Multiple sequence alignment - TraesCS1A01G380800

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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 TraesCS1A01G380800 chr1A 100.000 2570 0 0 1 2570 551814208 551811639 0.000000e+00 4747.0
1 TraesCS1A01G380800 chr1A 95.405 914 38 3 1 912 196412022 196411111 0.000000e+00 1452.0
2 TraesCS1A01G380800 chr1A 94.627 912 49 0 1 912 198199728 198200639 0.000000e+00 1413.0
3 TraesCS1A01G380800 chr5A 96.378 911 33 0 1 911 40881113 40880203 0.000000e+00 1500.0
4 TraesCS1A01G380800 chr5A 95.943 912 36 1 1 912 40908117 40907207 0.000000e+00 1478.0
5 TraesCS1A01G380800 chr5A 94.767 172 9 0 1631 1802 519947334 519947505 4.220000e-68 268.0
6 TraesCS1A01G380800 chr5A 85.714 91 11 2 2119 2207 707645484 707645574 7.570000e-16 95.3
7 TraesCS1A01G380800 chr6A 96.048 911 36 0 1 911 273158746 273159656 0.000000e+00 1483.0
8 TraesCS1A01G380800 chr6A 95.499 911 40 1 1 911 19128844 19127935 0.000000e+00 1454.0
9 TraesCS1A01G380800 chr6A 95.170 911 44 0 1 911 303420102 303419192 0.000000e+00 1439.0
10 TraesCS1A01G380800 chr6A 94.835 910 46 1 1 910 303432097 303431189 0.000000e+00 1419.0
11 TraesCS1A01G380800 chr4A 94.731 911 48 0 1 911 275324949 275325859 0.000000e+00 1417.0
12 TraesCS1A01G380800 chr1D 95.284 721 34 0 914 1634 460655856 460655136 0.000000e+00 1144.0
13 TraesCS1A01G380800 chr1D 93.208 795 25 6 1796 2570 460655137 460654352 0.000000e+00 1142.0
14 TraesCS1A01G380800 chr1D 96.364 165 6 0 1633 1797 356185937 356185773 3.260000e-69 272.0
15 TraesCS1A01G380800 chr2B 83.516 637 92 8 944 1569 749238556 749237922 1.330000e-162 582.0
16 TraesCS1A01G380800 chr2D 83.203 637 94 9 944 1569 614853915 614853281 2.870000e-159 571.0
17 TraesCS1A01G380800 chr2D 94.286 175 8 2 1632 1806 593801761 593801589 1.520000e-67 267.0
18 TraesCS1A01G380800 chr2D 89.231 65 7 0 2424 2488 614866884 614866820 5.890000e-12 82.4
19 TraesCS1A01G380800 chrUn 95.129 349 15 2 1796 2144 8040493 8040147 1.340000e-152 549.0
20 TraesCS1A01G380800 chrUn 95.129 349 15 2 1796 2144 8043366 8043020 1.340000e-152 549.0
21 TraesCS1A01G380800 chrUn 95.129 349 15 2 1796 2144 400811002 400811348 1.340000e-152 549.0
22 TraesCS1A01G380800 chrUn 95.847 313 13 0 1322 1634 8043677 8043365 8.210000e-140 507.0
23 TraesCS1A01G380800 chrUn 95.847 313 13 0 1322 1634 408486675 408486987 8.210000e-140 507.0
24 TraesCS1A01G380800 chrUn 95.527 313 14 0 1322 1634 8040804 8040492 3.820000e-138 501.0
25 TraesCS1A01G380800 chrUn 95.527 313 14 0 1322 1634 451344993 451344681 3.820000e-138 501.0
26 TraesCS1A01G380800 chrUn 93.596 203 13 0 912 1114 8041004 8040802 1.160000e-78 303.0
27 TraesCS1A01G380800 chrUn 93.596 203 13 0 912 1114 8043877 8043675 1.160000e-78 303.0
28 TraesCS1A01G380800 chrUn 93.103 203 14 0 912 1114 451345193 451344991 5.380000e-77 298.0
29 TraesCS1A01G380800 chrUn 93.750 176 11 0 1625 1800 382102453 382102278 5.450000e-67 265.0
