Multiple sequence alignment - TraesCS3D01G398000

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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 TraesCS3D01G398000 chr3D 100.000 6284 0 0 1 6284 512669976 512676259 0.000000e+00 11605.0
1 TraesCS3D01G398000 chr3A 90.749 5913 335 102 1 5780 648257345 648263178 0.000000e+00 7694.0
2 TraesCS3D01G398000 chr3A 93.556 419 16 8 5869 6284 648263369 648263779 1.160000e-171 614.0
3 TraesCS3D01G398000 chr3B 93.033 3976 143 57 2390 6284 675044370 675040448 0.000000e+00 5685.0
4 TraesCS3D01G398000 chr3B 90.873 1512 81 33 877 2358 675045854 675044370 0.000000e+00 1975.0
5 TraesCS3D01G398000 chr3B 81.760 625 67 25 154 756 675046700 675046101 4.410000e-131 479.0
6 TraesCS3D01G398000 chr3B 92.537 67 5 0 1 67 675054017 675053951 5.190000e-16 97.1
7 TraesCS3D01G398000 chr3B 80.612 98 5 7 56 152 675048987 675048903 5.260000e-06 63.9
8 TraesCS3D01G398000 chr1D 83.182 220 37 0 5878 6097 355470501 355470720 1.070000e-47 202.0
9 TraesCS3D01G398000 chr7A 85.128 195 18 7 3309 3492 39211290 39211484 8.320000e-44 189.0
10 TraesCS3D01G398000 chr1A 81.364 220 41 0 5878 6097 455819274 455819493 5.010000e-41 180.0
11 TraesCS3D01G398000 chr2D 74.477 239 54 6 5875 6107 398668239 398668476 5.190000e-16 97.1
12 TraesCS3D01G398000 chr2B 74.477 239 54 6 5878 6111 471322442 471322206 5.190000e-16 97.1
13 TraesCS3D01G398000 chr2A 73.222 239 57 6 5875 6107 535836616 535836853 5.220000e-11 80.5
14 TraesCS3D01G398000 chr6D 90.909 44 4 0 5538 5581 127138108 127138151 6.800000e-05 60.2
15 TraesCS3D01G398000 chr6B 90.909 44 4 0 5538 5581 226187671 226187714 6.800000e-05 60.2
16 TraesCS3D01G398000 chr6A 94.737 38 2 0 5544 5581 151491463 151491426 6.800000e-05 60.2


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 TraesCS3D01G398000 chr3D 512669976 512676259 6283 False 11605.000 11605 100.0000 1 6284 1 chr3D.!!$F1 6283
1 TraesCS3D01G398000 chr3A 648257345 648263779 6434 False 4154.000 7694 92.1525 1 6284 2 chr3A.!!$F1 6283
2 TraesCS3D01G398000 chr3B 675040448 675048987 8539 True 2050.725 5685 86.5695 56 6284 4 chr3B.!!$R2 6228

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 3358 0.028902 ACAACGAAAACCGCTCAAGC 59.971 50.0 0.00 0.00 43.32 4.01 F
1353 3786 0.324943 TACACCTCAGCAAAGCCTCC 59.675 55.0 0.00 0.00 0.00 4.30 F
2884 5332 0.097674 GCAATCGGCACTGTGTGATC 59.902 55.0 9.86 0.05 43.97 2.92 F
4004 6457 0.401738 AGGTGGGTCAGATGTTGGTG 59.598 55.0 0.00 0.00 0.00 4.17 F
4486 6941 0.249573 CTTTGCCCACTGCCAAACTG 60.250 55.0 0.00 0.00 40.16 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2884 5332 0.677731 ATCCCGGCACAAGTGACATG 60.678 55.000 6.88 0.00 38.95 3.21 R
