Multiple sequence alignment - TraesCS2D01G405300

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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 TraesCS2D01G405300 chr2D 100.000 5311 0 0 1 5311 520520233 520525543 0.000000e+00 9808.0
1 TraesCS2D01G405300 chr2B 93.282 5031 229 50 316 5311 612683241 612688197 0.000000e+00 7317.0
2 TraesCS2D01G405300 chr2B 92.361 288 18 2 1 284 612682865 612683152 1.780000e-109 407.0
3 TraesCS2D01G405300 chr2A 93.858 4510 204 38 831 5311 665705450 665709915 0.000000e+00 6726.0
4 TraesCS2D01G405300 chr2A 87.986 874 65 13 1 846 665704570 665705431 0.000000e+00 996.0
5 TraesCS2D01G405300 chr1B 89.728 662 54 10 502 1150 31629847 31630507 0.000000e+00 833.0
6 TraesCS2D01G405300 chr1B 82.022 356 35 14 89 430 31629511 31629851 5.240000e-70 276.0
7 TraesCS2D01G405300 chr1B 87.356 87 8 3 1358 1442 1833132 1833217 4.380000e-16 97.1
8 TraesCS2D01G405300 chr7B 91.743 109 7 1 325 431 297177593 297177485 3.310000e-32 150.0
9 TraesCS2D01G405300 chr7B 90.826 109 8 1 325 431 297163300 297163192 1.540000e-30 145.0
10 TraesCS2D01G405300 chr7B 87.671 73 7 1 1370 1442 696896087 696896017 3.410000e-12 84.2
11 TraesCS2D01G405300 chr7B 92.308 52 4 0 1391 1442 693245768 693245717 2.050000e-09 75.0
12 TraesCS2D01G405300 chr7D 92.381 105 6 1 329 431 87989977 87989873 1.190000e-31 148.0
13 TraesCS2D01G405300 chr7D 84.337 83 11 1 1360 1442 607611887 607611807 4.410000e-11 80.5
14 TraesCS2D01G405300 chr1D 91.667 108 7 1 326 431 17621902 17621795 1.190000e-31 148.0
15 TraesCS2D01G405300 chr7A 86.747 83 9 1 1360 1442 699839132 699839052 2.040000e-14 91.6
16 TraesCS2D01G405300 chr6A 85.057 87 8 5 1360 1442 117424681 117424596 3.410000e-12 84.2
17 TraesCS2D01G405300 chrUn 86.667 75 8 2 1373 1445 343707139 343707065 1.230000e-11 82.4
18 TraesCS2D01G405300 chrUn 85.526 76 9 2 1358 1431 343707064 343707139 1.590000e-10 78.7


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 TraesCS2D01G405300 chr2D 520520233 520525543 5310 False 9808.0 9808 100.0000 1 5311 1 chr2D.!!$F1 5310
1 TraesCS2D01G405300 chr2B 612682865 612688197 5332 False 3862.0 7317 92.8215 1 5311 2 chr2B.!!$F1 5310
2 TraesCS2D01G405300 chr2A 665704570 665709915 5345 False 3861.0 6726 90.9220 1 5311 2 chr2A.!!$F1 5310
3 TraesCS2D01G405300 chr1B 31629511 31630507 996 False 554.5 833 85.8750 89 1150 2 chr1B.!!$F2 1061

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
85 86 0.106918 TGGTTGTCACTTGGTGGGTC 60.107 55.0 0.0 0.0 33.87 4.46 F
1132 1267 0.537188 TCTTTCAGATGGGAGCCGAC 59.463 55.0 0.0 0.0 0.00 4.79 F
2301 2444 0.249238 GCATAGAGCAGTCGGAGGTG 60.249 60.0 0.0 0.0 44.79 4.00 F
3053 3202 0.250640 ACCAGTGCAAGCTCTTCAGG 60.251 55.0 0.0 0.0 0.00 3.86 F
3564 3719 0.751452 TGACATTTGCTTGCTTGCCA 59.249 45.0 0.0 0.0 0.00 4.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1287 1422 0.656259 CATCTGCAGCCGTGATTCTG 59.344 55.0 9.47 0.0 0.0 3.02 R
2498 2641 0.535102 ACTTTCAACCTGACCTGGCG 60.535 55.0 0.00 0.0 0.0 5.69 R
3502 3657 0.037882 ACGACTGCTGATGGACTGTG 60.038 55.0 0.00 0.0 0.0 3.66 R
4194 4351 0.324943 ATCCACGGTCCACTTTCCAG 59.675 55.0 0.00 0.0 0.0 3.86 R
