Multiple sequence alignment - TraesCS1A01G084500

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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 TraesCS1A01G084500 chr1A 100.000 3258 0 0 1 3258 70701104 70704361 0.000000e+00 6017
1 TraesCS1A01G084500 chr1D 92.727 2585 105 27 709 3258 70345774 70348310 0.000000e+00 3655
2 TraesCS1A01G084500 chr1D 92.699 452 18 5 122 565 70345325 70345769 3.550000e-179 638
3 TraesCS1A01G084500 chr1B 93.050 2446 94 29 665 3079 111669224 111671624 0.000000e+00 3506
4 TraesCS1A01G084500 chr1B 87.478 575 27 16 1 567 111668308 111668845 3.570000e-174 621
5 TraesCS1A01G084500 chr1B 93.407 182 11 1 3078 3258 111671786 111671967 5.360000e-68 268


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 TraesCS1A01G084500 chr1A 70701104 70704361 3257 False 6017.0 6017 100.000000 1 3258 1 chr1A.!!$F1 3257
1 TraesCS1A01G084500 chr1D 70345325 70348310 2985 False 2146.5 3655 92.713000 122 3258 2 chr1D.!!$F1 3136
2 TraesCS1A01G084500 chr1B 111668308 111671967 3659 False 1465.0 3506 91.311667 1 3258 3 chr1B.!!$F1 3257

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
588 909 0.02811 GCGTCCGAGGAAAATGCATC 59.972 55.0 0.0 0.0 0.0 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2583 2967 0.108585 TTCTCAACCAGAGCACCCAC 59.891 55.0 0.0 0.0 44.35 4.61 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
22 23 2.556189 TGCGCCTTGTGTGTGATTAATT 59.444 40.909 4.18 0.00 0.00 1.40
28 29 4.853196 CCTTGTGTGTGATTAATTGAAGCG 59.147 41.667 0.00 0.00 0.00 4.68
30 31 6.348132 CCTTGTGTGTGATTAATTGAAGCGTA 60.348 38.462 0.00 0.00 0.00 4.42
35 36 7.798516 GTGTGTGATTAATTGAAGCGTATATGG 59.201 37.037 0.00 0.00 0.00 2.74
60 61 4.459685 AGCAGAAGATGTACTCTACGTGTT 59.540 41.667 0.00 0.00 34.34 3.32
96 97 1.068281 CCTGATGACGGATCACCTGAG 59.932 57.143 0.00 0.00 37.79 3.35
97 98 1.068281 CTGATGACGGATCACCTGAGG 59.932 57.143 0.00 0.00 37.79 3.86
98 99 0.390860 GATGACGGATCACCTGAGGG 59.609 60.000 2.38 0.00 37.79 4.30
99 100 1.050988 ATGACGGATCACCTGAGGGG 61.051 60.000 2.38 0.00 37.79 4.79
100 101 3.083997 ACGGATCACCTGAGGGGC 61.084 66.667 2.38 0.00 39.10 5.80
101 102 4.227134 CGGATCACCTGAGGGGCG 62.227 72.222 2.38 0.00 39.10 6.13
102 103 4.554036 GGATCACCTGAGGGGCGC 62.554 72.222 2.38 0.00 39.10 6.53
103 104 4.899239 GATCACCTGAGGGGCGCG 62.899 72.222 2.38 0.00 39.10 6.86
152 153 1.221414 GTGCGTCTGAACAGAGCTTT 58.779 50.000 18.76 0.00 38.27 3.51
153 154 1.193426 GTGCGTCTGAACAGAGCTTTC 59.807 52.381 18.76 0.00 38.27 2.62
