Multiple sequence alignment - TraesCS2A01G260600

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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 TraesCS2A01G260600 chr2A 100.000 4187 0 0 1 4187 410850595 410854781 0.000000e+00 7733
1 TraesCS2A01G260600 chr2B 95.907 3274 102 12 102 3348 388598447 388595179 0.000000e+00 5275
2 TraesCS2A01G260600 chr2B 93.026 803 46 5 3392 4187 388595184 388594385 0.000000e+00 1164
3 TraesCS2A01G260600 chr2B 92.453 106 7 1 1 105 388598595 388598490 2.610000e-32 150
4 TraesCS2A01G260600 chr2D 94.911 3262 107 24 102 3348 320284509 320281292 0.000000e+00 5049
5 TraesCS2A01G260600 chr2D 91.905 803 44 7 3392 4187 320281297 320280509 0.000000e+00 1103
6 TraesCS2A01G260600 chr2D 87.500 104 12 1 3 105 320284655 320284552 7.350000e-23 119


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 TraesCS2A01G260600 chr2A 410850595 410854781 4186 False 7733.000000 7733 100.000000 1 4187 1 chr2A.!!$F1 4186
1 TraesCS2A01G260600 chr2B 388594385 388598595 4210 True 2196.333333 5275 93.795333 1 4187 3 chr2B.!!$R1 4186
2 TraesCS2A01G260600 chr2D 320280509 320284655 4146 True 2090.333333 5049 91.438667 3 4187 3 chr2D.!!$R1 4184

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
586 647 0.038343 CCGCCAAAAGGTTCACCATG 60.038 55.0 0.0 0.0 38.89 3.66 F
954 1015 0.179067 TTTCACACCCGACTCCACAC 60.179 55.0 0.0 0.0 0.00 3.82 F
2220 2281 0.473117 AAAGGAGAAGACGGACCCCA 60.473 55.0 0.0 0.0 0.00 4.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2220 2281 0.886490 CAGAGCGTCTTGGTTGCCTT 60.886 55.000 0.0 0.0 0.0 4.35 R
2459 2544 1.952296 CTTCTGCTTGGAACTGCTTGT 59.048 47.619 0.0 0.0 0.0 3.16 R
3594 3687 1.000145 GCAGAATTCGACGAGGGAAC 59.000 55.000 0.0 0.0 0.0 3.62 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
28 29 3.149196 AGAACCTAATGTGCACCTTGTG 58.851 45.455 15.69 8.89 36.51 3.33
83 84 9.220906 ACTTGGTTGTCTATTATTATAGGGACA 57.779 33.333 0.00 0.00 35.45 4.02
99 100 2.904835 ACATGCATTGTCCCCCATG 58.095 52.632 0.00 0.00 40.54 3.66
100 101 0.041535 ACATGCATTGTCCCCCATGT 59.958 50.000 0.00 0.00 42.32 3.21
105 153 1.935799 CATTGTCCCCCATGTTGGAA 58.064 50.000 2.24 0.00 40.96 3.53
222 270 9.601971 TTAAACAAAACATAATCTAGCGTTGAC 57.398 29.630 0.00 0.00 0.00 3.18
249 297 9.880064 GGAGTAGTTTTCATGTTCTTTTACTTC 57.120 33.333 0.00 0.00 0.00 3.01
