Multiple sequence alignment - TraesCS7D01G541900

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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 TraesCS7D01G541900 chr7D 100.000 2525 0 0 1 2525 631251738 631254262 0.000000e+00 4663.0
1 TraesCS7D01G541900 chr7D 94.408 1234 57 8 1 1228 630683853 630685080 0.000000e+00 1886.0
2 TraesCS7D01G541900 chr7D 90.185 703 66 3 1822 2523 120184785 120184085 0.000000e+00 913.0
3 TraesCS7D01G541900 chr7D 89.362 705 65 10 1826 2524 525279054 525279754 0.000000e+00 878.0
4 TraesCS7D01G541900 chr7D 90.223 583 34 10 1237 1818 630685151 630685711 0.000000e+00 739.0
5 TraesCS7D01G541900 chr7D 88.584 219 23 2 1017 1234 630833763 630833546 5.360000e-67 265.0
6 TraesCS7D01G541900 chr7D 88.584 219 23 2 1017 1234 631361197 631361414 5.360000e-67 265.0
7 TraesCS7D01G541900 chr7D 84.956 226 28 4 1015 1234 630678226 630678451 9.090000e-55 224.0
8 TraesCS7D01G541900 chr7D 87.952 166 18 2 122 287 454079409 454079246 7.130000e-46 195.0
9 TraesCS7D01G541900 chr7D 94.203 69 4 0 1756 1824 631253394 631253462 3.440000e-19 106.0
10 TraesCS7D01G541900 chr7D 94.203 69 4 0 1657 1725 631253493 631253561 3.440000e-19 106.0
11 TraesCS7D01G541900 chr7D 93.651 63 4 0 1657 1719 630685649 630685711 7.440000e-16 95.3
12 TraesCS7D01G541900 chr7D 97.500 40 1 0 1536 1575 630989303 630989342 4.510000e-08 69.4
13 TraesCS7D01G541900 chr5D 89.929 705 64 5 1823 2523 517711346 517712047 0.000000e+00 902.0
14 TraesCS7D01G541900 chr5D 89.586 701 71 2 1826 2525 341792810 341793509 0.000000e+00 889.0
15 TraesCS7D01G541900 chr5D 85.859 99 11 2 1711 1806 340103357 340103455 4.440000e-18 102.0
16 TraesCS7D01G541900 chr5D 88.889 72 6 2 1734 1804 400417561 400417631 1.240000e-13 87.9
17 TraesCS7D01G541900 chr6D 89.518 706 72 2 1821 2525 271598988 271598284 0.000000e+00 893.0
18 TraesCS7D01G541900 chr5A 89.331 703 70 5 1826 2525 313228104 313227404 0.000000e+00 878.0
19 TraesCS7D01G541900 chr5A 89.091 165 16 2 122 286 320214406 320214244 1.180000e-48 204.0
20 TraesCS7D01G541900 chr3D 89.078 705 75 2 1822 2525 137791695 137792398 0.000000e+00 874.0
21 TraesCS7D01G541900 chr3D 89.375 160 15 2 122 281 128214006 128214163 1.530000e-47 200.0
22 TraesCS7D01G541900 chr4D 89.047 703 75 2 1822 2523 293738802 293738101 0.000000e+00 870.0
23 TraesCS7D01G541900 chr4D 88.415 164 17 2 123 286 479687421 479687260 1.980000e-46 196.0
