.00 4.41
2512 2684 3.867493 GGGGACGTATAACTGCAAAGTAC 59.133 47.826 0.00 0.00 0.00 2.73
2538 2710 5.585047 GTGTCACTTTTTGTAGTCTTCACCT 59.415 40.000 0.00 0.00 0.00 4.00
2545 2717 5.899631 TTTGTAGTCTTCACCTAAACCCT 57.100 39.130 0.00 0.00 0.00 4.34
2566 2738 3.386932 TCCTGCCCTAGAATTTGCATT 57.613 42.857 0.00 0.00 32.53 3.56
2570 2742 2.159254 TGCCCTAGAATTTGCATTTCGC 60.159 45.455 0.00 0.00 42.89 4.70
2590 2762 1.004610 CATTCATGTAGCGACCAAGCG 60.005 52.381 0.00 0.00 43.00 4.68
2609 2782 1.145803 GGGTTACACTGCTTCACGTC 58.854 55.000 0.00 0.00 0.00 4.34
2652 2825 2.414138 GGTCGATGGTCCAAAGTAAACG 59.586 50.000 0.00 0.00 0.00 3.60
2667 2840 7.044314 CCAAAGTAAACGTTTTGCTAAGTTCAG 60.044 37.037 20.19 6.36 33.92 3.02
2668 2841 6.913873 AGTAAACGTTTTGCTAAGTTCAGA 57.086 33.333 20.19 0.00 0.00 3.27
2669 2842 6.712549 AGTAAACGTTTTGCTAAGTTCAGAC 58.287 36.000 20.19 6.25 0.00 3.51
2699 2873 4.082190 TCCGACTGTTTAGAGATTGTGAGG 60.082 45.833 0.00 0.00 0.00 3.86
2714 2888 2.235898 TGTGAGGCCAAAAGCAAAACTT 59.764 40.909 5.01 0.00 46.50 2.66
2715 2889 2.609002 GTGAGGCCAAAAGCAAAACTTG 59.391 45.455 5.01 0.00 46.50 3.16
2716 2890 2.212652 GAGGCCAAAAGCAAAACTTGG 58.787 47.619 5.01 0.00 46.50 3.61
2717 2891 1.559219 AGGCCAAAAGCAAAACTTGGT 59.441 42.857 5.01 0.00 46.50 3.67
2718 2892 2.769095 AGGCCAAAAGCAAAACTTGGTA 59.231 40.909 5.01 0.00 46.50 3.25
2719 2893 3.390967 AGGCCAAAAGCAAAACTTGGTAT 59.609 39.130 5.01 0.00 46.50 2.73
2768 2942 8.702438 ACTTTTTGTCAATGAATAAATCAAGCG 58.298 29.630 0.00 0.00 42.54 4.68
2783 2957 3.146066 TCAAGCGCTCACCAAAAGTAAT 58.854 40.909 12.06 0.00 0.00 1.89
2790 2964 3.857010 GCTCACCAAAAGTAATGTGGCAC 60.857 47.826 11.55 11.55 35.72 5.01
2808 3164 3.251004 GGCACAATTGGCTACTACTATGC 59.749 47.826 10.83 6.13 44.99 3.14
2816 3172 2.287103 GGCTACTACTATGCCGTTTTGC 59.713 50.000 0.00 0.00 37.11 3.68
2825 3181 5.424757 ACTATGCCGTTTTGCTGTCTTATA 58.575 37.500 0.00 0.00 0.00 0.98
2832 3188 6.258160 CCGTTTTGCTGTCTTATAAATGGAG 58.742 40.000 0.00 0.00 37.14 3.86
2838 3194 8.677148 TTGCTGTCTTATAAATGGAGATTACC 57.323 34.615 0.00 0.00 0.00 2.85
2840 3196 9.154632 TGCTGTCTTATAAATGGAGATTACCTA 57.845 33.333 0.00 0.00 0.00 3.08
2881 3239 4.030216 ACTGGGATTTTTGGTGTTGAACT 58.970 39.130 0.00 0.00 0.00 3.01
