Multiple sequence alignment - TraesCS4A01G105100

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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 TraesCS4A01G105100 chr4A 100.000 5704 0 0 1 5704 119081276 119075573 0.000000e+00 10534.0
1 TraesCS4A01G105100 chr4A 80.970 268 13 19 329 578 538908475 538908722 1.630000e-40 178.0
2 TraesCS4A01G105100 chr4D 93.369 3197 128 32 2572 5704 346456230 346459406 0.000000e+00 4652.0
3 TraesCS4A01G105100 chr4D 88.157 2322 103 59 294 2581 346453953 346456136 0.000000e+00 2606.0
4 TraesCS4A01G105100 chr4D 95.312 64 3 0 27 90 346453745 346453808 1.010000e-17 102.0
5 TraesCS4A01G105100 chr4B 93.380 1284 77 6 3550 4829 427502040 427503319 0.000000e+00 1893.0
6 TraesCS4A01G105100 chr4B 91.742 993 57 13 2572 3548 427501003 427501986 0.000000e+00 1356.0
7 TraesCS4A01G105100 chr4B 89.461 854 32 24 4886 5704 427503447 427504277 0.000000e+00 1026.0
8 TraesCS4A01G105100 chr4B 85.714 945 55 36 581 1512 427498986 427499863 0.000000e+00 924.0
9 TraesCS4A01G105100 chr4B 87.786 524 50 6 2064 2581 427500401 427500916 8.180000e-168 601.0
10 TraesCS4A01G105100 chr4B 84.946 558 34 10 1535 2044 427499857 427500412 2.360000e-143 520.0
11 TraesCS4A01G105100 chr4B 82.641 409 42 20 124 524 427498572 427498959 9.160000e-88 335.0
12 TraesCS4A01G105100 chr4B 80.669 269 18 9 329 581 385957703 385957453 1.630000e-40 178.0
13 TraesCS4A01G105100 chr4B 92.857 70 5 0 21 90 427498500 427498569 1.010000e-17 102.0
14 TraesCS4A01G105100 chr5D 81.920 896 112 25 3203 4073 497175556 497176426 0.000000e+00 712.0
15 TraesCS4A01G105100 chr5D 91.250 80 4 3 5419 5498 497177039 497177115 7.820000e-19 106.0
16 TraesCS4A01G105100 chr7D 81.818 902 113 26 3203 4079 637137795 637136920 0.000000e+00 710.0
17 TraesCS4A01G105100 chrUn 80.952 714 102 14 3102 3786 88524503 88523795 8.410000e-148 534.0
18 TraesCS4A01G105100 chrUn 87.218 266 24 5 3831 4093 88520891 88520633 1.550000e-75 294.0
19 TraesCS4A01G105100 chrUn 82.449 245 41 2 4402 4645 88520504 88520261 4.480000e-51 213.0
20 TraesCS4A01G105100 chrUn 89.286 56 4 2 4117 4170 88520630 88520575 1.030000e-07 69.4
21 TraesCS4A01G105100 chr7B 82.675 456 53 13 3343 3782 736105739 736106184 1.160000e-101 381.0
22 TraesCS4A01G105100 chr5A 93.082 159 10 1 268 426 692541651 692541494 1.240000e-56 231.0
23 TraesCS4A01G105100 chr5A 91.824 159 12 1 268 426 692548220 692548063 2.680000e-53 220.0
24 TraesCS4A01G105100 chr2A 90.000 160 14 2 268 426 737426043 737426201 7.490000e-49 206.0
25 TraesCS4A01G105100 chr1D 82.239 259 25 12 4607 4862 51040219 51040459 2.690000e-48 204.0
26 TraesCS4A01G105100 chr1D 81.923 260 25 13 4607 4862 50962008 50962249 3.490000e-47 200.0
27 TraesCS4A01G105100 chr2B 80.645 279 18 19 329 589 17219741 17220001 3.510000e-42 183.0
28 TraesCS4A01G105100 chr2B 80.669 269 18 17 329 581 127203102 127202852 1.630000e-40 178.0
29 TraesCS4A01G105100 chr2B 80.784 255 18 14 329 567 414953425 414953186 2.730000e-38 171.0
30 TraesCS4A01G105100 chr1A 83.636 165 15 6 4607 4770 49998677 49998830 1.660000e-30 145.0
31 TraesCS4A01G105100 chr1B 77.344 256 42 11 329 578 686995220 686995465 2.770000e-28 137.0
32 TraesCS4A01G105100 chr1B 85.321 109 10 6 4607 4714 77545915 77546018 2.170000e-19 108.0
33 TraesCS4A01G105100 chr2D 96.875 32 0 1 743 774 31954618 31954648 1.000000e-02 52.8


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 TraesCS4A01G105100 chr4A 119075573 119081276 5703 True 10534.000000 10534 100.000000 1 5704 1 chr4A.!!$R1 5703
1 TraesCS4A01G105100 chr4D 346453745 346459406 5661 False 2453.333333 4652 92.279333 27 5704 3 chr4D.!!$F1 5677
2 TraesCS4A01G105100 chr4B 427498500 427504277 5777 False 844.625000 1893 88.565875 21 5704 8 chr4B.!!$F1 5683
3 TraesCS4A01G105100 chr5D 497175556 497177115 1559 False 409.000000 712 86.585000 3203 5498 2 chr5D.!!$F1 2295
4 TraesCS4A01G105100 chr7D 637136920 637137795 875 True 710.000000 710 81.818000 3203 4079 1 chr7D.!!$R1 876
5 TraesCS4A01G105100 chrUn 88520261 88524503 4242 True 277.600000 534 84.976250 3102 4645 4 chrUn.!!$R1 1543

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
954 1002 0.178846 TTCCCTTCCACCATCCCTCA 60.179 55.0 0.00 0.0 0.0 3.86 F
2397 2512 0.033366 GTTGGATTGGTGTGTTGGCC 59.967 55.0 0.00 0.0 0.0 5.36 F
3049 3267 0.690762 ATAAAGGTGTGCTGGACGGT 59.309 50.0 0.00 0.0 0.0 4.83 F
