Multiple sequence alignment - TraesCS2D01G433900

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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 TraesCS2D01G433900 chr2D 100.000 4456 0 0 1 4456 545032527 545036982 0.000000e+00 8229.0
1 TraesCS2D01G433900 chr2D 82.162 185 25 6 2257 2437 545034963 545034783 7.720000e-33 152.0
2 TraesCS2D01G433900 chr2D 97.222 36 1 0 1621 1656 545034109 545034144 1.340000e-05 62.1
3 TraesCS2D01G433900 chr2D 97.222 36 1 0 1583 1618 545034147 545034182 1.340000e-05 62.1
4 TraesCS2D01G433900 chr2A 93.435 1965 97 14 2291 4233 688238427 688236473 0.000000e+00 2885.0
5 TraesCS2D01G433900 chr2A 90.380 1788 80 31 582 2299 688240615 688238850 0.000000e+00 2265.0
6 TraesCS2D01G433900 chr2A 86.081 467 28 21 2 438 688241290 688240831 6.750000e-128 468.0
7 TraesCS2D01G433900 chr2A 90.299 134 12 1 4219 4352 688236457 688236325 1.650000e-39 174.0
8 TraesCS2D01G433900 chr2A 84.667 150 15 5 2257 2402 688238281 688238426 4.650000e-30 143.0
9 TraesCS2D01G433900 chr2A 94.805 77 4 0 4380 4456 688236325 688236249 2.180000e-23 121.0
10 TraesCS2D01G433900 chr2B 94.082 1318 57 12 2474 3783 651926424 651927728 0.000000e+00 1982.0
11 TraesCS2D01G433900 chr2B 88.776 1078 52 34 582 1618 651924833 651925882 0.000000e+00 1256.0
12 TraesCS2D01G433900 chr2B 93.952 463 23 2 1785 2242 651925965 651926427 0.000000e+00 695.0
13 TraesCS2D01G433900 chr2B 87.117 489 29 15 1 464 651924272 651924751 1.420000e-144 523.0
14 TraesCS2D01G433900 chr2B 86.079 431 30 7 4042 4456 651929083 651929499 1.900000e-118 436.0
15 TraesCS2D01G433900 chr2B 89.161 286 9 8 3760 4045 651928587 651928850 1.990000e-88 337.0
16 TraesCS2D01G433900 chr2B 88.889 90 7 3 1605 1692 651925829 651925917 1.690000e-19 108.0


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 TraesCS2D01G433900 chr2D 545032527 545036982 4455 False 2784.400000 8229 98.148000 1 4456 3 chr2D.!!$F1 4455
1 TraesCS2D01G433900 chr2A 688236249 688241290 5041 True 1182.600000 2885 91.000000 2 4456 5 chr2A.!!$R1 4454
2 TraesCS2D01G433900 chr2B 651924272 651929499 5227 False 762.428571 1982 89.722286 1 4456 7 chr2B.!!$F1 4455

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
343 379 0.109342 CAGAAAGGGCACAGTGGAGT 59.891 55.000 1.84 0.0 0.00 3.85 F
501 603 0.890996 CAAACTCCTGGTGGTGAGCC 60.891 60.000 0.33 0.0 31.65 4.70 F
706 840 1.396996 ACGATGATAAAACTGCGGTGC 59.603 47.619 0.00 0.0 0.00 5.01 F
2154 2430 1.186200 GGAAAAGCCAGGGTGGAATC 58.814 55.000 0.00 0.0 40.96 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1282 1476 0.624254 TTAGAGAGGCGGAGGAGTGA 59.376 55.0 0.0 0.0 0.00 3.41 R
2017 2291 0.962489 CCTAGCCTCATACGGGACAG 59.038 60.0 0.0 0.0 0.00 3.51 R
