Multiple sequence alignment - TraesCS3A01G347700

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 TraesCS3A01G347700 chr3A 100.000 2831 0 0 1 2831 596753811 596750981 0.000000e+00 5228
1 TraesCS3A01G347700 chr3D 92.814 2171 86 36 644 2766 454678077 454675929 0.000000e+00 3081
2 TraesCS3A01G347700 chr3D 83.384 662 78 16 1 643 454686579 454685931 4.060000e-163 584
3 TraesCS3A01G347700 chr3B 93.307 1270 47 12 857 2121 597462173 597460937 0.000000e+00 1840
4 TraesCS3A01G347700 chr3B 92.541 724 31 7 2120 2831 597460909 597460197 0.000000e+00 1016
5 TraesCS3A01G347700 chr3B 83.636 660 82 15 1 643 597463132 597462482 5.220000e-167 597
6 TraesCS3A01G347700 chr1B 74.863 549 81 36 1146 1652 530610290 530610823 2.220000e-46 196
7 TraesCS3A01G347700 chr4A 84.516 155 20 3 1140 1292 139613122 139613274 1.760000e-32 150
8 TraesCS3A01G347700 chr4D 82.667 150 26 0 1143 1292 334110131 334109982 1.770000e-27 134
9 TraesCS3A01G347700 chr4B 82.667 150 26 0 1143 1292 412084722 412084573 1.770000e-27 134


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 TraesCS3A01G347700 chr3A 596750981 596753811 2830 True 5228 5228 100.000 1 2831 1 chr3A.!!$R1 2830
1 TraesCS3A01G347700 chr3D 454675929 454678077 2148 True 3081 3081 92.814 644 2766 1 chr3D.!!$R1 2122
2 TraesCS3A01G347700 chr3D 454685931 454686579 648 True 584 584 83.384 1 643 1 chr3D.!!$R2 642
3 TraesCS3A01G347700 chr3B 597460197 597463132 2935 True 1151 1840 89.828 1 2831 3 chr3B.!!$R1 2830

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
503 521 0.108138 GTGGACGACATTCTCCAGGG 60.108 60.0 0.0 0.0 37.23 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2089 2272 0.674269 TCGAAAACCCCGCATACACC 60.674 55.0 0.0 0.0 0.0 4.16 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
109 110 2.711547 GCCCAGGACACCCTCTATTAAT 59.288 50.000 0.00 0.00 42.02 1.40
111 112 4.718961 CCCAGGACACCCTCTATTAATTG 58.281 47.826 0.00 0.00 42.02 2.32
131 132 9.716507 TTAATTGAGAACGAGAGAAAAACAAAG 57.283 29.630 0.00 0.00 0.00 2.77
132 133 6.737254 TTGAGAACGAGAGAAAAACAAAGT 57.263 33.333 0.00 0.00 0.00 2.66
133 134 7.837202 TTGAGAACGAGAGAAAAACAAAGTA 57.163 32.000 0.00 0.00 0.00 2.24
134 135 8.433421 TTGAGAACGAGAGAAAAACAAAGTAT 57.567 30.769 0.00 0.00 0.00 2.12
175 176 7.393841 ACAAACTACATGAGGACTACTACTC 57.606 40.000 0.00 0.00 0.00 2.59
198 199 2.820197 TCAGTGTCATTGCTAGACTCGT 59.180 45.455 0.00 0.00 36.94 4.18