3268 5717 1.196354 CTTCAAAGAAGCAGCACCGAG 59.804 52.381 0.00 0.00 0.00 4.63 R
4100 6553 0.687354 AGATCCCCATATGGTCACGC 59.313 55.000 20.46 5.96 0.00 5.34 R
4896 7360 0.040646 TCGAGTTGAGGGGCCTTCTA 59.959 55.000 17.30 6.44 0.00 2.10 R
6116 8736 1.020437 GATAAGCCTCCTTGTGCTGC 58.980 55.000 0.00 0.00 38.00 5.25 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
23 24 3.222603 TCTCTTTTTGAAGGAAGGGCAC 58.777 45.455 0.00 0.00 0.00 5.01
45 46 8.094548 GGCACCCTTAGTTTTTCTATCATTTTT 58.905 33.333 0.00 0.00 0.00 1.94
57 58 8.857694 TTTCTATCATTTTTAAGAGAACCCGT 57.142 30.769 0.00 0.00 0.00 5.28
103 105 2.994186 TTACCTAACCGATGAAGCCC 57.006 50.000 0.00 0.00 0.00 5.19
210 2413 5.153513 GCTTATTGTGTCAAATTGCTCGAA 58.846 37.500 0.00 0.00 0.00 3.71
223 2426 2.020720 TGCTCGAAAAACACACATGGT 58.979 42.857 0.00 0.00 0.00 3.55
224 2427 2.425312 TGCTCGAAAAACACACATGGTT 59.575 40.909 0.00 0.00 37.33 3.67
227 2430 4.439776 GCTCGAAAAACACACATGGTTTAC 59.560 41.667 0.00 0.00 45.28 2.01
228 2431 5.732247 GCTCGAAAAACACACATGGTTTACT 60.732 40.000 0.00 0.00 45.28 2.24
229 2432 6.197364 TCGAAAAACACACATGGTTTACTT 57.803 33.333 0.00 0.00 45.28 2.24
230 2433 6.259638 TCGAAAAACACACATGGTTTACTTC 58.740 36.000 0.00 0.02 45.28 3.01
232 2435 6.695278 CGAAAAACACACATGGTTTACTTCAT 59.305 34.615 0.00 0.00 45.28 2.57
233 2436 7.221838 CGAAAAACACACATGGTTTACTTCATT 59.778 33.333 0.00 0.00 45.28 2.57
253 2456 0.178973 TGGGACAGACCAACTCGAGA 60.179 55.000 21.68 0.00 41.20 4.04
291 2494 6.840789 GCAGTTTCATTTCGTTTCAACAATTC 59.159 34.615 0.00 0.00 0.00 2.17
364 2587 6.561737 TTTCTTTGGTTTGTTGGTTTTTCC 57.438 33.333 0.00 0.00 0.00 3.13
366 2589 2.011540 TGGTTTGTTGGTTTTTCCGC 57.988 45.000 0.00 0.00 39.52 5.54
375 2598 4.099573 TGTTGGTTTTTCCGCTTCCATTTA 59.900 37.500 0.00 0.00 39.52 1.40
377 2600 3.239254 GGTTTTTCCGCTTCCATTTACG 58.761 45.455 0.00 0.00 0.00 3.18
423 2646 6.346096 TCTTTATTCCATCTTCACTAACCCG 58.654 40.000 0.00 0.00 0.00 5.28
492 2730 2.774687 TGGGCTTTTCTCGGTTACTTC 58.225 47.619 0.00 0.00 0.00 3.01
496 2734 2.411069 GCTTTTCTCGGTTACTTCGGAC 59.589 50.000 0.00 0.00 0.00 4.79
503 2741 5.644644 TCTCGGTTACTTCGGACTTATTTC 58.355 41.667 0.00 0.00 0.00 2.17
504 2742 5.183713 TCTCGGTTACTTCGGACTTATTTCA 59.816 40.000 0.00 0.00 0.00 2.69
510 2748 7.336176 GGTTACTTCGGACTTATTTCATCCTTT 59.664 37.037 0.00 0.00 0.00 3.11
557 2803 8.697507 ATTTACTGATCATGACTATTTTCCCC 57.302 34.615 0.00 0.00 0.00 4.81
559 2805 6.271585 ACTGATCATGACTATTTTCCCCAT 57.728 37.500 0.00 0.00 0.00 4.00
560 2806 6.676558 ACTGATCATGACTATTTTCCCCATT 58.323 36.000 0.00 0.00 0.00 3.16
561 2807 7.128077 ACTGATCATGACTATTTTCCCCATTT 58.872 34.615 0.00 0.00 0.00 2.32
562 2808 8.281531 ACTGATCATGACTATTTTCCCCATTTA 58.718 33.333 0.00 0.00 0.00 1.40