24 TraesCS7D01G541900 chr4D 81.600 125 14 6 1682 1806 52830297 52830182 7.440000e-16 95.3
25 TraesCS7D01G541900 chr2D 89.047 703 76 1 1822 2524 397912808 397913509 0.000000e+00 870.0
26 TraesCS7D01G541900 chr2D 88.820 161 16 2 123 283 134301488 134301646 1.980000e-46 196.0
27 TraesCS7D01G541900 chr2D 77.652 264 43 15 300 558 637980022 637979770 2.020000e-31 147.0
28 TraesCS7D01G541900 chrUn 78.958 518 83 21 1016 1515 364243352 364242843 1.870000e-86 329.0
29 TraesCS7D01G541900 chrUn 84.071 226 30 4 1015 1234 88643203 88643428 1.970000e-51 213.0
30 TraesCS7D01G541900 chrUn 84.071 226 30 4 1015 1234 283733294 283733519 1.970000e-51 213.0
31 TraesCS7D01G541900 chrUn 97.222 36 1 0 1199 1234 364243219 364243184 7.540000e-06 62.1
32 TraesCS7D01G541900 chr7A 85.590 229 24 5 1015 1234 727038229 727038001 5.430000e-57 231.0
33 TraesCS7D01G541900 chr2A 89.441 161 14 3 123 283 367649161 367649318 1.530000e-47 200.0
34 TraesCS7D01G541900 chr6B 88.485 165 16 3 120 283 36133500 36133662 1.980000e-46 196.0
35 TraesCS7D01G541900 chr6B 87.730 163 18 2 120 281 83138380 83138541 3.320000e-44 189.0
36 TraesCS7D01G541900 chr2B 88.372 86 9 1 1722 1806 38848145 38848060 4.440000e-18 102.0
37 TraesCS7D01G541900 chr2B 80.165 121 15 7 7 124 210827876 210827762 5.790000e-12 82.4
38 TraesCS7D01G541900 chr7B 84.848 99 12 2 1711 1806 750052401 750052499 2.070000e-16 97.1
39 TraesCS7D01G541900 chr7B 84.270 89 8 5 1729 1817 179332709 179332791 5.790000e-12 82.4
40 TraesCS7D01G541900 chr1D 97.059 34 1 0 1771 1804 373416379 373416412 9.760000e-05 58.4


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 TraesCS7D01G541900 chr7D 631251738 631254262 2524 False 1625.000000 4663 96.135333 1 2525 3 chr7D.!!$F6 2524
1 TraesCS7D01G541900 chr7D 120184085 120184785 700 True 913.000000 913 90.185000 1822 2523 1 chr7D.!!$R1 701
2 TraesCS7D01G541900 chr7D 630683853 630685711 1858 False 906.766667 1886 92.760667 1 1818 3 chr7D.!!$F5 1817
3 TraesCS7D01G541900 chr7D 525279054 525279754 700 False 878.000000 878 89.362000 1826 2524 1 chr7D.!!$F1 698
4 TraesCS7D01G541900 chr5D 517711346 517712047 701 False 902.000000 902 89.929000 1823 2523 1 chr5D.!!$F4 700
5 TraesCS7D01G541900 chr5D 341792810 341793509 699 False 889.000000 889 89.586000 1826 2525 1 chr5D.!!$F2 699
6 TraesCS7D01G541900 chr6D 271598284 271598988 704 True 893.000000 893 89.518000 1821 2525 1 chr6D.!!$R1 704
