Multiple sequence alignment - TraesCS5B01G143500

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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 TraesCS5B01G143500 chr5B 100.000 6185 0 0 1 6185 270859657 270865841 0.000000e+00 11422.0
1 TraesCS5B01G143500 chr5B 100.000 49 0 0 5661 5709 270865268 270865316 2.370000e-14 91.6
2 TraesCS5B01G143500 chr5B 100.000 49 0 0 5612 5660 270865317 270865365 2.370000e-14 91.6
3 TraesCS5B01G143500 chr5B 100.000 39 0 0 5901 5939 59694497 59694459 8.600000e-09 73.1
4 TraesCS5B01G143500 chr5D 94.375 5564 182 52 53 5519 233973687 233968158 0.000000e+00 8419.0
5 TraesCS5B01G143500 chr5D 97.802 182 4 0 5947 6128 233967048 233966867 1.290000e-81 315.0
6 TraesCS5B01G143500 chr5D 91.803 122 10 0 5781 5902 233967168 233967047 2.960000e-38 171.0
7 TraesCS5B01G143500 chr5D 85.827 127 1 5 5534 5660 233967762 233967653 1.090000e-22 119.0
8 TraesCS5B01G143500 chr5D 96.923 65 2 0 5661 5725 233967701 233967637 6.550000e-20 110.0
9 TraesCS5B01G143500 chr5D 97.674 43 0 1 5897 5939 521630301 521630342 8.600000e-09 73.1
10 TraesCS5B01G143500 chr5A 93.992 4544 171 45 39 4528 320558831 320563326 0.000000e+00 6785.0
11 TraesCS5B01G143500 chr5A 94.328 1093 44 7 4574 5660 320563322 320564402 0.000000e+00 1659.0
12 TraesCS5B01G143500 chr5A 96.943 229 6 1 5947 6175 320564595 320564822 3.500000e-102 383.0
13 TraesCS5B01G143500 chr5A 94.650 243 12 1 5661 5902 320564354 320564596 5.850000e-100 375.0
14 TraesCS5B01G143500 chr4D 85.874 446 59 4 2289 2732 103254840 103254397 7.260000e-129 472.0
15 TraesCS5B01G143500 chr4D 82.660 421 59 8 4061 4481 103252932 103252526 1.640000e-95 361.0
16 TraesCS5B01G143500 chr4D 88.542 192 21 1 3272 3462 103253945 103253754 1.340000e-56 231.0
17 TraesCS5B01G143500 chr4D 90.805 87 5 3 1026 1111 103255775 103255691 5.070000e-21 113.0
18 TraesCS5B01G143500 chr4A 87.811 402 46 3 2289 2688 471918724 471919124 9.390000e-128 468.0
19 TraesCS5B01G143500 chr4A 82.898 421 58 8 4061 4481 471920858 471921264 3.520000e-97 366.0
20 TraesCS5B01G143500 chr4A 88.360 189 21 1 3272 3459 471919639 471919827 6.240000e-55 226.0
21 TraesCS5B01G143500 chr4A 90.805 87 5 3 1026 1111 471917787 471917871 5.070000e-21 113.0
22 TraesCS5B01G143500 chr4B 85.523 449 60 5 2289 2734 147382253 147381807 1.210000e-126 464.0
23 TraesCS5B01G143500 chr4B 88.021 192 22 1 3272 3462 147381337 147381146 6.240000e-55 226.0
24 TraesCS5B01G143500 chr4B 90.805 87 5 3 1026 1111 147383206 147383122 5.070000e-21 113.0
25 TraesCS5B01G143500 chr1D 95.918 49 1 1 5901 5948 330534623 330534671 1.850000e-10 78.7
26 TraesCS5B01G143500 chr7D 97.674 43 1 0 5897 5939 190127596 190127554 2.390000e-09 75.0
27 TraesCS5B01G143500 chr6B 97.674 43 0 1 5897 5939 62536735 62536776 8.600000e-09 73.1
28 TraesCS5B01G143500 chr3B 95.652 46 0 2 5896 5939 323357062 323357107 8.600000e-09 73.1
29 TraesCS5B01G143500 chr3A 100.000 39 0 0 5901 5939 711080642 711080680 8.600000e-09 73.1
30 TraesCS5B01G143500 chr2B 95.652 46 0 1 5896 5939 771779629 771779674 8.600000e-09 73.1
31 TraesCS5B01G143500 chr2A 100.000 39 0 0 5901 5939 352437503 352437465 8.600000e-09 73.1


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5B01G143500 chr5B 270859657 270865841 6184 False 3868.400000 11422 100.000000 1 6185 3 chr5B.!!$F1 6184
1 TraesCS5B01G143500 chr5D 233966867 233973687 6820 True 1826.800000 8419 93.346000 53 6128 5 chr5D.!!$R1 6075
2 TraesCS5B01G143500 chr5A 320558831 320564822 5991 False 2300.500000 6785 94.978250 39 6175 4 chr5A.!!$F1 6136
3 TraesCS5B01G143500 chr4D 103252526 103255775 3249 True 294.250000 472 86.970250 1026 4481 4 chr4D.!!$R1 3455
4 TraesCS5B01G143500 chr4A 471917787 471921264 3477 False 293.250000 468 87.468500 1026 4481 4 chr4A.!!$F1 3455
5 TraesCS5B01G143500 chr4B 147381146 147383206 2060 True 267.666667 464 88.116333 1026 3462 3 chr4B.!!$R1 2436

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
911 958 0.106719 CTCCTCTCCGCTTCCTCTCT 60.107 60.000 0.00 0.0 0.00 3.10 F
1932 2279 0.822164 GCATTCAATGGCCTGCTCTT 59.178 50.000 3.32 0.0 0.00 2.85 F
3206 3643 1.608590 CGTGTTCAATGGCTTTGGTCT 59.391 47.619 12.54 0.0 35.92 3.85 F
3687 4140 1.238439 AGTGAACAATGCCCAGTTCG 58.762 50.000 0.00 0.0 45.34 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1981 2328 1.401931 CCCAAGCGCATCAACTTTCTG 60.402 52.381 11.47 0.0 0.00 3.02 R
3656 4109 2.268762 TGTTCACTTGGCTACATGCA 57.731 45.000 0.00 0.0 45.15 3.96 R
4729 5710 1.069823 AGCAGTCAAGTGACCTGTCAG 59.930 52.381 7.82 0.0 45.85 3.51 R
5673 7040 0.036952 AGTTCGACAGCCATCACCAG 60.037 55.000 0.00 0.0 0.00 4.00 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