343 351 1.243902 TTGGCTCCCGTTTCACATTC 58.756 50.000 0.00 0.00 0.00 2.67
362 374 4.041917 GGCCGCCATGTGTGTGTG 62.042 66.667 3.91 0.00 0.00 3.82
363 375 4.041917 GCCGCCATGTGTGTGTGG 62.042 66.667 0.00 0.00 38.55 4.17
364 376 3.364441 CCGCCATGTGTGTGTGGG 61.364 66.667 0.00 0.00 36.00 4.61
365 377 2.281414 CGCCATGTGTGTGTGGGA 60.281 61.111 0.00 0.00 36.00 4.37
397 409 2.357396 TGCGTCGCACATGCTTCT 60.357 55.556 17.58 0.00 37.96 2.85
408 420 2.807967 CACATGCTTCTCGGAGACAAAA 59.192 45.455 7.33 0.00 0.00 2.44
409 421 3.070018 ACATGCTTCTCGGAGACAAAAG 58.930 45.455 7.33 3.63 0.00 2.27
410 422 1.512926 TGCTTCTCGGAGACAAAAGC 58.487 50.000 18.19 18.19 40.03 3.51
511 523 0.373716 CTTGCACCGCGTTATCTTCC 59.626 55.000 4.92 0.00 0.00 3.46
525 537 5.467063 CGTTATCTTCCCTCCTTAATCAAGC 59.533 44.000 0.00 0.00 0.00 4.01
546 558 3.442625 GCGGCTTGGTTAACCTTAAAGAT 59.557 43.478 24.78 0.00 36.82 2.40
570 582 6.966021 TGAGTAAATTACAAGAAACACTGGC 58.034 36.000 5.89 0.00 0.00 4.85
571 583 5.997385 AGTAAATTACAAGAAACACTGGCG 58.003 37.500 5.89 0.00 0.00 5.69
574 586 1.873698 TACAAGAAACACTGGCGTCC 58.126 50.000 0.00 0.00 0.00 4.79
576 588 0.878523 CAAGAAACACTGGCGTCCGA 60.879 55.000 0.00 0.00 0.00 4.55
578 590 2.027625 GAAACACTGGCGTCCGAGG 61.028 63.158 0.00 0.00 0.00 4.63
588 909 0.028110 GCGTCCGAGGAAAATGCATC 59.972 55.000 0.00 0.00 0.00 3.91
608 929 2.833943 TCGCATGCCCATAGATAGATGT 59.166 45.455 13.15 0.00 0.00 3.06
615 936 5.368145 TGCCCATAGATAGATGTTGTGTTC 58.632 41.667 0.00 0.00 0.00 3.18
622 943 1.523758 AGATGTTGTGTTCGGAAGCC 58.476 50.000 0.00 0.00 0.00 4.35
649 970 5.931441 CGATAGGTGAAAGGAATGGATTC 57.069 43.478 0.00 0.00 36.08 2.52
650 971 5.615289 CGATAGGTGAAAGGAATGGATTCT 58.385 41.667 0.00 0.00 37.00 2.40
651 972 6.759272 CGATAGGTGAAAGGAATGGATTCTA 58.241 40.000 0.00 0.00 37.00 2.10
652 973 7.390027 CGATAGGTGAAAGGAATGGATTCTAT 58.610 38.462 0.00 0.00 37.00 1.98
653 974 7.880195 CGATAGGTGAAAGGAATGGATTCTATT 59.120 37.037 0.00 0.00 37.00 1.73
654 975 8.930846 ATAGGTGAAAGGAATGGATTCTATTG 57.069 34.615 0.00 0.00 37.00 1.90
655 976 5.595952 AGGTGAAAGGAATGGATTCTATTGC 59.404 40.000 6.20 6.20 37.00 3.56
656 977 5.360714 GGTGAAAGGAATGGATTCTATTGCA 59.639 40.000 14.89 0.00 37.00 4.08
657 978 6.127366 GGTGAAAGGAATGGATTCTATTGCAA 60.127 38.462 14.89 0.00 37.00 4.08
658 979 6.753744 GTGAAAGGAATGGATTCTATTGCAAC 59.246 38.462 14.89 7.40 37.00 4.17
659 980 5.505173 AAGGAATGGATTCTATTGCAACG 57.495 39.130 14.89 0.00 37.00 4.10
660 981 4.526970 AGGAATGGATTCTATTGCAACGT 58.473 39.130 14.89 0.00 37.00 3.99
