Multiple sequence alignment - TraesCS5D01G046500

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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 TraesCS5D01G046500 chr5D 100.000 3683 0 0 1 3683 45211806 45215488 0.000000e+00 6802.0
1 TraesCS5D01G046500 chr5D 84.932 219 21 7 2468 2686 45283909 45284115 1.040000e-50 211.0
2 TraesCS5D01G046500 chr5D 97.436 39 1 0 2810 2848 250406109 250406071 2.370000e-07 67.6
3 TraesCS5D01G046500 chr5D 87.931 58 5 2 2793 2848 556709648 556709705 2.370000e-07 67.6
4 TraesCS5D01G046500 chr5D 100.000 28 0 0 2855 2882 351799533 351799506 7.000000e-03 52.8
5 TraesCS5D01G046500 chr5A 87.038 1327 133 31 1367 2671 36075599 36076908 0.000000e+00 1461.0
6 TraesCS5D01G046500 chr5A 86.963 1327 135 30 1367 2671 36048825 36050135 0.000000e+00 1458.0
7 TraesCS5D01G046500 chr5A 86.888 1327 135 30 1367 2671 36194973 36196282 0.000000e+00 1450.0
8 TraesCS5D01G046500 chr5A 86.757 1329 135 31 1367 2671 36165938 36167249 0.000000e+00 1441.0
9 TraesCS5D01G046500 chr5A 91.980 985 69 2 1825 2806 36020911 36021888 0.000000e+00 1373.0
10 TraesCS5D01G046500 chr5A 84.835 877 94 31 1367 2221 36103760 36104619 0.000000e+00 846.0
11 TraesCS5D01G046500 chr5A 83.937 828 94 31 1367 2172 36132289 36133099 0.000000e+00 756.0
12 TraesCS5D01G046500 chr5A 88.110 656 27 28 559 1207 36019910 36020521 0.000000e+00 732.0
13 TraesCS5D01G046500 chr5A 91.803 366 25 4 852 1214 36074112 36074475 4.240000e-139 505.0
14 TraesCS5D01G046500 chr5A 91.803 366 25 4 852 1214 36193488 36193851 4.240000e-139 505.0
15 TraesCS5D01G046500 chr5A 91.530 366 26 4 852 1214 36102274 36102637 1.970000e-137 499.0
16 TraesCS5D01G046500 chr5A 91.530 366 26 4 852 1214 36130803 36131166 1.970000e-137 499.0
17 TraesCS5D01G046500 chr5A 91.530 366 26 4 852 1214 36164451 36164814 1.970000e-137 499.0
18 TraesCS5D01G046500 chr5A 91.798 317 26 0 2355 2671 36133093 36133409 3.380000e-120 442.0
19 TraesCS5D01G046500 chr5A 94.096 271 16 0 2401 2671 36104616 36104886 2.650000e-111 412.0
20 TraesCS5D01G046500 chr5A 87.003 377 30 8 48 414 36019440 36019807 1.230000e-109 407.0
21 TraesCS5D01G046500 chr5A 85.928 334 33 9 1650 1976 36034695 36035021 9.790000e-91 344.0
22 TraesCS5D01G046500 chr5A 91.837 49 3 1 2800 2848 683345236 683345283 2.370000e-07 67.6
23 TraesCS5D01G046500 chr5B 92.308 1014 68 4 1800 2806 45241952 45242962 0.000000e+00 1432.0
24 TraesCS5D01G046500 chr5B 84.032 883 78 33 47 877 45239925 45240796 0.000000e+00 791.0
25 TraesCS5D01G046500 chr5B 83.709 399 32 22 876 1270 45240897 45241266 2.720000e-91 346.0
26 TraesCS5D01G046500 chr5B 96.040 101 4 0 445 545 50175624 50175724 8.180000e-37 165.0
27 TraesCS5D01G046500 chr5B 94.231 104 6 0 446 549 91884434 91884537 3.810000e-35 159.0
28 TraesCS5D01G046500 chr2D 97.391 805 16 3 2880 3683 627827258 627828058 0.000000e+00 1365.0
29 TraesCS5D01G046500 chr2D 94.286 105 6 0 445 549 574067005 574067109 1.060000e-35 161.0
30 TraesCS5D01G046500 chr2D 97.561 41 1 0 2808 2848 603699138 603699178 1.830000e-08 71.3
31 TraesCS5D01G046500 chr7D 95.995 824 10 2 2880 3683 631359520 631358700 0.000000e+00 1317.0
32 TraesCS5D01G046500 chr6D 95.879 825 10 3 2880 3683 312193695 312194516 0.000000e+00 1314.0
33 TraesCS5D01G046500 chr6D 97.436 39 1 0 2810 2848 38162389 38162427 2.370000e-07 67.6
34 TraesCS5D01G046500 chr1D 94.639 858 20 9 2841 3683 399270868 399270022 0.000000e+00 1306.0
35 TraesCS5D01G046500 chr1D 76.230 833 170 23 1850 2665 62767988 62768809 2.050000e-112 416.0
36 TraesCS5D01G046500 chr1D 95.146 103 5 0 443 545 315817006 315816904 2.940000e-36 163.0
37 TraesCS5D01G046500 chr1D 83.133 83 13 1 1397 1478 485582793 485582875 1.420000e-09 75.0
38 TraesCS5D01G046500 chr3D 95.140 823 15 6 2880 3681 547772185 547773003 0.000000e+00 1275.0
39 TraesCS5D01G046500 chr3D 97.368 38 1 0 2845 2882 547772136 547772173 8.540000e-07 65.8
40 TraesCS5D01G046500 chr3A 93.103 841 34 6 2849 3675 610497096 610496266 0.000000e+00 1210.0
41 TraesCS5D01G046500 chr4D 91.882 850 43 11 2847 3675 423890309 423889465 0.000000e+00 1164.0
42 TraesCS5D01G046500 chr4D 92.000 50 1 3 2800 2848 490639838 490639791 2.370000e-07 67.6
43 TraesCS5D01G046500 chr6A 90.952 851 49 9 2849 3675 74420763 74419917 0.000000e+00 1120.0
44 TraesCS5D01G046500 chr4B 92.440 754 45 7 2880 3624 71004308 71003558 0.000000e+00 1066.0
45 TraesCS5D01G046500 chr4B 95.238 105 5 0 440 544 509166456 509166560 2.280000e-37 167.0
46 TraesCS5D01G046500 chr4B 95.146 103 5 0 441 543 185232398 185232500 2.940000e-36 163.0
47 TraesCS5D01G046500 chr4B 94.231 104 6 0 442 545 163759076 163758973 3.810000e-35 159.0
48 TraesCS5D01G046500 chrUn 92.361 432 33 0 1889 2320 476253797 476254228 1.880000e-172 616.0