4470 7707 1.257750 GGCCACCCCTTTGATCAACC 61.258 60.0 7.89 0.0 0.0 3.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2911 3129 0.463474 GCAGACCAGGGCTTGAGATC 60.463 60.000 0.00 0.0 0.00 2.75 R
3230 3467 1.402325 CCATAGCACAGAACGTCGACA 60.402 52.381 17.16 0.0 0.00 4.35 R
4538 7775 0.391597 TTCGAGCAACGGAAAGGACT 59.608 50.000 3.74 0.0 42.82 3.85 R
5389 8731 2.935849 TCGATGCGCAACATATTCTTGT 59.064 40.909 17.11 0.0 39.84 3.16 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
68 69 5.010922 TCACCTTGTCAAATTTTCTGATGGG 59.989 40.000 0.00 0.00 0.00 4.00
71 72 5.185635 CCTTGTCAAATTTTCTGATGGGCTA 59.814 40.000 0.00 0.00 0.00 3.93
90 91 6.013842 GGCTATCACCCATTTATTTACAGC 57.986 41.667 0.00 0.00 0.00 4.40
92 93 6.072452 GGCTATCACCCATTTATTTACAGCTC 60.072 42.308 0.00 0.00 0.00 4.09
94 95 7.013274 GCTATCACCCATTTATTTACAGCTCAA 59.987 37.037 0.00 0.00 0.00 3.02
98 99 7.831690 TCACCCATTTATTTACAGCTCAATACA 59.168 33.333 0.00 0.00 0.00 2.29
99 100 7.915397 CACCCATTTATTTACAGCTCAATACAC 59.085 37.037 0.00 0.00 0.00 2.90
100 101 7.834181 ACCCATTTATTTACAGCTCAATACACT 59.166 33.333 0.00 0.00 0.00 3.55
101 102 8.686334 CCCATTTATTTACAGCTCAATACACTT 58.314 33.333 0.00 0.00 0.00 3.16
109 110 9.462174 TTTACAGCTCAATACACTTTGATTTTG 57.538 29.630 0.00 0.00 35.20 2.44
110 111 6.449698 ACAGCTCAATACACTTTGATTTTGG 58.550 36.000 0.00 0.00 35.20 3.28
111 112 5.346822 CAGCTCAATACACTTTGATTTTGGC 59.653 40.000 0.00 0.00 35.20 4.52
112 113 4.627035 GCTCAATACACTTTGATTTTGGCC 59.373 41.667 0.00 0.00 35.20 5.36
113 114 5.146010 TCAATACACTTTGATTTTGGCCC 57.854 39.130 0.00 0.00 30.82 5.80
114 115 4.020662 TCAATACACTTTGATTTTGGCCCC 60.021 41.667 0.00 0.00 30.82 5.80
115 116 1.799933 ACACTTTGATTTTGGCCCCA 58.200 45.000 0.00 0.00 0.00 4.96
116 117 2.337849 ACACTTTGATTTTGGCCCCAT 58.662 42.857 0.00 0.00 0.00 4.00
117 118 2.302733 ACACTTTGATTTTGGCCCCATC 59.697 45.455 0.00 0.00 0.00 3.51
118 119 1.550072 ACTTTGATTTTGGCCCCATCG 59.450 47.619 0.00 0.00 0.00 3.84
119 120 1.824230 CTTTGATTTTGGCCCCATCGA 59.176 47.619 0.00 0.00 0.00 3.59
120 121 1.473258 TTGATTTTGGCCCCATCGAG 58.527 50.000 0.00 0.00 0.00 4.04
121 122 1.037030 TGATTTTGGCCCCATCGAGC 61.037 55.000 0.00 0.00 0.00 5.03
126 127 4.688966 GGCCCCATCGAGCCGATC 62.689 72.222 7.06 0.00 45.19 3.69
197 199 0.605589 ACAGCTCTGCAGTACTCACC 59.394 55.000 14.67 0.00 0.00 4.02
247 277 3.432608 CCGTGGTTAGGTTATGGTAAGGG 60.433 52.174 0.00 0.00 0.00 3.95
264 294 2.345991 GTGGTAGCAAGCACGGGA 59.654 61.111 0.00 0.00 43.60 5.14
265 295 1.302192 GTGGTAGCAAGCACGGGAA 60.302 57.895 0.00 0.00 43.60 3.97
266 296 1.003839 TGGTAGCAAGCACGGGAAG 60.004 57.895 0.00 0.00 0.00 3.46
267 297 1.003718 GGTAGCAAGCACGGGAAGT 60.004 57.895 0.00 0.00 0.00 3.01
277 307 3.702048 CGGGAAGTGCTCGGGGAA 61.702 66.667 0.00 0.00 36.65 3.97
278 308 2.754375 GGGAAGTGCTCGGGGAAA 59.246 61.111 0.00 0.00 0.00 3.13
279 309 1.303282 GGGAAGTGCTCGGGGAAAT 59.697 57.895 0.00 0.00 0.00 2.17
280 310 1.032114 GGGAAGTGCTCGGGGAAATG 61.032 60.000 0.00 0.00 0.00 2.32
281 311 1.657751 GGAAGTGCTCGGGGAAATGC 61.658 60.000 0.00 0.00 0.00 3.56
282 312 1.982073 GAAGTGCTCGGGGAAATGCG 61.982 60.000 0.00 0.00 0.00 4.73
283 313 3.508840 GTGCTCGGGGAAATGCGG 61.509 66.667 0.00 0.00 0.00 5.69
284 314 4.794648 TGCTCGGGGAAATGCGGG 62.795 66.667 0.00 0.00 0.00 6.13
285 315 4.796495 GCTCGGGGAAATGCGGGT 62.796 66.667 0.00 0.00 0.00 5.28
286 316 2.824041 CTCGGGGAAATGCGGGTG 60.824 66.667 0.00 0.00 0.00 4.61
287 317 3.323286 TCGGGGAAATGCGGGTGA 61.323 61.111 0.00 0.00 0.00 4.02
288 318 2.824041 CGGGGAAATGCGGGTGAG 60.824 66.667 0.00 0.00 0.00 3.51
289 319 3.140814 GGGGAAATGCGGGTGAGC 61.141 66.667 0.00 0.00 37.71 4.26
290 320 3.508840 GGGAAATGCGGGTGAGCG 61.509 66.667 0.00 0.00 40.67 5.03
291 321 3.508840 GGAAATGCGGGTGAGCGG 61.509 66.667 0.00 0.00 40.67 5.52
292 322 4.179579 GAAATGCGGGTGAGCGGC 62.180 66.667 7.26 7.26 40.67 6.53
529 565 4.598894 CATCTCCGCCTCGCCCAG 62.599 72.222 0.00 0.00 0.00 4.45
551 587 4.992511 CCCGGAAACCGCGACCAA 62.993 66.667 8.23 0.00 46.86 3.67
552 588 3.719144 CCGGAAACCGCGACCAAC 61.719 66.667 8.23 0.00 46.86 3.77
553 589 2.968156 CGGAAACCGCGACCAACA 60.968 61.111 8.23 0.00 41.17 3.33
554 590 2.943653 GGAAACCGCGACCAACAG 59.056 61.111 8.23 0.00 0.00 3.16
555 591 1.595929 GGAAACCGCGACCAACAGA 60.596 57.895 8.23 0.00 0.00 3.41
