Multiple sequence alignment - TraesCS6D01G050400

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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 TraesCS6D01G050400 chr6D 100.000 4502 0 0 1 4502 24299990 24295489 0.000000e+00 8314.0
1 TraesCS6D01G050400 chr6D 86.164 3845 405 63 1 3801 24428521 24432282 0.000000e+00 4036.0
2 TraesCS6D01G050400 chr6D 84.888 2402 314 32 1432 3800 24364541 24362156 0.000000e+00 2379.0
3 TraesCS6D01G050400 chr6D 84.792 2354 331 22 1457 3801 24403007 24405342 0.000000e+00 2338.0
4 TraesCS6D01G050400 chr6D 82.652 2640 392 43 1149 3746 24226396 24229011 0.000000e+00 2278.0
5 TraesCS6D01G050400 chr6D 84.089 2382 333 30 1433 3801 24357304 24354956 0.000000e+00 2257.0
6 TraesCS6D01G050400 chr6D 85.270 2057 281 17 1591 3639 24353405 24351363 0.000000e+00 2100.0
7 TraesCS6D01G050400 chr6D 86.556 1681 186 21 2151 3801 24339996 24338326 0.000000e+00 1816.0
8 TraesCS6D01G050400 chr6D 88.571 805 85 5 567 1369 24358122 24357323 0.000000e+00 970.0
9 TraesCS6D01G050400 chr6D 85.887 829 72 24 510 1326 24365334 24364539 0.000000e+00 841.0
10 TraesCS6D01G050400 chr6D 84.625 813 85 23 560 1359 24402178 24402963 0.000000e+00 773.0
11 TraesCS6D01G050400 chr6D 86.486 555 60 7 567 1109 24348840 24348289 3.000000e-166 595.0
12 TraesCS6D01G050400 chr6D 86.486 555 60 7 567 1109 24390487 24391038 3.000000e-166 595.0
13 TraesCS6D01G050400 chr6D 95.710 303 12 1 214 515 24366183 24365881 1.880000e-133 486.0
14 TraesCS6D01G050400 chr6D 99.505 202 1 0 4301 4502 24361670 24361469 7.110000e-98 368.0
15 TraesCS6D01G050400 chr6D 90.253 277 17 3 3764 4039 24405348 24405615 1.990000e-93 353.0
16 TraesCS6D01G050400 chr6D 82.768 354 41 10 3764 4104 24351173 24350827 9.470000e-77 298.0
17 TraesCS6D01G050400 chr6D 88.942 208 12 2 3764 3963 24362149 24361945 3.480000e-61 246.0
18 TraesCS6D01G050400 chr6D 82.043 323 22 19 3764 4078 24323344 24323050 4.500000e-60 243.0
19 TraesCS6D01G050400 chr6D 87.745 204 22 3 3881 4083 24338168 24337967 7.530000e-58 235.0
20 TraesCS6D01G050400 chr6D 87.745 204 22 3 3881 4083 24432440 24432641 7.530000e-58 235.0
21 TraesCS6D01G050400 chr6D 87.500 176 11 3 4077 4241 24361842 24361667 4.600000e-45 193.0
22 TraesCS6D01G050400 chr6D 96.190 105 4 0 4297 4401 24405846 24405950 5.990000e-39 172.0
23 TraesCS6D01G050400 chr6D 96.117 103 4 0 4297 4399 24322856 24322754 7.750000e-38 169.0
24 TraesCS6D01G050400 chr6D 88.525 122 14 0 4381 4502 24350420 24350299 1.010000e-31 148.0
25 TraesCS6D01G050400 chr6D 95.556 90 4 0 4297 4386 24354520 24354431 1.310000e-30 145.0
26 TraesCS6D01G050400 chr6D 91.667 48 3 1 4077 4124 24354669 24354623 1.050000e-06 65.8
27 TraesCS6D01G050400 chr6D 87.755 49 4 2 4077 4124 24323027 24322980 6.290000e-04 56.5
28 TraesCS6D01G050400 chr6A 85.919 3281 395 39 567 3801 23444106 23440847 0.000000e+00 3437.0
29 TraesCS6D01G050400 chr6A 84.812 3325 393 50 510 3797 23023012 23026261 0.000000e+00 3240.0
30 TraesCS6D01G050400 chr6A 83.660 3213 459 41 567 3738 22816008 22819195 0.000000e+00 2964.0
31 TraesCS6D01G050400 chr6A 83.166 3095 450 51 567 3628 22690877 22693933 0.000000e+00 2763.0
32 TraesCS6D01G050400 chr6A 88.673 980 106 4 2662 3639 22988236 22989212 0.000000e+00 1190.0
33 TraesCS6D01G050400 chr6A 86.133 750 48 19 3764 4480 22989380 22990106 0.000000e+00 758.0
34 TraesCS6D01G050400 chr6A 88.454 537 31 15 2 515 23022176 23022704 1.780000e-173 619.0
35 TraesCS6D01G050400 chr6A 80.122 654 85 20 3881 4502 23440689 23440049 3.200000e-121 446.0
36 TraesCS6D01G050400 chr6A 90.984 122 8 3 4349 4469 22824825 22824944 1.300000e-35 161.0
37 TraesCS6D01G050400 chr6B 82.967 2642 380 43 1149 3746 39193754 39196369 0.000000e+00 2322.0
38 TraesCS6D01G050400 chr6B 85.680 2095 276 18 1432 3517 39755570 39757649 0.000000e+00 2185.0
39 TraesCS6D01G050400 chr6B 85.935 775 88 13 567 1326 39754804 39755572 0.000000e+00 808.0
40 TraesCS6D01G050400 chr6B 89.703 573 59 0 537 1109 39431474 39432046 0.000000e+00 732.0
41 TraesCS6D01G050400 chr6B 85.792 549 61 8 576 1111 39193199 39193743 2.350000e-157 566.0
42 TraesCS6D01G050400 chr6B 91.457 199 15 2 3881 4078 39428757 39428954 5.740000e-69 272.0
43 TraesCS6D01G050400 chr6B 90.640 203 9 3 3764 3957 39757895 39758096 1.240000e-65 261.0
44 TraesCS6D01G050400 chr6B 88.182 220 21 5 4282 4499 39429018 39429234 1.610000e-64 257.0
45 TraesCS6D01G050400 chr6B 89.286 168 16 2 3902 4068 39456769 39456935 4.560000e-50 209.0
46 TraesCS6D01G050400 chr6B 86.765 204 8 6 4297 4499 39758528 39758713 4.560000e-50 209.0
47 TraesCS6D01G050400 chr6B 94.737 114 6 0 3764 3877 39426166 39426279 1.290000e-40 178.0
