Multiple sequence alignment - TraesCS5B01G516400

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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 TraesCS5B01G516400 chr5B 100.000 3101 0 0 1 3101 680606580 680603480 0.000000e+00 5727.0
1 TraesCS5B01G516400 chr5B 94.118 51 3 0 1916 1966 680604629 680604579 9.220000e-11 78.7
2 TraesCS5B01G516400 chr5B 94.118 51 3 0 1952 2002 680604665 680604615 9.220000e-11 78.7
3 TraesCS5B01G516400 chr5D 92.895 2421 118 20 713 3101 539027006 539024608 0.000000e+00 3469.0
4 TraesCS5B01G516400 chr5D 94.118 51 3 0 1916 1966 539025742 539025692 9.220000e-11 78.7
5 TraesCS5B01G516400 chr4A 91.653 1881 94 20 1232 3101 629475111 629476939 0.000000e+00 2545.0
6 TraesCS5B01G516400 chr4A 88.650 1348 74 31 1 1315 629473812 629475113 0.000000e+00 1568.0


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 TraesCS5B01G516400 chr5B 680603480 680606580 3100 True 1961.466667 5727 96.078667 1 3101 3 chr5B.!!$R1 3100
1 TraesCS5B01G516400 chr5D 539024608 539027006 2398 True 1773.850000 3469 93.506500 713 3101 2 chr5D.!!$R1 2388
2 TraesCS5B01G516400 chr4A 629473812 629476939 3127 False 2056.500000 2545 90.151500 1 3101 2 chr4A.!!$F1 3100

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
254 270 0.037697 TGTTTGCTCAGCCGTCGTAT 60.038 50.0 0.0 0.0 0.0 3.06 F
539 568 0.180642 TTCCAAACACAGGGCACGTA 59.819 50.0 0.0 0.0 0.0 3.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1536 1669 1.003580 ACCACCTGCACATTACCAGAG 59.996 52.381 0.00 0.00 0.0 3.35 R
2321 2467 0.611618 CAAACATGTAGGGCCCAGCA 60.612 55.000 27.56 22.47 0.0 4.41 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
20 21 1.530323 ATATAAAATCCCCGCGCCAC 58.470 50.000 0.00 0.00 0.00 5.01
28 29 2.202703 CCCGCGCCACTACTGTAC 60.203 66.667 0.00 0.00 0.00 2.90
71 72 0.250295 CTCTGCTCCGGTCAACCAAA 60.250 55.000 0.00 0.00 35.14 3.28
106 111 4.477975 CGCCCTCGTCTCCGTCAC 62.478 72.222 0.00 0.00 35.01 3.67
107 112 4.131088 GCCCTCGTCTCCGTCACC 62.131 72.222 0.00 0.00 35.01 4.02
108 113 3.812019 CCCTCGTCTCCGTCACCG 61.812 72.222 0.00 0.00 35.01 4.94
136 141 2.487428 CTCGCAGGTGAGGTCTCG 59.513 66.667 1.92 0.00 32.18 4.04
137 142 3.691744 CTCGCAGGTGAGGTCTCGC 62.692 68.421 1.92 3.14 39.26 5.03
177 182 0.789383 GCGACCAAGTTTCGATTGCG 60.789 55.000 1.17 0.00 38.85 4.85
218 234 0.536460 GAGTTTCGGCCCTGTTTCCA 60.536 55.000 0.00 0.00 0.00 3.53
246 262 4.389576 CCCGCGTGTTTGCTCAGC 62.390 66.667 4.92 0.00 0.00 4.26
250 266 2.551270 CGTGTTTGCTCAGCCGTC 59.449 61.111 0.00 0.00 0.00 4.79
