Multiple sequence alignment - TraesCS2D01G144000

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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 TraesCS2D01G144000 chr2D 100.000 4091 0 0 1 4091 85387527 85391617 0.000000e+00 7555.0
1 TraesCS2D01G144000 chr2D 93.394 1877 114 9 1332 3205 85673275 85675144 0.000000e+00 2771.0
2 TraesCS2D01G144000 chr2D 92.750 1862 116 13 1348 3205 84916312 84918158 0.000000e+00 2673.0
3 TraesCS2D01G144000 chr2D 85.083 1019 78 34 378 1358 85672349 85673331 0.000000e+00 972.0
4 TraesCS2D01G144000 chr2D 89.969 648 37 10 670 1298 84915691 84916329 0.000000e+00 811.0
5 TraesCS2D01G144000 chr2D 88.331 677 47 17 1 656 84914969 84915634 0.000000e+00 784.0
6 TraesCS2D01G144000 chr2D 90.674 386 31 3 9 391 85671951 85672334 3.650000e-140 508.0
7 TraesCS2D01G144000 chr2D 81.646 158 20 4 3930 4087 84928613 84928761 5.550000e-24 122.0
8 TraesCS2D01G144000 chr2D 79.048 105 12 6 1204 1298 142675724 142675620 3.410000e-06 63.9
9 TraesCS2D01G144000 chr2B 96.005 2453 64 14 1358 3804 137608121 137610545 0.000000e+00 3956.0
10 TraesCS2D01G144000 chr2B 96.413 2314 60 12 1492 3799 136951179 136953475 0.000000e+00 3792.0
11 TraesCS2D01G144000 chr2B 94.936 2350 68 21 1332 3677 136805982 136808284 0.000000e+00 3633.0
12 TraesCS2D01G144000 chr2B 92.702 1891 124 11 1318 3205 137188358 137190237 0.000000e+00 2715.0
13 TraesCS2D01G144000 chr2B 92.098 696 33 12 670 1358 136805358 136806038 0.000000e+00 961.0
14 TraesCS2D01G144000 chr2B 89.006 664 58 9 1 657 136949616 136950271 0.000000e+00 808.0
15 TraesCS2D01G144000 chr2B 92.495 533 30 8 9 535 137606948 137607476 0.000000e+00 754.0
16 TraesCS2D01G144000 chr2B 85.307 667 61 20 11 657 136804655 136805304 0.000000e+00 654.0
17 TraesCS2D01G144000 chr2B 87.544 570 41 20 673 1236 137187789 137188334 2.070000e-177 632.0
18 TraesCS2D01G144000 chr2B 93.059 389 13 5 573 955 137607469 137607849 1.280000e-154 556.0
19 TraesCS2D01G144000 chr2B 85.588 451 32 17 670 1113 136950327 136950751 3.750000e-120 442.0
20 TraesCS2D01G144000 chr2B 95.763 236 5 3 3861 4091 137610556 137610791 3.860000e-100 375.0
21 TraesCS2D01G144000 chr2B 92.653 245 18 0 1114 1358 136950886 136951130 1.810000e-93 353.0
22 TraesCS2D01G144000 chr2B 89.273 289 14 1 1039 1327 137607879 137608150 3.030000e-91 346.0
23 TraesCS2D01G144000 chr2B 86.192 239 22 8 252 485 137185818 137186050 8.780000e-62 248.0
24 TraesCS2D01G144000 chr2B 93.519 108 7 0 1332 1439 136951074 136951181 1.180000e-35 161.0
25 TraesCS2D01G144000 chr2B 92.174 115 8 1 146 260 137183049 137183162 1.180000e-35 161.0
26 TraesCS2D01G144000 chr2B 94.382 89 5 0 1 89 137144724 137144812 1.980000e-28 137.0
27 TraesCS2D01G144000 chr2B 94.382 89 5 0 1 89 137717598 137717686 1.980000e-28 137.0
28 TraesCS2D01G144000 chr2B 87.234 94 9 3 479 569 137187587 137187680 2.010000e-18 104.0
29 TraesCS2D01G144000 chr2A 89.463 1528 141 16 1687 3205 84154116 84152600 0.000000e+00 1912.0
