Multiple sequence alignment - TraesCS4D01G234500

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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 TraesCS4D01G234500 chr4D 100.000 7832 0 0 994 8825 394846401 394854232 0.000000e+00 14464.0
1 TraesCS4D01G234500 chr4D 100.000 620 0 0 1 620 394845408 394846027 0.000000e+00 1146.0
2 TraesCS4D01G234500 chr4D 95.238 126 6 0 2312 2437 394847644 394847769 5.400000e-47 200.0
3 TraesCS4D01G234500 chr4D 95.238 126 6 0 2237 2362 394847719 394847844 5.400000e-47 200.0
4 TraesCS4D01G234500 chr4A 96.037 7519 188 43 994 8431 76414796 76422285 0.000000e+00 12133.0
5 TraesCS4D01G234500 chr4A 88.753 409 21 12 8425 8825 76422307 76422698 2.230000e-130 477.0
6 TraesCS4D01G234500 chr4A 89.262 298 13 6 317 596 76413981 76414277 1.090000e-93 355.0
7 TraesCS4D01G234500 chr4A 96.825 126 4 0 2312 2437 76416033 76416158 2.500000e-50 211.0
8 TraesCS4D01G234500 chr4A 90.566 159 7 1 2237 2387 76416108 76416266 4.180000e-48 204.0
9 TraesCS4D01G234500 chr4A 95.652 46 2 0 254 299 76413949 76413994 3.420000e-09 75.0
10 TraesCS4D01G234500 chr4B 97.375 5752 117 21 2237 7968 485548018 485553755 0.000000e+00 9755.0
11 TraesCS4D01G234500 chr4B 96.980 861 25 1 2259 3119 485544794 485545653 0.000000e+00 1445.0
12 TraesCS4D01G234500 chr4B 93.892 835 36 3 1603 2437 485547324 485548143 0.000000e+00 1245.0
13 TraesCS4D01G234500 chr4B 92.029 828 41 9 994 1819 485546524 485547328 0.000000e+00 1140.0
14 TraesCS4D01G234500 chr4B 94.231 624 28 8 1 620 485545833 485546452 0.000000e+00 946.0
15 TraesCS4D01G234500 chr4B 91.379 464 24 4 7970 8424 485553798 485554254 9.730000e-174 621.0
16 TraesCS4D01G234500 chr4B 89.826 403 22 5 8425 8825 485554283 485554668 4.760000e-137 499.0
17 TraesCS4D01G234500 chr4B 96.032 126 5 0 2312 2437 485547943 485548068 1.160000e-48 206.0
18 TraesCS4D01G234500 chr4B 89.308 159 9 5 2237 2387 485548093 485548251 9.040000e-45 193.0
19 TraesCS4D01G234500 chr4B 86.792 159 13 5 2237 2387 485544847 485545005 4.240000e-38 171.0
20 TraesCS4D01G234500 chr4B 93.519 108 7 0 2330 2437 485544790 485544897 2.550000e-35 161.0
21 TraesCS4D01G234500 chr3A 93.333 45 2 1 7973 8016 566905208 566905164 2.060000e-06 65.8


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 TraesCS4D01G234500 chr4D 394845408 394854232 8824 False 7805.000000 14464 100.000000 1 8825 2 chr4D.!!$F1 8824
1 TraesCS4D01G234500 chr4A 76413949 76422285 8336 False 4187.666667 12133 93.650333 254 8431 3 chr4A.!!$F2 8177
2 TraesCS4D01G234500 chr4B 485544790 485553755 8965 False 1883.625000 9755 93.856250 1 7968 8 chr4B.!!$F2 7967
3 TraesCS4D01G234500 chr4B 485553798 485554668 870 False 560.000000 621 90.602500 7970 8825 2 chr4B.!!$F3 855

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
419 1464 0.034896 ACCAGATTTCGAACGCCTGT 59.965 50.000 15.24 2.6 0.00 4.00 F
1282 2469 1.153901 CGATTCCGTACTGTGCCGT 60.154 57.895 0.00 0.0 0.00 5.68 F
