Multiple sequence alignment - TraesCS6D01G341300

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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 TraesCS6D01G341300 chr6D 100.000 6110 0 0 1 6110 440372816 440366707 0.000000e+00 11284.0
1 TraesCS6D01G341300 chr6A 91.977 3889 171 45 1462 5255 588463363 588459521 0.000000e+00 5323.0
2 TraesCS6D01G341300 chr6A 93.005 872 40 7 2 853 588464951 588464081 0.000000e+00 1253.0
3 TraesCS6D01G341300 chr6A 93.944 677 32 5 5438 6110 588459263 588458592 0.000000e+00 1014.0
4 TraesCS6D01G341300 chr6A 92.553 564 34 6 853 1414 588463937 588463380 0.000000e+00 802.0
5 TraesCS6D01G341300 chr6A 88.235 170 9 6 5256 5421 588459480 588459318 6.250000e-45 193.0
6 TraesCS6D01G341300 chr6B 90.367 2803 160 34 2529 5251 665514652 665511880 0.000000e+00 3579.0
7 TraesCS6D01G341300 chr6B 90.892 1087 64 15 1462 2524 665515827 665514752 0.000000e+00 1426.0
8 TraesCS6D01G341300 chr6B 95.102 490 19 3 5256 5741 665511835 665511347 0.000000e+00 767.0
9 TraesCS6D01G341300 chr6B 90.832 469 27 6 950 1414 665516305 665515849 1.130000e-171 614.0
10 TraesCS6D01G341300 chr6B 92.683 410 20 4 2 407 665517324 665516921 3.170000e-162 582.0
11 TraesCS6D01G341300 chr6B 95.882 340 11 1 5771 6110 665511344 665511008 1.160000e-151 547.0
12 TraesCS6D01G341300 chr6B 88.184 457 30 14 403 838 665516874 665516421 1.950000e-144 523.0
13 TraesCS6D01G341300 chr3D 86.174 2893 256 71 1959 4747 346821596 346824448 0.000000e+00 2994.0
14 TraesCS6D01G341300 chr3A 86.023 1109 106 27 1985 3063 456909803 456908714 0.000000e+00 1144.0
15 TraesCS6D01G341300 chr3A 82.877 1133 94 30 3059 4138 456908541 456907456 0.000000e+00 926.0
16 TraesCS6D01G341300 chr3A 83.094 834 113 18 1127 1952 456910591 456909778 0.000000e+00 734.0
17 TraesCS6D01G341300 chr4A 77.188 697 111 23 4074 4747 356603711 356603040 4.500000e-96 363.0
18 TraesCS6D01G341300 chr4D 82.865 356 38 11 2081 2421 273541056 273541403 1.290000e-76 298.0
19 TraesCS6D01G341300 chr5D 88.889 54 4 2 2056 2108 143205918 143205970 1.420000e-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 TraesCS6D01G341300 chr6D 440366707 440372816 6109 True 11284.000000 11284 100.000000 1 6110 1 chr6D.!!$R1 6109
1 TraesCS6D01G341300 chr6A 588458592 588464951 6359 True 1717.000000 5323 91.942800 2 6110 5 chr6A.!!$R1 6108
2 TraesCS6D01G341300 chr6B 665511008 665517324 6316 True 1148.285714 3579 91.991714 2 6110 7 chr6B.!!$R1 6108
3 TraesCS6D01G341300 chr3D 346821596 346824448 2852 False 2994.000000 2994 86.174000 1959 4747 1 chr3D.!!$F1 2788
4 TraesCS6D01G341300 chr3A 456907456 456910591 3135 True 934.666667 1144 83.998000 1127 4138 3 chr3A.!!$R1 3011
5 TraesCS6D01G341300 chr4A 356603040 356603711 671 True 363.000000 363 77.188000 4074 4747 1 chr4A.!!$R1 673

