Multiple sequence alignment - TraesCS6D01G139200

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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 TraesCS6D01G139200 chr6D 100.000 5738 0 0 931 6668 108452126 108446389 0.000000e+00 10597.0
1 TraesCS6D01G139200 chr6D 100.000 369 0 0 1 369 108453056 108452688 0.000000e+00 682.0
2 TraesCS6D01G139200 chr6D 80.745 161 17 10 6255 6408 106970548 106970395 5.470000e-21 113.0
3 TraesCS6D01G139200 chr6D 80.247 162 18 10 6254 6408 408177285 408177131 7.070000e-20 110.0
4 TraesCS6D01G139200 chr6A 92.299 5558 277 51 1192 6668 133418841 133413354 0.000000e+00 7753.0
5 TraesCS6D01G139200 chr6A 91.620 358 7 7 18 369 133419543 133419203 2.180000e-129 473.0
6 TraesCS6D01G139200 chr6A 95.122 246 10 1 931 1174 133419079 133418834 2.920000e-103 387.0
7 TraesCS6D01G139200 chr6A 94.068 118 7 0 6549 6666 133412916 133412799 5.310000e-41 180.0
8 TraesCS6D01G139200 chr6B 92.702 3220 168 32 931 4117 195810347 195807162 0.000000e+00 4582.0
9 TraesCS6D01G139200 chr6B 89.957 2071 141 30 4163 6217 195806929 195804910 0.000000e+00 2610.0
10 TraesCS6D01G139200 chr6B 91.304 322 21 6 6347 6664 195787772 195787454 3.690000e-117 433.0
11 TraesCS6D01G139200 chr6B 92.035 113 7 2 6229 6341 195799391 195799281 2.490000e-34 158.0
12 TraesCS6D01G139200 chr6B 100.000 74 0 0 296 369 195810544 195810471 3.240000e-28 137.0
13 TraesCS6D01G139200 chr6B 85.185 108 11 4 2624 2730 553053350 553053453 9.150000e-19 106.0
14 TraesCS6D01G139200 chr3D 81.699 153 15 10 6254 6399 35715832 35715978 1.520000e-21 115.0
15 TraesCS6D01G139200 chr3D 90.909 44 4 0 3667 3710 29879960 29879917 7.220000e-05 60.2
16 TraesCS6D01G139200 chr2B 81.699 153 14 10 6254 6399 794641895 794642040 1.520000e-21 115.0
17 TraesCS6D01G139200 chr2B 81.699 153 14 10 6254 6399 794731470 794731615 1.520000e-21 115.0
18 TraesCS6D01G139200 chr4D 86.735 98 9 3 6254 6349 35385299 35385204 9.150000e-19 106.0
19 TraesCS6D01G139200 chr4A 86.735 98 9 4 6254 6349 659137350 659137445 9.150000e-19 106.0


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 TraesCS6D01G139200 chr6D 108446389 108453056 6667 True 5639.50 10597 100.000000 1 6668 2 chr6D.!!$R3 6667
1 TraesCS6D01G139200 chr6A 133412799 133419543 6744 True 2198.25 7753 93.277250 18 6668 4 chr6A.!!$R1 6650
2 TraesCS6D01G139200 chr6B 195804910 195810544 5634 True 2443.00 4582 94.219667 296 6217 3 chr6B.!!$R3 5921


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
66 69 0.458543 CACAACGACGGAGCAGCTAT 60.459 55.000 0.00 0.00 0.00 2.97 F
101 104 0.966920 ATCCACCAGACGAAACGACT 59.033 50.000 0.00 0.00 31.64 4.18 F
103 106 1.002250 CCACCAGACGAAACGACTCG 61.002 60.000 8.91 8.91 44.50 4.18 F
1467 1476 1.279025 AAGGCCACATACACCGGGAT 61.279 55.000 6.32 0.00 0.00 3.85 F
2943 2979 0.333312 AGAGAGAGGGGACGTGATGT 59.667 55.000 0.00 0.00 0.00 3.06 F
3110 3148 0.108520 GCGGGTGATTTGAGGTACGA 60.109 55.000 0.00 0.00 0.00 3.43 F
