Multiple sequence alignment - TraesCS3D01G107000

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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 TraesCS3D01G107000 chr3D 100.000 8469 0 0 1 8469 59282042 59290510 0.000000e+00 15640.0
1 TraesCS3D01G107000 chr3D 91.071 224 20 0 2437 2660 59284406 59284629 3.840000e-78 303.0
2 TraesCS3D01G107000 chr3D 91.071 224 20 0 2365 2588 59284478 59284701 3.840000e-78 303.0
3 TraesCS3D01G107000 chr3D 90.845 142 13 0 2519 2660 59284416 59284557 3.120000e-44 191.0
4 TraesCS3D01G107000 chr3D 92.647 68 4 1 5397 5464 71517744 71517678 7.000000e-16 97.1
5 TraesCS3D01G107000 chr3D 92.647 68 3 2 5397 5463 426451925 426451859 7.000000e-16 97.1
6 TraesCS3D01G107000 chr3B 90.832 3872 191 79 1 3745 95143899 95147733 0.000000e+00 5033.0
7 TraesCS3D01G107000 chr3B 94.056 2978 128 27 5506 8469 95149631 95152573 0.000000e+00 4473.0
8 TraesCS3D01G107000 chr3B 96.193 1760 64 2 3756 5512 95147716 95149475 0.000000e+00 2876.0
9 TraesCS3D01G107000 chr3B 91.964 224 18 0 2437 2660 95146343 95146566 1.770000e-81 315.0
10 TraesCS3D01G107000 chr3B 89.732 224 23 0 2365 2588 95146415 95146638 3.870000e-73 287.0
11 TraesCS3D01G107000 chr3B 91.549 142 12 0 2519 2660 95146353 95146494 6.710000e-46 196.0
12 TraesCS3D01G107000 chr3B 92.647 68 3 2 5397 5463 42630884 42630818 7.000000e-16 97.1
13 TraesCS3D01G107000 chr3A 95.353 3163 128 8 2365 5514 68276579 68279735 0.000000e+00 5009.0
14 TraesCS3D01G107000 chr3A 93.168 2737 121 37 5515 8225 68279897 68282593 0.000000e+00 3958.0
15 TraesCS3D01G107000 chr3A 87.875 1468 115 28 823 2270 68274904 68276328 0.000000e+00 1666.0
16 TraesCS3D01G107000 chr3A 92.453 477 36 0 2184 2660 68276326 68276802 0.000000e+00 682.0
17 TraesCS3D01G107000 chr3A 84.245 603 25 22 1 560 68274019 68274594 2.710000e-144 523.0
18 TraesCS3D01G107000 chr3A 87.539 321 22 8 8167 8469 68282619 68282939 1.050000e-93 355.0
19 TraesCS3D01G107000 chr3A 92.093 215 17 0 2374 2588 68276660 68276874 3.840000e-78 303.0
20 TraesCS3D01G107000 chr3A 90.367 218 21 0 2437 2654 68276507 68276724 3.870000e-73 287.0
21 TraesCS3D01G107000 chr3A 92.647 68 3 2 5397 5463 34532515 34532449 7.000000e-16 97.1
22 TraesCS3D01G107000 chr3A 88.235 51 2 3 5800 5846 642911571 642911621 3.300000e-04 58.4
23 TraesCS3D01G107000 chr5D 93.056 72 3 2 5397 5467 241947540 241947610 4.180000e-18 104.0
24 TraesCS3D01G107000 chr5D 92.958 71 3 2 5397 5466 294634422 294634491 1.500000e-17 102.0
25 TraesCS3D01G107000 chr5A 91.667 72 4 2 5397 5467 311937071 311937141 1.950000e-16 99.0
26 TraesCS3D01G107000 chr7D 90.698 43 3 1 5803 5845 154395980 154395939 1.000000e-03 56.5
27 TraesCS3D01G107000 chr2D 92.105 38 3 0 5654 5691 32067725 32067688 4.000000e-03 54.7


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 TraesCS3D01G107000 chr3D 59282042 59290510 8468 False 15640.000000 15640 100.000000 1 8469 1 chr3D.!!$F1 8468
1 TraesCS3D01G107000 chr3B 95143899 95152573 8674 False 2196.666667 5033 92.387667 1 8469 6 chr3B.!!$F1 8468
2 TraesCS3D01G107000 chr3A 68274019 68282939 8920 False 1597.875000 5009 90.386625 1 8469 8 chr3A.!!$F2 8468

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
493 527 0.036010 ACCAGGCCAAAGATCACGAG 60.036 55.0 5.01 0.00 0.00 4.18 F
1044 1228 0.108898 TGCTGCTTCTCGCTTCTCTC 60.109 55.0 0.00 0.00 40.11 3.20 F
1873 2071 0.179100 CGCCTGTCGATCAAGGACAT 60.179 55.0 14.09 0.00 42.97 3.06 F
2247 2529 0.549469 ACCTCCTCCGGTTGTGTTTT 59.451 50.0 0.00 0.00 31.94 2.43 F
2394 2676 0.689623 ACCTTCAGTTCAGGCTCCTG 59.310 55.0 9.61 9.61 44.86 3.86 F
3503 3867 0.782384 CCAACGAAAGGAGAACGTCG 59.218 55.0 0.00 0.00 39.31 5.12 F
4229 4620 0.032017 AGCCTCTAACGGATCCACCT 60.032 55.0 13.41 0.00 36.31 4.00 F
6026 6585 0.107508 ACCTCATGATTGCAGGGACG 60.108 55.0 0.00 0.00 0.00 4.79 F
6789 7348 0.323957 TCTCCTCCTCAACGTCTCGA 59.676 55.0 0.00 0.00 0.00 4.04 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1389 1573 0.036010 AAGGAGCACATGCGCTTAGT 60.036 50.000 10.05 0.83 44.01 2.24 R
