Multiple sequence alignment - TraesCS6D01G320400

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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 TraesCS6D01G320400 chr6D 100.000 6117 0 0 1 6117 428471299 428477415 0.000000e+00 11297.0
1 TraesCS6D01G320400 chr6D 95.385 130 6 0 5402 5531 354595823 354595694 2.230000e-49 207.0
2 TraesCS6D01G320400 chr6D 90.968 155 11 2 1335 1486 457345569 457345415 8.040000e-49 206.0
3 TraesCS6D01G320400 chr6D 88.095 84 9 1 2329 2411 414480290 414480207 1.400000e-16 99.0
4 TraesCS6D01G320400 chr6B 94.036 3018 116 27 2414 5397 644475711 644478698 0.000000e+00 4518.0
5 TraesCS6D01G320400 chr6B 85.842 1342 73 44 44 1329 644473586 644474866 0.000000e+00 1317.0
6 TraesCS6D01G320400 chr6B 92.164 587 36 4 5533 6117 644478801 644479379 0.000000e+00 821.0
7 TraesCS6D01G320400 chr6B 92.140 458 18 9 1896 2335 644475257 644475714 1.120000e-176 630.0
8 TraesCS6D01G320400 chr6B 94.118 255 10 3 1551 1800 644475004 644475258 3.460000e-102 383.0
9 TraesCS6D01G320400 chr6B 87.006 177 15 4 5537 5710 644478699 644478870 6.260000e-45 193.0
10 TraesCS6D01G320400 chr6A 96.399 2277 58 7 3861 6117 573194883 573197155 0.000000e+00 3729.0
11 TraesCS6D01G320400 chr6A 95.413 1439 53 5 2414 3852 573193414 573194839 0.000000e+00 2279.0
12 TraesCS6D01G320400 chr6A 90.340 911 43 21 444 1338 573191293 573192174 0.000000e+00 1153.0
13 TraesCS6D01G320400 chr6A 94.221 398 17 4 1551 1946 573192300 573192693 2.440000e-168 603.0
14 TraesCS6D01G320400 chr6A 97.170 318 9 0 2013 2330 573193095 573193412 6.980000e-149 538.0
15 TraesCS6D01G320400 chr6A 82.609 184 19 12 2 180 573190743 573190918 3.820000e-32 150.0
16 TraesCS6D01G320400 chr6A 92.647 68 3 1 1951 2016 573192723 573192790 5.050000e-16 97.1
17 TraesCS6D01G320400 chr6A 100.000 31 0 0 3378 3408 573194338 573194368 2.380000e-04 58.4
18 TraesCS6D01G320400 chr6A 100.000 29 0 0 421 449 573191260 573191288 3.000000e-03 54.7
19 TraesCS6D01G320400 chr3B 97.674 129 3 0 1334 1462 262424980 262425108 7.980000e-54 222.0
20 TraesCS6D01G320400 chr3B 96.923 130 4 0 1333 1462 42702211 42702340 1.030000e-52 219.0
21 TraesCS6D01G320400 chr3B 86.486 148 10 1 5402 5539 34644429 34644282 2.950000e-33 154.0
22 TraesCS6D01G320400 chr2D 96.923 130 4 0 1335 1464 492056537 492056408 1.030000e-52 219.0
23 TraesCS6D01G320400 chr2D 83.133 83 13 1 2339 2420 530555135 530555053 2.360000e-09 75.0
24 TraesCS6D01G320400 chr2D 94.737 38 2 0 1864 1901 315865635 315865672 6.620000e-05 60.2
25 TraesCS6D01G320400 chr1D 96.923 130 4 0 1335 1464 462925586 462925457 1.030000e-52 219.0
26 TraesCS6D01G320400 chr1D 96.923 130 4 0 1335 1464 462930176 462930047 1.030000e-52 219.0
27 TraesCS6D01G320400 chr1D 94.286 140 7 1 1332 1470 458871628 458871767 4.800000e-51 213.0
28 TraesCS6D01G320400 chr1D 88.112 143 7 1 5399 5531 212494808 212494666 1.760000e-35 161.0
29 TraesCS6D01G320400 chr7B 94.286 140 7 1 1335 1473 104514758 104514619 4.800000e-51 213.0
30 TraesCS6D01G320400 chr7B 92.481 133 10 0 5399 5531 606421915 606421783 2.250000e-44 191.0
31 TraesCS6D01G320400 chr7B 84.694 98 9 6 2334 2428 107127483 107127389 6.530000e-15 93.5
32 TraesCS6D01G320400 chr2A 94.286 140 7 1 1335 1473 425830069 425829930 4.800000e-51 213.0
33 TraesCS6D01G320400 chr2A 88.571 140 14 1 5394 5531 754448002 754448141 1.050000e-37 169.0
34 TraesCS6D01G320400 chr2A 87.013 77 5 5 2344 2416 454473523 454473598 1.410000e-11 82.4
35 TraesCS6D01G320400 chr4B 92.754 138 9 1 5395 5531 510830403 510830266 1.340000e-46 198.0
36 TraesCS6D01G320400 chr4A 92.593 135 10 0 5402 5536 668307632 668307498 1.740000e-45 195.0
37 TraesCS6D01G320400 chr5B 89.552 134 12 2 5399 5531 695656050 695656182 1.050000e-37 169.0
38 TraesCS6D01G320400 chr5A 86.364 154 10 3 5388 5531 600611482 600611330 2.280000e-34 158.0
39 TraesCS6D01G320400 chr2B 86.667 150 9 2 5393 5531 500456391 500456540 8.210000e-34 156.0
40 TraesCS6D01G320400 chr3D 91.429 70 6 0 1229 1298 210619672 210619741 5.050000e-16 97.1
41 TraesCS6D01G320400 chr3A 91.429 70 6 0 1229 1298 275293322 275293253 5.050000e-16 97.1
42 TraesCS6D01G320400 chr7D 85.057 87 12 1 2334 2419 610222483 610222569 3.040000e-13 87.9
43 TraesCS6D01G320400 chr7D 83.908 87 11 3 2339 2424 570639716 570639632 5.080000e-11 80.5
44 TraesCS6D01G320400 chr7A 83.721 86 13 1 2334 2418 699831095 699831010 5.080000e-11 80.5
45 TraesCS6D01G320400 chr7A 82.558 86 14 1 2334 2418 704453216 704453301 2.360000e-09 75.0
46 TraesCS6D01G320400 chrUn 82.558 86 14 1 2334 2418 83395544 83395459 2.360000e-09 75.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6D01G320400 chr6D 428471299 428477415 6116 False 11297.000000 11297 100.000000 1 6117 1 chr6D.!!$F1 6116
1 TraesCS6D01G320400 chr6B 644473586 644479379 5793 False 1310.333333 4518 90.884333 44 6117 6 chr6B.!!$F1 6073
2 TraesCS6D01G320400 chr6A 573190743 573197155 6412 False 962.466667 3729 94.311000 2 6117 9 chr6A.!!$F1 6115

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
83 84 0.108329 TTAGCCGCGAAGGAAGGAAG 60.108 55.000 8.23 0.0 45.00 3.46 F
1334 1579 0.036952 CAGGTTGGTCGCTCACTCAT 60.037 55.000 0.00 0.0 0.00 2.90 F
1340 1585 0.386113 GGTCGCTCACTCATACTCCC 59.614 60.000 0.00 0.0 0.00 4.30 F
