Multiple sequence alignment - TraesCS6B01G150400

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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 TraesCS6B01G150400 chr6B 100.000 7995 0 0 1 7995 151377318 151385312 0.000000e+00 14765.0
1 TraesCS6B01G150400 chr6B 84.639 3561 384 84 3824 7303 151300782 151297304 0.000000e+00 3395.0
2 TraesCS6B01G150400 chr6B 86.286 1823 205 25 1213 3015 151303565 151301768 0.000000e+00 1940.0
3 TraesCS6B01G150400 chr6B 84.909 656 76 15 3012 3657 151301688 151301046 6.760000e-180 641.0
4 TraesCS6B01G150400 chr6B 79.679 871 91 31 2 811 151304760 151303915 4.220000e-152 549.0
5 TraesCS6B01G150400 chr6B 81.410 624 104 8 1980 2598 151154100 151153484 4.310000e-137 499.0
6 TraesCS6B01G150400 chr6B 81.729 613 97 11 5228 5836 151151094 151150493 1.550000e-136 497.0
7 TraesCS6B01G150400 chr6B 86.957 391 51 0 6458 6848 151149284 151148894 2.650000e-119 440.0
8 TraesCS6B01G150400 chr6B 80.816 490 49 24 5991 6472 151149798 151149346 7.680000e-90 342.0
9 TraesCS6B01G150400 chr6B 89.947 189 19 0 997 1185 151303743 151303555 2.230000e-60 244.0
10 TraesCS6B01G150400 chr6D 94.323 4668 154 39 2771 7361 78760464 78765097 0.000000e+00 7049.0
11 TraesCS6B01G150400 chr6D 92.777 2658 79 34 1 2609 78757709 78760302 0.000000e+00 3740.0
12 TraesCS6B01G150400 chr6D 84.896 3562 388 81 3824 7303 78542155 78538662 0.000000e+00 3459.0
13 TraesCS6B01G150400 chr6D 86.993 1653 176 16 1213 2855 78544789 78543166 0.000000e+00 1825.0
14 TraesCS6B01G150400 chr6D 78.842 1295 179 51 5228 6479 78303959 78302717 0.000000e+00 785.0
15 TraesCS6B01G150400 chr6D 79.340 1273 141 54 2 1185 78546018 78544779 0.000000e+00 782.0
16 TraesCS6B01G150400 chr6D 93.388 484 20 9 7515 7995 78765975 78766449 0.000000e+00 706.0
17 TraesCS6B01G150400 chr6D 85.061 656 73 17 3012 3657 78543059 78542419 0.000000e+00 645.0
18 TraesCS6B01G150400 chr6D 78.345 1039 149 33 4711 5693 78357325 78356307 3.190000e-168 603.0
19 TraesCS6B01G150400 chr6D 78.918 906 133 25 4264 5127 78500934 78500045 5.420000e-156 562.0
20 TraesCS6B01G150400 chr6D 84.910 391 59 0 6458 6848 78302662 78302272 5.810000e-106 396.0
21 TraesCS6B01G150400 chr6D 94.611 167 7 1 7363 7527 78765791 78765957 2.860000e-64 257.0
22 TraesCS6B01G150400 chr6D 94.702 151 3 2 2594 2744 78760324 78760469 6.240000e-56 230.0
23 TraesCS6B01G150400 chr6D 80.682 264 45 6 4264 4526 78357777 78357519 4.890000e-47 200.0
24 TraesCS6B01G150400 chr6D 93.617 47 3 0 6552 6598 296824508 296824462 4.000000e-08 71.3
25 TraesCS6B01G150400 chr6A 93.203 2766 139 32 834 3559 94232460 94235216 0.000000e+00 4021.0
26 TraesCS6B01G150400 chr6A 84.642 3516 405 77 3852 7303 94200552 94197108 0.000000e+00 3376.0
27 TraesCS6B01G150400 chr6A 87.828 2136 166 45 3559 5631 94235342 94237446 0.000000e+00 2418.0
