Multiple sequence alignment - TraesCS2D01G403000

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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 TraesCS2D01G403000 chr2D 100.000 6173 0 0 1 6173 518034727 518028555 0.000000 11400.0
1 TraesCS2D01G403000 chr2B 93.867 4011 168 29 801 4766 609955367 609951390 0.000000 5973.0
2 TraesCS2D01G403000 chr2B 92.308 754 25 7 4758 5506 609951281 609950556 0.000000 1040.0
3 TraesCS2D01G403000 chr2B 90.012 821 47 19 2 815 609956116 609955324 0.000000 1029.0
4 TraesCS2D01G403000 chr2B 92.715 604 20 11 5573 6173 609950539 609949957 0.000000 850.0
5 TraesCS2D01G403000 chr2A 92.712 3485 140 41 800 4243 661721061 661717650 0.000000 4924.0
6 TraesCS2D01G403000 chr2A 95.273 1354 27 9 4227 5560 661716296 661714960 0.000000 2111.0
7 TraesCS2D01G403000 chr2A 95.556 540 11 8 5637 6173 661714756 661714227 0.000000 852.0
8 TraesCS2D01G403000 chr2A 91.916 569 24 7 3676 4243 661717029 661716482 0.000000 776.0
9 TraesCS2D01G403000 chr2A 91.901 568 24 7 3676 4242 661717653 661717107 0.000000 774.0
10 TraesCS2D01G403000 chr2A 89.172 628 34 15 2 620 661722077 661721475 0.000000 752.0
11 TraesCS2D01G403000 chr1D 91.667 48 3 1 1637 1684 305589038 305589084 0.000001 65.8
12 TraesCS2D01G403000 chr1A 91.667 48 3 1 1637 1684 384334587 384334633 0.000001 65.8
13 TraesCS2D01G403000 chr1B 87.719 57 4 3 1643 1698 370729982 370729928 0.000005 63.9
14 TraesCS2D01G403000 chr4D 89.796 49 3 2 1643 1690 119751926 119751879 0.000019 62.1
15 TraesCS2D01G403000 chr4B 91.304 46 3 1 1639 1684 182242816 182242860 0.000019 62.1
16 TraesCS2D01G403000 chr3D 88.679 53 3 3 1639 1690 454235682 454235632 0.000019 62.1
17 TraesCS2D01G403000 chr3B 87.037 54 4 3 1638 1690 596861809 596861758 0.000240 58.4


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 TraesCS2D01G403000 chr2D 518028555 518034727 6172 True 11400.000000 11400 100.0000 1 6173 1 chr2D.!!$R1 6172
1 TraesCS2D01G403000 chr2B 609949957 609956116 6159 True 2223.000000 5973 92.2255 2 6173 4 chr2B.!!$R1 6171
2 TraesCS2D01G403000 chr2A 661714227 661722077 7850 True 1698.166667 4924 92.7550 2 6173 6 chr2A.!!$R1 6171

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
816 1097 0.036875 AAAAGAAGCCAGAGTCCGGG 59.963 55.000 0.0 0.0 0.00 5.73 F
1385 1691 1.134788 CGATTTTCTCCTAGCCCGTGT 60.135 52.381 0.0 0.0 0.00 4.49 F
1684 2001 1.144969 TTGACGCTCAAACGGATGTC 58.855 50.000 0.0 0.0 32.71 3.06 F
1735 2052 1.562783 AGCCTTCCTACTGTCCACTC 58.437 55.000 0.0 0.0 0.00 3.51 F
1837 2154 1.927174 CAGGGTAATTCGTGCTTCTCG 59.073 52.381 0.0 0.0 0.00 4.04 F
2273 2590 2.030540 CAGGTGCACTTGTCTGGATTTG 60.031 50.000 20.1 0.0 0.00 2.32 F
2750 3069 2.291741 GTGCTTACTGCTCTTGTTTGCT 59.708 45.455 0.0 0.0 43.37 3.91 F
4204 5698 2.021355 AGAAATTGCAGCTCTCCTCG 57.979 50.000 0.0 0.0 0.00 4.63 F