7 TraesCS7D01G541900 chr5A 313227404 313228104 700 True 878.000000 878 89.331000 1826 2525 1 chr5A.!!$R1 699
8 TraesCS7D01G541900 chr3D 137791695 137792398 703 False 874.000000 874 89.078000 1822 2525 1 chr3D.!!$F2 703
9 TraesCS7D01G541900 chr4D 293738101 293738802 701 True 870.000000 870 89.047000 1822 2523 1 chr4D.!!$R2 701
10 TraesCS7D01G541900 chr2D 397912808 397913509 701 False 870.000000 870 89.047000 1822 2524 1 chr2D.!!$F2 702

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
228 229 6.15014 AGTGTAGATTCACTCATTTTGCTTCC 59.85 38.462 0.0 0.0 44.07 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1616 1686 0.09715 GCCAGGCGACGAATCTTTTC 59.903 55.0 0.0 0.0 0.0 2.29 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
228 229 6.150140 AGTGTAGATTCACTCATTTTGCTTCC 59.850 38.462 0.00 0.00 44.07 3.46
251 252 9.967346 TTCCTATGTAGTCTCTTATTGAAATCG 57.033 33.333 0.00 0.00 0.00 3.34
257 258 9.302345 TGTAGTCTCTTATTGAAATCGCTAAAG 57.698 33.333 0.00 0.00 0.00 1.85
258 259 7.778470 AGTCTCTTATTGAAATCGCTAAAGG 57.222 36.000 0.00 0.00 0.00 3.11
264 265 8.262227 TCTTATTGAAATCGCTAAAGGGAGTTA 58.738 33.333 9.31 0.00 43.52 2.24
283 284 7.395617 GGAGTTATATTTAGGAATGGAGGGAC 58.604 42.308 0.00 0.00 0.00 4.46
339 340 8.348507 CCTAAGAAGAAATGAATTAGTGGCATC 58.651 37.037 0.00 0.00 0.00 3.91
443 445 9.404848 GAATTAGTAGCTTTGGTATTACCCTTT 57.595 33.333 10.37 0.00 37.50 3.11
1030 1037 3.083349 CCATCTGCCGGGAGTCCA 61.083 66.667 23.44 3.75 0.00 4.02
1079 1086 1.187087 CTCAAGAAGGTAGTCGCCCT 58.813 55.000 0.00 0.00 0.00 5.19
1082 1089 1.321074 AAGAAGGTAGTCGCCCTCGG 61.321 60.000 0.00 0.00 36.13 4.63
1083 1090 3.427598 GAAGGTAGTCGCCCTCGGC 62.428 68.421 0.00 0.00 46.75 5.54
1107 1114 2.185350 CAGCCGCACCTCGATCTT 59.815 61.111 0.00 0.00 41.67 2.40
1197 1204 1.749638 CGAGTACTGGGAGGCGAGT 60.750 63.158 0.00 0.00 0.00 4.18
1204 1211 3.228017 GGGAGGCGAGTAGGGAGC 61.228 72.222 0.00 0.00 0.00 4.70
1228 1235 0.390472 GGACAAGGTGCTCTTCCTCG 60.390 60.000 0.00 0.00 33.76 4.63
1230 1237 1.078848 CAAGGTGCTCTTCCTCGGG 60.079 63.158 0.00 0.00 33.76 5.14
1384 1454 0.745845 CTTCAGGAAGGGCATGGTCG 60.746 60.000 1.01 0.00 34.87 4.79
1399 1469 4.373116 TCGGCGACTGGAGCAACC 62.373 66.667 4.99 0.00 39.54 3.77
1406 1476 1.676916 CGACTGGAGCAACCACATGAT 60.677 52.381 0.00 0.00 44.64 2.45
1447 1517 1.437573 GATGCCATCGTCGAGGACA 59.562 57.895 10.45 2.88 32.09 4.02
