Multiple sequence alignment - TraesCS3D01G165300

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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 TraesCS3D01G165300 chr3D 100.000 5205 0 0 1 5205 137001872 137007076 0.000000e+00 9612.0
1 TraesCS3D01G165300 chr3D 85.507 276 21 4 914 1189 500881613 500881357 2.390000e-68 270.0
2 TraesCS3D01G165300 chr3D 90.123 81 8 0 1109 1189 19368924 19368844 7.130000e-19 106.0
3 TraesCS3D01G165300 chr3B 94.014 2506 89 28 2727 5205 200482332 200479861 0.000000e+00 3740.0
4 TraesCS3D01G165300 chr3B 94.680 1485 51 10 1257 2728 200483884 200482415 0.000000e+00 2279.0
5 TraesCS3D01G165300 chr3B 96.516 1263 34 4 1 1260 200485261 200484006 0.000000e+00 2080.0
6 TraesCS3D01G165300 chr3B 87.350 585 64 8 1053 1632 420417635 420418214 0.000000e+00 662.0
7 TraesCS3D01G165300 chr3B 86.916 321 36 5 1311 1628 726627487 726627804 6.410000e-94 355.0
8 TraesCS3D01G165300 chr3B 86.335 322 28 3 774 1095 259400570 259400875 2.320000e-88 337.0
9 TraesCS3D01G165300 chr3B 83.750 80 7 6 3511 3587 200481637 200481561 2.600000e-08 71.3
10 TraesCS3D01G165300 chr3A 96.400 1250 28 9 3963 5205 155059520 155058281 0.000000e+00 2043.0
11 TraesCS3D01G165300 chr3A 91.838 1262 77 14 1 1260 155063743 155062506 0.000000e+00 1736.0
12 TraesCS3D01G165300 chr3A 93.726 1052 54 8 2082 3129 155061880 155060837 0.000000e+00 1567.0
13 TraesCS3D01G165300 chr3A 86.545 877 69 18 3125 3964 155060531 155059667 0.000000e+00 920.0
14 TraesCS3D01G165300 chr3A 90.000 370 31 4 1337 1700 155062242 155061873 1.700000e-129 473.0
15 TraesCS3D01G165300 chr3A 86.241 407 37 4 774 1180 136000441 136000054 1.730000e-114 424.0
16 TraesCS3D01G165300 chr3A 84.964 419 44 4 771 1189 648184053 648184452 1.740000e-109 407.0
17 TraesCS3D01G165300 chr6B 88.416 587 62 6 1053 1636 471231096 471231679 0.000000e+00 702.0
18 TraesCS3D01G165300 chr6B 85.588 340 28 7 774 1111 116276999 116276679 2.320000e-88 337.0
19 TraesCS3D01G165300 chr4B 86.058 416 36 8 776 1189 570893494 570893889 1.340000e-115 427.0
20 TraesCS3D01G165300 chr4B 85.167 418 40 8 774 1189 9940282 9939885 4.850000e-110 409.0
21 TraesCS3D01G165300 chr5A 84.856 416 48 11 1230 1636 10743287 10742878 6.280000e-109 405.0
22 TraesCS3D01G165300 chr5A 90.110 91 5 4 1539 1628 613927829 613927916 1.180000e-21 115.0
23 TraesCS3D01G165300 chr5D 86.707 331 36 5 1191 1517 458817350 458817676 1.380000e-95 361.0
24 TraesCS3D01G165300 chr5D 80.420 429 54 12 774 1189 555464458 555464047 3.050000e-77 300.0
