Multiple sequence alignment - TraesCS3A01G050400

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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 TraesCS3A01G050400 chr3A 100.000 2328 0 0 1 2328 26580209 26577882 0.000000e+00 4300.0
1 TraesCS3A01G050400 chr3A 95.815 454 19 0 1730 2183 483243129 483242676 0.000000e+00 734.0
2 TraesCS3A01G050400 chr3A 83.099 71 12 0 73 143 588536730 588536660 5.370000e-07 65.8
3 TraesCS3A01G050400 chr3D 90.398 1635 124 17 2 1610 19064173 19062546 0.000000e+00 2119.0
4 TraesCS3A01G050400 chr3D 80.556 288 40 11 73 352 418210289 418210568 8.430000e-50 207.0
5 TraesCS3A01G050400 chr3B 85.595 1673 177 33 4 1652 30909359 30907727 0.000000e+00 1696.0
6 TraesCS3A01G050400 chr3B 87.838 74 9 0 70 143 805311362 805311435 1.150000e-13 87.9
7 TraesCS3A01G050400 chr5D 94.816 598 30 1 1731 2328 523670425 523669829 0.000000e+00 931.0
8 TraesCS3A01G050400 chr6A 96.264 455 17 0 1726 2180 512815813 512816267 0.000000e+00 747.0
9 TraesCS3A01G050400 chr6A 94.553 459 23 2 1726 2183 183267581 183267124 0.000000e+00 708.0
10 TraesCS3A01G050400 chr6A 98.204 167 3 0 2162 2328 512816279 512816445 2.260000e-75 292.0
11 TraesCS3A01G050400 chr6A 95.322 171 4 1 2162 2328 183267100 183266930 3.810000e-68 268.0
12 TraesCS3A01G050400 chr7A 94.748 457 22 2 1728 2183 603089452 603088997 0.000000e+00 710.0
13 TraesCS3A01G050400 chr7A 79.167 168 33 2 253 419 509555993 509555827 5.260000e-22 115.0
14 TraesCS3A01G050400 chr7A 90.909 55 5 0 165 219 33355119 33355065 8.920000e-10 75.0
15 TraesCS3A01G050400 chr7A 87.273 55 7 0 73 127 674119664 674119610 1.930000e-06 63.9
16 TraesCS3A01G050400 chr6B 93.856 472 24 5 1715 2183 662144165 662143696 0.000000e+00 706.0
17 TraesCS3A01G050400 chr6B 95.322 171 4 1 2162 2328 662143672 662143502 3.810000e-68 268.0
18 TraesCS3A01G050400 chr1B 94.678 451 22 2 1731 2180 549691345 549691794 0.000000e+00 699.0
19 TraesCS3A01G050400 chr1B 95.322 171 4 1 2162 2328 549691822 549691992 3.810000e-68 268.0
20 TraesCS3A01G050400 chr5B 91.451 386 31 2 1729 2113 586472725 586473109 1.580000e-146 529.0
21 TraesCS3A01G050400 chr5B 95.783 166 4 1 2163 2328 586481290 586481452 4.930000e-67 265.0
22 TraesCS3A01G050400 chr5B 77.003 287 60 6 165 448 564983601 564983884 2.390000e-35 159.0
23 TraesCS3A01G050400 chr5B 75.918 245 59 0 165 409 564983934 564984178 2.430000e-25 126.0
24 TraesCS3A01G050400 chr5B 75.486 257 63 0 165 421 635774157 635774413 2.430000e-25 126.0
25 TraesCS3A01G050400 chr5B 79.195 149 31 0 162 310 664373606 664373754 1.140000e-18 104.0
26 TraesCS3A01G050400 chr7B 92.013 313 24 1 2017 2328 165104293 165104605 2.750000e-119 438.0
27 TraesCS3A01G050400 chr7B 85.849 212 25 3 531 737 540063459 540063248 1.080000e-53 220.0