5016 6824 2.237392 CAGGGGAGTTCCTAGAAAGGTG 59.763 54.545 0.0 0.0 44.09 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2162 2479 1.199789 TGTTGCTCTATTTTGCTGCGG 59.800 47.619 0.00 0.0 0.00 5.69 R
2844 3163 1.203523 GCGGCAACCATCCAAACAATA 59.796 47.619 0.00 0.0 0.00 1.90 R
3594 3936 1.549620 TGTTAAACGATAGGGACCGCA 59.450 47.619 0.00 0.0 43.77 5.69 R
3662 4004 5.273944 GCCTCATTATTTGGTAAAAGAGCG 58.726 41.667 0.00 0.0 31.94 5.03 R
3742 4085 4.021719 ACAGTCCCAATTGAAATCAAGCAG 60.022 41.667 7.12 0.0 39.47 4.24 R
3933 4806 0.035881 AGCATGCCCCAGATATGTCG 59.964 55.000 15.66 0.0 0.00 4.35 R
4411 6101 4.623932 TGTAGAGAGCAACAGTCCAAAT 57.376 40.909 0.00 0.0 0.00 2.32 R
5145 6953 0.833287 ACCGGCAGCAGATTACATCT 59.167 50.000 0.00 0.0 41.15 2.90 R
5862 7849 1.338200 GCCGAGTTCCAGTGAGTGAAT 60.338 52.381 0.00 0.0 0.00 2.57 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
20 21 2.126618 CTGGTGCATGCAACGCTG 60.127 61.111 29.46 18.32 36.20 5.18
104 108 2.027073 GCGCACGTTGATGACCAGA 61.027 57.895 0.30 0.00 0.00 3.86
130 134 0.171231 TTCGTCTGGCAGTCGATCTG 59.829 55.000 31.07 7.35 46.12 2.90
131 135 0.676782 TCGTCTGGCAGTCGATCTGA 60.677 55.000 28.12 10.09 46.27 3.27
137 141 2.430610 GCAGTCGATCTGAGGCCCT 61.431 63.158 16.09 0.00 46.27 5.19
186 190 5.874810 CCCTACAGAGATCGAAAATCAAACA 59.125 40.000 0.00 0.00 0.00 2.83
220 225 2.207590 CTCAGATGCAGCGCAGATTAA 58.792 47.619 11.47 0.00 43.65 1.40
222 227 3.009026 TCAGATGCAGCGCAGATTAAAA 58.991 40.909 11.47 0.00 43.65 1.52
223 228 3.103738 CAGATGCAGCGCAGATTAAAAC 58.896 45.455 11.47 0.00 43.65 2.43
226 231 1.262882 GCAGCGCAGATTAAAACAGC 58.737 50.000 11.47 0.00 0.00 4.40
228 233 2.921912 GCAGCGCAGATTAAAACAGCAA 60.922 45.455 11.47 0.00 0.00 3.91
229 234 3.504863 CAGCGCAGATTAAAACAGCAAT 58.495 40.909 11.47 0.00 0.00 3.56
230 235 4.661125 CAGCGCAGATTAAAACAGCAATA 58.339 39.130 11.47 0.00 0.00 1.90
240 245 8.960591 AGATTAAAACAGCAATACAGCAATAGT 58.039 29.630 0.00 0.00 36.85 2.12
252 257 3.243569 ACAGCAATAGTTAGCTAGGCTCG 60.244 47.826 11.13 9.89 38.74 5.03
297 304 3.358076 CTCCTCCGAGCGGGTTGAC 62.358 68.421 9.29 0.00 37.00 3.18
369 376 1.313812 GCGGAGAAGACGAGGGAGAA 61.314 60.000 0.00 0.00 0.00 2.87
393 400 4.814294 CGCGAGGGCCACCACTAC 62.814 72.222 6.18 0.00 40.13 2.73
394 401 3.391382 GCGAGGGCCACCACTACT 61.391 66.667 6.18 0.00 40.13 2.57
395 402 2.893398 CGAGGGCCACCACTACTC 59.107 66.667 6.18 0.00 40.13 2.59
396 403 2.893398 GAGGGCCACCACTACTCG 59.107 66.667 6.18 0.00 40.13 4.18
397 404 3.372554 GAGGGCCACCACTACTCGC 62.373 68.421 6.18 0.00 40.13 5.03
398 405 4.814294 GGGCCACCACTACTCGCG 62.814 72.222 4.39 0.00 36.50 5.87
444 451 3.522731 CGAGGGGCAGGAGACGAG 61.523 72.222 0.00 0.00 0.00 4.18
472 479 3.873026 GATGGGATGGCGCGGAGAG 62.873 68.421 8.83 0.00 0.00 3.20
482 491 2.045280 CGCGGAGAGGAGATGGATT 58.955 57.895 0.00 0.00 0.00 3.01
511 521 0.535328 CTCCGCGGGAGTAGAGATGA 60.535 60.000 27.83 0.00 44.25 2.92
515 525 1.883275 CGCGGGAGTAGAGATGAAGAT 59.117 52.381 0.00 0.00 0.00 2.40
