Multiple sequence alignment - TraesCS7B01G194700

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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 TraesCS7B01G194700 chr7B 100.000 3356 0 0 1 3356 334454342 334457697 0.000000e+00 6198.0
1 TraesCS7B01G194700 chr7A 88.806 2278 153 43 276 2500 194289923 194287695 0.000000e+00 2700.0
2 TraesCS7B01G194700 chr7A 92.115 279 11 6 1 270 194290269 194289993 1.890000e-102 383.0
3 TraesCS7B01G194700 chr7D 90.985 1919 129 14 619 2500 189912428 189914339 0.000000e+00 2545.0
4 TraesCS7B01G194700 chr7D 82.825 623 48 34 1 576 189910946 189911556 1.390000e-138 503.0
5 TraesCS7B01G194700 chr3B 92.162 842 66 0 2515 3356 421876527 421875686 0.000000e+00 1190.0
6 TraesCS7B01G194700 chr3B 85.325 845 114 9 2515 3354 491526814 491525975 0.000000e+00 865.0
7 TraesCS7B01G194700 chr3B 76.699 412 82 12 1151 1552 756823910 756823503 2.030000e-52 217.0
8 TraesCS7B01G194700 chr3B 76.156 411 85 11 1151 1552 756708778 756708372 1.580000e-48 204.0
9 TraesCS7B01G194700 chr5B 91.568 842 71 0 2515 3356 381385724 381384883 0.000000e+00 1162.0
10 TraesCS7B01G194700 chr5B 87.719 57 7 0 2396 2452 652628402 652628346 2.160000e-07 67.6
11 TraesCS7B01G194700 chr4B 86.730 844 110 2 2512 3354 609618532 609619374 0.000000e+00 937.0
12 TraesCS7B01G194700 chr4B 94.664 581 16 7 1 576 624107710 624107140 0.000000e+00 887.0
13 TraesCS7B01G194700 chr3A 84.121 825 127 4 2515 3337 713691922 713691100 0.000000e+00 795.0
14 TraesCS7B01G194700 chr3A 88.679 106 10 2 2393 2496 384190759 384190864 9.770000e-26 128.0
15 TraesCS7B01G194700 chr2A 82.521 841 145 2 2515 3354 608881215 608882054 0.000000e+00 737.0
16 TraesCS7B01G194700 chr2A 82.367 845 146 3 2512 3354 27596802 27595959 0.000000e+00 732.0
17 TraesCS7B01G194700 chr6A 82.588 827 142 2 2512 3337 93927108 93926283 0.000000e+00 728.0
18 TraesCS7B01G194700 chr5D 80.964 809 152 2 2547 3354 288560888 288560081 1.020000e-179 640.0
19 TraesCS7B01G194700 chr5D 88.636 88 9 1 2397 2483 525987603 525987690 4.580000e-19 106.0
20 TraesCS7B01G194700 chr5D 86.885 61 8 0 2393 2453 339646392 339646332 6.010000e-08 69.4


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 TraesCS7B01G194700 chr7B 334454342 334457697 3355 False 6198.0 6198 100.0000 1 3356 1 chr7B.!!$F1 3355
