Multiple sequence alignment - TraesCS2B01G043300

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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 TraesCS2B01G043300 chr2B 100.000 3932 0 0 1 3932 20076841 20072910 0.000000e+00 7262.0
1 TraesCS2B01G043300 chr2B 92.139 3600 249 17 1 3573 20364846 20368438 0.000000e+00 5049.0
2 TraesCS2B01G043300 chr2B 84.671 2766 372 28 210 2946 22782379 22785121 0.000000e+00 2712.0
3 TraesCS2B01G043300 chr2B 83.370 2760 412 24 210 2939 21909886 21912628 0.000000e+00 2510.0
4 TraesCS2B01G043300 chr2B 80.639 2815 499 28 159 2944 19396694 19393897 0.000000e+00 2137.0
5 TraesCS2B01G043300 chr2B 80.558 2865 478 47 129 2944 19441440 19444274 0.000000e+00 2132.0
6 TraesCS2B01G043300 chr2A 91.610 3957 260 25 1 3913 14471325 14467397 0.000000e+00 5402.0
7 TraesCS2B01G043300 chr2A 85.330 2679 366 9 210 2867 14300033 14302705 0.000000e+00 2745.0
8 TraesCS2B01G043300 chr2A 83.383 2696 407 16 210 2877 13850191 13847509 0.000000e+00 2459.0
9 TraesCS2B01G043300 chr2A 80.393 2851 497 34 129 2944 13137760 13134937 0.000000e+00 2111.0
10 TraesCS2B01G043300 chr7B 79.675 123 17 8 3611 3731 605890021 605889905 9.060000e-12 82.4


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 TraesCS2B01G043300 chr2B 20072910 20076841 3931 True 7262 7262 100.000 1 3932 1 chr2B.!!$R2 3931
1 TraesCS2B01G043300 chr2B 20364846 20368438 3592 False 5049 5049 92.139 1 3573 1 chr2B.!!$F2 3572
2 TraesCS2B01G043300 chr2B 22782379 22785121 2742 False 2712 2712 84.671 210 2946 1 chr2B.!!$F4 2736
3 TraesCS2B01G043300 chr2B 21909886 21912628 2742 False 2510 2510 83.370 210 2939 1 chr2B.!!$F3 2729
4 TraesCS2B01G043300 chr2B 19393897 19396694 2797 True 2137 2137 80.639 159 2944 1 chr2B.!!$R1 2785
5 TraesCS2B01G043300 chr2B 19441440 19444274 2834 False 2132 2132 80.558 129 2944 1 chr2B.!!$F1 2815
6 TraesCS2B01G043300 chr2A 14467397 14471325 3928 True 5402 5402 91.610 1 3913 1 chr2A.!!$R3 3912
7 TraesCS2B01G043300 chr2A 14300033 14302705 2672 False 2745 2745 85.330 210 2867 1 chr2A.!!$F1 2657
8 TraesCS2B01G043300 chr2A 13847509 13850191 2682 True 2459 2459 83.383 210 2877 1 chr2A.!!$R2 2667
9 TraesCS2B01G043300 chr2A 13134937 13137760 2823 True 2111 2111 80.393 129 2944 1 chr2A.!!$R1 2815

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
960 992 0.250684 TGTCTCGCCTTTGGATTGCA 60.251 50.0 0.0 0.0 0.0 4.08 F
1978 2034 0.388907 CAATTGCAGGAGTTTGGGCG 60.389 55.0 0.0 0.0 0.0 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2039 2095 1.133025 CATGTCCAATTCGGCCAACTC 59.867 52.381 2.24 0.0 33.14 3.01 R