207 208 1.001974 TGCTAGACTCGTGTGGCAAAT 59.998 47.619 2.84 0.00 0.00 2.32
210 211 0.396435 AGACTCGTGTGGCAAATGGA 59.604 50.000 0.00 0.00 0.00 3.41
212 213 1.227999 ACTCGTGTGGCAAATGGACG 61.228 55.000 0.00 0.00 0.00 4.79
223 224 3.657448 AATGGACGCCGACGATGCA 62.657 57.895 0.00 0.00 43.93 3.96
244 245 6.554784 TGCATTGGATATCCTGAAATGGTAT 58.445 36.000 24.26 5.70 36.82 2.73
245 246 6.434965 TGCATTGGATATCCTGAAATGGTATG 59.565 38.462 24.26 14.40 36.82 2.39
251 252 6.297243 GGATATCCTGAAATGGTATGTGGGAT 60.297 42.308 14.97 0.00 36.47 3.85
257 258 5.364778 TGAAATGGTATGTGGGATACTTCG 58.635 41.667 0.00 0.00 0.00 3.79
259 260 4.873746 ATGGTATGTGGGATACTTCGAG 57.126 45.455 0.00 0.00 0.00 4.04
260 261 3.905968 TGGTATGTGGGATACTTCGAGA 58.094 45.455 0.00 0.00 0.00 4.04
262 263 4.280929 TGGTATGTGGGATACTTCGAGATG 59.719 45.833 0.00 0.00 0.00 2.90
263 264 2.890808 TGTGGGATACTTCGAGATGC 57.109 50.000 0.00 0.00 0.00 3.91
264 265 2.107366 TGTGGGATACTTCGAGATGCA 58.893 47.619 0.00 0.00 0.00 3.96
265 266 2.159099 TGTGGGATACTTCGAGATGCAC 60.159 50.000 0.00 0.00 0.00 4.57
266 267 2.101582 GTGGGATACTTCGAGATGCACT 59.898 50.000 0.00 0.00 0.00 4.40
267 268 2.766263 TGGGATACTTCGAGATGCACTT 59.234 45.455 0.00 0.00 0.00 3.16
268 269 3.181475 TGGGATACTTCGAGATGCACTTC 60.181 47.826 0.00 0.00 0.00 3.01
280 295 5.278709 CGAGATGCACTTCAGATATGTACCT 60.279 44.000 0.00 0.00 0.00 3.08
281 296 6.491714 AGATGCACTTCAGATATGTACCTT 57.508 37.500 0.00 0.00 0.00 3.50
287 302 4.099573 ACTTCAGATATGTACCTTGTCCCG 59.900 45.833 0.00 0.00 0.00 5.14
290 305 5.202765 TCAGATATGTACCTTGTCCCGTTA 58.797 41.667 0.00 0.00 0.00 3.18
291 306 5.836898 TCAGATATGTACCTTGTCCCGTTAT 59.163 40.000 0.00 0.00 0.00 1.89
345 362 5.750067 ACGACTACTACGAATTGTGTGTTTT 59.250 36.000 0.00 0.00 34.70 2.43
357 374 3.360867 TGTGTGTTTTCTTGGATGTGGT 58.639 40.909 0.00 0.00 0.00 4.16
378 395 3.316308 GTGCCTATGATCACATTCAACCC 59.684 47.826 0.00 0.00 37.87 4.11
379 396 3.202818 TGCCTATGATCACATTCAACCCT 59.797 43.478 0.00 0.00 37.87 4.34
411 428 1.264045 TGGTGATCGTGCATGAGGGA 61.264 55.000 15.04 0.00 0.00 4.20
433 451 2.175715 GTTGGAAGGATCCCTAGCCAAT 59.824 50.000 21.11 0.00 44.30 3.16
492 510 2.677337 GTCTACTACAGAGGTGGACGAC 59.323 54.545 0.00 0.00 35.98 4.34
503 521 0.108138 GTGGACGACATTCTCCAGGG 60.108 60.000 0.00 0.00 37.23 4.45
529 547 5.819379 TGTTGAGGCAGAGCTAATAAATGAG 59.181 40.000 0.00 0.00 0.00 2.90
543 563 9.495572 GCTAATAAATGAGTTTATGAGGCTAGT 57.504 33.333 7.17 0.00 38.46 2.57
