Multiple sequence alignment - TraesCS1D01G315400

Loading Multiple Alignment...

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 TraesCS1D01G315400 chr1D 100.000 5882 0 0 1 5882 410512015 410506134 0.000000e+00 10863.0
1 TraesCS1D01G315400 chr1D 100.000 229 0 0 6151 6379 410505865 410505637 2.130000e-114 424.0
2 TraesCS1D01G315400 chr1B 95.378 5366 158 34 355 5670 553156699 553151374 0.000000e+00 8453.0
3 TraesCS1D01G315400 chr1B 96.522 230 7 1 6151 6379 553150707 553150478 4.670000e-101 379.0
4 TraesCS1D01G315400 chr1B 96.319 163 6 0 5690 5852 553151387 553151225 1.050000e-67 268.0
5 TraesCS1D01G315400 chr1B 100.000 36 0 0 5454 5489 553151564 553151529 4.130000e-07 67.6
6 TraesCS1D01G315400 chr1A 97.339 4510 93 15 532 5024 506558252 506553753 0.000000e+00 7638.0
7 TraesCS1D01G315400 chr1A 99.129 804 7 0 5049 5852 506553755 506552952 0.000000e+00 1447.0
8 TraesCS1D01G315400 chr1A 90.113 354 31 4 1 354 506558844 506558495 2.100000e-124 457.0
9 TraesCS1D01G315400 chr1A 99.563 229 1 0 6151 6379 506552540 506552312 9.890000e-113 418.0
10 TraesCS1D01G315400 chr1A 88.506 174 19 1 353 526 506558622 506558450 6.480000e-50 209.0
11 TraesCS1D01G315400 chr1A 100.000 36 0 0 5454 5489 506553323 506553288 4.130000e-07 67.6


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 TraesCS1D01G315400 chr1D 410505637 410512015 6378 True 5643.500000 10863 100.000 1 6379 2 chr1D.!!$R1 6378
1 TraesCS1D01G315400 chr1B 553150478 553156699 6221 True 3033.333333 8453 96.073 355 6379 3 chr1B.!!$R2 6024
2 TraesCS1D01G315400 chr1A 506552312 506558844 6532 True 1706.100000 7638 95.775 1 6379 6 chr1A.!!$R1 6378

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
597 744 0.248907 CGTAGTAGTGTCCCATGGCG 60.249 60.000 6.09 0.0 0.00 5.69 F
1399 1568 0.178861 AGGGGGTGTTGGAGATCTGT 60.179 55.000 0.00 0.0 0.00 3.41 F
1497 1666 2.152016 GCCTTTCTTTCAACGGTAGCT 58.848 47.619 0.00 0.0 0.00 3.32 F
1658 1827 2.258591 GACAAGGAGCTCGACGCA 59.741 61.111 7.83 0.0 42.61 5.24 F
2180 2354 2.549754 CTCATGACAAGAGTGCGGTTTT 59.450 45.455 0.00 0.0 0.00 2.43 F
3693 3875 1.620323 GGCCAGTGCAAGAAAGGAAAT 59.380 47.619 0.00 0.0 40.13 2.17 F
3985 4167 3.118956 GGCGATATAGGACCCTCATTCAG 60.119 52.174 0.00 0.0 0.00 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1501 1670 0.976963 CAGCAACATAAACAAGCGCG 59.023 50.000 0.00 0.00 0.00 6.86 R
