Multiple sequence alignment - TraesCS3D01G387800

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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 TraesCS3D01G387800 chr3D 100.000 2985 0 0 749 3733 502958458 502961442 0.000000e+00 5513.0
1 TraesCS3D01G387800 chr3D 100.000 431 0 0 1 431 502957710 502958140 0.000000e+00 797.0
2 TraesCS3D01G387800 chr3A 94.448 1513 72 6 2227 3733 641824814 641826320 0.000000e+00 2318.0
3 TraesCS3D01G387800 chr3A 94.033 419 20 5 1813 2226 641824363 641824781 6.800000e-177 630.0
4 TraesCS3D01G387800 chr3A 93.216 398 21 4 785 1179 641823002 641823396 6.950000e-162 580.0
5 TraesCS3D01G387800 chr3A 85.572 201 11 3 74 266 641822473 641822663 1.060000e-45 195.0
6 TraesCS3D01G387800 chr3A 83.981 206 17 3 1616 1821 641824137 641824326 2.290000e-42 183.0
7 TraesCS3D01G387800 chr3A 88.462 52 6 0 1519 1570 641824058 641824109 3.110000e-06 63.9
8 TraesCS3D01G387800 chr3A 96.875 32 0 1 3432 3463 597829817 597829787 7.000000e-03 52.8
9 TraesCS3D01G387800 chr3B 93.135 1515 69 16 2227 3733 664110711 664112198 0.000000e+00 2189.0
10 TraesCS3D01G387800 chr3B 88.902 874 45 24 753 1600 664109030 664109877 0.000000e+00 1029.0
11 TraesCS3D01G387800 chr3B 92.637 421 20 8 1814 2226 664110261 664110678 2.480000e-166 595.0
12 TraesCS3D01G387800 chr3B 78.808 453 31 16 3 403 664108453 664108892 1.040000e-60 244.0
13 TraesCS3D01G387800 chr7A 96.875 32 0 1 3432 3463 566028998 566028968 7.000000e-03 52.8
14 TraesCS3D01G387800 chr4A 96.875 32 0 1 3432 3463 174387645 174387615 7.000000e-03 52.8
15 TraesCS3D01G387800 chr4A 96.875 32 0 1 3432 3463 603658287 603658317 7.000000e-03 52.8


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 TraesCS3D01G387800 chr3D 502957710 502961442 3732 False 3155.00 5513 100.0000 1 3733 2 chr3D.!!$F1 3732
1 TraesCS3D01G387800 chr3A 641822473 641826320 3847 False 661.65 2318 89.9520 74 3733 6 chr3A.!!$F1 3659
2 TraesCS3D01G387800 chr3B 664108453 664112198 3745 False 1014.25 2189 88.3705 3 3733 4 chr3B.!!$F1 3730

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
47 48 0.104487 TCGTACTCGTTTTGTGCCCA 59.896 50.0 0.0 0.0 38.33 5.36 F
882 977 1.002242 AGTAGGAGGGAGGGAGGGAG 61.002 65.0 0.0 0.0 0.00 4.30 F
2188 2853 1.242076 GTTGAGTGCAAGCATCCTGT 58.758 50.0 0.0 0.0 34.01 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1183 1283 0.030603 GGGGAGGAGGAGGAGTGAAT 60.031 60.000 0.0 0.0 0.00 2.57 R
2643 3345 0.040958 GCGACAACCTGTGAGCAAAG 60.041 55.000 0.0 0.0 35.52 2.77 R
