Multiple sequence alignment - TraesCS1D01G187300

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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 TraesCS1D01G187300 chr1D 100.000 6279 0 0 1 6279 258582761 258576483 0.000000e+00 11596.0
1 TraesCS1D01G187300 chr1A 94.938 3793 106 38 467 4230 342386836 342390571 0.000000e+00 5862.0
2 TraesCS1D01G187300 chr1A 96.035 2068 51 8 4229 6279 342390614 342392667 0.000000e+00 3336.0
3 TraesCS1D01G187300 chr1A 92.488 426 17 12 1 423 342386267 342386680 4.190000e-166 595.0
4 TraesCS1D01G187300 chr1B 93.950 2281 84 24 569 2841 354228022 354230256 0.000000e+00 3398.0
5 TraesCS1D01G187300 chr1B 97.059 1156 30 3 4229 5381 354232097 354233251 0.000000e+00 1943.0
6 TraesCS1D01G187300 chr1B 95.952 1087 32 5 2829 3907 354230321 354231403 0.000000e+00 1753.0
7 TraesCS1D01G187300 chr1B 95.017 883 26 8 5375 6240 354233407 354234288 0.000000e+00 1371.0
8 TraesCS1D01G187300 chr1B 90.127 314 12 11 1 309 354227254 354227553 2.120000e-104 390.0
9 TraesCS1D01G187300 chr1B 92.969 256 7 2 3975 4230 354231810 354232054 4.630000e-96 363.0
10 TraesCS1D01G187300 chr1B 94.495 109 3 1 464 572 354227837 354227942 1.400000e-36 165.0
11 TraesCS1D01G187300 chr1B 96.471 85 2 1 3905 3989 354231563 354231646 8.490000e-29 139.0
12 TraesCS1D01G187300 chr1B 100.000 43 0 0 6237 6279 354234396 354234438 5.220000e-11 80.5
13 TraesCS1D01G187300 chr2A 100.000 28 0 0 5357 5384 318377907 318377880 1.100000e-02 52.8


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 TraesCS1D01G187300 chr1D 258576483 258582761 6278 True 11596.000000 11596 100.000000 1 6279 1 chr1D.!!$R1 6278
1 TraesCS1D01G187300 chr1A 342386267 342392667 6400 False 3264.333333 5862 94.487000 1 6279 3 chr1A.!!$F1 6278
2 TraesCS1D01G187300 chr1B 354227254 354234438 7184 False 1066.944444 3398 95.115556 1 6279 9 chr1B.!!$F1 6278

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
687 1096 0.107268 TGGCTCATCCATCCATCACG 59.893 55.000 0.00 0.0 40.72 4.35 F
689 1098 0.250209 GCTCATCCATCCATCACGCT 60.250 55.000 0.00 0.0 0.00 5.07 F
822 1233 0.752658 CTATGCTCATGTGGTCCCGA 59.247 55.000 0.00 0.0 0.00 5.14 F
1990 2418 0.746659 GCTGCTTCTGTTTGGGTTGT 59.253 50.000 0.00 0.0 0.00 3.32 F
2609 3039 1.451936 GGGCAGTCTGGAGTGTTGT 59.548 57.895 1.14 0.0 34.32 3.32 F
