Multiple sequence alignment - TraesCS2D01G365200

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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 TraesCS2D01G365200 chr2D 100.000 2993 0 0 1 2993 470214864 470217856 0.000000e+00 5528.0
1 TraesCS2D01G365200 chr2A 89.522 2195 161 27 832 2993 611945721 611947879 0.000000e+00 2715.0
2 TraesCS2D01G365200 chr2A 87.105 791 46 23 1 759 611944815 611945581 0.000000e+00 845.0
3 TraesCS2D01G365200 chr2B 94.157 1352 72 3 890 2234 549037598 549038949 0.000000e+00 2052.0
4 TraesCS2D01G365200 chr2B 86.032 315 27 8 449 759 549037287 549037588 3.720000e-84 322.0
5 TraesCS2D01G365200 chr2B 80.128 312 36 10 2465 2769 549039065 549039357 3.020000e-50 209.0
6 TraesCS2D01G365200 chr2B 79.100 311 42 14 116 424 549036797 549037086 3.040000e-45 193.0
7 TraesCS2D01G365200 chr2B 87.805 82 9 1 2285 2366 549038956 549039036 8.830000e-16 95.3


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 TraesCS2D01G365200 chr2D 470214864 470217856 2992 False 5528.00 5528 100.0000 1 2993 1 chr2D.!!$F1 2992
1 TraesCS2D01G365200 chr2A 611944815 611947879 3064 False 1780.00 2715 88.3135 1 2993 2 chr2A.!!$F1 2992
2 TraesCS2D01G365200 chr2B 549036797 549039357 2560 False 574.26 2052 85.4444 116 2769 5 chr2B.!!$F1 2653

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
522 722 0.03563 ATGAGGTGCAGCTGAGTTCC 60.036 55.0 25.6 12.86 0.0 3.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2172 2472 0.392706 TCCACTGTTCAGCATCACGT 59.607 50.0 0.0 0.0 0.0 4.49 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
29 30 3.630312 ACCGATATGGGGATTTTGTTTCG 59.370 43.478 8.78 0.00 44.64 3.46
45 46 7.966246 TTTGTTTCGGTTAATACAGAGCTTA 57.034 32.000 0.00 0.00 30.14 3.09
50 51 6.381481 TCGGTTAATACAGAGCTTATTCGA 57.619 37.500 0.00 0.00 0.00 3.71
74 75 6.147864 AGTTATGCAAAATGACACACACTT 57.852 33.333 0.00 0.00 0.00 3.16
87 88 5.583061 TGACACACACTTAAAGTACAGGTTG 59.417 40.000 0.00 0.00 0.00 3.77
135 139 0.037160 TGCTGCACAGATGTGGTGAT 59.963 50.000 14.44 0.00 45.72 3.06
148 152 1.737793 GTGGTGATTAGCTTGGGAACG 59.262 52.381 0.00 0.00 0.00 3.95
265 271 5.430417 TGGATTCAGGCCTAAATAGTTACCA 59.570 40.000 3.98 2.99 0.00 3.25
320 326 7.612633 GGGGACTTTGTATGTCTGGTTTTATAA 59.387 37.037 0.00 0.00 35.04 0.98
446 608 5.659440 TTTGTCTTTTGGCTTCAGTCTTT 57.341 34.783 0.00 0.00 0.00 2.52
448 610 5.659440 TGTCTTTTGGCTTCAGTCTTTTT 57.341 34.783 0.00 0.00 0.00 1.94
449 611 6.767524 TGTCTTTTGGCTTCAGTCTTTTTA 57.232 33.333 0.00 0.00 0.00 1.52
450 612 6.560711 TGTCTTTTGGCTTCAGTCTTTTTAC 58.439 36.000 0.00 0.00 0.00 2.01
451 613 6.377146 TGTCTTTTGGCTTCAGTCTTTTTACT 59.623 34.615 0.00 0.00 0.00 2.24
452 614 7.093945 TGTCTTTTGGCTTCAGTCTTTTTACTT 60.094 33.333 0.00 0.00 0.00 2.24
453 615 8.403236 GTCTTTTGGCTTCAGTCTTTTTACTTA 58.597 33.333 0.00 0.00 0.00 2.24
454 616 8.621286 TCTTTTGGCTTCAGTCTTTTTACTTAG 58.379 33.333 0.00 0.00 0.00 2.18
455 617 5.941948 TGGCTTCAGTCTTTTTACTTAGC 57.058 39.130 0.00 0.00 35.39 3.09
456 618 4.760204 TGGCTTCAGTCTTTTTACTTAGCC 59.240 41.667 15.18 15.18 45.97 3.93
