Multiple sequence alignment - TraesCS1A01G209700

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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 TraesCS1A01G209700 chr1A 100.000 2456 0 0 1 2456 372242652 372240197 0.000000e+00 4536.0
1 TraesCS1A01G209700 chr1A 88.387 155 15 1 399 553 146637476 146637627 1.500000e-42 183.0
2 TraesCS1A01G209700 chr1A 78.035 173 32 5 1281 1451 372467740 372467572 1.200000e-18 104.0
3 TraesCS1A01G209700 chr1A 93.651 63 4 0 7 69 547002253 547002315 7.230000e-16 95.3
4 TraesCS1A01G209700 chr1B 96.564 844 22 3 1414 2254 401624448 401623609 0.000000e+00 1391.0
5 TraesCS1A01G209700 chr1B 91.059 727 45 9 617 1339 401625155 401624445 0.000000e+00 965.0
6 TraesCS1A01G209700 chr1B 89.351 385 29 8 567 951 401813700 401813328 7.950000e-130 473.0
7 TraesCS1A01G209700 chr1B 96.020 201 6 2 2257 2456 401623444 401623245 2.360000e-85 326.0
8 TraesCS1A01G209700 chr1D 96.970 792 16 5 1669 2456 298573595 298572808 0.000000e+00 1323.0
9 TraesCS1A01G209700 chr1D 93.868 848 36 4 742 1580 298574599 298573759 0.000000e+00 1264.0
10 TraesCS1A01G209700 chr1D 83.451 284 23 15 68 347 3186324 3186587 2.440000e-60 243.0
11 TraesCS1A01G209700 chr1D 87.302 189 19 3 347 534 3186892 3187076 6.880000e-51 211.0
12 TraesCS1A01G209700 chr1D 89.076 119 9 3 627 742 298575945 298575828 7.080000e-31 145.0
13 TraesCS1A01G209700 chr1D 92.683 41 2 1 1600 1639 298573633 298573593 9.490000e-05 58.4
14 TraesCS1A01G209700 chr6D 86.824 296 30 8 61 348 336534340 336534634 3.050000e-84 322.0
15 TraesCS1A01G209700 chr6D 87.336 229 23 4 2227 2454 399037135 399036912 8.710000e-65 257.0
16 TraesCS1A01G209700 chr6D 88.112 143 12 4 412 553 336536633 336536771 5.430000e-37 165.0
17 TraesCS1A01G209700 chr6D 95.588 68 2 1 2 68 470407858 470407791 9.290000e-20 108.0
18 TraesCS1A01G209700 chr6D 92.424 66 5 0 7 72 329080222 329080287 7.230000e-16 95.3
19 TraesCS1A01G209700 chr7D 86.219 283 29 8 64 337 611053036 611053317 5.130000e-77 298.0
20 TraesCS1A01G209700 chr7D 88.439 173 18 2 347 519 611053596 611053766 8.900000e-50 207.0
21 TraesCS1A01G209700 chr7D 92.647 68 5 0 7 74 587178452 587178385 5.590000e-17 99.0
22 TraesCS1A01G209700 chr7B 85.764 288 31 9 67 347 538576064 538575780 1.850000e-76 296.0
23 TraesCS1A01G209700 chr7B 85.053 281 39 3 67 345 562379660 562379939 1.440000e-72 283.0
24 TraesCS1A01G209700 chr7B 88.995 209 17 4 347 553 648224203 648223999 1.130000e-63 254.0
25 TraesCS1A01G209700 chr7B 92.090 177 12 1 345 519 538575356 538575180 5.240000e-62 248.0
26 TraesCS1A01G209700 chr7B 86.667 225 25 5 2233 2454 634628064 634627842 6.780000e-61 244.0
27 TraesCS1A01G209700 chr7B 94.118 68 3 1 2 68 49587575 49587642 4.320000e-18 102.0
28 TraesCS1A01G209700 chr6B 85.764 288 32 7 67 347 497897262 497896977 1.850000e-76 296.0
