Multiple sequence alignment - TraesCS6B01G258600

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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 TraesCS6B01G258600 chr6B 100.000 4416 0 0 1 4416 465686477 465682062 0.000000e+00 8155.0
1 TraesCS6B01G258600 chr6B 87.981 208 25 0 3773 3980 298372048 298372255 3.410000e-61 246.0
2 TraesCS6B01G258600 chr6B 89.583 96 8 1 3543 3638 532146864 532146957 2.160000e-23 121.0
3 TraesCS6B01G258600 chr6A 95.700 3093 109 10 904 3980 416648245 416651329 0.000000e+00 4953.0
4 TraesCS6B01G258600 chr6A 94.570 442 23 1 3976 4416 416651358 416651799 0.000000e+00 682.0
5 TraesCS6B01G258600 chr6A 89.759 332 13 12 250 568 416643956 416644279 5.320000e-109 405.0
6 TraesCS6B01G258600 chr6A 97.059 238 7 0 1 238 416629374 416629611 6.880000e-108 401.0
7 TraesCS6B01G258600 chr6A 90.476 210 8 6 676 885 416648062 416648259 2.620000e-67 267.0
8 TraesCS6B01G258600 chr6D 96.012 2583 82 9 1138 3708 300898979 300896406 0.000000e+00 4180.0
9 TraesCS6B01G258600 chr6D 81.585 1754 315 8 1527 3276 300890848 300889099 0.000000e+00 1443.0
10 TraesCS6B01G258600 chr6D 95.918 441 18 0 3976 4416 300896155 300895715 0.000000e+00 715.0
11 TraesCS6B01G258600 chr6D 84.601 552 53 17 514 1055 300900853 300900324 1.820000e-143 520.0
12 TraesCS6B01G258600 chr6D 86.548 394 26 18 1 372 300901373 300900985 4.110000e-110 409.0
13 TraesCS6B01G258600 chr6D 95.089 224 11 0 3760 3983 300896404 300896181 1.950000e-93 353.0
14 TraesCS6B01G258600 chr6D 80.878 319 54 1 3662 3980 187022834 187023145 1.230000e-60 244.0
15 TraesCS6B01G258600 chr6D 97.500 40 0 1 906 944 300900513 300900474 2.850000e-07 67.6
16 TraesCS6B01G258600 chr2D 80.135 2079 405 7 1200 3274 156707518 156709592 0.000000e+00 1544.0
17 TraesCS6B01G258600 chr2D 79.923 2082 404 11 1200 3274 182575867 182573793 0.000000e+00 1517.0
18 TraesCS6B01G258600 chr2D 74.384 406 88 14 4018 4412 649650384 649650784 4.570000e-35 159.0
19 TraesCS6B01G258600 chr2A 79.827 2077 415 4 1200 3274 166628146 166630220 0.000000e+00 1511.0
20 TraesCS6B01G258600 chr2A 83.879 397 61 2 1138 1531 624359568 624359964 4.170000e-100 375.0
21 TraesCS6B01G258600 chr2B 79.672 2076 420 2 1200 3274 214281192 214283266 0.000000e+00 1495.0
22 TraesCS6B01G258600 chr1B 79.315 2103 427 8 1200 3300 148416235 148414139 0.000000e+00 1467.0
23 TraesCS6B01G258600 chr1B 91.429 105 9 0 3537 3641 359902042 359902146 1.280000e-30 145.0