49 TraesCS5D01G046500 chrUn 81.707 82 11 2 1397 1478 177151642 177151719 8.540000e-07 65.8
50 TraesCS5D01G046500 chr1A 92.991 214 15 0 2880 3093 532371862 532371649 2.760000e-81 313.0
51 TraesCS5D01G046500 chr1A 97.059 34 1 0 1397 1430 549164570 549164603 1.430000e-04 58.4
52 TraesCS5D01G046500 chr6B 93.519 108 5 2 437 542 113454853 113454746 3.810000e-35 159.0
53 TraesCS5D01G046500 chr6B 93.519 108 6 1 437 543 238301091 238301198 3.810000e-35 159.0
54 TraesCS5D01G046500 chr6B 97.561 41 1 0 2808 2848 551919450 551919410 1.830000e-08 71.3
55 TraesCS5D01G046500 chr2B 84.146 82 10 1 1397 1478 1345858 1345936 3.940000e-10 76.8
56 TraesCS5D01G046500 chr2B 81.707 82 11 2 1397 1478 3769241 3769164 8.540000e-07 65.8
57 TraesCS5D01G046500 chr2A 97.561 41 1 0 2808 2848 650606641 650606601 1.830000e-08 71.3
58 TraesCS5D01G046500 chr1B 97.561 41 1 0 2808 2848 630699376 630699336 1.830000e-08 71.3


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 TraesCS5D01G046500 chr5D 45211806 45215488 3682 False 6802.000000 6802 100.000000 1 3683 1 chr5D.!!$F1 3682
1 TraesCS5D01G046500 chr5A 36048825 36050135 1310 False 1458.000000 1458 86.963000 1367 2671 1 chr5A.!!$F2 1304
2 TraesCS5D01G046500 chr5A 36074112 36076908 2796 False 983.000000 1461 89.420500 852 2671 2 chr5A.!!$F5 1819
3 TraesCS5D01G046500 chr5A 36193488 36196282 2794 False 977.500000 1450 89.345500 852 2671 2 chr5A.!!$F9 1819
4 TraesCS5D01G046500 chr5A 36164451 36167249 2798 False 970.000000 1441 89.143500 852 2671 2 chr5A.!!$F8 1819
5 TraesCS5D01G046500 chr5A 36019440 36021888 2448 False 837.333333 1373 89.031000 48 2806 3 chr5A.!!$F4 2758
6 TraesCS5D01G046500 chr5A 36102274 36104886 2612 False 585.666667 846 90.153667 852 2671 3 chr5A.!!$F6 1819
7 TraesCS5D01G046500 chr5A 36130803 36133409 2606 False 565.666667 756 89.088333 852 2671 3 chr5A.!!$F7 1819
8 TraesCS5D01G046500 chr5B 45239925 45242962 3037 False 856.333333 1432 86.683000 47 2806 3 chr5B.!!$F3 2759
9 TraesCS5D01G046500 chr2D 627827258 627828058 800 False 1365.000000 1365 97.391000 2880 3683 1 chr2D.!!$F3 803
10 TraesCS5D01G046500 chr7D 631358700 631359520 820 True 1317.000000 1317 95.995000 2880 3683 1 chr7D.!!$R1 803
11 TraesCS5D01G046500 chr6D 312193695 312194516 821 False 1314.000000 1314 95.879000 2880 3683 1 chr6D.!!$F2 803
12 TraesCS5D01G046500 chr1D 399270022 399270868 846 True 1306.000000 1306 94.639000 2841 3683 1 chr1D.!!$R2 842
13 TraesCS5D01G046500 chr1D 62767988 62768809 821 False 416.000000 416 76.230000 1850 2665 1 chr1D.!!$F1 815
14 TraesCS5D01G046500 chr3D 547772136 547773003 867 False 670.400000 1275 96.254000 2845 3681 2 chr3D.!!$F1 836
15 TraesCS5D01G046500 chr3A 610496266 610497096 830 True 1210.000000 1210 93.103000 2849 3675 1 chr3A.!!$R1 826
16 TraesCS5D01G046500 chr4D 423889465 423890309 844 True 1164.000000 1164 91.882000 2847 3675 1 chr4D.!!$R1 828
17 TraesCS5D01G046500 chr6A 74419917 74420763 846 True 1120.000000 1120 90.952000 2849 3675 1 chr6A.!!$R1 826
18 TraesCS5D01G046500 chr4B 71003558 71004308 750 True 1066.000000 1066 92.440000 2880 3624 1 chr4B.!!$R1 744

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
546 569 1.020437 GGGACGAAGGGAGTACTACG 58.980 60.0 0.00 2.17 0.0 3.51 F
1313 1549 0.396556 TAGTACTCCCTCGCATGCCA 60.397 55.0 13.15 0.00 0.0 4.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1845 3586 0.107017 ATCCATCGCAACCCTGGAAG 60.107 55.0 0.00 0.00 42.12 3.46 R
2824 4764 0.242017 GCAATCTGTCACAGGGTTGC 59.758 55.0 23.82 23.82 41.74 4.17 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
52 53 6.706055 ACACAATGAACTGTACGTAAGATG 57.294 37.500 0.00 0.00 43.62 2.90
53 54 6.452242 ACACAATGAACTGTACGTAAGATGA 58.548 36.000 0.00 0.00 43.62 2.92
54 55 6.926826 ACACAATGAACTGTACGTAAGATGAA 59.073 34.615 0.00 0.00 43.62 2.57
55 56 7.095774 ACACAATGAACTGTACGTAAGATGAAC 60.096 37.037 0.00 0.00 43.62 3.18
56 57 6.926826 ACAATGAACTGTACGTAAGATGAACA 59.073 34.615 0.00 0.00 43.62 3.18
57 58 7.602644 ACAATGAACTGTACGTAAGATGAACAT 59.397 33.333 0.00 0.00 43.62 2.71
58 59 8.443160 CAATGAACTGTACGTAAGATGAACATT 58.557 33.333 0.00 1.90 43.62 2.71
144 145 2.010145 TTCACATGGCTAGAAGCGAC 57.990 50.000 0.00 0.00 43.62 5.19
161 163 3.432252 AGCGACGTATCCACTTTGAAAAG 59.568 43.478 0.00 1.22 41.73 2.27
178 180 6.083098 TGAAAAGACATGTGTTATGGTTGG 57.917 37.500 8.88 0.00 0.00 3.77
245 247 2.452600 AAATTGTGTGTGACCCACCT 57.547 45.000 0.00 0.00 43.85 4.00
249 251 1.227853 GTGTGTGACCCACCTCCAC 60.228 63.158 0.00 0.00 43.85 4.02
426 442 6.353082 CCCTCCTCCAGTTGTAATATCTTGTT 60.353 42.308 0.00 0.00 0.00 2.83
433 449 5.009631 AGTTGTAATATCTTGTTGCTGCCA 58.990 37.500 0.00 0.00 0.00 4.92
457 480 8.361139 CCATAAATATCATATACTCCCTCCGTC 58.639 40.741 0.00 0.00 0.00 4.79