548 568 8.723942 AAATGAGTTTATGAGGCTAGTAACAG 57.276 34.615 0.00 0.00 0.00 3.16
550 570 7.661536 TGAGTTTATGAGGCTAGTAACAGAT 57.338 36.000 0.00 0.00 0.00 2.90
552 572 7.981789 TGAGTTTATGAGGCTAGTAACAGATTG 59.018 37.037 0.00 0.00 0.00 2.67
553 573 8.079211 AGTTTATGAGGCTAGTAACAGATTGA 57.921 34.615 0.00 0.00 0.00 2.57
556 576 6.737720 ATGAGGCTAGTAACAGATTGATGA 57.262 37.500 0.00 0.00 0.00 2.92
563 583 6.258947 GCTAGTAACAGATTGATGAAAGGTCC 59.741 42.308 0.00 0.00 0.00 4.46
564 584 6.126863 AGTAACAGATTGATGAAAGGTCCA 57.873 37.500 0.00 0.00 0.00 4.02
566 586 4.647564 ACAGATTGATGAAAGGTCCACT 57.352 40.909 0.00 0.00 0.00 4.00
568 588 4.042062 ACAGATTGATGAAAGGTCCACTGA 59.958 41.667 0.00 0.00 0.00 3.41
576 596 4.899502 TGAAAGGTCCACTGAGAGAATTC 58.100 43.478 0.00 0.00 0.00 2.17
589 609 6.327104 ACTGAGAGAATTCTGCTATGAAGGAT 59.673 38.462 14.00 0.00 32.53 3.24
604 624 7.066766 GCTATGAAGGATTAGCCATGGAAATAG 59.933 40.741 18.40 7.59 40.02 1.73
618 638 5.116084 TGGAAATAGCTTAGCACCTTGAT 57.884 39.130 7.07 0.00 0.00 2.57
622 642 6.203723 GGAAATAGCTTAGCACCTTGATACAG 59.796 42.308 7.07 0.00 0.00 2.74
630 650 1.207488 ACCTTGATACAGCCCTGGCA 61.207 55.000 11.38 0.00 44.88 4.92
705 725 8.780616 ATGAATATGTAAACCAATCCATCCAA 57.219 30.769 0.00 0.00 0.00 3.53
714 734 3.287222 CCAATCCATCCAAACCGTGTAT 58.713 45.455 0.00 0.00 0.00 2.29
718 738 5.623956 ATCCATCCAAACCGTGTATTCTA 57.376 39.130 0.00 0.00 0.00 2.10
725 745 7.172868 TCCAAACCGTGTATTCTACTGATAA 57.827 36.000 0.00 0.00 0.00 1.75
728 748 4.604976 ACCGTGTATTCTACTGATAACGC 58.395 43.478 0.00 0.00 0.00 4.84
751 771 7.970061 ACGCTATGTAAAGTGTACTTTAATCGA 59.030 33.333 16.36 0.00 46.35 3.59
795 815 9.708222 CAACAATTACTCTATTATTGTGCACTC 57.292 33.333 19.41 0.00 40.54 3.51
797 817 9.672673 ACAATTACTCTATTATTGTGCACTCTT 57.327 29.630 19.41 5.22 40.08 2.85
907 1073 4.141937 GCCTAAAAAGGAAATGGATGGGTC 60.142 45.833 0.00 0.00 0.00 4.46
1014 1180 1.609841 GGCGCGCTATATAAACCCCTT 60.610 52.381 32.29 0.00 0.00 3.95
1055 1221 2.094286 TCACAACCCACAAGCAAACAAG 60.094 45.455 0.00 0.00 0.00 3.16
1125 1291 2.473760 CCGTCGACTCGAGCTCCAT 61.474 63.158 13.61 0.00 36.23 3.41
1444 1613 1.153469 CAGGAGGAAGAAGAGCCGC 60.153 63.158 0.00 0.00 0.00 6.53
1681 1859 6.616947 TCGAAGAGTTCTCTCATCTTTCTTC 58.383 40.000 2.69 0.00 42.66 2.87
1802 1983 3.963428 ACAGTGATGTACAGAGGGTTC 57.037 47.619 0.33 0.00 0.00 3.62
1811 1992 1.807814 ACAGAGGGTTCAGTGGTTCT 58.192 50.000 0.00 0.00 0.00 3.01
