Multiple sequence alignment - TraesCS2D01G256400

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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 TraesCS2D01G256400 chr2D 100.000 6151 0 0 1 6151 310306105 310299955 0.000000e+00 11359.0
1 TraesCS2D01G256400 chr2D 88.384 198 18 4 157 351 522506893 522507088 3.710000e-57 233.0
2 TraesCS2D01G256400 chr2D 85.821 134 15 4 404 534 619596500 619596368 8.310000e-29 139.0
3 TraesCS2D01G256400 chr2D 98.276 58 1 0 3971 4028 474500880 474500937 1.090000e-17 102.0
4 TraesCS2D01G256400 chr2D 100.000 50 0 0 3981 4030 44481338 44481387 6.560000e-15 93.5
5 TraesCS2D01G256400 chr2B 97.032 2325 51 10 625 2937 362017970 362020288 0.000000e+00 3895.0
6 TraesCS2D01G256400 chr2B 95.587 1994 63 9 3985 5961 362021184 362023169 0.000000e+00 3171.0
7 TraesCS2D01G256400 chr2B 93.258 712 18 7 3274 3983 362020468 362021151 0.000000e+00 1022.0
8 TraesCS2D01G256400 chr2B 86.184 456 31 8 27 455 362015726 362016176 1.210000e-126 464.0
9 TraesCS2D01G256400 chr2B 92.000 175 10 2 5980 6151 362023382 362023555 6.160000e-60 243.0
10 TraesCS2D01G256400 chr2B 87.817 197 15 5 452 644 362016211 362016402 8.030000e-54 222.0
11 TraesCS2D01G256400 chr2B 91.803 61 3 2 3981 4039 762517099 762517039 3.950000e-12 84.2
12 TraesCS2D01G256400 chr2B 100.000 29 0 0 3198 3226 362020337 362020365 3.000000e-03 54.7
13 TraesCS2D01G256400 chr2A 96.740 1503 38 4 355 1856 426381766 426380274 0.000000e+00 2494.0
14 TraesCS2D01G256400 chr2A 95.745 1034 27 7 1951 2971 426380266 426379237 0.000000e+00 1650.0
15 TraesCS2D01G256400 chr2A 94.967 1053 29 10 4937 5972 426376733 426375688 0.000000e+00 1629.0
16 TraesCS2D01G256400 chr2A 97.616 923 15 2 3985 4901 426377656 426376735 0.000000e+00 1576.0
17 TraesCS2D01G256400 chr2A 91.313 1036 52 19 2975 3983 426378713 426377689 0.000000e+00 1380.0
18 TraesCS2D01G256400 chr2A 90.698 172 11 2 5980 6151 426375480 426375314 2.230000e-54 224.0
19 TraesCS2D01G256400 chr7B 82.988 241 41 0 5718 5958 742270037 742269797 1.040000e-52 219.0
20 TraesCS2D01G256400 chr7B 89.706 68 4 3 3963 4028 678775337 678775403 3.950000e-12 84.2
21 TraesCS2D01G256400 chr1D 82.500 240 40 2 5720 5958 481442552 481442314 6.250000e-50 209.0
22 TraesCS2D01G256400 chr1D 82.843 204 33 2 5723 5926 462094855 462095056 1.360000e-41 182.0
23 TraesCS2D01G256400 chr1D 89.516 124 10 1 403 523 398872685 398872562 2.970000e-33 154.0
24 TraesCS2D01G256400 chrUn 89.831 118 11 1 403 520 51393651 51393535 3.840000e-32 150.0
25 TraesCS2D01G256400 chrUn 89.831 118 11 1 403 520 278335064 278335180 3.840000e-32 150.0
26 TraesCS2D01G256400 chr4D 87.402 127 16 0 403 529 100357433 100357559 4.970000e-31 147.0
