Multiple sequence alignment - TraesCS7A01G448100

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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 TraesCS7A01G448100 chr7A 100.000 2599 0 0 1 2599 642378235 642380833 0.000000e+00 4800.0
1 TraesCS7A01G448100 chr7A 87.376 1212 105 17 910 2103 642732807 642731626 0.000000e+00 1347.0
2 TraesCS7A01G448100 chr7A 95.442 373 14 1 534 903 65977082 65977454 2.230000e-165 592.0
3 TraesCS7A01G448100 chr7A 94.385 374 18 1 533 903 7286298 7286671 2.900000e-159 571.0
4 TraesCS7A01G448100 chr7A 91.530 366 26 3 173 536 642733302 642732940 1.390000e-137 499.0
5 TraesCS7A01G448100 chr7A 93.143 175 7 2 1 175 642733541 642733372 4.290000e-63 252.0
6 TraesCS7A01G448100 chr7D 94.717 2120 76 11 1 2103 556775916 556778016 0.000000e+00 3262.0
7 TraesCS7A01G448100 chr7D 92.308 377 14 9 536 903 47118259 47118629 2.960000e-144 521.0
8 TraesCS7A01G448100 chr7D 89.211 380 27 5 535 903 496720572 496720948 1.820000e-126 462.0
9 TraesCS7A01G448100 chr7D 86.869 198 16 5 2384 2573 556779524 556779719 2.030000e-51 213.0
10 TraesCS7A01G448100 chr7D 81.517 211 17 12 2104 2313 556778092 556778281 1.250000e-33 154.0
11 TraesCS7A01G448100 chr7B 91.338 785 58 7 910 1685 604331350 604332133 0.000000e+00 1064.0
12 TraesCS7A01G448100 chr7B 92.287 363 23 3 173 533 604330855 604331214 6.420000e-141 510.0
13 TraesCS7A01G448100 chr7B 80.775 671 66 26 1947 2576 604333992 604334640 1.410000e-127 466.0
14 TraesCS7A01G448100 chr7B 91.071 224 18 1 1737 1958 604332153 604332376 4.200000e-78 302.0
15 TraesCS7A01G448100 chr7B 91.429 175 10 2 1 175 604330615 604330784 4.320000e-58 235.0
16 TraesCS7A01G448100 chr6B 88.947 380 30 6 535 903 640627218 640626840 2.360000e-125 459.0
17 TraesCS7A01G448100 chr5D 88.947 380 28 7 536 904 446308060 446307684 8.480000e-125 457.0
18 TraesCS7A01G448100 chr3A 89.276 373 28 8 536 899 725451948 725451579 8.480000e-125 457.0
19 TraesCS7A01G448100 chr4D 88.918 379 29 8 535 903 60175493 60175118 3.050000e-124 455.0
20 TraesCS7A01G448100 chr4D 100.000 30 0 0 2378 2407 222349838 222349809 3.610000e-04 56.5
21 TraesCS7A01G448100 chr2A 84.158 101 13 1 2269 2369 137951005 137951102 7.660000e-16 95.3
22 TraesCS7A01G448100 chr2A 88.889 72 8 0 2298 2369 137942121 137942192 3.560000e-14 89.8
23 TraesCS7A01G448100 chr2A 92.308 52 1 1 2304 2355 138084166 138084214 1.290000e-08 71.3
