Multiple sequence alignment - TraesCS3D01G031400

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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 TraesCS3D01G031400 chr3D 100.000 4756 0 0 1 4756 11573794 11578549 0.000000e+00 8783
1 TraesCS3D01G031400 chr3A 88.197 4033 231 121 868 4754 25501437 25497504 0.000000e+00 4584
2 TraesCS3D01G031400 chr3A 87.117 326 27 11 554 868 25501790 25501469 5.850000e-94 355
3 TraesCS3D01G031400 chr3B 90.144 3054 156 57 1791 4756 16213573 16216569 0.000000e+00 3838
4 TraesCS3D01G031400 chr3B 86.266 881 27 30 936 1753 16212712 16213561 0.000000e+00 870
5 TraesCS3D01G031400 chr3B 88.018 217 15 8 636 844 16212458 16212671 3.680000e-61 246
6 TraesCS3D01G031400 chr6D 94.554 661 25 9 1 651 76350113 76350772 0.000000e+00 1011
7 TraesCS3D01G031400 chr6D 95.455 110 5 0 1555 1664 282609097 282609206 4.890000e-40 176
8 TraesCS3D01G031400 chr4D 94.554 661 24 8 1 651 306581469 306582127 0.000000e+00 1011
9 TraesCS3D01G031400 chr2D 94.554 661 24 8 1 651 541200632 541201290 0.000000e+00 1011
10 TraesCS3D01G031400 chr2D 94.436 665 21 8 1 651 291006813 291007475 0.000000e+00 1009
11 TraesCS3D01G031400 chrUn 94.144 666 22 9 1 651 10222452 10221789 0.000000e+00 998
12 TraesCS3D01G031400 chr7D 94.135 665 23 8 1 651 558366700 558366038 0.000000e+00 998
13 TraesCS3D01G031400 chr7D 92.029 414 18 7 251 651 434256180 434255769 6.910000e-158 568
14 TraesCS3D01G031400 chr7D 89.836 305 17 8 360 651 307352710 307352407 3.470000e-101 379
15 TraesCS3D01G031400 chr1D 94.135 665 23 8 1 651 190344294 190343632 0.000000e+00 998
16 TraesCS3D01G031400 chr1D 94.136 648 18 10 19 651 35492007 35491365 0.000000e+00 968
17 TraesCS3D01G031400 chr5D 93.985 665 25 8 1 651 23481397 23482060 0.000000e+00 992
18 TraesCS3D01G031400 chr1B 87.458 295 16 7 1387 1664 7249757 7249467 2.140000e-83 320


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 TraesCS3D01G031400 chr3D 11573794 11578549 4755 False 8783.000000 8783 100.000000 1 4756 1 chr3D.!!$F1 4755
1 TraesCS3D01G031400 chr3A 25497504 25501790 4286 True 2469.500000 4584 87.657000 554 4754 2 chr3A.!!$R1 4200
2 TraesCS3D01G031400 chr3B 16212458 16216569 4111 False 1651.333333 3838 88.142667 636 4756 3 chr3B.!!$F1 4120
3 TraesCS3D01G031400 chr6D 76350113 76350772 659 False 1011.000000 1011 94.554000 1 651 1 chr6D.!!$F1 650
4 TraesCS3D01G031400 chr4D 306581469 306582127 658 False 1011.000000 1011 94.554000 1 651 1 chr4D.!!$F1 650
5 TraesCS3D01G031400 chr2D 541200632 541201290 658 False 1011.000000 1011 94.554000 1 651 1 chr2D.!!$F2 650
6 TraesCS3D01G031400 chr2D 291006813 291007475 662 False 1009.000000 1009 94.436000 1 651 1 chr2D.!!$F1 650
7 TraesCS3D01G031400 chrUn 10221789 10222452 663 True 998.000000 998 94.144000 1 651 1 chrUn.!!$R1 650
8 TraesCS3D01G031400 chr7D 558366038 558366700 662 True 998.000000 998 94.135000 1 651 1 chr7D.!!$R3 650
9 TraesCS3D01G031400 chr1D 190343632 190344294 662 True 998.000000 998 94.135000 1 651 1 chr1D.!!$R2 650
10 TraesCS3D01G031400 chr1D 35491365 35492007 642 True 968.000000 968 94.136000 19 651 1 chr1D.!!$R1 632
11 TraesCS3D01G031400 chr5D 23481397 23482060 663 False 992.000000 992 93.985000 1 651 1 chr5D.!!$F1 650

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
970 1036 0.040425 GTGCGGTACAAACCTTGCAG 60.040 55.0 0.00 0.00 41.15 4.41 F
1303 1426 0.043334 TCCTCCCTCCTCCCAAAGAG 59.957 60.0 0.00 0.00 42.83 2.85 F
1524 1695 0.101939 GGGCTATGCTTGCTTGCTTC 59.898 55.0 3.47 0.00 0.00 3.86 F
2762 3004 0.034670 GGGACAAGATGAGCCAGCTT 60.035 55.0 0.00 0.58 40.92 3.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1773 1966 0.378257 ACAGCAAAGCGTGTGTCAAG 59.622 50.000 0.00 0.0 0.00 3.02 R
2348 2566 0.529555 GCTTCCTGATGAGCGTCTCC 60.530 60.000 4.73 0.0 0.00 3.71 R
3263 3514 1.135721 GGGTTGTAGTAGGCGGTGTAG 59.864 57.143 0.00 0.0 0.00 2.74 R
4095 4405 0.332632 TTCTGAAGCCCCCAATGGAG 59.667 55.000 0.00 0.0 35.39 3.86 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
150 154 9.654417 CTTTCCTTGTGATTTTTGCATTTTTAG 57.346 29.630 0.00 0.00 0.00 1.85
