Multiple sequence alignment - TraesCS3A01G389800

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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 TraesCS3A01G389800 chr3A 100.000 3813 0 0 1 3813 638205736 638201924 0.000000e+00 7042
1 TraesCS3A01G389800 chr3B 91.190 2395 136 41 1439 3804 655635241 655637589 0.000000e+00 3184
2 TraesCS3A01G389800 chr3B 88.166 1014 64 22 89 1067 655633741 655634733 0.000000e+00 1157
3 TraesCS3A01G389800 chr3B 90.991 222 16 2 1104 1325 655634735 655634952 2.880000e-76 296
4 TraesCS3A01G389800 chr3B 84.211 266 35 7 1906 2167 80773428 80773166 6.320000e-63 252
5 TraesCS3A01G389800 chr3B 87.912 91 5 2 1 86 655630775 655630864 6.740000e-18 102
6 TraesCS3A01G389800 chr3D 86.504 1519 129 40 2318 3802 496680296 496681772 0.000000e+00 1600
7 TraesCS3A01G389800 chr3D 87.952 1162 79 23 306 1436 496678275 496679406 0.000000e+00 1314
8 TraesCS3A01G389800 chr3D 87.875 866 70 18 1439 2288 496679449 496680295 0.000000e+00 985
9 TraesCS3A01G389800 chr3D 87.805 123 10 2 1 119 496677953 496678074 5.140000e-29 139
10 TraesCS3A01G389800 chr1B 83.019 265 37 8 1907 2167 486545345 486545085 2.290000e-57 233
11 TraesCS3A01G389800 chr1A 83.019 265 38 7 1907 2167 462436470 462436209 2.290000e-57 233
12 TraesCS3A01G389800 chr6B 82.642 265 39 7 1907 2167 44468466 44468205 1.070000e-55 228
13 TraesCS3A01G389800 chr1D 82.576 264 40 6 1907 2167 363281644 363281384 1.070000e-55 228


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 TraesCS3A01G389800 chr3A 638201924 638205736 3812 True 7042.00 7042 100.00000 1 3813 1 chr3A.!!$R1 3812
1 TraesCS3A01G389800 chr3B 655630775 655637589 6814 False 1184.75 3184 89.56475 1 3804 4 chr3B.!!$F1 3803
2 TraesCS3A01G389800 chr3D 496677953 496681772 3819 False 1009.50 1600 87.53400 1 3802 4 chr3D.!!$F1 3801

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
87 2967 0.179184 CGGCCAAATTTTACGGGTCG 60.179 55.0 2.24 5.07 42.52 4.79 F
483 3420 0.527817 GCGCGTCATTAGTGCTAGGT 60.528 55.0 8.43 0.00 41.45 3.08 F
1255 4248 0.602562 CATCCCCTTTTGCGCTTTCA 59.397 50.0 9.73 0.00 0.00 2.69 F
1543 4713 0.386858 CATGTTGCTGCAGTGTGCTC 60.387 55.0 16.64 0.00 45.31 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1133 4126 0.035820 GCACATCGACCAAACCCCTA 60.036 55.0 0.0 0.00 0.00 3.53 R
1436 4565 0.679002 ATGGCAGTGTCATGGCTCAC 60.679 55.0 10.0 3.83 45.51 3.51 R
2670 5867 0.321653 ATGGACAAACTCTCGGTGCC 60.322 55.0 0.0 0.00 0.00 5.01 R
2814 6011 1.021390 CCGCTCTTTGGTGCCTACTG 61.021 60.0 0.0 0.00 0.00 2.74 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
41 47 1.213296 ATCACGGGGTAGAAAGCCAT 58.787 50.000 0.00 0.00 45.66 4.40
79 85 1.132500 TGGGGAAACGGCCAAATTTT 58.868 45.000 2.24 0.00 0.00 1.82
80 86 2.037381 GTGGGGAAACGGCCAAATTTTA 59.963 45.455 2.24 0.00 0.00 1.52
87 2967 0.179184 CGGCCAAATTTTACGGGTCG 60.179 55.000 2.24 5.07 42.52 4.79
122 3011 3.951037 TGTAGTGTCCATTGCAACAGTTT 59.049 39.130 0.00 0.00 31.68 2.66
144 3037 3.165875 CATGTCGACCACCCTATAGGAT 58.834 50.000 21.07 0.00 39.89 3.24
166 3059 9.160412 AGGATTATTATTAGCAAGTACTGTCCT 57.840 33.333 0.00 0.00 0.00 3.85
193 3086 1.552792 TCATGCCGACCATACTGAACA 59.447 47.619 0.00 0.00 31.47 3.18