30 TraesCS1A01G380800 chr1B 95.129 349 15 2 1796 2144 632893643 632893297 1.340000e-152 549.0
31 TraesCS1A01G380800 chr1B 95.129 349 15 2 1796 2144 632896517 632896171 1.340000e-152 549.0
32 TraesCS1A01G380800 chr1B 95.129 349 15 2 1796 2144 632903377 632903031 1.340000e-152 549.0
33 TraesCS1A01G380800 chr1B 95.129 349 15 2 1796 2144 632906251 632905905 1.340000e-152 549.0
34 TraesCS1A01G380800 chr1B 94.842 349 16 2 1796 2144 632909125 632908779 6.250000e-151 544.0
35 TraesCS1A01G380800 chr1B 95.527 313 14 0 1322 1634 632893954 632893642 3.820000e-138 501.0
36 TraesCS1A01G380800 chr1B 95.527 313 14 0 1322 1634 632896828 632896516 3.820000e-138 501.0
37 TraesCS1A01G380800 chr1B 95.527 313 14 0 1322 1634 632903688 632903376 3.820000e-138 501.0
38 TraesCS1A01G380800 chr1B 95.527 313 14 0 1322 1634 632906562 632906250 3.820000e-138 501.0
39 TraesCS1A01G380800 chr1B 93.596 203 13 0 912 1114 632912510 632912308 1.160000e-78 303.0
40 TraesCS1A01G380800 chr1B 93.103 203 14 0 912 1114 632894154 632893952 5.380000e-77 298.0
41 TraesCS1A01G380800 chr1B 93.103 203 14 0 912 1114 632897028 632896826 5.380000e-77 298.0
42 TraesCS1A01G380800 chr1B 93.103 203 14 0 912 1114 632903888 632903686 5.380000e-77 298.0
43 TraesCS1A01G380800 chr1B 93.103 203 14 0 912 1114 632906762 632906560 5.380000e-77 298.0
44 TraesCS1A01G380800 chr6D 94.767 172 9 0 1631 1802 409753424 409753253 4.220000e-68 268.0
45 TraesCS1A01G380800 chr6D 94.286 175 9 1 1633 1807 104041326 104041153 1.520000e-67 267.0
46 TraesCS1A01G380800 chr5D 94.737 171 9 0 1633 1803 42949724 42949554 1.520000e-67 267.0
47 TraesCS1A01G380800 chr3D 95.238 168 8 0 1630 1797 145972542 145972709 1.520000e-67 267.0
48 TraesCS1A01G380800 chr7B 93.820 178 8 3 1633 1810 563739850 563740024 5.450000e-67 265.0
49 TraesCS1A01G380800 chr4B 76.359 368 54 19 1042 1383 673170763 673170403 1.580000e-37 167.0
50 TraesCS1A01G380800 chr4B 81.977 172 17 8 2296 2467 673169758 673169601 1.600000e-27 134.0


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 TraesCS1A01G380800 chr1A 551811639 551814208 2569 True 4747.000000 4747 100.000000 1 2570 1 chr1A.!!$R2 2569
1 TraesCS1A01G380800 chr1A 196411111 196412022 911 True 1452.000000 1452 95.405000 1 912 1 chr1A.!!$R1 911
2 TraesCS1A01G380800 chr1A 198199728 198200639 911 False 1413.000000 1413 94.627000 1 912 1 chr1A.!!$F1 911
3 TraesCS1A01G380800 chr5A 40880203 40881113 910 True 1500.000000 1500 96.378000 1 911 1 chr5A.!!$R1 910
4 TraesCS1A01G380800 chr5A 40907207 40908117 910 True 1478.000000 1478 95.943000 1 912 1 chr5A.!!$R2 911
5 TraesCS1A01G380800 chr6A 273158746 273159656 910 False 1483.000000 1483 96.048000 1 911 1 chr6A.!!$F1 910
6 TraesCS1A01G380800 chr6A 19127935 19128844 909 True 1454.000000 1454 95.499000 1 911 1 chr6A.!!$R1 910
7 TraesCS1A01G380800 chr6A 303419192 303420102 910 True 1439.000000 1439 95.170000 1 911 1 chr6A.!!$R2 910