251 267 2.551270 GTGTTTGCTCAGCCGTCG 59.449 61.111 0.00 0.00 0.00 5.12
252 268 2.108157 TGTTTGCTCAGCCGTCGT 59.892 55.556 0.00 0.00 0.00 4.34
253 269 0.942410 GTGTTTGCTCAGCCGTCGTA 60.942 55.000 0.00 0.00 0.00 3.43
254 270 0.037697 TGTTTGCTCAGCCGTCGTAT 60.038 50.000 0.00 0.00 0.00 3.06
255 271 1.202817 TGTTTGCTCAGCCGTCGTATA 59.797 47.619 0.00 0.00 0.00 1.47
256 272 1.852895 GTTTGCTCAGCCGTCGTATAG 59.147 52.381 0.00 0.00 0.00 1.31
257 273 0.248907 TTGCTCAGCCGTCGTATAGC 60.249 55.000 0.00 0.00 0.00 2.97
258 274 1.359117 GCTCAGCCGTCGTATAGCA 59.641 57.895 0.00 0.00 0.00 3.49
259 275 0.661780 GCTCAGCCGTCGTATAGCAG 60.662 60.000 0.00 0.00 0.00 4.24
260 276 0.945099 CTCAGCCGTCGTATAGCAGA 59.055 55.000 0.00 0.00 0.00 4.26
261 277 0.945099 TCAGCCGTCGTATAGCAGAG 59.055 55.000 0.00 0.00 0.00 3.35
262 278 0.663688 CAGCCGTCGTATAGCAGAGT 59.336 55.000 0.00 0.00 0.00 3.24
283 299 1.464997 CTGGTTTTGGTTAGAGAGCGC 59.535 52.381 0.00 0.00 0.00 5.92
286 302 2.143925 GTTTTGGTTAGAGAGCGCTGT 58.856 47.619 18.48 12.55 0.00 4.40
287 303 2.543777 TTTGGTTAGAGAGCGCTGTT 57.456 45.000 18.48 1.45 0.00 3.16
303 319 1.001974 CTGTTGAATCAGGTCGGGTGA 59.998 52.381 0.00 0.00 0.00 4.02
307 323 1.017387 GAATCAGGTCGGGTGATTGC 58.983 55.000 11.10 2.66 43.26 3.56
308 324 0.394352 AATCAGGTCGGGTGATTGCC 60.394 55.000 6.92 0.00 41.96 4.52
309 325 2.270874 ATCAGGTCGGGTGATTGCCC 62.271 60.000 0.00 0.00 45.21 5.36
318 334 1.114627 GGTGATTGCCCAGGATTTCC 58.885 55.000 0.00 0.00 0.00 3.13
319 335 1.619432 GGTGATTGCCCAGGATTTCCA 60.619 52.381 0.00 0.00 38.89 3.53
405 426 4.821805 CCCAACGGCACATCTAAGATTTAT 59.178 41.667 0.00 0.00 0.00 1.40
406 427 5.299279 CCCAACGGCACATCTAAGATTTATT 59.701 40.000 0.00 0.00 0.00 1.40
407 428 6.485313 CCCAACGGCACATCTAAGATTTATTA 59.515 38.462 0.00 0.00 0.00 0.98
425 446 1.922570 TAAGCTTACTGTAGCGCTGC 58.077 50.000 22.90 21.06 45.82 5.25
458 480 1.615262 CCCCCTGGATGGAAGAACC 59.385 63.158 0.00 0.00 38.35 3.62
469 491 1.168714 GGAAGAACCGAGCATGCTTT 58.831 50.000 23.61 12.64 0.00 3.51
479 501 2.618241 CGAGCATGCTTTTAGGGCATAA 59.382 45.455 23.61 0.00 46.94 1.90
480 502 3.254166 CGAGCATGCTTTTAGGGCATAAT 59.746 43.478 23.61 0.00 46.94 1.28
483 510 3.495753 GCATGCTTTTAGGGCATAATTGC 59.504 43.478 11.37 8.87 46.94 3.56
488 515 6.239402 ATGCTTTTAGGGCATAATTGCTAAGG 60.239 38.462 14.36 0.00 46.81 2.69
500 527 9.358872 GCATAATTGCTAAGGAATTATTAAGGC 57.641 33.333 8.98 6.86 45.77 4.35
501 528 9.559958 CATAATTGCTAAGGAATTATTAAGGCG 57.440 33.333 8.98 0.00 34.96 5.52
537 566 0.673437 ATTTCCAAACACAGGGCACG 59.327 50.000 0.00 0.00 0.00 5.34
