Multiple sequence alignment - TraesCS3D01G070200

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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 TraesCS3D01G070200 chr3D 100.000 6666 0 0 1 6666 31431328 31437993 0.000000e+00 12310.0
1 TraesCS3D01G070200 chr3D 89.179 1876 182 12 3474 5335 30985602 30983734 0.000000e+00 2320.0
2 TraesCS3D01G070200 chr3D 92.600 1027 59 7 981 1991 30988174 30987149 0.000000e+00 1459.0
3 TraesCS3D01G070200 chr3D 87.682 617 63 6 2817 3427 30986210 30985601 0.000000e+00 706.0
4 TraesCS3D01G070200 chr3D 75.391 1471 277 68 3883 5321 30428000 30429417 3.390000e-177 632.0
5 TraesCS3D01G070200 chr3D 74.462 1488 313 49 3875 5329 30412335 30410882 1.250000e-161 580.0
6 TraesCS3D01G070200 chr3D 78.419 797 141 24 1189 1971 30679170 30678391 2.160000e-134 490.0
7 TraesCS3D01G070200 chr3D 90.251 359 27 8 6307 6664 528551588 528551237 4.710000e-126 462.0
8 TraesCS3D01G070200 chr3D 91.798 317 23 3 2204 2517 30987022 30986706 7.940000e-119 438.0
9 TraesCS3D01G070200 chr3D 90.347 259 25 0 2552 2810 30986537 30986279 2.300000e-89 340.0
10 TraesCS3D01G070200 chr3D 82.216 343 51 9 1636 1973 30414488 30414151 3.040000e-73 287.0
11 TraesCS3D01G070200 chr3D 77.303 445 77 16 2232 2665 30678333 30677902 2.400000e-59 241.0
12 TraesCS3D01G070200 chr3D 76.826 397 77 10 2257 2650 30425092 30425476 6.770000e-50 209.0
13 TraesCS3D01G070200 chr3D 80.365 219 35 3 3476 3687 30370143 30369926 6.920000e-35 159.0
14 TraesCS3D01G070200 chr3D 76.374 182 35 7 6139 6314 441569223 441569044 2.560000e-14 91.6
15 TraesCS3D01G070200 chr3D 100.000 38 0 0 3619 3656 31434767 31434804 3.340000e-08 71.3
16 TraesCS3D01G070200 chr3D 100.000 38 0 0 3440 3477 31434946 31434983 3.340000e-08 71.3
17 TraesCS3D01G070200 chr3A 97.649 5786 99 14 909 6664 51773714 51767936 0.000000e+00 9897.0
18 TraesCS3D01G070200 chr3A 88.918 1886 175 22 3474 5335 44354340 44352465 0.000000e+00 2294.0
19 TraesCS3D01G070200 chr3A 93.294 1029 58 5 973 1991 44356523 44355496 0.000000e+00 1507.0
20 TraesCS3D01G070200 chr3A 97.990 796 10 4 1 794 51774728 51773937 0.000000e+00 1376.0
21 TraesCS3D01G070200 chr3A 87.687 804 81 7 2634 3427 44355134 44354339 0.000000e+00 920.0
22 TraesCS3D01G070200 chr3A 74.372 1592 335 55 3784 5330 42798185 42796622 4.420000e-171 612.0
23 TraesCS3D01G070200 chr3A 73.892 1647 348 57 3727 5329 42368008 42366400 9.630000e-163 584.0
24 TraesCS3D01G070200 chr3A 92.994 314 17 2 2226 2538 44355475 44355166 2.830000e-123 453.0
25 TraesCS3D01G070200 chr3A 81.818 341 56 6 1636 1973 43292686 43292349 1.420000e-71 281.0
26 TraesCS3D01G070200 chr3A 81.818 341 56 6 1636 1973 43876055 43875718 1.420000e-71 281.0
27 TraesCS3D01G070200 chr3A 96.273 161 4 2 787 946 51773899 51773740 5.130000e-66 263.0
