Multiple sequence alignment - TraesCS2A01G405300

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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 TraesCS2A01G405300 chr2A 100.000 4509 0 0 1 4509 661150262 661154770 0.000000e+00 8327.0
1 TraesCS2A01G405300 chr2A 83.111 1202 127 45 948 2113 661446582 661447743 0.000000e+00 1026.0
2 TraesCS2A01G405300 chr2A 82.892 1134 135 28 2234 3326 661448214 661449329 0.000000e+00 965.0
3 TraesCS2A01G405300 chr2A 80.500 1200 169 31 2173 3316 661082602 661083792 0.000000e+00 859.0
4 TraesCS2A01G405300 chr2A 84.994 833 73 24 1273 2072 661394536 661395349 0.000000e+00 798.0
5 TraesCS2A01G405300 chr2A 82.667 675 70 22 2179 2816 661395342 661396006 5.100000e-154 555.0
6 TraesCS2A01G405300 chr2A 83.469 369 49 8 474 833 661393176 661393541 2.600000e-87 333.0
7 TraesCS2A01G405300 chr2A 90.050 201 20 0 3126 3326 661403477 661403677 1.240000e-65 261.0
8 TraesCS2A01G405300 chr2A 92.778 180 10 1 2866 3042 661396102 661396281 1.610000e-64 257.0
9 TraesCS2A01G405300 chr2A 94.949 99 5 0 4027 4125 535802044 535802142 6.040000e-34 156.0
10 TraesCS2A01G405300 chr2A 80.095 211 31 9 632 832 480935590 480935381 3.630000e-31 147.0
11 TraesCS2A01G405300 chr2D 93.310 2616 124 27 948 3526 516924271 516926872 0.000000e+00 3814.0
12 TraesCS2A01G405300 chr2D 83.081 1188 121 39 948 2104 517086055 517087193 0.000000e+00 1007.0
13 TraesCS2A01G405300 chr2D 81.795 1181 157 34 2179 3315 516863174 516864340 0.000000e+00 937.0
14 TraesCS2A01G405300 chr2D 85.714 756 66 19 1273 2007 517037468 517038202 0.000000e+00 760.0
15 TraesCS2A01G405300 chr2D 84.171 796 96 17 4 794 516923109 516923879 0.000000e+00 745.0
16 TraesCS2A01G405300 chr2D 83.212 685 76 15 2151 2816 517087176 517087840 3.880000e-165 592.0
17 TraesCS2A01G405300 chr2D 87.794 467 48 4 2156 2613 517038200 517038666 5.130000e-149 538.0
18 TraesCS2A01G405300 chr2D 87.064 487 49 5 2846 3326 517087909 517088387 5.130000e-149 538.0
19 TraesCS2A01G405300 chr2D 86.574 432 19 16 3618 4038 516926884 516927287 1.490000e-119 440.0
20 TraesCS2A01G405300 chr2D 79.915 468 66 17 5 463 478696586 478696138 7.280000e-83 318.0
21 TraesCS2A01G405300 chr2D 92.500 200 12 1 2846 3042 517045658 517045857 2.660000e-72 283.0
22 TraesCS2A01G405300 chr2D 96.748 123 4 0 4384 4506 516928891 516929013 5.910000e-49 206.0
23 TraesCS2A01G405300 chr2D 87.425 167 21 0 467 633 516970233 516970399 4.600000e-45 193.0
24 TraesCS2A01G405300 chr2D 91.473 129 11 0 2688 2816 517045445 517045573 1.290000e-40 178.0
25 TraesCS2A01G405300 chr2D 84.762 105 16 0 460 564 516870493 516870597 6.170000e-19 106.0
26 TraesCS2A01G405300 chr2D 94.828 58 3 0 861 918 517085766 517085823 1.730000e-14 91.6
27 TraesCS2A01G405300 chr2B 92.273 1993 91 26 2087 4038 608667943 608669913 0.000000e+00 2769.0
28 TraesCS2A01G405300 chr2B 90.759 2056 107 33 173 2171 608665967 608667996 0.000000e+00 2667.0
29 TraesCS2A01G405300 chr2B 81.403 1183 159 34 2179 3316 608540772 608541938 0.000000e+00 909.0
30 TraesCS2A01G405300 chr2B 85.185 756 67 19 1273 2007 608801994 608802725 0.000000e+00 734.0
31 TraesCS2A01G405300 chr2B 95.408 392 17 1 4119 4509 608669910 608670301 1.380000e-174 623.0
32 TraesCS2A01G405300 chr2B 83.262 699 70 17 2156 2816 608802723 608803412 2.320000e-167 599.0
33 TraesCS2A01G405300 chr2B 88.000 250 29 1 3078 3326 608803767 608804016 1.230000e-75 294.0
34 TraesCS2A01G405300 chr2B 79.849 397 60 12 5 391 169868931 169868545 5.750000e-69 272.0
35 TraesCS2A01G405300 chr2B 86.722 241 18 4 2816 3042 608803457 608803697 5.790000e-64 255.0
36 TraesCS2A01G405300 chr2B 84.058 276 31 8 4 272 561261568 561261837 2.080000e-63 254.0
37 TraesCS2A01G405300 chr2B 78.987 395 51 13 6 389 495911146 495910773 1.620000e-59 241.0
38 TraesCS2A01G405300 chr5A 77.491 813 109 43 1138 1938 419361115 419361865 1.940000e-113 420.0
39 TraesCS2A01G405300 chr5B 80.632 475 65 12 4 462 539599050 539598587 4.320000e-90 342.0
40 TraesCS2A01G405300 chr4A 80.514 467 66 16 4 463 715642324 715641876 7.230000e-88 335.0
41 TraesCS2A01G405300 chr4A 80.573 314 38 11 1770 2072 541336410 541336109 2.110000e-53 220.0
42 TraesCS2A01G405300 chr3A 81.794 379 43 20 4 368 492732469 492732835 1.230000e-75 294.0
43 TraesCS2A01G405300 chr3A 98.876 89 1 0 4034 4122 60843327 60843415 4.670000e-35 159.0
44 TraesCS2A01G405300 chr3A 82.659 173 18 9 672 834 544968034 544968204 4.700000e-30 143.0
45 TraesCS2A01G405300 chr4D 79.750 400 46 14 6 391 49801820 49801442 1.610000e-64 257.0
