Multiple sequence alignment - TraesCS6A01G209500

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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 TraesCS6A01G209500 chr6A 100.000 2600 0 0 1 2600 379657061 379654462 0.000000e+00 4802.0
1 TraesCS6A01G209500 chr6D 95.303 1767 51 13 767 2513 266954100 266952346 0.000000e+00 2774.0
2 TraesCS6A01G209500 chr6D 95.146 103 5 0 673 775 266954682 266954580 2.070000e-36 163.0
3 TraesCS6A01G209500 chr6B 94.916 1377 42 14 779 2139 415035905 415034541 0.000000e+00 2130.0
4 TraesCS6A01G209500 chr6B 88.018 651 74 4 1 650 560790563 560789916 0.000000e+00 767.0
5 TraesCS6A01G209500 chr6B 95.441 329 13 2 2218 2545 415028964 415028637 8.240000e-145 523.0
6 TraesCS6A01G209500 chr6B 89.256 121 8 2 671 786 415036062 415035942 2.090000e-31 147.0
7 TraesCS6A01G209500 chr6B 96.296 54 2 0 2546 2599 415028576 415028523 3.560000e-14 89.8
8 TraesCS6A01G209500 chr6B 95.652 46 2 0 1353 1398 624698847 624698892 9.980000e-10 75.0
9 TraesCS6A01G209500 chr6B 93.478 46 3 0 1353 1398 195273270 195273315 4.640000e-08 69.4
10 TraesCS6A01G209500 chr1B 89.676 649 65 2 1 648 437539961 437539314 0.000000e+00 826.0
11 TraesCS6A01G209500 chr1B 89.009 646 69 2 1 646 8705890 8705247 0.000000e+00 798.0
12 TraesCS6A01G209500 chr1B 87.632 663 74 7 1 658 544764048 544763389 0.000000e+00 763.0
13 TraesCS6A01G209500 chr3D 89.767 645 65 1 1 645 380180540 380179897 0.000000e+00 824.0
14 TraesCS6A01G209500 chr3D 89.538 650 63 5 1 648 433443961 433443315 0.000000e+00 819.0
15 TraesCS6A01G209500 chr5B 89.645 647 63 3 1 646 356369829 356369186 0.000000e+00 821.0
16 TraesCS6A01G209500 chr7B 89.474 646 67 1 7 652 640720995 640720351 0.000000e+00 815.0
17 TraesCS6A01G209500 chr7B 88.854 646 70 2 1 645 110879384 110880028 0.000000e+00 793.0
18 TraesCS6A01G209500 chr5A 90.741 54 5 0 1345 1398 401505898 401505845 3.590000e-09 73.1
19 TraesCS6A01G209500 chr4D 93.478 46 3 0 1353 1398 358472686 358472641 4.640000e-08 69.4
20 TraesCS6A01G209500 chr1A 93.478 46 3 0 1353 1398 577819031 577819076 4.640000e-08 69.4


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 TraesCS6A01G209500 chr6A 379654462 379657061 2599 True 4802.0 4802 100.0000 1 2600 1 chr6A.!!$R1 2599
1 TraesCS6A01G209500 chr6D 266952346 266954682 2336 True 1468.5 2774 95.2245 673 2513 2 chr6D.!!$R1 1840
2 TraesCS6A01G209500 chr6B 415034541 415036062 1521 True 1138.5 2130 92.0860 671 2139 2 chr6B.!!$R3 1468
3 TraesCS6A01G209500 chr6B 560789916 560790563 647 True 767.0 767 88.0180 1 650 1 chr6B.!!$R1 649
4 TraesCS6A01G209500 chr1B 437539314 437539961 647 True 826.0 826 89.6760 1 648 1 chr1B.!!$R2 647
5 TraesCS6A01G209500 chr1B 8705247 8705890 643 True 798.0 798 89.0090 1 646 1 chr1B.!!$R1 645
6 TraesCS6A01G209500 chr1B 544763389 544764048 659 True 763.0 763 87.6320 1 658 1 chr1B.!!$R3 657
