Multiple sequence alignment - TraesCS7A01G080900

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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 TraesCS7A01G080900 chr7A 100.000 5544 0 0 1 5544 46709472 46715015 0.000000e+00 10238.0
1 TraesCS7A01G080900 chr7A 100.000 32 0 0 678 709 677865399 677865430 6.000000e-05 60.2
2 TraesCS7A01G080900 chr7D 94.376 2276 94 18 399 2668 44291682 44293929 0.000000e+00 3463.0
3 TraesCS7A01G080900 chr7D 94.368 2042 58 15 2624 4616 44293943 44295976 0.000000e+00 3081.0
4 TraesCS7A01G080900 chr7D 87.891 958 61 25 4614 5543 44296029 44296959 0.000000e+00 1075.0
5 TraesCS7A01G080900 chr7D 97.122 139 4 0 260 398 44291508 44291646 9.280000e-58 235.0
6 TraesCS7A01G080900 chr7D 96.610 118 3 1 1 117 44291094 44291211 1.580000e-45 195.0
7 TraesCS7A01G080900 chr7D 89.313 131 8 3 1 130 44045746 44045871 5.750000e-35 159.0
8 TraesCS7A01G080900 chr7D 85.315 143 17 2 1 143 44264606 44264744 1.610000e-30 145.0
9 TraesCS7A01G080900 chr4A 90.148 2304 136 50 399 2668 655250807 655253053 0.000000e+00 2913.0
10 TraesCS7A01G080900 chr4A 91.003 1934 112 33 3646 5544 655254287 655256193 0.000000e+00 2551.0
11 TraesCS7A01G080900 chr4A 93.979 1063 26 13 2624 3649 655253067 655254128 0.000000e+00 1574.0
12 TraesCS7A01G080900 chr4A 82.840 169 23 4 2 168 655246190 655246354 4.480000e-31 147.0
13 TraesCS7A01G080900 chr1A 81.368 1111 159 35 2445 3548 545889500 545890569 0.000000e+00 861.0
14 TraesCS7A01G080900 chr1A 76.788 685 88 49 3558 4197 545890619 545891277 8.960000e-83 318.0
15 TraesCS7A01G080900 chr1A 85.841 226 26 3 1366 1591 545888470 545888689 9.280000e-58 235.0
16 TraesCS7A01G080900 chr1A 83.916 143 21 2 1058 1199 545888299 545888440 9.690000e-28 135.0
17 TraesCS7A01G080900 chr1D 81.267 1105 155 34 2445 3533 451130288 451131356 0.000000e+00 846.0
18 TraesCS7A01G080900 chr1D 77.767 1066 155 49 1366 2388 451129270 451130296 1.040000e-161 580.0
19 TraesCS7A01G080900 chr1D 78.464 729 101 38 3610 4288 451131482 451132204 5.130000e-115 425.0
20 TraesCS7A01G080900 chr1D 86.957 115 13 2 1084 1197 451129125 451129238 1.620000e-25 128.0
21 TraesCS7A01G080900 chr1B 77.840 1065 151 50 1366 2388 619417124 619418145 1.040000e-161 580.0
22 TraesCS7A01G080900 chr1B 87.033 455 54 5 2904 3356 619418699 619419150 4.950000e-140 508.0
23 TraesCS7A01G080900 chr1B 78.912 735 93 45 3610 4290 619419508 619420234 5.100000e-120 442.0
24 TraesCS7A01G080900 chr1B 88.889 117 13 0 1083 1199 619416978 619417094 1.610000e-30 145.0
25 TraesCS7A01G080900 chr1B 89.130 92 10 0 2941 3032 619419114 619419205 1.260000e-21 115.0
26 TraesCS7A01G080900 chr5A 79.167 192 23 10 570 753 549941633 549941451 3.510000e-22 117.0
27 TraesCS7A01G080900 chr7B 79.755 163 24 5 560 713 623049800 623049638 5.870000e-20 110.0
28 TraesCS7A01G080900 chr7B 79.755 163 24 5 560 713 623099644 623099482 5.870000e-20 110.0
29 TraesCS7A01G080900 chr3D 80.282 142 22 4 562 699 305627442 305627581 9.830000e-18 102.0
