Multiple sequence alignment - TraesCS2A01G290800

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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 TraesCS2A01G290800 chr2A 100.000 3235 0 0 1 3235 501095228 501091994 0.000000e+00 5975
1 TraesCS2A01G290800 chr2D 91.597 2737 108 50 1 2708 370178024 370175381 0.000000e+00 3668
2 TraesCS2A01G290800 chr2B 95.868 1815 34 12 650 2449 439643366 439641578 0.000000e+00 2898
3 TraesCS2A01G290800 chr2B 83.237 519 70 11 2730 3233 68342000 68342516 8.180000e-126 460
4 TraesCS2A01G290800 chr2B 96.350 137 4 1 153 288 439651086 439650950 1.170000e-54 224
5 TraesCS2A01G290800 chr2B 90.210 143 12 1 273 413 439650892 439650750 5.510000e-43 185
6 TraesCS2A01G290800 chr2B 96.250 80 3 0 2442 2521 439626346 439626267 7.280000e-27 132
7 TraesCS2A01G290800 chr1A 82.745 510 64 14 2745 3233 32434945 32435451 1.780000e-117 433
8 TraesCS2A01G290800 chr1A 81.629 528 71 16 2729 3235 126535898 126535376 6.460000e-112 414
9 TraesCS2A01G290800 chr1A 81.629 528 71 16 2729 3235 465528254 465528776 6.460000e-112 414
10 TraesCS2A01G290800 chr6A 81.818 528 69 17 2729 3235 70602023 70601502 4.990000e-113 418
11 TraesCS2A01G290800 chr6B 81.629 528 71 16 2729 3235 696082437 696081915 6.460000e-112 414
12 TraesCS2A01G290800 chr5B 81.629 528 71 16 2729 3235 298322239 298321717 6.460000e-112 414
13 TraesCS2A01G290800 chr4A 81.629 528 71 16 2729 3235 602253725 602254247 6.460000e-112 414
14 TraesCS2A01G290800 chr1B 81.629 528 71 16 2729 3235 31472862 31473384 6.460000e-112 414


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 TraesCS2A01G290800 chr2A 501091994 501095228 3234 True 5975 5975 100.000 1 3235 1 chr2A.!!$R1 3234
1 TraesCS2A01G290800 chr2D 370175381 370178024 2643 True 3668 3668 91.597 1 2708 1 chr2D.!!$R1 2707
2 TraesCS2A01G290800 chr2B 439641578 439643366 1788 True 2898 2898 95.868 650 2449 1 chr2B.!!$R2 1799
3 TraesCS2A01G290800 chr2B 68342000 68342516 516 False 460 460 83.237 2730 3233 1 chr2B.!!$F1 503
4 TraesCS2A01G290800 chr1A 32434945 32435451 506 False 433 433 82.745 2745 3233 1 chr1A.!!$F1 488
5 TraesCS2A01G290800 chr1A 126535376 126535898 522 True 414 414 81.629 2729 3235 1 chr1A.!!$R1 506
6 TraesCS2A01G290800 chr1A 465528254 465528776 522 False 414 414 81.629 2729 3235 1 chr1A.!!$F2 506
7 TraesCS2A01G290800 chr6A 70601502 70602023 521 True 418 418 81.818 2729 3235 1 chr6A.!!$R1 506
8 TraesCS2A01G290800 chr6B 696081915 696082437 522 True 414 414 81.629 2729 3235 1 chr6B.!!$R1 506
9 TraesCS2A01G290800 chr5B 298321717 298322239 522 True 414 414 81.629 2729 3235 1 chr5B.!!$R1 506
10 TraesCS2A01G290800 chr4A 602253725 602254247 522 False 414 414 81.629 2729 3235 1 chr4A.!!$F1 506
