Multiple sequence alignment - TraesCS6A01G355200

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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 TraesCS6A01G355200 chr6A 100.000 8788 0 0 1 8788 586316126 586324913 0.000000e+00 16229
1 TraesCS6A01G355200 chr6A 83.504 879 137 7 2888 3765 586318908 586319779 0.000000e+00 813
2 TraesCS6A01G355200 chr6A 83.504 879 137 7 2783 3654 586319013 586319890 0.000000e+00 813
3 TraesCS6A01G355200 chr6A 83.073 768 126 4 3097 3862 586319000 586319765 0.000000e+00 695
4 TraesCS6A01G355200 chr6A 74.029 901 216 14 2871 3765 586318558 586319446 1.400000e-92 351
5 TraesCS6A01G355200 chr6D 97.227 6454 116 18 1091 7501 437944686 437951119 0.000000e+00 10868
6 TraesCS6A01G355200 chr6D 95.599 1227 40 10 7568 8788 437951111 437952329 0.000000e+00 1954
7 TraesCS6A01G355200 chr6D 84.597 1227 62 52 1 1161 437943549 437944714 0.000000e+00 1101
8 TraesCS6A01G355200 chr6D 84.528 879 131 5 2888 3765 437946381 437947255 0.000000e+00 865
9 TraesCS6A01G355200 chr6D 88.295 692 81 0 2963 3654 437946675 437947366 0.000000e+00 830
10 TraesCS6A01G355200 chr6D 83.270 789 126 6 3077 3862 437946456 437947241 0.000000e+00 721
11 TraesCS6A01G355200 chr6D 83.333 768 124 4 2875 3640 437946698 437947463 0.000000e+00 706
12 TraesCS6A01G355200 chr6D 74.582 956 217 19 2382 3321 437946421 437947366 6.390000e-106 396
13 TraesCS6A01G355200 chr6B 94.800 5596 188 42 3250 8787 662888721 662894271 0.000000e+00 8626
14 TraesCS6A01G355200 chr6B 95.000 2160 97 6 1085 3234 662886156 662888314 0.000000e+00 3380
15 TraesCS6A01G355200 chr6B 82.893 871 64 32 349 1161 662885347 662886190 0.000000e+00 704
16 TraesCS6A01G355200 chr6B 82.797 622 34 25 11 590 662884553 662885143 1.030000e-133 488
17 TraesCS6A01G355200 chr7D 100.000 40 0 0 1559 1598 592411177 592411216 3.400000e-09 75


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 TraesCS6A01G355200 chr6A 586316126 586324913 8787 False 16229.0 16229 100.0000 1 8788 1 chr6A.!!$F1 8787
1 TraesCS6A01G355200 chr6A 586318558 586319890 1332 False 668.0 813 81.0275 2783 3862 4 chr6A.!!$F2 1079
2 TraesCS6A01G355200 chr6D 437943549 437951119 7570 False 5984.5 10868 90.9120 1 7501 2 chr6D.!!$F1 7500
3 TraesCS6A01G355200 chr6D 437946381 437952329 5948 False 912.0 1954 84.9345 2382 8788 6 chr6D.!!$F2 6406
4 TraesCS6A01G355200 chr6B 662884553 662894271 9718 False 3299.5 8626 88.8725 11 8787 4 chr6B.!!$F1 8776

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
705 1243 0.034574 ATTATCGCCTGTTGCCACCA 60.035 50.000 0.00 0.0 36.24 4.17 F
752 1295 0.178961 AAAACAACCTCTGGCCCTCC 60.179 55.000 0.00 0.0 0.00 4.30 F
1682 2302 0.399454 ACTGACAAGATGCACAGGCT 59.601 50.000 4.94 0.0 41.91 4.58 F
2229 2849 0.600057 CAAGAAGGCCACTTGCTTCC 59.400 55.000 22.96 0.0 38.28 3.46 F
