Multiple sequence alignment - TraesCS4A01G012000

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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 TraesCS4A01G012000 chr4A 100.000 5764 0 0 1 5764 6894587 6888824 0.000000e+00 10645.0
1 TraesCS4A01G012000 chr4A 100.000 30 0 0 4914 4943 583946857 583946828 8.070000e-04 56.5
2 TraesCS4A01G012000 chr4D 90.284 3911 255 64 1942 5756 462840594 462836713 0.000000e+00 5001.0
3 TraesCS4A01G012000 chr4D 86.117 886 51 28 805 1661 462841837 462840995 0.000000e+00 889.0
4 TraesCS4A01G012000 chr4B 89.317 4053 294 75 869 4808 578036815 578040841 0.000000e+00 4957.0
5 TraesCS4A01G012000 chr4B 87.780 581 45 8 5021 5599 578041332 578041888 0.000000e+00 656.0
6 TraesCS4A01G012000 chr4B 97.917 48 1 0 808 855 578023622 578023575 3.700000e-12 84.2
7 TraesCS4A01G012000 chr1A 84.841 818 65 19 12 788 451741062 451740263 0.000000e+00 769.0
8 TraesCS4A01G012000 chr1A 92.453 53 3 1 3562 3613 524681711 524681763 2.230000e-09 75.0
9 TraesCS4A01G012000 chr7A 91.667 420 31 4 12 430 428385083 428384667 3.870000e-161 579.0
10 TraesCS4A01G012000 chr7A 85.484 434 54 8 2750 3180 731965218 731965645 1.470000e-120 444.0
11 TraesCS4A01G012000 chr7A 82.381 210 29 5 427 629 428384639 428384431 5.940000e-40 176.0
12 TraesCS4A01G012000 chr5B 85.766 555 49 18 12 539 507161661 507161110 1.400000e-155 560.0
13 TraesCS4A01G012000 chr7B 86.866 434 48 8 2750 3180 741716488 741716061 1.450000e-130 477.0
14 TraesCS4A01G012000 chr7B 84.586 266 39 2 3230 3494 741687904 741687640 4.430000e-66 263.0
15 TraesCS4A01G012000 chr7B 78.571 210 39 6 590 796 245118597 245118803 3.620000e-27 134.0
16 TraesCS4A01G012000 chr7D 84.703 438 55 10 2745 3180 634409212 634408785 1.480000e-115 427.0
17 TraesCS4A01G012000 chr7D 89.333 225 22 2 3391 3613 500954981 500954757 1.220000e-71 281.0
18 TraesCS4A01G012000 chr1B 83.908 435 29 12 12 430 422467783 422468192 1.520000e-100 377.0
19 TraesCS4A01G012000 chr1B 84.383 397 42 5 427 804 422468220 422468615 7.050000e-99 372.0
20 TraesCS4A01G012000 chr2B 83.641 434 30 12 12 429 133936436 133936028 2.540000e-98 370.0
21 TraesCS4A01G012000 chr2B 84.737 380 39 5 427 787 133935999 133935620 4.250000e-96 363.0
22 TraesCS4A01G012000 chr2B 84.979 233 30 5 14 244 378432263 378432034 1.250000e-56 231.0
23 TraesCS4A01G012000 chr2B 83.117 154 21 4 15 166 773464277 773464127 1.010000e-27 135.0
24 TraesCS4A01G012000 chr6B 84.169 379 41 5 427 788 658070881 658070505 3.310000e-92 350.0
25 TraesCS4A01G012000 chr6B 82.093 430 36 11 17 430 658071313 658070909 4.310000e-86 329.0
26 TraesCS4A01G012000 chr3B 82.468 154 22 4 15 166 543584964 543584814 4.690000e-26 130.0
27 TraesCS4A01G012000 chr2D 77.049 183 40 2 607 788 641676942 641677123 2.840000e-18 104.0
28 TraesCS4A01G012000 chr5A 75.676 185 40 5 607 788 40408737 40408555 2.860000e-13 87.9


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 TraesCS4A01G012000 chr4A 6888824 6894587 5763 True 10645.0 10645 100.0000 1 5764 1 chr4A.!!$R1 5763
1 TraesCS4A01G012000 chr4D 462836713 462841837 5124 True 2945.0 5001 88.2005 805 5756 2 chr4D.!!$R1 4951
2 TraesCS4A01G012000 chr4B 578036815 578041888 5073 False 2806.5 4957 88.5485 869 5599 2 chr4B.!!$F1 4730
3 TraesCS4A01G012000 chr1A 451740263 451741062 799 True 769.0 769 84.8410 12 788 1 chr1A.!!$R1 776
4 TraesCS4A01G012000 chr7A 428384431 428385083 652 True 377.5 579 87.0240 12 629 2 chr7A.!!$R1 617
5 TraesCS4A01G012000 chr5B 507161110 507161661 551 True 560.0 560 85.7660 12 539 1 chr5B.!!$R1 527
6 TraesCS4A01G012000 chr1B 422467783 422468615 832 False 374.5 377 84.1455 12 804 2 chr1B.!!$F1 792
7 TraesCS4A01G012000 chr2B 133935620 133936436 816 True 366.5 370 84.1890 12 787 2 chr2B.!!$R3 775
8 TraesCS4A01G012000 chr6B 658070505 658071313 808 True 339.5 350 83.1310 17 788 2 chr6B.!!$R1 771

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
858 942 0.033228 CATCGGCCATCTCTCTCACC 59.967 60.0 2.24 0.0 0.00 4.02 F
1193 1309 0.032714 AGTACGGGTTCCCTACTCCC 60.033 60.0 6.31 0.0 37.98 4.30 F
2527 2830 0.395586 TTCCACCCCATGCATAGTGC 60.396 55.0 14.97 0.0 45.29 4.40 F
3258 3585 0.751643 GGTTGCATATTGACCCGCCT 60.752 55.0 0.00 0.0 0.00 5.52 F
4169 4533 1.048601 TTCAGCCCTGAAGTCTCGTT 58.951 50.0 6.62 0.0 43.90 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2512 2815 1.055849 TATCGCACTATGCATGGGGT 58.944 50.000 14.36 4.00 45.36 4.95 R
2581 2884 1.610522 GAACAACTTGCTCTGCATGGT 59.389 47.619 9.60 0.92 38.76 3.55 R
4124 4488 0.027586 GTTTGCTCACACGGTCACAC 59.972 55.000 0.00 0.00 0.00 3.82 R
4331 4711 0.174389 GCAGCTCCTTCTCGATGTCA 59.826 55.000 0.00 0.00 0.00 3.58 R
4975 5481 0.251165 GTTAGGGGCTTGTTCTGGCA 60.251 55.000 0.00 0.00 0.00 4.92 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
59 61 0.033601 TTGGACTGTTTGGCTGGTGT 60.034 50.000 0.00 0.00 0.00 4.16
112 114 4.501743 GCTAGCCGTTTTCTCCTTAGCTAT 60.502 45.833 2.29 0.00 31.50 2.97
153 155 2.658422 CATGCACAAAGGCCACCC 59.342 61.111 5.01 0.00 0.00 4.61
166 168 1.829523 GCCACCCCACATGCACAAAT 61.830 55.000 0.00 0.00 0.00 2.32
251 261 1.705186 AGCTTACCAAAGAGGAGGCAA 59.295 47.619 0.00 0.00 41.22 4.52