24 TraesCS6B01G258600 chr1A 79.040 2104 427 13 1200 3300 90163447 90161355 0.000000e+00 1430.0
25 TraesCS6B01G258600 chr5A 88.152 422 49 1 3991 4411 94475153 94474732 6.590000e-138 501.0
26 TraesCS6B01G258600 chr5A 86.503 163 21 1 3818 3980 311516216 311516377 1.260000e-40 178.0
27 TraesCS6B01G258600 chr5A 90.000 100 10 0 3540 3639 110664987 110665086 3.580000e-26 130.0
28 TraesCS6B01G258600 chr5A 87.129 101 12 1 3543 3642 621874434 621874334 3.610000e-21 113.0
29 TraesCS6B01G258600 chr5D 79.602 603 98 18 3662 4242 10777346 10777945 4.110000e-110 409.0
30 TraesCS6B01G258600 chr7B 89.000 100 11 0 3544 3643 220135212 220135113 1.670000e-24 124.0
31 TraesCS6B01G258600 chr7B 90.805 87 8 0 3543 3629 3333704 3333618 2.790000e-22 117.0
32 TraesCS6B01G258600 chr3B 88.889 99 10 1 3543 3641 628403550 628403647 2.160000e-23 121.0


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 TraesCS6B01G258600 chr6B 465682062 465686477 4415 True 8155.000000 8155 100.000000 1 4416 1 chr6B.!!$R1 4415
1 TraesCS6B01G258600 chr6A 416643956 416651799 7843 False 1576.750000 4953 92.626250 250 4416 4 chr6A.!!$F2 4166
2 TraesCS6B01G258600 chr6D 300889099 300890848 1749 True 1443.000000 1443 81.585000 1527 3276 1 chr6D.!!$R1 1749
3 TraesCS6B01G258600 chr6D 300895715 300901373 5658 True 1040.766667 4180 92.611333 1 4416 6 chr6D.!!$R2 4415
4 TraesCS6B01G258600 chr2D 156707518 156709592 2074 False 1544.000000 1544 80.135000 1200 3274 1 chr2D.!!$F1 2074
5 TraesCS6B01G258600 chr2D 182573793 182575867 2074 True 1517.000000 1517 79.923000 1200 3274 1 chr2D.!!$R1 2074
6 TraesCS6B01G258600 chr2A 166628146 166630220 2074 False 1511.000000 1511 79.827000 1200 3274 1 chr2A.!!$F1 2074
7 TraesCS6B01G258600 chr2B 214281192 214283266 2074 False 1495.000000 1495 79.672000 1200 3274 1 chr2B.!!$F1 2074
8 TraesCS6B01G258600 chr1B 148414139 148416235 2096 True 1467.000000 1467 79.315000 1200 3300 1 chr1B.!!$R1 2100
9 TraesCS6B01G258600 chr1A 90161355 90163447 2092 True 1430.000000 1430 79.040000 1200 3300 1 chr1A.!!$R1 2100
10 TraesCS6B01G258600 chr5D 10777346 10777945 599 False 409.000000 409 79.602000 3662 4242 1 chr5D.!!$F1 580

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
308 336 0.031178 CAAGCACTGAACCAACAGCC 59.969 55.0 0.00 0.0 41.06 4.85 F
382 410 0.107703 CAGCTGGCCGGTAAGATGAA 60.108 55.0 14.55 0.0 31.44 2.57 F
1880 7008 0.992802 GCTTCTTCGAGCTACAACCG 59.007 55.0 0.00 0.0 39.57 4.44 F