5173 5356 0.030101 GAGTCGGCGAGGAAGATCTG 59.970 60.0 11.20 0.0 0.0 2.90 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
20 21 2.151202 GGAACACAAGGCGATTCAGAA 58.849 47.619 0.00 0.00 0.00 3.02
31 32 2.935201 GCGATTCAGAAGATTCAGCAGT 59.065 45.455 0.00 0.00 0.00 4.40
33 34 4.431809 CGATTCAGAAGATTCAGCAGTCT 58.568 43.478 0.00 0.00 0.00 3.24
37 38 4.965814 TCAGAAGATTCAGCAGTCTGTTT 58.034 39.130 0.93 0.00 41.10 2.83
39 40 6.524734 TCAGAAGATTCAGCAGTCTGTTTTA 58.475 36.000 0.93 0.00 41.10 1.52
85 86 0.106918 TGGTTGTCACTTGGTGGGTC 60.107 55.000 0.00 0.00 33.87 4.46
189 194 1.821216 ACTTGGCCCAATACGAACAG 58.179 50.000 0.00 0.00 0.00 3.16
343 414 6.373774 GGGAGATGCTTAATCCAACATGATAG 59.626 42.308 0.00 0.00 35.72 2.08
361 432 5.041287 TGATAGCTGTTCCTTTCGTTATCG 58.959 41.667 0.00 0.00 38.55 2.92
546 629 7.115378 GCATATTTGCCTTTTCAATATTCCGAG 59.885 37.037 0.00 0.00 43.38 4.63
606 689 5.120399 TCAAGTTCTTGTGACACGGTTAAT 58.880 37.500 11.52 0.00 0.00 1.40
608 691 3.739300 AGTTCTTGTGACACGGTTAATCG 59.261 43.478 6.57 6.57 0.00 3.34
706 793 2.159282 GCAATGTGATCCTTGCCTCTTG 60.159 50.000 11.63 0.00 41.45 3.02
790 881 7.033185 GCTGTATTTGTTTATGGGGTTAGTTG 58.967 38.462 0.00 0.00 0.00 3.16
827 918 9.612620 CACTAATTGGAACATACTTTGAGAAAC 57.387 33.333 0.00 0.00 39.30 2.78
893 1021 7.670364 GCTTTGGTTGCCATTATATATTCCTT 58.330 34.615 0.00 0.00 31.53 3.36
1044 1179 5.257082 ACAAAAGTTACAAACAGCGGAAT 57.743 34.783 0.00 0.00 0.00 3.01
1098 1233 1.736645 CCGCATGTTCGACTTCCGT 60.737 57.895 0.00 0.00 39.75 4.69
1131 1266 1.500474 ATCTTTCAGATGGGAGCCGA 58.500 50.000 0.00 0.00 32.80 5.54
1132 1267 0.537188 TCTTTCAGATGGGAGCCGAC 59.463 55.000 0.00 0.00 0.00 4.79
1140 1275 1.410850 ATGGGAGCCGACGGATGAAT 61.411 55.000 20.50 1.11 0.00 2.57
1160 1295 7.194112 TGAATACATATTCAGGTGAGGAACA 57.806 36.000 9.75 0.00 45.03 3.18
1162 1297 6.201044 GAATACATATTCAGGTGAGGAACACG 59.799 42.308 6.74 0.00 43.70 4.49
1163 1298 7.897332 GAATACATATTCAGGTGAGGAACACGA 60.897 40.741 6.74 0.00 43.70 4.35
1171 1306 1.131126 GTGAGGAACACGATGCCATTG 59.869 52.381 0.00 0.00 39.78 2.82
1178 1313 0.734309 CACGATGCCATTGCTTAGCA 59.266 50.000 1.39 1.39 41.50 3.49
1230 1365 5.902613 TCTGGTCCATGAATTTGCTAAAG 57.097 39.130 0.00 0.00 0.00 1.85
1231 1366 4.706476 TCTGGTCCATGAATTTGCTAAAGG 59.294 41.667 0.00 0.00 0.00 3.11
1242 1377 8.453238 TGAATTTGCTAAAGGTAAACTGTGTA 57.547 30.769 0.00 0.00 32.72 2.90
1272 1407 4.321750 GCAGTTAAAAGGGGTCTAAAAGGC 60.322 45.833 0.00 0.00 0.00 4.35
1278 1413 2.192263 AGGGGTCTAAAAGGCTCTGAG 58.808 52.381 0.00 0.00 0.00 3.35
1287 1422 6.314152 GTCTAAAAGGCTCTGAGGATTACAAC 59.686 42.308 6.83 0.00 0.00 3.32
1388 1528 6.778821 TCTCTGTCCCAAAATAAGTTCATGA 58.221 36.000 0.00 0.00 0.00 3.07
1465 1605 5.748592 CACAAAATAGCGCTATAAACCTCC 58.251 41.667 29.20 0.00 0.00 4.30
1631 1773 8.451748 GGAGTTTAACATGGTCAGAAGTATTTC 58.548 37.037 0.00 0.00 0.00 2.17
1695 1838 3.444029 TCAGAATGACAGAGACCATGGA 58.556 45.455 21.47 0.00 42.56 3.41
1705 1848 2.575279 AGAGACCATGGAGCTGAAACAT 59.425 45.455 21.47 0.00 0.00 2.71
1914 2057 3.058639 GTCACAATGGAAGTCAAGACAGC 60.059 47.826 2.72 0.00 0.00 4.40
