Multiple sequence alignment - TraesCS1D01G343000

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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 TraesCS1D01G343000 chr1D 100.000 3935 0 0 1 3935 432317487 432321421 0.000000e+00 7267.0
1 TraesCS1D01G343000 chr1D 85.417 96 10 4 1882 1977 19039915 19040006 3.240000e-16 97.1
2 TraesCS1D01G343000 chr1A 91.201 2273 68 49 1730 3935 530781098 530783305 0.000000e+00 2968.0
3 TraesCS1D01G343000 chr1A 84.581 1336 94 57 283 1531 530779408 530780718 0.000000e+00 1223.0
4 TraesCS1D01G343000 chr1A 88.406 207 24 0 2279 2485 390709560 390709766 2.350000e-62 250.0
5 TraesCS1D01G343000 chr1A 96.739 92 3 0 1629 1720 530780967 530781058 1.890000e-33 154.0
6 TraesCS1D01G343000 chr1B 91.808 1477 39 26 2490 3934 583760922 583762348 0.000000e+00 1982.0
7 TraesCS1D01G343000 chr1B 86.944 1754 114 39 1 1721 583758414 583760085 0.000000e+00 1864.0
8 TraesCS1D01G343000 chr1B 95.946 814 27 4 1728 2541 583760127 583760934 0.000000e+00 1315.0
9 TraesCS1D01G343000 chr3A 87.755 245 27 2 2261 2502 504024827 504025071 2.310000e-72 283.0
10 TraesCS1D01G343000 chr3A 93.805 113 4 1 1344 1456 504023769 504023878 2.430000e-37 167.0
11 TraesCS1D01G343000 chr3A 87.288 118 8 5 1814 1924 504024362 504024479 1.150000e-25 128.0
12 TraesCS1D01G343000 chr3B 88.889 225 25 0 2261 2485 496615074 496615298 1.080000e-70 278.0
13 TraesCS1D01G343000 chr3B 93.805 113 4 1 1344 1456 496614024 496614133 2.430000e-37 167.0
14 TraesCS1D01G343000 chr3B 89.474 114 6 4 1814 1921 496614609 496614722 5.300000e-29 139.0
15 TraesCS1D01G343000 chr3D 84.892 278 35 6 2261 2534 380815041 380815315 1.390000e-69 274.0
16 TraesCS1D01G343000 chr3D 92.920 113 5 1 1344 1456 380813992 380814101 1.130000e-35 161.0
17 TraesCS1D01G343000 chr3D 88.983 118 6 5 1814 1924 380814576 380814693 5.300000e-29 139.0
18 TraesCS1D01G343000 chr5A 89.623 212 22 0 2274 2485 696925398 696925187 1.800000e-68 270.0
19 TraesCS1D01G343000 chr4B 89.474 209 22 0 2274 2482 658212377 658212585 8.380000e-67 265.0
20 TraesCS1D01G343000 chr4D 88.679 212 24 0 2274 2485 509057231 509057020 3.900000e-65 259.0


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 TraesCS1D01G343000 chr1D 432317487 432321421 3934 False 7267.000000 7267 100.000000 1 3935 1 chr1D.!!$F2 3934
1 TraesCS1D01G343000 chr1A 530779408 530783305 3897 False 1448.333333 2968 90.840333 283 3935 3 chr1A.!!$F2 3652
2 TraesCS1D01G343000 chr1B 583758414 583762348 3934 False 1720.333333 1982 91.566000 1 3934 3 chr1B.!!$F1 3933

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
84 85 0.033504 AGTGACGCGTGAAGAACCAT 59.966 50.0 20.7 0.0 0.00 3.55 F