3393 4101 3.857157 TCCAGTGCCAAACTTAGAACT 57.143 42.857 0.0 0.0 36.83 3.01 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 1.706995 TAGCCCGTGACCCAACCAAA 61.707 55.000 0.00 0.00 0.00 3.28
30 31 1.130373 CGTGACCCAACCAAATCATCG 59.870 52.381 0.00 0.00 0.00 3.84
44 45 3.991605 ATCATCGTACTCGTTTTGTGC 57.008 42.857 0.00 0.00 38.33 4.57
45 46 2.063266 TCATCGTACTCGTTTTGTGCC 58.937 47.619 0.00 0.00 38.33 5.01
46 47 1.127951 CATCGTACTCGTTTTGTGCCC 59.872 52.381 0.00 0.00 38.33 5.36
47 48 0.104487 TCGTACTCGTTTTGTGCCCA 59.896 50.000 0.00 0.00 38.33 5.36
51 52 1.178534 ACTCGTTTTGTGCCCATGGG 61.179 55.000 27.87 27.87 38.57 4.00
64 69 1.307309 CATGGGCCATGGACCTGAA 59.693 57.895 36.85 18.60 45.59 3.02
69 74 1.450312 GCCATGGACCTGAACCGAG 60.450 63.158 18.40 0.00 0.00 4.63
162 175 2.072874 ATCTCATGATTGGGGCGGGG 62.073 60.000 0.00 0.00 0.00 5.73
206 230 4.803426 GCCGTCGGCTGAGGTCAG 62.803 72.222 28.98 2.37 46.69 3.51
207 231 3.374402 CCGTCGGCTGAGGTCAGT 61.374 66.667 13.88 0.00 45.45 3.41
208 232 2.179517 CGTCGGCTGAGGTCAGTC 59.820 66.667 7.08 5.18 45.45 3.51
212 236 4.803426 GGCTGAGGTCAGTCGCCG 62.803 72.222 8.74 0.00 45.45 6.46
213 237 4.057428 GCTGAGGTCAGTCGCCGT 62.057 66.667 8.74 0.00 45.45 5.68
214 238 2.179517 CTGAGGTCAGTCGCCGTC 59.820 66.667 0.00 0.00 39.09 4.79
215 239 3.669036 CTGAGGTCAGTCGCCGTCG 62.669 68.421 0.00 0.00 39.09 5.12
289 328 2.998316 TTTCCAAACAAAAGGCAGGG 57.002 45.000 0.00 0.00 0.00 4.45
393 477 3.809013 CCCTGATCCCCCAACCGG 61.809 72.222 0.00 0.00 0.00 5.28
394 478 4.506255 CCTGATCCCCCAACCGGC 62.506 72.222 0.00 0.00 0.00 6.13
395 479 3.727258 CTGATCCCCCAACCGGCA 61.727 66.667 0.00 0.00 0.00 5.69
396 480 3.020647 TGATCCCCCAACCGGCAT 61.021 61.111 0.00 0.00 0.00 4.40
397 481 2.203351 GATCCCCCAACCGGCATC 60.203 66.667 0.00 0.00 0.00 3.91
805 895 1.743589 TCTAGAGCGAGATAGGGGGA 58.256 55.000 0.00 0.00 0.00 4.81
808 898 1.710816 AGAGCGAGATAGGGGGAAAG 58.289 55.000 0.00 0.00 0.00 2.62
809 899 1.218196 AGAGCGAGATAGGGGGAAAGA 59.782 52.381 0.00 0.00 0.00 2.52
811 901 1.218196 AGCGAGATAGGGGGAAAGAGA 59.782 52.381 0.00 0.00 0.00 3.10
882 977 1.002242 AGTAGGAGGGAGGGAGGGAG 61.002 65.000 0.00 0.00 0.00 4.30
1168 1268 4.410883 TCAAGTTCTTCCTCACCAGGTAAA 59.589 41.667 0.00 0.00 41.28 2.01
1179 1279 4.991776 TCACCAGGTAAACCAATCAATCA 58.008 39.130 1.26 0.00 38.89 2.57
1180 1280 5.389520 TCACCAGGTAAACCAATCAATCAA 58.610 37.500 1.26 0.00 38.89 2.57
