Multiple sequence alignment - TraesCS5B01G214600

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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 TraesCS5B01G214600 chr5B 100.000 7388 0 0 1 7388 387733189 387740576 0.000000e+00 13644.0
1 TraesCS5B01G214600 chr5D 95.389 7439 202 57 1 7388 332033309 332040657 0.000000e+00 11707.0
2 TraesCS5B01G214600 chr5D 97.872 47 1 0 6906 6952 332040226 332040272 1.710000e-11 82.4
3 TraesCS5B01G214600 chr5A 94.710 4121 144 27 3190 7282 432439446 432443520 0.000000e+00 6335.0
4 TraesCS5B01G214600 chr5A 93.356 1731 44 25 1 1690 432436223 432437923 0.000000e+00 2494.0
5 TraesCS5B01G214600 chr5A 95.273 1481 35 13 1685 3155 432437992 432439447 0.000000e+00 2314.0
6 TraesCS5B01G214600 chr5A 95.283 106 3 2 7284 7388 432443683 432443787 4.580000e-37 167.0
7 TraesCS5B01G214600 chr5A 100.000 47 0 0 6906 6952 432443190 432443236 3.670000e-13 87.9
8 TraesCS5B01G214600 chrUn 86.123 454 47 10 6202 6644 83995116 83994668 6.710000e-130 475.0
9 TraesCS5B01G214600 chrUn 86.123 454 47 10 6202 6644 232033395 232032947 6.710000e-130 475.0
10 TraesCS5B01G214600 chrUn 86.123 454 47 10 6202 6644 232041602 232041154 6.710000e-130 475.0
11 TraesCS5B01G214600 chr7B 86.123 454 47 10 6202 6644 2315654 2315206 6.710000e-130 475.0
12 TraesCS5B01G214600 chr7B 100.000 41 0 0 1618 1658 686818549 686818509 7.950000e-10 76.8
13 TraesCS5B01G214600 chr7B 97.561 41 1 0 1618 1658 246008157 246008117 3.700000e-08 71.3
14 TraesCS5B01G214600 chr4A 86.031 451 50 9 6202 6644 731999332 731998887 8.680000e-129 472.0
15 TraesCS5B01G214600 chr7D 100.000 49 0 0 1618 1666 265703387 265703339 2.840000e-14 91.6
16 TraesCS5B01G214600 chr7D 100.000 49 0 0 1618 1666 604868053 604868101 2.840000e-14 91.6
17 TraesCS5B01G214600 chr7A 100.000 49 0 0 1618 1666 290922167 290922119 2.840000e-14 91.6
18 TraesCS5B01G214600 chr7A 94.340 53 3 0 3537 3589 117981072 117981020 1.710000e-11 82.4
19 TraesCS5B01G214600 chr6B 100.000 34 0 0 1619 1652 411102836 411102803 6.190000e-06 63.9
20 TraesCS5B01G214600 chr4B 100.000 33 0 0 1618 1650 120465086 120465118 2.230000e-05 62.1


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 TraesCS5B01G214600 chr5B 387733189 387740576 7387 False 13644.00 13644 100.0000 1 7388 1 chr5B.!!$F1 7387
1 TraesCS5B01G214600 chr5D 332033309 332040657 7348 False 5894.70 11707 96.6305 1 7388 2 chr5D.!!$F1 7387
2 TraesCS5B01G214600 chr5A 432436223 432443787 7564 False 2279.58 6335 95.7244 1 7388 5 chr5A.!!$F1 7387