7 TraesCS6A01G209500 chr3D 380179897 380180540 643 True 824.0 824 89.7670 1 645 1 chr3D.!!$R1 644
8 TraesCS6A01G209500 chr3D 433443315 433443961 646 True 819.0 819 89.5380 1 648 1 chr3D.!!$R2 647
9 TraesCS6A01G209500 chr5B 356369186 356369829 643 True 821.0 821 89.6450 1 646 1 chr5B.!!$R1 645
10 TraesCS6A01G209500 chr7B 640720351 640720995 644 True 815.0 815 89.4740 7 652 1 chr7B.!!$R1 645
11 TraesCS6A01G209500 chr7B 110879384 110880028 644 False 793.0 793 88.8540 1 645 1 chr7B.!!$F1 644

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
879 1385 0.038744 CAACTCTGGCCCATCCAACT 59.961 55.0 0.0 0.0 46.01 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2563 3088 0.377554 CGACGATTAGTGCTCCGAGT 59.622 55.0 0.0 0.0 0.0 4.18 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
54 55 1.511305 GGCGTCTCGGAGTTGATGA 59.489 57.895 4.69 0.00 0.00 2.92
95 96 0.681887 TCAGATCGGTGGCGTTAGGA 60.682 55.000 0.00 0.00 0.00 2.94
110 111 4.199310 CGTTAGGATTCATGGATGGTGTT 58.801 43.478 0.00 0.00 0.00 3.32
154 155 2.608261 CGTCAAGTGTGTCTCTCCTTCC 60.608 54.545 0.00 0.00 0.00 3.46
175 176 2.280524 CTGTCCCCGTTGTTGCGA 60.281 61.111 0.00 0.00 0.00 5.10
183 184 1.367195 CGTTGTTGCGACGTTGTCC 60.367 57.895 4.37 0.00 36.60 4.02
281 283 1.798626 AGATGGTGCATCTCCTGCTA 58.201 50.000 0.00 0.00 46.83 3.49
390 393 3.231736 AGAGACACGTTGCCCCGT 61.232 61.111 0.00 0.00 42.87 5.28
455 458 1.449778 GGAGGTCCGTAAAGCTGCC 60.450 63.158 0.00 0.00 0.00 4.85
473 476 1.227350 CGATCAGCGATGGAGCCAA 60.227 57.895 0.00 0.00 44.57 4.52
481 484 1.522580 GATGGAGCCAAGTCGAGCC 60.523 63.158 0.00 0.00 0.00 4.70
498 501 2.727392 CCCGGGTGAAGCGGTGATA 61.727 63.158 14.18 0.00 0.00 2.15
528 531 2.233305 TCCTTAGTGGAGAGGGACAC 57.767 55.000 0.00 0.00 40.56 3.67
531 534 1.255667 TTAGTGGAGAGGGACACGCC 61.256 60.000 0.00 0.00 42.25 5.68
590 600 9.524106 CAGTCCTATAATGTTGATGTTTACGTA 57.476 33.333 0.00 0.00 0.00 3.57
602 612 5.636121 TGATGTTTACGTAGCTTGTAACTGG 59.364 40.000 9.91 0.00 31.88 4.00
668 678 7.761038 AAAGACTTACATTTAGAAACAGGGG 57.239 36.000 0.00 0.00 0.00 4.79
669 679 5.816682 AGACTTACATTTAGAAACAGGGGG 58.183 41.667 0.00 0.00 0.00 5.40
691 701 8.599792 GGGGGAGTATATACTACTGCAAATTTA 58.400 37.037 21.91 0.00 37.32 1.40
733 748 7.840797 CGTTTGTGTTCTTAAAAATTGCAAGAG 59.159 33.333 4.94 0.00 30.43 2.85
777 1280 9.593134 AACTTTTCATGCACTATTTGTTTTACA 57.407 25.926 0.00 0.00 0.00 2.41
879 1385 0.038744 CAACTCTGGCCCATCCAACT 59.961 55.000 0.00 0.00 46.01 3.16
925 1431 2.631062 CCCTAACAAAAACCACCCCTTC 59.369 50.000 0.00 0.00 0.00 3.46
1158 1666 3.325753 GCAGTGGCCTCCCAGTCT 61.326 66.667 3.32 0.00 43.02 3.24
1527 2035 0.680280 GAGGTCAGCTCAGGGTCGTA 60.680 60.000 0.00 0.00 0.00 3.43
1608 2116 2.258591 GAGAACTGAGTCGCCGCA 59.741 61.111 0.00 0.00 0.00 5.69
1628 2136 5.008019 CCGCATATCTTTGCAATCTGTAACT 59.992 40.000 0.00 0.00 42.91 2.24
1694 2207 3.181541 GCCGATCAAAAATCAAACGCTTG 60.182 43.478 0.00 0.00 0.00 4.01