28 TraesCS3A01G050400 chr7B 74.912 283 70 1 167 449 4978321 4978602 6.750000e-26 128.0
29 TraesCS3A01G050400 chr7B 74.609 256 61 3 167 422 4976911 4977162 2.450000e-20 110.0
30 TraesCS3A01G050400 chr5A 92.013 313 24 1 2017 2328 553495401 553495089 2.750000e-119 438.0
31 TraesCS3A01G050400 chr4A 92.462 199 15 0 1733 1931 446625978 446626176 3.790000e-73 285.0
32 TraesCS3A01G050400 chr2B 82.985 335 26 11 1731 2036 779966264 779966596 8.200000e-70 274.0
33 TraesCS3A01G050400 chr2B 85.581 215 25 5 529 737 45729802 45729588 1.080000e-53 220.0
34 TraesCS3A01G050400 chr2B 85.185 216 23 8 531 737 24242055 24241840 1.810000e-51 213.0
35 TraesCS3A01G050400 chr7D 85.321 218 27 4 525 737 485106726 485106509 1.080000e-53 220.0
36 TraesCS3A01G050400 chr7D 85.377 212 26 4 531 737 199606876 199607087 5.040000e-52 215.0
37 TraesCS3A01G050400 chr2A 84.689 209 27 4 534 737 69311213 69311005 1.090000e-48 204.0
38 TraesCS3A01G050400 chr4B 84.186 215 27 7 527 737 541907424 541907213 3.920000e-48 202.0
39 TraesCS3A01G050400 chr6D 75.581 258 60 3 165 421 117168621 117168876 8.730000e-25 124.0
40 TraesCS3A01G050400 chr1A 85.135 74 11 0 70 143 51960951 51961024 2.480000e-10 76.8


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 TraesCS3A01G050400 chr3A 26577882 26580209 2327 True 4300.0 4300 100.0000 1 2328 1 chr3A.!!$R1 2327
1 TraesCS3A01G050400 chr3D 19062546 19064173 1627 True 2119.0 2119 90.3980 2 1610 1 chr3D.!!$R1 1608
2 TraesCS3A01G050400 chr3B 30907727 30909359 1632 True 1696.0 1696 85.5950 4 1652 1 chr3B.!!$R1 1648
3 TraesCS3A01G050400 chr5D 523669829 523670425 596 True 931.0 931 94.8160 1731 2328 1 chr5D.!!$R1 597
4 TraesCS3A01G050400 chr6A 512815813 512816445 632 False 519.5 747 97.2340 1726 2328 2 chr6A.!!$F1 602
5 TraesCS3A01G050400 chr6A 183266930 183267581 651 True 488.0 708 94.9375 1726 2328 2 chr6A.!!$R1 602
6 TraesCS3A01G050400 chr6B 662143502 662144165 663 True 487.0 706 94.5890 1715 2328 2 chr6B.!!$R1 613
7 TraesCS3A01G050400 chr1B 549691345 549691992 647 False 483.5 699 95.0000 1731 2328 2 chr1B.!!$F1 597

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
421 427 0.318441 ATAGGCATAGTCGCGCATGT 59.682 50.0 8.75 0.0 0.0 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1694 1732 0.108756 GGGAGGTGCGAAGAGTGTAC 60.109 60.0 0.0 0.0 0.0 2.9 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
18 19 1.807165 CGGGAGATGCTCACACACG 60.807 63.158 0.00 0.00 32.66 4.49
70 71 2.100031 GCACATGCGTGACCGATGA 61.100 57.895 14.17 0.00 46.80 2.92
93 99 3.990318 TGCACACTCTCATCGGTATAG 57.010 47.619 0.00 0.00 0.00 1.31
96 102 3.607310 GCACACTCTCATCGGTATAGTCG 60.607 52.174 0.00 0.00 0.00 4.18