18 19 3.240670 TCCATAGTCCGAGCCCATT 57.759 52.632 0.00 0.00 0.00 3.16
19 20 0.758734 TCCATAGTCCGAGCCCATTG 59.241 55.000 0.00 0.00 0.00 2.82
20 21 0.469917 CCATAGTCCGAGCCCATTGT 59.530 55.000 0.00 0.00 0.00 2.71
21 22 1.541233 CCATAGTCCGAGCCCATTGTC 60.541 57.143 0.00 0.00 0.00 3.18
22 23 1.138859 CATAGTCCGAGCCCATTGTCA 59.861 52.381 0.00 0.00 0.00 3.58
23 24 1.271856 TAGTCCGAGCCCATTGTCAA 58.728 50.000 0.00 0.00 0.00 3.18
24 25 0.321653 AGTCCGAGCCCATTGTCAAC 60.322 55.000 0.00 0.00 0.00 3.18
25 26 0.605319 GTCCGAGCCCATTGTCAACA 60.605 55.000 0.00 0.00 0.00 3.33
26 27 0.605319 TCCGAGCCCATTGTCAACAC 60.605 55.000 0.00 0.00 0.00 3.32
27 28 1.586154 CCGAGCCCATTGTCAACACC 61.586 60.000 0.00 0.00 0.00 4.16
28 29 1.586154 CGAGCCCATTGTCAACACCC 61.586 60.000 0.00 0.00 0.00 4.61
29 30 0.251341 GAGCCCATTGTCAACACCCT 60.251 55.000 0.00 0.00 0.00 4.34
30 31 1.004277 GAGCCCATTGTCAACACCCTA 59.996 52.381 0.00 0.00 0.00 3.53
31 32 1.004745 AGCCCATTGTCAACACCCTAG 59.995 52.381 0.00 0.00 0.00 3.02
32 33 1.004277 GCCCATTGTCAACACCCTAGA 59.996 52.381 0.00 0.00 0.00 2.43
33 34 2.711542 CCCATTGTCAACACCCTAGAC 58.288 52.381 0.00 0.00 0.00 2.59
34 35 2.618045 CCCATTGTCAACACCCTAGACC 60.618 54.545 0.00 0.00 0.00 3.85
35 36 2.618045 CCATTGTCAACACCCTAGACCC 60.618 54.545 0.00 0.00 0.00 4.46
36 37 2.112279 TTGTCAACACCCTAGACCCT 57.888 50.000 0.00 0.00 0.00 4.34
37 38 1.640917 TGTCAACACCCTAGACCCTC 58.359 55.000 0.00 0.00 0.00 4.30
42 43 3.655777 TCAACACCCTAGACCCTCAAAAT 59.344 43.478 0.00 0.00 0.00 1.82
49 50 4.473559 CCCTAGACCCTCAAAATACCTTCA 59.526 45.833 0.00 0.00 0.00 3.02
50 51 5.045140 CCCTAGACCCTCAAAATACCTTCAA 60.045 44.000 0.00 0.00 0.00 2.69
73 74 9.901172 TCAATATCCAAGGATCATAGATTGATG 57.099 33.333 15.33 0.00 45.29 3.07
80 81 9.901172 CCAAGGATCATAGATTGATGAATCATA 57.099 33.333 7.67 0.00 45.29 2.15
130 132 3.119388 TCGGTTGTACGATAAGGTTGGAG 60.119 47.826 0.00 0.00 38.06 3.86
135 137 2.693267 ACGATAAGGTTGGAGAAGGC 57.307 50.000 0.00 0.00 0.00 4.35
155 157 7.505923 AGAAGGCTAACCACTTGTTTCTAAAAT 59.494 33.333 0.00 0.00 38.42 1.82
205 225 3.963428 TGTGTAAAGAGGAAGAGCTCC 57.037 47.619 10.93 0.00 45.81 4.70
367 388 5.556915 AGAACGGTAAACCATCAAATCTCA 58.443 37.500 0.00 0.00 35.14 3.27
368 389 5.411669 AGAACGGTAAACCATCAAATCTCAC 59.588 40.000 0.00 0.00 35.14 3.51
373 394 5.355350 GGTAAACCATCAAATCTCACCTCTG 59.645 44.000 0.00 0.00 35.64 3.35
374 395 4.647564 AACCATCAAATCTCACCTCTGT 57.352 40.909 0.00 0.00 0.00 3.41
382 403 8.733458 CATCAAATCTCACCTCTGTTCATTTTA 58.267 33.333 0.00 0.00 0.00 1.52
447 469 2.939103 CGTAGCAAGAGGAATCTTTGGG 59.061 50.000 0.00 0.00 0.00 4.12
547 570 2.806244 CTGTTTACGGACCCTGTTTCTG 59.194 50.000 0.00 0.00 0.00 3.02
580 604 1.479709 TTTTGCATCCCCCGGTATTG 58.520 50.000 0.00 0.00 0.00 1.90
614 638 2.482414 TTCCTCCATACCGGTACCAT 57.518 50.000 18.55 0.00 35.57 3.55
633 661 4.040217 ACCATATTGGCTGCAAAAGTTCAA 59.960 37.500 0.50 0.00 42.67 2.69
640 668 6.338214 TGGCTGCAAAAGTTCAACAATATA 57.662 33.333 0.50 0.00 0.00 0.86
673 701 6.120220 AGTTACCACCAACTAATTATGAGGC 58.880 40.000 0.00 0.00 36.99 4.70
682 710 6.705381 CCAACTAATTATGAGGCTCTCTGAAG 59.295 42.308 16.72 8.62 0.00 3.02
692 720 4.322567 AGGCTCTCTGAAGAAATGTCAAC 58.677 43.478 0.00 0.00 0.00 3.18
694 722 4.083590 GGCTCTCTGAAGAAATGTCAACAC 60.084 45.833 0.00 0.00 0.00 3.32
798 845 2.946990 TGTCTGTCACTCGTCACAAGTA 59.053 45.455 0.00 0.00 0.00 2.24
903 950 1.979693 GACACACCTCCTCTCCGCT 60.980 63.158 0.00 0.00 0.00 5.52
904 951 1.534235 ACACACCTCCTCTCCGCTT 60.534 57.895 0.00 0.00 0.00 4.68
905 952 1.216710 CACACCTCCTCTCCGCTTC 59.783 63.158 0.00 0.00 0.00 3.86
906 953 1.985116 ACACCTCCTCTCCGCTTCC 60.985 63.158 0.00 0.00 0.00 3.46
907 954 1.684049 CACCTCCTCTCCGCTTCCT 60.684 63.158 0.00 0.00 0.00 3.36
908 955 1.380650 ACCTCCTCTCCGCTTCCTC 60.381 63.158 0.00 0.00 0.00 3.71
909 956 1.076339 CCTCCTCTCCGCTTCCTCT 60.076 63.158 0.00 0.00 0.00 3.69
910 957 1.106944 CCTCCTCTCCGCTTCCTCTC 61.107 65.000 0.00 0.00 0.00 3.20
911 958 0.106719 CTCCTCTCCGCTTCCTCTCT 60.107 60.000 0.00 0.00 0.00 3.10
916 963 1.283613 TCTCCGCTTCCTCTCTTCTCT 59.716 52.381 0.00 0.00 0.00 3.10
919 966 1.136110 CCGCTTCCTCTCTTCTCTTCC 59.864 57.143 0.00 0.00 0.00 3.46
932 979 4.045334 TCTTCTCTTCCCTTCTCTCCTCTT 59.955 45.833 0.00 0.00 0.00 2.85
1001 1048 4.052518 GGGCCACCACCAGCAGAT 62.053 66.667 4.39 0.00 36.50 2.90
1143 1194 2.776370 TAGTCACCCTTCCCGACGCT 62.776 60.000 0.00 0.00 34.80 5.07
1233 1284 0.830648 TGGTGGAATAGCCGGAAGAG 59.169 55.000 5.05 0.00 40.66 2.85
1255 1306 3.659108 GCGTTCTTTGCTTCGATTTTTGC 60.659 43.478 0.00 0.00 0.00 3.68