2601 2775 3.141398 CAGCAAGAGTAGCAACTTGGAA 58.859 45.455 0.00 0.00 42.26 3.53 R
3102 3283 4.056050 CCCGATACTTGTACAATGTAGCC 58.944 47.826 9.13 8.74 0.00 3.93 R
3507 3688 6.374333 ACATATGTCTTACATCAAACACCACC 59.626 38.462 1.41 0.00 39.88 4.61 R
3733 3915 3.964688 TCTTCTTGACTCCACAGGTTACA 59.035 43.478 0.00 0.00 0.00 2.41 R
4524 4706 0.107017 ATGAAGGGACGGCATTCCTG 60.107 55.000 3.27 0.00 35.76 3.86 R
5494 5706 0.841961 TGCAGATCAGGCCTAGCAAT 59.158 50.000 3.98 0.00 0.00 3.56 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
30 31 3.549898 AATCCCCTCTTCCTGCTTTTT 57.450 42.857 0.00 0.00 0.00 1.94
31 32 4.675063 AATCCCCTCTTCCTGCTTTTTA 57.325 40.909 0.00 0.00 0.00 1.52
33 34 4.236527 TCCCCTCTTCCTGCTTTTTATC 57.763 45.455 0.00 0.00 0.00 1.75
38 39 4.808364 CCTCTTCCTGCTTTTTATCTCTCG 59.192 45.833 0.00 0.00 0.00 4.04
72 73 5.070446 TCATCATAGCACGAATAAGAAGGGT 59.930 40.000 0.00 0.00 0.00 4.34
92 93 7.554959 AGGGTAGTTTGTTCAGATTCTTCTA 57.445 36.000 0.00 0.00 0.00 2.10
101 102 6.954944 TGTTCAGATTCTTCTACCAAAAACG 58.045 36.000 0.00 0.00 0.00 3.60
102 103 5.607119 TCAGATTCTTCTACCAAAAACGC 57.393 39.130 0.00 0.00 0.00 4.84
116 117 2.987213 AAACGCGCTCGACACACGTA 62.987 55.000 5.73 0.00 43.13 3.57
154 155 4.929211 CAGAAAGTCGTCATTACATGTGGA 59.071 41.667 9.11 0.24 0.00 4.02
157 158 4.736126 AGTCGTCATTACATGTGGATCA 57.264 40.909 9.11 0.00 0.00 2.92
196 197 0.536460 TTTTCCTCCGCGCCTCTTTT 60.536 50.000 0.00 0.00 0.00 2.27
209 210 2.093341 GCCTCTTTTACCATCCCACGTA 60.093 50.000 0.00 0.00 0.00 3.57
217 218 3.662759 ACCATCCCACGTAAAATGGAT 57.337 42.857 22.18 11.39 40.98 3.41
247 248 2.186903 CGAGGTATGCCAAGCCGT 59.813 61.111 1.54 0.00 37.19 5.68
249 250 1.883084 GAGGTATGCCAAGCCGTCG 60.883 63.158 1.54 0.00 37.19 5.12
262 263 3.118454 CGTCGTCGGCCAAGCAAT 61.118 61.111 2.24 0.00 0.00 3.56
267 268 2.045045 TCGGCCAAGCAATCCCTG 60.045 61.111 2.24 0.00 0.00 4.45
291 292 2.365293 GCCCTCCATTTTCACACAACTT 59.635 45.455 0.00 0.00 0.00 2.66
294 295 3.315191 CCTCCATTTTCACACAACTTCGT 59.685 43.478 0.00 0.00 0.00 3.85
309 310 2.359975 CGTGGGTTCCCTCCTTGC 60.360 66.667 9.43 0.00 0.00 4.01
311 312 3.646715 TGGGTTCCCTCCTTGCCG 61.647 66.667 9.43 0.00 0.00 5.69
316 317 2.150719 TTCCCTCCTTGCCGTTCCA 61.151 57.895 0.00 0.00 0.00 3.53
317 318 2.359975 CCCTCCTTGCCGTTCCAC 60.360 66.667 0.00 0.00 0.00 4.02
349 350 2.285977 CCCTACTAAAATCACCCACGC 58.714 52.381 0.00 0.00 0.00 5.34
