Multiple sequence alignment - TraesCS2D01G356600

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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 TraesCS2D01G356600 chr2D 100.000 7767 0 0 1 7767 459288221 459295987 0.000000e+00 14344.0
1 TraesCS2D01G356600 chr2D 81.359 515 77 13 1 505 617110738 617111243 1.210000e-107 401.0
2 TraesCS2D01G356600 chr2B 94.368 4670 153 35 528 5121 540423627 540428262 0.000000e+00 7066.0
3 TraesCS2D01G356600 chr2B 91.513 978 53 20 5118 6076 540428427 540429393 0.000000e+00 1319.0
4 TraesCS2D01G356600 chr2B 88.627 932 66 23 6075 6981 540429483 540430399 0.000000e+00 1098.0
5 TraesCS2D01G356600 chr2B 91.035 792 51 11 6990 7767 540430441 540431226 0.000000e+00 1051.0
6 TraesCS2D01G356600 chr2B 100.000 30 0 0 507 536 540423420 540423449 1.000000e-03 56.5
7 TraesCS2D01G356600 chr2A 96.152 2573 56 18 5214 7767 602443885 602446433 0.000000e+00 4163.0
8 TraesCS2D01G356600 chr2A 95.431 2364 45 14 2889 5205 602441374 602443721 0.000000e+00 3709.0
9 TraesCS2D01G356600 chr2A 93.564 1849 47 23 1039 2854 602439265 602441074 0.000000e+00 2689.0
10 TraesCS2D01G356600 chr2A 88.498 1052 89 15 1 1051 602438226 602439246 0.000000e+00 1243.0
11 TraesCS2D01G356600 chr2A 78.802 217 36 6 282 498 497693648 497693854 3.780000e-28 137.0
12 TraesCS2D01G356600 chr4D 79.545 484 88 9 1 480 46113180 46113656 1.250000e-87 335.0
13 TraesCS2D01G356600 chr4D 81.865 386 54 12 79 451 363251643 363251261 2.100000e-80 311.0
14 TraesCS2D01G356600 chr4D 78.218 505 75 15 6 497 500408155 500408637 2.740000e-74 291.0
15 TraesCS2D01G356600 chr3A 79.303 459 68 13 4 453 375022570 375022130 5.890000e-76 296.0
16 TraesCS2D01G356600 chr7D 78.587 467 81 13 4 463 491793317 491792863 2.740000e-74 291.0
17 TraesCS2D01G356600 chr4B 78.360 439 70 6 6 435 618376382 618376804 2.150000e-65 261.0
18 TraesCS2D01G356600 chr4B 78.505 321 50 12 1 318 633272517 633272213 7.950000e-45 193.0
19 TraesCS2D01G356600 chr3D 76.482 506 96 16 1 498 105107953 105108443 3.600000e-63 254.0
20 TraesCS2D01G356600 chr1D 76.647 501 89 20 5 498 204796139 204796618 1.290000e-62 252.0
21 TraesCS2D01G356600 chr1D 75.703 498 94 16 6 494 69614023 69614502 2.820000e-54 224.0
22 TraesCS2D01G356600 chr1D 84.264 197 25 2 4 200 215618713 215618523 3.700000e-43 187.0
23 TraesCS2D01G356600 chr5D 76.209 517 88 18 1 498 458557867 458558367 2.800000e-59 241.0
24 TraesCS2D01G356600 chr5B 79.464 224 36 6 284 498 149263324 149263102 4.850000e-32 150.0
25 TraesCS2D01G356600 chr7B 78.571 224 40 4 282 498 63132858 63132636 2.920000e-29 141.0
26 TraesCS2D01G356600 chr1A 77.515 169 35 3 317 484 546568823 546568657 1.780000e-16 99.0