48 TraesCS6D01G050400 chr6B 85.632 174 14 1 4077 4239 39758205 39758378 5.990000e-39 172.0
49 TraesCS6D01G050400 chr6B 94.444 54 3 0 383 436 39430945 39430998 2.890000e-12 84.2
50 TraesCS6D01G050400 chr6B 95.122 41 2 0 4077 4117 39428977 39429017 1.050000e-06 65.8
51 TraesCS6D01G050400 chrUn 100.000 32 0 0 3764 3795 278295554 278295585 4.860000e-05 60.2
52 TraesCS6D01G050400 chrUn 94.872 39 0 2 3764 3802 284474613 284474577 4.860000e-05 60.2


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 TraesCS6D01G050400 chr6D 24295489 24299990 4501 True 8314.000000 8314 100.000000 1 4502 1 chr6D.!!$R1 4501
1 TraesCS6D01G050400 chr6D 24226396 24229011 2615 False 2278.000000 2278 82.652000 1149 3746 1 chr6D.!!$F1 2597
2 TraesCS6D01G050400 chr6D 24428521 24432641 4120 False 2135.500000 4036 86.954500 1 4083 2 chr6D.!!$F4 4082
3 TraesCS6D01G050400 chr6D 24337967 24339996 2029 True 1025.500000 1816 87.150500 2151 4083 2 chr6D.!!$R3 1932
4 TraesCS6D01G050400 chr6D 24402178 24405950 3772 False 909.000000 2338 88.965000 560 4401 4 chr6D.!!$F3 3841
5 TraesCS6D01G050400 chr6D 24348289 24366183 17894 True 792.271429 2379 88.954571 214 4502 14 chr6D.!!$R4 4288
6 TraesCS6D01G050400 chr6D 24390487 24391038 551 False 595.000000 595 86.486000 567 1109 1 chr6D.!!$F2 542
7 TraesCS6D01G050400 chr6A 22816008 22819195 3187 False 2964.000000 2964 83.660000 567 3738 1 chr6A.!!$F2 3171
8 TraesCS6D01G050400 chr6A 22690877 22693933 3056 False 2763.000000 2763 83.166000 567 3628 1 chr6A.!!$F1 3061
9 TraesCS6D01G050400 chr6A 23440049 23444106 4057 True 1941.500000 3437 83.020500 567 4502 2 chr6A.!!$R1 3935
10 TraesCS6D01G050400 chr6A 23022176 23026261 4085 False 1929.500000 3240 86.633000 2 3797 2 chr6A.!!$F5 3795
11 TraesCS6D01G050400 chr6A 22988236 22990106 1870 False 974.000000 1190 87.403000 2662 4480 2 chr6A.!!$F4 1818
12 TraesCS6D01G050400 chr6B 39193199 39196369 3170 False 1444.000000 2322 84.379500 576 3746 2 chr6B.!!$F2 3170
13 TraesCS6D01G050400 chr6B 39754804 39758713 3909 False 727.000000 2185 86.930400 567 4499 5 chr6B.!!$F4 3932
14 TraesCS6D01G050400 chr6B 39426166 39432046 5880 False 264.833333 732 92.274167 383 4499 6 chr6B.!!$F3 4116

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
875 6135 0.030101 GTCAGGCTCGATCTCGGAAG 59.970 60.0 0.00 0.0 40.29 3.46 F
1704 6988 0.324943 TGACTAGAAGCCTGCCAACC 59.675 55.0 0.00 0.0 0.00 3.77 F
2759 8050 0.032912 ATCCATTGGACAGCCATGCA 60.033 50.0 7.76 0.0 45.46 3.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1807 7091 0.244721 GAGCCAAGGTCCAACATTGC 59.755 55.0 0.00 0.00 38.43 3.56 R
3291 19565 0.454600 CAGTTGCATCTCCATGGTGC 59.545 55.0 16.84 16.84 39.26 5.01 R
4268 20814 0.175760 GCAGAGGCAGACAACGGATA 59.824 55.0 0.00 0.00 40.72 2.59 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
207 216 5.567138 AAAAGAAAAGATATCACGGGCAG 57.433 39.130 5.32 0.00 0.00 4.85
211 220 0.759346 AAGATATCACGGGCAGGGAC 59.241 55.000 5.32 0.00 33.39 4.46
292 301 3.826754 CGCCAGCAGAGTAGCCGA 61.827 66.667 0.00 0.00 34.23 5.54
871 6131 0.171231 TGTTGTCAGGCTCGATCTCG 59.829 55.000 0.00 0.00 41.45 4.04
872 6132 0.526524 GTTGTCAGGCTCGATCTCGG 60.527 60.000 0.00 0.00 40.29 4.63
873 6133 0.679960 TTGTCAGGCTCGATCTCGGA 60.680 55.000 0.00 0.00 40.29 4.55
874 6134 0.679960 TGTCAGGCTCGATCTCGGAA 60.680 55.000 0.00 0.00 40.29 4.30
875 6135 0.030101 GTCAGGCTCGATCTCGGAAG 59.970 60.000 0.00 0.00 40.29 3.46
876 6136 1.299773 CAGGCTCGATCTCGGAAGC 60.300 63.158 5.08 5.08 38.14 3.86
877 6137 1.754621 AGGCTCGATCTCGGAAGCA 60.755 57.895 13.20 0.00 39.86 3.91
878 6138 1.590259 GGCTCGATCTCGGAAGCAC 60.590 63.158 13.20 2.45 39.86 4.40
879 6139 1.435515 GCTCGATCTCGGAAGCACT 59.564 57.895 8.02 0.00 38.55 4.40
880 6140 0.869454 GCTCGATCTCGGAAGCACTG 60.869 60.000 8.02 0.00 38.55 3.66
881 6141 0.735471 CTCGATCTCGGAAGCACTGA 59.265 55.000 0.00 0.00 40.29 3.41
882 6142 1.336440 CTCGATCTCGGAAGCACTGAT 59.664 52.381 0.00 0.00 40.29 2.90
883 6143 1.751351 TCGATCTCGGAAGCACTGATT 59.249 47.619 0.00 0.00 40.29 2.57
1040 6324 6.765512 CAGCTGAGATATCTCGACCTATCATA 59.234 42.308 24.27 5.31 45.72 2.15
1041 6325 7.445096 CAGCTGAGATATCTCGACCTATCATAT 59.555 40.741 24.27 1.82 45.72 1.78
1072 6356 0.616395 TGGAAGGATACCACCGCAGA 60.616 55.000 0.00 0.00 35.41 4.26
1093 6377 6.520272 CAGATGGGTAATCTCTCCAACTTAG 58.480 44.000 0.00 0.00 44.24 2.18
1116 6400 4.807304 GGATACTTAAATCTTGCGACCGAA 59.193 41.667 0.00 0.00 0.00 4.30
1117 6401 5.292589 GGATACTTAAATCTTGCGACCGAAA 59.707 40.000 0.00 0.00 0.00 3.46
1119 6403 5.622770 ACTTAAATCTTGCGACCGAAAAT 57.377 34.783 0.00 0.00 0.00 1.82