1959 2157 0.251922 AGGGCCTGCACATCAATGTT 60.252 50.000 4.50 0.00 39.39 2.71 R
3010 3364 0.592247 GTGCTTGTTGTTGAGGTGCG 60.592 55.000 0.00 0.00 0.00 5.34 R
3997 4388 2.158667 TGGGTTCTGTTTCAGGAGGAAC 60.159 50.000 0.00 0.00 34.56 3.62 R
4229 4620 4.783621 GCACATGGAGCTCCCGCA 62.784 66.667 29.95 12.34 39.10 5.69 R
5408 5805 0.253327 GTGGGGTCTGTGGAAGGATC 59.747 60.000 0.00 0.00 0.00 3.36 R
6177 6736 1.971695 CGAAGCCACCTTCCCCAAC 60.972 63.158 0.00 0.00 43.66 3.77 R
6832 7391 1.556564 CGTACTCCGGTGCAACATAG 58.443 55.000 0.98 0.00 39.98 2.23 R
8396 9100 0.926293 TGATTCCCCAGGGCTTTAGG 59.074 55.000 0.00 0.00 34.68 2.69 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
168 185 4.796495 GAACCGGGCCTGCCGAAT 62.796 66.667 5.85 0.00 36.85 3.34
169 186 4.360405 AACCGGGCCTGCCGAATT 62.360 61.111 5.85 0.00 36.85 2.17
170 187 3.879180 AACCGGGCCTGCCGAATTT 62.879 57.895 5.85 0.00 36.85 1.82
171 188 3.518068 CCGGGCCTGCCGAATTTC 61.518 66.667 5.85 0.00 36.85 2.17
172 189 2.438434 CGGGCCTGCCGAATTTCT 60.438 61.111 0.84 0.00 36.85 2.52
173 190 2.472909 CGGGCCTGCCGAATTTCTC 61.473 63.158 0.84 0.00 36.85 2.87
229 250 0.902531 ACGGCCACTACTACATTGCT 59.097 50.000 2.24 0.00 0.00 3.91
230 251 1.134788 ACGGCCACTACTACATTGCTC 60.135 52.381 2.24 0.00 0.00 4.26
231 252 1.137086 CGGCCACTACTACATTGCTCT 59.863 52.381 2.24 0.00 0.00 4.09
232 253 2.555199 GGCCACTACTACATTGCTCTG 58.445 52.381 0.00 0.00 0.00 3.35
233 254 2.093447 GGCCACTACTACATTGCTCTGT 60.093 50.000 0.00 0.00 0.00 3.41
234 255 2.932614 GCCACTACTACATTGCTCTGTG 59.067 50.000 2.48 0.00 0.00 3.66
235 256 3.617531 GCCACTACTACATTGCTCTGTGT 60.618 47.826 2.48 0.00 0.00 3.72
236 257 4.381612 GCCACTACTACATTGCTCTGTGTA 60.382 45.833 2.48 0.00 0.00 2.90
403 431 1.589716 GCAGCGCACTCCCAAAGATT 61.590 55.000 11.47 0.00 0.00 2.40
484 518 4.940905 GGTTAAACTAAACCAGGCCAAA 57.059 40.909 5.01 0.00 46.85 3.28
485 519 4.878439 GGTTAAACTAAACCAGGCCAAAG 58.122 43.478 5.01 0.00 46.85 2.77
486 520 4.585581 GGTTAAACTAAACCAGGCCAAAGA 59.414 41.667 5.01 0.00 46.85 2.52
487 521 5.245301 GGTTAAACTAAACCAGGCCAAAGAT 59.755 40.000 5.01 0.00 46.85 2.40
488 522 6.387465 GTTAAACTAAACCAGGCCAAAGATC 58.613 40.000 5.01 0.00 0.00 2.75
489 523 3.806949 ACTAAACCAGGCCAAAGATCA 57.193 42.857 5.01 0.00 0.00 2.92
490 524 3.421844 ACTAAACCAGGCCAAAGATCAC 58.578 45.455 5.01 0.00 0.00 3.06
491 525 1.247567 AAACCAGGCCAAAGATCACG 58.752 50.000 5.01 0.00 0.00 4.35
492 526 0.400213 AACCAGGCCAAAGATCACGA 59.600 50.000 5.01 0.00 0.00 4.35
493 527 0.036010 ACCAGGCCAAAGATCACGAG 60.036 55.000 5.01 0.00 0.00 4.18
609 716 3.732169 GCCGCTGCTTTCTCCTTTATTTC 60.732 47.826 0.00 0.00 33.53 2.17
613 720 6.038714 CCGCTGCTTTCTCCTTTATTTCTAAT 59.961 38.462 0.00 0.00 0.00 1.73
614 721 7.415653 CCGCTGCTTTCTCCTTTATTTCTAATT 60.416 37.037 0.00 0.00 0.00 1.40
644 751 5.662674 TTACTCTGCTAGGGTTCTCTTTC 57.337 43.478 0.00 0.00 0.00 2.62
669 776 4.760204 AGGGTGTGTGAATTTACTTGTAGC 59.240 41.667 1.75 0.00 0.00 3.58
685 792 3.896479 GCAGCTGCTACCACTTCC 58.104 61.111 31.33 0.00 38.21 3.46
691 798 1.550976 GCTGCTACCACTTCCAGTACT 59.449 52.381 0.00 0.00 0.00 2.73
693 800 3.181485 GCTGCTACCACTTCCAGTACTAG 60.181 52.174 0.00 0.00 0.00 2.57
760 867 4.453819 ACTGTACGAGTACTAGTGGTGTTC 59.546 45.833 17.80 0.00 37.00 3.18
794 929 2.613576 CTTCCCCCTCCTCCTCCTCC 62.614 70.000 0.00 0.00 0.00 4.30
958 1109 2.206536 CGGCTCTGATCCCCTCCTC 61.207 68.421 0.00 0.00 0.00 3.71
969 1120 4.834453 CCTCCTCCTGCTGCTGCG 62.834 72.222 11.21 5.84 43.34 5.18
1003 1187 4.538283 CGAGCGACGGCGAGATGT 62.538 66.667 18.90 0.00 46.35 3.06
1044 1228 0.108898 TGCTGCTTCTCGCTTCTCTC 60.109 55.000 0.00 0.00 40.11 3.20
1112 1296 0.467290 CTCTCCTCCTCTTCTCCCCG 60.467 65.000 0.00 0.00 0.00 5.73
1117 1301 0.910088 CTCCTCTTCTCCCCGGGTTT 60.910 60.000 21.85 0.00 0.00 3.27
1253 1437 0.731417 CTGAGCAATTTGAGGCGGAG 59.269 55.000 0.00 0.00 34.54 4.63
1266 1450 1.153349 GCGGAGACCTGTGGATTCC 60.153 63.158 0.00 0.00 0.00 3.01
1297 1481 3.755628 CAAATGCGCAGGCTGGCT 61.756 61.111 18.32 0.00 40.82 4.75
1330 1514 2.668550 AGGAAACCGCGCTTCACC 60.669 61.111 17.53 10.57 0.00 4.02