2440 3147 1.635817 TTGCCTGAGATGCCCCTACC 61.636 60.0 0.0 0.0 0.00 3.18 R
3988 5584 0.618458 AAGCTGGGATAACTCCGCAA 59.382 50.0 0.0 0.0 43.11 4.85 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
44 47 1.799258 AAGCAGTTCAAAGCAGCCGG 61.799 55.000 0.00 0.00 0.00 6.13
119 122 1.153066 TGACCGGCAAGCAAGAACA 60.153 52.632 0.00 0.00 0.00 3.18
169 176 5.509498 AGGCAATAGCATAGAGGTGAAAAA 58.491 37.500 0.00 0.00 44.61 1.94
170 177 6.131961 AGGCAATAGCATAGAGGTGAAAAAT 58.868 36.000 0.00 0.00 44.61 1.82
202 209 4.778415 CCGTCGCCGACAGTCCTG 62.778 72.222 18.40 0.00 35.63 3.86
228 235 2.370393 GGTGAAACGCCGAGACGAC 61.370 63.158 0.00 0.00 38.12 4.34
230 237 2.127118 GAAACGCCGAGACGACGA 60.127 61.111 0.00 0.00 36.09 4.20
311 320 3.565214 TGGCGTGACCACCACCAT 61.565 61.111 5.70 0.00 46.36 3.55
343 379 0.109342 CAGAAAGGGCACAGTGGAGT 59.891 55.000 1.84 0.00 0.00 3.85
424 465 7.777910 TCTTCTCACCTTGAATAAAGTTTCCAA 59.222 33.333 0.00 0.00 33.66 3.53
427 468 5.596361 TCACCTTGAATAAAGTTTCCAAGCA 59.404 36.000 14.74 4.28 33.66 3.91
495 597 2.026641 CATATGGCAAACTCCTGGTGG 58.973 52.381 0.00 0.00 0.00 4.61
496 598 1.072266 TATGGCAAACTCCTGGTGGT 58.928 50.000 0.00 0.00 34.23 4.16
501 603 0.890996 CAAACTCCTGGTGGTGAGCC 60.891 60.000 0.33 0.00 31.65 4.70
511 613 2.343758 GGTGAGCCAGCGTCTCAA 59.656 61.111 7.08 0.00 41.66 3.02
523 625 4.539870 CAGCGTCTCAAAATCAAATGTGT 58.460 39.130 0.00 0.00 0.00 3.72
524 626 4.977963 CAGCGTCTCAAAATCAAATGTGTT 59.022 37.500 0.00 0.00 0.00 3.32
527 629 7.167302 CAGCGTCTCAAAATCAAATGTGTTAAA 59.833 33.333 0.00 0.00 0.00 1.52
528 630 7.867403 AGCGTCTCAAAATCAAATGTGTTAAAT 59.133 29.630 0.00 0.00 0.00 1.40
529 631 9.123709 GCGTCTCAAAATCAAATGTGTTAAATA 57.876 29.630 0.00 0.00 0.00 1.40
694 828 4.746535 TCAGCCCAGTAAAACGATGATA 57.253 40.909 0.00 0.00 0.00 2.15
698 832 6.027749 CAGCCCAGTAAAACGATGATAAAAC 58.972 40.000 0.00 0.00 0.00 2.43
699 833 5.944007 AGCCCAGTAAAACGATGATAAAACT 59.056 36.000 0.00 0.00 0.00 2.66
700 834 6.027749 GCCCAGTAAAACGATGATAAAACTG 58.972 40.000 0.00 0.00 34.33 3.16
701 835 6.027749 CCCAGTAAAACGATGATAAAACTGC 58.972 40.000 0.00 0.00 33.44 4.40
704 838 4.759516 AAAACGATGATAAAACTGCGGT 57.240 36.364 0.00 0.00 0.00 5.68
705 839 3.740044 AACGATGATAAAACTGCGGTG 57.260 42.857 0.00 0.00 0.00 4.94
706 840 1.396996 ACGATGATAAAACTGCGGTGC 59.603 47.619 0.00 0.00 0.00 5.01
803 955 2.882137 TGGGCAGAAAAGTAAGAAACGG 59.118 45.455 0.00 0.00 0.00 4.44
990 1162 3.238241 CGTCGTCGTTGCTAGGCG 61.238 66.667 0.00 0.00 0.00 5.52
991 1163 3.542742 GTCGTCGTTGCTAGGCGC 61.543 66.667 0.00 0.00 39.77 6.53
1254 1444 4.797349 GTCAACAGATACAAGGTACGTAGC 59.203 45.833 16.85 16.85 0.00 3.58
1257 1447 3.181503 ACAGATACAAGGTACGTAGCGTG 60.182 47.826 30.25 30.25 41.39 5.34