517 527 2.609244 GCGGGAGTAGAGATGAAGATGC 60.609 54.545 0.00 0.00 0.00 3.91
581 594 4.176120 AGATGGAAATCTGTTGGGATCC 57.824 45.455 1.92 1.92 0.00 3.36
705 983 2.266055 CCTGACGGGCCAACTCTC 59.734 66.667 4.39 0.00 0.00 3.20
730 1009 2.083774 TGGATTTTCGCACATCTGGAC 58.916 47.619 0.00 0.00 0.00 4.02
783 1064 2.036992 CACACTGAAGAAGCCAGAGTCT 59.963 50.000 0.00 0.00 34.15 3.24
785 1066 2.036992 CACTGAAGAAGCCAGAGTCTGT 59.963 50.000 18.74 0.02 35.69 3.41
786 1067 3.256879 CACTGAAGAAGCCAGAGTCTGTA 59.743 47.826 18.74 0.00 35.69 2.74
791 1072 2.171840 GAAGCCAGAGTCTGTACCTCA 58.828 52.381 18.74 0.00 0.00 3.86
792 1073 2.310779 AGCCAGAGTCTGTACCTCAA 57.689 50.000 18.74 0.00 0.00 3.02
793 1074 2.609747 AGCCAGAGTCTGTACCTCAAA 58.390 47.619 18.74 0.00 0.00 2.69
794 1075 3.177228 AGCCAGAGTCTGTACCTCAAAT 58.823 45.455 18.74 0.00 0.00 2.32
795 1076 4.353777 AGCCAGAGTCTGTACCTCAAATA 58.646 43.478 18.74 0.00 0.00 1.40
796 1077 4.777896 AGCCAGAGTCTGTACCTCAAATAA 59.222 41.667 18.74 0.00 0.00 1.40
797 1078 5.248477 AGCCAGAGTCTGTACCTCAAATAAA 59.752 40.000 18.74 0.00 0.00 1.40
798 1079 5.938125 GCCAGAGTCTGTACCTCAAATAAAA 59.062 40.000 18.74 0.00 0.00 1.52
799 1080 6.430000 GCCAGAGTCTGTACCTCAAATAAAAA 59.570 38.462 18.74 0.00 0.00 1.94
815 1096 1.897560 AAAAAGAAGCCAGAGTCCGG 58.102 50.000 0.00 0.00 0.00 5.14
816 1097 0.036875 AAAAGAAGCCAGAGTCCGGG 59.963 55.000 0.00 0.00 0.00 5.73
861 1142 3.220110 GGGTCCGGGATAAAAAGAATCC 58.780 50.000 0.00 0.00 41.96 3.01
959 1245 2.266372 CGGTAACCATCGCCACCA 59.734 61.111 0.00 0.00 0.00 4.17
1276 1574 1.557832 GCCAGGACCAGTGGTATAACA 59.442 52.381 16.72 0.00 35.25 2.41
1380 1686 3.100658 GGAGTCGATTTTCTCCTAGCC 57.899 52.381 11.55 0.00 44.68 3.93
1385 1691 1.134788 CGATTTTCTCCTAGCCCGTGT 60.135 52.381 0.00 0.00 0.00 4.49
1506 1823 7.254455 CGAAGAATTGGAAGTGTATGTCCATAC 60.254 40.741 9.92 9.92 43.42 2.39
1574 1891 8.752766 ATGTTTGACAGCTTATTCAGAATTTG 57.247 30.769 0.00 0.00 0.00 2.32
1598 1915 9.645128 TTGATGGATACTGGAAATTCATTATGT 57.355 29.630 0.00 0.00 37.61 2.29
1652 1969 4.591072 GCATCTTGTTATCTACTCCCTCCT 59.409 45.833 0.00 0.00 0.00 3.69
1684 2001 1.144969 TTGACGCTCAAACGGATGTC 58.855 50.000 0.00 0.00 32.71 3.06
1688 2005 2.599082 GACGCTCAAACGGATGTCTTAG 59.401 50.000 0.00 0.00 37.37 2.18
1696 2013 7.439655 GCTCAAACGGATGTCTTAGAAGATATT 59.560 37.037 3.40 0.00 37.06 1.28
1735 2052 1.562783 AGCCTTCCTACTGTCCACTC 58.437 55.000 0.00 0.00 0.00 3.51
1837 2154 1.927174 CAGGGTAATTCGTGCTTCTCG 59.073 52.381 0.00 0.00 0.00 4.04
1857 2174 4.215908 TCGATGTTATTGAGCCCTAGAGT 58.784 43.478 0.00 0.00 0.00 3.24
1906 2223 4.798574 CCTTTTACACTGCACCTCATTTC 58.201 43.478 0.00 0.00 0.00 2.17
2003 2320 6.481976 ACAACGACAATCTCAAAGTAATGTCA 59.518 34.615 0.00 0.00 37.59 3.58
2162 2479 6.145535 CGGGAGCTTAAATTATTTCATGAGC 58.854 40.000 0.00 1.03 0.00 4.26
2273 2590 2.030540 CAGGTGCACTTGTCTGGATTTG 60.031 50.000 20.10 0.00 0.00 2.32