600 641 3.112709 GGACGTGCCTGAGCGAAC 61.113 66.667 0.00 0.00 44.31 3.95
617 659 3.312828 CGAACTCACAGAGACCAAAGAG 58.687 50.000 0.31 0.00 33.32 2.85
622 664 5.745227 ACTCACAGAGACCAAAGAGAAAAA 58.255 37.500 0.31 0.00 33.32 1.94
795 838 2.359230 GGCACCTGAGGACAGTGC 60.359 66.667 4.99 4.03 43.40 4.40
796 839 2.740055 GCACCTGAGGACAGTGCG 60.740 66.667 4.99 0.00 42.05 5.34
797 840 2.740055 CACCTGAGGACAGTGCGC 60.740 66.667 4.99 0.00 42.05 6.09
798 841 4.363990 ACCTGAGGACAGTGCGCG 62.364 66.667 4.99 0.00 42.05 6.86
801 844 4.377708 TGAGGACAGTGCGCGCAT 62.378 61.111 38.62 22.76 0.00 4.73
802 845 3.558411 GAGGACAGTGCGCGCATC 61.558 66.667 38.62 29.25 0.00 3.91
915 963 2.943978 CGTTCCAACCTCCGGCTCT 61.944 63.158 0.00 0.00 0.00 4.09
928 976 2.359230 GCTCTCAAACCCTGCGCT 60.359 61.111 9.73 0.00 0.00 5.92
929 977 2.684843 GCTCTCAAACCCTGCGCTG 61.685 63.158 9.73 8.47 0.00 5.18
930 978 2.669569 TCTCAAACCCTGCGCTGC 60.670 61.111 9.73 0.00 0.00 5.25
931 979 4.093952 CTCAAACCCTGCGCTGCG 62.094 66.667 19.17 19.17 0.00 5.18
942 990 3.793144 CGCTGCGCACTTCCCTTC 61.793 66.667 5.66 0.00 0.00 3.46
943 991 3.435186 GCTGCGCACTTCCCTTCC 61.435 66.667 5.66 0.00 0.00 3.46
944 992 2.032528 CTGCGCACTTCCCTTCCA 59.967 61.111 5.66 0.00 0.00 3.53
954 1002 0.178846 TTCCCTTCCACCATCCCTCA 60.179 55.000 0.00 0.00 0.00 3.86
969 1017 1.075600 CTCACTCCCTCCCTCCCTC 60.076 68.421 0.00 0.00 0.00 4.30
985 1033 1.296392 CTCCACCACTGCATTCCGA 59.704 57.895 0.00 0.00 0.00 4.55
986 1034 1.003839 TCCACCACTGCATTCCGAC 60.004 57.895 0.00 0.00 0.00 4.79
987 1035 2.390599 CCACCACTGCATTCCGACG 61.391 63.158 0.00 0.00 0.00 5.12
988 1036 1.374125 CACCACTGCATTCCGACGA 60.374 57.895 0.00 0.00 0.00 4.20
989 1037 1.079819 ACCACTGCATTCCGACGAG 60.080 57.895 0.00 0.00 0.00 4.18
990 1038 1.811266 CCACTGCATTCCGACGAGG 60.811 63.158 0.00 0.00 42.97 4.63
991 1039 2.125512 ACTGCATTCCGACGAGGC 60.126 61.111 0.00 0.00 40.77 4.70
1190 1244 1.657822 GTGCGGGAATTCTTCTCCTC 58.342 55.000 5.23 0.00 33.11 3.71
1193 1247 1.202592 GCGGGAATTCTTCTCCTCCTC 60.203 57.143 5.23 0.00 33.11 3.71
1204 1258 1.064314 TCTCCTCCTCCTTCTTCTCCG 60.064 57.143 0.00 0.00 0.00 4.63
1205 1259 1.000496 TCCTCCTCCTTCTTCTCCGA 59.000 55.000 0.00 0.00 0.00 4.55
1240 1294 2.030562 CGGTTCTTGGCCGTGTCT 59.969 61.111 0.00 0.00 43.84 3.41
1241 1295 1.597027 CGGTTCTTGGCCGTGTCTT 60.597 57.895 0.00 0.00 43.84 3.01
1315 1369 1.369625 GTGCGGTTGATCGGATTCTT 58.630 50.000 0.00 0.00 32.32 2.52
1379 1433 1.299976 GGCTGATCCCGTGGTTTCT 59.700 57.895 0.00 0.00 0.00 2.52
1393 1447 1.335964 GGTTTCTTTGGCGCTTCTTCC 60.336 52.381 7.64 0.00 0.00 3.46
1402 1456 0.729690 GCGCTTCTTCCCTTGATGTC 59.270 55.000 0.00 0.00 0.00 3.06
1420 1474 2.611751 TGTCTGGTTCGTGAAATGTGTG 59.388 45.455 0.00 0.00 0.00 3.82
1436 1490 1.356624 GTGCGGAATAGTGCCATGC 59.643 57.895 0.00 0.00 0.00 4.06
1467 1521 2.434359 GCCCGTCTTCGTTCCCAG 60.434 66.667 0.00 0.00 35.01 4.45
1474 1528 4.962384 CCGTCTTCGTTCCCAGAATTTGG 61.962 52.174 1.03 1.03 40.01 3.28
1490 1544 1.947597 TTGGGATGCCGCAATGCTTC 61.948 55.000 2.94 0.00 39.81 3.86
1503 1557 3.365820 GCAATGCTTCCTCGTGATTTTTG 59.634 43.478 0.00 0.00 0.00 2.44
1504 1558 3.855689 ATGCTTCCTCGTGATTTTTGG 57.144 42.857 0.00 0.00 0.00 3.28
1505 1559 1.885887 TGCTTCCTCGTGATTTTTGGG 59.114 47.619 0.00 0.00 0.00 4.12
1506 1560 1.886542 GCTTCCTCGTGATTTTTGGGT 59.113 47.619 0.00 0.00 0.00 4.51
1507 1561 3.078837 GCTTCCTCGTGATTTTTGGGTA 58.921 45.455 0.00 0.00 0.00 3.69
1508 1562 3.694566 GCTTCCTCGTGATTTTTGGGTAT 59.305 43.478 0.00 0.00 0.00 2.73
1509 1563 4.157840 GCTTCCTCGTGATTTTTGGGTATT 59.842 41.667 0.00 0.00 0.00 1.89
1510 1564 5.676331 GCTTCCTCGTGATTTTTGGGTATTC 60.676 44.000 0.00 0.00 0.00 1.75
1511 1565 5.174037 TCCTCGTGATTTTTGGGTATTCT 57.826 39.130 0.00 0.00 0.00 2.40
1512 1566 6.302535 TCCTCGTGATTTTTGGGTATTCTA 57.697 37.500 0.00 0.00 0.00 2.10
1513 1567 6.110707 TCCTCGTGATTTTTGGGTATTCTAC 58.889 40.000 0.00 0.00 0.00 2.59
1711 1780 4.184079 AGAAATTGCTGCATCTTTGGAC 57.816 40.909 1.84 0.00 0.00 4.02
1747 1816 1.868713 TTACCAATCGGCTACTCCCA 58.131 50.000 0.00 0.00 34.57 4.37
1784 1853 2.077579 TTGCAGGGCAATGGAGAGA 58.922 52.632 0.00 0.00 43.99 3.10
1808 1877 5.483811 TCTTGTTCGCTAATGTACCATGAA 58.516 37.500 0.00 0.00 0.00 2.57
1810 1879 6.428465 TCTTGTTCGCTAATGTACCATGAAAA 59.572 34.615 0.00 0.00 0.00 2.29
