Multiple sequence alignment - TraesCS6B01G316800

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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 TraesCS6B01G316800 chr6B 100.000 2561 0 0 1 2561 564570009 564567449 0.000000e+00 4730.0
1 TraesCS6B01G316800 chr6B 80.000 520 70 21 838 1348 564509340 564508846 1.130000e-93 353.0
2 TraesCS6B01G316800 chr6B 80.186 323 52 10 463 778 38213173 38213490 5.510000e-57 231.0
3 TraesCS6B01G316800 chr6B 92.424 66 1 3 2498 2561 331101766 331101829 9.760000e-15 91.6
4 TraesCS6B01G316800 chr6B 94.828 58 3 0 2504 2561 364466508 364466451 9.760000e-15 91.6
5 TraesCS6B01G316800 chr6D 91.039 2455 170 24 1 2436 378168704 378166281 0.000000e+00 3269.0
6 TraesCS6B01G316800 chr6D 80.115 523 70 20 835 1348 377975672 377975175 2.420000e-95 359.0
7 TraesCS6B01G316800 chr6D 80.000 315 51 11 460 769 336989549 336989242 3.320000e-54 222.0
8 TraesCS6B01G316800 chr6D 89.231 65 7 0 2437 2501 378165320 378165256 5.870000e-12 82.4
9 TraesCS6B01G316800 chr6A 90.169 2370 183 30 1 2349 519951317 519948977 0.000000e+00 3040.0
10 TraesCS6B01G316800 chr6A 79.623 530 64 23 835 1348 519596509 519596008 8.780000e-90 340.0
11 TraesCS6B01G316800 chr6A 98.148 54 1 0 2385 2438 519948766 519948713 7.540000e-16 95.3
12 TraesCS6B01G316800 chr6A 91.935 62 5 0 2437 2498 519947789 519947728 1.260000e-13 87.9
13 TraesCS6B01G316800 chr5A 80.573 314 44 12 463 770 244458221 244457919 2.560000e-55 226.0
14 TraesCS6B01G316800 chr2B 80.259 309 48 11 469 769 312176775 312176472 1.190000e-53 220.0
15 TraesCS6B01G316800 chr2B 80.259 309 48 11 469 769 312182319 312182016 1.190000e-53 220.0
16 TraesCS6B01G316800 chr2B 92.157 51 4 0 1679 1729 132762011 132761961 3.530000e-09 73.1
17 TraesCS6B01G316800 chr5D 80.756 291 46 9 462 748 41709048 41709332 4.290000e-53 219.0
18 TraesCS6B01G316800 chr1D 79.808 312 53 9 463 770 471008197 471007892 4.290000e-53 219.0
19 TraesCS6B01G316800 chr7B 83.784 111 14 3 1627 1737 410301254 410301148 4.510000e-18 102.0
20 TraesCS6B01G316800 chr7B 92.063 63 5 0 2499 2561 304087262 304087200 3.510000e-14 89.8
21 TraesCS6B01G316800 chr7D 93.846 65 2 2 2498 2561 269675884 269675947 2.100000e-16 97.1
22 TraesCS6B01G316800 chr3B 93.750 64 2 2 2499 2561 357244726 357244664 7.540000e-16 95.3
23 TraesCS6B01G316800 chr3B 91.935 62 5 0 2498 2559 293624861 293624800 1.260000e-13 87.9
24 TraesCS6B01G316800 chr3D 92.308 65 4 1 2498 2561 262696317 262696253 9.760000e-15 91.6
25 TraesCS6B01G316800 chr5B 92.063 63 5 0 2499 2561 171877170 171877108 3.510000e-14 89.8
26 TraesCS6B01G316800 chr1B 91.935 62 5 0 2498 2559 253767591 253767530 1.260000e-13 87.9
27 TraesCS6B01G316800 chr2D 83.158 95 14 1 1621 1715 477393157 477393249 4.540000e-13 86.1


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 TraesCS6B01G316800 chr6B 564567449 564570009 2560 True 4730.0 4730 100.000000 1 2561 1 chr6B.!!$R3 2560