2280 2597 5.716228 TGCACTTGTCTGGATTTGGAATTAT 59.284 36.000 0.00 0.00 0.00 1.28
2281 2598 6.211184 TGCACTTGTCTGGATTTGGAATTATT 59.789 34.615 0.00 0.00 0.00 1.40
2282 2599 7.395772 TGCACTTGTCTGGATTTGGAATTATTA 59.604 33.333 0.00 0.00 0.00 0.98
2318 2635 9.542462 CTCTTCCGAGGTGTAATTTTCAATATA 57.458 33.333 0.00 0.00 33.51 0.86
2357 2675 4.808895 TCGTTCTGTGATATGGTTGTATGC 59.191 41.667 0.00 0.00 0.00 3.14
2603 2922 9.770097 ATCAGTTGACTTACTATCATTGGTATG 57.230 33.333 0.00 0.00 0.00 2.39
2621 2940 5.994668 TGGTATGCGTATCATTTCAAGCATA 59.005 36.000 0.00 4.13 43.79 3.14
2681 3000 8.517062 AAGATCAGTAGAAAGCAATTAAGCAT 57.483 30.769 0.00 0.00 36.85 3.79
2750 3069 2.291741 GTGCTTACTGCTCTTGTTTGCT 59.708 45.455 0.00 0.00 43.37 3.91
2813 3132 4.746535 TCGTGACCAATGTGTACCATAT 57.253 40.909 0.00 0.00 31.97 1.78
2844 3163 3.390639 TGGGCATGACAGAAAAATTGGTT 59.609 39.130 0.00 0.00 0.00 3.67
2972 3291 7.068839 ACACCAAACACAACCTTAATGTATGAA 59.931 33.333 3.17 0.00 0.00 2.57
3055 3374 4.340097 TGTACCCCGTGAGTCACATATTAG 59.660 45.833 22.66 5.43 33.40 1.73
3174 3502 5.529060 GCATAAAGAACTAGTGCAGGCTTAT 59.471 40.000 3.00 0.00 35.93 1.73
3175 3503 6.038714 GCATAAAGAACTAGTGCAGGCTTATT 59.961 38.462 3.00 0.00 35.93 1.40
3176 3504 5.886960 AAAGAACTAGTGCAGGCTTATTG 57.113 39.130 3.00 0.00 0.00 1.90
3177 3505 4.826274 AGAACTAGTGCAGGCTTATTGA 57.174 40.909 3.00 0.00 0.00 2.57
3181 3509 3.515502 ACTAGTGCAGGCTTATTGACTCA 59.484 43.478 0.00 0.00 0.00 3.41
3200 3528 6.172136 ACTCAGCTCAGCATAATATTGAGT 57.828 37.500 9.14 9.14 40.29 3.41
3486 3827 8.519492 TTTACACATTTTGCAGCTTATCTTTC 57.481 30.769 0.00 0.00 0.00 2.62
3594 3936 5.632034 ACCTTCTCCAGTTTTTGTACTCT 57.368 39.130 0.00 0.00 0.00 3.24
3662 4004 4.236527 AGTTATGTTGGAATGGAGGACC 57.763 45.455 0.00 0.00 0.00 4.46
3716 4058 6.018262 CCTCATACTTTCTCGAGTCTCTACTG 60.018 46.154 13.13 4.06 35.56 2.74
3742 4085 9.303537 GTCTCTATATCACTGTTAACAAGGAAC 57.696 37.037 10.03 0.58 0.00 3.62
3760 4103 4.020839 AGGAACTGCTTGATTTCAATTGGG 60.021 41.667 5.42 0.00 37.18 4.12
3853 4726 3.840890 TTTGCCGTACAATCCATCAAC 57.159 42.857 0.00 0.00 38.31 3.18
3870 4743 5.980116 CCATCAACCTTTACTCAGATAGTCG 59.020 44.000 0.00 0.00 39.80 4.18
3928 4801 7.926674 TGATGTCATGTATCTTGTGAATGTT 57.073 32.000 11.89 0.00 0.00 2.71
3933 4806 8.506437 TGTCATGTATCTTGTGAATGTTCTTTC 58.494 33.333 0.00 0.00 0.00 2.62
4046 5540 5.305585 TGTGGCTCCTGTACTTCTTTTAAG 58.694 41.667 0.00 0.00 0.00 1.85
4088 5582 7.345691 TGGCAAGGAGAACTAATGATTATTGA 58.654 34.615 0.00 0.00 0.00 2.57
4127 5621 5.934625 CCCGATATAAGTAGAATTGCAGCTT 59.065 40.000 0.00 0.00 0.00 3.74
4204 5698 2.021355 AGAAATTGCAGCTCTCCTCG 57.979 50.000 0.00 0.00 0.00 4.63
4217 5711 5.819901 CAGCTCTCCTCGATTCCTTTATTTT 59.180 40.000 0.00 0.00 0.00 1.82
4218 5712 6.018343 CAGCTCTCCTCGATTCCTTTATTTTC 60.018 42.308 0.00 0.00 0.00 2.29
4411 6101 9.073475 ACATATTTGGACAAGCAAGTTTAGTTA 57.927 29.630 0.00 0.00 0.00 2.24