1282 1476 3.554342 CCTGCCGCAGCTCCCTAT 61.554 66.667 15.36 0.00 40.80 2.57
1317 1512 8.132362 CGCCTCTCTAATGGAGTAATGATATAC 58.868 40.741 0.00 0.00 42.40 1.47
1318 1513 9.196139 GCCTCTCTAATGGAGTAATGATATACT 57.804 37.037 0.00 0.00 42.40 2.12
1440 1635 2.221517 GCAATCTGCAACGCATTTTGTT 59.778 40.909 10.70 0.00 44.26 2.83
1505 1706 4.119155 TCCTTTTGGGATTGGTAGGAGAT 58.881 43.478 0.00 0.00 39.58 2.75
1527 1735 3.006752 TGTTCCCTTTGCTGCTTAAATGG 59.993 43.478 0.00 1.02 0.00 3.16
1571 1779 3.876320 GGAATCTCTGCTCCTGTTGAATC 59.124 47.826 0.00 0.00 0.00 2.52
1577 1785 1.881973 TGCTCCTGTTGAATCAGTTGC 59.118 47.619 0.00 0.00 34.02 4.17
1600 1846 8.010733 TGCTTATCCCTTCTAATTTTGGAATG 57.989 34.615 0.00 0.00 0.00 2.67
1601 1847 7.069826 TGCTTATCCCTTCTAATTTTGGAATGG 59.930 37.037 4.92 4.92 35.69 3.16
1602 1848 7.287696 GCTTATCCCTTCTAATTTTGGAATGGA 59.712 37.037 13.12 13.12 42.97 3.41
1603 1849 9.200817 CTTATCCCTTCTAATTTTGGAATGGAA 57.799 33.333 14.21 2.85 42.43 3.53
1604 1850 7.666063 ATCCCTTCTAATTTTGGAATGGAAG 57.334 36.000 14.21 6.96 42.43 3.46
1605 1851 6.561294 TCCCTTCTAATTTTGGAATGGAAGT 58.439 36.000 9.78 0.00 38.69 3.01
1606 1852 7.016296 TCCCTTCTAATTTTGGAATGGAAGTT 58.984 34.615 9.78 0.00 38.69 2.66
1607 1853 7.039082 TCCCTTCTAATTTTGGAATGGAAGTTG 60.039 37.037 9.78 0.57 38.69 3.16
1608 1854 7.039082 CCCTTCTAATTTTGGAATGGAAGTTGA 60.039 37.037 5.23 0.00 36.17 3.18
1609 1855 8.367156 CCTTCTAATTTTGGAATGGAAGTTGAA 58.633 33.333 0.00 0.00 35.93 2.69
1610 1856 9.933723 CTTCTAATTTTGGAATGGAAGTTGAAT 57.066 29.630 0.00 0.00 34.62 2.57
1716 1983 7.946237 GTGTTGAATTGCACATCTTTAATTTCG 59.054 33.333 0.00 0.00 35.81 3.46
1729 1996 1.842052 AATTTCGTGCCGGGGTAATT 58.158 45.000 2.18 0.00 0.00 1.40
1777 2046 6.101734 ACCTTCAATTTCCCAGATAGCTGATA 59.898 38.462 10.19 0.00 45.17 2.15
1954 2228 7.801783 CGAAAAAGTGTAGTATTCAGTTTTCCC 59.198 37.037 10.46 6.59 43.25 3.97
1955 2229 8.528044 AAAAAGTGTAGTATTCAGTTTTCCCA 57.472 30.769 10.46 0.00 43.25 4.37
2017 2291 3.262420 AGCTAATCCAACATGACACGAC 58.738 45.455 0.00 0.00 0.00 4.34
2021 2295 2.148916 TCCAACATGACACGACTGTC 57.851 50.000 0.00 0.00 46.34 3.51
2154 2430 1.186200 GGAAAAGCCAGGGTGGAATC 58.814 55.000 0.00 0.00 40.96 2.52
2177 2453 6.365520 TCTCTTTGCTTTAAGGGAAACTTCT 58.634 36.000 0.00 0.00 40.64 2.85
2348 3055 8.881743 GCATATAAATTTTGACATTTTGAGCCA 58.118 29.630 0.00 0.00 0.00 4.75
2419 3126 3.684788 ACTAGTGCTGTTCAAAATAGGCG 59.315 43.478 0.00 0.00 0.00 5.52
2422 3129 3.758554 AGTGCTGTTCAAAATAGGCGATT 59.241 39.130 0.00 0.00 0.00 3.34
2466 3173 1.340405 GGCATCTCAGGCAAAAGGAGA 60.340 52.381 0.00 0.00 41.50 3.71
2476 3183 4.038402 CAGGCAAAAGGAGAATGAAGTTGT 59.962 41.667 0.00 0.00 0.00 3.32
2578 3285 5.614324 TTTCAGGGGATAGACATGTACTG 57.386 43.478 0.00 0.00 0.00 2.74
