Multiple sequence alignment - TraesCS6B01G109100

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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 TraesCS6B01G109100 chr6B 100.000 2903 0 0 1 2903 89694977 89697879 0.000000e+00 5361
1 TraesCS6B01G109100 chr6D 96.419 1424 50 1 884 2306 38582626 38584049 0.000000e+00 2346
2 TraesCS6B01G109100 chr6D 93.946 892 45 7 1 884 38576491 38577381 0.000000e+00 1339
3 TraesCS6B01G109100 chr6D 93.548 248 14 1 2656 2903 38584310 38584555 4.570000e-98 368
4 TraesCS6B01G109100 chr6D 91.386 267 23 0 2361 2627 38584048 38584314 1.640000e-97 366
5 TraesCS6B01G109100 chr3A 85.241 2141 236 42 17 2095 102117510 102115388 0.000000e+00 2130
6 TraesCS6B01G109100 chr3D 84.967 2142 248 36 11 2095 85063059 85060935 0.000000e+00 2104
7 TraesCS6B01G109100 chr3B 84.562 2144 233 48 16 2095 130648648 130646539 0.000000e+00 2036
8 TraesCS6B01G109100 chr3B 85.504 1973 213 29 175 2095 134276161 134274210 0.000000e+00 1991
9 TraesCS6B01G109100 chrUn 93.530 1221 65 8 453 1660 114263417 114262198 0.000000e+00 1805
10 TraesCS6B01G109100 chrUn 96.302 649 24 0 1658 2306 114253137 114252489 0.000000e+00 1066
11 TraesCS6B01G109100 chrUn 91.791 268 20 2 2361 2627 114252490 114252224 3.530000e-99 372
12 TraesCS6B01G109100 chrUn 92.742 248 16 2 2656 2903 114252228 114251983 9.890000e-95 357
13 TraesCS6B01G109100 chr2B 76.594 1333 261 31 589 1884 760829842 760828524 0.000000e+00 686
14 TraesCS6B01G109100 chr2D 77.638 872 162 14 582 1428 620399298 620398435 1.550000e-137 499


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 TraesCS6B01G109100 chr6B 89694977 89697879 2902 False 5361.000000 5361 100.000000 1 2903 1 chr6B.!!$F1 2902
1 TraesCS6B01G109100 chr6D 38576491 38577381 890 False 1339.000000 1339 93.946000 1 884 1 chr6D.!!$F1 883
2 TraesCS6B01G109100 chr6D 38582626 38584555 1929 False 1026.666667 2346 93.784333 884 2903 3 chr6D.!!$F2 2019
3 TraesCS6B01G109100 chr3A 102115388 102117510 2122 True 2130.000000 2130 85.241000 17 2095 1 chr3A.!!$R1 2078
4 TraesCS6B01G109100 chr3D 85060935 85063059 2124 True 2104.000000 2104 84.967000 11 2095 1 chr3D.!!$R1 2084
5 TraesCS6B01G109100 chr3B 130646539 130648648 2109 True 2036.000000 2036 84.562000 16 2095 1 chr3B.!!$R1 2079
6 TraesCS6B01G109100 chr3B 134274210 134276161 1951 True 1991.000000 1991 85.504000 175 2095 1 chr3B.!!$R2 1920
7 TraesCS6B01G109100 chrUn 114262198 114263417 1219 True 1805.000000 1805 93.530000 453 1660 1 chrUn.!!$R1 1207
8 TraesCS6B01G109100 chrUn 114251983 114253137 1154 True 598.333333 1066 93.611667 1658 2903 3 chrUn.!!$R2 1245
9 TraesCS6B01G109100 chr2B 760828524 760829842 1318 True 686.000000 686 76.594000 589 1884 1 chr2B.!!$R1 1295
10 TraesCS6B01G109100 chr2D 620398435 620399298 863 True 499.000000 499 77.638000 582 1428 1 chr2D.!!$R1 846

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