285 296 2.154854 CACGACTTGTGTCACCTCAT 57.845 50.000 0.00 0.00 43.88 2.90
307 318 0.036010 ACTCATTGGCACTCTTCCGG 60.036 55.000 0.00 0.00 0.00 5.14
350 369 2.444706 TGCGCCTGGAGCTAGGAT 60.445 61.111 22.83 0.00 40.42 3.24
353 372 0.896019 GCGCCTGGAGCTAGGATCTA 60.896 60.000 15.58 0.00 40.42 1.98
482 532 5.261011 GCATGACACGTGATGCATCAAGT 62.261 47.826 33.64 33.64 46.95 3.16
514 564 2.528797 GCTTGGAAGCGAACGAAGA 58.471 52.632 0.00 0.00 42.88 2.87
539 589 1.169661 CGGCGAGACTATCTCCAGCT 61.170 60.000 0.00 0.00 40.34 4.24
566 646 1.336887 TGGAAGCGAACGAGGAAGAAG 60.337 52.381 0.00 0.00 0.00 2.85
570 650 1.340248 AGCGAACGAGGAAGAAGAACA 59.660 47.619 0.00 0.00 0.00 3.18
582 662 1.550976 AGAAGAACAAGACGGGCCTAG 59.449 52.381 0.84 0.00 0.00 3.02
588 668 1.697982 ACAAGACGGGCCTAGTTTCTT 59.302 47.619 0.84 0.80 0.00 2.52
657 741 6.591935 ACAGAGGAAATACTGTGTTTTGAGA 58.408 36.000 4.01 0.00 41.60 3.27
726 810 6.071952 AGCTCACTGTAATTAAAACCATGGTG 60.072 38.462 20.60 3.89 0.00 4.17
788 872 1.211457 AGAGCTATCAAACAGGGCCTG 59.789 52.381 31.62 31.62 37.52 4.85
791 875 1.065126 GCTATCAAACAGGGCCTGAGT 60.065 52.381 38.99 23.06 35.18 3.41
792 876 2.636830 CTATCAAACAGGGCCTGAGTG 58.363 52.381 38.99 31.10 35.18 3.51
793 877 0.773644 ATCAAACAGGGCCTGAGTGT 59.226 50.000 38.99 15.87 35.18 3.55
794 878 0.179020 TCAAACAGGGCCTGAGTGTG 60.179 55.000 38.99 26.59 35.18 3.82
795 879 0.466189 CAAACAGGGCCTGAGTGTGT 60.466 55.000 38.99 14.63 35.18 3.72
796 880 0.179018 AAACAGGGCCTGAGTGTGTC 60.179 55.000 38.99 0.00 35.18 3.67
797 881 1.056700 AACAGGGCCTGAGTGTGTCT 61.057 55.000 38.99 12.11 35.18 3.41
798 882 1.294780 CAGGGCCTGAGTGTGTCTC 59.705 63.158 29.96 0.00 43.03 3.36
856 940 1.752358 GCCATCGGCCATCTCTCTCA 61.752 60.000 2.24 0.00 44.06 3.27
858 942 0.033228 CATCGGCCATCTCTCTCACC 59.967 60.000 2.24 0.00 0.00 4.02
859 943 0.105760 ATCGGCCATCTCTCTCACCT 60.106 55.000 2.24 0.00 0.00 4.00
866 954 1.678627 CATCTCTCTCACCTACCACGG 59.321 57.143 0.00 0.00 0.00 4.94
871 959 4.642488 TCACCTACCACGGGCCCA 62.642 66.667 24.92 0.00 0.00 5.36
983 1079 0.597637 CGGTCCTCATATGCGGTGAC 60.598 60.000 11.45 3.60 0.00 3.67
996 1092 2.147820 GGTGACGTACGTTTCCAGC 58.852 57.895 23.70 20.34 0.00 4.85
1030 1127 3.308323 CACAAGAGAGAAATTAGGCGAGC 59.692 47.826 0.00 0.00 0.00 5.03
1067 1165 2.829458 GTCCGTCTCCCTCCCTCG 60.829 72.222 0.00 0.00 0.00 4.63
1068 1166 4.124943 TCCGTCTCCCTCCCTCGG 62.125 72.222 0.00 0.00 42.12 4.63
1193 1309 0.032714 AGTACGGGTTCCCTACTCCC 60.033 60.000 6.31 0.00 37.98 4.30
1194 1310 1.045350 GTACGGGTTCCCTACTCCCC 61.045 65.000 6.31 0.00 38.09 4.81
1196 1312 2.064581 CGGGTTCCCTACTCCCCAG 61.065 68.421 6.31 0.00 38.09 4.45
1197 1313 1.394963 GGGTTCCCTACTCCCCAGA 59.605 63.158 0.00 0.00 37.09 3.86
1198 1314 0.981801 GGGTTCCCTACTCCCCAGAC 60.982 65.000 0.00 0.00 37.09 3.51
1226 1342 1.067846 CGTCCATCAGTTCTCCGTTGA 60.068 52.381 0.00 0.00 0.00 3.18
1243 1359 4.334203 CCGTTGATTGATTTGACCCGATTA 59.666 41.667 0.00 0.00 0.00 1.75
1256 1372 2.230660 CCCGATTAGATTGCTTTCCCC 58.769 52.381 0.00 0.00 0.00 4.81
1275 1391 2.235016 CCGGGTTGAGATTTGGTTTCA 58.765 47.619 0.00 0.00 0.00 2.69
1333 1451 5.118642 ACGCGGTTTAGTAGGATCTTATC 57.881 43.478 12.47 0.00 0.00 1.75
1339 1457 6.071503 CGGTTTAGTAGGATCTTATCGGGATT 60.072 42.308 0.00 0.00 0.00 3.01
1454 1573 2.509131 TGATGCCATACAGACCCATTCA 59.491 45.455 0.00 0.00 0.00 2.57
1458 1577 3.134623 TGCCATACAGACCCATTCAGTAG 59.865 47.826 0.00 0.00 30.35 2.57
1460 1579 4.740934 GCCATACAGACCCATTCAGTAGTC 60.741 50.000 0.00 0.00 30.35 2.59
1461 1580 4.651503 CCATACAGACCCATTCAGTAGTCT 59.348 45.833 0.00 0.00 40.15 3.24
1475 1594 7.421530 TTCAGTAGTCTGCTAATGTGTTTTC 57.578 36.000 0.00 0.00 42.14 2.29
1485 1604 9.023962 TCTGCTAATGTGTTTTCTGGATATTTT 57.976 29.630 0.00 0.00 0.00 1.82
1491 1610 4.627035 GTGTTTTCTGGATATTTTGCAGCC 59.373 41.667 0.00 0.00 43.10 4.85
1511 1630 4.752101 AGCCGAATTTGATGCTGAGTATAC 59.248 41.667 0.00 0.00 31.70 1.47
1512 1631 4.511454 GCCGAATTTGATGCTGAGTATACA 59.489 41.667 5.50 0.00 0.00 2.29
1525 1644 7.781056 TGCTGAGTATACAGTGAAATGATGTA 58.219 34.615 5.50 0.00 39.73 2.29
1533 1652 4.142838 ACAGTGAAATGATGTACACATGCG 60.143 41.667 0.00 0.00 36.57 4.73
1558 1677 5.104776 TCCTCACTTAATCCAACATCAGAGG 60.105 44.000 0.00 0.00 40.10 3.69
1594 1713 5.755861 GGATTGCTTGAGTAGAACTGATACC 59.244 44.000 0.00 0.00 0.00 2.73
1616 1735 5.162925 ACCTCACTATGTTAGATAGAGGGCT 60.163 44.000 17.80 0.00 41.99 5.19
1688 1966 2.286365 ACCACAACGACATGGGATTT 57.714 45.000 0.00 0.00 40.59 2.17
1690 1968 3.757270 ACCACAACGACATGGGATTTAA 58.243 40.909 0.00 0.00 40.59 1.52
1691 1969 4.145807 ACCACAACGACATGGGATTTAAA 58.854 39.130 0.00 0.00 40.59 1.52
1693 1971 5.105917 ACCACAACGACATGGGATTTAAATC 60.106 40.000 18.22 18.22 40.59 2.17
1694 1972 5.027737 CACAACGACATGGGATTTAAATCG 58.972 41.667 19.41 11.73 36.27 3.34
1696 1974 5.890424 AACGACATGGGATTTAAATCGTT 57.110 34.783 19.41 16.75 44.04 3.85
1699 1977 4.574828 CGACATGGGATTTAAATCGTTCCT 59.425 41.667 19.41 4.50 36.27 3.36
1700 1978 5.277345 CGACATGGGATTTAAATCGTTCCTC 60.277 44.000 19.41 11.18 36.27 3.71
1703 1981 5.174037 TGGGATTTAAATCGTTCCTCACT 57.826 39.130 19.41 0.00 36.27 3.41
