Multiple sequence alignment - TraesCS4A01G208100

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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 TraesCS4A01G208100 chr4A 100.000 4174 0 0 1 4174 501141321 501137148 0.000000e+00 7709
1 TraesCS4A01G208100 chr4A 91.404 826 64 6 3354 4174 66584514 66585337 0.000000e+00 1125
2 TraesCS4A01G208100 chr4A 91.108 821 65 5 3357 4174 568320095 568320910 0.000000e+00 1105
3 TraesCS4A01G208100 chr4A 92.359 602 42 3 1 601 5619132 5619730 0.000000e+00 854
4 TraesCS4A01G208100 chr4A 91.542 603 49 2 1 602 566929369 566928768 0.000000e+00 830
5 TraesCS4A01G208100 chr4D 94.392 2657 108 19 713 3359 88158928 88156303 0.000000e+00 4043
6 TraesCS4A01G208100 chr4D 90.400 125 10 2 600 723 88470342 88470219 3.340000e-36 163
7 TraesCS4A01G208100 chr4B 93.638 2735 106 28 647 3359 125383688 125381000 0.000000e+00 4024
8 TraesCS4A01G208100 chr7A 93.057 821 54 3 3357 4174 18966614 18965794 0.000000e+00 1197
9 TraesCS4A01G208100 chr7A 93.398 727 44 4 3452 4174 18965960 18965234 0.000000e+00 1074
10 TraesCS4A01G208100 chr7A 91.188 783 54 3 3407 4174 652899805 652900587 0.000000e+00 1050
11 TraesCS4A01G208100 chr7A 92.680 724 51 2 3452 4174 652899307 652900029 0.000000e+00 1042
12 TraesCS4A01G208100 chr7A 92.359 602 41 4 1 601 624722722 624723319 0.000000e+00 852
13 TraesCS4A01G208100 chr7A 92.040 603 46 2 1 602 398742682 398743283 0.000000e+00 846
14 TraesCS4A01G208100 chr7A 91.362 602 48 3 1 601 554321359 554321957 0.000000e+00 821
15 TraesCS4A01G208100 chr3A 91.585 820 61 5 3358 4174 737116683 737115869 0.000000e+00 1125
16 TraesCS4A01G208100 chr1A 91.205 830 64 7 3350 4174 338306535 338307360 0.000000e+00 1120
17 TraesCS4A01G208100 chr1A 92.642 598 40 4 1 597 234738531 234737937 0.000000e+00 857
18 TraesCS4A01G208100 chr1A 91.820 599 45 4 1 597 104695011 104694415 0.000000e+00 832
19 TraesCS4A01G208100 chr6A 89.294 822 82 6 3358 4174 545539925 545539105 0.000000e+00 1026
20 TraesCS4A01G208100 chr2A 92.027 602 44 3 1 601 499961573 499962171 0.000000e+00 843
21 TraesCS4A01G208100 chr2A 87.825 616 53 11 3357 3952 674586135 674586748 0.000000e+00 702
22 TraesCS4A01G208100 chr2A 87.480 615 56 11 3357 3952 674701131 674701743 0.000000e+00 689
23 TraesCS4A01G208100 chr2A 85.495 455 44 10 3351 3785 98108783 98109235 4.920000e-124 455
24 TraesCS4A01G208100 chr5A 91.362 602 47 4 1 601 90743000 90742403 0.000000e+00 819


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 TraesCS4A01G208100 chr4A 501137148 501141321 4173 True 7709.0 7709 100.0000 1 4174 1 chr4A.!!$R1 4173
