Multiple sequence alignment - TraesCS1A01G359600

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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 TraesCS1A01G359600 chr1A 100.000 3098 0 0 1 3098 541075356 541072259 0.000000e+00 5722.0
1 TraesCS1A01G359600 chr1A 75.684 658 141 14 998 1644 541059646 541058997 8.340000e-81 311.0
2 TraesCS1A01G359600 chr1B 91.027 1616 122 7 651 2252 606697096 606695490 0.000000e+00 2159.0
3 TraesCS1A01G359600 chr1B 81.403 1269 201 19 992 2241 606681338 606680086 0.000000e+00 1003.0
4 TraesCS1A01G359600 chr1B 80.855 1029 173 16 952 1963 606687760 606686739 0.000000e+00 787.0
5 TraesCS1A01G359600 chr1B 77.557 1261 231 29 996 2240 606637431 606636207 0.000000e+00 713.0
6 TraesCS1A01G359600 chr1B 91.784 426 32 3 1821 2244 606639397 606638973 9.570000e-165 590.0
7 TraesCS1A01G359600 chr1B 83.206 262 29 7 2006 2252 606686735 606686474 3.110000e-55 226.0
8 TraesCS1A01G359600 chr7A 95.396 782 31 4 2319 3098 123276348 123277126 0.000000e+00 1240.0
9 TraesCS1A01G359600 chr7A 94.389 606 24 3 1 597 62583059 62583663 0.000000e+00 922.0
10 TraesCS1A01G359600 chr7A 95.588 68 3 0 2252 2319 471811814 471811747 3.270000e-20 110.0
11 TraesCS1A01G359600 chr4B 94.885 782 36 3 2319 3098 665863365 665864144 0.000000e+00 1219.0
12 TraesCS1A01G359600 chr4B 93.651 63 4 0 2252 2314 255342670 255342732 9.150000e-16 95.3
13 TraesCS1A01G359600 chr6A 94.878 781 35 4 2320 3098 52370616 52371393 0.000000e+00 1216.0
14 TraesCS1A01G359600 chr6A 96.000 600 21 1 1 597 5075680 5075081 0.000000e+00 972.0
15 TraesCS1A01G359600 chr6A 93.489 599 31 4 1 597 597904072 597904664 0.000000e+00 883.0
16 TraesCS1A01G359600 chr6A 90.566 53 3 2 598 649 60441898 60441847 5.540000e-08 69.4
17 TraesCS1A01G359600 chr2B 80.772 1503 242 23 718 2189 740730883 740732369 0.000000e+00 1131.0
18 TraesCS1A01G359600 chr3D 90.064 785 65 12 2319 3098 554726122 554725346 0.000000e+00 1005.0
19 TraesCS1A01G359600 chr3D 93.878 49 3 0 598 646 545836855 545836903 1.190000e-09 75.0
20 TraesCS1A01G359600 chr4A 95.183 602 24 2 1 597 164653894 164653293 0.000000e+00 946.0
21 TraesCS1A01G359600 chr2A 94.426 610 27 3 1 607 720316448 720315843 0.000000e+00 931.0
22 TraesCS1A01G359600 chr2A 94.833 600 25 3 1 597 758383376 758383972 0.000000e+00 931.0
23 TraesCS1A01G359600 chr2A 96.667 60 1 1 2252 2311 385442772 385442830 7.070000e-17 99.0
24 TraesCS1A01G359600 chr5A 94.949 594 26 3 2507 3098 705829493 705830084 0.000000e+00 928.0
25 TraesCS1A01G359600 chr5A 82.427 791 99 32 2322 3096 531515820 531516586 0.000000e+00 654.0