28 TraesCS3D01G070200 chr3A 84.030 263 32 7 5372 5626 44323032 44322772 1.860000e-60 244.0
29 TraesCS3D01G070200 chr3A 85.581 215 27 2 3476 3687 42034296 42034083 8.700000e-54 222.0
30 TraesCS3D01G070200 chr3A 83.475 236 39 0 2255 2490 43292292 43292057 3.130000e-53 220.0
31 TraesCS3D01G070200 chr3A 76.559 401 75 13 2257 2650 42379230 42379618 1.130000e-47 202.0
32 TraesCS3D01G070200 chr3A 82.353 170 23 5 3476 3640 42221596 42221429 2.510000e-29 141.0
33 TraesCS3D01G070200 chr3A 84.173 139 15 5 3507 3640 42248421 42248285 1.950000e-25 128.0
34 TraesCS3D01G070200 chr3A 88.462 104 8 3 5608 5708 44322406 44322304 9.080000e-24 122.0
35 TraesCS3D01G070200 chr3A 88.372 86 8 1 5625 5708 44313426 44313341 1.180000e-17 102.0
36 TraesCS3D01G070200 chr3A 94.118 51 1 2 2189 2238 551308638 551308589 7.170000e-10 76.8
37 TraesCS3D01G070200 chr3A 97.368 38 0 1 3440 3477 51771008 51770972 5.580000e-06 63.9
38 TraesCS3D01G070200 chr3B 89.510 1878 175 14 3474 5335 53576298 53574427 0.000000e+00 2357.0
39 TraesCS3D01G070200 chr3B 92.788 1026 65 5 973 1991 53580113 53579090 0.000000e+00 1476.0
40 TraesCS3D01G070200 chr3B 88.342 609 58 6 2825 3427 53576898 53576297 0.000000e+00 719.0
41 TraesCS3D01G070200 chr3B 87.582 612 49 8 2226 2836 53579069 53578484 0.000000e+00 684.0
42 TraesCS3D01G070200 chr3B 74.951 1521 315 54 3846 5329 53356201 53354710 7.290000e-179 638.0
43 TraesCS3D01G070200 chr3B 73.463 1594 310 84 3784 5329 53219104 53217576 4.640000e-136 496.0
44 TraesCS3D01G070200 chr3B 90.000 360 35 1 6307 6666 226807819 226808177 1.310000e-126 464.0
45 TraesCS3D01G070200 chr3B 76.854 445 79 16 2232 2665 53358095 53357664 5.200000e-56 230.0
46 TraesCS3D01G070200 chr1D 90.833 360 31 2 6306 6664 376968276 376967918 1.300000e-131 481.0
47 TraesCS3D01G070200 chr1D 89.972 359 34 2 6307 6664 344201053 344201410 4.710000e-126 462.0
48 TraesCS3D01G070200 chr1D 96.273 161 5 1 787 946 225419555 225419395 5.130000e-66 263.0
49 TraesCS3D01G070200 chr1D 95.652 161 6 1 787 946 193964244 193964404 2.390000e-64 257.0
50 TraesCS3D01G070200 chr2D 90.278 360 32 3 6307 6664 157604519 157604877 1.010000e-127 468.0
51 TraesCS3D01G070200 chr2D 92.453 53 4 0 2192 2244 46469894 46469842 7.170000e-10 76.8
52 TraesCS3D01G070200 chr7D 90.223 358 33 2 6308 6664 202305916 202306272 3.640000e-127 466.0
53 TraesCS3D01G070200 chr7D 89.972 359 34 2 6307 6664 242345828 242346185 4.710000e-126 462.0
54 TraesCS3D01G070200 chr7D 79.470 151 25 5 6167 6314 545261010 545260863 1.180000e-17 102.0
55 TraesCS3D01G070200 chr7D 80.282 142 23 5 6175 6314 609440900 609441038 1.180000e-17 102.0
56 TraesCS3D01G070200 chr4D 89.972 359 34 2 6307 6664 366499013 366498656 4.710000e-126 462.0