1182 1282 6.152661 TCACCAGGTAAACCAATCAATCAATC 59.847 38.462 1.26 0.00 38.89 2.67
1183 1283 6.015918 ACCAGGTAAACCAATCAATCAATCA 58.984 36.000 1.26 0.00 38.89 2.57
1184 1284 6.669154 ACCAGGTAAACCAATCAATCAATCAT 59.331 34.615 1.26 0.00 38.89 2.45
1185 1285 7.180766 ACCAGGTAAACCAATCAATCAATCATT 59.819 33.333 1.26 0.00 38.89 2.57
1186 1286 7.707893 CCAGGTAAACCAATCAATCAATCATTC 59.292 37.037 1.26 0.00 38.89 2.67
1187 1287 8.252417 CAGGTAAACCAATCAATCAATCATTCA 58.748 33.333 1.26 0.00 38.89 2.57
1189 1289 8.253113 GGTAAACCAATCAATCAATCATTCACT 58.747 33.333 0.00 0.00 35.64 3.41
1190 1290 9.294030 GTAAACCAATCAATCAATCATTCACTC 57.706 33.333 0.00 0.00 0.00 3.51
1192 1292 6.192773 ACCAATCAATCAATCATTCACTCCT 58.807 36.000 0.00 0.00 0.00 3.69
1193 1293 6.320672 ACCAATCAATCAATCATTCACTCCTC 59.679 38.462 0.00 0.00 0.00 3.71
1350 1469 2.750888 GCGTGGGGAATCGTTGAGC 61.751 63.158 0.00 0.00 0.00 4.26
1372 1504 1.382695 TCCGATCTGGTTCCCTCCC 60.383 63.158 3.97 0.00 39.52 4.30
1401 1538 2.832368 TTCTGCTCTGCTCTGCTCGC 62.832 60.000 0.00 0.00 0.00 5.03
1410 1547 4.166888 TCTGCTCGCTGGGGATGC 62.167 66.667 0.00 0.00 0.00 3.91
1412 1549 2.763710 TGCTCGCTGGGGATGCTA 60.764 61.111 0.00 0.00 0.00 3.49
1413 1550 2.030262 GCTCGCTGGGGATGCTAG 59.970 66.667 0.00 0.00 0.00 3.42
1418 1555 1.676384 GCTGGGGATGCTAGGCTAG 59.324 63.158 17.33 17.33 0.00 3.42
1472 1609 4.286813 ACTTCCATCTTATCTCAGGGGA 57.713 45.455 0.00 0.00 0.00 4.81
1473 1610 4.837218 ACTTCCATCTTATCTCAGGGGAT 58.163 43.478 0.00 0.00 0.00 3.85
1474 1611 5.230759 ACTTCCATCTTATCTCAGGGGATT 58.769 41.667 0.00 0.00 0.00 3.01
1476 1613 5.098575 TCCATCTTATCTCAGGGGATTCT 57.901 43.478 0.00 0.00 0.00 2.40
1477 1614 5.480710 TCCATCTTATCTCAGGGGATTCTT 58.519 41.667 0.00 0.00 0.00 2.52
1478 1615 5.913534 TCCATCTTATCTCAGGGGATTCTTT 59.086 40.000 0.00 0.00 0.00 2.52
1479 1616 6.391055 TCCATCTTATCTCAGGGGATTCTTTT 59.609 38.462 0.00 0.00 0.00 2.27
1480 1617 7.065504 CCATCTTATCTCAGGGGATTCTTTTT 58.934 38.462 0.00 0.00 0.00 1.94
1516 1655 4.632153 AGCATAATAAGAGAAATCGCCGT 58.368 39.130 0.00 0.00 0.00 5.68
1562 2021 2.745037 GTGGGTCCGTGCCTGTTA 59.255 61.111 0.00 0.00 0.00 2.41
1599 2211 4.630069 GCATTTCTTCAGCTTGAATGCATT 59.370 37.500 12.83 12.83 35.59 3.56
1604 2216 4.643334 TCTTCAGCTTGAATGCATTGCTAT 59.357 37.500 18.59 0.00 35.59 2.97
1611 2223 5.107607 GCTTGAATGCATTGCTATATTGCAC 60.108 40.000 18.59 1.63 45.31 4.57
1651 2263 2.226200 CGTTGCAATCCACATGTTCTCA 59.774 45.455 0.59 0.00 0.00 3.27