29 TraesCS1A01G209700 chr6B 90.047 211 16 2 345 553 497896553 497896346 4.030000e-68 268.0
30 TraesCS1A01G209700 chr3D 91.031 223 15 5 2231 2450 132924305 132924525 1.850000e-76 296.0
31 TraesCS1A01G209700 chr5B 90.047 211 13 5 347 553 711904404 711904198 1.450000e-67 267.0
32 TraesCS1A01G209700 chr5B 79.021 286 30 13 67 347 711905037 711904777 4.200000e-38 169.0
33 TraesCS1A01G209700 chr5B 95.588 68 2 1 2 68 639608387 639608454 9.290000e-20 108.0
34 TraesCS1A01G209700 chr7A 86.235 247 28 5 86 327 494129506 494129751 1.870000e-66 263.0
35 TraesCS1A01G209700 chr7A 86.979 192 13 7 369 553 494130065 494130251 3.200000e-49 206.0
36 TraesCS1A01G209700 chr7A 90.909 143 11 2 2312 2453 669275228 669275087 8.960000e-45 191.0
37 TraesCS1A01G209700 chr5D 82.414 290 33 14 67 347 7723555 7723275 1.140000e-58 237.0
38 TraesCS1A01G209700 chr2B 91.892 148 10 2 2228 2374 543512091 543512237 3.200000e-49 206.0
39 TraesCS1A01G209700 chr2B 82.326 215 25 8 2230 2439 543512251 543512457 9.030000e-40 174.0
40 TraesCS1A01G209700 chr2B 87.313 134 16 1 2235 2367 543512971 543513104 4.230000e-33 152.0
41 TraesCS1A01G209700 chr2B 95.714 70 2 1 2 70 666546798 666546867 7.180000e-21 111.0
42 TraesCS1A01G209700 chr2B 92.308 65 5 0 4 68 738945 738881 2.600000e-15 93.5
43 TraesCS1A01G209700 chr5A 84.091 220 25 9 2229 2445 609951930 609951718 1.150000e-48 204.0
44 TraesCS1A01G209700 chr5A 91.304 69 6 0 1301 1369 692198330 692198262 7.230000e-16 95.3
45 TraesCS1A01G209700 chr4B 87.640 89 11 0 1281 1369 654561112 654561024 1.200000e-18 104.0
46 TraesCS1A01G209700 chr4B 79.839 124 22 3 1301 1424 654728261 654728141 1.210000e-13 87.9
47 TraesCS1A01G209700 chrUn 87.356 87 9 2 1281 1366 154601802 154601887 5.590000e-17 99.0
48 TraesCS1A01G209700 chrUn 85.057 87 11 2 1281 1366 154587134 154587219 1.210000e-13 87.9
49 TraesCS1A01G209700 chr3B 93.548 62 4 0 7 68 18448266 18448327 2.600000e-15 93.5
50 TraesCS1A01G209700 chr2D 92.308 52 4 0 1170 1221 523738301 523738250 9.420000e-10 75.0
51 TraesCS1A01G209700 chr2A 92.157 51 3 1 1170 1219 669558144 669558094 1.220000e-08 71.3


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 TraesCS1A01G209700 chr1A 372240197 372242652 2455 True 4536.0 4536 100.000000 1 2456 1 chr1A.!!$R1 2455
1 TraesCS1A01G209700 chr1B 401623245 401625155 1910 True 894.0 1391 94.547667 617 2456 3 chr1B.!!$R2 1839
2 TraesCS1A01G209700 chr1D 298572808 298575945 3137 True 697.6 1323 93.149250 627 2456 4 chr1D.!!$R1 1829
3 TraesCS1A01G209700 chr1D 3186324 3187076 752 False 227.0 243 85.376500 68 534 2 chr1D.!!$F1 466
4 TraesCS1A01G209700 chr6D 336534340 336536771 2431 False 243.5 322 87.468000 61 553 2 chr6D.!!$F2 492
5 TraesCS1A01G209700 chr7D 611053036 611053766 730 False 252.5 298 87.329000 64 519 2 chr7D.!!$F1 455
6 TraesCS1A01G209700 chr7B 538575180 538576064 884 True 272.0 296 88.927000 67 519 2 chr7B.!!$R3 452
