Multiple sequence alignment - TraesCS3D01G095400

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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 TraesCS3D01G095400 chr3D 100.000 4933 0 0 1 4933 48427685 48422753 0.000000e+00 9110.0
1 TraesCS3D01G095400 chr3D 100.000 31 0 0 406 436 48427201 48427171 1.920000e-04 58.4
2 TraesCS3D01G095400 chr3D 100.000 31 0 0 485 515 48427280 48427250 1.920000e-04 58.4
3 TraesCS3D01G095400 chr3A 93.114 4865 184 57 1 4780 60634072 60629274 0.000000e+00 6988.0
4 TraesCS3D01G095400 chr3B 93.907 4152 153 40 548 4672 76485700 76481622 0.000000e+00 6174.0
5 TraesCS3D01G095400 chr3B 88.143 447 39 5 1 446 76489400 76488967 2.040000e-143 520.0
6 TraesCS3D01G095400 chr3B 84.286 140 9 1 4807 4933 76481485 76481346 1.860000e-24 124.0
7 TraesCS3D01G095400 chr3B 82.576 132 5 9 4667 4780 76481601 76481470 3.140000e-17 100.0
8 TraesCS3D01G095400 chr4B 79.670 182 37 0 3068 3249 379418503 379418684 1.110000e-26 132.0
9 TraesCS3D01G095400 chr4B 85.507 69 9 1 2424 2492 379417862 379417929 2.460000e-08 71.3
10 TraesCS3D01G095400 chr4D 87.879 66 6 2 2428 2492 304264974 304265038 5.300000e-10 76.8
11 TraesCS3D01G095400 chr4A 86.957 69 7 2 2428 2495 175001440 175001373 5.300000e-10 76.8
12 TraesCS3D01G095400 chr6A 97.059 34 0 1 3849 3882 520431344 520431376 6.900000e-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 TraesCS3D01G095400 chr3D 48422753 48427685 4932 True 3075.6 9110 100.000 1 4933 3 chr3D.!!$R1 4932
1 TraesCS3D01G095400 chr3A 60629274 60634072 4798 True 6988.0 6988 93.114 1 4780 1 chr3A.!!$R1 4779
2 TraesCS3D01G095400 chr3B 76481346 76489400 8054 True 1729.5 6174 87.228 1 4933 4 chr3B.!!$R1 4932

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
685 3866 0.469917 CCGCCTCTCTCTCTCTCTCT 59.530 60.000 0.0 0.0 0.00 3.10 F
1386 4586 0.248866 GGCAGTTTTGTGGTCAACGG 60.249 55.000 0.0 0.0 32.93 4.44 F
1822 5038 0.626916 AGCTTTTATTACCCCCGGCA 59.373 50.000 0.0 0.0 0.00 5.69 F
2159 5385 1.068588 GTGACCATAGCACGCCATCTA 59.931 52.381 0.0 0.0 0.00 1.98 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1660 4862 0.413832 TCAGAGGCCAGAGTTAGGGT 59.586 55.000 5.01 0.0 0.00 4.34 R
2271 5497 2.978156 TCCAGGAAGCAACTTTGGAT 57.022 45.000 0.00 0.0 33.21 3.41 R
2959 6187 4.633565 GGTGAGCTCCTCAGTTTCTTTATG 59.366 45.833 12.15 0.0 41.46 1.90 R
4001 7230 2.160417 GTCAGCTGTACAAAGTCATGGC 59.840 50.000 14.67 0.0 0.00 4.40 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
183 184 5.525378 TGACAACAATTAATTGGTTGCCAAC 59.475 36.000 27.43 19.01 46.95 3.77