2423 3892 0.471780 TCTCCTGAGGCACCTTGACA 60.472 55.000 0.00 0.0 0.00 3.58 F
2437 3906 0.534877 TTGACATTGCTGCACTCCGT 60.535 50.000 0.00 0.0 0.00 4.69 F
2443 3912 1.748329 TTGCTGCACTCCGTGTCTCT 61.748 55.000 0.00 0.0 35.75 3.10 F
3242 4711 2.036958 TCCTAATGCACCCGTCATTG 57.963 50.000 0.00 0.0 35.87 2.82 F
3646 5122 2.764010 TCTGCTTATATCCACCACGTGT 59.236 45.455 15.65 0.0 0.00 4.49 F
4469 5951 0.327259 TTGAGCATGCTGAAGAGGCT 59.673 50.000 28.27 0.0 37.56 4.58 F
6253 7744 0.108520 CCGCCGTGTTGGTAGTACAT 60.109 55.000 2.06 0.0 41.21 2.29 F
6849 8340 2.115052 ACATGCCCGCCTCACAAA 59.885 55.556 0.00 0.0 0.00 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1760 3145 0.036164 CCATCACCGACCACTCCAAA 59.964 55.000 0.0 0.0 0.00 3.28 R
2443 3912 0.250727 GTACAGCTCCAACCAAGGCA 60.251 55.000 0.0 0.0 0.00 4.75 R
3399 4868 2.102578 GTATTGCATGAAAGGTGGGCT 58.897 47.619 0.0 0.0 0.00 5.19 R
3504 4973 4.253685 GCTCAGTTGCTCACCTAAACATA 58.746 43.478 0.0 0.0 0.00 2.29 R
3538 5007 4.673534 ACTTGAACACGAAACGAAAAGT 57.326 36.364 0.0 0.0 0.00 2.66 R
4469 5951 2.753452 GTCACGTACATCCTCTTCCTCA 59.247 50.000 0.0 0.0 0.00 3.86 R
5209 6700 2.787473 TCCTGAATAGTTGCTGGTGG 57.213 50.000 0.0 0.0 0.00 4.61 R
6357 7848 0.182537 CCACTGGTTTGGGTGACTCA 59.817 55.000 0.0 0.0 35.69 3.41 R
7176 8667 0.252789 TTCCATGTCGGTAAGGGGGA 60.253 55.000 0.0 0.0 35.57 4.81 R
8681 10256 0.039256 CATTGTGGTCGGTTGCCTTG 60.039 55.000 0.0 0.0 0.00 3.61 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 1065 1.710244 AGTTGAATGGGGGATGACACA 59.290 47.619 0.00 0.00 0.00 3.72
24 1068 1.710244 TGAATGGGGGATGACACACTT 59.290 47.619 0.00 0.00 0.00 3.16
27 1071 2.038863 TGGGGGATGACACACTTACT 57.961 50.000 0.00 0.00 0.00 2.24
55 1099 1.463444 GTGGTAACTCCGCACAATGAC 59.537 52.381 0.00 0.00 45.32 3.06
76 1120 7.320443 TGACCATTATATCAAGCTCACAAAC 57.680 36.000 0.00 0.00 0.00 2.93
82 1126 9.926751 CATTATATCAAGCTCACAAACTACTTG 57.073 33.333 0.00 0.00 41.19 3.16
107 1151 8.941977 TGTACATACACATTCAAAGTATTCACC 58.058 33.333 0.00 0.00 0.00 4.02
108 1152 7.994425 ACATACACATTCAAAGTATTCACCA 57.006 32.000 0.00 0.00 0.00 4.17
112 1156 5.833131 ACACATTCAAAGTATTCACCAACCT 59.167 36.000 0.00 0.00 0.00 3.50
132 1176 2.046283 TCGTAAGAGTGCAACGACAG 57.954 50.000 6.48 0.00 45.86 3.51
134 1178 2.228103 TCGTAAGAGTGCAACGACAGAT 59.772 45.455 6.48 0.00 45.86 2.90
135 1179 2.594654 CGTAAGAGTGCAACGACAGATC 59.405 50.000 1.66 0.00 45.86 2.75
137 1181 4.436986 CGTAAGAGTGCAACGACAGATCTA 60.437 45.833 1.66 0.00 45.86 1.98
153 1198 6.842676 ACAGATCTAAAGAACCTTGGAAAGT 58.157 36.000 0.00 0.00 44.25 2.66
162 1207 5.131067 AGAACCTTGGAAAGTACAGGAAAC 58.869 41.667 1.89 0.00 44.25 2.78
176 1221 7.918643 AGTACAGGAAACAAAATTGCAATTTG 58.081 30.769 32.23 26.35 42.18 2.32
241 1286 4.317671 ACTCGGGATTAGTATTTCGGTG 57.682 45.455 0.00 0.00 0.00 4.94
243 1288 4.403432 ACTCGGGATTAGTATTTCGGTGAA 59.597 41.667 0.00 0.00 0.00 3.18