1 TraesCS6B01G316800 chr6D 378165256 378168704 3448 True 1675.7 3269 90.135000 1 2501 2 chr6D.!!$R3 2500
2 TraesCS6B01G316800 chr6A 519947728 519951317 3589 True 1074.4 3040 93.417333 1 2498 3 chr6A.!!$R2 2497
3 TraesCS6B01G316800 chr6A 519596008 519596509 501 True 340.0 340 79.623000 835 1348 1 chr6A.!!$R1 513

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
477 484 0.323178 GGTGTACTCCCTCCGTCTGA 60.323 60.0 2.33 0.0 0.0 3.27 F
767 778 0.635009 TATTCGTGGAGGGAGGGAGT 59.365 55.0 0.00 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1417 1451 0.539051 CCAGCTCCTCTTCGGTGAAT 59.461 55.0 0.00 0.00 0.0 2.57 R
2514 3693 0.109597 GAACCTTCTTGTGCATGCGG 60.110 55.0 14.09 8.61 0.0 5.69 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
62 64 8.279103 TCCAAATTTTGATACGAAATTTTGTGC 58.721 29.630 19.51 12.28 41.97 4.57
91 93 8.028354 CCATACATTGATGTTGTGTTAATGTGT 58.972 33.333 10.22 2.36 40.83 3.72
171 173 2.875933 CAATTACGGGTGCAACGGATAT 59.124 45.455 17.13 5.77 38.12 1.63
173 175 2.798976 TACGGGTGCAACGGATATAC 57.201 50.000 17.13 0.00 38.12 1.47
199 201 4.493747 GGACGAGGCTCCCGTTCG 62.494 72.222 9.32 0.00 40.67 3.95
236 238 1.000163 AGACACACAAGTCAGCTACGG 60.000 52.381 0.00 0.00 40.98 4.02
273 275 6.786967 TCTCTTTAATTTCTACTAGGCGGT 57.213 37.500 0.00 0.00 0.00 5.68
362 364 1.002868 CCAACCACCTCTGGCTCAG 60.003 63.158 0.00 0.00 42.08 3.35
366 368 0.764369 ACCACCTCTGGCTCAGTGAA 60.764 55.000 0.00 0.00 42.08 3.18
371 373 0.735632 CTCTGGCTCAGTGAAGTCGC 60.736 60.000 0.00 0.00 32.61 5.19
417 424 5.053145 CAGCAGGATAGTAATCACTTGGAC 58.947 45.833 0.00 0.00 36.14 4.02
472 479 1.379642 GGTACGGTGTACTCCCTCCG 61.380 65.000 8.36 9.64 46.98 4.63
475 482 1.378250 CGGTGTACTCCCTCCGTCT 60.378 63.158 8.36 0.00 38.45 4.18
477 484 0.323178 GGTGTACTCCCTCCGTCTGA 60.323 60.000 2.33 0.00 0.00 3.27
484 491 3.709587 ACTCCCTCCGTCTGAGAATAAA 58.290 45.455 0.00 0.00 44.42 1.40
489 496 5.068723 TCCCTCCGTCTGAGAATAAATGTAC 59.931 44.000 0.00 0.00 44.42 2.90
493 500 7.495934 CCTCCGTCTGAGAATAAATGTACATTT 59.504 37.037 30.81 30.81 44.42 2.32
494 501 9.529325 CTCCGTCTGAGAATAAATGTACATTTA 57.471 33.333 32.56 32.56 44.42 1.40
596 605 5.795972 TCACACGGTAATCAAGACCAATAA 58.204 37.500 0.00 0.00 36.72 1.40
603 612 7.065803 ACGGTAATCAAGACCAATAACATTCAG 59.934 37.037 0.00 0.00 36.72 3.02
607 616 8.585471 AATCAAGACCAATAACATTCAGACAT 57.415 30.769 0.00 0.00 0.00 3.06
646 655 5.847304 TCTACATGCACTTAGCTCATTAGG 58.153 41.667 0.00 0.00 45.94 2.69
648 657 3.144506 CATGCACTTAGCTCATTAGGGG 58.855 50.000 0.00 0.00 45.94 4.79
653 662 4.446371 CACTTAGCTCATTAGGGGTTGAG 58.554 47.826 0.00 0.00 0.00 3.02
707 716 6.815142 GCATCTTCCTAATGCATTTTTCACTT 59.185 34.615 18.75 0.00 46.93 3.16
767 778 0.635009 TATTCGTGGAGGGAGGGAGT 59.365 55.000 0.00 0.00 0.00 3.85
