Multiple sequence alignment - TraesCS3B01G272300

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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 TraesCS3B01G272300 chr3B 100.000 3408 0 0 1 3408 438539422 438536015 0.000000e+00 6294.0
1 TraesCS3B01G272300 chr3B 87.126 334 33 4 3076 3408 812677377 812677701 1.490000e-98 370.0
2 TraesCS3B01G272300 chr3B 100.000 31 0 0 2906 2936 29250801 29250771 1.320000e-04 58.4
3 TraesCS3B01G272300 chr3A 91.286 2100 66 40 869 2877 464913862 464915935 0.000000e+00 2756.0
4 TraesCS3B01G272300 chr3A 94.032 620 30 4 1 620 464913041 464913653 0.000000e+00 933.0
5 TraesCS3B01G272300 chr3A 83.333 216 5 4 655 867 464913638 464913825 1.630000e-38 171.0
6 TraesCS3B01G272300 chr3A 95.918 49 2 0 2939 2987 464917463 464917511 2.820000e-11 80.5
7 TraesCS3B01G272300 chr3D 92.632 1208 40 22 655 1836 339847834 339846650 0.000000e+00 1692.0
8 TraesCS3B01G272300 chr3D 91.981 1060 38 8 1844 2875 339846593 339845553 0.000000e+00 1443.0
9 TraesCS3B01G272300 chr3D 95.484 620 12 9 1 620 339848422 339847819 0.000000e+00 976.0
10 TraesCS3B01G272300 chr3D 88.462 260 19 1 2944 3192 339843964 339843705 1.540000e-78 303.0
11 TraesCS3B01G272300 chr3D 91.304 161 13 1 3249 3408 339843502 339843342 5.730000e-53 219.0
12 TraesCS3B01G272300 chr3D 100.000 49 0 0 2939 2987 339844004 339843956 1.300000e-14 91.6
13 TraesCS3B01G272300 chr1D 85.888 411 56 2 1974 2383 470075907 470075498 1.450000e-118 436.0
14 TraesCS3B01G272300 chr1D 84.047 257 38 3 1358 1611 470076737 470076481 9.450000e-61 244.0
15 TraesCS3B01G272300 chr1B 85.366 410 60 0 1974 2383 652458175 652457766 3.140000e-115 425.0
16 TraesCS3B01G272300 chr1B 86.364 220 30 0 1392 1611 652458941 652458722 1.220000e-59 241.0
17 TraesCS3B01G272300 chr1A 85.437 412 56 3 1974 2383 563685114 563684705 3.140000e-115 425.0
18 TraesCS3B01G272300 chr1A 84.615 247 37 1 1371 1616 563685887 563685641 9.450000e-61 244.0
19 TraesCS3B01G272300 chr5A 85.714 210 30 0 1403 1612 383883145 383882936 4.430000e-54 222.0
20 TraesCS3B01G272300 chr5A 80.383 209 39 2 1405 1612 526393850 526394057 1.270000e-34 158.0
21 TraesCS3B01G272300 chr5D 84.689 209 32 0 1403 1611 291501065 291500857 3.450000e-50 209.0
22 TraesCS3B01G272300 chr5B 84.689 209 32 0 1403 1611 332202989 332202781 3.450000e-50 209.0


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 TraesCS3B01G272300 chr3B 438536015 438539422 3407 True 6294.000000 6294 100.00000 1 3408 1 chr3B.!!$R2 3407
1 TraesCS3B01G272300 chr3A 464913041 464917511 4470 False 985.125000 2756 91.14225 1 2987 4 chr3A.!!$F1 2986
2 TraesCS3B01G272300 chr3D 339843342 339848422 5080 True 787.433333 1692 93.31050 1 3408 6 chr3D.!!$R1 3407
3 TraesCS3B01G272300 chr1D 470075498 470076737 1239 True 340.000000 436 84.96750 1358 2383 2 chr1D.!!$R1 1025