26 TraesCS1A01G359600 chr5A 92.557 309 20 2 2319 2625 705829187 705829494 1.020000e-119 440.0
27 TraesCS1A01G359600 chr5A 92.647 68 5 0 2252 2319 527937846 527937913 7.070000e-17 99.0
28 TraesCS1A01G359600 chr7D 94.881 586 23 4 1 582 597509063 597508481 0.000000e+00 909.0
29 TraesCS1A01G359600 chr7D 84.576 791 94 25 2319 3098 461236268 461235495 0.000000e+00 760.0
30 TraesCS1A01G359600 chr5D 93.603 594 33 5 1 592 495289433 495290023 0.000000e+00 881.0
31 TraesCS1A01G359600 chr5D 88.935 723 65 12 2323 3036 408218155 408218871 0.000000e+00 878.0
32 TraesCS1A01G359600 chr5D 98.413 63 0 1 2252 2314 446512304 446512365 3.270000e-20 110.0
33 TraesCS1A01G359600 chr3B 92.939 609 31 2 3 607 765782230 765781630 0.000000e+00 876.0
34 TraesCS1A01G359600 chr6D 82.890 789 105 27 2322 3097 471483447 471482676 0.000000e+00 682.0
35 TraesCS1A01G359600 chr6D 96.825 63 2 0 2252 2314 269967265 269967327 4.230000e-19 106.0
36 TraesCS1A01G359600 chr5B 95.522 67 2 1 2252 2318 439987149 439987214 4.230000e-19 106.0
37 TraesCS1A01G359600 chr4D 96.774 62 2 0 2253 2314 43263040 43263101 1.520000e-18 104.0
38 TraesCS1A01G359600 chr2D 95.312 64 3 0 2251 2314 54198145 54198082 5.470000e-18 102.0
39 TraesCS1A01G359600 chr1D 100.000 48 0 0 599 646 469070612 469070659 4.260000e-14 89.8


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 TraesCS1A01G359600 chr1A 541072259 541075356 3097 True 5722.0 5722 100.0000 1 3098 1 chr1A.!!$R2 3097
1 TraesCS1A01G359600 chr1A 541058997 541059646 649 True 311.0 311 75.6840 998 1644 1 chr1A.!!$R1 646
2 TraesCS1A01G359600 chr1B 606695490 606697096 1606 True 2159.0 2159 91.0270 651 2252 1 chr1B.!!$R2 1601
3 TraesCS1A01G359600 chr1B 606680086 606681338 1252 True 1003.0 1003 81.4030 992 2241 1 chr1B.!!$R1 1249
4 TraesCS1A01G359600 chr1B 606636207 606639397 3190 True 651.5 713 84.6705 996 2244 2 chr1B.!!$R3 1248
5 TraesCS1A01G359600 chr1B 606686474 606687760 1286 True 506.5 787 82.0305 952 2252 2 chr1B.!!$R4 1300
6 TraesCS1A01G359600 chr7A 123276348 123277126 778 False 1240.0 1240 95.3960 2319 3098 1 chr7A.!!$F2 779
7 TraesCS1A01G359600 chr7A 62583059 62583663 604 False 922.0 922 94.3890 1 597 1 chr7A.!!$F1 596
8 TraesCS1A01G359600 chr4B 665863365 665864144 779 False 1219.0 1219 94.8850 2319 3098 1 chr4B.!!$F2 779
9 TraesCS1A01G359600 chr6A 52370616 52371393 777 False 1216.0 1216 94.8780 2320 3098 1 chr6A.!!$F1 778
10 TraesCS1A01G359600 chr6A 5075081 5075680 599 True 972.0 972 96.0000 1 597 1 chr6A.!!$R1 596
11 TraesCS1A01G359600 chr6A 597904072 597904664 592 False 883.0 883 93.4890 1 597 1 chr6A.!!$F2 596
12 TraesCS1A01G359600 chr2B 740730883 740732369 1486 False 1131.0 1131 80.7720 718 2189 1 chr2B.!!$F1 1471