1090 1199 0.388294 GTAGAATTCGTCCGGGGAGG 59.612 60.0 0.0 1.0 42.97 4.30 F
1618 1943 1.029947 CCCATTAACACTCGCCCCAC 61.030 60.0 0.0 0.0 0.00 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1626 1951 0.040942 TTCATTCATGGGGTGGGGTG 59.959 55.0 0.0 0.0 0.00 4.61 R
2719 3139 2.196997 ATTGCTGCTGGGGCTAACGA 62.197 55.0 0.0 0.0 39.59 3.85 R
3227 3665 0.112218 TGGATTCAACACCACAGGGG 59.888 55.0 0.0 0.0 44.81 4.79 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
21 22 1.278302 TGGGGGAAGATTGGCGATGA 61.278 55.000 0.00 0.00 0.00 2.92
23 24 0.107214 GGGGAAGATTGGCGATGACA 60.107 55.000 0.00 0.00 0.00 3.58
28 29 1.671979 AGATTGGCGATGACATGTGG 58.328 50.000 1.15 0.00 0.00 4.17
49 50 2.815647 CGAGCTTGAACGGGGCTC 60.816 66.667 0.00 0.00 46.06 4.70
57 58 0.609957 TGAACGGGGCTCTAGACGAA 60.610 55.000 7.40 0.00 0.00 3.85
60 61 1.316651 ACGGGGCTCTAGACGAATAC 58.683 55.000 7.40 0.00 0.00 1.89
63 64 1.340568 GGGGCTCTAGACGAATACACC 59.659 57.143 0.00 0.00 0.00 4.16
70 71 5.306532 TCTAGACGAATACACCAAGTGAC 57.693 43.478 0.96 0.00 36.96 3.67
75 76 1.126113 GAATACACCAAGTGACGCGTG 59.874 52.381 20.70 2.70 36.96 5.34
84 85 0.033504 AGTGACGCGTGAAGAACCAT 59.966 50.000 20.70 0.00 0.00 3.55
89 90 3.123804 GACGCGTGAAGAACCATATGAT 58.876 45.455 20.70 0.00 0.00 2.45
96 97 6.516718 CGTGAAGAACCATATGATTAGGAGT 58.483 40.000 3.65 0.00 0.00 3.85
100 101 3.685139 ACCATATGATTAGGAGTGCGG 57.315 47.619 3.65 0.00 0.00 5.69
101 102 2.289694 ACCATATGATTAGGAGTGCGGC 60.290 50.000 3.65 0.00 0.00 6.53
109 110 2.238847 TAGGAGTGCGGCGATGCTTT 62.239 55.000 12.98 0.52 35.36 3.51
120 121 1.795162 GCGATGCTTTGATTTGTCCGG 60.795 52.381 0.00 0.00 0.00 5.14
153 154 1.034292 GGAGCACCATTTGAGGAGGC 61.034 60.000 0.00 0.00 35.97 4.70
159 160 1.651240 CCATTTGAGGAGGCAGCACG 61.651 60.000 0.00 0.00 0.00 5.34
166 167 1.812922 GGAGGCAGCACGACATGAG 60.813 63.158 0.00 0.00 0.00 2.90
169 170 0.461516 AGGCAGCACGACATGAGATG 60.462 55.000 0.00 0.00 0.00 2.90
176 177 2.537625 GCACGACATGAGATGCTAAGAC 59.462 50.000 0.00 0.00 35.16 3.01
179 180 3.696548 ACGACATGAGATGCTAAGACTGA 59.303 43.478 0.00 0.00 0.00 3.41
181 182 4.739228 CGACATGAGATGCTAAGACTGAAG 59.261 45.833 0.00 0.00 0.00 3.02
183 184 6.482898 ACATGAGATGCTAAGACTGAAGAT 57.517 37.500 0.00 0.00 0.00 2.40
186 187 6.647334 TGAGATGCTAAGACTGAAGATAGG 57.353 41.667 0.00 0.00 0.00 2.57
187 188 5.538053 TGAGATGCTAAGACTGAAGATAGGG 59.462 44.000 0.00 0.00 0.00 3.53
234 235 0.792640 GGAGCACATTGACACGAGTG 59.207 55.000 1.13 1.13 35.19 3.51
250 251 4.527944 ACGAGTGTGAGATAGATGGAGAA 58.472 43.478 0.00 0.00 0.00 2.87
409 412 7.013942 ACGCATATGTACTCCAACTATTCTGTA 59.986 37.037 4.29 0.00 0.00 2.74
