Multiple sequence alignment - TraesCS1D01G397000

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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 TraesCS1D01G397000 chr1D 100.000 3297 0 0 1 3297 464864146 464860850 0.000000e+00 6089.0
1 TraesCS1D01G397000 chr1B 92.128 1588 74 14 1155 2698 641630676 641629096 0.000000e+00 2193.0
2 TraesCS1D01G397000 chr1B 92.048 1094 61 13 1 1082 641631909 641630830 0.000000e+00 1515.0
3 TraesCS1D01G397000 chr1B 90.164 244 22 2 2780 3022 641628850 641628608 1.910000e-82 316.0
4 TraesCS1D01G397000 chr1B 96.045 177 6 1 3122 3297 641628579 641628403 1.500000e-73 287.0
5 TraesCS1D01G397000 chr1B 96.552 58 2 0 2721 2778 641629097 641629040 2.710000e-16 97.1
6 TraesCS1D01G397000 chr1A 88.684 1193 80 23 747 1915 557154123 557152962 0.000000e+00 1404.0
7 TraesCS1D01G397000 chr1A 94.391 624 14 10 1 603 557154885 557154262 0.000000e+00 939.0
8 TraesCS1D01G397000 chr1A 92.030 527 35 5 1946 2467 557152968 557152444 0.000000e+00 734.0
9 TraesCS1D01G397000 chr1A 86.782 174 19 2 1371 1544 327384474 327384305 1.210000e-44 191.0
10 TraesCS1D01G397000 chr1A 90.909 77 5 2 2698 2774 557152220 557152146 5.820000e-18 102.0
11 TraesCS1D01G397000 chr3B 93.368 573 26 8 1 568 657946286 657945721 0.000000e+00 837.0
12 TraesCS1D01G397000 chr5A 75.682 1649 244 91 747 2321 361446777 361448342 0.000000e+00 678.0
13 TraesCS1D01G397000 chr5A 81.989 372 60 4 206 575 361364997 361365363 3.200000e-80 309.0
14 TraesCS1D01G397000 chr5D 91.368 475 41 0 3 477 271480750 271481224 0.000000e+00 651.0
15 TraesCS1D01G397000 chr5D 90.949 453 41 0 6 458 271470333 271470785 7.820000e-171 610.0
16 TraesCS1D01G397000 chr5D 90.749 454 41 1 5 458 271475533 271475985 3.640000e-169 604.0
17 TraesCS1D01G397000 chr5D 90.487 452 43 0 5 456 271465116 271465567 6.090000e-167 597.0
18 TraesCS1D01G397000 chr5D 88.037 326 33 6 1196 1520 271708452 271708132 6.680000e-102 381.0
19 TraesCS1D01G397000 chr5B 89.873 316 27 5 1205 1520 307880979 307881289 5.120000e-108 401.0
20 TraesCS1D01G397000 chrUn 82.105 285 39 3 192 476 31027114 31027386 1.980000e-57 233.0
21 TraesCS1D01G397000 chr6B 86.782 174 19 2 1371 1544 185000391 185000560 1.210000e-44 191.0
22 TraesCS1D01G397000 chr2B 87.500 168 17 2 1377 1544 388578777 388578614 1.210000e-44 191.0
23 TraesCS1D01G397000 chr2B 87.500 168 17 2 1377 1544 746313155 746312992 1.210000e-44 191.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1D01G397000 chr1D 464860850 464864146 3296 True 6089.00 6089 100.0000 1 3297 1 chr1D.!!$R1 3296
1 TraesCS1D01G397000 chr1B 641628403 641631909 3506 True 881.62 2193 93.3874 1 3297 5 chr1B.!!$R1 3296
2 TraesCS1D01G397000 chr1A 557152146 557154885 2739 True 794.75 1404 91.5035 1 2774 4 chr1A.!!$R2 2773
3 TraesCS1D01G397000 chr3B 657945721 657946286 565 True 837.00 837 93.3680 1 568 1 chr3B.!!$R1 567
4 TraesCS1D01G397000 chr5A 361446777 361448342 1565 False 678.00 678 75.6820 747 2321 1 chr5A.!!$F2 1574