27 TraesCS2D01G256400 chr3A 88.000 125 13 2 397 519 21167623 21167747 4.970000e-31 147.0
28 TraesCS2D01G256400 chr3A 87.037 108 14 0 5718 5825 65997545 65997652 8.370000e-24 122.0
29 TraesCS2D01G256400 chr3B 88.889 117 12 1 403 519 464625828 464625943 6.430000e-30 143.0
30 TraesCS2D01G256400 chr7D 85.417 96 10 3 259 354 205239688 205239779 5.080000e-16 97.1
31 TraesCS2D01G256400 chr3D 93.443 61 3 1 3965 4025 386297107 386297048 8.490000e-14 89.8
32 TraesCS2D01G256400 chr3D 91.803 61 4 1 3968 4028 394624496 394624555 3.950000e-12 84.2
33 TraesCS2D01G256400 chr6D 93.103 58 4 0 3972 4029 242634233 242634290 1.100000e-12 86.1
34 TraesCS2D01G256400 chr6B 94.444 36 1 1 5606 5640 689518504 689518539 3.000000e-03 54.7
35 TraesCS2D01G256400 chr5D 96.774 31 1 0 5000 5030 311903632 311903602 1.100000e-02 52.8


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 TraesCS2D01G256400 chr2D 310299955 310306105 6150 True 11359.000000 11359 100.000000 1 6151 1 chr2D.!!$R1 6150
1 TraesCS2D01G256400 chr2B 362015726 362023555 7829 False 1295.957143 3895 93.125429 27 6151 7 chr2B.!!$F1 6124
2 TraesCS2D01G256400 chr2A 426375314 426381766 6452 True 1492.166667 2494 94.513167 355 6151 6 chr2A.!!$R1 5796

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
746 2407 0.252103 TATACATCTCCCCCTCCGCC 60.252 60.0 0.00 0.00 0.00 6.13 F
1843 3504 0.253583 TCCCTTCCATGACCCATCCA 60.254 55.0 0.00 0.00 0.00 3.41 F
2690 4364 0.247185 TCGTGTCGGGGGTATTCAAC 59.753 55.0 0.00 0.00 0.00 3.18 F
3517 5790 0.237498 GCGGTCTGTTTAAGGTGCAC 59.763 55.0 8.80 8.80 0.00 4.57 F
4252 6564 1.039068 CAACTGACAAACCATGGCCA 58.961 50.0 13.04 8.56 35.52 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2690 4364 0.729116 CACAAGCAGAATAGTGCCCG 59.271 55.000 0.00 0.0 45.20 6.13 R
3076 5271 0.460284 CTCTACGCGCAATTCACCCT 60.460 55.000 5.73 0.0 0.00 4.34 R
4545 6857 1.181098 AGCCAGCGCCTTCACATTTT 61.181 50.000 2.29 0.0 34.57 1.82 R
4915 7233 2.028567 CACCAAATTAACCAACCGGCAT 60.029 45.455 0.00 0.0 34.57 4.40 R
5977 8315 0.315886 ACACTACGCCGATGTTGACA 59.684 50.000 0.00 0.0 0.00 3.58 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
24 25 7.571097 CTAAAAACTTTACTGTCGTTGTTCG 57.429 36.000 0.00 0.00 41.41 3.95
25 26 5.783100 AAAACTTTACTGTCGTTGTTCGA 57.217 34.783 0.00 0.00 46.83 3.71
150 151 7.768240 TCATCTGAGTGTAACGCTATTCTAAA 58.232 34.615 0.00 0.00 45.86 1.85
151 152 8.248253 TCATCTGAGTGTAACGCTATTCTAAAA 58.752 33.333 0.00 0.00 45.86 1.52
152 153 9.035607 CATCTGAGTGTAACGCTATTCTAAAAT 57.964 33.333 0.00 0.00 45.86 1.82
153 154 8.407457 TCTGAGTGTAACGCTATTCTAAAATG 57.593 34.615 0.00 0.00 45.86 2.32
