Multiple sequence alignment - TraesCS6B01G146500

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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 TraesCS6B01G146500 chr6B 100.000 3168 0 0 1 3168 147055069 147058236 0.000000e+00 5851.0
1 TraesCS6B01G146500 chr6D 90.432 2059 100 43 693 2729 72405237 72407220 0.000000e+00 2621.0
2 TraesCS6B01G146500 chr6D 86.965 537 34 18 147 677 72404748 72405254 3.550000e-159 571.0
3 TraesCS6B01G146500 chr6D 88.670 406 31 8 2719 3116 72407272 72407670 6.150000e-132 481.0
4 TraesCS6B01G146500 chr6A 85.709 2533 191 83 693 3124 89302232 89304694 0.000000e+00 2514.0
5 TraesCS6B01G146500 chr6A 83.054 537 35 31 147 677 89301763 89302249 1.350000e-118 436.0
6 TraesCS6B01G146500 chr3A 71.640 878 175 56 1160 2004 113922422 113921586 1.170000e-39 174.0
7 TraesCS6B01G146500 chr3A 89.691 97 8 2 1412 1507 208222051 208222146 4.290000e-24 122.0
8 TraesCS6B01G146500 chr3A 95.000 60 3 0 1448 1507 208089754 208089695 9.350000e-16 95.3
9 TraesCS6B01G146500 chr3D 89.691 97 8 2 1412 1507 170659602 170659697 4.290000e-24 122.0
10 TraesCS6B01G146500 chr3D 85.870 92 13 0 1415 1506 170558070 170557979 7.230000e-17 99.0
11 TraesCS6B01G146500 chr3D 84.694 98 13 2 1159 1255 95840280 95840184 2.600000e-16 97.1
12 TraesCS6B01G146500 chr3D 95.000 60 3 0 1448 1507 170564417 170564358 9.350000e-16 95.3
13 TraesCS6B01G146500 chr3B 87.500 96 12 0 1412 1507 245964059 245963964 9.290000e-21 111.0
14 TraesCS6B01G146500 chr3B 96.667 60 2 0 1448 1507 245969767 245969708 2.010000e-17 100.0
15 TraesCS6B01G146500 chr3B 84.536 97 15 0 1159 1255 146706994 146706898 2.600000e-16 97.1
16 TraesCS6B01G146500 chr2D 71.591 440 103 17 1076 1507 55630258 55629833 2.010000e-17 100.0
17 TraesCS6B01G146500 chr4B 76.020 196 40 6 1320 1513 139399343 139399533 9.350000e-16 95.3
18 TraesCS6B01G146500 chr4B 76.020 196 40 6 1320 1513 139472488 139472678 9.350000e-16 95.3
19 TraesCS6B01G146500 chr4B 76.020 196 40 6 1320 1513 139510936 139511126 9.350000e-16 95.3
20 TraesCS6B01G146500 chr4B 100.000 29 0 0 47 75 559656413 559656441 2.000000e-03 54.7
21 TraesCS6B01G146500 chr4D 75.824 182 39 4 1320 1500 97605463 97605640 1.570000e-13 87.9
22 TraesCS6B01G146500 chr4D 75.000 196 42 6 1320 1513 97720838 97721028 2.020000e-12 84.2
23 TraesCS6B01G146500 chr4D 74.725 182 41 4 1320 1500 97766036 97765859 3.390000e-10 76.8
24 TraesCS6B01G146500 chr4A 74.872 195 42 6 1320 1512 478339829 478339640 7.280000e-12 82.4
25 TraesCS6B01G146500 chr7D 75.333 150 37 0 1102 1251 478333345 478333494 4.380000e-09 73.1
26 TraesCS6B01G146500 chr7B 75.333 150 37 0 1102 1251 503496241 503496390 4.380000e-09 73.1
27 TraesCS6B01G146500 chr7A 74.667 150 38 0 1102 1251 516990189 516990040 2.040000e-07 67.6


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 TraesCS6B01G146500 chr6B 147055069 147058236 3167 False 5851.000000 5851 100.0000 1 3168 1 chr6B.!!$F1 3167
1 TraesCS6B01G146500 chr6D 72404748 72407670 2922 False 1224.333333 2621 88.6890 147 3116 3 chr6D.!!$F1 2969
2 TraesCS6B01G146500 chr6A 89301763 89304694 2931 False 1475.000000 2514 84.3815 147 3124 2 chr6A.!!$F1 2977

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
718 750 0.179111 ATGGGATCGTACACTGTGCG 60.179 55.0 12.92 12.92 42.54 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2499 2616 0.036732 TCACACTGATTGGACTGGCC 59.963 55.0 0.0 0.0 37.1 5.36 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
60 61 9.561069 AAATTGCTTATCATATACTTTCTCCGT 57.439 29.630 0.00 0.00 0.00 4.69
61 62 9.561069 AATTGCTTATCATATACTTTCTCCGTT 57.439 29.630 0.00 0.00 0.00 4.44
62 63 8.589335 TTGCTTATCATATACTTTCTCCGTTC 57.411 34.615 0.00 0.00 0.00 3.95
63 64 7.152645 TGCTTATCATATACTTTCTCCGTTCC 58.847 38.462 0.00 0.00 0.00 3.62
64 65 7.152645 GCTTATCATATACTTTCTCCGTTCCA 58.847 38.462 0.00 0.00 0.00 3.53
65 66 7.656137 GCTTATCATATACTTTCTCCGTTCCAA 59.344 37.037 0.00 0.00 0.00 3.53
66 67 9.542462 CTTATCATATACTTTCTCCGTTCCAAA 57.458 33.333 0.00 0.00 0.00 3.28
67 68 9.893634 TTATCATATACTTTCTCCGTTCCAAAA 57.106 29.630 0.00 0.00 0.00 2.44
68 69 8.980481 ATCATATACTTTCTCCGTTCCAAAAT 57.020 30.769 0.00 0.00 0.00 1.82
70 71 9.893634 TCATATACTTTCTCCGTTCCAAAATAA 57.106 29.630 0.00 0.00 0.00 1.40
72 73 9.901172 ATATACTTTCTCCGTTCCAAAATAAGT 57.099 29.630 0.00 0.00 0.00 2.24
73 74 6.313744 ACTTTCTCCGTTCCAAAATAAGTG 57.686 37.500 0.00 0.00 0.00 3.16
74 75 5.826208 ACTTTCTCCGTTCCAAAATAAGTGT 59.174 36.000 0.00 0.00 0.00 3.55
