Multiple sequence alignment - TraesCS5B01G507100

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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 TraesCS5B01G507100 chr5B 100.000 5024 0 0 1 5024 672615888 672620911 0.000000e+00 9278.0
1 TraesCS5B01G507100 chr5D 89.941 2873 219 34 2160 5019 532553827 532556642 0.000000e+00 3640.0
2 TraesCS5B01G507100 chr5D 91.121 2140 100 32 4 2073 532551728 532553847 0.000000e+00 2817.0
3 TraesCS5B01G507100 chr5D 91.484 411 31 3 4 412 27805513 27805105 3.400000e-156 562.0
4 TraesCS5B01G507100 chr5D 74.014 558 104 33 377 919 403640378 403640909 6.640000e-44 189.0
5 TraesCS5B01G507100 chr4A 88.067 1961 163 41 2160 4086 639208141 639206218 0.000000e+00 2259.0
6 TraesCS5B01G507100 chr4A 85.800 1169 72 33 972 2074 639209261 639208121 0.000000e+00 1153.0
7 TraesCS5B01G507100 chr4A 83.069 821 118 11 108 920 31435561 31436368 0.000000e+00 726.0
8 TraesCS5B01G507100 chr4A 93.766 401 20 3 4619 5019 639205311 639204916 9.310000e-167 597.0
9 TraesCS5B01G507100 chr4A 82.045 440 55 19 1115 1545 545117384 545116960 2.220000e-93 353.0
10 TraesCS5B01G507100 chr4A 83.898 118 9 6 2997 3107 545115395 545115281 2.470000e-18 104.0
11 TraesCS5B01G507100 chr7D 89.290 775 63 12 4 775 631290767 631291524 0.000000e+00 953.0
12 TraesCS5B01G507100 chr3B 86.242 785 70 15 4 786 755169622 755170370 0.000000e+00 817.0
13 TraesCS5B01G507100 chr3B 81.667 900 136 19 4 885 734852164 734851276 0.000000e+00 721.0
14 TraesCS5B01G507100 chr3B 82.000 100 7 6 823 915 806078804 806078899 1.940000e-09 75.0
15 TraesCS5B01G507100 chr4D 84.236 831 109 12 98 920 436954378 436953562 0.000000e+00 789.0
16 TraesCS5B01G507100 chr4D 83.780 820 109 14 108 920 436960192 436959390 0.000000e+00 756.0
17 TraesCS5B01G507100 chr4D 81.348 445 54 23 1112 1545 51554021 51554447 8.060000e-88 335.0
18 TraesCS5B01G507100 chr4D 86.726 113 10 4 2997 3107 51555722 51555831 2.460000e-23 121.0
19 TraesCS5B01G507100 chr7B 89.366 489 47 5 433 919 13891408 13890923 1.200000e-170 610.0
20 TraesCS5B01G507100 chr4B 77.344 512 78 28 3555 4045 75739860 75740354 8.290000e-68 268.0
21 TraesCS5B01G507100 chr4B 83.955 268 33 10 1304 1561 75738090 75738357 1.080000e-61 248.0
22 TraesCS5B01G507100 chr4B 97.531 81 2 0 108 188 538968030 538967950 6.780000e-29 139.0
23 TraesCS5B01G507100 chr4B 85.841 113 11 4 2997 3107 75739570 75739679 1.140000e-21 115.0
24 TraesCS5B01G507100 chr4B 87.879 99 11 1 822 920 661628906 661629003 1.140000e-21 115.0
25 TraesCS5B01G507100 chr4B 92.453 53 2 2 2110 2162 562550977 562551027 1.940000e-09 75.0
26 TraesCS5B01G507100 chr3D 76.817 289 53 11 378 659 313709833 313710114 3.130000e-32 150.0
27 TraesCS5B01G507100 chr3D 83.333 96 12 4 822 916 48731394 48731486 8.960000e-13 86.1
28 TraesCS5B01G507100 chr3D 88.333 60 6 1 808 867 25149094 25149036 2.510000e-08 71.3
29 TraesCS5B01G507100 chr5A 78.661 239 40 9 408 642 103903031 103902800 1.130000e-31 148.0
30 TraesCS5B01G507100 chr2B 88.000 100 9 2 821 919 184882257 184882354 1.140000e-21 115.0
31 TraesCS5B01G507100 chrUn 88.312 77 6 3 501 574 385874907 385874983 6.930000e-14 89.8
32 TraesCS5B01G507100 chrUn 97.778 45 0 1 2118 2162 356995472 356995515 5.390000e-10 76.8
33 TraesCS5B01G507100 chrUn 90.909 55 4 1 2090 2143 35489620 35489674 6.980000e-09 73.1
34 TraesCS5B01G507100 chr1D 83.333 96 13 2 824 918 418635204 418635297 8.960000e-13 86.1
35 TraesCS5B01G507100 chr1A 86.250 80 8 2 2083 2161 515877084 515877161 3.220000e-12 84.2
36 TraesCS5B01G507100 chr1A 81.443 97 11 7 2071 2162 25888452 25888546 6.980000e-09 73.1
37 TraesCS5B01G507100 chr6D 85.000 80 10 2 2084 2162 105561913 105561991 4.170000e-11 80.5
38 TraesCS5B01G507100 chr2A 85.542 83 5 6 2084 2164 149348689 149348766 4.170000e-11 80.5
39 TraesCS5B01G507100 chr2A 84.211 76 5 5 2087 2159 470232196 470232125 3.250000e-07 67.6
40 TraesCS5B01G507100 chr7A 83.951 81 9 4 2084 2162 425314175 425314253 1.940000e-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 TraesCS5B01G507100 chr5B 672615888 672620911 5023 False 9278.000000 9278 100.0000 1 5024 1 chr5B.!!$F1 5023
1 TraesCS5B01G507100 chr5D 532551728 532556642 4914 False 3228.500000 3640 90.5310 4 5019 2 chr5D.!!$F2 5015
2 TraesCS5B01G507100 chr4A 639204916 639209261 4345 True 1336.333333 2259 89.2110 972 5019 3 chr4A.!!$R2 4047
3 TraesCS5B01G507100 chr4A 31435561 31436368 807 False 726.000000 726 83.0690 108 920 1 chr4A.!!$F1 812
4 TraesCS5B01G507100 chr4A 545115281 545117384 2103 True 228.500000 353 82.9715 1115 3107 2 chr4A.!!$R1 1992
5 TraesCS5B01G507100 chr7D 631290767 631291524 757 False 953.000000 953 89.2900 4 775 1 chr7D.!!$F1 771
6 TraesCS5B01G507100 chr3B 755169622 755170370 748 False 817.000000 817 86.2420 4 786 1 chr3B.!!$F1 782
7 TraesCS5B01G507100 chr3B 734851276 734852164 888 True 721.000000 721 81.6670 4 885 1 chr3B.!!$R1 881
8 TraesCS5B01G507100 chr4D 436953562 436954378 816 True 789.000000 789 84.2360 98 920 1 chr4D.!!$R1 822
9 TraesCS5B01G507100 chr4D 436959390 436960192 802 True 756.000000 756 83.7800 108 920 1 chr4D.!!$R2 812
10 TraesCS5B01G507100 chr4D 51554021 51555831 1810 False 228.000000 335 84.0370 1112 3107 2 chr4D.!!$F1 1995
11 TraesCS5B01G507100 chr4B 75738090 75740354 2264 False 210.333333 268 82.3800 1304 4045 3 chr4B.!!$F3 2741

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
