Multiple sequence alignment - TraesCS2A01G485500

Loading Multiple Alignment...

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 TraesCS2A01G485500 chr2A 100.000 3598 0 0 1 3598 720389102 720385505 0.000000e+00 6645.0
1 TraesCS2A01G485500 chr2A 100.000 563 0 0 3882 4444 720385221 720384659 0.000000e+00 1040.0
2 TraesCS2A01G485500 chr2A 91.223 638 48 7 914 1550 720354049 720353419 0.000000e+00 861.0
3 TraesCS2A01G485500 chr4A 91.590 2378 114 31 813 3115 687321186 687318820 0.000000e+00 3205.0
4 TraesCS2A01G485500 chr4A 90.249 441 27 7 3150 3587 687318823 687318396 3.000000e-156 562.0
5 TraesCS2A01G485500 chr4A 90.400 250 15 7 4197 4444 687317593 687317351 1.990000e-83 320.0
6 TraesCS2A01G485500 chr4A 97.000 100 3 0 10 109 687322592 687322493 7.640000e-38 169.0
7 TraesCS2A01G485500 chr4A 76.000 225 35 16 3882 4101 687317927 687317717 1.020000e-16 99.0
8 TraesCS2A01G485500 chr7D 96.011 1454 33 8 595 2031 37659364 37660809 0.000000e+00 2340.0
9 TraesCS2A01G485500 chr7D 90.558 932 68 9 2634 3565 37661132 37662043 0.000000e+00 1216.0
10 TraesCS2A01G485500 chr7D 90.977 665 52 4 886 1550 37625584 37626240 0.000000e+00 889.0
11 TraesCS2A01G485500 chr7D 95.639 321 11 2 2203 2520 37660803 37661123 3.070000e-141 512.0
12 TraesCS2A01G485500 chr7D 82.353 646 50 33 1 590 37658486 37659123 1.850000e-138 503.0
13 TraesCS2A01G485500 chr7D 84.483 348 26 9 109 444 37614803 37615134 7.170000e-83 318.0
14 TraesCS2A01G485500 chr7D 90.517 232 11 4 4220 4444 37662729 37662956 3.360000e-76 296.0
15 TraesCS2A01G485500 chr7D 100.000 28 0 0 529 556 3703511 3703484 8.000000e-03 52.8
16 TraesCS2A01G485500 chr3D 96.105 1412 31 8 637 2031 25527146 25525742 0.000000e+00 2281.0
17 TraesCS2A01G485500 chr3D 91.702 940 68 4 2634 3565 25525419 25524482 0.000000e+00 1295.0
18 TraesCS2A01G485500 chr3D 83.333 642 51 27 1 596 25528051 25527420 3.910000e-150 542.0
19 TraesCS2A01G485500 chr3D 95.950 321 10 2 2203 2520 25525748 25525428 6.590000e-143 518.0
20 TraesCS2A01G485500 chr3D 88.095 252 15 7 4202 4442 25523828 25523581 7.280000e-73 285.0
21 TraesCS2A01G485500 chr3D 89.231 65 6 1 515 578 61050522 61050586 3.680000e-11 80.5
22 TraesCS2A01G485500 chr3D 100.000 32 0 0 598 629 25527173 25527142 4.800000e-05 60.2
23 TraesCS2A01G485500 chr5B 88.776 1176 92 26 671 1828 325965667 325964514 0.000000e+00 1404.0
24 TraesCS2A01G485500 chr5B 78.349 642 81 36 2735 3354 325962693 325962088 3.270000e-96 363.0
25 TraesCS2A01G485500 chr5B 98.611 72 1 0 2463 2534 325964081 325964010 1.300000e-25 128.0
26 TraesCS2A01G485500 chr5D 88.137 1197 95 26 671 1833 287017761 287016578 0.000000e+00 1380.0
27 TraesCS2A01G485500 chr5D 76.774 930 102 46 2463 3354 287016179 287015326 2.470000e-112 416.0
28 TraesCS2A01G485500 chr5D 80.469 128 11 8 1843 1963 287016512 287016392 7.920000e-13 86.1
29 TraesCS2A01G485500 chr5A 88.186 1185 96 24 671 1828 379094448 379093281 0.000000e+00 1373.0
30 TraesCS2A01G485500 chr5A 77.292 938 107 57 2463 3354 379092845 379091968 5.240000e-124 455.0
31 TraesCS2A01G485500 chr5A 83.051 118 13 3 1833 1944 379093246 379093130 2.830000e-17 100.0
32 TraesCS2A01G485500 chr4D 88.344 163 14 3 2052 2210 428578398 428578559 1.630000e-44 191.0
33 TraesCS2A01G485500 chr4D 88.125 160 16 2 2054 2210 258893612 258893453 2.110000e-43 187.0
34 TraesCS2A01G485500 chr3B 86.905 168 19 2 2052 2216 276788487 276788654 7.590000e-43 185.0
35 TraesCS2A01G485500 chrUn 86.826 167 19 1 2052 2215 292404396 292404562 2.730000e-42 183.0
36 TraesCS2A01G485500 chrUn 86.826 167 19 1 2052 2215 292442935 292443101 2.730000e-42 183.0
37 TraesCS2A01G485500 chrUn 86.826 167 19 1 2052 2215 308913658 308913492 2.730000e-42 183.0
38 TraesCS2A01G485500 chr6D 87.273 165 16 4 2052 2212 436759244 436759081 2.730000e-42 183.0
39 TraesCS2A01G485500 chr2B 80.556 180 28 6 2052 2225 4217526 4217348 1.000000e-26 132.0
40 TraesCS2A01G485500 chr3A 75.824 182 42 2 2780 2960 456440834 456440654 1.700000e-14 91.6
41 TraesCS2A01G485500 chr1B 93.220 59 4 0 520 578 271099202 271099144 2.200000e-13 87.9
42 TraesCS2A01G485500 chr7A 89.831 59 6 0 520 578 141569804 141569862 4.770000e-10 76.8
43 TraesCS2A01G485500 chr7A 89.831 59 6 0 520 578 141850624 141850682 4.770000e-10 76.8
44 TraesCS2A01G485500 chr7A 89.831 59 6 0 520 578 142133509 142133567 4.770000e-10 76.8
45 TraesCS2A01G485500 chr2D 91.071 56 5 0 524 579 604310909 604310854 4.770000e-10 76.8


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 TraesCS2A01G485500 chr2A 720384659 720389102 4443 True 3842.500000 6645 100.000000 1 4444 2 chr2A.!!$R2 4443
1 TraesCS2A01G485500 chr2A 720353419 720354049 630 True 861.000000 861 91.223000 914 1550 1 chr2A.!!$R1 636
2 TraesCS2A01G485500 chr4A 687317351 687322592 5241 True 871.000000 3205 89.047800 10 4444 5 chr4A.!!$R1 4434
3 TraesCS2A01G485500 chr7D 37658486 37662956 4470 False 973.400000 2340 91.015600 1 4444 5 chr7D.!!$F3 4443
4 TraesCS2A01G485500 chr7D 37625584 37626240 656 False 889.000000 889 90.977000 886 1550 1 chr7D.!!$F2 664
5 TraesCS2A01G485500 chr3D 25523581 25528051 4470 True 830.200000 2281 92.530833 1 4442 6 chr3D.!!$R1 4441
6 TraesCS2A01G485500 chr5B 325962088 325965667 3579 True 631.666667 1404 88.578667 671 3354 3 chr5B.!!$R1 2683
