Multiple sequence alignment - TraesCS5A01G405400

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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 TraesCS5A01G405400 chr5A 100.000 5301 0 0 1 5301 597253201 597258501 0.000000e+00 9790.0
1 TraesCS5A01G405400 chr5A 86.598 97 11 2 3708 3803 437913606 437913511 7.260000e-19 106.0
2 TraesCS5A01G405400 chr5D 90.485 4351 189 90 600 4882 477983418 477987611 0.000000e+00 5533.0
3 TraesCS5A01G405400 chr5D 92.241 348 18 4 4887 5233 477990642 477990981 7.980000e-133 484.0
4 TraesCS5A01G405400 chr5D 87.629 97 10 2 3708 3803 336423180 336423085 1.560000e-20 111.0
5 TraesCS5A01G405400 chr5B 93.024 1964 83 26 2749 4696 585474690 585476615 0.000000e+00 2819.0
6 TraesCS5A01G405400 chr5B 89.084 2217 105 53 600 2764 585472540 585474671 0.000000e+00 2627.0
7 TraesCS5A01G405400 chr5B 95.047 424 13 2 4806 5229 585481458 585481873 0.000000e+00 660.0
8 TraesCS5A01G405400 chr5B 87.629 97 10 2 3708 3803 394744380 394744285 1.560000e-20 111.0
9 TraesCS5A01G405400 chr7A 96.970 594 16 2 1 593 57808783 57808191 0.000000e+00 996.0
10 TraesCS5A01G405400 chr4B 95.840 601 24 1 1 600 483883537 483882937 0.000000e+00 970.0
11 TraesCS5A01G405400 chr4B 85.827 127 16 2 3723 3848 493530205 493530330 3.330000e-27 134.0
12 TraesCS5A01G405400 chr4D 95.784 593 22 3 8 599 308857493 308858083 0.000000e+00 953.0
13 TraesCS5A01G405400 chr4D 87.402 127 14 2 3723 3848 399534243 399534368 1.540000e-30 145.0
14 TraesCS5A01G405400 chr4D 96.875 32 1 0 2643 2674 117734081 117734050 3.000000e-03 54.7
15 TraesCS5A01G405400 chrUn 95.183 602 25 4 4 602 30054732 30054132 0.000000e+00 948.0
16 TraesCS5A01G405400 chrUn 94.435 593 30 3 8 599 103403054 103403644 0.000000e+00 909.0
17 TraesCS5A01G405400 chr3D 94.992 599 20 2 1 599 578903325 578902737 0.000000e+00 931.0
18 TraesCS5A01G405400 chr4A 94.020 602 34 2 1 602 687201248 687200649 0.000000e+00 911.0
19 TraesCS5A01G405400 chr4A 86.614 127 15 2 3723 3848 57166250 57166375 7.160000e-29 139.0
20 TraesCS5A01G405400 chr2B 94.176 601 30 4 1 599 64035728 64035131 0.000000e+00 911.0
21 TraesCS5A01G405400 chr2B 91.367 139 12 0 2984 3122 361424348 361424210 1.950000e-44 191.0
22 TraesCS5A01G405400 chr2B 89.474 95 10 0 2605 2699 361424710 361424616 2.590000e-23 121.0
23 TraesCS5A01G405400 chr1B 92.941 595 38 4 7 599 7249899 7250491 0.000000e+00 863.0
24 TraesCS5A01G405400 chr1B 90.769 65 5 1 3816 3879 222294484 222294548 9.460000e-13 86.1
25 TraesCS5A01G405400 chr2D 91.367 139 12 0 2984 3122 311717425 311717563 1.950000e-44 191.0
26 TraesCS5A01G405400 chr2D 93.846 65 3 1 3816 3879 19223945 19224009 4.370000e-16 97.1
27 TraesCS5A01G405400 chr2A 90.647 139 13 0 2984 3122 428909939 428910077 9.070000e-43 185.0
28 TraesCS5A01G405400 chr2A 88.421 95 11 0 2605 2699 428909577 428909671 1.210000e-21 115.0
29 TraesCS5A01G405400 chr7D 93.846 65 3 1 3816 3879 112614435 112614499 4.370000e-16 97.1
30 TraesCS5A01G405400 chr6B 90.625 64 6 0 3816 3879 21012351 21012414 9.460000e-13 86.1


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 TraesCS5A01G405400 chr5A 597253201 597258501 5300 False 9790.0 9790 100.000 1 5301 1 chr5A.!!$F1 5300
1 TraesCS5A01G405400 chr5D 477983418 477990981 7563 False 3008.5 5533 91.363 600 5233 2 chr5D.!!$F1 4633
2 TraesCS5A01G405400 chr5B 585472540 585476615 4075 False 2723.0 2819 91.054 600 4696 2 chr5B.!!$F2 4096
3 TraesCS5A01G405400 chr7A 57808191 57808783 592 True 996.0 996 96.970 1 593 1 chr7A.!!$R1 592
4 TraesCS5A01G405400 chr4B 483882937 483883537 600 True 970.0 970 95.840 1 600 1 chr4B.!!$R1 599
5 TraesCS5A01G405400 chr4D 308857493 308858083 590 False 953.0 953 95.784 8 599 1 chr4D.!!$F1 591
6 TraesCS5A01G405400 chrUn 30054132 30054732 600 True 948.0 948 95.183 4 602 1 chrUn.!!$R1 598
7 TraesCS5A01G405400 chrUn 103403054 103403644 590 False 909.0 909 94.435 8 599 1 chrUn.!!$F1 591
8 TraesCS5A01G405400 chr3D 578902737 578903325 588 True 931.0 931 94.992 1 599 1 chr3D.!!$R1 598
9 TraesCS5A01G405400 chr4A 687200649 687201248 599 True 911.0 911 94.020 1 602 1 chr4A.!!$R1 601
10 TraesCS5A01G405400 chr2B 64035131 64035728 597 True 911.0 911 94.176 1 599 1 chr2B.!!$R1 598
11 TraesCS5A01G405400 chr1B 7249899 7250491 592 False 863.0 863 92.941 7 599 1 chr1B.!!$F1 592

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
637 653 0.038159 GTGTGGGAGGTCAAGACTCG 60.038 60.0 0.00 0.0 35.82 4.18 F
695 711 0.116143 TTAAAAGCCAGGCCCACCAT 59.884 50.0 8.22 0.0 39.06 3.55 F
696 712 0.116143 TAAAAGCCAGGCCCACCATT 59.884 50.0 8.22 0.0 39.06 3.16 F
740 761 0.258194 TACCCGACTCTCCCTCTTCC 59.742 60.0 0.00 0.0 0.00 3.46 F
848 874 0.890996 CCTTCAAACCCGCTGAGCTT 60.891 55.0 1.78 0.0 0.00 3.74 F
2293 2340 0.618981 AGTAGTAGCACTTTGCCCCC 59.381 55.0 0.00 0.0 46.52 5.40 F
2967 3097 0.179108 GGTGGATAGACACTCACGCC 60.179 60.0 0.00 0.0 41.09 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2081 2128 0.109086 AAGACGATGGCGACTCACTG 60.109 55.0 0.0 0.0 41.40 3.66 R
2082 2129 0.171455 GAAGACGATGGCGACTCACT 59.829 55.0 0.0 0.0 41.40 3.41 R
2085 2132 0.248702 GAGGAAGACGATGGCGACTC 60.249 60.0 0.0 0.0 41.40 3.36 R
2263 2310 0.311477 GCTACTACTACTCCGGCAGC 59.689 60.0 0.0 0.0 0.00 5.25 R
2589 2677 0.681175 ACCTGCCCAAATCAACAAGC 59.319 50.0 0.0 0.0 0.00 4.01 R
3210 3340 0.527113 TGCGGATTTGCATCTTGTGG 59.473 50.0 0.0 0.0 40.62 4.17 R
