Multiple sequence alignment - TraesCS2B01G267500

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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 TraesCS2B01G267500 chr2B 100.000 3206 0 0 1 3206 360483698 360480493 0.000000e+00 5921
1 TraesCS2B01G267500 chr2A 94.834 2284 85 15 1 2279 387774918 387777173 0.000000e+00 3533
2 TraesCS2B01G267500 chr2A 89.818 658 58 5 2262 2913 387777793 387778447 0.000000e+00 835
3 TraesCS2B01G267500 chr2A 89.147 129 11 1 3075 3203 387778447 387778572 1.190000e-34 158
4 TraesCS2B01G267500 chr2D 95.833 1680 33 8 701 2367 307155263 307156918 0.000000e+00 2680
5 TraesCS2B01G267500 chr2D 86.039 659 72 6 2553 3200 307156907 307157556 0.000000e+00 689
6 TraesCS2B01G267500 chr2D 88.849 278 22 6 226 502 307136963 307137232 1.840000e-87 333
7 TraesCS2B01G267500 chr2D 91.518 224 18 1 1 224 307129355 307129577 1.120000e-79 307
8 TraesCS2B01G267500 chr2D 86.813 182 21 3 497 678 307146716 307146894 1.950000e-47 200


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 TraesCS2B01G267500 chr2B 360480493 360483698 3205 True 5921.000000 5921 100.000000 1 3206 1 chr2B.!!$R1 3205
1 TraesCS2B01G267500 chr2A 387774918 387778572 3654 False 1508.666667 3533 91.266333 1 3203 3 chr2A.!!$F1 3202
2 TraesCS2B01G267500 chr2D 307155263 307157556 2293 False 1684.500000 2680 90.936000 701 3200 2 chr2D.!!$F4 2499

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
509 520 0.178068 ACGAGCGTTATTCCCTGCAT 59.822 50.0 0.0 0.0 0.0 3.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2475 3136 0.460459 TCGTCATCTCGAGCTCGACT 60.46 55.0 33.84 21.06 44.22 4.18 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
46 47 8.503196 GGGTCAAATTCCATCAAAATTAACAAC 58.497 33.333 0.00 0.00 0.00 3.32
51 52 8.879342 AATTCCATCAAAATTAACAACGAACA 57.121 26.923 0.00 0.00 0.00 3.18
54 55 6.799441 TCCATCAAAATTAACAACGAACATCG 59.201 34.615 0.00 0.00 46.93 3.84
69 70 1.995626 ATCGCTGGGGGCTTACACT 60.996 57.895 0.00 0.00 39.13 3.55
71 72 2.751837 GCTGGGGGCTTACACTGC 60.752 66.667 0.00 0.00 38.06 4.40
85 88 1.343142 ACACTGCGATTCACACACCTA 59.657 47.619 0.00 0.00 0.00 3.08
112 115 7.796838 TGAAGACTAATTTGTCATGTTTCTCG 58.203 34.615 19.82 0.00 39.27 4.04
113 116 7.655732 TGAAGACTAATTTGTCATGTTTCTCGA 59.344 33.333 19.82 0.00 39.27 4.04
133 136 5.724328 TCGATGCTTGAGATGTAGAACTTT 58.276 37.500 0.00 0.00 0.00 2.66
141 144 5.470368 TGAGATGTAGAACTTTCACCGAAG 58.530 41.667 0.00 0.00 0.00 3.79
142 145 5.010719 TGAGATGTAGAACTTTCACCGAAGT 59.989 40.000 0.00 0.00 41.44 3.01