1344 1589 0.671251 GCTCACTCATACTCCCTCCG 59.329 60.000 0.00 0.0 0.00 4.63 F
3027 3652 0.109597 CATTTGCTCCAGGTTCGCAC 60.110 55.000 1.13 0.0 32.71 5.34 F
4057 4724 2.267006 CAGGTGACGGCATCTGCT 59.733 61.111 20.70 0.0 45.49 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1939 2229 0.682292 TTGGGAAAACGGGGAAATGC 59.318 50.000 0.00 0.00 0.00 3.56 R
2610 3235 0.251341 GGAATGGAACCACAGCACCT 60.251 55.000 0.00 0.00 0.00 4.00 R
2697 3322 1.301244 AATCCATCTAGCCGCTGCG 60.301 57.895 16.34 16.34 44.33 5.18 R
3163 3788 4.815533 ATCCATGACCTAATCGATGGAG 57.184 45.455 8.68 4.86 42.89 3.86 R
4504 5182 0.323629 TGGTTTCCATCGTGGTCTCC 59.676 55.000 4.33 5.89 39.03 3.71 R
5504 6298 0.323957 GTTCGGTTAAGCCACTCCCT 59.676 55.000 0.00 0.00 36.97 4.20 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
79 80 3.400007 GCTTAGCCGCGAAGGAAG 58.600 61.111 8.23 6.67 45.00 3.46
81 82 1.515954 CTTAGCCGCGAAGGAAGGA 59.484 57.895 8.23 0.00 45.00 3.36
83 84 0.108329 TTAGCCGCGAAGGAAGGAAG 60.108 55.000 8.23 0.00 45.00 3.46
85 86 2.978824 CCGCGAAGGAAGGAAGGA 59.021 61.111 8.23 0.00 45.00 3.36
87 88 0.741221 CCGCGAAGGAAGGAAGGAAG 60.741 60.000 8.23 0.00 45.00 3.46
88 89 1.362406 CGCGAAGGAAGGAAGGAAGC 61.362 60.000 0.00 0.00 0.00 3.86
366 541 4.918201 CGCCCGAATCCAGCTCCC 62.918 72.222 0.00 0.00 0.00 4.30
367 542 4.918201 GCCCGAATCCAGCTCCCG 62.918 72.222 0.00 0.00 0.00 5.14
368 543 4.918201 CCCGAATCCAGCTCCCGC 62.918 72.222 0.00 0.00 0.00 6.13
384 559 1.443407 CGCTCCAGTCCCGATCAAT 59.557 57.895 0.00 0.00 0.00 2.57
569 770 3.279434 GAGTTTTGCCGATGGATAGGTT 58.721 45.455 0.00 0.00 0.00 3.50
592 793 3.181513 CCGGATGATACGATACGGTAGTG 60.182 52.174 0.00 0.00 43.85 2.74
593 794 3.434641 CGGATGATACGATACGGTAGTGT 59.565 47.826 0.00 0.00 0.00 3.55
594 795 4.435253 CGGATGATACGATACGGTAGTGTC 60.435 50.000 0.00 0.00 35.48 3.67
595 796 4.694509 GGATGATACGATACGGTAGTGTCT 59.305 45.833 0.00 0.00 36.50 3.41
596 797 5.390673 GGATGATACGATACGGTAGTGTCTG 60.391 48.000 0.00 0.00 36.50 3.51
597 798 4.445453 TGATACGATACGGTAGTGTCTGT 58.555 43.478 0.00 0.00 36.50 3.41
688 906 3.991121 GCTGCGGATAACTAGGATTTCTC 59.009 47.826 0.00 0.00 0.00 2.87
704 922 6.033966 GGATTTCTCTTTCGTTGTTGTTGTT 58.966 36.000 0.00 0.00 0.00 2.83
705 923 6.020678 GGATTTCTCTTTCGTTGTTGTTGTTG 60.021 38.462 0.00 0.00 0.00 3.33
706 924 5.365403 TTCTCTTTCGTTGTTGTTGTTGT 57.635 34.783 0.00 0.00 0.00 3.32
707 925 5.365403 TCTCTTTCGTTGTTGTTGTTGTT 57.635 34.783 0.00 0.00 0.00 2.83
708 926 5.150683 TCTCTTTCGTTGTTGTTGTTGTTG 58.849 37.500 0.00 0.00 0.00 3.33
709 927 4.861210 TCTTTCGTTGTTGTTGTTGTTGT 58.139 34.783 0.00 0.00 0.00 3.32
806 1033 1.061546 TCTGGTACCAGGTTTGACCC 58.938 55.000 35.94 0.00 43.75 4.46
849 1079 4.155709 TCTACAGTGGGAGGATCATCATC 58.844 47.826 9.94 1.52 36.25 2.92
850 1080 1.690893 ACAGTGGGAGGATCATCATCG 59.309 52.381 9.94 0.00 36.25 3.84
851 1081 0.683973 AGTGGGAGGATCATCATCGC 59.316 55.000 9.94 9.32 39.98 4.58
874 1104 5.656859 GCCAGAGATTAAATTAACCCAGGTT 59.343 40.000 7.34 7.34 41.65 3.50
877 1107 5.656859 AGAGATTAAATTAACCCAGGTTGCC 59.343 40.000 12.41 0.00 38.92 4.52
894 1124 4.081030 CGTCTGGCTGCGCAGTTG 62.081 66.667 35.80 25.04 0.00 3.16
895 1125 3.730761 GTCTGGCTGCGCAGTTGG 61.731 66.667 35.80 24.60 0.00 3.77
896 1126 4.254709 TCTGGCTGCGCAGTTGGT 62.255 61.111 35.80 0.00 0.00 3.67
897 1127 3.730761 CTGGCTGCGCAGTTGGTC 61.731 66.667 35.80 20.03 0.00 4.02
898 1128 4.560743 TGGCTGCGCAGTTGGTCA 62.561 61.111 35.80 22.71 0.00 4.02
899 1129 3.730761 GGCTGCGCAGTTGGTCAG 61.731 66.667 35.80 11.97 0.00 3.51
900 1130 2.974698 GCTGCGCAGTTGGTCAGT 60.975 61.111 35.80 0.00 0.00 3.41
901 1131 1.667830 GCTGCGCAGTTGGTCAGTA 60.668 57.895 35.80 0.00 0.00 2.74
902 1132 1.227999 GCTGCGCAGTTGGTCAGTAA 61.228 55.000 35.80 0.00 0.00 2.24
903 1133 0.512952 CTGCGCAGTTGGTCAGTAAC 59.487 55.000 29.24 0.00 0.00 2.50
909 1139 2.949644 GCAGTTGGTCAGTAACTTGGTT 59.050 45.455 0.00 0.00 36.29 3.67
910 1140 3.003378 GCAGTTGGTCAGTAACTTGGTTC 59.997 47.826 0.00 0.00 36.29 3.62
913 1143 3.102052 TGGTCAGTAACTTGGTTCGTC 57.898 47.619 0.00 0.00 0.00 4.20
936 1181 2.037687 CCCATTGGAGCCAAGGCA 59.962 61.111 14.40 0.00 44.88 4.75
940 1185 1.077985 ATTGGAGCCAAGGCAGCTT 59.922 52.632 14.40 0.00 41.75 3.74
943 1188 1.303970 GGAGCCAAGGCAGCTTCTT 60.304 57.895 14.40 0.00 41.75 2.52
944 1189 1.593296 GGAGCCAAGGCAGCTTCTTG 61.593 60.000 14.40 15.91 41.75 3.02
945 1190 2.210341 GAGCCAAGGCAGCTTCTTGC 62.210 60.000 14.40 13.31 41.75 4.01
952 1197 2.035312 CAGCTTCTTGCCAGGCCT 59.965 61.111 9.64 0.00 44.23 5.19
990 1235 1.354155 GTGGGGTTTATAAGCGCGC 59.646 57.895 26.66 26.66 43.78 6.86
991 1236 1.820481 TGGGGTTTATAAGCGCGCC 60.820 57.895 30.33 10.46 43.78 6.53
1059 1304 0.590230 CGCTGCTCTACTACACGCTC 60.590 60.000 0.00 0.00 0.00 5.03
1115 1360 3.878519 GGACTCGGACGGCGAGAG 61.879 72.222 16.62 20.40 37.25 3.20
1227 1472 0.039764 AGACCATCTCGACCCTGTCA 59.960 55.000 0.00 0.00 32.09 3.58
1329 1574 0.827925 AGAGACAGGTTGGTCGCTCA 60.828 55.000 0.00 0.00 43.14 4.26
1331 1576 1.115930 AGACAGGTTGGTCGCTCACT 61.116 55.000 0.00 0.00 42.62 3.41
1333 1578 1.367471 CAGGTTGGTCGCTCACTCA 59.633 57.895 0.00 0.00 0.00 3.41
1334 1579 0.036952 CAGGTTGGTCGCTCACTCAT 60.037 55.000 0.00 0.00 0.00 2.90