643 2908 8.417106 ACACACCATGAATTTTACAATAACACA 58.583 29.630 0.00 0.00 0.00 3.72
697 2962 7.066505 GTTTTTAAACATGCCAACGTATTTGG 58.933 34.615 0.10 0.10 46.23 3.28
827 3199 9.323985 TGAGTATTTCATTTTTCAGTTTTTGGG 57.676 29.630 0.00 0.00 0.00 4.12
833 3205 7.135591 TCATTTTTCAGTTTTTGGGAATCCT 57.864 32.000 0.00 0.00 0.00 3.24
960 3358 0.028902 ACAACGAAAACCGCTCAAGC 59.971 50.000 0.00 0.00 43.32 4.01
1019 3421 2.430921 CGTGGTGTCTCGCCTCAC 60.431 66.667 1.15 0.00 34.70 3.51
1036 3438 4.028490 CACCAACCCTAGCCGCCA 62.028 66.667 0.00 0.00 0.00 5.69
1037 3439 3.717294 ACCAACCCTAGCCGCCAG 61.717 66.667 0.00 0.00 0.00 4.85
1038 3440 4.489771 CCAACCCTAGCCGCCAGG 62.490 72.222 0.00 0.00 41.62 4.45
1039 3441 3.399181 CAACCCTAGCCGCCAGGA 61.399 66.667 6.40 0.00 41.02 3.86
1040 3442 3.083997 AACCCTAGCCGCCAGGAG 61.084 66.667 6.40 0.00 41.02 3.69
1041 3443 3.925914 AACCCTAGCCGCCAGGAGT 62.926 63.158 6.40 0.02 41.02 3.85
1042 3444 3.541713 CCCTAGCCGCCAGGAGTC 61.542 72.222 6.40 0.00 41.02 3.36
1043 3445 3.541713 CCTAGCCGCCAGGAGTCC 61.542 72.222 0.00 0.00 41.02 3.85
1050 3452 4.459089 GCCAGGAGTCCAGGACGC 62.459 72.222 24.24 14.81 37.67 5.19
1110 3537 3.702048 CGCTTTCGTCCTCCCCCA 61.702 66.667 0.00 0.00 0.00 4.96
1345 3778 2.304761 CCTTAAACCCTACACCTCAGCA 59.695 50.000 0.00 0.00 0.00 4.41
1346 3779 3.244770 CCTTAAACCCTACACCTCAGCAA 60.245 47.826 0.00 0.00 0.00 3.91
1352 3785 1.677217 CCTACACCTCAGCAAAGCCTC 60.677 57.143 0.00 0.00 0.00 4.70
1353 3786 0.324943 TACACCTCAGCAAAGCCTCC 59.675 55.000 0.00 0.00 0.00 4.30
1377 3810 1.512926 GACGCCATGTGAGACTGTTT 58.487 50.000 0.00 0.00 0.00 2.83
1381 3814 0.439985 CCATGTGAGACTGTTTCGCG 59.560 55.000 0.00 0.00 0.00 5.87
1468 3904 0.443869 CGCCGGATTGAAGTGAGTTG 59.556 55.000 5.05 0.00 0.00 3.16
1470 3906 1.197721 GCCGGATTGAAGTGAGTTGTG 59.802 52.381 5.05 0.00 0.00 3.33
1471 3907 2.766313 CCGGATTGAAGTGAGTTGTGA 58.234 47.619 0.00 0.00 0.00 3.58
1473 3909 2.155732 CGGATTGAAGTGAGTTGTGACG 59.844 50.000 0.00 0.00 0.00 4.35
1475 3911 2.017138 TTGAAGTGAGTTGTGACGCA 57.983 45.000 0.00 0.00 32.95 5.24
1482 3918 0.441533 GAGTTGTGACGCATGCTCTG 59.558 55.000 17.13 2.44 31.33 3.35
1497 3933 2.287970 TGCTCTGCTGTGAATTTTGCTG 60.288 45.455 0.00 0.00 0.00 4.41
1499 3935 3.058016 GCTCTGCTGTGAATTTTGCTGTA 60.058 43.478 0.00 0.00 0.00 2.74
1506 3942 5.119931 TGTGAATTTTGCTGTATGTGGTC 57.880 39.130 0.00 0.00 0.00 4.02
1575 4011 2.010145 TGGTGATTAGCGTTCTCAGC 57.990 50.000 6.90 6.90 37.79 4.26
1592 4036 4.082517 TCTCAGCCGAGTTGATATGATAGC 60.083 45.833 0.00 0.00 40.44 2.97
1603 4047 1.704641 TATGATAGCTCGTGGGCTGT 58.295 50.000 4.06 0.00 43.01 4.40
1638 4082 2.104111 TCGTTGGGTCTGAACTTCACAT 59.896 45.455 0.00 0.00 0.00 3.21
1746 4191 5.756195 TGGAATTCACTGTCAGAACTTTG 57.244 39.130 6.91 0.00 0.00 2.77
