Multiple sequence alignment - TraesCS7A01G066300

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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 TraesCS7A01G066300 chr7A 100.000 7901 0 0 1 7901 33202956 33195056 0.000000e+00 14591.0
1 TraesCS7A01G066300 chr7A 89.157 83 7 2 7820 7901 648953758 648953677 1.400000e-17 102.0
2 TraesCS7A01G066300 chr7A 87.356 87 11 0 7815 7901 700508857 700508943 5.040000e-17 100.0
3 TraesCS7A01G066300 chr7D 94.865 4557 134 34 604 5123 32960743 32956250 0.000000e+00 7027.0
4 TraesCS7A01G066300 chr7D 95.550 2000 73 6 5183 7179 32956234 32954248 0.000000e+00 3186.0
5 TraesCS7A01G066300 chr7D 87.018 570 58 9 7176 7744 32954154 32953600 5.200000e-176 628.0
6 TraesCS7A01G066300 chr7D 86.216 370 21 7 135 487 32961211 32960855 2.690000e-99 374.0
7 TraesCS7A01G066300 chr7D 85.437 103 1 3 520 613 32960867 32960770 2.350000e-15 95.3
8 TraesCS7A01G066300 chr4A 92.009 2578 114 28 4629 7153 692965465 692962927 0.000000e+00 3535.0
9 TraesCS7A01G066300 chr4A 95.512 1961 72 10 2677 4626 692967538 692965583 0.000000e+00 3120.0
10 TraesCS7A01G066300 chr4A 88.998 2136 141 40 607 2692 692969656 692967565 0.000000e+00 2556.0
11 TraesCS7A01G066300 chr4A 84.569 661 77 18 7176 7823 692962810 692962162 4.020000e-177 632.0
12 TraesCS7A01G066300 chr4A 78.629 496 45 27 23 487 692970245 692969780 1.010000e-68 272.0
13 TraesCS7A01G066300 chr4A 91.358 81 4 3 7823 7901 225310413 225310492 3.010000e-19 108.0
14 TraesCS7A01G066300 chr4A 89.535 86 7 2 7817 7901 584900763 584900847 3.010000e-19 108.0
15 TraesCS7A01G066300 chr6B 87.758 678 55 14 1146 1808 402446878 402447542 0.000000e+00 767.0
16 TraesCS7A01G066300 chr7B 86.008 486 49 7 3180 3650 685038632 685038151 3.290000e-138 503.0
17 TraesCS7A01G066300 chr7B 85.714 98 10 4 7807 7901 51080001 51080097 5.040000e-17 100.0
18 TraesCS7A01G066300 chr2B 85.161 465 51 11 3195 3650 152709860 152710315 2.010000e-125 460.0
19 TraesCS7A01G066300 chr5B 84.615 468 54 8 3180 3633 547361123 547360660 4.350000e-122 449.0
20 TraesCS7A01G066300 chr6A 83.468 496 64 13 3808 4301 454707873 454708352 5.630000e-121 446.0
21 TraesCS7A01G066300 chr6A 92.500 80 4 2 7823 7901 166310501 166310423 6.480000e-21 113.0
22 TraesCS7A01G066300 chr5A 82.812 512 66 15 3808 4317 548797309 548796818 9.410000e-119 438.0
23 TraesCS7A01G066300 chr5A 89.873 79 8 0 7823 7901 624607281 624607203 1.400000e-17 102.0
24 TraesCS7A01G066300 chr1A 84.653 404 49 8 3193 3588 417378141 417378539 2.670000e-104 390.0
25 TraesCS7A01G066300 chr1A 83.267 251 36 4 4067 4317 573211982 573211738 7.980000e-55 226.0
26 TraesCS7A01G066300 chr1A 90.361 83 6 2 7820 7901 271624635 271624554 3.010000e-19 108.0
27 TraesCS7A01G066300 chr3A 89.157 83 7 2 7820 7901 680673991 680673910 1.400000e-17 102.0
28 TraesCS7A01G066300 chr3D 92.308 52 4 0 4839 4890 2381013 2380962 3.060000e-09 75.0


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 TraesCS7A01G066300 chr7A 33195056 33202956 7900 True 14591.00 14591 100.0000 1 7901 1 chr7A.!!$R1 7900
1 TraesCS7A01G066300 chr7D 32953600 32961211 7611 True 2262.06 7027 89.8172 135 7744 5 chr7D.!!$R1 7609
2 TraesCS7A01G066300 chr4A 692962162 692970245 8083 True 2023.00 3535 87.9434 23 7823 5 chr4A.!!$R1 7800
3 TraesCS7A01G066300 chr6B 402446878 402447542 664 False 767.00 767 87.7580 1146 1808 1 chr6B.!!$F1 662

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
476 516 0.041135 CCTCGAGCGAATACGACCTC 60.041 60.000 6.99 0.00 42.66 3.85 F
1415 1562 0.101759 ATGCGCCAACAGATTGATGC 59.898 50.000 4.18 0.00 38.15 3.91 F
1416 1563 1.226773 GCGCCAACAGATTGATGCC 60.227 57.895 0.00 0.00 38.15 4.40 F
1701 1859 1.547372 ACATTTTGAGACCAGCATGCC 59.453 47.619 15.66 0.00 31.97 4.40 F
2734 2942 2.059756 TCTGTCTTTTCCCCATCCCT 57.940 50.000 0.00 0.00 0.00 4.20 F
2804 3012 2.642996 TACCGTGCCATGGAGCATCG 62.643 60.000 18.40 12.72 46.24 3.84 F
4408 4627 1.863454 GTGCCTCGAAGCATGACATAG 59.137 52.381 12.63 0.00 46.24 2.23 F
5755 6126 1.126113 GTGTGTTCATCTAACCGTGCG 59.874 52.381 0.00 0.00 37.27 5.34 F
6423 6809 0.694771 TGGCAAGCAGAGGAGACATT 59.305 50.000 0.00 0.00 0.00 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1604 1758 0.098552 TCACAATAAATGGCTGCGCG 59.901 50.000 0.00 0.0 0.00 6.86 R
2286 2452 3.632145 AGGCAATTAAGGGCAATACGAAG 59.368 43.478 6.31 0.0 0.00 3.79 R
2793 3001 3.787634 CGTTCATTTTTCGATGCTCCATG 59.212 43.478 0.00 0.0 0.00 3.66 R
3521 3732 2.693074 CCCAAGATAATTCAAACCCCCG 59.307 50.000 0.00 0.0 0.00 5.73 R
4203 4420 5.136828 ACAACCAATGGTTCAACTATGACA 58.863 37.500 15.79 0.0 43.05 3.58 R
4511 4730 5.189736 AGAAGGACAATCAAGTATGCCACTA 59.810 40.000 0.00 0.0 36.04 2.74 R
6183 6567 1.282157 AGGGCACTCTTGAATGTACCC 59.718 52.381 0.00 0.0 39.48 3.69 R
6795 7190 0.239879 GGAAAGGAATCGCAAACGCA 59.760 50.000 0.00 0.0 39.84 5.24 R
