Multiple sequence alignment - TraesCS2A01G371800

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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 TraesCS2A01G371800 chr2A 100.000 7138 0 0 1 7138 614000558 613993421 0.000000e+00 13182
1 TraesCS2A01G371800 chr2D 95.960 6436 155 43 780 7138 472478822 472472415 0.000000e+00 10347
2 TraesCS2A01G371800 chr2D 87.897 661 61 17 1 647 472481688 472481033 0.000000e+00 760
3 TraesCS2A01G371800 chr2B 94.227 3482 105 24 3678 7138 551643177 551639771 0.000000e+00 5228
4 TraesCS2A01G371800 chr2B 93.481 2838 108 38 28 2827 551647146 551644348 0.000000e+00 4145
5 TraesCS2A01G371800 chr2B 96.468 821 13 2 2889 3694 551644357 551643538 0.000000e+00 1341
6 TraesCS2A01G371800 chr7A 81.324 680 76 32 4731 5382 726602281 726601625 8.260000e-139 505
7 TraesCS2A01G371800 chr5D 81.796 412 64 10 4539 4946 208539713 208539309 1.150000e-87 335
8 TraesCS2A01G371800 chr5D 91.549 71 6 0 5312 5382 484657360 484657290 1.640000e-16 99
9 TraesCS2A01G371800 chr3A 80.230 435 73 12 4539 4967 745552497 745552924 1.490000e-81 315
10 TraesCS2A01G371800 chr5A 80.583 412 69 10 4539 4946 3456764 3456360 2.500000e-79 307
11 TraesCS2A01G371800 chr7B 91.549 71 6 0 5312 5382 102760785 102760715 1.640000e-16 99
12 TraesCS2A01G371800 chr6B 91.549 71 6 0 5312 5382 623362621 623362551 1.640000e-16 99


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 TraesCS2A01G371800 chr2A 613993421 614000558 7137 True 13182.000000 13182 100.000000 1 7138 1 chr2A.!!$R1 7137
1 TraesCS2A01G371800 chr2D 472472415 472481688 9273 True 5553.500000 10347 91.928500 1 7138 2 chr2D.!!$R1 7137
2 TraesCS2A01G371800 chr2B 551639771 551647146 7375 True 3571.333333 5228 94.725333 28 7138 3 chr2B.!!$R1 7110
3 TraesCS2A01G371800 chr7A 726601625 726602281 656 True 505.000000 505 81.324000 4731 5382 1 chr7A.!!$R1 651

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
282 285 0.037697 TCTACATGCGCCGACTTGTT 60.038 50.000 4.18 0.0 0.00 2.83 F
863 3070 0.179048 TTATGATCACCGCAGCCCAG 60.179 55.000 0.00 0.0 0.00 4.45 F
894 3101 0.853530 AGAGTTGGGCTTTTGAGGGT 59.146 50.000 0.00 0.0 0.00 4.34 F
1187 3407 0.981943 AACTACTCCAAACCCTCCCG 59.018 55.000 0.00 0.0 0.00 5.14 F
1272 3500 1.273666 ACGGGGGTCCTAGATTCAAGT 60.274 52.381 0.00 0.0 0.00 3.16 F
2667 4908 0.104120 CACGTCAGGACACTGTGGAA 59.896 55.000 13.09 0.0 45.14 3.53 F
3391 5647 1.338020 CTTCGGGTTTCTTTGCTTGCT 59.662 47.619 0.00 0.0 0.00 3.91 F
4161 6794 1.974028 TTGCCCTTCTATGGTACCCA 58.026 50.000 10.07 0.0 38.19 4.51 F