8 TraesCS1A01G380800 chr6A 303431189 303432097 908 True 1419.000000 1419 94.835000 1 910 1 chr6A.!!$R3 909
9 TraesCS1A01G380800 chr4A 275324949 275325859 910 False 1417.000000 1417 94.731000 1 911 1 chr4A.!!$F1 910
10 TraesCS1A01G380800 chr1D 460654352 460655856 1504 True 1143.000000 1144 94.246000 914 2570 2 chr1D.!!$R2 1656
11 TraesCS1A01G380800 chr2B 749237922 749238556 634 True 582.000000 582 83.516000 944 1569 1 chr2B.!!$R1 625
12 TraesCS1A01G380800 chr2D 614853281 614853915 634 True 571.000000 571 83.203000 944 1569 1 chr2D.!!$R2 625
13 TraesCS1A01G380800 chrUn 8040147 8043877 3730 True 452.000000 549 94.804000 912 2144 6 chrUn.!!$R2 1232
14 TraesCS1A01G380800 chrUn 451344681 451345193 512 True 399.500000 501 94.315000 912 1634 2 chrUn.!!$R3 722
15 TraesCS1A01G380800 chr1B 632893297 632897028 3731 True 449.333333 549 94.586333 912 2144 6 chr1B.!!$R1 1232
16 TraesCS1A01G380800 chr1B 632903031 632912510 9479 True 442.875000 549 94.494500 912 2144 8 chr1B.!!$R2 1232

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
342 343 0.179018 GCGAAGGGATACATGGGCTT 60.179 55.0 0.0 0.0 39.74 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1938 16156 0.104671 AACAAAGTGGCCACATGCAC 59.895 50.0 36.39 9.89 43.89 4.57 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
164 165 7.743857 CTCCAAAAGGAGGTCTTGAATCCAAG 61.744 46.154 3.58 0.00 40.20 3.61
227 228 0.534873 TCCGATGTGGATGAGCGAAA 59.465 50.000 0.00 0.00 43.74 3.46
257 258 7.476540 TCTCTAAGTATGAGCTAAACCAACA 57.523 36.000 0.00 0.00 0.00 3.33
313 314 1.684734 GTCTAGGGCCACGAAGGGA 60.685 63.158 6.18 0.00 38.09 4.20
342 343 0.179018 GCGAAGGGATACATGGGCTT 60.179 55.000 0.00 0.00 39.74 4.35
367 368 2.610433 CGATACACTGTGCACAGACAT 58.390 47.619 44.82 32.73 46.59 3.06
441 442 4.950744 CGGTACTTGTCGGACGTT 57.049 55.556 3.34 0.00 0.00 3.99
608 609 2.203182 TCCGGTGGGTCTTCAGGT 59.797 61.111 0.00 0.00 33.83 4.00
611 612 1.450211 CGGTGGGTCTTCAGGTGTT 59.550 57.895 0.00 0.00 0.00 3.32
679 682 1.822371 AGCTCTTCTTCTCGTTCCTCC 59.178 52.381 0.00 0.00 0.00 4.30
743 746 1.134310 TCCTGGTCATGCATAGCACAG 60.134 52.381 0.00 5.91 43.04 3.66
752 755 4.701171 TCATGCATAGCACAGATGTTTGAA 59.299 37.500 0.00 0.00 43.04 2.69
920 923 2.168313 TGCTCCGCATCATTACTCTCAA 59.832 45.455 0.00 0.00 31.71 3.02
930 933 6.202570 GCATCATTACTCTCAATGAAGAGACC 59.797 42.308 13.80 0.00 45.46 3.85
942 945 1.482593 GAAGAGACCATGGATGACCGT 59.517 52.381 21.47 0.00 39.42 4.83
1035 1038 1.079405 GACCTTTCATGTCGCCGGA 60.079 57.895 5.05 0.00 0.00 5.14
1037 1040 2.452813 CCTTTCATGTCGCCGGACG 61.453 63.158 5.05 9.12 46.49 4.79
1131 4008 4.388499 GAGAAAGCCGGCGGTCCA 62.388 66.667 28.82 0.00 0.00 4.02
1315 4201 3.739209 CGAGAGGCTGAAACTGATATGCA 60.739 47.826 0.00 0.00 0.00 3.96
1345 4231 2.011741 ATGCAGCCACATTGATGCCG 62.012 55.000 0.00 0.00 37.89 5.69