7798 8312 0.251341 TTTTGCCCTCTTCCTCTGCC 60.251 55.000 0.00 0.0 0.00 4.85 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
53 54 1.082104 GCAGGTGACGAAAAAGCCG 60.082 57.895 0.00 0.00 0.00 5.52
114 119 3.353239 CGCGTATCGTGTGCAAAAA 57.647 47.368 0.00 0.00 32.40 1.94
149 154 2.680352 TCCTCGCAGACCTGGACC 60.680 66.667 0.00 0.00 0.00 4.46
162 167 3.512516 GGACCGGACCCGTCTACG 61.513 72.222 9.46 0.00 37.81 3.51
205 211 3.952508 TTTCTCGCCAGCCAGCCA 61.953 61.111 0.00 0.00 0.00 4.75
206 212 3.907260 TTTCTCGCCAGCCAGCCAG 62.907 63.158 0.00 0.00 0.00 4.85
224 230 1.094785 AGCCGCCACACATACATTTC 58.905 50.000 0.00 0.00 0.00 2.17
234 246 4.032445 CACACATACATTTCCCTTCGTACG 59.968 45.833 9.53 9.53 0.00 3.67
240 252 3.184541 CATTTCCCTTCGTACGGTACAG 58.815 50.000 16.52 8.56 0.00 2.74
308 320 2.430921 GATGCGCGGTAGGATCGG 60.431 66.667 8.83 0.00 0.00 4.18
313 325 2.048127 GCGGTAGGATCGGGATGC 60.048 66.667 0.00 0.00 0.00 3.91
314 326 2.867855 GCGGTAGGATCGGGATGCA 61.868 63.158 3.00 0.00 0.00 3.96
425 448 3.680196 TACGGTCCTGCCCCTCCT 61.680 66.667 0.00 0.00 0.00 3.69
426 449 3.976490 TACGGTCCTGCCCCTCCTG 62.976 68.421 0.00 0.00 0.00 3.86
474 514 1.657794 GCCTCGAGCGAATACGACC 60.658 63.158 6.99 0.00 42.66 4.79
475 515 2.023318 CCTCGAGCGAATACGACCT 58.977 57.895 6.99 0.00 42.66 3.85
476 516 0.041135 CCTCGAGCGAATACGACCTC 60.041 60.000 6.99 0.00 42.66 3.85
477 517 0.041135 CTCGAGCGAATACGACCTCC 60.041 60.000 0.00 0.00 42.66 4.30
478 518 1.368969 CGAGCGAATACGACCTCCG 60.369 63.158 0.00 0.00 42.66 4.63
511 551 0.739561 TTTTTGAAACGTCACCGGGG 59.260 50.000 6.32 0.00 38.78 5.73
512 552 1.102222 TTTTGAAACGTCACCGGGGG 61.102 55.000 2.42 0.00 38.78 5.40
543 583 1.194772 GTTTCTTTTCCGACGAGCTGG 59.805 52.381 0.00 0.00 0.00 4.85
572 621 5.171337 CGTCCAGCGAAAATACATTTATTGC 59.829 40.000 0.00 0.00 44.77 3.56
641 741 2.617274 GCGCCCCAAAGAGTCACAC 61.617 63.158 0.00 0.00 0.00 3.82
642 742 2.317609 CGCCCCAAAGAGTCACACG 61.318 63.158 0.00 0.00 0.00 4.49
653 762 3.334751 TCACACGCGCGAGGTTTG 61.335 61.111 39.36 25.86 0.00 2.93
670 779 2.511600 GCAGATCGAACCCCGGTG 60.512 66.667 0.00 0.00 39.14 4.94
712 821 6.828785 AGTGCTCCTAAATAACGATGGAATTT 59.171 34.615 0.00 0.00 0.00 1.82
734 843 4.869215 TGTAAATGCCAGTCATGTTTGTG 58.131 39.130 0.00 0.00 35.13 3.33
737 847 2.049888 TGCCAGTCATGTTTGTGTCA 57.950 45.000 0.00 0.00 0.00 3.58
757 867 4.857037 GTCATGAACTAAAATGCGGGAAAC 59.143 41.667 0.00 0.00 0.00 2.78
824 934 2.997315 CGAGGTCAGGTCAGGCCA 60.997 66.667 5.01 0.00 40.61 5.36
1281 1423 4.453892 CGTACGTCCCCCTCCCCT 62.454 72.222 7.22 0.00 0.00 4.79
1282 1424 2.040114 GTACGTCCCCCTCCCCTT 59.960 66.667 0.00 0.00 0.00 3.95
1286 1428 3.015753 GTCCCCCTCCCCTTCCAC 61.016 72.222 0.00 0.00 0.00 4.02
1287 1429 4.364686 TCCCCCTCCCCTTCCACC 62.365 72.222 0.00 0.00 0.00 4.61
1353 1500 2.537625 CTGCTCCACGATTCGAGAAATC 59.462 50.000 13.95 2.75 40.42 2.17
1355 1502 2.537625 GCTCCACGATTCGAGAAATCAG 59.462 50.000 13.95 0.14 43.44 2.90
1357 1504 3.770666 TCCACGATTCGAGAAATCAGAC 58.229 45.455 13.95 0.00 43.44 3.51
1365 1512 6.473778 CGATTCGAGAAATCAGACACAGTATT 59.526 38.462 0.00 0.00 43.44 1.89
1380 1527 5.531659 ACACAGTATTACTCGATCGATTCCT 59.468 40.000 19.78 6.60 0.00 3.36
1381 1528 6.039493 ACACAGTATTACTCGATCGATTCCTT 59.961 38.462 19.78 5.68 0.00 3.36
1386 1533 5.578005 TTACTCGATCGATTCCTTGTTCT 57.422 39.130 19.78 0.00 0.00 3.01
1406 1553 4.360964 GCCTGCAATGCGCCAACA 62.361 61.111 4.18 0.00 41.33 3.33
1413 1560 1.470285 GCAATGCGCCAACAGATTGAT 60.470 47.619 17.18 0.00 38.15 2.57
1415 1562 0.101759 ATGCGCCAACAGATTGATGC 59.898 50.000 4.18 0.00 38.15 3.91
1416 1563 1.226773 GCGCCAACAGATTGATGCC 60.227 57.895 0.00 0.00 38.15 4.40
1417 1564 1.660560 GCGCCAACAGATTGATGCCT 61.661 55.000 0.00 0.00 38.15 4.75
1488 1638 4.207019 CGCGATGGATTTAGGAAATTTTGC 59.793 41.667 0.00 0.00 0.00 3.68
1604 1758 4.793201 AGGCTTATACCAGGGACAAAATC 58.207 43.478 0.00 0.00 0.00 2.17
1701 1859 1.547372 ACATTTTGAGACCAGCATGCC 59.453 47.619 15.66 0.00 31.97 4.40
1745 1903 9.528489 TCTAGGAACTTAGTTTAATTTTGGCAT 57.472 29.630 0.00 0.00 41.75 4.40
1860 2019 4.499696 GGCATTGCAATTGGTGGTAGATAC 60.500 45.833 9.83 0.00 0.00 2.24
1909 2072 3.067106 CAGACAAACAAGCCACTACGAT 58.933 45.455 0.00 0.00 0.00 3.73
1910 2073 4.021807 TCAGACAAACAAGCCACTACGATA 60.022 41.667 0.00 0.00 0.00 2.92
1911 2074 4.870426 CAGACAAACAAGCCACTACGATAT 59.130 41.667 0.00 0.00 0.00 1.63
1912 2075 6.040247 CAGACAAACAAGCCACTACGATATA 58.960 40.000 0.00 0.00 0.00 0.86
1940 2103 8.299990 TCAACCTCTTATTTTCCTCACAAAAA 57.700 30.769 0.00 0.00 0.00 1.94
1984 2147 3.008330 CCTCAGTTGAAAGCCTGATGAG 58.992 50.000 0.00 0.00 37.11 2.90
2058 2222 8.863049 GTTATTTCCGTACTTCTAAAATCGTCA 58.137 33.333 0.00 0.00 0.00 4.35
2059 2223 6.695292 TTTCCGTACTTCTAAAATCGTCAC 57.305 37.500 0.00 0.00 0.00 3.67