202 3095 4.151689 CGACCATACTGAACAAACATCGTT 59.848 41.667 0.00 0.00 0.00 3.85
211 3134 7.186804 ACTGAACAAACATCGTTAAAAGTCTG 58.813 34.615 0.00 0.00 0.00 3.51
257 3192 6.585695 ACATCAATGAGAACTTGCATTCTT 57.414 33.333 4.13 0.00 39.08 2.52
263 3198 3.251729 TGAGAACTTGCATTCTTGTGAGC 59.748 43.478 4.13 0.00 39.08 4.26
274 3209 0.588252 CTTGTGAGCTGGTTTCACCG 59.412 55.000 0.00 0.00 42.58 4.94
287 3222 4.041938 TGGTTTCACCGGAAAGTACCTAAT 59.958 41.667 9.46 0.00 43.35 1.73
292 3227 4.100498 TCACCGGAAAGTACCTAATCATCC 59.900 45.833 9.46 0.00 0.00 3.51
298 3233 2.249139 AGTACCTAATCATCCGAGGGC 58.751 52.381 0.00 0.00 34.41 5.19
300 3235 1.807814 ACCTAATCATCCGAGGGCTT 58.192 50.000 0.00 0.00 34.41 4.35
301 3236 2.972348 ACCTAATCATCCGAGGGCTTA 58.028 47.619 0.00 0.00 34.41 3.09
308 3243 1.115467 ATCCGAGGGCTTAGTGTCAG 58.885 55.000 0.00 0.00 0.00 3.51
325 3260 6.058183 AGTGTCAGGCCTAAATGATAATGTC 58.942 40.000 3.98 0.00 0.00 3.06
421 3358 7.621428 AACAAGATTATCATCAACCACTCTG 57.379 36.000 0.00 0.00 0.00 3.35
482 3419 1.215655 GGCGCGTCATTAGTGCTAGG 61.216 60.000 5.47 0.00 43.87 3.02
483 3420 0.527817 GCGCGTCATTAGTGCTAGGT 60.528 55.000 8.43 0.00 41.45 3.08
484 3421 1.268896 GCGCGTCATTAGTGCTAGGTA 60.269 52.381 8.43 0.00 41.45 3.08
485 3422 2.607282 GCGCGTCATTAGTGCTAGGTAT 60.607 50.000 8.43 0.00 41.45 2.73
486 3423 3.365666 GCGCGTCATTAGTGCTAGGTATA 60.366 47.826 8.43 0.00 41.45 1.47
487 3424 4.156915 CGCGTCATTAGTGCTAGGTATAC 58.843 47.826 0.00 0.00 0.00 1.47
549 3489 4.942090 GGTACGACGTCAACCGAA 57.058 55.556 18.30 0.00 40.70 4.30
576 3516 1.080366 TGGCCGACATACACGTCAC 60.080 57.895 0.00 0.00 35.54 3.67
590 3530 1.652563 GTCACAGTTTGGTTCGGCC 59.347 57.895 0.00 0.00 37.90 6.13
609 3549 2.175078 GTACTCTCGCGTGCACGA 59.825 61.111 41.19 21.53 43.02 4.35
671 3612 1.039233 CGTAGTCCACATACCCCGGT 61.039 60.000 0.00 0.00 0.00 5.28
854 3817 2.363147 GAGACCCTGCGTCCTCCT 60.363 66.667 0.00 0.00 43.08 3.69
1072 4038 4.787280 CTCCCCTCCTGCGGTCCT 62.787 72.222 0.00 0.00 0.00 3.85
1133 4126 2.717639 AGATGCGTGCCCTAATTTCT 57.282 45.000 0.00 0.00 0.00 2.52
1248 4241 0.817013 TGCGATTCATCCCCTTTTGC 59.183 50.000 0.00 0.00 0.00 3.68
1255 4248 0.602562 CATCCCCTTTTGCGCTTTCA 59.397 50.000 9.73 0.00 0.00 2.69
1269 4262 2.666026 GCTTTCAGGCTTGTTTAGTGC 58.334 47.619 0.00 0.00 0.00 4.40
1280 4273 4.576463 GCTTGTTTAGTGCCTGCTATGTAT 59.424 41.667 0.00 0.00 0.00 2.29
1281 4274 5.504665 GCTTGTTTAGTGCCTGCTATGTATG 60.505 44.000 0.00 0.00 0.00 2.39
1283 4276 5.739959 TGTTTAGTGCCTGCTATGTATGAA 58.260 37.500 0.00 0.00 0.00 2.57
1284 4277 5.817296 TGTTTAGTGCCTGCTATGTATGAAG 59.183 40.000 0.00 0.00 0.00 3.02
1285 4278 5.614324 TTAGTGCCTGCTATGTATGAAGT 57.386 39.130 0.00 0.00 0.00 3.01
1286 4279 6.724893 TTAGTGCCTGCTATGTATGAAGTA 57.275 37.500 0.00 0.00 0.00 2.24
1287 4280 5.815233 AGTGCCTGCTATGTATGAAGTAT 57.185 39.130 0.00 0.00 0.00 2.12
1288 4281 5.788450 AGTGCCTGCTATGTATGAAGTATC 58.212 41.667 0.00 0.00 0.00 2.24
1315 4308 2.191786 TATCCTGGTGCCACCGGTTG 62.192 60.000 21.05 1.36 43.22 3.77
1356 4353 4.271696 TCTGTGAGGGTGTTATCTGTTG 57.728 45.455 0.00 0.00 0.00 3.33
1357 4354 3.646162 TCTGTGAGGGTGTTATCTGTTGT 59.354 43.478 0.00 0.00 0.00 3.32