7 TraesCS1A01G209700 chr6B 497896346 497897262 916 True 282.0 296 87.905500 67 553 2 chr6B.!!$R1 486
8 TraesCS1A01G209700 chr5B 711904198 711905037 839 True 218.0 267 84.534000 67 553 2 chr5B.!!$R1 486
9 TraesCS1A01G209700 chr7A 494129506 494130251 745 False 234.5 263 86.607000 86 553 2 chr7A.!!$F1 467

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
554 2804 0.040958 GCAGCGCCAAATAGGAATCG 60.041 55.0 2.29 0.0 41.22 3.34 F
898 4381 0.787787 CGCAACTTTCGAACCGATGA 59.212 50.0 0.00 0.0 35.23 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1447 4939 0.179018 GACTTGGCTGGTCAGTTGGT 60.179 55.000 0.00 0.0 34.23 3.67 R
1759 5361 3.079578 CTGACAATGGCAGAACTGTGAT 58.920 45.455 11.37 0.0 35.39 3.06 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
24 25 7.914537 GGAGTGAAAGTTCATGTTTTTAGTG 57.085 36.000 0.00 0.00 39.73 2.74
25 26 7.480810 GGAGTGAAAGTTCATGTTTTTAGTGT 58.519 34.615 0.00 0.00 39.73 3.55
26 27 8.617809 GGAGTGAAAGTTCATGTTTTTAGTGTA 58.382 33.333 0.00 0.00 39.73 2.90
27 28 9.434559 GAGTGAAAGTTCATGTTTTTAGTGTAC 57.565 33.333 0.00 0.00 39.73 2.90
28 29 9.174166 AGTGAAAGTTCATGTTTTTAGTGTACT 57.826 29.630 0.00 0.00 39.73 2.73
29 30 9.783256 GTGAAAGTTCATGTTTTTAGTGTACTT 57.217 29.630 0.00 0.00 39.73 2.24
44 45 9.520204 TTTAGTGTACTTTATTAGGATACGTGC 57.480 33.333 0.00 0.00 46.39 5.34
45 46 6.204359 AGTGTACTTTATTAGGATACGTGCG 58.796 40.000 0.00 0.00 46.39 5.34
46 47 5.973565 GTGTACTTTATTAGGATACGTGCGT 59.026 40.000 0.00 2.05 46.39 5.24
47 48 6.473455 GTGTACTTTATTAGGATACGTGCGTT 59.527 38.462 1.66 0.00 46.39 4.84
48 49 5.961395 ACTTTATTAGGATACGTGCGTTG 57.039 39.130 1.66 0.00 46.39 4.10
49 50 4.269363 ACTTTATTAGGATACGTGCGTTGC 59.731 41.667 1.66 0.00 46.39 4.17
50 51 2.303163 ATTAGGATACGTGCGTTGCA 57.697 45.000 1.66 0.00 46.39 4.08
83 84 8.653338 CGCTTAATAGTGTTAACATACAAGTGT 58.347 33.333 12.26 0.00 0.00 3.55
95 96 4.283467 ACATACAAGTGTCACTAGCCAGAA 59.717 41.667 5.77 0.00 0.00 3.02
169 170 3.667261 GCTGCAGCGCTATTTTATTCATG 59.333 43.478 25.23 0.00 0.00 3.07
249 317 8.441312 AAAAGTTCATTGATCATGCAAAAAGT 57.559 26.923 0.00 0.00 32.13 2.66
250 318 8.441312 AAAGTTCATTGATCATGCAAAAAGTT 57.559 26.923 0.00 0.00 32.13 2.66
251 319 7.647907 AGTTCATTGATCATGCAAAAAGTTC 57.352 32.000 0.00 0.00 32.13 3.01
252 320 7.211573 AGTTCATTGATCATGCAAAAAGTTCA 58.788 30.769 0.00 0.00 32.13 3.18
253 321 7.876068 AGTTCATTGATCATGCAAAAAGTTCAT 59.124 29.630 0.00 0.00 32.13 2.57
254 322 7.821595 TCATTGATCATGCAAAAAGTTCATC 57.178 32.000 0.00 0.00 32.13 2.92
255 323 6.528774 TCATTGATCATGCAAAAAGTTCATCG 59.471 34.615 0.00 0.00 32.13 3.84
256 324 5.625921 TGATCATGCAAAAAGTTCATCGA 57.374 34.783 0.00 0.00 0.00 3.59
257 325 6.198650 TGATCATGCAAAAAGTTCATCGAT 57.801 33.333 0.00 0.00 0.00 3.59
335 1109 6.738114 TCACCTGATTTCAAAACAGTTCATC 58.262 36.000 6.65 0.00 0.00 2.92