1410 1490 6.316390 CGGCCTGACTAAATATTTCTTCTGTT 59.684 38.462 3.39 0.00 0.00 3.16
1498 1666 4.880696 CCCATTTGATTTCTCTCCTCTGAC 59.119 45.833 0.00 0.00 0.00 3.51
1589 1835 2.503356 TCTCCTTCCTCATCTTCTTGGC 59.497 50.000 0.00 0.00 0.00 4.52
1615 1861 5.447624 TGCATCATAAATCCTGCTTGATG 57.552 39.130 6.80 6.80 44.05 3.07
1932 2279 0.822164 GCATTCAATGGCCTGCTCTT 59.178 50.000 3.32 0.00 0.00 2.85
1981 2328 8.964420 TTTACAATTTACAGAGTTGCTAATGC 57.036 30.769 0.00 0.00 40.20 3.56
2032 2379 8.357402 AGACTTAACTGTCTTTCTTCTCTCTTC 58.643 37.037 0.00 0.00 44.01 2.87
2096 2443 9.626045 CAATCCCTCTGTAATTTTCAAACTAAC 57.374 33.333 0.00 0.00 0.00 2.34
2139 2486 7.468141 TGTACTACATGAGTGAGTTCAAGAT 57.532 36.000 0.00 0.00 39.39 2.40
2140 2487 7.539436 TGTACTACATGAGTGAGTTCAAGATC 58.461 38.462 0.00 0.00 39.39 2.75
2145 2492 7.432350 ACATGAGTGAGTTCAAGATCTTTTC 57.568 36.000 4.86 2.49 0.00 2.29
2167 2514 9.927668 TTTTCTTCTTGAATTCCATGGTTTATC 57.072 29.630 12.58 7.09 34.24 1.75
2230 2577 6.759497 ACCCTTTTTAATGTGATAGTCTGC 57.241 37.500 0.00 0.00 0.00 4.26
2399 2746 2.467880 TCAGATGTAAGTGACCCTCCC 58.532 52.381 0.00 0.00 0.00 4.30
3206 3643 1.608590 CGTGTTCAATGGCTTTGGTCT 59.391 47.619 12.54 0.00 35.92 3.85
3207 3644 2.811431 CGTGTTCAATGGCTTTGGTCTA 59.189 45.455 12.54 0.00 35.92 2.59
3208 3645 3.440173 CGTGTTCAATGGCTTTGGTCTAT 59.560 43.478 12.54 0.00 35.92 1.98
3209 3646 4.082787 CGTGTTCAATGGCTTTGGTCTATT 60.083 41.667 12.54 0.00 35.92 1.73
3210 3647 5.123186 CGTGTTCAATGGCTTTGGTCTATTA 59.877 40.000 12.54 0.00 35.92 0.98
3211 3648 6.183360 CGTGTTCAATGGCTTTGGTCTATTAT 60.183 38.462 12.54 0.00 35.92 1.28
3212 3649 7.547227 GTGTTCAATGGCTTTGGTCTATTATT 58.453 34.615 12.54 0.00 35.92 1.40
3213 3650 8.682710 GTGTTCAATGGCTTTGGTCTATTATTA 58.317 33.333 12.54 0.00 35.92 0.98
3214 3651 8.902806 TGTTCAATGGCTTTGGTCTATTATTAG 58.097 33.333 12.54 0.00 35.92 1.73
3215 3652 8.903820 GTTCAATGGCTTTGGTCTATTATTAGT 58.096 33.333 12.54 0.00 35.92 2.24
3479 3931 6.717997 TGGCAGCTCACATGATATCATAAAAT 59.282 34.615 17.77 1.95 34.26 1.82
3656 4109 7.678947 GCATTAGGCATCTTTATACACTCAT 57.321 36.000 0.00 0.00 43.97 2.90
3673 4126 3.011818 CTCATGCATGTAGCCAAGTGAA 58.988 45.455 25.43 1.46 44.83 3.18
3687 4140 1.238439 AGTGAACAATGCCCAGTTCG 58.762 50.000 0.00 0.00 45.34 3.95
4028 4996 5.934625 ACTTGTATCTGAGACAGCGAAAAAT 59.065 36.000 5.19 0.00 0.00 1.82
4508 5486 3.818961 ATTCGCTTAATGATGCCATCG 57.181 42.857 0.00 0.00 31.40 3.84
4637 5615 9.853177 ATTGGTTTTATTTGGTGTGGAATAAAA 57.147 25.926 8.93 8.93 41.62 1.52
4647 5625 9.549078 TTTGGTGTGGAATAAAATTTTTACCTC 57.451 29.630 9.06 10.96 0.00 3.85
4648 5626 8.251383 TGGTGTGGAATAAAATTTTTACCTCA 57.749 30.769 9.06 13.03 0.00 3.86
4729 5710 7.062749 TCACAACCTCATGAATATACCTACC 57.937 40.000 0.00 0.00 0.00 3.18
4730 5711 6.844388 TCACAACCTCATGAATATACCTACCT 59.156 38.462 0.00 0.00 0.00 3.08
5088 6069 3.851128 GGCGGCCTCCCTGACTAC 61.851 72.222 12.87 0.00 0.00 2.73
5233 6214 1.210478 CTACCCACTGCTGCAATAGGT 59.790 52.381 17.74 17.74 0.00 3.08
5276 6257 7.329226 AGCTTTTTCCGATGTGTAAATTTGATG 59.671 33.333 0.00 0.00 0.00 3.07
5277 6258 7.116233 GCTTTTTCCGATGTGTAAATTTGATGT 59.884 33.333 0.00 0.00 0.00 3.06
5382 6365 2.513897 GATCCCCGCTGAAACCGG 60.514 66.667 0.00 0.00 45.17 5.28
5474 6458 5.643777 GGAAGTTATGTCACATGTTGTAGCT 59.356 40.000 0.00 0.00 0.00 3.32
5487 6471 4.282496 TGTTGTAGCTTTTTCTTTCCCCA 58.718 39.130 0.00 0.00 0.00 4.96
5581 6948 6.842676 AGTTCTTGGTCATTTCCTTTCTAGT 58.157 36.000 0.00 0.00 0.00 2.57
5628 6995 2.821969 GCATGGTTTCTGATTGTCTGGT 59.178 45.455 0.00 0.00 0.00 4.00
5630 6997 3.855255 TGGTTTCTGATTGTCTGGTGA 57.145 42.857 0.00 0.00 0.00 4.02
5631 6998 4.371624 TGGTTTCTGATTGTCTGGTGAT 57.628 40.909 0.00 0.00 0.00 3.06
5632 6999 4.074259 TGGTTTCTGATTGTCTGGTGATG 58.926 43.478 0.00 0.00 0.00 3.07
5633 7000 3.441572 GGTTTCTGATTGTCTGGTGATGG 59.558 47.826 0.00 0.00 0.00 3.51
5634 7001 2.408271 TCTGATTGTCTGGTGATGGC 57.592 50.000 0.00 0.00 0.00 4.40
5635 7002 1.911357 TCTGATTGTCTGGTGATGGCT 59.089 47.619 0.00 0.00 0.00 4.75
5636 7003 2.014857 CTGATTGTCTGGTGATGGCTG 58.985 52.381 0.00 0.00 0.00 4.85
5637 7004 1.352017 TGATTGTCTGGTGATGGCTGT 59.648 47.619 0.00 0.00 0.00 4.40
5638 7005 2.012673 GATTGTCTGGTGATGGCTGTC 58.987 52.381 0.00 0.00 0.00 3.51
5639 7006 0.320683 TTGTCTGGTGATGGCTGTCG 60.321 55.000 0.00 0.00 0.00 4.35
5640 7007 1.184970 TGTCTGGTGATGGCTGTCGA 61.185 55.000 0.00 0.00 0.00 4.20
5641 7008 0.037326 GTCTGGTGATGGCTGTCGAA 60.037 55.000 0.00 0.00 0.00 3.71
5642 7009 0.037326 TCTGGTGATGGCTGTCGAAC 60.037 55.000 0.00 0.00 0.00 3.95
5643 7010 0.036952 CTGGTGATGGCTGTCGAACT 60.037 55.000 0.00 0.00 0.00 3.01