24 TraesCS7A01G448100 chr2D 83.168 101 14 2 2269 2369 131316563 131316660 3.560000e-14 89.8
25 TraesCS7A01G448100 chr2D 87.671 73 6 1 2298 2370 131295065 131295134 5.960000e-12 82.4
26 TraesCS7A01G448100 chr2B 90.625 64 3 1 2298 2361 184800014 184800074 5.960000e-12 82.4
27 TraesCS7A01G448100 chr2B 89.394 66 4 1 2304 2369 184928298 184928360 2.140000e-11 80.5
28 TraesCS7A01G448100 chr6D 100.000 30 0 0 2378 2407 418421015 418421044 3.610000e-04 56.5


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 TraesCS7A01G448100 chr7A 642378235 642380833 2598 False 4800.000000 4800 100.000 1 2599 1 chr7A.!!$F3 2598
1 TraesCS7A01G448100 chr7A 642731626 642733541 1915 True 699.333333 1347 90.683 1 2103 3 chr7A.!!$R1 2102
2 TraesCS7A01G448100 chr7D 556775916 556779719 3803 False 1209.666667 3262 87.701 1 2573 3 chr7D.!!$F3 2572
3 TraesCS7A01G448100 chr7B 604330615 604334640 4025 False 515.400000 1064 89.380 1 2576 5 chr7B.!!$F1 2575

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
74 75 0.476771 AACATTCCTGAACCCACCGT 59.523 50.0 0.0 0.0 0.0 4.83 F
77 78 0.616891 ATTCCTGAACCCACCGTACC 59.383 55.0 0.0 0.0 0.0 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1142 1227 0.544357 TGTCGAATGTGGGGTCCTCT 60.544 55.000 0.0 0.0 0.00 3.69 R
1850 1954 1.211703 TCAGGTCACTGCTTTGTTGGA 59.788 47.619 0.0 0.0 44.54 3.53 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
73 74 0.881118 CAACATTCCTGAACCCACCG 59.119 55.000 0.00 0.00 0.00 4.94
74 75 0.476771 AACATTCCTGAACCCACCGT 59.523 50.000 0.00 0.00 0.00 4.83
75 76 1.354101 ACATTCCTGAACCCACCGTA 58.646 50.000 0.00 0.00 0.00 4.02
76 77 1.002773 ACATTCCTGAACCCACCGTAC 59.997 52.381 0.00 0.00 0.00 3.67
77 78 0.616891 ATTCCTGAACCCACCGTACC 59.383 55.000 0.00 0.00 0.00 3.34
227 301 0.810426 GCTTAACGGCTCTGGGTAGC 60.810 60.000 0.00 0.00 41.99 3.58
262 337 5.029973 AGGAGCCCCAATCTATATACAGT 57.970 43.478 0.00 0.00 33.88 3.55
320 395 6.947464 TCCTTAGTCTGCAAAGCTAGTTATT 58.053 36.000 0.00 0.00 0.00 1.40
555 632 1.793134 CTAGAGAATACCCCGCGCGT 61.793 60.000 29.95 13.36 0.00 6.01
828 909 1.473258 TTTCCCATGCATGTAGTGGC 58.527 50.000 24.58 0.00 0.00 5.01
832 913 2.516930 ATGCATGTAGTGGCGGGC 60.517 61.111 0.00 0.00 0.00 6.13
907 991 7.806680 TCAACTTATGTATATAGGATGGGCA 57.193 36.000 0.00 0.00 0.00 5.36
1142 1227 5.401531 AGAAGAGTGTGCTTTTATACCGA 57.598 39.130 0.00 0.00 0.00 4.69