13 TraesCS1A01G359600 chr3D 554725346 554726122 776 True 1005.0 1005 90.0640 2319 3098 1 chr3D.!!$R1 779
14 TraesCS1A01G359600 chr4A 164653293 164653894 601 True 946.0 946 95.1830 1 597 1 chr4A.!!$R1 596
15 TraesCS1A01G359600 chr2A 720315843 720316448 605 True 931.0 931 94.4260 1 607 1 chr2A.!!$R1 606
16 TraesCS1A01G359600 chr2A 758383376 758383972 596 False 931.0 931 94.8330 1 597 1 chr2A.!!$F2 596
17 TraesCS1A01G359600 chr5A 705829187 705830084 897 False 684.0 928 93.7530 2319 3098 2 chr5A.!!$F3 779
18 TraesCS1A01G359600 chr5A 531515820 531516586 766 False 654.0 654 82.4270 2322 3096 1 chr5A.!!$F2 774
19 TraesCS1A01G359600 chr7D 597508481 597509063 582 True 909.0 909 94.8810 1 582 1 chr7D.!!$R2 581
20 TraesCS1A01G359600 chr7D 461235495 461236268 773 True 760.0 760 84.5760 2319 3098 1 chr7D.!!$R1 779
21 TraesCS1A01G359600 chr5D 495289433 495290023 590 False 881.0 881 93.6030 1 592 1 chr5D.!!$F3 591
22 TraesCS1A01G359600 chr5D 408218155 408218871 716 False 878.0 878 88.9350 2323 3036 1 chr5D.!!$F1 713
23 TraesCS1A01G359600 chr3B 765781630 765782230 600 True 876.0 876 92.9390 3 607 1 chr3B.!!$R1 604
24 TraesCS1A01G359600 chr6D 471482676 471483447 771 True 682.0 682 82.8900 2322 3097 1 chr6D.!!$R1 775

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
882 899 0.167470 TACGAAGACAAGGAGACGCG 59.833 55.0 3.53 3.53 0.00 6.01 F
1786 2779 1.032657 TAGTGACTCAGAGCCGGAGC 61.033 60.0 5.05 0.00 35.79 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1855 2851 0.393537 AGCTTTAGCCGCTGCAGATT 60.394 50.000 20.43 1.15 43.38 2.40 R
2772 3926 2.287915 GCTGAAGAAGTGTTTCGAGCAA 59.712 45.455 0.00 0.00 38.38 3.91 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
369 370 3.608662 CGGGTAAGGGCGGCGATA 61.609 66.667 12.98 0.00 0.00 2.92
553 562 0.324275 ACCGTATGCCCAAAATGCCT 60.324 50.000 0.00 0.00 0.00 4.75
601 614 3.704566 TGTACCGAAGCAGACCTCATATT 59.295 43.478 0.00 0.00 0.00 1.28
604 617 5.353394 ACCGAAGCAGACCTCATATTTAA 57.647 39.130 0.00 0.00 0.00 1.52
607 620 6.483640 ACCGAAGCAGACCTCATATTTAAATC 59.516 38.462 3.39 0.00 0.00 2.17
608 621 6.073003 CCGAAGCAGACCTCATATTTAAATCC 60.073 42.308 3.39 0.00 0.00 3.01
609 622 6.708054 CGAAGCAGACCTCATATTTAAATCCT 59.292 38.462 3.39 0.00 0.00 3.24
610 623 7.227512 CGAAGCAGACCTCATATTTAAATCCTT 59.772 37.037 3.39 0.00 0.00 3.36
612 625 8.910351 AGCAGACCTCATATTTAAATCCTTAC 57.090 34.615 3.39 0.00 0.00 2.34
613 626 8.494433 AGCAGACCTCATATTTAAATCCTTACA 58.506 33.333 3.39 0.00 0.00 2.41
616 629 9.628500 AGACCTCATATTTAAATCCTTACAACC 57.372 33.333 3.39 0.00 0.00 3.77