30 TraesCS2D01G144000 chr2A 85.294 170 14 5 490 657 84154957 84154797 9.100000e-37 165.0
31 TraesCS2D01G144000 chr2A 94.792 96 5 0 1065 1160 84154377 84154282 2.550000e-32 150.0
32 TraesCS2D01G144000 chr2A 88.136 59 5 2 3980 4037 172842603 172842546 7.340000e-08 69.4
33 TraesCS2D01G144000 chr2A 94.737 38 1 1 3965 4002 85600822 85600858 1.590000e-04 58.4
34 TraesCS2D01G144000 chr4B 94.761 649 17 7 3136 3779 446685640 446686276 0.000000e+00 994.0
35 TraesCS2D01G144000 chr3B 93.837 649 21 10 3136 3779 124618410 124619044 0.000000e+00 959.0
36 TraesCS2D01G144000 chr3B 75.971 1261 256 33 1929 3171 824391358 824392589 1.260000e-169 606.0
37 TraesCS2D01G144000 chr7A 91.455 550 20 5 3545 4091 571276065 571276590 0.000000e+00 730.0
38 TraesCS2D01G144000 chr7A 75.485 1289 251 48 1930 3189 32413303 32414555 1.650000e-158 569.0
39 TraesCS2D01G144000 chr7A 97.826 46 1 0 1348 1393 269271899 269271944 3.390000e-11 80.5
40 TraesCS2D01G144000 chr7A 82.022 89 8 4 1270 1358 733798047 733797967 7.340000e-08 69.4
41 TraesCS2D01G144000 chr7A 90.196 51 5 0 3841 3891 571276065 571276115 2.640000e-07 67.6
42 TraesCS2D01G144000 chrUn 75.610 1271 251 37 1929 3176 232156516 232157750 3.550000e-160 575.0
43 TraesCS2D01G144000 chr5A 95.745 47 2 0 1187 1233 613462677 613462723 4.390000e-10 76.8
44 TraesCS2D01G144000 chr5A 100.000 29 0 0 1270 1298 309313565 309313593 2.000000e-03 54.7
45 TraesCS2D01G144000 chr6B 85.135 74 8 3 3966 4037 318876096 318876168 5.670000e-09 73.1
46 TraesCS2D01G144000 chr6B 85.135 74 8 3 3966 4037 318988008 318988080 5.670000e-09 73.1
47 TraesCS2D01G144000 chr7D 80.198 101 12 4 1258 1358 633355340 633355432 7.340000e-08 69.4
48 TraesCS2D01G144000 chr7B 83.784 74 9 3 3966 4037 248701235 248701163 2.640000e-07 67.6
49 TraesCS2D01G144000 chr7B 76.429 140 21 9 1170 1298 600963435 600963573 9.490000e-07 65.8
50 TraesCS2D01G144000 chr5D 86.667 60 8 0 1334 1393 46603899 46603840 2.640000e-07 67.6
51 TraesCS2D01G144000 chr1B 83.784 74 9 3 3966 4037 510308651 510308579 2.640000e-07 67.6
52 TraesCS2D01G144000 chr1D 97.297 37 1 0 3386 3422 38596749 38596713 3.410000e-06 63.9
53 TraesCS2D01G144000 chr3A 88.462 52 4 2 3986 4037 180163066 180163115 1.230000e-05 62.1
54 TraesCS2D01G144000 chr1A 92.500 40 3 0 1364 1403 543652843 543652804 1.590000e-04 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 TraesCS2D01G144000 chr2D 85387527 85391617 4090 False 7555.000000 7555 100.000000 1 4091 1 chr2D.!!$F2 4090
1 TraesCS2D01G144000 chr2D 84914969 84918158 3189 False 1422.666667 2673 90.350000 1 3205 3 chr2D.!!$F3 3204
2 TraesCS2D01G144000 chr2D 85671951 85675144 3193 False 1417.000000 2771 89.717000 9 3205 3 chr2D.!!$F4 3196
3 TraesCS2D01G144000 chr2B 136804655 136808284 3629 False 1749.333333 3633 90.780333 11 3677 3 chr2B.!!$F3 3666
4 TraesCS2D01G144000 chr2B 137606948 137610791 3843 False 1197.400000 3956 93.319000 9 4091 5 chr2B.!!$F6 4082