127 133 1.131126 GCCGCGTAGTTACACACTCTA 59.869 52.381 4.92 0.00 36.88 2.43
128 134 2.778659 CCGCGTAGTTACACACTCTAC 58.221 52.381 4.92 0.00 36.88 2.59
130 136 3.484886 CCGCGTAGTTACACACTCTACTC 60.485 52.174 4.92 0.00 36.88 2.59
133 139 4.153835 GCGTAGTTACACACTCTACTCTGT 59.846 45.833 0.00 0.00 36.88 3.41
136 142 7.223582 GCGTAGTTACACACTCTACTCTGTATA 59.776 40.741 0.00 0.00 36.88 1.47
148 154 4.994220 ACTCTGTATAGTCGCATAGTCG 57.006 45.455 0.00 0.00 0.00 4.18
153 159 2.863401 ATAGTCGCATAGTCGCACAA 57.137 45.000 0.00 0.00 0.00 3.33
161 167 2.789092 GCATAGTCGCACAAGCACAATC 60.789 50.000 0.00 0.00 42.27 2.67
163 169 0.870393 AGTCGCACAAGCACAATCAG 59.130 50.000 0.00 0.00 42.27 2.90
173 179 0.524862 GCACAATCAGGGAGTTGCAG 59.475 55.000 0.00 0.00 0.00 4.41
215 221 0.968901 ATGCATGGCCACAGAGTTGG 60.969 55.000 8.16 0.00 39.98 3.77
219 225 4.065110 GGCCACAGAGTTGGACAC 57.935 61.111 0.00 0.00 45.27 3.67
229 235 1.794714 AGTTGGACACTCTCACCAGT 58.205 50.000 0.00 0.00 35.08 4.00
232 238 3.904339 AGTTGGACACTCTCACCAGTATT 59.096 43.478 0.00 0.00 35.08 1.89
238 244 1.135373 ACTCTCACCAGTATTGTCGCG 60.135 52.381 0.00 0.00 0.00 5.87
241 247 0.319986 TCACCAGTATTGTCGCGCAA 60.320 50.000 16.15 16.15 41.89 4.85
337 343 1.961277 GGGGTTGCACACTCTCGTG 60.961 63.158 0.00 0.00 46.63 4.35
362 368 3.952508 TCCCACATGCACGGCTGT 61.953 61.111 0.00 0.00 0.00 4.40
411 417 4.039004 AGTTGCAGACTCTCATAGGCATAG 59.961 45.833 0.00 0.00 34.57 2.23
416 422 1.537638 ACTCTCATAGGCATAGTCGCG 59.462 52.381 0.00 0.00 0.00 5.87
421 427 0.318441 ATAGGCATAGTCGCGCATGT 59.682 50.000 8.75 0.00 0.00 3.21
424 430 1.705337 GGCATAGTCGCGCATGTGTT 61.705 55.000 8.75 0.00 0.00 3.32
443 449 3.258123 TGTTATCACAGAGCTGCACACTA 59.742 43.478 1.02 0.00 0.00 2.74
446 452 1.135286 TCACAGAGCTGCACACTATCG 60.135 52.381 1.02 0.00 0.00 2.92
448 454 1.273606 ACAGAGCTGCACACTATCGTT 59.726 47.619 1.02 0.00 0.00 3.85
450 456 1.002366 GAGCTGCACACTATCGTTGG 58.998 55.000 1.02 0.00 0.00 3.77
451 457 0.321671 AGCTGCACACTATCGTTGGT 59.678 50.000 1.02 0.00 0.00 3.67
498 504 5.311265 TCTGAGATATTTGTCATGGGATGC 58.689 41.667 0.00 0.00 0.00 3.91
510 516 2.214376 TGGGATGCGATTGGTCTTTT 57.786 45.000 0.00 0.00 0.00 2.27
516 522 2.945278 TGCGATTGGTCTTTTCATTGC 58.055 42.857 0.00 0.00 0.00 3.56
525 531 4.022068 TGGTCTTTTCATTGCCTTTGCTAG 60.022 41.667 0.00 0.00 38.71 3.42
538 544 4.081031 GCCTTTGCTAGTAAGTACTCCCTT 60.081 45.833 0.00 0.00 37.73 3.95
713 725 6.204688 TGTGTAAGTTCAGATTGCTTTCGATT 59.795 34.615 0.00 0.00 0.00 3.34
773 797 6.459710 GCAAAATAAATAGAAACGGAGGGAGG 60.460 42.308 0.00 0.00 0.00 4.30
775 799 5.810080 ATAAATAGAAACGGAGGGAGGAG 57.190 43.478 0.00 0.00 0.00 3.69
776 800 3.399952 AATAGAAACGGAGGGAGGAGA 57.600 47.619 0.00 0.00 0.00 3.71