2070 2213 2.356695 CCATCAATCAGCGAATGCAGAA 59.643 45.455 0.00 0.00 46.23 3.02
2115 2258 2.932261 AGGTCCAAAGAACTGGTTGAC 58.068 47.619 0.00 0.00 39.15 3.18
2244 2387 1.065418 CCCAAGTTAGAACCCGCAGAT 60.065 52.381 0.00 0.00 0.00 2.90
2301 2444 0.249238 GCATAGAGCAGTCGGAGGTG 60.249 60.000 0.00 0.00 44.79 4.00
2452 2595 2.937433 GCAAGAAGTCAGGGTAGCCTTC 60.937 54.545 11.77 6.50 34.82 3.46
2589 2732 2.555199 CTTGCCACCATGAGTAGTAGC 58.445 52.381 0.00 0.00 0.00 3.58
2600 2743 4.785511 TGAGTAGTAGCACTTTCCAGAC 57.214 45.455 0.00 0.00 0.00 3.51
2842 2988 6.872547 TCAAGATGAAGACATTTCTCAGACTG 59.127 38.462 0.00 0.00 36.82 3.51
2847 2993 6.816136 TGAAGACATTTCTCAGACTGTACAA 58.184 36.000 1.59 0.00 0.00 2.41
2886 3032 5.130350 GGGAGATTAATTTCACATCCGGAA 58.870 41.667 9.01 0.00 0.00 4.30
2967 3113 4.250116 AGCTACAGACTCAAGTTCACAG 57.750 45.455 0.00 0.00 0.00 3.66
3019 3165 2.501223 TAGCCCACCAAGCGAAGACG 62.501 60.000 0.00 0.00 42.93 4.18
3031 3177 1.980156 GCGAAGACGAAGAGACAGAAC 59.020 52.381 0.00 0.00 42.66 3.01
3038 3184 1.401670 CGAAGAGACAGAACCGACCAG 60.402 57.143 0.00 0.00 0.00 4.00
3053 3202 0.250640 ACCAGTGCAAGCTCTTCAGG 60.251 55.000 0.00 0.00 0.00 3.86
3101 3250 4.649692 ACAGATCATGGCAACCATCTATC 58.350 43.478 0.00 3.66 43.15 2.08
3109 3258 1.964223 GCAACCATCTATCGGAGGAGA 59.036 52.381 0.00 0.00 0.00 3.71
3155 3304 4.333649 CGATGAAGGTATGTTGCTCATGTT 59.666 41.667 0.00 0.00 37.91 2.71
3157 3306 6.037062 CGATGAAGGTATGTTGCTCATGTTTA 59.963 38.462 0.00 0.00 37.91 2.01
3158 3307 7.254898 CGATGAAGGTATGTTGCTCATGTTTAT 60.255 37.037 0.00 0.81 37.91 1.40
3159 3308 7.087409 TGAAGGTATGTTGCTCATGTTTATG 57.913 36.000 0.00 0.00 37.91 1.90
3162 3311 7.325660 AGGTATGTTGCTCATGTTTATGAAG 57.674 36.000 0.00 0.00 42.48 3.02
3163 3312 6.886459 AGGTATGTTGCTCATGTTTATGAAGT 59.114 34.615 0.00 0.00 42.48 3.01
3165 3314 7.698130 GGTATGTTGCTCATGTTTATGAAGTTC 59.302 37.037 0.00 0.00 42.48 3.01
3272 3422 3.679389 AGATGCAGTGGAAAACCTACAG 58.321 45.455 0.00 0.00 0.00 2.74
3287 3437 2.645802 CTACAGCTCTCTACCGAGGTT 58.354 52.381 0.00 0.00 39.55 3.50
3294 3444 3.442977 GCTCTCTACCGAGGTTGAAACTA 59.557 47.826 0.00 0.00 37.86 2.24
3305 3455 5.500645 AGGTTGAAACTACAAGTGAAAGC 57.499 39.130 0.00 0.00 0.00 3.51
3329 3479 8.203485 AGCTTTGAACAAATAAATTCAGACCAA 58.797 29.630 0.44 0.00 36.26 3.67
3337 3487 9.349713 ACAAATAAATTCAGACCAAGTAAGTCA 57.650 29.630 0.00 0.00 36.68 3.41
3344 3494 6.681729 TCAGACCAAGTAAGTCAATACCTT 57.318 37.500 0.00 0.00 36.68 3.50
3374 3524 8.006027 GCAATTTCAATACAAAGTTGAGCTTTC 58.994 33.333 0.00 0.00 44.95 2.62
3378 3528 9.651913 TTTCAATACAAAGTTGAGCTTTCTTTT 57.348 25.926 0.00 0.00 44.95 2.27
3379 3529 8.856490 TCAATACAAAGTTGAGCTTTCTTTTC 57.144 30.769 0.00 0.00 44.95 2.29
3380 3530 8.686334 TCAATACAAAGTTGAGCTTTCTTTTCT 58.314 29.630 0.00 2.37 44.95 2.52
3381 3531 9.950680 CAATACAAAGTTGAGCTTTCTTTTCTA 57.049 29.630 0.00 3.91 44.95 2.10
3382 3532 9.952188 AATACAAAGTTGAGCTTTCTTTTCTAC 57.048 29.630 0.00 0.00 44.95 2.59
3435 3590 4.822026 AGTTATCTTCCGAAGAACCACAG 58.178 43.478 14.75 0.00 41.63 3.66