11 TraesCS2A01G290800 chr1B 31472862 31473384 522 False 414 414 81.629 2729 3235 1 chr1B.!!$F1 506

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
640 650 0.25316 TCAGGAGCCCATGGTAAGGT 60.253 55.0 11.73 0.17 0.0 3.5 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2310 2352 0.871057 CACACACACACACACACACA 59.129 50.0 0.0 0.0 0.0 3.72 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
24 25 7.615582 TGGAACATCTAACACTTGAATCATC 57.384 36.000 0.00 0.00 0.00 2.92
25 26 7.167535 TGGAACATCTAACACTTGAATCATCA 58.832 34.615 0.00 0.00 0.00 3.07
34 35 9.520204 CTAACACTTGAATCATCAACACTTTTT 57.480 29.630 0.00 0.00 40.59 1.94
37 38 8.465999 ACACTTGAATCATCAACACTTTTTGTA 58.534 29.630 0.00 0.00 40.59 2.41
48 49 7.356540 TCAACACTTTTTGTACAATATGACCG 58.643 34.615 9.56 4.71 37.51 4.79
62 63 6.073765 ACAATATGACCGAAATGTAATCTCGC 60.074 38.462 0.00 0.00 34.95 5.03
99 100 0.379316 GGTGACACCGTCCAAAACAC 59.621 55.000 9.33 0.00 0.00 3.32
103 104 1.741145 GACACCGTCCAAAACACTGTT 59.259 47.619 0.00 0.00 0.00 3.16
104 105 2.162809 GACACCGTCCAAAACACTGTTT 59.837 45.455 1.00 1.00 0.00 2.83
105 106 2.162809 ACACCGTCCAAAACACTGTTTC 59.837 45.455 7.62 0.00 0.00 2.78
106 107 1.399089 ACCGTCCAAAACACTGTTTCG 59.601 47.619 7.62 6.98 0.00 3.46
107 108 1.268335 CCGTCCAAAACACTGTTTCGG 60.268 52.381 14.58 14.58 0.00 4.30
108 109 1.399089 CGTCCAAAACACTGTTTCGGT 59.601 47.619 10.77 0.00 0.00 4.69
109 110 2.789779 CGTCCAAAACACTGTTTCGGTG 60.790 50.000 10.77 7.10 45.33 4.94
110 111 2.420722 GTCCAAAACACTGTTTCGGTGA 59.579 45.455 10.77 2.57 42.79 4.02
111 112 2.680841 TCCAAAACACTGTTTCGGTGAG 59.319 45.455 10.77 1.20 42.79 3.51
112 113 2.680841 CCAAAACACTGTTTCGGTGAGA 59.319 45.455 14.43 0.00 42.79 3.27
164 165 8.868522 TTGAGAAAGAATTGACTCAATATGGT 57.131 30.769 4.65 0.00 42.67 3.55
196 197 5.696270 CACAAAAATGAAAAGGCTAAGTCCC 59.304 40.000 0.00 0.00 0.00 4.46
203 204 6.388619 TGAAAAGGCTAAGTCCCTTAAGAT 57.611 37.500 3.36 0.00 41.70 2.40
204 205 7.504926 TGAAAAGGCTAAGTCCCTTAAGATA 57.495 36.000 3.36 0.00 41.70 1.98
205 206 7.336396 TGAAAAGGCTAAGTCCCTTAAGATAC 58.664 38.462 3.36 1.53 41.70 2.24
206 207 5.532664 AAGGCTAAGTCCCTTAAGATACG 57.467 43.478 3.36 0.00 40.79 3.06
207 208 4.544683 AGGCTAAGTCCCTTAAGATACGT 58.455 43.478 3.36 0.00 0.00 3.57
246 247 3.017048 CAATTAGGAGATTGGGGTGCA 57.983 47.619 0.00 0.00 34.20 4.57
252 253 1.177401 GAGATTGGGGTGCACTTTCC 58.823 55.000 17.98 15.85 0.00 3.13
253 254 0.482446 AGATTGGGGTGCACTTTCCA 59.518 50.000 17.98 18.17 0.00 3.53
267 268 4.726416 CACTTTCCATGGTGAATTCTTCG 58.274 43.478 12.58 0.00 35.69 3.79
365 366 4.196193 CCTAAGGGACGAATGCATGTTTA 58.804 43.478 0.00 0.00 33.58 2.01
409 410 5.963176 TTTTCGGGGGAAAAGTTATACAC 57.037 39.130 0.00 0.00 31.32 2.90
410 411 4.914177 TTCGGGGGAAAAGTTATACACT 57.086 40.909 0.00 0.00 37.30 3.55