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
833 891 1.133009 ACTTGTGAGTGTCTCCTCCCT 60.133 52.381 0.0 0.0 33.99 4.2 F
1128 1307 0.249447 GCCAACAACTTTGTGCTCCC 60.249 55.000 0.0 0.0 41.31 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1816 2033 0.478507 AGGCTTGGTTTGCTGTAGGT 59.521 50.0 0.0 0.0 0.00 3.08 R
3068 3561 0.039911 AGGCTAGAACCGAGTGGACT 59.960 55.0 0.0 0.0 39.21 3.85 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
532 548 4.683721 TTAGCGTGGCGGCGGAAA 62.684 61.111 9.78 0.00 38.18 3.13
657 690 2.048023 CGTCGTAGTACCTGGGCCA 61.048 63.158 5.85 5.85 0.00 5.36
698 731 1.764571 TAACAACTGGGCCAGCTCGT 61.765 55.000 33.04 23.23 34.37 4.18
699 732 2.743928 CAACTGGGCCAGCTCGTC 60.744 66.667 33.04 0.00 34.37 4.20
831 889 1.964223 TGACTTGTGAGTGTCTCCTCC 59.036 52.381 0.00 0.00 35.88 4.30
832 890 1.273886 GACTTGTGAGTGTCTCCTCCC 59.726 57.143 0.00 0.00 35.88 4.30
833 891 1.133009 ACTTGTGAGTGTCTCCTCCCT 60.133 52.381 0.00 0.00 33.99 4.20
834 892 1.548269 CTTGTGAGTGTCTCCTCCCTC 59.452 57.143 0.00 0.00 0.00 4.30
857 915 2.419021 CCTGGCGTCCTAAATTTCGGTA 60.419 50.000 8.48 0.00 0.00 4.02
907 978 1.401905 GACCTGTTCGATGAAATGCCC 59.598 52.381 0.00 0.00 0.00 5.36
975 1068 2.125552 TGAGCTCCGGCATCAACG 60.126 61.111 12.15 0.00 41.70 4.10
1021 1114 2.357517 GTGCAGGTGAGGACGTGG 60.358 66.667 0.00 0.00 38.23 4.94
1054 1147 2.501261 TCTCCTATGCAATGCTCATGC 58.499 47.619 6.82 2.57 44.08 4.06
1106 1285 6.481976 TGTTGTTACATTTAGATATCTGGCGG 59.518 38.462 15.79 5.28 0.00 6.13
1128 1307 0.249447 GCCAACAACTTTGTGCTCCC 60.249 55.000 0.00 0.00 41.31 4.30
1160 1339 0.393077 CCGTCATCTACCCCATCACC 59.607 60.000 0.00 0.00 0.00 4.02
1180 1359 4.036027 CACCAACTTGGCATCATAGATCAC 59.964 45.833 7.81 0.00 42.67 3.06
1317 1499 1.623973 GCGACCTGGTAAGTTGCGAC 61.624 60.000 0.00 0.00 35.04 5.19
1355 1537 3.869246 CGTAGGGGTGTAATGTTTAGCAG 59.131 47.826 0.00 0.00 0.00 4.24
1525 1717 7.760340 CCCTGTGTACTAATTTCAGAACTACTC 59.240 40.741 0.00 0.00 0.00 2.59
1529 1721 9.488124 GTGTACTAATTTCAGAACTACTCTACG 57.512 37.037 0.00 0.00 31.12 3.51
1532 1724 7.536855 ACTAATTTCAGAACTACTCTACGGTG 58.463 38.462 0.00 0.00 31.12 4.94
1549 1742 3.176708 CGGTGGTAATGTAGTTGACTCG 58.823 50.000 0.00 0.00 0.00 4.18
1576 1777 4.433186 TTTTATTTCGCACATCCACCAG 57.567 40.909 0.00 0.00 0.00 4.00
1577 1778 2.036958 TATTTCGCACATCCACCAGG 57.963 50.000 0.00 0.00 0.00 4.45
1727 1944 8.065557 CAAGAAAATCTTGCCAAAGTAGAAAC 57.934 34.615 7.13 0.00 46.03 2.78
1788 2005 3.243267 CCTGAACCGTTTTTGGTAGTTGG 60.243 47.826 0.00 0.00 42.89 3.77
1816 2033 8.855110 TGAGGAAACAGTTTATTGCTTCATTAA 58.145 29.630 0.00 0.00 0.00 1.40
1854 2071 0.687920 TGGCCTCCGTACATGTTTGA 59.312 50.000 2.30 0.00 0.00 2.69
2151 2413 9.168451 TGCTCTATCTAGTAGGATTTCTAATCG 57.832 37.037 0.00 0.00 0.00 3.34
2215 2477 2.035442 GTCGGAGCTTGGGTTCAGC 61.035 63.158 0.00 0.00 0.00 4.26
