Multiple sequence alignment - TraesCS3B01G466300

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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 TraesCS3B01G466300 chr3B 100.000 3296 0 0 1 3296 708912775 708909480 0.000000e+00 6087
1 TraesCS3B01G466300 chr3B 86.787 1945 133 62 605 2498 708502833 708504704 0.000000e+00 2054
2 TraesCS3B01G466300 chr3B 83.025 1514 150 58 193 1667 708496434 708497879 0.000000e+00 1273
3 TraesCS3B01G466300 chr3B 88.048 661 55 10 2603 3262 2122010 2122647 0.000000e+00 761
4 TraesCS3B01G466300 chr3B 87.083 689 61 10 2574 3262 188235425 188234765 0.000000e+00 754
5 TraesCS3B01G466300 chr3B 84.384 365 30 15 193 553 708499579 708499920 1.900000e-87 333
6 TraesCS3B01G466300 chr3B 77.285 383 82 5 1287 1666 708367622 708367242 1.540000e-53 220
7 TraesCS3B01G466300 chr3A 90.597 2446 112 56 229 2592 671766647 671764238 0.000000e+00 3134
8 TraesCS3B01G466300 chr3A 77.487 382 77 6 1287 1663 671697913 671697536 1.540000e-53 220
9 TraesCS3B01G466300 chr3A 89.062 128 10 2 2 125 671766830 671766703 4.400000e-34 156
10 TraesCS3B01G466300 chr3D 90.798 2369 97 55 164 2462 536339321 536337004 0.000000e+00 3055
11 TraesCS3B01G466300 chr3D 78.068 383 76 7 1287 1663 536027765 536028145 5.500000e-58 235
12 TraesCS3B01G466300 chr3D 98.230 113 2 0 1 113 536369192 536369080 7.210000e-47 198
13 TraesCS3B01G466300 chr5B 88.267 733 58 6 2576 3296 659735938 659735222 0.000000e+00 852
14 TraesCS3B01G466300 chr5B 80.670 388 58 11 2849 3229 559396890 559397267 5.380000e-73 285
15 TraesCS3B01G466300 chr7B 87.534 730 54 14 2578 3296 664321563 664320860 0.000000e+00 809
16 TraesCS3B01G466300 chr7B 87.994 708 53 12 2578 3262 126843907 126843209 0.000000e+00 808
17 TraesCS3B01G466300 chr7B 87.123 730 56 13 2578 3296 664349757 664349055 0.000000e+00 793
18 TraesCS3B01G466300 chr7B 82.114 492 47 16 2578 3057 615737379 615736917 1.860000e-102 383
19 TraesCS3B01G466300 chr5D 88.338 686 60 8 2578 3262 249086260 249085594 0.000000e+00 806
20 TraesCS3B01G466300 chr5D 80.172 696 85 32 2610 3296 442671713 442671062 3.850000e-129 472
21 TraesCS3B01G466300 chr6B 86.498 711 58 10 2576 3262 476733043 476733739 0.000000e+00 747
22 TraesCS3B01G466300 chr6B 87.168 678 60 10 2578 3242 95441039 95441702 0.000000e+00 745
23 TraesCS3B01G466300 chr2B 84.104 692 72 16 2573 3241 705151442 705152118 4.640000e-178 634
24 TraesCS3B01G466300 chr6D 82.345 742 93 13 2573 3293 25369911 25370635 7.820000e-171 610
25 TraesCS3B01G466300 chr4B 83.550 693 70 15 2576 3241 631062077 631062752 2.810000e-170 608