1909 2090 9.275398 TGAATTTTTCTGGGAAAATCTTTCATG 57.725 29.630 6.32 0.00 38.04 3.07
1950 2131 6.481954 AAACAAAGATATGGTTGAGTCGAC 57.518 37.500 7.70 7.70 0.00 4.20
2012 2194 3.182572 CCTCTCGTTCAAAACAGAAGACG 59.817 47.826 0.00 0.00 0.00 4.18
2077 2260 2.554032 CAAGCAGTAAACTCCACTTGGG 59.446 50.000 0.00 0.00 32.76 4.12
2083 2266 4.216257 CAGTAAACTCCACTTGGGACATTG 59.784 45.833 0.00 0.00 42.15 2.82
2086 2269 2.863809 ACTCCACTTGGGACATTGAAC 58.136 47.619 0.00 0.00 42.15 3.18
2089 2272 1.806542 CCACTTGGGACATTGAACTCG 59.193 52.381 0.00 0.00 39.30 4.18
2163 2375 1.490910 GCAGGGCAAGGTAGGTTATCT 59.509 52.381 0.00 0.00 0.00 1.98
2237 2449 4.200092 GCCGAGGAACTATTGAAGGAAAT 58.800 43.478 0.00 0.00 41.55 2.17
2238 2450 4.035675 GCCGAGGAACTATTGAAGGAAATG 59.964 45.833 0.00 0.00 41.55 2.32
2239 2451 5.428253 CCGAGGAACTATTGAAGGAAATGA 58.572 41.667 0.00 0.00 41.55 2.57
2240 2452 6.058183 CCGAGGAACTATTGAAGGAAATGAT 58.942 40.000 0.00 0.00 41.55 2.45
2241 2453 7.217200 CCGAGGAACTATTGAAGGAAATGATA 58.783 38.462 0.00 0.00 41.55 2.15
2242 2454 7.715249 CCGAGGAACTATTGAAGGAAATGATAA 59.285 37.037 0.00 0.00 41.55 1.75
2243 2455 8.552034 CGAGGAACTATTGAAGGAAATGATAAC 58.448 37.037 0.00 0.00 41.55 1.89
2244 2456 9.620259 GAGGAACTATTGAAGGAAATGATAACT 57.380 33.333 0.00 0.00 41.55 2.24
2292 2504 1.605753 ACACGAAAGGAAAGGGAAGC 58.394 50.000 0.00 0.00 0.00 3.86
2304 2516 3.451402 AAGGGAAGCGGAAAAAGGTAT 57.549 42.857 0.00 0.00 0.00 2.73
2435 2653 6.053650 AGTTTAAACCGCTACTTGAGAAACT 58.946 36.000 14.72 0.00 31.54 2.66
2589 2807 6.642707 TCTAATTTGGGTTGTTAACTGGTG 57.357 37.500 7.22 0.00 0.00 4.17
2590 2808 4.681074 AATTTGGGTTGTTAACTGGTGG 57.319 40.909 7.22 0.00 0.00 4.61
2591 2809 2.830651 TTGGGTTGTTAACTGGTGGT 57.169 45.000 7.22 0.00 0.00 4.16
2659 2877 3.368948 GCCCTTGGAATTTCGGCAAATTA 60.369 43.478 7.83 0.00 41.47 1.40
2767 2995 2.631062 CCCCGGTGCTGTAGATACATTA 59.369 50.000 0.00 0.00 35.36 1.90
2771 2999 4.245660 CGGTGCTGTAGATACATTATGGG 58.754 47.826 0.00 0.00 35.36 4.00
2810 3038 2.163613 CCGGTGCCATAAACCTCTTTTC 59.836 50.000 0.00 0.00 35.39 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 8.479313 AAAGTTTTCTCCAAAGATTTGTTGTC 57.521 30.769 4.71 0.00 36.45 3.18
72 73 3.988819 CTGGGCAGGATTTTTCGAAAAA 58.011 40.909 31.74 31.74 41.59 1.94
73 74 3.658757 CTGGGCAGGATTTTTCGAAAA 57.341 42.857 19.08 19.08 0.00 2.29
91 92 6.485830 TCTCAATTAATAGAGGGTGTCCTG 57.514 41.667 0.00 0.00 45.05 3.86
95 96 6.380274 TCTCGTTCTCAATTAATAGAGGGTGT 59.620 38.462 0.00 0.00 32.76 4.16