339 387 2.166459 CCACATGAGAAGAGCCGAGTAA 59.834 50.000 0.00 0.00 0.00 2.24
340 388 3.443037 CACATGAGAAGAGCCGAGTAAG 58.557 50.000 0.00 0.00 0.00 2.34
367 415 0.960364 GGGCGAAGAATGAGGTTGCA 60.960 55.000 0.00 0.00 0.00 4.08
368 416 0.881118 GGCGAAGAATGAGGTTGCAA 59.119 50.000 0.00 0.00 0.00 4.08
379 427 0.465460 AGGTTGCAAAGACGCCTTCA 60.465 50.000 0.00 0.00 0.00 3.02
381 429 0.944386 GTTGCAAAGACGCCTTCAGA 59.056 50.000 0.00 0.00 0.00 3.27
409 457 2.832129 AGTAGTGAATGTGATGGGTCGT 59.168 45.455 0.00 0.00 0.00 4.34
458 511 3.655615 TTTCGGCCCAACAATATAGGT 57.344 42.857 0.00 0.00 0.00 3.08
475 528 0.751643 GGTGCCAAATACGATGGGCT 60.752 55.000 0.00 0.00 46.53 5.19
579 640 1.404843 TAAGTTGCCGCCAAAAGGTT 58.595 45.000 0.00 0.00 31.68 3.50
585 646 1.815817 GCCGCCAAAAGGTTCACCAT 61.816 55.000 0.00 0.00 38.89 3.55
586 647 0.038343 CCGCCAAAAGGTTCACCATG 60.038 55.000 0.00 0.00 38.89 3.66
611 672 6.072452 GGCTAAGAAAATGCAGTGTAGAAACT 60.072 38.462 0.00 0.00 0.00 2.66
624 685 7.201145 CAGTGTAGAAACTTAGCACGGTATAT 58.799 38.462 0.00 0.00 35.46 0.86
709 770 5.347907 CAGTCACTAAACTAACAACCGGATC 59.652 44.000 9.46 0.00 0.00 3.36
739 800 3.199677 CCACTGTCACGACCAGTTAAAA 58.800 45.455 0.00 0.00 0.00 1.52
763 824 7.671495 ATTGCAAAACAAATGTATTCTTCCC 57.329 32.000 1.71 0.00 42.86 3.97
880 941 2.683867 CTCTTATCACTCCCGAGTCGTT 59.316 50.000 12.31 0.00 40.20 3.85
905 966 4.391830 TCGCTTCGTCTTTTTAATGATGCT 59.608 37.500 0.00 0.00 33.14 3.79
906 967 5.579119 TCGCTTCGTCTTTTTAATGATGCTA 59.421 36.000 0.00 0.00 33.14 3.49
926 987 2.614829 TAAGCCTTCACTATTCGGCC 57.385 50.000 0.00 0.00 43.48 6.13
944 1005 1.066215 GCCCATTCCATTTTCACACCC 60.066 52.381 0.00 0.00 0.00 4.61
954 1015 0.179067 TTTCACACCCGACTCCACAC 60.179 55.000 0.00 0.00 0.00 3.82
1109 1170 5.053145 GCTAGTCCAAGAACATGATAGGTG 58.947 45.833 0.00 0.00 0.00 4.00
1375 1436 5.141182 GAGAGATACCTGGTGAGTTATGGA 58.859 45.833 10.23 0.00 0.00 3.41
1473 1534 1.882623 CTGCAGAGTTTGGACCTTTCC 59.117 52.381 8.42 0.00 43.19 3.13
1562 1623 5.397221 GGATGTCTTCCAATTCTCTGGATGA 60.397 44.000 4.57 4.57 45.03 2.92
1822 1883 2.813901 AGCTGAGATCGCTGAGGC 59.186 61.111 7.51 2.53 36.15 4.70
1893 1954 1.001293 GTGGCACTGAGAGATCACACA 59.999 52.381 11.13 0.00 0.00 3.72
1936 1997 1.679898 CTCCCTGCGAAGGTTTCCT 59.320 57.895 9.15 0.00 33.87 3.36