947 966 0.099613 AGACATAGCTCTCGTGCGTG 59.900 55.0 0.00 0.0 38.13 5.34 F
1563 1614 0.183492 GCACTTAGGGGATCCATGCA 59.817 55.0 15.23 0.0 33.18 3.96 F
2092 2559 0.033601 TCTTGCCTTGGGTGTGTGTT 60.034 50.0 0.00 0.0 0.00 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2073 2540 0.033601 AACACACACCCAAGGCAAGA 60.034 50.000 0.00 0.00 0.00 3.02 R
2619 3146 2.158957 AGAAACTCCGAAGACAACAGCA 60.159 45.455 0.00 0.00 0.00 4.41 R
4082 4720 0.961857 TGCCTATGCAGTGCCAAGTG 60.962 55.000 13.72 5.48 44.23 3.16 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
204 205 1.028905 CCTTTCTTTGGCCGACAACA 58.971 50.000 0.00 0.00 39.19 3.33
205 206 1.613437 CCTTTCTTTGGCCGACAACAT 59.387 47.619 0.00 0.00 39.19 2.71
210 212 1.339610 CTTTGGCCGACAACATTTCCA 59.660 47.619 0.00 0.00 39.19 3.53
359 371 1.000233 CCCTTTGGCCTGCACCATA 60.000 57.895 3.32 0.00 40.13 2.74
561 577 1.306141 ATCGAGCCTGGGTGAAGGA 60.306 57.895 1.59 0.00 40.02 3.36
770 787 4.415881 AGTGTCTGTTCCACATTGTACA 57.584 40.909 0.00 0.00 35.24 2.90
777 794 7.446931 TGTCTGTTCCACATTGTACATTGTATT 59.553 33.333 19.92 0.00 0.00 1.89
869 888 4.679373 TGTTAATTCAAAGCCAGGCAAA 57.321 36.364 15.80 2.45 0.00 3.68
892 911 0.248843 CGAGCCTTTTCTCTGCCTCT 59.751 55.000 0.00 0.00 0.00 3.69
893 912 1.738700 CGAGCCTTTTCTCTGCCTCTC 60.739 57.143 0.00 0.00 0.00 3.20
894 913 0.248843 AGCCTTTTCTCTGCCTCTCG 59.751 55.000 0.00 0.00 0.00 4.04
895 914 0.742635 GCCTTTTCTCTGCCTCTCGG 60.743 60.000 0.00 0.00 0.00 4.63
944 963 4.039032 GTCTAAAGACATAGCTCTCGTGC 58.961 47.826 5.24 0.00 44.18 5.34
945 964 1.914634 AAAGACATAGCTCTCGTGCG 58.085 50.000 0.00 0.00 38.13 5.34
946 965 0.811915 AAGACATAGCTCTCGTGCGT 59.188 50.000 0.00 0.00 38.13 5.24
947 966 0.099613 AGACATAGCTCTCGTGCGTG 59.900 55.000 0.00 0.00 38.13 5.34
1295 1337 3.393149 GAGGCGCCCTTCCTCTTCC 62.393 68.421 26.15 0.00 45.13 3.46
1388 1439 2.182030 CTCAAGCCGACCTCGTCC 59.818 66.667 0.00 0.00 37.74 4.79
1547 1598 2.436115 GGTAACCAGGAGCCGCAC 60.436 66.667 0.00 0.00 0.00 5.34
1561 1612 3.312404 CGCACTTAGGGGATCCATG 57.688 57.895 15.23 2.74 34.83 3.66
1562 1613 0.886490 CGCACTTAGGGGATCCATGC 60.886 60.000 15.23 11.45 34.83 4.06
1563 1614 0.183492 GCACTTAGGGGATCCATGCA 59.817 55.000 15.23 0.00 33.18 3.96
1564 1615 1.202976 GCACTTAGGGGATCCATGCAT 60.203 52.381 15.23 0.00 33.18 3.96
1565 1616 2.787994 CACTTAGGGGATCCATGCATC 58.212 52.381 15.23 0.00 34.83 3.91
1566 1617 2.374504 CACTTAGGGGATCCATGCATCT 59.625 50.000 15.23 3.43 34.83 2.90
1567 1618 2.374504 ACTTAGGGGATCCATGCATCTG 59.625 50.000 15.23 0.00 34.83 2.90
1568 1619 0.694771 TAGGGGATCCATGCATCTGC 59.305 55.000 15.23 0.00 37.22 4.26
1581 1632 1.133853 GCATCTGCAATTCTCTCCCCT 60.134 52.381 0.00 0.00 41.59 4.79
1583 1634 3.737850 CATCTGCAATTCTCTCCCCTAC 58.262 50.000 0.00 0.00 0.00 3.18
1585 1636 1.141858 CTGCAATTCTCTCCCCTACCC 59.858 57.143 0.00 0.00 0.00 3.69
1611 1662 3.806949 ACCTGCCATTCTTAAGAACCA 57.193 42.857 19.94 15.17 36.80 3.67
1633 1685 5.327091 CATGTTTCACTCGACAATTGATCC 58.673 41.667 13.59 0.00 0.00 3.36
1641 1693 3.259064 TCGACAATTGATCCGAGGAAAC 58.741 45.455 13.59 0.00 0.00 2.78
1643 1695 3.062639 CGACAATTGATCCGAGGAAACTG 59.937 47.826 13.59 0.00 44.43 3.16
1644 1696 2.749621 ACAATTGATCCGAGGAAACTGC 59.250 45.455 13.59 0.00 44.43 4.40
1661 1713 0.972983 TGCCAGACAGAGAGTAGGGC 60.973 60.000 0.00 0.00 45.19 5.19
1662 1714 2.010582 GCCAGACAGAGAGTAGGGCG 62.011 65.000 0.00 0.00 39.02 6.13
1683 1761 0.734889 GATGTGGGTTCTGCATTCCG 59.265 55.000 0.00 0.00 0.00 4.30
1689 1767 1.068541 GGGTTCTGCATTCCGTTGTTC 60.069 52.381 0.00 0.00 0.00 3.18
1697 1775 1.012486 ATTCCGTTGTTCGTCGAGGC 61.012 55.000 0.00 0.00 37.94 4.70
1705 1783 1.270094 TGTTCGTCGAGGCAATTCACT 60.270 47.619 0.00 0.00 0.00 3.41
1709 1787 1.670087 CGTCGAGGCAATTCACTCTGT 60.670 52.381 0.00 0.00 0.00 3.41
1716 1803 4.067896 AGGCAATTCACTCTGTTACTGTG 58.932 43.478 0.00 0.00 0.00 3.66
1725 1812 5.237127 TCACTCTGTTACTGTGATTGCAAAG 59.763 40.000 1.71 0.00 36.03 2.77
1733 1823 2.540931 CTGTGATTGCAAAGTTTGGTGC 59.459 45.455 17.11 4.42 41.29 5.01
1735 1825 1.139163 GATTGCAAAGTTTGGTGCCG 58.861 50.000 17.11 0.00 40.14 5.69
1746 1849 3.440173 AGTTTGGTGCCGATTGATAACTG 59.560 43.478 0.00 0.00 0.00 3.16
1812 2219 3.562973 CCTGAATTCGACAATCCATCAGG 59.437 47.826 4.68 4.68 44.43 3.86
1819 2226 3.454447 TCGACAATCCATCAGGTTGGTAT 59.546 43.478 0.00 0.00 38.01 2.73
1823 2230 6.486657 CGACAATCCATCAGGTTGGTATATTT 59.513 38.462 0.00 0.00 38.01 1.40
1824 2231 7.013274 CGACAATCCATCAGGTTGGTATATTTT 59.987 37.037 0.00 0.00 38.01 1.82
1834 2241 7.335924 TCAGGTTGGTATATTTTGTAAGCAGAC 59.664 37.037 0.00 0.00 0.00 3.51
1890 2352 6.733145 ACTAGTTCTTCGTATTCGATAACCC 58.267 40.000 13.30 0.00 45.65 4.11
1912 2377 2.425539 GGTGGAAAATGCAAATGTGGG 58.574 47.619 0.00 0.00 0.00 4.61
1947 2412 0.934496 TCTGTTTCGCTTGGTCAACG 59.066 50.000 0.00 0.00 0.00 4.10
1952 2417 0.249531 TTCGCTTGGTCAACGTGCTA 60.250 50.000 0.00 0.00 0.00 3.49
1953 2418 0.666274 TCGCTTGGTCAACGTGCTAG 60.666 55.000 0.00 0.00 0.00 3.42
1988 2453 1.077501 CCGATTGCCATGGTCAGGT 60.078 57.895 14.67 4.93 0.00 4.00
1989 2454 1.378882 CCGATTGCCATGGTCAGGTG 61.379 60.000 14.67 5.37 0.00 4.00
2026 2491 9.208022 TCTTATTAGCACATTAATTCCTGATCG 57.792 33.333 0.00 0.00 0.00 3.69
2032 2497 6.543465 AGCACATTAATTCCTGATCGAAATCA 59.457 34.615 0.00 0.00 39.63 2.57
2033 2498 7.230108 AGCACATTAATTCCTGATCGAAATCAT 59.770 33.333 0.00 0.00 41.05 2.45