1120 6404 5.390613 ACTTAAATCTTGCGACCGAAAATG 58.609 37.500 0.00 0.00 0.00 2.32
1122 6406 4.701956 AAATCTTGCGACCGAAAATGAT 57.298 36.364 0.00 0.00 0.00 2.45
1129 6413 2.673368 GCGACCGAAAATGATGAGAGTT 59.327 45.455 0.00 0.00 0.00 3.01
1136 6420 9.261180 GACCGAAAATGATGAGAGTTATGATTA 57.739 33.333 0.00 0.00 0.00 1.75
1173 6457 4.202253 GGCACATACTCCACTGATATCACA 60.202 45.833 0.00 0.00 0.00 3.58
1194 6478 3.263489 TGGTTGTCACGGTTAACTTCA 57.737 42.857 5.42 0.00 0.00 3.02
1213 6497 4.944619 TCACTTGAGCACCTAGATATGG 57.055 45.455 0.00 0.00 0.00 2.74
1218 6502 1.618837 GAGCACCTAGATATGGCCGAA 59.381 52.381 0.00 0.00 0.00 4.30
1285 6569 4.336433 TGCTTCCAACTCTGAAAGTTCTTG 59.664 41.667 0.00 0.00 45.28 3.02
1320 6604 2.159028 CCAGCTTAGAAGTAGCCCTGAC 60.159 54.545 0.00 0.00 39.47 3.51
1341 6625 3.645687 ACTCTCTTCAGCTCTCAAACCTT 59.354 43.478 0.00 0.00 0.00 3.50
1354 6638 6.091986 GCTCTCAAACCTTACATCTCTTGAAG 59.908 42.308 0.00 0.00 0.00 3.02
1360 6644 4.187694 CCTTACATCTCTTGAAGCACTCC 58.812 47.826 0.00 0.00 0.00 3.85
1366 6650 2.037772 TCTCTTGAAGCACTCCACCTTC 59.962 50.000 0.00 0.00 38.30 3.46
1369 6653 1.067295 TGAAGCACTCCACCTTCCAT 58.933 50.000 0.00 0.00 37.29 3.41
1374 6658 2.578021 AGCACTCCACCTTCCATACAAT 59.422 45.455 0.00 0.00 0.00 2.71
1388 6672 5.376625 TCCATACAATGAGTTCCATAAGCC 58.623 41.667 0.00 0.00 34.45 4.35
1446 6730 4.676546 TCAAGCATCTAGACATCTCGTTG 58.323 43.478 0.00 0.00 0.00 4.10
1462 6746 3.941483 CTCGTTGAATGGTTTCTATGGCT 59.059 43.478 0.00 0.00 32.78 4.75
1471 6755 4.671831 TGGTTTCTATGGCTCATTTCCAA 58.328 39.130 0.00 0.00 37.13 3.53
1479 6763 2.749076 TGGCTCATTTCCAAACGAGATG 59.251 45.455 0.00 0.00 34.97 2.90
1481 6765 2.749621 GCTCATTTCCAAACGAGATGGT 59.250 45.455 0.00 0.00 39.09 3.55
1514 6798 4.658063 TCCATGGTGGAACTTTCGTTATT 58.342 39.130 12.58 0.00 45.00 1.40
1516 6800 6.419791 TCCATGGTGGAACTTTCGTTATTAT 58.580 36.000 12.58 0.00 45.00 1.28
1543 6827 1.064463 ACCTTGTGGGCATGATACCTG 60.064 52.381 0.00 0.00 39.10 4.00
1580 6864 8.409358 AACCTATGTAATTTGGAGGCATTATC 57.591 34.615 0.00 0.00 0.00 1.75
1587 6871 9.639563 TGTAATTTGGAGGCATTATCTTTATCA 57.360 29.630 0.00 0.00 0.00 2.15
1590 6874 4.655963 TGGAGGCATTATCTTTATCAGGC 58.344 43.478 0.00 0.00 0.00 4.85
1605 6889 7.779326 TCTTTATCAGGCAACAATATCAATGGA 59.221 33.333 0.00 0.00 41.41 3.41
1612 6896 9.630098 CAGGCAACAATATCAATGGAAATATAC 57.370 33.333 0.00 0.00 41.41 1.47
1613 6897 9.365906 AGGCAACAATATCAATGGAAATATACA 57.634 29.630 0.00 0.00 41.41 2.29
1661 6945 9.599322 CAGTTGTTCACAGAATAAACTACAATC 57.401 33.333 9.16 0.00 33.15 2.67
1670 6954 8.818057 ACAGAATAAACTACAATCGTTATCTGC 58.182 33.333 0.00 0.00 35.44 4.26
1674 6958 8.887036 ATAAACTACAATCGTTATCTGCATCA 57.113 30.769 0.00 0.00 0.00 3.07
1678 6962 6.818644 ACTACAATCGTTATCTGCATCAAACT 59.181 34.615 0.00 0.00 0.00 2.66
1690 6974 4.952262 GCATCAAACTGCAATCTGACTA 57.048 40.909 0.00 0.00 41.87 2.59
1704 6988 0.324943 TGACTAGAAGCCTGCCAACC 59.675 55.000 0.00 0.00 0.00 3.77
1720 7004 2.618045 CCAACCACACCAGTAGAATCCC 60.618 54.545 0.00 0.00 0.00 3.85
1729 7013 3.844211 ACCAGTAGAATCCCTAAGCAACA 59.156 43.478 0.00 0.00 0.00 3.33
1731 7015 5.665812 ACCAGTAGAATCCCTAAGCAACATA 59.334 40.000 0.00 0.00 0.00 2.29
1734 7018 7.275920 CAGTAGAATCCCTAAGCAACATAAGT 58.724 38.462 0.00 0.00 0.00 2.24
1750 7034 6.208988 ACATAAGTCAGCTGTTTCTCGATA 57.791 37.500 14.67 1.98 0.00 2.92
1771 7055 6.147821 CGATAAGAACAAACTCACTGGTCATT 59.852 38.462 0.00 0.00 32.63 2.57
1776 7060 1.238439 AACTCACTGGTCATTTGCCG 58.762 50.000 0.00 0.00 0.00 5.69
1777 7061 0.606401 ACTCACTGGTCATTTGCCGG 60.606 55.000 0.00 0.00 38.32 6.13
1778 7062 1.926511 CTCACTGGTCATTTGCCGGC 61.927 60.000 22.73 22.73 35.84 6.13
1786 7070 4.966787 ATTTGCCGGCGGTGTGGT 62.967 61.111 28.82 7.48 0.00 4.16
1791 7075 4.770874 CCGGCGGTGTGGTTAGGG 62.771 72.222 19.97 0.00 0.00 3.53
1803 7087 1.992557 TGGTTAGGGGAGCTCACAAAT 59.007 47.619 19.73 5.51 0.00 2.32
1807 7091 4.443598 GGTTAGGGGAGCTCACAAATCTAG 60.444 50.000 19.73 0.00 0.00 2.43
1854 7139 2.039480 CCTGGATGGGGTCATACATGAG 59.961 54.545 0.00 0.00 42.84 2.90
1875 7160 3.322254 AGGGCCATTTATCACGTCTAGAG 59.678 47.826 6.18 0.00 0.00 2.43
1882 7167 7.815068 GCCATTTATCACGTCTAGAGATGTTAT 59.185 37.037 1.50 3.19 41.97 1.89
1886 7171 9.570468 TTTATCACGTCTAGAGATGTTATACCT 57.430 33.333 1.50 0.00 41.97 3.08
1891 7176 8.237949 CACGTCTAGAGATGTTATACCTATTGG 58.762 40.741 1.50 0.00 41.97 3.16
1892 7177 8.162085 ACGTCTAGAGATGTTATACCTATTGGA 58.838 37.037 0.00 0.00 41.16 3.53
1902 7187 8.319057 TGTTATACCTATTGGACTTGTCAGAT 57.681 34.615 0.00 0.00 37.04 2.90
1923 7208 5.367937 AGATAACTCCATAGCCATCACAGTT 59.632 40.000 0.00 0.00 0.00 3.16