374 379 5.047566 TCCATCCACAACAAAAGAGAAGA 57.952 39.130 0.00 0.00 0.00 2.87
377 382 5.049129 CCATCCACAACAAAAGAGAAGAGAC 60.049 44.000 0.00 0.00 0.00 3.36
423 428 2.941064 GCTAATTAAACTGTCCCGGACC 59.059 50.000 15.24 0.00 0.00 4.46
493 499 4.223923 ACTCTAAGCATAGCAAGTCCACTT 59.776 41.667 0.00 0.00 36.45 3.16
496 502 6.106673 TCTAAGCATAGCAAGTCCACTTAAC 58.893 40.000 0.00 0.00 34.28 2.01
508 514 2.825532 TCCACTTAACACCGTACCCTAC 59.174 50.000 0.00 0.00 0.00 3.18
513 519 4.021981 ACTTAACACCGTACCCTACTCAAC 60.022 45.833 0.00 0.00 0.00 3.18
519 525 3.267483 CCGTACCCTACTCAACCAATTG 58.733 50.000 0.00 0.00 37.14 2.32
520 526 3.267483 CGTACCCTACTCAACCAATTGG 58.733 50.000 23.31 23.31 42.17 3.16
652 670 7.395206 ACCACTATTGTACTCTACACATGTGTA 59.605 37.037 31.33 31.33 44.42 2.90
656 674 7.884816 ATTGTACTCTACACATGTGTACAAC 57.115 36.000 31.59 25.00 46.90 3.32
657 675 5.775686 TGTACTCTACACATGTGTACAACC 58.224 41.667 30.31 18.36 44.42 3.77
684 705 2.813061 CCCACGTACGGGTTATTAGTG 58.187 52.381 21.06 4.99 41.83 2.74
685 706 2.195922 CCACGTACGGGTTATTAGTGC 58.804 52.381 21.06 0.00 0.00 4.40
776 808 2.772924 CAAAGCCCATCCCCCACT 59.227 61.111 0.00 0.00 0.00 4.00
861 893 1.675714 CCATCCTAACAAGAGCGTGCA 60.676 52.381 0.00 0.00 0.00 4.57
864 896 1.001974 TCCTAACAAGAGCGTGCATGT 59.998 47.619 7.93 0.00 0.00 3.21
877 941 2.159268 CGTGCATGTGTGAGAGAGAGAT 60.159 50.000 0.00 0.00 0.00 2.75
907 971 1.202582 CCACACTGTCCTAACGAGAGG 59.797 57.143 0.00 0.00 36.17 3.69
924 988 0.987294 AGGGTGTGAGACAATGAGGG 59.013 55.000 0.00 0.00 0.00 4.30
925 989 0.984230 GGGTGTGAGACAATGAGGGA 59.016 55.000 0.00 0.00 0.00 4.20
927 991 1.065854 GGTGTGAGACAATGAGGGAGG 60.066 57.143 0.00 0.00 0.00 4.30
929 993 0.107459 GTGAGACAATGAGGGAGGCC 60.107 60.000 0.00 0.00 0.00 5.19
930 994 1.144936 GAGACAATGAGGGAGGCCG 59.855 63.158 0.00 0.00 0.00 6.13
931 995 1.613630 AGACAATGAGGGAGGCCGT 60.614 57.895 0.00 0.00 0.00 5.68
932 996 1.450312 GACAATGAGGGAGGCCGTG 60.450 63.158 0.00 0.00 0.00 4.94
933 997 2.185310 GACAATGAGGGAGGCCGTGT 62.185 60.000 0.00 0.00 0.00 4.49
970 1036 0.040425 GTGCGGTACAAACCTTGCAG 60.040 55.000 0.00 0.00 41.15 4.41
975 1041 3.057806 GCGGTACAAACCTTGCAGTTTAT 60.058 43.478 3.97 0.00 44.35 1.40
976 1042 4.154556 GCGGTACAAACCTTGCAGTTTATA 59.845 41.667 3.97 0.00 44.35 0.98
991 1060 7.030768 TGCAGTTTATAAAATTTTACCGGAGC 58.969 34.615 9.46 12.55 0.00 4.70
1159 1263 1.604915 GAGGGGTGGCTTCTTCTCC 59.395 63.158 0.00 0.00 0.00 3.71
1160 1264 0.912006 GAGGGGTGGCTTCTTCTCCT 60.912 60.000 0.00 0.00 0.00 3.69
1161 1265 0.912006 AGGGGTGGCTTCTTCTCCTC 60.912 60.000 0.00 0.00 0.00 3.71
1261 1379 3.011517 CCCCTCCCTCCCACACAG 61.012 72.222 0.00 0.00 0.00 3.66
1276 1394 0.389166 CACAGACACGCTCTCTTCCC 60.389 60.000 0.00 0.00 0.00 3.97
1284 1402 1.414061 CGCTCTCTTCCCCCATCCAT 61.414 60.000 0.00 0.00 0.00 3.41
1290 1413 1.387347 TTCCCCCATCCATCCTCCC 60.387 63.158 0.00 0.00 0.00 4.30
1292 1415 1.849823 CCCCCATCCATCCTCCCTC 60.850 68.421 0.00 0.00 0.00 4.30
1303 1426 0.043334 TCCTCCCTCCTCCCAAAGAG 59.957 60.000 0.00 0.00 42.83 2.85
1310 1433 1.905215 CTCCTCCCAAAGAGAGCTTGA 59.095 52.381 0.00 0.00 46.50 3.02
1314 1437 1.421268 TCCCAAAGAGAGCTTGAGCAA 59.579 47.619 5.70 0.00 45.16 3.91
1317 1440 2.225963 CCAAAGAGAGCTTGAGCAACAG 59.774 50.000 5.70 0.00 45.16 3.16
1318 1441 1.521580 AAGAGAGCTTGAGCAACAGC 58.478 50.000 5.70 0.00 45.16 4.40
1319 1442 0.686224 AGAGAGCTTGAGCAACAGCT 59.314 50.000 5.70 3.40 45.16 4.24
1320 1443 1.072015 AGAGAGCTTGAGCAACAGCTT 59.928 47.619 5.70 0.00 45.16 3.74
1321 1444 1.197264 GAGAGCTTGAGCAACAGCTTG 59.803 52.381 5.70 0.00 45.16 4.01
1322 1445 0.240411 GAGCTTGAGCAACAGCTTGG 59.760 55.000 5.70 0.00 45.16 3.61
1323 1446 1.372623 GCTTGAGCAACAGCTTGGC 60.373 57.895 0.00 0.00 39.10 4.52
1324 1447 2.035421 CTTGAGCAACAGCTTGGCA 58.965 52.632 4.08 0.00 39.10 4.92
1325 1448 0.386476 CTTGAGCAACAGCTTGGCAA 59.614 50.000 0.00 0.00 39.10 4.52
1326 1449 0.102844 TTGAGCAACAGCTTGGCAAC 59.897 50.000 0.00 0.00 39.10 4.17
1327 1450 1.370900 GAGCAACAGCTTGGCAACG 60.371 57.895 0.00 0.00 39.10 4.10
1338 1461 4.947147 GGCAACGGTGGTGGCTCA 62.947 66.667 0.90 0.00 43.04 4.26