26 TraesCS3B01G466300 chr2A 82.192 730 98 20 2576 3296 47363679 47362973 1.690000e-167 599
27 TraesCS3B01G466300 chr4A 84.877 529 47 10 2792 3296 720075955 720076474 1.370000e-138 503
28 TraesCS3B01G466300 chr1B 80.315 381 52 15 2855 3231 670875932 670876293 1.950000e-67 267


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 TraesCS3B01G466300 chr3B 708909480 708912775 3295 True 6087 6087 100.0000 1 3296 1 chr3B.!!$R3 3295
1 TraesCS3B01G466300 chr3B 708496434 708504704 8270 False 1220 2054 84.7320 193 2498 3 chr3B.!!$F2 2305
2 TraesCS3B01G466300 chr3B 2122010 2122647 637 False 761 761 88.0480 2603 3262 1 chr3B.!!$F1 659
3 TraesCS3B01G466300 chr3B 188234765 188235425 660 True 754 754 87.0830 2574 3262 1 chr3B.!!$R1 688
4 TraesCS3B01G466300 chr3A 671764238 671766830 2592 True 1645 3134 89.8295 2 2592 2 chr3A.!!$R2 2590
5 TraesCS3B01G466300 chr3D 536337004 536339321 2317 True 3055 3055 90.7980 164 2462 1 chr3D.!!$R1 2298
6 TraesCS3B01G466300 chr5B 659735222 659735938 716 True 852 852 88.2670 2576 3296 1 chr5B.!!$R1 720
7 TraesCS3B01G466300 chr7B 664320860 664321563 703 True 809 809 87.5340 2578 3296 1 chr7B.!!$R3 718
8 TraesCS3B01G466300 chr7B 126843209 126843907 698 True 808 808 87.9940 2578 3262 1 chr7B.!!$R1 684
9 TraesCS3B01G466300 chr7B 664349055 664349757 702 True 793 793 87.1230 2578 3296 1 chr7B.!!$R4 718
10 TraesCS3B01G466300 chr5D 249085594 249086260 666 True 806 806 88.3380 2578 3262 1 chr5D.!!$R1 684
11 TraesCS3B01G466300 chr5D 442671062 442671713 651 True 472 472 80.1720 2610 3296 1 chr5D.!!$R2 686
12 TraesCS3B01G466300 chr6B 476733043 476733739 696 False 747 747 86.4980 2576 3262 1 chr6B.!!$F2 686
13 TraesCS3B01G466300 chr6B 95441039 95441702 663 False 745 745 87.1680 2578 3242 1 chr6B.!!$F1 664
14 TraesCS3B01G466300 chr2B 705151442 705152118 676 False 634 634 84.1040 2573 3241 1 chr2B.!!$F1 668
15 TraesCS3B01G466300 chr6D 25369911 25370635 724 False 610 610 82.3450 2573 3293 1 chr6D.!!$F1 720
16 TraesCS3B01G466300 chr4B 631062077 631062752 675 False 608 608 83.5500 2576 3241 1 chr4B.!!$F1 665
17 TraesCS3B01G466300 chr2A 47362973 47363679 706 True 599 599 82.1920 2576 3296 1 chr2A.!!$R1 720
18 TraesCS3B01G466300 chr4A 720075955 720076474 519 False 503 503 84.8770 2792 3296 1 chr4A.!!$F1 504

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
351 371 0.030908 CACTAGTAGGTAGGCGCTGC 59.969 60.0 7.64 0.0 32.29 5.25 F