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
866 1087 0.112412 TTTCACCTTCTCCCCTTGGC 59.888 55.000 0.00 0.0 0.00 4.52 F
1459 1696 0.036875 CACCCACCAGAAGTTCTCCC 59.963 60.000 1.26 0.0 0.00 4.30 F
3108 3704 1.076923 ATCTAGGGGTGTCGAGCGT 60.077 57.895 0.00 0.0 0.00 5.07 F
4933 5643 0.530650 AGCGCGATTTGACGATGGAT 60.531 50.000 12.10 0.0 35.09 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1778 2020 2.948115 TGCACAATAGGCAAGGCATAT 58.052 42.857 0.00 0.0 37.11 1.78 R
3138 3734 1.592081 GCAGAGCAGACTATCTTTGCG 59.408 52.381 4.43 0.0 42.47 4.85 R
5023 5733 0.251341 CTGGGGGTCAGTTGGAAAGG 60.251 60.000 0.00 0.0 38.64 3.11 R
5919 6746 1.144936 CATCTCCTCCGCAACCTCC 59.855 63.158 0.00 0.0 0.00 4.30 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
219 224 2.132762 GTAATTGTAGCGACCCATCCG 58.867 52.381 0.00 0.00 0.00 4.18
235 240 4.444876 CCCATCCGTAATTCCTGATGTCTT 60.445 45.833 2.60 0.00 34.22 3.01
281 286 5.565509 TCAAAATCATAACCCTAGTGTGCA 58.434 37.500 0.00 0.00 0.00 4.57
286 291 3.838317 TCATAACCCTAGTGTGCAGACTT 59.162 43.478 22.81 6.08 0.00 3.01
300 305 4.991056 GTGCAGACTTCAGAGACATAACAA 59.009 41.667 0.00 0.00 0.00 2.83
317 323 4.681074 AACAAAACCGGATTGGACAATT 57.319 36.364 22.43 9.48 42.00 2.32
623 683 2.359214 TCAGACTCGCCTAGTGCTAATG 59.641 50.000 2.39 0.00 39.07 1.90
789 866 1.719725 TTTTCTCAAAGGCGCACGCA 61.720 50.000 17.69 0.00 44.11 5.24
842 919 0.925267 CGTGCACGTTGAGCTGTTTG 60.925 55.000 30.50 0.00 34.11 2.93
866 1087 0.112412 TTTCACCTTCTCCCCTTGGC 59.888 55.000 0.00 0.00 0.00 4.52
1024 1248 2.680221 GCCATCATCAGCACTCTGTTCT 60.680 50.000 0.00 0.00 41.10 3.01
1079 1305 1.629297 CTTCCCTCCTCCCCTAGCT 59.371 63.158 0.00 0.00 0.00 3.32
1124 1350 1.768077 CTCCCCCATCTCCCTGGTC 60.768 68.421 0.00 0.00 34.23 4.02
1286 1515 2.687614 CGACCCCAGGTAGTACCATACA 60.688 54.545 21.49 0.00 41.95 2.29
1343 1575 2.877168 CAGTTATGGCCTGCTGAATCTC 59.123 50.000 3.32 0.00 0.00 2.75
1345 1577 3.201708 AGTTATGGCCTGCTGAATCTCTT 59.798 43.478 3.32 0.00 0.00 2.85
1353 1585 3.139850 CTGCTGAATCTCTTATGCTGGG 58.860 50.000 0.00 0.00 0.00 4.45
1358 1590 5.028549 TGAATCTCTTATGCTGGGTTCTC 57.971 43.478 0.00 0.00 0.00 2.87
1369 1601 4.272489 TGCTGGGTTCTCCAATTTGATAG 58.728 43.478 0.00 0.00 46.51 2.08
1372 1604 4.870636 TGGGTTCTCCAATTTGATAGCAT 58.129 39.130 0.00 0.00 43.84 3.79
1376 1608 6.064717 GGTTCTCCAATTTGATAGCATAGGT 58.935 40.000 0.00 0.00 0.00 3.08
1385 1617 0.886490 ATAGCATAGGTTGGCGCTGC 60.886 55.000 7.64 7.49 35.93 5.25
1403 1635 0.460987 GCTGCGCCTCACTGAATAGT 60.461 55.000 4.18 0.00 37.75 2.12
1416 1648 3.997021 ACTGAATAGTTTCTTGTGCTCCG 59.003 43.478 0.00 0.00 31.66 4.63
1419 1651 4.021456 TGAATAGTTTCTTGTGCTCCGAGA 60.021 41.667 0.00 0.00 32.78 4.04
1420 1652 2.447244 AGTTTCTTGTGCTCCGAGAG 57.553 50.000 0.00 0.00 34.96 3.20
1431 1663 2.107953 CCGAGAGCTTAGGCAGGC 59.892 66.667 0.00 0.00 41.70 4.85