1 TraesCS4A01G208100 chr4A 66584514 66585337 823 False 1125.0 1125 91.4040 3354 4174 1 chr4A.!!$F2 820
2 TraesCS4A01G208100 chr4A 568320095 568320910 815 False 1105.0 1105 91.1080 3357 4174 1 chr4A.!!$F3 817
3 TraesCS4A01G208100 chr4A 5619132 5619730 598 False 854.0 854 92.3590 1 601 1 chr4A.!!$F1 600
4 TraesCS4A01G208100 chr4A 566928768 566929369 601 True 830.0 830 91.5420 1 602 1 chr4A.!!$R2 601
5 TraesCS4A01G208100 chr4D 88156303 88158928 2625 True 4043.0 4043 94.3920 713 3359 1 chr4D.!!$R1 2646
6 TraesCS4A01G208100 chr4B 125381000 125383688 2688 True 4024.0 4024 93.6380 647 3359 1 chr4B.!!$R1 2712
7 TraesCS4A01G208100 chr7A 18965234 18966614 1380 True 1135.5 1197 93.2275 3357 4174 2 chr7A.!!$R1 817
8 TraesCS4A01G208100 chr7A 652899307 652900587 1280 False 1046.0 1050 91.9340 3407 4174 2 chr7A.!!$F4 767
9 TraesCS4A01G208100 chr7A 624722722 624723319 597 False 852.0 852 92.3590 1 601 1 chr7A.!!$F3 600
10 TraesCS4A01G208100 chr7A 398742682 398743283 601 False 846.0 846 92.0400 1 602 1 chr7A.!!$F1 601
11 TraesCS4A01G208100 chr7A 554321359 554321957 598 False 821.0 821 91.3620 1 601 1 chr7A.!!$F2 600
12 TraesCS4A01G208100 chr3A 737115869 737116683 814 True 1125.0 1125 91.5850 3358 4174 1 chr3A.!!$R1 816
13 TraesCS4A01G208100 chr1A 338306535 338307360 825 False 1120.0 1120 91.2050 3350 4174 1 chr1A.!!$F1 824
14 TraesCS4A01G208100 chr1A 234737937 234738531 594 True 857.0 857 92.6420 1 597 1 chr1A.!!$R2 596
15 TraesCS4A01G208100 chr1A 104694415 104695011 596 True 832.0 832 91.8200 1 597 1 chr1A.!!$R1 596
16 TraesCS4A01G208100 chr6A 545539105 545539925 820 True 1026.0 1026 89.2940 3358 4174 1 chr6A.!!$R1 816
17 TraesCS4A01G208100 chr2A 499961573 499962171 598 False 843.0 843 92.0270 1 601 1 chr2A.!!$F2 600
18 TraesCS4A01G208100 chr2A 674586135 674586748 613 False 702.0 702 87.8250 3357 3952 1 chr2A.!!$F3 595
19 TraesCS4A01G208100 chr2A 674701131 674701743 612 False 689.0 689 87.4800 3357 3952 1 chr2A.!!$F4 595
20 TraesCS4A01G208100 chr5A 90742403 90743000 597 True 819.0 819 91.3620 1 601 1 chr5A.!!$R1 600

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
631 636 0.170561 CGTCGTCGACATTTCCTCCT 59.829 55.0 24.13 0.00 39.71 3.69 F
1262 1282 0.034574 TCCCAGGTGCATGCGTTTAT 60.035 50.0 14.09 0.00 0.00 1.40 F
1404 1425 0.604780 TGTCCTGCAGAGAAGCTTGC 60.605 55.0 17.39 1.44 34.99 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2174 2200 2.325583 TCAACATTCCTCCGTATGGC 57.674 50.000 0.0 0.0 34.14 4.40 R
3058 3091 1.667724 CCATAGCCACTCTTTTCTGCG 59.332 52.381 0.0 0.0 0.00 5.18 R