617 630 8.762481 ACCTCATATTTAAATCCTTACAACCC 57.238 34.615 3.39 0.00 0.00 4.11
618 631 7.501225 ACCTCATATTTAAATCCTTACAACCCG 59.499 37.037 3.39 0.00 0.00 5.28
619 632 7.501225 CCTCATATTTAAATCCTTACAACCCGT 59.499 37.037 3.39 0.00 0.00 5.28
621 634 9.245481 TCATATTTAAATCCTTACAACCCGTTT 57.755 29.630 3.39 0.00 0.00 3.60
624 637 6.479095 TTAAATCCTTACAACCCGTTTACG 57.521 37.500 0.00 0.00 39.44 3.18
625 638 3.683365 ATCCTTACAACCCGTTTACGT 57.317 42.857 0.00 0.00 37.74 3.57
626 639 3.025287 TCCTTACAACCCGTTTACGTC 57.975 47.619 0.00 0.00 37.74 4.34
628 641 2.476241 CCTTACAACCCGTTTACGTCAC 59.524 50.000 0.00 0.00 37.74 3.67
629 642 2.147436 TACAACCCGTTTACGTCACC 57.853 50.000 0.00 0.00 37.74 4.02
633 646 3.244181 ACAACCCGTTTACGTCACCTTAT 60.244 43.478 0.00 0.00 37.74 1.73
634 647 3.683365 ACCCGTTTACGTCACCTTATT 57.317 42.857 0.00 0.00 37.74 1.40
635 648 4.799564 ACCCGTTTACGTCACCTTATTA 57.200 40.909 0.00 0.00 37.74 0.98
636 649 5.343307 ACCCGTTTACGTCACCTTATTAT 57.657 39.130 0.00 0.00 37.74 1.28
637 650 6.463995 ACCCGTTTACGTCACCTTATTATA 57.536 37.500 0.00 0.00 37.74 0.98
638 651 6.273071 ACCCGTTTACGTCACCTTATTATAC 58.727 40.000 0.00 0.00 37.74 1.47
640 653 6.980397 CCCGTTTACGTCACCTTATTATACTT 59.020 38.462 0.00 0.00 37.74 2.24
641 654 7.043192 CCCGTTTACGTCACCTTATTATACTTG 60.043 40.741 0.00 0.00 37.74 3.16
642 655 7.332530 CGTTTACGTCACCTTATTATACTTGC 58.667 38.462 0.00 0.00 34.11 4.01
643 656 7.221452 CGTTTACGTCACCTTATTATACTTGCT 59.779 37.037 0.00 0.00 34.11 3.91
645 658 6.466885 ACGTCACCTTATTATACTTGCTCT 57.533 37.500 0.00 0.00 0.00 4.09
646 659 7.578310 ACGTCACCTTATTATACTTGCTCTA 57.422 36.000 0.00 0.00 0.00 2.43
647 660 7.649973 ACGTCACCTTATTATACTTGCTCTAG 58.350 38.462 0.00 0.00 0.00 2.43
648 661 7.284944 ACGTCACCTTATTATACTTGCTCTAGT 59.715 37.037 0.00 0.00 0.00 2.57
649 662 8.136165 CGTCACCTTATTATACTTGCTCTAGTT 58.864 37.037 0.00 0.00 0.00 2.24
683 696 1.134965 AGACTACTCATGGTTGCTCGC 60.135 52.381 0.00 0.00 0.00 5.03
872 889 1.275010 TCAGGCTTGCATACGAAGACA 59.725 47.619 0.00 0.00 29.98 3.41
880 897 2.186076 GCATACGAAGACAAGGAGACG 58.814 52.381 0.00 0.00 0.00 4.18
882 899 0.167470 TACGAAGACAAGGAGACGCG 59.833 55.000 3.53 3.53 0.00 6.01
885 902 3.916392 AAGACAAGGAGACGCGCGG 62.916 63.158 35.22 16.69 0.00 6.46
991 1032 2.290641 CCTTGCACTTGCTAGTTCGTTT 59.709 45.455 11.01 0.00 41.24 3.60
992 1033 3.545633 CTTGCACTTGCTAGTTCGTTTC 58.454 45.455 0.00 0.00 42.66 2.78
993 1034 2.556257 TGCACTTGCTAGTTCGTTTCA 58.444 42.857 0.00 0.00 42.66 2.69
994 1035 2.286833 TGCACTTGCTAGTTCGTTTCAC 59.713 45.455 0.00 0.00 42.66 3.18
995 1036 2.544267 GCACTTGCTAGTTCGTTTCACT 59.456 45.455 0.00 0.00 38.21 3.41