3784 4798 1.340991 GCAGGGTTGCCTCTAATTCCA 60.341 52.381 0.00 0.0 44.74 3.53 F
4525 5539 2.760650 AGCGTGGATCTGACTGATAACA 59.239 45.455 0.00 0.0 35.14 2.41 F
4746 5760 2.941064 TCTACTACGTCCTTCATCACCG 59.059 50.000 0.00 0.0 0.00 4.94 F
5911 6956 3.713248 TCATGATGCAGATGGACTACCTT 59.287 43.478 8.29 0.0 37.04 3.50 F
7683 8737 2.029623 CCAGGCTTGAAGCTGCAATAT 58.970 47.619 17.59 0.0 41.99 1.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2158 2778 0.035439 TCTTTTCCAGGGACATCGGC 60.035 55.000 0.00 0.00 0.00 5.54 R
2283 2903 1.550976 GGAACCGAGGAGATGACTGTT 59.449 52.381 0.00 0.00 0.00 3.16 R
3784 4798 1.556911 ACTTCTCGACAGGGCATCAAT 59.443 47.619 0.00 0.00 0.00 2.57 R
4067 5081 4.689071 TGTGCCTACATTACCAGAATACG 58.311 43.478 0.00 0.00 0.00 3.06 R
5511 6528 2.181021 GCTGCCTTGATGCACTGC 59.819 61.111 0.00 0.00 36.04 4.40 R
6601 7648 1.280457 ACAATCAGGACCTCCAGGAC 58.720 55.000 0.00 0.00 38.89 3.85 R
6602 7649 2.044793 AACAATCAGGACCTCCAGGA 57.955 50.000 0.00 0.00 38.89 3.86 R
7685 8739 0.746659 AACAGCAAAGCACACCCTTC 59.253 50.000 0.00 0.00 0.00 3.46 R
8583 9654 0.163788 CTGTCAACCTAAGCAACGCG 59.836 55.000 3.53 3.53 0.00 6.01 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
110 111 1.144936 GAGCTAGCCGTTGCCATCT 59.855 57.895 12.13 0.00 38.69 2.90
111 112 1.153289 AGCTAGCCGTTGCCATCTG 60.153 57.895 12.13 0.00 38.69 2.90
151 161 4.168760 CGGCAACATTCCATTTCTCTTTC 58.831 43.478 0.00 0.00 0.00 2.62
152 162 4.082571 CGGCAACATTCCATTTCTCTTTCT 60.083 41.667 0.00 0.00 0.00 2.52
153 163 5.565439 CGGCAACATTCCATTTCTCTTTCTT 60.565 40.000 0.00 0.00 0.00 2.52
154 164 6.226052 GGCAACATTCCATTTCTCTTTCTTT 58.774 36.000 0.00 0.00 0.00 2.52
155 165 6.707608 GGCAACATTCCATTTCTCTTTCTTTT 59.292 34.615 0.00 0.00 0.00 2.27
156 166 7.095481 GGCAACATTCCATTTCTCTTTCTTTTC 60.095 37.037 0.00 0.00 0.00 2.29
157 167 7.439056 GCAACATTCCATTTCTCTTTCTTTTCA 59.561 33.333 0.00 0.00 0.00 2.69
158 168 9.485206 CAACATTCCATTTCTCTTTCTTTTCAT 57.515 29.630 0.00 0.00 0.00 2.57
175 185 6.440647 TCTTTTCATACTCATACTCCCACACT 59.559 38.462 0.00 0.00 0.00 3.55
229 240 0.461961 CTACCCGCCAGAGAGAAAGG 59.538 60.000 0.00 0.00 0.00 3.11
243 254 1.365368 GAAAGGGAGAGCAAGCGAGC 61.365 60.000 0.00 0.00 0.00 5.03
244 255 3.655810 AAGGGAGAGCAAGCGAGCG 62.656 63.158 0.00 0.00 40.15 5.03
245 256 4.135153 GGGAGAGCAAGCGAGCGA 62.135 66.667 0.00 0.00 40.15 4.93
247 258 2.487428 GAGAGCAAGCGAGCGAGA 59.513 61.111 0.00 0.00 40.15 4.04
248 259 1.586042 GAGAGCAAGCGAGCGAGAG 60.586 63.158 0.00 0.00 40.15 3.20
249 260 1.987704 GAGAGCAAGCGAGCGAGAGA 61.988 60.000 0.00 0.00 40.15 3.10
250 261 1.065600 GAGCAAGCGAGCGAGAGAT 59.934 57.895 0.00 0.00 40.15 2.75
251 262 1.208009 GAGCAAGCGAGCGAGAGATG 61.208 60.000 0.00 0.00 40.15 2.90
252 263 2.236382 GCAAGCGAGCGAGAGATGG 61.236 63.158 0.00 0.00 0.00 3.51
257 268 3.934962 GAGCGAGAGATGGCCCCC 61.935 72.222 0.00 0.00 0.00 5.40