75 76 5.682943 TTCTCCGTTCCAAAATAAGTGTG 57.317 39.130 0.00 0.00 0.00 3.82
76 77 4.710324 TCTCCGTTCCAAAATAAGTGTGT 58.290 39.130 0.00 0.00 0.00 3.72
77 78 5.127491 TCTCCGTTCCAAAATAAGTGTGTT 58.873 37.500 0.00 0.00 0.00 3.32
78 79 5.008217 TCTCCGTTCCAAAATAAGTGTGTTG 59.992 40.000 0.00 0.00 0.00 3.33
79 80 4.882427 TCCGTTCCAAAATAAGTGTGTTGA 59.118 37.500 0.00 0.00 0.00 3.18
80 81 5.008217 TCCGTTCCAAAATAAGTGTGTTGAG 59.992 40.000 0.00 0.00 0.00 3.02
81 82 4.675114 CGTTCCAAAATAAGTGTGTTGAGC 59.325 41.667 0.00 0.00 0.00 4.26
82 83 5.505654 CGTTCCAAAATAAGTGTGTTGAGCT 60.506 40.000 0.00 0.00 0.00 4.09
83 84 6.273071 GTTCCAAAATAAGTGTGTTGAGCTT 58.727 36.000 0.00 0.00 0.00 3.74
84 85 7.422399 GTTCCAAAATAAGTGTGTTGAGCTTA 58.578 34.615 0.00 0.00 0.00 3.09
85 86 7.202016 TCCAAAATAAGTGTGTTGAGCTTAG 57.798 36.000 0.00 0.00 0.00 2.18
86 87 6.770785 TCCAAAATAAGTGTGTTGAGCTTAGT 59.229 34.615 0.00 0.00 0.00 2.24
87 88 7.934665 TCCAAAATAAGTGTGTTGAGCTTAGTA 59.065 33.333 0.00 0.00 0.00 1.82
88 89 8.730680 CCAAAATAAGTGTGTTGAGCTTAGTAT 58.269 33.333 0.00 0.00 0.00 2.12
137 138 7.414814 AGTTAAAACATTTATTTTGGCACCG 57.585 32.000 0.00 0.00 33.80 4.94
138 139 7.210873 AGTTAAAACATTTATTTTGGCACCGA 58.789 30.769 0.00 0.00 33.80 4.69
139 140 7.383843 AGTTAAAACATTTATTTTGGCACCGAG 59.616 33.333 0.00 0.00 33.80 4.63
140 141 3.866883 ACATTTATTTTGGCACCGAGG 57.133 42.857 0.00 0.00 0.00 4.63
141 142 2.495669 ACATTTATTTTGGCACCGAGGG 59.504 45.455 0.00 0.00 0.00 4.30
142 143 2.588464 TTTATTTTGGCACCGAGGGA 57.412 45.000 0.00 0.00 0.00 4.20
143 144 2.122783 TTATTTTGGCACCGAGGGAG 57.877 50.000 0.00 0.00 0.00 4.30
144 145 0.988832 TATTTTGGCACCGAGGGAGT 59.011 50.000 0.00 0.00 0.00 3.85
145 146 0.988832 ATTTTGGCACCGAGGGAGTA 59.011 50.000 0.00 0.00 0.00 2.59
155 156 1.540267 CCGAGGGAGTATATCACGTGG 59.460 57.143 17.00 0.00 35.97 4.94
156 157 1.068472 CGAGGGAGTATATCACGTGGC 60.068 57.143 17.00 1.50 35.97 5.01
226 229 4.865925 TGATGTACTTTAACGGACGATTGG 59.134 41.667 0.00 0.00 0.00 3.16
287 295 1.305129 TCGACCGAACCCCACCATA 60.305 57.895 0.00 0.00 0.00 2.74
288 296 1.153509 CGACCGAACCCCACCATAC 60.154 63.158 0.00 0.00 0.00 2.39
289 297 1.890625 CGACCGAACCCCACCATACA 61.891 60.000 0.00 0.00 0.00 2.29
290 298 0.392060 GACCGAACCCCACCATACAC 60.392 60.000 0.00 0.00 0.00 2.90
296 304 2.280308 ACCCCACCATACACTACCAT 57.720 50.000 0.00 0.00 0.00 3.55
360 371 1.683441 CCTTCCCGGTATATGCCCC 59.317 63.158 4.03 0.00 0.00 5.80
402 413 1.262417 GAAAGAACCAACCGAACCGTC 59.738 52.381 0.00 0.00 0.00 4.79
404 415 2.946752 GAACCAACCGAACCGTCGC 61.947 63.158 0.00 0.00 46.28 5.19
405 416 4.974989 ACCAACCGAACCGTCGCC 62.975 66.667 0.00 0.00 46.28 5.54
513 534 1.065551 GATCTTCCCCGGCATTTTTCG 59.934 52.381 0.00 0.00 0.00 3.46
517 538 2.414785 CCCCGGCATTTTTCGAGGG 61.415 63.158 0.00 0.00 38.59 4.30
519 541 1.376609 CCCGGCATTTTTCGAGGGAG 61.377 60.000 0.00 0.00 41.26 4.30
525 547 3.182182 GCATTTTTCGAGGGAGCATTTC 58.818 45.455 0.00 0.00 0.00 2.17
529 551 4.701956 TTTTCGAGGGAGCATTTCATTC 57.298 40.909 0.00 0.00 0.00 2.67
583 605 2.744202 CCAGAGTTGTACCTGCAATCAC 59.256 50.000 0.00 0.00 0.00 3.06
586 608 0.179225 GTTGTACCTGCAATCACGCG 60.179 55.000 3.53 3.53 33.35 6.01
588 617 2.817834 TACCTGCAATCACGCGCC 60.818 61.111 5.73 0.00 33.35 6.53
632 661 2.413837 CACCGTCCACCTTTTAGACTG 58.586 52.381 0.00 0.00 0.00 3.51
633 662 2.044758 ACCGTCCACCTTTTAGACTGT 58.955 47.619 0.00 0.00 0.00 3.55
634 663 2.224209 ACCGTCCACCTTTTAGACTGTG 60.224 50.000 0.00 0.00 0.00 3.66
635 664 1.798813 CGTCCACCTTTTAGACTGTGC 59.201 52.381 0.00 0.00 0.00 4.57
636 665 2.548067 CGTCCACCTTTTAGACTGTGCT 60.548 50.000 0.00 0.00 0.00 4.40
637 666 3.305813 CGTCCACCTTTTAGACTGTGCTA 60.306 47.826 0.00 0.00 0.00 3.49
638 667 3.995048 GTCCACCTTTTAGACTGTGCTAC 59.005 47.826 0.00 0.00 0.00 3.58
639 668 3.901844 TCCACCTTTTAGACTGTGCTACT 59.098 43.478 0.00 0.00 0.00 2.57
640 669 4.021368 TCCACCTTTTAGACTGTGCTACTC 60.021 45.833 0.00 0.00 0.00 2.59
641 670 4.021016 CCACCTTTTAGACTGTGCTACTCT 60.021 45.833 0.00 0.00 0.00 3.24
646 678 5.821516 TTTAGACTGTGCTACTCTCTAGC 57.178 43.478 0.00 0.00 40.76 3.42
647 679 3.644966 AGACTGTGCTACTCTCTAGCT 57.355 47.619 0.00 0.00 40.95 3.32
649 681 2.357637 GACTGTGCTACTCTCTAGCTGG 59.642 54.545 0.00 0.00 40.95 4.85
677 709 4.656112 GGATGGGAGAATATGGGATCGTAT 59.344 45.833 0.00 0.00 0.00 3.06
679 711 6.498651 GGATGGGAGAATATGGGATCGTATAT 59.501 42.308 0.00 0.00 0.00 0.86