3797 3904 0.179215 CCTCAGTGCATTTCGTTCGC 60.179 55.000 0.00 0.0 0.00 4.70 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 53 1.601171 CAGGCTTGTCCCTCTCCTG 59.399 63.158 0.00 0.00 38.41 3.86
84 86 1.632589 GCCAGTTTTCCAATCCACCT 58.367 50.000 0.00 0.00 0.00 4.00
86 88 1.812571 CCAGTTTTCCAATCCACCTCG 59.187 52.381 0.00 0.00 0.00 4.63
87 89 1.812571 CAGTTTTCCAATCCACCTCGG 59.187 52.381 0.00 0.00 0.00 4.63
88 90 0.526211 GTTTTCCAATCCACCTCGGC 59.474 55.000 0.00 0.00 33.14 5.54
106 108 4.424430 CGCCGCTTGGTTTCGTCG 62.424 66.667 0.00 0.00 34.16 5.12
107 109 3.039588 GCCGCTTGGTTTCGTCGA 61.040 61.111 0.00 0.00 34.16 4.20
108 110 2.388232 GCCGCTTGGTTTCGTCGAT 61.388 57.895 0.00 0.00 34.16 3.59
111 113 0.999406 CGCTTGGTTTCGTCGATGAT 59.001 50.000 8.43 0.00 0.00 2.45
138 140 0.952010 GAACAACGGTGTATGGGCGT 60.952 55.000 6.49 0.00 36.80 5.68
143 145 1.153449 CGGTGTATGGGCGTGACAT 60.153 57.895 0.00 0.00 0.00 3.06
180 182 2.827423 CAGATGCTCATCCGGCCT 59.173 61.111 0.00 0.00 38.58 5.19
208 213 0.463474 GGCTTCACCAGAGAGGATGC 60.463 60.000 0.00 0.00 41.22 3.91
247 252 2.084546 GAGGAATTGGGAAGACAACGG 58.915 52.381 0.00 0.00 32.39 4.44
285 290 4.365714 TCAATGATGAAAGCGTCAGGCAA 61.366 43.478 0.00 0.00 42.90 4.52
334 339 3.117512 AGTTTCCAGTGTCTCCAACCAAT 60.118 43.478 0.00 0.00 0.00 3.16
375 383 2.620251 TAAGATCAGCCCAACCATCG 57.380 50.000 0.00 0.00 0.00 3.84
388 405 1.874129 ACCATCGTGGGTTGGATCTA 58.126 50.000 8.57 0.00 43.37 1.98
476 493 4.970711 AGATGCCTGATTGTTCTAGATGG 58.029 43.478 0.00 0.00 0.00 3.51
489 509 5.046663 TGTTCTAGATGGTGTATGCAACAGA 60.047 40.000 7.79 0.00 46.57 3.41
537 557 3.006323 TCACTCCTCTTCTTTCAGCAGAC 59.994 47.826 0.00 0.00 0.00 3.51
539 559 3.389329 ACTCCTCTTCTTTCAGCAGACAA 59.611 43.478 0.00 0.00 0.00 3.18
548 568 2.330440 TCAGCAGACAACAGAAGCAA 57.670 45.000 0.00 0.00 0.00 3.91
615 644 4.283467 TCACAGCTGTACACTGTAAATCCT 59.717 41.667 21.20 4.60 46.44 3.24
623 652 7.472100 GCTGTACACTGTAAATCCTCTGGATAT 60.472 40.741 0.00 0.00 42.27 1.63
625 654 7.563556 TGTACACTGTAAATCCTCTGGATATCA 59.436 37.037 4.83 0.28 42.27 2.15
628 657 8.153550 ACACTGTAAATCCTCTGGATATCAATC 58.846 37.037 4.83 0.00 42.27 2.67
673 702 4.352009 ACATGCTTTTCCCATTGATGGTA 58.648 39.130 9.07 0.00 46.65 3.25
694 723 5.163258 GGTAAGAATGTCCATCCAGATCTGT 60.163 44.000 21.11 0.60 0.00 3.41
703 732 6.611236 TGTCCATCCAGATCTGTAGTTGATTA 59.389 38.462 21.11 4.74 0.00 1.75
726 755 6.731292 AGGAGGAAAATTGCTACAAAAACT 57.269 33.333 0.00 0.00 30.85 2.66
772 801 1.602771 GTGGGAGGGTTGCTAGGAC 59.397 63.158 0.00 0.00 0.00 3.85
830 862 4.262851 GGAAACAGGGTTACAAAATGGCAT 60.263 41.667 0.00 0.00 0.00 4.40