1395 1536 3.469006 TCAAGATCCAGGTATCCCTCTCT 59.531 47.826 0.00 0.00 39.89 3.10
1400 1541 0.390860 CAGGTATCCCTCTCTTGGCG 59.609 60.000 0.00 0.00 39.89 5.69
1408 1549 4.087892 TCTCTTGGCGCCCTCTGC 62.088 66.667 26.77 0.00 0.00 4.26
1436 1577 8.210946 TCTGTTTCTTTCCATCTTTCTCTGTAA 58.789 33.333 0.00 0.00 0.00 2.41
1464 1605 1.026718 GTGGATTTGTGGGGAGCTCG 61.027 60.000 7.83 0.00 0.00 5.03
1475 1622 0.603569 GGGAGCTCGACTGTTCTTGA 59.396 55.000 7.83 0.00 0.00 3.02
1476 1623 1.403514 GGGAGCTCGACTGTTCTTGAG 60.404 57.143 7.83 0.00 0.00 3.02
1477 1624 1.542030 GGAGCTCGACTGTTCTTGAGA 59.458 52.381 7.83 0.00 0.00 3.27
1483 1653 2.227626 TCGACTGTTCTTGAGAGAGCTG 59.772 50.000 0.00 0.00 37.82 4.24
1510 1680 3.117663 ACTGTTCTTGTTTCTTGGGGCTA 60.118 43.478 0.00 0.00 0.00 3.93
1522 1693 1.755783 GGGGCTATGCTTGCTTGCT 60.756 57.895 3.47 0.00 0.00 3.91
1523 1694 1.325476 GGGGCTATGCTTGCTTGCTT 61.325 55.000 3.47 0.24 0.00 3.91
1524 1695 0.101939 GGGCTATGCTTGCTTGCTTC 59.898 55.000 3.47 0.00 0.00 3.86
1525 1696 0.248377 GGCTATGCTTGCTTGCTTCG 60.248 55.000 3.47 0.00 0.00 3.79
1526 1697 0.864797 GCTATGCTTGCTTGCTTCGC 60.865 55.000 3.47 1.83 0.00 4.70
1527 1698 0.248377 CTATGCTTGCTTGCTTCGCC 60.248 55.000 3.47 0.00 0.00 5.54
1528 1699 0.677731 TATGCTTGCTTGCTTCGCCT 60.678 50.000 3.47 0.00 0.00 5.52
1529 1700 1.930908 ATGCTTGCTTGCTTCGCCTC 61.931 55.000 3.47 0.00 0.00 4.70
1530 1701 2.331132 GCTTGCTTGCTTCGCCTCT 61.331 57.895 0.00 0.00 0.00 3.69
1673 1858 3.125656 TCCAATCCAATCCTCCATGTCT 58.874 45.455 0.00 0.00 0.00 3.41
1686 1871 4.342092 CCTCCATGTCTTTTCTGTTGGTTT 59.658 41.667 0.00 0.00 0.00 3.27
1724 1916 1.182667 TTCTAGCGGTCTAAGCTGCA 58.817 50.000 1.02 0.00 45.60 4.41
1742 1934 0.322975 CAGGTGGTGCTACTTGCTCT 59.677 55.000 0.00 0.00 43.37 4.09
1758 1951 5.048713 ACTTGCTCTTGTTGTTGTTATAGCC 60.049 40.000 0.00 0.00 0.00 3.93
1767 1960 4.120946 TGTTGTTATAGCCCCCACTTTT 57.879 40.909 0.00 0.00 0.00 2.27
1799 1992 2.542178 CACACGCTTTGCTGTAACTGTA 59.458 45.455 0.00 0.00 0.00 2.74
1800 1993 3.001838 CACACGCTTTGCTGTAACTGTAA 59.998 43.478 0.00 0.00 0.00 2.41
1801 1994 3.247648 ACACGCTTTGCTGTAACTGTAAG 59.752 43.478 0.00 0.00 42.29 2.34
1818 2011 6.449635 CTGTAAGTATCTCTTCTGCTCTGT 57.550 41.667 0.00 0.00 37.56 3.41
1959 2156 4.863152 GCCATGCCAATTAAATGTTCAC 57.137 40.909 0.00 0.00 0.00 3.18
1973 2170 6.847956 AAATGTTCACACCAAATTGATGTG 57.152 33.333 14.11 14.11 43.26 3.21
1976 2173 4.889995 TGTTCACACCAAATTGATGTGGTA 59.110 37.500 19.38 6.40 46.61 3.25
2044 2246 6.177610 TGATAGTTGGTGAATAGGTCCAAAC 58.822 40.000 0.00 0.00 41.86 2.93
2045 2247 4.724279 AGTTGGTGAATAGGTCCAAACT 57.276 40.909 0.00 0.00 41.86 2.66
2046 2248 4.652822 AGTTGGTGAATAGGTCCAAACTC 58.347 43.478 0.00 0.00 41.86 3.01
2047 2249 4.104102 AGTTGGTGAATAGGTCCAAACTCA 59.896 41.667 0.00 0.00 41.86 3.41
2048 2250 4.015872 TGGTGAATAGGTCCAAACTCAC 57.984 45.455 0.00 0.00 33.92 3.51
2051 2253 2.027561 TGAATAGGTCCAAACTCACCCG 60.028 50.000 0.00 0.00 32.45 5.28
2054 2256 0.324943 AGGTCCAAACTCACCCGATG 59.675 55.000 0.00 0.00 32.45 3.84
2071 2276 3.366476 CCGATGTATGTAGTAGCTGAGGC 60.366 52.174 0.00 0.00 39.06 4.70
2074 2279 2.617308 TGTATGTAGTAGCTGAGGCGAC 59.383 50.000 0.00 0.00 44.37 5.19
2075 2280 1.033574 ATGTAGTAGCTGAGGCGACC 58.966 55.000 0.00 0.00 43.47 4.79
2104 2309 3.186909 CGAATCTCACAAACGGCTGATA 58.813 45.455 0.00 0.00 0.00 2.15
2121 2326 4.697352 GCTGATAAGGAAATGACACACACT 59.303 41.667 0.00 0.00 0.00 3.55
2135 2348 2.092807 CACACACTGGATGGATGGATGA 60.093 50.000 0.00 0.00 0.00 2.92
2137 2350 2.947652 CACACTGGATGGATGGATGAAC 59.052 50.000 0.00 0.00 0.00 3.18
2149 2366 1.743995 GATGAACGAACCCCACCCG 60.744 63.158 0.00 0.00 0.00 5.28
2201 2419 6.316140 TGTGATGGTTCATTAGTTATGAGCAC 59.684 38.462 8.03 6.36 43.89 4.40
2207 2425 8.755028 TGGTTCATTAGTTATGAGCACTAGTAA 58.245 33.333 8.03 0.00 43.89 2.24
2221 2439 9.582431 TGAGCACTAGTAATTTGTACAGTAATC 57.418 33.333 0.00 0.00 0.00 1.75
2256 2474 1.000283 CGAGCAACCTGTGAACTCTCT 60.000 52.381 0.00 0.00 0.00 3.10
2258 2476 1.346068 AGCAACCTGTGAACTCTCTCC 59.654 52.381 0.00 0.00 0.00 3.71