1358 4355 4.102524 TCTGTGAGGGTGTTATCTGTTGTT 59.897 41.667 0.00 0.00 0.00 2.83
1381 4510 4.934001 TGTACTTGTGGTTGTCGTTTGTTA 59.066 37.500 0.00 0.00 0.00 2.41
1400 4529 2.400911 CATGTCAGCATGCGATGGT 58.599 52.632 13.01 0.00 44.87 3.55
1436 4565 2.019897 GCCGGCCAAATGATTCCTGG 62.020 60.000 18.11 0.00 0.00 4.45
1464 4633 1.550524 TGACACTGCCATCTGTAGGTC 59.449 52.381 0.00 0.00 31.95 3.85
1492 4662 9.073475 AGTTGCTAGTTATGTTGGTTGATAAAA 57.927 29.630 0.00 0.00 0.00 1.52
1516 4686 5.494632 AAAACAGTAAACAACCTCGAAGG 57.505 39.130 0.00 0.00 42.49 3.46
1536 4706 2.540931 GGTTTGTTTCATGTTGCTGCAG 59.459 45.455 10.11 10.11 0.00 4.41
1543 4713 0.386858 CATGTTGCTGCAGTGTGCTC 60.387 55.000 16.64 0.00 45.31 4.26
1551 4721 2.281276 CAGTGTGCTCTGCAGGCA 60.281 61.111 21.35 21.35 40.08 4.75
1552 4722 1.674651 CAGTGTGCTCTGCAGGCAT 60.675 57.895 25.84 12.59 40.08 4.40
1553 4723 1.074423 AGTGTGCTCTGCAGGCATT 59.926 52.632 25.84 15.38 40.08 3.56
1554 4724 1.211969 GTGTGCTCTGCAGGCATTG 59.788 57.895 25.84 9.36 40.08 2.82
1601 4788 4.207019 GTGTTTTGGACAAAGAGCATTTCG 59.793 41.667 0.00 0.00 40.65 3.46
1603 4790 4.488126 TTTGGACAAAGAGCATTTCGAG 57.512 40.909 0.00 0.00 0.00 4.04
1608 4795 4.676924 GGACAAAGAGCATTTCGAGTTTTG 59.323 41.667 0.00 0.00 0.00 2.44
1662 4849 6.259550 AGACAAATTGACTCTTGCATTACC 57.740 37.500 0.00 0.00 0.00 2.85
1675 4862 9.289782 ACTCTTGCATTACCTGGAATAATAATC 57.710 33.333 0.00 0.00 34.39 1.75
1695 4885 1.098050 GCATAGCTGGGTCTGTTTGG 58.902 55.000 0.00 0.00 0.00 3.28
1707 4897 1.071699 TCTGTTTGGGTAGCGCTCTTT 59.928 47.619 16.34 0.00 0.00 2.52
1738 4928 5.163488 TGTCTAGTTTTCTCGGTCACTTTCA 60.163 40.000 0.00 0.00 0.00 2.69
1757 4947 7.226720 CACTTTCATAGGTTGTTACACTCTGTT 59.773 37.037 0.00 0.00 0.00 3.16
1770 4960 2.547211 CACTCTGTTTGCTGTTCTGAGG 59.453 50.000 0.00 0.00 33.56 3.86
1776 4966 1.527034 TTGCTGTTCTGAGGCATCAC 58.473 50.000 0.00 0.00 35.84 3.06
1777 4967 0.689055 TGCTGTTCTGAGGCATCACT 59.311 50.000 0.00 0.00 0.00 3.41
1778 4968 1.085091 GCTGTTCTGAGGCATCACTG 58.915 55.000 0.00 0.00 0.00 3.66
1779 4969 1.338484 GCTGTTCTGAGGCATCACTGA 60.338 52.381 0.00 0.00 0.00 3.41
1780 4970 2.680221 GCTGTTCTGAGGCATCACTGAT 60.680 50.000 0.00 0.00 0.00 2.90
1781 4971 3.607741 CTGTTCTGAGGCATCACTGATT 58.392 45.455 0.00 0.00 0.00 2.57
1782 4972 3.603532 TGTTCTGAGGCATCACTGATTC 58.396 45.455 0.00 0.00 0.00 2.52
1783 4973 3.008266 TGTTCTGAGGCATCACTGATTCA 59.992 43.478 0.00 0.00 0.00 2.57
1824 5014 2.501723 TCTCTGGGCAATCCTAGTGTTC 59.498 50.000 0.00 0.00 41.33 3.18
1868 5058 6.860790 TGTAACATCCCTGTACACATCTTA 57.139 37.500 0.00 0.00 33.36 2.10
1869 5059 6.636705 TGTAACATCCCTGTACACATCTTAC 58.363 40.000 0.00 0.00 33.36 2.34
1871 5061 7.616542 TGTAACATCCCTGTACACATCTTACTA 59.383 37.037 0.00 0.00 33.36 1.82
1872 5062 6.466885 ACATCCCTGTACACATCTTACTAC 57.533 41.667 0.00 0.00 32.49 2.73
1873 5063 5.955959 ACATCCCTGTACACATCTTACTACA 59.044 40.000 0.00 0.00 32.49 2.74
1874 5064 6.096987 ACATCCCTGTACACATCTTACTACAG 59.903 42.308 0.00 0.00 37.09 2.74
1958 5148 2.087646 GGCAACTTGGATGAGAAGGTC 58.912 52.381 0.00 0.00 0.00 3.85
1994 5184 7.172361 GTCTTGTATGAGATTCTTATTCAGGCC 59.828 40.741 0.00 0.00 0.00 5.19
2082 5272 2.223782 GCTGAGTATGAGACAGAGGCAG 60.224 54.545 0.00 0.00 34.07 4.85