1741 2254 5.689383 AACTATGTGCTACTGTTTGGTTG 57.311 39.130 0.00 0.00 0.00 3.77
1814 2327 3.256631 GTGTCTGGCTTGATTGGTTTCAT 59.743 43.478 0.00 0.00 0.00 2.57
1905 2420 5.419788 TCTGATTCTTGATTTGGGATGTTGG 59.580 40.000 0.00 0.00 0.00 3.77
2032 2557 3.974401 CGGTACAGCACTCAAATTGTTTG 59.026 43.478 0.00 0.00 41.96 2.93
2047 2572 1.001487 TGTTTGGCAGTTTGATGAGCG 60.001 47.619 0.00 0.00 0.00 5.03
2048 2573 1.266718 GTTTGGCAGTTTGATGAGCGA 59.733 47.619 0.00 0.00 0.00 4.93
2049 2574 1.603456 TTGGCAGTTTGATGAGCGAA 58.397 45.000 0.00 0.00 0.00 4.70
2050 2575 0.874390 TGGCAGTTTGATGAGCGAAC 59.126 50.000 0.00 0.00 40.57 3.95
2066 2591 1.933181 CGAACTGCAATATTCGCCTCA 59.067 47.619 12.70 0.00 41.00 3.86
2087 2612 4.464244 TCAGGGACAACAAAACACAAATCA 59.536 37.500 0.00 0.00 0.00 2.57
2116 2641 4.351704 AGTTAAACACCCACTAAGCCCTTA 59.648 41.667 0.00 0.00 0.00 2.69
2117 2642 5.014860 AGTTAAACACCCACTAAGCCCTTAT 59.985 40.000 0.00 0.00 0.00 1.73
2145 2670 2.677914 TCAGGATCGGAAGGATAGCAA 58.322 47.619 0.00 0.00 34.82 3.91
2162 2687 8.156165 AGGATAGCAATTCTATTCTTCTTCCTG 58.844 37.037 0.00 0.00 40.02 3.86
2167 2692 7.126421 AGCAATTCTATTCTTCTTCCTGGTCTA 59.874 37.037 0.00 0.00 0.00 2.59
2168 2693 7.770897 GCAATTCTATTCTTCTTCCTGGTCTAA 59.229 37.037 0.00 0.00 0.00 2.10
2180 2705 4.800023 TCCTGGTCTAACATAGATCGGAA 58.200 43.478 7.84 0.00 43.54 4.30
2190 2715 0.968901 TAGATCGGAAGGCACACCGT 60.969 55.000 14.35 4.96 46.55 4.83
2223 2748 5.705441 TGAGTATGACTTGGTTGTGATTTCC 59.295 40.000 0.00 0.00 0.00 3.13
2467 2992 5.163844 GGAAGCTTGGTTCGACTAGAAAATC 60.164 44.000 2.10 0.00 41.10 2.17
2475 3000 5.704053 GGTTCGACTAGAAAATCCCTGAAAA 59.296 40.000 0.00 0.00 41.10 2.29
2510 3035 7.751768 ATTGAGATCAGTATGTGAGACGATA 57.248 36.000 0.00 0.00 39.07 2.92
2513 3038 8.257830 TGAGATCAGTATGTGAGACGATATAC 57.742 38.462 0.00 0.00 39.07 1.47
2514 3039 7.878127 TGAGATCAGTATGTGAGACGATATACA 59.122 37.037 0.00 0.00 39.07 2.29
2515 3040 8.800370 AGATCAGTATGTGAGACGATATACAT 57.200 34.615 0.00 0.00 39.07 2.29
2516 3041 8.672815 AGATCAGTATGTGAGACGATATACATG 58.327 37.037 0.00 0.00 39.07 3.21
2517 3042 6.612306 TCAGTATGTGAGACGATATACATGC 58.388 40.000 0.00 0.00 36.71 4.06
2518 3043 5.802451 CAGTATGTGAGACGATATACATGCC 59.198 44.000 0.00 0.00 37.00 4.40
2519 3044 3.660501 TGTGAGACGATATACATGCCC 57.339 47.619 0.00 0.00 0.00 5.36
2520 3045 2.962421 TGTGAGACGATATACATGCCCA 59.038 45.455 0.00 0.00 0.00 5.36
2521 3046 3.578282 TGTGAGACGATATACATGCCCAT 59.422 43.478 0.00 0.00 0.00 4.00
2522 3047 4.177026 GTGAGACGATATACATGCCCATC 58.823 47.826 0.00 0.00 0.00 3.51
2523 3048 3.119495 TGAGACGATATACATGCCCATCG 60.119 47.826 17.11 17.11 44.39 3.84
2526 3051 2.959516 CGATATACATGCCCATCGTGT 58.040 47.619 12.70 0.00 46.13 4.49
2527 3052 2.667969 CGATATACATGCCCATCGTGTG 59.332 50.000 12.70 0.00 44.24 3.82
2528 3053 1.877637 TATACATGCCCATCGTGTGC 58.122 50.000 0.00 0.00 44.24 4.57