2883 3241 5.301805 ACTGGGATTTTTGGTGTTGAACTAG 59.698 40.000 0.00 0.00 0.00 2.57
2889 3247 8.410912 GGATTTTTGGTGTTGAACTAGTAGTTT 58.589 33.333 16.56 1.20 38.80 2.66
2943 3307 7.465353 TTGCTGAATATTCCTTTTGTGATGA 57.535 32.000 12.90 0.00 0.00 2.92
3049 3414 6.234920 TCTTGGTCGATGATTAGTTTTCCAA 58.765 36.000 0.00 0.00 0.00 3.53
3055 3420 8.190784 GGTCGATGATTAGTTTTCCAAATGAAT 58.809 33.333 0.00 0.00 31.67 2.57
3113 3478 4.929211 GTCAATTATTGGGCAAACACTTCC 59.071 41.667 5.02 0.00 0.00 3.46
3114 3479 4.590647 TCAATTATTGGGCAAACACTTCCA 59.409 37.500 5.02 0.00 0.00 3.53
3119 3484 0.668535 GGGCAAACACTTCCAGACAC 59.331 55.000 0.00 0.00 0.00 3.67
3153 3518 2.018515 TCGTCACCGATATGTACAGCA 58.981 47.619 0.33 0.00 38.40 4.41
3214 3579 1.272769 ACCTCTAGCAAGTTGGTCGAC 59.727 52.381 11.55 7.13 0.00 4.20
3226 3591 1.301423 TGGTCGACCAAAAAGTTCGG 58.699 50.000 34.60 0.00 44.35 4.30
3227 3592 1.134461 TGGTCGACCAAAAAGTTCGGA 60.134 47.619 34.60 6.79 44.35 4.55
3230 3595 3.181498 GGTCGACCAAAAAGTTCGGAAAA 60.181 43.478 29.75 0.00 35.64 2.29
3231 3596 4.033019 GTCGACCAAAAAGTTCGGAAAAG 58.967 43.478 3.51 0.00 0.00 2.27
3232 3597 3.940221 TCGACCAAAAAGTTCGGAAAAGA 59.060 39.130 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 8.815565 TGCCATTAGTTTGACCTAATCATTTA 57.184 30.769 0.00 0.00 35.87 1.40
10 11 6.945435 TCTTTGCCATTAGTTTGACCTAATCA 59.055 34.615 0.00 0.00 35.87 2.57
24 25 5.192176 TGTATGCTGTCATCTTTGCCATTA 58.808 37.500 0.00 0.00 34.22 1.90
51 52 7.334056 GATCACGAATCAAGTTGGAAACCCC 62.334 48.000 2.34 0.00 40.07 4.95
52 53 4.379499 GATCACGAATCAAGTTGGAAACCC 60.379 45.833 2.34 0.00 40.07 4.11
53 54 4.215399 TGATCACGAATCAAGTTGGAAACC 59.785 41.667 2.34 0.00 43.11 3.27
105 106 2.002586 CATTTTCCGATCGCACTCAGT 58.997 47.619 10.32 0.00 0.00 3.41
256 263 9.693739 TGGCAATCTTCCAAGAATATAGTTTTA 57.306 29.630 0.00 0.00 38.77 1.52
260 267 7.141758 TCTGGCAATCTTCCAAGAATATAGT 57.858 36.000 0.00 0.00 38.77 2.12
262 269 7.013655 GCTTTCTGGCAATCTTCCAAGAATATA 59.986 37.037 0.00 0.00 38.77 0.86
263 270 6.183360 GCTTTCTGGCAATCTTCCAAGAATAT 60.183 38.462 0.00 0.00 38.77 1.28
270 277 1.888512 GTGCTTTCTGGCAATCTTCCA 59.111 47.619 0.00 0.00 44.18 3.53