163 166 4.103785 AGTCTAGCAATCAGGGCATGTAAT 59.896 41.667 0.00 0.00 0.00 1.89
185 188 1.577328 GCCACATCACCACAACTCGG 61.577 60.000 0.00 0.00 0.00 4.63
202 205 2.165301 GGTCGCCGAGAATTGACCG 61.165 63.158 0.00 0.00 41.26 4.79
215 218 5.063880 AGAATTGACCGAACAAAGCTACTT 58.936 37.500 0.00 0.00 33.44 2.24
228 231 0.457853 GCTACTTGACATGGCGACGA 60.458 55.000 0.00 0.00 0.00 4.20
295 298 1.429930 TGGAGAGTAGGCCAACAACA 58.570 50.000 5.01 0.00 0.00 3.33
301 304 1.985159 AGTAGGCCAACAACAGATGGA 59.015 47.619 5.01 0.00 39.12 3.41
303 306 2.380064 AGGCCAACAACAGATGGAAA 57.620 45.000 5.01 0.00 39.12 3.13
305 308 1.273327 GGCCAACAACAGATGGAAAGG 59.727 52.381 0.00 0.00 39.12 3.11
308 311 2.229784 CCAACAACAGATGGAAAGGCTC 59.770 50.000 0.00 0.00 39.12 4.70
323 326 0.596083 GGCTCATGTCATCGACGGAG 60.596 60.000 9.85 9.85 38.62 4.63
339 342 1.141053 CGGAGAGTTAGGGATTTGGGG 59.859 57.143 0.00 0.00 0.00 4.96
345 348 1.279846 GTTAGGGATTTGGGGTCGTCA 59.720 52.381 0.00 0.00 0.00 4.35
346 349 1.200519 TAGGGATTTGGGGTCGTCAG 58.799 55.000 0.00 0.00 0.00 3.51
347 350 0.546747 AGGGATTTGGGGTCGTCAGA 60.547 55.000 0.00 0.00 0.00 3.27
348 351 0.546598 GGGATTTGGGGTCGTCAGAT 59.453 55.000 0.00 0.00 0.00 2.90
368 371 4.166919 AGATGAGAAGTTAGGGATTTGGGG 59.833 45.833 0.00 0.00 0.00 4.96
373 376 4.665483 AGAAGTTAGGGATTTGGGGGATAG 59.335 45.833 0.00 0.00 0.00 2.08
394 397 7.066404 GGATAGGAATTTTTGAAGAGAGGTGAC 59.934 40.741 0.00 0.00 0.00 3.67
396 399 4.827284 GGAATTTTTGAAGAGAGGTGACCA 59.173 41.667 3.63 0.00 0.00 4.02
461 472 4.062293 TCATTTCACTTAACACCGAGTGG 58.938 43.478 8.57 0.00 42.67 4.00
471 482 1.304217 ACCGAGTGGAGTCGTGGAT 60.304 57.895 3.35 0.00 38.32 3.41
481 492 2.489971 GAGTCGTGGATTGGTCAACAA 58.510 47.619 0.00 0.00 44.54 2.83
498 509 3.844577 ACAATGACTAGTACGAGCGTT 57.155 42.857 0.00 1.71 0.00 4.84
499 510 4.952262 ACAATGACTAGTACGAGCGTTA 57.048 40.909 0.00 0.00 0.00 3.18
500 511 5.496133 ACAATGACTAGTACGAGCGTTAT 57.504 39.130 0.00 0.00 0.00 1.89
501 512 5.888105 ACAATGACTAGTACGAGCGTTATT 58.112 37.500 0.00 0.00 0.00 1.40
502 513 5.970023 ACAATGACTAGTACGAGCGTTATTC 59.030 40.000 0.00 0.00 0.00 1.75
504 515 3.313526 TGACTAGTACGAGCGTTATTCCC 59.686 47.826 0.00 0.00 0.00 3.97
505 516 3.549794 ACTAGTACGAGCGTTATTCCCT 58.450 45.455 0.00 0.00 0.00 4.20
506 517 2.865343 AGTACGAGCGTTATTCCCTG 57.135 50.000 0.00 0.00 0.00 4.45
507 518 1.202382 AGTACGAGCGTTATTCCCTGC 60.202 52.381 0.00 0.00 0.00 4.85
508 519 0.818938 TACGAGCGTTATTCCCTGCA 59.181 50.000 0.00 0.00 0.00 4.41
509 520 0.178068 ACGAGCGTTATTCCCTGCAT 59.822 50.000 0.00 0.00 0.00 3.96
