Multiple sequence alignment - TraesCS5A01G294900

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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 TraesCS5A01G294900 chr5A 100.000 3006 0 0 1 3006 503621871 503624876 0.000000e+00 5552.0
1 TraesCS5A01G294900 chr5A 86.532 297 32 4 102 396 503544693 503544983 1.340000e-83 320.0
2 TraesCS5A01G294900 chr5A 75.228 549 92 32 1161 1693 503233496 503234016 1.400000e-53 220.0
3 TraesCS5A01G294900 chr5A 86.928 153 18 2 1161 1312 503320288 503320439 1.430000e-38 171.0
4 TraesCS5A01G294900 chr5A 83.088 136 18 3 1165 1296 503493049 503493183 5.260000e-23 119.0
5 TraesCS5A01G294900 chr5A 80.208 96 10 6 2805 2892 585407102 585407008 2.500000e-06 63.9
6 TraesCS5A01G294900 chr5B 88.679 1590 109 34 166 1714 478513781 478515340 0.000000e+00 1873.0
7 TraesCS5A01G294900 chr5B 87.730 978 84 12 2057 3006 478515807 478516776 0.000000e+00 1109.0
8 TraesCS5A01G294900 chr5B 92.222 180 13 1 1809 1987 478515345 478515524 1.380000e-63 254.0
9 TraesCS5A01G294900 chr5B 91.304 138 6 3 1 137 478513483 478513615 1.840000e-42 183.0
10 TraesCS5A01G294900 chr5B 89.130 138 9 5 1 137 478502301 478502433 1.850000e-37 167.0
11 TraesCS5A01G294900 chr5B 87.805 82 10 0 1734 1815 47661441 47661522 2.470000e-16 97.1
12 TraesCS5A01G294900 chr5D 92.238 1211 69 11 517 1719 398547300 398548493 0.000000e+00 1692.0
13 TraesCS5A01G294900 chr5D 82.867 572 64 9 2057 2602 398548908 398549471 1.620000e-132 483.0
14 TraesCS5A01G294900 chr5D 91.860 258 19 2 197 452 398546545 398546802 2.850000e-95 359.0
15 TraesCS5A01G294900 chr5D 89.105 257 21 4 1806 2056 398548494 398548749 2.250000e-81 313.0
16 TraesCS5A01G294900 chr5D 88.148 135 16 0 1161 1295 398255301 398255435 8.620000e-36 161.0
17 TraesCS5A01G294900 chr5D 84.967 153 21 2 1161 1312 398124882 398125033 1.440000e-33 154.0
18 TraesCS5A01G294900 chr5D 95.946 74 3 0 1734 1807 412962040 412962113 1.460000e-23 121.0
19 TraesCS5A01G294900 chr5D 91.379 58 3 2 2749 2806 398550501 398550556 8.930000e-11 78.7
20 TraesCS5A01G294900 chr6D 91.139 79 5 1 1737 1815 454822353 454822277 4.100000e-19 106.0
21 TraesCS5A01G294900 chr7D 92.958 71 5 0 1737 1807 549512425 549512355 1.470000e-18 104.0
22 TraesCS5A01G294900 chr7A 92.958 71 5 0 1737 1807 634960732 634960662 1.470000e-18 104.0
23 TraesCS5A01G294900 chr6B 91.892 74 6 0 1734 1807 136094588 136094661 1.470000e-18 104.0
24 TraesCS5A01G294900 chr6B 93.056 72 4 1 1736 1807 433707833 433707903 1.470000e-18 104.0
25 TraesCS5A01G294900 chr6B 86.567 67 7 2 2600 2666 245721075 245721139 4.160000e-09 73.1
26 TraesCS5A01G294900 chr6B 93.182 44 3 0 2803 2846 636978278 636978235 6.960000e-07 65.8
27 TraesCS5A01G294900 chr3D 87.805 82 10 0 1734 1815 311300955 311301036 2.470000e-16 97.1
28 TraesCS5A01G294900 chr3D 90.000 50 4 1 2796 2845 69853479 69853527 2.500000e-06 63.9
29 TraesCS5A01G294900 chr1A 88.608 79 9 0 1737 1815 459632406 459632328 2.470000e-16 97.1
30 TraesCS5A01G294900 chr4A 93.333 45 3 0 2802 2846 697826548 697826592 1.930000e-07 67.6
31 TraesCS5A01G294900 chr4A 95.122 41 2 0 2806 2846 157207380 157207340 6.960000e-07 65.8
32 TraesCS5A01G294900 chr4A 93.182 44 3 0 2803 2846 698043005 698043048 6.960000e-07 65.8
33 TraesCS5A01G294900 chr4D 91.111 45 3 1 2793 2837 493836407 493836450 3.240000e-05 60.2
34 TraesCS5A01G294900 chr1D 97.143 35 1 0 2812 2846 403328217 403328183 3.240000e-05 60.2


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 TraesCS5A01G294900 chr5A 503621871 503624876 3005 False 5552.00 5552 100.00000 1 3006 1 chr5A.!!$F5 3005
1 TraesCS5A01G294900 chr5A 503233496 503234016 520 False 220.00 220 75.22800 1161 1693 1 chr5A.!!$F1 532
2 TraesCS5A01G294900 chr5B 478513483 478516776 3293 False 854.75 1873 89.98375 1 3006 4 chr5B.!!$F3 3005
3 TraesCS5A01G294900 chr5D 398546545 398550556 4011 False 585.14 1692 89.48980 197 2806 5 chr5D.!!$F4 2609

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
138 139 0.043053 CAGTTTGCTGACACGACGTG 60.043 55.0 25.72 25.72 45.28 4.49 F
203 341 0.174845 AGCGCACGGTATGTATGTGT 59.825 50.0 11.47 0.00 36.04 3.72 F
692 1325 0.324943 ACTTGGTTGGATCGTCCCAG 59.675 55.0 2.23 0.00 37.53 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1060 1714 0.322277 ACTGAAGTGCCCTGCTGATG 60.322 55.0 0.00 0.00 0.00 3.07 R
1743 2409 0.530744 ATGGACTGCTTTGCATGCTG 59.469 50.0 20.33 10.18 38.13 4.41 R
2471 3406 0.178068 GGCACCCGCTCTCAAGATAA 59.822 55.0 0.00 0.00 38.60 1.75 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