353 354 4.216687 CCTACTAAAATCACCCACGCAAAA 59.783 41.667 0.00 0.00 0.00 2.44
370 371 3.625314 AAAAACCCAGGTCTGCCAA 57.375 47.368 0.00 0.00 37.19 4.52
373 374 3.513750 AACCCAGGTCTGCCAAGCC 62.514 63.158 0.00 0.00 37.19 4.35
395 396 1.223487 GTCGGCCAAGCAATCCCTA 59.777 57.895 2.24 0.00 0.00 3.53
402 403 0.842635 CAAGCAATCCCTAGAGCCCT 59.157 55.000 0.00 0.00 0.00 5.19
412 413 2.422093 CCCTAGAGCCCTCCATTTTCAC 60.422 54.545 0.00 0.00 0.00 3.18
414 415 2.206576 AGAGCCCTCCATTTTCACAC 57.793 50.000 0.00 0.00 0.00 3.82
422 423 1.606668 TCCATTTTCACACAACTCCGC 59.393 47.619 0.00 0.00 0.00 5.54
423 424 1.662876 CCATTTTCACACAACTCCGCG 60.663 52.381 0.00 0.00 0.00 6.46
428 429 2.184167 CACACAACTCCGCGGGTTT 61.184 57.895 27.83 15.99 0.00 3.27
449 450 4.735132 CCTCGCCGTTCCGCTTGA 62.735 66.667 0.00 0.00 0.00 3.02
454 455 0.655733 CGCCGTTCCGCTTGAAATAT 59.344 50.000 0.00 0.00 33.94 1.28
506 507 2.943036 TCCGCTTGGAATAATACCCC 57.057 50.000 0.00 0.00 39.40 4.95
580 727 1.684983 TCCTCTGTTTTCCGAAGACGT 59.315 47.619 0.00 0.00 37.88 4.34
597 744 0.248907 CGTAGTAGTGTCCCATGGCG 60.249 60.000 6.09 0.00 0.00 5.69
944 1105 4.500826 GTCCCCTCCCTCCCTCCC 62.501 77.778 0.00 0.00 0.00 4.30
945 1106 4.761304 TCCCCTCCCTCCCTCCCT 62.761 72.222 0.00 0.00 0.00 4.20
947 1108 4.179599 CCCTCCCTCCCTCCCTCC 62.180 77.778 0.00 0.00 0.00 4.30
948 1109 3.368501 CCTCCCTCCCTCCCTCCA 61.369 72.222 0.00 0.00 0.00 3.86
950 1111 3.695825 TCCCTCCCTCCCTCCACC 61.696 72.222 0.00 0.00 0.00 4.61
951 1112 4.024984 CCCTCCCTCCCTCCACCA 62.025 72.222 0.00 0.00 0.00 4.17
1155 1323 0.946221 CCGGCGCTTCTCATGGTATC 60.946 60.000 7.64 0.00 0.00 2.24
1176 1344 0.396811 CCCCTCGATCGCCCTTTAAT 59.603 55.000 11.09 0.00 0.00 1.40
1242 1410 1.064803 TGCGTGATTGCTTTGAAACGT 59.935 42.857 0.00 0.00 35.36 3.99
1298 1466 1.560505 GGTGGGGAAAATGCACATCT 58.439 50.000 0.00 0.00 0.00 2.90
1300 1468 2.354003 GGTGGGGAAAATGCACATCTTG 60.354 50.000 0.00 0.00 0.00 3.02
1399 1568 0.178861 AGGGGGTGTTGGAGATCTGT 60.179 55.000 0.00 0.00 0.00 3.41
1423 1592 4.202441 AGAAGGCGAGAAATTATGCATGT 58.798 39.130 10.16 0.00 0.00 3.21
1481 1650 2.743928 CTGAGCCTTTCGCGCCTT 60.744 61.111 0.00 0.00 44.76 4.35
1483 1652 2.245714 CTGAGCCTTTCGCGCCTTTC 62.246 60.000 0.00 0.00 44.76 2.62
1497 1666 2.152016 GCCTTTCTTTCAACGGTAGCT 58.848 47.619 0.00 0.00 0.00 3.32
1501 1670 4.319549 CCTTTCTTTCAACGGTAGCTGTTC 60.320 45.833 0.00 0.00 29.62 3.18