680 712 6.978674 TGGGAGAATATGGGATCGTATATC 57.021 41.667 2.06 0.00 0.00 1.63
681 713 6.440354 TGGGAGAATATGGGATCGTATATCA 58.560 40.000 2.06 0.00 0.00 2.15
682 714 6.900743 TGGGAGAATATGGGATCGTATATCAA 59.099 38.462 2.06 0.00 0.00 2.57
683 715 7.401782 TGGGAGAATATGGGATCGTATATCAAA 59.598 37.037 2.06 0.00 0.00 2.69
684 716 8.265055 GGGAGAATATGGGATCGTATATCAAAA 58.735 37.037 2.06 0.00 0.00 2.44
685 717 9.667107 GGAGAATATGGGATCGTATATCAAAAA 57.333 33.333 2.06 0.00 0.00 1.94
705 737 6.855375 AAAAAGGAGAGGAGAATATGGGAT 57.145 37.500 0.00 0.00 0.00 3.85
706 738 6.446909 AAAAGGAGAGGAGAATATGGGATC 57.553 41.667 0.00 0.00 0.00 3.36
707 739 3.707316 AGGAGAGGAGAATATGGGATCG 58.293 50.000 0.00 0.00 0.00 3.69
708 740 3.076785 AGGAGAGGAGAATATGGGATCGT 59.923 47.826 0.00 0.00 0.00 3.73
709 741 4.292571 AGGAGAGGAGAATATGGGATCGTA 59.707 45.833 0.00 0.00 0.00 3.43
710 742 4.399934 GGAGAGGAGAATATGGGATCGTAC 59.600 50.000 0.00 0.00 0.00 3.67
711 743 4.999310 AGAGGAGAATATGGGATCGTACA 58.001 43.478 0.00 0.00 0.00 2.90
712 744 4.767928 AGAGGAGAATATGGGATCGTACAC 59.232 45.833 0.00 0.00 0.00 2.90
713 745 4.742012 AGGAGAATATGGGATCGTACACT 58.258 43.478 0.00 0.00 0.00 3.55
714 746 4.524714 AGGAGAATATGGGATCGTACACTG 59.475 45.833 0.00 0.00 0.00 3.66
715 747 4.281182 GGAGAATATGGGATCGTACACTGT 59.719 45.833 0.00 0.00 0.00 3.55
716 748 5.201713 AGAATATGGGATCGTACACTGTG 57.798 43.478 6.19 6.19 0.00 3.66
717 749 2.882927 TATGGGATCGTACACTGTGC 57.117 50.000 7.90 0.00 0.00 4.57
718 750 0.179111 ATGGGATCGTACACTGTGCG 60.179 55.000 12.92 12.92 42.54 5.34
814 860 1.379977 CTAGCCAGAGTCCGTCCCA 60.380 63.158 0.00 0.00 0.00 4.37
819 865 2.915659 AGAGTCCGTCCCACGCAA 60.916 61.111 0.00 0.00 40.91 4.85
835 881 4.988598 AACACGCCTGGCTGGACG 62.989 66.667 17.92 18.00 39.83 4.79
930 990 4.456806 GGCAGTTTCCGAGTGTGT 57.543 55.556 0.00 0.00 0.00 3.72
945 1006 2.986979 TGTGCTAGTGCGGTCGGA 60.987 61.111 0.00 0.00 43.34 4.55
946 1007 2.202623 GTGCTAGTGCGGTCGGAG 60.203 66.667 0.00 0.00 43.34 4.63
947 1008 3.449227 TGCTAGTGCGGTCGGAGG 61.449 66.667 0.00 0.00 43.34 4.30
948 1009 3.450115 GCTAGTGCGGTCGGAGGT 61.450 66.667 0.00 0.00 0.00 3.85
949 1010 2.799371 CTAGTGCGGTCGGAGGTC 59.201 66.667 0.00 0.00 0.00 3.85
972 1033 2.107141 CTTCCTCCGATCGGGTGC 59.893 66.667 32.79 0.00 37.00 5.01
1020 1081 3.471806 GCCTCCTTCCCCTCCGTC 61.472 72.222 0.00 0.00 0.00 4.79
1025 1086 2.362632 CTTCCCCTCCGTCTCCGT 60.363 66.667 0.00 0.00 0.00 4.69
1056 1117 2.726351 GCCGAGACCCTTCCTCCTG 61.726 68.421 0.00 0.00 0.00 3.86
1254 1315 0.029834 ACTGCTTCGTCAACGTACGT 59.970 50.000 16.72 16.72 43.31 3.57
1256 1317 0.029167 TGCTTCGTCAACGTACGTGA 59.971 50.000 23.57 17.79 43.31 4.35
1258 1319 1.745566 CTTCGTCAACGTACGTGACA 58.254 50.000 31.24 22.27 43.31 3.58
1268 1330 1.654602 CGTACGTGACACAACACAACA 59.345 47.619 7.22 0.00 40.34 3.33
1270 1332 0.800012 ACGTGACACAACACAACACC 59.200 50.000 6.37 0.00 40.34 4.16
1271 1333 1.083489 CGTGACACAACACAACACCT 58.917 50.000 6.37 0.00 40.34 4.00
1274 1336 3.241701 GTGACACAACACAACACCTTTG 58.758 45.455 0.00 0.00 40.11 2.77
1275 1337 3.057876 GTGACACAACACAACACCTTTGA 60.058 43.478 0.00 0.00 40.11 2.69
1279 1341 5.167845 ACACAACACAACACCTTTGATTTC 58.832 37.500 0.00 0.00 0.00 2.17
1280 1342 4.566360 CACAACACAACACCTTTGATTTCC 59.434 41.667 0.00 0.00 0.00 3.13
1281 1343 3.708563 ACACAACACCTTTGATTTCCG 57.291 42.857 0.00 0.00 0.00 4.30
1282 1344 2.360801 ACACAACACCTTTGATTTCCGG 59.639 45.455 0.00 0.00 0.00 5.14
1283 1345 2.360801 CACAACACCTTTGATTTCCGGT 59.639 45.455 0.00 0.00 0.00 5.28
1284 1346 3.028130 ACAACACCTTTGATTTCCGGTT 58.972 40.909 0.00 0.00 0.00 4.44
1285 1347 3.067601 ACAACACCTTTGATTTCCGGTTC 59.932 43.478 0.00 0.00 0.00 3.62
1307 1369 6.720112 TCATCCCCTTTGATTGAATTGATC 57.280 37.500 0.00 0.00 0.00 2.92
1314 1376 6.984474 CCCTTTGATTGAATTGATCTGAATGG 59.016 38.462 0.00 0.00 0.00 3.16
1528 1598 1.003233 GTCAACCTGGTCAGCCTCC 60.003 63.158 0.00 0.00 35.27 4.30
1529 1599 2.046892 CAACCTGGTCAGCCTCCG 60.047 66.667 0.00 0.00 35.27 4.63
1546 1616 1.179174 CCGTCTCCACTCCACACTCA 61.179 60.000 0.00 0.00 0.00 3.41
1547 1617 0.891373 CGTCTCCACTCCACACTCAT 59.109 55.000 0.00 0.00 0.00 2.90
1568 1640 2.109128 TGCTACCAATTCTTCCCCAACA 59.891 45.455 0.00 0.00 0.00 3.33
1569 1641 2.492088 GCTACCAATTCTTCCCCAACAC 59.508 50.000 0.00 0.00 0.00 3.32
1574 1646 0.768622 ATTCTTCCCCAACACACGGA 59.231 50.000 0.00 0.00 0.00 4.69
2014 2090 0.603975 AGGAGCTCTTCAACAACGGC 60.604 55.000 14.64 0.00 0.00 5.68