2278 2540 2.910688 TGGAGAGTCCAACAAGTGAC 57.089 50.000 0.00 0.00 45.00 3.67
2325 2587 8.515414 GTTCAACTTGCAAGTTCCTTATCTAAT 58.485 33.333 35.97 13.33 45.65 1.73
2536 2802 7.801104 TGCTGAACCCTAATAATCATGAGTTA 58.199 34.615 0.00 0.69 0.00 2.24
2537 2803 8.439971 TGCTGAACCCTAATAATCATGAGTTAT 58.560 33.333 0.00 3.08 0.00 1.89
2539 2805 8.621532 TGAACCCTAATAATCATGAGTTATGC 57.378 34.615 0.00 0.00 36.70 3.14
2592 2859 6.430925 AGCATTACTAAAATCAGCTTGTGACA 59.569 34.615 0.00 0.00 38.28 3.58
2695 2981 7.789831 AGTCTATATCCCCTAAAAGATGACACA 59.210 37.037 0.00 0.00 0.00 3.72
2696 2982 8.091449 GTCTATATCCCCTAAAAGATGACACAG 58.909 40.741 0.00 0.00 0.00 3.66
2719 3024 0.618458 TCTTCATGGTGGCTGGTACC 59.382 55.000 4.43 4.43 38.71 3.34
2728 3033 0.322098 TGGCTGGTACCGGAATTGTG 60.322 55.000 25.59 0.00 0.00 3.33
2778 3083 1.677633 GGAACATGTTGTCCCCGGG 60.678 63.158 17.58 15.80 0.00 5.73
2787 3280 3.647771 GTCCCCGGGAAGCTTGGT 61.648 66.667 26.32 0.00 31.38 3.67
2805 3298 1.597937 GGTCTGACAAAGCAAGCGTTG 60.598 52.381 17.03 17.03 40.35 4.10
2806 3299 1.330521 GTCTGACAAAGCAAGCGTTGA 59.669 47.619 23.65 5.11 38.45 3.18
2818 3311 3.668656 GCAAGCGTTGATTCCTTGTTAAC 59.331 43.478 0.00 0.00 38.50 2.01
2820 3313 5.460646 CAAGCGTTGATTCCTTGTTAACAT 58.539 37.500 9.56 0.00 33.17 2.71
2833 3326 6.201425 TCCTTGTTAACATCGTCAAACTGTAC 59.799 38.462 9.56 0.00 0.00 2.90
2846 3339 6.183360 CGTCAAACTGTACAGAAGGTTTCTTT 60.183 38.462 29.30 13.11 38.11 2.52
2862 3355 8.045176 AGGTTTCTTTATATCAGTTCTTGTGC 57.955 34.615 0.00 0.00 0.00 4.57
2867 3360 8.492673 TCTTTATATCAGTTCTTGTGCGAAAT 57.507 30.769 0.00 0.00 0.00 2.17
2891 3384 3.128764 CACAGTAGTCGCTACAGGATTCA 59.871 47.826 15.98 0.00 39.22 2.57
2926 3419 7.084486 GTGTCCTTGTTTATTTGATCTGTTCC 58.916 38.462 0.00 0.00 0.00 3.62
2927 3420 7.004086 TGTCCTTGTTTATTTGATCTGTTCCT 58.996 34.615 0.00 0.00 0.00 3.36
2928 3421 7.505585 TGTCCTTGTTTATTTGATCTGTTCCTT 59.494 33.333 0.00 0.00 0.00 3.36
2940 3433 9.658799 TTTGATCTGTTCCTTATTGTCTTCTAG 57.341 33.333 0.00 0.00 0.00 2.43
2949 3442 2.113860 TTGTCTTCTAGGCATGTGGC 57.886 50.000 0.00 0.00 43.74 5.01
2985 3478 9.509956 TTGTCGATCTTTTCCTAATTCCTTTTA 57.490 29.630 0.00 0.00 0.00 1.52
2991 3484 8.863872 TCTTTTCCTAATTCCTTTTACTCCAG 57.136 34.615 0.00 0.00 0.00 3.86
3004 3497 7.681168 TCCTTTTACTCCAGGGAGATACTTTTA 59.319 37.037 21.73 0.00 44.53 1.52
3034 3527 5.886960 ATCTTACAAATGCCAGACTTGTC 57.113 39.130 0.00 0.00 35.09 3.18
3035 3528 4.713553 TCTTACAAATGCCAGACTTGTCA 58.286 39.130 3.49 0.00 35.09 3.58
3036 3529 4.515191 TCTTACAAATGCCAGACTTGTCAC 59.485 41.667 3.49 0.00 35.09 3.67
3037 3530 1.956477 ACAAATGCCAGACTTGTCACC 59.044 47.619 3.49 0.00 0.00 4.02
3038 3531 1.955778 CAAATGCCAGACTTGTCACCA 59.044 47.619 3.49 0.00 0.00 4.17
3040 3533 0.250901 ATGCCAGACTTGTCACCACC 60.251 55.000 3.49 0.00 0.00 4.61
3041 3534 1.148273 GCCAGACTTGTCACCACCA 59.852 57.895 3.49 0.00 0.00 4.17
3042 3535 0.250901 GCCAGACTTGTCACCACCAT 60.251 55.000 3.49 0.00 0.00 3.55