28 TraesCS6B01G150400 chr6A 92.683 1599 88 15 5940 7531 94238698 94240274 0.000000e+00 2278.0
29 TraesCS6B01G150400 chr6A 87.701 1496 155 18 1213 2700 94210871 94209397 0.000000e+00 1716.0
30 TraesCS6B01G150400 chr6A 83.989 712 91 15 2957 3657 94207292 94206593 0.000000e+00 662.0
31 TraesCS6B01G150400 chr6A 79.299 884 113 39 5630 6472 93891464 93890610 9.070000e-154 555.0
32 TraesCS6B01G150400 chr6A 84.725 491 43 21 1 481 94231731 94232199 5.650000e-126 462.0
33 TraesCS6B01G150400 chr6A 85.934 391 55 0 6458 6848 93890543 93890153 1.240000e-112 418.0
34 TraesCS6B01G150400 chr6A 83.333 468 60 15 5234 5692 94070351 94069893 4.460000e-112 416.0
35 TraesCS6B01G150400 chr6A 93.358 271 18 0 5623 5893 94238424 94238694 1.250000e-107 401.0
36 TraesCS6B01G150400 chr6A 85.100 349 32 10 2 331 94212163 94211816 9.940000e-89 339.0
37 TraesCS6B01G150400 chr6A 82.967 364 47 7 823 1185 94211210 94210861 1.670000e-81 315.0
38 TraesCS6B01G150400 chr6A 86.957 138 8 6 7518 7647 94240290 94240425 6.470000e-31 147.0
39 TraesCS6B01G150400 chr6A 84.516 155 10 10 597 740 94232273 94232424 3.010000e-29 141.0


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 TraesCS6B01G150400 chr6B 151377318 151385312 7994 False 14765.000000 14765 100.000000 1 7995 1 chr6B.!!$F1 7994
1 TraesCS6B01G150400 chr6B 151297304 151304760 7456 True 1353.800000 3395 85.092000 2 7303 5 chr6B.!!$R2 7301
2 TraesCS6B01G150400 chr6B 151148894 151154100 5206 True 444.500000 499 82.728000 1980 6848 4 chr6B.!!$R1 4868
3 TraesCS6B01G150400 chr6D 78757709 78766449 8740 False 2396.400000 7049 93.960200 1 7995 5 chr6D.!!$F1 7994
4 TraesCS6B01G150400 chr6D 78538662 78546018 7356 True 1677.750000 3459 84.072500 2 7303 4 chr6D.!!$R5 7301
5 TraesCS6B01G150400 chr6D 78302272 78303959 1687 True 590.500000 785 81.876000 5228 6848 2 chr6D.!!$R3 1620
6 TraesCS6B01G150400 chr6D 78500045 78500934 889 True 562.000000 562 78.918000 4264 5127 1 chr6D.!!$R1 863
7 TraesCS6B01G150400 chr6D 78356307 78357777 1470 True 401.500000 603 79.513500 4264 5693 2 chr6D.!!$R4 1429
8 TraesCS6B01G150400 chr6A 94197108 94200552 3444 True 3376.000000 3376 84.642000 3852 7303 1 chr6A.!!$R2 3451
9 TraesCS6B01G150400 chr6A 94231731 94240425 8694 False 1409.714286 4021 89.038571 1 7647 7 chr6A.!!$F1 7646
10 TraesCS6B01G150400 chr6A 94206593 94212163 5570 True 758.000000 1716 84.939250 2 3657 4 chr6A.!!$R4 3655
11 TraesCS6B01G150400 chr6A 93890153 93891464 1311 True 486.500000 555 82.616500 5630 6848 2 chr6A.!!$R3 1218

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
831 997 0.320247 GCACTAGCTCACTGCACACT 60.320 55.000 0.00 0.0 45.94 3.55 F
1906 2163 0.249447 CGGTCGCTGAATATCCTGCA 60.249 55.000 0.00 0.0 0.00 4.41 F
1959 2225 0.107361 ACCGCCGCTTTTAGCCTTAT 60.107 50.000 0.00 0.0 38.18 1.73 F