1954 2015 1.347050 CCTCTCCTATGCCATCACCTG 59.653 57.143 0.00 0.00 0.00 4.00
1962 2023 2.601240 TGCCATCACCTGAAATGGAA 57.399 45.000 5.58 0.00 44.37 3.53
1971 2032 6.131972 TCACCTGAAATGGAAGAGATTTCT 57.868 37.500 0.00 0.00 39.55 2.52
2043 2104 5.104527 TGAAGTATTTACAGTCATCCCCCAG 60.105 44.000 0.00 0.00 0.00 4.45
2085 2146 2.281484 GAGGCAAACCGAGGCACA 60.281 61.111 0.00 0.00 42.76 4.57
2169 2230 2.806244 GGTGTTAGTCGTCATTGTTGCT 59.194 45.455 0.00 0.00 0.00 3.91
2173 2234 4.447724 TGTTAGTCGTCATTGTTGCTCTTC 59.552 41.667 0.00 0.00 0.00 2.87
2220 2281 0.473117 AAAGGAGAAGACGGACCCCA 60.473 55.000 0.00 0.00 0.00 4.96
2316 2401 4.844884 ACATTGGAGCTTCCCTAACTTAC 58.155 43.478 0.00 0.00 35.03 2.34
2349 2434 2.499693 CCGGGCCACTGGAAATTTTAAT 59.500 45.455 4.39 0.00 46.80 1.40
2393 2478 0.512952 GGCTTTGGCGCGACATATAG 59.487 55.000 19.26 15.36 39.81 1.31
2458 2543 1.208535 CTATTGGGAGGCAACACGGTA 59.791 52.381 0.00 0.00 41.41 4.02
2459 2544 0.402504 ATTGGGAGGCAACACGGTAA 59.597 50.000 0.00 0.00 41.41 2.85
2611 2696 3.888930 GGAGAGGTTCATACAGGAGAGAG 59.111 52.174 0.00 0.00 0.00 3.20
2784 2869 3.717707 TCTCTCCGATTTTGGATTAGCG 58.282 45.455 0.00 0.00 37.41 4.26
2838 2923 3.243068 CCACAAGTGTTGCTGGTACTTTC 60.243 47.826 0.00 0.00 32.69 2.62
2864 2949 3.925238 CGCGCCGGAGTATGCAAC 61.925 66.667 5.05 0.00 0.00 4.17
3097 3182 2.952310 GTTGAGATTATGAACCTGGGGC 59.048 50.000 0.00 0.00 0.00 5.80
3345 3431 7.612668 GGAAAGTTCCAGTAGTAATTTCCTC 57.387 40.000 5.16 0.00 46.76 3.71
3346 3432 7.395617 GGAAAGTTCCAGTAGTAATTTCCTCT 58.604 38.462 5.16 0.00 46.76 3.69
3347 3433 7.883833 GGAAAGTTCCAGTAGTAATTTCCTCTT 59.116 37.037 5.16 0.00 46.76 2.85
3348 3434 9.286170 GAAAGTTCCAGTAGTAATTTCCTCTTT 57.714 33.333 0.00 0.00 0.00 2.52
3349 3435 9.642343 AAAGTTCCAGTAGTAATTTCCTCTTTT 57.358 29.630 0.00 0.00 0.00 2.27
3350 3436 9.642343 AAGTTCCAGTAGTAATTTCCTCTTTTT 57.358 29.630 0.00 0.00 0.00 1.94
3369 3455 5.913137 TTTTTCCTCAACAGTGTGAATGT 57.087 34.783 0.00 0.00 0.00 2.71
3370 3456 5.913137 TTTTCCTCAACAGTGTGAATGTT 57.087 34.783 0.00 0.00 41.47 2.71
3371 3457 5.913137 TTTCCTCAACAGTGTGAATGTTT 57.087 34.783 0.00 0.00 38.80 2.83
3372 3458 4.898829 TCCTCAACAGTGTGAATGTTTG 57.101 40.909 0.00 0.00 38.80 2.93
3373 3459 3.066621 TCCTCAACAGTGTGAATGTTTGC 59.933 43.478 0.00 0.00 38.80 3.68
3374 3460 3.067180 CCTCAACAGTGTGAATGTTTGCT 59.933 43.478 0.00 0.00 38.80 3.91