1221 1306 1.344393 TGGAGGTGACCTATGCCATCT 60.344 52.381 2.97 0.00 31.76 2.90
1262 1347 1.807142 GAAGTTGCTGTGAGGCTTACC 59.193 52.381 6.99 0.00 0.00 2.85
1287 1372 5.707242 TCGCGATGTAAAAGATCCTATCT 57.293 39.130 3.71 0.00 42.61 1.98
1388 1473 3.721035 CATATGTGCACGATCAGGAGAA 58.279 45.455 13.13 0.00 0.00 2.87
1404 1489 2.751806 GGAGAACTGATTCCTTTGGCTG 59.248 50.000 0.00 0.00 35.18 4.85
1436 1521 0.521291 CGGTGCCATTGTACAAGGTG 59.479 55.000 18.13 10.39 0.00 4.00
1451 1536 5.138125 ACAAGGTGCTGGTAATTGAATTG 57.862 39.130 0.00 0.00 0.00 2.32
1538 1623 2.395690 GATCAAACGGCGCGTCTG 59.604 61.111 9.90 8.55 39.99 3.51
1571 1656 5.607477 AGTGGTACTCAAATCGAAGTGAAA 58.393 37.500 0.00 0.00 0.00 2.69
1605 1690 8.967664 TTCACAGTATTTTAGGTAGTGTGTTT 57.032 30.769 16.33 0.00 46.32 2.83
1681 1776 1.271926 GCCCAGTCCCTTGTGTTGTAT 60.272 52.381 0.00 0.00 0.00 2.29
1682 1777 2.026636 GCCCAGTCCCTTGTGTTGTATA 60.027 50.000 0.00 0.00 0.00 1.47
1683 1778 3.606687 CCCAGTCCCTTGTGTTGTATAC 58.393 50.000 0.00 0.00 0.00 1.47
1684 1779 3.263425 CCCAGTCCCTTGTGTTGTATACT 59.737 47.826 4.17 0.00 0.00 2.12
1685 1780 4.263331 CCCAGTCCCTTGTGTTGTATACTT 60.263 45.833 4.17 0.00 0.00 2.24
1686 1781 4.695455 CCAGTCCCTTGTGTTGTATACTTG 59.305 45.833 4.17 0.00 0.00 3.16
1687 1782 5.305585 CAGTCCCTTGTGTTGTATACTTGT 58.694 41.667 4.17 0.00 0.00 3.16
1688 1783 6.460781 CAGTCCCTTGTGTTGTATACTTGTA 58.539 40.000 4.17 0.00 0.00 2.41
1689 1784 7.103641 CAGTCCCTTGTGTTGTATACTTGTAT 58.896 38.462 4.17 0.00 0.00 2.29
1721 1816 9.809096 CACAAGCTTCTTCTACTCTCATATTAA 57.191 33.333 0.00 0.00 0.00 1.40
1726 1821 9.134734 GCTTCTTCTACTCTCATATTAATTCCG 57.865 37.037 0.00 0.00 0.00 4.30
1815 1919 9.883142 TGAAATTCTAAGTTCATGTTGGTTTTT 57.117 25.926 1.73 0.00 37.99 1.94
1879 1983 0.947244 CAGTGACCTGACCTTTGTGC 59.053 55.000 0.00 0.00 41.50 4.57
1891 1996 5.486526 TGACCTTTGTGCAGAATTTTGTTT 58.513 33.333 0.00 0.00 0.00 2.83
1943 2048 3.131400 TGTTGTTCTTGGTTAAACCTGGC 59.869 43.478 0.00 0.00 39.58 4.85
1976 3708 7.800380 CGTGATGAATAAGAATTTCTACATGCC 59.200 37.037 0.00 0.00 0.00 4.40
1978 3710 9.412460 TGATGAATAAGAATTTCTACATGCCTT 57.588 29.630 0.00 0.00 0.00 4.35
1981 3713 9.859427 TGAATAAGAATTTCTACATGCCTTTTG 57.141 29.630 0.00 0.00 0.00 2.44
1982 3714 9.305925 GAATAAGAATTTCTACATGCCTTTTGG 57.694 33.333 0.00 0.00 44.18 3.28