25 TraesCS3D01G165300 chr5D 86.911 191 23 1 2488 2676 491000007 490999817 4.080000e-51 213.0
26 TraesCS3D01G165300 chr5D 90.123 81 8 0 1109 1189 370302543 370302463 7.130000e-19 106.0
27 TraesCS3D01G165300 chr1B 84.840 343 31 7 771 1111 84961959 84962282 5.030000e-85 326.0
28 TraesCS3D01G165300 chr7A 86.806 288 30 5 1347 1628 628829846 628829561 1.090000e-81 315.0
29 TraesCS3D01G165300 chr1D 82.807 285 43 4 1347 1628 468134223 468133942 3.110000e-62 250.0
30 TraesCS3D01G165300 chr5B 89.697 165 17 0 2512 2676 605787627 605787463 1.470000e-50 211.0
31 TraesCS3D01G165300 chr2B 88.415 164 16 1 1017 1180 639526095 639525935 1.480000e-45 195.0


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 TraesCS3D01G165300 chr3D 137001872 137007076 5204 False 9612.000 9612 100.0000 1 5205 1 chr3D.!!$F1 5204
1 TraesCS3D01G165300 chr3B 200479861 200485261 5400 True 2042.575 3740 92.2400 1 5205 4 chr3B.!!$R1 5204
2 TraesCS3D01G165300 chr3B 420417635 420418214 579 False 662.000 662 87.3500 1053 1632 1 chr3B.!!$F2 579
3 TraesCS3D01G165300 chr3A 155058281 155063743 5462 True 1347.800 2043 91.7018 1 5205 5 chr3A.!!$R2 5204
4 TraesCS3D01G165300 chr6B 471231096 471231679 583 False 702.000 702 88.4160 1053 1636 1 chr6B.!!$F1 583

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
505 510 0.175760 GGTCTGCGATGAAGTGGCTA 59.824 55.000 0.00 0.00 32.08 3.93 F
1638 1874 0.184933 TGTGGGAAAGGGTTGGTGAG 59.815 55.000 0.00 0.00 0.00 3.51 F
1747 1985 0.684805 GAGGGGCCGAGAGAGAAAGA 60.685 60.000 0.00 0.00 0.00 2.52 F
2389 2631 0.690192 TTCGAGAGGGTCAATGGCAA 59.310 50.000 0.00 0.00 0.00 4.52 F
3825 4481 2.032054 TGCAAGCGAGCATACTTATTGC 59.968 45.455 1.83 8.39 40.11 3.56 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1905 2143 0.321210 CTACAATGTGGGCCGTGACA 60.321 55.000 0.00 0.0 0.00 3.58 R
3628 4277 0.033504 TCCACTGACAAGTCGAAGGC 59.966 55.000 0.00 0.0 32.98 4.35 R
3630 4279 4.568359 CCATAATCCACTGACAAGTCGAAG 59.432 45.833 0.00 0.0 32.98 3.79 R
3853 4515 1.066143 ACACCGGAAGTAGCCAATCAG 60.066 52.381 9.46 0.0 0.00 2.90 R
4658 5487 3.806316 ATCGTGTGAATTTTCCGTGTC 57.194 42.857 0.00 0.0 0.00 3.67 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
31 32 2.125912 CTCCCTCACTCAACGCGG 60.126 66.667 12.47 0.00 0.00 6.46
40 43 1.300620 CTCAACGCGGACCAGAACA 60.301 57.895 12.47 0.00 0.00 3.18
50 53 2.805353 CCAGAACACGACGCGAGG 60.805 66.667 15.93 6.33 0.00 4.63
51 54 3.470567 CAGAACACGACGCGAGGC 61.471 66.667 15.93 0.00 0.00 4.70
194 198 0.317160 TCGTGCAGGATCTGTTCGTT 59.683 50.000 4.68 0.00 34.06 3.85