154 155 8.248253 TCTGAGTGTAACGCTATTCTAAAATGA 58.752 33.333 0.00 0.00 45.86 2.57
161 185 6.243216 ACGCTATTCTAAAATGAACCCCTA 57.757 37.500 0.00 0.00 0.00 3.53
162 186 6.655930 ACGCTATTCTAAAATGAACCCCTAA 58.344 36.000 0.00 0.00 0.00 2.69
248 276 8.921353 TGCTACCCAAGTTTGTAATTTAGTAA 57.079 30.769 0.00 0.00 0.00 2.24
249 277 9.523168 TGCTACCCAAGTTTGTAATTTAGTAAT 57.477 29.630 0.00 0.00 0.00 1.89
330 358 8.136165 CGTTACTGAGGTGTAGAATAAGCTATT 58.864 37.037 0.00 0.00 0.00 1.73
331 359 9.819267 GTTACTGAGGTGTAGAATAAGCTATTT 57.181 33.333 0.00 0.00 0.00 1.40
412 440 7.602644 CACTATAAGGTTTTGAGCTTGTAGTCA 59.397 37.037 18.47 0.00 33.57 3.41
414 442 9.167311 CTATAAGGTTTTGAGCTTGTAGTCATT 57.833 33.333 11.52 0.00 0.00 2.57
430 458 2.426024 GTCATTGCTAGGTGGTCTACGA 59.574 50.000 0.00 0.00 0.00 3.43
443 471 5.221461 GGTGGTCTACGAATCTGGATGTAAT 60.221 44.000 0.00 0.00 0.00 1.89
585 654 3.965347 ACTGGACCATAACCGTTATAGCT 59.035 43.478 3.42 0.00 0.00 3.32
586 655 5.142639 ACTGGACCATAACCGTTATAGCTA 58.857 41.667 3.42 0.00 0.00 3.32
587 656 5.243283 ACTGGACCATAACCGTTATAGCTAG 59.757 44.000 3.42 6.33 0.00 3.42
588 657 4.021719 TGGACCATAACCGTTATAGCTAGC 60.022 45.833 6.62 6.62 0.00 3.42
746 2407 0.252103 TATACATCTCCCCCTCCGCC 60.252 60.000 0.00 0.00 0.00 6.13
1011 2672 6.417258 TGTTAATTTGCTCATGGATCAGAGA 58.583 36.000 11.79 0.00 33.74 3.10
1334 2995 6.678878 TCGACTGCCAGAAAGTACATATATC 58.321 40.000 0.00 0.00 0.00 1.63
1373 3034 9.868277 AAATTGCTAATTTCATTAATCCAACGA 57.132 25.926 0.00 0.00 36.38 3.85
1426 3087 3.361627 GCGTTTTTCTTTTGCGTGATTCC 60.362 43.478 0.00 0.00 0.00 3.01
1843 3504 0.253583 TCCCTTCCATGACCCATCCA 60.254 55.000 0.00 0.00 0.00 3.41
1853 3514 4.594920 CCATGACCCATCCAATCTACTAGT 59.405 45.833 0.00 0.00 0.00 2.57
1854 3515 5.780282 CCATGACCCATCCAATCTACTAGTA 59.220 44.000 1.89 1.89 0.00 1.82
1855 3516 6.295349 CCATGACCCATCCAATCTACTAGTAC 60.295 46.154 0.00 0.00 0.00 2.73
1995 3656 3.084786 GGATCATAGCCATTGTTAGCCC 58.915 50.000 0.00 0.00 0.00 5.19
2069 3730 1.683385 GGCAGAGACCTTTGCTTTGTT 59.317 47.619 11.50 0.00 40.15 2.83
2072 3733 3.429410 GCAGAGACCTTTGCTTTGTTTGT 60.429 43.478 5.42 0.00 37.35 2.83
2160 3824 2.371841 TCTGAAGCTAGCTTTGGTTGGA 59.628 45.455 29.84 17.55 36.26 3.53
2163 3827 4.917385 TGAAGCTAGCTTTGGTTGGAATA 58.083 39.130 29.84 5.39 36.26 1.75
2274 3938 3.495331 TGCTGGCTTTTCAACTAATCCA 58.505 40.909 0.00 0.00 0.00 3.41
2322 3986 6.619801 TCTCTCCTTTTTCTTTTCCTTTCG 57.380 37.500 0.00 0.00 0.00 3.46
2513 4181 4.082026 AGCCTTGTGAAAACTCCATTATGC 60.082 41.667 0.00 0.00 0.00 3.14
2585 4254 2.841442 AGTACTGTTCCAAGGACTGC 57.159 50.000 0.00 0.00 40.02 4.40