510 521 1.299541 CGAGCGTTATTCCCTGCATT 58.700 50.000 0.00 0.00 0.00 3.56
536 547 4.385825 ACCGTACATTCATGTCTTGTTGT 58.614 39.130 0.00 0.00 41.97 3.32
583 594 5.139435 TCTTGAGTACAGTGATGAAGGTG 57.861 43.478 0.00 0.00 0.00 4.00
587 598 5.321927 TGAGTACAGTGATGAAGGTGAGTA 58.678 41.667 0.00 0.00 0.00 2.59
590 601 5.775701 AGTACAGTGATGAAGGTGAGTACTT 59.224 40.000 0.00 0.00 38.09 2.24
591 602 5.140747 ACAGTGATGAAGGTGAGTACTTC 57.859 43.478 0.00 0.00 43.52 3.01
592 603 4.021016 ACAGTGATGAAGGTGAGTACTTCC 60.021 45.833 0.00 3.30 42.79 3.46
599 610 2.054799 AGGTGAGTACTTCCTGGCAAA 58.945 47.619 16.40 0.00 0.00 3.68
609 620 9.120538 GAGTACTTCCTGGCAAATTTAATGATA 57.879 33.333 0.00 0.00 0.00 2.15
612 623 7.955918 ACTTCCTGGCAAATTTAATGATATCC 58.044 34.615 0.00 0.00 0.00 2.59
667 678 6.319658 TCTTTGATTTGATCTGCTGGGATTAC 59.680 38.462 0.00 0.00 0.00 1.89
771 782 4.054085 CCAGTGTGTGACAGGCAG 57.946 61.111 0.00 0.00 0.00 4.85
934 945 1.527034 CCAACTCCATCCACACACAG 58.473 55.000 0.00 0.00 0.00 3.66
1179 1194 1.618640 GAAGAACGACGAGGCTGCAC 61.619 60.000 0.00 0.00 0.00 4.57
1295 1310 1.313812 ACGGAGAAGCAGGTACGAGG 61.314 60.000 0.00 0.00 0.00 4.63
1334 1349 0.038526 CGACAGCGACTGTAGGGTTT 60.039 55.000 11.60 0.00 45.44 3.27
1552 1568 3.069158 ACCTCTCCGTTATAATCAACCCG 59.931 47.826 0.00 0.00 0.00 5.28
1677 1693 5.221283 CCGAGGTCTAATAACTCCTTCCTTC 60.221 48.000 0.00 0.00 0.00 3.46
1678 1694 5.221283 CGAGGTCTAATAACTCCTTCCTTCC 60.221 48.000 0.00 0.00 0.00 3.46
1679 1695 5.855988 AGGTCTAATAACTCCTTCCTTCCT 58.144 41.667 0.00 0.00 0.00 3.36
1680 1696 6.273104 AGGTCTAATAACTCCTTCCTTCCTT 58.727 40.000 0.00 0.00 0.00 3.36
1681 1697 6.736179 AGGTCTAATAACTCCTTCCTTCCTTT 59.264 38.462 0.00 0.00 0.00 3.11
1682 1698 7.049133 GGTCTAATAACTCCTTCCTTCCTTTC 58.951 42.308 0.00 0.00 0.00 2.62
1683 1699 7.092802 GGTCTAATAACTCCTTCCTTCCTTTCT 60.093 40.741 0.00 0.00 0.00 2.52
1685 1701 8.891501 TCTAATAACTCCTTCCTTCCTTTCTTT 58.108 33.333 0.00 0.00 0.00 2.52
1742 1758 1.499056 CCAAGTGTGCTGACGATGC 59.501 57.895 0.00 0.00 0.00 3.91
2321 2976 6.021596 GCTAACTGGAATGTAAAATCACGTG 58.978 40.000 9.94 9.94 0.00 4.49
2411 3072 2.813908 GTTGTAGGCCCACGCGAG 60.814 66.667 15.93 4.16 35.02 5.03
2413 3074 2.874664 TTGTAGGCCCACGCGAGTT 61.875 57.895 15.93 0.00 46.40 3.01
2431 3092 2.427095 AGTTGAAGGTTTTGACAGGTGC 59.573 45.455 0.00 0.00 0.00 5.01
2459 3120 4.200092 GGGTCCATATGTTTTCAGTCTCC 58.800 47.826 1.24 0.00 0.00 3.71
2471 3132 2.631384 TCAGTCTCCCTTTGGATTGGA 58.369 47.619 0.00 0.00 40.80 3.53
2475 3136 2.305927 GTCTCCCTTTGGATTGGACAGA 59.694 50.000 0.00 0.00 40.80 3.41