1452 1522 0.668535 CCATCGTCGAGGACATGCTA 59.331 55.000 10.45 0.00 32.09 3.49
1486 1556 4.322574 GGGGCTTCTCGTTTACTAACTCTT 60.323 45.833 0.00 0.00 31.89 2.85
1491 1561 5.401531 TCTCGTTTACTAACTCTTGCCAT 57.598 39.130 0.00 0.00 31.89 4.40
1493 1563 3.682858 TCGTTTACTAACTCTTGCCATGC 59.317 43.478 0.00 0.00 31.89 4.06
1509 1579 2.815647 GCGGAAGAAGGTGCTCCG 60.816 66.667 5.39 5.39 45.67 4.63
1513 1583 3.591254 GAAGAAGGTGCTCCGCCGT 62.591 63.158 0.00 0.00 39.30 5.68
1515 1585 1.614241 AAGAAGGTGCTCCGCCGTAT 61.614 55.000 0.00 0.00 39.30 3.06
1549 1619 6.037098 CGGGTGAAAGTTTTTATTGTGTTGA 58.963 36.000 0.00 0.00 0.00 3.18
1616 1686 2.351738 GGTCGGCCAACTGATTCTTTTG 60.352 50.000 0.00 0.00 32.57 2.44
1624 1694 6.707608 GGCCAACTGATTCTTTTGAAAAGATT 59.292 34.615 19.81 16.26 42.31 2.40
1630 1700 5.851177 TGATTCTTTTGAAAAGATTCGTCGC 59.149 36.000 25.17 11.73 42.31 5.19
1649 1719 0.604780 CCTGGCGAGCTATCCCATTG 60.605 60.000 0.00 0.00 0.00 2.82
1650 1720 1.227943 TGGCGAGCTATCCCATTGC 60.228 57.895 0.00 0.00 0.00 3.56
1661 1731 1.107945 TCCCATTGCGTGATACGAGA 58.892 50.000 5.44 0.00 46.05 4.04
1662 1732 1.478916 TCCCATTGCGTGATACGAGAA 59.521 47.619 5.44 0.00 46.05 2.87
1663 1733 1.593006 CCCATTGCGTGATACGAGAAC 59.407 52.381 5.44 0.00 46.05 3.01
1665 1735 2.930040 CCATTGCGTGATACGAGAACTT 59.070 45.455 5.44 0.00 46.05 2.66
1666 1736 3.370978 CCATTGCGTGATACGAGAACTTT 59.629 43.478 5.44 0.00 46.05 2.66
1667 1737 4.142902 CCATTGCGTGATACGAGAACTTTT 60.143 41.667 5.44 0.00 46.05 2.27
1668 1738 4.640805 TTGCGTGATACGAGAACTTTTC 57.359 40.909 5.44 0.00 46.05 2.29
1670 1740 5.050644 TGCGTGATACGAGAACTTTTCTA 57.949 39.130 5.44 0.00 46.05 2.10
1671 1741 4.855388 TGCGTGATACGAGAACTTTTCTAC 59.145 41.667 5.44 0.00 46.05 2.59
1672 1742 4.028670 GCGTGATACGAGAACTTTTCTACG 60.029 45.833 5.44 0.00 46.05 3.51
1673 1743 5.319139 CGTGATACGAGAACTTTTCTACGA 58.681 41.667 11.90 1.61 46.05 3.43
1674 1744 5.791974 CGTGATACGAGAACTTTTCTACGAA 59.208 40.000 11.90 0.00 46.05 3.85
1675 1745 6.303970 CGTGATACGAGAACTTTTCTACGAAA 59.696 38.462 11.90 0.00 46.05 3.46
1676 1746 7.008086 CGTGATACGAGAACTTTTCTACGAAAT 59.992 37.037 11.90 7.09 46.05 2.17
1677 1747 8.312524 GTGATACGAGAACTTTTCTACGAAATC 58.687 37.037 11.90 12.62 40.87 2.17
1678 1748 8.242053 TGATACGAGAACTTTTCTACGAAATCT 58.758 33.333 11.90 0.00 40.87 2.40
1679 1749 6.931243 ACGAGAACTTTTCTACGAAATCTC 57.069 37.500 11.90 7.74 40.87 2.75
1682 1752 6.251801 CGAGAACTTTTCTACGAAATCTCCTC 59.748 42.308 10.47 0.00 40.87 3.71