910 942 6.047870 TGCTTCACATATTGCAGTTTGTTTT 58.952 32.000 2.58 0.00 0.00 2.43
924 956 7.500892 TGCAGTTTGTTTTCAGAGGACTATAAA 59.499 33.333 0.00 0.00 0.00 1.40
945 977 5.733620 AATTTGATCCAGCACATTTGTCT 57.266 34.783 0.00 0.00 0.00 3.41
960 992 0.250684 TGTCTCGCCTTTGGATTGCA 60.251 50.000 0.00 0.00 0.00 4.08
961 993 1.098050 GTCTCGCCTTTGGATTGCAT 58.902 50.000 0.00 0.00 0.00 3.96
986 1018 3.068873 GGTTTTGTACATCCACAAGGCAA 59.931 43.478 0.00 0.00 39.46 4.52
1015 1047 5.679601 AGAAAAGGATGGAAGACATAGCTC 58.320 41.667 0.00 0.00 40.72 4.09
1057 1089 3.253188 CCTTTCACGCTCATTTTTCCAGA 59.747 43.478 0.00 0.00 0.00 3.86
1119 1151 3.255642 GCCTACTCCATGAACTTGCAAAA 59.744 43.478 0.00 0.00 0.00 2.44
1163 1195 3.667360 TCCGTATTGATGATGGCATGAG 58.333 45.455 3.81 0.00 34.11 2.90
1254 1286 0.953960 CCGGGCTAGAAAAGTTGCGT 60.954 55.000 0.00 0.00 0.00 5.24
1261 1293 3.667166 GCTAGAAAAGTTGCGTACCTTGC 60.667 47.826 0.00 0.00 0.00 4.01
1283 1315 4.646492 GCTAATCCAACCATCACTTCCATT 59.354 41.667 0.00 0.00 0.00 3.16
1391 1447 5.873732 CTCTAAAGAGTTGCCTAATTGCAC 58.126 41.667 0.00 0.00 35.56 4.57
1394 1450 3.146104 AGAGTTGCCTAATTGCACTGT 57.854 42.857 0.00 0.00 41.88 3.55
1398 1454 3.254166 AGTTGCCTAATTGCACTGTTGAG 59.746 43.478 0.00 0.00 41.88 3.02
1410 1466 3.004734 GCACTGTTGAGTTATTGCACCTT 59.995 43.478 0.00 0.00 0.00 3.50
1431 1487 4.448720 TCGTTACCTCTCTATCCATGGA 57.551 45.455 18.88 18.88 0.00 3.41
1608 1664 2.902343 GGCATTGGTCGGCTAGCC 60.902 66.667 24.75 24.75 34.71 3.93
1690 1746 5.388654 AGTTGAGGAACATCAATGGTCTTT 58.611 37.500 7.89 0.00 43.90 2.52
1753 1809 4.036027 GCTATGAAGAAGCATGCAAAGCTA 59.964 41.667 21.98 2.10 42.53 3.32
1932 1988 1.899814 CCCAGTTGGCTACAGTCACTA 59.100 52.381 1.24 0.00 0.00 2.74
1978 2034 0.388907 CAATTGCAGGAGTTTGGGCG 60.389 55.000 0.00 0.00 0.00 6.13
2010 2066 4.225717 CCATTGGGAAATTTGGGATCACTT 59.774 41.667 0.00 0.00 35.59 3.16
2014 2070 5.509498 TGGGAAATTTGGGATCACTTAGAG 58.491 41.667 0.00 0.00 0.00 2.43
2045 2101 2.237143 TGAAGGAGCTATGTGGAGTTGG 59.763 50.000 0.00 0.00 0.00 3.77
2171 2227 6.385176 ACAGAGGACAAGATCTCATTTCCATA 59.615 38.462 0.00 0.00 32.76 2.74
2258 2314 3.244078 ACTCGTGAAGTTACCATTGAGCA 60.244 43.478 0.00 0.00 33.03 4.26
2343 2399 2.605338 CGATGTTTGCACAACTTCTGGG 60.605 50.000 17.27 6.47 36.16 4.45
2376 2432 4.061596 GGTTACTCCATAAGCAGCATCTC 58.938 47.826 0.00 0.00 40.40 2.75
2389 2445 3.641434 AGCATCTCAAGGCTGTTGTAT 57.359 42.857 0.00 0.00 41.88 2.29
2402 2458 8.686334 CAAGGCTGTTGTATCCTTAAACATAAT 58.314 33.333 0.00 0.00 38.08 1.28
2407 2463 8.887264 TGTTGTATCCTTAAACATAATTGGGT 57.113 30.769 0.00 0.00 0.00 4.51
2419 2475 5.630121 ACATAATTGGGTCTGAACAAGTCA 58.370 37.500 0.00 0.00 34.17 3.41