2015 2091 1.578206 GGAGCTCTTCAACAACGGCC 61.578 60.000 14.64 0.00 0.00 6.13
2016 2092 0.884704 GAGCTCTTCAACAACGGCCA 60.885 55.000 6.43 0.00 0.00 5.36
2017 2093 0.886490 AGCTCTTCAACAACGGCCAG 60.886 55.000 2.24 0.00 0.00 4.85
2018 2094 1.576421 CTCTTCAACAACGGCCAGC 59.424 57.895 2.24 0.00 0.00 4.85
2035 2111 4.087892 CTGGACTCCCTGGTGCGG 62.088 72.222 0.00 0.00 0.00 5.69
2160 2236 4.656041 CTCGATTGCAGGAAAGTCAATTC 58.344 43.478 0.00 0.00 31.30 2.17
2161 2237 4.326826 TCGATTGCAGGAAAGTCAATTCT 58.673 39.130 0.00 0.00 31.30 2.40
2162 2238 4.761739 TCGATTGCAGGAAAGTCAATTCTT 59.238 37.500 0.00 0.00 31.30 2.52
2255 2333 6.536731 GATGAAATCGACTAAGCATGACAT 57.463 37.500 0.00 0.00 31.13 3.06
2256 2334 5.973651 TGAAATCGACTAAGCATGACATC 57.026 39.130 0.00 0.00 0.00 3.06
2412 2519 7.929159 TGAACGATATGAAATGCACATTACAT 58.071 30.769 0.00 0.00 0.00 2.29
2415 2522 9.663904 AACGATATGAAATGCACATTACATTAC 57.336 29.630 0.00 0.00 36.74 1.89
2427 2534 8.338986 TGCACATTACATTACATATTTGGTACG 58.661 33.333 0.00 0.00 0.00 3.67
2456 2572 9.570488 GAGTACTCTATTTGGTACTTTAGTGTG 57.430 37.037 15.91 0.00 45.59 3.82
2476 2592 1.369091 GCGATCAGTGGCGTGGAAAT 61.369 55.000 7.86 0.00 0.00 2.17
2497 2614 3.701205 TTGAAGCTAACAGCAGATCCA 57.299 42.857 0.38 0.00 45.56 3.41
2498 2615 3.920231 TGAAGCTAACAGCAGATCCAT 57.080 42.857 0.38 0.00 45.56 3.41
2499 2616 3.538591 TGAAGCTAACAGCAGATCCATG 58.461 45.455 0.38 0.00 45.56 3.66
2500 2617 2.634815 AGCTAACAGCAGATCCATGG 57.365 50.000 4.97 4.97 45.56 3.66
2501 2618 0.950116 GCTAACAGCAGATCCATGGC 59.050 55.000 6.96 0.00 41.89 4.40
2502 2619 1.602311 CTAACAGCAGATCCATGGCC 58.398 55.000 6.96 0.00 0.00 5.36
2503 2620 0.918258 TAACAGCAGATCCATGGCCA 59.082 50.000 8.56 8.56 0.00 5.36
2504 2621 0.395311 AACAGCAGATCCATGGCCAG 60.395 55.000 13.05 3.10 0.00 4.85
2505 2622 1.226542 CAGCAGATCCATGGCCAGT 59.773 57.895 13.05 0.00 0.00 4.00
2506 2623 0.818445 CAGCAGATCCATGGCCAGTC 60.818 60.000 13.05 6.85 0.00 3.51
2507 2624 1.527844 GCAGATCCATGGCCAGTCC 60.528 63.158 13.05 0.00 0.00 3.85
2523 2663 3.189910 CCAGTCCAATCAGTGTGACATTG 59.810 47.826 1.22 1.22 32.70 2.82
2531 2671 6.017192 CCAATCAGTGTGACATTGTTTACTCA 60.017 38.462 7.96 0.00 0.00 3.41
2542 2682 5.106712 ACATTGTTTACTCATACGCTGGTTG 60.107 40.000 0.00 0.00 0.00 3.77
2633 2784 8.556194 CGTTGCTACATATAAATAGCTGGAAAA 58.444 33.333 15.76 3.56 43.54 2.29
2647 2798 4.120331 AAAATGCTGGGCGCGCTC 62.120 61.111 32.29 30.04 43.27 5.03
2730 2886 9.658475 TGTTTCAGAGTCGTAAATAATGTTTTG 57.342 29.630 0.00 0.00 0.00 2.44
2731 2887 9.872757 GTTTCAGAGTCGTAAATAATGTTTTGA 57.127 29.630 0.00 0.00 0.00 2.69
2736 2951 9.877178 AGAGTCGTAAATAATGTTTTGAGATCT 57.123 29.630 0.00 0.00 0.00 2.75
2799 3014 1.136147 CGTACGTCAAGTCCCTCGG 59.864 63.158 7.22 0.00 0.00 4.63
2807 3022 2.093447 GTCAAGTCCCTCGGTCATGATT 60.093 50.000 0.00 0.00 0.00 2.57
2822 3037 4.706476 GTCATGATTTGGTTCCTGGAATGA 59.294 41.667 13.07 6.70 0.00 2.57
2894 3109 2.032426 GTCTCTAGTTCTAGCCGTGCTC 59.968 54.545 1.46 0.00 40.44 4.26
2895 3110 2.017782 CTCTAGTTCTAGCCGTGCTCA 58.982 52.381 1.46 0.00 40.44 4.26
2913 3131 1.139654 TCAGAGCAGCGCTAATCCATT 59.860 47.619 10.99 0.00 39.88 3.16
2915 3133 0.590195 GAGCAGCGCTAATCCATTGG 59.410 55.000 10.99 0.00 39.88 3.16
2916 3134 0.181114 AGCAGCGCTAATCCATTGGA 59.819 50.000 10.99 8.08 36.99 3.53
2917 3135 1.202855 AGCAGCGCTAATCCATTGGAT 60.203 47.619 10.99 12.62 45.46 3.41
2919 3137 2.775890 CAGCGCTAATCCATTGGATCT 58.224 47.619 18.45 8.18 42.27 2.75
2943 3165 5.913946 AAATATCTACTCCAAAGAGGGGG 57.086 43.478 0.00 0.00 44.86 5.40
2948 3170 2.133858 ACTCCAAAGAGGGGGAAAGA 57.866 50.000 0.00 0.00 44.86 2.52
2958 3180 5.236425 AGAGGGGGAAAGAAAGACCTATA 57.764 43.478 0.00 0.00 0.00 1.31
2960 3182 6.946526 AGAGGGGGAAAGAAAGACCTATATA 58.053 40.000 0.00 0.00 0.00 0.86
2961 3183 7.558192 AGAGGGGGAAAGAAAGACCTATATAT 58.442 38.462 0.00 0.00 0.00 0.86
2962 3184 7.680739 AGAGGGGGAAAGAAAGACCTATATATC 59.319 40.741 0.00 0.00 0.00 1.63
2972 3194 8.371699 AGAAAGACCTATATATCAAGACTTGGC 58.628 37.037 15.13 0.00 0.00 4.52
3052 3283 4.586421 TGTGGACACCATTTTGCAGATAAA 59.414 37.500 0.00 0.00 35.28 1.40
3086 3317 5.407407 TGCCACTTGTTAAAGTTTGGAAA 57.593 34.783 0.00 0.00 44.47 3.13
3100 3331 2.472695 TGGAAATGGAAGGTCACTCG 57.527 50.000 0.00 0.00 0.00 4.18
3116 3347 2.868583 CACTCGGCACTCAGGATATTTG 59.131 50.000 0.00 0.00 0.00 2.32
3118 3349 1.486310 TCGGCACTCAGGATATTTGCT 59.514 47.619 0.00 0.00 33.55 3.91
3124 3355 5.358160 GGCACTCAGGATATTTGCTTTACTT 59.642 40.000 0.00 0.00 33.55 2.24