246 1291 5.813672 TCGGGATTAGTATTTCGGTGAAAAG 59.186 40.000 0.00 0.00 35.11 2.27
306 1351 1.959085 CACACCATGTGTTGCCTCC 59.041 57.895 0.00 0.00 45.08 4.30
419 1464 0.034896 ACCAGATTTCGAACGCCTGT 59.965 50.000 15.24 2.60 0.00 4.00
495 1541 2.099921 CAGTAGAACGGACCCATGAGAG 59.900 54.545 0.00 0.00 0.00 3.20
1282 2469 1.153901 CGATTCCGTACTGTGCCGT 60.154 57.895 0.00 0.00 0.00 5.68
1321 2508 3.501040 AATTGGGGTTCGGCGGTGT 62.501 57.895 7.21 0.00 0.00 4.16
1392 2579 1.445582 GCTCGGGTTCGGTGTGTAG 60.446 63.158 0.00 0.00 36.95 2.74
1460 2649 4.035091 TGGTGATATCAAAAAGGATTCGCG 59.965 41.667 7.07 0.00 0.00 5.87
1608 2797 2.472029 AGTTACTCTGTGGGCAGCTAT 58.528 47.619 0.00 0.00 42.29 2.97
1642 2831 1.881973 TGAGTTGGTGCATTGCTCTTC 59.118 47.619 10.49 4.65 0.00 2.87
1721 2910 5.474876 CAGGATTGGGCCTTATTGATACTTC 59.525 44.000 4.53 0.00 35.66 3.01
1760 3145 4.879295 TGGTATGGGTTGAATTGGAGAT 57.121 40.909 0.00 0.00 0.00 2.75
1772 3157 2.472695 TTGGAGATTTGGAGTGGTCG 57.527 50.000 0.00 0.00 0.00 4.79
1825 3210 7.283329 AGACACTTGATTTAGAACTGGTTTCT 58.717 34.615 0.00 0.00 46.91 2.52
1951 3336 7.775053 AAACTATTGGCTCAAAACAGGATAA 57.225 32.000 0.00 0.00 0.00 1.75
1953 3338 7.775053 ACTATTGGCTCAAAACAGGATAAAA 57.225 32.000 0.00 0.00 0.00 1.52
1958 3343 9.603921 ATTGGCTCAAAACAGGATAAAAATATG 57.396 29.630 0.00 0.00 0.00 1.78
2067 3452 7.725844 ACTTTACATCTTTCACTTCCTTCCATT 59.274 33.333 0.00 0.00 0.00 3.16
2177 3565 4.594123 TGTTTTGTATCTCTGTCGTGGA 57.406 40.909 0.00 0.00 0.00 4.02
2178 3566 4.951254 TGTTTTGTATCTCTGTCGTGGAA 58.049 39.130 0.00 0.00 0.00 3.53
2179 3567 5.547465 TGTTTTGTATCTCTGTCGTGGAAT 58.453 37.500 0.00 0.00 0.00 3.01
2180 3568 6.693466 TGTTTTGTATCTCTGTCGTGGAATA 58.307 36.000 0.00 0.00 0.00 1.75
2181 3569 7.327975 TGTTTTGTATCTCTGTCGTGGAATAT 58.672 34.615 0.00 0.00 0.00 1.28
2182 3570 7.822334 TGTTTTGTATCTCTGTCGTGGAATATT 59.178 33.333 0.00 0.00 0.00 1.28
2255 3649 5.540911 ACCTTCGATTTTCCGTTACAACTA 58.459 37.500 0.00 0.00 0.00 2.24
2285 3679 0.886490 CCTTGACTTTGCCGCACTCT 60.886 55.000 0.00 0.00 0.00 3.24
2423 3892 0.471780 TCTCCTGAGGCACCTTGACA 60.472 55.000 0.00 0.00 0.00 3.58
2437 3906 0.534877 TTGACATTGCTGCACTCCGT 60.535 50.000 0.00 0.00 0.00 4.69
2443 3912 1.748329 TTGCTGCACTCCGTGTCTCT 61.748 55.000 0.00 0.00 35.75 3.10
2534 4003 6.447084 TCCATAATAGAGTTTTCTTGTCCCCT 59.553 38.462 0.00 0.00 34.79 4.79
2806 4275 4.858935 TGCTTCTGGAAAATTTCAAGTCG 58.141 39.130 9.71 4.13 32.34 4.18
3009 4478 7.594758 CCAGAATGTAAGTGTAAACAATTGTGG 59.405 37.037 12.82 6.24 35.62 4.17
3132 4601 3.679980 TGTCTGAACTAATCGCTCTTTGC 59.320 43.478 0.00 0.00 38.57 3.68
3237 4706 3.454812 ACTCTATTTCCTAATGCACCCGT 59.545 43.478 0.00 0.00 0.00 5.28
3242 4711 2.036958 TCCTAATGCACCCGTCATTG 57.963 50.000 0.00 0.00 35.87 2.82
3399 4868 3.678289 AGAAACATGTGCTCTGCATACA 58.322 40.909 0.00 0.00 41.91 2.29
3504 4973 7.180663 AGGAGGATGATTTCATTGAAAGACTT 58.819 34.615 16.34 10.97 34.92 3.01