1253 7345 0.035534 TGCTCTTCGGCCATTTGCTA 60.036 50.0 2.24 0.0 40.92 3.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1700 7813 2.281762 CGATCGATGTCCCGAAAGAAAC 59.718 50.0 10.26 0.0 42.22 2.78 R
2515 8677 0.035881 ATCCACCGGAGCATAGCATG 59.964 55.0 9.46 0.0 34.05 4.06 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
42 43 5.625568 AGTCAGTTTAACCACCTAACAGT 57.374 39.130 0.00 0.00 0.00 3.55
56 57 7.452501 ACCACCTAACAGTAAGTACTATCACAA 59.547 37.037 0.00 0.00 34.13 3.33
64 65 8.972127 ACAGTAAGTACTATCACAATCACAGAT 58.028 33.333 0.00 0.00 34.13 2.90
113 118 3.025866 CTGGTACGGTGTCGCTAAC 57.974 57.895 0.00 0.00 40.63 2.34
114 119 0.241749 CTGGTACGGTGTCGCTAACA 59.758 55.000 0.00 0.00 40.63 2.41
115 120 0.889994 TGGTACGGTGTCGCTAACAT 59.110 50.000 0.00 0.00 40.80 2.71
116 121 1.274596 GGTACGGTGTCGCTAACATG 58.725 55.000 0.00 0.00 40.80 3.21
117 122 1.403249 GGTACGGTGTCGCTAACATGT 60.403 52.381 0.00 0.00 40.80 3.21
118 123 1.916000 GTACGGTGTCGCTAACATGTC 59.084 52.381 0.00 0.00 40.80 3.06
119 124 0.315886 ACGGTGTCGCTAACATGTCA 59.684 50.000 0.00 0.00 40.80 3.58
120 125 1.269883 ACGGTGTCGCTAACATGTCAA 60.270 47.619 0.00 0.00 40.80 3.18
121 126 1.795872 CGGTGTCGCTAACATGTCAAA 59.204 47.619 0.00 0.00 40.80 2.69
122 127 2.159841 CGGTGTCGCTAACATGTCAAAG 60.160 50.000 0.00 0.00 40.80 2.77
123 128 3.064207 GGTGTCGCTAACATGTCAAAGA 58.936 45.455 0.00 0.00 40.80 2.52
124 129 3.496884 GGTGTCGCTAACATGTCAAAGAA 59.503 43.478 0.00 0.00 40.80 2.52
125 130 4.154195 GGTGTCGCTAACATGTCAAAGAAT 59.846 41.667 0.00 0.00 40.80 2.40
126 131 5.334879 GGTGTCGCTAACATGTCAAAGAATT 60.335 40.000 0.00 0.00 40.80 2.17
127 132 5.790495 GTGTCGCTAACATGTCAAAGAATTC 59.210 40.000 0.00 0.00 40.80 2.17
128 133 5.106712 TGTCGCTAACATGTCAAAGAATTCC 60.107 40.000 0.00 0.00 31.20 3.01
129 134 4.394920 TCGCTAACATGTCAAAGAATTCCC 59.605 41.667 0.00 0.00 0.00 3.97
130 135 4.438744 CGCTAACATGTCAAAGAATTCCCC 60.439 45.833 0.00 0.00 0.00 4.81
131 136 4.438744 GCTAACATGTCAAAGAATTCCCCG 60.439 45.833 0.00 0.00 0.00 5.73
132 137 1.818674 ACATGTCAAAGAATTCCCCGC 59.181 47.619 0.65 0.00 0.00 6.13
133 138 1.818060 CATGTCAAAGAATTCCCCGCA 59.182 47.619 0.65 0.00 0.00 5.69
134 139 1.988293 TGTCAAAGAATTCCCCGCAA 58.012 45.000 0.65 0.00 0.00 4.85
135 140 2.311463 TGTCAAAGAATTCCCCGCAAA 58.689 42.857 0.65 0.00 0.00 3.68
136 141 2.695666 TGTCAAAGAATTCCCCGCAAAA 59.304 40.909 0.65 0.00 0.00 2.44
137 142 3.133003 TGTCAAAGAATTCCCCGCAAAAA 59.867 39.130 0.65 0.00 0.00 1.94
196 214 1.227943 GCTTCATATGGAGGCGGCA 60.228 57.895 13.10 0.00 38.95 5.69
351 371 0.030908 CACTAGTAGGTAGGCGCTGC 59.969 60.000 7.64 0.00 32.29 5.25