1811 1880 6.561737 TGTTCGCTAATGTACCATGAAAAA 57.438 33.333 0.00 0.00 0.00 1.94
1813 1882 8.270080 TGTTCGCTAATGTACCATGAAAAATA 57.730 30.769 0.00 0.00 0.00 1.40
1815 1884 9.169468 GTTCGCTAATGTACCATGAAAAATATG 57.831 33.333 0.00 0.00 0.00 1.78
1817 1886 9.549078 TCGCTAATGTACCATGAAAAATATGTA 57.451 29.630 0.00 0.00 0.00 2.29
1986 2081 1.358152 TGAACTTGTGGTCCTAGGGG 58.642 55.000 9.46 0.00 0.00 4.79
2044 2152 7.550906 GCACAGTCTTGAGGTCTTCTATATTTT 59.449 37.037 0.00 0.00 0.00 1.82
2045 2153 9.442047 CACAGTCTTGAGGTCTTCTATATTTTT 57.558 33.333 0.00 0.00 0.00 1.94
2184 2294 5.839606 ACTAACCTCCTAGAACAGAAAGTGT 59.160 40.000 0.00 0.00 43.24 3.55
2332 2447 4.923281 GCGATGCTATGTGTGATGTATACA 59.077 41.667 8.27 8.27 34.75 2.29
2357 2472 3.934457 ACATGTTCCCGGTCAAATTTC 57.066 42.857 0.00 0.00 0.00 2.17
2386 2501 5.870978 CCTTTTTCTTGCTATGGTTGGATTG 59.129 40.000 0.00 0.00 0.00 2.67
2397 2512 0.033366 GTTGGATTGGTGTGTTGGCC 59.967 55.000 0.00 0.00 0.00 5.36
2400 2515 0.755686 GGATTGGTGTGTTGGCCAAA 59.244 50.000 22.47 8.06 46.34 3.28
2403 2518 3.948702 GGTGTGTTGGCCAAACCT 58.051 55.556 24.77 0.00 46.63 3.50
2405 2520 1.326951 GGTGTGTTGGCCAAACCTGT 61.327 55.000 24.77 0.00 46.63 4.00
2477 2592 6.466308 TTGAATATGTGCAGTACGATATGC 57.534 37.500 0.00 0.00 42.86 3.14
2566 2681 9.197306 ACAACTGTATACATCTATGTGTTCCTA 57.803 33.333 5.91 0.00 41.89 2.94
2786 3004 2.362717 CCCACATAAACGGGTGTTGTTT 59.637 45.455 0.00 0.00 41.97 2.83
2822 3040 7.054491 AGTGTTTAGGCTTTTTCATGTGATT 57.946 32.000 0.00 0.00 0.00 2.57
2836 3054 5.062528 TCATGTGATTGCTGACAACTACAA 58.937 37.500 0.00 0.00 38.99 2.41
2911 3129 2.173382 GCCGTGCGCACTAAGTTG 59.827 61.111 35.27 19.85 37.47 3.16
2928 3146 1.280421 GTTGATCTCAAGCCCTGGTCT 59.720 52.381 0.00 0.00 36.39 3.85
2947 3165 2.899900 TCTGCATACCAATCGCCTATCT 59.100 45.455 0.00 0.00 0.00 1.98
3004 3222 3.119101 GCTTCCCACGAGATCACTTTCTA 60.119 47.826 0.00 0.00 0.00 2.10
3049 3267 0.690762 ATAAAGGTGTGCTGGACGGT 59.309 50.000 0.00 0.00 0.00 4.83
3075 3293 4.564372 CGAGGTGAGTTCATGTGTTCTATG 59.436 45.833 0.00 0.00 0.00 2.23
3097 3319 7.673641 ATGGGCAGTTCAATAATTGGAATTA 57.326 32.000 0.00 0.00 35.52 1.40
3098 3320 7.673641 TGGGCAGTTCAATAATTGGAATTAT 57.326 32.000 0.00 0.00 41.94 1.28
3289 3526 5.437289 TGTTATGAAAAGTGAGGCTTGTG 57.563 39.130 0.00 0.00 37.52 3.33
3290 3527 5.129634 TGTTATGAAAAGTGAGGCTTGTGA 58.870 37.500 0.00 0.00 37.52 3.58
3326 3567 9.193133 GTGTACTATATGATTCGCTTGTATGTT 57.807 33.333 0.00 0.00 0.00 2.71
3631 3957 1.944588 TCTTCCCAGATCTTCCCCCTA 59.055 52.381 0.00 0.00 0.00 3.53
3666 3992 7.995488 CCTCTTGACTGGAATACAAGGATAAAT 59.005 37.037 0.00 0.00 40.60 1.40
4022 7235 3.301794 TGCTGAATGGGTAAGCATCAT 57.698 42.857 0.00 0.00 41.83 2.45
4064 7279 8.258708 TCTTTTATAGAACTACTCCTTGCTTCC 58.741 37.037 0.00 0.00 0.00 3.46
4105 7320 5.183140 GCTGTACCAAGGACAATATTGTGTT 59.817 40.000 25.42 14.99 42.43 3.32
4178 7414 6.604795 ACTGGCAGAAGCATCATAAGTTTATT 59.395 34.615 23.66 0.00 44.61 1.40
4256 7492 3.887716 GGTCTTGCCATTGCTGAGATAAT 59.112 43.478 0.00 0.00 38.71 1.28
4304 7540 5.645056 TCCTCATATGGAAGCCACAATAA 57.355 39.130 2.13 0.00 35.80 1.40
4399 7636 9.218359 CTTGTCTAAAAAGTAAAACGAGTTTCC 57.782 33.333 1.39 0.00 31.45 3.13
4406 7643 8.510243 AAAAGTAAAACGAGTTTCCCTTTCTA 57.490 30.769 17.73 0.45 34.35 2.10
4426 7663 9.214953 CTTTCTACGATGAAGATTAATTGTTGC 57.785 33.333 0.00 0.00 0.00 4.17
4431 7668 5.898606 CGATGAAGATTAATTGTTGCGACTC 59.101 40.000 5.50 0.00 0.00 3.36
4470 7707 1.257750 GGCCACCCCTTTGATCAACC 61.258 60.000 7.89 0.00 0.00 3.77
4538 7775 4.713553 ACAACATGACATCACTGTACCAA 58.286 39.130 0.00 0.00 35.14 3.67
4703 7940 4.287585 CACCAACCCGGGGAAGATATATAA 59.712 45.833 27.92 0.00 43.25 0.98
4762 7999 4.362279 AGTGCAAAGCAATGTAGTGTTTG 58.638 39.130 0.00 0.00 41.47 2.93
4771 8008 4.736168 GCAATGTAGTGTTTGTGGCTTTGA 60.736 41.667 0.00 0.00 0.00 2.69
4788 8031 9.121658 GTGGCTTTGATATGATGATGATGATAT 57.878 33.333 0.00 0.00 0.00 1.63
4789 8032 9.338622 TGGCTTTGATATGATGATGATGATATC 57.661 33.333 4.98 4.98 36.32 1.63
4801 8044 9.315525 GATGATGATGATATCGTGATCAAGAAT 57.684 33.333 24.83 12.68 38.59 2.40
4864 8107 5.196341 GGGGGAAGTTTTGTTTGTAGAAG 57.804 43.478 0.00 0.00 0.00 2.85
4868 8111 6.040054 GGGGAAGTTTTGTTTGTAGAAGCTAA 59.960 38.462 0.00 0.00 0.00 3.09
4899 8213 6.136857 AGAGTAGAGTAGGTGCAAATATCCA 58.863 40.000 0.00 0.00 0.00 3.41