3180 3220 3.572682 TCTTCACTAGGCACTCGAAGAAA 59.427 43.478 6.89 0.00 41.85 2.52 F
4207 4447 1.789464 GATAGATTTGCACCGCGAGAG 59.211 52.381 8.23 0.00 0.00 3.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1281 1290 0.250295 CGTCTTGGGTGAAGGAGCAA 60.250 55.000 0.00 0.00 31.85 3.91 R
1598 1610 0.521291 TTCCGAAATCCGCAAGCTTG 59.479 50.000 22.44 22.44 36.84 4.01 R
1631 1643 3.312697 TCCTGTTGATCATCGAGTCGTAG 59.687 47.826 13.12 6.54 0.00 3.51 R
3077 3113 0.031449 ACCCGCAAACATTCAAACCG 59.969 50.000 0.00 0.00 0.00 4.44 R
4186 4426 0.504384 CTCGCGGTGCAAATCTATCG 59.496 55.000 6.13 0.00 0.00 2.92 R
4201 4441 1.066908 AGATGTTGAGCTAGCTCTCGC 59.933 52.381 37.42 27.61 43.12 5.03 R
4473 4719 1.338020 CTCAAGTTGTTTCCCACTGGC 59.662 52.381 2.11 0.00 0.00 4.85 R
5962 6227 1.295020 AAGGAAATCGGGATCCACCA 58.705 50.000 15.23 0.00 41.20 4.17 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
37 38 5.490159 CCTAATTACAACTTCCACCCGTAA 58.510 41.667 0.00 0.00 0.00 3.18
65 68 1.080772 CACAACGACGGAGCAGCTA 60.081 57.895 0.00 0.00 0.00 3.32
66 69 0.458543 CACAACGACGGAGCAGCTAT 60.459 55.000 0.00 0.00 0.00 2.97
91 94 1.386550 TGGACTCCGATCCACCAGA 59.613 57.895 0.00 0.00 44.14 3.86
101 104 0.966920 ATCCACCAGACGAAACGACT 59.033 50.000 0.00 0.00 31.64 4.18
103 106 1.002250 CCACCAGACGAAACGACTCG 61.002 60.000 8.91 8.91 44.50 4.18
156 159 2.732619 GGAATCGACCGGAAGCCCT 61.733 63.158 9.46 0.00 0.00 5.19
258 261 3.576356 CGCCAGCCAACCATAGCG 61.576 66.667 0.00 0.00 37.39 4.26
261 264 3.211963 CAGCCAACCATAGCGCCC 61.212 66.667 2.29 0.00 0.00 6.13
280 283 2.863988 CCACCCCCTCCCACCTTT 60.864 66.667 0.00 0.00 0.00 3.11
281 284 2.763902 CACCCCCTCCCACCTTTC 59.236 66.667 0.00 0.00 0.00 2.62
282 285 2.534533 ACCCCCTCCCACCTTTCC 60.535 66.667 0.00 0.00 0.00 3.13
283 286 3.347590 CCCCCTCCCACCTTTCCC 61.348 72.222 0.00 0.00 0.00 3.97
1113 1120 4.761058 TCCCTCCGCTCCGAAGCT 62.761 66.667 0.00 0.00 46.91 3.74
1162 1171 7.607607 TCCACTCAATATATCAATCAATTCCCG 59.392 37.037 0.00 0.00 0.00 5.14
1281 1290 1.690219 CCAACCTCCTCAGCGCCTAT 61.690 60.000 2.29 0.00 0.00 2.57
1467 1476 1.279025 AAGGCCACATACACCGGGAT 61.279 55.000 6.32 0.00 0.00 3.85
1529 1541 8.281194 TGAAGATTACGTCACTTCGTATATCTC 58.719 37.037 17.75 12.54 43.96 2.75
1531 1543 9.486497 AAGATTACGTCACTTCGTATATCTCTA 57.514 33.333 15.93 0.00 43.96 2.43
1537 1549 6.246748 CGTCACTTCGTATATCTCTAAATCGC 59.753 42.308 0.00 0.00 0.00 4.58
1542 1554 7.534578 ACTTCGTATATCTCTAAATCGCTTTCG 59.465 37.037 0.00 0.00 0.00 3.46
1682 1694 3.268603 CACACGCTTGTCGGCACA 61.269 61.111 0.00 0.00 43.86 4.57
1725 1737 9.628746 TTAAAAGTTGTTGTTTTTAGGACTGTC 57.371 29.630 0.00 0.00 32.27 3.51
1801 1814 5.174395 ACTGACATTCTACTGATTCAGTGC 58.826 41.667 26.01 9.27 45.01 4.40
1809 1822 5.473931 TCTACTGATTCAGTGCTCTGTTTC 58.526 41.667 26.01 12.84 45.01 2.78
2464 2483 6.375455 ACGACATTCATTTGCCTTCTCTATTT 59.625 34.615 0.00 0.00 0.00 1.40
2598 2617 9.950496 AAAGAGAAGACATCACATGTTAGTATT 57.050 29.630 0.00 0.00 45.03 1.89