3368 3875 1.949525 TGCCAAAGTCTGTTCTTGAGC 59.050 47.619 0.00 0.0 0.00 4.26 F
4532 5432 1.202110 GCACTCACATTCTGCAATCCG 60.202 52.381 0.00 0.0 0.00 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1695 2122 0.172352 GAGCAGGAGACCACGAGAAG 59.828 60.000 0.0 0.0 0.00 2.85 R
1990 2418 0.250989 CGCCCTGGTAACCTTCCAAA 60.251 55.000 0.0 0.0 34.35 3.28 R
2155 2583 1.153369 GGACTGCTGCCGCTATTCA 60.153 57.895 0.7 0.0 36.97 2.57 R
2857 3364 0.246635 TCAAGTAGAGCCGGTCAAGC 59.753 55.000 1.9 0.0 0.00 4.01 R
4067 4923 0.105964 TGATCGCCCCAACTTATCGG 59.894 55.000 0.0 0.0 0.00 4.18 R
5079 5979 1.948834 CAGGCTCATGACACAACACAA 59.051 47.619 0.0 0.0 0.00 3.33 R
5610 6677 0.689080 AGACAGGATCATCGGCACCT 60.689 55.000 0.0 0.0 0.00 4.00 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
205 208 2.304470 TGGACATCATCGGAGGACAAAA 59.696 45.455 0.00 0.00 0.00 2.44
245 248 3.126879 TGATTTGCGAGCGCCCAG 61.127 61.111 12.70 0.00 41.09 4.45
275 482 0.396811 GCCCGCCTACCATATTGACT 59.603 55.000 0.00 0.00 0.00 3.41
291 498 9.090692 CCATATTGACTCCATTTTTGTTTCATC 57.909 33.333 0.00 0.00 0.00 2.92
352 559 5.755813 AGTGTATAATACAAGTAGGACGCG 58.244 41.667 3.53 3.53 40.93 6.01
353 560 4.380974 GTGTATAATACAAGTAGGACGCGC 59.619 45.833 5.73 0.00 40.93 6.86
447 738 7.972277 ACAAGTGTATAATACAACTAGGACACG 59.028 37.037 0.00 0.00 40.93 4.49
448 739 7.636150 AGTGTATAATACAACTAGGACACGT 57.364 36.000 0.00 0.00 40.93 4.49
455 746 2.367567 ACAACTAGGACACGTTGGACAT 59.632 45.455 7.02 0.00 43.52 3.06
465 756 3.070748 CACGTTGGACATCACCATACAA 58.929 45.455 0.00 0.00 39.82 2.41
632 1036 1.519455 CGGGCTCACTAAAGGCGAG 60.519 63.158 0.00 0.00 42.50 5.03
643 1047 2.140065 AAAGGCGAGCAAAAAGAAGC 57.860 45.000 0.00 0.00 0.00 3.86
663 1072 6.589907 AGAAGCGAAAAACAACAACTTGAAAT 59.410 30.769 0.00 0.00 0.00 2.17
664 1073 6.331170 AGCGAAAAACAACAACTTGAAATC 57.669 33.333 0.00 0.00 0.00 2.17
665 1074 6.099341 AGCGAAAAACAACAACTTGAAATCT 58.901 32.000 0.00 0.00 0.00 2.40
666 1075 6.253512 AGCGAAAAACAACAACTTGAAATCTC 59.746 34.615 0.00 0.00 0.00 2.75
667 1076 6.618198 CGAAAAACAACAACTTGAAATCTCG 58.382 36.000 0.00 0.00 0.00 4.04
668 1077 6.250527 CGAAAAACAACAACTTGAAATCTCGT 59.749 34.615 0.00 0.00 0.00 4.18
669 1078 6.869421 AAAACAACAACTTGAAATCTCGTG 57.131 33.333 0.00 0.00 0.00 4.35