1989 3721 4.331968 TCTACATGCCTTTTGGTTGGTAG 58.668 43.478 0.00 0.00 42.99 3.18
2069 3801 0.752009 CAGAGTAGGTGCGAGGGCTA 60.752 60.000 0.00 0.00 40.82 3.93
2108 3916 3.726144 TGCGCCATGGTCCCATCA 61.726 61.111 14.67 0.00 33.90 3.07
2178 3986 1.373590 CCAAGCCGACCAATTACCGG 61.374 60.000 0.00 0.00 45.51 5.28
2201 4009 4.371855 ACATGCATTGATTTGAGAGCAG 57.628 40.909 0.00 0.00 35.26 4.24
2223 4032 6.627065 GCAGAGTAGACACTAGAGCTTGAAAT 60.627 42.308 0.00 0.00 34.21 2.17
2229 4038 6.940739 AGACACTAGAGCTTGAAATGTACAT 58.059 36.000 1.41 1.41 0.00 2.29
2231 4040 7.332926 AGACACTAGAGCTTGAAATGTACATTG 59.667 37.037 21.46 10.18 0.00 2.82
2232 4041 6.128172 ACACTAGAGCTTGAAATGTACATTGC 60.128 38.462 21.46 19.87 0.00 3.56
2233 4042 4.346734 AGAGCTTGAAATGTACATTGCG 57.653 40.909 21.46 9.20 0.00 4.85
2234 4043 3.753272 AGAGCTTGAAATGTACATTGCGT 59.247 39.130 21.46 6.41 0.00 5.24
2235 4044 4.935205 AGAGCTTGAAATGTACATTGCGTA 59.065 37.500 21.46 10.78 0.00 4.42
2236 4045 5.586243 AGAGCTTGAAATGTACATTGCGTAT 59.414 36.000 21.46 5.64 31.20 3.06
2237 4046 5.810525 AGCTTGAAATGTACATTGCGTATC 58.189 37.500 21.46 14.65 31.20 2.24
2238 4047 5.353956 AGCTTGAAATGTACATTGCGTATCA 59.646 36.000 21.46 16.91 31.20 2.15
2239 4048 5.452302 GCTTGAAATGTACATTGCGTATCAC 59.548 40.000 21.46 6.90 31.20 3.06
2240 4049 5.478233 TGAAATGTACATTGCGTATCACC 57.522 39.130 21.46 4.22 31.20 4.02
2241 4050 4.033472 TGAAATGTACATTGCGTATCACCG 59.967 41.667 21.46 0.00 31.20 4.94
2242 4051 2.943449 TGTACATTGCGTATCACCGA 57.057 45.000 0.00 0.00 31.20 4.69
2243 4052 3.233684 TGTACATTGCGTATCACCGAA 57.766 42.857 0.00 0.00 31.20 4.30
2256 4065 2.479837 TCACCGAAACATATCATCGCC 58.520 47.619 0.00 0.00 35.35 5.54
2264 4073 4.890158 AACATATCATCGCCCATGTCTA 57.110 40.909 0.00 0.00 33.66 2.59
2271 4080 8.982685 CATATCATCGCCCATGTCTAAATATAC 58.017 37.037 0.00 0.00 33.66 1.47
2314 4144 3.133362 AGACCGAAGTCAGTAAACAACCA 59.867 43.478 0.00 0.00 46.15 3.67
2315 4145 3.200483 ACCGAAGTCAGTAAACAACCAC 58.800 45.455 0.00 0.00 0.00 4.16
2316 4146 2.546789 CCGAAGTCAGTAAACAACCACC 59.453 50.000 0.00 0.00 0.00 4.61
2317 4147 2.220133 CGAAGTCAGTAAACAACCACCG 59.780 50.000 0.00 0.00 0.00 4.94
2318 4148 3.460103 GAAGTCAGTAAACAACCACCGA 58.540 45.455 0.00 0.00 0.00 4.69
2319 4149 3.107642 AGTCAGTAAACAACCACCGAG 57.892 47.619 0.00 0.00 0.00 4.63
2320 4150 2.696707 AGTCAGTAAACAACCACCGAGA 59.303 45.455 0.00 0.00 0.00 4.04