2697 7825 0.835941 CCTCTGCCAGGCTATTGACT 59.164 55.0 14.15 0.0 34.56 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1880 7008 0.462759 CCATGGCGAGACCTTCCTTC 60.463 60.000 0.00 0.0 40.22 3.46 R
2697 7825 0.821301 TTCACCTCAATGTGGCGCAA 60.821 50.000 10.83 0.0 36.87 4.85 R
2867 7995 0.255890 GATAGTTGGGGCTGCAAGGA 59.744 55.000 0.50 0.0 0.00 3.36 R
4232 9463 2.392662 TGGGGCAAACAATTCTCACAA 58.607 42.857 0.00 0.0 0.00 3.33 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
54 55 6.762187 TGCAAATGTTGACAACTTCATGAAAT 59.238 30.769 18.73 0.00 32.84 2.17
81 82 0.881118 TGACTTTCCTGGCAATTCGC 59.119 50.000 0.00 0.00 41.28 4.70
98 99 1.135373 TCGCGTCCAGTCTTCAGATTC 60.135 52.381 5.77 0.00 0.00 2.52
108 109 8.041323 GTCCAGTCTTCAGATTCCTGTTAATTA 58.959 37.037 0.00 0.00 41.16 1.40
109 110 8.260818 TCCAGTCTTCAGATTCCTGTTAATTAG 58.739 37.037 0.00 0.00 41.16 1.73
110 111 8.043710 CCAGTCTTCAGATTCCTGTTAATTAGT 58.956 37.037 0.00 0.00 41.16 2.24
139 140 2.544694 CCAGTGTAGATGCGGATGACTC 60.545 54.545 0.00 0.00 0.00 3.36
156 157 5.026038 TGACTCAAACTCCCGTCTTTTTA 57.974 39.130 0.00 0.00 0.00 1.52
184 185 4.560128 CCGAATTGAAGTCAGAACTCAGA 58.440 43.478 0.00 0.00 33.48 3.27
193 194 3.886505 AGTCAGAACTCAGAACGAGACTT 59.113 43.478 0.00 0.00 45.45 3.01
261 274 1.441729 ACGTGTGGTGAGAGTGTGG 59.558 57.895 0.00 0.00 0.00 4.17
286 314 1.413812 TCGACATGATGCTACAGCCAT 59.586 47.619 0.00 0.00 41.18 4.40
302 330 1.608055 CCATGTCAAGCACTGAACCA 58.392 50.000 0.00 0.00 35.22 3.67
304 332 2.287788 CCATGTCAAGCACTGAACCAAC 60.288 50.000 0.00 0.00 35.22 3.77
305 333 2.121291 TGTCAAGCACTGAACCAACA 57.879 45.000 0.00 0.00 35.22 3.33
306 334 2.016318 TGTCAAGCACTGAACCAACAG 58.984 47.619 0.00 0.00 42.78 3.16
307 335 1.024271 TCAAGCACTGAACCAACAGC 58.976 50.000 0.00 0.00 41.06 4.40
308 336 0.031178 CAAGCACTGAACCAACAGCC 59.969 55.000 0.00 0.00 41.06 4.85
309 337 0.395586 AAGCACTGAACCAACAGCCA 60.396 50.000 0.00 0.00 41.06 4.75
310 338 1.103398 AGCACTGAACCAACAGCCAC 61.103 55.000 0.00 0.00 41.06 5.01
311 339 2.032981 CACTGAACCAACAGCCACC 58.967 57.895 0.00 0.00 41.06 4.61
312 340 1.525995 ACTGAACCAACAGCCACCG 60.526 57.895 0.00 0.00 41.06 4.94
343 371 0.397941 CCTGCAGGTTGGAGAACTGA 59.602 55.000 25.53 0.00 38.14 3.41
382 410 0.107703 CAGCTGGCCGGTAAGATGAA 60.108 55.000 14.55 0.00 31.44 2.57
482 510 8.617290 AACTTAGTCTTTTGTCGGTTCAATAT 57.383 30.769 0.00 0.00 0.00 1.28
483 511 9.715121 AACTTAGTCTTTTGTCGGTTCAATATA 57.285 29.630 0.00 0.00 0.00 0.86
484 512 9.715121 ACTTAGTCTTTTGTCGGTTCAATATAA 57.285 29.630 0.00 0.00 0.00 0.98