1960 2226 1.139455 ACCGCCGCTTTTAGCCTTATA 59.861 47.619 0.00 0.0 38.18 0.98 F
3597 6024 0.035458 GGATATTCTCCCCACCTGCG 59.965 60.000 0.00 0.0 38.19 5.18 F
4261 7043 0.817634 TCTGGGCACAACTGTTTCCG 60.818 55.000 0.00 0.0 0.00 4.30 F
5017 7938 1.202989 TGGCAATGGTACTTCCTGCAA 60.203 47.619 10.42 0.0 38.60 4.08 F
5232 8206 3.530265 ATGCTTGCCATTACATTGTGG 57.470 42.857 0.00 0.0 38.55 4.17 F
6649 11323 1.108776 GCATGAGCATCCACATTGGT 58.891 50.000 0.00 0.0 38.69 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1934 2200 0.096454 CTAAAAGCGGCGGTTACAGC 59.904 55.000 25.54 0.00 0.00 4.40 R
3257 5551 1.852157 ATTTCAGAGGGGCTTGCCGA 61.852 55.000 5.49 0.00 0.00 5.54 R
3416 5714 3.381272 CCAAAGGAAGACAAGTTTCTGCA 59.619 43.478 0.00 0.00 0.00 4.41 R
3664 6095 5.470368 GTCTGCGAATTAGGTGCATATAGA 58.530 41.667 0.00 0.00 38.07 1.98 R
5232 8206 4.319118 GCCTTTCGCTTAGCTGAATACATC 60.319 45.833 1.76 0.00 0.00 3.06 R
5880 9940 2.030628 GCTGGTTTAGTGCGCCTAAAAA 60.031 45.455 23.66 16.95 44.98 1.94 R
6374 10957 1.091771 CAATGGTACCAGCTGGCTCG 61.092 60.000 33.06 9.57 39.32 5.03 R
6793 11467 1.105167 CCACGACCTCCGCCATAGTA 61.105 60.000 0.00 0.00 43.32 1.82 R
7538 12956 0.179156 CACGTTGCCATCTTGCATCC 60.179 55.000 0.00 0.00 41.70 3.51 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
125 138 2.203153 GGTGCGGTGGTGTCTTGT 60.203 61.111 0.00 0.00 0.00 3.16
341 377 3.748048 TGAAAAATCAGGACTTCTCTGCG 59.252 43.478 0.00 0.00 32.63 5.18
379 425 9.439500 TGTTAAAATTATTAACTGCTCCGTAGT 57.561 29.630 16.86 0.00 36.23 2.73
385 431 2.381725 AACTGCTCCGTAGTTAAGCC 57.618 50.000 0.00 0.00 36.77 4.35
386 432 0.535797 ACTGCTCCGTAGTTAAGCCC 59.464 55.000 0.00 0.00 35.12 5.19
387 433 0.535335 CTGCTCCGTAGTTAAGCCCA 59.465 55.000 0.00 0.00 35.12 5.36
388 434 1.139058 CTGCTCCGTAGTTAAGCCCAT 59.861 52.381 0.00 0.00 35.12 4.00
389 435 2.364324 CTGCTCCGTAGTTAAGCCCATA 59.636 50.000 0.00 0.00 35.12 2.74
390 436 2.364324 TGCTCCGTAGTTAAGCCCATAG 59.636 50.000 0.00 0.00 35.12 2.23
437 483 7.013369 GGCACCTTATTCTTCCCTAACTTTATG 59.987 40.741 0.00 0.00 0.00 1.90
468 520 4.933400 GCCACTTGTAAGATTCGTTAGGAA 59.067 41.667 0.00 0.00 39.42 3.36
484 536 9.545105 TTCGTTAGGAACATCTTGTTAGTTTAA 57.455 29.630 0.00 0.00 41.28 1.52
510 580 6.080406 GCACAAGCTTTAGCAGTTAAGTTAG 58.920 40.000 13.51 0.00 45.16 2.34
604 750 5.245301 CCATTCCGGAGATTAGTACATACCA 59.755 44.000 3.34 0.00 36.56 3.25
615 761 9.277783 AGATTAGTACATACCATGAAATGCTTC 57.722 33.333 0.00 0.00 44.97 3.86
658 816 9.998106 TGCCCTTCTGATTTATTATTCTACTAC 57.002 33.333 0.00 0.00 0.00 2.73
819 985 5.096482 TGTTTCCAAACAGCTGCACTAGC 62.096 47.826 15.27 0.00 43.45 3.42
828 994 2.453843 CTGCACTAGCTCACTGCAC 58.546 57.895 8.42 0.00 45.94 4.57
831 997 0.320247 GCACTAGCTCACTGCACACT 60.320 55.000 0.00 0.00 45.94 3.55