2034 2499 7.325338 GCACATTAATTCCTGATCGAAATCATG 59.675 37.037 0.00 0.00 41.05 3.07
2052 2519 4.665451 TCATGTTTCATGTCCTGGATGTT 58.335 39.130 0.00 0.00 0.00 2.71
2064 2531 5.163205 TGTCCTGGATGTTTTCTCTTTCTGA 60.163 40.000 0.00 0.00 0.00 3.27
2065 2532 5.765182 GTCCTGGATGTTTTCTCTTTCTGAA 59.235 40.000 0.00 0.00 0.00 3.02
2066 2533 6.263168 GTCCTGGATGTTTTCTCTTTCTGAAA 59.737 38.462 0.00 2.44 0.00 2.69
2067 2534 7.006509 TCCTGGATGTTTTCTCTTTCTGAAAT 58.993 34.615 2.88 0.00 34.04 2.17
2068 2535 8.163408 TCCTGGATGTTTTCTCTTTCTGAAATA 58.837 33.333 2.88 0.00 34.04 1.40
2070 2537 8.690203 TGGATGTTTTCTCTTTCTGAAATACA 57.310 30.769 2.88 2.94 34.04 2.29
2071 2538 9.300681 TGGATGTTTTCTCTTTCTGAAATACAT 57.699 29.630 2.88 6.96 37.56 2.29
2079 2546 8.668510 TCTCTTTCTGAAATACATATCTTGCC 57.331 34.615 2.88 0.00 0.00 4.52
2080 2547 8.489489 TCTCTTTCTGAAATACATATCTTGCCT 58.511 33.333 2.88 0.00 0.00 4.75
2081 2548 9.118300 CTCTTTCTGAAATACATATCTTGCCTT 57.882 33.333 2.88 0.00 0.00 4.35
2082 2549 8.896744 TCTTTCTGAAATACATATCTTGCCTTG 58.103 33.333 2.88 0.00 0.00 3.61
2083 2550 7.572523 TTCTGAAATACATATCTTGCCTTGG 57.427 36.000 0.00 0.00 0.00 3.61
2084 2551 6.064060 TCTGAAATACATATCTTGCCTTGGG 58.936 40.000 0.00 0.00 0.00 4.12
2085 2552 5.765510 TGAAATACATATCTTGCCTTGGGT 58.234 37.500 0.00 0.00 0.00 4.51
2086 2553 5.593909 TGAAATACATATCTTGCCTTGGGTG 59.406 40.000 0.00 0.00 0.00 4.61
2087 2554 4.796110 ATACATATCTTGCCTTGGGTGT 57.204 40.909 0.00 0.00 0.00 4.16
2088 2555 2.726821 ACATATCTTGCCTTGGGTGTG 58.273 47.619 0.00 0.00 0.00 3.82
2089 2556 2.041620 ACATATCTTGCCTTGGGTGTGT 59.958 45.455 0.00 0.00 0.00 3.72
2090 2557 2.198827 TATCTTGCCTTGGGTGTGTG 57.801 50.000 0.00 0.00 0.00 3.82
2091 2558 0.185901 ATCTTGCCTTGGGTGTGTGT 59.814 50.000 0.00 0.00 0.00 3.72
2092 2559 0.033601 TCTTGCCTTGGGTGTGTGTT 60.034 50.000 0.00 0.00 0.00 3.32
2093 2560 0.823460 CTTGCCTTGGGTGTGTGTTT 59.177 50.000 0.00 0.00 0.00 2.83
2094 2561 0.534412 TTGCCTTGGGTGTGTGTTTG 59.466 50.000 0.00 0.00 0.00 2.93
2095 2562 0.613292 TGCCTTGGGTGTGTGTTTGT 60.613 50.000 0.00 0.00 0.00 2.83
2096 2563 1.341089 TGCCTTGGGTGTGTGTTTGTA 60.341 47.619 0.00 0.00 0.00 2.41
2097 2564 1.960689 GCCTTGGGTGTGTGTTTGTAT 59.039 47.619 0.00 0.00 0.00 2.29
2098 2565 2.030274 GCCTTGGGTGTGTGTTTGTATC 60.030 50.000 0.00 0.00 0.00 2.24
2099 2566 2.225491 CCTTGGGTGTGTGTTTGTATCG 59.775 50.000 0.00 0.00 0.00 2.92
2100 2567 1.885560 TGGGTGTGTGTTTGTATCGG 58.114 50.000 0.00 0.00 0.00 4.18
2101 2568 1.141254 TGGGTGTGTGTTTGTATCGGT 59.859 47.619 0.00 0.00 0.00 4.69
2102 2569 1.533731 GGGTGTGTGTTTGTATCGGTG 59.466 52.381 0.00 0.00 0.00 4.94
2103 2570 1.069500 GGTGTGTGTTTGTATCGGTGC 60.069 52.381 0.00 0.00 0.00 5.01
2104 2571 1.871039 GTGTGTGTTTGTATCGGTGCT 59.129 47.619 0.00 0.00 0.00 4.40
2105 2572 2.096417 GTGTGTGTTTGTATCGGTGCTC 60.096 50.000 0.00 0.00 0.00 4.26
2106 2573 2.224185 TGTGTGTTTGTATCGGTGCTCT 60.224 45.455 0.00 0.00 0.00 4.09
2107 2574 2.412089 GTGTGTTTGTATCGGTGCTCTC 59.588 50.000 0.00 0.00 0.00 3.20
2108 2575 2.036604 TGTGTTTGTATCGGTGCTCTCA 59.963 45.455 0.00 0.00 0.00 3.27
2109 2576 2.668457 GTGTTTGTATCGGTGCTCTCAG 59.332 50.000 0.00 0.00 0.00 3.35
2110 2577 2.560981 TGTTTGTATCGGTGCTCTCAGA 59.439 45.455 0.00 0.00 0.00 3.27
2116 2583 0.390340 TCGGTGCTCTCAGATGTTGC 60.390 55.000 0.00 0.00 0.00 4.17
2117 2584 1.690283 CGGTGCTCTCAGATGTTGCG 61.690 60.000 0.00 0.00 0.00 4.85
2118 2585 0.390340 GGTGCTCTCAGATGTTGCGA 60.390 55.000 0.00 0.00 0.00 5.10
2125 2592 2.079158 CTCAGATGTTGCGATGTTGGT 58.921 47.619 0.00 0.00 0.00 3.67
2130 2597 0.743688 TGTTGCGATGTTGGTTGCTT 59.256 45.000 0.00 0.00 0.00 3.91
2132 2599 2.359214 TGTTGCGATGTTGGTTGCTTTA 59.641 40.909 0.00 0.00 0.00 1.85
2133 2600 3.005261 TGTTGCGATGTTGGTTGCTTTAT 59.995 39.130 0.00 0.00 0.00 1.40
2134 2601 4.216472 TGTTGCGATGTTGGTTGCTTTATA 59.784 37.500 0.00 0.00 0.00 0.98
2135 2602 5.157781 GTTGCGATGTTGGTTGCTTTATAA 58.842 37.500 0.00 0.00 0.00 0.98
2137 2604 6.685527 TGCGATGTTGGTTGCTTTATAATA 57.314 33.333 0.00 0.00 0.00 0.98
2138 2605 7.270757 TGCGATGTTGGTTGCTTTATAATAT 57.729 32.000 0.00 0.00 0.00 1.28
2139 2606 8.384607 TGCGATGTTGGTTGCTTTATAATATA 57.615 30.769 0.00 0.00 0.00 0.86
2140 2607 8.841300 TGCGATGTTGGTTGCTTTATAATATAA 58.159 29.630 0.00 0.00 0.00 0.98
2141 2608 9.672086 GCGATGTTGGTTGCTTTATAATATAAA 57.328 29.630 5.46 5.46 0.00 1.40
2148 2615 7.507616 TGGTTGCTTTATAATATAAAGTGGGGG 59.492 37.037 25.08 8.22 37.00 5.40
2184 2651 8.561932 TTCATCTTTCTGAAATACGATACGAG 57.438 34.615 2.88 0.00 32.35 4.18
2209 2713 9.073475 AGTACTCAAATACTCATGGATAGTCTC 57.927 37.037 0.00 0.00 28.86 3.36
2314 2818 6.017934 GTGTTTCTTGTCAATGTAGAGAGCAA 60.018 38.462 0.00 0.00 0.00 3.91
2341 2854 5.404466 TGTTTGAGGCAATAAATTGAGGG 57.596 39.130 6.87 0.00 40.14 4.30
2360 2873 4.642429 AGGGTTTTCACTAGTGACATGAC 58.358 43.478 25.13 18.46 39.66 3.06
2388 2901 6.395426 TTGACATAATTGCTTCCATCATCC 57.605 37.500 0.00 0.00 0.00 3.51
2515 3036 5.534654 AGCTGCTGTTTATTGTTGGTTCTTA 59.465 36.000 0.00 0.00 0.00 2.10
2516 3037 6.209391 AGCTGCTGTTTATTGTTGGTTCTTAT 59.791 34.615 0.00 0.00 0.00 1.73
2551 3072 2.023673 TGGTGGCAGTTGAAACTCAAG 58.976 47.619 0.00 0.00 37.00 3.02
2552 3073 2.024414 GGTGGCAGTTGAAACTCAAGT 58.976 47.619 0.00 0.00 40.42 3.16
2631 3166 2.033801 ACAGTTGCATGCTGTTGTCTTC 59.966 45.455 20.33 0.00 43.87 2.87
2683 3235 5.626543 CAGCTATGCATAAATAAAACCAGCG 59.373 40.000 8.00 0.00 0.00 5.18