1694 1764 9.458374 CTACGAAATCTCCTCTTCTCTAATTTC 57.542 37.037 0.00 0.00 0.00 2.17
1705 1775 7.094032 CCTCTTCTCTAATTTCCTGCAACAATT 60.094 37.037 0.00 0.00 0.00 2.32
1707 1777 7.448161 TCTTCTCTAATTTCCTGCAACAATTCA 59.552 33.333 0.00 0.00 0.00 2.57
1708 1778 6.913170 TCTCTAATTTCCTGCAACAATTCAC 58.087 36.000 0.00 0.00 0.00 3.18
1709 1779 6.716628 TCTCTAATTTCCTGCAACAATTCACT 59.283 34.615 0.00 0.00 0.00 3.41
1710 1780 7.231317 TCTCTAATTTCCTGCAACAATTCACTT 59.769 33.333 0.00 0.00 0.00 3.16
1711 1781 7.147312 TCTAATTTCCTGCAACAATTCACTTG 58.853 34.615 0.00 0.00 40.90 3.16
1818 1888 4.400884 TGCAACAAGTCACCTGTTACAATT 59.599 37.500 0.00 0.00 0.00 2.32
1819 1889 5.105554 TGCAACAAGTCACCTGTTACAATTT 60.106 36.000 0.00 0.00 0.00 1.82
1824 1894 8.057536 ACAAGTCACCTGTTACAATTTTTGTA 57.942 30.769 0.00 0.00 43.27 2.41
1833 1903 8.413229 CCTGTTACAATTTTTGTAGGGGATATG 58.587 37.037 0.91 0.00 45.92 1.78
1896 1967 4.516698 CCACTTGCGGCTTATAATGAAGAT 59.483 41.667 0.00 0.00 0.00 2.40
1948 2019 0.543749 AGCGAGCTTATTGAAGGCCT 59.456 50.000 0.00 0.00 32.84 5.19
1958 2029 0.545787 TTGAAGGCCTAAGACCCGGA 60.546 55.000 5.16 0.00 0.00 5.14
2140 2215 7.489160 GGGTTAACTCAAGAAAACAACTCATT 58.511 34.615 5.42 0.00 0.00 2.57
2163 2238 4.142227 TGAGAACTAGGTCAAGCGTATTCC 60.142 45.833 11.14 0.00 0.00 3.01
2183 2258 1.557832 CCTCCCTGGTAATCGAAACCA 59.442 52.381 18.81 18.81 44.75 3.67
2241 2316 1.757118 CGTTGAGAGGGGCTGAATCTA 59.243 52.381 0.00 0.00 0.00 1.98
2316 2394 3.693807 ACGATGACTCCACACCTAAGTA 58.306 45.455 0.00 0.00 0.00 2.24
2318 2396 3.181489 CGATGACTCCACACCTAAGTACC 60.181 52.174 0.00 0.00 0.00 3.34
2326 2404 4.594062 TCCACACCTAAGTACCTTTGCTAA 59.406 41.667 0.00 0.00 0.00 3.09
2362 2440 3.276091 TCCACAACAGTTGGCGCG 61.276 61.111 17.76 0.00 34.12 6.86
2365 2443 3.286751 ACAACAGTTGGCGCGCAT 61.287 55.556 34.42 12.76 34.12 4.73
2370 2448 2.436469 AGTTGGCGCGCATCATGA 60.436 55.556 34.42 5.47 0.00 3.07
2376 2454 2.898840 CGCGCATCATGAGGCCTT 60.899 61.111 25.30 0.00 34.12 4.35
2404 2482 4.855340 AGTGGTTTCAAGTTCTTGAAGGA 58.145 39.130 21.64 10.46 41.38 3.36
2435 2513 1.611673 GGGATCAAGGGATACGCCATG 60.612 57.143 0.00 0.00 34.97 3.66
2459 2537 3.665675 GATGACCAAGAGCCGCCGT 62.666 63.158 0.00 0.00 0.00 5.68
2480 2558 1.469251 GGCAAGCTCTACATCGACGAA 60.469 52.381 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