568 644 2.334006 TCCTGGAGAAAGGAGAGCTT 57.666 50.000 0.00 0.00 41.60 3.74
569 645 1.905215 TCCTGGAGAAAGGAGAGCTTG 59.095 52.381 0.00 0.00 41.60 4.01
573 649 2.039084 TGGAGAAAGGAGAGCTTGAACC 59.961 50.000 0.00 0.00 0.00 3.62
586 662 3.082548 GCTTGAACCCTTTCCTACTTCC 58.917 50.000 0.00 0.00 0.00 3.46
599 675 7.227512 CCTTTCCTACTTCCAATGATATGACAC 59.772 40.741 0.00 0.00 0.00 3.67
602 678 5.468072 CCTACTTCCAATGATATGACACAGC 59.532 44.000 0.00 0.00 0.00 4.40
678 758 2.426024 GCTACTACCTGACATCGGTTGA 59.574 50.000 3.00 0.00 35.98 3.18
693 4493 8.561738 ACATCGGTTGAAACAAGTAATTATCT 57.438 30.769 0.00 0.00 0.00 1.98
820 4620 2.518349 CAACAACCACAGCCCGGT 60.518 61.111 0.00 0.00 38.85 5.28
891 4692 5.961395 AAAAATACGCACCTACTCATACG 57.039 39.130 0.00 0.00 0.00 3.06
892 4693 4.644103 AAATACGCACCTACTCATACGT 57.356 40.909 0.00 0.00 37.53 3.57
893 4694 3.892918 ATACGCACCTACTCATACGTC 57.107 47.619 0.00 0.00 35.15 4.34
894 4695 1.456296 ACGCACCTACTCATACGTCA 58.544 50.000 0.00 0.00 0.00 4.35
895 4696 1.814394 ACGCACCTACTCATACGTCAA 59.186 47.619 0.00 0.00 0.00 3.18
896 4697 2.229543 ACGCACCTACTCATACGTCAAA 59.770 45.455 0.00 0.00 0.00 2.69
897 4698 3.247442 CGCACCTACTCATACGTCAAAA 58.753 45.455 0.00 0.00 0.00 2.44
898 4699 3.676172 CGCACCTACTCATACGTCAAAAA 59.324 43.478 0.00 0.00 0.00 1.94
978 4816 3.275999 CCACGGTCCCTATTTAAACCTG 58.724 50.000 0.00 0.00 0.00 4.00
979 4817 2.681344 CACGGTCCCTATTTAAACCTGC 59.319 50.000 0.00 0.00 0.00 4.85
980 4818 2.574824 ACGGTCCCTATTTAAACCTGCT 59.425 45.455 0.00 0.00 0.00 4.24
1037 4877 1.550524 CCAGTTCCAGCTACACTGCTA 59.449 52.381 11.84 0.00 45.78 3.49
1041 4881 3.118592 AGTTCCAGCTACACTGCTATTCC 60.119 47.826 0.00 0.00 45.78 3.01
1116 4960 3.876274 TCAGACTAGTGCTTTAGCCAG 57.124 47.619 0.00 0.00 41.18 4.85
1133 4977 3.567797 GCTCGTCCATCCGCAAGC 61.568 66.667 0.00 0.00 0.00 4.01
1373 6501 2.348998 GAGGTGGTGGTGGAGCTG 59.651 66.667 0.00 0.00 0.00 4.24
1385 6513 2.347322 GGAGCTGGACGAGTCTGCT 61.347 63.158 18.17 18.17 40.08 4.24
1802 6930 2.046314 AACTCCGTGGCGATTGGG 60.046 61.111 0.00 0.00 0.00 4.12
1880 7008 0.992802 GCTTCTTCGAGCTACAACCG 59.007 55.000 0.00 0.00 39.57 4.44
2697 7825 0.835941 CCTCTGCCAGGCTATTGACT 59.164 55.000 14.15 0.00 34.56 3.41
2713 7841 1.228245 ACTTGCGCCACATTGAGGT 60.228 52.632 4.18 0.00 0.00 3.85
2747 7875 2.425312 TGCCGTCAAAAGTTGTGTGATT 59.575 40.909 0.00 0.00 0.00 2.57
2867 7995 1.808390 GTTTGCCTACGCCGACGAT 60.808 57.895 0.00 0.00 43.93 3.73