5644 7011 1.204704 CTGGTGATGGCTGTCGAACTA 59.795 52.381 0.00 0.00 0.00 2.24
5645 7012 1.204704 TGGTGATGGCTGTCGAACTAG 59.795 52.381 0.00 0.00 0.00 2.57
5646 7013 1.281899 GTGATGGCTGTCGAACTAGC 58.718 55.000 8.59 8.59 39.17 3.42
5647 7014 0.894835 TGATGGCTGTCGAACTAGCA 59.105 50.000 16.36 1.57 41.63 3.49
5648 7015 1.482182 TGATGGCTGTCGAACTAGCAT 59.518 47.619 16.36 9.64 41.63 3.79
5649 7016 2.131183 GATGGCTGTCGAACTAGCATC 58.869 52.381 16.36 13.21 41.63 3.91
5650 7017 0.894835 TGGCTGTCGAACTAGCATCA 59.105 50.000 16.36 6.29 41.63 3.07
5651 7018 1.281899 GGCTGTCGAACTAGCATCAC 58.718 55.000 16.36 0.00 41.63 3.06
5652 7019 1.281899 GCTGTCGAACTAGCATCACC 58.718 55.000 11.40 0.00 39.67 4.02
5653 7020 1.404181 GCTGTCGAACTAGCATCACCA 60.404 52.381 11.40 0.00 39.67 4.17
5654 7021 2.739932 GCTGTCGAACTAGCATCACCAT 60.740 50.000 11.40 0.00 39.67 3.55
5655 7022 3.490933 GCTGTCGAACTAGCATCACCATA 60.491 47.826 11.40 0.00 39.67 2.74
5656 7023 4.682787 CTGTCGAACTAGCATCACCATAA 58.317 43.478 0.00 0.00 0.00 1.90
5657 7024 5.276461 TGTCGAACTAGCATCACCATAAT 57.724 39.130 0.00 0.00 0.00 1.28
5658 7025 6.399639 TGTCGAACTAGCATCACCATAATA 57.600 37.500 0.00 0.00 0.00 0.98
5659 7026 6.811954 TGTCGAACTAGCATCACCATAATAA 58.188 36.000 0.00 0.00 0.00 1.40
5660 7027 6.923508 TGTCGAACTAGCATCACCATAATAAG 59.076 38.462 0.00 0.00 0.00 1.73
5661 7028 6.366332 GTCGAACTAGCATCACCATAATAAGG 59.634 42.308 0.00 0.00 0.00 2.69
5662 7029 6.041637 TCGAACTAGCATCACCATAATAAGGT 59.958 38.462 0.00 0.00 40.85 3.50
5663 7030 6.706270 CGAACTAGCATCACCATAATAAGGTT 59.294 38.462 0.00 0.00 37.23 3.50
5664 7031 7.226720 CGAACTAGCATCACCATAATAAGGTTT 59.773 37.037 0.00 0.00 37.23 3.27
5665 7032 8.451908 AACTAGCATCACCATAATAAGGTTTC 57.548 34.615 0.00 0.00 37.23 2.78
5666 7033 7.806180 ACTAGCATCACCATAATAAGGTTTCT 58.194 34.615 0.00 0.00 37.23 2.52
5667 7034 6.949352 AGCATCACCATAATAAGGTTTCTG 57.051 37.500 0.00 0.00 37.23 3.02
5668 7035 6.662755 AGCATCACCATAATAAGGTTTCTGA 58.337 36.000 0.00 0.00 37.23 3.27
5669 7036 7.293073 AGCATCACCATAATAAGGTTTCTGAT 58.707 34.615 0.00 0.00 37.23 2.90
5670 7037 7.781693 AGCATCACCATAATAAGGTTTCTGATT 59.218 33.333 0.00 0.00 37.23 2.57
5671 7038 7.864379 GCATCACCATAATAAGGTTTCTGATTG 59.136 37.037 0.00 0.00 37.23 2.67
5672 7039 8.906867 CATCACCATAATAAGGTTTCTGATTGT 58.093 33.333 0.00 0.00 37.23 2.71
5673 7040 8.506168 TCACCATAATAAGGTTTCTGATTGTC 57.494 34.615 0.00 0.00 37.23 3.18
5674 7041 8.328758 TCACCATAATAAGGTTTCTGATTGTCT 58.671 33.333 0.00 0.00 37.23 3.41
5675 7042 8.400947 CACCATAATAAGGTTTCTGATTGTCTG 58.599 37.037 0.00 0.00 37.23 3.51
5676 7043 7.557719 ACCATAATAAGGTTTCTGATTGTCTGG 59.442 37.037 0.00 0.00 35.33 3.86
5677 7044 7.557719 CCATAATAAGGTTTCTGATTGTCTGGT 59.442 37.037 0.00 0.00 0.00 4.00
5678 7045 6.824305 AATAAGGTTTCTGATTGTCTGGTG 57.176 37.500 0.00 0.00 0.00 4.17
5790 7570 4.752146 TGAGCAATCAGTGTGATCTACTG 58.248 43.478 18.74 18.74 45.30 2.74
5906 7687 9.573133 CAATCAATTCAAGTGTAAATTACTCCC 57.427 33.333 4.67 0.00 0.00 4.30
5907 7688 9.533831 AATCAATTCAAGTGTAAATTACTCCCT 57.466 29.630 4.67 0.00 0.00 4.20
5908 7689 8.561738 TCAATTCAAGTGTAAATTACTCCCTC 57.438 34.615 4.67 0.00 0.00 4.30
5909 7690 7.610305 TCAATTCAAGTGTAAATTACTCCCTCC 59.390 37.037 4.67 0.00 0.00 4.30
5910 7691 5.080969 TCAAGTGTAAATTACTCCCTCCG 57.919 43.478 4.67 0.00 0.00 4.63
5911 7692 4.529377 TCAAGTGTAAATTACTCCCTCCGT 59.471 41.667 4.67 0.00 0.00 4.69
5912 7693 4.732672 AGTGTAAATTACTCCCTCCGTC 57.267 45.455 4.67 0.00 0.00 4.79
5913 7694 3.450096 AGTGTAAATTACTCCCTCCGTCC 59.550 47.826 4.67 0.00 0.00 4.79
5914 7695 3.450096 GTGTAAATTACTCCCTCCGTCCT 59.550 47.826 4.67 0.00 0.00 3.85
5915 7696 4.646492 GTGTAAATTACTCCCTCCGTCCTA 59.354 45.833 4.67 0.00 0.00 2.94
5916 7697 5.303845 GTGTAAATTACTCCCTCCGTCCTAT 59.696 44.000 4.67 0.00 0.00 2.57
5917 7698 6.491403 GTGTAAATTACTCCCTCCGTCCTATA 59.509 42.308 4.67 0.00 0.00 1.31
5918 7699 7.014615 GTGTAAATTACTCCCTCCGTCCTATAA 59.985 40.741 4.67 0.00 0.00 0.98
5919 7700 7.731688 TGTAAATTACTCCCTCCGTCCTATAAT 59.268 37.037 4.67 0.00 0.00 1.28
5920 7701 6.607004 AATTACTCCCTCCGTCCTATAATG 57.393 41.667 0.00 0.00 0.00 1.90
5921 7702 3.614568 ACTCCCTCCGTCCTATAATGT 57.385 47.619 0.00 0.00 0.00 2.71
5922 7703 4.736611 ACTCCCTCCGTCCTATAATGTA 57.263 45.455 0.00 0.00 0.00 2.29
5923 7704 5.070823 ACTCCCTCCGTCCTATAATGTAA 57.929 43.478 0.00 0.00 0.00 2.41
5924 7705 5.078256 ACTCCCTCCGTCCTATAATGTAAG 58.922 45.833 0.00 0.00 0.00 2.34
5925 7706 5.163012 ACTCCCTCCGTCCTATAATGTAAGA 60.163 44.000 0.00 0.00 0.00 2.10
5926 7707 5.075493 TCCCTCCGTCCTATAATGTAAGAC 58.925 45.833 0.00 0.00 0.00 3.01