3043 3536 1.819305 GCCAGACTTGTCACCACCATT 60.819 52.381 3.49 0.00 0.00 3.16
3044 3537 1.881973 CCAGACTTGTCACCACCATTG 59.118 52.381 3.49 0.00 0.00 2.82
3045 3538 2.575532 CAGACTTGTCACCACCATTGT 58.424 47.619 3.49 0.00 0.00 2.71
3046 3539 2.291465 CAGACTTGTCACCACCATTGTG 59.709 50.000 3.49 0.00 42.39 3.33
3059 3552 3.226346 CCATTGTGGTTCTGCATTCTG 57.774 47.619 0.00 0.00 31.35 3.02
3060 3553 2.602878 CATTGTGGTTCTGCATTCTGC 58.397 47.619 0.00 0.00 45.29 4.26
3061 3554 0.961019 TTGTGGTTCTGCATTCTGCC 59.039 50.000 0.00 0.00 44.23 4.85
3062 3555 0.895100 TGTGGTTCTGCATTCTGCCC 60.895 55.000 0.00 0.00 44.23 5.36
3063 3556 0.895100 GTGGTTCTGCATTCTGCCCA 60.895 55.000 0.00 0.00 44.23 5.36
3064 3557 0.040058 TGGTTCTGCATTCTGCCCAT 59.960 50.000 0.00 0.00 44.23 4.00
3065 3558 0.458669 GGTTCTGCATTCTGCCCATG 59.541 55.000 0.00 0.00 44.23 3.66
3066 3559 0.458669 GTTCTGCATTCTGCCCATGG 59.541 55.000 4.14 4.14 44.23 3.66
3067 3560 0.040058 TTCTGCATTCTGCCCATGGT 59.960 50.000 11.73 0.00 44.23 3.55
3068 3561 0.918258 TCTGCATTCTGCCCATGGTA 59.082 50.000 11.73 0.00 44.23 3.25
3069 3562 1.134007 TCTGCATTCTGCCCATGGTAG 60.134 52.381 11.73 8.92 44.23 3.18
3070 3563 0.625316 TGCATTCTGCCCATGGTAGT 59.375 50.000 11.73 0.00 44.23 2.73
3071 3564 1.312815 GCATTCTGCCCATGGTAGTC 58.687 55.000 11.73 0.00 37.42 2.59
3072 3565 1.972872 CATTCTGCCCATGGTAGTCC 58.027 55.000 11.73 0.00 36.77 3.85
3073 3566 4.660880 GCATTCTGCCCATGGTAGTCCA 62.661 54.545 11.73 0.00 42.17 4.02
3082 3575 3.759865 TGGTAGTCCACTCGGTTCT 57.240 52.632 0.00 0.00 39.03 3.01
3083 3576 2.885135 TGGTAGTCCACTCGGTTCTA 57.115 50.000 0.00 0.00 39.03 2.10
3084 3577 2.719739 TGGTAGTCCACTCGGTTCTAG 58.280 52.381 0.00 0.00 39.03 2.43
3085 3578 1.404748 GGTAGTCCACTCGGTTCTAGC 59.595 57.143 0.00 0.00 34.27 3.42
3086 3579 1.404748 GTAGTCCACTCGGTTCTAGCC 59.595 57.143 0.00 0.00 0.00 3.93
3087 3580 0.039911 AGTCCACTCGGTTCTAGCCT 59.960 55.000 0.00 0.00 0.00 4.58
3088 3581 0.896226 GTCCACTCGGTTCTAGCCTT 59.104 55.000 0.00 0.00 0.00 4.35
3089 3582 1.135053 GTCCACTCGGTTCTAGCCTTC 60.135 57.143 0.00 0.00 0.00 3.46
3090 3583 1.187087 CCACTCGGTTCTAGCCTTCT 58.813 55.000 0.00 0.00 0.00 2.85
3091 3584 1.134965 CCACTCGGTTCTAGCCTTCTG 60.135 57.143 0.00 0.00 0.00 3.02
3092 3585 1.819288 CACTCGGTTCTAGCCTTCTGA 59.181 52.381 0.00 0.00 0.00 3.27
3093 3586 2.231478 CACTCGGTTCTAGCCTTCTGAA 59.769 50.000 0.00 0.00 0.00 3.02
3094 3587 2.897969 ACTCGGTTCTAGCCTTCTGAAA 59.102 45.455 0.00 0.00 0.00 2.69
3095 3588 3.056465 ACTCGGTTCTAGCCTTCTGAAAG 60.056 47.826 0.00 0.00 0.00 2.62
3096 3589 3.162666 TCGGTTCTAGCCTTCTGAAAGA 58.837 45.455 0.00 0.00 44.68 2.52
3109 3602 4.487714 TCTGAAAGACTGAAACCACTGT 57.512 40.909 0.00 0.00 38.67 3.55
3110 3603 4.191544 TCTGAAAGACTGAAACCACTGTG 58.808 43.478 0.00 0.00 38.67 3.66
3111 3604 3.941483 CTGAAAGACTGAAACCACTGTGT 59.059 43.478 7.08 0.00 34.07 3.72
3112 3605 5.092554 TGAAAGACTGAAACCACTGTGTA 57.907 39.130 7.08 0.00 0.00 2.90