3538 5007 3.453717 AGCAACTGAGCATAATGGAGAGA 59.546 43.478 0.00 0.00 36.85 3.10
3550 5019 4.992381 AATGGAGAGACTTTTCGTTTCG 57.008 40.909 0.00 0.00 32.31 3.46
3646 5122 2.764010 TCTGCTTATATCCACCACGTGT 59.236 45.455 15.65 0.00 0.00 4.49
4409 5891 2.976490 GCTGGTGCTGGGAGATGGT 61.976 63.158 0.00 0.00 36.03 3.55
4469 5951 0.327259 TTGAGCATGCTGAAGAGGCT 59.673 50.000 28.27 0.00 37.56 4.58
5042 6525 9.903682 AATAAATGTGTTCTCTTTCTGTTGATG 57.096 29.630 0.00 0.00 0.00 3.07
5056 6539 8.961294 TTTCTGTTGATGAATGGATTGTTTTT 57.039 26.923 0.00 0.00 0.00 1.94
5071 6554 7.148154 TGGATTGTTTTTAGGTGATTGATACGG 60.148 37.037 0.00 0.00 0.00 4.02
5186 6677 1.143684 TGGACAAGCTCTTTTCCTGCT 59.856 47.619 13.94 0.00 39.51 4.24
5209 6700 7.140048 GCTATACTATTGGTGTGACTGTAGTC 58.860 42.308 5.09 5.09 44.97 2.59
5429 6920 6.279882 ACATTGGAAAAACAGGTATGTGTTG 58.720 36.000 0.00 0.00 39.82 3.33
5431 6922 5.923733 TGGAAAAACAGGTATGTGTTGTT 57.076 34.783 0.00 0.00 40.02 2.83
6180 7671 2.111582 GCCAACAGCTAGAGCAGGC 61.112 63.158 4.01 7.77 45.16 4.85
6253 7744 0.108520 CCGCCGTGTTGGTAGTACAT 60.109 55.000 2.06 0.00 41.21 2.29
6293 7784 5.313712 TCCAAAACAAGTATGGGAGAGAAC 58.686 41.667 5.46 0.00 34.89 3.01
6387 7878 4.335416 CCAAACCAGTGGAATGTGATACT 58.665 43.478 18.40 0.00 41.65 2.12
6415 7906 3.554934 TGTGAAAAGCTTGACACAGGAT 58.445 40.909 24.99 0.00 38.14 3.24
6480 7971 9.055248 GTTTGTAAATCAGAAACAGATCAATCG 57.945 33.333 0.00 0.00 39.57 3.34
6516 8007 5.051891 AGGAAAATCAATCTGCTTGTTCG 57.948 39.130 0.00 0.00 36.20 3.95
6545 8036 7.827236 TGGAACTCCTATGACGAATAAACAAAT 59.173 33.333 0.00 0.00 36.82 2.32
6759 8250 5.363562 ACATCATTACAGAAGCTCCATCA 57.636 39.130 0.00 0.00 0.00 3.07
6849 8340 2.115052 ACATGCCCGCCTCACAAA 59.885 55.556 0.00 0.00 0.00 2.83
7122 8613 4.157840 CCTGCTTTTAGTTGTATTCACCCC 59.842 45.833 0.00 0.00 0.00 4.95
7251 8742 5.178096 TGAATCCAGACAGGCTTAATTCA 57.822 39.130 6.11 6.11 34.77 2.57
7392 8883 4.508662 CCAAAGATGGTAAGAGTGGAGAC 58.491 47.826 0.00 0.00 42.18 3.36
7395 8886 8.526065 CCAAAGATGGTAAGAGTGGAGACTCC 62.526 50.000 15.13 15.13 44.46 3.85
7414 8905 1.223487 GTAGGAAGGATGCCGCCAA 59.777 57.895 0.00 0.00 40.87 4.52
7560 9051 4.083802 ACGTGCTCTTCTCATTTTTACTGC 60.084 41.667 0.00 0.00 0.00 4.40
7593 9084 7.200455 TGTATACGGTGAGTGATTGTATCAAG 58.800 38.462 0.00 0.00 41.69 3.02
7835 9341 3.882888 TGAATGAGTTGGTTCCTGTGTTC 59.117 43.478 0.00 0.00 0.00 3.18
7838 9344 3.541632 TGAGTTGGTTCCTGTGTTCTTC 58.458 45.455 0.00 0.00 0.00 2.87
7844 9350 5.623956 TGGTTCCTGTGTTCTTCTCTTTA 57.376 39.130 0.00 0.00 0.00 1.85
7845 9351 5.996644 TGGTTCCTGTGTTCTTCTCTTTAA 58.003 37.500 0.00 0.00 0.00 1.52
7847 9353 7.060421 TGGTTCCTGTGTTCTTCTCTTTAATT 58.940 34.615 0.00 0.00 0.00 1.40
8102 9635 2.169144 TGGGTATCTCATGTGCTCTGTG 59.831 50.000 0.00 0.00 0.00 3.66
8103 9636 2.484417 GGGTATCTCATGTGCTCTGTGG 60.484 54.545 0.00 0.00 0.00 4.17
8104 9637 2.208431 GTATCTCATGTGCTCTGTGGC 58.792 52.381 0.00 0.00 0.00 5.01