57 TraesCS3D01G070200 chr4D 95.031 161 7 1 787 946 220344996 220345156 1.110000e-62 252.0
58 TraesCS3D01G070200 chr4D 82.517 143 19 5 6175 6314 414059670 414059809 3.260000e-23 121.0
59 TraesCS3D01G070200 chrUn 83.013 312 51 2 1636 1946 332582554 332582864 1.420000e-71 281.0
60 TraesCS3D01G070200 chrUn 83.475 236 39 0 2255 2490 332582948 332583183 3.130000e-53 220.0
61 TraesCS3D01G070200 chrUn 85.981 107 9 4 6209 6312 467340291 467340188 7.070000e-20 110.0
62 TraesCS3D01G070200 chrUn 94.000 50 2 1 2182 2230 95223426 95223377 2.580000e-09 75.0
63 TraesCS3D01G070200 chr2B 95.625 160 6 1 788 946 168845038 168845197 8.580000e-64 255.0
64 TraesCS3D01G070200 chr2B 89.655 58 4 1 2189 2244 691994735 691994678 9.270000e-09 73.1
65 TraesCS3D01G070200 chr7B 95.031 161 7 1 787 946 444462425 444462585 1.110000e-62 252.0
66 TraesCS3D01G070200 chr7B 78.974 195 31 10 6123 6313 609256754 609256942 2.520000e-24 124.0
67 TraesCS3D01G070200 chr6D 95.031 161 7 1 787 946 296696762 296696602 1.110000e-62 252.0
68 TraesCS3D01G070200 chr6D 81.325 166 26 5 6152 6314 139585748 139585911 5.420000e-26 130.0
69 TraesCS3D01G070200 chr4A 95.031 161 7 1 787 946 379019637 379019797 1.110000e-62 252.0
70 TraesCS3D01G070200 chr2A 95.031 161 7 1 787 946 119318134 119318294 1.110000e-62 252.0
71 TraesCS3D01G070200 chr1A 81.013 158 25 4 6161 6314 488106612 488106768 3.260000e-23 121.0
72 TraesCS3D01G070200 chr1A 87.671 73 9 0 5176 5248 382745157 382745229 1.190000e-12 86.1
73 TraesCS3D01G070200 chr6B 84.821 112 15 2 5166 5277 608182774 608182665 1.970000e-20 111.0
74 TraesCS3D01G070200 chr5D 83.929 112 16 2 5166 5277 437562464 437562355 9.140000e-19 106.0
75 TraesCS3D01G070200 chr5D 80.702 114 20 2 5165 5278 437696736 437696847 3.310000e-13 87.9
76 TraesCS3D01G070200 chr5A 83.051 118 18 2 5183 5299 547032906 547032790 9.140000e-19 106.0
77 TraesCS3D01G070200 chr5A 87.013 77 8 2 5165 5241 552676743 552676817 1.190000e-12 86.1
78 TraesCS3D01G070200 chr4B 80.822 146 18 6 6175 6314 44926058 44925917 9.140000e-19 106.0
79 TraesCS3D01G070200 chr4B 94.118 51 2 1 2189 2238 91298352 91298302 7.170000e-10 76.8
80 TraesCS3D01G070200 chr6A 91.228 57 2 3 2175 2231 74246271 74246324 2.580000e-09 75.0
81 TraesCS3D01G070200 chr5B 90.909 55 3 2 2175 2227 338716757 338716811 9.270000e-09 73.1


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 TraesCS3D01G070200 chr3D 31431328 31437993 6665 False 4150.866667 12310 100.00000 1 6666 3 chr3D.!!$F2 6665
1 TraesCS3D01G070200 chr3D 30983734 30988174 4440 True 1052.600000 2320 90.32120 981 5335 5 chr3D.!!$R6 4354
2 TraesCS3D01G070200 chr3D 30410882 30414488 3606 True 433.500000 580 78.33900 1636 5329 2 chr3D.!!$R4 3693
3 TraesCS3D01G070200 chr3D 30425092 30429417 4325 False 420.500000 632 76.10850 2257 5321 2 chr3D.!!$F1 3064
