Multiple sequence alignment - TraesCS5B01G431800

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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 TraesCS5B01G431800 chr5B 100.000 2626 0 0 1 2626 606546309 606543684 0.000000e+00 4850.0
1 TraesCS5B01G431800 chr5B 79.252 535 76 16 1083 1596 606596419 606595899 9.000000e-90 340.0
2 TraesCS5B01G431800 chr5B 81.720 186 34 0 1083 1268 606485282 606485097 3.500000e-34 156.0
3 TraesCS5B01G431800 chr5B 100.000 31 0 0 483 513 592070541 592070511 1.020000e-04 58.4
4 TraesCS5B01G431800 chr1B 95.597 863 28 8 1702 2560 295768717 295769573 0.000000e+00 1375.0
5 TraesCS5B01G431800 chr2B 96.514 832 25 3 1720 2549 316103251 316104080 0.000000e+00 1373.0
6 TraesCS5B01G431800 chr2B 96.519 833 21 5 1722 2549 296026329 296027158 0.000000e+00 1371.0
7 TraesCS5B01G431800 chr6B 95.887 851 28 6 1715 2562 67945400 67946246 0.000000e+00 1371.0
8 TraesCS5B01G431800 chr6B 96.394 832 25 4 1720 2549 179995373 179996201 0.000000e+00 1365.0
9 TraesCS5B01G431800 chr4B 96.510 831 23 4 1720 2549 662088251 662087426 0.000000e+00 1369.0
10 TraesCS5B01G431800 chr4A 96.154 832 30 2 1721 2550 647597376 647598207 0.000000e+00 1358.0
11 TraesCS5B01G431800 chr4A 95.933 836 30 3 1719 2553 151959373 151958541 0.000000e+00 1352.0
12 TraesCS5B01G431800 chr3A 96.265 830 28 3 1721 2549 522043380 522044207 0.000000e+00 1358.0
13 TraesCS5B01G431800 chr5D 93.201 706 39 7 1002 1701 491660679 491659977 0.000000e+00 1029.0
14 TraesCS5B01G431800 chr5D 87.801 582 42 13 422 999 491661319 491660763 0.000000e+00 654.0
15 TraesCS5B01G431800 chr5D 82.659 519 66 12 1085 1596 491669217 491668716 3.100000e-119 438.0
16 TraesCS5B01G431800 chr5D 84.615 117 12 3 303 413 98814491 98814375 7.680000e-21 111.0
17 TraesCS5B01G431800 chr5A 90.759 606 39 7 1116 1717 613929406 613928814 0.000000e+00 793.0
18 TraesCS5B01G431800 chr5A 90.141 426 29 6 7 423 613930580 613930159 2.300000e-150 542.0
19 TraesCS5B01G431800 chr5A 89.939 328 21 5 685 1003 613929771 613929447 1.880000e-111 412.0
20 TraesCS5B01G431800 chr5A 88.129 278 25 5 422 692 613930122 613929846 9.070000e-85 324.0
21 TraesCS5B01G431800 chr5A 78.481 237 37 9 191 417 540789699 540789931 2.720000e-30 143.0
22 TraesCS5B01G431800 chr5A 78.059 237 38 9 191 417 540818653 540818885 1.270000e-28 137.0
23 TraesCS5B01G431800 chr5A 86.957 69 8 1 451 518 342240499 342240431 2.800000e-10 76.8
24 TraesCS5B01G431800 chr6A 83.673 196 21 6 236 421 8798924 8798730 9.660000e-40 174.0