4867 5025 0.244721 GCCTTCCAATCCAACAGTGC 59.755 55.0 0.0 0.0 0.00 4.40 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
97 98 4.980592 TGGAGCAGGGGTGGAGCA 62.981 66.667 0.00 0.00 0.00 4.26
114 115 1.819229 CAGCGTCCTCCATAGCACT 59.181 57.895 0.00 0.00 0.00 4.40
339 341 1.153901 GAACTCAATCCGTCGCCGA 60.154 57.895 0.00 0.00 35.63 5.54
340 342 0.734942 GAACTCAATCCGTCGCCGAA 60.735 55.000 0.00 0.00 35.63 4.30
578 594 1.493772 AAAAAGACGTCGCGACATCA 58.506 45.000 33.34 0.00 0.00 3.07
604 620 1.172175 GAACGGAGGGAGTAGTTCGT 58.828 55.000 0.00 0.00 34.54 3.85
621 637 4.393680 AGTTCGTAAAATGTGTGTGTGTGT 59.606 37.500 0.00 0.00 0.00 3.72
625 641 2.136298 AAATGTGTGTGTGTGTGGGA 57.864 45.000 0.00 0.00 0.00 4.37
626 642 1.679139 AATGTGTGTGTGTGTGGGAG 58.321 50.000 0.00 0.00 0.00 4.30
629 645 0.814010 GTGTGTGTGTGTGGGAGGTC 60.814 60.000 0.00 0.00 0.00 3.85
630 646 1.268283 TGTGTGTGTGTGGGAGGTCA 61.268 55.000 0.00 0.00 0.00 4.02
631 647 0.107410 GTGTGTGTGTGGGAGGTCAA 60.107 55.000 0.00 0.00 0.00 3.18
632 648 0.180171 TGTGTGTGTGGGAGGTCAAG 59.820 55.000 0.00 0.00 0.00 3.02
633 649 0.468226 GTGTGTGTGGGAGGTCAAGA 59.532 55.000 0.00 0.00 0.00 3.02
634 650 0.468226 TGTGTGTGGGAGGTCAAGAC 59.532 55.000 0.00 0.00 0.00 3.01
637 653 0.038159 GTGTGGGAGGTCAAGACTCG 60.038 60.000 0.00 0.00 35.82 4.18
641 657 1.006043 TGGGAGGTCAAGACTCGAGAT 59.994 52.381 21.68 4.01 35.82 2.75
671 687 1.002576 CTCATTCGCTTTGCACACACA 60.003 47.619 0.00 0.00 0.00 3.72
672 688 1.122849 CATTCGCTTTGCACACACAC 58.877 50.000 0.00 0.00 0.00 3.82
673 689 0.316937 ATTCGCTTTGCACACACACG 60.317 50.000 0.00 0.00 0.00 4.49
674 690 1.640210 TTCGCTTTGCACACACACGT 61.640 50.000 0.00 0.00 0.00 4.49
675 691 1.226267 CGCTTTGCACACACACGTT 60.226 52.632 0.00 0.00 0.00 3.99
686 702 3.545873 CACACACACGTTTTAAAAGCCAG 59.454 43.478 0.00 0.00 0.00 4.85
692 708 1.604438 CGTTTTAAAAGCCAGGCCCAC 60.604 52.381 8.22 0.00 0.00 4.61
693 709 1.052617 TTTTAAAAGCCAGGCCCACC 58.947 50.000 8.22 0.00 0.00 4.61
695 711 0.116143 TTAAAAGCCAGGCCCACCAT 59.884 50.000 8.22 0.00 39.06 3.55
696 712 0.116143 TAAAAGCCAGGCCCACCATT 59.884 50.000 8.22 0.00 39.06 3.16
698 714 3.944250 AAGCCAGGCCCACCATTCG 62.944 63.158 8.22 0.00 39.06 3.34
704 725 3.140814 GCCCACCATTCGGCCTTC 61.141 66.667 0.00 0.00 39.39 3.46
719 740 1.519455 CTTCTCCGCCGATCACACC 60.519 63.158 0.00 0.00 0.00 4.16
720 741 2.225791 CTTCTCCGCCGATCACACCA 62.226 60.000 0.00 0.00 0.00 4.17
721 742 1.613317 TTCTCCGCCGATCACACCAT 61.613 55.000 0.00 0.00 0.00 3.55
722 743 0.753848 TCTCCGCCGATCACACCATA 60.754 55.000 0.00 0.00 0.00 2.74
740 761 0.258194 TACCCGACTCTCCCTCTTCC 59.742 60.000 0.00 0.00 0.00 3.46
807 828 3.131478 GGCATACCCCGCACACAC 61.131 66.667 0.00 0.00 0.00 3.82
808 829 3.496131 GCATACCCCGCACACACG 61.496 66.667 0.00 0.00 0.00 4.49
809 830 3.496131 CATACCCCGCACACACGC 61.496 66.667 0.00 0.00 0.00 5.34
848 874 0.890996 CCTTCAAACCCGCTGAGCTT 60.891 55.000 1.78 0.00 0.00 3.74
899 925 2.658285 TGTGCTCCCCAATGATTGATC 58.342 47.619 6.76 0.00 0.00 2.92
900 926 1.959282 GTGCTCCCCAATGATTGATCC 59.041 52.381 6.76 0.00 0.00 3.36
1086 1115 4.400109 TCGCTGTCGCCTCACGTC 62.400 66.667 0.00 0.00 44.19 4.34
1095 1124 2.202797 CCTCACGTCGCCATGGAG 60.203 66.667 18.40 13.80 0.00 3.86
1209 1238 1.831736 CCCATGTCCTTCTACTTCGGT 59.168 52.381 0.00 0.00 0.00 4.69
1212 1241 1.263356 TGTCCTTCTACTTCGGTGGG 58.737 55.000 0.00 0.00 0.00 4.61
1213 1242 1.203087 TGTCCTTCTACTTCGGTGGGA 60.203 52.381 0.00 0.00 0.00 4.37
1357 1386 6.512253 CGGTAAATATCTGCACAGTACTACGA 60.512 42.308 0.00 0.00 0.00 3.43
1383 1412 5.529800 TCTTACTTTGCTACAGTTTGGGTTC 59.470 40.000 0.00 0.00 0.00 3.62
1385 1414 3.222603 CTTTGCTACAGTTTGGGTTCCT 58.777 45.455 0.00 0.00 0.00 3.36
1386 1415 2.270352 TGCTACAGTTTGGGTTCCTG 57.730 50.000 0.00 0.00 0.00 3.86
1387 1416 1.771854 TGCTACAGTTTGGGTTCCTGA 59.228 47.619 0.00 0.00 0.00 3.86
1388 1417 2.224523 TGCTACAGTTTGGGTTCCTGAG 60.225 50.000 0.00 0.00 0.00 3.35
1400 1429 1.882623 GTTCCTGAGGTTCTTGGCTTG 59.117 52.381 0.00 0.00 0.00 4.01
1411 1440 4.680237 TGGCTTGTAGCTGCGCGT 62.680 61.111 8.43 0.00 41.99 6.01
1436 1465 4.522789 TCTCTTTATGTTTCTTGGTTGGGC 59.477 41.667 0.00 0.00 0.00 5.36
1448 1477 2.193536 GTTGGGCTTGCGGTCTGTT 61.194 57.895 0.00 0.00 0.00 3.16
1531 1560 1.739562 GCTGAGCCTGGACAACTCG 60.740 63.158 0.00 0.00 32.98 4.18
1849 1887 3.695606 TCCCAGTCCAGCTGCGTC 61.696 66.667 8.66 0.29 43.71 5.19
2021 2065 2.048503 AGCGCACGTCCAAGTACC 60.049 61.111 11.47 0.00 0.00 3.34
2063 2110 1.678970 GGCACAACCCATCTCACCC 60.679 63.158 0.00 0.00 0.00 4.61
2080 2127 2.027929 CACCCCATTGCATGTCATTTGT 60.028 45.455 0.00 0.00 0.00 2.83
2081 2128 2.234414 ACCCCATTGCATGTCATTTGTC 59.766 45.455 0.00 0.00 0.00 3.18
2082 2129 2.234168 CCCCATTGCATGTCATTTGTCA 59.766 45.455 0.00 0.00 0.00 3.58
2083 2130 3.517602 CCCATTGCATGTCATTTGTCAG 58.482 45.455 0.00 0.00 0.00 3.51
2084 2131 3.056393 CCCATTGCATGTCATTTGTCAGT 60.056 43.478 0.00 0.00 0.00 3.41
2085 2132 3.924073 CCATTGCATGTCATTTGTCAGTG 59.076 43.478 0.00 0.00 0.00 3.66
2086 2133 4.321378 CCATTGCATGTCATTTGTCAGTGA 60.321 41.667 0.00 0.00 0.00 3.41
2087 2134 4.492791 TTGCATGTCATTTGTCAGTGAG 57.507 40.909 0.00 0.00 0.00 3.51
2088 2135 3.479489 TGCATGTCATTTGTCAGTGAGT 58.521 40.909 0.00 0.00 0.00 3.41
2250 2297 4.201950 CCAAGCTCCAACCTTAATCAATCG 60.202 45.833 0.00 0.00 0.00 3.34
2262 2309 5.453339 CCTTAATCAATCGAGCTCCCTAACA 60.453 44.000 8.47 0.00 0.00 2.41
2263 2310 3.742433 ATCAATCGAGCTCCCTAACAG 57.258 47.619 8.47 0.00 0.00 3.16