313 317 5.041191 AGAACCTATGCATTTGACTAGGG 57.959 43.478 3.54 0.00 35.97 3.53
399 405 8.209917 AGACACTTCTAAATTAAAATAGGCGG 57.790 34.615 0.00 0.00 0.00 6.13
450 456 7.238710 AGACTTGGTTTTATTAGTTCCCATGT 58.761 34.615 0.00 0.00 34.29 3.21
507 3578 9.660180 AATTTCTGAGAAGTACTTATCCAAGAC 57.340 33.333 23.75 3.51 35.60 3.01
508 3579 8.423906 TTTCTGAGAAGTACTTATCCAAGACT 57.576 34.615 23.75 8.14 35.60 3.24
510 3581 7.831753 TCTGAGAAGTACTTATCCAAGACTTG 58.168 38.462 23.75 8.31 34.80 3.16
673 3854 4.075793 TCCTGCCTACCCGCCTCT 62.076 66.667 0.00 0.00 0.00 3.69
674 3855 3.541713 CCTGCCTACCCGCCTCTC 61.542 72.222 0.00 0.00 0.00 3.20
675 3856 2.443016 CTGCCTACCCGCCTCTCT 60.443 66.667 0.00 0.00 0.00 3.10
676 3857 2.442272 TGCCTACCCGCCTCTCTC 60.442 66.667 0.00 0.00 0.00 3.20
677 3858 2.123640 GCCTACCCGCCTCTCTCT 60.124 66.667 0.00 0.00 0.00 3.10
678 3859 2.197605 GCCTACCCGCCTCTCTCTC 61.198 68.421 0.00 0.00 0.00 3.20
679 3860 1.534697 CCTACCCGCCTCTCTCTCT 59.465 63.158 0.00 0.00 0.00 3.10
680 3861 0.536460 CCTACCCGCCTCTCTCTCTC 60.536 65.000 0.00 0.00 0.00 3.20
681 3862 0.472471 CTACCCGCCTCTCTCTCTCT 59.528 60.000 0.00 0.00 0.00 3.10
682 3863 0.470766 TACCCGCCTCTCTCTCTCTC 59.529 60.000 0.00 0.00 0.00 3.20
683 3864 1.279025 ACCCGCCTCTCTCTCTCTCT 61.279 60.000 0.00 0.00 0.00 3.10
684 3865 0.535102 CCCGCCTCTCTCTCTCTCTC 60.535 65.000 0.00 0.00 0.00 3.20
685 3866 0.469917 CCGCCTCTCTCTCTCTCTCT 59.530 60.000 0.00 0.00 0.00 3.10
686 3867 1.541233 CCGCCTCTCTCTCTCTCTCTC 60.541 61.905 0.00 0.00 0.00 3.20
687 3868 1.414181 CGCCTCTCTCTCTCTCTCTCT 59.586 57.143 0.00 0.00 0.00 3.10
698 3879 4.017591 TCTCTCTCTCTCTCTGTCCCATTT 60.018 45.833 0.00 0.00 0.00 2.32
699 3880 4.277476 TCTCTCTCTCTCTGTCCCATTTC 58.723 47.826 0.00 0.00 0.00 2.17
700 3881 3.370104 TCTCTCTCTCTGTCCCATTTCC 58.630 50.000 0.00 0.00 0.00 3.13
778 3962 2.210116 ACTATTAATGGCTGCCGTTCG 58.790 47.619 28.23 17.11 34.27 3.95
803 3987 2.332063 AATCACGGAGGCCATTACTG 57.668 50.000 5.01 0.67 0.00 2.74
845 4029 1.376166 CCCCATAAACACCGTCGCA 60.376 57.895 0.00 0.00 0.00 5.10
894 4078 4.697756 GTGCCGCTGGTGGTAGCA 62.698 66.667 2.05 0.00 43.87 3.49
903 4087 1.376037 GGTGGTAGCAGCAGTGGTC 60.376 63.158 18.66 0.00 35.51 4.02
1012 4196 4.530857 GGGAGATGGTCGTGGCGG 62.531 72.222 0.00 0.00 0.00 6.13
1267 4451 5.542251 AGGAGTAAGTGCTCTCTTCTTCTTT 59.458 40.000 0.00 0.00 35.89 2.52
1268 4452 6.042666 AGGAGTAAGTGCTCTCTTCTTCTTTT 59.957 38.462 0.00 0.00 35.89 2.27
1285 4485 3.395941 TCTTTTTCTTCCTCTTGCTCCCT 59.604 43.478 0.00 0.00 0.00 4.20