46 TraesCS2A01G405300 chr4D 93.269 104 6 1 4023 4126 494781688 494781790 7.810000e-33 152.0
47 TraesCS2A01G405300 chr3D 83.582 268 38 3 5 272 526993700 526993439 3.480000e-61 246.0
48 TraesCS2A01G405300 chr1D 76.220 492 73 21 5 475 490554390 490554858 2.110000e-53 220.0
49 TraesCS2A01G405300 chr7D 92.593 108 6 2 4016 4122 70086436 70086542 2.170000e-33 154.0
50 TraesCS2A01G405300 chr7D 88.776 98 11 0 3625 3722 404045822 404045919 2.200000e-23 121.0
51 TraesCS2A01G405300 chr7B 93.204 103 6 1 4020 4122 458165622 458165723 2.810000e-32 150.0
52 TraesCS2A01G405300 chr7B 89.796 98 10 0 3625 3722 413560050 413560147 4.740000e-25 126.0
53 TraesCS2A01G405300 chr6D 94.000 100 5 1 4023 4122 303549105 303549203 2.810000e-32 150.0
54 TraesCS2A01G405300 chr7A 81.250 192 27 7 631 813 127861425 127861616 3.630000e-31 147.0
55 TraesCS2A01G405300 chr7A 80.851 188 27 7 631 809 727826748 727826935 6.080000e-29 139.0
56 TraesCS2A01G405300 chr7A 80.588 170 26 6 672 834 259832012 259831843 1.700000e-24 124.0
57 TraesCS2A01G405300 chr6B 89.565 115 8 4 4011 4125 409930112 409930002 4.700000e-30 143.0
58 TraesCS2A01G405300 chr6B 89.565 115 8 4 4011 4125 409981762 409981652 4.700000e-30 143.0
59 TraesCS2A01G405300 chr6B 89.565 115 8 4 4011 4125 410394229 410394119 4.700000e-30 143.0
60 TraesCS2A01G405300 chr6B 89.583 48 4 1 3524 3571 513155905 513155951 4.870000e-05 60.2
61 TraesCS2A01G405300 chr5D 83.125 160 23 3 632 787 479689679 479689838 4.700000e-30 143.0
62 TraesCS2A01G405300 chr1A 80.203 197 28 8 631 817 25949939 25949744 2.190000e-28 137.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2A01G405300 chr2A 661150262 661154770 4508 False 8327.000000 8327 100.000000 1 4509 1 chr2A.!!$F3 4508
1 TraesCS2A01G405300 chr2A 661446582 661449329 2747 False 995.500000 1026 83.001500 948 3326 2 chr2A.!!$F6 2378
2 TraesCS2A01G405300 chr2A 661082602 661083792 1190 False 859.000000 859 80.500000 2173 3316 1 chr2A.!!$F2 1143
3 TraesCS2A01G405300 chr2A 661393176 661396281 3105 False 485.750000 798 85.977000 474 3042 4 chr2A.!!$F5 2568
4 TraesCS2A01G405300 chr2D 516923109 516929013 5904 False 1301.250000 3814 90.200750 4 4506 4 chr2D.!!$F4 4502
5 TraesCS2A01G405300 chr2D 516863174 516864340 1166 False 937.000000 937 81.795000 2179 3315 1 chr2D.!!$F1 1136
6 TraesCS2A01G405300 chr2D 517037468 517038666 1198 False 649.000000 760 86.754000 1273 2613 2 chr2D.!!$F5 1340
7 TraesCS2A01G405300 chr2D 517085766 517088387 2621 False 557.150000 1007 87.046250 861 3326 4 chr2D.!!$F7 2465
8 TraesCS2A01G405300 chr2B 608665967 608670301 4334 False 2019.666667 2769 92.813333 173 4509 3 chr2B.!!$F3 4336
9 TraesCS2A01G405300 chr2B 608540772 608541938 1166 False 909.000000 909 81.403000 2179 3316 1 chr2B.!!$F2 1137
10 TraesCS2A01G405300 chr2B 608801994 608804016 2022 False 470.500000 734 85.792250 1273 3326 4 chr2B.!!$F4 2053
11 TraesCS2A01G405300 chr5A 419361115 419361865 750 False 420.000000 420 77.491000 1138 1938 1 chr5A.!!$F1 800

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
93 94 0.034059 GTCGATGCCTACATGGAGGG 59.966 60.000 25.94 8.88 41.08 4.30 F
146 147 0.114364 AAGGGGTTGGCGAGGAAATT 59.886 50.000 0.00 0.00 0.00 1.82 F
1302 2194 0.179048 CTTGCAGGGTATCATCGGCA 60.179 55.000 0.00 0.00 32.72 5.69 F
1303 2195 0.473755 TTGCAGGGTATCATCGGCAT 59.526 50.000 0.00 0.00 34.44 4.40 F
1496 2408 0.923403 TTGCGCTCTCGATCGAAATG 59.077 50.000 19.92 12.52 38.10 2.32 F
1709 2628 1.132640 GCATGCACCGTTCGTCTTC 59.867 57.895 14.21 0.00 0.00 2.87 F
3320 4919 1.287739 CCCCAAGATCCCTTGCCTTAA 59.712 52.381 0.00 0.00 46.42 1.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1475 2387 0.388006 TTTCGATCGAGAGCGCAACA 60.388 50.000 18.54 0.00 40.42 3.33 R
1496 2408 1.331138 CATCCGTCACGTAGGTCTCTC 59.669 57.143 0.00 0.00 0.00 3.20 R
3061 4608 0.179215 CCAGAAGACGCGCAAACATC 60.179 55.000 5.73 0.00 0.00 3.06 R
3069 4662 0.242825 TAAGACACCCAGAAGACGCG 59.757 55.000 3.53 3.53 0.00 6.01 R
3330 4932 0.676736 ATCGCCTTCTACCTGCTAGC 59.323 55.000 8.10 8.10 0.00 3.42 R
3355 4978 1.665282 ACACATAAACACGCGCGGA 60.665 52.632 35.22 13.81 0.00 5.54 R
4402 7387 2.017049 CTTCCGGCTTTCATGTTAGGG 58.983 52.381 0.00 0.00 0.00 3.53 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
29 30 0.962855 CAGCTCCGACTCTGACCTGA 60.963 60.000 0.00 0.00 32.26 3.86
36 37 1.924320 GACTCTGACCTGACGGACGG 61.924 65.000 0.00 0.00 33.35 4.79
79 80 4.796231 GCACCTCCGCACGTCGAT 62.796 66.667 0.00 0.00 41.67 3.59
