Multiple sequence alignment - TraesCS5A01G180300

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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 TraesCS5A01G180300 chr5A 100.000 4192 0 0 1 4192 379095108 379090917 0.000000e+00 7742.0
1 TraesCS5A01G180300 chr5A 80.324 432 41 18 3794 4192 379040928 379040508 1.910000e-73 287.0
2 TraesCS5A01G180300 chr5A 93.333 60 4 0 3709 3768 379041067 379041008 5.770000e-14 89.8
3 TraesCS5A01G180300 chr5D 92.278 2046 69 39 1 1997 287018399 287016394 0.000000e+00 2820.0
4 TraesCS5A01G180300 chr5D 90.786 1704 79 25 2094 3788 287016351 287014717 0.000000e+00 2206.0
5 TraesCS5A01G180300 chr5D 90.025 401 18 9 3794 4192 287014672 287014292 2.250000e-137 499.0
6 TraesCS5A01G180300 chr5D 93.443 61 4 0 3708 3768 286949778 286949718 1.600000e-14 91.6
7 TraesCS5A01G180300 chr5B 94.290 1261 41 16 621 1873 325965707 325964470 0.000000e+00 1901.0
8 TraesCS5A01G180300 chr5B 91.574 1080 61 7 2389 3467 325962814 325961764 0.000000e+00 1463.0
9 TraesCS5A01G180300 chr5B 96.178 628 20 4 1 624 325966414 325965787 0.000000e+00 1024.0
10 TraesCS5A01G180300 chr5B 89.000 400 25 7 3795 4192 325961444 325961062 1.050000e-130 477.0
11 TraesCS5A01G180300 chr5B 91.901 284 13 5 3507 3790 325961763 325961490 5.080000e-104 388.0
12 TraesCS5A01G180300 chr5B 93.089 246 12 3 2094 2335 325964254 325964010 5.150000e-94 355.0
13 TraesCS5A01G180300 chr5B 83.280 311 27 9 3797 4083 325942981 325942672 3.210000e-66 263.0
14 TraesCS5A01G180300 chr5B 90.698 129 10 2 1870 1997 325964424 325964297 2.000000e-38 171.0
15 TraesCS5A01G180300 chr7D 86.064 1471 120 43 661 2092 37659440 37660864 0.000000e+00 1502.0
16 TraesCS5A01G180300 chr7D 86.418 751 69 14 805 1547 37625515 37626240 0.000000e+00 791.0
17 TraesCS5A01G180300 chr7D 90.000 80 7 1 2097 2175 37660843 37660922 7.410000e-18 102.0
18 TraesCS5A01G180300 chr7D 91.525 59 4 1 2264 2321 37661065 37661123 3.470000e-11 80.5
19 TraesCS5A01G180300 chr3D 85.870 1472 122 42 661 2092 25527112 25525687 0.000000e+00 1487.0
20 TraesCS5A01G180300 chr3D 90.000 80 7 1 2097 2175 25525708 25525629 7.410000e-18 102.0
21 TraesCS5A01G180300 chr3D 93.220 59 3 1 2264 2321 25525486 25525428 7.470000e-13 86.1
22 TraesCS5A01G180300 chr2A 88.186 1185 96 24 661 1828 720388432 720387275 0.000000e+00 1373.0
23 TraesCS5A01G180300 chr2A 87.888 644 50 18 914 1547 720354044 720353419 0.000000e+00 732.0
24 TraesCS5A01G180300 chr2A 77.292 938 107 57 2264 3141 720386640 720385749 4.940000e-124 455.0
25 TraesCS5A01G180300 chr2A 83.051 118 13 3 1863 1979 720387270 720387159 2.670000e-17 100.0
26 TraesCS5A01G180300 chr4A 87.997 1183 94 26 808 1979 687321183 687320038 0.000000e+00 1354.0


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 TraesCS5A01G180300 chr5A 379090917 379095108 4191 True 7742.000000 7742 100.000000 1 4192 1 chr5A.!!$R1 4191
1 TraesCS5A01G180300 chr5D 287014292 287018399 4107 True 1841.666667 2820 91.029667 1 4192 3 chr5D.!!$R2 4191