2442 2498 5.755409 TTGCTACTGAAGAAATAGGGTCA 57.245 39.130 0.00 0.00 0.00 4.02
2445 2501 5.105310 TGCTACTGAAGAAATAGGGTCACTC 60.105 44.000 0.00 0.00 0.00 3.51
2467 2523 4.058817 CGTTTCTCTACAAAGGCTTCAGT 58.941 43.478 0.00 5.33 0.00 3.41
2576 2632 5.483937 TGCCTAACTTAACATCTCTTCCAGA 59.516 40.000 0.00 0.00 34.78 3.86
2662 2731 3.069300 GCAGTCTCTATCCTCATTGCAGA 59.931 47.826 0.00 0.00 0.00 4.26
2740 2809 5.183140 ACATCATTTCCGTTGAACTTTAGGG 59.817 40.000 0.00 0.00 0.00 3.53
2765 2834 2.168326 TCATCGCTCAAAGTGCTGAA 57.832 45.000 0.00 0.00 29.20 3.02
2799 2868 3.452627 TCTCAGAGCTCCAATCTTTACCC 59.547 47.826 10.93 0.00 0.00 3.69
2811 2880 2.596346 TCTTTACCCGTGTGTGGTCTA 58.404 47.619 0.00 0.00 37.31 2.59
2925 3008 4.344359 TGCAATTGTACCTAGTGTGTCA 57.656 40.909 7.40 0.00 0.00 3.58
2929 3012 6.264292 TGCAATTGTACCTAGTGTGTCAATTT 59.736 34.615 7.40 8.14 38.99 1.82
2948 3031 8.169268 GTCAATTTAGTGACAGAGTATTTTCGG 58.831 37.037 5.53 0.00 46.00 4.30
2949 3032 6.663944 ATTTAGTGACAGAGTATTTTCGGC 57.336 37.500 0.00 0.00 0.00 5.54
2951 3034 4.273148 AGTGACAGAGTATTTTCGGCTT 57.727 40.909 0.00 0.00 0.00 4.35
2952 3035 3.997021 AGTGACAGAGTATTTTCGGCTTG 59.003 43.478 0.00 0.00 0.00 4.01
2953 3036 3.746492 GTGACAGAGTATTTTCGGCTTGT 59.254 43.478 0.00 0.00 0.00 3.16
2954 3037 4.927425 GTGACAGAGTATTTTCGGCTTGTA 59.073 41.667 0.00 0.00 0.00 2.41
2955 3038 5.407387 GTGACAGAGTATTTTCGGCTTGTAA 59.593 40.000 0.00 0.00 0.00 2.41
2956 3039 5.407387 TGACAGAGTATTTTCGGCTTGTAAC 59.593 40.000 0.00 0.00 0.00 2.50
2957 3040 5.548406 ACAGAGTATTTTCGGCTTGTAACT 58.452 37.500 0.00 0.00 0.00 2.24
2987 3070 2.031157 GTGTTTCCACAAGTTCATCGGG 60.031 50.000 0.00 0.00 41.44 5.14
3027 3110 3.192844 AGATGGCAACTCAAATGCTCTTG 59.807 43.478 0.00 0.00 43.34 3.02
3090 3173 3.554934 TGTACATGCCCTGATGAAATCC 58.445 45.455 0.00 0.00 44.73 3.01
3091 3174 3.202818 TGTACATGCCCTGATGAAATCCT 59.797 43.478 0.00 0.00 44.73 3.24
3097 3180 1.133668 CCCTGATGAAATCCTGGACCC 60.134 57.143 0.00 0.00 44.73 4.46
3100 3183 2.240667 CTGATGAAATCCTGGACCCTGT 59.759 50.000 0.00 0.00 44.73 4.00
3108 3191 4.779993 ATCCTGGACCCTGTAGAAAATC 57.220 45.455 0.00 0.00 0.00 2.17
3133 3216 1.166129 CATTTGCAGCAGAGCAGTCT 58.834 50.000 0.00 0.00 46.54 3.24
3162 3245 4.488770 TGGCAAAAAGAAGGGTAAATCCT 58.511 39.130 0.00 0.00 39.17 3.24
3205 3289 5.146010 GGCAACAATCATACAAAAGGGAA 57.854 39.130 0.00 0.00 0.00 3.97
3262 3346 5.266733 GCTCATTGCCAAAGATTTATCCA 57.733 39.130 0.00 0.00 35.15 3.41
3269 3353 4.097741 TGCCAAAGATTTATCCATGTTCGG 59.902 41.667 0.00 0.00 0.00 4.30
3293 3377 0.179073 CGACAATCCTTCGCCATCCT 60.179 55.000 0.00 0.00 0.00 3.24
