Multiple sequence alignment - TraesCS3B01G533400

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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 TraesCS3B01G533400 chr3B 100.000 3176 0 0 1 3176 773746050 773749225 0.000000e+00 5866.0
1 TraesCS3B01G533400 chr3B 90.664 482 39 3 1920 2396 773882267 773881787 1.240000e-178 636.0
2 TraesCS3B01G533400 chr3B 83.838 594 51 16 979 1566 773882821 773882267 1.010000e-144 523.0
3 TraesCS3B01G533400 chr3B 79.636 550 66 21 12 525 773762423 773762962 1.400000e-93 353.0
4 TraesCS3B01G533400 chr3B 88.739 222 22 3 992 1213 752973257 752973039 5.220000e-68 268.0
5 TraesCS3B01G533400 chr3B 79.830 352 55 9 115 462 773883695 773883356 3.170000e-60 243.0
6 TraesCS3B01G533400 chr3B 81.271 299 45 5 2097 2386 684636527 684636231 6.850000e-57 231.0
7 TraesCS3B01G533400 chr3B 73.451 452 104 12 1713 2153 754331007 754331453 4.240000e-34 156.0
8 TraesCS3B01G533400 chr3B 76.250 320 48 18 2667 2973 601374559 601374863 9.180000e-31 145.0
9 TraesCS3B01G533400 chr3B 94.737 76 2 2 2562 2637 674058070 674058143 2.000000e-22 117.0
10 TraesCS3B01G533400 chr3B 100.000 37 0 0 2251 2287 685396179 685396215 5.680000e-08 69.4
11 TraesCS3B01G533400 chr3B 100.000 33 0 0 744 776 773882990 773882958 9.510000e-06 62.1
12 TraesCS3B01G533400 chr3D 88.521 1690 144 27 744 2396 579583081 579581405 0.000000e+00 2001.0
13 TraesCS3B01G533400 chr3D 91.667 1368 103 4 1034 2396 579398533 579399894 0.000000e+00 1884.0
14 TraesCS3B01G533400 chr3D 86.216 370 31 7 2642 3003 579402430 579402787 1.790000e-102 383.0
15 TraesCS3B01G533400 chr3D 88.760 258 23 5 60 315 579425756 579426009 8.550000e-81 311.0
16 TraesCS3B01G533400 chr3D 92.647 204 15 0 2751 2954 579556596 579556393 8.620000e-76 294.0
17 TraesCS3B01G533400 chr3D 92.647 204 15 0 2751 2954 579578258 579578055 8.620000e-76 294.0
18 TraesCS3B01G533400 chr3D 92.157 204 16 0 2751 2954 579567521 579567318 4.010000e-74 289.0
19 TraesCS3B01G533400 chr3D 80.711 394 55 13 991 1375 565641909 565642290 1.440000e-73 287.0
20 TraesCS3B01G533400 chr3D 80.435 414 46 21 176 570 579397722 579398119 1.860000e-72 283.0
21 TraesCS3B01G533400 chr3D 91.667 204 17 0 2751 2954 579562009 579561806 1.860000e-72 283.0
22 TraesCS3B01G533400 chr3D 82.796 279 45 2 991 1269 565830738 565831013 2.450000e-61 246.0
23 TraesCS3B01G533400 chr3D 89.881 168 15 2 1 166 579425555 579425722 6.900000e-52 215.0
24 TraesCS3B01G533400 chr3D 91.034 145 10 3 3002 3143 579417914 579418058 3.230000e-45 193.0
25 TraesCS3B01G533400 chr3D 81.818 242 25 9 331 561 579425996 579426229 5.410000e-43 185.0
26 TraesCS3B01G533400 chr3D 84.507 142 10 5 2420 2550 579556785 579556645 2.570000e-26 130.0
27 TraesCS3B01G533400 chr3D 84.028 144 11 5 2420 2552 579562198 579562056 9.250000e-26 128.0
28 TraesCS3B01G533400 chr3D 84.028 144 11 8 2420 2552 579567710 579567568 9.250000e-26 128.0
29 TraesCS3B01G533400 chr3A 89.978 1357 101 9 937 2281 714595562 714596895 0.000000e+00 1720.0
30 TraesCS3B01G533400 chr3A 87.771 507 46 9 2643 3137 714599412 714599914 2.120000e-161 579.0
31 TraesCS3B01G533400 chr3A 73.706 1198 225 47 991 2176 655920287 655921406 4.970000e-103 385.0
32 TraesCS3B01G533400 chr3A 80.052 386 66 8 991 1375 702407891 702407516 3.120000e-70 276.0
33 TraesCS3B01G533400 chr3A 97.368 76 2 0 813 888 714595422 714595497 2.570000e-26 130.0
34 TraesCS3B01G533400 chr3A 90.698 86 7 1 12 96 714594202 714594287 2.590000e-21 113.0
35 TraesCS3B01G533400 chr3A 97.674 43 0 1 874 916 714595515 714595556 4.390000e-09 73.1
36 TraesCS3B01G533400 chr4A 78.650 548 69 15 12 536 714667860 714667338 1.420000e-83 320.0
37 TraesCS3B01G533400 chr4A 80.745 161 28 3 2028 2186 648794328 648794169 4.300000e-24 122.0
38 TraesCS3B01G533400 chr4B 77.555 548 75 19 12 536 430672758 430672236 1.440000e-73 287.0
39 TraesCS3B01G533400 chr4B 91.358 81 3 4 2556 2636 585426249 585426325 1.200000e-19 108.0
40 TraesCS3B01G533400 chr4B 95.385 65 3 0 2572 2636 56560412 56560348 1.560000e-18 104.0
41 TraesCS3B01G533400 chr7A 72.671 483 114 16 1679 2152 41048137 41047664 9.180000e-31 145.0
42 TraesCS3B01G533400 chr7D 72.211 511 121 17 1679 2177 41601215 41600714 1.540000e-28 137.0
43 TraesCS3B01G533400 chr7D 93.103 87 4 2 2556 2641 460654203 460654288 3.330000e-25 126.0
44 TraesCS3B01G533400 chr4D 95.062 81 3 1 2556 2636 497170673 497170752 3.330000e-25 126.0
45 TraesCS3B01G533400 chr6B 96.000 75 2 1 2562 2636 134677429 134677356 1.550000e-23 121.0
46 TraesCS3B01G533400 chrUn 78.355 231 17 7 325 536 230760114 230759898 5.570000e-23 119.0
47 TraesCS3B01G533400 chrUn 96.364 55 2 0 12 66 230760181 230760127 1.210000e-14 91.6
48 TraesCS3B01G533400 chrUn 96.364 55 2 0 12 66 341498617 341498563 1.210000e-14 91.6