1826 4271 6.347483 CGGCTTAAAACAACTTAGGTTCTCTC 60.347 42.308 0.00 0.00 32.73 3.20
1858 4303 5.574188 AGCTCAGTATTCTTTGGAAACCAT 58.426 37.500 0.00 0.00 34.90 3.55
1862 4307 7.657354 GCTCAGTATTCTTTGGAAACCATTTTT 59.343 33.333 0.00 0.00 34.90 1.94
2029 4474 5.536554 AATGTGAGTCATTGATGTCGAAC 57.463 39.130 0.00 0.00 44.06 3.95
2081 4526 7.992754 ATCTGGATTATCATAGGTGCTTTTC 57.007 36.000 0.00 0.00 0.00 2.29
2229 4674 8.038862 AGAGTCAGGTACATGGATTATTGATT 57.961 34.615 7.81 0.00 0.00 2.57
2337 4784 1.151668 GAAACATGCGAGTCACTGCT 58.848 50.000 0.00 0.00 0.00 4.24
2356 4803 2.035066 GCTTGTCCTTGCATGTTCTGTT 59.965 45.455 0.00 0.00 0.00 3.16
2392 4839 8.479313 TGTGATGACATATCAGTTTACAACTC 57.521 34.615 0.00 0.00 40.46 3.01
2414 4861 8.603242 ACTCGATTAAGAAAAAGAACAGCTAA 57.397 30.769 0.00 0.00 0.00 3.09
2661 5108 6.371548 TCAAATCAAAGCGTGACTATTTAGCT 59.628 34.615 0.00 0.00 39.72 3.32
2707 5154 1.141881 CTATCACGACTTGCGGCCT 59.858 57.895 0.00 0.00 46.49 5.19
2884 5332 0.097674 GCAATCGGCACTGTGTGATC 59.902 55.000 9.86 0.05 43.97 2.92
2971 5419 5.860611 TCATGAGTCTTTTTCCCTTTACGA 58.139 37.500 0.00 0.00 0.00 3.43
2982 5430 2.486982 TCCCTTTACGAAGAGACTGACG 59.513 50.000 0.00 0.00 34.71 4.35
3140 5588 8.434392 TCAATATCATGGTACTACTTTTACCCC 58.566 37.037 0.00 0.00 38.66 4.95
3177 5625 3.006967 ACACTCGGATAAGTCAGCTTGTT 59.993 43.478 0.00 0.00 36.22 2.83
3186 5634 6.372659 GGATAAGTCAGCTTGTTCATTCTTCA 59.627 38.462 0.00 0.00 36.22 3.02
3377 5827 1.876799 TCAAGGTTTGCCATGTGTACG 59.123 47.619 0.00 0.00 35.18 3.67
3381 5831 2.292292 AGGTTTGCCATGTGTACGAAAC 59.708 45.455 0.00 0.00 37.19 2.78
3396 5846 3.855858 ACGAAACAAAACACATGCCTTT 58.144 36.364 0.00 0.00 0.00 3.11
3521 5971 9.959721 TCTTACCCTATATTTTATCCTTCATGC 57.040 33.333 0.00 0.00 0.00 4.06
3646 6096 9.436957 GCATATTCTAATAGCTAAAGCCTAACA 57.563 33.333 0.00 0.00 43.38 2.41
3666 6116 3.118261 ACAGAGGACTGCTTTCTGTTCAA 60.118 43.478 0.81 0.00 46.89 2.69
4004 6457 0.401738 AGGTGGGTCAGATGTTGGTG 59.598 55.000 0.00 0.00 0.00 4.17
4100 6553 6.552445 TTTGGTTAATGTTGATAATGGGGG 57.448 37.500 0.00 0.00 0.00 5.40
4111 6564 1.440618 TAATGGGGGCGTGACCATAT 58.559 50.000 7.20 2.50 46.38 1.78
4153 6606 7.212976 TGCACTTTTTGAAGGCAATAACATTA 58.787 30.769 0.00 0.00 33.25 1.90
4154 6607 7.877097 TGCACTTTTTGAAGGCAATAACATTAT 59.123 29.630 0.00 0.00 33.25 1.28
4361 6816 5.045359 TGAGGATTCAACATCAGAACAGGAT 60.045 40.000 0.00 0.00 0.00 3.24
4440 6895 8.609483 ACCAGGTATTGATCTGCATCTAAATAT 58.391 33.333 0.00 0.00 0.00 1.28
4483 6938 1.336632 AAGCTTTGCCCACTGCCAAA 61.337 50.000 0.00 0.00 40.16 3.28
4486 6941 0.249573 CTTTGCCCACTGCCAAACTG 60.250 55.000 0.00 0.00 40.16 3.16