4 TraesCS3B01G272300 chr1B 652457766 652458941 1175 True 333.000000 425 85.86500 1392 2383 2 chr1B.!!$R1 991
5 TraesCS3B01G272300 chr1A 563684705 563685887 1182 True 334.500000 425 85.02600 1371 2383 2 chr1A.!!$R1 1012

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
720 721 0.037605 AGTGGCTGTACCGTACAAGC 60.038 55.0 12.39 15.60 43.94 4.01 F
1022 1059 0.472044 TATGTACATGCATGCCCGGT 59.528 50.0 26.53 12.87 0.00 5.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1632 1724 0.540830 ATACAGGTGGCGGGCAAAAA 60.541 50.0 5.57 0.00 0.00 1.94 R
2772 3278 0.391661 GACATCGCCGGCATATCCAT 60.392 55.0 28.98 3.98 34.01 3.41 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
45 46 8.567285 AGAAGTGGATAACAAACAGGATTAAG 57.433 34.615 0.00 0.00 0.00 1.85
261 262 7.455953 ACATACAGTGTATCATATGGTGGATCT 59.544 37.037 13.00 0.00 39.91 2.75
415 416 3.963374 TGGAGAGATTGGTCTGATAGTGG 59.037 47.826 0.00 0.00 33.97 4.00
516 517 2.222213 CGTGCAGTTTGGTCGAAACATA 59.778 45.455 12.30 0.00 45.69 2.29
547 548 1.535015 CCTCGAATCTGAACTCGCTCC 60.535 57.143 7.44 0.00 35.04 4.70
549 550 2.614520 CTCGAATCTGAACTCGCTCCTA 59.385 50.000 7.44 0.00 35.04 2.94
560 561 2.766263 ACTCGCTCCTATTTGTGATGGA 59.234 45.455 0.00 0.00 0.00 3.41
565 566 6.353323 TCGCTCCTATTTGTGATGGAATTTA 58.647 36.000 0.00 0.00 0.00 1.40
610 611 9.814899 TCATGTGTATTTTCTGTCATTGTTTTT 57.185 25.926 0.00 0.00 0.00 1.94
677 678 8.307921 AGTGTTTTCGTATCTTTTAAGGAGAC 57.692 34.615 0.00 0.00 0.00 3.36
678 679 7.929785 AGTGTTTTCGTATCTTTTAAGGAGACA 59.070 33.333 3.02 0.00 0.00 3.41
679 680 8.718734 GTGTTTTCGTATCTTTTAAGGAGACAT 58.281 33.333 3.02 0.00 0.00 3.06
720 721 0.037605 AGTGGCTGTACCGTACAAGC 60.038 55.000 12.39 15.60 43.94 4.01
794 795 2.121786 GCGCCGTACTTGATCGAAATA 58.878 47.619 0.00 0.00 0.00 1.40
885 921 5.473162 TGATGAGCGAAAATGAAAGGAGAAA 59.527 36.000 0.00 0.00 0.00 2.52
890 926 6.337356 AGCGAAAATGAAAGGAGAAACAAAA 58.663 32.000 0.00 0.00 0.00 2.44
891 927 6.476706 AGCGAAAATGAAAGGAGAAACAAAAG 59.523 34.615 0.00 0.00 0.00 2.27
892 928 6.475402 GCGAAAATGAAAGGAGAAACAAAAGA 59.525 34.615 0.00 0.00 0.00 2.52
893 929 7.306225 GCGAAAATGAAAGGAGAAACAAAAGAG 60.306 37.037 0.00 0.00 0.00 2.85
895 931 9.586435 GAAAATGAAAGGAGAAACAAAAGAGAA 57.414 29.630 0.00 0.00 0.00 2.87
897 933 9.538508 AAATGAAAGGAGAAACAAAAGAGAATG 57.461 29.630 0.00 0.00 0.00 2.67
898 934 6.507023 TGAAAGGAGAAACAAAAGAGAATGC 58.493 36.000 0.00 0.00 0.00 3.56
899 935 6.322201 TGAAAGGAGAAACAAAAGAGAATGCT 59.678 34.615 0.00 0.00 0.00 3.79
900 936 7.502226 TGAAAGGAGAAACAAAAGAGAATGCTA 59.498 33.333 0.00 0.00 0.00 3.49
1011 1048 5.720202 AGTCGTTGACACATGTATGTACAT 58.280 37.500 13.93 13.93 40.08 2.29
1021 1058 0.874390 GTATGTACATGCATGCCCGG 59.126 55.000 26.53 7.02 0.00 5.73