7 TraesCS2A01G485500 chr5D 287015326 287017761 2435 True 627.366667 1380 81.793333 671 3354 3 chr5D.!!$R1 2683
8 TraesCS2A01G485500 chr5A 379091968 379094448 2480 True 642.666667 1373 82.843000 671 3354 3 chr5A.!!$R1 2683

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
521 619 0.750249 CCCCCGAAAAAGTTTGCACT 59.250 50.0 0.00 0.00 33.11 4.40 F
2035 2991 0.251165 GGCTTTGGAGGCCTTGTACA 60.251 55.0 6.77 0.82 45.57 2.90 F
2189 3145 0.246635 TCCGAAGCACTCTAAGCACC 59.753 55.0 0.00 0.00 0.00 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2170 3126 0.246635 GGTGCTTAGAGTGCTTCGGA 59.753 55.000 0.0 0.0 0.0 4.55 R
3299 5735 0.528470 CTTCCACCGTCTCCTCTGTC 59.472 60.000 0.0 0.0 0.0 3.51 R
4007 6666 1.066605 GCAGCCAATCAATAGCACAGG 59.933 52.381 0.0 0.0 0.0 4.00 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
227 289 1.469767 CCTTGGCGCATTTCTTTAGGC 60.470 52.381 10.83 0.00 0.00 3.93
282 356 2.255430 GGAGACGAGACAAGACGGT 58.745 57.895 0.00 0.00 0.00 4.83
313 387 1.744368 ATGAGCTTCACGGCAGCAG 60.744 57.895 0.00 0.00 39.99 4.24
334 408 2.840038 GCTTGATTTCCTCCCCCAAATT 59.160 45.455 0.00 0.00 0.00 1.82
355 429 2.043349 GGTTATTTGGCCCGCCCT 60.043 61.111 0.00 0.00 34.56 5.19
424 498 4.093998 CCATGCTGTTGACTTGTCATCTAC 59.906 45.833 4.18 1.25 0.00 2.59
425 499 4.335400 TGCTGTTGACTTGTCATCTACA 57.665 40.909 4.18 5.61 35.88 2.74
426 500 4.309933 TGCTGTTGACTTGTCATCTACAG 58.690 43.478 20.79 20.79 46.33 2.74
427 501 4.202253 TGCTGTTGACTTGTCATCTACAGT 60.202 41.667 23.47 0.00 45.74 3.55
428 502 5.010617 TGCTGTTGACTTGTCATCTACAGTA 59.989 40.000 23.47 19.73 45.74 2.74
475 551 4.759516 ATGTCCATGGTTTTACAACGAC 57.240 40.909 12.58 0.00 33.13 4.34
503 579 8.306761 CAAATATGTTAATTTATGCTCCCTCCC 58.693 37.037 0.00 0.00 0.00 4.30
504 580 4.178956 TGTTAATTTATGCTCCCTCCCC 57.821 45.455 0.00 0.00 0.00 4.81
521 619 0.750249 CCCCCGAAAAAGTTTGCACT 59.250 50.000 0.00 0.00 33.11 4.40
522 620 1.537990 CCCCCGAAAAAGTTTGCACTG 60.538 52.381 0.00 0.00 31.60 3.66
524 622 2.459934 CCCGAAAAAGTTTGCACTGAC 58.540 47.619 0.00 0.00 31.60 3.51
527 625 3.547468 CCGAAAAAGTTTGCACTGACTTG 59.453 43.478 9.35 0.00 36.31 3.16
551 649 6.126796 TGGTGCTAGATACATCAATTTGAGGA 60.127 38.462 17.21 1.21 31.79 3.71
596 694 6.348540 GGGAGTATTCAACAAGAATGTGTGAC 60.349 42.308 0.85 0.00 46.24 3.67
1021 1863 7.607991 ACATAATGGCAGATATACAGTTAAGCC 59.392 37.037 0.00 0.00 41.15 4.35
1276 2126 6.145209 TGTTTACATCATTTTTGTGCCATTCG 59.855 34.615 0.00 0.00 0.00 3.34
1278 2128 4.880759 ACATCATTTTTGTGCCATTCGAA 58.119 34.783 0.00 0.00 0.00 3.71
1287 2139 5.545658 TTGTGCCATTCGAAAAGATAGTC 57.454 39.130 0.00 0.00 0.00 2.59
1291 2143 4.137543 GCCATTCGAAAAGATAGTCCCAT 58.862 43.478 0.00 0.00 0.00 4.00
1399 2251 3.962063 TCTATGATTTGCACCATGGCATT 59.038 39.130 13.04 0.00 44.48 3.56
1411 2263 3.721575 ACCATGGCATTCTGGGTATCTAA 59.278 43.478 13.04 0.00 36.82 2.10
1639 2499 5.975693 TCACTTTTTCCAGTCACAAGTTT 57.024 34.783 0.00 0.00 0.00 2.66
1656 2516 5.594317 ACAAGTTTATCTTTGTTGACCTGCT 59.406 36.000 0.00 0.00 33.63 4.24
1692 2555 8.270744 GTTCTTATCATCTATGGAGCCCATATT 58.729 37.037 12.60 3.77 44.33 1.28
1982 2938 4.080582 TGGGAATAAGTGATGGTACCTGTG 60.081 45.833 14.36 0.00 0.00 3.66
2024 2980 2.229792 CTTGTGTTAGCTGGCTTTGGA 58.770 47.619 0.00 0.00 0.00 3.53
2025 2981 1.896220 TGTGTTAGCTGGCTTTGGAG 58.104 50.000 0.00 0.00 0.00 3.86
2026 2982 1.168714 GTGTTAGCTGGCTTTGGAGG 58.831 55.000 0.00 0.00 0.00 4.30
2034 2990 2.568003 GGCTTTGGAGGCCTTGTAC 58.432 57.895 6.77 0.00 45.57 2.90
2035 2991 0.251165 GGCTTTGGAGGCCTTGTACA 60.251 55.000 6.77 0.82 45.57 2.90
2036 2992 1.616159 GCTTTGGAGGCCTTGTACAA 58.384 50.000 6.77 8.28 0.00 2.41
2037 2993 2.171003 GCTTTGGAGGCCTTGTACAAT 58.829 47.619 6.77 0.00 0.00 2.71
2038 2994 2.094545 GCTTTGGAGGCCTTGTACAATG 60.095 50.000 6.77 13.13 0.00 2.82
2039 2995 1.544724 TTGGAGGCCTTGTACAATGC 58.455 50.000 23.06 23.06 0.00 3.56
2040 2996 0.403655 TGGAGGCCTTGTACAATGCA 59.596 50.000 29.20 15.48 34.30 3.96
2041 2997 1.202989 TGGAGGCCTTGTACAATGCAA 60.203 47.619 29.20 14.05 34.30 4.08
2042 2998 1.474077 GGAGGCCTTGTACAATGCAAG 59.526 52.381 29.20 10.69 42.00 4.01
2047 3003 2.352503 CTTGTACAATGCAAGGTGCC 57.647 50.000 9.13 0.00 44.23 5.01
2048 3004 1.888512 CTTGTACAATGCAAGGTGCCT 59.111 47.619 9.13 0.00 44.23 4.75
2049 3005 2.869101 TGTACAATGCAAGGTGCCTA 57.131 45.000 0.00 0.00 44.23 3.93
2050 3006 2.710377 TGTACAATGCAAGGTGCCTAG 58.290 47.619 0.00 0.00 44.23 3.02
2051 3007 2.039746 TGTACAATGCAAGGTGCCTAGT 59.960 45.455 0.00 0.00 44.23 2.57
2052 3008 3.262151 TGTACAATGCAAGGTGCCTAGTA 59.738 43.478 0.00 0.00 44.23 1.82
2053 3009 2.991250 ACAATGCAAGGTGCCTAGTAG 58.009 47.619 0.00 0.00 44.23 2.57
2054 3010 2.571653 ACAATGCAAGGTGCCTAGTAGA 59.428 45.455 0.00 0.00 44.23 2.59
2055 3011 3.201290 CAATGCAAGGTGCCTAGTAGAG 58.799 50.000 0.00 0.00 44.23 2.43
2056 3012 2.231716 TGCAAGGTGCCTAGTAGAGA 57.768 50.000 0.00 0.00 44.23 3.10
2057 3013 2.536066 TGCAAGGTGCCTAGTAGAGAA 58.464 47.619 0.00 0.00 44.23 2.87
2058 3014 2.903784 TGCAAGGTGCCTAGTAGAGAAA 59.096 45.455 0.00 0.00 44.23 2.52
2059 3015 3.519510 TGCAAGGTGCCTAGTAGAGAAAT 59.480 43.478 0.00 0.00 44.23 2.17
2060 3016 4.714802 TGCAAGGTGCCTAGTAGAGAAATA 59.285 41.667 0.00 0.00 44.23 1.40
2061 3017 5.188948 TGCAAGGTGCCTAGTAGAGAAATAA 59.811 40.000 0.00 0.00 44.23 1.40
2062 3018 6.113411 GCAAGGTGCCTAGTAGAGAAATAAA 58.887 40.000 0.00 0.00 37.42 1.40