85 86 2.285977 CCCAGCCACTAATAACCGTTC 58.714 52.381 0.00 0.00 0.00 3.95
88 89 3.754323 CCAGCCACTAATAACCGTTCAAA 59.246 43.478 0.00 0.00 0.00 2.69
102 103 2.982470 CGTTCAAACCACCTCTACGTAC 59.018 50.000 0.00 0.00 0.00 3.67
103 104 2.982470 GTTCAAACCACCTCTACGTACG 59.018 50.000 15.01 15.01 0.00 3.67
104 105 2.229792 TCAAACCACCTCTACGTACGT 58.770 47.619 25.98 25.98 0.00 3.57
105 106 2.030893 TCAAACCACCTCTACGTACGTG 60.031 50.000 30.25 19.22 0.00 4.49
137 138 0.459585 ACAGTTTGCTGACACGACGT 60.460 50.000 0.00 0.00 45.28 4.34
138 139 0.043053 CAGTTTGCTGACACGACGTG 60.043 55.000 25.72 25.72 45.28 4.49
139 140 1.151777 AGTTTGCTGACACGACGTGG 61.152 55.000 29.86 14.70 37.94 4.94
140 141 2.530497 TTTGCTGACACGACGTGGC 61.530 57.895 29.86 28.50 42.82 5.01
141 142 2.916502 TTTGCTGACACGACGTGGCT 62.917 55.000 32.22 13.11 42.96 4.75
142 143 3.406361 GCTGACACGACGTGGCTG 61.406 66.667 32.22 31.04 42.96 4.85
148 149 4.415332 ACGACGTGGCTGCCGTAG 62.415 66.667 14.98 11.59 38.92 3.51
162 163 3.188773 CGTAGGTTCGCTGAACACA 57.811 52.632 18.49 6.84 43.54 3.72
163 164 0.782384 CGTAGGTTCGCTGAACACAC 59.218 55.000 18.49 14.49 43.54 3.82
164 165 1.860676 GTAGGTTCGCTGAACACACA 58.139 50.000 18.49 3.11 43.54 3.72
187 325 4.625311 ACACAAACCTGAAAAGAAAAAGCG 59.375 37.500 0.00 0.00 0.00 4.68
203 341 0.174845 AGCGCACGGTATGTATGTGT 59.825 50.000 11.47 0.00 36.04 3.72
207 345 1.931172 GCACGGTATGTATGTGTGGTC 59.069 52.381 0.00 0.00 36.04 4.02
212 350 4.951715 ACGGTATGTATGTGTGGTCTTCTA 59.048 41.667 0.00 0.00 0.00 2.10
215 353 6.016192 CGGTATGTATGTGTGGTCTTCTATCT 60.016 42.308 0.00 0.00 0.00 1.98
220 369 3.664107 TGTGTGGTCTTCTATCTGTTGC 58.336 45.455 0.00 0.00 0.00 4.17
337 487 3.147595 TCGATGGTGGAGGAGGCG 61.148 66.667 0.00 0.00 0.00 5.52
357 507 3.787676 CGCGCGCAGTTGATCCAA 61.788 61.111 32.61 0.00 0.00 3.53
358 508 2.099062 GCGCGCAGTTGATCCAAG 59.901 61.111 29.10 0.00 0.00 3.61
359 509 2.099062 CGCGCAGTTGATCCAAGC 59.901 61.111 8.75 0.00 0.00 4.01
360 510 2.679934 CGCGCAGTTGATCCAAGCA 61.680 57.895 8.75 0.00 0.00 3.91
361 511 1.136147 GCGCAGTTGATCCAAGCAG 59.864 57.895 0.30 0.00 0.00 4.24
362 512 1.798735 CGCAGTTGATCCAAGCAGG 59.201 57.895 0.00 0.00 39.47 4.85
383 548 1.833630 AGCTGCACAAGGATAGCACTA 59.166 47.619 1.02 0.00 38.59 2.74
386 551 3.193263 CTGCACAAGGATAGCACTACAG 58.807 50.000 0.00 0.00 34.13 2.74
446 628 2.097038 CCTGGCTTTCTCGACTGCG 61.097 63.158 0.00 0.00 39.35 5.18
452 634 1.660333 GCTTTCTCGACTGCGTTTTGG 60.660 52.381 0.00 0.00 38.98 3.28
455 637 1.597027 CTCGACTGCGTTTTGGGGT 60.597 57.895 0.00 0.00 38.98 4.95
465 647 1.676006 CGTTTTGGGGTCAGATATGCC 59.324 52.381 0.00 0.00 0.00 4.40
466 648 2.683742 CGTTTTGGGGTCAGATATGCCT 60.684 50.000 1.73 0.00 0.00 4.75
467 649 3.365472 GTTTTGGGGTCAGATATGCCTT 58.635 45.455 1.73 0.00 0.00 4.35
468 650 3.297134 TTTGGGGTCAGATATGCCTTC 57.703 47.619 1.73 0.00 0.00 3.46
469 651 0.758734 TGGGGTCAGATATGCCTTCG 59.241 55.000 1.73 0.00 0.00 3.79
496 1126 3.189702 GCCAGTTGAATAAAGTGCCGTAA 59.810 43.478 0.00 0.00 37.81 3.18
497 1127 4.671766 GCCAGTTGAATAAAGTGCCGTAAG 60.672 45.833 0.00 0.00 37.81 2.34
556 1187 1.364626 GCACACAGGATCGCAAGGAG 61.365 60.000 0.00 0.00 38.47 3.69
603 1234 4.261994 GGTTTGGTTGCTTCTGCTTCATAA 60.262 41.667 0.00 0.00 40.48 1.90
604 1235 4.771590 TTGGTTGCTTCTGCTTCATAAG 57.228 40.909 0.00 0.00 40.48 1.73
645 1278 5.067153 CCATGTTTGATTAGTCGCCCATTTA 59.933 40.000 0.00 0.00 0.00 1.40
646 1279 6.239008 CCATGTTTGATTAGTCGCCCATTTAT 60.239 38.462 0.00 0.00 0.00 1.40
657 1290 2.016318 GCCCATTTATTTTGCTTGCCC 58.984 47.619 0.00 0.00 0.00 5.36
686 1319 4.142687 GGTATTGTGAACTTGGTTGGATCG 60.143 45.833 0.00 0.00 0.00 3.69
687 1320 2.631160 TGTGAACTTGGTTGGATCGT 57.369 45.000 0.00 0.00 0.00 3.73
688 1321 2.489971 TGTGAACTTGGTTGGATCGTC 58.510 47.619 0.00 0.00 0.00 4.20
692 1325 0.324943 ACTTGGTTGGATCGTCCCAG 59.675 55.000 2.23 0.00 37.53 4.45
747 1390 7.985752 ACCTAATTGGAACTAATACTTTCTCCG 59.014 37.037 0.00 0.00 39.71 4.63
759 1404 9.819267 CTAATACTTTCTCCGTATTTTTCCTCT 57.181 33.333 0.00 0.00 38.25 3.69
806 1451 3.238597 TGCCTTTTACCTTTGCTTCCAT 58.761 40.909 0.00 0.00 0.00 3.41
862 1511 5.236263 GCCGAATTGTTTTCTCCAAAATGTT 59.764 36.000 0.00 0.00 33.98 2.71
963 1612 2.877582 CACGCCCAGTACGTACGC 60.878 66.667 19.49 15.60 42.96 4.42
964 1613 3.058160 ACGCCCAGTACGTACGCT 61.058 61.111 19.49 1.80 43.02 5.07
1004 1653 1.004044 CTTGTGGCTCCAGGACAAGAT 59.996 52.381 11.74 0.00 46.31 2.40