1453 10087 1.462616 CAATTTGGAGGCGGTGATGA 58.537 50.000 0.00 0.00 0.00 2.92
1500 10134 1.609239 CAGTTGCCCATCTGCCCTA 59.391 57.895 0.00 0.00 0.00 3.53
1629 13137 6.208988 TCTATGCACGTCTCAGATTAGTTT 57.791 37.500 0.00 0.00 0.00 2.66
1634 13142 5.862323 TGCACGTCTCAGATTAGTTTTCTAC 59.138 40.000 0.00 0.00 31.46 2.59
1635 13143 6.094061 GCACGTCTCAGATTAGTTTTCTACT 58.906 40.000 0.00 0.00 41.04 2.57
1636 13144 6.251801 GCACGTCTCAGATTAGTTTTCTACTC 59.748 42.308 0.00 0.00 38.33 2.59
1637 13145 6.748198 CACGTCTCAGATTAGTTTTCTACTCC 59.252 42.308 0.00 0.00 38.33 3.85
1638 13146 6.127675 ACGTCTCAGATTAGTTTTCTACTCCC 60.128 42.308 0.00 0.00 38.33 4.30
1639 13147 6.095720 CGTCTCAGATTAGTTTTCTACTCCCT 59.904 42.308 0.00 0.00 38.33 4.20
1640 13148 7.485810 GTCTCAGATTAGTTTTCTACTCCCTC 58.514 42.308 0.00 0.00 38.33 4.30
1641 13149 6.608002 TCTCAGATTAGTTTTCTACTCCCTCC 59.392 42.308 0.00 0.00 38.33 4.30
1642 13150 5.360144 TCAGATTAGTTTTCTACTCCCTCCG 59.640 44.000 0.00 0.00 38.33 4.63
1643 13151 5.127356 CAGATTAGTTTTCTACTCCCTCCGT 59.873 44.000 0.00 0.00 38.33 4.69
1644 13152 5.720520 AGATTAGTTTTCTACTCCCTCCGTT 59.279 40.000 0.00 0.00 38.33 4.44
1645 13153 5.813513 TTAGTTTTCTACTCCCTCCGTTT 57.186 39.130 0.00 0.00 38.33 3.60
1646 13154 4.268797 AGTTTTCTACTCCCTCCGTTTC 57.731 45.455 0.00 0.00 28.23 2.78
1647 13155 3.007723 AGTTTTCTACTCCCTCCGTTTCC 59.992 47.826 0.00 0.00 28.23 3.13
1648 13156 2.314071 TTCTACTCCCTCCGTTTCCA 57.686 50.000 0.00 0.00 0.00 3.53
1649 13157 2.314071 TCTACTCCCTCCGTTTCCAA 57.686 50.000 0.00 0.00 0.00 3.53
1650 13158 2.612000 TCTACTCCCTCCGTTTCCAAA 58.388 47.619 0.00 0.00 0.00 3.28
1651 13159 3.178865 TCTACTCCCTCCGTTTCCAAAT 58.821 45.455 0.00 0.00 0.00 2.32
1652 13160 4.355549 TCTACTCCCTCCGTTTCCAAATA 58.644 43.478 0.00 0.00 0.00 1.40
1653 13161 4.966805 TCTACTCCCTCCGTTTCCAAATAT 59.033 41.667 0.00 0.00 0.00 1.28
1654 13162 6.138263 TCTACTCCCTCCGTTTCCAAATATA 58.862 40.000 0.00 0.00 0.00 0.86
1655 13163 5.703730 ACTCCCTCCGTTTCCAAATATAA 57.296 39.130 0.00 0.00 0.00 0.98
1656 13164 5.681639 ACTCCCTCCGTTTCCAAATATAAG 58.318 41.667 0.00 0.00 0.00 1.73
1657 13165 5.191124 ACTCCCTCCGTTTCCAAATATAAGT 59.809 40.000 0.00 0.00 0.00 2.24
1659 13167 5.427481 TCCCTCCGTTTCCAAATATAAGTCT 59.573 40.000 0.00 0.00 0.00 3.24
1660 13168 6.069847 TCCCTCCGTTTCCAAATATAAGTCTT 60.070 38.462 0.00 0.00 0.00 3.01
1661 13169 6.602009 CCCTCCGTTTCCAAATATAAGTCTTT 59.398 38.462 0.00 0.00 0.00 2.52
1662 13170 7.201705 CCCTCCGTTTCCAAATATAAGTCTTTC 60.202 40.741 0.00 0.00 0.00 2.62
1663 13171 7.553044 CCTCCGTTTCCAAATATAAGTCTTTCT 59.447 37.037 0.00 0.00 0.00 2.52
1665 13173 9.595823 TCCGTTTCCAAATATAAGTCTTTCTAG 57.404 33.333 0.00 0.00 0.00 2.43
1680 13188 8.600449 AGTCTTTCTAGAGATTTCAACAAGTG 57.400 34.615 0.00 0.00 0.00 3.16
1681 13189 8.424918 AGTCTTTCTAGAGATTTCAACAAGTGA 58.575 33.333 0.00 0.00 0.00 3.41
1685 13329 9.477484 TTTCTAGAGATTTCAACAAGTGACTAC 57.523 33.333 0.00 0.00 35.39 2.73