1707 1985 6.702282 GGGATTTAAATCGTTCCTCACTAGAG 59.298 42.308 19.41 0.00 37.68 2.43
1720 1998 4.493547 CTCACTAGAGTCAGGCAAGAAAG 58.506 47.826 0.00 0.00 37.11 2.62
1734 2012 4.335594 GGCAAGAAAGTAATCCATTACGCT 59.664 41.667 4.21 1.78 45.48 5.07
1754 2032 7.034685 ACGCTACAAAATCCAAGTTTTAAGT 57.965 32.000 0.00 0.00 30.56 2.24
1757 2035 6.645003 GCTACAAAATCCAAGTTTTAAGTGGG 59.355 38.462 0.00 0.00 32.95 4.61
1762 2040 6.405278 AATCCAAGTTTTAAGTGGGTTCAG 57.595 37.500 0.00 0.00 29.43 3.02
1801 2080 6.714810 TGAACAAAGGTGAATACAGCATAACT 59.285 34.615 0.00 0.00 45.57 2.24
1893 2174 4.796946 GCAAAGTGGAAACATGATGCAGAA 60.797 41.667 0.00 0.00 46.14 3.02
1897 2178 4.828939 AGTGGAAACATGATGCAGAAAAGA 59.171 37.500 0.00 0.00 46.14 2.52
1970 2265 5.521010 TGCGTAATTAGGATCACCTTAAACG 59.479 40.000 9.31 0.00 45.36 3.60
1972 2267 6.697019 GCGTAATTAGGATCACCTTAAACGTA 59.303 38.462 9.31 0.00 45.36 3.57
2041 2342 6.909550 AAGTTGAAGCCAATGTGGTAATAA 57.090 33.333 0.00 0.00 40.46 1.40
2046 2347 5.067674 TGAAGCCAATGTGGTAATAATCTGC 59.932 40.000 0.00 0.00 40.46 4.26
2099 2401 8.127954 GCATTTCTTTTATTTTGGTTTTGCTCA 58.872 29.630 0.00 0.00 0.00 4.26
2115 2417 4.327982 TGCTCATACCAAGCAGATAGTC 57.672 45.455 0.00 0.00 44.51 2.59
2116 2418 3.706086 TGCTCATACCAAGCAGATAGTCA 59.294 43.478 0.00 0.00 44.51 3.41
2134 2436 1.527034 CAGGTGTCCTGTTCCATGTG 58.473 55.000 7.55 0.00 45.82 3.21
2136 2438 1.072331 AGGTGTCCTGTTCCATGTGAC 59.928 52.381 0.00 0.00 29.57 3.67
2137 2439 1.072331 GGTGTCCTGTTCCATGTGACT 59.928 52.381 0.00 0.00 0.00 3.41
2138 2440 2.146342 GTGTCCTGTTCCATGTGACTG 58.854 52.381 0.00 0.00 0.00 3.51
2140 2442 2.172505 TGTCCTGTTCCATGTGACTGTT 59.827 45.455 0.00 0.00 0.00 3.16
2159 2461 3.244009 TGTTTATGTTGTTGGGTGCCATG 60.244 43.478 0.00 0.00 31.53 3.66
2169 2471 3.668141 TGGGTGCCATGTCATTAATCT 57.332 42.857 0.00 0.00 0.00 2.40
2170 2472 3.979911 TGGGTGCCATGTCATTAATCTT 58.020 40.909 0.00 0.00 0.00 2.40
2172 2474 3.491447 GGGTGCCATGTCATTAATCTTGC 60.491 47.826 0.00 0.00 0.00 4.01
2175 2477 5.353938 GTGCCATGTCATTAATCTTGCATT 58.646 37.500 0.00 0.00 0.00 3.56
2176 2478 5.233476 GTGCCATGTCATTAATCTTGCATTG 59.767 40.000 0.00 0.00 0.00 2.82
2177 2479 4.210537 GCCATGTCATTAATCTTGCATTGC 59.789 41.667 0.46 0.46 0.00 3.56
2210 2513 2.289002 CCAGATGGCTCTTAATGAACGC 59.711 50.000 0.00 0.00 0.00 4.84
2294 2597 2.223805 CCAAGCTTCAACCACAAAGTCC 60.224 50.000 0.00 0.00 0.00 3.85
2464 2767 8.565416 AGTTATTGAACTGCTTTACAAGGTAAC 58.435 33.333 0.00 0.00 44.50 2.50
2497 2800 5.014123 AGTTCAACTTGATGGGATTACCTCA 59.986 40.000 0.00 0.00 41.11 3.86
2500 2803 4.342862 ACTTGATGGGATTACCTCATCG 57.657 45.455 0.00 0.00 41.91 3.84
2512 2815 5.880164 TTACCTCATCGTCCATTATTCCA 57.120 39.130 0.00 0.00 0.00 3.53
2527 2830 0.395586 TTCCACCCCATGCATAGTGC 60.396 55.000 14.97 0.00 45.29 4.40
2544 2847 3.650139 AGTGCGATACGTTTCTCTGTTT 58.350 40.909 0.00 0.00 0.00 2.83
2553 2856 7.110216 CGATACGTTTCTCTGTTTTCTGTTTTG 59.890 37.037 0.00 0.00 0.00 2.44
2590 2894 8.651589 AGCTAGTAGTATTAATACCATGCAGA 57.348 34.615 19.74 1.72 33.79 4.26
2599 2903 2.566833 TACCATGCAGAGCAAGTTGT 57.433 45.000 4.48 0.00 43.62 3.32
2602 2906 1.884579 CCATGCAGAGCAAGTTGTTCT 59.115 47.619 15.74 15.74 43.62 3.01
2618 2936 5.105146 AGTTGTTCTGAGCCTTATAGGACAG 60.105 44.000 11.44 11.44 37.67 3.51
2619 2937 3.133003 TGTTCTGAGCCTTATAGGACAGC 59.867 47.826 12.32 0.00 39.42 4.40
2621 2939 2.961741 TCTGAGCCTTATAGGACAGCAG 59.038 50.000 12.32 0.00 39.42 4.24
2629 2947 4.818546 CCTTATAGGACAGCAGGTGATTTG 59.181 45.833 6.61 0.00 37.67 2.32
2637 2955 4.012374 ACAGCAGGTGATTTGTTGGATAG 58.988 43.478 6.61 0.00 31.92 2.08
2641 2959 4.220602 GCAGGTGATTTGTTGGATAGGTTT 59.779 41.667 0.00 0.00 0.00 3.27
2643 2961 5.476599 CAGGTGATTTGTTGGATAGGTTTCA 59.523 40.000 0.00 0.00 0.00 2.69
2656 2974 5.880332 GGATAGGTTTCACTGTTGCTTATGA 59.120 40.000 0.00 0.00 0.00 2.15
2664 2982 6.245115 TCACTGTTGCTTATGATGTCTTTG 57.755 37.500 0.00 0.00 0.00 2.77
2678 2996 8.655935 ATGATGTCTTTGGGTTAGAGAAAAAT 57.344 30.769 0.00 0.00 0.00 1.82
2679 2997 7.885297 TGATGTCTTTGGGTTAGAGAAAAATG 58.115 34.615 0.00 0.00 0.00 2.32
2683 3002 7.041644 TGTCTTTGGGTTAGAGAAAAATGTACG 60.042 37.037 0.00 0.00 0.00 3.67
2690 3009 6.369615 GGTTAGAGAAAAATGTACGGTGCTAA 59.630 38.462 0.00 0.00 0.00 3.09
2693 3012 9.656040 TTAGAGAAAAATGTACGGTGCTAATTA 57.344 29.630 0.00 0.00 0.00 1.40
2705 3024 5.307196 ACGGTGCTAATTATCTCTGGGTAAT 59.693 40.000 3.14 0.00 0.00 1.89
2716 3035 8.882415 TTATCTCTGGGTAATGATAAAACGAC 57.118 34.615 0.00 0.00 31.14 4.34
2721 3040 5.806818 TGGGTAATGATAAAACGACCAGAA 58.193 37.500 0.00 0.00 0.00 3.02
2735 3054 4.160439 ACGACCAGAACAGTGATGTCATAT 59.840 41.667 0.00 0.00 0.00 1.78
2817 3138 3.752665 TGGTGGTCCTAACGCAAAAATA 58.247 40.909 0.00 0.00 34.23 1.40
2823 3144 5.584649 TGGTCCTAACGCAAAAATAGAGATG 59.415 40.000 0.00 0.00 0.00 2.90
2834 3155 9.559958 CGCAAAAATAGAGATGTTTATTCAAGT 57.440 29.630 0.00 0.00 0.00 3.16
2845 3166 8.836413 AGATGTTTATTCAAGTCTGAAAAACGA 58.164 29.630 0.00 8.65 44.64 3.85
2862 3183 5.957842 AAACGATTCTGCACCTTATTTCA 57.042 34.783 0.00 0.00 0.00 2.69
2947 3270 8.938906 AGTAACAAAAAGAACGTTCTCTTACAA 58.061 29.630 29.82 11.34 36.28 2.41
3107 3430 3.182967 GGCAGTCTTTGATAGTCTGACG 58.817 50.000 1.52 0.00 40.97 4.35