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
408 440 0.179084 GAATCCCCGCGTGATTCTCA 60.179 55.000 27.78 0.00 43.01 3.27 F
1253 1301 1.000359 ATGGAAGGGGGCTTTTCGG 60.000 57.895 0.00 0.00 0.00 4.30 F
2051 2177 2.218603 AGTGTAGTTGGAAAGGTTGCG 58.781 47.619 0.00 0.00 0.00 4.85 F
2591 2717 0.898326 TCTCTGCGGAGTACCAAGCA 60.898 55.000 21.88 6.58 40.29 3.91 F
4231 4370 1.715993 GACCGAGCCTTTCACTTCTC 58.284 55.000 0.00 0.00 0.00 2.87 F
5872 6017 0.790207 TCGAGTGAAATGCTGAACGC 59.210 50.000 0.00 0.00 39.77 4.84 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1503 1551 2.133742 CTTGAACTTGCCGCCACCAG 62.134 60.000 0.00 0.00 0.00 4.00 R
2479 2605 1.027357 CAGCCATTTCATTCTCGGGG 58.973 55.000 0.00 0.00 0.00 5.73 R
3725 3863 0.759959 TACCAACAAAGGCTCACCGA 59.240 50.000 0.00 0.00 42.76 4.69 R
4345 4484 1.271271 TGCACACATCAGCACACCATA 60.271 47.619 0.00 0.00 35.51 2.74 R
6141 6297 0.811616 GCCCTTGCCGTCTATCACAG 60.812 60.000 0.00 0.00 0.00 3.66 R
7206 7376 0.036388 AACGACTTCCATGGACGCAT 60.036 50.000 15.91 5.17 0.00 4.73 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
20 21 3.887335 TTTCCTTTCCGTCGCCCCG 62.887 63.158 0.00 0.00 0.00 5.73
264 281 1.295020 TCCAATCTTTGACGGGGGAT 58.705 50.000 0.00 0.00 0.00 3.85
371 403 0.329261 TGGTTGCTGCTAATCAGGCT 59.671 50.000 0.00 0.00 43.06 4.58
408 440 0.179084 GAATCCCCGCGTGATTCTCA 60.179 55.000 27.78 0.00 43.01 3.27
715 762 1.365699 TTCGTTATCCTCCTTTGCGC 58.634 50.000 0.00 0.00 0.00 6.09
912 959 1.410224 GGATTTGTGGTCTGATCCCCC 60.410 57.143 0.00 0.00 33.50 5.40
976 1024 4.332828 CCGAGGTTAATTTCTGGGTCTTT 58.667 43.478 0.00 0.00 0.00 2.52
977 1025 4.156008 CCGAGGTTAATTTCTGGGTCTTTG 59.844 45.833 0.00 0.00 0.00 2.77
978 1026 4.379499 CGAGGTTAATTTCTGGGTCTTTGC 60.379 45.833 0.00 0.00 0.00 3.68
979 1027 4.479158 AGGTTAATTTCTGGGTCTTTGCA 58.521 39.130 0.00 0.00 0.00 4.08
980 1028 4.524328 AGGTTAATTTCTGGGTCTTTGCAG 59.476 41.667 0.00 0.00 0.00 4.41
981 1029 4.321974 GGTTAATTTCTGGGTCTTTGCAGG 60.322 45.833 0.00 0.00 0.00 4.85
1185 1233 2.211250 TGGAGGTCAGTTAGTAGCGT 57.789 50.000 0.00 0.00 0.00 5.07
1199 1247 1.194772 GTAGCGTCCTCACTTTGTTGC 59.805 52.381 0.00 0.00 0.00 4.17
1253 1301 1.000359 ATGGAAGGGGGCTTTTCGG 60.000 57.895 0.00 0.00 0.00 4.30
1495 1543 5.008019 ACTGTCTGCAATGCTATTTATTCCG 59.992 40.000 6.82 0.00 0.00 4.30
1503 1551 5.751243 ATGCTATTTATTCCGTGGTTGAC 57.249 39.130 0.00 0.00 0.00 3.18
1593 1642 2.549754 CTCGCTGACATGTTTTGGAGTT 59.450 45.455 0.00 0.00 0.00 3.01
1603 1652 9.126151 TGACATGTTTTGGAGTTAACATTCTAA 57.874 29.630 8.61 0.00 41.65 2.10