670 1079 4.552166 ACAACAACTTGAAATCTCGTGG 57.448 40.909 0.00 0.00 0.00 4.94
671 1080 3.243068 ACAACAACTTGAAATCTCGTGGC 60.243 43.478 0.00 0.00 0.00 5.01
672 1081 2.851195 ACAACTTGAAATCTCGTGGCT 58.149 42.857 0.00 0.00 0.00 4.75
673 1082 2.808543 ACAACTTGAAATCTCGTGGCTC 59.191 45.455 0.00 0.00 0.00 4.70
674 1083 2.807967 CAACTTGAAATCTCGTGGCTCA 59.192 45.455 0.00 0.00 0.00 4.26
675 1084 3.340814 ACTTGAAATCTCGTGGCTCAT 57.659 42.857 0.00 0.00 0.00 2.90
676 1085 3.265791 ACTTGAAATCTCGTGGCTCATC 58.734 45.455 0.00 0.00 0.00 2.92
677 1086 2.315925 TGAAATCTCGTGGCTCATCC 57.684 50.000 0.00 0.00 0.00 3.51
678 1087 1.554617 TGAAATCTCGTGGCTCATCCA 59.445 47.619 0.00 0.00 44.18 3.41
687 1096 0.107268 TGGCTCATCCATCCATCACG 59.893 55.000 0.00 0.00 40.72 4.35
688 1097 1.233285 GGCTCATCCATCCATCACGC 61.233 60.000 0.00 0.00 34.01 5.34
689 1098 0.250209 GCTCATCCATCCATCACGCT 60.250 55.000 0.00 0.00 0.00 5.07
690 1099 1.813092 GCTCATCCATCCATCACGCTT 60.813 52.381 0.00 0.00 0.00 4.68
709 1119 3.934068 CTTCATCCAAGCAAGCCAAAAT 58.066 40.909 0.00 0.00 0.00 1.82
752 1162 4.589908 ACCATCATCTAAACCAACTCCAC 58.410 43.478 0.00 0.00 0.00 4.02
753 1163 4.289672 ACCATCATCTAAACCAACTCCACT 59.710 41.667 0.00 0.00 0.00 4.00
754 1164 4.878397 CCATCATCTAAACCAACTCCACTC 59.122 45.833 0.00 0.00 0.00 3.51
755 1165 4.553330 TCATCTAAACCAACTCCACTCC 57.447 45.455 0.00 0.00 0.00 3.85
756 1166 3.907474 TCATCTAAACCAACTCCACTCCA 59.093 43.478 0.00 0.00 0.00 3.86
807 1218 3.584406 AGCTGCCGCTACTAATCTATG 57.416 47.619 0.00 0.00 46.79 2.23
822 1233 0.752658 CTATGCTCATGTGGTCCCGA 59.247 55.000 0.00 0.00 0.00 5.14
844 1255 2.199291 GCACATGAGCCATGCTAAAC 57.801 50.000 13.19 0.00 44.80 2.01
848 1259 3.064958 CACATGAGCCATGCTAAACAGAG 59.935 47.826 13.19 0.00 44.80 3.35
851 1262 5.163269 ACATGAGCCATGCTAAACAGAGATA 60.163 40.000 13.19 0.00 44.80 1.98
853 1264 5.933617 TGAGCCATGCTAAACAGAGATATT 58.066 37.500 0.00 0.00 39.88 1.28
857 1268 9.658799 GAGCCATGCTAAACAGAGATATTTATA 57.341 33.333 0.00 0.00 39.88 0.98
1390 1813 2.411904 GCTCTCCCTTGCGATTCTATG 58.588 52.381 0.00 0.00 0.00 2.23
1391 1814 2.411904 CTCTCCCTTGCGATTCTATGC 58.588 52.381 0.00 0.00 0.00 3.14
1428 1854 4.142469 GGTTTCCCGTTCGATTTGATTCAT 60.142 41.667 0.00 0.00 0.00 2.57
1434 1860 4.260375 CCGTTCGATTTGATTCATGGACTC 60.260 45.833 0.00 0.00 0.00 3.36
