Multiple sequence alignment - TraesCS3A01G494800

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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 TraesCS3A01G494800 chr3A 100.000 3686 0 0 1 3686 721084724 721088409 0.000000e+00 6807.0
1 TraesCS3A01G494800 chr3A 89.408 1605 142 13 1096 2686 721223520 721221930 0.000000e+00 1997.0
2 TraesCS3A01G494800 chr3A 87.317 205 25 1 271 474 721224177 721223973 2.210000e-57 233.0
3 TraesCS3A01G494800 chr3B 89.917 2995 174 63 1 2939 790520175 790523097 0.000000e+00 3740.0
4 TraesCS3A01G494800 chr3B 88.949 1674 142 27 1096 2744 790542777 790541122 0.000000e+00 2026.0
5 TraesCS3A01G494800 chr3B 86.891 534 30 17 3164 3686 790523550 790524054 2.490000e-156 562.0
6 TraesCS3A01G494800 chr3B 83.213 417 49 10 114 525 790519038 790519438 2.710000e-96 363.0
7 TraesCS3A01G494800 chr3B 86.207 174 14 5 458 630 790571400 790571236 2.920000e-41 180.0
8 TraesCS3A01G494800 chr3B 88.710 124 11 2 2984 3106 790523352 790523473 8.250000e-32 148.0
9 TraesCS3A01G494800 chr3D 90.917 2213 107 36 805 2982 590526177 590524024 0.000000e+00 2887.0
10 TraesCS3A01G494800 chr3D 88.889 1746 151 21 1096 2826 590678105 590676388 0.000000e+00 2109.0
11 TraesCS3A01G494800 chr3D 84.393 519 42 14 3153 3653 590523760 590523263 1.200000e-129 473.0
12 TraesCS3A01G494800 chr3D 94.257 296 17 0 2298 2593 360589894 360590189 1.560000e-123 453.0
13 TraesCS3A01G494800 chr3D 89.474 361 28 8 3 363 590526934 590526584 7.260000e-122 448.0
14 TraesCS3A01G494800 chr3D 87.500 240 16 5 538 774 590526475 590526247 7.850000e-67 265.0
15 TraesCS3A01G494800 chr3D 93.204 103 6 1 400 502 590526576 590526475 2.290000e-32 150.0
16 TraesCS3A01G494800 chr3D 85.526 76 9 2 2290 2363 7229200 7229275 1.100000e-10 78.7
17 TraesCS3A01G494800 chr6B 87.879 66 8 0 2295 2360 718344381 718344316 1.100000e-10 78.7
18 TraesCS3A01G494800 chr6A 87.879 66 8 0 2295 2360 616832948 616833013 1.100000e-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 TraesCS3A01G494800 chr3A 721084724 721088409 3685 False 6807.00 6807 100.00000 1 3686 1 chr3A.!!$F1 3685
1 TraesCS3A01G494800 chr3A 721221930 721224177 2247 True 1115.00 1997 88.36250 271 2686 2 chr3A.!!$R1 2415
2 TraesCS3A01G494800 chr3B 790541122 790542777 1655 True 2026.00 2026 88.94900 1096 2744 1 chr3B.!!$R1 1648
3 TraesCS3A01G494800 chr3B 790519038 790524054 5016 False 1203.25 3740 87.18275 1 3686 4 chr3B.!!$F1 3685
4 TraesCS3A01G494800 chr3D 590676388 590678105 1717 True 2109.00 2109 88.88900 1096 2826 1 chr3D.!!$R1 1730
5 TraesCS3A01G494800 chr3D 590523263 590526934 3671 True 844.60 2887 89.09760 3 3653 5 chr3D.!!$R2 3650