1058 1712 3.636300 AGCACTGTTCCATCTCTAGCTAG 59.364 47.826 15.01 15.01 0.00 3.42
1059 1713 3.798548 GCACTGTTCCATCTCTAGCTAGC 60.799 52.174 16.35 6.62 0.00 3.42
1060 1714 2.962421 ACTGTTCCATCTCTAGCTAGCC 59.038 50.000 16.35 0.00 0.00 3.93
1061 1715 2.961741 CTGTTCCATCTCTAGCTAGCCA 59.038 50.000 16.35 4.92 0.00 4.75
1283 1937 3.362399 CTCGCACAGGATCCACGCT 62.362 63.158 15.82 0.00 0.00 5.07
1381 2044 4.157958 GGTCGTCCTCGTCCGTCG 62.158 72.222 0.00 0.00 35.87 5.12
1397 2060 3.444642 CGTCGTAACGCCACTGAC 58.555 61.111 0.00 0.00 42.82 3.51
1416 2079 1.552337 ACATCTCTGATCAGTTGGCGT 59.448 47.619 21.92 11.24 0.00 5.68
1484 2147 0.817654 TGCACTCCATCTTCGACGAT 59.182 50.000 0.00 0.00 0.00 3.73
1531 2197 2.658593 GGGCGACGACGATGATGG 60.659 66.667 12.29 0.00 42.66 3.51
1654 2320 1.560923 GTGGACGATGAGATTGACCG 58.439 55.000 0.00 0.00 32.07 4.79
1683 2349 3.733337 GGCATATTCATCACGAGGTTCT 58.267 45.455 0.00 0.00 0.00 3.01
1740 2406 6.433847 TCATACTCCCTCTTTCACTTTTCA 57.566 37.500 0.00 0.00 0.00 2.69
1741 2407 6.467677 TCATACTCCCTCTTTCACTTTTCAG 58.532 40.000 0.00 0.00 0.00 3.02
1742 2408 6.270000 TCATACTCCCTCTTTCACTTTTCAGA 59.730 38.462 0.00 0.00 0.00 3.27
1743 2409 4.709250 ACTCCCTCTTTCACTTTTCAGAC 58.291 43.478 0.00 0.00 0.00 3.51
1744 2410 4.164221 ACTCCCTCTTTCACTTTTCAGACA 59.836 41.667 0.00 0.00 0.00 3.41
1745 2411 4.708177 TCCCTCTTTCACTTTTCAGACAG 58.292 43.478 0.00 0.00 0.00 3.51
1746 2412 3.251972 CCCTCTTTCACTTTTCAGACAGC 59.748 47.826 0.00 0.00 0.00 4.40
1747 2413 3.879295 CCTCTTTCACTTTTCAGACAGCA 59.121 43.478 0.00 0.00 0.00 4.41
1748 2414 4.518211 CCTCTTTCACTTTTCAGACAGCAT 59.482 41.667 0.00 0.00 0.00 3.79
1749 2415 5.428496 TCTTTCACTTTTCAGACAGCATG 57.572 39.130 0.00 0.00 46.00 4.06
1750 2416 3.631145 TTCACTTTTCAGACAGCATGC 57.369 42.857 10.51 10.51 42.53 4.06
1751 2417 2.574450 TCACTTTTCAGACAGCATGCA 58.426 42.857 21.98 0.00 42.53 3.96
1752 2418 2.950975 TCACTTTTCAGACAGCATGCAA 59.049 40.909 21.98 0.36 42.53 4.08
1753 2419 3.380954 TCACTTTTCAGACAGCATGCAAA 59.619 39.130 21.98 7.52 42.53 3.68
1754 2420 3.734231 CACTTTTCAGACAGCATGCAAAG 59.266 43.478 21.98 19.46 42.53 2.77
1755 2421 2.427232 TTTCAGACAGCATGCAAAGC 57.573 45.000 21.98 6.10 42.53 3.51
1756 2422 1.320507 TTCAGACAGCATGCAAAGCA 58.679 45.000 21.98 0.00 42.53 3.91
1757 2423 0.879090 TCAGACAGCATGCAAAGCAG 59.121 50.000 21.98 10.62 43.65 4.24
1758 2424 0.596577 CAGACAGCATGCAAAGCAGT 59.403 50.000 21.98 13.53 43.65 4.40
1759 2425 0.879765 AGACAGCATGCAAAGCAGTC 59.120 50.000 23.46 23.46 45.41 3.51
1760 2426 0.109412 GACAGCATGCAAAGCAGTCC 60.109 55.000 21.98 9.70 43.65 3.85
1761 2427 0.824595 ACAGCATGCAAAGCAGTCCA 60.825 50.000 21.98 0.00 43.65 4.02
1762 2428 0.530744 CAGCATGCAAAGCAGTCCAT 59.469 50.000 21.98 0.00 43.65 3.41
1763 2429 1.067142 CAGCATGCAAAGCAGTCCATT 60.067 47.619 21.98 0.00 43.65 3.16
1764 2430 1.621814 AGCATGCAAAGCAGTCCATTT 59.378 42.857 21.98 0.00 43.65 2.32
1765 2431 2.038033 AGCATGCAAAGCAGTCCATTTT 59.962 40.909 21.98 0.00 43.65 1.82
1766 2432 2.414138 GCATGCAAAGCAGTCCATTTTC 59.586 45.455 14.21 0.00 43.65 2.29
1767 2433 3.655486 CATGCAAAGCAGTCCATTTTCA 58.345 40.909 0.00 0.00 43.65 2.69
1768 2434 3.374220 TGCAAAGCAGTCCATTTTCAG 57.626 42.857 0.00 0.00 33.32 3.02
1769 2435 2.694628 TGCAAAGCAGTCCATTTTCAGT 59.305 40.909 0.00 0.00 33.32 3.41
1770 2436 3.132646 TGCAAAGCAGTCCATTTTCAGTT 59.867 39.130 0.00 0.00 33.32 3.16
1771 2437 3.492011 GCAAAGCAGTCCATTTTCAGTTG 59.508 43.478 0.00 0.00 0.00 3.16
1772 2438 4.685924 CAAAGCAGTCCATTTTCAGTTGT 58.314 39.130 0.00 0.00 0.00 3.32
1773 2439 4.574599 AAGCAGTCCATTTTCAGTTGTC 57.425 40.909 0.00 0.00 0.00 3.18
1774 2440 3.825328 AGCAGTCCATTTTCAGTTGTCT 58.175 40.909 0.00 0.00 0.00 3.41
1775 2441 3.567164 AGCAGTCCATTTTCAGTTGTCTG 59.433 43.478 0.00 0.00 42.54 3.51
1792 2458 7.964545 GTTGTCTGAAACGACTTACAAAAAT 57.035 32.000 0.00 0.00 38.97 1.82
1793 2459 7.817831 GTTGTCTGAAACGACTTACAAAAATG 58.182 34.615 0.00 0.00 38.97 2.32
1794 2460 7.310072 TGTCTGAAACGACTTACAAAAATGA 57.690 32.000 0.00 0.00 35.00 2.57
1795 2461 7.753659 TGTCTGAAACGACTTACAAAAATGAA 58.246 30.769 0.00 0.00 35.00 2.57
1796 2462 7.694784 TGTCTGAAACGACTTACAAAAATGAAC 59.305 33.333 0.00 0.00 35.00 3.18
1797 2463 6.902948 TCTGAAACGACTTACAAAAATGAACG 59.097 34.615 0.00 0.00 0.00 3.95
1798 2464 5.966503 TGAAACGACTTACAAAAATGAACGG 59.033 36.000 0.00 0.00 0.00 4.44
1799 2465 5.738118 AACGACTTACAAAAATGAACGGA 57.262 34.783 0.00 0.00 0.00 4.69
1800 2466 5.338614 ACGACTTACAAAAATGAACGGAG 57.661 39.130 0.00 0.00 0.00 4.63