396 516 4.021807 TCGAGTGAAATTACAGTGCAGGTA 60.022 41.667 0.00 0.00 0.00 3.08
403 523 6.231211 AGTTTCCATCGAGTGAAATTACAGT 58.769 36.000 13.32 0.00 0.00 3.55
404 524 6.727824 AGTTTCCATCGAGTGAAATTACAG 57.272 37.500 13.32 0.00 0.00 2.74
438 558 1.411246 ACAGTGCTTGGTCGTGACTAA 59.589 47.619 0.00 0.00 0.00 2.24
445 565 7.090808 ACATGTATATATACAGTGCTTGGTCG 58.909 38.462 25.52 9.81 45.46 4.79
446 566 8.712363 CAACATGTATATATACAGTGCTTGGTC 58.288 37.037 25.52 0.00 45.46 4.02
447 567 8.210946 ACAACATGTATATATACAGTGCTTGGT 58.789 33.333 25.52 16.65 45.46 3.67
448 568 8.607441 ACAACATGTATATATACAGTGCTTGG 57.393 34.615 25.52 15.19 45.46 3.61
449 569 9.260002 TGACAACATGTATATATACAGTGCTTG 57.740 33.333 25.52 24.09 45.46 4.01
450 570 9.830975 TTGACAACATGTATATATACAGTGCTT 57.169 29.630 25.52 16.95 45.46 3.91
452 572 8.214472 CGTTGACAACATGTATATATACAGTGC 58.786 37.037 25.52 18.43 45.46 4.40
453 573 9.458374 TCGTTGACAACATGTATATATACAGTG 57.542 33.333 25.52 23.11 45.46 3.66
457 577 9.472361 ACCTTCGTTGACAACATGTATATATAC 57.528 33.333 18.09 14.86 0.00 1.47
458 578 9.687210 GACCTTCGTTGACAACATGTATATATA 57.313 33.333 18.09 0.00 0.00 0.86
459 579 8.201464 TGACCTTCGTTGACAACATGTATATAT 58.799 33.333 18.09 0.00 0.00 0.86
460 580 7.490079 GTGACCTTCGTTGACAACATGTATATA 59.510 37.037 18.09 0.00 0.00 0.86
461 581 6.312918 GTGACCTTCGTTGACAACATGTATAT 59.687 38.462 18.09 0.00 0.00 0.86
462 582 5.636121 GTGACCTTCGTTGACAACATGTATA 59.364 40.000 18.09 0.00 0.00 1.47
463 583 4.451096 GTGACCTTCGTTGACAACATGTAT 59.549 41.667 18.09 0.47 0.00 2.29
464 584 3.805422 GTGACCTTCGTTGACAACATGTA 59.195 43.478 18.09 0.00 0.00 2.29
465 585 2.612212 GTGACCTTCGTTGACAACATGT 59.388 45.455 18.09 8.58 0.00 3.21
499 620 5.168569 CGAGCAAGTAGAACTAATTGGACA 58.831 41.667 18.80 0.00 40.32 4.02
502 623 6.147164 TCAAACGAGCAAGTAGAACTAATTGG 59.853 38.462 18.80 8.73 40.32 3.16
509 632 4.318831 CCAGTTCAAACGAGCAAGTAGAAC 60.319 45.833 15.40 15.40 38.46 3.01
520 645 1.138069 TCACTGCTCCAGTTCAAACGA 59.862 47.619 0.00 0.00 42.59 3.85
522 647 2.805099 CTCTCACTGCTCCAGTTCAAAC 59.195 50.000 0.00 0.00 42.59 2.93
555 680 1.665679 CACACACCCGTGATAGATTGC 59.334 52.381 0.96 0.00 46.80 3.56
608 734 5.811399 TTACTTGCCATGTAAGGAATTCG 57.189 39.130 10.57 0.00 29.74 3.34