1658 1827 2.258591 GACAAGGAGCTCGACGCA 59.741 61.111 7.83 0.00 42.61 5.24
2005 2175 2.556622 AGTAAATGTTGAGGCAAACCCG 59.443 45.455 1.28 0.00 39.21 5.28
2087 2257 3.862877 TGGCATATATGGTGAAGTGCT 57.137 42.857 14.51 0.00 33.38 4.40
2127 2299 3.437741 TGATTACTGCTGTGCTGATGTTG 59.562 43.478 6.48 0.00 0.00 3.33
2180 2354 2.549754 CTCATGACAAGAGTGCGGTTTT 59.450 45.455 0.00 0.00 0.00 2.43
2462 2636 3.114065 CGCAGACCTTTCTATTACGGTC 58.886 50.000 0.00 0.00 44.84 4.79
2568 2742 4.704540 CCTTGTGTACCATTATTCTTGGCA 59.295 41.667 0.00 0.00 37.81 4.92
2587 2761 2.760092 GCAGAATTGGGCTCCACAAATA 59.240 45.455 0.00 0.00 30.78 1.40
2588 2762 3.195396 GCAGAATTGGGCTCCACAAATAA 59.805 43.478 0.00 0.00 30.78 1.40
2703 2878 8.409358 TCATGCTATAAGCTATCACTAACTGA 57.591 34.615 0.03 0.00 42.97 3.41
2720 2895 7.752239 CACTAACTGATTTGTTTGCTCCTATTG 59.248 37.037 0.00 0.00 0.00 1.90
2786 2961 6.349300 CCATGGTAAAGCTAACACTCTATGT 58.651 40.000 2.57 0.00 46.42 2.29
2976 3153 4.219115 TGGAGTCAGTCATAGGGATCTTC 58.781 47.826 0.00 0.00 0.00 2.87
2987 3164 8.910944 AGTCATAGGGATCTTCAATCAAATTTG 58.089 33.333 12.15 12.15 0.00 2.32
3485 3666 5.362430 TGTGCACTAGGAATTTTGAACCTTT 59.638 36.000 19.41 0.00 35.52 3.11
3507 3688 9.013490 CCTTTGAACAATATTTCTATCTTTGCG 57.987 33.333 0.00 0.00 0.00 4.85
3693 3875 1.620323 GGCCAGTGCAAGAAAGGAAAT 59.380 47.619 0.00 0.00 40.13 2.17
3713 3895 6.460676 GGAAATAATTGCACTTCTCCTCATGG 60.461 42.308 0.00 0.00 0.00 3.66
3733 3915 3.204382 TGGAAGAGAGGGTTCTGGTTTTT 59.796 43.478 0.00 0.00 32.53 1.94
3985 4167 3.118956 GGCGATATAGGACCCTCATTCAG 60.119 52.174 0.00 0.00 0.00 3.02
4524 4706 4.048241 CTTCTCGAGGAATTACTCACCC 57.952 50.000 17.92 0.00 37.34 4.61
5021 5206 6.183360 GGTGAAAGCTTTTGAAAGAACCAAAG 60.183 38.462 14.05 0.00 38.28 2.77
5022 5207 6.589907 GTGAAAGCTTTTGAAAGAACCAAAGA 59.410 34.615 14.05 0.00 38.28 2.52
5023 5208 7.278646 GTGAAAGCTTTTGAAAGAACCAAAGAT 59.721 33.333 14.05 0.00 38.28 2.40
5024 5209 7.278424 TGAAAGCTTTTGAAAGAACCAAAGATG 59.722 33.333 14.05 0.00 38.28 2.90
5025 5210 5.604565 AGCTTTTGAAAGAACCAAAGATGG 58.395 37.500 7.63 0.00 44.48 3.51
5026 5211 5.363580 AGCTTTTGAAAGAACCAAAGATGGA 59.636 36.000 7.63 0.00 42.93 3.41
5027 5212 5.693555 GCTTTTGAAAGAACCAAAGATGGAG 59.306 40.000 7.63 0.00 42.93 3.86
5028 5213 5.693555 CTTTTGAAAGAACCAAAGATGGAGC 59.306 40.000 1.10 0.00 42.93 4.70
5029 5214 6.683610 CTTTTGAAAGAACCAAAGATGGAGCA 60.684 38.462 1.10 0.00 42.93 4.26