1666 1718 4.376920 GGCTTTGTTGTTGTTGTTGTTGTC 60.377 41.667 0.00 0.00 0.00 3.18
1979 2105 7.116948 CAGTTCACTCAAAGGTAGACACATTAG 59.883 40.741 0.00 0.00 0.00 1.73
2051 2177 2.218603 AGTGTAGTTGGAAAGGTTGCG 58.781 47.619 0.00 0.00 0.00 4.85
2094 2220 7.762382 ACCTGTCTTAAGTTTCACAAAAGAAG 58.238 34.615 1.63 0.00 0.00 2.85
2095 2221 7.393515 ACCTGTCTTAAGTTTCACAAAAGAAGT 59.606 33.333 1.63 0.00 0.00 3.01
2479 2605 4.395231 GCTCCAAAGGTAAATGTAGTCACC 59.605 45.833 0.00 0.00 0.00 4.02
2506 2632 4.525024 AGAATGAAATGGCTGAGGAAGAG 58.475 43.478 0.00 0.00 0.00 2.85
2591 2717 0.898326 TCTCTGCGGAGTACCAAGCA 60.898 55.000 21.88 6.58 40.29 3.91
2919 3053 6.207417 ACAACAACCTTCATGACAATCTAAGG 59.793 38.462 0.00 0.00 42.01 2.69
3010 3146 8.267620 TGGATGTTATCACATTTACACTCTTG 57.732 34.615 0.00 0.00 44.22 3.02
3011 3147 7.148255 TGGATGTTATCACATTTACACTCTTGC 60.148 37.037 0.00 0.00 44.22 4.01
3173 3309 2.221169 ACGCAGCTTGAGTTCATTCAA 58.779 42.857 0.00 0.00 35.83 2.69
3327 3463 7.698836 TCTTTTACTACTTGTCGGTAAACAC 57.301 36.000 9.65 0.00 35.87 3.32
3334 3470 3.751175 ACTTGTCGGTAAACACATGGATG 59.249 43.478 0.00 0.00 0.00 3.51
3410 3546 5.474876 CCAGGATTTGTTCAGCTAACTCTTT 59.525 40.000 0.00 0.00 38.99 2.52
3432 3568 6.603237 TTATCTATCAATCTTTGTGCCACG 57.397 37.500 0.00 0.00 0.00 4.94
3586 3722 5.073144 TCTGTTGGGGTTGAGAATTCTTACT 59.927 40.000 9.87 0.00 0.00 2.24
3671 3809 7.655328 AGCTAGCTCTACTATTGTTGCTTATTG 59.345 37.037 12.68 0.00 31.99 1.90
3714 3852 6.051946 AGGGAGGGGACAAGTAGATTATTA 57.948 41.667 0.00 0.00 0.00 0.98
3818 3956 2.291741 CACCCTGTGCAAGAAGTCTTTC 59.708 50.000 0.00 0.00 33.11 2.62
3894 4032 4.469657 TGTGGGTAAAGCAGAAACTGATT 58.530 39.130 2.81 0.00 42.09 2.57
3985 4123 3.266510 ACCATGCGTTGTGATATGACT 57.733 42.857 0.00 0.00 0.00 3.41
4062 4200 7.402054 TGTTTTGATGACCAGGTACAGATTAT 58.598 34.615 0.00 0.00 0.00 1.28
4100 4239 3.013921 TCTTGACTTGACCACACAAACC 58.986 45.455 0.00 0.00 0.00 3.27
4105 4244 3.219281 ACTTGACCACACAAACCCATAC 58.781 45.455 0.00 0.00 0.00 2.39
4140 4279 2.238144 TCTGCAGCTTCTAGAAAGCCAT 59.762 45.455 9.47 4.09 44.01 4.40
4231 4370 1.715993 GACCGAGCCTTTCACTTCTC 58.284 55.000 0.00 0.00 0.00 2.87
4345 4484 8.289939 ACAGATATGCAACAGATTTGAATTCT 57.710 30.769 7.05 0.00 0.00 2.40
4465 4604 6.636454 TTATGTGGACTCCTTATGACCTTT 57.364 37.500 0.00 0.00 0.00 3.11
4528 4667 9.684448 TCAATTTTCGTCTATATCTGATGACTC 57.316 33.333 0.00 0.00 0.00 3.36
4583 4723 7.211966 GCATCTAGCACCAGAAATTTCATAT 57.788 36.000 19.99 1.88 44.79 1.78
4610 4750 2.487265 CCTAGTTGCACTTGGAGTTGGT 60.487 50.000 9.86 0.00 42.55 3.67