661 982 4.336433 AGGAATGGATTCTATTGCAACGTG 59.664 41.667 14.89 0.00 37.00 4.49
662 983 4.096382 GGAATGGATTCTATTGCAACGTGT 59.904 41.667 0.00 0.00 37.00 4.49
663 984 4.882671 ATGGATTCTATTGCAACGTGTC 57.117 40.909 0.00 0.00 0.00 3.67
670 991 4.503910 TCTATTGCAACGTGTCATTAGCT 58.496 39.130 0.00 0.00 0.00 3.32
672 993 6.103330 TCTATTGCAACGTGTCATTAGCTTA 58.897 36.000 0.00 0.00 0.00 3.09
697 1018 5.935448 GCACGTTTTTGCAGTTTAACTTA 57.065 34.783 0.00 0.00 42.49 2.24
710 1031 9.757227 TGCAGTTTAACTTACTTTTGCAATAAT 57.243 25.926 0.00 0.00 0.00 1.28
726 1047 4.807304 GCAATAATGGGTTGAGATGCTTTG 59.193 41.667 0.00 0.00 0.00 2.77
729 1050 2.957402 TGGGTTGAGATGCTTTGACT 57.043 45.000 0.00 0.00 0.00 3.41
731 1052 3.942829 TGGGTTGAGATGCTTTGACTAG 58.057 45.455 0.00 0.00 0.00 2.57
740 1061 7.857456 TGAGATGCTTTGACTAGGGTAATTTA 58.143 34.615 0.00 0.00 0.00 1.40
746 1067 9.120538 TGCTTTGACTAGGGTAATTTAATCATC 57.879 33.333 0.00 0.00 0.00 2.92
747 1068 8.568794 GCTTTGACTAGGGTAATTTAATCATCC 58.431 37.037 0.00 0.00 0.00 3.51
748 1069 9.627123 CTTTGACTAGGGTAATTTAATCATCCA 57.373 33.333 0.00 0.00 0.00 3.41
753 1074 9.720769 ACTAGGGTAATTTAATCATCCATAACG 57.279 33.333 0.00 0.00 0.00 3.18
754 1075 7.448748 AGGGTAATTTAATCATCCATAACGC 57.551 36.000 0.00 0.00 0.00 4.84
755 1076 7.001674 AGGGTAATTTAATCATCCATAACGCA 58.998 34.615 0.00 0.00 0.00 5.24
757 1078 8.303876 GGGTAATTTAATCATCCATAACGCAAT 58.696 33.333 0.00 0.00 0.00 3.56
758 1079 9.128107 GGTAATTTAATCATCCATAACGCAATG 57.872 33.333 0.00 0.00 0.00 2.82
759 1080 7.642071 AATTTAATCATCCATAACGCAATGC 57.358 32.000 0.00 0.00 0.00 3.56
760 1081 5.764487 TTAATCATCCATAACGCAATGCA 57.236 34.783 5.91 0.00 0.00 3.96
761 1082 3.631145 ATCATCCATAACGCAATGCAC 57.369 42.857 5.91 0.00 0.00 4.57
802 1123 7.041721 TGTAGTAGTAAGCATTTCATCTGTGG 58.958 38.462 0.00 0.00 0.00 4.17
805 1126 7.620880 AGTAGTAAGCATTTCATCTGTGGTAA 58.379 34.615 0.00 0.00 0.00 2.85
806 1127 6.992063 AGTAAGCATTTCATCTGTGGTAAG 57.008 37.500 0.00 0.00 0.00 2.34
807 1128 6.476378 AGTAAGCATTTCATCTGTGGTAAGT 58.524 36.000 0.00 0.00 0.00 2.24
808 1129 7.620880 AGTAAGCATTTCATCTGTGGTAAGTA 58.379 34.615 0.00 0.00 0.00 2.24
809 1130 8.100791 AGTAAGCATTTCATCTGTGGTAAGTAA 58.899 33.333 0.00 0.00 0.00 2.24
810 1131 7.944729 AAGCATTTCATCTGTGGTAAGTAAT 57.055 32.000 0.00 0.00 0.00 1.89
811 1132 7.944729 AGCATTTCATCTGTGGTAAGTAATT 57.055 32.000 0.00 0.00 0.00 1.40
812 1133 8.353423 AGCATTTCATCTGTGGTAAGTAATTT 57.647 30.769 0.00 0.00 0.00 1.82
813 1134 8.806146 AGCATTTCATCTGTGGTAAGTAATTTT 58.194 29.630 0.00 0.00 0.00 1.82