5030 5215 8.111959 CTTTTGAAAGAACCAAAGATGGAGCAA 61.112 37.037 1.10 0.00 42.93 3.91
5038 5223 4.012319 CAAAGATGGAGCAATTGACGAG 57.988 45.455 10.34 0.00 0.00 4.18
5039 5224 3.616956 AAGATGGAGCAATTGACGAGA 57.383 42.857 10.34 0.00 0.00 4.04
5040 5225 3.616956 AGATGGAGCAATTGACGAGAA 57.383 42.857 10.34 0.00 0.00 2.87
5041 5226 3.942829 AGATGGAGCAATTGACGAGAAA 58.057 40.909 10.34 0.00 0.00 2.52
5042 5227 4.326826 AGATGGAGCAATTGACGAGAAAA 58.673 39.130 10.34 0.00 0.00 2.29
5043 5228 3.896648 TGGAGCAATTGACGAGAAAAC 57.103 42.857 10.34 0.00 0.00 2.43
5044 5229 2.223144 TGGAGCAATTGACGAGAAAACG 59.777 45.455 10.34 0.00 39.31 3.60
5045 5230 2.478894 GGAGCAATTGACGAGAAAACGA 59.521 45.455 10.34 0.00 37.03 3.85
5046 5231 3.423645 GGAGCAATTGACGAGAAAACGAG 60.424 47.826 10.34 0.00 37.03 4.18
5047 5232 2.480419 AGCAATTGACGAGAAAACGAGG 59.520 45.455 10.34 0.00 37.03 4.63
5390 5602 5.105187 TGGTACAAGATGAGATCCAGACTTG 60.105 44.000 19.46 19.46 42.83 3.16
5494 5706 1.141657 GGCCTGATCTGCAGTCCAATA 59.858 52.381 14.67 0.00 42.26 1.90
5567 5779 3.810310 ACAGGCTTAGTCAGACTATGC 57.190 47.619 28.66 28.66 39.95 3.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 4.080072 AGAGATAAAAAGCAGGAAGAGGGG 60.080 45.833 0.00 0.00 0.00 4.79
14 15 5.109500 AGAGATAAAAAGCAGGAAGAGGG 57.891 43.478 0.00 0.00 0.00 4.30
30 31 1.376543 GACACCGGTCACGAGAGATA 58.623 55.000 2.59 0.00 43.73 1.98
31 32 2.181584 GACACCGGTCACGAGAGAT 58.818 57.895 2.59 0.00 43.73 2.75
72 73 9.621629 TTTTGGTAGAAGAATCTGAACAAACTA 57.378 29.630 3.65 0.00 35.52 2.24
92 93 2.174969 TGTCGAGCGCGTTTTTGGT 61.175 52.632 10.30 0.00 38.98 3.67
101 102 2.556677 CGATACGTGTGTCGAGCGC 61.557 63.158 12.96 0.00 45.16 5.92
102 103 1.933041 CCGATACGTGTGTCGAGCG 60.933 63.158 18.76 3.25 45.16 5.03
116 117 2.214376 TTCTGCAAATGGTTCCCGAT 57.786 45.000 0.00 0.00 0.00 4.18
157 158 7.051000 GGAAAATATTCAAGTCAGGCTAGACT 58.949 38.462 12.05 12.05 40.11 3.24
196 197 4.781775 ATCCATTTTACGTGGGATGGTA 57.218 40.909 19.04 10.71 38.67 3.25
231 232 1.883084 CGACGGCTTGGCATACCTC 60.883 63.158 4.96 1.74 36.63 3.85
247 248 2.435938 GGATTGCTTGGCCGACGA 60.436 61.111 0.00 0.00 0.00 4.20
249 250 2.044946 AGGGATTGCTTGGCCGAC 60.045 61.111 0.00 0.00 0.00 4.79
253 254 2.421399 GCTCCAGGGATTGCTTGGC 61.421 63.158 1.08 0.00 31.94 4.52
330 331 2.980568 TGCGTGGGTGATTTTAGTAGG 58.019 47.619 0.00 0.00 0.00 3.18
331 332 5.365403 TTTTGCGTGGGTGATTTTAGTAG 57.635 39.130 0.00 0.00 0.00 2.57