4744 7205 3.549471 CGAGAACAAATCGACAGATCCAG 59.451 47.826 0.00 0.00 42.76 3.86
4830 7294 4.085733 CTGAGGATACCGAGGATGAAGAT 58.914 47.826 0.00 0.00 37.17 2.40
4938 7402 2.327200 ACGCTTACAAGGATAAGGGC 57.673 50.000 8.91 0.00 44.75 5.19
4988 7452 0.680618 CAAGCCTGCCAATGGTGAAA 59.319 50.000 0.00 0.00 0.00 2.69
5015 7479 0.550914 TGGTCCTGCTTGTTTCTGGT 59.449 50.000 0.00 0.00 0.00 4.00
5030 7494 5.163205 TGTTTCTGGTTGGAGATCTCAAGAA 60.163 40.000 23.85 18.34 0.00 2.52
5279 7750 0.589708 GTGTAACCAGTTGCCGTTCC 59.410 55.000 0.00 0.00 0.00 3.62
5288 7761 0.743345 GTTGCCGTTCCCGCTAGATT 60.743 55.000 0.00 0.00 0.00 2.40
5329 7828 3.073062 ACACTTCAATCTACCTTGGCAGT 59.927 43.478 0.00 0.00 0.00 4.40
5331 7830 3.327757 ACTTCAATCTACCTTGGCAGTGA 59.672 43.478 0.00 0.00 0.00 3.41
5512 8011 1.133216 TGCTCGTCGAAGATCTCCTTG 59.867 52.381 0.35 0.00 40.67 3.61
5535 8034 2.514824 GAAGGTCCCCATCTGCGC 60.515 66.667 0.00 0.00 0.00 6.09
5635 8134 1.419387 AGCTGTCTTTGAGCCTGAACT 59.581 47.619 0.00 0.00 37.12 3.01
5637 8136 2.031333 GCTGTCTTTGAGCCTGAACTTG 60.031 50.000 0.00 0.00 0.00 3.16
5651 8157 4.441913 CCTGAACTTGAAAAACATGGCTGT 60.442 41.667 0.00 0.00 37.12 4.40
5659 8165 3.294079 AACATGGCTGTTTGCTTGC 57.706 47.368 0.00 0.00 43.05 4.01
5660 8166 0.754472 AACATGGCTGTTTGCTTGCT 59.246 45.000 0.00 0.00 43.05 3.91
5661 8167 0.754472 ACATGGCTGTTTGCTTGCTT 59.246 45.000 0.00 0.00 42.39 3.91
5662 8168 1.269936 ACATGGCTGTTTGCTTGCTTC 60.270 47.619 0.00 0.00 42.39 3.86
5663 8169 1.000506 CATGGCTGTTTGCTTGCTTCT 59.999 47.619 0.00 0.00 42.39 2.85
5664 8170 1.113788 TGGCTGTTTGCTTGCTTCTT 58.886 45.000 0.00 0.00 42.39 2.52
5665 8171 1.481772 TGGCTGTTTGCTTGCTTCTTT 59.518 42.857 0.00 0.00 42.39 2.52
5671 8177 5.501413 GCTGTTTGCTTGCTTCTTTTTCTTC 60.501 40.000 0.00 0.00 38.95 2.87
5672 8178 5.477510 TGTTTGCTTGCTTCTTTTTCTTCA 58.522 33.333 0.00 0.00 0.00 3.02
5693 8201 6.951062 TCATAATGAGAAGAGTGAGACGAT 57.049 37.500 0.00 0.00 0.00 3.73
5701 8213 1.137872 AGAGTGAGACGATGGATTGCC 59.862 52.381 0.00 0.00 0.00 4.52
5785 8297 2.900122 CGTAGGTGGTCTTGCAAATG 57.100 50.000 0.00 0.00 0.00 2.32
5834 8351 4.343526 CAGTTAGTCACTAGCATCCATCCT 59.656 45.833 1.08 0.00 32.76 3.24
5835 8352 4.586841 AGTTAGTCACTAGCATCCATCCTC 59.413 45.833 1.08 0.00 31.97 3.71
6257 8890 2.821546 TCAGCAAGTGGTATACGATGC 58.178 47.619 5.58 5.58 43.14 3.91
6260 8893 1.261619 GCAAGTGGTATACGATGCTGC 59.738 52.381 6.30 0.00 41.10 5.25
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 2.297315 GGTGCCCTTCCTTCAAAAAGAG 59.703 50.000 0.00 0.00 34.14 2.85
9 10 4.018195 AGGGTGCCCTTCCTTCAA 57.982 55.556 3.45 0.00 45.70 2.69
54 55 8.644318 AGTACTTGCACTAATAAAGATAACGG 57.356 34.615 0.00 0.00 0.00 4.44
103 105 2.305927 AGTTGTAAGGTGGATGGGACTG 59.694 50.000 0.00 0.00 0.00 3.51