30 TraesCS7A01G080900 chr2A 88.095 84 8 2 564 646 733354125 733354043 1.270000e-16 99.0


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 TraesCS7A01G080900 chr7A 46709472 46715015 5543 False 10238.00 10238 100.00000 1 5544 1 chr7A.!!$F1 5543
1 TraesCS7A01G080900 chr7D 44291094 44296959 5865 False 1609.80 3463 94.07340 1 5543 5 chr7D.!!$F3 5542
2 TraesCS7A01G080900 chr4A 655250807 655256193 5386 False 2346.00 2913 91.71000 399 5544 3 chr4A.!!$F2 5145
3 TraesCS7A01G080900 chr1A 545888299 545891277 2978 False 387.25 861 81.97825 1058 4197 4 chr1A.!!$F1 3139
4 TraesCS7A01G080900 chr1D 451129125 451132204 3079 False 494.75 846 81.11375 1084 4288 4 chr1D.!!$F1 3204
5 TraesCS7A01G080900 chr1B 619416978 619420234 3256 False 358.00 580 84.36080 1083 4290 5 chr1B.!!$F1 3207

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
323 479 0.397957 GAGGGAGGGAGAGAGGTTCC 60.398 65.000 0.00 0.0 0.00 3.62 F
926 1144 1.720781 AAAGATTGGGCAGTTTGGCT 58.279 45.000 2.60 0.0 43.20 4.75 F
1670 1923 0.167908 TGCCAGCTTTGTAATTCGCG 59.832 50.000 0.00 0.0 0.00 5.87 F
2529 2821 0.627451 TGGCAAGCCATCAGGATCTT 59.373 50.000 10.24 0.0 41.89 2.40 F
3863 4656 1.211949 GACTTATAGGGGTGCCAAGCA 59.788 52.381 0.00 0.0 35.60 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1231 1449 0.749454 ATGGCGCACTCTTGGGAATC 60.749 55.000 10.83 0.0 37.91 2.52 R
2153 2442 1.879380 CAATCGAACTTGGAAGGTGCA 59.121 47.619 0.00 0.0 0.00 4.57 R
2690 3048 2.456577 ACCCAGCCATGTTTTCCATAC 58.543 47.619 0.00 0.0 30.71 2.39 R
3949 4757 1.134371 GCCTTGCTAAGATCTTCCGGT 60.134 52.381 12.24 0.0 0.00 5.28 R
4761 5654 0.036388 ATGGTTGGTAGACGGCAGTG 60.036 55.000 0.00 0.0 0.00 3.66 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
18 19 2.047560 GTAGAAAGCCCGCCACGT 60.048 61.111 0.00 0.00 0.00 4.49
193 195 3.394836 GTGGCGAGCCTCTCCCTT 61.395 66.667 15.75 0.00 36.94 3.95
194 196 3.077556 TGGCGAGCCTCTCCCTTC 61.078 66.667 15.75 0.00 36.94 3.46
195 197 3.855853 GGCGAGCCTCTCCCTTCC 61.856 72.222 6.90 0.00 0.00 3.46
196 198 3.855853 GCGAGCCTCTCCCTTCCC 61.856 72.222 0.00 0.00 0.00 3.97
197 199 3.532155 CGAGCCTCTCCCTTCCCG 61.532 72.222 0.00 0.00 0.00 5.14
198 200 3.855853 GAGCCTCTCCCTTCCCGC 61.856 72.222 0.00 0.00 0.00 6.13
199 201 4.406763 AGCCTCTCCCTTCCCGCT 62.407 66.667 0.00 0.00 0.00 5.52
200 202 3.855853 GCCTCTCCCTTCCCGCTC 61.856 72.222 0.00 0.00 0.00 5.03
201 203 2.042435 CCTCTCCCTTCCCGCTCT 60.042 66.667 0.00 0.00 0.00 4.09
202 204 2.131067 CCTCTCCCTTCCCGCTCTC 61.131 68.421 0.00 0.00 0.00 3.20
203 205 1.076339 CTCTCCCTTCCCGCTCTCT 60.076 63.158 0.00 0.00 0.00 3.10
204 206 1.076632 TCTCCCTTCCCGCTCTCTC 60.077 63.158 0.00 0.00 0.00 3.20
205 207 1.076339 CTCCCTTCCCGCTCTCTCT 60.076 63.158 0.00 0.00 0.00 3.10
206 208 0.686112 CTCCCTTCCCGCTCTCTCTT 60.686 60.000 0.00 0.00 0.00 2.85
207 209 0.684805 TCCCTTCCCGCTCTCTCTTC 60.685 60.000 0.00 0.00 0.00 2.87
208 210 1.681486 CCCTTCCCGCTCTCTCTTCC 61.681 65.000 0.00 0.00 0.00 3.46
209 211 1.435515 CTTCCCGCTCTCTCTTCCG 59.564 63.158 0.00 0.00 0.00 4.30