3375 3461 4.275689 CCTCAACAGTGTGAATGTTTGCTA 59.724 41.667 0.00 0.00 38.80 3.49
3376 3462 5.168526 TCAACAGTGTGAATGTTTGCTAC 57.831 39.130 0.00 0.00 38.80 3.58
3377 3463 4.881273 TCAACAGTGTGAATGTTTGCTACT 59.119 37.500 0.00 0.00 38.80 2.57
3378 3464 5.356751 TCAACAGTGTGAATGTTTGCTACTT 59.643 36.000 0.00 0.00 38.80 2.24
3379 3465 5.424121 ACAGTGTGAATGTTTGCTACTTC 57.576 39.130 0.00 0.00 0.00 3.01
3380 3466 5.126067 ACAGTGTGAATGTTTGCTACTTCT 58.874 37.500 0.00 0.00 0.00 2.85
3381 3467 6.288294 ACAGTGTGAATGTTTGCTACTTCTA 58.712 36.000 0.00 0.00 0.00 2.10
3382 3468 6.202954 ACAGTGTGAATGTTTGCTACTTCTAC 59.797 38.462 0.00 0.00 0.00 2.59
3383 3469 6.425114 CAGTGTGAATGTTTGCTACTTCTACT 59.575 38.462 0.00 0.00 0.00 2.57
3384 3470 6.992715 AGTGTGAATGTTTGCTACTTCTACTT 59.007 34.615 0.00 0.00 0.00 2.24
3385 3471 7.499232 AGTGTGAATGTTTGCTACTTCTACTTT 59.501 33.333 0.00 0.00 0.00 2.66
3386 3472 8.129211 GTGTGAATGTTTGCTACTTCTACTTTT 58.871 33.333 0.00 0.00 0.00 2.27
3387 3473 8.682710 TGTGAATGTTTGCTACTTCTACTTTTT 58.317 29.630 0.00 0.00 0.00 1.94
3388 3474 9.170584 GTGAATGTTTGCTACTTCTACTTTTTC 57.829 33.333 0.00 0.00 0.00 2.29
3389 3475 9.120538 TGAATGTTTGCTACTTCTACTTTTTCT 57.879 29.630 0.00 0.00 0.00 2.52
3390 3476 9.952188 GAATGTTTGCTACTTCTACTTTTTCTT 57.048 29.630 0.00 0.00 0.00 2.52
3426 3512 5.988287 TCATACAATGTAGATTCCTGTGCA 58.012 37.500 0.00 0.00 0.00 4.57
3436 3529 2.543777 TTCCTGTGCAAGTGTCCTAC 57.456 50.000 0.00 0.00 0.00 3.18
3454 3547 2.798976 ACGGTTAGTGCGTCAGTTTA 57.201 45.000 0.00 0.00 0.00 2.01
3455 3548 3.308438 ACGGTTAGTGCGTCAGTTTAT 57.692 42.857 0.00 0.00 0.00 1.40
3456 3549 4.439305 ACGGTTAGTGCGTCAGTTTATA 57.561 40.909 0.00 0.00 0.00 0.98
3463 3556 5.607119 AGTGCGTCAGTTTATAAACAAGG 57.393 39.130 26.06 19.44 41.30 3.61
3467 3560 6.092259 GTGCGTCAGTTTATAAACAAGGAGAT 59.908 38.462 26.06 4.90 41.30 2.75
3481 3574 5.988287 ACAAGGAGATCATCTTTCCTTCTC 58.012 41.667 9.63 0.00 45.78 2.87
3498 3591 8.761575 TTCCTTCTCATTTTTCATAAATGTGC 57.238 30.769 9.33 0.00 38.44 4.57
3518 3611 6.526526 TGTGCTATATTAGTAAAATCGCCCA 58.473 36.000 0.00 0.00 0.00 5.36
3543 3636 9.096160 CATACAGATGTGAATAATCTCTATGGC 57.904 37.037 0.00 0.00 33.13 4.40
3566 3659 5.106118 GCCTTCTTTTCTTTTCGGCTTCTAT 60.106 40.000 0.00 0.00 33.47 1.98
3594 3687 9.277565 GCATTGTGCAATATATTTATAAGGACG 57.722 33.333 0.00 0.00 44.26 4.79