2529 3054 0.181114 ATACATGCCCATCGTGTGCT 59.819 50.000 0.00 0.00 44.24 4.40
2530 3055 0.827368 TACATGCCCATCGTGTGCTA 59.173 50.000 0.00 0.00 44.24 3.49
2531 3056 0.462581 ACATGCCCATCGTGTGCTAG 60.463 55.000 0.00 0.00 42.99 3.42
2532 3057 0.462581 CATGCCCATCGTGTGCTAGT 60.463 55.000 0.00 0.00 0.00 2.57
2533 3058 1.119684 ATGCCCATCGTGTGCTAGTA 58.880 50.000 0.00 0.00 0.00 1.82
2534 3059 0.174845 TGCCCATCGTGTGCTAGTAC 59.825 55.000 3.70 3.70 0.00 2.73
2535 3060 0.460311 GCCCATCGTGTGCTAGTACT 59.540 55.000 12.42 0.00 0.00 2.73
2536 3061 1.134788 GCCCATCGTGTGCTAGTACTT 60.135 52.381 12.42 0.00 0.00 2.24
2537 3062 2.540515 CCCATCGTGTGCTAGTACTTG 58.459 52.381 12.42 0.00 0.00 3.16
2538 3063 2.540515 CCATCGTGTGCTAGTACTTGG 58.459 52.381 12.42 9.70 0.00 3.61
2539 3064 2.094182 CCATCGTGTGCTAGTACTTGGT 60.094 50.000 12.42 0.00 0.00 3.67
2540 3065 3.129813 CCATCGTGTGCTAGTACTTGGTA 59.870 47.826 12.42 0.00 0.00 3.25
2541 3066 3.837213 TCGTGTGCTAGTACTTGGTAC 57.163 47.619 12.42 5.32 39.10 3.34
2542 3067 3.148412 TCGTGTGCTAGTACTTGGTACA 58.852 45.455 12.42 7.95 41.03 2.90
2558 3083 4.057432 TGGTACAACGTAACAGCTTAACC 58.943 43.478 0.00 0.00 31.92 2.85
2559 3084 4.202243 TGGTACAACGTAACAGCTTAACCT 60.202 41.667 0.00 0.00 31.92 3.50
2560 3085 5.010516 TGGTACAACGTAACAGCTTAACCTA 59.989 40.000 0.00 0.00 31.92 3.08
2561 3086 6.101997 GGTACAACGTAACAGCTTAACCTAT 58.898 40.000 0.00 0.00 0.00 2.57
2562 3087 7.093988 TGGTACAACGTAACAGCTTAACCTATA 60.094 37.037 0.00 0.00 31.92 1.31
2563 3088 7.759433 GGTACAACGTAACAGCTTAACCTATAA 59.241 37.037 0.00 0.00 0.00 0.98
2564 3089 7.586714 ACAACGTAACAGCTTAACCTATAAC 57.413 36.000 0.00 0.00 0.00 1.89
2565 3090 7.381323 ACAACGTAACAGCTTAACCTATAACT 58.619 34.615 0.00 0.00 0.00 2.24
2566 3091 7.543520 ACAACGTAACAGCTTAACCTATAACTC 59.456 37.037 0.00 0.00 0.00 3.01
2567 3092 6.261118 ACGTAACAGCTTAACCTATAACTCG 58.739 40.000 0.00 0.00 0.00 4.18
2568 3093 5.684626 CGTAACAGCTTAACCTATAACTCGG 59.315 44.000 0.00 0.00 0.00 4.63
2569 3094 5.927281 AACAGCTTAACCTATAACTCGGA 57.073 39.130 0.00 0.00 0.00 4.55
2570 3095 5.517322 ACAGCTTAACCTATAACTCGGAG 57.483 43.478 2.83 2.83 0.00 4.63
2571 3096 4.202131 ACAGCTTAACCTATAACTCGGAGC 60.202 45.833 4.58 0.00 0.00 4.70
2572 3097 3.958798 AGCTTAACCTATAACTCGGAGCA 59.041 43.478 4.58 0.00 0.00 4.26
2573 3098 4.049869 GCTTAACCTATAACTCGGAGCAC 58.950 47.826 4.58 0.00 0.00 4.40
2574 3099 4.202131 GCTTAACCTATAACTCGGAGCACT 60.202 45.833 4.58 0.00 0.00 4.40
2575 3100 5.009410 GCTTAACCTATAACTCGGAGCACTA 59.991 44.000 4.58 0.00 0.00 2.74
2576 3101 6.460676 GCTTAACCTATAACTCGGAGCACTAA 60.461 42.308 4.58 0.00 0.00 2.24
2577 3102 7.592885 TTAACCTATAACTCGGAGCACTAAT 57.407 36.000 4.58 0.00 0.00 1.73
2578 3103 5.708877 ACCTATAACTCGGAGCACTAATC 57.291 43.478 4.58 0.00 0.00 1.75
2579 3104 4.215827 ACCTATAACTCGGAGCACTAATCG 59.784 45.833 4.58 0.00 0.00 3.34