1801 2467 4.212636 ACGACTTACAAAAATGAACGGAGG 59.787 41.667 0.00 0.00 0.00 4.30
1802 2468 4.378046 CGACTTACAAAAATGAACGGAGGG 60.378 45.833 0.00 0.00 0.00 4.30
1803 2469 4.721132 ACTTACAAAAATGAACGGAGGGA 58.279 39.130 0.00 0.00 0.00 4.20
1804 2470 4.760204 ACTTACAAAAATGAACGGAGGGAG 59.240 41.667 0.00 0.00 0.00 4.30
1905 2575 9.520515 CATATTAGCTATAGGGGTGAAAAATGT 57.479 33.333 1.04 0.00 0.00 2.71
1920 2590 6.601741 GAAAAATGTCATGGCTGTTTTTCA 57.398 33.333 28.88 1.86 43.21 2.69
1957 2628 1.407299 CCCCACTTCTGCATCGATTGA 60.407 52.381 0.00 0.00 0.00 2.57
1970 2641 4.614535 GCATCGATTGAATATGGTGAAGGC 60.615 45.833 0.00 0.00 0.00 4.35
1978 2649 5.538118 TGAATATGGTGAAGGCGTACATAG 58.462 41.667 0.00 0.00 0.00 2.23
1993 2664 6.417044 GGCGTACATAGATATATAAAGCGGTG 59.583 42.308 0.00 0.00 0.00 4.94
1994 2665 6.971184 GCGTACATAGATATATAAAGCGGTGT 59.029 38.462 0.00 0.00 0.00 4.16
1999 2670 9.350357 ACATAGATATATAAAGCGGTGTTTACG 57.650 33.333 0.00 0.00 0.00 3.18
2000 2671 9.563898 CATAGATATATAAAGCGGTGTTTACGA 57.436 33.333 0.00 0.00 0.00 3.43
2041 2712 8.796475 ACAGCAATGTTTACTGTGAAAGATTAT 58.204 29.630 0.00 0.00 42.83 1.28
2043 2714 8.796475 AGCAATGTTTACTGTGAAAGATTATGT 58.204 29.630 0.00 0.00 32.28 2.29
2070 2981 2.568090 GTTCCAAGCATGTGCCCG 59.432 61.111 0.57 0.00 43.38 6.13
2122 3033 6.374333 TGTTCTAGTGAAATTTATCCACCTGC 59.626 38.462 5.20 0.00 33.52 4.85
2230 3163 4.579869 TGGAGAACTCTATCAAAACAGGC 58.420 43.478 1.86 0.00 0.00 4.85
2231 3164 3.619038 GGAGAACTCTATCAAAACAGGCG 59.381 47.826 1.86 0.00 0.00 5.52
2237 3170 2.073816 CTATCAAAACAGGCGTTCGGT 58.926 47.619 0.00 0.00 32.91 4.69
2241 3174 2.928642 AAAACAGGCGTTCGGTCCGT 62.929 55.000 11.88 0.00 32.91 4.69
2254 3187 7.222654 GCGTTCGGTCCGTTTTATATATAAAG 58.777 38.462 15.65 7.49 34.13 1.85
2255 3188 7.222654 CGTTCGGTCCGTTTTATATATAAAGC 58.777 38.462 17.54 17.54 34.13 3.51
2291 3226 1.340991 ACACAACCAAGTCAAGTGCCT 60.341 47.619 0.00 0.00 33.69 4.75
2307 3242 8.988934 GTCAAGTGCCTCATCGAATATAAAATA 58.011 33.333 0.00 0.00 0.00 1.40
2308 3243 9.208022 TCAAGTGCCTCATCGAATATAAAATAG 57.792 33.333 0.00 0.00 0.00 1.73
2313 3248 8.585018 TGCCTCATCGAATATAAAATAGTCTGA 58.415 33.333 0.00 0.00 0.00 3.27
2337 3272 2.159212 GGGTAAAAACACAAACACGCCT 60.159 45.455 0.00 0.00 0.00 5.52
2342 3277 3.963383 AAACACAAACACGCCTAAGAG 57.037 42.857 0.00 0.00 0.00 2.85
2359 3294 7.641802 CGCCTAAGAGAAATCATAAAAGAAAGC 59.358 37.037 0.00 0.00 0.00 3.51
2367 3302 9.702494 AGAAATCATAAAAGAAAGCAGAAAAGG 57.298 29.630 0.00 0.00 0.00 3.11
2369 3304 9.702494 AAATCATAAAAGAAAGCAGAAAAGGAG 57.298 29.630 0.00 0.00 0.00 3.69
2370 3305 8.641498 ATCATAAAAGAAAGCAGAAAAGGAGA 57.359 30.769 0.00 0.00 0.00 3.71
2372 3307 5.521906 AAAAGAAAGCAGAAAAGGAGACC 57.478 39.130 0.00 0.00 0.00 3.85
2373 3308 3.864789 AGAAAGCAGAAAAGGAGACCA 57.135 42.857 0.00 0.00 0.00 4.02
2374 3309 4.379302 AGAAAGCAGAAAAGGAGACCAT 57.621 40.909 0.00 0.00 0.00 3.55
2375 3310 4.331108 AGAAAGCAGAAAAGGAGACCATC 58.669 43.478 0.00 0.00 0.00 3.51
2377 3312 3.795688 AGCAGAAAAGGAGACCATCAA 57.204 42.857 0.00 0.00 0.00 2.57
2378 3313 4.313020 AGCAGAAAAGGAGACCATCAAT 57.687 40.909 0.00 0.00 0.00 2.57
2406 3341 1.930100 GATCAAGTGATCTGCGGCG 59.070 57.895 13.03 0.51 45.60 6.46
2471 3406 0.606401 CAAGCCGGTCACAATCCTGT 60.606 55.000 1.90 0.00 35.63 4.00
2477 3412 3.873910 CCGGTCACAATCCTGTTATCTT 58.126 45.455 0.00 0.00 31.64 2.40
2534 3469 1.403814 TGAAGATAGTCAGAGGCCCG 58.596 55.000 0.00 0.00 0.00 6.13
2537 3472 2.041922 ATAGTCAGAGGCCCGCCA 60.042 61.111 8.74 0.00 38.92 5.69
2561 3498 2.029838 AAGATCCGCTCAATCACCAC 57.970 50.000 0.00 0.00 0.00 4.16
2563 3500 0.815615 GATCCGCTCAATCACCACCC 60.816 60.000 0.00 0.00 0.00 4.61
2587 3525 4.938226 TGTTGCGAATGTCCACATGTAATA 59.062 37.500 0.00 0.00 36.56 0.98
2606 3544 5.749596 AATAAATTCATGATGCGACCGAA 57.250 34.783 0.00 0.00 0.00 4.30
2671 3609 9.209175 TGTCCGGTTTCAAAAATAAATAAATGG 57.791 29.630 0.00 0.00 0.00 3.16
2705 3643 3.770666 TCTCGCATGTCTAGTTTAGCAC 58.229 45.455 0.00 0.00 0.00 4.40
2709 3647 3.334691 GCATGTCTAGTTTAGCACCACA 58.665 45.455 0.00 0.00 0.00 4.17
2710 3648 3.125316 GCATGTCTAGTTTAGCACCACAC 59.875 47.826 0.00 0.00 0.00 3.82
2711 3649 4.314961 CATGTCTAGTTTAGCACCACACA 58.685 43.478 0.00 0.00 0.00 3.72
2712 3650 4.617253 TGTCTAGTTTAGCACCACACAT 57.383 40.909 0.00 0.00 0.00 3.21
2713 3651 5.731957 TGTCTAGTTTAGCACCACACATA 57.268 39.130 0.00 0.00 0.00 2.29
2714 3652 5.475719 TGTCTAGTTTAGCACCACACATAC 58.524 41.667 0.00 0.00 0.00 2.39