27 TraesCS2D01G356600 chr6A 75.824 182 43 1 317 498 167669838 167670018 2.980000e-14 91.6


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 TraesCS2D01G356600 chr2D 459288221 459295987 7766 False 14344.0 14344 100.00000 1 7767 1 chr2D.!!$F1 7766
1 TraesCS2D01G356600 chr2D 617110738 617111243 505 False 401.0 401 81.35900 1 505 1 chr2D.!!$F2 504
2 TraesCS2D01G356600 chr2B 540423420 540431226 7806 False 2118.1 7066 93.10860 507 7767 5 chr2B.!!$F1 7260
3 TraesCS2D01G356600 chr2A 602438226 602446433 8207 False 2951.0 4163 93.41125 1 7767 4 chr2A.!!$F2 7766
4 TraesCS2D01G356600 chr5D 458557867 458558367 500 False 241.0 241 76.20900 1 498 1 chr5D.!!$F1 497

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
500 534 0.534203 TCGGCACTTTGGAGTTGTCC 60.534 55.000 0.00 0.00 44.24 4.02 F
1166 1420 0.315568 GTAGGAGTAGGGCTGCGATG 59.684 60.000 0.00 0.00 40.77 3.84 F
1965 2252 1.275573 ACTTCTTTACTGGAGGACCGC 59.724 52.381 0.00 0.00 39.42 5.68 F
1977 2264 1.476891 GAGGACCGCAGACAGATAACA 59.523 52.381 0.00 0.00 0.00 2.41 F
3489 4047 3.855255 TGTCTTTCAGGACAACATGGA 57.145 42.857 0.00 0.00 42.35 3.41 F
3877 4435 4.854291 CGTGTTTTAAGAGTGTGTGCAAAA 59.146 37.500 0.00 0.00 0.00 2.44 F
4110 4690 7.628769 TGCTCTTTAGTATTTTGATGCATCA 57.371 32.000 25.42 25.42 34.44 3.07 F
4819 5425 0.039437 CTAACCGTGTGACGCTCAGT 60.039 55.000 0.00 0.00 40.91 3.41 F
5680 6609 0.542467 ATGCATGTTGGCCTGGAACA 60.542 50.000 9.36 9.36 37.70 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1552 1817 1.068895 CTTGTCATTTGCCACAAGCCA 59.931 47.619 0.00 0.00 42.23 4.75 R
1977 2264 1.971357 AGCTGTAGCGGCTACCATAAT 59.029 47.619 31.14 14.05 45.07 1.28 R
2834 3125 2.555325 CTGAAACAAGCATCAGAAGGCA 59.445 45.455 0.00 0.00 44.64 4.75 R
3757 4315 3.004171 CCAAAAACATGTGCCATCATGG 58.996 45.455 0.00 0.00 46.39 3.66 R
4302 4882 0.177604 CTGACTGGCCTGGATCTGTC 59.822 60.000 14.82 15.34 34.06 3.51 R
4686 5292 0.180406 AGTGCCTGTTGGTCGAGTTT 59.820 50.000 0.00 0.00 35.27 2.66 R
5666 6595 0.770499 TCATCTGTTCCAGGCCAACA 59.230 50.000 5.01 6.20 32.75 3.33 R
6716 7765 0.179000 AGGAAGGCCATACAAGCTCG 59.821 55.000 5.01 0.00 36.29 5.03 R
7029 8125 1.337823 ACCTGAACACCTCGTATGTGC 60.338 52.381 0.00 0.00 37.22 4.57 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
49 50 1.623542 GCCTCCGGCCCTTTCTCTTA 61.624 60.000 0.00 0.00 44.06 2.10
162 166 1.289066 CGGAGCTGACGAAGGTGAA 59.711 57.895 0.00 0.00 36.52 3.18
187 191 4.761058 AAGGCGAGGGAGGCGAGA 62.761 66.667 0.00 0.00 41.99 4.04
280 292 1.153349 GGAGGGAAGTGATGGTCGC 60.153 63.158 0.00 0.00 0.00 5.19
317 329 1.222113 GCCAGGTGGAGAAGTAGGC 59.778 63.158 0.00 0.00 37.39 3.93
325 355 3.398353 GAGAAGTAGGCGCGCGTCT 62.398 63.158 40.13 40.13 0.00 4.18