460 461 6.938596 ACGTTGCTAACTTAAAAAGGAGGTAT 59.061 34.615 0.00 0.00 0.00 2.73
461 462 7.446319 ACGTTGCTAACTTAAAAAGGAGGTATT 59.554 33.333 0.00 0.00 0.00 1.89
462 463 8.938906 CGTTGCTAACTTAAAAAGGAGGTATTA 58.061 33.333 0.00 0.00 0.00 0.98
476 477 9.950496 AAAGGAGGTATTACATCATGCTAATAG 57.050 33.333 10.35 0.00 29.10 1.73
533 541 3.372206 AGCATATGTGACTGTTTCTTCGC 59.628 43.478 4.29 0.00 0.00 4.70
534 542 3.485877 GCATATGTGACTGTTTCTTCGCC 60.486 47.826 4.29 0.00 0.00 5.54
535 543 1.523758 ATGTGACTGTTTCTTCGCCC 58.476 50.000 0.00 0.00 0.00 6.13
536 544 0.468226 TGTGACTGTTTCTTCGCCCT 59.532 50.000 0.00 0.00 0.00 5.19
537 545 1.134220 TGTGACTGTTTCTTCGCCCTT 60.134 47.619 0.00 0.00 0.00 3.95
538 546 1.531578 GTGACTGTTTCTTCGCCCTTC 59.468 52.381 0.00 0.00 0.00 3.46
539 547 1.157585 GACTGTTTCTTCGCCCTTCC 58.842 55.000 0.00 0.00 0.00 3.46
540 548 0.765510 ACTGTTTCTTCGCCCTTCCT 59.234 50.000 0.00 0.00 0.00 3.36
541 549 1.975680 ACTGTTTCTTCGCCCTTCCTA 59.024 47.619 0.00 0.00 0.00 2.94
542 550 2.289506 ACTGTTTCTTCGCCCTTCCTAC 60.290 50.000 0.00 0.00 0.00 3.18
543 551 1.002773 TGTTTCTTCGCCCTTCCTACC 59.997 52.381 0.00 0.00 0.00 3.18
544 552 1.278413 GTTTCTTCGCCCTTCCTACCT 59.722 52.381 0.00 0.00 0.00 3.08
618 628 2.050168 GCGCCACCATTGTGTGTG 60.050 61.111 0.00 0.00 41.09 3.82
620 630 2.554636 CGCCACCATTGTGTGTGCT 61.555 57.895 0.00 0.00 41.09 4.40
640 650 0.253160 TCAGGAGCCCATGGTAAGGT 60.253 55.000 11.73 0.17 0.00 3.50
652 674 5.515886 CCCATGGTAAGGTCCAAAACTAGAA 60.516 44.000 11.73 0.00 41.09 2.10
731 753 1.141053 AGACAAAGGAAACAGCGACCT 59.859 47.619 0.00 0.00 35.36 3.85
767 792 4.124351 CACGTAGCTCCCGCGGAA 62.124 66.667 30.73 4.60 42.32 4.30
802 827 2.972819 GCCACCCCCACTCCTCTTC 61.973 68.421 0.00 0.00 0.00 2.87
941 967 3.323115 GCAGATCAGTGATCCTACCATCA 59.677 47.826 26.14 0.00 39.66 3.07
943 969 5.722263 CAGATCAGTGATCCTACCATCATC 58.278 45.833 26.14 1.94 39.66 2.92
944 970 4.776837 AGATCAGTGATCCTACCATCATCC 59.223 45.833 26.14 0.95 39.66 3.51
945 971 4.204792 TCAGTGATCCTACCATCATCCT 57.795 45.455 0.00 0.00 35.23 3.24
946 972 4.560739 TCAGTGATCCTACCATCATCCTT 58.439 43.478 0.00 0.00 35.23 3.36
948 974 3.649981 AGTGATCCTACCATCATCCTTGG 59.350 47.826 0.00 0.00 40.26 3.61
949 975 2.373169 TGATCCTACCATCATCCTTGGC 59.627 50.000 0.00 0.00 37.81 4.52
950 976 0.758734 TCCTACCATCATCCTTGGCG 59.241 55.000 0.00 0.00 37.81 5.69
951 977 0.469917 CCTACCATCATCCTTGGCGT 59.530 55.000 0.00 0.00 37.81 5.68
952 978 1.134098 CCTACCATCATCCTTGGCGTT 60.134 52.381 0.00 0.00 37.81 4.84
953 979 2.213499 CTACCATCATCCTTGGCGTTC 58.787 52.381 0.00 0.00 37.81 3.95
954 980 0.327924 ACCATCATCCTTGGCGTTCA 59.672 50.000 0.00 0.00 37.81 3.18
1390 1428 0.110486 ACCTCACAATTCGGCCACTT 59.890 50.000 2.24 0.00 0.00 3.16