1 TraesCS7B01G194700 chr7A 194287695 194290269 2574 True 1541.5 2700 90.4605 1 2500 2 chr7A.!!$R1 2499
2 TraesCS7B01G194700 chr7D 189910946 189914339 3393 False 1524.0 2545 86.9050 1 2500 2 chr7D.!!$F1 2499
3 TraesCS7B01G194700 chr3B 421875686 421876527 841 True 1190.0 1190 92.1620 2515 3356 1 chr3B.!!$R1 841
4 TraesCS7B01G194700 chr3B 491525975 491526814 839 True 865.0 865 85.3250 2515 3354 1 chr3B.!!$R2 839
5 TraesCS7B01G194700 chr5B 381384883 381385724 841 True 1162.0 1162 91.5680 2515 3356 1 chr5B.!!$R1 841
6 TraesCS7B01G194700 chr4B 609618532 609619374 842 False 937.0 937 86.7300 2512 3354 1 chr4B.!!$F1 842
7 TraesCS7B01G194700 chr4B 624107140 624107710 570 True 887.0 887 94.6640 1 576 1 chr4B.!!$R1 575
8 TraesCS7B01G194700 chr3A 713691100 713691922 822 True 795.0 795 84.1210 2515 3337 1 chr3A.!!$R1 822
9 TraesCS7B01G194700 chr2A 608881215 608882054 839 False 737.0 737 82.5210 2515 3354 1 chr2A.!!$F1 839
10 TraesCS7B01G194700 chr2A 27595959 27596802 843 True 732.0 732 82.3670 2512 3354 1 chr2A.!!$R1 842
11 TraesCS7B01G194700 chr6A 93926283 93927108 825 True 728.0 728 82.5880 2512 3337 1 chr6A.!!$R1 825
12 TraesCS7B01G194700 chr5D 288560081 288560888 807 True 640.0 640 80.9640 2547 3354 1 chr5D.!!$R1 807

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
689 1651 0.598065 AAACAAAGACGGGCTCATGC 59.402 50.0 0.0 0.0 38.76 4.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2608 3612 0.03213 TGCAGAAGCGAGTCGACTTT 59.968 50.0 21.08 10.32 46.23 2.66 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
40 45 4.889856 TCCATGTGATCGCCGCCG 62.890 66.667 3.31 0.00 0.00 6.46
67 72 2.661566 CGGTTCAGCTGCTCGTGTG 61.662 63.158 9.47 0.00 0.00 3.82
68 73 1.595382 GGTTCAGCTGCTCGTGTGT 60.595 57.895 9.47 0.00 0.00 3.72
358 457 6.128445 GCGAGATATGTGTATTTCTTGGGATG 60.128 42.308 0.00 0.00 30.62 3.51
491 598 8.779354 AGATACATAAGACTTTTGACTGGAAC 57.221 34.615 11.97 0.00 0.00 3.62
544 669 6.707440 AGAGTACCAGATGTCATCACTAAG 57.293 41.667 15.20 1.59 0.00 2.18
606 1568 2.582052 TGGAAACGATTGCTTCTGGTT 58.418 42.857 0.00 0.00 0.00 3.67
611 1573 3.126001 ACGATTGCTTCTGGTTCTGAA 57.874 42.857 0.00 0.00 0.00 3.02
612 1574 2.808543 ACGATTGCTTCTGGTTCTGAAC 59.191 45.455 12.05 12.05 0.00 3.18
646 1608 3.553917 CGGTTGAACAAATTCACCAAACC 59.446 43.478 0.00 0.00 44.66 3.27