2694 3246 3.859411 AAAACCAGCGACAAACTTGAA 57.141 38.095 0.00 0.00 0.00 2.69
2719 3271 4.814147 TGTAGTCTCAGAAGTTGCATCTG 58.186 43.478 9.15 9.15 44.53 2.90
2811 3363 5.860941 TTCTATCTTCTTCCACCTAGCAG 57.139 43.478 0.00 0.00 0.00 4.24
2836 3388 8.157476 AGATCTGACATAATGGTTTGGGTATAC 58.843 37.037 0.00 0.00 0.00 1.47
2846 3399 4.279671 TGGTTTGGGTATACTTTGTGCAAG 59.720 41.667 2.25 0.00 38.64 4.01
2914 3469 3.828451 TCCCCTTCATTGCAAAAAGAGAG 59.172 43.478 20.63 11.73 0.00 3.20
2932 3487 8.445275 AAAGAGAGAAGAAAGAAAGAAGAACC 57.555 34.615 0.00 0.00 0.00 3.62
2933 3488 7.373617 AGAGAGAAGAAAGAAAGAAGAACCT 57.626 36.000 0.00 0.00 0.00 3.50
2935 3490 9.100197 AGAGAGAAGAAAGAAAGAAGAACCTAT 57.900 33.333 0.00 0.00 0.00 2.57
3119 3679 2.565834 TCCAAAGACTGGTGTACTAGGC 59.434 50.000 0.00 0.00 46.51 3.93
3121 3681 1.183549 AAGACTGGTGTACTAGGCGG 58.816 55.000 0.00 0.00 37.57 6.13
3128 3688 0.458669 GTGTACTAGGCGGCAGCTTA 59.541 55.000 13.08 4.41 44.37 3.09
3190 3751 8.659569 GTGTATCAGAAACACACATAAACATG 57.340 34.615 7.94 0.00 45.26 3.21
3243 3804 4.927422 TCAAAAACGGTTTGAGATCAACC 58.073 39.130 6.92 3.81 35.28 3.77
3261 3822 2.830104 ACCGTGGAAACTGTAGTTCAC 58.170 47.619 0.00 2.72 37.25 3.18
3264 3825 3.493503 CCGTGGAAACTGTAGTTCACTTC 59.506 47.826 12.08 1.94 37.25 3.01
3269 3830 7.208080 GTGGAAACTGTAGTTCACTTCTCTTA 58.792 38.462 8.51 0.00 37.25 2.10
3270 3831 7.382759 GTGGAAACTGTAGTTCACTTCTCTTAG 59.617 40.741 8.51 0.00 37.25 2.18
3362 3935 5.415077 TCCAAACCGTTTTTGAACACTCTTA 59.585 36.000 8.03 0.00 0.00 2.10
3495 4083 9.125026 ACTTAAAATGATACAGGTGATTCCATC 57.875 33.333 0.00 0.00 39.02 3.51
3551 4172 3.859386 GTCAATGATGGTTTCCGCATTTC 59.141 43.478 0.00 0.00 31.85 2.17
3553 4174 3.508744 ATGATGGTTTCCGCATTTCAC 57.491 42.857 0.00 0.00 0.00 3.18
3845 4472 6.362551 CGGTAATGACATATCCTTTCTACACG 59.637 42.308 0.00 0.00 0.00 4.49
3851 4478 5.892568 ACATATCCTTTCTACACGACTGTC 58.107 41.667 0.00 0.00 0.00 3.51
3869 4496 4.580995 ACTGTCTTAGTGTATCGGAGGATG 59.419 45.833 0.00 0.00 38.49 3.51
3939 4575 0.252197 GTGTAGGCCCTGTCCGAATT 59.748 55.000 0.00 0.00 0.00 2.17
4020 4656 1.808411 GCAGTCGGACATTTTCTCCA 58.192 50.000 11.27 0.00 0.00 3.86
4032 4668 6.040166 GGACATTTTCTCCATGATGTAGCAAT 59.960 38.462 0.00 0.00 33.21 3.56
4045 4682 8.833493 CATGATGTAGCAATCAAGAAACTATGA 58.167 33.333 1.50 0.00 39.90 2.15
4064 4701 5.830799 ATGATCTGGTATGAATGCCTACA 57.169 39.130 0.00 0.00 33.30 2.74
4067 4704 5.072193 TGATCTGGTATGAATGCCTACATGT 59.928 40.000 2.69 2.69 36.36 3.21
4075 4713 6.932356 ATGAATGCCTACATGTACTTTCTG 57.068 37.500 16.44 3.32 36.36 3.02
4082 4720 6.538742 TGCCTACATGTACTTTCTGCTTTATC 59.461 38.462 0.08 0.00 0.00 1.75
4097 4904 3.378112 GCTTTATCACTTGGCACTGCATA 59.622 43.478 2.82 0.00 0.00 3.14
4099 4906 2.048444 ATCACTTGGCACTGCATAGG 57.952 50.000 2.82 0.00 0.00 2.57
4159 4966 3.316029 CAGTGAACAATCTGCACTTTCCA 59.684 43.478 0.00 0.00 40.63 3.53
4195 5002 2.052157 GATTTGATCCGATCGTCGACC 58.948 52.381 15.09 0.00 43.74 4.79
4206 5013 0.604511 TCGTCGACCTGTGCTGTCTA 60.605 55.000 10.58 0.00 0.00 2.59
4211 5018 1.433534 GACCTGTGCTGTCTACAAGC 58.566 55.000 0.00 0.00 0.00 4.01
4217 5024 1.194772 GTGCTGTCTACAAGCGAAACC 59.805 52.381 0.00 0.00 0.00 3.27
4222 5029 2.364324 TGTCTACAAGCGAAACCAGAGT 59.636 45.455 0.00 0.00 0.00 3.24
4223 5030 2.731976 GTCTACAAGCGAAACCAGAGTG 59.268 50.000 0.00 0.00 0.00 3.51
4229 5036 0.880278 GCGAAACCAGAGTGCAGTCA 60.880 55.000 23.21 0.00 0.00 3.41
4230 5037 0.861837 CGAAACCAGAGTGCAGTCAC 59.138 55.000 23.21 0.00 43.44 3.67
4244 5053 2.150397 AGTCACGACTGCCTTGTAAC 57.850 50.000 0.00 0.00 40.75 2.50
4247 5056 1.411246 TCACGACTGCCTTGTAACTGT 59.589 47.619 0.00 0.00 0.00 3.55
4248 5057 1.526887 CACGACTGCCTTGTAACTGTG 59.473 52.381 0.00 0.00 0.00 3.66
4275 5084 0.107459 GCACCATTCTGGAGTCTCCC 60.107 60.000 16.60 0.00 40.96 4.30
4280 5089 3.456277 ACCATTCTGGAGTCTCCCATTAC 59.544 47.826 16.60 0.00 40.96 1.89
4287 5096 2.223433 GGAGTCTCCCATTACGTGTACG 60.223 54.545 7.78 2.43 46.33 3.67
4294 5103 5.075858 TCCCATTACGTGTACGATTCTTT 57.924 39.130 11.79 0.00 43.02 2.52
4317 5126 8.871629 TTTTAAGCTGGAAGTATTTATGGTCA 57.128 30.769 0.00 0.00 35.30 4.02
4319 5128 5.700402 AGCTGGAAGTATTTATGGTCAGT 57.300 39.130 0.00 0.00 35.30 3.41
4320 5129 6.808321 AGCTGGAAGTATTTATGGTCAGTA 57.192 37.500 0.00 0.00 35.30 2.74
4322 5131 5.992217 GCTGGAAGTATTTATGGTCAGTAGG 59.008 44.000 0.00 0.00 35.30 3.18
4325 5134 4.602340 AGTATTTATGGTCAGTAGGCCG 57.398 45.455 0.00 0.00 0.00 6.13
4327 5136 4.652421 AGTATTTATGGTCAGTAGGCCGAA 59.348 41.667 0.00 0.00 0.00 4.30
4333 5142 0.032952 GTCAGTAGGCCGAACACACA 59.967 55.000 13.01 0.00 0.00 3.72
4336 5145 1.464608 CAGTAGGCCGAACACACAATG 59.535 52.381 13.01 0.00 0.00 2.82
4346 5156 2.869233 ACACACAATGCTTCCACAAC 57.131 45.000 0.00 0.00 0.00 3.32
4377 5187 4.989279 ACAAGCATCTTGTGTTTCTGTT 57.011 36.364 10.98 0.00 0.00 3.16
4393 5203 9.760660 GTGTTTCTGTTAGATAAAGCTGTAATG 57.239 33.333 0.00 0.00 0.00 1.90
4400 5210 5.957771 AGATAAAGCTGTAATGTCCCTCA 57.042 39.130 0.00 0.00 0.00 3.86
4416 5227 2.165167 CCTCATTCTGCAACATGTGGT 58.835 47.619 0.00 0.00 31.88 4.16
4453 5264 7.177407 TCAGTTTATGTTGAATAAATCGTCGC 58.823 34.615 0.00 0.00 0.00 5.19
4461 5272 4.004314 TGAATAAATCGTCGCTTTTCCCA 58.996 39.130 0.00 0.00 0.00 4.37
4462 5273 4.094294 TGAATAAATCGTCGCTTTTCCCAG 59.906 41.667 0.00 0.00 0.00 4.45
4463 5274 1.892209 AAATCGTCGCTTTTCCCAGT 58.108 45.000 0.00 0.00 0.00 4.00
