Multiple sequence alignment - TraesCS1D01G240400

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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 TraesCS1D01G240400 chr1D 100.000 4708 0 0 1 4708 330524796 330529503 0.000000e+00 8695.0
1 TraesCS1D01G240400 chr1A 94.342 4012 184 25 472 4463 427481795 427485783 0.000000e+00 6111.0
2 TraesCS1D01G240400 chr1A 92.787 305 18 2 4404 4708 427485774 427486074 5.590000e-119 438.0
3 TraesCS1D01G240400 chr1A 95.000 60 3 0 388 447 427401958 427402017 1.390000e-15 95.3
4 TraesCS1D01G240400 chr1B 94.659 2621 94 12 1 2613 445177324 445179906 0.000000e+00 4023.0
5 TraesCS1D01G240400 chr1B 90.147 1979 114 34 2642 4609 445179903 445181811 0.000000e+00 2499.0
6 TraesCS1D01G240400 chr1B 93.137 102 5 2 4608 4708 445181955 445182055 1.060000e-31 148.0
7 TraesCS1D01G240400 chr5D 85.987 314 42 2 136 448 42986670 42986982 7.550000e-88 335.0
8 TraesCS1D01G240400 chr5D 84.496 129 18 2 1 129 42986499 42986625 4.950000e-25 126.0
9 TraesCS1D01G240400 chr5D 83.077 130 22 0 1 130 359161163 359161292 8.280000e-23 119.0
10 TraesCS1D01G240400 chr2D 80.938 320 57 4 134 451 203750617 203750300 2.810000e-62 250.0
11 TraesCS1D01G240400 chr2D 85.124 121 18 0 9 129 333832738 333832618 1.780000e-24 124.0
12 TraesCS1D01G240400 chr2D 83.594 128 18 3 1 127 569414590 569414715 2.980000e-22 117.0
13 TraesCS1D01G240400 chr3A 87.597 129 16 0 1 129 157656625 157656497 2.930000e-32 150.0
14 TraesCS1D01G240400 chr7B 85.039 127 19 0 1 127 463828312 463828186 3.820000e-26 130.0
15 TraesCS1D01G240400 chr3B 85.039 127 17 2 1 126 547483295 547483420 1.380000e-25 128.0
16 TraesCS1D01G240400 chr2B 83.077 130 21 1 1 130 402010469 402010597 2.980000e-22 117.0
17 TraesCS1D01G240400 chr2B 80.247 162 24 6 136 296 438438499 438438345 1.070000e-21 115.0
18 TraesCS1D01G240400 chr5B 82.979 94 16 0 462 555 424433439 424433532 8.390000e-13 86.1
19 TraesCS1D01G240400 chr6B 84.211 76 9 2 468 543 7116289 7116361 2.350000e-08 71.3
20 TraesCS1D01G240400 chr6D 100.000 30 0 0 622 651 280863083 280863112 6.580000e-04 56.5


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 TraesCS1D01G240400 chr1D 330524796 330529503 4707 False 8695.000000 8695 100.000000 1 4708 1 chr1D.!!$F1 4707
1 TraesCS1D01G240400 chr1A 427481795 427486074 4279 False 3274.500000 6111 93.564500 472 4708 2 chr1A.!!$F2 4236
2 TraesCS1D01G240400 chr1B 445177324 445182055 4731 False 2223.333333 4023 92.647667 1 4708 3 chr1B.!!$F1 4707

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
766 772 0.036388 ACATTGCCGTAGACACTGGG 60.036 55.000 0.0 0.0 0.0 4.45 F