1999 7284 3.217626 CAGCTAGGGCCTAAATTTCCAG 58.782 50.000 15.43 2.81 39.73 3.86
2022 7307 1.483827 TGGCTTCAATGGCAAACACAA 59.516 42.857 0.00 0.00 39.58 3.33
2043 7328 8.353684 ACACAAGTAAGGAGTCTTGATATATCG 58.646 37.037 8.19 0.00 42.22 2.92
2055 7340 7.383572 AGTCTTGATATATCGAACACAAGCATC 59.616 37.037 8.19 1.63 35.97 3.91
2090 7375 5.982890 CCAGATTGGTTTTGGATAACAGT 57.017 39.130 0.00 0.00 33.76 3.55
2095 7380 6.553100 AGATTGGTTTTGGATAACAGTTTCCA 59.447 34.615 11.20 11.20 40.24 3.53
2100 7385 3.788227 TGGATAACAGTTTCCACAGCT 57.212 42.857 11.20 0.00 37.10 4.24
2104 7389 4.576463 GGATAACAGTTTCCACAGCTATGG 59.424 45.833 4.04 4.04 41.57 2.74
2107 7392 4.634012 ACAGTTTCCACAGCTATGGTTA 57.366 40.909 11.64 0.00 40.95 2.85
2165 7450 5.890985 TCCCGTCAACAATGGAATTTATGAT 59.109 36.000 0.00 0.00 35.91 2.45
2166 7451 6.379703 TCCCGTCAACAATGGAATTTATGATT 59.620 34.615 0.00 0.00 35.91 2.57
2169 7454 6.291217 CGTCAACAATGGAATTTATGATTGCG 60.291 38.462 0.00 0.00 31.22 4.85
2170 7455 6.531240 GTCAACAATGGAATTTATGATTGCGT 59.469 34.615 0.00 0.00 31.22 5.24
2213 7498 3.855689 CCAGCTTGGTGGTTCAATAAG 57.144 47.619 10.40 0.00 31.35 1.73
2218 7503 5.473504 CAGCTTGGTGGTTCAATAAGTAAGT 59.526 40.000 0.00 0.00 0.00 2.24
2228 7513 7.393234 TGGTTCAATAAGTAAGTTTCCCATCAG 59.607 37.037 0.00 0.00 0.00 2.90
2260 7545 3.384789 CCTGGATCTCAGTCGGAACAATA 59.615 47.826 9.47 0.00 41.83 1.90
2298 7583 2.217038 AGACTTTGGAGCGCCAGGA 61.217 57.895 9.79 1.70 46.91 3.86
2302 7587 1.301677 CTTTGGAGCGCCAGGACTTC 61.302 60.000 9.79 0.00 46.91 3.01
2385 7670 2.286067 GCGATCATTGCAGCTGTTAGAC 60.286 50.000 16.64 0.00 0.00 2.59
2425 7710 5.015515 TCAATGGGTCAATTACTGATTGCA 58.984 37.500 0.00 0.00 43.93 4.08
2435 7720 8.400947 GTCAATTACTGATTGCATAGTCAATGT 58.599 33.333 2.50 0.08 43.93 2.71
2446 7731 6.762333 TGCATAGTCAATGTATCTAGCACAT 58.238 36.000 4.48 4.48 38.25 3.21
2532 7823 0.529378 CACTTCTGCAGAAATGCCCC 59.471 55.000 28.16 0.00 33.07 5.80
2620 7911 6.183360 GGAGAAGCTATTGTCTTTGTCATTCC 60.183 42.308 0.00 0.00 0.00 3.01
2704 7995 4.671831 TCTTCAATATTTGGACCTTGCCA 58.328 39.130 0.00 0.00 35.78 4.92
2715 8006 6.463995 TTGGACCTTGCCAACAATAATATC 57.536 37.500 0.00 0.00 42.75 1.63
2739 8030 4.774726 TCAGGGAGCATACCAAGATCTATC 59.225 45.833 0.00 0.00 0.00 2.08
2743 8034 5.396213 GGGAGCATACCAAGATCTATCATCC 60.396 48.000 0.00 0.00 0.00 3.51
2753 8044 5.163281 AGATCTATCATCCATTGGACAGC 57.837 43.478 7.76 0.00 32.98 4.40
2758 8049 0.387929 CATCCATTGGACAGCCATGC 59.612 55.000 7.76 0.00 45.46 4.06
2759 8050 0.032912 ATCCATTGGACAGCCATGCA 60.033 50.000 7.76 0.00 45.46 3.96
2764 8055 0.675083 TTGGACAGCCATGCAACAAG 59.325 50.000 0.00 0.00 45.46 3.16
2790 8084 5.385198 AGAGGCACCTTTGTTTATCTTCAA 58.615 37.500 0.00 0.00 0.00 2.69
2797 8091 6.700960 CACCTTTGTTTATCTTCAACATGCAA 59.299 34.615 0.00 0.00 34.13 4.08
2804 8098 8.791675 TGTTTATCTTCAACATGCAATCAGTTA 58.208 29.630 0.00 0.00 0.00 2.24
2808 8102 5.711506 TCTTCAACATGCAATCAGTTATGGT 59.288 36.000 0.00 0.00 0.00 3.55
2813 8107 1.818060 TGCAATCAGTTATGGTGGTGC 59.182 47.619 0.00 0.00 0.00 5.01
2814 8108 1.818060 GCAATCAGTTATGGTGGTGCA 59.182 47.619 0.00 0.00 0.00 4.57
2820 8114 0.519961 GTTATGGTGGTGCACGGTTC 59.480 55.000 11.45 0.00 34.83 3.62
2830 8124 0.033642 TGCACGGTTCGGTGACAATA 59.966 50.000 13.24 0.00 40.38 1.90
2832 8126 1.735571 GCACGGTTCGGTGACAATAAT 59.264 47.619 13.24 0.00 40.38 1.28
2881 8175 4.212214 CAGTACTCACAAAAGGTCAAGAGC 59.788 45.833 0.00 0.00 0.00 4.09
2899 8193 7.539366 GTCAAGAGCGATTATATACAGGAGAAC 59.461 40.741 0.00 0.00 0.00 3.01
2901 8195 7.768807 AGAGCGATTATATACAGGAGAACTT 57.231 36.000 0.00 0.00 0.00 2.66
2964 8258 4.226168 ACCGGAGAGATTCCTGAAGAAATT 59.774 41.667 9.46 0.00 44.41 1.82
2966 8260 6.070194 ACCGGAGAGATTCCTGAAGAAATTAA 60.070 38.462 9.46 0.00 44.41 1.40
3098 15620 4.970662 ATGATTTGTCTGGTGAAATCCG 57.029 40.909 0.00 0.00 37.65 4.18
3131 15653 0.593618 GCTCTCACGTCACTGAGTCA 59.406 55.000 0.00 0.00 39.08 3.41
3156 19430 4.894784 TGAACCTGTCCTACAACAATCTC 58.105 43.478 0.00 0.00 0.00 2.75
3253 19527 0.181587 CTGCGGTCCTCCTCTCTCTA 59.818 60.000 0.00 0.00 0.00 2.43
3265 19539 7.013464 GTCCTCCTCTCTCTATAAATTGTTCGA 59.987 40.741 0.00 0.00 0.00 3.71
3275 19549 4.128139 TTGTTCGACACAACCCGG 57.872 55.556 0.00 0.00 40.71 5.73
3291 19565 1.153086 CGGGCCAATTCCAGGAGAG 60.153 63.158 4.39 0.00 0.00 3.20
3292 19566 1.454663 GGGCCAATTCCAGGAGAGC 60.455 63.158 4.39 0.00 0.00 4.09
3308 19582 0.737219 GAGCACCATGGAGATGCAAC 59.263 55.000 23.44 14.79 41.97 4.17
3356 19633 3.661944 CCATGAGCTCTGGATATGTGAC 58.338 50.000 21.15 0.00 35.70 3.67