778 802 2.255770 AGAAACGGAGGGAGGAGAAT 57.744 50.000 0.00 0.00 0.00 2.40
781 805 1.952621 AACGGAGGGAGGAGAATGAA 58.047 50.000 0.00 0.00 0.00 2.57
782 806 1.490574 ACGGAGGGAGGAGAATGAAG 58.509 55.000 0.00 0.00 0.00 3.02
783 807 1.007238 ACGGAGGGAGGAGAATGAAGA 59.993 52.381 0.00 0.00 0.00 2.87
784 808 1.686052 CGGAGGGAGGAGAATGAAGAG 59.314 57.143 0.00 0.00 0.00 2.85
858 891 5.249393 AGCTTATCCAGTCTTCTTCTTTGGA 59.751 40.000 0.00 0.00 41.75 3.53
942 975 2.962421 TCATTTTCTTTCCCGGCAACTT 59.038 40.909 0.00 0.00 0.00 2.66
952 986 2.775384 TCCCGGCAACTTATACTCCAAT 59.225 45.455 0.00 0.00 0.00 3.16
957 991 6.231211 CCGGCAACTTATACTCCAATAATCT 58.769 40.000 0.00 0.00 0.00 2.40
1029 1063 1.388547 CTCTAGCGCTTCTCCTGACT 58.611 55.000 18.68 0.00 0.00 3.41
1131 1165 9.902196 AAATTATATATGTGCATGATGTGTGTG 57.098 29.630 0.00 0.00 0.00 3.82
1168 1202 4.010349 GCTATTTTGTAGGTGTGGAAGCT 58.990 43.478 0.00 0.00 40.55 3.74
1184 1218 3.932710 GGAAGCTGATTGTACGACATCAA 59.067 43.478 0.00 0.00 0.00 2.57
1282 1316 3.367932 GCGATCAATGTCGTCTTCAGAAA 59.632 43.478 0.00 0.00 43.27 2.52
1560 1598 3.119708 GCAATCTTGAACCCAGCAGTAAG 60.120 47.826 0.00 0.00 0.00 2.34
1606 1644 0.253160 ATTAGGGCTGAGTGGGGACA 60.253 55.000 0.00 0.00 38.70 4.02
1610 1648 0.983378 GGGCTGAGTGGGGACATAGT 60.983 60.000 0.00 0.00 46.14 2.12
1616 1654 2.035632 GAGTGGGGACATAGTGAGGAG 58.964 57.143 0.00 0.00 46.14 3.69
1635 1673 3.885901 GGAGCCCAGTCCATTTCTATTTC 59.114 47.826 0.00 0.00 36.51 2.17
1656 1694 7.852971 TTTCCCCATGTTTTAGTAGATAACG 57.147 36.000 0.00 0.00 0.00 3.18
1657 1695 5.920903 TCCCCATGTTTTAGTAGATAACGG 58.079 41.667 0.00 0.00 0.00 4.44
1658 1696 5.061179 CCCCATGTTTTAGTAGATAACGGG 58.939 45.833 0.00 0.00 0.00 5.28
1659 1697 4.514066 CCCATGTTTTAGTAGATAACGGGC 59.486 45.833 0.00 0.00 0.00 6.13
1660 1698 4.514066 CCATGTTTTAGTAGATAACGGGCC 59.486 45.833 0.00 0.00 0.00 5.80
1661 1699 4.141233 TGTTTTAGTAGATAACGGGCCC 57.859 45.455 13.57 13.57 0.00 5.80
1662 1700 3.118298 TGTTTTAGTAGATAACGGGCCCC 60.118 47.826 18.66 0.30 0.00 5.80
1663 1701 2.475339 TTAGTAGATAACGGGCCCCA 57.525 50.000 18.66 1.04 0.00 4.96
1664 1702 1.708341 TAGTAGATAACGGGCCCCAC 58.292 55.000 18.66 3.03 0.00 4.61
1665 1703 0.031414 AGTAGATAACGGGCCCCACT 60.031 55.000 18.66 10.90 0.00 4.00
1666 1704 0.391966 GTAGATAACGGGCCCCACTC 59.608 60.000 18.66 8.24 0.00 3.51
1667 1705 0.031917 TAGATAACGGGCCCCACTCA 60.032 55.000 18.66 0.00 0.00 3.41
1668 1706 1.153229 GATAACGGGCCCCACTCAC 60.153 63.158 18.66 0.00 0.00 3.51
1669 1707 1.906105 GATAACGGGCCCCACTCACA 61.906 60.000 18.66 0.00 0.00 3.58
1670 1708 1.279025 ATAACGGGCCCCACTCACAT 61.279 55.000 18.66 0.00 0.00 3.21
1671 1709 1.493854 TAACGGGCCCCACTCACATT 61.494 55.000 18.66 0.33 0.00 2.71
