Multiple sequence alignment - TraesCS6A01G365700

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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 TraesCS6A01G365700 chr6A 100.000 2495 0 0 1 2495 593776193 593778687 0.000000e+00 4608.0
1 TraesCS6A01G365700 chr6A 86.194 536 59 10 995 1518 593785719 593786251 1.300000e-157 566.0
2 TraesCS6A01G365700 chr6A 81.101 545 57 29 987 1519 593792297 593792807 6.470000e-106 394.0
3 TraesCS6A01G365700 chr6A 78.407 565 70 26 970 1519 593732831 593733358 1.110000e-83 320.0
4 TraesCS6A01G365700 chr6A 81.362 279 33 11 208 475 593791732 593792002 2.510000e-50 209.0
5 TraesCS6A01G365700 chr6A 84.615 117 10 5 212 323 593930675 593930562 2.620000e-20 110.0
6 TraesCS6A01G365700 chr6A 100.000 31 0 0 478 508 593732046 593732076 9.640000e-05 58.4
7 TraesCS6A01G365700 chr6D 84.787 1433 93 38 168 1558 446901225 446902574 0.000000e+00 1323.0
8 TraesCS6A01G365700 chr6D 87.114 551 48 12 992 1519 446934805 446935355 9.870000e-169 603.0
9 TraesCS6A01G365700 chr6D 85.690 580 38 23 1722 2285 446903168 446903718 1.000000e-158 569.0
10 TraesCS6A01G365700 chr6D 80.109 548 74 18 981 1516 446882306 446882830 2.340000e-100 375.0
11 TraesCS6A01G365700 chr6D 90.361 166 11 2 2 167 446901009 446901169 1.940000e-51 213.0
12 TraesCS6A01G365700 chr6D 77.745 337 42 22 1657 1982 447277865 447277551 2.550000e-40 176.0
13 TraesCS6A01G365700 chr6D 79.853 273 24 14 216 474 446947897 446948152 1.190000e-38 171.0
14 TraesCS6A01G365700 chr6D 86.047 129 11 2 1854 1982 447738836 447738957 5.600000e-27 132.0
15 TraesCS6A01G365700 chr6D 84.091 132 14 3 212 342 447214593 447214468 1.210000e-23 121.0
16 TraesCS6A01G365700 chr6D 90.909 88 2 2 1568 1653 446903041 446903124 2.030000e-21 113.0
17 TraesCS6A01G365700 chr6D 89.773 88 5 2 265 352 446728795 446728712 2.620000e-20 110.0
18 TraesCS6A01G365700 chr6D 83.784 111 14 3 227 334 447737168 447737277 4.390000e-18 102.0
19 TraesCS6A01G365700 chr6D 92.157 51 4 0 257 307 447279628 447279578 3.440000e-09 73.1
20 TraesCS6A01G365700 chr6D 100.000 31 0 0 476 506 446881316 446881346 9.640000e-05 58.4
21 TraesCS6A01G365700 chr6D 100.000 29 0 0 481 509 447510999 447510971 1.000000e-03 54.7
22 TraesCS6A01G365700 chr6B 88.773 962 74 19 777 1720 675626947 675626002 0.000000e+00 1147.0
23 TraesCS6A01G365700 chr6B 83.124 557 69 14 995 1539 676123577 676124120 3.730000e-133 484.0