767 773 0.249120 CATTGCCGTAGACACTGGGA 59.751 55.000 0.0 0.0 0.0 4.37 F
769 775 0.249120 TTGCCGTAGACACTGGGATG 59.751 55.000 0.0 0.0 0.0 3.51 F
912 921 0.608640 ACCGCTCCTCACCAGTAAAG 59.391 55.000 0.0 0.0 0.0 1.85 F
1726 1737 1.066430 TCAATCTGTCCTACAACCGGC 60.066 52.381 0.0 0.0 0.0 6.13 F
2179 2193 1.303317 AAAGGACATGGTGCGGGTC 60.303 57.895 0.0 0.0 0.0 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2097 2108 1.266175 GCAATGATCAAGATCCCTGCG 59.734 52.381 14.00 0.00 35.86 5.18 R
2461 2475 1.606224 CCTCAAGGCAACAATGTTGGC 60.606 52.381 35.60 35.60 44.22 4.52 R
2624 2639 4.090642 GTCAACAGTTCTATGAAGCGACAG 59.909 45.833 0.00 0.00 0.00 3.51 R
2819 2834 4.073549 ACAGAGTACCACTGAGACAGTAC 58.926 47.826 19.81 0.44 43.43 2.73 R
3566 3584 0.533032 CTTCCTGTTCCGAGTCCCTC 59.467 60.000 0.00 0.00 0.00 4.30 R
3716 3734 2.798148 ATCACCGCCCTTTCGTGGTC 62.798 60.000 0.00 0.00 44.91 4.02 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
134 135 7.013942 ACGAATAATAGTACACCATCAGCAGTA 59.986 37.037 0.00 0.00 0.00 2.74
145 146 5.352569 CACCATCAGCAGTAACTTCCTTAAG 59.647 44.000 0.00 0.00 38.77 1.85
165 166 7.440856 CCTTAAGAGATGACTAAGAATTGCCTC 59.559 40.741 3.36 0.00 0.00 4.70
195 196 2.383298 TGCTTCTTTTGAAACGCTCG 57.617 45.000 0.00 0.00 38.07 5.03
198 199 2.095718 GCTTCTTTTGAAACGCTCGGAT 60.096 45.455 0.00 0.00 38.07 4.18
267 268 6.149308 TGCTTCAATTTGAGCTCTTCGATTTA 59.851 34.615 16.19 0.00 0.00 1.40
306 307 7.118971 ACAAAGTACTGCATTCTGATCTTCTTC 59.881 37.037 0.00 0.00 0.00 2.87
309 310 7.164122 AGTACTGCATTCTGATCTTCTTCAAA 58.836 34.615 0.00 0.00 0.00 2.69
310 311 6.497785 ACTGCATTCTGATCTTCTTCAAAG 57.502 37.500 0.00 0.00 0.00 2.77
334 335 1.689959 CAATCGCTGCTTTTGTGTCC 58.310 50.000 0.00 0.00 0.00 4.02
355 356 3.875134 CCGACTCTTGTGTTGTAACCTTT 59.125 43.478 0.00 0.00 0.00 3.11
378 379 2.808523 TCTAGCTCTCGGATGCATTG 57.191 50.000 0.00 0.00 0.00 2.82
448 449 1.971357 TCGAAGGAGCACTTTTCCTCT 59.029 47.619 0.00 0.00 44.24 3.69
449 450 2.368875 TCGAAGGAGCACTTTTCCTCTT 59.631 45.455 0.00 0.00 44.24 2.85
470 471 1.540707 TGTGGTACGTGTTGCGATCTA 59.459 47.619 0.00 0.00 44.77 1.98
545 546 4.923281 GGCTCGCACAATACTTTTGAAATT 59.077 37.500 0.00 0.00 0.00 1.82
588 589 2.091541 CTATGCGCAAAAGAAAGGGGA 58.908 47.619 17.11 0.00 0.00 4.81
605 606 5.808366 AGGGGAAAAGAGGTCAAAATTTC 57.192 39.130 0.00 0.00 0.00 2.17
714 720 0.179100 AGCGAAGGATGGACGACATG 60.179 55.000 2.29 0.00 40.72 3.21
736 742 2.159099 TCCTTCGATTGAATGACCTCCG 60.159 50.000 0.00 0.00 32.61 4.63
742 748 2.149803 TTGAATGACCTCCGACGCGT 62.150 55.000 13.85 13.85 0.00 6.01