2690 4364 0.247185 TCGTGTCGGGGGTATTCAAC 59.753 55.000 0.00 0.00 0.00 3.18
2847 4523 2.453080 GTTGTGGTATGCATGCATTCG 58.547 47.619 36.23 0.00 37.82 3.34
2940 4616 7.228507 TGTGTACAGAATAATGGCCATGTAATC 59.771 37.037 21.63 15.16 0.00 1.75
3014 5209 6.756542 AGAACATTTTAACTGCAACTTGAACC 59.243 34.615 0.00 0.00 0.00 3.62
3035 5230 7.723616 TGAACCAAATGTTTCATCTCTTAGGAA 59.276 33.333 0.00 0.00 37.29 3.36
3080 5275 3.709567 GCCTCGTAGGTGAAGGGT 58.290 61.111 3.38 0.00 37.80 4.34
3081 5276 1.218316 GCCTCGTAGGTGAAGGGTG 59.782 63.158 3.38 0.00 37.80 4.61
3082 5277 1.255667 GCCTCGTAGGTGAAGGGTGA 61.256 60.000 3.38 0.00 37.80 4.02
3100 5295 2.279136 GTGAATTGCGCGTAGAGTAGTG 59.721 50.000 8.43 0.00 0.00 2.74
3102 5297 2.190325 ATTGCGCGTAGAGTAGTGTC 57.810 50.000 8.43 0.00 0.00 3.67
3123 5318 5.536161 TGTCCAGGGAAAAGAAATTCTTGAG 59.464 40.000 9.21 0.00 36.71 3.02
3133 5328 7.776933 AAAGAAATTCTTGAGGCTGTTTTTC 57.223 32.000 9.21 0.00 36.71 2.29
3194 5389 8.553459 AAGACACGAAACATTAGAATCTCAAT 57.447 30.769 0.00 0.00 0.00 2.57
3232 5503 9.692325 AAATCTAGATCTTGTTTATTCAGCCTT 57.308 29.630 5.51 0.00 0.00 4.35
3253 5524 6.536224 GCCTTTGCATCAAATTTAGCAACTAT 59.464 34.615 18.65 0.00 45.53 2.12
3254 5525 7.464977 GCCTTTGCATCAAATTTAGCAACTATG 60.465 37.037 18.65 11.47 45.53 2.23
3255 5526 7.546667 CCTTTGCATCAAATTTAGCAACTATGT 59.453 33.333 18.65 0.00 45.53 2.29
3256 5527 9.571810 CTTTGCATCAAATTTAGCAACTATGTA 57.428 29.630 18.65 7.59 45.53 2.29
3257 5528 8.909708 TTGCATCAAATTTAGCAACTATGTAC 57.090 30.769 16.31 0.00 41.55 2.90
3258 5529 8.279970 TGCATCAAATTTAGCAACTATGTACT 57.720 30.769 9.00 0.00 33.48 2.73
3259 5530 9.389755 TGCATCAAATTTAGCAACTATGTACTA 57.610 29.630 9.00 0.00 33.48 1.82
3364 5637 2.676839 GTGCATGTGGAGAGACAATGAG 59.323 50.000 0.00 0.00 0.00 2.90
3391 5664 6.645306 AGTTTTGTCCTCCTATTCTTCTAGC 58.355 40.000 0.00 0.00 0.00 3.42
3400 5673 6.015772 CCTCCTATTCTTCTAGCACCTCTAAC 60.016 46.154 0.00 0.00 0.00 2.34
3422 5695 4.142315 ACATCATTTGAGCTAACCATGTGC 60.142 41.667 0.00 0.00 0.00 4.57
3517 5790 0.237498 GCGGTCTGTTTAAGGTGCAC 59.763 55.000 8.80 8.80 0.00 4.57
3541 5814 4.625311 GCACACCAATTTAAGGTTGCATAC 59.375 41.667 0.00 0.00 40.09 2.39
3816 6097 8.691661 TTAATATAAGCAATTGGGTTCCTCTC 57.308 34.615 7.72 0.00 38.39 3.20
3875 6156 8.840867 CGTTTGCTCATTTTCATTTACTACTTC 58.159 33.333 0.00 0.00 0.00 3.01
3919 6200 9.308318 GTTTGGCAAATTTCTTAGAAAACAGTA 57.692 29.630 16.74 0.00 0.00 2.74
3967 6248 7.040755 CCAATATTCATCATGCCATGCAAAAAT 60.041 33.333 0.00 0.55 43.62 1.82
3983 6264 7.156876 TGCAAAAATAATTACTCCCTCAGTG 57.843 36.000 0.00 0.00 36.43 3.66
3990 6302 8.834004 AATAATTACTCCCTCAGTGTAGTGTA 57.166 34.615 0.00 0.00 36.43 2.90