1359 1543 6.855763 TTATTCAGGATTTGAGCAAACCAT 57.144 33.333 13.27 0.00 37.07 3.55
1371 1555 4.761739 TGAGCAAACCATAGGAGAGTTTTG 59.238 41.667 0.00 0.00 31.54 2.44
1373 1557 4.762251 AGCAAACCATAGGAGAGTTTTGTC 59.238 41.667 0.00 0.00 31.54 3.18
1381 1565 3.217626 AGGAGAGTTTTGTCAAGCTTGG 58.782 45.455 25.73 8.01 0.00 3.61
1384 1568 4.214332 GGAGAGTTTTGTCAAGCTTGGTAG 59.786 45.833 25.73 0.38 0.00 3.18
1409 1593 1.207089 ACTAAGCGCATGTGCTCCTTA 59.793 47.619 32.41 20.21 46.60 2.69
1431 1615 8.040132 CCTTACTTCTGAATTCTCATCAAGAGT 58.960 37.037 7.05 3.63 44.98 3.24
1456 1640 3.039202 GCAATGTCGGCGTCTTGGG 62.039 63.158 6.85 0.00 0.00 4.12
1546 1730 1.741732 GCTGCCTCATCTACCTGTGTG 60.742 57.143 0.00 0.00 0.00 3.82
1596 1780 1.080995 TAATTTTTGGCCGCATGCGC 61.081 50.000 34.00 26.77 42.61 6.09
1625 1811 4.804868 TGCATCACTATGTGCCATTTTT 57.195 36.364 0.00 0.00 40.56 1.94
1632 1818 6.389091 TCACTATGTGCCATTTTTCATGTTC 58.611 36.000 0.00 0.00 32.98 3.18
1711 1904 1.889573 GCCTCCGATAGCAACCTGC 60.890 63.158 0.00 0.00 45.46 4.85
1873 2071 0.179100 CGCCTGTCGATCAAGGACAT 60.179 55.000 14.09 0.00 42.97 3.06
1958 2156 7.457024 TCTGAATTTTCAAAGATCATCAGCA 57.543 32.000 0.00 0.00 36.64 4.41
1959 2157 7.888424 TCTGAATTTTCAAAGATCATCAGCAA 58.112 30.769 0.00 0.00 36.64 3.91
2011 2209 2.361230 GTTGCAGCACCCCCTACC 60.361 66.667 0.00 0.00 0.00 3.18
2012 2210 3.657350 TTGCAGCACCCCCTACCC 61.657 66.667 0.00 0.00 0.00 3.69
2063 2261 4.704833 TGAGCCCTGCAGTTCCGC 62.705 66.667 13.81 8.50 0.00 5.54
2189 2387 1.865865 ATGTAGGTTCTAATGCGCCG 58.134 50.000 4.18 0.00 0.00 6.46
2228 2489 3.051210 CCTCCAGTCGTGTCTGCA 58.949 61.111 0.00 0.00 34.47 4.41
2245 2527 1.450211 CACCTCCTCCGGTTGTGTT 59.550 57.895 0.00 0.00 34.29 3.32
2247 2529 0.549469 ACCTCCTCCGGTTGTGTTTT 59.451 50.000 0.00 0.00 31.94 2.43
2287 2569 1.336632 GCTCCTCCTCCTGCTGTCAT 61.337 60.000 0.00 0.00 0.00 3.06
2394 2676 0.689623 ACCTTCAGTTCAGGCTCCTG 59.310 55.000 9.61 9.61 44.86 3.86
2396 2678 1.004560 TTCAGTTCAGGCTCCTGCG 60.005 57.895 10.99 0.53 43.31 5.18
2425 2707 2.035530 GCTGTGAAGCCTAATCTGCT 57.964 50.000 0.00 0.00 41.89 4.24
2501 2783 2.304470 TGTGAAGCCTAATGTGCCACTA 59.696 45.455 0.00 0.00 0.00 2.74
2700 3054 6.270231 AGGTAGACCAATTGGATCAGGTATAC 59.730 42.308 31.22 17.13 44.15 1.47
2752 3106 3.173668 TCCCGAATTCTTGATGTACCG 57.826 47.619 3.52 0.00 0.00 4.02
2753 3107 2.159014 TCCCGAATTCTTGATGTACCGG 60.159 50.000 0.00 0.00 35.88 5.28
2809 3163 4.891756 CCCTCATTATTCACTCCTGCATTT 59.108 41.667 0.00 0.00 0.00 2.32
2818 3172 1.283321 ACTCCTGCATTTTCCCTCTCC 59.717 52.381 0.00 0.00 0.00 3.71
2825 3179 3.017442 GCATTTTCCCTCTCCAGGTAAC 58.983 50.000 0.00 0.00 38.30 2.50
2829 3183 3.675348 TTCCCTCTCCAGGTAACGATA 57.325 47.619 0.00 0.00 46.39 2.92
2837 3191 2.178325 TCCAGGTAACGATATCCCTCCA 59.822 50.000 0.00 0.00 46.39 3.86
2968 3322 4.461781 CCGTTCTTCTTAGTAGTTCCTCCA 59.538 45.833 0.00 0.00 0.00 3.86
3010 3364 3.173668 TCACCACCTATTATCGCACAC 57.826 47.619 0.00 0.00 0.00 3.82
3096 3452 8.891671 ATTCTGTTGCTATTTGTTTGACAATT 57.108 26.923 0.00 0.00 38.00 2.32
3097 3453 7.697352 TCTGTTGCTATTTGTTTGACAATTG 57.303 32.000 3.24 3.24 38.00 2.32
3251 3615 2.295909 CACCGGTTCACAAATCACCAAT 59.704 45.455 2.97 0.00 0.00 3.16
3307 3671 5.280945 GCAGCTTGTTTGTGAAAGACAATA 58.719 37.500 0.00 0.00 44.23 1.90
3421 3785 1.135603 CATCAACGGTTCCACATGCTG 60.136 52.381 0.00 0.00 0.00 4.41
3503 3867 0.782384 CCAACGAAAGGAGAACGTCG 59.218 55.000 0.00 0.00 39.31 5.12
3716 4080 6.017934 CCGATGATTCAAGGTAATGGTAGTTG 60.018 42.308 0.00 0.00 0.00 3.16
3729 4093 9.543783 GGTAATGGTAGTTGTTCCTTCTATAAG 57.456 37.037 0.00 0.00 0.00 1.73
3740 4104 8.561738 TGTTCCTTCTATAAGACATTGGTTTC 57.438 34.615 0.00 0.00 34.37 2.78
3741 4105 8.160765 TGTTCCTTCTATAAGACATTGGTTTCA 58.839 33.333 0.00 0.00 34.37 2.69
3742 4106 9.178758 GTTCCTTCTATAAGACATTGGTTTCAT 57.821 33.333 0.00 0.00 34.37 2.57
3743 4107 9.753674 TTCCTTCTATAAGACATTGGTTTCATT 57.246 29.630 0.00 0.00 34.37 2.57
3744 4108 9.753674 TCCTTCTATAAGACATTGGTTTCATTT 57.246 29.630 0.00 0.00 34.37 2.32