679 1641 1.595794 TCGCCGACTGAAAACAAAGAC 59.404 47.619 0.00 0.00 0.00 3.01
680 1642 1.656429 CGCCGACTGAAAACAAAGACG 60.656 52.381 0.00 0.00 0.00 4.18
689 1651 0.598065 AAACAAAGACGGGCTCATGC 59.402 50.000 0.00 0.00 38.76 4.06
769 1731 2.487934 CTCGATTGGCTGGACCTAATG 58.512 52.381 0.00 0.00 40.22 1.90
792 1754 6.563422 TGGTGATTGAAAAGAAAGAACAGTG 58.437 36.000 0.00 0.00 0.00 3.66
797 1759 9.173021 TGATTGAAAAGAAAGAACAGTGTTCTA 57.827 29.630 33.12 17.84 31.41 2.10
830 1793 7.010183 GGGGAAAAGAAAAGAAAAGAAAGAACG 59.990 37.037 0.00 0.00 0.00 3.95
835 1798 5.417894 AGAAAAGAAAAGAAAGAACGGTGGT 59.582 36.000 0.00 0.00 0.00 4.16
935 1902 3.706594 CCCAGAGACTTTACCAGCATCTA 59.293 47.826 0.00 0.00 0.00 1.98
939 1906 3.983741 AGACTTTACCAGCATCTATCGC 58.016 45.455 0.00 0.00 0.00 4.58
952 1919 3.944055 TCTATCGCCTTCCTAATCTGC 57.056 47.619 0.00 0.00 0.00 4.26
971 1938 1.807755 GCATCTTGCAGGCGTGAGATA 60.808 52.381 11.29 0.00 44.26 1.98
1085 2052 2.762887 CCAGTCTGCAGGTATCTTCTCA 59.237 50.000 15.13 0.00 0.00 3.27
1109 2076 0.592637 TTGCTTGATTCACAGCCGTG 59.407 50.000 14.24 0.00 45.08 4.94
1118 2098 2.594592 ACAGCCGTGCTTGTTCCC 60.595 61.111 0.00 0.00 36.40 3.97
1149 2129 3.627395 TTCACCTAGCTGTTACCATGG 57.373 47.619 11.19 11.19 0.00 3.66
1155 2135 3.197766 CCTAGCTGTTACCATGGAACTCA 59.802 47.826 21.47 10.69 0.00 3.41
1176 2156 0.947660 TTGCAGAACGCTGAGCAGAG 60.948 55.000 4.88 0.14 45.17 3.35
1220 2200 1.080434 GCCATCGCCGATCTACTCC 60.080 63.158 0.00 0.00 0.00 3.85
1222 2202 1.235281 CCATCGCCGATCTACTCCGA 61.235 60.000 0.00 0.00 0.00 4.55
1262 2242 4.760047 GCATGGTGGTCGCGGACT 62.760 66.667 6.13 0.00 32.47 3.85
1303 2283 2.653702 GCGCTCACTCTGGTGTCT 59.346 61.111 0.00 0.00 43.41 3.41
1344 2324 0.391597 GGTCAGTGTCTTCGTTCCCA 59.608 55.000 0.00 0.00 0.00 4.37
1351 2331 2.032528 CTTCGTTCCCAGCAGCCA 59.967 61.111 0.00 0.00 0.00 4.75
1396 2376 3.056821 TCAACGATCTTCCAGACAACGAT 60.057 43.478 0.00 0.00 0.00 3.73
1439 2419 2.518112 TGGCGTTCCAGCAAAGCA 60.518 55.556 0.00 0.00 40.97 3.91
1450 2430 0.751643 AGCAAAGCAACAGGTCGGTT 60.752 50.000 0.00 0.00 0.00 4.44
1515 2495 1.078848 GTGGCTCCTTGCATCTCGT 60.079 57.895 0.00 0.00 45.15 4.18
1561 2544 3.561725 GGCTCTCCGAGGTATGAATTTTG 59.438 47.826 0.00 0.00 0.00 2.44
1573 2556 0.237235 GAATTTTGCACGGCTCGACA 59.763 50.000 1.50 0.00 0.00 4.35