49 TraesCS3B01G533400 chr5A 93.333 75 2 3 2562 2636 665614796 665614725 1.200000e-19 108.0
50 TraesCS3B01G533400 chr2A 95.385 65 1 2 2572 2636 709415703 709415765 5.600000e-18 102.0
51 TraesCS3B01G533400 chr7B 93.846 65 3 1 2572 2636 104752816 104752753 2.610000e-16 97.1


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 TraesCS3B01G533400 chr3B 773746050 773749225 3175 False 5866.000 5866 100.000000 1 3176 1 chr3B.!!$F5 3175
1 TraesCS3B01G533400 chr3B 773881787 773883695 1908 True 366.025 636 88.583000 115 2396 4 chr3B.!!$R3 2281
2 TraesCS3B01G533400 chr3B 773762423 773762962 539 False 353.000 353 79.636000 12 525 1 chr3B.!!$F6 513
3 TraesCS3B01G533400 chr3D 579578055 579583081 5026 True 1147.500 2001 90.584000 744 2954 2 chr3D.!!$R4 2210
4 TraesCS3B01G533400 chr3D 579397722 579402787 5065 False 850.000 1884 86.106000 176 3003 3 chr3D.!!$F4 2827
5 TraesCS3B01G533400 chr3D 579425555 579426229 674 False 237.000 311 86.819667 1 561 3 chr3D.!!$F5 560
6 TraesCS3B01G533400 chr3A 714594202 714599914 5712 False 523.020 1720 92.697800 12 3137 5 chr3A.!!$F2 3125
7 TraesCS3B01G533400 chr3A 655920287 655921406 1119 False 385.000 385 73.706000 991 2176 1 chr3A.!!$F1 1185
8 TraesCS3B01G533400 chr4A 714667338 714667860 522 True 320.000 320 78.650000 12 536 1 chr4A.!!$R2 524
9 TraesCS3B01G533400 chr4B 430672236 430672758 522 True 287.000 287 77.555000 12 536 1 chr4B.!!$R2 524

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
719 1378 0.108329 ACATTCGCGGTAGGGTTCAG 60.108 55.0 6.13 0.0 0.0 3.02 F
720 1379 0.174845 CATTCGCGGTAGGGTTCAGA 59.825 55.0 6.13 0.0 0.0 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1822 2648 0.031178 GCAGCATCATTAAAGCCGGG 59.969 55.0 2.18 0.0 0.0 5.73 R
2596 6521 0.323451 GGCTTCACCCCTTCCGATTT 60.323 55.0 0.00 0.0 0.0 2.17 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
48 49 8.519799 AAGTTCAGAGAAGAGATCTAACTAGG 57.480 38.462 0.00 0.00 38.96 3.02
66 67 6.759497 ACTAGGGCTTCACATTTTTATCAC 57.241 37.500 0.00 0.00 0.00 3.06
192 749 2.756760 CCCAATAGCTCAATTGCACAGT 59.243 45.455 0.00 0.00 35.85 3.55
196 753 6.204359 CCAATAGCTCAATTGCACAGTTATC 58.796 40.000 0.00 0.00 35.85 1.75
235 794 9.104965 TCGAGATTTAACGATCCAACAAAATAT 57.895 29.630 0.00 0.00 33.62 1.28
286 845 9.520515 AATAGTACAAGACAACATTTTCTGGAT 57.479 29.630 0.00 0.00 0.00 3.41
317 876 4.557205 ACACGAGGTTTCAGATTCTGTAC 58.443 43.478 13.23 11.92 32.61 2.90
318 877 4.281182 ACACGAGGTTTCAGATTCTGTACT 59.719 41.667 13.23 7.52 32.61 2.73
337 896 7.504238 TCTGTACTGTTAATTGGTTGGTTTCAT 59.496 33.333 0.00 0.00 0.00 2.57
432 1006 2.265904 GGAGAAAACCCCCACGCAC 61.266 63.158 0.00 0.00 0.00 5.34
457 1031 0.385390 CAAGGAAACCACACACTGGC 59.615 55.000 0.00 0.00 45.32 4.85
461 1036 1.205893 GGAAACCACACACTGGCAAAA 59.794 47.619 0.00 0.00 45.32 2.44
463 1038 0.534873 AACCACACACTGGCAAAACC 59.465 50.000 0.00 0.00 45.32 3.27
465 1040 0.179113 CCACACACTGGCAAAACCAC 60.179 55.000 0.00 0.00 46.36 4.16
468 1043 0.529833 CACACTGGCAAAACCACACA 59.470 50.000 0.00 0.00 46.36 3.72
470 1045 1.136695 ACACTGGCAAAACCACACATG 59.863 47.619 0.00 0.00 46.36 3.21
525 1126 6.226787 GGATACATATTGCTCTGCTTGTAGT 58.773 40.000 0.00 0.00 0.00 2.73
561 1162 1.410517 CGTGTACTGGATCCTGCATCT 59.589 52.381 17.94 1.88 0.00 2.90
562 1163 2.544694 CGTGTACTGGATCCTGCATCTC 60.545 54.545 17.94 8.74 0.00 2.75
563 1164 2.697751 GTGTACTGGATCCTGCATCTCT 59.302 50.000 17.94 0.81 0.00 3.10
580 1181 3.659334 TGCACTTGTAGCAGCTGC 58.341 55.556 31.53 31.53 37.02 5.25
581 1182 1.227913 TGCACTTGTAGCAGCTGCA 60.228 52.632 38.24 22.31 45.16 4.41
582 1183 1.232621 TGCACTTGTAGCAGCTGCAG 61.233 55.000 38.24 28.16 45.16 4.41
583 1184 0.952497 GCACTTGTAGCAGCTGCAGA 60.952 55.000 38.24 24.02 45.16 4.26
637 1238 3.314541 ACACTTAACATCTCACCGACC 57.685 47.619 0.00 0.00 0.00 4.79
638 1239 2.897969 ACACTTAACATCTCACCGACCT 59.102 45.455 0.00 0.00 0.00 3.85
639 1240 4.084287 ACACTTAACATCTCACCGACCTA 58.916 43.478 0.00 0.00 0.00 3.08
640 1241 4.525487 ACACTTAACATCTCACCGACCTAA 59.475 41.667 0.00 0.00 0.00 2.69
641 1242 5.187186 ACACTTAACATCTCACCGACCTAAT 59.813 40.000 0.00 0.00 0.00 1.73
642 1243 5.749109 CACTTAACATCTCACCGACCTAATC 59.251 44.000 0.00 0.00 0.00 1.75
643 1244 5.657302 ACTTAACATCTCACCGACCTAATCT 59.343 40.000 0.00 0.00 0.00 2.40
644 1245 6.832384 ACTTAACATCTCACCGACCTAATCTA 59.168 38.462 0.00 0.00 0.00 1.98
646 1247 5.517322 ACATCTCACCGACCTAATCTAAC 57.483 43.478 0.00 0.00 0.00 2.34
647 1248 4.954202 ACATCTCACCGACCTAATCTAACA 59.046 41.667 0.00 0.00 0.00 2.41
648 1249 5.067936 ACATCTCACCGACCTAATCTAACAG 59.932 44.000 0.00 0.00 0.00 3.16
649 1250 4.597004 TCTCACCGACCTAATCTAACAGT 58.403 43.478 0.00 0.00 0.00 3.55
651 1252 5.587844 TCTCACCGACCTAATCTAACAGTAC 59.412 44.000 0.00 0.00 0.00 2.73