1433 1665 1.227205 CGAGAGCTTAGGCAGGCTG 60.227 63.158 10.94 10.94 41.70 4.85
1434 1666 1.523484 GAGAGCTTAGGCAGGCTGC 60.523 63.158 30.93 30.93 44.08 5.25
1457 1694 0.108585 TGCACCCACCAGAAGTTCTC 59.891 55.000 1.26 0.00 0.00 2.87
1458 1695 0.606673 GCACCCACCAGAAGTTCTCC 60.607 60.000 1.26 0.00 0.00 3.71
1459 1696 0.036875 CACCCACCAGAAGTTCTCCC 59.963 60.000 1.26 0.00 0.00 4.30
1460 1697 1.134438 ACCCACCAGAAGTTCTCCCC 61.134 60.000 1.26 0.00 0.00 4.81
1470 1707 3.846588 AGAAGTTCTCCCCTTAGCATTGA 59.153 43.478 0.00 0.00 0.00 2.57
1488 1725 3.607422 TGACTGCATCAGTTTTGTTCG 57.393 42.857 0.66 0.00 45.44 3.95
1496 1733 5.156355 GCATCAGTTTTGTTCGATGTCATT 58.844 37.500 0.00 0.00 38.01 2.57
1531 1768 4.990543 TCACTTGCTTTACATGTTCGAG 57.009 40.909 2.30 0.84 34.59 4.04
1549 1786 6.817641 TGTTCGAGTTGGTCTACTTTGTTTAA 59.182 34.615 0.00 0.00 0.00 1.52
1592 1830 5.922544 CCCTTTTAACTCTGCAAACATCTTG 59.077 40.000 0.00 0.00 0.00 3.02
1604 1842 6.620678 TGCAAACATCTTGGAAAATACTAGC 58.379 36.000 0.00 0.00 0.00 3.42
1606 1844 7.093814 TGCAAACATCTTGGAAAATACTAGCAT 60.094 33.333 0.00 0.00 0.00 3.79
1607 1845 7.221452 GCAAACATCTTGGAAAATACTAGCATG 59.779 37.037 0.00 0.00 0.00 4.06
1623 1865 1.945394 GCATGAACTGAGGGCTATGTG 59.055 52.381 0.00 0.00 0.00 3.21
1624 1866 1.945394 CATGAACTGAGGGCTATGTGC 59.055 52.381 0.00 0.00 41.94 4.57
1648 1890 4.085357 TGTTACACAGATTGGCAGAAGT 57.915 40.909 0.00 0.00 0.00 3.01
1650 1892 1.901591 ACACAGATTGGCAGAAGTGG 58.098 50.000 13.36 0.00 0.00 4.00
1745 1987 6.648725 GTGCTTTTCAGAGGGATATCTGTATC 59.351 42.308 2.05 0.00 45.70 2.24
1778 2020 1.452145 GGTCCGGCAAAACTCTTGCA 61.452 55.000 11.25 0.00 46.58 4.08
1866 2108 2.685850 ACCTACACGGGATTTAGCAC 57.314 50.000 0.00 0.00 36.97 4.40
1915 2167 8.015185 ACCTTCTAGAAACTTGTGTACACTAA 57.985 34.615 25.60 16.57 0.00 2.24
1918 2170 9.141400 CTTCTAGAAACTTGTGTACACTAATCC 57.859 37.037 25.60 11.12 0.00 3.01
1928 2180 6.863275 TGTGTACACTAATCCATACTGTCAG 58.137 40.000 25.60 0.00 0.00 3.51
2363 2621 2.039084 ACCATTTCTGTCTCCTCACACC 59.961 50.000 0.00 0.00 0.00 4.16
2366 2624 3.685139 TTTCTGTCTCCTCACACCATC 57.315 47.619 0.00 0.00 0.00 3.51
2428 2699 7.676683 ATGTCCTGTTATACATAGTTGAGGT 57.323 36.000 0.00 0.00 34.61 3.85
2429 2700 7.490657 TGTCCTGTTATACATAGTTGAGGTT 57.509 36.000 0.00 0.00 0.00 3.50
2430 2701 8.598202 TGTCCTGTTATACATAGTTGAGGTTA 57.402 34.615 0.00 0.00 0.00 2.85
2431 2702 8.472413 TGTCCTGTTATACATAGTTGAGGTTAC 58.528 37.037 0.00 0.00 0.00 2.50
2432 2703 8.472413 GTCCTGTTATACATAGTTGAGGTTACA 58.528 37.037 0.00 0.00 0.00 2.41
2443 2715 5.348164 AGTTGAGGTTACAATTGTTTGTGC 58.652 37.500 17.78 5.07 45.56 4.57
2475 2764 2.248135 TTTGTGTGCCGCAGTACCG 61.248 57.895 0.00 0.00 0.00 4.02
2588 2973 4.573900 TGATTATTTTGGCGCATTTTGGT 58.426 34.783 10.83 0.00 0.00 3.67