3362 3448 5.612725 TCTTTCCAGCAACCTTCAAAAAT 57.387 34.783 0.00 0.00 0.00 1.82
3376 3462 1.115467 AAAAATGGTGTGGGCGACAA 58.885 45.000 3.20 0.00 35.91 3.18
3557 3651 8.678593 TTTCCTAGTTCCTTTCTCTTTCTTTC 57.321 34.615 0.00 0.00 0.00 2.62
3567 3661 7.067494 TCCTTTCTCTTTCTTTCCTTGTTCTTG 59.933 37.037 0.00 0.00 0.00 3.02
3570 3664 7.321745 TCTCTTTCTTTCCTTGTTCTTGTTC 57.678 36.000 0.00 0.00 0.00 3.18
3758 3865 7.319646 TGATGAACATTTTCTAAAAATCCGGG 58.680 34.615 0.00 0.00 32.36 5.73
3766 3873 9.816354 CATTTTCTAAAAATCCGGGAACATTAT 57.184 29.630 0.00 0.00 0.00 1.28
3776 3883 4.812091 TCCGGGAACATTATTGAATACACG 59.188 41.667 0.00 0.00 0.00 4.49
3843 3950 1.990799 TGACGAGTGGTTAATGAGCG 58.009 50.000 0.00 0.00 0.00 5.03
3844 3951 1.278238 GACGAGTGGTTAATGAGCGG 58.722 55.000 0.00 0.00 0.00 5.52
3913 4020 3.527641 CACCGACTAGGAGCTCCC 58.472 66.667 29.54 12.87 45.00 4.30
3915 4022 1.104577 CACCGACTAGGAGCTCCCTC 61.105 65.000 29.54 19.09 43.31 4.30
3916 4023 1.894756 CCGACTAGGAGCTCCCTCG 60.895 68.421 29.54 27.97 43.31 4.63
3917 4024 1.146485 CGACTAGGAGCTCCCTCGA 59.854 63.158 28.76 14.38 43.31 4.04
3918 4025 1.161563 CGACTAGGAGCTCCCTCGAC 61.162 65.000 28.76 17.85 43.31 4.20
3919 4026 1.153127 ACTAGGAGCTCCCTCGACG 60.153 63.158 29.54 13.18 43.31 5.12
3920 4027 2.516460 TAGGAGCTCCCTCGACGC 60.516 66.667 29.54 1.26 43.31 5.19
3925 4032 3.224324 GCTCCCTCGACGCCCATA 61.224 66.667 0.00 0.00 0.00 2.74
3926 4033 3.043419 CTCCCTCGACGCCCATAG 58.957 66.667 0.00 0.00 0.00 2.23
3927 4034 2.520982 TCCCTCGACGCCCATAGG 60.521 66.667 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 2.676839 CTGCGAGCTTTCTCATTCACAT 59.323 45.455 0.00 0.00 39.30 3.21
51 53 1.303643 CTGGCCTTCACCCTTGTCC 60.304 63.158 3.32 0.00 0.00 4.02
60 62 2.247358 GGATTGGAAAACTGGCCTTCA 58.753 47.619 3.32 0.00 0.00 3.02
61 63 2.029020 GTGGATTGGAAAACTGGCCTTC 60.029 50.000 3.32 0.00 0.00 3.46
88 90 4.084888 GACGAAACCAAGCGGCGG 62.085 66.667 9.78 0.00 34.57 6.13
91 93 1.011968 TCATCGACGAAACCAAGCGG 61.012 55.000 0.00 0.00 38.77 5.52
106 108 2.782192 CCGTTGTTCGACGAGTATCATC 59.218 50.000 13.29 0.00 45.47 2.92
107 109 2.163010 ACCGTTGTTCGACGAGTATCAT 59.837 45.455 13.29 0.00 45.47 2.45
108 110 1.536766 ACCGTTGTTCGACGAGTATCA 59.463 47.619 13.29 0.00 45.47 2.15
111 113 0.662619 ACACCGTTGTTCGACGAGTA 59.337 50.000 13.29 0.00 45.47 2.59
120 122 1.071814 ACGCCCATACACCGTTGTT 59.928 52.632 0.00 0.00 37.15 2.83
124 126 1.895020 ATGTCACGCCCATACACCGT 61.895 55.000 0.00 0.00 35.29 4.83
125 127 1.153449 ATGTCACGCCCATACACCG 60.153 57.895 0.00 0.00 0.00 4.94
138 140 1.008815 ACCTCATCCCTCTCCATGTCA 59.991 52.381 0.00 0.00 0.00 3.58