4 TraesCS3D01G070200 chr3D 30677902 30679170 1268 True 365.500000 490 77.86100 1189 2665 2 chr3D.!!$R5 1476
5 TraesCS3D01G070200 chr3A 51767936 51774728 6792 True 2899.975000 9897 97.32000 1 6664 4 chr3A.!!$R12 6663
6 TraesCS3D01G070200 chr3A 44352465 44356523 4058 True 1293.500000 2294 90.72325 973 5335 4 chr3A.!!$R11 4362
7 TraesCS3D01G070200 chr3A 42796622 42798185 1563 True 612.000000 612 74.37200 3784 5330 1 chr3A.!!$R5 1546
8 TraesCS3D01G070200 chr3A 42366400 42368008 1608 True 584.000000 584 73.89200 3727 5329 1 chr3A.!!$R4 1602
9 TraesCS3D01G070200 chr3A 43292057 43292686 629 True 250.500000 281 82.64650 1636 2490 2 chr3A.!!$R9 854
10 TraesCS3D01G070200 chr3B 53574427 53580113 5686 True 1309.000000 2357 89.55550 973 5335 4 chr3B.!!$R3 4362
11 TraesCS3D01G070200 chr3B 53217576 53219104 1528 True 496.000000 496 73.46300 3784 5329 1 chr3B.!!$R1 1545
12 TraesCS3D01G070200 chr3B 53354710 53358095 3385 True 434.000000 638 75.90250 2232 5329 2 chr3B.!!$R2 3097
13 TraesCS3D01G070200 chrUn 332582554 332583183 629 False 250.500000 281 83.24400 1636 2490 2 chrUn.!!$F1 854

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
276 277 1.026182 TATCACGGTCGCACCTACGT 61.026 55.000 0.0 0.0 40.6 3.57 F
352 353 1.145738 CTTATGCCCCAGCTAACCCAT 59.854 52.381 0.0 0.0 40.8 4.00 F
3011 5492 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.0 0.0 0.0 3.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2121 2281 2.338785 GCTTGAAGCCCAGTCCTGC 61.339 63.158 5.74 0.0 34.48 4.85 R
4015 7794 3.125146 GTGAAGCAATTAGTGACGATGCA 59.875 43.478 0.00 0.0 39.42 3.96 R
6385 10221 0.869068 TAACACCGAACAATGCACCG 59.131 50.000 0.00 0.0 0.00 4.94 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
276 277 1.026182 TATCACGGTCGCACCTACGT 61.026 55.000 0.00 0.00 40.60 3.57
348 349 1.166531 CCGCTTATGCCCCAGCTAAC 61.167 60.000 0.00 0.00 40.80 2.34
352 353 1.145738 CTTATGCCCCAGCTAACCCAT 59.854 52.381 0.00 0.00 40.80 4.00
379 380 8.079809 CCAAGTTTTACTGGGTTGTTAGTTATG 58.920 37.037 0.00 0.00 34.47 1.90
545 546 4.512914 GCCCCTGCCCCTGATCAC 62.513 72.222 0.00 0.00 0.00 3.06
546 547 2.693864 CCCCTGCCCCTGATCACT 60.694 66.667 0.00 0.00 0.00 3.41
547 548 2.311854 CCCCTGCCCCTGATCACTT 61.312 63.158 0.00 0.00 0.00 3.16
571 572 2.025727 CCGCCGACCACGTCTATC 59.974 66.667 0.00 0.00 37.88 2.08
638 639 3.532155 GGCGCCTCCTGTCTCGAT 61.532 66.667 22.15 0.00 0.00 3.59
673 674 4.736896 GTCGTCCGGCTCACCACC 62.737 72.222 0.00 0.00 34.57 4.61
770 772 6.161381 ACCAACTTCTATAGTGTTTGTACGG 58.839 40.000 12.56 11.34 37.12 4.02
781 783 5.543714 AGTGTTTGTACGGTAATGATGACA 58.456 37.500 0.00 0.00 0.00 3.58
863 911 1.408683 GGTTCTGGCACATGGATAGCA 60.409 52.381 0.00 0.00 38.20 3.49