5 TraesCS2D01G144000 chr2B 136949616 136953475 3859 False 1111.200000 3792 91.435800 1 3799 5 chr2B.!!$F4 3798
6 TraesCS2D01G144000 chr2B 137183049 137190237 7188 False 772.000000 2715 89.169200 146 3205 5 chr2B.!!$F5 3059
7 TraesCS2D01G144000 chr2A 84152600 84154957 2357 True 742.333333 1912 89.849667 490 3205 3 chr2A.!!$R2 2715
8 TraesCS2D01G144000 chr4B 446685640 446686276 636 False 994.000000 994 94.761000 3136 3779 1 chr4B.!!$F1 643
9 TraesCS2D01G144000 chr3B 124618410 124619044 634 False 959.000000 959 93.837000 3136 3779 1 chr3B.!!$F1 643
10 TraesCS2D01G144000 chr3B 824391358 824392589 1231 False 606.000000 606 75.971000 1929 3171 1 chr3B.!!$F2 1242
11 TraesCS2D01G144000 chr7A 32413303 32414555 1252 False 569.000000 569 75.485000 1930 3189 1 chr7A.!!$F1 1259
12 TraesCS2D01G144000 chr7A 571276065 571276590 525 False 398.800000 730 90.825500 3545 4091 2 chr7A.!!$F3 546
13 TraesCS2D01G144000 chrUn 232156516 232157750 1234 False 575.000000 575 75.610000 1929 3176 1 chrUn.!!$F1 1247

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
81 83 0.178903 AGCTGTGTGGAGGGTCCTTA 60.179 55.0 0.0 0.0 37.46 2.69 F
160 163 0.873743 GCATAGTGCTCTGTCGCTCC 60.874 60.0 0.0 0.0 40.96 4.70 F
1011 5356 1.027357 GGCCACGAATGAATGATGCT 58.973 50.0 0.0 0.0 0.00 3.79 F
1631 6202 0.551131 AGGGGGAGAATTGGCTGACT 60.551 55.0 0.0 0.0 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1240 5810 0.178861 AGCTCCTTCCTTCCCTCCAA 60.179 55.0 0.00 0.0 0.00 3.53 R
1321 5891 0.246635 GGTCGCCTGCAAGACTAAGA 59.753 55.0 13.86 0.0 37.52 2.10 R
2855 7612 0.453390 GGCTGAAGAATCAAAGCGGG 59.547 55.0 0.00 0.0 34.49 6.13 R
3224 7986 0.531090 AACGCTTGCCACTGTCGTTA 60.531 50.0 1.55 0.0 40.88 3.18 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
81 83 0.178903 AGCTGTGTGGAGGGTCCTTA 60.179 55.000 0.00 0.00 37.46 2.69
130 132 3.126073 CCATCTCGATGATTCTTCGCAA 58.874 45.455 15.05 7.52 41.20 4.85
137 140 1.164411 TGATTCTTCGCAACGCCAAT 58.836 45.000 0.00 0.00 0.00 3.16
160 163 0.873743 GCATAGTGCTCTGTCGCTCC 60.874 60.000 0.00 0.00 40.96 4.70
282 2949 3.119849 CGGTCATTGGTTGCTTCCTTTAG 60.120 47.826 0.00 0.00 0.00 1.85
295 2962 3.217681 TCCTTTAGGTCAAACCGCTTT 57.782 42.857 0.00 0.00 44.90 3.51
383 3080 4.095632 TGGTTTATATTGTGTCCATGTGCG 59.904 41.667 0.00 0.00 0.00 5.34
485 3191 7.663043 AAATCCTTGCCCCGTTTATTTATAA 57.337 32.000 0.00 0.00 0.00 0.98
487 3193 7.849322 ATCCTTGCCCCGTTTATTTATAAAT 57.151 32.000 14.86 14.86 35.02 1.40
550 4816 5.125097 TGGTAGAAGAAAGACGAGTGATACC 59.875 44.000 0.00 0.00 0.00 2.73
633 4917 4.415783 GGTGGCTTCCATCGGTTT 57.584 55.556 0.00 0.00 35.28 3.27
862 5204 2.158004 TCTCCCTCCCTCTCTTTTTCCA 60.158 50.000 0.00 0.00 0.00 3.53
864 5206 3.268072 CTCCCTCCCTCTCTTTTTCCATT 59.732 47.826 0.00 0.00 0.00 3.16
1011 5356 1.027357 GGCCACGAATGAATGATGCT 58.973 50.000 0.00 0.00 0.00 3.79
1180 5749 7.394816 AGTACAAACATCACCAGTTTAGCTAT 58.605 34.615 0.00 0.00 37.10 2.97
1237 5807 2.178912 TTTCGCGTGAAGGAAGGAAT 57.821 45.000 11.77 0.00 35.06 3.01