87 88 1.588932 CGCACGTCGATGCCTACAT 60.589 57.895 4.06 0.00 42.99 2.29
88 89 1.811217 CGCACGTCGATGCCTACATG 61.811 60.000 4.06 0.00 42.99 3.21
93 94 0.034059 GTCGATGCCTACATGGAGGG 59.966 60.000 25.94 8.88 41.08 4.30
115 116 2.887568 GGGACAGCTGCATCGACG 60.888 66.667 15.27 0.00 0.00 5.12
133 134 1.541620 GACCTGAAGGGGAAGGGGT 60.542 63.158 0.56 0.00 40.27 4.95
134 135 1.072143 ACCTGAAGGGGAAGGGGTT 60.072 57.895 0.56 0.00 40.27 4.11
138 139 3.938637 GAAGGGGAAGGGGTTGGCG 62.939 68.421 0.00 0.00 0.00 5.69
146 147 0.114364 AAGGGGTTGGCGAGGAAATT 59.886 50.000 0.00 0.00 0.00 1.82
245 253 2.027625 CTGTCCGCCGTTGAACTCC 61.028 63.158 0.00 0.00 0.00 3.85
271 279 2.973945 ACTATGTTCCTCTTGTTCGGC 58.026 47.619 0.00 0.00 0.00 5.54
272 280 2.301870 ACTATGTTCCTCTTGTTCGGCA 59.698 45.455 0.00 0.00 0.00 5.69
296 304 7.760794 GCAATGAAATGTTGATCCATTGAACTA 59.239 33.333 17.48 0.00 43.87 2.24
316 324 6.012658 ACTACGCATTGATCATGTTTTTGT 57.987 33.333 0.00 0.00 34.98 2.83
379 387 4.215109 GGGTGTGGAAGGCAACATATAAT 58.785 43.478 0.00 0.00 41.41 1.28
382 390 5.221048 GGTGTGGAAGGCAACATATAATGTC 60.221 44.000 0.00 0.00 44.07 3.06
395 412 0.908910 TAATGTCAGTGCCCGTGGAT 59.091 50.000 0.00 0.00 0.00 3.41
405 422 2.028190 CCGTGGATGCGCCTAGAG 59.972 66.667 4.18 0.00 37.63 2.43
462 479 2.158900 GCCTGGCTGTAGATGCTCTTAA 60.159 50.000 12.43 0.00 0.00 1.85
471 488 7.605691 GGCTGTAGATGCTCTTAATGATGTATT 59.394 37.037 0.00 0.00 0.00 1.89
516 534 6.512741 GCATTTGGTGAGAGAAAACTTACGAA 60.513 38.462 0.00 0.00 0.00 3.85
519 537 6.539649 TGGTGAGAGAAAACTTACGAAATG 57.460 37.500 0.00 0.00 0.00 2.32
522 540 6.347483 GGTGAGAGAAAACTTACGAAATGTCC 60.347 42.308 0.00 0.00 0.00 4.02
690 714 8.416329 AGATGGTCAATTTTTATAAGATGGCAC 58.584 33.333 0.00 0.00 0.00 5.01
849 960 5.975988 ATCATACTCCCAATACAACCAGT 57.024 39.130 0.00 0.00 0.00 4.00
859 970 6.380274 TCCCAATACAACCAGTCTACTAAGAG 59.620 42.308 0.00 0.00 30.45 2.85
921 1443 1.513178 CATCTGCGTGATCGAACGTAC 59.487 52.381 10.99 0.00 45.32 3.67
924 1446 1.917955 CTGCGTGATCGAACGTACATT 59.082 47.619 10.99 0.00 45.32 2.71
926 1448 3.500014 TGCGTGATCGAACGTACATTTA 58.500 40.909 10.99 0.00 45.32 1.40
927 1449 3.544682 TGCGTGATCGAACGTACATTTAG 59.455 43.478 10.99 0.00 45.32 1.85
928 1450 3.598670 GCGTGATCGAACGTACATTTAGC 60.599 47.826 10.99 0.00 45.32 3.09
929 1451 3.544682 CGTGATCGAACGTACATTTAGCA 59.455 43.478 1.48 0.00 38.74 3.49
931 1453 5.276207 CGTGATCGAACGTACATTTAGCATT 60.276 40.000 1.48 0.00 38.74 3.56
932 1454 6.075257 CGTGATCGAACGTACATTTAGCATTA 60.075 38.462 1.48 0.00 38.74 1.90
933 1455 7.055598 GTGATCGAACGTACATTTAGCATTAC 58.944 38.462 0.00 0.00 0.00 1.89
935 1457 6.801367 TCGAACGTACATTTAGCATTACTC 57.199 37.500 0.00 0.00 0.00 2.59
936 1458 6.558009 TCGAACGTACATTTAGCATTACTCT 58.442 36.000 0.00 0.00 0.00 3.24
987 1848 9.886132 GTACATATATATACCCCCACAGAAAAG 57.114 37.037 0.00 0.00 0.00 2.27
1054 1915 1.185618 TGCAGCGACAGTAGGGACTT 61.186 55.000 0.00 0.00 41.75 3.01
1095 1956 2.280823 GACGACCTTACGAGCCCCTG 62.281 65.000 0.00 0.00 37.03 4.45
1169 2054 4.445385 GCATTTCACAAAGTTTGCTCGAAT 59.555 37.500 15.59 8.07 0.00 3.34
1224 2116 1.909700 AACAACCACTATGTGCTGGG 58.090 50.000 0.00 0.00 31.34 4.45
1282 2174 6.452090 CGTGTGAGACGTGCTTACTAATTAAC 60.452 42.308 0.00 0.00 43.50 2.01
1298 2190 6.998673 ACTAATTAACCTTGCAGGGTATCATC 59.001 38.462 22.32 0.00 37.41 2.92
1299 2191 2.332063 AACCTTGCAGGGTATCATCG 57.668 50.000 22.32 0.00 40.58 3.84
1300 2192 0.469917 ACCTTGCAGGGTATCATCGG 59.530 55.000 20.60 0.00 40.58 4.18
1301 2193 0.886490 CCTTGCAGGGTATCATCGGC 60.886 60.000 6.72 0.00 0.00 5.54
1302 2194 0.179048 CTTGCAGGGTATCATCGGCA 60.179 55.000 0.00 0.00 32.72 5.69
1303 2195 0.473755 TTGCAGGGTATCATCGGCAT 59.526 50.000 0.00 0.00 34.44 4.40
1496 2408 0.923403 TTGCGCTCTCGATCGAAATG 59.077 50.000 19.92 12.52 38.10 2.32
1709 2628 1.132640 GCATGCACCGTTCGTCTTC 59.867 57.895 14.21 0.00 0.00 2.87
1730 2649 7.504238 GTCTTCCCTGATCTTGTCTTAGATCTA 59.496 40.741 13.10 0.00 46.94 1.98
1978 2922 4.442706 ACTCGTCTCTTGCAAGAAAGAAA 58.557 39.130 28.16 13.92 35.79 2.52
1985 2929 8.070171 CGTCTCTTGCAAGAAAGAAAGAAAATA 58.930 33.333 28.16 2.76 35.79 1.40
2479 3890 3.545481 CGACGGCGTGCACATCTC 61.545 66.667 21.19 0.00 0.00 2.75
2483 3894 2.359850 GGCGTGCACATCTCCCAA 60.360 61.111 18.64 0.00 0.00 4.12
2490 3901 2.622942 GTGCACATCTCCCAAAGTGAAA 59.377 45.455 13.17 0.00 33.99 2.69
2622 4037 4.775664 CGTAAGGTAACAAAGGTTTTCCG 58.224 43.478 0.00 0.00 42.67 4.30