1624 2607 6.588204 TGAGCAGTAAGTTTAACTTTGGAGA 58.412 36.000 15.83 0.00 39.51 3.71
1628 2611 7.389053 AGCAGTAAGTTTAACTTTGGAGATGAG 59.611 37.037 15.83 0.00 39.51 2.90
1717 2700 0.949105 GAAGACGGCGTGTGGTCATT 60.949 55.000 21.19 0.00 35.63 2.57
1729 2712 0.918258 TGGTCATTGGAGCCTATGCA 59.082 50.000 6.14 0.00 40.83 3.96
1730 2713 1.284491 TGGTCATTGGAGCCTATGCAA 59.716 47.619 6.14 0.00 44.01 4.08
1792 2775 1.506262 CAAAGAATTGGTCGCCGGG 59.494 57.895 2.18 0.00 32.69 5.73
1870 2853 1.637553 ACTCATGCCTGGGAATCAGTT 59.362 47.619 0.00 0.00 41.83 3.16
1888 2871 8.451908 AATCAGTTGCCCTTATATTAAGTGAC 57.548 34.615 0.00 0.00 34.60 3.67
1893 2876 6.260700 TGCCCTTATATTAAGTGACATGGT 57.739 37.500 0.00 0.00 0.00 3.55
1987 2974 5.244626 TGTGACTGACATCTTGATCTTCTGA 59.755 40.000 0.00 0.00 0.00 3.27
1988 2975 6.162079 GTGACTGACATCTTGATCTTCTGAA 58.838 40.000 0.00 0.00 0.00 3.02
2075 3063 1.045350 TCCGATGAAGAGCTGAGGGG 61.045 60.000 0.00 0.00 0.00 4.79
2161 3149 0.107945 GGAAAGCACGCTGATCTCCT 60.108 55.000 0.00 0.00 0.00 3.69
2262 3250 2.424956 GGATGAATTTGTGAGGACTGCC 59.575 50.000 0.00 0.00 0.00 4.85
2276 3264 4.287781 TGCCGAACGACGCTGGAA 62.288 61.111 4.94 0.00 41.07 3.53
2279 3267 2.355363 CGAACGACGCTGGAACCA 60.355 61.111 0.00 0.00 34.51 3.67
2315 3303 1.519455 CGGAGCTGGCTAGAAACCG 60.519 63.158 0.00 8.38 32.59 4.44
2340 3328 4.553938 CGAGTTATTTTGGTTGTGTCGCTT 60.554 41.667 0.00 0.00 0.00 4.68
2372 3360 4.202182 GGTATAACGTGTTAGGGCATCTCA 60.202 45.833 0.00 0.00 0.00 3.27
2405 3393 1.880646 GCTCGGGCAGTAAAGGACAAA 60.881 52.381 0.00 0.00 38.54 2.83
2438 3426 6.819649 TCAAATAAAAGTCCGATCCATAACGT 59.180 34.615 0.00 0.00 0.00 3.99
2466 3470 3.244009 GGATCACATGTCCGATCACATCT 60.244 47.826 21.36 0.00 39.88 2.90
2504 3508 9.262472 GTATGCTTAAGTTTTACATGTCTTTCG 57.738 33.333 0.00 0.00 0.00 3.46
2505 3509 7.254227 TGCTTAAGTTTTACATGTCTTTCGT 57.746 32.000 0.00 0.00 0.00 3.85
2506 3510 7.349711 TGCTTAAGTTTTACATGTCTTTCGTC 58.650 34.615 0.00 0.00 0.00 4.20
2507 3511 6.795593 GCTTAAGTTTTACATGTCTTTCGTCC 59.204 38.462 0.00 0.00 0.00 4.79
2508 3512 7.519328 GCTTAAGTTTTACATGTCTTTCGTCCA 60.519 37.037 0.00 0.00 0.00 4.02
2509 3513 5.668558 AGTTTTACATGTCTTTCGTCCAC 57.331 39.130 0.00 0.00 0.00 4.02
2510 3514 5.365619 AGTTTTACATGTCTTTCGTCCACT 58.634 37.500 0.00 0.00 0.00 4.00