459 482 2.599408 TCATATACTCCCTCCGTCCC 57.401 55.000 0.00 0.00 0.00 4.46
466 489 2.271777 ACTCCCTCCGTCCCAAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
467 490 2.026542 ACTCCCTCCGTCCCAAAATAAC 60.027 50.000 0.00 0.00 0.00 1.89
470 493 2.290705 CCCTCCGTCCCAAAATAACTGT 60.291 50.000 0.00 0.00 0.00 3.55
473 496 4.324267 CTCCGTCCCAAAATAACTGTCTT 58.676 43.478 0.00 0.00 0.00 3.01
476 499 5.702209 TCCGTCCCAAAATAACTGTCTTAAC 59.298 40.000 0.00 0.00 0.00 2.01
489 512 9.857957 ATAACTGTCTTAACTTTGTACTAGCTC 57.142 33.333 0.00 0.00 0.00 4.09
491 514 8.632906 ACTGTCTTAACTTTGTACTAGCTCTA 57.367 34.615 0.00 0.00 0.00 2.43
492 515 8.732531 ACTGTCTTAACTTTGTACTAGCTCTAG 58.267 37.037 0.00 2.55 39.04 2.43
494 517 9.730705 TGTCTTAACTTTGTACTAGCTCTAGTA 57.269 33.333 11.59 11.59 43.98 1.82
528 551 9.774742 GTACTAAGCTCAAGACATTTATTTTGG 57.225 33.333 3.19 0.00 0.00 3.28
529 552 7.830739 ACTAAGCTCAAGACATTTATTTTGGG 58.169 34.615 3.19 0.00 0.00 4.12
533 556 5.106317 GCTCAAGACATTTATTTTGGGACGA 60.106 40.000 0.00 0.00 0.00 4.20
542 565 2.845363 TTTTGGGACGAAGGGAGTAC 57.155 50.000 0.00 0.00 0.00 2.73
545 568 2.134789 TGGGACGAAGGGAGTACTAC 57.865 55.000 0.00 0.00 0.00 2.73
546 569 1.020437 GGGACGAAGGGAGTACTACG 58.980 60.000 0.00 2.17 0.00 3.51
547 570 1.680249 GGGACGAAGGGAGTACTACGT 60.680 57.143 0.00 0.00 36.71 3.57
548 571 2.420129 GGGACGAAGGGAGTACTACGTA 60.420 54.545 0.00 0.00 34.26 3.57
549 572 3.270877 GGACGAAGGGAGTACTACGTAA 58.729 50.000 0.00 0.00 34.26 3.18
550 573 3.879892 GGACGAAGGGAGTACTACGTAAT 59.120 47.826 0.00 0.00 34.26 1.89
551 574 4.260948 GGACGAAGGGAGTACTACGTAATG 60.261 50.000 0.00 0.00 34.26 1.90
631 660 3.033094 CGTAACCGTTGCACATACATG 57.967 47.619 0.13 0.00 0.00 3.21
697 727 7.796660 CACGATCAATTAGAAAAACACGAAAGA 59.203 33.333 0.00 0.00 0.00 2.52
891 1055 5.590530 AGGAGCTATTATCCATGATCGTC 57.409 43.478 0.00 0.00 39.47 4.20
935 1101 1.409427 CTCCTCCACCTTAAGCTACCG 59.591 57.143 0.00 0.00 0.00 4.02
976 1142 6.092807 AGCAGCAGTTTATCTTAGCAAACTAC 59.907 38.462 10.08 6.49 41.78 2.73
977 1143 6.092807 GCAGCAGTTTATCTTAGCAAACTACT 59.907 38.462 10.08 8.14 41.78 2.57
978 1144 7.277981 GCAGCAGTTTATCTTAGCAAACTACTA 59.722 37.037 10.08 0.00 41.78 1.82
979 1145 8.812329 CAGCAGTTTATCTTAGCAAACTACTAG 58.188 37.037 10.08 0.00 41.78 2.57
980 1146 7.492994 AGCAGTTTATCTTAGCAAACTACTAGC 59.507 37.037 10.08 9.63 41.78 3.42
981 1147 7.492994 GCAGTTTATCTTAGCAAACTACTAGCT 59.507 37.037 10.08 0.00 41.78 3.32
987 1153 6.660800 TCTTAGCAAACTACTAGCTAGGAGA 58.339 40.000 35.12 12.42 40.55 3.71
1198 1364 3.617263 CGACTGCTGGGTTAATGTAAGTC 59.383 47.826 0.00 0.00 0.00 3.01
1199 1365 3.939592 GACTGCTGGGTTAATGTAAGTCC 59.060 47.826 0.00 0.00 0.00 3.85
1215 1381 6.252233 TGTAAGTCCCCATCAATTGATTTCA 58.748 36.000 18.41 4.78 31.21 2.69
1218 1384 9.082313 GTAAGTCCCCATCAATTGATTTCATAT 57.918 33.333 18.41 5.55 31.21 1.78
1220 1386 9.659135 AAGTCCCCATCAATTGATTTCATATAA 57.341 29.630 18.41 0.00 31.21 0.98
1221 1387 9.305555 AGTCCCCATCAATTGATTTCATATAAG 57.694 33.333 18.41 4.14 31.21 1.73
1222 1388 8.031277 GTCCCCATCAATTGATTTCATATAAGC 58.969 37.037 18.41 0.00 31.21 3.09
1224 1390 8.033038 CCCCATCAATTGATTTCATATAAGCTG 58.967 37.037 18.41 4.21 31.21 4.24
1225 1391 8.799367 CCCATCAATTGATTTCATATAAGCTGA 58.201 33.333 18.41 0.00 31.21 4.26
1234 1453 4.972514 TCATATAAGCTGATCGATCGCT 57.027 40.909 27.54 27.54 37.94 4.93
1239 1458 7.645735 TCATATAAGCTGATCGATCGCTTAATC 59.354 37.037 37.73 19.52 44.04 1.75
1245 1481 5.188327 TGATCGATCGCTTAATCTGTCTT 57.812 39.130 20.03 0.00 0.00 3.01
1270 1506 7.735917 TGTTTCACCATGGACTATATCTTAGG 58.264 38.462 21.47 0.00 0.00 2.69
1275 1511 5.659079 ACCATGGACTATATCTTAGGCTAGC 59.341 44.000 21.47 6.04 0.00 3.42
1279 1515 5.017490 GGACTATATCTTAGGCTAGCCACA 58.983 45.833 34.70 19.67 38.92 4.17
1280 1516 5.480772 GGACTATATCTTAGGCTAGCCACAA 59.519 44.000 34.70 24.98 38.92 3.33
1288 1524 0.464554 GGCTAGCCACAATGGGTCTC 60.465 60.000 29.33 0.00 46.99 3.36
1292 1528 3.433598 GCTAGCCACAATGGGTCTCATAA 60.434 47.826 2.29 0.00 46.99 1.90
1293 1529 3.737559 AGCCACAATGGGTCTCATAAA 57.262 42.857 0.00 0.00 46.99 1.40
1294 1530 4.255510 AGCCACAATGGGTCTCATAAAT 57.744 40.909 0.00 0.00 46.99 1.40
1296 1532 5.380043 AGCCACAATGGGTCTCATAAATAG 58.620 41.667 0.00 0.00 46.99 1.73
1297 1533 5.103940 AGCCACAATGGGTCTCATAAATAGT 60.104 40.000 0.00 0.00 46.99 2.12
1300 1536 7.509546 CCACAATGGGTCTCATAAATAGTACT 58.490 38.462 0.00 0.00 34.44 2.73
1301 1537 7.657761 CCACAATGGGTCTCATAAATAGTACTC 59.342 40.741 0.00 0.00 34.44 2.59
1302 1538 7.657761 CACAATGGGTCTCATAAATAGTACTCC 59.342 40.741 0.00 0.00 34.44 3.85
1303 1539 6.936968 ATGGGTCTCATAAATAGTACTCCC 57.063 41.667 0.00 0.00 33.61 4.30
1306 1542 5.183522 GGGTCTCATAAATAGTACTCCCTCG 59.816 48.000 0.00 0.00 0.00 4.63