2321 4151 3.323979 AGTCAGTAAACAACCACCGAGAT 59.676 43.478 0.00 0.00 0.00 2.75
2322 4152 3.432252 GTCAGTAAACAACCACCGAGATG 59.568 47.826 0.00 0.00 0.00 2.90
2323 4153 2.159627 CAGTAAACAACCACCGAGATGC 59.840 50.000 0.00 0.00 0.00 3.91
2324 4154 2.147958 GTAAACAACCACCGAGATGCA 58.852 47.619 0.00 0.00 0.00 3.96
2325 4155 1.238439 AAACAACCACCGAGATGCAG 58.762 50.000 0.00 0.00 0.00 4.41
2326 4156 0.606401 AACAACCACCGAGATGCAGG 60.606 55.000 0.00 0.00 0.00 4.85
2327 4157 1.003355 CAACCACCGAGATGCAGGT 60.003 57.895 0.00 0.00 42.34 4.00
2331 4161 2.982130 ACCGAGATGCAGGTGACC 59.018 61.111 0.00 0.00 39.66 4.02
2344 4174 2.067197 GTGACCTACCAACAGGCCT 58.933 57.895 0.00 0.00 39.53 5.19
2361 4191 2.514458 CCTCCAAGGCACCATAGTTT 57.486 50.000 0.00 0.00 0.00 2.66
2422 5445 9.339492 GTCTTATATTATGTTAGTGTACGGAGC 57.661 37.037 0.00 0.00 0.00 4.70
2423 5446 9.293404 TCTTATATTATGTTAGTGTACGGAGCT 57.707 33.333 0.00 0.00 0.00 4.09
2433 5456 3.439476 AGTGTACGGAGCTTAGTAGTGTG 59.561 47.826 2.94 0.00 0.00 3.82
2434 5457 2.163010 TGTACGGAGCTTAGTAGTGTGC 59.837 50.000 2.94 0.00 0.00 4.57
2459 5482 6.243900 CCATCTGGATTTTGGAGTGCTATAT 58.756 40.000 0.00 0.00 37.39 0.86
2494 5525 4.219392 TCTCTTATCTCCCACCCATCAT 57.781 45.455 0.00 0.00 0.00 2.45
2544 5575 1.004610 CACACAGACAAGAAGCACACG 60.005 52.381 0.00 0.00 0.00 4.49
2576 5607 1.886222 GCTGGGCAAGAACACCATGTA 60.886 52.381 0.00 0.00 33.07 2.29
2577 5608 2.086869 CTGGGCAAGAACACCATGTAG 58.913 52.381 0.00 0.00 33.07 2.74
2578 5609 1.271871 TGGGCAAGAACACCATGTAGG 60.272 52.381 0.00 0.00 45.67 3.18
2579 5610 1.463674 GGCAAGAACACCATGTAGGG 58.536 55.000 0.00 0.00 43.89 3.53
2580 5611 1.271926 GGCAAGAACACCATGTAGGGT 60.272 52.381 0.00 0.00 43.89 4.34
2586 5617 4.579354 ACCATGTAGGGTGCCTGA 57.421 55.556 0.00 0.00 43.89 3.86
2587 5618 2.785743 ACCATGTAGGGTGCCTGAA 58.214 52.632 0.00 0.00 43.89 3.02
2588 5619 0.328258 ACCATGTAGGGTGCCTGAAC 59.672 55.000 0.00 0.00 43.89 3.18
2589 5620 0.620556 CCATGTAGGGTGCCTGAACT 59.379 55.000 0.00 0.00 34.61 3.01
2590 5621 1.407437 CCATGTAGGGTGCCTGAACTC 60.407 57.143 0.00 0.00 34.61 3.01
2591 5622 0.912486 ATGTAGGGTGCCTGAACTCC 59.088 55.000 0.00 0.00 34.61 3.85
2592 5623 1.198759 TGTAGGGTGCCTGAACTCCC 61.199 60.000 0.00 0.00 42.62 4.30
2593 5624 1.159905 TAGGGTGCCTGAACTCCCA 59.840 57.895 4.63 0.00 44.37 4.37
2594 5625 0.253160 TAGGGTGCCTGAACTCCCAT 60.253 55.000 4.63 0.00 44.37 4.00