1022 1059 0.472044 TATGTACATGCATGCCCGGT 59.528 50.000 26.53 12.87 0.00 5.28
1059 1096 3.316573 GAAGCCAGGACCGGGACAG 62.317 68.421 15.76 0.00 0.00 3.51
1245 1287 1.080298 CACCGCGTTGCCTTTGTATA 58.920 50.000 4.92 0.00 0.00 1.47
1246 1288 1.668751 CACCGCGTTGCCTTTGTATAT 59.331 47.619 4.92 0.00 0.00 0.86
1251 1293 2.286184 GCGTTGCCTTTGTATATCGTGG 60.286 50.000 0.00 0.00 0.00 4.94
1314 1376 2.780010 GGAGGGGAAGGAGATCAAATCA 59.220 50.000 0.00 0.00 0.00 2.57
1315 1377 3.181446 GGAGGGGAAGGAGATCAAATCAG 60.181 52.174 0.00 0.00 0.00 2.90
1316 1378 3.713764 GAGGGGAAGGAGATCAAATCAGA 59.286 47.826 0.00 0.00 0.00 3.27
1317 1379 4.314238 AGGGGAAGGAGATCAAATCAGAT 58.686 43.478 0.00 0.00 0.00 2.90
1318 1380 4.350520 AGGGGAAGGAGATCAAATCAGATC 59.649 45.833 0.00 0.00 43.73 2.75
1319 1381 4.103785 GGGGAAGGAGATCAAATCAGATCA 59.896 45.833 6.70 0.00 45.39 2.92
1320 1382 5.398353 GGGGAAGGAGATCAAATCAGATCAA 60.398 44.000 6.70 0.00 45.39 2.57
1321 1383 6.125029 GGGAAGGAGATCAAATCAGATCAAA 58.875 40.000 6.70 0.00 45.39 2.69
1322 1384 6.039159 GGGAAGGAGATCAAATCAGATCAAAC 59.961 42.308 6.70 0.00 45.39 2.93
1323 1385 6.039159 GGAAGGAGATCAAATCAGATCAAACC 59.961 42.308 6.70 6.70 45.39 3.27
1621 1696 4.566907 GCCAAGAAAGGTACCAATACTCCA 60.567 45.833 15.94 0.00 0.00 3.86
1622 1697 5.566469 CCAAGAAAGGTACCAATACTCCAA 58.434 41.667 15.94 0.00 0.00 3.53
1632 1724 5.584551 ACCAATACTCCAACCTCTTTCTT 57.415 39.130 0.00 0.00 0.00 2.52
1678 1786 1.900498 GCTGCTTTGCCTGTCCACT 60.900 57.895 0.00 0.00 0.00 4.00
1684 1792 2.884639 GCTTTGCCTGTCCACTTCTTTA 59.115 45.455 0.00 0.00 0.00 1.85
1809 1966 4.746729 TGCCATGCTTGTGATTTCAATAC 58.253 39.130 0.00 0.00 0.00 1.89
1812 1969 5.682990 GCCATGCTTGTGATTTCAATACCAT 60.683 40.000 0.00 0.00 0.00 3.55
1813 1970 5.981315 CCATGCTTGTGATTTCAATACCATC 59.019 40.000 0.00 0.00 0.00 3.51
1814 1971 6.183360 CCATGCTTGTGATTTCAATACCATCT 60.183 38.462 0.00 0.00 0.00 2.90
1815 1972 6.198650 TGCTTGTGATTTCAATACCATCTG 57.801 37.500 0.00 0.00 0.00 2.90
1836 1995 4.780815 TGGAACAACTCATTCTCAACTGT 58.219 39.130 0.00 0.00 31.92 3.55
1837 1996 4.576053 TGGAACAACTCATTCTCAACTGTG 59.424 41.667 0.00 0.00 31.92 3.66
1839 1998 2.880890 ACAACTCATTCTCAACTGTGGC 59.119 45.455 0.00 0.00 0.00 5.01
1840 1999 2.880268 CAACTCATTCTCAACTGTGGCA 59.120 45.455 0.00 0.00 0.00 4.92
1841 2000 3.213206 ACTCATTCTCAACTGTGGCAA 57.787 42.857 0.00 0.00 0.00 4.52
1842 2001 3.144506 ACTCATTCTCAACTGTGGCAAG 58.855 45.455 0.00 0.00 0.00 4.01
1846 2024 4.937620 TCATTCTCAACTGTGGCAAGTATC 59.062 41.667 0.00 0.00 0.00 2.24
2425 2898 3.951680 CCTAGTCAAACTCTCTCCCTCTC 59.048 52.174 0.00 0.00 0.00 3.20
2426 2899 3.825908 AGTCAAACTCTCTCCCTCTCT 57.174 47.619 0.00 0.00 0.00 3.10
2427 2900 4.938575 AGTCAAACTCTCTCCCTCTCTA 57.061 45.455 0.00 0.00 0.00 2.43