3440 3595 1.966451 CCGAAGAACCACAGCCCAC 60.966 63.158 0.00 0.00 0.00 4.61
3463 3618 0.753867 TGCGTTACCAGAAGTGACCA 59.246 50.000 0.00 0.00 31.34 4.02
3478 3633 1.307097 GACCATGCATTCTCCTGAGC 58.693 55.000 0.00 0.00 0.00 4.26
3502 3657 1.993370 CCGTTGAGGAACAAGACGATC 59.007 52.381 0.00 0.00 45.00 3.69
3503 3658 2.609491 CCGTTGAGGAACAAGACGATCA 60.609 50.000 0.00 0.00 45.00 2.92
3564 3719 0.751452 TGACATTTGCTTGCTTGCCA 59.249 45.000 0.00 0.00 0.00 4.92
3597 3752 5.471456 TGATGAAAAAGAGGAGAAACTGAGC 59.529 40.000 0.00 0.00 0.00 4.26
3644 3799 2.645297 TGGCAAATAGTACCAGTCCCAA 59.355 45.455 0.00 0.00 0.00 4.12
3926 4083 4.820775 AGAGGTGGTATATGGATGTGTCT 58.179 43.478 0.00 0.00 0.00 3.41
3977 4134 2.159043 AGGAATGTCATACTGCCTGACG 60.159 50.000 5.93 0.00 44.77 4.35
4016 4173 7.169158 TCTTTTTGATTGTGTTGAGGAAGTT 57.831 32.000 0.00 0.00 0.00 2.66
4094 4251 1.227527 CAACGTGAGACCAGCACCA 60.228 57.895 0.00 0.00 32.74 4.17
4194 4351 0.108585 TGAGGTGGTGCTGAAAGACC 59.891 55.000 0.00 0.00 34.07 3.85
4238 4395 2.133553 CTTCGATGCGATGCTGAAGAT 58.866 47.619 11.06 0.00 36.17 2.40
4262 4419 1.406539 GTCATTGATGTGTGGGATGGC 59.593 52.381 0.00 0.00 0.00 4.40
4378 4535 2.348243 CCTTTTGGCCGTACGGGA 59.652 61.111 33.98 0.00 38.47 5.14
4379 4536 1.302671 CCTTTTGGCCGTACGGGAA 60.303 57.895 33.98 5.27 38.47 3.97
4581 4742 1.227102 CCATTTCCCGGATGGAGCA 59.773 57.895 14.17 0.00 46.24 4.26
4594 4755 5.124776 CCGGATGGAGCAAATAACAGTTTTA 59.875 40.000 0.00 0.00 37.49 1.52
4608 4771 1.544246 AGTTTTATTTCACAGCCCGGC 59.456 47.619 0.00 0.00 0.00 6.13
4674 4837 8.519526 CACTAGGAATTGTTTGGTTATGCTTTA 58.480 33.333 0.00 0.00 0.00 1.85
4685 4848 7.435068 TTGGTTATGCTTTACTTCTCACTTC 57.565 36.000 0.00 0.00 0.00 3.01
4689 4852 7.414540 GGTTATGCTTTACTTCTCACTTCATGG 60.415 40.741 0.00 0.00 0.00 3.66
4696 4859 3.117888 ACTTCTCACTTCATGGTGTTGGT 60.118 43.478 0.00 0.00 38.28 3.67
4752 4915 4.881850 GGGTGTGTATAGATTGTTCCCTTG 59.118 45.833 0.00 0.00 0.00 3.61
4860 5026 2.170397 TGTCAGTTGCCAACTTGAGAGA 59.830 45.455 7.51 0.00 40.46 3.10
4883 5055 2.107031 CCATGCCCATCCATACAAGAGA 59.893 50.000 0.00 0.00 0.00 3.10
4922 5094 4.111375 AGTGATACTGTACTCTTTGGCG 57.889 45.455 0.00 0.00 0.00 5.69
4934 5106 2.083774 TCTTTGGCGTCCATTGTCATC 58.916 47.619 0.00 0.00 31.53 2.92
4943 5115 4.261783 GCGTCCATTGTCATCATAGAGAGA 60.262 45.833 0.00 0.00 0.00 3.10
4944 5116 5.737349 GCGTCCATTGTCATCATAGAGAGAA 60.737 44.000 0.00 0.00 0.00 2.87
4974 5151 0.184451 CTGAGGGACCATGGGAATGG 59.816 60.000 18.09 3.16 46.92 3.16
4975 5152 0.253583 TGAGGGACCATGGGAATGGA 60.254 55.000 18.09 0.00 44.39 3.41
4976 5153 0.926293 GAGGGACCATGGGAATGGAA 59.074 55.000 18.09 0.00 44.39 3.53
4977 5154 1.500736 GAGGGACCATGGGAATGGAAT 59.499 52.381 18.09 0.00 44.39 3.01
4978 5155 1.218704 AGGGACCATGGGAATGGAATG 59.781 52.381 18.09 0.00 44.39 2.67
5010 5187 4.730487 CATGGCTATGCTAGGGCC 57.270 61.111 0.00 0.00 45.45 5.80
5037 5214 0.392060 CCTACTGTGCTCATGCTGCA 60.392 55.000 4.13 4.13 40.48 4.41
5052 5229 3.689347 TGCTGCAATCTTCCATTAGTGT 58.311 40.909 0.00 0.00 0.00 3.55
5053 5230 4.842574 TGCTGCAATCTTCCATTAGTGTA 58.157 39.130 0.00 0.00 0.00 2.90