3601 3694 8.880750 GCAATATATTTATAAGGACGTTCCCTC 58.119 37.037 0.00 0.00 37.19 4.30
3624 3717 7.044706 CCTCGTCGAATTCTGCAAATAAAATTC 60.045 37.037 3.52 0.00 35.67 2.17
3630 3723 7.253883 CGAATTCTGCAAATAAAATTCAGGCTC 60.254 37.037 3.52 0.00 37.77 4.70
3642 3735 2.561209 TCAGGCTCCCCTATGTGTTA 57.439 50.000 0.00 0.00 40.33 2.41
3646 3739 3.709653 CAGGCTCCCCTATGTGTTAACTA 59.290 47.826 7.22 0.00 40.33 2.24
3673 3766 4.574599 AGAAGCAAGTTTGGATGACAAC 57.425 40.909 0.00 0.00 39.19 3.32
3888 3981 6.378710 AGTCACACCTAGAAAAGAAAAAGC 57.621 37.500 0.00 0.00 0.00 3.51
3927 4020 2.945447 TGAAGCTGCACATAATTGGC 57.055 45.000 1.02 0.00 0.00 4.52
3943 4036 2.831685 TGGCCATCGATGTGGTATAC 57.168 50.000 23.27 6.47 41.47 1.47
3982 4075 6.579666 TTCAAGGGAAATCTCACTTTGATG 57.420 37.500 0.00 0.00 43.08 3.07
4013 4106 2.997986 CCTGGCTGTCAAAATCATTTGC 59.002 45.455 0.00 0.00 44.52 3.68
4034 4127 3.011818 CTGGTTCAGCATAAGATGTGCA 58.988 45.455 2.00 0.00 44.87 4.57
4101 4194 7.514784 TTCATTAATGTTGCATCCAGATAGG 57.485 36.000 14.97 0.00 39.47 2.57
4135 4228 8.375493 TGGTTACCTTTATTAGAGACTGATGT 57.625 34.615 2.07 0.00 0.00 3.06
4136 4229 8.822805 TGGTTACCTTTATTAGAGACTGATGTT 58.177 33.333 2.07 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 0.041576 GTGGAGTGAAAAACGGCGTC 60.042 55.000 15.17 0.09 0.00 5.19
62 63 9.672673 ATGCATGTCCCTATAATAATAGACAAC 57.327 33.333 0.00 0.00 37.84 3.32
83 84 1.196911 CAACATGGGGGACAATGCAT 58.803 50.000 0.00 0.00 0.00 3.96
94 95 0.903942 CCCATTGGTTCCAACATGGG 59.096 55.000 21.55 21.55 42.62 4.00
157 205 8.632679 AGTTTTATCATGTCAAATGTGTTCACT 58.367 29.630 4.59 0.00 0.00 3.41
222 270 8.084590 AGTAAAAGAACATGAAAACTACTCCG 57.915 34.615 0.00 0.00 0.00 4.63
228 276 8.190784 CCACAGAAGTAAAAGAACATGAAAACT 58.809 33.333 0.00 0.00 0.00 2.66
238 286 9.273016 CAAATCTACTCCACAGAAGTAAAAGAA 57.727 33.333 0.00 0.00 0.00 2.52
249 297 8.954950 ACTCAATAATCAAATCTACTCCACAG 57.045 34.615 0.00 0.00 0.00 3.66
351 399 3.665323 CGTCTTTGCAACCTCATTCTTCG 60.665 47.826 0.00 0.00 0.00 3.79
367 415 0.387929 TCGTGTCTGAAGGCGTCTTT 59.612 50.000 2.60 0.00 32.52 2.52
368 416 0.387929 TTCGTGTCTGAAGGCGTCTT 59.612 50.000 0.00 0.00 35.62 3.01
379 427 5.196341 TCACATTCACTACTTTCGTGTCT 57.804 39.130 0.00 0.00 34.14 3.41
381 429 4.690748 CCATCACATTCACTACTTTCGTGT 59.309 41.667 0.00 0.00 34.14 4.49