1672 1710 2.035626 CGGGCCCCACTCACATTT 59.964 61.111 18.66 0.00 0.00 2.32
1673 1711 1.606313 CGGGCCCCACTCACATTTT 60.606 57.895 18.66 0.00 0.00 1.82
1674 1712 1.876497 CGGGCCCCACTCACATTTTG 61.876 60.000 18.66 0.00 0.00 2.44
1675 1713 1.293179 GGCCCCACTCACATTTTGC 59.707 57.895 0.00 0.00 0.00 3.68
1676 1714 1.187567 GGCCCCACTCACATTTTGCT 61.188 55.000 0.00 0.00 0.00 3.91
1677 1715 0.244721 GCCCCACTCACATTTTGCTC 59.755 55.000 0.00 0.00 0.00 4.26
1678 1716 0.890683 CCCCACTCACATTTTGCTCC 59.109 55.000 0.00 0.00 0.00 4.70
1679 1717 0.890683 CCCACTCACATTTTGCTCCC 59.109 55.000 0.00 0.00 0.00 4.30
1680 1718 0.523072 CCACTCACATTTTGCTCCCG 59.477 55.000 0.00 0.00 0.00 5.14
1681 1719 1.522668 CACTCACATTTTGCTCCCGA 58.477 50.000 0.00 0.00 0.00 5.14
1682 1720 1.466167 CACTCACATTTTGCTCCCGAG 59.534 52.381 0.00 0.00 0.00 4.63
1692 1730 4.528674 CTCCCGAGCAGTCCAATG 57.471 61.111 0.00 0.00 0.00 2.82
1693 1731 1.817099 CTCCCGAGCAGTCCAATGC 60.817 63.158 0.00 0.00 46.88 3.56
1700 1738 2.840974 GCAGTCCAATGCGTACACT 58.159 52.632 0.00 0.00 36.28 3.55
1701 1739 0.721718 GCAGTCCAATGCGTACACTC 59.278 55.000 0.00 0.00 36.28 3.51
1702 1740 1.673033 GCAGTCCAATGCGTACACTCT 60.673 52.381 0.00 0.00 36.28 3.24
1703 1741 2.688507 CAGTCCAATGCGTACACTCTT 58.311 47.619 0.00 0.00 0.00 2.85
1704 1742 2.668457 CAGTCCAATGCGTACACTCTTC 59.332 50.000 0.00 0.00 0.00 2.87
1705 1743 1.654105 GTCCAATGCGTACACTCTTCG 59.346 52.381 0.00 0.00 0.00 3.79
1711 1749 3.017232 CGTACACTCTTCGCACCTC 57.983 57.895 0.00 0.00 0.00 3.85
1712 1750 0.456312 CGTACACTCTTCGCACCTCC 60.456 60.000 0.00 0.00 0.00 4.30
1713 1751 0.108756 GTACACTCTTCGCACCTCCC 60.109 60.000 0.00 0.00 0.00 4.30
1714 1752 0.541063 TACACTCTTCGCACCTCCCA 60.541 55.000 0.00 0.00 0.00 4.37
1715 1753 1.371183 CACTCTTCGCACCTCCCAA 59.629 57.895 0.00 0.00 0.00 4.12
1716 1754 0.951040 CACTCTTCGCACCTCCCAAC 60.951 60.000 0.00 0.00 0.00 3.77
1717 1755 1.738099 CTCTTCGCACCTCCCAACG 60.738 63.158 0.00 0.00 0.00 4.10
1718 1756 2.030562 CTTCGCACCTCCCAACGT 59.969 61.111 0.00 0.00 0.00 3.99
1719 1757 1.597027 CTTCGCACCTCCCAACGTT 60.597 57.895 0.00 0.00 0.00 3.99
1720 1758 1.153127 TTCGCACCTCCCAACGTTT 60.153 52.632 0.00 0.00 0.00 3.60
1721 1759 0.748729 TTCGCACCTCCCAACGTTTT 60.749 50.000 0.00 0.00 0.00 2.43
1722 1760 0.748729 TCGCACCTCCCAACGTTTTT 60.749 50.000 0.00 0.00 0.00 1.94
1745 1783 3.392285 TCCCATCACTAGTAAGCATGCAT 59.608 43.478 21.98 11.22 0.00 3.96
1864 1902 8.128582 CGCAAAAAGCATATAATTCCTAACTCA 58.871 33.333 0.00 0.00 46.13 3.41
2005 2044 2.254546 AGTGCATCTCGACAACCAAA 57.745 45.000 0.00 0.00 0.00 3.28
2030 2070 1.364626 GACCAACATCTCGCCAGCAG 61.365 60.000 0.00 0.00 0.00 4.24
2137 2177 9.787532 AATTGACATAATTCACCAGTTATTTCG 57.212 29.630 0.00 0.00 0.00 3.46