4646 4786 2.562738 TCCTGTTGCTTCATTCGAGAGA 59.437 45.455 0.00 0.00 39.20 3.10
5003 5143 2.263741 GCCAGTTGCTCCACCTGTG 61.264 63.158 0.00 0.00 36.87 3.66
5009 5149 0.819259 TTGCTCCACCTGTGAAGCAC 60.819 55.000 10.90 0.00 43.94 4.40
5175 5315 4.011966 TGCTTCTTTGAGCTTGATGAGA 57.988 40.909 0.00 0.00 43.11 3.27
5431 5571 9.307121 CAGTGTACTCTAATGATTAAAGAGGTG 57.693 37.037 9.17 0.00 40.88 4.00
5467 5607 7.816995 GTGCATTTTGTTAATCATTGTTCCCTA 59.183 33.333 0.00 0.00 0.00 3.53
5571 5711 1.148310 CGAAGATGCGAAACCACACT 58.852 50.000 0.00 0.00 0.00 3.55
5593 5733 9.204570 ACACTGTAACAAATAGAATGACTGTAC 57.795 33.333 0.00 0.00 0.00 2.90
5668 5810 5.994250 TCCTTTAGCTATCAATGCTGAAGT 58.006 37.500 15.48 0.00 46.17 3.01
5669 5811 6.418101 TCCTTTAGCTATCAATGCTGAAGTT 58.582 36.000 15.48 0.00 46.17 2.66
5732 5877 8.503458 TTTCCATTTCAATTTTGAACATGTGT 57.497 26.923 0.00 0.00 45.99 3.72
5734 5879 9.605275 TTCCATTTCAATTTTGAACATGTGTTA 57.395 25.926 0.00 0.00 45.99 2.41
5735 5880 9.258826 TCCATTTCAATTTTGAACATGTGTTAG 57.741 29.630 0.00 2.23 45.99 2.34
5773 5918 9.123902 TCTGGTCTCCATGATAACAATTAATTG 57.876 33.333 23.60 23.60 37.02 2.32
5812 5957 8.859236 TTCTCTGAAATTTCATGATCACTTCT 57.141 30.769 20.76 0.00 36.46 2.85
5872 6017 0.790207 TCGAGTGAAATGCTGAACGC 59.210 50.000 0.00 0.00 39.77 4.84
6045 6201 5.105392 TGCTTTGGATTTCAAGTTTGTCACT 60.105 36.000 0.00 0.00 36.62 3.41
6046 6202 5.232838 GCTTTGGATTTCAAGTTTGTCACTG 59.767 40.000 0.00 0.00 35.12 3.66
6111 6267 1.457346 CTGGAGATTGGGTGAACTGC 58.543 55.000 0.00 0.00 0.00 4.40
6141 6297 1.356624 CGAATGGGCTCATTTCGGC 59.643 57.895 14.31 0.00 43.08 5.54
6188 6344 5.518847 GCACTTTCAAGGTAAAAACTTGTCC 59.481 40.000 4.72 0.00 44.29 4.02
6190 6346 6.751888 CACTTTCAAGGTAAAAACTTGTCCTG 59.248 38.462 4.72 0.00 44.29 3.86
6193 6349 6.930667 TCAAGGTAAAAACTTGTCCTGTAC 57.069 37.500 4.72 0.00 44.29 2.90
6194 6350 5.824097 TCAAGGTAAAAACTTGTCCTGTACC 59.176 40.000 4.72 0.00 44.29 3.34
6261 6420 1.083489 CCTTGCAGGATTACGCGAAA 58.917 50.000 15.93 0.00 37.67 3.46
6345 6504 0.394352 CGCCCCAGAAAGTAGCCAAT 60.394 55.000 0.00 0.00 0.00 3.16
6412 6572 5.300286 TCCTCTTCTTTTCTTGCTTTTCCTG 59.700 40.000 0.00 0.00 0.00 3.86
6591 6753 1.273324 ACAGGGAGGCTACTTACTGCT 60.273 52.381 0.00 0.00 35.45 4.24
6651 6813 5.446260 AAGTTAATCTGTATCCCCGGTTT 57.554 39.130 0.00 0.00 0.00 3.27
6653 6815 4.132336 GTTAATCTGTATCCCCGGTTTCC 58.868 47.826 0.00 0.00 0.00 3.13
6654 6816 1.887797 ATCTGTATCCCCGGTTTCCA 58.112 50.000 0.00 0.00 0.00 3.53