3113 3606 5.116180 TGAAAGACTGAAACCACTGTGTAG 58.884 41.667 7.08 0.00 0.00 2.74
3114 3607 5.105106 TGAAAGACTGAAACCACTGTGTAGA 60.105 40.000 7.08 0.00 0.00 2.59
3115 3608 5.552870 AAGACTGAAACCACTGTGTAGAT 57.447 39.130 7.08 0.00 0.00 1.98
3116 3609 4.887748 AGACTGAAACCACTGTGTAGATG 58.112 43.478 7.08 0.00 0.00 2.90
3117 3610 3.403038 ACTGAAACCACTGTGTAGATGC 58.597 45.455 7.08 0.00 0.00 3.91
3118 3611 3.181455 ACTGAAACCACTGTGTAGATGCA 60.181 43.478 7.08 0.00 0.00 3.96
3119 3612 3.402110 TGAAACCACTGTGTAGATGCAG 58.598 45.455 7.08 0.00 38.58 4.41
3120 3613 3.181455 TGAAACCACTGTGTAGATGCAGT 60.181 43.478 7.08 0.00 45.69 4.40
3173 3666 2.069273 CGACTTTGGGCTACTCAACTG 58.931 52.381 0.00 0.00 0.00 3.16
3219 3712 2.166050 GGTTGTGTTGATATGCCATGCA 59.834 45.455 0.00 0.00 44.86 3.96
3235 3728 2.429930 CACTTTCCTCGGTGGCCA 59.570 61.111 0.00 0.00 35.26 5.36
3239 3732 0.537371 CTTTCCTCGGTGGCCAGTTT 60.537 55.000 5.11 0.00 35.26 2.66
3279 3773 9.832445 AAAGATACATGGACAGTAAATAATCGT 57.168 29.630 0.00 0.00 0.00 3.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
532 548 0.047176 TCCTCCTCCTCCTCTCCTCT 59.953 60.000 0.00 0.00 0.00 3.69
559 580 2.998670 TCTCGTATAATAGGGTCTCGCG 59.001 50.000 0.00 0.00 0.00 5.87
674 707 2.972021 AGCTGGCCCAGTTGTTATTTTT 59.028 40.909 13.35 0.00 33.43 1.94
675 708 2.562738 GAGCTGGCCCAGTTGTTATTTT 59.437 45.455 13.35 0.00 33.43 1.82
676 709 2.171003 GAGCTGGCCCAGTTGTTATTT 58.829 47.619 13.35 0.00 33.43 1.40
677 710 1.839424 GAGCTGGCCCAGTTGTTATT 58.161 50.000 13.35 0.00 33.43 1.40
678 711 0.392998 CGAGCTGGCCCAGTTGTTAT 60.393 55.000 13.35 0.00 33.43 1.89
680 713 2.281761 CGAGCTGGCCCAGTTGTT 60.282 61.111 13.35 0.00 33.43 2.83
682 715 2.743928 GACGAGCTGGCCCAGTTG 60.744 66.667 13.35 5.06 33.43 3.16
698 731 2.604686 AGAGGAAGCAGCGTGGGA 60.605 61.111 0.00 0.00 0.00 4.37
699 732 2.125350 GAGAGGAAGCAGCGTGGG 60.125 66.667 0.00 0.00 0.00 4.61
701 734 0.739112 GAAGGAGAGGAAGCAGCGTG 60.739 60.000 0.00 0.00 0.00 5.34
702 735 1.594310 GAAGGAGAGGAAGCAGCGT 59.406 57.895 0.00 0.00 0.00 5.07
703 736 1.153469 GGAAGGAGAGGAAGCAGCG 60.153 63.158 0.00 0.00 0.00 5.18
704 737 0.177836 GAGGAAGGAGAGGAAGCAGC 59.822 60.000 0.00 0.00 0.00 5.25
808 866 2.766263 AGGAGACACTCACAAGTCACAA 59.234 45.455 0.00 0.00 37.23 3.33
831 889 1.123928 ATTTAGGACGCCAGGAGAGG 58.876 55.000 0.00 0.00 0.00 3.69
832 890 2.990066 AATTTAGGACGCCAGGAGAG 57.010 50.000 0.00 0.00 0.00 3.20
833 891 2.418197 CGAAATTTAGGACGCCAGGAGA 60.418 50.000 0.00 0.00 0.00 3.71
834 892 1.933853 CGAAATTTAGGACGCCAGGAG 59.066 52.381 0.00 0.00 0.00 3.69
857 915 3.005050 CGCCCAATGTCATGCATAGATTT 59.995 43.478 0.00 0.00 36.67 2.17
885 947 2.487762 GGCATTTCATCGAACAGGTCAA 59.512 45.455 0.00 0.00 0.00 3.18
907 978 1.268539 GCACAAGTCAACCAAGGTTCG 60.269 52.381 0.51 0.00 36.00 3.95
1106 1285 0.175531 AGCACAAAGTTGTTGGCCAC 59.824 50.000 3.88 0.75 39.91 5.01
