Multiple sequence alignment - TraesCS7D01G086300

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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 TraesCS7D01G086300 chr7D 100.000 4289 0 0 1 4289 53259121 53263409 0.000000e+00 7921.0
1 TraesCS7D01G086300 chr7D 75.800 500 111 10 84 576 116602473 116601977 1.190000e-60 244.0
2 TraesCS7D01G086300 chr7D 74.777 448 93 16 92 529 621202382 621201945 2.630000e-42 183.0
3 TraesCS7D01G086300 chr4A 88.565 2606 215 49 35 2573 667356257 667353668 0.000000e+00 3085.0
4 TraesCS7D01G086300 chr4A 95.021 482 24 0 2571 3052 667353586 667353105 0.000000e+00 758.0
5 TraesCS7D01G086300 chr4A 85.574 714 70 23 3051 3732 667352857 667352145 0.000000e+00 717.0
6 TraesCS7D01G086300 chr4A 73.481 543 123 18 129 660 433710057 433710589 7.320000e-43 185.0
7 TraesCS7D01G086300 chr4A 93.750 48 3 0 1611 1658 708849262 708849215 5.950000e-09 73.1
8 TraesCS7D01G086300 chr7A 96.490 1738 31 14 2552 4289 55003515 55001808 0.000000e+00 2844.0
9 TraesCS7D01G086300 chr7A 93.126 1804 86 16 774 2554 55005397 55003609 0.000000e+00 2610.0
10 TraesCS7D01G086300 chr7A 85.573 811 89 9 1 786 55006220 55005413 0.000000e+00 824.0
11 TraesCS7D01G086300 chr7A 87.119 590 67 6 1 587 55010159 55009576 0.000000e+00 660.0
12 TraesCS7D01G086300 chr7A 75.586 512 110 15 74 576 670686626 670686121 5.540000e-59 239.0
13 TraesCS7D01G086300 chr2B 89.474 950 82 7 1153 2085 37465953 37465005 0.000000e+00 1184.0
14 TraesCS7D01G086300 chr2B 93.496 123 7 1 1156 1278 747749270 747749149 9.470000e-42 182.0
15 TraesCS7D01G086300 chr1D 88.397 948 73 15 1153 2085 416261049 416260124 0.000000e+00 1107.0
16 TraesCS7D01G086300 chr1D 87.129 101 13 0 1276 1376 406702866 406702966 9.750000e-22 115.0
17 TraesCS7D01G086300 chr1A 92.500 280 20 1 1153 1432 532975462 532975740 2.400000e-107 399.0
18 TraesCS7D01G086300 chrUn 75.195 512 111 16 74 576 434814399 434813895 1.200000e-55 228.0
19 TraesCS7D01G086300 chr5D 95.122 123 5 1 1156 1278 231602723 231602602 4.380000e-45 193.0
20 TraesCS7D01G086300 chr5D 73.346 514 104 26 91 582 322584465 322584967 4.440000e-35 159.0
21 TraesCS7D01G086300 chr5D 92.222 90 7 0 1287 1376 448501115 448501204 1.250000e-25 128.0
22 TraesCS7D01G086300 chr5D 95.745 47 2 0 1611 1657 327296121 327296075 4.600000e-10 76.8
23 TraesCS7D01G086300 chr5A 76.215 391 74 14 87 471 547660478 547660855 5.660000e-44 189.0