2497 3158 1.010574 GAGCTCGAGATGACGACGG 60.011 63.158 18.75 0.00 37.37 4.79
2498 3159 1.707239 GAGCTCGAGATGACGACGGT 61.707 60.000 18.75 0.00 37.37 4.83
2502 3163 1.514228 CGAGATGACGACGGTGTGG 60.514 63.158 0.00 0.00 35.09 4.17
2518 3179 1.478916 TGTGGCCGATATCTTTGTCGA 59.521 47.619 0.00 0.00 38.61 4.20
2556 3217 1.000283 CGCTGGAGGTTAGGATAGCAG 60.000 57.143 0.00 0.00 0.00 4.24
2565 3226 2.553172 GTTAGGATAGCAGACGACGGAT 59.447 50.000 0.00 0.00 0.00 4.18
2573 3234 2.261671 GACGACGGATGTGCTGGT 59.738 61.111 0.00 0.00 0.00 4.00
2613 3274 3.785859 GACGCTCTGGATGGCCCA 61.786 66.667 0.00 0.00 44.25 5.36
2625 3286 4.666253 GGCCCACTCCTGCAGCAA 62.666 66.667 8.66 0.00 0.00 3.91
2671 3343 2.907897 CTAAGGGGAACGGCGCAGAG 62.908 65.000 16.26 4.70 0.00 3.35
2696 3368 1.444933 TGGTTGGTCTGATGGTCCTT 58.555 50.000 0.00 0.00 0.00 3.36
2818 3490 1.686236 ATGGGGGTTGAGATCTTGGT 58.314 50.000 0.00 0.00 0.00 3.67
2879 3551 2.765969 CCAGGGCATTGGACTGGT 59.234 61.111 1.30 0.00 45.21 4.00
2885 3557 0.895100 GGCATTGGACTGGTTGCTCA 60.895 55.000 0.00 0.00 35.46 4.26
2890 3562 2.029844 GGACTGGTTGCTCAGCGAC 61.030 63.158 8.75 8.75 41.81 5.19
2900 3572 1.935327 GCTCAGCGACCGGAGTTACT 61.935 60.000 9.46 0.00 35.94 2.24
2915 3587 0.692476 TTACTGGCTGCCATGAGTGT 59.308 50.000 23.64 18.01 30.82 3.55
2929 3601 2.512515 GTGTCCCTCATCCGCTGC 60.513 66.667 0.00 0.00 0.00 5.25
2995 3667 1.746615 CACGGGCTTGTCATCAGGG 60.747 63.158 0.00 0.00 0.00 4.45
2996 3668 2.224159 ACGGGCTTGTCATCAGGGT 61.224 57.895 0.00 0.00 0.00 4.34
3001 3673 1.559682 GGCTTGTCATCAGGGTAGGAA 59.440 52.381 0.00 0.00 0.00 3.36
3018 3690 2.922283 AGGAATTTGACATGGTCCTCCT 59.078 45.455 0.00 0.00 33.26 3.69
3023 3695 1.222936 GACATGGTCCTCCTGCCTG 59.777 63.158 0.00 0.00 34.23 4.85
3029 3701 2.935481 TCCTCCTGCCTGGGGTTG 60.935 66.667 0.00 0.00 33.29 3.77
3052 3724 1.599047 CTCCTCAAGCGGGTCATGT 59.401 57.895 0.00 0.00 0.00 3.21
3062 3734 2.048597 GGTCATGTCGCGGTGTCA 60.049 61.111 6.13 1.15 0.00 3.58
3088 3760 3.838271 TCGGGATGCTCGGCTGTC 61.838 66.667 0.00 0.00 0.00 3.51
3098 3770 2.032071 CGGCTGTCGGTCCCTTTT 59.968 61.111 0.00 0.00 34.75 2.27
3104 3776 0.768622 TGTCGGTCCCTTTTGGTCAT 59.231 50.000 0.00 0.00 38.10 3.06
3203 3875 4.314440 GACTCTGTGGTGCCGGCA 62.314 66.667 29.03 29.03 0.00 5.69
3204 3876 4.320456 ACTCTGTGGTGCCGGCAG 62.320 66.667 33.73 18.75 0.00 4.85
3205 3877 4.007644 CTCTGTGGTGCCGGCAGA 62.008 66.667 33.73 22.25 37.63 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 3.443052 TGATGGAATTTGACCCATGCTT 58.557 40.909 1.29 0.00 42.80 3.91