2215 2381 7.934120 AGTTACTTTAGCCATATCTGTTGATCC 59.066 37.037 0.00 0.00 34.32 3.36
2286 2452 8.549338 AAGCCTCACAGTACTTTTCTTATAAC 57.451 34.615 0.00 0.00 0.00 1.89
2289 2455 8.657729 GCCTCACAGTACTTTTCTTATAACTTC 58.342 37.037 0.00 0.00 0.00 3.01
2501 2667 8.675705 ATATCGATCACATGTACCAAATGAAA 57.324 30.769 0.00 0.00 0.00 2.69
2734 2942 2.059756 TCTGTCTTTTCCCCATCCCT 57.940 50.000 0.00 0.00 0.00 4.20
2804 3012 2.642996 TACCGTGCCATGGAGCATCG 62.643 60.000 18.40 12.72 46.24 3.84
3043 3251 5.393135 GGGTAATCTGCTGTTTCTTTTAGCC 60.393 44.000 0.00 0.00 36.64 3.93
3147 3356 5.417580 TCACCCATGCATACTTAAAAGGTTC 59.582 40.000 0.00 0.00 0.00 3.62
3150 3359 5.888161 CCCATGCATACTTAAAAGGTTCTCT 59.112 40.000 0.00 0.00 0.00 3.10
3240 3451 3.009143 TCAAAGGGGAGCTCTCTTTTACC 59.991 47.826 21.98 8.74 0.00 2.85
3281 3492 3.476552 TGTCTTGTCTCACCACATTTCC 58.523 45.455 0.00 0.00 0.00 3.13
3362 3573 8.540492 GGACGATGTGTTTATTTCTGTGTATAG 58.460 37.037 0.00 0.00 0.00 1.31
3401 3612 6.959639 TCTGTTTGCTTTCAGGAGTAAAAT 57.040 33.333 0.00 0.00 33.93 1.82
3521 3732 6.641474 ACAAGGTATGCTAGTACTTCCTTTC 58.359 40.000 0.00 0.00 32.48 2.62
3597 3813 9.057089 GGAGAAACTTTGTCTCATTTCTTAGAA 57.943 33.333 4.01 0.00 42.85 2.10
3984 4200 8.103305 ACATTTAAGTTCTCTGCTAAATCTGGA 58.897 33.333 0.00 0.00 0.00 3.86
4037 4253 8.647143 AAGTACCAACAATTCAGTGAAATTTG 57.353 30.769 10.14 12.98 0.00 2.32
4150 4367 6.202188 ACTGTTAAACTCTGGTACACGAAATG 59.798 38.462 0.00 0.00 0.00 2.32
4203 4420 2.849943 TGTAGATATTGTGCCCCTGGTT 59.150 45.455 0.00 0.00 0.00 3.67
4295 4512 5.301551 TCACTTTTGTTGCATAACCATGTCT 59.698 36.000 0.00 0.00 35.92 3.41
4408 4627 1.863454 GTGCCTCGAAGCATGACATAG 59.137 52.381 12.63 0.00 46.24 2.23
4590 4809 2.514205 AGGTTCATGTTTGTTGCAGC 57.486 45.000 0.00 0.00 0.00 5.25
4720 5058 2.430546 GCAGTAGCTATGATCGTGCT 57.569 50.000 13.85 13.85 40.43 4.40
4730 5068 5.049060 AGCTATGATCGTGCTACTGTTCTAG 60.049 44.000 9.31 0.00 35.05 2.43
4935 5273 8.220755 AGTAATTCAAAGCAGTTAAACAGACA 57.779 30.769 0.00 0.00 0.00 3.41
5070 5434 6.301486 TGATTCTTGATATCATGACCCTTGG 58.699 40.000 18.23 0.00 31.00 3.61
5159 5524 5.221521 GGCCCATTTTCCCTGAGATAATTTC 60.222 44.000 0.00 0.00 0.00 2.17
5181 5546 3.609853 GCAATCATGGGAGAAGTGTACA 58.390 45.455 0.00 0.00 0.00 2.90
5609 5980 5.979517 GCACCATGCCTTATTTATTGTCTTC 59.020 40.000 0.00 0.00 37.42 2.87
5755 6126 1.126113 GTGTGTTCATCTAACCGTGCG 59.874 52.381 0.00 0.00 37.27 5.34
5794 6165 5.458041 AAGCTTGCTTCTTATTTTCTGCA 57.542 34.783 0.00 0.00 0.00 4.41
5815 6198 5.384063 CATTGGTTGCAGTTACATTACCA 57.616 39.130 0.00 0.00 34.08 3.25
5816 6199 5.401550 CATTGGTTGCAGTTACATTACCAG 58.598 41.667 3.08 0.00 37.03 4.00
5817 6200 4.093472 TGGTTGCAGTTACATTACCAGT 57.907 40.909 0.00 0.00 32.30 4.00
5818 6201 4.465886 TGGTTGCAGTTACATTACCAGTT 58.534 39.130 0.00 0.00 32.30 3.16
5819 6202 4.890581 TGGTTGCAGTTACATTACCAGTTT 59.109 37.500 0.00 0.00 32.30 2.66
5876 6259 4.875544 TGGAAGAATGTATTGCTTACGC 57.124 40.909 0.00 0.00 33.15 4.42
5877 6260 3.625764 TGGAAGAATGTATTGCTTACGCC 59.374 43.478 0.00 0.00 33.15 5.68
5957 6341 5.334421 TCTAGATAAGGGCTGATAAGGTCC 58.666 45.833 0.00 0.00 0.00 4.46
6073 6457 1.604147 ATGACCGAGATGGCACGACA 61.604 55.000 0.00 0.00 43.94 4.35
6129 6513 4.650972 AAAAGGTATCTGCCCTGTACAA 57.349 40.909 0.00 0.00 30.99 2.41
6183 6567 2.412089 CCCAAAGCTTCTAGTTTCGACG 59.588 50.000 0.00 0.00 0.00 5.12
6193 6577 3.758023 TCTAGTTTCGACGGGTACATTCA 59.242 43.478 0.00 0.00 0.00 2.57
6286 6670 6.761312 ACATTGATGTGACAAATCCATTTGT 58.239 32.000 15.93 15.93 46.46 2.83
6288 6672 8.533657 ACATTGATGTGACAAATCCATTTGTAT 58.466 29.630 15.96 7.84 46.97 2.29
6302 6686 7.558161 TCCATTTGTATCAGAAGTTGCATAG 57.442 36.000 0.00 0.00 0.00 2.23
6394 6780 8.600625 CAATGATCGTCGTATTTTTCTCCTTTA 58.399 33.333 0.00 0.00 0.00 1.85
6423 6809 0.694771 TGGCAAGCAGAGGAGACATT 59.305 50.000 0.00 0.00 0.00 2.71
6677 7072 4.824479 TCACTTCACTCTGATATTGGCA 57.176 40.909 0.00 0.00 0.00 4.92
6790 7185 6.575162 AGGTTATTCACTTGCTTACCTTTG 57.425 37.500 0.00 0.00 30.68 2.77
6795 7190 9.476202 GTTATTCACTTGCTTACCTTTGATTTT 57.524 29.630 0.00 0.00 0.00 1.82
7033 7433 5.421277 TGTTTTCAGACCGACTTTAGTCAA 58.579 37.500 10.27 0.00 44.99 3.18
7088 7488 4.167268 TGCACAAAGGTAAACACGTTTTC 58.833 39.130 0.00 0.00 34.23 2.29
7111 7511 2.932614 CTCTGTTTCTCCCAACGCATAG 59.067 50.000 0.00 0.00 0.00 2.23
7133 7533 0.179092 TCTCGCACTGCATCTCATGG 60.179 55.000 1.11 0.00 0.00 3.66
7135 7535 0.460811 TCGCACTGCATCTCATGGTC 60.461 55.000 1.11 0.00 0.00 4.02
7140 7540 2.941064 CACTGCATCTCATGGTCGATTT 59.059 45.455 0.00 0.00 0.00 2.17
7144 7544 3.562557 TGCATCTCATGGTCGATTTCATG 59.437 43.478 15.61 15.61 41.35 3.07
7153 7553 3.926527 TGGTCGATTTCATGTCTTCTTCG 59.073 43.478 0.00 0.00 0.00 3.79
7154 7554 3.927142 GGTCGATTTCATGTCTTCTTCGT 59.073 43.478 0.00 0.00 0.00 3.85