2063 3019 6.037281 GCAAGGTGCCTAGTAGAGAAATAAAC 59.963 42.308 0.00 0.00 37.42 2.01
2064 3020 6.236558 AGGTGCCTAGTAGAGAAATAAACC 57.763 41.667 0.00 0.00 0.00 3.27
2065 3021 5.724854 AGGTGCCTAGTAGAGAAATAAACCA 59.275 40.000 0.00 0.00 0.00 3.67
2066 3022 6.049790 GGTGCCTAGTAGAGAAATAAACCAG 58.950 44.000 0.00 0.00 0.00 4.00
2067 3023 6.351966 GGTGCCTAGTAGAGAAATAAACCAGT 60.352 42.308 0.00 0.00 0.00 4.00
2068 3024 7.104290 GTGCCTAGTAGAGAAATAAACCAGTT 58.896 38.462 0.00 0.00 0.00 3.16
2069 3025 7.606839 GTGCCTAGTAGAGAAATAAACCAGTTT 59.393 37.037 0.00 0.86 36.63 2.66
2070 3026 8.161425 TGCCTAGTAGAGAAATAAACCAGTTTT 58.839 33.333 0.37 0.00 34.23 2.43
2071 3027 9.011095 GCCTAGTAGAGAAATAAACCAGTTTTT 57.989 33.333 0.37 0.00 34.23 1.94
2075 3031 9.286170 AGTAGAGAAATAAACCAGTTTTTCCTC 57.714 33.333 0.37 5.01 34.23 3.71
2076 3032 9.063615 GTAGAGAAATAAACCAGTTTTTCCTCA 57.936 33.333 0.37 0.00 34.23 3.86
2077 3033 8.533569 AGAGAAATAAACCAGTTTTTCCTCAA 57.466 30.769 0.37 0.00 34.23 3.02
2078 3034 8.633561 AGAGAAATAAACCAGTTTTTCCTCAAG 58.366 33.333 0.37 0.00 34.23 3.02
2079 3035 7.210174 AGAAATAAACCAGTTTTTCCTCAAGC 58.790 34.615 0.37 0.00 34.23 4.01
2080 3036 6.478512 AATAAACCAGTTTTTCCTCAAGCA 57.521 33.333 0.37 0.00 34.23 3.91
2081 3037 3.801114 AACCAGTTTTTCCTCAAGCAC 57.199 42.857 0.00 0.00 0.00 4.40
2082 3038 2.031870 ACCAGTTTTTCCTCAAGCACC 58.968 47.619 0.00 0.00 0.00 5.01
2083 3039 1.001378 CCAGTTTTTCCTCAAGCACCG 60.001 52.381 0.00 0.00 0.00 4.94
2084 3040 1.001378 CAGTTTTTCCTCAAGCACCGG 60.001 52.381 0.00 0.00 0.00 5.28
2085 3041 1.029681 GTTTTTCCTCAAGCACCGGT 58.970 50.000 0.00 0.00 0.00 5.28
2086 3042 1.028905 TTTTTCCTCAAGCACCGGTG 58.971 50.000 30.66 30.66 0.00 4.94
2100 3056 2.936498 CACCGGTGCTTATTTGTAGAGG 59.064 50.000 24.02 0.00 0.00 3.69
2101 3057 1.940613 CCGGTGCTTATTTGTAGAGGC 59.059 52.381 0.00 0.00 0.00 4.70
2102 3058 2.420129 CCGGTGCTTATTTGTAGAGGCT 60.420 50.000 0.00 0.00 0.00 4.58
2103 3059 3.181469 CCGGTGCTTATTTGTAGAGGCTA 60.181 47.826 0.00 0.00 0.00 3.93
2104 3060 4.051922 CGGTGCTTATTTGTAGAGGCTAG 58.948 47.826 0.00 0.00 0.00 3.42
2105 3061 4.202121 CGGTGCTTATTTGTAGAGGCTAGA 60.202 45.833 0.00 0.00 0.00 2.43
2106 3062 5.509840 CGGTGCTTATTTGTAGAGGCTAGAT 60.510 44.000 0.00 0.00 0.00 1.98
2107 3063 5.698545 GGTGCTTATTTGTAGAGGCTAGATG 59.301 44.000 0.00 0.00 0.00 2.90
2108 3064 5.178438 GTGCTTATTTGTAGAGGCTAGATGC 59.822 44.000 0.00 0.00 41.94 3.91
2109 3065 5.070981 TGCTTATTTGTAGAGGCTAGATGCT 59.929 40.000 0.00 0.00 42.39 3.79
2110 3066 5.994668 GCTTATTTGTAGAGGCTAGATGCTT 59.005 40.000 0.00 0.00 42.39 3.91
2111 3067 7.155328 GCTTATTTGTAGAGGCTAGATGCTTA 58.845 38.462 0.00 0.00 42.39 3.09
2112 3068 7.657761 GCTTATTTGTAGAGGCTAGATGCTTAA 59.342 37.037 0.00 0.00 42.39 1.85
2113 3069 9.717942 CTTATTTGTAGAGGCTAGATGCTTAAT 57.282 33.333 0.00 0.00 42.39 1.40
2116 3072 9.717942 ATTTGTAGAGGCTAGATGCTTAATTAG 57.282 33.333 0.00 0.00 42.39 1.73
2117 3073 7.233389 TGTAGAGGCTAGATGCTTAATTAGG 57.767 40.000 0.00 0.00 42.39 2.69
2118 3074 5.159273 AGAGGCTAGATGCTTAATTAGGC 57.841 43.478 12.39 12.39 42.39 3.93
2119 3075 4.594920 AGAGGCTAGATGCTTAATTAGGCA 59.405 41.667 22.66 22.66 42.60 4.75
2126 3082 3.508845 TGCTTAATTAGGCATCCCTCC 57.491 47.619 17.47 0.00 41.75 4.30
2127 3083 3.056080 TGCTTAATTAGGCATCCCTCCT 58.944 45.455 17.47 0.00 41.75 3.69
2128 3084 3.181440 TGCTTAATTAGGCATCCCTCCTG 60.181 47.826 17.47 0.00 41.75 3.86
2129 3085 3.181439 GCTTAATTAGGCATCCCTCCTGT 60.181 47.826 14.21 0.00 41.75 4.00
2130 3086 4.041691 GCTTAATTAGGCATCCCTCCTGTA 59.958 45.833 14.21 0.00 41.75 2.74
2131 3087 5.799213 CTTAATTAGGCATCCCTCCTGTAG 58.201 45.833 0.00 0.00 41.75 2.74
2132 3088 3.637821 ATTAGGCATCCCTCCTGTAGA 57.362 47.619 0.00 0.00 41.75 2.59
2133 3089 3.414759 TTAGGCATCCCTCCTGTAGAA 57.585 47.619 0.00 0.00 41.75 2.10
2134 3090 2.270434 AGGCATCCCTCCTGTAGAAA 57.730 50.000 0.00 0.00 36.46 2.52
2135 3091 2.781667 AGGCATCCCTCCTGTAGAAAT 58.218 47.619 0.00 0.00 36.46 2.17
2136 3092 3.941629 AGGCATCCCTCCTGTAGAAATA 58.058 45.455 0.00 0.00 36.46 1.40
2137 3093 4.307259 AGGCATCCCTCCTGTAGAAATAA 58.693 43.478 0.00 0.00 36.46 1.40
2138 3094 4.349342 AGGCATCCCTCCTGTAGAAATAAG 59.651 45.833 0.00 0.00 36.46 1.73
2139 3095 4.068599 GCATCCCTCCTGTAGAAATAAGC 58.931 47.826 0.00 0.00 0.00 3.09
2140 3096 4.444876 GCATCCCTCCTGTAGAAATAAGCA 60.445 45.833 0.00 0.00 0.00 3.91
2141 3097 4.755266 TCCCTCCTGTAGAAATAAGCAC 57.245 45.455 0.00 0.00 0.00 4.40
2142 3098 4.362677 TCCCTCCTGTAGAAATAAGCACT 58.637 43.478 0.00 0.00 0.00 4.40
2143 3099 4.162320 TCCCTCCTGTAGAAATAAGCACTG 59.838 45.833 0.00 0.00 0.00 3.66
2144 3100 4.446371 CCTCCTGTAGAAATAAGCACTGG 58.554 47.826 0.00 0.00 0.00 4.00
2145 3101 4.080863 CCTCCTGTAGAAATAAGCACTGGT 60.081 45.833 0.00 0.00 33.23 4.00
2146 3102 4.832248 TCCTGTAGAAATAAGCACTGGTG 58.168 43.478 0.00 0.00 33.23 4.17
2162 3118 5.043248 CACTGGTGCTTAAGAAAAACTTGG 58.957 41.667 6.67 0.00 39.38 3.61
2163 3119 4.709886 ACTGGTGCTTAAGAAAAACTTGGT 59.290 37.500 6.67 0.00 39.38 3.67
2164 3120 5.186992 ACTGGTGCTTAAGAAAAACTTGGTT 59.813 36.000 6.67 0.00 39.38 3.67
2165 3121 6.043854 TGGTGCTTAAGAAAAACTTGGTTT 57.956 33.333 6.67 0.00 39.38 3.27
2166 3122 7.093684 ACTGGTGCTTAAGAAAAACTTGGTTTA 60.094 33.333 6.67 0.00 39.38 2.01