457 619 5.004448 GGCTTCAGTCTTTTTACTTAGCCT 58.996 41.667 14.93 0.00 44.21 4.58
458 620 5.473846 GGCTTCAGTCTTTTTACTTAGCCTT 59.526 40.000 14.93 0.00 44.21 4.35
459 621 6.348622 GGCTTCAGTCTTTTTACTTAGCCTTC 60.349 42.308 14.93 0.00 44.21 3.46
460 622 6.428465 GCTTCAGTCTTTTTACTTAGCCTTCT 59.572 38.462 0.00 0.00 32.36 2.85
461 623 7.041030 GCTTCAGTCTTTTTACTTAGCCTTCTT 60.041 37.037 0.00 0.00 32.36 2.52
462 624 7.730364 TCAGTCTTTTTACTTAGCCTTCTTG 57.270 36.000 0.00 0.00 0.00 3.02
463 625 7.506114 TCAGTCTTTTTACTTAGCCTTCTTGA 58.494 34.615 0.00 0.00 0.00 3.02
464 626 7.441458 TCAGTCTTTTTACTTAGCCTTCTTGAC 59.559 37.037 0.00 0.00 0.00 3.18
465 627 7.442666 CAGTCTTTTTACTTAGCCTTCTTGACT 59.557 37.037 0.00 0.00 0.00 3.41
474 673 6.931840 ACTTAGCCTTCTTGACTCTTGTTAAG 59.068 38.462 0.00 0.00 40.02 1.85
483 682 6.929606 TCTTGACTCTTGTTAAGCTTTAGGTC 59.070 38.462 3.20 5.06 38.97 3.85
496 695 5.423886 AGCTTTAGGTCTGATAGCAACTTC 58.576 41.667 0.00 0.00 34.37 3.01
500 699 4.734398 AGGTCTGATAGCAACTTCTCTG 57.266 45.455 0.00 0.00 0.00 3.35
520 720 2.038952 TGTAATGAGGTGCAGCTGAGTT 59.961 45.455 25.60 16.31 0.00 3.01
522 722 0.035630 ATGAGGTGCAGCTGAGTTCC 60.036 55.000 25.60 12.86 0.00 3.62
523 723 1.372683 GAGGTGCAGCTGAGTTCCA 59.627 57.895 25.60 1.69 0.00 3.53
557 757 5.469479 CATGTTTTACCATGTTTCCTGTCC 58.531 41.667 0.00 0.00 37.91 4.02
588 788 6.856426 GTCAAAAGTATGCTTCCAGTTACAAC 59.144 38.462 0.00 0.00 33.01 3.32
592 792 7.668525 AAGTATGCTTCCAGTTACAACTTAC 57.331 36.000 0.00 0.00 37.08 2.34
593 793 6.765403 AGTATGCTTCCAGTTACAACTTACA 58.235 36.000 0.00 0.00 37.08 2.41
594 794 7.221450 AGTATGCTTCCAGTTACAACTTACAA 58.779 34.615 0.00 0.00 37.08 2.41
599 799 9.073475 TGCTTCCAGTTACAACTTACAAATTAT 57.927 29.630 0.00 0.00 37.08 1.28
603 803 9.953565 TCCAGTTACAACTTACAAATTATAGCT 57.046 29.630 0.00 0.00 37.08 3.32
629 851 7.094508 TCAGTTAGCAAAAACAATCACAAGA 57.905 32.000 0.00 0.00 0.00 3.02
652 874 4.068599 GCTGAAGCTGGAGTTCTTTACTT 58.931 43.478 0.00 0.00 36.10 2.24
658 880 8.403236 TGAAGCTGGAGTTCTTTACTTAAAAAC 58.597 33.333 0.00 0.00 37.17 2.43
696 923 6.643388 AGTATCACAGTAACTGCAATCATGA 58.357 36.000 0.00 0.00 34.37 3.07
753 980 2.476185 GGATTCTGCAATTCGTCGTTGG 60.476 50.000 0.00 0.00 0.00 3.77
763 1023 1.005512 CGTCGTTGGGACATGGACA 60.006 57.895 0.00 0.00 46.42 4.02
765 1025 1.156736 GTCGTTGGGACATGGACAAG 58.843 55.000 0.00 0.00 45.36 3.16
766 1026 0.605319 TCGTTGGGACATGGACAAGC 60.605 55.000 0.00 0.00 39.30 4.01
818 1080 1.882912 TGAGTGACATGCCAAGACAC 58.117 50.000 0.00 0.00 33.02 3.67
822 1084 3.225104 AGTGACATGCCAAGACACAAAT 58.775 40.909 5.44 0.00 34.81 2.32
824 1086 3.004629 GTGACATGCCAAGACACAAATGA 59.995 43.478 0.00 0.00 33.08 2.57
830 1092 2.223782 GCCAAGACACAAATGACAAGCA 60.224 45.455 0.00 0.00 0.00 3.91
904 1198 6.803154 AGCCTGTGTTTGAGTTTATCTTAC 57.197 37.500 0.00 0.00 0.00 2.34
988 1287 5.336150 TCTTTTGCAGTGTTGGAATTTGA 57.664 34.783 0.00 0.00 34.44 2.69
990 1289 2.772568 TGCAGTGTTGGAATTTGACG 57.227 45.000 0.00 0.00 0.00 4.35
1088 1387 2.969628 AGACTTACGAGATTGCCCAG 57.030 50.000 0.00 0.00 0.00 4.45
1138 1437 3.249799 GGGCCACTTTAAAAACATTGCAC 59.750 43.478 4.39 0.00 0.00 4.57