2428 2901 5.466127 AGTCAAACTCTCTCCCTCTCTAT 57.534 43.478 0.00 0.00 0.00 1.98
2429 2902 5.445964 AGTCAAACTCTCTCCCTCTCTATC 58.554 45.833 0.00 0.00 0.00 2.08
2515 2988 2.209273 TGCGACCGTGATGATTATTGG 58.791 47.619 0.00 0.00 0.00 3.16
2593 3069 6.056428 TGATACTACTACATACAGCGTGTG 57.944 41.667 4.45 4.45 0.00 3.82
2648 3127 4.858680 TTGCAACCACGGTCCGCA 62.859 61.111 12.28 8.73 35.56 5.69
2772 3278 3.342627 CGGCCGTCGTGCAGAAAA 61.343 61.111 19.50 0.00 0.00 2.29
2775 3281 1.154225 GCCGTCGTGCAGAAAATGG 60.154 57.895 0.00 0.00 0.00 3.16
2936 3481 6.086222 CCAAGTTTATTCATCAAAGTCCACG 58.914 40.000 0.00 0.00 0.00 4.94
2937 3482 5.880054 AGTTTATTCATCAAAGTCCACGG 57.120 39.130 0.00 0.00 0.00 4.94
2981 5019 2.414161 GGTTAACCAAGCAGTTGCGATC 60.414 50.000 20.12 0.00 40.25 3.69
3038 5076 3.389656 TGATCCACTTTACCAGACACACA 59.610 43.478 0.00 0.00 0.00 3.72
3052 5090 5.240183 CCAGACACACACTCTCATTTGAAAT 59.760 40.000 0.00 0.00 0.00 2.17
3074 5112 0.040058 TGCCTACGGGTAGAACCTCA 59.960 55.000 7.41 0.00 38.64 3.86
3134 5183 1.746171 GCCGGAGTACCCAAATTCCTC 60.746 57.143 5.05 0.00 34.14 3.71
3136 5185 2.629051 CGGAGTACCCAAATTCCTCAC 58.371 52.381 0.00 0.00 34.14 3.51
3137 5186 2.027561 CGGAGTACCCAAATTCCTCACA 60.028 50.000 0.00 0.00 34.14 3.58
3140 5189 4.254492 GAGTACCCAAATTCCTCACAGTC 58.746 47.826 0.00 0.00 0.00 3.51
3142 5191 1.780309 ACCCAAATTCCTCACAGTCCA 59.220 47.619 0.00 0.00 0.00 4.02
3150 5199 2.601666 TCACAGTCCAGCGAGGCT 60.602 61.111 0.00 0.00 40.77 4.58
3174 5223 1.003839 GTTGGGGCGTGAGTCATCA 60.004 57.895 0.00 0.00 37.54 3.07
3187 5236 4.214332 GTGAGTCATCAAGGTCCAGAAAAC 59.786 45.833 0.00 0.00 37.14 2.43
3192 5241 4.039973 TCATCAAGGTCCAGAAAACGTACT 59.960 41.667 0.00 0.00 0.00 2.73
3193 5242 5.244402 TCATCAAGGTCCAGAAAACGTACTA 59.756 40.000 0.00 0.00 0.00 1.82
3194 5243 5.733620 TCAAGGTCCAGAAAACGTACTAT 57.266 39.130 0.00 0.00 0.00 2.12
3195 5244 5.475719 TCAAGGTCCAGAAAACGTACTATG 58.524 41.667 0.00 0.00 0.00 2.23
3196 5245 5.011329 TCAAGGTCCAGAAAACGTACTATGT 59.989 40.000 0.00 0.00 0.00 2.29
3197 5246 6.209192 TCAAGGTCCAGAAAACGTACTATGTA 59.791 38.462 0.00 0.00 0.00 2.29
3198 5247 6.786967 AGGTCCAGAAAACGTACTATGTAT 57.213 37.500 0.00 0.00 0.00 2.29
3199 5248 7.886629 AGGTCCAGAAAACGTACTATGTATA 57.113 36.000 0.00 0.00 0.00 1.47
3200 5249 7.938715 AGGTCCAGAAAACGTACTATGTATAG 58.061 38.462 0.00 0.00 36.46 1.31
3201 5250 7.559170 AGGTCCAGAAAACGTACTATGTATAGT 59.441 37.037 9.31 9.31 45.08 2.12
3202 5251 7.646922 GGTCCAGAAAACGTACTATGTATAGTG 59.353 40.741 13.42 2.26 43.10 2.74
3203 5252 7.167136 GTCCAGAAAACGTACTATGTATAGTGC 59.833 40.741 13.42 11.28 43.10 4.40
3204 5253 6.976349 CCAGAAAACGTACTATGTATAGTGCA 59.024 38.462 16.65 0.00 43.41 4.57
3205 5254 7.652105 CCAGAAAACGTACTATGTATAGTGCAT 59.348 37.037 16.65 2.70 43.41 3.96