1289 4489 1.203364 TCTTCCTCTTGCTCCCTCCTT 60.203 52.381 0.00 0.00 0.00 3.36
1310 4510 2.237893 TCCCTTCCGTGGAATTTAGTCC 59.762 50.000 1.02 0.00 38.27 3.85
1386 4586 0.248866 GGCAGTTTTGTGGTCAACGG 60.249 55.000 0.00 0.00 32.93 4.44
1451 4651 2.480244 GGCGATTCTGAGGCCAATTTTC 60.480 50.000 5.01 0.00 46.13 2.29
1455 4655 2.291209 TCTGAGGCCAATTTTCTGCA 57.709 45.000 5.01 0.00 0.00 4.41
1456 4656 2.596346 TCTGAGGCCAATTTTCTGCAA 58.404 42.857 5.01 0.00 0.00 4.08
1459 4659 3.167485 TGAGGCCAATTTTCTGCAATCT 58.833 40.909 5.01 0.00 0.00 2.40
1471 4671 2.781757 TCTGCAATCTTGGGATCTCCAT 59.218 45.455 4.04 0.00 46.52 3.41
1472 4672 3.203710 TCTGCAATCTTGGGATCTCCATT 59.796 43.478 4.04 0.00 46.52 3.16
1491 4691 2.203669 TGCATTGGGGCTGCAACT 60.204 55.556 0.50 0.00 46.06 3.16
1492 4692 2.263540 GCATTGGGGCTGCAACTG 59.736 61.111 0.50 0.00 39.46 3.16
1493 4693 2.263540 CATTGGGGCTGCAACTGC 59.736 61.111 0.50 0.00 42.50 4.40
1515 4715 1.588674 ACGTTCTGAATTTGCGGTCA 58.411 45.000 0.00 0.00 0.00 4.02
1529 4729 1.000506 GCGGTCACTTCTTGGTAGACA 59.999 52.381 0.00 0.00 0.00 3.41
1607 4809 3.306849 CCTGTGCTGCTCATATGCTATCT 60.307 47.826 4.73 0.00 0.00 1.98
1608 4810 3.922910 TGTGCTGCTCATATGCTATCTC 58.077 45.455 0.00 0.00 0.00 2.75
1660 4862 2.026729 TGGAACATCCAATCGTAAGGCA 60.027 45.455 0.00 0.00 45.00 4.75
1662 4864 2.038387 ACATCCAATCGTAAGGCACC 57.962 50.000 0.00 0.00 38.47 5.01
1665 4867 1.868713 TCCAATCGTAAGGCACCCTA 58.131 50.000 0.00 0.00 31.13 3.53
1666 4868 2.189676 TCCAATCGTAAGGCACCCTAA 58.810 47.619 0.00 0.00 31.13 2.69
1714 4930 5.695816 CCTTTGCTGCTTTATGTTGCTAAAA 59.304 36.000 0.00 0.00 0.00 1.52
1715 4931 6.202570 CCTTTGCTGCTTTATGTTGCTAAAAA 59.797 34.615 0.00 0.00 0.00 1.94
1716 4932 7.095102 CCTTTGCTGCTTTATGTTGCTAAAAAT 60.095 33.333 0.00 0.00 0.00 1.82
1717 4933 7.727331 TTGCTGCTTTATGTTGCTAAAAATT 57.273 28.000 0.00 0.00 0.00 1.82
1720 4936 8.924691 TGCTGCTTTATGTTGCTAAAAATTAAG 58.075 29.630 0.00 0.00 0.00 1.85
1821 5037 1.679680 GAAGCTTTTATTACCCCCGGC 59.320 52.381 0.00 0.00 0.00 6.13
1822 5038 0.626916 AGCTTTTATTACCCCCGGCA 59.373 50.000 0.00 0.00 0.00 5.69
1833 5049 1.376086 CCCCGGCATCTGCATCATA 59.624 57.895 0.00 0.00 44.36 2.15
1836 5052 1.436600 CCGGCATCTGCATCATAGAC 58.563 55.000 4.33 0.00 44.36 2.59
2003 5226 3.760580 AATGGCTATCTGCTAGTGACC 57.239 47.619 0.00 0.00 42.39 4.02
2047 5270 3.253838 AGCCGGGGTTTGTGCCTA 61.254 61.111 2.18 0.00 0.00 3.93
2055 5278 2.633488 GGGTTTGTGCCTAAGCTAGAG 58.367 52.381 0.00 0.00 40.80 2.43
2070 5295 9.547753 CCTAAGCTAGAGTAGATTATTTTTGCA 57.452 33.333 0.00 0.00 36.24 4.08