8147 9680 3.806521 GCTCACACCATGCTAATCTACAG 59.193 47.826 0.00 0.00 0.00 2.74
8150 9683 6.538945 TCACACCATGCTAATCTACAGTTA 57.461 37.500 0.00 0.00 0.00 2.24
8260 9802 1.243902 TGCAAAGGGGAAAGCTAACG 58.756 50.000 0.00 0.00 0.00 3.18
8347 9889 0.599558 CTCCACACATTGGCACCAAG 59.400 55.000 8.30 3.24 46.47 3.61
8353 9895 1.187567 ACATTGGCACCAAGGAAGGC 61.188 55.000 20.03 0.00 39.72 4.35
8380 9922 3.383229 TGCAGCAAAGCATGGCAT 58.617 50.000 0.00 0.00 40.11 4.40
8427 9974 5.215069 AGATCATGGTGTCTAGAACAGGAT 58.785 41.667 15.84 15.84 38.97 3.24
8431 10005 3.371965 TGGTGTCTAGAACAGGATACCC 58.628 50.000 0.00 0.00 41.15 3.69
8454 10028 2.042831 CCCTTGCCTTGGCTCGAAG 61.043 63.158 13.18 8.02 0.00 3.79
8457 10031 2.754664 CTTGCCTTGGCTCGAAGGGT 62.755 60.000 13.18 0.00 42.63 4.34
8481 10055 4.321082 GCCGTACCATTGGAGTATAGAGAC 60.321 50.000 10.37 0.00 0.00 3.36
8490 10064 2.573369 GAGTATAGAGACGCTCACCCA 58.427 52.381 9.09 0.00 32.06 4.51
8493 10067 2.145397 ATAGAGACGCTCACCCAAGA 57.855 50.000 9.09 0.00 32.06 3.02
8520 10094 0.899717 GGATGCCAACCTCAAAGCCA 60.900 55.000 0.00 0.00 0.00 4.75
8557 10132 3.432051 CTCGATCCGGGCACACCTC 62.432 68.421 0.00 0.00 36.97 3.85
8567 10142 4.662961 CACACCTCGCCGACAGCA 62.663 66.667 0.00 0.00 44.04 4.41
8568 10143 4.664677 ACACCTCGCCGACAGCAC 62.665 66.667 0.00 0.00 44.04 4.40
8572 10147 4.363990 CTCGCCGACAGCACCAGT 62.364 66.667 0.00 0.00 44.04 4.00
8593 10168 1.679139 CACCACTGCTGTCCAAGAAA 58.321 50.000 0.00 0.00 0.00 2.52
8645 10220 0.108615 ATTGTCGTCGAAGGAGGCAG 60.109 55.000 0.00 0.00 0.00 4.85
8651 10226 3.710722 CGAAGGAGGCAGCAGGGT 61.711 66.667 0.00 0.00 0.00 4.34
8677 10252 0.110464 GTGAACGAAGAGCAGCAAGC 60.110 55.000 0.00 0.00 46.19 4.01
8707 10282 1.324383 ACCGACCACAATGGAAAACC 58.676 50.000 0.84 0.00 40.96 3.27
8770 10345 2.122369 CCCTATCCCCTTCCGCCT 60.122 66.667 0.00 0.00 0.00 5.52
8771 10346 2.520536 CCCTATCCCCTTCCGCCTG 61.521 68.421 0.00 0.00 0.00 4.85
8775 10350 1.352622 TATCCCCTTCCGCCTGCATT 61.353 55.000 0.00 0.00 0.00 3.56
8785 10360 3.197790 CCTGCATTGAGGACGCCG 61.198 66.667 0.00 0.00 34.69 6.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 1.818674 GTGTGTCATCCCCCATTCAAC 59.181 52.381 0.00 0.00 0.00 3.18
21 1065 6.703165 CGGAGTTACCACTTGTAAAAGTAAGT 59.297 38.462 0.00 2.17 41.00 2.24
24 1068 4.990426 GCGGAGTTACCACTTGTAAAAGTA 59.010 41.667 0.00 0.00 41.00 2.24
27 1071 3.560896 GTGCGGAGTTACCACTTGTAAAA 59.439 43.478 0.00 0.00 41.00 1.52
39 1083 2.779755 ATGGTCATTGTGCGGAGTTA 57.220 45.000 0.00 0.00 0.00 2.24
49 1093 7.500720 TGTGAGCTTGATATAATGGTCATTG 57.499 36.000 10.22 0.00 38.80 2.82
55 1099 8.668510 AGTAGTTTGTGAGCTTGATATAATGG 57.331 34.615 0.00 0.00 0.00 3.16
82 1126 8.941977 TGGTGAATACTTTGAATGTGTATGTAC 58.058 33.333 0.00 0.00 0.00 2.90
106 1150 2.163818 TGCACTCTTACGAAGGTTGG 57.836 50.000 0.00 0.00 0.00 3.77
107 1151 2.096909 CGTTGCACTCTTACGAAGGTTG 60.097 50.000 1.66 0.00 37.47 3.77