2580 3105 4.215827 CCTATAACTCGGAGCACTAATCGT 59.784 45.833 4.58 0.00 0.00 3.73
2581 3106 2.563471 AACTCGGAGCACTAATCGTC 57.437 50.000 4.58 0.00 0.00 4.20
2582 3107 0.377554 ACTCGGAGCACTAATCGTCG 59.622 55.000 4.58 0.00 0.00 5.12
2583 3108 0.656259 CTCGGAGCACTAATCGTCGA 59.344 55.000 0.00 0.00 0.00 4.20
2584 3109 1.264557 CTCGGAGCACTAATCGTCGAT 59.735 52.381 0.75 0.75 0.00 3.59
2585 3110 1.674441 TCGGAGCACTAATCGTCGATT 59.326 47.619 23.01 23.01 36.20 3.34
2586 3111 2.098607 TCGGAGCACTAATCGTCGATTT 59.901 45.455 24.43 7.28 33.95 2.17
2587 3112 2.858344 CGGAGCACTAATCGTCGATTTT 59.142 45.455 24.43 10.37 33.95 1.82
2588 3113 3.301835 CGGAGCACTAATCGTCGATTTTG 60.302 47.826 24.43 20.81 33.95 2.44
2589 3114 3.544244 GGAGCACTAATCGTCGATTTTGC 60.544 47.826 29.33 29.33 38.75 3.68
2590 3115 3.262420 AGCACTAATCGTCGATTTTGCT 58.738 40.909 31.52 31.52 41.28 3.91
2591 3116 3.307242 AGCACTAATCGTCGATTTTGCTC 59.693 43.478 31.52 17.83 41.79 4.26
2592 3117 3.837838 GCACTAATCGTCGATTTTGCTCG 60.838 47.826 29.27 15.52 37.12 5.03
2593 3118 2.281762 ACTAATCGTCGATTTTGCTCGC 59.718 45.455 24.43 0.00 38.52 5.03
2594 3119 1.075542 AATCGTCGATTTTGCTCGCA 58.924 45.000 14.69 0.00 38.52 5.10
2595 3120 1.075542 ATCGTCGATTTTGCTCGCAA 58.924 45.000 0.75 0.00 38.52 4.85
2596 3121 0.862490 TCGTCGATTTTGCTCGCAAA 59.138 45.000 12.62 12.62 43.23 3.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 2.045926 GCCGCCATGGAAGACACT 60.046 61.111 18.40 0.00 42.00 3.55
27 28 4.812476 CGAGACGCCGCCATGGAA 62.812 66.667 18.40 0.00 42.00 3.53
54 55 0.796312 GATCGGCAAACACACGATGT 59.204 50.000 3.36 0.00 46.12 3.06
85 86 2.487086 CCATCCATGAATCCTAACGCCA 60.487 50.000 0.00 0.00 0.00 5.69
95 96 1.105457 CGCCAACACCATCCATGAAT 58.895 50.000 0.00 0.00 0.00 2.57
134 135 2.608261 CGGAAGGAGAGACACACTTGAC 60.608 54.545 0.00 0.00 0.00 3.18
138 139 0.540830 AGCGGAAGGAGAGACACACT 60.541 55.000 0.00 0.00 0.00 3.55
154 155 2.030562 AACAACGGGGACAGAGCG 59.969 61.111 0.00 0.00 0.00 5.03
183 184 4.402528 TTCCACCATGGCGTCGGG 62.403 66.667 13.04 6.15 37.47 5.14
275 277 1.202879 TCCAACCACAAACCTAGCAGG 60.203 52.381 1.16 1.16 42.49 4.85
276 278 2.154462 CTCCAACCACAAACCTAGCAG 58.846 52.381 0.00 0.00 0.00 4.24
281 283 0.468029 CAGCCTCCAACCACAAACCT 60.468 55.000 0.00 0.00 0.00 3.50
347 350 4.281182 ACACACCATCGAACTCTAGAACTT 59.719 41.667 0.00 0.00 0.00 2.66
354 357 1.338107 TGGACACACCATCGAACTCT 58.662 50.000 0.00 0.00 44.64 3.24
390 393 5.242838 ACCATTGCCGTTGAAAGAATTAGAA 59.757 36.000 0.00 0.00 0.00 2.10
455 458 1.220169 CTTGGCTCCATCGCTGATCG 61.220 60.000 0.00 0.00 40.15 3.69
473 476 3.382832 CTTCACCCGGGCTCGACT 61.383 66.667 24.08 0.00 39.00 4.18
491 494 7.815068 CACTAAGGAAAAGGAGATATATCACCG 59.185 40.741 19.68 8.00 41.64 4.94
578 588 5.636121 CCAGTTACAAGCTACGTAAACATCA 59.364 40.000 9.56 0.00 30.96 3.07
653 663 8.881262 AGTATATACTCCCCCTGTTTCTAAATG 58.119 37.037 9.71 0.00 0.00 2.32