2511 3515 6.518493 AGTTTTACATGTCTTTCGTCCACTA 58.482 36.000 0.00 0.00 0.00 2.74
2512 3516 6.423001 AGTTTTACATGTCTTTCGTCCACTAC 59.577 38.462 0.00 0.00 0.00 2.73
2513 3517 3.314541 ACATGTCTTTCGTCCACTACC 57.685 47.619 0.00 0.00 0.00 3.18
2532 3536 1.500474 CTGGCATCTTCTCCCCACTA 58.500 55.000 0.00 0.00 0.00 2.74
2535 3539 1.501582 GCATCTTCTCCCCACTACCT 58.498 55.000 0.00 0.00 0.00 3.08
2563 3567 0.841961 TGCCAGCATGAGGATTAGCT 59.158 50.000 8.66 0.00 39.69 3.32
2608 3612 1.073125 TCGCCAACCCAATCAAAGAGA 59.927 47.619 0.00 0.00 0.00 3.10
2610 3614 2.295909 CGCCAACCCAATCAAAGAGAAA 59.704 45.455 0.00 0.00 0.00 2.52
2628 3632 0.387878 AAGTCGACTCGCTTCTGCAG 60.388 55.000 20.33 7.63 39.64 4.41
2643 3647 3.759581 TCTGCAGCTCCTCAATCTTTTT 58.240 40.909 9.47 0.00 0.00 1.94
2645 3649 3.489355 TGCAGCTCCTCAATCTTTTTGA 58.511 40.909 0.00 0.00 0.00 2.69
2715 3719 6.263842 CCATGATTAGGTGCAACAATGTAGAT 59.736 38.462 3.64 0.00 39.98 1.98
2757 3761 2.832201 GGCGGCTCCGTAGTAGGT 60.832 66.667 10.24 0.00 42.09 3.08
2802 3806 1.409427 CCGGTCTCCACTGGTAGAATC 59.591 57.143 0.00 0.00 43.54 2.52
2989 3993 0.251341 GGACATTGACAAGGCCAGGT 60.251 55.000 5.01 1.07 0.00 4.00
3009 4013 1.222115 GACGATTCCTATGGGCGCAC 61.222 60.000 10.83 6.04 0.00 5.34
3042 4046 0.040067 CAGGCGGAAAGTGCAAAGTC 60.040 55.000 0.00 0.00 0.00 3.01
3108 4112 5.279657 GGGCATTCAAAATCTCCAACTCTTT 60.280 40.000 0.00 0.00 0.00 2.52
3133 4137 1.807886 GCACTACGTCTCCGATGGT 59.192 57.895 0.00 0.00 37.88 3.55
3135 4139 1.909376 CACTACGTCTCCGATGGTTG 58.091 55.000 0.00 0.00 37.88 3.77
3216 4220 3.429410 GCAATGACAAGGCCCTATTCAAC 60.429 47.826 0.00 0.00 0.00 3.18
3220 4224 4.415596 TGACAAGGCCCTATTCAACAAAT 58.584 39.130 0.00 0.00 0.00 2.32
3225 4229 4.415596 AGGCCCTATTCAACAAATTCACA 58.584 39.130 0.00 0.00 0.00 3.58
3258 4262 0.514691 GAGACGGCAAGACAGCAAAG 59.485 55.000 0.00 0.00 35.83 2.77
3308 4313 3.493767 ACCTCTCTGTCAAACTTTCCC 57.506 47.619 0.00 0.00 0.00 3.97
3320 4325 5.290885 GTCAAACTTTCCCAATGTTGTTCAC 59.709 40.000 0.00 0.00 0.00 3.18
3338 4343 2.079925 CACAAGGGCTAGAAGCAAGTC 58.920 52.381 0.00 0.00 44.75 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 54 2.356313 ACACGAGCAGCTGAACCG 60.356 61.111 20.43 18.43 0.00 4.44
67 72 1.212616 GCTGCGTATCATGGACAGAC 58.787 55.000 0.00 0.00 0.00 3.51
68 73 0.823460 TGCTGCGTATCATGGACAGA 59.177 50.000 0.00 0.00 0.00 3.41