197 201 1.464997 GTGCAGGATCTGTTCGTTTCC 59.535 52.381 0.00 0.00 33.43 3.13
242 247 2.653702 GATCGATCTGGGGAGCCG 59.346 66.667 18.29 0.00 0.00 5.52
272 277 4.653888 CGGGGAAGCGGGGTGTTT 62.654 66.667 0.00 0.00 0.00 2.83
288 293 1.339610 TGTTTGTTGCGCCATTTAGCT 59.660 42.857 4.18 0.00 0.00 3.32
314 319 3.369385 CGTAGCGGTGGATTAGTTGTAG 58.631 50.000 0.00 0.00 0.00 2.74
315 320 2.311124 AGCGGTGGATTAGTTGTAGC 57.689 50.000 0.00 0.00 0.00 3.58
316 321 1.134491 AGCGGTGGATTAGTTGTAGCC 60.134 52.381 0.00 0.00 0.00 3.93
317 322 1.949465 CGGTGGATTAGTTGTAGCCC 58.051 55.000 0.00 0.00 0.00 5.19
318 323 1.485066 CGGTGGATTAGTTGTAGCCCT 59.515 52.381 0.00 0.00 0.00 5.19
467 472 3.056179 TCGCTGAACCAAGTGATCATGTA 60.056 43.478 0.00 0.00 31.84 2.29
505 510 0.175760 GGTCTGCGATGAAGTGGCTA 59.824 55.000 0.00 0.00 32.08 3.93
635 640 2.563179 CTGGGTGTTCACTAGTAGCACT 59.437 50.000 17.42 0.00 0.00 4.40
688 693 4.634883 ACAATTTGTTGCAAAATGCTGTGA 59.365 33.333 0.00 0.00 45.31 3.58
898 903 5.593502 GGATAAGTAGGATCCACTATACCGG 59.406 48.000 15.82 0.00 42.26 5.28
1239 1244 7.426169 CAGCATTTTAGTTTCTGTTTTGCAAAC 59.574 33.333 12.39 8.01 0.00 2.93
1360 1574 5.501156 ACTTCCTGAATCCTCCATGTTTAC 58.499 41.667 0.00 0.00 0.00 2.01
1391 1605 4.756642 TGTGATTCCTTGTAGTTGCTTCAG 59.243 41.667 0.00 0.00 0.00 3.02
1405 1624 6.583562 AGTTGCTTCAGTAGTAGTCAAAGTT 58.416 36.000 0.00 0.00 0.00 2.66
1406 1625 6.480320 AGTTGCTTCAGTAGTAGTCAAAGTTG 59.520 38.462 0.00 0.00 0.00 3.16
1407 1626 5.914033 TGCTTCAGTAGTAGTCAAAGTTGT 58.086 37.500 0.00 0.00 0.00 3.32
1408 1627 6.346096 TGCTTCAGTAGTAGTCAAAGTTGTT 58.654 36.000 0.00 0.00 0.00 2.83
1409 1628 6.821665 TGCTTCAGTAGTAGTCAAAGTTGTTT 59.178 34.615 0.00 0.00 0.00 2.83
1429 1648 4.589216 TTCTGCAAGTCAATTTTGGGAG 57.411 40.909 0.00 0.00 33.76 4.30
1432 1651 4.037923 TCTGCAAGTCAATTTTGGGAGTTC 59.962 41.667 0.00 0.00 33.76 3.01
1631 1866 1.710809 ACTGCTTATGTGGGAAAGGGT 59.289 47.619 0.00 0.00 0.00 4.34
1638 1874 0.184933 TGTGGGAAAGGGTTGGTGAG 59.815 55.000 0.00 0.00 0.00 3.51
1711 1949 2.203195 TGTGTGCAGTGGTGGAGC 60.203 61.111 0.00 0.00 0.00 4.70
1716 1954 2.046892 GCAGTGGTGGAGCGTGAT 60.047 61.111 0.00 0.00 0.00 3.06
1745 1983 1.686110 GGAGGGGCCGAGAGAGAAA 60.686 63.158 0.00 0.00 0.00 2.52
1747 1985 0.684805 GAGGGGCCGAGAGAGAAAGA 60.685 60.000 0.00 0.00 0.00 2.52
1758 1996 6.456718 GCCGAGAGAGAAAGAAAAATGATCTG 60.457 42.308 0.00 0.00 0.00 2.90
1798 2036 2.814280 GGACAAGAAGACCGTTCAGA 57.186 50.000 0.00 0.00 0.00 3.27
1799 2037 3.320673 GGACAAGAAGACCGTTCAGAT 57.679 47.619 0.00 0.00 0.00 2.90