4209 6521 1.112113 TCGGAACTGGTCTATCAGGC 58.888 55.000 0.00 0.00 38.98 4.85
4252 6564 1.039068 CAACTGACAAACCATGGCCA 58.961 50.000 13.04 8.56 35.52 5.36
4342 6654 8.594550 ACTACTAGATGTCCAAAATTACACTGT 58.405 33.333 0.00 0.00 0.00 3.55
4357 6669 4.330944 ACACTGTTTACACTCGAATCCA 57.669 40.909 0.00 0.00 0.00 3.41
4887 7205 7.201427 CGCATGTAATTTCCATCAAAACGAAAT 60.201 33.333 0.00 0.00 37.72 2.17
4915 7233 9.806203 TGCGTTATGTATTCTTACTAAAGCTTA 57.194 29.630 0.00 0.00 33.34 3.09
4931 7249 3.361786 AGCTTATGCCGGTTGGTTAATT 58.638 40.909 1.90 0.00 40.80 1.40
5054 7372 1.480212 AACCGTCTGAGGACATGCCA 61.480 55.000 8.58 0.00 42.21 4.92
5136 7454 3.064416 TGGCTGACGGCATGTACA 58.936 55.556 8.86 0.00 44.01 2.90
5187 7506 1.672881 GATCTGGCGAAAGGTGATTGG 59.327 52.381 0.00 0.00 0.00 3.16
5216 7536 7.011389 CGTTGGAAAGATATCTGTATTCAGCAA 59.989 37.037 5.86 4.96 41.10 3.91
5475 7796 3.782523 ACAGTTGAGGTGGATATGGTCAT 59.217 43.478 0.00 0.00 0.00 3.06
5493 7814 7.940178 TGGTCATGATAACGTGTATATTGTC 57.060 36.000 0.00 0.00 34.90 3.18
5517 7852 5.051816 TGAAAATTTCAGCAGCTTTCCTTG 58.948 37.500 4.03 0.00 34.08 3.61
5520 7855 0.467844 TTCAGCAGCTTTCCTTGGCA 60.468 50.000 0.00 0.00 0.00 4.92
5539 7874 3.555966 GCATTACCCAGTTGAATAGGCT 58.444 45.455 0.00 0.00 0.00 4.58
5540 7875 3.316308 GCATTACCCAGTTGAATAGGCTG 59.684 47.826 0.00 0.00 0.00 4.85
5589 7926 5.825593 ACTGTCTTAAGATTTCCCTGTGA 57.174 39.130 8.75 0.00 0.00 3.58
5811 8148 6.870971 AGGAAGCGACAAATGTAGTTTTTA 57.129 33.333 0.00 0.00 0.00 1.52
5815 8152 7.424452 GGAAGCGACAAATGTAGTTTTTATACG 59.576 37.037 0.00 0.00 0.00 3.06
5839 8176 5.463392 GCGTGATGAGACAATCAAATAGCTA 59.537 40.000 0.00 0.00 42.53 3.32
5961 8299 1.343465 CGACCGGATACCAAATAGGCT 59.657 52.381 9.46 0.00 43.14 4.58
5962 8300 2.559668 CGACCGGATACCAAATAGGCTA 59.440 50.000 9.46 0.00 43.14 3.93
5965 8303 5.105635 CGACCGGATACCAAATAGGCTATAA 60.106 44.000 9.46 0.00 43.14 0.98
5967 8305 5.189145 ACCGGATACCAAATAGGCTATAAGG 59.811 44.000 9.46 18.51 43.14 2.69
5972 8310 7.093024 GGATACCAAATAGGCTATAAGGTGCTA 60.093 40.741 27.86 16.20 43.14 3.49
5973 8311 5.866207 ACCAAATAGGCTATAAGGTGCTAC 58.134 41.667 22.72 0.00 43.14 3.58
5974 8312 5.368523 ACCAAATAGGCTATAAGGTGCTACA 59.631 40.000 22.72 0.00 43.14 2.74
5975 8313 5.934625 CCAAATAGGCTATAAGGTGCTACAG 59.065 44.000 7.59 0.00 0.00 2.74
5977 8315 6.749036 AATAGGCTATAAGGTGCTACAGTT 57.251 37.500 7.59 0.00 0.00 3.16
5978 8316 4.408182 AGGCTATAAGGTGCTACAGTTG 57.592 45.455 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.393327 TCGAACAACGACAGTAAAGTTTTTAG 58.607 34.615 0.00 0.00 46.45 1.85
1 2 7.288317 TCGAACAACGACAGTAAAGTTTTTA 57.712 32.000 0.00 0.00 46.45 1.52