3446 19723 2.203070 CAGCCTGTATGACCGGGC 60.203 66.667 6.32 1.57 44.38 6.13
3502 19782 7.502561 CCTTGAGAGGTAAAATTAATGGGTAGG 59.497 40.741 0.00 0.00 38.32 3.18
3517 19798 3.238597 GGGTAGGAGCTGAGATGAGATT 58.761 50.000 0.00 0.00 0.00 2.40
3547 19828 3.565307 TGGTTCTTGGTTTGCTCTCATT 58.435 40.909 0.00 0.00 0.00 2.57
3693 20011 3.197549 ACATTGGTTCTTGGTTTGCTGTT 59.802 39.130 0.00 0.00 0.00 3.16
3696 20014 2.828520 TGGTTCTTGGTTTGCTGTTGAA 59.171 40.909 0.00 0.00 0.00 2.69
3747 20067 8.843885 ATCATGAATGTATCAATCGATGTTCT 57.156 30.769 0.00 0.00 42.54 3.01
3855 20232 8.076178 GTGTTATCTATGTGCTTTCTGTTGTTT 58.924 33.333 0.00 0.00 0.00 2.83
3865 20243 4.388469 GCTTTCTGTTGTTTGTGCTTTTCA 59.612 37.500 0.00 0.00 0.00 2.69
3930 20335 7.486407 AAACTCAAATGGCAAAGATAAGGAT 57.514 32.000 0.00 0.00 0.00 3.24
3969 20374 4.524749 GCAAGAATGATGATGACATGACG 58.475 43.478 0.00 0.00 36.82 4.35
4003 20408 4.797471 TGATTCTGATTTTTGTTCTGGCG 58.203 39.130 0.00 0.00 0.00 5.69
4061 20472 5.580998 AGAAGAACCCAGACAGTACTATGA 58.419 41.667 0.00 0.00 0.00 2.15
4062 20473 5.654650 AGAAGAACCCAGACAGTACTATGAG 59.345 44.000 0.00 0.00 0.00 2.90
4065 20476 4.864483 ACCCAGACAGTACTATGAGAGA 57.136 45.455 0.00 0.00 0.00 3.10
4106 20583 1.609072 GAGGTGGTCTCTGTTTTTGCC 59.391 52.381 0.00 0.00 39.38 4.52
4122 20599 3.981308 CCTACAACCGTTGGCTGG 58.019 61.111 15.60 9.92 31.12 4.85
4239 20785 4.509970 CCATTGTCAAACTGTCGAACTGTA 59.490 41.667 0.00 0.00 29.85 2.74
4242 20788 4.304110 TGTCAAACTGTCGAACTGTATCC 58.696 43.478 0.00 0.00 29.85 2.59
4243 20789 4.202172 TGTCAAACTGTCGAACTGTATCCA 60.202 41.667 0.00 0.00 29.85 3.41
4244 20790 4.150098 GTCAAACTGTCGAACTGTATCCAC 59.850 45.833 0.00 0.00 29.85 4.02
4245 20791 3.314541 AACTGTCGAACTGTATCCACC 57.685 47.619 0.00 0.00 29.85 4.61
4246 20792 1.549170 ACTGTCGAACTGTATCCACCC 59.451 52.381 0.00 0.00 0.00 4.61
4247 20793 1.825474 CTGTCGAACTGTATCCACCCT 59.175 52.381 0.00 0.00 0.00 4.34
4248 20794 1.548719 TGTCGAACTGTATCCACCCTG 59.451 52.381 0.00 0.00 0.00 4.45
4249 20795 1.549170 GTCGAACTGTATCCACCCTGT 59.451 52.381 0.00 0.00 0.00 4.00
4250 20796 1.548719 TCGAACTGTATCCACCCTGTG 59.451 52.381 0.00 0.00 0.00 3.66
4264 20810 5.097742 CACCCTGTGGTAATGAGTAATGA 57.902 43.478 0.00 0.00 45.57 2.57
4265 20811 4.876107 CACCCTGTGGTAATGAGTAATGAC 59.124 45.833 0.00 0.00 45.57 3.06
4266 20812 4.783227 ACCCTGTGGTAATGAGTAATGACT 59.217 41.667 0.00 0.00 45.45 3.41
4267 20813 5.118990 CCCTGTGGTAATGAGTAATGACTG 58.881 45.833 0.00 0.00 35.45 3.51
4268 20814 5.338381 CCCTGTGGTAATGAGTAATGACTGT 60.338 44.000 0.00 0.00 35.45 3.55
4269 20815 6.127168 CCCTGTGGTAATGAGTAATGACTGTA 60.127 42.308 0.00 0.00 35.45 2.74
4270 20816 7.419057 CCCTGTGGTAATGAGTAATGACTGTAT 60.419 40.741 0.00 0.00 35.45 2.29
4271 20817 7.653713 CCTGTGGTAATGAGTAATGACTGTATC 59.346 40.741 0.00 0.00 35.45 2.24
4272 20818 7.497595 TGTGGTAATGAGTAATGACTGTATCC 58.502 38.462 0.00 0.00 35.45 2.59
4294 20840 3.307242 CGTTGTCTGCCTCTGCTTTATAC 59.693 47.826 0.00 0.00 38.71 1.47
4406 21175 7.306749 GCACATGTTATTGCATATGTAAAAGGC 60.307 37.037 10.40 2.83 38.68 4.35
4410 21179 8.472683 TGTTATTGCATATGTAAAAGGCAAAC 57.527 30.769 10.40 8.58 46.15 2.93
4422 21191 5.596836 AAAAGGCAAACATGAGTTCAGAA 57.403 34.783 0.00 0.00 36.84 3.02
4428 21197 4.151157 GCAAACATGAGTTCAGAAAATGCC 59.849 41.667 0.00 0.00 36.84 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 2.040813 AGCACTCTGACCATCACCAAAT 59.959 45.455 0.00 0.00 0.00 2.32
94 97 5.471116 GCATCCATCAAGAATATACACAGCA 59.529 40.000 0.00 0.00 0.00 4.41
102 105 6.938596 TCTCAAATCGCATCCATCAAGAATAT 59.061 34.615 0.00 0.00 0.00 1.28
207 216 2.635427 GTGGGGATGAAGATCTAGTCCC 59.365 54.545 22.79 22.79 46.30 4.46
211 220 2.036475 CACCGTGGGGATGAAGATCTAG 59.964 54.545 0.00 0.00 36.97 2.43
401 4799 4.166888 GCGATCTGGAGGCTGGCA 62.167 66.667 3.38 0.00 0.00 4.92
765 6025 3.322318 GAGGCTGGCAGGGTCTGAC 62.322 68.421 17.64 0.00 40.49 3.51
871 6131 3.061697 CCGTTTACGTAATCAGTGCTTCC 59.938 47.826 9.18 0.00 37.74 3.46
872 6132 3.061697 CCCGTTTACGTAATCAGTGCTTC 59.938 47.826 9.18 0.00 37.74 3.86
873 6133 2.997986 CCCGTTTACGTAATCAGTGCTT 59.002 45.455 9.18 0.00 37.74 3.91
874 6134 2.613691 CCCGTTTACGTAATCAGTGCT 58.386 47.619 9.18 0.00 37.74 4.40
875 6135 1.061566 GCCCGTTTACGTAATCAGTGC 59.938 52.381 9.18 7.31 37.74 4.40
876 6136 2.339418 TGCCCGTTTACGTAATCAGTG 58.661 47.619 9.18 1.33 37.74 3.66
877 6137 2.613691 CTGCCCGTTTACGTAATCAGT 58.386 47.619 9.18 0.00 37.74 3.41
878 6138 1.931172 CCTGCCCGTTTACGTAATCAG 59.069 52.381 9.18 10.79 37.74 2.90
879 6139 2.008045 GCCTGCCCGTTTACGTAATCA 61.008 52.381 9.18 2.37 37.74 2.57
880 6140 0.654160 GCCTGCCCGTTTACGTAATC 59.346 55.000 9.18 7.57 37.74 1.75