4781 6589 8.321353 AGGAATATCTTACATGTTGTGAAGTCA 58.679 33.333 2.30 0.00 0.00 3.41
4887 6695 6.267817 CAAACGACATATGAAATTGCCAGAT 58.732 36.000 10.38 0.00 0.00 2.90
4965 6773 7.997482 TCGTTATATTTGCTTGTCTCTAGTCT 58.003 34.615 0.00 0.00 0.00 3.24
5016 6824 2.237392 CAGGGGAGTTCCTAGAAAGGTG 59.763 54.545 0.00 0.00 44.09 4.00
5145 6953 0.395311 CTAGACCCTACACCTGCCGA 60.395 60.000 0.00 0.00 0.00 5.54
5263 7075 4.576053 GGCTCATTGATGTTGTACAGCATA 59.424 41.667 23.14 10.89 44.56 3.14
5264 7076 5.240183 GGCTCATTGATGTTGTACAGCATAT 59.760 40.000 23.14 12.60 44.56 1.78
5265 7077 6.427853 GGCTCATTGATGTTGTACAGCATATA 59.572 38.462 23.14 14.90 44.56 0.86
5266 7078 7.293745 GCTCATTGATGTTGTACAGCATATAC 58.706 38.462 23.14 12.77 44.56 1.47
5267 7079 7.172190 GCTCATTGATGTTGTACAGCATATACT 59.828 37.037 23.14 8.79 44.56 2.12
5268 7080 8.593492 TCATTGATGTTGTACAGCATATACTC 57.407 34.615 23.14 13.03 44.56 2.59
5269 7081 7.657354 TCATTGATGTTGTACAGCATATACTCC 59.343 37.037 23.14 11.49 44.56 3.85
5270 7082 6.731292 TGATGTTGTACAGCATATACTCCT 57.269 37.500 23.14 1.63 39.86 3.69
5294 7106 8.598041 CCTATATATAGGCACCTTTTTGTCTCT 58.402 37.037 22.98 0.00 43.08 3.10
5309 7121 9.118300 CTTTTTGTCTCTTATAGAATGCATCCT 57.882 33.333 0.00 0.00 35.47 3.24
5479 7291 6.843069 ATGTTAAATGCACAACTGAAAACC 57.157 33.333 0.00 0.00 0.00 3.27
5506 7318 7.394872 GTTCGTTCTGTATCTGATGATTGTTC 58.605 38.462 0.00 0.00 34.32 3.18
5507 7319 6.867550 TCGTTCTGTATCTGATGATTGTTCT 58.132 36.000 0.00 0.00 34.32 3.01
5591 7423 6.552629 ACGATTATACGTACATATCAGCTGG 58.447 40.000 15.13 0.00 44.72 4.85
5618 7450 8.392612 TCTTAAGGTTTTTAGACACTGAAAACG 58.607 33.333 18.34 9.65 44.96 3.60
5625 7457 6.091169 TTTTTAGACACTGAAAACGACGAAGT 59.909 34.615 0.00 0.00 31.37 3.01
5737 7721 8.136165 CAGGTTCCAGTACAAGACATAGTATAC 58.864 40.741 0.00 0.00 0.00 1.47
5782 7769 4.109766 CAAGCCAGCATTACATCACATTG 58.890 43.478 0.00 0.00 0.00 2.82
5786 7773 5.240183 AGCCAGCATTACATCACATTGATAC 59.760 40.000 0.00 0.00 34.28 2.24
5868 7855 9.822185 AAACTTGCTTTCATCTTTAAATTCACT 57.178 25.926 0.00 0.00 0.00 3.41
5869 7856 9.468532 AACTTGCTTTCATCTTTAAATTCACTC 57.531 29.630 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.300080 GCGTTGCATGCACCAGTTT 60.300 52.632 22.58 0.00 0.00 2.66
20 21 5.502153 TTAGCTTACTCGAGACATTCCTC 57.498 43.478 21.68 0.00 0.00 3.71
104 108 0.033504 ACTGCCAGACGAACGACAAT 59.966 50.000 0.00 0.00 0.00 2.71
130 134 2.361737 GGCAGTTTCCAGGGCCTC 60.362 66.667 0.95 0.00 43.09 4.70
131 135 3.984732 GGGCAGTTTCCAGGGCCT 61.985 66.667 0.00 0.00 45.68 5.19
137 141 0.109532 TGATCAACGGGCAGTTTCCA 59.890 50.000 0.00 0.00 42.02 3.53
186 190 0.956633 TCTGAGGTTAACTGCGACGT 59.043 50.000 5.42 0.00 0.00 4.34
220 225 6.375455 AGCTAACTATTGCTGTATTGCTGTTT 59.625 34.615 0.00 0.00 38.21 2.83
222 227 5.431765 AGCTAACTATTGCTGTATTGCTGT 58.568 37.500 0.00 0.00 38.21 4.40
223 228 5.998454 AGCTAACTATTGCTGTATTGCTG 57.002 39.130 0.00 0.00 38.21 4.41