814 1135 9.423061 GCATTTCATCTGTGGTAAGTAATTTTT 57.577 29.630 0.00 0.00 0.00 1.94
819 1140 9.104965 TCATCTGTGGTAAGTAATTTTTATCGG 57.895 33.333 0.00 0.00 0.00 4.18
820 1141 7.311364 TCTGTGGTAAGTAATTTTTATCGGC 57.689 36.000 0.00 0.00 0.00 5.54
821 1142 7.107542 TCTGTGGTAAGTAATTTTTATCGGCT 58.892 34.615 0.00 0.00 0.00 5.52
822 1143 7.279313 TCTGTGGTAAGTAATTTTTATCGGCTC 59.721 37.037 0.00 0.00 0.00 4.70
823 1144 6.036300 TGTGGTAAGTAATTTTTATCGGCTCG 59.964 38.462 0.00 0.00 0.00 5.03
824 1145 5.006941 TGGTAAGTAATTTTTATCGGCTCGC 59.993 40.000 0.00 0.00 0.00 5.03
825 1146 3.854286 AGTAATTTTTATCGGCTCGCG 57.146 42.857 0.00 0.00 0.00 5.87
826 1147 2.542595 AGTAATTTTTATCGGCTCGCGG 59.457 45.455 6.13 0.00 0.00 6.46
856 1177 3.848272 ACATGTTTGTAAAGCGATGGG 57.152 42.857 0.00 0.00 33.16 4.00
1071 1393 2.202676 GCCGAAGCCAGAGAGACG 60.203 66.667 0.00 0.00 0.00 4.18
1461 1789 2.696238 CTCGACGTCGTCTCCTCG 59.304 66.667 34.40 10.27 40.80 4.63
1623 1951 1.001633 GACTTCGGCAACTTCCAGGTA 59.998 52.381 0.00 0.00 0.00 3.08
1770 2098 4.564110 CGATTCCCCTTCCGCCCC 62.564 72.222 0.00 0.00 0.00 5.80
2182 2563 2.738846 CACCTTCTTCGACAACTGGATG 59.261 50.000 0.00 0.00 0.00 3.51
2283 2664 0.618981 CGCTCCCCTTTCCCTTAGTT 59.381 55.000 0.00 0.00 0.00 2.24
2434 2818 1.433534 CGAACTGACCTGCTCTTTCC 58.566 55.000 0.00 0.00 0.00 3.13
2452 2836 7.619964 TCTTTCCTTAGTTTCGTCAAAGTTT 57.380 32.000 0.00 0.00 0.00 2.66
2455 2839 9.777575 CTTTCCTTAGTTTCGTCAAAGTTTTTA 57.222 29.630 0.00 0.00 0.00 1.52
2515 2899 3.081554 AGCCATCGCTGGTTTCCT 58.918 55.556 7.21 0.00 46.19 3.36
2551 2935 6.519679 TCGAAACCTGTTCATAGTAGCTAA 57.480 37.500 0.00 0.00 0.00 3.09
2583 2967 4.691860 ACGATTTGGAGAAATGCAGAAG 57.308 40.909 0.00 0.00 31.58 2.85
2664 3048 1.442769 TCTCGTTCTGATTGGCAAGC 58.557 50.000 8.86 8.86 0.00 4.01
2675 3059 3.195396 TGATTGGCAAGCTTATTTGGACC 59.805 43.478 17.21 0.00 0.00 4.46
2690 3074 5.486735 TTTGGACCATGCTCATTGAATTT 57.513 34.783 0.00 0.00 0.00 1.82
2772 3157 2.045536 CAGAAGGGGGTGCTCTGC 60.046 66.667 0.00 0.00 30.91 4.26
2794 3179 1.273495 TGAGAGCAGATCCTTGGGAGT 60.273 52.381 0.00 0.00 34.05 3.85
2881 3266 7.685481 TGGTTCAATCTCTAACCTGTTCATAA 58.315 34.615 5.88 0.00 44.55 1.90
2907 3292 8.802267 ACTAGACTCTGAATATGATTTAGGCTC 58.198 37.037 0.00 0.00 0.00 4.70
3073 3458 6.293298 GCTAGATATGGTTCTGCATGTTTCTG 60.293 42.308 0.00 0.00 0.00 3.02
3107 3655 4.497291 ACAACCACAGTCCTTTTCTACA 57.503 40.909 0.00 0.00 0.00 2.74
3113 3661 4.214332 CCACAGTCCTTTTCTACAGCTTTC 59.786 45.833 0.00 0.00 0.00 2.62