1427 1469 7.203910 CGACCAAGAAATATTAGTAGCAGAGT 58.796 38.462 0.00 0.00 0.00 3.24
1430 1472 8.145122 ACCAAGAAATATTAGTAGCAGAGTAGC 58.855 37.037 0.00 0.00 0.00 3.58
1431 1473 8.144478 CCAAGAAATATTAGTAGCAGAGTAGCA 58.856 37.037 0.00 0.00 36.85 3.49
1432 1474 9.703892 CAAGAAATATTAGTAGCAGAGTAGCAT 57.296 33.333 0.00 0.00 36.85 3.79
1457 1499 6.627243 ACTAGCATGTCGTTTATGAACAGTA 58.373 36.000 0.95 0.00 35.44 2.74
1469 1511 0.925466 GAACAGTACGTGCGTGTGTT 59.075 50.000 19.78 19.78 38.47 3.32
1690 1732 2.674220 CCCCAAGCTCCTCACTCCC 61.674 68.421 0.00 0.00 0.00 4.30
1821 1863 8.821147 TCCCATTAATTACATGTACGTGATAC 57.179 34.615 21.82 0.00 0.00 2.24
1822 1864 8.644216 TCCCATTAATTACATGTACGTGATACT 58.356 33.333 21.82 1.62 34.56 2.12
1823 1865 8.922676 CCCATTAATTACATGTACGTGATACTC 58.077 37.037 21.82 0.00 34.56 2.59
1824 1866 9.692749 CCATTAATTACATGTACGTGATACTCT 57.307 33.333 21.82 0.50 34.56 3.24
1892 1934 2.825836 CTGCTGGGCGTGGAATCC 60.826 66.667 0.00 0.00 0.00 3.01
1994 2036 4.498520 ACCGCGCACATCTCCGAG 62.499 66.667 8.75 0.00 0.00 4.63
2021 2063 3.093172 GAGCTTGGGAGGAGGGGG 61.093 72.222 0.00 0.00 0.00 5.40
2311 2353 9.866798 AGTTGTAGACTATATGCATCATACATG 57.133 33.333 0.19 0.00 36.65 3.21
2312 2354 9.645059 GTTGTAGACTATATGCATCATACATGT 57.355 33.333 0.19 2.69 0.00 3.21
2313 2355 9.643693 TTGTAGACTATATGCATCATACATGTG 57.356 33.333 9.11 0.00 0.00 3.21
2314 2356 8.806146 TGTAGACTATATGCATCATACATGTGT 58.194 33.333 9.11 0.00 0.00 3.72
2315 2357 9.080915 GTAGACTATATGCATCATACATGTGTG 57.919 37.037 15.88 15.88 0.00 3.82
2316 2358 7.674120 AGACTATATGCATCATACATGTGTGT 58.326 34.615 20.39 7.09 42.39 3.72
2317 2359 7.601508 AGACTATATGCATCATACATGTGTGTG 59.398 37.037 20.39 17.66 39.39 3.82
2318 2360 7.219322 ACTATATGCATCATACATGTGTGTGT 58.781 34.615 20.39 9.39 39.39 3.72
2319 2361 4.625972 ATGCATCATACATGTGTGTGTG 57.374 40.909 20.39 19.44 45.59 3.82
2320 2362 3.410508 TGCATCATACATGTGTGTGTGT 58.589 40.909 20.39 4.96 44.81 3.72
2321 2363 3.188873 TGCATCATACATGTGTGTGTGTG 59.811 43.478 20.39 15.47 44.81 3.82
2322 2364 3.189080 GCATCATACATGTGTGTGTGTGT 59.811 43.478 20.39 1.27 44.81 3.72
2323 2365 4.714851 CATCATACATGTGTGTGTGTGTG 58.285 43.478 20.39 8.71 44.81 3.82
2324 2366 3.802866 TCATACATGTGTGTGTGTGTGT 58.197 40.909 20.39 0.00 44.81 3.72
2325 2367 3.559242 TCATACATGTGTGTGTGTGTGTG 59.441 43.478 20.39 0.00 44.81 3.82
2497 2539 4.136796 CCACTGAGAACCATTGACTTTGA 58.863 43.478 0.00 0.00 0.00 2.69
2505 2547 2.375174 ACCATTGACTTTGAGGCCTACA 59.625 45.455 4.42 2.40 0.00 2.74
2621 2663 3.093172 CTCCAGCCTTCCTCCCCC 61.093 72.222 0.00 0.00 0.00 5.40
2687 2739 2.754375 GACGGGCCCTTCTTTCCA 59.246 61.111 22.43 0.00 0.00 3.53
2693 2745 2.391389 GCCCTTCTTTCCACGCTCG 61.391 63.158 0.00 0.00 0.00 5.03