757 763 1.447140 GCGTCCAGACATTGCCGTA 60.447 57.895 0.00 0.00 0.00 4.02
762 768 1.067142 TCCAGACATTGCCGTAGACAC 60.067 52.381 0.00 0.00 0.00 3.67
766 772 0.036388 ACATTGCCGTAGACACTGGG 60.036 55.000 0.00 0.00 0.00 4.45
767 773 0.249120 CATTGCCGTAGACACTGGGA 59.751 55.000 0.00 0.00 0.00 4.37
768 774 1.134401 CATTGCCGTAGACACTGGGAT 60.134 52.381 0.00 0.00 0.00 3.85
769 775 0.249120 TTGCCGTAGACACTGGGATG 59.751 55.000 0.00 0.00 0.00 3.51
912 921 0.608640 ACCGCTCCTCACCAGTAAAG 59.391 55.000 0.00 0.00 0.00 1.85
960 971 3.762674 GGAGGATTCCGGTGAGAAC 57.237 57.895 0.00 0.00 32.79 3.01
987 998 7.053200 CAGTTAAACACGAAACTACAACGTAG 58.947 38.462 0.00 0.00 38.47 3.51
988 999 6.751888 AGTTAAACACGAAACTACAACGTAGT 59.248 34.615 0.94 0.94 36.77 2.73
989 1000 7.913297 AGTTAAACACGAAACTACAACGTAGTA 59.087 33.333 7.20 0.00 34.85 1.82
992 1003 5.207768 ACACGAAACTACAACGTAGTACAG 58.792 41.667 7.20 4.76 45.00 2.74
1053 1064 2.659757 TCTTCATAAACGCAACGACTCG 59.340 45.455 0.00 0.00 0.00 4.18
1576 1587 2.131854 TCTTGGACCTTTCCTCCAACA 58.868 47.619 0.00 0.00 41.92 3.33
1577 1588 2.512056 TCTTGGACCTTTCCTCCAACAA 59.488 45.455 0.00 0.00 41.92 2.83
1655 1666 2.046314 CGGCCGGAACAACCTCAT 60.046 61.111 20.10 0.00 36.31 2.90
1726 1737 1.066430 TCAATCTGTCCTACAACCGGC 60.066 52.381 0.00 0.00 0.00 6.13
1788 1799 2.361771 GAGGGGACGGTGGACCTA 59.638 66.667 0.00 0.00 32.42 3.08
1923 1934 4.572571 GACAACCGTGGCCCCACA 62.573 66.667 16.94 0.00 46.47 4.17
2097 2108 1.474077 GCCATTGTTCTGGGTGATGTC 59.526 52.381 0.00 0.00 36.75 3.06
2179 2193 1.303317 AAAGGACATGGTGCGGGTC 60.303 57.895 0.00 0.00 0.00 4.46
2298 2312 2.935201 GTTTGATCTCGATGAGCTGCTT 59.065 45.455 2.53 0.00 31.32 3.91
2461 2475 2.053865 ATTGGCAAGGTCCGGCATG 61.054 57.895 5.96 0.00 38.88 4.06
2600 2614 1.883275 TCGAGCTCTCTAATGCCTAGC 59.117 52.381 12.85 0.00 0.00 3.42
2624 2639 9.807649 AGCTTACATCATGTTTCCATTATTTTC 57.192 29.630 0.00 0.00 0.00 2.29
2629 2644 7.970061 ACATCATGTTTCCATTATTTTCTGTCG 59.030 33.333 0.00 0.00 0.00 4.35
2630 2645 6.321717 TCATGTTTCCATTATTTTCTGTCGC 58.678 36.000 0.00 0.00 0.00 5.19
2634 2649 6.016693 TGTTTCCATTATTTTCTGTCGCTTCA 60.017 34.615 0.00 0.00 0.00 3.02
2641 2656 8.607459 CATTATTTTCTGTCGCTTCATAGAACT 58.393 33.333 0.00 0.00 0.00 3.01
2679 2694 6.987386 AGTAATTTGTAGATCAGGATCCTCG 58.013 40.000 12.69 8.09 38.58 4.63
2693 2708 7.175797 TCAGGATCCTCGTACTGATATAATGT 58.824 38.462 12.69 0.00 35.24 2.71
2718 2733 4.695217 TCGACATTGATTAGTTTTGCCC 57.305 40.909 0.00 0.00 0.00 5.36
2719 2734 3.442273 TCGACATTGATTAGTTTTGCCCC 59.558 43.478 0.00 0.00 0.00 5.80