108 1152 2.132762 CGTTGCACTCTTACGAAGGTT 58.867 47.619 1.66 0.00 37.47 3.50
112 1156 2.033675 TCTGTCGTTGCACTCTTACGAA 59.966 45.455 11.81 3.22 44.71 3.85
120 1164 4.521130 TCTTTAGATCTGTCGTTGCACT 57.479 40.909 5.18 0.00 0.00 4.40
126 1170 4.527038 TCCAAGGTTCTTTAGATCTGTCGT 59.473 41.667 5.18 0.00 0.00 4.34
127 1171 5.073311 TCCAAGGTTCTTTAGATCTGTCG 57.927 43.478 5.18 0.00 0.00 4.35
129 1173 6.842676 ACTTTCCAAGGTTCTTTAGATCTGT 58.157 36.000 5.18 0.00 0.00 3.41
130 1174 7.878127 TGTACTTTCCAAGGTTCTTTAGATCTG 59.122 37.037 5.18 0.00 0.00 2.90
132 1176 7.334671 CCTGTACTTTCCAAGGTTCTTTAGATC 59.665 40.741 0.00 0.00 0.00 2.75
134 1178 6.328148 TCCTGTACTTTCCAAGGTTCTTTAGA 59.672 38.462 0.00 0.00 0.00 2.10
135 1179 6.531021 TCCTGTACTTTCCAAGGTTCTTTAG 58.469 40.000 0.00 0.00 0.00 1.85
137 1181 5.382664 TCCTGTACTTTCCAAGGTTCTTT 57.617 39.130 0.00 0.00 0.00 2.52
153 1198 7.856145 ACAAATTGCAATTTTGTTTCCTGTA 57.144 28.000 30.13 0.00 36.52 2.74
203 1248 7.798596 TCCCGAGTAGTAGAATAACTTACAG 57.201 40.000 0.00 0.00 0.00 2.74
235 1280 4.701651 AGAATGCATGATCTTTTCACCGAA 59.298 37.500 0.00 0.00 37.11 4.30
241 1286 9.286946 CTAAACTTGAGAATGCATGATCTTTTC 57.713 33.333 0.00 0.00 0.00 2.29
243 1288 8.345724 ACTAAACTTGAGAATGCATGATCTTT 57.654 30.769 0.00 1.74 0.00 2.52
246 1291 7.312657 TGACTAAACTTGAGAATGCATGATC 57.687 36.000 0.00 1.79 0.00 2.92
306 1351 2.772568 TGATGTGCCACTTGTTTTCG 57.227 45.000 0.00 0.00 0.00 3.46
495 1541 1.527188 GCGCGGTTCGATTTCTCTTTC 60.527 52.381 8.83 0.00 41.67 2.62
1282 2469 7.372714 CAATTCTCACATCTCAAATGAAACCA 58.627 34.615 0.00 0.00 0.00 3.67
1321 2508 1.215382 CACAGATTCGCAGGGACGA 59.785 57.895 0.00 0.00 41.04 4.20
1392 2579 2.292292 ACACGGTGCCTTTTATGTGAAC 59.708 45.455 8.30 0.00 0.00 3.18
1608 2797 5.771469 CACCAACTCAAAGTCAATGCAATA 58.229 37.500 0.00 0.00 0.00 1.90
1736 2925 5.016173 TCTCCAATTCAACCCATACCAAAG 58.984 41.667 0.00 0.00 0.00 2.77
1760 3145 0.036164 CCATCACCGACCACTCCAAA 59.964 55.000 0.00 0.00 0.00 3.28
1772 3157 1.226717 GCGAGACGACTCCATCACC 60.227 63.158 9.30 0.00 39.76 4.02
1825 3210 6.791867 TCCTTCTCGAATGAGGAAGAATTA 57.208 37.500 11.72 0.00 42.79 1.40
1887 3272 6.706295 TGACAGAATTTTGTTTTCCCAACTT 58.294 32.000 2.77 0.00 0.00 2.66
1951 3336 7.872483 ACTCGGTGAAAATTTCAAGCATATTTT 59.128 29.630 10.27 0.00 42.15 1.82
1953 3338 6.924111 ACTCGGTGAAAATTTCAAGCATATT 58.076 32.000 10.27 0.00 42.15 1.28
1956 3341 4.853924 ACTCGGTGAAAATTTCAAGCAT 57.146 36.364 10.27 0.00 42.15 3.79
1958 3343 4.207019 CACAACTCGGTGAAAATTTCAAGC 59.793 41.667 10.27 4.03 42.15 4.01
1972 3357 2.230025 ACTCAGTCTCATCACAACTCGG 59.770 50.000 0.00 0.00 0.00 4.63
2067 3452 8.001881 GCTTGCTAGCTTATCATCCTACTATA 57.998 38.462 17.23 0.00 44.27 1.31
2255 3649 1.201429 AAGTCAAGGTGCCTCGGGAT 61.201 55.000 0.00 0.00 0.00 3.85
2285 3679 2.356665 TTACAGCTTCAACCAAGGCA 57.643 45.000 0.00 0.00 31.94 4.75
2437 3906 0.397941 CTCCAACCAAGGCAGAGACA 59.602 55.000 0.00 0.00 0.00 3.41