2267 2485 2.094234 GTGAACTCTCTCCCTCTGCTTC 60.094 54.545 0.00 0.00 0.00 3.86
2268 2486 2.225242 TGAACTCTCTCCCTCTGCTTCT 60.225 50.000 0.00 0.00 0.00 2.85
2272 2490 1.898472 TCTCTCCCTCTGCTTCTTGTG 59.102 52.381 0.00 0.00 0.00 3.33
2273 2491 1.622811 CTCTCCCTCTGCTTCTTGTGT 59.377 52.381 0.00 0.00 0.00 3.72
2274 2492 1.345741 TCTCCCTCTGCTTCTTGTGTG 59.654 52.381 0.00 0.00 0.00 3.82
2275 2493 1.071385 CTCCCTCTGCTTCTTGTGTGT 59.929 52.381 0.00 0.00 0.00 3.72
2276 2494 1.070758 TCCCTCTGCTTCTTGTGTGTC 59.929 52.381 0.00 0.00 0.00 3.67
2277 2495 1.143305 CCTCTGCTTCTTGTGTGTCG 58.857 55.000 0.00 0.00 0.00 4.35
2480 2716 2.916052 GCAGAAGCAGCAGCAGCAA 61.916 57.895 12.92 0.00 45.49 3.91
2483 2719 1.371389 GAAGCAGCAGCAGCAACAC 60.371 57.895 12.92 0.00 45.49 3.32
2561 2800 3.011517 GGGCAGAAGGAGCAGGGA 61.012 66.667 0.00 0.00 0.00 4.20
2570 2809 2.346541 GGAGCAGGGAAAGCTTGGC 61.347 63.158 0.00 0.00 43.58 4.52
2762 3004 0.034670 GGGACAAGATGAGCCAGCTT 60.035 55.000 0.00 0.58 40.92 3.74
2942 3184 1.114627 GGAATGCCAAGATGGGGAAC 58.885 55.000 0.00 0.00 38.19 3.62
2958 3200 1.945776 GAACGGCGCTCAGAAGAACG 61.946 60.000 6.90 0.55 36.47 3.95
3263 3514 2.040464 TCTCCCCAGATCAGCCCC 60.040 66.667 0.00 0.00 0.00 5.80
3466 3723 1.221840 GAGCTTGGGCGATGAGGAA 59.778 57.895 0.00 0.00 44.37 3.36
3468 3725 0.465097 AGCTTGGGCGATGAGGAATG 60.465 55.000 0.00 0.00 44.37 2.67
3474 3731 0.759346 GGCGATGAGGAATGGGTAGT 59.241 55.000 0.00 0.00 0.00 2.73
3502 3759 2.100749 TGGTGATGCAGTCGTACTATGG 59.899 50.000 0.00 0.00 0.00 2.74
3561 3818 7.870509 TTTCTCCTGTATCAAGAATGAATGG 57.129 36.000 0.00 0.00 39.49 3.16
3627 3907 3.088259 GTGGTGCCACTGTGTGTAA 57.912 52.632 13.68 0.00 43.12 2.41
3629 3909 1.953686 GTGGTGCCACTGTGTGTAATT 59.046 47.619 13.68 0.00 43.12 1.40
3631 3911 3.188460 GTGGTGCCACTGTGTGTAATTAG 59.812 47.826 13.68 0.00 43.12 1.73
3738 4020 3.576648 GTGCTGAGTAGTTGTCAGTACC 58.423 50.000 9.42 0.00 46.28 3.34
3743 4025 1.076024 AGTAGTTGTCAGTACCGGGGA 59.924 52.381 6.32 0.00 29.82 4.81
3756 4038 2.490148 CGGGGAGCTGTATCGCTGA 61.490 63.158 0.00 0.00 41.08 4.26
3757 4039 1.810606 CGGGGAGCTGTATCGCTGAT 61.811 60.000 0.00 0.00 41.08 2.90
3774 4058 4.009675 GCTGATAGAAATTGTCCCACACA 58.990 43.478 0.00 0.00 0.00 3.72
3775 4059 4.142600 GCTGATAGAAATTGTCCCACACAC 60.143 45.833 0.00 0.00 33.41 3.82
3776 4060 4.331968 TGATAGAAATTGTCCCACACACC 58.668 43.478 0.00 0.00 33.41 4.16
3777 4061 2.746279 AGAAATTGTCCCACACACCA 57.254 45.000 0.00 0.00 33.41 4.17
3778 4062 3.025322 AGAAATTGTCCCACACACCAA 57.975 42.857 0.00 0.00 33.41 3.67
3779 4063 2.693074 AGAAATTGTCCCACACACCAAC 59.307 45.455 0.00 0.00 33.41 3.77
3780 4064 2.151502 AATTGTCCCACACACCAACA 57.848 45.000 0.00 0.00 33.41 3.33
3781 4065 1.398692 ATTGTCCCACACACCAACAC 58.601 50.000 0.00 0.00 33.41 3.32
3782 4066 0.681564 TTGTCCCACACACCAACACC 60.682 55.000 0.00 0.00 33.41 4.16
3797 4081 3.198068 CAACACCGTCCTAAGGATGATG 58.802 50.000 0.00 0.00 40.94 3.07
3827 4111 2.057830 ACATGAGTGAAGCCGGTGA 58.942 52.632 1.90 0.00 0.00 4.02
3828 4112 0.036952 ACATGAGTGAAGCCGGTGAG 60.037 55.000 1.90 0.00 0.00 3.51
3829 4113 1.078848 ATGAGTGAAGCCGGTGAGC 60.079 57.895 1.90 0.00 0.00 4.26
3831 4115 1.739562 GAGTGAAGCCGGTGAGCTG 60.740 63.158 1.90 0.00 44.11 4.24
3832 4116 2.031163 GTGAAGCCGGTGAGCTGT 59.969 61.111 1.90 0.00 44.11 4.40
3833 4117 2.031012 TGAAGCCGGTGAGCTGTG 59.969 61.111 1.90 0.00 44.11 3.66
3848 4132 0.733150 CTGTGAGCATGCCATGTGAG 59.267 55.000 15.66 0.00 0.00 3.51
3853 4137 0.748367 AGCATGCCATGTGAGCAGAG 60.748 55.000 15.66 0.00 44.90 3.35
3874 4167 8.066595 GCAGAGAATAAACATTAGCATGTACTG 58.933 37.037 0.00 0.00 43.34 2.74
3900 4193 5.615925 AATTAAGTACAGGCTACAGAGGG 57.384 43.478 0.00 0.00 0.00 4.30
4093 4403 1.838077 ACGATTTGTAAGGGAGGAGGG 59.162 52.381 0.00 0.00 0.00 4.30
4094 4404 2.116238 CGATTTGTAAGGGAGGAGGGA 58.884 52.381 0.00 0.00 0.00 4.20
4095 4405 2.158943 CGATTTGTAAGGGAGGAGGGAC 60.159 54.545 0.00 0.00 0.00 4.46
4117 4428 1.551883 CCATTGGGGGCTTCAGAAAAG 59.448 52.381 0.00 0.00 0.00 2.27
4157 4468 2.102925 CCAAAGGCGGCCAATTATGATT 59.897 45.455 23.09 0.31 0.00 2.57