1852 2090 5.774498 GGGAACAGAAGAAAAGTTCACAT 57.226 39.130 0.00 0.00 43.37 3.21
1862 2100 7.766278 AGAAGAAAAGTTCACATATACAGCGAT 59.234 33.333 0.00 0.00 0.00 4.58
1866 2104 6.775939 AAGTTCACATATACAGCGATCATG 57.224 37.500 0.00 0.00 0.00 3.07
1868 2106 4.255833 TCACATATACAGCGATCATGCA 57.744 40.909 0.00 0.00 37.31 3.96
1883 2121 1.002257 TGCATCGGGTGTGCAGATT 60.002 52.632 0.00 0.00 46.76 2.40
1952 2190 1.134098 GCCCATAGAAGCAGCCACTTA 60.134 52.381 0.00 0.00 0.00 2.24
1972 2210 6.319658 CACTTACACTGGCCAGATCAAATAAT 59.680 38.462 39.19 10.61 0.00 1.28
1999 2237 6.357367 GGTGACTGATCTAAATTGTATGGGT 58.643 40.000 0.00 0.00 0.00 4.51
2031 2269 9.699703 ACGTAGGTATTTGTATTTTGCAATTTT 57.300 25.926 0.00 0.00 0.00 1.82
2043 2281 0.879090 GCAATTTTCGAAGACCGGGT 59.121 50.000 6.32 0.00 39.14 5.28
2072 2310 2.264794 GTGGTCCCCACGTAGCTG 59.735 66.667 0.00 0.00 44.95 4.24
2225 2467 6.932960 GTCAGTAGTTTTAGCCTGTTTTCCTA 59.067 38.462 0.00 0.00 0.00 2.94
2227 2469 7.015877 TCAGTAGTTTTAGCCTGTTTTCCTAGA 59.984 37.037 0.00 0.00 0.00 2.43
2291 2533 2.286294 CAGTTACATCATTGAGAGCCGC 59.714 50.000 0.00 0.00 0.00 6.53
2389 2631 0.690192 TTCGAGAGGGTCAATGGCAA 59.310 50.000 0.00 0.00 0.00 4.52
2569 2811 7.079451 ACTATATTTGGATACCAGAACCCAG 57.921 40.000 0.00 0.00 33.81 4.45
2919 3246 4.142038 TGCTTCTTTTGGAAACCCTAGTC 58.858 43.478 0.00 0.00 33.07 2.59
2954 3281 8.608844 AAGTATTATGACTGCCTTAATGCTAC 57.391 34.615 4.32 0.00 37.07 3.58
3020 3347 6.566141 TGTCTGCATGATTGAATTGGTATTG 58.434 36.000 0.00 0.00 0.00 1.90
3105 3434 3.127030 CGTTTCCCCTTTAGCATGACTTC 59.873 47.826 0.00 0.00 0.00 3.01
3404 4053 5.100344 AGTATGTCTGGTAGTCTTCTCGA 57.900 43.478 0.00 0.00 0.00 4.04
3434 4083 9.767228 TTTTGCCATATCATCATTCTTAAATGG 57.233 29.630 0.00 0.00 42.19 3.16
3628 4277 9.606631 GAAGGTTCCATAATTAGATATAGGCTG 57.393 37.037 0.00 0.00 0.00 4.85
3630 4279 6.768381 GGTTCCATAATTAGATATAGGCTGCC 59.232 42.308 11.65 11.65 0.00 4.85
3635 4284 7.417911 CCATAATTAGATATAGGCTGCCTTCGA 60.418 40.741 28.55 12.01 34.61 3.71
3825 4481 2.032054 TGCAAGCGAGCATACTTATTGC 59.968 45.455 1.83 8.39 40.11 3.56
3853 4515 4.454504 TCCCTTGTGCTTTCGATTTTAGTC 59.545 41.667 0.00 0.00 0.00 2.59
3869 4531 2.969628 AGTCTGATTGGCTACTTCCG 57.030 50.000 0.00 0.00 0.00 4.30
3884 4560 2.904434 ACTTCCGGTGTAATCCTCACTT 59.096 45.455 0.00 0.00 36.25 3.16
3885 4561 3.262420 CTTCCGGTGTAATCCTCACTTG 58.738 50.000 0.00 0.00 36.25 3.16
4184 5009 5.059833 GGATAGTACTGATGCTCTTTTGGG 58.940 45.833 5.39 0.00 0.00 4.12
4450 5278 8.424918 ACCATGAACTATTCTATTAGAGGTGTG 58.575 37.037 0.00 0.00 0.00 3.82