2595 5626 1.077429 GGGTGCCTGAACTCCCATC 60.077 63.158 0.00 0.00 42.01 3.51
2596 5627 1.450312 GGTGCCTGAACTCCCATCG 60.450 63.158 0.00 0.00 0.00 3.84
2597 5628 2.109126 GTGCCTGAACTCCCATCGC 61.109 63.158 0.00 0.00 0.00 4.58
2598 5629 2.268920 GCCTGAACTCCCATCGCA 59.731 61.111 0.00 0.00 0.00 5.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
271 346 1.153369 CAGTGCCTGGTACGATGGG 60.153 63.158 9.33 0.00 0.00 4.00
320 395 1.871418 AGAGCCAGCATGTCCTCTTA 58.129 50.000 0.00 0.00 39.04 2.10
401 476 8.304596 TCTTTCTTCTATTATCAACACACGACT 58.695 33.333 0.00 0.00 0.00 4.18
555 632 0.108709 GCAATTGATTCCCGCAGCAA 60.109 50.000 10.34 0.00 0.00 3.91
828 909 1.750399 CCACCTCATCAAAGGCCCG 60.750 63.158 0.00 0.00 40.34 6.13
832 913 1.475280 CACATGCCACCTCATCAAAGG 59.525 52.381 0.00 0.00 42.55 3.11
879 960 9.218525 CCCATCCTATATACATAAGTTGATCCT 57.781 37.037 0.00 0.00 0.00 3.24
1011 1095 4.323485 CCAGGACCAGTTAGCACAAGATTA 60.323 45.833 0.00 0.00 0.00 1.75
1142 1227 0.544357 TGTCGAATGTGGGGTCCTCT 60.544 55.000 0.00 0.00 0.00 3.69
1221 1306 1.887956 GCATTCAACTCCCTGGCTCAA 60.888 52.381 0.00 0.00 0.00 3.02
1262 1347 3.393800 AGGATCTTTTACATCGCGATGG 58.606 45.455 42.28 28.38 42.91 3.51
1287 1372 2.295909 CGACAATTCTCCCAAAAAGGCA 59.704 45.455 0.00 0.00 35.39 4.75
1388 1473 1.425066 TGTCCAGCCAAAGGAATCAGT 59.575 47.619 0.00 0.00 36.80 3.41
1397 1482 1.250328 CAAGCAGATGTCCAGCCAAA 58.750 50.000 0.00 0.00 0.00 3.28
1404 1489 3.044059 GCACCGCAAGCAGATGTCC 62.044 63.158 0.00 0.00 0.00 4.02
1436 1521 4.098349 TGCAGATCCAATTCAATTACCAGC 59.902 41.667 0.00 0.00 0.00 4.85
1451 1536 2.286872 CCACAATCAGAGTGCAGATCC 58.713 52.381 0.00 0.00 35.69 3.36
1538 1623 3.876274 TGAGTACCACTCTTGCTGATC 57.124 47.619 7.75 0.00 45.27 2.92
1589 1674 5.648526 TGAGCAACAAACACACTACCTAAAA 59.351 36.000 0.00 0.00 0.00 1.52
1605 1690 1.227943 GTGACCCAGCTGAGCAACA 60.228 57.895 17.39 5.17 0.00 3.33
1684 1779 9.635520 GTAGAAGAAGCTTGTGTAGTAATACAA 57.364 33.333 2.10 0.00 35.66 2.41
1685 1780 9.021807 AGTAGAAGAAGCTTGTGTAGTAATACA 57.978 33.333 2.10 0.00 0.00 2.29
1686 1781 9.505995 GAGTAGAAGAAGCTTGTGTAGTAATAC 57.494 37.037 2.10 0.00 0.00 1.89
1687 1782 9.463902 AGAGTAGAAGAAGCTTGTGTAGTAATA 57.536 33.333 2.10 0.00 0.00 0.98
1688 1783 8.356000 AGAGTAGAAGAAGCTTGTGTAGTAAT 57.644 34.615 2.10 0.00 0.00 1.89
1689 1784 7.447545 TGAGAGTAGAAGAAGCTTGTGTAGTAA 59.552 37.037 2.10 0.00 0.00 2.24