1535 1962 5.533154 CAGGTAGATCTTTCTGTCCGAGTAT 59.467 44.000 0.00 0.00 34.55 2.12
1540 1967 6.744112 AGATCTTTCTGTCCGAGTATCATTC 58.256 40.000 0.00 0.00 33.17 2.67
1555 1982 7.503902 CGAGTATCATTCCATGGATAGGATAGA 59.496 40.741 17.06 6.95 32.18 1.98
1556 1983 9.378504 GAGTATCATTCCATGGATAGGATAGAT 57.621 37.037 17.06 13.23 34.99 1.98
1605 2032 6.699204 AGATCTGTCATTTATACGTGCTGAAG 59.301 38.462 0.00 0.00 0.00 3.02
1680 2107 4.680440 GCAATATCGGGACAAGCCAAAAAT 60.680 41.667 0.00 0.00 38.95 1.82
1696 2123 6.622833 CCAAAAATTGAATTCTTGTTGGCT 57.377 33.333 13.62 0.00 0.00 4.75
1713 2140 1.882989 GCTTCTCGTGGTCTCCTGCT 61.883 60.000 0.00 0.00 0.00 4.24
1775 2202 6.405286 CGATCAGTCTCTACAATCCTTTCTGT 60.405 42.308 0.00 0.00 0.00 3.41
1778 2205 6.267699 TCAGTCTCTACAATCCTTTCTGTGAA 59.732 38.462 0.00 0.00 0.00 3.18
1990 2418 0.746659 GCTGCTTCTGTTTGGGTTGT 59.253 50.000 0.00 0.00 0.00 3.32
2155 2583 2.045524 AGATGGCGGTGATTCTCAGAT 58.954 47.619 0.00 0.00 0.00 2.90
2426 2854 2.104622 TGTCTCAGCTGTCACATTTCCA 59.895 45.455 14.67 0.00 0.00 3.53
2429 2857 4.331168 GTCTCAGCTGTCACATTTCCATAC 59.669 45.833 14.67 0.00 0.00 2.39
2506 2934 9.790344 ATGCAGTAGATAATGCTATTCTTTCTT 57.210 29.630 12.82 0.00 46.39 2.52
2609 3039 1.451936 GGGCAGTCTGGAGTGTTGT 59.548 57.895 1.14 0.00 34.32 3.32
2808 3238 6.812656 TGCTCAATTATTAATGCCAAGTTGTG 59.187 34.615 1.45 0.00 0.00 3.33
2832 3339 8.643752 GTGTTTCAAAATATTTATTGACCGTGG 58.356 33.333 0.01 0.00 35.42 4.94
2836 3343 6.977502 TCAAAATATTTATTGACCGTGGCATG 59.022 34.615 0.01 0.00 30.94 4.06
3096 3603 3.244457 GGTTAGTGCCTAACAACTCACCT 60.244 47.826 19.97 0.00 45.57 4.00
3108 3615 4.196971 ACAACTCACCTTACACCACTTTC 58.803 43.478 0.00 0.00 0.00 2.62
3167 3674 9.349145 ACAACTGTTACTTTTATGAACAACAAC 57.651 29.630 0.00 0.00 32.94 3.32
3196 3703 5.759963 CTGCTTGATTTCTGAATCTATGCC 58.240 41.667 0.00 0.00 41.80 4.40
3287 3794 6.905736 TCAATTGGGCCAGTTTATGTATCTA 58.094 36.000 12.09 0.00 0.00 1.98
3368 3875 1.949525 TGCCAAAGTCTGTTCTTGAGC 59.050 47.619 0.00 0.00 0.00 4.26
3375 3882 2.435805 AGTCTGTTCTTGAGCTGGAACA 59.564 45.455 18.93 18.93 46.08 3.18
3423 3933 9.173939 CTTATCTTGTGTTTTGTCATCTTCAAC 57.826 33.333 0.00 0.00 0.00 3.18
3493 4003 6.016276 TGCCTTTCTTGACTTATTTCACCTTC 60.016 38.462 0.00 0.00 0.00 3.46