332 348 0.818938 TTATCACTCCTACGCCGCAA 59.181 50.000 0.00 0.00 0.00 4.85
333 349 0.101759 TATCACTCCTACGCCGCAAC 59.898 55.000 0.00 0.00 0.00 4.17
334 350 2.884087 ATCACTCCTACGCCGCAACG 62.884 60.000 0.00 0.00 39.50 4.10
372 403 5.232202 CGTACTAATCATCGCATTCAGTTGT 59.768 40.000 0.00 0.00 0.00 3.32
412 448 0.958876 GTCCTTAACCCCAGCCAACG 60.959 60.000 0.00 0.00 0.00 4.10
498 997 0.680280 CTCCGTTTCTCTCTCCCCGA 60.680 60.000 0.00 0.00 0.00 5.14
527 1037 2.709475 CCATTACTCGGCTTGCGC 59.291 61.111 0.00 0.00 0.00 6.09
596 1106 1.222936 CTCCCTCCATCAGGTGCAC 59.777 63.158 8.80 8.80 41.51 4.57
600 1111 1.002990 CTCCATCAGGTGCACAGCA 60.003 57.895 20.43 0.68 35.60 4.41
692 1230 5.997007 CGCGTACGTTGGTAAATTATTATCG 59.003 40.000 17.90 1.38 33.53 2.92
693 1231 5.780269 GCGTACGTTGGTAAATTATTATCGC 59.220 40.000 17.90 0.00 0.00 4.58
695 1233 6.144402 CGTACGTTGGTAAATTATTATCGCCT 59.856 38.462 7.22 0.00 0.00 5.52
696 1234 6.295039 ACGTTGGTAAATTATTATCGCCTG 57.705 37.500 0.00 0.00 0.00 4.85
697 1235 5.818857 ACGTTGGTAAATTATTATCGCCTGT 59.181 36.000 0.00 0.00 0.00 4.00
698 1236 6.316890 ACGTTGGTAAATTATTATCGCCTGTT 59.683 34.615 0.00 0.00 0.00 3.16
699 1237 6.631238 CGTTGGTAAATTATTATCGCCTGTTG 59.369 38.462 0.00 0.00 0.00 3.33
700 1238 6.067263 TGGTAAATTATTATCGCCTGTTGC 57.933 37.500 0.00 0.00 0.00 4.17
701 1239 5.009210 TGGTAAATTATTATCGCCTGTTGCC 59.991 40.000 0.00 0.00 36.24 4.52
702 1240 5.009210 GGTAAATTATTATCGCCTGTTGCCA 59.991 40.000 0.00 0.00 36.24 4.92
703 1241 4.568152 AATTATTATCGCCTGTTGCCAC 57.432 40.909 0.00 0.00 36.24 5.01
704 1242 1.961793 TATTATCGCCTGTTGCCACC 58.038 50.000 0.00 0.00 36.24 4.61
705 1243 0.034574 ATTATCGCCTGTTGCCACCA 60.035 50.000 0.00 0.00 36.24 4.17
707 1245 0.250945 TATCGCCTGTTGCCACCAAA 60.251 50.000 0.00 0.00 36.24 3.28
710 1248 2.133641 GCCTGTTGCCACCAAAGGT 61.134 57.895 0.00 0.00 34.50 3.50
721 1259 3.090765 CAAAGGTGGAGGGAGGGG 58.909 66.667 0.00 0.00 0.00 4.79
722 1260 1.541368 CAAAGGTGGAGGGAGGGGA 60.541 63.158 0.00 0.00 0.00 4.81
744 1287 1.430992 TCCTCCGGAAAACAACCTCT 58.569 50.000 5.23 0.00 0.00 3.69
752 1295 0.178961 AAAACAACCTCTGGCCCTCC 60.179 55.000 0.00 0.00 0.00 4.30
754 1297 3.732849 CAACCTCTGGCCCTCCCC 61.733 72.222 0.00 0.00 0.00 4.81
755 1298 3.960313 AACCTCTGGCCCTCCCCT 61.960 66.667 0.00 0.00 0.00 4.79
756 1299 3.952799 AACCTCTGGCCCTCCCCTC 62.953 68.421 0.00 0.00 0.00 4.30
770 1313 2.675371 CCTCCCGTCCCCTTTTCC 59.325 66.667 0.00 0.00 0.00 3.13
775 1318 0.611062 CCCGTCCCCTTTTCCTTTCC 60.611 60.000 0.00 0.00 0.00 3.13
785 1331 2.741486 TTTCCTTTCCTCCACCCGCG 62.741 60.000 0.00 0.00 0.00 6.46
845 1392 1.303309 GTCTGATTCTGCGGGATTGG 58.697 55.000 0.00 0.00 0.00 3.16
862 1409 3.670377 GTCTGCCGGTTGGTTGCC 61.670 66.667 1.90 0.00 37.67 4.52
885 1432 1.503542 CCTGTCTGAACCGCATTGC 59.496 57.895 0.00 0.00 0.00 3.56