3125 3356 6.127619 GGCACTCAGGATATTTGCTTTACTTT 60.128 38.462 0.00 0.00 33.55 2.66
3126 3357 7.315890 GCACTCAGGATATTTGCTTTACTTTT 58.684 34.615 0.00 0.00 0.00 2.27
3127 3358 7.814587 GCACTCAGGATATTTGCTTTACTTTTT 59.185 33.333 0.00 0.00 0.00 1.94
3164 3395 9.474313 AAAAGGATATTTGCTTTACTATGGTCA 57.526 29.630 3.26 0.00 42.01 4.02
3165 3396 8.451908 AAGGATATTTGCTTTACTATGGTCAC 57.548 34.615 0.00 0.00 27.49 3.67
3166 3397 7.573710 AGGATATTTGCTTTACTATGGTCACA 58.426 34.615 0.00 0.00 0.00 3.58
3167 3398 7.499232 AGGATATTTGCTTTACTATGGTCACAC 59.501 37.037 0.00 0.00 0.00 3.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 9.561069 ACGGAGAAAGTATATGATAAGCAATTT 57.439 29.630 0.00 0.00 0.00 1.82
35 36 9.561069 AACGGAGAAAGTATATGATAAGCAATT 57.439 29.630 0.00 0.00 0.00 2.32
36 37 9.209175 GAACGGAGAAAGTATATGATAAGCAAT 57.791 33.333 0.00 0.00 0.00 3.56
37 38 7.656137 GGAACGGAGAAAGTATATGATAAGCAA 59.344 37.037 0.00 0.00 0.00 3.91
38 39 7.152645 GGAACGGAGAAAGTATATGATAAGCA 58.847 38.462 0.00 0.00 0.00 3.91
39 40 7.152645 TGGAACGGAGAAAGTATATGATAAGC 58.847 38.462 0.00 0.00 0.00 3.09
40 41 9.542462 TTTGGAACGGAGAAAGTATATGATAAG 57.458 33.333 0.00 0.00 0.00 1.73
41 42 9.893634 TTTTGGAACGGAGAAAGTATATGATAA 57.106 29.630 0.00 0.00 0.00 1.75
43 44 8.980481 ATTTTGGAACGGAGAAAGTATATGAT 57.020 30.769 0.00 0.00 0.00 2.45
44 45 9.893634 TTATTTTGGAACGGAGAAAGTATATGA 57.106 29.630 0.00 0.00 0.00 2.15
46 47 9.901172 ACTTATTTTGGAACGGAGAAAGTATAT 57.099 29.630 0.00 0.00 0.00 0.86
47 48 9.158233 CACTTATTTTGGAACGGAGAAAGTATA 57.842 33.333 0.00 0.00 0.00 1.47
48 49 7.664318 ACACTTATTTTGGAACGGAGAAAGTAT 59.336 33.333 0.00 0.00 0.00 2.12
49 50 6.993902 ACACTTATTTTGGAACGGAGAAAGTA 59.006 34.615 0.00 0.00 0.00 2.24
50 51 5.826208 ACACTTATTTTGGAACGGAGAAAGT 59.174 36.000 0.00 0.00 0.00 2.66
51 52 6.142817 CACACTTATTTTGGAACGGAGAAAG 58.857 40.000 0.00 0.00 0.00 2.62
52 53 5.591067 ACACACTTATTTTGGAACGGAGAAA 59.409 36.000 0.00 0.00 0.00 2.52
53 54 5.127491 ACACACTTATTTTGGAACGGAGAA 58.873 37.500 0.00 0.00 0.00 2.87
54 55 4.710324 ACACACTTATTTTGGAACGGAGA 58.290 39.130 0.00 0.00 0.00 3.71
55 56 5.008217 TCAACACACTTATTTTGGAACGGAG 59.992 40.000 0.00 0.00 0.00 4.63
56 57 4.882427 TCAACACACTTATTTTGGAACGGA 59.118 37.500 0.00 0.00 0.00 4.69
57 58 5.176407 TCAACACACTTATTTTGGAACGG 57.824 39.130 0.00 0.00 0.00 4.44
58 59 4.675114 GCTCAACACACTTATTTTGGAACG 59.325 41.667 0.00 0.00 0.00 3.95
59 60 5.831997 AGCTCAACACACTTATTTTGGAAC 58.168 37.500 0.00 0.00 0.00 3.62
60 61 6.463995 AAGCTCAACACACTTATTTTGGAA 57.536 33.333 0.00 0.00 0.00 3.53
61 62 6.770785 ACTAAGCTCAACACACTTATTTTGGA 59.229 34.615 0.00 0.00 0.00 3.53
62 63 6.970484 ACTAAGCTCAACACACTTATTTTGG 58.030 36.000 0.00 0.00 0.00 3.28
111 112 8.338986 CGGTGCCAAAATAAATGTTTTAACTTT 58.661 29.630 0.00 0.00 30.56 2.66
112 113 7.711339 TCGGTGCCAAAATAAATGTTTTAACTT 59.289 29.630 0.00 0.00 30.56 2.66
113 114 7.210873 TCGGTGCCAAAATAAATGTTTTAACT 58.789 30.769 0.00 0.00 30.56 2.24
114 115 7.359681 CCTCGGTGCCAAAATAAATGTTTTAAC 60.360 37.037 0.00 0.00 30.56 2.01
115 116 6.647067 CCTCGGTGCCAAAATAAATGTTTTAA 59.353 34.615 0.00 0.00 30.56 1.52
116 117 6.159988 CCTCGGTGCCAAAATAAATGTTTTA 58.840 36.000 0.00 0.00 30.56 1.52
117 118 4.994217 CCTCGGTGCCAAAATAAATGTTTT 59.006 37.500 0.00 0.00 0.00 2.43
118 119 4.562552 CCCTCGGTGCCAAAATAAATGTTT 60.563 41.667 0.00 0.00 0.00 2.83
119 120 3.056179 CCCTCGGTGCCAAAATAAATGTT 60.056 43.478 0.00 0.00 0.00 2.71
120 121 2.495669 CCCTCGGTGCCAAAATAAATGT 59.504 45.455 0.00 0.00 0.00 2.71
121 122 2.757868 TCCCTCGGTGCCAAAATAAATG 59.242 45.455 0.00 0.00 0.00 2.32
122 123 3.023832 CTCCCTCGGTGCCAAAATAAAT 58.976 45.455 0.00 0.00 0.00 1.40
123 124 2.224917 ACTCCCTCGGTGCCAAAATAAA 60.225 45.455 0.00 0.00 0.00 1.40
124 125 1.353022 ACTCCCTCGGTGCCAAAATAA 59.647 47.619 0.00 0.00 0.00 1.40
125 126 0.988832 ACTCCCTCGGTGCCAAAATA 59.011 50.000 0.00 0.00 0.00 1.40
126 127 0.988832 TACTCCCTCGGTGCCAAAAT 59.011 50.000 0.00 0.00 0.00 1.82
127 128 0.988832 ATACTCCCTCGGTGCCAAAA 59.011 50.000 0.00 0.00 0.00 2.44
128 129 1.868713 TATACTCCCTCGGTGCCAAA 58.131 50.000 0.00 0.00 0.00 3.28
129 130 1.968493 GATATACTCCCTCGGTGCCAA 59.032 52.381 0.00 0.00 0.00 4.52
130 131 1.133294 TGATATACTCCCTCGGTGCCA 60.133 52.381 0.00 0.00 0.00 4.92
131 132 1.272769 GTGATATACTCCCTCGGTGCC 59.727 57.143 0.00 0.00 0.00 5.01
132 133 1.068472 CGTGATATACTCCCTCGGTGC 60.068 57.143 0.00 0.00 0.00 5.01
133 134 2.031069 CACGTGATATACTCCCTCGGTG 60.031 54.545 10.90 0.00 0.00 4.94