5054 5231 4.635765 TGCTGCAATCTTCCATTAGTGTAC 59.364 41.667 0.00 0.00 0.00 2.90
5127 5304 2.403259 GACCGGCATTTTGGTTTTCTG 58.597 47.619 0.00 0.00 38.99 3.02
5128 5305 1.069978 ACCGGCATTTTGGTTTTCTGG 59.930 47.619 0.00 0.00 33.81 3.86
5129 5306 1.069978 CCGGCATTTTGGTTTTCTGGT 59.930 47.619 0.00 0.00 0.00 4.00
5130 5307 2.403259 CGGCATTTTGGTTTTCTGGTC 58.597 47.619 0.00 0.00 0.00 4.02
5131 5308 2.766313 GGCATTTTGGTTTTCTGGTCC 58.234 47.619 0.00 0.00 0.00 4.46
5132 5309 2.103941 GGCATTTTGGTTTTCTGGTCCA 59.896 45.455 0.00 0.00 0.00 4.02
5301 5484 2.546494 AACGTCCTGCAGCACAAGC 61.546 57.895 8.83 0.00 42.56 4.01
5303 5486 2.545596 CGTCCTGCAGCACAAGCAA 61.546 57.895 8.83 0.00 45.49 3.91
5304 5487 1.859427 CGTCCTGCAGCACAAGCAAT 61.859 55.000 8.83 0.00 45.49 3.56
5305 5488 0.109412 GTCCTGCAGCACAAGCAATC 60.109 55.000 8.66 0.00 45.49 2.67
5307 5490 0.109272 CCTGCAGCACAAGCAATCAG 60.109 55.000 8.66 0.00 45.49 2.90
5308 5491 0.879090 CTGCAGCACAAGCAATCAGA 59.121 50.000 0.00 0.00 45.49 3.27
5309 5492 1.472878 CTGCAGCACAAGCAATCAGAT 59.527 47.619 0.00 0.00 45.49 2.90
5310 5493 1.890489 TGCAGCACAAGCAATCAGATT 59.110 42.857 0.00 0.00 45.49 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 6.291377 TCTTGTAAAACAGACTGCTGAATCT 58.709 36.000 1.25 0.00 45.17 2.40
33 34 5.123227 CCTGACCTCTGTTCTTGTAAAACA 58.877 41.667 0.00 0.00 35.44 2.83
37 38 2.038557 GCCCTGACCTCTGTTCTTGTAA 59.961 50.000 0.00 0.00 0.00 2.41
39 40 0.398318 GCCCTGACCTCTGTTCTTGT 59.602 55.000 0.00 0.00 0.00 3.16
66 67 0.106918 GACCCACCAAGTGACAACCA 60.107 55.000 0.00 0.00 35.23 3.67
76 77 1.144691 TTGATCACAGGACCCACCAA 58.855 50.000 0.00 0.00 42.04 3.67
139 144 4.223032 ACTGTCTAACCAGATGAACGGAAT 59.777 41.667 0.00 0.00 36.30 3.01
284 297 0.446616 GACCGAAATGCCCGTTCTTC 59.553 55.000 0.00 0.00 0.00 2.87
285 298 0.250553 TGACCGAAATGCCCGTTCTT 60.251 50.000 0.00 0.00 0.00 2.52
343 414 2.613691 TCCGATAACGAAAGGAACAGC 58.386 47.619 0.00 0.00 42.66 4.40
375 452 8.400184 TGTGAACTCTGAAGATTTCAATTCAT 57.600 30.769 12.93 0.00 42.62 2.57
524 607 6.773976 TCTCGGAATATTGAAAAGGCAAAT 57.226 33.333 0.00 0.00 0.00 2.32
546 629 2.316119 AATTTGACGCACGAAGCTTC 57.684 45.000 16.84 16.84 41.56 3.86
706 793 5.163754 CCCAAAAGACAAAGACCATATCGAC 60.164 44.000 0.00 0.00 0.00 4.20
790 881 3.088532 TCCAATTAGTGAATGGTGGCAC 58.911 45.455 9.70 9.70 35.30 5.01
827 918 2.498167 CCAAGTCCCAACAACTCAGAG 58.502 52.381 0.00 0.00 0.00 3.35
893 1021 5.124617 TGTGAACACTGAACAGCACAAAATA 59.875 36.000 6.51 0.00 33.81 1.40
930 1058 4.838959 GCATAAAGCACACGCGTT 57.161 50.000 10.22 0.00 45.49 4.84
950 1078 3.506455 TCTCTTCAGACGAGTTAACCTGG 59.494 47.826 0.88 0.00 0.00 4.45
1044 1179 2.241176 ACAACCAACCTGAACCTTCTCA 59.759 45.455 0.00 0.00 0.00 3.27
1140 1275 4.707934 TCGTGTTCCTCACCTGAATATGTA 59.292 41.667 0.00 0.00 43.51 2.29
1160 1295 1.019673 CTGCTAAGCAATGGCATCGT 58.980 50.000 0.00 0.00 45.23 3.73
1193 1328 7.290948 TCATGGACCAGATGATACATTAACTCT 59.709 37.037 0.00 0.00 0.00 3.24
1206 1341 5.840243 TTAGCAAATTCATGGACCAGATG 57.160 39.130 0.00 0.00 0.00 2.90
1230 1365 4.334481 ACTGCACAAAGTACACAGTTTACC 59.666 41.667 0.00 0.00 38.38 2.85