5928 7709 4.518211 CCTCCGTCCTATAATGTAAGACGT 59.482 45.833 9.63 0.00 46.62 4.34
5929 7710 5.009410 CCTCCGTCCTATAATGTAAGACGTT 59.991 44.000 9.63 0.00 46.62 3.99
5930 7711 6.455360 TCCGTCCTATAATGTAAGACGTTT 57.545 37.500 9.63 0.00 46.62 3.60
5931 7712 6.866480 TCCGTCCTATAATGTAAGACGTTTT 58.134 36.000 9.63 0.00 46.62 2.43
5932 7713 7.322664 TCCGTCCTATAATGTAAGACGTTTTT 58.677 34.615 9.63 0.00 46.62 1.94
6028 7809 2.271821 TACATGATCGTCGTGTGTGG 57.728 50.000 17.58 0.00 45.40 4.17
6040 7821 0.602638 GTGTGTGGCGTGGATCAAGA 60.603 55.000 0.00 0.00 0.00 3.02
6157 7938 9.050154 TGTATATGTCCATGGATTGATGTATCT 57.950 33.333 19.62 0.68 0.00 1.98
6175 7956 6.512297 TGTATCTTTTTCTTTTGAAGCCCAC 58.488 36.000 0.00 0.00 39.88 4.61
6176 7957 5.612725 ATCTTTTTCTTTTGAAGCCCACA 57.387 34.783 0.00 0.00 39.88 4.17
6177 7958 5.413309 TCTTTTTCTTTTGAAGCCCACAA 57.587 34.783 0.00 0.00 39.88 3.33
6178 7959 5.988287 TCTTTTTCTTTTGAAGCCCACAAT 58.012 33.333 0.00 0.00 39.88 2.71
6179 7960 7.118496 TCTTTTTCTTTTGAAGCCCACAATA 57.882 32.000 0.00 0.00 39.88 1.90
6180 7961 7.734942 TCTTTTTCTTTTGAAGCCCACAATAT 58.265 30.769 0.00 0.00 39.88 1.28
6181 7962 8.210265 TCTTTTTCTTTTGAAGCCCACAATATT 58.790 29.630 0.00 0.00 39.88 1.28
6182 7963 8.744568 TTTTTCTTTTGAAGCCCACAATATTT 57.255 26.923 0.00 0.00 39.88 1.40
6183 7964 8.744568 TTTTCTTTTGAAGCCCACAATATTTT 57.255 26.923 0.00 0.00 39.88 1.82
6184 7965 8.744568 TTTCTTTTGAAGCCCACAATATTTTT 57.255 26.923 0.00 0.00 39.88 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.758734 CAATGGGCTCGGACTATGGA 59.241 55.000 0.00 0.00 0.00 3.41
1 2 0.469917 ACAATGGGCTCGGACTATGG 59.530 55.000 0.00 0.00 0.00 2.74
2 3 1.138859 TGACAATGGGCTCGGACTATG 59.861 52.381 0.00 0.00 0.00 2.23
3 4 1.496060 TGACAATGGGCTCGGACTAT 58.504 50.000 0.00 0.00 0.00 2.12
4 5 1.066430 GTTGACAATGGGCTCGGACTA 60.066 52.381 0.00 0.00 0.00 2.59
5 6 0.321653 GTTGACAATGGGCTCGGACT 60.322 55.000 0.00 0.00 0.00 3.85
6 7 0.605319 TGTTGACAATGGGCTCGGAC 60.605 55.000 0.00 0.00 0.00 4.79
7 8 0.605319 GTGTTGACAATGGGCTCGGA 60.605 55.000 0.00 0.00 0.00 4.55
8 9 1.586154 GGTGTTGACAATGGGCTCGG 61.586 60.000 0.00 0.00 0.00 4.63
9 10 1.586154 GGGTGTTGACAATGGGCTCG 61.586 60.000 0.00 0.00 0.00 5.03
10 11 0.251341 AGGGTGTTGACAATGGGCTC 60.251 55.000 0.00 0.00 0.00 4.70
11 12 1.004745 CTAGGGTGTTGACAATGGGCT 59.995 52.381 0.00 0.00 0.00 5.19
12 13 1.004277 TCTAGGGTGTTGACAATGGGC 59.996 52.381 0.00 0.00 0.00 5.36
13 14 2.618045 GGTCTAGGGTGTTGACAATGGG 60.618 54.545 0.00 0.00 32.84 4.00
14 15 2.618045 GGGTCTAGGGTGTTGACAATGG 60.618 54.545 0.00 0.00 32.84 3.16
15 16 2.305927 AGGGTCTAGGGTGTTGACAATG 59.694 50.000 0.00 0.00 32.84 2.82
16 17 2.572104 GAGGGTCTAGGGTGTTGACAAT 59.428 50.000 0.00 0.00 32.84 2.71
17 18 1.975680 GAGGGTCTAGGGTGTTGACAA 59.024 52.381 0.00 0.00 32.84 3.18
18 19 1.132977 TGAGGGTCTAGGGTGTTGACA 60.133 52.381 0.00 0.00 32.84 3.58
19 20 1.640917 TGAGGGTCTAGGGTGTTGAC 58.359 55.000 0.00 0.00 0.00 3.18
20 21 2.409064 TTGAGGGTCTAGGGTGTTGA 57.591 50.000 0.00 0.00 0.00 3.18
21 22 3.502123 TTTTGAGGGTCTAGGGTGTTG 57.498 47.619 0.00 0.00 0.00 3.33
22 23 4.018688 GGTATTTTGAGGGTCTAGGGTGTT 60.019 45.833 0.00 0.00 0.00 3.32
23 24 3.522343 GGTATTTTGAGGGTCTAGGGTGT 59.478 47.826 0.00 0.00 0.00 4.16
24 25 3.780850 AGGTATTTTGAGGGTCTAGGGTG 59.219 47.826 0.00 0.00 0.00 4.61
25 26 4.090027 AGGTATTTTGAGGGTCTAGGGT 57.910 45.455 0.00 0.00 0.00 4.34
26 27 4.473559 TGAAGGTATTTTGAGGGTCTAGGG 59.526 45.833 0.00 0.00 0.00 3.53
27 28 5.693769 TGAAGGTATTTTGAGGGTCTAGG 57.306 43.478 0.00 0.00 0.00 3.02
28 29 9.495572 GATATTGAAGGTATTTTGAGGGTCTAG 57.504 37.037 0.00 0.00 0.00 2.43
29 30 8.437575 GGATATTGAAGGTATTTTGAGGGTCTA 58.562 37.037 0.00 0.00 0.00 2.59
30 31 7.091993 TGGATATTGAAGGTATTTTGAGGGTCT 60.092 37.037 0.00 0.00 0.00 3.85
31 32 7.060421 TGGATATTGAAGGTATTTTGAGGGTC 58.940 38.462 0.00 0.00 0.00 4.46
32 33 6.980577 TGGATATTGAAGGTATTTTGAGGGT 58.019 36.000 0.00 0.00 0.00 4.34
33 34 7.014615 CCTTGGATATTGAAGGTATTTTGAGGG 59.985 40.741 5.80 0.00 35.01 4.30
34 35 7.779798 TCCTTGGATATTGAAGGTATTTTGAGG 59.220 37.037 11.55 0.00 39.91 3.86
35 36 8.752005 TCCTTGGATATTGAAGGTATTTTGAG 57.248 34.615 11.55 0.00 39.91 3.02
36 37 9.354673 GATCCTTGGATATTGAAGGTATTTTGA 57.645 33.333 1.65 0.00 39.91 2.69
37 38 9.135189 TGATCCTTGGATATTGAAGGTATTTTG 57.865 33.333 1.65 0.00 39.91 2.44
42 43 8.972662 TCTATGATCCTTGGATATTGAAGGTA 57.027 34.615 1.65 2.75 39.91 3.08
102 103 3.428452 CCTTATCGTACAACCGAGAGCAA 60.428 47.826 0.00 0.00 40.68 3.91
103 104 2.098607 CCTTATCGTACAACCGAGAGCA 59.901 50.000 0.00 0.00 40.68 4.26
130 132 6.628919 TTTAGAAACAAGTGGTTAGCCTTC 57.371 37.500 0.00 0.00 39.29 3.46