2694 2746 1.004918 CCCTTCTTTCCACGCTCGT 60.005 57.895 0.00 0.00 0.00 4.18
2719 2773 2.281484 CACGGGGTTCTGTGGGTG 60.281 66.667 0.00 0.00 44.41 4.61
2720 2774 2.446994 ACGGGGTTCTGTGGGTGA 60.447 61.111 0.00 0.00 0.00 4.02
2721 2775 2.347490 CGGGGTTCTGTGGGTGAG 59.653 66.667 0.00 0.00 0.00 3.51
2722 2776 2.757077 GGGGTTCTGTGGGTGAGG 59.243 66.667 0.00 0.00 0.00 3.86
2723 2777 2.757077 GGGTTCTGTGGGTGAGGG 59.243 66.667 0.00 0.00 0.00 4.30
2724 2778 2.034221 GGTTCTGTGGGTGAGGGC 59.966 66.667 0.00 0.00 0.00 5.19
2725 2779 2.829384 GGTTCTGTGGGTGAGGGCA 61.829 63.158 0.00 0.00 0.00 5.36
2726 2780 1.600916 GTTCTGTGGGTGAGGGCAC 60.601 63.158 0.00 0.00 44.39 5.01
2727 2781 1.770110 TTCTGTGGGTGAGGGCACT 60.770 57.895 0.00 0.00 44.52 4.40
2740 2794 4.819761 GCACTCCTCATGCGGCGA 62.820 66.667 12.98 0.00 32.45 5.54
2924 2991 2.016393 CTCCTTCGGCCGATGTGCTA 62.016 60.000 31.56 12.27 0.00 3.49
2927 2994 0.739462 CTTCGGCCGATGTGCTACAA 60.739 55.000 31.56 9.71 0.00 2.41
2929 2996 1.739929 CGGCCGATGTGCTACAACA 60.740 57.895 24.07 0.00 0.00 3.33
2932 2999 1.368641 GCCGATGTGCTACAACATGA 58.631 50.000 0.00 0.00 40.87 3.07
2933 3000 1.942657 GCCGATGTGCTACAACATGAT 59.057 47.619 0.00 0.00 40.87 2.45
2992 3059 1.002502 GTTCGGGCCTGGTAAGCTT 60.003 57.895 12.87 3.48 0.00 3.74
3016 3083 2.362503 TCATGTCCGGTCGGCTCT 60.363 61.111 0.00 0.00 34.68 4.09
3121 3188 3.311110 GTGTCGGTGGCCTCAGGA 61.311 66.667 3.32 0.00 0.00 3.86
3125 3192 1.306141 TCGGTGGCCTCAGGAAGAT 60.306 57.895 3.32 0.00 0.00 2.40
3131 3198 0.103937 GGCCTCAGGAAGATGACGAG 59.896 60.000 0.00 0.00 0.00 4.18
3190 3257 0.466189 CAGGTCTGGTGGTGCACTTT 60.466 55.000 17.98 0.00 34.40 2.66
3191 3258 0.466189 AGGTCTGGTGGTGCACTTTG 60.466 55.000 17.98 3.36 34.40 2.77
3192 3259 0.465460 GGTCTGGTGGTGCACTTTGA 60.465 55.000 17.98 5.71 34.40 2.69
3200 3267 0.521735 GGTGCACTTTGAATCGTCCC 59.478 55.000 17.98 0.00 0.00 4.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 8.854979 TGTACAAAAAGTGTTGATGATTCAAG 57.145 30.769 0.00 0.00 42.41 3.02
24 25 7.356540 TCGGTCATATTGTACAAAAAGTGTTG 58.643 34.615 13.23 3.41 41.98 3.33
25 26 7.499321 TCGGTCATATTGTACAAAAAGTGTT 57.501 32.000 13.23 0.00 41.98 3.32
34 35 9.256477 GAGATTACATTTCGGTCATATTGTACA 57.744 33.333 0.00 0.00 0.00 2.90
37 38 6.073765 GCGAGATTACATTTCGGTCATATTGT 60.074 38.462 0.00 0.00 35.05 2.71
42 43 3.131396 GGCGAGATTACATTTCGGTCAT 58.869 45.455 0.00 0.00 35.05 3.06
48 49 2.919228 AGGGTGGCGAGATTACATTTC 58.081 47.619 0.00 0.00 0.00 2.17
62 63 2.038659 ACCAAAATGTCACAAGGGTGG 58.961 47.619 0.00 0.00 45.32 4.61
99 100 5.424121 ACTTCAAAATCTCACCGAAACAG 57.576 39.130 0.00 0.00 0.00 3.16
103 104 6.486657 AGATCAAACTTCAAAATCTCACCGAA 59.513 34.615 0.00 0.00 0.00 4.30
104 105 5.997746 AGATCAAACTTCAAAATCTCACCGA 59.002 36.000 0.00 0.00 0.00 4.69