6655 6817 1.887797 TCTGTATCCCCGGTTTCCAT 58.112 50.000 0.00 0.00 0.00 3.41
6657 6819 0.466543 TGTATCCCCGGTTTCCATCG 59.533 55.000 0.00 0.00 0.00 3.84
6728 6890 4.133078 GGATCCTCTGAATGTTGGATGTC 58.867 47.826 3.84 0.00 39.19 3.06
6796 6958 5.922544 CGTTGCACTATGACTATGATCATCA 59.077 40.000 12.53 5.64 39.97 3.07
6815 6977 2.758089 CGGCAATGAGACAGGCAGC 61.758 63.158 0.00 0.00 0.00 5.25
6829 6991 1.625818 AGGCAGCTACATATACCAGGC 59.374 52.381 0.00 0.00 0.00 4.85
6850 7012 3.665544 GCACTTTGCAGAGCCAAAA 57.334 47.368 3.74 0.00 44.26 2.44
6854 7016 2.798283 CACTTTGCAGAGCCAAAATGTG 59.202 45.455 3.74 0.00 34.59 3.21
6898 7060 0.105964 CAGGGAAGGACGAACACACA 59.894 55.000 0.00 0.00 0.00 3.72
6984 7146 2.656947 ATTGGCAGTACAACACAGGT 57.343 45.000 0.00 0.00 32.39 4.00
6995 7157 7.916450 GCAGTACAACACAGGTTTAATTTACAA 59.084 33.333 0.00 0.00 34.21 2.41
7001 7163 8.626526 CAACACAGGTTTAATTTACAAGGTAGT 58.373 33.333 0.00 0.00 34.21 2.73
7003 7165 7.994334 ACACAGGTTTAATTTACAAGGTAGTGA 59.006 33.333 0.00 0.00 0.00 3.41
7019 7189 2.743636 GTGAAGATCACACCTTCGGA 57.256 50.000 5.65 0.00 46.22 4.55
7047 7217 3.987404 GCCTGTGGCTTGTGTAGG 58.013 61.111 0.73 0.00 46.69 3.18
7052 7222 2.571212 CTGTGGCTTGTGTAGGTGAAA 58.429 47.619 0.00 0.00 0.00 2.69
7053 7223 2.549754 CTGTGGCTTGTGTAGGTGAAAG 59.450 50.000 0.00 0.00 0.00 2.62
7071 7241 2.358615 TGCGCATCAGCTTCGGTT 60.359 55.556 5.66 0.00 39.10 4.44
7124 7294 3.790334 TTGAGGCGCGGGATCATCG 62.790 63.158 8.83 0.00 0.00 3.84
7206 7376 2.281484 GCGCCCAGACACCTTTGA 60.281 61.111 0.00 0.00 0.00 2.69
7330 7661 6.952358 AGTACTAGACAACACCATCTTCCTTA 59.048 38.462 0.00 0.00 0.00 2.69
7369 7700 9.499479 CTTACAGATGCAGTCCTGATAAATAAT 57.501 33.333 17.10 0.00 34.65 1.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 1.809651 GCTGCCTCCTCATTACTGCTC 60.810 57.143 0.00 0.00 0.00 4.26
153 166 4.241590 TGCGATGGATGGATTATTTTGC 57.758 40.909 0.00 0.00 0.00 3.68
189 202 2.976185 CTCTATCCCTTCCCTTCCCTTC 59.024 54.545 0.00 0.00 0.00 3.46
190 203 2.597304 TCTCTATCCCTTCCCTTCCCTT 59.403 50.000 0.00 0.00 0.00 3.95
191 204 2.236851 TCTCTATCCCTTCCCTTCCCT 58.763 52.381 0.00 0.00 0.00 4.20
192 205 2.797285 TCTCTATCCCTTCCCTTCCC 57.203 55.000 0.00 0.00 0.00 3.97
193 206 4.299485 TCTTTCTCTATCCCTTCCCTTCC 58.701 47.826 0.00 0.00 0.00 3.46
345 374 0.825840 TTAGCAGCAACCACCAACCC 60.826 55.000 0.00 0.00 0.00 4.11
408 440 0.322546 GAAGCCGACCAAACTGGGAT 60.323 55.000 0.00 0.00 43.37 3.85
663 710 1.590147 GGGAGAAGACGAAGGCGAA 59.410 57.895 0.00 0.00 41.64 4.70
667 714 1.597461 GTGGGGGAGAAGACGAAGG 59.403 63.158 0.00 0.00 0.00 3.46