210 212 2.621371 CTTCCCGCTCTCTCTTCCGC 62.621 65.000 0.00 0.00 0.00 5.54
211 213 4.560856 CCCGCTCTCTCTTCCGCG 62.561 72.222 0.00 0.00 44.69 6.46
286 442 4.695231 CGTGAAGGCGACGACCGT 62.695 66.667 0.00 0.00 39.21 4.83
323 479 0.397957 GAGGGAGGGAGAGAGGTTCC 60.398 65.000 0.00 0.00 0.00 3.62
340 496 2.301583 GTTCCTCTCAGGTCAGCTTCTT 59.698 50.000 0.00 0.00 36.53 2.52
443 634 2.587522 TGGATCTCGGACGATGAAGAT 58.412 47.619 0.00 0.00 0.00 2.40
444 635 2.959030 TGGATCTCGGACGATGAAGATT 59.041 45.455 0.00 0.00 0.00 2.40
566 767 4.245660 GCCTGAATTTCTTTTAAGGGTGC 58.754 43.478 0.00 0.00 0.00 5.01
573 774 1.903860 TCTTTTAAGGGTGCGGCTAGA 59.096 47.619 0.00 0.00 0.00 2.43
586 787 2.484651 GCGGCTAGATCTCAGTCGATTA 59.515 50.000 22.13 0.00 43.67 1.75
675 890 4.260132 GCACAAATCTCTACGCAAGATCTG 60.260 45.833 0.00 0.00 43.62 2.90
690 905 6.018913 CGCAAGATCTGATGAATATAGCATCC 60.019 42.308 13.12 2.18 39.92 3.51
926 1144 1.720781 AAAGATTGGGCAGTTTGGCT 58.279 45.000 2.60 0.00 43.20 4.75
1204 1422 2.766263 TCGCCTCAGTAGTGATTTCCAT 59.234 45.455 0.00 0.00 30.18 3.41
1520 1741 4.552365 ATGCCCGACCTCATGCGG 62.552 66.667 0.00 0.00 46.80 5.69
1580 1801 2.026641 CAGCTGTGGTTTATCCCATGG 58.973 52.381 4.14 4.14 36.74 3.66
1603 1856 3.221771 TCATTGTGTTTGCTGGCTACTT 58.778 40.909 0.00 0.00 0.00 2.24
1628 1881 6.924913 TGCTATATTCTTGCATCCTAGAGT 57.075 37.500 0.00 0.00 30.37 3.24
1670 1923 0.167908 TGCCAGCTTTGTAATTCGCG 59.832 50.000 0.00 0.00 0.00 5.87
1698 1955 9.561270 GTCAATTTAGAACATTAGAAGGCTTTC 57.439 33.333 0.00 0.00 0.00 2.62
1760 2017 6.431234 CCTAGACTTTTTCCATTGCTTGTAGT 59.569 38.462 0.00 0.00 0.00 2.73
1808 2082 8.498054 TGTTCTTTCCAGCAAGATAGATTTAG 57.502 34.615 0.00 0.00 32.69 1.85
1892 2180 8.306038 CCATGAACATCAATCTGGTTCTTTTTA 58.694 33.333 0.00 0.00 41.07 1.52
1977 2265 5.123027 GCCTAAAATATATGGTCTGCAGCTC 59.877 44.000 9.47 4.44 0.00 4.09
2202 2493 6.095377 ACTGCAGCTAAAAACTCAAATATGC 58.905 36.000 15.27 0.00 0.00 3.14
2237 2528 6.573094 GCCCTATGAAAAGCTTTCTGTTGATT 60.573 38.462 13.10 0.00 0.00 2.57
2272 2563 5.819991 TGGCACTTGATCCTCTTTTCTATT 58.180 37.500 0.00 0.00 0.00 1.73
2368 2659 5.702670 ACAACTTGATGACTATCACAAGGTG 59.297 40.000 23.07 23.07 46.39 4.00
2393 2684 1.488812 TGCCAGTACAGTTTGTCCTGT 59.511 47.619 0.00 0.00 46.94 4.00
2417 2708 8.372459 TGTATTTTGCTAGAGTTCTGTTCCTAA 58.628 33.333 0.00 0.00 0.00 2.69
2529 2821 0.627451 TGGCAAGCCATCAGGATCTT 59.373 50.000 10.24 0.00 41.89 2.40
2558 2850 5.093457 CACAAGCTGACTTTGATTGCATAG 58.907 41.667 0.00 0.00 34.59 2.23
2619 2911 3.438434 GGTCTCCATTCTGCTTTCAGTTC 59.562 47.826 0.00 0.00 41.10 3.01
2627 2919 4.006780 TCTGCTTTCAGTTCACATGCTA 57.993 40.909 0.00 0.00 41.10 3.49
2690 3048 9.853177 AAACTGTTAAATCCTCCCTTATCTATG 57.147 33.333 0.00 0.00 0.00 2.23
2783 3141 7.656948 CCATGTACATGAAACTGAAAACCATTT 59.343 33.333 32.72 0.00 41.20 2.32
2933 3419 8.033178 TCATATTGATGTATCCCTTGAGTTGA 57.967 34.615 0.00 0.00 34.41 3.18
3118 3604 4.281182 AGCGAAGGATGGTACCAAGTATAG 59.719 45.833 20.76 10.71 0.00 1.31