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
934 2203 0.033504 TCTGTGGGAGAAACTGACGC 59.966 55.000 0.00 0.0 0.0 5.19 F
936 2205 2.027625 GTGGGAGAAACTGACGCGG 61.028 63.158 12.47 0.0 0.0 6.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2628 3971 1.298014 CAGCTTCCTCAGGGTGTCC 59.702 63.158 0.0 0.0 0.00 4.02 R
2807 4163 1.404477 CAACAAAACGGTTGCGATCC 58.596 50.000 0.0 0.0 41.37 3.36 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
62 1200 3.118149 GGTTAGTGTACTGGGTATTGGGG 60.118 52.174 0.00 0.00 0.00 4.96
89 1227 7.175119 GGAAATGCACTAGGATATAGGGAAAAC 59.825 40.741 0.00 0.00 0.00 2.43
92 1230 7.924358 TGCACTAGGATATAGGGAAAACTAA 57.076 36.000 0.00 0.00 0.00 2.24
95 1233 8.648693 GCACTAGGATATAGGGAAAACTAAGAA 58.351 37.037 0.00 0.00 0.00 2.52
133 1271 9.609346 GAATAAACTAGCCCAATACACTAGAAA 57.391 33.333 0.00 0.00 37.44 2.52
139 1277 5.390387 AGCCCAATACACTAGAAACCAAAA 58.610 37.500 0.00 0.00 0.00 2.44
157 1295 9.875691 AAACCAAAAATGATTCTAGGAATAAGC 57.124 29.630 0.00 0.00 0.00 3.09
162 1300 2.364324 TGATTCTAGGAATAAGCGGCGT 59.636 45.455 9.37 0.00 0.00 5.68
173 1311 3.949031 AGCGGCGTTTTGCTTTTTA 57.051 42.105 9.37 0.00 45.43 1.52
186 1324 8.455682 CGTTTTGCTTTTTAGTAGGGATAATCA 58.544 33.333 0.00 0.00 0.00 2.57
216 1354 5.945144 TCCCTGGAAATACACTAGTAACC 57.055 43.478 0.00 0.00 33.13 2.85
217 1355 5.343715 TCCCTGGAAATACACTAGTAACCA 58.656 41.667 0.00 0.00 33.13 3.67
218 1356 5.786457 TCCCTGGAAATACACTAGTAACCAA 59.214 40.000 0.00 0.00 34.30 3.67
219 1357 6.272792 TCCCTGGAAATACACTAGTAACCAAA 59.727 38.462 0.00 0.00 34.30 3.28
220 1358 6.943718 CCCTGGAAATACACTAGTAACCAAAA 59.056 38.462 0.00 0.00 34.30 2.44
252 1394 3.415212 CAGAAATGTGTGTGTGAGGGAT 58.585 45.455 0.00 0.00 0.00 3.85
371 1514 1.530013 GCTGGTTGTCAATGGCTGCT 61.530 55.000 0.00 0.00 0.00 4.24
394 1538 6.018669 GCTTGTTATAGCCTGTTCTGTCATAC 60.019 42.308 0.00 0.00 35.06 2.39
445 1589 0.321653 CACTCACTTACCACCCCAGC 60.322 60.000 0.00 0.00 0.00 4.85
513 1701 3.117776 TGCATGGAGAGCACATAGGAAAT 60.118 43.478 0.00 0.00 37.02 2.17
514 1702 3.252701 GCATGGAGAGCACATAGGAAATG 59.747 47.826 0.00 0.00 0.00 2.32
536 1724 4.754618 TGGATTTGACCATCGTATGCATAC 59.245 41.667 24.27 24.27 34.77 2.39
555 1743 2.970324 TTCACACTCAACCGCCGC 60.970 61.111 0.00 0.00 0.00 6.53
576 1764 1.612442 GGCCGGCTATCCCTCCATA 60.612 63.158 28.56 0.00 0.00 2.74
577 1765 1.597461 GCCGGCTATCCCTCCATAC 59.403 63.158 22.15 0.00 0.00 2.39
578 1766 0.905337 GCCGGCTATCCCTCCATACT 60.905 60.000 22.15 0.00 0.00 2.12
579 1767 1.187087 CCGGCTATCCCTCCATACTC 58.813 60.000 0.00 0.00 0.00 2.59
580 1768 1.187087 CGGCTATCCCTCCATACTCC 58.813 60.000 0.00 0.00 0.00 3.85