469 492 2.579518 GGCATTTAGTTGGCGCGC 60.580 61.111 25.94 25.94 32.10 6.86
470 493 2.579518 GCATTTAGTTGGCGCGCC 60.580 61.111 42.35 42.35 0.00 6.53
471 494 2.277247 CATTTAGTTGGCGCGCCG 60.277 61.111 41.73 23.24 39.42 6.46
519 544 1.567357 GAAGCTTCTCCTCCACCTCT 58.433 55.000 19.44 0.00 0.00 3.69
563 608 1.141019 GAGGCATGGCGAACTCGTA 59.859 57.895 14.30 0.00 42.22 3.43
564 609 0.459585 GAGGCATGGCGAACTCGTAA 60.460 55.000 14.30 0.00 42.22 3.18
565 610 0.178068 AGGCATGGCGAACTCGTAAT 59.822 50.000 14.30 0.00 42.22 1.89
567 612 2.159014 AGGCATGGCGAACTCGTAATAA 60.159 45.455 14.30 0.00 42.22 1.40
568 613 2.610374 GGCATGGCGAACTCGTAATAAA 59.390 45.455 2.41 0.00 42.22 1.40
572 617 5.395486 GCATGGCGAACTCGTAATAAAAATC 59.605 40.000 0.51 0.00 42.22 2.17
577 622 5.782255 CGAACTCGTAATAAAAATCGCTGT 58.218 37.500 0.00 0.00 34.11 4.40
579 624 6.476243 AACTCGTAATAAAAATCGCTGTGT 57.524 33.333 0.00 0.00 0.00 3.72
580 625 5.854157 ACTCGTAATAAAAATCGCTGTGTG 58.146 37.500 0.00 0.00 0.00 3.82
619 670 0.462375 TAATTAAGCTCGGCTGCGGA 59.538 50.000 9.62 9.62 39.62 5.54
634 686 0.793250 GCGGAAGTTCTGAGACTTGC 59.207 55.000 16.15 10.29 42.45 4.01
684 743 1.158434 GTCGGTTTGATTACGGGCAA 58.842 50.000 0.00 0.00 0.00 4.52
733 6780 1.925185 GACCTCGCGTTTGATTAGTCC 59.075 52.381 5.77 0.00 0.00 3.85
750 6797 1.061566 GTCCATGGCGCGTTAGTTAAC 59.938 52.381 6.96 0.00 0.00 2.01
763 6810 0.109153 AGTTAACCACCCCGTCAACC 59.891 55.000 0.88 0.00 0.00 3.77
861 6914 2.377193 AGTACAGTGAGAGTGGAGAGGT 59.623 50.000 0.00 0.00 0.00 3.85
932 7005 4.825085 GCTGGTAGAGCTATAGCCTATAGG 59.175 50.000 21.17 15.01 45.21 2.57
933 7006 5.398126 GCTGGTAGAGCTATAGCCTATAGGA 60.398 48.000 23.61 2.39 45.21 2.94
934 7007 6.653790 TGGTAGAGCTATAGCCTATAGGAA 57.346 41.667 23.61 9.80 43.38 3.36
937 7010 5.466127 AGAGCTATAGCCTATAGGAAGCT 57.534 43.478 25.89 25.89 43.38 3.74
938 7011 5.200483 AGAGCTATAGCCTATAGGAAGCTG 58.800 45.833 28.56 15.72 43.38 4.24
939 7012 3.704061 AGCTATAGCCTATAGGAAGCTGC 59.296 47.826 25.39 20.25 43.38 5.25
941 7014 1.645710 TAGCCTATAGGAAGCTGCCC 58.354 55.000 23.61 1.53 37.45 5.36
942 7015 1.130678 AGCCTATAGGAAGCTGCCCC 61.131 60.000 23.61 0.00 34.99 5.80
943 7016 1.674057 CCTATAGGAAGCTGCCCCG 59.326 63.158 14.11 0.00 37.39 5.73
944 7017 0.832135 CCTATAGGAAGCTGCCCCGA 60.832 60.000 14.11 0.00 37.39 5.14
945 7018 1.270907 CTATAGGAAGCTGCCCCGAT 58.729 55.000 7.30 0.90 0.00 4.18
977 7055 1.755783 CTTTCCCCTGCATGCCTCC 60.756 63.158 16.68 0.00 0.00 4.30
1016 7104 1.162800 GGCATGGCGATCTCCAAGAC 61.163 60.000 8.83 2.15 39.96 3.01