2686 4134 2.288642 AATGATGTGATGGCCGGGCT 62.289 55.000 29.87 14.71 0.00 5.19
2782 4230 2.910688 ACGTCCACTTCATCAACACT 57.089 45.000 0.00 0.00 0.00 3.55
2827 4325 3.884900 CAGGTAAACCGGCCTTCG 58.115 61.111 0.00 0.00 42.08 3.79
2843 4341 3.550436 GCCTTCGCTTACTAACGAGCTAT 60.550 47.826 0.00 0.00 39.81 2.97
2853 4375 1.320344 AACGAGCTATCTGACGCCCA 61.320 55.000 0.00 0.00 0.00 5.36
2876 4398 4.271049 AGGTGATCATATTGTTTCTTCGCG 59.729 41.667 0.00 0.00 0.00 5.87
2977 4499 5.186215 TCATCAACCAATTCTACGTAGACCA 59.814 40.000 24.60 12.01 30.81 4.02
3042 4578 3.272581 TGGACGATCTGTATACGTGTGA 58.727 45.455 0.00 0.00 40.29 3.58
3043 4579 3.881089 TGGACGATCTGTATACGTGTGAT 59.119 43.478 0.00 0.00 40.29 3.06
3044 4580 4.219802 GGACGATCTGTATACGTGTGATG 58.780 47.826 0.00 0.00 40.29 3.07
3045 4581 4.261072 GGACGATCTGTATACGTGTGATGT 60.261 45.833 0.00 0.00 40.29 3.06
3046 4582 4.598062 ACGATCTGTATACGTGTGATGTG 58.402 43.478 0.00 0.00 38.79 3.21
3059 4606 2.831526 TGTGATGTGGAGCAGCTAGTAA 59.168 45.455 0.00 0.00 34.02 2.24
3061 4608 3.806521 GTGATGTGGAGCAGCTAGTAATG 59.193 47.826 0.00 0.00 34.02 1.90
3069 4662 4.260948 GGAGCAGCTAGTAATGATGTTTGC 60.261 45.833 0.00 0.00 0.00 3.68
3181 4777 2.954753 GCCGTGGACTTCAACTGCG 61.955 63.158 0.00 0.00 0.00 5.18
3219 4815 3.770666 CACGAATATCCACGTCAACTCT 58.229 45.455 0.00 0.00 40.76 3.24
3320 4919 1.287739 CCCCAAGATCCCTTGCCTTAA 59.712 52.381 0.00 0.00 46.42 1.85
3355 4978 2.362717 GCAGGTAGAAGGCGATCTAAGT 59.637 50.000 4.91 0.00 33.86 2.24
3430 5053 0.251608 GTGGCAGTGGTATTGGGGTT 60.252 55.000 0.00 0.00 0.00 4.11
3433 5056 1.549037 GGCAGTGGTATTGGGGTTGAA 60.549 52.381 0.00 0.00 0.00 2.69
3466 5090 8.019669 CGAATGAATCTTTTTGACAGACTTCAT 58.980 33.333 0.00 0.00 34.01 2.57
3528 5152 7.787725 ATCCGGAATCAGTTGTTTATTACTC 57.212 36.000 9.01 0.00 0.00 2.59
3530 5154 5.296035 CCGGAATCAGTTGTTTATTACTCCC 59.704 44.000 0.00 0.00 0.00 4.30
3533 5157 7.339482 GGAATCAGTTGTTTATTACTCCCTCT 58.661 38.462 0.00 0.00 0.00 3.69
3536 5160 6.698380 TCAGTTGTTTATTACTCCCTCTGTC 58.302 40.000 0.00 0.00 0.00 3.51
3538 5162 5.785940 AGTTGTTTATTACTCCCTCTGTCCT 59.214 40.000 0.00 0.00 0.00 3.85
3553 5177 7.453752 TCCCTCTGTCCTATAATATAAAAGCGT 59.546 37.037 0.00 0.00 0.00 5.07
3586 5210 8.737175 ACATTAGTATAGTGTCGAAAACTCTCA 58.263 33.333 5.34 0.00 36.80 3.27
3608 5232 7.067615 TCTCATATATTATGAGACGGAGGAAGC 59.932 40.741 18.66 0.00 46.66 3.86
3629 5257 6.005583 AGCATTTGACACAACTTATGTCTG 57.994 37.500 2.01 0.00 45.58 3.51
3678 5306 6.500684 ACAGAAATTCAACGCATATGTCTT 57.499 33.333 4.29 0.00 0.00 3.01
3697 5325 3.064820 TCTTGGTGAAAAGTCAACTTCGC 59.935 43.478 0.00 0.00 42.46 4.70
3753 5388 5.398126 GGGTATATTCATGTGGGTTGTACCA 60.398 44.000 0.00 0.00 41.02 3.25
3768 5403 6.597562 GGTTGTACCATATAACCAATCCAGA 58.402 40.000 9.02 0.00 45.83 3.86
3888 5526 5.481105 AGAAATTCATGTACGGACGGTTTA 58.519 37.500 0.00 0.00 0.00 2.01
4006 5645 4.637534 AGAAGGACATCATTTGATCAACCG 59.362 41.667 7.89 2.12 31.21 4.44
4046 5685 8.582437 TGAATTGTTTATATAGTACTCCCTCCG 58.418 37.037 0.00 0.00 0.00 4.63
4047 5686 8.488308 AATTGTTTATATAGTACTCCCTCCGT 57.512 34.615 0.00 0.00 0.00 4.69
4048 5687 7.902920 TTGTTTATATAGTACTCCCTCCGTT 57.097 36.000 0.00 0.00 0.00 4.44
4049 5688 7.516198 TGTTTATATAGTACTCCCTCCGTTC 57.484 40.000 0.00 0.00 0.00 3.95
4050 5689 6.491403 TGTTTATATAGTACTCCCTCCGTTCC 59.509 42.308 0.00 0.00 0.00 3.62
4051 5690 4.736611 ATATAGTACTCCCTCCGTTCCA 57.263 45.455 0.00 0.00 0.00 3.53
4052 5691 3.614568 ATAGTACTCCCTCCGTTCCAT 57.385 47.619 0.00 0.00 0.00 3.41
4053 5692 4.736611 ATAGTACTCCCTCCGTTCCATA 57.263 45.455 0.00 0.00 0.00 2.74
4054 5693 3.614568 AGTACTCCCTCCGTTCCATAT 57.385 47.619 0.00 0.00 0.00 1.78
4055 5694 3.924922 AGTACTCCCTCCGTTCCATATT 58.075 45.455 0.00 0.00 0.00 1.28
4056 5695 5.070823 AGTACTCCCTCCGTTCCATATTA 57.929 43.478 0.00 0.00 0.00 0.98
4057 5696 5.652324 AGTACTCCCTCCGTTCCATATTAT 58.348 41.667 0.00 0.00 0.00 1.28
4058 5697 6.082707 AGTACTCCCTCCGTTCCATATTATT 58.917 40.000 0.00 0.00 0.00 1.40
4059 5698 5.906772 ACTCCCTCCGTTCCATATTATTT 57.093 39.130 0.00 0.00 0.00 1.40
4060 5699 5.621193 ACTCCCTCCGTTCCATATTATTTG 58.379 41.667 0.00 0.00 0.00 2.32
4061 5700 5.132144 ACTCCCTCCGTTCCATATTATTTGT 59.868 40.000 0.00 0.00 0.00 2.83
4062 5701 5.617252 TCCCTCCGTTCCATATTATTTGTC 58.383 41.667 0.00 0.00 0.00 3.18
4063 5702 4.451096 CCCTCCGTTCCATATTATTTGTCG 59.549 45.833 0.00 0.00 0.00 4.35
4064 5703 5.054477 CCTCCGTTCCATATTATTTGTCGT 58.946 41.667 0.00 0.00 0.00 4.34
4065 5704 5.050363 CCTCCGTTCCATATTATTTGTCGTG 60.050 44.000 0.00 0.00 0.00 4.35