3753 4117 9.447157 AAGACATTGGTTTCATTTTCTTGAAAA 57.553 25.926 10.41 10.41 44.71 2.29
3754 4118 9.447157 AGACATTGGTTTCATTTTCTTGAAAAA 57.553 25.926 11.78 0.00 44.71 1.94
3971 4362 4.090761 AGCTTCAGTCATTTTCAGGACA 57.909 40.909 0.00 0.00 36.50 4.02
3972 4363 3.817647 AGCTTCAGTCATTTTCAGGACAC 59.182 43.478 0.00 0.00 36.50 3.67
3973 4364 3.364366 GCTTCAGTCATTTTCAGGACACG 60.364 47.826 0.00 0.00 36.50 4.49
3997 4388 3.578716 TGTTTCTCCTACTCTTCCACCAG 59.421 47.826 0.00 0.00 0.00 4.00
4047 4438 2.917933 TCAACTCATCCTATTTGGGCG 58.082 47.619 0.00 0.00 36.20 6.13
4132 4523 9.542462 TCCTTTCAAACTTTATATACTGGATCG 57.458 33.333 0.00 0.00 0.00 3.69
4179 4570 6.810182 TGATTCTTACCTAGTGAAGCGTTAAC 59.190 38.462 0.00 0.00 0.00 2.01
4229 4620 0.032017 AGCCTCTAACGGATCCACCT 60.032 55.000 13.41 0.00 36.31 4.00
4471 4862 6.648879 TTTTGATAAAGCTACTGCCTTGTT 57.351 33.333 0.00 0.00 40.80 2.83
4563 4954 7.298374 TCTCTATGTTGTCTATCCAGGTATGT 58.702 38.462 0.00 0.00 0.00 2.29
4564 4955 8.445588 TCTCTATGTTGTCTATCCAGGTATGTA 58.554 37.037 0.00 0.00 0.00 2.29
4566 4957 9.601810 TCTATGTTGTCTATCCAGGTATGTATT 57.398 33.333 0.00 0.00 0.00 1.89
4568 4959 6.745116 TGTTGTCTATCCAGGTATGTATTCG 58.255 40.000 0.00 0.00 0.00 3.34
4569 4960 5.386958 TGTCTATCCAGGTATGTATTCGC 57.613 43.478 0.00 0.00 0.00 4.70
4571 4962 5.048013 TGTCTATCCAGGTATGTATTCGCTG 60.048 44.000 0.00 0.00 0.00 5.18
4572 4963 2.526304 TCCAGGTATGTATTCGCTGC 57.474 50.000 0.00 0.00 0.00 5.25
4701 5096 3.497262 CAGTGCGTCATGCTCATCATATT 59.503 43.478 0.00 0.00 46.63 1.28
4864 5259 2.453521 GGTTGATGTAGGAAAACCCCC 58.546 52.381 0.00 0.00 36.81 5.40
5108 5503 2.742053 GCCTTAGCTGTTCGATTGACAA 59.258 45.455 0.00 0.00 35.50 3.18
5225 5620 1.364269 TTGGGAGGGAACACCGTATT 58.636 50.000 0.00 0.00 46.96 1.89
5240 5635 6.557110 ACACCGTATTGTTGGCATATTTTAC 58.443 36.000 0.00 0.00 0.00 2.01
5269 5664 1.289160 TGAGATACAGCCTTGGCCTT 58.711 50.000 3.32 0.00 0.00 4.35
5298 5695 1.086696 ACATGCTTTCGAACATCCCG 58.913 50.000 0.00 0.00 0.00 5.14
5323 5720 4.806640 AGAAAAACTGCACCCCATAATG 57.193 40.909 0.00 0.00 0.00 1.90
5331 5728 7.436320 AACTGCACCCCATAATGATATTTTT 57.564 32.000 0.00 0.00 0.00 1.94
5398 5795 3.436704 AGACATGTAAAGCCACGATGTTG 59.563 43.478 0.00 0.00 0.00 3.33
5408 5805 2.193447 CCACGATGTTGTCCTCGTATG 58.807 52.381 0.00 0.00 45.63 2.39
5481 5878 7.974675 TGTCTTTATAGAAAATGGAAGCTTCG 58.025 34.615 19.91 1.42 30.65 3.79
5514 5911 2.806818 CTCGGCATCATCCTTCATGAAG 59.193 50.000 25.75 25.75 45.06 3.02
5675 6233 4.011966 AGACTTGATGATGTGCAACTCA 57.988 40.909 2.25 2.25 38.04 3.41
5703 6261 7.685481 TGACCCAGAAATAACAATTACTCAGA 58.315 34.615 0.00 0.00 0.00 3.27
5726 6284 6.036517 AGACGAGTGACAAATATCAAATCTGC 59.963 38.462 0.00 0.00 0.00 4.26
5830 6388 0.929244 ATAACCCCAGCCTCTGCATT 59.071 50.000 0.00 0.00 41.13 3.56
5894 6452 3.957497 ACATTTCAACTGCTAACCCACAA 59.043 39.130 0.00 0.00 0.00 3.33
6026 6585 0.107508 ACCTCATGATTGCAGGGACG 60.108 55.000 0.00 0.00 0.00 4.79
6059 6618 0.392863 TAGCTGGTCGCCGTAGTACA 60.393 55.000 0.00 0.00 40.39 2.90
6086 6645 1.351017 GGTCCATCAAGTTCACTGGGA 59.649 52.381 0.00 0.00 0.00 4.37
6177 6736 4.051237 TGGCTTTGATGATTCGTCGATAG 58.949 43.478 0.00 0.70 0.00 2.08
6401 6960 7.902920 ATATGAACTTATTCCAAATGGCAGT 57.097 32.000 0.00 0.00 33.49 4.40
6459 7018 4.067896 AGATTTAACTCCGCCAGCATATG 58.932 43.478 0.00 0.00 0.00 1.78
6510 7069 8.040716 ACTAATTACTTAATGTGTTGGCTCAC 57.959 34.615 6.48 6.48 38.63 3.51
6682 7241 5.769662 AGAGCATGATTTCACACCAAAAGTA 59.230 36.000 0.00 0.00 0.00 2.24
6685 7244 6.435277 AGCATGATTTCACACCAAAAGTATCT 59.565 34.615 0.00 0.00 0.00 1.98
6739 7298 0.326264 GGAACCAGCACATCTCCACT 59.674 55.000 0.00 0.00 0.00 4.00
6787 7346 3.547746 ACTATCTCCTCCTCAACGTCTC 58.452 50.000 0.00 0.00 0.00 3.36
6789 7348 0.323957 TCTCCTCCTCAACGTCTCGA 59.676 55.000 0.00 0.00 0.00 4.04
6832 7391 8.977505 GTATGATATTCTGTCTTTCTTCTCAGC 58.022 37.037 0.00 0.00 0.00 4.26
6898 7457 5.398603 AGAGTGATGTATACAGCTATGGC 57.601 43.478 20.91 7.17 39.06 4.40
6913 7472 3.669122 GCTATGGCGTCGTATTACTTGAG 59.331 47.826 0.00 0.00 0.00 3.02