1128 1307 0.108804 ATGACGGGTAACACGCTGAG 60.109 55.000 0.00 0.00 39.74 3.35
1160 1339 4.637091 TGTGTGATCTATGATGCCAAGTTG 59.363 41.667 0.00 0.00 0.00 3.16
1180 1359 2.039974 TTATGCAGCGGCTGGTGTG 61.040 57.895 29.44 6.96 45.36 3.82
1317 1499 2.412089 CCTACGAGAAAAACAAGAGCGG 59.588 50.000 0.00 0.00 0.00 5.52
1525 1717 5.320549 AGTCAACTACATTACCACCGTAG 57.679 43.478 0.00 0.00 38.83 3.51
1529 1721 2.928116 GCGAGTCAACTACATTACCACC 59.072 50.000 0.00 0.00 0.00 4.61
1532 1724 3.187700 CAGGCGAGTCAACTACATTACC 58.812 50.000 0.00 0.00 0.00 2.85
1549 1742 3.612423 GGATGTGCGAAATAAAAACAGGC 59.388 43.478 0.00 0.00 0.00 4.85
1576 1777 3.898482 AGTGCACCCTAAATCATTACCC 58.102 45.455 14.63 0.00 0.00 3.69
1577 1778 4.440112 GCAAGTGCACCCTAAATCATTACC 60.440 45.833 14.63 0.00 41.59 2.85
1727 1944 4.970003 GCTGCGGCAATAAATAAACTGTAG 59.030 41.667 14.08 0.00 38.54 2.74
1788 2005 5.009610 TGAAGCAATAAACTGTTTCCTCACC 59.990 40.000 9.38 0.00 36.13 4.02
1816 2033 0.478507 AGGCTTGGTTTGCTGTAGGT 59.521 50.000 0.00 0.00 0.00 3.08
1843 2060 7.067494 AGAGGAGGCAAATAATCAAACATGTAC 59.933 37.037 0.00 0.00 0.00 2.90
1938 2155 8.919777 AGAAGGCTAAAACAAGTAGTTACATT 57.080 30.769 0.00 0.00 40.26 2.71
2122 2384 7.759489 AGAAATCCTACTAGATAGAGCAGTG 57.241 40.000 0.00 0.00 31.83 3.66
2151 2413 3.304257 CCTGGATTGCACAAGAATATCGC 60.304 47.826 0.00 0.00 0.00 4.58
2325 2587 5.603395 TGGGAGTACCGAATGATATTAACCA 59.397 40.000 0.00 0.00 44.64 3.67
2346 2608 4.736464 GCACTTCCTAAAACTTGTGTTGGG 60.736 45.833 0.24 0.24 36.39 4.12
2392 2657 8.821686 TGATTATTCTTTTGCCCTTAAGATGA 57.178 30.769 3.36 0.00 31.00 2.92
2506 2772 7.560991 TCATGATTATTAGGGTTCAGCAACAAT 59.439 33.333 0.00 0.00 33.70 2.71
2536 2802 2.347490 GTGGTCTGGTCACCGCAT 59.653 61.111 0.00 0.00 45.07 4.73
2558 2825 6.403049 TGATTTTAGTAATGCTCTCGAACCA 58.597 36.000 0.00 0.00 0.00 3.67
2570 2837 6.430925 TGCTGTCACAAGCTGATTTTAGTAAT 59.569 34.615 0.00 0.00 43.90 1.89
2695 2981 2.679716 GCCACCATGAAGAGGCCT 59.320 61.111 3.86 3.86 41.25 5.19
2719 3024 2.665519 GCAGTTAGCACACACAATTCCG 60.666 50.000 0.00 0.00 44.79 4.30
2773 3078 2.045926 CAGACCAAGCTTCCCGGG 60.046 66.667 16.85 16.85 0.00 5.73
2778 3083 1.949525 TGCTTTGTCAGACCAAGCTTC 59.050 47.619 29.85 10.77 0.00 3.86
2787 3280 1.662517 TCAACGCTTGCTTTGTCAGA 58.337 45.000 10.75 0.00 0.00 3.27
2805 3298 6.797033 CAGTTTGACGATGTTAACAAGGAATC 59.203 38.462 13.23 4.24 0.00 2.52
2806 3299 6.262273 ACAGTTTGACGATGTTAACAAGGAAT 59.738 34.615 13.23 0.00 0.00 3.01
2818 3311 4.307432 ACCTTCTGTACAGTTTGACGATG 58.693 43.478 21.99 4.20 0.00 3.84
2820 3313 4.395959 AACCTTCTGTACAGTTTGACGA 57.604 40.909 21.99 0.00 0.00 4.20
2846 3339 6.048073 GCATTTCGCACAAGAACTGATATA 57.952 37.500 2.05 0.00 41.79 0.86
2861 3354 0.247301 GCGACTACTGTGCATTTCGC 60.247 55.000 9.63 9.63 44.22 4.70
2862 3355 1.350193 AGCGACTACTGTGCATTTCG 58.650 50.000 0.00 0.00 0.00 3.46
2867 3360 0.526211 CCTGTAGCGACTACTGTGCA 59.474 55.000 15.00 0.00 37.78 4.57