1308 1544 5.241064 GTCTCATAAATAGTACTCCCTCGCA 59.759 44.000 0.00 0.00 0.00 5.10
1309 1545 6.010850 TCTCATAAATAGTACTCCCTCGCAT 58.989 40.000 0.00 0.00 0.00 4.73
1310 1546 6.025749 TCATAAATAGTACTCCCTCGCATG 57.974 41.667 0.00 0.00 0.00 4.06
1312 1548 0.969894 ATAGTACTCCCTCGCATGCC 59.030 55.000 13.15 0.00 0.00 4.40
1313 1549 0.396556 TAGTACTCCCTCGCATGCCA 60.397 55.000 13.15 0.00 0.00 4.92
1315 1551 0.882042 GTACTCCCTCGCATGCCATG 60.882 60.000 13.15 0.00 0.00 3.66
1316 1552 1.337384 TACTCCCTCGCATGCCATGT 61.337 55.000 13.15 5.48 0.00 3.21
1319 1555 2.777972 CCCTCGCATGCCATGTTGG 61.778 63.158 13.15 6.21 41.55 3.77
1331 1567 3.249986 CCATGTTGGCAAAAATCCGAT 57.750 42.857 0.00 0.00 0.00 4.18
1332 1568 2.931325 CCATGTTGGCAAAAATCCGATG 59.069 45.455 0.00 0.00 0.00 3.84
1334 1570 3.023946 TGTTGGCAAAAATCCGATGTG 57.976 42.857 0.00 0.00 0.00 3.21
1335 1571 2.288702 TGTTGGCAAAAATCCGATGTGG 60.289 45.455 0.00 0.00 40.09 4.17
1338 1574 2.490115 TGGCAAAAATCCGATGTGGTAC 59.510 45.455 0.00 0.00 39.52 3.34
1341 1577 3.917985 GCAAAAATCCGATGTGGTACAAC 59.082 43.478 0.00 0.00 44.16 3.32
1342 1578 4.557695 GCAAAAATCCGATGTGGTACAACA 60.558 41.667 5.32 5.32 44.16 3.33
1343 1579 5.524284 CAAAAATCCGATGTGGTACAACAA 58.476 37.500 7.28 0.00 44.16 2.83
1344 1580 5.975693 AAAATCCGATGTGGTACAACAAT 57.024 34.783 7.28 0.00 44.16 2.71
1345 1581 5.975693 AAATCCGATGTGGTACAACAATT 57.024 34.783 7.28 0.00 44.16 2.32
1346 1582 7.455641 AAAATCCGATGTGGTACAACAATTA 57.544 32.000 7.28 0.00 44.16 1.40
1390 2557 8.004585 GTGGTATCATAGCACGTAAAACTATC 57.995 38.462 11.16 0.00 45.66 2.08
1395 2562 8.897457 ATCATAGCACGTAAAACTATCGATAG 57.103 34.615 27.15 27.15 36.46 2.08
1438 2605 8.552083 TTCGATCTATTCATCAAATACCATGG 57.448 34.615 11.19 11.19 0.00 3.66
1439 2606 6.595326 TCGATCTATTCATCAAATACCATGGC 59.405 38.462 13.04 0.00 0.00 4.40
1441 2608 7.094677 CGATCTATTCATCAAATACCATGGCAA 60.095 37.037 13.04 0.00 0.00 4.52
1442 2609 8.660295 ATCTATTCATCAAATACCATGGCAAT 57.340 30.769 13.04 2.51 0.00 3.56
1485 2654 8.945481 CAATAAAAATTGCATCCATACCAAGA 57.055 30.769 0.00 0.00 0.00 3.02
1504 2673 7.985476 ACCAAGATATTTTAATGACAAGTCGG 58.015 34.615 0.00 0.00 0.00 4.79
1507 2676 8.883731 CAAGATATTTTAATGACAAGTCGGTCT 58.116 33.333 0.00 0.00 38.61 3.85
1529 2698 8.952278 GGTCTTGTACACATATTTGTATTGGAA 58.048 33.333 5.07 0.00 34.50 3.53
1598 2767 8.895141 TGATACTATATGCATTACAGGGTAGT 57.105 34.615 3.54 5.46 32.06 2.73
1599 2768 8.749354 TGATACTATATGCATTACAGGGTAGTG 58.251 37.037 3.54 0.00 30.71 2.74
1600 2769 6.996180 ACTATATGCATTACAGGGTAGTGT 57.004 37.500 3.54 0.00 34.21 3.55
1601 2770 6.994221 ACTATATGCATTACAGGGTAGTGTC 58.006 40.000 3.54 0.00 31.46 3.67
1602 2771 6.782988 ACTATATGCATTACAGGGTAGTGTCT 59.217 38.462 3.54 0.00 31.46 3.41
1603 2772 7.948447 ACTATATGCATTACAGGGTAGTGTCTA 59.052 37.037 3.54 0.00 31.46 2.59
1604 2773 4.730949 TGCATTACAGGGTAGTGTCTAC 57.269 45.455 0.00 0.00 31.46 2.59
1605 2774 4.090819 TGCATTACAGGGTAGTGTCTACA 58.909 43.478 8.78 0.00 31.46 2.74
1606 2775 4.528987 TGCATTACAGGGTAGTGTCTACAA 59.471 41.667 8.78 0.00 31.46 2.41
1607 2776 5.012251 TGCATTACAGGGTAGTGTCTACAAA 59.988 40.000 8.78 0.00 31.46 2.83
1608 2777 5.350640 GCATTACAGGGTAGTGTCTACAAAC 59.649 44.000 8.78 0.00 31.46 2.93
1609 2778 6.460781 CATTACAGGGTAGTGTCTACAAACA 58.539 40.000 8.78 0.00 31.46 2.83
1610 2779 6.482898 TTACAGGGTAGTGTCTACAAACAA 57.517 37.500 8.78 0.00 31.46 2.83
1611 2780 5.362105 ACAGGGTAGTGTCTACAAACAAA 57.638 39.130 8.78 0.00 0.00 2.83
1612 2781 5.937111 ACAGGGTAGTGTCTACAAACAAAT 58.063 37.500 8.78 0.00 0.00 2.32
1613 2782 7.069877 ACAGGGTAGTGTCTACAAACAAATA 57.930 36.000 8.78 0.00 0.00 1.40
1614 2783 7.511268 ACAGGGTAGTGTCTACAAACAAATAA 58.489 34.615 8.78 0.00 0.00 1.40
1615 2784 7.994334 ACAGGGTAGTGTCTACAAACAAATAAA 59.006 33.333 8.78 0.00 0.00 1.40
1616 2785 9.010029 CAGGGTAGTGTCTACAAACAAATAAAT 57.990 33.333 8.78 0.00 0.00 1.40
1659 2828 9.456147 ACTACTATATGATCCTATGTCACACTC 57.544 37.037 1.11 0.00 0.00 3.51
1660 2829 7.710676 ACTATATGATCCTATGTCACACTCC 57.289 40.000 1.11 0.00 0.00 3.85
1661 2830 7.241628 ACTATATGATCCTATGTCACACTCCA 58.758 38.462 1.11 0.00 0.00 3.86
1662 2831 7.898100 ACTATATGATCCTATGTCACACTCCAT 59.102 37.037 1.11 0.00 0.00 3.41
1665 2834 6.161855 TGATCCTATGTCACACTCCATTAC 57.838 41.667 0.00 0.00 0.00 1.89
1666 2835 5.660864 TGATCCTATGTCACACTCCATTACA 59.339 40.000 0.00 0.00 0.00 2.41
1668 2837 5.977635 TCCTATGTCACACTCCATTACAAG 58.022 41.667 0.00 0.00 0.00 3.16
1669 2838 5.719563 TCCTATGTCACACTCCATTACAAGA 59.280 40.000 0.00 0.00 0.00 3.02
1670 2839 6.045318 CCTATGTCACACTCCATTACAAGAG 58.955 44.000 0.00 0.00 36.16 2.85
1673 2897 2.571653 TCACACTCCATTACAAGAGGGG 59.428 50.000 0.00 0.00 37.87 4.79
1701 2980 5.165961 ACTCCTAGCACTAAAATCAAGCA 57.834 39.130 0.00 0.00 0.00 3.91