3206 5255 8.480066 CAGAAAACGTACTATGTATAGTGCATG 58.520 37.037 16.65 6.68 43.41 4.06
3207 5256 7.652105 AGAAAACGTACTATGTATAGTGCATGG 59.348 37.037 16.65 6.50 43.41 3.66
3208 5257 4.806330 ACGTACTATGTATAGTGCATGGC 58.194 43.478 16.65 0.00 43.41 4.40
3209 5258 3.851969 CGTACTATGTATAGTGCATGGCG 59.148 47.826 16.65 7.98 43.41 5.69
3210 5259 3.319137 ACTATGTATAGTGCATGGCGG 57.681 47.619 3.84 0.00 41.77 6.13
3211 5260 2.897326 ACTATGTATAGTGCATGGCGGA 59.103 45.455 3.84 0.00 41.77 5.54
3212 5261 2.462456 ATGTATAGTGCATGGCGGAG 57.538 50.000 0.00 0.00 0.00 4.63
3232 5281 3.190878 GCCTCTTGTGGCGATTGG 58.809 61.111 0.00 0.00 43.74 3.16
3233 5282 2.409870 GCCTCTTGTGGCGATTGGG 61.410 63.158 0.00 0.00 43.74 4.12
3234 5283 1.750399 CCTCTTGTGGCGATTGGGG 60.750 63.158 0.00 0.00 0.00 4.96
3235 5284 1.750399 CTCTTGTGGCGATTGGGGG 60.750 63.158 0.00 0.00 0.00 5.40
3236 5285 2.196997 CTCTTGTGGCGATTGGGGGA 62.197 60.000 0.00 0.00 0.00 4.81
3237 5286 1.750399 CTTGTGGCGATTGGGGGAG 60.750 63.158 0.00 0.00 0.00 4.30
3238 5287 3.280938 TTGTGGCGATTGGGGGAGG 62.281 63.158 0.00 0.00 0.00 4.30
3239 5288 4.506255 GTGGCGATTGGGGGAGGG 62.506 72.222 0.00 0.00 0.00 4.30
3274 5469 0.033894 GGGGACGAGAGAGAGGAAGT 60.034 60.000 0.00 0.00 0.00 3.01
3289 5484 1.001406 GGAAGTATGGGGCTGAGATCG 59.999 57.143 0.00 0.00 0.00 3.69
3305 5501 0.982852 ATCGGACATGAGGAAGGCCA 60.983 55.000 5.01 0.00 36.29 5.36
3314 5510 1.202806 TGAGGAAGGCCAACTGAACAG 60.203 52.381 5.01 0.00 36.29 3.16
3317 5513 2.087646 GGAAGGCCAACTGAACAGATC 58.912 52.381 5.01 0.00 0.00 2.75
3318 5514 2.553028 GGAAGGCCAACTGAACAGATCA 60.553 50.000 5.01 0.00 36.38 2.92
3349 5545 1.595357 GAAGTGGTAGTGGGGGTCG 59.405 63.158 0.00 0.00 0.00 4.79
3360 5556 2.358247 GGGGTCGCGAAGAAGCAA 60.358 61.111 12.06 0.00 36.85 3.91
3369 5565 1.009829 CGAAGAAGCAAATCGGGAGG 58.990 55.000 0.00 0.00 33.15 4.30
3373 5569 1.839994 AGAAGCAAATCGGGAGGATCA 59.160 47.619 0.00 0.00 36.25 2.92
3374 5570 2.441001 AGAAGCAAATCGGGAGGATCAT 59.559 45.455 0.00 0.00 36.25 2.45
3405 5601 5.280062 GGGCCTATACCTAACCTTGAAGATC 60.280 48.000 0.84 0.00 0.00 2.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 46 5.965918 GTCGGAAGCAAATAACTGATAAAGC 59.034 40.000 0.00 0.00 0.00 3.51
261 262 4.157246 TGCCACTCTAAGAGTTACCTTCA 58.843 43.478 0.00 0.00 41.37 3.02
415 416 3.890936 AACTCAGTGCTCGGCTGGC 62.891 63.158 0.00 0.00 34.89 4.85
516 517 6.318900 AGTTCAGATTCGAGGTTTTGTTTCTT 59.681 34.615 0.00 0.00 0.00 2.52
584 585 9.814899 AAAAACAATGACAGAAAATACACATGA 57.185 25.926 0.00 0.00 0.00 3.07
651 652 9.415544 GTCTCCTTAAAAGATACGAAAACACTA 57.584 33.333 0.00 0.00 0.00 2.74
652 653 7.929785 TGTCTCCTTAAAAGATACGAAAACACT 59.070 33.333 0.00 0.00 0.00 3.55
653 654 8.080083 TGTCTCCTTAAAAGATACGAAAACAC 57.920 34.615 0.00 0.00 0.00 3.32
654 655 8.842358 ATGTCTCCTTAAAAGATACGAAAACA 57.158 30.769 0.00 0.00 0.00 2.83