24 TraesCS7D01G086300 chr5A 80.738 244 39 7 74 314 169306268 169306030 2.630000e-42 183.0
25 TraesCS7D01G086300 chr4D 73.311 592 127 19 74 660 504283284 504283849 5.660000e-44 189.0
26 TraesCS7D01G086300 chr3B 76.353 351 71 10 120 463 799813780 799813435 1.230000e-40 178.0
27 TraesCS7D01G086300 chr4B 92.683 123 8 1 1156 1278 488124805 488124684 4.410000e-40 176.0
28 TraesCS7D01G086300 chr2D 73.653 501 112 19 86 576 629380073 629380563 4.410000e-40 176.0
29 TraesCS7D01G086300 chr2D 91.089 101 9 0 1276 1376 607129589 607129489 2.080000e-28 137.0
30 TraesCS7D01G086300 chr6B 92.000 125 6 4 1156 1278 244748253 244748131 5.700000e-39 172.0
31 TraesCS7D01G086300 chr5B 89.691 97 10 0 1280 1376 521831891 521831795 1.620000e-24 124.0


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 TraesCS7D01G086300 chr7D 53259121 53263409 4288 False 7921.0 7921 100.000 1 4289 1 chr7D.!!$F1 4288
1 TraesCS7D01G086300 chr4A 667352145 667356257 4112 True 1520.0 3085 89.720 35 3732 3 chr4A.!!$R2 3697
2 TraesCS7D01G086300 chr7A 55001808 55010159 8351 True 1734.5 2844 90.577 1 4289 4 chr7A.!!$R2 4288
3 TraesCS7D01G086300 chr7A 670686121 670686626 505 True 239.0 239 75.586 74 576 1 chr7A.!!$R1 502
4 TraesCS7D01G086300 chr2B 37465005 37465953 948 True 1184.0 1184 89.474 1153 2085 1 chr2B.!!$R1 932
5 TraesCS7D01G086300 chr1D 416260124 416261049 925 True 1107.0 1107 88.397 1153 2085 1 chr1D.!!$R1 932
6 TraesCS7D01G086300 chrUn 434813895 434814399 504 True 228.0 228 75.195 74 576 1 chrUn.!!$R1 502

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
314 317 0.179056 AGAACCAACACACCAGGACG 60.179 55.000 0.0 0.00 0.00 4.79 F
1285 5315 1.000612 TAATTTGGGGCCCCGGTTC 59.999 57.895 36.0 12.61 39.42 3.62 F
1470 5500 0.535335 TCGTTGAGGTCATACAGGGC 59.465 55.000 0.0 0.00 0.00 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1288 5318 0.103026 TGACAGATCCGCCGAATCAG 59.897 55.000 0.00 0.0 0.0 2.90 R
2155 6208 5.619132 TCCAGTCATTCATAGCAATCTCA 57.381 39.130 0.00 0.0 0.0 3.27 R
3352 7845 3.509575 TCCCAAATGTATTGTGCACCTTC 59.490 43.478 15.69 3.0 0.0 3.46 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
31 32 5.710513 AGAGATATGTGAGAGATGAGTGC 57.289 43.478 0.00 0.00 0.00 4.40
43 44 5.527951 AGAGATGAGTGCGTAATTCTGATC 58.472 41.667 0.00 0.00 0.00 2.92
78 80 4.400529 ACCACCCACACAATTCTTTTTC 57.599 40.909 0.00 0.00 0.00 2.29