538 567 0.681564 TTTCCAAACACAGGGCACGT 60.682 50.000 0.00 0.00 0.00 4.49
539 568 0.180642 TTCCAAACACAGGGCACGTA 59.819 50.000 0.00 0.00 0.00 3.57
540 569 0.250124 TCCAAACACAGGGCACGTAG 60.250 55.000 0.00 0.00 0.00 3.51
541 570 0.250124 CCAAACACAGGGCACGTAGA 60.250 55.000 0.00 0.00 0.00 2.59
542 571 1.148310 CAAACACAGGGCACGTAGAG 58.852 55.000 0.00 0.00 0.00 2.43
545 574 1.251527 ACACAGGGCACGTAGAGGAG 61.252 60.000 0.00 0.00 0.00 3.69
560 589 2.090606 AGAGGAGAGGAAGATCCAGCAT 60.091 50.000 0.00 0.00 39.61 3.79
564 593 4.531732 AGGAGAGGAAGATCCAGCATAATC 59.468 45.833 0.00 0.00 39.61 1.75
573 602 3.281727 TCCAGCATAATCGCTTTTCCT 57.718 42.857 0.00 0.00 41.38 3.36
593 622 8.682936 TTTCCTTTTATTTTGCAATTTAGCCA 57.317 26.923 0.00 0.00 0.00 4.75
600 629 1.381735 GCAATTTAGCCAGGGCCCT 60.382 57.895 22.28 22.28 43.17 5.19
627 656 1.144565 CTCAGGACAGCGAATCTGCG 61.145 60.000 0.00 0.00 46.76 5.18
636 665 0.385223 GCGAATCTGCGATGCCATTC 60.385 55.000 0.00 2.17 0.00 2.67
641 670 1.825090 TCTGCGATGCCATTCTGTTT 58.175 45.000 0.00 0.00 0.00 2.83
647 676 2.855963 CGATGCCATTCTGTTTTGATGC 59.144 45.455 0.00 0.00 0.00 3.91
706 735 0.604780 TTCTCTTCTGCTGTGCTGCC 60.605 55.000 0.00 0.00 0.00 4.85
729 758 3.817647 CTGCTTCTGCTTCCTGTAAACTT 59.182 43.478 0.00 0.00 40.48 2.66
733 762 3.751518 TCTGCTTCCTGTAAACTTTCCC 58.248 45.455 0.00 0.00 0.00 3.97
747 776 3.989056 ACTTTCCCCTTCTCCACAAAAA 58.011 40.909 0.00 0.00 0.00 1.94
805 835 2.867975 GCCTATTGACAAATTGCCATGC 59.132 45.455 0.00 0.00 0.00 4.06
815 845 4.247258 CAAATTGCCATGCTCAGCTTTTA 58.753 39.130 0.00 0.00 0.00 1.52
858 896 4.715527 ACTAACTCTTTGCGGTACCTAG 57.284 45.455 10.90 4.02 0.00 3.02
862 901 2.100989 CTCTTTGCGGTACCTAGGAGT 58.899 52.381 17.98 0.00 0.00 3.85
871 915 4.800914 GCGGTACCTAGGAGTACTTATCGA 60.801 50.000 17.98 0.00 41.93 3.59
874 918 6.429385 CGGTACCTAGGAGTACTTATCGATTT 59.571 42.308 17.98 0.00 41.93 2.17
877 921 5.539193 ACCTAGGAGTACTTATCGATTTGGG 59.461 44.000 17.98 0.00 0.00 4.12
904 948 7.872483 GGGTGAATGAACAGAAATATTTGTTGT 59.128 33.333 5.17 7.21 37.63 3.32
965 1011 4.284746 AGCTCTAACAGTTTCTTACCTGCT 59.715 41.667 0.00 0.00 0.00 4.24
979 1025 1.074405 ACCTGCTCATGTGTTGGATGT 59.926 47.619 12.69 0.00 0.00 3.06
981 1027 0.883153 TGCTCATGTGTTGGATGTGC 59.117 50.000 0.00 0.00 39.61 4.57
1154 1201 8.044060 TGGTCATTGATTCTCTGTTTACAATC 57.956 34.615 0.00 0.00 0.00 2.67
1168 1215 7.013750 TCTGTTTACAATCCAACAACTGCATAA 59.986 33.333 0.00 0.00 32.53 1.90
1296 1346 5.256474 TGTCTTGGAGATCAATCTTTTCCC 58.744 41.667 0.00 0.00 37.25 3.97
1302 1352 5.252863 TGGAGATCAATCTTTTCCCCAGTTA 59.747 40.000 0.00 0.00 37.25 2.24