7157 7557 6.916387 GGTCGATTTCATGTCTTCTTCGTATA 59.084 38.462 0.00 0.00 0.00 1.47
7169 7569 1.729276 TCGTATAACGACGGGGCTG 59.271 57.895 0.00 0.00 46.73 4.85
7187 7683 4.248058 GGCTGTAACCGAGCTAGTAAAAA 58.752 43.478 0.00 0.00 36.63 1.94
7193 7689 6.813152 TGTAACCGAGCTAGTAAAAATGTACC 59.187 38.462 0.00 0.00 0.00 3.34
7230 7726 7.484007 CCATTTGATTTCTTGTTGAGATCGAAG 59.516 37.037 0.00 0.00 40.67 3.79
7231 7727 6.486253 TTGATTTCTTGTTGAGATCGAAGG 57.514 37.500 0.00 0.00 38.65 3.46
7239 7735 0.737367 TGAGATCGAAGGCGTTGCAG 60.737 55.000 0.00 0.00 38.98 4.41
7240 7736 0.737715 GAGATCGAAGGCGTTGCAGT 60.738 55.000 0.00 0.00 38.98 4.40
7243 7739 1.730064 GATCGAAGGCGTTGCAGTTTA 59.270 47.619 0.00 0.00 38.98 2.01
7247 7743 2.661979 CGAAGGCGTTGCAGTTTAAGTC 60.662 50.000 0.00 0.00 0.00 3.01
7248 7744 1.961793 AGGCGTTGCAGTTTAAGTCA 58.038 45.000 0.00 0.00 0.00 3.41
7275 7771 1.270907 GACACTGTCCTCCTCCACAT 58.729 55.000 0.00 0.00 0.00 3.21
7285 7781 2.432510 CCTCCTCCACATCTTGTAGGTC 59.567 54.545 0.00 0.00 30.13 3.85
7318 7815 3.099002 GGAGAGTAGGACTCCGACC 57.901 63.158 4.79 2.06 46.18 4.79
7356 7854 8.509690 CAAGATGGATGAAGCGATACATTATTT 58.490 33.333 0.00 0.00 25.94 1.40
7360 7858 5.182001 GGATGAAGCGATACATTATTTGCCT 59.818 40.000 0.00 0.00 0.00 4.75
7362 7860 6.060028 TGAAGCGATACATTATTTGCCTTC 57.940 37.500 0.00 0.00 0.00 3.46
7376 7874 2.381445 CCTTCAAGGCACCCTCTCT 58.619 57.895 0.00 0.00 30.89 3.10
7380 7878 2.530151 AAGGCACCCTCTCTGGCA 60.530 61.111 0.00 0.00 36.66 4.92
7391 7889 1.817099 CTCTGGCAATCTCCGGCAC 60.817 63.158 0.00 0.00 34.84 5.01
7474 7975 0.454600 CGGCTCAACGTAGCTCCTTA 59.545 55.000 10.03 0.00 42.37 2.69
7509 8010 2.412323 CGGAAGATCGTCGGTCCCA 61.412 63.158 0.82 0.00 0.00 4.37
7624 8135 4.039092 CCTGGTGGTGGGCTCTGG 62.039 72.222 0.00 0.00 0.00 3.86
7626 8137 2.449518 TGGTGGTGGGCTCTGGAA 60.450 61.111 0.00 0.00 0.00 3.53
7657 8171 2.627945 GACACCACCGCAAATCATCTA 58.372 47.619 0.00 0.00 0.00 1.98
7682 8196 1.197721 AGTTGTTCGCTTGCTGTATGC 59.802 47.619 0.00 0.00 43.25 3.14
7700 8214 1.203288 TGCCATTGATCCCCCAGTTTT 60.203 47.619 0.00 0.00 0.00 2.43
7714 8228 3.824443 CCCAGTTTTCCGTTCCTTTATGT 59.176 43.478 0.00 0.00 0.00 2.29
7744 8258 7.042051 GCAAAATGTTTCTCCTTAGTTTTTCCC 60.042 37.037 0.00 0.00 0.00 3.97
7745 8259 6.665992 AATGTTTCTCCTTAGTTTTTCCCC 57.334 37.500 0.00 0.00 0.00 4.81
7746 8260 5.132043 TGTTTCTCCTTAGTTTTTCCCCA 57.868 39.130 0.00 0.00 0.00 4.96
7747 8261 5.137551 TGTTTCTCCTTAGTTTTTCCCCAG 58.862 41.667 0.00 0.00 0.00 4.45
7749 8263 2.041216 TCTCCTTAGTTTTTCCCCAGGC 59.959 50.000 0.00 0.00 0.00 4.85
7750 8264 1.076513 TCCTTAGTTTTTCCCCAGGCC 59.923 52.381 0.00 0.00 0.00 5.19
7751 8265 1.077169 CCTTAGTTTTTCCCCAGGCCT 59.923 52.381 0.00 0.00 0.00 5.19
7756 8270 2.654896 AGTTTTTCCCCAGGCCTTATCT 59.345 45.455 0.00 0.00 0.00 1.98
7770 8284 4.083590 GGCCTTATCTTGAATGAATCTCGC 60.084 45.833 0.00 0.00 0.00 5.03
7771 8285 4.512944 GCCTTATCTTGAATGAATCTCGCA 59.487 41.667 0.00 0.00 0.00 5.10
7773 8287 6.620303 GCCTTATCTTGAATGAATCTCGCATC 60.620 42.308 0.00 0.00 0.00 3.91
7775 8289 7.119407 CCTTATCTTGAATGAATCTCGCATCAT 59.881 37.037 0.00 0.00 37.88 2.45
7783 8297 2.616634 ATCTCGCATCATGAAGCTGT 57.383 45.000 19.71 1.57 0.00 4.40
7791 8305 3.439476 GCATCATGAAGCTGTCAACTCTT 59.561 43.478 15.45 0.00 40.50 2.85
7794 8308 4.903054 TCATGAAGCTGTCAACTCTTGAT 58.097 39.130 0.00 0.00 42.47 2.57
7798 8312 5.240891 TGAAGCTGTCAACTCTTGATAAGG 58.759 41.667 0.00 0.00 42.47 2.69
7819 8335 1.819305 GCAGAGGAAGAGGGCAAAACA 60.819 52.381 0.00 0.00 0.00 2.83
7823 8339 4.766891 CAGAGGAAGAGGGCAAAACATTTA 59.233 41.667 0.00 0.00 0.00 1.40
7824 8340 5.012893 AGAGGAAGAGGGCAAAACATTTAG 58.987 41.667 0.00 0.00 0.00 1.85
7825 8341 4.089361 AGGAAGAGGGCAAAACATTTAGG 58.911 43.478 0.00 0.00 0.00 2.69
7826 8342 3.195610 GGAAGAGGGCAAAACATTTAGGG 59.804 47.826 0.00 0.00 0.00 3.53
7827 8343 2.179427 AGAGGGCAAAACATTTAGGGC 58.821 47.619 0.00 0.00 0.00 5.19
7828 8344 1.207089 GAGGGCAAAACATTTAGGGCC 59.793 52.381 0.00 0.00 39.23 5.80
7829 8345 0.980423 GGGCAAAACATTTAGGGCCA 59.020 50.000 6.18 0.00 43.09 5.36
7830 8346 1.066215 GGGCAAAACATTTAGGGCCAG 60.066 52.381 6.18 0.00 43.09 4.85
7831 8347 1.623311 GGCAAAACATTTAGGGCCAGT 59.377 47.619 6.18 0.00 41.02 4.00
7832 8348 2.038426 GGCAAAACATTTAGGGCCAGTT 59.962 45.455 6.18 0.00 41.02 3.16
7833 8349 3.325870 GCAAAACATTTAGGGCCAGTTC 58.674 45.455 6.18 0.00 0.00 3.01
7834 8350 3.006859 GCAAAACATTTAGGGCCAGTTCT 59.993 43.478 6.18 0.00 0.00 3.01
7835 8351 4.503123 GCAAAACATTTAGGGCCAGTTCTT 60.503 41.667 6.18 0.00 0.00 2.52
7836 8352 5.610398 CAAAACATTTAGGGCCAGTTCTTT 58.390 37.500 6.18 0.00 0.00 2.52
7837 8353 5.887214 AAACATTTAGGGCCAGTTCTTTT 57.113 34.783 6.18 0.00 0.00 2.27
7838 8354 4.871933 ACATTTAGGGCCAGTTCTTTTG 57.128 40.909 6.18 0.00 0.00 2.44