4479 5307 5.657474 GACCGACATAGTAATTGGTCTTCA 58.343 41.667 13.57 0.00 42.00 3.02
4624 5453 6.889019 TTACCAAATTTTGTTCGGTGAAAC 57.111 33.333 8.26 0.00 0.00 2.78
4658 5487 6.015504 CGGAAAATTCACACGATTCTAGTTG 58.984 40.000 0.00 0.00 0.00 3.16
4659 5488 6.128661 CGGAAAATTCACACGATTCTAGTTGA 60.129 38.462 0.00 0.00 0.00 3.18
4660 5489 7.015877 GGAAAATTCACACGATTCTAGTTGAC 58.984 38.462 0.00 0.00 0.00 3.18
4661 5490 7.307751 GGAAAATTCACACGATTCTAGTTGACA 60.308 37.037 0.00 0.00 0.00 3.58
4662 5491 6.467723 AATTCACACGATTCTAGTTGACAC 57.532 37.500 0.00 0.00 0.00 3.67
4665 5494 2.555325 ACACGATTCTAGTTGACACGGA 59.445 45.455 0.00 0.00 0.00 4.69
4668 5497 4.446385 CACGATTCTAGTTGACACGGAAAA 59.554 41.667 0.00 0.00 0.00 2.29
4672 5501 6.128661 CGATTCTAGTTGACACGGAAAATTCA 60.129 38.462 0.00 0.00 0.00 2.57
4757 5589 2.298661 CCCCAAACCCCGAGCTAGT 61.299 63.158 0.00 0.00 0.00 2.57
4760 5592 1.481871 CCAAACCCCGAGCTAGTAGA 58.518 55.000 0.00 0.00 0.00 2.59
4803 5637 2.355986 AAGCACCCTGCCGTCGATA 61.356 57.895 0.00 0.00 46.52 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 2.232696 GAGTGAGGGAGAGAGGTGAAAC 59.767 54.545 0.00 0.00 0.00 2.78
31 32 2.050714 TCGCGTCGTGTTCTGGTC 60.051 61.111 5.77 0.00 0.00 4.02
62 65 2.860628 CGTGCTTACCATCTCGCGC 61.861 63.158 0.00 0.00 0.00 6.86
123 127 4.101448 GATGCAGCGGACCCCTGT 62.101 66.667 7.96 0.00 32.93 4.00
143 147 2.279186 CCGCGCGGATCACATGTA 60.279 61.111 44.86 0.00 37.50 2.29
170 174 3.456365 AGATCCTGCACGAGCGCT 61.456 61.111 11.27 11.27 46.23 5.92
194 198 0.320073 AGCGAATCCAAACGACGGAA 60.320 50.000 0.00 0.00 35.77 4.30
197 201 0.366871 CTCAGCGAATCCAAACGACG 59.633 55.000 0.00 0.00 0.00 5.12
242 247 0.540133 TTCCCCGCCAAAACCCTAAC 60.540 55.000 0.00 0.00 0.00 2.34
272 277 1.594194 CCCAGCTAAATGGCGCAACA 61.594 55.000 10.83 0.00 39.17 3.33
354 359 2.644418 GCGCAGAAACCACATGCA 59.356 55.556 0.30 0.00 39.97 3.96
635 640 3.002791 GCATCGACTGACCTTGATTCAA 58.997 45.455 0.00 0.00 0.00 2.69
1327 1457 4.343814 AGGATTCAGGAAGTAGAAGCTAGC 59.656 45.833 6.62 6.62 31.29 3.42
1360 1574 5.595885 ACTACAAGGAATCACAGATCATCG 58.404 41.667 0.00 0.00 0.00 3.84
1391 1605 6.598753 TGCAGAAACAACTTTGACTACTAC 57.401 37.500 0.00 0.00 0.00 2.73
1405 1624 4.161189 TCCCAAAATTGACTTGCAGAAACA 59.839 37.500 0.00 0.00 0.00 2.83
1406 1625 4.692228 TCCCAAAATTGACTTGCAGAAAC 58.308 39.130 0.00 0.00 0.00 2.78
1407 1626 4.405358 ACTCCCAAAATTGACTTGCAGAAA 59.595 37.500 0.00 0.00 0.00 2.52
1408 1627 3.960102 ACTCCCAAAATTGACTTGCAGAA 59.040 39.130 0.00 0.00 0.00 3.02