2 TraesCS5A01G180300 chr5B 325961062 325966414 5352 True 825.571429 1901 92.390000 1 4192 7 chr5B.!!$R2 4191
3 TraesCS5A01G180300 chr7D 37625515 37626240 725 False 791.000000 791 86.418000 805 1547 1 chr7D.!!$F1 742
4 TraesCS5A01G180300 chr7D 37659440 37661123 1683 False 561.500000 1502 89.196333 661 2321 3 chr7D.!!$F2 1660
5 TraesCS5A01G180300 chr3D 25525428 25527112 1684 True 558.366667 1487 89.696667 661 2321 3 chr3D.!!$R1 1660
6 TraesCS5A01G180300 chr2A 720353419 720354044 625 True 732.000000 732 87.888000 914 1547 1 chr2A.!!$R1 633
7 TraesCS5A01G180300 chr2A 720385749 720388432 2683 True 642.666667 1373 82.843000 661 3141 3 chr2A.!!$R2 2480
8 TraesCS5A01G180300 chr4A 687320038 687321183 1145 True 1354.000000 1354 87.997000 808 1979 1 chr4A.!!$R1 1171

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
974 1082 2.108952 ACCAATTCTTGTCTTGCTCCCT 59.891 45.455 0.00 0.0 0.0 4.20 F
1999 2209 0.249120 TCCGTGATGGCTACCTGTTG 59.751 55.000 0.00 0.0 37.8 3.33 F
2065 2463 0.250209 CATGGAATCAGGGGAGCTCG 60.250 60.000 7.83 0.0 0.0 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2342 2821 0.184692 TCACCACAGGGCATGTTTCA 59.815 50.0 0.14 0.0 41.41 2.69 R
3059 4749 0.597568 TGAAGGAGTTTGCAATGCCG 59.402 50.0 1.53 0.0 0.00 5.69 R
3845 5578 0.603975 AGAGCACGAAACTCCCAAGC 60.604 55.0 0.00 0.0 34.56 4.01 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
33 34 3.960571 AGTTGGCAGCAACAGATTAGAT 58.039 40.909 3.63 0.00 37.52 1.98
411 416 6.311735 ACCTTTGGGTTGTGATGTTTACTAT 58.688 36.000 0.00 0.00 44.73 2.12
478 483 6.290605 GCATATTTTGCCCAGGTGATAAATT 58.709 36.000 0.00 0.00 46.15 1.82
505 510 8.922931 TGCTGATAATGGCTTTCTCATAATTA 57.077 30.769 2.41 0.00 0.00 1.40
602 607 9.487790 TTTTTGATTTGACATTCCTTAATCACC 57.512 29.630 0.00 0.00 35.59 4.02
825 914 5.237344 GCAGAGTAACACTGTCTTCATTTGT 59.763 40.000 0.00 0.00 37.64 2.83
863 952 7.090173 GCAAGTATTTGTGCTCCTATTTTTGA 58.910 34.615 0.00 0.00 37.78 2.69
973 1081 2.229784 CACCAATTCTTGTCTTGCTCCC 59.770 50.000 0.00 0.00 0.00 4.30
974 1082 2.108952 ACCAATTCTTGTCTTGCTCCCT 59.891 45.455 0.00 0.00 0.00 4.20
975 1083 3.160269 CCAATTCTTGTCTTGCTCCCTT 58.840 45.455 0.00 0.00 0.00 3.95
976 1084 3.575687 CCAATTCTTGTCTTGCTCCCTTT 59.424 43.478 0.00 0.00 0.00 3.11
977 1085 4.553323 CAATTCTTGTCTTGCTCCCTTTG 58.447 43.478 0.00 0.00 0.00 2.77
978 1086 3.297134 TTCTTGTCTTGCTCCCTTTGT 57.703 42.857 0.00 0.00 0.00 2.83
1428 1547 6.126185 ACTGGGTATTTACATATTCTTGGGCT 60.126 38.462 0.00 0.00 0.00 5.19
1618 1751 4.401837 AGATTACTACCCGAGAACTTCACC 59.598 45.833 0.00 0.00 0.00 4.02
1623 1756 3.292492 ACCCGAGAACTTCACCTTTTT 57.708 42.857 0.00 0.00 0.00 1.94
1635 1768 2.687935 TCACCTTTTTCAGCCACAAGTC 59.312 45.455 0.00 0.00 0.00 3.01
1667 1800 0.466189 CCTGCCCACTGTTCAGTTGT 60.466 55.000 2.47 0.00 0.00 3.32
1687 1820 7.984050 CAGTTGTTCTTATCATGTATGGAGTCT 59.016 37.037 0.00 0.00 0.00 3.24
1710 1844 8.237267 GTCTAAATTGACCAAAACTCATCGAAT 58.763 33.333 0.00 0.00 0.00 3.34