2874 3367 1.681793 GCCTGAATCCTGTAGCGACTA 59.318 52.381 0.00 0.00 0.00 2.59
2926 3419 4.274459 GCCACATGCCTAGAAGACAATAAG 59.726 45.833 0.00 0.00 0.00 1.73
2927 3420 4.199310 GCCACATGCCTAGAAGACAATAA 58.801 43.478 0.00 0.00 0.00 1.40
2928 3421 3.199727 TGCCACATGCCTAGAAGACAATA 59.800 43.478 0.00 0.00 40.16 1.90
2940 3433 0.609662 AATTTCTGGTGCCACATGCC 59.390 50.000 0.00 0.00 40.16 4.40
2949 3442 5.858581 GGAAAAGATCGACAAATTTCTGGTG 59.141 40.000 11.95 0.00 32.14 4.17
3008 3501 9.277783 GACAAGTCTGGCATTTGTAAGATATAT 57.722 33.333 10.78 0.00 35.35 0.86
3009 3502 8.264347 TGACAAGTCTGGCATTTGTAAGATATA 58.736 33.333 10.78 0.00 34.82 0.86
3010 3503 7.066284 GTGACAAGTCTGGCATTTGTAAGATAT 59.934 37.037 10.78 0.00 44.43 1.63
3011 3504 6.371548 GTGACAAGTCTGGCATTTGTAAGATA 59.628 38.462 10.78 0.00 44.43 1.98
3012 3505 5.182001 GTGACAAGTCTGGCATTTGTAAGAT 59.818 40.000 10.78 0.00 44.43 2.40
3014 3507 4.320494 GGTGACAAGTCTGGCATTTGTAAG 60.320 45.833 10.78 0.00 44.43 2.34
3022 3515 1.148273 GGTGGTGACAAGTCTGGCA 59.852 57.895 1.53 0.00 46.06 4.92
3023 3516 0.250901 ATGGTGGTGACAAGTCTGGC 60.251 55.000 1.53 0.00 46.06 4.85
3024 3517 1.881973 CAATGGTGGTGACAAGTCTGG 59.118 52.381 1.53 0.00 46.06 3.86
3025 3518 2.291465 CACAATGGTGGTGACAAGTCTG 59.709 50.000 1.53 0.00 46.06 3.51
3053 3546 1.212688 TGGACTACCATGGGCAGAATG 59.787 52.381 18.09 0.26 41.77 2.67
3054 3547 1.595311 TGGACTACCATGGGCAGAAT 58.405 50.000 18.09 0.00 41.77 2.40
3055 3548 3.096852 TGGACTACCATGGGCAGAA 57.903 52.632 18.09 2.08 41.77 3.02
3056 3549 4.908333 TGGACTACCATGGGCAGA 57.092 55.556 18.09 0.00 41.77 4.26
3064 3557 2.719739 CTAGAACCGAGTGGACTACCA 58.280 52.381 0.00 0.00 44.76 3.25
3065 3558 1.404748 GCTAGAACCGAGTGGACTACC 59.595 57.143 0.00 0.00 39.21 3.18
3066 3559 1.404748 GGCTAGAACCGAGTGGACTAC 59.595 57.143 0.00 0.00 39.21 2.73
3067 3560 1.284198 AGGCTAGAACCGAGTGGACTA 59.716 52.381 0.00 0.00 39.21 2.59
3068 3561 0.039911 AGGCTAGAACCGAGTGGACT 59.960 55.000 0.00 0.00 39.21 3.85
3069 3562 0.896226 AAGGCTAGAACCGAGTGGAC 59.104 55.000 0.00 0.00 39.21 4.02
3070 3563 1.183549 GAAGGCTAGAACCGAGTGGA 58.816 55.000 0.00 0.00 39.21 4.02
3071 3564 1.134965 CAGAAGGCTAGAACCGAGTGG 60.135 57.143 0.00 0.00 42.84 4.00
3072 3565 1.819288 TCAGAAGGCTAGAACCGAGTG 59.181 52.381 0.00 0.00 33.69 3.51
3073 3566 2.217510 TCAGAAGGCTAGAACCGAGT 57.782 50.000 0.00 0.00 33.69 4.18
3074 3567 3.193691 TCTTTCAGAAGGCTAGAACCGAG 59.806 47.826 0.00 0.00 33.56 4.63
3075 3568 3.056749 GTCTTTCAGAAGGCTAGAACCGA 60.057 47.826 0.00 0.00 34.63 4.69
3076 3569 3.056465 AGTCTTTCAGAAGGCTAGAACCG 60.056 47.826 0.00 0.00 45.68 4.44
3077 3570 4.021016 TCAGTCTTTCAGAAGGCTAGAACC 60.021 45.833 0.00 0.00 45.77 3.62
3078 3571 5.140747 TCAGTCTTTCAGAAGGCTAGAAC 57.859 43.478 0.00 0.00 45.77 3.01
3079 3572 5.808366 TTCAGTCTTTCAGAAGGCTAGAA 57.192 39.130 0.00 0.00 45.77 2.10
3080 3573 5.511545 GGTTTCAGTCTTTCAGAAGGCTAGA 60.512 44.000 0.00 0.00 45.77 2.43