135 137 9.965824 ATGTTGATTTTAGAAACAAGTGGTTAG 57.034 29.630 0.00 0.00 39.29 2.34
175 177 9.658799 CTCTTCCTCTTTACACATCTTGAATAA 57.341 33.333 0.00 0.00 0.00 1.40
176 178 7.766278 GCTCTTCCTCTTTACACATCTTGAATA 59.234 37.037 0.00 0.00 0.00 1.75
177 179 6.597280 GCTCTTCCTCTTTACACATCTTGAAT 59.403 38.462 0.00 0.00 0.00 2.57
180 182 5.486526 AGCTCTTCCTCTTTACACATCTTG 58.513 41.667 0.00 0.00 0.00 3.02
181 183 5.337975 GGAGCTCTTCCTCTTTACACATCTT 60.338 44.000 14.64 0.00 43.16 2.40
182 184 4.161377 GGAGCTCTTCCTCTTTACACATCT 59.839 45.833 14.64 0.00 43.16 2.90
183 185 4.438148 GGAGCTCTTCCTCTTTACACATC 58.562 47.826 14.64 0.00 43.16 3.06
205 225 0.602905 ACAGAAGAAACGGGAAGGCG 60.603 55.000 0.00 0.00 0.00 5.52
367 388 6.365520 ACTTGGACTTAAAATGAACAGAGGT 58.634 36.000 0.00 0.00 0.00 3.85
368 389 6.072452 GGACTTGGACTTAAAATGAACAGAGG 60.072 42.308 0.00 0.00 0.00 3.69
373 394 7.214467 TCATGGACTTGGACTTAAAATGAAC 57.786 36.000 0.00 0.00 0.00 3.18
374 395 6.071952 GCTCATGGACTTGGACTTAAAATGAA 60.072 38.462 0.00 0.00 0.00 2.57
382 403 3.087031 CAATGCTCATGGACTTGGACTT 58.913 45.455 0.00 0.00 0.00 3.01
462 484 3.188460 ACAATGTACGAACCATGAACAGC 59.812 43.478 0.00 0.00 0.00 4.40
500 523 3.133901 ACTTGGTGGATTTGTTTGGGAAC 59.866 43.478 0.00 0.00 36.29 3.62
547 570 4.531332 GATGCAAAATTAGTCTCCATCGC 58.469 43.478 0.00 0.00 0.00 4.58
614 638 4.662468 TGTTGAACTTTTGCAGCCAATA 57.338 36.364 0.00 0.00 0.00 1.90
651 679 6.157994 AGAGCCTCATAATTAGTTGGTGGTAA 59.842 38.462 0.00 0.00 0.00 2.85
673 701 4.984785 TCGTGTTGACATTTCTTCAGAGAG 59.015 41.667 0.00 0.00 32.44 3.20
682 710 6.198687 TCACTTCATTTCGTGTTGACATTTC 58.801 36.000 0.00 0.00 33.07 2.17
692 720 2.910482 CGCCATTTCACTTCATTTCGTG 59.090 45.455 0.00 0.00 0.00 4.35
694 722 2.095263 ACCGCCATTTCACTTCATTTCG 60.095 45.455 0.00 0.00 0.00 3.46
760 807 3.446516 CAGACAGGACTGATGAGTGATGA 59.553 47.826 6.29 0.00 39.94 2.92
798 845 2.614734 GGCAGAGCCTTAACCGTTACTT 60.615 50.000 0.00 0.00 46.69 2.24
895 942 1.676006 GAGAAGAGAGGAAGCGGAGAG 59.324 57.143 0.00 0.00 0.00 3.20
896 943 1.283613 AGAGAAGAGAGGAAGCGGAGA 59.716 52.381 0.00 0.00 0.00 3.71
898 945 2.096248 GAAGAGAAGAGAGGAAGCGGA 58.904 52.381 0.00 0.00 0.00 5.54
900 947 1.136110 GGGAAGAGAAGAGAGGAAGCG 59.864 57.143 0.00 0.00 0.00 4.68
903 950 4.045334 AGAGAAGGGAAGAGAAGAGAGGAA 59.955 45.833 0.00 0.00 0.00 3.36
904 951 3.596046 AGAGAAGGGAAGAGAAGAGAGGA 59.404 47.826 0.00 0.00 0.00 3.71
905 952 3.954258 GAGAGAAGGGAAGAGAAGAGAGG 59.046 52.174 0.00 0.00 0.00 3.69
906 953 3.954258 GGAGAGAAGGGAAGAGAAGAGAG 59.046 52.174 0.00 0.00 0.00 3.20
907 954 3.596046 AGGAGAGAAGGGAAGAGAAGAGA 59.404 47.826 0.00 0.00 0.00 3.10
908 955 3.954258 GAGGAGAGAAGGGAAGAGAAGAG 59.046 52.174 0.00 0.00 0.00 2.85
909 956 3.596046 AGAGGAGAGAAGGGAAGAGAAGA 59.404 47.826 0.00 0.00 0.00 2.87
910 957 3.981212 AGAGGAGAGAAGGGAAGAGAAG 58.019 50.000 0.00 0.00 0.00 2.85
911 958 4.045334 AGAAGAGGAGAGAAGGGAAGAGAA 59.955 45.833 0.00 0.00 0.00 2.87
916 963 3.309556 GGAGAGAAGAGGAGAGAAGGGAA 60.310 52.174 0.00 0.00 0.00 3.97
919 966 3.053693 TGAGGAGAGAAGAGGAGAGAAGG 60.054 52.174 0.00 0.00 0.00 3.46
992 1039 1.612726 GGCTCTTGTTCATCTGCTGGT 60.613 52.381 0.00 0.00 0.00 4.00
995 1042 0.034670 GGGGCTCTTGTTCATCTGCT 60.035 55.000 0.00 0.00 0.00 4.24
1001 1048 3.126703 TTGGCGGGGCTCTTGTTCA 62.127 57.895 0.00 0.00 0.00 3.18
1143 1194 0.544120 GGCAAGAAATCCCCAACCCA 60.544 55.000 0.00 0.00 0.00 4.51
1180 1231 1.596477 GGATCTCAGCATCCACCGC 60.596 63.158 0.00 0.00 42.02 5.68
1187 1238 1.606480 CCATAACGCGGATCTCAGCAT 60.606 52.381 12.47 0.00 36.87 3.79
1223 1274 0.951040 CAAAGAACGCTCTTCCGGCT 60.951 55.000 0.75 0.00 41.23 5.52
1233 1284 3.659108 GCAAAAATCGAAGCAAAGAACGC 60.659 43.478 0.00 0.00 0.00 4.84
1255 1306 0.525242 TAATAAACCGGACGCCGTCG 60.525 55.000 9.46 6.63 46.80 5.12
1351 1402 8.654094 AGATTTCAATCAATCAAAACCCTCTTT 58.346 29.630 2.43 0.00 37.89 2.52
1410 1490 2.018515 GCAAAATCCCCCGTTCGAATA 58.981 47.619 0.00 0.00 0.00 1.75
1452 1614 4.338118 GGATTCAAGACACCAAAGTTGACA 59.662 41.667 0.00 0.00 0.00 3.58
1498 1666 8.131100 ACAGTTGAACAAAAGTTGATACTCATG 58.869 33.333 0.00 0.00 31.99 3.07
1555 1794 3.054508 AGGAAGGAGAGAAGAATGGCAAG 60.055 47.826 0.00 0.00 0.00 4.01
1589 1835 5.298527 TCAAGCAGGATTTATGATGCAAGAG 59.701 40.000 0.00 0.00 41.14 2.85
1615 1861 4.695928 GGTAAATATTTCCCGATGAGCTCC 59.304 45.833 12.15 0.00 0.00 4.70
1624 1870 1.202842 AGGGCCGGTAAATATTTCCCG 60.203 52.381 21.64 21.64 40.12 5.14
1887 2234 5.337652 GGCTTGGACTATGTTTCTGAGTACT 60.338 44.000 0.00 0.00 0.00 2.73
1981 2328 1.401931 CCCAAGCGCATCAACTTTCTG 60.402 52.381 11.47 0.00 0.00 3.02
2096 2443 2.499289 ACATAGAGCTGAGTCAAGGTGG 59.501 50.000 0.00 0.00 0.00 4.61