2806 4706 7.753309 TTGCTTGGCAAGAAAATAGTTACTA 57.247 32.000 30.45 0.00 43.99 1.82
2815 4715 7.580882 GCAAGAAAATAGTTACTACTCCCTCCA 60.581 40.741 0.00 0.00 35.78 3.86
2818 4718 8.706521 AGAAAATAGTTACTACTCCCTCCAATC 58.293 37.037 0.00 0.00 35.78 2.67
2826 4726 6.936968 ACTACTCCCTCCAATCCATATTAC 57.063 41.667 0.00 0.00 0.00 1.89
2832 4732 5.911178 TCCCTCCAATCCATATTACTTGTCT 59.089 40.000 0.00 0.00 0.00 3.41
2859 4759 7.437748 AGATTTTTCTAGTGTCTATGGATCGG 58.562 38.462 0.00 0.00 0.00 4.18
2874 4774 4.344978 TGGATCGGAGGGAGTAATAGATG 58.655 47.826 0.00 0.00 0.00 2.90
2880 4780 6.371278 TCGGAGGGAGTAATAGATGTTAGTT 58.629 40.000 0.00 0.00 0.00 2.24
2890 4790 7.928706 AGTAATAGATGTTAGTTCCAGTGATGC 59.071 37.037 0.00 0.00 0.00 3.91
2892 4792 4.910195 AGATGTTAGTTCCAGTGATGCAA 58.090 39.130 0.00 0.00 0.00 4.08
2902 4802 4.151121 TCCAGTGATGCAAAATTGGAGAA 58.849 39.130 10.94 0.00 31.50 2.87
2912 4812 7.230849 TGCAAAATTGGAGAACTCACATAAT 57.769 32.000 4.23 0.00 0.00 1.28
2914 4814 7.177216 TGCAAAATTGGAGAACTCACATAATCT 59.823 33.333 4.23 0.00 0.00 2.40
2931 4831 6.485984 ACATAATCTGCAGAGCTTATCCTTTG 59.514 38.462 22.96 12.77 0.00 2.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 6.317140 TCATGAAGGTGTATGCTCATTTCTTC 59.683 38.462 0.00 0.00 0.00 2.87
76 77 3.782656 AGAGGTGGTTTGAACGGTTAT 57.217 42.857 0.00 0.00 0.00 1.89
85 86 2.322161 CACGTACGTAGAGGTGGTTTG 58.678 52.381 22.34 0.00 0.00 2.93
88 89 0.890542 TGCACGTACGTAGAGGTGGT 60.891 55.000 22.34 0.00 0.00 4.16
105 106 0.801836 AAACTGTTTGCTGCGTGTGC 60.802 50.000 4.73 0.00 43.20 4.57
130 131 4.710695 TACGGCAGCCACGTCGTG 62.711 66.667 18.54 18.54 44.37 4.35
131 132 4.415332 CTACGGCAGCCACGTCGT 62.415 66.667 13.30 5.51 44.37 4.34
133 134 3.584868 AACCTACGGCAGCCACGTC 62.585 63.158 13.30 0.00 44.37 4.34
137 138 4.752879 GCGAACCTACGGCAGCCA 62.753 66.667 13.30 0.00 0.00 4.75
138 139 4.452733 AGCGAACCTACGGCAGCC 62.453 66.667 0.00 0.00 0.00 4.85
139 140 3.188786 CAGCGAACCTACGGCAGC 61.189 66.667 0.00 0.00 0.00 5.25
140 141 1.080093 TTCAGCGAACCTACGGCAG 60.080 57.895 0.00 0.00 0.00 4.85
141 142 1.373748 GTTCAGCGAACCTACGGCA 60.374 57.895 9.40 0.00 36.65 5.69
142 143 1.373748 TGTTCAGCGAACCTACGGC 60.374 57.895 15.49 0.00 41.35 5.68
145 146 1.525619 GTGTGTGTTCAGCGAACCTAC 59.474 52.381 15.49 14.15 41.35 3.18
146 147 1.137282 TGTGTGTGTTCAGCGAACCTA 59.863 47.619 15.49 5.32 41.35 3.08
148 149 0.027586 GTGTGTGTGTTCAGCGAACC 59.972 55.000 15.49 9.51 41.35 3.62
149 150 0.724549 TGTGTGTGTGTTCAGCGAAC 59.275 50.000 12.53 12.53 42.26 3.95
150 151 1.443802 TTGTGTGTGTGTTCAGCGAA 58.556 45.000 0.00 0.00 0.00 4.70
151 152 1.129624 GTTTGTGTGTGTGTTCAGCGA 59.870 47.619 0.00 0.00 0.00 4.93
152 153 1.534028 GTTTGTGTGTGTGTTCAGCG 58.466 50.000 0.00 0.00 0.00 5.18
153 154 1.472480 AGGTTTGTGTGTGTGTTCAGC 59.528 47.619 0.00 0.00 0.00 4.26
154 155 2.746904 TCAGGTTTGTGTGTGTGTTCAG 59.253 45.455 0.00 0.00 0.00 3.02
155 156 2.784347 TCAGGTTTGTGTGTGTGTTCA 58.216 42.857 0.00 0.00 0.00 3.18
156 157 3.840890 TTCAGGTTTGTGTGTGTGTTC 57.159 42.857 0.00 0.00 0.00 3.18
159 160 4.433186 TCTTTTCAGGTTTGTGTGTGTG 57.567 40.909 0.00 0.00 0.00 3.82
160 161 5.461032 TTTCTTTTCAGGTTTGTGTGTGT 57.539 34.783 0.00 0.00 0.00 3.72
161 162 6.618379 GCTTTTTCTTTTCAGGTTTGTGTGTG 60.618 38.462 0.00 0.00 0.00 3.82
162 163 5.408299 GCTTTTTCTTTTCAGGTTTGTGTGT 59.592 36.000 0.00 0.00 0.00 3.72
163 164 5.444481 CGCTTTTTCTTTTCAGGTTTGTGTG 60.444 40.000 0.00 0.00 0.00 3.82
164 165 4.625311 CGCTTTTTCTTTTCAGGTTTGTGT 59.375 37.500 0.00 0.00 0.00 3.72
187 325 1.931172 GACCACACATACATACCGTGC 59.069 52.381 0.00 0.00 33.89 5.34
203 341 1.559682 GGGGCAACAGATAGAAGACCA 59.440 52.381 0.00 0.00 39.74 4.02
207 345 2.636830 CACTGGGGCAACAGATAGAAG 58.363 52.381 14.27 0.00 40.97 2.85
212 350 2.036256 GGCACTGGGGCAACAGAT 59.964 61.111 14.27 0.00 40.97 2.90
246 395 1.597027 GTGGTGTTGGACGGACAGG 60.597 63.158 0.00 0.00 0.00 4.00
314 464 0.830648 TCCTCCACCATCGACCAATC 59.169 55.000 0.00 0.00 0.00 2.67
343 493 1.136147 CTGCTTGGATCAACTGCGC 59.864 57.895 0.00 0.00 0.00 6.09
359 509 1.950828 CTATCCTTGTGCAGCTCCTG 58.049 55.000 0.00 0.00 34.12 3.86
360 510 0.179936 GCTATCCTTGTGCAGCTCCT 59.820 55.000 0.00 0.00 0.00 3.69
361 511 0.107508 TGCTATCCTTGTGCAGCTCC 60.108 55.000 0.00 0.00 35.05 4.70
362 512 1.012841 GTGCTATCCTTGTGCAGCTC 58.987 55.000 0.00 0.00 37.39 4.09
363 513 0.617413 AGTGCTATCCTTGTGCAGCT 59.383 50.000 0.00 0.00 37.39 4.24
364 514 1.936547 GTAGTGCTATCCTTGTGCAGC 59.063 52.381 0.00 0.00 37.39 5.25
365 515 3.193263 CTGTAGTGCTATCCTTGTGCAG 58.807 50.000 0.00 0.00 37.39 4.41