2083 5308 2.880963 TTTTGCACTGTAGTTTGGGC 57.119 45.000 0.00 0.00 0.00 5.36
2159 5385 1.068588 GTGACCATAGCACGCCATCTA 59.931 52.381 0.00 0.00 0.00 1.98
2261 5487 9.852481 CAACATTGTTTCAATAACATCAAACAG 57.148 29.630 0.00 0.00 39.31 3.16
2295 5521 3.070015 CCAAAGTTGCTTCCTGGAAACAT 59.930 43.478 12.92 0.00 41.51 2.71
2298 5524 6.458210 CAAAGTTGCTTCCTGGAAACATATT 58.542 36.000 12.92 8.36 41.51 1.28
2310 5536 7.282224 TCCTGGAAACATATTAACATGTGCTAC 59.718 37.037 0.00 0.00 39.10 3.58
2311 5537 7.328277 TGGAAACATATTAACATGTGCTACC 57.672 36.000 0.00 3.16 39.10 3.18
2313 5539 7.559533 TGGAAACATATTAACATGTGCTACCAT 59.440 33.333 0.00 0.00 39.10 3.55
2336 5564 7.218773 CCATCTTGTGCTATTGTAAATGTTTCG 59.781 37.037 0.00 0.00 0.00 3.46
2540 5768 4.287720 CGTTGAAACTCCAGCTAAAAACC 58.712 43.478 0.00 0.00 0.00 3.27
2959 6187 1.870055 CTGCACACATGGCTGTTCCC 61.870 60.000 0.00 0.00 31.62 3.97
3195 6424 5.250774 AGCTCTAGGGTTTTCAAAGGATACA 59.749 40.000 0.00 0.00 41.41 2.29
3722 6951 5.256474 ACCATCTTATTGGACAGGACAAAG 58.744 41.667 0.00 0.00 39.25 2.77
3953 7182 3.080300 TGATACCCGGAAAAGCATTGT 57.920 42.857 0.73 0.00 0.00 2.71
4273 7512 2.308866 TCTCCATTCCCCCTTCTTGTTC 59.691 50.000 0.00 0.00 0.00 3.18
4363 7602 7.739498 TTCCTCCAATGTTCTTTTGTACTAC 57.261 36.000 0.00 0.00 0.00 2.73
4364 7603 6.235664 TCCTCCAATGTTCTTTTGTACTACC 58.764 40.000 0.00 0.00 0.00 3.18
4365 7604 6.001460 CCTCCAATGTTCTTTTGTACTACCA 58.999 40.000 0.00 0.00 0.00 3.25
4366 7605 6.149474 CCTCCAATGTTCTTTTGTACTACCAG 59.851 42.308 0.00 0.00 0.00 4.00
4367 7606 6.597562 TCCAATGTTCTTTTGTACTACCAGT 58.402 36.000 0.00 0.00 0.00 4.00
4368 7607 7.057894 TCCAATGTTCTTTTGTACTACCAGTT 58.942 34.615 0.00 0.00 0.00 3.16
4370 7609 8.287503 CCAATGTTCTTTTGTACTACCAGTTAC 58.712 37.037 0.00 0.00 0.00 2.50
4371 7610 7.974482 ATGTTCTTTTGTACTACCAGTTACC 57.026 36.000 0.00 0.00 0.00 2.85
4372 7611 6.887013 TGTTCTTTTGTACTACCAGTTACCA 58.113 36.000 0.00 0.00 0.00 3.25
4373 7612 7.337167 TGTTCTTTTGTACTACCAGTTACCAA 58.663 34.615 0.00 0.00 0.00 3.67
4374 7613 7.828223 TGTTCTTTTGTACTACCAGTTACCAAA 59.172 33.333 0.00 0.00 0.00 3.28
4375 7614 8.843262 GTTCTTTTGTACTACCAGTTACCAAAT 58.157 33.333 0.00 0.00 0.00 2.32
4431 7670 3.153919 TGACAAACATTAACCTGGAGCC 58.846 45.455 0.00 0.00 0.00 4.70
4525 7765 4.843147 TGTTGAACTGTATGCAAACTTCG 58.157 39.130 0.00 0.00 0.00 3.79
4571 7811 0.040514 TGCGAATTTGACCTGCAACG 60.041 50.000 0.00 0.00 35.91 4.10
4627 7868 4.368565 ACCAGCTGATCTCATGCATATT 57.631 40.909 17.39 0.00 0.00 1.28