1759 3218 8.651391 TGAAATGATACAATCCATTGAAATGC 57.349 30.769 6.29 0.00 40.14 3.56
1760 3219 8.258708 TGAAATGATACAATCCATTGAAATGCA 58.741 29.630 6.29 0.00 40.14 3.96
1761 3220 9.268268 GAAATGATACAATCCATTGAAATGCAT 57.732 29.630 6.29 0.00 40.14 3.96
1764 3223 9.869757 ATGATACAATCCATTGAAATGCATATG 57.130 29.630 0.00 0.00 40.14 1.78
1831 3572 2.774687 TGATCGATGAGGAATGCATGG 58.225 47.619 0.54 0.00 0.00 3.66
1885 3629 0.033504 GGTGCTCTTGGACAAGACGA 59.966 55.000 10.52 0.00 42.06 4.20
2050 3794 2.671276 TGAGCGGCGGCAAAATCA 60.671 55.556 19.21 10.22 43.41 2.57
2142 3886 2.778299 CAATCCACCTTCGAGTTCCAA 58.222 47.619 0.00 0.00 0.00 3.53
2586 4522 2.279918 AACAACGACTTCGCCGCT 60.280 55.556 0.00 0.00 44.43 5.52
2628 4564 2.123982 CCGGCCGAGGGTAGTACT 60.124 66.667 30.73 0.00 0.00 2.73
2698 4634 1.009829 CTAGAAGCAACGGCATCACC 58.990 55.000 0.00 0.00 44.61 4.02
2699 4635 0.613260 TAGAAGCAACGGCATCACCT 59.387 50.000 0.00 0.00 44.61 4.00
2700 4636 0.613260 AGAAGCAACGGCATCACCTA 59.387 50.000 0.00 0.00 44.61 3.08
2701 4637 0.727398 GAAGCAACGGCATCACCTAC 59.273 55.000 0.00 0.00 44.61 3.18
2703 4639 0.391661 AGCAACGGCATCACCTACAG 60.392 55.000 0.00 0.00 44.61 2.74
2704 4640 1.369091 GCAACGGCATCACCTACAGG 61.369 60.000 0.00 0.00 40.72 4.00
2755 4695 5.415701 TGTATTTTGAAGGCTCTGTTCCATC 59.584 40.000 0.00 0.00 0.00 3.51
2768 4708 7.224297 GCTCTGTTCCATCCCTAATTTGTATA 58.776 38.462 0.00 0.00 0.00 1.47
2806 4746 9.566624 CACTGCAAAATAAAACGACAATAAAAG 57.433 29.630 0.00 0.00 0.00 2.27
2807 4747 9.522804 ACTGCAAAATAAAACGACAATAAAAGA 57.477 25.926 0.00 0.00 0.00 2.52
2810 4750 9.285387 GCAAAATAAAACGACAATAAAAGAACG 57.715 29.630 0.00 0.00 0.00 3.95
2829 4769 8.474006 AAGAACGAAAAATATATTTGGCAACC 57.526 30.769 11.42 1.66 0.00 3.77
2830 4770 7.039270 AGAACGAAAAATATATTTGGCAACCC 58.961 34.615 11.42 0.36 0.00 4.11
2831 4771 6.538945 ACGAAAAATATATTTGGCAACCCT 57.461 33.333 11.42 0.00 0.00 4.34
2832 4772 6.337356 ACGAAAAATATATTTGGCAACCCTG 58.663 36.000 11.42 0.00 0.00 4.45
2833 4773 6.071051 ACGAAAAATATATTTGGCAACCCTGT 60.071 34.615 11.42 0.00 0.00 4.00
2834 4774 6.255453 CGAAAAATATATTTGGCAACCCTGTG 59.745 38.462 11.42 0.00 0.00 3.66
2835 4775 6.865834 AAAATATATTTGGCAACCCTGTGA 57.134 33.333 11.42 0.00 0.00 3.58
2836 4776 5.852282 AATATATTTGGCAACCCTGTGAC 57.148 39.130 0.00 0.00 0.00 3.67
2837 4777 2.666272 TATTTGGCAACCCTGTGACA 57.334 45.000 0.00 0.00 33.59 3.58
2838 4778 1.331214 ATTTGGCAACCCTGTGACAG 58.669 50.000 5.42 5.42 37.96 3.51
2839 4779 0.257328 TTTGGCAACCCTGTGACAGA 59.743 50.000 15.33 0.00 37.96 3.41
2840 4780 0.478072 TTGGCAACCCTGTGACAGAT 59.522 50.000 15.33 0.00 37.96 2.90
2841 4781 0.478072 TGGCAACCCTGTGACAGATT 59.522 50.000 15.33 5.19 29.08 2.40
2842 4782 0.883833 GGCAACCCTGTGACAGATTG 59.116 55.000 15.33 17.71 32.44 2.67
2843 4783 0.242017 GCAACCCTGTGACAGATTGC 59.758 55.000 26.96 26.96 36.07 3.56
2872 4812 2.197577 GCTGCTAAATCTCAGTCGACC 58.802 52.381 13.01 0.00 33.09 4.79
3177 5205 6.007703 TGGGTTGTTATGTTTTAGGGAGAAG 58.992 40.000 0.00 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 9.511144 CATCTTACGTACAGTTCATTGTGTATA 57.489 33.333 0.00 0.00 31.95 1.47
27 28 8.248253 TCATCTTACGTACAGTTCATTGTGTAT 58.752 33.333 0.00 0.00 31.95 2.29
28 29 7.595604 TCATCTTACGTACAGTTCATTGTGTA 58.404 34.615 0.00 0.00 32.56 2.90
29 30 6.452242 TCATCTTACGTACAGTTCATTGTGT 58.548 36.000 0.00 0.00 32.56 3.72
30 31 6.944557 TCATCTTACGTACAGTTCATTGTG 57.055 37.500 0.00 0.00 32.56 3.33
31 32 6.926826 TGTTCATCTTACGTACAGTTCATTGT 59.073 34.615 0.00 0.00 35.09 2.71
32 33 7.346208 TGTTCATCTTACGTACAGTTCATTG 57.654 36.000 0.00 0.00 0.00 2.82
33 34 8.547967 AATGTTCATCTTACGTACAGTTCATT 57.452 30.769 0.00 0.00 0.00 2.57
34 35 8.547967 AAATGTTCATCTTACGTACAGTTCAT 57.452 30.769 0.00 0.00 0.00 2.57
35 36 7.956420 AAATGTTCATCTTACGTACAGTTCA 57.044 32.000 0.00 0.00 0.00 3.18
121 122 4.009675 TCGCTTCTAGCCATGTGAAAAAT 58.990 39.130 0.00 0.00 38.18 1.82
144 145 6.079763 CACATGTCTTTTCAAAGTGGATACG 58.920 40.000 0.00 0.00 37.31 3.06
161 163 3.081061 TGAGCCAACCATAACACATGTC 58.919 45.455 0.00 0.00 0.00 3.06
245 247 2.109739 ATAAAATGCGCGCCGTGGA 61.110 52.632 30.77 10.13 0.00 4.02
426 442 7.127801 AGGGAGTATATGATATTTATGGCAGCA 59.872 37.037 0.00 0.00 0.00 4.41
433 449 7.509659 GGGACGGAGGGAGTATATGATATTTAT 59.490 40.741 0.00 0.00 0.00 1.40
457 480 9.673454 GTACAAAGTTAAGACAGTTATTTTGGG 57.327 33.333 0.00 0.00 0.00 4.12
466 489 7.527568 AGAGCTAGTACAAAGTTAAGACAGT 57.472 36.000 0.00 0.00 0.00 3.55
467 490 8.732531 ACTAGAGCTAGTACAAAGTTAAGACAG 58.267 37.037 8.35 0.00 43.98 3.51
502 525 9.774742 CCAAAATAAATGTCTTGAGCTTAGTAC 57.225 33.333 0.00 0.00 0.00 2.73
503 526 8.956426 CCCAAAATAAATGTCTTGAGCTTAGTA 58.044 33.333 0.00 0.00 0.00 1.82
504 527 7.669722 TCCCAAAATAAATGTCTTGAGCTTAGT 59.330 33.333 0.00 0.00 0.00 2.24