720 721 7.391833 AGAGTTCTAGGGCAAAACTATCTTTTG 59.608 37.037 1.88 1.88 41.09 2.44
763 764 1.445410 TACGGCGCACAAGCTAGTG 60.445 57.895 10.83 0.00 42.37 2.74
794 795 0.890542 TCTCAAGGCAGCAACGCAAT 60.891 50.000 0.00 0.00 0.00 3.56
885 921 9.245481 AGTAGTAGTAGTAGCATTCTCTTTTGT 57.755 33.333 0.00 0.00 0.00 2.83
890 926 9.496873 CATGTAGTAGTAGTAGTAGCATTCTCT 57.503 37.037 0.00 0.00 0.00 3.10
891 927 9.491675 TCATGTAGTAGTAGTAGTAGCATTCTC 57.508 37.037 0.00 0.00 0.00 2.87
892 928 9.848710 TTCATGTAGTAGTAGTAGTAGCATTCT 57.151 33.333 0.00 0.00 0.00 2.40
895 931 7.175293 GGCTTCATGTAGTAGTAGTAGTAGCAT 59.825 40.741 1.02 4.41 0.00 3.79
896 932 6.485984 GGCTTCATGTAGTAGTAGTAGTAGCA 59.514 42.308 1.02 2.76 0.00 3.49
897 933 6.485984 TGGCTTCATGTAGTAGTAGTAGTAGC 59.514 42.308 1.02 0.00 0.00 3.58
898 934 8.447924 TTGGCTTCATGTAGTAGTAGTAGTAG 57.552 38.462 1.02 0.00 0.00 2.57
899 935 8.051535 ACTTGGCTTCATGTAGTAGTAGTAGTA 58.948 37.037 1.02 0.00 0.00 1.82
900 936 6.890814 ACTTGGCTTCATGTAGTAGTAGTAGT 59.109 38.462 1.02 0.00 0.00 2.73
1225 1267 2.195123 ATACAAAGGCAACGCGGTGC 62.195 55.000 39.90 39.90 44.14 5.01
1226 1268 1.080298 TATACAAAGGCAACGCGGTG 58.920 50.000 22.40 22.40 46.39 4.94
1245 1287 4.342378 TCTTGAGCTAAATAGAGCCACGAT 59.658 41.667 0.00 0.00 43.97 3.73
1246 1288 3.699538 TCTTGAGCTAAATAGAGCCACGA 59.300 43.478 0.00 0.00 43.97 4.35
1251 1293 5.278957 CCTCTCCTCTTGAGCTAAATAGAGC 60.279 48.000 0.00 0.00 41.18 4.09
1294 1346 3.713764 TCTGATTTGATCTCCTTCCCCTC 59.286 47.826 0.00 0.00 0.00 4.30
1314 1376 4.514401 GATGGTTTCCTACGGTTTGATCT 58.486 43.478 0.00 0.00 0.00 2.75
1315 1377 3.308866 CGATGGTTTCCTACGGTTTGATC 59.691 47.826 0.00 0.00 0.00 2.92
1316 1378 3.055675 TCGATGGTTTCCTACGGTTTGAT 60.056 43.478 0.00 0.00 0.00 2.57
1317 1379 2.299582 TCGATGGTTTCCTACGGTTTGA 59.700 45.455 0.00 0.00 0.00 2.69
1318 1380 2.690786 TCGATGGTTTCCTACGGTTTG 58.309 47.619 0.00 0.00 0.00 2.93
1319 1381 3.622166 ATCGATGGTTTCCTACGGTTT 57.378 42.857 0.00 0.00 0.00 3.27
1320 1382 3.055675 TCAATCGATGGTTTCCTACGGTT 60.056 43.478 0.00 0.00 30.27 4.44
1321 1383 2.498481 TCAATCGATGGTTTCCTACGGT 59.502 45.455 0.00 0.00 0.00 4.83
1322 1384 3.173668 TCAATCGATGGTTTCCTACGG 57.826 47.619 0.00 0.00 0.00 4.02
1323 1385 4.974103 GATCAATCGATGGTTTCCTACG 57.026 45.455 0.00 0.00 29.66 3.51
1338 1400 2.963854 CGCCGCTGCTCGATCAAT 60.964 61.111 0.00 0.00 41.67 2.57
1434 1509 3.303189 CTGTCCCCGATCAGCACT 58.697 61.111 0.00 0.00 0.00 4.40
1632 1724 0.540830 ATACAGGTGGCGGGCAAAAA 60.541 50.000 5.57 0.00 0.00 1.94
1678 1786 3.682858 CGAGCGGTGGAAGAAATAAAGAA 59.317 43.478 0.00 0.00 0.00 2.52
1684 1792 0.736325 CGACGAGCGGTGGAAGAAAT 60.736 55.000 2.87 0.00 36.03 2.17
1754 1869 2.158449 GTCATCGCAAGTCCTTGAGTTG 59.842 50.000 11.12 12.06 43.49 3.16