1231 1366 5.479716 ACTGCACAAAGTACACAGTTTAC 57.520 39.130 0.00 0.00 38.38 2.01
1242 1377 3.371034 ACCCCTTTTAACTGCACAAAGT 58.629 40.909 0.00 0.00 0.00 2.66
1272 1407 5.518128 CGTGATTCTGTTGTAATCCTCAGAG 59.482 44.000 0.00 0.00 38.03 3.35
1278 1413 3.063997 CAGCCGTGATTCTGTTGTAATCC 59.936 47.826 0.00 0.00 33.28 3.01
1287 1422 0.656259 CATCTGCAGCCGTGATTCTG 59.344 55.000 9.47 0.00 0.00 3.02
1398 1538 6.639563 AGTGTTGTGGCTTTAGTTCAAATTT 58.360 32.000 0.00 0.00 0.00 1.82
1399 1539 6.220726 AGTGTTGTGGCTTTAGTTCAAATT 57.779 33.333 0.00 0.00 0.00 1.82
1400 1540 5.852282 AGTGTTGTGGCTTTAGTTCAAAT 57.148 34.783 0.00 0.00 0.00 2.32
1401 1541 5.652994 AAGTGTTGTGGCTTTAGTTCAAA 57.347 34.783 0.00 0.00 0.00 2.69
1404 1544 7.169140 CCAAAATAAGTGTTGTGGCTTTAGTTC 59.831 37.037 0.00 0.00 0.00 3.01
1405 1545 6.983890 CCAAAATAAGTGTTGTGGCTTTAGTT 59.016 34.615 0.00 0.00 0.00 2.24
1406 1546 6.462347 CCCAAAATAAGTGTTGTGGCTTTAGT 60.462 38.462 0.00 0.00 0.00 2.24
1407 1547 5.925969 CCCAAAATAAGTGTTGTGGCTTTAG 59.074 40.000 0.00 0.00 0.00 1.85
1408 1548 5.598830 TCCCAAAATAAGTGTTGTGGCTTTA 59.401 36.000 0.00 0.00 0.00 1.85
1409 1549 4.407296 TCCCAAAATAAGTGTTGTGGCTTT 59.593 37.500 0.00 0.00 0.00 3.51
1410 1550 3.964031 TCCCAAAATAAGTGTTGTGGCTT 59.036 39.130 0.00 0.00 0.00 4.35
1411 1551 3.320826 GTCCCAAAATAAGTGTTGTGGCT 59.679 43.478 0.00 0.00 0.00 4.75
1412 1552 3.649073 GTCCCAAAATAAGTGTTGTGGC 58.351 45.455 0.00 0.00 0.00 5.01
1413 1553 3.305064 CCGTCCCAAAATAAGTGTTGTGG 60.305 47.826 0.00 0.00 0.00 4.17
1414 1554 3.566322 TCCGTCCCAAAATAAGTGTTGTG 59.434 43.478 0.00 0.00 0.00 3.33
1415 1555 3.818773 CTCCGTCCCAAAATAAGTGTTGT 59.181 43.478 0.00 0.00 0.00 3.32
1416 1556 3.190535 CCTCCGTCCCAAAATAAGTGTTG 59.809 47.826 0.00 0.00 0.00 3.33
1417 1557 3.418047 CCTCCGTCCCAAAATAAGTGTT 58.582 45.455 0.00 0.00 0.00 3.32
1465 1605 6.805713 AGAAGTTCCAAAGTTACCACATTTG 58.194 36.000 0.00 0.00 34.45 2.32
1588 1730 4.389890 ACTCCAACGTACCGCATATAAA 57.610 40.909 0.00 0.00 0.00 1.40
1601 1743 4.062293 TCTGACCATGTTAAACTCCAACG 58.938 43.478 0.00 0.00 0.00 4.10
1695 1838 2.825532 ACCGGCATAAAATGTTTCAGCT 59.174 40.909 0.00 0.00 0.00 4.24
2070 2213 0.880278 CGCCGCTGCTGGTTATGTAT 60.880 55.000 11.14 0.00 34.43 2.29
2107 2250 2.941333 CTGCAGTGCGTCAACCAG 59.059 61.111 11.20 0.00 0.00 4.00
2115 2258 3.789858 CTCAGCAGCTGCAGTGCG 61.790 66.667 38.24 20.96 46.06 5.34
2244 2387 7.173218 CCTTGCAACTTAGTTACTTCATCAGAA 59.827 37.037 0.00 0.00 0.00 3.02
2301 2444 4.893424 TCTTTGCACTTTACTTGGTGAC 57.107 40.909 0.00 0.00 35.69 3.67
2452 2595 6.864165 GGTGAAGAAGTTACACTACTTGAGAG 59.136 42.308 0.00 0.00 38.43 3.20
2498 2641 0.535102 ACTTTCAACCTGACCTGGCG 60.535 55.000 0.00 0.00 0.00 5.69
2589 2732 2.289882 TGGATCAGCAGTCTGGAAAGTG 60.290 50.000 1.14 0.00 40.69 3.16
2600 2743 1.001764 TGCTTGGGTGGATCAGCAG 60.002 57.895 0.00 0.00 33.07 4.24
2628 2771 8.475331 TTTCTGAACTTATCGACATACTTTCC 57.525 34.615 0.00 0.00 0.00 3.13
2842 2988 7.122650 TCTCCCAATGGATTCTGATTTTTGTAC 59.877 37.037 0.00 0.00 40.80 2.90
2847 2993 8.843308 TTAATCTCCCAATGGATTCTGATTTT 57.157 30.769 0.00 0.00 40.80 1.82