912 959 1.082104 GCAACCGCGAAACAGAAGG 60.082 57.895 8.23 0.00 0.00 3.46
913 960 0.384725 CTGCAACCGCGAAACAGAAG 60.385 55.000 8.23 0.00 42.97 2.85
914 961 1.646540 CTGCAACCGCGAAACAGAA 59.353 52.632 8.23 0.00 42.97 3.02
915 962 2.250939 CCTGCAACCGCGAAACAGA 61.251 57.895 8.23 0.00 42.97 3.41
916 963 2.252260 CCTGCAACCGCGAAACAG 59.748 61.111 8.23 9.57 42.97 3.16
961 1009 3.075283 TCCCTGCAAAGACCCAGAAATTA 59.925 43.478 0.00 0.00 0.00 1.40
976 1024 0.104671 GCAAGCAAAAACTCCCTGCA 59.895 50.000 0.00 0.00 38.58 4.41
977 1025 0.940991 CGCAAGCAAAAACTCCCTGC 60.941 55.000 0.00 0.00 36.29 4.85
978 1026 0.318955 CCGCAAGCAAAAACTCCCTG 60.319 55.000 0.00 0.00 0.00 4.45
979 1027 2.041153 CCGCAAGCAAAAACTCCCT 58.959 52.632 0.00 0.00 0.00 4.20
980 1028 1.664649 GCCGCAAGCAAAAACTCCC 60.665 57.895 0.00 0.00 42.97 4.30
981 1029 1.664649 GGCCGCAAGCAAAAACTCC 60.665 57.895 0.00 0.00 46.50 3.85
1155 1203 2.936032 ACCTCCAACCTCCCAGCC 60.936 66.667 0.00 0.00 0.00 4.85
1158 1206 0.401395 AACTGACCTCCAACCTCCCA 60.401 55.000 0.00 0.00 0.00 4.37
1185 1233 1.148273 AGGCGCAACAAAGTGAGGA 59.852 52.632 10.83 0.00 0.00 3.71
1199 1247 1.999634 AATCCTTCCATCCCCAGGCG 62.000 60.000 0.00 0.00 0.00 5.52
1387 1435 2.509336 GGGTCAGACATGTCGGCG 60.509 66.667 19.74 12.78 34.09 6.46
1444 1492 6.681777 AGAGAAAATTTCTGCGCTTACAATT 58.318 32.000 13.55 5.31 40.87 2.32
1495 1543 2.978010 CCGCCACCAGTCAACCAC 60.978 66.667 0.00 0.00 0.00 4.16
1503 1551 2.133742 CTTGAACTTGCCGCCACCAG 62.134 60.000 0.00 0.00 0.00 4.00
1603 1652 7.639062 AGTTGGGATAGATTAGTCATGGAAT 57.361 36.000 0.00 0.00 0.00 3.01
1666 1718 6.851222 ATTGCAGTTATGGAACTAGAATCG 57.149 37.500 0.00 0.00 44.39 3.34
2051 2177 6.095720 AGACAGGTTACTAGATACTTCTGTGC 59.904 42.308 0.00 0.41 34.83 4.57
2144 2270 5.982890 ATACCCTGAAATGAAACAACCAG 57.017 39.130 0.00 0.00 0.00 4.00
2337 2463 3.244215 CCATGTATGGCTCACCGAACTAT 60.244 47.826 0.00 0.00 41.75 2.12
2479 2605 1.027357 CAGCCATTTCATTCTCGGGG 58.973 55.000 0.00 0.00 0.00 5.73
2887 3020 7.581213 TGTCATGAAGGTTGTTGTTAGAATT 57.419 32.000 0.00 0.00 0.00 2.17
3010 3146 7.169645 TGAAACAAGAGCATAAATGTTTTGAGC 59.830 33.333 4.47 0.00 43.77 4.26
3011 3147 8.578308 TGAAACAAGAGCATAAATGTTTTGAG 57.422 30.769 4.47 0.00 43.77 3.02
3173 3309 8.736244 ACTAGTCTTGTTGTTTTGTGTACAAAT 58.264 29.630 10.63 0.00 44.30 2.32
3267 3403 2.494073 ACGGTGTTTTTGGATGTGTGTT 59.506 40.909 0.00 0.00 0.00 3.32
3327 3463 5.352016 CCCTTGTTTTATTTGTGCATCCATG 59.648 40.000 0.00 0.00 0.00 3.66
3334 3470 4.329462 TGGTCCCTTGTTTTATTTGTGC 57.671 40.909 0.00 0.00 0.00 4.57