778 789 1.007359 GGGAGGGAGTAGGTGAGAAGT 59.993 57.143 0.00 0.00 0.00 3.01
794 810 3.952811 GTGAAGAGCACACCGGTC 58.047 61.111 2.59 0.00 46.91 4.79
1028 1048 2.303163 AGTTCACAACGCACACACTA 57.697 45.000 0.00 0.00 36.23 2.74
1032 1052 5.962714 AGTTCACAACGCACACACTAAGTG 61.963 45.833 0.00 0.00 44.65 3.16
1169 1203 6.337356 GGTTCTGATTTGTTTCTGGTTTTGA 58.663 36.000 0.00 0.00 0.00 2.69
1177 1211 4.692228 TGTTTCTGGTTTTGATTTCAGGC 58.308 39.130 0.00 0.00 0.00 4.85
1282 1316 4.803426 CCGACGAGGCAGGTGCTC 62.803 72.222 1.26 0.00 41.70 4.26
1426 1460 1.017177 GCGTGCCAGTATTCACCGAA 61.017 55.000 0.00 0.00 0.00 4.30
1491 1525 1.663702 GATATTAGCGGTGCGGCGT 60.664 57.895 9.37 0.00 38.18 5.68
1550 1584 2.878117 GCGGGGCATGGCTATAAATGTA 60.878 50.000 19.78 0.00 0.00 2.29
1554 1588 3.191371 GGGCATGGCTATAAATGTAGTGC 59.809 47.826 19.78 0.00 0.00 4.40
1557 1591 4.614535 GCATGGCTATAAATGTAGTGCTGC 60.615 45.833 0.00 0.00 0.00 5.25
1618 1655 5.653255 ATAATACATTCAACCTCAGCCCT 57.347 39.130 0.00 0.00 0.00 5.19
1619 1656 2.787473 TACATTCAACCTCAGCCCTG 57.213 50.000 0.00 0.00 0.00 4.45
1625 1662 4.591321 TTCAACCTCAGCCCTGAATTAT 57.409 40.909 0.00 0.00 39.39 1.28
1632 1669 4.337555 CCTCAGCCCTGAATTATTTGTCTG 59.662 45.833 0.00 0.00 39.39 3.51
1634 1671 5.188434 TCAGCCCTGAATTATTTGTCTGAG 58.812 41.667 0.00 0.00 36.53 3.35
1738 1775 2.885894 GGACGAATGGAGGGAGTACTAG 59.114 54.545 0.00 0.00 0.00 2.57
1754 1791 7.427214 GGAGTACTAGTGACATATTCAGAACC 58.573 42.308 5.39 0.00 33.71 3.62
1755 1792 7.285858 GGAGTACTAGTGACATATTCAGAACCT 59.714 40.741 5.39 0.00 33.71 3.50
1756 1793 8.228035 AGTACTAGTGACATATTCAGAACCTC 57.772 38.462 5.39 0.00 33.71 3.85
1760 1797 8.275758 ACTAGTGACATATTCAGAACCTCTCTA 58.724 37.037 0.00 0.00 33.71 2.43
1778 1817 4.115516 CTCTATGTGTGAATGTCTTCGGG 58.884 47.826 0.00 0.00 33.86 5.14
1893 1932 8.633408 CGTTCAACAAAAATGCAAAATTTGAAA 58.367 25.926 21.68 13.03 37.46 2.69
1956 1995 6.757897 TCCAAGAAATGAATAGCGACAAAT 57.242 33.333 0.00 0.00 0.00 2.32
1962 2001 1.396648 TGAATAGCGACAAATGGTGCG 59.603 47.619 0.00 0.00 0.00 5.34
1978 2017 5.950758 TGGTGCGTCACTATTTTTGTATT 57.049 34.783 9.31 0.00 34.40 1.89
1982 2021 7.380065 TGGTGCGTCACTATTTTTGTATTTTTC 59.620 33.333 9.31 0.00 34.40 2.29
2098 2138 7.789273 TCTTTGAAAGAAAACGTGGTATGTA 57.211 32.000 4.94 0.00 33.83 2.29
2131 2171 3.988379 TGCAACTGATTTCAACCAGAC 57.012 42.857 0.00 0.00 34.65 3.51
2221 2261 3.183775 GCGAAAGAGCGAGTGTTTTTCTA 59.816 43.478 0.00 0.00 0.00 2.10
2228 2268 7.964604 AGAGCGAGTGTTTTTCTATTAGTTT 57.035 32.000 0.00 0.00 0.00 2.66
2230 2270 8.283291 AGAGCGAGTGTTTTTCTATTAGTTTTG 58.717 33.333 0.00 0.00 0.00 2.44
2233 2273 7.642586 GCGAGTGTTTTTCTATTAGTTTTGTGT 59.357 33.333 0.00 0.00 0.00 3.72
2374 2416 0.102120 CAATGGCACCGTGTGTTGTT 59.898 50.000 0.00 0.00 35.75 2.83
2427 2644 5.625150 ACAATCCTAAGGGCATCTACATTC 58.375 41.667 0.00 0.00 0.00 2.67