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 TraesCS5B01G431800 chr5B 606543684 606546309 2625 True 4850.00 4850 100.000 1 2626 1 chr5B.!!$R3 2625
1 TraesCS5B01G431800 chr5B 606595899 606596419 520 True 340.00 340 79.252 1083 1596 1 chr5B.!!$R4 513
2 TraesCS5B01G431800 chr1B 295768717 295769573 856 False 1375.00 1375 95.597 1702 2560 1 chr1B.!!$F1 858
3 TraesCS5B01G431800 chr2B 316103251 316104080 829 False 1373.00 1373 96.514 1720 2549 1 chr2B.!!$F2 829
4 TraesCS5B01G431800 chr2B 296026329 296027158 829 False 1371.00 1371 96.519 1722 2549 1 chr2B.!!$F1 827
5 TraesCS5B01G431800 chr6B 67945400 67946246 846 False 1371.00 1371 95.887 1715 2562 1 chr6B.!!$F1 847
6 TraesCS5B01G431800 chr6B 179995373 179996201 828 False 1365.00 1365 96.394 1720 2549 1 chr6B.!!$F2 829
7 TraesCS5B01G431800 chr4B 662087426 662088251 825 True 1369.00 1369 96.510 1720 2549 1 chr4B.!!$R1 829
8 TraesCS5B01G431800 chr4A 647597376 647598207 831 False 1358.00 1358 96.154 1721 2550 1 chr4A.!!$F1 829
9 TraesCS5B01G431800 chr4A 151958541 151959373 832 True 1352.00 1352 95.933 1719 2553 1 chr4A.!!$R1 834
10 TraesCS5B01G431800 chr3A 522043380 522044207 827 False 1358.00 1358 96.265 1721 2549 1 chr3A.!!$F1 828
11 TraesCS5B01G431800 chr5D 491659977 491661319 1342 True 841.50 1029 90.501 422 1701 2 chr5D.!!$R3 1279
12 TraesCS5B01G431800 chr5D 491668716 491669217 501 True 438.00 438 82.659 1085 1596 1 chr5D.!!$R2 511
13 TraesCS5B01G431800 chr5A 613928814 613930580 1766 True 517.75 793 89.742 7 1717 4 chr5A.!!$R2 1710

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
576 625 0.032403 TGGTTACACTTCACGACCCG 59.968 55.0 0.0 0.0 0.0 5.28 F
1075 1302 0.096976 CACGCCATTGTTCGATCCAC 59.903 55.0 0.0 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1554 1810 0.236711 CGACGACGACCGGCTATTAT 59.763 55.000 0.0 0.0 46.22 1.28 R
2599 2870 1.065251 CGTTCGCTAGTTAGAGGGTCC 59.935 57.143 0.0 0.0 0.00 4.46 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
44 45 6.093633 GGACTTCGAAGTGCTTATAAATTGGT 59.906 38.462 34.31 8.69 43.15 3.67
128 129 3.496331 GGACCTTTGGAACCTCATTTGA 58.504 45.455 0.00 0.00 0.00 2.69
166 167 6.241207 TCCTAATTCAGAGTTTTTGCTTCG 57.759 37.500 0.00 0.00 0.00 3.79
189 190 3.057969 TGCAACTATGAACAGTCCCTG 57.942 47.619 0.00 0.00 37.52 4.45
199 200 2.640316 ACAGTCCCTGTTGAAAGTCC 57.360 50.000 0.00 0.00 42.59 3.85
211 212 6.274157 TGTTGAAAGTCCTTGCTGTTAAAA 57.726 33.333 0.00 0.00 0.00 1.52