20 21 8.503196 GTTGTTAATTTTGATGGAATTTGACCC 58.497 33.333 0.00 0.00 0.00 4.46
23 24 9.534565 TTCGTTGTTAATTTTGATGGAATTTGA 57.465 25.926 0.00 0.00 0.00 2.69
54 55 2.751837 GCAGTGTAAGCCCCCAGC 60.752 66.667 0.00 0.00 44.25 4.85
69 70 3.326836 TCAATAGGTGTGTGAATCGCA 57.673 42.857 0.00 0.00 0.00 5.10
71 72 5.171476 AGTCTTCAATAGGTGTGTGAATCG 58.829 41.667 0.00 0.00 31.21 3.34
112 115 6.183360 GGTGAAAGTTCTACATCTCAAGCATC 60.183 42.308 0.00 0.00 0.00 3.91
113 116 5.645497 GGTGAAAGTTCTACATCTCAAGCAT 59.355 40.000 0.00 0.00 0.00 3.79
133 136 2.166459 CCTGATTGCTAGACTTCGGTGA 59.834 50.000 0.00 0.00 0.00 4.02
141 144 2.338577 ACATGCCCTGATTGCTAGAC 57.661 50.000 0.00 0.00 0.00 2.59
142 145 4.102996 TCATTACATGCCCTGATTGCTAGA 59.897 41.667 0.00 0.00 0.00 2.43
163 166 0.473755 AGTTGTGGTGATGTGGCTCA 59.526 50.000 0.00 0.00 0.00 4.26
185 188 0.734942 TTCGGTCAATTCTCGGCGAC 60.735 55.000 4.99 0.00 0.00 5.19
200 203 3.120199 CCATGTCAAGTAGCTTTGTTCGG 60.120 47.826 0.00 0.00 0.00 4.30
202 205 3.667960 CGCCATGTCAAGTAGCTTTGTTC 60.668 47.826 0.00 0.00 0.00 3.18
215 218 2.126618 GTCGTCGTCGCCATGTCA 60.127 61.111 0.00 0.00 36.96 3.58
235 238 4.776322 CGCCATCGCCCACCTTCA 62.776 66.667 0.00 0.00 0.00 3.02
295 298 3.743584 CGATGACATGAGCCTTTCCATCT 60.744 47.826 0.00 0.00 0.00 2.90
301 304 1.645034 CGTCGATGACATGAGCCTTT 58.355 50.000 0.00 0.00 32.09 3.11
303 306 1.037579 TCCGTCGATGACATGAGCCT 61.038 55.000 6.11 0.00 32.09 4.58
305 308 0.382158 TCTCCGTCGATGACATGAGC 59.618 55.000 6.11 0.00 33.76 4.26
308 311 2.568696 AACTCTCCGTCGATGACATG 57.431 50.000 6.11 0.00 32.09 3.21
323 326 1.558294 ACGACCCCAAATCCCTAACTC 59.442 52.381 0.00 0.00 0.00 3.01
339 342 3.695060 TCCCTAACTTCTCATCTGACGAC 59.305 47.826 0.00 0.00 0.00 4.34
345 348 4.166919 CCCCAAATCCCTAACTTCTCATCT 59.833 45.833 0.00 0.00 0.00 2.90
346 349 4.464947 CCCCAAATCCCTAACTTCTCATC 58.535 47.826 0.00 0.00 0.00 2.92
347 350 3.205282 CCCCCAAATCCCTAACTTCTCAT 59.795 47.826 0.00 0.00 0.00 2.90
348 351 2.580783 CCCCCAAATCCCTAACTTCTCA 59.419 50.000 0.00 0.00 0.00 3.27
368 371 7.066404 GTCACCTCTCTTCAAAAATTCCTATCC 59.934 40.741 0.00 0.00 0.00 2.59
373 376 4.827284 TGGTCACCTCTCTTCAAAAATTCC 59.173 41.667 0.00 0.00 0.00 3.01
419 429 3.580895 TGACCCACTATGTATGTGTGTGT 59.419 43.478 0.00 0.00 33.92 3.72
420 430 4.200838 TGACCCACTATGTATGTGTGTG 57.799 45.455 0.00 0.00 33.92 3.82
421 431 5.435686 AATGACCCACTATGTATGTGTGT 57.564 39.130 0.00 0.00 33.92 3.72
422 432 5.879777 TGAAATGACCCACTATGTATGTGTG 59.120 40.000 0.00 0.00 33.92 3.82