1304 1354 7.128728 TGGAGATCAATCTTTTCCCCAGTTATA 59.871 37.037 0.00 0.00 37.25 0.98
1308 1439 9.136323 GATCAATCTTTTCCCCAGTTATATGTT 57.864 33.333 0.00 0.00 0.00 2.71
1318 1449 5.357032 CCCCAGTTATATGTTCAACCTTGAC 59.643 44.000 0.00 0.00 36.83 3.18
1335 1466 4.878397 CCTTGACACAATAGAGCTTTAGGG 59.122 45.833 0.00 0.00 0.00 3.53
1341 1472 5.104527 ACACAATAGAGCTTTAGGGCATACA 60.105 40.000 0.00 0.00 34.17 2.29
1342 1473 5.822519 CACAATAGAGCTTTAGGGCATACAA 59.177 40.000 0.00 0.00 34.17 2.41
1351 1482 6.268387 AGCTTTAGGGCATACAATTGCATATT 59.732 34.615 5.05 0.00 44.59 1.28
1437 1568 7.583230 TGAATTGTTTTGCAAATATTGGCTTC 58.417 30.769 13.65 9.46 40.91 3.86
1460 1591 2.636647 TTGGTTGACTGAGTGATGCA 57.363 45.000 0.00 0.00 0.00 3.96
1461 1592 2.865119 TGGTTGACTGAGTGATGCAT 57.135 45.000 0.00 0.00 0.00 3.96
1462 1593 3.144657 TGGTTGACTGAGTGATGCATT 57.855 42.857 0.00 0.00 0.00 3.56
1463 1594 3.489355 TGGTTGACTGAGTGATGCATTT 58.511 40.909 0.00 0.00 0.00 2.32
1494 1627 6.984474 ACCTTCACAACTATTCCACATATACG 59.016 38.462 0.00 0.00 0.00 3.06
1499 1632 8.198778 TCACAACTATTCCACATATACGCTTTA 58.801 33.333 0.00 0.00 0.00 1.85
1557 1690 1.003118 TCTGGTAATGTGCAGGTGGTC 59.997 52.381 0.00 0.00 0.00 4.02
1818 1957 0.179018 GTGGGGACTGCTTCAAGTGT 60.179 55.000 0.00 0.00 0.00 3.55
1860 1999 0.835941 GAGAGTGCCCAGATGGTGAT 59.164 55.000 0.00 0.00 36.04 3.06
1925 2064 1.272258 TGGTGGTAGATCTGACCGTGA 60.272 52.381 5.18 0.00 40.09 4.35
2152 2297 6.996180 TCCAGGTATGAAAACCCTATCTAG 57.004 41.667 0.00 0.00 40.71 2.43
2321 2467 2.905736 ACTTGGCCATAAAATGCTTGGT 59.094 40.909 6.09 0.00 32.90 3.67
2385 2531 0.957888 GCTTGGTTGAGAGGTGGCTC 60.958 60.000 0.00 0.00 35.46 4.70
2535 2681 9.598517 ACTAAACTTTGCTTGAAAAATTCATCA 57.401 25.926 0.00 0.00 39.84 3.07
2615 2762 5.835257 TCTCTTTCAATGCTCTGTTTTTGG 58.165 37.500 0.00 0.00 0.00 3.28
2625 2772 5.136828 TGCTCTGTTTTTGGGATTGAGTTA 58.863 37.500 0.00 0.00 0.00 2.24
2689 2836 5.238432 CCTTTTGGGTTGCTTATTTTGTTCC 59.762 40.000 0.00 0.00 35.46 3.62
2734 2881 8.533657 TCTTCCTTCCGTTGTTGTCTAATAATA 58.466 33.333 0.00 0.00 0.00 0.98
2737 2884 7.550196 TCCTTCCGTTGTTGTCTAATAATAACC 59.450 37.037 0.00 0.00 0.00 2.85
2742 2889 6.019318 CGTTGTTGTCTAATAATAACCGAGGG 60.019 42.308 0.00 0.00 0.00 4.30
2823 2970 1.820519 CTGCAGCCTGCCTAAAAATGA 59.179 47.619 15.29 0.00 44.23 2.57
2826 2973 2.817901 CAGCCTGCCTAAAAATGATGC 58.182 47.619 0.00 0.00 0.00 3.91
2840 2988 1.079612 GATGCTTGTGCCTTTGCCC 60.080 57.895 0.00 0.00 38.71 5.36
2846 2994 1.398958 TTGTGCCTTTGCCCCTGTTC 61.399 55.000 0.00 0.00 36.33 3.18