505 528 7.970614 GTCCCAAAATAAATGTCTTGAGCTTAG 59.029 37.037 0.00 0.00 0.00 2.18
509 532 5.095490 CGTCCCAAAATAAATGTCTTGAGC 58.905 41.667 0.00 0.00 0.00 4.26
510 533 6.494893 TCGTCCCAAAATAAATGTCTTGAG 57.505 37.500 0.00 0.00 0.00 3.02
512 535 6.092748 CCTTCGTCCCAAAATAAATGTCTTG 58.907 40.000 0.00 0.00 0.00 3.02
513 536 5.185056 CCCTTCGTCCCAAAATAAATGTCTT 59.815 40.000 0.00 0.00 0.00 3.01
516 539 4.668636 TCCCTTCGTCCCAAAATAAATGT 58.331 39.130 0.00 0.00 0.00 2.71
520 543 4.533311 AGTACTCCCTTCGTCCCAAAATAA 59.467 41.667 0.00 0.00 0.00 1.40
528 551 1.743996 ACGTAGTACTCCCTTCGTCC 58.256 55.000 0.00 0.00 41.94 4.79
529 552 4.260948 CCATTACGTAGTACTCCCTTCGTC 60.261 50.000 0.00 0.00 45.76 4.20
533 556 2.697229 GCCCATTACGTAGTACTCCCTT 59.303 50.000 0.00 0.00 45.76 3.95
542 565 0.650512 CTGCGTTGCCCATTACGTAG 59.349 55.000 0.00 0.00 42.33 3.51
545 568 0.027979 CATCTGCGTTGCCCATTACG 59.972 55.000 0.00 0.00 40.55 3.18
546 569 1.094785 ACATCTGCGTTGCCCATTAC 58.905 50.000 0.00 0.00 0.00 1.89
547 570 2.700722 TACATCTGCGTTGCCCATTA 57.299 45.000 0.00 0.00 0.00 1.90
548 571 2.057137 ATACATCTGCGTTGCCCATT 57.943 45.000 0.00 0.00 0.00 3.16
549 572 2.104792 AGTATACATCTGCGTTGCCCAT 59.895 45.455 5.50 0.00 0.00 4.00
550 573 1.484653 AGTATACATCTGCGTTGCCCA 59.515 47.619 5.50 0.00 0.00 5.36
551 574 2.135933 GAGTATACATCTGCGTTGCCC 58.864 52.381 5.50 0.00 0.00 5.36
627 656 2.233431 GAGAACTGCTGAGAGGACATGT 59.767 50.000 0.00 0.00 0.00 3.21
631 660 4.727507 TTATGAGAACTGCTGAGAGGAC 57.272 45.455 0.00 0.00 0.00 3.85
901 1065 4.036971 GGTGGAGGAGTATATATAGCAGCG 59.963 50.000 0.00 0.00 0.00 5.18
935 1101 2.607892 GCTGTGGTCCGTGTGCTTC 61.608 63.158 0.00 0.00 0.00 3.86
976 1142 7.441890 TCTTAATTCGATGTCTCCTAGCTAG 57.558 40.000 14.20 14.20 0.00 3.42
977 1143 7.094162 CCATCTTAATTCGATGTCTCCTAGCTA 60.094 40.741 13.51 0.00 37.22 3.32
978 1144 6.295011 CCATCTTAATTCGATGTCTCCTAGCT 60.295 42.308 13.51 0.00 37.22 3.32
979 1145 5.866633 CCATCTTAATTCGATGTCTCCTAGC 59.133 44.000 13.51 0.00 37.22 3.42
980 1146 5.866633 GCCATCTTAATTCGATGTCTCCTAG 59.133 44.000 13.51 0.00 37.22 3.02
981 1147 5.279506 GGCCATCTTAATTCGATGTCTCCTA 60.280 44.000 0.00 0.00 37.22 2.94
983 1149 3.748568 GGCCATCTTAATTCGATGTCTCC 59.251 47.826 0.00 9.31 37.22 3.71
987 1153 3.885297 CCTTGGCCATCTTAATTCGATGT 59.115 43.478 6.09 0.00 37.22 3.06
1072 1238 4.814294 GTCCACGTAGGCGGCCTG 62.814 72.222 31.26 17.89 43.45 4.85
1198 1364 8.033038 CAGCTTATATGAAATCAATTGATGGGG 58.967 37.037 21.39 6.23 34.49 4.96
1199 1365 8.799367 TCAGCTTATATGAAATCAATTGATGGG 58.201 33.333 21.39 5.81 34.49 4.00
1215 1381 7.647318 CAGATTAAGCGATCGATCAGCTTATAT 59.353 37.037 36.38 32.01 42.44 0.86
1218 1384 5.157067 CAGATTAAGCGATCGATCAGCTTA 58.843 41.667 34.67 34.67 42.27 3.09
1219 1385 3.986572 CAGATTAAGCGATCGATCAGCTT 59.013 43.478 36.03 36.03 43.50 3.74
1220 1386 3.005261 ACAGATTAAGCGATCGATCAGCT 59.995 43.478 27.54 27.54 37.94 4.24
1221 1387 3.312828 ACAGATTAAGCGATCGATCAGC 58.687 45.455 24.40 24.69 0.00 4.26
1222 1388 4.793071 AGACAGATTAAGCGATCGATCAG 58.207 43.478 24.40 17.27 0.00 2.90
1224 1390 4.979197 ACAAGACAGATTAAGCGATCGATC 59.021 41.667 21.57 15.68 0.00 3.69
1225 1391 4.938080 ACAAGACAGATTAAGCGATCGAT 58.062 39.130 21.57 10.64 0.00 3.59
1227 1393 5.062183 TGAAACAAGACAGATTAAGCGATCG 59.938 40.000 11.69 11.69 0.00 3.69
1234 1453 6.206634 GTCCATGGTGAAACAAGACAGATTAA 59.793 38.462 12.58 0.00 39.98 1.40
1239 1458 3.480470 AGTCCATGGTGAAACAAGACAG 58.520 45.455 12.58 0.00 39.98 3.51
1245 1481 7.689313 GCCTAAGATATAGTCCATGGTGAAACA 60.689 40.741 12.58 0.00 39.98 2.83
1270 1506 0.253044 TGAGACCCATTGTGGCTAGC 59.747 55.000 6.04 6.04 35.79 3.42
1275 1511 7.509546 AGTACTATTTATGAGACCCATTGTGG 58.490 38.462 0.00 0.00 36.71 4.17
1279 1515 7.082972 AGGGAGTACTATTTATGAGACCCATT 58.917 38.462 10.59 0.00 36.71 3.16
1280 1516 6.635021 AGGGAGTACTATTTATGAGACCCAT 58.365 40.000 10.59 0.00 39.25 4.00
1285 1521 5.382616 TGCGAGGGAGTACTATTTATGAGA 58.617 41.667 0.00 0.00 0.00 3.27
1288 1524 4.627467 GCATGCGAGGGAGTACTATTTATG 59.373 45.833 0.00 0.00 0.00 1.90
1292 1528 1.344763 GGCATGCGAGGGAGTACTATT 59.655 52.381 12.44 0.00 0.00 1.73
1293 1529 0.969894 GGCATGCGAGGGAGTACTAT 59.030 55.000 12.44 0.00 0.00 2.12
1294 1530 0.396556 TGGCATGCGAGGGAGTACTA 60.397 55.000 12.44 0.00 0.00 1.82
1296 1532 0.882042 CATGGCATGCGAGGGAGTAC 60.882 60.000 15.53 0.00 0.00 2.73
1297 1533 1.337384 ACATGGCATGCGAGGGAGTA 61.337 55.000 26.70 0.00 0.00 2.59
1300 1536 1.750018 CAACATGGCATGCGAGGGA 60.750 57.895 26.70 0.00 0.00 4.20
1301 1537 2.777972 CCAACATGGCATGCGAGGG 61.778 63.158 26.70 17.99 0.00 4.30
1302 1538 2.802792 CCAACATGGCATGCGAGG 59.197 61.111 26.70 20.62 0.00 4.63
1312 1548 3.368539 CACATCGGATTTTTGCCAACATG 59.631 43.478 0.00 0.00 0.00 3.21