2594 2979 1.539157 TGGCGCATTTTGGTATGACA 58.461 45.000 10.83 0.00 0.00 3.58
2702 3102 2.035066 CCCTGCTTGTGTTCTTTCCAAG 59.965 50.000 0.00 0.00 38.83 3.61
2815 3234 5.347635 TCTTATTAGTGTTGCGTACTTGCTG 59.652 40.000 0.00 0.00 35.36 4.41
2861 3280 3.995199 TCAGGTTGTTGATGAGACAGAC 58.005 45.455 0.00 0.00 0.00 3.51
3001 3420 5.886474 TGACTACCATCAGAAGATCGTAAGT 59.114 40.000 0.00 0.00 29.34 2.24
3021 3440 8.228464 CGTAAGTCTTGCTCTACGATATCAATA 58.772 37.037 3.12 0.00 36.87 1.90
3071 3667 6.968131 TCACTTTATGTTTCAATCGAGGAG 57.032 37.500 0.00 0.00 0.00 3.69
3108 3704 1.076923 ATCTAGGGGTGTCGAGCGT 60.077 57.895 0.00 0.00 0.00 5.07
3138 3734 8.732746 TTAAAGGTAAATGCTATCCAAGACTC 57.267 34.615 0.00 0.00 0.00 3.36
3241 3853 3.538634 ATAGTGGGAAGAAGCGTTACC 57.461 47.619 0.00 0.00 0.00 2.85
3357 4000 3.686016 ACTGTCCCATGCGTTCTTATTT 58.314 40.909 0.00 0.00 0.00 1.40
3399 4042 8.729756 CAGATCTGTACATCAAACATAAAACCA 58.270 33.333 14.95 0.00 0.00 3.67
3584 4229 9.491675 TCGAAGGTAATTACTCATGTTTGTTTA 57.508 29.630 15.05 0.00 0.00 2.01
3625 4270 2.074230 TTTCTTGCGCTGGTTGCAGG 62.074 55.000 9.73 0.00 44.28 4.85
3687 4332 7.282585 TGACTGAATATGCCTTATACAAGCTT 58.717 34.615 0.00 0.00 0.00 3.74
3710 4356 7.425577 TTCATGGATCATATTTGTTAGAGCG 57.574 36.000 0.00 0.00 0.00 5.03
3910 4556 9.632807 GATATAATGGCTCGAGGAATACATATC 57.367 37.037 15.58 2.75 0.00 1.63
4236 4923 8.065473 TGGTGTTAATAACTGTTACTATCGGA 57.935 34.615 1.73 0.00 0.00 4.55
4242 4929 7.982371 AATAACTGTTACTATCGGAACTTCG 57.018 36.000 1.73 0.00 0.00 3.79
4562 5262 2.350895 CCATCACCCACGCCTTCA 59.649 61.111 0.00 0.00 0.00 3.02
4572 5272 1.200020 CCACGCCTTCAATGTTCTTCC 59.800 52.381 0.00 0.00 0.00 3.46
4730 5440 3.057946 CGGGAGCTTTGAAAAGAAAGAGG 60.058 47.826 6.98 0.00 38.28 3.69
4749 5459 1.892474 GGGGCAAGCAAACATGAAGTA 59.108 47.619 0.00 0.00 0.00 2.24
4751 5461 3.429410 GGGGCAAGCAAACATGAAGTATC 60.429 47.826 0.00 0.00 0.00 2.24
4752 5462 3.445096 GGGCAAGCAAACATGAAGTATCT 59.555 43.478 0.00 0.00 0.00 1.98
4753 5463 4.439289 GGGCAAGCAAACATGAAGTATCTC 60.439 45.833 0.00 0.00 0.00 2.75
4754 5464 4.397417 GGCAAGCAAACATGAAGTATCTCT 59.603 41.667 0.00 0.00 0.00 3.10
4757 5467 6.348786 GCAAGCAAACATGAAGTATCTCTGAA 60.349 38.462 0.00 0.00 0.00 3.02
4758 5468 7.627939 GCAAGCAAACATGAAGTATCTCTGAAT 60.628 37.037 0.00 0.00 0.00 2.57
4759 5469 7.934855 AGCAAACATGAAGTATCTCTGAATT 57.065 32.000 0.00 0.00 0.00 2.17
4760 5470 7.759465 AGCAAACATGAAGTATCTCTGAATTG 58.241 34.615 0.00 0.00 0.00 2.32
4761 5471 7.392673 AGCAAACATGAAGTATCTCTGAATTGT 59.607 33.333 0.00 0.00 0.00 2.71
4886 5596 6.238759 CCCCTGTTTGCTTTTCTATATGTAGC 60.239 42.308 0.00 0.00 0.00 3.58
4888 5598 7.013655 CCCTGTTTGCTTTTCTATATGTAGCAT 59.986 37.037 0.00 0.00 41.06 3.79
4909 5619 3.552875 TCTCTGTTACCCCTACTGATCG 58.447 50.000 0.00 0.00 0.00 3.69