1652 2264 3.119743 CGTTGCAATCCACATGTTCTCAT 60.120 43.478 0.59 0.00 34.21 2.90
1671 2283 3.060138 TCATACTGCGTGTTTCGTTTCAC 60.060 43.478 0.00 0.00 42.13 3.18
1674 2286 2.160813 ACTGCGTGTTTCGTTTCACTTT 59.839 40.909 0.00 0.00 42.13 2.66
1679 2291 4.965158 GCGTGTTTCGTTTCACTTTCATTA 59.035 37.500 0.00 0.00 42.13 1.90
1708 2320 5.046663 GCCCTTAACCTTGATCATCCAAAAA 60.047 40.000 0.00 0.00 0.00 1.94
1767 2380 5.652994 TTCAATAAATTTGGGCGTTAGCT 57.347 34.783 0.00 0.00 44.37 3.32
1810 2423 7.337167 TGGATTTTGTGATTAATTCCCCATTG 58.663 34.615 0.00 0.00 0.00 2.82
1811 2424 7.181665 TGGATTTTGTGATTAATTCCCCATTGA 59.818 33.333 0.00 0.00 0.00 2.57
1840 2498 3.122297 TGTGCTTGTTAATTGTTGCAGC 58.878 40.909 0.00 0.00 0.00 5.25
2080 2739 5.305644 GTGTGGTAGGTTATCCATCTCATCT 59.694 44.000 0.00 0.00 36.09 2.90
2109 2771 5.218885 CGCATCACCTGTTTGTTTATGAAA 58.781 37.500 0.00 0.00 0.00 2.69
2185 2850 3.308438 AAATGTTGAGTGCAAGCATCC 57.692 42.857 0.00 0.00 34.01 3.51
2188 2853 1.242076 GTTGAGTGCAAGCATCCTGT 58.758 50.000 0.00 0.00 34.01 4.00
2190 2855 2.813754 GTTGAGTGCAAGCATCCTGTAA 59.186 45.455 0.00 0.00 34.01 2.41
2297 2996 1.466950 GCAAGCAGCGGTATGTAACAA 59.533 47.619 0.00 0.00 0.00 2.83
2310 3009 6.455646 CGGTATGTAACAACTGCTCTGATTTC 60.456 42.308 0.00 0.00 0.00 2.17
2367 3066 4.979388 CAACTATGCTGAGCTTTTTCCTC 58.021 43.478 5.83 0.00 0.00 3.71
2369 3068 4.853007 ACTATGCTGAGCTTTTTCCTCAT 58.147 39.130 5.83 0.00 38.54 2.90
2373 3072 4.874970 TGCTGAGCTTTTTCCTCATTTTC 58.125 39.130 5.83 0.00 38.54 2.29
2510 3209 6.550854 TCAAGTGTCCTTTTCATTCTCCATTT 59.449 34.615 0.00 0.00 0.00 2.32
2513 3212 7.436933 AGTGTCCTTTTCATTCTCCATTTTTC 58.563 34.615 0.00 0.00 0.00 2.29
2530 3231 6.866248 CCATTTTTCGTATAGTTTGGCAGTTT 59.134 34.615 0.00 0.00 0.00 2.66
2616 3318 1.358787 AGGTTTGCCCTTCCATGATCA 59.641 47.619 0.00 0.00 42.73 2.92
2619 3321 3.960102 GGTTTGCCCTTCCATGATCATAA 59.040 43.478 8.15 0.00 0.00 1.90
2651 3353 1.202521 TCGCTCACTCAACTTTGCTCA 60.203 47.619 0.00 0.00 0.00 4.26
2737 3439 5.049198 CAGTGACAAGTGTTGTATGATGCTT 60.049 40.000 0.00 0.00 45.52 3.91
2738 3440 5.049198 AGTGACAAGTGTTGTATGATGCTTG 60.049 40.000 0.00 0.00 45.52 4.01
2739 3441 4.161333 GACAAGTGTTGTATGATGCTTGC 58.839 43.478 0.00 0.00 45.52 4.01
2740 3442 3.057315 ACAAGTGTTGTATGATGCTTGCC 60.057 43.478 0.00 0.00 43.27 4.52
2842 3544 4.098960 AGGTATCGGTTCGATGTGTAATGT 59.901 41.667 12.35 0.00 46.43 2.71
2848 3550 3.188460 GGTTCGATGTGTAATGTTGTGCT 59.812 43.478 0.00 0.00 0.00 4.40