3532 4042 6.512415 GCTGTTCAGACACCATATAATGCTTC 60.512 42.308 3.84 0.00 0.00 3.86
3573 4083 9.204337 TCCATGTTCAATATTCAAAATGAGGAT 57.796 29.630 3.92 0.00 0.00 3.24
4067 4923 6.721321 TCTTTTATCACAAACTCGAAACACC 58.279 36.000 0.00 0.00 0.00 4.16
4135 4991 7.019388 AGGAGGCTCATATTTCTGTATCCTTA 58.981 38.462 17.69 0.00 29.21 2.69
4182 5038 5.017294 TGTGAATTCCCTTGTTTCAAACC 57.983 39.130 2.27 0.00 31.66 3.27
4196 5052 8.948631 TTGTTTCAAACCATGCTAATAAACAA 57.051 26.923 16.18 16.18 37.90 2.83
4235 5135 6.334989 ACATGAAACCGAATACGAAGTCATA 58.665 36.000 0.00 0.00 43.93 2.15
4298 5198 4.134563 ACAGTACACCACCAGATGAAAAC 58.865 43.478 0.00 0.00 0.00 2.43
4320 5220 3.616219 TGCAATGGTGGTATCCTAACAC 58.384 45.455 0.00 0.00 45.54 3.32
4475 5375 7.558161 TGGAATAATGTCATTCACTAAGCTG 57.442 36.000 0.07 0.00 36.77 4.24
4532 5432 1.202110 GCACTCACATTCTGCAATCCG 60.202 52.381 0.00 0.00 0.00 4.18
4742 5642 1.900351 CTCCGAGGTGCAATCTCCA 59.100 57.895 11.34 0.53 0.00 3.86
4984 5884 2.618709 CGGCTGTGTTTCTTTTTCTCCT 59.381 45.455 0.00 0.00 0.00 3.69
5079 5979 9.587772 GTATTGTAACATTCGGCTCATATCTAT 57.412 33.333 0.00 0.00 0.00 1.98
5096 5998 5.808042 ATCTATTGTGTTGTGTCATGAGC 57.192 39.130 0.00 0.00 0.00 4.26
5268 6170 7.326454 CCCCTGATGATATATAGATTATGCCG 58.674 42.308 0.00 0.00 0.00 5.69
5271 6173 7.544915 CCTGATGATATATAGATTATGCCGCAG 59.455 40.741 0.00 0.00 0.00 5.18
5347 6249 4.156455 TGCATTTCCTCCCTTCACTATC 57.844 45.455 0.00 0.00 0.00 2.08
5353 6256 6.500589 TTTCCTCCCTTCACTATCATAAGG 57.499 41.667 0.00 0.00 39.63 2.69
5393 6458 3.782046 ACGGACTACATACATGCTGAAC 58.218 45.455 3.07 0.00 0.00 3.18
5418 6485 3.728718 GTGAACAAACACACTAAATGCGG 59.271 43.478 0.00 0.00 40.11 5.69
5477 6544 7.351166 TCTTATAATTTTGGAACGGAGGGAAT 58.649 34.615 0.00 0.00 0.00 3.01
5484 6551 4.417426 TGGAACGGAGGGAATAATCTTC 57.583 45.455 0.00 0.00 0.00 2.87
5667 6734 3.260100 CAGGAAGTGCCCCACCCT 61.260 66.667 0.00 0.00 37.37 4.34
5934 7017 1.067212 GCATCAGGGTCGTACGAGATT 59.933 52.381 20.18 3.73 0.00 2.40
6035 7118 2.856988 AGGGCGTTGGGGAAGGAA 60.857 61.111 0.00 0.00 0.00 3.36
6073 7156 4.052518 GGAGGTGGGCAGCCATGT 62.053 66.667 15.19 0.00 0.00 3.21
6116 7199 2.106131 CACGGCGCATAGTAGGCA 59.894 61.111 10.83 0.00 0.00 4.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 32 2.271800 CTATTGAACAGGTCGCAGTCC 58.728 52.381 0.00 0.00 35.48 3.85