2264 2311 1.137086 TCAATCGAGCTCCCTAACAGC 59.863 52.381 8.47 0.00 37.12 4.40
2268 2315 2.993853 AGCTCCCTAACAGCTGCC 59.006 61.111 15.27 0.00 45.85 4.85
2269 2316 2.512515 GCTCCCTAACAGCTGCCG 60.513 66.667 15.27 1.72 33.75 5.69
2270 2317 2.187946 CTCCCTAACAGCTGCCGG 59.812 66.667 15.27 11.52 0.00 6.13
2277 2324 2.022195 CTAACAGCTGCCGGAGTAGTA 58.978 52.381 15.27 0.00 0.00 1.82
2293 2340 0.618981 AGTAGTAGCACTTTGCCCCC 59.381 55.000 0.00 0.00 46.52 5.40
2315 2364 6.126854 CCCCAGTACCATTTTAGTTAGTAGCT 60.127 42.308 0.00 0.00 0.00 3.32
2334 2396 7.422399 AGTAGCTGTACGTACTACTAGTAGTC 58.578 42.308 33.47 23.66 43.61 2.59
2335 2397 5.277825 AGCTGTACGTACTACTAGTAGTCG 58.722 45.833 33.47 32.10 44.58 4.18
2337 2399 6.038382 AGCTGTACGTACTACTAGTAGTCGTA 59.962 42.308 34.08 34.08 44.58 3.43
2338 2400 6.358558 GCTGTACGTACTACTAGTAGTCGTAG 59.641 46.154 35.92 31.70 44.58 3.51
2339 2401 7.317842 TGTACGTACTACTAGTAGTCGTAGT 57.682 40.000 35.92 30.11 44.58 2.73
2340 2402 7.187480 TGTACGTACTACTAGTAGTCGTAGTG 58.813 42.308 35.92 25.08 44.28 2.74
2341 2403 6.197364 ACGTACTACTAGTAGTCGTAGTGT 57.803 41.667 34.09 23.93 44.28 3.55
2342 2404 7.317842 ACGTACTACTAGTAGTCGTAGTGTA 57.682 40.000 34.09 19.51 44.28 2.90
2436 2503 2.797278 GCCTGGGGATCGATCGTGT 61.797 63.158 18.81 5.18 0.00 4.49
2437 2504 1.364171 CCTGGGGATCGATCGTGTC 59.636 63.158 18.81 13.97 0.00 3.67
2439 2506 1.605753 CTGGGGATCGATCGTGTCTA 58.394 55.000 18.81 6.06 0.00 2.59
2440 2507 1.267261 CTGGGGATCGATCGTGTCTAC 59.733 57.143 18.81 11.40 0.00 2.59
2441 2508 1.315690 GGGGATCGATCGTGTCTACA 58.684 55.000 18.81 0.00 0.00 2.74
2467 2544 5.086104 TCAGTTTATCTTGGTGAGTAGCC 57.914 43.478 0.00 0.00 0.00 3.93
2468 2545 4.777896 TCAGTTTATCTTGGTGAGTAGCCT 59.222 41.667 0.00 0.00 0.00 4.58
2469 2546 4.872691 CAGTTTATCTTGGTGAGTAGCCTG 59.127 45.833 0.00 0.00 0.00 4.85
2470 2547 4.532521 AGTTTATCTTGGTGAGTAGCCTGT 59.467 41.667 0.00 0.00 0.00 4.00
2471 2548 5.013183 AGTTTATCTTGGTGAGTAGCCTGTT 59.987 40.000 0.00 0.00 0.00 3.16
2472 2549 2.839486 TCTTGGTGAGTAGCCTGTTG 57.161 50.000 0.00 0.00 0.00 3.33
2473 2550 1.160137 CTTGGTGAGTAGCCTGTTGC 58.840 55.000 0.00 0.00 41.71 4.17
2510 2597 6.317391 GCTCCTATCACTTTGCTTAATCTTGT 59.683 38.462 0.00 0.00 0.00 3.16
2523 2610 5.415701 GCTTAATCTTGTTGGGATCAGTCAA 59.584 40.000 0.00 0.00 0.00 3.18
2537 2624 8.421784 TGGGATCAGTCAATACAAATACTAGTC 58.578 37.037 0.00 0.00 0.00 2.59
2539 2626 7.873505 GGATCAGTCAATACAAATACTAGTCCC 59.126 40.741 0.00 0.00 0.00 4.46
2541 2628 8.008513 TCAGTCAATACAAATACTAGTCCCTC 57.991 38.462 0.00 0.00 0.00 4.30
2545 2632 6.382859 TCAATACAAATACTAGTCCCTCTGCA 59.617 38.462 0.00 0.00 0.00 4.41
2552 2640 6.808321 ATACTAGTCCCTCTGCATGTTTAA 57.192 37.500 0.00 0.00 0.00 1.52
2573 2661 2.930562 GAGGGAGTGGTGGTGCCT 60.931 66.667 0.00 0.00 38.72 4.75
2574 2662 1.612442 GAGGGAGTGGTGGTGCCTA 60.612 63.158 0.00 0.00 35.54 3.93
2575 2663 1.151899 AGGGAGTGGTGGTGCCTAA 60.152 57.895 0.00 0.00 33.18 2.69
2578 2666 1.141053 GGGAGTGGTGGTGCCTAATAG 59.859 57.143 0.00 0.00 38.35 1.73
2589 2677 6.539103 GGTGGTGCCTAATAGAACTAAAAGAG 59.461 42.308 0.00 0.00 0.00 2.85
2747 2848 1.396996 CCGGTGTACTACATTGCTTGC 59.603 52.381 0.00 0.00 0.00 4.01
2764 2883 0.249155 TGCTTGCTTGCTTGCTTGTC 60.249 50.000 10.35 0.00 0.00 3.18
2786 2905 5.124457 GTCATCACAATGTAGCCAGTGATTT 59.876 40.000 4.33 0.00 46.35 2.17
2805 2924 2.949451 TTGACCATTGTTTGCGTGTT 57.051 40.000 0.00 0.00 0.00 3.32
2919 3040 0.806868 ATCACATGCTTGCCTGAACG 59.193 50.000 4.98 0.00 0.00 3.95
2920 3041 0.250252 TCACATGCTTGCCTGAACGA 60.250 50.000 4.98 0.00 0.00 3.85
2922 3043 1.237285 ACATGCTTGCCTGAACGACC 61.237 55.000 4.98 0.00 0.00 4.79
2924 3045 2.032681 GCTTGCCTGAACGACCCT 59.967 61.111 0.00 0.00 0.00 4.34
2954 3084 0.249615 CACTCGATCGCATGGTGGAT 60.250 55.000 11.09 0.00 0.00 3.41
2956 3086 1.270826 ACTCGATCGCATGGTGGATAG 59.729 52.381 11.09 0.61 0.00 2.08
2957 3087 1.541588 CTCGATCGCATGGTGGATAGA 59.458 52.381 11.09 0.00 0.00 1.98
2961 3091 1.485124 TCGCATGGTGGATAGACACT 58.515 50.000 0.00 0.00 41.09 3.55
2963 3093 1.136891 CGCATGGTGGATAGACACTCA 59.863 52.381 0.00 0.00 41.09 3.41
2964 3094 2.555199 GCATGGTGGATAGACACTCAC 58.445 52.381 0.00 0.00 41.09 3.51
2965 3095 2.814269 CATGGTGGATAGACACTCACG 58.186 52.381 0.00 0.00 41.09 4.35
2966 3096 0.530744 TGGTGGATAGACACTCACGC 59.469 55.000 0.00 0.00 41.09 5.34
2967 3097 0.179108 GGTGGATAGACACTCACGCC 60.179 60.000 0.00 0.00 41.09 5.68
2968 3098 0.525668 GTGGATAGACACTCACGCCG 60.526 60.000 0.00 0.00 38.32 6.46
2969 3099 1.065928 GGATAGACACTCACGCCGG 59.934 63.158 0.00 0.00 0.00 6.13
2970 3100 1.589196 GATAGACACTCACGCCGGC 60.589 63.158 19.07 19.07 0.00 6.13
2971 3101 3.411418 ATAGACACTCACGCCGGCG 62.411 63.158 44.88 44.88 46.03 6.46
3172 3302 2.294074 GTTGCCGCCATTAATCAGGTA 58.706 47.619 0.00 0.00 0.00 3.08
3205 3335 2.727777 CAATCTTGCAATCTCGCCATG 58.272 47.619 0.00 0.00 0.00 3.66
3206 3336 1.315690 ATCTTGCAATCTCGCCATGG 58.684 50.000 7.63 7.63 0.00 3.66
3207 3337 0.749091 TCTTGCAATCTCGCCATGGG 60.749 55.000 15.13 3.69 0.00 4.00
3208 3338 2.345880 CTTGCAATCTCGCCATGGGC 62.346 60.000 15.13 6.92 46.75 5.36
3226 3356 1.404583 GGCACCACAAGATGCAAATCC 60.405 52.381 0.00 0.00 43.93 3.01
3537 3671 2.110990 GTGGGTTTACGTTTTTGCGTC 58.889 47.619 0.00 0.00 44.55 5.19
3602 3736 1.073216 CATGCTCTCGTCGCTTTCGT 61.073 55.000 0.00 0.00 36.96 3.85