1240 5810 1.822990 TCGCGTGAAGGAAGGAATAGT 59.177 47.619 5.77 0.00 0.00 2.12
1322 5892 1.926108 AGGCGACCCTGGTATCTATC 58.074 55.000 0.00 0.00 40.94 2.08
1323 5893 1.429687 AGGCGACCCTGGTATCTATCT 59.570 52.381 0.00 0.00 40.94 1.98
1324 5894 2.158295 AGGCGACCCTGGTATCTATCTT 60.158 50.000 0.00 0.00 40.94 2.40
1325 5895 3.075582 AGGCGACCCTGGTATCTATCTTA 59.924 47.826 0.00 0.00 40.94 2.10
1326 5896 3.444388 GGCGACCCTGGTATCTATCTTAG 59.556 52.174 0.00 0.00 0.00 2.18
1327 5897 4.080687 GCGACCCTGGTATCTATCTTAGT 58.919 47.826 0.00 0.00 0.00 2.24
1328 5898 4.156373 GCGACCCTGGTATCTATCTTAGTC 59.844 50.000 0.00 0.00 0.00 2.59
1329 5899 5.562635 CGACCCTGGTATCTATCTTAGTCT 58.437 45.833 0.00 0.00 0.00 3.24
1330 5900 6.005198 CGACCCTGGTATCTATCTTAGTCTT 58.995 44.000 0.00 0.00 0.00 3.01
1331 5901 6.072397 CGACCCTGGTATCTATCTTAGTCTTG 60.072 46.154 0.00 0.00 0.00 3.02
1332 5902 5.540719 ACCCTGGTATCTATCTTAGTCTTGC 59.459 44.000 0.00 0.00 0.00 4.01
1333 5903 5.540337 CCCTGGTATCTATCTTAGTCTTGCA 59.460 44.000 0.00 0.00 0.00 4.08
1567 6138 3.495377 CACGTATCGGTTTGAGGTTGAAA 59.505 43.478 0.00 0.00 0.00 2.69
1631 6202 0.551131 AGGGGGAGAATTGGCTGACT 60.551 55.000 0.00 0.00 0.00 3.41
1785 6498 0.729116 CTGTTGGCTATTCTGCGGTG 59.271 55.000 0.00 0.00 0.00 4.94
1909 6626 5.950549 ACTGCAGTAAGAGCCTAAGTACTAA 59.049 40.000 20.16 0.00 0.00 2.24
2008 6732 1.227556 GTGGTTGTCGCAGAGTGGT 60.228 57.895 0.00 0.00 36.95 4.16
2022 6746 6.042777 CGCAGAGTGGTCATCTAAGAAAATA 58.957 40.000 0.00 0.00 0.00 1.40
2087 6814 2.288025 GGGCAGACCTACCGGACAA 61.288 63.158 9.46 0.00 35.85 3.18
2199 6926 7.391833 GTCTTTTCCTTCCCATCATCCATATAC 59.608 40.741 0.00 0.00 0.00 1.47
2481 7217 2.099405 CCCAAACTCCACACAAACAGT 58.901 47.619 0.00 0.00 0.00 3.55
2582 7318 0.773644 ATCTTCCAGTGGCAGGTTGT 59.226 50.000 9.08 0.00 0.00 3.32
2788 7533 1.071434 TGATCCATGGTTGGTGGTCA 58.929 50.000 12.58 3.61 44.06 4.02
2822 7567 4.380233 GCTTCTCATGGTTGATCTTGTTGG 60.380 45.833 0.00 0.00 0.00 3.77
2945 7702 5.905331 TCTTTATCAGCCTTGATAGGAGGAA 59.095 40.000 0.00 0.00 44.75 3.36
3057 7817 1.020437 GGATTGCTGTAGAGCTTGGC 58.980 55.000 13.66 0.24 46.39 4.52
3089 7849 6.866010 TTACAGTATAACTCGCTCGGATTA 57.134 37.500 0.00 0.00 0.00 1.75
3224 7986 0.982704 AGTGAGCCTCTGCATCAGTT 59.017 50.000 0.00 0.00 41.13 3.16
3290 8053 6.004574 GGGAAGGAACTGAAGTGTCTAATTT 58.995 40.000 0.00 0.00 40.86 1.82
3291 8054 6.072452 GGGAAGGAACTGAAGTGTCTAATTTG 60.072 42.308 0.00 0.00 40.86 2.32
3292 8055 6.486993 GGAAGGAACTGAAGTGTCTAATTTGT 59.513 38.462 0.00 0.00 40.86 2.83
3294 8057 7.964604 AGGAACTGAAGTGTCTAATTTGTAC 57.035 36.000 0.00 0.00 37.18 2.90
3295 8058 7.506114 AGGAACTGAAGTGTCTAATTTGTACA 58.494 34.615 0.00 0.00 37.18 2.90
3296 8059 7.990886 AGGAACTGAAGTGTCTAATTTGTACAA 59.009 33.333 3.59 3.59 37.18 2.41
3297 8060 8.617809 GGAACTGAAGTGTCTAATTTGTACAAA 58.382 33.333 22.58 22.58 34.46 2.83
3298 8061 9.434559 GAACTGAAGTGTCTAATTTGTACAAAC 57.565 33.333 22.78 11.39 32.51 2.93