2886 3032 1.009997 TGGGAGAAAATGCCCCATCT 58.990 50.000 0.00 0.00 44.67 2.90
2891 3037 2.149973 ATGACTGGGAGAAAATGCCC 57.850 50.000 0.00 0.00 44.93 5.36
2967 3113 8.229137 GCTGAACTATCATCTTGCTCAATTATC 58.771 37.037 0.00 0.00 34.37 1.75
3019 3165 1.614413 ACTGGTCGGTTCTGTCTCTTC 59.386 52.381 0.00 0.00 0.00 2.87
3031 3177 1.294659 GAAGAGCTTGCACTGGTCGG 61.295 60.000 11.01 0.00 37.07 4.79
3038 3184 2.464157 ACTACCTGAAGAGCTTGCAC 57.536 50.000 0.00 0.00 0.00 4.57
3109 3258 6.096987 TCGATTAGCTCCTGAGAAATAGTGTT 59.903 38.462 0.00 0.00 0.00 3.32
3155 3304 4.601857 AGAAGGGGGTCTTGAACTTCATAA 59.398 41.667 0.00 0.00 39.87 1.90
3157 3306 2.989571 AGAAGGGGGTCTTGAACTTCAT 59.010 45.455 0.00 0.00 39.87 2.57
3158 3307 2.372172 GAGAAGGGGGTCTTGAACTTCA 59.628 50.000 0.00 0.00 39.87 3.02
3159 3308 2.640332 AGAGAAGGGGGTCTTGAACTTC 59.360 50.000 0.00 0.00 38.20 3.01
3162 3311 2.372172 TGAAGAGAAGGGGGTCTTGAAC 59.628 50.000 0.00 0.00 35.50 3.18
3163 3312 2.639839 CTGAAGAGAAGGGGGTCTTGAA 59.360 50.000 0.00 0.00 35.50 2.69
3165 3314 1.339535 GCTGAAGAGAAGGGGGTCTTG 60.340 57.143 0.00 0.00 35.50 3.02
3251 3401 3.679389 CTGTAGGTTTTCCACTGCATCT 58.321 45.455 0.00 0.00 43.73 2.90
3287 3437 6.751514 TCAAAGCTTTCACTTGTAGTTTCA 57.248 33.333 9.23 0.00 0.00 2.69
3294 3444 8.770438 TTTATTTGTTCAAAGCTTTCACTTGT 57.230 26.923 9.23 2.66 0.00 3.16
3305 3455 9.533253 ACTTGGTCTGAATTTATTTGTTCAAAG 57.467 29.630 4.37 0.00 34.26 2.77
3344 3494 8.977505 GCTCAACTTTGTATTGAAATTGCTAAA 58.022 29.630 0.00 0.00 35.70 1.85
3378 3528 8.041323 GGGAGAAGTTTATTCATCAACTGTAGA 58.959 37.037 0.00 0.00 33.38 2.59
3379 3529 7.281100 GGGGAGAAGTTTATTCATCAACTGTAG 59.719 40.741 0.00 0.00 33.38 2.74
3380 3530 7.037586 AGGGGAGAAGTTTATTCATCAACTGTA 60.038 37.037 0.00 0.00 33.38 2.74
3381 3531 5.946377 GGGGAGAAGTTTATTCATCAACTGT 59.054 40.000 0.00 0.00 33.38 3.55
3382 3532 6.183347 AGGGGAGAAGTTTATTCATCAACTG 58.817 40.000 0.00 0.00 33.38 3.16
3440 3595 2.092211 GTCACTTCTGGTAACGCATTCG 59.908 50.000 0.00 0.00 42.51 3.34
3463 3618 0.106819 GGGTGCTCAGGAGAATGCAT 60.107 55.000 0.00 0.00 37.76 3.96
3478 3633 0.107831 TCTTGTTCCTCAACGGGGTG 59.892 55.000 0.00 0.00 34.95 4.61
3502 3657 0.037882 ACGACTGCTGATGGACTGTG 60.038 55.000 0.00 0.00 0.00 3.66
3503 3658 0.681733 AACGACTGCTGATGGACTGT 59.318 50.000 0.00 0.00 0.00 3.55
3564 3719 5.813383 TCCTCTTTTTCATCAGCATTCTCT 58.187 37.500 0.00 0.00 0.00 3.10
3597 3752 0.108138 GATCCAGAACCGAGTGTGGG 60.108 60.000 2.36 0.00 0.00 4.61
3644 3799 4.142038 ACCTTGCTTTCGAGTTTTATGGT 58.858 39.130 0.00 0.00 0.00 3.55
3926 4083 4.256110 CCAATACAGATGTCTCAAGCACA 58.744 43.478 0.00 0.00 0.00 4.57
3977 4134 4.274950 TCAAAAAGAAGAACCACATCGTCC 59.725 41.667 0.00 0.00 0.00 4.79
4016 4173 7.495901 AGAAATCATCGCTTATCTTGAGAAGA 58.504 34.615 8.92 0.00 42.69 2.87
4094 4251 1.831736 CTAACGAGTTCCATCCCCAGT 59.168 52.381 0.00 0.00 0.00 4.00
4194 4351 0.324943 ATCCACGGTCCACTTTCCAG 59.675 55.000 0.00 0.00 0.00 3.86
4238 4395 1.073603 TCCCACACATCAATGACAGCA 59.926 47.619 0.00 0.00 0.00 4.41
4262 4419 2.926200 CTCCAGTAAGTCGTCAAGCATG 59.074 50.000 0.00 0.00 0.00 4.06
4569 4730 1.949525 CTGTTATTTGCTCCATCCGGG 59.050 52.381 0.00 0.00 38.37 5.73