832 998 1.875576 GCACTAGCTCACTGCACACTT 60.876 52.381 0.00 0.00 45.94 3.16
839 1031 1.620819 CTCACTGCACACTTACCCTCT 59.379 52.381 0.00 0.00 0.00 3.69
904 1097 1.678101 GCATTTGCTACTCCCATGGAC 59.322 52.381 15.22 0.00 38.21 4.02
916 1111 4.537288 ACTCCCATGGACATGCATATATGA 59.463 41.667 15.22 2.36 37.49 2.15
989 1241 5.077564 TCTCCTAGTTTGCTCACAAGAGTA 58.922 41.667 0.00 0.00 44.00 2.59
1005 1257 8.939929 TCACAAGAGTAAAGAATAAGCATGAAG 58.060 33.333 0.00 0.00 0.00 3.02
1006 1258 8.725148 CACAAGAGTAAAGAATAAGCATGAAGT 58.275 33.333 0.00 0.00 0.00 3.01
1073 1325 2.615912 GACAGCCTGATTATCAAGGTGC 59.384 50.000 19.17 10.71 39.26 5.01
1113 1366 9.561069 TCTTATTTCTTACTGCTCTTTCTGTTT 57.439 29.630 0.00 0.00 0.00 2.83
1172 1425 7.450014 TCATAGCCAAAAGTTTATTCAAGGTCA 59.550 33.333 0.00 0.00 0.00 4.02
1309 1562 8.044908 TCTACCTACCAAGATTCCATTACAAAC 58.955 37.037 0.00 0.00 0.00 2.93
1384 1637 1.688735 TCCTCAGATTACATGGAGCCG 59.311 52.381 0.00 0.00 0.00 5.52
1432 1685 1.226030 GGTTCTTTCCACACGGTCCG 61.226 60.000 10.48 10.48 0.00 4.79
1579 1832 7.883311 ACAAACTACTGGCATGAAGTTAACTAT 59.117 33.333 8.92 0.00 32.09 2.12
1780 2033 2.473070 TCTAATCGGTTCCACATGGGA 58.527 47.619 0.00 0.00 46.61 4.37
1906 2163 0.249447 CGGTCGCTGAATATCCTGCA 60.249 55.000 0.00 0.00 0.00 4.41
1959 2225 0.107361 ACCGCCGCTTTTAGCCTTAT 60.107 50.000 0.00 0.00 38.18 1.73
1960 2226 1.139455 ACCGCCGCTTTTAGCCTTATA 59.861 47.619 0.00 0.00 38.18 0.98
1961 2227 1.529865 CCGCCGCTTTTAGCCTTATAC 59.470 52.381 0.00 0.00 38.18 1.47
1962 2228 1.191647 CGCCGCTTTTAGCCTTATACG 59.808 52.381 0.00 0.00 38.18 3.06
2093 2364 1.479730 CTAAACAGGTACCCCTCGGAC 59.520 57.143 8.74 0.00 39.89 4.79
2141 2412 7.497579 ACATATAATGCAATTCCGAACTGTACA 59.502 33.333 0.00 0.00 37.87 2.90
2143 2414 3.889196 TGCAATTCCGAACTGTACAAC 57.111 42.857 0.00 0.00 0.00 3.32
2474 2745 6.743575 AATTATAGTGTCTCACTTGTTGCC 57.256 37.500 7.70 0.00 42.59 4.52
2533 2804 4.974645 TGGAGATGTACTTGGTGAAACT 57.025 40.909 0.00 0.00 36.74 2.66
2805 4799 8.405418 AGTCTCACTAGTGATTTAGTGTAACA 57.595 34.615 25.35 0.00 46.75 2.41
3042 5322 4.820894 TTTCCTAGCAGTAAAGAGGGTC 57.179 45.455 0.00 0.00 0.00 4.46
3257 5551 7.327064 AGAGGATTAAACTGCTCATATCCAT 57.673 36.000 0.00 0.00 36.17 3.41
3405 5702 3.669536 AGAGAAGCTAACTGTTCTTGGC 58.330 45.455 0.00 0.00 33.04 4.52
3410 5708 4.625607 AGCTAACTGTTCTTGGCTTACT 57.374 40.909 0.00 0.00 34.53 2.24
3463 5761 4.473477 AGTTGGTGCCATCTCTACTAAC 57.527 45.455 0.00 0.00 36.44 2.34
3487 5785 3.608316 AGAGATCTCAAAGCACTCCAC 57.392 47.619 24.39 0.00 0.00 4.02
3548 5847 8.677300 CACTGTGGAATTTTAACATGCTACTAT 58.323 33.333 0.00 0.00 0.00 2.12
3597 6024 0.035458 GGATATTCTCCCCACCTGCG 59.965 60.000 0.00 0.00 38.19 5.18
3664 6095 5.007682 ACACGAAGGTTTGTATAAGCCAAT 58.992 37.500 7.80 0.00 39.43 3.16