341 371 1.069090 TCTGTTTCTTGTCCGCGCT 59.931 52.632 5.56 0.00 0.00 5.92
378 408 5.534207 TCAAATTTGAGCCTGAAATGTGT 57.466 34.783 16.91 0.00 32.12 3.72
379 409 5.531634 TCAAATTTGAGCCTGAAATGTGTC 58.468 37.500 16.91 0.00 32.12 3.67
380 410 5.068855 TCAAATTTGAGCCTGAAATGTGTCA 59.931 36.000 16.91 0.00 32.12 3.58
387 421 1.241165 CTGAAATGTGTCAGCAGGCA 58.759 50.000 0.00 0.00 38.74 4.75
404 438 1.646540 CAGACAAAAAGCGGACGCA 59.353 52.632 19.48 0.00 44.88 5.24
410 444 1.707239 AAAAAGCGGACGCACGTTCA 61.707 50.000 19.48 0.00 44.88 3.18
414 448 0.668096 AGCGGACGCACGTTCATTTA 60.668 50.000 19.48 0.00 44.88 1.40
419 453 2.927477 GGACGCACGTTCATTTAGATCA 59.073 45.455 0.00 0.00 0.00 2.92
443 477 1.029681 GTTGGGCCGACTTTTCTGTT 58.970 50.000 17.07 0.00 0.00 3.16
454 488 3.793775 TTTCTGTTCGCGGCGACCA 62.794 57.895 26.40 23.52 34.89 4.02
498 532 1.523758 GATCGGCACTTTGGAGTTGT 58.476 50.000 0.00 0.00 32.54 3.32
499 533 1.464997 GATCGGCACTTTGGAGTTGTC 59.535 52.381 0.00 0.00 32.54 3.18
500 534 0.534203 TCGGCACTTTGGAGTTGTCC 60.534 55.000 0.00 0.00 44.24 4.02
501 535 0.535102 CGGCACTTTGGAGTTGTCCT 60.535 55.000 0.00 0.00 44.30 3.85
502 536 1.270625 CGGCACTTTGGAGTTGTCCTA 60.271 52.381 0.00 0.00 44.30 2.94
504 538 2.427506 GCACTTTGGAGTTGTCCTAGG 58.572 52.381 0.82 0.82 44.30 3.02
505 539 2.427506 CACTTTGGAGTTGTCCTAGGC 58.572 52.381 2.96 0.00 44.30 3.93
547 768 2.359975 CGGGGTGGACAAAGGAGC 60.360 66.667 0.00 0.00 0.00 4.70
634 855 2.047844 CCGCACTCCCACTGACAG 60.048 66.667 0.00 0.00 0.00 3.51
656 877 2.283173 GGCCAGAACCCAACCCAG 60.283 66.667 0.00 0.00 0.00 4.45
657 878 2.840753 GGCCAGAACCCAACCCAGA 61.841 63.158 0.00 0.00 0.00 3.86
658 879 1.603739 GCCAGAACCCAACCCAGAC 60.604 63.158 0.00 0.00 0.00 3.51
659 880 1.074951 CCAGAACCCAACCCAGACC 59.925 63.158 0.00 0.00 0.00 3.85
660 881 1.074951 CAGAACCCAACCCAGACCC 59.925 63.158 0.00 0.00 0.00 4.46
661 882 1.386772 AGAACCCAACCCAGACCCA 60.387 57.895 0.00 0.00 0.00 4.51
662 883 1.228459 GAACCCAACCCAGACCCAC 60.228 63.158 0.00 0.00 0.00 4.61
731 953 1.229400 TTTACCAGTCGCCTCCCCT 60.229 57.895 0.00 0.00 0.00 4.79
983 1205 1.158466 TGAGTCCCTGCTTCCTCCA 59.842 57.895 0.00 0.00 0.00 3.86
1043 1296 1.073284 GTGGTTAGGTTGCTTCCCTGA 59.927 52.381 0.00 0.00 33.35 3.86
1057 1310 3.939740 TCCCTGATTGATTGCTAGCTT 57.060 42.857 17.23 3.07 0.00 3.74
1063 1316 1.755179 TTGATTGCTAGCTTGCCTCC 58.245 50.000 17.57 6.73 0.00 4.30
1111 1364 1.298859 CCCTAGTGCCGTGTTCTTGC 61.299 60.000 0.00 0.00 0.00 4.01
1112 1365 1.298859 CCTAGTGCCGTGTTCTTGCC 61.299 60.000 0.00 0.00 0.00 4.52
1130 1383 2.445525 TGCCTTCTTGGGGTTACTTCTT 59.554 45.455 0.00 0.00 36.00 2.52
1166 1420 0.315568 GTAGGAGTAGGGCTGCGATG 59.684 60.000 0.00 0.00 40.77 3.84