703 1923 4.762251 GGAGAACTAATGCCATTGTATCCC 59.238 45.833 0.00 0.00 0.00 3.85
705 1925 5.133221 AGAACTAATGCCATTGTATCCCAC 58.867 41.667 0.00 0.00 0.00 4.61
729 1949 8.239314 CACTGGTAGTAGACGTAGAATTGTTTA 58.761 37.037 0.00 0.00 0.00 2.01
799 2024 9.745880 AAAAGGTATATAGTACAACGAGATGTG 57.254 33.333 0.00 0.00 34.75 3.21
801 2026 7.872881 AGGTATATAGTACAACGAGATGTGTG 58.127 38.462 0.00 0.00 34.75 3.82
802 2027 7.040617 AGGTATATAGTACAACGAGATGTGTGG 60.041 40.741 0.00 0.00 34.75 4.17
803 2028 6.710597 ATATAGTACAACGAGATGTGTGGT 57.289 37.500 0.00 0.00 34.75 4.16
815 2081 0.675083 TGTGTGGTGTACGTGTAGGG 59.325 55.000 0.00 0.00 0.00 3.53
917 2186 0.118144 AGGCTGGGGACTTCTTCTCT 59.882 55.000 0.00 0.00 0.00 3.10
919 2188 0.980423 GCTGGGGACTTCTTCTCTGT 59.020 55.000 0.00 0.00 0.00 3.41
920 2189 1.338579 GCTGGGGACTTCTTCTCTGTG 60.339 57.143 0.00 0.00 0.00 3.66
922 2191 0.615850 GGGGACTTCTTCTCTGTGGG 59.384 60.000 0.00 0.00 0.00 4.61
924 2193 1.552792 GGGACTTCTTCTCTGTGGGAG 59.447 57.143 0.00 0.00 43.12 4.30
934 2203 0.033504 TCTGTGGGAGAAACTGACGC 59.966 55.000 0.00 0.00 0.00 5.19
936 2205 2.027625 GTGGGAGAAACTGACGCGG 61.028 63.158 12.47 0.00 0.00 6.46
2059 3375 2.522436 ACAACCGGACCCTCGTCA 60.522 61.111 9.46 0.00 41.13 4.35
2361 3704 2.359230 AAGCTGCTGTTCCTCCGC 60.359 61.111 1.35 0.00 0.00 5.54
2514 3857 3.573491 GTGCGCAAGTATCCGGCC 61.573 66.667 14.00 0.00 41.68 6.13
2746 4102 1.489070 GACGAGCTGCTGCATGCTAG 61.489 60.000 20.33 21.63 43.37 3.42
2747 4103 2.883468 CGAGCTGCTGCATGCTAGC 61.883 63.158 25.69 25.69 42.18 3.42
2754 4110 3.821636 CTGCATGCTAGCCGAGGGG 62.822 68.421 20.33 0.00 0.00 4.79
2758 4114 3.088090 ATGCTAGCCGAGGGGAGGA 62.088 63.158 13.29 0.00 34.06 3.71
2807 4163 2.202987 GTGAGAGGGCGCTGGATG 60.203 66.667 8.56 0.00 0.00 3.51
2837 4193 3.119637 ACCGTTTTGTTGGACTCTTGTTG 60.120 43.478 0.00 0.00 0.00 3.33
2901 4257 6.583050 TCGTTTTGTTTGTGGACAAGTTAAAG 59.417 34.615 0.00 0.00 40.33 1.85
2990 4556 2.965831 TCTCGAAATATAGTGCCAGGCT 59.034 45.455 14.15 0.00 0.00 4.58
3088 4662 3.621268 TGGAACTAACTATGTTCATGCGC 59.379 43.478 0.00 0.00 43.84 6.09
3105 4679 2.472909 GCTATGCCCCTGCGTTGAC 61.473 63.158 0.00 0.00 41.78 3.18
3129 4709 1.745489 CCAGGGCGGCAGAACTAAC 60.745 63.158 12.47 0.00 0.00 2.34
3138 4718 4.093261 GGCGGCAGAACTAACGTTTATTTA 59.907 41.667 5.91 0.00 32.39 1.40
3150 4730 9.766277 ACTAACGTTTATTTACTCTACTTCTCG 57.234 33.333 5.91 0.00 0.00 4.04
3152 4732 6.615088 ACGTTTATTTACTCTACTTCTCGCA 58.385 36.000 0.00 0.00 0.00 5.10
3153 4733 6.525976 ACGTTTATTTACTCTACTTCTCGCAC 59.474 38.462 0.00 0.00 0.00 5.34