24 TraesCS6A01G365700 chr6B 83.197 488 55 13 996 1474 676136381 676136850 2.970000e-114 422.0
25 TraesCS6A01G365700 chr6B 88.806 268 14 4 445 712 675627196 675626945 5.180000e-82 315.0
26 TraesCS6A01G365700 chr6B 78.625 538 68 26 989 1519 676036440 676036937 1.860000e-81 313.0
27 TraesCS6A01G365700 chr6B 89.212 241 20 3 166 406 675627735 675627501 1.880000e-76 296.0
28 TraesCS6A01G365700 chr6B 91.781 146 12 0 995 1140 675614415 675614270 1.170000e-48 204.0
29 TraesCS6A01G365700 chr6B 81.852 270 24 12 1722 1982 678091776 678091523 1.170000e-48 204.0
30 TraesCS6A01G365700 chr6B 78.797 316 48 10 980 1287 676865799 676865495 7.040000e-46 195.0
31 TraesCS6A01G365700 chr6B 79.856 278 21 16 1712 1972 676037084 676037343 1.190000e-38 171.0
32 TraesCS6A01G365700 chr6B 78.723 282 26 19 1717 1982 677777673 677777410 9.240000e-35 158.0
33 TraesCS6A01G365700 chr6B 78.723 282 27 18 1717 1982 677909954 677909690 9.240000e-35 158.0
34 TraesCS6A01G365700 chr6B 78.369 282 28 18 1717 1982 677087472 677087208 4.300000e-33 152.0
35 TraesCS6A01G365700 chr6B 82.249 169 18 6 205 361 676035627 676035795 4.330000e-28 135.0
36 TraesCS6A01G365700 chr6B 77.122 271 32 20 225 476 677046419 677046160 2.010000e-26 130.0
37 TraesCS6A01G365700 chr6B 84.286 140 12 4 214 347 676731349 676731214 7.240000e-26 128.0
38 TraesCS6A01G365700 chr6B 81.366 161 20 5 1823 1982 676864844 676864693 3.370000e-24 122.0
39 TraesCS6A01G365700 chr6B 91.304 92 3 2 1745 1835 675625842 675625755 1.210000e-23 121.0
40 TraesCS6A01G365700 chr6B 92.308 52 4 0 429 480 677089109 677089058 9.570000e-10 75.0
41 TraesCS6A01G365700 chr6B 91.071 56 4 1 423 477 678354156 678354211 9.570000e-10 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 TraesCS6A01G365700 chr6A 593776193 593778687 2494 False 4608.000000 4608 100.000000 1 2495 1 chr6A.!!$F1 2494
1 TraesCS6A01G365700 chr6A 593785719 593786251 532 False 566.000000 566 86.194000 995 1518 1 chr6A.!!$F2 523
2 TraesCS6A01G365700 chr6A 593791732 593792807 1075 False 301.500000 394 81.231500 208 1519 2 chr6A.!!$F4 1311
3 TraesCS6A01G365700 chr6D 446934805 446935355 550 False 603.000000 603 87.114000 992 1519 1 chr6D.!!$F1 527
4 TraesCS6A01G365700 chr6D 446901009 446903718 2709 False 554.500000 1323 87.936750 2 2285 4 chr6D.!!$F4 2283
5 TraesCS6A01G365700 chr6D 446881316 446882830 1514 False 216.700000 375 90.054500 476 1516 2 chr6D.!!$F3 1040
6 TraesCS6A01G365700 chr6B 676123577 676124120 543 False 484.000000 484 83.124000 995 1539 1 chr6B.!!$F1 544