881 6141 1.085501 CGCCTGCCCGTTTACGTAAT 61.086 55.000 9.18 0.00 37.74 1.89
882 6142 1.737371 CGCCTGCCCGTTTACGTAA 60.737 57.895 3.29 3.29 37.74 3.18
883 6143 2.125991 CGCCTGCCCGTTTACGTA 60.126 61.111 1.28 0.00 37.74 3.57
1040 6324 5.888161 GGTATCCTTCCAATGAACTGTGAAT 59.112 40.000 0.00 0.00 0.00 2.57
1041 6325 5.222027 TGGTATCCTTCCAATGAACTGTGAA 60.222 40.000 0.00 0.00 31.50 3.18
1072 6356 5.538877 TCCTAAGTTGGAGAGATTACCCAT 58.461 41.667 0.00 0.00 0.00 4.00
1129 6413 7.724951 TGTGCCATGATGGAAAGAATAATCATA 59.275 33.333 17.22 0.00 40.96 2.15
1136 6420 5.452255 AGTATGTGCCATGATGGAAAGAAT 58.548 37.500 17.22 2.21 40.96 2.40
1147 6431 2.696989 TCAGTGGAGTATGTGCCATG 57.303 50.000 0.00 0.00 36.41 3.66
1173 6457 3.562557 GTGAAGTTAACCGTGACAACCAT 59.437 43.478 0.88 0.00 0.00 3.55
1194 6478 2.370189 GGCCATATCTAGGTGCTCAAGT 59.630 50.000 0.00 0.00 0.00 3.16
1213 6497 1.000506 TGTACTGAGGTTCACTTCGGC 59.999 52.381 0.00 0.00 32.20 5.54
1218 6502 5.680619 TGAACAATTGTACTGAGGTTCACT 58.319 37.500 12.39 0.00 39.51 3.41
1285 6569 2.416680 AGCTGGCAAGAGGAAAGATC 57.583 50.000 0.00 0.00 0.00 2.75
1320 6604 3.959535 AGGTTTGAGAGCTGAAGAGAG 57.040 47.619 0.00 0.00 34.08 3.20
1341 6625 3.055819 GGTGGAGTGCTTCAAGAGATGTA 60.056 47.826 0.00 0.00 0.00 2.29
1354 6638 2.489938 TTGTATGGAAGGTGGAGTGC 57.510 50.000 0.00 0.00 0.00 4.40
1360 6644 4.588899 TGGAACTCATTGTATGGAAGGTG 58.411 43.478 0.00 0.00 0.00 4.00
1366 6650 5.380043 AGGCTTATGGAACTCATTGTATGG 58.620 41.667 0.00 0.00 37.30 2.74
1369 6653 5.130311 TGCTAGGCTTATGGAACTCATTGTA 59.870 40.000 0.00 0.00 37.30 2.41
1374 6658 2.159099 CGTGCTAGGCTTATGGAACTCA 60.159 50.000 0.00 0.00 0.00 3.41
1388 6672 0.889186 AAACCAGTTGGGCGTGCTAG 60.889 55.000 2.79 0.00 42.05 3.42
1446 6730 5.360714 TGGAAATGAGCCATAGAAACCATTC 59.639 40.000 0.00 0.00 35.70 2.67
1462 6746 8.620416 CATATTAACCATCTCGTTTGGAAATGA 58.380 33.333 7.80 0.00 37.69 2.57
1471 6755 5.365605 TGGAGGTCATATTAACCATCTCGTT 59.634 40.000 6.77 0.00 39.39 3.85
1514 6798 9.899661 GTATCATGCCCACAAGGTTATTATATA 57.100 33.333 0.00 0.00 38.26 0.86
1516 6800 7.018149 AGGTATCATGCCCACAAGGTTATTATA 59.982 37.037 0.00 0.00 38.26 0.98
1543 6827 3.470645 ACATAGGTTCTTCATACCGGC 57.529 47.619 0.00 0.00 40.69 6.13
1546 6830 8.974060 TCCAAATTACATAGGTTCTTCATACC 57.026 34.615 0.00 0.00 35.85 2.73
1580 6864 7.944061 TCCATTGATATTGTTGCCTGATAAAG 58.056 34.615 0.00 0.00 0.00 1.85
1584 6868 6.795144 TTTCCATTGATATTGTTGCCTGAT 57.205 33.333 0.00 0.00 0.00 2.90
1587 6871 9.365906 TGTATATTTCCATTGATATTGTTGCCT 57.634 29.630 0.00 0.00 0.00 4.75
1612 6896 7.040961 ACTGGGCAATTGATTGAAAAATTCTTG 60.041 33.333 10.34 0.00 40.14 3.02
1613 6897 6.999871 ACTGGGCAATTGATTGAAAAATTCTT 59.000 30.769 10.34 0.00 40.14 2.52
1620 6904 4.686191 ACAACTGGGCAATTGATTGAAA 57.314 36.364 10.34 0.00 40.14 2.69
1628 6912 2.665165 TCTGTGAACAACTGGGCAATT 58.335 42.857 0.00 0.00 0.00 2.32
1632 6916 4.278419 AGTTTATTCTGTGAACAACTGGGC 59.722 41.667 6.14 0.00 0.00 5.36
1669 6953 3.844577 AGTCAGATTGCAGTTTGATGC 57.155 42.857 5.72 0.00 46.68 3.91
1670 6954 6.675002 GCTTCTAGTCAGATTGCAGTTTGATG 60.675 42.308 5.72 1.05 33.44 3.07
1674 6958 4.006319 GGCTTCTAGTCAGATTGCAGTTT 58.994 43.478 0.00 0.00 34.32 2.66
1678 6962 2.679059 GCAGGCTTCTAGTCAGATTGCA 60.679 50.000 11.96 0.00 34.32 4.08
1690 6974 1.529244 GTGTGGTTGGCAGGCTTCT 60.529 57.895 0.00 0.00 0.00 2.85
1704 6988 3.197766 TGCTTAGGGATTCTACTGGTGTG 59.802 47.826 0.00 0.00 0.00 3.82
1720 7004 5.869753 AACAGCTGACTTATGTTGCTTAG 57.130 39.130 23.35 0.00 35.89 2.18
1729 7013 7.101652 TCTTATCGAGAAACAGCTGACTTAT 57.898 36.000 23.35 10.43 0.00 1.73
1731 7015 5.392767 TCTTATCGAGAAACAGCTGACTT 57.607 39.130 23.35 13.18 0.00 3.01
1734 7018 5.134202 TGTTCTTATCGAGAAACAGCTGA 57.866 39.130 23.35 0.00 45.59 4.26
1750 7034 5.679638 GCAAATGACCAGTGAGTTTGTTCTT 60.680 40.000 0.00 0.00 33.53 2.52
1771 7055 4.251771 TAACCACACCGCCGGCAA 62.252 61.111 28.98 0.00 0.00 4.52
1776 7060 3.324108 TCCCCTAACCACACCGCC 61.324 66.667 0.00 0.00 0.00 6.13
1777 7061 2.267961 CTCCCCTAACCACACCGC 59.732 66.667 0.00 0.00 0.00 5.68
1778 7062 2.240162 GAGCTCCCCTAACCACACCG 62.240 65.000 0.87 0.00 0.00 4.94
1786 7070 3.134804 GCTAGATTTGTGAGCTCCCCTAA 59.865 47.826 12.15 5.59 33.28 2.69
1791 7075 3.944015 ACATTGCTAGATTTGTGAGCTCC 59.056 43.478 12.15 3.09 37.12 4.70
1803 7087 2.879756 GCCAAGGTCCAACATTGCTAGA 60.880 50.000 0.00 0.00 38.43 2.43
1807 7091 0.244721 GAGCCAAGGTCCAACATTGC 59.755 55.000 0.00 0.00 38.43 3.56
1854 7139 3.321111 TCTCTAGACGTGATAAATGGCCC 59.679 47.826 0.00 0.00 0.00 5.80
1875 7160 8.421784 TCTGACAAGTCCAATAGGTATAACATC 58.578 37.037 0.00 0.00 35.89 3.06