3199 3232 2.744202 CACTCTACACCTGATGGCAAAC 59.256 50.000 0.0 0.0 36.63 2.93 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
129 130 1.421410 CGTGGAGCCATCGCAACTAC 61.421 60.000 0.00 0.00 37.52 2.73
149 150 8.570488 CAACTACGAAGTTTAAAGGGGTTAATT 58.430 33.333 0.00 0.00 43.60 1.40
520 524 6.594788 AACCGTCACCTTGTATACTCTTTA 57.405 37.500 4.17 0.00 0.00 1.85
548 552 2.570415 TTGAAGTAACCCGCCATTGA 57.430 45.000 0.00 0.00 0.00 2.57
559 563 1.462616 CGCCATTGAGATTGACCCAA 58.537 50.000 0.00 0.00 0.00 4.12
597 602 3.038280 CACACCTGGTAGTCATATCCCA 58.962 50.000 0.00 0.00 0.00 4.37
599 604 3.454812 ACACCTGGTAGTCATATCCCAAC 59.545 47.826 0.00 0.00 0.00 3.77
600 605 3.454447 CACCTGGTAGTCATATCCCAACA 59.546 47.826 0.00 0.00 0.00 3.33
601 606 3.711704 ACCTGGTAGTCATATCCCAACAG 59.288 47.826 0.00 0.00 0.00 3.16
602 607 3.967326 CCTGGTAGTCATATCCCAACAGA 59.033 47.826 0.00 0.00 0.00 3.41
603 608 4.408921 CCTGGTAGTCATATCCCAACAGAA 59.591 45.833 0.00 0.00 0.00 3.02
604 609 5.072329 CCTGGTAGTCATATCCCAACAGAAT 59.928 44.000 0.00 0.00 0.00 2.40
605 610 5.928976 TGGTAGTCATATCCCAACAGAATG 58.071 41.667 0.00 0.00 46.00 2.67
606 611 5.163205 TGGTAGTCATATCCCAACAGAATGG 60.163 44.000 0.00 0.00 43.62 3.16
612 617 4.344237 CCAACAGAATGGGAGGCC 57.656 61.111 0.00 0.00 43.62 5.19
613 618 1.750399 CCAACAGAATGGGAGGCCG 60.750 63.158 0.00 0.00 43.62 6.13
614 619 1.002134 CAACAGAATGGGAGGCCGT 60.002 57.895 0.00 0.00 43.62 5.68
615 620 1.026718 CAACAGAATGGGAGGCCGTC 61.027 60.000 0.00 0.00 43.62 4.79
616 621 2.202932 CAGAATGGGAGGCCGTCG 60.203 66.667 0.00 0.00 0.00 5.12
617 622 2.683933 AGAATGGGAGGCCGTCGT 60.684 61.111 0.00 0.00 0.00 4.34
618 623 2.202892 GAATGGGAGGCCGTCGTC 60.203 66.667 0.00 0.00 0.00 4.20
619 624 4.143333 AATGGGAGGCCGTCGTCG 62.143 66.667 0.00 0.00 0.00 5.12
623 628 3.823330 GGAGGCCGTCGTCGACAT 61.823 66.667 24.13 7.55 39.71 3.06
624 629 2.181021 GAGGCCGTCGTCGACATT 59.819 61.111 24.13 6.88 39.71 2.71
625 630 1.445582 GAGGCCGTCGTCGACATTT 60.446 57.895 24.13 7.22 39.71 2.32
626 631 1.411493 GAGGCCGTCGTCGACATTTC 61.411 60.000 24.13 12.07 39.71 2.17
627 632 2.450345 GGCCGTCGTCGACATTTCC 61.450 63.158 24.13 14.45 39.71 3.13
628 633 1.445582 GCCGTCGTCGACATTTCCT 60.446 57.895 24.13 0.00 39.71 3.36
629 634 1.411493 GCCGTCGTCGACATTTCCTC 61.411 60.000 24.13 2.20 39.71 3.71
630 635 0.801067 CCGTCGTCGACATTTCCTCC 60.801 60.000 24.13 0.00 39.71 4.30
631 636 0.170561 CGTCGTCGACATTTCCTCCT 59.829 55.000 24.13 0.00 39.71 3.69
632 637 1.794437 CGTCGTCGACATTTCCTCCTC 60.794 57.143 24.13 0.00 39.71 3.71