105 106 6.246420 AGATCAAACTTCAAAATCTCACCG 57.754 37.500 0.00 0.00 0.00 4.94
106 107 9.965824 TTAAAGATCAAACTTCAAAATCTCACC 57.034 29.630 0.00 0.00 0.00 4.02
111 112 9.965824 TGTCCTTAAAGATCAAACTTCAAAATC 57.034 29.630 0.00 0.00 0.00 2.17
241 242 1.327303 TTCACCATGGAAAGTGCACC 58.673 50.000 21.47 0.00 33.90 5.01
267 268 9.330063 TGATTAATAGGTCATGTCAGTTGAATC 57.670 33.333 0.00 0.00 0.00 2.52
321 322 9.590828 TTAGGGCTTATTTGGTTTACTAGTTTT 57.409 29.630 0.00 0.00 0.00 2.43
335 336 4.461198 CATTCGTCCCTTAGGGCTTATTT 58.539 43.478 13.54 0.00 43.94 1.40
387 388 5.633117 AGTGTATAACTTTTCCCCCGAAAA 58.367 37.500 0.00 0.00 43.97 2.29
453 454 9.726438 AAACTATTAGCATGATGTAATACCTCC 57.274 33.333 0.00 0.00 0.00 4.30
460 461 9.679661 TGAAAGGAAACTATTAGCATGATGTAA 57.320 29.630 0.00 0.00 42.68 2.41
461 462 9.679661 TTGAAAGGAAACTATTAGCATGATGTA 57.320 29.630 0.00 0.00 42.68 2.29
462 463 8.579850 TTGAAAGGAAACTATTAGCATGATGT 57.420 30.769 0.00 0.00 42.68 3.06
476 477 2.952310 AGGACAGTGCTTGAAAGGAAAC 59.048 45.455 0.00 0.00 0.00 2.78
484 485 3.455910 AGGCATTATAGGACAGTGCTTGA 59.544 43.478 0.00 0.00 36.15 3.02
533 541 4.837972 CTCAGAAAGAAAGGTAGGAAGGG 58.162 47.826 0.00 0.00 0.00 3.95
534 542 4.257731 GCTCAGAAAGAAAGGTAGGAAGG 58.742 47.826 0.00 0.00 0.00 3.46
535 543 3.929610 CGCTCAGAAAGAAAGGTAGGAAG 59.070 47.826 0.00 0.00 0.00 3.46
536 544 3.864921 GCGCTCAGAAAGAAAGGTAGGAA 60.865 47.826 0.00 0.00 0.00 3.36
537 545 2.353803 GCGCTCAGAAAGAAAGGTAGGA 60.354 50.000 0.00 0.00 0.00 2.94
538 546 2.003301 GCGCTCAGAAAGAAAGGTAGG 58.997 52.381 0.00 0.00 0.00 3.18
539 547 2.413453 GTGCGCTCAGAAAGAAAGGTAG 59.587 50.000 9.73 0.00 0.00 3.18
540 548 2.224185 TGTGCGCTCAGAAAGAAAGGTA 60.224 45.455 9.73 0.00 0.00 3.08
541 549 1.230324 GTGCGCTCAGAAAGAAAGGT 58.770 50.000 9.73 0.00 0.00 3.50
542 550 1.229428 TGTGCGCTCAGAAAGAAAGG 58.771 50.000 9.73 0.00 0.00 3.11
543 551 2.473540 CGATGTGCGCTCAGAAAGAAAG 60.474 50.000 17.93 0.00 0.00 2.62
544 552 1.460743 CGATGTGCGCTCAGAAAGAAA 59.539 47.619 17.93 0.00 0.00 2.52
620 630 0.918983 CCTTACCATGGGCTCCTGAA 59.081 55.000 18.09 0.00 0.00 3.02
632 642 6.544564 CAGTTTTCTAGTTTTGGACCTTACCA 59.455 38.462 0.00 0.00 38.24 3.25
640 650 5.189928 TCTGTGCAGTTTTCTAGTTTTGGA 58.810 37.500 0.00 0.00 0.00 3.53
652 674 2.486203 TGTGACGTTTTCTGTGCAGTTT 59.514 40.909 0.00 0.00 0.00 2.66
941 967 1.534729 GGAGTTTGAACGCCAAGGAT 58.465 50.000 11.13 0.00 46.56 3.24
948 974 0.234884 CGAGTTGGGAGTTTGAACGC 59.765 55.000 0.00 0.00 0.00 4.84
949 975 1.260561 CACGAGTTGGGAGTTTGAACG 59.739 52.381 0.00 0.00 0.00 3.95
950 976 2.557317 TCACGAGTTGGGAGTTTGAAC 58.443 47.619 0.00 0.00 0.00 3.18
951 977 2.992124 TCACGAGTTGGGAGTTTGAA 57.008 45.000 0.00 0.00 0.00 2.69