2848 2996 4.056125 GCCTTTGCCCCTGTTCGC 62.056 66.667 0.00 0.00 0.00 4.70
2857 3005 2.978010 CCTGTTCGCCGGCTTTGT 60.978 61.111 26.68 0.00 0.00 2.83
2974 3122 0.235926 TCGTCGCTAGAGATGCATCG 59.764 55.000 20.67 8.90 0.00 3.84
2981 3129 1.069823 CTAGAGATGCATCGTTGGGCT 59.930 52.381 20.67 13.72 0.00 5.19
3002 3150 1.514228 GTTCGTCGCGAGAGATGCA 60.514 57.895 10.24 0.00 43.49 3.96
3007 3155 1.298638 TCGCGAGAGATGCACATCG 60.299 57.895 3.71 0.00 42.48 3.84
3018 3166 3.750130 AGATGCACATCGGAATAATGCTC 59.250 43.478 5.04 0.00 42.48 4.26
3025 3175 4.202253 ACATCGGAATAATGCTCAGCTACA 60.202 41.667 0.00 0.00 0.00 2.74
3033 3183 2.827800 TGCTCAGCTACATGGCTATC 57.172 50.000 0.00 0.00 41.00 2.08
3049 3199 2.542411 GCTATCCTTCTTTGGCAATGCG 60.542 50.000 0.00 0.00 0.00 4.73
3085 3235 5.100259 CAGGTTCCGTTAGTATGTAGTGTG 58.900 45.833 0.00 0.00 0.00 3.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 0.026027 GAGACCGCGTCGTACAGTAG 59.974 60.000 4.92 0.00 37.67 2.57
28 29 3.878519 GGAGGAGAGACCGCGTCG 61.879 72.222 4.92 0.00 44.74 5.12
49 50 0.179097 GGTTGACCGGAGCAGAGATC 60.179 60.000 9.46 0.00 0.00 2.75
71 72 2.592308 GCTTGGGAAGCGGAGGAT 59.408 61.111 0.00 0.00 45.74 3.24
157 162 0.454452 GCAATCGAAACTTGGTCGCC 60.454 55.000 0.00 0.00 38.39 5.54
177 182 3.462678 GGAGAGCCACCTCCCGTC 61.463 72.222 6.21 0.00 45.44 4.79
228 244 2.972505 CTGAGCAAACACGCGGGT 60.973 61.111 9.01 9.01 36.85 5.28
235 251 0.037697 ATACGACGGCTGAGCAAACA 60.038 50.000 6.82 0.00 0.00 2.83
246 262 1.264557 CCAGACTCTGCTATACGACGG 59.735 57.143 0.00 0.00 0.00 4.79
250 266 3.865745 CCAAAACCAGACTCTGCTATACG 59.134 47.826 0.00 0.00 0.00 3.06
251 267 4.833390 ACCAAAACCAGACTCTGCTATAC 58.167 43.478 0.00 0.00 0.00 1.47
252 268 5.499004 AACCAAAACCAGACTCTGCTATA 57.501 39.130 0.00 0.00 0.00 1.31
253 269 4.373156 AACCAAAACCAGACTCTGCTAT 57.627 40.909 0.00 0.00 0.00 2.97
254 270 3.857157 AACCAAAACCAGACTCTGCTA 57.143 42.857 0.00 0.00 0.00 3.49
255 271 2.736670 AACCAAAACCAGACTCTGCT 57.263 45.000 0.00 0.00 0.00 4.24
256 272 3.740115 TCTAACCAAAACCAGACTCTGC 58.260 45.455 0.00 0.00 0.00 4.26
257 273 5.215252 TCTCTAACCAAAACCAGACTCTG 57.785 43.478 0.00 0.00 0.00 3.35
258 274 4.262678 GCTCTCTAACCAAAACCAGACTCT 60.263 45.833 0.00 0.00 0.00 3.24
259 275 3.997681 GCTCTCTAACCAAAACCAGACTC 59.002 47.826 0.00 0.00 0.00 3.36
260 276 3.555168 CGCTCTCTAACCAAAACCAGACT 60.555 47.826 0.00 0.00 0.00 3.24
261 277 2.737252 CGCTCTCTAACCAAAACCAGAC 59.263 50.000 0.00 0.00 0.00 3.51
262 278 2.870435 GCGCTCTCTAACCAAAACCAGA 60.870 50.000 0.00 0.00 0.00 3.86