900 960 0.242825 CGTACAGCCTCGTGGAGAAA 59.757 55.0 7.92 0.0 34.57 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2424 2513 0.321564 TCACCTTCACATTGCCCGAG 60.322 55.0 0.0 0.0 0.0 4.63 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
219 231 0.889638 TCACGCTCTGTCTCCTCGTT 60.890 55.000 0.00 0.00 0.00 3.85
245 257 2.266554 CCGAACTGTGATCTTGAGCTC 58.733 52.381 6.82 6.82 0.00 4.09
303 316 1.084370 GGATTCGGTTCAGTCCTGCG 61.084 60.000 0.00 0.00 0.00 5.18
355 371 1.425412 ACCCGTTCGATTCAAAGTCG 58.575 50.000 0.00 0.00 40.30 4.18
365 381 4.212636 TCGATTCAAAGTCGGAACCTTTTC 59.787 41.667 0.00 0.00 39.45 2.29
407 440 1.340017 CCAATTTCCGGCAGAAGGAGA 60.340 52.381 0.00 0.00 39.22 3.71
410 449 0.984230 TTTCCGGCAGAAGGAGACAT 59.016 50.000 0.00 0.00 39.22 3.06
484 523 1.068541 GGATTGCAACCTTCCAACGAC 60.069 52.381 11.87 0.00 0.00 4.34
493 533 2.621526 ACCTTCCAACGACCAATTGTTC 59.378 45.455 4.43 0.00 29.14 3.18
524 567 1.541588 GCCGATTTATCTCCAATGGGC 59.458 52.381 0.00 3.34 44.95 5.36
548 591 3.022557 ACCTGTAGCGTATCCAAGGTA 57.977 47.619 0.00 0.00 0.00 3.08
556 599 2.351544 GCGTATCCAAGGTATCGAGTCC 60.352 54.545 0.00 0.00 0.00 3.85
569 612 1.607801 CGAGTCCAGCCATCCACAGA 61.608 60.000 0.00 0.00 0.00 3.41
774 823 3.677284 CTGATGCGTGCCTGCTCCT 62.677 63.158 0.00 0.00 35.36 3.69
900 960 0.242825 CGTACAGCCTCGTGGAGAAA 59.757 55.000 7.92 0.00 34.57 2.52
962 1022 2.777459 AGGTATCTGATCGGGTCCTT 57.223 50.000 0.62 0.00 0.00 3.36
963 1023 2.320781 AGGTATCTGATCGGGTCCTTG 58.679 52.381 0.62 0.00 0.00 3.61
978 1038 1.845791 TCCTTGAATGGCTGGCTGATA 59.154 47.619 2.00 0.00 0.00 2.15
984 1044 0.256752 ATGGCTGGCTGATAACTGCA 59.743 50.000 2.00 0.00 41.61 4.41
1025 1087 5.242171 TGCATATTGTCAATCCCATCACATC 59.758 40.000 0.07 0.00 0.00 3.06
1044 1106 0.103937 CTGAACAGATCGCTCTCCCC 59.896 60.000 0.00 0.00 0.00 4.81
1263 1335 4.077108 TGCTTATTCATGATCCAGATGGC 58.923 43.478 0.00 0.00 34.44 4.40
1384 1458 2.945668 GTGGCATCGCTAGGAGAAATTT 59.054 45.455 0.00 0.00 0.00 1.82
1400 1474 5.175859 AGAAATTTACGCCTTCGATCTCAA 58.824 37.500 0.00 0.00 39.41 3.02
1476 1550 8.203485 AGTTGTCCAACATTTTACATTGTTCAT 58.797 29.630 12.32 0.00 43.47 2.57
1613 1687 4.072131 GTTGTGACTATGCCTGAAAAGGA 58.928 43.478 0.00 0.00 0.00 3.36
1656 1730 2.610232 GGATCATGTGTTGTTGGTTGGC 60.610 50.000 0.00 0.00 0.00 4.52
1725 1799 5.385509 AGGCAAACAATGTGTATGTTACC 57.614 39.130 0.00 0.00 39.98 2.85
2022 2110 4.065088 GACATTGCAGTTGGTGAGAGTTA 58.935 43.478 4.06 0.00 0.00 2.24
2232 2320 4.946157 ACTTGCCTCTTATTCATCAAGGTG 59.054 41.667 0.00 0.00 36.26 4.00
2283 2372 6.294843 GGAGAATCTAGGCCTGTAGATACAAC 60.295 46.154 17.99 9.15 38.57 3.32
2285 2374 6.266558 AGAATCTAGGCCTGTAGATACAACTG 59.733 42.308 17.99 0.00 38.57 3.16
2315 2404 1.946768 TGTTCTGAACAAAAGCCTCCG 59.053 47.619 20.14 0.00 38.72 4.63
2316 2405 1.266989 GTTCTGAACAAAAGCCTCCGG 59.733 52.381 15.34 0.00 0.00 5.14
2317 2406 0.472471 TCTGAACAAAAGCCTCCGGT 59.528 50.000 0.00 0.00 0.00 5.28
2318 2407 0.593128 CTGAACAAAAGCCTCCGGTG 59.407 55.000 0.00 0.00 0.00 4.94
2319 2408 0.181587 TGAACAAAAGCCTCCGGTGA 59.818 50.000 4.76 0.00 0.00 4.02