3275 3761 5.548056 TCTCCCTAAAGTTGAGAATGAGGTT 59.452 40.000 0.00 0.00 32.45 3.50
3497 4042 8.678199 CCCTCTGGACTGTTATTCTTTTTATTC 58.322 37.037 0.00 0.00 0.00 1.75
3806 4591 4.014406 TCAGAGATGCAGGTACGTCTTAA 58.986 43.478 0.00 0.00 36.04 1.85
3863 4656 1.211949 GACTTATAGGGGTGCCAAGCA 59.788 52.381 0.00 0.00 35.60 3.91
3877 4670 4.740695 GTGCCAAGCATAAAAACGTTACAA 59.259 37.500 0.00 0.00 41.91 2.41
3879 4672 6.583050 GTGCCAAGCATAAAAACGTTACAATA 59.417 34.615 0.00 0.00 41.91 1.90
3949 4757 2.230664 AGGTCTTTGCCACCTGACA 58.769 52.632 0.00 0.00 43.10 3.58
4018 4826 3.993081 CTGACTTCCAAACTACAGCAGAG 59.007 47.826 0.00 0.00 0.00 3.35
4077 4885 4.271776 CCTTTATTCTAAACCCTAACCGCG 59.728 45.833 0.00 0.00 0.00 6.46
4201 5028 3.113514 TTGGAGCGACAGGCCAACA 62.114 57.895 5.01 0.00 45.17 3.33
4236 5066 1.928653 CAAGACCGACGAAAACGCA 59.071 52.632 0.00 0.00 0.00 5.24
4251 5081 3.490890 GCAAAGAGGAAGCGCGAT 58.509 55.556 12.10 0.00 0.00 4.58
4431 5263 2.979678 ACACCTGACCTGGTCTAATGTT 59.020 45.455 26.03 9.97 38.45 2.71
4609 5446 7.228706 TCCTGAAGAAAACAACAGAGGTTATTC 59.771 37.037 0.00 0.00 34.87 1.75
4619 5511 7.882179 ACAACAGAGGTTATTCATTGGTAAAC 58.118 34.615 0.00 0.00 34.87 2.01
4623 5515 7.119262 ACAGAGGTTATTCATTGGTAAACTTCG 59.881 37.037 3.06 0.00 33.05 3.79
4752 5645 5.151454 TCAAAGGGGTTTGATTGTATGGTT 58.849 37.500 0.00 0.00 36.15 3.67
4753 5646 5.245075 TCAAAGGGGTTTGATTGTATGGTTC 59.755 40.000 0.00 0.00 36.15 3.62
4754 5647 4.396357 AGGGGTTTGATTGTATGGTTCA 57.604 40.909 0.00 0.00 0.00 3.18
4756 5649 3.194755 GGGGTTTGATTGTATGGTTCACC 59.805 47.826 0.00 0.00 0.00 4.02
4757 5650 4.086457 GGGTTTGATTGTATGGTTCACCT 58.914 43.478 0.00 0.00 36.82 4.00
4759 5652 4.764823 GGTTTGATTGTATGGTTCACCTCA 59.235 41.667 0.00 0.00 36.82 3.86
4760 5653 5.335661 GGTTTGATTGTATGGTTCACCTCAC 60.336 44.000 0.00 0.00 36.82 3.51
4761 5654 3.950397 TGATTGTATGGTTCACCTCACC 58.050 45.455 0.00 0.00 36.82 4.02
4766 5659 1.148273 TGGTTCACCTCACCACTGC 59.852 57.895 0.00 0.00 39.53 4.40
4768 5661 1.961277 GTTCACCTCACCACTGCCG 60.961 63.158 0.00 0.00 0.00 5.69
4769 5662 2.439960 TTCACCTCACCACTGCCGT 61.440 57.895 0.00 0.00 0.00 5.68
4845 5750 6.427853 TGCAAGATACCATACATTAGCATCAC 59.572 38.462 0.00 0.00 0.00 3.06
4881 5792 5.468592 AGCATAATGAAACAACATTCGCAA 58.531 33.333 0.33 0.00 40.36 4.85
4884 5795 7.922278 AGCATAATGAAACAACATTCGCAATAT 59.078 29.630 0.33 0.00 40.36 1.28
5005 5920 1.137825 GAACGTCCCTGCGAGAGAG 59.862 63.158 0.00 0.00 35.59 3.20
5006 5921 1.303398 AACGTCCCTGCGAGAGAGA 60.303 57.895 0.00 0.00 35.59 3.10
5007 5922 0.681564 AACGTCCCTGCGAGAGAGAT 60.682 55.000 0.00 0.00 35.59 2.75
5008 5923 0.681564 ACGTCCCTGCGAGAGAGATT 60.682 55.000 0.00 0.00 35.59 2.40
5065 5980 3.743911 GGGAACAAACAAAATAAAGGCGG 59.256 43.478 0.00 0.00 0.00 6.13
5073 5988 2.929398 CAAAATAAAGGCGGCACCATTC 59.071 45.455 13.08 0.00 43.14 2.67
5080 5995 0.667184 GGCGGCACCATTCAAAACAG 60.667 55.000 3.07 0.00 38.86 3.16
5119 6034 5.091431 CCATCTTTTCTGCGATGACTTTTC 58.909 41.667 0.00 0.00 39.43 2.29