2167 3123 7.787028 TGGTGCTTAAGAAAAACTTGGTTTAT 58.213 30.769 6.67 0.00 39.38 1.40
2168 3124 8.261522 TGGTGCTTAAGAAAAACTTGGTTTATT 58.738 29.630 6.67 0.00 39.38 1.40
2169 3125 9.104965 GGTGCTTAAGAAAAACTTGGTTTATTT 57.895 29.630 6.67 0.00 39.38 1.40
2176 3132 8.642908 AGAAAAACTTGGTTTATTTTCCGAAG 57.357 30.769 6.29 0.00 40.77 3.79
2177 3133 6.838198 AAAACTTGGTTTATTTTCCGAAGC 57.162 33.333 0.00 0.00 34.43 3.86
2178 3134 5.523438 AACTTGGTTTATTTTCCGAAGCA 57.477 34.783 0.00 0.00 0.00 3.91
2179 3135 4.866921 ACTTGGTTTATTTTCCGAAGCAC 58.133 39.130 0.00 0.00 31.35 4.40
2180 3136 4.583073 ACTTGGTTTATTTTCCGAAGCACT 59.417 37.500 0.00 0.00 31.35 4.40
2181 3137 4.759516 TGGTTTATTTTCCGAAGCACTC 57.240 40.909 0.00 0.00 0.00 3.51
2182 3138 4.394729 TGGTTTATTTTCCGAAGCACTCT 58.605 39.130 0.00 0.00 0.00 3.24
2183 3139 5.553123 TGGTTTATTTTCCGAAGCACTCTA 58.447 37.500 0.00 0.00 0.00 2.43
2184 3140 5.998981 TGGTTTATTTTCCGAAGCACTCTAA 59.001 36.000 0.00 0.00 0.00 2.10
2185 3141 6.148811 TGGTTTATTTTCCGAAGCACTCTAAG 59.851 38.462 0.00 0.00 0.00 2.18
2186 3142 5.796350 TTATTTTCCGAAGCACTCTAAGC 57.204 39.130 0.00 0.00 0.00 3.09
2187 3143 2.831685 TTTCCGAAGCACTCTAAGCA 57.168 45.000 0.00 0.00 0.00 3.91
2188 3144 2.080286 TTCCGAAGCACTCTAAGCAC 57.920 50.000 0.00 0.00 0.00 4.40
2189 3145 0.246635 TCCGAAGCACTCTAAGCACC 59.753 55.000 0.00 0.00 0.00 5.01
2190 3146 0.247736 CCGAAGCACTCTAAGCACCT 59.752 55.000 0.00 0.00 0.00 4.00
2191 3147 1.338200 CCGAAGCACTCTAAGCACCTT 60.338 52.381 0.00 0.00 0.00 3.50
2192 3148 1.728971 CGAAGCACTCTAAGCACCTTG 59.271 52.381 0.00 0.00 0.00 3.61
2193 3149 1.466558 GAAGCACTCTAAGCACCTTGC 59.533 52.381 0.00 0.00 45.46 4.01
2474 3677 6.602803 ACATCTTGTAATGGACAATGCACATA 59.397 34.615 0.00 0.00 46.95 2.29
2568 3772 1.580942 CCCTGTGTGGTGAAATGCG 59.419 57.895 0.00 0.00 0.00 4.73
2600 4970 7.039082 TGGCAGAAGCATTTTTCTAGGTAAAAT 60.039 33.333 9.37 9.37 44.61 1.82
2727 5125 3.502979 GGCTAGATCACCTAACTAGACCG 59.497 52.174 0.00 0.00 36.57 4.79
2843 5241 4.599047 TGGGAAAATCGCAGTTTTTGAT 57.401 36.364 0.00 0.00 34.23 2.57
2936 5334 1.469940 CGAGTGGATGACTACTGGCAC 60.470 57.143 0.00 0.00 37.94 5.01
2991 5389 2.223711 GGTTTGTCTGCCATTTGTCGTT 60.224 45.455 0.00 0.00 0.00 3.85
3014 5412 8.374728 CGTTGTTGCGTAAATTAGTTATACAGA 58.625 33.333 0.00 0.00 0.00 3.41
3030 5428 1.751924 ACAGATGACCTTCTAGACGCC 59.248 52.381 0.00 0.00 0.00 5.68
3035 5433 2.307768 TGACCTTCTAGACGCCCATAG 58.692 52.381 0.00 0.00 0.00 2.23
3130 5551 6.627065 GCAATTTTTCCCATATCCTTTCGACA 60.627 38.462 0.00 0.00 0.00 4.35
3148 5569 3.775654 CAGACGGTGCCTCCTCCC 61.776 72.222 0.00 0.00 0.00 4.30
3165 5595 3.939592 CCTCCCTTTACCAATCGAGTTTC 59.060 47.826 0.00 0.00 0.00 2.78
3191 5621 3.830178 TCTTCCGTGGTTTCTCAGTGATA 59.170 43.478 0.00 0.00 0.00 2.15
3427 5863 1.614241 GCCCTGAGAGACGCCCTAAA 61.614 60.000 0.00 0.00 0.00 1.85
3569 6007 4.020662 ACACTTTGGTTTGATTGGTGTGTT 60.021 37.500 0.00 0.00 35.54 3.32
3594 6032 2.944129 ACCTGCTGGTGTTTTGTATGT 58.056 42.857 15.36 0.00 46.51 2.29
3595 6033 4.093472 ACCTGCTGGTGTTTTGTATGTA 57.907 40.909 15.36 0.00 46.51 2.29
3596 6034 4.662278 ACCTGCTGGTGTTTTGTATGTAT 58.338 39.130 15.36 0.00 46.51 2.29
3597 6035 4.458989 ACCTGCTGGTGTTTTGTATGTATG 59.541 41.667 15.36 0.00 46.51 2.39
3904 6521 6.573664 TGTTTGTTAGAGGTTGATTGGATG 57.426 37.500 0.00 0.00 0.00 3.51
3912 6529 2.311542 AGGTTGATTGGATGGTTAGGCA 59.688 45.455 0.00 0.00 0.00 4.75
3924 6541 2.237143 TGGTTAGGCAAGTGAGGATCTG 59.763 50.000 0.00 0.00 34.92 2.90
3926 6543 0.833287 TAGGCAAGTGAGGATCTGGC 59.167 55.000 0.00 0.00 34.92 4.85
3927 6544 1.817099 GGCAAGTGAGGATCTGGCG 60.817 63.158 0.00 0.00 33.08 5.69
3930 6547 0.742281 CAAGTGAGGATCTGGCGTGG 60.742 60.000 0.00 0.00 34.92 4.94
3932 6549 0.324368 AGTGAGGATCTGGCGTGGTA 60.324 55.000 0.00 0.00 34.92 3.25
3933 6550 0.179108 GTGAGGATCTGGCGTGGTAC 60.179 60.000 0.00 0.00 34.92 3.34
3934 6551 0.613572 TGAGGATCTGGCGTGGTACA 60.614 55.000 0.00 0.00 34.92 2.90
3936 6553 1.139058 GAGGATCTGGCGTGGTACATT 59.861 52.381 0.00 0.00 44.52 2.71
3954 6573 6.769822 GGTACATTACCTAGTCAGTGCTAGTA 59.230 42.308 15.79 8.85 45.52 1.82
4013 6672 3.456280 TGATTGCTTTTTCAACCTGTGC 58.544 40.909 0.00 0.00 0.00 4.57
4015 6674 4.340666 TGATTGCTTTTTCAACCTGTGCTA 59.659 37.500 0.00 0.00 0.00 3.49
4016 6675 4.935352 TTGCTTTTTCAACCTGTGCTAT 57.065 36.364 0.00 0.00 0.00 2.97
4017 6676 4.935352 TGCTTTTTCAACCTGTGCTATT 57.065 36.364 0.00 0.00 0.00 1.73
4019 6678 4.340666 TGCTTTTTCAACCTGTGCTATTGA 59.659 37.500 0.00 0.00 0.00 2.57
4023 6682 5.389859 TTTCAACCTGTGCTATTGATTGG 57.610 39.130 0.00 0.00 32.61 3.16
4024 6683 2.754552 TCAACCTGTGCTATTGATTGGC 59.245 45.455 0.00 0.00 0.00 4.52
4032 6691 2.092807 TGCTATTGATTGGCTGCTCAGA 60.093 45.455 0.00 0.00 0.00 3.27
4045 6704 3.144506 CTGCTCAGATCAACTGGTTTGT 58.855 45.455 0.00 0.00 45.76 2.83
4047 6706 4.713553 TGCTCAGATCAACTGGTTTGTTA 58.286 39.130 0.00 0.00 45.76 2.41
4095 6762 2.507058 TGCTAACATGCAGGGATTCTCT 59.493 45.455 2.31 0.00 38.12 3.10
4096 6763 3.711190 TGCTAACATGCAGGGATTCTCTA 59.289 43.478 2.31 0.00 38.12 2.43
4098 6765 4.754114 GCTAACATGCAGGGATTCTCTAAG 59.246 45.833 2.31 0.00 0.00 2.18
4099 6766 4.851639 AACATGCAGGGATTCTCTAAGT 57.148 40.909 2.31 0.00 0.00 2.24
4100 6767 5.957771 AACATGCAGGGATTCTCTAAGTA 57.042 39.130 2.31 0.00 0.00 2.24
4101 6768 5.283457 ACATGCAGGGATTCTCTAAGTAC 57.717 43.478 2.31 0.00 0.00 2.73