1210 1509 0.463295 AGAGGACGATGCCAGCATTG 60.463 55.000 16.67 16.67 42.12 2.82
1257 1556 4.683781 GCTATTGATACAGAAGAAGCTCCG 59.316 45.833 0.00 0.00 0.00 4.63
1452 1751 1.070445 CGCTGGCCTTCTATCCCTG 59.930 63.158 3.32 0.00 0.00 4.45
1473 1772 0.532573 TGGGACTCGACTGCATCTTC 59.467 55.000 0.00 0.00 0.00 2.87
1512 1811 1.153449 CTTCCTTATGGCCGACGCA 60.153 57.895 0.00 0.00 36.38 5.24
1515 1814 1.523711 CCTTATGGCCGACGCATGT 60.524 57.895 0.00 0.00 36.38 3.21
1536 1835 1.610624 GGGCGTCCAGAGAACAATTCA 60.611 52.381 0.00 0.00 0.00 2.57
1641 1940 0.388006 TGCTTTTCGCGTCTCATCGA 60.388 50.000 5.77 0.00 43.27 3.59
1872 2171 2.437359 ATGGTGCAGAGCCTTCGC 60.437 61.111 0.00 0.00 0.00 4.70
1926 2225 1.506309 TTCAGTTGATGCGCGTTGCT 61.506 50.000 8.43 0.00 46.63 3.91
1957 2256 1.639298 GCTCAGTTCCGCAAGCGATT 61.639 55.000 16.97 0.00 42.83 3.34
1959 2258 0.320334 TCAGTTCCGCAAGCGATTCA 60.320 50.000 16.97 0.00 42.83 2.57
1963 2262 1.922135 TTCCGCAAGCGATTCAAGCC 61.922 55.000 16.97 0.00 42.83 4.35
1965 2264 1.430632 CGCAAGCGATTCAAGCCAT 59.569 52.632 9.11 0.00 42.83 4.40
1974 2273 2.843701 GATTCAAGCCATGGATCGAGT 58.156 47.619 18.40 0.00 34.34 4.18
2052 2351 3.821033 GGATAGAATGGGTGCCATGTTAC 59.179 47.826 0.00 0.00 44.40 2.50
2062 2361 0.447801 GCCATGTTACTTCTGGTGCG 59.552 55.000 0.00 0.00 32.42 5.34
2099 2398 2.413796 TGCGGTGCACGTAGAATAAAAG 59.586 45.455 11.45 0.00 46.52 2.27
2101 2400 3.255725 CGGTGCACGTAGAATAAAAGGA 58.744 45.455 11.45 0.00 37.93 3.36
2134 2434 6.602179 TGATAGAAACTTTGAATCGTGCAAG 58.398 36.000 0.00 0.00 0.00 4.01
2147 2447 3.605634 TCGTGCAAGTGCTTTGGTATAT 58.394 40.909 4.69 0.00 42.66 0.86
2289 2591 2.420547 CCATTTCCTCGGAAGATCTGCA 60.421 50.000 2.29 0.00 40.84 4.41
2346 2648 9.442047 GATATGGTATCCTTCCTTTATTCACAG 57.558 37.037 0.00 0.00 0.00 3.66
2389 2691 3.496331 TCTTTTGGTGGGTTCAGGATTC 58.504 45.455 0.00 0.00 0.00 2.52
2395 2697 1.354368 GTGGGTTCAGGATTCTGGGAA 59.646 52.381 0.00 0.00 41.23 3.97
2419 2728 0.826715 TGGAGGAGGCTCAAGATTCG 59.173 55.000 17.69 0.00 0.00 3.34
2421 2730 0.105778 GAGGAGGCTCAAGATTCGGG 59.894 60.000 17.69 0.00 0.00 5.14
2462 2771 1.514678 GGCCAACATTCGTGTGCAGA 61.515 55.000 0.00 0.00 0.00 4.26
2538 2860 9.127277 ACTAGTTATGTCTTTCTCAGATACTCC 57.873 37.037 0.00 0.00 32.60 3.85
2539 2861 9.349713 CTAGTTATGTCTTTCTCAGATACTCCT 57.650 37.037 0.00 0.00 32.60 3.69
2540 2862 8.602472 AGTTATGTCTTTCTCAGATACTCCTT 57.398 34.615 0.00 0.00 32.60 3.36
2541 2863 9.041354 AGTTATGTCTTTCTCAGATACTCCTTT 57.959 33.333 0.00 0.00 32.60 3.11
2542 2864 9.660180 GTTATGTCTTTCTCAGATACTCCTTTT 57.340 33.333 0.00 0.00 32.60 2.27
2543 2865 9.658799 TTATGTCTTTCTCAGATACTCCTTTTG 57.341 33.333 0.00 0.00 32.60 2.44
2544 2866 6.467677 TGTCTTTCTCAGATACTCCTTTTGG 58.532 40.000 0.00 0.00 35.67 3.28
2545 2867 5.352846 GTCTTTCTCAGATACTCCTTTTGGC 59.647 44.000 0.00 0.00 34.78 4.52
2546 2868 3.526931 TCTCAGATACTCCTTTTGGCG 57.473 47.619 0.00 0.00 40.12 5.69
2547 2869 2.832129 TCTCAGATACTCCTTTTGGCGT 59.168 45.455 0.00 0.00 41.06 5.68
2548 2870 2.932614 CTCAGATACTCCTTTTGGCGTG 59.067 50.000 0.00 0.00 38.14 5.34