2267 2353 2.962089 GCCATTGCCAATAAGCACG 58.038 52.632 6.72 0.00 43.97 5.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 4.876701 ACAACCGTGTGTGAGCAT 57.123 50.000 0.00 0.00 36.31 3.79
14 15 1.078072 TGCAACTCCACAACCGTGT 60.078 52.632 0.00 0.00 41.93 4.49
18 19 2.793831 AGTGTGCAACTCCACAACC 58.206 52.632 7.79 0.00 46.28 3.77
41 42 2.397751 GCATGTGCGACTATGCCTT 58.602 52.632 6.86 0.00 42.88 4.35
70 71 0.681733 ACCGATGAGAGTGTGCAACT 59.318 50.000 0.00 0.00 43.85 3.16
118 124 4.571580 GCGACTATACAGAGTAGAGTGTGT 59.428 45.833 8.96 0.00 0.00 3.72
127 133 3.186817 GCGACTATGCGACTATACAGAGT 59.813 47.826 0.00 0.00 40.83 3.24
128 134 3.186613 TGCGACTATGCGACTATACAGAG 59.813 47.826 0.00 0.00 37.81 3.35
130 136 3.227147 GTGCGACTATGCGACTATACAG 58.773 50.000 0.00 0.00 37.81 2.74
133 139 3.852205 GCTTGTGCGACTATGCGACTATA 60.852 47.826 0.00 0.00 37.81 1.31
136 142 1.078759 GCTTGTGCGACTATGCGACT 61.079 55.000 0.00 0.00 37.81 4.18
148 154 0.524862 CTCCCTGATTGTGCTTGTGC 59.475 55.000 0.00 0.00 40.20 4.57
153 159 0.111061 TGCAACTCCCTGATTGTGCT 59.889 50.000 0.00 0.00 0.00 4.40
200 206 0.250901 GTGTCCAACTCTGTGGCCAT 60.251 55.000 9.72 0.00 38.68 4.40
215 221 3.502920 CGACAATACTGGTGAGAGTGTC 58.497 50.000 0.00 0.00 0.00 3.67
219 225 1.550065 CGCGACAATACTGGTGAGAG 58.450 55.000 0.00 0.00 0.00 3.20
241 247 3.319198 ATCTCCCGCACCCGTGTT 61.319 61.111 0.00 0.00 0.00 3.32
268 274 1.303561 GTCTGCAACTCCATGGCCA 60.304 57.895 8.56 8.56 0.00 5.36
293 299 1.153188 CGCATGTGGGACTATGCCA 60.153 57.895 0.00 0.00 43.09 4.92
317 323 3.050275 GAGAGTGTGCAACCCCGC 61.050 66.667 0.00 0.00 34.36 6.13
337 343 1.819208 TGCATGTGGGACTATGCGC 60.819 57.895 0.00 0.00 46.71 6.09
362 368 3.311110 GTCCGTGAGTGCCTCCCA 61.311 66.667 0.50 0.00 0.00 4.37
369 375 3.403057 CGCAACCGTCCGTGAGTG 61.403 66.667 0.00 0.00 0.00 3.51
370 376 4.657824 CCGCAACCGTCCGTGAGT 62.658 66.667 0.00 0.00 0.00 3.41
377 383 2.954753 CTGCAACTCCGCAACCGTC 61.955 63.158 0.00 0.00 42.45 4.79
411 417 3.491934 GTGATAACACATGCGCGAC 57.508 52.632 12.10 0.88 45.32 5.19
421 427 2.037641 AGTGTGCAGCTCTGTGATAACA 59.962 45.455 0.00 0.00 0.00 2.41
424 430 3.243201 CGATAGTGTGCAGCTCTGTGATA 60.243 47.826 0.00 0.00 0.00 2.15
498 504 3.855689 AGGCAATGAAAAGACCAATCG 57.144 42.857 0.00 0.00 0.00 3.34
510 516 6.049955 AGTACTTACTAGCAAAGGCAATGA 57.950 37.500 9.54 0.00 44.61 2.57
516 522 5.187186 TGAAGGGAGTACTTACTAGCAAAGG 59.813 44.000 0.00 0.00 36.50 3.11
554 560 9.625747 TTTGACCTGAGACATAATTAATATGCA 57.374 29.630 0.00 0.00 44.46 3.96
577 583 6.569780 ACTTTGCCTAAGTTTACAAGGTTTG 58.430 36.000 0.00 0.00 44.73 2.93
613 619 8.980481 ATTGACTTCGTATCCTGGATTTTAAT 57.020 30.769 15.55 2.89 0.00 1.40
617 623 6.126883 TGGTATTGACTTCGTATCCTGGATTT 60.127 38.462 15.55 0.00 0.00 2.17