4464 5275 1.892209 AATCGTCGCTTTTCCCAGTT 58.108 45.000 0.00 0.00 0.00 3.16
4465 5276 1.892209 ATCGTCGCTTTTCCCAGTTT 58.108 45.000 0.00 0.00 0.00 2.66
4466 5277 1.670791 TCGTCGCTTTTCCCAGTTTT 58.329 45.000 0.00 0.00 0.00 2.43
4467 5278 2.836262 TCGTCGCTTTTCCCAGTTTTA 58.164 42.857 0.00 0.00 0.00 1.52
4468 5279 3.204526 TCGTCGCTTTTCCCAGTTTTAA 58.795 40.909 0.00 0.00 0.00 1.52
4469 5280 3.002553 TCGTCGCTTTTCCCAGTTTTAAC 59.997 43.478 0.00 0.00 0.00 2.01
4470 5281 3.635331 GTCGCTTTTCCCAGTTTTAACC 58.365 45.455 0.00 0.00 0.00 2.85
4477 5288 4.668138 TTCCCAGTTTTAACCCAGCTAT 57.332 40.909 0.00 0.00 0.00 2.97
4481 5292 4.331968 CCAGTTTTAACCCAGCTATGACA 58.668 43.478 0.00 0.00 0.00 3.58
4488 5299 2.162681 ACCCAGCTATGACAAAACTGC 58.837 47.619 0.00 0.00 0.00 4.40
4495 5306 3.304928 GCTATGACAAAACTGCAGCACTT 60.305 43.478 15.27 1.62 0.00 3.16
4516 5327 6.974622 CACTTGTGAAGAAACTTGTAAATGCT 59.025 34.615 0.00 0.00 0.00 3.79
4575 5386 5.372343 AACTATGGCTCATGTTATCCACA 57.628 39.130 0.00 0.00 40.71 4.17
4594 5405 3.949754 CACATGAGTATTTCAGGGCATGT 59.050 43.478 0.00 0.00 44.90 3.21
4596 5407 5.766670 CACATGAGTATTTCAGGGCATGTAT 59.233 40.000 0.00 0.00 42.93 2.29
4614 5426 6.449698 CATGTATCAACAGGCTTTGAAGTTT 58.550 36.000 13.46 3.65 38.95 2.66
4615 5427 7.592938 CATGTATCAACAGGCTTTGAAGTTTA 58.407 34.615 13.46 2.93 38.95 2.01
4629 5441 7.565073 GCTTTGAAGTTTAACAAGTTGCATACG 60.565 37.037 1.81 0.00 0.00 3.06
4650 5673 1.337071 AGTATCTCACGGCCACATACG 59.663 52.381 2.24 0.00 0.00 3.06
4653 5676 2.433491 TCACGGCCACATACGCAC 60.433 61.111 2.24 0.00 0.00 5.34
4659 5682 1.374560 GGCCACATACGCACATACAA 58.625 50.000 0.00 0.00 0.00 2.41
4662 5685 2.418628 GCCACATACGCACATACAAGTT 59.581 45.455 0.00 0.00 0.00 2.66
4664 5687 4.647964 CCACATACGCACATACAAGTTTC 58.352 43.478 0.00 0.00 0.00 2.78
4980 6003 0.764369 TCAGCTCCCAGTTCCTGTGT 60.764 55.000 0.00 0.00 0.00 3.72
4989 6012 3.817084 CCCAGTTCCTGTGTATATGCATG 59.183 47.826 10.16 0.00 0.00 4.06
4997 6020 5.363580 TCCTGTGTATATGCATGTTCAGAGA 59.636 40.000 22.26 14.28 0.00 3.10
4999 6022 6.709397 CCTGTGTATATGCATGTTCAGAGATT 59.291 38.462 22.26 0.00 0.00 2.40
5000 6023 7.874528 CCTGTGTATATGCATGTTCAGAGATTA 59.125 37.037 22.26 0.00 0.00 1.75
5001 6024 8.593492 TGTGTATATGCATGTTCAGAGATTAC 57.407 34.615 10.16 0.00 0.00 1.89
5002 6025 8.424133 TGTGTATATGCATGTTCAGAGATTACT 58.576 33.333 10.16 0.00 0.00 2.24
5019 6042 8.928448 AGAGATTACTACTATTTCCTGATGCAA 58.072 33.333 0.00 0.00 0.00 4.08
5020 6043 9.717942 GAGATTACTACTATTTCCTGATGCAAT 57.282 33.333 0.00 0.00 0.00 3.56
5021 6044 9.717942 AGATTACTACTATTTCCTGATGCAATC 57.282 33.333 0.00 0.00 45.83 2.67
5022 6045 8.854614 ATTACTACTATTTCCTGATGCAATCC 57.145 34.615 0.00 0.00 44.73 3.01
5023 6046 6.506538 ACTACTATTTCCTGATGCAATCCT 57.493 37.500 0.00 0.00 44.73 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.952296 GCTAGCACATGGGAAGGAATG 59.048 52.381 10.63 0.00 0.00 2.67
1 2 1.849039 AGCTAGCACATGGGAAGGAAT 59.151 47.619 18.83 0.00 0.00 3.01
238 240 2.844362 CCTAGCAGATCCCGGCCA 60.844 66.667 2.24 0.00 33.86 5.36
288 291 3.244875 TGGAGATAAGAGCAAGCCAACAA 60.245 43.478 0.00 0.00 0.00 2.83
794 811 6.854496 AGAACATTACAGCGAAGTAAACAA 57.146 33.333 4.57 0.00 37.50 2.83
805 824 9.331282 AGGATTACAAGATTAGAACATTACAGC 57.669 33.333 0.00 0.00 0.00 4.40
869 888 1.609320 GGCAGAGAAAAGGCTCGAACT 60.609 52.381 0.00 0.00 39.87 3.01
895 914 2.989422 TTTTAGAGAAAAGGCGCAGC 57.011 45.000 10.83 0.00 40.64 5.25
1242 1279 4.097361 GGTCGGTCAGGAAGGGGC 62.097 72.222 0.00 0.00 0.00 5.80
1271 1310 4.610714 GAAGGGCGCCTCGGGATC 62.611 72.222 28.56 7.55 30.89 3.36
1295 1337 1.634702 CGCGGGAAGAAGAAGAAGAG 58.365 55.000 0.00 0.00 0.00 2.85
1547 1598 2.878935 GCAGATGCATGGATCCCCTAAG 60.879 54.545 22.14 7.98 41.59 2.18
1561 1612 1.133853 AGGGGAGAGAATTGCAGATGC 60.134 52.381 0.00 0.00 42.50 3.91
1562 1613 3.495806 GGTAGGGGAGAGAATTGCAGATG 60.496 52.174 0.00 0.00 0.00 2.90
1563 1614 2.708325 GGTAGGGGAGAGAATTGCAGAT 59.292 50.000 0.00 0.00 0.00 2.90
1564 1615 2.119495 GGTAGGGGAGAGAATTGCAGA 58.881 52.381 0.00 0.00 0.00 4.26
1565 1616 1.141858 GGGTAGGGGAGAGAATTGCAG 59.858 57.143 0.00 0.00 0.00 4.41
1566 1617 1.213296 GGGTAGGGGAGAGAATTGCA 58.787 55.000 0.00 0.00 0.00 4.08
1567 1618 0.474614 GGGGTAGGGGAGAGAATTGC 59.525 60.000 0.00 0.00 0.00 3.56
1568 1619 0.759346 CGGGGTAGGGGAGAGAATTG 59.241 60.000 0.00 0.00 0.00 2.32
1569 1620 0.640495 TCGGGGTAGGGGAGAGAATT 59.360 55.000 0.00 0.00 0.00 2.17
1570 1621 0.868186 ATCGGGGTAGGGGAGAGAAT 59.132 55.000 0.00 0.00 0.00 2.40
1571 1622 0.640495 AATCGGGGTAGGGGAGAGAA 59.360 55.000 0.00 0.00 0.00 2.87
1572 1623 1.146566 GTAATCGGGGTAGGGGAGAGA 59.853 57.143 0.00 0.00 0.00 3.10
1573 1624 1.630223 GTAATCGGGGTAGGGGAGAG 58.370 60.000 0.00 0.00 0.00 3.20
1574 1625 0.189327 GGTAATCGGGGTAGGGGAGA 59.811 60.000 0.00 0.00 0.00 3.71
1581 1632 1.418637 GAATGGCAGGTAATCGGGGTA 59.581 52.381 0.00 0.00 0.00 3.69
1583 1634 0.474184 AGAATGGCAGGTAATCGGGG 59.526 55.000 0.00 0.00 0.00 5.73
1585 1636 4.703897 TCTTAAGAATGGCAGGTAATCGG 58.296 43.478 1.68 0.00 0.00 4.18
1611 1662 4.093408 CGGATCAATTGTCGAGTGAAACAT 59.907 41.667 5.13 0.00 41.43 2.71
1633 1685 0.318441 TCTGTCTGGCAGTTTCCTCG 59.682 55.000 15.27 0.00 45.23 4.63
1641 1693 1.110442 CCCTACTCTCTGTCTGGCAG 58.890 60.000 8.58 8.58 46.34 4.85
1643 1695 1.819905 GCCCTACTCTCTGTCTGGC 59.180 63.158 0.00 0.00 37.98 4.85