444 447 2.741878 CGTGTAATGCTACCTCCCCTTG 60.742 54.545 0.00 0.00 0.00 3.61
472 476 2.559330 GATCGCGGCGGTTTTTGT 59.441 55.556 23.46 0.07 0.00 2.83
502 506 7.155328 TGATTTTGTACAAAAACCAACACAGT 58.845 30.769 31.40 15.06 42.71 3.55
525 530 7.178451 CAGTGTAAATCCTCAATAAAAACCCCT 59.822 37.037 0.00 0.00 0.00 4.79
653 673 6.669125 ACTCACCAAAAATGATCCAATCAA 57.331 33.333 0.00 0.00 43.50 2.57
743 777 1.141881 CAGATGTCGTCTTCCCCGG 59.858 63.158 0.00 0.00 34.00 5.73
774 814 1.257743 GGGGAGCTGTTTCCTTTTCC 58.742 55.000 0.00 0.00 37.40 3.13
779 832 3.078097 GAGCTGTTTCCTTTTCCTCTCC 58.922 50.000 0.00 0.00 0.00 3.71
792 845 4.988716 TCTCCCTCACCGCCGTGT 62.989 66.667 5.09 0.00 41.09 4.49
874 946 0.545646 AGGCCATTCCAGAGAAGAGC 59.454 55.000 5.01 0.00 34.86 4.09
875 947 0.465278 GGCCATTCCAGAGAAGAGCC 60.465 60.000 0.00 3.88 43.17 4.70
935 1039 3.952799 GAGCTTGACCCCTCCCCCT 62.953 68.421 0.00 0.00 0.00 4.79
936 1040 3.412408 GCTTGACCCCTCCCCCTC 61.412 72.222 0.00 0.00 0.00 4.30
1090 1199 0.388294 GTAGAATTCGTCCGGGGAGG 59.612 60.000 0.00 1.00 42.97 4.30
1466 1599 5.302360 TGCGAGCCGGTAATTATTAATTCT 58.698 37.500 1.90 0.00 32.38 2.40
1473 1606 7.878644 AGCCGGTAATTATTAATTCTTCTCCTC 59.121 37.037 1.90 0.00 32.38 3.71
1484 1617 2.008400 TCTTCTCCTCTTACCCTCCCA 58.992 52.381 0.00 0.00 0.00 4.37
1502 1638 2.034558 CCCATGTCCATTAATTCACGCC 59.965 50.000 0.00 0.00 0.00 5.68
1516 1652 2.343101 TCACGCCTTATTCCTTCGTTG 58.657 47.619 0.00 0.00 0.00 4.10
1520 1656 2.010043 GCCTTATTCCTTCGTTGGCGA 61.010 52.381 0.00 0.00 46.36 5.54
1534 1675 5.704888 TCGTTGGCGAACAAATTTATCAAT 58.295 33.333 12.30 0.00 44.92 2.57
1537 1678 6.947680 CGTTGGCGAACAAATTTATCAATTTC 59.052 34.615 12.30 0.00 41.58 2.17
1552 1697 4.965062 TCAATTTCTGGCGAACGAATTAC 58.035 39.130 0.00 0.00 0.00 1.89
1567 1712 5.095691 CGAATTACTCGGAATTTCCATGG 57.904 43.478 15.58 4.97 44.20 3.66
1568 1713 4.554723 CGAATTACTCGGAATTTCCATGGC 60.555 45.833 15.58 0.00 44.20 4.40
1569 1714 3.644966 TTACTCGGAATTTCCATGGCT 57.355 42.857 15.58 0.00 35.91 4.75
1570 1715 4.764050 TTACTCGGAATTTCCATGGCTA 57.236 40.909 15.58 0.00 35.91 3.93
1571 1716 3.199880 ACTCGGAATTTCCATGGCTAG 57.800 47.619 15.58 5.17 35.91 3.42
1572 1717 1.876156 CTCGGAATTTCCATGGCTAGC 59.124 52.381 15.58 6.04 35.91 3.42
1573 1718 1.490490 TCGGAATTTCCATGGCTAGCT 59.510 47.619 15.72 0.00 35.91 3.32
1574 1719 1.605710 CGGAATTTCCATGGCTAGCTG 59.394 52.381 15.72 5.79 35.91 4.24
1575 1720 1.959282 GGAATTTCCATGGCTAGCTGG 59.041 52.381 15.72 15.48 36.28 4.85
1576 1721 2.423373 GGAATTTCCATGGCTAGCTGGA 60.423 50.000 19.10 19.10 39.78 3.86