4911 8225 3.701040 GCAAATATCCATGTGTCCCTTGT 59.299 43.478 0.00 0.00 0.00 3.16
4913 8227 5.359576 GCAAATATCCATGTGTCCCTTGTTA 59.640 40.000 0.00 0.00 0.00 2.41
4925 8239 0.698818 CCTTGTTAAGGGCCTGAGGT 59.301 55.000 6.92 0.00 45.27 3.85
4940 8254 4.335416 CCTGAGGTTTGTCATATGTGGTT 58.665 43.478 1.90 0.00 0.00 3.67
4945 8259 4.283212 AGGTTTGTCATATGTGGTTTTGGG 59.717 41.667 1.90 0.00 0.00 4.12
4946 8260 4.282195 GGTTTGTCATATGTGGTTTTGGGA 59.718 41.667 1.90 0.00 0.00 4.37
4968 8283 7.093068 TGGGAACATAGCTTCATAGTAGTTGAA 60.093 37.037 0.00 0.00 33.40 2.69
5022 8337 2.880268 CCTCTTGTTGACATGTTGCTGA 59.120 45.455 0.00 0.00 0.00 4.26
5025 8340 3.253921 TCTTGTTGACATGTTGCTGATGG 59.746 43.478 0.00 0.00 0.00 3.51
5026 8341 2.585330 TGTTGACATGTTGCTGATGGT 58.415 42.857 0.00 0.00 0.00 3.55
5027 8342 2.957680 TGTTGACATGTTGCTGATGGTT 59.042 40.909 0.00 0.00 0.00 3.67
5028 8343 3.384146 TGTTGACATGTTGCTGATGGTTT 59.616 39.130 0.00 0.00 0.00 3.27
5031 8346 3.384146 TGACATGTTGCTGATGGTTTTGT 59.616 39.130 0.00 0.00 0.00 2.83
5032 8347 4.141981 TGACATGTTGCTGATGGTTTTGTT 60.142 37.500 0.00 0.00 0.00 2.83
5033 8348 4.121317 ACATGTTGCTGATGGTTTTGTTG 58.879 39.130 0.00 0.00 0.00 3.33
5034 8349 4.141981 ACATGTTGCTGATGGTTTTGTTGA 60.142 37.500 0.00 0.00 0.00 3.18
5037 8352 3.663995 TGCTGATGGTTTTGTTGATGG 57.336 42.857 0.00 0.00 0.00 3.51
5039 8354 3.387374 TGCTGATGGTTTTGTTGATGGTT 59.613 39.130 0.00 0.00 0.00 3.67
5047 8362 3.467374 TTTGTTGATGGTTTTCAGCCC 57.533 42.857 0.00 0.00 0.00 5.19
5144 8461 9.567776 TCATTTCTAACACAAAAATCTAGGTCA 57.432 29.630 0.00 0.00 0.00 4.02
5231 8571 3.964688 TCCAACTGTTCCTGACTCTTGTA 59.035 43.478 0.00 0.00 0.00 2.41
5389 8731 8.840833 TGTCTTTTACACTAAGCAACATATGA 57.159 30.769 10.38 0.00 31.43 2.15
5405 8747 5.751680 ACATATGACAAGAATATGTTGCGC 58.248 37.500 10.38 0.00 44.88 6.09
5522 8873 6.295349 CCAGTATAACCCTATGACATCCTCAC 60.295 46.154 0.00 0.00 0.00 3.51
5557 8908 1.153046 ACAGGGGGTTTCGTGTGTG 60.153 57.895 0.00 0.00 34.90 3.82
5647 8998 1.636148 ACATGGATGCCTTGCAAAGT 58.364 45.000 0.00 0.00 44.25 2.66
5648 8999 1.274167 ACATGGATGCCTTGCAAAGTG 59.726 47.619 0.00 0.00 44.25 3.16
5649 9000 1.546923 CATGGATGCCTTGCAAAGTGA 59.453 47.619 0.00 0.00 44.25 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 7.550597 TCTGGGTATAGAATCTACTCGTAGA 57.449 40.000 9.04 9.04 45.24 2.59
20 21 8.041919 TGATCTGGGTATAGAATCTACTCGTAG 58.958 40.741 0.00 0.00 34.56 3.51
21 22 7.823310 GTGATCTGGGTATAGAATCTACTCGTA 59.177 40.741 0.00 0.00 0.00 3.43
22 23 6.655848 GTGATCTGGGTATAGAATCTACTCGT 59.344 42.308 0.00 0.00 0.00 4.18
23 24 6.094325 GGTGATCTGGGTATAGAATCTACTCG 59.906 46.154 0.00 0.00 0.00 4.18
68 69 6.486657 TGAGCTGTAAATAAATGGGTGATAGC 59.513 38.462 0.00 0.00 0.00 2.97
71 72 7.902920 ATTGAGCTGTAAATAAATGGGTGAT 57.097 32.000 0.00 0.00 0.00 3.06
90 91 5.170748 GGGCCAAAATCAAAGTGTATTGAG 58.829 41.667 4.39 0.00 42.21 3.02
92 93 4.252878 GGGGCCAAAATCAAAGTGTATTG 58.747 43.478 4.39 0.00 0.00 1.90
94 95 3.515562 TGGGGCCAAAATCAAAGTGTAT 58.484 40.909 4.39 0.00 0.00 2.29
98 99 1.550072 CGATGGGGCCAAAATCAAAGT 59.450 47.619 4.39 0.00 0.00 2.66
99 100 1.824230 TCGATGGGGCCAAAATCAAAG 59.176 47.619 4.39 0.00 0.00 2.77
100 101 1.824230 CTCGATGGGGCCAAAATCAAA 59.176 47.619 4.39 0.00 0.00 2.69
101 102 1.473258 CTCGATGGGGCCAAAATCAA 58.527 50.000 4.39 0.00 0.00 2.57
102 103 1.037030 GCTCGATGGGGCCAAAATCA 61.037 55.000 4.39 0.00 0.00 2.57
103 104 1.735973 GCTCGATGGGGCCAAAATC 59.264 57.895 4.39 4.37 0.00 2.17
104 105 1.758122 GGCTCGATGGGGCCAAAAT 60.758 57.895 14.68 0.00 46.84 1.82
105 106 2.362375 GGCTCGATGGGGCCAAAA 60.362 61.111 14.68 0.00 46.84 2.44
109 110 4.688966 GATCGGCTCGATGGGGCC 62.689 72.222 8.90 8.90 47.00 5.80
110 111 2.738213 ATTGATCGGCTCGATGGGGC 62.738 60.000 13.68 0.00 47.00 5.80
111 112 0.671781 GATTGATCGGCTCGATGGGG 60.672 60.000 13.68 0.00 47.00 4.96
112 113 1.010935 CGATTGATCGGCTCGATGGG 61.011 60.000 13.68 0.00 47.00 4.00
113 114 0.039165 TCGATTGATCGGCTCGATGG 60.039 55.000 13.68 0.00 47.00 3.51
114 115 1.988063 ATCGATTGATCGGCTCGATG 58.012 50.000 19.70 1.38 47.00 3.84
123 124 3.792294 CGCTTACTTGCATCGATTGATC 58.208 45.455 0.00 0.00 30.49 2.92
124 125 2.032549 GCGCTTACTTGCATCGATTGAT 60.033 45.455 0.00 0.00 34.28 2.57
125 126 1.327460 GCGCTTACTTGCATCGATTGA 59.673 47.619 0.00 0.00 0.00 2.57
126 127 1.062440 TGCGCTTACTTGCATCGATTG 59.938 47.619 9.73 0.00 35.90 2.67