5221 7882 1.073763 CATTGGACTGAAGTGGGACCA 59.926 52.381 0.00 0.0 0.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1211 3431 1.345415 GTTCCTACGGTCCCAACTCAA 59.655 52.381 0.00 0.00 0.00 3.02 R
2267 4508 1.549037 GCACCCTTTCCCCATAACACA 60.549 52.381 0.00 0.00 0.00 3.72 R
2599 4840 1.562008 TGGTGTGTTCAAGTTCCTCCA 59.438 47.619 0.00 0.00 0.00 3.86 R
2667 4908 2.045438 TCAATCCGGCGTGCCAAT 60.045 55.556 12.06 0.68 35.37 3.16 R
3084 5340 3.826729 AGGCTGACATAAGGAAAACAACC 59.173 43.478 0.00 0.00 0.00 3.77 R
4250 6883 1.795170 ATCCAGCGGCACACACAAAC 61.795 55.000 1.45 0.00 0.00 2.93 R
4270 6903 2.050691 GCTGCCAAAATACACACAACG 58.949 47.619 0.00 0.00 0.00 4.10 R
5413 8075 2.071778 AAGCCTTGCTGTCTTTTCCA 57.928 45.000 0.00 0.00 39.62 3.53 R
6856 9576 0.394899 GATCTCCCACCCCAGCTTTG 60.395 60.000 0.00 0.00 0.00 2.77 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
21 22 4.314440 TGTCGTCTGGCCAGGCAC 62.314 66.667 35.25 29.04 31.14 5.01
22 23 4.008933 GTCGTCTGGCCAGGCACT 62.009 66.667 35.25 0.00 43.88 4.40
23 24 2.283604 TCGTCTGGCCAGGCACTA 60.284 61.111 35.25 18.31 36.02 2.74
24 25 2.185350 CGTCTGGCCAGGCACTAG 59.815 66.667 35.25 16.59 36.02 2.57
25 26 2.124942 GTCTGGCCAGGCACTAGC 60.125 66.667 32.45 10.11 43.86 3.42
26 27 2.284921 TCTGGCCAGGCACTAGCT 60.285 61.111 32.23 0.00 44.10 3.32
108 109 4.824537 TGGAACAAAATTCTCAACCATCGA 59.175 37.500 0.00 0.00 31.92 3.59
170 173 2.642982 TCCTCTTCCCTTTTGGATGGA 58.357 47.619 0.00 0.00 44.66 3.41
198 201 8.945481 AACATGAACATGAAAACATTTTCTCA 57.055 26.923 19.56 11.94 45.14 3.27
216 219 8.737168 TTTTCTCACATATCCTTACAATCCAG 57.263 34.615 0.00 0.00 0.00 3.86
241 244 0.182537 TCAGTGGACACCAAACCCTG 59.817 55.000 0.00 0.00 34.18 4.45
282 285 0.037697 TCTACATGCGCCGACTTGTT 60.038 50.000 4.18 0.00 0.00 2.83
283 286 0.370273 CTACATGCGCCGACTTGTTC 59.630 55.000 4.18 0.00 0.00 3.18
307 310 5.349817 CGAGATGAGTTTTGCTATGACTTGT 59.650 40.000 0.00 0.00 0.00 3.16
314 317 2.391616 TGCTATGACTTGTGGCTCAG 57.608 50.000 0.00 0.00 0.00 3.35
353 356 3.878519 CCCGCCTCTCGAGACGAC 61.879 72.222 22.69 10.04 41.67 4.34
361 364 4.405671 TCGAGACGACCGCCCTCT 62.406 66.667 0.00 0.00 0.00 3.69
365 368 3.519930 GACGACCGCCCTCTCCTC 61.520 72.222 0.00 0.00 0.00 3.71
371 374 2.506061 CCGCCCTCTCCTCCATCTG 61.506 68.421 0.00 0.00 0.00 2.90
372 375 1.456518 CGCCCTCTCCTCCATCTGA 60.457 63.158 0.00 0.00 0.00 3.27
374 377 0.689080 GCCCTCTCCTCCATCTGACA 60.689 60.000 0.00 0.00 0.00 3.58
376 379 1.484240 CCCTCTCCTCCATCTGACAAC 59.516 57.143 0.00 0.00 0.00 3.32
377 380 2.465813 CCTCTCCTCCATCTGACAACT 58.534 52.381 0.00 0.00 0.00 3.16