3675 6122 7.921786 TTGTATAAGCCAATCTATATGCACC 57.078 36.000 0.00 0.00 0.00 5.01
3688 6135 1.290203 ATGCACCTAATTCGCAGACG 58.710 50.000 0.00 0.00 39.39 4.18
3769 6233 9.581289 TTGTTTATGGAGAGAATTACCTGAAAA 57.419 29.630 0.00 0.00 0.00 2.29
3821 6286 4.715534 TGAACTTCCCAGTGGATAACAA 57.284 40.909 11.95 0.00 41.40 2.83
3884 6414 9.490379 GGAAAAAGAAAGAACTGTCTGTATCTA 57.510 33.333 0.00 0.00 33.05 1.98
3943 6473 3.302870 CGTTTTTCTACACCGTTCACCAG 60.303 47.826 0.00 0.00 0.00 4.00
4001 6768 4.323868 GGAGACAAACGTAACTCTTCATCG 59.676 45.833 0.00 0.00 0.00 3.84
4030 6797 5.583854 CAGTGACTAGATGCATACTTTTGCT 59.416 40.000 0.00 0.00 43.18 3.91
4091 6859 5.127356 ACTTCCAAAAACGTTGTATTTCCCA 59.873 36.000 0.00 0.00 0.00 4.37
4095 6863 5.460748 CCAAAAACGTTGTATTTCCCACTTC 59.539 40.000 0.00 0.00 0.00 3.01
4108 6876 2.172717 TCCCACTTCCCTTATTAGCTGC 59.827 50.000 0.00 0.00 0.00 5.25
4261 7043 0.817634 TCTGGGCACAACTGTTTCCG 60.818 55.000 0.00 0.00 0.00 4.30
4639 7476 7.011482 GCTGGAAAGATAAGTTACGTCATCATT 59.989 37.037 0.00 0.00 0.00 2.57
4654 7491 8.630278 ACGTCATCATTACTTATCAACTGTAC 57.370 34.615 0.00 0.00 0.00 2.90
5017 7938 1.202989 TGGCAATGGTACTTCCTGCAA 60.203 47.619 10.42 0.00 38.60 4.08
5141 8068 4.475944 CGCTCAAAGGAAAAGGTAACATG 58.524 43.478 0.00 0.00 41.41 3.21
5232 8206 3.530265 ATGCTTGCCATTACATTGTGG 57.470 42.857 0.00 0.00 38.55 4.17
6374 10957 6.238022 GCGACTCCAAAACACATATAACTACC 60.238 42.308 0.00 0.00 0.00 3.18
6419 11002 7.959689 GTACTTAGATCCTGAGTACGTCATA 57.040 40.000 11.50 0.00 41.33 2.15
6646 11320 2.022195 GACAGCATGAGCATCCACATT 58.978 47.619 0.00 0.00 45.49 2.71
6649 11323 1.108776 GCATGAGCATCCACATTGGT 58.891 50.000 0.00 0.00 38.69 3.67
6939 11613 6.147000 GCACTTGAGGTAGAAGAAGAAGAAAG 59.853 42.308 0.00 0.00 0.00 2.62
7007 11693 7.700505 TGCAATGAGATGATAGTTTTGATGAC 58.299 34.615 0.00 0.00 0.00 3.06
7013 11699 9.383519 TGAGATGATAGTTTTGATGACCTTAAC 57.616 33.333 0.00 0.00 0.00 2.01
7274 11962 4.219033 GTTGGCATGTTCGTCTTAGTTTG 58.781 43.478 0.00 0.00 0.00 2.93
7275 11963 3.472652 TGGCATGTTCGTCTTAGTTTGT 58.527 40.909 0.00 0.00 0.00 2.83
7276 11964 3.496884 TGGCATGTTCGTCTTAGTTTGTC 59.503 43.478 0.00 0.00 0.00 3.18
7314 12002 5.431765 TGTTTCTCTCCTCTTGGCAATATC 58.568 41.667 0.00 0.00 0.00 1.63
7397 12783 2.107366 GCTGGGGGCAAATAAAGCTTA 58.893 47.619 0.00 0.00 41.35 3.09
7407 12795 7.308830 GGGGCAAATAAAGCTTACATCATCTAG 60.309 40.741 0.00 0.00 0.00 2.43
7440 12828 1.896755 GCATTGGATGGTTGGTTCCCT 60.897 52.381 0.00 0.00 0.00 4.20
7441 12829 1.826720 CATTGGATGGTTGGTTCCCTG 59.173 52.381 0.00 0.00 0.00 4.45
7509 12897 3.412237 TGTGATGATCGATGATGCCAT 57.588 42.857 0.54 0.00 35.29 4.40
7538 12956 6.261826 AGGAATTTCTTGATTCTTAGGATGCG 59.738 38.462 0.00 0.00 36.50 4.73
7573 12991 4.230657 CAACGTGTGAAAACCTTGAAACA 58.769 39.130 0.00 0.00 0.00 2.83