338 1112 5.853282 CCTGATTTCAAAACAGTTCATCGAC 59.147 40.000 6.65 0.00 0.00 4.20
381 1468 2.037901 TGGTGGTGTCGTAGTGGTTAA 58.962 47.619 0.00 0.00 0.00 2.01
382 1469 2.036217 TGGTGGTGTCGTAGTGGTTAAG 59.964 50.000 0.00 0.00 0.00 1.85
394 1481 4.749245 AGTGGTTAAGTCGATTTGCTTG 57.251 40.909 3.04 0.00 0.00 4.01
433 2679 1.215382 CGAATCTGGGTCACGCTGA 59.785 57.895 3.84 3.84 0.00 4.26
518 2768 1.165270 GCCCGTTTGTAGATTGCACT 58.835 50.000 0.00 0.00 0.00 4.40
519 2769 2.352388 GCCCGTTTGTAGATTGCACTA 58.648 47.619 0.00 0.00 0.00 2.74
520 2770 2.943033 GCCCGTTTGTAGATTGCACTAT 59.057 45.455 0.00 0.00 0.00 2.12
553 2803 1.002033 CTGCAGCGCCAAATAGGAATC 60.002 52.381 2.29 0.00 41.22 2.52
554 2804 0.040958 GCAGCGCCAAATAGGAATCG 60.041 55.000 2.29 0.00 41.22 3.34
555 2805 1.299541 CAGCGCCAAATAGGAATCGT 58.700 50.000 2.29 0.00 41.22 3.73
556 2806 1.003545 CAGCGCCAAATAGGAATCGTG 60.004 52.381 2.29 0.00 41.22 4.35
557 2807 1.014352 GCGCCAAATAGGAATCGTGT 58.986 50.000 0.00 0.00 41.22 4.49
558 2808 1.268032 GCGCCAAATAGGAATCGTGTG 60.268 52.381 0.00 0.00 41.22 3.82
559 2809 1.330521 CGCCAAATAGGAATCGTGTGG 59.669 52.381 0.00 0.00 41.22 4.17
560 2810 2.639065 GCCAAATAGGAATCGTGTGGA 58.361 47.619 6.40 0.00 41.22 4.02
561 2811 3.214328 GCCAAATAGGAATCGTGTGGAT 58.786 45.455 6.40 0.00 41.22 3.41
562 2812 4.385825 GCCAAATAGGAATCGTGTGGATA 58.614 43.478 6.40 0.00 41.22 2.59
563 2813 4.452455 GCCAAATAGGAATCGTGTGGATAG 59.548 45.833 6.40 0.00 41.22 2.08
564 2814 4.997395 CCAAATAGGAATCGTGTGGATAGG 59.003 45.833 0.00 0.00 41.22 2.57
565 2815 3.963428 ATAGGAATCGTGTGGATAGGC 57.037 47.619 0.00 0.00 34.08 3.93
566 2816 1.496060 AGGAATCGTGTGGATAGGCA 58.504 50.000 0.00 0.00 34.08 4.75
567 2817 2.050144 AGGAATCGTGTGGATAGGCAT 58.950 47.619 0.00 0.00 34.08 4.40
568 2818 3.239449 AGGAATCGTGTGGATAGGCATA 58.761 45.455 0.00 0.00 34.08 3.14
569 2819 3.259374 AGGAATCGTGTGGATAGGCATAG 59.741 47.826 0.00 0.00 34.08 2.23
570 2820 3.258372 GGAATCGTGTGGATAGGCATAGA 59.742 47.826 0.00 0.00 34.08 1.98
571 2821 4.262463 GGAATCGTGTGGATAGGCATAGAA 60.262 45.833 0.00 0.00 34.08 2.10
572 2822 3.728076 TCGTGTGGATAGGCATAGAAC 57.272 47.619 0.00 0.00 0.00 3.01
573 2823 3.028130 TCGTGTGGATAGGCATAGAACA 58.972 45.455 0.00 0.00 0.00 3.18
574 2824 3.068165 TCGTGTGGATAGGCATAGAACAG 59.932 47.826 0.00 0.00 0.00 3.16
575 2825 3.134458 GTGTGGATAGGCATAGAACAGC 58.866 50.000 0.00 0.00 0.00 4.40
576 2826 2.771372 TGTGGATAGGCATAGAACAGCA 59.229 45.455 0.00 0.00 0.00 4.41
577 2827 3.392285 TGTGGATAGGCATAGAACAGCAT 59.608 43.478 0.00 0.00 0.00 3.79
578 2828 4.592778 TGTGGATAGGCATAGAACAGCATA 59.407 41.667 0.00 0.00 0.00 3.14
579 2829 4.932200 GTGGATAGGCATAGAACAGCATAC 59.068 45.833 0.00 0.00 29.19 2.39
580 2830 4.840680 TGGATAGGCATAGAACAGCATACT 59.159 41.667 0.00 0.00 29.19 2.12
627 2877 7.685481 TGAACCTTTCTTTTCCTTTTCCTTTT 58.315 30.769 0.00 0.00 0.00 2.27