4224 4539 6.299023 TGAATGCGGACATGATTGTAATAC 57.701 37.500 0.00 0.00 36.36 1.89
4241 4556 1.117150 TACGTAGCCCCCTTCATGAC 58.883 55.000 0.00 0.00 0.00 3.06
4299 4615 5.003804 TCCTCAAAGATTTTGCCAGACTAC 58.996 41.667 0.00 0.00 0.00 2.73
4301 4617 5.335191 CCTCAAAGATTTTGCCAGACTACAC 60.335 44.000 0.00 0.00 0.00 2.90
4410 4727 6.974622 AGTGTTATCTGTTTTTCAAGCAGTTG 59.025 34.615 0.97 0.00 34.67 3.16
4413 4730 2.159114 TCTGTTTTTCAAGCAGTTGGCC 60.159 45.455 0.00 0.00 46.50 5.36
4433 4751 3.734902 GCCAACTGTGTCCTTTTGAAGTG 60.735 47.826 0.00 0.00 0.00 3.16
4507 4825 3.057245 GGAAAGGAAATTGCTCTGTGGAC 60.057 47.826 0.00 0.00 0.00 4.02
4608 4927 0.887387 GCGAACACCCCTAACAGCAA 60.887 55.000 0.00 0.00 0.00 3.91
4627 4946 2.254546 AAGATGGTCAACTCAACGCA 57.745 45.000 0.00 0.00 0.00 5.24
4637 4956 3.005554 CAACTCAACGCAAGATCCAGAT 58.994 45.455 0.00 0.00 43.62 2.90
4641 4960 0.749454 AACGCAAGATCCAGATGGGC 60.749 55.000 0.00 0.00 43.62 5.36
4644 4963 1.453762 GCAAGATCCAGATGGGCAGC 61.454 60.000 0.00 0.00 36.21 5.25
4648 4967 2.276391 AGATCCAGATGGGCAGCATAT 58.724 47.619 0.00 0.00 36.21 1.78
4649 4968 2.026169 AGATCCAGATGGGCAGCATATG 60.026 50.000 0.00 0.00 36.21 1.78
4650 4969 1.142936 TCCAGATGGGCAGCATATGT 58.857 50.000 4.29 0.00 36.21 2.29
4694 5020 1.098050 CTGCAGGGGAAGAAATTCCG 58.902 55.000 5.57 0.00 42.02 4.30
4721 5047 4.164822 CACAGTTGGTGCAAGGATAAAG 57.835 45.455 0.00 0.00 41.36 1.85
4733 5063 4.453819 GCAAGGATAAAGCCTAGCATAGTG 59.546 45.833 0.00 0.00 37.26 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
150 154 1.279271 AGGGTGCTGAGTCCAACATAC 59.721 52.381 0.00 0.00 0.00 2.39
374 379 8.144478 AGTAATAATGTGCAGTTATCATCGTCT 58.856 33.333 5.10 0.00 0.00 4.18
377 382 7.513132 CCAGTAATAATGTGCAGTTATCATCG 58.487 38.462 5.10 0.00 0.00 3.84
438 444 2.270986 GCTTGAGGCAGGGTTGGTG 61.271 63.158 0.00 0.00 41.35 4.17
493 499 2.825532 GGTTGAGTAGGGTACGGTGTTA 59.174 50.000 0.00 0.00 0.00 2.41
496 502 1.259609 TGGTTGAGTAGGGTACGGTG 58.740 55.000 0.00 0.00 0.00 4.94
513 519 2.403378 CCGGCCGTGTACCAATTGG 61.403 63.158 26.12 23.31 42.17 3.16
617 635 5.591067 AGAGTACAATAGTGGTAGCTGACTC 59.409 44.000 0.00 0.00 0.00 3.36
652 670 1.624479 TACGTGGGTGTGTGGGTTGT 61.624 55.000 0.00 0.00 0.00 3.32
655 673 2.823829 GTACGTGGGTGTGTGGGT 59.176 61.111 0.00 0.00 0.00 4.51
656 674 2.356553 CGTACGTGGGTGTGTGGG 60.357 66.667 7.22 0.00 0.00 4.61
657 675 2.356553 CCGTACGTGGGTGTGTGG 60.357 66.667 15.21 0.00 0.00 4.17
675 696 0.928229 CGGTCCAGCGCACTAATAAC 59.072 55.000 11.47 0.00 0.00 1.89
676 697 0.533491 ACGGTCCAGCGCACTAATAA 59.467 50.000 11.47 0.00 0.00 1.40
677 698 0.179121 CACGGTCCAGCGCACTAATA 60.179 55.000 11.47 0.00 0.00 0.98
678 699 1.447838 CACGGTCCAGCGCACTAAT 60.448 57.895 11.47 0.00 0.00 1.73
680 701 4.063967 CCACGGTCCAGCGCACTA 62.064 66.667 11.47 0.00 0.00 2.74
703 729 7.453126 AGGGTTGTACCATGATAAAATTGTGAA 59.547 33.333 0.00 0.00 41.02 3.18
776 808 4.382541 TCTGGAGAGGCTGGCCGA 62.383 66.667 5.93 0.00 41.95 5.54
907 971 1.065854 CCTCCCTCATTGTCTCACACC 60.066 57.143 0.00 0.00 0.00 4.16
924 988 2.025418 CACGGTTACACACGGCCTC 61.025 63.158 0.00 0.00 0.00 4.70
925 989 2.029964 CACGGTTACACACGGCCT 59.970 61.111 0.00 0.00 0.00 5.19
927 991 2.322081 ATGCACGGTTACACACGGC 61.322 57.895 0.00 0.00 0.00 5.68
929 993 1.125384 GTACATGCACGGTTACACACG 59.875 52.381 0.00 0.00 0.00 4.49
930 994 1.461897 GGTACATGCACGGTTACACAC 59.538 52.381 0.00 0.00 0.00 3.82
931 995 1.798283 GGTACATGCACGGTTACACA 58.202 50.000 0.00 0.00 0.00 3.72
932 996 0.717224 CGGTACATGCACGGTTACAC 59.283 55.000 0.00 0.00 0.00 2.90
933 997 0.317799 ACGGTACATGCACGGTTACA 59.682 50.000 3.55 0.00 0.00 2.41
1159 1263 1.457455 GCAGGAGGAGGAGGAGGAG 60.457 68.421 0.00 0.00 0.00 3.69
1160 1264 1.815384 TTGCAGGAGGAGGAGGAGGA 61.815 60.000 0.00 0.00 0.00 3.71
1161 1265 1.306482 TTGCAGGAGGAGGAGGAGG 60.306 63.158 0.00 0.00 0.00 4.30
1209 1313 3.134127 GTGGGGAAGTGATGGCGC 61.134 66.667 0.00 0.00 0.00 6.53
1211 1315 1.077429 GGAGTGGGGAAGTGATGGC 60.077 63.158 0.00 0.00 0.00 4.40
1261 1379 1.617947 ATGGGGGAAGAGAGCGTGTC 61.618 60.000 0.00 0.00 0.00 3.67
1276 1394 0.839853 GAGGAGGGAGGATGGATGGG 60.840 65.000 0.00 0.00 0.00 4.00