2440 3619 2.292569 TCTACATTCGAGGGTATGTCGC 59.707 50.000 3.79 0.00 35.94 5.19
2445 3624 2.184830 CGAGGGTATGTCGCGAGGA 61.185 63.158 10.24 0.00 0.00 3.71
2448 3627 1.884579 GAGGGTATGTCGCGAGGAATA 59.115 52.381 10.24 5.45 0.00 1.75
2462 3641 5.289595 GCGAGGAATAGTGACAACATATGA 58.710 41.667 10.38 0.00 0.00 2.15
2498 3677 5.097742 TGGACGAACATGATTAGGTTGAT 57.902 39.130 0.00 0.00 29.76 2.57
2501 3680 5.006746 GGACGAACATGATTAGGTTGATGTC 59.993 44.000 0.00 0.00 29.76 3.06
2502 3681 5.487433 ACGAACATGATTAGGTTGATGTCA 58.513 37.500 0.00 0.00 29.76 3.58
2503 3682 5.582269 ACGAACATGATTAGGTTGATGTCAG 59.418 40.000 0.00 0.00 29.76 3.51
2504 3683 5.812127 CGAACATGATTAGGTTGATGTCAGA 59.188 40.000 0.00 0.00 29.76 3.27
2505 3684 6.481313 CGAACATGATTAGGTTGATGTCAGAT 59.519 38.462 0.00 0.00 29.76 2.90
2506 3685 7.011763 CGAACATGATTAGGTTGATGTCAGATT 59.988 37.037 0.00 0.00 29.76 2.40
2507 3686 7.798596 ACATGATTAGGTTGATGTCAGATTC 57.201 36.000 0.00 0.00 0.00 2.52
2508 3687 7.341030 ACATGATTAGGTTGATGTCAGATTCA 58.659 34.615 0.00 0.00 0.00 2.57
2509 3688 7.498239 ACATGATTAGGTTGATGTCAGATTCAG 59.502 37.037 0.00 0.00 0.00 3.02
2510 3689 6.351711 TGATTAGGTTGATGTCAGATTCAGG 58.648 40.000 0.00 0.00 0.00 3.86
2511 3690 3.641434 AGGTTGATGTCAGATTCAGGG 57.359 47.619 0.00 0.00 0.00 4.45
2512 3691 2.019984 GGTTGATGTCAGATTCAGGGC 58.980 52.381 0.00 0.00 0.00 5.19
2513 3692 2.356535 GGTTGATGTCAGATTCAGGGCT 60.357 50.000 0.00 0.00 0.00 5.19
2514 3693 2.941720 GTTGATGTCAGATTCAGGGCTC 59.058 50.000 0.00 0.00 0.00 4.70
2515 3694 1.487976 TGATGTCAGATTCAGGGCTCC 59.512 52.381 0.00 0.00 0.00 4.70
2516 3695 0.467384 ATGTCAGATTCAGGGCTCCG 59.533 55.000 0.00 0.00 0.00 4.63
2517 3696 1.522580 GTCAGATTCAGGGCTCCGC 60.523 63.158 0.00 0.00 0.00 5.54
2518 3697 1.989508 TCAGATTCAGGGCTCCGCA 60.990 57.895 0.00 0.00 0.00 5.69
2519 3698 1.147824 CAGATTCAGGGCTCCGCAT 59.852 57.895 0.00 0.00 0.00 4.73
2520 3699 1.147824 AGATTCAGGGCTCCGCATG 59.852 57.895 0.00 0.00 0.00 4.06
2521 3700 2.517875 ATTCAGGGCTCCGCATGC 60.518 61.111 7.91 7.91 0.00 4.06
2522 3701 3.348554 ATTCAGGGCTCCGCATGCA 62.349 57.895 19.57 0.00 0.00 3.96
2523 3702 4.783621 TCAGGGCTCCGCATGCAC 62.784 66.667 19.57 3.38 0.00 4.57
2525 3704 4.349503 AGGGCTCCGCATGCACAA 62.350 61.111 19.57 0.63 36.08 3.33
2526 3705 3.818787 GGGCTCCGCATGCACAAG 61.819 66.667 19.57 12.19 33.38 3.16
2527 3706 2.747460 GGCTCCGCATGCACAAGA 60.747 61.111 19.57 7.49 0.00 3.02
2528 3707 2.334946 GGCTCCGCATGCACAAGAA 61.335 57.895 19.57 0.00 0.00 2.52
2529 3708 1.136147 GCTCCGCATGCACAAGAAG 59.864 57.895 19.57 6.10 0.00 2.85
2530 3709 1.798735 CTCCGCATGCACAAGAAGG 59.201 57.895 19.57 8.88 0.00 3.46
2531 3710 0.957395 CTCCGCATGCACAAGAAGGT 60.957 55.000 19.57 0.00 0.00 3.50
2532 3711 0.537143 TCCGCATGCACAAGAAGGTT 60.537 50.000 19.57 0.00 0.00 3.50