143 145 3.621715 GCCAAATCACTAGTTAACCCTCG 59.378 47.826 0.88 0.00 0.00 4.63
210 2413 7.279758 CCAAATGAAGTAAACCATGTGTGTTTT 59.720 33.333 4.26 0.00 37.18 2.43
223 2426 5.055265 TGGTCTGTCCCAAATGAAGTAAA 57.945 39.130 0.00 0.00 34.77 2.01
224 2427 4.715534 TGGTCTGTCCCAAATGAAGTAA 57.284 40.909 0.00 0.00 34.77 2.24
225 2428 4.104102 AGTTGGTCTGTCCCAAATGAAGTA 59.896 41.667 0.00 0.00 45.72 2.24
227 2430 3.490348 AGTTGGTCTGTCCCAAATGAAG 58.510 45.455 0.00 0.00 45.72 3.02
228 2431 3.486383 GAGTTGGTCTGTCCCAAATGAA 58.514 45.455 6.56 0.00 45.72 2.57
229 2432 2.549992 CGAGTTGGTCTGTCCCAAATGA 60.550 50.000 6.56 0.00 45.72 2.57
230 2433 1.806542 CGAGTTGGTCTGTCCCAAATG 59.193 52.381 6.56 0.00 45.72 2.32
232 2435 1.070134 CTCGAGTTGGTCTGTCCCAAA 59.930 52.381 3.62 0.00 45.72 3.28
233 2436 0.679505 CTCGAGTTGGTCTGTCCCAA 59.320 55.000 3.62 0.00 42.16 4.12
253 2456 2.158957 TGAAACTGCTTCCGAGTCACTT 60.159 45.455 0.00 0.00 32.53 3.16
262 2465 4.606961 TGAAACGAAATGAAACTGCTTCC 58.393 39.130 0.00 0.00 32.53 3.46
291 2494 3.442977 CCAGAAAAGGAAAGATGAGCCAG 59.557 47.826 0.00 0.00 0.00 4.85
339 2562 7.081349 GGAAAAACCAACAAACCAAAGAAAAG 58.919 34.615 0.00 0.00 38.79 2.27
364 2587 8.173130 AGAATAAAAAGTACGTAAATGGAAGCG 58.827 33.333 0.00 0.00 0.00 4.68
404 2627 2.238646 TGCGGGTTAGTGAAGATGGAAT 59.761 45.455 0.00 0.00 0.00 3.01
406 2629 1.271856 TGCGGGTTAGTGAAGATGGA 58.728 50.000 0.00 0.00 0.00 3.41
407 2630 2.107950 TTGCGGGTTAGTGAAGATGG 57.892 50.000 0.00 0.00 0.00 3.51
408 2631 4.497473 TTTTTGCGGGTTAGTGAAGATG 57.503 40.909 0.00 0.00 0.00 2.90
461 2686 0.758734 AAAAGCCCAAAGGAAGTGGC 59.241 50.000 0.00 0.00 44.35 5.01
463 2688 2.030805 CGAGAAAAGCCCAAAGGAAGTG 60.031 50.000 0.00 0.00 33.47 3.16
492 2730 9.129209 GAAAAAGAAAAGGATGAAATAAGTCCG 57.871 33.333 0.00 0.00 37.12 4.79
496 2734 8.374743 TGGGGAAAAAGAAAAGGATGAAATAAG 58.625 33.333 0.00 0.00 0.00 1.73
503 2741 7.822161 AAAAATGGGGAAAAAGAAAAGGATG 57.178 32.000 0.00 0.00 0.00 3.51
618 2881 8.809159 TGTGTTATTGTAAAATTCATGGTGTG 57.191 30.769 0.00 0.00 0.00 3.82
671 2936 7.621991 CAAATACGTTGGCATGTTTAAAAACA 58.378 30.769 10.47 10.47 41.95 2.83
810 3182 7.498570 TGAAGGATTCCCAAAAACTGAAAAATG 59.501 33.333 0.00 0.00 46.93 2.32
815 3187 6.552445 TTTGAAGGATTCCCAAAAACTGAA 57.448 33.333 0.00 0.00 46.93 3.02
965 3363 1.195347 CACTCTGACGATAAGCGCAG 58.805 55.000 11.47 0.00 46.04 5.18
971 3369 1.672854 CCGGCCCACTCTGACGATAA 61.673 60.000 0.00 0.00 0.00 1.75
972 3370 2.125326 CCGGCCCACTCTGACGATA 61.125 63.158 0.00 0.00 0.00 2.92
1019 3421 3.976701 CTGGCGGCTAGGGTTGGTG 62.977 68.421 11.43 0.00 0.00 4.17
1141 3574 2.363147 AGAGGAGGAGGTGGTCGC 60.363 66.667 0.00 0.00 0.00 5.19
1352 3785 4.386951 TCACATGGCGTCGGGTGG 62.387 66.667 10.42 0.00 32.29 4.61