1204 7292 1.202313 CGAAGGCTTCTTCTCCTACCG 60.202 57.143 23.74 4.57 43.46 4.02
1205 7293 0.537653 AAGGCTTCTTCTCCTACCGC 59.462 55.000 0.00 0.00 31.24 5.68
1207 7295 1.063867 AGGCTTCTTCTCCTACCGCTA 60.064 52.381 0.00 0.00 0.00 4.26
1209 7297 1.067364 GCTTCTTCTCCTACCGCTACC 59.933 57.143 0.00 0.00 0.00 3.18
1210 7298 2.376109 CTTCTTCTCCTACCGCTACCA 58.624 52.381 0.00 0.00 0.00 3.25
1211 7299 2.519771 TCTTCTCCTACCGCTACCAA 57.480 50.000 0.00 0.00 0.00 3.67
1212 7300 3.028094 TCTTCTCCTACCGCTACCAAT 57.972 47.619 0.00 0.00 0.00 3.16
1213 7301 2.693591 TCTTCTCCTACCGCTACCAATG 59.306 50.000 0.00 0.00 0.00 2.82
1214 7302 0.750850 TCTCCTACCGCTACCAATGC 59.249 55.000 0.00 0.00 0.00 3.56
1249 7341 2.097466 CGTATTTGCTCTTCGGCCATTT 59.903 45.455 2.24 0.00 0.00 2.32
1250 7342 2.660189 ATTTGCTCTTCGGCCATTTG 57.340 45.000 2.24 0.00 0.00 2.32
1251 7343 0.038343 TTTGCTCTTCGGCCATTTGC 60.038 50.000 2.24 0.11 40.16 3.68
1252 7344 0.895100 TTGCTCTTCGGCCATTTGCT 60.895 50.000 2.24 0.00 40.92 3.91
1253 7345 0.035534 TGCTCTTCGGCCATTTGCTA 60.036 50.000 2.24 0.00 40.92 3.49
1287 7385 1.781025 CGGTTTCCTTTGCGCAGACA 61.781 55.000 11.31 0.00 0.00 3.41
1565 7666 4.821589 CCTCTCCGGCGCCAAGAC 62.822 72.222 28.98 0.00 0.00 3.01
1679 7785 1.226379 GTCGTCGCCATTGCCATTG 60.226 57.895 0.00 0.00 0.00 2.82
1766 7879 7.515528 CGTTAGAAATAATAATCGTGCCGACAA 60.516 37.037 0.00 0.00 39.18 3.18
2305 8440 6.477669 AGTGCATACATTGATTGATCGATC 57.522 37.500 18.72 18.72 0.00 3.69
2306 8441 5.410746 AGTGCATACATTGATTGATCGATCC 59.589 40.000 22.31 8.00 0.00 3.36
2327 8473 3.392882 CATTGATTGATGGGATCGACGA 58.607 45.455 0.00 0.00 0.00 4.20
2405 8557 2.342279 CTTCCGGCCTGTCGTTGA 59.658 61.111 0.00 0.00 0.00 3.18
2467 8626 9.594478 TTTAGTACACACATGACATATACCTTG 57.406 33.333 0.00 0.00 0.00 3.61
2468 8627 7.418337 AGTACACACATGACATATACCTTGA 57.582 36.000 0.00 0.00 0.00 3.02
2474 8635 8.729756 CACACATGACATATACCTTGAGAAAAA 58.270 33.333 0.00 0.00 0.00 1.94
2475 8636 9.466497 ACACATGACATATACCTTGAGAAAAAT 57.534 29.630 0.00 0.00 0.00 1.82
2487 8648 5.630680 CCTTGAGAAAAATGTACACACATGC 59.369 40.000 0.00 0.00 44.83 4.06
2498 8659 6.809630 TGTACACACATGCTATGCTTTTTA 57.190 33.333 0.00 0.00 0.00 1.52
2499 8660 6.607689 TGTACACACATGCTATGCTTTTTAC 58.392 36.000 0.00 0.00 0.00 2.01
2502 8663 5.473162 ACACACATGCTATGCTTTTTACAGA 59.527 36.000 0.00 0.00 0.00 3.41
2503 8664 5.796935 CACACATGCTATGCTTTTTACAGAC 59.203 40.000 0.00 0.00 0.00 3.51
2514 8676 8.621532 ATGCTTTTTACAGACAGAAGAATACA 57.378 30.769 0.00 0.00 0.00 2.29