2533 3712 0.109597 CCGCATGCACAAGAAGGTTC 60.110 55.000 19.57 0.00 0.00 3.62
2534 3713 0.453282 CGCATGCACAAGAAGGTTCG 60.453 55.000 19.57 0.00 0.00 3.95
2535 3714 0.874390 GCATGCACAAGAAGGTTCGA 59.126 50.000 14.21 0.00 0.00 3.71
2536 3715 1.266718 GCATGCACAAGAAGGTTCGAA 59.733 47.619 14.21 0.00 0.00 3.71
2537 3716 2.918131 GCATGCACAAGAAGGTTCGAAC 60.918 50.000 20.14 20.14 0.00 3.95
2538 3717 2.325583 TGCACAAGAAGGTTCGAACT 57.674 45.000 26.32 9.06 0.00 3.01
2539 3718 2.210116 TGCACAAGAAGGTTCGAACTC 58.790 47.619 26.32 17.34 0.00 3.01
2540 3719 2.158957 TGCACAAGAAGGTTCGAACTCT 60.159 45.455 26.32 19.22 0.00 3.24
2541 3720 3.069016 TGCACAAGAAGGTTCGAACTCTA 59.931 43.478 26.32 5.70 0.00 2.43
2542 3721 3.675698 GCACAAGAAGGTTCGAACTCTAG 59.324 47.826 26.32 15.75 0.00 2.43
2543 3722 4.238514 CACAAGAAGGTTCGAACTCTAGG 58.761 47.826 26.32 18.43 0.00 3.02
2544 3723 3.258622 ACAAGAAGGTTCGAACTCTAGGG 59.741 47.826 26.32 16.42 0.00 3.53
2545 3724 1.826096 AGAAGGTTCGAACTCTAGGGC 59.174 52.381 26.32 9.09 0.00 5.19
2546 3725 0.531200 AAGGTTCGAACTCTAGGGCG 59.469 55.000 26.32 0.00 0.00 6.13
2547 3726 0.611340 AGGTTCGAACTCTAGGGCGT 60.611 55.000 26.32 0.00 0.00 5.68
2548 3727 0.458025 GGTTCGAACTCTAGGGCGTG 60.458 60.000 26.32 0.00 0.00 5.34
2549 3728 0.243095 GTTCGAACTCTAGGGCGTGT 59.757 55.000 20.97 0.00 0.00 4.49
2550 3729 0.242825 TTCGAACTCTAGGGCGTGTG 59.757 55.000 0.00 0.00 0.00 3.82
2551 3730 1.805945 CGAACTCTAGGGCGTGTGC 60.806 63.158 0.00 0.00 41.71 4.57
2552 3731 1.805945 GAACTCTAGGGCGTGTGCG 60.806 63.158 0.00 0.00 44.10 5.34
2553 3732 2.209064 GAACTCTAGGGCGTGTGCGA 62.209 60.000 0.00 0.00 44.10 5.10
2554 3733 1.812686 AACTCTAGGGCGTGTGCGAA 61.813 55.000 0.00 0.00 44.10 4.70
2555 3734 1.517257 CTCTAGGGCGTGTGCGAAG 60.517 63.158 0.00 0.00 44.10 3.79
2556 3735 1.934220 CTCTAGGGCGTGTGCGAAGA 61.934 60.000 0.00 0.00 44.10 2.87
2557 3736 1.141881 CTAGGGCGTGTGCGAAGAT 59.858 57.895 0.00 0.00 44.10 2.40
2558 3737 0.872021 CTAGGGCGTGTGCGAAGATC 60.872 60.000 0.00 0.00 44.10 2.75
2559 3738 1.320344 TAGGGCGTGTGCGAAGATCT 61.320 55.000 0.00 0.00 44.10 2.75
2560 3739 2.167861 GGGCGTGTGCGAAGATCTC 61.168 63.158 0.00 0.00 44.10 2.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 39 7.533561 GGCACAAAATTTCGTATCAAAATTTGG 59.466 33.333 5.83 8.12 42.51 3.28
46 48 4.167554 TGGTGGCACAAAATTTCGTATC 57.832 40.909 20.82 0.00 44.16 2.24
62 64 5.389859 AACACAACATCAATGTATGGTGG 57.610 39.130 18.53 6.64 46.76 4.61
111 113 6.275335 CACCAAATGCCATAGGACATTTTAG 58.725 40.000 0.00 0.00 42.34 1.85
130 132 1.376683 GATGCTACCGGTGCACCAA 60.377 57.895 34.16 18.27 43.59 3.67
131 133 2.267642 GATGCTACCGGTGCACCA 59.732 61.111 34.16 15.28 43.59 4.17
199 201 4.142578 TGTGTCTCGCTTCTCTATCAACTC 60.143 45.833 0.00 0.00 0.00 3.01
273 275 1.140161 CGCGTTCTCCCATCCGTTA 59.860 57.895 0.00 0.00 0.00 3.18
362 364 1.370172 AGACGACGTGCGACTTCAC 60.370 57.895 4.58 0.00 42.06 3.18