1644 1696 0.394488 TCGCCCTACTCTCTGTCTGG 60.394 60.000 0.00 0.00 0.00 3.86
1652 1704 0.757188 CCCACATCTCGCCCTACTCT 60.757 60.000 0.00 0.00 0.00 3.24
1654 1706 0.617820 AACCCACATCTCGCCCTACT 60.618 55.000 0.00 0.00 0.00 2.57
1655 1707 0.179081 GAACCCACATCTCGCCCTAC 60.179 60.000 0.00 0.00 0.00 3.18
1656 1708 0.325296 AGAACCCACATCTCGCCCTA 60.325 55.000 0.00 0.00 0.00 3.53
1657 1709 1.613630 AGAACCCACATCTCGCCCT 60.614 57.895 0.00 0.00 0.00 5.19
1658 1710 1.450312 CAGAACCCACATCTCGCCC 60.450 63.158 0.00 0.00 0.00 6.13
1661 1713 1.667724 GAATGCAGAACCCACATCTCG 59.332 52.381 0.00 0.00 0.00 4.04
1662 1714 2.019984 GGAATGCAGAACCCACATCTC 58.980 52.381 0.00 0.00 0.00 2.75
1683 1761 1.529438 TGAATTGCCTCGACGAACAAC 59.471 47.619 13.40 5.05 0.00 3.32
1689 1767 0.994995 CAGAGTGAATTGCCTCGACG 59.005 55.000 0.00 0.00 32.88 5.12
1697 1775 6.082338 GCAATCACAGTAACAGAGTGAATTG 58.918 40.000 0.00 0.00 44.47 2.32
1705 1783 6.264832 CAAACTTTGCAATCACAGTAACAGA 58.735 36.000 0.00 0.00 32.45 3.41
1709 1787 5.347342 CACCAAACTTTGCAATCACAGTAA 58.653 37.500 0.00 0.00 32.45 2.24
1716 1803 1.139163 CGGCACCAAACTTTGCAATC 58.861 50.000 0.00 0.00 40.75 2.67
1725 1812 3.438781 TCAGTTATCAATCGGCACCAAAC 59.561 43.478 0.00 0.00 0.00 2.93
1746 1849 7.267857 GCATGGGGCATATCCTAATTAATTTC 58.732 38.462 5.91 0.00 43.97 2.17
1763 2169 2.512974 GCATTTGCAGCATGGGGC 60.513 61.111 0.00 0.00 45.30 5.80
1783 2189 2.559698 TGTCGAATTCAGGCTCCAAA 57.440 45.000 6.22 0.00 0.00 3.28
1791 2197 4.194640 ACCTGATGGATTGTCGAATTCAG 58.805 43.478 6.22 0.00 30.11 3.02
1812 2219 8.263940 TCAGTCTGCTTACAAAATATACCAAC 57.736 34.615 0.00 0.00 0.00 3.77
1819 2226 6.875948 TTGCTTCAGTCTGCTTACAAAATA 57.124 33.333 0.00 0.00 0.00 1.40
1823 2230 4.214119 GTCATTGCTTCAGTCTGCTTACAA 59.786 41.667 0.00 0.00 0.00 2.41
1824 2231 3.748048 GTCATTGCTTCAGTCTGCTTACA 59.252 43.478 0.00 0.00 0.00 2.41
1834 2241 5.649395 TGGAATTCCTAAGTCATTGCTTCAG 59.351 40.000 24.73 0.00 36.82 3.02
1888 2350 0.612744 ATTTGCATTTTCCACCGGGG 59.387 50.000 6.32 0.00 38.37 5.73
1890 2352 2.067766 CACATTTGCATTTTCCACCGG 58.932 47.619 0.00 0.00 0.00 5.28
1912 2377 6.322491 CGAAACAGATTTCCTATTCCAAACC 58.678 40.000 0.00 0.00 41.12 3.27
1988 2453 9.797642 AATGTGCTAATAAGATATTGTCATCCA 57.202 29.630 0.00 0.00 0.00 3.41
2000 2465 9.208022 CGATCAGGAATTAATGTGCTAATAAGA 57.792 33.333 0.00 0.00 0.00 2.10
2021 2486 5.882000 AGGACATGAAACATGATTTCGATCA 59.118 36.000 16.86 0.00 34.73 2.92
2026 2491 5.902613 TCCAGGACATGAAACATGATTTC 57.097 39.130 16.86 6.76 0.00 2.17
2032 2497 5.776716 AGAAAACATCCAGGACATGAAACAT 59.223 36.000 0.00 0.00 0.00 2.71
2033 2498 5.139727 AGAAAACATCCAGGACATGAAACA 58.860 37.500 0.00 0.00 0.00 2.83
2034 2499 5.474876 AGAGAAAACATCCAGGACATGAAAC 59.525 40.000 0.00 0.00 0.00 2.78
2064 2531 5.360714 CACACCCAAGGCAAGATATGTATTT 59.639 40.000 0.00 0.00 0.00 1.40
2065 2532 4.889409 CACACCCAAGGCAAGATATGTATT 59.111 41.667 0.00 0.00 0.00 1.89
2066 2533 4.079787 ACACACCCAAGGCAAGATATGTAT 60.080 41.667 0.00 0.00 0.00 2.29
2067 2534 3.265737 ACACACCCAAGGCAAGATATGTA 59.734 43.478 0.00 0.00 0.00 2.29
2068 2535 2.041620 ACACACCCAAGGCAAGATATGT 59.958 45.455 0.00 0.00 0.00 2.29
2070 2537 2.041620 ACACACACCCAAGGCAAGATAT 59.958 45.455 0.00 0.00 0.00 1.63
2071 2538 1.423541 ACACACACCCAAGGCAAGATA 59.576 47.619 0.00 0.00 0.00 1.98
2072 2539 0.185901 ACACACACCCAAGGCAAGAT 59.814 50.000 0.00 0.00 0.00 2.40
2073 2540 0.033601 AACACACACCCAAGGCAAGA 60.034 50.000 0.00 0.00 0.00 3.02
2074 2541 0.823460 AAACACACACCCAAGGCAAG 59.177 50.000 0.00 0.00 0.00 4.01
2075 2542 0.534412 CAAACACACACCCAAGGCAA 59.466 50.000 0.00 0.00 0.00 4.52
2076 2543 0.613292 ACAAACACACACCCAAGGCA 60.613 50.000 0.00 0.00 0.00 4.75
2077 2544 1.394618 TACAAACACACACCCAAGGC 58.605 50.000 0.00 0.00 0.00 4.35
2078 2545 2.225491 CGATACAAACACACACCCAAGG 59.775 50.000 0.00 0.00 0.00 3.61
2079 2546 2.225491 CCGATACAAACACACACCCAAG 59.775 50.000 0.00 0.00 0.00 3.61
2080 2547 2.222886 CCGATACAAACACACACCCAA 58.777 47.619 0.00 0.00 0.00 4.12
2081 2548 1.141254 ACCGATACAAACACACACCCA 59.859 47.619 0.00 0.00 0.00 4.51
2082 2549 1.533731 CACCGATACAAACACACACCC 59.466 52.381 0.00 0.00 0.00 4.61
2083 2550 1.069500 GCACCGATACAAACACACACC 60.069 52.381 0.00 0.00 0.00 4.16
2084 2551 1.871039 AGCACCGATACAAACACACAC 59.129 47.619 0.00 0.00 0.00 3.82
2085 2552 2.139917 GAGCACCGATACAAACACACA 58.860 47.619 0.00 0.00 0.00 3.72
2086 2553 2.412089 GAGAGCACCGATACAAACACAC 59.588 50.000 0.00 0.00 0.00 3.82
2087 2554 2.036604 TGAGAGCACCGATACAAACACA 59.963 45.455 0.00 0.00 0.00 3.72
2088 2555 2.668457 CTGAGAGCACCGATACAAACAC 59.332 50.000 0.00 0.00 0.00 3.32
2089 2556 2.560981 TCTGAGAGCACCGATACAAACA 59.439 45.455 0.00 0.00 0.00 2.83
2090 2557 3.232213 TCTGAGAGCACCGATACAAAC 57.768 47.619 0.00 0.00 0.00 2.93
2091 2558 3.195610 ACATCTGAGAGCACCGATACAAA 59.804 43.478 0.00 0.00 0.00 2.83
2092 2559 2.760650 ACATCTGAGAGCACCGATACAA 59.239 45.455 0.00 0.00 0.00 2.41
2093 2560 2.379005 ACATCTGAGAGCACCGATACA 58.621 47.619 0.00 0.00 0.00 2.29
2094 2561 3.119291 CAACATCTGAGAGCACCGATAC 58.881 50.000 0.00 0.00 0.00 2.24
2095 2562 2.481969 GCAACATCTGAGAGCACCGATA 60.482 50.000 0.00 0.00 0.00 2.92
2096 2563 1.741732 GCAACATCTGAGAGCACCGAT 60.742 52.381 0.00 0.00 0.00 4.18
2097 2564 0.390340 GCAACATCTGAGAGCACCGA 60.390 55.000 0.00 0.00 0.00 4.69
2098 2565 1.690283 CGCAACATCTGAGAGCACCG 61.690 60.000 0.00 0.00 0.00 4.94