890 1437 0.537143 TCTGAACCGCATTGCCTTGT 60.537 50.000 2.41 0.00 0.00 3.16
1205 1822 2.993853 GAAGAGGCCCCAGTCCAG 59.006 66.667 0.00 0.00 0.00 3.86
1682 2302 0.399454 ACTGACAAGATGCACAGGCT 59.601 50.000 4.94 0.00 41.91 4.58
1713 2333 2.111999 CTTCACCCAAGAGGACGGCA 62.112 60.000 0.00 0.00 39.89 5.69
1791 2411 1.064296 CCGATTGGTCTCCTCGTCG 59.936 63.158 0.00 0.00 0.00 5.12
1792 2412 1.586564 CGATTGGTCTCCTCGTCGC 60.587 63.158 0.00 0.00 0.00 5.19
1834 2454 3.899726 AGATCATCTGCTTCAAATGGCT 58.100 40.909 0.00 0.00 0.00 4.75
1914 2534 1.139853 GCAGTTCCATCGAGAGGGATT 59.860 52.381 7.35 0.00 41.34 3.01
2229 2849 0.600057 CAAGAAGGCCACTTGCTTCC 59.400 55.000 22.96 0.00 38.28 3.46
2250 2870 4.814234 TCCGATGGTGTTAATGCTATTGTC 59.186 41.667 0.00 0.00 0.00 3.18
2268 2888 8.057742 GCTATTGTCAAAAATATGGATTTTGCG 58.942 33.333 6.82 0.00 43.10 4.85
2271 2891 6.459066 TGTCAAAAATATGGATTTTGCGGAA 58.541 32.000 6.82 0.00 43.10 4.30
2283 2903 2.779755 TTGCGGAAAAGGATAGCAGA 57.220 45.000 0.00 0.00 39.11 4.26
3784 4798 1.340991 GCAGGGTTGCCTCTAATTCCA 60.341 52.381 0.00 0.00 44.74 3.53
4067 5081 6.813649 TGTAGTGATGATACTTCAGAAAGCAC 59.186 38.462 0.00 0.00 35.81 4.40
4479 5493 4.925054 TCTACACGAAAAATACTTGGACCG 59.075 41.667 0.00 0.00 0.00 4.79
4525 5539 2.760650 AGCGTGGATCTGACTGATAACA 59.239 45.455 0.00 0.00 35.14 2.41
4746 5760 2.941064 TCTACTACGTCCTTCATCACCG 59.059 50.000 0.00 0.00 0.00 4.94
5511 6528 7.333528 AGTAATAACATTGTGGGCATTAGTG 57.666 36.000 0.00 0.00 0.00 2.74
5627 6645 5.567138 AAATTCCCGATCATGTCTGTTTC 57.433 39.130 0.00 0.00 0.00 2.78
5740 6782 6.935208 ACTGGTTGGAAGACTAAGTTTACATC 59.065 38.462 0.00 0.00 0.00 3.06
5744 6786 9.498176 GGTTGGAAGACTAAGTTTACATCTTTA 57.502 33.333 0.00 0.00 29.85 1.85
5796 6841 5.435686 TTTATATTCTGTGGAGGTGCACT 57.564 39.130 17.98 2.27 0.00 4.40
5911 6956 3.713248 TCATGATGCAGATGGACTACCTT 59.287 43.478 8.29 0.00 37.04 3.50
6125 7170 7.097834 GGAGTAAAGCTAACTTCTGTACATGT 58.902 38.462 2.69 2.69 34.05 3.21
6602 7649 9.872684 ATTCAGTTATTATGATTCAATGGAGGT 57.127 29.630 0.00 0.00 0.00 3.85
6603 7650 8.908786 TCAGTTATTATGATTCAATGGAGGTC 57.091 34.615 0.00 0.00 0.00 3.85
6604 7651 7.939039 TCAGTTATTATGATTCAATGGAGGTCC 59.061 37.037 0.00 0.00 0.00 4.46
6605 7652 7.941238 CAGTTATTATGATTCAATGGAGGTCCT 59.059 37.037 0.00 0.00 36.82 3.85
6606 7653 7.941238 AGTTATTATGATTCAATGGAGGTCCTG 59.059 37.037 0.00 0.00 36.82 3.86
6607 7654 3.589951 ATGATTCAATGGAGGTCCTGG 57.410 47.619 0.00 0.00 36.82 4.45
6608 7655 2.561187 TGATTCAATGGAGGTCCTGGA 58.439 47.619 0.00 0.00 36.82 3.86
6872 7921 4.458989 TGATGTTTGAGTTCTGGCATTACC 59.541 41.667 0.00 0.00 39.84 2.85
6945 7994 7.885009 TTCATTGATTGCCATAATCTTCTGA 57.115 32.000 0.00 0.00 0.00 3.27
7028 8077 4.095782 CAGTTAGAGGCTACACACTCTCTC 59.904 50.000 0.00 0.00 42.73 3.20
7132 8181 5.235186 CACTGCAGGTACAAGCTTGATATAC 59.765 44.000 32.50 22.18 32.89 1.47