1213 1474 4.870426 TCGCTTGTTTAATCTGGAAGCTAG 59.130 41.667 0.00 0.00 37.48 3.42
1214 1475 4.034510 CGCTTGTTTAATCTGGAAGCTAGG 59.965 45.833 0.00 0.00 37.48 3.02
1215 1476 5.186198 GCTTGTTTAATCTGGAAGCTAGGA 58.814 41.667 0.00 0.00 36.83 2.94
1216 1477 5.295540 GCTTGTTTAATCTGGAAGCTAGGAG 59.704 44.000 0.00 0.00 36.83 3.69
1217 1478 4.770795 TGTTTAATCTGGAAGCTAGGAGC 58.229 43.478 0.00 0.00 42.84 4.70
1404 1668 1.464997 GGGTGAATTTGTCTCTCGTGC 59.535 52.381 0.00 0.00 0.00 5.34
1494 1758 2.217750 AGTTGCGTGCATTGTCAAGTA 58.782 42.857 0.00 0.00 0.00 2.24
1495 1759 2.616376 AGTTGCGTGCATTGTCAAGTAA 59.384 40.909 0.00 0.00 0.00 2.24
1496 1760 2.967459 TGCGTGCATTGTCAAGTAAG 57.033 45.000 0.00 0.00 0.00 2.34
1497 1761 1.535028 TGCGTGCATTGTCAAGTAAGG 59.465 47.619 0.00 0.00 0.00 2.69
1547 1812 5.853936 AGTGTTGTACTGCATGTAGAAAGA 58.146 37.500 18.40 4.84 38.49 2.52
1549 1814 5.465390 GTGTTGTACTGCATGTAGAAAGACA 59.535 40.000 18.40 12.82 36.39 3.41
1550 1815 6.147821 GTGTTGTACTGCATGTAGAAAGACAT 59.852 38.462 18.40 0.00 40.78 3.06
1552 1817 8.040727 TGTTGTACTGCATGTAGAAAGACATAT 58.959 33.333 18.40 0.00 37.99 1.78
1553 1818 8.331022 GTTGTACTGCATGTAGAAAGACATATG 58.669 37.037 18.40 0.00 37.99 1.78
1555 1820 4.818546 ACTGCATGTAGAAAGACATATGGC 59.181 41.667 18.40 3.43 37.99 4.40
1672 1959 7.382759 CCTCGAGTTGTAGCTATTCCTTTATTC 59.617 40.741 12.31 0.00 0.00 1.75
1896 2183 2.162408 GTCTGGAGGCAAACTATTGTGC 59.838 50.000 0.00 0.00 38.85 4.57
1965 2252 1.275573 ACTTCTTTACTGGAGGACCGC 59.724 52.381 0.00 0.00 39.42 5.68
1977 2264 1.476891 GAGGACCGCAGACAGATAACA 59.523 52.381 0.00 0.00 0.00 2.41
2106 2393 5.278315 GCAAAAGACGGAAATTCCTGTAAGT 60.278 40.000 10.64 0.00 33.30 2.24
2517 2807 9.457436 CTATTAAAAGGGCAAGAAAGGTAGTTA 57.543 33.333 0.00 0.00 0.00 2.24
2639 2929 6.258068 GCTAAAAGCCTAATTAGACACGACAT 59.742 38.462 14.28 0.00 34.48 3.06
2834 3125 7.508636 TGGATGGTTTGTAATATACAATGGCAT 59.491 33.333 0.00 0.00 46.89 4.40
2897 3453 6.454795 TGGGCTGAAACATTTTTAGATTGTC 58.545 36.000 0.00 0.00 0.00 3.18
3016 3572 5.084818 TCCATATGTGTGTAGACCAACAG 57.915 43.478 1.24 0.00 0.00 3.16
3198 3756 5.824097 GGTACCTTCACTTCTTTTTACACCA 59.176 40.000 4.06 0.00 0.00 4.17
3201 3759 5.589050 ACCTTCACTTCTTTTTACACCAGTC 59.411 40.000 0.00 0.00 0.00 3.51
3446 4004 6.094603 GCTGCTTTATTTGATTCCTTCTCAGA 59.905 38.462 0.00 0.00 0.00 3.27
3489 4047 3.855255 TGTCTTTCAGGACAACATGGA 57.145 42.857 0.00 0.00 42.35 3.41
3612 4170 8.289618 TGTTTTCATTTGCTGAGTATAGAACAC 58.710 33.333 0.00 0.00 34.68 3.32
3757 4315 6.628919 AATTTGTGGGTACTTGTCAGTTAC 57.371 37.500 0.00 0.00 34.06 2.50
3770 4328 9.641135 TACTTGTCAGTTACCATGATGGCACAT 62.641 40.741 12.25 0.00 37.56 3.21
3877 4435 4.854291 CGTGTTTTAAGAGTGTGTGCAAAA 59.146 37.500 0.00 0.00 0.00 2.44