212 213 6.329496 TGTTGAAAGTCCTTGCTGTTAAAAG 58.671 36.000 0.00 0.00 0.00 2.27
222 223 8.084684 GTCCTTGCTGTTAAAAGAAATCTCATT 58.915 33.333 0.00 0.00 0.00 2.57
227 228 8.412456 TGCTGTTAAAAGAAATCTCATTGTCAA 58.588 29.630 0.00 0.00 0.00 3.18
253 254 5.065218 GTGTTATCATGAGATGGTTGGTGTC 59.935 44.000 0.09 0.00 35.67 3.67
254 255 5.045651 TGTTATCATGAGATGGTTGGTGTCT 60.046 40.000 0.09 0.00 35.67 3.41
260 261 5.551305 TGAGATGGTTGGTGTCTATATGG 57.449 43.478 0.00 0.00 0.00 2.74
266 267 5.436175 TGGTTGGTGTCTATATGGTCATTG 58.564 41.667 0.00 0.00 0.00 2.82
267 268 4.275936 GGTTGGTGTCTATATGGTCATTGC 59.724 45.833 0.00 0.00 0.00 3.56
268 269 4.085357 TGGTGTCTATATGGTCATTGCC 57.915 45.455 0.00 0.00 0.00 4.52
269 270 3.457749 TGGTGTCTATATGGTCATTGCCA 59.542 43.478 2.90 2.90 43.48 4.92
284 285 0.536260 TGCCATAGTTTGCCCATTGC 59.464 50.000 0.00 0.00 41.77 3.56
295 296 2.110967 CCCATTGCAGAGCTGGTCG 61.111 63.158 0.00 0.00 0.00 4.79
313 318 5.099575 TGGTCGCTTTTGTTTTCTTTTCTC 58.900 37.500 0.00 0.00 0.00 2.87
370 380 2.440539 TGGTTTGTTTTTGTGCGTGT 57.559 40.000 0.00 0.00 0.00 4.49
375 385 4.201542 GGTTTGTTTTTGTGCGTGTGTTAG 60.202 41.667 0.00 0.00 0.00 2.34
376 386 4.421033 TTGTTTTTGTGCGTGTGTTAGA 57.579 36.364 0.00 0.00 0.00 2.10
377 387 4.624336 TGTTTTTGTGCGTGTGTTAGAT 57.376 36.364 0.00 0.00 0.00 1.98
378 388 4.346970 TGTTTTTGTGCGTGTGTTAGATG 58.653 39.130 0.00 0.00 0.00 2.90
380 390 4.624336 TTTTGTGCGTGTGTTAGATGTT 57.376 36.364 0.00 0.00 0.00 2.71
382 392 2.827652 TGTGCGTGTGTTAGATGTTGA 58.172 42.857 0.00 0.00 0.00 3.18
389 399 5.139482 CGTGTGTTAGATGTTGATTGTGTG 58.861 41.667 0.00 0.00 0.00 3.82
398 408 4.764679 TGTTGATTGTGTGCATCCTAAC 57.235 40.909 0.00 0.00 0.00 2.34
399 409 3.505680 TGTTGATTGTGTGCATCCTAACC 59.494 43.478 0.00 0.00 0.00 2.85
410 420 0.106519 ATCCTAACCATGCACAGGCC 60.107 55.000 6.93 0.00 40.13 5.19
428 438 0.891449 CCGGGTGTGTGTGCCAATAA 60.891 55.000 0.00 0.00 0.00 1.40
432 442 3.584834 GGGTGTGTGTGCCAATAAAATC 58.415 45.455 0.00 0.00 0.00 2.17
435 445 4.502259 GGTGTGTGTGCCAATAAAATCCAA 60.502 41.667 0.00 0.00 0.00 3.53
440 487 6.926272 GTGTGTGCCAATAAAATCCAACTTTA 59.074 34.615 0.00 0.00 0.00 1.85
441 488 7.602265 GTGTGTGCCAATAAAATCCAACTTTAT 59.398 33.333 0.00 0.00 31.71 1.40
442 489 7.816995 TGTGTGCCAATAAAATCCAACTTTATC 59.183 33.333 0.00 0.00 30.41 1.75
443 490 7.009174 GTGTGCCAATAAAATCCAACTTTATCG 59.991 37.037 0.00 0.00 30.41 2.92
444 491 6.475402 GTGCCAATAAAATCCAACTTTATCGG 59.525 38.462 0.00 0.00 29.50 4.18