2169 5359 4.854399 TGCGGTATGTTTCTTCTTTTGTG 58.146 39.130 0.00 0.00 0.00 3.33
2230 5420 5.838529 ACCTTGCAAATTAACACTGGTTAC 58.161 37.500 0.00 0.00 39.14 2.50
2240 5430 7.707774 ATTAACACTGGTTACAAATTGCAAC 57.292 32.000 0.00 0.59 39.14 4.17
2244 5434 5.105554 ACACTGGTTACAAATTGCAACTTGA 60.106 36.000 25.93 7.99 0.00 3.02
2255 5449 3.435105 TGCAACTTGATTGGAACACAC 57.565 42.857 0.00 0.00 39.29 3.82
2306 5500 7.818446 ACCGTGTATACATATGTGTGTTTTGTA 59.182 33.333 18.81 0.00 39.39 2.41
2307 5501 8.822855 CCGTGTATACATATGTGTGTTTTGTAT 58.177 33.333 18.81 3.11 39.39 2.29
2342 5536 7.117956 GCAAGGTCTAATCCCTAAATTCGTATC 59.882 40.741 0.00 0.00 0.00 2.24
2359 5553 5.938322 TCGTATCAATTTTGACAGCTTTCC 58.062 37.500 0.00 0.00 40.49 3.13
2374 5568 0.882927 TTTCCGGACAAGACAAGCCG 60.883 55.000 1.83 0.00 43.20 5.52
2461 5655 6.463360 TCAGTTTGTGCATTCTAGTGATACA 58.537 36.000 0.00 0.00 0.00 2.29
2617 5814 6.328410 TCCAGGATACATGACTTGATCTCATT 59.672 38.462 0.00 0.00 41.41 2.57
2618 5815 6.427242 CCAGGATACATGACTTGATCTCATTG 59.573 42.308 0.00 0.00 41.41 2.82
2636 5833 8.099364 TCTCATTGTGTTCTATTGTTTTCTCC 57.901 34.615 0.00 0.00 0.00 3.71
2670 5867 4.082523 ACCTCGACCCGTGCATGG 62.083 66.667 18.73 18.73 0.00 3.66
2794 5991 2.025037 TGGAGCTATGAGGCAACCAATT 60.025 45.455 0.00 0.00 37.72 2.32
2814 6011 6.884836 CCAATTATTTACCCATCCTACTAGGC 59.115 42.308 0.00 0.00 34.61 3.93
2815 6012 7.458397 CAATTATTTACCCATCCTACTAGGCA 58.542 38.462 0.00 0.00 34.61 4.75
2935 6132 4.403113 TGCACTTCATTTCCATGCATGTAT 59.597 37.500 24.58 12.26 41.18 2.29
2953 6150 6.572509 GCATGTATATAGGGCTGGTATATCCG 60.573 46.154 0.00 0.00 39.52 4.18
3050 6247 3.384467 AGCCTGCTAGATCTGTTCTCTTC 59.616 47.826 5.18 0.00 35.79 2.87
3078 6281 6.756074 TGGAAAATAAAGAAATGCAATAGCGG 59.244 34.615 0.00 0.00 46.23 5.52
3104 6309 2.359230 GCACCCCTGCTGACTCAC 60.359 66.667 0.00 0.00 40.63 3.51
3156 6361 4.700213 TGAGTTATTCCTAAAGTGCCTTGC 59.300 41.667 0.00 0.00 0.00 4.01
3157 6362 4.923415 AGTTATTCCTAAAGTGCCTTGCT 58.077 39.130 0.00 0.00 0.00 3.91
3209 6414 1.931841 CCAGCAGATGTTGATGTCTCG 59.068 52.381 0.00 0.00 41.61 4.04
3216 6421 1.248101 TGTTGATGTCTCGGCTCCGA 61.248 55.000 10.84 10.84 46.87 4.55
3267 6472 3.244561 ACTGTCCTATGTTTGTGTCCCTG 60.245 47.826 0.00 0.00 0.00 4.45
3268 6473 2.084546 GTCCTATGTTTGTGTCCCTGC 58.915 52.381 0.00 0.00 0.00 4.85
3271 6476 2.238646 CCTATGTTTGTGTCCCTGCCTA 59.761 50.000 0.00 0.00 0.00 3.93
3272 6477 3.117888 CCTATGTTTGTGTCCCTGCCTAT 60.118 47.826 0.00 0.00 0.00 2.57
3273 6478 2.489938 TGTTTGTGTCCCTGCCTATC 57.510 50.000 0.00 0.00 0.00 2.08
3348 6569 4.379499 GCACCTTGTTGTATTACTTGGCTC 60.379 45.833 0.00 0.00 0.00 4.70
3459 6685 2.102252 CTCTGCCCAGTACATCTCCTTC 59.898 54.545 0.00 0.00 0.00 3.46
3474 6700 6.892456 ACATCTCCTTCCTTTTCTTTAATCCC 59.108 38.462 0.00 0.00 0.00 3.85
3581 6814 4.805719 GCTCGCGGATTAATGATCATATCA 59.194 41.667 9.04 0.00 44.55 2.15
3645 6878 4.785658 GCACTCGAATGATCATTGCTCTTG 60.786 45.833 25.37 15.14 0.00 3.02
3716 6951 1.829533 CTGTGTTTGTGGCCCTGCT 60.830 57.895 0.00 0.00 0.00 4.24
3721 6956 1.202989 TGTTTGTGGCCCTGCTTATCA 60.203 47.619 0.00 0.00 0.00 2.15
3727 6962 1.098050 GGCCCTGCTTATCAACACAG 58.902 55.000 0.00 0.00 0.00 3.66