143 144 6.489675 AGTTGAGAAATTATGTAAGCATGCG 58.510 36.000 13.01 0.00 36.58 4.73
147 148 9.719355 TGTCTTAGTTGAGAAATTATGTAAGCA 57.281 29.630 0.00 0.00 0.00 3.91
181 183 1.001406 ACTTGGTGAGTACTGCAGAGC 59.999 52.381 23.35 12.38 36.65 4.09
197 199 4.629634 TGTCTCACACACACTTGTTACTTG 59.370 41.667 0.00 0.00 31.66 3.16
247 277 1.298859 CTTCCCGTGCTTGCTACCAC 61.299 60.000 0.00 0.00 0.00 4.16
260 290 2.536997 ATTTCCCCGAGCACTTCCCG 62.537 60.000 0.00 0.00 0.00 5.14
261 291 1.032114 CATTTCCCCGAGCACTTCCC 61.032 60.000 0.00 0.00 0.00 3.97
262 292 1.657751 GCATTTCCCCGAGCACTTCC 61.658 60.000 0.00 0.00 0.00 3.46
263 293 1.803289 GCATTTCCCCGAGCACTTC 59.197 57.895 0.00 0.00 0.00 3.01
264 294 2.040544 CGCATTTCCCCGAGCACTT 61.041 57.895 0.00 0.00 0.00 3.16
265 295 2.436646 CGCATTTCCCCGAGCACT 60.437 61.111 0.00 0.00 0.00 4.40
266 296 3.508840 CCGCATTTCCCCGAGCAC 61.509 66.667 0.00 0.00 0.00 4.40
267 297 4.794648 CCCGCATTTCCCCGAGCA 62.795 66.667 0.00 0.00 0.00 4.26
268 298 4.796495 ACCCGCATTTCCCCGAGC 62.796 66.667 0.00 0.00 0.00 5.03
269 299 2.824041 CACCCGCATTTCCCCGAG 60.824 66.667 0.00 0.00 0.00 4.63
270 300 3.323286 TCACCCGCATTTCCCCGA 61.323 61.111 0.00 0.00 0.00 5.14
271 301 2.824041 CTCACCCGCATTTCCCCG 60.824 66.667 0.00 0.00 0.00 5.73
272 302 3.140814 GCTCACCCGCATTTCCCC 61.141 66.667 0.00 0.00 0.00 4.81
273 303 3.508840 CGCTCACCCGCATTTCCC 61.509 66.667 0.00 0.00 0.00 3.97
274 304 3.508840 CCGCTCACCCGCATTTCC 61.509 66.667 0.00 0.00 0.00 3.13
275 305 4.179579 GCCGCTCACCCGCATTTC 62.180 66.667 0.00 0.00 0.00 2.17
292 322 3.400599 AAGATGGTAAGCGCCCCGG 62.401 63.158 2.29 0.00 0.00 5.73
498 534 3.925090 GATGGGGGAGTACGGCGG 61.925 72.222 13.24 0.00 0.00 6.13
537 573 1.595929 TCTGTTGGTCGCGGTTTCC 60.596 57.895 6.13 4.91 0.00 3.13
538 574 0.878961 AGTCTGTTGGTCGCGGTTTC 60.879 55.000 6.13 0.00 0.00 2.78
539 575 1.145377 AGTCTGTTGGTCGCGGTTT 59.855 52.632 6.13 0.00 0.00 3.27
540 576 1.594293 CAGTCTGTTGGTCGCGGTT 60.594 57.895 6.13 0.00 0.00 4.44
541 577 2.029073 CAGTCTGTTGGTCGCGGT 59.971 61.111 6.13 0.00 0.00 5.68
542 578 3.414700 GCAGTCTGTTGGTCGCGG 61.415 66.667 6.13 0.00 0.00 6.46
543 579 3.767230 CGCAGTCTGTTGGTCGCG 61.767 66.667 0.00 0.00 36.47 5.87
544 580 3.414700 CCGCAGTCTGTTGGTCGC 61.415 66.667 0.93 0.00 0.00 5.19
545 581 3.414700 GCCGCAGTCTGTTGGTCG 61.415 66.667 12.92 3.20 0.00 4.79
546 582 3.414700 CGCCGCAGTCTGTTGGTC 61.415 66.667 12.92 6.45 0.00 4.02
547 583 4.988598 CCGCCGCAGTCTGTTGGT 62.989 66.667 12.92 0.00 0.00 3.67
572 608 3.423154 CACGTCCTTCCTTGCGCC 61.423 66.667 4.18 0.00 0.00 6.53
575 611 2.032681 AGGCACGTCCTTCCTTGC 59.967 61.111 1.23 0.00 44.75 4.01
576 612 0.671781 CTCAGGCACGTCCTTCCTTG 60.672 60.000 4.08 0.00 44.75 3.61
578 614 2.948720 GCTCAGGCACGTCCTTCCT 61.949 63.158 4.08 0.00 44.75 3.36
622 664 3.491342 GCCTTCCTTTGGACTCTTCTTT 58.509 45.455 0.00 0.00 0.00 2.52
625 667 1.270893 ACGCCTTCCTTTGGACTCTTC 60.271 52.381 0.00 0.00 0.00 2.87
626 668 0.765510 ACGCCTTCCTTTGGACTCTT 59.234 50.000 0.00 0.00 0.00 2.85
627 669 1.275573 GTACGCCTTCCTTTGGACTCT 59.724 52.381 0.00 0.00 0.00 3.24
628 670 1.275573 AGTACGCCTTCCTTTGGACTC 59.724 52.381 0.00 0.00 0.00 3.36
798 841 1.153147 GGAAGGACGGAAGGGATGC 60.153 63.158 0.00 0.00 0.00 3.91
799 842 0.466124 GAGGAAGGACGGAAGGGATG 59.534 60.000 0.00 0.00 0.00 3.51
800 843 1.043673 CGAGGAAGGACGGAAGGGAT 61.044 60.000 0.00 0.00 0.00 3.85
801 844 1.681327 CGAGGAAGGACGGAAGGGA 60.681 63.158 0.00 0.00 0.00 4.20
802 845 2.893398 CGAGGAAGGACGGAAGGG 59.107 66.667 0.00 0.00 0.00 3.95
928 976 2.281484 GTGGAAGGGAAGTGCGCA 60.281 61.111 5.66 5.66 0.00 6.09
929 977 3.056328 GGTGGAAGGGAAGTGCGC 61.056 66.667 0.00 0.00 0.00 6.09
930 978 1.002134 ATGGTGGAAGGGAAGTGCG 60.002 57.895 0.00 0.00 0.00 5.34
931 979 0.681243 GGATGGTGGAAGGGAAGTGC 60.681 60.000 0.00 0.00 0.00 4.40
942 990 1.307343 AGGGAGTGAGGGATGGTGG 60.307 63.158 0.00 0.00 0.00 4.61
943 991 1.341156 GGAGGGAGTGAGGGATGGTG 61.341 65.000 0.00 0.00 0.00 4.17
944 992 1.003573 GGAGGGAGTGAGGGATGGT 59.996 63.158 0.00 0.00 0.00 3.55
954 1002 2.540910 TGGAGGGAGGGAGGGAGT 60.541 66.667 0.00 0.00 0.00 3.85
969 1017 2.390599 CGTCGGAATGCAGTGGTGG 61.391 63.158 0.00 0.00 0.00 4.61
1119 1173 2.509336 GCGCACGTACCAGCTGAT 60.509 61.111 17.39 0.00 0.00 2.90
1190 1244 1.066303 CGTCATCGGAGAAGAAGGAGG 59.934 57.143 0.00 0.00 43.58 4.30