7839 8355 4.479158 ACATTTAGGGCCAGTTCTTTTGA 58.521 39.130 6.18 0.00 0.00 2.69
7840 8356 4.898861 ACATTTAGGGCCAGTTCTTTTGAA 59.101 37.500 6.18 0.00 35.84 2.69
7853 8369 4.617253 TCTTTTGAACGATTCTCCCAGA 57.383 40.909 0.00 0.00 0.00 3.86
7854 8370 4.968259 TCTTTTGAACGATTCTCCCAGAA 58.032 39.130 0.00 0.00 38.78 3.02
7855 8371 5.560724 TCTTTTGAACGATTCTCCCAGAAT 58.439 37.500 0.00 0.00 46.84 2.40
7856 8372 6.149474 TTCTTTTGAACGATTCTCCCAGAATC 59.851 38.462 14.00 14.00 43.36 2.52
7861 8377 1.839894 ATTCTCCCAGAATCGCCCC 59.160 57.895 0.00 0.00 40.75 5.80
7862 8378 1.709994 ATTCTCCCAGAATCGCCCCC 61.710 60.000 0.00 0.00 40.75 5.40
7876 8392 3.744155 CCCCCTCCCCAGCTTTCC 61.744 72.222 0.00 0.00 0.00 3.13
7877 8393 3.744155 CCCCTCCCCAGCTTTCCC 61.744 72.222 0.00 0.00 0.00 3.97
7878 8394 2.615288 CCCTCCCCAGCTTTCCCT 60.615 66.667 0.00 0.00 0.00 4.20
7879 8395 1.307866 CCCTCCCCAGCTTTCCCTA 60.308 63.158 0.00 0.00 0.00 3.53
7880 8396 1.348775 CCCTCCCCAGCTTTCCCTAG 61.349 65.000 0.00 0.00 0.00 3.02
7881 8397 0.326618 CCTCCCCAGCTTTCCCTAGA 60.327 60.000 0.00 0.00 0.00 2.43
7882 8398 1.584724 CTCCCCAGCTTTCCCTAGAA 58.415 55.000 0.00 0.00 0.00 2.10
7883 8399 2.131023 CTCCCCAGCTTTCCCTAGAAT 58.869 52.381 0.00 0.00 0.00 2.40
7884 8400 2.511637 CTCCCCAGCTTTCCCTAGAATT 59.488 50.000 0.00 0.00 0.00 2.17
7885 8401 2.242196 TCCCCAGCTTTCCCTAGAATTG 59.758 50.000 0.00 0.00 0.00 2.32
7886 8402 2.024941 CCCCAGCTTTCCCTAGAATTGT 60.025 50.000 0.00 0.00 0.00 2.71
7887 8403 3.282885 CCCAGCTTTCCCTAGAATTGTC 58.717 50.000 0.00 0.00 0.00 3.18
7888 8404 3.282885 CCAGCTTTCCCTAGAATTGTCC 58.717 50.000 0.00 0.00 0.00 4.02
7889 8405 3.282885 CAGCTTTCCCTAGAATTGTCCC 58.717 50.000 0.00 0.00 0.00 4.46
7890 8406 3.054065 CAGCTTTCCCTAGAATTGTCCCT 60.054 47.826 0.00 0.00 0.00 4.20
7891 8407 3.201045 AGCTTTCCCTAGAATTGTCCCTC 59.799 47.826 0.00 0.00 0.00 4.30
7892 8408 3.685835 GCTTTCCCTAGAATTGTCCCTCC 60.686 52.174 0.00 0.00 0.00 4.30
7893 8409 2.961536 TCCCTAGAATTGTCCCTCCA 57.038 50.000 0.00 0.00 0.00 3.86
7894 8410 3.438131 TCCCTAGAATTGTCCCTCCAT 57.562 47.619 0.00 0.00 0.00 3.41
7895 8411 4.569676 TCCCTAGAATTGTCCCTCCATA 57.430 45.455 0.00 0.00 0.00 2.74
7896 8412 5.106631 TCCCTAGAATTGTCCCTCCATAT 57.893 43.478 0.00 0.00 0.00 1.78
7897 8413 5.486332 TCCCTAGAATTGTCCCTCCATATT 58.514 41.667 0.00 0.00 0.00 1.28
7898 8414 5.917087 TCCCTAGAATTGTCCCTCCATATTT 59.083 40.000 0.00 0.00 0.00 1.40
7899 8415 6.392842 TCCCTAGAATTGTCCCTCCATATTTT 59.607 38.462 0.00 0.00 0.00 1.82
7900 8416 7.069344 CCCTAGAATTGTCCCTCCATATTTTT 58.931 38.462 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 4.596585 GTGGGGTGGGGTGTGGTG 62.597 72.222 0.00 0.00 0.00 4.17
31 32 0.041312 CTTTTTCGTCACCTGCGTGG 60.041 55.000 0.00 0.00 40.65 4.94
60 61 4.016706 GGGACGGGACTGGTGGTG 62.017 72.222 0.00 0.00 0.00 4.17
74 79 2.434185 GAATGTGTCGCAGCGGGA 60.434 61.111 16.42 0.00 0.00 5.14
81 86 2.778679 GCGTGGAGAATGTGTCGC 59.221 61.111 0.00 0.00 37.17 5.19
84 89 1.797713 CGATACGCGTGGAGAATGTGT 60.798 52.381 24.59 0.00 41.43 3.72
149 154 3.740397 TGTGCGTAGACGGGTCCG 61.740 66.667 7.97 7.97 46.03 4.79
205 211 1.094785 GAAATGTATGTGTGGCGGCT 58.905 50.000 11.43 0.00 0.00 5.52
206 212 0.100503 GGAAATGTATGTGTGGCGGC 59.899 55.000 0.00 0.00 0.00 6.53
207 213 0.738389 GGGAAATGTATGTGTGGCGG 59.262 55.000 0.00 0.00 0.00 6.13
208 214 1.750193 AGGGAAATGTATGTGTGGCG 58.250 50.000 0.00 0.00 0.00 5.69
211 217 4.032445 CGTACGAAGGGAAATGTATGTGTG 59.968 45.833 10.44 0.00 0.00 3.82
224 230 0.179145 CAGCTGTACCGTACGAAGGG 60.179 60.000 18.76 1.74 36.67 3.95
234 246 2.103042 CGCTTGCTCCAGCTGTACC 61.103 63.158 13.81 0.21 42.66 3.34
240 252 3.854459 GTACGCGCTTGCTCCAGC 61.854 66.667 5.73 0.00 42.50 4.85
298 310 0.034059 CTGTGCATCCCGATCCTACC 59.966 60.000 0.00 0.00 0.00 3.18
314 326 4.760220 ATTCCCTCCCCCGCCTGT 62.760 66.667 0.00 0.00 0.00 4.00
425 448 4.293648 AGGTGTACACGCAGCGCA 62.294 61.111 16.61 0.89 41.28 6.09
426 449 3.777925 CAGGTGTACACGCAGCGC 61.778 66.667 16.61 0.00 41.28 5.92
427 450 2.355837 ACAGGTGTACACGCAGCG 60.356 61.111 19.41 14.82 41.28 5.18
428 451 2.027625 GGACAGGTGTACACGCAGC 61.028 63.158 19.41 9.09 37.16 5.25
509 549 0.323451 AGAAACGGAATTCTGCCCCC 60.323 55.000 14.40 1.80 38.22 5.40
510 550 1.545841 AAGAAACGGAATTCTGCCCC 58.454 50.000 14.40 3.52 39.54 5.80
511 551 3.575630 GAAAAGAAACGGAATTCTGCCC 58.424 45.455 14.40 3.87 39.54 5.36
512 552 3.575630 GGAAAAGAAACGGAATTCTGCC 58.424 45.455 14.40 4.22 39.54 4.85
513 553 3.058501 TCGGAAAAGAAACGGAATTCTGC 60.059 43.478 14.40 0.00 39.54 4.26
514 554 4.464112 GTCGGAAAAGAAACGGAATTCTG 58.536 43.478 12.91 12.91 39.54 3.02
515 555 3.185797 CGTCGGAAAAGAAACGGAATTCT 59.814 43.478 5.23 0.00 41.34 2.40
516 556 3.184986 TCGTCGGAAAAGAAACGGAATTC 59.815 43.478 0.00 0.00 35.89 2.17
517 557 3.132925 TCGTCGGAAAAGAAACGGAATT 58.867 40.909 0.00 0.00 35.89 2.17