1714 1848 3.751175 TGACCAAAACTCATCGAATGACC 59.249 43.478 0.00 0.00 35.06 4.02
1748 1882 7.712639 CAGCTTTATGATAATGTCACTACTGGT 59.287 37.037 0.00 0.00 40.28 4.00
1793 1927 5.192927 AGTGTCATCAAAGAAGGTCACAAA 58.807 37.500 0.00 0.00 0.00 2.83
1843 1977 9.823647 ATGTAAGTGATGACCTGAATACTTAAG 57.176 33.333 0.00 0.00 33.85 1.85
1880 2063 7.287927 TGTTTCCTTTGGTAATATTGGTGTCAA 59.712 33.333 0.00 0.00 37.28 3.18
1941 2129 9.774742 CTTTAAAACTCCATTACATACTTGAGC 57.225 33.333 0.00 0.00 0.00 4.26
1942 2130 6.759497 AAAACTCCATTACATACTTGAGCC 57.241 37.500 0.00 0.00 0.00 4.70
1998 2208 0.249398 GTCCGTGATGGCTACCTGTT 59.751 55.000 0.00 0.00 37.80 3.16
1999 2209 0.249120 TCCGTGATGGCTACCTGTTG 59.751 55.000 0.00 0.00 37.80 3.33
2005 2215 3.317993 GTGATGGCTACCTGTTGTTTTGT 59.682 43.478 0.00 0.00 0.00 2.83
2026 2236 2.132996 TTGGTTGGGCTGCTTGTGG 61.133 57.895 0.00 0.00 0.00 4.17
2028 2238 2.730094 GTTGGGCTGCTTGTGGTG 59.270 61.111 0.00 0.00 0.00 4.17
2053 2451 2.648059 GCTTAGTGGCAGTCATGGAAT 58.352 47.619 0.00 0.00 0.00 3.01
2065 2463 0.250209 CATGGAATCAGGGGAGCTCG 60.250 60.000 7.83 0.00 0.00 5.03
2096 2494 2.658422 GCCACAATTGGGCCACAG 59.342 61.111 21.04 0.74 45.87 3.66
2097 2495 2.946346 GCCACAATTGGGCCACAGG 61.946 63.158 21.04 5.04 45.87 4.00
2098 2496 1.533753 CCACAATTGGGCCACAGGT 60.534 57.895 5.23 0.58 39.57 4.00
2099 2497 1.667151 CACAATTGGGCCACAGGTG 59.333 57.895 5.23 11.11 0.00 4.00
2136 2534 2.740055 CGAGACAGCCTGGTGCAC 60.740 66.667 8.80 8.80 44.83 4.57
2155 2553 1.331214 CTGGCCACTTTGGTGTGATT 58.669 50.000 0.00 0.00 40.46 2.57
2182 2581 2.357836 CCAGGAAGTGGCAGGCAT 59.642 61.111 0.00 0.00 40.39 4.40
2191 2590 2.180017 GGCAGGCATGAAAGTGCG 59.820 61.111 0.62 0.00 45.97 5.34
2193 2592 2.180017 CAGGCATGAAAGTGCGGC 59.820 61.111 0.00 0.00 45.97 6.53
2243 2646 1.003355 TGCTTGGTGTAGGAGCAGC 60.003 57.895 0.00 0.00 41.15 5.25
2251 2654 1.066573 GTGTAGGAGCAGCTGTGTGAT 60.067 52.381 16.64 0.71 0.00 3.06
2316 2795 1.149077 ACCCCACAAAATTGGCCTAGT 59.851 47.619 3.32 0.00 35.00 2.57
2338 2817 3.391296 TCTTAGCCTTGTCTCAAGGTTGT 59.609 43.478 23.61 14.26 39.60 3.32
2341 2820 2.706190 AGCCTTGTCTCAAGGTTGTAGT 59.294 45.455 23.61 5.55 39.60 2.73
2342 2821 3.136626 AGCCTTGTCTCAAGGTTGTAGTT 59.863 43.478 23.61 5.01 39.60 2.24
2343 2822 3.251004 GCCTTGTCTCAAGGTTGTAGTTG 59.749 47.826 23.61 2.58 39.60 3.16
2365 2846 2.897271 ACATGCCCTGTGGTGAAATA 57.103 45.000 0.00 0.00 36.48 1.40
2429 4070 8.689972 AGTTTTTAGGCCAATTCAATATCTGAG 58.310 33.333 5.01 0.00 34.81 3.35
2432 4073 4.723309 AGGCCAATTCAATATCTGAGGTC 58.277 43.478 5.01 0.00 34.81 3.85
2440 4081 2.621998 CAATATCTGAGGTCGGGTACGT 59.378 50.000 0.00 0.00 41.85 3.57
2445 4086 1.246056 TGAGGTCGGGTACGTCAAGG 61.246 60.000 0.00 0.00 46.96 3.61
2447 4088 2.505557 GTCGGGTACGTCAAGGCG 60.506 66.667 0.00 0.00 41.85 5.52
2481 4128 2.027377 AGGCACATCTAGCATCTATGGC 60.027 50.000 0.00 0.00 0.00 4.40
2498 4145 2.862541 TGGCAGTGCTGTTACAATTCT 58.137 42.857 16.11 0.00 0.00 2.40
2515 4162 6.248433 ACAATTCTGTCAAATAGGTCATGGT 58.752 36.000 0.00 0.00 0.00 3.55