692 704 8.547967 AGTTAATCGAAAGCAATCTGAACTTA 57.452 30.769 0.00 0.00 0.00 2.24
698 710 6.602179 TGACAAGTTAATCGAAAGCAATCTG 58.398 36.000 0.00 0.00 0.00 2.90
750 774 6.965607 TCCTCCCTCCGTTTCTATTTATTTT 58.034 36.000 0.00 0.00 0.00 1.82
753 777 5.464984 TCTCCTCCCTCCGTTTCTATTTAT 58.535 41.667 0.00 0.00 0.00 1.40
760 784 1.831736 TCATTCTCCTCCCTCCGTTTC 59.168 52.381 0.00 0.00 0.00 2.78
826 859 2.171448 AGACTGGATAAGCTTCGCCAAT 59.829 45.455 17.80 10.57 0.00 3.16
912 945 3.056536 GGGAAAGAAAATGAGAGGGCAAC 60.057 47.826 0.00 0.00 0.00 4.17
942 975 9.837681 TCACCCAAGATAGATTATTGGAGTATA 57.162 33.333 4.79 0.00 45.19 1.47
1029 1063 4.226427 TGCTAGTAAGAGGACGGTAAGA 57.774 45.455 0.00 0.00 0.00 2.10
1158 1192 2.412089 GTCGTACAATCAGCTTCCACAC 59.588 50.000 0.00 0.00 0.00 3.82
1168 1202 7.254286 CGGTTGATAATTGATGTCGTACAATCA 60.254 37.037 0.00 0.00 35.99 2.57
1184 1218 7.825270 TGTACACTTATTTGGACGGTTGATAAT 59.175 33.333 0.00 0.00 32.30 1.28
1258 1292 1.067213 TGAAGACGACATTGATCGCCA 60.067 47.619 0.00 1.58 46.22 5.69
1282 1316 2.143876 ACTTTCCAACACAACTGGCT 57.856 45.000 0.00 0.00 33.63 4.75
1517 1555 0.833287 AATCTGTCATGCCGCCTAGT 59.167 50.000 0.00 0.00 0.00 2.57
1519 1557 1.270305 GCTAATCTGTCATGCCGCCTA 60.270 52.381 0.00 0.00 0.00 3.93
1560 1598 7.627340 TGTGAGTTTGTCTTCGATACTTTTTC 58.373 34.615 0.00 0.00 0.00 2.29
1606 1644 0.339859 TGGACTGGGCTCCTCACTAT 59.660 55.000 0.00 0.00 0.00 2.12
1610 1648 0.620556 GAAATGGACTGGGCTCCTCA 59.379 55.000 0.00 0.00 0.00 3.86
1616 1654 2.959030 GGGAAATAGAAATGGACTGGGC 59.041 50.000 0.00 0.00 0.00 5.36
1635 1673 5.061179 CCCGTTATCTACTAAAACATGGGG 58.939 45.833 0.00 0.00 0.00 4.96
1652 1690 1.493854 AATGTGAGTGGGGCCCGTTA 61.494 55.000 19.83 0.88 0.00 3.18
1653 1691 2.366153 AAATGTGAGTGGGGCCCGTT 62.366 55.000 19.83 8.45 0.00 4.44
1654 1692 2.366153 AAAATGTGAGTGGGGCCCGT 62.366 55.000 19.83 7.69 0.00 5.28
1655 1693 1.606313 AAAATGTGAGTGGGGCCCG 60.606 57.895 19.83 0.00 0.00 6.13
1656 1694 1.974543 CAAAATGTGAGTGGGGCCC 59.025 57.895 18.17 18.17 0.00 5.80
1657 1695 1.187567 AGCAAAATGTGAGTGGGGCC 61.188 55.000 0.00 0.00 0.00 5.80
1658 1696 0.244721 GAGCAAAATGTGAGTGGGGC 59.755 55.000 0.00 0.00 0.00 5.80
1659 1697 0.890683 GGAGCAAAATGTGAGTGGGG 59.109 55.000 0.00 0.00 0.00 4.96
1660 1698 0.890683 GGGAGCAAAATGTGAGTGGG 59.109 55.000 0.00 0.00 0.00 4.61
1661 1699 0.523072 CGGGAGCAAAATGTGAGTGG 59.477 55.000 0.00 0.00 0.00 4.00
1662 1700 1.466167 CTCGGGAGCAAAATGTGAGTG 59.534 52.381 0.00 0.00 0.00 3.51
1663 1701 1.813513 CTCGGGAGCAAAATGTGAGT 58.186 50.000 0.00 0.00 0.00 3.41
1675 1713 1.817099 GCATTGGACTGCTCGGGAG 60.817 63.158 0.00 0.00 39.12 4.30
1676 1714 2.268920 GCATTGGACTGCTCGGGA 59.731 61.111 0.00 0.00 39.12 5.14