423 433 5.880332 GTGAAATGACCCACTATGTATGTGT 59.120 40.000 0.00 0.00 33.92 3.72
424 434 6.115446 AGTGAAATGACCCACTATGTATGTG 58.885 40.000 0.00 0.00 41.38 3.21
426 436 8.612619 GTTAAGTGAAATGACCCACTATGTATG 58.387 37.037 0.00 0.00 42.25 2.39
427 437 8.325787 TGTTAAGTGAAATGACCCACTATGTAT 58.674 33.333 0.00 0.00 42.25 2.29
428 438 7.604927 GTGTTAAGTGAAATGACCCACTATGTA 59.395 37.037 0.00 0.00 42.25 2.29
429 439 6.430000 GTGTTAAGTGAAATGACCCACTATGT 59.570 38.462 0.00 0.00 42.25 2.29
430 440 6.128007 GGTGTTAAGTGAAATGACCCACTATG 60.128 42.308 0.00 0.00 42.25 2.23
431 441 5.944007 GGTGTTAAGTGAAATGACCCACTAT 59.056 40.000 0.00 0.00 42.25 2.12
432 442 5.310451 GGTGTTAAGTGAAATGACCCACTA 58.690 41.667 0.00 0.00 42.25 2.74
461 472 2.163818 TGTTGACCAATCCACGACTC 57.836 50.000 0.00 0.00 0.00 3.36
481 492 4.023365 GGGAATAACGCTCGTACTAGTCAT 60.023 45.833 0.00 0.00 0.00 3.06
498 509 1.280710 ACGGTCACAATGCAGGGAATA 59.719 47.619 0.00 0.00 0.00 1.75
499 510 0.038166 ACGGTCACAATGCAGGGAAT 59.962 50.000 0.00 0.00 0.00 3.01
500 511 0.687920 TACGGTCACAATGCAGGGAA 59.312 50.000 0.00 0.00 0.00 3.97
501 512 0.036765 GTACGGTCACAATGCAGGGA 60.037 55.000 0.00 0.00 0.00 4.20
502 513 0.321210 TGTACGGTCACAATGCAGGG 60.321 55.000 0.00 0.00 0.00 4.45
504 515 2.741517 TGAATGTACGGTCACAATGCAG 59.258 45.455 0.00 0.00 30.84 4.41
505 516 2.772287 TGAATGTACGGTCACAATGCA 58.228 42.857 0.00 0.00 30.84 3.96
506 517 3.126858 ACATGAATGTACGGTCACAATGC 59.873 43.478 0.00 0.00 39.68 3.56
507 518 4.631377 AGACATGAATGTACGGTCACAATG 59.369 41.667 0.00 0.00 41.95 2.82
508 519 4.832248 AGACATGAATGTACGGTCACAAT 58.168 39.130 0.00 0.00 41.95 2.71
509 520 4.265904 AGACATGAATGTACGGTCACAA 57.734 40.909 0.00 0.00 41.95 3.33
510 521 3.953712 AGACATGAATGTACGGTCACA 57.046 42.857 0.00 0.00 41.95 3.58
556 567 9.201989 ACCTTCATCACTGTACTCAAGAATATA 57.798 33.333 0.00 0.00 0.00 0.86
558 569 7.178451 TCACCTTCATCACTGTACTCAAGAATA 59.822 37.037 0.00 0.00 0.00 1.75
562 573 5.139435 TCACCTTCATCACTGTACTCAAG 57.861 43.478 0.00 0.00 0.00 3.02
577 588 1.623811 TGCCAGGAAGTACTCACCTTC 59.376 52.381 15.95 12.18 38.05 3.46
580 591 2.561478 TTTGCCAGGAAGTACTCACC 57.439 50.000 10.06 10.06 0.00 4.02
583 594 7.391148 TCATTAAATTTGCCAGGAAGTACTC 57.609 36.000 0.00 0.00 0.00 2.59
587 598 7.255590 CGGATATCATTAAATTTGCCAGGAAGT 60.256 37.037 4.83 0.00 0.00 3.01
590 601 6.303054 TCGGATATCATTAAATTTGCCAGGA 58.697 36.000 4.83 0.00 0.00 3.86
591 602 6.573664 TCGGATATCATTAAATTTGCCAGG 57.426 37.500 4.83 0.00 0.00 4.45
592 603 6.529125 GCATCGGATATCATTAAATTTGCCAG 59.471 38.462 4.83 0.00 0.00 4.85