4628 7869 4.726583 ACCAGCTGATCTCATGCATATTT 58.273 39.130 17.39 0.00 0.00 1.40
4633 7874 7.201652 CCAGCTGATCTCATGCATATTTATCTG 60.202 40.741 17.39 6.04 0.00 2.90
4712 7997 6.928348 TGTGTCCTAGAGATTTGGTTTAGA 57.072 37.500 0.00 0.00 0.00 2.10
4724 8009 5.616488 TTTGGTTTAGAGTAATCGGTTGC 57.384 39.130 0.00 0.00 0.00 4.17
4725 8010 4.546829 TGGTTTAGAGTAATCGGTTGCT 57.453 40.909 0.00 0.00 32.62 3.91
4780 8065 6.037500 GCTTGGTTTGAAAAGAAAATGCTCTT 59.962 34.615 0.00 0.00 37.24 2.85
4781 8066 7.224557 GCTTGGTTTGAAAAGAAAATGCTCTTA 59.775 33.333 0.00 0.00 34.49 2.10
4782 8067 9.264719 CTTGGTTTGAAAAGAAAATGCTCTTAT 57.735 29.630 0.00 0.00 34.49 1.73
4783 8068 9.612066 TTGGTTTGAAAAGAAAATGCTCTTATT 57.388 25.926 0.00 0.00 34.49 1.40
4784 8069 9.260002 TGGTTTGAAAAGAAAATGCTCTTATTC 57.740 29.630 0.00 0.00 34.49 1.75
4785 8070 8.427774 GGTTTGAAAAGAAAATGCTCTTATTCG 58.572 33.333 0.00 0.00 34.49 3.34
4786 8071 7.566858 TTGAAAAGAAAATGCTCTTATTCGC 57.433 32.000 0.00 0.00 34.49 4.70
4787 8072 6.676950 TGAAAAGAAAATGCTCTTATTCGCA 58.323 32.000 0.00 0.00 40.87 5.10
4788 8073 7.144661 TGAAAAGAAAATGCTCTTATTCGCAA 58.855 30.769 0.00 0.00 39.89 4.85
4789 8074 7.651304 TGAAAAGAAAATGCTCTTATTCGCAAA 59.349 29.630 0.00 0.00 39.89 3.68
4790 8075 7.945033 AAAGAAAATGCTCTTATTCGCAAAA 57.055 28.000 0.00 0.00 39.89 2.44
4791 8076 7.945033 AAGAAAATGCTCTTATTCGCAAAAA 57.055 28.000 0.00 0.00 39.89 1.94
4876 8161 7.009265 GTCTGAACTTGGTTTTGTCTTTTTAGC 59.991 37.037 0.00 0.00 0.00 3.09
4884 8169 6.128795 TGGTTTTGTCTTTTTAGCGTTTGTTG 60.129 34.615 0.00 0.00 0.00 3.33
4899 8197 5.386627 GCGTTTGTTGAATTTACGGCTAAAC 60.387 40.000 0.00 0.00 33.17 2.01
4907 8205 7.266922 TGAATTTACGGCTAAACTTTCAACT 57.733 32.000 0.00 0.00 0.00 3.16
4911 8209 6.774354 TTACGGCTAAACTTTCAACTGTAG 57.226 37.500 0.00 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
131 132 1.234821 TCGGTTGCTTCGAAATGCTT 58.765 45.000 10.33 0.00 33.42 3.91
300 304 9.155975 CATACTACAATATCCCTAGTCAAATGC 57.844 37.037 0.00 0.00 0.00 3.56
406 412 7.831753 CAAGTCTTGGATAAGTACTTCTCAGA 58.168 38.462 19.27 12.80 34.76 3.27
426 432 7.462571 ACATGGGAACTAATAAAACCAAGTC 57.537 36.000 0.00 0.00 0.00 3.01
505 3576 3.365364 CCTCGAAATGCTGAAACCAAGTC 60.365 47.826 0.00 0.00 0.00 3.01
507 3578 2.095059 CCCTCGAAATGCTGAAACCAAG 60.095 50.000 0.00 0.00 0.00 3.61
508 3579 1.885887 CCCTCGAAATGCTGAAACCAA 59.114 47.619 0.00 0.00 0.00 3.67
510 3581 1.821216 TCCCTCGAAATGCTGAAACC 58.179 50.000 0.00 0.00 0.00 3.27
673 3854 2.771943 GGGACAGAGAGAGAGAGAGAGA 59.228 54.545 0.00 0.00 0.00 3.10
674 3855 2.505407 TGGGACAGAGAGAGAGAGAGAG 59.495 54.545 0.00 0.00 0.00 3.20