358 457 6.410540 ACAATTTACTCAGGGTCATCTTCTC 58.589 40.000 0.00 0.00 0.00 2.87
416 515 4.515191 GGAAATCACAACAGCAGTTCTACA 59.485 41.667 0.00 0.00 35.28 2.74
491 598 2.287608 TGTTATACGATGAGCAGCGGAG 60.288 50.000 12.89 0.00 45.50 4.63
544 669 7.095102 GGATACCGACTTCTCTTCTAGTGTATC 60.095 44.444 0.00 0.00 33.67 2.24
576 701 9.271828 AGAAGCAATCGTTTCCAAATTTTAATT 57.728 25.926 0.00 0.00 33.11 1.40
606 1568 2.171027 ACCGTTGGTTACTTGGTTCAGA 59.829 45.455 0.00 0.00 27.29 3.27
611 1573 2.684374 GTTCAACCGTTGGTTACTTGGT 59.316 45.455 11.35 0.00 45.01 3.67
612 1574 2.683867 TGTTCAACCGTTGGTTACTTGG 59.316 45.455 11.35 0.00 45.01 3.61
613 1575 4.358494 TTGTTCAACCGTTGGTTACTTG 57.642 40.909 11.35 0.00 45.01 3.16
614 1576 5.585820 ATTTGTTCAACCGTTGGTTACTT 57.414 34.783 11.35 0.00 45.01 2.24
615 1577 5.125739 TGAATTTGTTCAACCGTTGGTTACT 59.874 36.000 11.35 0.00 45.01 2.24
616 1578 5.230516 GTGAATTTGTTCAACCGTTGGTTAC 59.769 40.000 11.35 7.95 45.01 2.50
617 1579 5.341617 GTGAATTTGTTCAACCGTTGGTTA 58.658 37.500 11.35 0.00 45.01 2.85
662 1624 1.263217 CCCGTCTTTGTTTTCAGTCGG 59.737 52.381 0.00 0.00 37.04 4.79
664 1626 1.947456 AGCCCGTCTTTGTTTTCAGTC 59.053 47.619 0.00 0.00 0.00 3.51
680 1642 2.747460 TTGTCAGCGCATGAGCCC 60.747 61.111 18.40 7.08 39.07 5.19
689 1651 2.341257 AGCACTATGAAGTTGTCAGCG 58.659 47.619 0.00 0.00 40.43 5.18
769 1731 6.564328 ACACTGTTCTTTCTTTTCAATCACC 58.436 36.000 0.00 0.00 0.00 4.02
804 1767 7.010183 CGTTCTTTCTTTTCTTTTCTTTTCCCC 59.990 37.037 0.00 0.00 0.00 4.81
810 1773 6.071560 ACCACCGTTCTTTCTTTTCTTTTCTT 60.072 34.615 0.00 0.00 0.00 2.52
811 1774 5.417894 ACCACCGTTCTTTCTTTTCTTTTCT 59.582 36.000 0.00 0.00 0.00 2.52
812 1775 5.647589 ACCACCGTTCTTTCTTTTCTTTTC 58.352 37.500 0.00 0.00 0.00 2.29
813 1776 5.417894 AGACCACCGTTCTTTCTTTTCTTTT 59.582 36.000 0.00 0.00 0.00 2.27
814 1777 4.948004 AGACCACCGTTCTTTCTTTTCTTT 59.052 37.500 0.00 0.00 0.00 2.52
830 1793 3.626930 TGGCACCAATAATTAGACCACC 58.373 45.455 0.00 0.00 0.00 4.61
935 1902 2.636893 AGATGCAGATTAGGAAGGCGAT 59.363 45.455 0.00 0.00 0.00 4.58
952 1919 2.133553 CTATCTCACGCCTGCAAGATG 58.866 52.381 6.59 0.00 34.07 2.90
965 1932 2.037901 CAGGCTGAGCTTCCTATCTCA 58.962 52.381 9.42 0.00 37.70 3.27
1085 2052 3.015327 GGCTGTGAATCAAGCAAGAGAT 58.985 45.455 15.44 0.00 0.00 2.75