952 978 2.367241 TGATCACGAGTTGGGAGTTTGA 59.633 45.455 0.00 0.00 0.00 2.69
953 979 2.766313 TGATCACGAGTTGGGAGTTTG 58.234 47.619 0.00 0.00 0.00 2.93
954 980 3.703001 ATGATCACGAGTTGGGAGTTT 57.297 42.857 0.00 0.00 0.00 2.66
1427 1469 6.977213 TCATAAACGACATGCTAGTATGCTA 58.023 36.000 19.44 5.46 0.00 3.49
1430 1472 7.222805 ACTGTTCATAAACGACATGCTAGTATG 59.777 37.037 18.12 18.12 38.28 2.39
1431 1473 7.265673 ACTGTTCATAAACGACATGCTAGTAT 58.734 34.615 0.00 0.00 38.28 2.12
1432 1474 6.627243 ACTGTTCATAAACGACATGCTAGTA 58.373 36.000 0.00 0.00 38.28 1.82
1433 1475 5.479306 ACTGTTCATAAACGACATGCTAGT 58.521 37.500 0.00 0.00 38.28 2.57
1434 1476 6.291112 CGTACTGTTCATAAACGACATGCTAG 60.291 42.308 0.00 0.00 38.28 3.42
1457 1499 2.099446 GCACAAACACACGCACGT 59.901 55.556 0.00 0.00 0.00 4.49
1469 1511 2.334946 GCTTGATCGCCCTGCACAA 61.335 57.895 0.00 0.00 0.00 3.33
1648 1690 4.189188 CCGACGTAGCCGGTCAGG 62.189 72.222 1.90 0.00 41.91 3.86
1690 1732 0.974010 TACGTACCCTTCTGGCCTGG 60.974 60.000 10.07 3.85 37.83 4.45
1821 1863 8.851416 CACAGAAGTACGACAAGTTAATTAGAG 58.149 37.037 0.00 0.00 0.00 2.43
1822 1864 8.570488 TCACAGAAGTACGACAAGTTAATTAGA 58.430 33.333 0.00 0.00 0.00 2.10
1823 1865 8.738199 TCACAGAAGTACGACAAGTTAATTAG 57.262 34.615 0.00 0.00 0.00 1.73
1824 1866 9.701098 AATCACAGAAGTACGACAAGTTAATTA 57.299 29.630 0.00 0.00 0.00 1.40
1825 1867 8.495949 CAATCACAGAAGTACGACAAGTTAATT 58.504 33.333 0.00 0.00 0.00 1.40
1920 1962 2.577112 CAGTCCGCGCTCGTACAG 60.577 66.667 5.56 0.00 0.00 2.74
1994 2036 3.793144 CCAAGCTCGTTCCGCAGC 61.793 66.667 0.00 0.00 35.73 5.25
2021 2063 1.677637 CTAGCCCCTCGTCCTTCACC 61.678 65.000 0.00 0.00 0.00 4.02
2183 2225 2.751837 GCGCCCTGGGGAAAGAAG 60.752 66.667 16.03 0.00 37.50 2.85
2310 2352 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2311 2353 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2312 2354 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2313 2355 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2314 2356 1.152510 GACACACACACACACACACA 58.847 50.000 0.00 0.00 0.00 3.72
2315 2357 1.438651 AGACACACACACACACACAC 58.561 50.000 0.00 0.00 0.00 3.82
2316 2358 1.803555 CAAGACACACACACACACACA 59.196 47.619 0.00 0.00 0.00 3.72
2317 2359 1.804151 ACAAGACACACACACACACAC 59.196 47.619 0.00 0.00 0.00 3.82
2318 2360 2.073056 GACAAGACACACACACACACA 58.927 47.619 0.00 0.00 0.00 3.72
2319 2361 1.396996 GGACAAGACACACACACACAC 59.603 52.381 0.00 0.00 0.00 3.82
2320 2362 1.277842 AGGACAAGACACACACACACA 59.722 47.619 0.00 0.00 0.00 3.72
2321 2363 2.024176 AGGACAAGACACACACACAC 57.976 50.000 0.00 0.00 0.00 3.82
2322 2364 2.779755 AAGGACAAGACACACACACA 57.220 45.000 0.00 0.00 0.00 3.72
2323 2365 3.498397 CCATAAGGACAAGACACACACAC 59.502 47.826 0.00 0.00 36.89 3.82