2748 2763 9.388346 GTGATACGATTTTTGTTGTTAATGACA 57.612 29.630 0.00 0.00 36.19 3.58
2819 2834 9.345517 CAGTCCATGTAAATTGTTTTGATACAG 57.654 33.333 0.00 0.00 0.00 2.74
2830 2845 7.946655 TTGTTTTGATACAGTACTGTCTCAG 57.053 36.000 30.96 8.74 44.02 3.35
2940 2958 9.090103 TGTCTCTTATATTTATGTACAGAGGGG 57.910 37.037 0.33 0.00 0.00 4.79
2944 2962 9.543231 TCTTATATTTATGTACAGAGGGGGTAG 57.457 37.037 0.33 0.00 0.00 3.18
2985 3003 3.969553 ACTAGAGTACATCCTCACTGCA 58.030 45.455 0.00 0.00 33.75 4.41
2986 3004 4.344978 ACTAGAGTACATCCTCACTGCAA 58.655 43.478 0.00 0.00 33.75 4.08
2987 3005 4.959210 ACTAGAGTACATCCTCACTGCAAT 59.041 41.667 0.00 0.00 33.75 3.56
2990 3008 4.019860 AGAGTACATCCTCACTGCAATGTT 60.020 41.667 4.87 0.00 34.39 2.71
2997 3015 3.072330 TCCTCACTGCAATGTTGAACCTA 59.928 43.478 0.00 0.00 0.00 3.08
3075 3093 2.228822 GGGACAATGACATTCACACCAC 59.771 50.000 0.00 0.00 0.00 4.16
3158 3176 5.163713 GCATGAATTCAGTCCCAAGAAGTAC 60.164 44.000 14.54 0.00 0.00 2.73
3354 3372 1.956477 GCCCTCTTGTGAGCAAAGAAA 59.044 47.619 0.00 0.00 38.93 2.52
3428 3446 2.609747 TGGGATGTCTACTCCTATGGC 58.390 52.381 0.00 0.00 33.05 4.40
3566 3584 2.202623 CTCGACCCTTTCCTCGCG 60.203 66.667 0.00 0.00 0.00 5.87
3842 3860 6.016610 ACCATGTAAAATTATCGATTTCGGGG 60.017 38.462 1.71 0.00 36.96 5.73
3865 3883 6.353342 GGGCCTTTAACAAGTTAGGTACCTAT 60.353 42.308 22.36 8.95 0.00 2.57
3923 3944 9.692749 GCATGTAGTATCTGTTAGTATTTGCTA 57.307 33.333 0.00 0.00 30.91 3.49
3945 3966 6.094325 GCTACTGTAGTACTCTGTGTGAGAAT 59.906 42.308 15.71 0.00 45.39 2.40
4026 4048 4.151121 TGAAGACTTGCAATGAAATCCCA 58.849 39.130 0.00 0.00 0.00 4.37
4060 4082 7.112122 TGTTGTCTATCCTTGCAGTGAATATT 58.888 34.615 0.00 0.00 0.00 1.28
4216 4238 1.028330 CGCATGGTCAGGCATGTTCT 61.028 55.000 8.31 0.00 38.12 3.01
4266 4288 6.625532 TTAGATAGGATGGAAGCATGCATA 57.374 37.500 21.98 2.89 37.78 3.14
4272 4294 6.378661 AGGATGGAAGCATGCATAATAGTA 57.621 37.500 21.98 0.00 37.78 1.82
4287 4309 7.653311 TGCATAATAGTAGCATAGTGTTGAGTG 59.347 37.037 0.00 0.00 32.55 3.51
4342 4365 7.004086 ACTTTTGGTTCCTCAGATATCACAAA 58.996 34.615 5.32 0.00 0.00 2.83
4349 4372 3.629398 CCTCAGATATCACAAACCTTGGC 59.371 47.826 5.32 0.00 34.12 4.52
4352 4377 4.883585 TCAGATATCACAAACCTTGGCATC 59.116 41.667 5.32 0.00 34.12 3.91
4400 4425 8.688747 TGAAATGTCATGTATGTATATTGCCA 57.311 30.769 0.00 0.00 0.00 4.92
4431 4506 7.841729 TGTTCTAAGGACCTCTCTGATCTAAAT 59.158 37.037 0.00 0.00 0.00 1.40
4463 4538 8.542080 TCTATTCGGATTTTAGAGGGTTGTAAA 58.458 33.333 0.00 0.00 0.00 2.01
4498 4573 3.670625 TCTTCGTGGGGTTGTTTGATAG 58.329 45.455 0.00 0.00 0.00 2.08