682 1315 9.193133 CTGAATCAATGCATATCCTTCAATTTC 57.807 33.333 0.00 0.00 0.00 2.17
686 1345 7.864686 TCAATGCATATCCTTCAATTTCTACG 58.135 34.615 0.00 0.00 0.00 3.51
714 1373 2.828877 TGAATAACATTCGCGGTAGGG 58.171 47.619 6.13 0.00 0.00 3.53
717 1376 2.298411 TAACATTCGCGGTAGGGTTC 57.702 50.000 6.13 0.00 0.00 3.62
718 1377 0.322322 AACATTCGCGGTAGGGTTCA 59.678 50.000 6.13 0.00 0.00 3.18
719 1378 0.108329 ACATTCGCGGTAGGGTTCAG 60.108 55.000 6.13 0.00 0.00 3.02
720 1379 0.174845 CATTCGCGGTAGGGTTCAGA 59.825 55.000 6.13 0.00 0.00 3.27
721 1380 0.460311 ATTCGCGGTAGGGTTCAGAG 59.540 55.000 6.13 0.00 0.00 3.35
722 1381 2.202756 CGCGGTAGGGTTCAGAGC 60.203 66.667 0.00 0.00 0.00 4.09
723 1382 2.711922 CGCGGTAGGGTTCAGAGCT 61.712 63.158 0.00 0.00 0.00 4.09
724 1383 1.597461 GCGGTAGGGTTCAGAGCTT 59.403 57.895 0.00 0.00 0.00 3.74
795 1553 4.840005 GGCGTACTGGGCTGGCTC 62.840 72.222 0.00 0.00 0.00 4.70
797 1555 3.077556 CGTACTGGGCTGGCTCCT 61.078 66.667 0.00 0.00 0.00 3.69
799 1557 2.688666 TACTGGGCTGGCTCCTGG 60.689 66.667 0.00 0.00 0.00 4.45
806 1564 4.478371 CTGGCTCCTGGCGCATCA 62.478 66.667 10.83 0.00 42.94 3.07
807 1565 4.478371 TGGCTCCTGGCGCATCAG 62.478 66.667 10.83 8.37 42.94 2.90
811 1569 2.747460 TCCTGGCGCATCAGCAAC 60.747 61.111 10.83 0.00 42.27 4.17
866 1633 4.299796 GCCCAGGTTTGGCCCAGA 62.300 66.667 0.00 0.00 43.58 3.86
901 1700 1.095600 TCAATCCACGAGACGAGAGG 58.904 55.000 0.00 0.00 0.00 3.69
925 1724 1.470448 AACCTACCTCCCCTCCCCTT 61.470 60.000 0.00 0.00 0.00 3.95
926 1725 1.074395 CCTACCTCCCCTCCCCTTC 60.074 68.421 0.00 0.00 0.00 3.46
975 1774 0.179045 ACAAGCAGTCCACCACTCAC 60.179 55.000 0.00 0.00 30.26 3.51
976 1775 0.886490 CAAGCAGTCCACCACTCACC 60.886 60.000 0.00 0.00 30.26 4.02
1086 1906 1.454111 CTGGGAGATCCTCGTCCGT 60.454 63.158 0.00 0.00 36.20 4.69
1381 2201 2.683933 TGGTCCTCTCCTTCCGCC 60.684 66.667 0.00 0.00 0.00 6.13
1611 2431 2.279582 ACATCTTCACGTTAGGCTCG 57.720 50.000 0.00 0.00 0.00 5.03
1689 2509 1.646189 GATCTCTCCTGTTTCGTGGC 58.354 55.000 0.00 0.00 0.00 5.01
1690 2510 1.205893 GATCTCTCCTGTTTCGTGGCT 59.794 52.381 0.00 0.00 0.00 4.75
1715 2535 3.892104 ATTGGCACCCACCAGGCAG 62.892 63.158 0.00 0.00 41.82 4.85
1724 2547 1.369091 CCACCAGGCAGCACGATAAC 61.369 60.000 0.00 0.00 0.00 1.89
1764 2587 0.250467 AGTTGTTCTGGCAGATGCGT 60.250 50.000 19.50 0.00 43.26 5.24
1777 2600 1.004320 ATGCGTGCTCCGGTTGTTA 60.004 52.632 0.00 0.00 36.94 2.41
1839 2665 0.395586 TGCCCGGCTTTAATGATGCT 60.396 50.000 11.61 0.00 0.00 3.79
1846 2672 2.540361 GGCTTTAATGATGCTGCGACAG 60.540 50.000 0.00 2.92 34.12 3.51
1875 2701 2.687200 TGGGTGGCGCAGGACTAT 60.687 61.111 10.83 0.00 0.00 2.12
1881 2707 1.365633 GGCGCAGGACTATGAGAGG 59.634 63.158 10.83 0.00 0.00 3.69
1918 2744 4.443034 GCAAATACCGGGTAGACTTCTCAT 60.443 45.833 13.15 0.00 0.00 2.90
1944 2770 0.536006 ACCTCACTCTGCAGTTTGGC 60.536 55.000 14.67 0.00 0.00 4.52
1950 2776 1.406539 ACTCTGCAGTTTGGCAAGTTG 59.593 47.619 14.67 4.39 44.40 3.16
1974 2800 0.261696 AAAGTTCTTGGGTGGTGGCT 59.738 50.000 0.00 0.00 0.00 4.75
2005 2831 0.538746 TGGTGACGTGCTCCTACTGA 60.539 55.000 0.00 0.00 0.00 3.41
2020 2846 4.943705 TCCTACTGATCAATTTTGGTGAGC 59.056 41.667 0.00 0.00 32.00 4.26
2063 2889 0.796927 GGCAAGTTGGTCGCTACTTC 59.203 55.000 4.75 0.00 32.50 3.01
2139 2965 5.763204 TCAACATACCTTCTTTCCAACACTC 59.237 40.000 0.00 0.00 0.00 3.51
2163 2989 1.885887 GGTTATGTTGCCAACTCTGCA 59.114 47.619 9.30 0.00 36.84 4.41
2211 3041 2.644798 AGTGGTGATTCTAGCCCAACTT 59.355 45.455 0.00 0.00 0.00 2.66
2301 3131 8.146479 TGATGCATAGACAAGTTATGATCAAC 57.854 34.615 0.00 0.00 30.79 3.18
2365 3195 0.615331 CTTCTGGGCTGAAGTGGCTA 59.385 55.000 10.91 0.00 38.76 3.93
2367 3197 0.545309 TCTGGGCTGAAGTGGCTACT 60.545 55.000 0.00 0.00 39.32 2.57
2386 3216 5.814705 GCTACTGTGAGTCTTGATGCTAAAT 59.185 40.000 0.00 0.00 0.00 1.40
2388 3218 6.492007 ACTGTGAGTCTTGATGCTAAATTG 57.508 37.500 0.00 0.00 0.00 2.32
2389 3219 5.106396 ACTGTGAGTCTTGATGCTAAATTGC 60.106 40.000 0.00 0.00 0.00 3.56
2411 4040 5.473504 TGCAAGTCTTTCTTAAAGGTCATCC 59.526 40.000 0.00 0.00 39.01 3.51
2421 4050 3.884037 AAAGGTCATCCAGTGGTTTCT 57.116 42.857 9.54 0.00 35.89 2.52
2422 4051 2.867109 AGGTCATCCAGTGGTTTCTG 57.133 50.000 9.54 3.46 35.89 3.02
2424 4053 2.443255 AGGTCATCCAGTGGTTTCTGTT 59.557 45.455 9.54 0.00 35.89 3.16
2425 4054 2.554032 GGTCATCCAGTGGTTTCTGTTG 59.446 50.000 9.54 0.00 34.02 3.33
2426 4055 3.214328 GTCATCCAGTGGTTTCTGTTGT 58.786 45.455 9.54 0.00 34.02 3.32
2427 4056 4.385825 GTCATCCAGTGGTTTCTGTTGTA 58.614 43.478 9.54 0.00 34.02 2.41
2428 4057 4.819630 GTCATCCAGTGGTTTCTGTTGTAA 59.180 41.667 9.54 0.00 34.02 2.41
2429 4058 5.473504 GTCATCCAGTGGTTTCTGTTGTAAT 59.526 40.000 9.54 0.00 34.02 1.89
2430 4059 6.016276 GTCATCCAGTGGTTTCTGTTGTAATT 60.016 38.462 9.54 0.00 34.02 1.40