4066 5705 4.812091 TCCGTTCCATATTATTTGTCGTGG 59.188 41.667 0.00 0.00 0.00 4.94
4067 5706 4.573201 CCGTTCCATATTATTTGTCGTGGT 59.427 41.667 0.00 0.00 0.00 4.16
4068 5707 5.065474 CCGTTCCATATTATTTGTCGTGGTT 59.935 40.000 0.00 0.00 0.00 3.67
4069 5708 6.403855 CCGTTCCATATTATTTGTCGTGGTTT 60.404 38.462 0.00 0.00 0.00 3.27
4070 5709 7.024768 CGTTCCATATTATTTGTCGTGGTTTT 58.975 34.615 0.00 0.00 0.00 2.43
4071 5710 8.176365 CGTTCCATATTATTTGTCGTGGTTTTA 58.824 33.333 0.00 0.00 0.00 1.52
4072 5711 9.498307 GTTCCATATTATTTGTCGTGGTTTTAG 57.502 33.333 0.00 0.00 0.00 1.85
4073 5712 8.795842 TCCATATTATTTGTCGTGGTTTTAGT 57.204 30.769 0.00 0.00 0.00 2.24
4074 5713 9.233649 TCCATATTATTTGTCGTGGTTTTAGTT 57.766 29.630 0.00 0.00 0.00 2.24
4075 5714 9.498307 CCATATTATTTGTCGTGGTTTTAGTTC 57.502 33.333 0.00 0.00 0.00 3.01
4079 5718 9.974980 ATTATTTGTCGTGGTTTTAGTTCAAAT 57.025 25.926 0.00 0.00 37.75 2.32
4080 5719 9.804758 TTATTTGTCGTGGTTTTAGTTCAAATT 57.195 25.926 0.00 0.00 36.28 1.82
4081 5720 8.710835 ATTTGTCGTGGTTTTAGTTCAAATTT 57.289 26.923 0.00 0.00 32.73 1.82
4082 5721 7.513190 TTGTCGTGGTTTTAGTTCAAATTTG 57.487 32.000 12.15 12.15 0.00 2.32
4083 5722 6.853720 TGTCGTGGTTTTAGTTCAAATTTGA 58.146 32.000 16.91 16.91 34.92 2.69
4084 5723 7.313646 TGTCGTGGTTTTAGTTCAAATTTGAA 58.686 30.769 26.01 26.01 44.31 2.69
4097 5736 7.743520 TTCAAATTTGAACTAAAACCACGAC 57.256 32.000 26.01 0.00 41.88 4.34
4098 5737 6.853720 TCAAATTTGAACTAAAACCACGACA 58.146 32.000 18.45 0.00 33.55 4.35
4099 5738 7.313646 TCAAATTTGAACTAAAACCACGACAA 58.686 30.769 18.45 0.00 33.55 3.18
4100 5739 7.486551 TCAAATTTGAACTAAAACCACGACAAG 59.513 33.333 18.45 0.00 33.55 3.16
4101 5740 5.883503 TTTGAACTAAAACCACGACAAGT 57.116 34.783 0.00 0.00 0.00 3.16
4102 5741 6.981762 TTTGAACTAAAACCACGACAAGTA 57.018 33.333 0.00 0.00 0.00 2.24
4103 5742 6.981762 TTGAACTAAAACCACGACAAGTAA 57.018 33.333 0.00 0.00 0.00 2.24
4104 5743 7.556733 TTGAACTAAAACCACGACAAGTAAT 57.443 32.000 0.00 0.00 0.00 1.89
4105 5744 7.556733 TGAACTAAAACCACGACAAGTAATT 57.443 32.000 0.00 0.00 0.00 1.40
4106 5745 7.987649 TGAACTAAAACCACGACAAGTAATTT 58.012 30.769 0.00 0.00 0.00 1.82
4107 5746 7.911205 TGAACTAAAACCACGACAAGTAATTTG 59.089 33.333 0.00 0.00 42.68 2.32
4108 5747 6.731164 ACTAAAACCACGACAAGTAATTTGG 58.269 36.000 0.00 0.00 41.25 3.28
4109 5748 5.838531 AAAACCACGACAAGTAATTTGGA 57.161 34.783 0.00 0.00 41.25 3.53
4110 5749 5.838531 AAACCACGACAAGTAATTTGGAA 57.161 34.783 0.00 0.00 41.25 3.53
4111 5750 4.823790 ACCACGACAAGTAATTTGGAAC 57.176 40.909 0.00 0.00 41.25 3.62
4112 5751 3.249080 ACCACGACAAGTAATTTGGAACG 59.751 43.478 0.00 0.00 41.25 3.95
4113 5752 3.364565 CCACGACAAGTAATTTGGAACGG 60.365 47.826 0.00 0.00 41.25 4.44
4114 5753 3.495377 CACGACAAGTAATTTGGAACGGA 59.505 43.478 0.00 0.00 41.25 4.69
4115 5754 3.744426 ACGACAAGTAATTTGGAACGGAG 59.256 43.478 0.00 0.00 41.25 4.63
4116 5755 3.124636 CGACAAGTAATTTGGAACGGAGG 59.875 47.826 0.00 0.00 41.25 4.30
4117 5756 3.418047 ACAAGTAATTTGGAACGGAGGG 58.582 45.455 0.00 0.00 41.25 4.30
4131 5770 2.561858 ACGGAGGGAGTAGTTCTCAAAC 59.438 50.000 0.00 0.00 44.40 2.93
4179 5818 9.543018 GAAACTTCATGTAAGAAAAACCTATCG 57.457 33.333 10.61 0.00 38.67 2.92
4281 5920 3.919223 AGTAGACTTCACCGTGACTTC 57.081 47.619 0.00 0.66 0.00 3.01
4323 5962 6.627395 TTCTGAAACTTGCCTCGAAAAATA 57.373 33.333 0.00 0.00 0.00 1.40
4337 5976 7.625553 CCTCGAAAAATATGTCTGAAGATCAC 58.374 38.462 0.00 0.00 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.048222 CGGAGCTGCACCTTTCGA 60.048 61.111 14.15 0.00 0.00 3.71
1 2 2.048222 TCGGAGCTGCACCTTTCG 60.048 61.111 14.15 0.00 0.00 3.46
2 3 1.004440 AGTCGGAGCTGCACCTTTC 60.004 57.895 14.15 4.60 0.00 2.62
16 17 1.502640 GTCCGTCAGGTCAGAGTCG 59.497 63.158 0.00 0.00 39.05 4.18
41 42 1.136391 GTCGTCGTCGTAGCTATAGGC 60.136 57.143 0.00 0.00 38.60 3.93
45 46 1.275066 GCGTCGTCGTCGTAGCTAT 59.725 57.895 13.09 0.00 39.49 2.97
51 52 4.380628 GAGGTGCGTCGTCGTCGT 62.381 66.667 13.09 0.00 39.49 4.34
69 70 1.588932 ATGTAGGCATCGACGTGCG 60.589 57.895 13.58 0.00 45.97 5.34
75 76 1.121407 CCCCTCCATGTAGGCATCGA 61.121 60.000 0.00 0.00 37.29 3.59
98 99 2.887568 CGTCGATGCAGCTGTCCC 60.888 66.667 16.64 3.50 0.00 4.46
99 100 2.161486 GTCGTCGATGCAGCTGTCC 61.161 63.158 16.64 0.00 0.00 4.02
100 101 2.161486 GGTCGTCGATGCAGCTGTC 61.161 63.158 16.64 8.39 0.00 3.51
102 103 2.163390 CAGGTCGTCGATGCAGCTG 61.163 63.158 10.11 10.11 0.00 4.24
103 104 1.877576 TTCAGGTCGTCGATGCAGCT 61.878 55.000 0.00 1.59 0.00 4.24