609 737 8.903820 AGTTATTACTTGCCATGTAAGGAATTC 58.096 33.333 17.60 12.93 35.77 2.17
694 826 1.000843 TCTTGATGTGACGGTGTCTGG 59.999 52.381 0.00 0.00 33.15 3.86
714 846 6.061441 GGATGTTTGGGGAATTTTGTTTTCT 58.939 36.000 0.00 0.00 0.00 2.52
796 932 8.655935 AGGGTTGACAATCTTAATTTGATCTT 57.344 30.769 0.00 0.00 0.00 2.40
803 939 6.472887 TCGAGAAGGGTTGACAATCTTAATT 58.527 36.000 0.00 0.00 0.00 1.40
804 940 6.049955 TCGAGAAGGGTTGACAATCTTAAT 57.950 37.500 0.00 0.00 0.00 1.40
805 941 5.477607 TCGAGAAGGGTTGACAATCTTAA 57.522 39.130 0.00 0.00 0.00 1.85
806 942 5.677319 ATCGAGAAGGGTTGACAATCTTA 57.323 39.130 0.00 0.00 0.00 2.10
884 1026 4.621510 GCACACAAGGATCATGTACTGAGA 60.622 45.833 3.37 0.00 37.28 3.27
886 1028 3.007831 TGCACACAAGGATCATGTACTGA 59.992 43.478 3.37 0.00 38.53 3.41
1109 1255 2.581354 GCACGATGCTCTCCAGGT 59.419 61.111 0.00 0.00 40.96 4.00
1270 1416 3.308053 CACACACATCGATCAATCACTCC 59.692 47.826 0.00 0.00 0.00 3.85
1394 1540 2.567049 GACCCTCACCGTCTCGTG 59.433 66.667 0.00 0.00 34.93 4.35
1501 1647 0.249868 TAGAGGTGTGCTGTGTGTGC 60.250 55.000 0.00 0.00 0.00 4.57
1508 1658 4.662468 ATGTACAGATAGAGGTGTGCTG 57.338 45.455 0.33 0.00 31.24 4.41
1510 1660 5.447818 GCAAAATGTACAGATAGAGGTGTGC 60.448 44.000 0.33 0.00 0.00 4.57
1511 1661 5.643348 TGCAAAATGTACAGATAGAGGTGTG 59.357 40.000 0.33 0.00 0.00 3.82
1512 1662 5.643777 GTGCAAAATGTACAGATAGAGGTGT 59.356 40.000 0.33 0.00 33.03 4.16
1513 1663 5.065218 GGTGCAAAATGTACAGATAGAGGTG 59.935 44.000 0.33 0.00 34.53 4.00
1516 1666 4.271049 CCGGTGCAAAATGTACAGATAGAG 59.729 45.833 0.33 0.00 34.53 2.43
1517 1667 4.081365 TCCGGTGCAAAATGTACAGATAGA 60.081 41.667 0.00 0.00 34.53 1.98
1518 1668 4.034048 GTCCGGTGCAAAATGTACAGATAG 59.966 45.833 0.00 0.00 34.53 2.08
1519 1669 3.936453 GTCCGGTGCAAAATGTACAGATA 59.064 43.478 0.00 0.00 34.53 1.98
1527 1686 0.737019 GGCATGTCCGGTGCAAAATG 60.737 55.000 16.44 2.48 44.25 2.32
1545 1704 1.406539 CATGAAAATTCAGGCTCCGGG 59.593 52.381 0.00 0.00 41.08 5.73
1547 1706 3.855689 AACATGAAAATTCAGGCTCCG 57.144 42.857 7.65 0.00 42.28 4.63
1549 1708 7.515643 CAAATCAAACATGAAAATTCAGGCTC 58.484 34.615 7.65 0.00 42.28 4.70
1551 1710 6.081693 GCAAATCAAACATGAAAATTCAGGC 58.918 36.000 7.65 0.00 42.28 4.85