3299 8062 8.500753 ACTGAAGTGTCTAATTTGTACAAACA 57.499 30.769 22.78 13.86 32.51 2.83
3300 8063 9.120538 ACTGAAGTGTCTAATTTGTACAAACAT 57.879 29.630 22.78 16.52 34.97 2.71
3301 8064 9.950680 CTGAAGTGTCTAATTTGTACAAACATT 57.049 29.630 22.78 16.14 34.97 2.71
3304 8067 8.574196 AGTGTCTAATTTGTACAAACATTTGC 57.426 30.769 22.78 12.04 41.79 3.68
3609 8377 6.097696 TCTCGATGGAAGGTGTTATTATCACA 59.902 38.462 7.10 0.00 37.52 3.58
3611 8379 7.279615 TCGATGGAAGGTGTTATTATCACAAT 58.720 34.615 7.10 0.00 37.52 2.71
3824 8592 2.441750 TGAGGAGGGCAACTGTAAAACT 59.558 45.455 0.00 0.00 0.00 2.66
3825 8593 2.814336 GAGGAGGGCAACTGTAAAACTG 59.186 50.000 0.00 0.00 0.00 3.16
3827 8595 2.583143 GAGGGCAACTGTAAAACTGGT 58.417 47.619 0.00 0.00 0.00 4.00
3828 8596 3.497227 GGAGGGCAACTGTAAAACTGGTA 60.497 47.826 0.00 0.00 0.00 3.25
3829 8597 3.483421 AGGGCAACTGTAAAACTGGTAC 58.517 45.455 0.00 0.00 0.00 3.34
3830 8598 3.117813 AGGGCAACTGTAAAACTGGTACA 60.118 43.478 0.00 0.00 0.00 2.90
3831 8599 3.633065 GGGCAACTGTAAAACTGGTACAA 59.367 43.478 0.00 0.00 38.70 2.41
3832 8600 4.498513 GGGCAACTGTAAAACTGGTACAAC 60.499 45.833 0.00 0.00 38.70 3.32
3833 8601 4.276460 GCAACTGTAAAACTGGTACAACG 58.724 43.478 0.00 0.00 38.70 4.10
3834 8602 4.787245 GCAACTGTAAAACTGGTACAACGG 60.787 45.833 0.00 0.00 38.70 4.44
3835 8603 4.405116 ACTGTAAAACTGGTACAACGGA 57.595 40.909 0.00 0.00 38.70 4.69
3836 8604 4.768583 ACTGTAAAACTGGTACAACGGAA 58.231 39.130 0.00 0.00 38.70 4.30
3837 8605 4.571984 ACTGTAAAACTGGTACAACGGAAC 59.428 41.667 0.00 0.00 38.70 3.62
3838 8606 4.511527 TGTAAAACTGGTACAACGGAACA 58.488 39.130 0.00 0.00 38.70 3.18
3839 8607 4.571580 TGTAAAACTGGTACAACGGAACAG 59.428 41.667 0.00 0.00 38.70 3.16
3840 8608 2.994186 AACTGGTACAACGGAACAGT 57.006 45.000 0.00 0.00 43.61 3.55
3841 8609 2.234300 ACTGGTACAACGGAACAGTG 57.766 50.000 0.00 0.00 40.56 3.66
3842 8610 1.483415 ACTGGTACAACGGAACAGTGT 59.517 47.619 0.00 0.00 40.56 3.55
3843 8611 2.694628 ACTGGTACAACGGAACAGTGTA 59.305 45.455 0.00 0.00 40.56 2.90
3844 8612 3.243636 ACTGGTACAACGGAACAGTGTAG 60.244 47.826 0.00 0.00 40.56 2.74
3845 8613 2.694628 TGGTACAACGGAACAGTGTAGT 59.305 45.455 0.00 0.00 31.92 2.73
3846 8614 3.054878 GGTACAACGGAACAGTGTAGTG 58.945 50.000 0.00 0.00 0.00 2.74
3847 8615 1.578583 ACAACGGAACAGTGTAGTGC 58.421 50.000 0.00 0.00 0.00 4.40
3848 8616 1.134640 ACAACGGAACAGTGTAGTGCA 60.135 47.619 0.00 0.00 0.00 4.57
3849 8617 1.937223 CAACGGAACAGTGTAGTGCAA 59.063 47.619 0.00 0.00 0.00 4.08
3850 8618 1.865865 ACGGAACAGTGTAGTGCAAG 58.134 50.000 0.00 0.00 0.00 4.01
3851 8619 1.138266 ACGGAACAGTGTAGTGCAAGT 59.862 47.619 0.00 0.00 0.00 3.16
3875 8643 9.331282 AGTTCCTCTTTGCTAATGTATTACATC 57.669 33.333 9.68 0.00 37.97 3.06
3891 8659 8.475639 TGTATTACATCTAGTTCTTGAGGGAAC 58.524 37.037 0.00 0.00 44.02 3.62
4065 8838 3.253188 ACCGTTTCATCATCCAACACTTG 59.747 43.478 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