1809 1966 4.582869 TGAGAATGAGTTGTTCCAGATGG 58.417 43.478 0.00 0.00 0.00 3.51
1812 1969 5.059161 CAGTTGAGAATGAGTTGTTCCAGA 58.941 41.667 0.00 0.00 0.00 3.86
1813 1970 4.818546 ACAGTTGAGAATGAGTTGTTCCAG 59.181 41.667 0.00 0.00 0.00 3.86
1814 1971 4.576053 CACAGTTGAGAATGAGTTGTTCCA 59.424 41.667 0.00 0.00 0.00 3.53
1815 1972 4.023707 CCACAGTTGAGAATGAGTTGTTCC 60.024 45.833 0.00 0.00 0.00 3.62
1836 1995 4.015764 TGCATTGCTAAAGATACTTGCCA 58.984 39.130 10.49 0.00 0.00 4.92
1837 1996 4.637483 TGCATTGCTAAAGATACTTGCC 57.363 40.909 10.49 0.00 0.00 4.52
1839 1998 6.020121 GCACATTGCATTGCTAAAGATACTTG 60.020 38.462 10.49 0.00 44.26 3.16
1840 1999 6.038356 GCACATTGCATTGCTAAAGATACTT 58.962 36.000 10.49 0.00 44.26 2.24
1841 2000 5.585390 GCACATTGCATTGCTAAAGATACT 58.415 37.500 10.49 0.00 44.26 2.12
1842 2001 5.878261 GCACATTGCATTGCTAAAGATAC 57.122 39.130 10.49 0.00 44.26 2.24
1919 2375 2.159947 CGCACGTACGCAAAGTGATTAA 60.160 45.455 16.72 0.00 39.66 1.40
1960 2420 1.132643 CGGTACCTACACACAGAGAGC 59.867 57.143 10.90 0.00 0.00 4.09
2332 2805 1.672854 CGTCGATGGTCTTGCCCCTA 61.673 60.000 0.00 0.00 36.04 3.53
2515 2988 3.365969 CCCAGAGCGTTTTGACCAATAAC 60.366 47.826 0.00 0.00 0.00 1.89
2576 3049 3.378112 GGTACCACACGCTGTATGTAGTA 59.622 47.826 7.15 0.00 0.00 1.82
2577 3050 2.165030 GGTACCACACGCTGTATGTAGT 59.835 50.000 7.15 0.00 0.00 2.73
2578 3051 2.793585 CGGTACCACACGCTGTATGTAG 60.794 54.545 13.54 0.00 0.00 2.74
2593 3069 1.805910 GACGTCTTCTCCCGGTACC 59.194 63.158 8.70 0.16 0.00 3.34
2648 3127 2.705658 TGGACCTGAACTGAACACAGAT 59.294 45.455 0.00 0.00 35.80 2.90
2772 3278 0.391661 GACATCGCCGGCATATCCAT 60.392 55.000 28.98 3.98 34.01 3.41
2775 3281 3.876300 GGACATCGCCGGCATATC 58.124 61.111 28.98 16.94 0.00 1.63
2902 3447 8.325421 TGATGAATAAACTTGGCTTTTACGTA 57.675 30.769 0.00 0.00 0.00 3.57
2903 3448 7.209471 TGATGAATAAACTTGGCTTTTACGT 57.791 32.000 0.00 0.00 0.00 3.57
2904 3449 8.514136 TTTGATGAATAAACTTGGCTTTTACG 57.486 30.769 0.00 0.00 0.00 3.18
2905 3450 9.476202 ACTTTGATGAATAAACTTGGCTTTTAC 57.524 29.630 0.00 0.00 0.00 2.01
2937 3482 1.064824 AAGCCCATCTGATCTCCCCC 61.065 60.000 0.00 0.00 0.00 5.40
2981 5019 1.222936 GGTCCACTGCCCTCATCTG 59.777 63.158 0.00 0.00 0.00 2.90
2987 5025 1.072266 TTACATTGGTCCACTGCCCT 58.928 50.000 9.07 0.00 0.00 5.19
3038 5076 3.679389 AGGCACGATTTCAAATGAGAGT 58.321 40.909 0.00 0.00 0.00 3.24
3114 5163 0.255033 AGGAATTTGGGTACTCCGGC 59.745 55.000 0.00 0.00 38.76 6.13
3116 5165 2.027561 TGTGAGGAATTTGGGTACTCCG 60.028 50.000 0.00 0.00 38.76 4.63
3134 5183 1.294659 GAAAGCCTCGCTGGACTGTG 61.295 60.000 0.00 0.00 39.62 3.66
3136 5185 1.743252 GGAAAGCCTCGCTGGACTG 60.743 63.158 0.00 0.00 39.62 3.51
3137 5186 2.665603 GGAAAGCCTCGCTGGACT 59.334 61.111 0.00 0.00 39.62 3.85
3140 5189 3.901797 AACGGGAAAGCCTCGCTGG 62.902 63.158 0.00 0.00 39.62 4.85