1689 13333 8.764524 AGAGATTTCAACAAGTGACTACATAC 57.235 34.615 0.00 0.00 35.39 2.39
1690 13334 7.542477 AGAGATTTCAACAAGTGACTACATACG 59.458 37.037 0.00 0.00 35.39 3.06
1696 13340 8.136800 TTCAACAAGTGACTACATACGAAGTAA 58.863 33.333 0.00 0.00 41.03 2.24
1713 13357 8.240883 ACGAAGTAAAATGAGTGAATCTACAC 57.759 34.615 0.00 0.00 41.94 2.90
1751 13395 4.720090 CATACATCCGTATGTCGTAGTCC 58.280 47.826 0.00 0.00 46.70 3.85
1752 13396 2.646930 ACATCCGTATGTCGTAGTCCA 58.353 47.619 0.00 0.00 42.92 4.02
1753 13397 3.220110 ACATCCGTATGTCGTAGTCCAT 58.780 45.455 0.00 0.00 42.92 3.41
1761 14738 7.223193 TCCGTATGTCGTAGTCCATTTAAAATG 59.777 37.037 0.00 0.00 37.94 2.32
1763 14740 5.554822 TGTCGTAGTCCATTTAAAATGCC 57.445 39.130 0.00 0.00 0.00 4.40
1766 14743 6.879993 TGTCGTAGTCCATTTAAAATGCCTAA 59.120 34.615 0.00 0.00 0.00 2.69
1768 14745 8.238631 GTCGTAGTCCATTTAAAATGCCTAAAA 58.761 33.333 0.00 0.00 0.00 1.52
1769 14746 8.794553 TCGTAGTCCATTTAAAATGCCTAAAAA 58.205 29.630 0.00 0.00 0.00 1.94
1770 14747 9.072294 CGTAGTCCATTTAAAATGCCTAAAAAG 57.928 33.333 0.00 0.00 0.00 2.27
1791 14768 8.959705 AAAAGACTTATATTTAGGAACGGAGG 57.040 34.615 0.00 0.00 0.00 4.30
1793 14770 6.379579 AGACTTATATTTAGGAACGGAGGGA 58.620 40.000 0.00 0.00 0.00 4.20
1794 14771 6.494146 AGACTTATATTTAGGAACGGAGGGAG 59.506 42.308 0.00 0.00 0.00 4.30
1798 16016 9.471702 CTTATATTTAGGAACGGAGGGAGTATA 57.528 37.037 0.00 0.00 0.00 1.47
1821 16039 1.423541 TGGTTGGATGTGTGCCTTAGT 59.576 47.619 0.00 0.00 0.00 2.24
1826 16044 4.471904 TGGATGTGTGCCTTAGTAGAAG 57.528 45.455 0.00 0.00 0.00 2.85
1829 16047 5.012664 TGGATGTGTGCCTTAGTAGAAGAAA 59.987 40.000 0.00 0.00 0.00 2.52
1830 16048 5.938125 GGATGTGTGCCTTAGTAGAAGAAAA 59.062 40.000 0.00 0.00 0.00 2.29
1831 16049 6.430000 GGATGTGTGCCTTAGTAGAAGAAAAA 59.570 38.462 0.00 0.00 0.00 1.94
1883 16101 3.562973 ACTCTGCAGTTTCATGTTCTGTG 59.437 43.478 14.67 8.56 0.00 3.66
1885 16103 1.002576 TGCAGTTTCATGTTCTGTGCG 60.003 47.619 12.90 0.00 31.99 5.34
1932 16150 8.328758 TCTCTTCTAGGGCTTAAATGAAATTGA 58.671 33.333 0.00 0.00 36.10 2.57
1933 16151 8.877864 TCTTCTAGGGCTTAAATGAAATTGAA 57.122 30.769 0.00 0.00 36.10 2.69
1938 16156 3.303229 GGCTTAAATGAAATTGAACGCCG 59.697 43.478 0.00 0.00 36.10 6.46
2099 16318 4.984161 CAGTTTTGTTATGTTCTGCAAGGG 59.016 41.667 0.00 0.00 0.00 3.95
2228 16447 3.084786 AGGTTTCAGCCTTTGTCTATGC 58.915 45.455 0.00 0.00 34.71 3.14
2229 16448 3.084786 GGTTTCAGCCTTTGTCTATGCT 58.915 45.455 0.00 0.00 33.52 3.79
2230 16449 6.780712 AAGGTTTCAGCCTTTGTCTATGCTG 61.781 44.000 4.05 4.05 45.91 4.41
2273 16492 5.404366 TCGTTGTAGAAGATAACAAGTGCAC 59.596 40.000 9.40 9.40 36.33 4.57
2276 16495 6.346477 TGTAGAAGATAACAAGTGCACTCT 57.654 37.500 21.95 12.03 0.00 3.24
2311 16549 3.127425 AGAGTAACTGTTTGTCCTGGC 57.873 47.619 0.00 0.00 0.00 4.85
2315 16553 1.692411 AACTGTTTGTCCTGGCTTCC 58.308 50.000 0.00 0.00 0.00 3.46
2343 16581 4.864704 AGAAGCGAAGATATCCCTCTTC 57.135 45.455 13.41 13.41 45.03 2.87