366 368 2.185103 GAGGAAGACGACGTGCGACT 62.185 60.000 4.58 9.67 46.42 4.18
371 373 1.464355 CGAAGAGAGGAAGACGACGTG 60.464 57.143 4.58 0.00 0.00 4.49
417 424 5.678483 CGGTGATTAGCATTGAATCTTTTCG 59.322 40.000 0.00 0.00 34.88 3.46
464 471 4.100189 ACATTTATTCTCAGACGGAGGGAG 59.900 45.833 2.63 0.00 44.19 4.30
470 477 8.276325 GCTAAATGTACATTTATTCTCAGACGG 58.724 37.037 31.34 20.17 41.02 4.79
565 574 7.033791 GTCTTGATTACCGTGTGATAAGAGAA 58.966 38.462 0.00 0.00 0.00 2.87
571 580 5.408880 TTGGTCTTGATTACCGTGTGATA 57.591 39.130 0.00 0.00 40.08 2.15
578 587 7.279981 TCTGAATGTTATTGGTCTTGATTACCG 59.720 37.037 0.00 0.00 40.08 4.02
615 624 9.008965 TGAGCTAAGTGCATGTAGAAATAAAAA 57.991 29.630 10.04 0.00 45.94 1.94
616 625 8.560355 TGAGCTAAGTGCATGTAGAAATAAAA 57.440 30.769 10.04 0.00 45.94 1.52
619 628 9.481340 CTAATGAGCTAAGTGCATGTAGAAATA 57.519 33.333 10.04 0.00 45.94 1.40
630 639 2.945668 CAACCCCTAATGAGCTAAGTGC 59.054 50.000 0.00 0.00 43.29 4.40
632 641 4.104831 ACTCAACCCCTAATGAGCTAAGT 58.895 43.478 2.86 0.00 45.50 2.24
637 646 7.773690 TCTTTAATTACTCAACCCCTAATGAGC 59.226 37.037 2.86 0.00 45.50 4.26
640 649 9.681062 TTCTCTTTAATTACTCAACCCCTAATG 57.319 33.333 0.00 0.00 0.00 1.90
646 655 9.503399 TCTCTTTTCTCTTTAATTACTCAACCC 57.497 33.333 0.00 0.00 0.00 4.11
667 676 4.699257 GGAAGATGCAAATCACTGTCTCTT 59.301 41.667 0.00 0.00 0.00 2.85
673 682 5.279384 GCATTAGGAAGATGCAAATCACTG 58.721 41.667 0.00 0.00 46.96 3.66
734 743 9.496873 CCCTCCACGAATAAATGTACATATAAA 57.503 33.333 9.21 0.00 0.00 1.40
735 744 8.872134 TCCCTCCACGAATAAATGTACATATAA 58.128 33.333 9.21 0.00 0.00 0.98
736 745 8.425237 TCCCTCCACGAATAAATGTACATATA 57.575 34.615 9.21 0.00 0.00 0.86
767 778 3.005897 GTGTGCTCTTCACTTCTCACCTA 59.994 47.826 0.00 0.00 45.81 3.08
778 789 2.741092 GGACCGGTGTGCTCTTCA 59.259 61.111 14.63 0.00 0.00 3.02
832 848 1.428370 GAGCCATGCATGCGTTACGA 61.428 55.000 21.69 0.00 0.00 3.43
908 924 4.073200 GTGCCATGCCAAGGTGCC 62.073 66.667 0.00 0.00 0.00 5.01
997 1015 3.309682 CGTTGTGAACTTGTGATGAGTGT 59.690 43.478 0.00 0.00 0.00 3.55
999 1017 2.287915 GCGTTGTGAACTTGTGATGAGT 59.712 45.455 0.00 0.00 0.00 3.41
1028 1048 7.578310 TCTGTCACTTACTTACTACACACTT 57.422 36.000 0.00 0.00 0.00 3.16
1032 1052 8.913656 GTTCAATCTGTCACTTACTTACTACAC 58.086 37.037 0.00 0.00 0.00 2.90
1033 1053 8.635328 TGTTCAATCTGTCACTTACTTACTACA 58.365 33.333 0.00 0.00 0.00 2.74
1169 1203 2.040544 CCTTCGCACCGCCTGAAAT 61.041 57.895 0.00 0.00 0.00 2.17
1275 1309 4.052229 CGTTCGACGGGAGCACCT 62.052 66.667 0.00 0.00 38.08 4.00
1410 1444 1.207089 CCTCTTCGGTGAATACTGGCA 59.793 52.381 0.00 0.00 33.84 4.92
1417 1451 0.539051 CCAGCTCCTCTTCGGTGAAT 59.461 55.000 0.00 0.00 0.00 2.57
1491 1525 2.666190 GTGGCTGACGAGCTTGCA 60.666 61.111 0.00 0.00 45.44 4.08
1550 1584 1.683943 TCTTCAAGCAAAGCAGCACT 58.316 45.000 0.00 0.00 36.85 4.40