3742 6977 3.744940 ACACAGTTGAATCCCCATCAT 57.255 42.857 0.00 0.00 0.00 2.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 53 0.969917 TTCCCCACATTTCCCGCATG 60.970 55.000 0.00 0.00 0.00 4.06
79 85 5.849510 ACAAATCATTATCATCGACCCGTA 58.150 37.500 0.00 0.00 0.00 4.02
80 86 4.703897 ACAAATCATTATCATCGACCCGT 58.296 39.130 0.00 0.00 0.00 5.28
87 2967 9.888878 CAATGGACACTACAAATCATTATCATC 57.111 33.333 0.00 0.00 0.00 2.92
122 3011 2.176148 TCCTATAGGGTGGTCGACATGA 59.824 50.000 18.97 0.00 36.25 3.07
178 3071 3.062099 CGATGTTTGTTCAGTATGGTCGG 59.938 47.826 0.00 0.00 36.16 4.79
186 3079 7.065324 TCAGACTTTTAACGATGTTTGTTCAGT 59.935 33.333 0.00 0.00 0.00 3.41
237 3160 5.532032 TCACAAGAATGCAAGTTCTCATTGA 59.468 36.000 3.10 4.24 37.46 2.57
243 3166 3.252701 CAGCTCACAAGAATGCAAGTTCT 59.747 43.478 0.00 0.00 40.05 3.01
244 3167 3.562505 CAGCTCACAAGAATGCAAGTTC 58.437 45.455 0.00 0.00 0.00 3.01
247 3170 1.884579 ACCAGCTCACAAGAATGCAAG 59.115 47.619 0.00 0.00 0.00 4.01
251 3186 3.893720 GTGAAACCAGCTCACAAGAATG 58.106 45.455 0.00 0.00 42.32 2.67
274 3209 4.262506 CCCTCGGATGATTAGGTACTTTCC 60.263 50.000 0.00 0.00 41.75 3.13
275 3210 4.799917 GCCCTCGGATGATTAGGTACTTTC 60.800 50.000 0.00 0.00 41.75 2.62
287 3222 1.112113 GACACTAAGCCCTCGGATGA 58.888 55.000 0.00 0.00 0.00 2.92
292 3227 1.153549 GCCTGACACTAAGCCCTCG 60.154 63.158 0.00 0.00 0.00 4.63
298 3233 7.716998 ACATTATCATTTAGGCCTGACACTAAG 59.283 37.037 17.99 0.00 31.48 2.18
300 3235 7.071196 AGACATTATCATTTAGGCCTGACACTA 59.929 37.037 17.99 0.00 0.00 2.74
301 3236 6.006275 ACATTATCATTTAGGCCTGACACT 57.994 37.500 17.99 0.00 0.00 3.55
308 3243 8.416329 ACAATGAAAGACATTATCATTTAGGCC 58.584 33.333 0.00 0.00 46.01 5.19
325 3260 3.557577 TGTCGCAATGGACAATGAAAG 57.442 42.857 2.80 0.00 43.55 2.62
421 3358 0.108472 GCCAACCACCCGTAGAGTAC 60.108 60.000 0.00 0.00 0.00 2.73
483 3420 9.866798 CGATGACACTATACTAGTACAGGTATA 57.133 37.037 12.69 13.53 37.23 1.47
484 3421 7.333921 GCGATGACACTATACTAGTACAGGTAT 59.666 40.741 12.69 12.90 37.23 2.73
485 3422 6.648310 GCGATGACACTATACTAGTACAGGTA 59.352 42.308 12.69 0.00 37.23 3.08
486 3423 5.469421 GCGATGACACTATACTAGTACAGGT 59.531 44.000 12.69 7.44 37.23 4.00
487 3424 5.106634 GGCGATGACACTATACTAGTACAGG 60.107 48.000 12.69 4.49 37.23 4.00
490 3427 6.017275 ACAAGGCGATGACACTATACTAGTAC 60.017 42.308 4.31 0.00 37.23 2.73
491 3428 6.060136 ACAAGGCGATGACACTATACTAGTA 58.940 40.000 4.77 4.77 37.23 1.82
492 3429 4.888239 ACAAGGCGATGACACTATACTAGT 59.112 41.667 0.00 0.00 40.28 2.57
493 3430 5.440234 ACAAGGCGATGACACTATACTAG 57.560 43.478 0.26 0.00 0.00 2.57
508 3448 2.780643 CTGCATGTCGACAAGGCG 59.219 61.111 28.87 22.33 34.33 5.52
546 3486 2.024868 TCGGCCACATCACGTTTCG 61.025 57.895 2.24 0.00 0.00 3.46
549 3489 0.248012 TATGTCGGCCACATCACGTT 59.752 50.000 19.83 3.87 42.62 3.99
576 3516 1.301874 TACCGGCCGAACCAAACTG 60.302 57.895 30.73 8.96 39.03 3.16
590 3530 2.874780 GTGCACGCGAGAGTACCG 60.875 66.667 15.93 0.00 31.78 4.02
763 3720 1.364171 CGCCTCGAGATTCGGGAAT 59.636 57.895 15.71 0.00 44.60 3.01
766 3723 4.951963 GCCGCCTCGAGATTCGGG 62.952 72.222 28.61 17.55 40.73 5.14
854 3817 3.798650 CGAATTGCGGCGCAGGAA 61.799 61.111 34.19 21.25 40.61 3.36