518 558 2.735134 CTCGTCGGAAAAGAAACGGAAT 59.265 45.455 0.00 0.00 35.89 3.01
572 621 2.584791 CGCGAGGAAAACAAATCCAAG 58.415 47.619 0.00 0.00 39.55 3.61
625 725 2.617274 GCGTGTGACTCTTTGGGGC 61.617 63.158 0.00 0.00 0.00 5.80
633 733 4.702081 ACCTCGCGCGTGTGACTC 62.702 66.667 30.98 0.00 0.00 3.36
641 741 3.425938 GATCTGCAAACCTCGCGCG 62.426 63.158 26.76 26.76 0.00 6.86
642 742 2.401195 GATCTGCAAACCTCGCGC 59.599 61.111 0.00 0.00 0.00 6.86
653 762 2.511600 CACCGGGGTTCGATCTGC 60.512 66.667 6.32 0.00 42.43 4.26
670 779 1.298859 ACTCCGCAAATTCCGCAGTC 61.299 55.000 1.28 0.00 0.00 3.51
688 797 6.619801 AATTCCATCGTTATTTAGGAGCAC 57.380 37.500 0.00 0.00 0.00 4.40
696 805 8.037758 TGGCATTTACAAATTCCATCGTTATTT 58.962 29.630 2.43 0.00 36.89 1.40
697 806 7.551585 TGGCATTTACAAATTCCATCGTTATT 58.448 30.769 2.43 0.00 36.89 1.40
712 821 4.340666 ACACAAACATGACTGGCATTTACA 59.659 37.500 0.00 0.00 34.15 2.41
725 834 7.503991 GCATTTTAGTTCATGACACAAACATG 58.496 34.615 0.00 0.00 44.20 3.21
726 835 6.363088 CGCATTTTAGTTCATGACACAAACAT 59.637 34.615 0.00 0.00 0.00 2.71
734 843 4.695217 TTCCCGCATTTTAGTTCATGAC 57.305 40.909 0.00 0.00 0.00 3.06
737 847 4.279671 TGTGTTTCCCGCATTTTAGTTCAT 59.720 37.500 0.00 0.00 0.00 2.57
742 852 2.094752 CCCTGTGTTTCCCGCATTTTAG 60.095 50.000 0.00 0.00 31.99 1.85
744 854 0.678950 CCCTGTGTTTCCCGCATTTT 59.321 50.000 0.00 0.00 31.99 1.82
1005 1141 1.010574 CATCTCCTCGTCGTCGCTC 60.011 63.158 0.00 0.00 36.96 5.03
1287 1429 3.878667 GAAGGAGGGATGGGCGGG 61.879 72.222 0.00 0.00 0.00 6.13
1289 1431 3.878667 GGGAAGGAGGGATGGGCG 61.879 72.222 0.00 0.00 0.00 6.13
1290 1432 2.368878 AGGGAAGGAGGGATGGGC 60.369 66.667 0.00 0.00 0.00 5.36
1291 1433 1.772156 GGAGGGAAGGAGGGATGGG 60.772 68.421 0.00 0.00 0.00 4.00
1294 1436 2.712746 GGGGAGGGAAGGAGGGAT 59.287 66.667 0.00 0.00 0.00 3.85
1353 1500 5.405331 TCGATCGAGTAATACTGTGTCTG 57.595 43.478 15.15 0.00 0.00 3.51
1355 1502 5.852229 GGAATCGATCGAGTAATACTGTGTC 59.148 44.000 23.84 4.59 0.00 3.67
1357 1504 6.003234 AGGAATCGATCGAGTAATACTGTG 57.997 41.667 23.84 0.00 0.00 3.66
1365 1512 4.733815 GCAGAACAAGGAATCGATCGAGTA 60.734 45.833 23.84 0.00 0.00 2.59
1406 1553 1.202903 GGCATGAGGAGGCATCAATCT 60.203 52.381 0.00 0.00 0.00 2.40
1413 1560 1.078214 CGAAAGGCATGAGGAGGCA 60.078 57.895 0.00 0.00 0.00 4.75
1415 1562 2.176273 CGCGAAAGGCATGAGGAGG 61.176 63.158 0.00 0.00 43.84 4.30
1416 1563 1.448540 ACGCGAAAGGCATGAGGAG 60.449 57.895 15.93 0.00 43.84 3.69
1417 1564 1.741401 CACGCGAAAGGCATGAGGA 60.741 57.895 15.93 0.00 36.86 3.71
1498 1648 3.722147 ACGCTGCTCCATAATTAGAGTG 58.278 45.455 0.00 0.00 32.47 3.51
1514 1667 2.017049 CTTGGAAAGGGGAATACGCTG 58.983 52.381 0.00 0.00 42.22 5.18
1604 1758 0.098552 TCACAATAAATGGCTGCGCG 59.901 50.000 0.00 0.00 0.00 6.86
1701 1859 5.070981 TCCTAGAGTTTCAGAATGGCATAGG 59.929 44.000 0.00 0.00 36.16 2.57
1745 1903 5.701569 CAGAATGCTGCCATGGTACATCAA 61.702 45.833 14.67 0.00 38.20 2.57
1860 2019 1.203050 CCCCCTAGCCCCATACATTTG 60.203 57.143 0.00 0.00 0.00 2.32
1912 2075 9.753674 TTTGTGAGGAAAATAAGAGGTTGATAT 57.246 29.630 0.00 0.00 0.00 1.63
1940 2103 8.310122 AGGAGGCATCAATAACACATTTATTT 57.690 30.769 0.00 0.00 0.00 1.40
1943 2106 6.422333 TGAGGAGGCATCAATAACACATTTA 58.578 36.000 0.00 0.00 0.00 1.40
2058 2222 2.488153 GGTTTATCCTTTTGCTCGCTGT 59.512 45.455 0.00 0.00 0.00 4.40
2059 2223 2.159379 GGGTTTATCCTTTTGCTCGCTG 60.159 50.000 0.00 0.00 36.25 5.18
2215 2381 5.834169 TGCAGCACATAATGTTTCCATATG 58.166 37.500 0.00 0.00 0.00 1.78
2234 2400 8.524870 AAGAGCAAAATAAAATAACACTGCAG 57.475 30.769 13.48 13.48 0.00 4.41
2286 2452 3.632145 AGGCAATTAAGGGCAATACGAAG 59.368 43.478 6.31 0.00 0.00 3.79
2289 2455 4.134563 ACTAGGCAATTAAGGGCAATACG 58.865 43.478 0.00 0.00 0.00 3.06
2523 2689 9.460019 TGAATGATGTAACAAATCACCAGATAA 57.540 29.630 0.00 0.00 36.89 1.75
2530 2696 8.075574 TGACAACTGAATGATGTAACAAATCAC 58.924 33.333 0.00 0.00 36.89 3.06
2793 3001 3.787634 CGTTCATTTTTCGATGCTCCATG 59.212 43.478 0.00 0.00 0.00 3.66
2804 3012 6.033966 AGTGACAGGTTTTCGTTCATTTTTC 58.966 36.000 0.00 0.00 0.00 2.29
3024 3232 4.655963 TGAGGCTAAAAGAAACAGCAGAT 58.344 39.130 0.00 0.00 37.02 2.90
3043 3251 6.149633 GCTAGTGTGGTTGGTAAAATTTGAG 58.850 40.000 0.00 0.00 0.00 3.02
3147 3356 9.817809 ACATACATGTATACCAGTGTTAAAGAG 57.182 33.333 17.86 3.06 39.68 2.85
3150 3359 7.707464 CCGACATACATGTATACCAGTGTTAAA 59.293 37.037 17.86 0.00 41.95 1.52
3240 3451 9.073368 CAAGACAAAATGCAGATAAAGAGAATG 57.927 33.333 0.00 0.00 0.00 2.67
3362 3573 4.900635 AACAGAATTGAAGGTCACACAC 57.099 40.909 0.00 0.00 0.00 3.82
3401 3612 4.832823 TGTCACTTCTCACTCCAACTGATA 59.167 41.667 0.00 0.00 0.00 2.15
3521 3732 2.693074 CCCAAGATAATTCAAACCCCCG 59.307 50.000 0.00 0.00 0.00 5.73
3984 4200 9.997482 CAGTAACAAAGTAAACAACAGTACATT 57.003 29.630 0.00 0.00 0.00 2.71