3156 4736 8.870879 GTTTATTTACTCTACTTCTCGCACAAT 58.129 33.333 0.00 0.00 0.00 2.71
3157 4737 6.893958 ATTTACTCTACTTCTCGCACAATG 57.106 37.500 0.00 0.00 0.00 2.82
3161 4741 4.867047 ACTCTACTTCTCGCACAATGATTG 59.133 41.667 3.16 3.16 0.00 2.67
3194 4819 2.440560 GCTGTTGCTGCAAACAAAAC 57.559 45.000 17.80 4.72 39.47 2.43
3195 4820 1.731160 GCTGTTGCTGCAAACAAAACA 59.269 42.857 17.80 9.46 39.47 2.83
3196 4821 2.159234 GCTGTTGCTGCAAACAAAACAA 59.841 40.909 17.80 0.00 39.47 2.83
3223 4848 0.179092 TGGCAGATCATCGTGCAGAG 60.179 55.000 6.95 0.00 41.75 3.35
3240 4865 0.876342 GAGGCATCGTCCATCCGTTC 60.876 60.000 0.00 0.00 0.00 3.95
3250 4875 2.080693 TCCATCCGTTCGTTTGATTGG 58.919 47.619 0.00 0.00 0.00 3.16
3273 4900 4.656731 CGAAGAGTAGTATTTCGTTCGC 57.343 45.455 7.99 0.00 38.96 4.70
3274 4901 4.341099 CGAAGAGTAGTATTTCGTTCGCT 58.659 43.478 7.99 0.00 38.96 4.93
3275 4902 4.202558 CGAAGAGTAGTATTTCGTTCGCTG 59.797 45.833 7.99 0.00 38.96 5.18
3276 4903 4.698583 AGAGTAGTATTTCGTTCGCTGT 57.301 40.909 0.00 0.00 0.00 4.40
3277 4904 5.808042 AGAGTAGTATTTCGTTCGCTGTA 57.192 39.130 0.00 0.00 0.00 2.74
3278 4905 5.567552 AGAGTAGTATTTCGTTCGCTGTAC 58.432 41.667 0.00 0.00 0.00 2.90
3279 4906 5.122869 AGAGTAGTATTTCGTTCGCTGTACA 59.877 40.000 0.00 0.00 0.00 2.90
3280 4907 5.702865 AGTAGTATTTCGTTCGCTGTACAA 58.297 37.500 0.00 0.00 0.00 2.41
3281 4908 4.898328 AGTATTTCGTTCGCTGTACAAC 57.102 40.909 0.00 0.00 0.00 3.32
3322 4971 4.503714 AAGGAACATACCATGTGTAGGG 57.496 45.455 9.68 0.00 44.07 3.53
3332 4981 1.909302 CATGTGTAGGGAGTGGACCTT 59.091 52.381 0.00 0.00 39.54 3.50
3350 5000 5.177696 GGACCTTCGTGCATTTGATATAGTC 59.822 44.000 0.00 0.00 0.00 2.59
3351 5001 4.745125 ACCTTCGTGCATTTGATATAGTCG 59.255 41.667 0.00 0.00 0.00 4.18
3352 5002 4.982295 CCTTCGTGCATTTGATATAGTCGA 59.018 41.667 0.00 0.00 0.00 4.20
3353 5003 5.107837 CCTTCGTGCATTTGATATAGTCGAC 60.108 44.000 7.70 7.70 0.00 4.20
3384 5034 2.251642 ACGGAGTTTGAACAGCGGC 61.252 57.895 0.00 0.00 37.78 6.53
3408 5058 2.360844 GAGAAGTTTCTTAGGCAGGCC 58.639 52.381 0.97 0.97 37.73 5.19
3409 5059 1.705186 AGAAGTTTCTTAGGCAGGCCA 59.295 47.619 13.63 0.00 34.21 5.36
3410 5060 2.087646 GAAGTTTCTTAGGCAGGCCAG 58.912 52.381 13.63 0.00 38.92 4.85
3411 5061 0.322906 AGTTTCTTAGGCAGGCCAGC 60.323 55.000 12.53 12.53 38.92 4.85
3412 5062 1.377202 TTTCTTAGGCAGGCCAGCG 60.377 57.895 14.62 0.00 38.92 5.18
3462 5112 1.676916 CCGATGCAGTTGACATGGACT 60.677 52.381 0.00 0.00 0.00 3.85
3464 5114 2.485426 CGATGCAGTTGACATGGACTTT 59.515 45.455 0.00 0.00 0.00 2.66
3465 5115 3.668757 CGATGCAGTTGACATGGACTTTG 60.669 47.826 0.00 0.00 0.00 2.77
3466 5116 2.929641 TGCAGTTGACATGGACTTTGA 58.070 42.857 0.00 0.00 0.00 2.69