2602 2621 9.950496 AGAAGACATCACATGTTAGTATTTCTT 57.050 29.630 0.00 2.36 45.03 2.52
2644 2663 0.833287 AGCATCTCCATTACCGTGCT 59.167 50.000 0.00 0.00 38.03 4.40
2646 2665 1.743772 GCATCTCCATTACCGTGCTGT 60.744 52.381 0.00 0.00 0.00 4.40
2677 2696 1.444895 CTAAACGTCCGTGGACCCG 60.445 63.158 13.24 5.48 41.76 5.28
2694 2713 2.029221 GAATACGGGAGCTCGCCC 59.971 66.667 23.61 12.70 45.10 6.13
2710 2729 1.133792 CGCCCTCCAAATCCATACCTT 60.134 52.381 0.00 0.00 0.00 3.50
2836 2855 6.537301 CCGTCAAATAAGAACCACTAGCAATA 59.463 38.462 0.00 0.00 0.00 1.90
2894 2913 2.912956 TGGTCTCCTTCTGCCAAATAGT 59.087 45.455 0.00 0.00 0.00 2.12
2900 2919 2.420129 CCTTCTGCCAAATAGTAGCGGT 60.420 50.000 0.00 0.00 34.43 5.68
2916 2935 2.268920 GTCTTCCGCCATCCTGCA 59.731 61.111 0.00 0.00 0.00 4.41
2928 2947 1.000359 TCCTGCACGGATGGAGAGA 60.000 57.895 0.00 0.00 46.84 3.10
2929 2948 1.039785 TCCTGCACGGATGGAGAGAG 61.040 60.000 0.00 0.00 46.84 3.20
2930 2949 1.039785 CCTGCACGGATGGAGAGAGA 61.040 60.000 0.00 0.00 46.84 3.10
2934 2970 1.112315 CACGGATGGAGAGAGAGGGG 61.112 65.000 0.00 0.00 0.00 4.79
2943 2979 0.333312 AGAGAGAGGGGACGTGATGT 59.667 55.000 0.00 0.00 0.00 3.06
3014 3050 4.933400 TCTAGTTTAGTGAAATTCGGCCAC 59.067 41.667 2.24 0.00 0.00 5.01
3054 3090 1.948104 TATGCGGCACTATGTTGGAC 58.052 50.000 4.03 0.00 0.00 4.02
3076 3112 3.628017 GACAAAAATGGTCCGAACACTG 58.372 45.455 0.00 0.00 0.00 3.66
3077 3113 2.223711 ACAAAAATGGTCCGAACACTGC 60.224 45.455 0.00 0.00 0.00 4.40
3084 3122 3.725819 CCGAACACTGCGGTTTGA 58.274 55.556 0.00 0.00 43.66 2.69
3110 3148 0.108520 GCGGGTGATTTGAGGTACGA 60.109 55.000 0.00 0.00 0.00 3.43
3180 3220 3.572682 TCTTCACTAGGCACTCGAAGAAA 59.427 43.478 6.89 0.00 41.85 2.52
3182 3222 4.537135 TCACTAGGCACTCGAAGAAATT 57.463 40.909 0.00 0.00 41.75 1.82
3183 3223 5.654603 TCACTAGGCACTCGAAGAAATTA 57.345 39.130 0.00 0.00 41.75 1.40
3184 3224 6.222038 TCACTAGGCACTCGAAGAAATTAT 57.778 37.500 0.00 0.00 41.75 1.28
3185 3225 7.342769 TCACTAGGCACTCGAAGAAATTATA 57.657 36.000 0.00 0.00 41.75 0.98
3186 3226 7.952671 TCACTAGGCACTCGAAGAAATTATAT 58.047 34.615 0.00 0.00 41.75 0.86
3187 3227 9.074576 TCACTAGGCACTCGAAGAAATTATATA 57.925 33.333 0.00 0.00 41.75 0.86
3188 3228 9.130312 CACTAGGCACTCGAAGAAATTATATAC 57.870 37.037 0.00 0.00 41.75 1.47
3855 3903 8.630037 CCTCAAAGGTTGGGATGTTTAATATAC 58.370 37.037 0.00 0.00 30.85 1.47
3857 3905 9.762381 TCAAAGGTTGGGATGTTTAATATACTT 57.238 29.630 0.00 0.00 0.00 2.24
3921 3970 9.691362 GACAAATTCACAACCATAAACAAGTAT 57.309 29.630 0.00 0.00 0.00 2.12
4051 4103 5.471556 TTCTACGGGAGTTAAACATGTCA 57.528 39.130 0.00 0.00 43.33 3.58
4206 4446 1.852942 GATAGATTTGCACCGCGAGA 58.147 50.000 8.23 0.00 0.00 4.04
4207 4447 1.789464 GATAGATTTGCACCGCGAGAG 59.211 52.381 8.23 0.00 0.00 3.20
4225 4465 4.274705 CGAGAGCTAGCTCAACATCTTCTA 59.725 45.833 38.86 0.00 44.99 2.10
4311 4553 8.206189 TCTATGTTGCATCTGATCTACAAATGA 58.794 33.333 0.00 5.42 29.19 2.57