196 199 3.325870 CGATGACTACAAGCACTGGAAA 58.674 45.455 0.00 0.00 0.00 3.13
212 215 1.032014 GAAAGAGCCAAAGGTGCACA 58.968 50.000 20.43 0.00 0.00 4.57
225 228 1.303155 TGCACAACCATCATCGCCA 60.303 52.632 0.00 0.00 0.00 5.69
261 264 2.546789 CCGGACAAACCTTGTTGTAGTC 59.453 50.000 0.00 0.00 45.52 2.59
262 265 3.199677 CGGACAAACCTTGTTGTAGTCA 58.800 45.455 0.00 0.00 45.52 3.41
283 286 2.546778 ACAGTCGTGAAATTGTCGTGT 58.453 42.857 0.00 0.00 0.00 4.49
314 317 0.179056 AGAACCAACACACCAGGACG 60.179 55.000 0.00 0.00 0.00 4.79
343 346 5.489249 TGTTACCATTGAATAGGCGTGTAA 58.511 37.500 0.00 0.00 0.00 2.41
384 388 2.300152 AGACACATGAACACAGACGGAT 59.700 45.455 0.00 0.00 0.00 4.18
529 536 4.667573 GGGGGAATCTTATTCCATCTTCC 58.332 47.826 17.98 10.42 40.32 3.46
548 555 2.359169 GGGAGCCGTCACCATCTGA 61.359 63.158 0.00 0.00 0.00 3.27
550 557 1.608717 GGAGCCGTCACCATCTGACT 61.609 60.000 0.00 0.00 46.50 3.41
561 568 3.750130 CACCATCTGACTTTCCTGAACAG 59.250 47.826 0.00 0.00 0.00 3.16
562 569 3.648067 ACCATCTGACTTTCCTGAACAGA 59.352 43.478 3.19 0.00 40.88 3.41
566 573 4.697514 TCTGACTTTCCTGAACAGAACAG 58.302 43.478 3.19 0.00 35.20 3.16
588 4536 4.271776 AGAAACCCTAAACGAACACGAAAG 59.728 41.667 0.00 0.00 0.00 2.62
594 4542 2.012937 AACGAACACGAAAGGACACA 57.987 45.000 0.00 0.00 0.00 3.72
641 4589 4.016706 AAGGGCCGAGAACCACCG 62.017 66.667 0.00 0.00 0.00 4.94
660 4608 1.686325 GCGCCTCCATGGTCTAAGGA 61.686 60.000 19.11 0.00 38.35 3.36
667 4615 1.139853 CCATGGTCTAAGGAGGCAGAC 59.860 57.143 2.57 0.00 40.40 3.51
761 4752 6.500684 AGACATACACACATCAATGAAACC 57.499 37.500 0.00 0.00 0.00 3.27
779 4798 7.095695 TGAAACCCTCAAAACTTCTGTTAAG 57.904 36.000 0.00 0.00 34.96 1.85
807 4828 1.004918 CCACAGTCCCTTCCACGAC 60.005 63.158 0.00 0.00 0.00 4.34
895 4916 2.562298 CCATGGCAGCAGTCCTTTAAAA 59.438 45.455 0.00 0.00 0.00 1.52
946 4967 2.046285 CCATCCTCCCAAACCGCAC 61.046 63.158 0.00 0.00 0.00 5.34
971 4992 2.368011 CCCTCCCGTCTTTCCTCCC 61.368 68.421 0.00 0.00 0.00 4.30
979 5000 3.798511 CTTTCCTCCCCTCCCGCC 61.799 72.222 0.00 0.00 0.00 6.13
1278 5308 1.338674 GGTTTGCTGTAATTTGGGGCC 60.339 52.381 0.00 0.00 0.00 5.80
1283 5313 2.361375 GTAATTTGGGGCCCCGGT 59.639 61.111 36.00 21.18 39.42 5.28
1285 5315 1.000612 TAATTTGGGGCCCCGGTTC 59.999 57.895 36.00 12.61 39.42 3.62
1455 5485 4.446413 GGGGTCGCCGACATCGTT 62.446 66.667 20.08 0.00 37.74 3.85
1464 5494 1.202371 GCCGACATCGTTGAGGTCATA 60.202 52.381 11.51 0.00 42.49 2.15