996 1037 3.363084 GCACTTGCTAGTTCGTTTCACTC 60.363 47.826 0.00 0.00 38.21 3.51
1182 2169 1.879575 TCAGGGTTGGAGGGTATCTG 58.120 55.000 0.00 0.00 0.00 2.90
1308 2295 5.278660 GCAGTTCAGGTTCAGTTTCATTGAT 60.279 40.000 0.00 0.00 0.00 2.57
1317 2304 5.089970 TCAGTTTCATTGATCAGTCCGAT 57.910 39.130 0.00 0.00 36.91 4.18
1331 2318 3.034635 AGTCCGATAAGCAGGAGTCAAT 58.965 45.455 0.00 0.00 35.38 2.57
1379 2369 5.347635 CCTTTCGTGACAAATCTCGTGAATA 59.652 40.000 0.00 0.00 41.48 1.75
1656 2649 2.961741 CCTTGCAGCCAGATCTAGAGTA 59.038 50.000 0.00 0.00 0.00 2.59
1665 2658 4.283212 GCCAGATCTAGAGTATTCAAGGCT 59.717 45.833 15.10 0.00 34.59 4.58
1727 2720 2.224305 GGGCCATACACATAGAGGACAC 60.224 54.545 4.39 0.00 0.00 3.67
1776 2769 5.063438 GCTTGCGTTCATTTATAGTGACTCA 59.937 40.000 0.00 0.00 0.00 3.41
1786 2779 1.032657 TAGTGACTCAGAGCCGGAGC 61.033 60.000 5.05 0.00 35.79 4.70
1855 2851 0.671796 CATCGCGGTGGATAGGTACA 59.328 55.000 12.68 0.00 0.00 2.90
1885 2881 2.679837 CGGCTAAAGCTCATGTGTGAAT 59.320 45.455 1.39 0.00 41.70 2.57
1908 2904 3.297134 AAGATATGCGGGTTCATTGGT 57.703 42.857 0.00 0.00 0.00 3.67
1938 2934 0.458543 CGACGACCATCCTGGAACTG 60.459 60.000 0.00 0.00 40.96 3.16
1980 2976 1.826024 CCTGAGGAAGGCGTGCTAT 59.174 57.895 0.00 0.00 39.93 2.97
1989 2985 4.816925 AGGAAGGCGTGCTATAATTTTCTC 59.183 41.667 0.00 0.00 0.00 2.87
2196 3208 0.523072 CATTTGGTCTCTGCCGGTTG 59.477 55.000 1.90 0.00 0.00 3.77
2231 3251 1.795286 GACTTGCAACTTCTCTGGTCG 59.205 52.381 0.00 0.00 0.00 4.79
2260 3280 1.975660 TTTGTTTTCTCGGTCCTGGG 58.024 50.000 0.00 0.00 0.00 4.45
2261 3281 0.109723 TTGTTTTCTCGGTCCTGGGG 59.890 55.000 0.00 0.00 0.00 4.96
2262 3282 1.674651 GTTTTCTCGGTCCTGGGGC 60.675 63.158 0.00 0.00 0.00 5.80
2263 3283 2.150719 TTTTCTCGGTCCTGGGGCA 61.151 57.895 0.00 0.00 0.00 5.36
2264 3284 2.124507 TTTTCTCGGTCCTGGGGCAG 62.125 60.000 0.00 0.00 0.00 4.85
2301 3321 4.293671 CCGGGCCCCCAAAAGTCA 62.294 66.667 18.66 0.00 35.37 3.41
2302 3322 2.203567 CGGGCCCCCAAAAGTCAA 60.204 61.111 18.66 0.00 35.37 3.18
2303 3323 2.275380 CGGGCCCCCAAAAGTCAAG 61.275 63.158 18.66 0.00 35.37 3.02
2304 3324 1.913262 GGGCCCCCAAAAGTCAAGG 60.913 63.158 12.23 0.00 35.81 3.61
2305 3325 1.913262 GGCCCCCAAAAGTCAAGGG 60.913 63.158 0.00 0.00 42.44 3.95
2308 3328 3.791640 CCCAAAAGTCAAGGGGCC 58.208 61.111 0.00 0.00 38.98 5.80
2309 3329 1.913262 CCCAAAAGTCAAGGGGCCC 60.913 63.158 17.12 17.12 38.98 5.80
2310 3330 1.913262 CCAAAAGTCAAGGGGCCCC 60.913 63.158 35.90 35.90 0.00 5.80
2405 3425 7.145932 ACAACTAGCAGAAAATAAAAGCGAT 57.854 32.000 0.00 0.00 0.00 4.58
2421 3441 3.516615 AGCGATGAAACTAAGCTGTCTC 58.483 45.455 0.00 0.00 36.73 3.36