7375 8425 7.081349 TGAAACAGTTAAATAAGATGCCAACG 58.919 34.615 0.00 0.00 0.00 4.10
7501 8552 7.360607 GGAAATGCTTTTTGAGTGGATCATTTG 60.361 37.037 0.00 0.00 37.89 2.32
7540 8591 6.795098 TCTTGTTACCATGTGTTACATCAC 57.205 37.500 6.89 0.00 36.53 3.06
7586 8640 9.464714 TCTTTATGATCAGTTTCTAGATAACGC 57.535 33.333 0.09 0.00 0.00 4.84
7596 8650 8.350722 CAGTTTCTAGATAACGCAGTCCTATTA 58.649 37.037 0.00 0.00 45.00 0.98
7683 8737 2.029623 CCAGGCTTGAAGCTGCAATAT 58.970 47.619 17.59 0.00 41.99 1.28
7685 8739 3.252701 CCAGGCTTGAAGCTGCAATATAG 59.747 47.826 17.59 0.00 41.99 1.31
7772 8826 3.005554 CAGCCTAAGGACACAACTCATG 58.994 50.000 0.00 0.00 0.00 3.07
7795 8849 5.048083 TGCAAGAAACAGAGTGAACAACTTT 60.048 36.000 0.00 0.00 40.07 2.66
7941 9000 4.673968 AGGTACCCCCAAATTTCTCTTTC 58.326 43.478 8.74 0.00 34.66 2.62
7997 9056 3.057969 TGTACAACCTGCATGGAAGAG 57.942 47.619 8.91 0.00 39.71 2.85
8093 9152 1.186200 CTGAGGATGTCGAGGTTCCA 58.814 55.000 10.04 0.00 31.65 3.53
8094 9153 1.135915 CTGAGGATGTCGAGGTTCCAG 59.864 57.143 10.04 0.05 31.65 3.86
8305 9369 0.672889 TACCTACACGTTTGCGGTCA 59.327 50.000 1.42 0.00 43.45 4.02
8308 9372 1.562575 CTACACGTTTGCGGTCACCC 61.563 60.000 0.00 0.00 43.45 4.61
8350 9416 6.913170 ACGCTTTCTTGATATGTCAATGTTT 58.087 32.000 5.26 0.00 43.08 2.83
8373 9439 6.573664 TTTCAGTTCTATGAAATGTGTGGG 57.426 37.500 7.46 0.00 42.68 4.61
8380 9450 6.367374 TCTATGAAATGTGTGGGTTGTCTA 57.633 37.500 0.00 0.00 0.00 2.59
8413 9483 4.272018 GCTCATTATAGTGCTGGAACTGTG 59.728 45.833 0.00 0.00 0.00 3.66
8557 9628 7.764443 TGTCCTCAAAGAATGTATACAACTAGC 59.236 37.037 10.14 0.00 0.00 3.42
8573 9644 3.112263 ACTAGCTTAGTTGGGCCATACA 58.888 45.455 7.26 0.00 34.86 2.29
8583 9654 0.251341 GGGCCATACACCATCATCCC 60.251 60.000 4.39 0.00 0.00 3.85
8621 9692 1.075374 AGCCACTGTTTAGCCCATGAA 59.925 47.619 0.00 0.00 0.00 2.57
8624 9696 3.055891 GCCACTGTTTAGCCCATGAATTT 60.056 43.478 0.00 0.00 0.00 1.82
8661 9733 2.492753 GGAAAATGGGTCCTCCTTTGGT 60.493 50.000 0.00 0.00 33.70 3.67
8771 9846 6.543465 CCCATGTAGATCAGCAACTTTTATCA 59.457 38.462 0.00 0.00 0.00 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
151 161 6.644347 AGTGTGGGAGTATGAGTATGAAAAG 58.356 40.000 0.00 0.00 0.00 2.27
152 162 6.620877 AGTGTGGGAGTATGAGTATGAAAA 57.379 37.500 0.00 0.00 0.00 2.29
153 163 6.620877 AAGTGTGGGAGTATGAGTATGAAA 57.379 37.500 0.00 0.00 0.00 2.69
154 164 6.620877 AAAGTGTGGGAGTATGAGTATGAA 57.379 37.500 0.00 0.00 0.00 2.57
155 165 6.620877 AAAAGTGTGGGAGTATGAGTATGA 57.379 37.500 0.00 0.00 0.00 2.15
200 211 4.713321 TCTCTGGCGGGTAGTAGTAAAAAT 59.287 41.667 0.00 0.00 0.00 1.82
205 216 2.121948 TCTCTCTGGCGGGTAGTAGTA 58.878 52.381 0.00 0.00 0.00 1.82
206 217 0.917533 TCTCTCTGGCGGGTAGTAGT 59.082 55.000 0.00 0.00 0.00 2.73
207 218 2.054232 TTCTCTCTGGCGGGTAGTAG 57.946 55.000 0.00 0.00 0.00 2.57