2889 8017 0.630673 TTGCAGCCCCAACTATCCAT 59.369 50.000 0.00 0.00 0.00 3.41
3140 8268 3.570550 GTGAGGAGCTCGGAACTGTATAT 59.429 47.826 7.83 0.00 32.35 0.86
3146 8274 5.474189 GGAGCTCGGAACTGTATATCTAACT 59.526 44.000 7.83 0.00 0.00 2.24
3255 8383 1.371183 CTCAAGGAGTGGAACGGCA 59.629 57.895 0.00 0.00 45.86 5.69
3565 8709 3.225940 CTCCCTCCATCCCAAAATAAGC 58.774 50.000 0.00 0.00 0.00 3.09
3570 8714 3.541632 TCCATCCCAAAATAAGCGTCTC 58.458 45.455 0.00 0.00 0.00 3.36
3580 8724 6.307155 CAAAATAAGCGTCTCAACCTTAGTG 58.693 40.000 0.00 0.00 0.00 2.74
3652 8796 3.639625 AGGAGTATAAGCTAAGCCCCT 57.360 47.619 0.00 0.00 0.00 4.79
3658 8802 5.973905 AGTATAAGCTAAGCCCCTAGGTAA 58.026 41.667 8.29 0.00 34.57 2.85
3659 8803 6.572569 AGTATAAGCTAAGCCCCTAGGTAAT 58.427 40.000 8.29 0.00 34.57 1.89
3660 8804 5.763876 ATAAGCTAAGCCCCTAGGTAATG 57.236 43.478 8.29 0.00 34.57 1.90
3707 8852 8.780846 ACAATCGTTCTGTGGTATTTACATTA 57.219 30.769 0.00 0.00 0.00 1.90
3708 8853 9.391006 ACAATCGTTCTGTGGTATTTACATTAT 57.609 29.630 0.00 0.00 0.00 1.28
3741 8886 8.771920 AAGTACATGAAGTTACAAATCGATCA 57.228 30.769 0.00 0.00 0.00 2.92
3742 8887 8.771920 AGTACATGAAGTTACAAATCGATCAA 57.228 30.769 0.00 0.00 0.00 2.57
3743 8888 8.656849 AGTACATGAAGTTACAAATCGATCAAC 58.343 33.333 0.00 1.36 0.00 3.18
3744 8889 6.842163 ACATGAAGTTACAAATCGATCAACC 58.158 36.000 0.00 0.00 0.00 3.77
3745 8890 6.429692 ACATGAAGTTACAAATCGATCAACCA 59.570 34.615 0.00 0.00 0.00 3.67
3746 8891 6.869315 TGAAGTTACAAATCGATCAACCAA 57.131 33.333 0.00 0.00 0.00 3.67
3747 8892 7.447374 TGAAGTTACAAATCGATCAACCAAT 57.553 32.000 0.00 0.00 0.00 3.16
3748 8893 8.554835 TGAAGTTACAAATCGATCAACCAATA 57.445 30.769 0.00 0.00 0.00 1.90
3749 8894 8.447833 TGAAGTTACAAATCGATCAACCAATAC 58.552 33.333 0.00 0.00 0.00 1.89
3750 8895 8.561738 AAGTTACAAATCGATCAACCAATACT 57.438 30.769 0.00 0.00 0.00 2.12
3751 8896 9.661563 AAGTTACAAATCGATCAACCAATACTA 57.338 29.630 0.00 0.00 0.00 1.82
3752 8897 9.314321 AGTTACAAATCGATCAACCAATACTAG 57.686 33.333 0.00 0.00 0.00 2.57
3753 8898 9.095065 GTTACAAATCGATCAACCAATACTAGT 57.905 33.333 0.00 0.00 0.00 2.57
3754 8899 9.661563 TTACAAATCGATCAACCAATACTAGTT 57.338 29.630 0.00 0.00 0.00 2.24
3920 9117 8.859090 TGAGGTGTTGTTGATCTGAATATTTTT 58.141 29.630 0.00 0.00 0.00 1.94
3965 9162 6.008331 ACTCCAACATCCCATGATAATGATG 58.992 40.000 0.00 1.27 40.28 3.07
3982 9212 9.321562 GATAATGATGTCCAAAGCAATTTCATT 57.678 29.630 0.00 0.00 36.72 2.57
4137 9367 5.350365 TCCAGATACATGCTTTTACGTTGTC 59.650 40.000 0.00 0.00 0.00 3.18