2 3 6.168164 TCGAACAACGACAGTAAAGTTTTT 57.832 33.333 0.00 0.00 46.45 1.94
3 4 5.783100 TCGAACAACGACAGTAAAGTTTT 57.217 34.783 0.00 0.00 46.45 2.43
16 17 4.092120 TCAAACAACAACATCGAACAACG 58.908 39.130 0.00 0.00 44.09 4.10
17 18 7.672351 TTATCAAACAACAACATCGAACAAC 57.328 32.000 0.00 0.00 0.00 3.32
95 96 9.442047 AGTGAATACCTTTTTACTCAGATGAAG 57.558 33.333 0.00 0.00 0.00 3.02
131 132 8.114905 GGTTCATTTTAGAATAGCGTTACACTC 58.885 37.037 0.00 0.00 0.00 3.51
218 243 8.972458 AAATTACAAACTTGGGTAGCAAATTT 57.028 26.923 0.00 0.00 0.00 1.82
220 245 8.866093 ACTAAATTACAAACTTGGGTAGCAAAT 58.134 29.630 0.00 0.00 0.00 2.32
296 324 9.750783 ATTCTACACCTCAGTAACGGTATATAT 57.249 33.333 0.00 0.00 30.91 0.86
303 331 5.041940 GCTTATTCTACACCTCAGTAACGG 58.958 45.833 0.00 0.00 0.00 4.44
304 332 5.892568 AGCTTATTCTACACCTCAGTAACG 58.107 41.667 0.00 0.00 0.00 3.18
412 440 3.961408 AGATTCGTAGACCACCTAGCAAT 59.039 43.478 0.00 0.00 34.32 3.56
414 442 2.688446 CAGATTCGTAGACCACCTAGCA 59.312 50.000 0.00 0.00 34.32 3.49
707 2364 1.729586 TGTACACCTGCTTCCTTCCT 58.270 50.000 0.00 0.00 0.00 3.36
708 2365 2.789409 ATGTACACCTGCTTCCTTCC 57.211 50.000 0.00 0.00 0.00 3.46
709 2366 5.914033 TGTATATGTACACCTGCTTCCTTC 58.086 41.667 0.00 0.00 35.94 3.46
710 2367 5.950544 TGTATATGTACACCTGCTTCCTT 57.049 39.130 0.00 0.00 35.94 3.36
746 2407 3.121944 CCTCTTTCTCACGTCAAATCACG 59.878 47.826 0.00 0.00 45.65 4.35
1011 2672 1.680249 GCTCCGAGATTCCCAAAGCTT 60.680 52.381 0.00 0.00 29.40 3.74
1334 2995 7.919313 AATTAGCAATTTTCATGAGCGTATG 57.081 32.000 0.00 0.00 0.00 2.39
1373 3034 1.546029 TGCTTGCTGATACAGTCGAGT 59.454 47.619 0.00 0.00 33.43 4.18
1591 3252 2.605818 CGGCGGATGAAGAATTAAACGA 59.394 45.455 0.00 0.00 0.00 3.85
1766 3427 3.770040 CCGCCGGTGATGGAGTCA 61.770 66.667 18.79 0.00 0.00 3.41
1853 3514 4.577693 CGAACAGGCATGTACTAGTAGGTA 59.422 45.833 3.57 0.00 39.29 3.08
1854 3515 3.380637 CGAACAGGCATGTACTAGTAGGT 59.619 47.826 3.57 0.00 39.29 3.08
1855 3516 3.380637 ACGAACAGGCATGTACTAGTAGG 59.619 47.826 3.57 0.00 39.29 3.18
2160 3824 2.114616 CTCCTCACTGTGCCCTCTATT 58.885 52.381 2.12 0.00 0.00 1.73
2163 3827 2.289532 GCTCCTCACTGTGCCCTCT 61.290 63.158 2.12 0.00 0.00 3.69
2322 3986 3.284323 TCTAGTGTCTTGTCGTGAAGC 57.716 47.619 0.00 0.00 0.00 3.86
2381 4045 2.035576 TGCATGGAGATCGATGACTCTG 59.964 50.000 0.54 1.01 34.54 3.35
2690 4364 0.729116 CACAAGCAGAATAGTGCCCG 59.271 55.000 0.00 0.00 45.20 6.13
2847 4523 3.269178 CCTTGAGCTGTTGATCTCCTTC 58.731 50.000 0.00 0.00 0.00 3.46
2880 4556 7.898014 TCTCTGAACACATATATACCACAGT 57.102 36.000 0.00 0.00 0.00 3.55
2940 4616 6.964741 TTATGCATTTTGTAATGTGCCTTG 57.035 33.333 3.54 0.00 42.56 3.61