1721 1816 2.312424 TTTTACCTTTGGCCCGGAAT 57.688 45.000 0.73 0.00 0.00 3.01
1726 1821 2.811431 GCAAACATTTTACCTTTGGCCC 59.189 45.455 0.00 0.00 0.00 5.80
1850 1954 1.211703 TCAGGTCACTGCTTTGTTGGA 59.788 47.619 0.00 0.00 44.54 3.53
1851 1955 1.334869 GTCAGGTCACTGCTTTGTTGG 59.665 52.381 0.00 0.00 44.54 3.77
1879 1983 4.496175 GCCCAGCAAACAAACAAAATTCTG 60.496 41.667 0.00 0.00 0.00 3.02
1891 1996 2.101783 CAATATCTGGCCCAGCAAACA 58.898 47.619 5.66 0.00 0.00 2.83
1976 3708 5.008712 GGTCAGTTCTTCTACCAACCAAAAG 59.991 44.000 0.00 0.00 32.04 2.27
1978 3710 4.165372 AGGTCAGTTCTTCTACCAACCAAA 59.835 41.667 0.00 0.00 34.29 3.28
1979 3711 3.714798 AGGTCAGTTCTTCTACCAACCAA 59.285 43.478 0.00 0.00 34.29 3.67
1980 3712 3.314693 AGGTCAGTTCTTCTACCAACCA 58.685 45.455 0.00 0.00 34.29 3.67
1981 3713 3.323979 TGAGGTCAGTTCTTCTACCAACC 59.676 47.826 0.00 0.00 34.29 3.77
1982 3714 4.202223 TGTGAGGTCAGTTCTTCTACCAAC 60.202 45.833 0.00 0.00 34.29 3.77
2091 3824 3.702529 CTGATGGGACCATGGCGCA 62.703 63.158 21.80 21.80 36.70 6.09
2123 3931 2.126424 GACGCGAAGAACGGCTCT 60.126 61.111 15.93 0.00 42.83 4.09
2161 3969 0.325602 TTCCGGTAATTGGTCGGCTT 59.674 50.000 0.00 0.00 43.10 4.35
2178 3986 4.740268 TGCTCTCAAATCAATGCATGTTC 58.260 39.130 0.00 0.00 0.00 3.18
2201 4009 6.626302 ACATTTCAAGCTCTAGTGTCTACTC 58.374 40.000 0.00 0.00 38.36 2.59
2223 4032 2.943449 TCGGTGATACGCAATGTACA 57.057 45.000 0.00 0.00 35.44 2.90
2229 4038 4.434520 TGATATGTTTCGGTGATACGCAA 58.565 39.130 0.00 0.00 0.00 4.85
2231 4040 4.201494 CGATGATATGTTTCGGTGATACGC 60.201 45.833 0.00 0.00 0.00 4.42
2232 4041 4.201494 GCGATGATATGTTTCGGTGATACG 60.201 45.833 0.00 0.00 33.62 3.06
2233 4042 4.091509 GGCGATGATATGTTTCGGTGATAC 59.908 45.833 0.00 0.00 33.62 2.24
2234 4043 4.242475 GGCGATGATATGTTTCGGTGATA 58.758 43.478 0.00 0.00 33.62 2.15
2235 4044 3.067106 GGCGATGATATGTTTCGGTGAT 58.933 45.455 0.00 0.00 33.62 3.06
2236 4045 2.479837 GGCGATGATATGTTTCGGTGA 58.520 47.619 0.00 0.00 33.62 4.02
2237 4046 1.531149 GGGCGATGATATGTTTCGGTG 59.469 52.381 0.00 0.00 33.62 4.94
2238 4047 1.140052 TGGGCGATGATATGTTTCGGT 59.860 47.619 0.00 0.00 33.62 4.69
2239 4048 1.877637 TGGGCGATGATATGTTTCGG 58.122 50.000 0.00 0.00 33.62 4.30
2240 4049 2.807967 ACATGGGCGATGATATGTTTCG 59.192 45.455 16.77 0.00 35.80 3.46
2241 4050 4.067896 AGACATGGGCGATGATATGTTTC 58.932 43.478 16.77 1.45 34.18 2.78