2358 16596 4.887655 TCCCTCTTCTGTTTTTGTTTCTCC 59.112 41.667 0.00 0.00 0.00 3.71
2467 16705 3.005684 TGGTTGATTGTGATTCCAAGCAC 59.994 43.478 0.62 0.62 45.04 4.40
2486 16724 6.787085 AGCACAGAGTTCTTGTGTTATTAC 57.213 37.500 7.16 0.00 36.09 1.89
2528 16766 4.521639 ACATACTGGAATGCATGCTATTGG 59.478 41.667 20.33 7.35 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
75 76 3.737266 TGTATCGTCCGTTGTTGACTTTC 59.263 43.478 0.00 0.00 0.00 2.62
164 165 1.044611 CCTCTTCGGAGAAGATCCCC 58.955 60.000 12.21 0.00 46.50 4.81
227 228 9.292195 GGTTTAGCTCATACTTAGAGATAGAGT 57.708 37.037 0.00 0.00 35.65 3.24
257 258 2.308866 CCTCCACCATTTGAGGGTTAGT 59.691 50.000 0.00 0.00 43.69 2.24
313 314 1.807814 ATCCCTTCGCCCTCACTTAT 58.192 50.000 0.00 0.00 0.00 1.73
342 343 2.267642 GCACAGTGTATCGGGCCA 59.732 61.111 4.39 0.00 0.00 5.36
441 442 4.612412 ACCGAGCCAAAACGCCGA 62.612 61.111 0.00 0.00 0.00 5.54
504 505 1.281960 CGGACGTTCGACACACTCT 59.718 57.895 11.86 0.00 0.00 3.24
743 746 6.109359 AGACATGGCTACTACTTCAAACATC 58.891 40.000 0.00 0.00 0.00 3.06
752 755 2.724454 ACGTGAGACATGGCTACTACT 58.276 47.619 0.00 0.00 0.00 2.57
920 923 2.103771 CGGTCATCCATGGTCTCTTCAT 59.896 50.000 12.58 0.00 0.00 2.57
930 933 3.307674 CACAACAAAACGGTCATCCATG 58.692 45.455 0.00 0.00 0.00 3.66
1031 1034 2.104331 CCGAGAACATCCGTCCGG 59.896 66.667 0.00 0.00 0.00 5.14
1035 1038 1.046472 TATGGGCCGAGAACATCCGT 61.046 55.000 0.00 0.00 0.00 4.69
1037 1040 0.035458 CCTATGGGCCGAGAACATCC 59.965 60.000 6.83 0.00 0.00 3.51
1101 1104 1.340405 GCTTTCTCCTTCATGGCTCCA 60.340 52.381 0.00 0.00 35.26 3.86
1156 4033 3.446873 TGGAGCAAACACTTGAACACATT 59.553 39.130 0.00 0.00 34.14 2.71
1315 4201 1.270550 GTGGCTGCATAACTTGTGCTT 59.729 47.619 11.33 0.00 42.92 3.91
1345 4231 4.760047 ACTGGTCGCCGCCATGTC 62.760 66.667 0.89 0.00 37.96 3.06
1447 10081 3.599343 TGTAGCCATCACTTGTCATCAC 58.401 45.455 0.00 0.00 0.00 3.06
1453 10087 2.566833 TGCTTGTAGCCATCACTTGT 57.433 45.000 0.00 0.00 41.51 3.16
1500 10134 3.615155 GAGCCTAGCAATCAACTCCTTT 58.385 45.455 0.00 0.00 0.00 3.11
1614 13122 6.095720 AGGGAGTAGAAAACTAATCTGAGACG 59.904 42.308 0.00 0.00 39.07 4.18
1629 13137 2.314071 TGGAAACGGAGGGAGTAGAA 57.686 50.000 0.00 0.00 0.00 2.10
1634 13142 5.681639 ACTTATATTTGGAAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
1635 13143 5.427481 AGACTTATATTTGGAAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
1636 13144 5.681639 AGACTTATATTTGGAAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
1637 13145 7.553044 AGAAAGACTTATATTTGGAAACGGAGG 59.447 37.037 0.00 0.00 0.00 4.30
1638 13146 8.494016 AGAAAGACTTATATTTGGAAACGGAG 57.506 34.615 0.00 0.00 0.00 4.63
1639 13147 9.595823 CTAGAAAGACTTATATTTGGAAACGGA 57.404 33.333 0.00 0.00 0.00 4.69
1640 13148 9.595823 TCTAGAAAGACTTATATTTGGAAACGG 57.404 33.333 0.00 0.00 0.00 4.44
1654 13162 9.050601 CACTTGTTGAAATCTCTAGAAAGACTT 57.949 33.333 0.00 0.00 0.00 3.01