4336 4578 7.271511 ACTCTTCAAGGAAATCTAGCATACAG 58.728 38.462 0.00 0.00 0.00 2.74
4398 4644 2.008242 ATGCTACCTTTTTGGGTGCA 57.992 45.000 11.01 11.01 42.59 4.57
4473 4719 8.925161 TTGTTTTCTGACATAAGGTTTTTCTG 57.075 30.769 0.00 0.00 0.00 3.02
4544 4790 4.645667 TGAGTCATTTGAACGACATTCG 57.354 40.909 0.00 0.00 46.93 3.34
4568 4814 4.017177 AGTACCTACCAAGCAACTTTCC 57.983 45.455 0.00 0.00 0.00 3.13
4579 4825 1.542492 CAACTTTCCAGAGCAGGCAT 58.458 50.000 0.00 0.00 0.00 4.40
4619 4865 4.710423 ATGTCTATAGCTAGGATGCACG 57.290 45.455 0.00 0.00 34.99 5.34
4768 5019 5.583061 TCCAATGTTACGTGTATGGATGAAC 59.417 40.000 0.00 0.00 32.28 3.18
4771 5022 7.225734 CCAATGTTACGTGTATGGATGAACATA 59.774 37.037 0.00 0.00 35.56 2.29
4800 5051 1.241315 CGGCCATTCAAAAGGGTCGT 61.241 55.000 9.02 0.00 44.32 4.34
4931 5182 8.682710 TGGCACTATCATTTCTTATTTGGTTAC 58.317 33.333 0.00 0.00 0.00 2.50
5109 5361 1.973281 CAATCCTGTGCACCGCCTT 60.973 57.895 15.69 1.09 0.00 4.35
5153 5408 5.587043 TGGGACCGAAACATATTTGTACATC 59.413 40.000 0.00 0.00 34.06 3.06
5207 5462 9.487442 TCTACATGTCCTACATATGCCATATTA 57.513 33.333 0.00 0.00 36.53 0.98
5213 5468 8.601546 TGTCCTACATATGCCATATTAACATCA 58.398 33.333 1.58 0.00 0.00 3.07
5658 5918 6.320494 TGCGTCCAACAAAATAAAGTACAT 57.680 33.333 0.00 0.00 0.00 2.29
5670 5930 9.950680 CAAAATAAAGTACATGGGCTATAGTTG 57.049 33.333 0.84 0.00 0.00 3.16
5923 6187 9.643693 TTTTCCTAGTAATTTAGTACTCCAACG 57.356 33.333 0.00 0.00 35.85 4.10
5945 6209 8.328864 CAACGCACTAATAGATTCTTTACCTTC 58.671 37.037 0.00 0.00 0.00 3.46
6005 6270 9.634163 CTTTAGTAGAAACCAAAACAAAACTGT 57.366 29.630 0.00 0.00 0.00 3.55
6026 6292 3.845781 ACCATCTCACACATCATACCC 57.154 47.619 0.00 0.00 0.00 3.69
6085 6351 7.041721 CGATGTAATATAGCAAAGAGGCCATA 58.958 38.462 5.01 0.00 0.00 2.74
6093 6363 3.118223 AGCAAAGAGGCCATACTAGGAAC 60.118 47.826 5.01 0.00 0.00 3.62
6094 6364 3.809905 CAAAGAGGCCATACTAGGAACC 58.190 50.000 5.01 0.00 0.00 3.62
6095 6365 1.705873 AGAGGCCATACTAGGAACCG 58.294 55.000 5.01 0.00 0.00 4.44
6135 6405 1.204704 CGGTGAGCTGAACATAGGACA 59.795 52.381 0.00 0.00 0.00 4.02
6157 6427 6.725246 ACACACAATAAAAGGAAAGAAGACG 58.275 36.000 0.00 0.00 0.00 4.18
6201 6471 4.040461 TCTCGTTCCTCAGTTTTGGAATCT 59.960 41.667 0.00 0.00 43.25 2.40
6217 6487 4.080356 TGGAATCTATGGGGTTCACTTCTG 60.080 45.833 0.00 0.00 0.00 3.02
6220 6490 4.061131 TCTATGGGGTTCACTTCTGAGA 57.939 45.455 0.00 0.00 0.00 3.27
6221 6491 4.624913 TCTATGGGGTTCACTTCTGAGAT 58.375 43.478 0.00 0.00 0.00 2.75
6222 6492 3.641434 ATGGGGTTCACTTCTGAGATG 57.359 47.619 0.00 0.00 0.00 2.90
6223 6493 1.630369 TGGGGTTCACTTCTGAGATGG 59.370 52.381 0.29 0.00 0.00 3.51
6224 6494 1.065126 GGGGTTCACTTCTGAGATGGG 60.065 57.143 0.29 0.00 0.00 4.00
6234 6528 3.340814 TCTGAGATGGGAGCAAAAGAC 57.659 47.619 0.00 0.00 0.00 3.01
6248 6542 0.657840 AAAGACGTGTCTGTTGCTGC 59.342 50.000 2.78 0.00 40.36 5.25
6258 6552 1.680735 TCTGTTGCTGCGTGGAAAATT 59.319 42.857 0.00 0.00 0.00 1.82
6264 6558 1.269448 GCTGCGTGGAAAATTTGAGGA 59.731 47.619 0.00 0.00 0.00 3.71