7 TraesCS6A01G365700 chr6B 675625755 675627735 1980 True 469.750000 1147 89.523750 166 1835 4 chr6B.!!$R7 1669
8 TraesCS6A01G365700 chr6B 676035627 676037343 1716 False 206.333333 313 80.243333 205 1972 3 chr6B.!!$F4 1767

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
976 1944 0.03467 AACATCCCTGCTCTGCTTCC 60.035 55.0 0.0 0.0 0.0 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2154 3801 0.0293 TGTTGCGCAAGTTCAAGAGC 59.971 50.0 25.78 8.94 41.68 4.09 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
26 27 2.729882 CACTTACCAACGAAAGAGACGG 59.270 50.000 0.00 0.00 34.93 4.79
69 70 3.617284 ACCATAATCGAAGGAAACCCAC 58.383 45.455 0.00 0.00 0.00 4.61
102 103 3.556817 TGGCAACAGCGATCAGATT 57.443 47.368 0.00 0.00 46.17 2.40
103 104 2.689553 TGGCAACAGCGATCAGATTA 57.310 45.000 0.00 0.00 46.17 1.75
245 301 3.267900 CCATTACGGCGACTGGTAG 57.732 57.895 16.62 0.00 0.00 3.18
361 429 1.281960 CGTCACGTCGTTCAGGTCT 59.718 57.895 0.00 0.00 0.00 3.85
362 430 0.317603 CGTCACGTCGTTCAGGTCTT 60.318 55.000 0.00 0.00 0.00 3.01
363 431 1.069703 CGTCACGTCGTTCAGGTCTTA 60.070 52.381 0.00 0.00 0.00 2.10
364 432 2.413765 CGTCACGTCGTTCAGGTCTTAT 60.414 50.000 0.00 0.00 0.00 1.73
368 436 4.696877 TCACGTCGTTCAGGTCTTATCTAA 59.303 41.667 0.00 0.00 0.00 2.10
426 506 1.391485 CGCACTCGAGGATGACTTTTG 59.609 52.381 18.41 3.39 38.10 2.44
555 918 4.166011 GCATCGGCAGTTCGGCAC 62.166 66.667 0.00 0.00 41.26 5.01
556 919 2.434884 CATCGGCAGTTCGGCACT 60.435 61.111 0.00 0.00 41.26 4.40
557 920 2.034879 CATCGGCAGTTCGGCACTT 61.035 57.895 0.00 0.00 41.26 3.16
558 921 1.302511 ATCGGCAGTTCGGCACTTT 60.303 52.632 0.00 0.00 41.26 2.66
559 922 0.889186 ATCGGCAGTTCGGCACTTTT 60.889 50.000 0.00 0.00 41.26 2.27
560 923 1.098712 TCGGCAGTTCGGCACTTTTT 61.099 50.000 0.00 0.00 41.26 1.94
573 936 4.159120 GGCACTTTTTCTTACGAATCAGC 58.841 43.478 0.00 0.00 0.00 4.26
588 951 2.356313 AGCGCAGTTCACACGGAG 60.356 61.111 11.47 0.00 0.00 4.63
754 1628 3.615592 GCTGGCATGCATACAATATTGGG 60.616 47.826 21.36 9.54 0.00 4.12
762 1636 4.353489 TGCATACAATATTGGGAGATGGGA 59.647 41.667 19.37 0.93 0.00 4.37
846 1744 1.528129 CCACTGCTTCACTTCTTCCC 58.472 55.000 0.00 0.00 0.00 3.97
878 1814 0.919710 GTTACCAGAATGCCCCTCCT 59.080 55.000 0.00 0.00 31.97 3.69
938 1895 5.698545 CAGTTTACTCTCAACTCTCCCAAAG 59.301 44.000 0.00 0.00 31.83 2.77
958 1915 1.381056 ACCAGGCAACCACAGCAAA 60.381 52.632 0.00 0.00 37.17 3.68