675 3856 2.556766 TGGGACAGAGAGAGAGAGAGA 58.443 52.381 0.00 0.00 0.00 3.10
698 3879 3.458118 AGAAGAGAAGAGATCGAGGAGGA 59.542 47.826 0.00 0.00 0.00 3.71
699 3880 3.820557 AGAAGAGAAGAGATCGAGGAGG 58.179 50.000 0.00 0.00 0.00 4.30
700 3881 4.275936 GGAAGAAGAGAAGAGATCGAGGAG 59.724 50.000 0.00 0.00 0.00 3.69
778 3962 2.396590 TGGCCTCCGTGATTAGTTTC 57.603 50.000 3.32 0.00 0.00 2.78
803 3987 1.660560 TAACTACGCCGTCAGGAGCC 61.661 60.000 0.00 0.00 41.37 4.70
845 4029 0.318762 GCGAAGGATTAGAGCGGGAT 59.681 55.000 0.00 0.00 0.00 3.85
894 4078 1.174783 CTAGTACCACGACCACTGCT 58.825 55.000 0.00 0.00 0.00 4.24
903 4087 1.880819 AACCGCCACCTAGTACCACG 61.881 60.000 0.00 0.00 0.00 4.94
990 4174 2.687566 ACGACCATCTCCCCACCC 60.688 66.667 0.00 0.00 0.00 4.61
1267 4451 1.630878 GGAGGGAGCAAGAGGAAGAAA 59.369 52.381 0.00 0.00 0.00 2.52
1268 4452 1.203364 AGGAGGGAGCAAGAGGAAGAA 60.203 52.381 0.00 0.00 0.00 2.52
1285 4485 1.368374 AATTCCACGGAAGGGAAGGA 58.632 50.000 4.58 0.00 46.85 3.36
1289 4489 2.237893 GGACTAAATTCCACGGAAGGGA 59.762 50.000 4.58 0.00 37.56 4.20
1416 4616 1.026182 ATCGCCATTTCGAGCTTGCA 61.026 50.000 0.00 0.00 42.14 4.08
1451 4651 2.723322 TGGAGATCCCAAGATTGCAG 57.277 50.000 0.84 0.00 43.29 4.41
1493 4693 2.719046 GACCGCAAATTCAGAACGTTTG 59.281 45.455 0.46 3.17 36.26 2.93
1494 4694 2.356382 TGACCGCAAATTCAGAACGTTT 59.644 40.909 0.46 0.00 0.00 3.60
1495 4695 1.944024 TGACCGCAAATTCAGAACGTT 59.056 42.857 0.00 0.00 0.00 3.99
1496 4696 1.263217 GTGACCGCAAATTCAGAACGT 59.737 47.619 0.00 0.00 0.00 3.99
1515 4715 4.649674 TCAGAACAGTGTCTACCAAGAAGT 59.350 41.667 0.00 0.00 32.16 3.01
1529 4729 1.417890 CAGGTCCAGGTTCAGAACAGT 59.582 52.381 15.36 0.00 0.00 3.55
1607 4809 4.898320 TGCTTACAAATCAGCTCTCAAGA 58.102 39.130 0.00 0.00 36.92 3.02
1608 4810 5.353400 TCATGCTTACAAATCAGCTCTCAAG 59.647 40.000 0.00 0.00 36.92 3.02
1660 4862 0.413832 TCAGAGGCCAGAGTTAGGGT 59.586 55.000 5.01 0.00 0.00 4.34
1662 4864 4.651503 TCTTAATCAGAGGCCAGAGTTAGG 59.348 45.833 5.01 0.00 0.00 2.69
1665 4867 4.718774 TCATCTTAATCAGAGGCCAGAGTT 59.281 41.667 5.01 0.00 33.87 3.01
1666 4868 4.293494 TCATCTTAATCAGAGGCCAGAGT 58.707 43.478 5.01 1.22 33.87 3.24
1716 4932 9.653287 CTCCACTCTGTATCATTTGTTACTTAA 57.347 33.333 1.70 0.00 0.00 1.85
1717 4933 8.812972 ACTCCACTCTGTATCATTTGTTACTTA 58.187 33.333 1.70 0.00 0.00 2.24
1720 4936 9.601217 AATACTCCACTCTGTATCATTTGTTAC 57.399 33.333 0.00 0.00 0.00 2.50
1736 4952 2.066262 CGTGTTGCGAAATACTCCACT 58.934 47.619 1.21 0.00 44.77 4.00