134 135 2.228059 CACGTGATATACTCCCTCGGT 58.772 52.381 10.90 0.00 0.00 4.69
135 136 1.540267 CCACGTGATATACTCCCTCGG 59.460 57.143 19.30 0.00 0.00 4.63
136 137 1.068472 GCCACGTGATATACTCCCTCG 60.068 57.143 19.30 0.00 0.00 4.63
137 138 1.068472 CGCCACGTGATATACTCCCTC 60.068 57.143 19.30 0.00 0.00 4.30
138 139 0.959553 CGCCACGTGATATACTCCCT 59.040 55.000 19.30 0.00 0.00 4.20
139 140 0.672342 ACGCCACGTGATATACTCCC 59.328 55.000 19.30 0.00 39.18 4.30
140 141 3.631145 TTACGCCACGTGATATACTCC 57.369 47.619 19.30 0.00 41.39 3.85
141 142 5.217393 TGATTTACGCCACGTGATATACTC 58.783 41.667 19.30 6.07 41.39 2.59
142 143 5.009310 TCTGATTTACGCCACGTGATATACT 59.991 40.000 19.30 0.00 41.39 2.12
143 144 5.116680 GTCTGATTTACGCCACGTGATATAC 59.883 44.000 19.30 0.00 41.39 1.47
144 145 5.217393 GTCTGATTTACGCCACGTGATATA 58.783 41.667 19.30 2.66 41.39 0.86
145 146 4.049186 GTCTGATTTACGCCACGTGATAT 58.951 43.478 19.30 3.74 41.39 1.63
155 156 0.997196 GGGTCGTGTCTGATTTACGC 59.003 55.000 7.04 0.00 37.70 4.42
156 157 2.649331 AGGGTCGTGTCTGATTTACG 57.351 50.000 5.94 5.94 39.04 3.18
287 295 2.268920 CGCTGCCCATGGTAGTGT 59.731 61.111 11.73 0.00 40.23 3.55
288 296 3.204827 GCGCTGCCCATGGTAGTG 61.205 66.667 11.73 15.54 46.13 2.74
289 297 4.489771 GGCGCTGCCCATGGTAGT 62.490 66.667 11.73 0.00 44.06 2.73
493 514 1.065551 CGAAAAATGCCGGGGAAGATC 59.934 52.381 2.18 0.00 0.00 2.75
513 534 1.943340 GTCCGAATGAAATGCTCCCTC 59.057 52.381 0.00 0.00 0.00 4.30
517 538 1.594862 CGAGGTCCGAATGAAATGCTC 59.405 52.381 0.00 0.00 41.76 4.26
519 541 1.651987 TCGAGGTCCGAATGAAATGC 58.348 50.000 0.00 0.00 45.43 3.56
541 563 0.179084 TGAATCGGAATCAGACGGGC 60.179 55.000 0.00 0.00 0.00 6.13
545 567 3.861840 TCTGGTTGAATCGGAATCAGAC 58.138 45.455 0.00 0.00 35.97 3.51
604 633 3.712881 GTGGACGGTGCGTTGAGC 61.713 66.667 0.00 0.00 41.37 4.26
605 634 2.989055 AAGGTGGACGGTGCGTTGAG 62.989 60.000 0.00 0.00 41.37 3.02
606 635 2.596553 AAAGGTGGACGGTGCGTTGA 62.597 55.000 0.00 0.00 41.37 3.18
607 636 1.720694 AAAAGGTGGACGGTGCGTTG 61.721 55.000 0.00 0.00 41.37 4.10
608 637 0.179051 TAAAAGGTGGACGGTGCGTT 60.179 50.000 0.00 0.00 41.37 4.84
609 638 0.601841 CTAAAAGGTGGACGGTGCGT 60.602 55.000 0.00 0.00 45.10 5.24
610 639 0.320073 TCTAAAAGGTGGACGGTGCG 60.320 55.000 0.00 0.00 0.00 5.34
611 640 1.154197 GTCTAAAAGGTGGACGGTGC 58.846 55.000 0.00 0.00 0.00 5.01
632 661 1.398692 AGCCAGCTAGAGAGTAGCAC 58.601 55.000 6.79 0.00 42.68 4.40
633 662 3.153130 CATAGCCAGCTAGAGAGTAGCA 58.847 50.000 5.49 0.00 42.68 3.49
634 663 2.491693 CCATAGCCAGCTAGAGAGTAGC 59.508 54.545 5.49 0.00 40.67 3.58
635 664 4.027674 TCCATAGCCAGCTAGAGAGTAG 57.972 50.000 5.49 0.00 31.45 2.57
636 665 4.339748 CATCCATAGCCAGCTAGAGAGTA 58.660 47.826 5.49 0.00 31.45 2.59
637 666 3.164268 CATCCATAGCCAGCTAGAGAGT 58.836 50.000 5.49 0.00 31.45 3.24
638 667 2.496871 CCATCCATAGCCAGCTAGAGAG 59.503 54.545 5.49 0.00 31.45 3.20
639 668 2.533916 CCATCCATAGCCAGCTAGAGA 58.466 52.381 5.49 4.91 31.45 3.10
640 669 1.554160 CCCATCCATAGCCAGCTAGAG 59.446 57.143 5.49 0.78 31.45 2.43
641 670 1.149923 TCCCATCCATAGCCAGCTAGA 59.850 52.381 5.49 0.00 31.45 2.43
646 678 4.384978 CCATATTCTCCCATCCATAGCCAG 60.385 50.000 0.00 0.00 0.00 4.85
647 679 3.524789 CCATATTCTCCCATCCATAGCCA 59.475 47.826 0.00 0.00 0.00 4.75
649 681 3.782523 TCCCATATTCTCCCATCCATAGC 59.217 47.826 0.00 0.00 0.00 2.97
682 714 6.465035 CGATCCCATATTCTCCTCTCCTTTTT 60.465 42.308 0.00 0.00 0.00 1.94
683 715 5.012561 CGATCCCATATTCTCCTCTCCTTTT 59.987 44.000 0.00 0.00 0.00 2.27
684 716 4.530161 CGATCCCATATTCTCCTCTCCTTT 59.470 45.833 0.00 0.00 0.00 3.11
685 717 4.093011 CGATCCCATATTCTCCTCTCCTT 58.907 47.826 0.00 0.00 0.00 3.36
686 718 3.076785 ACGATCCCATATTCTCCTCTCCT 59.923 47.826 0.00 0.00 0.00 3.69
687 719 3.436243 ACGATCCCATATTCTCCTCTCC 58.564 50.000 0.00 0.00 0.00 3.71
688 720 5.010933 TGTACGATCCCATATTCTCCTCTC 58.989 45.833 0.00 0.00 0.00 3.20
689 721 4.767928 GTGTACGATCCCATATTCTCCTCT 59.232 45.833 0.00 0.00 0.00 3.69
690 722 4.767928 AGTGTACGATCCCATATTCTCCTC 59.232 45.833 0.00 0.00 0.00 3.71
691 723 4.524714 CAGTGTACGATCCCATATTCTCCT 59.475 45.833 0.00 0.00 0.00 3.69
692 724 4.281182 ACAGTGTACGATCCCATATTCTCC 59.719 45.833 0.00 0.00 0.00 3.71
693 725 5.223382 CACAGTGTACGATCCCATATTCTC 58.777 45.833 0.00 0.00 0.00 2.87
694 726 4.501571 GCACAGTGTACGATCCCATATTCT 60.502 45.833 1.61 0.00 0.00 2.40
695 727 3.741344 GCACAGTGTACGATCCCATATTC 59.259 47.826 1.61 0.00 0.00 1.75