5123 6038 2.724977 TCTGCGATGACTTTTCGTCT 57.275 45.000 0.00 0.00 43.25 4.18
5124 6039 3.026630 TCTGCGATGACTTTTCGTCTT 57.973 42.857 0.00 0.00 43.25 3.01
5140 6055 9.663904 CTTTTCGTCTTAGATTTGAATGTTGAA 57.336 29.630 0.00 0.00 0.00 2.69
5154 6069 9.650539 TTTGAATGTTGAAAGAACAGAAATTGA 57.349 25.926 0.00 0.00 33.18 2.57
5155 6070 8.861033 TGAATGTTGAAAGAACAGAAATTGAG 57.139 30.769 0.00 0.00 33.18 3.02
5157 6072 9.178427 GAATGTTGAAAGAACAGAAATTGAGAG 57.822 33.333 0.00 0.00 33.18 3.20
5218 6133 0.392461 GGCGCCTCCTGTAAATGTCA 60.392 55.000 22.15 0.00 0.00 3.58
5261 6176 1.066858 GCATCGTCTCCTTGTTCTCCA 60.067 52.381 0.00 0.00 0.00 3.86
5362 6283 2.673368 GAGTGACAACCTAAATCAGCGG 59.327 50.000 0.00 0.00 0.00 5.52
5386 6307 0.394216 CCCAATGTGCGATGAAGGGA 60.394 55.000 0.00 0.00 36.96 4.20
5391 6312 1.452110 TGTGCGATGAAGGGACATTG 58.548 50.000 0.00 0.00 35.45 2.82
5395 6316 3.006940 TGCGATGAAGGGACATTGTTAC 58.993 45.455 0.00 0.00 34.98 2.50
5396 6317 2.030457 GCGATGAAGGGACATTGTTACG 59.970 50.000 0.00 0.00 34.98 3.18
5413 6334 5.720202 TGTTACGATGTAATCTGTTCTGCT 58.280 37.500 0.00 0.00 42.58 4.24
5418 6339 5.358442 ACGATGTAATCTGTTCTGCTACTCT 59.642 40.000 0.00 0.00 42.58 3.24
5422 6343 6.184068 TGTAATCTGTTCTGCTACTCTCTCT 58.816 40.000 0.00 0.00 0.00 3.10
5430 6351 2.077627 TGCTACTCTCTCTGTCGTCAC 58.922 52.381 0.00 0.00 0.00 3.67
5444 6365 4.168014 TGTCGTCACATATCGGTTGTAAC 58.832 43.478 0.00 0.00 0.00 2.50
5455 6376 8.826710 ACATATCGGTTGTAACAACATCTTATG 58.173 33.333 5.09 8.31 0.00 1.90
5468 6394 4.637276 ACATCTTATGTTGTGTTGGACGA 58.363 39.130 0.00 0.00 41.63 4.20
5478 6404 1.082756 GTTGGACGAAAGCACTGCG 60.083 57.895 0.00 0.00 0.00 5.18
5486 6412 2.094700 ACGAAAGCACTGCGAATCTCTA 60.095 45.455 0.00 0.00 0.00 2.43
5495 6421 2.857152 CTGCGAATCTCTAGTGAACAGC 59.143 50.000 0.00 5.42 0.00 4.40
5496 6422 2.231235 TGCGAATCTCTAGTGAACAGCA 59.769 45.455 13.61 13.61 0.00 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 56 2.233305 ACAGAACAGATACGGGTCCT 57.767 50.000 0.00 0.00 0.00 3.85
176 178 3.378399 GAAGGGAGAGGCTCGCCAC 62.378 68.421 33.58 23.66 43.17 5.01
177 179 3.077556 GAAGGGAGAGGCTCGCCA 61.078 66.667 33.58 0.00 43.17 5.69
178 180 3.855853 GGAAGGGAGAGGCTCGCC 61.856 72.222 27.02 27.02 43.17 5.54
179 181 3.855853 GGGAAGGGAGAGGCTCGC 61.856 72.222 10.01 10.01 42.60 5.03
180 182 3.532155 CGGGAAGGGAGAGGCTCG 61.532 72.222 9.22 0.00 0.00 5.03
181 183 3.855853 GCGGGAAGGGAGAGGCTC 61.856 72.222 6.34 6.34 0.00 4.70
182 184 4.406763 AGCGGGAAGGGAGAGGCT 62.407 66.667 0.00 0.00 0.00 4.58
183 185 3.855853 GAGCGGGAAGGGAGAGGC 61.856 72.222 0.00 0.00 0.00 4.70
184 186 2.042435 AGAGCGGGAAGGGAGAGG 60.042 66.667 0.00 0.00 0.00 3.69
185 187 1.076339 AGAGAGCGGGAAGGGAGAG 60.076 63.158 0.00 0.00 0.00 3.20
186 188 1.076632 GAGAGAGCGGGAAGGGAGA 60.077 63.158 0.00 0.00 0.00 3.71
187 189 0.686112 AAGAGAGAGCGGGAAGGGAG 60.686 60.000 0.00 0.00 0.00 4.30
188 190 0.684805 GAAGAGAGAGCGGGAAGGGA 60.685 60.000 0.00 0.00 0.00 4.20
189 191 1.681486 GGAAGAGAGAGCGGGAAGGG 61.681 65.000 0.00 0.00 0.00 3.95