2517 4164 7.233348 ACAATTCTGTCAAATAGGTCATGGTTT 59.767 33.333 0.00 0.00 0.00 3.27
2532 4195 8.497745 AGGTCATGGTTTGATCATCTAATAACT 58.502 33.333 0.00 0.00 37.99 2.24
2538 4201 8.946085 TGGTTTGATCATCTAATAACTGTGTTC 58.054 33.333 0.00 0.00 0.00 3.18
2574 4244 7.466804 TGTGTTAATCTATTCCAGGGTCTTTT 58.533 34.615 0.00 0.00 0.00 2.27
2652 4322 5.393027 CCGTAAAGGTCATATTGCAAAGCTT 60.393 40.000 1.71 5.27 34.51 3.74
2655 4325 5.473066 AAGGTCATATTGCAAAGCTTTGT 57.527 34.783 33.47 20.27 40.24 2.83
2752 4422 0.395586 TGTGGTTGCAGGAGCTGTTT 60.396 50.000 0.00 0.00 42.74 2.83
2842 4520 8.396272 TGCCTATAATTATTTTCTTCTCCTGC 57.604 34.615 2.68 0.00 0.00 4.85
2886 4564 2.294233 TCTCACAGTGGCTTCATTTTGC 59.706 45.455 0.00 0.00 0.00 3.68
2907 4585 4.682787 GCTACCTGCAATTTTTCCCATAC 58.317 43.478 0.00 0.00 42.31 2.39
2950 4628 7.176165 GTGCCTCCTTTTACCTGTTTTATTACT 59.824 37.037 0.00 0.00 0.00 2.24
2994 4681 8.684386 TCCATGTTTTTCAGTGATAACAGTAA 57.316 30.769 19.75 9.63 34.37 2.24
3080 4770 1.615392 GGCATTGCAAACTCCTTCAGT 59.385 47.619 11.39 0.00 36.64 3.41
3215 4909 0.750911 ACCGGATCAGACGACTACCC 60.751 60.000 9.46 0.00 0.00 3.69
3216 4910 0.750546 CCGGATCAGACGACTACCCA 60.751 60.000 0.00 0.00 0.00 4.51
3257 4951 2.893489 ACCTTCTTCATGGGCTTGTTTC 59.107 45.455 0.00 0.00 0.00 2.78
3280 4974 2.124403 CACATGGCAGGGGAGAGC 60.124 66.667 3.46 0.00 0.00 4.09
3281 4975 2.611800 ACATGGCAGGGGAGAGCA 60.612 61.111 3.46 0.00 0.00 4.26
3282 4976 2.192443 CATGGCAGGGGAGAGCAG 59.808 66.667 0.00 0.00 0.00 4.24
3476 5170 6.187125 TGTTGCATTATTTCTTGCTCTCTC 57.813 37.500 0.00 0.00 39.60 3.20
3477 5171 5.942236 TGTTGCATTATTTCTTGCTCTCTCT 59.058 36.000 0.00 0.00 39.60 3.10
3488 5182 2.364842 TCTCTCTGCCCCCTGAGC 60.365 66.667 0.00 0.00 37.07 4.26
3497 5191 4.421554 CCCCTGAGCCCCTGAGGA 62.422 72.222 0.00 0.00 37.01 3.71
3498 5192 2.040043 CCCTGAGCCCCTGAGGAT 60.040 66.667 0.00 0.00 37.01 3.24
3499 5193 2.450320 CCCTGAGCCCCTGAGGATG 61.450 68.421 0.00 0.00 37.01 3.51
3501 5195 1.692042 CTGAGCCCCTGAGGATGGT 60.692 63.158 0.00 0.00 38.24 3.55
3503 5197 1.225704 GAGCCCCTGAGGATGGTTG 59.774 63.158 0.00 0.00 38.24 3.77
3504 5198 1.542375 AGCCCCTGAGGATGGTTGT 60.542 57.895 0.00 0.00 38.24 3.32
3505 5199 1.142688 AGCCCCTGAGGATGGTTGTT 61.143 55.000 0.00 0.00 38.24 2.83
3550 5244 7.597288 AGCAGTATGTATACATGGTTGACTA 57.403 36.000 25.48 2.85 39.31 2.59
3551 5245 7.434492 AGCAGTATGTATACATGGTTGACTAC 58.566 38.462 25.48 15.53 39.31 2.73
3552 5246 7.287927 AGCAGTATGTATACATGGTTGACTACT 59.712 37.037 25.48 17.21 39.31 2.57
3553 5247 7.926555 GCAGTATGTATACATGGTTGACTACTT 59.073 37.037 25.48 0.71 39.31 2.24
3554 5248 9.249457 CAGTATGTATACATGGTTGACTACTTG 57.751 37.037 25.48 8.03 37.15 3.16
3555 5249 9.197306 AGTATGTATACATGGTTGACTACTTGA 57.803 33.333 25.48 0.32 37.15 3.02
3556 5250 9.245962 GTATGTATACATGGTTGACTACTTGAC 57.754 37.037 25.48 8.81 37.15 3.18
3557 5251 7.476540 TGTATACATGGTTGACTACTTGACT 57.523 36.000 0.08 0.00 0.00 3.41