1336 1581 1.204941 AGGTTGGTCGCTCACTCATAC 59.795 52.381 0.00 0.00 0.00 2.39
1337 1582 1.204941 GGTTGGTCGCTCACTCATACT 59.795 52.381 0.00 0.00 0.00 2.12
1339 1584 1.103803 TGGTCGCTCACTCATACTCC 58.896 55.000 0.00 0.00 0.00 3.85
1340 1585 0.386113 GGTCGCTCACTCATACTCCC 59.614 60.000 0.00 0.00 0.00 4.30
1342 1587 1.335496 GTCGCTCACTCATACTCCCTC 59.665 57.143 0.00 0.00 0.00 4.30
1344 1589 0.671251 GCTCACTCATACTCCCTCCG 59.329 60.000 0.00 0.00 0.00 4.63
1345 1590 2.024825 GCTCACTCATACTCCCTCCGT 61.025 57.143 0.00 0.00 0.00 4.69
1346 1591 2.379972 CTCACTCATACTCCCTCCGTT 58.620 52.381 0.00 0.00 0.00 4.44
1347 1592 2.359531 CTCACTCATACTCCCTCCGTTC 59.640 54.545 0.00 0.00 0.00 3.95
1348 1593 1.409427 CACTCATACTCCCTCCGTTCC 59.591 57.143 0.00 0.00 0.00 3.62
1349 1594 1.006758 ACTCATACTCCCTCCGTTCCA 59.993 52.381 0.00 0.00 0.00 3.53
1350 1595 1.409427 CTCATACTCCCTCCGTTCCAC 59.591 57.143 0.00 0.00 0.00 4.02
1351 1596 1.191535 CATACTCCCTCCGTTCCACA 58.808 55.000 0.00 0.00 0.00 4.17
1352 1597 1.553248 CATACTCCCTCCGTTCCACAA 59.447 52.381 0.00 0.00 0.00 3.33
1353 1598 1.946984 TACTCCCTCCGTTCCACAAT 58.053 50.000 0.00 0.00 0.00 2.71
1354 1599 1.946984 ACTCCCTCCGTTCCACAATA 58.053 50.000 0.00 0.00 0.00 1.90
1355 1600 1.553704 ACTCCCTCCGTTCCACAATAC 59.446 52.381 0.00 0.00 0.00 1.89
1356 1601 1.831736 CTCCCTCCGTTCCACAATACT 59.168 52.381 0.00 0.00 0.00 2.12
1357 1602 2.236395 CTCCCTCCGTTCCACAATACTT 59.764 50.000 0.00 0.00 0.00 2.24
1358 1603 2.027561 TCCCTCCGTTCCACAATACTTG 60.028 50.000 0.00 0.00 0.00 3.16
1359 1604 1.737793 CCTCCGTTCCACAATACTTGC 59.262 52.381 0.00 0.00 0.00 4.01
1360 1605 1.737793 CTCCGTTCCACAATACTTGCC 59.262 52.381 0.00 0.00 0.00 4.52
1361 1606 1.349688 TCCGTTCCACAATACTTGCCT 59.650 47.619 0.00 0.00 0.00 4.75
1362 1607 2.159382 CCGTTCCACAATACTTGCCTT 58.841 47.619 0.00 0.00 0.00 4.35
1363 1608 2.556622 CCGTTCCACAATACTTGCCTTT 59.443 45.455 0.00 0.00 0.00 3.11
1364 1609 3.365969 CCGTTCCACAATACTTGCCTTTC 60.366 47.826 0.00 0.00 0.00 2.62
1365 1610 3.365969 CGTTCCACAATACTTGCCTTTCC 60.366 47.826 0.00 0.00 0.00 3.13
1366 1611 3.806949 TCCACAATACTTGCCTTTCCT 57.193 42.857 0.00 0.00 0.00 3.36
1367 1612 4.112634 TCCACAATACTTGCCTTTCCTT 57.887 40.909 0.00 0.00 0.00 3.36
1368 1613 4.479158 TCCACAATACTTGCCTTTCCTTT 58.521 39.130 0.00 0.00 0.00 3.11
1369 1614 4.280677 TCCACAATACTTGCCTTTCCTTTG 59.719 41.667 0.00 0.00 0.00 2.77
1370 1615 4.039124 CCACAATACTTGCCTTTCCTTTGT 59.961 41.667 0.00 0.00 0.00 2.83
1371 1616 5.222631 CACAATACTTGCCTTTCCTTTGTC 58.777 41.667 0.00 0.00 0.00 3.18
1372 1617 4.892934 ACAATACTTGCCTTTCCTTTGTCA 59.107 37.500 0.00 0.00 0.00 3.58
1373 1618 5.362430 ACAATACTTGCCTTTCCTTTGTCAA 59.638 36.000 0.00 0.00 0.00 3.18
1374 1619 6.127196 ACAATACTTGCCTTTCCTTTGTCAAA 60.127 34.615 0.00 0.00 0.00 2.69
1375 1620 4.817318 ACTTGCCTTTCCTTTGTCAAAA 57.183 36.364 0.00 0.00 0.00 2.44
1376 1621 5.357742 ACTTGCCTTTCCTTTGTCAAAAT 57.642 34.783 0.00 0.00 0.00 1.82
1377 1622 6.478512 ACTTGCCTTTCCTTTGTCAAAATA 57.521 33.333 0.00 0.00 0.00 1.40
1378 1623 7.066307 ACTTGCCTTTCCTTTGTCAAAATAT 57.934 32.000 0.00 0.00 0.00 1.28
1379 1624 8.189119 ACTTGCCTTTCCTTTGTCAAAATATA 57.811 30.769 0.00 0.00 0.00 0.86
1380 1625 8.306761 ACTTGCCTTTCCTTTGTCAAAATATAG 58.693 33.333 0.00 0.00 0.00 1.31
1381 1626 8.415950 TTGCCTTTCCTTTGTCAAAATATAGA 57.584 30.769 0.00 0.00 0.00 1.98
1382 1627 8.593945 TGCCTTTCCTTTGTCAAAATATAGAT 57.406 30.769 0.00 0.00 0.00 1.98
1383 1628 8.469200 TGCCTTTCCTTTGTCAAAATATAGATG 58.531 33.333 0.00 0.00 0.00 2.90
1384 1629 8.470002 GCCTTTCCTTTGTCAAAATATAGATGT 58.530 33.333 0.00 0.00 0.00 3.06
1448 1693 8.748412 TGGATAAATGGAAGTCAAGTATTTTGG 58.252 33.333 0.00 0.00 0.00 3.28
1449 1694 8.966868 GGATAAATGGAAGTCAAGTATTTTGGA 58.033 33.333 0.00 0.00 0.00 3.53
1452 1697 5.682943 TGGAAGTCAAGTATTTTGGAACG 57.317 39.130 0.00 0.00 0.00 3.95
1453 1698 4.517453 TGGAAGTCAAGTATTTTGGAACGG 59.483 41.667 0.00 0.00 0.00 4.44
1454 1699 4.758165 GGAAGTCAAGTATTTTGGAACGGA 59.242 41.667 0.00 0.00 0.00 4.69
1455 1700 5.106673 GGAAGTCAAGTATTTTGGAACGGAG 60.107 44.000 0.00 0.00 0.00 4.63
1456 1701 4.324267 AGTCAAGTATTTTGGAACGGAGG 58.676 43.478 0.00 0.00 0.00 4.30
1457 1702 3.439129 GTCAAGTATTTTGGAACGGAGGG 59.561 47.826 0.00 0.00 0.00 4.30
1458 1703 3.328343 TCAAGTATTTTGGAACGGAGGGA 59.672 43.478 0.00 0.00 0.00 4.20
1459 1704 3.629142 AGTATTTTGGAACGGAGGGAG 57.371 47.619 0.00 0.00 0.00 4.30
1460 1705 2.910977 AGTATTTTGGAACGGAGGGAGT 59.089 45.455 0.00 0.00 0.00 3.85
1461 1706 4.098894 AGTATTTTGGAACGGAGGGAGTA 58.901 43.478 0.00 0.00 0.00 2.59
1462 1707 2.845363 TTTTGGAACGGAGGGAGTAC 57.155 50.000 0.00 0.00 0.00 2.73
1463 1708 2.019807 TTTGGAACGGAGGGAGTACT 57.980 50.000 0.00 0.00 0.00 2.73
1464 1709 2.019807 TTGGAACGGAGGGAGTACTT 57.980 50.000 0.00 0.00 0.00 2.24
1465 1710 2.019807 TGGAACGGAGGGAGTACTTT 57.980 50.000 0.00 0.00 0.00 2.66
1466 1711 1.621814 TGGAACGGAGGGAGTACTTTG 59.378 52.381 0.00 0.00 0.00 2.77
1467 1712 1.622312 GGAACGGAGGGAGTACTTTGT 59.378 52.381 0.00 0.00 0.00 2.83
1470 1715 1.270678 ACGGAGGGAGTACTTTGTTGC 60.271 52.381 0.00 0.00 0.00 4.17
1481 1726 5.555017 AGTACTTTGTTGCTGATGTGATCT 58.445 37.500 0.00 0.00 0.00 2.75
1603 1888 4.770795 ACATAGGCATCACACTCCTTAAC 58.229 43.478 0.00 0.00 0.00 2.01