2549 2871 1.398390 CAGATACTCCTTTTGGCGTGC 59.602 52.381 0.00 0.00 38.14 5.34
2550 2872 0.373716 GATACTCCTTTTGGCGTGCG 59.626 55.000 0.00 0.00 38.14 5.34
2551 2873 0.321298 ATACTCCTTTTGGCGTGCGT 60.321 50.000 0.00 0.00 38.14 5.24
2552 2874 0.317799 TACTCCTTTTGGCGTGCGTA 59.682 50.000 0.00 0.00 38.14 4.42
2553 2875 1.226030 ACTCCTTTTGGCGTGCGTAC 61.226 55.000 0.00 0.00 35.96 3.67
2557 2879 1.908066 CTTTTGGCGTGCGTACTCCC 61.908 60.000 10.28 6.72 30.42 4.30
2564 2887 0.742505 CGTGCGTACTCCCCTTGATA 59.257 55.000 1.24 0.00 0.00 2.15
2567 2890 2.093869 GTGCGTACTCCCCTTGATACAA 60.094 50.000 0.00 0.00 0.00 2.41
2614 2939 1.624813 CTAAACACCCGACCTAACCCA 59.375 52.381 0.00 0.00 0.00 4.51
2615 2940 1.069775 AAACACCCGACCTAACCCAT 58.930 50.000 0.00 0.00 0.00 4.00
2616 2941 0.326927 AACACCCGACCTAACCCATG 59.673 55.000 0.00 0.00 0.00 3.66
2617 2942 0.838987 ACACCCGACCTAACCCATGT 60.839 55.000 0.00 0.00 0.00 3.21
2618 2943 0.392461 CACCCGACCTAACCCATGTG 60.392 60.000 0.00 0.00 0.00 3.21
2620 2945 1.451387 CCGACCTAACCCATGTGCC 60.451 63.158 0.00 0.00 0.00 5.01
2621 2946 1.602237 CGACCTAACCCATGTGCCT 59.398 57.895 0.00 0.00 0.00 4.75
2669 3000 6.236409 TCTGTTGAATTTCAGAGAGAGCAAT 58.764 36.000 0.00 0.00 36.04 3.56
2673 3004 6.889301 TGAATTTCAGAGAGAGCAATTGTT 57.111 33.333 7.40 0.00 0.00 2.83
2674 3005 6.906659 TGAATTTCAGAGAGAGCAATTGTTC 58.093 36.000 13.90 13.90 0.00 3.18
2683 3014 6.492772 AGAGAGAGCAATTGTTCAAAGGAATT 59.507 34.615 22.26 0.99 35.05 2.17
2684 3015 6.453092 AGAGAGCAATTGTTCAAAGGAATTG 58.547 36.000 22.26 0.00 39.20 2.32
2691 3022 4.599047 TGTTCAAAGGAATTGGCGAAAT 57.401 36.364 0.00 0.00 39.62 2.17
2692 3023 4.555262 TGTTCAAAGGAATTGGCGAAATC 58.445 39.130 0.00 0.00 39.62 2.17
2699 3030 2.879026 GGAATTGGCGAAATCCTAGACC 59.121 50.000 8.22 0.00 0.00 3.85
2706 3037 2.930682 GCGAAATCCTAGACCTGTCAAC 59.069 50.000 0.00 0.00 0.00 3.18
2714 3045 1.048601 AGACCTGTCAACCACACGAT 58.951 50.000 0.00 0.00 0.00 3.73
2727 3058 0.037697 ACACGATAAGCCAAGCGACA 60.038 50.000 0.17 0.00 0.00 4.35
2728 3059 1.290203 CACGATAAGCCAAGCGACAT 58.710 50.000 0.17 0.00 0.00 3.06
2742 3074 1.864435 GCGACATGGCTTACGACCTAG 60.864 57.143 0.00 0.00 0.00 3.02
2744 3076 2.159282 CGACATGGCTTACGACCTAGTT 60.159 50.000 0.00 0.00 0.00 2.24
2769 3101 0.030638 ATTCAACACTGTTGGCGTGC 59.969 50.000 19.60 0.00 35.84 5.34
2794 3126 1.125021 CACGTCTGAGTTCGATTGTGC 59.875 52.381 6.78 0.00 0.00 4.57
2813 3145 3.059665 GTGCAGGCACAACTAAAATTTGC 60.060 43.478 18.84 0.00 45.53 3.68
2820 3158 5.845433 GGCACAACTAAAATTTGCAAATTCG 59.155 36.000 31.78 24.52 37.62 3.34
2827 3165 2.267002 AATTTGCAAATTCGCCGCAGG 61.267 47.619 27.73 0.00 42.53 4.85
2828 3166 4.545572 AATTTGCAAATTCGCCGCAGGA 62.546 45.455 27.73 0.00 42.33 3.86
2829 3167 5.960800 AATTTGCAAATTCGCCGCAGGAA 62.961 43.478 27.73 0.00 42.33 3.36
2898 3236 3.553828 TTGAAATGTAGATCCGGACCC 57.446 47.619 6.12 0.90 0.00 4.46
2900 3238 2.841266 TGAAATGTAGATCCGGACCCAA 59.159 45.455 6.12 0.00 0.00 4.12
2904 3242 1.272816 TGTAGATCCGGACCCAAGTGA 60.273 52.381 6.12 0.00 0.00 3.41
2906 3244 0.613777 AGATCCGGACCCAAGTGAAC 59.386 55.000 6.12 0.00 0.00 3.18