7150 7709 1.408702 GAAGTTGTGCAGGCCTTGAAA 59.591 47.619 0.00 0.00 0.00 2.69
7177 7736 3.474570 AGCGAGGGTGATGAGGGC 61.475 66.667 0.00 0.00 0.00 5.19
7384 7943 3.845781 AACAAGAAGTTCTGGCAGAGA 57.154 42.857 17.91 6.31 34.74 3.10
7414 7973 4.846040 ACTTGTCGAGAGGTAGTATGAGT 58.154 43.478 0.00 0.00 0.00 3.41
7470 8029 3.832490 TCACAGTGTAGCAATAGGTGAGT 59.168 43.478 0.00 0.00 30.99 3.41
7562 8121 7.490962 TTGAAGACCTAGTTTGTGTACATTG 57.509 36.000 0.00 0.00 0.00 2.82
7618 8180 2.055042 AGCAGAGTAGCAGACCGGG 61.055 63.158 6.32 0.00 36.85 5.73
7658 8220 4.472833 ACCAGAGGCTTGAATAAGATCTGT 59.527 41.667 0.00 0.00 42.14 3.41
7691 8263 2.304761 TCCTCATTTAACGGGTTCTGCT 59.695 45.455 0.00 0.00 0.00 4.24
7692 8264 3.516300 TCCTCATTTAACGGGTTCTGCTA 59.484 43.478 0.00 0.00 0.00 3.49
7739 8311 1.676006 CGCCTGCCTTCCGATTTTTAT 59.324 47.619 0.00 0.00 0.00 1.40
7777 8349 4.377431 CGGCATGTCAGTTTGAGTTAGTTC 60.377 45.833 0.00 0.00 0.00 3.01
7788 8360 6.376299 AGTTTGAGTTAGTTCGTTTTCCCTTT 59.624 34.615 0.00 0.00 0.00 3.11
7789 8361 6.762702 TTGAGTTAGTTCGTTTTCCCTTTT 57.237 33.333 0.00 0.00 0.00 2.27
8020 8605 5.712917 GTCAGGTCTTCTTTCTCTCCTCTAA 59.287 44.000 0.00 0.00 0.00 2.10
8029 8614 8.601047 TTCTTTCTCTCCTCTAATCAGATTGA 57.399 34.615 5.85 1.21 0.00 2.57
8052 8643 9.681692 TTGAATATATATGTCAATTGTTGCTGC 57.318 29.630 5.13 0.00 0.00 5.25
8054 8645 7.671495 ATATATATGTCAATTGTTGCTGCGA 57.329 32.000 5.13 0.00 0.00 5.10
8078 8669 9.530129 CGAAACTTGTTAAGAACTGATGTATTC 57.470 33.333 0.00 0.00 0.00 1.75
8129 8720 4.431661 AAAAATTCTGCAGCACTCTAGC 57.568 40.909 9.47 0.00 0.00 3.42
8132 8723 0.972134 TTCTGCAGCACTCTAGCACT 59.028 50.000 9.47 0.00 36.85 4.40
8133 8724 0.972134 TCTGCAGCACTCTAGCACTT 59.028 50.000 9.47 0.00 36.85 3.16
8134 8725 2.171003 TCTGCAGCACTCTAGCACTTA 58.829 47.619 9.47 0.00 36.85 2.24
8135 8726 2.094494 TCTGCAGCACTCTAGCACTTAC 60.094 50.000 9.47 0.00 36.85 2.34
8148 8739 2.152016 GCACTTACCACCCTTCAGAAC 58.848 52.381 0.00 0.00 0.00 3.01
8156 8747 2.224621 CCACCCTTCAGAACACATGAGT 60.225 50.000 0.00 0.00 0.00 3.41
8163 8754 6.166279 CCTTCAGAACACATGAGTTTAGCTA 58.834 40.000 9.96 0.00 0.00 3.32
8190 8781 9.509278 TAAGGGCACTTTCTTTTCCTGAAAAGC 62.509 40.741 21.85 12.97 44.60 3.51
8206 8894 4.892934 TGAAAAGCCACTTCATTAGTTGGT 59.107 37.500 0.00 0.00 33.85 3.67
8209 8897 3.412386 AGCCACTTCATTAGTTGGTGAC 58.588 45.455 0.00 0.00 33.85 3.67
8308 8999 1.507141 CCCTTTCTGCGTGGTGTGAC 61.507 60.000 0.00 0.00 0.00 3.67
8310 9001 1.229428 CTTTCTGCGTGGTGTGACAT 58.771 50.000 0.00 0.00 0.00 3.06
8327 9018 3.226346 ACATTGCTGTCATCACATTGC 57.774 42.857 0.00 0.00 0.00 3.56
8396 9100 5.983720 TGACAGACTGTTAGAAGTAGCAAAC 59.016 40.000 10.01 0.00 0.00 2.93
8441 9145 0.811281 GGATCTTGCCGTGAAAAGGG 59.189 55.000 0.00 0.00 35.32 3.95
8456 9160 6.156519 GTGAAAAGGGCACGAAAAGATAATT 58.843 36.000 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
156 173 2.121538 GGAGAAATTCGGCAGGCCC 61.122 63.158 0.00 0.00 0.00 5.80
159 176 0.749454 CCCTGGAGAAATTCGGCAGG 60.749 60.000 0.00 0.00 35.90 4.85
160 177 0.749454 CCCCTGGAGAAATTCGGCAG 60.749 60.000 0.00 0.00 0.00 4.85
161 178 1.302949 CCCCTGGAGAAATTCGGCA 59.697 57.895 0.00 0.00 0.00 5.69
162 179 2.121538 GCCCCTGGAGAAATTCGGC 61.122 63.158 0.00 0.00 0.00 5.54
165 182 0.253327 ACGAGCCCCTGGAGAAATTC 59.747 55.000 0.00 0.00 0.00 2.17
166 183 0.035056 CACGAGCCCCTGGAGAAATT 60.035 55.000 0.00 0.00 0.00 1.82
167 184 1.604378 CACGAGCCCCTGGAGAAAT 59.396 57.895 0.00 0.00 0.00 2.17
168 185 3.068881 CACGAGCCCCTGGAGAAA 58.931 61.111 0.00 0.00 0.00 2.52
169 186 3.706373 GCACGAGCCCCTGGAGAA 61.706 66.667 0.00 0.00 33.58 2.87
170 187 4.704103 AGCACGAGCCCCTGGAGA 62.704 66.667 0.00 0.00 43.56 3.71
171 188 4.463879 CAGCACGAGCCCCTGGAG 62.464 72.222 0.00 0.00 43.56 3.86
219 240 3.936372 ACGTACACAGAGCAATGTAGT 57.064 42.857 0.00 0.00 32.05 2.73
419 447 4.203076 GTGGTACCGCCGCGAGAT 62.203 66.667 15.93 1.62 41.21 2.75
484 518 2.507102 CGCCGTTGCTCGTGATCT 60.507 61.111 0.00 0.00 37.94 2.75
485 519 3.554692 CCGCCGTTGCTCGTGATC 61.555 66.667 0.00 0.00 37.94 2.92