3194 3744 4.437682 TTGAGAAAGTGGACACCAGAAT 57.562 40.909 0.00 0.00 32.34 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 4.418013 TCAATTAATCACACACAAGGCG 57.582 40.909 0.00 0.00 0.00 5.52
22 23 4.583073 TCTTCTGCTACCATATACGCTTCA 59.417 41.667 0.00 0.00 0.00 3.02
28 29 8.343168 AGAGTACATCTTCTGCTACCATATAC 57.657 38.462 0.00 0.00 32.99 1.47
30 31 7.119992 CGTAGAGTACATCTTCTGCTACCATAT 59.880 40.741 0.00 0.00 39.64 1.78
35 36 5.064962 ACACGTAGAGTACATCTTCTGCTAC 59.935 44.000 0.00 0.00 39.64 3.58
78 79 1.114627 CCTCAGGTGATCCGTCATCA 58.885 55.000 0.00 0.00 37.97 3.07
82 83 3.095347 GCCCCTCAGGTGATCCGTC 62.095 68.421 0.00 0.00 38.26 4.79
104 105 4.760047 CCTCGGCCTGAACGTGGG 62.760 72.222 0.00 0.00 40.27 4.61
118 119 3.414700 CACAGCGAACACGGCCTC 61.415 66.667 0.00 0.00 0.00 4.70
132 133 0.104855 AAGCTCTGTTCAGACGCACA 59.895 50.000 18.52 0.00 0.00 4.57
179 180 4.091939 GGTGTAGGGGGCGTGTCC 62.092 72.222 0.00 0.00 0.00 4.02
280 288 2.432628 GTTCCCTGCTCCACGACG 60.433 66.667 0.00 0.00 0.00 5.12
359 371 0.391927 CGCGAAAATACCCTCCCACA 60.392 55.000 0.00 0.00 0.00 4.17
360 372 1.093496 CCGCGAAAATACCCTCCCAC 61.093 60.000 8.23 0.00 0.00 4.61
361 373 1.222387 CCGCGAAAATACCCTCCCA 59.778 57.895 8.23 0.00 0.00 4.37
362 374 1.093496 CACCGCGAAAATACCCTCCC 61.093 60.000 8.23 0.00 0.00 4.30
363 375 1.712018 GCACCGCGAAAATACCCTCC 61.712 60.000 8.23 0.00 0.00 4.30
364 376 1.719709 GCACCGCGAAAATACCCTC 59.280 57.895 8.23 0.00 0.00 4.30
365 377 3.899395 GCACCGCGAAAATACCCT 58.101 55.556 8.23 0.00 0.00 4.34
397 409 1.230635 GCTGCTGCTTTTGTCTCCGA 61.231 55.000 8.53 0.00 36.03 4.55
511 523 1.672881 CAAGCCGCTTGATTAAGGAGG 59.327 52.381 26.07 0.00 43.42 4.30
525 537 4.698304 TCATCTTTAAGGTTAACCAAGCCG 59.302 41.667 26.26 13.95 38.89 5.52
546 558 6.293190 CGCCAGTGTTTCTTGTAATTTACTCA 60.293 38.462 7.99 0.00 0.00 3.41
567 579 2.038269 GCATTTTCCTCGGACGCCA 61.038 57.895 0.00 0.00 0.00 5.69
570 582 0.301687 CGATGCATTTTCCTCGGACG 59.698 55.000 0.00 0.00 0.00 4.79
571 583 0.028110 GCGATGCATTTTCCTCGGAC 59.972 55.000 0.00 0.00 0.00 4.79
588 909 3.257469 ACATCTATCTATGGGCATGCG 57.743 47.619 12.44 0.00 0.00 4.73
593 914 4.449068 CGAACACAACATCTATCTATGGGC 59.551 45.833 0.00 0.00 0.00 5.36
594 915 4.991056 CCGAACACAACATCTATCTATGGG 59.009 45.833 0.00 0.00 0.00 4.00
622 943 3.728076 TTCCTTTCACCTATCGGATCG 57.272 47.619 0.00 0.00 0.00 3.69
624 945 3.973973 TCCATTCCTTTCACCTATCGGAT 59.026 43.478 0.00 0.00 0.00 4.18
625 946 3.380393 TCCATTCCTTTCACCTATCGGA 58.620 45.455 0.00 0.00 0.00 4.55