4499 4574 3.071892 TCTTCGTGGGGTTGTTTGATAGT 59.928 43.478 0.00 0.00 0.00 2.12
4500 4575 4.283978 TCTTCGTGGGGTTGTTTGATAGTA 59.716 41.667 0.00 0.00 0.00 1.82
4501 4576 4.829872 TCGTGGGGTTGTTTGATAGTAT 57.170 40.909 0.00 0.00 0.00 2.12
4502 4577 5.936187 TCGTGGGGTTGTTTGATAGTATA 57.064 39.130 0.00 0.00 0.00 1.47
4503 4578 6.488769 TCGTGGGGTTGTTTGATAGTATAT 57.511 37.500 0.00 0.00 0.00 0.86
4504 4579 7.600231 TCGTGGGGTTGTTTGATAGTATATA 57.400 36.000 0.00 0.00 0.00 0.86
4505 4580 7.436118 TCGTGGGGTTGTTTGATAGTATATAC 58.564 38.462 4.60 4.60 0.00 1.47
4559 4637 7.710475 GGAAAAACTTTCCATCAACTGAATTCA 59.290 33.333 8.12 8.12 38.45 2.57
4633 4856 3.434641 GGTCATGATAATGTCATCCTGCG 59.565 47.826 0.00 0.00 45.76 5.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
145 146 5.028549 TGGAGGCAATTCTTAGTCATCTC 57.971 43.478 0.00 0.00 0.00 2.75
165 166 8.216453 CGTTTCAAAAGAAGCAATAAGAAATGG 58.784 33.333 0.00 0.00 30.92 3.16
195 196 2.999331 TGGATCGGGACAGAAAAATCC 58.001 47.619 0.00 0.00 34.54 3.01
198 199 4.009675 CAAGATGGATCGGGACAGAAAAA 58.990 43.478 0.00 0.00 0.00 1.94
306 307 4.874534 CAGCGATTGCCACCTTTG 57.125 55.556 0.00 0.00 44.31 2.77
334 335 4.785341 GCAAAGGTTACAACACAAGAGTCG 60.785 45.833 0.00 0.00 0.00 4.18
355 356 0.387202 GCATCCGAGAGCTAGAAGCA 59.613 55.000 1.22 0.00 45.56 3.91
378 379 7.092137 TCATCACATGATTCATCCTTTGAAC 57.908 36.000 0.00 0.00 46.80 3.18
448 449 1.527736 GATCGCAACACGTACCACAAA 59.472 47.619 0.00 0.00 44.19 2.83
449 450 1.141645 GATCGCAACACGTACCACAA 58.858 50.000 0.00 0.00 44.19 3.33
470 471 4.771590 ACAACGCTTTCAATCATGATGT 57.228 36.364 9.46 0.00 34.96 3.06
545 546 4.436317 GCGTGCGGTGATTCTAATGTTTTA 60.436 41.667 0.00 0.00 0.00 1.52
583 584 4.593206 GGAAATTTTGACCTCTTTTCCCCT 59.407 41.667 0.00 0.00 39.48 4.79
588 589 6.560003 AACCTGGAAATTTTGACCTCTTTT 57.440 33.333 0.00 0.00 0.00 2.27
719 725 1.202256 CGTCGGAGGTCATTCAATCGA 60.202 52.381 0.00 0.00 0.00 3.59
736 742 2.740714 GGCAATGTCTGGACGCGTC 61.741 63.158 30.67 30.67 0.00 5.19
742 748 1.067142 GTGTCTACGGCAATGTCTGGA 60.067 52.381 0.00 0.00 0.00 3.86
745 751 1.066858 CCAGTGTCTACGGCAATGTCT 60.067 52.381 0.00 0.00 30.97 3.41
757 763 4.033009 TGTACATCATCATCCCAGTGTCT 58.967 43.478 0.00 0.00 0.00 3.41
762 768 4.319984 CGCAAATGTACATCATCATCCCAG 60.320 45.833 9.23 0.00 35.48 4.45
766 772 5.809464 TCAACGCAAATGTACATCATCATC 58.191 37.500 9.23 0.00 35.48 2.92
767 773 5.816449 TCAACGCAAATGTACATCATCAT 57.184 34.783 9.23 0.00 35.48 2.45
768 774 5.411053 TCTTCAACGCAAATGTACATCATCA 59.589 36.000 9.23 0.00 35.48 3.07
769 775 5.868257 TCTTCAACGCAAATGTACATCATC 58.132 37.500 9.23 0.24 35.48 2.92