7584 13003 8.428063 TGAAAACCTTGAAACAATATTGATGGT 58.572 29.630 22.16 13.12 0.00 3.55
7872 13300 9.278978 ACATAAAAATGTGGTAAAAATGGGAAC 57.721 29.630 0.00 0.00 32.79 3.62
7876 13304 9.554395 AAAAATGTGGTAAAAATGGGAACTTAG 57.446 29.630 0.00 0.00 0.00 2.18
7877 13305 8.485578 AAATGTGGTAAAAATGGGAACTTAGA 57.514 30.769 0.00 0.00 0.00 2.10
7878 13306 7.703058 ATGTGGTAAAAATGGGAACTTAGAG 57.297 36.000 0.00 0.00 0.00 2.43
7879 13307 6.007703 TGTGGTAAAAATGGGAACTTAGAGG 58.992 40.000 0.00 0.00 0.00 3.69
7956 13385 4.751600 CCACAAATTGAGGAAAAGAAAGCC 59.248 41.667 3.23 0.00 28.90 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
370 416 2.364647 ACTATGGGCTTAACTACGGAGC 59.635 50.000 0.00 0.00 35.71 4.70
371 417 4.826183 AGTACTATGGGCTTAACTACGGAG 59.174 45.833 0.00 0.00 0.00 4.63
373 419 6.639632 TTAGTACTATGGGCTTAACTACGG 57.360 41.667 2.79 0.00 0.00 4.02
374 420 9.837525 CTTATTAGTACTATGGGCTTAACTACG 57.162 37.037 2.79 0.00 0.00 3.51
387 433 9.930693 GCCTCATTGCTTACTTATTAGTACTAT 57.069 33.333 2.79 0.00 36.61 2.12
388 434 8.920174 TGCCTCATTGCTTACTTATTAGTACTA 58.080 33.333 0.00 0.00 36.61 1.82
389 435 7.711339 GTGCCTCATTGCTTACTTATTAGTACT 59.289 37.037 0.00 0.00 36.61 2.73
390 436 7.041984 GGTGCCTCATTGCTTACTTATTAGTAC 60.042 40.741 0.00 0.00 36.61 2.73
468 520 6.918022 GCTTGTGCTTTAAACTAACAAGATGT 59.082 34.615 23.96 0.00 46.81 3.06
556 626 5.376854 AACAGTGTGGAACTAATTGCATC 57.623 39.130 0.00 0.00 38.55 3.91
595 741 5.506317 GGCTGAAGCATTTCATGGTATGTAC 60.506 44.000 4.43 0.00 42.19 2.90
604 750 1.760613 CCCATGGCTGAAGCATTTCAT 59.239 47.619 6.09 0.00 42.19 2.57
615 761 0.532115 GCAAGTAAACCCCATGGCTG 59.468 55.000 6.09 1.56 33.59 4.85
658 816 1.739466 CCATGTGGTTTGGTCATCTCG 59.261 52.381 0.00 0.00 0.00 4.04
796 962 1.134946 AGTGCAGCTGTTTGGAAACAC 59.865 47.619 16.64 11.77 43.45 3.32
819 985 1.620819 AGAGGGTAAGTGTGCAGTGAG 59.379 52.381 0.00 0.00 0.00 3.51
821 987 2.146342 CAAGAGGGTAAGTGTGCAGTG 58.854 52.381 0.00 0.00 0.00 3.66
822 988 2.047061 TCAAGAGGGTAAGTGTGCAGT 58.953 47.619 0.00 0.00 0.00 4.40
823 989 2.839486 TCAAGAGGGTAAGTGTGCAG 57.161 50.000 0.00 0.00 0.00 4.41
824 990 2.906389 AGATCAAGAGGGTAAGTGTGCA 59.094 45.455 0.00 0.00 0.00 4.57
827 993 7.682787 AATGATAGATCAAGAGGGTAAGTGT 57.317 36.000 0.00 0.00 40.69 3.55
828 994 9.650539 CATAATGATAGATCAAGAGGGTAAGTG 57.349 37.037 0.00 0.00 40.69 3.16
831 997 8.972662 TCCATAATGATAGATCAAGAGGGTAA 57.027 34.615 0.00 0.00 40.69 2.85
832 998 8.972662 TTCCATAATGATAGATCAAGAGGGTA 57.027 34.615 0.00 0.00 40.69 3.69
904 1097 7.121611 AGAGAGAGAGACTGTCATATATGCATG 59.878 40.741 10.16 0.00 40.74 4.06
916 1111 4.357325 AGAGAGAGAGAGAGAGAGACTGT 58.643 47.826 0.00 0.00 0.00 3.55
1005 1257 6.651225 AGAAAAGGAGAACTGCTACACATAAC 59.349 38.462 0.00 0.00 0.00 1.89