958 3924 3.151022 GCGTGGAGGAGGAGGAGG 61.151 72.222 0.00 0.00 0.00 4.30
959 3925 3.151022 GGCGTGGAGGAGGAGGAG 61.151 72.222 0.00 0.00 0.00 3.69
960 3926 4.779733 GGGCGTGGAGGAGGAGGA 62.780 72.222 0.00 0.00 0.00 3.71
961 3927 4.787280 AGGGCGTGGAGGAGGAGG 62.787 72.222 0.00 0.00 0.00 4.30
1094 4060 5.539582 TCTAATTCAATCCGAACCAAACG 57.460 39.130 0.00 0.00 36.12 3.60
1095 4061 5.743872 GCATCTAATTCAATCCGAACCAAAC 59.256 40.000 0.00 0.00 36.12 2.93
1096 4062 5.448496 CGCATCTAATTCAATCCGAACCAAA 60.448 40.000 0.00 0.00 36.12 3.28
1097 4063 4.035091 CGCATCTAATTCAATCCGAACCAA 59.965 41.667 0.00 0.00 36.12 3.67
1098 4064 3.559655 CGCATCTAATTCAATCCGAACCA 59.440 43.478 0.00 0.00 36.12 3.67
1099 4065 3.560068 ACGCATCTAATTCAATCCGAACC 59.440 43.478 0.00 0.00 36.12 3.62
1100 4066 4.518217 CACGCATCTAATTCAATCCGAAC 58.482 43.478 0.00 0.00 36.12 3.95
1101 4067 3.002246 GCACGCATCTAATTCAATCCGAA 59.998 43.478 0.00 0.00 38.22 4.30
1102 4068 2.543848 GCACGCATCTAATTCAATCCGA 59.456 45.455 0.00 0.00 0.00 4.55
1133 4126 0.035820 GCACATCGACCAAACCCCTA 60.036 55.000 0.00 0.00 0.00 3.53
1248 4241 2.918131 GCACTAAACAAGCCTGAAAGCG 60.918 50.000 0.00 0.00 38.01 4.68
1269 4262 7.658982 ACATTGTGATACTTCATACATAGCAGG 59.341 37.037 0.00 0.00 33.56 4.85
1280 4273 6.823182 CACCAGGATAACATTGTGATACTTCA 59.177 38.462 0.00 0.00 0.00 3.02
1281 4274 6.238484 GCACCAGGATAACATTGTGATACTTC 60.238 42.308 0.00 0.00 0.00 3.01
1283 4276 5.126067 GCACCAGGATAACATTGTGATACT 58.874 41.667 0.00 0.00 0.00 2.12
1284 4277 4.275936 GGCACCAGGATAACATTGTGATAC 59.724 45.833 0.00 0.00 0.00 2.24
1285 4278 4.080072 TGGCACCAGGATAACATTGTGATA 60.080 41.667 0.00 0.00 0.00 2.15
1286 4279 3.290710 GGCACCAGGATAACATTGTGAT 58.709 45.455 0.00 0.00 0.00 3.06
1287 4280 2.040947 TGGCACCAGGATAACATTGTGA 59.959 45.455 0.00 0.00 0.00 3.58
1288 4281 2.164219 GTGGCACCAGGATAACATTGTG 59.836 50.000 6.29 0.00 0.00 3.33
1325 4318 4.536765 ACACCCTCACAGAAGAATTGTTT 58.463 39.130 0.00 0.00 0.00 2.83
1326 4319 4.170468 ACACCCTCACAGAAGAATTGTT 57.830 40.909 0.00 0.00 0.00 2.83
1328 4321 6.093219 CAGATAACACCCTCACAGAAGAATTG 59.907 42.308 0.00 0.00 0.00 2.32
1329 4322 6.176183 CAGATAACACCCTCACAGAAGAATT 58.824 40.000 0.00 0.00 0.00 2.17
1330 4323 5.249393 ACAGATAACACCCTCACAGAAGAAT 59.751 40.000 0.00 0.00 0.00 2.40
1356 4353 4.092816 CAAACGACAACCACAAGTACAAC 58.907 43.478 0.00 0.00 0.00 3.32
1357 4354 3.752222 ACAAACGACAACCACAAGTACAA 59.248 39.130 0.00 0.00 0.00 2.41
1358 4355 3.336468 ACAAACGACAACCACAAGTACA 58.664 40.909 0.00 0.00 0.00 2.90
1400 4529 6.535540 TGGCCGGCAAATTAGAACTATATAA 58.464 36.000 30.85 0.00 0.00 0.98
1436 4565 0.679002 ATGGCAGTGTCATGGCTCAC 60.679 55.000 10.00 3.83 45.51 3.51
1464 4633 4.688879 TCAACCAACATAACTAGCAACTCG 59.311 41.667 0.00 0.00 0.00 4.18
1509 4679 3.730715 GCAACATGAAACAAACCTTCGAG 59.269 43.478 0.00 0.00 0.00 4.04
1512 4682 3.245990 GCAGCAACATGAAACAAACCTTC 59.754 43.478 0.00 0.00 0.00 3.46
1516 4686 3.000523 CACTGCAGCAACATGAAACAAAC 59.999 43.478 15.27 0.00 0.00 2.93
1536 4706 1.211969 CAATGCCTGCAGAGCACAC 59.788 57.895 25.68 6.07 44.40 3.82
1546 4716 7.458409 AAGGATAATTATACTGCAATGCCTG 57.542 36.000 11.09 0.00 0.00 4.85