2971 3679 3.646162 TCTGGTGAAAGCTAGAAAGTGGA 59.354 43.478 0.00 0.00 33.76 4.02
2975 3683 3.002791 TGAAAGCTAGAAAGTGGATGCG 58.997 45.455 0.00 0.00 0.00 4.73
3076 3784 7.255569 GGGTTTAGTGCATAATAAAACTCACC 58.744 38.462 13.45 7.38 35.13 4.02
3184 3892 3.636764 GTCCAAACACTCCCTGTTGATTT 59.363 43.478 0.00 0.00 42.70 2.17
3190 3898 4.985538 ACACTCCCTGTTGATTTGTACAT 58.014 39.130 0.00 0.00 0.00 2.29
3198 3906 5.375417 TGTTGATTTGTACATGAAGCTGG 57.625 39.130 0.00 0.00 0.00 4.85
3219 3927 3.565902 GGACAGCCAACATATCTAAAGCC 59.434 47.826 0.00 0.00 0.00 4.35
3225 3933 4.217118 GCCAACATATCTAAAGCCTGATGG 59.783 45.833 0.00 0.00 34.09 3.51
3320 4028 6.596888 ACCAACATGTGTGAGAAGATATCAAG 59.403 38.462 0.00 0.00 0.00 3.02
3406 4114 2.225727 GTGGCCGAAGTTCTAAGTTTGG 59.774 50.000 10.97 10.97 43.14 3.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 0.322187 GTTGGGTCACGGGCTATGTT 60.322 55.000 0.00 0.00 0.00 2.71
2 3 1.298667 GTTGGGTCACGGGCTATGT 59.701 57.895 0.00 0.00 0.00 2.29
3 4 1.451387 GGTTGGGTCACGGGCTATG 60.451 63.158 0.00 0.00 0.00 2.23
4 5 1.493854 TTGGTTGGGTCACGGGCTAT 61.494 55.000 0.00 0.00 0.00 2.97
24 25 2.671396 GGCACAAAACGAGTACGATGAT 59.329 45.455 0.00 0.00 42.66 2.45
30 31 1.199097 CCATGGGCACAAAACGAGTAC 59.801 52.381 2.85 0.00 0.00 2.73
46 47 1.039233 GTTCAGGTCCATGGCCCATG 61.039 60.000 15.64 17.16 41.10 3.66
47 48 1.307647 GTTCAGGTCCATGGCCCAT 59.692 57.895 15.64 0.00 0.00 4.00
51 52 1.450312 CTCGGTTCAGGTCCATGGC 60.450 63.158 6.96 1.78 0.00 4.40
52 53 0.391661 CACTCGGTTCAGGTCCATGG 60.392 60.000 4.97 4.97 0.00 3.66
53 54 0.608130 TCACTCGGTTCAGGTCCATG 59.392 55.000 0.00 0.00 0.00 3.66
59 64 2.101582 CCCTATCTTCACTCGGTTCAGG 59.898 54.545 0.00 0.00 0.00 3.86
61 66 2.108168 CCCCTATCTTCACTCGGTTCA 58.892 52.381 0.00 0.00 0.00 3.18
62 67 1.202545 GCCCCTATCTTCACTCGGTTC 60.203 57.143 0.00 0.00 0.00 3.62
64 69 0.325296 TGCCCCTATCTTCACTCGGT 60.325 55.000 0.00 0.00 0.00 4.69
69 74 1.883084 CGCGTGCCCCTATCTTCAC 60.883 63.158 0.00 0.00 0.00 3.18
162 175 2.124151 AAGGTGATGATGGCCCGC 60.124 61.111 0.00 0.00 0.00 6.13
198 222 3.733960 CGACGGCGACTGACCTCA 61.734 66.667 16.62 0.00 40.82 3.86
273 309 0.033920 GCTCCCTGCCTTTTGTTTGG 59.966 55.000 0.00 0.00 35.15 3.28
286 322 5.367945 TTTGTCCGATTAATTAGCTCCCT 57.632 39.130 0.00 0.00 0.00 4.20
289 328 6.679327 AGGTTTTGTCCGATTAATTAGCTC 57.321 37.500 0.00 0.00 0.00 4.09
344 404 1.380302 GAATATGCTGGGGGCCGAT 59.620 57.895 0.00 0.00 40.92 4.18
345 405 2.836154 GAATATGCTGGGGGCCGA 59.164 61.111 0.00 0.00 40.92 5.54