2515 8677 7.861630 TGCTTTTTACAGACAGAAGAATACAC 58.138 34.615 0.00 0.00 0.00 2.90
2536 8699 0.179048 TGCTATGCTCCGGTGGATTG 60.179 55.000 15.92 14.55 0.00 2.67
2539 8702 2.289694 GCTATGCTCCGGTGGATTGTAT 60.290 50.000 15.92 0.00 0.00 2.29
2544 8707 0.544223 TCCGGTGGATTGTATGGTGG 59.456 55.000 0.00 0.00 0.00 4.61
2547 8710 2.557317 CGGTGGATTGTATGGTGGTAC 58.443 52.381 0.00 0.00 0.00 3.34
2569 8732 3.420576 CACCGTAATTTTTGTTGCTGTCG 59.579 43.478 0.00 0.00 0.00 4.35
2654 8823 2.387445 CGAACCGGCGCAAGATTGA 61.387 57.895 10.83 0.00 43.02 2.57
2679 8850 2.031465 GGTTCGGTTCGCTCCCAA 59.969 61.111 0.00 0.00 0.00 4.12
2740 8912 5.262422 GTTTCAAAATTTTGCAAACTCGGG 58.738 37.500 28.52 2.23 36.46 5.14
3280 9576 2.203070 GGCGCCCTCGTTGATGAT 60.203 61.111 18.11 0.00 38.14 2.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.244044 ACTTTGCTCTGACCTCTGAGAAC 60.244 47.826 6.17 0.34 42.37 3.01
2 3 2.560542 GACTTTGCTCTGACCTCTGAGA 59.439 50.000 6.17 0.00 42.37 3.27
4 5 2.298446 CTGACTTTGCTCTGACCTCTGA 59.702 50.000 0.00 0.00 0.00 3.27
64 65 3.202906 GTGTTAGAACAAGGCAGTCACA 58.797 45.455 0.00 0.00 41.21 3.58
68 69 2.572290 GTGGTGTTAGAACAAGGCAGT 58.428 47.619 0.00 0.00 41.21 4.40
70 71 1.812324 CGGTGGTGTTAGAACAAGGCA 60.812 52.381 0.00 0.00 41.21 4.75
75 80 1.121378 TGGACGGTGGTGTTAGAACA 58.879 50.000 0.00 0.00 36.38 3.18
110 115 3.442273 GCGGGGAATTCTTTGACATGTTA 59.558 43.478 0.00 0.00 0.00 2.41
112 117 1.818674 GCGGGGAATTCTTTGACATGT 59.181 47.619 0.00 0.00 0.00 3.21
113 118 1.818060 TGCGGGGAATTCTTTGACATG 59.182 47.619 5.23 0.00 0.00 3.21
114 119 2.214376 TGCGGGGAATTCTTTGACAT 57.786 45.000 5.23 0.00 0.00 3.06
115 120 1.988293 TTGCGGGGAATTCTTTGACA 58.012 45.000 5.23 0.00 0.00 3.58
116 121 3.378911 TTTTGCGGGGAATTCTTTGAC 57.621 42.857 5.23 0.00 0.00 3.18
139 144 4.024977 GGCGCAATTCTTTGACATGTTTTT 60.025 37.500 10.83 0.00 34.60 1.94
140 145 3.494251 GGCGCAATTCTTTGACATGTTTT 59.506 39.130 10.83 0.00 34.60 2.43
141 146 3.059166 GGCGCAATTCTTTGACATGTTT 58.941 40.909 10.83 0.00 34.60 2.83
142 147 2.035704 TGGCGCAATTCTTTGACATGTT 59.964 40.909 10.83 0.00 34.60 2.71
143 148 1.612950 TGGCGCAATTCTTTGACATGT 59.387 42.857 10.83 0.00 34.60 3.21
148 153 1.669502 GCACATGGCGCAATTCTTTGA 60.670 47.619 10.83 0.00 34.60 2.69
174 192 1.224075 CGCCTCCATATGAAGCAGTG 58.776 55.000 3.65 0.00 30.35 3.66
177 195 1.227943 GCCGCCTCCATATGAAGCA 60.228 57.895 3.65 0.00 30.35 3.91
181 199 3.150949 CCTGCCGCCTCCATATGA 58.849 61.111 3.65 0.00 0.00 2.15
196 214 2.759795 GGAAACAGAGCCCTGCCT 59.240 61.111 0.00 0.00 44.16 4.75