3651 5345 2.993264 GTCGGACCGGGACTGGAA 60.993 66.667 15.25 0.00 0.00 3.53
3657 5351 1.420430 GACCGGGACTGGAATGGATA 58.580 55.000 6.32 0.00 0.00 2.59
3658 5352 1.766496 GACCGGGACTGGAATGGATAA 59.234 52.381 6.32 0.00 0.00 1.75
3676 5370 4.202050 GGATAACCCATTGCAAAGCTGTAG 60.202 45.833 1.71 0.00 34.14 2.74
3694 5388 4.571919 TGTAGTCGGGTAAAGTTCCATTG 58.428 43.478 0.00 0.00 0.00 2.82
3704 5398 5.177327 GGTAAAGTTCCATTGCATGTTGTTG 59.823 40.000 0.00 0.00 0.00 3.33
3747 5441 4.011698 CCACATTCAGTTCACATGGATGA 58.988 43.478 0.00 0.00 35.95 2.92
3768 5462 7.653713 GGATGACATTATATTCAACTCGAGTGT 59.346 37.037 20.85 8.32 0.00 3.55
3779 5473 1.224069 CTCGAGTGTGTGCCTTGGTG 61.224 60.000 3.62 0.00 0.00 4.17
3780 5474 1.523711 CGAGTGTGTGCCTTGGTGT 60.524 57.895 0.00 0.00 0.00 4.16
3782 5476 0.663153 GAGTGTGTGCCTTGGTGTTC 59.337 55.000 0.00 0.00 0.00 3.18
3788 5482 3.764434 TGTGTGCCTTGGTGTTCTTTTTA 59.236 39.130 0.00 0.00 0.00 1.52
3789 5483 4.404073 TGTGTGCCTTGGTGTTCTTTTTAT 59.596 37.500 0.00 0.00 0.00 1.40
3790 5484 5.594725 TGTGTGCCTTGGTGTTCTTTTTATA 59.405 36.000 0.00 0.00 0.00 0.98
3792 5486 7.448777 TGTGTGCCTTGGTGTTCTTTTTATATA 59.551 33.333 0.00 0.00 0.00 0.86
3863 5596 1.869690 GCTTGGGAGTTTCGTGCTC 59.130 57.895 0.00 0.00 0.00 4.26
3881 5614 2.796304 CTCTGAGTGACGAGAGAATGC 58.204 52.381 8.47 0.00 38.42 3.56
3929 5662 6.539464 GCATTAATCTTTGATTTTGGCATCCA 59.461 34.615 0.00 0.00 0.00 3.41
3943 5676 4.758688 TGGCATCCAATATATAGCGACTG 58.241 43.478 0.00 0.00 0.00 3.51
4069 5804 3.225235 GAGAAGCCATCTCGCCCT 58.775 61.111 1.72 0.00 44.89 5.19
4117 5858 4.899239 GCGCCGGCTGACAGCTAT 62.899 66.667 26.68 0.00 41.99 2.97
4118 5859 2.659897 CGCCGGCTGACAGCTATC 60.660 66.667 26.68 13.79 41.99 2.08
4119 5860 2.280457 GCCGGCTGACAGCTATCC 60.280 66.667 25.92 9.21 41.99 2.59
4120 5861 3.094062 GCCGGCTGACAGCTATCCA 62.094 63.158 25.92 0.00 41.99 3.41
4121 5862 1.227380 CCGGCTGACAGCTATCCAC 60.227 63.158 25.92 8.12 41.99 4.02
4122 5863 1.227380 CGGCTGACAGCTATCCACC 60.227 63.158 25.92 7.41 41.99 4.61
4123 5864 1.907739 GGCTGACAGCTATCCACCA 59.092 57.895 25.92 0.00 41.99 4.17
4183 5924 3.397906 GCTTCTCCAGCTCCAGGT 58.602 61.111 0.00 0.00 46.27 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 9.967451 TCAGAAATGTAATTAAATACCAGGACA 57.033 29.630 0.00 0.00 33.67 4.02
303 307 7.230510 GGCCAGTATAACCAATTCAACATGATA 59.769 37.037 0.00 0.00 0.00 2.15
318 322 3.432326 CCACTTCAGAGGGCCAGTATAAC 60.432 52.174 6.18 0.00 0.00 1.89
411 416 8.836413 CCACAGTAGATAAAAAGTTTGTTCTCA 58.164 33.333 0.00 0.00 0.00 3.27
478 483 9.524496 AATTATGAGAAAGCCATTATCAGCATA 57.476 29.630 3.92 0.00 42.16 3.14
529 534 1.009078 CGAGCATGAAAATCCTCGCA 58.991 50.000 0.00 0.00 40.35 5.10
784 872 3.754965 TCTGCTTGACTGGCTTTTGTAT 58.245 40.909 0.00 0.00 0.00 2.29
825 914 7.304735 CACAAATACTTGCAGTTGTAGCATTA 58.695 34.615 0.00 0.00 42.33 1.90
1252 1366 6.086222 GGCACACAAAATGATGTAAGTAGTG 58.914 40.000 0.00 0.00 30.84 2.74
1253 1367 5.767665 TGGCACACAAAATGATGTAAGTAGT 59.232 36.000 0.00 0.00 30.84 2.73