1470 5500 0.535335 TCGTTGAGGTCATACAGGGC 59.465 55.000 0.00 0.00 0.00 5.19
1523 5553 3.532950 GCGAGTCTTTTCGTTTCTTGAC 58.467 45.455 0.00 0.00 42.38 3.18
1527 5557 4.766375 AGTCTTTTCGTTTCTTGACTCCA 58.234 39.130 0.00 0.00 30.08 3.86
1544 5574 5.637810 TGACTCCATCTTACATTTGTTCGTC 59.362 40.000 0.00 0.00 0.00 4.20
1613 5644 6.072286 GGAGTGATATCCCAGCAATATTGTTG 60.072 42.308 21.60 21.60 38.85 3.33
1718 5757 6.728200 AGTATTGATCAGTTTGTTGTGTGTG 58.272 36.000 0.00 0.00 0.00 3.82
1879 5926 6.088824 AGCATTCTTGAATTCTAAGTTTGCG 58.911 36.000 22.23 11.39 38.21 4.85
2155 6208 6.099557 TGGGTGACAAAAAGATGGAAGATTTT 59.900 34.615 0.00 0.00 0.00 1.82
2550 6606 6.070424 TGCACCTAATAGGCCTGTAATATACC 60.070 42.308 17.99 0.00 39.63 2.73
2637 6873 7.452880 TTCTCACTTCCATAACCATTCTTTG 57.547 36.000 0.00 0.00 0.00 2.77
3060 7545 5.132897 TGCTGAATTTTCTAACGGCAATT 57.867 34.783 0.00 0.00 40.82 2.32
3106 7599 4.276926 GTCTGACAGCCATTTGTTTCTTCT 59.723 41.667 2.24 0.00 0.00 2.85
3352 7845 3.915437 ACCCATTCAGTTTTTAGCGTG 57.085 42.857 0.00 0.00 0.00 5.34
3504 8023 2.336667 TGTGTGCTATCATGTGTCGTG 58.663 47.619 0.00 0.00 0.00 4.35
3581 8103 6.920758 GTGTGTTTGTTTTTCATAGTATGGCA 59.079 34.615 10.26 0.00 0.00 4.92
3677 8199 5.569059 GCCAGAGATTTTGTTTGTTGTATCG 59.431 40.000 0.00 0.00 0.00 2.92
3748 8270 6.036191 GCCTCTAGATTAGAAGTTGGTTTTCG 59.964 42.308 0.00 0.00 33.75 3.46
3749 8271 7.321153 CCTCTAGATTAGAAGTTGGTTTTCGA 58.679 38.462 0.00 0.00 33.75 3.71
3759 8281 1.234821 TGGTTTTCGATGCCTGTCAC 58.765 50.000 0.00 0.00 0.00 3.67
3832 8354 4.467438 TGAGCTGTTATTCAGTGAGATCCA 59.533 41.667 0.00 0.00 45.23 3.41
3833 8355 5.129980 TGAGCTGTTATTCAGTGAGATCCAT 59.870 40.000 0.00 0.00 45.23 3.41
3834 8356 5.609423 AGCTGTTATTCAGTGAGATCCATC 58.391 41.667 0.00 0.00 45.23 3.51
3835 8357 5.366186 AGCTGTTATTCAGTGAGATCCATCT 59.634 40.000 0.00 0.00 45.23 2.90
3836 8358 5.466058 GCTGTTATTCAGTGAGATCCATCTG 59.534 44.000 0.00 0.00 45.23 2.90
3837 8359 6.684865 GCTGTTATTCAGTGAGATCCATCTGA 60.685 42.308 7.08 7.08 45.23 3.27
3838 8360 6.577103 TGTTATTCAGTGAGATCCATCTGAC 58.423 40.000 9.74 0.00 40.67 3.51
3847 8369 7.624360 GTGAGATCCATCTGACTATACCTAG 57.376 44.000 0.00 0.00 37.92 3.02
3848 8370 7.398829 GTGAGATCCATCTGACTATACCTAGA 58.601 42.308 0.00 0.00 37.92 2.43
3849 8371 8.052748 GTGAGATCCATCTGACTATACCTAGAT 58.947 40.741 0.00 0.00 37.92 1.98
3850 8372 8.619281 TGAGATCCATCTGACTATACCTAGATT 58.381 37.037 0.00 0.00 37.25 2.40