656 666 8.740512 AGTAGTATATACTCCCCCTGTTTCTAA 58.259 37.037 18.68 0.00 37.73 2.10
657 667 8.168725 CAGTAGTATATACTCCCCCTGTTTCTA 58.831 40.741 18.68 0.00 37.73 2.10
658 668 7.011382 CAGTAGTATATACTCCCCCTGTTTCT 58.989 42.308 18.68 1.85 37.73 2.52
659 669 6.295180 GCAGTAGTATATACTCCCCCTGTTTC 60.295 46.154 18.68 5.73 37.73 2.78
660 670 5.543020 GCAGTAGTATATACTCCCCCTGTTT 59.457 44.000 18.68 0.00 37.73 2.83
661 671 5.085219 GCAGTAGTATATACTCCCCCTGTT 58.915 45.833 18.68 0.00 37.73 3.16
662 672 4.107473 TGCAGTAGTATATACTCCCCCTGT 59.893 45.833 18.68 0.00 37.73 4.00
663 673 4.673968 TGCAGTAGTATATACTCCCCCTG 58.326 47.826 18.68 18.47 37.73 4.45
664 674 5.349738 TTGCAGTAGTATATACTCCCCCT 57.650 43.478 18.68 8.25 37.73 4.79
665 675 6.622427 ATTTGCAGTAGTATATACTCCCCC 57.378 41.667 18.68 7.45 37.73 5.40
666 676 9.433153 GTAAATTTGCAGTAGTATATACTCCCC 57.567 37.037 18.68 8.52 37.73 4.81
667 677 9.991906 TGTAAATTTGCAGTAGTATATACTCCC 57.008 33.333 18.68 10.85 37.73 4.30
691 701 6.503524 ACACAAACGCTTATTTTTCTCATGT 58.496 32.000 0.00 0.00 0.00 3.21
733 748 8.145122 TGAAAAGTTGTTATTCCACCCATTAAC 58.855 33.333 0.00 0.00 0.00 2.01
828 1333 3.199946 TGGAAGGCCCATTTCACTACTAG 59.800 47.826 0.00 0.00 40.82 2.57
925 1431 2.685380 AAGAGGGACTGGAGGCGG 60.685 66.667 0.00 0.00 41.55 6.13
1126 1634 3.573772 CTGCACGGAGCTTGGACGA 62.574 63.158 7.82 0.00 45.94 4.20
1608 2116 8.757982 ATTGGAGTTACAGATTGCAAAGATAT 57.242 30.769 1.71 0.00 29.67 1.63
1628 2136 9.995003 ATTGAAAAGCATTACTACAAAATTGGA 57.005 25.926 0.00 0.00 0.00 3.53
1694 2207 8.671384 TTCATATACCATACCAAAGTAACTGC 57.329 34.615 0.00 0.00 30.59 4.40
1814 2327 2.346766 AACATCAGCAGTTCACCACA 57.653 45.000 0.00 0.00 0.00 4.17
1905 2420 3.814945 GCGCAAAGCTATTATCATCCAC 58.185 45.455 0.30 0.00 44.04 4.02
1950 2465 6.009589 TGATAAAAGAATGAAGCTCACCCAA 58.990 36.000 0.00 0.00 0.00 4.12
1951 2466 5.569355 TGATAAAAGAATGAAGCTCACCCA 58.431 37.500 0.00 0.00 0.00 4.51
1954 2469 6.128063 ACAGCTGATAAAAGAATGAAGCTCAC 60.128 38.462 23.35 0.00 37.42 3.51
1967 2490 5.584649 CGGGTTCTTATCACAGCTGATAAAA 59.415 40.000 23.35 8.32 45.01 1.52
2032 2557 1.135859 CAGTTCGCTCATCAAACTGCC 60.136 52.381 1.96 0.00 42.23 4.85
2047 2572 2.289002 CCTGAGGCGAATATTGCAGTTC 59.711 50.000 0.00 0.00 0.00 3.01
2048 2573 2.292267 CCTGAGGCGAATATTGCAGTT 58.708 47.619 0.00 0.00 0.00 3.16
2049 2574 1.475751 CCCTGAGGCGAATATTGCAGT 60.476 52.381 0.00 0.00 0.00 4.40
2050 2575 1.202687 TCCCTGAGGCGAATATTGCAG 60.203 52.381 0.00 0.00 0.00 4.41
2066 2591 5.413309 TTGATTTGTGTTTTGTTGTCCCT 57.587 34.783 0.00 0.00 0.00 4.20
2087 2612 6.183360 GGCTTAGTGGGTGTTTAACTTCTTTT 60.183 38.462 0.00 0.00 0.00 2.27
2116 2641 4.412199 TCCTTCCGATCCTGAACCAAATAT 59.588 41.667 0.00 0.00 0.00 1.28
2117 2642 3.778075 TCCTTCCGATCCTGAACCAAATA 59.222 43.478 0.00 0.00 0.00 1.40
2145 2670 8.380742 TGTTAGACCAGGAAGAAGAATAGAAT 57.619 34.615 0.00 0.00 0.00 2.40