4104 6771 6.041069 ACATGCAGGGATTCTCTAAGTACTAC 59.959 42.308 2.31 0.00 0.00 2.73
4105 6772 4.894114 TGCAGGGATTCTCTAAGTACTACC 59.106 45.833 0.00 0.00 0.00 3.18
4106 6773 4.894114 GCAGGGATTCTCTAAGTACTACCA 59.106 45.833 0.00 0.00 0.00 3.25
4108 6775 6.127140 GCAGGGATTCTCTAAGTACTACCAAA 60.127 42.308 0.00 0.00 0.00 3.28
4110 6777 8.487028 CAGGGATTCTCTAAGTACTACCAAATT 58.513 37.037 0.00 0.00 0.00 1.82
4111 6778 9.059023 AGGGATTCTCTAAGTACTACCAAATTT 57.941 33.333 0.00 0.00 0.00 1.82
4112 6779 9.682465 GGGATTCTCTAAGTACTACCAAATTTT 57.318 33.333 0.00 0.00 0.00 1.82
4115 6782 9.740710 ATTCTCTAAGTACTACCAAATTTTGCT 57.259 29.630 0.00 0.00 0.00 3.91
4116 6783 8.547967 TCTCTAAGTACTACCAAATTTTGCTG 57.452 34.615 0.00 0.00 0.00 4.41
4121 6788 4.670896 ACTACCAAATTTTGCTGCTGTT 57.329 36.364 3.50 0.00 0.00 3.16
4125 6792 4.009002 ACCAAATTTTGCTGCTGTTTTGT 58.991 34.783 3.50 0.00 0.00 2.83
4160 6827 9.739276 ATGTAATACAGTTCAGAAAATCTTCCA 57.261 29.630 0.00 0.00 31.28 3.53
4166 7097 5.297776 CAGTTCAGAAAATCTTCCACACTGT 59.702 40.000 0.00 0.00 32.47 3.55
4173 7104 4.900635 AATCTTCCACACTGTCAAACAC 57.099 40.909 0.00 0.00 0.00 3.32
4180 7111 4.104776 CCACACTGTCAAACACAAATCAC 58.895 43.478 0.00 0.00 33.31 3.06
4181 7112 4.142403 CCACACTGTCAAACACAAATCACT 60.142 41.667 0.00 0.00 33.31 3.41
4182 7113 4.794762 CACACTGTCAAACACAAATCACTG 59.205 41.667 0.00 0.00 33.31 3.66
4183 7114 4.699735 ACACTGTCAAACACAAATCACTGA 59.300 37.500 0.00 0.00 33.31 3.41
4184 7115 5.182950 ACACTGTCAAACACAAATCACTGAA 59.817 36.000 0.00 0.00 33.31 3.02
4185 7116 5.740569 CACTGTCAAACACAAATCACTGAAG 59.259 40.000 0.00 0.00 33.31 3.02
4187 7118 6.319658 ACTGTCAAACACAAATCACTGAAGAT 59.680 34.615 0.00 0.00 33.31 2.40
4189 7120 8.394971 TGTCAAACACAAATCACTGAAGATAT 57.605 30.769 0.00 0.00 29.30 1.63
4190 7121 8.506437 TGTCAAACACAAATCACTGAAGATATC 58.494 33.333 0.00 0.00 29.30 1.63
4192 7156 9.065798 TCAAACACAAATCACTGAAGATATCAA 57.934 29.630 5.32 0.00 37.67 2.57
4200 7164 6.037786 TCACTGAAGATATCAAGGAAACGT 57.962 37.500 5.32 0.00 37.67 3.99
4218 7182 8.701895 AGGAAACGTTACCAAATCTCATAGATA 58.298 33.333 0.00 0.00 32.89 1.98
4249 7217 6.565811 CGATCCATGTATAAACATTCAACCCG 60.566 42.308 0.00 0.00 44.07 5.28
4272 7240 0.248458 CACACAACAGGGCAACGAAC 60.248 55.000 0.00 0.00 37.60 3.95
4286 7254 4.219033 GCAACGAACGAAAATTGACAGAT 58.781 39.130 0.14 0.00 0.00 2.90
4287 7255 5.379003 GCAACGAACGAAAATTGACAGATA 58.621 37.500 0.14 0.00 0.00 1.98
4297 7268 9.226606 ACGAAAATTGACAGATAATTTAGGACA 57.773 29.630 0.00 0.00 36.89 4.02
4298 7269 9.708222 CGAAAATTGACAGATAATTTAGGACAG 57.292 33.333 0.00 0.00 36.89 3.51
4420 7396 7.958088 TCCACCCTTGTAAAAAGATTTAAAGG 58.042 34.615 0.00 0.00 38.03 3.11
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
207 264 1.469767 GCCTAAAGAAATGCGCCAAGG 60.470 52.381 4.18 0.96 0.00 3.61
227 289 4.093952 CTGCAGCGGGAAAGCACG 62.094 66.667 0.00 0.00 45.74 5.34
264 338 0.109689 CACCGTCTTGTCTCGTCTCC 60.110 60.000 0.00 0.00 0.00 3.71
273 347 2.661866 GCGTCAGCACCGTCTTGT 60.662 61.111 0.00 0.00 44.35 3.16
313 387 1.937191 TTTGGGGGAGGAAATCAAGC 58.063 50.000 0.00 0.00 0.00 4.01
334 408 1.379309 GCGGGCCAAATAACCTGGA 60.379 57.895 4.39 0.00 35.85 3.86
355 429 9.716556 AGTACTAAGAGGAAGATTAGGATTCAA 57.283 33.333 0.00 0.00 34.05 2.69
475 551 9.683069 GAGGGAGCATAAATTAACATATTTGTG 57.317 33.333 0.00 0.00 38.72 3.33
503 579 1.407258 TCAGTGCAAACTTTTTCGGGG 59.593 47.619 0.00 0.00 0.00 5.73
504 580 2.099098 AGTCAGTGCAAACTTTTTCGGG 59.901 45.455 0.00 0.00 0.00 5.14
507 583 4.327087 CACCAAGTCAGTGCAAACTTTTTC 59.673 41.667 7.46 0.00 33.53 2.29
521 619 5.675684 TTGATGTATCTAGCACCAAGTCA 57.324 39.130 0.00 0.00 0.00 3.41
522 620 7.280876 TCAAATTGATGTATCTAGCACCAAGTC 59.719 37.037 0.00 0.00 0.00 3.01
524 622 7.255035 CCTCAAATTGATGTATCTAGCACCAAG 60.255 40.741 0.00 0.00 0.00 3.61
527 625 6.291377 TCCTCAAATTGATGTATCTAGCACC 58.709 40.000 0.00 0.00 0.00 5.01
551 649 2.295070 CCTCCGTCGGGAAAAATTTGTT 59.705 45.455 12.29 0.00 43.27 2.83
564 662 1.475280 TGTTGAATACTCCCTCCGTCG 59.525 52.381 0.00 0.00 0.00 5.12
596 694 2.808543 GACAGGTAAGTTGTTCAGCAGG 59.191 50.000 0.00 0.00 0.00 4.85
1011 1853 7.381323 ACTTTATAGTGTAACGGCTTAACTGT 58.619 34.615 0.00 0.00 45.86 3.55
1021 1863 5.909477 TCCATGGGACTTTATAGTGTAACG 58.091 41.667 13.02 0.00 45.86 3.18
1276 2126 9.841880 GAGTTACAAAAATGGGACTATCTTTTC 57.158 33.333 0.00 0.00 0.00 2.29
1278 2128 8.793592 GTGAGTTACAAAAATGGGACTATCTTT 58.206 33.333 0.00 0.00 0.00 2.52
1287 2139 7.360269 GCAAATCATGTGAGTTACAAAAATGGG 60.360 37.037 0.00 0.00 43.77 4.00
1291 2143 6.700960 CCTGCAAATCATGTGAGTTACAAAAA 59.299 34.615 0.00 0.00 43.77 1.94
1399 2251 7.733047 TGCCTAAGAATATGTTAGATACCCAGA 59.267 37.037 6.66 0.00 30.21 3.86
1450 2302 7.948513 ATACGTGTTTCGAATTATTTCTTGC 57.051 32.000 0.00 0.00 42.86 4.01
1639 2499 5.316167 ACAATGAGCAGGTCAACAAAGATA 58.684 37.500 6.36 0.00 39.19 1.98
1656 2516 9.551734 CCATAGATGATAAGAACTGAACAATGA 57.448 33.333 0.00 0.00 0.00 2.57
1692 2555 3.813166 GTCCTTCGATGAGTTTTGGTCAA 59.187 43.478 0.00 0.00 0.00 3.18
1739 2603 3.806591 GCACAGAACGCCAGTAGTA 57.193 52.632 0.00 0.00 0.00 1.82
1982 2938 1.433053 GCCCAACCAACCGCAAAAAC 61.433 55.000 0.00 0.00 0.00 2.43
2038 2994 3.611766 TTTCTCTACTAGGCACCTTGC 57.388 47.619 0.00 0.00 44.08 4.01