3258 3585 0.751643 GGTTGCATATTGACCCGCCT 60.752 55.000 0.00 0.00 0.00 5.52
3396 3723 5.010112 CGTATTGGATGATCTACAGGTGACT 59.990 44.000 0.00 0.00 46.44 3.41
3397 3724 6.206829 CGTATTGGATGATCTACAGGTGACTA 59.793 42.308 0.00 0.00 40.21 2.59
3402 3729 8.127150 TGGATGATCTACAGGTGACTATATTG 57.873 38.462 0.00 0.00 40.21 1.90
3411 3738 6.779860 ACAGGTGACTATATTGTTCTTGGTT 58.220 36.000 0.00 0.00 40.21 3.67
3439 3766 4.640771 TTTGAGAAATCTGGTAGGTGCT 57.359 40.909 0.00 0.00 0.00 4.40
3489 3817 8.324163 AGTTTGATGGTTGAACTAACTGTATC 57.676 34.615 0.00 0.00 39.31 2.24
3528 3856 7.093902 CCAAGTAGTCTTATGTACAGAGGTTCA 60.094 40.741 0.33 0.00 32.07 3.18
3532 3860 6.926313 AGTCTTATGTACAGAGGTTCAAGAC 58.074 40.000 8.90 8.90 34.75 3.01
3543 3871 6.828785 ACAGAGGTTCAAGACTTTAATGTTGT 59.171 34.615 0.00 0.00 0.00 3.32
3600 3928 9.623350 GTATATGTAAAGTACAGTTAGCTAGGC 57.377 37.037 0.00 0.00 42.77 3.93
3606 3934 3.447944 AGTACAGTTAGCTAGGCTTCCAC 59.552 47.826 0.00 0.00 40.44 4.02
3687 4019 3.528597 ATTAACAGGGTCTCGAGCTTC 57.471 47.619 7.81 0.45 0.00 3.86
3701 4033 5.421056 TCTCGAGCTTCTATGGAGGTTAAAA 59.579 40.000 7.81 0.00 0.00 1.52
3751 4083 5.647658 TGCACTTCTAGTGGTTATTGGAATG 59.352 40.000 8.73 0.00 46.01 2.67
3778 4110 6.472016 TCAATGGTTGATTACTTCACTGCTA 58.528 36.000 0.00 0.00 34.08 3.49
3824 4156 1.361271 CACAACAGCACAGCCCTTG 59.639 57.895 0.00 0.00 0.00 3.61
3825 4157 1.829533 ACAACAGCACAGCCCTTGG 60.830 57.895 0.00 0.00 0.00 3.61
3835 4167 2.234296 AGCCCTTGGGCTAAGCACT 61.234 57.895 29.89 5.96 44.06 4.40
3840 4172 3.365472 CCCTTGGGCTAAGCACTAAAAT 58.635 45.455 4.89 0.00 34.96 1.82
3866 4198 8.299262 TCGATATTTAGTTAGCTTGAATCAGC 57.701 34.615 0.00 0.00 40.44 4.26
3930 4270 4.799564 TTTGCTTGGAAACAGTGTTTCT 57.200 36.364 35.54 13.52 44.54 2.52
3981 4321 7.977789 TGAATCAGTGAAATTACTTGCAGTA 57.022 32.000 0.00 0.00 0.00 2.74
4018 4358 8.977267 ATTCTTTTCTGCAGATAAATAGAGCT 57.023 30.769 19.04 2.22 0.00 4.09
4027 4367 5.508872 CAGATAAATAGAGCTGCAAAGCAC 58.491 41.667 1.02 0.00 37.25 4.40
4029 4369 2.099141 AATAGAGCTGCAAAGCACGA 57.901 45.000 1.02 0.00 37.25 4.35
4030 4370 2.322355 ATAGAGCTGCAAAGCACGAT 57.678 45.000 1.02 0.00 37.25 3.73
4031 4371 2.099141 TAGAGCTGCAAAGCACGATT 57.901 45.000 1.02 0.00 37.25 3.34
4032 4372 2.099141 AGAGCTGCAAAGCACGATTA 57.901 45.000 1.02 0.00 37.25 1.75
4033 4373 2.005451 AGAGCTGCAAAGCACGATTAG 58.995 47.619 1.02 0.00 37.25 1.73
4044 4385 6.622896 GCAAAGCACGATTAGTTAGTTCCAAT 60.623 38.462 0.00 0.00 0.00 3.16
4048 4389 8.813643 AGCACGATTAGTTAGTTCCAATATAC 57.186 34.615 0.00 0.00 0.00 1.47
4066 4407 2.301577 ACTGAAACTAGGCAGATCGC 57.698 50.000 14.10 1.55 41.28 4.58
4082 4423 5.582550 CAGATCGCTTACTGATCAGTGTTA 58.417 41.667 33.76 19.29 43.73 2.41
4103 4467 8.225777 GTGTTAAGTATTGGTGTTACTTGTAGC 58.774 37.037 6.40 0.00 39.56 3.58
4104 4468 8.152246 TGTTAAGTATTGGTGTTACTTGTAGCT 58.848 33.333 6.40 0.00 39.56 3.32
4108 4472 7.871853 AGTATTGGTGTTACTTGTAGCTTTTG 58.128 34.615 0.00 0.00 0.00 2.44
4124 4488 3.549070 GCTTTTGCTCTTTATCGCAATGG 59.451 43.478 0.00 0.00 44.60 3.16
4125 4489 4.737054 CTTTTGCTCTTTATCGCAATGGT 58.263 39.130 0.00 0.00 44.60 3.55
4126 4490 3.763097 TTGCTCTTTATCGCAATGGTG 57.237 42.857 0.00 0.00 40.84 4.17
4127 4491 2.710377 TGCTCTTTATCGCAATGGTGT 58.290 42.857 0.00 0.00 32.40 4.16
4128 4492 2.419673 TGCTCTTTATCGCAATGGTGTG 59.580 45.455 0.00 0.00 36.54 3.82
4130 4494 3.485877 GCTCTTTATCGCAATGGTGTGAC 60.486 47.826 0.00 0.00 46.70 3.67
4131 4495 3.006940 TCTTTATCGCAATGGTGTGACC 58.993 45.455 0.00 0.00 46.70 4.02
4158 4522 1.928868 CAAACCAGGAATTCAGCCCT 58.071 50.000 7.93 0.00 0.00 5.19
4169 4533 1.048601 TTCAGCCCTGAAGTCTCGTT 58.951 50.000 6.62 0.00 43.90 3.85
4171 4535 1.416401 TCAGCCCTGAAGTCTCGTTTT 59.584 47.619 0.00 0.00 36.53 2.43
4172 4536 1.801178 CAGCCCTGAAGTCTCGTTTTC 59.199 52.381 0.00 0.00 0.00 2.29
4173 4537 1.694696 AGCCCTGAAGTCTCGTTTTCT 59.305 47.619 0.00 0.00 0.00 2.52
4174 4538 1.801178 GCCCTGAAGTCTCGTTTTCTG 59.199 52.381 0.00 0.00 0.00 3.02
4175 4539 1.801178 CCCTGAAGTCTCGTTTTCTGC 59.199 52.381 0.00 0.00 0.00 4.26
4176 4540 2.548920 CCCTGAAGTCTCGTTTTCTGCT 60.549 50.000 0.00 0.00 0.00 4.24
4177 4541 3.134458 CCTGAAGTCTCGTTTTCTGCTT 58.866 45.455 0.00 0.00 0.00 3.91
4178 4542 4.307432 CCTGAAGTCTCGTTTTCTGCTTA 58.693 43.478 0.00 0.00 0.00 3.09
4179 4543 4.932200 CCTGAAGTCTCGTTTTCTGCTTAT 59.068 41.667 0.00 0.00 0.00 1.73
4205 4585 2.082231 CTCAAAGCCTCTGGTGATGTG 58.918 52.381 0.00 0.00 0.00 3.21
4331 4711 1.750399 GCTGCCACGGGACATGATT 60.750 57.895 0.00 0.00 0.00 2.57
4516 4896 3.047877 GTTCGACCTGCCCCGTTG 61.048 66.667 0.00 0.00 0.00 4.10
4543 4923 4.560108 GCAAGAAGCAAATGGGGCATATAG 60.560 45.833 0.00 0.00 44.79 1.31
4549 4929 3.640967 GCAAATGGGGCATATAGGTTTCA 59.359 43.478 0.00 0.00 0.00 2.69
4566 4946 4.262592 GGTTTCAGGGCATTTCTTCATGTT 60.263 41.667 0.00 0.00 0.00 2.71
4632 5012 3.517901 CTGTGTTACTCTACCATTGGGGA 59.482 47.826 7.78 4.21 41.15 4.81
4659 5039 5.765176 TGACTTGATGCATCTCAAAACTTG 58.235 37.500 26.32 6.49 34.86 3.16
4853 5317 0.977395 CCGTCTCTCAAGAACCCCTT 59.023 55.000 0.00 0.00 31.93 3.95
4857 5321 4.184629 CGTCTCTCAAGAACCCCTTTATG 58.815 47.826 0.00 0.00 31.93 1.90