2099 2566 0.390340 TCGCAACATCTGAGAGCACC 60.390 55.000 0.00 0.00 29.52 5.01
2100 2567 1.326852 CATCGCAACATCTGAGAGCAC 59.673 52.381 0.00 0.00 37.27 4.40
2101 2568 1.066645 ACATCGCAACATCTGAGAGCA 60.067 47.619 0.00 0.00 37.27 4.26
2102 2569 1.649664 ACATCGCAACATCTGAGAGC 58.350 50.000 0.00 0.00 37.27 4.09
2103 2570 2.350804 CCAACATCGCAACATCTGAGAG 59.649 50.000 0.00 0.00 37.27 3.20
2104 2571 2.289631 ACCAACATCGCAACATCTGAGA 60.290 45.455 0.00 0.00 38.31 3.27
2105 2572 2.079158 ACCAACATCGCAACATCTGAG 58.921 47.619 0.00 0.00 0.00 3.35
2106 2573 2.183478 ACCAACATCGCAACATCTGA 57.817 45.000 0.00 0.00 0.00 3.27
2107 2574 2.587956 CAACCAACATCGCAACATCTG 58.412 47.619 0.00 0.00 0.00 2.90
2108 2575 1.068333 GCAACCAACATCGCAACATCT 60.068 47.619 0.00 0.00 0.00 2.90
2109 2576 1.068333 AGCAACCAACATCGCAACATC 60.068 47.619 0.00 0.00 0.00 3.06
2110 2577 0.961019 AGCAACCAACATCGCAACAT 59.039 45.000 0.00 0.00 0.00 2.71
2148 2615 6.405278 TCAGAAAGATGAAAAAGGGTTTCC 57.595 37.500 0.00 0.00 0.00 3.13
2159 2626 8.188799 ACTCGTATCGTATTTCAGAAAGATGAA 58.811 33.333 14.87 4.26 37.41 2.57
2161 2628 7.916128 ACTCGTATCGTATTTCAGAAAGATG 57.084 36.000 3.65 3.65 0.00 2.90
2162 2629 8.838365 AGTACTCGTATCGTATTTCAGAAAGAT 58.162 33.333 1.28 2.06 0.00 2.40
2163 2630 8.206325 AGTACTCGTATCGTATTTCAGAAAGA 57.794 34.615 1.28 0.00 0.00 2.52
2165 2632 7.977904 TGAGTACTCGTATCGTATTTCAGAAA 58.022 34.615 17.85 0.00 0.00 2.52
2167 2634 7.543947 TTGAGTACTCGTATCGTATTTCAGA 57.456 36.000 17.85 0.00 0.00 3.27
2168 2635 8.783999 ATTTGAGTACTCGTATCGTATTTCAG 57.216 34.615 17.85 0.00 0.00 3.02
2184 2651 8.018520 CGAGACTATCCATGAGTATTTGAGTAC 58.981 40.741 0.00 0.00 0.00 2.73
2209 2713 3.713288 TCACTCAAGACTACACCAAACG 58.287 45.455 0.00 0.00 0.00 3.60
2263 2767 1.150536 GAGTGAACCCCAACCTGCA 59.849 57.895 0.00 0.00 0.00 4.41
2314 2818 7.388500 CCTCAATTTATTGCCTCAAACATTTGT 59.612 33.333 4.36 0.00 37.29 2.83
2341 2854 8.745837 CAAATTTGTCATGTCACTAGTGAAAAC 58.254 33.333 26.74 17.40 41.85 2.43
2360 2873 8.481974 TGATGGAAGCAATTATGTCAAATTTG 57.518 30.769 12.15 12.15 0.00 2.32
2388 2901 3.508744 AGCGCATAACCTGGAAAATTG 57.491 42.857 11.47 0.00 0.00 2.32
2551 3072 7.810658 TCAAGTTTGAATGCTCTTTCTATCAC 58.189 34.615 0.00 0.00 33.55 3.06
2552 3073 7.984422 TCAAGTTTGAATGCTCTTTCTATCA 57.016 32.000 0.00 0.00 33.55 2.15
2598 3119 9.874205 ACAGCATGCAACTGTTTTAATATATTT 57.126 25.926 21.98 0.00 46.01 1.40
2611 3132 2.658285 GAAGACAACAGCATGCAACTG 58.342 47.619 21.98 15.18 42.53 3.16
2619 3146 2.158957 AGAAACTCCGAAGACAACAGCA 60.159 45.455 0.00 0.00 0.00 4.41
2631 3166 5.466728 TGATCAGTCAAAAGAAGAAACTCCG 59.533 40.000 0.00 0.00 0.00 4.63
2683 3235 8.142994 TCTGAGACTACAATTTCAAGTTTGTC 57.857 34.615 0.00 0.00 37.29 3.18
2694 3246 6.370994 CAGATGCAACTTCTGAGACTACAATT 59.629 38.462 9.76 0.00 42.63 2.32
2719 3271 6.622896 GCTTGTGATTTATGAACTGGTACACC 60.623 42.308 0.00 0.00 0.00 4.16
2756 3308 6.056884 CACATATAACTAGCCCCGGTAAAAA 58.943 40.000 0.00 0.00 0.00 1.94
2761 3313 2.686119 ACACATATAACTAGCCCCGGT 58.314 47.619 0.00 0.00 0.00 5.28
2762 3314 3.764237 AACACATATAACTAGCCCCGG 57.236 47.619 0.00 0.00 0.00 5.73
2763 3315 5.204409 TGTAACACATATAACTAGCCCCG 57.796 43.478 0.00 0.00 0.00 5.73
2776 3328 9.606631 GGAAGAAGATAGAAAGATGTAACACAT 57.393 33.333 0.00 0.00 42.43 3.21
2811 3363 8.157476 AGTATACCCAAACCATTATGTCAGATC 58.843 37.037 0.00 0.00 0.00 2.75
2836 3388 8.853345 CAATTATTTACTACAGCTTGCACAAAG 58.147 33.333 0.00 0.00 39.07 2.77
3128 3688 7.992754 ATGAGAAGAAAAAGTAACAGCTCAT 57.007 32.000 0.00 0.00 36.18 2.90
3194 3755 7.546316 GCTCCCTTAGTTTCAGTCTAACTTTAG 59.454 40.741 0.00 0.00 37.12 1.85
3243 3804 4.369182 AGAAGTGAACTACAGTTTCCACG 58.631 43.478 7.78 0.00 41.56 4.94
3261 3822 7.067737 AGTGGCTTAAGCTAGTACTAAGAGAAG 59.932 40.741 25.88 6.92 41.70 2.85
3264 3825 6.319152 TGAGTGGCTTAAGCTAGTACTAAGAG 59.681 42.308 25.88 0.00 41.70 2.85
3269 3830 4.345854 ACTGAGTGGCTTAAGCTAGTACT 58.654 43.478 25.88 22.06 41.70 2.73
3270 3831 4.722361 ACTGAGTGGCTTAAGCTAGTAC 57.278 45.455 25.88 18.42 41.70 2.73
3362 3935 6.319658 CAGTACATATTCCATTGGCTTCACTT 59.680 38.462 0.00 0.00 0.00 3.16
3430 4016 5.324409 AGCCCTTTTCATGTCATTGACTTA 58.676 37.500 17.26 0.00 33.15 2.24
3431 4017 4.154942 AGCCCTTTTCATGTCATTGACTT 58.845 39.130 17.26 8.72 33.15 3.01
3495 4083 9.987272 TGGAAGTGAGAGTACATATTCATAATG 57.013 33.333 0.00 0.00 0.00 1.90
3551 4172 2.624838 ACAGCTGATTTTGGAACCTGTG 59.375 45.455 23.35 0.00 31.54 3.66
3553 4174 2.229784 GGACAGCTGATTTTGGAACCTG 59.770 50.000 23.35 0.00 0.00 4.00
3636 4258 7.024340 TCTACTACTACTTTAGGTCGCAATG 57.976 40.000 0.00 0.00 0.00 2.82
3845 4472 4.197750 TCCTCCGATACACTAAGACAGTC 58.802 47.826 0.00 0.00 34.26 3.51
3851 4478 4.098044 ACACACATCCTCCGATACACTAAG 59.902 45.833 0.00 0.00 0.00 2.18
3869 4496 3.056891 CCCATCAATAACCCACAACACAC 60.057 47.826 0.00 0.00 0.00 3.82
3939 4575 2.373169 ACCAGCTTTGATCTTCTGTCCA 59.627 45.455 0.00 0.00 0.00 4.02
4020 4656 8.969260 TCATAGTTTCTTGATTGCTACATCAT 57.031 30.769 0.00 0.00 0.00 2.45
4032 4668 9.551734 CATTCATACCAGATCATAGTTTCTTGA 57.448 33.333 0.00 0.00 0.00 3.02
4045 4682 5.573380 ACATGTAGGCATTCATACCAGAT 57.427 39.130 0.00 0.00 31.99 2.90
4064 4701 6.127897 GCCAAGTGATAAAGCAGAAAGTACAT 60.128 38.462 0.00 0.00 0.00 2.29
4067 4704 5.181245 GTGCCAAGTGATAAAGCAGAAAGTA 59.819 40.000 0.00 0.00 33.37 2.24
4075 4713 1.541147 TGCAGTGCCAAGTGATAAAGC 59.459 47.619 13.72 0.00 0.00 3.51