627 948 5.615289 AGAATCCATTCCTTTCACCTATCG 58.385 41.667 0.00 0.00 37.51 2.92
633 954 6.455360 TGCAATAGAATCCATTCCTTTCAC 57.545 37.500 0.00 0.00 37.51 3.18
636 957 5.418840 ACGTTGCAATAGAATCCATTCCTTT 59.581 36.000 0.59 0.00 37.51 3.11
637 958 4.949856 ACGTTGCAATAGAATCCATTCCTT 59.050 37.500 0.59 0.00 37.51 3.36
638 959 4.336433 CACGTTGCAATAGAATCCATTCCT 59.664 41.667 0.59 0.00 37.51 3.36
639 960 4.096382 ACACGTTGCAATAGAATCCATTCC 59.904 41.667 0.59 0.00 37.51 3.01
640 961 5.163764 TGACACGTTGCAATAGAATCCATTC 60.164 40.000 0.59 0.00 37.06 2.67
641 962 4.699735 TGACACGTTGCAATAGAATCCATT 59.300 37.500 0.59 0.00 0.00 3.16
642 963 4.260985 TGACACGTTGCAATAGAATCCAT 58.739 39.130 0.59 0.00 0.00 3.41
643 964 3.669536 TGACACGTTGCAATAGAATCCA 58.330 40.909 0.59 0.00 0.00 3.41
644 965 4.882671 ATGACACGTTGCAATAGAATCC 57.117 40.909 0.59 0.00 0.00 3.01
645 966 5.904080 GCTAATGACACGTTGCAATAGAATC 59.096 40.000 0.59 4.62 0.00 2.52
646 967 5.586243 AGCTAATGACACGTTGCAATAGAAT 59.414 36.000 0.59 0.00 0.00 2.40
647 968 4.935205 AGCTAATGACACGTTGCAATAGAA 59.065 37.500 0.59 0.00 0.00 2.10
648 969 4.503910 AGCTAATGACACGTTGCAATAGA 58.496 39.130 0.59 0.00 0.00 1.98
649 970 4.864916 AGCTAATGACACGTTGCAATAG 57.135 40.909 0.59 2.53 0.00 1.73
650 971 6.918892 ATAAGCTAATGACACGTTGCAATA 57.081 33.333 0.59 0.00 0.00 1.90
651 972 5.818136 ATAAGCTAATGACACGTTGCAAT 57.182 34.783 0.59 0.00 0.00 3.56
652 973 5.389778 CAATAAGCTAATGACACGTTGCAA 58.610 37.500 0.00 0.00 0.00 4.08
653 974 4.671508 GCAATAAGCTAATGACACGTTGCA 60.672 41.667 0.00 0.00 39.22 4.08
654 975 3.786048 GCAATAAGCTAATGACACGTTGC 59.214 43.478 0.00 0.00 41.15 4.17
655 976 4.788100 GTGCAATAAGCTAATGACACGTTG 59.212 41.667 0.00 0.00 45.94 4.10
656 977 4.435518 CGTGCAATAAGCTAATGACACGTT 60.436 41.667 18.06 0.00 45.94 3.99
657 978 3.062099 CGTGCAATAAGCTAATGACACGT 59.938 43.478 18.06 0.00 45.94 4.49
658 979 3.597324 CGTGCAATAAGCTAATGACACG 58.403 45.455 14.39 14.39 45.94 4.49
659 980 4.600012 ACGTGCAATAAGCTAATGACAC 57.400 40.909 0.00 0.00 45.94 3.67
660 981 5.621197 AAACGTGCAATAAGCTAATGACA 57.379 34.783 0.00 0.00 45.94 3.58
661 982 6.667386 GCAAAAACGTGCAATAAGCTAATGAC 60.667 38.462 0.00 0.00 44.29 3.06
662 983 5.344665 GCAAAAACGTGCAATAAGCTAATGA 59.655 36.000 0.00 0.00 44.29 2.57
663 984 5.541008 GCAAAAACGTGCAATAAGCTAATG 58.459 37.500 0.00 0.00 44.29 1.90
687 1008 9.705290 CCCATTATTGCAAAAGTAAGTTAAACT 57.295 29.630 1.71 0.00 0.00 2.66
697 1018 6.400568 CATCTCAACCCATTATTGCAAAAGT 58.599 36.000 1.71 0.00 0.00 2.66
710 1031 2.957402 AGTCAAAGCATCTCAACCCA 57.043 45.000 0.00 0.00 0.00 4.51