1655 13163 8.424918 TCACTTGTTGAAATCTCTAGAAAGACT 58.575 33.333 0.00 0.00 0.00 3.24
1656 13164 8.491950 GTCACTTGTTGAAATCTCTAGAAAGAC 58.508 37.037 0.00 0.00 35.39 3.01
1657 13165 8.424918 AGTCACTTGTTGAAATCTCTAGAAAGA 58.575 33.333 0.00 0.00 35.39 2.52
1659 13167 9.477484 GTAGTCACTTGTTGAAATCTCTAGAAA 57.523 33.333 0.00 0.00 35.39 2.52
1660 13168 8.638873 TGTAGTCACTTGTTGAAATCTCTAGAA 58.361 33.333 0.00 0.00 35.39 2.10
1661 13169 8.178313 TGTAGTCACTTGTTGAAATCTCTAGA 57.822 34.615 0.00 0.00 35.39 2.43
1662 13170 8.994429 ATGTAGTCACTTGTTGAAATCTCTAG 57.006 34.615 0.00 0.00 35.39 2.43
1663 13171 9.856488 GTATGTAGTCACTTGTTGAAATCTCTA 57.144 33.333 0.00 0.00 35.39 2.43
1665 13173 7.541091 TCGTATGTAGTCACTTGTTGAAATCTC 59.459 37.037 0.00 0.00 35.39 2.75
1668 13176 7.656137 ACTTCGTATGTAGTCACTTGTTGAAAT 59.344 33.333 0.00 0.00 35.39 2.17
1669 13177 6.982141 ACTTCGTATGTAGTCACTTGTTGAAA 59.018 34.615 0.00 0.00 35.39 2.69
1670 13178 6.509656 ACTTCGTATGTAGTCACTTGTTGAA 58.490 36.000 0.00 0.00 35.39 2.69
1671 13179 6.080648 ACTTCGTATGTAGTCACTTGTTGA 57.919 37.500 0.00 0.00 0.00 3.18
1672 13180 7.862741 TTACTTCGTATGTAGTCACTTGTTG 57.137 36.000 0.00 0.00 0.00 3.33
1674 13182 8.922676 CATTTTACTTCGTATGTAGTCACTTGT 58.077 33.333 0.00 0.00 0.00 3.16
1676 13184 9.355215 CTCATTTTACTTCGTATGTAGTCACTT 57.645 33.333 0.00 0.00 0.00 3.16
1677 13185 8.521176 ACTCATTTTACTTCGTATGTAGTCACT 58.479 33.333 0.00 0.00 0.00 3.41
1678 13186 8.584600 CACTCATTTTACTTCGTATGTAGTCAC 58.415 37.037 0.00 0.00 0.00 3.67
1680 13188 8.906636 TCACTCATTTTACTTCGTATGTAGTC 57.093 34.615 0.00 0.00 0.00 2.59
1681 13189 9.871238 ATTCACTCATTTTACTTCGTATGTAGT 57.129 29.630 0.00 0.00 0.00 2.73
1688 13332 8.088981 AGTGTAGATTCACTCATTTTACTTCGT 58.911 33.333 0.00 0.00 44.07 3.85
1689 13333 8.467402 AGTGTAGATTCACTCATTTTACTTCG 57.533 34.615 0.00 0.00 44.07 3.79
1730 13374 4.392047 TGGACTACGACATACGGATGTAT 58.608 43.478 14.70 7.78 46.64 2.29
1738 13382 7.012044 AGGCATTTTAAATGGACTACGACATAC 59.988 37.037 17.89 0.00 0.00 2.39
1739 13383 7.051623 AGGCATTTTAAATGGACTACGACATA 58.948 34.615 17.89 0.00 0.00 2.29
1743 13387 7.925043 TTTAGGCATTTTAAATGGACTACGA 57.075 32.000 17.89 2.13 0.00 3.43
1744 13388 8.973835 TTTTTAGGCATTTTAAATGGACTACG 57.026 30.769 17.89 0.00 0.00 3.51
1748 13392 9.489084 AAGTCTTTTTAGGCATTTTAAATGGAC 57.511 29.630 17.89 13.22 0.00 4.02
1766 14743 7.991460 CCCTCCGTTCCTAAATATAAGTCTTTT 59.009 37.037 0.00 0.00 0.00 2.27
1768 14745 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
1769 14746 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
1770 14747 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
1771 14748 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
1776 14753 9.417561 CATATATACTCCCTCCGTTCCTAAATA 57.582 37.037 0.00 0.00 0.00 1.40
1781 14758 4.045590 ACCATATATACTCCCTCCGTTCCT 59.954 45.833 0.00 0.00 0.00 3.36