3467 5117 3.489355 TGCAGTTGACATGGACTTTGAT 58.511 40.909 0.00 0.00 0.00 2.57
3480 5130 1.205893 ACTTTGATCGAGAGTCCAGCC 59.794 52.381 3.20 0.00 0.00 4.85
3518 5168 4.801330 ACGAGAATGACATGGAACTGTA 57.199 40.909 0.00 0.00 0.00 2.74
3555 5213 1.367471 CAGCCACCTGTTGACGAGA 59.633 57.895 0.00 0.00 34.31 4.04
3559 5217 0.946221 CCACCTGTTGACGAGAGCAC 60.946 60.000 0.00 0.00 0.00 4.40
3560 5218 0.946221 CACCTGTTGACGAGAGCACC 60.946 60.000 0.00 0.00 0.00 5.01
3561 5219 1.367471 CCTGTTGACGAGAGCACCA 59.633 57.895 0.00 0.00 0.00 4.17
3613 5271 0.750850 GTACCAGCTGGCCTCGATTA 59.249 55.000 33.06 12.78 39.32 1.75
3644 5302 2.159043 ACCCATCTCATCTACTTGCACG 60.159 50.000 0.00 0.00 0.00 5.34
3659 5320 1.269361 TGCACGCAAGACTTTCTACGA 60.269 47.619 0.00 0.00 43.62 3.43
3677 5338 6.127101 TCTACGAATAATTCTCAGGGTCAGA 58.873 40.000 0.00 0.00 0.00 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.613506 GCGGTTTGACGGGGACTTG 61.614 63.158 0.00 0.00 0.00 3.16
1 2 2.281276 GCGGTTTGACGGGGACTT 60.281 61.111 0.00 0.00 0.00 3.01
11 1149 1.291906 GATTGGGGGTTGCGGTTTG 59.708 57.895 0.00 0.00 0.00 2.93
62 1200 4.783227 TCCCTATATCCTAGTGCATTTCCC 59.217 45.833 0.00 0.00 0.00 3.97
102 1240 7.128263 AGTGTATTGGGCTAGTTTATTCCCTTA 59.872 37.037 2.95 0.00 39.49 2.69
105 1243 5.691896 AGTGTATTGGGCTAGTTTATTCCC 58.308 41.667 0.00 0.00 39.22 3.97
133 1271 7.201821 CCGCTTATTCCTAGAATCATTTTTGGT 60.202 37.037 0.00 0.00 0.00 3.67
139 1277 3.997021 CGCCGCTTATTCCTAGAATCATT 59.003 43.478 0.00 0.00 0.00 2.57
157 1295 3.231160 CCTACTAAAAAGCAAAACGCCG 58.769 45.455 0.00 0.00 44.04 6.46
227 1365 0.314935 CACACACACATTTCTGGGGC 59.685 55.000 0.00 0.00 0.00 5.80
228 1366 1.881973 CTCACACACACATTTCTGGGG 59.118 52.381 0.00 0.00 0.00 4.96
252 1394 0.541063 TGGTGCTCGGAGTTGGACTA 60.541 55.000 6.90 0.00 0.00 2.59
371 1514 7.182817 AGTATGACAGAACAGGCTATAACAA 57.817 36.000 0.00 0.00 0.00 2.83
385 1529 6.636454 ATTGGGGAGTTTTAGTATGACAGA 57.364 37.500 0.00 0.00 0.00 3.41
394 1538 3.193479 GCTGTCCAATTGGGGAGTTTTAG 59.807 47.826 24.29 11.39 37.71 1.85
445 1589 5.066375 TCTGCATTCGTATTGATTTTCCAGG 59.934 40.000 0.00 0.00 0.00 4.45
499 1643 5.221126 GGTCAAATCCATTTCCTATGTGCTC 60.221 44.000 0.00 0.00 0.00 4.26
501 1689 4.402155 TGGTCAAATCCATTTCCTATGTGC 59.598 41.667 0.00 0.00 31.96 4.57
506 1694 5.110814 ACGATGGTCAAATCCATTTCCTA 57.889 39.130 0.00 0.00 46.72 2.94
513 1701 3.274095 TGCATACGATGGTCAAATCCA 57.726 42.857 0.00 0.00 42.01 3.41
514 1702 5.283060 GTATGCATACGATGGTCAAATCC 57.717 43.478 20.52 0.00 0.00 3.01
536 1724 2.935955 GGCGGTTGAGTGTGAACG 59.064 61.111 0.00 0.00 0.00 3.95