633 638 0.815734 TCGTCGACATTTCCTCCTCC 59.184 55.000 17.16 0.00 0.00 4.30
634 639 0.530744 CGTCGACATTTCCTCCTCCA 59.469 55.000 17.16 0.00 0.00 3.86
635 640 1.736032 CGTCGACATTTCCTCCTCCAC 60.736 57.143 17.16 0.00 0.00 4.02
636 641 1.550976 GTCGACATTTCCTCCTCCACT 59.449 52.381 11.55 0.00 0.00 4.00
637 642 1.550524 TCGACATTTCCTCCTCCACTG 59.449 52.381 0.00 0.00 0.00 3.66
638 643 1.406069 CGACATTTCCTCCTCCACTGG 60.406 57.143 0.00 0.00 0.00 4.00
639 644 0.329596 ACATTTCCTCCTCCACTGGC 59.670 55.000 0.00 0.00 0.00 4.85
640 645 0.329261 CATTTCCTCCTCCACTGGCA 59.671 55.000 0.00 0.00 0.00 4.92
641 646 0.329596 ATTTCCTCCTCCACTGGCAC 59.670 55.000 0.00 0.00 0.00 5.01
642 647 1.059584 TTTCCTCCTCCACTGGCACA 61.060 55.000 0.00 0.00 0.00 4.57
643 648 1.768684 TTCCTCCTCCACTGGCACAC 61.769 60.000 0.00 0.00 0.00 3.82
644 649 2.519622 CCTCCTCCACTGGCACACA 61.520 63.158 0.00 0.00 0.00 3.72
645 650 1.451504 CTCCTCCACTGGCACACAA 59.548 57.895 0.00 0.00 0.00 3.33
660 665 2.738314 CACACAATGCATTCAGTCTCGA 59.262 45.455 9.53 0.00 0.00 4.04
662 667 1.995484 ACAATGCATTCAGTCTCGACG 59.005 47.619 9.53 0.00 36.20 5.12
665 670 2.148916 TGCATTCAGTCTCGACGTTT 57.851 45.000 0.00 0.00 36.20 3.60
673 678 2.218759 CAGTCTCGACGTTTGGTCTTTG 59.781 50.000 0.00 0.00 43.79 2.77
677 682 0.231279 CGACGTTTGGTCTTTGTCGG 59.769 55.000 5.25 0.00 46.19 4.79
679 684 0.463116 ACGTTTGGTCTTTGTCGGCT 60.463 50.000 0.00 0.00 0.00 5.52
724 737 8.996024 TTTCCGTGAAAAGAAAAGAAAAGATT 57.004 26.923 0.00 0.00 0.00 2.40
754 767 5.851047 AACGTCAAAACCGATTTAGGTAG 57.149 39.130 0.00 0.00 45.21 3.18
769 782 7.660208 CGATTTAGGTAGCCCATACATACTTTT 59.340 37.037 0.00 0.00 35.96 2.27
953 968 1.230182 TCCCTCCCTTTCTTCCCCC 60.230 63.158 0.00 0.00 0.00 5.40
1065 1081 1.276421 CAGGATTCCGTGAGTGACCTT 59.724 52.381 0.00 0.00 0.00 3.50
1074 1094 0.119155 TGAGTGACCTTCCTCCCCAT 59.881 55.000 0.00 0.00 0.00 4.00
1096 1116 2.683933 CCGCTCCTACACCCACCT 60.684 66.667 0.00 0.00 0.00 4.00
1158 1178 6.129326 CGCTATTCACGAATCTGAGATGTTAC 60.129 42.308 0.00 0.00 32.50 2.50
1213 1233 1.153229 GAGGTCCGGTAATGTGGGC 60.153 63.158 0.00 0.00 0.00 5.36
1235 1255 1.146982 ACCTGTATTGGGGCTTTGTGT 59.853 47.619 0.00 0.00 0.00 3.72
1262 1282 0.034574 TCCCAGGTGCATGCGTTTAT 60.035 50.000 14.09 0.00 0.00 1.40
1287 1308 4.272489 CTTGGATCCATTGCAGGACTTAA 58.728 43.478 17.06 0.00 41.30 1.85
1320 1341 3.118775 TGACGGTGTAAATCTGAGATGGG 60.119 47.826 0.00 0.00 0.00 4.00
1404 1425 0.604780 TGTCCTGCAGAGAAGCTTGC 60.605 55.000 17.39 1.44 34.99 4.01
1415 1436 3.137533 GAGAAGCTTGCCTATGATGTCC 58.862 50.000 2.10 0.00 0.00 4.02