4885 5349 4.036734 CACCAGTGTAATGATGGCAATACC 59.963 45.833 0.00 0.00 37.64 2.73
4924 5429 9.332502 TGAAAAGGATTCGGATCGATTATAAAA 57.667 29.630 0.00 0.00 35.23 1.52
4953 5459 6.485830 TCAGAAGTACAAATCATCCCTAGG 57.514 41.667 0.06 0.06 0.00 3.02
4956 5462 2.368875 AGTACAAATCATCCCTAGGCCG 59.631 50.000 2.05 0.00 0.00 6.13
4975 5481 1.872237 CGGTGAACGACCATTGTCACT 60.872 52.381 0.00 0.00 46.55 3.41
4979 5485 0.179032 AACGACCATTGTCACTGCCA 60.179 50.000 0.00 0.00 41.85 4.92
4989 5495 1.228245 TCACTGCCAGAACAAGCCC 60.228 57.895 0.00 0.00 0.00 5.19
5053 5719 5.834742 TCCATCCATGATCACTAAATTTGGG 59.165 40.000 6.50 0.00 0.00 4.12
5180 5846 2.683362 GGCTACTGGATTTGCCTAACAC 59.317 50.000 0.00 0.00 41.92 3.32
5182 5848 3.375299 GCTACTGGATTTGCCTAACACAG 59.625 47.826 0.00 0.00 37.63 3.66
5187 5853 3.947196 TGGATTTGCCTAACACAGCATAG 59.053 43.478 0.00 0.00 39.11 2.23
5397 6065 5.710099 TCAAGGTTTCAGAAGTGAACTTGTT 59.290 36.000 9.86 0.00 42.60 2.83
5517 6185 4.354662 ACCCCAACTTGTACTTTTTCCAA 58.645 39.130 0.00 0.00 0.00 3.53
5639 6308 6.775708 ACAGTTGTGAGGGTTTAGCTTATTA 58.224 36.000 0.00 0.00 0.00 0.98
5643 6312 6.614694 TGTGAGGGTTTAGCTTATTACAGA 57.385 37.500 0.00 0.00 0.00 3.41
5644 6313 7.195374 TGTGAGGGTTTAGCTTATTACAGAT 57.805 36.000 0.00 0.00 0.00 2.90
5646 6315 8.107095 TGTGAGGGTTTAGCTTATTACAGATTT 58.893 33.333 0.00 0.00 0.00 2.17
5647 6316 8.398665 GTGAGGGTTTAGCTTATTACAGATTTG 58.601 37.037 0.00 0.00 0.00 2.32
5648 6317 7.556275 TGAGGGTTTAGCTTATTACAGATTTGG 59.444 37.037 0.00 0.00 0.00 3.28
5649 6318 6.321435 AGGGTTTAGCTTATTACAGATTTGGC 59.679 38.462 0.00 0.00 0.00 4.52
5650 6319 6.321435 GGGTTTAGCTTATTACAGATTTGGCT 59.679 38.462 0.00 0.00 0.00 4.75
5651 6320 7.418408 GGTTTAGCTTATTACAGATTTGGCTC 58.582 38.462 0.00 0.00 0.00 4.70
5653 6322 8.624776 GTTTAGCTTATTACAGATTTGGCTCAT 58.375 33.333 0.00 0.00 0.00 2.90
5654 6323 6.630444 AGCTTATTACAGATTTGGCTCATG 57.370 37.500 0.00 0.00 0.00 3.07
5655 6324 5.009410 AGCTTATTACAGATTTGGCTCATGC 59.991 40.000 0.00 0.00 38.76 4.06
5657 6326 6.681120 GCTTATTACAGATTTGGCTCATGCAA 60.681 38.462 0.00 0.00 41.91 4.08
5658 6327 4.707030 TTACAGATTTGGCTCATGCAAG 57.293 40.909 0.00 0.00 41.91 4.01
5659 6328 2.522185 ACAGATTTGGCTCATGCAAGT 58.478 42.857 0.00 0.00 41.91 3.16
5660 6329 2.895404 ACAGATTTGGCTCATGCAAGTT 59.105 40.909 0.00 0.00 41.91 2.66
5662 6331 4.708421 ACAGATTTGGCTCATGCAAGTTAT 59.292 37.500 0.00 0.00 41.91 1.89
5760 6452 2.202570 CCGTTCGGTCGGCACTAG 60.203 66.667 2.82 0.00 43.96 2.57
5761 6453 2.879462 CGTTCGGTCGGCACTAGC 60.879 66.667 0.00 0.00 41.10 3.42
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 0.385390 CAACACCAGCCAAACAGTCC 59.615 55.000 0.00 0.00 0.00 3.85
59 61 5.767665 AGCCAATTTACGTGGATATATGCAA 59.232 36.000 8.67 0.00 38.54 4.08
112 114 3.623960 CCGTTGAGTTTGTAACAACTGGA 59.376 43.478 0.00 0.00 40.80 3.86
153 155 4.614078 GCCATTCAAAATTTGTGCATGTGG 60.614 41.667 5.56 7.30 0.00 4.17
166 168 2.924757 TTGTGCATGGCCATTCAAAA 57.075 40.000 20.11 17.98 0.00 2.44
227 237 3.680196 GCCTCCTCTTTGGTAAGCTACAG 60.680 52.174 0.00 0.00 37.07 2.74
251 261 2.295349 AGTCGTGTTGTGGTAGTTCGAT 59.705 45.455 0.00 0.00 0.00 3.59
285 296 2.783135 GGAAGAGTGCCAATGAGTTCA 58.217 47.619 0.00 0.00 0.00 3.18
307 318 1.598701 GATGCCCCTTGACAGCAACC 61.599 60.000 0.00 0.00 40.46 3.77
338 349 2.298729 GGCTGTTAGATCCTAGCTCCAG 59.701 54.545 0.00 0.00 36.45 3.86
350 369 1.666553 CGTGTTGCGGGCTGTTAGA 60.667 57.895 0.00 0.00 36.85 2.10
397 416 0.179200 CGGTTCCAGTTTATGCGCAC 60.179 55.000 14.90 0.00 0.00 5.34
482 532 2.344592 TCCAAGCCACCTCCTTTCTTA 58.655 47.619 0.00 0.00 0.00 2.10
514 564 1.066587 GATAGTCTCGCCGCTGCTT 59.933 57.895 0.00 0.00 34.43 3.91
566 646 2.074576 GAAACTAGGCCCGTCTTGTTC 58.925 52.381 0.00 0.00 33.07 3.18
570 650 1.610886 GCAAGAAACTAGGCCCGTCTT 60.611 52.381 0.00 0.00 0.00 3.01
582 662 7.589574 TTTTTAAACTGAACAGGCAAGAAAC 57.410 32.000 6.76 0.00 0.00 2.78
788 872 1.269723 TCACGGTCATGAGACACACTC 59.730 52.381 0.00 0.00 46.80 3.51
796 880 1.947456 TCGATACCTCACGGTCATGAG 59.053 52.381 0.00 0.00 44.21 2.90
797 881 1.947456 CTCGATACCTCACGGTCATGA 59.053 52.381 0.00 0.00 44.21 3.07
798 882 1.947456 TCTCGATACCTCACGGTCATG 59.053 52.381 0.00 0.00 44.21 3.07
799 883 2.343484 TCTCGATACCTCACGGTCAT 57.657 50.000 0.00 0.00 44.21 3.06
800 884 2.014857 CTTCTCGATACCTCACGGTCA 58.985 52.381 0.00 0.00 44.21 4.02
801 885 1.334243 CCTTCTCGATACCTCACGGTC 59.666 57.143 0.00 0.00 44.21 4.79
803 887 1.604755 CTCCTTCTCGATACCTCACGG 59.395 57.143 0.00 0.00 0.00 4.94
815 899 1.599576 GGTGGACTGGCTCCTTCTC 59.400 63.158 0.00 0.00 40.26 2.87
856 940 3.407967 CATGGGCCCGTGGTAGGT 61.408 66.667 33.41 1.57 0.00 3.08
904 994 4.447290 GGCTAAAGAGGAGGATGTTTCTC 58.553 47.826 0.00 0.00 0.00 2.87
948 1038 0.984230 ACCGGAATGATGTGAGTGGT 59.016 50.000 9.46 0.00 0.00 4.16
983 1079 2.726691 CTGCGGCTGGAAACGTACG 61.727 63.158 15.01 15.01 0.00 3.67
989 1085 4.386951 TAGCGCTGCGGCTGGAAA 62.387 61.111 22.90 3.62 44.50 3.13
996 1092 3.857854 CTTGTGCTAGCGCTGCGG 61.858 66.667 27.36 11.31 36.97 5.69
1030 1127 4.399395 TGCTGCCTCGCTTCCTGG 62.399 66.667 0.00 0.00 0.00 4.45