1712 2000 8.270744 ACCTAAACAGCTCTCAGATTCATTTAT 58.729 33.333 0.00 0.00 0.00 1.40
1824 2114 1.366435 AGGTACTCCCTCTGTCCCATT 59.634 52.381 0.00 0.00 40.71 3.16
1827 2117 4.422592 AGGTACTCCCTCTGTCCCATTATA 59.577 45.833 0.00 0.00 40.71 0.98
1835 2125 6.673978 TCCCTCTGTCCCATTATATAAGATGG 59.326 42.308 7.81 7.81 41.99 3.51
1837 2127 7.623677 CCCTCTGTCCCATTATATAAGATGGTA 59.376 40.741 12.20 0.00 40.98 3.25
1892 2182 9.798994 GTAATAACATCTTATAGTATGGGACGG 57.201 37.037 0.00 0.00 0.00 4.79
1893 2183 8.660295 AATAACATCTTATAGTATGGGACGGA 57.340 34.615 0.00 0.00 0.00 4.69
1948 2238 7.530426 AGATTATCACATTTAGCATTTCCCC 57.470 36.000 0.00 0.00 0.00 4.81
1949 2239 5.766150 TTATCACATTTAGCATTTCCCCG 57.234 39.130 0.00 0.00 0.00 5.73
1954 2269 4.625311 CACATTTAGCATTTCCCCGTTTTC 59.375 41.667 0.00 0.00 0.00 2.29
2050 2675 3.853355 AGGCCAGAATCATAGGACAAG 57.147 47.619 5.01 0.00 30.87 3.16
2332 2957 9.553064 AAGCAGGAGTAAGTGAAATCTATATTG 57.447 33.333 0.00 0.00 0.00 1.90
2333 2958 8.709308 AGCAGGAGTAAGTGAAATCTATATTGT 58.291 33.333 0.00 0.00 0.00 2.71
2334 2959 9.982651 GCAGGAGTAAGTGAAATCTATATTGTA 57.017 33.333 0.00 0.00 0.00 2.41
2337 2962 9.708092 GGAGTAAGTGAAATCTATATTGTACCC 57.292 37.037 0.00 0.00 0.00 3.69
2338 2963 9.708092 GAGTAAGTGAAATCTATATTGTACCCC 57.292 37.037 0.00 0.00 0.00 4.95
2339 2964 8.657712 AGTAAGTGAAATCTATATTGTACCCCC 58.342 37.037 0.00 0.00 0.00 5.40
2340 2965 7.707467 AAGTGAAATCTATATTGTACCCCCT 57.293 36.000 0.00 0.00 0.00 4.79
2341 2966 7.079451 AGTGAAATCTATATTGTACCCCCTG 57.921 40.000 0.00 0.00 0.00 4.45
2342 2967 6.619852 AGTGAAATCTATATTGTACCCCCTGT 59.380 38.462 0.00 0.00 0.00 4.00
2343 2968 6.710744 GTGAAATCTATATTGTACCCCCTGTG 59.289 42.308 0.00 0.00 0.00 3.66
2344 2969 6.388689 TGAAATCTATATTGTACCCCCTGTGT 59.611 38.462 0.00 0.00 0.00 3.72
2345 2970 7.569485 TGAAATCTATATTGTACCCCCTGTGTA 59.431 37.037 0.00 0.00 0.00 2.90
2346 2971 7.941053 AATCTATATTGTACCCCCTGTGTAA 57.059 36.000 0.00 0.00 0.00 2.41
2347 2972 7.941053 ATCTATATTGTACCCCCTGTGTAAA 57.059 36.000 0.00 0.00 0.00 2.01
2348 2973 7.369551 TCTATATTGTACCCCCTGTGTAAAG 57.630 40.000 0.00 0.00 0.00 1.85
2349 2974 7.134162 TCTATATTGTACCCCCTGTGTAAAGA 58.866 38.462 0.00 0.00 0.00 2.52
2350 2975 6.645884 ATATTGTACCCCCTGTGTAAAGAA 57.354 37.500 0.00 0.00 0.00 2.52
2351 2976 3.775261 TGTACCCCCTGTGTAAAGAAC 57.225 47.619 0.00 0.00 0.00 3.01
2352 2977 3.320129 TGTACCCCCTGTGTAAAGAACT 58.680 45.455 0.00 0.00 0.00 3.01
2353 2978 2.951229 ACCCCCTGTGTAAAGAACTG 57.049 50.000 0.00 0.00 0.00 3.16
2354 2979 2.132686 ACCCCCTGTGTAAAGAACTGT 58.867 47.619 0.00 0.00 0.00 3.55
2355 2980 3.320129 ACCCCCTGTGTAAAGAACTGTA 58.680 45.455 0.00 0.00 0.00 2.74
2356 2981 3.717913 ACCCCCTGTGTAAAGAACTGTAA 59.282 43.478 0.00 0.00 0.00 2.41
2357 2982 4.202430 ACCCCCTGTGTAAAGAACTGTAAG 60.202 45.833 0.00 0.00 42.29 2.34
2358 2983 4.041198 CCCCCTGTGTAAAGAACTGTAAGA 59.959 45.833 0.00 0.00 37.43 2.10
2359 2984 4.995487 CCCCTGTGTAAAGAACTGTAAGAC 59.005 45.833 0.00 0.00 37.43 3.01
2360 2985 4.684703 CCCTGTGTAAAGAACTGTAAGACG 59.315 45.833 0.00 0.00 37.43 4.18
2361 2986 5.287226 CCTGTGTAAAGAACTGTAAGACGT 58.713 41.667 0.00 0.00 37.43 4.34
2362 2987 5.751990 CCTGTGTAAAGAACTGTAAGACGTT 59.248 40.000 0.00 0.00 37.43 3.99
2363 2988 6.257193 CCTGTGTAAAGAACTGTAAGACGTTT 59.743 38.462 0.00 0.00 37.43 3.60
2364 2989 7.201582 CCTGTGTAAAGAACTGTAAGACGTTTT 60.202 37.037 0.00 0.00 37.43 2.43
2365 2990 8.700722 TGTGTAAAGAACTGTAAGACGTTTTA 57.299 30.769 0.00 0.00 37.43 1.52
2366 2991 8.810427 TGTGTAAAGAACTGTAAGACGTTTTAG 58.190 33.333 0.00 0.00 37.43 1.85
2367 2992 8.271487 GTGTAAAGAACTGTAAGACGTTTTAGG 58.729 37.037 0.00 0.00 37.43 2.69
2368 2993 7.981225 TGTAAAGAACTGTAAGACGTTTTAGGT 59.019 33.333 0.00 0.00 37.43 3.08
2369 2994 7.474398 AAAGAACTGTAAGACGTTTTAGGTC 57.526 36.000 0.00 0.00 37.43 3.85
2370 2995 6.152932 AGAACTGTAAGACGTTTTAGGTCA 57.847 37.500 8.78 0.05 35.60 4.02
2371 2996 5.981915 AGAACTGTAAGACGTTTTAGGTCAC 59.018 40.000 8.78 0.00 35.60 3.67
2372 2997 5.526506 ACTGTAAGACGTTTTAGGTCACT 57.473 39.130 0.00 0.00 35.60 3.41
2373 2998 6.639632 ACTGTAAGACGTTTTAGGTCACTA 57.360 37.500 0.00 0.00 35.60 2.74
2374 2999 7.042797 ACTGTAAGACGTTTTAGGTCACTAA 57.957 36.000 0.00 0.00 35.60 2.24
2375 3000 7.664758 ACTGTAAGACGTTTTAGGTCACTAAT 58.335 34.615 0.00 0.00 36.83 1.73
2376 3001 8.146412 ACTGTAAGACGTTTTAGGTCACTAATT 58.854 33.333 0.00 0.00 36.83 1.40
2377 3002 9.630098 CTGTAAGACGTTTTAGGTCACTAATTA 57.370 33.333 0.00 0.00 35.93 1.40
2378 3003 9.630098 TGTAAGACGTTTTAGGTCACTAATTAG 57.370 33.333 11.05 11.05 38.87 1.73
2379 3004 9.631452 GTAAGACGTTTTAGGTCACTAATTAGT 57.369 33.333 12.50 12.50 38.87 2.24
2382 3007 9.631452 AGACGTTTTAGGTCACTAATTAGTAAC 57.369 33.333 17.62 13.74 38.87 2.50
2383 3008 8.763049 ACGTTTTAGGTCACTAATTAGTAACC 57.237 34.615 25.24 25.24 43.65 2.85
2391 3016 8.763049 GGTCACTAATTAGTAACCTAAAACGT 57.237 34.615 25.29 0.00 40.74 3.99
2392 3017 8.864024 GGTCACTAATTAGTAACCTAAAACGTC 58.136 37.037 25.29 6.01 40.74 4.34
2393 3018 9.631452 GTCACTAATTAGTAACCTAAAACGTCT 57.369 33.333 17.62 0.00 36.76 4.18
2610 3235 1.757118 GATACCCTGACAGCTGCTACA 59.243 52.381 15.27 10.94 0.00 2.74
2673 3298 6.231211 AGGTGGTGTTAGTGATCTAGTTTTG 58.769 40.000 0.00 0.00 0.00 2.44