229 240 2.581953 CTCGCTCGCTTGCTCTCC 60.582 66.667 0.00 0.00 0.00 3.71
257 268 1.396653 GATCAATGCAAGTGGGGAGG 58.603 55.000 0.00 0.00 29.44 4.30
259 270 0.033208 GGGATCAATGCAAGTGGGGA 60.033 55.000 0.00 0.00 29.44 4.81
260 271 1.044790 GGGGATCAATGCAAGTGGGG 61.045 60.000 0.00 0.00 29.44 4.96
301 312 7.360607 GCGTAGGAGTGATAAAAGCAAGTTTAA 60.361 37.037 0.00 0.00 0.00 1.52
302 313 6.091713 GCGTAGGAGTGATAAAAGCAAGTTTA 59.908 38.462 0.00 0.00 0.00 2.01
303 314 5.106673 GCGTAGGAGTGATAAAAGCAAGTTT 60.107 40.000 0.00 0.00 0.00 2.66
304 315 4.392138 GCGTAGGAGTGATAAAAGCAAGTT 59.608 41.667 0.00 0.00 0.00 2.66
309 320 1.859080 CGGCGTAGGAGTGATAAAAGC 59.141 52.381 0.00 0.00 0.00 3.51
317 328 3.179265 CGTTGCGGCGTAGGAGTG 61.179 66.667 9.37 0.00 0.00 3.51
334 350 1.203313 GTACGCCGCATTAATCCGC 59.797 57.895 0.00 0.00 0.00 5.54
335 351 2.054687 TAGTACGCCGCATTAATCCG 57.945 50.000 0.00 0.00 0.00 4.18
336 352 3.991773 TGATTAGTACGCCGCATTAATCC 59.008 43.478 9.29 0.00 32.43 3.01
337 353 5.498700 CGATGATTAGTACGCCGCATTAATC 60.499 44.000 5.83 5.83 33.47 1.75
338 354 4.326278 CGATGATTAGTACGCCGCATTAAT 59.674 41.667 0.00 0.00 0.00 1.40
339 355 3.671459 CGATGATTAGTACGCCGCATTAA 59.329 43.478 0.00 0.00 0.00 1.40
341 357 2.058798 CGATGATTAGTACGCCGCATT 58.941 47.619 0.00 0.00 0.00 3.56
342 358 1.698165 CGATGATTAGTACGCCGCAT 58.302 50.000 0.00 0.00 0.00 4.73
343 359 0.937699 GCGATGATTAGTACGCCGCA 60.938 55.000 0.00 0.00 44.27 5.69
344 360 1.773496 GCGATGATTAGTACGCCGC 59.227 57.895 0.00 0.00 44.27 6.53
372 403 2.793946 GGGCGACGCGACTAACTA 59.206 61.111 15.93 0.00 34.07 2.24
412 448 1.002011 GGAGGCCACCACTTCCTTC 60.002 63.158 15.24 0.00 0.00 3.46
596 1106 1.575576 GACTCAGTGCTGGCTTGCTG 61.576 60.000 0.00 0.98 0.00 4.41
600 1111 1.072159 GGTGACTCAGTGCTGGCTT 59.928 57.895 0.00 0.00 0.00 4.35
677 1215 5.009210 GGCAACAGGCGATAATAATTTACCA 59.991 40.000 0.00 0.00 46.16 3.25
678 1216 5.009210 TGGCAACAGGCGATAATAATTTACC 59.991 40.000 0.00 0.00 46.17 2.85
679 1217 6.067263 TGGCAACAGGCGATAATAATTTAC 57.933 37.500 0.00 0.00 46.17 2.01
702 1240 1.852626 CCCTCCCTCCACCTTTGGT 60.853 63.158 0.00 0.00 44.35 3.67
703 1241 2.616458 CCCCTCCCTCCACCTTTGG 61.616 68.421 0.00 0.00 45.56 3.28
704 1242 1.140134 TTCCCCTCCCTCCACCTTTG 61.140 60.000 0.00 0.00 0.00 2.77
705 1243 0.178801 ATTCCCCTCCCTCCACCTTT 60.179 55.000 0.00 0.00 0.00 3.11
707 1245 0.624795 GAATTCCCCTCCCTCCACCT 60.625 60.000 0.00 0.00 0.00 4.00
710 1248 0.327576 GAGGAATTCCCCTCCCTCCA 60.328 60.000 21.22 0.00 45.44 3.86
711 1249 2.545969 GAGGAATTCCCCTCCCTCC 58.454 63.158 21.22 0.00 45.44 4.30
752 1295 2.675371 GAAAAGGGGACGGGAGGG 59.325 66.667 0.00 0.00 0.00 4.30
754 1297 0.404426 AAAGGAAAAGGGGACGGGAG 59.596 55.000 0.00 0.00 0.00 4.30
755 1298 0.402887 GAAAGGAAAAGGGGACGGGA 59.597 55.000 0.00 0.00 0.00 5.14
756 1299 0.611062 GGAAAGGAAAAGGGGACGGG 60.611 60.000 0.00 0.00 0.00 5.28