696 728 3.728845 GCACAGTGTACGATCCCATATT 58.271 45.455 1.61 0.00 0.00 1.28
697 729 2.288213 CGCACAGTGTACGATCCCATAT 60.288 50.000 10.46 0.00 0.00 1.78
698 730 1.066454 CGCACAGTGTACGATCCCATA 59.934 52.381 10.46 0.00 0.00 2.74
699 731 0.179111 CGCACAGTGTACGATCCCAT 60.179 55.000 10.46 0.00 0.00 4.00
700 732 1.214325 CGCACAGTGTACGATCCCA 59.786 57.895 10.46 0.00 0.00 4.37
701 733 0.525668 CTCGCACAGTGTACGATCCC 60.526 60.000 18.47 0.00 30.77 3.85
702 734 0.170561 ACTCGCACAGTGTACGATCC 59.829 55.000 18.47 0.00 30.77 3.36
703 735 1.260206 CACTCGCACAGTGTACGATC 58.740 55.000 18.47 0.00 46.81 3.69
704 736 3.401577 CACTCGCACAGTGTACGAT 57.598 52.632 18.47 6.97 46.81 3.73
705 737 4.935630 CACTCGCACAGTGTACGA 57.064 55.556 17.29 17.29 46.81 3.43
714 746 4.293626 AAACGCACGCACTCGCAC 62.294 61.111 0.00 0.00 39.84 5.34
715 747 4.292208 CAAACGCACGCACTCGCA 62.292 61.111 0.00 0.00 39.84 5.10
717 749 3.506312 AAGCAAACGCACGCACTCG 62.506 57.895 0.00 0.00 42.43 4.18
718 750 1.722507 GAAGCAAACGCACGCACTC 60.723 57.895 0.00 0.00 0.00 3.51
719 751 2.327940 GAAGCAAACGCACGCACT 59.672 55.556 0.00 0.00 0.00 4.40
720 752 2.725815 GGAAGCAAACGCACGCAC 60.726 61.111 0.00 0.00 0.00 5.34
721 753 3.179869 CTGGAAGCAAACGCACGCA 62.180 57.895 0.00 0.00 0.00 5.24
722 754 2.427410 CTGGAAGCAAACGCACGC 60.427 61.111 0.00 0.00 0.00 5.34
744 776 1.811266 CGTCCGCCTTCATGTGGAG 60.811 63.158 10.79 7.70 45.19 3.86
795 841 1.076923 GGGACGGACTCTGGCTAGA 60.077 63.158 0.00 0.00 0.00 2.43
797 843 1.681327 GTGGGACGGACTCTGGCTA 60.681 63.158 0.00 0.00 0.00 3.93
930 990 3.449227 CCTCCGACCGCACTAGCA 61.449 66.667 0.00 0.00 42.27 3.49
947 1008 1.874872 CGATCGGAGGAAGGTAGAGAC 59.125 57.143 7.38 0.00 0.00 3.36
948 1009 1.202782 CCGATCGGAGGAAGGTAGAGA 60.203 57.143 30.62 0.00 37.50 3.10
949 1010 1.240256 CCGATCGGAGGAAGGTAGAG 58.760 60.000 30.62 0.00 37.50 2.43
972 1033 2.357517 GCGACCACAGTCCACAGG 60.358 66.667 0.00 0.00 40.12 4.00
1006 1067 2.363361 GGAGACGGAGGGGAAGGA 59.637 66.667 0.00 0.00 0.00 3.36
1254 1315 3.149981 TCAAAGGTGTTGTGTTGTGTCA 58.850 40.909 0.00 0.00 0.00 3.58
1256 1317 4.799564 AATCAAAGGTGTTGTGTTGTGT 57.200 36.364 0.00 0.00 0.00 3.72
1258 1319 4.676723 CGGAAATCAAAGGTGTTGTGTTGT 60.677 41.667 0.00 0.00 0.00 3.32
1268 1330 3.089284 GGATGAACCGGAAATCAAAGGT 58.911 45.455 9.46 0.00 38.88 3.50
1270 1332 2.427095 GGGGATGAACCGGAAATCAAAG 59.573 50.000 9.46 0.00 40.11 2.77
1271 1333 2.042433 AGGGGATGAACCGGAAATCAAA 59.958 45.455 9.46 0.00 40.11 2.69
1274 1336 2.427095 CAAAGGGGATGAACCGGAAATC 59.573 50.000 9.46 7.88 40.11 2.17
1275 1337 2.042433 TCAAAGGGGATGAACCGGAAAT 59.958 45.455 9.46 0.00 40.11 2.17
1279 1341 1.750778 CAATCAAAGGGGATGAACCGG 59.249 52.381 0.00 0.00 40.11 5.28
1280 1342 2.722094 TCAATCAAAGGGGATGAACCG 58.278 47.619 0.00 0.00 40.11 4.44
1281 1343 5.187576 TCAATTCAATCAAAGGGGATGAACC 59.812 40.000 0.00 0.00 38.08 3.62
1282 1344 6.284891 TCAATTCAATCAAAGGGGATGAAC 57.715 37.500 0.00 0.00 0.00 3.18
1283 1345 6.899075 AGATCAATTCAATCAAAGGGGATGAA 59.101 34.615 0.00 0.00 0.00 2.57
1284 1346 6.322969 CAGATCAATTCAATCAAAGGGGATGA 59.677 38.462 0.00 0.00 0.00 2.92
1285 1347 6.322969 TCAGATCAATTCAATCAAAGGGGATG 59.677 38.462 0.00 0.00 0.00 3.51
1528 1598 0.891373 ATGAGTGTGGAGTGGAGACG 59.109 55.000 0.00 0.00 0.00 4.18
1529 1599 1.674221 GCATGAGTGTGGAGTGGAGAC 60.674 57.143 0.00 0.00 0.00 3.36
1546 1616 3.245586 TGTTGGGGAAGAATTGGTAGCAT 60.246 43.478 0.00 0.00 0.00 3.79
1547 1617 2.109128 TGTTGGGGAAGAATTGGTAGCA 59.891 45.455 0.00 0.00 0.00 3.49
1574 1646 2.661675 CGACGAGTGTTTCATTCACGAT 59.338 45.455 0.00 0.00 40.28 3.73
2014 2090 2.608988 ACCAGGGAGTCCAGCTGG 60.609 66.667 27.87 27.87 38.41 4.85
2015 2091 2.667418 CACCAGGGAGTCCAGCTG 59.333 66.667 12.30 6.78 34.83 4.24
2016 2092 3.325753 GCACCAGGGAGTCCAGCT 61.326 66.667 12.30 0.00 34.83 4.24
2017 2093 4.767255 CGCACCAGGGAGTCCAGC 62.767 72.222 12.30 5.67 34.83 4.85
2018 2094 4.087892 CCGCACCAGGGAGTCCAG 62.088 72.222 12.30 2.42 34.83 3.86
2035 2111 2.820037 GGGTTGGCGCTGTAGAGC 60.820 66.667 7.64 0.76 42.37 4.09
2056 2132 1.374252 GAAGTCGGCCGAGAAAGCA 60.374 57.895 31.97 0.87 0.00 3.91
2059 2135 2.431942 GCGAAGTCGGCCGAGAAA 60.432 61.111 31.97 3.34 40.23 2.52
2244 2322 1.068434 TCCGATGCGATGTCATGCTTA 59.932 47.619 0.00 0.00 0.00 3.09
2325 2419 9.899661 TCCTAAAAATAGCAAAGCTCTACAATA 57.100 29.630 0.00 0.00 40.44 1.90
2409 2516 9.956720 GTACTCTACGTACCAAATATGTAATGT 57.043 33.333 0.00 0.00 42.14 2.71