393 407 5.116180 TGACAACTTCAACTCTTCGTCAAT 58.884 37.500 0.00 0.00 0.00 2.57
429 443 1.661463 TGATCCTCTCTGGCCTTTGT 58.339 50.000 3.32 0.00 35.26 2.83
430 444 1.988107 TGATCCTCTCTGGCCTTTGTT 59.012 47.619 3.32 0.00 35.26 2.83
470 484 2.154462 CTAGGGTTGAAAGCAGTGGTG 58.846 52.381 0.00 0.00 0.00 4.17
508 522 2.923655 AGCACACACGAAATGTCTATCG 59.076 45.455 0.00 0.00 40.64 2.92
554 568 3.284793 ACTAGACTGTAGACTCGGCAT 57.715 47.619 0.00 0.00 0.00 4.40
641 656 2.038033 CCTTAACGGAGAGAACCAACCA 59.962 50.000 0.00 0.00 33.16 3.67
672 2850 0.611062 ACACGAGGGATCGACCTTGA 60.611 55.000 14.70 0.00 43.58 3.02
756 2958 6.421801 CACAATTTGCTCTAAAAGAAACCAGG 59.578 38.462 0.00 0.00 0.00 4.45
757 2959 4.584327 TTTGCTCTAAAAGAAACCAGGC 57.416 40.909 0.00 0.00 0.00 4.85
758 2960 3.508845 TGCTCTAAAAGAAACCAGGCT 57.491 42.857 0.00 0.00 0.00 4.58
759 2961 3.832527 TGCTCTAAAAGAAACCAGGCTT 58.167 40.909 0.00 0.00 0.00 4.35
760 2962 3.821033 TGCTCTAAAAGAAACCAGGCTTC 59.179 43.478 0.00 0.00 0.00 3.86
761 2963 4.075682 GCTCTAAAAGAAACCAGGCTTCT 58.924 43.478 0.00 0.00 34.56 2.85
762 2964 4.520874 GCTCTAAAAGAAACCAGGCTTCTT 59.479 41.667 11.55 11.55 43.38 2.52
863 3070 0.179048 TTATGATCACCGCAGCCCAG 60.179 55.000 0.00 0.00 0.00 4.45
894 3101 0.853530 AGAGTTGGGCTTTTGAGGGT 59.146 50.000 0.00 0.00 0.00 4.34
1060 3267 2.747443 GGGGTAGCAAGGAGAGGGC 61.747 68.421 0.00 0.00 0.00 5.19
1187 3407 0.981943 AACTACTCCAAACCCTCCCG 59.018 55.000 0.00 0.00 0.00 5.14
1272 3500 1.273666 ACGGGGGTCCTAGATTCAAGT 60.274 52.381 0.00 0.00 0.00 3.16
1276 3504 2.701423 GGGGTCCTAGATTCAAGTCTCC 59.299 54.545 0.00 0.00 0.00 3.71
1422 3659 3.447586 TCTCTTGTAGTCGGAAATCAGGG 59.552 47.826 0.00 0.00 0.00 4.45
1600 3840 6.889177 TCCTTGCCACATATTTCTTCAACATA 59.111 34.615 0.00 0.00 0.00 2.29
1601 3841 7.395772 TCCTTGCCACATATTTCTTCAACATAA 59.604 33.333 0.00 0.00 0.00 1.90
1602 3842 8.034215 CCTTGCCACATATTTCTTCAACATAAA 58.966 33.333 0.00 0.00 0.00 1.40
1909 4149 6.896883 TCTGAGATGATTCTTGGATGTGATT 58.103 36.000 0.00 0.00 30.30 2.57
1997 4238 3.634910 ACAACTTAACGCCACTGGATTTT 59.365 39.130 0.00 0.00 0.00 1.82
2267 4508 4.755123 ACAGCGAATAACTTAAAGTGCACT 59.245 37.500 15.25 15.25 0.00 4.40
2550 4791 7.907214 ACTTTCATGCCTTGTACTTTACTAG 57.093 36.000 0.00 0.00 0.00 2.57
2592 4833 9.034544 GCAAATTATTCCATGTAGATTTTGACC 57.965 33.333 9.41 0.00 0.00 4.02
2599 4840 6.009589 TCCATGTAGATTTTGACCACATTGT 58.990 36.000 0.00 0.00 0.00 2.71
2667 4908 0.104120 CACGTCAGGACACTGTGGAA 59.896 55.000 13.09 0.00 45.14 3.53
2833 5074 3.302365 AACACCCAAGATTGCAAATCG 57.698 42.857 1.71 0.00 0.00 3.34