1617 1942 1.301623 CCCATTAACACTCGCCCCA 59.698 57.895 0.00 0.00 0.00 4.96
1618 1943 1.029947 CCCATTAACACTCGCCCCAC 61.030 60.000 0.00 0.00 0.00 4.61
1619 1944 1.029947 CCATTAACACTCGCCCCACC 61.030 60.000 0.00 0.00 0.00 4.61
1620 1945 1.029947 CATTAACACTCGCCCCACCC 61.030 60.000 0.00 0.00 0.00 4.61
1621 1946 2.206182 ATTAACACTCGCCCCACCCC 62.206 60.000 0.00 0.00 0.00 4.95
1712 2037 2.403378 GCGGCCGGAAATAGCAACA 61.403 57.895 29.38 0.00 0.00 3.33
1721 2046 5.472137 GCCGGAAATAGCAACATCCTAAATA 59.528 40.000 5.05 0.00 0.00 1.40
1722 2047 6.348540 GCCGGAAATAGCAACATCCTAAATAG 60.349 42.308 5.05 0.00 0.00 1.73
1723 2048 6.348540 CCGGAAATAGCAACATCCTAAATAGC 60.349 42.308 0.00 0.00 0.00 2.97
1724 2049 6.204688 CGGAAATAGCAACATCCTAAATAGCA 59.795 38.462 0.00 0.00 0.00 3.49
1725 2050 7.255104 CGGAAATAGCAACATCCTAAATAGCAA 60.255 37.037 0.00 0.00 0.00 3.91
1780 2141 2.165301 CGCCCGTCTCGTTCCATTC 61.165 63.158 0.00 0.00 0.00 2.67
1789 2150 4.154195 CGTCTCGTTCCATTCCTGAAAATT 59.846 41.667 0.00 0.00 0.00 1.82
1802 2163 2.536803 CTGAAAATTGTGTGCTGTGTGC 59.463 45.455 0.00 0.00 43.25 4.57
2488 2857 4.680237 CGGCGCCAGAAGGACACA 62.680 66.667 28.98 0.00 36.89 3.72
2515 2884 2.882876 CAGCTGCTGCACCATTCC 59.117 61.111 17.73 0.00 42.74 3.01
2522 2891 2.283101 TGCACCATTCCCAGCACC 60.283 61.111 0.00 0.00 31.05 5.01
2719 3139 1.415200 GCCTAGGAGGAGGATCGTTT 58.585 55.000 14.75 0.00 37.67 3.60
2921 3343 6.509386 TCCTTAGAAACTAATCCTAGGGTGT 58.491 40.000 9.46 0.00 33.12 4.16
2925 3347 6.793505 AGAAACTAATCCTAGGGTGTAGTG 57.206 41.667 9.46 0.00 0.00 2.74
2927 3349 3.990369 ACTAATCCTAGGGTGTAGTGCA 58.010 45.455 9.46 0.00 0.00 4.57
2932 3357 2.301870 TCCTAGGGTGTAGTGCAGTTTG 59.698 50.000 9.46 0.00 0.00 2.93
2933 3358 2.038557 CCTAGGGTGTAGTGCAGTTTGT 59.961 50.000 0.00 0.00 0.00 2.83
2934 3359 2.729028 AGGGTGTAGTGCAGTTTGTT 57.271 45.000 0.00 0.00 0.00 2.83
3141 3575 5.234466 ACTAGTGAGATTGAGCAAAGGTT 57.766 39.130 0.00 0.00 0.00 3.50
3225 3663 0.400975 GATGATGATGCCTCTGCCCT 59.599 55.000 0.00 0.00 36.33 5.19
3226 3664 0.110678 ATGATGATGCCTCTGCCCTG 59.889 55.000 0.00 0.00 36.33 4.45
3227 3665 1.897615 GATGATGCCTCTGCCCTGC 60.898 63.158 0.00 0.00 36.33 4.85
3228 3666 3.432445 ATGATGCCTCTGCCCTGCC 62.432 63.158 0.00 0.00 36.33 4.85
3229 3667 4.891037 GATGCCTCTGCCCTGCCC 62.891 72.222 0.00 0.00 36.33 5.36
3248 3686 2.094675 CCCTGTGGTGTTGAATCCATC 58.905 52.381 0.00 0.00 36.09 3.51
3249 3687 2.094675 CCTGTGGTGTTGAATCCATCC 58.905 52.381 0.00 0.00 36.09 3.51
3292 3736 6.156083 ACAAAACAAATGGTATGATAAGGGGG 59.844 38.462 0.00 0.00 0.00 5.40
3294 3738 5.324832 ACAAATGGTATGATAAGGGGGAG 57.675 43.478 0.00 0.00 0.00 4.30