2320 2409 1.314730 GAACAAAAGCCTCCGGTGAA 58.685 50.000 4.76 0.00 0.00 3.18
2321 2410 1.886542 GAACAAAAGCCTCCGGTGAAT 59.113 47.619 4.76 0.00 0.00 2.57
2322 2411 1.247567 ACAAAAGCCTCCGGTGAATG 58.752 50.000 4.76 0.00 0.00 2.67
2323 2412 0.527565 CAAAAGCCTCCGGTGAATGG 59.472 55.000 4.76 0.65 0.00 3.16
2324 2413 0.404040 AAAAGCCTCCGGTGAATGGA 59.596 50.000 4.76 0.00 0.00 3.41
2325 2414 0.404040 AAAGCCTCCGGTGAATGGAA 59.596 50.000 4.76 0.00 34.44 3.53
2326 2415 0.404040 AAGCCTCCGGTGAATGGAAA 59.596 50.000 4.76 0.00 34.44 3.13
2327 2416 0.322546 AGCCTCCGGTGAATGGAAAC 60.323 55.000 4.76 0.00 34.44 2.78
2328 2417 1.644786 GCCTCCGGTGAATGGAAACG 61.645 60.000 4.76 0.00 34.44 3.60
2329 2418 1.644786 CCTCCGGTGAATGGAAACGC 61.645 60.000 4.76 0.00 34.44 4.84
2330 2419 0.953471 CTCCGGTGAATGGAAACGCA 60.953 55.000 0.00 0.00 34.44 5.24
2331 2420 0.953471 TCCGGTGAATGGAAACGCAG 60.953 55.000 0.00 0.00 30.98 5.18
2332 2421 0.953471 CCGGTGAATGGAAACGCAGA 60.953 55.000 0.00 0.00 0.00 4.26
2333 2422 1.086696 CGGTGAATGGAAACGCAGAT 58.913 50.000 0.00 0.00 0.00 2.90
2334 2423 1.202065 CGGTGAATGGAAACGCAGATG 60.202 52.381 0.00 0.00 0.00 2.90
2335 2424 2.083774 GGTGAATGGAAACGCAGATGA 58.916 47.619 0.00 0.00 0.00 2.92
2336 2425 2.159517 GGTGAATGGAAACGCAGATGAC 60.160 50.000 0.00 0.00 0.00 3.06
2337 2426 2.083774 TGAATGGAAACGCAGATGACC 58.916 47.619 0.00 0.00 0.00 4.02
2338 2427 2.290260 TGAATGGAAACGCAGATGACCT 60.290 45.455 0.00 0.00 0.00 3.85
2339 2428 2.496899 ATGGAAACGCAGATGACCTT 57.503 45.000 0.00 0.00 0.00 3.50
2340 2429 1.522668 TGGAAACGCAGATGACCTTG 58.477 50.000 0.00 0.00 0.00 3.61
2341 2430 1.071542 TGGAAACGCAGATGACCTTGA 59.928 47.619 0.00 0.00 0.00 3.02
2342 2431 2.151202 GGAAACGCAGATGACCTTGAA 58.849 47.619 0.00 0.00 0.00 2.69
2343 2432 2.095718 GGAAACGCAGATGACCTTGAAC 60.096 50.000 0.00 0.00 0.00 3.18
2344 2433 2.254546 AACGCAGATGACCTTGAACA 57.745 45.000 0.00 0.00 0.00 3.18
2345 2434 1.800805 ACGCAGATGACCTTGAACAG 58.199 50.000 0.00 0.00 0.00 3.16
2346 2435 1.344438 ACGCAGATGACCTTGAACAGA 59.656 47.619 0.00 0.00 0.00 3.41
2347 2436 2.027745 ACGCAGATGACCTTGAACAGAT 60.028 45.455 0.00 0.00 0.00 2.90
2348 2437 3.005554 CGCAGATGACCTTGAACAGATT 58.994 45.455 0.00 0.00 0.00 2.40
2349 2438 3.438087 CGCAGATGACCTTGAACAGATTT 59.562 43.478 0.00 0.00 0.00 2.17
2350 2439 4.670992 CGCAGATGACCTTGAACAGATTTG 60.671 45.833 0.00 0.00 0.00 2.32
2351 2440 4.380233 GCAGATGACCTTGAACAGATTTGG 60.380 45.833 0.00 0.00 0.00 3.28
2352 2441 5.005740 CAGATGACCTTGAACAGATTTGGA 58.994 41.667 0.00 0.00 0.00 3.53
2353 2442 5.651139 CAGATGACCTTGAACAGATTTGGAT 59.349 40.000 0.00 0.00 0.00 3.41
2354 2443 6.825213 CAGATGACCTTGAACAGATTTGGATA 59.175 38.462 0.00 0.00 0.00 2.59
2355 2444 7.337689 CAGATGACCTTGAACAGATTTGGATAA 59.662 37.037 0.00 0.00 0.00 1.75
2356 2445 7.555554 AGATGACCTTGAACAGATTTGGATAAG 59.444 37.037 0.00 0.00 0.00 1.73
2357 2446 6.778821 TGACCTTGAACAGATTTGGATAAGA 58.221 36.000 0.00 0.00 0.00 2.10
2358 2447 7.405292 TGACCTTGAACAGATTTGGATAAGAT 58.595 34.615 0.00 0.00 0.00 2.40