4139 9369 6.183360 CCAGATACATGCTTTTACGTTGTCAT 60.183 38.462 0.00 0.00 0.00 3.06
4232 9463 8.386264 AGGTGCTCCATAGTTGCTTAAATATAT 58.614 33.333 7.70 0.00 35.89 0.86
4265 9496 0.036199 TGCCCCAATGATTGCTTTGC 60.036 50.000 0.00 0.14 0.00 3.68
4285 9516 6.734502 TTGCACATTTTCATGGATGGATAT 57.265 33.333 0.00 0.00 34.27 1.63
4359 9590 5.389859 TTGTTGCCAATAAGGTCATTCAG 57.610 39.130 0.00 0.00 40.61 3.02
4392 9623 4.953667 TGTTGATAAGCCTGCAGAGATAG 58.046 43.478 17.39 0.00 0.00 2.08
4411 9642 6.644347 AGATAGTGGTCTATGAAAGTGTTGG 58.356 40.000 0.00 0.00 37.05 3.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 55 2.297701 GCCAGGAAAGTCACTTGTTCA 58.702 47.619 0.00 0.00 0.00 3.18
55 56 2.297701 TGCCAGGAAAGTCACTTGTTC 58.702 47.619 0.00 0.00 0.00 3.18
64 65 0.889186 ACGCGAATTGCCAGGAAAGT 60.889 50.000 15.93 0.00 42.08 2.66
69 70 2.745884 TGGACGCGAATTGCCAGG 60.746 61.111 15.93 0.00 42.08 4.45
81 82 2.232452 ACAGGAATCTGAAGACTGGACG 59.768 50.000 0.00 0.00 43.49 4.79
98 99 8.483758 ACACTGGGAACTATACTAATTAACAGG 58.516 37.037 0.00 0.00 0.00 4.00
108 109 4.278669 CGCATCTACACTGGGAACTATACT 59.721 45.833 0.00 0.00 0.00 2.12
109 110 4.547532 CGCATCTACACTGGGAACTATAC 58.452 47.826 0.00 0.00 0.00 1.47
110 111 3.572682 CCGCATCTACACTGGGAACTATA 59.427 47.826 0.00 0.00 0.00 1.31
111 112 2.365617 CCGCATCTACACTGGGAACTAT 59.634 50.000 0.00 0.00 0.00 2.12
112 113 1.754803 CCGCATCTACACTGGGAACTA 59.245 52.381 0.00 0.00 0.00 2.24
113 114 0.537188 CCGCATCTACACTGGGAACT 59.463 55.000 0.00 0.00 0.00 3.01
156 157 1.808945 CTGACTTCAATTCGGCAGCTT 59.191 47.619 0.00 0.00 0.00 3.74
184 185 0.896226 GTCCTGGGCTAAGTCTCGTT 59.104 55.000 0.00 0.00 0.00 3.85
193 194 0.970937 CTCGGTCAAGTCCTGGGCTA 60.971 60.000 0.00 0.00 0.00 3.93
261 274 2.526077 TGTAGCATCATGTCGAACGTC 58.474 47.619 0.00 0.00 0.00 4.34
286 314 2.016318 CTGTTGGTTCAGTGCTTGACA 58.984 47.619 0.00 0.00 34.94 3.58
302 330 2.743718 CTGGTCTCGGTGGCTGTT 59.256 61.111 0.00 0.00 0.00 3.16
304 332 4.087892 CCCTGGTCTCGGTGGCTG 62.088 72.222 0.00 0.00 0.00 4.85
305 333 3.625632 ATCCCTGGTCTCGGTGGCT 62.626 63.158 0.00 0.00 0.00 4.75
306 334 3.083997 ATCCCTGGTCTCGGTGGC 61.084 66.667 0.00 0.00 0.00 5.01
307 335 2.435693 GGATCCCTGGTCTCGGTGG 61.436 68.421 0.00 0.00 0.00 4.61
308 336 1.381872 AGGATCCCTGGTCTCGGTG 60.382 63.158 8.55 0.00 29.57 4.94
309 337 3.110552 AGGATCCCTGGTCTCGGT 58.889 61.111 8.55 0.00 29.57 4.69
333 361 2.567169 ACCATGAATCGTCAGTTCTCCA 59.433 45.455 0.00 0.00 37.14 3.86