104 105 1.416813 CTTCAGGTCGTCGATGCAGC 61.417 60.000 0.00 0.00 0.00 5.25
105 106 0.803768 CCTTCAGGTCGTCGATGCAG 60.804 60.000 0.00 0.00 0.00 4.41
106 107 1.215382 CCTTCAGGTCGTCGATGCA 59.785 57.895 0.00 0.00 0.00 3.96
109 110 0.613853 TTCCCCTTCAGGTCGTCGAT 60.614 55.000 0.00 0.00 0.00 3.59
110 111 1.228644 TTCCCCTTCAGGTCGTCGA 60.229 57.895 0.00 0.00 0.00 4.20
111 112 1.215647 CTTCCCCTTCAGGTCGTCG 59.784 63.158 0.00 0.00 0.00 5.12
112 113 1.597461 CCTTCCCCTTCAGGTCGTC 59.403 63.158 0.00 0.00 0.00 4.20
115 116 1.140772 AACCCCTTCCCCTTCAGGTC 61.141 60.000 0.00 0.00 0.00 3.85
133 134 4.173036 GAAATCACAATTTCCTCGCCAA 57.827 40.909 0.41 0.00 43.30 4.52
134 135 3.848272 GAAATCACAATTTCCTCGCCA 57.152 42.857 0.41 0.00 43.30 5.69
146 147 0.035439 GAAGGGCGGAGGAAATCACA 60.035 55.000 0.00 0.00 0.00 3.58
245 253 5.004821 CGAACAAGAGGAACATAGTTCATCG 59.995 44.000 15.89 7.93 36.16 3.84
271 279 9.079833 GTAGTTCAATGGATCAACATTTCATTG 57.920 33.333 10.57 10.57 43.31 2.82
272 280 7.970061 CGTAGTTCAATGGATCAACATTTCATT 59.030 33.333 0.00 0.00 38.94 2.57
296 304 4.619973 ACACAAAAACATGATCAATGCGT 58.380 34.783 0.00 0.00 40.22 5.24
316 324 2.419673 CCTCAAATCATGCAACGCTACA 59.580 45.455 0.00 0.00 0.00 2.74
379 387 2.347114 CATCCACGGGCACTGACA 59.653 61.111 0.00 0.00 38.67 3.58
401 418 3.884350 CGCCTGCGTACGCCTCTA 61.884 66.667 35.11 17.31 41.09 2.43
414 431 4.394712 CCGGCCTCTCAAACGCCT 62.395 66.667 0.00 0.00 40.70 5.52
516 534 2.665649 TAACATCGAGCGTGGACATT 57.334 45.000 0.00 0.00 0.00 2.71
519 537 2.273370 TCTTAACATCGAGCGTGGAC 57.727 50.000 0.00 0.00 0.00 4.02
522 540 8.227731 TGATATTAATCTTAACATCGAGCGTG 57.772 34.615 0.00 0.00 31.00 5.34
590 608 8.748380 TTCATAGTCAAAGATATGATGTAGCG 57.252 34.615 0.00 0.00 38.02 4.26
617 635 4.139786 TCTCATTACGGTTAGGCGTATCT 58.860 43.478 0.00 0.00 0.00 1.98
666 690 8.076910 TGTGCCATCTTATAAAAATTGACCAT 57.923 30.769 0.00 0.00 0.00 3.55
668 692 8.770438 TTTGTGCCATCTTATAAAAATTGACC 57.230 30.769 0.00 0.00 0.00 4.02
839 950 5.191426 TCGCTCTTAGTAGACTGGTTGTAT 58.809 41.667 0.00 0.00 0.00 2.29
849 960 7.868922 TGTGTAAACAATTTCGCTCTTAGTAGA 59.131 33.333 0.00 0.00 0.00 2.59
859 970 7.530190 CCAAATTGAATGTGTAAACAATTTCGC 59.470 33.333 0.00 0.00 45.06 4.70
921 1443 6.199908 CGGAAGTCTCAGAGTAATGCTAAATG 59.800 42.308 0.00 0.00 0.00 2.32
924 1446 4.098044 CCGGAAGTCTCAGAGTAATGCTAA 59.902 45.833 0.00 0.00 0.00 3.09
926 1448 2.428890 CCGGAAGTCTCAGAGTAATGCT 59.571 50.000 0.00 0.00 0.00 3.79
927 1449 2.427453 TCCGGAAGTCTCAGAGTAATGC 59.573 50.000 0.00 0.00 0.00 3.56
928 1450 3.487711 CGTCCGGAAGTCTCAGAGTAATG 60.488 52.174 5.23 0.00 0.00 1.90
929 1451 2.683867 CGTCCGGAAGTCTCAGAGTAAT 59.316 50.000 5.23 0.00 0.00 1.89
931 1453 1.735386 CGTCCGGAAGTCTCAGAGTA 58.265 55.000 5.23 0.00 0.00 2.59
932 1454 1.587933 GCGTCCGGAAGTCTCAGAGT 61.588 60.000 18.88 0.00 0.00 3.24
933 1455 1.137825 GCGTCCGGAAGTCTCAGAG 59.862 63.158 18.88 0.00 0.00 3.35
935 1457 0.456995 GAAGCGTCCGGAAGTCTCAG 60.457 60.000 18.88 0.22 0.00 3.35
936 1458 0.894184 AGAAGCGTCCGGAAGTCTCA 60.894 55.000 18.88 0.00 0.00 3.27
964 1825 7.402054 TGCTTTTCTGTGGGGGTATATATATG 58.598 38.462 5.44 0.00 0.00 1.78
965 1826 7.582909 TGCTTTTCTGTGGGGGTATATATAT 57.417 36.000 0.00 0.00 0.00 0.86
987 1848 4.333926 AGCTCTGTTTCGATCCTAAAATGC 59.666 41.667 0.00 0.00 0.00 3.56
1001 1862 2.057137 TCAAGTGCCAAGCTCTGTTT 57.943 45.000 0.00 0.00 32.56 2.83
1054 1915 1.537638 ACACGTGCAAAACTGTTGTGA 59.462 42.857 17.22 0.00 0.00 3.58
1095 1956 6.812998 TCAAGTTAGTATGTACCATAGGTGC 58.187 40.000 0.00 0.00 38.78 5.01
1301 2193 4.552365 AGGATGGCCGTGCGGATG 62.552 66.667 15.45 0.00 39.96 3.51
1302 2194 4.552365 CAGGATGGCCGTGCGGAT 62.552 66.667 15.45 0.00 39.96 4.18
1427 2328 0.516877 TACGTACCTTGGTGTCGTCG 59.483 55.000 20.69 11.98 36.24 5.12
1475 2387 0.388006 TTTCGATCGAGAGCGCAACA 60.388 50.000 18.54 0.00 40.42 3.33
1496 2408 1.331138 CATCCGTCACGTAGGTCTCTC 59.669 57.143 0.00 0.00 0.00 3.20
1960 2904 9.905171 ATATTTTCTTTCTTTCTTGCAAGAGAC 57.095 29.630 27.02 0.00 36.22 3.36
2079 3028 4.458989 GGTGAGTGGAAACTGATAAATGCA 59.541 41.667 0.00 0.00 0.00 3.96
2253 3654 3.436700 TGCACGTCGATCTATGAATGT 57.563 42.857 0.00 0.00 0.00 2.71
2450 3861 3.697747 CCGTCGGTGTTGGGGCTA 61.698 66.667 2.08 0.00 0.00 3.93
2478 3889 2.018515 GTGGACGTTTTCACTTTGGGA 58.981 47.619 9.40 0.00 0.00 4.37
2479 3890 1.268335 CGTGGACGTTTTCACTTTGGG 60.268 52.381 13.13 0.00 34.11 4.12
2622 4037 1.997669 AGAGGAAAACGCAGATCGAC 58.002 50.000 0.00 0.00 41.67 4.20