1737 4953 1.463528 GCGTGTTGCGAAATACTCCAC 60.464 52.381 1.21 0.00 44.77 4.02
1738 4954 0.793861 GCGTGTTGCGAAATACTCCA 59.206 50.000 1.21 0.00 44.77 3.86
1739 4955 3.580658 GCGTGTTGCGAAATACTCC 57.419 52.632 1.21 0.00 44.77 3.85
1836 5052 1.596260 CAATCAGTGAGGCTGTATGCG 59.404 52.381 0.00 0.00 45.23 4.73
2003 5226 1.017387 GATTAAGGCCTCCGTTGCAG 58.983 55.000 5.23 0.00 0.00 4.41
2043 5266 8.499967 GCAAAAATAATCTACTCTAGCTTAGGC 58.500 37.037 0.00 0.00 39.06 3.93
2047 5270 8.887717 CAGTGCAAAAATAATCTACTCTAGCTT 58.112 33.333 0.00 0.00 0.00 3.74
2055 5278 9.341899 CCAAACTACAGTGCAAAAATAATCTAC 57.658 33.333 0.00 0.00 0.00 2.59
2070 5295 1.247567 GCATGTGCCCAAACTACAGT 58.752 50.000 0.00 0.00 34.31 3.55
2083 5308 3.338818 AAATTAGAATCGCGGCATGTG 57.661 42.857 6.13 0.00 0.00 3.21
2159 5385 6.313519 TCAGGGAGCACTAATGTTAGATTT 57.686 37.500 6.78 0.00 34.84 2.17
2223 5449 7.536895 TGAAACAATGTTGAATGGAAAACTG 57.463 32.000 0.00 0.00 0.00 3.16
2261 5487 3.507622 AGCAACTTTGGATAAACAGCTCC 59.492 43.478 0.00 0.00 0.00 4.70
2271 5497 2.978156 TCCAGGAAGCAACTTTGGAT 57.022 45.000 0.00 0.00 33.21 3.41
2278 5504 6.919721 TGTTAATATGTTTCCAGGAAGCAAC 58.080 36.000 21.44 14.92 36.46 4.17
2295 5521 6.038161 GCACAAGATGGTAGCACATGTTAATA 59.962 38.462 0.00 0.00 33.20 0.98
2298 5524 3.689161 GCACAAGATGGTAGCACATGTTA 59.311 43.478 0.00 0.00 33.20 2.41
2310 5536 7.218773 CGAAACATTTACAATAGCACAAGATGG 59.781 37.037 0.00 0.00 0.00 3.51
2311 5537 7.750458 ACGAAACATTTACAATAGCACAAGATG 59.250 33.333 0.00 0.00 0.00 2.90
2313 5539 7.197071 ACGAAACATTTACAATAGCACAAGA 57.803 32.000 0.00 0.00 0.00 3.02
2336 5564 7.509659 TCCTATTTTACTCTGAGATAAGGGGAC 59.490 40.741 12.44 0.00 0.00 4.46
2540 5768 4.509600 GGCATCGAATAAAGTCTTCTCCTG 59.490 45.833 0.00 0.00 0.00 3.86
2959 6187 4.633565 GGTGAGCTCCTCAGTTTCTTTATG 59.366 45.833 12.15 0.00 41.46 1.90
3195 6424 9.986157 ATTTCACCAGAGGCAATATATATCAAT 57.014 29.630 0.00 0.00 0.00 2.57
3722 6951 6.849588 AAATGATCCAAAAGTTCAACAAGC 57.150 33.333 0.00 0.00 0.00 4.01
3953 7182 6.888105 TCAGGTCAGCATCAATACTCATTTA 58.112 36.000 0.00 0.00 0.00 1.40
4001 7230 2.160417 GTCAGCTGTACAAAGTCATGGC 59.840 50.000 14.67 0.00 0.00 4.40
4235 7471 7.503566 GGAATGGAGAGTGAAATGAAATGGATA 59.496 37.037 0.00 0.00 0.00 2.59
4273 7512 3.244146 CCATGATAAGAGTCAGAGCCCTG 60.244 52.174 0.00 0.00 41.74 4.45
4370 7609 9.826574 ATGACCTGAAATTTCATAATGATTTGG 57.173 29.630 20.76 16.30 36.46 3.28
4375 7614 9.904198 TCTGTATGACCTGAAATTTCATAATGA 57.096 29.630 20.76 8.84 34.73 2.57
4455 7694 7.951530 CAGTTGCTGGAAAGAAATAAAATGT 57.048 32.000 0.00 0.00 0.00 2.71