2039 2995 6.539103 GGTTTATTTCTCTACTAGGCACCTTG 59.461 42.308 0.00 0.00 0.00 3.61
2040 2996 6.214819 TGGTTTATTTCTCTACTAGGCACCTT 59.785 38.462 0.00 0.00 0.00 3.50
2041 2997 5.724854 TGGTTTATTTCTCTACTAGGCACCT 59.275 40.000 0.00 0.00 0.00 4.00
2042 2998 5.985911 TGGTTTATTTCTCTACTAGGCACC 58.014 41.667 0.00 0.00 0.00 5.01
2043 2999 6.641474 ACTGGTTTATTTCTCTACTAGGCAC 58.359 40.000 0.00 0.00 0.00 5.01
2044 3000 6.869206 ACTGGTTTATTTCTCTACTAGGCA 57.131 37.500 0.00 0.00 0.00 4.75
2045 3001 8.563123 AAAACTGGTTTATTTCTCTACTAGGC 57.437 34.615 0.00 0.00 31.63 3.93
2049 3005 9.286170 GAGGAAAAACTGGTTTATTTCTCTACT 57.714 33.333 14.66 5.40 30.87 2.57
2050 3006 9.063615 TGAGGAAAAACTGGTTTATTTCTCTAC 57.936 33.333 18.49 8.54 32.58 2.59
2051 3007 9.635404 TTGAGGAAAAACTGGTTTATTTCTCTA 57.365 29.630 18.49 13.50 32.58 2.43
2052 3008 8.533569 TTGAGGAAAAACTGGTTTATTTCTCT 57.466 30.769 18.49 11.64 32.58 3.10
2053 3009 7.382488 GCTTGAGGAAAAACTGGTTTATTTCTC 59.618 37.037 14.86 14.86 32.31 2.87
2054 3010 7.147742 TGCTTGAGGAAAAACTGGTTTATTTCT 60.148 33.333 0.00 1.70 31.63 2.52
2055 3011 6.983890 TGCTTGAGGAAAAACTGGTTTATTTC 59.016 34.615 0.00 1.58 31.63 2.17
2056 3012 6.761242 GTGCTTGAGGAAAAACTGGTTTATTT 59.239 34.615 0.00 0.00 31.63 1.40
2057 3013 6.280643 GTGCTTGAGGAAAAACTGGTTTATT 58.719 36.000 0.00 0.00 31.63 1.40
2058 3014 5.221441 GGTGCTTGAGGAAAAACTGGTTTAT 60.221 40.000 0.00 0.00 31.63 1.40
2059 3015 4.098807 GGTGCTTGAGGAAAAACTGGTTTA 59.901 41.667 0.00 0.00 31.63 2.01
2060 3016 3.118775 GGTGCTTGAGGAAAAACTGGTTT 60.119 43.478 0.00 0.00 0.00 3.27
2061 3017 2.430694 GGTGCTTGAGGAAAAACTGGTT 59.569 45.455 0.00 0.00 0.00 3.67
2062 3018 2.031870 GGTGCTTGAGGAAAAACTGGT 58.968 47.619 0.00 0.00 0.00 4.00
2063 3019 1.001378 CGGTGCTTGAGGAAAAACTGG 60.001 52.381 0.00 0.00 0.00 4.00
2064 3020 1.001378 CCGGTGCTTGAGGAAAAACTG 60.001 52.381 0.00 0.00 0.00 3.16
2065 3021 1.318576 CCGGTGCTTGAGGAAAAACT 58.681 50.000 0.00 0.00 0.00 2.66
2066 3022 1.029681 ACCGGTGCTTGAGGAAAAAC 58.970 50.000 6.12 0.00 0.00 2.43
2067 3023 1.028905 CACCGGTGCTTGAGGAAAAA 58.971 50.000 24.02 0.00 0.00 1.94
2068 3024 2.714259 CACCGGTGCTTGAGGAAAA 58.286 52.632 24.02 0.00 0.00 2.29
2069 3025 4.473643 CACCGGTGCTTGAGGAAA 57.526 55.556 24.02 0.00 0.00 3.13
2079 3035 2.936498 CCTCTACAAATAAGCACCGGTG 59.064 50.000 30.66 30.66 0.00 4.94
2080 3036 2.679930 GCCTCTACAAATAAGCACCGGT 60.680 50.000 0.00 0.00 0.00 5.28
2081 3037 1.940613 GCCTCTACAAATAAGCACCGG 59.059 52.381 0.00 0.00 0.00 5.28
2082 3038 2.906354 AGCCTCTACAAATAAGCACCG 58.094 47.619 0.00 0.00 0.00 4.94
2083 3039 5.277857 TCTAGCCTCTACAAATAAGCACC 57.722 43.478 0.00 0.00 0.00 5.01
2084 3040 5.178438 GCATCTAGCCTCTACAAATAAGCAC 59.822 44.000 0.00 0.00 37.23 4.40
2085 3041 5.300752 GCATCTAGCCTCTACAAATAAGCA 58.699 41.667 0.00 0.00 37.23 3.91
2086 3042 5.854431 GCATCTAGCCTCTACAAATAAGC 57.146 43.478 0.00 0.00 37.23 3.09
2094 3050 7.580495 ATGCCTAATTAAGCATCTAGCCTCTAC 60.580 40.741 14.55 0.00 46.58 2.59
2095 3051 6.441924 ATGCCTAATTAAGCATCTAGCCTCTA 59.558 38.462 14.55 0.00 46.58 2.43
2096 3052 5.250313 ATGCCTAATTAAGCATCTAGCCTCT 59.750 40.000 14.55 0.00 46.58 3.69
2097 3053 5.495640 ATGCCTAATTAAGCATCTAGCCTC 58.504 41.667 14.55 0.00 46.58 4.70
2098 3054 5.511386 ATGCCTAATTAAGCATCTAGCCT 57.489 39.130 14.55 0.00 46.58 4.58
2106 3062 3.056080 AGGAGGGATGCCTAATTAAGCA 58.944 45.455 5.42 11.06 44.45 3.91
2107 3063 3.181439 ACAGGAGGGATGCCTAATTAAGC 60.181 47.826 5.42 0.00 33.51 3.09
2108 3064 4.713792 ACAGGAGGGATGCCTAATTAAG 57.286 45.455 5.42 0.00 33.51 1.85
2109 3065 5.473273 TCTACAGGAGGGATGCCTAATTAA 58.527 41.667 5.42 0.00 33.51 1.40
2110 3066 5.087923 TCTACAGGAGGGATGCCTAATTA 57.912 43.478 5.42 0.00 33.51 1.40
2111 3067 3.941629 TCTACAGGAGGGATGCCTAATT 58.058 45.455 5.42 0.00 33.51 1.40
2112 3068 3.637821 TCTACAGGAGGGATGCCTAAT 57.362 47.619 5.42 0.00 33.51 1.73
2113 3069 3.414759 TTCTACAGGAGGGATGCCTAA 57.585 47.619 5.42 0.00 33.51 2.69
2114 3070 3.414759 TTTCTACAGGAGGGATGCCTA 57.585 47.619 5.42 0.00 33.51 3.93
2115 3071 2.270434 TTTCTACAGGAGGGATGCCT 57.730 50.000 4.97 4.97 35.75 4.75
2116 3072 4.646572 CTTATTTCTACAGGAGGGATGCC 58.353 47.826 0.00 0.00 0.00 4.40
2117 3073 4.068599 GCTTATTTCTACAGGAGGGATGC 58.931 47.826 0.00 0.00 0.00 3.91
2118 3074 5.059833 GTGCTTATTTCTACAGGAGGGATG 58.940 45.833 0.00 0.00 0.00 3.51
2119 3075 4.971924 AGTGCTTATTTCTACAGGAGGGAT 59.028 41.667 0.00 0.00 0.00 3.85
2120 3076 4.162320 CAGTGCTTATTTCTACAGGAGGGA 59.838 45.833 0.00 0.00 0.00 4.20
2121 3077 4.446371 CAGTGCTTATTTCTACAGGAGGG 58.554 47.826 0.00 0.00 0.00 4.30
2122 3078 4.080863 ACCAGTGCTTATTTCTACAGGAGG 60.081 45.833 0.00 0.00 0.00 4.30
2123 3079 4.872691 CACCAGTGCTTATTTCTACAGGAG 59.127 45.833 0.00 0.00 0.00 3.69
2124 3080 4.832248 CACCAGTGCTTATTTCTACAGGA 58.168 43.478 0.00 0.00 0.00 3.86
2138 3094 4.504097 CAAGTTTTTCTTAAGCACCAGTGC 59.496 41.667 14.91 14.91 44.50 4.40
2139 3095 5.043248 CCAAGTTTTTCTTAAGCACCAGTG 58.957 41.667 0.00 0.00 34.66 3.66
2140 3096 4.709886 ACCAAGTTTTTCTTAAGCACCAGT 59.290 37.500 0.00 0.00 34.66 4.00
2141 3097 5.262588 ACCAAGTTTTTCTTAAGCACCAG 57.737 39.130 0.00 0.00 34.66 4.00
2142 3098 5.669164 AACCAAGTTTTTCTTAAGCACCA 57.331 34.783 0.00 0.00 34.66 4.17
2143 3099 8.657074 AATAAACCAAGTTTTTCTTAAGCACC 57.343 30.769 0.00 0.00 37.01 5.01