2156 2681 4.827835 TCCGATCTATGTTAGACCAGGAAG 59.172 45.833 0.00 0.00 37.69 3.46
2162 2687 3.321111 TGCCTTCCGATCTATGTTAGACC 59.679 47.826 0.00 0.00 37.69 3.85
2167 2692 2.420129 GGTGTGCCTTCCGATCTATGTT 60.420 50.000 0.00 0.00 0.00 2.71
2168 2693 1.139058 GGTGTGCCTTCCGATCTATGT 59.861 52.381 0.00 0.00 0.00 2.29
2180 2705 2.046892 GCTGATCACGGTGTGCCT 60.047 61.111 8.17 0.00 32.98 4.75
2190 2715 4.223700 ACCAAGTCATACTCAAGCTGATCA 59.776 41.667 0.00 0.00 0.00 2.92
2223 2748 0.647410 CACGATCCTTTGTAGCAGCG 59.353 55.000 0.00 0.00 0.00 5.18
2467 2992 6.015180 TCTCAATTTCCATCTGTTTTTCAGGG 60.015 38.462 0.00 0.00 43.76 4.45
2475 3000 8.051535 ACATACTGATCTCAATTTCCATCTGTT 58.948 33.333 0.00 0.00 31.93 3.16
2517 3042 2.540515 CAAGTACTAGCACACGATGGG 58.459 52.381 0.00 0.00 0.00 4.00
2518 3043 2.094182 ACCAAGTACTAGCACACGATGG 60.094 50.000 0.00 0.00 34.58 3.51
2519 3044 3.232213 ACCAAGTACTAGCACACGATG 57.768 47.619 0.00 0.00 0.00 3.84
2520 3045 3.760151 TGTACCAAGTACTAGCACACGAT 59.240 43.478 0.00 0.00 39.49 3.73
2521 3046 3.148412 TGTACCAAGTACTAGCACACGA 58.852 45.455 0.00 0.00 39.49 4.35
2522 3047 3.564235 TGTACCAAGTACTAGCACACG 57.436 47.619 0.00 0.00 39.49 4.49
2523 3048 3.671928 CGTTGTACCAAGTACTAGCACAC 59.328 47.826 0.00 0.00 39.49 3.82
2524 3049 3.318839 ACGTTGTACCAAGTACTAGCACA 59.681 43.478 0.00 0.00 39.49 4.57
2525 3050 3.905784 ACGTTGTACCAAGTACTAGCAC 58.094 45.455 0.00 0.00 39.49 4.40
2526 3051 5.009510 TGTTACGTTGTACCAAGTACTAGCA 59.990 40.000 0.00 0.00 39.49 3.49
2527 3052 5.460646 TGTTACGTTGTACCAAGTACTAGC 58.539 41.667 0.00 0.00 39.49 3.42
2528 3053 5.570589 GCTGTTACGTTGTACCAAGTACTAG 59.429 44.000 0.00 0.00 39.49 2.57
2529 3054 5.241506 AGCTGTTACGTTGTACCAAGTACTA 59.758 40.000 0.00 0.00 39.49 1.82
2530 3055 4.038402 AGCTGTTACGTTGTACCAAGTACT 59.962 41.667 0.00 0.00 39.49 2.73
2531 3056 4.301628 AGCTGTTACGTTGTACCAAGTAC 58.698 43.478 0.00 0.00 39.24 2.73
2532 3057 4.589216 AGCTGTTACGTTGTACCAAGTA 57.411 40.909 0.00 0.00 0.00 2.24
2533 3058 3.464111 AGCTGTTACGTTGTACCAAGT 57.536 42.857 0.00 0.00 0.00 3.16
2534 3059 5.333568 GGTTAAGCTGTTACGTTGTACCAAG 60.334 44.000 0.00 0.00 0.00 3.61
2535 3060 4.511082 GGTTAAGCTGTTACGTTGTACCAA 59.489 41.667 0.00 0.00 0.00 3.67
2536 3061 4.057432 GGTTAAGCTGTTACGTTGTACCA 58.943 43.478 0.00 0.00 0.00 3.25
2537 3062 4.309933 AGGTTAAGCTGTTACGTTGTACC 58.690 43.478 6.33 0.00 0.00 3.34
2538 3063 8.587111 GTTATAGGTTAAGCTGTTACGTTGTAC 58.413 37.037 17.34 0.00 0.00 2.90
2539 3064 8.522830 AGTTATAGGTTAAGCTGTTACGTTGTA 58.477 33.333 17.34 0.00 0.00 2.41
2540 3065 7.381323 AGTTATAGGTTAAGCTGTTACGTTGT 58.619 34.615 17.34 0.00 0.00 3.32
2541 3066 7.253552 CGAGTTATAGGTTAAGCTGTTACGTTG 60.254 40.741 17.34 6.43 0.00 4.10
2542 3067 6.749118 CGAGTTATAGGTTAAGCTGTTACGTT 59.251 38.462 17.34 0.28 0.00 3.99
2543 3068 6.261118 CGAGTTATAGGTTAAGCTGTTACGT 58.739 40.000 17.34 0.00 0.00 3.57