1006 1258 6.769512 AGAAAAGGAGAACTGCTACACATAA 58.230 36.000 0.00 0.00 0.00 1.90
1073 1325 4.399303 AGAAATAAGAATTGAGGGGCAACG 59.601 41.667 0.00 0.00 39.78 4.10
1113 1366 3.812609 TGCTTCTCGTTGTGCATTTTCTA 59.187 39.130 0.00 0.00 0.00 2.10
1127 1380 0.320247 AGCAACAGAGGTGCTTCTCG 60.320 55.000 3.28 0.00 38.71 4.04
1172 1425 7.663081 ACTTATGCATCACGGATTTCTATCATT 59.337 33.333 0.19 0.00 32.09 2.57
1238 1491 4.846779 TGCTTATGAAACCTGGAAACAC 57.153 40.909 0.00 0.00 35.60 3.32
1432 1685 2.501723 TCTCAGGGTGTAGCAATTCCTC 59.498 50.000 0.00 0.00 0.00 3.71
1489 1742 8.820831 CCATCATAGTTTCCATAGTAGAAGGAT 58.179 37.037 0.00 0.00 0.00 3.24
1679 1932 1.821136 CCTCAAATCCAGCCCAGAAAC 59.179 52.381 0.00 0.00 0.00 2.78
1780 2033 5.653769 CCTGATTATTGAATTGTCTGTGGGT 59.346 40.000 0.00 0.00 0.00 4.51
1887 2144 0.249447 TGCAGGATATTCAGCGACCG 60.249 55.000 0.00 0.00 0.00 4.79
1934 2200 0.096454 CTAAAAGCGGCGGTTACAGC 59.904 55.000 25.54 0.00 0.00 4.40
1945 2211 4.085210 GCAGTACGTATAAGGCTAAAAGCG 60.085 45.833 0.00 0.00 43.62 4.68
1959 2225 7.036829 TGCAGATAAAACTTATGCAGTACGTA 58.963 34.615 0.00 0.00 41.65 3.57
1960 2226 5.872617 TGCAGATAAAACTTATGCAGTACGT 59.127 36.000 0.00 0.00 41.65 3.57
1961 2227 6.344572 TGCAGATAAAACTTATGCAGTACG 57.655 37.500 0.00 0.00 41.65 3.67
1962 2228 7.148239 ACCTTGCAGATAAAACTTATGCAGTAC 60.148 37.037 0.00 0.00 46.51 2.73
2093 2364 2.511452 CCAGATGCGGTCTAGGGGG 61.511 68.421 0.00 0.00 34.69 5.40
2141 2412 4.406648 TGGAGATGTTGCAGATATCGTT 57.593 40.909 0.00 0.00 31.70 3.85
2143 2414 4.378149 GCATTGGAGATGTTGCAGATATCG 60.378 45.833 0.00 0.00 35.22 2.92
2711 4667 8.504005 GTCAATCGAAAGGTTTTAGAATTCAGA 58.496 33.333 8.44 0.00 26.76 3.27
2768 4724 3.666345 AGTGAGACTACCCGAGGTTAT 57.334 47.619 0.72 0.00 37.09 1.89
2769 4725 3.521126 ACTAGTGAGACTACCCGAGGTTA 59.479 47.826 0.00 0.00 37.09 2.85
2805 4799 2.033911 TGGACACGTGGCATGCAT 59.966 55.556 25.47 0.00 0.00 3.96
3025 5305 2.376109 TCCGACCCTCTTTACTGCTAG 58.624 52.381 0.00 0.00 0.00 3.42
3042 5322 8.425577 AATGTGATAAAGAACAGTCTAATCCG 57.574 34.615 0.00 0.00 32.16 4.18
3211 5505 6.049149 TCTCCATATAAAAGCTTTCGGAGTG 58.951 40.000 25.17 16.48 39.82 3.51
3257 5551 1.852157 ATTTCAGAGGGGCTTGCCGA 61.852 55.000 5.49 0.00 0.00 5.54
3320 5614 3.938963 TCAGCGTATGAGAATGGGTTTTC 59.061 43.478 0.00 0.00 32.77 2.29
3416 5714 3.381272 CCAAAGGAAGACAAGTTTCTGCA 59.619 43.478 0.00 0.00 0.00 4.41
3463 5761 5.580297 GTGGAGTGCTTTGAGATCTCTAAAG 59.420 44.000 26.60 26.60 34.21 1.85
3664 6095 5.470368 GTCTGCGAATTAGGTGCATATAGA 58.530 41.667 0.00 0.00 38.07 1.98
3675 6122 6.911484 AATTTTCAAACGTCTGCGAATTAG 57.089 33.333 0.00 0.00 42.00 1.73
3884 6414 7.914427 TCATGTAACCAGAGTTCCTATATGT 57.086 36.000 0.00 0.00 37.42 2.29
4030 6797 6.631971 TCACTGCATGACTGAATACAAAAA 57.368 33.333 0.00 0.00 29.99 1.94