1552 1711 7.192148 TGCAAATCAAACATGAAAATTCAGG 57.808 32.000 0.00 6.28 43.96 3.86
1553 1712 7.270365 GCATGCAAATCAAACATGAAAATTCAG 59.730 33.333 14.21 0.00 43.04 3.02
1554 1713 7.078851 GCATGCAAATCAAACATGAAAATTCA 58.921 30.769 14.21 0.00 43.04 2.57
1555 1714 7.078851 TGCATGCAAATCAAACATGAAAATTC 58.921 30.769 20.30 0.00 43.04 2.17
1556 1715 6.971602 TGCATGCAAATCAAACATGAAAATT 58.028 28.000 20.30 0.00 43.04 1.82
1557 1716 6.428465 TCTGCATGCAAATCAAACATGAAAAT 59.572 30.769 22.88 0.00 43.04 1.82
1558 1717 5.758784 TCTGCATGCAAATCAAACATGAAAA 59.241 32.000 22.88 0.00 43.04 2.29
1559 1718 5.298347 TCTGCATGCAAATCAAACATGAAA 58.702 33.333 22.88 0.00 43.04 2.69
1560 1719 4.884247 TCTGCATGCAAATCAAACATGAA 58.116 34.783 22.88 0.00 43.04 2.57
1561 1720 4.490743 CTCTGCATGCAAATCAAACATGA 58.509 39.130 22.88 10.10 43.04 3.07
1755 1914 1.678598 TACGGTTGGGAGGCGTATGG 61.679 60.000 0.00 0.00 0.00 2.74
1757 1916 1.679559 GGTACGGTTGGGAGGCGTAT 61.680 60.000 0.00 0.00 0.00 3.06
1794 1959 4.995124 ACTGTTATGTTAGCAGGAGTACG 58.005 43.478 3.89 0.00 40.77 3.67
1798 1963 5.295292 CCATGAACTGTTATGTTAGCAGGAG 59.705 44.000 0.00 0.00 40.77 3.69
1799 1964 5.185454 CCATGAACTGTTATGTTAGCAGGA 58.815 41.667 0.00 0.00 40.77 3.86
1800 1965 4.201950 GCCATGAACTGTTATGTTAGCAGG 60.202 45.833 0.00 0.00 40.77 4.85
1802 1967 4.395854 CAGCCATGAACTGTTATGTTAGCA 59.604 41.667 0.00 0.00 0.00 3.49
1803 1968 4.201950 CCAGCCATGAACTGTTATGTTAGC 60.202 45.833 12.83 0.00 33.09 3.09
2073 2238 1.893168 GCGTGCGGTTGTCGTTGTAT 61.893 55.000 0.00 0.00 41.72 2.29
2094 2259 2.261671 CACGAGTTGACGAGGGGG 59.738 66.667 0.00 0.00 37.03 5.40
2169 2334 4.353437 GACTTGACCCCGACGCGT 62.353 66.667 13.85 13.85 0.00 6.01
2199 2364 3.296516 GCACTGCTTGCGTATGTTC 57.703 52.632 0.00 0.00 42.79 3.18
2282 2452 1.374758 ACACTAACTCAGCCAGCGC 60.375 57.895 0.00 0.00 0.00 5.92
2306 2476 0.521867 CTTTGACGCATGCACCGATG 60.522 55.000 19.57 2.13 0.00 3.84
2307 2477 1.647545 CCTTTGACGCATGCACCGAT 61.648 55.000 19.57 0.00 0.00 4.18
2308 2478 2.324330 CCTTTGACGCATGCACCGA 61.324 57.895 19.57 5.30 0.00 4.69
2309 2479 2.176546 CCTTTGACGCATGCACCG 59.823 61.111 19.57 3.77 0.00 4.94
2310 2480 1.081242 CACCTTTGACGCATGCACC 60.081 57.895 19.57 8.95 0.00 5.01