4110 4690 7.628769 TGCTCTTTAGTATTTTGATGCATCA 57.371 32.000 25.42 25.42 34.44 3.07
4786 5392 2.129785 GGATGGGATGGGCAAGCAC 61.130 63.158 0.00 0.00 0.00 4.40
4807 5413 1.407979 CGGTGCCTCTAATCTAACCGT 59.592 52.381 3.96 0.00 44.17 4.83
4819 5425 0.039437 CTAACCGTGTGACGCTCAGT 60.039 55.000 0.00 0.00 40.91 3.41
4859 5465 5.186198 ACAGAAATGTAGTACTCAATGCCC 58.814 41.667 0.00 0.00 0.00 5.36
4894 5500 8.849168 TCAAGAATGAGCTTCAGAACATAAAAA 58.151 29.630 0.00 0.00 36.24 1.94
5169 5943 6.680874 AAAACACACACCAGTAATCGTTAA 57.319 33.333 0.00 0.00 0.00 2.01
5244 6172 5.914898 AGGTTTGGTATAATGCCTTTGAC 57.085 39.130 0.00 0.00 0.00 3.18
5254 6182 3.763671 CCTTTGACGCAGGCCTTT 58.236 55.556 0.00 0.00 0.00 3.11
5309 6237 3.081061 CTGGATCCAATGTTGACCGAAA 58.919 45.455 17.00 0.00 0.00 3.46
5562 6491 2.629656 GGCTGAACATTGCCGTGCT 61.630 57.895 0.00 0.00 39.71 4.40
5666 6595 7.558161 TGTTTAAGAGATCGATTTGATGCAT 57.442 32.000 0.00 0.00 37.47 3.96
5671 6600 4.275196 AGAGATCGATTTGATGCATGTTGG 59.725 41.667 2.46 0.00 37.47 3.77
5680 6609 0.542467 ATGCATGTTGGCCTGGAACA 60.542 50.000 9.36 9.36 37.70 3.18
5785 6722 8.188531 TGTGTGTGTAGTTTTAGAAACTGTAC 57.811 34.615 14.50 12.84 0.00 2.90
5963 6909 2.430465 AGTCATTGCAGCCTTGTACAG 58.570 47.619 0.00 0.00 0.00 2.74
6012 6959 7.060059 CGTTTGTTTGGGTTCAATTTTGTTTTC 59.940 33.333 0.00 0.00 32.28 2.29
6066 7013 3.567797 GCCTCATCTTGGCGTCGC 61.568 66.667 9.22 9.22 41.03 5.19
6112 7150 4.478206 TTGGGTGCATGTTGAAGAAAAA 57.522 36.364 0.00 0.00 0.00 1.94
6167 7205 9.865484 GTTTGACTTAAACTCATAAGAACACTC 57.135 33.333 1.38 0.00 44.18 3.51
6168 7206 9.832445 TTTGACTTAAACTCATAAGAACACTCT 57.168 29.630 1.38 0.00 36.57 3.24
6392 7437 0.592637 TGAACAAATCCACAGCAGCG 59.407 50.000 0.00 0.00 0.00 5.18
6716 7765 8.882415 AATCAAAATGTATTTCATCATCCAGC 57.118 30.769 0.00 0.00 35.48 4.85
6728 7777 1.202568 TCATCCAGCGAGCTTGTATGG 60.203 52.381 17.13 17.13 0.00 2.74
6908 7967 3.807553 TCTTCTGACATGTTTGACTGCA 58.192 40.909 0.00 0.00 0.00 4.41
6925 7984 1.134128 TGCAAACTGGAACTCTGCTCA 60.134 47.619 0.00 0.00 34.10 4.26
7235 8332 4.057432 ACAATAACTGTGCAAAATGTGGC 58.943 39.130 0.00 0.00 36.69 5.01
7333 8435 4.261801 TCAACTGCTAAGCCCTATGAAAC 58.738 43.478 0.00 0.00 0.00 2.78
7557 8660 4.686191 TGGAAAGGATTGCACACAAAAT 57.314 36.364 0.00 0.00 39.77 1.82
7559 8662 4.815308 TGGAAAGGATTGCACACAAAATTG 59.185 37.500 0.00 0.00 39.77 2.32
7561 8664 5.178067 GGAAAGGATTGCACACAAAATTGAG 59.822 40.000 0.00 0.00 39.77 3.02
7563 8666 3.007182 AGGATTGCACACAAAATTGAGGG 59.993 43.478 0.00 0.00 39.77 4.30
7569 8673 3.305950 GCACACAAAATTGAGGGCACATA 60.306 43.478 12.06 0.00 45.64 2.29
7586 8690 8.903820 AGGGCACATAATCTTGTAGAATTTAAC 58.096 33.333 0.00 0.00 0.00 2.01