1882 7167 7.069578 GGAGTTATCTGACAAGTCCAATAGGTA 59.930 40.741 15.90 0.00 42.68 3.08
1891 7176 5.163405 TGGCTATGGAGTTATCTGACAAGTC 60.163 44.000 0.00 0.00 0.00 3.01
1892 7177 4.716784 TGGCTATGGAGTTATCTGACAAGT 59.283 41.667 0.00 0.00 0.00 3.16
1902 7187 5.661312 ACTAACTGTGATGGCTATGGAGTTA 59.339 40.000 0.00 0.00 0.00 2.24
1923 7208 1.004277 GGAGGAACCCATGTTGCACTA 59.996 52.381 0.00 0.00 44.50 2.74
1927 7212 1.546029 GAAAGGAGGAACCCATGTTGC 59.454 52.381 0.00 0.00 42.60 4.17
1999 7284 1.202510 TGTTTGCCATTGAAGCCACAC 60.203 47.619 0.00 0.00 0.00 3.82
2022 7307 8.569641 GTGTTCGATATATCAAGACTCCTTACT 58.430 37.037 13.11 0.00 0.00 2.24
2043 7328 7.645340 GGTACAATATCATTGATGCTTGTGTTC 59.355 37.037 24.84 18.33 34.03 3.18
2086 7371 3.508845 AACCATAGCTGTGGAAACTGT 57.491 42.857 33.60 9.33 42.02 3.55
2090 7375 7.665559 GGATATTGATAACCATAGCTGTGGAAA 59.334 37.037 33.60 20.95 42.02 3.13
2095 7380 6.605471 TCGGATATTGATAACCATAGCTGT 57.395 37.500 0.00 0.00 0.00 4.40
2145 7430 6.531240 ACGCAATCATAAATTCCATTGTTGAC 59.469 34.615 0.00 0.00 0.00 3.18
2165 7450 5.957842 ACTGAAATCCATTTCTAACGCAA 57.042 34.783 12.22 0.00 44.85 4.85
2166 7451 5.705441 AGAACTGAAATCCATTTCTAACGCA 59.295 36.000 12.22 0.00 44.85 5.24
2170 7455 9.231297 CTGGTTAGAACTGAAATCCATTTCTAA 57.769 33.333 12.22 11.17 46.08 2.10
2212 7497 5.337330 CGGTTAGACTGATGGGAAACTTACT 60.337 44.000 0.00 0.00 0.00 2.24
2213 7498 4.868734 CGGTTAGACTGATGGGAAACTTAC 59.131 45.833 0.00 0.00 0.00 2.34
2218 7503 3.604875 GTCGGTTAGACTGATGGGAAA 57.395 47.619 0.00 0.00 46.13 3.13
2260 7545 4.406003 GTCTGATGGTAGTGGTCCAACTAT 59.594 45.833 0.00 0.00 38.52 2.12
2298 7583 6.072838 TGTCGTATAGAAGAAGTGTTCGAAGT 60.073 38.462 0.00 0.00 34.02 3.01
2302 7587 5.854866 TGTTGTCGTATAGAAGAAGTGTTCG 59.145 40.000 0.00 0.00 34.02 3.95
2385 7670 8.930846 ACCCATTGAGATTATTTCTTGATAGG 57.069 34.615 0.00 0.00 33.74 2.57
2425 7710 9.866798 CATGTATGTGCTAGATACATTGACTAT 57.133 33.333 15.43 5.91 42.01 2.12
2435 7720 4.021104 GGCCTGTCATGTATGTGCTAGATA 60.021 45.833 0.00 0.00 0.00 1.98
2446 7731 3.642141 TGATACTCAGGCCTGTCATGTA 58.358 45.455 31.58 25.85 0.00 2.29
2478 7769 4.640201 CCAGAGAGGTTGTTGTTTCTGAAA 59.360 41.667 0.00 0.00 35.28 2.69
2532 7823 4.569966 CCGAGATCAAGAAAGATGAGTTGG 59.430 45.833 0.00 0.00 0.00 3.77
2620 7911 9.698309 ATAAAACATATTGGATCTCAGTCGTAG 57.302 33.333 0.00 0.00 0.00 3.51
2680 7971 5.127519 TGGCAAGGTCCAAATATTGAAGATG 59.872 40.000 0.00 0.00 32.18 2.90
2704 7995 7.017551 TGGTATGCTCCCTGAGATATTATTGTT 59.982 37.037 0.00 0.00 0.00 2.83
2715 8006 2.971330 AGATCTTGGTATGCTCCCTGAG 59.029 50.000 0.00 0.00 0.00 3.35
2758 8049 1.035139 AAGGTGCCTCTTGCTTGTTG 58.965 50.000 0.00 0.00 42.00 3.33
2759 8050 1.410153 CAAAGGTGCCTCTTGCTTGTT 59.590 47.619 0.00 0.00 42.00 2.83
2764 8055 3.507622 AGATAAACAAAGGTGCCTCTTGC 59.492 43.478 10.73 0.00 41.77 4.01
2771 8065 5.119125 GCATGTTGAAGATAAACAAAGGTGC 59.881 40.000 0.00 0.00 40.69 5.01
2790 8084 3.444742 CACCACCATAACTGATTGCATGT 59.555 43.478 0.00 0.00 0.00 3.21
2797 8091 1.678728 CCGTGCACCACCATAACTGAT 60.679 52.381 12.15 0.00 0.00 2.90
2804 8098 2.668212 CGAACCGTGCACCACCAT 60.668 61.111 12.15 0.00 0.00 3.55
2808 8102 3.851128 TCACCGAACCGTGCACCA 61.851 61.111 12.15 0.00 33.57 4.17
2813 8107 2.350498 GGATTATTGTCACCGAACCGTG 59.650 50.000 0.00 0.00 34.93 4.94
2814 8108 2.027929 TGGATTATTGTCACCGAACCGT 60.028 45.455 0.00 0.00 0.00 4.83
2820 8114 4.253685 AGTCAACTGGATTATTGTCACCG 58.746 43.478 0.00 0.00 0.00 4.94
2830 8124 9.388506 CAAATTCTCAGTATAGTCAACTGGATT 57.611 33.333 3.60 0.76 43.69 3.01
2832 8126 8.035394 GTCAAATTCTCAGTATAGTCAACTGGA 58.965 37.037 3.60 0.00 43.69 3.86
2928 8222 7.177041 GGAATCTCTCCGGTAAGACTATTACAT 59.823 40.741 0.00 0.00 33.37 2.29
2966 8260 8.772250 TCAGGTTCTTCAATTCCATAAGAGTAT 58.228 33.333 0.00 0.00 31.30 2.12
3098 15620 2.605366 GTGAGAGCCGATAAGCTTGAAC 59.395 50.000 9.86 0.00 45.15 3.18
3131 15653 2.404559 TGTTGTAGGACAGGTTCAGGT 58.595 47.619 0.00 0.00 0.00 4.00
3156 19430 4.826274 TCCAGTTGGTATCTTTCCTCTG 57.174 45.455 0.00 0.00 36.34 3.35
3265 19539 1.906333 GAATTGGCCCGGGTTGTGT 60.906 57.895 24.63 4.91 0.00 3.72
3270 19544 4.060667 CCTGGAATTGGCCCGGGT 62.061 66.667 24.63 0.00 43.71 5.28
3275 19549 1.034292 GTGCTCTCCTGGAATTGGCC 61.034 60.000 0.00 0.00 0.00 5.36
3291 19565 0.454600 CAGTTGCATCTCCATGGTGC 59.545 55.000 16.84 16.84 39.26 5.01
3292 19566 1.100510 CCAGTTGCATCTCCATGGTG 58.899 55.000 12.58 9.91 0.00 4.17
3308 19582 0.661020 AAACGAAACCAAGTCGCCAG 59.339 50.000 0.00 0.00 42.27 4.85
3356 19633 1.889530 GAAGACCACCCAGAGACCCG 61.890 65.000 0.00 0.00 0.00 5.28