2579 3286 4.265856 TCAGGGGATAGACATGTACTGT 57.734 45.455 0.00 0.00 42.15 3.55
2581 3288 5.138276 TCAGGGGATAGACATGTACTGTAC 58.862 45.833 10.98 10.98 38.54 2.90
2582 3289 5.103643 TCAGGGGATAGACATGTACTGTACT 60.104 44.000 17.98 0.00 38.54 2.73
2583 3290 6.102174 TCAGGGGATAGACATGTACTGTACTA 59.898 42.308 17.98 6.12 38.54 1.82
2584 3291 6.207025 CAGGGGATAGACATGTACTGTACTAC 59.793 46.154 17.98 7.56 38.54 2.73
2585 3292 6.066690 GGGGATAGACATGTACTGTACTACA 58.933 44.000 17.98 1.97 38.54 2.74
2586 3293 6.720288 GGGGATAGACATGTACTGTACTACAT 59.280 42.308 17.98 4.34 38.54 2.29
2587 3294 7.232941 GGGGATAGACATGTACTGTACTACATT 59.767 40.741 17.98 5.16 38.54 2.71
2588 3295 9.293404 GGGATAGACATGTACTGTACTACATTA 57.707 37.037 17.98 6.93 38.54 1.90
2651 3358 0.388520 GACGCTGATTTGGGGTTTGC 60.389 55.000 0.00 0.00 0.00 3.68
2688 3396 6.098266 ACCAGTTTCAAGCTTTCAGGTAAAAT 59.902 34.615 0.00 0.00 0.00 1.82
2689 3397 6.421801 CCAGTTTCAAGCTTTCAGGTAAAATG 59.578 38.462 0.00 1.10 0.00 2.32
2690 3398 6.980397 CAGTTTCAAGCTTTCAGGTAAAATGT 59.020 34.615 0.00 0.00 0.00 2.71
2691 3399 8.134895 CAGTTTCAAGCTTTCAGGTAAAATGTA 58.865 33.333 0.00 0.00 0.00 2.29
2732 3441 5.009610 ACAATGTGTCGCCTAATTTGTTTCT 59.990 36.000 0.00 0.00 0.00 2.52
2736 3445 5.049954 TGTGTCGCCTAATTTGTTTCTGTAC 60.050 40.000 0.00 0.00 0.00 2.90
2743 3452 8.328864 CGCCTAATTTGTTTCTGTACTATCTTC 58.671 37.037 0.00 0.00 0.00 2.87
2820 3529 3.902261 TTGCTGTGTGATTGCAACTAG 57.098 42.857 0.00 0.00 41.06 2.57
2833 3545 9.765795 GTGATTGCAACTAGGATTTATAGTACT 57.234 33.333 0.00 0.00 33.15 2.73
2862 3574 6.068461 TGTTTAGTCTATGGGGCAATAACA 57.932 37.500 0.00 0.00 0.00 2.41
2868 3580 5.652452 AGTCTATGGGGCAATAACACTTTTC 59.348 40.000 0.00 0.00 0.00 2.29
2897 3609 4.021102 TCAGGGGAAAGAAACATCTGAC 57.979 45.455 0.00 0.00 0.00 3.51
3426 4138 1.480212 TTCGCTCATGACCACCCTGT 61.480 55.000 0.00 0.00 0.00 4.00
3537 4249 7.430502 CCATGTTTCATCGATTCTTTTTAGCTC 59.569 37.037 0.00 0.00 0.00 4.09
3549 4261 3.302365 TTTTAGCTCTTGCAACATGCC 57.698 42.857 0.00 0.00 44.23 4.40
3553 4265 0.318955 GCTCTTGCAACATGCCGTTT 60.319 50.000 0.00 0.00 44.23 3.60
3554 4266 1.411394 CTCTTGCAACATGCCGTTTG 58.589 50.000 0.00 0.00 44.23 2.93
3555 4267 0.743688 TCTTGCAACATGCCGTTTGT 59.256 45.000 0.00 0.00 44.23 2.83
3557 4269 0.249238 TTGCAACATGCCGTTTGTCC 60.249 50.000 0.00 0.00 44.23 4.02
3730 4444 0.671472 CAGGCATCAGTCGTCTTGCA 60.671 55.000 8.28 0.00 36.82 4.08
3732 4446 1.482182 AGGCATCAGTCGTCTTGCATA 59.518 47.619 8.28 0.00 36.82 3.14
3745 4459 5.049474 TCGTCTTGCATAAATATCATGTGCC 60.049 40.000 7.44 0.00 35.03 5.01
3800 5396 7.004555 TGTGAACTTGTAATGTAGACTGGAT 57.995 36.000 0.00 0.00 0.00 3.41
3862 5458 4.396790 GCCATGTAAACCGATTGGAACTTA 59.603 41.667 5.81 0.00 39.21 2.24