2359 2448 7.337689 TGACCTTGAACAGATTTGGATAAGATG 59.662 37.037 0.00 0.00 0.00 2.90
2360 2449 6.096001 ACCTTGAACAGATTTGGATAAGATGC 59.904 38.462 0.00 0.00 0.00 3.91
2361 2450 6.095860 CCTTGAACAGATTTGGATAAGATGCA 59.904 38.462 0.00 0.00 0.00 3.96
2367 2456 8.070034 ACAGATTTGGATAAGATGCATTGAAA 57.930 30.769 0.00 0.00 0.00 2.69
2422 2511 7.094118 GCTTTTTGACCATGGTAAACTGGTATA 60.094 37.037 19.80 0.00 45.70 1.47
2424 2513 5.031066 TGACCATGGTAAACTGGTATAGC 57.969 43.478 19.80 0.39 45.70 2.97
2427 2516 4.202223 ACCATGGTAAACTGGTATAGCTCG 60.202 45.833 18.10 0.00 43.91 5.03
2444 2533 0.109532 TCGGGCAATGTGAAGGTGAA 59.890 50.000 0.00 0.00 0.00 3.18
2466 2555 7.973944 GTGAACATATCTTGTGTTATTTTCCCC 59.026 37.037 0.00 0.00 39.72 4.81
2475 2564 4.202131 TGTGTTATTTTCCCCGGTTTGAAC 60.202 41.667 0.00 0.00 0.00 3.18
2481 2570 0.701731 TCCCCGGTTTGAACATGGAT 59.298 50.000 0.00 0.00 0.00 3.41
2484 2573 2.166829 CCCGGTTTGAACATGGATCAA 58.833 47.619 10.98 10.98 35.11 2.57
2496 2585 4.419282 ACATGGATCAAACTGAAATGGGT 58.581 39.130 0.00 0.00 0.00 4.51
2501 2590 4.528206 GGATCAAACTGAAATGGGTTCCTT 59.472 41.667 0.00 0.00 35.12 3.36
2511 2600 8.723365 ACTGAAATGGGTTCCTTATCATGTATA 58.277 33.333 0.00 0.00 35.12 1.47
2526 2615 7.870509 ATCATGTATACATTGCTGTTGAACT 57.129 32.000 15.85 0.00 36.79 3.01
2543 2632 7.847487 TGTTGAACTACTTGTAATGTTTCTCG 58.153 34.615 0.00 0.00 0.00 4.04
2550 2639 4.819630 ACTTGTAATGTTTCTCGCCAAAGA 59.180 37.500 0.00 0.00 0.00 2.52
2559 2648 6.837992 TGTTTCTCGCCAAAGATAAATACAC 58.162 36.000 0.00 0.00 0.00 2.90
2632 2721 7.700322 TTAGTTTGATCTTGAGACATATCGC 57.300 36.000 0.00 0.00 0.00 4.58
2633 2722 5.664457 AGTTTGATCTTGAGACATATCGCA 58.336 37.500 0.00 0.00 32.15 5.10
2634 2723 5.521735 AGTTTGATCTTGAGACATATCGCAC 59.478 40.000 0.00 0.00 33.99 5.34
2635 2724 3.982475 TGATCTTGAGACATATCGCACC 58.018 45.455 0.00 0.00 33.99 5.01
2636 2725 3.638627 TGATCTTGAGACATATCGCACCT 59.361 43.478 0.00 0.00 33.99 4.00
2637 2726 4.827284 TGATCTTGAGACATATCGCACCTA 59.173 41.667 0.00 0.00 33.99 3.08
2638 2727 5.478332 TGATCTTGAGACATATCGCACCTAT 59.522 40.000 0.00 0.00 33.99 2.57
2639 2728 5.791336 TCTTGAGACATATCGCACCTATT 57.209 39.130 0.00 0.00 33.99 1.73
2640 2729 6.161855 TCTTGAGACATATCGCACCTATTT 57.838 37.500 0.00 0.00 33.99 1.40
2641 2730 5.985530 TCTTGAGACATATCGCACCTATTTG 59.014 40.000 0.00 0.00 33.99 2.32
2642 2731 4.631131 TGAGACATATCGCACCTATTTGG 58.369 43.478 0.00 0.00 42.93 3.28
2643 2732 3.403038 AGACATATCGCACCTATTTGGC 58.597 45.455 0.00 0.00 40.22 4.52
2644 2733 3.138304 GACATATCGCACCTATTTGGCA 58.862 45.455 0.00 0.00 40.22 4.92
2645 2734 3.141398 ACATATCGCACCTATTTGGCAG 58.859 45.455 0.00 0.00 40.22 4.85
2646 2735 3.181455 ACATATCGCACCTATTTGGCAGA 60.181 43.478 0.00 0.00 40.22 4.26
2647 2736 2.418368 ATCGCACCTATTTGGCAGAA 57.582 45.000 0.00 0.00 40.22 3.02
2648 2737 1.737838 TCGCACCTATTTGGCAGAAG 58.262 50.000 0.00 0.00 40.22 2.85
2649 2738 1.003118 TCGCACCTATTTGGCAGAAGT 59.997 47.619 0.00 0.00 40.22 3.01