143 145 0.684479 CACGACCTCATCCCTCTCCA 60.684 60.000 0.00 0.00 0.00 3.86
180 182 4.966787 GGTGAAGCCCCACCGCAA 62.967 66.667 9.06 0.00 46.00 4.85
188 190 0.179936 CATCCTCTCTGGTGAAGCCC 59.820 60.000 0.00 0.00 37.07 5.19
208 213 3.369261 CCTCCATCACCAACAAGAGAGAG 60.369 52.174 0.00 0.00 0.00 3.20
247 252 6.988580 TCATCATTGAATACCATCTGAGTGAC 59.011 38.462 0.00 0.00 0.00 3.67
334 339 1.611474 ATCTCTGCTGCGAGCTCCAA 61.611 55.000 8.47 0.00 42.97 3.53
375 383 5.359194 TCTTCTCATTAGATCCAACCCAC 57.641 43.478 0.00 0.00 0.00 4.61
388 405 6.950041 TGAAAATCCACCATCTTCTTCTCATT 59.050 34.615 0.00 0.00 0.00 2.57
476 493 5.627499 TTCATCCTTTCTGTTGCATACAC 57.373 39.130 0.00 0.00 32.10 2.90
489 509 4.410099 TGTCCAGCAAGATTTCATCCTTT 58.590 39.130 0.00 0.00 0.00 3.11
537 557 5.581874 AGTCACCAAAATTTTGCTTCTGTTG 59.418 36.000 22.90 10.75 36.86 3.33
539 559 5.343307 AGTCACCAAAATTTTGCTTCTGT 57.657 34.783 22.90 13.24 36.86 3.41
548 568 4.278170 TCATGCGAGAAGTCACCAAAATTT 59.722 37.500 0.00 0.00 0.00 1.82
615 644 5.396772 GGACCAACAGTGATTGATATCCAGA 60.397 44.000 0.00 0.00 31.40 3.86
623 652 1.545428 GCAGGGACCAACAGTGATTGA 60.545 52.381 0.00 0.00 0.00 2.57
625 654 0.773644 AGCAGGGACCAACAGTGATT 59.226 50.000 0.00 0.00 0.00 2.57
628 657 0.179020 TTGAGCAGGGACCAACAGTG 60.179 55.000 0.00 0.00 0.00 3.66
673 702 5.664908 ACTACAGATCTGGATGGACATTCTT 59.335 40.000 26.08 3.43 34.19 2.52
694 723 8.325787 TGTAGCAATTTTCCTCCTAATCAACTA 58.674 33.333 0.00 0.00 0.00 2.24
703 732 6.731292 AGTTTTTGTAGCAATTTTCCTCCT 57.269 33.333 0.00 0.00 0.00 3.69
726 755 2.378038 GCAGCCAAAGGTGATCCATTA 58.622 47.619 0.00 0.00 44.53 1.90
772 801 0.248990 TGCGCTTTGCTCCTTGTTTG 60.249 50.000 9.73 0.00 46.63 2.93
830 862 4.102524 TCAAGAGTAGGGCAGAGAAAACAA 59.897 41.667 0.00 0.00 0.00 2.83
910 942 7.147497 TGCTGGATCAAATTTATAGTCCTCTGA 60.147 37.037 0.00 0.00 0.00 3.27
924 956 4.142534 CGAGACAAATGTGCTGGATCAAAT 60.143 41.667 0.00 0.00 0.00 2.32
945 977 1.679139 CCTATGCAATCCAAAGGCGA 58.321 50.000 0.00 0.00 0.00 5.54
960 992 5.261216 CCTTGTGGATGTACAAAACCCTAT 58.739 41.667 0.00 0.00 39.81 2.57
961 993 4.658063 CCTTGTGGATGTACAAAACCCTA 58.342 43.478 0.00 0.00 39.81 3.53
986 1018 2.915604 TCTTCCATCCTTTTCTCAGCCT 59.084 45.455 0.00 0.00 0.00 4.58
1015 1047 6.857777 AAGGAGCTGATCAAAATATTCTCG 57.142 37.500 0.00 0.00 0.00 4.04
1057 1089 4.646492 AGTCTTGTGTCCAAGCTTGATTTT 59.354 37.500 28.05 0.00 46.33 1.82
1119 1151 0.042431 AGTCCTCCTCCACAGCAGAT 59.958 55.000 0.00 0.00 0.00 2.90
1127 1159 1.984570 CGGAAGCAGTCCTCCTCCA 60.985 63.158 5.06 0.00 45.36 3.86
1163 1195 3.058016 CACTGTTGATGGGATGTCACAAC 60.058 47.826 0.00 0.00 40.44 3.32