1554 1588 4.450080 GGGATTTTTCTTCAAGCAAAGCAG 59.550 41.667 0.00 0.00 0.00 4.24
1557 1591 4.870363 TCGGGATTTTTCTTCAAGCAAAG 58.130 39.130 0.00 0.00 0.00 2.77
1605 1639 4.591321 AATAATTCAGGGCTGAGGTTGA 57.409 40.909 0.00 0.00 41.13 3.18
1606 1640 4.463891 ACAAATAATTCAGGGCTGAGGTTG 59.536 41.667 0.00 0.00 41.13 3.77
1607 1641 4.677182 ACAAATAATTCAGGGCTGAGGTT 58.323 39.130 0.00 0.00 41.13 3.50
1610 1644 5.188434 TCAGACAAATAATTCAGGGCTGAG 58.812 41.667 0.00 0.00 41.13 3.35
1613 1647 5.441718 TCTCAGACAAATAATTCAGGGCT 57.558 39.130 0.00 0.00 0.00 5.19
1700 1737 8.413229 CCATTCGTCCCAAATTAATTGTCTTAT 58.587 33.333 0.39 0.00 37.32 1.73
1709 1746 3.267291 TCCCTCCATTCGTCCCAAATTAA 59.733 43.478 0.00 0.00 0.00 1.40
1724 1761 5.664815 ATATGTCACTAGTACTCCCTCCA 57.335 43.478 0.00 0.00 0.00 3.86
1738 1775 7.651304 CACATAGAGAGGTTCTGAATATGTCAC 59.349 40.741 8.40 0.00 36.61 3.67
1754 1791 5.039984 CCGAAGACATTCACACATAGAGAG 58.960 45.833 0.00 0.00 34.94 3.20
1755 1792 4.142160 CCCGAAGACATTCACACATAGAGA 60.142 45.833 0.00 0.00 34.94 3.10
1756 1793 4.115516 CCCGAAGACATTCACACATAGAG 58.884 47.826 0.00 0.00 34.94 2.43
1760 1797 2.859165 ACCCGAAGACATTCACACAT 57.141 45.000 0.00 0.00 34.94 3.21
1778 1817 3.975168 TGCCCTGTTTCTAGTTCCTAC 57.025 47.619 0.00 0.00 0.00 3.18
1893 1932 9.341078 ACCTTGCAAATGAATTTTAGTTTGAAT 57.659 25.926 0.00 0.00 34.38 2.57
1956 1995 5.950758 AATACAAAAATAGTGACGCACCA 57.049 34.783 6.39 0.00 34.49 4.17
1972 2011 8.770010 TTTGGAAGGTAAGGAGAAAAATACAA 57.230 30.769 0.00 0.00 0.00 2.41
1978 2017 8.950007 AATACATTTGGAAGGTAAGGAGAAAA 57.050 30.769 0.00 0.00 30.82 2.29
2075 2115 8.286800 TCATACATACCACGTTTTCTTTCAAAG 58.713 33.333 0.00 0.00 0.00 2.77
2076 2116 8.155821 TCATACATACCACGTTTTCTTTCAAA 57.844 30.769 0.00 0.00 0.00 2.69
2077 2117 7.731882 TCATACATACCACGTTTTCTTTCAA 57.268 32.000 0.00 0.00 0.00 2.69
2078 2118 7.442969 ACTTCATACATACCACGTTTTCTTTCA 59.557 33.333 0.00 0.00 0.00 2.69
2079 2119 7.803724 ACTTCATACATACCACGTTTTCTTTC 58.196 34.615 0.00 0.00 0.00 2.62
2080 2120 7.739498 ACTTCATACATACCACGTTTTCTTT 57.261 32.000 0.00 0.00 0.00 2.52
2131 2171 7.095270 ACGTTGTAAGGTATTCCTAGAAAGTG 58.905 38.462 0.00 0.00 44.35 3.16
2160 2200 1.639635 GGGTGCATCCTCTCCCACAT 61.640 60.000 9.39 0.00 39.10 3.21
2161 2201 2.300967 GGGTGCATCCTCTCCCACA 61.301 63.158 9.39 0.00 39.10 4.17
2361 2403 2.281517 TGAACCTAACAACACACGGTG 58.718 47.619 6.58 6.58 39.75 4.94
2364 2406 6.592607 ACCTATAATGAACCTAACAACACACG 59.407 38.462 0.00 0.00 0.00 4.49
2374 2416 6.119536 CCTGTTGCAACCTATAATGAACCTA 58.880 40.000 26.14 1.82 0.00 3.08
2427 2644 1.721664 TTCCTCGCGACATACCCTCG 61.722 60.000 3.71 0.00 0.00 4.63
2440 3619 6.367149 CCATCATATGTTGTCACTATTCCTCG 59.633 42.308 11.82 0.00 0.00 4.63
2445 3624 7.828717 TGTGTTCCATCATATGTTGTCACTATT 59.171 33.333 20.96 0.00 0.00 1.73