99 100 9.587772 TTTTCTCTCGTTCTCAATTAATAGAGG 57.412 33.333 7.45 0.00 32.09 3.69
109 110 6.737254 ACTTTGTTTTTCTCTCGTTCTCAA 57.263 33.333 0.00 0.00 0.00 3.02
111 112 9.717892 AAAATACTTTGTTTTTCTCTCGTTCTC 57.282 29.630 0.00 0.00 0.00 2.87
142 143 9.959721 AGTCCTCATGTAGTTTGTACATATTTT 57.040 29.630 0.00 0.00 36.49 1.82
145 146 9.422681 AGTAGTCCTCATGTAGTTTGTACATAT 57.577 33.333 0.00 0.00 36.49 1.78
175 176 3.733380 CGAGTCTAGCAATGACACTGAGG 60.733 52.174 6.55 0.00 36.94 3.86
182 183 2.263077 CCACACGAGTCTAGCAATGAC 58.737 52.381 0.00 0.00 34.88 3.06
207 208 3.657448 AATGCATCGTCGGCGTCCA 62.657 57.895 10.18 5.54 39.49 4.02
210 211 2.923426 ATCCAATGCATCGTCGGCGT 62.923 55.000 10.18 0.00 39.49 5.68
212 213 1.394917 GATATCCAATGCATCGTCGGC 59.605 52.381 0.00 0.00 0.00 5.54
223 224 6.950041 CCACATACCATTTCAGGATATCCAAT 59.050 38.462 23.81 11.73 38.89 3.16
244 245 2.107366 TGCATCTCGAAGTATCCCACA 58.893 47.619 0.00 0.00 0.00 4.17
245 246 2.101582 AGTGCATCTCGAAGTATCCCAC 59.898 50.000 0.00 0.00 0.00 4.61
251 252 4.991153 ATCTGAAGTGCATCTCGAAGTA 57.009 40.909 0.00 0.00 0.00 2.24
257 258 6.095432 AGGTACATATCTGAAGTGCATCTC 57.905 41.667 0.00 0.00 0.00 2.75
259 260 6.051717 ACAAGGTACATATCTGAAGTGCATC 58.948 40.000 0.00 0.00 0.00 3.91
260 261 5.994250 ACAAGGTACATATCTGAAGTGCAT 58.006 37.500 0.00 0.00 0.00 3.96
262 263 4.811557 GGACAAGGTACATATCTGAAGTGC 59.188 45.833 0.00 0.00 0.00 4.40
263 264 5.360591 GGGACAAGGTACATATCTGAAGTG 58.639 45.833 0.00 0.00 0.00 3.16
264 265 4.099573 CGGGACAAGGTACATATCTGAAGT 59.900 45.833 0.00 0.00 0.00 3.01
265 266 4.099573 ACGGGACAAGGTACATATCTGAAG 59.900 45.833 0.00 0.00 0.00 3.02
266 267 4.028131 ACGGGACAAGGTACATATCTGAA 58.972 43.478 0.00 0.00 0.00 3.02
267 268 3.638860 ACGGGACAAGGTACATATCTGA 58.361 45.455 0.00 0.00 0.00 3.27
268 269 4.402056 AACGGGACAAGGTACATATCTG 57.598 45.455 0.00 0.00 0.00 2.90
280 295 2.152830 CGGGTGAAAATAACGGGACAA 58.847 47.619 0.00 0.00 0.00 3.18
281 296 1.810959 CGGGTGAAAATAACGGGACA 58.189 50.000 0.00 0.00 0.00 4.02
287 302 2.156098 TGTGGAGCGGGTGAAAATAAC 58.844 47.619 0.00 0.00 0.00 1.89
290 305 1.545582 CATTGTGGAGCGGGTGAAAAT 59.454 47.619 0.00 0.00 0.00 1.82
291 306 0.958091 CATTGTGGAGCGGGTGAAAA 59.042 50.000 0.00 0.00 0.00 2.29
345 362 2.195727 TCATAGGCACCACATCCAAGA 58.804 47.619 0.00 0.00 0.00 3.02
357 374 3.202818 AGGGTTGAATGTGATCATAGGCA 59.797 43.478 0.00 0.00 33.49 4.75