458 511 0.034574 ACAGCCCATCGTATTTGGCA 60.035 50.000 1.86 0.00 46.45 4.92
475 528 6.294010 GCTGATATCGACACATACTCCTAACA 60.294 42.308 0.00 0.00 0.00 2.41
543 602 7.967854 CGGCAACTTAAAGATCATTCATGTTTA 59.032 33.333 0.00 0.00 30.70 2.01
547 606 4.736793 GCGGCAACTTAAAGATCATTCATG 59.263 41.667 0.00 0.00 0.00 3.07
548 607 4.202050 GGCGGCAACTTAAAGATCATTCAT 60.202 41.667 3.07 0.00 0.00 2.57
549 608 3.128589 GGCGGCAACTTAAAGATCATTCA 59.871 43.478 3.07 0.00 0.00 2.57
550 609 3.128589 TGGCGGCAACTTAAAGATCATTC 59.871 43.478 10.22 0.00 0.00 2.67
551 610 3.088532 TGGCGGCAACTTAAAGATCATT 58.911 40.909 10.22 0.00 0.00 2.57
553 612 2.192664 TGGCGGCAACTTAAAGATCA 57.807 45.000 10.22 0.00 0.00 2.92
554 613 3.569250 TTTGGCGGCAACTTAAAGATC 57.431 42.857 25.48 0.00 0.00 2.75
559 620 1.404843 ACCTTTTGGCGGCAACTTAA 58.595 45.000 25.48 15.11 45.59 1.85
579 640 3.429492 TGCATTTTCTTAGCCATGGTGA 58.571 40.909 14.67 4.27 0.00 4.02
585 646 4.905429 TCTACACTGCATTTTCTTAGCCA 58.095 39.130 0.00 0.00 0.00 4.75
586 647 5.880054 TTCTACACTGCATTTTCTTAGCC 57.120 39.130 0.00 0.00 0.00 3.93
713 774 0.682292 TGGTCGTGACAGTGGCAATA 59.318 50.000 0.00 0.00 0.00 1.90
728 789 8.180920 ACATTTGTTTTGCAATTTTAACTGGTC 58.819 29.630 0.00 0.00 36.89 4.02
739 800 7.222872 TGGGAAGAATACATTTGTTTTGCAAT 58.777 30.769 0.00 0.00 36.89 3.56
763 824 9.057089 CCTAGTACCTTTCTTGGCTATATTTTG 57.943 37.037 0.00 0.00 0.00 2.44
880 941 5.617609 CATCATTAAAAAGACGAAGCGACA 58.382 37.500 0.00 0.00 0.00 4.35
926 987 2.094752 GTCGGGTGTGAAAATGGAATGG 60.095 50.000 0.00 0.00 0.00 3.16
944 1005 2.219325 GAGCAGAGGGTGTGGAGTCG 62.219 65.000 0.00 0.00 0.00 4.18
1109 1170 0.179936 CATGAGTTGGAGGAGAGCCC 59.820 60.000 0.00 0.00 33.31 5.19
1164 1225 0.526662 CTGAGTCCGGTGACCAGTAC 59.473 60.000 1.11 0.00 42.81 2.73
1375 1436 2.600729 CCTCCAGGTTCTGCAGCCT 61.601 63.158 9.47 8.08 35.04 4.58
1562 1623 2.579873 CAATCTGCGGAGGGATGAAAT 58.420 47.619 3.37 0.00 0.00 2.17
1818 1879 3.347216 TGAGGACAAATTTAGCAGCCTC 58.653 45.455 0.00 0.00 40.56 4.70
1893 1954 5.184864 CAGATCACTGTCAAGGAGTAGAACT 59.815 44.000 0.00 0.00 39.11 3.01
1936 1997 2.477104 TCAGGTGATGGCATAGGAGA 57.523 50.000 0.00 0.00 0.00 3.71
1954 2015 7.173907 TGTCACTTGAGAAATCTCTTCCATTTC 59.826 37.037 11.45 0.00 43.25 2.17
1962 2023 4.282957 TCAGCTGTCACTTGAGAAATCTCT 59.717 41.667 14.67 0.00 43.25 3.10