1478 1597 6.880484 TGAGCACCGAATAAAGAATACCTAA 58.120 36.000 0.00 0.00 0.00 2.69
1618 1751 3.571401 AGATGGACTTGTGGCTGAAAAAG 59.429 43.478 0.00 0.00 0.00 2.27
1623 1756 2.158623 ACAAAGATGGACTTGTGGCTGA 60.159 45.455 0.00 0.00 38.98 4.26
1635 1768 0.890683 GGGCAGGTCAACAAAGATGG 59.109 55.000 0.00 0.00 0.00 3.51
1687 1820 8.020819 GTCATTCGATGAGTTTTGGTCAATTTA 58.979 33.333 0.00 0.00 40.53 1.40
1710 1844 4.724399 TCATAAAGCTGAAAACAGGGTCA 58.276 39.130 0.00 0.00 0.00 4.02
1714 1848 8.461222 TGACATTATCATAAAGCTGAAAACAGG 58.539 33.333 0.00 0.00 29.99 4.00
1880 2063 2.165030 GCATAGCTGACCAACAAATGCT 59.835 45.455 0.00 0.00 36.81 3.79
1986 2177 2.627699 CCACAAAACAACAGGTAGCCAT 59.372 45.455 0.00 0.00 0.00 4.40
1990 2181 3.445805 ACCAACCACAAAACAACAGGTAG 59.554 43.478 0.00 0.00 31.10 3.18
1998 2208 0.250513 GCCCAACCAACCACAAAACA 59.749 50.000 0.00 0.00 0.00 2.83
1999 2209 0.539518 AGCCCAACCAACCACAAAAC 59.460 50.000 0.00 0.00 0.00 2.43
2005 2215 2.132996 CAAGCAGCCCAACCAACCA 61.133 57.895 0.00 0.00 0.00 3.67
2026 2236 2.034066 TGCCACTAAGCCAGCCAC 59.966 61.111 0.00 0.00 0.00 5.01
2028 2238 1.746991 GACTGCCACTAAGCCAGCC 60.747 63.158 0.00 0.00 0.00 4.85
2053 2451 2.363018 CTGTCCGAGCTCCCCTGA 60.363 66.667 8.47 0.00 0.00 3.86
2100 2498 3.210302 GCCCAATTGTGGCCTAGC 58.790 61.111 21.04 0.00 44.46 3.42
2106 2504 0.888736 TGTCTCGTGCCCAATTGTGG 60.889 55.000 4.43 6.64 45.53 4.17
2107 2505 0.518636 CTGTCTCGTGCCCAATTGTG 59.481 55.000 4.43 0.00 0.00 3.33
2108 2506 1.237285 GCTGTCTCGTGCCCAATTGT 61.237 55.000 4.43 0.00 0.00 2.71
2109 2507 1.503542 GCTGTCTCGTGCCCAATTG 59.496 57.895 0.00 0.00 0.00 2.32
2110 2508 1.675641 GGCTGTCTCGTGCCCAATT 60.676 57.895 0.00 0.00 43.11 2.32
2111 2509 2.045926 GGCTGTCTCGTGCCCAAT 60.046 61.111 0.00 0.00 43.11 3.16
2116 2514 2.740055 CACCAGGCTGTCTCGTGC 60.740 66.667 14.43 0.00 28.46 5.34
2117 2515 2.740055 GCACCAGGCTGTCTCGTG 60.740 66.667 14.43 14.64 37.60 4.35
2155 2553 1.679139 CACTTCCTGGTTCACTGCAA 58.321 50.000 0.00 0.00 0.00 4.08
2193 2592 1.156736 CTAAACTGGAAGGTGGCACG 58.843 55.000 12.17 0.00 39.30 5.34
2199 2601 3.074538 ACCAAGCATCTAAACTGGAAGGT 59.925 43.478 0.00 0.00 39.30 3.50
2240 2643 7.118245 TGTCTAATCAAACTAATCACACAGCTG 59.882 37.037 13.48 13.48 0.00 4.24
2243 2646 9.764870 CATTGTCTAATCAAACTAATCACACAG 57.235 33.333 0.00 0.00 0.00 3.66
2251 2654 8.334263 TGATGTGCATTGTCTAATCAAACTAA 57.666 30.769 0.00 0.00 0.00 2.24
2316 2795 3.391296 ACAACCTTGAGACAAGGCTAAGA 59.609 43.478 24.58 0.00 41.10 2.10
2338 2817 2.158534 ACCACAGGGCATGTTTCAACTA 60.159 45.455 0.14 0.00 41.41 2.24
2341 2820 1.039068 CACCACAGGGCATGTTTCAA 58.961 50.000 0.14 0.00 41.41 2.69
2342 2821 0.184692 TCACCACAGGGCATGTTTCA 59.815 50.000 0.14 0.00 41.41 2.69
2343 2822 1.327303 TTCACCACAGGGCATGTTTC 58.673 50.000 0.14 0.00 41.41 2.78
2365 2846 3.498774 AATGCTTCTGACTGGACTTGT 57.501 42.857 0.00 0.00 0.00 3.16
2426 4067 1.246056 CCTTGACGTACCCGACCTCA 61.246 60.000 0.00 0.00 37.88 3.86
2429 4070 2.125793 GCCTTGACGTACCCGACC 60.126 66.667 0.00 0.00 37.88 4.79