576 1764 3.519510 TGGAAGCTTGCTAACTATGGAGT 59.480 43.478 19.34 0.00 37.59 3.85
577 1765 4.142609 TGGAAGCTTGCTAACTATGGAG 57.857 45.455 19.34 0.00 0.00 3.86
578 1766 4.568072 TTGGAAGCTTGCTAACTATGGA 57.432 40.909 19.34 0.00 0.00 3.41
579 1767 5.128919 AGATTGGAAGCTTGCTAACTATGG 58.871 41.667 19.34 0.00 0.00 2.74
580 1768 6.493116 CAAGATTGGAAGCTTGCTAACTATG 58.507 40.000 19.34 11.72 44.19 2.23
703 1923 6.192234 ACAATTCTACGTCTACTACCAGTG 57.808 41.667 0.00 0.00 0.00 3.66
705 1925 9.448294 GATAAACAATTCTACGTCTACTACCAG 57.552 37.037 0.00 0.00 0.00 4.00
778 2003 7.590322 CACCACACATCTCGTTGTACTATATAC 59.410 40.741 0.00 0.00 0.00 1.47
785 2010 2.750948 ACACCACACATCTCGTTGTAC 58.249 47.619 0.00 0.00 0.00 2.90
791 2016 1.335597 ACACGTACACCACACATCTCG 60.336 52.381 0.00 0.00 0.00 4.04
794 2019 2.602878 CCTACACGTACACCACACATC 58.397 52.381 0.00 0.00 0.00 3.06
797 2022 0.037975 CCCCTACACGTACACCACAC 60.038 60.000 0.00 0.00 0.00 3.82
799 2024 0.244721 GTCCCCTACACGTACACCAC 59.755 60.000 0.00 0.00 0.00 4.16
801 2026 0.529378 CAGTCCCCTACACGTACACC 59.471 60.000 0.00 0.00 0.00 4.16
802 2027 0.529378 CCAGTCCCCTACACGTACAC 59.471 60.000 0.00 0.00 0.00 2.90
803 2028 0.612732 CCCAGTCCCCTACACGTACA 60.613 60.000 0.00 0.00 0.00 2.90
815 2081 3.626924 ACACGCTCCACCCAGTCC 61.627 66.667 0.00 0.00 0.00 3.85
840 2106 2.678324 GTCTTCAGAGACCAGTTTCCG 58.322 52.381 0.00 0.00 45.34 4.30
917 2186 1.300620 CGCGTCAGTTTCTCCCACA 60.301 57.895 0.00 0.00 0.00 4.17
919 2188 2.342279 CCGCGTCAGTTTCTCCCA 59.658 61.111 4.92 0.00 0.00 4.37
920 2189 2.434359 CCCGCGTCAGTTTCTCCC 60.434 66.667 4.92 0.00 0.00 4.30
922 2191 3.479269 CGCCCGCGTCAGTTTCTC 61.479 66.667 4.92 0.00 34.35 2.87
924 2193 3.479269 CTCGCCCGCGTCAGTTTC 61.479 66.667 4.92 0.00 40.74 2.78
1027 2308 0.754217 TTATGTAGGCCGGCGAGAGT 60.754 55.000 22.54 8.98 0.00 3.24
1051 2337 2.452813 CCGGTTTGATCAGGTCGCG 61.453 63.158 0.00 0.00 0.00 5.87
1243 2544 2.288273 CGAAGAAGAAGTGGACGAACCT 60.288 50.000 0.00 0.00 39.86 3.50
1404 2708 2.688666 TCGCCCTCATTGCCTCCT 60.689 61.111 0.00 0.00 0.00 3.69
1405 2709 2.514824 GTCGCCCTCATTGCCTCC 60.515 66.667 0.00 0.00 0.00 4.30
1406 2710 2.892425 CGTCGCCCTCATTGCCTC 60.892 66.667 0.00 0.00 0.00 4.70
1613 2929 3.157949 CCCGCTCCTCCTTCTCCC 61.158 72.222 0.00 0.00 0.00 4.30
1923 3239 1.317431 TCACGTGGTGGTCCGATAGG 61.317 60.000 17.00 0.00 46.14 2.57
1926 3242 1.515954 GATCACGTGGTGGTCCGAT 59.484 57.895 17.00 0.00 37.68 4.18
2031 3347 2.358247 CGGTTGTCCTTGGTCCGG 60.358 66.667 0.00 0.00 37.92 5.14
2059 3375 3.888093 CGAGGAAGTCGTGGAAGTT 57.112 52.632 0.00 0.00 44.20 2.66
2415 3758 3.047718 CTTCTCGTAGCACCCGCGA 62.048 63.158 8.23 0.00 45.49 5.87