1547 4717 9.759473 ATTAAGGATAATTATACTGCAATGCCT 57.241 29.630 11.09 1.26 0.00 4.75
1548 4718 9.793252 CATTAAGGATAATTATACTGCAATGCC 57.207 33.333 21.29 8.36 30.02 4.40
1549 4719 9.793252 CCATTAAGGATAATTATACTGCAATGC 57.207 33.333 24.44 0.00 41.22 3.56
1553 4723 9.860650 ACAACCATTAAGGATAATTATACTGCA 57.139 29.630 11.09 1.56 41.22 4.41
1564 4751 6.778069 TGTCCAAAACACAACCATTAAGGATA 59.222 34.615 0.00 0.00 34.96 2.59
1568 4755 7.038659 TCTTTGTCCAAAACACAACCATTAAG 58.961 34.615 0.00 0.00 37.70 1.85
1601 4788 4.021544 TCCCCAAATACATGTGCAAAACTC 60.022 41.667 9.11 0.00 0.00 3.01
1603 4790 4.264460 TCCCCAAATACATGTGCAAAAC 57.736 40.909 9.11 0.00 0.00 2.43
1608 4795 4.649218 AGGTAATTCCCCAAATACATGTGC 59.351 41.667 9.11 0.00 36.75 4.57
1655 4842 6.494893 TGCGATTATTATTCCAGGTAATGC 57.505 37.500 0.00 0.00 0.00 3.56
1662 4849 5.295292 CCCAGCTATGCGATTATTATTCCAG 59.705 44.000 0.00 0.00 0.00 3.86
1675 4862 0.729116 CAAACAGACCCAGCTATGCG 59.271 55.000 0.00 0.00 0.00 4.73
1695 4885 3.522553 ACAGTGATAAAAGAGCGCTACC 58.477 45.455 11.50 0.00 30.86 3.18
1707 4897 6.208007 TGACCGAGAAAACTAGACAGTGATAA 59.792 38.462 0.00 0.00 34.36 1.75
1738 4928 5.470098 CAGCAAACAGAGTGTAACAACCTAT 59.530 40.000 0.00 0.00 41.43 2.57
1757 4947 1.072806 AGTGATGCCTCAGAACAGCAA 59.927 47.619 0.00 0.00 40.46 3.91
1770 4960 3.624410 TGCATACAGTGAATCAGTGATGC 59.376 43.478 28.33 28.33 42.05 3.91
1776 4966 5.761726 ACACCATATGCATACAGTGAATCAG 59.238 40.000 30.51 13.53 0.00 2.90
1777 4967 5.683681 ACACCATATGCATACAGTGAATCA 58.316 37.500 30.51 3.39 0.00 2.57
1778 4968 6.484643 AGAACACCATATGCATACAGTGAATC 59.515 38.462 30.51 26.28 0.00 2.52
1779 4969 6.359804 AGAACACCATATGCATACAGTGAAT 58.640 36.000 30.51 22.30 0.00 2.57
1780 4970 5.744171 AGAACACCATATGCATACAGTGAA 58.256 37.500 30.51 5.40 0.00 3.18
1781 4971 5.129320 AGAGAACACCATATGCATACAGTGA 59.871 40.000 30.51 6.07 0.00 3.41
1782 4972 5.363101 AGAGAACACCATATGCATACAGTG 58.637 41.667 25.57 25.57 0.00 3.66
1783 4973 5.365025 AGAGAGAACACCATATGCATACAGT 59.635 40.000 8.99 6.60 0.00 3.55
1824 5014 9.931210 GTTACATAAATCATAGAAAAAGGACCG 57.069 33.333 0.00 0.00 0.00 4.79
1868 5058 8.582437 TGCTTAAGTAATACAACAGACTGTAGT 58.418 33.333 8.91 0.00 35.32 2.73
1869 5059 8.981724 TGCTTAAGTAATACAACAGACTGTAG 57.018 34.615 8.91 0.00 35.32 2.74
1871 5061 8.721478 CATTGCTTAAGTAATACAACAGACTGT 58.279 33.333 17.06 1.07 0.00 3.55
1872 5062 8.721478 ACATTGCTTAAGTAATACAACAGACTG 58.279 33.333 17.06 0.00 0.00 3.51
1873 5063 8.848474 ACATTGCTTAAGTAATACAACAGACT 57.152 30.769 17.06 0.00 0.00 3.24
1874 5064 9.893305 AAACATTGCTTAAGTAATACAACAGAC 57.107 29.630 17.06 0.00 0.00 3.51
1958 5148 5.667539 TCTCATACAAGACTCTTTCAGGG 57.332 43.478 0.00 0.00 0.00 4.45
2188 5378 6.363626 GCAAGGTAATGATCGTACAGATGTAG 59.636 42.308 8.24 0.00 40.26 2.74
2192 5382 5.276461 TGCAAGGTAATGATCGTACAGAT 57.724 39.130 8.24 0.00 43.51 2.90
2230 5420 5.293814 TGTGTTCCAATCAAGTTGCAATTTG 59.706 36.000 24.31 24.31 36.46 2.32
2240 5430 6.144402 GCAACAATTAGTGTGTTCCAATCAAG 59.856 38.462 0.00 0.00 40.60 3.02
2244 5434 4.262420 GGGCAACAATTAGTGTGTTCCAAT 60.262 41.667 0.00 0.00 40.60 3.16
2250 5444 4.725490 AGTAAGGGCAACAATTAGTGTGT 58.275 39.130 0.00 0.00 40.60 3.72
2316 5510 5.123936 ACGAATTTAGGGATTAGACCTTGC 58.876 41.667 0.00 0.00 39.54 4.01