3901 5497 2.769095 AGAGACCTTGCCTGATAGAACC 59.231 50.000 0.00 0.00 0.00 3.62
3972 5568 8.022550 GGCATTCAAAAAGTTAAATTCATTGGG 58.977 33.333 11.71 6.03 0.00 4.12
3988 5584 2.034221 GGCTCGGCACTCCCTTTT 59.966 61.111 0.00 0.00 0.00 2.27
3989 5585 1.603739 GGCTCGGCACTCCCTTTTT 60.604 57.895 0.00 0.00 0.00 1.94
4111 5955 5.478679 CGAAGGTATCCTCCTCTTGATGTAT 59.521 44.000 0.00 0.00 36.74 2.29
4181 6030 5.277825 GTTCAATCGTGGTTGTCAAATTCA 58.722 37.500 0.00 0.00 0.00 2.57
4183 6032 5.459768 TCAATCGTGGTTGTCAAATTCATG 58.540 37.500 0.00 0.00 0.00 3.07
4212 6061 5.824904 ACATTCCTTTGATCTTGATTCCG 57.175 39.130 0.00 0.00 0.00 4.30
4213 6062 5.256474 ACATTCCTTTGATCTTGATTCCGT 58.744 37.500 0.00 0.00 0.00 4.69
4214 6063 6.414732 ACATTCCTTTGATCTTGATTCCGTA 58.585 36.000 0.00 0.00 0.00 4.02
4215 6064 6.540189 ACATTCCTTTGATCTTGATTCCGTAG 59.460 38.462 0.00 0.00 0.00 3.51
4216 6065 4.442706 TCCTTTGATCTTGATTCCGTAGC 58.557 43.478 0.00 0.00 0.00 3.58
4217 6066 4.081142 TCCTTTGATCTTGATTCCGTAGCA 60.081 41.667 0.00 0.00 0.00 3.49
4218 6067 4.635765 CCTTTGATCTTGATTCCGTAGCAA 59.364 41.667 0.00 0.00 0.00 3.91
4219 6068 5.447818 CCTTTGATCTTGATTCCGTAGCAAC 60.448 44.000 0.00 0.00 0.00 4.17
4220 6069 3.531538 TGATCTTGATTCCGTAGCAACC 58.468 45.455 0.00 0.00 0.00 3.77
4221 6070 3.197766 TGATCTTGATTCCGTAGCAACCT 59.802 43.478 0.00 0.00 0.00 3.50
4222 6071 4.404394 TGATCTTGATTCCGTAGCAACCTA 59.596 41.667 0.00 0.00 0.00 3.08
4223 6072 4.386867 TCTTGATTCCGTAGCAACCTAG 57.613 45.455 0.00 0.00 0.00 3.02
4224 6073 4.021229 TCTTGATTCCGTAGCAACCTAGA 58.979 43.478 0.00 0.00 0.00 2.43
4225 6074 4.649674 TCTTGATTCCGTAGCAACCTAGAT 59.350 41.667 0.00 0.00 0.00 1.98
4238 6087 4.081420 GCAACCTAGATCCTCTTTGACTCA 60.081 45.833 0.00 0.00 0.00 3.41
4277 6170 7.621832 TGTAATGAAAGAAAGCAAACGAATG 57.378 32.000 0.00 0.00 0.00 2.67
4287 6180 1.268999 GCAAACGAATGAAGTGGCACA 60.269 47.619 21.41 0.00 0.00 4.57
4295 6188 0.396435 TGAAGTGGCACATCCGTTCT 59.604 50.000 21.41 0.00 44.52 3.01
4309 6202 7.549134 GCACATCCGTTCTAATCCAATATGATA 59.451 37.037 0.00 0.00 0.00 2.15
4369 6262 4.318332 CAAGAGGTCTGAGTGCATGTAAA 58.682 43.478 0.00 0.00 0.00 2.01
4370 6263 3.931578 AGAGGTCTGAGTGCATGTAAAC 58.068 45.455 0.00 0.00 0.00 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 23 0.386476 TGCTTTGAACTGCTTGCTGG 59.614 50.000 4.64 0.00 0.00 4.85
60 63 3.261137 AGTGCTTTCCTGGTTCCTACTAC 59.739 47.826 0.00 0.00 0.00 2.73
119 122 0.754587 TTTTTACCACGGCCCGGTTT 60.755 50.000 16.38 0.00 37.99 3.27
169 176 0.322187 ACGGCGTGCCCTTCTTAAAT 60.322 50.000 13.76 0.00 0.00 1.40
170 177 0.952010 GACGGCGTGCCCTTCTTAAA 60.952 55.000 21.19 0.00 0.00 1.52
333 369 3.181495 GCTGCTACTACTACTCCACTGTG 60.181 52.174 0.00 0.00 0.00 3.66