6281 6575 9.584008 AATTTGAGGAGTGATATTTGATATGCT 57.416 29.630 0.00 0.00 0.00 3.79
6282 6576 7.974482 TTGAGGAGTGATATTTGATATGCTG 57.026 36.000 0.00 0.00 0.00 4.41
6409 6704 4.216902 AGGAAAAACCCATACGTTAGTTGC 59.783 41.667 0.00 0.00 40.05 4.17
6422 6717 5.642686 ACGTTAGTTGCTTTTTGCTTTGTA 58.357 33.333 0.00 0.00 43.37 2.41
6432 6727 7.145323 TGCTTTTTGCTTTGTATACTTCCTTC 58.855 34.615 4.17 0.00 43.37 3.46
6470 6765 5.028549 ACACCATATGATCCTGTGAAGAC 57.971 43.478 13.79 0.00 0.00 3.01
6519 6816 8.511321 TGATGCAAAACCACATAGTAAACTTAG 58.489 33.333 0.00 0.00 0.00 2.18
6523 6820 7.361799 GCAAAACCACATAGTAAACTTAGAGGG 60.362 40.741 0.00 0.00 0.00 4.30
6524 6821 5.952347 ACCACATAGTAAACTTAGAGGGG 57.048 43.478 0.00 0.00 0.00 4.79
6527 6824 6.502863 ACCACATAGTAAACTTAGAGGGGAAA 59.497 38.462 0.00 0.00 0.00 3.13
6599 7453 1.801178 CTTGCAAACCTCGAAGTCCTC 59.199 52.381 0.00 0.00 0.00 3.71
6607 7461 4.853507 CGAAGTCCTCGCGTACAA 57.146 55.556 5.77 0.00 41.49 2.41
6666 7520 7.272244 TGGCAAAGACTTTGAGAATATATCGA 58.728 34.615 28.15 4.89 43.26 3.59
6667 7521 7.224753 TGGCAAAGACTTTGAGAATATATCGAC 59.775 37.037 28.15 8.13 43.26 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.822822 AGTTGTAATTAGGCACGTCTTATCTTT 59.177 33.333 0.00 0.00 0.00 2.52
1 2 7.328737 AGTTGTAATTAGGCACGTCTTATCTT 58.671 34.615 0.00 0.00 0.00 2.40
2 3 6.875076 AGTTGTAATTAGGCACGTCTTATCT 58.125 36.000 0.00 0.00 0.00 1.98
3 4 7.254353 GGAAGTTGTAATTAGGCACGTCTTATC 60.254 40.741 0.00 0.00 0.00 1.75
4 5 6.537660 GGAAGTTGTAATTAGGCACGTCTTAT 59.462 38.462 0.00 0.00 0.00 1.73
5 6 5.870978 GGAAGTTGTAATTAGGCACGTCTTA 59.129 40.000 0.00 0.00 0.00 2.10
6 7 4.694037 GGAAGTTGTAATTAGGCACGTCTT 59.306 41.667 0.00 0.00 0.00 3.01
7 8 4.251268 GGAAGTTGTAATTAGGCACGTCT 58.749 43.478 0.00 0.00 0.00 4.18
8 9 3.998341 TGGAAGTTGTAATTAGGCACGTC 59.002 43.478 0.00 0.00 0.00 4.34
9 10 3.749609 GTGGAAGTTGTAATTAGGCACGT 59.250 43.478 0.00 0.00 0.00 4.49
10 11 3.126343 GGTGGAAGTTGTAATTAGGCACG 59.874 47.826 0.00 0.00 0.00 5.34
11 12 3.442625 GGGTGGAAGTTGTAATTAGGCAC 59.557 47.826 0.00 0.00 0.00 5.01
12 13 3.692690 GGGTGGAAGTTGTAATTAGGCA 58.307 45.455 0.00 0.00 0.00 4.75
13 14 2.681344 CGGGTGGAAGTTGTAATTAGGC 59.319 50.000 0.00 0.00 0.00 3.93
14 15 3.946606 ACGGGTGGAAGTTGTAATTAGG 58.053 45.455 0.00 0.00 0.00 2.69
15 16 6.168389 ACTTACGGGTGGAAGTTGTAATTAG 58.832 40.000 0.00 0.00 31.83 1.73
16 17 6.112927 ACTTACGGGTGGAAGTTGTAATTA 57.887 37.500 0.00 0.00 31.83 1.40
37 38 0.168348 CGTCGTTGTGATCGAGGACT 59.832 55.000 11.83 0.00 42.95 3.85
65 68 1.486726 GGATCGGAGTCCAACCAAGAT 59.513 52.381 10.49 2.18 38.20 2.40
66 69 0.902531 GGATCGGAGTCCAACCAAGA 59.097 55.000 10.49 0.00 38.20 3.02
91 94 0.950116 AAGAGTCCGAGTCGTTTCGT 59.050 50.000 12.31 1.62 38.88 3.85
119 122 1.266989 CCGTTTCTGTTTTGCCTCCTC 59.733 52.381 0.00 0.00 0.00 3.71
120 123 1.133915 TCCGTTTCTGTTTTGCCTCCT 60.134 47.619 0.00 0.00 0.00 3.69
121 124 1.314730 TCCGTTTCTGTTTTGCCTCC 58.685 50.000 0.00 0.00 0.00 4.30