2872 5113 1.774110 ATGCATGGCCATTCGGTTTA 58.226 45.000 17.92 0.00 33.28 2.01
2885 5126 8.192110 GGCCATTCGGTTTATTAGAATTTTGTA 58.808 33.333 0.00 0.00 32.87 2.41
3000 5256 9.719355 GATTTACTTTGTAATCCATTGGGTTTT 57.281 29.630 6.50 0.00 34.93 2.43
3084 5340 4.372656 GACCCTAGGATCATTTTCGAGTG 58.627 47.826 11.48 0.00 0.00 3.51
3391 5647 1.338020 CTTCGGGTTTCTTTGCTTGCT 59.662 47.619 0.00 0.00 0.00 3.91
4161 6794 1.974028 TTGCCCTTCTATGGTACCCA 58.026 50.000 10.07 0.00 38.19 4.51
4250 6883 4.141892 TGCAAGATGCCATTTTTCATAGGG 60.142 41.667 0.00 0.00 44.23 3.53
4270 6903 1.514678 TTTGTGTGTGCCGCTGGATC 61.515 55.000 0.00 0.00 0.00 3.36
4620 7253 2.821437 TCCTCCCTTACTGTCTCCTTG 58.179 52.381 0.00 0.00 0.00 3.61
4703 7336 3.258123 TGGTAGCCTTGAAATTGCCTTTC 59.742 43.478 2.70 2.70 43.05 2.62
5068 7728 3.673746 TTGCGTTGTTGAAGTTCTCTG 57.326 42.857 4.17 0.00 0.00 3.35
5208 7869 4.275936 GTCTGTATGGGTTATGCATTGGAC 59.724 45.833 3.54 1.53 30.73 4.02
5221 7882 1.073763 CATTGGACTGAAGTGGGACCA 59.926 52.381 0.00 0.00 0.00 4.02
5413 8075 6.312672 AGTTGCAACTTCGTAAAAATTGCTTT 59.687 30.769 26.36 0.00 44.69 3.51
5714 8381 3.674997 TGTTTTCTCCGGAGATCTTTGG 58.325 45.455 33.97 5.80 37.29 3.28
5782 8449 0.032403 GCTTTTGCACTGTGCCATCA 59.968 50.000 28.17 8.38 44.23 3.07
6030 8700 0.543277 TTCTGCCAATCTGGATCGCT 59.457 50.000 0.00 0.00 40.96 4.93
6085 8755 6.588719 TCATGTTATTTGGGAAGTTCAAGG 57.411 37.500 5.01 0.00 0.00 3.61
6234 8904 5.194432 TGTGTGGGTTTGTACTTTGTACAT 58.806 37.500 10.75 0.00 0.00 2.29
6295 8965 2.227194 CTACGGCCTTGGTTTTGTTCT 58.773 47.619 0.00 0.00 0.00 3.01
6299 8969 2.560504 GGCCTTGGTTTTGTTCTTTGG 58.439 47.619 0.00 0.00 0.00 3.28
6421 9095 5.405797 CGTGACATCATAGACCATATGAGG 58.594 45.833 3.65 7.72 40.38 3.86
6450 9124 6.620877 TGCTATTTCTTCTGGAAGGACTTA 57.379 37.500 10.01 0.00 38.88 2.24
6457 9131 9.620259 ATTTCTTCTGGAAGGACTTATTGATAC 57.380 33.333 10.01 0.00 38.88 2.24
6571 9251 5.741673 GCAATGCTTTCTTCTTTGGGGTAAA 60.742 40.000 0.00 0.00 0.00 2.01
6597 9277 8.984891 TCAAACCAATTTTACTGAGCAATATG 57.015 30.769 0.00 0.00 0.00 1.78
6613 9293 9.932207 TGAGCAATATGTTTTTCATCAAAAGAT 57.068 25.926 0.00 0.00 40.54 2.40
6656 9336 9.939802 AGAAAGAGAGTAAACCATATTTACGTT 57.060 29.630 0.00 0.00 39.25 3.99
6738 9444 1.212688 CTGGATCTTGTGGCATGGGTA 59.787 52.381 0.00 0.00 0.00 3.69
6768 9474 1.335496 GTCAGCCGTCAGGATCTCTAC 59.665 57.143 0.00 0.00 41.02 2.59
6769 9475 1.213182 TCAGCCGTCAGGATCTCTACT 59.787 52.381 0.00 0.00 41.02 2.57
6770 9476 2.438392 TCAGCCGTCAGGATCTCTACTA 59.562 50.000 0.00 0.00 41.02 1.82