2686 4134 3.380004 CCACACTAGCCAAGAAACACAAA 59.620 43.478 0.00 0.00 0.00 2.83
2782 4230 3.011144 TCTTGATCCTTGCCCCATTTGTA 59.989 43.478 0.00 0.00 0.00 2.41
2827 4325 4.212911 CGTCAGATAGCTCGTTAGTAAGC 58.787 47.826 0.00 0.00 38.84 3.09
2843 4341 0.977627 ATGATCACCTGGGCGTCAGA 60.978 55.000 0.00 0.00 46.18 3.27
2853 4375 4.271049 CGCGAAGAAACAATATGATCACCT 59.729 41.667 0.00 0.00 0.00 4.00
2876 4398 2.677875 CCTTTCCCACCCTGCAGC 60.678 66.667 8.66 0.00 0.00 5.25
2977 4499 3.030873 CCATATTTGGGACATGGTGGT 57.969 47.619 0.00 0.00 39.30 4.16
3042 4578 4.102210 ACATCATTACTAGCTGCTCCACAT 59.898 41.667 4.91 0.00 0.00 3.21
3043 4579 3.452264 ACATCATTACTAGCTGCTCCACA 59.548 43.478 4.91 0.00 0.00 4.17
3044 4580 4.065321 ACATCATTACTAGCTGCTCCAC 57.935 45.455 4.91 0.00 0.00 4.02
3045 4581 4.760530 AACATCATTACTAGCTGCTCCA 57.239 40.909 4.91 0.00 0.00 3.86
3046 4582 4.260948 GCAAACATCATTACTAGCTGCTCC 60.261 45.833 4.91 0.00 0.00 4.70
3059 4606 1.129251 CAGAAGACGCGCAAACATCAT 59.871 47.619 5.73 0.00 0.00 2.45
3061 4608 0.179215 CCAGAAGACGCGCAAACATC 60.179 55.000 5.73 0.00 0.00 3.06
3069 4662 0.242825 TAAGACACCCAGAAGACGCG 59.757 55.000 3.53 3.53 0.00 6.01
3112 4708 5.049954 GGTTCTTGTACGTTATGTTGCTCAA 60.050 40.000 0.00 0.00 0.00 3.02
3320 4919 8.261522 GCCTTCTACCTGCTAGCTATTATTATT 58.738 37.037 17.23 0.00 0.00 1.40
3330 4932 0.676736 ATCGCCTTCTACCTGCTAGC 59.323 55.000 8.10 8.10 0.00 3.42
3355 4978 1.665282 ACACATAAACACGCGCGGA 60.665 52.632 35.22 13.81 0.00 5.54
3390 5013 6.210784 GCCACCCCTTCTCTTACTTTAAAAAT 59.789 38.462 0.00 0.00 0.00 1.82
3430 5053 5.437289 AAAGATTCATTCGCAACTGTTCA 57.563 34.783 0.00 0.00 0.00 3.18
3433 5056 5.687285 GTCAAAAAGATTCATTCGCAACTGT 59.313 36.000 0.00 0.00 0.00 3.55
3466 5090 7.230510 AGTCTACCAGTGTGCAATGAAAATTTA 59.769 33.333 0.89 0.00 0.00 1.40
3528 5152 7.612677 ACGCTTTTATATTATAGGACAGAGGG 58.387 38.462 0.00 0.00 0.00 4.30
3586 5210 7.667575 ATGCTTCCTCCGTCTCATAATATAT 57.332 36.000 0.00 0.00 0.00 0.86
3593 5217 2.237143 TCAAATGCTTCCTCCGTCTCAT 59.763 45.455 0.00 0.00 0.00 2.90
3608 5232 5.048504 AGCCAGACATAAGTTGTGTCAAATG 60.049 40.000 27.93 19.29 46.46 2.32
3629 5257 5.700722 TGATGCATCAGATTTTGATAGCC 57.299 39.130 25.42 0.00 44.76 3.93
3678 5306 2.360844 TGCGAAGTTGACTTTTCACCA 58.639 42.857 0.00 0.00 36.11 4.17
3697 5325 5.886715 TGATTTTGAACTTGCAACGATTG 57.113 34.783 0.00 0.00 0.00 2.67
3753 5388 6.006275 AGTGCAGTTCTGGATTGGTTATAT 57.994 37.500 0.00 0.00 0.00 0.86
3768 5403 6.607600 TCATAATACTACAGGAGAGTGCAGTT 59.392 38.462 0.00 0.00 0.00 3.16
3804 5439 2.092914 ACTTTGATAGCACTACCCAGGC 60.093 50.000 0.00 0.00 0.00 4.85
3837 5475 7.732222 AATGGGTGCAAAATAGGAAATTCTA 57.268 32.000 0.00 0.00 0.00 2.10
3911 5549 2.078849 TCTGTCTGTGCACGTTATGG 57.921 50.000 13.13 0.88 0.00 2.74
4034 5673 3.614568 ATATGGAACGGAGGGAGTACT 57.385 47.619 0.00 0.00 0.00 2.73
4035 5674 5.997384 ATAATATGGAACGGAGGGAGTAC 57.003 43.478 0.00 0.00 0.00 2.73
4036 5675 6.328148 ACAAATAATATGGAACGGAGGGAGTA 59.672 38.462 0.00 0.00 0.00 2.59
4037 5676 5.132144 ACAAATAATATGGAACGGAGGGAGT 59.868 40.000 0.00 0.00 0.00 3.85
4038 5677 5.621193 ACAAATAATATGGAACGGAGGGAG 58.379 41.667 0.00 0.00 0.00 4.30
4039 5678 5.617252 GACAAATAATATGGAACGGAGGGA 58.383 41.667 0.00 0.00 0.00 4.20
4040 5679 4.451096 CGACAAATAATATGGAACGGAGGG 59.549 45.833 0.00 0.00 0.00 4.30
4041 5680 5.050363 CACGACAAATAATATGGAACGGAGG 60.050 44.000 0.00 0.00 0.00 4.30
4042 5681 5.050363 CCACGACAAATAATATGGAACGGAG 60.050 44.000 0.00 0.00 0.00 4.63
4043 5682 4.812091 CCACGACAAATAATATGGAACGGA 59.188 41.667 0.00 0.00 0.00 4.69
4044 5683 4.573201 ACCACGACAAATAATATGGAACGG 59.427 41.667 0.00 0.00 0.00 4.44
4045 5684 5.728351 ACCACGACAAATAATATGGAACG 57.272 39.130 0.00 0.00 0.00 3.95
4046 5685 9.498307 CTAAAACCACGACAAATAATATGGAAC 57.502 33.333 0.00 0.00 0.00 3.62
4047 5686 9.233649 ACTAAAACCACGACAAATAATATGGAA 57.766 29.630 0.00 0.00 0.00 3.53
4048 5687 8.795842 ACTAAAACCACGACAAATAATATGGA 57.204 30.769 0.00 0.00 0.00 3.41
4049 5688 9.498307 GAACTAAAACCACGACAAATAATATGG 57.502 33.333 0.00 0.00 0.00 2.74
4053 5692 9.974980 ATTTGAACTAAAACCACGACAAATAAT 57.025 25.926 0.00 0.00 35.79 1.28
4054 5693 9.804758 AATTTGAACTAAAACCACGACAAATAA 57.195 25.926 0.00 0.00 36.27 1.40
4055 5694 9.804758 AAATTTGAACTAAAACCACGACAAATA 57.195 25.926 0.00 0.00 36.27 1.40
4056 5695 8.599774 CAAATTTGAACTAAAACCACGACAAAT 58.400 29.630 13.08 0.00 38.00 2.32
4057 5696 7.813148 TCAAATTTGAACTAAAACCACGACAAA 59.187 29.630 18.45 0.00 33.55 2.83