283 299 1.001974 TCACCCGACCTGATTCAACAG 59.998 52.381 0.00 0.00 37.61 3.16
286 302 2.710377 CAATCACCCGACCTGATTCAA 58.290 47.619 0.00 0.00 36.42 2.69
287 303 1.678728 GCAATCACCCGACCTGATTCA 60.679 52.381 0.00 0.00 36.42 2.57
303 319 2.967887 GCTATTGGAAATCCTGGGCAAT 59.032 45.455 0.44 0.00 36.82 3.56
307 323 2.590821 CAGGCTATTGGAAATCCTGGG 58.409 52.381 0.44 0.00 40.34 4.45
308 324 1.959282 GCAGGCTATTGGAAATCCTGG 59.041 52.381 8.44 0.00 43.31 4.45
309 325 2.941480 AGCAGGCTATTGGAAATCCTG 58.059 47.619 0.44 2.43 45.26 3.86
310 326 3.718956 AGTAGCAGGCTATTGGAAATCCT 59.281 43.478 4.06 0.00 36.82 3.24
311 327 4.068599 GAGTAGCAGGCTATTGGAAATCC 58.931 47.826 4.06 0.00 0.00 3.01
312 328 4.068599 GGAGTAGCAGGCTATTGGAAATC 58.931 47.826 4.06 0.00 0.00 2.17
313 329 3.495100 CGGAGTAGCAGGCTATTGGAAAT 60.495 47.826 4.06 0.00 0.00 2.17
314 330 2.158957 CGGAGTAGCAGGCTATTGGAAA 60.159 50.000 4.06 0.00 0.00 3.13
315 331 1.412710 CGGAGTAGCAGGCTATTGGAA 59.587 52.381 4.06 0.00 0.00 3.53
316 332 1.040646 CGGAGTAGCAGGCTATTGGA 58.959 55.000 4.06 0.00 0.00 3.53
317 333 1.040646 TCGGAGTAGCAGGCTATTGG 58.959 55.000 4.06 0.00 0.00 3.16
318 334 2.681706 CATCGGAGTAGCAGGCTATTG 58.318 52.381 4.06 0.00 0.00 1.90
319 335 1.001406 GCATCGGAGTAGCAGGCTATT 59.999 52.381 4.06 0.00 0.00 1.73
348 364 1.449956 GAGGCAGAAGGAGCAGCAG 60.450 63.158 0.00 0.00 0.00 4.24
405 426 2.094182 AGCAGCGCTACAGTAAGCTTAA 60.094 45.455 10.99 0.00 40.49 1.85
406 427 1.476891 AGCAGCGCTACAGTAAGCTTA 59.523 47.619 10.99 0.86 40.49 3.09
407 428 0.247736 AGCAGCGCTACAGTAAGCTT 59.752 50.000 10.99 3.48 40.49 3.74
446 468 1.303309 CATGCTCGGTTCTTCCATCC 58.697 55.000 0.00 0.00 35.57 3.51
454 476 1.401905 CCCTAAAAGCATGCTCGGTTC 59.598 52.381 22.93 0.00 0.00 3.62
458 480 2.481212 TGCCCTAAAAGCATGCTCG 58.519 52.632 22.93 9.79 34.69 5.03
479 501 5.048013 GCCGCCTTAATAATTCCTTAGCAAT 60.048 40.000 0.00 0.00 0.00 3.56
480 502 4.277423 GCCGCCTTAATAATTCCTTAGCAA 59.723 41.667 0.00 0.00 0.00 3.91
483 510 4.652822 AGGCCGCCTTAATAATTCCTTAG 58.347 43.478 5.94 0.00 0.00 2.18
488 515 3.304726 GCAGAAGGCCGCCTTAATAATTC 60.305 47.826 24.89 10.64 44.82 2.17
499 526 0.038343 TGAATTTTGCAGAAGGCCGC 60.038 50.000 0.00 0.00 43.89 6.53
500 527 2.660189 ATGAATTTTGCAGAAGGCCG 57.340 45.000 0.00 0.00 43.89 6.13
501 528 3.686241 GGAAATGAATTTTGCAGAAGGCC 59.314 43.478 0.00 0.00 43.89 5.19
537 566 2.890945 GCTGGATCTTCCTCTCCTCTAC 59.109 54.545 0.00 0.00 37.46 2.59
538 567 2.515853 TGCTGGATCTTCCTCTCCTCTA 59.484 50.000 0.00 0.00 37.46 2.43
539 568 1.290431 TGCTGGATCTTCCTCTCCTCT 59.710 52.381 0.00 0.00 37.46 3.69