2150 3106 9.093970 CTTCGGAAAATAAACCAAGTTTTTCTT 57.906 29.630 0.00 0.00 37.89 2.52
2151 3107 7.223971 GCTTCGGAAAATAAACCAAGTTTTTCT 59.776 33.333 0.00 0.00 37.89 2.52
2152 3108 7.010645 TGCTTCGGAAAATAAACCAAGTTTTTC 59.989 33.333 0.00 0.00 37.01 2.29
2153 3109 6.819146 TGCTTCGGAAAATAAACCAAGTTTTT 59.181 30.769 0.00 0.00 37.01 1.94
2154 3110 6.256975 GTGCTTCGGAAAATAAACCAAGTTTT 59.743 34.615 0.00 0.00 37.01 2.43
2155 3111 5.751509 GTGCTTCGGAAAATAAACCAAGTTT 59.248 36.000 0.00 0.00 39.24 2.66
2156 3112 5.068591 AGTGCTTCGGAAAATAAACCAAGTT 59.931 36.000 0.00 0.00 0.00 2.66
2157 3113 4.583073 AGTGCTTCGGAAAATAAACCAAGT 59.417 37.500 0.00 0.00 0.00 3.16
2158 3114 5.048713 AGAGTGCTTCGGAAAATAAACCAAG 60.049 40.000 0.00 0.00 0.00 3.61
2159 3115 4.825085 AGAGTGCTTCGGAAAATAAACCAA 59.175 37.500 0.00 0.00 0.00 3.67
2160 3116 4.394729 AGAGTGCTTCGGAAAATAAACCA 58.605 39.130 0.00 0.00 0.00 3.67
2161 3117 6.490566 TTAGAGTGCTTCGGAAAATAAACC 57.509 37.500 0.00 0.00 0.00 3.27
2162 3118 6.022208 GCTTAGAGTGCTTCGGAAAATAAAC 58.978 40.000 0.00 0.00 0.00 2.01
2163 3119 5.703592 TGCTTAGAGTGCTTCGGAAAATAAA 59.296 36.000 0.00 0.00 0.00 1.40
2164 3120 5.121768 GTGCTTAGAGTGCTTCGGAAAATAA 59.878 40.000 0.00 0.00 0.00 1.40
2165 3121 4.630069 GTGCTTAGAGTGCTTCGGAAAATA 59.370 41.667 0.00 0.00 0.00 1.40
2166 3122 3.437049 GTGCTTAGAGTGCTTCGGAAAAT 59.563 43.478 0.00 0.00 0.00 1.82
2167 3123 2.806244 GTGCTTAGAGTGCTTCGGAAAA 59.194 45.455 0.00 0.00 0.00 2.29
2168 3124 2.413837 GTGCTTAGAGTGCTTCGGAAA 58.586 47.619 0.00 0.00 0.00 3.13
2169 3125 1.337823 GGTGCTTAGAGTGCTTCGGAA 60.338 52.381 0.00 0.00 0.00 4.30
2170 3126 0.246635 GGTGCTTAGAGTGCTTCGGA 59.753 55.000 0.00 0.00 0.00 4.55
2171 3127 0.247736 AGGTGCTTAGAGTGCTTCGG 59.752 55.000 0.00 0.00 0.00 4.30
2172 3128 1.728971 CAAGGTGCTTAGAGTGCTTCG 59.271 52.381 0.00 0.00 0.00 3.79
2173 3129 1.466558 GCAAGGTGCTTAGAGTGCTTC 59.533 52.381 0.00 0.00 40.96 3.86
2174 3130 1.202806 TGCAAGGTGCTTAGAGTGCTT 60.203 47.619 1.43 0.00 45.31 3.91
2175 3131 0.397941 TGCAAGGTGCTTAGAGTGCT 59.602 50.000 1.43 0.00 45.31 4.40
2176 3132 1.457346 ATGCAAGGTGCTTAGAGTGC 58.543 50.000 0.00 0.00 45.31 4.40
2177 3133 2.816087 ACAATGCAAGGTGCTTAGAGTG 59.184 45.455 0.00 0.00 45.31 3.51
2178 3134 3.146104 ACAATGCAAGGTGCTTAGAGT 57.854 42.857 0.00 0.00 45.31 3.24
2179 3135 4.002982 TGTACAATGCAAGGTGCTTAGAG 58.997 43.478 9.81 0.00 45.31 2.43
2180 3136 4.014569 TGTACAATGCAAGGTGCTTAGA 57.985 40.909 9.81 0.00 45.31 2.10
2181 3137 4.726416 CTTGTACAATGCAAGGTGCTTAG 58.274 43.478 9.13 4.87 45.31 2.18
2182 3138 4.764679 CTTGTACAATGCAAGGTGCTTA 57.235 40.909 9.13 0.00 45.31 3.09
2183 3139 3.648339 CTTGTACAATGCAAGGTGCTT 57.352 42.857 9.13 0.00 45.31 3.91
2189 3145 3.758554 ACTAAGGCCTTGTACAATGCAAG 59.241 43.478 29.20 24.25 42.00 4.01
2190 3146 3.505680 CACTAAGGCCTTGTACAATGCAA 59.494 43.478 29.20 16.92 34.30 4.08
2191 3147 3.081061 CACTAAGGCCTTGTACAATGCA 58.919 45.455 29.20 13.85 34.30 3.96
2192 3148 2.423538 CCACTAAGGCCTTGTACAATGC 59.576 50.000 28.77 23.06 0.00 3.56
2266 3439 4.428845 CCAATGCCAGGCTGTCTT 57.571 55.556 14.15 0.00 0.00 3.01
2456 3659 6.435430 TGACTTATGTGCATTGTCCATTAC 57.565 37.500 0.00 0.00 0.00 1.89
2474 3677 5.940470 GGGTCTCTAATCAAACACATGACTT 59.060 40.000 0.00 0.00 30.82 3.01
2568 3772 1.831580 AAATGCTTCTGCCAGGACTC 58.168 50.000 0.00 0.00 38.71 3.36
2600 4970 6.211184 ACTGAATTGGCCTGAAAACATATTGA 59.789 34.615 3.32 0.00 0.00 2.57
2665 5052 7.748683 CGCAATTGTAACAACACTACAACATAT 59.251 33.333 7.40 0.00 40.94 1.78
2843 5241 2.605837 TTGCGATATGGCCTTTACGA 57.394 45.000 3.32 0.00 0.00 3.43
2936 5334 1.603678 GCAAACACATCTTGCCAGTGG 60.604 52.381 4.20 4.20 42.74 4.00
2957 5355 4.443457 GCAGACAAACCTATGATAGCTCCA 60.443 45.833 0.00 0.00 0.00 3.86
2991 5389 9.589111 TCATCTGTATAACTAATTTACGCAACA 57.411 29.630 0.00 0.00 0.00 3.33
3014 5412 1.794714 ATGGGCGTCTAGAAGGTCAT 58.205 50.000 7.81 1.62 0.00 3.06
3130 5551 2.997897 GGAGGAGGCACCGTCTGT 60.998 66.667 0.00 0.00 44.74 3.41
3165 5595 1.000607 TGAGAAACCACGGAAGACTCG 60.001 52.381 0.00 0.00 0.00 4.18
3175 5605 8.604890 GCTAAGTATTTATCACTGAGAAACCAC 58.395 37.037 0.93 3.52 0.00 4.16
3191 5621 9.686683 ATGGAAATCAGTACTTGCTAAGTATTT 57.313 29.630 10.56 8.59 45.05 1.40
3207 5637 4.430007 CACAATCCTGCAATGGAAATCAG 58.570 43.478 0.00 0.00 39.85 2.90
3208 5638 3.196039 CCACAATCCTGCAATGGAAATCA 59.804 43.478 0.00 0.00 39.85 2.57
3299 5735 0.528470 CTTCCACCGTCTCCTCTGTC 59.472 60.000 0.00 0.00 0.00 3.51
3302 5738 1.551452 CTTCTTCCACCGTCTCCTCT 58.449 55.000 0.00 0.00 0.00 3.69
3367 5803 1.671845 CTTCTTCTACCGTCTCCTCCG 59.328 57.143 0.00 0.00 0.00 4.63
3427 5863 7.995488 CCTTCCACTCCTAGTTTTCATCATATT 59.005 37.037 0.00 0.00 0.00 1.28
3458 5894 3.065925 GTCGTTGTAGTTAGGGTATCGCT 59.934 47.826 0.00 0.00 0.00 4.93
3459 5895 3.366719 GTCGTTGTAGTTAGGGTATCGC 58.633 50.000 0.00 0.00 0.00 4.58
3463 5899 2.747446 GACGGTCGTTGTAGTTAGGGTA 59.253 50.000 0.00 0.00 0.00 3.69
3887 6499 5.631481 GCCTAACCATCCAATCAACCTCTAA 60.631 44.000 0.00 0.00 0.00 2.10
3904 6521 2.420687 CCAGATCCTCACTTGCCTAACC 60.421 54.545 0.00 0.00 0.00 2.85
3912 6529 1.194781 ACCACGCCAGATCCTCACTT 61.195 55.000 0.00 0.00 0.00 3.16
3930 6547 6.696441 ACTAGCACTGACTAGGTAATGTAC 57.304 41.667 11.98 0.00 43.34 2.90
3932 6549 7.899648 ATTACTAGCACTGACTAGGTAATGT 57.100 36.000 11.98 0.00 43.34 2.71