2628 3971 1.298014 CAGCTTCCTCAGGGTGTCC 59.702 63.158 0.00 0.00 0.00 4.02
2679 4022 2.436646 CAACCAGCCAGCTACGGG 60.437 66.667 3.91 3.91 0.00 5.28
2794 4150 2.031768 GATCCATCCAGCGCCCTC 59.968 66.667 2.29 0.00 0.00 4.30
2807 4163 1.404477 CAACAAAACGGTTGCGATCC 58.596 50.000 0.00 0.00 41.37 3.36
2837 4193 2.526304 TTGTGTAGTCTGTGCTGTCC 57.474 50.000 0.00 0.00 0.00 4.02
2877 4233 6.363896 ACTTTAACTTGTCCACAAACAAAACG 59.636 34.615 0.00 0.00 38.60 3.60
2901 4257 4.505556 GGAGTATTCGACGGTTAAATGGAC 59.494 45.833 0.00 0.00 0.00 4.02
2947 4303 8.847567 CGAGACAACGAACCATATATATACAAC 58.152 37.037 0.00 0.00 35.09 3.32
2966 4322 4.693283 CCTGGCACTATATTTCGAGACAA 58.307 43.478 0.00 0.00 0.00 3.18
3057 4628 5.297547 ACATAGTTAGTTCCATATGTGGCG 58.702 41.667 3.06 0.00 45.63 5.69
3058 4629 6.765989 TGAACATAGTTAGTTCCATATGTGGC 59.234 38.462 3.06 0.00 45.63 5.01
3075 4649 1.466167 GGGCATAGCGCATGAACATAG 59.534 52.381 19.56 0.00 45.17 2.23
3088 4662 1.819632 GGTCAACGCAGGGGCATAG 60.820 63.158 0.00 0.00 41.24 2.23
3100 4674 2.991540 GCCCTGGCCTTGGTCAAC 60.992 66.667 3.32 0.00 34.56 3.18
3124 4704 9.766277 CGAGAAGTAGAGTAAATAAACGTTAGT 57.234 33.333 0.00 0.00 0.00 2.24
3129 4709 6.525628 TGTGCGAGAAGTAGAGTAAATAAACG 59.474 38.462 0.00 0.00 0.00 3.60
3138 4718 4.727507 ATCATTGTGCGAGAAGTAGAGT 57.272 40.909 0.00 0.00 0.00 3.24
3150 4730 3.163594 GCACGTTACTCAATCATTGTGC 58.836 45.455 0.00 0.00 43.66 4.57
3152 4732 4.314961 TCTGCACGTTACTCAATCATTGT 58.685 39.130 0.00 0.00 0.00 2.71
3153 4733 4.726021 GCTCTGCACGTTACTCAATCATTG 60.726 45.833 0.00 0.00 0.00 2.82
3156 4736 2.029020 AGCTCTGCACGTTACTCAATCA 60.029 45.455 0.00 0.00 0.00 2.57
3157 4737 2.346847 CAGCTCTGCACGTTACTCAATC 59.653 50.000 0.00 0.00 0.00 2.67
3161 4741 1.457303 CAACAGCTCTGCACGTTACTC 59.543 52.381 0.00 0.00 0.00 2.59
3192 4817 3.937814 TGATCTGCCAACGATACTTGTT 58.062 40.909 0.00 0.00 0.00 2.83
3193 4818 3.610040 TGATCTGCCAACGATACTTGT 57.390 42.857 0.00 0.00 0.00 3.16
3194 4819 3.183172 CGATGATCTGCCAACGATACTTG 59.817 47.826 0.00 0.00 34.84 3.16
3195 4820 3.181475 ACGATGATCTGCCAACGATACTT 60.181 43.478 0.00 0.00 36.14 2.24
3196 4821 2.362397 ACGATGATCTGCCAACGATACT 59.638 45.455 0.00 0.00 36.14 2.12
3223 4848 2.237751 CGAACGGATGGACGATGCC 61.238 63.158 0.00 0.00 37.61 4.40
3240 4865 4.235360 ACTACTCTTCGTCCAATCAAACG 58.765 43.478 0.00 0.00 40.17 3.60
3269 4896 3.132925 GGGTTTGTAGTTGTACAGCGAA 58.867 45.455 3.90 0.00 40.33 4.70
3271 4898 2.478894 CTGGGTTTGTAGTTGTACAGCG 59.521 50.000 3.90 0.00 40.33 5.18
3272 4899 3.497262 GTCTGGGTTTGTAGTTGTACAGC 59.503 47.826 0.72 0.72 40.33 4.40