1546 1571 5.847817 TCCTAGAACCAGTCCCTTTCTTTTA 59.152 40.000 0.00 0.00 31.93 1.52
1588 1614 1.337118 TGTTTCCTTGCCCCATTGTC 58.663 50.000 0.00 0.00 0.00 3.18
1724 1750 2.496070 TGGCAGGTACACTAGCTTACAG 59.504 50.000 0.00 0.00 33.57 2.74
1735 1761 6.929625 ACACTAGCTTACAGCCATATCTATG 58.070 40.000 0.00 0.00 43.77 2.23
1828 1854 7.064134 TCGTATTTTGGGCAATGATATCGTATC 59.936 37.037 0.00 0.00 0.00 2.24
1852 1878 5.163622 CGATAAGGTTAAGAGGTGGTCGTTA 60.164 44.000 0.00 0.00 0.00 3.18
1869 1895 5.523916 GGTCGTTATACAAATCATGTGCTCT 59.476 40.000 0.00 0.00 43.77 4.09
1964 1990 5.934625 TGAGTTAGAGAAGGCAATTTCTGTC 59.065 40.000 2.56 0.00 37.53 3.51
2062 2088 4.819630 CCGCAACCAGGTATGTTATTACAT 59.180 41.667 2.50 2.50 46.49 2.29
2128 2154 4.142038 ACCCGAAGTTCAGTAGCAAATTT 58.858 39.130 3.32 0.00 0.00 1.82
2174 2200 7.745620 AACTTGAAATTGTTCTAGGTGGTAG 57.254 36.000 0.00 0.00 39.90 3.18
2491 2518 8.669243 GTTGTAAGTAGAAGCTCTGCATTTTAT 58.331 33.333 0.00 0.00 31.12 1.40
2747 2777 8.189119 TGTTGGTTGCTTTCTTTTCCTATATT 57.811 30.769 0.00 0.00 0.00 1.28
2946 2976 1.384525 CCAGGACACGTTGTTTGGAA 58.615 50.000 12.75 0.00 37.50 3.53
2947 2977 1.064952 CCAGGACACGTTGTTTGGAAC 59.935 52.381 12.75 0.00 37.50 3.62
2951 2981 1.004292 GACACGTTGTTTGGAACTCCG 60.004 52.381 0.00 0.00 39.43 4.63
3045 3078 2.484770 CCAACGGACTGAAACTTCTCCA 60.485 50.000 0.00 0.00 0.00 3.86
3058 3091 4.830826 ACTTCTCCACCGTTTTTGATTC 57.169 40.909 0.00 0.00 0.00 2.52
3199 3232 5.413833 AGATGGAGTTTAAGTTGCATGAGTG 59.586 40.000 0.00 0.00 0.00 3.51
3219 3252 2.371841 TGTTTGCCATCAGGTGTAGAGT 59.628 45.455 0.00 0.00 37.19 3.24
3220 3253 2.744202 GTTTGCCATCAGGTGTAGAGTG 59.256 50.000 0.00 0.00 37.19 3.51
3221 3254 0.250234 TGCCATCAGGTGTAGAGTGC 59.750 55.000 0.00 0.00 37.19 4.40
3281 3314 5.766174 TCTGGCCGTTATAGTTTTGTTCTTT 59.234 36.000 0.00 0.00 0.00 2.52
3337 3370 6.910433 GTCATTTTTCGTGTAATATGGCGAAT 59.090 34.615 0.00 0.00 41.85 3.34
3475 3527 0.193574 TTGTCCCCTCTCTCCACCTT 59.806 55.000 0.00 0.00 0.00 3.50
3497 3550 4.759516 ATTGGTTTATTTTCGCGTCACT 57.240 36.364 5.77 0.00 0.00 3.41
3502 3555 4.860907 GGTTTATTTTCGCGTCACTCTCTA 59.139 41.667 5.77 0.00 0.00 2.43
3542 3596 5.668471 TGAGCAGATCAGAACTTTCCATAG 58.332 41.667 0.00 0.00 32.77 2.23
3587 4200 7.905604 TGTAGAATCAATCACGAACAATCTT 57.094 32.000 0.00 0.00 0.00 2.40
3713 4326 8.954950 AACCTTATCTTAACTCACAGATGATG 57.045 34.615 0.00 0.00 33.22 3.07
3732 4345 7.832685 AGATGATGATCAATCTCCAAACAAAGA 59.167 33.333 0.00 0.00 36.15 2.52
3765 4378 7.862675 ACATAGAGGGAGCAGTAAATAAACTT 58.137 34.615 0.00 0.00 0.00 2.66