540 569 1.786937 TGCTGGATCTTCCTCTCCTC 58.213 55.000 0.00 0.00 37.46 3.71
541 570 2.493099 ATGCTGGATCTTCCTCTCCT 57.507 50.000 0.00 0.00 37.46 3.69
542 571 4.620332 CGATTATGCTGGATCTTCCTCTCC 60.620 50.000 0.00 0.00 37.46 3.71
545 574 2.999355 GCGATTATGCTGGATCTTCCTC 59.001 50.000 0.00 0.00 37.46 3.71
560 589 8.594881 TTGCAAAATAAAAGGAAAAGCGATTA 57.405 26.923 0.00 0.00 0.00 1.75
564 593 9.316859 CTAAATTGCAAAATAAAAGGAAAAGCG 57.683 29.630 1.71 0.00 0.00 4.68
573 602 5.414144 GCCCTGGCTAAATTGCAAAATAAAA 59.586 36.000 1.71 0.00 38.26 1.52
600 629 2.673200 GCTGTCCTGAGATGCCCCA 61.673 63.158 0.00 0.00 0.00 4.96
613 642 1.275066 GCATCGCAGATTCGCTGTC 59.725 57.895 0.00 0.00 46.62 3.51
627 656 3.192466 GGCATCAAAACAGAATGGCATC 58.808 45.455 0.00 0.00 43.62 3.91
636 665 1.891150 AGAAGCTGGGCATCAAAACAG 59.109 47.619 0.00 0.00 0.00 3.16
641 670 3.548770 CAGAATAGAAGCTGGGCATCAA 58.451 45.455 0.00 0.00 0.00 2.57
706 735 2.479566 TTACAGGAAGCAGAAGCAGG 57.520 50.000 0.00 0.00 45.49 4.85
747 776 8.147704 GCTCTTCTAAGCTAAACTGGATATCTT 58.852 37.037 2.05 0.00 39.27 2.40
828 866 6.225318 ACCGCAAAGAGTTAGTACATGTTAA 58.775 36.000 2.30 0.00 0.00 2.01
832 870 4.565564 GGTACCGCAAAGAGTTAGTACATG 59.434 45.833 0.00 0.00 33.41 3.21
858 896 4.004196 CCCCCAAATCGATAAGTACTCC 57.996 50.000 0.00 0.00 0.00 3.85
877 921 6.935167 ACAAATATTTCTGTTCATTCACCCC 58.065 36.000 0.00 0.00 0.00 4.95
904 948 6.701340 AGAGCAATACAGATTATATGGCGAA 58.299 36.000 0.00 0.00 34.61 4.70
965 1011 2.585330 ACAAGCACATCCAACACATGA 58.415 42.857 0.00 0.00 0.00 3.07
979 1025 2.642311 TCACTGGGAGGATAAACAAGCA 59.358 45.455 0.00 0.00 0.00 3.91
981 1027 4.202441 CCATCACTGGGAGGATAAACAAG 58.798 47.826 0.00 0.00 39.04 3.16
1118 1165 6.243900 AGAATCAATGACCAAGAGATTGTGT 58.756 36.000 0.00 0.00 0.00 3.72
1154 1201 4.481930 TTCGAACTTATGCAGTTGTTGG 57.518 40.909 0.00 5.31 46.53 3.77
1168 1215 7.438459 CGTAGGATCAGGAAAATAATTCGAACT 59.562 37.037 0.00 0.00 0.00 3.01
1203 1250 6.954487 ATTGCTTCATCAATGCTCTATCAA 57.046 33.333 0.00 0.00 35.52 2.57
1278 1328 3.593328 ACTGGGGAAAAGATTGATCTCCA 59.407 43.478 0.00 0.00 35.76 3.86
1279 1329 4.242336 ACTGGGGAAAAGATTGATCTCC 57.758 45.455 0.00 0.00 35.76 3.71
1296 1346 6.429692 TGTGTCAAGGTTGAACATATAACTGG 59.570 38.462 0.00 0.00 39.21 4.00
1302 1352 7.066284 GCTCTATTGTGTCAAGGTTGAACATAT 59.934 37.037 0.00 2.76 39.21 1.78
1304 1354 5.182001 GCTCTATTGTGTCAAGGTTGAACAT 59.818 40.000 0.00 0.00 39.21 2.71
1308 1439 4.623932 AGCTCTATTGTGTCAAGGTTGA 57.376 40.909 0.00 0.00 34.20 3.18