2431 4060 6.206634 TCATCCAGTGGTTTCTGTTGTAATTC 59.793 38.462 9.54 0.00 34.02 2.17
2432 4061 4.825085 TCCAGTGGTTTCTGTTGTAATTCC 59.175 41.667 9.54 0.00 34.02 3.01
2433 4062 4.827284 CCAGTGGTTTCTGTTGTAATTCCT 59.173 41.667 0.00 0.00 34.02 3.36
2516 6431 9.798885 GAATTAATAGTGCATATGAAGTTCGAC 57.201 33.333 6.97 0.00 0.00 4.20
2531 6456 8.244494 TGAAGTTCGACTCTGAAGAAATAATG 57.756 34.615 0.00 0.00 0.00 1.90
2562 6487 4.882671 ACAAGCAGAAGTTTGTACTGTG 57.117 40.909 0.00 0.00 45.64 3.66
2563 6488 4.261801 ACAAGCAGAAGTTTGTACTGTGT 58.738 39.130 0.00 0.00 45.64 3.72
2564 6489 4.332819 ACAAGCAGAAGTTTGTACTGTGTC 59.667 41.667 0.00 0.00 45.64 3.67
2565 6490 4.408182 AGCAGAAGTTTGTACTGTGTCT 57.592 40.909 0.00 0.00 34.01 3.41
2566 6491 5.531122 AGCAGAAGTTTGTACTGTGTCTA 57.469 39.130 0.00 0.00 34.01 2.59
2567 6492 5.533482 AGCAGAAGTTTGTACTGTGTCTAG 58.467 41.667 0.00 0.00 34.01 2.43
2568 6493 4.686554 GCAGAAGTTTGTACTGTGTCTAGG 59.313 45.833 0.00 0.00 34.01 3.02
2569 6494 5.230942 CAGAAGTTTGTACTGTGTCTAGGG 58.769 45.833 0.00 0.00 34.01 3.53
2570 6495 5.010719 CAGAAGTTTGTACTGTGTCTAGGGA 59.989 44.000 0.00 0.00 34.01 4.20
2571 6496 5.780793 AGAAGTTTGTACTGTGTCTAGGGAT 59.219 40.000 0.00 0.00 34.01 3.85
2572 6497 5.407407 AGTTTGTACTGTGTCTAGGGATG 57.593 43.478 0.00 0.00 31.99 3.51
2573 6498 4.223032 AGTTTGTACTGTGTCTAGGGATGG 59.777 45.833 0.00 0.00 31.99 3.51
2574 6499 3.750501 TGTACTGTGTCTAGGGATGGA 57.249 47.619 0.00 0.00 0.00 3.41
2575 6500 4.265856 TGTACTGTGTCTAGGGATGGAT 57.734 45.455 0.00 0.00 0.00 3.41
2576 6501 3.960755 TGTACTGTGTCTAGGGATGGATG 59.039 47.826 0.00 0.00 0.00 3.51
2577 6502 1.765314 ACTGTGTCTAGGGATGGATGC 59.235 52.381 0.00 0.00 0.00 3.91
2578 6503 2.045524 CTGTGTCTAGGGATGGATGCT 58.954 52.381 0.00 0.00 0.00 3.79
2579 6504 2.437281 CTGTGTCTAGGGATGGATGCTT 59.563 50.000 0.00 0.00 0.00 3.91
2580 6505 2.171237 TGTGTCTAGGGATGGATGCTTG 59.829 50.000 0.00 0.00 0.00 4.01
2581 6506 1.770658 TGTCTAGGGATGGATGCTTGG 59.229 52.381 0.00 0.00 0.00 3.61
2582 6507 1.072965 GTCTAGGGATGGATGCTTGGG 59.927 57.143 0.00 0.00 0.00 4.12
2583 6508 1.143813 CTAGGGATGGATGCTTGGGT 58.856 55.000 0.00 0.00 0.00 4.51
2584 6509 1.496429 CTAGGGATGGATGCTTGGGTT 59.504 52.381 0.00 0.00 0.00 4.11
2585 6510 0.712380 AGGGATGGATGCTTGGGTTT 59.288 50.000 0.00 0.00 0.00 3.27
2586 6511 1.079323 AGGGATGGATGCTTGGGTTTT 59.921 47.619 0.00 0.00 0.00 2.43
2587 6512 1.482182 GGGATGGATGCTTGGGTTTTC 59.518 52.381 0.00 0.00 0.00 2.29
2588 6513 2.178580 GGATGGATGCTTGGGTTTTCA 58.821 47.619 0.00 0.00 0.00 2.69
2589 6514 2.767960 GGATGGATGCTTGGGTTTTCAT 59.232 45.455 0.00 0.00 0.00 2.57
2590 6515 3.198417 GGATGGATGCTTGGGTTTTCATT 59.802 43.478 0.00 0.00 0.00 2.57
2591 6516 4.405358 GGATGGATGCTTGGGTTTTCATTA 59.595 41.667 0.00 0.00 0.00 1.90
2592 6517 5.104982 GGATGGATGCTTGGGTTTTCATTAA 60.105 40.000 0.00 0.00 0.00 1.40
2593 6518 6.408434 GGATGGATGCTTGGGTTTTCATTAAT 60.408 38.462 0.00 0.00 0.00 1.40
2594 6519 5.732633 TGGATGCTTGGGTTTTCATTAATG 58.267 37.500 9.29 9.29 0.00 1.90
2595 6520 5.483231 TGGATGCTTGGGTTTTCATTAATGA 59.517 36.000 14.23 14.23 34.44 2.57
2596 6521 6.013898 TGGATGCTTGGGTTTTCATTAATGAA 60.014 34.615 23.86 23.86 44.42 2.57
2608 6533 6.463995 TTCATTAATGAAAATCGGAAGGGG 57.536 37.500 25.11 0.00 43.26 4.79
2609 6534 5.515106 TCATTAATGAAAATCGGAAGGGGT 58.485 37.500 15.82 0.00 33.08 4.95
2610 6535 5.359576 TCATTAATGAAAATCGGAAGGGGTG 59.640 40.000 15.82 0.00 33.08 4.61
2611 6536 3.449746 AATGAAAATCGGAAGGGGTGA 57.550 42.857 0.00 0.00 0.00 4.02
2612 6537 2.961531 TGAAAATCGGAAGGGGTGAA 57.038 45.000 0.00 0.00 0.00 3.18
2613 6538 2.790433 TGAAAATCGGAAGGGGTGAAG 58.210 47.619 0.00 0.00 0.00 3.02
2614 6539 1.472878 GAAAATCGGAAGGGGTGAAGC 59.527 52.381 0.00 0.00 0.00 3.86
2615 6540 0.323451 AAATCGGAAGGGGTGAAGCC 60.323 55.000 0.00 0.00 0.00 4.35
2629 6554 5.722021 GGTGAAGCCCTTCTTTTATTCAA 57.278 39.130 9.23 0.00 40.14 2.69
2630 6555 6.096673 GGTGAAGCCCTTCTTTTATTCAAA 57.903 37.500 9.23 0.00 40.14 2.69
2631 6556 6.521162 GGTGAAGCCCTTCTTTTATTCAAAA 58.479 36.000 9.23 0.00 40.14 2.44
2632 6557 6.989759 GGTGAAGCCCTTCTTTTATTCAAAAA 59.010 34.615 9.23 0.00 40.14 1.94
2660 6585 6.488006 AGCTAACAAGCAGAAGAAAAGATTGA 59.512 34.615 0.00 0.00 37.25 2.57
2671 6596 4.990526 AGAAAAGATTGACATGGTCAGGT 58.009 39.130 0.00 0.00 43.69 4.00
2672 6597 5.006386 AGAAAAGATTGACATGGTCAGGTC 58.994 41.667 8.59 8.59 43.69 3.85
2674 6599 1.561542 AGATTGACATGGTCAGGTCCC 59.438 52.381 12.30 3.44 43.69 4.46
2675 6600 1.281867 GATTGACATGGTCAGGTCCCA 59.718 52.381 12.30 1.22 43.69 4.37
2676 6601 1.144691 TTGACATGGTCAGGTCCCAA 58.855 50.000 12.30 0.56 43.69 4.12
2677 6602 1.144691 TGACATGGTCAGGTCCCAAA 58.855 50.000 12.30 0.00 41.02 3.28