2650 2739 1.131126 CGCACCTATTTGGCAGAAGTG 59.869 52.381 0.00 0.00 40.22 3.16
2668 2757 5.180868 AGAAGTGCATCAGACACAATTTCTC 59.819 40.000 0.00 0.00 40.59 2.87
2692 2781 4.684134 TTGGCCTTGGCCTCCAGC 62.684 66.667 28.37 1.14 42.60 4.85
2726 2815 2.906354 CCACATCCACTAGGTTACAGC 58.094 52.381 0.00 0.00 35.89 4.40
2790 2879 7.645340 GCTATAAAATGGGCTGAATAATATGCG 59.355 37.037 0.00 0.00 0.00 4.73
2794 2883 2.553602 TGGGCTGAATAATATGCGCAAG 59.446 45.455 17.11 5.49 43.45 4.01
2810 2899 3.393800 CGCAAGTCATTACCAGATAGGG 58.606 50.000 0.00 0.00 43.89 3.53
2824 2913 7.989947 ACCAGATAGGGAAGTATTTCTAACA 57.010 36.000 0.00 0.00 43.89 2.41
2838 2927 9.231297 AGTATTTCTAACAATTGCAGCTTCTTA 57.769 29.630 5.05 0.00 0.00 2.10
2898 2987 4.101585 TGGACACCATATCAAGAGACATCC 59.898 45.833 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
219 231 0.317160 AGATCACAGTTCGGCGAACA 59.683 50.000 42.65 28.46 44.11 3.18
303 316 4.828925 GAGTGCTGGCGCTCCTCC 62.829 72.222 21.23 1.54 45.02 4.30
355 371 1.911057 CCACTCCCAGAAAAGGTTCC 58.089 55.000 0.00 0.00 33.92 3.62
365 381 2.046892 CGACAAGGCCACTCCCAG 60.047 66.667 5.01 0.00 34.51 4.45
407 440 2.769663 TCTTGGGCGTACTTATGGATGT 59.230 45.455 0.00 0.00 0.00 3.06
410 449 1.138266 GCTCTTGGGCGTACTTATGGA 59.862 52.381 0.00 0.00 0.00 3.41
484 523 4.301628 GGCACTTTCAGAAGAACAATTGG 58.698 43.478 10.83 0.00 36.69 3.16
493 533 5.007136 GGAGATAAATCGGCACTTTCAGAAG 59.993 44.000 0.00 0.00 38.87 2.85
524 567 1.311859 TGGATACGCTACAGGTACCG 58.688 55.000 6.18 4.16 42.51 4.02
548 591 0.977627 TGTGGATGGCTGGACTCGAT 60.978 55.000 0.00 0.00 0.00 3.59
556 599 2.092538 AGATTCCTTCTGTGGATGGCTG 60.093 50.000 0.00 0.00 36.90 4.85
569 612 2.360801 GACTAGAGAGCGCAGATTCCTT 59.639 50.000 11.47 0.00 0.00 3.36
900 960 4.020128 GGGAGAGTCAACTTGTATGACCTT 60.020 45.833 3.23 0.00 46.60 3.50
962 1022 2.646930 CAGTTATCAGCCAGCCATTCA 58.353 47.619 0.00 0.00 0.00 2.57
963 1023 1.336125 GCAGTTATCAGCCAGCCATTC 59.664 52.381 0.00 0.00 0.00 2.67
978 1038 0.534412 CGGACCTCTCATCTGCAGTT 59.466 55.000 14.67 1.65 0.00 3.16
984 1044 1.327303 GCATCTCGGACCTCTCATCT 58.673 55.000 0.00 0.00 0.00 2.90
1025 1087 0.103937 GGGGAGAGCGATCTGTTCAG 59.896 60.000 8.50 0.00 0.00 3.02
1074 1136 2.293399 GGCACCTGTTTCATCGAAAACT 59.707 45.455 12.58 0.00 39.39 2.66
1178 1249 3.826157 TGCCTTTTTCTGGAGGTATTGTG 59.174 43.478 0.00 0.00 35.42 3.33
1263 1335 4.082571 CCTAACCAAGCAAATGAGAGTTGG 60.083 45.833 0.00 0.00 42.89 3.77
1400 1474 3.884774 TTGCGACCACAGGGCCTT 61.885 61.111 1.32 0.00 37.90 4.35
1433 1507 3.118112 ACAACTGAAGATATCTGCCCAGG 60.118 47.826 22.98 14.28 0.00 4.45
1476 1550 0.621280 TCAGATCCCCACATGGAGCA 60.621 55.000 0.00 0.00 43.36 4.26
1595 1669 4.264253 CACATCCTTTTCAGGCATAGTCA 58.736 43.478 0.00 0.00 40.58 3.41
1613 1687 6.672593 TCCTTCAAGCTATTTATTCCCACAT 58.327 36.000 0.00 0.00 0.00 3.21
1656 1730 4.392940 AGAGACAAAGTGATTGGTTCTGG 58.607 43.478 0.00 0.00 43.66 3.86
1725 1799 7.596749 AAAAGTTAGATACTTGTGGTCATCG 57.403 36.000 0.00 0.00 46.34 3.84