2460 3484 1.833630 CACTGCATTGAGGTAGGAGGA 59.166 52.381 0.00 0.00 0.00 3.71
2478 3502 0.258774 GAAAGCCATCCCTTGCCCTA 59.741 55.000 0.00 0.00 0.00 3.53
2515 3539 0.035881 CAGTGCAGAGCTTCCCAAGA 59.964 55.000 0.00 0.00 0.00 3.02
2549 3694 1.915078 CTGGGCTCAAATCCGGTCCT 61.915 60.000 0.00 0.00 0.00 3.85
2557 3702 0.988832 AAATCCGGTCCTAGCACCAA 59.011 50.000 3.15 0.00 36.01 3.67
2597 3746 9.780186 AAAGTCTTTAGAACAGTAGCTAAACAT 57.220 29.630 0.00 0.00 34.10 2.71
2652 3801 6.884295 TCTTCTCTGAAGGACAAAGACAAAAA 59.116 34.615 7.37 0.00 0.00 1.94
2657 3806 4.142182 TGAAGGACAAAGACAAAAAGCAGG 60.142 41.667 0.00 0.00 0.00 4.85
2772 3926 2.665000 CAGTCGCCACCCATGAGT 59.335 61.111 0.00 0.00 0.00 3.41
2820 3974 2.093973 CACCGATCTGCTTTAGTCCAGT 60.094 50.000 0.00 0.00 0.00 4.00
2839 3993 7.772757 AGTCCAGTCTCCATCATTTTATTTCTC 59.227 37.037 0.00 0.00 0.00 2.87
2910 4064 0.478072 TTGACAGGCACACAGGGATT 59.522 50.000 0.00 0.00 0.00 3.01
3052 4206 3.117776 CCCTCATCACCAGATCCAAATCA 60.118 47.826 0.00 0.00 34.07 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
171 172 2.261671 GTGATGTCGCCTCCGTGT 59.738 61.111 0.00 0.00 35.54 4.49
298 299 1.406539 GATCACGCTGCCAATTCCAAT 59.593 47.619 0.00 0.00 0.00 3.16
436 445 1.457643 CGCATCTACCCTCTCCCCA 60.458 63.158 0.00 0.00 0.00 4.96
490 499 1.523032 GGCGTGCCCATACAGGTAC 60.523 63.158 0.00 0.00 38.99 3.34
553 562 3.457610 CCCCCTCGCTTAACGTATAAA 57.542 47.619 0.00 0.00 44.19 1.40
601 614 5.994668 ACGTAAACGGGTTGTAAGGATTTAA 59.005 36.000 7.50 0.00 44.95 1.52
604 617 3.996363 GACGTAAACGGGTTGTAAGGATT 59.004 43.478 7.50 0.00 44.95 3.01
607 620 2.476241 GTGACGTAAACGGGTTGTAAGG 59.524 50.000 7.50 0.00 44.95 2.69
608 621 2.476241 GGTGACGTAAACGGGTTGTAAG 59.524 50.000 7.50 0.00 44.95 2.34
609 622 2.102252 AGGTGACGTAAACGGGTTGTAA 59.898 45.455 7.50 0.00 44.95 2.41
610 623 1.686052 AGGTGACGTAAACGGGTTGTA 59.314 47.619 7.50 0.00 44.95 2.41
612 625 1.585297 AAGGTGACGTAAACGGGTTG 58.415 50.000 7.50 0.00 44.95 3.77
613 626 3.683365 ATAAGGTGACGTAAACGGGTT 57.317 42.857 7.50 0.00 44.95 4.11
615 628 6.507023 AGTATAATAAGGTGACGTAAACGGG 58.493 40.000 7.50 0.00 44.95 5.28
616 629 7.515684 GCAAGTATAATAAGGTGACGTAAACGG 60.516 40.741 7.50 0.00 44.95 4.44
617 630 7.221452 AGCAAGTATAATAAGGTGACGTAAACG 59.779 37.037 0.04 0.04 46.33 3.60
618 631 8.416485 AGCAAGTATAATAAGGTGACGTAAAC 57.584 34.615 0.00 0.00 0.00 2.01
619 632 8.472413 AGAGCAAGTATAATAAGGTGACGTAAA 58.528 33.333 0.00 0.00 0.00 2.01
621 634 7.578310 AGAGCAAGTATAATAAGGTGACGTA 57.422 36.000 0.00 0.00 0.00 3.57
622 635 6.466885 AGAGCAAGTATAATAAGGTGACGT 57.533 37.500 0.00 0.00 0.00 4.34