3446 19723 3.119849 GGTAACAGCCACTTGCACATAAG 60.120 47.826 0.00 0.00 44.83 1.73
3502 19782 3.069300 TGCTGGTAATCTCATCTCAGCTC 59.931 47.826 13.13 0.00 45.29 4.09
3715 20035 9.798994 TCGATTGATACATTCATGATAGATCTG 57.201 33.333 5.18 0.00 33.34 2.90
3751 20071 7.989741 GCATGGCTAGTTCCATATCTACAATAT 59.010 37.037 1.95 0.00 44.63 1.28
3759 20080 3.743521 TGTGCATGGCTAGTTCCATATC 58.256 45.455 1.95 0.00 44.63 1.63
3760 20081 3.862877 TGTGCATGGCTAGTTCCATAT 57.137 42.857 1.95 0.00 44.63 1.78
3761 20082 3.117926 ACATGTGCATGGCTAGTTCCATA 60.118 43.478 15.52 0.00 44.63 2.74
3834 20211 6.441274 CACAAACAACAGAAAGCACATAGAT 58.559 36.000 0.00 0.00 0.00 1.98
3878 20256 7.461749 CCCAAGGTATCAGTATTTACCATGAT 58.538 38.462 0.00 0.00 38.74 2.45
3879 20284 6.690460 GCCCAAGGTATCAGTATTTACCATGA 60.690 42.308 0.00 0.00 38.74 3.07
3900 20305 1.126488 TGCCATTTGAGTTTTGCCCA 58.874 45.000 0.00 0.00 0.00 5.36
3930 20335 1.602323 GCCATCACCGGTTTCACCA 60.602 57.895 2.97 0.00 38.47 4.17
3969 20374 3.272574 TCAGAATCAGCTTCATCACCC 57.727 47.619 0.00 0.00 36.24 4.61
4003 20408 1.596727 GCAGAATCGAGCATCTTCCAC 59.403 52.381 0.00 0.00 0.00 4.02
4035 20440 4.421131 AGTACTGTCTGGGTTCTTCTCAT 58.579 43.478 0.00 0.00 0.00 2.90
4061 20472 9.071276 TCTTTGCATAGACTTCAATTTTTCTCT 57.929 29.630 2.39 0.00 0.00 3.10
4062 20473 9.339492 CTCTTTGCATAGACTTCAATTTTTCTC 57.661 33.333 2.39 0.00 0.00 2.87
4065 20476 7.869429 CACCTCTTTGCATAGACTTCAATTTTT 59.131 33.333 2.39 0.00 0.00 1.94
4106 20583 1.314730 AAACCAGCCAACGGTTGTAG 58.685 50.000 18.73 6.46 46.12 2.74
4122 20599 3.284617 ACGGGGGCATGACTATAAAAAC 58.715 45.455 0.00 0.00 0.00 2.43
4242 20788 7.347117 CAGTCATTACTCATTACCACAGGGTG 61.347 46.154 0.00 0.00 40.36 4.61
4243 20789 5.338381 CAGTCATTACTCATTACCACAGGGT 60.338 44.000 0.00 0.00 42.14 4.34
4244 20790 5.118990 CAGTCATTACTCATTACCACAGGG 58.881 45.833 0.00 0.00 35.01 4.45
4245 20791 5.734720 ACAGTCATTACTCATTACCACAGG 58.265 41.667 0.00 0.00 31.97 4.00
4246 20792 7.653713 GGATACAGTCATTACTCATTACCACAG 59.346 40.741 0.00 0.00 31.97 3.66
4247 20793 7.497595 GGATACAGTCATTACTCATTACCACA 58.502 38.462 0.00 0.00 31.97 4.17
4248 20794 6.641314 CGGATACAGTCATTACTCATTACCAC 59.359 42.308 0.00 0.00 31.97 4.16
4249 20795 6.322969 ACGGATACAGTCATTACTCATTACCA 59.677 38.462 0.00 0.00 31.97 3.25
4250 20796 6.746120 ACGGATACAGTCATTACTCATTACC 58.254 40.000 0.00 0.00 31.97 2.85
4251 20797 7.705325 ACAACGGATACAGTCATTACTCATTAC 59.295 37.037 0.00 0.00 31.97 1.89
4252 20798 7.778083 ACAACGGATACAGTCATTACTCATTA 58.222 34.615 0.00 0.00 31.97 1.90
4253 20799 6.640518 ACAACGGATACAGTCATTACTCATT 58.359 36.000 0.00 0.00 31.97 2.57
4254 20800 6.096987 AGACAACGGATACAGTCATTACTCAT 59.903 38.462 0.00 0.00 35.63 2.90
4255 20801 5.417894 AGACAACGGATACAGTCATTACTCA 59.582 40.000 0.00 0.00 35.63 3.41
4256 20802 5.744345 CAGACAACGGATACAGTCATTACTC 59.256 44.000 0.00 0.00 35.63 2.59
4257 20803 5.651530 CAGACAACGGATACAGTCATTACT 58.348 41.667 0.00 0.00 35.63 2.24
4258 20804 4.267928 GCAGACAACGGATACAGTCATTAC 59.732 45.833 0.00 0.00 35.63 1.89
4259 20805 4.430007 GCAGACAACGGATACAGTCATTA 58.570 43.478 0.00 0.00 35.63 1.90
4260 20806 3.262420 GCAGACAACGGATACAGTCATT 58.738 45.455 0.00 0.00 35.63 2.57
4261 20807 2.418746 GGCAGACAACGGATACAGTCAT 60.419 50.000 0.00 0.00 35.63 3.06
4262 20808 1.067142 GGCAGACAACGGATACAGTCA 60.067 52.381 0.00 0.00 35.63 3.41
4263 20809 1.204941 AGGCAGACAACGGATACAGTC 59.795 52.381 0.00 0.00 33.99 3.51
4264 20810 1.204941 GAGGCAGACAACGGATACAGT 59.795 52.381 0.00 0.00 0.00 3.55
4265 20811 1.478510 AGAGGCAGACAACGGATACAG 59.521 52.381 0.00 0.00 0.00 2.74
4266 20812 1.204704 CAGAGGCAGACAACGGATACA 59.795 52.381 0.00 0.00 0.00 2.29
4267 20813 1.927895 CAGAGGCAGACAACGGATAC 58.072 55.000 0.00 0.00 0.00 2.24
4268 20814 0.175760 GCAGAGGCAGACAACGGATA 59.824 55.000 0.00 0.00 40.72 2.59
4269 20815 1.078848 GCAGAGGCAGACAACGGAT 60.079 57.895 0.00 0.00 40.72 4.18
4270 20816 1.758440 AAGCAGAGGCAGACAACGGA 61.758 55.000 0.00 0.00 44.61 4.69
4271 20817 0.886490 AAAGCAGAGGCAGACAACGG 60.886 55.000 0.00 0.00 44.61 4.44
4272 20818 1.795768 TAAAGCAGAGGCAGACAACG 58.204 50.000 0.00 0.00 44.61 4.10
4401 21170 5.596836 TTTCTGAACTCATGTTTGCCTTT 57.403 34.783 0.00 0.00 36.39 3.11
4403 21172 5.535333 CATTTTCTGAACTCATGTTTGCCT 58.465 37.500 0.00 0.00 36.39 4.75
4406 21175 5.404366 CAGGCATTTTCTGAACTCATGTTTG 59.596 40.000 0.00 0.00 36.39 2.93
4410 21179 4.778534 ACAGGCATTTTCTGAACTCATG 57.221 40.909 0.00 0.00 36.22 3.07
4422 21191 8.571336 GCAAATATCTACAAGATACAGGCATTT 58.429 33.333 0.00 0.00 39.76 2.32


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

AutoCloner maintained by Alex Coulton.