346 406 2.669569 CGAATATGCTGGGGGCCG 60.670 66.667 0.00 0.00 40.92 6.13
347 407 2.985847 GCGAATATGCTGGGGGCC 60.986 66.667 0.00 0.00 40.92 5.80
348 408 2.985847 GGCGAATATGCTGGGGGC 60.986 66.667 0.00 0.00 42.22 5.80
349 409 1.302832 GAGGCGAATATGCTGGGGG 60.303 63.158 0.00 0.00 34.52 5.40
352 412 0.886490 GGTGGAGGCGAATATGCTGG 60.886 60.000 0.00 0.00 34.52 4.85
393 477 4.081030 CCGATGCCGATGCGATGC 62.081 66.667 0.00 0.00 41.78 3.91
394 478 4.081030 GCCGATGCCGATGCGATG 62.081 66.667 0.00 0.00 41.78 3.84
395 479 3.889134 ATGCCGATGCCGATGCGAT 62.889 57.895 0.00 0.00 41.78 4.58
396 480 4.607325 ATGCCGATGCCGATGCGA 62.607 61.111 0.00 0.00 41.78 5.10
397 481 4.081030 GATGCCGATGCCGATGCG 62.081 66.667 0.00 0.00 41.78 4.73
749 833 6.731448 ACTATTATAACTCTCTTGGATCCCCC 59.269 42.308 9.90 0.00 0.00 5.40
750 834 7.800300 ACTATTATAACTCTCTTGGATCCCC 57.200 40.000 9.90 0.00 0.00 4.81
751 835 9.713713 GAAACTATTATAACTCTCTTGGATCCC 57.286 37.037 9.90 0.00 0.00 3.85
805 895 8.414778 CGATTCACCCTACTTATACTTCTCTTT 58.585 37.037 0.00 0.00 0.00 2.52
808 898 6.151004 GCGATTCACCCTACTTATACTTCTC 58.849 44.000 0.00 0.00 0.00 2.87
809 899 5.010820 GGCGATTCACCCTACTTATACTTCT 59.989 44.000 0.00 0.00 0.00 2.85
811 901 4.261909 CGGCGATTCACCCTACTTATACTT 60.262 45.833 0.00 0.00 0.00 2.24
852 947 5.398012 CCCTCCCTCCTACTATTCCAAAAAG 60.398 48.000 0.00 0.00 0.00 2.27
882 977 5.278512 GCAGCACTAAATTTATAGCCTTCCC 60.279 44.000 14.75 1.49 0.00 3.97
972 1067 3.352338 CTTTCCTCCCGGACGGACG 62.352 68.421 13.13 2.36 39.60 4.79
973 1068 1.538687 TTCTTTCCTCCCGGACGGAC 61.539 60.000 13.13 0.00 39.60 4.79
1168 1268 6.192773 AGGAGTGAATGATTGATTGATTGGT 58.807 36.000 0.00 0.00 0.00 3.67
1179 1279 3.044894 GGAGGAGGAGGAGTGAATGATT 58.955 50.000 0.00 0.00 0.00 2.57
1180 1280 2.688477 GGAGGAGGAGGAGTGAATGAT 58.312 52.381 0.00 0.00 0.00 2.45
1182 1282 1.127343 GGGAGGAGGAGGAGTGAATG 58.873 60.000 0.00 0.00 0.00 2.67
1183 1283 0.030603 GGGGAGGAGGAGGAGTGAAT 60.031 60.000 0.00 0.00 0.00 2.57
1184 1284 1.392534 GGGGAGGAGGAGGAGTGAA 59.607 63.158 0.00 0.00 0.00 3.18
1185 1285 1.231751 ATGGGGAGGAGGAGGAGTGA 61.232 60.000 0.00 0.00 0.00 3.41
1186 1286 0.327000 AATGGGGAGGAGGAGGAGTG 60.327 60.000 0.00 0.00 0.00 3.51
1187 1287 0.423544 AAATGGGGAGGAGGAGGAGT 59.576 55.000 0.00 0.00 0.00 3.85
1189 1289 0.624500 CCAAATGGGGAGGAGGAGGA 60.625 60.000 0.00 0.00 0.00 3.71
1190 1290 1.925888 CCAAATGGGGAGGAGGAGG 59.074 63.158 0.00 0.00 0.00 4.30