1318 1449 5.368145 TGTATGCCCTAAAGCTCTATTGTG 58.632 41.667 0.00 0.00 0.00 3.33
1360 1491 9.116080 ACATTCCAGATATAATCAATACTGGGA 57.884 33.333 0.00 0.00 38.53 4.37
1407 1538 8.732531 CCAATATTTGCAAAACAATTCAGGAAT 58.267 29.630 17.19 0.00 38.31 3.01
1437 1568 4.637091 TGCATCACTCAGTCAACCAATATG 59.363 41.667 0.00 0.00 0.00 1.78
1494 1627 5.909610 GCTCATGATGAATAAACGGTAAAGC 59.090 40.000 0.00 0.00 0.00 3.51
1499 1632 6.515272 AAAAGCTCATGATGAATAAACGGT 57.485 33.333 0.00 0.00 0.00 4.83
1533 1666 3.614092 CACCTGCACATTACCAGAGAAT 58.386 45.455 0.00 0.00 0.00 2.40
1536 1669 1.003580 ACCACCTGCACATTACCAGAG 59.996 52.381 0.00 0.00 0.00 3.35
1557 1690 2.878406 ACGTCCAGAAAACTTGTCCATG 59.122 45.455 0.00 0.00 0.00 3.66
1795 1928 1.352622 TTGAAGCAGTCCCCACCACT 61.353 55.000 0.00 0.00 0.00 4.00
1818 1957 1.110442 CAAAGTGTCCAGGTTTGCCA 58.890 50.000 0.00 0.00 37.19 4.92
1925 2064 4.657824 CGCCACGGTCAGAACGGT 62.658 66.667 13.63 0.00 39.31 4.83
2152 2297 5.003804 ACAAGGAAACACACCTCATGATAC 58.996 41.667 0.00 0.00 36.67 2.24
2321 2467 0.611618 CAAACATGTAGGGCCCAGCA 60.612 55.000 27.56 22.47 0.00 4.41
2385 2531 2.534019 AACACACAGCGCGACCAAG 61.534 57.895 12.10 0.00 0.00 3.61
2535 2681 1.145119 GTCACCTCCCCCTTTTCTTGT 59.855 52.381 0.00 0.00 0.00 3.16
2689 2836 1.010419 AACCGAACGAAACCGATCCG 61.010 55.000 0.00 0.00 0.00 4.18
2734 2881 1.152830 AACCAACATGCCCTCGGTT 59.847 52.632 0.00 0.00 35.13 4.44
2737 2884 1.133025 GAATCAACCAACATGCCCTCG 59.867 52.381 0.00 0.00 0.00 4.63
2767 2914 4.256920 CTCCAATGGCTATGGTATACTGC 58.743 47.826 2.25 2.97 39.09 4.40
2823 2970 3.062639 GGGCAAAGGCACAAGCAT 58.937 55.556 0.00 0.00 45.12 3.79
2840 2988 1.231958 TAACAAAGCCGGCGAACAGG 61.232 55.000 23.20 11.27 0.00 4.00
2846 2994 2.686816 CCAGGTAACAAAGCCGGCG 61.687 63.158 23.20 9.91 41.41 6.46
2848 2996 0.250553 TGACCAGGTAACAAAGCCGG 60.251 55.000 0.00 0.00 41.41 6.13
2857 3005 2.775384 ACAAACTCCAGTGACCAGGTAA 59.225 45.455 0.00 0.00 0.00 2.85
2974 3122 2.935955 CGACGAACACAGCCCAAC 59.064 61.111 0.00 0.00 0.00 3.77
2981 3129 0.454452 CATCTCTCGCGACGAACACA 60.454 55.000 3.71 0.00 34.74 3.72
3002 3150 3.482156 AGCTGAGCATTATTCCGATGT 57.518 42.857 7.39 0.00 0.00 3.06
3007 3155 3.190118 GCCATGTAGCTGAGCATTATTCC 59.810 47.826 7.39 0.00 0.00 3.01
3018 3166 4.348863 AAGAAGGATAGCCATGTAGCTG 57.651 45.455 0.00 0.00 44.67 4.24
3025 3175 3.386932 TTGCCAAAGAAGGATAGCCAT 57.613 42.857 0.00 0.00 36.29 4.40
3033 3183 4.173971 GCGCATTGCCAAAGAAGG 57.826 55.556 0.30 0.00 37.76 3.46


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

AutoCloner maintained by Alex Coulton.