1137 1251 2.202743 CGATCCGGCAAGCTCGAA 60.203 61.111 0.00 0.00 33.07 3.71
1226 1342 5.829924 AGCAATCTAATCGGGTCAAATCAAT 59.170 36.000 0.00 0.00 0.00 2.57
1243 1359 0.611896 CAACCCGGGGAAAGCAATCT 60.612 55.000 27.92 0.00 0.00 2.40
1256 1372 4.941263 TCTATGAAACCAAATCTCAACCCG 59.059 41.667 0.00 0.00 0.00 5.28
1275 1391 3.487372 TCCCGATCACGATTCAGTCTAT 58.513 45.455 0.00 0.00 42.66 1.98
1333 1451 3.002656 CGTTCCATCAAGATTCAATCCCG 59.997 47.826 0.00 0.00 0.00 5.14
1339 1457 4.535526 TCACTCGTTCCATCAAGATTCA 57.464 40.909 0.00 0.00 0.00 2.57
1454 1573 5.934625 CCAGAAAACACATTAGCAGACTACT 59.065 40.000 0.00 0.00 0.00 2.57
1458 1577 5.886960 ATCCAGAAAACACATTAGCAGAC 57.113 39.130 0.00 0.00 0.00 3.51
1460 1579 9.079833 CAAAATATCCAGAAAACACATTAGCAG 57.920 33.333 0.00 0.00 0.00 4.24
1461 1580 7.545265 GCAAAATATCCAGAAAACACATTAGCA 59.455 33.333 0.00 0.00 0.00 3.49
1475 1594 3.996150 ATTCGGCTGCAAAATATCCAG 57.004 42.857 0.50 0.00 0.00 3.86
1485 1604 0.171679 CAGCATCAAATTCGGCTGCA 59.828 50.000 0.50 0.00 46.00 4.41
1491 1610 6.476706 TCACTGTATACTCAGCATCAAATTCG 59.523 38.462 4.17 0.00 38.84 3.34
1511 1630 4.142838 ACGCATGTGTACATCATTTCACTG 60.143 41.667 10.90 0.00 33.61 3.66
1512 1631 4.002982 ACGCATGTGTACATCATTTCACT 58.997 39.130 10.90 0.00 33.61 3.41
1525 1644 2.831685 TTAAGTGAGGACGCATGTGT 57.168 45.000 12.68 12.68 0.00 3.72
1533 1652 5.734720 TCTGATGTTGGATTAAGTGAGGAC 58.265 41.667 0.00 0.00 0.00 3.85
1558 1677 4.309099 TCAAGCAATCCACAAAAATCAGC 58.691 39.130 0.00 0.00 0.00 4.26
1567 1686 4.040339 TCAGTTCTACTCAAGCAATCCACA 59.960 41.667 0.00 0.00 0.00 4.17
1594 1713 6.007076 TGAGCCCTCTATCTAACATAGTGAG 58.993 44.000 0.00 0.00 0.00 3.51
1616 1735 9.617523 ATTATGTTCAGATCACATGTGTTATGA 57.382 29.630 23.67 23.67 35.57 2.15
1688 1966 6.438259 CTGACTCTAGTGAGGAACGATTTA 57.562 41.667 0.00 0.00 44.29 1.40
1690 1968 4.974368 CTGACTCTAGTGAGGAACGATT 57.026 45.455 0.00 0.00 44.29 3.34
1699 1977 3.898123 ACTTTCTTGCCTGACTCTAGTGA 59.102 43.478 0.00 0.00 0.00 3.41
1700 1978 4.264460 ACTTTCTTGCCTGACTCTAGTG 57.736 45.455 0.00 0.00 0.00 2.74
1703 1981 5.483937 TGGATTACTTTCTTGCCTGACTCTA 59.516 40.000 0.00 0.00 0.00 2.43
1707 1985 5.904362 AATGGATTACTTTCTTGCCTGAC 57.096 39.130 0.00 0.00 0.00 3.51
1720 1998 7.254227 TGGATTTTGTAGCGTAATGGATTAC 57.746 36.000 0.15 0.15 39.32 1.89
1734 2012 7.663043 ACCCACTTAAAACTTGGATTTTGTA 57.337 32.000 0.00 0.00 33.80 2.41
1754 2032 2.173782 TCCAACTTAAGTGCTGAACCCA 59.826 45.455 9.34 0.00 0.00 4.51
1757 2035 5.008613 TGTTCATCCAACTTAAGTGCTGAAC 59.991 40.000 26.40 26.40 40.82 3.18
1762 2040 5.221244 ACCTTTGTTCATCCAACTTAAGTGC 60.221 40.000 9.34 0.00 35.79 4.40
1823 2102 2.818130 TGGCATTCCAACAAGCTTTC 57.182 45.000 0.00 0.00 39.99 2.62
1854 2135 4.275689 CACTTTGCATTCAGTGTGTCCTTA 59.724 41.667 11.36 0.00 36.44 2.69
1855 2136 3.067180 CACTTTGCATTCAGTGTGTCCTT 59.933 43.478 11.36 0.00 36.44 3.36
1934 2215 9.216117 GATCCTAATTACGCAATACCTTTACAT 57.784 33.333 0.00 0.00 0.00 2.29
1935 2216 8.205512 TGATCCTAATTACGCAATACCTTTACA 58.794 33.333 0.00 0.00 0.00 2.41
1936 2217 8.493547 GTGATCCTAATTACGCAATACCTTTAC 58.506 37.037 0.00 0.00 0.00 2.01
1939 2220 5.995897 GGTGATCCTAATTACGCAATACCTT 59.004 40.000 0.00 0.00 0.00 3.50
1948 2243 7.917505 AGTACGTTTAAGGTGATCCTAATTACG 59.082 37.037 0.00 0.00 44.35 3.18
2003 2304 9.912634 TGGCTTCAACTTTGATATTTTCTAAAG 57.087 29.630 0.00 0.00 37.00 1.85
2026 2327 3.891366 AGGCAGATTATTACCACATTGGC 59.109 43.478 0.00 0.00 42.67 4.52
2041 2342 1.180029 GCATGTTGAACCAGGCAGAT 58.820 50.000 0.00 0.00 41.53 2.90
2046 2347 1.321474 ACACTGCATGTTGAACCAGG 58.679 50.000 5.34 0.00 38.98 4.45
2099 2401 4.033709 ACACCTGACTATCTGCTTGGTAT 58.966 43.478 0.00 0.00 0.00 2.73
2102 2404 2.419297 GGACACCTGACTATCTGCTTGG 60.419 54.545 0.00 0.00 0.00 3.61
2105 2407 2.541233 AGGACACCTGACTATCTGCT 57.459 50.000 0.00 0.00 29.57 4.24
2116 2418 1.072331 GTCACATGGAACAGGACACCT 59.928 52.381 0.00 0.00 46.40 4.00
2134 2436 3.552068 GGCACCCAACAACATAAACAGTC 60.552 47.826 0.00 0.00 0.00 3.51
2136 2438 2.363680 TGGCACCCAACAACATAAACAG 59.636 45.455 0.00 0.00 0.00 3.16
2137 2439 2.388735 TGGCACCCAACAACATAAACA 58.611 42.857 0.00 0.00 0.00 2.83
2138 2440 3.244044 ACATGGCACCCAACAACATAAAC 60.244 43.478 0.00 0.00 36.95 2.01
2140 2442 2.560542 GACATGGCACCCAACAACATAA 59.439 45.455 0.00 0.00 36.95 1.90
2159 2461 6.278363 AGATTGGCAATGCAAGATTAATGAC 58.722 36.000 19.07 0.00 0.00 3.06
2176 2478 4.107136 GCCATCTGGACCAAAGATTGGC 62.107 54.545 9.00 13.74 44.74 4.52
2177 2479 1.753073 GCCATCTGGACCAAAGATTGG 59.247 52.381 7.56 7.56 45.64 3.16
2210 2513 5.049167 TGCTGTTGTTTAAATTTGCTGAGG 58.951 37.500 0.00 0.00 0.00 3.86
2294 2597 2.237143 TCTAGACCTTGGAGCATTGTGG 59.763 50.000 0.00 0.00 0.00 4.17
2327 2630 1.600636 TTTTGCTGGAGCTGACGGG 60.601 57.895 0.00 0.00 42.66 5.28
2378 2681 5.068855 TGAATTGATGTGTTGAAGCCTTTCA 59.931 36.000 0.00 0.00 41.44 2.69
2420 2723 7.828717 TCAATAACTAATTTGATCTGTGCTCCA 59.171 33.333 0.00 0.00 0.00 3.86
2464 2767 4.508861 CCATCAAGTTGAACTTTTGGCAAG 59.491 41.667 18.47 4.07 36.03 4.01
2497 2800 2.131854 TGGGGTGGAATAATGGACGAT 58.868 47.619 0.00 0.00 0.00 3.73
2500 2803 1.963515 GCATGGGGTGGAATAATGGAC 59.036 52.381 0.00 0.00 0.00 4.02