2697 3322 3.181476 GGTATGCACATTTTGGGATGGTC 60.181 47.826 0.00 0.00 0.00 4.02
2766 3391 7.066284 ACAGAAGCATTACATTTGTATCCAGAC 59.934 37.037 0.00 0.00 0.00 3.51
2800 3425 2.032680 ACGGCACAAGTGTACAGTTT 57.967 45.000 13.37 0.00 0.00 2.66
2822 3447 9.505995 AGTTTACAGTATTTTTGTTTTGTACCG 57.494 29.630 0.00 0.00 0.00 4.02
2833 3458 3.148412 GTTTTGTACCGCCTTTTCCCTA 58.852 45.455 0.00 0.00 0.00 3.53
2859 3484 9.938280 ATATTCTTTGCTAGTAGTGTTGTGTTA 57.062 29.630 0.00 0.00 0.00 2.41
2912 3537 5.125900 TGATGGTGTCTCTGGCAAATATTTG 59.874 40.000 21.54 21.54 41.03 2.32
3027 3652 0.109597 CATTTGCTCCAGGTTCGCAC 60.110 55.000 1.13 0.00 32.71 5.34
3142 3767 6.590677 GGTTCTCCAGTGTACTTGTAATCTTC 59.409 42.308 0.00 0.00 0.00 2.87
3329 3954 6.348786 CGGATCATAAAATAGGAACTGCCATG 60.349 42.308 0.00 0.00 41.52 3.66
3365 3990 6.464222 TCCTAAAAATGGTACTGTCAGACTG 58.536 40.000 6.91 5.91 0.00 3.51
3459 4084 3.131396 CCCAGCTTATGTACGAACCATC 58.869 50.000 0.00 0.00 0.00 3.51
3548 4173 2.868583 CTGGTGCAGACTTGGATATTCG 59.131 50.000 0.00 0.00 32.44 3.34
3569 4194 6.812879 TCGGATCTAAGAACATCGCTTATA 57.187 37.500 0.00 0.00 0.00 0.98
3581 4206 9.646427 AGAACATCGCTTATATTTCTCCTTATC 57.354 33.333 0.00 0.00 0.00 1.75
3635 4260 5.107220 CCTTTCACAAGATTGCAATTCTTGC 60.107 40.000 30.53 15.47 43.93 4.01
3825 4451 7.018851 TCAGAGGTACCCTTTTATTTACCCTTT 59.981 37.037 8.74 0.00 35.50 3.11
3826 4452 7.338703 CAGAGGTACCCTTTTATTTACCCTTTC 59.661 40.741 8.74 0.00 35.50 2.62
3827 4453 7.241251 AGAGGTACCCTTTTATTTACCCTTTCT 59.759 37.037 8.74 0.00 35.50 2.52
3828 4454 7.772686 AGGTACCCTTTTATTTACCCTTTCTT 58.227 34.615 8.74 0.00 35.50 2.52
3866 4527 9.332502 TGCCATAACTGTTAATTCAATACGTAT 57.667 29.630 1.14 1.14 0.00 3.06
4057 4724 2.267006 CAGGTGACGGCATCTGCT 59.733 61.111 20.70 0.00 45.49 4.24
4084 4751 4.588899 TGAATGATCTCCGTCACCAAATT 58.411 39.130 0.00 0.00 0.00 1.82
4299 4971 9.544579 TTCATAAATCCATTGGCATTATCCATA 57.455 29.630 0.00 0.00 35.77 2.74
4474 5152 8.706322 AAGAAATAACAACTTCCACTACCAAT 57.294 30.769 0.00 0.00 0.00 3.16
4504 5182 5.410924 TCTGAATCCACTTCACTATTGACG 58.589 41.667 0.00 0.00 38.97 4.35
5132 5813 0.824759 GTAGGTGGTAGCCCTGACAG 59.175 60.000 11.01 0.00 33.35 3.51
5284 5965 4.551603 CGCTTGTCACAACTTTTCTCAGAG 60.552 45.833 0.00 0.00 0.00 3.35
5289 5973 7.895975 TGTCACAACTTTTCTCAGAGATATG 57.104 36.000 0.00 1.73 0.00 1.78
5290 5974 7.670364 TGTCACAACTTTTCTCAGAGATATGA 58.330 34.615 0.00 0.00 0.00 2.15
5291 5975 8.316946 TGTCACAACTTTTCTCAGAGATATGAT 58.683 33.333 0.00 0.00 0.00 2.45
5292 5976 9.809096 GTCACAACTTTTCTCAGAGATATGATA 57.191 33.333 0.00 0.00 0.00 2.15
5416 6210 6.555812 AATCTTTTAGGTCTTGTTCGGTTC 57.444 37.500 0.00 0.00 0.00 3.62
5435 6229 3.634397 TCCATGACAAATGAGAGGGAC 57.366 47.619 0.00 0.00 0.00 4.46
5504 6298 3.849574 TCCATTCCACTCCAATCCACTTA 59.150 43.478 0.00 0.00 0.00 2.24
5563 6359 5.707298 AGCAGCAGTGTTTGATTACTGTAAT 59.293 36.000 12.62 12.62 44.66 1.89
5604 6400 7.721399 ACATTCCTACTGTGAAAGTTTGATTCT 59.279 33.333 0.00 0.00 40.56 2.40
5652 6448 4.898320 TCTTTCATTGAGAAGCAGCACTA 58.102 39.130 0.00 0.00 37.57 2.74
5744 6541 7.656137 TCAACATGTAAAACAGAGAAGTAGTCC 59.344 37.037 0.00 0.00 0.00 3.85
5857 6654 1.271379 GCCCTAGAAGAACTGGTTGCA 60.271 52.381 0.00 0.00 0.00 4.08
5951 6748 1.851666 CATCTCTTCTCGCTTCTTCGC 59.148 52.381 0.00 0.00 0.00 4.70
5955 6752 1.132643 TCTTCTCGCTTCTTCGCCTAC 59.867 52.381 0.00 0.00 0.00 3.18
6016 6813 2.783135 TCAGTTGAAGCCATGGTCTTC 58.217 47.619 28.06 28.06 40.13 2.87
6052 6849 1.733041 CTCGGTTTTCGCGAGCTCA 60.733 57.895 15.40 0.00 39.05 4.26
6054 6851 0.171679 TCGGTTTTCGCGAGCTCATA 59.828 50.000 15.40 0.00 39.05 2.15
6088 6885 0.881118 CTGCTGGCTTTTCCGCTTTA 59.119 50.000 0.00 0.00 37.80 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 47 1.647545 AAGCGGCGCGTACTGTACTA 61.648 55.000 27.59 0.00 0.00 1.82
47 48 1.647545 TAAGCGGCGCGTACTGTACT 61.648 55.000 27.59 1.71 0.00 2.73
48 49 1.198608 CTAAGCGGCGCGTACTGTAC 61.199 60.000 27.59 7.90 0.00 2.90
49 50 1.063006 CTAAGCGGCGCGTACTGTA 59.937 57.895 27.59 6.64 0.00 2.74
50 51 2.202570 CTAAGCGGCGCGTACTGT 60.203 61.111 27.59 4.38 0.00 3.55
51 52 3.617538 GCTAAGCGGCGCGTACTG 61.618 66.667 27.59 17.10 0.00 2.74
79 80 0.037882 GGCTTTGCTTGCTTCCTTCC 60.038 55.000 0.00 0.00 0.00 3.46
81 82 1.662044 CGGCTTTGCTTGCTTCCTT 59.338 52.632 0.00 0.00 0.00 3.36
83 84 2.431430 GCGGCTTTGCTTGCTTCC 60.431 61.111 0.00 0.00 0.00 3.46
85 86 4.347453 CCGCGGCTTTGCTTGCTT 62.347 61.111 14.67 0.00 0.00 3.91
315 489 3.596459 TTGGGAGGGGAAGGGAGGG 62.596 68.421 0.00 0.00 0.00 4.30
322 496 1.378732 CTAGGGTTTTGGGAGGGGAA 58.621 55.000 0.00 0.00 0.00 3.97
363 538 4.458829 ATCGGGACTGGAGCGGGA 62.459 66.667 0.00 0.00 0.00 5.14
366 541 0.598680 GATTGATCGGGACTGGAGCG 60.599 60.000 0.00 0.00 0.00 5.03
367 542 0.598680 CGATTGATCGGGACTGGAGC 60.599 60.000 5.51 0.00 45.93 4.70
368 543 3.577231 CGATTGATCGGGACTGGAG 57.423 57.895 5.51 0.00 45.93 3.86
378 553 3.038417 CGGGCGGCTCGATTGATC 61.038 66.667 19.23 0.00 0.00 2.92
569 770 2.189594 ACCGTATCGTATCATCCGGA 57.810 50.000 6.61 6.61 38.75 5.14
635 844 1.663074 GCAGCCGCCGATAGAGAAG 60.663 63.158 0.00 0.00 39.76 2.85
688 906 4.915085 AGACAACAACAACAACAACGAAAG 59.085 37.500 0.00 0.00 0.00 2.62
704 922 2.862541 CAGGGAATCAACCAGACAACA 58.137 47.619 0.00 0.00 0.00 3.33