343 379 9.967451 AATAGAATAGATCTGCTGCTACTACTA 57.033 33.333 5.18 0.00 39.30 1.82
464 566 7.721399 AGGAGTTTGCCATATGGAGTAATAAAG 59.279 37.037 26.47 0.00 37.39 1.85
467 569 6.465751 CCAGGAGTTTGCCATATGGAGTAATA 60.466 42.308 26.47 0.83 37.39 0.98
469 571 4.385199 CCAGGAGTTTGCCATATGGAGTAA 60.385 45.833 26.47 13.39 37.39 2.24
470 572 3.136443 CCAGGAGTTTGCCATATGGAGTA 59.864 47.826 26.47 7.79 37.39 2.59
471 573 2.092212 CCAGGAGTTTGCCATATGGAGT 60.092 50.000 26.47 7.48 37.39 3.85
472 574 2.092212 ACCAGGAGTTTGCCATATGGAG 60.092 50.000 26.47 0.00 37.39 3.86
474 576 2.026641 CACCAGGAGTTTGCCATATGG 58.973 52.381 18.07 18.07 38.53 2.74
475 577 2.026641 CCACCAGGAGTTTGCCATATG 58.973 52.381 0.00 0.00 36.89 1.78
476 578 1.640670 ACCACCAGGAGTTTGCCATAT 59.359 47.619 0.00 0.00 38.69 1.78
477 579 1.072266 ACCACCAGGAGTTTGCCATA 58.928 50.000 0.00 0.00 38.69 2.74
478 580 0.540365 CACCACCAGGAGTTTGCCAT 60.540 55.000 0.00 0.00 38.69 4.40
479 581 1.152777 CACCACCAGGAGTTTGCCA 60.153 57.895 0.00 0.00 38.69 4.92
480 582 0.890996 CTCACCACCAGGAGTTTGCC 60.891 60.000 0.00 0.00 38.69 4.52
481 583 1.518903 GCTCACCACCAGGAGTTTGC 61.519 60.000 0.00 0.00 38.69 3.68
482 584 0.890996 GGCTCACCACCAGGAGTTTG 60.891 60.000 0.00 0.00 38.69 2.93
483 585 1.352622 TGGCTCACCACCAGGAGTTT 61.353 55.000 0.00 0.00 42.67 2.66
484 586 1.770110 TGGCTCACCACCAGGAGTT 60.770 57.895 0.00 0.00 42.67 3.01
495 597 1.129437 GATTTTGAGACGCTGGCTCAC 59.871 52.381 12.71 0.03 41.72 3.51
496 598 1.270785 TGATTTTGAGACGCTGGCTCA 60.271 47.619 9.61 9.61 40.41 4.26
501 603 4.539870 ACACATTTGATTTTGAGACGCTG 58.460 39.130 0.00 0.00 0.00 5.18
527 629 9.941325 TGCCTAAACAAACAAAAATGATCATAT 57.059 25.926 9.04 0.00 0.00 1.78
528 630 9.421806 CTGCCTAAACAAACAAAAATGATCATA 57.578 29.630 9.04 0.00 0.00 2.15
529 631 8.149647 TCTGCCTAAACAAACAAAAATGATCAT 58.850 29.630 1.18 1.18 0.00 2.45
530 632 7.495901 TCTGCCTAAACAAACAAAAATGATCA 58.504 30.769 0.00 0.00 0.00 2.92
531 633 7.945033 TCTGCCTAAACAAACAAAAATGATC 57.055 32.000 0.00 0.00 0.00 2.92
532 634 8.203485 TCTTCTGCCTAAACAAACAAAAATGAT 58.797 29.630 0.00 0.00 0.00 2.45
533 635 7.551585 TCTTCTGCCTAAACAAACAAAAATGA 58.448 30.769 0.00 0.00 0.00 2.57
534 636 7.769272 TCTTCTGCCTAAACAAACAAAAATG 57.231 32.000 0.00 0.00 0.00 2.32
571 673 2.945890 GCCTCCCATCCCTTTTACTGTG 60.946 54.545 0.00 0.00 0.00 3.66
704 838 3.986006 GTCGTCCGTCCACCTGCA 61.986 66.667 0.00 0.00 0.00 4.41
705 839 3.916392 CTGTCGTCCGTCCACCTGC 62.916 68.421 0.00 0.00 0.00 4.85
706 840 2.258591 CTGTCGTCCGTCCACCTG 59.741 66.667 0.00 0.00 0.00 4.00
713 856 0.887836 TCACACTAGCTGTCGTCCGT 60.888 55.000 0.00 0.00 0.00 4.69
892 1059 3.288308 CTCTGCCACGCGACCTTCT 62.288 63.158 15.93 0.00 0.00 2.85
913 1080 2.181975 CTGGATTGATTTTGGGTGGCT 58.818 47.619 0.00 0.00 0.00 4.75