875 923 1.638467 GATAGCAAGCTTCCACGCG 59.362 57.895 3.53 3.53 34.40 6.01
904 953 3.464907 CATGGCTAGTTCTCTGGTGATG 58.535 50.000 0.00 0.00 0.00 3.07
1009 1121 6.368805 TCTCTAGGTAGAAAGATGCAGATCA 58.631 40.000 0.00 0.00 0.00 2.92
1373 1498 6.341316 TCTGTACCTGATCATTAGTTGCTTC 58.659 40.000 0.00 0.00 0.00 3.86
1611 1744 7.774625 TGATGGTAATCATTCTGCAAACTGATA 59.225 33.333 0.00 0.00 37.91 2.15
2121 2281 2.343163 TTTGTTCTGTTTGGCCCGCG 62.343 55.000 0.00 0.00 0.00 6.46
2690 3360 3.407424 TGCTCTTTATGCGGCAGATAT 57.593 42.857 9.25 0.00 0.00 1.63
3008 5489 2.816672 TGAAATGTGTGTGTGTGTGTGT 59.183 40.909 0.00 0.00 0.00 3.72
3009 5490 2.917701 AATGTGTGTGTGTGTGTGTG 57.082 45.000 0.00 0.00 0.00 3.82
3010 5491 1.819928 ATGTGTGTGTGTGTGTGTGT 58.180 45.000 0.00 0.00 0.00 3.72
3011 5492 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
3385 6876 1.956477 CCTGCCACTGCTTAACACTTT 59.044 47.619 0.00 0.00 38.71 2.66
4362 8155 4.635765 TGCCATGTTTCTGTAACTAGATGC 59.364 41.667 0.00 0.00 37.64 3.91
5003 8806 4.641989 GCAAGTGGGATAGTGATCAACAAT 59.358 41.667 0.00 0.00 33.27 2.71
5369 9190 6.978659 TCGCCTCTTGTCTTACATATTAACTG 59.021 38.462 0.00 0.00 0.00 3.16
5425 9246 5.140454 ACTGCTGATTTTACCAAAGTTCCT 58.860 37.500 0.00 0.00 0.00 3.36
5481 9302 6.376978 CATTCAACAAGACCTTGATTCAGAC 58.623 40.000 15.84 0.00 42.93 3.51
5606 9427 4.889409 AGACTTGCTGGAATTTCTTGAACA 59.111 37.500 0.00 0.00 0.00 3.18
5777 9598 2.293677 TATGTTGTGCCAGCTAGTCG 57.706 50.000 0.00 0.00 0.00 4.18
5813 9635 4.074970 AGACCTCTTGTTGCTTTATGTGG 58.925 43.478 0.00 0.00 0.00 4.17
5956 9778 7.253917 CGTTTGTGCATCATGTGTCTTTTTAAA 60.254 33.333 0.00 0.00 0.00 1.52
6042 9864 3.701664 AGCTAACCAATAAGCCTGCTTT 58.298 40.909 10.01 0.00 39.64 3.51
6074 9896 4.310769 GTTAGTAGTAGGATCGCGACCTA 58.689 47.826 24.40 24.40 38.76 3.08
6097 9924 0.253327 GGGGCGATCAGGTTTTCTCT 59.747 55.000 0.00 0.00 0.00 3.10
6113 9940 6.757010 GGTTTTCTCTGTTTTCTTTCCCTTTC 59.243 38.462 0.00 0.00 0.00 2.62
6114 9941 7.363880 GGTTTTCTCTGTTTTCTTTCCCTTTCT 60.364 37.037 0.00 0.00 0.00 2.52
6115 9942 6.944234 TTCTCTGTTTTCTTTCCCTTTCTC 57.056 37.500 0.00 0.00 0.00 2.87
6116 9943 6.001449 TCTCTGTTTTCTTTCCCTTTCTCA 57.999 37.500 0.00 0.00 0.00 3.27
6117 9944 6.058183 TCTCTGTTTTCTTTCCCTTTCTCAG 58.942 40.000 0.00 0.00 0.00 3.35
6118 9945 6.001449 TCTGTTTTCTTTCCCTTTCTCAGA 57.999 37.500 0.00 0.00 0.00 3.27
6328 10164 7.484975 TCAAATACTTGGTGTTAAGGTTTGTG 58.515 34.615 0.29 0.00 37.91 3.33
6334 10170 3.892588 TGGTGTTAAGGTTTGTGATTCCC 59.107 43.478 0.00 0.00 0.00 3.97
6338 10174 7.114095 GGTGTTAAGGTTTGTGATTCCCTATA 58.886 38.462 0.00 0.00 0.00 1.31
6387 10223 6.861065 AATACAATTACATCCTACTTGCGG 57.139 37.500 0.00 0.00 0.00 5.69
6394 10230 1.064505 CATCCTACTTGCGGTGCATTG 59.935 52.381 0.00 0.00 38.76 2.82