2443 3912 0.250727 GTACAGCTCCAACCAAGGCA 60.251 55.000 0.00 0.00 0.00 4.75
2806 4275 1.605710 TCTGAAACTTCTTGCTGCAGC 59.394 47.619 31.89 31.89 42.50 5.25
3237 4706 8.642935 TGTCAAATACCTGATTAAACCAATGA 57.357 30.769 0.00 0.00 0.00 2.57
3242 4711 7.275560 GTGCATTGTCAAATACCTGATTAAACC 59.724 37.037 0.00 0.00 0.00 3.27
3399 4868 2.102578 GTATTGCATGAAAGGTGGGCT 58.897 47.619 0.00 0.00 0.00 5.19
3504 4973 4.253685 GCTCAGTTGCTCACCTAAACATA 58.746 43.478 0.00 0.00 0.00 2.29
3538 5007 4.673534 ACTTGAACACGAAACGAAAAGT 57.326 36.364 0.00 0.00 0.00 2.66
3550 5019 9.434559 GTGTTTTATGTCTCTTAACTTGAACAC 57.565 33.333 0.00 0.00 0.00 3.32
3646 5122 7.923344 GCTAAGATTGTTCTCTAGTGCATCTTA 59.077 37.037 0.00 0.00 0.00 2.10
4409 5891 6.531503 TCACCCTTTGTAATTGTCACAAAA 57.468 33.333 0.00 0.00 43.31 2.44
4469 5951 2.753452 GTCACGTACATCCTCTTCCTCA 59.247 50.000 0.00 0.00 0.00 3.86
4528 6010 8.338259 AGTATTACAAATGCTCTCAATTAAGCG 58.662 33.333 0.00 0.00 41.51 4.68
4555 6037 5.416952 CCTCCTGCTCATGTTTTCATTAGTT 59.583 40.000 0.00 0.00 38.64 2.24
4820 6303 6.035758 GCTAAGACACCTTAATTTGGTAGACG 59.964 42.308 3.01 0.00 35.80 4.18
5186 6677 7.067859 GTGGACTACAGTCACACCAATAGTATA 59.932 40.741 11.31 0.00 46.47 1.47
5209 6700 2.787473 TCCTGAATAGTTGCTGGTGG 57.213 50.000 0.00 0.00 0.00 4.61
6180 7671 2.723322 TTGCCATCTTCATCTCCCTG 57.277 50.000 0.00 0.00 0.00 4.45
6253 7744 6.016693 TGTTTTGGAATTGCATTTCTCTCGTA 60.017 34.615 18.11 2.80 0.00 3.43
6293 7784 3.187700 CCAGTCTTTTTCCGAGTATCCG 58.812 50.000 0.00 0.00 0.00 4.18
6357 7848 0.182537 CCACTGGTTTGGGTGACTCA 59.817 55.000 0.00 0.00 35.69 3.41
6387 7878 4.515191 GTGTCAAGCTTTTCACATCCACTA 59.485 41.667 19.57 0.00 0.00 2.74
6415 7906 2.066340 CCTGGCCTAGTGGTTCACA 58.934 57.895 3.32 0.00 36.74 3.58
6444 7935 7.439157 TTCTGATTTACAAACATCAGTGGAG 57.561 36.000 8.61 0.00 44.68 3.86
6477 7968 0.248907 CCTCGCGTTGTCCATACGAT 60.249 55.000 5.77 0.00 41.33 3.73
6478 7969 1.138036 CCTCGCGTTGTCCATACGA 59.862 57.895 5.77 0.00 41.33 3.43
6480 7971 1.717194 TTTCCTCGCGTTGTCCATAC 58.283 50.000 5.77 0.00 0.00 2.39
6516 8007 4.608948 ATTCGTCATAGGAGTTCCATCC 57.391 45.455 0.28 0.00 39.89 3.51
6545 8036 6.663093 ACCTTCATTATTTGTTGAGTGGCATA 59.337 34.615 0.00 0.00 0.00 3.14
6759 8250 3.675467 GAACGTGAAGCAGTTCTTGTT 57.325 42.857 0.00 0.00 42.34 2.83
6849 8340 6.365970 AGTACACTGAATCCAAATCTGTCT 57.634 37.500 0.00 0.00 0.00 3.41
7122 8613 2.159787 CGGTGTCTTGAGAATTTGCTCG 60.160 50.000 0.00 0.00 37.73 5.03
7176 8667 0.252789 TTCCATGTCGGTAAGGGGGA 60.253 55.000 0.00 0.00 35.57 4.81
7251 8742 1.188863 GGCCCATCAGCTTCAACATT 58.811 50.000 0.00 0.00 0.00 2.71
7262 8753 2.918248 CATCCTTCGGGCCCATCA 59.082 61.111 24.92 0.68 34.44 3.07
7392 8883 1.364171 CGGCATCCTTCCTACGGAG 59.636 63.158 0.00 0.00 33.29 4.63
7395 8886 2.280186 GGCGGCATCCTTCCTACG 60.280 66.667 3.07 0.00 0.00 3.51
7400 8891 1.227060 GCAATTGGCGGCATCCTTC 60.227 57.895 14.32 0.00 0.00 3.46