226 231 6.226787 AGCCTAGCTAACTATTGCTGTATTG 58.773 40.000 0.00 0.00 40.08 1.90
228 233 5.336055 CGAGCCTAGCTAACTATTGCTGTAT 60.336 44.000 0.00 0.00 39.88 2.29
229 234 4.023107 CGAGCCTAGCTAACTATTGCTGTA 60.023 45.833 0.00 0.00 39.88 2.74
230 235 3.243569 CGAGCCTAGCTAACTATTGCTGT 60.244 47.826 0.00 0.00 39.88 4.40
240 245 8.577048 ACATATATAGTTTCGAGCCTAGCTAA 57.423 34.615 0.00 0.00 39.88 3.09
252 257 5.577164 CCGCAGCAGGTACATATATAGTTTC 59.423 44.000 0.00 0.00 0.00 2.78
304 311 0.680280 TCGACTGGGAGGTCAGCTAC 60.680 60.000 0.00 0.00 38.26 3.58
308 315 1.067495 GTTCTTCGACTGGGAGGTCAG 60.067 57.143 0.00 0.00 40.40 3.51
357 364 1.303398 TGCGTCTTCTCCCTCGTCT 60.303 57.895 0.00 0.00 0.00 4.18
440 447 1.090625 CCCATCTCGTCTCGTCTCGT 61.091 60.000 0.00 0.00 0.00 4.18
441 448 0.810426 TCCCATCTCGTCTCGTCTCG 60.810 60.000 0.00 0.00 0.00 4.04
442 449 1.265635 CATCCCATCTCGTCTCGTCTC 59.734 57.143 0.00 0.00 0.00 3.36
443 450 1.313772 CATCCCATCTCGTCTCGTCT 58.686 55.000 0.00 0.00 0.00 4.18
444 451 0.312416 CCATCCCATCTCGTCTCGTC 59.688 60.000 0.00 0.00 0.00 4.20
472 479 4.383989 GGAGCCATCTATCAATCCATCTCC 60.384 50.000 0.00 0.00 0.00 3.71
705 983 0.171007 ATGTGCGAAAATCCAAGCCG 59.829 50.000 0.00 0.00 0.00 5.52
796 1077 1.545651 CCCGGACTCTGGCTTCTTTTT 60.546 52.381 0.73 0.00 0.00 1.94
797 1078 0.036875 CCCGGACTCTGGCTTCTTTT 59.963 55.000 0.73 0.00 0.00 2.27
798 1079 1.679898 CCCGGACTCTGGCTTCTTT 59.320 57.895 0.73 0.00 0.00 2.52
799 1080 2.960688 GCCCGGACTCTGGCTTCTT 61.961 63.158 0.73 0.00 44.46 2.52
800 1081 3.394836 GCCCGGACTCTGGCTTCT 61.395 66.667 0.73 0.00 44.46 2.85
805 1086 4.492604 TTTTTGCCCGGACTCTGG 57.507 55.556 0.73 0.00 0.00 3.86
861 1142 0.244994 CTGGAAGTGGACGGACTCTG 59.755 60.000 0.00 0.00 0.00 3.35
950 1236 3.083997 GAGGGAGGTGGTGGCGAT 61.084 66.667 0.00 0.00 0.00 4.58
959 1245 2.329399 GGAGGAGGAGGAGGGAGGT 61.329 68.421 0.00 0.00 0.00 3.85
1086 1372 2.319025 ACCCCCAAATCGAACCAATT 57.681 45.000 0.00 0.00 0.00 2.32
1136 1431 3.204827 CTGCGCTCAAATCCCCGG 61.205 66.667 9.73 0.00 0.00 5.73
1137 1432 3.204827 CCTGCGCTCAAATCCCCG 61.205 66.667 9.73 0.00 0.00 5.73
1259 1557 1.838077 GCCTGTTATACCACTGGTCCT 59.162 52.381 3.21 0.00 37.92 3.85
1263 1561 0.182775 GGGGCCTGTTATACCACTGG 59.817 60.000 0.84 0.00 38.50 4.00
1380 1686 1.137404 GCAATAGCTGCCAACACGG 59.863 57.895 0.00 0.00 46.13 4.94
1506 1823 4.944962 TTCTTCAAACATATCAGGCACG 57.055 40.909 0.00 0.00 0.00 5.34
1541 1858 4.749245 AAGCTGTCAAACATTAGAACCG 57.251 40.909 0.00 0.00 0.00 4.44
1598 1915 7.692460 AAAACAGAGAACAGATGCATGATAA 57.308 32.000 2.46 0.00 0.00 1.75
1605 1922 6.525976 GCTAATGAAAAACAGAGAACAGATGC 59.474 38.462 0.00 0.00 0.00 3.91
1606 1923 7.587629 TGCTAATGAAAAACAGAGAACAGATG 58.412 34.615 0.00 0.00 0.00 2.90
1652 1969 7.254852 GTTTGAGCGTCAATTAATATGGGAAA 58.745 34.615 0.00 0.00 36.11 3.13
1688 2005 9.606631 AAGACAGATGACCAGTAAAATATCTTC 57.393 33.333 0.00 0.00 0.00 2.87