1118 2098 2.503356 AGCTAGGTGAATCAGTTCTGGG 59.497 50.000 0.00 0.00 35.33 4.45
1149 2129 3.736581 GCGTTCTGCAAGTGAGTTC 57.263 52.632 0.00 0.00 45.45 3.01
1176 2156 3.092511 TGAGGGGCCTCATCCTGC 61.093 66.667 4.79 0.00 46.80 4.85
1303 2283 0.387929 GGATGGCGTCAACGGAGATA 59.612 55.000 9.27 0.00 40.23 1.98
1351 2331 3.222354 GACGCAGACTTCCACCGGT 62.222 63.158 0.00 0.00 0.00 5.28
1396 2376 2.622942 GCTCTTCACCACCATGTTGAAA 59.377 45.455 0.00 0.00 0.00 2.69
1439 2419 1.487558 ACCTGTAACAACCGACCTGTT 59.512 47.619 0.00 0.00 40.13 3.16
1584 2567 1.522676 GCTCAAAAAGAAACAAGCCGC 59.477 47.619 0.00 0.00 0.00 6.53
1585 2568 2.791004 CTGCTCAAAAAGAAACAAGCCG 59.209 45.455 0.00 0.00 0.00 5.52
1586 2569 3.785486 ACTGCTCAAAAAGAAACAAGCC 58.215 40.909 0.00 0.00 0.00 4.35
1587 2570 6.036470 ACTTACTGCTCAAAAAGAAACAAGC 58.964 36.000 0.00 0.00 0.00 4.01
1624 2607 1.202330 CTTCAGGAGCCTGGACTCAT 58.798 55.000 16.06 9.20 43.75 2.90
1628 2611 0.980423 AGTTCTTCAGGAGCCTGGAC 59.020 55.000 16.06 9.94 43.75 4.02
1729 2712 4.473444 TGAAATCTTTCCTGAACTGCCTT 58.527 39.130 0.48 0.00 36.36 4.35
1730 2713 4.104383 TGAAATCTTTCCTGAACTGCCT 57.896 40.909 0.48 0.00 36.36 4.75
1789 2772 0.891904 AAACAACCAATCGACCCCCG 60.892 55.000 0.00 0.00 40.25 5.73
1792 2775 0.885879 GGGAAACAACCAATCGACCC 59.114 55.000 0.00 0.00 0.00 4.46
1870 2853 6.101150 AGACCATGTCACTTAATATAAGGGCA 59.899 38.462 2.53 1.74 34.60 5.36
1888 2871 6.764308 AATCAATGTACCTTTGAGACCATG 57.236 37.500 12.27 0.00 36.60 3.66
1921 2904 7.962918 CGTTTAGGAATGGTAGAAATGAAACAG 59.037 37.037 0.00 0.00 0.00 3.16
2075 3063 2.725221 ACCCTCTGCTTGAATGATCC 57.275 50.000 0.00 0.00 0.00 3.36
2161 3149 1.219124 GACTGGCCATCTTGCTCGA 59.781 57.895 5.51 0.00 0.00 4.04
2262 3250 2.355363 TGGTTCCAGCGTCGTTCG 60.355 61.111 0.00 0.00 43.12 3.95
2276 3264 4.673375 CCAAGCTGCCCTGCTGGT 62.673 66.667 9.00 0.00 43.24 4.00
2279 3267 2.035312 CTTCCAAGCTGCCCTGCT 59.965 61.111 0.00 0.00 46.40 4.24
2315 3303 3.561503 GACACAACCAAAATAACTCGCC 58.438 45.455 0.00 0.00 0.00 5.54
2317 3305 3.059188 AGCGACACAACCAAAATAACTCG 60.059 43.478 0.00 0.00 0.00 4.18
2340 3328 7.334171 GCCCTAACACGTTATACCTTCTTTTTA 59.666 37.037 0.00 0.00 0.00 1.52
2389 3377 4.864704 TTCAATTTGTCCTTTACTGCCC 57.135 40.909 0.00 0.00 0.00 5.36
2405 3393 9.586435 GGATCGGACTTTTATTTGAATTTCAAT 57.414 29.630 12.39 6.11 36.11 2.57