248 267 0.592637 ACGTGTTGGTCGTCGTATCA 59.407 50.000 0.00 0.00 36.85 2.15
351 371 1.443872 GTCCGTCACCAGCGTGTAG 60.444 63.158 0.00 0.00 41.09 2.74
514 539 4.626081 GTGCACACGGCCAGAGGT 62.626 66.667 13.17 0.00 43.89 3.85
575 620 0.945743 GCGACAGATGACTGCACACA 60.946 55.000 0.00 0.00 46.95 3.72
576 621 1.784062 GCGACAGATGACTGCACAC 59.216 57.895 0.00 0.00 46.95 3.82
577 622 1.734117 CGCGACAGATGACTGCACA 60.734 57.895 0.00 0.00 46.95 4.57
579 624 1.006220 AACGCGACAGATGACTGCA 60.006 52.632 15.93 0.00 46.95 4.41
580 625 1.704582 GAACGCGACAGATGACTGC 59.295 57.895 15.93 0.00 46.95 4.40
619 670 2.373169 TCATGGGCAAGTCTCAGAACTT 59.627 45.455 0.00 0.00 40.08 2.66
733 6780 1.080298 TGGTTAACTAACGCGCCATG 58.920 50.000 5.73 0.00 37.07 3.66
763 6810 0.747644 TTATGCATCACGGGTGGCTG 60.748 55.000 0.19 0.00 0.00 4.85
836 6889 5.104859 CCTCTCCACTCTCACTGTACTACTA 60.105 48.000 0.00 0.00 0.00 1.82
837 6890 4.323945 CCTCTCCACTCTCACTGTACTACT 60.324 50.000 0.00 0.00 0.00 2.57
838 6891 3.942748 CCTCTCCACTCTCACTGTACTAC 59.057 52.174 0.00 0.00 0.00 2.73
926 6999 1.205893 GATCGGGGCAGCTTCCTATAG 59.794 57.143 1.39 0.00 0.00 1.31
927 7000 1.267121 GATCGGGGCAGCTTCCTATA 58.733 55.000 1.39 0.00 0.00 1.31
929 7002 2.498941 CGATCGGGGCAGCTTCCTA 61.499 63.158 7.38 0.00 0.00 2.94
930 7003 3.854669 CGATCGGGGCAGCTTCCT 61.855 66.667 7.38 0.00 0.00 3.36
932 7005 2.279784 CTCGATCGGGGCAGCTTC 60.280 66.667 16.41 0.00 0.00 3.86
933 7006 4.537433 GCTCGATCGGGGCAGCTT 62.537 66.667 18.35 0.00 0.00 3.74
938 7011 4.918201 CAAGGGCTCGATCGGGGC 62.918 72.222 31.80 31.80 40.81 5.80
939 7012 4.918201 GCAAGGGCTCGATCGGGG 62.918 72.222 18.35 10.67 36.96 5.73
977 7055 2.806856 GAGCAGCTGGATCAACGCG 61.807 63.158 17.12 3.53 0.00 6.01
1120 7208 1.573436 GAGTGAACTCCGTCGTCGT 59.427 57.895 0.71 0.00 37.02 4.34
1209 7297 2.307929 CGAGTAGATCGTACCGCATTG 58.692 52.381 0.00 0.00 46.62 2.82
1210 7298 2.682952 CGAGTAGATCGTACCGCATT 57.317 50.000 0.00 0.00 46.62 3.56
1249 7341 5.531122 ACCGTTAAGCAGATTAGATAGCA 57.469 39.130 0.00 0.00 0.00 3.49
1250 7342 6.073711 GGAAACCGTTAAGCAGATTAGATAGC 60.074 42.308 0.00 0.00 0.00 2.97
1251 7343 7.210873 AGGAAACCGTTAAGCAGATTAGATAG 58.789 38.462 0.00 0.00 0.00 2.08
1252 7344 7.120923 AGGAAACCGTTAAGCAGATTAGATA 57.879 36.000 0.00 0.00 0.00 1.98
1253 7345 5.990668 AGGAAACCGTTAAGCAGATTAGAT 58.009 37.500 0.00 0.00 0.00 1.98
1565 7666 3.375699 AGGTAGTCCTTGGTCATGTAGG 58.624 50.000 0.00 0.00 42.12 3.18
1700 7813 2.281762 CGATCGATGTCCCGAAAGAAAC 59.718 50.000 10.26 0.00 42.22 2.78