1696 2013 5.248477 AGGCTAAAGACAGATGACCAGTAAA 59.752 40.000 0.00 0.00 0.00 2.01
1735 2052 2.715046 ACACATGTACCTGGCATCAAG 58.285 47.619 0.00 0.00 0.00 3.02
1837 2154 6.267928 TCCTTACTCTAGGGCTCAATAACATC 59.732 42.308 0.00 0.00 35.90 3.06
1857 2174 5.011635 TCGCTGTTCCTATGCATAATCCTTA 59.988 40.000 8.00 0.00 0.00 2.69
1906 2223 3.119101 ACATACCTAACAGCAAGAGGACG 60.119 47.826 1.43 0.00 34.24 4.79
2003 2320 6.649155 ACCAAGGCAAAACAAAAGAACTTAT 58.351 32.000 0.00 0.00 0.00 1.73
2162 2479 1.199789 TGTTGCTCTATTTTGCTGCGG 59.800 47.619 0.00 0.00 0.00 5.69
2318 2635 6.648310 CACAGAACGAAGATAGATGGCAATAT 59.352 38.462 0.00 0.00 0.00 1.28
2332 2649 6.510157 GCATACAACCATATCACAGAACGAAG 60.510 42.308 0.00 0.00 0.00 3.79
2357 2675 6.873605 GGTCAAATCCCTAAACAAAATGGAAG 59.126 38.462 0.00 0.00 0.00 3.46
2603 2922 5.914085 AGTCTATGCTTGAAATGATACGC 57.086 39.130 0.00 0.00 0.00 4.42
2681 3000 5.559770 ACATATTGGACATGACACAAGACA 58.440 37.500 0.00 0.00 0.00 3.41
2750 3069 6.022107 TCTAGGGTACAGCTTCATAGGTAA 57.978 41.667 0.00 0.00 0.00 2.85
2813 3132 7.894753 TTTTCTGTCATGCCCATAATAATGA 57.105 32.000 0.00 0.00 34.84 2.57
2844 3163 1.203523 GCGGCAACCATCCAAACAATA 59.796 47.619 0.00 0.00 0.00 1.90
2972 3291 2.171448 CTCTAGGCCATAACTGGTGCTT 59.829 50.000 5.01 0.00 45.10 3.91
3055 3374 7.442666 AGTGATAGAAAGTCTTCTTGTGGTTTC 59.557 37.037 0.00 0.00 42.17 2.78
3086 3405 8.106462 TGTCAGATTGGTAAATGGTAATGAAGA 58.894 33.333 0.00 0.00 0.00 2.87
3174 3502 6.585416 TCAATATTATGCTGAGCTGAGTCAA 58.415 36.000 5.83 0.00 0.00 3.18
3175 3503 6.165700 TCAATATTATGCTGAGCTGAGTCA 57.834 37.500 5.83 0.75 0.00 3.41
3176 3504 6.222389 ACTCAATATTATGCTGAGCTGAGTC 58.778 40.000 14.89 0.00 38.22 3.36
3177 3505 6.172136 ACTCAATATTATGCTGAGCTGAGT 57.828 37.500 14.89 14.89 40.23 3.41
3181 3509 6.825213 TCACAAACTCAATATTATGCTGAGCT 59.175 34.615 5.83 0.00 40.23 4.09
3371 3712 8.680001 TGATGATCAAATTGGAGAATACACTTG 58.320 33.333 0.00 0.00 0.00 3.16
3378 3719 7.830697 TGTACAGTGATGATCAAATTGGAGAAT 59.169 33.333 0.00 0.00 0.00 2.40
3428 3769 3.829601 ACCAAAAACGGCAATGATTCCTA 59.170 39.130 0.00 0.00 0.00 2.94
3486 3827 5.449113 GTGCATTCGAGATTTAATGTGTTCG 59.551 40.000 0.00 0.00 35.86 3.95
3594 3936 1.549620 TGTTAAACGATAGGGACCGCA 59.450 47.619 0.00 0.00 43.77 5.69
3662 4004 5.273944 GCCTCATTATTTGGTAAAAGAGCG 58.726 41.667 0.00 0.00 31.94 5.03
3716 4058 9.303537 GTTCCTTGTTAACAGTGATATAGAGAC 57.696 37.037 8.56 1.02 0.00 3.36
3742 4085 4.021719 ACAGTCCCAATTGAAATCAAGCAG 60.022 41.667 7.12 0.00 39.47 4.24
3760 4103 4.184629 GGAATGGTCATCAGTACACAGTC 58.815 47.826 0.00 0.00 0.00 3.51
3853 4726 7.660617 TGGTAGATACGACTATCTGAGTAAAGG 59.339 40.741 5.95 0.00 39.65 3.11
3870 4743 7.280205 CACTGGTAACTGGATTTTGGTAGATAC 59.720 40.741 0.00 0.00 40.36 2.24
3928 4801 2.115427 TGCCCCAGATATGTCGAAAGA 58.885 47.619 0.00 0.00 38.16 2.52
3933 4806 0.035881 AGCATGCCCCAGATATGTCG 59.964 55.000 15.66 0.00 0.00 4.35