2678 6603 1.710244 TGACATGGTCAGGTCCCAAAT 59.290 47.619 12.30 0.00 41.02 2.32
2679 6604 2.109834 TGACATGGTCAGGTCCCAAATT 59.890 45.455 12.30 0.00 41.02 1.82
2680 6605 3.332187 TGACATGGTCAGGTCCCAAATTA 59.668 43.478 12.30 0.00 41.02 1.40
2681 6606 4.017591 TGACATGGTCAGGTCCCAAATTAT 60.018 41.667 12.30 0.00 41.02 1.28
2682 6607 4.280819 ACATGGTCAGGTCCCAAATTATG 58.719 43.478 0.00 0.00 35.14 1.90
2685 6610 4.340617 TGGTCAGGTCCCAAATTATGTTC 58.659 43.478 0.00 0.00 0.00 3.18
2705 6638 1.680338 GTGTTGAGGCACTGGAACTT 58.320 50.000 0.00 0.00 41.55 2.66
2729 6662 4.409570 CAGCCATGTTCATTTTTCTCTCG 58.590 43.478 0.00 0.00 0.00 4.04
2730 6663 4.154737 CAGCCATGTTCATTTTTCTCTCGA 59.845 41.667 0.00 0.00 0.00 4.04
2731 6664 4.394300 AGCCATGTTCATTTTTCTCTCGAG 59.606 41.667 5.93 5.93 0.00 4.04
2733 6666 4.437930 CCATGTTCATTTTTCTCTCGAGGC 60.438 45.833 13.56 0.00 0.00 4.70
2775 6708 1.473677 TCATTGGCCGAAAGCAGATTG 59.526 47.619 0.00 0.00 46.50 2.67
2776 6709 0.174162 ATTGGCCGAAAGCAGATTGC 59.826 50.000 0.00 0.00 46.50 3.56
2813 6750 4.282957 ACACCATGATTTGTGTGGCAATAA 59.717 37.500 4.88 0.00 43.69 1.40
2946 6886 7.018635 TGCATGTGTGAGATAAATGTACATG 57.981 36.000 9.63 0.00 43.93 3.21
2954 6894 5.877564 TGAGATAAATGTACATGTTGGCGAA 59.122 36.000 9.63 0.00 0.00 4.70
2958 6898 5.898630 AAATGTACATGTTGGCGAAAAAC 57.101 34.783 9.63 0.00 0.00 2.43
2964 6904 6.858993 TGTACATGTTGGCGAAAAACTATTTC 59.141 34.615 2.30 0.00 0.00 2.17
2981 6921 3.889196 TTTCGATTGTGTGGTTACAGC 57.111 42.857 0.00 0.00 37.52 4.40
2992 6932 4.561606 GTGTGGTTACAGCTTACACTATCG 59.438 45.833 0.00 0.00 38.76 2.92
3017 6957 8.667463 CGATGCAATATATATGTTTGACATCCA 58.333 33.333 21.87 11.44 39.88 3.41
3058 6998 4.973396 TGTTTGATCGATCTGAAACATGC 58.027 39.130 27.31 11.99 34.27 4.06
3059 6999 4.455190 TGTTTGATCGATCTGAAACATGCA 59.545 37.500 27.31 13.76 34.27 3.96
3083 7023 7.063426 GCAAAAAGTCTTTTCAGCTTAAACTGT 59.937 33.333 20.04 0.00 38.84 3.55
3108 7051 0.662619 CTGCTTTTTGTGTCGAGCCA 59.337 50.000 0.00 0.00 34.30 4.75
3114 7057 2.442212 TTTGTGTCGAGCCAATACGA 57.558 45.000 0.00 0.00 36.18 3.43
3125 7068 4.291783 GAGCCAATACGACATCTGAGTAC 58.708 47.826 0.00 0.00 0.00 2.73
3137 7080 3.516981 TCTGAGTACATGAGCAAGAGC 57.483 47.619 0.00 0.00 42.56 4.09
3148 7091 3.151461 GCAAGAGCTGAAGTCCTCC 57.849 57.895 0.00 0.00 37.91 4.30
3149 7092 0.612744 GCAAGAGCTGAAGTCCTCCT 59.387 55.000 0.00 0.00 37.91 3.69
3150 7093 1.003003 GCAAGAGCTGAAGTCCTCCTT 59.997 52.381 0.00 0.00 37.91 3.36
3151 7094 2.551938 GCAAGAGCTGAAGTCCTCCTTT 60.552 50.000 0.00 0.00 37.91 3.11
3152 7095 3.072944 CAAGAGCTGAAGTCCTCCTTTG 58.927 50.000 0.00 0.00 32.03 2.77
3153 7096 1.627834 AGAGCTGAAGTCCTCCTTTGG 59.372 52.381 0.00 0.00 32.03 3.28
3154 7097 0.037447 AGCTGAAGTCCTCCTTTGGC 59.963 55.000 0.00 0.00 32.03 4.52
3155 7098 0.037447 GCTGAAGTCCTCCTTTGGCT 59.963 55.000 0.00 0.00 32.03 4.75
3156 7099 1.279271 GCTGAAGTCCTCCTTTGGCTA 59.721 52.381 0.00 0.00 32.03 3.93
3157 7100 2.290323 GCTGAAGTCCTCCTTTGGCTAA 60.290 50.000 0.00 0.00 32.03 3.09
3158 7101 3.810743 GCTGAAGTCCTCCTTTGGCTAAA 60.811 47.826 0.00 0.00 32.03 1.85
3159 7102 4.593956 CTGAAGTCCTCCTTTGGCTAAAT 58.406 43.478 0.00 0.00 32.03 1.40
3160 7103 4.998051 TGAAGTCCTCCTTTGGCTAAATT 58.002 39.130 0.00 0.00 32.03 1.82
3161 7104 6.134535 TGAAGTCCTCCTTTGGCTAAATTA 57.865 37.500 0.00 0.00 32.03 1.40
3162 7105 6.731467 TGAAGTCCTCCTTTGGCTAAATTAT 58.269 36.000 0.00 0.00 32.03 1.28
3163 7106 7.182060 TGAAGTCCTCCTTTGGCTAAATTATT 58.818 34.615 0.00 0.00 32.03 1.40
3164 7107 7.122650 TGAAGTCCTCCTTTGGCTAAATTATTG 59.877 37.037 0.00 0.00 32.03 1.90
3165 7108 6.494059 AGTCCTCCTTTGGCTAAATTATTGT 58.506 36.000 0.00 0.00 0.00 2.71
3166 7109 6.378280 AGTCCTCCTTTGGCTAAATTATTGTG 59.622 38.462 0.00 0.00 0.00 3.33
3167 7110 6.152831 GTCCTCCTTTGGCTAAATTATTGTGT 59.847 38.462 0.00 0.00 0.00 3.72
3168 7111 6.723977 TCCTCCTTTGGCTAAATTATTGTGTT 59.276 34.615 0.00 0.00 0.00 3.32
3169 7112 6.813152 CCTCCTTTGGCTAAATTATTGTGTTG 59.187 38.462 0.00 0.00 0.00 3.33
3170 7113 6.162777 TCCTTTGGCTAAATTATTGTGTTGC 58.837 36.000 0.00 0.00 0.00 4.17
3171 7114 6.014669 TCCTTTGGCTAAATTATTGTGTTGCT 60.015 34.615 0.00 0.00 0.00 3.91
3172 7115 6.650390 CCTTTGGCTAAATTATTGTGTTGCTT 59.350 34.615 0.00 0.00 0.00 3.91
3173 7116 7.173047 CCTTTGGCTAAATTATTGTGTTGCTTT 59.827 33.333 0.00 0.00 0.00 3.51
3174 7117 7.418840 TTGGCTAAATTATTGTGTTGCTTTG 57.581 32.000 0.00 0.00 0.00 2.77
3175 7118 6.753180 TGGCTAAATTATTGTGTTGCTTTGA 58.247 32.000 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 6.389091 TCATGTGTGATAAAAATGTGAAGCC 58.611 36.000 0.00 0.00 0.00 4.35
66 67 9.109533 GCTTTTTGCTTAAATTTTCATCATGTG 57.890 29.630 0.00 0.00 38.95 3.21
196 753 8.955002 TCGTTAAATCTCGATTTCTAATTCTCG 58.045 33.333 8.07 0.70 40.99 4.04