1783 14760 5.337330 CCAACCATATATACTCCCTCCGTTC 60.337 48.000 0.00 0.00 0.00 3.95
1784 14761 4.530946 CCAACCATATATACTCCCTCCGTT 59.469 45.833 0.00 0.00 0.00 4.44
1785 14762 4.094476 CCAACCATATATACTCCCTCCGT 58.906 47.826 0.00 0.00 0.00 4.69
1787 14764 5.726793 ACATCCAACCATATATACTCCCTCC 59.273 44.000 0.00 0.00 0.00 4.30
1788 14765 6.213600 ACACATCCAACCATATATACTCCCTC 59.786 42.308 0.00 0.00 0.00 4.30
1789 14766 6.013379 CACACATCCAACCATATATACTCCCT 60.013 42.308 0.00 0.00 0.00 4.20
1790 14767 6.173339 CACACATCCAACCATATATACTCCC 58.827 44.000 0.00 0.00 0.00 4.30
1791 14768 5.643777 GCACACATCCAACCATATATACTCC 59.356 44.000 0.00 0.00 0.00 3.85
1793 14770 5.310594 AGGCACACATCCAACCATATATACT 59.689 40.000 0.00 0.00 0.00 2.12
1794 14771 5.560724 AGGCACACATCCAACCATATATAC 58.439 41.667 0.00 0.00 0.00 1.47
1798 16016 3.386932 AAGGCACACATCCAACCATAT 57.613 42.857 0.00 0.00 0.00 1.78
1821 16039 9.574516 AGATAGCAGGTTTTTCTTTTTCTTCTA 57.425 29.630 0.00 0.00 0.00 2.10
1826 16044 9.914131 AACATAGATAGCAGGTTTTTCTTTTTC 57.086 29.630 0.00 0.00 0.00 2.29
1829 16047 8.860088 ACAAACATAGATAGCAGGTTTTTCTTT 58.140 29.630 0.00 0.00 29.89 2.52
1830 16048 8.409358 ACAAACATAGATAGCAGGTTTTTCTT 57.591 30.769 0.00 0.00 29.89 2.52
1831 16049 8.299570 CAACAAACATAGATAGCAGGTTTTTCT 58.700 33.333 0.00 0.00 29.89 2.52
1883 16101 3.687572 TTAGAGTTCGATACAGACCGC 57.312 47.619 0.00 0.00 0.00 5.68
1885 16103 7.708998 AGAGAAATTAGAGTTCGATACAGACC 58.291 38.462 0.00 0.00 0.00 3.85
1938 16156 0.104671 AACAAAGTGGCCACATGCAC 59.895 50.000 36.39 9.89 43.89 4.57
2053 16271 3.849527 ACCAAGCAGAAATCCCTCTTTT 58.150 40.909 0.00 0.00 0.00 2.27
2099 16318 8.443937 CAAAGTAAAACTCCACATAGAGTAAGC 58.556 37.037 0.00 0.00 46.44 3.09
2208 16427 3.084786 AGCATAGACAAAGGCTGAAACC 58.915 45.455 0.00 0.00 34.83 3.27
2226 16445 1.408702 GGCAGTCCAAAAGAAACAGCA 59.591 47.619 0.00 0.00 0.00 4.41
2227 16446 1.269778 GGGCAGTCCAAAAGAAACAGC 60.270 52.381 0.00 0.00 35.00 4.40
2228 16447 1.341209 GGGGCAGTCCAAAAGAAACAG 59.659 52.381 0.00 0.00 37.22 3.16
2229 16448 1.063266 AGGGGCAGTCCAAAAGAAACA 60.063 47.619 0.00 0.00 37.22 2.83
2230 16449 1.613925 GAGGGGCAGTCCAAAAGAAAC 59.386 52.381 0.00 0.00 37.22 2.78
2231 16450 1.817740 CGAGGGGCAGTCCAAAAGAAA 60.818 52.381 0.00 0.00 37.22 2.52
2232 16451 0.250727 CGAGGGGCAGTCCAAAAGAA 60.251 55.000 0.00 0.00 37.22 2.52
2287 16506 5.794894 CCAGGACAAACAGTTACTCTACAT 58.205 41.667 0.00 0.00 0.00 2.29
2315 16553 3.978217 GGATATCTTCGCTTCTTCAGTCG 59.022 47.826 2.05 0.00 0.00 4.18
2343 16581 9.377312 TGGAAATAAAAGGAGAAACAAAAACAG 57.623 29.630 0.00 0.00 0.00 3.16
2358 16596 7.651808 AGTCACACTGAACATGGAAATAAAAG 58.348 34.615 0.00 0.00 0.00 2.27
2467 16705 6.785488 TGCAGTAATAACACAAGAACTCTG 57.215 37.500 0.00 0.00 0.00 3.35
2486 16724 4.690184 TGTCTGAACAATATGCTTGCAG 57.310 40.909 0.87 0.00 30.70 4.41
2528 16766 4.252073 AGTGTTCATGCTCAGATTCAGTC 58.748 43.478 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.