161 162 5.836898 ACATCCGTATGTAGTCCCTTATTGA 59.163 40.000 0.00 0.00 44.66 2.57
251 252 9.232473 CCATTCCTAAATATAACTCCCTTTAGC 57.768 37.037 0.00 0.00 32.40 3.09
257 258 6.504279 TCCCTCCATTCCTAAATATAACTCCC 59.496 42.308 0.00 0.00 0.00 4.30
258 259 7.237887 AGTCCCTCCATTCCTAAATATAACTCC 59.762 40.741 0.00 0.00 0.00 3.85
264 265 6.032693 CCCTAGTCCCTCCATTCCTAAATAT 58.967 44.000 0.00 0.00 0.00 1.28
283 284 9.336171 CTTCCTTTTCTATGAGAATTTCCCTAG 57.664 37.037 0.00 0.00 33.67 3.02
318 319 5.066505 ACCGATGCCACTAATTCATTTCTTC 59.933 40.000 0.00 0.00 0.00 2.87
322 323 6.959639 ATTACCGATGCCACTAATTCATTT 57.040 33.333 0.00 0.00 0.00 2.32
327 328 5.298989 TGGTATTACCGATGCCACTAATT 57.701 39.130 8.32 0.00 44.44 1.40
413 415 9.053840 GGTAATACCAAAGCTACTAATTCCTTC 57.946 37.037 4.24 0.00 38.42 3.46
416 418 7.515586 AGGGTAATACCAAAGCTACTAATTCC 58.484 38.462 12.03 0.00 41.02 3.01
771 776 8.326765 TCTTCTTAAAGGGTATGGCACTAATA 57.673 34.615 0.00 0.00 33.03 0.98
823 828 9.988350 ATTCTTCGCATACTATTAAAAAGTGTG 57.012 29.630 11.44 11.44 38.63 3.82
913 918 6.662755 TGATCTATGGGTATATTTGGGATGC 58.337 40.000 0.00 0.00 0.00 3.91
1013 1020 2.599645 CTTGGACTCCCGGCAGATGG 62.600 65.000 0.00 0.00 34.29 3.51
1021 1028 2.261671 CACGTCCTTGGACTCCCG 59.738 66.667 16.60 6.98 34.29 5.14
1030 1037 1.066858 CCATGACACTAGCACGTCCTT 60.067 52.381 0.00 0.00 0.00 3.36
1100 1107 0.098905 CTCGGCGAAGTCAAGATCGA 59.901 55.000 12.13 0.00 41.43 3.59
1107 1114 1.213013 GAAGAGCTCGGCGAAGTCA 59.787 57.895 12.13 0.00 0.00 3.41
1234 1241 1.680522 CCTCCTCCTCCACCGTGATG 61.681 65.000 0.00 0.00 0.00 3.07
1241 1310 2.447714 GGGCATCCTCCTCCTCCAC 61.448 68.421 0.00 0.00 0.00 4.02
1242 1311 2.040464 GGGCATCCTCCTCCTCCA 60.040 66.667 0.00 0.00 0.00 3.86
1269 1338 1.654954 GCACAGCTCCAAGATGGCAG 61.655 60.000 0.00 0.00 35.60 4.85
1340 1409 2.338620 CGTTGGAGTCGGTGCTCA 59.661 61.111 0.00 0.00 37.24 4.26
1341 1410 1.733399 GACGTTGGAGTCGGTGCTC 60.733 63.158 0.00 0.00 34.89 4.26
1342 1411 2.338984 GACGTTGGAGTCGGTGCT 59.661 61.111 0.00 0.00 0.00 4.40
1399 1469 2.725641 CATGGCGGGCATCATGTG 59.274 61.111 14.79 0.49 36.82 3.21
1463 1533 3.195182 AGAGTTAGTAAACGAGAAGCCCC 59.805 47.826 0.00 0.00 40.73 5.80
1486 1556 1.675310 CACCTTCTTCCGCATGGCA 60.675 57.895 0.00 0.00 34.14 4.92
1491 1561 2.347490 GGAGCACCTTCTTCCGCA 59.653 61.111 0.00 0.00 0.00 5.69
1513 1583 3.448301 ACTTTCACCCGTCAACCGATATA 59.552 43.478 0.00 0.00 39.56 0.86