628 2878 7.822334 TGAACCTTTCTTTTCCTTTTCCTTTTC 59.178 33.333 0.00 0.00 0.00 2.29
641 2891 7.827236 TCCTTTTCCTTTTCCTTTTCCTTTTTC 59.173 33.333 0.00 0.00 0.00 2.29
676 2926 1.403249 GCAAACTGAGCCATGCGAAAT 60.403 47.619 0.00 0.00 0.00 2.17
677 2927 2.159393 GCAAACTGAGCCATGCGAAATA 60.159 45.455 0.00 0.00 0.00 1.40
678 2928 3.489738 GCAAACTGAGCCATGCGAAATAT 60.490 43.478 0.00 0.00 0.00 1.28
679 2929 4.285292 CAAACTGAGCCATGCGAAATATC 58.715 43.478 0.00 0.00 0.00 1.63
680 2930 3.482156 ACTGAGCCATGCGAAATATCT 57.518 42.857 0.00 0.00 0.00 1.98
682 2932 4.202441 ACTGAGCCATGCGAAATATCTTT 58.798 39.130 0.00 0.00 0.00 2.52
799 4282 4.919774 ACATTCCCTACATGTTGTACCA 57.080 40.909 2.30 0.00 30.22 3.25
811 4294 5.699458 ACATGTTGTACCAAAGCTACAGTAC 59.301 40.000 11.31 11.31 36.47 2.73
812 4295 5.279255 TGTTGTACCAAAGCTACAGTACA 57.721 39.130 15.15 15.15 42.36 2.90
879 4362 4.389077 CGGACACCTGACTCAAGTAAATTC 59.611 45.833 0.00 0.00 0.00 2.17
898 4381 0.787787 CGCAACTTTCGAACCGATGA 59.212 50.000 0.00 0.00 35.23 2.92
1044 4527 1.523711 CACGGTGGTTGCACTGTCT 60.524 57.895 0.00 0.00 42.26 3.41
1078 4564 2.791868 GCGAGCTTCCTCCTCCTCC 61.792 68.421 0.00 0.00 34.49 4.30
1086 4572 2.517402 CTCCTCCTCCCCGTCTCG 60.517 72.222 0.00 0.00 0.00 4.04
1087 4573 3.336568 TCCTCCTCCCCGTCTCGT 61.337 66.667 0.00 0.00 0.00 4.18
1176 4668 4.484872 GGCGGAGGTAAGTGCCCC 62.485 72.222 0.00 0.00 41.70 5.80
1301 4793 3.782244 GTGCTGCGAGCTCGTTGG 61.782 66.667 34.46 24.39 42.97 3.77
1459 4951 4.885426 AGTGCACCAACTGACCAG 57.115 55.556 14.63 0.00 0.00 4.00
1462 4954 2.203337 GCACCAACTGACCAGCCA 60.203 61.111 0.00 0.00 0.00 4.75
1528 5020 1.798079 GCTAGTAGTGGTACGTGCTGC 60.798 57.143 3.01 0.00 33.97 5.25
1757 5359 8.612619 ACATTATACATGCAGCTTTACAAGTAC 58.387 33.333 0.00 0.00 0.00 2.73
1758 5360 8.830580 CATTATACATGCAGCTTTACAAGTACT 58.169 33.333 0.00 0.00 0.00 2.73
1763 5365 6.313905 ACATGCAGCTTTACAAGTACTATCAC 59.686 38.462 0.00 0.00 0.00 3.06
2225 5827 6.811665 GGCATCCTTCTTTACCAATTTACAAC 59.188 38.462 0.00 0.00 0.00 3.32
2311 6075 5.303165 CACATCACCTAGTCATGCATGTAT 58.697 41.667 25.43 17.19 0.00 2.29
2315 6079 6.178607 TCACCTAGTCATGCATGTATTCAT 57.821 37.500 25.43 6.95 34.21 2.57
2369 6134 2.747467 GCATACCACCTCATGCATGACT 60.747 50.000 25.42 10.61 45.51 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.480810 ACACTAAAAACATGAACTTTCACTCC 58.519 34.615 0.00 0.00 40.49 3.85
1 2 9.434559 GTACACTAAAAACATGAACTTTCACTC 57.565 33.333 0.00 0.00 40.49 3.51
3 4 9.783256 AAGTACACTAAAAACATGAACTTTCAC 57.217 29.630 0.00 0.00 40.49 3.18
18 19 9.520204 GCACGTATCCTAATAAAGTACACTAAA 57.480 33.333 0.00 0.00 0.00 1.85
19 20 7.857389 CGCACGTATCCTAATAAAGTACACTAA 59.143 37.037 0.00 0.00 0.00 2.24
20 21 7.012327 ACGCACGTATCCTAATAAAGTACACTA 59.988 37.037 0.00 0.00 0.00 2.74
21 22 6.183360 ACGCACGTATCCTAATAAAGTACACT 60.183 38.462 0.00 0.00 0.00 3.55