974 1942 1.542492 CAAACATCCCTGCTCTGCTT 58.458 50.000 0.00 0.00 0.00 3.91
975 1943 1.471684 CAAACATCCCTGCTCTGCTTC 59.528 52.381 0.00 0.00 0.00 3.86
976 1944 0.034670 AACATCCCTGCTCTGCTTCC 60.035 55.000 0.00 0.00 0.00 3.46
977 1945 1.523258 CATCCCTGCTCTGCTTCCG 60.523 63.158 0.00 0.00 0.00 4.30
978 1946 2.739996 ATCCCTGCTCTGCTTCCGG 61.740 63.158 0.00 0.00 0.00 5.14
981 1949 4.093291 CTGCTCTGCTTCCGGCCT 62.093 66.667 0.00 0.00 40.92 5.19
1090 2069 4.821589 CCCGCGTCAAGCTCTCCC 62.822 72.222 4.92 0.00 45.59 4.30
1188 2179 2.048222 CGTCGGTCCTGCATGTGT 60.048 61.111 0.00 0.00 0.00 3.72
1527 2541 5.007234 CGTCGACATGCCATAGGAAAATTAA 59.993 40.000 17.16 0.00 0.00 1.40
1597 3068 9.154847 GAAAGAAATTCCCCAAATAATTCACAG 57.845 33.333 0.00 0.00 31.44 3.66
1598 3069 7.186570 AGAAATTCCCCAAATAATTCACAGG 57.813 36.000 0.00 0.00 0.00 4.00
1599 3070 5.357742 AATTCCCCAAATAATTCACAGGC 57.642 39.130 0.00 0.00 0.00 4.85
1608 3079 2.198304 AATTCACAGGCCGGGGTCTC 62.198 60.000 4.63 0.00 0.00 3.36
1642 3115 8.635765 TGCAGAAAATTGGAGTTTTAGAGTAT 57.364 30.769 0.00 0.00 31.80 2.12
1675 3158 2.043450 CGTCCTCTCCCCTCTGCT 60.043 66.667 0.00 0.00 0.00 4.24
1687 3170 0.747255 CCTCTGCTGTGTATACGCCT 59.253 55.000 13.71 0.00 0.00 5.52
1693 3176 1.802880 GCTGTGTATACGCCTGGAGTG 60.803 57.143 13.68 0.00 0.00 3.51
1710 3193 7.719633 GCCTGGAGTGTCTTTTTGGATAATATA 59.280 37.037 0.00 0.00 0.00 0.86
1711 3194 9.799106 CCTGGAGTGTCTTTTTGGATAATATAT 57.201 33.333 0.00 0.00 0.00 0.86
1713 3196 9.573166 TGGAGTGTCTTTTTGGATAATATATGG 57.427 33.333 0.00 0.00 0.00 2.74
1776 3393 4.007644 CTGCTCTGCCCCGTGACA 62.008 66.667 0.00 0.00 0.00 3.58
1781 3398 2.046892 CTGCCCCGTGACAAGAGG 60.047 66.667 0.00 0.00 0.00 3.69
1782 3399 4.329545 TGCCCCGTGACAAGAGGC 62.330 66.667 6.97 6.97 44.13 4.70
1783 3400 4.021925 GCCCCGTGACAAGAGGCT 62.022 66.667 6.67 0.00 40.57 4.58
1784 3401 2.750350 CCCCGTGACAAGAGGCTT 59.250 61.111 0.00 0.00 0.00 4.35
1835 3467 3.243201 CCCAACAACTTTCTGCTTCTGTC 60.243 47.826 0.00 0.00 0.00 3.51
1850 3486 4.021894 GCTTCTGTCTCTGTTTCTGGAGTA 60.022 45.833 0.00 0.00 0.00 2.59
1860 3498 2.145397 TTCTGGAGTACATCTCGCCT 57.855 50.000 0.00 0.00 43.60 5.52
1867 3505 3.368531 GGAGTACATCTCGCCTCTGTTTT 60.369 47.826 0.00 0.00 43.60 2.43
1868 3506 3.589988 AGTACATCTCGCCTCTGTTTTG 58.410 45.455 0.00 0.00 0.00 2.44
1892 3531 3.297391 GGATAAGCTCCGCAAGAGG 57.703 57.895 3.14 0.00 43.46 3.69