4914 5624 2.756760 GTTACCCCTACTGATCGACACA 59.243 50.000 0.00 0.00 0.00 3.72
4926 5636 1.225475 CGACACAGCGCGATTTGAC 60.225 57.895 18.37 10.31 0.00 3.18
4933 5643 0.530650 AGCGCGATTTGACGATGGAT 60.531 50.000 12.10 0.00 35.09 3.41
4956 5666 1.342076 TGTGGTTTAGTGGGTTTGGCA 60.342 47.619 0.00 0.00 0.00 4.92
4994 5704 8.024145 ACATTTGTGGGTAAACCTGAAAATTA 57.976 30.769 0.00 0.00 41.11 1.40
5003 5713 7.069455 GGGTAAACCTGAAAATTATAGGTGCAT 59.931 37.037 8.47 3.12 43.75 3.96
5006 5716 6.455360 ACCTGAAAATTATAGGTGCATGTG 57.545 37.500 7.24 0.00 42.95 3.21
5076 5805 4.278170 CCCTTGTTCAAATGCTACAAGTCA 59.722 41.667 18.39 0.00 44.46 3.41
5109 5838 4.380531 TCCTTGTTCATCAGAGTTGTCAC 58.619 43.478 0.00 0.00 0.00 3.67
5113 5842 3.070018 GTTCATCAGAGTTGTCACTGGG 58.930 50.000 0.00 0.00 34.04 4.45
5117 5846 4.777366 TCATCAGAGTTGTCACTGGGATTA 59.223 41.667 0.00 0.00 34.04 1.75
5118 5847 4.808414 TCAGAGTTGTCACTGGGATTAG 57.192 45.455 0.00 0.00 34.04 1.73
5141 5871 3.423996 TTTTGGTTAACAAGCACGGTC 57.576 42.857 8.10 0.00 40.82 4.79
5142 5872 2.039818 TTGGTTAACAAGCACGGTCA 57.960 45.000 8.10 0.00 38.84 4.02
5158 5888 5.547465 CACGGTCAAAGATGCCCTAATATA 58.453 41.667 0.00 0.00 0.00 0.86
5159 5889 6.173339 CACGGTCAAAGATGCCCTAATATAT 58.827 40.000 0.00 0.00 0.00 0.86
5160 5890 7.327975 CACGGTCAAAGATGCCCTAATATATA 58.672 38.462 0.00 0.00 0.00 0.86
5161 5891 7.987458 CACGGTCAAAGATGCCCTAATATATAT 59.013 37.037 0.00 0.00 0.00 0.86
5182 5912 3.857052 TCTTCAGCGGATCACGTAATTT 58.143 40.909 0.00 0.00 46.52 1.82
5185 5915 4.112716 TCAGCGGATCACGTAATTTACA 57.887 40.909 7.31 0.00 46.52 2.41
5190 5933 3.061403 CGGATCACGTAATTTACACGCTC 60.061 47.826 7.31 0.00 43.10 5.03
5224 5967 0.888619 TTGACGCTCTGAGGATCGTT 59.111 50.000 6.83 0.00 43.03 3.85
5254 6037 3.535561 CTTGTTACCACCTGCATCCTAG 58.464 50.000 0.00 0.00 0.00 3.02
5393 6177 1.425412 CAGCTTTGCATTTGTGCCTC 58.575 50.000 0.00 0.00 0.00 4.70
5402 6187 6.543430 TTGCATTTGTGCCTCCTATAAAAT 57.457 33.333 0.00 0.00 0.00 1.82
5403 6188 7.652524 TTGCATTTGTGCCTCCTATAAAATA 57.347 32.000 0.00 0.00 0.00 1.40
5501 6324 0.318762 ACAAGAGGAACGACAGCTCC 59.681 55.000 0.00 0.00 32.85 4.70
5549 6372 1.663695 AGAGACTAGAGCAGCTCGAC 58.336 55.000 16.99 9.45 35.36 4.20
5726 6553 1.005450 TGGCAATTCTACCCCCAGAAC 59.995 52.381 0.00 0.00 37.37 3.01
5729 6556 2.026262 GCAATTCTACCCCCAGAACTCA 60.026 50.000 0.00 0.00 37.37 3.41
5741 6568 3.565902 CCCAGAACTCAAACCTTCTGAAC 59.434 47.826 8.63 0.00 44.22 3.18
5871 6698 1.509923 GCTACCGCCTTCGTGTAGT 59.490 57.895 11.74 0.00 39.46 2.73
5940 6767 1.519455 GGTTGCGGAGGAGATGACG 60.519 63.158 0.00 0.00 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.366590 GGATGGAATGGGGATTCAAAGC 59.633 50.000 0.00 0.00 32.39 3.51
68 69 0.035317 GTCTCATGCACCACACTCCA 59.965 55.000 0.00 0.00 0.00 3.86
219 224 6.529220 AGGCATAGAAGACATCAGGAATTAC 58.471 40.000 0.00 0.00 0.00 1.89