22 23 5.973565 ACGCACGTATCCTAATAAAGTACAC 59.026 40.000 0.00 0.00 0.00 2.90
23 24 6.135290 ACGCACGTATCCTAATAAAGTACA 57.865 37.500 0.00 0.00 0.00 2.90
24 25 6.560983 GCAACGCACGTATCCTAATAAAGTAC 60.561 42.308 0.00 0.00 0.00 2.73
25 26 5.459762 GCAACGCACGTATCCTAATAAAGTA 59.540 40.000 0.00 0.00 0.00 2.24
26 27 4.269363 GCAACGCACGTATCCTAATAAAGT 59.731 41.667 0.00 0.00 0.00 2.66
27 28 4.269123 TGCAACGCACGTATCCTAATAAAG 59.731 41.667 0.00 0.00 31.71 1.85
28 29 4.182339 TGCAACGCACGTATCCTAATAAA 58.818 39.130 0.00 0.00 31.71 1.40
29 30 3.783191 TGCAACGCACGTATCCTAATAA 58.217 40.909 0.00 0.00 31.71 1.40
30 31 3.439895 TGCAACGCACGTATCCTAATA 57.560 42.857 0.00 0.00 31.71 0.98
31 32 2.303163 TGCAACGCACGTATCCTAAT 57.697 45.000 0.00 0.00 31.71 1.73
32 33 3.816580 TGCAACGCACGTATCCTAA 57.183 47.368 0.00 0.00 31.71 2.69
48 49 0.719465 ACTATTAAGCGTGCACGTGC 59.281 50.000 36.80 33.11 42.22 5.34
49 50 1.724623 ACACTATTAAGCGTGCACGTG 59.275 47.619 36.80 26.41 42.22 4.49
50 51 2.074547 ACACTATTAAGCGTGCACGT 57.925 45.000 36.80 22.79 42.22 4.49
51 52 4.143284 TGTTAACACTATTAAGCGTGCACG 60.143 41.667 34.01 34.01 43.27 5.34
52 53 5.272167 TGTTAACACTATTAAGCGTGCAC 57.728 39.130 6.82 6.82 34.58 4.57
53 54 6.590677 TGTATGTTAACACTATTAAGCGTGCA 59.409 34.615 11.22 0.00 34.58 4.57
54 55 6.996106 TGTATGTTAACACTATTAAGCGTGC 58.004 36.000 11.22 0.00 34.58 5.34
55 56 8.653338 ACTTGTATGTTAACACTATTAAGCGTG 58.347 33.333 11.22 5.62 37.18 5.34
56 57 8.653338 CACTTGTATGTTAACACTATTAAGCGT 58.347 33.333 11.22 0.00 0.00 5.07
57 58 8.653338 ACACTTGTATGTTAACACTATTAAGCG 58.347 33.333 11.22 8.06 0.00 4.68
58 59 9.968743 GACACTTGTATGTTAACACTATTAAGC 57.031 33.333 11.22 0.00 31.24 3.09
65 66 6.645415 GCTAGTGACACTTGTATGTTAACACT 59.355 38.462 14.50 0.00 39.03 3.55
83 84 3.741245 AGTAGGTCTTCTGGCTAGTGA 57.259 47.619 0.00 0.00 0.00 3.41
95 96 3.788227 TCAACAATGGCAAGTAGGTCT 57.212 42.857 0.00 0.00 0.00 3.85
238 306 6.693761 TGAAATCGATGAACTTTTTGCATG 57.306 33.333 0.00 0.00 0.00 4.06
239 307 7.712264 TTTGAAATCGATGAACTTTTTGCAT 57.288 28.000 0.00 0.00 0.00 3.96
240 308 7.531280 TTTTGAAATCGATGAACTTTTTGCA 57.469 28.000 0.00 0.00 0.00 4.08
316 387 6.618287 AGTCGATGAACTGTTTTGAAATCA 57.382 33.333 0.00 0.00 0.00 2.57
327 399 6.087291 GCAATCTTTTCAAAGTCGATGAACTG 59.913 38.462 0.00 0.00 36.57 3.16
335 1109 4.618489 GGTCATGCAATCTTTTCAAAGTCG 59.382 41.667 0.00 0.00 37.31 4.18
338 1112 4.885413 TGGGTCATGCAATCTTTTCAAAG 58.115 39.130 0.00 0.00 37.36 2.77
381 1468 3.201290 CTCCATAGCAAGCAAATCGACT 58.799 45.455 0.00 0.00 0.00 4.18
382 1469 2.939103 ACTCCATAGCAAGCAAATCGAC 59.061 45.455 0.00 0.00 0.00 4.20
394 1481 3.526534 GAACTCAAGACCACTCCATAGC 58.473 50.000 0.00 0.00 0.00 2.97
451 2701 4.814234 GGCCCGTTCTTCATTTTTCTTTTT 59.186 37.500 0.00 0.00 0.00 1.94
508 2758 4.124238 GCCCGTTACAATAGTGCAATCTA 58.876 43.478 0.00 0.00 0.00 1.98