2512 2815 1.055849 TATCGCACTATGCATGGGGT 58.944 50.000 14.36 4.00 45.36 4.95
2527 2830 5.824243 ACAGAAAACAGAGAAACGTATCG 57.176 39.130 0.00 0.00 0.00 2.92
2534 2837 5.659440 AGGCAAAACAGAAAACAGAGAAA 57.341 34.783 0.00 0.00 0.00 2.52
2537 2840 3.553105 GCAAGGCAAAACAGAAAACAGAG 59.447 43.478 0.00 0.00 0.00 3.35
2553 2856 7.497925 AATACTACTAGCTATTTTGCAAGGC 57.502 36.000 0.00 3.57 34.99 4.35
2570 2873 7.657761 ACTTGCTCTGCATGGTATTAATACTAC 59.342 37.037 21.86 9.56 38.76 2.73
2581 2884 1.610522 GAACAACTTGCTCTGCATGGT 59.389 47.619 9.60 0.92 38.76 3.55
2582 2885 1.884579 AGAACAACTTGCTCTGCATGG 59.115 47.619 9.60 2.10 38.76 3.66
2589 2893 1.889545 AGGCTCAGAACAACTTGCTC 58.110 50.000 0.00 0.00 0.00 4.26
2590 2894 2.355010 AAGGCTCAGAACAACTTGCT 57.645 45.000 0.00 0.00 0.00 3.91
2599 2903 3.374764 TGCTGTCCTATAAGGCTCAGAA 58.625 45.455 16.46 7.82 38.41 3.02
2602 2906 2.042464 CCTGCTGTCCTATAAGGCTCA 58.958 52.381 0.00 0.00 34.61 4.26
2603 2907 2.043227 ACCTGCTGTCCTATAAGGCTC 58.957 52.381 0.00 0.00 34.61 4.70
2604 2908 1.765314 CACCTGCTGTCCTATAAGGCT 59.235 52.381 0.00 0.00 34.61 4.58
2605 2909 1.762957 TCACCTGCTGTCCTATAAGGC 59.237 52.381 0.00 0.00 34.61 4.35
2606 2910 4.696479 AATCACCTGCTGTCCTATAAGG 57.304 45.455 0.00 0.00 36.46 2.69
2618 2936 3.356290 ACCTATCCAACAAATCACCTGC 58.644 45.455 0.00 0.00 0.00 4.85
2619 2937 5.476599 TGAAACCTATCCAACAAATCACCTG 59.523 40.000 0.00 0.00 0.00 4.00
2621 2939 5.476945 AGTGAAACCTATCCAACAAATCACC 59.523 40.000 0.00 0.00 37.80 4.02
2629 2947 3.821033 AGCAACAGTGAAACCTATCCAAC 59.179 43.478 0.00 0.00 37.80 3.77
2637 2955 5.182001 AGACATCATAAGCAACAGTGAAACC 59.818 40.000 0.00 0.00 37.80 3.27
2641 2959 5.181811 CCAAAGACATCATAAGCAACAGTGA 59.818 40.000 0.00 0.00 0.00 3.41
2643 2961 4.460382 CCCAAAGACATCATAAGCAACAGT 59.540 41.667 0.00 0.00 0.00 3.55
2656 2974 7.839680 ACATTTTTCTCTAACCCAAAGACAT 57.160 32.000 0.00 0.00 0.00 3.06
2664 2982 4.142752 GCACCGTACATTTTTCTCTAACCC 60.143 45.833 0.00 0.00 0.00 4.11
2678 2996 4.038763 CCCAGAGATAATTAGCACCGTACA 59.961 45.833 3.17 0.00 0.00 2.90
2679 2997 4.038883 ACCCAGAGATAATTAGCACCGTAC 59.961 45.833 3.17 0.00 0.00 3.67
2683 3002 6.769512 TCATTACCCAGAGATAATTAGCACC 58.230 40.000 3.17 0.00 0.00 5.01
2690 3009 9.490379 GTCGTTTTATCATTACCCAGAGATAAT 57.510 33.333 0.00 0.00 34.16 1.28
2693 3012 6.126883 TGGTCGTTTTATCATTACCCAGAGAT 60.127 38.462 0.00 0.00 0.00 2.75
2705 3024 4.951254 TCACTGTTCTGGTCGTTTTATCA 58.049 39.130 0.00 0.00 0.00 2.15
2716 3035 8.843885 AATATCATATGACATCACTGTTCTGG 57.156 34.615 7.78 0.00 35.14 3.86
2735 3054 8.840833 TGTCACTAAAAGCAACAGTAATATCA 57.159 30.769 0.00 0.00 0.00 2.15
2770 3091 9.053840 AGTATCTGATAATTGAGAGTGCAATTG 57.946 33.333 11.39 0.00 45.31 2.32
2784 3105 6.015350 CGTTAGGACCACCAGTATCTGATAAT 60.015 42.308 0.00 0.00 38.94 1.28
2823 3144 9.665264 AGAATCGTTTTTCAGACTTGAATAAAC 57.335 29.630 12.63 12.63 42.60 2.01
2834 3155 3.476552 AGGTGCAGAATCGTTTTTCAGA 58.523 40.909 0.00 0.00 0.00 3.27
2843 3164 4.944962 TGTGAAATAAGGTGCAGAATCG 57.055 40.909 0.00 0.00 0.00 3.34
2897 3220 9.490379 ACTGTACTACAAAGTCTTTCATTAAGG 57.510 33.333 0.00 0.00 37.15 2.69
2913 3236 8.477984 AACGTTCTTTTTGTTACTGTACTACA 57.522 30.769 0.00 0.00 0.00 2.74
2914 3237 8.811378 AGAACGTTCTTTTTGTTACTGTACTAC 58.189 33.333 24.93 0.00 32.55 2.73
3107 3430 7.331687 CCATCAAATTGTACTTTGGGATTGTTC 59.668 37.037 7.51 0.00 36.87 3.18
3202 3525 6.451064 ACGAAGTCTTTCACAAAGGAAAAT 57.549 33.333 0.00 0.00 29.74 1.82
3223 3547 6.851222 ATGCAACCTAATATGAGAAAGACG 57.149 37.500 0.00 0.00 0.00 4.18
3231 3555 5.937540 CGGGTCAATATGCAACCTAATATGA 59.062 40.000 4.57 0.00 33.42 2.15
3232 3556 5.391950 GCGGGTCAATATGCAACCTAATATG 60.392 44.000 4.57 0.00 33.42 1.78
3233 3557 4.700213 GCGGGTCAATATGCAACCTAATAT 59.300 41.667 4.57 0.00 33.42 1.28
3258 3585 5.851720 TGCTTGGACTGCATAATTTCAAAA 58.148 33.333 0.00 0.00 35.31 2.44
3424 3751 8.686334 CAAAATAATGTAGCACCTACCAGATTT 58.314 33.333 0.40 1.59 36.24 2.17
3462 3789 7.730364 ACAGTTAGTTCAACCATCAAACTAG 57.270 36.000 0.00 0.00 36.96 2.57
3463 3790 9.431887 GATACAGTTAGTTCAACCATCAAACTA 57.568 33.333 0.00 0.00 37.93 2.24
3465 3792 8.230486 CAGATACAGTTAGTTCAACCATCAAAC 58.770 37.037 0.00 0.00 37.93 2.93
3489 3817 9.877178 ATAAGACTACTTGGTTTCTGAATACAG 57.123 33.333 0.00 0.00 39.90 2.74
3528 3856 9.899226 GCTAAAAGATCACAACATTAAAGTCTT 57.101 29.630 0.00 0.00 0.00 3.01
3532 3860 9.214953 GATCGCTAAAAGATCACAACATTAAAG 57.785 33.333 0.00 0.00 42.86 1.85
3543 3871 6.817765 AAAACAAGGATCGCTAAAAGATCA 57.182 33.333 8.24 0.00 44.58 2.92
3600 3928 5.782893 TTTTGGAACATAACCAGTGGAAG 57.217 39.130 18.40 4.78 39.30 3.46
3632 3960 1.401552 GTGGCTTTGCGCATTATGAGA 59.598 47.619 12.75 0.00 41.67 3.27
3634 3962 0.455410 GGTGGCTTTGCGCATTATGA 59.545 50.000 12.75 0.00 41.67 2.15
3636 3964 1.185315 AAGGTGGCTTTGCGCATTAT 58.815 45.000 12.75 0.00 41.67 1.28
3643 3971 1.412343 TCCAAGAAAAGGTGGCTTTGC 59.588 47.619 0.00 0.00 34.68 3.68
3650 3978 6.701400 CCTGTTAATTGTTCCAAGAAAAGGTG 59.299 38.462 0.00 0.00 0.00 4.00
3656 3986 5.701224 AGACCCTGTTAATTGTTCCAAGAA 58.299 37.500 0.00 0.00 0.00 2.52
3701 4033 7.984617 ACACAAAGGCAACAACTAACATTAAAT 59.015 29.630 0.00 0.00 41.41 1.40