3363 3807 2.109387 TGTGTCCAACCGAACCCG 59.891 61.111 0.00 0.00 0.00 5.28
3366 3810 2.047560 GTCCAACCGAACCCGAGG 60.048 66.667 0.00 0.00 38.22 4.63
3392 3836 1.475169 CCGAGCATGGCATAGGAGGA 61.475 60.000 0.00 0.00 0.00 3.71
3530 3983 1.003116 GGCATCATCATCGTCAACAGC 60.003 52.381 0.00 0.00 0.00 4.40
3696 4177 0.108520 GATCCAACCACTTCGCCGTA 60.109 55.000 0.00 0.00 0.00 4.02
3698 4179 1.005394 CCAACCACTTCGCCGTAGT 60.005 57.895 0.00 0.00 0.00 2.73
3805 4291 2.012948 GCCTCGTTCGTTCGTTCGT 61.013 57.895 9.89 0.00 0.00 3.85
3806 4292 1.543106 GCCTCGTTCGTTCGTTCGTT 61.543 55.000 9.89 0.00 0.00 3.85
3807 4293 0.428618 CCTCGTTCGTTCGTTCGTTC 59.571 55.000 9.89 0.00 0.00 3.95
3808 4294 1.114842 CTCGTTCGTTCGTTCGTTCA 58.885 50.000 9.89 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 1.605710 CATGTCATCGCCAATCTTCCC 59.394 52.381 0.00 0.00 0.00 3.97
12 13 2.397754 CGCCACATGTCATCGCCAA 61.398 57.895 0.00 0.00 0.00 4.52
13 14 2.819154 CGCCACATGTCATCGCCA 60.819 61.111 0.00 0.00 0.00 5.69
15 16 4.241999 GCCGCCACATGTCATCGC 62.242 66.667 0.00 0.00 0.00 4.58
21 22 4.704833 AAGCTCGCCGCCACATGT 62.705 61.111 0.00 0.00 40.39 3.21
23 24 3.899981 TTCAAGCTCGCCGCCACAT 62.900 57.895 0.00 0.00 40.39 3.21
38 39 0.609957 TTCGTCTAGAGCCCCGTTCA 60.610 55.000 0.00 0.00 0.00 3.18
41 42 1.316651 GTATTCGTCTAGAGCCCCGT 58.683 55.000 0.00 0.00 0.00 5.28
43 44 1.340568 GGTGTATTCGTCTAGAGCCCC 59.659 57.143 0.00 0.00 0.00 5.80
48 49 4.142752 CGTCACTTGGTGTATTCGTCTAGA 60.143 45.833 0.00 0.00 34.79 2.43
49 50 4.096311 CGTCACTTGGTGTATTCGTCTAG 58.904 47.826 0.00 0.00 34.79 2.43
57 58 0.315886 TCACGCGTCACTTGGTGTAT 59.684 50.000 9.86 0.00 34.79 2.29
60 61 0.874175 TCTTCACGCGTCACTTGGTG 60.874 55.000 9.86 0.00 34.45 4.17
63 64 0.232303 GGTTCTTCACGCGTCACTTG 59.768 55.000 9.86 0.00 0.00 3.16
70 71 4.150627 CCTAATCATATGGTTCTTCACGCG 59.849 45.833 4.00 3.53 0.00 6.01
75 76 5.406780 CGCACTCCTAATCATATGGTTCTTC 59.593 44.000 4.00 0.00 0.00 2.87
84 85 1.324383 TCGCCGCACTCCTAATCATA 58.676 50.000 0.00 0.00 0.00 2.15
89 90 2.202878 GCATCGCCGCACTCCTAA 60.203 61.111 0.00 0.00 0.00 2.69
96 97 0.456482 CAAATCAAAGCATCGCCGCA 60.456 50.000 0.00 0.00 0.00 5.69
100 101 1.538276 CGGACAAATCAAAGCATCGC 58.462 50.000 0.00 0.00 0.00 4.58
101 102 1.795162 GCCGGACAAATCAAAGCATCG 60.795 52.381 5.05 0.00 0.00 3.84
109 110 2.359354 CCACCGCCGGACAAATCA 60.359 61.111 11.71 0.00 0.00 2.57
120 121 3.787001 CTCCCTCCCTTCCACCGC 61.787 72.222 0.00 0.00 0.00 5.68
136 137 0.323178 CTGCCTCCTCAAATGGTGCT 60.323 55.000 0.00 0.00 0.00 4.40
153 154 2.214387 TAGCATCTCATGTCGTGCTG 57.786 50.000 22.46 5.12 46.48 4.41
159 160 5.900425 TCTTCAGTCTTAGCATCTCATGTC 58.100 41.667 0.00 0.00 0.00 3.06