156 159 0.033920 CGGATCCGGATCTCATGCAA 59.966 55.000 36.72 0.00 37.92 4.08
268 271 3.347590 GGGGGAAAGGTGGGAGGG 61.348 72.222 0.00 0.00 0.00 4.30
283 286 2.125512 CGCTTTCTCGTGAGGGGG 60.126 66.667 0.00 0.00 0.00 5.40
1188 1197 1.204941 AGAGACGCCGATTAGTGCTTT 59.795 47.619 0.00 0.00 0.00 3.51
1281 1290 0.250295 CGTCTTGGGTGAAGGAGCAA 60.250 55.000 0.00 0.00 31.85 3.91
1467 1476 4.081420 GGAGAGAGCTCAATTACCTTGACA 60.081 45.833 17.77 0.00 43.14 3.58
1484 1493 3.437213 TCAAATTCAGTACCGGGAGAGA 58.563 45.455 6.32 0.00 0.00 3.10
1529 1541 3.404564 CCGAAACACGAAAGCGATTTAG 58.595 45.455 0.00 0.70 45.77 1.85
1531 1543 1.069500 CCCGAAACACGAAAGCGATTT 60.069 47.619 0.00 0.00 45.77 2.17
1537 1549 1.083015 CACGCCCGAAACACGAAAG 60.083 57.895 0.00 0.00 45.77 2.62
1542 1554 1.010462 GTGTTCACGCCCGAAACAC 60.010 57.895 19.32 19.32 0.00 3.32
1598 1610 0.521291 TTCCGAAATCCGCAAGCTTG 59.479 50.000 22.44 22.44 36.84 4.01
1631 1643 3.312697 TCCTGTTGATCATCGAGTCGTAG 59.687 47.826 13.12 6.54 0.00 3.51
1696 1708 9.850628 AGTCCTAAAAACAACAACTTTTAAGAC 57.149 29.630 7.49 7.49 38.04 3.01
1701 1713 7.094631 GGACAGTCCTAAAAACAACAACTTTT 58.905 34.615 12.94 0.00 32.53 2.27
1725 1737 7.878547 ACCCATTGGCAAAAATATTAATTGG 57.121 32.000 3.01 2.94 33.59 3.16
1735 1747 4.637387 ATCATCAACCCATTGGCAAAAA 57.363 36.364 3.01 0.00 36.39 1.94
1801 1814 5.123027 GTGCCATCCTTAAGAAGAAACAGAG 59.877 44.000 3.36 0.00 0.00 3.35
1809 1822 3.634397 TCAGGTGCCATCCTTAAGAAG 57.366 47.619 3.36 0.00 35.37 2.85
2073 2092 4.279671 ACCTCAGTAACTTCTCACAGACAG 59.720 45.833 0.00 0.00 0.00 3.51
2368 2387 3.957671 AGCATGCATCTTACGTGATTG 57.042 42.857 21.98 0.00 0.00 2.67
2464 2483 3.682372 TGCGCGCACATAAAAATGATA 57.318 38.095 33.09 0.66 0.00 2.15
2476 2495 0.110688 CACCACATATATGCGCGCAC 60.111 55.000 39.05 6.30 0.00 5.34
2610 2629 5.130975 TGGAGATGCTCTTAGCTATGGAAAA 59.869 40.000 6.78 0.00 42.97 2.29
2632 2651 2.286833 CCGATTTACAGCACGGTAATGG 59.713 50.000 0.00 0.00 40.42 3.16
2635 2654 2.029200 TGTCCGATTTACAGCACGGTAA 60.029 45.455 0.00 0.00 44.72 2.85
2644 2663 4.619973 ACGTTTAGTGTGTCCGATTTACA 58.380 39.130 0.00 0.00 0.00 2.41
2646 2665 4.236935 GGACGTTTAGTGTGTCCGATTTA 58.763 43.478 0.00 0.00 42.42 1.40
2677 2696 2.029221 GGGCGAGCTCCCGTATTC 59.971 66.667 8.47 0.00 36.38 1.75
2694 2713 6.017109 CGGACATTTAAGGTATGGATTTGGAG 60.017 42.308 0.00 0.00 0.00 3.86
2734 2753 9.834628 CGGAAGACATTGCTACTATTTTAAAAA 57.165 29.630 4.44 0.00 0.00 1.94
2735 2754 7.966204 GCGGAAGACATTGCTACTATTTTAAAA 59.034 33.333 2.51 2.51 0.00 1.52
2736 2755 7.414762 GGCGGAAGACATTGCTACTATTTTAAA 60.415 37.037 0.00 0.00 40.66 1.52
2737 2756 6.037830 GGCGGAAGACATTGCTACTATTTTAA 59.962 38.462 0.00 0.00 40.66 1.52
2738 2757 5.526111 GGCGGAAGACATTGCTACTATTTTA 59.474 40.000 0.00 0.00 40.66 1.52
2865 2884 3.416156 GCAGAAGGAGACCAACTTTGAT 58.584 45.455 0.00 0.00 0.00 2.57
2900 2919 2.268920 GTGCAGGATGGCGGAAGA 59.731 61.111 0.00 0.00 35.86 2.87