1353 3786 2.815211 CTCACATGGCGTCGGGTG 60.815 66.667 4.66 4.66 0.00 4.61
1381 3814 1.725973 GCAAAACCGAAGCGTCAGC 60.726 57.895 0.00 0.00 45.58 4.26
1475 3911 2.561419 AGCAAAATTCACAGCAGAGCAT 59.439 40.909 0.00 0.00 0.00 3.79
1482 3918 3.922240 CCACATACAGCAAAATTCACAGC 59.078 43.478 0.00 0.00 0.00 4.40
1483 3919 5.048504 AGACCACATACAGCAAAATTCACAG 60.049 40.000 0.00 0.00 0.00 3.66
1497 3933 4.202050 GCATCAATTTCCCAGACCACATAC 60.202 45.833 0.00 0.00 0.00 2.39
1499 3935 2.762327 GCATCAATTTCCCAGACCACAT 59.238 45.455 0.00 0.00 0.00 3.21
1506 3942 1.479323 CCACAGGCATCAATTTCCCAG 59.521 52.381 0.00 0.00 0.00 4.45
1592 4036 2.009774 CCTTAAATGACAGCCCACGAG 58.990 52.381 0.00 0.00 0.00 4.18
1603 4047 6.373216 CAGACCCAACGATTAACCTTAAATGA 59.627 38.462 0.00 0.00 0.00 2.57
1638 4082 3.878103 TGCAAAGCTTAACCGAAACACTA 59.122 39.130 0.00 0.00 0.00 2.74
1746 4191 2.618709 GGACATTACATTACTGCAGCCC 59.381 50.000 15.27 0.00 0.00 5.19
1826 4271 6.312426 CCAAAGAATACTGAGCTCTAACACAG 59.688 42.308 16.19 5.77 34.79 3.66
2008 4453 3.935203 GGTTCGACATCAATGACTCACAT 59.065 43.478 0.00 0.00 41.45 3.21
2029 4474 7.486647 ACATCTAAGCATAAAATGAAGCAAGG 58.513 34.615 0.00 0.00 0.00 3.61
2229 4674 9.146586 AGGCAAAATATATAAAATGAGCAGGAA 57.853 29.630 0.00 0.00 0.00 3.36
2337 4784 8.046708 AGTATATAACAGAACATGCAAGGACAA 58.953 33.333 0.00 0.00 0.00 3.18
2386 4833 7.012421 AGCTGTTCTTTTTCTTAATCGAGTTGT 59.988 33.333 0.00 0.00 0.00 3.32
2414 4861 7.724061 ACATGATTGGGTGTTTAGAACTTTAGT 59.276 33.333 0.00 0.00 0.00 2.24
2661 5108 1.275291 CAGTTAAAGCTCCTCCGGTGA 59.725 52.381 4.76 0.31 0.00 4.02
2884 5332 0.677731 ATCCCGGCACAAGTGACATG 60.678 55.000 6.88 0.00 38.95 3.21
2971 5419 2.288273 GCAACACCTACGTCAGTCTCTT 60.288 50.000 0.00 0.00 0.00 2.85
3177 5625 8.915057 ACAAGAAAGAGAGAAATGAAGAATGA 57.085 30.769 0.00 0.00 0.00 2.57
3186 5634 8.302438 CAAAGGCAATACAAGAAAGAGAGAAAT 58.698 33.333 0.00 0.00 0.00 2.17
3221 5670 7.559486 ACATGATGCAGAAACTACAGAATCTA 58.441 34.615 0.00 0.00 0.00 1.98
3268 5717 1.196354 CTTCAAAGAAGCAGCACCGAG 59.804 52.381 0.00 0.00 0.00 4.63
3362 5812 3.341857 TGTTTCGTACACATGGCAAAC 57.658 42.857 0.00 0.00 0.00 2.93
3377 5827 7.179410 CAGTTTAAAGGCATGTGTTTTGTTTC 58.821 34.615 0.00 0.00 0.00 2.78
3381 5831 4.024977 GGCAGTTTAAAGGCATGTGTTTTG 60.025 41.667 12.37 0.00 0.00 2.44
3396 5846 4.576873 TGTTCAACTCGAAATGGCAGTTTA 59.423 37.500 0.19 0.00 34.69 2.01
3521 5971 5.496387 GTCAATCTGCAGAACATCAATACG 58.504 41.667 22.50 0.00 0.00 3.06
3646 6096 3.845781 TTGAACAGAAAGCAGTCCTCT 57.154 42.857 0.00 0.00 0.00 3.69
3666 6116 6.875195 CCTGCAAAAACAAACCTCATGAATAT 59.125 34.615 0.00 0.00 0.00 1.28
3769 6221 9.479549 AAAATCAGTTGTAATGGATAAGATGGT 57.520 29.630 0.00 0.00 0.00 3.55