2923 3261 8.190784 CCAAGTGAACTTCAAGACACTTTTTAT 58.809 33.333 22.26 7.80 46.69 1.40
2924 3262 9.573133 CAAGTGAACTTCAAGACACTTTTTATT 57.427 29.630 22.26 7.30 46.69 1.40
2970 3308 2.798499 GCCATTGCAAATGCTAGAGCAG 60.798 50.000 10.44 0.00 45.95 4.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 3.630312 ACCGAAACAAAATCCCCATATCG 59.370 43.478 0.00 0.00 0.00 2.92
29 30 8.421673 AACTTCGAATAAGCTCTGTATTAACC 57.578 34.615 0.00 0.00 0.00 2.85
45 46 6.582295 GTGTGTCATTTTGCATAACTTCGAAT 59.418 34.615 0.00 0.00 0.00 3.34
50 51 6.147864 AGTGTGTGTCATTTTGCATAACTT 57.852 33.333 0.00 0.00 0.00 2.66
87 88 7.172190 GGTACTAAACACCAGAAACTTAAGGAC 59.828 40.741 7.53 0.00 36.01 3.85
135 139 3.555586 GGTTACTGACGTTCCCAAGCTAA 60.556 47.826 0.00 0.00 0.00 3.09
148 152 5.465724 ACAATCTGTCGAAAAGGTTACTGAC 59.534 40.000 0.00 0.00 0.00 3.51
357 363 6.163476 TCTAGCACACGTGAGATTTAACATT 58.837 36.000 25.01 0.00 0.00 2.71
427 589 6.796426 AGTAAAAAGACTGAAGCCAAAAGAC 58.204 36.000 0.00 0.00 0.00 3.01
446 608 6.827727 ACAAGAGTCAAGAAGGCTAAGTAAA 58.172 36.000 0.00 0.00 27.31 2.01
448 610 6.420913 AACAAGAGTCAAGAAGGCTAAGTA 57.579 37.500 0.00 0.00 27.31 2.24
449 611 4.965200 ACAAGAGTCAAGAAGGCTAAGT 57.035 40.909 0.00 0.00 27.31 2.24
450 612 6.128418 GCTTAACAAGAGTCAAGAAGGCTAAG 60.128 42.308 0.00 0.00 27.31 2.18
451 613 5.701290 GCTTAACAAGAGTCAAGAAGGCTAA 59.299 40.000 0.00 0.00 27.31 3.09
452 614 5.012148 AGCTTAACAAGAGTCAAGAAGGCTA 59.988 40.000 0.00 0.00 27.31 3.93
453 615 4.068599 GCTTAACAAGAGTCAAGAAGGCT 58.931 43.478 0.00 0.00 32.36 4.58
454 616 4.068599 AGCTTAACAAGAGTCAAGAAGGC 58.931 43.478 0.00 0.00 0.00 4.35
455 617 6.625873 AAAGCTTAACAAGAGTCAAGAAGG 57.374 37.500 0.00 0.00 0.00 3.46
456 618 7.442666 ACCTAAAGCTTAACAAGAGTCAAGAAG 59.557 37.037 0.00 0.00 0.00 2.85
457 619 7.280356 ACCTAAAGCTTAACAAGAGTCAAGAA 58.720 34.615 0.00 0.00 0.00 2.52
458 620 6.827727 ACCTAAAGCTTAACAAGAGTCAAGA 58.172 36.000 0.00 0.00 0.00 3.02
459 621 6.931840 AGACCTAAAGCTTAACAAGAGTCAAG 59.068 38.462 0.00 0.00 0.00 3.02
460 622 6.706270 CAGACCTAAAGCTTAACAAGAGTCAA 59.294 38.462 0.00 0.00 0.00 3.18
461 623 6.041637 TCAGACCTAAAGCTTAACAAGAGTCA 59.958 38.462 0.00 0.00 0.00 3.41
462 624 6.456501 TCAGACCTAAAGCTTAACAAGAGTC 58.543 40.000 0.00 5.70 0.00 3.36
463 625 6.420913 TCAGACCTAAAGCTTAACAAGAGT 57.579 37.500 0.00 0.00 0.00 3.24
464 626 7.223777 GCTATCAGACCTAAAGCTTAACAAGAG 59.776 40.741 0.00 0.00 0.00 2.85
465 627 7.042335 GCTATCAGACCTAAAGCTTAACAAGA 58.958 38.462 0.00 0.00 0.00 3.02
474 673 5.423886 AGAAGTTGCTATCAGACCTAAAGC 58.576 41.667 0.00 0.00 0.00 3.51
483 682 6.700960 CCTCATTACAGAGAAGTTGCTATCAG 59.299 42.308 0.00 0.00 37.87 2.90
496 695 2.093816 TCAGCTGCACCTCATTACAGAG 60.094 50.000 9.47 0.00 35.39 3.35
500 699 2.393271 ACTCAGCTGCACCTCATTAC 57.607 50.000 9.47 0.00 0.00 1.89
557 757 3.127030 GGAAGCATACTTTTGACTTCCGG 59.873 47.826 0.00 0.00 44.92 5.14
603 803 8.845227 TCTTGTGATTGTTTTTGCTAACTGATA 58.155 29.630 0.00 0.00 0.00 2.15
604 804 7.715657 TCTTGTGATTGTTTTTGCTAACTGAT 58.284 30.769 0.00 0.00 0.00 2.90
605 805 7.094508 TCTTGTGATTGTTTTTGCTAACTGA 57.905 32.000 0.00 0.00 0.00 3.41