2429 2536 9.531158 ACACTAAAGTACCAAATAGAGTACTCT 57.469 33.333 27.72 27.72 46.50 3.24
2430 2537 9.570488 CACACTAAAGTACCAAATAGAGTACTC 57.430 37.037 15.41 15.41 46.50 2.59
2432 2539 7.277319 GCCACACTAAAGTACCAAATAGAGTAC 59.723 40.741 0.00 0.00 39.31 2.73
2433 2540 7.325694 GCCACACTAAAGTACCAAATAGAGTA 58.674 38.462 0.00 0.00 0.00 2.59
2434 2541 6.171213 GCCACACTAAAGTACCAAATAGAGT 58.829 40.000 0.00 0.00 0.00 3.24
2435 2542 5.291128 CGCCACACTAAAGTACCAAATAGAG 59.709 44.000 0.00 0.00 0.00 2.43
2436 2543 5.047164 TCGCCACACTAAAGTACCAAATAGA 60.047 40.000 0.00 0.00 0.00 1.98
2437 2544 5.172934 TCGCCACACTAAAGTACCAAATAG 58.827 41.667 0.00 0.00 0.00 1.73
2438 2545 5.149973 TCGCCACACTAAAGTACCAAATA 57.850 39.130 0.00 0.00 0.00 1.40
2446 2553 2.612972 CCACTGATCGCCACACTAAAGT 60.613 50.000 0.00 0.00 0.00 2.66
2449 2556 0.391130 GCCACTGATCGCCACACTAA 60.391 55.000 0.00 0.00 0.00 2.24
2456 2572 3.950794 TTCCACGCCACTGATCGCC 62.951 63.158 0.00 0.00 0.00 5.54
2476 2592 4.019792 TGGATCTGCTGTTAGCTTCAAA 57.980 40.909 0.00 0.00 42.97 2.69
2499 2616 0.036732 TCACACTGATTGGACTGGCC 59.963 55.000 0.00 0.00 37.10 5.36
2500 2617 1.160137 GTCACACTGATTGGACTGGC 58.840 55.000 0.00 0.00 0.00 4.85
2501 2618 2.549064 TGTCACACTGATTGGACTGG 57.451 50.000 0.00 0.00 0.00 4.00
2502 2619 3.817084 ACAATGTCACACTGATTGGACTG 59.183 43.478 0.00 0.00 0.00 3.51
2503 2620 4.090761 ACAATGTCACACTGATTGGACT 57.909 40.909 0.00 0.00 0.00 3.85
2504 2621 4.836125 AACAATGTCACACTGATTGGAC 57.164 40.909 0.00 0.00 0.00 4.02
2505 2622 6.061441 AGTAAACAATGTCACACTGATTGGA 58.939 36.000 0.00 0.00 0.00 3.53
2506 2623 6.017192 TGAGTAAACAATGTCACACTGATTGG 60.017 38.462 0.00 0.00 0.00 3.16
2507 2624 6.958255 TGAGTAAACAATGTCACACTGATTG 58.042 36.000 0.00 0.00 0.00 2.67
2523 2663 3.124636 CCACAACCAGCGTATGAGTAAAC 59.875 47.826 0.00 0.00 0.00 2.01
2531 2671 1.377202 CCTGCCACAACCAGCGTAT 60.377 57.895 0.00 0.00 0.00 3.06
2647 2798 1.638133 CAACTGATCAGAGAGCCACG 58.362 55.000 29.27 0.11 0.00 4.94
2729 2885 1.986882 TGCTCTATCCGCAGATCTCA 58.013 50.000 0.00 0.00 33.67 3.27
2736 2951 2.800541 CCCAGCTGCTCTATCCGCA 61.801 63.158 8.66 0.00 35.80 5.69
2778 2993 3.177249 GGGACTTGACGTACGCGC 61.177 66.667 16.72 8.55 42.83 6.86
2799 3014 4.706476 TCATTCCAGGAACCAAATCATGAC 59.294 41.667 3.18 0.00 33.08 3.06
2807 3022 1.075374 CAGGGTCATTCCAGGAACCAA 59.925 52.381 3.18 0.00 44.88 3.67
2822 3037 0.317479 CTTTCGAGACGGTTCAGGGT 59.683 55.000 0.00 0.00 0.00 4.34
2894 3109 1.263484 CAATGGATTAGCGCTGCTCTG 59.737 52.381 22.90 7.22 40.44 3.35
2895 3110 1.590932 CAATGGATTAGCGCTGCTCT 58.409 50.000 22.90 0.66 40.44 4.09
2901 3116 5.689383 TTTTAGATCCAATGGATTAGCGC 57.311 39.130 16.90 0.00 43.27 5.92
2915 3133 9.936759 CCCTCTTTGGAGTAGATATTTTAGATC 57.063 37.037 0.00 0.00 37.86 2.75
2916 3134 8.885346 CCCCTCTTTGGAGTAGATATTTTAGAT 58.115 37.037 0.00 0.00 37.86 1.98
2917 3135 7.292591 CCCCCTCTTTGGAGTAGATATTTTAGA 59.707 40.741 0.00 0.00 37.86 2.10
2919 3137 7.143741 TCCCCCTCTTTGGAGTAGATATTTTA 58.856 38.462 0.00 0.00 37.86 1.52
2929 3147 2.133858 TCTTTCCCCCTCTTTGGAGT 57.866 50.000 0.00 0.00 37.86 3.85
2931 3152 3.060611 TCTTTCTTTCCCCCTCTTTGGA 58.939 45.455 0.00 0.00 38.35 3.53
2948 3170 7.155328 CGCCAAGTCTTGATATATAGGTCTTT 58.845 38.462 14.42 0.00 0.00 2.52
2958 3180 4.769688 TGATCAACGCCAAGTCTTGATAT 58.230 39.130 14.42 0.00 32.20 1.63
2960 3182 3.057969 TGATCAACGCCAAGTCTTGAT 57.942 42.857 14.42 0.00 34.10 2.57
2961 3183 2.542020 TGATCAACGCCAAGTCTTGA 57.458 45.000 14.42 0.00 0.00 3.02
2962 3184 2.730090 GCATGATCAACGCCAAGTCTTG 60.730 50.000 0.00 5.53 0.00 3.02
2972 3194 1.264020 CCGTTATGGGCATGATCAACG 59.736 52.381 0.00 2.11 38.68 4.10
2984 3206 4.766375 ACACCTTATCTTCACCGTTATGG 58.234 43.478 0.00 0.00 46.41 2.74
3052 3283 1.688197 CAAGTGGCAAACTGGACCAAT 59.312 47.619 0.00 0.00 39.81 3.16
3086 3317 1.194781 AGTGCCGAGTGACCTTCCAT 61.195 55.000 0.00 0.00 0.00 3.41
3100 3331 4.884164 AGTAAAGCAAATATCCTGAGTGCC 59.116 41.667 0.00 0.00 35.80 5.01
3138 3369 9.474313 TGACCATAGTAAAGCAAATATCCTTTT 57.526 29.630 0.00 0.00 33.64 2.27
3139 3370 8.903820 GTGACCATAGTAAAGCAAATATCCTTT 58.096 33.333 0.00 0.00 35.60 3.11
3140 3371 8.052748 TGTGACCATAGTAAAGCAAATATCCTT 58.947 33.333 0.00 0.00 0.00 3.36
3141 3372 7.499232 GTGTGACCATAGTAAAGCAAATATCCT 59.501 37.037 0.00 0.00 0.00 3.24
3142 3373 7.639945 GTGTGACCATAGTAAAGCAAATATCC 58.360 38.462 0.00 0.00 0.00 2.59


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

AutoCloner maintained by Alex Coulton.