1515 1585 1.619827 ACTTTCACCCGTCAACCGATA 59.380 47.619 0.00 0.00 39.56 2.92
1571 1641 3.712091 AGCGCGCCCTTATAGTATATC 57.288 47.619 30.33 0.00 0.00 1.63
1594 1664 0.322546 AAGAATCAGTTGGCCGACCC 60.323 55.000 20.18 4.41 33.59 4.46
1602 1672 8.566008 ACGAATCTTTTCAAAAGAATCAGTTG 57.434 30.769 22.30 11.77 0.00 3.16
1616 1686 0.097150 GCCAGGCGACGAATCTTTTC 59.903 55.000 0.00 0.00 0.00 2.29
1630 1700 0.604780 CAATGGGATAGCTCGCCAGG 60.605 60.000 7.05 0.00 33.54 4.45
1649 1719 4.028670 CGTAGAAAAGTTCTCGTATCACGC 60.029 45.833 0.00 0.00 42.21 5.34
1650 1720 5.319139 TCGTAGAAAAGTTCTCGTATCACG 58.681 41.667 0.00 0.00 44.19 4.35
1661 1731 7.672240 AGAAGAGGAGATTTCGTAGAAAAGTT 58.328 34.615 0.00 0.00 45.90 2.66
1662 1732 7.177744 AGAGAAGAGGAGATTTCGTAGAAAAGT 59.822 37.037 0.00 0.00 45.90 2.66
1663 1733 7.543756 AGAGAAGAGGAGATTTCGTAGAAAAG 58.456 38.462 0.00 0.00 45.90 2.27
1665 1735 8.577048 TTAGAGAAGAGGAGATTTCGTAGAAA 57.423 34.615 0.00 0.00 45.90 2.52
1666 1736 8.754991 ATTAGAGAAGAGGAGATTTCGTAGAA 57.245 34.615 0.00 0.00 45.90 2.10
1667 1737 8.754991 AATTAGAGAAGAGGAGATTTCGTAGA 57.245 34.615 0.00 0.00 0.00 2.59
1668 1738 9.458374 GAAATTAGAGAAGAGGAGATTTCGTAG 57.542 37.037 0.00 0.00 0.00 3.51
1670 1740 7.125053 AGGAAATTAGAGAAGAGGAGATTTCGT 59.875 37.037 0.00 0.00 34.51 3.85
1671 1741 7.437862 CAGGAAATTAGAGAAGAGGAGATTTCG 59.562 40.741 0.00 0.00 34.51 3.46
1672 1742 7.226523 GCAGGAAATTAGAGAAGAGGAGATTTC 59.773 40.741 0.00 0.00 33.51 2.17
1673 1743 7.053498 GCAGGAAATTAGAGAAGAGGAGATTT 58.947 38.462 0.00 0.00 0.00 2.17
1674 1744 6.157645 TGCAGGAAATTAGAGAAGAGGAGATT 59.842 38.462 0.00 0.00 0.00 2.40
1675 1745 5.664908 TGCAGGAAATTAGAGAAGAGGAGAT 59.335 40.000 0.00 0.00 0.00 2.75
1676 1746 5.026121 TGCAGGAAATTAGAGAAGAGGAGA 58.974 41.667 0.00 0.00 0.00 3.71
1677 1747 5.350504 TGCAGGAAATTAGAGAAGAGGAG 57.649 43.478 0.00 0.00 0.00 3.69
1678 1748 5.013079 TGTTGCAGGAAATTAGAGAAGAGGA 59.987 40.000 0.00 0.00 0.00 3.71
1679 1749 5.248640 TGTTGCAGGAAATTAGAGAAGAGG 58.751 41.667 0.00 0.00 0.00 3.69
1682 1752 7.540055 GTGAATTGTTGCAGGAAATTAGAGAAG 59.460 37.037 4.02 0.00 0.00 2.85
1707 1777 9.278978 AGGTTTTCAACAAAAATTGTAACAAGT 57.721 25.926 0.00 0.00 44.59 3.16
1708 1778 9.753669 GAGGTTTTCAACAAAAATTGTAACAAG 57.246 29.630 0.00 0.00 44.59 3.16
1709 1779 8.722394 GGAGGTTTTCAACAAAAATTGTAACAA 58.278 29.630 0.00 0.00 44.59 2.83
1710 1780 8.097662 AGGAGGTTTTCAACAAAAATTGTAACA 58.902 29.630 0.00 0.00 44.59 2.41