3410 3546 5.670485 ACGTGGCACAAAGATTGATAGATA 58.330 37.500 19.09 0.00 44.16 1.98
3586 3722 4.777896 AGCACTCTACAGGAAGGTTATCAA 59.222 41.667 0.00 0.00 0.00 2.57
3671 3809 7.766738 CCTCCCTCTCTTTCATTTAGTAAGAAC 59.233 40.741 0.00 0.00 33.90 3.01
3714 3852 6.071391 ACAAAGGCTCACCGATTCATTTTAAT 60.071 34.615 0.00 0.00 42.76 1.40
3725 3863 0.759959 TACCAACAAAGGCTCACCGA 59.240 50.000 0.00 0.00 42.76 4.69
3727 3865 2.224548 ACTCTACCAACAAAGGCTCACC 60.225 50.000 0.00 0.00 0.00 4.02
3778 3916 5.592104 GGTGACCCCAATATTTACAAAGG 57.408 43.478 0.00 0.00 0.00 3.11
3868 4006 3.636764 AGTTTCTGCTTTACCCACAAAGG 59.363 43.478 0.00 0.00 36.27 3.11
3894 4032 1.632920 TGCCACATATGAGAACACCCA 59.367 47.619 10.38 0.00 0.00 4.51
3967 4105 5.731278 CAAGTAGTCATATCACAACGCATG 58.269 41.667 0.00 0.00 0.00 4.06
4062 4200 5.544176 AGTCAAGAAAGTCTCAAGTATGGGA 59.456 40.000 0.00 0.00 32.15 4.37
4100 4239 4.299155 CAGACATAGTAAGCACCGTATGG 58.701 47.826 0.00 0.00 42.84 2.74
4105 4244 2.196749 CTGCAGACATAGTAAGCACCG 58.803 52.381 8.42 0.00 0.00 4.94
4334 4473 6.441093 TCAGCACACCATAGAATTCAAATC 57.559 37.500 8.44 0.00 0.00 2.17
4345 4484 1.271271 TGCACACATCAGCACACCATA 60.271 47.619 0.00 0.00 35.51 2.74
4610 4750 3.328382 ACAGGAGTAGCATTTACGCAA 57.672 42.857 0.00 0.00 0.00 4.85
4646 4786 5.943013 AAAGAAGGCGGTCTGCATCTTGT 62.943 47.826 19.12 5.81 45.20 3.16
4850 4990 4.453480 TTTTCCCTTGAAGGATGTCAGT 57.547 40.909 13.97 0.00 37.67 3.41
5003 5143 3.019564 AGGTGCTGAATTATGGTGCTTC 58.980 45.455 0.00 0.00 0.00 3.86
5175 5315 8.189460 GTGGTCTTAGTATAGAGACATTTCGTT 58.811 37.037 11.05 0.00 43.14 3.85
5431 5571 9.823098 TGATTAACAAAATGCACATTTATTTGC 57.177 25.926 8.92 0.00 39.88 3.68
5593 5733 3.966154 AGCGAAGTGAATAGTGGATACG 58.034 45.455 0.00 0.00 42.51 3.06
5647 5787 7.312657 TGAACTTCAGCATTGATAGCTAAAG 57.687 36.000 0.00 0.00 41.98 1.85
5725 5870 7.094634 CCAGATCAAAACTAAGCTAACACATGT 60.095 37.037 0.00 0.00 0.00 3.21
5732 5877 6.013725 TGGAGACCAGATCAAAACTAAGCTAA 60.014 38.462 0.00 0.00 0.00 3.09
5734 5879 4.287067 TGGAGACCAGATCAAAACTAAGCT 59.713 41.667 0.00 0.00 0.00 3.74
5735 5880 4.579869 TGGAGACCAGATCAAAACTAAGC 58.420 43.478 0.00 0.00 0.00 3.09
5812 5957 6.500589 AACTTGCTATGAAGGGAGCTAATA 57.499 37.500 0.00 0.00 39.54 0.98
5872 6017 9.878599 CACCCTAAATATAGCAAAATTAGAACG 57.121 33.333 0.00 0.00 0.00 3.95
5900 6056 3.013921 GTGTCTTTTCAGTGTGTTCCCA 58.986 45.455 0.00 0.00 0.00 4.37
6045 6201 5.197451 ACAAAGATGGTGTTAGGTTTCACA 58.803 37.500 0.00 0.00 36.43 3.58