343 371 1.078709 CGTTGAGCACCATGAATCGT 58.921 50.000 0.00 0.00 0.00 3.73
382 410 1.137872 GATGACCAGGATCTCAGCGTT 59.862 52.381 0.00 0.00 0.00 4.84
485 513 9.487790 TGCATTCGTTCAACTATCATCATATTA 57.512 29.630 0.00 0.00 0.00 0.98
486 514 8.382030 TGCATTCGTTCAACTATCATCATATT 57.618 30.769 0.00 0.00 0.00 1.28
568 644 4.352595 TCATTGGAAGTAGGAAAGGGTTCA 59.647 41.667 0.00 0.00 35.25 3.18
569 645 4.918588 TCATTGGAAGTAGGAAAGGGTTC 58.081 43.478 0.00 0.00 0.00 3.62
573 649 7.227512 GTGTCATATCATTGGAAGTAGGAAAGG 59.772 40.741 0.00 0.00 0.00 3.11
586 662 3.065786 GGTGTGGCTGTGTCATATCATTG 59.934 47.826 0.00 0.00 0.00 2.82
599 675 1.985447 GCATGATCACGGTGTGGCTG 61.985 60.000 8.17 3.98 33.87 4.85
602 678 0.959867 TTGGCATGATCACGGTGTGG 60.960 55.000 8.17 0.00 33.87 4.17
657 737 2.426024 TCAACCGATGTCAGGTAGTAGC 59.574 50.000 0.00 0.00 41.95 3.58
693 4493 1.530323 GCGTGCCTTTTCCTAAGGAA 58.470 50.000 1.27 1.27 40.27 3.36
820 4620 3.573772 CTTCGTGACTGGCGGCAGA 62.574 63.158 41.51 20.80 0.00 4.26
869 4670 5.413499 ACGTATGAGTAGGTGCGTATTTTT 58.587 37.500 0.00 0.00 34.98 1.94
876 4677 2.554806 TTGACGTATGAGTAGGTGCG 57.445 50.000 0.00 0.00 0.00 5.34
904 4705 1.601477 CGGGGTAGGTGCGGTTTTT 60.601 57.895 0.00 0.00 0.00 1.94
905 4706 2.032987 CGGGGTAGGTGCGGTTTT 59.967 61.111 0.00 0.00 0.00 2.43
906 4707 2.924101 TCGGGGTAGGTGCGGTTT 60.924 61.111 0.00 0.00 0.00 3.27
907 4708 3.698820 GTCGGGGTAGGTGCGGTT 61.699 66.667 0.00 0.00 0.00 4.44
946 4784 1.447643 GACCGTGGGATGAGGATGG 59.552 63.158 0.00 0.00 0.00 3.51
978 4816 0.849417 AGAGGAATGGATGGGGAAGC 59.151 55.000 0.00 0.00 0.00 3.86
979 4817 1.423161 GGAGAGGAATGGATGGGGAAG 59.577 57.143 0.00 0.00 0.00 3.46
980 4818 1.274943 TGGAGAGGAATGGATGGGGAA 60.275 52.381 0.00 0.00 0.00 3.97
1037 4877 2.808206 GGGGCTCGATCGTGGGAAT 61.808 63.158 15.94 0.00 0.00 3.01
1041 4881 4.899239 GCAGGGGCTCGATCGTGG 62.899 72.222 15.94 10.45 36.96 4.94
1116 4960 3.567797 GCTTGCGGATGGACGAGC 61.568 66.667 0.00 0.00 35.47 5.03
1880 7008 0.462759 CCATGGCGAGACCTTCCTTC 60.463 60.000 0.00 0.00 40.22 3.46
2697 7825 0.821301 TTCACCTCAATGTGGCGCAA 60.821 50.000 10.83 0.00 36.87 4.85
2713 7841 1.069978 TGACGGCACTCTTGACATTCA 59.930 47.619 0.00 0.00 0.00 2.57
2747 7875 3.788227 AGTGTCTTCTTTGCCACCATA 57.212 42.857 0.00 0.00 0.00 2.74
2867 7995 0.255890 GATAGTTGGGGCTGCAAGGA 59.744 55.000 0.50 0.00 0.00 3.36
2889 8017 3.244078 ACACCACGTAGCTTCTTCATCAA 60.244 43.478 0.00 0.00 0.00 2.57
3140 8268 2.515854 AGTGTCTTCTCGCCAGTTAGA 58.484 47.619 0.00 0.00 0.00 2.10