1284 1402 0.043334 CTCTTTGGGAGGAGGGAGGA 59.957 60.000 0.00 0.00 38.35 3.71
1290 1413 1.905215 TCAAGCTCTCTTTGGGAGGAG 59.095 52.381 0.00 0.00 42.10 3.69
1292 1415 1.678425 GCTCAAGCTCTCTTTGGGAGG 60.678 57.143 0.00 0.00 42.10 4.30
1314 1437 2.906897 CCACCGTTGCCAAGCTGT 60.907 61.111 0.00 0.00 0.00 4.40
1317 1440 3.977244 CCACCACCGTTGCCAAGC 61.977 66.667 0.00 0.00 0.00 4.01
1318 1441 3.977244 GCCACCACCGTTGCCAAG 61.977 66.667 0.00 0.00 0.00 3.61
1319 1442 4.514585 AGCCACCACCGTTGCCAA 62.515 61.111 0.00 0.00 30.94 4.52
1320 1443 4.947147 GAGCCACCACCGTTGCCA 62.947 66.667 0.00 0.00 30.94 4.92
1321 1444 4.947147 TGAGCCACCACCGTTGCC 62.947 66.667 0.00 0.00 30.94 4.52
1322 1445 3.357079 CTGAGCCACCACCGTTGC 61.357 66.667 0.00 0.00 0.00 4.17
1323 1446 3.357079 GCTGAGCCACCACCGTTG 61.357 66.667 0.00 0.00 0.00 4.10
1324 1447 3.832237 CTGCTGAGCCACCACCGTT 62.832 63.158 0.23 0.00 0.00 4.44
1325 1448 4.320456 CTGCTGAGCCACCACCGT 62.320 66.667 0.23 0.00 0.00 4.83
1326 1449 3.947132 CTCTGCTGAGCCACCACCG 62.947 68.421 7.75 0.00 33.12 4.94
1327 1450 1.908340 ATCTCTGCTGAGCCACCACC 61.908 60.000 15.31 0.00 40.03 4.61
1338 1461 3.118334 CCTCATCTTTGGTCATCTCTGCT 60.118 47.826 0.00 0.00 0.00 4.24
1400 1541 1.902938 AAGAAACAGAAGCAGAGGGC 58.097 50.000 0.00 0.00 45.30 5.19
1408 1549 7.228308 ACAGAGAAAGATGGAAAGAAACAGAAG 59.772 37.037 0.00 0.00 0.00 2.85
1436 1577 1.962807 CCACAAATCCACACACCACAT 59.037 47.619 0.00 0.00 0.00 3.21
1464 1605 3.932545 TCAGCTCTCTCAAGAACAGTC 57.067 47.619 0.00 0.00 0.00 3.51
1475 1622 6.107901 ACAAGAACAGTTTATCAGCTCTCT 57.892 37.500 0.00 0.00 0.00 3.10
1476 1623 6.793492 AACAAGAACAGTTTATCAGCTCTC 57.207 37.500 0.00 0.00 0.00 3.20
1477 1624 6.995091 AGAAACAAGAACAGTTTATCAGCTCT 59.005 34.615 0.00 0.00 39.15 4.09
1483 1653 6.447162 CCCCAAGAAACAAGAACAGTTTATC 58.553 40.000 0.00 0.00 39.15 1.75
1522 1693 1.293498 GTCTGCAGGAAGAGGCGAA 59.707 57.895 15.13 0.00 0.00 4.70
1523 1694 2.650116 GGTCTGCAGGAAGAGGCGA 61.650 63.158 15.13 0.00 0.00 5.54
1524 1695 2.125350 GGTCTGCAGGAAGAGGCG 60.125 66.667 15.13 0.00 0.00 5.52
1525 1696 1.919600 ATGGGTCTGCAGGAAGAGGC 61.920 60.000 15.13 0.00 0.00 4.70
1526 1697 0.107312 CATGGGTCTGCAGGAAGAGG 60.107 60.000 15.13 0.00 0.00 3.69
1527 1698 0.617413 ACATGGGTCTGCAGGAAGAG 59.383 55.000 15.13 2.73 0.00 2.85
1528 1699 0.615331 GACATGGGTCTGCAGGAAGA 59.385 55.000 15.13 0.00 40.99 2.87
1529 1700 0.393537 GGACATGGGTCTGCAGGAAG 60.394 60.000 15.13 1.06 43.77 3.46
1530 1701 0.842030 AGGACATGGGTCTGCAGGAA 60.842 55.000 15.13 0.00 43.77 3.36
1673 1858 5.167845 GTGCAAGAAGAAACCAACAGAAAA 58.832 37.500 0.00 0.00 0.00 2.29
1686 1871 0.961857 ATGGCGCATGTGCAAGAAGA 60.962 50.000 30.73 8.85 42.21 2.87
1742 1934 3.158676 GTGGGGGCTATAACAACAACAA 58.841 45.455 0.00 0.00 0.00 2.83
1767 1960 3.730662 GCAAAGCGTGTGTCAAGAGAAAA 60.731 43.478 0.00 0.00 0.00 2.29
1771 1964 0.940126 AGCAAAGCGTGTGTCAAGAG 59.060 50.000 0.00 0.00 0.00 2.85
1773 1966 0.378257 ACAGCAAAGCGTGTGTCAAG 59.622 50.000 0.00 0.00 0.00 3.02
1779 1972 1.663695 ACAGTTACAGCAAAGCGTGT 58.336 45.000 0.00 0.00 0.00 4.49
1801 1994 9.255304 CCTTTATTAACAGAGCAGAAGAGATAC 57.745 37.037 0.00 0.00 0.00 2.24
1802 1995 7.928706 GCCTTTATTAACAGAGCAGAAGAGATA 59.071 37.037 0.00 0.00 0.00 1.98
1803 1996 6.765512 GCCTTTATTAACAGAGCAGAAGAGAT 59.234 38.462 0.00 0.00 0.00 2.75
1804 1997 6.109359 GCCTTTATTAACAGAGCAGAAGAGA 58.891 40.000 0.00 0.00 0.00 3.10
1805 1998 5.295540 GGCCTTTATTAACAGAGCAGAAGAG 59.704 44.000 0.00 0.00 0.00 2.85
1806 1999 5.045578 AGGCCTTTATTAACAGAGCAGAAGA 60.046 40.000 0.00 0.00 0.00 2.87
1807 2000 5.065731 CAGGCCTTTATTAACAGAGCAGAAG 59.934 44.000 0.00 0.00 0.00 2.85
1808 2001 4.943705 CAGGCCTTTATTAACAGAGCAGAA 59.056 41.667 0.00 0.00 0.00 3.02
1809 2002 4.225042 TCAGGCCTTTATTAACAGAGCAGA 59.775 41.667 0.00 0.00 0.00 4.26
1810 2003 4.517285 TCAGGCCTTTATTAACAGAGCAG 58.483 43.478 0.00 0.00 0.00 4.24
1811 2004 4.568072 TCAGGCCTTTATTAACAGAGCA 57.432 40.909 0.00 0.00 0.00 4.26
1812 2005 4.201960 GCTTCAGGCCTTTATTAACAGAGC 60.202 45.833 0.00 0.00 34.27 4.09