7734 8842 8.424918 TCAATTTTAAAGGACATTAACAAGCCA 58.575 29.630 0.00 0.00 0.00 4.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
84 85 0.884514 GCCACCCAAGAAGAAGAAGC 59.115 55.000 0.00 0.00 0.00 3.86
86 87 0.889186 GCGCCACCCAAGAAGAAGAA 60.889 55.000 0.00 0.00 0.00 2.52
150 154 2.204461 TCCGGCTTCACCTTCGTCA 61.204 57.895 0.00 0.00 35.61 4.35
304 316 2.886124 GCGCGCCTACTTCTCCAC 60.886 66.667 23.24 0.00 0.00 4.02
305 317 4.492160 CGCGCGCCTACTTCTCCA 62.492 66.667 27.72 0.00 0.00 3.86
317 329 1.154836 GACAAGAAACAGACGCGCG 60.155 57.895 30.96 30.96 0.00 6.86
325 355 0.602638 ATCAGCGCGGACAAGAAACA 60.603 50.000 13.72 0.00 0.00 2.83
341 371 6.983984 TCAAATTTGAGTCTCATTTGCATCA 58.016 32.000 16.91 4.77 30.50 3.07
368 398 1.199327 CTGCCTGCTGACACATTTCAG 59.801 52.381 0.00 0.00 45.15 3.02
369 399 1.202794 TCTGCCTGCTGACACATTTCA 60.203 47.619 0.00 0.00 0.00 2.69
371 401 1.242076 GTCTGCCTGCTGACACATTT 58.758 50.000 20.08 0.00 42.15 2.32
377 407 1.601412 GCTTTTTGTCTGCCTGCTGAC 60.601 52.381 18.71 18.71 42.65 3.51
378 408 0.670162 GCTTTTTGTCTGCCTGCTGA 59.330 50.000 0.00 0.00 0.00 4.26
379 409 0.662374 CGCTTTTTGTCTGCCTGCTG 60.662 55.000 0.00 0.00 0.00 4.41
380 410 1.656441 CGCTTTTTGTCTGCCTGCT 59.344 52.632 0.00 0.00 0.00 4.24
387 421 1.647084 GTGCGTCCGCTTTTTGTCT 59.353 52.632 13.31 0.00 42.51 3.41
404 438 1.588404 CGCGCTGATCTAAATGAACGT 59.412 47.619 5.56 0.00 0.00 3.99
410 444 1.299541 CCCAACGCGCTGATCTAAAT 58.700 50.000 11.83 0.00 0.00 1.40
443 477 3.342627 CTGTTTTGGTCGCCGCGA 61.343 61.111 12.39 12.39 0.00 5.87
487 521 1.275291 TCGCCTAGGACAACTCCAAAG 59.725 52.381 14.75 0.00 39.39 2.77
498 532 1.464376 GGCATGCTACTCGCCTAGGA 61.464 60.000 18.92 0.00 42.78 2.94
499 533 1.005630 GGCATGCTACTCGCCTAGG 60.006 63.158 18.92 3.67 42.78 3.02
500 534 4.663444 GGCATGCTACTCGCCTAG 57.337 61.111 18.92 0.00 42.78 3.02
689 911 0.450583 GCCGACGGAGGGAATTTTTC 59.549 55.000 20.50 0.00 0.00 2.29
1043 1296 2.305009 GGAGGCAAGCTAGCAATCAAT 58.695 47.619 18.83 0.00 35.83 2.57
1092 1345 1.298859 GCAAGAACACGGCACTAGGG 61.299 60.000 0.00 0.00 0.00 3.53
1130 1383 6.610830 ACTCCTACAAAGAATCCCAGAAAAA 58.389 36.000 0.00 0.00 0.00 1.94
1135 1388 4.101741 CCCTACTCCTACAAAGAATCCCAG 59.898 50.000 0.00 0.00 0.00 4.45
1219 1480 1.782028 AAACAACACCGCGAGAAGCC 61.782 55.000 8.23 0.00 44.76 4.35
1221 1482 1.070577 CAGAAACAACACCGCGAGAAG 60.071 52.381 8.23 0.00 0.00 2.85
1222 1483 0.934496 CAGAAACAACACCGCGAGAA 59.066 50.000 8.23 0.00 0.00 2.87
1223 1484 0.103390 TCAGAAACAACACCGCGAGA 59.897 50.000 8.23 0.00 0.00 4.04
1404 1668 6.017026 TGCACTTATAGACAGATCGAACTAGG 60.017 42.308 0.00 0.00 0.00 3.02
1494 1758 7.880195 CCTCTGCATATTTATAGTAAGCACCTT 59.120 37.037 0.00 0.00 0.00 3.50