51 54 3.935818 AGCTCTACTGCTCTAGGTGTA 57.064 47.619 0.00 0.00 39.34 2.90
57 60 8.379331 TGATTTATCTCTAGCTCTACTGCTCTA 58.621 37.037 0.00 0.00 42.97 2.43
58 61 7.174946 GTGATTTATCTCTAGCTCTACTGCTCT 59.825 40.741 0.00 0.00 42.97 4.09
59 62 7.040755 TGTGATTTATCTCTAGCTCTACTGCTC 60.041 40.741 0.00 0.00 42.97 4.26
60 63 6.775142 TGTGATTTATCTCTAGCTCTACTGCT 59.225 38.462 0.00 0.00 46.11 4.24
61 64 6.976088 TGTGATTTATCTCTAGCTCTACTGC 58.024 40.000 0.00 0.00 0.00 4.40
62 65 9.409312 CAATGTGATTTATCTCTAGCTCTACTG 57.591 37.037 0.00 0.00 0.00 2.74
63 66 8.584157 CCAATGTGATTTATCTCTAGCTCTACT 58.416 37.037 0.00 0.00 0.00 2.57
64 67 7.816995 CCCAATGTGATTTATCTCTAGCTCTAC 59.183 40.741 0.00 0.00 0.00 2.59
205 208 1.339247 TGTTTTGATATGGACGGCGGT 60.339 47.619 13.24 0.00 0.00 5.68
331 538 4.036616 TGCGCGTCCTACTTGTATTATACA 59.963 41.667 8.43 0.29 36.79 2.29
352 559 1.079336 GGTAACTCGGGTGAGGTGC 60.079 63.158 0.00 0.00 43.67 5.01
447 738 5.880332 ACATACTTGTATGGTGATGTCCAAC 59.120 40.000 20.56 0.00 41.09 3.77
448 739 6.061022 ACATACTTGTATGGTGATGTCCAA 57.939 37.500 20.56 0.00 41.09 3.53
548 869 5.003804 AGTAACCACTAATTGACCTGCTTG 58.996 41.667 0.00 0.00 31.45 4.01
549 870 5.242795 AGTAACCACTAATTGACCTGCTT 57.757 39.130 0.00 0.00 31.45 3.91
550 871 4.910458 AGTAACCACTAATTGACCTGCT 57.090 40.909 0.00 0.00 31.45 4.24
632 1036 4.952097 TGTTGTTTTTCGCTTCTTTTTGC 58.048 34.783 0.00 0.00 0.00 3.68
643 1047 6.250527 ACGAGATTTCAAGTTGTTGTTTTTCG 59.749 34.615 2.11 7.79 34.98 3.46
669 1078 1.233285 GCGTGATGGATGGATGAGCC 61.233 60.000 0.00 0.00 37.10 4.70
670 1079 0.250209 AGCGTGATGGATGGATGAGC 60.250 55.000 0.00 0.00 0.00 4.26
671 1080 2.141517 GAAGCGTGATGGATGGATGAG 58.858 52.381 0.00 0.00 0.00 2.90
672 1081 1.485895 TGAAGCGTGATGGATGGATGA 59.514 47.619 0.00 0.00 0.00 2.92
673 1082 1.957668 TGAAGCGTGATGGATGGATG 58.042 50.000 0.00 0.00 0.00 3.51
674 1083 2.551721 GGATGAAGCGTGATGGATGGAT 60.552 50.000 0.00 0.00 0.00 3.41
675 1084 1.202687 GGATGAAGCGTGATGGATGGA 60.203 52.381 0.00 0.00 0.00 3.41
676 1085 1.233019 GGATGAAGCGTGATGGATGG 58.767 55.000 0.00 0.00 0.00 3.51
677 1086 1.957668 TGGATGAAGCGTGATGGATG 58.042 50.000 0.00 0.00 0.00 3.51
678 1087 2.569059 CTTGGATGAAGCGTGATGGAT 58.431 47.619 0.00 0.00 0.00 3.41
679 1088 2.028420 CTTGGATGAAGCGTGATGGA 57.972 50.000 0.00 0.00 0.00 3.41