1971 2032 4.814147 CTGAACTATCAGCTGTCACTTGA 58.186 43.478 14.67 0.00 46.11 3.02
2043 2104 3.136009 AGTACCCAGGTGCTTTTGTAC 57.864 47.619 1.05 0.00 37.82 2.90
2169 2230 1.429930 TGGTGGCCACAACTAGAAGA 58.570 50.000 35.78 6.01 34.61 2.87
2173 2234 3.181469 ACGTATATGGTGGCCACAACTAG 60.181 47.826 35.78 21.45 35.80 2.57
2220 2281 0.886490 CAGAGCGTCTTGGTTGCCTT 60.886 55.000 0.00 0.00 0.00 4.35
2316 2401 3.508840 GCCCGGACAATTGCCTCG 61.509 66.667 0.73 7.00 0.00 4.63
2458 2543 2.057137 TCTGCTTGGAACTGCTTGTT 57.943 45.000 0.00 0.00 42.38 2.83
2459 2544 1.952296 CTTCTGCTTGGAACTGCTTGT 59.048 47.619 0.00 0.00 0.00 3.16
2501 2586 5.026121 TGAGAGTGACAAGATTAGGATGGT 58.974 41.667 0.00 0.00 0.00 3.55
2611 2696 2.825532 TCCAACCAATTTGCCTCTTAGC 59.174 45.455 0.00 0.00 33.34 3.09
2784 2869 3.944422 TGTGAGTTGCGAAGAAGTTTC 57.056 42.857 0.00 0.00 0.00 2.78
2838 2923 4.858433 TCCGGCGCGACATAACCG 62.858 66.667 14.85 13.59 45.21 4.44
3097 3182 4.689484 CTCCACAGTGCACAGGAG 57.311 61.111 27.53 27.53 41.43 3.69
3282 3368 7.118825 CACATCAACATAGGTATAAGCATCCAG 59.881 40.741 0.00 0.00 0.00 3.86
3347 3433 5.913137 ACATTCACACTGTTGAGGAAAAA 57.087 34.783 0.00 0.00 0.00 1.94
3348 3434 5.913137 AACATTCACACTGTTGAGGAAAA 57.087 34.783 0.00 0.00 35.57 2.29
3349 3435 5.649557 CAAACATTCACACTGTTGAGGAAA 58.350 37.500 0.00 0.00 36.95 3.13
3350 3436 4.439974 GCAAACATTCACACTGTTGAGGAA 60.440 41.667 0.00 0.00 36.95 3.36
3351 3437 3.066621 GCAAACATTCACACTGTTGAGGA 59.933 43.478 0.00 0.00 36.95 3.71
3352 3438 3.067180 AGCAAACATTCACACTGTTGAGG 59.933 43.478 0.00 0.00 36.95 3.86
3353 3439 4.297299 AGCAAACATTCACACTGTTGAG 57.703 40.909 0.00 0.00 36.95 3.02
3354 3440 4.881273 AGTAGCAAACATTCACACTGTTGA 59.119 37.500 0.00 0.00 36.95 3.18
3355 3441 5.173774 AGTAGCAAACATTCACACTGTTG 57.826 39.130 0.00 0.00 36.95 3.33
3356 3442 5.590259 AGAAGTAGCAAACATTCACACTGTT 59.410 36.000 0.00 0.00 38.44 3.16
3357 3443 5.126067 AGAAGTAGCAAACATTCACACTGT 58.874 37.500 0.00 0.00 0.00 3.55
3358 3444 5.679734 AGAAGTAGCAAACATTCACACTG 57.320 39.130 0.00 0.00 0.00 3.66
3359 3445 6.525629 AGTAGAAGTAGCAAACATTCACACT 58.474 36.000 0.00 0.00 0.00 3.55
3360 3446 6.787085 AGTAGAAGTAGCAAACATTCACAC 57.213 37.500 0.00 0.00 0.00 3.82
3361 3447 7.801716 AAAGTAGAAGTAGCAAACATTCACA 57.198 32.000 0.00 0.00 0.00 3.58