190 192 1.819905 GGAAGAGAGAGCGGGAAGG 59.180 63.158 0.00 0.00 0.00 3.46
191 193 1.435515 CGGAAGAGAGAGCGGGAAG 59.564 63.158 0.00 0.00 0.00 3.46
192 194 2.711922 GCGGAAGAGAGAGCGGGAA 61.712 63.158 0.00 0.00 0.00 3.97
193 195 3.141488 GCGGAAGAGAGAGCGGGA 61.141 66.667 0.00 0.00 0.00 5.14
286 442 4.802051 GAATGGGGCCGCTGCTGA 62.802 66.667 21.80 0.00 37.74 4.26
306 462 0.397957 GAGGAACCTCTCTCCCTCCC 60.398 65.000 12.98 0.00 39.33 4.30
323 479 2.992543 CGAAAAGAAGCTGACCTGAGAG 59.007 50.000 0.00 0.00 0.00 3.20
340 496 1.148310 CGCTTGAGAGAAAGGCGAAA 58.852 50.000 0.00 0.00 32.24 3.46
530 730 5.823861 AATTCAGGCCAAAACTTAACCAT 57.176 34.783 5.01 0.00 0.00 3.55
566 767 4.452795 TCTTAATCGACTGAGATCTAGCCG 59.547 45.833 0.00 0.00 0.00 5.52
573 774 9.877178 ACTTGTTAAATCTTAATCGACTGAGAT 57.123 29.630 0.00 0.00 0.00 2.75
586 787 9.342308 TCACTTGATTGAGACTTGTTAAATCTT 57.658 29.630 0.00 0.00 0.00 2.40
656 871 6.154203 TCATCAGATCTTGCGTAGAGATTT 57.846 37.500 0.00 0.00 36.02 2.17
675 890 6.695429 TGTCTCAGTGGATGCTATATTCATC 58.305 40.000 8.39 8.39 39.56 2.92
926 1144 1.607178 CCATGTTTGCTCTGCCCCA 60.607 57.895 0.00 0.00 0.00 4.96
1165 1383 2.527100 CGAGACGGAAACTGATACCAC 58.473 52.381 0.00 0.00 0.00 4.16
1231 1449 0.749454 ATGGCGCACTCTTGGGAATC 60.749 55.000 10.83 0.00 37.91 2.52
1334 1552 3.007398 AGTCTGAGACAACTTTGCCCTAG 59.993 47.826 15.86 0.00 34.60 3.02
1520 1741 1.792949 CGAATGATACCGGTAAGCTGC 59.207 52.381 20.22 7.68 0.00 5.25
1580 1801 2.514205 AGCCAGCAAACACAATGAAC 57.486 45.000 0.00 0.00 0.00 3.18
1624 1877 5.048507 GTCCGACTTTCTAAAACACACTCT 58.951 41.667 0.00 0.00 0.00 3.24
1628 1881 4.124238 CCAGTCCGACTTTCTAAAACACA 58.876 43.478 0.00 0.00 0.00 3.72
1670 1923 8.499403 AGCCTTCTAATGTTCTAAATTGACTC 57.501 34.615 0.00 0.00 0.00 3.36
1710 1967 5.852827 TGCCACATTAGTCAATATCGATCA 58.147 37.500 0.00 0.00 0.00 2.92
1711 1968 6.347725 GGTTGCCACATTAGTCAATATCGATC 60.348 42.308 0.00 0.00 0.00 3.69
1712 1969 5.470098 GGTTGCCACATTAGTCAATATCGAT 59.530 40.000 2.16 2.16 0.00 3.59
1714 1971 4.816385 AGGTTGCCACATTAGTCAATATCG 59.184 41.667 0.00 0.00 0.00 2.92
1715 1972 7.171678 GTCTAGGTTGCCACATTAGTCAATATC 59.828 40.741 0.00 0.00 0.00 1.63
1716 1973 6.992715 GTCTAGGTTGCCACATTAGTCAATAT 59.007 38.462 0.00 0.00 0.00 1.28
1808 2082 7.325660 TGTAGCAGAAATCTTGATTCCATTC 57.674 36.000 0.00 0.00 0.00 2.67
1892 2180 2.371841 TGGTCTACCAATGAACACAGCT 59.628 45.455 0.00 0.00 44.35 4.24
1989 2277 7.122799 GGGCTTTTTAGTTAGGTTCAGATGATT 59.877 37.037 0.00 0.00 0.00 2.57
2047 2335 9.659135 TGAATCAATCCCAAAAGTATATCCAAT 57.341 29.630 0.00 0.00 0.00 3.16
2052 2340 8.695456 GTGGTTGAATCAATCCCAAAAGTATAT 58.305 33.333 6.86 0.00 0.00 0.86
2057 2345 5.473066 AGTGGTTGAATCAATCCCAAAAG 57.527 39.130 6.86 0.00 0.00 2.27
2138 2427 6.601613 TGGAAGGTGCATAAAGAACGATAAAT 59.398 34.615 0.00 0.00 0.00 1.40
2153 2442 1.879380 CAATCGAACTTGGAAGGTGCA 59.121 47.619 0.00 0.00 0.00 4.57
2185 2475 9.994432 AAAGAGATCGCATATTTGAGTTTTTAG 57.006 29.630 0.00 0.00 0.00 1.85