623 636 7.649973 ACTAGAGCAAGTATAATAAGGTGACG 58.350 38.462 0.00 0.00 0.00 4.35
633 646 9.463902 ACTCTGAACTAACTAGAGCAAGTATAA 57.536 33.333 0.00 0.00 41.20 0.98
634 647 9.463902 AACTCTGAACTAACTAGAGCAAGTATA 57.536 33.333 0.00 0.00 41.20 1.47
635 648 7.948034 ACTCTGAACTAACTAGAGCAAGTAT 57.052 36.000 0.00 0.00 41.20 2.12
636 649 7.762588 AACTCTGAACTAACTAGAGCAAGTA 57.237 36.000 0.00 0.00 41.20 2.24
637 650 6.658188 AACTCTGAACTAACTAGAGCAAGT 57.342 37.500 0.00 0.00 41.20 3.16
638 651 9.134734 CTTAAACTCTGAACTAACTAGAGCAAG 57.865 37.037 0.00 0.00 41.20 4.01
640 653 8.298140 GTCTTAAACTCTGAACTAACTAGAGCA 58.702 37.037 0.00 0.00 41.20 4.26
641 654 8.517056 AGTCTTAAACTCTGAACTAACTAGAGC 58.483 37.037 0.00 0.00 41.20 4.09
646 659 9.352191 TGAGTAGTCTTAAACTCTGAACTAACT 57.648 33.333 6.59 0.00 42.17 2.24
649 662 8.740906 CCATGAGTAGTCTTAAACTCTGAACTA 58.259 37.037 0.00 0.00 42.17 2.24
670 683 0.175760 GTCTAGGCGAGCAACCATGA 59.824 55.000 0.00 0.00 0.00 3.07
683 696 1.272490 TGCCTTTCAGACGTGTCTAGG 59.728 52.381 11.38 11.38 37.98 3.02
943 983 4.408921 AGGTTGGAAATATGGATCACGAGA 59.591 41.667 0.00 0.00 0.00 4.04
991 1032 1.443702 CGAACGACATGGCGAGTGA 60.444 57.895 31.27 0.00 34.83 3.41
992 1033 3.071459 GCGAACGACATGGCGAGTG 62.071 63.158 31.27 17.00 34.83 3.51
993 1034 2.809601 GCGAACGACATGGCGAGT 60.810 61.111 31.27 15.51 34.83 4.18
994 1035 2.507102 AGCGAACGACATGGCGAG 60.507 61.111 31.27 19.01 34.83 5.03
995 1036 2.809174 CAGCGAACGACATGGCGA 60.809 61.111 31.27 0.00 34.83 5.54
996 1037 3.853330 CCAGCGAACGACATGGCG 61.853 66.667 21.98 21.98 37.29 5.69
1182 2169 3.699413 AGGGTAGTACTTGAGAGACCAC 58.301 50.000 11.44 2.77 0.00 4.16
1222 2209 2.200370 AGATACATCGCCGGGGGA 59.800 61.111 19.63 16.73 0.00 4.81
1223 2210 2.343758 CAGATACATCGCCGGGGG 59.656 66.667 19.63 4.42 0.00 5.40
1231 2218 2.216898 GACAAGGGCAGCAGATACATC 58.783 52.381 0.00 0.00 0.00 3.06
1308 2295 2.025155 GACTCCTGCTTATCGGACTGA 58.975 52.381 0.00 0.00 0.00 3.41
1317 2304 4.380550 CGAGTGTGTATTGACTCCTGCTTA 60.381 45.833 0.00 0.00 36.07 3.09
1331 2318 2.160205 CTCCTCCAGAACGAGTGTGTA 58.840 52.381 0.00 0.00 0.00 2.90
1364 2354 6.183360 GGTGTTCGAATATTCACGAGATTTGT 60.183 38.462 15.57 0.00 39.59 2.83
1379 2369 3.034721 TGCTCGTTAAGGTGTTCGAAT 57.965 42.857 0.00 0.00 32.12 3.34
1656 2649 1.406614 CCGAAGAGCTCAGCCTTGAAT 60.407 52.381 17.77 0.00 31.69 2.57
1665 2658 0.397114 TCATAGGGCCGAAGAGCTCA 60.397 55.000 17.77 0.00 34.85 4.26
1680 2673 1.035385 TCGCCGTGCTCTCCTTCATA 61.035 55.000 0.00 0.00 0.00 2.15
1727 2720 1.798813 CCTTGAAAACTCGAGGTTCCG 59.201 52.381 17.67 11.95 37.12 4.30