1893 1970 9.958180 TGGACATGAAGAAAAACTCATAGATTA 57.042 29.630 0.00 0.00 0.00 1.75
2022 2110 5.015284 ACCTTAGAGCTGGATTTTAACCCTT 59.985 40.000 0.00 0.00 0.00 3.95
2227 2315 4.618920 AATGTCGTTTAGTCTCCACCTT 57.381 40.909 0.00 0.00 0.00 3.50
2232 2320 3.119955 GGCCAAAATGTCGTTTAGTCTCC 60.120 47.826 0.00 0.00 0.00 3.71
2283 2372 6.618287 TTGTTCAGAACAATTCCTGTACAG 57.382 37.500 22.53 16.34 45.79 2.74
2311 2400 0.953471 TGCGTTTCCATTCACCGGAG 60.953 55.000 9.46 0.00 33.01 4.63
2312 2401 0.953471 CTGCGTTTCCATTCACCGGA 60.953 55.000 9.46 0.00 0.00 5.14
2313 2402 0.953471 TCTGCGTTTCCATTCACCGG 60.953 55.000 0.00 0.00 0.00 5.28
2314 2403 1.086696 ATCTGCGTTTCCATTCACCG 58.913 50.000 0.00 0.00 0.00 4.94
2315 2404 2.083774 TCATCTGCGTTTCCATTCACC 58.916 47.619 0.00 0.00 0.00 4.02
2316 2405 2.159517 GGTCATCTGCGTTTCCATTCAC 60.160 50.000 0.00 0.00 0.00 3.18
2317 2406 2.083774 GGTCATCTGCGTTTCCATTCA 58.916 47.619 0.00 0.00 0.00 2.57
2318 2407 2.359900 AGGTCATCTGCGTTTCCATTC 58.640 47.619 0.00 0.00 0.00 2.67
2319 2408 2.489329 CAAGGTCATCTGCGTTTCCATT 59.511 45.455 0.00 0.00 0.00 3.16
2320 2409 2.086869 CAAGGTCATCTGCGTTTCCAT 58.913 47.619 0.00 0.00 0.00 3.41
2321 2410 1.071542 TCAAGGTCATCTGCGTTTCCA 59.928 47.619 0.00 0.00 0.00 3.53
2322 2411 1.808411 TCAAGGTCATCTGCGTTTCC 58.192 50.000 0.00 0.00 0.00 3.13
2323 2412 2.548057 TGTTCAAGGTCATCTGCGTTTC 59.452 45.455 0.00 0.00 0.00 2.78
2324 2413 2.549754 CTGTTCAAGGTCATCTGCGTTT 59.450 45.455 0.00 0.00 0.00 3.60
2325 2414 2.146342 CTGTTCAAGGTCATCTGCGTT 58.854 47.619 0.00 0.00 0.00 4.84
2326 2415 1.344438 TCTGTTCAAGGTCATCTGCGT 59.656 47.619 0.00 0.00 0.00 5.24
2327 2416 2.084610 TCTGTTCAAGGTCATCTGCG 57.915 50.000 0.00 0.00 0.00 5.18
2328 2417 4.380233 CCAAATCTGTTCAAGGTCATCTGC 60.380 45.833 0.00 0.00 0.00 4.26
2329 2418 5.005740 TCCAAATCTGTTCAAGGTCATCTG 58.994 41.667 0.00 0.00 0.00 2.90
2330 2419 5.246981 TCCAAATCTGTTCAAGGTCATCT 57.753 39.130 0.00 0.00 0.00 2.90
2331 2420 7.554118 TCTTATCCAAATCTGTTCAAGGTCATC 59.446 37.037 0.00 0.00 0.00 2.92
2332 2421 7.405292 TCTTATCCAAATCTGTTCAAGGTCAT 58.595 34.615 0.00 0.00 0.00 3.06
2333 2422 6.778821 TCTTATCCAAATCTGTTCAAGGTCA 58.221 36.000 0.00 0.00 0.00 4.02
2334 2423 7.680588 GCATCTTATCCAAATCTGTTCAAGGTC 60.681 40.741 0.00 0.00 0.00 3.85
2335 2424 6.096001 GCATCTTATCCAAATCTGTTCAAGGT 59.904 38.462 0.00 0.00 0.00 3.50
2336 2425 6.095860 TGCATCTTATCCAAATCTGTTCAAGG 59.904 38.462 0.00 0.00 0.00 3.61
2337 2426 7.092137 TGCATCTTATCCAAATCTGTTCAAG 57.908 36.000 0.00 0.00 0.00 3.02
2338 2427 7.649533 ATGCATCTTATCCAAATCTGTTCAA 57.350 32.000 0.00 0.00 0.00 2.69
2339 2428 7.339976 TCAATGCATCTTATCCAAATCTGTTCA 59.660 33.333 0.00 0.00 0.00 3.18
2340 2429 7.709947 TCAATGCATCTTATCCAAATCTGTTC 58.290 34.615 0.00 0.00 0.00 3.18
2341 2430 7.649533 TCAATGCATCTTATCCAAATCTGTT 57.350 32.000 0.00 0.00 0.00 3.16
2342 2431 7.649533 TTCAATGCATCTTATCCAAATCTGT 57.350 32.000 0.00 0.00 0.00 3.41
2343 2432 8.814235 GTTTTCAATGCATCTTATCCAAATCTG 58.186 33.333 0.00 0.00 0.00 2.90