4046 5540 7.330262 TCCTTGCCATTATTTTTCCTTTGATC 58.670 34.615 0.00 0.00 0.00 2.92
4065 5559 8.897752 AGTTCAATAATCATTAGTTCTCCTTGC 58.102 33.333 0.00 0.00 0.00 4.01
4217 5711 6.519679 TTAAGAGGACATAGCTGTTAACGA 57.480 37.500 0.00 0.00 35.14 3.85
4218 5712 8.916654 CATATTAAGAGGACATAGCTGTTAACG 58.083 37.037 0.00 0.00 35.14 3.18
4411 6101 4.623932 TGTAGAGAGCAACAGTCCAAAT 57.376 40.909 0.00 0.00 0.00 2.32
4887 6695 5.601313 ACCTTAGGTAAGATATTCGCTTCCA 59.399 40.000 0.15 0.00 35.33 3.53
4965 6773 8.773645 GTGTCATTTGATCGATTCATTATGGTA 58.226 33.333 0.00 0.00 33.34 3.25
5040 6848 2.102252 GCAGAGGTCATAGAGGTTCCTG 59.898 54.545 0.00 0.00 0.00 3.86
5145 6953 0.833287 ACCGGCAGCAGATTACATCT 59.167 50.000 0.00 0.00 41.15 2.90
5294 7106 7.216494 TCGTTTGATCAGGATGCATTCTATAA 58.784 34.615 7.32 0.00 34.76 0.98
5309 7121 5.821995 TCAATCTAATGGCATCGTTTGATCA 59.178 36.000 0.00 0.00 34.77 2.92
5479 7291 4.028852 TCATCAGATACAGAACGAACGG 57.971 45.455 0.00 0.00 0.00 4.44
5506 7318 9.286946 GACAACCGAGGACGAAATATATATAAG 57.713 37.037 0.00 0.00 42.66 1.73
5507 7319 8.795513 TGACAACCGAGGACGAAATATATATAA 58.204 33.333 0.00 0.00 42.66 0.98
5570 7402 7.704578 AGACCAGCTGATATGTACGTATAAT 57.295 36.000 17.39 0.00 0.00 1.28
5571 7403 7.520451 AAGACCAGCTGATATGTACGTATAA 57.480 36.000 17.39 0.00 0.00 0.98
5572 7404 8.625786 TTAAGACCAGCTGATATGTACGTATA 57.374 34.615 17.39 0.00 0.00 1.47
5573 7405 7.309255 CCTTAAGACCAGCTGATATGTACGTAT 60.309 40.741 17.39 7.33 0.00 3.06
5574 7406 6.016527 CCTTAAGACCAGCTGATATGTACGTA 60.017 42.308 17.39 0.00 0.00 3.57
5575 7407 5.221263 CCTTAAGACCAGCTGATATGTACGT 60.221 44.000 17.39 0.70 0.00 3.57
5576 7408 5.221263 ACCTTAAGACCAGCTGATATGTACG 60.221 44.000 17.39 0.00 0.00 3.67
5577 7409 6.163135 ACCTTAAGACCAGCTGATATGTAC 57.837 41.667 17.39 0.00 0.00 2.90
5591 7423 9.499585 GTTTTCAGTGTCTAAAAACCTTAAGAC 57.500 33.333 3.36 0.00 37.06 3.01
5661 7645 6.560253 AGCTGAATCTACGTTTCAAACATT 57.440 33.333 0.22 0.00 32.98 2.71
5662 7646 6.560253 AAGCTGAATCTACGTTTCAAACAT 57.440 33.333 0.22 0.00 32.98 2.71
5663 7647 6.371809 AAAGCTGAATCTACGTTTCAAACA 57.628 33.333 0.22 0.00 32.98 2.83
5664 7648 7.547119 CAAAAAGCTGAATCTACGTTTCAAAC 58.453 34.615 0.00 0.00 32.98 2.93
5665 7649 6.198216 GCAAAAAGCTGAATCTACGTTTCAAA 59.802 34.615 0.00 0.00 41.15 2.69
5737 7721 9.962759 CTTGTTTTTCATTTTGTTTCTGAGAAG 57.037 29.630 0.00 0.00 0.00 2.85
5786 7773 6.637795 TGTCTAATCCACCAACGGAAGACG 62.638 50.000 7.11 0.00 42.33 4.18
5852 7839 7.939039 AGTTCCAGTGAGTGAATTTAAAGATGA 59.061 33.333 0.00 0.00 0.00 2.92
5862 7849 1.338200 GCCGAGTTCCAGTGAGTGAAT 60.338 52.381 0.00 0.00 0.00 2.57
5866 7853 2.651361 CGCCGAGTTCCAGTGAGT 59.349 61.111 0.00 0.00 0.00 3.41
5867 7854 2.125912 CCGCCGAGTTCCAGTGAG 60.126 66.667 0.00 0.00 0.00 3.51
5868 7855 3.691342 CCCGCCGAGTTCCAGTGA 61.691 66.667 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.