81 83 2.667318 CGCTTGTCGTCGTTGCCAT 61.667 57.895 0.00 0.00 0.00 4.40
130 132 0.734889 GCACTATGCAAGATTGGCGT 59.265 50.000 0.00 0.00 44.26 5.68
160 163 5.186996 CAACAATGGATCCGGGAATAAAG 57.813 43.478 7.39 0.00 0.00 1.85
197 200 3.981211 AGCCAAATGAACAACACACATC 58.019 40.909 0.00 0.00 0.00 3.06
282 2949 1.866925 CCGAGAAAGCGGTTTGACC 59.133 57.895 18.67 3.08 46.07 4.02
295 2962 2.177016 TCATCACCTATTCTCCCCGAGA 59.823 50.000 0.00 0.00 36.86 4.04
383 3080 8.494016 AAGAGCAATAAACTATACAACTCACC 57.506 34.615 0.00 0.00 0.00 4.02
494 3200 7.599998 ACACATGGAGAAGCAAAACATATTTTC 59.400 33.333 0.00 0.00 35.79 2.29
550 4816 1.991430 CCGTTCGATCTCGCTGTTG 59.009 57.895 0.00 0.00 39.60 3.33
826 5162 1.755008 GAGAGGTCACGGGAGAGGG 60.755 68.421 0.00 0.00 0.00 4.30
827 5163 1.755008 GGAGAGGTCACGGGAGAGG 60.755 68.421 0.00 0.00 0.00 3.69
828 5164 1.755008 GGGAGAGGTCACGGGAGAG 60.755 68.421 0.00 0.00 0.00 3.20
829 5165 2.212794 GAGGGAGAGGTCACGGGAGA 62.213 65.000 0.00 0.00 0.00 3.71
830 5166 1.755008 GAGGGAGAGGTCACGGGAG 60.755 68.421 0.00 0.00 0.00 4.30
831 5167 2.359404 GAGGGAGAGGTCACGGGA 59.641 66.667 0.00 0.00 0.00 5.14
862 5204 7.373493 CAACAAATTTGCACTAGGAAGAGAAT 58.627 34.615 18.12 0.00 0.00 2.40
864 5206 5.241506 CCAACAAATTTGCACTAGGAAGAGA 59.758 40.000 18.12 0.00 0.00 3.10
1011 5356 2.434843 CGTGCATCTAGGCAGGGGA 61.435 63.158 1.65 0.00 45.96 4.81
1180 5749 8.997323 CAAATTATAAATTCAGGCAACCACAAA 58.003 29.630 0.00 0.00 37.17 2.83
1237 5807 2.834113 CTCCTTCCTTCCCTCCAACTA 58.166 52.381 0.00 0.00 0.00 2.24
1240 5810 0.178861 AGCTCCTTCCTTCCCTCCAA 60.179 55.000 0.00 0.00 0.00 3.53
1304 5874 1.926108 AGATAGATACCAGGGTCGCC 58.074 55.000 0.00 0.00 0.00 5.54
1305 5875 4.080687 ACTAAGATAGATACCAGGGTCGC 58.919 47.826 0.00 0.00 0.00 5.19
1306 5876 5.562635 AGACTAAGATAGATACCAGGGTCG 58.437 45.833 0.00 0.00 0.00 4.79
1307 5877 6.294843 GCAAGACTAAGATAGATACCAGGGTC 60.295 46.154 0.00 0.00 0.00 4.46
1308 5878 5.540719 GCAAGACTAAGATAGATACCAGGGT 59.459 44.000 0.00 0.00 0.00 4.34
1309 5879 5.540337 TGCAAGACTAAGATAGATACCAGGG 59.460 44.000 0.00 0.00 0.00 4.45
1310 5880 6.295011 CCTGCAAGACTAAGATAGATACCAGG 60.295 46.154 0.00 0.00 34.07 4.45
1311 5881 6.686630 CCTGCAAGACTAAGATAGATACCAG 58.313 44.000 0.00 0.00 34.07 4.00
1312 5882 5.011125 GCCTGCAAGACTAAGATAGATACCA 59.989 44.000 0.00 0.00 34.07 3.25
1313 5883 5.474825 GCCTGCAAGACTAAGATAGATACC 58.525 45.833 0.00 0.00 34.07 2.73
1314 5884 5.048643 TCGCCTGCAAGACTAAGATAGATAC 60.049 44.000 0.00 0.00 34.07 2.24
1315 5885 5.048643 GTCGCCTGCAAGACTAAGATAGATA 60.049 44.000 8.77 0.00 34.07 1.98
1316 5886 3.891977 TCGCCTGCAAGACTAAGATAGAT 59.108 43.478 0.00 0.00 34.07 1.98
1317 5887 3.066900 GTCGCCTGCAAGACTAAGATAGA 59.933 47.826 8.77 0.00 34.07 1.98
1318 5888 3.376540 GTCGCCTGCAAGACTAAGATAG 58.623 50.000 8.77 0.00 34.07 2.08
1319 5889 2.100916 GGTCGCCTGCAAGACTAAGATA 59.899 50.000 13.86 0.00 37.52 1.98
1320 5890 1.134670 GGTCGCCTGCAAGACTAAGAT 60.135 52.381 13.86 0.00 37.52 2.40