378 395 1.877637 TCACCAATCGGTCAACACAG 58.122 50.000 0.00 0.00 44.71 3.66
379 396 2.422597 GATCACCAATCGGTCAACACA 58.577 47.619 0.00 0.00 44.71 3.72
395 412 0.904649 AACTCCCTCATGCACGATCA 59.095 50.000 0.00 0.00 0.00 2.92
405 422 1.584724 GGATCCTTCCAACTCCCTCA 58.415 55.000 3.84 0.00 42.12 3.86
411 428 1.274416 TGGCTAGGGATCCTTCCAACT 60.274 52.381 12.58 1.13 44.60 3.16
463 481 5.186021 CCACCTCTGTAGTAGACTGTCATTT 59.814 44.000 10.88 0.00 0.00 2.32
480 498 1.187087 GGAGAATGTCGTCCACCTCT 58.813 55.000 0.00 0.00 32.55 3.69
492 510 2.440409 CCTCAACAACCCTGGAGAATG 58.560 52.381 0.00 0.00 0.00 2.67
503 521 5.880054 TTTATTAGCTCTGCCTCAACAAC 57.120 39.130 0.00 0.00 0.00 3.32
529 547 8.768955 CATCAATCTGTTACTAGCCTCATAAAC 58.231 37.037 0.00 0.00 0.00 2.01
543 563 5.939883 CAGTGGACCTTTCATCAATCTGTTA 59.060 40.000 0.00 0.00 0.00 2.41
548 568 4.836825 TCTCAGTGGACCTTTCATCAATC 58.163 43.478 0.00 0.00 0.00 2.67
550 570 3.903714 TCTCTCAGTGGACCTTTCATCAA 59.096 43.478 0.00 0.00 0.00 2.57
552 572 4.543590 TTCTCTCAGTGGACCTTTCATC 57.456 45.455 0.00 0.00 0.00 2.92
553 573 5.250313 AGAATTCTCTCAGTGGACCTTTCAT 59.750 40.000 0.88 0.00 0.00 2.57
556 576 4.805609 GCAGAATTCTCTCAGTGGACCTTT 60.806 45.833 4.57 0.00 0.00 3.11
563 583 5.754406 CCTTCATAGCAGAATTCTCTCAGTG 59.246 44.000 4.57 1.89 0.00 3.66
564 584 5.660417 TCCTTCATAGCAGAATTCTCTCAGT 59.340 40.000 4.57 0.00 0.00 3.41
566 586 6.744175 ATCCTTCATAGCAGAATTCTCTCA 57.256 37.500 4.57 0.00 0.00 3.27
568 588 7.160726 GCTAATCCTTCATAGCAGAATTCTCT 58.839 38.462 4.57 8.60 43.16 3.10
576 596 4.008330 CCATGGCTAATCCTTCATAGCAG 58.992 47.826 0.00 0.00 44.99 4.24
589 609 4.821805 GTGCTAAGCTATTTCCATGGCTAA 59.178 41.667 6.96 4.08 46.09 3.09
604 624 1.943340 GGCTGTATCAAGGTGCTAAGC 59.057 52.381 0.00 0.00 0.00 3.09
618 638 3.882102 ATTTGATATGCCAGGGCTGTA 57.118 42.857 12.19 5.26 42.51 2.74
622 642 4.405116 TCAAAATTTGATATGCCAGGGC 57.595 40.909 4.03 2.62 36.82 5.19
696 716 4.503714 AGAATACACGGTTTGGATGGAT 57.496 40.909 0.00 0.00 0.00 3.41
705 725 5.039333 GCGTTATCAGTAGAATACACGGTT 58.961 41.667 0.00 0.00 46.26 4.44
714 734 8.464404 ACACTTTACATAGCGTTATCAGTAGAA 58.536 33.333 0.00 0.00 0.00 2.10
718 738 7.769220 AGTACACTTTACATAGCGTTATCAGT 58.231 34.615 0.00 0.00 0.00 3.41
725 745 7.970061 TCGATTAAAGTACACTTTACATAGCGT 59.030 33.333 12.89 0.00 45.11 5.07
757 777 9.838339 ATAGAGTAATTGTTGATCGGAATCTTT 57.162 29.630 0.00 0.00 32.75 2.52
765 785 9.586150 GCACAATAATAGAGTAATTGTTGATCG 57.414 33.333 11.44 3.37 40.83 3.69