2432 4073 4.728102 TGCGCCTTGACGTACCCG 62.728 66.667 4.18 0.00 40.83 5.28
2440 4081 1.896220 AATGAAAGACTGCGCCTTGA 58.104 45.000 4.18 0.00 0.00 3.02
2445 4086 1.086696 TGCCTAATGAAAGACTGCGC 58.913 50.000 0.00 0.00 0.00 6.09
2447 4088 3.944015 AGATGTGCCTAATGAAAGACTGC 59.056 43.478 0.00 0.00 0.00 4.40
2481 4128 5.422666 TTGACAGAATTGTAACAGCACTG 57.577 39.130 0.00 0.00 37.76 3.66
2498 4145 6.244654 TGATCAAACCATGACCTATTTGACA 58.755 36.000 0.00 2.22 42.22 3.58
2532 4195 3.950397 ACACAAGGTGAAAGAGAACACA 58.050 40.909 2.98 0.00 38.57 3.72
2538 4201 8.669243 GGAATAGATTAACACAAGGTGAAAGAG 58.331 37.037 2.98 0.00 36.96 2.85
2652 4322 9.595823 GTAAGTAGAGGCAGAACAATAATACAA 57.404 33.333 0.00 0.00 0.00 2.41
2655 4325 7.926555 GCAGTAAGTAGAGGCAGAACAATAATA 59.073 37.037 0.00 0.00 0.00 0.98
2752 4422 5.766174 AGAACTACGAAAATGGCAAACCTAA 59.234 36.000 0.00 0.00 36.63 2.69
2842 4520 0.961753 GCAAAGGGAACAGGGAACAG 59.038 55.000 0.00 0.00 0.00 3.16
2886 4564 4.099419 GGGTATGGGAAAAATTGCAGGTAG 59.901 45.833 0.00 0.00 0.00 3.18
2907 4585 1.884579 GCACCATCTGCATCATAAGGG 59.115 52.381 0.00 0.00 46.29 3.95
2950 4628 6.432783 ACATGGAGGAACACAAAAATCGATAA 59.567 34.615 0.00 0.00 0.00 1.75
2957 4635 6.467677 TGAAAAACATGGAGGAACACAAAAA 58.532 32.000 0.00 0.00 0.00 1.94
2961 4639 4.097741 CACTGAAAAACATGGAGGAACACA 59.902 41.667 0.00 0.00 0.00 3.72
2963 4641 4.531854 TCACTGAAAAACATGGAGGAACA 58.468 39.130 0.00 0.00 0.00 3.18
2966 4644 6.303054 TGTTATCACTGAAAAACATGGAGGA 58.697 36.000 0.00 0.00 0.00 3.71
2967 4645 6.207417 ACTGTTATCACTGAAAAACATGGAGG 59.793 38.462 9.56 3.23 31.88 4.30
2968 4646 7.206981 ACTGTTATCACTGAAAAACATGGAG 57.793 36.000 9.56 3.49 31.88 3.86
2969 4647 8.564574 GTTACTGTTATCACTGAAAAACATGGA 58.435 33.333 9.56 1.82 31.88 3.41
2994 4681 2.366266 ACAGTCCTGCAATGCAAATTGT 59.634 40.909 9.92 10.58 38.41 2.71
3059 4749 0.597568 TGAAGGAGTTTGCAATGCCG 59.402 50.000 1.53 0.00 0.00 5.69
3215 4909 3.865745 GTCAGGACGATCATGGTACTTTG 59.134 47.826 0.00 0.00 0.00 2.77
3216 4910 3.118738 GGTCAGGACGATCATGGTACTTT 60.119 47.826 0.00 0.00 0.00 2.66
3275 4969 2.159544 GCATGAGAAAACAGCTGCTCTC 60.160 50.000 24.16 24.16 35.82 3.20
3280 4974 2.292569 ACTGTGCATGAGAAAACAGCTG 59.707 45.455 13.48 13.48 43.04 4.24
3281 4975 2.579873 ACTGTGCATGAGAAAACAGCT 58.420 42.857 0.00 0.00 43.04 4.24
3282 4976 3.360249 AACTGTGCATGAGAAAACAGC 57.640 42.857 0.00 0.00 43.04 4.40
3443 5137 3.781079 ATAATGCAACATGTTCACCGG 57.219 42.857 8.48 0.00 0.00 5.28
3488 5182 0.698238 TCAACAACCATCCTCAGGGG 59.302 55.000 0.00 0.00 0.00 4.79
3496 5190 4.699257 AGAGCAAGAAGATCAACAACCATC 59.301 41.667 0.00 0.00 34.30 3.51
3497 5191 4.660168 AGAGCAAGAAGATCAACAACCAT 58.340 39.130 0.00 0.00 34.30 3.55
3498 5192 4.090761 AGAGCAAGAAGATCAACAACCA 57.909 40.909 0.00 0.00 34.30 3.67
3499 5193 4.516698 TCAAGAGCAAGAAGATCAACAACC 59.483 41.667 0.00 0.00 34.30 3.77
3501 5195 5.936686 CTCAAGAGCAAGAAGATCAACAA 57.063 39.130 0.00 0.00 34.30 2.83
3550 5244 2.538449 CACTTCGCGTAACAAGTCAAGT 59.462 45.455 5.77 1.66 30.06 3.16