608 808 5.979517 AGCTCTTGTGATTGTTTTTGCTAAC 59.020 36.000 0.00 0.00 0.00 2.34
609 809 5.978919 CAGCTCTTGTGATTGTTTTTGCTAA 59.021 36.000 0.00 0.00 0.00 3.09
610 810 5.299028 TCAGCTCTTGTGATTGTTTTTGCTA 59.701 36.000 0.00 0.00 0.00 3.49
629 851 3.326297 AGTAAAGAACTCCAGCTTCAGCT 59.674 43.478 0.00 0.00 43.86 4.24
658 880 9.653287 TTACTGTGATACTTCTTATTCAACAGG 57.347 33.333 0.00 0.00 34.13 4.00
753 980 3.367703 CCAAAGATTGCTTGTCCATGTCC 60.368 47.826 0.00 0.00 33.79 4.02
790 1050 4.343231 TGGCATGTCACTCAACCATTTAT 58.657 39.130 0.00 0.00 33.37 1.40
818 1080 7.935338 AGAGTAAAACAATGCTTGTCATTTG 57.065 32.000 2.65 0.00 44.59 2.32
822 1084 6.449635 ACAAGAGTAAAACAATGCTTGTCA 57.550 33.333 0.00 0.00 44.59 3.58
824 1086 6.449635 TGACAAGAGTAAAACAATGCTTGT 57.550 33.333 0.00 0.00 45.87 3.16
830 1092 7.027778 GTCAGGTTGACAAGAGTAAAACAAT 57.972 36.000 4.42 0.00 46.22 2.71
858 1152 8.170553 GGCTAACAATGAAATGCAATAAAGTTG 58.829 33.333 0.00 0.00 0.00 3.16
860 1154 7.546667 CAGGCTAACAATGAAATGCAATAAAGT 59.453 33.333 0.00 0.00 0.00 2.66
863 1157 6.812656 CACAGGCTAACAATGAAATGCAATAA 59.187 34.615 0.00 0.00 0.00 1.40
904 1198 1.135546 CGTGGCGAGATATCTAGCAGG 60.136 57.143 30.88 20.52 44.78 4.85
915 1209 3.371063 GTCTGGACCGTGGCGAGA 61.371 66.667 0.00 0.00 0.00 4.04
967 1266 4.026640 CGTCAAATTCCAACACTGCAAAAG 60.027 41.667 0.00 0.00 0.00 2.27
988 1287 0.249398 GAAGCCATGGTACAGGACGT 59.751 55.000 14.67 0.00 46.40 4.34
990 1289 2.749621 CAAAGAAGCCATGGTACAGGAC 59.250 50.000 14.67 0.00 46.40 3.85
1138 1437 3.103738 GCAAATTCTTAGTGCATCGCAG 58.896 45.455 0.00 0.00 40.08 5.18
1210 1509 3.252215 TCGACAACATTTGTTCCCATGAC 59.748 43.478 0.00 0.00 45.52 3.06
1233 1532 4.994217 GGAGCTTCTTCTGTATCAATAGCC 59.006 45.833 0.00 0.00 0.00 3.93
1257 1556 3.044894 ACTCTGGAGGATTGGAATCTCC 58.955 50.000 0.00 0.00 35.30 3.71
1362 1661 2.837532 TACCGGTAACCAACAGAACC 57.162 50.000 13.14 0.00 0.00 3.62
1452 1751 1.153549 GATGCAGTCGAGTCCCACC 60.154 63.158 0.00 0.00 0.00 4.61
1473 1772 0.892755 ACAGCATTGCTCCCATGTTG 59.107 50.000 8.54 0.00 36.40 3.33
1512 1811 1.296715 GTTCTCTGGACGCCCACAT 59.703 57.895 0.00 0.00 37.58 3.21
1515 1814 0.400213 AATTGTTCTCTGGACGCCCA 59.600 50.000 0.00 0.00 40.95 5.36
1536 1835 0.976641 TCTGCCTTGTCAGGTCGAAT 59.023 50.000 0.00 0.00 43.18 3.34
1593 1892 3.563223 AGGAGCAACGAAGCCTAGTATA 58.437 45.455 0.00 0.00 34.23 1.47
1665 1964 1.880027 AGCACCAAGAACGGAATGAAC 59.120 47.619 0.00 0.00 0.00 3.18
1872 2171 2.669569 CACCAGGACACCAAGCCG 60.670 66.667 0.00 0.00 0.00 5.52
1926 2225 2.032528 CTGAGCCCAGCGAACCAA 59.967 61.111 0.00 0.00 33.07 3.67
1957 2256 1.194218 TCACTCGATCCATGGCTTGA 58.806 50.000 6.96 6.06 0.00 3.02
1959 2258 1.764723 TCATCACTCGATCCATGGCTT 59.235 47.619 6.96 0.00 0.00 4.35
1963 2262 3.986277 TCACATCATCACTCGATCCATG 58.014 45.455 0.00 0.00 0.00 3.66
1965 2264 3.195396 TGTTCACATCATCACTCGATCCA 59.805 43.478 0.00 0.00 0.00 3.41
1974 2273 6.950842 AGAAACCTATCTGTTCACATCATCA 58.049 36.000 0.00 0.00 0.00 3.07
2030 2329 2.664402 ACATGGCACCCATTCTATCC 57.336 50.000 0.00 0.00 42.23 2.59