2344 2433 8.755977 AGTTTTCAATGCATCTTATCCAAATCT 58.244 29.630 0.00 0.00 0.00 2.40
2345 2434 8.814235 CAGTTTTCAATGCATCTTATCCAAATC 58.186 33.333 0.00 0.00 0.00 2.17
2346 2435 8.316214 ACAGTTTTCAATGCATCTTATCCAAAT 58.684 29.630 0.00 0.00 0.00 2.32
2347 2436 7.669427 ACAGTTTTCAATGCATCTTATCCAAA 58.331 30.769 0.00 0.00 0.00 3.28
2348 2437 7.039853 TGACAGTTTTCAATGCATCTTATCCAA 60.040 33.333 0.00 0.00 0.00 3.53
2349 2438 6.433716 TGACAGTTTTCAATGCATCTTATCCA 59.566 34.615 0.00 0.00 0.00 3.41
2350 2439 6.749118 GTGACAGTTTTCAATGCATCTTATCC 59.251 38.462 0.00 0.00 0.00 2.59
2351 2440 7.533426 AGTGACAGTTTTCAATGCATCTTATC 58.467 34.615 0.00 0.00 0.00 1.75
2352 2441 7.362401 GGAGTGACAGTTTTCAATGCATCTTAT 60.362 37.037 0.00 0.00 32.76 1.73
2353 2442 6.072508 GGAGTGACAGTTTTCAATGCATCTTA 60.073 38.462 0.00 0.00 32.76 2.10
2354 2443 5.278660 GGAGTGACAGTTTTCAATGCATCTT 60.279 40.000 0.00 0.00 32.76 2.40
2355 2444 4.217118 GGAGTGACAGTTTTCAATGCATCT 59.783 41.667 0.00 0.00 32.76 2.90
2356 2445 4.022935 TGGAGTGACAGTTTTCAATGCATC 60.023 41.667 0.00 0.00 37.06 3.91
2357 2446 3.890756 TGGAGTGACAGTTTTCAATGCAT 59.109 39.130 0.00 0.00 37.06 3.96
2358 2447 3.286353 TGGAGTGACAGTTTTCAATGCA 58.714 40.909 0.00 0.00 39.24 3.96
2359 2448 3.854784 GCTGGAGTGACAGTTTTCAATGC 60.855 47.826 0.00 0.00 40.59 3.56
2360 2449 3.316029 TGCTGGAGTGACAGTTTTCAATG 59.684 43.478 0.00 0.00 40.59 2.82
2361 2450 3.316308 GTGCTGGAGTGACAGTTTTCAAT 59.684 43.478 0.00 0.00 40.59 2.57
2367 2456 2.224606 CAATGTGCTGGAGTGACAGTT 58.775 47.619 0.00 0.00 40.59 3.16
2422 2511 1.377725 CCTTCACATTGCCCGAGCT 60.378 57.895 0.00 0.00 40.80 4.09
2424 2513 0.321564 TCACCTTCACATTGCCCGAG 60.322 55.000 0.00 0.00 0.00 4.63
2427 2516 1.327303 TGTTCACCTTCACATTGCCC 58.673 50.000 0.00 0.00 0.00 5.36
2444 2533 5.592688 CCGGGGAAAATAACACAAGATATGT 59.407 40.000 0.00 0.00 45.34 2.29
2475 2564 5.410355 AACCCATTTCAGTTTGATCCATG 57.590 39.130 0.00 0.00 0.00 3.66
2481 2570 6.310941 TGATAAGGAACCCATTTCAGTTTGA 58.689 36.000 0.00 0.00 35.70 2.69
2484 2573 6.256053 ACATGATAAGGAACCCATTTCAGTT 58.744 36.000 0.00 0.00 35.70 3.16
2496 2585 8.839343 CAACAGCAATGTATACATGATAAGGAA 58.161 33.333 18.94 0.00 36.56 3.36
2501 2590 8.962884 AGTTCAACAGCAATGTATACATGATA 57.037 30.769 18.94 1.41 36.56 2.15
2511 2600 6.935741 TTACAAGTAGTTCAACAGCAATGT 57.064 33.333 0.00 0.00 0.00 2.71
2526 2615 5.992829 TCTTTGGCGAGAAACATTACAAGTA 59.007 36.000 0.00 0.00 0.00 2.24
2543 2632 5.123820 TGTGCTCTGTGTATTTATCTTTGGC 59.876 40.000 0.00 0.00 0.00 4.52
2550 2639 7.772292 ACTGATCAATGTGCTCTGTGTATTTAT 59.228 33.333 0.00 0.00 0.00 1.40
2559 2648 5.624344 AAAGAACTGATCAATGTGCTCTG 57.376 39.130 0.00 0.00 0.00 3.35
2611 2700 5.277058 GGTGCGATATGTCTCAAGATCAAAC 60.277 44.000 0.00 0.00 0.00 2.93
2612 2701 4.811024 GGTGCGATATGTCTCAAGATCAAA 59.189 41.667 0.00 0.00 0.00 2.69
2615 2704 4.250116 AGGTGCGATATGTCTCAAGATC 57.750 45.455 0.00 0.00 0.00 2.75
2622 2711 3.181455 TGCCAAATAGGTGCGATATGTCT 60.181 43.478 0.00 0.00 40.61 3.41