3851 8373 8.821686 AGATCCATCTGACTATACCTAGATTG 57.178 38.462 0.00 0.00 35.42 2.67
3852 8374 6.842437 TCCATCTGACTATACCTAGATTGC 57.158 41.667 0.00 0.00 0.00 3.56
3853 8375 6.556639 TCCATCTGACTATACCTAGATTGCT 58.443 40.000 0.00 0.00 0.00 3.91
3854 8376 7.013220 TCCATCTGACTATACCTAGATTGCTT 58.987 38.462 0.00 0.00 0.00 3.91
3855 8377 7.510685 TCCATCTGACTATACCTAGATTGCTTT 59.489 37.037 0.00 0.00 0.00 3.51
3856 8378 7.601886 CCATCTGACTATACCTAGATTGCTTTG 59.398 40.741 0.00 0.00 0.00 2.77
3857 8379 7.898014 TCTGACTATACCTAGATTGCTTTGA 57.102 36.000 0.00 0.00 0.00 2.69
3858 8380 7.717568 TCTGACTATACCTAGATTGCTTTGAC 58.282 38.462 0.00 0.00 0.00 3.18
3859 8381 7.561722 TCTGACTATACCTAGATTGCTTTGACT 59.438 37.037 0.00 0.00 0.00 3.41
3860 8382 8.079211 TGACTATACCTAGATTGCTTTGACTT 57.921 34.615 0.00 0.00 0.00 3.01
3861 8383 8.540388 TGACTATACCTAGATTGCTTTGACTTT 58.460 33.333 0.00 0.00 0.00 2.66
3862 8384 9.384764 GACTATACCTAGATTGCTTTGACTTTT 57.615 33.333 0.00 0.00 0.00 2.27
3863 8385 9.167311 ACTATACCTAGATTGCTTTGACTTTTG 57.833 33.333 0.00 0.00 0.00 2.44
3864 8386 9.383519 CTATACCTAGATTGCTTTGACTTTTGA 57.616 33.333 0.00 0.00 0.00 2.69
3875 8397 9.677567 TTGCTTTGACTTTTGATAGTAATTCAC 57.322 29.630 0.00 0.00 0.00 3.18
4077 8599 5.726980 ACCATTGTGAGTGCATTTTGTAT 57.273 34.783 0.00 0.00 0.00 2.29
4080 8602 6.991531 ACCATTGTGAGTGCATTTTGTATTTT 59.008 30.769 0.00 0.00 0.00 1.82
4086 8608 7.222417 TGTGAGTGCATTTTGTATTTTTGTCAG 59.778 33.333 0.00 0.00 0.00 3.51
4107 8629 5.353400 TCAGAGATTTTGCTTGCTGTATCAG 59.647 40.000 0.00 0.00 34.12 2.90
4153 8675 3.472652 TGCCTGTGATGTAACTTTCGTT 58.527 40.909 0.00 0.00 37.15 3.85
4214 8736 6.942532 AAGATAGACTGAACTGTTTTTGCA 57.057 33.333 0.00 0.00 0.00 4.08
4234 8756 1.607148 AGTTTGTTTTAGCTGGTCGGC 59.393 47.619 0.00 0.00 0.00 5.54
4256 8778 6.238211 CGGCAATCTAGTTCCATTTTGACTAG 60.238 42.308 3.92 3.92 42.56 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 6.093909 CGCACTCATCTCTCACATATCTCTAT 59.906 42.308 0.00 0.00 0.00 1.98
13 14 5.774498 TTACGCACTCATCTCTCACATAT 57.226 39.130 0.00 0.00 0.00 1.78
14 15 5.774498 ATTACGCACTCATCTCTCACATA 57.226 39.130 0.00 0.00 0.00 2.29
31 32 5.985530 TGCATCCAACTAGATCAGAATTACG 59.014 40.000 0.00 0.00 0.00 3.18
43 44 2.172505 TGGGTGGTATGCATCCAACTAG 59.827 50.000 23.72 0.00 41.87 2.57
78 80 1.202348 GATTGAAAGGTTTCCCGCCAG 59.798 52.381 0.05 0.00 36.36 4.85