6046 6202 5.767816 ACAAAGATGGTGTTAGGTTTCAC 57.232 39.130 0.00 0.00 0.00 3.18
6111 6267 1.010125 CCATTCGCCGCATAAACCG 60.010 57.895 0.00 0.00 0.00 4.44
6141 6297 0.811616 GCCCTTGCCGTCTATCACAG 60.812 60.000 0.00 0.00 0.00 3.66
6190 6346 2.043941 AGGGGGTGGGGATGGTAC 59.956 66.667 0.00 0.00 0.00 3.34
6193 6349 2.774351 GAGAGGGGGTGGGGATGG 60.774 72.222 0.00 0.00 0.00 3.51
6194 6350 2.774351 GGAGAGGGGGTGGGGATG 60.774 72.222 0.00 0.00 0.00 3.51
6261 6420 5.456921 AGATGTATTCCAACCCATCTGTT 57.543 39.130 0.00 0.00 41.74 3.16
6345 6504 1.579084 GCACGGTATTCGCAAACCCA 61.579 55.000 0.00 0.00 43.89 4.51
6412 6572 0.606673 AGGGCAGAGAGGCGAAAAAC 60.607 55.000 0.00 0.00 45.36 2.43
6489 6651 8.084985 TGGGATAATACAGATCAACACTACAA 57.915 34.615 0.00 0.00 0.00 2.41
6490 6652 7.669089 TGGGATAATACAGATCAACACTACA 57.331 36.000 0.00 0.00 0.00 2.74
6591 6753 2.371841 ACACTGAATCTGGCCAACTACA 59.628 45.455 7.01 4.52 0.00 2.74
6651 6813 1.078918 CAAGCAGTCTGGCGATGGA 60.079 57.895 1.14 0.00 39.27 3.41
6653 6815 0.952497 ACACAAGCAGTCTGGCGATG 60.952 55.000 1.14 2.65 39.27 3.84
6654 6816 0.250467 AACACAAGCAGTCTGGCGAT 60.250 50.000 1.14 0.00 39.27 4.58
6655 6817 1.146041 AACACAAGCAGTCTGGCGA 59.854 52.632 1.14 0.00 39.27 5.54
6657 6819 0.308993 GACAACACAAGCAGTCTGGC 59.691 55.000 1.14 0.00 0.00 4.85
6728 6890 2.743664 TGATTCTGCACCTCAATTCACG 59.256 45.455 0.00 0.00 0.00 4.35
6796 6958 1.376424 CTGCCTGTCTCATTGCCGT 60.376 57.895 0.00 0.00 0.00 5.68
6815 6977 4.342862 AGTGCAAGCCTGGTATATGTAG 57.657 45.455 0.00 0.00 0.00 2.74
6854 7016 4.766404 ATTAAGCCTGTGTTGCTGTAAC 57.234 40.909 1.39 1.39 39.48 2.50
6898 7060 6.358974 ACCAATAAATAAACTTTGGCAGCT 57.641 33.333 0.62 0.00 41.89 4.24
7019 7189 3.699894 CACAGGCCGGTCAGAGCT 61.700 66.667 9.71 0.00 0.00 4.09
7047 7217 0.239347 AAGCTGATGCGCACTTTCAC 59.761 50.000 14.90 8.00 45.42 3.18
7052 7222 2.816958 CCGAAGCTGATGCGCACT 60.817 61.111 14.90 1.08 45.42 4.40
7053 7223 2.680913 AACCGAAGCTGATGCGCAC 61.681 57.895 14.90 7.75 45.42 5.34
7071 7241 1.428448 CTTCATGAACGAGTTCCGCA 58.572 50.000 3.38 0.00 43.32 5.69
7124 7294 1.092345 GGCGAGGACAAGATCAAGGC 61.092 60.000 0.00 0.00 0.00 4.35
7206 7376 0.036388 AACGACTTCCATGGACGCAT 60.036 50.000 15.91 5.17 0.00 4.73
7264 7434 9.282569 TGCACATGCATATGTTACAAGATATTA 57.717 29.630 6.86 0.00 45.01 0.98
7282 7613 2.443887 AGTTGTTTCCATGCACATGC 57.556 45.000 5.06 0.00 37.49 4.06
7346 7677 9.851686 TTTATTATTTATCAGGACTGCATCTGT 57.148 29.630 10.34 0.00 33.13 3.41


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

AutoCloner maintained by Alex Coulton.