4082 4720 0.961857 TGCCTATGCAGTGCCAAGTG 60.962 55.000 13.72 5.48 44.23 3.16
4097 4904 7.911651 ACAGATTATAGCAATATACAGTGCCT 58.088 34.615 0.00 0.00 46.84 4.75
4139 4946 3.066621 TGTGGAAAGTGCAGATTGTTCAC 59.933 43.478 0.00 0.00 0.00 3.18
4184 4991 1.869574 CAGCACAGGTCGACGATCG 60.870 63.158 14.88 14.88 42.10 3.69
4186 4993 1.213013 GACAGCACAGGTCGACGAT 59.787 57.895 9.92 0.00 0.00 3.73
4187 4994 0.604511 TAGACAGCACAGGTCGACGA 60.605 55.000 9.92 0.00 40.20 4.20
4195 5002 1.783284 TTCGCTTGTAGACAGCACAG 58.217 50.000 0.00 0.00 0.00 3.66
4206 5013 0.463654 TGCACTCTGGTTTCGCTTGT 60.464 50.000 0.00 0.00 0.00 3.16
4211 5018 0.861837 GTGACTGCACTCTGGTTTCG 59.138 55.000 0.00 0.00 41.84 3.46
4229 5036 1.411246 TCACAGTTACAAGGCAGTCGT 59.589 47.619 0.00 0.00 0.00 4.34
4230 5037 2.148916 TCACAGTTACAAGGCAGTCG 57.851 50.000 0.00 0.00 0.00 4.18
4231 5038 3.437049 GGAATCACAGTTACAAGGCAGTC 59.563 47.826 0.00 0.00 0.00 3.51
4234 5041 2.422597 CGGAATCACAGTTACAAGGCA 58.577 47.619 0.00 0.00 0.00 4.75
4235 5042 1.130561 GCGGAATCACAGTTACAAGGC 59.869 52.381 0.00 0.00 0.00 4.35
4236 5043 1.393539 CGCGGAATCACAGTTACAAGG 59.606 52.381 0.00 0.00 0.00 3.61
4237 5044 1.201921 GCGCGGAATCACAGTTACAAG 60.202 52.381 8.83 0.00 0.00 3.16
4238 5045 0.793861 GCGCGGAATCACAGTTACAA 59.206 50.000 8.83 0.00 0.00 2.41
4240 5047 0.094730 GTGCGCGGAATCACAGTTAC 59.905 55.000 8.83 0.00 33.63 2.50
4241 5048 1.017177 GGTGCGCGGAATCACAGTTA 61.017 55.000 8.83 0.00 35.04 2.24
4244 5053 1.647545 AATGGTGCGCGGAATCACAG 61.648 55.000 8.83 0.00 35.04 3.66
4247 5056 1.078497 AGAATGGTGCGCGGAATCA 60.078 52.632 8.83 7.91 0.00 2.57
4248 5057 1.353103 CAGAATGGTGCGCGGAATC 59.647 57.895 8.83 1.07 0.00 2.52
4275 5084 7.630987 CAGCTTAAAAGAATCGTACACGTAATG 59.369 37.037 1.19 0.00 40.80 1.90
4280 5089 4.624024 TCCAGCTTAAAAGAATCGTACACG 59.376 41.667 0.00 0.00 41.45 4.49
4294 5103 7.630082 ACTGACCATAAATACTTCCAGCTTAA 58.370 34.615 0.00 0.00 0.00 1.85
4317 5126 1.808411 CATTGTGTGTTCGGCCTACT 58.192 50.000 0.00 0.00 0.00 2.57
4319 5128 0.036164 AGCATTGTGTGTTCGGCCTA 59.964 50.000 0.00 0.00 0.00 3.93
4320 5129 0.823356 AAGCATTGTGTGTTCGGCCT 60.823 50.000 0.00 0.00 0.00 5.19
4322 5131 0.387239 GGAAGCATTGTGTGTTCGGC 60.387 55.000 0.00 0.00 0.00 5.54
4325 5134 3.115554 GTTGTGGAAGCATTGTGTGTTC 58.884 45.455 0.00 0.00 0.00 3.18
4327 5136 2.378038 AGTTGTGGAAGCATTGTGTGT 58.622 42.857 0.00 0.00 0.00 3.72
4333 5142 3.197549 ACCAACAAAGTTGTGGAAGCATT 59.802 39.130 15.23 0.00 41.31 3.56
4336 5145 2.959507 ACCAACAAAGTTGTGGAAGC 57.040 45.000 15.23 0.00 41.31 3.86
4346 5156 4.977963 CACAAGATGCTTGTACCAACAAAG 59.022 41.667 11.98 0.00 44.79 2.77
4359 5169 8.621532 TTTATCTAACAGAAACACAAGATGCT 57.378 30.769 0.00 0.00 0.00 3.79
4361 5171 8.725148 AGCTTTATCTAACAGAAACACAAGATG 58.275 33.333 0.00 0.00 0.00 2.90
4377 5187 7.618019 ATGAGGGACATTACAGCTTTATCTA 57.382 36.000 0.00 0.00 35.45 1.98
4393 5203 2.163010 CACATGTTGCAGAATGAGGGAC 59.837 50.000 15.39 0.00 39.69 4.46
4416 5227 9.645059 TTCAACATAAACTGAATGTGTTTTCAA 57.355 25.926 0.00 0.00 37.62 2.69
4453 5264 3.641436 AGCTGGGTTAAAACTGGGAAAAG 59.359 43.478 0.00 0.00 0.00 2.27
4461 5272 6.549736 AGTTTTGTCATAGCTGGGTTAAAACT 59.450 34.615 18.79 18.79 40.33 2.66
4462 5273 6.640907 CAGTTTTGTCATAGCTGGGTTAAAAC 59.359 38.462 16.17 16.17 37.16 2.43
4463 5274 6.737346 GCAGTTTTGTCATAGCTGGGTTAAAA 60.737 38.462 8.73 0.00 0.00 1.52
4464 5275 5.278758 GCAGTTTTGTCATAGCTGGGTTAAA 60.279 40.000 8.73 0.00 0.00 1.52
4465 5276 4.217550 GCAGTTTTGTCATAGCTGGGTTAA 59.782 41.667 8.73 0.00 0.00 2.01
4466 5277 3.756434 GCAGTTTTGTCATAGCTGGGTTA 59.244 43.478 8.73 0.00 0.00 2.85
4467 5278 2.558359 GCAGTTTTGTCATAGCTGGGTT 59.442 45.455 8.73 0.00 0.00 4.11
4468 5279 2.162681 GCAGTTTTGTCATAGCTGGGT 58.837 47.619 8.73 0.00 0.00 4.51
4469 5280 2.161855 TGCAGTTTTGTCATAGCTGGG 58.838 47.619 8.73 0.00 0.00 4.45
4470 5281 2.415090 GCTGCAGTTTTGTCATAGCTGG 60.415 50.000 16.64 0.00 0.00 4.85
4477 5288 1.818060 ACAAGTGCTGCAGTTTTGTCA 59.182 42.857 19.51 0.00 0.00 3.58
4481 5292 2.754552 TCTTCACAAGTGCTGCAGTTTT 59.245 40.909 19.51 11.37 0.00 2.43
4488 5299 4.361451 ACAAGTTTCTTCACAAGTGCTG 57.639 40.909 0.00 0.00 0.00 4.41
4495 5306 9.677567 GAATAAGCATTTACAAGTTTCTTCACA 57.322 29.630 0.00 0.00 0.00 3.58
4544 5355 7.612065 AACATGAGCCATAGTTATACACCTA 57.388 36.000 0.00 0.00 0.00 3.08
4552 5363 6.493189 TGTGGATAACATGAGCCATAGTTA 57.507 37.500 0.00 0.00 37.20 2.24
4575 5386 6.191657 TGATACATGCCCTGAAATACTCAT 57.808 37.500 0.00 0.00 32.14 2.90
4580 5391 5.132502 CCTGTTGATACATGCCCTGAAATA 58.867 41.667 0.00 0.00 32.86 1.40
4588 5399 2.754552 TCAAAGCCTGTTGATACATGCC 59.245 45.455 0.00 0.00 44.16 4.40
4594 5405 7.575414 TGTTAAACTTCAAAGCCTGTTGATA 57.425 32.000 0.00 0.00 37.36 2.15
4596 5407 5.906113 TGTTAAACTTCAAAGCCTGTTGA 57.094 34.783 0.00 0.00 35.72 3.18
4614 5426 6.750501 GTGAGATACTCGTATGCAACTTGTTA 59.249 38.462 0.00 0.00 32.35 2.41
4615 5427 5.577164 GTGAGATACTCGTATGCAACTTGTT 59.423 40.000 0.00 0.00 32.35 2.83
4629 5441 2.604855 CGTATGTGGCCGTGAGATACTC 60.605 54.545 0.00 0.00 0.00 2.59
4997 6020 8.664079 AGGATTGCATCAGGAAATAGTAGTAAT 58.336 33.333 0.00 0.00 0.00 1.89
4999 6022 7.618019 AGGATTGCATCAGGAAATAGTAGTA 57.382 36.000 0.00 0.00 0.00 1.82
5000 6023 6.506538 AGGATTGCATCAGGAAATAGTAGT 57.493 37.500 0.00 0.00 0.00 2.73


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

AutoCloner maintained by Alex Coulton.