1254 1286 4.227300 AGTGATGGTTGGATTAGCAAGGTA 59.773 41.667 0.00 0.00 0.00 3.08
1261 1293 6.125029 AGAATGGAAGTGATGGTTGGATTAG 58.875 40.000 0.00 0.00 0.00 1.73
1283 1315 1.349026 CTTGGAAGCAACTGGAGGAGA 59.651 52.381 0.00 0.00 0.00 3.71
1391 1447 3.498397 ACGAAGGTGCAATAACTCAACAG 59.502 43.478 0.00 0.00 0.00 3.16
1394 1450 4.453136 GGTAACGAAGGTGCAATAACTCAA 59.547 41.667 0.00 0.00 0.00 3.02
1398 1454 4.251268 AGAGGTAACGAAGGTGCAATAAC 58.749 43.478 0.00 0.00 46.39 1.89
1410 1466 4.448720 TCCATGGATAGAGAGGTAACGA 57.551 45.455 11.44 0.00 46.39 3.85
1431 1487 1.138568 CAGGAAGCCTCTGGATGGAT 58.861 55.000 0.00 0.00 0.00 3.41
1608 1664 3.626670 GCTCAAGTGATCCCTGAAGATTG 59.373 47.826 0.00 0.00 0.00 2.67
1690 1746 7.235804 AGACCTTTTATTTTTAGTAGCCCACA 58.764 34.615 0.00 0.00 0.00 4.17
1932 1988 1.201181 TGCAAAGAACGCACTTGTTGT 59.799 42.857 0.00 0.00 33.55 3.32
1978 2034 2.899303 TTTCCCAATGGAGGAAGGAC 57.101 50.000 0.00 0.00 44.07 3.85
2010 2066 6.798427 AGCTCCTTCATGTGTAAATCTCTA 57.202 37.500 0.00 0.00 0.00 2.43
2014 2070 6.017605 CCACATAGCTCCTTCATGTGTAAATC 60.018 42.308 20.00 0.00 45.17 2.17
2039 2095 1.133025 CATGTCCAATTCGGCCAACTC 59.867 52.381 2.24 0.00 33.14 3.01
2045 2101 3.575965 AAAACTCATGTCCAATTCGGC 57.424 42.857 0.00 0.00 33.14 5.54
2098 2154 6.603201 GGGAAGTCATCAAATTCAAGGATACA 59.397 38.462 0.00 0.00 41.41 2.29
2101 2157 5.582953 TGGGAAGTCATCAAATTCAAGGAT 58.417 37.500 0.00 0.00 0.00 3.24
2171 2227 7.020827 TCCACTAGAATCAATCTTTCAAGGT 57.979 36.000 0.00 0.00 39.71 3.50
2322 2378 2.605338 CCCAGAAGTTGTGCAAACATCG 60.605 50.000 12.28 7.59 0.00 3.84
2343 2399 1.154197 GGAGTAACCCGTTGAAGTGC 58.846 55.000 0.00 0.00 0.00 4.40
2389 2445 7.235079 TGTTCAGACCCAATTATGTTTAAGGA 58.765 34.615 0.00 0.00 0.00 3.36
2402 2458 2.622942 GCAATGACTTGTTCAGACCCAA 59.377 45.455 0.00 0.00 37.77 4.12
2407 2463 5.213891 TCAGTAGCAATGACTTGTTCAGA 57.786 39.130 0.00 0.00 37.77 3.27
2419 2475 6.069963 AGTGACCCTATTTCTTCAGTAGCAAT 60.070 38.462 0.00 0.00 0.00 3.56
2442 2498 4.202223 TGAAGCCTTTGTAGAGAAACGAGT 60.202 41.667 0.00 0.00 0.00 4.18
2445 2501 4.058817 ACTGAAGCCTTTGTAGAGAAACG 58.941 43.478 0.00 0.00 0.00 3.60
2467 2523 3.496507 TCAGTGAAATCGCATCGACAAAA 59.503 39.130 0.00 0.00 39.18 2.44
2576 2632 6.268847 TGTGCTAACCCCAAATGTTTCTAATT 59.731 34.615 0.00 0.00 0.00 1.40
2740 2809 2.413371 GCACTTTGAGCGATGAAAGACC 60.413 50.000 19.33 5.68 34.02 3.85
2765 2834 5.188555 TGGAGCTCTGAGAAGTGTGATATTT 59.811 40.000 14.64 0.00 0.00 1.40
2777 2846 3.452627 GGGTAAAGATTGGAGCTCTGAGA 59.547 47.826 14.64 0.00 0.00 3.27
2925 3008 6.879458 AGCCGAAAATACTCTGTCACTAAATT 59.121 34.615 0.00 0.00 0.00 1.82