1711 1781 8.487313 AGGAGGTTTTCAACAAAAATTGTAAC 57.513 30.769 0.00 0.00 44.59 2.50
1712 1782 8.536175 AGAGGAGGTTTTCAACAAAAATTGTAA 58.464 29.630 0.00 0.00 44.59 2.41
1713 1783 8.073467 AGAGGAGGTTTTCAACAAAAATTGTA 57.927 30.769 0.00 0.00 44.59 2.41
1715 1785 7.765819 AGAAGAGGAGGTTTTCAACAAAAATTG 59.234 33.333 0.00 0.00 39.01 2.32
1716 1786 7.851228 AGAAGAGGAGGTTTTCAACAAAAATT 58.149 30.769 0.00 0.00 39.01 1.82
1717 1787 7.343057 AGAGAAGAGGAGGTTTTCAACAAAAAT 59.657 33.333 0.00 0.00 39.01 1.82
1718 1788 6.663523 AGAGAAGAGGAGGTTTTCAACAAAAA 59.336 34.615 0.00 0.00 33.17 1.94
1732 1802 9.712305 TTGTTACAGAAAATTAGAGAAGAGGAG 57.288 33.333 0.00 0.00 0.00 3.69
1818 1888 5.368523 CCCAGTAGTCATATCCCCTACAAAA 59.631 44.000 0.00 0.00 34.78 2.44
1819 1889 4.905456 CCCAGTAGTCATATCCCCTACAAA 59.095 45.833 0.00 0.00 34.78 2.83
1824 1894 4.360140 TCATACCCAGTAGTCATATCCCCT 59.640 45.833 0.00 0.00 0.00 4.79
1878 1948 2.813754 GGCATCTTCATTATAAGCCGCA 59.186 45.455 0.00 0.00 0.00 5.69
1888 1959 8.945195 TTCATATATTCTTGGGCATCTTCATT 57.055 30.769 0.00 0.00 0.00 2.57
1896 1967 5.012239 GCCATCTTCATATATTCTTGGGCA 58.988 41.667 0.00 0.00 36.57 5.36
1948 2019 2.426024 CTCAAATCGTCTCCGGGTCTTA 59.574 50.000 0.00 0.00 33.95 2.10
1958 2029 1.079127 CGTGGGCCTCAAATCGTCT 60.079 57.895 4.53 0.00 0.00 4.18
2140 2215 4.142227 GGAATACGCTTGACCTAGTTCTCA 60.142 45.833 0.00 0.00 0.00 3.27
2163 2238 1.557832 TGGTTTCGATTACCAGGGAGG 59.442 52.381 14.10 0.00 40.65 4.30
2183 2258 5.391312 CCTGCTTTAGGTTGTATTGCTTT 57.609 39.130 0.00 0.00 42.00 3.51
2234 2309 7.016268 AGGACACAAAGAGTTTACCTAGATTCA 59.984 37.037 0.00 0.00 0.00 2.57
2241 2316 5.506708 ACAAAGGACACAAAGAGTTTACCT 58.493 37.500 0.00 0.00 0.00 3.08
2295 2372 2.526432 ACTTAGGTGTGGAGTCATCGT 58.474 47.619 0.00 0.00 0.00 3.73
2362 2440 1.170919 ATGCGAAGGCCTCATGATGC 61.171 55.000 5.23 13.99 38.85 3.91
2365 2443 1.123077 ACTATGCGAAGGCCTCATGA 58.877 50.000 5.23 0.00 38.85 3.07
2370 2448 0.328258 AAACCACTATGCGAAGGCCT 59.672 50.000 0.00 0.00 38.85 5.19
2375 2453 4.385825 AGAACTTGAAACCACTATGCGAA 58.614 39.130 0.00 0.00 0.00 4.70
2376 2454 4.002906 AGAACTTGAAACCACTATGCGA 57.997 40.909 0.00 0.00 0.00 5.10
2404 2482 2.507471 CCCTTGATCCCTAAGAAGCTGT 59.493 50.000 0.00 0.00 0.00 4.40
2459 2537 0.179137 CGTCGATGTAGAGCTTGCCA 60.179 55.000 0.00 0.00 0.00 4.92


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

AutoCloner maintained by Alex Coulton.