103 105 8.058667 TCTTTGTACTTCCACGACTATTGATA 57.941 34.615 0.00 0.00 0.00 2.15
196 199 1.109323 GGTTGTGCACCTTTGGCTCT 61.109 55.000 15.69 0.00 43.29 4.09
212 215 0.552848 AGGGAATGGCGATGATGGTT 59.447 50.000 0.00 0.00 0.00 3.67
225 228 0.996583 TCCGGCTTTGGTAAGGGAAT 59.003 50.000 0.00 0.00 31.76 3.01
261 264 3.242284 ACACGACAATTTCACGACTGTTG 60.242 43.478 0.00 0.00 0.00 3.33
262 265 2.933906 ACACGACAATTTCACGACTGTT 59.066 40.909 0.00 0.00 0.00 3.16
265 268 4.210537 CCTTAACACGACAATTTCACGACT 59.789 41.667 0.00 0.00 0.00 4.18
274 277 2.851263 TGAGGCCTTAACACGACAAT 57.149 45.000 6.77 0.00 0.00 2.71
283 286 4.042311 TGTGTTGGTTCTATGAGGCCTTAA 59.958 41.667 6.77 0.00 0.00 1.85
343 346 7.817478 TGTGTCTACATGTTGATACTTTCGATT 59.183 33.333 27.53 0.00 30.61 3.34
376 380 1.141881 CCCGGTCTTCATCCGTCTG 59.858 63.158 0.00 0.00 45.63 3.51
384 388 1.203087 TCTACTTGGACCCGGTCTTCA 60.203 52.381 17.27 5.01 32.47 3.02
492 498 3.148279 CCCGCTTAGCCTCCGTCT 61.148 66.667 0.00 0.00 0.00 4.18
548 555 4.640647 GGTTTCTGTTCTGTTCAGGAAAGT 59.359 41.667 0.00 0.00 33.01 2.66
550 557 3.951680 GGGTTTCTGTTCTGTTCAGGAAA 59.048 43.478 0.00 0.16 33.01 3.13
561 568 4.551410 CGTGTTCGTTTAGGGTTTCTGTTC 60.551 45.833 0.00 0.00 0.00 3.18
562 569 3.310501 CGTGTTCGTTTAGGGTTTCTGTT 59.689 43.478 0.00 0.00 0.00 3.16
566 573 4.521010 CTTTCGTGTTCGTTTAGGGTTTC 58.479 43.478 0.00 0.00 38.33 2.78
610 4558 3.080121 CCTTGCCGAGGGAGAGCT 61.080 66.667 0.00 0.00 42.26 4.09
641 4589 1.227674 CCTTAGACCATGGAGGCGC 60.228 63.158 21.47 0.00 43.14 6.53
668 4616 4.170062 CTGCCGACAATGCCGCAG 62.170 66.667 0.00 3.06 0.00 5.18
671 4619 3.197790 CTCCTGCCGACAATGCCG 61.198 66.667 0.00 0.00 0.00 5.69
676 4624 4.069232 CTCGCCTCCTGCCGACAA 62.069 66.667 0.00 0.00 36.24 3.18
678 4626 3.296709 TTTCTCGCCTCCTGCCGAC 62.297 63.158 0.00 0.00 36.24 4.79
761 4752 6.693315 TGAACCTTAACAGAAGTTTTGAGG 57.307 37.500 0.00 0.00 39.15 3.86
835 4856 1.944024 TGCTTTAATATTCGTGCCCGG 59.056 47.619 0.00 0.00 33.95 5.73
838 4859 4.976116 GGATTGTGCTTTAATATTCGTGCC 59.024 41.667 0.00 0.00 0.00 5.01
839 4860 5.577835 TGGATTGTGCTTTAATATTCGTGC 58.422 37.500 0.00 0.00 0.00 5.34
895 4916 3.175786 AGGGTTTATGGGGTAGGGATT 57.824 47.619 0.00 0.00 0.00 3.01
946 4967 0.250597 AAAGACGGGAGGGGTTTTCG 60.251 55.000 0.00 0.00 0.00 3.46
1288 5318 0.103026 TGACAGATCCGCCGAATCAG 59.897 55.000 0.00 0.00 0.00 2.90
1455 5485 0.546507 TGGTGCCCTGTATGACCTCA 60.547 55.000 0.00 0.00 0.00 3.86