2081 2380 4.251268 ACTCCTTTTATTCTACGTGCACC 58.749 43.478 12.15 0.00 0.00 5.01
2099 2398 8.154649 TCAAAGTTTCTATCAGTCAAAACTCC 57.845 34.615 0.00 0.00 40.16 3.85
2172 2472 0.392706 TCCACTGTTCAGCATCACGT 59.607 50.000 0.00 0.00 0.00 4.49
2225 2527 7.625817 GCAACAGCTTGGAGCATATATATTCTG 60.626 40.741 0.00 0.00 45.56 3.02
2346 2648 2.519302 ACCTGGCAGTGCACAACC 60.519 61.111 21.04 19.60 0.00 3.77
2389 2691 1.409381 GCCTCCTCCAGATTTTCCCAG 60.409 57.143 0.00 0.00 0.00 4.45
2395 2697 2.555664 TCTTGAGCCTCCTCCAGATTT 58.444 47.619 0.00 0.00 35.58 2.17
2419 2728 3.063743 CTTTTGGCCGATTCCGCCC 62.064 63.158 12.61 0.00 33.27 6.13
2421 2730 0.456142 GTTCTTTTGGCCGATTCCGC 60.456 55.000 0.00 0.00 0.00 5.54
2447 2756 3.565482 AGTTGATTCTGCACACGAATGTT 59.435 39.130 4.53 0.00 36.72 2.71
2462 2771 2.306847 GACACACCCAACCAGTTGATT 58.693 47.619 12.06 0.00 42.93 2.57
2514 2836 9.702253 AAGGAGTATCTGAGAAAGACATAACTA 57.298 33.333 0.00 0.00 37.88 2.24
2535 2857 0.949105 AGTACGCACGCCAAAAGGAG 60.949 55.000 0.00 0.00 0.00 3.69
2536 2858 0.947180 GAGTACGCACGCCAAAAGGA 60.947 55.000 0.00 0.00 0.00 3.36
2537 2859 1.495951 GAGTACGCACGCCAAAAGG 59.504 57.895 0.00 0.00 0.00 3.11
2538 2860 1.495951 GGAGTACGCACGCCAAAAG 59.504 57.895 3.36 0.00 43.63 2.27
2539 2861 1.962306 GGGAGTACGCACGCCAAAA 60.962 57.895 10.92 0.00 45.81 2.44
2540 2862 2.357760 GGGAGTACGCACGCCAAA 60.358 61.111 10.92 0.00 45.81 3.28
2541 2863 4.382320 GGGGAGTACGCACGCCAA 62.382 66.667 10.92 0.00 45.81 4.52
2543 2865 4.078516 AAGGGGAGTACGCACGCC 62.079 66.667 0.00 0.00 43.46 5.68
2544 2866 2.573609 ATCAAGGGGAGTACGCACGC 62.574 60.000 0.00 0.00 33.80 5.34
2545 2867 0.742505 TATCAAGGGGAGTACGCACG 59.257 55.000 0.00 0.00 33.80 5.34
2546 2868 1.479323 TGTATCAAGGGGAGTACGCAC 59.521 52.381 0.00 0.00 33.80 5.34
2547 2869 1.855295 TGTATCAAGGGGAGTACGCA 58.145 50.000 0.00 0.00 33.80 5.24
2548 2870 2.973694 TTGTATCAAGGGGAGTACGC 57.026 50.000 0.00 0.00 0.00 4.42
2549 2871 5.018539 TGATTTGTATCAAGGGGAGTACG 57.981 43.478 0.00 0.00 37.83 3.67
2564 2887 3.488047 GCGTGATATGCTGCTTGATTTGT 60.488 43.478 0.00 0.00 0.00 2.83
2567 2890 2.291365 TGCGTGATATGCTGCTTGATT 58.709 42.857 0.00 0.00 0.00 2.57
2614 2939 1.656652 GTACGCATCTCAAGGCACAT 58.343 50.000 0.00 0.00 30.94 3.21
2615 2940 0.735978 CGTACGCATCTCAAGGCACA 60.736 55.000 0.52 0.00 30.94 4.57
2616 2941 1.421410 CCGTACGCATCTCAAGGCAC 61.421 60.000 10.49 0.00 30.94 5.01
2617 2942 1.153647 CCGTACGCATCTCAAGGCA 60.154 57.895 10.49 0.00 30.94 4.75
2618 2943 0.739813 AACCGTACGCATCTCAAGGC 60.740 55.000 10.49 0.00 0.00 4.35
2620 2945 0.914551 CGAACCGTACGCATCTCAAG 59.085 55.000 10.49 0.00 0.00 3.02
2621 2946 3.024423 CGAACCGTACGCATCTCAA 57.976 52.632 10.49 0.00 0.00 3.02
2664 2995 4.067192 GCCAATTCCTTTGAACAATTGCT 58.933 39.130 5.05 0.00 37.53 3.91
2669 3000 4.392921 TTTCGCCAATTCCTTTGAACAA 57.607 36.364 0.00 0.00 37.53 2.83
2673 3004 3.430453 AGGATTTCGCCAATTCCTTTGA 58.570 40.909 2.08 0.00 38.67 2.69
2674 3005 3.874392 AGGATTTCGCCAATTCCTTTG 57.126 42.857 2.08 0.00 38.67 2.77
2683 3014 1.480954 GACAGGTCTAGGATTTCGCCA 59.519 52.381 0.00 0.00 0.00 5.69