282 841 2.104111 ACCTCGTGTTCAACTCAATCCA 59.896 45.455 0.00 0.00 0.00 3.41
286 845 3.601435 TGAAACCTCGTGTTCAACTCAA 58.399 40.909 0.00 0.00 35.67 3.02
317 876 9.357652 CAGAATATGAAACCAACCAATTAACAG 57.642 33.333 0.00 0.00 0.00 3.16
318 877 7.816995 GCAGAATATGAAACCAACCAATTAACA 59.183 33.333 0.00 0.00 0.00 2.41
337 896 1.477700 GCCATGGTTTGCTGCAGAATA 59.522 47.619 20.43 0.00 0.00 1.75
394 967 3.267860 GCGCCCATCTGCTTCTCG 61.268 66.667 0.00 0.00 0.00 4.04
424 997 0.958091 TCCTTGAAAATGTGCGTGGG 59.042 50.000 0.00 0.00 0.00 4.61
432 1006 4.805192 CAGTGTGTGGTTTCCTTGAAAATG 59.195 41.667 0.00 0.00 33.14 2.32
463 1038 1.061131 GAATTCGAGTCGCCATGTGTG 59.939 52.381 7.92 0.00 0.00 3.82
464 1039 1.337728 TGAATTCGAGTCGCCATGTGT 60.338 47.619 7.92 0.00 0.00 3.72
465 1040 1.358877 TGAATTCGAGTCGCCATGTG 58.641 50.000 7.92 0.00 0.00 3.21
468 1043 2.905075 TCAATGAATTCGAGTCGCCAT 58.095 42.857 7.92 5.77 0.00 4.40
470 1045 2.673368 ACTTCAATGAATTCGAGTCGCC 59.327 45.455 7.92 0.00 0.00 5.54
471 1046 3.999229 ACTTCAATGAATTCGAGTCGC 57.001 42.857 7.92 0.00 0.00 5.19
472 1047 5.346011 TCTGAACTTCAATGAATTCGAGTCG 59.654 40.000 6.09 6.09 0.00 4.18
477 1070 6.082338 CCTGTTCTGAACTTCAATGAATTCG 58.918 40.000 20.18 1.47 0.00 3.34
525 1126 5.049198 CAGTACACGTCTGGTTCTGTAACTA 60.049 44.000 0.00 0.00 35.81 2.24
563 1164 1.227913 TGCAGCTGCTACAAGTGCA 60.228 52.632 36.61 13.77 41.72 4.57
565 1166 0.795085 GTCTGCAGCTGCTACAAGTG 59.205 55.000 36.61 18.03 42.66 3.16
566 1167 0.683973 AGTCTGCAGCTGCTACAAGT 59.316 50.000 36.61 19.56 42.66 3.16
567 1168 2.662006 TAGTCTGCAGCTGCTACAAG 57.338 50.000 36.61 25.86 42.66 3.16
568 1169 3.196469 AGATTAGTCTGCAGCTGCTACAA 59.804 43.478 36.61 26.33 42.66 2.41
570 1171 3.451141 AGATTAGTCTGCAGCTGCTAC 57.549 47.619 36.61 31.32 42.66 3.58
571 1172 4.402474 TGTTAGATTAGTCTGCAGCTGCTA 59.598 41.667 36.61 23.26 42.66 3.49
572 1173 3.196469 TGTTAGATTAGTCTGCAGCTGCT 59.804 43.478 36.61 20.81 42.66 4.24
573 1174 3.525537 TGTTAGATTAGTCTGCAGCTGC 58.474 45.455 31.89 31.89 42.50 5.25
574 1175 4.753233 ACTGTTAGATTAGTCTGCAGCTG 58.247 43.478 10.11 10.11 39.90 4.24
575 1176 5.419155 TGTACTGTTAGATTAGTCTGCAGCT 59.581 40.000 9.47 12.20 39.90 4.24
576 1177 5.651530 TGTACTGTTAGATTAGTCTGCAGC 58.348 41.667 9.47 4.26 39.90 5.25
577 1178 7.090808 TGTTGTACTGTTAGATTAGTCTGCAG 58.909 38.462 7.63 7.63 40.98 4.41
578 1179 6.988522 TGTTGTACTGTTAGATTAGTCTGCA 58.011 36.000 0.00 0.00 35.87 4.41
579 1180 8.383619 CAATGTTGTACTGTTAGATTAGTCTGC 58.616 37.037 0.00 0.00 35.87 4.26
580 1181 9.639601 TCAATGTTGTACTGTTAGATTAGTCTG 57.360 33.333 0.00 0.00 35.87 3.51
647 1248 7.443575 GGATATGCATTGATTCAGTCTTGTACT 59.556 37.037 3.54 0.00 39.81 2.73
648 1249 7.443575 AGGATATGCATTGATTCAGTCTTGTAC 59.556 37.037 3.54 0.00 0.00 2.90
649 1250 7.512130 AGGATATGCATTGATTCAGTCTTGTA 58.488 34.615 3.54 0.00 0.00 2.41
651 1252 6.879276 AGGATATGCATTGATTCAGTCTTG 57.121 37.500 3.54 0.00 0.00 3.02
667 1268 8.520835 TCGAATCGTAGAAATTGAAGGATATG 57.479 34.615 1.52 0.00 43.58 1.78
706 1365 0.036294 AAAGCTCTGAACCCTACCGC 60.036 55.000 0.00 0.00 0.00 5.68
733 1392 4.503296 GCTCTGAACCCTACTTGTCTCAAA 60.503 45.833 0.00 0.00 0.00 2.69
734 1393 3.006967 GCTCTGAACCCTACTTGTCTCAA 59.993 47.826 0.00 0.00 0.00 3.02
737 1396 2.564947 CAGCTCTGAACCCTACTTGTCT 59.435 50.000 0.00 0.00 0.00 3.41
738 1397 2.563179 TCAGCTCTGAACCCTACTTGTC 59.437 50.000 0.00 0.00 36.53 3.18
739 1398 2.609747 TCAGCTCTGAACCCTACTTGT 58.390 47.619 0.00 0.00 36.53 3.16
740 1399 3.594134 CTTCAGCTCTGAACCCTACTTG 58.406 50.000 8.14 0.00 43.90 3.16
741 1400 2.569404 CCTTCAGCTCTGAACCCTACTT 59.431 50.000 8.14 0.00 43.90 2.24
742 1401 2.183679 CCTTCAGCTCTGAACCCTACT 58.816 52.381 8.14 0.00 43.90 2.57
794 1552 2.747460 GTTGCTGATGCGCCAGGA 60.747 61.111 14.34 9.48 43.34 3.86
795 1553 4.170062 CGTTGCTGATGCGCCAGG 62.170 66.667 14.34 0.00 43.34 4.45
806 1564 3.616721 AGACACTCGGCCGTTGCT 61.617 61.111 27.15 19.43 37.74 3.91
807 1565 3.414700 CAGACACTCGGCCGTTGC 61.415 66.667 27.15 17.71 0.00 4.17
808 1566 2.738521 CCAGACACTCGGCCGTTG 60.739 66.667 27.15 24.46 0.00 4.10
809 1567 4.003788 CCCAGACACTCGGCCGTT 62.004 66.667 27.15 11.00 0.00 4.44
866 1633 0.475044 TTGAACTGGGCCTAAACGGT 59.525 50.000 4.53 0.00 34.25 4.83
901 1700 0.034380 GAGGGGAGGTAGGTTTTGCC 60.034 60.000 0.00 0.00 37.58 4.52
1053 1873 1.063642 TCCCAGATGGTGATCTCGTCT 60.064 52.381 0.00 0.03 36.75 4.18
1158 1978 2.285368 TGGTGGGCGAGGAGGAAT 60.285 61.111 0.00 0.00 0.00 3.01
1365 2185 2.683933 TGGCGGAAGGAGAGGACC 60.684 66.667 0.00 0.00 0.00 4.46
1381 2201 3.036084 GTCACGGACGCTGGTGTG 61.036 66.667 0.00 0.00 35.67 3.82
1440 2260 3.056754 ATAAGGCAACGGGAGGGGC 62.057 63.158 0.00 0.00 46.39 5.80
1573 2393 2.873557 TAGGAGCCGTCTTCAGGGGG 62.874 65.000 0.00 0.00 0.00 5.40