1897 3536 2.659610 GCTCCGCAAGAGGTCAGT 59.340 61.111 3.14 0.00 43.46 3.41
1898 3537 1.890894 GCTCCGCAAGAGGTCAGTA 59.109 57.895 3.14 0.00 43.46 2.74
1899 3538 0.458716 GCTCCGCAAGAGGTCAGTAC 60.459 60.000 3.14 0.00 43.46 2.73
1934 3581 2.202570 CCGCTTACTCCGGTCACG 60.203 66.667 0.00 0.00 40.84 4.35
1935 3582 2.879462 CGCTTACTCCGGTCACGC 60.879 66.667 0.00 0.00 39.22 5.34
1936 3583 2.879462 GCTTACTCCGGTCACGCG 60.879 66.667 3.53 3.53 39.22 6.01
1937 3584 2.202570 CTTACTCCGGTCACGCGG 60.203 66.667 12.47 0.00 39.22 6.46
1938 3585 4.424566 TTACTCCGGTCACGCGGC 62.425 66.667 12.47 0.00 39.22 6.53
1982 3629 1.751927 GATCAGGCCAGCCACTTGG 60.752 63.158 12.03 0.00 41.35 3.61
1984 3631 1.578215 ATCAGGCCAGCCACTTGGAT 61.578 55.000 12.03 3.07 40.87 3.41
1994 3641 2.092538 AGCCACTTGGATGGAGATTGAG 60.093 50.000 0.00 0.00 43.02 3.02
2025 3672 3.525268 ATCCCGGCAAAATTTCATGAC 57.475 42.857 0.00 0.00 0.00 3.06
2029 3676 0.366534 GGCAAAATTTCATGACGCGC 59.633 50.000 5.73 0.00 0.00 6.86
2032 3679 0.109781 AAAATTTCATGACGCGCGCT 60.110 45.000 32.58 17.75 0.00 5.92
2065 3712 4.359434 ACTGAGGACTTTTCTTCTTCCC 57.641 45.455 0.00 0.00 0.00 3.97
2137 3784 4.681978 GAAGGACGGCGTGGCAGT 62.682 66.667 21.19 0.00 40.02 4.40
2172 3819 0.993746 CGCTCTTGAACTTGCGCAAC 60.994 55.000 21.02 10.74 41.85 4.17
2205 3859 4.927782 GGTGGGCGCACACAGACA 62.928 66.667 40.65 2.24 43.08 3.41
2231 3885 1.297664 CAGCTGGCTCTTGCTATCAC 58.702 55.000 5.57 0.00 37.81 3.06
2234 3888 2.026449 AGCTGGCTCTTGCTATCACTTT 60.026 45.455 0.00 0.00 37.81 2.66
2237 3891 3.084039 TGGCTCTTGCTATCACTTTTGG 58.916 45.455 0.00 0.00 39.59 3.28
2253 3907 0.965439 TTGGTTCTTGGCCGGAAATG 59.035 50.000 5.05 0.00 0.00 2.32
2254 3908 0.178975 TGGTTCTTGGCCGGAAATGT 60.179 50.000 5.05 0.00 0.00 2.71
2269 3923 0.103937 AATGTGTTGCGTTGGGTTGG 59.896 50.000 0.00 0.00 0.00 3.77
2285 3939 2.161078 TTGGCGCCATGTACGTCAGA 62.161 55.000 33.25 8.24 46.90 3.27
2286 3940 1.227263 GGCGCCATGTACGTCAGAT 60.227 57.895 24.80 0.00 34.67 2.90
2287 3941 0.031585 GGCGCCATGTACGTCAGATA 59.968 55.000 24.80 0.00 34.67 1.98
2288 3942 1.409412 GCGCCATGTACGTCAGATAG 58.591 55.000 0.00 0.00 0.00 2.08
2289 3943 1.269102 GCGCCATGTACGTCAGATAGT 60.269 52.381 0.00 0.00 0.00 2.12
2290 3944 2.031420 GCGCCATGTACGTCAGATAGTA 60.031 50.000 0.00 0.00 0.00 1.82
2291 3945 3.552541 CGCCATGTACGTCAGATAGTAC 58.447 50.000 0.00 10.56 42.43 2.73
2296 3950 4.611310 TGTACGTCAGATAGTACACTGC 57.389 45.455 14.36 0.00 45.49 4.40