281 286 5.696724 CGGTTTTGTTATGTCTCTGAAGTCT 59.303 40.000 0.00 0.00 0.00 3.24
286 291 4.610605 TCCGGTTTTGTTATGTCTCTGA 57.389 40.909 0.00 0.00 0.00 3.27
300 305 6.041069 TGTCTTTAAATTGTCCAATCCGGTTT 59.959 34.615 0.00 0.00 35.57 3.27
623 683 9.853921 CATTTATTTGAGCAAAGAGAAACAAAC 57.146 29.630 1.92 0.00 33.32 2.93
789 866 5.359716 TTTTATGCGGATTTTGTACGTGT 57.640 34.783 0.00 0.00 36.21 4.49
842 919 4.462834 CCAAGGGGAGAAGGTGAAAAATAC 59.537 45.833 0.00 0.00 35.59 1.89
866 1087 1.532604 GCCGGTGAAAAGGGGAAAGG 61.533 60.000 1.90 0.00 0.00 3.11
1141 1367 1.372087 CTGCCCCTTCGTCTTCATGC 61.372 60.000 0.00 0.00 0.00 4.06
1286 1515 1.076044 GGCACAGGCATGGGGTATT 60.076 57.895 1.37 0.00 43.71 1.89
1353 1585 7.420800 CAACCTATGCTATCAAATTGGAGAAC 58.579 38.462 0.00 0.00 0.00 3.01
1358 1590 4.557296 CGCCAACCTATGCTATCAAATTGG 60.557 45.833 0.00 0.00 38.69 3.16
1369 1601 2.825836 AGCAGCGCCAACCTATGC 60.826 61.111 2.29 5.43 37.15 3.14
1385 1617 2.015736 AACTATTCAGTGAGGCGCAG 57.984 50.000 10.83 0.00 34.36 5.18
1391 1623 5.121454 GGAGCACAAGAAACTATTCAGTGAG 59.879 44.000 14.30 3.32 42.03 3.51
1416 1648 1.523484 GCAGCCTGCCTAAGCTCTC 60.523 63.158 5.06 0.00 37.18 3.20
1419 1651 1.676967 GTTGCAGCCTGCCTAAGCT 60.677 57.895 15.29 0.00 44.23 3.74
1420 1652 1.676967 AGTTGCAGCCTGCCTAAGC 60.677 57.895 15.29 0.00 44.23 3.09
1421 1653 2.177950 CAGTTGCAGCCTGCCTAAG 58.822 57.895 15.29 0.00 44.23 2.18
1433 1665 1.799258 CTTCTGGTGGGTGCAGTTGC 61.799 60.000 0.00 0.00 42.50 4.17
1434 1666 0.466189 ACTTCTGGTGGGTGCAGTTG 60.466 55.000 0.00 0.00 0.00 3.16
1438 1670 0.108585 GAGAACTTCTGGTGGGTGCA 59.891 55.000 0.00 0.00 0.00 4.57
1439 1671 0.606673 GGAGAACTTCTGGTGGGTGC 60.607 60.000 0.00 0.00 0.00 5.01
1440 1672 0.036875 GGGAGAACTTCTGGTGGGTG 59.963 60.000 0.00 0.00 0.00 4.61
1444 1676 2.355209 GCTAAGGGGAGAACTTCTGGTG 60.355 54.545 0.00 0.00 0.00 4.17
1447 1679 3.922171 ATGCTAAGGGGAGAACTTCTG 57.078 47.619 0.00 0.00 0.00 3.02
1479 1716 4.739716 AGTGCAAATGACATCGAACAAAAC 59.260 37.500 0.00 0.00 0.00 2.43
1488 1725 7.237173 GTGAAACTACTAGTGCAAATGACATC 58.763 38.462 5.39 0.00 0.00 3.06
1531 1768 6.373186 AGCAGTTAAACAAAGTAGACCAAC 57.627 37.500 0.00 0.00 0.00 3.77
1549 1786 4.407365 AGGGCACAAAGTTAATAAGCAGT 58.593 39.130 0.00 0.00 0.00 4.40
1592 1830 5.529060 CCCTCAGTTCATGCTAGTATTTTCC 59.471 44.000 0.00 0.00 0.00 3.13
1604 1842 1.945394 GCACATAGCCCTCAGTTCATG 59.055 52.381 0.00 0.00 37.23 3.07
1606 1844 0.983467 TGCACATAGCCCTCAGTTCA 59.017 50.000 0.00 0.00 44.83 3.18
1607 1845 1.065854 AGTGCACATAGCCCTCAGTTC 60.066 52.381 21.04 0.00 44.83 3.01
1648 1890 2.891941 GATTCCCATCCGCTGCACCA 62.892 60.000 0.00 0.00 0.00 4.17
1650 1892 2.537560 CGATTCCCATCCGCTGCAC 61.538 63.158 0.00 0.00 0.00 4.57
1778 2020 2.948115 TGCACAATAGGCAAGGCATAT 58.052 42.857 0.00 0.00 37.11 1.78