2199 2490 2.369860 TCATAGGGCAAAGAGATCGCAT 59.630 45.455 0.00 0.00 0.00 4.73
2202 2493 4.260948 GCTTTTCATAGGGCAAAGAGATCG 60.261 45.833 4.70 0.00 30.31 3.69
2237 2528 5.221009 GGATCAAGTGCCAAATTTTGCAAAA 60.221 36.000 25.76 25.76 39.57 2.44
2393 2684 9.383519 CATTAGGAACAGAACTCTAGCAAAATA 57.616 33.333 0.00 0.00 0.00 1.40
2479 2771 7.394816 AGGTCATGCAAACTATAAACAGTACT 58.605 34.615 0.00 0.00 0.00 2.73
2529 2821 6.255453 GCAATCAAAGTCAGCTTGTGTTTTTA 59.745 34.615 0.00 0.00 34.71 1.52
2627 2919 7.281040 TGAAAATCTTCTCAGAAAGTGCAAT 57.719 32.000 0.00 0.00 30.76 3.56
2690 3048 2.456577 ACCCAGCCATGTTTTCCATAC 58.543 47.619 0.00 0.00 30.71 2.39
2783 3141 9.823647 GATGATTACAATCTTAGAGTTCCAAGA 57.176 33.333 3.76 0.00 36.39 3.02
2967 3453 3.125316 CCAACGAAGCAACTCCATCTTAC 59.875 47.826 0.00 0.00 0.00 2.34
3097 3583 6.040616 ACTTCTATACTTGGTACCATCCTTCG 59.959 42.308 17.17 3.98 0.00 3.79
3497 4042 6.021596 GTGCTAAAATCAATACCGACACAAG 58.978 40.000 0.00 0.00 0.00 3.16
3515 4060 6.317893 TGAGTCGAAGTCAGTATATGTGCTAA 59.682 38.462 0.00 0.00 0.00 3.09
3516 4061 5.820947 TGAGTCGAAGTCAGTATATGTGCTA 59.179 40.000 0.00 0.00 0.00 3.49
3554 4117 6.991938 ACAAAAAGCTAAATGATAACAGCCA 58.008 32.000 0.00 0.00 34.49 4.75
3806 4591 6.381801 CAAAAGGCATGAGATAAACGTCTTT 58.618 36.000 0.00 0.00 0.00 2.52
3949 4757 1.134371 GCCTTGCTAAGATCTTCCGGT 60.134 52.381 12.24 0.00 0.00 5.28
4018 4826 1.351017 TCCATGTCAAGGTCCACTTCC 59.649 52.381 0.00 0.00 37.29 3.46
4077 4885 3.807538 CAGTGTGGCGCATGGAGC 61.808 66.667 10.83 0.00 40.87 4.70
4236 5066 3.318275 TGTAGATATCGCGCTTCCTCTTT 59.682 43.478 5.56 0.00 0.00 2.52
4251 5081 6.090483 GTCTTGGCTAGAGCATTGTAGATA 57.910 41.667 3.54 0.00 44.36 1.98
4291 5121 1.364171 CTGAACCGGGCTATCTCCG 59.636 63.158 6.32 0.00 46.43 4.63
4609 5446 7.359262 TGATGAGTTACGAAGTTTACCAATG 57.641 36.000 0.00 0.00 37.78 2.82
4619 5511 4.489810 AGTGAAGCTGATGAGTTACGAAG 58.510 43.478 0.00 0.00 0.00 3.79
4623 5515 6.478344 CCTATGAAGTGAAGCTGATGAGTTAC 59.522 42.308 0.00 0.00 0.00 2.50
4700 5593 5.418840 TCTTTCACCCCAAAGATAAGAATGC 59.581 40.000 0.00 0.00 37.45 3.56
4752 5645 2.842462 ACGGCAGTGGTGAGGTGA 60.842 61.111 0.00 0.00 0.00 4.02
4753 5646 1.532604 TAGACGGCAGTGGTGAGGTG 61.533 60.000 0.00 0.00 0.00 4.00
4754 5647 1.228769 TAGACGGCAGTGGTGAGGT 60.229 57.895 0.00 0.00 0.00 3.85
4756 5649 1.215647 GGTAGACGGCAGTGGTGAG 59.784 63.158 0.00 0.00 0.00 3.51
4757 5650 1.116536 TTGGTAGACGGCAGTGGTGA 61.117 55.000 0.00 0.00 0.00 4.02
4759 5652 1.370064 GTTGGTAGACGGCAGTGGT 59.630 57.895 0.00 0.00 0.00 4.16
4760 5653 1.375523 GGTTGGTAGACGGCAGTGG 60.376 63.158 0.00 0.00 0.00 4.00
4761 5654 0.036388 ATGGTTGGTAGACGGCAGTG 60.036 55.000 0.00 0.00 0.00 3.66
4762 5655 0.249398 GATGGTTGGTAGACGGCAGT 59.751 55.000 0.00 0.00 0.00 4.40
4763 5656 0.249120 TGATGGTTGGTAGACGGCAG 59.751 55.000 0.00 0.00 0.00 4.85
4764 5657 0.249120 CTGATGGTTGGTAGACGGCA 59.751 55.000 0.00 0.00 0.00 5.69
4765 5658 0.462047 CCTGATGGTTGGTAGACGGC 60.462 60.000 0.00 0.00 0.00 5.68