7414 8905 2.690778 GCGCTTGAACCGGAGCAAT 61.691 57.895 9.46 0.00 38.81 3.56
7560 9051 4.397103 TCACTCACCGTATACAGTTGTAGG 59.603 45.833 3.32 0.00 33.52 3.18
7593 9084 5.854338 TCAAAACATCCTTTATTTCGTTCGC 59.146 36.000 0.00 0.00 0.00 4.70
7808 9314 3.192001 CAGGAACCAACTCATTCACATGG 59.808 47.826 0.00 0.00 37.19 3.66
7935 9450 4.409718 TTACATCCCTAATAACGCTGCA 57.590 40.909 0.00 0.00 0.00 4.41
8102 9635 3.192922 ATACGTTTCTGCGCCGCC 61.193 61.111 6.63 0.00 34.88 6.13
8103 9636 2.021380 CATACGTTTCTGCGCCGC 59.979 61.111 4.18 0.00 34.88 6.53
8104 9637 2.021380 GCATACGTTTCTGCGCCG 59.979 61.111 4.18 2.53 34.88 6.46
8150 9683 9.397280 GGCTAATCTAGAACCTTTTGTCTAAAT 57.603 33.333 0.00 0.00 0.00 1.40
8260 9802 3.064271 TGCTCGTAGTGGTTTTTGTTGTC 59.936 43.478 0.00 0.00 0.00 3.18
8347 9889 2.496291 GCATCTGCCATGGCCTTCC 61.496 63.158 33.44 14.29 41.09 3.46
8353 9895 0.179111 CTTTGCTGCATCTGCCATGG 60.179 55.000 7.63 7.63 41.18 3.66
8380 9922 4.085733 CAAACCCCTGTGATGATTGGTTA 58.914 43.478 0.00 0.00 35.14 2.85
8427 9974 1.518367 CAAGGCAAGGGGATAGGGTA 58.482 55.000 0.00 0.00 0.00 3.69
8431 10005 0.179006 GAGCCAAGGCAAGGGGATAG 60.179 60.000 14.40 0.00 44.88 2.08
8440 10014 3.249189 ACCCTTCGAGCCAAGGCA 61.249 61.111 14.40 0.00 41.69 4.75
8441 10015 2.747855 CACCCTTCGAGCCAAGGC 60.748 66.667 2.02 2.02 41.69 4.35
8457 10031 3.568443 TCTATACTCCAATGGTACGGCA 58.432 45.455 0.00 0.00 0.00 5.69
8460 10034 4.613167 GCGTCTCTATACTCCAATGGTACG 60.613 50.000 0.00 0.00 0.00 3.67
8490 10064 2.165998 GTTGGCATCCTTCTTGCTCTT 58.834 47.619 0.00 0.00 40.03 2.85
8493 10067 0.407139 AGGTTGGCATCCTTCTTGCT 59.593 50.000 11.39 0.00 40.03 3.91
8520 10094 1.375268 GTCGCTCTGAGGCTGCTTT 60.375 57.895 6.83 0.00 0.00 3.51
8593 10168 1.421646 CTTTCCAGTCCCACTTGGTCT 59.578 52.381 0.00 0.00 32.16 3.85
8645 10220 1.079336 GTTCACCTCGGTACCCTGC 60.079 63.158 6.25 0.00 0.00 4.85
8651 10226 0.524862 GCTCTTCGTTCACCTCGGTA 59.475 55.000 0.00 0.00 0.00 4.02
8677 10252 3.423154 GGTCGGTTGCCTTGCTCG 61.423 66.667 0.00 0.00 0.00 5.03
8678 10253 2.281484 TGGTCGGTTGCCTTGCTC 60.281 61.111 0.00 0.00 0.00 4.26
8679 10254 2.594592 GTGGTCGGTTGCCTTGCT 60.595 61.111 0.00 0.00 0.00 3.91
8680 10255 1.805428 ATTGTGGTCGGTTGCCTTGC 61.805 55.000 0.00 0.00 0.00 4.01
8681 10256 0.039256 CATTGTGGTCGGTTGCCTTG 60.039 55.000 0.00 0.00 0.00 3.61
8682 10257 1.178534 CCATTGTGGTCGGTTGCCTT 61.179 55.000 0.00 0.00 31.35 4.35
8683 10258 1.603455 CCATTGTGGTCGGTTGCCT 60.603 57.895 0.00 0.00 31.35 4.75
8684 10259 1.175983 TTCCATTGTGGTCGGTTGCC 61.176 55.000 0.00 0.00 39.03 4.52
8770 10345 4.695993 TGCGGCGTCCTCAATGCA 62.696 61.111 9.37 0.00 42.04 3.96
8771 10346 4.166011 GTGCGGCGTCCTCAATGC 62.166 66.667 9.37 0.00 39.33 3.56
8785 10360 3.050275 GCTCAGTTCCGGTGGTGC 61.050 66.667 0.00 0.00 0.00 5.01
8792 10367 2.720758 CTCGCGTTGCTCAGTTCCG 61.721 63.158 5.77 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.