3273 4900 4.750098 CAGTCTGGGTTTGTAGTTGTACAG 59.250 45.833 0.00 0.00 40.33 2.74
3274 4901 4.406326 TCAGTCTGGGTTTGTAGTTGTACA 59.594 41.667 0.00 0.00 37.38 2.90
3275 4902 4.748600 GTCAGTCTGGGTTTGTAGTTGTAC 59.251 45.833 0.00 0.00 0.00 2.90
3276 4903 4.202284 GGTCAGTCTGGGTTTGTAGTTGTA 60.202 45.833 0.00 0.00 0.00 2.41
3277 4904 3.433173 GGTCAGTCTGGGTTTGTAGTTGT 60.433 47.826 0.00 0.00 0.00 3.32
3278 4905 3.139077 GGTCAGTCTGGGTTTGTAGTTG 58.861 50.000 0.00 0.00 0.00 3.16
3279 4906 2.775384 TGGTCAGTCTGGGTTTGTAGTT 59.225 45.455 0.00 0.00 0.00 2.24
3280 4907 2.404559 TGGTCAGTCTGGGTTTGTAGT 58.595 47.619 0.00 0.00 0.00 2.73
3281 4908 3.485463 TTGGTCAGTCTGGGTTTGTAG 57.515 47.619 0.00 0.00 0.00 2.74
3322 4971 1.197721 CAAATGCACGAAGGTCCACTC 59.802 52.381 0.00 0.00 0.00 3.51
3332 4981 4.295870 GGTCGACTATATCAAATGCACGA 58.704 43.478 16.46 0.00 0.00 4.35
3384 5034 3.604582 CTGCCTAAGAAACTTCTCCCAG 58.395 50.000 0.00 0.00 36.28 4.45
3408 5058 2.030562 AACTCAACCCCGTCGCTG 59.969 61.111 0.00 0.00 0.00 5.18
3409 5059 2.030562 CAACTCAACCCCGTCGCT 59.969 61.111 0.00 0.00 0.00 4.93
3410 5060 1.595929 TTCAACTCAACCCCGTCGC 60.596 57.895 0.00 0.00 0.00 5.19
3411 5061 1.554042 CGTTCAACTCAACCCCGTCG 61.554 60.000 0.00 0.00 0.00 5.12
3412 5062 1.226030 CCGTTCAACTCAACCCCGTC 61.226 60.000 0.00 0.00 0.00 4.79
3445 5095 3.489355 TCAAAGTCCATGTCAACTGCAT 58.511 40.909 0.00 0.00 0.00 3.96
3462 5112 0.173481 CGGCTGGACTCTCGATCAAA 59.827 55.000 0.00 0.00 0.00 2.69
3464 5114 2.775856 GCGGCTGGACTCTCGATCA 61.776 63.158 0.00 0.00 0.00 2.92
3465 5115 2.026879 GCGGCTGGACTCTCGATC 59.973 66.667 0.00 0.00 0.00 3.69
3466 5116 3.893763 CGCGGCTGGACTCTCGAT 61.894 66.667 0.00 0.00 0.00 3.59
3518 5168 4.471726 GTCGTCGCCGTCGGATGT 62.472 66.667 17.49 0.00 36.13 3.06
3533 5183 2.280797 TCAACAGGTGGCTGCGTC 60.281 61.111 0.00 0.00 0.00 5.19
3559 5217 0.179936 GGACAGAGGAAGGCAGATGG 59.820 60.000 0.00 0.00 0.00 3.51
3560 5218 0.179936 GGGACAGAGGAAGGCAGATG 59.820 60.000 0.00 0.00 0.00 2.90
3561 5219 0.043940 AGGGACAGAGGAAGGCAGAT 59.956 55.000 0.00 0.00 0.00 2.90
3613 5271 1.276859 TGAGATGGGTGCAGATGCCT 61.277 55.000 1.72 0.00 41.18 4.75
3644 5302 8.186178 TGAGAATTATTCGTAGAAAGTCTTGC 57.814 34.615 0.00 0.00 45.90 4.01
3648 5306 7.266400 ACCCTGAGAATTATTCGTAGAAAGTC 58.734 38.462 11.20 0.00 45.90 3.01
3649 5307 7.093465 TGACCCTGAGAATTATTCGTAGAAAGT 60.093 37.037 11.20 7.04 45.90 2.66
3650 5308 7.265673 TGACCCTGAGAATTATTCGTAGAAAG 58.734 38.462 11.20 4.82 45.90 2.62
3659 5320 3.782523 TGCCTCTGACCCTGAGAATTATT 59.217 43.478 0.00 0.00 32.36 1.40


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

AutoCloner maintained by Alex Coulton.