166 167 4.020662 CCCCCTATCTTCAGTCTTAGCATC 60.021 50.000 0.00 0.00 0.00 3.91
195 196 2.895372 ATCGTCAATTCCGCCGCC 60.895 61.111 0.00 0.00 0.00 6.13
196 197 2.324477 CATCGTCAATTCCGCCGC 59.676 61.111 0.00 0.00 0.00 6.53
202 203 2.076100 TGTGCTCCACATCGTCAATTC 58.924 47.619 0.00 0.00 39.62 2.17
223 224 4.142381 CCATCTATCTCACACTCGTGTCAA 60.142 45.833 0.00 0.00 42.83 3.18
226 227 3.621558 TCCATCTATCTCACACTCGTGT 58.378 45.455 0.00 0.00 46.17 4.49
228 229 4.157849 TCTCCATCTATCTCACACTCGT 57.842 45.455 0.00 0.00 0.00 4.18
234 235 2.887783 TCGCCTTCTCCATCTATCTCAC 59.112 50.000 0.00 0.00 0.00 3.51
235 236 3.153130 CTCGCCTTCTCCATCTATCTCA 58.847 50.000 0.00 0.00 0.00 3.27
269 270 4.603946 GTAGTCGCCGCCATCCCC 62.604 72.222 0.00 0.00 0.00 4.81
270 271 3.379865 TTGTAGTCGCCGCCATCCC 62.380 63.158 0.00 0.00 0.00 3.85
398 401 3.927142 GCTCGCAACACTACAGAATAGTT 59.073 43.478 0.00 0.00 0.00 2.24
409 412 0.038618 TACACGATGCTCGCAACACT 60.039 50.000 0.00 0.00 45.12 3.55
424 427 2.504175 TCAAGGGGAGGTAGCATTACAC 59.496 50.000 0.00 0.00 0.00 2.90
502 506 9.777008 ATTAGGGGTTTTTATTGAGGATTTACA 57.223 29.630 0.00 0.00 0.00 2.41
623 634 8.421249 TGGATCATTTTTGGTGAGTTAGAATT 57.579 30.769 0.00 0.00 0.00 2.17
628 648 7.773489 TGATTGGATCATTTTTGGTGAGTTA 57.227 32.000 0.00 0.00 33.59 2.24
653 673 0.742990 CATGTACGGCAACATCGGGT 60.743 55.000 0.00 0.00 38.01 5.28
666 686 0.457853 TGCTCGTCGCCTTCATGTAC 60.458 55.000 0.00 0.00 38.05 2.90
727 761 2.056223 TCCCGGGGAAGACGACATC 61.056 63.158 23.50 0.00 0.00 3.06
743 777 0.765510 AGCTCCCCGATTTATGGTCC 59.234 55.000 0.00 0.00 0.00 4.46
792 845 4.036941 AGCCTGTTAAATCGGGGTTTTA 57.963 40.909 0.00 0.00 41.12 1.52
861 917 0.979665 CCACTGGCTCTTCTCTGGAA 59.020 55.000 0.00 0.00 0.00 3.53
862 918 1.548357 GCCACTGGCTCTTCTCTGGA 61.548 60.000 13.28 0.00 46.69 3.86
875 947 4.265073 AGTAAATAAAGCCAGAGCCACTG 58.735 43.478 2.06 2.06 45.36 3.66
935 1039 1.669927 GGAGAGAGATGGGAGGGGGA 61.670 65.000 0.00 0.00 0.00 4.81
936 1040 1.152139 GGAGAGAGATGGGAGGGGG 60.152 68.421 0.00 0.00 0.00 5.40
945 1049 0.467290 GCGGAGTGGAGGAGAGAGAT 60.467 60.000 0.00 0.00 0.00 2.75
1090 1199 0.996762 TCCTCCTCCTCCTCCTCCTC 60.997 65.000 0.00 0.00 0.00 3.71
1091 1200 0.998945 CTCCTCCTCCTCCTCCTCCT 60.999 65.000 0.00 0.00 0.00 3.69
1092 1201 1.541672 CTCCTCCTCCTCCTCCTCC 59.458 68.421 0.00 0.00 0.00 4.30
1093 1202 0.996762 TCCTCCTCCTCCTCCTCCTC 60.997 65.000 0.00 0.00 0.00 3.71
1094 1203 0.998945 CTCCTCCTCCTCCTCCTCCT 60.999 65.000 0.00 0.00 0.00 3.69
1095 1204 1.541672 CTCCTCCTCCTCCTCCTCC 59.458 68.421 0.00 0.00 0.00 4.30
1096 1205 1.541672 CCTCCTCCTCCTCCTCCTC 59.458 68.421 0.00 0.00 0.00 3.71