1193 1247 0.528684 GGCGTCATCGGAGAAGAAGG 60.529 60.000 0.00 0.00 43.58 3.46
1292 1346 0.875908 ATCCGATCAACCGCACGATG 60.876 55.000 0.00 0.00 0.00 3.84
1379 1433 0.179004 TCAAGGGAAGAAGCGCCAAA 60.179 50.000 2.29 0.00 0.00 3.28
1393 1447 2.455674 TCACGAACCAGACATCAAGG 57.544 50.000 0.00 0.00 0.00 3.61
1402 1456 1.660052 CGCACACATTTCACGAACCAG 60.660 52.381 0.00 0.00 0.00 4.00
1420 1474 1.174712 ATGGCATGGCACTATTCCGC 61.175 55.000 25.84 0.00 0.00 5.54
1467 1521 1.574134 CATTGCGGCATCCCAAATTC 58.426 50.000 2.28 0.00 0.00 2.17
1474 1528 2.414594 GGAAGCATTGCGGCATCC 59.585 61.111 2.28 3.30 43.47 3.51
1490 1544 5.006358 CGTAGAATACCCAAAAATCACGAGG 59.994 44.000 0.00 0.00 38.71 4.63
1503 1557 0.782384 CGATTGCGCGTAGAATACCC 59.218 55.000 8.43 0.00 38.71 3.69
1504 1558 1.484356 ACGATTGCGCGTAGAATACC 58.516 50.000 8.43 0.00 43.61 2.73
1505 1559 2.406863 CGAACGATTGCGCGTAGAATAC 60.407 50.000 8.43 0.00 44.86 1.89
1506 1560 1.776897 CGAACGATTGCGCGTAGAATA 59.223 47.619 8.43 0.00 44.86 1.75
1507 1561 0.570734 CGAACGATTGCGCGTAGAAT 59.429 50.000 8.43 3.74 44.86 2.40
1508 1562 0.454789 TCGAACGATTGCGCGTAGAA 60.455 50.000 8.43 0.00 44.86 2.10
1509 1563 0.860203 CTCGAACGATTGCGCGTAGA 60.860 55.000 8.43 0.00 44.86 2.59
1510 1564 1.132199 ACTCGAACGATTGCGCGTAG 61.132 55.000 8.43 0.00 44.86 3.51
1511 1565 1.129879 GACTCGAACGATTGCGCGTA 61.130 55.000 8.43 0.00 44.86 4.42
1513 1567 2.313374 GACTCGAACGATTGCGCG 59.687 61.111 0.00 0.00 42.48 6.86
2007 2115 1.605753 AGACTGTGCTCTGACGTGTA 58.394 50.000 0.00 0.00 0.00 2.90
2044 2152 6.522054 AGAAGAAGACTACCGATGTTCAAAA 58.478 36.000 0.00 0.00 0.00 2.44
2045 2153 6.097915 AGAAGAAGACTACCGATGTTCAAA 57.902 37.500 0.00 0.00 0.00 2.69
2048 2156 9.968870 AAATATAGAAGAAGACTACCGATGTTC 57.031 33.333 0.00 0.00 0.00 3.18
2184 2294 4.037446 GTGCAGTTTCAATACCCAGAACAA 59.963 41.667 0.00 0.00 0.00 2.83
2195 2305 9.573133 GCTAGTAAAATAATGTGCAGTTTCAAT 57.427 29.630 0.00 0.00 0.00 2.57
2291 2402 1.153823 CGATCGGGACACAGTGGTC 60.154 63.158 7.38 0.00 37.06 4.02
2292 2403 2.970639 CGATCGGGACACAGTGGT 59.029 61.111 7.38 0.00 0.00 4.16
2294 2405 2.613739 ATCGCGATCGGGACACAGTG 62.614 60.000 33.45 0.00 39.84 3.66
2295 2406 2.415608 ATCGCGATCGGGACACAGT 61.416 57.895 33.45 17.09 39.84 3.55
2296 2407 1.946156 CATCGCGATCGGGACACAG 60.946 63.158 33.45 20.37 39.84 3.66
2297 2408 2.104132 CATCGCGATCGGGACACA 59.896 61.111 33.45 14.81 39.84 3.72
2298 2409 2.402282 TAGCATCGCGATCGGGACAC 62.402 60.000 33.45 26.80 39.84 3.67
2300 2411 1.073216 CATAGCATCGCGATCGGGAC 61.073 60.000 33.45 22.62 39.84 4.46
2301 2412 1.212751 CATAGCATCGCGATCGGGA 59.787 57.895 32.97 32.97 41.24 5.14
2332 2447 7.559897 AGAAATTTGACCGGGAACATGTATTAT 59.440 33.333 6.32 0.00 0.00 1.28
2348 2463 6.018751 GCAAGAAAAAGGGACAGAAATTTGAC 60.019 38.462 0.00 0.00 0.00 3.18
2357 2472 4.082125 ACCATAGCAAGAAAAAGGGACAG 58.918 43.478 0.00 0.00 0.00 3.51
2397 2512 8.712363 CATCTATATCACCGAAATACAGGTTTG 58.288 37.037 0.00 0.00 39.00 2.93
2400 2515 7.776618 TCATCTATATCACCGAAATACAGGT 57.223 36.000 0.00 0.00 42.34 4.00
2477 2592 6.279882 ACAACATGTAACCTGTTTCATTTGG 58.720 36.000 0.00 8.07 34.69 3.28
2624 2842 4.707030 TCCATGTTGAAGCAATCATGTC 57.293 40.909 15.04 0.00 38.03 3.06
2719 2937 8.269317 AGGAACCGAACAATTCCAATTAGTATA 58.731 33.333 5.84 0.00 45.90 1.47
2786 3004 5.826643 AGCCTAAACACTTCCATTATCCAA 58.173 37.500 0.00 0.00 0.00 3.53
2822 3040 2.158682 ACCACCATTGTAGTTGTCAGCA 60.159 45.455 0.00 0.00 0.00 4.41
2836 3054 5.481473 AGAAACAAAATAGATGCACCACCAT 59.519 36.000 0.00 0.00 0.00 3.55
2911 3129 0.463474 GCAGACCAGGGCTTGAGATC 60.463 60.000 0.00 0.00 0.00 2.75
2928 3146 3.769739 AAGATAGGCGATTGGTATGCA 57.230 42.857 0.00 0.00 0.00 3.96
3004 3222 2.284699 CCGAACCCACCCTCTCCT 60.285 66.667 0.00 0.00 0.00 3.69
3049 3267 4.038763 AGAACACATGAACTCACCTCGTTA 59.961 41.667 0.00 0.00 0.00 3.18
3075 3293 9.077885 TCTATAATTCCAATTATTGAACTGCCC 57.922 33.333 6.50 0.00 40.85 5.36
3230 3467 1.402325 CCATAGCACAGAACGTCGACA 60.402 52.381 17.16 0.00 0.00 4.35
3238 3475 4.286032 ACCTCAGTAAACCATAGCACAGAA 59.714 41.667 0.00 0.00 0.00 3.02
3242 3479 4.324267 ACAACCTCAGTAAACCATAGCAC 58.676 43.478 0.00 0.00 0.00 4.40
3290 3527 9.126151 CGAATCATATAGTACACCATATCCTCT 57.874 37.037 0.00 0.00 0.00 3.69
3617 3943 5.513962 GGCTTCTTATTAGGGGGAAGATCTG 60.514 48.000 0.00 0.00 37.84 2.90