757 1300 0.404426 AGGAAAGGAAAAGGGGACGG 59.596 55.000 0.00 0.00 0.00 4.79
770 1313 3.702048 TCCGCGGGTGGAGGAAAG 61.702 66.667 27.83 0.00 42.12 2.62
819 1366 1.212616 CGCAGAATCAGACCGGAATC 58.787 55.000 9.46 0.00 0.00 2.52
825 1372 1.303309 CAATCCCGCAGAATCAGACC 58.697 55.000 0.00 0.00 0.00 3.85
829 1376 0.911769 AGACCAATCCCGCAGAATCA 59.088 50.000 0.00 0.00 0.00 2.57
845 1392 3.670377 GGCAACCAACCGGCAGAC 61.670 66.667 0.00 0.00 34.57 3.51
868 1415 0.957395 AGGCAATGCGGTTCAGACAG 60.957 55.000 0.00 0.00 0.00 3.51
885 1432 1.665169 GCCTGCACAACAAAAACAAGG 59.335 47.619 0.00 0.00 0.00 3.61
890 1437 0.805322 CAGCGCCTGCACAACAAAAA 60.805 50.000 2.29 0.00 46.23 1.94
1025 1579 3.093278 CGTCAGATTTCCGCAGCC 58.907 61.111 0.00 0.00 0.00 4.85
1305 1922 2.271497 GAGGAGGACGAGGACGGA 59.729 66.667 0.00 0.00 44.46 4.69
1698 2318 2.990479 GATGCCGTCCTCTTGGGT 59.010 61.111 0.00 0.00 36.25 4.51
1713 2333 0.813610 TTGCGGCGGATGAAATCGAT 60.814 50.000 9.78 0.00 46.86 3.59
1788 2408 3.519930 GACTCCTCCCCTCGCGAC 61.520 72.222 3.71 0.00 0.00 5.19
1791 2411 2.569218 TAGGTGACTCCTCCCCTCGC 62.569 65.000 0.00 0.00 44.42 5.03
1792 2412 0.466555 CTAGGTGACTCCTCCCCTCG 60.467 65.000 0.00 0.00 44.42 4.63
1834 2454 4.142534 GCTGCTTTTTGATGTATCAGCTGA 60.143 41.667 20.79 20.79 41.37 4.26
2112 2732 1.015109 CACCAGATGCTGCTGATGTC 58.985 55.000 0.00 0.00 38.14 3.06
2158 2778 0.035439 TCTTTTCCAGGGACATCGGC 60.035 55.000 0.00 0.00 0.00 5.54
2229 2849 5.733226 TGACAATAGCATTAACACCATCG 57.267 39.130 0.00 0.00 0.00 3.84
2250 2870 7.118971 TCCTTTTCCGCAAAATCCATATTTTTG 59.881 33.333 6.70 6.70 41.50 2.44
2266 2886 2.352960 CTGTTCTGCTATCCTTTTCCGC 59.647 50.000 0.00 0.00 0.00 5.54
2268 2888 4.579869 TGACTGTTCTGCTATCCTTTTCC 58.420 43.478 0.00 0.00 0.00 3.13
2271 2891 5.396213 GGAGATGACTGTTCTGCTATCCTTT 60.396 44.000 0.00 0.00 0.00 3.11
2283 2903 1.550976 GGAACCGAGGAGATGACTGTT 59.449 52.381 0.00 0.00 0.00 3.16
3784 4798 1.556911 ACTTCTCGACAGGGCATCAAT 59.443 47.619 0.00 0.00 0.00 2.57
4067 5081 4.689071 TGTGCCTACATTACCAGAATACG 58.311 43.478 0.00 0.00 0.00 3.06
4479 5493 1.610522 GACATGGCATTAGCACCATCC 59.389 52.381 0.00 0.00 44.97 3.51
4746 5760 3.084039 TGATGTTGATGAAGCCTTGGTC 58.916 45.455 0.00 0.00 0.00 4.02
5093 6107 7.921304 ATTTTCCAAAATTTCCTAAGCAGGAT 58.079 30.769 0.00 0.00 39.52 3.24
5094 6108 7.315066 ATTTTCCAAAATTTCCTAAGCAGGA 57.685 32.000 0.00 0.00 40.91 3.86
5095 6109 7.984422 AATTTTCCAAAATTTCCTAAGCAGG 57.016 32.000 4.48 0.00 43.91 4.85
5511 6528 2.181021 GCTGCCTTGATGCACTGC 59.819 61.111 0.00 0.00 36.04 4.40
5627 6645 5.776173 ACTAGGACAATCTATCTCAACCG 57.224 43.478 0.00 0.00 0.00 4.44
5911 6956 1.451504 CAACTCTGCCCAGTGGTCA 59.548 57.895 8.74 0.00 0.00 4.02
6125 7170 7.562454 AGAATCAAACGGAAGACTTGTTTAA 57.438 32.000 0.00 0.00 34.29 1.52