1464 5494 2.204136 TCCTCCATGGTGCCCTGT 60.204 61.111 12.58 0.00 37.07 4.00
1523 5553 4.332819 GGGACGAACAAATGTAAGATGGAG 59.667 45.833 0.00 0.00 0.00 3.86
1527 5557 5.160607 TCAGGGACGAACAAATGTAAGAT 57.839 39.130 0.00 0.00 0.00 2.40
1544 5574 4.036734 CCAAATGTTACCATCGATTCAGGG 59.963 45.833 0.00 0.00 0.00 4.45
1567 5598 2.047560 AGCCAACGCCGGTACTTC 60.048 61.111 1.90 0.00 34.57 3.01
1613 5644 3.801114 AGACTTGGCCTTTTTGTTGTC 57.199 42.857 3.32 0.91 0.00 3.18
1718 5757 3.843999 TCAACTGCAGTTCCAAAAACAC 58.156 40.909 28.97 0.00 35.83 3.32
1888 5940 9.362151 AGTTCTGGTAAGAAAATTCAATACCAA 57.638 29.630 21.25 14.20 44.24 3.67
1915 5968 6.243148 TGATCAGGCTGCATATAACAATCAT 58.757 36.000 10.34 0.00 0.00 2.45
1993 6046 5.335191 GGGTGTTGATTGTCATCTTTCAGAC 60.335 44.000 0.00 0.00 35.37 3.51
2005 6058 5.363580 ACAAAATCAGAAGGGTGTTGATTGT 59.636 36.000 0.26 0.00 39.82 2.71
2155 6208 5.619132 TCCAGTCATTCATAGCAATCTCA 57.381 39.130 0.00 0.00 0.00 3.27
2507 6560 5.945784 AGGTGCAAGTCATTTATAAGCTTCA 59.054 36.000 0.00 0.00 0.00 3.02
2637 6873 7.025963 CCAAATTGAAGACTGCAGAAGAATAC 58.974 38.462 23.35 5.47 0.00 1.89
3352 7845 3.509575 TCCCAAATGTATTGTGCACCTTC 59.490 43.478 15.69 3.00 0.00 3.46
3504 8023 1.539827 AGGTTTTTGATACGGCACAGC 59.460 47.619 0.00 0.00 0.00 4.40
3581 8103 6.665680 TGTATTACACAAAGGTTGGCCATTAT 59.334 34.615 6.09 0.00 33.33 1.28
3748 8270 4.319177 AGTTGAACTAAGTGACAGGCATC 58.681 43.478 0.00 0.00 0.00 3.91
3749 8271 4.357918 AGTTGAACTAAGTGACAGGCAT 57.642 40.909 0.00 0.00 0.00 4.40
3759 8281 5.123227 TCAGTGAACCCAAGTTGAACTAAG 58.877 41.667 3.87 0.00 35.94 2.18
3832 8354 8.364142 GTCAAAGCAATCTAGGTATAGTCAGAT 58.636 37.037 0.00 0.00 0.00 2.90
3833 8355 7.561722 AGTCAAAGCAATCTAGGTATAGTCAGA 59.438 37.037 0.00 0.00 0.00 3.27
3834 8356 7.721402 AGTCAAAGCAATCTAGGTATAGTCAG 58.279 38.462 0.00 0.00 0.00 3.51
3835 8357 7.661536 AGTCAAAGCAATCTAGGTATAGTCA 57.338 36.000 0.00 0.00 0.00 3.41
3836 8358 8.950208 AAAGTCAAAGCAATCTAGGTATAGTC 57.050 34.615 0.00 0.00 0.00 2.59
3837 8359 9.167311 CAAAAGTCAAAGCAATCTAGGTATAGT 57.833 33.333 0.00 0.00 0.00 2.12
3838 8360 9.383519 TCAAAAGTCAAAGCAATCTAGGTATAG 57.616 33.333 0.00 0.00 0.00 1.31
3839 8361 9.905713 ATCAAAAGTCAAAGCAATCTAGGTATA 57.094 29.630 0.00 0.00 0.00 1.47
3840 8362 8.814038 ATCAAAAGTCAAAGCAATCTAGGTAT 57.186 30.769 0.00 0.00 0.00 2.73
3841 8363 9.383519 CTATCAAAAGTCAAAGCAATCTAGGTA 57.616 33.333 0.00 0.00 0.00 3.08