3944 6563 9.846248 AAAAGCAAGAAATAATTACTAGCACTG 57.154 29.630 0.00 0.00 0.00 3.66
3998 6657 6.366877 CCAATCAATAGCACAGGTTGAAAAAG 59.633 38.462 0.00 0.00 35.70 2.27
4002 6661 3.193267 GCCAATCAATAGCACAGGTTGAA 59.807 43.478 0.00 0.00 35.70 2.69
4004 6663 2.756760 AGCCAATCAATAGCACAGGTTG 59.243 45.455 0.00 0.00 0.00 3.77
4005 6664 2.756760 CAGCCAATCAATAGCACAGGTT 59.243 45.455 0.00 0.00 0.00 3.50
4006 6665 2.372264 CAGCCAATCAATAGCACAGGT 58.628 47.619 0.00 0.00 0.00 4.00
4007 6666 1.066605 GCAGCCAATCAATAGCACAGG 59.933 52.381 0.00 0.00 0.00 4.00
4008 6667 2.022195 AGCAGCCAATCAATAGCACAG 58.978 47.619 0.00 0.00 0.00 3.66
4010 6669 2.019249 TGAGCAGCCAATCAATAGCAC 58.981 47.619 0.00 0.00 0.00 4.40
4012 6671 2.569059 TCTGAGCAGCCAATCAATAGC 58.431 47.619 0.00 0.00 0.00 2.97
4013 6672 4.386711 TGATCTGAGCAGCCAATCAATAG 58.613 43.478 0.00 0.00 0.00 1.73
4015 6674 3.292492 TGATCTGAGCAGCCAATCAAT 57.708 42.857 0.00 0.00 0.00 2.57
4016 6675 2.751259 GTTGATCTGAGCAGCCAATCAA 59.249 45.455 0.00 8.26 34.80 2.57
4017 6676 2.026542 AGTTGATCTGAGCAGCCAATCA 60.027 45.455 6.14 3.44 0.00 2.57
4019 6678 2.366533 CAGTTGATCTGAGCAGCCAAT 58.633 47.619 6.14 0.00 46.27 3.16
4023 6682 1.818642 AACCAGTTGATCTGAGCAGC 58.181 50.000 1.26 1.26 46.27 5.25
4024 6683 3.144506 ACAAACCAGTTGATCTGAGCAG 58.855 45.455 0.00 0.00 46.27 4.24
4032 6691 7.233348 ACATCTTTGGATAACAAACCAGTTGAT 59.767 33.333 0.00 0.00 43.81 2.57
4095 6762 6.488683 ACAGCAGCAAAATTTGGTAGTACTTA 59.511 34.615 10.23 0.00 39.79 2.24
4096 6763 5.301805 ACAGCAGCAAAATTTGGTAGTACTT 59.698 36.000 10.23 0.00 39.79 2.24
4098 6765 5.121221 ACAGCAGCAAAATTTGGTAGTAC 57.879 39.130 10.23 1.40 39.79 2.73
4099 6766 5.782893 AACAGCAGCAAAATTTGGTAGTA 57.217 34.783 10.23 0.00 39.79 1.82
4100 6767 4.670896 AACAGCAGCAAAATTTGGTAGT 57.329 36.364 10.23 6.99 39.79 2.73
4101 6768 5.294060 ACAAAACAGCAGCAAAATTTGGTAG 59.706 36.000 10.23 6.40 39.79 3.18
4104 6771 4.619437 ACAAAACAGCAGCAAAATTTGG 57.381 36.364 7.89 0.00 33.31 3.28
4105 6772 9.881529 AAATATACAAAACAGCAGCAAAATTTG 57.118 25.926 0.57 0.57 34.75 2.32
4108 6775 8.830201 TGAAATATACAAAACAGCAGCAAAAT 57.170 26.923 0.00 0.00 0.00 1.82
4110 6777 8.710551 CATTGAAATATACAAAACAGCAGCAAA 58.289 29.630 0.00 0.00 0.00 3.68
4111 6778 7.871973 ACATTGAAATATACAAAACAGCAGCAA 59.128 29.630 0.00 0.00 0.00 3.91
4112 6779 7.377398 ACATTGAAATATACAAAACAGCAGCA 58.623 30.769 0.00 0.00 0.00 4.41
4113 6780 7.816945 ACATTGAAATATACAAAACAGCAGC 57.183 32.000 0.00 0.00 0.00 5.25
4144 6811 5.296780 TGACAGTGTGGAAGATTTTCTGAAC 59.703 40.000 0.00 0.00 33.68 3.18
4145 6812 5.436175 TGACAGTGTGGAAGATTTTCTGAA 58.564 37.500 0.00 0.00 33.68 3.02
4146 6813 5.034852 TGACAGTGTGGAAGATTTTCTGA 57.965 39.130 0.00 0.00 33.68 3.27
4149 6816 5.743872 GTGTTTGACAGTGTGGAAGATTTTC 59.256 40.000 0.00 0.00 0.00 2.29
4150 6817 5.184864 TGTGTTTGACAGTGTGGAAGATTTT 59.815 36.000 0.00 0.00 0.00 1.82
4151 6818 4.704540 TGTGTTTGACAGTGTGGAAGATTT 59.295 37.500 0.00 0.00 0.00 2.17
4153 6820 3.884895 TGTGTTTGACAGTGTGGAAGAT 58.115 40.909 0.00 0.00 0.00 2.40
4154 6821 3.342377 TGTGTTTGACAGTGTGGAAGA 57.658 42.857 0.00 0.00 0.00 2.87
4155 6822 4.433186 TTTGTGTTTGACAGTGTGGAAG 57.567 40.909 0.00 0.00 35.44 3.46
4156 6823 4.460731 TGATTTGTGTTTGACAGTGTGGAA 59.539 37.500 0.00 0.00 35.44 3.53
4157 6824 4.013050 TGATTTGTGTTTGACAGTGTGGA 58.987 39.130 0.00 0.00 35.44 4.02
4158 6825 4.104776 GTGATTTGTGTTTGACAGTGTGG 58.895 43.478 0.00 0.00 35.44 4.17
4159 6826 4.794762 CAGTGATTTGTGTTTGACAGTGTG 59.205 41.667 0.00 0.00 35.44 3.82
4160 6827 4.699735 TCAGTGATTTGTGTTTGACAGTGT 59.300 37.500 0.00 0.00 35.44 3.55
4166 7097 8.620116 TGATATCTTCAGTGATTTGTGTTTGA 57.380 30.769 3.98 0.00 0.00 2.69
4173 7104 7.907045 CGTTTCCTTGATATCTTCAGTGATTTG 59.093 37.037 3.98 0.00 35.27 2.32
4180 7111 6.816640 TGGTAACGTTTCCTTGATATCTTCAG 59.183 38.462 22.46 0.00 42.51 3.02
4181 7112 6.703319 TGGTAACGTTTCCTTGATATCTTCA 58.297 36.000 22.46 0.00 42.51 3.02
4182 7113 7.605410 TTGGTAACGTTTCCTTGATATCTTC 57.395 36.000 22.46 0.00 42.51 2.87
4183 7114 7.989416 TTTGGTAACGTTTCCTTGATATCTT 57.011 32.000 22.46 0.00 42.51 2.40
4184 7115 8.047310 AGATTTGGTAACGTTTCCTTGATATCT 58.953 33.333 22.46 17.67 42.51 1.98
4185 7116 8.209917 AGATTTGGTAACGTTTCCTTGATATC 57.790 34.615 22.46 16.20 42.51 1.63
4187 7118 7.162761 TGAGATTTGGTAACGTTTCCTTGATA 58.837 34.615 22.46 1.48 42.51 2.15
4189 7120 5.369833 TGAGATTTGGTAACGTTTCCTTGA 58.630 37.500 22.46 10.31 42.51 3.02
4190 7121 5.682943 TGAGATTTGGTAACGTTTCCTTG 57.317 39.130 22.46 0.00 42.51 3.61
4192 7156 6.942976 TCTATGAGATTTGGTAACGTTTCCT 58.057 36.000 22.46 4.82 42.51 3.36
4218 7182 9.283768 TGAATGTTTATACATGGATCGCTATTT 57.716 29.630 0.00 0.00 44.14 1.40
4249 7217 2.422231 TTGCCCTGTTGTGTGTGCC 61.422 57.895 0.00 0.00 0.00 5.01
4272 7240 9.708222 CTGTCCTAAATTATCTGTCAATTTTCG 57.292 33.333 7.08 0.00 36.99 3.46
4286 7254 7.966339 TCTAAGTGCCTACTGTCCTAAATTA 57.034 36.000 0.00 0.00 37.19 1.40
4287 7255 6.869206 TCTAAGTGCCTACTGTCCTAAATT 57.131 37.500 0.00 0.00 37.19 1.82
4297 7268 4.678309 GCTTCGTGATTCTAAGTGCCTACT 60.678 45.833 0.00 0.00 39.32 2.57
4298 7269 3.552294 GCTTCGTGATTCTAAGTGCCTAC 59.448 47.826 0.00 0.00 0.00 3.18
4420 7396 2.566833 TGCTACCCCATGATATGTGC 57.433 50.000 0.00 0.00 0.00 4.57


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

AutoCloner maintained by Alex Coulton.