3838 4452 6.071334 AGTGTTCTTGATTCTTGAGACCGATA 60.071 38.462 0.00 0.00 0.00 2.92
3963 4578 0.251787 GGCTTCCCACCTTTCATGGT 60.252 55.000 0.00 0.00 41.77 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 5.073144 TGGATTTGAGTTCTTGAAGGGTAGT 59.927 40.000 0.00 0.00 0.00 2.73
129 130 5.477637 TCCCAATTAACCCCTTTAAACTTCG 59.522 40.000 0.00 0.00 33.26 3.79
149 150 0.679505 CTCTCGTGTCCTTTGTCCCA 59.320 55.000 0.00 0.00 0.00 4.37
264 267 0.175302 ACAGATCGAGAGCCAAGCTG 59.825 55.000 0.00 0.00 39.88 4.24
310 314 4.660168 ACCCGTGTATATAAGAGGACGAT 58.340 43.478 0.00 0.00 0.00 3.73
317 321 5.827797 AGGACGTTAACCCGTGTATATAAGA 59.172 40.000 0.00 0.00 41.98 2.10
442 446 1.426816 GCGACTTAAGGCCCGTAAGC 61.427 60.000 19.22 12.85 32.74 3.09
472 476 5.932619 TGATAAAGCTTGTAGTAGGCTCA 57.067 39.130 0.00 0.00 41.43 4.26
520 524 3.146847 CGGGTTACTTCAAAGAAAGCCT 58.853 45.455 0.00 0.00 37.35 4.58
548 552 0.178831 AGGAGGGGTTGGGTCAATCT 60.179 55.000 0.00 0.00 0.00 2.40
597 602 1.299976 GACGGCCTCCCATTCTGTT 59.700 57.895 0.00 0.00 0.00 3.16
599 604 2.202932 CGACGGCCTCCCATTCTG 60.203 66.667 0.00 0.00 0.00 3.02
600 605 2.683933 ACGACGGCCTCCCATTCT 60.684 61.111 0.00 0.00 0.00 2.40
601 606 2.202892 GACGACGGCCTCCCATTC 60.203 66.667 0.00 0.00 0.00 2.67
602 607 4.143333 CGACGACGGCCTCCCATT 62.143 66.667 0.00 0.00 35.72 3.16
606 611 2.830704 AAATGTCGACGACGGCCTCC 62.831 60.000 22.06 0.00 43.97 4.30
607 612 1.411493 GAAATGTCGACGACGGCCTC 61.411 60.000 22.06 12.26 43.97 4.70
608 613 1.445582 GAAATGTCGACGACGGCCT 60.446 57.895 22.06 7.38 43.97 5.19
609 614 2.450345 GGAAATGTCGACGACGGCC 61.450 63.158 22.06 15.83 43.97 6.13
610 615 1.411493 GAGGAAATGTCGACGACGGC 61.411 60.000 22.06 4.63 44.90 5.68
611 616 0.801067 GGAGGAAATGTCGACGACGG 60.801 60.000 22.06 0.00 40.21 4.79
612 617 0.170561 AGGAGGAAATGTCGACGACG 59.829 55.000 22.06 0.00 34.95 5.12
613 618 1.469423 GGAGGAGGAAATGTCGACGAC 60.469 57.143 20.97 20.97 0.00 4.34
614 619 0.815734 GGAGGAGGAAATGTCGACGA 59.184 55.000 11.62 0.00 0.00 4.20
615 620 0.530744 TGGAGGAGGAAATGTCGACG 59.469 55.000 11.62 0.00 0.00 5.12
616 621 1.550976 AGTGGAGGAGGAAATGTCGAC 59.449 52.381 9.11 9.11 0.00 4.20
617 622 1.550524 CAGTGGAGGAGGAAATGTCGA 59.449 52.381 0.00 0.00 0.00 4.20
618 623 1.406069 CCAGTGGAGGAGGAAATGTCG 60.406 57.143 1.68 0.00 0.00 4.35
619 624 1.680249 GCCAGTGGAGGAGGAAATGTC 60.680 57.143 15.20 0.00 0.00 3.06
620 625 0.329596 GCCAGTGGAGGAGGAAATGT 59.670 55.000 15.20 0.00 0.00 2.71
621 626 0.329261 TGCCAGTGGAGGAGGAAATG 59.671 55.000 15.20 0.00 0.00 2.32
622 627 0.329596 GTGCCAGTGGAGGAGGAAAT 59.670 55.000 15.20 0.00 0.00 2.17