1576 2396 1.067821 GATGTAGGAGCCGTCTTCAGG 59.932 57.143 0.00 0.00 0.00 3.86
1579 2399 3.086818 GAAGATGTAGGAGCCGTCTTC 57.913 52.381 6.61 6.61 43.71 2.87
1715 2535 0.364515 GTCGAACACCGTTATCGTGC 59.635 55.000 0.00 0.00 39.75 5.34
1740 2563 3.866066 GCATCTGCCAGAACAACTCAGTA 60.866 47.826 0.00 0.00 34.31 2.74
1764 2587 1.302192 GCCAGTAACAACCGGAGCA 60.302 57.895 9.46 0.00 0.00 4.26
1777 2600 2.292828 AACAACTTAGCATGGCCAGT 57.707 45.000 13.05 0.00 0.00 4.00
1822 2648 0.031178 GCAGCATCATTAAAGCCGGG 59.969 55.000 2.18 0.00 0.00 5.73
1839 2665 2.486918 CAGATATCAATGGCTGTCGCA 58.513 47.619 5.32 0.00 38.10 5.10
1846 2672 1.251251 GCCACCCAGATATCAATGGC 58.749 55.000 18.12 18.12 45.26 4.40
1875 2701 2.039624 GCCCAGACCTCCCTCTCA 59.960 66.667 0.00 0.00 0.00 3.27
1881 2707 2.505364 ATTTGCAGGCCCAGACCTCC 62.505 60.000 0.00 0.00 38.26 4.30
1937 2763 1.757682 TTCGTCCAACTTGCCAAACT 58.242 45.000 0.00 0.00 0.00 2.66
1944 2770 3.243068 CCCAAGAACTTTCGTCCAACTTG 60.243 47.826 0.00 0.00 34.85 3.16
1950 2776 1.235724 CCACCCAAGAACTTTCGTCC 58.764 55.000 0.00 0.00 0.00 4.79
1974 2800 1.074775 GTCACCATCCCAAGGCACA 59.925 57.895 0.00 0.00 0.00 4.57
2005 2831 1.549203 AGCCGCTCACCAAAATTGAT 58.451 45.000 0.00 0.00 0.00 2.57
2020 2846 2.386661 ATGTCAACCTGAAGTAGCCG 57.613 50.000 0.00 0.00 0.00 5.52
2063 2889 4.598894 CGAGGCCTCTGCGATGGG 62.599 72.222 29.73 8.40 38.85 4.00
2301 3131 3.996150 ACCATGAAACAGTCAAGCTTG 57.004 42.857 20.81 20.81 40.50 4.01
2337 3167 5.649395 CACTTCAGCCCAGAAGAATATTCAA 59.351 40.000 17.56 0.00 46.18 2.69
2365 3195 5.106396 GCAATTTAGCATCAAGACTCACAGT 60.106 40.000 0.00 0.00 0.00 3.55
2367 3197 4.761227 TGCAATTTAGCATCAAGACTCACA 59.239 37.500 0.00 0.00 40.11 3.58
2386 3216 6.016276 GGATGACCTTTAAGAAAGACTTGCAA 60.016 38.462 0.00 0.00 41.02 4.08
2388 3218 5.473504 TGGATGACCTTTAAGAAAGACTTGC 59.526 40.000 0.47 0.00 41.02 4.01
2389 3219 6.712547 ACTGGATGACCTTTAAGAAAGACTTG 59.287 38.462 0.47 0.00 41.02 3.16
2390 3220 6.712547 CACTGGATGACCTTTAAGAAAGACTT 59.287 38.462 0.47 0.00 41.02 3.01
2411 4040 6.391227 AAGGAATTACAACAGAAACCACTG 57.609 37.500 0.00 0.00 42.78 3.66
2446 6360 7.581213 AAGTGAGACACAATTCCAAACAATA 57.419 32.000 4.75 0.00 36.74 1.90
2498 6413 4.158579 TCAGAGTCGAACTTCATATGCACT 59.841 41.667 0.00 0.00 0.00 4.40
2501 6416 5.344066 TCTTCAGAGTCGAACTTCATATGC 58.656 41.667 0.00 0.00 0.00 3.14
2509 6424 6.402222 AGCATTATTTCTTCAGAGTCGAACT 58.598 36.000 0.00 0.00 0.00 3.01
2516 6431 8.816144 GTCAGTAGAAGCATTATTTCTTCAGAG 58.184 37.037 5.02 0.00 40.72 3.35
2552 6477 4.422057 TCCATCCCTAGACACAGTACAAA 58.578 43.478 0.00 0.00 0.00 2.83
2553 6478 4.055710 TCCATCCCTAGACACAGTACAA 57.944 45.455 0.00 0.00 0.00 2.41
2554 6479 3.750501 TCCATCCCTAGACACAGTACA 57.249 47.619 0.00 0.00 0.00 2.90
2556 6481 2.965831 GCATCCATCCCTAGACACAGTA 59.034 50.000 0.00 0.00 0.00 2.74
2558 6483 2.045524 AGCATCCATCCCTAGACACAG 58.954 52.381 0.00 0.00 0.00 3.66
2561 6486 1.770658 CCAAGCATCCATCCCTAGACA 59.229 52.381 0.00 0.00 0.00 3.41
2562 6487 1.072965 CCCAAGCATCCATCCCTAGAC 59.927 57.143 0.00 0.00 0.00 2.59
2563 6488 1.345422 ACCCAAGCATCCATCCCTAGA 60.345 52.381 0.00 0.00 0.00 2.43
2564 6489 1.143813 ACCCAAGCATCCATCCCTAG 58.856 55.000 0.00 0.00 0.00 3.02
2565 6490 1.607225 AACCCAAGCATCCATCCCTA 58.393 50.000 0.00 0.00 0.00 3.53
2566 6491 0.712380 AAACCCAAGCATCCATCCCT 59.288 50.000 0.00 0.00 0.00 4.20
2567 6492 1.482182 GAAAACCCAAGCATCCATCCC 59.518 52.381 0.00 0.00 0.00 3.85
2568 6493 2.178580 TGAAAACCCAAGCATCCATCC 58.821 47.619 0.00 0.00 0.00 3.51
2569 6494 4.476628 AATGAAAACCCAAGCATCCATC 57.523 40.909 0.00 0.00 0.00 3.51
2570 6495 6.156602 TCATTAATGAAAACCCAAGCATCCAT 59.843 34.615 15.82 0.00 33.08 3.41
2571 6496 5.483231 TCATTAATGAAAACCCAAGCATCCA 59.517 36.000 15.82 0.00 33.08 3.41
2572 6497 5.976458 TCATTAATGAAAACCCAAGCATCC 58.024 37.500 15.82 0.00 33.08 3.51
2585 6510 5.955355 ACCCCTTCCGATTTTCATTAATGAA 59.045 36.000 23.86 23.86 44.42 2.57
2586 6511 5.359576 CACCCCTTCCGATTTTCATTAATGA 59.640 40.000 14.23 14.23 34.44 2.57
2587 6512 5.359576 TCACCCCTTCCGATTTTCATTAATG 59.640 40.000 9.29 9.29 0.00 1.90
2588 6513 5.515106 TCACCCCTTCCGATTTTCATTAAT 58.485 37.500 0.00 0.00 0.00 1.40
2589 6514 4.924625 TCACCCCTTCCGATTTTCATTAA 58.075 39.130 0.00 0.00 0.00 1.40
2590 6515 4.577988 TCACCCCTTCCGATTTTCATTA 57.422 40.909 0.00 0.00 0.00 1.90
2591 6516 3.449746 TCACCCCTTCCGATTTTCATT 57.550 42.857 0.00 0.00 0.00 2.57
2592 6517 3.356290 CTTCACCCCTTCCGATTTTCAT 58.644 45.455 0.00 0.00 0.00 2.57
2593 6518 2.790433 CTTCACCCCTTCCGATTTTCA 58.210 47.619 0.00 0.00 0.00 2.69
2594 6519 1.472878 GCTTCACCCCTTCCGATTTTC 59.527 52.381 0.00 0.00 0.00 2.29
2595 6520 1.545841 GCTTCACCCCTTCCGATTTT 58.454 50.000 0.00 0.00 0.00 1.82
2596 6521 0.323451 GGCTTCACCCCTTCCGATTT 60.323 55.000 0.00 0.00 0.00 2.17