481 530 7.285401 AGACATTTGACAGTCCAATTTACACTT 59.715 33.333 0.00 0.00 35.38 3.16
542 591 4.040095 AGTTACAAACACTCCACTAGTCCC 59.960 45.833 0.00 0.00 35.76 4.46
545 594 2.368875 CAAACACTCCACTAGTCCCTGT 59.631 50.000 0.00 0.00 35.76 4.00
549 598 2.755655 CACTCCACTAGTCCCTGTACAG 59.244 54.545 16.34 16.34 35.76 2.74
576 625 0.032403 TGGTTACACTTCACGACCCG 59.968 55.000 0.00 0.00 0.00 5.28
581 630 4.309950 ACTTCACGACCCGCCCAC 62.310 66.667 0.00 0.00 0.00 4.61
582 631 4.003788 CTTCACGACCCGCCCACT 62.004 66.667 0.00 0.00 0.00 4.00
588 637 4.699522 GACCCGCCCACTGTCACC 62.700 72.222 0.00 0.00 0.00 4.02
616 665 0.251634 CACCAGAGAGGAAGAAGGCC 59.748 60.000 0.00 0.00 41.22 5.19
648 701 2.763039 TGACCAGATCCCTCATAGCAA 58.237 47.619 0.00 0.00 0.00 3.91
699 836 3.001365 CGAATAAAGTAGTTCGCCACGAC 60.001 47.826 0.00 0.00 40.39 4.34
742 888 0.750850 CTCGTTGGACGGGGACATAT 59.249 55.000 0.27 0.00 42.81 1.78
743 889 0.748450 TCGTTGGACGGGGACATATC 59.252 55.000 0.27 0.00 42.81 1.63
748 894 2.536066 TGGACGGGGACATATCCTATG 58.464 52.381 0.00 0.00 45.46 2.23
755 901 2.769095 GGGACATATCCTATGCTCTCCC 59.231 54.545 0.00 5.87 45.46 4.30
758 904 3.957497 GACATATCCTATGCTCTCCCGAT 59.043 47.826 0.00 0.00 0.00 4.18
804 950 2.575805 CTCCAAAGCACCTTCCTTCT 57.424 50.000 0.00 0.00 0.00 2.85
842 988 1.605712 CCTGAGAAGACGAAAACCGCT 60.606 52.381 0.00 0.00 43.32 5.52
863 1009 0.388134 GACGCGAAACTCCTGCACTA 60.388 55.000 15.93 0.00 0.00 2.74
926 1072 5.588696 AACCTATTGTTGACTCGGTACGGA 61.589 45.833 2.87 2.87 44.85 4.69
946 1092 4.628074 GGAACTGCTAGCGTAATCCATTA 58.372 43.478 18.40 0.00 0.00 1.90
948 1094 5.701290 GGAACTGCTAGCGTAATCCATTATT 59.299 40.000 18.40 0.31 0.00 1.40
988 1134 5.122239 TCTGAGAAACTCCAATGCAATTACG 59.878 40.000 0.00 0.00 32.46 3.18
1018 1245 5.122512 ACTGTTATATAACGCTCGAGCAT 57.877 39.130 34.69 24.97 42.21 3.79
1033 1260 2.190578 CATCTCCTTGGACCCGGC 59.809 66.667 0.00 0.00 0.00 6.13
1075 1302 0.096976 CACGCCATTGTTCGATCCAC 59.903 55.000 0.00 0.00 0.00 4.02
1120 1347 2.721797 GCTGACGTTGAGCAAACATACG 60.722 50.000 13.93 0.00 38.84 3.06
1251 1504 0.302890 CTAGTACTACCGTGCCGTCG 59.697 60.000 0.00 0.00 0.00 5.12
1379 1632 0.247736 GACATCCTCGAGTGGCTTGT 59.752 55.000 12.31 7.12 0.00 3.16
1458 1711 4.148825 GACAGGTGCCTCCGCGAT 62.149 66.667 8.23 0.00 41.99 4.58
1464 1717 1.153549 GTGCCTCCGCGATCTCTTT 60.154 57.895 8.23 0.00 38.08 2.52
1492 1745 2.815647 CGGTCGGCAAGCTCTTCC 60.816 66.667 0.00 0.00 0.00 3.46
1585 1848 1.805945 GTCGTCGTCCAGGCATGTC 60.806 63.158 0.00 0.00 0.00 3.06