6429 10265 8.208718 AGTTATGCTTAATGCTCGTTAATGAA 57.791 30.769 0.00 0.00 43.37 2.57
6458 10294 3.428862 CGTTTCTTGGTTGGTTGCTTCTT 60.429 43.478 0.00 0.00 0.00 2.52
6462 10298 5.705609 TCTTGGTTGGTTGCTTCTTAATC 57.294 39.130 0.00 0.00 0.00 1.75
6473 10309 7.014230 TGGTTGCTTCTTAATCTTTTTGCTAGT 59.986 33.333 0.00 0.00 0.00 2.57
6476 10312 8.034058 TGCTTCTTAATCTTTTTGCTAGTCTC 57.966 34.615 0.00 0.00 0.00 3.36
6485 10321 6.769512 TCTTTTTGCTAGTCTCCACTTGTAT 58.230 36.000 0.00 0.00 33.62 2.29
6526 10362 9.435688 ACTTATGCATTCAAAATCTTTAAACCC 57.564 29.630 3.54 0.00 0.00 4.11
6548 10384 4.012374 CAGTTTTGCCATATGAGTCCACT 58.988 43.478 3.65 0.00 0.00 4.00
6572 10408 9.129532 ACTATACCTACCTATATGCGGTATTTC 57.870 37.037 11.94 0.00 40.41 2.17
6573 10409 5.672421 ACCTACCTATATGCGGTATTTCC 57.328 43.478 6.28 0.00 36.49 3.13
6574 10410 5.088730 ACCTACCTATATGCGGTATTTCCA 58.911 41.667 6.28 0.00 36.49 3.53
6577 10413 5.499004 ACCTATATGCGGTATTTCCATGT 57.501 39.130 0.00 0.00 35.57 3.21
6578 10414 5.876357 ACCTATATGCGGTATTTCCATGTT 58.124 37.500 0.00 0.00 35.57 2.71
6582 10418 4.799564 ATGCGGTATTTCCATGTTGTTT 57.200 36.364 0.00 0.00 35.57 2.83
6646 10482 5.883503 TTTCCTTTTTGTGTGTTCGTACT 57.116 34.783 0.00 0.00 0.00 2.73
6664 10500 4.838152 GCTCATGAAGCGGCGGGA 62.838 66.667 9.78 0.00 42.21 5.14
6665 10501 2.587194 CTCATGAAGCGGCGGGAG 60.587 66.667 9.78 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 53 5.633830 AATGAGATAAAATATGCTGCCGG 57.366 39.130 0.00 0.00 0.00 6.13
276 277 2.889512 TCTCACAGACTTAGAGGCCAA 58.110 47.619 5.01 0.00 0.00 4.52
352 353 5.757988 ACTAACAACCCAGTAAAACTTGGA 58.242 37.500 4.33 0.00 34.82 3.53
379 380 4.022329 CCAAAGTTTGGTGGGTGATAAGTC 60.022 45.833 24.17 0.00 45.93 3.01
545 546 2.815647 GGTCGGCGGCAGAAGAAG 60.816 66.667 15.59 0.00 0.00 2.85
546 547 3.621805 TGGTCGGCGGCAGAAGAA 61.622 61.111 15.59 0.00 0.00 2.52
547 548 4.373116 GTGGTCGGCGGCAGAAGA 62.373 66.667 15.59 0.00 0.00 2.87
571 572 1.754621 TCAGCTGGGTAGGAGCTCG 60.755 63.158 15.13 0.00 45.24 5.03
638 639 2.687805 CGGCGAGACAGGAACGAGA 61.688 63.158 0.00 0.00 0.00 4.04
673 674 5.883673 AGGCCTCTTATATAGAAGCTAGTCG 59.116 44.000 0.00 0.00 39.76 4.18
770 772 6.074356 GCTTGTTTGGTTGTTGTCATCATTAC 60.074 38.462 0.00 0.00 0.00 1.89
781 783 0.829990 CCCCAGCTTGTTTGGTTGTT 59.170 50.000 0.00 0.00 33.73 2.83
904 953 2.367241 GAGGGATCTTAAGGACTGGAGC 59.633 54.545 1.85 0.00 0.00 4.70
1009 1121 0.322546 GGTTGAACATCCCCTCGCTT 60.323 55.000 0.00 0.00 0.00 4.68
2121 2281 2.338785 GCTTGAAGCCCAGTCCTGC 61.339 63.158 5.74 0.00 34.48 4.85
4015 7794 3.125146 GTGAAGCAATTAGTGACGATGCA 59.875 43.478 0.00 0.00 39.42 3.96
4362 8155 1.922570 ACTATAACGCAGACGCTTGG 58.077 50.000 0.00 0.00 45.53 3.61
4476 8269 6.354130 AGCTTGTAACCAATACGATTACCAT 58.646 36.000 0.00 0.00 37.32 3.55