729 1050 8.158132 TGCGTTATGGATGATTAAATTACCCTA 58.842 33.333 0.00 0.00 0.00 3.53
731 1052 7.209471 TGCGTTATGGATGATTAAATTACCC 57.791 36.000 0.00 0.00 0.00 3.69
740 1061 3.380954 TGTGCATTGCGTTATGGATGATT 59.619 39.130 3.84 0.00 0.00 2.57
746 1067 2.565210 ACATGTGCATTGCGTTATGG 57.435 45.000 17.91 4.63 0.00 2.74
747 1068 6.386897 TTTTAACATGTGCATTGCGTTATG 57.613 33.333 0.00 14.27 0.00 1.90
748 1069 6.644592 AGTTTTTAACATGTGCATTGCGTTAT 59.355 30.769 0.00 0.00 0.00 1.89
749 1070 5.980116 AGTTTTTAACATGTGCATTGCGTTA 59.020 32.000 0.00 3.72 0.00 3.18
753 1074 4.905295 GCAAGTTTTTAACATGTGCATTGC 59.095 37.500 0.00 0.46 36.53 3.56
754 1075 6.130723 CAGCAAGTTTTTAACATGTGCATTG 58.869 36.000 0.00 0.00 37.97 2.82
755 1076 5.816777 ACAGCAAGTTTTTAACATGTGCATT 59.183 32.000 0.00 0.00 37.97 3.56
757 1078 4.753233 ACAGCAAGTTTTTAACATGTGCA 58.247 34.783 0.00 0.00 37.97 4.57
758 1079 5.977129 ACTACAGCAAGTTTTTAACATGTGC 59.023 36.000 0.00 0.00 36.67 4.57
759 1080 8.342634 ACTACTACAGCAAGTTTTTAACATGTG 58.657 33.333 0.00 0.00 32.96 3.21
760 1081 8.446599 ACTACTACAGCAAGTTTTTAACATGT 57.553 30.769 0.00 0.00 32.96 3.21
802 1123 5.128468 CGCGAGCCGATAAAAATTACTTAC 58.872 41.667 0.00 0.00 40.02 2.34
805 1126 2.542595 CCGCGAGCCGATAAAAATTACT 59.457 45.455 8.23 0.00 40.02 2.24
806 1127 2.286025 ACCGCGAGCCGATAAAAATTAC 59.714 45.455 8.23 0.00 40.02 1.89
807 1128 2.285756 CACCGCGAGCCGATAAAAATTA 59.714 45.455 8.23 0.00 40.02 1.40
808 1129 1.063469 CACCGCGAGCCGATAAAAATT 59.937 47.619 8.23 0.00 40.02 1.82
809 1130 0.655733 CACCGCGAGCCGATAAAAAT 59.344 50.000 8.23 0.00 40.02 1.82
810 1131 1.363145 CCACCGCGAGCCGATAAAAA 61.363 55.000 8.23 0.00 40.02 1.94
811 1132 1.812093 CCACCGCGAGCCGATAAAA 60.812 57.895 8.23 0.00 40.02 1.52
812 1133 1.665264 TACCACCGCGAGCCGATAAA 61.665 55.000 8.23 0.00 40.02 1.40
813 1134 2.067091 CTACCACCGCGAGCCGATAA 62.067 60.000 8.23 0.00 40.02 1.75
814 1135 2.516695 TACCACCGCGAGCCGATA 60.517 61.111 8.23 0.00 40.02 2.92
815 1136 3.900892 CTACCACCGCGAGCCGAT 61.901 66.667 8.23 0.00 40.02 4.18
818 1139 3.146726 TATGCTACCACCGCGAGCC 62.147 63.158 8.23 0.00 35.24 4.70
819 1140 1.949631 GTATGCTACCACCGCGAGC 60.950 63.158 8.23 9.07 36.72 5.03
820 1141 0.032130 ATGTATGCTACCACCGCGAG 59.968 55.000 8.23 0.00 0.00 5.03
821 1142 0.249280 CATGTATGCTACCACCGCGA 60.249 55.000 8.23 0.00 0.00 5.87
822 1143 0.529773 ACATGTATGCTACCACCGCG 60.530 55.000 0.00 0.00 0.00 6.46
823 1144 1.663695 AACATGTATGCTACCACCGC 58.336 50.000 0.00 0.00 0.00 5.68