1682 1945 4.293494 ACCAGGCTCAGAGATTCATCTTA 58.707 43.478 0.00 0.00 37.25 2.10
1747 2010 1.295792 CACTAACTGCCACACGTGTT 58.704 50.000 20.79 5.94 0.00 3.32
2113 2376 8.814038 ATTAAGAAACTAGACTTGCCATGAAT 57.186 30.769 0.00 0.00 0.00 2.57
2161 2424 3.063485 GCACGTAAAATTGCCATGGTTT 58.937 40.909 14.67 8.41 32.21 3.27
2247 2511 8.121305 TGCCATGATCTACAAACTAAAATTGT 57.879 30.769 0.00 0.00 43.14 2.71
2343 2611 7.389803 AAATGTCGAAACATATCAACATGGA 57.610 32.000 0.00 0.00 45.48 3.41
2446 2717 6.986904 ACATTTTTAAGCCGAAAACCAAAA 57.013 29.167 0.00 0.00 0.00 2.44
2447 2718 7.379098 ACATTTTTAAGCCGAAAACCAAAAA 57.621 28.000 0.00 0.00 31.65 1.94
2477 2748 9.438228 AATTCTGCTGATGTCATCTATTCATAG 57.562 33.333 13.90 2.53 0.00 2.23
2550 2821 4.054671 CACATGTGGGCGTTAACATTTTT 58.945 39.130 18.51 0.00 34.81 1.94
2555 2826 5.657474 TGTGGGCGTTAACATTTTTGTTTA 58.343 33.333 6.39 0.00 33.59 2.01
2605 2876 9.915564 ATATTAGGACTATCTTTTAAGGACCCT 57.084 33.333 0.00 0.00 0.00 4.34
2606 2877 7.672122 TTAGGACTATCTTTTAAGGACCCTC 57.328 40.000 0.00 0.00 0.00 4.30
2607 2878 5.855988 AGGACTATCTTTTAAGGACCCTCT 58.144 41.667 0.00 0.00 0.00 3.69
2608 2879 6.994582 AGGACTATCTTTTAAGGACCCTCTA 58.005 40.000 0.00 0.00 0.00 2.43
2609 2880 7.428335 AGGACTATCTTTTAAGGACCCTCTAA 58.572 38.462 0.00 0.00 0.00 2.10
2610 2881 7.345132 AGGACTATCTTTTAAGGACCCTCTAAC 59.655 40.741 0.00 0.00 0.00 2.34
2611 2882 7.345132 GGACTATCTTTTAAGGACCCTCTAACT 59.655 40.741 0.00 0.00 0.00 2.24
2612 2883 9.418839 GACTATCTTTTAAGGACCCTCTAACTA 57.581 37.037 0.00 0.00 0.00 2.24
2613 2884 9.423964 ACTATCTTTTAAGGACCCTCTAACTAG 57.576 37.037 0.00 0.00 0.00 2.57
2614 2885 6.541934 TCTTTTAAGGACCCTCTAACTAGC 57.458 41.667 0.00 0.00 0.00 3.42
2615 2886 4.996788 TTTAAGGACCCTCTAACTAGCG 57.003 45.455 0.00 0.00 0.00 4.26
2616 2887 2.822707 AAGGACCCTCTAACTAGCGA 57.177 50.000 0.00 0.00 0.00 4.93
2617 2888 2.822707 AGGACCCTCTAACTAGCGAA 57.177 50.000 0.00 0.00 0.00 4.70
2618 2889 2.377073 AGGACCCTCTAACTAGCGAAC 58.623 52.381 0.00 0.00 0.00 3.95
2619 2890 1.065251 GGACCCTCTAACTAGCGAACG 59.935 57.143 0.00 0.00 0.00 3.95
2620 2891 1.742268 GACCCTCTAACTAGCGAACGT 59.258 52.381 0.00 0.00 0.00 3.99
2621 2892 2.163211 GACCCTCTAACTAGCGAACGTT 59.837 50.000 0.00 0.00 0.00 3.99
2622 2893 2.094854 ACCCTCTAACTAGCGAACGTTG 60.095 50.000 5.00 0.00 0.00 4.10
2623 2894 2.527100 CCTCTAACTAGCGAACGTTGG 58.473 52.381 5.00 5.50 0.00 3.77
2624 2895 1.918609 CTCTAACTAGCGAACGTTGGC 59.081 52.381 25.54 25.54 0.00 4.52