332 333 5.769484 TTTTTGCGTGGGTGATTTTAGTA 57.231 34.783 0.00 0.00 0.00 1.82
353 354 1.115326 GCTTGGCAGACCTGGGTTTT 61.115 55.000 0.00 0.00 36.63 2.43
382 383 0.179006 GGGCTCTAGGGATTGCTTGG 60.179 60.000 0.00 0.00 0.00 3.61
388 389 2.522013 AATGGAGGGCTCTAGGGATT 57.478 50.000 0.00 0.00 0.00 3.01
395 396 1.425066 TGTGTGAAAATGGAGGGCTCT 59.575 47.619 0.00 0.00 0.00 4.09
402 403 1.606668 GCGGAGTTGTGTGAAAATGGA 59.393 47.619 0.00 0.00 0.00 3.41
412 413 2.613506 GGAAACCCGCGGAGTTGTG 61.614 63.158 30.73 11.56 0.00 3.33
414 415 2.032071 AGGAAACCCGCGGAGTTG 59.968 61.111 30.73 12.89 0.00 3.16
422 423 4.814294 CGGCGAGGAGGAAACCCG 62.814 72.222 0.00 0.00 0.00 5.28
423 424 3.249837 AACGGCGAGGAGGAAACCC 62.250 63.158 16.62 0.00 0.00 4.11
449 450 7.472240 GCGGGTGATTTTAATGGGGTAATATTT 60.472 37.037 0.00 0.00 0.00 1.40
454 455 3.025262 GCGGGTGATTTTAATGGGGTAA 58.975 45.455 0.00 0.00 0.00 2.85
491 492 8.132995 GTGATTTTAACGGGGTATTATTCCAAG 58.867 37.037 0.00 0.00 0.00 3.61
506 507 0.110147 TTGCGCGGGTGATTTTAACG 60.110 50.000 8.83 0.00 0.00 3.18
597 744 2.046285 CAAGGTGCCCCGGACATTC 61.046 63.158 0.73 0.00 35.12 2.67
659 806 1.407979 GCCTTCATTCATTGCTCCCAG 59.592 52.381 0.00 0.00 0.00 4.45
941 1102 2.221299 CGAGGGTTTGGTGGAGGGA 61.221 63.158 0.00 0.00 0.00 4.20
944 1105 1.374252 CGACGAGGGTTTGGTGGAG 60.374 63.158 0.00 0.00 0.00 3.86
945 1106 2.738480 CGACGAGGGTTTGGTGGA 59.262 61.111 0.00 0.00 0.00 4.02
947 1108 3.047877 GGCGACGAGGGTTTGGTG 61.048 66.667 0.00 0.00 0.00 4.17
1172 1340 1.411246 ACCGGTAGAGCATGCGATTAA 59.589 47.619 4.49 0.00 0.00 1.40
1176 1344 0.818938 TTAACCGGTAGAGCATGCGA 59.181 50.000 8.00 0.00 0.00 5.10
1242 1410 0.461548 CCTCGCCTGCACAGATCTAA 59.538 55.000 0.00 0.00 0.00 2.10
1269 1437 1.497309 TTTCCCCACCGGATCTTGCT 61.497 55.000 9.46 0.00 41.63 3.91
1271 1439 1.750778 CATTTTCCCCACCGGATCTTG 59.249 52.381 9.46 0.00 41.63 3.02
1281 1449 2.607499 ACAAGATGTGCATTTTCCCCA 58.393 42.857 0.00 0.00 0.00 4.96
1314 1482 7.849804 AACAACTTAGCGAGTATCAATCAAT 57.150 32.000 0.00 0.00 37.72 2.57
1315 1483 7.667043 AAACAACTTAGCGAGTATCAATCAA 57.333 32.000 0.00 0.00 37.72 2.57
1328 1496 4.976116 CCTACACAAGCAAAACAACTTAGC 59.024 41.667 0.00 0.00 0.00 3.09
1399 1568 5.822519 ACATGCATAATTTCTCGCCTTCTAA 59.177 36.000 0.00 0.00 0.00 2.10
1423 1592 4.105057 TCCAAGGCAAACCCTAGAAAACTA 59.895 41.667 0.00 0.00 45.62 2.24