2597 6522 1.303282 GGCTTCACCCCTTCCGATT 59.697 57.895 0.00 0.00 0.00 3.34
2598 6523 2.998949 GGCTTCACCCCTTCCGAT 59.001 61.111 0.00 0.00 0.00 4.18
2605 6530 9.315914 TTTTGAATAAAAGAAGGGCTTCACCCC 62.316 40.741 0.00 0.00 43.91 4.95
2606 6531 6.463755 TTTTGAATAAAAGAAGGGCTTCACCC 60.464 38.462 0.00 0.00 43.57 4.61
2607 6532 5.722021 TTGAATAAAAGAAGGGCTTCACC 57.278 39.130 0.00 0.00 41.84 4.02
2637 6562 7.642669 TGTCAATCTTTTCTTCTGCTTGTTAG 58.357 34.615 0.00 0.00 0.00 2.34
2638 6563 7.566760 TGTCAATCTTTTCTTCTGCTTGTTA 57.433 32.000 0.00 0.00 0.00 2.41
2639 6564 6.455360 TGTCAATCTTTTCTTCTGCTTGTT 57.545 33.333 0.00 0.00 0.00 2.83
2640 6565 6.444633 CATGTCAATCTTTTCTTCTGCTTGT 58.555 36.000 0.00 0.00 0.00 3.16
2660 6585 2.999185 AATTTGGGACCTGACCATGT 57.001 45.000 0.00 0.00 37.93 3.21
2671 6596 4.457603 CCTCAACACGAACATAATTTGGGA 59.542 41.667 0.00 0.00 0.00 4.37
2672 6597 4.732784 CCTCAACACGAACATAATTTGGG 58.267 43.478 0.00 0.00 0.00 4.12
2674 6599 4.616802 GTGCCTCAACACGAACATAATTTG 59.383 41.667 0.00 0.00 0.00 2.32
2675 6600 4.518970 AGTGCCTCAACACGAACATAATTT 59.481 37.500 0.00 0.00 45.45 1.82
2676 6601 4.072131 AGTGCCTCAACACGAACATAATT 58.928 39.130 0.00 0.00 45.45 1.40
2677 6602 3.436704 CAGTGCCTCAACACGAACATAAT 59.563 43.478 0.00 0.00 45.45 1.28
2678 6603 2.805671 CAGTGCCTCAACACGAACATAA 59.194 45.455 0.00 0.00 45.45 1.90
2679 6604 2.412870 CAGTGCCTCAACACGAACATA 58.587 47.619 0.00 0.00 45.45 2.29
2680 6605 1.229428 CAGTGCCTCAACACGAACAT 58.771 50.000 0.00 0.00 45.45 2.71
2681 6606 0.813610 CCAGTGCCTCAACACGAACA 60.814 55.000 0.00 0.00 45.45 3.18
2682 6607 0.531974 TCCAGTGCCTCAACACGAAC 60.532 55.000 0.00 0.00 45.45 3.95
2685 6610 0.532862 AGTTCCAGTGCCTCAACACG 60.533 55.000 0.00 0.00 45.45 4.49
2705 6638 4.410099 AGAGAAAAATGAACATGGCTGGA 58.590 39.130 0.00 0.00 0.00 3.86
2747 6680 3.316308 GCTTTCGGCCAATGATACTCAAT 59.684 43.478 2.24 0.00 34.27 2.57
2749 6682 2.288666 GCTTTCGGCCAATGATACTCA 58.711 47.619 2.24 0.00 34.27 3.41
2762 6695 1.250154 TTGGGGCAATCTGCTTTCGG 61.250 55.000 0.00 0.00 44.28 4.30
2775 6708 2.048603 GTGTGATCCTGCTTGGGGC 61.049 63.158 0.00 0.00 42.22 5.80
2776 6709 1.379044 GGTGTGATCCTGCTTGGGG 60.379 63.158 0.00 0.00 36.20 4.96
2836 6776 5.296780 CAGTAACAAATGACCAGAGTGTGTT 59.703 40.000 0.00 0.00 0.00 3.32
2837 6777 4.816385 CAGTAACAAATGACCAGAGTGTGT 59.184 41.667 0.00 0.00 0.00 3.72
2838 6778 4.214119 CCAGTAACAAATGACCAGAGTGTG 59.786 45.833 0.00 0.00 0.00 3.82
2954 6894 7.932335 TGTAACCACACAATCGAAATAGTTTT 58.068 30.769 0.00 0.00 0.00 2.43
2958 6898 5.351465 AGCTGTAACCACACAATCGAAATAG 59.649 40.000 0.00 0.00 0.00 1.73
2964 6904 3.743911 TGTAAGCTGTAACCACACAATCG 59.256 43.478 0.00 0.00 0.00 3.34
2992 6932 9.999009 CTGGATGTCAAACATATATATTGCATC 57.001 33.333 21.30 21.30 39.27 3.91
3017 6957 9.857656 ATCAAACATACTGGAATACATCAATCT 57.142 29.630 0.00 0.00 0.00 2.40
3023 6963 8.370940 AGATCGATCAAACATACTGGAATACAT 58.629 33.333 26.47 0.00 0.00 2.29
3025 6965 7.867909 TCAGATCGATCAAACATACTGGAATAC 59.132 37.037 26.47 0.00 0.00 1.89
3058 6998 8.466086 ACAGTTTAAGCTGAAAAGACTTTTTG 57.534 30.769 24.12 11.23 36.66 2.44
3083 7023 5.064707 GGCTCGACACAAAAAGCAGATAATA 59.935 40.000 0.00 0.00 36.47 0.98
3087 7027 1.537202 GGCTCGACACAAAAAGCAGAT 59.463 47.619 0.00 0.00 36.47 2.90
3108 7051 5.067805 TGCTCATGTACTCAGATGTCGTATT 59.932 40.000 0.00 0.00 0.00 1.89
3114 7057 4.680172 GCTCTTGCTCATGTACTCAGATGT 60.680 45.833 0.00 0.00 36.03 3.06
3137 7080 3.703001 TTAGCCAAAGGAGGACTTCAG 57.297 47.619 0.00 0.00 38.85 3.02
3138 7081 4.657814 ATTTAGCCAAAGGAGGACTTCA 57.342 40.909 0.00 0.00 38.85 3.02
3139 7082 7.122799 ACAATAATTTAGCCAAAGGAGGACTTC 59.877 37.037 0.00 0.00 38.85 3.01
3140 7083 6.954102 ACAATAATTTAGCCAAAGGAGGACTT 59.046 34.615 0.00 0.00 42.52 3.01
3141 7084 6.378280 CACAATAATTTAGCCAAAGGAGGACT 59.622 38.462 0.00 0.00 0.00 3.85
3142 7085 6.152831 ACACAATAATTTAGCCAAAGGAGGAC 59.847 38.462 0.00 0.00 0.00 3.85
3143 7086 6.252995 ACACAATAATTTAGCCAAAGGAGGA 58.747 36.000 0.00 0.00 0.00 3.71
3144 7087 6.530019 ACACAATAATTTAGCCAAAGGAGG 57.470 37.500 0.00 0.00 0.00 4.30
3145 7088 6.311200 GCAACACAATAATTTAGCCAAAGGAG 59.689 38.462 0.00 0.00 0.00 3.69
3146 7089 6.014669 AGCAACACAATAATTTAGCCAAAGGA 60.015 34.615 0.00 0.00 0.00 3.36
3147 7090 6.165577 AGCAACACAATAATTTAGCCAAAGG 58.834 36.000 0.00 0.00 0.00 3.11
3148 7091 7.656707 AAGCAACACAATAATTTAGCCAAAG 57.343 32.000 0.00 0.00 0.00 2.77
3149 7092 7.712639 TCAAAGCAACACAATAATTTAGCCAAA 59.287 29.630 0.00 0.00 0.00 3.28
3150 7093 7.212976 TCAAAGCAACACAATAATTTAGCCAA 58.787 30.769 0.00 0.00 0.00 4.52
3151 7094 6.753180 TCAAAGCAACACAATAATTTAGCCA 58.247 32.000 0.00 0.00 0.00 4.75


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

AutoCloner maintained by Alex Coulton.