705 923 1.541588 GCAGGGAATCAACCAGACAAC 59.458 52.381 0.00 0.00 0.00 3.32
706 924 1.881925 CGCAGGGAATCAACCAGACAA 60.882 52.381 0.00 0.00 0.00 3.18
707 925 0.321564 CGCAGGGAATCAACCAGACA 60.322 55.000 0.00 0.00 0.00 3.41
708 926 2.471255 CGCAGGGAATCAACCAGAC 58.529 57.895 0.00 0.00 0.00 3.51
754 981 6.575162 AGATCCGAGTTTTTATTTGCAGTT 57.425 33.333 0.00 0.00 0.00 3.16
755 982 6.349363 GGAAGATCCGAGTTTTTATTTGCAGT 60.349 38.462 0.00 0.00 0.00 4.40
756 983 6.030228 GGAAGATCCGAGTTTTTATTTGCAG 58.970 40.000 0.00 0.00 0.00 4.41
757 984 5.710099 AGGAAGATCCGAGTTTTTATTTGCA 59.290 36.000 0.00 0.00 42.75 4.08
758 985 6.094186 AGAGGAAGATCCGAGTTTTTATTTGC 59.906 38.462 0.00 0.00 42.75 3.68
759 986 7.119846 ACAGAGGAAGATCCGAGTTTTTATTTG 59.880 37.037 0.00 0.00 42.75 2.32
806 1033 2.190578 GATCTTGGGGCGGGACAG 59.809 66.667 0.00 0.00 0.00 3.51
849 1079 4.275936 CCTGGGTTAATTTAATCTCTGGCG 59.724 45.833 0.00 0.00 0.00 5.69
850 1080 5.201243 ACCTGGGTTAATTTAATCTCTGGC 58.799 41.667 0.00 0.00 0.00 4.85
851 1081 6.405842 GCAACCTGGGTTAATTTAATCTCTGG 60.406 42.308 4.58 6.30 36.46 3.86
890 1120 3.118519 ACGAACCAAGTTACTGACCAACT 60.119 43.478 0.00 0.00 37.85 3.16
892 1122 3.118702 TGACGAACCAAGTTACTGACCAA 60.119 43.478 0.00 0.00 0.00 3.67
893 1123 2.431419 TGACGAACCAAGTTACTGACCA 59.569 45.455 0.00 0.00 0.00 4.02
894 1124 2.798847 GTGACGAACCAAGTTACTGACC 59.201 50.000 0.00 0.00 0.00 4.02
895 1125 3.714391 AGTGACGAACCAAGTTACTGAC 58.286 45.455 0.00 0.00 37.12 3.51
898 1128 2.480845 GCAGTGACGAACCAAGTTACT 58.519 47.619 0.00 0.00 38.69 2.24
899 1129 1.529865 GGCAGTGACGAACCAAGTTAC 59.470 52.381 0.00 0.00 0.00 2.50
900 1130 1.541670 GGGCAGTGACGAACCAAGTTA 60.542 52.381 0.00 0.00 0.00 2.24
901 1131 0.818040 GGGCAGTGACGAACCAAGTT 60.818 55.000 0.00 0.00 0.00 2.66
902 1132 1.227853 GGGCAGTGACGAACCAAGT 60.228 57.895 0.00 0.00 0.00 3.16
903 1133 1.966451 GGGGCAGTGACGAACCAAG 60.966 63.158 0.00 0.00 0.00 3.61
909 1139 2.184020 CTCCAATGGGGCAGTGACGA 62.184 60.000 0.00 0.00 36.21 4.20
910 1140 1.746615 CTCCAATGGGGCAGTGACG 60.747 63.158 0.00 0.00 36.21 4.35
913 1143 2.757099 GGCTCCAATGGGGCAGTG 60.757 66.667 27.13 0.00 36.21 3.66
936 1181 2.354343 GAGGCCTGGCAAGAAGCT 59.646 61.111 22.05 6.81 44.79 3.74
1068 1313 2.031516 CAGCTTCTCCGTGTGCAGG 61.032 63.158 0.00 0.00 0.00 4.85
1329 1574 1.006758 TGGAACGGAGGGAGTATGAGT 59.993 52.381 0.00 0.00 0.00 3.41
1331 1576 1.272816 TGTGGAACGGAGGGAGTATGA 60.273 52.381 0.00 0.00 42.39 2.15
1333 1578 1.946984 TTGTGGAACGGAGGGAGTAT 58.053 50.000 0.00 0.00 42.39 2.12
1334 1579 1.946984 ATTGTGGAACGGAGGGAGTA 58.053 50.000 0.00 0.00 42.39 2.59
1336 1581 1.831736 AGTATTGTGGAACGGAGGGAG 59.168 52.381 0.00 0.00 42.39 4.30
1337 1582 1.946984 AGTATTGTGGAACGGAGGGA 58.053 50.000 0.00 0.00 42.39 4.20
1351 1596 6.478512 TTTGACAAAGGAAAGGCAAGTATT 57.521 33.333 0.00 0.00 0.00 1.89
1352 1597 6.478512 TTTTGACAAAGGAAAGGCAAGTAT 57.521 33.333 0.10 0.00 0.00 2.12
1353 1598 5.923733 TTTTGACAAAGGAAAGGCAAGTA 57.076 34.783 0.10 0.00 0.00 2.24
1354 1599 4.817318 TTTTGACAAAGGAAAGGCAAGT 57.183 36.364 0.10 0.00 0.00 3.16
1355 1600 8.522830 TCTATATTTTGACAAAGGAAAGGCAAG 58.477 33.333 0.10 0.00 0.00 4.01
1356 1601 8.415950 TCTATATTTTGACAAAGGAAAGGCAA 57.584 30.769 0.10 0.00 0.00 4.52
1357 1602 8.469200 CATCTATATTTTGACAAAGGAAAGGCA 58.531 33.333 0.10 0.00 0.00 4.75
1358 1603 8.470002 ACATCTATATTTTGACAAAGGAAAGGC 58.530 33.333 0.10 0.00 0.00 4.35
1422 1667 8.748412 CCAAAATACTTGACTTCCATTTATCCA 58.252 33.333 0.00 0.00 0.00 3.41
1423 1668 8.966868 TCCAAAATACTTGACTTCCATTTATCC 58.033 33.333 0.00 0.00 0.00 2.59
1426 1671 8.293867 CGTTCCAAAATACTTGACTTCCATTTA 58.706 33.333 0.00 0.00 0.00 1.40
1427 1672 7.145323 CGTTCCAAAATACTTGACTTCCATTT 58.855 34.615 0.00 0.00 0.00 2.32
1428 1673 6.294508 CCGTTCCAAAATACTTGACTTCCATT 60.295 38.462 0.00 0.00 0.00 3.16
1429 1674 5.183140 CCGTTCCAAAATACTTGACTTCCAT 59.817 40.000 0.00 0.00 0.00 3.41
1430 1675 4.517453 CCGTTCCAAAATACTTGACTTCCA 59.483 41.667 0.00 0.00 0.00 3.53
1431 1676 4.758165 TCCGTTCCAAAATACTTGACTTCC 59.242 41.667 0.00 0.00 0.00 3.46
1432 1677 5.106673 CCTCCGTTCCAAAATACTTGACTTC 60.107 44.000 0.00 0.00 0.00 3.01
1433 1678 4.760204 CCTCCGTTCCAAAATACTTGACTT 59.240 41.667 0.00 0.00 0.00 3.01
1434 1679 4.324267 CCTCCGTTCCAAAATACTTGACT 58.676 43.478 0.00 0.00 0.00 3.41
1435 1680 3.439129 CCCTCCGTTCCAAAATACTTGAC 59.561 47.826 0.00 0.00 0.00 3.18
1436 1681 3.328343 TCCCTCCGTTCCAAAATACTTGA 59.672 43.478 0.00 0.00 0.00 3.02
1437 1682 3.681593 TCCCTCCGTTCCAAAATACTTG 58.318 45.455 0.00 0.00 0.00 3.16
1438 1683 3.329814 ACTCCCTCCGTTCCAAAATACTT 59.670 43.478 0.00 0.00 0.00 2.24
1439 1684 2.910977 ACTCCCTCCGTTCCAAAATACT 59.089 45.455 0.00 0.00 0.00 2.12
1440 1685 3.345508 ACTCCCTCCGTTCCAAAATAC 57.654 47.619 0.00 0.00 0.00 1.89
1441 1686 4.098894 AGTACTCCCTCCGTTCCAAAATA 58.901 43.478 0.00 0.00 0.00 1.40
1442 1687 2.910977 AGTACTCCCTCCGTTCCAAAAT 59.089 45.455 0.00 0.00 0.00 1.82
1443 1688 2.332117 AGTACTCCCTCCGTTCCAAAA 58.668 47.619 0.00 0.00 0.00 2.44
1444 1689 2.019807 AGTACTCCCTCCGTTCCAAA 57.980 50.000 0.00 0.00 0.00 3.28
1445 1690 2.019807 AAGTACTCCCTCCGTTCCAA 57.980 50.000 0.00 0.00 0.00 3.53
1446 1691 1.621814 CAAAGTACTCCCTCCGTTCCA 59.378 52.381 0.00 0.00 0.00 3.53