6771 9477 2.550606 CAGCCGTCAGGATCTCTACTAC 59.449 54.545 0.00 0.00 41.02 2.73
6772 9478 2.440253 AGCCGTCAGGATCTCTACTACT 59.560 50.000 0.00 0.00 41.02 2.57
6773 9479 2.809696 GCCGTCAGGATCTCTACTACTC 59.190 54.545 0.00 0.00 41.02 2.59
6854 9574 7.819900 CAGAAACTCCTAGCACTACATTAGTTT 59.180 37.037 0.00 0.00 38.31 2.66
6856 9576 8.999220 AAACTCCTAGCACTACATTAGTTTAC 57.001 34.615 0.00 0.00 36.76 2.01
6860 9580 8.997621 TCCTAGCACTACATTAGTTTACAAAG 57.002 34.615 0.00 0.00 36.76 2.77
6891 9611 4.972514 GAGATCAAACACCCAAATCTCC 57.027 45.455 0.00 0.00 37.47 3.71
6924 9645 8.363390 TGGTCTGTAATATCTCATCTGAACATC 58.637 37.037 0.00 0.00 0.00 3.06
6984 9705 6.819397 TCAGGTTATCGATCCATGTACTAG 57.181 41.667 0.00 0.00 0.00 2.57
6985 9706 6.304624 TCAGGTTATCGATCCATGTACTAGT 58.695 40.000 0.00 0.00 0.00 2.57
7018 9739 0.106149 ACTCACCCGGTTCTGAACAC 59.894 55.000 21.01 10.18 0.00 3.32
7020 9741 0.542333 TCACCCGGTTCTGAACACAA 59.458 50.000 21.01 0.00 0.00 3.33
7023 9744 0.306533 CCCGGTTCTGAACACAAACG 59.693 55.000 21.01 14.24 0.00 3.60
7028 9749 3.966218 CGGTTCTGAACACAAACGAAATC 59.034 43.478 21.01 0.00 0.00 2.17
7061 9782 2.917971 GCAGACAGCAGTTCTAGTTACG 59.082 50.000 0.00 0.00 44.79 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 2.283604 TAGTGCCTGGCCAGACGA 60.284 61.111 34.91 18.27 0.00 4.20
9 10 1.001631 TAGCTAGTGCCTGGCCAGA 59.998 57.895 34.91 12.85 38.77 3.86
13 14 4.844420 CACTAGCTAGTGCCTGGC 57.156 61.111 34.51 12.87 46.03 4.85
83 84 6.015519 TCGATGGTTGAGAATTTTGTTCCAAT 60.016 34.615 0.00 0.00 0.00 3.16
85 86 4.824537 TCGATGGTTGAGAATTTTGTTCCA 59.175 37.500 0.00 0.00 0.00 3.53
108 109 2.158081 TGGGAATTTGGTAAGGCCCTTT 60.158 45.455 0.00 0.00 33.73 3.11
163 164 3.266513 TCATGTTCATGTTCCTCCATCCA 59.733 43.478 11.73 0.00 0.00 3.41
198 201 3.074538 GGGCCTGGATTGTAAGGATATGT 59.925 47.826 0.84 0.00 35.40 2.29
216 219 2.034221 GGTGTCCACTGAAGGGCC 59.966 66.667 0.00 0.00 30.21 5.80
254 257 0.598680 GCGCATGTAGAGGCACTAGG 60.599 60.000 0.30 0.00 41.55 3.02
282 285 5.330455 AGTCATAGCAAAACTCATCTCGA 57.670 39.130 0.00 0.00 0.00 4.04
283 286 5.349817 ACAAGTCATAGCAAAACTCATCTCG 59.650 40.000 0.00 0.00 0.00 4.04
353 356 2.123077 AGATGGAGGAGAGGGCGG 60.123 66.667 0.00 0.00 0.00 6.13
361 364 3.648067 AGTTGAAGTTGTCAGATGGAGGA 59.352 43.478 0.00 0.00 37.61 3.71
365 368 4.151335 CGAAGAGTTGAAGTTGTCAGATGG 59.849 45.833 0.00 0.00 37.61 3.51
366 369 4.747108 ACGAAGAGTTGAAGTTGTCAGATG 59.253 41.667 0.00 0.00 37.61 2.90
367 370 4.950050 ACGAAGAGTTGAAGTTGTCAGAT 58.050 39.130 0.00 0.00 37.61 2.90
371 374 5.333416 GGATTGACGAAGAGTTGAAGTTGTC 60.333 44.000 0.00 0.00 0.00 3.18