623 628 1.059584 TGTGCCAGTGGAGGAGGAAA 61.060 55.000 15.20 0.00 0.00 3.13
624 629 1.461268 TGTGCCAGTGGAGGAGGAA 60.461 57.895 15.20 0.00 0.00 3.36
625 630 2.204034 TGTGCCAGTGGAGGAGGA 59.796 61.111 15.20 0.00 0.00 3.71
626 631 2.055689 TTGTGTGCCAGTGGAGGAGG 62.056 60.000 15.20 0.00 0.00 4.30
627 632 0.037303 ATTGTGTGCCAGTGGAGGAG 59.963 55.000 15.20 0.00 0.00 3.69
628 633 0.250858 CATTGTGTGCCAGTGGAGGA 60.251 55.000 15.20 0.00 0.00 3.71
629 634 2.260247 CATTGTGTGCCAGTGGAGG 58.740 57.895 15.20 0.00 0.00 4.30
639 644 2.738314 TCGAGACTGAATGCATTGTGTG 59.262 45.455 18.59 6.36 0.00 3.82
640 645 2.738846 GTCGAGACTGAATGCATTGTGT 59.261 45.455 18.59 14.68 0.00 3.72
641 646 2.222663 CGTCGAGACTGAATGCATTGTG 60.223 50.000 18.59 11.43 0.00 3.33
642 647 1.995484 CGTCGAGACTGAATGCATTGT 59.005 47.619 18.59 9.58 0.00 2.71
643 648 1.995484 ACGTCGAGACTGAATGCATTG 59.005 47.619 18.59 5.89 0.00 2.82
644 649 2.370281 ACGTCGAGACTGAATGCATT 57.630 45.000 12.83 12.83 0.00 3.56
645 650 2.370281 AACGTCGAGACTGAATGCAT 57.630 45.000 0.00 0.00 0.00 3.96
660 665 0.463116 AGCCGACAAAGACCAAACGT 60.463 50.000 0.00 0.00 0.00 3.99
662 667 1.305201 TCAGCCGACAAAGACCAAAC 58.695 50.000 0.00 0.00 0.00 2.93
665 670 0.884704 GCTTCAGCCGACAAAGACCA 60.885 55.000 0.00 0.00 34.31 4.02
677 682 1.089920 ATTGTCATCGTGGCTTCAGC 58.910 50.000 0.00 0.00 41.14 4.26
679 684 4.582701 AAAAATTGTCATCGTGGCTTCA 57.417 36.364 0.00 0.00 0.00 3.02
703 708 8.393395 TGACAATCTTTTCTTTTCTTTTCACG 57.607 30.769 0.00 0.00 0.00 4.35
724 737 5.676532 ATCGGTTTTGACGTTTATTGACA 57.323 34.783 0.00 0.00 0.00 3.58
754 767 3.154710 GGGCCTAAAAGTATGTATGGGC 58.845 50.000 0.84 0.00 37.82 5.36
782 795 1.634702 GAGTGAGCTTACAGGCTTCG 58.365 55.000 11.65 0.00 43.20 3.79
913 927 1.539929 CGATGAGCTGATCTGAACCCC 60.540 57.143 11.54 0.00 0.00 4.95
953 968 2.762006 GATCGGGAGCAGCTGGATCG 62.762 65.000 17.12 0.00 30.89 3.69
1065 1081 3.416880 GCGGGGAAATGGGGAGGA 61.417 66.667 0.00 0.00 0.00 3.71
1074 1094 2.295602 GGGTGTAGGAGCGGGGAAA 61.296 63.158 0.00 0.00 0.00 3.13
1158 1178 1.007848 CGCAGATCATGGCTAGAGCG 61.008 60.000 0.00 0.00 43.26 5.03
1213 1233 3.016736 CACAAAGCCCCAATACAGGTAG 58.983 50.000 0.00 0.00 0.00 3.18
1235 1255 1.561769 ATGCACCTGGGATCCGAACA 61.562 55.000 5.45 0.00 0.00 3.18
1262 1282 1.845791 TCCTGCAATGGATCCAAGCTA 59.154 47.619 30.84 20.75 33.92 3.32
1320 1341 3.202097 CACACCCAAAATGTTTGGTTCC 58.798 45.455 16.49 0.00 37.88 3.62
1404 1425 1.802960 GCAGCAATCGGACATCATAGG 59.197 52.381 0.00 0.00 0.00 2.57
1546 1571 8.948631 ACAAGTTGTTATAGACATCATCGAAT 57.051 30.769 1.64 0.00 38.26 3.34