1321 5891 0.246635 GGTCGCCTGCAAGACTAAGA 59.753 55.000 13.86 0.00 37.52 2.10
1322 5892 0.741221 GGGTCGCCTGCAAGACTAAG 60.741 60.000 13.86 0.00 37.52 2.18
1323 5893 1.295423 GGGTCGCCTGCAAGACTAA 59.705 57.895 13.86 0.00 37.52 2.24
1324 5894 2.656069 GGGGTCGCCTGCAAGACTA 61.656 63.158 13.86 0.00 37.52 2.59
1325 5895 4.021925 GGGGTCGCCTGCAAGACT 62.022 66.667 13.86 0.00 37.52 3.24
1331 5901 4.603946 GATACCGGGGTCGCCTGC 62.604 72.222 6.32 0.00 34.56 4.85
1332 5902 0.898789 ATAGATACCGGGGTCGCCTG 60.899 60.000 6.32 0.00 34.56 4.85
1333 5903 0.611340 GATAGATACCGGGGTCGCCT 60.611 60.000 6.32 0.00 34.56 5.52
1567 6138 5.380043 AGATCCAACGGATAATGCTTCATT 58.620 37.500 0.00 0.00 43.27 2.57
1631 6202 3.311322 AGTCGCGTGAAAATCTGAAAACA 59.689 39.130 5.77 0.00 0.00 2.83
1737 6450 4.158579 TGCTCAGTACGACAGAATTCAGAT 59.841 41.667 8.44 0.00 0.00 2.90
1739 6452 3.838120 TGCTCAGTACGACAGAATTCAG 58.162 45.455 8.44 1.65 0.00 3.02
1740 6453 3.934457 TGCTCAGTACGACAGAATTCA 57.066 42.857 8.44 0.00 0.00 2.57
1741 6454 4.424626 TGATGCTCAGTACGACAGAATTC 58.575 43.478 0.00 0.00 0.00 2.17
1742 6455 4.456280 TGATGCTCAGTACGACAGAATT 57.544 40.909 0.00 0.00 0.00 2.17
1785 6498 6.626302 TGGCACACTACAATTAAAATAAGCC 58.374 36.000 0.00 0.00 36.50 4.35
1869 6583 6.354794 ACTGCAGTACTACACATTAAAGGA 57.645 37.500 20.16 0.00 0.00 3.36
1995 6712 1.834188 TAGATGACCACTCTGCGACA 58.166 50.000 0.00 0.00 0.00 4.35
2008 6732 6.359804 AGCAGTGGCATATTTTCTTAGATGA 58.640 36.000 0.00 0.00 44.61 2.92
2087 6814 3.019564 GCAATGATTAGGTGAAGCAGGT 58.980 45.455 0.00 0.00 36.75 4.00
2199 6926 0.955919 GAGGTGGGAAGACAAAGGCG 60.956 60.000 0.00 0.00 0.00 5.52
2481 7217 3.118811 TGGCACTATCGATCACACAATCA 60.119 43.478 0.00 0.00 0.00 2.57
2582 7318 5.280317 GGGTACTCTGTCCAGGAATTTGTTA 60.280 44.000 0.00 0.00 0.00 2.41
2822 7567 3.428045 GGTGCCATTGCTTATCAAGTCAC 60.428 47.826 0.00 0.00 38.22 3.67
2855 7612 0.453390 GGCTGAAGAATCAAAGCGGG 59.547 55.000 0.00 0.00 34.49 6.13
2945 7702 4.220602 GGTTCATGCAAGAAAATGTAGGGT 59.779 41.667 5.85 0.00 0.00 4.34
3057 7817 4.804139 CGAGTTATACTGTAAACTGCCTGG 59.196 45.833 15.29 0.00 36.10 4.45
3089 7849 7.466746 TTGCTTTTGCCTTCTAGAATGTATT 57.533 32.000 5.44 0.00 46.87 1.89
3224 7986 0.531090 AACGCTTGCCACTGTCGTTA 60.531 50.000 1.55 0.00 40.88 3.18
3292 8055 5.691305 GCATTTCAGAGTGCAAATGTTTGTA 59.309 36.000 8.03 0.03 40.63 2.41
3294 8057 4.748102 AGCATTTCAGAGTGCAAATGTTTG 59.252 37.500 11.25 1.19 43.63 2.93
3295 8058 4.748102 CAGCATTTCAGAGTGCAAATGTTT 59.252 37.500 11.25 0.00 43.63 2.83
3296 8059 4.038282 TCAGCATTTCAGAGTGCAAATGTT 59.962 37.500 11.25 0.32 43.63 2.71
3297 8060 3.570975 TCAGCATTTCAGAGTGCAAATGT 59.429 39.130 11.25 0.00 43.63 2.71
3298 8061 4.168922 TCAGCATTTCAGAGTGCAAATG 57.831 40.909 11.25 2.77 43.63 2.32
3299 8062 4.859304 TTCAGCATTTCAGAGTGCAAAT 57.141 36.364 11.25 0.00 43.63 2.32
3300 8063 4.098349 ACTTTCAGCATTTCAGAGTGCAAA 59.902 37.500 11.25 4.72 43.63 3.68
3301 8064 3.633525 ACTTTCAGCATTTCAGAGTGCAA 59.366 39.130 11.25 0.00 43.63 4.08