2684 3015 1.480954 TGACAGGTCTAGGATTTCGCC 59.519 52.381 0.65 0.00 0.00 5.54
2691 3022 1.968493 GTGTGGTTGACAGGTCTAGGA 59.032 52.381 0.65 0.00 34.28 2.94
2692 3023 1.336887 CGTGTGGTTGACAGGTCTAGG 60.337 57.143 0.65 0.00 35.99 3.02
2699 3030 1.732259 GGCTTATCGTGTGGTTGACAG 59.268 52.381 0.00 0.00 34.28 3.51
2706 3037 0.739462 TCGCTTGGCTTATCGTGTGG 60.739 55.000 0.00 0.00 0.00 4.17
2727 3058 4.708421 TCAACTAACTAGGTCGTAAGCCAT 59.292 41.667 0.00 0.00 36.22 4.40
2728 3059 4.081406 TCAACTAACTAGGTCGTAAGCCA 58.919 43.478 0.00 0.00 36.22 4.75
2742 3074 4.976116 GCCAACAGTGTTGAATCAACTAAC 59.024 41.667 32.72 16.00 43.85 2.34
2744 3076 3.249799 CGCCAACAGTGTTGAATCAACTA 59.750 43.478 32.72 10.22 43.85 2.24
2774 3106 1.125021 GCACAATCGAACTCAGACGTG 59.875 52.381 0.00 0.00 0.00 4.49
2775 3107 1.269569 TGCACAATCGAACTCAGACGT 60.270 47.619 0.00 0.00 0.00 4.34
2782 3114 2.247790 GTGCCTGCACAATCGAACT 58.752 52.632 16.95 0.00 45.53 3.01
2794 3126 5.731599 TTTGCAAATTTTAGTTGTGCCTG 57.268 34.783 8.05 0.00 34.25 4.85
2801 3133 4.376920 GCGGCGAATTTGCAAATTTTAGTT 60.377 37.500 32.09 14.90 38.64 2.24
2802 3134 3.122780 GCGGCGAATTTGCAAATTTTAGT 59.877 39.130 32.09 14.91 38.64 2.24
2804 3136 3.059884 TGCGGCGAATTTGCAAATTTTA 58.940 36.364 32.09 15.65 38.64 1.52
2805 3137 1.869767 TGCGGCGAATTTGCAAATTTT 59.130 38.095 32.09 16.99 38.64 1.82
2808 3140 0.737019 CCTGCGGCGAATTTGCAAAT 60.737 50.000 18.99 18.99 38.30 2.32
2810 3142 1.800283 TTCCTGCGGCGAATTTGCAA 61.800 50.000 19.31 0.00 38.30 4.08
2811 3143 1.800283 TTTCCTGCGGCGAATTTGCA 61.800 50.000 19.31 7.59 36.28 4.08
2813 3145 2.842208 TATTTCCTGCGGCGAATTTG 57.158 45.000 12.98 0.00 0.00 2.32
2820 3158 9.093970 ACTAAATTTTATTTTATTTCCTGCGGC 57.906 29.630 0.00 0.00 0.00 6.53
2856 3194 9.874205 TTCAAAAATAGCTAAATATGCAGCTTT 57.126 25.926 14.61 6.36 45.80 3.51
2871 3209 7.132863 GTCCGGATCTACATTTCAAAAATAGC 58.867 38.462 7.81 0.00 0.00 2.97
2898 3236 9.573133 AATAAAAAGTGTCTTGAAGTTCACTTG 57.427 29.630 25.30 0.00 46.06 3.16
2924 3262 8.400947 GCCGATCGTATGTTAGATAGGTATAAA 58.599 37.037 15.09 0.00 40.36 1.40
2926 3264 6.484643 GGCCGATCGTATGTTAGATAGGTATA 59.515 42.308 15.09 0.00 40.36 1.47
2927 3265 5.298777 GGCCGATCGTATGTTAGATAGGTAT 59.701 44.000 15.09 0.00 40.36 2.73
2928 3266 4.637534 GGCCGATCGTATGTTAGATAGGTA 59.362 45.833 15.09 0.00 40.36 3.08
2929 3267 3.442977 GGCCGATCGTATGTTAGATAGGT 59.557 47.826 15.09 0.00 40.36 3.08
2930 3268 3.442625 TGGCCGATCGTATGTTAGATAGG 59.557 47.826 15.09 1.13 40.92 2.57
2931 3269 4.696899 TGGCCGATCGTATGTTAGATAG 57.303 45.455 15.09 0.00 0.00 2.08
2932 3270 5.407502 CAATGGCCGATCGTATGTTAGATA 58.592 41.667 15.09 0.00 0.00 1.98
2933 3271 4.245660 CAATGGCCGATCGTATGTTAGAT 58.754 43.478 15.09 0.00 0.00 1.98
2941 3279 1.333308 CATTTGCAATGGCCGATCGTA 59.667 47.619 15.09 0.04 40.13 3.43
2944 3282 0.103572 AGCATTTGCAATGGCCGATC 59.896 50.000 16.50 0.00 45.16 3.69
2948 3286 1.537562 GCTCTAGCATTTGCAATGGCC 60.538 52.381 16.50 0.00 45.16 5.36
2970 3308 4.184629 ACTTTTACATCATCTGTCGGAGC 58.815 43.478 0.00 0.00 39.39 4.70


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

AutoCloner maintained by Alex Coulton.