3362 3448 9.170584 GAAAAAGTAGAAGTAGCAAACATTCAC 57.829 33.333 0.00 0.00 0.00 3.18
3363 3449 9.120538 AGAAAAAGTAGAAGTAGCAAACATTCA 57.879 29.630 0.00 0.00 0.00 2.57
3364 3450 9.952188 AAGAAAAAGTAGAAGTAGCAAACATTC 57.048 29.630 0.00 0.00 0.00 2.67
3365 3451 9.952188 GAAGAAAAAGTAGAAGTAGCAAACATT 57.048 29.630 0.00 0.00 0.00 2.71
3366 3452 9.343539 AGAAGAAAAAGTAGAAGTAGCAAACAT 57.656 29.630 0.00 0.00 0.00 2.71
3367 3453 8.732746 AGAAGAAAAAGTAGAAGTAGCAAACA 57.267 30.769 0.00 0.00 0.00 2.83
3414 3500 1.701847 AGGACACTTGCACAGGAATCT 59.298 47.619 0.00 0.00 0.00 2.40
3436 3529 5.118971 TGTTTATAAACTGACGCACTAACCG 59.881 40.000 24.81 0.00 39.59 4.44
3463 3556 8.954350 TGAAAAATGAGAAGGAAAGATGATCTC 58.046 33.333 0.00 0.00 37.60 2.75
3514 3607 6.471146 AGAGATTATTCACATCTGTATGGGC 58.529 40.000 0.00 0.00 36.37 5.36
3518 3611 8.263640 GGCCATAGAGATTATTCACATCTGTAT 58.736 37.037 0.00 0.00 37.60 2.29
3524 3617 7.327064 AGAAGGCCATAGAGATTATTCACAT 57.673 36.000 5.01 0.00 0.00 3.21
3543 3636 4.837896 AGAAGCCGAAAAGAAAAGAAGG 57.162 40.909 0.00 0.00 0.00 3.46
3594 3687 1.000145 GCAGAATTCGACGAGGGAAC 59.000 55.000 0.00 0.00 0.00 3.62
3601 3694 7.253420 CCTGAATTTTATTTGCAGAATTCGACG 60.253 37.037 0.00 0.00 39.93 5.12
3624 3717 2.505819 AGTTAACACATAGGGGAGCCTG 59.494 50.000 8.61 0.00 0.00 4.85
3630 3723 7.419711 TCTTTCTCTAGTTAACACATAGGGG 57.580 40.000 8.61 0.00 0.00 4.79
3642 3735 6.357367 TCCAAACTTGCTTCTTTCTCTAGTT 58.643 36.000 0.00 0.00 0.00 2.24
3646 3739 5.240403 GTCATCCAAACTTGCTTCTTTCTCT 59.760 40.000 0.00 0.00 0.00 3.10
3673 3766 5.107220 GCCATCTGCTTTGAGAAACAAATTG 60.107 40.000 0.00 0.00 45.63 2.32
3888 3981 7.495606 AGCTTCAAAAATACAACCAAAAAGAGG 59.504 33.333 0.00 0.00 0.00 3.69
3927 4020 7.065803 GGGAAAATATGTATACCACATCGATGG 59.934 40.741 28.09 16.54 44.99 3.51
3943 4036 5.830991 TCCCTTGAATAACGGGGAAAATATG 59.169 40.000 0.00 0.00 44.10 1.78
3953 4046 5.186198 AGTGAGATTTCCCTTGAATAACGG 58.814 41.667 0.00 0.00 0.00 4.44
3982 4075 1.930908 GACAGCCAGGCATGTTCAGC 61.931 60.000 15.80 0.00 0.00 4.26
4013 4106 3.011818 TGCACATCTTATGCTGAACCAG 58.988 45.455 0.00 0.00 43.77 4.00
4063 4156 9.599322 CAACATTAATGAAACTAGAGACACAAC 57.401 33.333 22.16 0.00 0.00 3.32
4101 4194 9.930693 CTCTAATAAAGGTAACCATGACTATCC 57.069 37.037 0.00 0.00 37.17 2.59


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

AutoCloner maintained by Alex Coulton.