3302 8065 3.216800 ACTTTCAGCATTTCAGAGTGCA 58.783 40.909 11.25 0.00 43.63 4.57
3303 8066 3.911661 ACTTTCAGCATTTCAGAGTGC 57.088 42.857 2.43 2.43 41.57 4.40
3304 8067 4.999950 AGGTACTTTCAGCATTTCAGAGTG 59.000 41.667 0.00 0.00 27.25 3.51
3609 8377 2.400573 AGGCTGATGCTCTCTCTGATT 58.599 47.619 0.00 0.00 39.59 2.57
3611 8379 2.744352 TAGGCTGATGCTCTCTCTGA 57.256 50.000 0.00 0.00 39.59 3.27
3677 8445 4.572985 TTCTTGAGTTGCAAATCACTGG 57.427 40.909 27.66 19.56 35.74 4.00
3736 8504 4.720649 AGCTAAGTCGCTTGATTAGACA 57.279 40.909 0.00 0.00 36.74 3.41
3794 8562 2.368548 GTTGCCCTCCTCAACCAAAAAT 59.631 45.455 0.00 0.00 38.21 1.82
3824 8592 2.694628 ACTACACTGTTCCGTTGTACCA 59.305 45.455 0.00 0.00 0.00 3.25
3825 8593 3.054878 CACTACACTGTTCCGTTGTACC 58.945 50.000 0.00 0.00 0.00 3.34
3827 8595 2.101082 TGCACTACACTGTTCCGTTGTA 59.899 45.455 0.00 0.00 0.00 2.41
3828 8596 1.134640 TGCACTACACTGTTCCGTTGT 60.135 47.619 0.00 0.00 0.00 3.32
3829 8597 1.577468 TGCACTACACTGTTCCGTTG 58.423 50.000 0.00 0.00 0.00 4.10
3830 8598 2.210116 CTTGCACTACACTGTTCCGTT 58.790 47.619 0.00 0.00 0.00 4.44
3831 8599 1.138266 ACTTGCACTACACTGTTCCGT 59.862 47.619 0.00 0.00 0.00 4.69
3832 8600 1.865865 ACTTGCACTACACTGTTCCG 58.134 50.000 0.00 0.00 0.00 4.30
3833 8601 2.548480 GGAACTTGCACTACACTGTTCC 59.452 50.000 0.00 0.00 46.16 3.62
3834 8602 3.467803 AGGAACTTGCACTACACTGTTC 58.532 45.455 0.00 0.00 39.43 3.18
3835 8603 3.134804 AGAGGAACTTGCACTACACTGTT 59.865 43.478 0.00 0.00 41.55 3.16
3836 8604 2.700897 AGAGGAACTTGCACTACACTGT 59.299 45.455 0.00 0.00 41.55 3.55
3837 8605 3.393089 AGAGGAACTTGCACTACACTG 57.607 47.619 0.00 0.00 41.55 3.66
3838 8606 4.130118 CAAAGAGGAACTTGCACTACACT 58.870 43.478 0.00 0.00 41.55 3.55
3839 8607 3.304057 GCAAAGAGGAACTTGCACTACAC 60.304 47.826 2.07 0.00 41.55 2.90
3840 8608 2.878406 GCAAAGAGGAACTTGCACTACA 59.122 45.455 2.07 0.00 41.55 2.74
3841 8609 3.142174 AGCAAAGAGGAACTTGCACTAC 58.858 45.455 9.24 0.00 41.55 2.73
3842 8610 3.492102 AGCAAAGAGGAACTTGCACTA 57.508 42.857 9.24 0.00 41.55 2.74
3843 8611 2.355010 AGCAAAGAGGAACTTGCACT 57.645 45.000 9.24 0.00 41.55 4.40
3844 8612 4.022849 ACATTAGCAAAGAGGAACTTGCAC 60.023 41.667 9.24 0.00 41.55 4.57
3845 8613 4.144297 ACATTAGCAAAGAGGAACTTGCA 58.856 39.130 9.24 0.00 41.55 4.08
3846 8614 4.773323 ACATTAGCAAAGAGGAACTTGC 57.227 40.909 0.00 0.00 41.55 4.01
3847 8615 8.946085 TGTAATACATTAGCAAAGAGGAACTTG 58.054 33.333 0.00 0.00 41.55 3.16
3848 8616 9.686683 ATGTAATACATTAGCAAAGAGGAACTT 57.313 29.630 0.00 0.00 34.49 2.66
3849 8617 9.331282 GATGTAATACATTAGCAAAGAGGAACT 57.669 33.333 7.39 0.00 39.94 3.01
3850 8618 9.331282 AGATGTAATACATTAGCAAAGAGGAAC 57.669 33.333 7.39 0.00 39.27 3.62
3891 8659 6.149308 TGTTTGTGATAATTACAGTGCTGAGG 59.851 38.462 6.17 0.00 0.00 3.86
4065 8838 4.248691 AGTTCTGCTGCATTTTTCTTCC 57.751 40.909 1.31 0.00 0.00 3.46


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

AutoCloner maintained by Alex Coulton.