366 516 2.093500 CCTGTAGTGCTATCCTTGTGCA 60.093 50.000 0.00 0.00 0.00 4.57
367 517 2.093447 ACCTGTAGTGCTATCCTTGTGC 60.093 50.000 0.00 0.00 0.00 4.57
368 518 3.895232 ACCTGTAGTGCTATCCTTGTG 57.105 47.619 0.00 0.00 0.00 3.33
369 519 6.561519 ATTAACCTGTAGTGCTATCCTTGT 57.438 37.500 0.00 0.00 0.00 3.16
383 548 6.259550 ACGTACTCGAGTTAATTAACCTGT 57.740 37.500 25.44 17.05 40.62 4.00
386 551 7.537306 TGTGTAACGTACTCGAGTTAATTAACC 59.463 37.037 25.44 13.63 42.39 2.85
446 628 3.018423 AGGCATATCTGACCCCAAAAC 57.982 47.619 0.00 0.00 0.00 2.43
452 634 0.394565 AGCGAAGGCATATCTGACCC 59.605 55.000 0.00 0.00 43.41 4.46
455 637 2.140065 CGAAGCGAAGGCATATCTGA 57.860 50.000 0.00 0.00 43.41 3.27
556 1187 0.679505 GTGGCTTTTCCTTTGGGGTC 59.320 55.000 0.00 0.00 36.25 4.46
603 1234 0.541863 GGCTGGTGTAGTGGTATGCT 59.458 55.000 0.00 0.00 0.00 3.79
604 1235 0.251916 TGGCTGGTGTAGTGGTATGC 59.748 55.000 0.00 0.00 0.00 3.14
645 1278 1.535204 CCTCCGTGGGCAAGCAAAAT 61.535 55.000 0.00 0.00 0.00 1.82
646 1279 2.199652 CCTCCGTGGGCAAGCAAAA 61.200 57.895 0.00 0.00 0.00 2.44
657 1290 2.742053 CCAAGTTCACAATACCTCCGTG 59.258 50.000 0.00 0.00 0.00 4.94
686 1319 0.179936 CCTGATTGGCTCTCTGGGAC 59.820 60.000 5.35 0.00 0.00 4.46
687 1320 2.612760 CCTGATTGGCTCTCTGGGA 58.387 57.895 5.35 0.00 0.00 4.37
688 1321 1.530771 CCCTGATTGGCTCTCTGGG 59.469 63.158 14.19 14.19 43.04 4.45
744 1387 1.203052 ACGCGAGAGGAAAAATACGGA 59.797 47.619 15.93 0.00 0.00 4.69
747 1390 4.085721 CGTGATACGCGAGAGGAAAAATAC 60.086 45.833 15.93 0.00 39.94 1.89
862 1511 3.228188 AGTCCAAAGCACATGAAAGGA 57.772 42.857 0.00 0.00 0.00 3.36
1004 1653 3.700538 CTTCAGGGTTTGGATTCATGGA 58.299 45.455 0.00 0.00 0.00 3.41
1059 1713 1.001764 TGAAGTGCCCTGCTGATGG 60.002 57.895 0.00 0.00 0.00 3.51
1060 1714 0.322277 ACTGAAGTGCCCTGCTGATG 60.322 55.000 0.00 0.00 0.00 3.07
1061 1715 0.322277 CACTGAAGTGCCCTGCTGAT 60.322 55.000 0.00 0.00 39.39 2.90
1108 1762 0.749649 GATGATGACCGAGGAGCTGT 59.250 55.000 0.00 0.00 0.00 4.40
1301 1955 2.362120 TCGAGGTCCTTCCCCGAC 60.362 66.667 0.00 0.00 36.75 4.79
1381 2044 0.989890 GATGTCAGTGGCGTTACGAC 59.010 55.000 9.62 6.20 34.27 4.34
1397 2060 2.306341 ACGCCAACTGATCAGAGATG 57.694 50.000 29.27 21.33 0.00 2.90
1667 2333 3.600388 GTTCCAGAACCTCGTGATGAAT 58.400 45.455 0.00 0.00 35.36 2.57
1683 2349 1.229690 TCCCATTCCTCCGGTTCCA 60.230 57.895 0.00 0.00 0.00 3.53
1719 2385 6.043243 TGTCTGAAAAGTGAAAGAGGGAGTAT 59.957 38.462 0.00 0.00 0.00 2.12
1720 2386 5.365605 TGTCTGAAAAGTGAAAGAGGGAGTA 59.634 40.000 0.00 0.00 0.00 2.59
1721 2387 4.164221 TGTCTGAAAAGTGAAAGAGGGAGT 59.836 41.667 0.00 0.00 0.00 3.85
1722 2388 4.708177 TGTCTGAAAAGTGAAAGAGGGAG 58.292 43.478 0.00 0.00 0.00 4.30
1723 2389 4.708177 CTGTCTGAAAAGTGAAAGAGGGA 58.292 43.478 0.00 0.00 0.00 4.20
1724 2390 3.251972 GCTGTCTGAAAAGTGAAAGAGGG 59.748 47.826 0.00 0.00 0.00 4.30
1725 2391 3.879295 TGCTGTCTGAAAAGTGAAAGAGG 59.121 43.478 0.00 0.00 0.00 3.69
1726 2392 5.450171 CATGCTGTCTGAAAAGTGAAAGAG 58.550 41.667 0.00 0.00 0.00 2.85
1727 2393 4.261322 GCATGCTGTCTGAAAAGTGAAAGA 60.261 41.667 11.37 0.00 0.00 2.52
1728 2394 3.979495 GCATGCTGTCTGAAAAGTGAAAG 59.021 43.478 11.37 0.00 0.00 2.62
1729 2395 3.380954 TGCATGCTGTCTGAAAAGTGAAA 59.619 39.130 20.33 0.00 0.00 2.69
1730 2396 2.950975 TGCATGCTGTCTGAAAAGTGAA 59.049 40.909 20.33 0.00 0.00 3.18
1731 2397 2.574450 TGCATGCTGTCTGAAAAGTGA 58.426 42.857 20.33 0.00 0.00 3.41
1732 2398 3.358707 TTGCATGCTGTCTGAAAAGTG 57.641 42.857 20.33 0.00 0.00 3.16
1733 2399 3.797865 GCTTTGCATGCTGTCTGAAAAGT 60.798 43.478 20.33 0.00 40.16 2.66
1734 2400 2.729882 GCTTTGCATGCTGTCTGAAAAG 59.270 45.455 20.33 17.77 40.72 2.27
1735 2401 2.101082 TGCTTTGCATGCTGTCTGAAAA 59.899 40.909 20.33 8.03 31.71 2.29
1736 2402 1.682323 TGCTTTGCATGCTGTCTGAAA 59.318 42.857 20.33 8.76 31.71 2.69
1737 2403 1.268625 CTGCTTTGCATGCTGTCTGAA 59.731 47.619 20.33 0.00 38.13 3.02
1738 2404 0.879090 CTGCTTTGCATGCTGTCTGA 59.121 50.000 20.33 0.00 38.13 3.27
1739 2405 0.596577 ACTGCTTTGCATGCTGTCTG 59.403 50.000 20.33 11.24 38.13 3.51
1740 2406 3.031916 ACTGCTTTGCATGCTGTCT 57.968 47.368 20.33 0.00 38.13 3.41
1741 2407 3.396491 GACTGCTTTGCATGCTGTC 57.604 52.632 24.65 24.65 46.31 3.51
1742 2408 0.824595 TGGACTGCTTTGCATGCTGT 60.825 50.000 20.33 19.19 43.43 4.40
1743 2409 0.530744 ATGGACTGCTTTGCATGCTG 59.469 50.000 20.33 10.18 38.13 4.41
1744 2410 1.263356 AATGGACTGCTTTGCATGCT 58.737 45.000 20.33 0.00 38.13 3.79