822 828 1.010419 TTCGAGAAAGTAACGCGGCC 61.010 55.000 12.47 0.00 0.00 6.13
912 921 5.742446 CGCTTGCTATTCTATTTCCACTTC 58.258 41.667 0.00 0.00 0.00 3.01
918 927 4.802876 ACTGCGCTTGCTATTCTATTTC 57.197 40.909 9.73 0.00 40.12 2.17
919 928 5.237344 CCTAACTGCGCTTGCTATTCTATTT 59.763 40.000 9.73 0.00 40.12 1.40
929 938 0.462759 ATCCTCCTAACTGCGCTTGC 60.463 55.000 9.73 0.00 39.78 4.01
960 971 5.504392 GTTGTAGTTTCGTGTTTAACTGGG 58.496 41.667 0.00 0.00 36.16 4.45
987 998 4.537015 GCGATGGCATTATTTTCCTGTAC 58.463 43.478 0.00 0.00 39.62 2.90
988 999 3.568007 GGCGATGGCATTATTTTCCTGTA 59.432 43.478 0.00 0.00 42.47 2.74
989 1000 2.362077 GGCGATGGCATTATTTTCCTGT 59.638 45.455 0.00 0.00 42.47 4.00
992 1003 2.362077 ACTGGCGATGGCATTATTTTCC 59.638 45.455 0.00 0.00 42.47 3.13
1053 1064 2.267324 GGCACTGAGTGAGGCTCC 59.733 66.667 18.18 3.41 43.48 4.70
1103 1114 3.839432 GAGGAGGAGGAACGCGGG 61.839 72.222 12.47 0.00 0.00 6.13
1141 1152 0.112412 GCTAGGAGGAGGAGGAGGAG 59.888 65.000 0.00 0.00 0.00 3.69
1566 1577 1.476110 CCGTTGAGGTTGTTGGAGGAA 60.476 52.381 0.00 0.00 34.51 3.36
1576 1587 1.545706 GGGAGAGAGCCGTTGAGGTT 61.546 60.000 0.00 0.00 43.70 3.50
1577 1588 1.985116 GGGAGAGAGCCGTTGAGGT 60.985 63.158 0.00 0.00 43.70 3.85
1788 1799 1.645034 CGGAGAAGTCATTGTGCGAT 58.355 50.000 0.00 0.00 44.68 4.58
1923 1934 2.597510 GGGTTGCCCAAGAACGCT 60.598 61.111 0.00 0.00 44.65 5.07
2097 2108 1.266175 GCAATGATCAAGATCCCTGCG 59.734 52.381 14.00 0.00 35.86 5.18
2163 2177 3.717294 GGACCCGCACCATGTCCT 61.717 66.667 0.00 0.00 44.17 3.85
2461 2475 1.606224 CCTCAAGGCAACAATGTTGGC 60.606 52.381 35.60 35.60 44.22 4.52
2496 2510 9.269453 TCATATATCAGCAACTTCTCATCAAAG 57.731 33.333 0.00 0.00 0.00 2.77
2624 2639 4.090642 GTCAACAGTTCTATGAAGCGACAG 59.909 45.833 0.00 0.00 0.00 3.51
2629 2644 4.935885 CTGGTCAACAGTTCTATGAAGC 57.064 45.455 0.00 0.00 42.42 3.86
2641 2656 8.590204 TCTACAAATTACTATCACTGGTCAACA 58.410 33.333 0.00 0.00 0.00 3.33
2661 2676 4.822350 CAGTACGAGGATCCTGATCTACAA 59.178 45.833 22.02 0.00 37.92 2.41
2693 2708 6.128117 GGGCAAAACTAATCAATGTCGAAGTA 60.128 38.462 0.00 0.00 0.00 2.24
2718 2733 8.789881 TTAACAACAAAAATCGTATCACAAGG 57.210 30.769 0.00 0.00 0.00 3.61
2748 2763 4.593634 ACTTGAACTCCAGGTACTAGCTTT 59.406 41.667 0.00 0.00 36.02 3.51
2819 2834 4.073549 ACAGAGTACCACTGAGACAGTAC 58.926 47.826 19.81 0.44 43.43 2.73
2822 2837 5.707242 TTAACAGAGTACCACTGAGACAG 57.293 43.478 19.81 0.00 38.55 3.51
2830 2845 7.549615 AAGTCAAACTTTAACAGAGTACCAC 57.450 36.000 0.00 0.00 34.11 4.16
2916 2934 8.239478 ACCCCCTCTGTACATAAATATAAGAGA 58.761 37.037 0.00 0.00 0.00 3.10