1447 1692 1.622312 ACAAAGTACTCCCTCCGTTCC 59.378 52.381 0.00 0.00 0.00 3.62
1448 1693 3.064931 CAACAAAGTACTCCCTCCGTTC 58.935 50.000 0.00 0.00 0.00 3.95
1449 1694 2.809299 GCAACAAAGTACTCCCTCCGTT 60.809 50.000 0.00 0.00 0.00 4.44
1450 1695 1.270678 GCAACAAAGTACTCCCTCCGT 60.271 52.381 0.00 0.00 0.00 4.69
1451 1696 1.002087 AGCAACAAAGTACTCCCTCCG 59.998 52.381 0.00 0.00 0.00 4.63
1452 1697 2.038557 TCAGCAACAAAGTACTCCCTCC 59.961 50.000 0.00 0.00 0.00 4.30
1453 1698 3.402628 TCAGCAACAAAGTACTCCCTC 57.597 47.619 0.00 0.00 0.00 4.30
1454 1699 3.073062 ACATCAGCAACAAAGTACTCCCT 59.927 43.478 0.00 0.00 0.00 4.20
1455 1700 3.189287 CACATCAGCAACAAAGTACTCCC 59.811 47.826 0.00 0.00 0.00 4.30
1456 1701 4.065088 TCACATCAGCAACAAAGTACTCC 58.935 43.478 0.00 0.00 0.00 3.85
1457 1702 5.641209 AGATCACATCAGCAACAAAGTACTC 59.359 40.000 0.00 0.00 0.00 2.59
1458 1703 5.410746 CAGATCACATCAGCAACAAAGTACT 59.589 40.000 0.00 0.00 0.00 2.73
1459 1704 5.180117 ACAGATCACATCAGCAACAAAGTAC 59.820 40.000 0.00 0.00 0.00 2.73
1460 1705 5.308014 ACAGATCACATCAGCAACAAAGTA 58.692 37.500 0.00 0.00 0.00 2.24
1461 1706 4.139786 ACAGATCACATCAGCAACAAAGT 58.860 39.130 0.00 0.00 0.00 2.66
1462 1707 4.761235 ACAGATCACATCAGCAACAAAG 57.239 40.909 0.00 0.00 0.00 2.77
1463 1708 4.793678 GCAACAGATCACATCAGCAACAAA 60.794 41.667 0.00 0.00 0.00 2.83
1464 1709 3.304861 GCAACAGATCACATCAGCAACAA 60.305 43.478 0.00 0.00 0.00 2.83
1465 1710 2.227149 GCAACAGATCACATCAGCAACA 59.773 45.455 0.00 0.00 0.00 3.33
1466 1711 2.486982 AGCAACAGATCACATCAGCAAC 59.513 45.455 0.00 0.00 0.00 4.17
1467 1712 2.745821 GAGCAACAGATCACATCAGCAA 59.254 45.455 0.00 0.00 0.00 3.91
1470 1715 4.936411 AGAAAGAGCAACAGATCACATCAG 59.064 41.667 0.00 0.00 0.00 2.90
1481 1726 9.944376 AAGTATCATAGTTAAGAAAGAGCAACA 57.056 29.630 0.00 0.00 0.00 3.33
1511 1756 0.830648 TCCCTATCGGCTTCCAACAG 59.169 55.000 0.00 0.00 0.00 3.16
1537 1782 7.490840 TCCTACATGGCAATGTTTATGATTTG 58.509 34.615 13.06 0.00 44.94 2.32
1603 1888 8.028354 AGAAGCGATAAGAACAGATGATAGATG 58.972 37.037 0.00 0.00 0.00 2.90
1651 1939 9.530633 CAACTATATGGTAAGACTAAGACAACC 57.469 37.037 0.00 0.00 0.00 3.77
1749 2039 2.743664 TCGTTCATGCAGTTTCATCAGG 59.256 45.455 0.00 0.00 0.00 3.86
1882 2172 3.253677 CAGATACTCACTCCGTCCCATAC 59.746 52.174 0.00 0.00 0.00 2.39
1888 2178 5.123502 TCACTTAACAGATACTCACTCCGTC 59.876 44.000 0.00 0.00 0.00 4.79
1889 2179 5.008331 TCACTTAACAGATACTCACTCCGT 58.992 41.667 0.00 0.00 0.00 4.69
1890 2180 5.562506 TCACTTAACAGATACTCACTCCG 57.437 43.478 0.00 0.00 0.00 4.63
1892 2182 6.688578 TGGTTCACTTAACAGATACTCACTC 58.311 40.000 0.00 0.00 40.08 3.51
1893 2183 6.665992 TGGTTCACTTAACAGATACTCACT 57.334 37.500 0.00 0.00 40.08 3.41
1895 2185 7.676004 TGAATGGTTCACTTAACAGATACTCA 58.324 34.615 0.00 0.00 40.08 3.41
1935 2225 2.563620 GGGAAAACGGGGAAATGCTAAA 59.436 45.455 0.00 0.00 0.00 1.85
1939 2229 0.682292 TTGGGAAAACGGGGAAATGC 59.318 50.000 0.00 0.00 0.00 3.56
1946 2236 4.036380 GCAGTAATCTATTGGGAAAACGGG 59.964 45.833 0.00 0.00 0.00 5.28
1948 2238 4.881850 AGGCAGTAATCTATTGGGAAAACG 59.118 41.667 0.00 0.00 0.00 3.60
1949 2239 6.826741 TGTAGGCAGTAATCTATTGGGAAAAC 59.173 38.462 0.00 0.00 0.00 2.43
1954 2269 5.182001 GCATTGTAGGCAGTAATCTATTGGG 59.818 44.000 0.00 0.00 0.00 4.12
2050 2675 9.434559 GTTCAAGTCATTAACAGTTCAAAGTAC 57.565 33.333 0.00 0.00 0.00 2.73
2325 2950 7.369551 TCTTTACACAGGGGGTACAATATAG 57.630 40.000 0.00 0.00 0.00 1.31
2331 2956 3.071892 CAGTTCTTTACACAGGGGGTACA 59.928 47.826 0.00 0.00 0.00 2.90
2332 2957 3.072038 ACAGTTCTTTACACAGGGGGTAC 59.928 47.826 0.00 0.00 0.00 3.34
2333 2958 3.320129 ACAGTTCTTTACACAGGGGGTA 58.680 45.455 0.00 0.00 0.00 3.69
2334 2959 2.132686 ACAGTTCTTTACACAGGGGGT 58.867 47.619 0.00 0.00 0.00 4.95
2335 2960 2.951229 ACAGTTCTTTACACAGGGGG 57.049 50.000 0.00 0.00 0.00 5.40
2336 2961 4.995487 GTCTTACAGTTCTTTACACAGGGG 59.005 45.833 0.00 0.00 0.00 4.79
2337 2962 4.684703 CGTCTTACAGTTCTTTACACAGGG 59.315 45.833 0.00 0.00 0.00 4.45
2338 2963 5.287226 ACGTCTTACAGTTCTTTACACAGG 58.713 41.667 0.00 0.00 0.00 4.00
2339 2964 6.823678 AACGTCTTACAGTTCTTTACACAG 57.176 37.500 0.00 0.00 0.00 3.66
2340 2965 7.599630 AAAACGTCTTACAGTTCTTTACACA 57.400 32.000 0.00 0.00 0.00 3.72
2341 2966 8.271487 CCTAAAACGTCTTACAGTTCTTTACAC 58.729 37.037 0.00 0.00 0.00 2.90
2342 2967 7.981225 ACCTAAAACGTCTTACAGTTCTTTACA 59.019 33.333 0.00 0.00 0.00 2.41
2343 2968 8.357796 ACCTAAAACGTCTTACAGTTCTTTAC 57.642 34.615 0.00 0.00 0.00 2.01
2344 2969 8.196771 TGACCTAAAACGTCTTACAGTTCTTTA 58.803 33.333 0.00 0.00 0.00 1.85
2345 2970 7.010830 GTGACCTAAAACGTCTTACAGTTCTTT 59.989 37.037 0.00 0.00 0.00 2.52
2346 2971 6.478016 GTGACCTAAAACGTCTTACAGTTCTT 59.522 38.462 0.00 0.00 0.00 2.52
2347 2972 5.981915 GTGACCTAAAACGTCTTACAGTTCT 59.018 40.000 0.00 0.00 0.00 3.01
2348 2973 5.981915 AGTGACCTAAAACGTCTTACAGTTC 59.018 40.000 0.00 0.00 0.00 3.01
2349 2974 5.910614 AGTGACCTAAAACGTCTTACAGTT 58.089 37.500 0.00 0.00 0.00 3.16
2350 2975 5.526506 AGTGACCTAAAACGTCTTACAGT 57.473 39.130 0.00 0.00 0.00 3.55
2351 2976 8.530269 AATTAGTGACCTAAAACGTCTTACAG 57.470 34.615 0.00 0.00 36.76 2.74
2352 2977 9.630098 CTAATTAGTGACCTAAAACGTCTTACA 57.370 33.333 4.18 0.00 36.76 2.41