609 620 4.887071 TGGCTTAAGTAAAATGCATCGGAT 59.113 37.500 0.00 0.00 0.00 4.18
612 623 6.942886 TTTTGGCTTAAGTAAAATGCATCG 57.057 33.333 0.00 0.00 0.00 3.84
629 640 7.599630 TCAAATCAAAGATTAGCATTTTGGC 57.400 32.000 0.00 0.00 33.70 4.52
667 678 0.304705 AGCACAAAAGAGTTGCGACG 59.695 50.000 0.00 0.00 0.00 5.12
771 782 1.363744 GATCCGCATCGAATGATCCC 58.636 55.000 0.00 0.00 30.49 3.85
934 945 1.071567 GCGCGAGAGTACTTGTGGTC 61.072 60.000 12.10 0.00 38.18 4.02
1295 1310 1.922570 CTCACATACACGGCCACTAC 58.077 55.000 2.24 0.00 0.00 2.73
1334 1349 2.609491 CGAAGTCACTCATCCGAAACCA 60.609 50.000 0.00 0.00 0.00 3.67
1417 1433 2.042261 AACCCCTCCCCGCTGTAT 59.958 61.111 0.00 0.00 0.00 2.29
1426 1442 2.879103 TCATCAGTTTGAACCCCTCC 57.121 50.000 0.00 0.00 0.00 4.30
1552 1568 2.427506 GTGATGGTCTTCTTGGTGGTC 58.572 52.381 0.00 0.00 0.00 4.02
1681 1697 8.391106 CGACAAAGAAGAAGAAGAAGAAAAAGA 58.609 33.333 0.00 0.00 0.00 2.52
1682 1698 7.164990 GCGACAAAGAAGAAGAAGAAGAAAAAG 59.835 37.037 0.00 0.00 0.00 2.27
1683 1699 6.967199 GCGACAAAGAAGAAGAAGAAGAAAAA 59.033 34.615 0.00 0.00 0.00 1.94
1685 1701 5.584649 TGCGACAAAGAAGAAGAAGAAGAAA 59.415 36.000 0.00 0.00 0.00 2.52
2061 2077 0.731417 CGATCGGTCTCTACACGGTT 59.269 55.000 7.38 0.00 0.00 4.44
2300 2955 5.763204 ACTCACGTGATTTTACATTCCAGTT 59.237 36.000 20.40 0.00 0.00 3.16
2321 2976 2.429610 TCGATGGCTACCCTTGTTACTC 59.570 50.000 0.00 0.00 0.00 2.59
2403 3064 0.661020 AAAACCTTCAACTCGCGTGG 59.339 50.000 13.32 6.71 0.00 4.94
2406 3067 1.329292 TGTCAAAACCTTCAACTCGCG 59.671 47.619 0.00 0.00 0.00 5.87
2411 3072 2.794631 CGCACCTGTCAAAACCTTCAAC 60.795 50.000 0.00 0.00 0.00 3.18
2412 3073 1.403679 CGCACCTGTCAAAACCTTCAA 59.596 47.619 0.00 0.00 0.00 2.69
2413 3074 1.021202 CGCACCTGTCAAAACCTTCA 58.979 50.000 0.00 0.00 0.00 3.02
2459 3120 2.028112 TCGACTCTGTCCAATCCAAAGG 60.028 50.000 0.00 0.00 0.00 3.11
2471 3132 1.013596 CATCTCGAGCTCGACTCTGT 58.986 55.000 33.84 15.14 44.22 3.41
2475 3136 0.460459 TCGTCATCTCGAGCTCGACT 60.460 55.000 33.84 21.06 44.22 4.18
2497 3158 1.593006 CGACAAAGATATCGGCCACAC 59.407 52.381 2.24 0.00 34.67 3.82
2498 3159 1.478916 TCGACAAAGATATCGGCCACA 59.521 47.619 2.24 0.00 38.86 4.17
2502 3163 1.784525 CCCTCGACAAAGATATCGGC 58.215 55.000 0.00 0.00 38.86 5.54
2506 3167 3.068873 GTCTGAGCCCTCGACAAAGATAT 59.931 47.826 12.21 0.00 35.13 1.63
2536 3197 1.000283 CTGCTATCCTAACCTCCAGCG 60.000 57.143 0.00 0.00 0.00 5.18
2538 3199 2.294791 CGTCTGCTATCCTAACCTCCAG 59.705 54.545 0.00 0.00 0.00 3.86
2556 3217 2.094659 CACCAGCACATCCGTCGTC 61.095 63.158 0.00 0.00 0.00 4.20