518 2768 1.816259 GCAGGCGCCCGTTACAATA 60.816 57.895 26.15 0.00 0.00 1.90
519 2769 3.131478 GCAGGCGCCCGTTACAAT 61.131 61.111 26.15 0.00 0.00 2.71
520 2770 4.627801 TGCAGGCGCCCGTTACAA 62.628 61.111 26.15 0.00 37.32 2.41
553 2803 3.384668 CTGTTCTATGCCTATCCACACG 58.615 50.000 0.00 0.00 0.00 4.49
554 2804 3.134458 GCTGTTCTATGCCTATCCACAC 58.866 50.000 0.00 0.00 0.00 3.82
555 2805 2.771372 TGCTGTTCTATGCCTATCCACA 59.229 45.455 0.00 0.00 0.00 4.17
556 2806 3.475566 TGCTGTTCTATGCCTATCCAC 57.524 47.619 0.00 0.00 0.00 4.02
557 2807 4.840680 AGTATGCTGTTCTATGCCTATCCA 59.159 41.667 0.00 0.00 0.00 3.41
558 2808 5.047021 TCAGTATGCTGTTCTATGCCTATCC 60.047 44.000 10.80 0.00 43.05 2.59
559 2809 6.030548 TCAGTATGCTGTTCTATGCCTATC 57.969 41.667 10.80 0.00 43.05 2.08
560 2810 5.777223 TCTCAGTATGCTGTTCTATGCCTAT 59.223 40.000 10.80 0.00 43.05 2.57
561 2811 5.140454 TCTCAGTATGCTGTTCTATGCCTA 58.860 41.667 10.80 0.00 43.05 3.93
562 2812 3.963374 TCTCAGTATGCTGTTCTATGCCT 59.037 43.478 10.80 0.00 43.05 4.75
563 2813 4.327982 TCTCAGTATGCTGTTCTATGCC 57.672 45.455 10.80 0.00 43.05 4.40
564 2814 6.073331 GGAAATCTCAGTATGCTGTTCTATGC 60.073 42.308 10.80 0.00 43.05 3.14
565 2815 7.215789 AGGAAATCTCAGTATGCTGTTCTATG 58.784 38.462 10.80 0.00 43.05 2.23
566 2816 7.070447 TGAGGAAATCTCAGTATGCTGTTCTAT 59.930 37.037 10.80 1.41 46.71 1.98
567 2817 6.381133 TGAGGAAATCTCAGTATGCTGTTCTA 59.619 38.462 10.80 0.00 46.71 2.10
568 2818 5.188555 TGAGGAAATCTCAGTATGCTGTTCT 59.811 40.000 10.80 0.00 46.71 3.01
569 2819 5.423015 TGAGGAAATCTCAGTATGCTGTTC 58.577 41.667 10.80 6.97 46.71 3.18
570 2820 5.426689 TGAGGAAATCTCAGTATGCTGTT 57.573 39.130 10.80 0.00 46.71 3.16
597 2847 8.956426 GGAAAAGGAAAAGAAAGGTTCAATTTT 58.044 29.630 0.00 0.00 31.91 1.82
598 2848 8.328758 AGGAAAAGGAAAAGAAAGGTTCAATTT 58.671 29.630 0.00 0.00 0.00 1.82
599 2849 7.861629 AGGAAAAGGAAAAGAAAGGTTCAATT 58.138 30.769 0.00 0.00 0.00 2.32
600 2850 7.437713 AGGAAAAGGAAAAGAAAGGTTCAAT 57.562 32.000 0.00 0.00 0.00 2.57
601 2851 6.867519 AGGAAAAGGAAAAGAAAGGTTCAA 57.132 33.333 0.00 0.00 0.00 2.69
602 2852 6.867519 AAGGAAAAGGAAAAGAAAGGTTCA 57.132 33.333 0.00 0.00 0.00 3.18
603 2853 7.280205 GGAAAAGGAAAAGGAAAAGAAAGGTTC 59.720 37.037 0.00 0.00 0.00 3.62
604 2854 7.037586 AGGAAAAGGAAAAGGAAAAGAAAGGTT 60.038 33.333 0.00 0.00 0.00 3.50
605 2855 6.443849 AGGAAAAGGAAAAGGAAAAGAAAGGT 59.556 34.615 0.00 0.00 0.00 3.50
606 2856 6.889198 AGGAAAAGGAAAAGGAAAAGAAAGG 58.111 36.000 0.00 0.00 0.00 3.11
607 2857 8.792830 AAAGGAAAAGGAAAAGGAAAAGAAAG 57.207 30.769 0.00 0.00 0.00 2.62
608 2858 9.226606 GAAAAGGAAAAGGAAAAGGAAAAGAAA 57.773 29.630 0.00 0.00 0.00 2.52
609 2859 7.827236 GGAAAAGGAAAAGGAAAAGGAAAAGAA 59.173 33.333 0.00 0.00 0.00 2.52
610 2860 7.182026 AGGAAAAGGAAAAGGAAAAGGAAAAGA 59.818 33.333 0.00 0.00 0.00 2.52
611 2861 7.338710 AGGAAAAGGAAAAGGAAAAGGAAAAG 58.661 34.615 0.00 0.00 0.00 2.27