2916 2935 1.231641 CCCCTCTCTCTCCATCCGT 59.768 63.158 0.00 0.00 0.00 4.69
2928 2947 1.645710 AAAGACATCACGTCCCCTCT 58.354 50.000 0.00 0.00 46.69 3.69
2929 2948 2.076863 CAAAAGACATCACGTCCCCTC 58.923 52.381 0.00 0.00 46.69 4.30
2930 2949 1.697432 TCAAAAGACATCACGTCCCCT 59.303 47.619 0.00 0.00 46.69 4.79
2934 2970 4.213270 TGGACAATCAAAAGACATCACGTC 59.787 41.667 0.00 0.00 45.77 4.34
2943 2979 1.073125 TCCGCCTGGACAATCAAAAGA 59.927 47.619 0.00 0.00 40.17 2.52
3054 3090 2.289547 AGTGTTCGGACCATTTTTGTCG 59.710 45.455 0.00 0.00 33.46 4.35
3076 3112 1.281566 CCCGCAAACATTCAAACCGC 61.282 55.000 0.00 0.00 0.00 5.68
3077 3113 0.031449 ACCCGCAAACATTCAAACCG 59.969 50.000 0.00 0.00 0.00 4.44
3084 3122 2.029110 CCTCAAATCACCCGCAAACATT 60.029 45.455 0.00 0.00 0.00 2.71
3110 3148 1.568504 TCTTAGGGCATCTCCAACGT 58.431 50.000 0.00 0.00 36.21 3.99
3437 3477 9.632807 TTATTGCACAAGTAAAATCATACCAAC 57.367 29.630 0.00 0.00 0.00 3.77
3513 3553 7.339721 TCATTCTCTTCCGAGTACTAGAAATGT 59.660 37.037 4.34 0.00 38.45 2.71
3801 3849 2.435372 TTGGAGTTGTTGAGCTTGGT 57.565 45.000 0.00 0.00 0.00 3.67
3857 3905 8.687242 ACGAAGTGACTATCATTCTATCAAGAA 58.313 33.333 0.00 0.00 42.98 2.52
3931 3980 4.852609 ACGGTATAGTTTCACATTTCGC 57.147 40.909 0.00 0.00 0.00 4.70
3983 4032 1.060409 GCACGTTTTGCCAACAACTTG 59.940 47.619 0.00 5.33 46.63 3.16
4067 4119 8.659925 AGAACAATGCAATTTTGATGTAAACA 57.340 26.923 5.55 0.00 31.22 2.83
4178 4418 4.569162 CGGTGCAAATCTATCGAAACCTAA 59.431 41.667 0.00 0.00 0.00 2.69
4186 4426 0.504384 CTCGCGGTGCAAATCTATCG 59.496 55.000 6.13 0.00 0.00 2.92
4201 4441 1.066908 AGATGTTGAGCTAGCTCTCGC 59.933 52.381 37.42 27.61 43.12 5.03
4206 4446 5.186797 AGTGTTAGAAGATGTTGAGCTAGCT 59.813 40.000 19.45 19.45 0.00 3.32
4207 4447 5.415221 AGTGTTAGAAGATGTTGAGCTAGC 58.585 41.667 6.62 6.62 0.00 3.42
4208 4448 6.625362 TGAGTGTTAGAAGATGTTGAGCTAG 58.375 40.000 0.00 0.00 0.00 3.42
4209 4449 6.590234 TGAGTGTTAGAAGATGTTGAGCTA 57.410 37.500 0.00 0.00 0.00 3.32
4294 4536 8.713737 TTGAAGAGTCATTTGTAGATCAGATG 57.286 34.615 0.00 0.00 39.20 2.90
4311 4553 7.093112 ACTGTATGCTAGATTTCCTTGAAGAGT 60.093 37.037 0.00 0.00 0.00 3.24
4473 4719 1.338020 CTCAAGTTGTTTCCCACTGGC 59.662 52.381 2.11 0.00 0.00 4.85
4544 4790 5.048921 GGAAAGTTGCTTGGTAGGTACTTTC 60.049 44.000 14.06 14.06 45.19 2.62
4568 4814 2.008329 GAGAAGAACATGCCTGCTCTG 58.992 52.381 13.73 0.00 34.24 3.35
4579 4825 9.793259 ATAGACATTTTACTTTGGAGAAGAACA 57.207 29.630 0.00 0.00 0.00 3.18
4607 4853 5.931441 AAATATTCTTCGTGCATCCTAGC 57.069 39.130 0.00 0.00 0.00 3.42
4800 5051 6.966066 CCGTTTCTTCCGTTGTTACTTTAAAA 59.034 34.615 0.00 0.00 0.00 1.52
5104 5356 6.992063 AATATAGGCAAGATTATCAAGGCG 57.008 37.500 0.00 0.00 0.00 5.52
5109 5361 7.669722 GGTCCCAAAATATAGGCAAGATTATCA 59.330 37.037 0.00 0.00 0.00 2.15
5175 5430 4.855715 ATGTAGGACATGTAGATGACCG 57.144 45.455 14.07 0.00 45.82 4.79
5557 5813 7.542130 CCCTTTTGCATCTGTTAAACAACTATC 59.458 37.037 0.00 0.00 0.00 2.08