1097 1206 2.018086 CCCTCCTCCTCCTCCTCCT 61.018 68.421 0.00 0.00 0.00 3.69
1466 1599 2.045885 ACATGGGAGGGTAAGAGGAGAA 59.954 50.000 0.00 0.00 0.00 2.87
1473 1606 4.788925 TTAATGGACATGGGAGGGTAAG 57.211 45.455 0.00 0.00 0.00 2.34
1484 1617 6.016276 GGAATAAGGCGTGAATTAATGGACAT 60.016 38.462 0.00 0.00 0.00 3.06
1516 1652 6.455513 GCCAGAAATTGATAAATTTGTTCGCC 60.456 38.462 5.44 0.00 32.92 5.54
1520 1656 7.148820 CGTTCGCCAGAAATTGATAAATTTGTT 60.149 33.333 5.44 0.00 38.23 2.83
1523 1659 6.616947 TCGTTCGCCAGAAATTGATAAATTT 58.383 32.000 0.00 0.00 38.23 1.82
1534 1675 2.664568 CGAGTAATTCGTTCGCCAGAAA 59.335 45.455 0.00 0.00 44.27 2.52
1552 1697 1.876156 GCTAGCCATGGAAATTCCGAG 59.124 52.381 18.40 3.14 40.17 4.63
1555 1700 1.959282 CCAGCTAGCCATGGAAATTCC 59.041 52.381 18.40 4.79 39.02 3.01
1556 1701 2.936202 TCCAGCTAGCCATGGAAATTC 58.064 47.619 20.35 0.00 42.61 2.17
1561 1706 1.522092 CGTTCCAGCTAGCCATGGA 59.478 57.895 19.10 19.10 43.87 3.41
1562 1707 1.524621 CCGTTCCAGCTAGCCATGG 60.525 63.158 15.30 15.30 37.97 3.66
1563 1708 0.811616 GACCGTTCCAGCTAGCCATG 60.812 60.000 12.13 3.78 0.00 3.66
1564 1709 1.264749 TGACCGTTCCAGCTAGCCAT 61.265 55.000 12.13 0.00 0.00 4.40
1565 1710 1.476845 TTGACCGTTCCAGCTAGCCA 61.477 55.000 12.13 0.00 0.00 4.75
1566 1711 0.107654 ATTGACCGTTCCAGCTAGCC 60.108 55.000 12.13 0.00 0.00 3.93
1567 1712 1.009829 CATTGACCGTTCCAGCTAGC 58.990 55.000 6.62 6.62 0.00 3.42
1568 1713 1.009829 GCATTGACCGTTCCAGCTAG 58.990 55.000 0.00 0.00 0.00 3.42
1569 1714 0.739462 CGCATTGACCGTTCCAGCTA 60.739 55.000 0.00 0.00 0.00 3.32
1570 1715 2.034879 CGCATTGACCGTTCCAGCT 61.035 57.895 0.00 0.00 0.00 4.24
1571 1716 1.852067 AACGCATTGACCGTTCCAGC 61.852 55.000 0.00 0.00 44.70 4.85
1572 1717 2.244000 AACGCATTGACCGTTCCAG 58.756 52.632 0.00 0.00 44.70 3.86
1573 1718 4.466133 AACGCATTGACCGTTCCA 57.534 50.000 0.00 0.00 44.70 3.53
1624 1949 2.635596 ATTCATGGGGTGGGGTGGG 61.636 63.158 0.00 0.00 0.00 4.61
1625 1950 1.381599 CATTCATGGGGTGGGGTGG 60.382 63.158 0.00 0.00 0.00 4.61
1626 1951 0.040942 TTCATTCATGGGGTGGGGTG 59.959 55.000 0.00 0.00 0.00 4.61
1627 1952 0.336048 CTTCATTCATGGGGTGGGGT 59.664 55.000 0.00 0.00 0.00 4.95
1628 1953 0.397535 CCTTCATTCATGGGGTGGGG 60.398 60.000 0.00 0.00 0.00 4.96
1629 1954 1.044790 GCCTTCATTCATGGGGTGGG 61.045 60.000 0.00 0.00 0.00 4.61
1630 1955 0.324552 TGCCTTCATTCATGGGGTGG 60.325 55.000 0.00 0.00 0.00 4.61
1631 1956 1.108776 CTGCCTTCATTCATGGGGTG 58.891 55.000 0.00 0.00 0.00 4.61
1632 1957 0.685458 GCTGCCTTCATTCATGGGGT 60.685 55.000 0.00 0.00 0.00 4.95
1672 1997 4.495184 GCGGGTTTCATCGGTTACTATTTG 60.495 45.833 0.00 0.00 0.00 2.32