372 375 4.511826 GGATTGACGAAGAGTTGAAGTTGT 59.488 41.667 0.00 0.00 0.00 3.32
374 377 4.962155 AGGATTGACGAAGAGTTGAAGTT 58.038 39.130 0.00 0.00 0.00 2.66
376 379 4.390297 GGAAGGATTGACGAAGAGTTGAAG 59.610 45.833 0.00 0.00 0.00 3.02
377 380 4.202315 TGGAAGGATTGACGAAGAGTTGAA 60.202 41.667 0.00 0.00 0.00 2.69
393 407 2.268796 TCATGGATCAGGTGGAAGGA 57.731 50.000 0.00 0.00 0.00 3.36
429 443 2.289547 GCTTCGGTTGTCTGTTTGCTAA 59.710 45.455 0.00 0.00 0.00 3.09
430 444 1.871039 GCTTCGGTTGTCTGTTTGCTA 59.129 47.619 0.00 0.00 0.00 3.49
458 472 1.337703 TGATTGTGCACCACTGCTTTC 59.662 47.619 15.69 0.00 44.57 2.62
460 474 1.624336 ATGATTGTGCACCACTGCTT 58.376 45.000 15.69 0.00 44.57 3.91
470 484 2.507484 TGCTAGGGCATATGATTGTGC 58.493 47.619 6.97 5.29 44.28 4.57
478 492 7.886989 ACATTTCGTGTGTGCTAGGGCATAT 62.887 44.000 0.00 0.00 41.41 1.78
508 522 3.684788 ACTTGTCCATATCGTGCTTTCAC 59.315 43.478 0.00 0.00 39.78 3.18
515 529 3.861840 AGTTCCACTTGTCCATATCGTG 58.138 45.455 0.00 0.00 0.00 4.35
527 541 4.696402 CGAGTCTACAGTCTAGTTCCACTT 59.304 45.833 0.00 0.00 0.00 3.16
554 568 0.179018 TCGCCGGAGAGATCAGATCA 60.179 55.000 5.05 0.00 0.00 2.92
602 616 2.202824 TAGGCGATTTCGTGGCGG 60.203 61.111 1.55 0.00 42.22 6.13
663 2841 4.060205 TCATACGATCGTATCAAGGTCGA 58.940 43.478 32.40 22.72 39.07 4.20
665 2843 5.359716 ACTCATACGATCGTATCAAGGTC 57.640 43.478 32.40 0.00 39.07 3.85
762 2964 6.767524 TTCTGGTGTCTTTTAGAGCAAAAA 57.232 33.333 0.00 0.00 35.71 1.94
763 2965 6.959639 ATTCTGGTGTCTTTTAGAGCAAAA 57.040 33.333 0.00 0.00 34.89 2.44
764 2966 6.959639 AATTCTGGTGTCTTTTAGAGCAAA 57.040 33.333 0.00 0.00 0.00 3.68
765 2967 6.959639 AAATTCTGGTGTCTTTTAGAGCAA 57.040 33.333 0.00 0.00 0.00 3.91
766 2968 6.959639 AAAATTCTGGTGTCTTTTAGAGCA 57.040 33.333 0.00 0.00 0.00 4.26
863 3070 1.301677 CCAACTCTTCTTGCTCGGGC 61.302 60.000 0.00 0.00 39.26 6.13
894 3101 1.746220 CACGTTTCTTGTTGGGTTGGA 59.254 47.619 0.00 0.00 0.00 3.53
908 3115 0.673644 CCGGATCCTCTTGCACGTTT 60.674 55.000 10.75 0.00 0.00 3.60
991 3198 0.735632 GACAGTGCCGCAGAGAAGAG 60.736 60.000 0.00 0.00 0.00 2.85
1206 3426 2.359975 GGTCCCAACTCAAGCGGG 60.360 66.667 0.00 0.00 41.76 6.13
1211 3431 1.345415 GTTCCTACGGTCCCAACTCAA 59.655 52.381 0.00 0.00 0.00 3.02
1272 3500 2.515853 TCCTGCTCTAGATTCAGGGAGA 59.484 50.000 27.54 14.69 45.58 3.71
1276 3504 3.110447 GCTTCCTGCTCTAGATTCAGG 57.890 52.381 24.65 24.65 46.60 3.86
1468 3708 6.414408 ACAAAGAGCTAAATCAGTTCATCG 57.586 37.500 0.00 0.00 36.98 3.84
1601 3841 9.830186 AGGATAGTTCCACATATGACTAGTATT 57.170 33.333 10.38 0.00 45.30 1.89