2353 2978 9.631452 ACTAATTAGTGACCTAAAACGTCTTAC 57.369 33.333 17.35 0.00 36.76 2.34
2356 2981 9.631452 GTTACTAATTAGTGACCTAAAACGTCT 57.369 33.333 25.27 0.00 36.98 4.18
2367 2992 9.631452 AGACGTTTTAGGTTACTAATTAGTGAC 57.369 33.333 25.02 25.02 40.76 3.67
2452 3077 7.103641 TCAGTCAACAGTAAACAGTTCTTCTT 58.896 34.615 0.00 0.00 0.00 2.52
2453 3078 6.640518 TCAGTCAACAGTAAACAGTTCTTCT 58.359 36.000 0.00 0.00 0.00 2.85
2454 3079 6.903883 TCAGTCAACAGTAAACAGTTCTTC 57.096 37.500 0.00 0.00 0.00 2.87
2610 3235 0.251341 GGAATGGAACCACAGCACCT 60.251 55.000 0.00 0.00 0.00 4.00
2673 3298 1.859302 TCCCAAAATGTGCATACCCC 58.141 50.000 0.00 0.00 0.00 4.95
2697 3322 1.301244 AATCCATCTAGCCGCTGCG 60.301 57.895 16.34 16.34 44.33 5.18
2766 3391 8.120465 CACTTGTGCCGTACCTTTATTTTATAG 58.880 37.037 0.00 0.00 0.00 1.31
2800 3425 6.262720 AGGCGGTACAAAACAAAAATACTGTA 59.737 34.615 0.00 0.00 0.00 2.74
2822 3447 6.773200 ACTAGCAAAGAATATAGGGAAAAGGC 59.227 38.462 0.00 0.00 0.00 4.35
2833 3458 8.848474 AACACAACACTACTAGCAAAGAATAT 57.152 30.769 0.00 0.00 0.00 1.28
2912 3537 5.507315 CCAAGTGAATGTCCAACAACCTAAC 60.507 44.000 0.00 0.00 0.00 2.34
3027 3652 7.796838 TCTTCAGACAGAAAAACATCATAACG 58.203 34.615 0.00 0.00 35.40 3.18
3163 3788 4.815533 ATCCATGACCTAATCGATGGAG 57.184 45.455 8.68 4.86 42.89 3.86
3166 3791 8.552083 TCATTTAATCCATGACCTAATCGATG 57.448 34.615 0.00 0.00 0.00 3.84
3171 3796 7.395489 GGATGCTCATTTAATCCATGACCTAAT 59.605 37.037 0.00 0.00 39.79 1.73
3216 3841 8.677148 TTAGAAGATAGTGCATTGGGTATTTC 57.323 34.615 0.00 0.00 0.00 2.17
3304 3929 5.063204 TGGCAGTTCCTATTTTATGATCCG 58.937 41.667 0.00 0.00 35.26 4.18
3305 3930 6.716628 TCATGGCAGTTCCTATTTTATGATCC 59.283 38.462 0.00 0.00 35.26 3.36
3329 3954 9.952188 GTACCATTTTTAGGATAGCTTGAAATC 57.048 33.333 0.00 0.00 0.00 2.17
3365 3990 6.097839 TGACAGTACCATTTACCTGAGATACC 59.902 42.308 0.00 0.00 0.00 2.73
3459 4084 4.212214 GGGAGAGCATCACTTATTTAAGCG 59.788 45.833 0.00 0.00 37.82 4.68
3548 4173 9.646427 AGAAATATAAGCGATGTTCTTAGATCC 57.354 33.333 0.00 0.00 29.63 3.36
3569 4194 9.244292 GACTTTTTGTTAGGGATAAGGAGAAAT 57.756 33.333 0.00 0.00 0.00 2.17
3581 4206 3.473625 AGTGGTCGACTTTTTGTTAGGG 58.526 45.455 16.46 0.00 0.00 3.53
3635 4260 9.220767 GGCTAAATCACAACTATATTCTAAGGG 57.779 37.037 0.00 0.00 0.00 3.95
3639 4264 9.778741 CAAGGGCTAAATCACAACTATATTCTA 57.221 33.333 0.00 0.00 0.00 2.10
3789 4415 3.067721 GGTACCTCTGAACGAAGATCG 57.932 52.381 4.06 0.00 46.93 3.69
3825 4451 8.100791 ACAGTTATGGCATTACTAACAAGAAGA 58.899 33.333 17.79 0.00 0.00 2.87
3826 4452 8.268850 ACAGTTATGGCATTACTAACAAGAAG 57.731 34.615 17.79 6.77 0.00 2.85
3827 4453 8.630054 AACAGTTATGGCATTACTAACAAGAA 57.370 30.769 17.79 0.00 0.00 2.52
3828 4454 9.727859 TTAACAGTTATGGCATTACTAACAAGA 57.272 29.630 17.79 1.70 0.00 3.02
3866 4527 9.515226 AGATCTTACTGGTGCAAATAAGTTAAA 57.485 29.630 0.00 0.00 0.00 1.52
4057 4724 1.554617 TGACGGAGATCATTCAGCCAA 59.445 47.619 0.00 0.00 0.00 4.52
4084 4751 3.261643 TGCTCAGGATTCTAGTTTGCTCA 59.738 43.478 0.00 0.00 0.00 4.26
4232 4899 2.608623 AGGGGGTCAAACAAAAGATGG 58.391 47.619 0.00 0.00 0.00 3.51
4299 4971 3.321682 ACACATTGCCAACATTGCTAGTT 59.678 39.130 0.00 0.00 31.69 2.24
4504 5182 0.323629 TGGTTTCCATCGTGGTCTCC 59.676 55.000 4.33 5.89 39.03 3.71
5101 5782 0.616111 CCACCTACAGAGCCAGGTCT 60.616 60.000 0.00 0.00 43.45 3.85
5132 5813 3.129287 ACCAGCAAGCTGTATTGTATTGC 59.871 43.478 19.60 1.00 45.05 3.56
5284 5965 9.624697 GTGAGAAGAGTTGACAGATATCATATC 57.375 37.037 5.32 0.00 0.00 1.63
5289 5973 6.127479 ACCTGTGAGAAGAGTTGACAGATATC 60.127 42.308 0.00 0.00 36.89 1.63
5290 5974 5.719085 ACCTGTGAGAAGAGTTGACAGATAT 59.281 40.000 0.00 0.00 36.89 1.63
5291 5975 5.080337 ACCTGTGAGAAGAGTTGACAGATA 58.920 41.667 0.00 0.00 36.89 1.98
5292 5976 3.900601 ACCTGTGAGAAGAGTTGACAGAT 59.099 43.478 0.00 0.00 36.89 2.90
5294 5978 3.742433 ACCTGTGAGAAGAGTTGACAG 57.258 47.619 0.00 0.00 34.95 3.51
5295 5979 3.706594 AGAACCTGTGAGAAGAGTTGACA 59.293 43.478 0.00 0.00 0.00 3.58
5296 5980 4.202161 TGAGAACCTGTGAGAAGAGTTGAC 60.202 45.833 0.00 0.00 0.00 3.18
5297 5981 3.960755 TGAGAACCTGTGAGAAGAGTTGA 59.039 43.478 0.00 0.00 0.00 3.18
5404 6198 2.920724 TGTCATGGAACCGAACAAGA 57.079 45.000 0.00 0.00 0.00 3.02
5405 6199 3.980646 TTTGTCATGGAACCGAACAAG 57.019 42.857 0.00 0.00 0.00 3.16
5416 6210 3.054875 TCAGTCCCTCTCATTTGTCATGG 60.055 47.826 0.00 0.00 0.00 3.66
5435 6229 7.961351 ACTAGATGAGATTTAATCCCTGTCAG 58.039 38.462 0.00 0.00 0.00 3.51
5468 6262 0.936691 AATGGAGGGGATTTGGGGAG 59.063 55.000 0.00 0.00 0.00 4.30
5469 6263 0.933700 GAATGGAGGGGATTTGGGGA 59.066 55.000 0.00 0.00 0.00 4.81
5504 6298 0.323957 GTTCGGTTAAGCCACTCCCT 59.676 55.000 0.00 0.00 36.97 4.20
5563 6359 9.219603 CAGTAGGAATGTGACTAGAATTTTTGA 57.780 33.333 0.00 0.00 0.00 2.69
5604 6400 5.087323 TCCTCTCTTAAAAGGAGAAGCTGA 58.913 41.667 0.00 0.00 39.04 4.26
5652 6448 7.744087 TTGCTGATACAGTAATCAAACACTT 57.256 32.000 0.00 0.00 35.51 3.16
5744 6541 8.503458 ACATCAAAGAAGATGAAACTATGAGG 57.497 34.615 10.59 0.00 46.51 3.86
5857 6654 1.627297 GCCAGAAGGGAAGGGATCGT 61.627 60.000 0.00 0.00 40.01 3.73
5955 6752 1.001974 TGTCACCACCTGAGAAATCCG 59.998 52.381 0.00 0.00 0.00 4.18
6016 6813 1.396301 GAGCCTTCTGATGAGTTTGCG 59.604 52.381 0.00 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.