4150 4367 7.256286 CCCTACGCATATACTGGATAAACTAC 58.744 42.308 0.00 0.00 0.00 2.73
4203 4420 5.136828 ACAACCAATGGTTCAACTATGACA 58.863 37.500 15.79 0.00 43.05 3.58
4304 4521 8.336801 ACCAAAATAAAAGGTAGCTTCAGTAG 57.663 34.615 7.80 0.00 32.92 2.57
4305 4522 9.223099 GTACCAAAATAAAAGGTAGCTTCAGTA 57.777 33.333 7.80 1.74 38.49 2.74
4306 4523 7.722285 TGTACCAAAATAAAAGGTAGCTTCAGT 59.278 33.333 7.80 0.00 38.49 3.41
4408 4627 6.147164 TGAACGGTACAAGAATCAATGTCTTC 59.853 38.462 0.00 0.00 32.96 2.87
4447 4666 6.603997 TGTTACACCAACAAAACTATTCAGGT 59.396 34.615 0.00 0.00 44.20 4.00
4511 4730 5.189736 AGAAGGACAATCAAGTATGCCACTA 59.810 40.000 0.00 0.00 36.04 2.74
4515 4734 7.391148 TTTTAGAAGGACAATCAAGTATGCC 57.609 36.000 0.00 0.00 0.00 4.40
4730 5068 7.277981 TCTCGGAACTGTAATCTTCAATTTAGC 59.722 37.037 0.00 0.00 0.00 3.09
5024 5362 6.834107 TCATCTGCCAATGAGATTAATGAGA 58.166 36.000 0.00 0.00 32.03 3.27
5070 5434 4.952460 TGTAGGGTTTGCTAATATCCGTC 58.048 43.478 0.00 0.00 0.00 4.79
5145 5510 5.335426 CCATGATTGCGAAATTATCTCAGGG 60.335 44.000 0.00 0.00 28.28 4.45
5159 5524 1.742761 ACACTTCTCCCATGATTGCG 58.257 50.000 0.00 0.00 0.00 4.85
5175 5540 8.547894 TCGATATAAGAAATTGCATGTGTACAC 58.452 33.333 19.36 19.36 0.00 2.90
5181 5546 7.498900 TGTTCCTCGATATAAGAAATTGCATGT 59.501 33.333 0.00 0.00 0.00 3.21
5755 6126 6.698359 CAAGCTTACTTGTGAAGACTAGTC 57.302 41.667 15.41 15.41 46.84 2.59
5794 6165 5.076873 ACTGGTAATGTAACTGCAACCAAT 58.923 37.500 4.33 0.00 36.62 3.16
5876 6259 9.326413 ACAACAGAAATATTTATAAGACCTCGG 57.674 33.333 0.00 0.00 0.00 4.63
6073 6457 4.082949 AGAGCTTTAAATTTAAACGCGCCT 60.083 37.500 25.86 23.05 34.73 5.52
6077 6461 4.920927 TGGCAGAGCTTTAAATTTAAACGC 59.079 37.500 23.33 23.33 32.24 4.84
6162 6546 2.412089 CGTCGAAACTAGAAGCTTTGGG 59.588 50.000 0.00 0.00 0.00 4.12
6163 6547 2.412089 CCGTCGAAACTAGAAGCTTTGG 59.588 50.000 0.00 0.00 0.00 3.28
6183 6567 1.282157 AGGGCACTCTTGAATGTACCC 59.718 52.381 0.00 0.00 39.48 3.69
6286 6670 7.776933 GTTGATCACTATGCAACTTCTGATA 57.223 36.000 0.00 0.00 38.96 2.15
6394 6780 3.698040 CCTCTGCTTGCCAATATCTGTTT 59.302 43.478 0.00 0.00 0.00 2.83
6423 6809 5.127845 TCTTTTGGCAGTTTGAAATACACCA 59.872 36.000 0.00 0.00 0.00 4.17
6534 6922 4.223032 TCCTAGGATTGTCAACCAGAAGAC 59.777 45.833 7.62 0.00 35.37 3.01
6790 7185 2.595386 AGGAATCGCAAACGCAAAATC 58.405 42.857 0.00 0.00 39.84 2.17
6795 7190 0.239879 GGAAAGGAATCGCAAACGCA 59.760 50.000 0.00 0.00 39.84 5.24
6807 7202 6.517194 GCACTTTGAATTCAAGATGGAAAGGA 60.517 38.462 24.17 8.19 37.15 3.36
6945 7344 8.101654 AGTGAGAAGCGACCTATAAGTAATAG 57.898 38.462 0.00 0.00 37.84 1.73
7088 7488 0.955919 GCGTTGGGAGAAACAGAGGG 60.956 60.000 0.00 0.00 0.00 4.30
7111 7511 1.432514 TGAGATGCAGTGCGAGAAAC 58.567 50.000 11.20 0.52 0.00 2.78
7133 7533 6.814076 ATACGAAGAAGACATGAAATCGAC 57.186 37.500 0.00 0.00 33.42 4.20
7135 7535 7.267318 CGTTATACGAAGAAGACATGAAATCG 58.733 38.462 0.00 3.30 46.05 3.34
7153 7553 2.463876 GTTACAGCCCCGTCGTTATAC 58.536 52.381 0.00 0.00 0.00 1.47
7154 7554 1.408702 GGTTACAGCCCCGTCGTTATA 59.591 52.381 0.00 0.00 0.00 0.98
7157 7557 2.344872 GGTTACAGCCCCGTCGTT 59.655 61.111 0.00 0.00 0.00 3.85
7163 7563 1.328430 ACTAGCTCGGTTACAGCCCC 61.328 60.000 0.00 0.00 37.63 5.80
7164 7564 1.396653 TACTAGCTCGGTTACAGCCC 58.603 55.000 0.00 0.00 37.63 5.19
7166 7566 5.350640 ACATTTTTACTAGCTCGGTTACAGC 59.649 40.000 0.00 0.00 37.12 4.40
7167 7567 6.963049 ACATTTTTACTAGCTCGGTTACAG 57.037 37.500 0.00 0.00 0.00 2.74
7169 7569 6.020360 CGGTACATTTTTACTAGCTCGGTTAC 60.020 42.308 0.00 0.00 0.00 2.50
7187 7683 5.941058 TCAAATGGTTGTAATGTCGGTACAT 59.059 36.000 0.00 0.00 40.71 2.29
7193 7689 7.594758 ACAAGAAATCAAATGGTTGTAATGTCG 59.405 33.333 0.00 0.00 36.07 4.35
7205 7701 7.484007 CCTTCGATCTCAACAAGAAATCAAATG 59.516 37.037 0.00 0.00 37.61 2.32
7206 7702 7.533426 CCTTCGATCTCAACAAGAAATCAAAT 58.467 34.615 0.00 0.00 37.61 2.32
7208 7704 5.106555 GCCTTCGATCTCAACAAGAAATCAA 60.107 40.000 0.00 0.00 37.61 2.57
7230 7726 1.663161 GCTGACTTAAACTGCAACGCC 60.663 52.381 0.00 0.00 33.57 5.68
7231 7727 1.002900 TGCTGACTTAAACTGCAACGC 60.003 47.619 9.98 0.00 38.74 4.84
7239 7735 7.133891 ACAGTGTCAATATGCTGACTTAAAC 57.866 36.000 8.60 0.18 45.03 2.01
7240 7736 6.371548 GGACAGTGTCAATATGCTGACTTAAA 59.628 38.462 24.20 0.00 45.03 1.52
7243 7739 4.019860 AGGACAGTGTCAATATGCTGACTT 60.020 41.667 24.20 0.00 45.03 3.01
7247 7743 3.118482 AGGAGGACAGTGTCAATATGCTG 60.118 47.826 24.20 0.00 33.68 4.41
7248 7744 3.110705 AGGAGGACAGTGTCAATATGCT 58.889 45.455 24.20 13.85 33.68 3.79
7285 7781 5.292101 CCTACTCTCCAAAATTAGACGCTTG 59.708 44.000 0.00 0.00 0.00 4.01
7318 7815 7.011857 GCTTCATCCATCTTGTTAGACTTAAGG 59.988 40.741 7.53 0.00 31.99 2.69
7360 7858 2.069776 CCAGAGAGGGTGCCTTGAA 58.930 57.895 0.00 0.00 31.76 2.69
7362 7860 2.045536 GCCAGAGAGGGTGCCTTG 60.046 66.667 0.00 0.00 38.09 3.61