3824 6277 6.148480 CACCTTTCTCTGTAAGATTGAACCTG 59.852 42.308 0.00 0.00 45.62 4.00
4060 6513 3.440173 ACCAAATGACAATACTTCTGCCG 59.560 43.478 0.00 0.00 0.00 5.69
4071 6524 9.650539 CCATTATCAACATTAACCAAATGACAA 57.349 29.630 4.82 0.00 46.81 3.18
4100 6553 0.687354 AGATCCCCATATGGTCACGC 59.313 55.000 20.46 5.96 0.00 5.34
4111 6564 1.075212 TGCATTGTCACAAGATCCCCA 59.925 47.619 0.00 0.00 0.00 4.96
4204 6657 8.172484 TGTAAAATTAATACGACTGCACATGAC 58.828 33.333 0.00 0.00 0.00 3.06
4361 6816 4.932789 GCATCGCCACCTTCACTA 57.067 55.556 0.00 0.00 0.00 2.74
4486 6941 4.699257 AGAAAACTGAATCTGCTGGATGAC 59.301 41.667 0.00 0.00 34.45 3.06
4760 7221 2.365105 CGGCTCCCTTAGGGTCCA 60.365 66.667 23.26 4.88 44.74 4.02
4818 7282 2.145958 ATGCGTCATCTTCATCCTCG 57.854 50.000 0.00 0.00 0.00 4.63
4896 7360 0.040646 TCGAGTTGAGGGGCCTTCTA 59.959 55.000 17.30 6.44 0.00 2.10
4938 7402 0.251297 TGGAGTTCATGGTGCCCTTG 60.251 55.000 0.00 1.99 0.00 3.61
4988 7452 0.468029 CAAGCAGGACCAACCAACCT 60.468 55.000 0.00 0.00 42.04 3.50
5015 7479 4.104738 ACCAAACCTTCTTGAGATCTCCAA 59.895 41.667 20.03 12.62 0.00 3.53
5030 7494 0.535102 CTCAAGACCGCACCAAACCT 60.535 55.000 0.00 0.00 0.00 3.50
5076 7540 6.642683 AAACTGACAACGGAAATATACTCG 57.357 37.500 0.00 0.00 0.00 4.18
5206 7677 3.990318 AGTAAACTGCCAAAGAGCAAC 57.010 42.857 0.00 0.00 43.52 4.17
5279 7750 4.371855 TCAGTAAGACACAATCTAGCGG 57.628 45.455 0.00 0.00 36.27 5.52
5416 7915 4.728110 AAGGATGCTGCTGCCGCA 62.728 61.111 20.66 20.66 45.60 5.69
5651 8157 8.767085 CATTATGAAGAAAAAGAAGCAAGCAAA 58.233 29.630 0.00 0.00 0.00 3.68
5658 8164 9.771915 CTCTTCTCATTATGAAGAAAAAGAAGC 57.228 33.333 11.04 0.00 46.03 3.86
5664 8170 9.429359 GTCTCACTCTTCTCATTATGAAGAAAA 57.571 33.333 7.45 0.00 46.03 2.29
5665 8171 7.757173 CGTCTCACTCTTCTCATTATGAAGAAA 59.243 37.037 7.45 0.00 46.03 2.52
5671 8177 5.919707 CCATCGTCTCACTCTTCTCATTATG 59.080 44.000 0.00 0.00 0.00 1.90
5672 8178 5.830457 TCCATCGTCTCACTCTTCTCATTAT 59.170 40.000 0.00 0.00 0.00 1.28
5688 8196 1.077787 TGGGTGGCAATCCATCGTC 60.078 57.895 6.72 0.00 44.65 4.20
5693 8201 4.358841 CGGGTGGGTGGCAATCCA 62.359 66.667 6.72 6.72 40.85 3.41
5701 8213 2.184322 CTCGTCATCGGGTGGGTG 59.816 66.667 0.00 0.00 37.69 4.61
5705 8217 2.105128 GAGGCTCGTCATCGGGTG 59.895 66.667 0.00 0.00 40.06 4.61
5785 8297 2.169561 TCTGTTGGGTTTTCCTTTTGCC 59.830 45.455 0.00 0.00 40.46 4.52
5788 8300 4.159693 GTGTCTCTGTTGGGTTTTCCTTTT 59.840 41.667 0.00 0.00 40.46 2.27
6116 8736 1.020437 GATAAGCCTCCTTGTGCTGC 58.980 55.000 0.00 0.00 38.00 5.25
6257 8890 5.940192 TCCAGTGTTTACAACTATTGCAG 57.060 39.130 0.00 0.00 0.00 4.41


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

AutoCloner maintained by Alex Coulton.