1766 7879 2.672307 AACGCCTCGGTCGAGAGT 60.672 61.111 20.34 16.05 44.53 3.24
1926 8061 3.334691 CGTGGCCTTGAAGTAGATGAAA 58.665 45.455 3.32 0.00 0.00 2.69
2133 8268 3.126879 ATGTGCACGGTGGCGATG 61.127 61.111 13.13 0.00 36.28 3.84
2305 8440 2.481568 CGTCGATCCCATCAATCAATGG 59.518 50.000 0.00 0.00 44.96 3.16
2306 8441 3.392882 TCGTCGATCCCATCAATCAATG 58.607 45.455 0.00 0.00 0.00 2.82
2327 8473 3.606662 CCCGCATCGATCGGTCCT 61.607 66.667 24.71 0.00 45.09 3.85
2405 8557 2.884012 TGAACAGAATGGCGAAACACAT 59.116 40.909 0.00 0.00 43.62 3.21
2463 8622 5.630680 GCATGTGTGTACATTTTTCTCAAGG 59.369 40.000 0.00 0.00 45.01 3.61
2464 8623 6.441274 AGCATGTGTGTACATTTTTCTCAAG 58.559 36.000 0.00 0.00 45.01 3.02
2467 8626 6.470235 GCATAGCATGTGTGTACATTTTTCTC 59.530 38.462 0.00 0.00 45.01 2.87
2468 8627 6.151648 AGCATAGCATGTGTGTACATTTTTCT 59.848 34.615 0.00 0.00 45.01 2.52
2475 8636 5.703978 AAAAAGCATAGCATGTGTGTACA 57.296 34.783 0.00 0.00 41.89 2.90
2498 8659 5.157940 AGCATGTGTATTCTTCTGTCTGT 57.842 39.130 0.00 0.00 0.00 3.41
2499 8660 6.292757 GCATAGCATGTGTATTCTTCTGTCTG 60.293 42.308 0.00 0.00 0.00 3.51
2502 8663 5.678583 AGCATAGCATGTGTATTCTTCTGT 58.321 37.500 0.00 0.00 0.00 3.41
2503 8664 5.178996 GGAGCATAGCATGTGTATTCTTCTG 59.821 44.000 0.00 0.00 0.00 3.02
2514 8676 1.146930 CCACCGGAGCATAGCATGT 59.853 57.895 9.46 0.00 0.00 3.21
2515 8677 0.035881 ATCCACCGGAGCATAGCATG 59.964 55.000 9.46 0.00 34.05 4.06
2544 8707 5.275494 ACAGCAACAAAAATTACGGTGTAC 58.725 37.500 0.00 0.00 33.70 2.90
2547 8710 3.420576 CGACAGCAACAAAAATTACGGTG 59.579 43.478 0.00 0.00 0.00 4.94
2550 8713 3.357823 GCTCGACAGCAACAAAAATTACG 59.642 43.478 0.00 0.00 46.06 3.18
2569 8732 2.802774 GCTGGAGATGCTCTAACTGCTC 60.803 54.545 0.00 0.00 30.97 4.26
2604 8773 0.887387 TCTTTTTCGGCGTCTTGGGG 60.887 55.000 6.85 0.00 0.00 4.96
2605 8774 0.517316 CTCTTTTTCGGCGTCTTGGG 59.483 55.000 6.85 0.00 0.00 4.12
2606 8775 0.110192 GCTCTTTTTCGGCGTCTTGG 60.110 55.000 6.85 0.00 0.00 3.61
2607 8776 0.451135 CGCTCTTTTTCGGCGTCTTG 60.451 55.000 6.85 0.00 43.28 3.02
2608 8777 1.566018 CCGCTCTTTTTCGGCGTCTT 61.566 55.000 6.85 0.00 46.23 3.01
2610 8779 2.474712 CCGCTCTTTTTCGGCGTC 59.525 61.111 6.85 0.00 46.23 5.19
2679 8850 2.805546 CGACCGTGGGACGATGAT 59.194 61.111 0.27 0.00 46.05 2.45
2740 8912 1.402852 GCCGAGTTCCTGCAAAAATCC 60.403 52.381 4.05 0.00 0.00 3.01
2933 9165 4.124943 CAGGGCTGCAGCAGGGAT 62.125 66.667 37.63 16.69 44.36 3.85


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

AutoCloner maintained by Alex Coulton.