2625 2896 1.542915 TCTAACTAGCGAACGTTGGCT 59.457 47.619 34.71 34.71 44.57 4.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 6.031471 GCACTTCGAAGTCCAAACTTAAAAA 58.969 36.000 27.54 0.00 45.80 1.94
9 10 5.355910 AGCACTTCGAAGTCCAAACTTAAAA 59.644 36.000 27.54 0.00 45.80 1.52
10 11 4.879545 AGCACTTCGAAGTCCAAACTTAAA 59.120 37.500 27.54 0.00 45.80 1.52
11 12 4.448210 AGCACTTCGAAGTCCAAACTTAA 58.552 39.130 27.54 0.00 45.80 1.85
12 13 4.067972 AGCACTTCGAAGTCCAAACTTA 57.932 40.909 27.54 0.00 45.80 2.24
44 45 2.831685 AGTTACATTCTCGTGTGGCA 57.168 45.000 0.00 0.00 33.62 4.92
75 76 5.400066 TCACGATGTCACTCTATTGGAAA 57.600 39.130 0.00 0.00 0.00 3.13
84 85 2.271800 GGTCCATTCACGATGTCACTC 58.728 52.381 0.00 0.00 33.71 3.51
166 167 2.098117 GGGACTGTTCATAGTTGCATGC 59.902 50.000 11.82 11.82 0.00 4.06
189 190 6.560711 TCTTTTAACAGCAAGGACTTTCAAC 58.439 36.000 0.00 0.00 0.00 3.18
197 198 7.765695 ATGAGATTTCTTTTAACAGCAAGGA 57.234 32.000 0.00 0.00 0.00 3.36
199 200 8.807667 ACAATGAGATTTCTTTTAACAGCAAG 57.192 30.769 0.00 0.00 0.00 4.01
211 212 9.234827 TGATAACACATTGACAATGAGATTTCT 57.765 29.630 30.23 9.89 41.46 2.52
222 223 6.417258 ACCATCTCATGATAACACATTGACA 58.583 36.000 0.00 0.00 0.00 3.58
227 228 5.591472 CACCAACCATCTCATGATAACACAT 59.409 40.000 0.00 0.00 0.00 3.21
232 233 5.698741 AGACACCAACCATCTCATGATAA 57.301 39.130 0.00 0.00 0.00 1.75
234 235 5.901413 ATAGACACCAACCATCTCATGAT 57.099 39.130 0.00 0.00 0.00 2.45
295 296 4.112634 AGGCGAGAAAAGAAAACAAAAGC 58.887 39.130 0.00 0.00 0.00 3.51
313 318 0.810031 ACCAAAGCTATGCGTAGGCG 60.810 55.000 14.75 0.00 44.10 5.52
370 380 5.106197 GGATGCACACAATCAACATCTAACA 60.106 40.000 0.00 0.00 37.77 2.41
375 385 5.335127 GTTAGGATGCACACAATCAACATC 58.665 41.667 0.00 0.00 37.09 3.06
376 386 4.158394 GGTTAGGATGCACACAATCAACAT 59.842 41.667 0.00 0.00 0.00 2.71
377 387 3.505680 GGTTAGGATGCACACAATCAACA 59.494 43.478 0.00 0.00 0.00 3.33
378 388 3.505680 TGGTTAGGATGCACACAATCAAC 59.494 43.478 0.00 0.00 0.00 3.18
380 390 3.431673 TGGTTAGGATGCACACAATCA 57.568 42.857 0.00 0.00 0.00 2.57
382 392 2.428171 GCATGGTTAGGATGCACACAAT 59.572 45.455 0.00 0.00 44.74 2.71
389 399 1.027357 CCTGTGCATGGTTAGGATGC 58.973 55.000 0.00 0.00 45.45 3.91
410 420 0.955178 TTTATTGGCACACACACCCG 59.045 50.000 0.00 0.00 39.29 5.28
542 591 1.967319 AACCAAGGTGTGCTGTACAG 58.033 50.000 18.93 18.93 40.69 2.74
545 594 2.436542 AGTGTAACCAAGGTGTGCTGTA 59.563 45.455 0.00 0.00 37.80 2.74