3633 3767 2.359975 CCTGTCCTTTGACCGCCC 60.360 66.667 0.00 0.00 41.01 6.13
3655 3789 2.477972 GAAAGCCCGGCTGCTGTTTC 62.478 60.000 14.19 8.89 41.80 2.78
3799 3939 0.165944 CCAACTTCGACATCAACCGC 59.834 55.000 0.00 0.00 0.00 5.68
4330 4479 0.947180 TACAGCGTCGTCCTTTTGGC 60.947 55.000 0.00 0.00 40.12 4.52
4331 4480 2.668550 AGCGTCGTCCTTTTGGCC 60.669 61.111 0.00 0.00 40.12 5.36
4356 4505 1.403814 TCCACGAGGAGATAGCAAGG 58.596 55.000 0.00 0.00 39.61 3.61
4358 4507 1.482593 CCACGAGGAGATAGCAAGGTT 59.517 52.381 0.00 0.00 36.89 3.50
4370 4519 7.253905 AGATAGCAAGGTTGTTTAACTAGGA 57.746 36.000 0.00 0.00 36.99 2.94
4379 4528 5.702670 GGTTGTTTAACTAGGACTGGTTACC 59.297 44.000 7.65 5.09 36.48 2.85
4420 4569 2.174854 AGCAAGGAACTGTAAGGTGGTT 59.825 45.455 0.00 0.00 40.86 3.67
4487 4636 1.079057 GGCTCTCGTGGTTCCTTCC 60.079 63.158 0.00 0.00 0.00 3.46
4602 4755 1.476007 ATCGGAGCTGGATGGGTAGC 61.476 60.000 0.00 0.00 40.18 3.58
4651 4804 8.550376 CCTAACTTTCATCAAACCAAAATGTTG 58.450 33.333 0.00 0.00 34.25 3.33
4665 4818 1.508632 ATGTTGGACCTTCGTGTTCG 58.491 50.000 0.00 0.00 38.55 3.95
4670 4823 1.219522 GGACCTTCGTGTTCGTGTGG 61.220 60.000 0.00 0.00 38.33 4.17
4672 4825 2.604174 CCTTCGTGTTCGTGTGGCC 61.604 63.158 0.00 0.00 38.33 5.36
4674 4827 1.557443 CTTCGTGTTCGTGTGGCCTC 61.557 60.000 3.32 0.00 38.33 4.70
4692 4845 4.210304 GCGGCGCGTCTGAACATC 62.210 66.667 19.09 0.00 0.00 3.06
4693 4846 2.507102 CGGCGCGTCTGAACATCT 60.507 61.111 9.90 0.00 0.00 2.90
4694 4847 2.792290 CGGCGCGTCTGAACATCTG 61.792 63.158 9.90 0.00 0.00 2.90
4695 4848 1.446099 GGCGCGTCTGAACATCTGA 60.446 57.895 8.43 0.00 0.00 3.27
4696 4849 0.807667 GGCGCGTCTGAACATCTGAT 60.808 55.000 8.43 0.00 0.00 2.90
4697 4850 1.002366 GCGCGTCTGAACATCTGATT 58.998 50.000 8.43 0.00 0.00 2.57
4698 4851 1.394917 GCGCGTCTGAACATCTGATTT 59.605 47.619 8.43 0.00 0.00 2.17
4699 4852 2.159653 GCGCGTCTGAACATCTGATTTT 60.160 45.455 8.43 0.00 0.00 1.82
4700 4853 3.667960 GCGCGTCTGAACATCTGATTTTT 60.668 43.478 8.43 0.00 0.00 1.94
4735 4888 4.583871 AGGGTAAGCATCTGAACTTTCTG 58.416 43.478 2.22 0.00 0.00 3.02
4736 4889 4.287067 AGGGTAAGCATCTGAACTTTCTGA 59.713 41.667 1.54 1.54 39.07 3.27
4746 4904 5.065914 TCTGAACTTTCTGATGGGTTTCTG 58.934 41.667 0.00 0.00 31.41 3.02
4759 4917 0.040067 GTTTCTGTTTGCTCGGGCTG 60.040 55.000 9.62 0.00 39.59 4.85
4760 4918 0.465460 TTTCTGTTTGCTCGGGCTGT 60.465 50.000 9.62 0.00 39.59 4.40
4761 4919 1.165907 TTCTGTTTGCTCGGGCTGTG 61.166 55.000 9.62 0.00 39.59 3.66
4762 4920 1.893808 CTGTTTGCTCGGGCTGTGT 60.894 57.895 9.62 0.00 39.59 3.72
4776 4934 1.930817 GCTGTGTGTGTAGTCACGGAG 60.931 57.143 8.08 0.00 46.49 4.63
4780 4938 0.728466 GTGTGTAGTCACGGAGTCGC 60.728 60.000 0.00 0.00 46.49 5.19
4815 4973 1.149174 CCCCGGGATCCTCATGTTG 59.851 63.158 26.32 0.00 0.00 3.33
4818 4976 0.179045 CCGGGATCCTCATGTTGGAC 60.179 60.000 12.58 6.84 36.30 4.02
4820 4978 0.541863 GGGATCCTCATGTTGGACGT 59.458 55.000 12.58 0.00 36.30 4.34
4821 4979 1.656652 GGATCCTCATGTTGGACGTG 58.343 55.000 3.84 0.00 36.30 4.49
4856 5014 1.522580 GGAATCGCTGGCTGTCCTC 60.523 63.158 0.00 0.00 0.00 3.71
4882 5040 2.562298 GGATTTGCACTGTTGGATTGGA 59.438 45.455 0.00 0.00 0.00 3.53
4883 5041 3.006752 GGATTTGCACTGTTGGATTGGAA 59.993 43.478 0.00 0.00 0.00 3.53
4885 5043 1.619654 TGCACTGTTGGATTGGAAGG 58.380 50.000 0.00 0.00 0.00 3.46
4899 8083 4.171103 AAGGCGGCCGGGTCATAC 62.171 66.667 29.38 7.82 0.00 2.39
5084 8269 3.294493 GGCTGTTTGCTGGGCGAA 61.294 61.111 0.00 0.00 42.39 4.70
5086 8271 2.260869 GCTGTTTGCTGGGCGAAGA 61.261 57.895 0.00 0.00 38.95 2.87
5158 8343 4.244802 CGTCGGCTCCTCTCGCTC 62.245 72.222 0.00 0.00 0.00 5.03
5159 8344 2.826738 GTCGGCTCCTCTCGCTCT 60.827 66.667 0.00 0.00 0.00 4.09
5173 8358 2.289532 GCTCTCTCTGGTGCCCACT 61.290 63.158 0.00 0.00 0.00 4.00
5175 8360 2.046507 CTCTCTGGTGCCCACTGC 60.047 66.667 0.00 0.00 41.77 4.40
5244 8429 3.381136 CCCCGGGCAAATGTGGTG 61.381 66.667 17.73 0.00 0.00 4.17
5245 8430 3.381136 CCCGGGCAAATGTGGTGG 61.381 66.667 8.08 0.00 0.00 4.61
5246 8431 2.600173 CCGGGCAAATGTGGTGGT 60.600 61.111 0.00 0.00 0.00 4.16
5247 8432 2.650196 CGGGCAAATGTGGTGGTG 59.350 61.111 0.00 0.00 0.00 4.17
5248 8433 2.199652 CGGGCAAATGTGGTGGTGT 61.200 57.895 0.00 0.00 0.00 4.16
5249 8434 1.367102 GGGCAAATGTGGTGGTGTG 59.633 57.895 0.00 0.00 0.00 3.82
5250 8435 1.398958 GGGCAAATGTGGTGGTGTGT 61.399 55.000 0.00 0.00 0.00 3.72
5251 8436 0.249405 GGCAAATGTGGTGGTGTGTG 60.249 55.000 0.00 0.00 0.00 3.82
5252 8437 0.249405 GCAAATGTGGTGGTGTGTGG 60.249 55.000 0.00 0.00 0.00 4.17
5253 8438 1.110442 CAAATGTGGTGGTGTGTGGT 58.890 50.000 0.00 0.00 0.00 4.16
5254 8439 1.110442 AAATGTGGTGGTGTGTGGTG 58.890 50.000 0.00 0.00 0.00 4.17
5255 8440 0.754957 AATGTGGTGGTGTGTGGTGG 60.755 55.000 0.00 0.00 0.00 4.61
5256 8441 1.932156 ATGTGGTGGTGTGTGGTGGT 61.932 55.000 0.00 0.00 0.00 4.16
5257 8442 2.118404 GTGGTGGTGTGTGGTGGTG 61.118 63.158 0.00 0.00 0.00 4.17
5258 8443 2.274104 GGTGGTGTGTGGTGGTGT 59.726 61.111 0.00 0.00 0.00 4.16
5259 8444 2.118404 GGTGGTGTGTGGTGGTGTG 61.118 63.158 0.00 0.00 0.00 3.82
5260 8445 2.439338 TGGTGTGTGGTGGTGTGC 60.439 61.111 0.00 0.00 0.00 4.57
5261 8446 3.216292 GGTGTGTGGTGGTGTGCC 61.216 66.667 0.00 0.00 0.00 5.01
5262 8447 2.124320 GTGTGTGGTGGTGTGCCT 60.124 61.111 0.00 0.00 35.27 4.75
5263 8448 1.752694 GTGTGTGGTGGTGTGCCTT 60.753 57.895 0.00 0.00 35.27 4.35
5264 8449 1.453015 TGTGTGGTGGTGTGCCTTC 60.453 57.895 0.00 0.00 35.27 3.46