1813 2006 5.189180 AGCTTCAGGCCTTTATTAACAGAG 58.811 41.667 0.00 0.00 43.05 3.35
1814 2007 5.179452 AGCTTCAGGCCTTTATTAACAGA 57.821 39.130 0.00 0.00 43.05 3.41
1815 2008 5.904362 AAGCTTCAGGCCTTTATTAACAG 57.096 39.130 0.00 0.00 43.05 3.16
1816 2009 5.566627 GCAAAGCTTCAGGCCTTTATTAACA 60.567 40.000 0.00 0.00 43.05 2.41
1817 2010 4.864806 GCAAAGCTTCAGGCCTTTATTAAC 59.135 41.667 0.00 0.00 43.05 2.01
1818 2011 4.772100 AGCAAAGCTTCAGGCCTTTATTAA 59.228 37.500 0.00 0.00 43.05 1.40
1866 2059 3.365265 CGTGGGGGTGCTTTCAGC 61.365 66.667 0.00 0.00 42.82 4.26
1945 2140 9.814507 CATCAATTTGGTGTGAACATTTAATTG 57.185 29.630 1.28 14.43 34.52 2.32
1959 2156 9.787532 CTTTACTTATACCACATCAATTTGGTG 57.212 33.333 8.12 8.12 46.03 4.17
2044 2246 3.821600 AGCTACTACATACATCGGGTGAG 59.178 47.826 0.00 0.00 0.00 3.51
2045 2247 3.568430 CAGCTACTACATACATCGGGTGA 59.432 47.826 0.00 0.00 0.00 4.02
2046 2248 3.568430 TCAGCTACTACATACATCGGGTG 59.432 47.826 0.00 0.00 0.00 4.61
2047 2249 3.821600 CTCAGCTACTACATACATCGGGT 59.178 47.826 0.00 0.00 0.00 5.28
2048 2250 3.191581 CCTCAGCTACTACATACATCGGG 59.808 52.174 0.00 0.00 0.00 5.14
2051 2253 3.502595 TCGCCTCAGCTACTACATACATC 59.497 47.826 0.00 0.00 36.60 3.06
2054 2256 2.030981 GGTCGCCTCAGCTACTACATAC 60.031 54.545 0.00 0.00 35.13 2.39
2071 2276 3.554692 GATTCGGCACAGCGGTCG 61.555 66.667 0.00 0.00 0.00 4.79
2074 2279 2.125552 TGAGATTCGGCACAGCGG 60.126 61.111 0.00 0.00 0.00 5.52
2075 2280 1.291184 TTGTGAGATTCGGCACAGCG 61.291 55.000 12.78 0.00 44.80 5.18
2104 2309 3.576078 TCCAGTGTGTGTCATTTCCTT 57.424 42.857 0.00 0.00 0.00 3.36
2121 2326 2.421388 GGTTCGTTCATCCATCCATCCA 60.421 50.000 0.00 0.00 0.00 3.41
2135 2348 3.944945 GTCCGGGTGGGGTTCGTT 61.945 66.667 0.00 0.00 36.01 3.85
2137 2350 4.078516 GAGTCCGGGTGGGGTTCG 62.079 72.222 0.00 0.00 36.01 3.95
2149 2366 2.143925 GTAGGTTTGTGCAGTGAGTCC 58.856 52.381 0.00 0.00 0.00 3.85
2207 2425 7.834181 AGCCATGGTAAAGATTACTGTACAAAT 59.166 33.333 14.67 0.00 38.28 2.32
2256 2474 1.070758 GACACACAAGAAGCAGAGGGA 59.929 52.381 0.00 0.00 0.00 4.20
2258 2476 1.143305 CGACACACAAGAAGCAGAGG 58.857 55.000 0.00 0.00 0.00 3.69
2267 2485 1.009675 GCCTGCAACGACACACAAG 60.010 57.895 0.00 0.00 0.00 3.16
2268 2486 2.818487 CGCCTGCAACGACACACAA 61.818 57.895 2.74 0.00 0.00 3.33
2272 2490 1.372499 TAGACGCCTGCAACGACAC 60.372 57.895 15.03 6.56 0.00 3.67
2273 2491 1.372499 GTAGACGCCTGCAACGACA 60.372 57.895 15.03 0.00 0.00 4.35
2274 2492 1.071567 GAGTAGACGCCTGCAACGAC 61.072 60.000 15.03 9.15 0.00 4.34
2275 2493 1.211969 GAGTAGACGCCTGCAACGA 59.788 57.895 15.03 0.00 0.00 3.85
2276 2494 2.152699 CGAGTAGACGCCTGCAACG 61.153 63.158 7.21 7.21 0.00 4.10
2277 2495 1.805945 CCGAGTAGACGCCTGCAAC 60.806 63.158 0.00 0.00 0.00 4.17
2348 2566 0.529555 GCTTCCTGATGAGCGTCTCC 60.530 60.000 4.73 0.00 0.00 3.71
2361 2579 1.614824 CCCCTCTGGTGAGCTTCCT 60.615 63.158 9.68 0.00 38.93 3.36
2418 2636 1.326213 TTGTGGCCCTGGTTGTTGTG 61.326 55.000 0.00 0.00 0.00 3.33
2480 2716 1.600076 CTTCTGCTGCTGCTGGTGT 60.600 57.895 19.63 0.00 40.48 4.16
2483 2719 2.671963 TGCTTCTGCTGCTGCTGG 60.672 61.111 19.63 11.50 40.48 4.85
2561 2800 4.643387 ACTCCGCCGCCAAGCTTT 62.643 61.111 0.00 0.00 0.00 3.51
2579 2821 4.559063 CCCTGCATGAGGCTCCCG 62.559 72.222 12.86 3.84 45.15 5.14
2663 2905 9.209048 TCATCCTCATCATCATACATATCATCA 57.791 33.333 0.00 0.00 0.00 3.07
2762 3004 4.478371 CGCTGCCTGAGGATGCCA 62.478 66.667 0.65 0.00 0.00 4.92
2871 3113 1.881973 CTGGTTGTTCTGATGGTGGTG 59.118 52.381 0.00 0.00 0.00 4.17
3263 3514 1.135721 GGGTTGTAGTAGGCGGTGTAG 59.864 57.143 0.00 0.00 0.00 2.74
3466 3723 2.274542 TCACCATTCACCACTACCCAT 58.725 47.619 0.00 0.00 0.00 4.00
3468 3725 2.643551 CATCACCATTCACCACTACCC 58.356 52.381 0.00 0.00 0.00 3.69
3474 3731 1.825090 GACTGCATCACCATTCACCA 58.175 50.000 0.00 0.00 0.00 4.17
3509 3766 6.884295 ACATAAAGGCAGCAAAATACTAGTGA 59.116 34.615 5.39 0.00 0.00 3.41
3561 3818 2.094675 CCCAAGTCAACACCCATGATC 58.905 52.381 0.00 0.00 0.00 2.92
3627 3907 8.320338 AGGCAGTCAAAGGTAATACTACTAAT 57.680 34.615 0.00 0.00 0.00 1.73
3629 3909 7.179694 ACAAGGCAGTCAAAGGTAATACTACTA 59.820 37.037 0.00 0.00 0.00 1.82