1313 1549 3.587923 CACATCGGATTTTTGCCAACAT 58.412 40.909 0.00 0.00 0.00 2.71
1315 1551 2.288763 ACCACATCGGATTTTTGCCAAC 60.289 45.455 0.00 0.00 38.63 3.77
1316 1552 1.967066 ACCACATCGGATTTTTGCCAA 59.033 42.857 0.00 0.00 38.63 4.52
1319 1555 3.840890 TGTACCACATCGGATTTTTGC 57.159 42.857 0.00 0.00 38.63 3.68
1320 1556 5.114785 TGTTGTACCACATCGGATTTTTG 57.885 39.130 0.00 0.00 38.63 2.44
1321 1557 5.776173 TTGTTGTACCACATCGGATTTTT 57.224 34.783 0.00 0.00 38.63 1.94
1322 1558 5.975693 ATTGTTGTACCACATCGGATTTT 57.024 34.783 0.00 0.00 38.63 1.82
1323 1559 5.975693 AATTGTTGTACCACATCGGATTT 57.024 34.783 0.00 0.00 38.63 2.17
1324 1560 7.639113 ATTAATTGTTGTACCACATCGGATT 57.361 32.000 0.00 0.99 38.63 3.01
1325 1561 8.740123 TTATTAATTGTTGTACCACATCGGAT 57.260 30.769 0.00 0.00 38.63 4.18
1327 1563 8.670135 TCTTTATTAATTGTTGTACCACATCGG 58.330 33.333 0.00 0.00 42.50 4.18
1357 1732 4.217334 CGTGCTATGATACCACTCTCATCT 59.783 45.833 0.00 0.00 34.14 2.90
1358 1733 4.022762 ACGTGCTATGATACCACTCTCATC 60.023 45.833 0.00 0.00 34.14 2.92
1361 1736 3.992260 ACGTGCTATGATACCACTCTC 57.008 47.619 0.00 0.00 0.00 3.20
1362 1737 5.847111 TTTACGTGCTATGATACCACTCT 57.153 39.130 0.00 0.00 0.00 3.24
1363 1738 6.040878 AGTTTTACGTGCTATGATACCACTC 58.959 40.000 0.00 0.00 0.00 3.51
1365 1740 7.149015 CGATAGTTTTACGTGCTATGATACCAC 60.149 40.741 0.00 0.00 0.00 4.16
1395 2562 7.350467 AGATCGAAAGTTTTCCTCGTAAAAAC 58.650 34.615 11.93 11.93 43.63 2.43
1400 2567 7.541162 TGAATAGATCGAAAGTTTTCCTCGTA 58.459 34.615 0.00 0.00 33.68 3.43
1401 2568 6.395629 TGAATAGATCGAAAGTTTTCCTCGT 58.604 36.000 0.00 0.00 33.68 4.18
1402 2569 6.887376 TGAATAGATCGAAAGTTTTCCTCG 57.113 37.500 0.00 0.00 33.68 4.63
1403 2570 8.425577 TGATGAATAGATCGAAAGTTTTCCTC 57.574 34.615 0.00 0.00 33.68 3.71
1404 2571 8.792830 TTGATGAATAGATCGAAAGTTTTCCT 57.207 30.769 0.00 0.00 33.68 3.36
1416 2583 7.692460 TGCCATGGTATTTGATGAATAGATC 57.308 36.000 14.67 0.00 31.01 2.75
1471 2640 9.846248 GTCATTAAAATATCTTGGTATGGATGC 57.154 33.333 0.00 0.00 0.00 3.91
1480 2649 7.985476 ACCGACTTGTCATTAAAATATCTTGG 58.015 34.615 1.59 0.00 0.00 3.61
1482 2651 9.449719 AAGACCGACTTGTCATTAAAATATCTT 57.550 29.630 1.59 0.00 37.73 2.40
1503 2672 8.500753 TCCAATACAAATATGTGTACAAGACC 57.499 34.615 7.94 0.00 40.84 3.85
1573 2742 8.749354 CACTACCCTGTAATGCATATAGTATCA 58.251 37.037 0.00 0.00 0.00 2.15
1574 2743 8.750298 ACACTACCCTGTAATGCATATAGTATC 58.250 37.037 0.00 0.00 0.00 2.24
1575 2744 8.666129 ACACTACCCTGTAATGCATATAGTAT 57.334 34.615 0.00 0.00 0.00 2.12
1576 2745 7.948447 AGACACTACCCTGTAATGCATATAGTA 59.052 37.037 0.00 0.00 0.00 1.82
1577 2746 6.782988 AGACACTACCCTGTAATGCATATAGT 59.217 38.462 0.00 0.00 0.00 2.12
1578 2747 7.233389 AGACACTACCCTGTAATGCATATAG 57.767 40.000 0.00 0.00 0.00 1.31
1579 2748 7.726738 TGTAGACACTACCCTGTAATGCATATA 59.273 37.037 0.00 0.00 0.00 0.86
1580 2749 6.553476 TGTAGACACTACCCTGTAATGCATAT 59.447 38.462 0.00 0.00 0.00 1.78
1581 2750 5.894964 TGTAGACACTACCCTGTAATGCATA 59.105 40.000 0.00 0.00 0.00 3.14
1582 2751 4.714802 TGTAGACACTACCCTGTAATGCAT 59.285 41.667 0.00 0.00 0.00 3.96
1583 2752 4.090819 TGTAGACACTACCCTGTAATGCA 58.909 43.478 6.49 0.00 0.00 3.96
1584 2753 4.730949 TGTAGACACTACCCTGTAATGC 57.269 45.455 6.49 0.00 0.00 3.56
1585 2754 6.460781 TGTTTGTAGACACTACCCTGTAATG 58.539 40.000 6.49 0.00 0.00 1.90
1586 2755 6.675413 TGTTTGTAGACACTACCCTGTAAT 57.325 37.500 6.49 0.00 0.00 1.89
1587 2756 6.482898 TTGTTTGTAGACACTACCCTGTAA 57.517 37.500 6.49 0.00 0.00 2.41
1588 2757 6.482898 TTTGTTTGTAGACACTACCCTGTA 57.517 37.500 6.49 0.00 0.00 2.74
1589 2758 5.362105 TTTGTTTGTAGACACTACCCTGT 57.638 39.130 6.49 0.00 0.00 4.00
1590 2759 7.972832 TTATTTGTTTGTAGACACTACCCTG 57.027 36.000 6.49 0.00 0.00 4.45
1646 2815 5.977635 TCTTGTAATGGAGTGTGACATAGG 58.022 41.667 0.00 0.00 0.00 2.57
1652 2821 2.571653 CCCCTCTTGTAATGGAGTGTGA 59.428 50.000 0.00 0.00 0.00 3.58
1653 2822 2.571653 TCCCCTCTTGTAATGGAGTGTG 59.428 50.000 0.00 0.00 0.00 3.82
1654 2823 2.915869 TCCCCTCTTGTAATGGAGTGT 58.084 47.619 0.00 0.00 0.00 3.55
1655 2824 4.301072 TTTCCCCTCTTGTAATGGAGTG 57.699 45.455 0.00 0.00 0.00 3.51
1713 2992 7.953158 TTCATGTGTTTTTGTGTGAGAAAAA 57.047 28.000 0.00 0.00 31.43 1.94
1714 2993 7.953158 TTTCATGTGTTTTTGTGTGAGAAAA 57.047 28.000 0.00 0.00 0.00 2.29
1757 3216 6.546772 TGCATTGAAAAGGAGTATCATATGCA 59.453 34.615 14.69 14.69 40.70 3.96
1758 3217 6.973843 TGCATTGAAAAGGAGTATCATATGC 58.026 36.000 0.00 0.00 37.68 3.14
1759 3218 9.406828 CAATGCATTGAAAAGGAGTATCATATG 57.593 33.333 31.47 0.32 40.14 1.78
1760 3219 8.582437 CCAATGCATTGAAAAGGAGTATCATAT 58.418 33.333 35.47 0.00 40.14 1.78
1761 3220 7.779326 TCCAATGCATTGAAAAGGAGTATCATA 59.221 33.333 35.47 2.25 40.14 2.15
1762 3221 6.608405 TCCAATGCATTGAAAAGGAGTATCAT 59.392 34.615 35.47 0.00 40.14 2.45