7368 7866 1.333636 CGGAGATTGCCAGAGAGGGT 61.334 60.000 0.00 0.00 38.09 4.34
7374 7872 2.268920 GTGCCGGAGATTGCCAGA 59.731 61.111 5.05 0.00 0.00 3.86
7376 7874 4.776322 CGGTGCCGGAGATTGCCA 62.776 66.667 5.05 0.00 35.56 4.92
7404 7902 3.385384 TGGTCTCTGGGAGCAGCG 61.385 66.667 5.11 0.00 45.96 5.18
7490 7991 2.278661 GGACCGACGATCTTCCGC 60.279 66.667 0.00 0.00 0.00 5.54
7492 7993 0.464452 AATGGGACCGACGATCTTCC 59.536 55.000 0.00 0.00 0.00 3.46
7494 7995 2.290071 ACAAAATGGGACCGACGATCTT 60.290 45.455 0.00 0.00 0.00 2.40
7558 8059 1.152567 CCCCACAACACACCACCAT 60.153 57.895 0.00 0.00 0.00 3.55
7624 8135 2.156310 GGTGGTGTCGTCGTTACAATTC 59.844 50.000 0.00 0.00 0.00 2.17
7626 8137 1.787012 GGTGGTGTCGTCGTTACAAT 58.213 50.000 0.00 0.00 0.00 2.71
7682 8196 2.110578 GGAAAACTGGGGGATCAATGG 58.889 52.381 0.00 0.00 0.00 3.16
7700 8214 1.626321 TGCAGGACATAAAGGAACGGA 59.374 47.619 0.00 0.00 0.00 4.69
7714 8228 5.385198 ACTAAGGAGAAACATTTTGCAGGA 58.615 37.500 0.00 0.00 0.00 3.86
7744 8258 5.383476 AGATTCATTCAAGATAAGGCCTGG 58.617 41.667 5.69 0.00 0.00 4.45
7745 8259 5.178996 CGAGATTCATTCAAGATAAGGCCTG 59.821 44.000 5.69 0.00 0.00 4.85
7746 8260 5.303971 CGAGATTCATTCAAGATAAGGCCT 58.696 41.667 0.00 0.00 0.00 5.19
7747 8261 4.083590 GCGAGATTCATTCAAGATAAGGCC 60.084 45.833 0.00 0.00 0.00 5.19
7749 8263 6.426025 TGATGCGAGATTCATTCAAGATAAGG 59.574 38.462 0.00 0.00 0.00 2.69
7750 8264 7.417496 TGATGCGAGATTCATTCAAGATAAG 57.583 36.000 0.00 0.00 0.00 1.73
7751 8265 7.658575 TCATGATGCGAGATTCATTCAAGATAA 59.341 33.333 0.00 0.00 30.24 1.75
7756 8270 5.505159 GCTTCATGATGCGAGATTCATTCAA 60.505 40.000 16.79 0.00 30.24 2.69
7770 8284 4.694037 TCAAGAGTTGACAGCTTCATGATG 59.306 41.667 0.00 0.00 38.19 3.07
7771 8285 4.903054 TCAAGAGTTGACAGCTTCATGAT 58.097 39.130 0.00 0.00 34.08 2.45
7773 8287 6.183360 CCTTATCAAGAGTTGACAGCTTCATG 60.183 42.308 0.00 0.00 43.48 3.07
7775 8289 5.240891 CCTTATCAAGAGTTGACAGCTTCA 58.759 41.667 0.00 0.00 43.48 3.02
7783 8297 3.198635 CCTCTGCCCTTATCAAGAGTTGA 59.801 47.826 0.00 0.00 45.01 3.18
7791 8305 2.402564 CCTCTTCCTCTGCCCTTATCA 58.597 52.381 0.00 0.00 0.00 2.15
7794 8308 0.983378 GCCCTCTTCCTCTGCCCTTA 60.983 60.000 0.00 0.00 0.00 2.69
7798 8312 0.251341 TTTTGCCCTCTTCCTCTGCC 60.251 55.000 0.00 0.00 0.00 4.85
7819 8335 4.022329 CGTTCAAAAGAACTGGCCCTAAAT 60.022 41.667 0.00 0.00 33.21 1.40
7823 8339 1.133915 TCGTTCAAAAGAACTGGCCCT 60.134 47.619 0.00 0.00 33.21 5.19
7824 8340 1.314730 TCGTTCAAAAGAACTGGCCC 58.685 50.000 0.00 0.00 33.21 5.80
7825 8341 3.253432 AGAATCGTTCAAAAGAACTGGCC 59.747 43.478 0.00 0.00 33.21 5.36
7826 8342 4.467735 GAGAATCGTTCAAAAGAACTGGC 58.532 43.478 6.77 0.00 33.21 4.85
7827 8343 4.083271 GGGAGAATCGTTCAAAAGAACTGG 60.083 45.833 6.77 0.00 34.37 4.00
7828 8344 4.515191 TGGGAGAATCGTTCAAAAGAACTG 59.485 41.667 6.77 1.59 34.37 3.16
7829 8345 4.714632 TGGGAGAATCGTTCAAAAGAACT 58.285 39.130 6.77 0.00 34.37 3.01
7830 8346 4.755123 TCTGGGAGAATCGTTCAAAAGAAC 59.245 41.667 0.00 0.00 34.37 3.01
7831 8347 4.968259 TCTGGGAGAATCGTTCAAAAGAA 58.032 39.130 1.58 0.00 34.37 2.52
7832 8348 4.617253 TCTGGGAGAATCGTTCAAAAGA 57.383 40.909 1.58 0.00 34.37 2.52
7833 8349 5.886960 ATTCTGGGAGAATCGTTCAAAAG 57.113 39.130 0.00 0.00 40.75 2.27
7843 8359 1.709994 GGGGGCGATTCTGGGAGAAT 61.710 60.000 0.00 0.00 46.84 2.40
7844 8360 2.375345 GGGGGCGATTCTGGGAGAA 61.375 63.158 0.00 0.00 38.78 2.87
7845 8361 2.768344 GGGGGCGATTCTGGGAGA 60.768 66.667 0.00 0.00 0.00 3.71
7859 8375 3.744155 GGAAAGCTGGGGAGGGGG 61.744 72.222 0.00 0.00 0.00 5.40
7860 8376 2.857998 TAGGGAAAGCTGGGGAGGGG 62.858 65.000 0.00 0.00 0.00 4.79
7861 8377 1.307866 TAGGGAAAGCTGGGGAGGG 60.308 63.158 0.00 0.00 0.00 4.30
7862 8378 0.326618 TCTAGGGAAAGCTGGGGAGG 60.327 60.000 0.00 0.00 0.00 4.30
7863 8379 1.584724 TTCTAGGGAAAGCTGGGGAG 58.415 55.000 0.00 0.00 0.00 4.30
7864 8380 2.242196 CAATTCTAGGGAAAGCTGGGGA 59.758 50.000 0.00 0.00 34.90 4.81
7865 8381 2.024941 ACAATTCTAGGGAAAGCTGGGG 60.025 50.000 0.00 0.00 34.90 4.96
7866 8382 3.282885 GACAATTCTAGGGAAAGCTGGG 58.717 50.000 0.00 0.00 34.90 4.45
7867 8383 3.282885 GGACAATTCTAGGGAAAGCTGG 58.717 50.000 0.00 0.00 34.90 4.85
7868 8384 3.054065 AGGGACAATTCTAGGGAAAGCTG 60.054 47.826 0.00 0.00 34.90 4.24
7869 8385 3.193782 AGGGACAATTCTAGGGAAAGCT 58.806 45.455 0.00 0.00 34.90 3.74
7870 8386 3.546724 GAGGGACAATTCTAGGGAAAGC 58.453 50.000 0.00 0.00 34.90 3.51
7871 8387 3.523564 TGGAGGGACAATTCTAGGGAAAG 59.476 47.826 0.00 0.00 34.90 2.62
7872 8388 3.537337 TGGAGGGACAATTCTAGGGAAA 58.463 45.455 0.00 0.00 34.90 3.13
7873 8389 3.214694 TGGAGGGACAATTCTAGGGAA 57.785 47.619 0.00 0.00 35.78 3.97
7874 8390 2.961536 TGGAGGGACAATTCTAGGGA 57.038 50.000 0.00 0.00 0.00 4.20
7875 8391 5.850046 AATATGGAGGGACAATTCTAGGG 57.150 43.478 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.