2383 2555 2.238521 ACCATGTACAAGCCAAACAGG 58.761 47.619 0.00 0.00 41.84 4.00
2388 2560 6.094742 CACATATACAACCATGTACAAGCCAA 59.905 38.462 0.00 0.00 44.47 4.52
2506 2678 7.822822 AGACTACAAAAAGTGACACAGTACTTT 59.177 33.333 8.59 0.00 46.03 2.66
2512 2684 6.456988 GGTGAAGACTACAAAAAGTGACACAG 60.457 42.308 8.59 0.00 31.22 3.66
2538 2710 2.653543 TCTAGGGCAGGAAGGGTTTA 57.346 50.000 0.00 0.00 0.00 2.01
2545 2717 2.897271 TGCAAATTCTAGGGCAGGAA 57.103 45.000 0.00 0.00 0.00 3.36
2570 2742 1.004610 CGCTTGGTCGCTACATGAATG 60.005 52.381 0.00 0.00 0.00 2.67
2590 2762 1.145803 GACGTGAAGCAGTGTAACCC 58.854 55.000 0.00 0.00 37.80 4.11
2609 2782 3.163594 GACTTCAATGCGGTTTTCATCG 58.836 45.455 0.00 0.00 0.00 3.84
2652 2825 5.344207 ACGATGTCTGAACTTAGCAAAAC 57.656 39.130 0.00 0.00 0.00 2.43
2688 2862 1.888512 TGCTTTTGGCCTCACAATCTC 59.111 47.619 3.32 0.00 40.92 2.75
2699 2873 5.778862 TCTATACCAAGTTTTGCTTTTGGC 58.221 37.500 2.58 0.00 44.06 4.52
2742 2916 8.702438 CGCTTGATTTATTCATTGACAAAAAGT 58.298 29.630 0.00 0.00 33.34 2.66
2754 2928 3.342719 TGGTGAGCGCTTGATTTATTCA 58.657 40.909 13.26 0.00 0.00 2.57
2768 2942 2.295909 TGCCACATTACTTTTGGTGAGC 59.704 45.455 0.00 0.00 33.16 4.26
2783 2957 2.039746 AGTAGTAGCCAATTGTGCCACA 59.960 45.455 15.60 0.00 0.00 4.17
2805 3161 5.637006 TTTATAAGACAGCAAAACGGCAT 57.363 34.783 0.00 0.00 35.83 4.40
2808 3164 6.093495 TCTCCATTTATAAGACAGCAAAACGG 59.907 38.462 0.00 0.00 0.00 4.44
2832 3188 8.358895 GTCCTTGGTAACTAGTCATAGGTAATC 58.641 40.741 0.00 0.00 37.78 1.75
2838 3194 6.405953 CCAGTGTCCTTGGTAACTAGTCATAG 60.406 46.154 0.00 0.00 37.78 2.23
2840 3196 4.223032 CCAGTGTCCTTGGTAACTAGTCAT 59.777 45.833 0.00 0.00 37.78 3.06
2842 3198 3.056035 CCCAGTGTCCTTGGTAACTAGTC 60.056 52.174 0.00 0.00 37.78 2.59
2906 3264 9.860898 GGAATATTCAGCAAATCAAAACTAGTT 57.139 29.630 17.07 1.12 0.00 2.24
3113 3478 1.603802 AGATGCCGTGTTTTGTGTCTG 59.396 47.619 0.00 0.00 0.00 3.51
3114 3479 1.873591 GAGATGCCGTGTTTTGTGTCT 59.126 47.619 0.00 0.00 0.00 3.41
3119 3484 0.865111 TGACGAGATGCCGTGTTTTG 59.135 50.000 0.00 0.00 43.49 2.44
3153 3518 0.475632 TCACCCCCTGTCAAGGTCAT 60.476 55.000 0.00 0.00 42.74 3.06


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

AutoCloner maintained by Alex Coulton.