824 1145 3.006940 ACAAACATGTATGCTACCACCG 58.993 45.455 0.00 0.00 0.00 4.94
825 1146 6.503589 TTTACAAACATGTATGCTACCACC 57.496 37.500 0.00 0.00 0.00 4.61
826 1147 6.027749 GCTTTACAAACATGTATGCTACCAC 58.972 40.000 0.00 0.00 0.00 4.16
1110 1432 2.719798 CAACAAACTCTGGCAAGTTCG 58.280 47.619 13.03 7.07 38.52 3.95
1742 2070 4.918201 GGAATCGGAGCGGGCAGG 62.918 72.222 0.00 0.00 0.00 4.85
1743 2071 4.918201 GGGAATCGGAGCGGGCAG 62.918 72.222 0.00 0.00 0.00 4.85
1805 2186 1.212751 GGAAACCTGCATTGCGACC 59.787 57.895 3.84 0.00 0.00 4.79
1806 2187 0.109597 CAGGAAACCTGCATTGCGAC 60.110 55.000 3.84 0.00 45.13 5.19
2182 2563 1.608046 CCCCTCCTCTAGCGGATCC 60.608 68.421 0.94 0.00 31.43 3.36
2190 2571 2.708132 CCCCCTCCCCCTCCTCTA 60.708 72.222 0.00 0.00 0.00 2.43
2211 2592 2.125512 CTTCTTCCTGGCGGTCGG 60.126 66.667 0.00 0.00 0.00 4.79
2225 2606 3.265791 ACTTGATCTTGCCATCGTCTTC 58.734 45.455 0.00 0.00 0.00 2.87
2374 2758 5.495926 TCTTGCCATTCTCTTCTTCTTCT 57.504 39.130 0.00 0.00 0.00 2.85
2375 2759 5.006552 CGATCTTGCCATTCTCTTCTTCTTC 59.993 44.000 0.00 0.00 0.00 2.87
2376 2760 4.874966 CGATCTTGCCATTCTCTTCTTCTT 59.125 41.667 0.00 0.00 0.00 2.52
2455 2839 9.319143 GAACACACTATAGCAGTATCAAATCTT 57.681 33.333 0.00 0.00 34.98 2.40
2472 2856 2.367529 TCCATGGCGGAACACACTA 58.632 52.632 6.96 0.00 42.52 2.74
2473 2857 3.156714 TCCATGGCGGAACACACT 58.843 55.556 6.96 0.00 42.52 3.55
2551 2935 7.921786 TTTCTCCAAATCGTATCTCAATGTT 57.078 32.000 0.00 0.00 0.00 2.71
2583 2967 0.108585 TTCTCAACCAGAGCACCCAC 59.891 55.000 0.00 0.00 44.35 4.61
2664 3048 5.840243 TCAATGAGCATGGTCCAAATAAG 57.160 39.130 21.58 6.19 0.00 1.73
2675 3059 4.092821 CAGGTTGCAAATTCAATGAGCATG 59.907 41.667 0.00 0.00 34.87 4.06
2690 3074 5.546621 AGAACTACTAAGAACAGGTTGCA 57.453 39.130 0.00 0.00 0.00 4.08
2772 3157 1.836166 TCCCAAGGATCTGCTCTCAAG 59.164 52.381 0.00 0.00 0.00 3.02
2784 3169 7.056522 TCCAGATATATCATACTCCCAAGGA 57.943 40.000 15.08 3.77 0.00 3.36
2881 3266 8.719645 AGCCTAAATCATATTCAGAGTCTAGT 57.280 34.615 0.00 0.00 0.00 2.57
3063 3448 9.624697 TTGTTAATTGTTAGATCAGAAACATGC 57.375 29.630 8.54 0.00 35.64 4.06
3073 3458 7.390718 AGGACTGTGGTTGTTAATTGTTAGATC 59.609 37.037 0.00 0.00 0.00 2.75
3137 3687 9.626045 GTAAACTCCTCACAAAAGATAAAATGG 57.374 33.333 0.00 0.00 0.00 3.16
3140 3690 8.846211 CCTGTAAACTCCTCACAAAAGATAAAA 58.154 33.333 0.00 0.00 0.00 1.52
3182 3732 8.097038 GCTCAGATAATAATATTCTGGTGTCCA 58.903 37.037 0.00 0.00 0.00 4.02
3184 3734 9.664332 ATGCTCAGATAATAATATTCTGGTGTC 57.336 33.333 0.00 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.