1409 1628 3.565307 ACTCCCAAAATTGACTTGCAGA 58.435 40.909 0.00 0.00 0.00 4.26
1429 1648 6.989169 TCCTAGACTTATACAGGTACTCGAAC 59.011 42.308 0.00 0.00 34.60 3.95
1432 1651 6.202570 GTGTCCTAGACTTATACAGGTACTCG 59.797 46.154 0.00 0.00 31.39 4.18
1556 1783 6.041409 TGCAAACCAGGTGATTTCAATTCTTA 59.959 34.615 0.00 0.00 0.00 2.10
1557 1784 5.163322 TGCAAACCAGGTGATTTCAATTCTT 60.163 36.000 0.00 0.00 0.00 2.52
1558 1785 4.344679 TGCAAACCAGGTGATTTCAATTCT 59.655 37.500 0.00 0.00 0.00 2.40
1559 1786 4.630111 TGCAAACCAGGTGATTTCAATTC 58.370 39.130 0.00 0.00 0.00 2.17
1560 1787 4.686191 TGCAAACCAGGTGATTTCAATT 57.314 36.364 0.00 0.00 0.00 2.32
1593 1820 6.485830 AGCAGTATGTTATCTTTGCCTCTA 57.514 37.500 0.00 0.00 39.31 2.43
1628 1863 5.975693 TTCATTATTCAACTCACCAACCC 57.024 39.130 0.00 0.00 0.00 4.11
1631 1866 9.513906 TTCTGTATTCATTATTCAACTCACCAA 57.486 29.630 0.00 0.00 0.00 3.67
1706 1944 3.369471 CCTTCCTTTCTTATCACGCTCCA 60.369 47.826 0.00 0.00 0.00 3.86
1711 1949 3.432326 CCCCTCCTTCCTTTCTTATCACG 60.432 52.174 0.00 0.00 0.00 4.35
1716 1954 1.296002 GGCCCCTCCTTCCTTTCTTA 58.704 55.000 0.00 0.00 0.00 2.10
1745 1983 6.441924 TCTCCACTAGTCCAGATCATTTTTCT 59.558 38.462 0.00 0.00 0.00 2.52
1747 1985 6.627087 TCTCCACTAGTCCAGATCATTTTT 57.373 37.500 0.00 0.00 0.00 1.94
1866 2104 1.430632 CAATCTGCACACCCGATGC 59.569 57.895 0.00 0.00 43.68 3.91
1868 2106 3.909662 GCAATCTGCACACCCGAT 58.090 55.556 0.00 0.00 44.26 4.18
1905 2143 0.321210 CTACAATGTGGGCCGTGACA 60.321 55.000 0.00 0.00 0.00 3.58
1952 2190 4.403432 CCAATTATTTGATCTGGCCAGTGT 59.597 41.667 31.58 21.42 34.60 3.55
1972 2210 6.828273 CCATACAATTTAGATCAGTCACCCAA 59.172 38.462 0.00 0.00 0.00 4.12
2009 2247 9.482627 TTCGAAAATTGCAAAATACAAATACCT 57.517 25.926 1.71 0.00 0.00 3.08
2010 2248 9.739786 CTTCGAAAATTGCAAAATACAAATACC 57.260 29.630 1.71 0.00 0.00 2.73
2030 2268 2.646719 CACGACCCGGTCTTCGAA 59.353 61.111 20.50 0.00 42.43 3.71
2031 2269 3.367743 CCACGACCCGGTCTTCGA 61.368 66.667 20.50 0.00 42.43 3.71
2043 2281 3.936203 GACCACACAGGGCCACGA 61.936 66.667 6.18 0.00 40.85 4.35
2072 2310 0.670546 ATACACACAGTCACCTGCGC 60.671 55.000 0.00 0.00 42.81 6.09
2184 2426 4.090761 ACTGACAAGGATTTGCTTCTCA 57.909 40.909 0.00 0.00 37.85 3.27
2225 2467 7.472334 ACAAGAGTGCCATGATAATTTTTCT 57.528 32.000 0.00 0.00 0.00 2.52
2227 2469 6.369615 GCAACAAGAGTGCCATGATAATTTTT 59.630 34.615 0.00 0.00 0.00 1.94
2291 2533 3.907788 CACACATTGTCAAATAGCACACG 59.092 43.478 0.00 0.00 0.00 4.49
2389 2631 3.460103 CTTGCAGCAGTTTCAATTTGGT 58.540 40.909 0.00 0.00 0.00 3.67