4766 5659 0.462047 GCCTGATGGTTGGTAGACGG 60.462 60.000 0.00 0.00 35.27 4.79
4768 5661 0.912486 AGGCCTGATGGTTGGTAGAC 59.088 55.000 3.11 0.00 35.27 2.59
4769 5662 1.204146 GAGGCCTGATGGTTGGTAGA 58.796 55.000 12.00 0.00 35.27 2.59
5005 5920 6.387465 CACCATGATTATGCCATCTTCAATC 58.613 40.000 0.00 0.00 32.79 2.67
5006 5921 5.279306 GCACCATGATTATGCCATCTTCAAT 60.279 40.000 0.00 0.00 33.06 2.57
5007 5922 4.038282 GCACCATGATTATGCCATCTTCAA 59.962 41.667 0.00 0.00 33.06 2.69
5008 5923 3.570975 GCACCATGATTATGCCATCTTCA 59.429 43.478 0.00 0.00 33.06 3.02
5065 5980 8.810652 TTAAGTTAATCTGTTTTGAATGGTGC 57.189 30.769 0.00 0.00 0.00 5.01
5073 5988 9.696917 ATGGAAGCTTTAAGTTAATCTGTTTTG 57.303 29.630 0.00 0.00 0.00 2.44
5092 6007 2.679837 TCATCGCAGAAAAGATGGAAGC 59.320 45.455 5.73 0.00 43.58 3.86
5119 6034 9.107367 GTTCTTTCAACATTCAAATCTAAGACG 57.893 33.333 0.00 0.00 0.00 4.18
5140 6055 4.599241 TCCCCTCTCTCAATTTCTGTTCTT 59.401 41.667 0.00 0.00 0.00 2.52
5151 6066 0.987294 CCTGCTTTCCCCTCTCTCAA 59.013 55.000 0.00 0.00 0.00 3.02
5152 6067 0.911525 CCCTGCTTTCCCCTCTCTCA 60.912 60.000 0.00 0.00 0.00 3.27
5153 6068 1.631071 CCCCTGCTTTCCCCTCTCTC 61.631 65.000 0.00 0.00 0.00 3.20
5154 6069 1.617839 CCCCTGCTTTCCCCTCTCT 60.618 63.158 0.00 0.00 0.00 3.10
5155 6070 1.208165 TTCCCCTGCTTTCCCCTCTC 61.208 60.000 0.00 0.00 0.00 3.20
5157 6072 1.304617 CTTCCCCTGCTTTCCCCTC 59.695 63.158 0.00 0.00 0.00 4.30
5218 6133 1.056125 TGCATCTCATCACCCCGGAT 61.056 55.000 0.73 0.00 0.00 4.18
5261 6176 1.135373 CGTTCTGGCTGTCATAGACGT 60.135 52.381 0.00 0.00 37.17 4.34
5311 6226 3.495377 TCTTCGTTCCCGTATGTTTGTTG 59.505 43.478 0.00 0.00 35.01 3.33
5312 6227 3.731089 TCTTCGTTCCCGTATGTTTGTT 58.269 40.909 0.00 0.00 35.01 2.83
5313 6228 3.389925 TCTTCGTTCCCGTATGTTTGT 57.610 42.857 0.00 0.00 35.01 2.83
5362 6283 0.679640 TCATCGCACATTGGGGGTTC 60.680 55.000 2.62 0.00 0.00 3.62
5386 6307 7.413000 GCAGAACAGATTACATCGTAACAATGT 60.413 37.037 0.00 0.00 40.37 2.71
5391 6312 6.973474 AGTAGCAGAACAGATTACATCGTAAC 59.027 38.462 0.00 0.00 0.00 2.50
5395 6316 5.826586 AGAGTAGCAGAACAGATTACATCG 58.173 41.667 0.00 0.00 0.00 3.84
5396 6317 7.013274 AGAGAGAGTAGCAGAACAGATTACATC 59.987 40.741 0.00 0.00 0.00 3.06
5413 6334 4.745620 CGATATGTGACGACAGAGAGAGTA 59.254 45.833 0.00 0.00 34.87 2.59
5418 6339 2.640184 ACCGATATGTGACGACAGAGA 58.360 47.619 0.00 0.00 34.87 3.10
5422 6343 4.168014 GTTACAACCGATATGTGACGACA 58.832 43.478 0.00 0.00 36.22 4.35
5430 6351 8.826710 ACATAAGATGTTGTTACAACCGATATG 58.173 33.333 23.20 23.14 41.63 1.78
5455 6376 1.400494 AGTGCTTTCGTCCAACACAAC 59.600 47.619 0.00 0.00 33.69 3.32
5466 6387 1.354040 AGAGATTCGCAGTGCTTTCG 58.646 50.000 14.33 0.00 0.00 3.46
5468 6394 3.056536 TCACTAGAGATTCGCAGTGCTTT 60.057 43.478 14.33 0.00 35.60 3.51
5478 6404 5.407995 GGCATATGCTGTTCACTAGAGATTC 59.592 44.000 26.12 0.51 41.70 2.52
5486 6412 3.137176 AGGTATGGCATATGCTGTTCACT 59.863 43.478 26.12 14.69 41.70 3.41


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

AutoCloner maintained by Alex Coulton.