3711 4043 0.894141 TGCACACAAAGGCAACAACT 59.106 45.000 0.00 0.00 37.03 3.16
3720 4052 3.206150 ACCACTAGAAGTGCACACAAAG 58.794 45.455 21.04 13.07 44.63 2.77
3751 4083 6.363357 GCAGTGAAGTAATCAACCATTGAAAC 59.637 38.462 0.00 0.00 43.95 2.78
3801 4133 1.021202 GGCTGTGCTGTTGTGTACAA 58.979 50.000 0.00 0.00 36.02 2.41
3824 4156 6.803154 ATATCGAATTTTAGTGCTTAGCCC 57.197 37.500 0.29 0.00 0.00 5.19
3825 4157 9.813080 CTAAATATCGAATTTTAGTGCTTAGCC 57.187 33.333 16.53 0.00 32.98 3.93
3840 4172 8.765219 GCTGATTCAAGCTAACTAAATATCGAA 58.235 33.333 0.00 0.00 40.20 3.71
3855 4187 5.871524 TCATATATTCCTCGCTGATTCAAGC 59.128 40.000 0.00 0.00 39.94 4.01
3862 4194 6.405278 TCAACTTCATATATTCCTCGCTGA 57.595 37.500 0.00 0.00 0.00 4.26
3866 4198 7.116948 GGACACATCAACTTCATATATTCCTCG 59.883 40.741 0.00 0.00 0.00 4.63
3930 4270 2.948979 GTTGTGTTCCATCAGACACCAA 59.051 45.455 4.40 0.00 44.18 3.67
3993 4333 8.838365 CAGCTCTATTTATCTGCAGAAAAGAAT 58.162 33.333 22.50 18.47 0.00 2.40
4018 4358 4.153475 GGAACTAACTAATCGTGCTTTGCA 59.847 41.667 0.00 0.00 35.60 4.08
4023 4363 8.639761 AGTATATTGGAACTAACTAATCGTGCT 58.360 33.333 0.00 0.00 0.00 4.40
4024 4364 8.700644 CAGTATATTGGAACTAACTAATCGTGC 58.299 37.037 0.00 0.00 0.00 5.34
4025 4365 9.961265 TCAGTATATTGGAACTAACTAATCGTG 57.039 33.333 0.00 0.00 0.00 4.35
4033 4373 9.043079 GCCTAGTTTCAGTATATTGGAACTAAC 57.957 37.037 22.58 16.41 44.50 2.34
4044 4385 5.122512 GCGATCTGCCTAGTTTCAGTATA 57.877 43.478 0.00 0.00 37.76 1.47
4066 4407 8.873830 CACCAATACTTAACACTGATCAGTAAG 58.126 37.037 27.44 26.18 40.20 2.34
4082 4423 8.349983 CAAAAGCTACAAGTAACACCAATACTT 58.650 33.333 0.00 0.00 42.73 2.24
4108 4472 2.677836 TCACACCATTGCGATAAAGAGC 59.322 45.455 0.00 0.00 0.00 4.09
4114 4478 0.248012 ACGGTCACACCATTGCGATA 59.752 50.000 0.00 0.00 38.47 2.92
4117 4481 2.250939 ACACGGTCACACCATTGCG 61.251 57.895 0.00 0.00 38.47 4.85
4124 4488 0.027586 GTTTGCTCACACGGTCACAC 59.972 55.000 0.00 0.00 0.00 3.82
4125 4489 1.092921 GGTTTGCTCACACGGTCACA 61.093 55.000 0.00 0.00 0.00 3.58
4126 4490 1.092921 TGGTTTGCTCACACGGTCAC 61.093 55.000 0.00 0.00 0.00 3.67
4127 4491 0.813610 CTGGTTTGCTCACACGGTCA 60.814 55.000 0.00 0.00 0.00 4.02
4128 4492 1.507141 CCTGGTTTGCTCACACGGTC 61.507 60.000 0.00 0.00 0.00 4.79
4129 4493 1.525995 CCTGGTTTGCTCACACGGT 60.526 57.895 0.00 0.00 0.00 4.83
4130 4494 0.817634 TTCCTGGTTTGCTCACACGG 60.818 55.000 0.00 0.00 0.00 4.94
4131 4495 1.238439 ATTCCTGGTTTGCTCACACG 58.762 50.000 0.00 0.00 0.00 4.49
4158 4522 6.100004 CCTATAAGCAGAAAACGAGACTTCA 58.900 40.000 0.00 0.00 0.00 3.02
4166 4530 4.433615 TGAGAGCCTATAAGCAGAAAACG 58.566 43.478 0.00 0.00 34.23 3.60
4167 4531 6.676700 GCTTTGAGAGCCTATAAGCAGAAAAC 60.677 42.308 0.00 0.00 46.01 2.43
4169 4533 4.878397 GCTTTGAGAGCCTATAAGCAGAAA 59.122 41.667 0.00 0.00 46.01 2.52
4171 4535 4.065321 GCTTTGAGAGCCTATAAGCAGA 57.935 45.455 0.00 0.00 46.01 4.26
4196 4576 1.228215 CAGCCACCACACATCACCA 60.228 57.895 0.00 0.00 0.00 4.17
4205 4585 1.582968 CATGCTTGACAGCCACCAC 59.417 57.895 0.00 0.00 46.74 4.16
4331 4711 0.174389 GCAGCTCCTTCTCGATGTCA 59.826 55.000 0.00 0.00 0.00 3.58
4409 4789 2.676121 TTTGGTCGCTGGCCATGG 60.676 61.111 5.51 7.63 35.71 3.66
4430 4810 2.664402 TCTGCTTCTTCTTGGCCTTT 57.336 45.000 3.32 0.00 0.00 3.11
4516 4896 0.457337 CCCATTTGCTTCTTGCGCTC 60.457 55.000 9.73 0.00 46.63 5.03
4543 4923 3.259123 ACATGAAGAAATGCCCTGAAACC 59.741 43.478 0.00 0.00 0.00 3.27
4549 4929 3.094572 CTCCAACATGAAGAAATGCCCT 58.905 45.455 0.00 0.00 0.00 5.19
4632 5012 7.439381 AGTTTTGAGATGCATCAAGTCATTTT 58.561 30.769 27.81 4.17 40.16 1.82
4659 5039 2.206576 AGCATCCCAACCTCAGTTTC 57.793 50.000 0.00 0.00 32.45 2.78
4853 5317 5.685520 TCATTACACTGGTGCCTACATAA 57.314 39.130 0.17 0.00 0.00 1.90
4857 5321 3.206150 CCATCATTACACTGGTGCCTAC 58.794 50.000 0.17 0.00 0.00 3.18
4885 5349 8.768955 CCGAATCCTTTTCATAAGAGAAGTATG 58.231 37.037 0.00 0.00 34.94 2.39
4886 5350 8.705594 TCCGAATCCTTTTCATAAGAGAAGTAT 58.294 33.333 0.00 0.00 34.94 2.12
4924 5429 6.825721 GGGATGATTTGTACTTCTGATGAACT 59.174 38.462 0.00 0.00 0.00 3.01
4943 5449 1.002403 TTCACCGGCCTAGGGATGA 59.998 57.895 11.72 0.00 35.02 2.92
4947 5453 3.072468 TCGTTCACCGGCCTAGGG 61.072 66.667 11.72 0.00 37.11 3.53
4975 5481 0.251165 GTTAGGGGCTTGTTCTGGCA 60.251 55.000 0.00 0.00 0.00 4.92
4979 5485 1.207329 CTAGCGTTAGGGGCTTGTTCT 59.793 52.381 0.00 0.00 41.80 3.01
4989 5495 3.881937 AAACAGTACCCTAGCGTTAGG 57.118 47.619 17.81 17.81 45.23 2.69
5053 5719 5.391310 CCAGTGATCAAAGTTACTGCATGAC 60.391 44.000 0.00 0.00 39.27 3.06
5180 5846 4.867047 ACGAATTCTTCACACTCTATGCTG 59.133 41.667 3.52 0.00 0.00 4.41
5182 5848 6.037098 AGTACGAATTCTTCACACTCTATGC 58.963 40.000 3.52 0.00 0.00 3.14
5187 5853 4.174762 GGGAGTACGAATTCTTCACACTC 58.825 47.826 3.52 4.58 38.46 3.51
5397 6065 5.163447 CCTTATCCAACCACTCGATGTTCTA 60.163 44.000 0.00 0.00 0.00 2.10
5639 6308 2.522185 ACTTGCATGAGCCAAATCTGT 58.478 42.857 6.60 0.00 41.13 3.41
5698 6390 9.722056 CACAGCCTGATTATAGATTAAAAACAC 57.278 33.333 0.00 0.00 0.00 3.32
5744 6436 2.879462 GCTAGTGCCGACCGAACG 60.879 66.667 0.00 0.00 0.00 3.95


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

AutoCloner maintained by Alex Coulton.