2544 3069 5.684626 CCGAGTTATAGGTTAAGCTGTTACG 59.315 44.000 17.34 13.41 0.00 3.18
2545 3070 6.799512 TCCGAGTTATAGGTTAAGCTGTTAC 58.200 40.000 17.34 13.93 0.00 2.50
2546 3071 6.460676 GCTCCGAGTTATAGGTTAAGCTGTTA 60.461 42.308 17.34 1.58 0.00 2.41
2547 3072 5.681695 GCTCCGAGTTATAGGTTAAGCTGTT 60.682 44.000 17.34 7.24 0.00 3.16
2548 3073 4.202131 GCTCCGAGTTATAGGTTAAGCTGT 60.202 45.833 17.34 13.04 0.00 4.40
2549 3074 4.202121 TGCTCCGAGTTATAGGTTAAGCTG 60.202 45.833 17.34 0.00 0.00 4.24
2550 3075 3.958798 TGCTCCGAGTTATAGGTTAAGCT 59.041 43.478 12.54 12.54 0.00 3.74
2551 3076 4.049869 GTGCTCCGAGTTATAGGTTAAGC 58.950 47.826 0.00 0.00 0.00 3.09
2552 3077 5.517322 AGTGCTCCGAGTTATAGGTTAAG 57.483 43.478 0.00 0.00 0.00 1.85
2553 3078 7.521099 CGATTAGTGCTCCGAGTTATAGGTTAA 60.521 40.741 0.00 0.00 0.00 2.01
2554 3079 6.072838 CGATTAGTGCTCCGAGTTATAGGTTA 60.073 42.308 0.00 0.00 0.00 2.85
2555 3080 5.278364 CGATTAGTGCTCCGAGTTATAGGTT 60.278 44.000 0.00 0.00 0.00 3.50
2556 3081 4.215827 CGATTAGTGCTCCGAGTTATAGGT 59.784 45.833 0.00 0.00 0.00 3.08
2557 3082 4.215827 ACGATTAGTGCTCCGAGTTATAGG 59.784 45.833 0.00 0.00 0.00 2.57
2558 3083 5.359716 ACGATTAGTGCTCCGAGTTATAG 57.640 43.478 0.00 0.00 0.00 1.31
2559 3084 4.084171 CGACGATTAGTGCTCCGAGTTATA 60.084 45.833 0.00 0.00 0.00 0.98
2560 3085 3.303857 CGACGATTAGTGCTCCGAGTTAT 60.304 47.826 0.00 0.00 0.00 1.89
2561 3086 2.031314 CGACGATTAGTGCTCCGAGTTA 59.969 50.000 0.00 0.00 0.00 2.24
2562 3087 1.202154 CGACGATTAGTGCTCCGAGTT 60.202 52.381 0.00 0.00 0.00 3.01
2563 3088 0.377554 CGACGATTAGTGCTCCGAGT 59.622 55.000 0.00 0.00 0.00 4.18
2564 3089 0.656259 TCGACGATTAGTGCTCCGAG 59.344 55.000 0.00 0.00 0.00 4.63
2565 3090 1.306148 ATCGACGATTAGTGCTCCGA 58.694 50.000 4.05 0.00 31.52 4.55
2566 3091 2.121116 AATCGACGATTAGTGCTCCG 57.879 50.000 21.10 0.00 29.72 4.63
2567 3092 3.544244 GCAAAATCGACGATTAGTGCTCC 60.544 47.826 31.85 16.56 38.76 4.70
2568 3093 3.307242 AGCAAAATCGACGATTAGTGCTC 59.693 43.478 34.08 20.17 43.59 4.26
2569 3094 3.262420 AGCAAAATCGACGATTAGTGCT 58.738 40.909 34.08 34.08 42.93 4.40
2570 3095 3.598330 GAGCAAAATCGACGATTAGTGC 58.402 45.455 31.97 31.97 40.44 4.40
2571 3096 3.837838 GCGAGCAAAATCGACGATTAGTG 60.838 47.826 22.55 21.84 45.56 2.74
2572 3097 2.281762 GCGAGCAAAATCGACGATTAGT 59.718 45.455 22.55 11.55 45.56 2.24
2573 3098 2.281498 TGCGAGCAAAATCGACGATTAG 59.719 45.455 22.55 18.21 45.56 1.73
2574 3099 2.263945 TGCGAGCAAAATCGACGATTA 58.736 42.857 22.55 2.54 45.56 1.75
2575 3100 1.075542 TGCGAGCAAAATCGACGATT 58.924 45.000 17.19 17.19 45.56 3.34
2576 3101 1.075542 TTGCGAGCAAAATCGACGAT 58.924 45.000 8.17 4.05 45.56 3.73
2577 3102 0.862490 TTTGCGAGCAAAATCGACGA 59.138 45.000 19.38 0.00 45.56 4.20
2578 3103 1.669184 TTTTGCGAGCAAAATCGACG 58.331 45.000 26.14 0.00 46.80 5.12


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

AutoCloner maintained by Alex Coulton.