1786 2779 3.517100 TCTTCACCATCTTCCTTCTCCAG 59.483 47.826 0.00 0.00 0.00 3.86
1837 2833 1.405872 TTGTACCTATCCACCGCGAT 58.594 50.000 8.23 0.00 0.00 4.58
1844 2840 2.224042 CGCTGCAGATTGTACCTATCCA 60.224 50.000 20.43 0.00 0.00 3.41
1855 2851 0.393537 AGCTTTAGCCGCTGCAGATT 60.394 50.000 20.43 1.15 43.38 2.40
1885 2881 4.102524 ACCAATGAACCCGCATATCTTAGA 59.897 41.667 0.00 0.00 0.00 2.10
1908 2904 1.227031 GGTCGTCGTGGTGTTGACA 60.227 57.895 0.00 0.00 34.78 3.58
1938 2934 0.886490 CACAGTGGTGGTTCTCAGCC 60.886 60.000 0.00 0.00 42.81 4.85
1980 2976 3.095032 GGCGCGCCGAGAAAATTA 58.905 55.556 37.24 0.00 0.00 1.40
2139 3147 3.425193 CGATTGCTTTTTCCGTTCCTTTG 59.575 43.478 0.00 0.00 0.00 2.77
2196 3208 3.572255 TGCAAGTCCAGTAACCCATTTTC 59.428 43.478 0.00 0.00 0.00 2.29
2244 3264 1.674651 GCCCCAGGACCGAGAAAAC 60.675 63.158 0.00 0.00 0.00 2.43
2245 3265 2.124507 CTGCCCCAGGACCGAGAAAA 62.125 60.000 0.00 0.00 0.00 2.29
2284 3304 3.819016 TTGACTTTTGGGGGCCCGG 62.819 63.158 17.79 6.53 39.42 5.73
2285 3305 2.203567 TTGACTTTTGGGGGCCCG 60.204 61.111 17.79 4.39 39.42 6.13
2286 3306 1.913262 CCTTGACTTTTGGGGGCCC 60.913 63.158 15.76 15.76 0.00 5.80
2287 3307 1.913262 CCCTTGACTTTTGGGGGCC 60.913 63.158 0.00 0.00 37.37 5.80
2288 3308 3.791640 CCCTTGACTTTTGGGGGC 58.208 61.111 0.00 0.00 37.37 5.80
2291 3311 1.913262 GGGCCCCTTGACTTTTGGG 60.913 63.158 12.23 0.00 41.23 4.12
2292 3312 1.913262 GGGGCCCCTTGACTTTTGG 60.913 63.158 35.49 0.00 0.00 3.28
2293 3313 1.156095 AGGGGCCCCTTGACTTTTG 59.844 57.895 39.79 0.00 45.70 2.44
2294 3314 3.701991 AGGGGCCCCTTGACTTTT 58.298 55.556 39.79 14.35 45.70 2.27
2303 3323 0.412244 AAAAACTTAGGAGGGGCCCC 59.588 55.000 35.90 35.90 37.37 5.80
2405 3425 1.628846 GGGGGAGACAGCTTAGTTTCA 59.371 52.381 0.00 0.00 0.00 2.69
2515 3539 1.003573 CCAGGCCTTAGGTCTCCCT 59.996 63.158 0.00 0.00 45.51 4.20
2549 3694 9.127277 ACTTTTTAAACTCTAATGTTGGTGCTA 57.873 29.630 0.00 0.00 0.00 3.49
2587 3736 6.331845 TGTTTCCGTTATCGATGTTTAGCTA 58.668 36.000 8.54 0.00 39.71 3.32
2597 3746 5.119588 GTGTTGAGATTGTTTCCGTTATCGA 59.880 40.000 0.00 0.00 39.71 3.59
2652 3801 2.634453 CCTTCCCATTGTTTTTCCTGCT 59.366 45.455 0.00 0.00 0.00 4.24
2657 3806 4.309933 CTCAAGCCTTCCCATTGTTTTTC 58.690 43.478 0.00 0.00 0.00 2.29
2772 3926 2.287915 GCTGAAGAAGTGTTTCGAGCAA 59.712 45.455 0.00 0.00 38.38 3.91
2820 3974 6.779049 CCCCATGAGAAATAAAATGATGGAGA 59.221 38.462 0.00 0.00 32.20 3.71
2839 3993 2.892852 TCTCTTGCAGAAAAACCCCATG 59.107 45.455 0.00 0.00 0.00 3.66
3052 4206 9.282569 GCTTTCAATCTCAAAGATATACCAGAT 57.717 33.333 0.00 0.00 32.89 2.90


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

AutoCloner maintained by Alex Coulton.