2139 2486 7.601705 AACCATGGAATTCAAGAAGAAAAGA 57.398 32.000 21.47 0.00 40.22 2.52
2140 2487 9.933723 ATAAACCATGGAATTCAAGAAGAAAAG 57.066 29.630 21.47 0.00 40.22 2.27
2145 2492 9.880157 AAATGATAAACCATGGAATTCAAGAAG 57.120 29.630 21.47 0.00 0.00 2.85
2230 2577 6.662414 TGCATCAGTCGGATAAACTAAAAG 57.338 37.500 0.00 0.00 33.95 2.27
2399 2746 4.034510 GCATCTTCGATTTTCCTAGGTGTG 59.965 45.833 9.08 0.00 0.00 3.82
2937 3355 3.743521 TCCAGTTTCCACATTCTGAGTG 58.256 45.455 0.00 0.00 36.76 3.51
3479 3931 9.625747 TGTAAAGATATGATGCCACAGAAATTA 57.374 29.630 0.00 0.00 0.00 1.40
3493 3945 8.847982 TCGGGGGAATATATGTAAAGATATGA 57.152 34.615 0.00 0.00 0.00 2.15
3643 4096 5.759763 TGGCTACATGCATGAGTGTATAAAG 59.240 40.000 32.75 14.50 45.15 1.85
3656 4109 2.268762 TGTTCACTTGGCTACATGCA 57.731 45.000 0.00 0.00 45.15 3.96
3673 4126 3.672293 CAGCGAACTGGGCATTGT 58.328 55.556 0.00 0.00 40.48 2.71
3687 4140 6.603940 ATTCTAGATCAGGGAAGATACAGC 57.396 41.667 0.00 0.00 0.00 4.40
3922 4448 9.100554 CAATTTTTGCAATTTGGATATAGCTCA 57.899 29.630 0.00 0.00 0.00 4.26
4012 4980 4.085415 GCAAAACATTTTTCGCTGTCTCAG 60.085 41.667 0.00 0.00 34.12 3.35
4016 4984 3.796178 TCAGCAAAACATTTTTCGCTGTC 59.204 39.130 15.03 0.00 42.75 3.51
4028 4996 3.845781 AGAGAAGGAGTCAGCAAAACA 57.154 42.857 0.00 0.00 0.00 2.83
4068 5046 1.683418 CCCAGGGTAACGGAGTAGCC 61.683 65.000 0.00 3.77 45.00 3.93
4176 5154 5.045286 AGAGTCCAGCAGAATATTTGAGGTT 60.045 40.000 0.00 0.00 0.00 3.50
4317 5295 2.533266 AGCAGTATAATCCTGTGGCG 57.467 50.000 0.00 0.00 32.41 5.69
4661 5641 2.284627 GCATTTTTCGCATCGCATCAAC 60.285 45.455 0.00 0.00 0.00 3.18
4700 5681 3.641434 ATTCATGAGGTTGTGAGGAGG 57.359 47.619 0.00 0.00 0.00 4.30
4706 5687 6.931281 CAGGTAGGTATATTCATGAGGTTGTG 59.069 42.308 0.00 0.00 0.00 3.33
4707 5688 6.844388 TCAGGTAGGTATATTCATGAGGTTGT 59.156 38.462 0.00 0.00 0.00 3.32
4729 5710 1.069823 AGCAGTCAAGTGACCTGTCAG 59.930 52.381 7.82 0.00 45.85 3.51
4730 5711 1.123077 AGCAGTCAAGTGACCTGTCA 58.877 50.000 7.82 0.00 45.85 3.58
4746 5727 4.019858 AGCTGTAGACATCACTTCTAGCA 58.980 43.478 0.00 0.00 0.00 3.49
5022 6003 4.728409 CCACTCTGCAATGGCTCA 57.272 55.556 0.00 0.00 41.91 4.26
5233 6214 2.862541 AGCTTGCAATGTACAACTGGA 58.137 42.857 0.00 0.00 0.00 3.86
5276 6257 0.457681 AAAACAACAGTGGCACGCAC 60.458 50.000 12.71 0.00 44.14 5.34
5277 6258 0.244994 AAAAACAACAGTGGCACGCA 59.755 45.000 12.71 0.00 44.14 5.24
5297 6280 1.608590 GCCTTACAAGCAGCAGAAACA 59.391 47.619 0.00 0.00 0.00 2.83
5429 6412 3.822735 CCATAGTTCCATACCATTGCCAG 59.177 47.826 0.00 0.00 0.00 4.85
5474 6458 4.732065 ACCGATAACTGGGGAAAGAAAAA 58.268 39.130 0.00 0.00 0.00 1.94
5487 6471 2.119495 AGCAATCCAGGACCGATAACT 58.881 47.619 0.00 0.00 0.00 2.24
5581 6948 8.627403 CAACATACTCCGGTACTCTAATTCTTA 58.373 37.037 0.00 0.00 0.00 2.10
5596 6963 3.009723 AGAAACCATGCAACATACTCCG 58.990 45.455 0.00 0.00 0.00 4.63
5628 6995 0.894835 TGCTAGTTCGACAGCCATCA 59.105 50.000 9.64 0.00 36.95 3.07
5630 6997 1.482182 TGATGCTAGTTCGACAGCCAT 59.518 47.619 9.64 4.68 36.95 4.40
5631 6998 0.894835 TGATGCTAGTTCGACAGCCA 59.105 50.000 9.64 0.66 36.95 4.75
5632 6999 1.281899 GTGATGCTAGTTCGACAGCC 58.718 55.000 9.64 0.00 36.95 4.85
5633 7000 1.281899 GGTGATGCTAGTTCGACAGC 58.718 55.000 6.01 6.01 38.31 4.40
5634 7001 2.654749 TGGTGATGCTAGTTCGACAG 57.345 50.000 0.00 0.00 0.00 3.51
5635 7002 4.729227 TTATGGTGATGCTAGTTCGACA 57.271 40.909 0.00 0.00 0.00 4.35
5636 7003 6.366332 CCTTATTATGGTGATGCTAGTTCGAC 59.634 42.308 0.00 0.00 0.00 4.20
5637 7004 6.041637 ACCTTATTATGGTGATGCTAGTTCGA 59.958 38.462 0.64 0.00 36.30 3.71
5638 7005 6.223852 ACCTTATTATGGTGATGCTAGTTCG 58.776 40.000 0.64 0.00 36.30 3.95
5639 7006 8.451908 AAACCTTATTATGGTGATGCTAGTTC 57.548 34.615 2.24 0.00 37.93 3.01
5640 7007 8.275040 AGAAACCTTATTATGGTGATGCTAGTT 58.725 33.333 2.24 0.00 37.93 2.24
5641 7008 7.716998 CAGAAACCTTATTATGGTGATGCTAGT 59.283 37.037 2.24 0.00 37.93 2.57
5642 7009 7.933577 TCAGAAACCTTATTATGGTGATGCTAG 59.066 37.037 2.24 0.00 37.93 3.42
5643 7010 7.801104 TCAGAAACCTTATTATGGTGATGCTA 58.199 34.615 2.24 0.00 37.93 3.49
5644 7011 6.662755 TCAGAAACCTTATTATGGTGATGCT 58.337 36.000 2.24 0.00 37.93 3.79
5645 7012 6.942532 TCAGAAACCTTATTATGGTGATGC 57.057 37.500 2.24 0.00 37.93 3.91
5646 7013 8.906867 ACAATCAGAAACCTTATTATGGTGATG 58.093 33.333 2.24 3.01 37.93 3.07
5647 7014 9.125026 GACAATCAGAAACCTTATTATGGTGAT 57.875 33.333 2.24 0.00 37.93 3.06
5648 7015 8.328758 AGACAATCAGAAACCTTATTATGGTGA 58.671 33.333 2.24 0.00 37.93 4.02
5649 7016 8.400947 CAGACAATCAGAAACCTTATTATGGTG 58.599 37.037 2.24 0.00 37.93 4.17