3551 5245 2.538449 ACACTTCGCGTAACAAGTCAAG 59.462 45.455 5.77 0.93 30.06 3.02
3552 5246 2.283086 CACACTTCGCGTAACAAGTCAA 59.717 45.455 5.77 0.00 30.06 3.18
3553 5247 1.855978 CACACTTCGCGTAACAAGTCA 59.144 47.619 5.77 0.00 30.06 3.41
3554 5248 2.121786 TCACACTTCGCGTAACAAGTC 58.878 47.619 5.77 0.00 30.06 3.01
3555 5249 2.212869 TCACACTTCGCGTAACAAGT 57.787 45.000 5.77 5.43 32.87 3.16
3556 5250 2.538449 ACTTCACACTTCGCGTAACAAG 59.462 45.455 5.77 4.67 0.00 3.16
3557 5251 2.542597 ACTTCACACTTCGCGTAACAA 58.457 42.857 5.77 0.00 0.00 2.83
3657 5351 2.558359 GACTACAGCTTTGCAATGGGTT 59.442 45.455 13.62 0.00 0.00 4.11
3658 5352 2.162681 GACTACAGCTTTGCAATGGGT 58.837 47.619 13.62 6.63 0.00 4.51
3676 5370 2.156098 TGCAATGGAACTTTACCCGAC 58.844 47.619 0.00 0.00 0.00 4.79
3694 5388 5.699839 CCCTACTTCTTAACAACAACATGC 58.300 41.667 0.00 0.00 0.00 4.06
3704 5398 3.607741 GTTCCAGGCCCTACTTCTTAAC 58.392 50.000 0.00 0.00 0.00 2.01
3747 5441 6.036083 GCACACACTCGAGTTGAATATAATGT 59.964 38.462 24.80 11.84 0.00 2.71
3768 5462 6.909550 ATATAAAAAGAACACCAAGGCACA 57.090 33.333 0.00 0.00 0.00 4.57
3845 5578 0.603975 AGAGCACGAAACTCCCAAGC 60.604 55.000 0.00 0.00 34.56 4.01
3846 5579 1.151668 CAGAGCACGAAACTCCCAAG 58.848 55.000 0.00 0.00 34.56 3.61
3863 5596 1.131315 TCGCATTCTCTCGTCACTCAG 59.869 52.381 0.00 0.00 0.00 3.35
3881 5614 3.579709 AGATAATACGAAGGCAGCATCG 58.420 45.455 15.94 15.94 44.33 3.84
3929 5662 5.571285 TCTCCAGTCCAGTCGCTATATATT 58.429 41.667 0.00 0.00 0.00 1.28
3943 5676 4.679373 TGATAATTGCTCTCTCCAGTCC 57.321 45.455 0.00 0.00 0.00 3.85
4102 5843 2.280457 GGATAGCTGTCAGCCGGC 60.280 66.667 21.89 21.89 43.77 6.13
4103 5844 1.227380 GTGGATAGCTGTCAGCCGG 60.227 63.158 21.32 0.00 43.77 6.13
4104 5845 1.227380 GGTGGATAGCTGTCAGCCG 60.227 63.158 21.32 0.00 43.77 5.52
4106 5847 0.462759 GGTGGTGGATAGCTGTCAGC 60.463 60.000 17.48 17.48 42.84 4.26
4107 5848 0.904649 TGGTGGTGGATAGCTGTCAG 59.095 55.000 12.91 0.00 0.00 3.51
4108 5849 0.613260 GTGGTGGTGGATAGCTGTCA 59.387 55.000 12.91 0.00 0.00 3.58
4109 5850 0.107654 GGTGGTGGTGGATAGCTGTC 60.108 60.000 1.05 1.05 0.00 3.51
4111 5852 0.392998 GTGGTGGTGGTGGATAGCTG 60.393 60.000 0.00 0.00 0.00 4.24
4112 5853 1.562672 GGTGGTGGTGGTGGATAGCT 61.563 60.000 0.00 0.00 0.00 3.32
4113 5854 1.077716 GGTGGTGGTGGTGGATAGC 60.078 63.158 0.00 0.00 0.00 2.97
4114 5855 0.035439 GTGGTGGTGGTGGTGGATAG 60.035 60.000 0.00 0.00 0.00 2.08
4115 5856 1.493854 GGTGGTGGTGGTGGTGGATA 61.494 60.000 0.00 0.00 0.00 2.59
4116 5857 2.840753 GGTGGTGGTGGTGGTGGAT 61.841 63.158 0.00 0.00 0.00 3.41
4117 5858 3.494254 GGTGGTGGTGGTGGTGGA 61.494 66.667 0.00 0.00 0.00 4.02
4118 5859 3.790416 CTGGTGGTGGTGGTGGTGG 62.790 68.421 0.00 0.00 0.00 4.61
4119 5860 2.203337 CTGGTGGTGGTGGTGGTG 60.203 66.667 0.00 0.00 0.00 4.17
4120 5861 4.204028 GCTGGTGGTGGTGGTGGT 62.204 66.667 0.00 0.00 0.00 4.16
4149 5890 0.252881 AGCATGAGGAGGAGGGACAA 60.253 55.000 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.