2438 3426 2.511373 GACATGTGATCCGGCGCA 60.511 61.111 10.83 0.00 0.00 6.09
2507 3511 1.139853 GGGAGAAGATGCCAGGTAGTG 59.860 57.143 0.00 0.00 39.77 2.74
2508 3512 1.501582 GGGAGAAGATGCCAGGTAGT 58.498 55.000 0.00 0.00 39.77 2.73
2509 3513 0.761802 GGGGAGAAGATGCCAGGTAG 59.238 60.000 0.00 0.00 42.44 3.18
2510 3514 0.044092 TGGGGAGAAGATGCCAGGTA 59.956 55.000 0.00 0.00 42.44 3.08
2511 3515 1.229951 TGGGGAGAAGATGCCAGGT 60.230 57.895 0.00 0.00 42.44 4.00
2512 3516 1.225704 GTGGGGAGAAGATGCCAGG 59.774 63.158 0.00 0.00 42.44 4.45
2513 3517 1.139853 GTAGTGGGGAGAAGATGCCAG 59.860 57.143 0.00 0.00 42.44 4.85
2532 3536 2.373707 GCTGGCATCTCTCCCAGGT 61.374 63.158 8.58 0.00 46.87 4.00
2535 3539 0.984432 TCATGCTGGCATCTCTCCCA 60.984 55.000 4.98 0.00 33.90 4.37
2543 3547 1.424302 AGCTAATCCTCATGCTGGCAT 59.576 47.619 1.86 1.86 37.08 4.40
2563 3567 4.320608 TCACAGCATCATCAGCGTATAA 57.679 40.909 0.00 0.00 37.01 0.98
2608 3612 0.032130 TGCAGAAGCGAGTCGACTTT 59.968 50.000 21.08 10.32 46.23 2.66
2610 3614 1.211449 CTGCAGAAGCGAGTCGACT 59.789 57.895 20.18 20.18 46.23 4.18
2645 3649 2.344203 CGAAGACCAGAGGCGTCCT 61.344 63.158 2.06 0.00 36.03 3.85
2757 3761 3.971971 GGCCTAGGTAAGTCATAGGGAAA 59.028 47.826 11.31 0.00 46.88 3.13
2802 3806 3.617263 GGAACTGCAGATGTACTAAACGG 59.383 47.826 23.35 0.00 0.00 4.44
2889 3893 0.317103 CGCTACGGACGAGGATTCTG 60.317 60.000 0.00 0.00 0.00 3.02
2964 3968 2.029918 GGCCTTGTCAATGTCCTTCAAC 60.030 50.000 0.00 0.00 0.00 3.18
2965 3969 2.238521 GGCCTTGTCAATGTCCTTCAA 58.761 47.619 0.00 0.00 0.00 2.69
2989 3993 1.069090 GCGCCCATAGGAATCGTCA 59.931 57.895 0.00 0.00 33.47 4.35
3009 4013 0.366871 CGCCTGACAAATCTTCGTCG 59.633 55.000 0.00 0.00 34.78 5.12
3133 4137 1.894466 CTGCATCCATTCCAACCACAA 59.106 47.619 0.00 0.00 0.00 3.33
3135 4139 0.174162 GCTGCATCCATTCCAACCAC 59.826 55.000 0.00 0.00 0.00 4.16
3216 4220 3.787634 CGATGGCGATCTTTGTGAATTTG 59.212 43.478 7.15 0.00 40.82 2.32
3220 4224 1.066502 TCCGATGGCGATCTTTGTGAA 60.067 47.619 7.15 0.00 40.82 3.18
3225 4229 0.249073 CGTCTCCGATGGCGATCTTT 60.249 55.000 7.15 0.00 40.82 2.52
3308 4313 3.820467 TCTAGCCCTTGTGAACAACATTG 59.180 43.478 0.00 0.00 38.99 2.82
3320 4325 1.003580 TGGACTTGCTTCTAGCCCTTG 59.996 52.381 0.00 0.00 41.51 3.61


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

AutoCloner maintained by Alex Coulton.