1020 1208 4.416601 AACCCTCCTCCCCCTCCG 62.417 72.222 0.00 0.00 0.00 4.63
1021 1209 2.367107 GAACCCTCCTCCCCCTCC 60.367 72.222 0.00 0.00 0.00 4.30
1022 1210 1.690985 CTGAACCCTCCTCCCCCTC 60.691 68.421 0.00 0.00 0.00 4.30
1023 1211 2.456840 CTGAACCCTCCTCCCCCT 59.543 66.667 0.00 0.00 0.00 4.79
1282 1476 0.624254 TTAGAGAGGCGGAGGAGTGA 59.376 55.000 0.00 0.00 0.00 3.41
1317 1512 4.337145 AGACACCAGACAGTTACTCCTAG 58.663 47.826 0.00 0.00 0.00 3.02
1318 1513 4.333690 GAGACACCAGACAGTTACTCCTA 58.666 47.826 0.00 0.00 0.00 2.94
1505 1706 3.006752 CCATTTAAGCAGCAAAGGGAACA 59.993 43.478 3.36 0.00 38.75 3.18
1527 1735 5.418840 TCCTCCCTTTGATTGAAATGTTAGC 59.581 40.000 0.00 0.00 0.00 3.09
1571 1779 7.122650 TCCAAAATTAGAAGGGATAAGCAACTG 59.877 37.037 0.00 0.00 0.00 3.16
1577 1785 8.766994 TCCATTCCAAAATTAGAAGGGATAAG 57.233 34.615 12.55 0.00 45.32 1.73
1614 1860 7.293535 TCCATTCCAAAATTAGAAGGGGAAAAA 59.706 33.333 13.40 0.00 42.72 1.94
1615 1861 6.789959 TCCATTCCAAAATTAGAAGGGGAAAA 59.210 34.615 13.40 0.00 42.72 2.29
1616 1862 6.326970 TCCATTCCAAAATTAGAAGGGGAAA 58.673 36.000 13.40 0.00 42.72 3.13
1617 1863 5.909760 TCCATTCCAAAATTAGAAGGGGAA 58.090 37.500 13.40 0.00 42.72 3.97
1618 1864 5.544441 TCCATTCCAAAATTAGAAGGGGA 57.456 39.130 13.40 9.29 42.72 4.81
1619 1865 5.721480 ACTTCCATTCCAAAATTAGAAGGGG 59.279 40.000 13.40 7.71 42.72 4.79
1620 1866 6.857437 ACTTCCATTCCAAAATTAGAAGGG 57.143 37.500 9.17 9.17 43.60 3.95
1621 1867 7.895759 TCAACTTCCATTCCAAAATTAGAAGG 58.104 34.615 0.00 0.00 37.18 3.46
1622 1868 9.933723 ATTCAACTTCCATTCCAAAATTAGAAG 57.066 29.630 0.00 0.00 38.02 2.85
1777 2046 5.703730 TGGATTTTAAACTCCGGGTATCT 57.296 39.130 17.09 0.00 34.05 1.98
1889 2162 6.312426 CACAACTATACTCAGAAAAGCCTCAG 59.688 42.308 0.00 0.00 0.00 3.35
1954 2228 8.767085 ACAATGAACAAAGTGAAATGCTAAATG 58.233 29.630 0.00 0.00 0.00 2.32
1955 2229 8.891671 ACAATGAACAAAGTGAAATGCTAAAT 57.108 26.923 0.00 0.00 0.00 1.40
2017 2291 0.962489 CCTAGCCTCATACGGGACAG 59.038 60.000 0.00 0.00 0.00 3.51
2021 2295 2.496470 GGTTATCCTAGCCTCATACGGG 59.504 54.545 0.00 0.00 0.00 5.28
2154 2430 6.039829 ACAGAAGTTTCCCTTAAAGCAAAGAG 59.960 38.462 0.00 0.00 32.03 2.85
2177 2453 5.497464 TCCATTCTGGATAGTTTGTCACA 57.503 39.130 0.00 0.00 42.67 3.58
2223 2499 6.539324 CCACACACAAAAATAGTACGGTATG 58.461 40.000 0.00 0.00 0.00 2.39
2228 2504 4.475763 TGCCACACACAAAAATAGTACG 57.524 40.909 0.00 0.00 0.00 3.67
2278 2554 5.221165 GCAGTAAACTAGGGCTGTTCAAAAA 60.221 40.000 0.00 0.00 0.00 1.94
2327 3034 8.729805 AAAGTGGCTCAAAATGTCAAAATTTA 57.270 26.923 0.00 0.00 0.00 1.40
2416 3123 8.410912 ACCTTTTGTTATCCTAATTTAATCGCC 58.589 33.333 0.00 0.00 0.00 5.54
2422 3129 7.781219 GCCCCTACCTTTTGTTATCCTAATTTA 59.219 37.037 0.00 0.00 0.00 1.40