1745 2411 2.088950 AAATGGACTGCTTTGCATGC 57.911 45.000 11.82 11.82 38.13 4.06
1746 2412 3.655486 TGAAAATGGACTGCTTTGCATG 58.345 40.909 0.00 0.00 38.13 4.06
1747 2413 3.322828 ACTGAAAATGGACTGCTTTGCAT 59.677 39.130 0.00 0.00 38.13 3.96
1748 2414 2.694628 ACTGAAAATGGACTGCTTTGCA 59.305 40.909 0.00 0.00 36.92 4.08
1749 2415 3.375782 ACTGAAAATGGACTGCTTTGC 57.624 42.857 0.00 0.00 0.00 3.68
1750 2416 4.685924 ACAACTGAAAATGGACTGCTTTG 58.314 39.130 0.00 0.00 0.00 2.77
1751 2417 4.646492 AGACAACTGAAAATGGACTGCTTT 59.354 37.500 0.00 0.00 0.00 3.51
1752 2418 4.037208 CAGACAACTGAAAATGGACTGCTT 59.963 41.667 0.00 0.00 46.03 3.91
1753 2419 3.567164 CAGACAACTGAAAATGGACTGCT 59.433 43.478 0.00 0.00 46.03 4.24
1754 2420 3.893720 CAGACAACTGAAAATGGACTGC 58.106 45.455 0.00 0.00 46.03 4.40
1766 2432 5.712217 TTGTAAGTCGTTTCAGACAACTG 57.288 39.130 0.00 0.00 43.24 3.16
1767 2433 6.730960 TTTTGTAAGTCGTTTCAGACAACT 57.269 33.333 0.00 0.00 43.24 3.16
1768 2434 7.694784 TCATTTTTGTAAGTCGTTTCAGACAAC 59.305 33.333 0.00 0.00 43.24 3.32
1769 2435 7.753659 TCATTTTTGTAAGTCGTTTCAGACAA 58.246 30.769 0.00 0.00 43.24 3.18
1770 2436 7.310072 TCATTTTTGTAAGTCGTTTCAGACA 57.690 32.000 0.00 0.00 43.24 3.41
1771 2437 7.097570 CGTTCATTTTTGTAAGTCGTTTCAGAC 60.098 37.037 0.00 0.00 41.23 3.51
1772 2438 6.902948 CGTTCATTTTTGTAAGTCGTTTCAGA 59.097 34.615 0.00 0.00 0.00 3.27
1773 2439 6.140108 CCGTTCATTTTTGTAAGTCGTTTCAG 59.860 38.462 0.00 0.00 0.00 3.02
1774 2440 5.966503 CCGTTCATTTTTGTAAGTCGTTTCA 59.033 36.000 0.00 0.00 0.00 2.69
1775 2441 6.193761 TCCGTTCATTTTTGTAAGTCGTTTC 58.806 36.000 0.00 0.00 0.00 2.78
1776 2442 6.121613 TCCGTTCATTTTTGTAAGTCGTTT 57.878 33.333 0.00 0.00 0.00 3.60
1777 2443 5.277634 CCTCCGTTCATTTTTGTAAGTCGTT 60.278 40.000 0.00 0.00 0.00 3.85
1778 2444 4.212636 CCTCCGTTCATTTTTGTAAGTCGT 59.787 41.667 0.00 0.00 0.00 4.34
1779 2445 4.378046 CCCTCCGTTCATTTTTGTAAGTCG 60.378 45.833 0.00 0.00 0.00 4.18
1780 2446 4.758165 TCCCTCCGTTCATTTTTGTAAGTC 59.242 41.667 0.00 0.00 0.00 3.01
1781 2447 4.721132 TCCCTCCGTTCATTTTTGTAAGT 58.279 39.130 0.00 0.00 0.00 2.24
1782 2448 4.760204 ACTCCCTCCGTTCATTTTTGTAAG 59.240 41.667 0.00 0.00 0.00 2.34
1783 2449 4.721132 ACTCCCTCCGTTCATTTTTGTAA 58.279 39.130 0.00 0.00 0.00 2.41
1784 2450 4.360951 ACTCCCTCCGTTCATTTTTGTA 57.639 40.909 0.00 0.00 0.00 2.41
1785 2451 3.223674 ACTCCCTCCGTTCATTTTTGT 57.776 42.857 0.00 0.00 0.00 2.83
1786 2452 3.127030 GCTACTCCCTCCGTTCATTTTTG 59.873 47.826 0.00 0.00 0.00 2.44
1787 2453 3.009143 AGCTACTCCCTCCGTTCATTTTT 59.991 43.478 0.00 0.00 0.00 1.94
1788 2454 2.572104 AGCTACTCCCTCCGTTCATTTT 59.428 45.455 0.00 0.00 0.00 1.82
1789 2455 2.188817 AGCTACTCCCTCCGTTCATTT 58.811 47.619 0.00 0.00 0.00 2.32
1790 2456 1.867363 AGCTACTCCCTCCGTTCATT 58.133 50.000 0.00 0.00 0.00 2.57
1791 2457 1.482593 CAAGCTACTCCCTCCGTTCAT 59.517 52.381 0.00 0.00 0.00 2.57
1792 2458 0.895530 CAAGCTACTCCCTCCGTTCA 59.104 55.000 0.00 0.00 0.00 3.18
1793 2459 0.896226 ACAAGCTACTCCCTCCGTTC 59.104 55.000 0.00 0.00 0.00 3.95
1794 2460 1.349067 AACAAGCTACTCCCTCCGTT 58.651 50.000 0.00 0.00 0.00 4.44
1795 2461 1.349067 AAACAAGCTACTCCCTCCGT 58.651 50.000 0.00 0.00 0.00 4.69
1796 2462 2.347731 GAAAACAAGCTACTCCCTCCG 58.652 52.381 0.00 0.00 0.00 4.63
1797 2463 2.306219 AGGAAAACAAGCTACTCCCTCC 59.694 50.000 0.00 0.00 0.00 4.30
1798 2464 3.704800 AGGAAAACAAGCTACTCCCTC 57.295 47.619 0.00 0.00 0.00 4.30
1799 2465 4.455070 AAAGGAAAACAAGCTACTCCCT 57.545 40.909 0.00 0.00 0.00 4.20
1800 2466 4.796290 GCAAAAGGAAAACAAGCTACTCCC 60.796 45.833 0.00 0.00 0.00 4.30
1801 2467 4.202111 TGCAAAAGGAAAACAAGCTACTCC 60.202 41.667 0.00 0.00 0.00 3.85
1802 2468 4.740205 GTGCAAAAGGAAAACAAGCTACTC 59.260 41.667 0.00 0.00 0.00 2.59
1803 2469 4.402474 AGTGCAAAAGGAAAACAAGCTACT 59.598 37.500 0.00 0.00 0.00 2.57
1804 2470 4.504097 CAGTGCAAAAGGAAAACAAGCTAC 59.496 41.667 0.00 0.00 0.00 3.58
1883 2553 6.964464 TGACATTTTTCACCCCTATAGCTAA 58.036 36.000 0.00 0.00 0.00 3.09
1905 2575 5.358922 CCTCTTTTTGAAAAACAGCCATGA 58.641 37.500 0.00 0.00 0.00 3.07
1941 2611 5.237996 CACCATATTCAATCGATGCAGAAGT 59.762 40.000 0.00 0.00 0.00 3.01
1957 2628 5.801531 TCTATGTACGCCTTCACCATATT 57.198 39.130 0.00 0.00 0.00 1.28
1970 2641 8.906636 AACACCGCTTTATATATCTATGTACG 57.093 34.615 0.00 0.00 0.00 3.67
1978 2649 9.919348 TTTTTCGTAAACACCGCTTTATATATC 57.081 29.630 0.00 0.00 0.00 1.63
2041 2712 2.235016 GCTTGGAACCAACCATGTACA 58.765 47.619 0.00 0.00 39.82 2.90
2043 2714 2.666272 TGCTTGGAACCAACCATGTA 57.334 45.000 1.83 0.00 39.82 2.29