1466 1635 1.578206 AAGAAAGGCGCGAAAGGCTC 61.578 55.000 12.10 0.00 46.87 4.70
1481 1650 2.798283 CGAACAGCTACCGTTGAAAGAA 59.202 45.455 0.00 0.00 0.00 2.52
1483 1652 1.136336 GCGAACAGCTACCGTTGAAAG 60.136 52.381 0.00 0.00 44.04 2.62
1497 1666 2.645163 CAACATAAACAAGCGCGAACA 58.355 42.857 12.10 0.00 0.00 3.18
1501 1670 0.976963 CAGCAACATAAACAAGCGCG 59.023 50.000 0.00 0.00 0.00 6.86
1658 1827 6.653989 AGCTGCTTCACCTACTTAAATACAT 58.346 36.000 0.00 0.00 0.00 2.29
2005 2175 5.095490 CCTTCGACAAAATTAGCAACATCC 58.905 41.667 0.00 0.00 0.00 3.51
2127 2299 2.604912 AAACAATTGACCCTCTCCCC 57.395 50.000 13.59 0.00 0.00 4.81
2462 2636 7.934120 AGATTCCAGGAAATTATAAGAAGTCCG 59.066 37.037 5.81 0.00 0.00 4.79
2568 2742 4.415596 TGTTATTTGTGGAGCCCAATTCT 58.584 39.130 0.00 0.00 34.18 2.40
2601 2775 3.141398 CAGCAAGAGTAGCAACTTGGAA 58.859 45.455 0.00 0.00 42.26 3.53
2703 2878 7.284034 CAGAGGATACAATAGGAGCAAACAAAT 59.716 37.037 0.00 0.00 41.41 2.32
2720 2895 6.441088 AATAGGGTTGGAATCAGAGGATAC 57.559 41.667 0.00 0.00 32.09 2.24
2976 3153 9.846248 CCTAGGAGTAAGAAACAAATTTGATTG 57.154 33.333 24.64 0.00 36.37 2.67
2987 3164 6.879458 TGCAAGATTTCCTAGGAGTAAGAAAC 59.121 38.462 12.26 2.01 31.51 2.78
3081 3258 4.638865 GCCGACATACACCTAAAGGATTTT 59.361 41.667 2.23 0.00 40.09 1.82
3082 3259 4.080526 AGCCGACATACACCTAAAGGATTT 60.081 41.667 2.23 0.00 43.42 2.17
3102 3283 4.056050 CCCGATACTTGTACAATGTAGCC 58.944 47.826 9.13 8.74 0.00 3.93
3485 3666 7.415095 CCACCGCAAAGATAGAAATATTGTTCA 60.415 37.037 0.00 0.00 0.00 3.18
3507 3688 6.374333 ACATATGTCTTACATCAAACACCACC 59.626 38.462 1.41 0.00 39.88 4.61
3693 3875 4.842531 TCCATGAGGAGAAGTGCAATTA 57.157 40.909 0.00 0.00 39.61 1.40
3713 3895 4.207955 ACAAAAACCAGAACCCTCTCTTC 58.792 43.478 0.00 0.00 0.00 2.87
3733 3915 3.964688 TCTTCTTGACTCCACAGGTTACA 59.035 43.478 0.00 0.00 0.00 2.41
3985 4167 4.499183 CCCTATGATCTTCGCCATAAGAC 58.501 47.826 0.00 0.00 38.28 3.01
4524 4706 0.107017 ATGAAGGGACGGCATTCCTG 60.107 55.000 3.27 0.00 35.76 3.86
4730 4912 6.712095 TCATATGGACTATTTGAAGGTGATGC 59.288 38.462 2.13 0.00 0.00 3.91
4894 5076 9.236006 GACATATTCCTTGCCAACTTATCATAT 57.764 33.333 0.00 0.00 0.00 1.78
5021 5206 4.406943 GTTTTCTCGTCAATTGCTCCATC 58.593 43.478 0.00 0.00 0.00 3.51
5022 5207 3.120199 CGTTTTCTCGTCAATTGCTCCAT 60.120 43.478 0.00 0.00 0.00 3.41
5023 5208 2.223144 CGTTTTCTCGTCAATTGCTCCA 59.777 45.455 0.00 0.00 0.00 3.86