5265 8450 2.193536 GTGTGGTGGTGTGCCTTCC 61.194 63.158 0.00 0.00 35.27 3.46
5266 8451 2.382770 TGTGGTGGTGTGCCTTCCT 61.383 57.895 0.00 0.00 35.27 3.36
5267 8452 1.898574 GTGGTGGTGTGCCTTCCTG 60.899 63.158 0.00 0.00 35.27 3.86
5268 8453 2.382770 TGGTGGTGTGCCTTCCTGT 61.383 57.895 0.00 0.00 35.27 4.00
5269 8454 1.898574 GGTGGTGTGCCTTCCTGTG 60.899 63.158 0.00 0.00 35.27 3.66
5270 8455 1.152963 GTGGTGTGCCTTCCTGTGT 60.153 57.895 0.00 0.00 35.27 3.72
5271 8456 1.152984 TGGTGTGCCTTCCTGTGTG 60.153 57.895 0.00 0.00 35.27 3.82
5272 8457 1.898574 GGTGTGCCTTCCTGTGTGG 60.899 63.158 0.00 0.00 37.10 4.17
5273 8458 1.898574 GTGTGCCTTCCTGTGTGGG 60.899 63.158 0.00 0.00 36.20 4.61
5274 8459 2.382770 TGTGCCTTCCTGTGTGGGT 61.383 57.895 0.00 0.00 36.20 4.51
5275 8460 1.152756 GTGCCTTCCTGTGTGGGTT 60.153 57.895 0.00 0.00 36.20 4.11
5276 8461 1.152777 TGCCTTCCTGTGTGGGTTG 60.153 57.895 0.00 0.00 36.20 3.77
5277 8462 1.152756 GCCTTCCTGTGTGGGTTGT 60.153 57.895 0.00 0.00 36.20 3.32
5278 8463 0.755327 GCCTTCCTGTGTGGGTTGTT 60.755 55.000 0.00 0.00 36.20 2.83
5279 8464 1.032014 CCTTCCTGTGTGGGTTGTTG 58.968 55.000 0.00 0.00 36.20 3.33
5280 8465 1.032014 CTTCCTGTGTGGGTTGTTGG 58.968 55.000 0.00 0.00 36.20 3.77
5281 8466 0.333312 TTCCTGTGTGGGTTGTTGGT 59.667 50.000 0.00 0.00 36.20 3.67
5282 8467 0.395036 TCCTGTGTGGGTTGTTGGTG 60.395 55.000 0.00 0.00 36.20 4.17
5283 8468 1.391157 CCTGTGTGGGTTGTTGGTGG 61.391 60.000 0.00 0.00 0.00 4.61
5284 8469 1.380515 TGTGTGGGTTGTTGGTGGG 60.381 57.895 0.00 0.00 0.00 4.61
5285 8470 2.443016 TGTGGGTTGTTGGTGGGC 60.443 61.111 0.00 0.00 0.00 5.36
5286 8471 3.601685 GTGGGTTGTTGGTGGGCG 61.602 66.667 0.00 0.00 0.00 6.13
5287 8472 4.130554 TGGGTTGTTGGTGGGCGT 62.131 61.111 0.00 0.00 0.00 5.68
5288 8473 3.292159 GGGTTGTTGGTGGGCGTC 61.292 66.667 0.00 0.00 0.00 5.19
5289 8474 2.517402 GGTTGTTGGTGGGCGTCA 60.517 61.111 0.00 0.00 0.00 4.35
5290 8475 1.901464 GGTTGTTGGTGGGCGTCAT 60.901 57.895 0.00 0.00 0.00 3.06
5291 8476 1.579429 GTTGTTGGTGGGCGTCATC 59.421 57.895 0.00 0.00 0.00 2.92
5292 8477 1.963855 TTGTTGGTGGGCGTCATCG 60.964 57.895 0.00 0.00 40.37 3.84
5293 8478 2.358247 GTTGGTGGGCGTCATCGT 60.358 61.111 0.00 0.00 39.49 3.73
5294 8479 1.964373 GTTGGTGGGCGTCATCGTT 60.964 57.895 0.00 0.00 39.49 3.85
5295 8480 1.963855 TTGGTGGGCGTCATCGTTG 60.964 57.895 0.00 0.00 39.49 4.10
5296 8481 2.358247 GGTGGGCGTCATCGTTGT 60.358 61.111 0.00 0.00 39.49 3.32
5297 8482 2.677003 GGTGGGCGTCATCGTTGTG 61.677 63.158 0.00 0.00 39.49 3.33
5298 8483 2.358125 TGGGCGTCATCGTTGTGG 60.358 61.111 0.00 0.00 39.49 4.17
5299 8484 3.124921 GGGCGTCATCGTTGTGGG 61.125 66.667 0.00 0.00 39.49 4.61
5300 8485 2.358247 GGCGTCATCGTTGTGGGT 60.358 61.111 0.00 0.00 39.49 4.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
339 341 0.040499 AGCTCCTCTCCTCGTTCCTT 59.960 55.000 0.00 0.00 0.00 3.36
340 342 0.395173 GAGCTCCTCTCCTCGTTCCT 60.395 60.000 0.87 0.00 35.77 3.36
463 478 1.941734 GTCCGCTCGATGCTCTTCG 60.942 63.158 5.53 0.00 40.11 3.79
491 506 1.408961 CCTCACTCTCTTCTCCGGCTA 60.409 57.143 0.00 0.00 0.00 3.93
578 594 0.981943 ACTCCCTCCGTTCGGATTTT 59.018 50.000 14.34 0.00 33.34 1.82
604 620 3.621558 TCCCACACACACACACATTTTA 58.378 40.909 0.00 0.00 0.00 1.52
621 637 0.404426 TCTCGAGTCTTGACCTCCCA 59.596 55.000 13.13 0.00 0.00 4.37
625 641 3.691575 TCTTGATCTCGAGTCTTGACCT 58.308 45.455 13.13 0.00 0.00 3.85
626 642 3.733684 GCTCTTGATCTCGAGTCTTGACC 60.734 52.174 13.13 1.41 0.00 4.02
629 645 3.500558 TGCTCTTGATCTCGAGTCTTG 57.499 47.619 13.13 6.84 0.00 3.02
630 646 3.509575 AGTTGCTCTTGATCTCGAGTCTT 59.490 43.478 13.13 0.00 0.00 3.01
631 647 3.088532 AGTTGCTCTTGATCTCGAGTCT 58.911 45.455 13.13 0.67 0.00 3.24
632 648 3.119673 TGAGTTGCTCTTGATCTCGAGTC 60.120 47.826 13.13 9.92 0.00 3.36
633 649 2.822561 TGAGTTGCTCTTGATCTCGAGT 59.177 45.455 13.13 0.00 0.00 4.18
634 650 3.500558 TGAGTTGCTCTTGATCTCGAG 57.499 47.619 5.93 5.93 0.00 4.04
637 653 3.001127 GCGAATGAGTTGCTCTTGATCTC 59.999 47.826 0.00 0.00 0.00 2.75
641 657 2.462456 AGCGAATGAGTTGCTCTTGA 57.538 45.000 0.00 0.00 32.44 3.02
671 687 0.677288 GGGCCTGGCTTTTAAAACGT 59.323 50.000 19.68 0.00 0.00 3.99
672 688 0.676736 TGGGCCTGGCTTTTAAAACG 59.323 50.000 19.68 0.00 0.00 3.60
673 689 1.270625 GGTGGGCCTGGCTTTTAAAAC 60.271 52.381 19.68 6.51 0.00 2.43
674 690 1.052617 GGTGGGCCTGGCTTTTAAAA 58.947 50.000 19.68 0.00 0.00 1.52
675 691 0.105453 TGGTGGGCCTGGCTTTTAAA 60.105 50.000 19.68 0.00 35.27 1.52
699 715 2.586357 GTGATCGGCGGAGAAGGC 60.586 66.667 7.21 0.00 0.00 4.35
704 725 0.597637 GTATGGTGTGATCGGCGGAG 60.598 60.000 7.21 0.00 0.00 4.63
719 740 1.957877 GAAGAGGGAGAGTCGGGTATG 59.042 57.143 0.00 0.00 0.00 2.39
720 741 1.133419 GGAAGAGGGAGAGTCGGGTAT 60.133 57.143 0.00 0.00 0.00 2.73
721 742 0.258194 GGAAGAGGGAGAGTCGGGTA 59.742 60.000 0.00 0.00 0.00 3.69
722 743 1.000612 GGAAGAGGGAGAGTCGGGT 59.999 63.158 0.00 0.00 0.00 5.28
763 784 1.740296 CGCTTCTTGTACCCCGTGG 60.740 63.158 0.00 0.00 37.80 4.94
807 828 4.724697 CTTTGGTCTGTGCGCGCG 62.725 66.667 28.44 28.44 0.00 6.86
808 829 3.579626 GACTTTGGTCTGTGCGCGC 62.580 63.158 27.26 27.26 39.24 6.86
809 830 2.551270 GACTTTGGTCTGTGCGCG 59.449 61.111 0.00 0.00 39.24 6.86
810 831 2.617274 GGGACTTTGGTCTGTGCGC 61.617 63.158 0.00 0.00 41.82 6.09
848 874 2.437180 CCGCTGCTCTCCATTGCA 60.437 61.111 0.00 0.00 37.63 4.08
882 908 2.107901 AGAGGATCAATCATTGGGGAGC 59.892 50.000 0.00 0.00 37.82 4.70
899 925 5.083122 TCTAGCTTAGATGGGAATGAGAGG 58.917 45.833 0.00 0.00 0.00 3.69