1866 2108 9.301153 GGTAAAATAAATATCACAAACCTGCAG 57.699 33.333 6.78 6.78 0.00 4.41
1915 2167 8.727100 TGGAATAAGATACTGACAGTATGGAT 57.273 34.615 28.65 16.71 41.21 3.41
1918 2170 7.436933 TGCTGGAATAAGATACTGACAGTATG 58.563 38.462 28.65 14.01 41.21 2.39
2363 2621 5.105187 TGAACTCAGTCCATTGTAGAGGATG 60.105 44.000 0.00 0.00 36.11 3.51
2366 2624 4.808414 TGAACTCAGTCCATTGTAGAGG 57.192 45.455 0.00 0.00 0.00 3.69
2431 2702 3.307674 ACTATGCACGCACAAACAATTG 58.692 40.909 3.24 3.24 42.46 2.32
2432 2703 3.641437 ACTATGCACGCACAAACAATT 57.359 38.095 0.00 0.00 0.00 2.32
2443 2715 3.845775 GCACACAAACAATACTATGCACG 59.154 43.478 0.00 0.00 0.00 5.34
2475 2764 4.032900 CCAGCATACTGTTCGACATTACAC 59.967 45.833 0.00 0.00 42.81 2.90
2588 2973 8.677300 GGTGAATCTAGAAAATTGCTTGTCATA 58.323 33.333 0.00 0.00 0.00 2.15
2594 2979 6.491403 AGTGTGGTGAATCTAGAAAATTGCTT 59.509 34.615 0.00 0.00 0.00 3.91
2702 3102 3.381590 GGCCCTGTTGACTGAATAATTCC 59.618 47.826 0.00 0.00 0.00 3.01
2835 3254 3.882888 GTCTCATCAACAACCTGAAACCA 59.117 43.478 0.00 0.00 0.00 3.67
2861 3280 6.106648 TGATATGCCTCTCTTAACATCCTG 57.893 41.667 0.00 0.00 0.00 3.86
3001 3420 8.567285 TGAGATATTGATATCGTAGAGCAAGA 57.433 34.615 0.00 0.00 43.63 3.02
3065 3484 5.154932 CCATAGCGTAGAATTAACTCCTCG 58.845 45.833 0.00 0.00 0.00 4.63
3071 3667 6.531948 CCTAGATGCCATAGCGTAGAATTAAC 59.468 42.308 0.00 0.00 44.31 2.01
3108 3704 6.494952 TGGATAGCATTTACCTTTAAACCCA 58.505 36.000 0.00 0.00 29.77 4.51
3138 3734 1.592081 GCAGAGCAGACTATCTTTGCG 59.408 52.381 4.43 0.00 42.47 4.85
3241 3853 3.600388 ACTCCAGCTTTGTAGGAATTCG 58.400 45.455 0.00 0.00 0.00 3.34
3357 4000 4.397103 CAGATCTGCAATAACAGCAAGGAA 59.603 41.667 10.38 0.00 42.17 3.36
3399 4042 4.101585 TGGAGAAGAACAATGAGACACAGT 59.898 41.667 0.00 0.00 0.00 3.55
3587 4232 9.415544 GCAAGAAAATGAACTCTGATTTACAAT 57.584 29.630 0.00 0.00 0.00 2.71
3625 4270 6.674066 TGTAGTTACTTATTTTTGTGGCTGC 58.326 36.000 0.00 0.00 0.00 5.25
3687 4332 6.424812 CACGCTCTAACAAATATGATCCATGA 59.575 38.462 0.00 0.00 0.00 3.07
3710 4356 4.207019 GCTTTCTTATGTTTGCACACACAC 59.793 41.667 8.06 0.00 35.03 3.82
3910 4556 8.370493 AGTTGATAACATATCTCAAACCATCG 57.630 34.615 0.00 0.00 31.21 3.84
4091 4755 7.365497 AGACATGTCAGTACAATATCATGGA 57.635 36.000 27.02 0.00 39.58 3.41
4217 4904 8.677300 ACGAAGTTCCGATAGTAACAGTTATTA 58.323 33.333 0.00 0.00 37.78 0.98
4218 4905 7.487189 CACGAAGTTCCGATAGTAACAGTTATT 59.513 37.037 0.00 0.00 41.61 1.40
4236 4923 2.105821 TCCTGACCCAAATCACGAAGTT 59.894 45.455 0.00 0.00 41.61 2.66
4242 4929 3.000727 CGTAAGTCCTGACCCAAATCAC 58.999 50.000 0.00 0.00 0.00 3.06
4730 5440 3.445096 AGATACTTCATGTTTGCTTGCCC 59.555 43.478 0.00 0.00 0.00 5.36
4754 5464 3.559655 CAGAACACCGACTGAACAATTCA 59.440 43.478 0.00 0.00 36.38 2.57
4757 5467 3.469008 TCAGAACACCGACTGAACAAT 57.531 42.857 0.00 0.00 39.68 2.71