1495 1759 7.390027 CCTCTGCATATTTATAGTAAGCACCT 58.610 38.462 0.00 0.00 0.00 4.00
1496 1760 6.092807 GCCTCTGCATATTTATAGTAAGCACC 59.907 42.308 0.00 0.00 37.47 5.01
1497 1761 6.092807 GGCCTCTGCATATTTATAGTAAGCAC 59.907 42.308 0.00 0.00 40.13 4.40
1535 1800 5.297776 ACAAGCCATATGTCTTTCTACATGC 59.702 40.000 0.00 0.00 40.29 4.06
1542 1807 2.754552 TGCCACAAGCCATATGTCTTTC 59.245 45.455 0.00 0.00 42.71 2.62
1545 1810 2.512692 TTGCCACAAGCCATATGTCT 57.487 45.000 1.24 0.00 42.71 3.41
1547 1812 3.098377 TCATTTGCCACAAGCCATATGT 58.902 40.909 1.24 0.00 42.71 2.29
1549 1814 3.098377 TGTCATTTGCCACAAGCCATAT 58.902 40.909 0.00 0.00 42.71 1.78
1550 1815 2.523245 TGTCATTTGCCACAAGCCATA 58.477 42.857 0.00 0.00 42.71 2.74
1552 1817 1.068895 CTTGTCATTTGCCACAAGCCA 59.931 47.619 0.00 0.00 42.23 4.75
1553 1818 1.340889 TCTTGTCATTTGCCACAAGCC 59.659 47.619 6.89 0.00 46.19 4.35
1672 1959 8.697846 ATTTAGTCATTTGTGCTGAATGAATG 57.302 30.769 15.37 5.49 43.06 2.67
1965 2252 5.635280 CGGCTACCATAATGTTATCTGTCTG 59.365 44.000 0.00 0.00 0.00 3.51
1977 2264 1.971357 AGCTGTAGCGGCTACCATAAT 59.029 47.619 31.14 14.05 45.07 1.28
2106 2393 9.938670 CCCGTATATGAAAATTCGTCATTTTTA 57.061 29.630 9.24 6.18 43.89 1.52
2191 2478 8.768955 GTGTTGATAACCACAAAATTTGCATTA 58.231 29.630 5.52 2.96 0.00 1.90
2834 3125 2.555325 CTGAAACAAGCATCAGAAGGCA 59.445 45.455 0.00 0.00 44.64 4.75
2897 3453 4.039004 AGCAGTGGATGATAAGCTCAGTAG 59.961 45.833 0.00 0.00 37.28 2.57
3016 3572 6.942532 TGATGCATAACCCTGTTATTCTTC 57.057 37.500 0.00 2.37 0.00 2.87
3198 3756 5.393569 CCGTATCAGAATCACAAGTCAGACT 60.394 44.000 0.00 0.00 0.00 3.24
3201 3759 4.748892 ACCGTATCAGAATCACAAGTCAG 58.251 43.478 0.00 0.00 0.00 3.51
3489 4047 3.744530 GCTGACCGAAGCCCAATATTAGT 60.745 47.826 0.00 0.00 37.20 2.24
3743 4301 4.332819 GCCATCATGGTAACTGACAAGTAC 59.667 45.833 5.31 0.00 40.46 2.73
3757 4315 3.004171 CCAAAAACATGTGCCATCATGG 58.996 45.455 0.00 0.00 46.39 3.66
3770 4328 7.012799 GGACAGCCAAAATAATTTCCAAAAACA 59.987 33.333 0.00 0.00 0.00 2.83
3846 4404 4.062991 CACTCTTAAAACACGTTAGGCCT 58.937 43.478 11.78 11.78 0.00 5.19
4110 4690 3.740115 AGAATGCGTCTGTTTACCTGTT 58.260 40.909 0.00 0.00 34.29 3.16
4302 4882 0.177604 CTGACTGGCCTGGATCTGTC 59.822 60.000 14.82 15.34 34.06 3.51
4686 5292 0.180406 AGTGCCTGTTGGTCGAGTTT 59.820 50.000 0.00 0.00 35.27 2.66
4786 5392 1.269621 CGGTTAGATTAGAGGCACCGG 60.270 57.143 0.00 0.00 42.80 5.28
4807 5413 3.446310 TGTAAGAAACTGAGCGTCACA 57.554 42.857 0.00 0.00 0.00 3.58
4819 5425 8.250332 ACATTTCTGTTTTCTGCTTGTAAGAAA 58.750 29.630 0.00 0.00 40.88 2.52
4859 5465 4.871993 AGCTCATTCTTGAAACTATGCG 57.128 40.909 0.00 0.00 0.00 4.73