900 926 6.664816 AGATCTAGCTTAGATGGGAATGAGAG 59.335 42.308 9.53 0.00 45.16 3.20
1146 1175 2.417649 GATAGTAGACCCCGCCGTGC 62.418 65.000 0.00 0.00 0.00 5.34
1263 1292 1.979693 GTCGGACCTGAGAGGCAGT 60.980 63.158 0.00 0.00 43.33 4.40
1357 1386 6.068670 ACCCAAACTGTAGCAAAGTAAGAAT 58.931 36.000 0.00 0.00 0.00 2.40
1383 1412 2.704572 CTACAAGCCAAGAACCTCAGG 58.295 52.381 0.00 0.00 0.00 3.86
1385 1414 1.699634 AGCTACAAGCCAAGAACCTCA 59.300 47.619 0.00 0.00 43.77 3.86
1386 1415 2.079925 CAGCTACAAGCCAAGAACCTC 58.920 52.381 0.00 0.00 43.77 3.85
1387 1416 1.884067 GCAGCTACAAGCCAAGAACCT 60.884 52.381 0.00 0.00 43.77 3.50
1388 1417 0.523519 GCAGCTACAAGCCAAGAACC 59.476 55.000 0.00 0.00 43.77 3.62
1411 1440 5.534654 CCCAACCAAGAAACATAAAGAGACA 59.465 40.000 0.00 0.00 0.00 3.41
1436 1465 1.672356 CCCCTGAACAGACCGCAAG 60.672 63.158 3.19 0.00 0.00 4.01
1518 1547 2.656069 TAGCCCGAGTTGTCCAGGC 61.656 63.158 0.00 0.00 38.44 4.85
1531 1560 3.037428 CCGCCGTAGTAGTAGCCC 58.963 66.667 0.00 0.00 0.00 5.19
2021 2065 4.143333 CTACCTGGTGACGCCCCG 62.143 72.222 10.23 0.00 36.04 5.73
2046 2090 1.678970 GGGGTGAGATGGGTTGTGC 60.679 63.158 0.00 0.00 0.00 4.57
2048 2092 1.084018 AATGGGGTGAGATGGGTTGT 58.916 50.000 0.00 0.00 0.00 3.32
2080 2127 0.960861 AGACGATGGCGACTCACTGA 60.961 55.000 0.00 0.00 38.03 3.41
2081 2128 0.109086 AAGACGATGGCGACTCACTG 60.109 55.000 0.00 0.00 41.40 3.66
2082 2129 0.171455 GAAGACGATGGCGACTCACT 59.829 55.000 0.00 0.00 41.40 3.41
2083 2130 0.802607 GGAAGACGATGGCGACTCAC 60.803 60.000 0.00 0.00 41.40 3.51
2084 2131 0.965866 AGGAAGACGATGGCGACTCA 60.966 55.000 0.00 0.00 41.40 3.41
2085 2132 0.248702 GAGGAAGACGATGGCGACTC 60.249 60.000 0.00 0.00 41.40 3.36
2086 2133 1.668101 GGAGGAAGACGATGGCGACT 61.668 60.000 0.00 0.00 43.94 4.18
2087 2134 1.227002 GGAGGAAGACGATGGCGAC 60.227 63.158 0.00 0.00 41.64 5.19
2088 2135 1.379977 AGGAGGAAGACGATGGCGA 60.380 57.895 0.00 0.00 41.64 5.54
2250 2297 1.153269 GGCAGCTGTTAGGGAGCTC 60.153 63.158 16.64 4.71 45.24 4.09
2262 2309 1.970092 CTACTACTACTCCGGCAGCT 58.030 55.000 0.00 0.00 0.00 4.24
2263 2310 0.311477 GCTACTACTACTCCGGCAGC 59.689 60.000 0.00 0.00 0.00 5.25
2264 2311 1.334243 GTGCTACTACTACTCCGGCAG 59.666 57.143 0.00 0.00 0.00 4.85
2266 2313 1.677942 AGTGCTACTACTACTCCGGC 58.322 55.000 0.00 0.00 0.00 6.13
2268 2315 3.436496 GCAAAGTGCTACTACTACTCCG 58.564 50.000 0.00 0.00 40.96 4.63
2269 2316 3.430513 GGGCAAAGTGCTACTACTACTCC 60.431 52.174 0.00 0.00 44.28 3.85
2270 2317 3.430513 GGGGCAAAGTGCTACTACTACTC 60.431 52.174 0.00 0.00 44.28 2.59
2277 2324 1.380302 CTGGGGGCAAAGTGCTACT 59.620 57.895 0.00 0.00 44.28 2.57
2293 2340 9.298774 GTACAGCTACTAACTAAAATGGTACTG 57.701 37.037 0.00 0.00 0.00 2.74
2334 2396 7.299787 TCACATCACTACTTAGTACACTACG 57.700 40.000 0.00 0.00 34.13 3.51
2335 2397 9.504710 CAATCACATCACTACTTAGTACACTAC 57.495 37.037 0.00 0.00 34.13 2.73
2337 2399 7.036220 GCAATCACATCACTACTTAGTACACT 58.964 38.462 0.00 0.00 34.13 3.55
2338 2400 6.811665 TGCAATCACATCACTACTTAGTACAC 59.188 38.462 0.00 0.00 34.13 2.90
2339 2401 6.811665 GTGCAATCACATCACTACTTAGTACA 59.188 38.462 0.00 0.00 42.66 2.90
2340 2402 7.036220 AGTGCAATCACATCACTACTTAGTAC 58.964 38.462 0.00 0.00 45.49 2.73
2341 2403 7.170393 AGTGCAATCACATCACTACTTAGTA 57.830 36.000 0.00 0.00 45.49 1.82
2342 2404 6.042638 AGTGCAATCACATCACTACTTAGT 57.957 37.500 0.00 0.00 45.49 2.24
2436 2503 8.134202 TCACCAAGATAAACTGAAGATGTAGA 57.866 34.615 0.00 0.00 0.00 2.59
2437 2504 8.037758 ACTCACCAAGATAAACTGAAGATGTAG 58.962 37.037 0.00 0.00 0.00 2.74
2439 2506 6.773638 ACTCACCAAGATAAACTGAAGATGT 58.226 36.000 0.00 0.00 0.00 3.06
2440 2507 7.010923 GCTACTCACCAAGATAAACTGAAGATG 59.989 40.741 0.00 0.00 0.00 2.90
2441 2508 7.044798 GCTACTCACCAAGATAAACTGAAGAT 58.955 38.462 0.00 0.00 0.00 2.40
2467 2544 1.310933 GCATCACTCCCAGGCAACAG 61.311 60.000 0.00 0.00 41.41 3.16
2468 2545 1.303561 GCATCACTCCCAGGCAACA 60.304 57.895 0.00 0.00 41.41 3.33
2469 2546 1.001641 AGCATCACTCCCAGGCAAC 60.002 57.895 0.00 0.00 0.00 4.17
2470 2547 1.300963 GAGCATCACTCCCAGGCAA 59.699 57.895 0.00 0.00 39.75 4.52
2471 2548 2.993008 GAGCATCACTCCCAGGCA 59.007 61.111 0.00 0.00 39.75 4.75
2510 2597 8.768397 ACTAGTATTTGTATTGACTGATCCCAA 58.232 33.333 0.00 0.00 0.00 4.12
2523 2610 6.327626 ACATGCAGAGGGACTAGTATTTGTAT 59.672 38.462 0.00 0.00 41.55 2.29
2541 2628 4.334759 CACTCCCTCTGATTAAACATGCAG 59.665 45.833 0.00 0.00 0.00 4.41
2545 2632 4.324563 CCACCACTCCCTCTGATTAAACAT 60.325 45.833 0.00 0.00 0.00 2.71
2552 2640 1.557269 GCACCACCACTCCCTCTGAT 61.557 60.000 0.00 0.00 0.00 2.90
2578 2666 6.642540 CCCAAATCAACAAGCTCTTTTAGTTC 59.357 38.462 0.00 0.00 0.00 3.01
2589 2677 0.681175 ACCTGCCCAAATCAACAAGC 59.319 50.000 0.00 0.00 0.00 4.01
2650 2738 3.545481 CAGTACTTGAGCGCCGCG 61.545 66.667 8.83 8.83 0.00 6.46
2747 2848 2.287970 TGATGACAAGCAAGCAAGCAAG 60.288 45.455 3.19 0.00 36.85 4.01
2764 2883 5.571784 AAATCACTGGCTACATTGTGATG 57.428 39.130 8.00 0.00 45.74 3.07
2786 2905 2.926200 CAAACACGCAAACAATGGTCAA 59.074 40.909 0.00 0.00 0.00 3.18
2899 3018 1.466866 CGTTCAGGCAAGCATGTGATG 60.467 52.381 6.60 0.00 0.00 3.07
2919 3040 2.160417 CGAGTGCAAATTTCTCAGGGTC 59.840 50.000 0.00 0.00 0.00 4.46
2920 3041 2.154462 CGAGTGCAAATTTCTCAGGGT 58.846 47.619 0.00 0.00 0.00 4.34
2922 3043 3.242220 CGATCGAGTGCAAATTTCTCAGG 60.242 47.826 10.26 0.00 0.00 3.86
2924 3045 2.094258 GCGATCGAGTGCAAATTTCTCA 59.906 45.455 21.57 0.00 0.00 3.27