2565 3226 0.394192 CAAGAGGTCTCACCAGCACA 59.606 55.000 0.55 0.00 41.95 4.57
2573 3234 2.061220 CCCACTGCAAGAGGTCTCA 58.939 57.895 0.55 0.00 43.89 3.27
2613 3274 2.256591 CGCAAGTTGCTGCAGGAGT 61.257 57.895 24.61 0.44 42.25 3.85
2671 3343 0.967380 CATCAGACCAACCAAGGCCC 60.967 60.000 0.00 0.00 0.00 5.80
2681 3353 1.279496 CCTGAAGGACCATCAGACCA 58.721 55.000 25.00 0.00 45.74 4.02
2696 3368 2.520458 CCACCCAAGGTTGCCTGA 59.480 61.111 0.00 0.00 31.02 3.86
2732 3404 4.796495 GGCCGCCGGTTCTCCATT 62.796 66.667 4.45 0.00 0.00 3.16
2781 3453 1.267574 ATTCTCTGCTCCGCCTCCAA 61.268 55.000 0.00 0.00 0.00 3.53
2791 3463 0.622665 CTCAACCCCCATTCTCTGCT 59.377 55.000 0.00 0.00 0.00 4.24
2829 3501 2.596338 CAAACACACCCCGTCCCC 60.596 66.667 0.00 0.00 0.00 4.81
2839 3511 1.619654 CCATTGGCTCCTCAAACACA 58.380 50.000 0.00 0.00 0.00 3.72
2879 3551 1.529152 TAACTCCGGTCGCTGAGCAA 61.529 55.000 4.88 0.00 31.65 3.91
2885 3557 3.003113 GCCAGTAACTCCGGTCGCT 62.003 63.158 0.00 0.00 0.00 4.93
2890 3562 2.125106 GGCAGCCAGTAACTCCGG 60.125 66.667 6.55 0.00 0.00 5.14
2900 3572 2.352422 GGACACTCATGGCAGCCA 59.648 61.111 18.99 18.99 34.30 4.75
2977 3649 1.746615 CCCTGATGACAAGCCCGTG 60.747 63.158 0.00 0.00 0.00 4.94
2978 3650 0.907704 TACCCTGATGACAAGCCCGT 60.908 55.000 0.00 0.00 0.00 5.28
2979 3651 0.179073 CTACCCTGATGACAAGCCCG 60.179 60.000 0.00 0.00 0.00 6.13
2980 3652 0.181350 CCTACCCTGATGACAAGCCC 59.819 60.000 0.00 0.00 0.00 5.19
2989 3661 4.230502 ACCATGTCAAATTCCTACCCTGAT 59.769 41.667 0.00 0.00 0.00 2.90
2991 3663 3.947834 GACCATGTCAAATTCCTACCCTG 59.052 47.826 0.00 0.00 32.09 4.45
2995 3667 4.080299 AGGAGGACCATGTCAAATTCCTAC 60.080 45.833 0.00 2.25 36.80 3.18
2996 3668 4.080356 CAGGAGGACCATGTCAAATTCCTA 60.080 45.833 0.00 0.00 36.80 2.94
3001 3673 1.341383 GGCAGGAGGACCATGTCAAAT 60.341 52.381 0.00 0.00 38.94 2.32
3023 3695 3.210012 TTGAGGAGCAGCCAACCCC 62.210 63.158 0.00 0.00 40.02 4.95
3049 3721 1.749063 TCTAAGATGACACCGCGACAT 59.251 47.619 8.23 7.74 32.41 3.06
3052 3724 1.400846 GACTCTAAGATGACACCGCGA 59.599 52.381 8.23 0.00 0.00 5.87
3058 3730 2.362397 GCATCCCGACTCTAAGATGACA 59.638 50.000 3.15 0.00 38.72 3.58
3062 3734 1.883275 CGAGCATCCCGACTCTAAGAT 59.117 52.381 0.00 0.00 0.00 2.40
3088 3760 1.595093 GGCATGACCAAAAGGGACCG 61.595 60.000 0.00 0.00 41.15 4.79
3104 3776 2.430610 GCAAACACCCACCTTGGCA 61.431 57.895 0.00 0.00 35.79 4.92
3157 3829 3.093172 TGCCACAGACCACCACCA 61.093 61.111 0.00 0.00 0.00 4.17


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

AutoCloner maintained by Alex Coulton.