4473 7713 1.267806 CACACTCAATGACCCAGTTGC 59.732 52.381 0.00 0.00 0.00 4.17
4486 7726 8.394877 CAGTTCAACAAAGTAATAACACACTCA 58.605 33.333 0.00 0.00 0.00 3.41
4538 7778 1.674359 TTCGCAGAAGCAAGGACAAA 58.326 45.000 0.00 0.00 45.90 2.83
4571 7811 1.092345 GGTCAGCTGATTCCTTCGCC 61.092 60.000 21.47 9.89 0.00 5.54
4712 7997 4.072131 ACATGTTTGAGCAACCGATTACT 58.928 39.130 0.00 0.00 33.97 2.24
4795 8080 9.881649 AGAGCATTTTCTTTTCTTTTCTTTTCT 57.118 25.926 0.00 0.00 0.00 2.52
4802 8087 9.617975 CGATTCTAGAGCATTTTCTTTTCTTTT 57.382 29.630 0.00 0.00 0.00 2.27
4803 8088 8.787852 ACGATTCTAGAGCATTTTCTTTTCTTT 58.212 29.630 0.00 0.00 0.00 2.52
4804 8089 8.329203 ACGATTCTAGAGCATTTTCTTTTCTT 57.671 30.769 0.00 0.00 0.00 2.52
4805 8090 7.913674 ACGATTCTAGAGCATTTTCTTTTCT 57.086 32.000 0.00 0.00 0.00 2.52
4806 8091 8.844690 CAAACGATTCTAGAGCATTTTCTTTTC 58.155 33.333 0.00 0.00 0.00 2.29
4807 8092 7.809806 CCAAACGATTCTAGAGCATTTTCTTTT 59.190 33.333 0.00 0.00 0.00 2.27
4808 8093 7.040409 ACCAAACGATTCTAGAGCATTTTCTTT 60.040 33.333 0.00 0.00 0.00 2.52
4809 8094 6.431234 ACCAAACGATTCTAGAGCATTTTCTT 59.569 34.615 0.00 0.00 0.00 2.52
4810 8095 5.940470 ACCAAACGATTCTAGAGCATTTTCT 59.060 36.000 0.00 0.00 0.00 2.52
4811 8096 6.183309 ACCAAACGATTCTAGAGCATTTTC 57.817 37.500 0.00 0.00 0.00 2.29
4812 8097 7.865706 ATACCAAACGATTCTAGAGCATTTT 57.134 32.000 0.00 0.00 0.00 1.82
4813 8098 7.865706 AATACCAAACGATTCTAGAGCATTT 57.134 32.000 0.00 0.00 0.00 2.32
4814 8099 7.865706 AAATACCAAACGATTCTAGAGCATT 57.134 32.000 0.00 0.00 0.00 3.56
4815 8100 7.770897 AGAAAATACCAAACGATTCTAGAGCAT 59.229 33.333 0.00 0.00 0.00 3.79
4816 8101 7.064609 CAGAAAATACCAAACGATTCTAGAGCA 59.935 37.037 0.00 0.00 0.00 4.26
4817 8102 7.064728 ACAGAAAATACCAAACGATTCTAGAGC 59.935 37.037 0.00 0.00 0.00 4.09
4818 8103 8.383619 CACAGAAAATACCAAACGATTCTAGAG 58.616 37.037 0.00 0.00 0.00 2.43
4819 8104 8.092068 TCACAGAAAATACCAAACGATTCTAGA 58.908 33.333 0.00 0.00 0.00 2.43
4820 8105 8.251750 TCACAGAAAATACCAAACGATTCTAG 57.748 34.615 0.00 0.00 0.00 2.43
4861 8146 7.040056 TCAACAAACGCTAAAAAGACAAAAC 57.960 32.000 0.00 0.00 0.00 2.43
4866 8151 7.988859 CGTAAATTCAACAAACGCTAAAAAGAC 59.011 33.333 0.00 0.00 0.00 3.01
4869 8154 6.291690 GCCGTAAATTCAACAAACGCTAAAAA 60.292 34.615 0.00 0.00 32.43 1.94
4876 8161 5.910723 AGTTTAGCCGTAAATTCAACAAACG 59.089 36.000 0.00 0.00 30.76 3.60
4884 8169 7.136772 ACAGTTGAAAGTTTAGCCGTAAATTC 58.863 34.615 0.00 0.00 30.76 2.17


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

AutoCloner maintained by Alex Coulton.