4058 5697 7.313646 TCAAATTTGAACTAAAACCACGACAA 58.686 30.769 18.45 0.00 33.55 3.18
4059 5698 6.853720 TCAAATTTGAACTAAAACCACGACA 58.146 32.000 18.45 0.00 33.55 4.35
4060 5699 7.743520 TTCAAATTTGAACTAAAACCACGAC 57.256 32.000 26.01 0.00 41.88 4.34
4073 5712 7.313646 TGTCGTGGTTTTAGTTCAAATTTGAA 58.686 30.769 26.01 26.01 44.31 2.69
4074 5713 6.853720 TGTCGTGGTTTTAGTTCAAATTTGA 58.146 32.000 16.91 16.91 34.92 2.69
4075 5714 7.274686 ACTTGTCGTGGTTTTAGTTCAAATTTG 59.725 33.333 12.15 12.15 0.00 2.32
4076 5715 7.317390 ACTTGTCGTGGTTTTAGTTCAAATTT 58.683 30.769 0.00 0.00 0.00 1.82
4077 5716 6.859017 ACTTGTCGTGGTTTTAGTTCAAATT 58.141 32.000 0.00 0.00 0.00 1.82
4078 5717 6.445357 ACTTGTCGTGGTTTTAGTTCAAAT 57.555 33.333 0.00 0.00 0.00 2.32
4079 5718 5.883503 ACTTGTCGTGGTTTTAGTTCAAA 57.116 34.783 0.00 0.00 0.00 2.69
4080 5719 6.981762 TTACTTGTCGTGGTTTTAGTTCAA 57.018 33.333 0.00 0.00 0.00 2.69
4081 5720 7.556733 AATTACTTGTCGTGGTTTTAGTTCA 57.443 32.000 0.00 0.00 0.00 3.18
4082 5721 7.377662 CCAAATTACTTGTCGTGGTTTTAGTTC 59.622 37.037 0.00 0.00 32.65 3.01
4083 5722 7.067251 TCCAAATTACTTGTCGTGGTTTTAGTT 59.933 33.333 0.00 0.00 32.65 2.24
4084 5723 6.543100 TCCAAATTACTTGTCGTGGTTTTAGT 59.457 34.615 0.00 0.00 32.65 2.24
4085 5724 6.961576 TCCAAATTACTTGTCGTGGTTTTAG 58.038 36.000 0.00 0.00 32.65 1.85
4086 5725 6.939132 TCCAAATTACTTGTCGTGGTTTTA 57.061 33.333 0.00 0.00 32.65 1.52
4087 5726 5.838531 TCCAAATTACTTGTCGTGGTTTT 57.161 34.783 0.00 0.00 32.65 2.43
4088 5727 5.584442 GTTCCAAATTACTTGTCGTGGTTT 58.416 37.500 0.00 0.00 32.65 3.27
4089 5728 4.260866 CGTTCCAAATTACTTGTCGTGGTT 60.261 41.667 0.00 0.00 32.65 3.67
4090 5729 3.249080 CGTTCCAAATTACTTGTCGTGGT 59.751 43.478 0.00 0.00 32.65 4.16
4091 5730 3.364565 CCGTTCCAAATTACTTGTCGTGG 60.365 47.826 0.00 0.00 32.65 4.94
4092 5731 3.495377 TCCGTTCCAAATTACTTGTCGTG 59.505 43.478 0.00 0.00 32.65 4.35
4093 5732 3.731089 TCCGTTCCAAATTACTTGTCGT 58.269 40.909 0.00 0.00 32.65 4.34
4094 5733 3.124636 CCTCCGTTCCAAATTACTTGTCG 59.875 47.826 0.00 0.00 32.65 4.35
4095 5734 3.439129 CCCTCCGTTCCAAATTACTTGTC 59.561 47.826 0.00 0.00 32.65 3.18
4096 5735 3.073356 TCCCTCCGTTCCAAATTACTTGT 59.927 43.478 0.00 0.00 32.65 3.16
4097 5736 3.681593 TCCCTCCGTTCCAAATTACTTG 58.318 45.455 0.00 0.00 34.52 3.16
4098 5737 3.329814 ACTCCCTCCGTTCCAAATTACTT 59.670 43.478 0.00 0.00 0.00 2.24
4099 5738 2.910977 ACTCCCTCCGTTCCAAATTACT 59.089 45.455 0.00 0.00 0.00 2.24
4100 5739 3.345508 ACTCCCTCCGTTCCAAATTAC 57.654 47.619 0.00 0.00 0.00 1.89
4101 5740 4.098894 ACTACTCCCTCCGTTCCAAATTA 58.901 43.478 0.00 0.00 0.00 1.40
4102 5741 2.910977 ACTACTCCCTCCGTTCCAAATT 59.089 45.455 0.00 0.00 0.00 1.82
4103 5742 2.547990 ACTACTCCCTCCGTTCCAAAT 58.452 47.619 0.00 0.00 0.00 2.32
4104 5743 2.019807 ACTACTCCCTCCGTTCCAAA 57.980 50.000 0.00 0.00 0.00 3.28
4105 5744 1.897802 GAACTACTCCCTCCGTTCCAA 59.102 52.381 0.00 0.00 31.89 3.53
4106 5745 1.076677 AGAACTACTCCCTCCGTTCCA 59.923 52.381 0.00 0.00 37.15 3.53
4107 5746 1.750206 GAGAACTACTCCCTCCGTTCC 59.250 57.143 0.00 0.00 39.53 3.62
4108 5747 2.444421 TGAGAACTACTCCCTCCGTTC 58.556 52.381 0.00 0.00 44.34 3.95
4109 5748 2.599408 TGAGAACTACTCCCTCCGTT 57.401 50.000 0.00 0.00 44.34 4.44
4110 5749 2.561858 GTTTGAGAACTACTCCCTCCGT 59.438 50.000 0.00 0.00 44.34 4.69
4111 5750 2.094130 GGTTTGAGAACTACTCCCTCCG 60.094 54.545 0.00 0.00 44.34 4.63
4112 5751 2.904434 TGGTTTGAGAACTACTCCCTCC 59.096 50.000 0.00 0.00 44.34 4.30
4113 5752 4.618920 TTGGTTTGAGAACTACTCCCTC 57.381 45.455 0.00 0.00 44.34 4.30
4114 5753 4.658901 TCTTTGGTTTGAGAACTACTCCCT 59.341 41.667 0.00 0.00 44.34 4.20
4115 5754 4.969484 TCTTTGGTTTGAGAACTACTCCC 58.031 43.478 0.00 0.00 44.34 4.30
4116 5755 5.049336 GCTTCTTTGGTTTGAGAACTACTCC 60.049 44.000 0.00 0.00 44.34 3.85
4117 5756 5.049336 GGCTTCTTTGGTTTGAGAACTACTC 60.049 44.000 0.00 0.00 45.11 2.59
4131 5770 8.978539 GTTTCTAAATTAGTTTGGCTTCTTTGG 58.021 33.333 0.00 0.00 0.00 3.28
4204 5843 6.620877 TCTTTGATGTGGGAACTACTGTAT 57.379 37.500 0.00 0.00 0.00 2.29
4263 5902 2.497138 TCGAAGTCACGGTGAAGTCTA 58.503 47.619 13.23 2.69 0.00 2.59
4291 5930 4.704057 AGGCAAGTTTCAGAATTCTCCATC 59.296 41.667 4.57 0.00 0.00 3.51
4323 5962 5.917447 CGTGATATTCGTGATCTTCAGACAT 59.083 40.000 0.00 0.00 0.00 3.06
4337 5976 3.494626 AGCCTAATTGCACGTGATATTCG 59.505 43.478 22.23 12.66 0.00 3.34
4402 7387 2.017049 CTTCCGGCTTTCATGTTAGGG 58.983 52.381 0.00 0.00 0.00 3.53


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

AutoCloner maintained by Alex Coulton.