486 520 4.373116 ACCGCCGTTGCTCGTGAT 62.373 61.111 0.00 0.00 37.94 3.06
617 724 7.735326 AGAGAACCCTAGCAGAGTAAATAAA 57.265 36.000 0.00 0.00 0.00 1.40
644 751 6.092259 GCTACAAGTAAATTCACACACCCTAG 59.908 42.308 0.00 0.00 0.00 3.02
669 776 3.149899 CTGGAAGTGGTAGCAGCTG 57.850 57.895 10.11 10.11 0.00 4.24
685 792 6.388278 GGGAAGAAACTGTGTACTAGTACTG 58.612 44.000 28.56 20.99 37.00 2.74
691 798 4.504340 GCAAGGGGAAGAAACTGTGTACTA 60.504 45.833 0.00 0.00 0.00 1.82
693 800 2.552743 GCAAGGGGAAGAAACTGTGTAC 59.447 50.000 0.00 0.00 0.00 2.90
778 913 4.179599 GGGAGGAGGAGGAGGGGG 62.180 77.778 0.00 0.00 0.00 5.40
969 1120 3.198489 GTAGCAAGAGCCGCAGCC 61.198 66.667 0.00 0.00 43.56 4.85
1019 1203 2.031012 CGAGAAGCAGCACCACCA 59.969 61.111 0.00 0.00 0.00 4.17
1044 1228 1.279496 TCTCACCTGTGGATCCAAGG 58.721 55.000 27.86 27.86 0.00 3.61
1112 1296 0.319469 CAAACCACGCCATGAAACCC 60.319 55.000 0.00 0.00 0.00 4.11
1117 1301 0.387202 CCAAACAAACCACGCCATGA 59.613 50.000 0.00 0.00 0.00 3.07
1234 1418 0.731417 CTCCGCCTCAAATTGCTCAG 59.269 55.000 0.00 0.00 0.00 3.35
1266 1450 4.025061 TGCGCATTTGGAAGAAAAATTGTG 60.025 37.500 5.66 0.00 0.00 3.33
1297 1481 0.688749 TCCTGGCAGCAGATCAGCTA 60.689 55.000 12.76 0.00 44.54 3.32
1359 1543 4.141482 ACCAAGCTTGACAAAACTCTCCTA 60.141 41.667 28.05 0.00 0.00 2.94
1381 1565 1.212616 CATGCGCTTAGTCCTGCTAC 58.787 55.000 9.73 0.00 0.00 3.58
1384 1568 1.717937 CACATGCGCTTAGTCCTGC 59.282 57.895 9.73 0.00 0.00 4.85
1387 1571 1.432270 GGAGCACATGCGCTTAGTCC 61.432 60.000 10.05 2.78 44.01 3.85
1388 1572 0.460987 AGGAGCACATGCGCTTAGTC 60.461 55.000 10.05 0.00 44.01 2.59
1389 1573 0.036010 AAGGAGCACATGCGCTTAGT 60.036 50.000 10.05 0.83 44.01 2.24
1409 1593 6.873076 GTCACTCTTGATGAGAATTCAGAAGT 59.127 38.462 8.44 0.00 45.39 3.01
1456 1640 1.304134 ACAGGGGAACGGGAAATGC 60.304 57.895 0.00 0.00 0.00 3.56
1546 1730 0.730265 TGCGATATCACGGCCAAAAC 59.270 50.000 2.24 0.00 0.00 2.43
1596 1780 2.740447 CACATAGTGATGCATCATCCGG 59.260 50.000 30.89 21.91 39.87 5.14
1625 1811 6.591062 GCAATTATTGAAAGCTTGGAACATGA 59.409 34.615 9.36 0.00 39.30 3.07
1632 1818 5.063060 GCAAGAGCAATTATTGAAAGCTTGG 59.937 40.000 19.91 10.06 41.58 3.61
1698 1891 2.283298 ACAATCTGCAGGTTGCTATCG 58.717 47.619 34.34 14.40 45.31 2.92
1727 1920 9.372369 GTGTAATGACTAAGCTCTGAGTTTAAT 57.628 33.333 13.76 5.32 0.00 1.40
1728 1921 8.364894 TGTGTAATGACTAAGCTCTGAGTTTAA 58.635 33.333 13.76 1.93 0.00 1.52
1771 1969 3.450904 TCAGGGAGCAGGTAAAGTATGT 58.549 45.455 0.00 0.00 0.00 2.29
1810 2008 3.741249 CGCCAGATCAGTACCTAGAGTA 58.259 50.000 0.00 0.00 0.00 2.59
1958 2156 0.609662 GGGCCTGCACATCAATGTTT 59.390 50.000 0.84 0.00 39.39 2.83
1959 2157 0.251922 AGGGCCTGCACATCAATGTT 60.252 50.000 4.50 0.00 39.39 2.71
2011 2209 2.123982 GGAGGGCTTGCTGATGGG 60.124 66.667 0.00 0.00 0.00 4.00
2012 2210 2.123982 GGGAGGGCTTGCTGATGG 60.124 66.667 0.00 0.00 0.00 3.51
2100 2298 6.155221 TCTGACTGAATGTGAGCTACCTTTAT 59.845 38.462 0.00 0.00 29.74 1.40
2245 2527 2.487265 GGCTCAACTGGAGGAGACAAAA 60.487 50.000 0.00 0.00 44.22 2.44
2247 2529 0.687354 GGCTCAACTGGAGGAGACAA 59.313 55.000 0.00 0.00 44.22 3.18
2425 2707 2.176889 GTGAAGCAGGAGGTGGTAGTA 58.823 52.381 0.00 0.00 35.15 1.82
2501 2783 1.840635 GGTATTGAAGGAGGAGGTGCT 59.159 52.381 0.00 0.00 0.00 4.40
2700 3054 6.603237 TTATGAATCGTTACCAGCAGAATG 57.397 37.500 0.00 0.00 40.87 2.67
2767 3121 4.613437 AGGGAAGGAACATATTTGCACAT 58.387 39.130 0.00 0.00 0.00 3.21
2809 3163 2.544844 ATCGTTACCTGGAGAGGGAA 57.455 50.000 0.00 0.00 44.84 3.97
2818 3172 5.069251 GGATATGGAGGGATATCGTTACCTG 59.931 48.000 3.25 0.00 36.53 4.00
2825 3179 3.133003 GTGGTGGATATGGAGGGATATCG 59.867 52.174 0.00 0.00 36.53 2.92
2829 3183 1.226750 AGGTGGTGGATATGGAGGGAT 59.773 52.381 0.00 0.00 0.00 3.85
2837 3191 1.595311 TGCCTTCAGGTGGTGGATAT 58.405 50.000 0.00 0.00 37.57 1.63
2968 3322 5.598005 TGAAATTGGAGGTTTCACATGTTCT 59.402 36.000 0.00 0.00 39.81 3.01
3010 3364 0.592247 GTGCTTGTTGTTGAGGTGCG 60.592 55.000 0.00 0.00 0.00 5.34
3126 3490 4.157105 GGTGCCGTGTTTCCTACAATAAAT 59.843 41.667 0.00 0.00 38.80 1.40