1192 1292 2.316586 GGCCAAATGGGGAGGAGGA 61.317 63.158 0.00 0.00 37.04 3.71
1193 1293 1.878799 AAGGCCAAATGGGGAGGAGG 61.879 60.000 5.01 0.00 37.04 4.30
1288 1400 4.660938 ACCAGCTTTGACCCGGGC 62.661 66.667 24.08 14.70 0.00 6.13
1372 1504 2.103432 AGCAGAGCAGAATCAGAGGATG 59.897 50.000 0.00 0.00 32.92 3.51
1401 1538 1.835927 GCCTAGCCTAGCATCCCCAG 61.836 65.000 0.00 0.00 0.00 4.45
1410 1547 1.001860 GCATTCTCCAGCCTAGCCTAG 59.998 57.143 0.00 0.00 0.00 3.02
1412 1549 1.835693 GCATTCTCCAGCCTAGCCT 59.164 57.895 0.00 0.00 0.00 4.58
1413 1550 1.596477 CGCATTCTCCAGCCTAGCC 60.596 63.158 0.00 0.00 0.00 3.93
1418 1555 1.169034 GGGAATCGCATTCTCCAGCC 61.169 60.000 8.23 0.00 39.24 4.85
1447 1584 6.851836 TCCCCTGAGATAAGATGGAAGTAAAT 59.148 38.462 0.00 0.00 0.00 1.40
1450 1587 5.418692 TCCCCTGAGATAAGATGGAAGTA 57.581 43.478 0.00 0.00 0.00 2.24
1481 1618 6.489603 TCTTATTATGCTCCCAGACCAAAAA 58.510 36.000 0.00 0.00 0.00 1.94
1482 1619 6.069673 TCTCTTATTATGCTCCCAGACCAAAA 60.070 38.462 0.00 0.00 0.00 2.44
1483 1620 5.428457 TCTCTTATTATGCTCCCAGACCAAA 59.572 40.000 0.00 0.00 0.00 3.28
1484 1621 4.968719 TCTCTTATTATGCTCCCAGACCAA 59.031 41.667 0.00 0.00 0.00 3.67
1516 1655 8.975663 ATCTCATGCTTAATTTGAAGAGATCA 57.024 30.769 0.00 0.00 37.08 2.92
1562 2021 4.914177 AGAAATGCAAATTTCACCCCAT 57.086 36.364 13.74 0.00 41.63 4.00
1599 2211 5.430886 AGATGTGTGAAGTGCAATATAGCA 58.569 37.500 0.00 0.00 43.35 3.49
1604 2216 7.503521 TTGTTTAGATGTGTGAAGTGCAATA 57.496 32.000 0.00 0.00 0.00 1.90
1611 2223 5.171337 GCAACGTTTGTTTAGATGTGTGAAG 59.829 40.000 0.00 0.00 35.72 3.02
1651 2263 3.128349 AGTGAAACGAAACACGCAGTAT 58.872 40.909 0.00 0.00 45.86 2.12
1652 2264 2.542597 AGTGAAACGAAACACGCAGTA 58.457 42.857 0.00 0.00 45.86 2.74
1671 2283 5.510430 AGGTTAAGGGCCTCTTAATGAAAG 58.490 41.667 21.81 0.00 46.10 2.62
1674 2286 4.538490 TCAAGGTTAAGGGCCTCTTAATGA 59.462 41.667 21.81 18.91 46.10 2.57
1679 2291 2.919602 TGATCAAGGTTAAGGGCCTCTT 59.080 45.455 6.46 2.30 39.40 2.85
1724 2336 7.022055 TGAATTTCTCGCTTGTTTTTGTCTA 57.978 32.000 0.00 0.00 0.00 2.59
1737 2349 5.276348 CGCCCAAATTTATTGAATTTCTCGC 60.276 40.000 0.00 0.00 44.16 5.03
1767 2380 7.649533 AAATCCATTGCTTATGTCAGATCAA 57.350 32.000 0.00 0.00 31.99 2.57
1840 2498 6.089016 CAGCAGCATTTGTCTATGAAAACTTG 59.911 38.462 0.00 0.00 0.00 3.16
1874 2532 5.997129 TCAGTCAAGAAGTAATGCACATCAA 59.003 36.000 0.00 0.00 0.00 2.57
2080 2739 1.805943 CAAACAGGTGATGCGTGATGA 59.194 47.619 0.00 0.00 36.83 2.92