5561 5817 5.356426 ACCCTTTTGCATCTGTTAAACAAC 58.644 37.500 0.00 0.00 0.00 3.32
5658 5918 3.118038 CCACCTTAAGCAACTATAGCCCA 60.118 47.826 0.00 0.00 0.00 5.36
5670 5930 5.416013 AGCTATGAAAAGAACCACCTTAAGC 59.584 40.000 0.00 0.00 0.00 3.09
5746 6007 4.563061 ACTACTTTAAGTAAGTGGCACCG 58.437 43.478 15.27 0.00 46.15 4.94
5781 6042 9.571810 CAAAATAAATGAAGCTAATGCACTACA 57.428 29.630 0.00 0.00 42.74 2.74
5806 6067 7.851228 TCTTCTAGAAGCACAATCTATTTCCA 58.149 34.615 25.04 1.88 38.28 3.53
5919 6183 7.772332 AGGTAAAGAATCTATTAGTGCGTTG 57.228 36.000 0.00 0.00 0.00 4.10
5923 6187 8.819643 ATCGAAGGTAAAGAATCTATTAGTGC 57.180 34.615 0.00 0.00 0.00 4.40
5962 6227 1.295020 AAGGAAATCGGGATCCACCA 58.705 50.000 15.23 0.00 41.20 4.17
6005 6270 3.320826 CGGGTATGATGTGTGAGATGGTA 59.679 47.826 0.00 0.00 0.00 3.25
6085 6351 5.198965 TCTAGATAACTTGCGGTTCCTAGT 58.801 41.667 18.89 0.00 39.53 2.57
6093 6363 5.276868 CCGTTTTGATCTAGATAACTTGCGG 60.277 44.000 4.89 11.55 0.00 5.69
6094 6364 5.291128 ACCGTTTTGATCTAGATAACTTGCG 59.709 40.000 4.89 6.65 0.00 4.85
6095 6365 6.312918 TCACCGTTTTGATCTAGATAACTTGC 59.687 38.462 4.89 0.00 0.00 4.01
6135 6405 5.298276 TGCGTCTTCTTTCCTTTTATTGTGT 59.702 36.000 0.00 0.00 0.00 3.72
6157 6427 1.454653 GACGTTGGACGACTAGTTTGC 59.545 52.381 7.54 0.00 46.05 3.68
6201 6471 3.455910 CCATCTCAGAAGTGAACCCCATA 59.544 47.826 0.00 0.00 30.14 2.74
6217 6487 1.734465 CACGTCTTTTGCTCCCATCTC 59.266 52.381 0.00 0.00 0.00 2.75
6220 6490 1.072331 AGACACGTCTTTTGCTCCCAT 59.928 47.619 0.00 0.00 36.31 4.00
6221 6491 0.468226 AGACACGTCTTTTGCTCCCA 59.532 50.000 0.00 0.00 36.31 4.37
6222 6492 0.868406 CAGACACGTCTTTTGCTCCC 59.132 55.000 0.00 0.00 37.98 4.30
6223 6493 1.583054 ACAGACACGTCTTTTGCTCC 58.417 50.000 0.00 0.00 37.98 4.70
6224 6494 2.974165 CAACAGACACGTCTTTTGCTC 58.026 47.619 11.87 0.00 39.54 4.26
6234 6528 2.246397 CACGCAGCAACAGACACG 59.754 61.111 0.00 0.00 0.00 4.49
6248 6542 6.683974 ATATCACTCCTCAAATTTTCCACG 57.316 37.500 0.00 0.00 0.00 4.94
6258 6552 6.429078 GCAGCATATCAAATATCACTCCTCAA 59.571 38.462 0.00 0.00 0.00 3.02
6281 6575 5.175859 CCGAGTTTGAAGGAGTATTTAGCA 58.824 41.667 0.00 0.00 0.00 3.49
6282 6576 5.063564 CACCGAGTTTGAAGGAGTATTTAGC 59.936 44.000 0.00 0.00 0.00 3.09
6422 6717 7.756614 ACCCAAGACTTTTTAGAAGGAAGTAT 58.243 34.615 0.00 0.00 34.02 2.12
6490 6785 7.230510 AGTTTACTATGTGGTTTTGCATCAAGA 59.769 33.333 0.00 0.00 0.00 3.02
6496 6793 7.174253 CCTCTAAGTTTACTATGTGGTTTTGCA 59.826 37.037 0.00 0.00 0.00 4.08
6504 6801 8.857694 TTTTTCCCCTCTAAGTTTACTATGTG 57.142 34.615 0.00 0.00 0.00 3.21
6506 6803 9.462606 ACATTTTTCCCCTCTAAGTTTACTATG 57.537 33.333 0.00 0.00 0.00 2.23
6508 6805 7.392393 GCACATTTTTCCCCTCTAAGTTTACTA 59.608 37.037 0.00 0.00 0.00 1.82
6519 6816 5.596836 TCATATTGCACATTTTTCCCCTC 57.403 39.130 0.00 0.00 0.00 4.30
6599 7453 6.711579 AGTATGTTAATGGAATTTGTACGCG 58.288 36.000 3.53 3.53 37.87 6.01



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

AutoCloner maintained by Alex Coulton.