1602 3842 9.830186 AAGGATAGTTCCACATATGACTAGTAT 57.170 33.333 10.38 4.68 45.30 2.12
1926 4166 4.524328 AGCAGTCCTTAAATTTGTTCCCTG 59.476 41.667 0.00 3.20 0.00 4.45
1997 4238 4.141824 GGAGAACATGGGGAACAAACAAAA 60.142 41.667 0.00 0.00 0.00 2.44
2001 4242 2.558359 CTGGAGAACATGGGGAACAAAC 59.442 50.000 0.00 0.00 0.00 2.93
2267 4508 1.549037 GCACCCTTTCCCCATAACACA 60.549 52.381 0.00 0.00 0.00 3.72
2364 4605 7.396540 ACACCTGATGAGGATGAAAAATTAC 57.603 36.000 4.75 0.00 42.93 1.89
2397 4638 4.807834 CCCATGTTGATATCTATAGCAGCG 59.192 45.833 3.98 0.00 33.44 5.18
2550 4791 4.861102 ATTTGCATAGCCTGAATAAGCC 57.139 40.909 0.00 0.00 0.00 4.35
2592 4833 3.631686 TGTTCAAGTTCCTCCACAATGTG 59.368 43.478 6.37 6.37 0.00 3.21
2599 4840 1.562008 TGGTGTGTTCAAGTTCCTCCA 59.438 47.619 0.00 0.00 0.00 3.86
2667 4908 2.045438 TCAATCCGGCGTGCCAAT 60.045 55.556 12.06 0.68 35.37 3.16
2776 5017 4.039852 ACCCTTTAAAAACACGAATGGCAT 59.960 37.500 0.00 0.00 0.00 4.40
2885 5126 9.106070 GATTTAAGTCGTATCAATTTGGGTACT 57.894 33.333 0.00 0.00 0.00 2.73
3084 5340 3.826729 AGGCTGACATAAGGAAAACAACC 59.173 43.478 0.00 0.00 0.00 3.77
3520 5776 7.331440 TGCTTGTTTGCGAATGAATATTTTCAT 59.669 29.630 5.65 5.65 43.58 2.57
4161 6794 7.734410 ACCATAAATTTGGGCAGTATTATCCAT 59.266 33.333 0.00 0.00 41.35 3.41
4250 6883 1.795170 ATCCAGCGGCACACACAAAC 61.795 55.000 1.45 0.00 0.00 2.93
4270 6903 2.050691 GCTGCCAAAATACACACAACG 58.949 47.619 0.00 0.00 0.00 4.10
4462 7095 8.507582 TCTCTCTGTACTAGATAGGTGGAATA 57.492 38.462 0.00 0.00 34.21 1.75
4502 7135 6.359804 AGCTCTCAACAGGCAATATTATCAA 58.640 36.000 0.00 0.00 0.00 2.57
4620 7253 7.425606 TGCAGTTTGATCCTTAGTTTTCTTTC 58.574 34.615 0.00 0.00 0.00 2.62
4703 7336 8.166422 ACCTACTCCTTCAGTTGTAAATTTTG 57.834 34.615 0.00 0.00 36.43 2.44
4918 7561 6.731292 AGAGGTTAGCAAAATCCTGTTTTT 57.269 33.333 0.00 0.00 0.00 1.94
5068 7728 6.890663 TGAGCACATTATTAAATTTGCAGC 57.109 33.333 10.75 4.44 46.60 5.25
5208 7869 3.007940 TCATGTACTTGGTCCCACTTCAG 59.992 47.826 8.74 0.00 0.00 3.02
5261 7922 4.522689 AGCACGCACACCGACACA 62.523 61.111 0.00 0.00 41.02 3.72
5413 8075 2.071778 AAGCCTTGCTGTCTTTTCCA 57.928 45.000 0.00 0.00 39.62 3.53
5454 8116 3.003689 CACAGTCCACAGTCATGAAAACC 59.996 47.826 0.00 0.00 0.00 3.27
5714 8381 9.727627 GATATGTGAATTTCTCCAAAACTCATC 57.272 33.333 0.00 0.00 0.00 2.92
5782 8449 7.370905 TCAGTTGATCTTGATCAGATACCAT 57.629 36.000 12.31 0.00 42.92 3.55
6030 8700 6.883756 TCAATAATACATGACACAGCCTTTCA 59.116 34.615 0.00 0.00 0.00 2.69
6190 8860 6.309737 ACACAACGATCGTTTCTAAGGAATAC 59.690 38.462 29.89 0.00 36.00 1.89