1721 2046 9.467258 CGGAAATGATAATAAATTGATGTTGCT 57.533 29.630 0.00 0.00 0.00 3.91
1722 2047 9.462174 TCGGAAATGATAATAAATTGATGTTGC 57.538 29.630 0.00 0.00 0.00 4.17
1769 2129 5.156355 CACAATTTTCAGGAATGGAACGAG 58.844 41.667 0.00 0.00 0.00 4.18
1780 2141 3.117794 CACACAGCACACAATTTTCAGG 58.882 45.455 0.00 0.00 0.00 3.86
1802 2163 1.732259 GTCGTACTGCAAATCCACAGG 59.268 52.381 0.00 0.00 38.25 4.00
2695 3115 2.723464 ATCCTCCTCCTAGGCGAGCC 62.723 65.000 16.50 5.89 36.51 4.70
2719 3139 2.196997 ATTGCTGCTGGGGCTAACGA 62.197 55.000 0.00 0.00 39.59 3.85
2921 3343 5.437060 AGAGAAGGAAAACAAACTGCACTA 58.563 37.500 0.00 0.00 0.00 2.74
2925 3347 5.506686 AGAAGAGAAGGAAAACAAACTGC 57.493 39.130 0.00 0.00 0.00 4.40
2967 3392 8.695456 AGAAGAAACTCTATGGAAAAGCAAAAA 58.305 29.630 0.00 0.00 0.00 1.94
2968 3393 8.237811 AGAAGAAACTCTATGGAAAAGCAAAA 57.762 30.769 0.00 0.00 0.00 2.44
2989 3414 8.077991 TGACTGCATTACAAGAAAATGAAGAAG 58.922 33.333 10.13 0.74 40.96 2.85
3079 3509 3.865011 TCAAAGAAAAACACTGCTGCA 57.135 38.095 0.88 0.88 0.00 4.41
3225 3663 0.539438 GATTCAACACCACAGGGGCA 60.539 55.000 0.00 0.00 42.05 5.36
3226 3664 1.250840 GGATTCAACACCACAGGGGC 61.251 60.000 0.00 0.00 42.05 5.80
3227 3665 0.112218 TGGATTCAACACCACAGGGG 59.888 55.000 0.00 0.00 44.81 4.79
3228 3666 2.094675 GATGGATTCAACACCACAGGG 58.905 52.381 0.00 0.00 39.06 4.45
3229 3667 2.094675 GGATGGATTCAACACCACAGG 58.905 52.381 0.00 0.00 39.06 4.00
3248 3686 3.392882 TGTTTGATCGATCGATGGATGG 58.607 45.455 33.86 0.00 34.60 3.51
3249 3687 5.408204 TTTGTTTGATCGATCGATGGATG 57.592 39.130 33.86 2.68 34.60 3.51
3376 3820 1.132913 TCTCTCCTCCTATGCCATGCT 60.133 52.381 0.00 0.00 0.00 3.79
3392 3836 2.043450 CGCTCCCCTCCACTCTCT 60.043 66.667 0.00 0.00 0.00 3.10
3530 3983 2.033141 CACACAGGGCCAGTGAGG 59.967 66.667 32.53 20.37 40.16 3.86
3552 4008 1.400494 ACGTATCGGCTTTCAATTGCC 59.600 47.619 0.00 0.00 45.25 4.52
3553 4009 2.095213 TGACGTATCGGCTTTCAATTGC 59.905 45.455 0.00 0.00 35.04 3.56
3580 4040 9.634163 GAAAAGATATTTACTCTAGAGCTAGGC 57.366 37.037 19.97 3.88 34.06 3.93
3663 4138 1.080839 GGATCCGATCTCTCGCAGC 60.081 63.158 8.29 0.00 43.66 5.25
3696 4177 5.923684 CCGCACCAAAAACAATTTACATACT 59.076 36.000 0.00 0.00 0.00 2.12
3698 4179 4.686554 GCCGCACCAAAAACAATTTACATA 59.313 37.500 0.00 0.00 0.00 2.29
3805 4291 0.178947 AAAAAGGTGGCCCGGATGAA 60.179 50.000 0.73 0.00 35.12 2.57
3806 4292 1.462928 AAAAAGGTGGCCCGGATGA 59.537 52.632 0.73 0.00 35.12 2.92
3807 4293 4.111967 AAAAAGGTGGCCCGGATG 57.888 55.556 0.73 0.00 35.12 3.51


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

AutoCloner maintained by Alex Coulton.