612 2862 7.265599 AGGAAAAGGAAAAGGAAAAGGAAAA 57.734 32.000 0.00 0.00 0.00 2.29
613 2863 6.884472 AGGAAAAGGAAAAGGAAAAGGAAA 57.116 33.333 0.00 0.00 0.00 3.13
614 2864 6.884472 AAGGAAAAGGAAAAGGAAAAGGAA 57.116 33.333 0.00 0.00 0.00 3.36
615 2865 6.884472 AAAGGAAAAGGAAAAGGAAAAGGA 57.116 33.333 0.00 0.00 0.00 3.36
627 2877 3.449377 ACGCCAAAGAAAAAGGAAAAGGA 59.551 39.130 0.00 0.00 0.00 3.36
628 2878 3.555547 CACGCCAAAGAAAAAGGAAAAGG 59.444 43.478 0.00 0.00 0.00 3.11
641 2891 0.662619 TTTGCTGTCTCACGCCAAAG 59.337 50.000 0.00 0.00 0.00 2.77
700 2954 4.451096 GCGTGGTCACTTTGATAGAGAAAA 59.549 41.667 0.00 0.00 0.00 2.29
702 2956 3.585862 GCGTGGTCACTTTGATAGAGAA 58.414 45.455 0.00 0.00 0.00 2.87
703 2957 2.415491 CGCGTGGTCACTTTGATAGAGA 60.415 50.000 0.00 0.00 0.00 3.10
799 4282 3.679980 CGTGCAATCTGTACTGTAGCTTT 59.320 43.478 0.00 0.00 30.49 3.51
879 4362 0.787787 TCATCGGTTCGAAAGTTGCG 59.212 50.000 0.00 0.00 39.99 4.85
898 4381 2.574824 GTGGTGGTATTTGTAGGGGAGT 59.425 50.000 0.00 0.00 0.00 3.85
946 4429 5.175491 CGACGAGAGAATGAGTACCTAGTAC 59.825 48.000 0.00 0.00 39.10 2.73
947 4430 5.068329 TCGACGAGAGAATGAGTACCTAGTA 59.932 44.000 0.00 0.00 0.00 1.82
948 4431 4.121317 CGACGAGAGAATGAGTACCTAGT 58.879 47.826 0.00 0.00 0.00 2.57
949 4432 4.370049 TCGACGAGAGAATGAGTACCTAG 58.630 47.826 0.00 0.00 0.00 3.02
950 4433 4.397481 TCGACGAGAGAATGAGTACCTA 57.603 45.455 0.00 0.00 0.00 3.08
951 4434 3.263489 TCGACGAGAGAATGAGTACCT 57.737 47.619 0.00 0.00 0.00 3.08
952 4435 3.810941 AGATCGACGAGAGAATGAGTACC 59.189 47.826 3.01 0.00 0.00 3.34
1044 4527 2.838225 GCCGCTAGAGCCAGGGTA 60.838 66.667 0.00 0.00 37.91 3.69
1066 4549 2.226149 GAGACGGGGAGGAGGAGGAA 62.226 65.000 0.00 0.00 0.00 3.36
1078 4564 4.180946 CGCCTCTGACGAGACGGG 62.181 72.222 0.00 0.00 39.15 5.28
1447 4939 0.179018 GACTTGGCTGGTCAGTTGGT 60.179 55.000 0.00 0.00 34.23 3.67
1449 4941 1.230635 CGGACTTGGCTGGTCAGTTG 61.231 60.000 11.19 0.00 35.61 3.16
1456 4948 2.813908 GCGTACGGACTTGGCTGG 60.814 66.667 18.39 0.00 0.00 4.85
1459 4951 3.475774 CGTGCGTACGGACTTGGC 61.476 66.667 32.32 10.91 46.23 4.52
1528 5020 6.032042 AGACAAACTTAATTAAAATTCGCGCG 59.968 34.615 26.76 26.76 0.00 6.86
1588 5080 2.859526 TTACGTTACCACACGACACA 57.140 45.000 0.00 0.00 43.15 3.72
1757 5359 4.256110 TGACAATGGCAGAACTGTGATAG 58.744 43.478 0.00 0.00 0.00 2.08
1758 5360 4.256110 CTGACAATGGCAGAACTGTGATA 58.744 43.478 11.37 0.00 35.39 2.15
1759 5361 3.079578 CTGACAATGGCAGAACTGTGAT 58.920 45.455 11.37 0.00 35.39 3.06
1763 5365 5.215160 GTTTTACTGACAATGGCAGAACTG 58.785 41.667 24.73 0.00 36.86 3.16
1993 5595 4.619336 GTGTTTGTTGTCGTTTGTCATGTT 59.381 37.500 0.00 0.00 0.00 2.71
2254 5856 6.632672 GCATGGAGAGGAAAATTAGGTAGTGA 60.633 42.308 0.00 0.00 0.00 3.41
2255 5857 5.529060 GCATGGAGAGGAAAATTAGGTAGTG 59.471 44.000 0.00 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.