4581 4742 6.866248 CGGGCTGTGAAATAAAACTGTTATTT 59.134 34.615 4.22 4.22 37.31 1.40
4608 4771 7.715265 ATTCAGGATTATACAACTAACAGCG 57.285 36.000 0.00 0.00 0.00 5.18
4674 4837 3.117888 ACCAACACCATGAAGTGAGAAGT 60.118 43.478 8.84 0.00 40.34 3.01
4685 4848 3.383185 ACACCTTTACAACCAACACCATG 59.617 43.478 0.00 0.00 0.00 3.66
4689 4852 3.942748 TCTCACACCTTTACAACCAACAC 59.057 43.478 0.00 0.00 0.00 3.32
4752 4915 7.106239 TGAGGGAAATTATTCTTCAGACAGTC 58.894 38.462 0.00 0.00 35.79 3.51
4814 4977 7.239763 TGATTCACCAGAGTATGAACTGTAA 57.760 36.000 0.00 0.00 37.64 2.41
4817 4980 6.111382 ACATGATTCACCAGAGTATGAACTG 58.889 40.000 0.00 0.00 37.64 3.16
4818 4981 6.070596 TGACATGATTCACCAGAGTATGAACT 60.071 38.462 0.00 0.00 37.64 3.01
4860 5026 0.932955 TTGTATGGATGGGCATGGGT 59.067 50.000 0.00 0.00 0.00 4.51
4883 5055 5.895636 TCACTTGTCACTTGTGAATGTTT 57.104 34.783 4.93 0.00 37.71 2.83
4922 5094 6.147492 GCATTCTCTCTATGATGACAATGGAC 59.853 42.308 0.00 0.00 0.00 4.02
4934 5106 5.296035 TCAGTTGCATTGCATTCTCTCTATG 59.704 40.000 12.95 3.16 38.76 2.23
4943 5115 1.547372 GTCCCTCAGTTGCATTGCATT 59.453 47.619 12.95 1.06 38.76 3.56
4944 5116 1.180029 GTCCCTCAGTTGCATTGCAT 58.820 50.000 12.95 0.00 38.76 3.96
4974 5151 2.378038 TGCTTGGGGCTACATTCATTC 58.622 47.619 0.00 0.00 42.39 2.67
4975 5152 2.530460 TGCTTGGGGCTACATTCATT 57.470 45.000 0.00 0.00 42.39 2.57
4976 5153 2.313317 CATGCTTGGGGCTACATTCAT 58.687 47.619 0.00 0.00 42.39 2.57
4977 5154 1.685803 CCATGCTTGGGGCTACATTCA 60.686 52.381 10.81 0.00 39.56 2.57
4978 5155 1.035139 CCATGCTTGGGGCTACATTC 58.965 55.000 10.81 0.00 39.56 2.67
5008 5185 1.437986 CACAGTAGGCTACTCCGGC 59.562 63.158 23.95 0.00 40.77 6.13
5009 5186 1.038130 AGCACAGTAGGCTACTCCGG 61.038 60.000 23.95 15.45 40.47 5.14
5010 5187 0.382515 GAGCACAGTAGGCTACTCCG 59.617 60.000 23.95 17.82 42.78 4.63
5037 5214 8.693625 GTGGTAGTAGTACACTAATGGAAGATT 58.306 37.037 9.89 0.00 41.45 2.40
5052 5229 6.834969 TGCCATAACATGTAGTGGTAGTAGTA 59.165 38.462 23.08 0.68 32.45 1.82
5053 5230 5.659525 TGCCATAACATGTAGTGGTAGTAGT 59.340 40.000 23.08 0.00 32.45 2.73
5054 5231 6.156748 TGCCATAACATGTAGTGGTAGTAG 57.843 41.667 23.08 5.11 32.45 2.57
5111 5288 2.103941 TGGACCAGAAAACCAAAATGCC 59.896 45.455 0.00 0.00 0.00 4.40
5127 5304 2.203938 TGGACCTGGACCTGGACC 60.204 66.667 25.42 25.42 37.66 4.46
5128 5305 2.294078 CCTGGACCTGGACCTGGAC 61.294 68.421 28.41 16.79 45.37 4.02
5129 5306 2.122729 CCTGGACCTGGACCTGGA 59.877 66.667 28.41 4.64 45.37 3.86
5130 5307 3.721706 GCCTGGACCTGGACCTGG 61.722 72.222 28.13 28.13 45.33 4.45
5131 5308 2.930019 TGCCTGGACCTGGACCTG 60.930 66.667 21.06 14.74 0.00 4.00
5132 5309 2.608988 CTGCCTGGACCTGGACCT 60.609 66.667 21.06 0.00 0.00 3.85
5172 5355 0.394488 AGTCGGCGAGGAAGATCTGA 60.394 55.000 11.20 0.00 0.00 3.27
5173 5356 0.030101 GAGTCGGCGAGGAAGATCTG 59.970 60.000 11.20 0.00 0.00 2.90
5174 5357 1.440938 CGAGTCGGCGAGGAAGATCT 61.441 60.000 11.20 0.65 0.00 2.75
5283 5466 2.546494 GCTTGTGCTGCAGGACGTT 61.546 57.895 29.82 0.00 39.39 3.99


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

AutoCloner maintained by Alex Coulton.