3631 3911 6.092259 CACAAGGCAGTCAAAGGTAATACTAC 59.908 42.308 0.00 0.00 0.00 2.73
3756 4038 4.380843 TGGTGTGTGGGACAATTTCTAT 57.619 40.909 0.00 0.00 44.16 1.98
3757 4039 3.866703 TGGTGTGTGGGACAATTTCTA 57.133 42.857 0.00 0.00 44.16 2.10
3774 4058 1.278127 CATCCTTAGGACGGTGTTGGT 59.722 52.381 1.74 0.00 32.98 3.67
3775 4059 1.553248 TCATCCTTAGGACGGTGTTGG 59.447 52.381 1.74 0.00 32.98 3.77
3776 4060 3.118775 TCATCATCCTTAGGACGGTGTTG 60.119 47.826 7.50 6.33 32.98 3.33
3777 4061 3.104512 TCATCATCCTTAGGACGGTGTT 58.895 45.455 7.50 0.00 32.98 3.32
3778 4062 2.747177 TCATCATCCTTAGGACGGTGT 58.253 47.619 7.50 0.00 32.98 4.16
3779 4063 3.321968 TGATCATCATCCTTAGGACGGTG 59.678 47.826 1.74 1.05 32.98 4.94
3780 4064 3.576861 TGATCATCATCCTTAGGACGGT 58.423 45.455 1.74 0.00 32.98 4.83
3781 4065 4.753233 GATGATCATCATCCTTAGGACGG 58.247 47.826 27.30 0.00 45.66 4.79
3797 4081 3.473625 TCACTCATGTGCCATGATGATC 58.526 45.455 15.42 0.00 43.49 2.92
3827 4111 1.001269 ACATGGCATGCTCACAGCT 60.001 52.632 26.70 2.08 42.97 4.24
3828 4112 1.138883 CACATGGCATGCTCACAGC 59.861 57.895 26.70 0.00 42.82 4.40
3829 4113 0.733150 CTCACATGGCATGCTCACAG 59.267 55.000 26.70 11.54 0.00 3.66
3830 4114 1.310216 GCTCACATGGCATGCTCACA 61.310 55.000 26.70 7.69 0.00 3.58
3831 4115 1.310216 TGCTCACATGGCATGCTCAC 61.310 55.000 26.70 14.61 34.56 3.51
3832 4116 1.001887 TGCTCACATGGCATGCTCA 60.002 52.632 26.70 14.25 34.56 4.26
3833 4117 0.746923 TCTGCTCACATGGCATGCTC 60.747 55.000 26.70 13.44 39.07 4.26
3848 4132 8.066595 CAGTACATGCTAATGTTTATTCTCTGC 58.933 37.037 0.00 0.00 44.94 4.26
3874 4167 6.985059 CCTCTGTAGCCTGTACTTAATTTACC 59.015 42.308 0.00 0.00 0.00 2.85
3900 4193 2.675032 GCTTAAAATTGCCCAGTCCAGC 60.675 50.000 0.00 0.00 0.00 4.85
3924 4218 3.433274 TGGTACTATAAGATACGGCGTCG 59.567 47.826 19.21 8.42 43.02 5.12
3960 4255 2.282462 CACCCAGAACACTGCCCC 60.282 66.667 0.00 0.00 0.00 5.80
4093 4403 0.394899 CTGAAGCCCCCAATGGAGTC 60.395 60.000 0.00 0.00 35.39 3.36
4094 4404 0.846427 TCTGAAGCCCCCAATGGAGT 60.846 55.000 0.00 0.00 35.39 3.85
4095 4405 0.332632 TTCTGAAGCCCCCAATGGAG 59.667 55.000 0.00 0.00 35.39 3.86
4096 4406 0.783206 TTTCTGAAGCCCCCAATGGA 59.217 50.000 0.00 0.00 35.39 3.41
4098 4408 1.551883 CCTTTTCTGAAGCCCCCAATG 59.448 52.381 0.00 0.00 0.00 2.82
4099 4409 1.942776 CCTTTTCTGAAGCCCCCAAT 58.057 50.000 0.00 0.00 0.00 3.16
4101 4411 1.228862 GCCTTTTCTGAAGCCCCCA 60.229 57.895 0.00 0.00 0.00 4.96
4102 4412 1.077445 AGCCTTTTCTGAAGCCCCC 59.923 57.895 0.00 0.00 0.00 5.40
4180 4495 4.714308 TCATTTTCAACCACCTTTTCCAGT 59.286 37.500 0.00 0.00 0.00 4.00
4224 4539 1.146263 GGTCATGAAGGGGGCTACG 59.854 63.158 0.00 0.00 0.00 3.51
4259 4574 9.305555 TCTTTGAGGAGATCAGAATTCATTTTT 57.694 29.630 8.44 0.00 39.68 1.94
4299 4615 3.627577 GCCATTATGAACCCTGTACTGTG 59.372 47.826 0.00 0.00 0.00 3.66
4301 4617 3.214328 GGCCATTATGAACCCTGTACTG 58.786 50.000 0.00 0.00 0.00 2.74
4413 4730 3.443681 ACCACTTCAAAAGGACACAGTTG 59.556 43.478 0.00 0.00 0.00 3.16
4423 4741 3.546020 CGTACTGTGCACCACTTCAAAAG 60.546 47.826 15.69 3.83 35.11 2.27
4433 4751 0.878523 TCAACTGCGTACTGTGCACC 60.879 55.000 15.69 0.00 37.44 5.01
4507 4825 7.042187 CCAGAGATCGAGGAATAAACAAATCTG 60.042 40.741 0.00 0.00 0.00 2.90
4519 4837 4.081642 CAGTTTAACCCAGAGATCGAGGAA 60.082 45.833 0.00 0.00 0.00 3.36
4608 4927 2.254546 TGCGTTGAGTTGACCATCTT 57.745 45.000 0.00 0.00 0.00 2.40
4627 4946 0.851469 ATGCTGCCCATCTGGATCTT 59.149 50.000 0.00 0.00 37.39 2.40
4637 4956 4.022603 ACAATTTGTACATATGCTGCCCA 58.977 39.130 1.58 0.00 0.00 5.36
4641 4960 6.252015 GCACTTGACAATTTGTACATATGCTG 59.748 38.462 1.58 0.00 0.00 4.41
4644 4963 7.529158 TCTGCACTTGACAATTTGTACATATG 58.471 34.615 1.15 0.00 0.00 1.78
4648 4967 4.261155 GCTCTGCACTTGACAATTTGTACA 60.261 41.667 1.15 0.00 0.00 2.90
4649 4968 4.023707 AGCTCTGCACTTGACAATTTGTAC 60.024 41.667 1.15 0.00 0.00 2.90
4650 4969 4.136796 AGCTCTGCACTTGACAATTTGTA 58.863 39.130 1.15 0.00 0.00 2.41
4721 5047 3.821421 ACAGTTACCACTATGCTAGGC 57.179 47.619 0.00 0.00 0.00 3.93


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

AutoCloner maintained by Alex Coulton.