3503 3867 4.584743 GTGGGTAAGATGGGGAAAATGATC 59.415 45.833 0.00 0.00 0.00 2.92
3716 4080 8.561738 TGAAACCAATGTCTTATAGAAGGAAC 57.438 34.615 0.00 0.00 33.09 3.62
3971 4362 2.561858 GGAAGAGTAGGAGAAACACCGT 59.438 50.000 0.00 0.00 0.00 4.83
3972 4363 2.561419 TGGAAGAGTAGGAGAAACACCG 59.439 50.000 0.00 0.00 0.00 4.94
3973 4364 3.306849 GGTGGAAGAGTAGGAGAAACACC 60.307 52.174 0.00 0.00 39.01 4.16
3997 4388 2.158667 TGGGTTCTGTTTCAGGAGGAAC 60.159 50.000 0.00 0.00 34.56 3.62
4132 4523 6.237901 TCATCAGTATTACCCAATATGCACC 58.762 40.000 0.00 0.00 0.00 5.01
4229 4620 4.783621 GCACATGGAGCTCCCGCA 62.784 66.667 29.95 12.34 39.10 5.69
4471 4862 4.572985 CTCCACAAGCTTTGAAATGTCA 57.427 40.909 0.00 0.00 0.00 3.58
4563 4954 2.076100 CAAGGACACAAGCAGCGAATA 58.924 47.619 0.00 0.00 0.00 1.75
4564 4955 0.877071 CAAGGACACAAGCAGCGAAT 59.123 50.000 0.00 0.00 0.00 3.34
4566 4957 1.597854 CCAAGGACACAAGCAGCGA 60.598 57.895 0.00 0.00 0.00 4.93
4568 4959 0.536006 AGTCCAAGGACACAAGCAGC 60.536 55.000 20.52 0.00 46.76 5.25
4569 4960 1.071385 AGAGTCCAAGGACACAAGCAG 59.929 52.381 20.52 0.00 46.76 4.24
4571 4962 1.346068 AGAGAGTCCAAGGACACAAGC 59.654 52.381 20.52 8.57 46.76 4.01
4572 4963 3.760580 AAGAGAGTCCAAGGACACAAG 57.239 47.619 20.52 0.00 46.76 3.16
4701 5096 9.033481 CAGAAGTTCAAAATGCTTAACAATGAA 57.967 29.630 5.50 0.00 31.15 2.57
4867 5262 5.469479 CAATTACGCTCCCATTCACTTTTT 58.531 37.500 0.00 0.00 0.00 1.94
5108 5503 5.009911 TGAAAATGTGCAGCTATTGTTCTGT 59.990 36.000 0.00 0.00 33.09 3.41
5217 5612 6.690957 CAGTAAAATATGCCAACAATACGGTG 59.309 38.462 0.00 0.00 0.00 4.94
5240 5635 1.938577 GCTGTATCTCATGTGGCACAG 59.061 52.381 26.04 16.98 41.80 3.66
5298 5695 7.284489 TCATTATGGGGTGCAGTTTTTCTATAC 59.716 37.037 0.00 0.00 0.00 1.47
5331 5728 7.037438 GTGTCTACGACCAGGACAAAATATTA 58.963 38.462 0.00 0.00 40.86 0.98
5367 5764 9.602568 TCGTGGCTTTACATGTCTATTTTATAA 57.397 29.630 0.00 0.00 0.00 0.98
5398 5795 2.693591 TGTGGAAGGATCATACGAGGAC 59.306 50.000 0.00 0.00 0.00 3.85
5408 5805 0.253327 GTGGGGTCTGTGGAAGGATC 59.747 60.000 0.00 0.00 0.00 3.36
5500 5897 5.641789 ATCATCCACTTCATGAAGGATGA 57.358 39.130 36.93 36.93 43.48 2.92
5514 5911 8.822652 AAGAATCAACTTTCAAAATCATCCAC 57.177 30.769 0.00 0.00 0.00 4.02
5558 6116 7.989826 ACCTATTTTCTAACATTTGCAGCTAG 58.010 34.615 0.00 0.00 0.00 3.42
5675 6233 7.942341 TGAGTAATTGTTATTTCTGGGTCAACT 59.058 33.333 0.00 0.00 0.00 3.16
5703 6261 5.643348 TGCAGATTTGATATTTGTCACTCGT 59.357 36.000 0.00 0.00 0.00 4.18
5871 6429 4.720046 TGTGGGTTAGCAGTTGAAATGTA 58.280 39.130 0.00 0.00 0.00 2.29
5881 6439 3.119990 CCATAAACGTTGTGGGTTAGCAG 60.120 47.826 19.98 0.00 38.18 4.24
5894 6452 6.112734 TCATCTGAAATGCTACCATAAACGT 58.887 36.000 0.00 0.00 0.00 3.99
6026 6585 7.739286 GCGACCAGCTAAAAGTGTGTTACAC 62.739 48.000 8.76 8.76 45.34 2.90
6059 6618 4.074970 GTGAACTTGATGGACCTGATTGT 58.925 43.478 0.00 0.00 0.00 2.71
6177 6736 1.971695 CGAAGCCACCTTCCCCAAC 60.972 63.158 0.00 0.00 43.66 3.77
6365 6924 6.971726 ATAAGTTCATATACCAGACACCGA 57.028 37.500 0.00 0.00 0.00 4.69
6401 6960 1.894466 CCATGCAAATGGGACTCAACA 59.106 47.619 0.00 0.00 38.04 3.33
6459 7018 0.947244 CAACTGCTGACACCACTTCC 59.053 55.000 0.00 0.00 0.00 3.46
6463 7022 2.221169 TCAATCAACTGCTGACACCAC 58.779 47.619 0.00 0.00 36.69 4.16
6464 7023 2.636647 TCAATCAACTGCTGACACCA 57.363 45.000 0.00 0.00 36.69 4.17
6465 7024 3.316308 AGTTTCAATCAACTGCTGACACC 59.684 43.478 0.00 0.00 36.69 4.16
6510 7069 2.050895 CGCGATCGGCTCCTACAG 60.051 66.667 18.30 0.00 40.44 2.74
6682 7241 0.904865 TGGCCAGTCCGAAGTCAGAT 60.905 55.000 0.00 0.00 37.80 2.90
6685 7244 2.583441 CCTGGCCAGTCCGAAGTCA 61.583 63.158 30.63 0.00 37.80 3.41
6691 7250 4.767255 GCAGTCCTGGCCAGTCCG 62.767 72.222 30.63 16.20 37.80 4.79
6739 7298 1.674519 CCGAATGTTCCCATGACACGA 60.675 52.381 0.00 0.00 0.00 4.35
6832 7391 1.556564 CGTACTCCGGTGCAACATAG 58.443 55.000 0.98 0.00 39.98 2.23
6898 7457 4.496183 GTGAGAAGCTCAAGTAATACGACG 59.504 45.833 0.00 0.00 42.46 5.12
7150 7709 2.345244 CCCTCGCTGCAGACAAGT 59.655 61.111 20.43 0.00 0.00 3.16