2440 3147 1.635817 TTGCCTGAGATGCCCCTACC 61.636 60.000 0.00 0.00 0.00 3.18
2466 3173 3.306780 CCTCCGGAGTGTACAACTTCATT 60.307 47.826 29.25 0.00 40.07 2.57
2476 3183 2.907696 TCCATTTTTCCTCCGGAGTGTA 59.092 45.455 29.25 12.25 31.21 2.90
2667 3375 7.381408 GGTACATTTTACCTGAAAGCTTGAAAC 59.619 37.037 0.00 0.00 34.82 2.78
2746 3455 2.334838 GTGTAGTGGAATGTCGTCACC 58.665 52.381 0.00 0.00 32.29 4.02
2833 3545 5.575157 TGCCCCATAGACTAAACAATGAAA 58.425 37.500 0.00 0.00 0.00 2.69
2847 3559 6.530019 AAGAAAAGTGTTATTGCCCCATAG 57.470 37.500 0.00 0.00 0.00 2.23
2862 3574 6.611236 TCTTTCCCCTGATGAAAAAGAAAAGT 59.389 34.615 0.00 0.00 34.10 2.66
2868 3580 6.160576 TGTTTCTTTCCCCTGATGAAAAAG 57.839 37.500 0.00 0.00 31.77 2.27
2897 3609 3.408634 ACATTGTCTACCGTTTTCTGGG 58.591 45.455 0.00 0.00 0.00 4.45
3317 4029 1.446791 CATCAGCCTCTCCTGCTCC 59.553 63.158 0.00 0.00 36.81 4.70
3426 4138 8.964476 AGATCTTCTTGTAAGAGTTTGTTCAA 57.036 30.769 0.00 0.00 36.22 2.69
3472 4184 6.593382 GTCTAGTACATTATCTACCCGTCGAT 59.407 42.308 0.00 0.00 0.00 3.59
3549 4261 4.811555 TCAAACATCTTCTGGACAAACG 57.188 40.909 0.00 0.00 0.00 3.60
3553 4265 4.937620 GCTACATCAAACATCTTCTGGACA 59.062 41.667 0.00 0.00 0.00 4.02
3554 4266 5.181748 AGCTACATCAAACATCTTCTGGAC 58.818 41.667 0.00 0.00 0.00 4.02
3555 4267 5.426689 AGCTACATCAAACATCTTCTGGA 57.573 39.130 0.00 0.00 0.00 3.86
3745 4459 4.395959 ACAATGCCATGAAAATGCTAGG 57.604 40.909 0.00 0.00 0.00 3.02
3862 5458 2.629617 CTCTTGTGGGCTCAAACCAAAT 59.370 45.455 0.00 0.00 40.24 2.32
3972 5568 1.581447 CAAAAAGGGAGTGCCGAGC 59.419 57.895 0.00 0.00 33.83 5.03
3988 5584 0.618458 AAGCTGGGATAACTCCGCAA 59.382 50.000 0.00 0.00 43.11 4.85
3989 5585 0.618458 AAAGCTGGGATAACTCCGCA 59.382 50.000 0.00 0.00 43.11 5.69
4077 5909 7.071321 AGAGGAGGATACCTTCGTTTGATATTT 59.929 37.037 0.00 0.00 40.73 1.40
4081 5913 4.290942 AGAGGAGGATACCTTCGTTTGAT 58.709 43.478 0.00 0.00 40.73 2.57
4205 6054 3.321111 GGATCTAGGTTGCTACGGAATCA 59.679 47.826 0.00 0.00 0.00 2.57
4223 6072 9.388506 TGATAATCTTTTGAGTCAAAGAGGATC 57.611 33.333 17.36 18.77 34.72 3.36
4224 6073 9.171877 GTGATAATCTTTTGAGTCAAAGAGGAT 57.828 33.333 17.36 17.37 34.72 3.24
4225 6074 8.156820 TGTGATAATCTTTTGAGTCAAAGAGGA 58.843 33.333 17.36 16.15 34.72 3.71
4257 6150 6.418819 CACTTCATTCGTTTGCTTTCTTTCAT 59.581 34.615 0.00 0.00 0.00 2.57
4277 6170 2.380084 TAGAACGGATGTGCCACTTC 57.620 50.000 2.25 2.25 35.94 3.01
4369 6262 4.894784 TGCACTCGATTTTAGAGGAAAGT 58.105 39.130 0.00 0.00 39.90 2.66
4370 6263 5.862924 TTGCACTCGATTTTAGAGGAAAG 57.137 39.130 0.00 0.00 39.90 2.62
4429 6322 1.936547 GCCGTCTGATTGTCAGGATTC 59.063 52.381 7.08 0.00 44.39 2.52


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

AutoCloner maintained by Alex Coulton.