2342 5536 3.243367 TGTCCGGAAAGCTGTCAAAATTG 60.243 43.478 5.23 0.00 0.00 2.32
2359 5553 3.550656 GACGGCTTGTCTTGTCCG 58.449 61.111 0.00 0.00 44.58 4.79
2374 5568 6.152932 ACTGGATTATTGCCATTTGATGAC 57.847 37.500 0.00 0.00 34.33 3.06
2461 5655 1.535462 GCTGGTTTATGCGACACAAGT 59.465 47.619 0.00 0.00 0.00 3.16
2609 5805 9.766277 GAGAAAACAATAGAACACAATGAGATC 57.234 33.333 0.00 0.00 0.00 2.75
2617 5814 7.201785 GGTGAAAGGAGAAAACAATAGAACACA 60.202 37.037 0.00 0.00 0.00 3.72
2618 5815 7.139392 GGTGAAAGGAGAAAACAATAGAACAC 58.861 38.462 0.00 0.00 0.00 3.32
2636 5833 2.749621 GAGGTGGTAATGCTGGTGAAAG 59.250 50.000 0.00 0.00 0.00 2.62
2670 5867 0.321653 ATGGACAAACTCTCGGTGCC 60.322 55.000 0.00 0.00 0.00 5.01
2794 5991 5.723355 ACTGCCTAGTAGGATGGGTAAATA 58.277 41.667 21.02 0.00 37.67 1.40
2814 6011 1.021390 CCGCTCTTTGGTGCCTACTG 61.021 60.000 0.00 0.00 0.00 2.74
2815 6012 1.296715 CCGCTCTTTGGTGCCTACT 59.703 57.895 0.00 0.00 0.00 2.57
2844 6041 8.122472 AGCTACATTTAACCTGCATACTTTTT 57.878 30.769 0.00 0.00 0.00 1.94
2845 6042 7.703058 AGCTACATTTAACCTGCATACTTTT 57.297 32.000 0.00 0.00 0.00 2.27
2935 6132 7.620491 TGATAAAACGGATATACCAGCCCTATA 59.380 37.037 0.00 0.00 38.90 1.31
3050 6247 8.606602 GCTATTGCATTTCTTTATTTTCCAAGG 58.393 33.333 0.00 0.00 39.41 3.61
3104 6309 6.885735 TCCACGCATATGATCATTAATACG 57.114 37.500 14.65 11.09 0.00 3.06
3156 6361 6.644181 ACAGCAATGATCATTCGAGTACATAG 59.356 38.462 18.16 4.54 0.00 2.23
3157 6362 6.515832 ACAGCAATGATCATTCGAGTACATA 58.484 36.000 18.16 0.00 0.00 2.29
3193 6398 2.200067 GAGCCGAGACATCAACATCTG 58.800 52.381 0.00 0.00 0.00 2.90
3216 6421 6.718593 TGAACTTATGATTATATGGGGCCT 57.281 37.500 0.84 0.00 0.00 5.19
3253 6458 2.308570 TGATAGGCAGGGACACAAACAT 59.691 45.455 0.00 0.00 0.00 2.71
3267 6472 6.205658 GGAGGTTAAATTCTGTGATGATAGGC 59.794 42.308 0.00 0.00 0.00 3.93
3268 6473 7.282585 TGGAGGTTAAATTCTGTGATGATAGG 58.717 38.462 0.00 0.00 0.00 2.57
3271 6476 7.348815 TGATGGAGGTTAAATTCTGTGATGAT 58.651 34.615 0.00 0.00 0.00 2.45
3272 6477 6.720309 TGATGGAGGTTAAATTCTGTGATGA 58.280 36.000 0.00 0.00 0.00 2.92
3273 6478 6.039047 CCTGATGGAGGTTAAATTCTGTGATG 59.961 42.308 0.00 0.00 37.02 3.07
3348 6569 9.121517 CAGAAATCACAAACAACAAAGCTATAG 57.878 33.333 0.00 0.00 0.00 1.31
3358 6579 5.687285 CCTAAGCACAGAAATCACAAACAAC 59.313 40.000 0.00 0.00 0.00 3.32
3459 6685 7.883311 TCTGTTAGACAGGGATTAAAGAAAAGG 59.117 37.037 8.11 0.00 45.94 3.11
3490 6716 6.010219 CCCAGGAAAAGAAAAGATCTACCAA 58.990 40.000 0.00 0.00 37.42 3.67
3496 6722 6.840780 TGATTCCCAGGAAAAGAAAAGATC 57.159 37.500 2.65 0.00 37.69 2.75
3553 6785 1.143305 CATTAATCCGCGAGCCAGAG 58.857 55.000 8.23 0.00 0.00 3.35
3563 6796 9.333724 TCATCCATTGATATGATCATTAATCCG 57.666 33.333 14.65 3.65 39.39 4.18
3645 6878 1.666054 CAGAGCTGAGAAATCTGGGC 58.334 55.000 0.00 0.00 37.41 5.36
3716 6951 4.991776 TGGGGATTCAACTGTGTTGATAA 58.008 39.130 12.95 1.40 0.00 1.75
3721 6956 3.524095 TGATGGGGATTCAACTGTGTT 57.476 42.857 0.00 0.00 0.00 3.32
3727 6962 3.017048 TGTCCATGATGGGGATTCAAC 57.983 47.619 12.26 0.80 38.32 3.18
3742 6977 5.690865 ACATTCCAGAAACTTAGTTGTCCA 58.309 37.500 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.