2971 4647 9.606631 AAATGTTCTCATCTTTGACCTATAGAC 57.393 33.333 0.00 0.00 32.56 2.59
2977 4653 8.571336 CAGTTAAAATGTTCTCATCTTTGACCT 58.429 33.333 0.00 0.00 32.56 3.85
2978 4654 7.327032 GCAGTTAAAATGTTCTCATCTTTGACC 59.673 37.037 0.00 0.00 32.56 4.02
2979 4655 7.862372 TGCAGTTAAAATGTTCTCATCTTTGAC 59.138 33.333 0.00 0.00 32.56 3.18
2981 4657 8.482429 GTTGCAGTTAAAATGTTCTCATCTTTG 58.518 33.333 0.00 0.00 32.56 2.77
2982 4658 8.416329 AGTTGCAGTTAAAATGTTCTCATCTTT 58.584 29.630 0.00 0.00 32.56 2.52
2983 4659 7.945134 AGTTGCAGTTAAAATGTTCTCATCTT 58.055 30.769 0.00 0.00 32.56 2.40
2985 4661 7.862372 TCAAGTTGCAGTTAAAATGTTCTCATC 59.138 33.333 0.00 0.00 32.56 2.92
2986 4662 7.715657 TCAAGTTGCAGTTAAAATGTTCTCAT 58.284 30.769 0.00 0.00 35.59 2.90
3014 5209 8.103948 ACACTTCCTAAGAGATGAAACATTTG 57.896 34.615 0.00 0.00 0.00 2.32
3035 5230 3.387050 GGGTGGATCCGATAGTTTACACT 59.613 47.826 7.39 0.00 37.00 3.55
3076 5271 0.460284 CTCTACGCGCAATTCACCCT 60.460 55.000 5.73 0.00 0.00 4.34
3077 5272 0.739813 ACTCTACGCGCAATTCACCC 60.740 55.000 5.73 0.00 0.00 4.61
3078 5273 1.852895 CTACTCTACGCGCAATTCACC 59.147 52.381 5.73 0.00 0.00 4.02
3079 5274 2.279136 CACTACTCTACGCGCAATTCAC 59.721 50.000 5.73 0.00 0.00 3.18
3080 5275 2.094906 ACACTACTCTACGCGCAATTCA 60.095 45.455 5.73 0.00 0.00 2.57
3081 5276 2.527100 ACACTACTCTACGCGCAATTC 58.473 47.619 5.73 0.00 0.00 2.17
3082 5277 2.527100 GACACTACTCTACGCGCAATT 58.473 47.619 5.73 0.00 0.00 2.32
3100 5295 5.047731 CCTCAAGAATTTCTTTTCCCTGGAC 60.048 44.000 8.95 0.00 33.78 4.02
3102 5297 4.322273 GCCTCAAGAATTTCTTTTCCCTGG 60.322 45.833 8.95 6.67 33.78 4.45
3166 5361 7.872993 TGAGATTCTAATGTTTCGTGTCTTCTT 59.127 33.333 0.00 0.00 0.00 2.52
3167 5362 7.378966 TGAGATTCTAATGTTTCGTGTCTTCT 58.621 34.615 0.00 0.00 0.00 2.85
3168 5363 7.582435 TGAGATTCTAATGTTTCGTGTCTTC 57.418 36.000 0.00 0.00 0.00 2.87
3232 5503 8.739039 AGTACATAGTTGCTAAATTTGATGCAA 58.261 29.630 17.80 17.80 42.16 4.08
3309 5582 3.509740 TGTGTGCACATTCAACAAACAG 58.490 40.909 24.69 0.00 36.21 3.16
3310 5583 3.192212 TCTGTGTGCACATTCAACAAACA 59.808 39.130 24.69 11.62 41.01 2.83
3364 5637 6.645306 AGAAGAATAGGAGGACAAAACTAGC 58.355 40.000 0.00 0.00 0.00 3.42
3391 5664 6.037610 GGTTAGCTCAAATGATGTTAGAGGTG 59.962 42.308 0.00 0.00 37.58 4.00
3400 5673 4.357142 GCACATGGTTAGCTCAAATGATG 58.643 43.478 0.00 0.00 0.00 3.07
3422 5695 7.175641 ACCTCACTTGTTTGATCTCTTAATTGG 59.824 37.037 0.00 0.00 0.00 3.16
3517 5790 2.058057 GCAACCTTAAATTGGTGTGCG 58.942 47.619 0.00 0.00 37.93 5.34
3689 5970 8.791327 TCAGTTCAGATGTGCAAGAATAATAA 57.209 30.769 0.00 0.00 0.00 1.40
3816 6097 4.082081 AGACAAAATGTGCACCATACCATG 60.082 41.667 15.69 6.91 31.97 3.66