875 1040 6.767423 CCATTTCCTTTTTAGGCCATATTTGG 59.233 38.462 5.01 0.00 46.66 3.28
907 1073 1.340248 CTACGGCCACACCTAGGTATG 59.660 57.143 15.80 14.63 35.61 2.39
1055 1221 1.728425 GCTTGTTTAATTGGCTGCTGC 59.272 47.619 7.10 7.10 38.76 5.25
1423 1592 1.270907 GGCTCTTCTTCCTCCTGTCA 58.729 55.000 0.00 0.00 0.00 3.58
1444 1613 1.675641 CTTCTTGTTGGAGCCCGGG 60.676 63.158 19.09 19.09 0.00 5.73
1453 1622 1.871772 CCGCCTGCTCTTCTTGTTG 59.128 57.895 0.00 0.00 0.00 3.33
1454 1623 1.968540 GCCGCCTGCTCTTCTTGTT 60.969 57.895 0.00 0.00 36.87 2.83
1455 1624 2.359230 GCCGCCTGCTCTTCTTGT 60.359 61.111 0.00 0.00 36.87 3.16
1509 1678 3.733344 TTATCCTGCTCCGCGGTGC 62.733 63.158 37.92 37.92 32.22 5.01
1525 1703 0.815734 GCAGCTCCGTCAGGTAGTTA 59.184 55.000 0.00 0.00 39.05 2.24
1681 1859 3.875571 AGAATAATAGGAGGAGGGGGTG 58.124 50.000 0.00 0.00 0.00 4.61
1802 1983 4.339530 TCATCTCCGATCTAAGAACCACTG 59.660 45.833 0.00 0.00 0.00 3.66
1811 1992 6.791867 TTTTTCCTCTCATCTCCGATCTAA 57.208 37.500 0.00 0.00 0.00 2.10
1930 2111 5.957910 GAGTCGACTCAACCATATCTTTG 57.042 43.478 34.97 0.00 42.42 2.77
2062 2245 4.394729 TCAATGTCCCAAGTGGAGTTTAC 58.605 43.478 0.00 0.00 46.38 2.01
2077 2260 2.029244 CGCATACACCGAGTTCAATGTC 59.971 50.000 0.00 0.00 0.00 3.06
2083 2266 1.520787 CCCCGCATACACCGAGTTC 60.521 63.158 0.00 0.00 0.00 3.01
2086 2269 0.675522 AAAACCCCGCATACACCGAG 60.676 55.000 0.00 0.00 0.00 4.63
2089 2272 0.674269 TCGAAAACCCCGCATACACC 60.674 55.000 0.00 0.00 0.00 4.16
2117 2300 5.891551 ACTTTGGTTGTGTTCCTTTCACTAT 59.108 36.000 0.00 0.00 36.83 2.12
2122 2334 3.780902 CCACTTTGGTTGTGTTCCTTTC 58.219 45.455 0.00 0.00 33.92 2.62
2254 2466 5.066764 TCGTGTAGTATCCGATTCATGTTGA 59.933 40.000 0.00 0.00 0.00 3.18
2292 2504 2.097036 GGGGTTGGATACCTTTTTCCG 58.903 52.381 0.00 0.00 46.86 4.30
2304 2516 2.309162 TCGGACAATAATTGGGGTTGGA 59.691 45.455 0.00 0.00 34.12 3.53
2409 2627 6.535274 TTCTCAAGTAGCGGTTTAAACTTC 57.465 37.500 17.50 9.69 29.93 3.01
2435 2653 8.984891 ATTCGCAACAAGATTTATCATTTTGA 57.015 26.923 0.00 0.00 0.00 2.69
2659 2877 8.671384 AACAATACGTATTTAGCATACCACAT 57.329 30.769 18.06 0.00 0.00 3.21
2724 2952 1.002868 AGGTGCATCAGACACTGGC 60.003 57.895 0.00 0.00 38.14 4.85
2725 2953 0.322648 TGAGGTGCATCAGACACTGG 59.677 55.000 0.00 0.00 38.14 4.00
2771 2999 1.182667 GGTGTTAGTGAATTGGCCCC 58.817 55.000 0.00 0.00 0.00 5.80


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

AutoCloner maintained by Alex Coulton.