6234 8904 8.325421 TCTACGCAATAACAAATCCTACAAAA 57.675 30.769 0.00 0.00 0.00 2.44
6277 8947 1.480789 AAGAACAAAACCAAGGCCGT 58.519 45.000 0.00 0.00 0.00 5.68
6295 8965 1.868713 ATGCATGGGATGAAGCCAAA 58.131 45.000 0.00 0.00 0.00 3.28
6299 8969 4.371855 CATCATATGCATGGGATGAAGC 57.628 45.455 26.09 0.00 39.52 3.86
6325 8995 2.082231 CTGTCAGAGCAACCAGATTGG 58.918 52.381 0.00 0.00 45.02 3.16
6362 9032 6.543831 ACTTTGTGCTTCCAGAATCCATATAC 59.456 38.462 0.00 0.00 0.00 1.47
6363 9033 6.662755 ACTTTGTGCTTCCAGAATCCATATA 58.337 36.000 0.00 0.00 0.00 0.86
6364 9034 5.513233 ACTTTGTGCTTCCAGAATCCATAT 58.487 37.500 0.00 0.00 0.00 1.78
6421 9095 5.065731 CCTTCCAGAAGAAATAGCATGTGAC 59.934 44.000 9.00 0.00 40.79 3.67
6496 9171 3.508744 AAATAATTGGTCCGCTGCAAG 57.491 42.857 0.00 0.00 0.00 4.01
6526 9201 1.063942 TCTGGGCATCTAGAAGACGGA 60.064 52.381 0.00 0.00 0.00 4.69
6553 9228 6.929049 GGTTTGATTTACCCCAAAGAAGAAAG 59.071 38.462 0.00 0.00 33.52 2.62
6557 9232 5.799827 TGGTTTGATTTACCCCAAAGAAG 57.200 39.130 0.00 0.00 33.52 2.85
6571 9251 9.590451 CATATTGCTCAGTAAAATTGGTTTGAT 57.410 29.630 0.00 0.00 0.00 2.57
6673 9353 8.941977 AGCGTGTTGAACATATTTTTACAGATA 58.058 29.630 0.00 0.00 0.00 1.98
6768 9474 9.692749 TGAATATTTCGTTTATGCTAGGAGTAG 57.307 33.333 0.00 0.00 0.00 2.57
6769 9475 9.692749 CTGAATATTTCGTTTATGCTAGGAGTA 57.307 33.333 0.00 0.00 0.00 2.59
6770 9476 8.421784 TCTGAATATTTCGTTTATGCTAGGAGT 58.578 33.333 0.00 0.00 0.00 3.85
6771 9477 8.818141 TCTGAATATTTCGTTTATGCTAGGAG 57.182 34.615 0.00 0.00 0.00 3.69
6772 9478 9.778741 AATCTGAATATTTCGTTTATGCTAGGA 57.221 29.630 0.00 0.00 0.00 2.94
6854 9574 0.474854 TCTCCCACCCCAGCTTTGTA 60.475 55.000 0.00 0.00 0.00 2.41
6856 9576 0.394899 GATCTCCCACCCCAGCTTTG 60.395 60.000 0.00 0.00 0.00 2.77
6860 9580 0.681243 GTTTGATCTCCCACCCCAGC 60.681 60.000 0.00 0.00 0.00 4.85
6903 9624 9.330063 GGTTTGATGTTCAGATGAGATATTACA 57.670 33.333 0.00 0.00 0.00 2.41
6944 9665 3.003275 ACCTGAATGTAAAGTGTTGTGCG 59.997 43.478 0.00 0.00 0.00 5.34
6984 9705 3.314357 GGGTGAGTTTCTTTGTGTGGTAC 59.686 47.826 0.00 0.00 0.00 3.34
6985 9706 3.547746 GGGTGAGTTTCTTTGTGTGGTA 58.452 45.455 0.00 0.00 0.00 3.25
7018 9739 5.163824 TGCTAGCATCTTCAGATTTCGTTTG 60.164 40.000 14.93 0.00 31.21 2.93
7020 9741 4.507710 TGCTAGCATCTTCAGATTTCGTT 58.492 39.130 14.93 0.00 31.21 3.85
7023 9744 5.114780 TGTCTGCTAGCATCTTCAGATTTC 58.885 41.667 19.72 0.06 37.81 2.17
7028 9749 2.203401 GCTGTCTGCTAGCATCTTCAG 58.797 52.381 19.72 21.57 40.81 3.02


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

AutoCloner maintained by Alex Coulton.