2141 3052 8.298854 TCAACTACGTTTGTCATAGCTAAAGTA 58.701 33.333 0.00 0.00 0.00 2.24
2159 3070 5.049198 TCCAAGTAGTACACAGTCAACTACG 60.049 44.000 13.03 4.31 46.53 3.51
2214 3125 2.993899 CGAACGCCTGTTTTGATAGAGT 59.006 45.455 0.00 0.00 38.78 3.24
2219 3152 0.872388 GACCGAACGCCTGTTTTGAT 59.128 50.000 0.00 0.00 38.78 2.57
2230 3163 7.096106 TGCTTTATATATAAAACGGACCGAACG 60.096 37.037 23.38 0.00 32.39 3.95
2231 3164 8.006027 GTGCTTTATATATAAAACGGACCGAAC 58.994 37.037 23.38 6.57 32.39 3.95
2237 3170 8.734218 TGGTTGTGCTTTATATATAAAACGGA 57.266 30.769 16.69 6.90 32.39 4.69
2254 3187 3.257393 TGTGTGAATTTGTTGGTTGTGC 58.743 40.909 0.00 0.00 0.00 4.57
2255 3188 4.092675 GGTTGTGTGAATTTGTTGGTTGTG 59.907 41.667 0.00 0.00 0.00 3.33
2291 3226 9.875691 CCCATCAGACTATTTTATATTCGATGA 57.124 33.333 0.00 0.00 30.53 2.92
2307 3242 4.447138 TGTGTTTTTACCCCATCAGACT 57.553 40.909 0.00 0.00 0.00 3.24
2308 3243 5.163499 TGTTTGTGTTTTTACCCCATCAGAC 60.163 40.000 0.00 0.00 0.00 3.51
2313 3248 3.738590 GCGTGTTTGTGTTTTTACCCCAT 60.739 43.478 0.00 0.00 0.00 4.00
2322 3257 3.537580 TCTCTTAGGCGTGTTTGTGTTT 58.462 40.909 0.00 0.00 0.00 2.83
2342 3277 9.696917 TCCTTTTCTGCTTTCTTTTATGATTTC 57.303 29.630 0.00 0.00 0.00 2.17
2359 3294 5.320549 CCAATTGATGGTCTCCTTTTCTG 57.679 43.478 7.12 0.00 44.85 3.02
2372 3307 4.401519 ACTTGATCTTCTGGCCAATTGATG 59.598 41.667 7.01 3.33 0.00 3.07
2373 3308 4.401519 CACTTGATCTTCTGGCCAATTGAT 59.598 41.667 7.01 10.31 0.00 2.57
2374 3309 3.760151 CACTTGATCTTCTGGCCAATTGA 59.240 43.478 7.01 5.20 0.00 2.57
2375 3310 3.760151 TCACTTGATCTTCTGGCCAATTG 59.240 43.478 7.01 0.00 0.00 2.32
2377 3312 3.726557 TCACTTGATCTTCTGGCCAAT 57.273 42.857 7.01 0.00 0.00 3.16
2378 3313 3.614092 GATCACTTGATCTTCTGGCCAA 58.386 45.455 7.01 0.00 45.60 4.52
2406 3341 1.336887 TGCCACACTTCGACTAGCTTC 60.337 52.381 0.00 0.00 0.00 3.86
2418 3353 1.097547 GTGTTGACTGCTGCCACACT 61.098 55.000 0.00 0.00 0.00 3.55
2423 3358 2.607892 GGACGTGTTGACTGCTGCC 61.608 63.158 0.00 0.00 0.00 4.85
2471 3406 0.178068 GGCACCCGCTCTCAAGATAA 59.822 55.000 0.00 0.00 38.60 1.75
2477 3412 4.007644 CACTGGCACCCGCTCTCA 62.008 66.667 0.00 0.00 38.60 3.27
2509 3444 5.397334 GGGCCTCTGACTATCTTCAAATTCT 60.397 44.000 0.84 0.00 0.00 2.40
2521 3456 1.899437 CTTTGGCGGGCCTCTGACTA 61.899 60.000 11.55 0.00 36.94 2.59
2526 3461 1.303643 CTTTCTTTGGCGGGCCTCT 60.304 57.895 11.55 0.00 36.94 3.69
2534 3469 1.453155 TGAGCGGATCTTTCTTTGGC 58.547 50.000 0.00 0.00 0.00 4.52
2537 3472 3.691609 GGTGATTGAGCGGATCTTTCTTT 59.308 43.478 0.00 0.00 0.00 2.52
2561 3498 0.888736 TGTGGACATTCGCAACAGGG 60.889 55.000 0.00 0.00 0.00 4.45
2563 3500 1.536766 ACATGTGGACATTCGCAACAG 59.463 47.619 0.00 0.00 33.61 3.16
2587 3525 3.009723 AGTTCGGTCGCATCATGAATTT 58.990 40.909 0.00 0.00 0.00 1.82
2634 3572 4.204012 TGAAACCGGACAAAAGATTCACT 58.796 39.130 9.46 0.00 0.00 3.41
2637 3575 6.895607 TTTTTGAAACCGGACAAAAGATTC 57.104 33.333 24.56 11.83 43.47 2.52
2671 3609 2.010145 TGCGAGAGATTAACTGGCAC 57.990 50.000 0.00 0.00 42.25 5.01
2705 3643 4.877823 AGCTCATTACATGTGTATGTGTGG 59.122 41.667 9.11 6.18 46.63 4.17
2709 3647 6.585416 TCATGAGCTCATTACATGTGTATGT 58.415 36.000 26.70 0.00 41.51 2.29
2710 3648 7.519002 CATCATGAGCTCATTACATGTGTATG 58.481 38.462 26.70 12.41 41.14 2.39
2711 3649 6.148976 GCATCATGAGCTCATTACATGTGTAT 59.851 38.462 26.70 8.07 41.14 2.29
2712 3650 5.467735 GCATCATGAGCTCATTACATGTGTA 59.532 40.000 26.70 6.22 41.14 2.90
2713 3651 4.275196 GCATCATGAGCTCATTACATGTGT 59.725 41.667 26.70 7.62 41.14 3.72
2714 3652 4.320275 GGCATCATGAGCTCATTACATGTG 60.320 45.833 26.70 15.14 41.14 3.21
2806 4706 5.672194 ACAAGTAATATGGATTGGAGGGAGT 59.328 40.000 0.00 0.00 0.00 3.85
2832 4732 9.967346 CGATCCATAGACACTAGAAAAATCTAA 57.033 33.333 0.00 0.00 0.00 2.10
2859 4759 7.288158 ACTGGAACTAACATCTATTACTCCCTC 59.712 40.741 0.00 0.00 0.00 4.30
2874 4774 5.634859 CCAATTTTGCATCACTGGAACTAAC 59.365 40.000 0.00 0.00 31.84 2.34
2880 4780 3.765381 TCTCCAATTTTGCATCACTGGA 58.235 40.909 7.61 7.61 0.00 3.86
2890 4790 7.487189 GCAGATTATGTGAGTTCTCCAATTTTG 59.513 37.037 0.00 0.00 0.00 2.44
2892 4792 6.660521 TGCAGATTATGTGAGTTCTCCAATTT 59.339 34.615 0.00 0.00 0.00 1.82
2902 4802 4.484537 AAGCTCTGCAGATTATGTGAGT 57.515 40.909 18.63 0.00 35.48 3.41
2912 4812 3.517100 AGACAAAGGATAAGCTCTGCAGA 59.483 43.478 17.19 17.19 0.00 4.26
2914 4814 3.369892 GGAGACAAAGGATAAGCTCTGCA 60.370 47.826 0.00 0.00 0.00 4.41


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

AutoCloner maintained by Alex Coulton.