7177 7736 1.880027 CTGAAACTTCCCGAACCAAGG 59.120 52.381 0.00 0.00 0.00 3.61
7384 7943 2.069273 CCTCTCGACAAGTTTCGCATT 58.931 47.619 3.51 0.00 38.95 3.56
7426 7985 4.780815 AGTGTGTCTCAAAATCTGGTGAA 58.219 39.130 0.00 0.00 0.00 3.18
7477 8036 1.701847 ACTGGAAGCTGGACAGAACAT 59.298 47.619 16.61 0.00 37.60 2.71
7562 8121 2.648059 AGCCTTTATCTCCACATGCAC 58.352 47.619 0.00 0.00 0.00 4.57
7618 8180 3.136443 TCTGGTGATCCATAACCCATGAC 59.864 47.826 0.00 0.00 43.43 3.06
7638 8200 6.155910 TCTGAACAGATCTTATTCAAGCCTCT 59.844 38.462 16.39 0.00 32.19 3.69
7658 8220 5.874810 CGTTAAATGAGGAACCAGATCTGAA 59.125 40.000 24.62 2.69 0.00 3.02
7672 8234 6.201044 CAGTATAGCAGAACCCGTTAAATGAG 59.799 42.308 0.00 0.00 0.00 2.90
7691 8263 4.591072 TGTGTATGGCCACATAGCAGTATA 59.409 41.667 8.16 0.00 40.30 1.47
7692 8264 3.390967 TGTGTATGGCCACATAGCAGTAT 59.609 43.478 8.16 0.00 40.30 2.12
7788 8360 5.153950 ACCAAACAGCTAACCAAACAAAA 57.846 34.783 0.00 0.00 0.00 2.44
7789 8361 4.810191 ACCAAACAGCTAACCAAACAAA 57.190 36.364 0.00 0.00 0.00 2.83
7838 8410 3.309296 TGGCCAAATGTAGTCCCAAAAA 58.691 40.909 0.61 0.00 0.00 1.94
7839 8411 2.964209 TGGCCAAATGTAGTCCCAAAA 58.036 42.857 0.61 0.00 0.00 2.44
7843 8415 1.750778 CACATGGCCAAATGTAGTCCC 59.249 52.381 10.96 0.00 38.75 4.46
8029 8614 8.098220 TCGCAGCAACAATTGACATATATATT 57.902 30.769 13.59 0.00 0.00 1.28
8038 8623 2.731217 AGTTTCGCAGCAACAATTGAC 58.269 42.857 13.59 0.97 0.00 3.18
8040 8625 2.859538 ACAAGTTTCGCAGCAACAATTG 59.140 40.909 3.24 3.24 0.00 2.32
8045 8636 3.947626 TCTTAACAAGTTTCGCAGCAAC 58.052 40.909 0.00 0.00 0.00 4.17
8052 8643 9.530129 GAATACATCAGTTCTTAACAAGTTTCG 57.470 33.333 0.00 0.00 0.00 3.46
8078 8669 5.065731 GCACAGATCCAAGTTTCCTATTCAG 59.934 44.000 0.00 0.00 0.00 3.02
8120 8711 1.405661 GGGTGGTAAGTGCTAGAGTGC 60.406 57.143 0.00 0.00 0.00 4.40
8123 8714 2.832129 TGAAGGGTGGTAAGTGCTAGAG 59.168 50.000 0.00 0.00 0.00 2.43
8126 8717 2.897350 TCTGAAGGGTGGTAAGTGCTA 58.103 47.619 0.00 0.00 0.00 3.49
8129 8720 3.139077 GTGTTCTGAAGGGTGGTAAGTG 58.861 50.000 0.00 0.00 0.00 3.16
8132 8723 3.392947 TCATGTGTTCTGAAGGGTGGTAA 59.607 43.478 0.00 0.00 0.00 2.85
8133 8724 2.976185 TCATGTGTTCTGAAGGGTGGTA 59.024 45.455 0.00 0.00 0.00 3.25
8134 8725 1.774254 TCATGTGTTCTGAAGGGTGGT 59.226 47.619 0.00 0.00 0.00 4.16
8135 8726 2.224621 ACTCATGTGTTCTGAAGGGTGG 60.225 50.000 0.00 0.00 0.00 4.61
8148 8739 5.237344 GTGCCCTTATAGCTAAACTCATGTG 59.763 44.000 0.00 0.00 0.00 3.21
8156 8747 7.122204 GGAAAAGAAAGTGCCCTTATAGCTAAA 59.878 37.037 0.00 0.00 0.00 1.85
8163 8754 4.998051 TCAGGAAAAGAAAGTGCCCTTAT 58.002 39.130 0.00 0.00 0.00 1.73
8190 8781 3.750371 TGGTCACCAACTAATGAAGTGG 58.250 45.455 0.00 0.00 38.88 4.00
8191 8782 5.278463 CCTTTGGTCACCAACTAATGAAGTG 60.278 44.000 9.45 0.00 43.82 3.16
8192 8783 4.827284 CCTTTGGTCACCAACTAATGAAGT 59.173 41.667 9.45 0.00 43.82 3.01
8194 8785 4.798882 ACCTTTGGTCACCAACTAATGAA 58.201 39.130 9.45 0.00 43.82 2.57
8195 8786 4.447138 ACCTTTGGTCACCAACTAATGA 57.553 40.909 9.45 0.00 43.82 2.57
8196 8787 5.068460 TGAAACCTTTGGTCACCAACTAATG 59.932 40.000 9.45 0.00 43.82 1.90
8197 8788 5.205056 TGAAACCTTTGGTCACCAACTAAT 58.795 37.500 9.45 0.00 43.82 1.73
8198 8789 4.601084 TGAAACCTTTGGTCACCAACTAA 58.399 39.130 9.45 0.00 43.82 2.24
8206 8894 1.140052 TCGAGCTGAAACCTTTGGTCA 59.860 47.619 0.00 0.00 33.12 4.02
8209 8897 2.154462 ACATCGAGCTGAAACCTTTGG 58.846 47.619 0.00 0.00 0.00 3.28
8277 8965 3.614870 CGCAGAAAGGGGAAATGGAAAAG 60.615 47.826 0.00 0.00 0.00 2.27
8280 8970 1.203001 ACGCAGAAAGGGGAAATGGAA 60.203 47.619 0.00 0.00 33.80 3.53
8308 8999 2.159490 TCGCAATGTGATGACAGCAATG 60.159 45.455 0.00 0.00 34.87 2.82
8310 9001 1.521580 TCGCAATGTGATGACAGCAA 58.478 45.000 0.00 0.00 34.87 3.91
8359 9050 6.412362 ACAGTCTGTCACTCTGTTTAATCT 57.588 37.500 0.00 0.00 39.00 2.40
8396 9100 0.926293 TGATTCCCCAGGGCTTTAGG 59.074 55.000 0.00 0.00 34.68 2.69
8441 9145 8.227791 TGAACACTTCTAATTATCTTTTCGTGC 58.772 33.333 0.00 0.00 0.00 5.34


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

AutoCloner maintained by Alex Coulton.