3142 5191 2.358737 CAACGGGAAAGCCTCGCT 60.359 61.111 0.00 0.00 42.56 4.93
3164 5213 3.685139 TTCTGGACCTTGATGACTCAC 57.315 47.619 0.00 0.00 0.00 3.51
3174 5223 5.479124 ACATAGTACGTTTTCTGGACCTT 57.521 39.130 0.00 0.00 0.00 3.50
3187 5236 3.851969 CGCCATGCACTATACATAGTACG 59.148 47.826 1.64 0.00 41.44 3.67
3192 5241 2.353704 GCTCCGCCATGCACTATACATA 60.354 50.000 0.00 0.00 0.00 2.29
3193 5242 1.609061 GCTCCGCCATGCACTATACAT 60.609 52.381 0.00 0.00 0.00 2.29
3194 5243 0.249868 GCTCCGCCATGCACTATACA 60.250 55.000 0.00 0.00 0.00 2.29
3195 5244 2.533318 GCTCCGCCATGCACTATAC 58.467 57.895 0.00 0.00 0.00 1.47
3216 5265 1.750399 CCCCAATCGCCACAAGAGG 60.750 63.158 0.00 0.00 0.00 3.69
3217 5266 1.750399 CCCCCAATCGCCACAAGAG 60.750 63.158 0.00 0.00 0.00 2.85
3218 5267 2.196997 CTCCCCCAATCGCCACAAGA 62.197 60.000 0.00 0.00 0.00 3.02
3219 5268 1.750399 CTCCCCCAATCGCCACAAG 60.750 63.158 0.00 0.00 0.00 3.16
3220 5269 2.354729 CTCCCCCAATCGCCACAA 59.645 61.111 0.00 0.00 0.00 3.33
3221 5270 3.727258 CCTCCCCCAATCGCCACA 61.727 66.667 0.00 0.00 0.00 4.17
3222 5271 4.506255 CCCTCCCCCAATCGCCAC 62.506 72.222 0.00 0.00 0.00 5.01
3238 5287 1.380380 CCAGAACCATGCTTCCCCC 60.380 63.158 0.00 0.00 0.00 5.40
3239 5288 1.380380 CCCAGAACCATGCTTCCCC 60.380 63.158 0.00 0.00 0.00 4.81
3240 5289 1.380380 CCCCAGAACCATGCTTCCC 60.380 63.158 0.00 0.00 0.00 3.97
3241 5290 0.681243 GTCCCCAGAACCATGCTTCC 60.681 60.000 0.00 0.00 0.00 3.46
3242 5291 1.026718 CGTCCCCAGAACCATGCTTC 61.027 60.000 0.00 0.00 0.00 3.86
3243 5292 1.002134 CGTCCCCAGAACCATGCTT 60.002 57.895 0.00 0.00 0.00 3.91
3244 5293 1.903877 CTCGTCCCCAGAACCATGCT 61.904 60.000 0.00 0.00 0.00 3.79
3245 5294 1.450312 CTCGTCCCCAGAACCATGC 60.450 63.158 0.00 0.00 0.00 4.06
3246 5295 0.176680 CTCTCGTCCCCAGAACCATG 59.823 60.000 0.00 0.00 0.00 3.66
3247 5296 0.041238 TCTCTCGTCCCCAGAACCAT 59.959 55.000 0.00 0.00 0.00 3.55
3274 5469 0.105709 TGTCCGATCTCAGCCCCATA 60.106 55.000 0.00 0.00 0.00 2.74
3289 5484 0.329596 AGTTGGCCTTCCTCATGTCC 59.670 55.000 3.32 0.00 0.00 4.02
3314 5510 3.044894 ACTTCCTCCATCTTCCCTGATC 58.955 50.000 0.00 0.00 0.00 2.92
3317 5513 1.211457 CCACTTCCTCCATCTTCCCTG 59.789 57.143 0.00 0.00 0.00 4.45
3318 5514 1.203492 ACCACTTCCTCCATCTTCCCT 60.203 52.381 0.00 0.00 0.00 4.20
3323 5519 2.472029 CCACTACCACTTCCTCCATCT 58.528 52.381 0.00 0.00 0.00 2.90
3349 5545 0.375106 CTCCCGATTTGCTTCTTCGC 59.625 55.000 0.00 0.00 0.00 4.70
3360 5556 2.639839 CCCAAGTATGATCCTCCCGATT 59.360 50.000 0.00 0.00 0.00 3.34
3369 5565 3.200165 GGTATAGGCCCCCAAGTATGATC 59.800 52.174 0.00 0.00 0.00 2.92
3373 5569 4.173594 GTTAGGTATAGGCCCCCAAGTAT 58.826 47.826 0.00 0.00 0.00 2.12
3374 5570 3.590714 GTTAGGTATAGGCCCCCAAGTA 58.409 50.000 0.00 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.