4091 6859 5.358160 GTGAATTGCAGCTAATAAGGGAAGT 59.642 40.000 0.00 0.00 0.00 3.01
4095 6863 5.357878 TCTTGTGAATTGCAGCTAATAAGGG 59.642 40.000 0.00 0.00 0.00 3.95
4108 6876 7.148340 GGAAGGAGTAACAGATCTTGTGAATTG 60.148 40.741 0.00 0.00 40.74 2.32
4294 7081 3.173953 TCATTGCTGGACAAATCCCTT 57.826 42.857 0.00 0.00 45.59 3.95
5017 7938 5.182001 CCATTGATCTTCTTTCGAACTGGTT 59.818 40.000 0.00 0.00 0.00 3.67
5141 8068 4.952335 AGAAACCATCATTTCCATCTGACC 59.048 41.667 0.00 0.00 39.05 4.02
5226 8200 4.512944 CGCTTAGCTGAATACATCCACAAT 59.487 41.667 1.76 0.00 0.00 2.71
5232 8206 4.319118 GCCTTTCGCTTAGCTGAATACATC 60.319 45.833 1.76 0.00 0.00 3.06
5880 9940 2.030628 GCTGGTTTAGTGCGCCTAAAAA 60.031 45.455 23.66 16.95 44.98 1.94
6374 10957 1.091771 CAATGGTACCAGCTGGCTCG 61.092 60.000 33.06 9.57 39.32 5.03
6419 11002 5.104610 ACAGGAGAAGATATTGATGCTGTGT 60.105 40.000 7.86 0.00 40.45 3.72
6646 11320 3.157949 TCGTGCACCCACTCACCA 61.158 61.111 12.15 0.00 39.86 4.17
6649 11323 1.806461 GACTCTCGTGCACCCACTCA 61.806 60.000 12.15 0.00 39.86 3.41
6667 11341 1.890489 TCGATGTTTCCTTGGTCGAGA 59.110 47.619 0.00 0.00 36.52 4.04
6676 11350 3.005554 CACAATGCTCTCGATGTTTCCT 58.994 45.455 0.00 0.00 0.00 3.36
6793 11467 1.105167 CCACGACCTCCGCCATAGTA 61.105 60.000 0.00 0.00 43.32 1.82
6939 11613 1.334869 CTCCACCTTGTTGCTGTTGTC 59.665 52.381 0.00 0.00 0.00 3.18
7007 11693 4.536765 ACCTCCAGCATTTATGGTTAAGG 58.463 43.478 13.70 13.70 40.53 2.69
7012 11698 2.311542 TCCAACCTCCAGCATTTATGGT 59.688 45.455 0.00 0.00 39.01 3.55
7013 11699 2.954318 CTCCAACCTCCAGCATTTATGG 59.046 50.000 0.00 0.00 39.33 2.74
7274 11962 3.328237 AACATCAAAAACACGGACGAC 57.672 42.857 0.00 0.00 0.00 4.34
7275 11963 3.623960 AGAAACATCAAAAACACGGACGA 59.376 39.130 0.00 0.00 0.00 4.20
7276 11964 3.947626 AGAAACATCAAAAACACGGACG 58.052 40.909 0.00 0.00 0.00 4.79
7344 12038 7.347252 TCCTAAGACGATGTATATAGCCAGAT 58.653 38.462 0.00 0.00 0.00 2.90
7345 12039 6.718294 TCCTAAGACGATGTATATAGCCAGA 58.282 40.000 0.00 0.00 0.00 3.86
7356 12050 3.226777 CCTCTGGATCCTAAGACGATGT 58.773 50.000 14.23 0.00 0.00 3.06
7397 12783 8.459911 TGCATGATTGATTTTCTAGATGATGT 57.540 30.769 0.00 0.00 0.00 3.06
7407 12795 6.053005 ACCATCCAATGCATGATTGATTTTC 58.947 36.000 0.00 0.00 43.87 2.29
7440 12828 4.753516 TCAGAAAGAAGTGTCACCTTCA 57.246 40.909 13.92 0.00 42.68 3.02
7441 12829 7.913674 AATATCAGAAAGAAGTGTCACCTTC 57.086 36.000 0.00 3.52 40.95 3.46
7509 12897 5.653769 CCTAAGAATCAAGAAATTCCTGCCA 59.346 40.000 0.00 0.00 36.49 4.92
7538 12956 0.179156 CACGTTGCCATCTTGCATCC 60.179 55.000 0.00 0.00 41.70 3.51
7573 12991 6.108015 GTGTGAAATGCCAACCATCAATATT 58.892 36.000 0.00 0.00 31.43 1.28
7876 13304 9.634021 AACTTCCTTGGATATTAGATTTTCCTC 57.366 33.333 0.00 0.00 0.00 3.71


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

AutoCloner maintained by Alex Coulton.