3631 3957 5.505181 TTCCAGTCAAGAGGCTTCTTATT 57.495 39.130 11.17 0.00 41.71 1.40
3690 4016 5.224888 CAGTTAACATGCAAATGCTTCAGT 58.775 37.500 8.61 0.00 42.66 3.41
4064 7279 2.173519 CAGCCATTATAGCATTGGGGG 58.826 52.381 0.00 0.00 0.00 5.40
4081 7296 4.700213 ACACAATATTGTCCTTGGTACAGC 59.300 41.667 18.25 0.00 38.70 4.40
4105 7320 7.402071 AGAACTCACCAAAGATATACCAGGTAA 59.598 37.037 2.53 0.00 0.00 2.85
4256 7492 9.425248 AATTATGGAGAAATGCCAAGAAGAATA 57.575 29.630 0.00 0.00 39.21 1.75
4304 7540 5.483685 TTCTGTCTAGTGTATGCCAAACT 57.516 39.130 0.00 0.00 0.00 2.66
4399 7636 9.708222 CAACAATTAATCTTCATCGTAGAAAGG 57.292 33.333 0.00 0.00 43.58 3.11
4406 7643 5.351465 AGTCGCAACAATTAATCTTCATCGT 59.649 36.000 0.00 0.00 0.00 3.73
4426 7663 7.359262 TGAAATTATACACCAACAAGAGTCG 57.641 36.000 0.00 0.00 0.00 4.18
4431 7668 5.184864 TGGCCTGAAATTATACACCAACAAG 59.815 40.000 3.32 0.00 0.00 3.16
4470 7707 2.609350 CAACATTGCAAAATCCCTCCG 58.391 47.619 1.71 0.00 0.00 4.63
4502 7739 4.216257 GTCATGTTGTACTGATTGCCAAGT 59.784 41.667 0.00 0.00 0.00 3.16
4538 7775 0.391597 TTCGAGCAACGGAAAGGACT 59.608 50.000 3.74 0.00 42.82 3.85
4762 7999 6.812879 TCATCATCATCATATCAAAGCCAC 57.187 37.500 0.00 0.00 0.00 5.01
4788 8031 5.133941 AGTAGAGCCTATTCTTGATCACGA 58.866 41.667 0.00 0.00 0.00 4.35
4789 8032 5.446143 AGTAGAGCCTATTCTTGATCACG 57.554 43.478 0.00 0.00 0.00 4.35
4801 8044 1.480683 CGGAATGGGGAGTAGAGCCTA 60.481 57.143 0.00 0.00 0.00 3.93
4864 8107 8.671028 GCACCTACTCTACTCTATCTATTTAGC 58.329 40.741 0.00 0.00 0.00 3.09
4868 8111 8.998277 TTTGCACCTACTCTACTCTATCTATT 57.002 34.615 0.00 0.00 0.00 1.73
4911 8225 1.777878 TGACAAACCTCAGGCCCTTAA 59.222 47.619 0.00 0.00 0.00 1.85
4913 8227 0.779997 ATGACAAACCTCAGGCCCTT 59.220 50.000 0.00 0.00 0.00 3.95
4925 8239 5.363868 TGTTCCCAAAACCACATATGACAAA 59.636 36.000 10.38 0.00 0.00 2.83
4940 8254 7.195374 ACTACTATGAAGCTATGTTCCCAAA 57.805 36.000 0.00 0.00 0.00 3.28
4968 8283 4.835615 AGATTAAGCGTCATGGAGGTATCT 59.164 41.667 0.00 0.00 0.00 1.98
4974 8289 2.219674 GCGAAGATTAAGCGTCATGGAG 59.780 50.000 7.41 0.00 0.00 3.86
5022 8337 4.815846 GCTGAAAACCATCAACAAAACCAT 59.184 37.500 0.00 0.00 0.00 3.55
5025 8340 3.559655 GGGCTGAAAACCATCAACAAAAC 59.440 43.478 0.00 0.00 0.00 2.43
5026 8341 3.739519 CGGGCTGAAAACCATCAACAAAA 60.740 43.478 0.00 0.00 0.00 2.44
5027 8342 2.223923 CGGGCTGAAAACCATCAACAAA 60.224 45.455 0.00 0.00 0.00 2.83
5028 8343 1.339610 CGGGCTGAAAACCATCAACAA 59.660 47.619 0.00 0.00 0.00 2.83
5031 8346 2.156098 GTACGGGCTGAAAACCATCAA 58.844 47.619 0.00 0.00 0.00 2.57
5032 8347 1.612199 GGTACGGGCTGAAAACCATCA 60.612 52.381 0.00 0.00 0.00 3.07
5033 8348 1.092348 GGTACGGGCTGAAAACCATC 58.908 55.000 0.00 0.00 0.00 3.51
5034 8349 0.696501 AGGTACGGGCTGAAAACCAT 59.303 50.000 15.90 3.23 32.43 3.55
5037 8352 3.817084 ACTTTTAGGTACGGGCTGAAAAC 59.183 43.478 0.00 0.00 0.00 2.43
5039 8354 3.181452 ACACTTTTAGGTACGGGCTGAAA 60.181 43.478 0.00 0.00 0.00 2.69
5047 8362 5.934935 AACCATCAACACTTTTAGGTACG 57.065 39.130 0.00 0.00 0.00 3.67
5136 8453 9.851686 ATAGTGAAAAATATGCAATGACCTAGA 57.148 29.630 0.00 0.00 0.00 2.43
5137 8454 9.888878 CATAGTGAAAAATATGCAATGACCTAG 57.111 33.333 0.00 0.00 0.00 3.02
5138 8455 9.407380 ACATAGTGAAAAATATGCAATGACCTA 57.593 29.630 0.00 0.00 33.53 3.08
5139 8456 8.297470 ACATAGTGAAAAATATGCAATGACCT 57.703 30.769 0.00 0.00 33.53 3.85
5140 8457 9.669353 CTACATAGTGAAAAATATGCAATGACC 57.331 33.333 0.00 0.00 33.53 4.02
5231 8571 1.604593 GGACATGCAACTGCCTGGT 60.605 57.895 11.01 1.57 40.31 4.00
5342 8684 6.785191 ACAAAGTATCTGTTGATTATTGCCG 58.215 36.000 0.00 0.00 34.32 5.69
5389 8731 2.935849 TCGATGCGCAACATATTCTTGT 59.064 40.909 17.11 0.00 39.84 3.16
5404 8746 6.521133 CAGTGTCTTATTTGTTCTTTCGATGC 59.479 38.462 0.00 0.00 0.00 3.91
5405 8747 7.017645 CCAGTGTCTTATTTGTTCTTTCGATG 58.982 38.462 0.00 0.00 0.00 3.84
5470 8821 6.212888 AGAGCATGTTTTGTTTCTCTTGTT 57.787 33.333 0.00 0.00 0.00 2.83
5522 8873 4.277423 CCCCTGTGTTGTTAGGTTAGTTTG 59.723 45.833 0.00 0.00 31.99 2.93
5624 8975 3.591196 TTGCAAGGCATCCATGTAAAC 57.409 42.857 0.00 0.00 38.76 2.01
5647 8998 4.422057 TGGAGTTATGTTGGTAGGTCTCA 58.578 43.478 0.00 0.00 0.00 3.27
5648 8999 5.364157 AGATGGAGTTATGTTGGTAGGTCTC 59.636 44.000 0.00 0.00 0.00 3.36
5649 9000 5.129485 CAGATGGAGTTATGTTGGTAGGTCT 59.871 44.000 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.