2569 2811 1.981256 TCAACTTGGCAAGGTTCCTC 58.019 50.000 29.26 0.00 0.00 3.71
2919 3246 9.561069 AGGCAGTCATAATACTTTTATACAAGG 57.439 33.333 3.78 0.00 0.00 3.61
2954 3281 8.717821 TCAAACAATAGGAGTATCAAGAAAACG 58.282 33.333 0.00 0.00 36.25 3.60
3043 3370 8.781067 TCAAAACACGAAGATGAAATGTTAAG 57.219 30.769 0.00 0.00 33.27 1.85
3105 3434 6.143118 GCTAATACATTAGAACAGACTGCGAG 59.857 42.308 12.20 0.00 41.72 5.03
3149 3787 5.164620 TGTCTTAATTGACATGGCTGAGA 57.835 39.130 0.00 0.00 41.43 3.27
3461 4110 4.298332 CCTGTGATGCTTACAAACCAAAC 58.702 43.478 0.00 0.00 0.00 2.93
3606 4255 7.569240 AGGCAGCCTATATCTAATTATGGAAC 58.431 38.462 14.18 0.00 28.47 3.62
3628 4277 0.033504 TCCACTGACAAGTCGAAGGC 59.966 55.000 0.00 0.00 32.98 4.35
3630 4279 4.568359 CCATAATCCACTGACAAGTCGAAG 59.432 45.833 0.00 0.00 32.98 3.79
3635 4284 8.522830 CAAAATTACCATAATCCACTGACAAGT 58.477 33.333 0.00 0.00 36.98 3.16
3812 4468 4.808042 AGGGAAATGGCAATAAGTATGCT 58.192 39.130 0.00 0.00 43.34 3.79
3825 4481 1.885887 TCGAAAGCACAAGGGAAATGG 59.114 47.619 0.00 0.00 0.00 3.16
3853 4515 1.066143 ACACCGGAAGTAGCCAATCAG 60.066 52.381 9.46 0.00 0.00 2.90
3869 4531 6.385649 TTTGTTTCAAGTGAGGATTACACC 57.614 37.500 0.00 0.00 38.82 4.16
3906 4582 5.254339 ACGGGACCGAGTTAGTTTTATAG 57.746 43.478 18.80 0.00 42.83 1.31
3909 4585 3.069443 ACAACGGGACCGAGTTAGTTTTA 59.931 43.478 18.80 0.00 42.83 1.52
3920 4596 2.100631 GCAGATCACAACGGGACCG 61.101 63.158 9.56 9.56 46.03 4.79
4184 5009 4.330074 CGGTCACCATATCTTGTTCTTGAC 59.670 45.833 0.00 0.00 0.00 3.18
4450 5278 4.684703 CCAATTACTATGTCGGTCGAATCC 59.315 45.833 0.00 0.00 0.00 3.01
4479 5307 4.832266 TCTTACATGTTGGGCTCACAAAAT 59.168 37.500 2.30 0.00 31.17 1.82
4612 5441 2.483106 TGTCAAAACGTTTCACCGAACA 59.517 40.909 15.01 9.45 0.00 3.18
4624 5453 4.028026 GTGTGAATTTTCCGTGTCAAAACG 60.028 41.667 0.00 0.00 43.20 3.60
4658 5487 3.806316 ATCGTGTGAATTTTCCGTGTC 57.194 42.857 0.00 0.00 0.00 3.67
4659 5488 3.813166 AGAATCGTGTGAATTTTCCGTGT 59.187 39.130 0.00 0.00 0.00 4.49
4660 5489 4.404507 AGAATCGTGTGAATTTTCCGTG 57.595 40.909 0.00 0.00 0.00 4.94
4661 5490 5.235516 ACTAGAATCGTGTGAATTTTCCGT 58.764 37.500 0.00 0.00 0.00 4.69
4662 5491 5.779806 ACTAGAATCGTGTGAATTTTCCG 57.220 39.130 0.00 0.00 0.00 4.30
4665 5494 9.965824 AATTTCAACTAGAATCGTGTGAATTTT 57.034 25.926 0.00 0.00 35.83 1.82
4668 5497 7.023575 GCAATTTCAACTAGAATCGTGTGAAT 58.976 34.615 0.00 0.00 35.83 2.57
4672 5501 6.017109 ACAAGCAATTTCAACTAGAATCGTGT 60.017 34.615 0.00 0.00 35.83 4.49


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

AutoCloner maintained by Alex Coulton.