688 1097 3.389925 TTTTGGCTTGCTTGGATGAAG 57.610 42.857 0.00 0.00 34.41 3.02
689 1098 3.071312 ACATTTTGGCTTGCTTGGATGAA 59.929 39.130 0.00 0.00 0.00 2.57
690 1099 2.633967 ACATTTTGGCTTGCTTGGATGA 59.366 40.909 0.00 0.00 0.00 2.92
709 1119 1.040339 ACGGGCCAAGCTTTTTCACA 61.040 50.000 4.39 0.00 0.00 3.58
752 1162 3.599730 TGTGCTTAGTGACTGATGGAG 57.400 47.619 0.00 0.00 0.00 3.86
753 1163 4.020307 TGATTGTGCTTAGTGACTGATGGA 60.020 41.667 0.00 0.00 0.00 3.41
754 1164 4.093998 GTGATTGTGCTTAGTGACTGATGG 59.906 45.833 0.00 0.00 0.00 3.51
755 1165 4.692155 TGTGATTGTGCTTAGTGACTGATG 59.308 41.667 0.00 0.00 0.00 3.07
756 1166 4.692625 GTGTGATTGTGCTTAGTGACTGAT 59.307 41.667 0.00 0.00 0.00 2.90
807 1218 2.509336 CGTCGGGACCACATGAGC 60.509 66.667 0.00 0.00 0.00 4.26
894 1314 7.668469 TCATCCTCGCTTTATATACTCTTGGTA 59.332 37.037 0.00 0.00 34.62 3.25
1540 1967 7.454380 GGAGATTCCTATCTATCCTATCCATGG 59.546 44.444 4.97 4.97 41.23 3.66
1615 2042 1.731969 ACTAGAAACACGACGCGGC 60.732 57.895 12.47 6.41 0.00 6.53
1680 2107 3.882888 ACGAGAAGCCAACAAGAATTCAA 59.117 39.130 8.44 0.00 0.00 2.69
1695 2122 0.172352 GAGCAGGAGACCACGAGAAG 59.828 60.000 0.00 0.00 0.00 2.85
1696 2123 0.251386 AGAGCAGGAGACCACGAGAA 60.251 55.000 0.00 0.00 0.00 2.87
1775 2202 7.558161 ACAATCAGCTAAATGATTCGATTCA 57.442 32.000 12.05 12.05 44.68 2.57
1778 2205 9.079833 CAAAAACAATCAGCTAAATGATTCGAT 57.920 29.630 0.00 0.00 44.68 3.59
1934 2361 1.066071 GTCTCAGGGCAGAAAGGTACC 60.066 57.143 2.73 2.73 0.00 3.34
1990 2418 0.250989 CGCCCTGGTAACCTTCCAAA 60.251 55.000 0.00 0.00 34.35 3.28
2155 2583 1.153369 GGACTGCTGCCGCTATTCA 60.153 57.895 0.70 0.00 36.97 2.57
2426 2854 9.273016 CCTATCAAATTTGATGTAGTTCCGTAT 57.727 33.333 33.94 13.73 46.68 3.06
2429 2857 6.430451 GCCTATCAAATTTGATGTAGTTCCG 58.570 40.000 33.94 17.20 46.68 4.30
2507 2935 9.768662 TTGAGAACTCGTTTTATTTTAGGTACT 57.231 29.630 0.00 0.00 46.37 2.73
2609 3039 7.632898 GCTCCTTTATGACAGTAACATACCTGA 60.633 40.741 0.00 0.00 31.26 3.86
2808 3238 7.329717 TGCCACGGTCAATAAATATTTTGAAAC 59.670 33.333 5.91 1.82 33.90 2.78
2857 3364 0.246635 TCAAGTAGAGCCGGTCAAGC 59.753 55.000 1.90 0.00 0.00 4.01
3167 3674 2.071540 TCAGAAATCAAGCAGCACTCG 58.928 47.619 0.00 0.00 0.00 4.18
3196 3703 4.864247 CACCCTTGTGTGTTTTCTCAAAAG 59.136 41.667 0.00 0.00 37.98 2.27