1588 1614 7.582435 ATCTTGTACTTTGTCAATCTGTACG 57.418 36.000 14.03 0.00 37.04 3.67
1735 1761 4.384940 GGACAGAGGATTAGAATCTTGCC 58.615 47.826 2.44 0.00 35.73 4.52
1828 1854 3.129988 ACGACCACCTCTTAACCTTATCG 59.870 47.826 0.00 0.00 0.00 2.92
1843 1869 5.064707 AGCACATGATTTGTATAACGACCAC 59.935 40.000 0.00 0.00 36.57 4.16
1852 1878 7.039504 ACAAAAGGAAGAGCACATGATTTGTAT 60.040 33.333 0.00 0.00 36.89 2.29
1869 1895 5.055812 ACACGGTAAATACGACAAAAGGAA 58.944 37.500 0.00 0.00 34.93 3.36
1916 1942 8.370940 TCATCCACCTTAATTGCAACATTAAAA 58.629 29.630 0.00 0.00 0.00 1.52
2079 2105 7.770433 TGTAGCTTAATCATTCATGTTAGCAGT 59.230 33.333 0.00 0.00 0.00 4.40
2149 2175 7.255486 GCTACCACCTAGAACAATTTCAAGTTT 60.255 37.037 0.00 0.00 33.72 2.66
2159 2185 3.131577 CGTATGGCTACCACCTAGAACAA 59.868 47.826 0.00 0.00 35.80 2.83
2174 2200 2.325583 TCAACATTCCTCCGTATGGC 57.674 50.000 0.00 0.00 34.14 4.40
2442 2469 6.479006 ACATCATGATTCTGTGAGGAAGAAA 58.521 36.000 5.16 0.00 37.22 2.52
2491 2518 3.719871 TCCTCTGGAAGGTAGCATTACA 58.280 45.455 0.00 0.00 46.32 2.41
2747 2777 1.906574 AGTTAACCGGGCTCTTCATGA 59.093 47.619 6.32 0.00 0.00 3.07
2946 2976 3.568093 GCAAAAACATGCACGGAGT 57.432 47.368 0.00 0.00 45.70 3.85
3045 3078 3.701532 TTTCTGCGAATCAAAAACGGT 57.298 38.095 0.00 0.00 0.00 4.83
3058 3091 1.667724 CCATAGCCACTCTTTTCTGCG 59.332 52.381 0.00 0.00 0.00 5.18
3199 3232 2.744202 CACTCTACACCTGATGGCAAAC 59.256 50.000 0.00 0.00 36.63 2.93
3281 3314 3.092511 GGCAGAGGCAGATCCCCA 61.093 66.667 3.14 0.00 43.71 4.96
3475 3527 5.640357 AGAGTGACGCGAAAATAAACCAATA 59.360 36.000 15.93 0.00 0.00 1.90
3522 3576 4.574013 CCACTATGGAAAGTTCTGATCTGC 59.426 45.833 0.00 0.00 40.96 4.26
3542 3596 5.875930 ACATTACTAAATAACTTGCGCCAC 58.124 37.500 4.18 0.00 0.00 5.01
3695 4308 8.702819 AGATTGATCATCATCTGTGAGTTAAGA 58.297 33.333 8.77 0.00 37.87 2.10
3711 4324 8.423349 TGTTTTCTTTGTTTGGAGATTGATCAT 58.577 29.630 0.00 0.00 0.00 2.45
3713 4326 8.647143 TTGTTTTCTTTGTTTGGAGATTGATC 57.353 30.769 0.00 0.00 0.00 2.92
3732 4345 6.067217 ACTGCTCCCTCTATGTATTGTTTT 57.933 37.500 0.00 0.00 0.00 2.43
3793 4406 3.128349 CTCGACAACGGAAAGGAAAGAA 58.872 45.455 0.00 0.00 40.21 2.52
3798 4411 0.748450 ACACTCGACAACGGAAAGGA 59.252 50.000 0.00 0.00 40.21 3.36
3802 4415 2.159212 TCAAGAACACTCGACAACGGAA 60.159 45.455 0.00 0.00 40.21 4.30
3838 4452 2.281070 CAGTGACGCAGCCCAAGT 60.281 61.111 0.00 0.00 0.00 3.16
3977 4594 0.841289 AAACCAACGAAGGTGGGAGA 59.159 50.000 9.11 0.00 39.95 3.71


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

AutoCloner maintained by Alex Coulton.