2324 2366 3.389656 TCCATAAGGACAAGACACACACA 59.610 43.478 0.00 0.00 39.61 3.72
2325 2367 4.002906 TCCATAAGGACAAGACACACAC 57.997 45.455 0.00 0.00 39.61 3.82
2485 2527 3.071874 TGTAGGCCTCAAAGTCAATGG 57.928 47.619 9.68 0.00 0.00 3.16
2497 2539 7.037730 AGCTGAATATCTTCATAATGTAGGCCT 60.038 37.037 11.78 11.78 40.52 5.19
2505 2547 9.638176 AAAACCTCAGCTGAATATCTTCATAAT 57.362 29.630 18.85 0.00 40.52 1.28
2594 2636 3.151022 GGCTGGAGGAGAGGACGG 61.151 72.222 0.00 0.00 0.00 4.79
2673 2725 3.062466 GCGTGGAAAGAAGGGCCC 61.062 66.667 16.46 16.46 0.00 5.80
2674 2726 2.034221 AGCGTGGAAAGAAGGGCC 59.966 61.111 0.00 0.00 0.00 5.80
2703 2757 2.446994 TCACCCACAGAACCCCGT 60.447 61.111 0.00 0.00 0.00 5.28
2708 2762 1.600916 GTGCCCTCACCCACAGAAC 60.601 63.158 0.00 0.00 37.24 3.01
2709 2763 1.768684 GAGTGCCCTCACCCACAGAA 61.769 60.000 0.00 0.00 44.16 3.02
2710 2764 2.122413 AGTGCCCTCACCCACAGA 60.122 61.111 0.00 0.00 44.16 3.41
2711 2765 2.348998 GAGTGCCCTCACCCACAG 59.651 66.667 0.00 0.00 44.16 3.66
2712 2766 3.249189 GGAGTGCCCTCACCCACA 61.249 66.667 0.00 0.00 44.16 4.17
2713 2767 2.930562 AGGAGTGCCCTCACCCAC 60.931 66.667 0.00 0.00 43.31 4.61
2723 2777 4.819761 TCGCCGCATGAGGAGTGC 62.820 66.667 20.86 2.32 39.18 4.40
2724 2778 2.887568 GTCGCCGCATGAGGAGTG 60.888 66.667 20.86 8.02 32.66 3.51
2725 2779 4.498520 CGTCGCCGCATGAGGAGT 62.499 66.667 20.86 0.00 32.66 3.85
2726 2780 4.498520 ACGTCGCCGCATGAGGAG 62.499 66.667 20.86 16.79 37.70 3.69
2727 2781 4.794439 CACGTCGCCGCATGAGGA 62.794 66.667 20.86 0.00 37.70 3.71
2796 2850 1.626356 AAAGGGCCTAGATCTGCGCA 61.626 55.000 19.88 10.98 42.32 6.09
2799 2853 1.685148 CCAAAAGGGCCTAGATCTGC 58.315 55.000 6.41 0.23 0.00 4.26
2909 2976 1.017177 GTTGTAGCACATCGGCCGAA 61.017 55.000 34.66 16.30 0.00 4.30
2918 2985 2.086094 CTGCCATCATGTTGTAGCACA 58.914 47.619 3.19 0.00 0.00 4.57
2924 2991 0.114954 AACCCCTGCCATCATGTTGT 59.885 50.000 3.19 0.00 0.00 3.32
2927 2994 0.323725 GACAACCCCTGCCATCATGT 60.324 55.000 0.00 0.00 0.00 3.21
2929 2996 1.307647 GGACAACCCCTGCCATCAT 59.692 57.895 0.00 0.00 0.00 2.45
2932 2999 4.047125 CCGGACAACCCCTGCCAT 62.047 66.667 0.00 0.00 0.00 4.40
2976 3043 1.612442 AGAAGCTTACCAGGCCCGA 60.612 57.895 0.00 0.00 0.00 5.14
2992 3059 1.880894 GACCGGACATGACGACAGA 59.119 57.895 9.46 0.00 0.00 3.41
3073 3140 3.379445 GGGACGAGGAGCCAACGA 61.379 66.667 11.65 0.00 0.00 3.85
3121 3188 1.337823 CCGAACCAACCTCGTCATCTT 60.338 52.381 0.00 0.00 34.46 2.40
3125 3192 1.068417 CACCGAACCAACCTCGTCA 59.932 57.895 0.00 0.00 34.46 4.35
3147 3214 1.186917 CCACCAACATGTGCCACCAT 61.187 55.000 0.00 0.00 34.85 3.55
3200 3267 1.758906 AAACCCAAACCACCACCCG 60.759 57.895 0.00 0.00 0.00 5.28


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

AutoCloner maintained by Alex Coulton.