2623 2712 3.138304 TGCCAAATAGGTGCGATATGTC 58.862 45.455 0.00 0.00 40.61 3.06
2624 2713 3.141398 CTGCCAAATAGGTGCGATATGT 58.859 45.455 0.00 0.00 40.61 2.29
2625 2714 3.402110 TCTGCCAAATAGGTGCGATATG 58.598 45.455 0.00 0.00 40.61 1.78
2626 2715 3.769739 TCTGCCAAATAGGTGCGATAT 57.230 42.857 0.00 0.00 40.61 1.63
2627 2716 3.118408 ACTTCTGCCAAATAGGTGCGATA 60.118 43.478 0.00 0.00 40.61 2.92
2628 2717 2.292267 CTTCTGCCAAATAGGTGCGAT 58.708 47.619 0.00 0.00 40.61 4.58
2629 2718 1.003118 ACTTCTGCCAAATAGGTGCGA 59.997 47.619 0.00 0.00 40.61 5.10
2630 2719 1.131126 CACTTCTGCCAAATAGGTGCG 59.869 52.381 0.00 0.00 40.61 5.34
2631 2720 1.135286 GCACTTCTGCCAAATAGGTGC 60.135 52.381 0.00 0.00 40.91 5.01
2632 2721 2.161855 TGCACTTCTGCCAAATAGGTG 58.838 47.619 0.00 0.00 43.51 4.00
2633 2722 2.584835 TGCACTTCTGCCAAATAGGT 57.415 45.000 0.00 0.00 43.51 3.08
2634 2723 3.018856 TGATGCACTTCTGCCAAATAGG 58.981 45.455 0.00 0.00 43.51 2.57
2635 2724 3.943381 TCTGATGCACTTCTGCCAAATAG 59.057 43.478 0.00 0.00 43.51 1.73
2636 2725 3.691118 GTCTGATGCACTTCTGCCAAATA 59.309 43.478 0.00 0.00 43.51 1.40
2637 2726 2.490903 GTCTGATGCACTTCTGCCAAAT 59.509 45.455 0.00 0.00 43.51 2.32
2638 2727 1.881973 GTCTGATGCACTTCTGCCAAA 59.118 47.619 0.00 0.00 43.51 3.28
2639 2728 1.202794 TGTCTGATGCACTTCTGCCAA 60.203 47.619 0.00 0.00 43.51 4.52
2640 2729 0.397564 TGTCTGATGCACTTCTGCCA 59.602 50.000 0.00 0.00 43.51 4.92
2641 2730 0.801251 GTGTCTGATGCACTTCTGCC 59.199 55.000 0.00 0.00 43.51 4.85
2642 2731 1.516161 TGTGTCTGATGCACTTCTGC 58.484 50.000 0.00 0.00 44.52 4.26
2643 2732 4.761235 AATTGTGTCTGATGCACTTCTG 57.239 40.909 0.00 0.00 37.70 3.02
2644 2733 5.068636 AGAAATTGTGTCTGATGCACTTCT 58.931 37.500 0.00 0.00 37.70 2.85
2645 2734 5.180868 AGAGAAATTGTGTCTGATGCACTTC 59.819 40.000 0.00 0.00 37.70 3.01
2646 2735 5.068636 AGAGAAATTGTGTCTGATGCACTT 58.931 37.500 0.00 0.00 37.70 3.16
2647 2736 4.649692 AGAGAAATTGTGTCTGATGCACT 58.350 39.130 0.00 0.00 37.70 4.40
2648 2737 4.694509 AGAGAGAAATTGTGTCTGATGCAC 59.305 41.667 0.00 0.00 37.37 4.57
2649 2738 4.903054 AGAGAGAAATTGTGTCTGATGCA 58.097 39.130 0.00 0.00 27.65 3.96
2650 2739 5.180868 ACAAGAGAGAAATTGTGTCTGATGC 59.819 40.000 0.00 0.00 38.19 3.91
2651 2740 6.798315 ACAAGAGAGAAATTGTGTCTGATG 57.202 37.500 0.00 0.00 38.19 3.07
2652 2741 7.255381 CCAAACAAGAGAGAAATTGTGTCTGAT 60.255 37.037 0.00 0.00 39.50 2.90
2653 2742 6.038603 CCAAACAAGAGAGAAATTGTGTCTGA 59.961 38.462 0.00 0.00 39.50 3.27
2654 2743 6.204359 CCAAACAAGAGAGAAATTGTGTCTG 58.796 40.000 0.00 0.00 39.50 3.51
2692 2781 2.559440 GATGTGGCTCCAGCTAAGAAG 58.441 52.381 0.00 0.00 41.70 2.85
2772 2861 2.794103 TGCGCATATTATTCAGCCCAT 58.206 42.857 5.66 0.00 0.00 4.00
2790 2879 4.689612 TCCCTATCTGGTAATGACTTGC 57.310 45.455 0.00 0.00 0.00 4.01
2794 2883 8.652290 AGAAATACTTCCCTATCTGGTAATGAC 58.348 37.037 0.00 0.00 31.28 3.06
2810 2899 8.239998 AGAAGCTGCAATTGTTAGAAATACTTC 58.760 33.333 7.40 12.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.