1763 3222 5.951148 TCCAATGCATTGAAAAGGAGTATCA 59.049 36.000 35.47 3.59 40.14 2.15
1764 3223 6.455360 TCCAATGCATTGAAAAGGAGTATC 57.545 37.500 35.47 0.00 40.14 2.24
1831 3572 3.129287 CCCTGGAAGTTAACACATGCATC 59.871 47.826 8.61 0.00 0.00 3.91
1837 3578 2.303175 GCAACCCTGGAAGTTAACACA 58.697 47.619 8.61 3.11 0.00 3.72
1845 3586 0.107017 ATCCATCGCAACCCTGGAAG 60.107 55.000 0.00 0.00 42.12 3.46
1846 3587 0.107214 GATCCATCGCAACCCTGGAA 60.107 55.000 0.00 0.00 42.12 3.53
1847 3588 1.526887 GATCCATCGCAACCCTGGA 59.473 57.895 0.00 0.00 42.95 3.86
1885 3629 4.977393 GGTATTGCCACCGGATGT 57.023 55.556 9.46 0.00 37.17 3.06
2050 3794 0.324460 CCTGAGGGAACGGAGTAGGT 60.324 60.000 0.00 0.00 45.00 3.08
2142 3886 0.597637 CGAAGTTGTCCACGAGCTGT 60.598 55.000 0.00 0.00 0.00 4.40
2418 4279 2.824489 TTTGCCGCGGTGTTCACA 60.824 55.556 28.70 12.30 0.00 3.58
2433 4363 1.600916 GTTGTCCAGAGCGCCCTTT 60.601 57.895 2.29 0.00 0.00 3.11
2442 4372 2.561419 GTGGTAGTAGCTGTTGTCCAGA 59.439 50.000 0.00 0.00 44.49 3.86
2586 4522 1.676635 GCTGAGCTTGACCATGGCA 60.677 57.895 13.04 8.31 0.00 4.92
2610 4546 3.909285 GTACTACCCTCGGCCGGC 61.909 72.222 27.83 21.18 0.00 6.13
2628 4564 5.675575 GCAGTTCTTCCTTATCTCGTAACGA 60.676 44.000 0.00 0.00 0.00 3.85
2704 4640 1.450531 GCATCCATGGCACCTGTAGC 61.451 60.000 6.96 0.00 0.00 3.58
2755 4695 9.621629 TGAGTATTGTGGTTATACAAATTAGGG 57.378 33.333 0.00 0.00 43.13 3.53
2768 4708 5.789643 ATTTTGCAGTGAGTATTGTGGTT 57.210 34.783 0.00 0.00 0.00 3.67
2806 4746 7.010091 CAGGGTTGCCAAATATATTTTTCGTTC 59.990 37.037 8.01 0.00 0.00 3.95
2807 4747 6.816140 CAGGGTTGCCAAATATATTTTTCGTT 59.184 34.615 8.01 0.00 0.00 3.85
2808 4748 6.071051 ACAGGGTTGCCAAATATATTTTTCGT 60.071 34.615 8.01 0.00 0.00 3.85
2809 4749 6.255453 CACAGGGTTGCCAAATATATTTTTCG 59.745 38.462 8.01 0.94 0.00 3.46
2810 4750 7.277760 GTCACAGGGTTGCCAAATATATTTTTC 59.722 37.037 8.01 4.15 0.00 2.29
2811 4751 7.102993 GTCACAGGGTTGCCAAATATATTTTT 58.897 34.615 8.01 0.00 0.00 1.94
2812 4752 6.212388 TGTCACAGGGTTGCCAAATATATTTT 59.788 34.615 8.01 0.00 0.00 1.82
2813 4753 5.719085 TGTCACAGGGTTGCCAAATATATTT 59.281 36.000 4.81 4.81 0.00 1.40
2814 4754 5.268387 TGTCACAGGGTTGCCAAATATATT 58.732 37.500 0.00 0.00 0.00 1.28
2815 4755 4.865905 TGTCACAGGGTTGCCAAATATAT 58.134 39.130 0.00 0.00 0.00 0.86
2816 4756 4.018870 TCTGTCACAGGGTTGCCAAATATA 60.019 41.667 4.57 0.00 31.51 0.86
2817 4757 3.091545 CTGTCACAGGGTTGCCAAATAT 58.908 45.455 0.00 0.00 0.00 1.28
2818 4758 2.107378 TCTGTCACAGGGTTGCCAAATA 59.893 45.455 4.57 0.00 31.51 1.40
2819 4759 1.133513 TCTGTCACAGGGTTGCCAAAT 60.134 47.619 4.57 0.00 31.51 2.32
2820 4760 0.257328 TCTGTCACAGGGTTGCCAAA 59.743 50.000 4.57 0.00 31.51 3.28
2821 4761 0.478072 ATCTGTCACAGGGTTGCCAA 59.522 50.000 4.57 0.00 31.51 4.52
2822 4762 0.478072 AATCTGTCACAGGGTTGCCA 59.522 50.000 4.57 0.00 31.51 4.92
2823 4763 0.883833 CAATCTGTCACAGGGTTGCC 59.116 55.000 4.57 0.00 31.51 4.52
2824 4764 0.242017 GCAATCTGTCACAGGGTTGC 59.758 55.000 23.82 23.82 41.74 4.17
2825 4765 1.608055 TGCAATCTGTCACAGGGTTG 58.392 50.000 15.52 15.52 33.80 3.77
2826 4766 2.363306 TTGCAATCTGTCACAGGGTT 57.637 45.000 4.57 0.00 31.51 4.11
2827 4767 2.362077 GTTTTGCAATCTGTCACAGGGT 59.638 45.455 4.57 0.00 31.51 4.34
2828 4768 2.605338 CGTTTTGCAATCTGTCACAGGG 60.605 50.000 4.57 0.00 31.51 4.45
2829 4769 2.605338 CCGTTTTGCAATCTGTCACAGG 60.605 50.000 4.57 0.00 31.51 4.00
2830 4770 2.033299 ACCGTTTTGCAATCTGTCACAG 59.967 45.455 0.00 0.00 0.00 3.66
2831 4771 2.020720 ACCGTTTTGCAATCTGTCACA 58.979 42.857 0.00 0.00 0.00 3.58
2832 4772 2.384382 CACCGTTTTGCAATCTGTCAC 58.616 47.619 0.00 0.00 0.00 3.67
2833 4773 1.268999 GCACCGTTTTGCAATCTGTCA 60.269 47.619 0.00 0.00 42.49 3.58
2834 4774 1.001378 AGCACCGTTTTGCAATCTGTC 60.001 47.619 0.00 0.00 45.62 3.51
2835 4775 1.032014 AGCACCGTTTTGCAATCTGT 58.968 45.000 0.00 0.00 45.62 3.41
2836 4776 1.411394 CAGCACCGTTTTGCAATCTG 58.589 50.000 0.00 0.00 45.62 2.90
2837 4777 0.318955 GCAGCACCGTTTTGCAATCT 60.319 50.000 0.00 0.00 45.62 2.40
2838 4778 0.318955 AGCAGCACCGTTTTGCAATC 60.319 50.000 0.00 0.00 45.62 2.67
2839 4779 0.958091 TAGCAGCACCGTTTTGCAAT 59.042 45.000 0.00 0.00 45.62 3.56
2840 4780 0.741326 TTAGCAGCACCGTTTTGCAA 59.259 45.000 0.00 0.00 45.62 4.08
2841 4781 0.741326 TTTAGCAGCACCGTTTTGCA 59.259 45.000 0.00 0.00 45.62 4.08
2842 4782 1.985684 GATTTAGCAGCACCGTTTTGC 59.014 47.619 0.00 0.00 43.34 3.68
2843 4783 3.058293 TGAGATTTAGCAGCACCGTTTTG 60.058 43.478 0.00 0.00 0.00 2.44
2872 4812 2.573689 GGACGCGTCGAAGTCTCG 60.574 66.667 30.99 6.20 46.87 4.04
3177 5205 7.083875 TGAAAAGAAATGGACGAATACCATC 57.916 36.000 0.00 0.00 45.89 3.51


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

AutoCloner maintained by Alex Coulton.