6519 7565 9.224267 AGTGTGCCAATGCTAATTATAGATTAG 57.776 33.333 2.25 2.25 38.71 1.73
6601 7648 1.280457 ACAATCAGGACCTCCAGGAC 58.720 55.000 0.00 0.00 38.89 3.85
6602 7649 2.044793 AACAATCAGGACCTCCAGGA 57.955 50.000 0.00 0.00 38.89 3.86
6603 7650 3.107601 TCTAACAATCAGGACCTCCAGG 58.892 50.000 0.00 0.00 38.89 4.45
6604 7651 3.772025 ACTCTAACAATCAGGACCTCCAG 59.228 47.826 0.00 0.00 38.89 3.86
6605 7652 3.791320 ACTCTAACAATCAGGACCTCCA 58.209 45.455 0.00 0.00 38.89 3.86
6606 7653 4.020128 ACAACTCTAACAATCAGGACCTCC 60.020 45.833 0.00 0.00 0.00 4.30
6607 7654 4.932200 CACAACTCTAACAATCAGGACCTC 59.068 45.833 0.00 0.00 0.00 3.85
6608 7655 4.593206 TCACAACTCTAACAATCAGGACCT 59.407 41.667 0.00 0.00 0.00 3.85
6789 7836 4.466370 AGATCATCTGGAACGGTCAAGTTA 59.534 41.667 4.38 0.00 34.00 2.24
6872 7921 4.401519 AGAAAATCAGCATCCACTTCCATG 59.598 41.667 0.00 0.00 0.00 3.66
7028 8077 3.290308 ACAGCTGAGAGTTCTGTAACG 57.710 47.619 23.35 0.00 39.08 3.18
7061 8110 5.360144 TCTGTACTCATTAAGGGTAGTGCTC 59.640 44.000 0.00 0.00 0.00 4.26
7375 8425 3.857549 TCAGTCAGTGTCTCAGCATAC 57.142 47.619 0.00 0.00 0.00 2.39
7439 8490 8.299570 GTGATGAGAAATCCGGCAATATTAAAT 58.700 33.333 0.00 0.00 0.00 1.40
7501 8552 3.604582 ACAAGAAATAGCAGTCAGAGGC 58.395 45.455 0.00 0.00 0.00 4.70
7540 8591 7.798596 AAAGAGGTTGCACAGATATAGATTG 57.201 36.000 0.00 0.00 0.00 2.67
7683 8737 1.142870 ACAGCAAAGCACACCCTTCTA 59.857 47.619 0.00 0.00 0.00 2.10
7685 8739 0.746659 AACAGCAAAGCACACCCTTC 59.253 50.000 0.00 0.00 0.00 3.46
7772 8826 4.622701 AGTTGTTCACTCTGTTTCTTGC 57.377 40.909 0.00 0.00 0.00 4.01
8093 9152 7.597288 ATTTACAACAGGCTTTAAGGTTTCT 57.403 32.000 0.00 0.00 0.00 2.52
8094 9153 9.923143 ATAATTTACAACAGGCTTTAAGGTTTC 57.077 29.630 0.00 0.00 0.00 2.78
8240 9303 5.103643 ACCTGTCATCATCTACTACCCTGTA 60.104 44.000 0.00 0.00 0.00 2.74
8305 9369 4.383118 CGTCACCATATCTCTTGAAAGGGT 60.383 45.833 0.00 0.00 0.00 4.34
8308 9372 4.437239 AGCGTCACCATATCTCTTGAAAG 58.563 43.478 0.00 0.00 0.00 2.62
8350 9416 6.068010 ACCCACACATTTCATAGAACTGAAA 58.932 36.000 4.43 2.11 46.13 2.69
8356 9422 5.630121 AGACAACCCACACATTTCATAGAA 58.370 37.500 0.00 0.00 0.00 2.10
8380 9450 7.066284 CCAGCACTATAATGAGCAGTAAAAAGT 59.934 37.037 0.00 0.00 0.00 2.66
8413 9483 6.363357 GCATCACTAGAATCAACAAAAACCAC 59.637 38.462 0.00 0.00 0.00 4.16
8557 9628 2.799126 TGGTGTATGGCCCAACTAAG 57.201 50.000 0.00 0.00 0.00 2.18
8573 9644 2.819984 AAGCAACGCGGGATGATGGT 62.820 55.000 12.47 6.14 0.00 3.55
8583 9654 0.163788 CTGTCAACCTAAGCAACGCG 59.836 55.000 3.53 3.53 0.00 6.01
8624 9696 6.709846 CCCATTTTCCTTTGCAACTGATAAAA 59.290 34.615 0.00 2.94 0.00 1.52
8661 9733 4.045781 ATCATGCGCCCCACACCA 62.046 61.111 4.18 0.00 0.00 4.17
8717 9791 9.270640 AGCATCATCTCTTATCTTATGAACAAC 57.729 33.333 0.00 0.00 32.47 3.32


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

AutoCloner maintained by Alex Coulton.