2242 4051 4.090761 AGACATGGGCGATGATATGTTT 57.909 40.909 16.77 0.00 34.18 2.83
2243 4052 3.777106 AGACATGGGCGATGATATGTT 57.223 42.857 16.77 0.00 34.18 2.71
2256 4065 7.814587 TCAATCTCTGCGTATATTTAGACATGG 59.185 37.037 0.00 0.00 0.00 3.66
2264 4073 5.119279 GCGTGATCAATCTCTGCGTATATTT 59.881 40.000 0.00 0.00 0.00 1.40
2271 4080 1.215244 ATGCGTGATCAATCTCTGCG 58.785 50.000 0.00 0.00 0.00 5.18
2314 4144 0.324368 TAGGTCACCTGCATCTCGGT 60.324 55.000 6.61 0.00 34.61 4.69
2315 4145 0.103208 GTAGGTCACCTGCATCTCGG 59.897 60.000 6.61 0.00 36.26 4.63
2316 4146 0.103208 GGTAGGTCACCTGCATCTCG 59.897 60.000 14.66 0.00 44.79 4.04
2325 4155 1.489560 AGGCCTGTTGGTAGGTCACC 61.490 60.000 3.11 0.00 45.03 4.02
2326 4156 0.036294 GAGGCCTGTTGGTAGGTCAC 60.036 60.000 12.00 0.00 45.03 3.67
2327 4157 1.198759 GGAGGCCTGTTGGTAGGTCA 61.199 60.000 12.00 0.00 45.03 4.02
2328 4158 1.198759 TGGAGGCCTGTTGGTAGGTC 61.199 60.000 12.00 0.00 42.89 3.85
2329 4159 0.770557 TTGGAGGCCTGTTGGTAGGT 60.771 55.000 12.00 0.00 40.11 3.08
2330 4160 0.035056 CTTGGAGGCCTGTTGGTAGG 60.035 60.000 12.00 0.00 40.95 3.18
2331 4161 0.035056 CCTTGGAGGCCTGTTGGTAG 60.035 60.000 12.00 0.00 35.27 3.18
2344 4174 3.585289 TGACTAAACTATGGTGCCTTGGA 59.415 43.478 0.00 0.00 0.00 3.53
2418 5441 0.902531 TGGGCACACTACTAAGCTCC 59.097 55.000 0.00 0.00 0.00 4.70
2422 5445 2.766263 TCCAGATGGGCACACTACTAAG 59.234 50.000 0.00 0.00 36.21 2.18
2423 5446 2.827755 TCCAGATGGGCACACTACTAA 58.172 47.619 0.00 0.00 36.21 2.24
2433 5456 1.753073 CACTCCAAAATCCAGATGGGC 59.247 52.381 0.00 0.00 36.21 5.36
2434 5457 1.753073 GCACTCCAAAATCCAGATGGG 59.247 52.381 0.00 0.00 34.89 4.00
2459 5482 7.553402 GGGAGATAAGAGAACGCTGATACTATA 59.447 40.741 0.00 0.00 0.00 1.31
2466 5497 2.427453 GTGGGAGATAAGAGAACGCTGA 59.573 50.000 0.00 0.00 0.00 4.26
2512 5543 0.460811 TCTGTGTGCATCGATCAGCC 60.461 55.000 0.00 0.00 0.00 4.85
2576 5607 1.542375 ATGGGAGTTCAGGCACCCT 60.542 57.895 0.00 0.00 42.49 4.34
2577 5608 1.077429 GATGGGAGTTCAGGCACCC 60.077 63.158 0.00 0.00 42.37 4.61
2578 5609 1.450312 CGATGGGAGTTCAGGCACC 60.450 63.158 0.00 0.00 0.00 5.01
2579 5610 2.109126 GCGATGGGAGTTCAGGCAC 61.109 63.158 0.00 0.00 0.00 5.01
2580 5611 2.268920 GCGATGGGAGTTCAGGCA 59.731 61.111 0.00 0.00 0.00 4.75
2581 5612 2.268920 TGCGATGGGAGTTCAGGC 59.731 61.111 0.00 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.