3081 3574 4.693095 GGTTTCAGTCTTTCAGAAGGCTAG 59.307 45.833 0.00 0.00 45.77 3.42
3082 3575 4.102524 TGGTTTCAGTCTTTCAGAAGGCTA 59.897 41.667 0.00 0.00 45.77 3.93
3084 3577 3.003793 GTGGTTTCAGTCTTTCAGAAGGC 59.996 47.826 0.00 0.00 37.77 4.35
3085 3578 4.274459 CAGTGGTTTCAGTCTTTCAGAAGG 59.726 45.833 0.00 0.00 33.56 3.46
3086 3579 4.878397 ACAGTGGTTTCAGTCTTTCAGAAG 59.122 41.667 0.00 0.00 0.00 2.85
3087 3580 4.635765 CACAGTGGTTTCAGTCTTTCAGAA 59.364 41.667 0.00 0.00 0.00 3.02
3088 3581 4.191544 CACAGTGGTTTCAGTCTTTCAGA 58.808 43.478 0.00 0.00 0.00 3.27
3089 3582 3.941483 ACACAGTGGTTTCAGTCTTTCAG 59.059 43.478 5.31 0.00 0.00 3.02
3090 3583 3.950397 ACACAGTGGTTTCAGTCTTTCA 58.050 40.909 5.31 0.00 0.00 2.69
3091 3584 5.357257 TCTACACAGTGGTTTCAGTCTTTC 58.643 41.667 5.31 0.00 0.00 2.62
3092 3585 5.353394 TCTACACAGTGGTTTCAGTCTTT 57.647 39.130 5.31 0.00 0.00 2.52
3093 3586 5.300752 CATCTACACAGTGGTTTCAGTCTT 58.699 41.667 5.31 0.00 0.00 3.01
3094 3587 4.800914 GCATCTACACAGTGGTTTCAGTCT 60.801 45.833 5.31 0.00 0.00 3.24
3095 3588 3.433615 GCATCTACACAGTGGTTTCAGTC 59.566 47.826 5.31 0.00 0.00 3.51
3096 3589 3.181455 TGCATCTACACAGTGGTTTCAGT 60.181 43.478 5.31 0.00 0.00 3.41
3097 3590 3.402110 TGCATCTACACAGTGGTTTCAG 58.598 45.455 5.31 0.00 0.00 3.02
3098 3591 3.181455 ACTGCATCTACACAGTGGTTTCA 60.181 43.478 5.31 0.00 45.19 2.69
3099 3592 3.403038 ACTGCATCTACACAGTGGTTTC 58.597 45.455 5.31 0.00 45.19 2.78
3100 3593 3.492102 ACTGCATCTACACAGTGGTTT 57.508 42.857 5.31 0.00 45.19 3.27
3101 3594 3.492102 AACTGCATCTACACAGTGGTT 57.508 42.857 5.31 0.00 46.17 3.67
3102 3595 3.617531 GCTAACTGCATCTACACAGTGGT 60.618 47.826 5.31 0.00 46.17 4.16
3103 3596 2.932614 GCTAACTGCATCTACACAGTGG 59.067 50.000 5.31 0.00 46.17 4.00
3104 3597 3.854666 AGCTAACTGCATCTACACAGTG 58.145 45.455 0.00 0.00 46.17 3.66
3106 3599 4.436584 GCAAAGCTAACTGCATCTACACAG 60.437 45.833 9.78 0.00 45.94 3.66
3107 3600 3.436704 GCAAAGCTAACTGCATCTACACA 59.563 43.478 9.78 0.00 45.94 3.72
3108 3601 3.181506 GGCAAAGCTAACTGCATCTACAC 60.182 47.826 15.03 0.00 45.94 2.90
3109 3602 3.009723 GGCAAAGCTAACTGCATCTACA 58.990 45.455 15.03 0.00 45.94 2.74
3110 3603 3.009723 TGGCAAAGCTAACTGCATCTAC 58.990 45.455 15.03 1.29 45.94 2.59
3111 3604 3.009723 GTGGCAAAGCTAACTGCATCTA 58.990 45.455 15.03 0.00 45.94 1.98
3112 3605 1.815003 GTGGCAAAGCTAACTGCATCT 59.185 47.619 15.03 0.00 45.94 2.90
3113 3606 1.815003 AGTGGCAAAGCTAACTGCATC 59.185 47.619 15.03 8.50 45.94 3.91
3114 3607 1.915141 AGTGGCAAAGCTAACTGCAT 58.085 45.000 15.03 1.07 45.94 3.96
3115 3608 1.337703 CAAGTGGCAAAGCTAACTGCA 59.662 47.619 15.03 0.00 45.94 4.41
3116 3609 1.932156 GCAAGTGGCAAAGCTAACTGC 60.932 52.381 6.78 6.78 43.97 4.40
3117 3610 2.056094 GCAAGTGGCAAAGCTAACTG 57.944 50.000 0.00 0.00 43.97 3.16
3219 3712 1.705997 AACTGGCCACCGAGGAAAGT 61.706 55.000 0.00 0.00 41.22 2.66
3277 3771 2.857592 TAAAGGCCTTACTCGCTACG 57.142 50.000 20.84 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.