2929 3012 5.168569 CAAGCCGAAAATACTCTGTCACTA 58.831 41.667 0.00 0.00 0.00 2.74
2975 3058 2.482721 AGTTAAACGCCCGATGAACTTG 59.517 45.455 0.00 0.00 0.00 3.16
2987 3070 3.863142 TCTCTCCCTACAGTTAAACGC 57.137 47.619 0.00 0.00 0.00 4.84
3027 3110 1.327303 TTCAATCACACTGGGTTGCC 58.673 50.000 0.00 0.00 0.00 4.52
3032 3115 4.549458 GTGAACAATTCAATCACACTGGG 58.451 43.478 8.99 0.00 42.15 4.45
3090 3173 3.264450 ACCAGATTTTCTACAGGGTCCAG 59.736 47.826 0.00 0.00 0.00 3.86
3091 3174 3.256704 ACCAGATTTTCTACAGGGTCCA 58.743 45.455 0.00 0.00 0.00 4.02
3097 3180 6.680810 TGCAAATGAACCAGATTTTCTACAG 58.319 36.000 0.00 0.00 0.00 2.74
3100 3183 5.243507 TGCTGCAAATGAACCAGATTTTCTA 59.756 36.000 0.00 0.00 0.00 2.10
3108 3191 1.402456 GCTCTGCTGCAAATGAACCAG 60.402 52.381 3.02 0.00 0.00 4.00
3144 3227 5.084519 GACCCAGGATTTACCCTTCTTTTT 58.915 41.667 0.00 0.00 40.05 1.94
3145 3228 4.107311 TGACCCAGGATTTACCCTTCTTTT 59.893 41.667 0.00 0.00 40.05 2.27
3149 3232 3.459969 AGATGACCCAGGATTTACCCTTC 59.540 47.826 0.00 0.00 40.05 3.46
3150 3233 3.474920 AGATGACCCAGGATTTACCCTT 58.525 45.455 0.00 0.00 40.05 3.95
3162 3245 4.780815 CCACTTTGCTATAAGATGACCCA 58.219 43.478 0.00 0.00 0.00 4.51
3216 3300 8.267894 AGCCAAGATACTACATACAATCAAACT 58.732 33.333 0.00 0.00 0.00 2.66
3225 3309 6.473397 GCAATGAGCCAAGATACTACATAC 57.527 41.667 0.00 0.00 37.23 2.39
3269 3353 3.564027 CGAAGGATTGTCGGGCGC 61.564 66.667 0.00 0.00 34.85 6.53
3293 3377 4.555709 GGACGGGGTGTGTGCACA 62.556 66.667 17.42 17.42 46.95 4.57
3341 3425 4.512571 CCATTTTTGAAGGTTGCTGGAAAG 59.487 41.667 0.00 0.00 0.00 2.62
3342 3426 4.080638 ACCATTTTTGAAGGTTGCTGGAAA 60.081 37.500 0.00 0.00 29.58 3.13
3345 3429 3.132925 CACCATTTTTGAAGGTTGCTGG 58.867 45.455 0.00 0.00 32.15 4.85
3347 3431 3.432046 CCACACCATTTTTGAAGGTTGCT 60.432 43.478 0.00 0.00 32.15 3.91
3348 3432 2.871633 CCACACCATTTTTGAAGGTTGC 59.128 45.455 0.00 0.00 32.15 4.17
3349 3433 3.465871 CCCACACCATTTTTGAAGGTTG 58.534 45.455 0.00 0.00 32.15 3.77
3362 3448 1.511318 CGAAATTGTCGCCCACACCA 61.511 55.000 0.00 0.00 44.14 4.17
3376 3462 2.353803 CGAGGGGTCTTGAGTTCGAAAT 60.354 50.000 0.00 0.00 0.00 2.17
3547 3641 7.326968 AGAACAAGAACAAGGAAAGAAAGAG 57.673 36.000 0.00 0.00 0.00 2.85
3673 3780 5.903764 TTGCTTTTGGAAAAATGTCATCG 57.096 34.783 0.00 0.00 0.00 3.84
3766 3873 6.496571 ACGGTTGAAAAATTCGTGTATTCAA 58.503 32.000 0.00 0.00 37.59 2.69
3797 3904 0.179215 CCTCAGTGCATTTCGTTCGC 60.179 55.000 0.00 0.00 0.00 4.70
3810 3917 2.673523 GTCATGCAGGCCCTCAGT 59.326 61.111 0.00 0.00 0.00 3.41
3812 3919 3.002583 TCGTCATGCAGGCCCTCA 61.003 61.111 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.