5024 5209 2.478894 TCGTTTTCTCGTCAATTGCTCC 59.521 45.455 0.00 0.00 0.00 4.70
5025 5210 3.423645 CCTCGTTTTCTCGTCAATTGCTC 60.424 47.826 0.00 0.00 0.00 4.26
5026 5211 2.480419 CCTCGTTTTCTCGTCAATTGCT 59.520 45.455 0.00 0.00 0.00 3.91
5027 5212 2.412847 CCCTCGTTTTCTCGTCAATTGC 60.413 50.000 0.00 0.00 0.00 3.56
5028 5213 3.064207 TCCCTCGTTTTCTCGTCAATTG 58.936 45.455 0.00 0.00 0.00 2.32
5029 5214 3.396260 TCCCTCGTTTTCTCGTCAATT 57.604 42.857 0.00 0.00 0.00 2.32
5030 5215 3.611766 ATCCCTCGTTTTCTCGTCAAT 57.388 42.857 0.00 0.00 0.00 2.57
5031 5216 3.396260 AATCCCTCGTTTTCTCGTCAA 57.604 42.857 0.00 0.00 0.00 3.18
5032 5217 4.730949 ATAATCCCTCGTTTTCTCGTCA 57.269 40.909 0.00 0.00 0.00 4.35
5033 5218 5.006455 GGAAATAATCCCTCGTTTTCTCGTC 59.994 44.000 0.00 0.00 43.00 4.20
5034 5219 4.874396 GGAAATAATCCCTCGTTTTCTCGT 59.126 41.667 0.00 0.00 43.00 4.18
5035 5220 4.025979 CGGAAATAATCCCTCGTTTTCTCG 60.026 45.833 0.00 0.00 46.39 4.04
5036 5221 4.874396 ACGGAAATAATCCCTCGTTTTCTC 59.126 41.667 0.00 0.00 46.39 2.87
5037 5222 4.840271 ACGGAAATAATCCCTCGTTTTCT 58.160 39.130 0.00 0.00 46.39 2.52
5038 5223 6.856135 ATACGGAAATAATCCCTCGTTTTC 57.144 37.500 0.00 0.00 46.39 2.29
5039 5224 6.824704 TGAATACGGAAATAATCCCTCGTTTT 59.175 34.615 0.00 0.00 46.39 2.43
5040 5225 6.350906 TGAATACGGAAATAATCCCTCGTTT 58.649 36.000 0.00 0.00 46.39 3.60
5041 5226 5.920903 TGAATACGGAAATAATCCCTCGTT 58.079 37.500 0.00 0.00 46.39 3.85
5042 5227 5.540400 TGAATACGGAAATAATCCCTCGT 57.460 39.130 0.00 0.00 46.39 4.18
5043 5228 7.298122 CAAATGAATACGGAAATAATCCCTCG 58.702 38.462 0.00 0.00 46.39 4.63
5044 5229 7.593825 CCAAATGAATACGGAAATAATCCCTC 58.406 38.462 0.00 0.00 46.39 4.30
5045 5230 6.015434 GCCAAATGAATACGGAAATAATCCCT 60.015 38.462 0.00 0.00 46.39 4.20
5046 5231 6.156519 GCCAAATGAATACGGAAATAATCCC 58.843 40.000 0.00 0.00 46.39 3.85
5047 5232 6.744112 TGCCAAATGAATACGGAAATAATCC 58.256 36.000 0.00 0.00 45.57 3.01
5390 5602 2.615912 GGTGATGGAGCTCAGCATTTAC 59.384 50.000 17.19 12.66 44.14 2.01
5494 5706 0.841961 TGCAGATCAGGCCTAGCAAT 59.158 50.000 3.98 0.00 0.00 3.56
5567 5779 9.715121 TTAAAACTCCACCATAAAGTACTACTG 57.285 33.333 0.00 0.00 0.00 2.74
5731 5943 6.612247 ACAAAATGAACAACGATGACACTA 57.388 33.333 0.00 0.00 0.00 2.74
5796 6008 1.047002 CCCCCAATCAAGCACAACAA 58.953 50.000 0.00 0.00 0.00 2.83


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

AutoCloner maintained by Alex Coulton.