5003 8806 6.612247 TCTTTGCAATCGAGTTTACTTTCA 57.388 33.333 0.00 0.00 0.00 2.69
5481 9302 6.932356 AAGTAAGTCCATGAATAGTGCATG 57.068 37.500 0.00 0.00 42.07 4.06
5606 9427 8.492673 TTCACATTAGTCATAGCGAAATTCTT 57.507 30.769 0.00 0.00 0.00 2.52
5777 9598 2.300437 AGAGGTCTTGTGTAAGTGCCTC 59.700 50.000 17.20 17.20 45.82 4.70
5813 9635 9.052759 CCACCTTATAGATTACATGTGGTTTAC 57.947 37.037 9.11 0.00 37.74 2.01
5852 9674 4.096382 CGGCAACTAGTGATTTGGCTAATT 59.904 41.667 14.66 0.00 44.08 1.40
5908 9730 9.581099 AAACGCGATAATTCTTTTGGATTTAAT 57.419 25.926 15.93 0.00 0.00 1.40
5914 9736 5.150683 CACAAACGCGATAATTCTTTTGGA 58.849 37.500 15.93 0.00 0.00 3.53
5931 9753 5.971895 AAAAAGACACATGATGCACAAAC 57.028 34.783 0.00 0.00 0.00 2.93
6042 9864 7.255381 GCGATCCTACTACTAACCATTAACTGA 60.255 40.741 0.00 0.00 0.00 3.41
6074 9896 1.209747 GAAAACCTGATCGCCCCTAGT 59.790 52.381 0.00 0.00 0.00 2.57
6085 9912 5.359860 GGGAAAGAAAACAGAGAAAACCTGA 59.640 40.000 0.00 0.00 35.69 3.86
6097 9924 7.660030 AAATCTGAGAAAGGGAAAGAAAACA 57.340 32.000 0.00 0.00 0.00 2.83
6328 10164 5.116882 ACTTTCGTGCTTGTATAGGGAATC 58.883 41.667 0.00 0.00 0.00 2.52
6334 10170 7.488150 TGACTATTGACTTTCGTGCTTGTATAG 59.512 37.037 0.00 0.00 0.00 1.31
6338 10174 4.377021 TGACTATTGACTTTCGTGCTTGT 58.623 39.130 0.00 0.00 0.00 3.16
6363 10199 7.439955 CACCGCAAGTAGGATGTAATTGTATTA 59.560 37.037 0.00 0.00 0.00 0.98
6367 10203 3.938963 CACCGCAAGTAGGATGTAATTGT 59.061 43.478 0.00 0.00 0.00 2.71
6368 10204 3.242739 GCACCGCAAGTAGGATGTAATTG 60.243 47.826 0.00 0.00 0.00 2.32
6369 10205 2.943033 GCACCGCAAGTAGGATGTAATT 59.057 45.455 0.00 0.00 0.00 1.40
6385 10221 0.869068 TAACACCGAACAATGCACCG 59.131 50.000 0.00 0.00 0.00 4.94
6387 10223 3.619233 AACTAACACCGAACAATGCAC 57.381 42.857 0.00 0.00 0.00 4.57
6394 10230 5.963586 GCATTAAGCATAACTAACACCGAAC 59.036 40.000 0.00 0.00 44.79 3.95
6429 10265 5.163804 GCAACCAACCAAGAAACGAAAATTT 60.164 36.000 0.00 0.00 0.00 1.82
6458 10294 7.224297 ACAAGTGGAGACTAGCAAAAAGATTA 58.776 34.615 0.00 0.00 0.00 1.75
6462 10298 7.440523 AATACAAGTGGAGACTAGCAAAAAG 57.559 36.000 0.00 0.00 0.00 2.27
6501 10337 9.434420 TGGGTTTAAAGATTTTGAATGCATAAG 57.566 29.630 0.00 0.00 0.00 1.73
6506 10342 7.728847 AACTGGGTTTAAAGATTTTGAATGC 57.271 32.000 0.00 0.00 0.00 3.56
6510 10346 6.540551 GGCAAAACTGGGTTTAAAGATTTTGA 59.459 34.615 17.68 0.00 37.62 2.69
6511 10347 6.317391 TGGCAAAACTGGGTTTAAAGATTTTG 59.683 34.615 13.04 13.04 34.43 2.44
6518 10354 6.268847 ACTCATATGGCAAAACTGGGTTTAAA 59.731 34.615 2.13 0.00 34.43 1.52
6526 10362 4.012374 AGTGGACTCATATGGCAAAACTG 58.988 43.478 2.13 0.00 0.00 3.16
6548 10384 8.060689 TGGAAATACCGCATATAGGTAGGTATA 58.939 37.037 19.47 7.96 46.17 1.47


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

AutoCloner maintained by Alex Coulton.