3875 6156 9.647797 TTGCCAAACTATATATATCTTACACCG 57.352 33.333 0.00 0.00 0.00 4.94
3967 6248 8.654485 TTTACACTACACTGAGGGAGTAATTA 57.346 34.615 0.00 0.00 31.73 1.40
3996 6308 4.440250 CCTCCGTCCCATAATATAAGAGCG 60.440 50.000 0.00 0.00 0.00 5.03
4209 6521 6.375174 TGAAACTGATACCAATCTGACCATTG 59.625 38.462 0.07 0.00 35.60 2.82
4342 6654 2.677836 GCATGCTGGATTCGAGTGTAAA 59.322 45.455 11.37 0.00 0.00 2.01
4357 6669 8.418597 AATCTATCATTTTAGGAATGCATGCT 57.581 30.769 20.33 0.00 0.00 3.79
4545 6857 1.181098 AGCCAGCGCCTTCACATTTT 61.181 50.000 2.29 0.00 34.57 1.82
4887 7205 8.195436 AGCTTTAGTAAGAATACATAACGCAGA 58.805 33.333 0.00 0.00 34.29 4.26
4915 7233 2.028567 CACCAAATTAACCAACCGGCAT 60.029 45.455 0.00 0.00 34.57 4.40
4931 7249 3.238788 TCTGTCTCCTACACTCACCAA 57.761 47.619 0.00 0.00 33.45 3.67
5187 7506 6.257849 TGAATACAGATATCTTTCCAACGTGC 59.742 38.462 1.33 0.00 0.00 5.34
5191 7510 7.792374 TGCTGAATACAGATATCTTTCCAAC 57.208 36.000 1.33 0.00 46.03 3.77
5216 7536 7.775053 ACAATGTCCATGTATTTTAACCAGT 57.225 32.000 0.00 0.00 0.00 4.00
5517 7852 2.623416 GCCTATTCAACTGGGTAATGCC 59.377 50.000 0.00 0.00 0.00 4.40
5520 7855 4.018415 ACACAGCCTATTCAACTGGGTAAT 60.018 41.667 0.00 0.00 45.94 1.89
5539 7874 4.299586 TGGATGAAATTCTGGCTACACA 57.700 40.909 0.00 0.00 0.00 3.72
5540 7875 4.883585 TGATGGATGAAATTCTGGCTACAC 59.116 41.667 0.00 0.00 0.00 2.90
5589 7926 8.421249 TGGATCATTAGGTGTTTCAGAAATTT 57.579 30.769 0.00 0.00 0.00 1.82
5718 8055 8.964772 CCCTTCAAAGATTCTACATGAAAATCT 58.035 33.333 0.00 7.83 40.55 2.40
5730 8067 4.221482 GCACAAATCCCCTTCAAAGATTCT 59.779 41.667 0.00 0.00 30.06 2.40
5811 8148 3.436700 TGATTGTCTCATCACGCGTAT 57.563 42.857 13.44 3.13 0.00 3.06
5815 8152 4.272018 AGCTATTTGATTGTCTCATCACGC 59.728 41.667 0.00 0.00 32.72 5.34
5961 8299 6.104146 TGTTGACAACTGTAGCACCTTATA 57.896 37.500 18.73 0.00 0.00 0.98
5962 8300 4.968259 TGTTGACAACTGTAGCACCTTAT 58.032 39.130 18.73 0.00 0.00 1.73
5965 8303 3.403038 GATGTTGACAACTGTAGCACCT 58.597 45.455 18.73 0.00 0.00 4.00
5967 8305 2.157668 CCGATGTTGACAACTGTAGCAC 59.842 50.000 18.73 2.90 0.00 4.40
5972 8310 0.531974 ACGCCGATGTTGACAACTGT 60.532 50.000 18.73 8.03 0.00 3.55
5973 8311 1.390123 CTACGCCGATGTTGACAACTG 59.610 52.381 18.73 8.90 0.00 3.16
5974 8312 1.000506 ACTACGCCGATGTTGACAACT 59.999 47.619 18.73 5.08 0.00 3.16
5975 8313 1.126113 CACTACGCCGATGTTGACAAC 59.874 52.381 11.54 11.54 0.00 3.32
5977 8315 0.315886 ACACTACGCCGATGTTGACA 59.684 50.000 0.00 0.00 0.00 3.58
5978 8316 1.389106 GAACACTACGCCGATGTTGAC 59.611 52.381 10.01 0.00 36.70 3.18


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

AutoCloner maintained by Alex Coulton.