2115 2777 1.734465 GTCCAAGAAGAGGCAACATCG 59.266 52.381 0.00 0.00 41.41 3.84
2116 2778 2.783135 TGTCCAAGAAGAGGCAACATC 58.217 47.619 0.00 0.00 41.41 3.06
2119 2781 4.579869 TCTTATGTCCAAGAAGAGGCAAC 58.420 43.478 0.00 0.00 31.63 4.17
2121 2783 3.840666 ACTCTTATGTCCAAGAAGAGGCA 59.159 43.478 18.80 0.00 46.92 4.75
2122 2784 4.479786 ACTCTTATGTCCAAGAAGAGGC 57.520 45.455 18.80 0.00 46.92 4.70
2123 2785 6.293004 AGAACTCTTATGTCCAAGAAGAGG 57.707 41.667 18.80 7.86 46.92 3.69
2125 2787 6.724441 TGGTAGAACTCTTATGTCCAAGAAGA 59.276 38.462 0.00 0.00 34.22 2.87
2210 2877 5.220381 GCCAATCATCATGAATTAGCACAG 58.780 41.667 0.00 0.00 0.00 3.66
2212 2879 5.190992 TGCCAATCATCATGAATTAGCAC 57.809 39.130 8.56 0.00 0.00 4.40
2215 2882 5.533528 TCACCTGCCAATCATCATGAATTAG 59.466 40.000 0.00 0.00 0.00 1.73
2217 2884 4.283337 TCACCTGCCAATCATCATGAATT 58.717 39.130 0.00 0.00 0.00 2.17
2362 3061 7.394359 CACCTAAAGAATGGAGAAAATGAGGAA 59.606 37.037 0.00 0.00 0.00 3.36
2367 3066 7.885297 TCAACACCTAAAGAATGGAGAAAATG 58.115 34.615 0.00 0.00 0.00 2.32
2369 3068 7.201875 GGTTCAACACCTAAAGAATGGAGAAAA 60.202 37.037 0.00 0.00 43.29 2.29
2373 3072 5.629079 GGTTCAACACCTAAAGAATGGAG 57.371 43.478 0.00 0.00 43.29 3.86
2510 3209 6.621316 TTCAAACTGCCAAACTATACGAAA 57.379 33.333 0.00 0.00 0.00 3.46
2513 3212 4.851558 GCTTTCAAACTGCCAAACTATACG 59.148 41.667 0.00 0.00 0.00 3.06
2530 3231 5.587289 GGTAAAAATATGGCATCGCTTTCA 58.413 37.500 1.65 0.00 0.00 2.69
2635 3337 2.092968 ACCTGTGAGCAAAGTTGAGTGA 60.093 45.455 0.00 0.00 0.00 3.41
2643 3345 0.040958 GCGACAACCTGTGAGCAAAG 60.041 55.000 0.00 0.00 35.52 2.77
2737 3439 2.280797 GCACCTTGAGACACGGCA 60.281 61.111 0.00 0.00 0.00 5.69
2738 3440 2.280797 TGCACCTTGAGACACGGC 60.281 61.111 0.00 0.00 0.00 5.68
2739 3441 1.669115 CCTGCACCTTGAGACACGG 60.669 63.158 0.00 0.00 0.00 4.94
2740 3442 0.668706 CTCCTGCACCTTGAGACACG 60.669 60.000 0.00 0.00 0.00 4.49
2842 3544 2.158971 TCTCAACAGCACTACAGCACAA 60.159 45.455 0.00 0.00 36.85 3.33
2848 3550 4.960938 ACTTGATTCTCAACAGCACTACA 58.039 39.130 0.00 0.00 32.21 2.74
2971 3679 6.143496 CGAGACATTATAACTAGTGACGCAT 58.857 40.000 0.00 0.00 0.00 4.73
2975 3683 9.680315 AATTAGCGAGACATTATAACTAGTGAC 57.320 33.333 0.00 0.00 0.00 3.67
3198 3906 4.274459 CAGGCTTTAGATATGTTGGCTGTC 59.726 45.833 0.00 0.00 41.23 3.51
3393 4101 3.857157 TCCAGTGCCAAACTTAGAACT 57.143 42.857 0.00 0.00 36.83 3.01


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

AutoCloner maintained by Alex Coulton.