2954 3084 4.111016 CGCCGGCGTGAGTGTCTA 62.111 66.667 39.71 0.00 34.35 2.59
2970 3100 3.803082 CTGCACCAATGGCGGTCG 61.803 66.667 0.00 0.00 37.07 4.79
2971 3101 3.443045 CCTGCACCAATGGCGGTC 61.443 66.667 0.00 0.00 37.07 4.79
2972 3102 3.505790 TTCCTGCACCAATGGCGGT 62.506 57.895 0.00 0.00 41.07 5.68
3019 3149 1.885163 CTGGTGACTCCCCGGTACAC 61.885 65.000 0.00 3.04 34.77 2.90
3152 3282 1.102978 ACCTGATTAATGGCGGCAAC 58.897 50.000 18.31 6.16 0.00 4.17
3202 3332 1.252215 TGCATCTTGTGGTGCCCATG 61.252 55.000 0.00 0.00 40.56 3.66
3203 3333 0.542467 TTGCATCTTGTGGTGCCCAT 60.542 50.000 0.00 0.00 40.56 4.00
3204 3334 0.758310 TTTGCATCTTGTGGTGCCCA 60.758 50.000 0.00 0.00 40.56 5.36
3205 3335 0.609662 ATTTGCATCTTGTGGTGCCC 59.390 50.000 0.00 0.00 40.56 5.36
3206 3336 1.404583 GGATTTGCATCTTGTGGTGCC 60.405 52.381 0.00 0.00 40.56 5.01
3207 3337 1.733389 CGGATTTGCATCTTGTGGTGC 60.733 52.381 0.00 0.00 41.61 5.01
3208 3338 1.733389 GCGGATTTGCATCTTGTGGTG 60.733 52.381 0.00 0.00 34.15 4.17
3209 3339 0.527565 GCGGATTTGCATCTTGTGGT 59.472 50.000 0.00 0.00 34.15 4.16
3210 3340 0.527113 TGCGGATTTGCATCTTGTGG 59.473 50.000 0.00 0.00 40.62 4.17
3211 3341 1.904144 CTGCGGATTTGCATCTTGTG 58.096 50.000 0.00 0.00 45.26 3.33
3238 3368 4.333095 GTGATGATGATGCATGATAGGAGC 59.667 45.833 2.46 0.00 0.00 4.70
3239 3369 4.876679 GGTGATGATGATGCATGATAGGAG 59.123 45.833 2.46 0.00 0.00 3.69
3240 3370 4.622220 CGGTGATGATGATGCATGATAGGA 60.622 45.833 2.46 0.00 0.00 2.94
3241 3371 3.621715 CGGTGATGATGATGCATGATAGG 59.378 47.826 2.46 0.00 0.00 2.57
3242 3372 4.501071 TCGGTGATGATGATGCATGATAG 58.499 43.478 2.46 0.00 0.00 2.08
3243 3373 4.540359 TCGGTGATGATGATGCATGATA 57.460 40.909 2.46 0.00 0.00 2.15
3244 3374 3.412237 TCGGTGATGATGATGCATGAT 57.588 42.857 2.46 0.00 0.00 2.45
3245 3375 2.914695 TCGGTGATGATGATGCATGA 57.085 45.000 2.46 0.00 0.00 3.07
3246 3376 3.500680 TGAATCGGTGATGATGATGCATG 59.499 43.478 2.46 0.00 0.00 4.06
3247 3377 3.501062 GTGAATCGGTGATGATGATGCAT 59.499 43.478 0.00 0.00 30.63 3.96
3248 3378 2.874086 GTGAATCGGTGATGATGATGCA 59.126 45.455 0.00 0.00 0.00 3.96
3249 3379 2.225019 GGTGAATCGGTGATGATGATGC 59.775 50.000 0.00 0.00 0.00 3.91
3537 3671 1.212616 CCTTATGAGAAAGGCGAGCG 58.787 55.000 0.00 0.00 39.69 5.03
3602 3736 2.757508 CAGGAGAGGAGCCGAGCA 60.758 66.667 0.00 0.00 0.00 4.26
3642 3776 2.256461 GCTTGAAACAGCAGCCGG 59.744 61.111 0.00 0.00 39.83 6.13
3655 3789 1.297819 CACACACACACGCAGCTTG 60.298 57.895 0.00 0.00 0.00 4.01
3799 3939 2.913777 TGATCTTGTCCACGTCGTAG 57.086 50.000 0.00 0.00 0.00 3.51
4330 4479 1.406065 ATCTCCTCGTGGATGCAGGG 61.406 60.000 6.68 1.08 42.29 4.45
4331 4480 1.271934 CTATCTCCTCGTGGATGCAGG 59.728 57.143 6.68 0.00 42.29 4.85
4356 4505 6.528321 AGGTAACCAGTCCTAGTTAAACAAC 58.472 40.000 0.00 0.00 30.64 3.32
4358 4507 7.472334 CTAGGTAACCAGTCCTAGTTAAACA 57.528 40.000 9.33 0.00 44.71 2.83
4370 4519 5.069251 CAGCTACTAATGCTAGGTAACCAGT 59.931 44.000 0.00 0.00 38.92 4.00
4602 4755 3.118038 AGGTCTAGAGACAGGAGCTACAG 60.118 52.174 11.64 0.00 46.47 2.74
4603 4756 2.847449 AGGTCTAGAGACAGGAGCTACA 59.153 50.000 11.64 0.00 46.47 2.74
4618 4771 6.271391 TGGTTTGATGAAAGTTAGGAGGTCTA 59.729 38.462 0.00 0.00 0.00 2.59
4651 4804 1.219522 CCACACGAACACGAAGGTCC 61.220 60.000 0.00 0.00 0.00 4.46
4677 4830 0.807667 ATCAGATGTTCAGACGCGCC 60.808 55.000 5.73 0.00 0.00 6.53
4707 4860 5.385198 AGTTCAGATGCTTACCCTCAAAAA 58.615 37.500 0.00 0.00 0.00 1.94
4708 4861 4.985538 AGTTCAGATGCTTACCCTCAAAA 58.014 39.130 0.00 0.00 0.00 2.44
4709 4862 4.640771 AGTTCAGATGCTTACCCTCAAA 57.359 40.909 0.00 0.00 0.00 2.69
4710 4863 4.640771 AAGTTCAGATGCTTACCCTCAA 57.359 40.909 0.00 0.00 0.00 3.02
4711 4864 4.287067 AGAAAGTTCAGATGCTTACCCTCA 59.713 41.667 0.00 0.00 0.00 3.86
4712 4865 4.633565 CAGAAAGTTCAGATGCTTACCCTC 59.366 45.833 0.00 0.00 0.00 4.30
4713 4866 4.287067 TCAGAAAGTTCAGATGCTTACCCT 59.713 41.667 0.00 0.00 0.00 4.34
4714 4867 4.579869 TCAGAAAGTTCAGATGCTTACCC 58.420 43.478 0.00 0.00 0.00 3.69
4715 4868 5.065731 CCATCAGAAAGTTCAGATGCTTACC 59.934 44.000 16.76 0.00 44.81 2.85
4716 4869 5.065731 CCCATCAGAAAGTTCAGATGCTTAC 59.934 44.000 16.76 0.00 44.81 2.34
4717 4870 5.188434 CCCATCAGAAAGTTCAGATGCTTA 58.812 41.667 16.76 0.00 44.81 3.09
4718 4871 4.015084 CCCATCAGAAAGTTCAGATGCTT 58.985 43.478 16.76 0.00 44.81 3.91
4719 4872 3.009916 ACCCATCAGAAAGTTCAGATGCT 59.990 43.478 16.76 5.46 44.81 3.79
4720 4873 3.350833 ACCCATCAGAAAGTTCAGATGC 58.649 45.455 16.76 0.00 44.81 3.91
4721 4874 5.709164 AGAAACCCATCAGAAAGTTCAGATG 59.291 40.000 15.73 15.73 45.37 2.90
4722 4875 5.709164 CAGAAACCCATCAGAAAGTTCAGAT 59.291 40.000 0.00 0.00 34.28 2.90
4735 4888 1.200020 CCGAGCAAACAGAAACCCATC 59.800 52.381 0.00 0.00 0.00 3.51
4736 4889 1.247567 CCGAGCAAACAGAAACCCAT 58.752 50.000 0.00 0.00 0.00 4.00
4741 4899 0.465460 ACAGCCCGAGCAAACAGAAA 60.465 50.000 0.00 0.00 43.56 2.52
4746 4904 2.186826 ACACACAGCCCGAGCAAAC 61.187 57.895 0.00 0.00 43.56 2.93
4759 4917 1.662309 CGACTCCGTGACTACACACAC 60.662 57.143 0.00 0.00 46.20 3.82
4760 4918 0.589708 CGACTCCGTGACTACACACA 59.410 55.000 0.00 0.00 46.20 3.72
4761 4919 0.728466 GCGACTCCGTGACTACACAC 60.728 60.000 0.00 0.00 46.20 3.82
4762 4920 1.577922 GCGACTCCGTGACTACACA 59.422 57.895 0.00 0.00 46.20 3.72
4789 4947 4.570874 GATCCCGGGGAAGCCAGC 62.571 72.222 23.50 0.00 34.34 4.85
4790 4948 3.878667 GGATCCCGGGGAAGCCAG 61.879 72.222 23.50 0.00 34.34 4.85