3287 3794 1.895131 AGAAACCATTGCAATTCCGCT 59.105 42.857 9.83 1.08 0.00 5.52
3326 3833 0.403655 TGCCTTGTTCAGGTATGCCA 59.596 50.000 1.54 0.00 46.07 4.92
3368 3875 7.798596 AATATTTGCTCTATGTCTGTTCCAG 57.201 36.000 0.00 0.00 0.00 3.86
3493 4003 2.480037 TGAACAGCAAGCACTTGTATCG 59.520 45.455 11.77 1.67 42.31 2.92
3532 4042 5.353956 TGAACATGGAAGTGTCGATAATTGG 59.646 40.000 0.00 0.00 0.00 3.16
3573 4083 1.065401 CAAAAGAGCCGACAAGTGCAA 59.935 47.619 0.00 0.00 0.00 4.08
3835 4350 4.974645 TTGGATTAGACAGGACTGTGTT 57.025 40.909 10.08 0.79 45.05 3.32
3922 4599 2.094894 CGAAGATGACTCATTGGTGCAC 59.905 50.000 8.80 8.80 0.00 4.57
4067 4923 0.105964 TGATCGCCCCAACTTATCGG 59.894 55.000 0.00 0.00 0.00 4.18
4135 4991 0.178068 GTGGCATCATACGACCCTGT 59.822 55.000 0.00 0.00 0.00 4.00
4182 5038 9.135843 CTGCCATTATCATTGTTTATTAGCATG 57.864 33.333 0.00 0.00 0.00 4.06
4196 5052 6.576185 GGTTTCATGTTTCTGCCATTATCAT 58.424 36.000 0.00 0.00 0.00 2.45
4298 5198 3.627577 GTGTTAGGATACCACCATTGCAG 59.372 47.826 0.00 0.00 37.17 4.41
4475 5375 3.858868 TTCTGTCGGTGTGCTCGGC 62.859 63.158 0.00 0.00 0.00 5.54
4532 5432 4.165779 CAGAACGGGTATTCAAAATGCAC 58.834 43.478 0.00 0.00 0.00 4.57
4640 5540 2.114670 CGACGGAAATGGGCTGCAT 61.115 57.895 0.50 0.00 0.00 3.96
5079 5979 1.948834 CAGGCTCATGACACAACACAA 59.051 47.619 0.00 0.00 0.00 3.33
5096 5998 5.048782 GCTATGATCTAGACTCACTCACAGG 60.049 48.000 0.00 0.00 0.00 4.00
5268 6170 4.622701 ACAAACAAACTGAAGAGACTGC 57.377 40.909 0.00 0.00 0.00 4.40
5271 6173 6.663944 ACTGTACAAACAAACTGAAGAGAC 57.336 37.500 0.00 0.00 34.49 3.36
5393 6458 4.670621 GCATTTAGTGTGTTTGTTCACTCG 59.329 41.667 1.08 0.00 42.77 4.18
5477 6544 7.458409 AGCAATGCTGAAGAAAAGAAGATTA 57.542 32.000 7.07 0.00 37.57 1.75
5484 6551 4.516365 AGGAAGCAATGCTGAAGAAAAG 57.484 40.909 9.14 0.00 39.62 2.27
5610 6677 0.689080 AGACAGGATCATCGGCACCT 60.689 55.000 0.00 0.00 0.00 4.00
5667 6734 4.129737 GCTACCACGAGCTCGCCA 62.130 66.667 34.83 16.50 44.43 5.69
5934 7017 1.565390 CCTCAGCTCCCCCATTGTCA 61.565 60.000 0.00 0.00 0.00 3.58
5984 7067 1.692042 CCTCATGGCCCTCTCCACT 60.692 63.158 0.00 0.00 39.25 4.00
6107 7190 1.067582 GCTCCGCGTTGCCTACTAT 59.932 57.895 4.92 0.00 0.00 2.12


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

AutoCloner maintained by Alex Coulton.