2448 3627 5.559770 TGTGTTCCATCATATGTTGTCACT 58.440 37.500 20.96 0.00 0.00 3.41
2454 3633 8.632679 GTCCAAATATGTGTTCCATCATATGTT 58.367 33.333 1.90 0.00 37.34 2.71
2462 3641 5.007034 TGTTCGTCCAAATATGTGTTCCAT 58.993 37.500 0.00 0.00 37.58 3.41
2498 3677 1.900351 CGGAGCCCTGAATCTGACA 59.100 57.895 0.00 0.00 0.00 3.58
2512 3691 0.957395 ACCTTCTTGTGCATGCGGAG 60.957 55.000 14.09 10.59 0.00 4.63
2513 3692 0.537143 AACCTTCTTGTGCATGCGGA 60.537 50.000 14.09 5.82 0.00 5.54
2514 3693 0.109597 GAACCTTCTTGTGCATGCGG 60.110 55.000 14.09 8.61 0.00 5.69
2515 3694 0.453282 CGAACCTTCTTGTGCATGCG 60.453 55.000 14.09 0.00 0.00 4.73
2516 3695 0.874390 TCGAACCTTCTTGTGCATGC 59.126 50.000 11.82 11.82 0.00 4.06
2517 3696 2.549754 AGTTCGAACCTTCTTGTGCATG 59.450 45.455 24.22 0.00 0.00 4.06
2518 3697 2.808543 GAGTTCGAACCTTCTTGTGCAT 59.191 45.455 24.22 1.13 0.00 3.96
2519 3698 2.158957 AGAGTTCGAACCTTCTTGTGCA 60.159 45.455 24.22 0.00 0.00 4.57
2520 3699 2.484889 AGAGTTCGAACCTTCTTGTGC 58.515 47.619 24.22 3.65 0.00 4.57
2521 3700 4.238514 CCTAGAGTTCGAACCTTCTTGTG 58.761 47.826 24.22 13.65 0.00 3.33
2522 3701 3.258622 CCCTAGAGTTCGAACCTTCTTGT 59.741 47.826 24.22 7.00 0.00 3.16
2523 3702 3.851098 CCCTAGAGTTCGAACCTTCTTG 58.149 50.000 24.22 19.65 0.00 3.02
2524 3703 2.234168 GCCCTAGAGTTCGAACCTTCTT 59.766 50.000 24.22 5.64 0.00 2.52
2525 3704 1.826096 GCCCTAGAGTTCGAACCTTCT 59.174 52.381 24.22 21.80 0.00 2.85
2526 3705 1.469423 CGCCCTAGAGTTCGAACCTTC 60.469 57.143 24.22 16.07 0.00 3.46
2527 3706 0.531200 CGCCCTAGAGTTCGAACCTT 59.469 55.000 24.22 15.01 0.00 3.50
2528 3707 0.611340 ACGCCCTAGAGTTCGAACCT 60.611 55.000 24.22 21.11 0.00 3.50
2529 3708 0.458025 CACGCCCTAGAGTTCGAACC 60.458 60.000 24.22 15.46 0.00 3.62
2530 3709 0.243095 ACACGCCCTAGAGTTCGAAC 59.757 55.000 20.71 20.71 0.00 3.95
2531 3710 0.242825 CACACGCCCTAGAGTTCGAA 59.757 55.000 0.00 0.00 0.00 3.71
2532 3711 1.880894 CACACGCCCTAGAGTTCGA 59.119 57.895 0.00 0.00 0.00 3.71
2533 3712 1.805945 GCACACGCCCTAGAGTTCG 60.806 63.158 0.00 0.00 0.00 3.95
2534 3713 1.805945 CGCACACGCCCTAGAGTTC 60.806 63.158 0.00 0.00 33.11 3.01
2535 3714 1.812686 TTCGCACACGCCCTAGAGTT 61.813 55.000 0.00 0.00 39.84 3.01
2536 3715 2.214181 CTTCGCACACGCCCTAGAGT 62.214 60.000 0.00 0.00 39.84 3.24
2537 3716 1.517257 CTTCGCACACGCCCTAGAG 60.517 63.158 0.00 0.00 39.84 2.43
2538 3717 1.320344 ATCTTCGCACACGCCCTAGA 61.320 55.000 0.00 0.00 39.84 2.43
2539 3718 0.872021 GATCTTCGCACACGCCCTAG 60.872 60.000 0.00 0.00 39.84 3.02
2540 3719 1.141019 GATCTTCGCACACGCCCTA 59.859 57.895 0.00 0.00 39.84 3.53
2541 3720 2.125512 GATCTTCGCACACGCCCT 60.126 61.111 0.00 0.00 39.84 5.19
2542 3721 2.125512 AGATCTTCGCACACGCCC 60.126 61.111 0.00 0.00 39.84 6.13
2543 3722 3.389206 GAGATCTTCGCACACGCC 58.611 61.111 0.00 0.00 39.84 5.68


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

AutoCloner maintained by Alex Coulton.