4791 4949 4.431524 AGGATCCCGGGGAAGCCA 62.432 66.667 29.42 0.00 34.34 4.75
4792 4950 3.561241 GAGGATCCCGGGGAAGCC 61.561 72.222 23.50 23.07 34.34 4.35
4793 4951 2.150051 ATGAGGATCCCGGGGAAGC 61.150 63.158 23.50 15.00 34.34 3.86
4794 4952 1.056700 ACATGAGGATCCCGGGGAAG 61.057 60.000 23.50 6.74 34.34 3.46
4795 4953 0.623324 AACATGAGGATCCCGGGGAA 60.623 55.000 23.50 1.15 34.34 3.97
4796 4954 1.004230 AACATGAGGATCCCGGGGA 59.996 57.895 23.50 20.15 35.55 4.81
4797 4955 1.149174 CAACATGAGGATCCCGGGG 59.851 63.158 23.50 6.77 0.00 5.73
4815 4973 0.878961 ACGAAACTGAAGCCACGTCC 60.879 55.000 0.00 0.00 0.00 4.79
4818 4976 0.788391 GGTACGAAACTGAAGCCACG 59.212 55.000 0.00 0.00 0.00 4.94
4856 5014 1.069022 CCAACAGTGCAAATCCTGTCG 60.069 52.381 8.02 0.00 40.91 4.35
4861 5019 2.562298 TCCAATCCAACAGTGCAAATCC 59.438 45.455 0.00 0.00 0.00 3.01
4862 5020 3.940209 TCCAATCCAACAGTGCAAATC 57.060 42.857 0.00 0.00 0.00 2.17
4867 5025 0.244721 GCCTTCCAATCCAACAGTGC 59.755 55.000 0.00 0.00 0.00 4.40
4882 5040 4.171103 GTATGACCCGGCCGCCTT 62.171 66.667 22.85 5.11 0.00 4.35
4923 8107 2.767697 GTGCGTTACGAGCGGAAC 59.232 61.111 9.62 7.88 37.44 3.62
4945 8129 2.985847 GGCCAACAGTGTCTGCCC 60.986 66.667 20.20 7.09 36.07 5.36
5107 8292 2.266055 GACAAGACTCGCCTGGGG 59.734 66.667 4.03 4.03 0.00 4.96
5149 8334 2.003658 GCACCAGAGAGAGCGAGAGG 62.004 65.000 0.00 0.00 0.00 3.69
5183 8368 2.636462 CACGTTGTTGCATGCGGA 59.364 55.556 14.09 0.63 0.00 5.54
5233 8418 0.249405 CCACACACCACCACATTTGC 60.249 55.000 0.00 0.00 0.00 3.68
5234 8419 1.110442 ACCACACACCACCACATTTG 58.890 50.000 0.00 0.00 0.00 2.32
5235 8420 1.110442 CACCACACACCACCACATTT 58.890 50.000 0.00 0.00 0.00 2.32
5236 8421 0.754957 CCACCACACACCACCACATT 60.755 55.000 0.00 0.00 0.00 2.71
5237 8422 1.152777 CCACCACACACCACCACAT 60.153 57.895 0.00 0.00 0.00 3.21
5238 8423 2.273776 CCACCACACACCACCACA 59.726 61.111 0.00 0.00 0.00 4.17
5239 8424 2.118404 CACCACCACACACCACCAC 61.118 63.158 0.00 0.00 0.00 4.16
5240 8425 2.273776 CACCACCACACACCACCA 59.726 61.111 0.00 0.00 0.00 4.17
5241 8426 2.118404 CACACCACCACACACCACC 61.118 63.158 0.00 0.00 0.00 4.61
5242 8427 2.770589 GCACACCACCACACACCAC 61.771 63.158 0.00 0.00 0.00 4.16
5243 8428 2.439338 GCACACCACCACACACCA 60.439 61.111 0.00 0.00 0.00 4.17
5244 8429 3.216292 GGCACACCACCACACACC 61.216 66.667 0.00 0.00 35.26 4.16
5245 8430 1.724582 GAAGGCACACCACCACACAC 61.725 60.000 0.00 0.00 39.06 3.82
5246 8431 1.453015 GAAGGCACACCACCACACA 60.453 57.895 0.00 0.00 39.06 3.72
5247 8432 2.193536 GGAAGGCACACCACCACAC 61.194 63.158 0.00 0.00 39.06 3.82
5248 8433 2.194597 GGAAGGCACACCACCACA 59.805 61.111 0.00 0.00 39.06 4.17
5249 8434 1.898574 CAGGAAGGCACACCACCAC 60.899 63.158 0.00 0.00 39.06 4.16
5250 8435 2.382770 ACAGGAAGGCACACCACCA 61.383 57.895 0.00 0.00 39.06 4.17
5251 8436 1.898574 CACAGGAAGGCACACCACC 60.899 63.158 0.00 0.00 39.06 4.61
5252 8437 1.152963 ACACAGGAAGGCACACCAC 60.153 57.895 0.00 0.00 39.06 4.16
5253 8438 1.152984 CACACAGGAAGGCACACCA 60.153 57.895 0.00 0.00 39.06 4.17
5254 8439 1.898574 CCACACAGGAAGGCACACC 60.899 63.158 0.00 0.00 41.22 4.16
5255 8440 1.898574 CCCACACAGGAAGGCACAC 60.899 63.158 0.00 0.00 41.22 3.82
5256 8441 1.932156 AACCCACACAGGAAGGCACA 61.932 55.000 0.00 0.00 41.22 4.57
5257 8442 1.152756 AACCCACACAGGAAGGCAC 60.153 57.895 0.00 0.00 41.22 5.01
5258 8443 1.152777 CAACCCACACAGGAAGGCA 60.153 57.895 0.00 0.00 41.22 4.75
5259 8444 0.755327 AACAACCCACACAGGAAGGC 60.755 55.000 0.00 0.00 41.22 4.35
5260 8445 1.032014 CAACAACCCACACAGGAAGG 58.968 55.000 0.00 0.00 41.22 3.46
5261 8446 1.032014 CCAACAACCCACACAGGAAG 58.968 55.000 0.00 0.00 41.22 3.46
5262 8447 0.333312 ACCAACAACCCACACAGGAA 59.667 50.000 0.00 0.00 41.22 3.36
5263 8448 0.395036 CACCAACAACCCACACAGGA 60.395 55.000 0.00 0.00 41.22 3.86
5264 8449 1.391157 CCACCAACAACCCACACAGG 61.391 60.000 0.00 0.00 37.03 4.00
5265 8450 1.391157 CCCACCAACAACCCACACAG 61.391 60.000 0.00 0.00 0.00 3.66
5266 8451 1.380515 CCCACCAACAACCCACACA 60.381 57.895 0.00 0.00 0.00 3.72
5267 8452 2.791868 GCCCACCAACAACCCACAC 61.792 63.158 0.00 0.00 0.00 3.82
5268 8453 2.443016 GCCCACCAACAACCCACA 60.443 61.111 0.00 0.00 0.00 4.17
5269 8454 3.601685 CGCCCACCAACAACCCAC 61.602 66.667 0.00 0.00 0.00 4.61
5270 8455 4.130554 ACGCCCACCAACAACCCA 62.131 61.111 0.00 0.00 0.00 4.51
5271 8456 3.292159 GACGCCCACCAACAACCC 61.292 66.667 0.00 0.00 0.00 4.11
5272 8457 1.862602 GATGACGCCCACCAACAACC 61.863 60.000 0.00 0.00 0.00 3.77
5273 8458 1.579429 GATGACGCCCACCAACAAC 59.421 57.895 0.00 0.00 0.00 3.32
5274 8459 1.963855 CGATGACGCCCACCAACAA 60.964 57.895 0.00 0.00 0.00 2.83
5275 8460 2.358125 CGATGACGCCCACCAACA 60.358 61.111 0.00 0.00 0.00 3.33
5276 8461 1.964373 AACGATGACGCCCACCAAC 60.964 57.895 0.00 0.00 43.96 3.77
5277 8462 1.963855 CAACGATGACGCCCACCAA 60.964 57.895 0.00 0.00 43.96 3.67
5278 8463 2.358125 CAACGATGACGCCCACCA 60.358 61.111 0.00 0.00 43.96 4.17
5279 8464 2.358247 ACAACGATGACGCCCACC 60.358 61.111 0.00 0.00 43.96 4.61
5280 8465 2.677003 CCACAACGATGACGCCCAC 61.677 63.158 0.00 0.00 43.96 4.61
5281 8466 2.358125 CCACAACGATGACGCCCA 60.358 61.111 0.00 0.00 43.96 5.36
5282 8467 3.124921 CCCACAACGATGACGCCC 61.125 66.667 0.00 0.00 43.96 6.13
5283 8468 2.358247 ACCCACAACGATGACGCC 60.358 61.111 0.00 0.00 43.96 5.68


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

AutoCloner maintained by Alex Coulton.