3146 8274 1.476891 GGTGATAGTGTCTTCTCGCCA 59.523 52.381 0.00 0.00 38.03 5.69
3255 8383 2.037847 GCAGATGGGCAGGGGTTT 59.962 61.111 0.00 0.00 0.00 3.27
3417 8547 7.898014 CCTAAAAGGCCTCAAGGTAAATAAT 57.102 36.000 5.23 0.00 37.57 1.28
3444 8574 8.706035 GCGATACTTCAAAAGTTACAGTTTAGA 58.294 33.333 0.00 0.00 42.81 2.10
3565 8709 2.755650 AGTTGCACTAAGGTTGAGACG 58.244 47.619 0.00 0.00 0.00 4.18
3715 8860 9.863845 TGATCGATTTGTAACTTCATGTACTTA 57.136 29.630 0.00 0.00 0.00 2.24
3716 8861 8.771920 TGATCGATTTGTAACTTCATGTACTT 57.228 30.769 0.00 0.00 0.00 2.24
3717 8862 8.656849 GTTGATCGATTTGTAACTTCATGTACT 58.343 33.333 0.00 0.00 0.00 2.73
3718 8863 7.903431 GGTTGATCGATTTGTAACTTCATGTAC 59.097 37.037 0.00 0.00 0.00 2.90
3719 8864 7.604545 TGGTTGATCGATTTGTAACTTCATGTA 59.395 33.333 0.00 0.00 0.00 2.29
3720 8865 6.429692 TGGTTGATCGATTTGTAACTTCATGT 59.570 34.615 0.00 0.00 0.00 3.21
3721 8866 6.841119 TGGTTGATCGATTTGTAACTTCATG 58.159 36.000 0.00 0.00 0.00 3.07
3722 8867 7.447374 TTGGTTGATCGATTTGTAACTTCAT 57.553 32.000 0.00 0.00 0.00 2.57
3723 8868 6.869315 TTGGTTGATCGATTTGTAACTTCA 57.131 33.333 0.00 0.00 0.00 3.02
3724 8869 8.665685 AGTATTGGTTGATCGATTTGTAACTTC 58.334 33.333 0.00 0.00 0.00 3.01
3725 8870 8.561738 AGTATTGGTTGATCGATTTGTAACTT 57.438 30.769 0.00 0.00 0.00 2.66
3726 8871 9.314321 CTAGTATTGGTTGATCGATTTGTAACT 57.686 33.333 0.00 0.00 0.00 2.24
3727 8872 9.095065 ACTAGTATTGGTTGATCGATTTGTAAC 57.905 33.333 0.00 3.54 0.00 2.50
3728 8873 9.661563 AACTAGTATTGGTTGATCGATTTGTAA 57.338 29.630 0.00 0.00 0.00 2.41
3730 8875 9.832445 ATAACTAGTATTGGTTGATCGATTTGT 57.168 29.630 0.00 0.00 0.00 2.83
3920 9117 6.042093 GGAGTATATGGTCACTGAGGAATGAA 59.958 42.308 0.00 0.00 0.00 2.57
3931 9128 4.102524 TGGGATGTTGGAGTATATGGTCAC 59.897 45.833 0.00 0.00 0.00 3.67
3965 9162 8.250332 TCAACCTATAATGAAATTGCTTTGGAC 58.750 33.333 0.00 0.00 36.99 4.02
4137 9367 4.848357 AGGGTGAACACAAGGAATCTATG 58.152 43.478 7.25 0.00 0.00 2.23
4139 9369 5.724370 TGATAGGGTGAACACAAGGAATCTA 59.276 40.000 7.25 0.00 0.00 1.98
4232 9463 2.392662 TGGGGCAAACAATTCTCACAA 58.607 42.857 0.00 0.00 0.00 3.33
4265 9496 7.436970 CACACAATATCCATCCATGAAAATGTG 59.563 37.037 0.00 0.00 0.00 3.21
4359 9590 4.706962 AGGCTTATCAACAATTCAACTCCC 59.293 41.667 0.00 0.00 0.00 4.30
4392 9623 3.189287 CAGCCAACACTTTCATAGACCAC 59.811 47.826 0.00 0.00 0.00 4.16


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

AutoCloner maintained by Alex Coulton.