4758 5468 2.971660 TCAGAACACCGACTGAACAA 57.028 45.000 0.00 0.00 39.68 2.83
4759 5469 2.971660 TTCAGAACACCGACTGAACA 57.028 45.000 0.00 0.00 44.59 3.18
4765 5475 4.970003 CAGAAAACAATTCAGAACACCGAC 59.030 41.667 0.00 0.00 0.00 4.79
4860 5570 5.826643 ACATATAGAAAAGCAAACAGGGGA 58.173 37.500 0.00 0.00 0.00 4.81
4886 5596 4.022762 CGATCAGTAGGGGTAACAGAGATG 60.023 50.000 0.00 0.00 39.74 2.90
4888 5598 3.201487 TCGATCAGTAGGGGTAACAGAGA 59.799 47.826 0.00 0.00 39.74 3.10
4909 5619 1.225475 CGTCAAATCGCGCTGTGTC 60.225 57.895 5.56 0.00 0.00 3.67
4914 5624 0.530650 ATCCATCGTCAAATCGCGCT 60.531 50.000 5.56 0.00 0.00 5.92
4933 5643 2.290464 CAAACCCACTAAACCACACGA 58.710 47.619 0.00 0.00 0.00 4.35
4939 5649 1.989706 TCTGCCAAACCCACTAAACC 58.010 50.000 0.00 0.00 0.00 3.27
4956 5666 6.306987 ACCCACAAATGTTCAGACTAAATCT 58.693 36.000 0.00 0.00 38.66 2.40
4977 5687 6.378848 TGCACCTATAATTTTCAGGTTTACCC 59.621 38.462 3.29 0.00 40.77 3.69
4994 5704 7.466746 AAAAATTACTGTCACATGCACCTAT 57.533 32.000 0.00 0.00 0.00 2.57
5023 5733 0.251341 CTGGGGGTCAGTTGGAAAGG 60.251 60.000 0.00 0.00 38.64 3.11
5076 5805 2.936202 TGAACAAGGAGAAGCAGCTTT 58.064 42.857 9.62 0.00 0.00 3.51
5142 5872 9.844257 GCTGAAGATATATATTAGGGCATCTTT 57.156 33.333 7.33 0.00 33.93 2.52
5158 5888 4.848562 TTACGTGATCCGCTGAAGATAT 57.151 40.909 0.00 0.00 41.42 1.63
5159 5889 4.848562 ATTACGTGATCCGCTGAAGATA 57.151 40.909 0.00 0.00 41.42 1.98
5160 5890 3.735237 ATTACGTGATCCGCTGAAGAT 57.265 42.857 0.00 0.00 41.42 2.40
5161 5891 3.520290 AATTACGTGATCCGCTGAAGA 57.480 42.857 0.00 0.00 41.42 2.87
5167 5897 2.595881 GCGTGTAAATTACGTGATCCGC 60.596 50.000 0.00 2.14 43.09 5.54
5190 5933 5.809562 AGAGCGTCAAGAACTCAAGATATTG 59.190 40.000 0.00 0.00 32.71 1.90
5254 6037 7.590689 GTCAGATAACCTTAGTTATAGTGCGTC 59.409 40.741 0.00 0.00 46.83 5.19
5337 6121 7.734865 TGGAAGATAATCTACCTATCATGTGGT 59.265 37.037 11.24 11.24 40.12 4.16
5402 6187 9.742144 TTATAGGAGGTACAAATGCAAAGTTTA 57.258 29.630 0.00 0.00 0.00 2.01
5403 6188 8.644374 TTATAGGAGGTACAAATGCAAAGTTT 57.356 30.769 0.00 0.00 0.00 2.66
5609 6432 2.168496 GCCCTACCTTTTTCCTGTTCC 58.832 52.381 0.00 0.00 0.00 3.62
5726 6553 4.035675 GGACAGTTGTTCAGAAGGTTTGAG 59.964 45.833 0.00 0.00 0.00 3.02
5729 6556 3.053619 AGGGACAGTTGTTCAGAAGGTTT 60.054 43.478 0.00 0.00 0.00 3.27
5741 6568 1.202806 TCTTTCAGCCAGGGACAGTTG 60.203 52.381 0.00 0.00 0.00 3.16
5769 6596 1.745890 CGGTGGACAGTGAAGTGGA 59.254 57.895 0.00 0.00 0.00 4.02
5824 6651 4.973055 TCGGTTGGTGAACGGCGG 62.973 66.667 13.24 0.00 33.51 6.13
5825 6652 3.411351 CTCGGTTGGTGAACGGCG 61.411 66.667 4.80 4.80 33.51 6.46
5919 6746 1.144936 CATCTCCTCCGCAACCTCC 59.855 63.158 0.00 0.00 0.00 4.30
5940 6767 2.825264 CCGATCTCCCTTGCCTCC 59.175 66.667 0.00 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.