5164 5938 3.733337 AGATGGGATAAGCAGCTTAACG 58.267 45.455 18.87 0.00 29.35 3.18
5169 5943 3.560882 GGCAATAGATGGGATAAGCAGCT 60.561 47.826 0.00 0.00 0.00 4.24
5244 6172 2.540265 ATATCTCTCAAAGGCCTGCG 57.460 50.000 5.69 0.00 0.00 5.18
5254 6182 6.767902 GGACATTGCCTTTGTTATATCTCTCA 59.232 38.462 0.00 0.00 0.00 3.27
5296 6224 4.571580 TCGTTTACTGTTTCGGTCAACATT 59.428 37.500 6.59 0.00 36.08 2.71
5666 6595 0.770499 TCATCTGTTCCAGGCCAACA 59.230 50.000 5.01 6.20 32.75 3.33
5671 6600 1.672881 CGGAATTCATCTGTTCCAGGC 59.327 52.381 7.93 0.00 43.22 4.85
5680 6609 2.766263 TGCCTCTACACGGAATTCATCT 59.234 45.455 7.93 0.00 0.00 2.90
5785 6722 6.647212 TCTTATACAAGTCGACAATGCTTG 57.353 37.500 19.50 14.93 43.56 4.01
5942 6888 3.007940 ACTGTACAAGGCTGCAATGACTA 59.992 43.478 10.34 0.00 0.00 2.59
5963 6909 5.556947 CGGAAGAAGCTGCAAAAATTTGAAC 60.557 40.000 9.96 0.00 40.55 3.18
6012 6959 0.958822 AAAACAAACCCAGGCTAGCG 59.041 50.000 9.00 0.00 0.00 4.26
6062 7009 6.073440 TGAGTTGTTTTGTATTAGAAGGCGAC 60.073 38.462 0.00 0.00 0.00 5.19
6066 7013 9.965824 AAATGTGAGTTGTTTTGTATTAGAAGG 57.034 29.630 0.00 0.00 0.00 3.46
6112 7150 6.569226 CGTGCTTGGATTTGAAGAGATCTTTT 60.569 38.462 0.00 0.00 36.11 2.27
6167 7205 6.469410 TGGGGTCAGTTTTTGTGTATACTAG 58.531 40.000 4.17 0.00 0.00 2.57
6168 7206 6.436738 TGGGGTCAGTTTTTGTGTATACTA 57.563 37.500 4.17 0.00 0.00 1.82
6392 7437 1.474077 CTTGCTTTGGGGTCTGCATAC 59.526 52.381 0.00 0.00 35.27 2.39
6437 7482 6.381498 TTGGTCATACTGGTCCTTAATTCA 57.619 37.500 0.00 0.00 0.00 2.57
6620 7666 5.855045 ACTTCTTCGCTCTTAAGAAAAGGA 58.145 37.500 6.63 4.97 41.21 3.36
6716 7765 0.179000 AGGAAGGCCATACAAGCTCG 59.821 55.000 5.01 0.00 36.29 5.03
6728 7777 3.574826 ACGTTCTATATCTGGAGGAAGGC 59.425 47.826 0.00 0.00 0.00 4.35
6908 7967 3.584848 ACCTATGAGCAGAGTTCCAGTTT 59.415 43.478 0.00 0.00 0.00 2.66
6917 7976 3.488721 GCAATTGCAACCTATGAGCAGAG 60.489 47.826 25.36 0.00 39.72 3.35
6925 7984 6.588719 TTCAACTTAGCAATTGCAACCTAT 57.411 33.333 30.89 12.66 45.16 2.57
7029 8125 1.337823 ACCTGAACACCTCGTATGTGC 60.338 52.381 0.00 0.00 37.22 4.57
7235 8332 3.558505 CAAGGAAGCTCATGTTGTTTCG 58.441 45.455 0.00 0.00 0.00 3.46
7545 8648 1.483827 TGCCCTCAATTTTGTGTGCAA 59.516 42.857 0.00 0.00 0.00 4.08
7557 8660 5.692115 TCTACAAGATTATGTGCCCTCAA 57.308 39.130 0.00 0.00 34.75 3.02
7559 8662 7.573968 AAATTCTACAAGATTATGTGCCCTC 57.426 36.000 0.00 0.00 34.75 4.30
7561 8664 8.903820 AGTTAAATTCTACAAGATTATGTGCCC 58.096 33.333 0.00 0.00 34.75 5.36
7563 8666 9.937175 GGAGTTAAATTCTACAAGATTATGTGC 57.063 33.333 0.00 0.00 34.75 4.57
7734 8842 5.325239 CTTCCTTTTTGGGATTCACTAGGT 58.675 41.667 0.00 0.00 35.07 3.08


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

AutoCloner maintained by Alex Coulton.