549 598 2.032924 GTGAAGTGTAACCAAGGTGTGC 59.967 50.000 0.00 0.00 37.80 4.57
576 625 0.668535 GAGTTTTGGTGACAGTGGGC 59.331 55.000 0.00 0.00 44.54 5.36
581 630 1.318576 GGTGGGAGTTTTGGTGACAG 58.681 55.000 0.00 0.00 44.54 3.51
582 631 0.626382 TGGTGGGAGTTTTGGTGACA 59.374 50.000 0.00 0.00 39.83 3.58
588 637 1.699634 TCCTCTCTGGTGGGAGTTTTG 59.300 52.381 0.00 0.00 37.07 2.44
616 665 1.676635 CTGGTCATGGTGGGTGCTG 60.677 63.158 0.00 0.00 0.00 4.41
712 849 2.100631 CCAACGAGTCACATCGGCC 61.101 63.158 0.00 0.00 46.91 6.13
722 859 0.612732 TATGTCCCCGTCCAACGAGT 60.613 55.000 0.24 0.00 46.05 4.18
742 888 2.088104 ACAATCGGGAGAGCATAGGA 57.912 50.000 0.00 0.00 45.48 2.94
743 889 4.039245 TCTTTACAATCGGGAGAGCATAGG 59.961 45.833 0.00 0.00 45.48 2.57
748 894 3.119101 TGAGTCTTTACAATCGGGAGAGC 60.119 47.826 0.00 0.00 45.48 4.09
755 901 6.758416 TGAATGGAGATGAGTCTTTACAATCG 59.242 38.462 0.00 0.00 33.97 3.34
758 904 7.335171 CACATGAATGGAGATGAGTCTTTACAA 59.665 37.037 0.00 0.00 33.97 2.41
842 988 2.357034 GCAGGAGTTTCGCGTCCA 60.357 61.111 15.02 0.00 35.02 4.02
863 1009 7.039882 CGTTATGTAACCTCAATTACAGACCT 58.960 38.462 4.82 0.00 45.68 3.85
926 1072 8.094548 TGATAATAATGGATTACGCTAGCAGTT 58.905 33.333 16.45 0.21 32.72 3.16
988 1134 4.738740 AGCGTTATATAACAGTCGTCAAGC 59.261 41.667 22.27 14.54 35.99 4.01
1018 1245 3.943137 ATGGCCGGGTCCAAGGAGA 62.943 63.158 13.04 0.00 39.96 3.71
1120 1347 1.336125 GATCTTGCCTGCCATTGCTAC 59.664 52.381 0.00 0.00 38.71 3.58
1180 1407 0.608640 GTTGGAGTGGACGTGAGGAT 59.391 55.000 0.00 0.00 0.00 3.24
1428 1681 4.803426 CTGTCGCCGACCCTCTGC 62.803 72.222 15.60 0.00 0.00 4.26
1458 1711 1.595993 CCGCAGAGTCGGGAAAGAGA 61.596 60.000 0.00 0.00 45.38 3.10
1492 1745 1.229336 AGTGACTGACCAGGGGAGG 60.229 63.158 1.82 0.00 0.00 4.30
1552 1808 2.096268 CGACGACGACCGGCTATTATTA 60.096 50.000 0.00 0.00 46.22 0.98
1553 1809 1.334419 CGACGACGACCGGCTATTATT 60.334 52.381 0.00 0.00 46.22 1.40
1554 1810 0.236711 CGACGACGACCGGCTATTAT 59.763 55.000 0.00 0.00 46.22 1.28
1585 1848 2.890109 GCGGATGCCTTGAGATGCG 61.890 63.158 0.00 0.00 36.58 4.73
1711 1974 7.640240 GCAGTTAGTGCGATCCTAAATAAAAAG 59.360 37.037 0.00 0.00 43.99 2.27
1729 1992 1.295792 CAACACGTGTGGCAGTTAGT 58.704 50.000 24.16 0.00 34.19 2.24
1747 2010 2.922503 TGCGTCTCCCTTCCTGCA 60.923 61.111 0.00 0.00 0.00 4.41
2247 2511 5.278758 GGCTTAAACTAAAGTTGCCATGTGA 60.279 40.000 14.54 0.00 41.51 3.58
2343 2611 5.411977 TCGACGAGATCTTCAAAACTAGACT 59.588 40.000 0.00 0.00 0.00 3.24