2987 3005 8.682710 GCCTGAAATAAATACATAGGTTCAACA 58.317 33.333 0.00 0.00 0.00 3.33
2990 3008 9.778741 CTAGCCTGAAATAAATACATAGGTTCA 57.221 33.333 0.00 0.00 0.00 3.18
2997 3015 6.513393 GCAACGCTAGCCTGAAATAAATACAT 60.513 38.462 9.66 0.00 0.00 2.29
3158 3176 1.214589 CCTCAAGTCCCCGTGTACG 59.785 63.158 0.00 0.00 39.44 3.67
3428 3446 4.526970 AATCATTTCGAGCAAGATCACG 57.473 40.909 0.00 0.00 0.00 4.35
3566 3584 0.533032 CTTCCTGTTCCGAGTCCCTC 59.467 60.000 0.00 0.00 0.00 4.30
3716 3734 2.798148 ATCACCGCCCTTTCGTGGTC 62.798 60.000 0.00 0.00 44.91 4.02
3732 3750 5.476254 TCACATGTTTTCTGCAACCATATCA 59.524 36.000 0.00 0.00 0.00 2.15
3833 3851 2.823747 ACTTGTTAAAGGCCCCGAAATC 59.176 45.455 0.00 0.00 37.76 2.17
3834 3852 2.884320 ACTTGTTAAAGGCCCCGAAAT 58.116 42.857 0.00 0.00 37.76 2.17
3842 3860 7.333323 TGATAGGTACCTAACTTGTTAAAGGC 58.667 38.462 25.25 0.00 37.76 4.35
3865 3883 6.239008 CCCAAAGAAGAAAAGCTAACACATGA 60.239 38.462 0.00 0.00 0.00 3.07
3923 3944 6.004574 TCATTCTCACACAGAGTACTACAGT 58.995 40.000 0.00 0.00 44.98 3.55
3924 3945 6.502136 TCATTCTCACACAGAGTACTACAG 57.498 41.667 0.00 0.00 44.98 2.74
3925 3946 6.894339 TTCATTCTCACACAGAGTACTACA 57.106 37.500 0.00 0.00 44.98 2.74
3926 3947 8.247562 AGAATTCATTCTCACACAGAGTACTAC 58.752 37.037 8.44 0.00 43.27 2.73
3927 3948 8.246871 CAGAATTCATTCTCACACAGAGTACTA 58.753 37.037 8.44 0.00 44.84 1.82
4026 4048 5.591877 GCAAGGATAGACAACAATCAGGAAT 59.408 40.000 0.00 0.00 0.00 3.01
4188 4210 3.211963 GACCATGCGTCCATGCCC 61.212 66.667 3.65 0.00 45.97 5.36
4266 4288 5.129485 AGGCACTCAACACTATGCTACTATT 59.871 40.000 0.00 0.00 38.18 1.73
4272 4294 2.867109 AAGGCACTCAACACTATGCT 57.133 45.000 0.00 0.00 38.49 3.79
4287 4309 0.034756 ATCCCCGCAAAACAAAAGGC 59.965 50.000 0.00 0.00 0.00 4.35
4342 4365 6.855763 TTTTTCTAATGATGATGCCAAGGT 57.144 33.333 0.00 0.00 0.00 3.50
4381 4406 7.872993 ACACTAGTGGCAATATACATACATGAC 59.127 37.037 26.12 0.00 34.19 3.06
4400 4425 5.014333 TCAGAGAGGTCCTTAGAACACTAGT 59.986 44.000 0.00 0.00 29.91 2.57
4431 4506 8.272173 ACCCTCTAAAATCCGAATAGAAAATCA 58.728 33.333 0.00 0.00 0.00 2.57
4502 4577 9.924650 GTAGTGAAAATTATGGATCCTACGTAT 57.075 33.333 14.23 0.00 0.00 3.06
4503 4578 8.916062 TGTAGTGAAAATTATGGATCCTACGTA 58.084 33.333 14.23 0.00 0.00 3.57
4504 4579 7.788026 TGTAGTGAAAATTATGGATCCTACGT 58.212 34.615 14.23 0.00 0.00 3.57
4505 4580 8.833231 ATGTAGTGAAAATTATGGATCCTACG 57.167 34.615 14.23 0.00 0.00 3.51
4654 4877 9.362539 CTTTGATTCACCTAATTCAAAAGATGG 57.637 33.333 0.00 0.00 31.23 3.51


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

AutoCloner maintained by Alex Coulton.