1677 1715 2.572095 TACGCATTGGACTGCTCGGG 62.572 60.000 0.00 0.00 40.06 5.14
1678 1716 1.153647 TACGCATTGGACTGCTCGG 60.154 57.895 0.00 0.00 40.06 4.63
1679 1717 0.735978 TGTACGCATTGGACTGCTCG 60.736 55.000 0.00 0.00 40.06 5.03
1680 1718 0.721718 GTGTACGCATTGGACTGCTC 59.278 55.000 0.39 0.00 40.06 4.26
1681 1719 0.321671 AGTGTACGCATTGGACTGCT 59.678 50.000 9.48 0.00 40.06 4.24
1682 1720 0.721718 GAGTGTACGCATTGGACTGC 59.278 55.000 9.48 0.00 38.81 4.40
1683 1721 2.370281 AGAGTGTACGCATTGGACTG 57.630 50.000 9.48 0.00 0.00 3.51
1684 1722 2.671351 CGAAGAGTGTACGCATTGGACT 60.671 50.000 9.48 0.00 0.00 3.85
1685 1723 1.654105 CGAAGAGTGTACGCATTGGAC 59.346 52.381 9.48 0.00 0.00 4.02
1686 1724 1.990799 CGAAGAGTGTACGCATTGGA 58.009 50.000 9.48 0.00 0.00 3.53
1693 1731 0.456312 GGAGGTGCGAAGAGTGTACG 60.456 60.000 0.00 0.00 0.00 3.67
1694 1732 0.108756 GGGAGGTGCGAAGAGTGTAC 60.109 60.000 0.00 0.00 0.00 2.90
1695 1733 0.541063 TGGGAGGTGCGAAGAGTGTA 60.541 55.000 0.00 0.00 0.00 2.90
1696 1734 1.407656 TTGGGAGGTGCGAAGAGTGT 61.408 55.000 0.00 0.00 0.00 3.55
1697 1735 0.951040 GTTGGGAGGTGCGAAGAGTG 60.951 60.000 0.00 0.00 0.00 3.51
1698 1736 1.371558 GTTGGGAGGTGCGAAGAGT 59.628 57.895 0.00 0.00 0.00 3.24
1699 1737 1.738099 CGTTGGGAGGTGCGAAGAG 60.738 63.158 0.00 0.00 0.00 2.85
1700 1738 2.035237 AACGTTGGGAGGTGCGAAGA 62.035 55.000 0.00 0.00 0.00 2.87
1701 1739 1.164041 AAACGTTGGGAGGTGCGAAG 61.164 55.000 0.00 0.00 0.00 3.79
1702 1740 0.748729 AAAACGTTGGGAGGTGCGAA 60.749 50.000 0.00 0.00 0.00 4.70
1703 1741 0.748729 AAAAACGTTGGGAGGTGCGA 60.749 50.000 0.00 0.00 0.00 5.10
1704 1742 1.731093 AAAAACGTTGGGAGGTGCG 59.269 52.632 0.00 0.00 0.00 5.34
1719 1757 5.125417 GCATGCTTACTAGTGATGGGAAAAA 59.875 40.000 11.37 0.00 0.00 1.94
1720 1758 4.640201 GCATGCTTACTAGTGATGGGAAAA 59.360 41.667 11.37 0.00 0.00 2.29
1721 1759 4.199310 GCATGCTTACTAGTGATGGGAAA 58.801 43.478 11.37 0.00 0.00 3.13
1722 1760 3.199727 TGCATGCTTACTAGTGATGGGAA 59.800 43.478 20.33 0.00 0.00 3.97
1723 1761 2.771372 TGCATGCTTACTAGTGATGGGA 59.229 45.455 20.33 0.00 0.00 4.37
1724 1762 3.198409 TGCATGCTTACTAGTGATGGG 57.802 47.619 20.33 0.00 0.00 4.00
1728 1766 2.938451 GCACATGCATGCTTACTAGTGA 59.062 45.455 26.53 0.00 42.62 3.41
1812 1850 6.088016 AGATTGCAGCTGTTCAAAATGTAA 57.912 33.333 16.64 0.00 0.00 2.41
1905 1943 1.105457 TGCTAAGCAATGGACATGGC 58.895 50.000 3.44 3.44 38.03 4.40
2005 2044 0.745845 GCGAGATGTTGGTCATGGCT 60.746 55.000 0.00 0.00 36.83 4.75
2030 2070 5.491070 TGAATATCTATATGGCACTGTGGC 58.509 41.667 25.55 25.55 44.03 5.01
2137 2177 6.228995 TGGATGCAATGATGACTCTAAGATC 58.771 40.000 0.00 0.00 0.00 2.75
2281 2367 1.139989 CCTCTGTACACACACTTGCG 58.860 55.000 0.00 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.