3842 8364 7.885399 ACTATCAAAAGTCAAAGCAATCTAGGT 59.115 33.333 0.00 0.00 0.00 3.08
3843 8365 8.273780 ACTATCAAAAGTCAAAGCAATCTAGG 57.726 34.615 0.00 0.00 0.00 3.02
3849 8371 9.677567 GTGAATTACTATCAAAAGTCAAAGCAA 57.322 29.630 0.00 0.00 32.21 3.91
3850 8372 8.845227 TGTGAATTACTATCAAAAGTCAAAGCA 58.155 29.630 0.00 0.00 32.21 3.91
3851 8373 9.846248 ATGTGAATTACTATCAAAAGTCAAAGC 57.154 29.630 0.00 0.00 32.21 3.51
3854 8376 9.430623 TCGATGTGAATTACTATCAAAAGTCAA 57.569 29.630 0.00 0.00 32.21 3.18
3855 8377 8.869897 GTCGATGTGAATTACTATCAAAAGTCA 58.130 33.333 0.00 0.00 0.00 3.41
3856 8378 8.869897 TGTCGATGTGAATTACTATCAAAAGTC 58.130 33.333 0.00 0.00 0.00 3.01
3857 8379 8.771920 TGTCGATGTGAATTACTATCAAAAGT 57.228 30.769 0.00 0.00 0.00 2.66
3858 8380 9.087424 TCTGTCGATGTGAATTACTATCAAAAG 57.913 33.333 0.00 0.00 0.00 2.27
3859 8381 8.996024 TCTGTCGATGTGAATTACTATCAAAA 57.004 30.769 0.00 0.00 0.00 2.44
3860 8382 8.996024 TTCTGTCGATGTGAATTACTATCAAA 57.004 30.769 0.00 0.00 0.00 2.69
3861 8383 8.251026 ACTTCTGTCGATGTGAATTACTATCAA 58.749 33.333 0.00 0.00 0.00 2.57
3862 8384 7.772166 ACTTCTGTCGATGTGAATTACTATCA 58.228 34.615 0.00 0.00 0.00 2.15
3863 8385 8.535592 CAACTTCTGTCGATGTGAATTACTATC 58.464 37.037 0.00 0.00 0.00 2.08
3864 8386 8.251026 TCAACTTCTGTCGATGTGAATTACTAT 58.749 33.333 0.00 0.00 0.00 2.12
3875 8397 6.035435 CAGAAATACCTCAACTTCTGTCGATG 59.965 42.308 0.00 0.00 39.83 3.84
3878 8400 4.627467 CCAGAAATACCTCAACTTCTGTCG 59.373 45.833 9.19 0.00 42.03 4.35
3963 8485 5.657474 ACATCAGATAAAATTGCCAAGCAG 58.343 37.500 0.00 0.00 40.61 4.24
4077 8599 5.521010 CAGCAAGCAAAATCTCTGACAAAAA 59.479 36.000 0.00 0.00 0.00 1.94
4080 8602 3.633525 ACAGCAAGCAAAATCTCTGACAA 59.366 39.130 0.00 0.00 0.00 3.18
4086 8608 5.557891 ACTGATACAGCAAGCAAAATCTC 57.442 39.130 0.00 0.00 34.37 2.75
4107 8629 7.851387 TTGGAAGGAAAACCAACAAAATTAC 57.149 32.000 0.00 0.00 40.59 1.89
4153 8675 3.065233 GTGAGCACAAACACATCAGTTGA 59.935 43.478 0.00 0.00 37.05 3.18
4214 8736 1.607148 GCCGACCAGCTAAAACAAACT 59.393 47.619 0.00 0.00 0.00 2.66
4217 8739 1.681538 TTGCCGACCAGCTAAAACAA 58.318 45.000 0.00 0.00 0.00 2.83
4218 8740 1.810151 GATTGCCGACCAGCTAAAACA 59.190 47.619 0.00 0.00 0.00 2.83
4234 8756 9.442047 AGTTCTAGTCAAAATGGAACTAGATTG 57.558 33.333 11.14 0.00 42.85 2.67


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

AutoCloner maintained by Alex Coulton.