2380 2648 5.008316 AGCGAACTAAAAATCCGTTTTCACT 59.992 36.000 0.00 0.00 40.07 3.41
2477 2748 3.429822 CCATCATCACTCATTTTGCCACC 60.430 47.826 0.00 0.00 0.00 4.61
2579 2850 9.915564 AGGGTCCTTAAAAGATAGTCCTAATAT 57.084 33.333 0.00 0.00 0.00 1.28
2580 2851 9.377238 GAGGGTCCTTAAAAGATAGTCCTAATA 57.623 37.037 0.00 0.00 0.00 0.98
2581 2852 8.074991 AGAGGGTCCTTAAAAGATAGTCCTAAT 58.925 37.037 0.00 0.00 0.00 1.73
2582 2853 7.428335 AGAGGGTCCTTAAAAGATAGTCCTAA 58.572 38.462 0.00 0.00 0.00 2.69
2583 2854 6.994582 AGAGGGTCCTTAAAAGATAGTCCTA 58.005 40.000 0.00 0.00 0.00 2.94
2584 2855 5.855988 AGAGGGTCCTTAAAAGATAGTCCT 58.144 41.667 0.00 0.00 0.00 3.85
2585 2856 7.345132 AGTTAGAGGGTCCTTAAAAGATAGTCC 59.655 40.741 0.00 0.00 0.00 3.85
2586 2857 8.308851 AGTTAGAGGGTCCTTAAAAGATAGTC 57.691 38.462 0.00 0.00 0.00 2.59
2587 2858 9.423964 CTAGTTAGAGGGTCCTTAAAAGATAGT 57.576 37.037 0.00 0.00 0.00 2.12
2588 2859 8.361889 GCTAGTTAGAGGGTCCTTAAAAGATAG 58.638 40.741 0.00 0.00 0.00 2.08
2589 2860 7.014038 CGCTAGTTAGAGGGTCCTTAAAAGATA 59.986 40.741 0.00 0.00 0.00 1.98
2590 2861 6.183360 CGCTAGTTAGAGGGTCCTTAAAAGAT 60.183 42.308 0.00 0.00 0.00 2.40
2591 2862 5.126707 CGCTAGTTAGAGGGTCCTTAAAAGA 59.873 44.000 0.00 0.00 0.00 2.52
2592 2863 5.126707 TCGCTAGTTAGAGGGTCCTTAAAAG 59.873 44.000 0.00 0.00 0.00 2.27
2593 2864 5.018809 TCGCTAGTTAGAGGGTCCTTAAAA 58.981 41.667 0.00 0.00 0.00 1.52
2594 2865 4.603131 TCGCTAGTTAGAGGGTCCTTAAA 58.397 43.478 0.00 0.00 0.00 1.52
2595 2866 4.240881 TCGCTAGTTAGAGGGTCCTTAA 57.759 45.455 0.00 0.00 0.00 1.85
2596 2867 3.939740 TCGCTAGTTAGAGGGTCCTTA 57.060 47.619 0.00 0.00 0.00 2.69
2597 2868 2.759535 GTTCGCTAGTTAGAGGGTCCTT 59.240 50.000 0.00 0.00 0.00 3.36
2598 2869 2.377073 GTTCGCTAGTTAGAGGGTCCT 58.623 52.381 0.00 0.00 0.00 3.85
2599 2870 1.065251 CGTTCGCTAGTTAGAGGGTCC 59.935 57.143 0.00 0.00 0.00 4.46
2600 2871 1.742268 ACGTTCGCTAGTTAGAGGGTC 59.258 52.381 0.00 0.00 0.00 4.46
2601 2872 1.831580 ACGTTCGCTAGTTAGAGGGT 58.168 50.000 0.00 0.00 0.00 4.34
2602 2873 2.527100 CAACGTTCGCTAGTTAGAGGG 58.473 52.381 0.00 0.00 0.00 4.30
2603 2874 2.527100 CCAACGTTCGCTAGTTAGAGG 58.473 52.381 0.00 0.00 0.00 3.69
2604 2875 1.918609 GCCAACGTTCGCTAGTTAGAG 59.081 52.381 10.84 0.00 0.00 2.43
2605 2876 1.542915 AGCCAACGTTCGCTAGTTAGA 59.457 47.619 19.16 0.00 32.26 2.10
2606 2877 1.992170 AGCCAACGTTCGCTAGTTAG 58.008 50.000 19.16 0.00 32.26 2.34


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

AutoCloner maintained by Alex Coulton.