5650 7017 7.557719 CCAGACAATCAGAAACCTTATTATGGT 59.442 37.037 0.00 0.00 39.91 3.55
5651 7018 7.557719 ACCAGACAATCAGAAACCTTATTATGG 59.442 37.037 0.00 0.00 0.00 2.74
5652 7019 8.400947 CACCAGACAATCAGAAACCTTATTATG 58.599 37.037 0.00 0.00 0.00 1.90
5653 7020 8.328758 TCACCAGACAATCAGAAACCTTATTAT 58.671 33.333 0.00 0.00 0.00 1.28
5654 7021 7.685481 TCACCAGACAATCAGAAACCTTATTA 58.315 34.615 0.00 0.00 0.00 0.98
5655 7022 6.542821 TCACCAGACAATCAGAAACCTTATT 58.457 36.000 0.00 0.00 0.00 1.40
5656 7023 6.126863 TCACCAGACAATCAGAAACCTTAT 57.873 37.500 0.00 0.00 0.00 1.73
5657 7024 5.560722 TCACCAGACAATCAGAAACCTTA 57.439 39.130 0.00 0.00 0.00 2.69
5658 7025 4.437682 TCACCAGACAATCAGAAACCTT 57.562 40.909 0.00 0.00 0.00 3.50
5659 7026 4.330250 CATCACCAGACAATCAGAAACCT 58.670 43.478 0.00 0.00 0.00 3.50
5660 7027 3.441572 CCATCACCAGACAATCAGAAACC 59.558 47.826 0.00 0.00 0.00 3.27
5661 7028 3.119708 GCCATCACCAGACAATCAGAAAC 60.120 47.826 0.00 0.00 0.00 2.78
5662 7029 3.084039 GCCATCACCAGACAATCAGAAA 58.916 45.455 0.00 0.00 0.00 2.52
5663 7030 2.306805 AGCCATCACCAGACAATCAGAA 59.693 45.455 0.00 0.00 0.00 3.02
5664 7031 1.911357 AGCCATCACCAGACAATCAGA 59.089 47.619 0.00 0.00 0.00 3.27
5665 7032 2.014857 CAGCCATCACCAGACAATCAG 58.985 52.381 0.00 0.00 0.00 2.90
5666 7033 1.352017 ACAGCCATCACCAGACAATCA 59.648 47.619 0.00 0.00 0.00 2.57
5667 7034 2.012673 GACAGCCATCACCAGACAATC 58.987 52.381 0.00 0.00 0.00 2.67
5668 7035 1.676916 CGACAGCCATCACCAGACAAT 60.677 52.381 0.00 0.00 0.00 2.71
5669 7036 0.320683 CGACAGCCATCACCAGACAA 60.321 55.000 0.00 0.00 0.00 3.18
5670 7037 1.184970 TCGACAGCCATCACCAGACA 61.185 55.000 0.00 0.00 0.00 3.41
5671 7038 0.037326 TTCGACAGCCATCACCAGAC 60.037 55.000 0.00 0.00 0.00 3.51
5672 7039 0.037326 GTTCGACAGCCATCACCAGA 60.037 55.000 0.00 0.00 0.00 3.86
5673 7040 0.036952 AGTTCGACAGCCATCACCAG 60.037 55.000 0.00 0.00 0.00 4.00
5674 7041 1.204704 CTAGTTCGACAGCCATCACCA 59.795 52.381 0.00 0.00 0.00 4.17
5675 7042 1.927895 CTAGTTCGACAGCCATCACC 58.072 55.000 0.00 0.00 0.00 4.02
5676 7043 1.281899 GCTAGTTCGACAGCCATCAC 58.718 55.000 2.17 0.00 0.00 3.06
5677 7044 0.894835 TGCTAGTTCGACAGCCATCA 59.105 50.000 9.64 0.00 36.95 3.07
5678 7045 2.131183 GATGCTAGTTCGACAGCCATC 58.869 52.381 9.64 8.84 36.95 3.51
5725 7092 0.459489 TGTTGCAAGGCAGGTCAAAC 59.541 50.000 0.00 0.00 40.61 2.93
5790 7570 2.614057 GCCATGTGCATAGACAACTACC 59.386 50.000 0.00 0.00 40.77 3.18
5870 7651 6.071728 ACACTTGAATTGATTGAGAATGACCC 60.072 38.462 0.00 0.00 0.00 4.46
5901 7682 3.614568 ACATTATAGGACGGAGGGAGT 57.385 47.619 0.00 0.00 0.00 3.85
5902 7683 5.183522 GTCTTACATTATAGGACGGAGGGAG 59.816 48.000 0.00 0.00 0.00 4.30
5903 7684 5.075493 GTCTTACATTATAGGACGGAGGGA 58.925 45.833 0.00 0.00 0.00 4.20
5904 7685 4.082895 CGTCTTACATTATAGGACGGAGGG 60.083 50.000 9.88 0.00 43.69 4.30
5905 7686 5.044428 CGTCTTACATTATAGGACGGAGG 57.956 47.826 9.88 0.00 43.69 4.30
5929 7710 5.534207 TTACTACTCCCTCGTGTCAAAAA 57.466 39.130 0.00 0.00 0.00 1.94
5930 7711 5.534207 TTTACTACTCCCTCGTGTCAAAA 57.466 39.130 0.00 0.00 0.00 2.44
5931 7712 5.733620 ATTTACTACTCCCTCGTGTCAAA 57.266 39.130 0.00 0.00 0.00 2.69
5932 7713 5.475719 CAATTTACTACTCCCTCGTGTCAA 58.524 41.667 0.00 0.00 0.00 3.18
5933 7714 4.081862 CCAATTTACTACTCCCTCGTGTCA 60.082 45.833 0.00 0.00 0.00 3.58
5934 7715 4.081807 ACCAATTTACTACTCCCTCGTGTC 60.082 45.833 0.00 0.00 0.00 3.67
5935 7716 3.836562 ACCAATTTACTACTCCCTCGTGT 59.163 43.478 0.00 0.00 0.00 4.49
5936 7717 4.181578 CACCAATTTACTACTCCCTCGTG 58.818 47.826 0.00 0.00 0.00 4.35
5937 7718 3.836562 ACACCAATTTACTACTCCCTCGT 59.163 43.478 0.00 0.00 0.00 4.18
5938 7719 4.181578 CACACCAATTTACTACTCCCTCG 58.818 47.826 0.00 0.00 0.00 4.63
5939 7720 4.019591 ACCACACCAATTTACTACTCCCTC 60.020 45.833 0.00 0.00 0.00 4.30
5940 7721 3.914435 ACCACACCAATTTACTACTCCCT 59.086 43.478 0.00 0.00 0.00 4.20
5941 7722 4.007659 CACCACACCAATTTACTACTCCC 58.992 47.826 0.00 0.00 0.00 4.30
5942 7723 3.439129 GCACCACACCAATTTACTACTCC 59.561 47.826 0.00 0.00 0.00 3.85
5943 7724 3.439129 GGCACCACACCAATTTACTACTC 59.561 47.826 0.00 0.00 0.00 2.59
5944 7725 3.181438 TGGCACCACACCAATTTACTACT 60.181 43.478 0.00 0.00 33.12 2.57
5945 7726 3.150767 TGGCACCACACCAATTTACTAC 58.849 45.455 0.00 0.00 33.12 2.73
5946 7727 3.510531 TGGCACCACACCAATTTACTA 57.489 42.857 0.00 0.00 33.12 1.82
6028 7809 2.541762 GCTTATCTGTCTTGATCCACGC 59.458 50.000 0.00 0.00 0.00 5.34
6154 7935 5.612725 TGTGGGCTTCAAAAGAAAAAGAT 57.387 34.783 0.00 0.00 0.00 2.40
6157 7938 8.744568 AAATATTGTGGGCTTCAAAAGAAAAA 57.255 26.923 0.00 0.00 0.00 1.94


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

AutoCloner maintained by Alex Coulton.