2297 3951 4.004982 TGTACGTCAGATAGTACACTGCA 58.995 43.478 14.36 0.00 45.49 4.41
2298 3952 3.489180 ACGTCAGATAGTACACTGCAC 57.511 47.619 0.00 2.54 34.57 4.57
2299 3953 2.817844 ACGTCAGATAGTACACTGCACA 59.182 45.455 0.00 0.00 34.57 4.57
2300 3954 3.172050 CGTCAGATAGTACACTGCACAC 58.828 50.000 0.00 0.00 34.57 3.82
2301 3955 3.512680 GTCAGATAGTACACTGCACACC 58.487 50.000 0.00 0.00 34.57 4.16
2302 3956 2.163613 TCAGATAGTACACTGCACACCG 59.836 50.000 0.00 0.00 34.57 4.94
2303 3957 1.135083 AGATAGTACACTGCACACCGC 60.135 52.381 0.00 0.00 42.89 5.68
2304 3958 0.457853 ATAGTACACTGCACACCGCG 60.458 55.000 0.00 0.00 46.97 6.46
2305 3959 1.798234 TAGTACACTGCACACCGCGT 61.798 55.000 4.92 0.00 46.97 6.01
2309 3963 4.539083 ACTGCACACCGCGTGGAA 62.539 61.111 24.59 0.42 46.30 3.53
2310 3964 3.049674 CTGCACACCGCGTGGAAT 61.050 61.111 24.59 5.91 46.30 3.01
2311 3965 2.593148 TGCACACCGCGTGGAATT 60.593 55.556 24.59 1.48 43.83 2.17
2312 3966 2.128853 CTGCACACCGCGTGGAATTT 62.129 55.000 24.59 0.00 46.30 1.82
2313 3967 1.442017 GCACACCGCGTGGAATTTC 60.442 57.895 24.59 2.62 46.45 2.17
2314 3968 1.209127 CACACCGCGTGGAATTTCC 59.791 57.895 24.59 8.59 42.34 3.13
2315 3969 1.969589 ACACCGCGTGGAATTTCCC 60.970 57.895 24.59 3.74 37.94 3.97
2316 3970 1.674322 CACCGCGTGGAATTTCCCT 60.674 57.895 24.59 0.00 39.21 4.20
2317 3971 1.074248 ACCGCGTGGAATTTCCCTT 59.926 52.632 24.59 0.00 39.21 3.95
2318 3972 0.538746 ACCGCGTGGAATTTCCCTTT 60.539 50.000 24.59 0.00 39.21 3.11
2319 3973 0.601057 CCGCGTGGAATTTCCCTTTT 59.399 50.000 10.20 0.00 35.03 2.27
2320 3974 1.402325 CCGCGTGGAATTTCCCTTTTC 60.402 52.381 10.20 0.00 35.03 2.29
2321 3975 1.539827 CGCGTGGAATTTCCCTTTTCT 59.460 47.619 12.90 0.00 35.03 2.52
2322 3976 2.030274 CGCGTGGAATTTCCCTTTTCTT 60.030 45.455 12.90 0.00 35.03 2.52
2323 3977 3.189702 CGCGTGGAATTTCCCTTTTCTTA 59.810 43.478 12.90 0.00 35.03 2.10
2324 3978 4.142469 CGCGTGGAATTTCCCTTTTCTTAT 60.142 41.667 12.90 0.00 35.03 1.73
2325 3979 5.340803 GCGTGGAATTTCCCTTTTCTTATC 58.659 41.667 12.90 0.00 35.03 1.75
2326 3980 5.569413 CGTGGAATTTCCCTTTTCTTATCG 58.431 41.667 12.90 0.00 35.03 2.92
2327 3981 5.353123 CGTGGAATTTCCCTTTTCTTATCGA 59.647 40.000 12.90 0.00 35.03 3.59
2328 3982 6.128117 CGTGGAATTTCCCTTTTCTTATCGAA 60.128 38.462 12.90 0.00 35.03 3.71
2329 3983 7.027760 GTGGAATTTCCCTTTTCTTATCGAAC 58.972 38.462 12.90 0.00 35.03 3.95
2330 3984 6.128117 TGGAATTTCCCTTTTCTTATCGAACG 60.128 38.462 12.90 0.00 35.03 3.95
2331 3985 6.093082 GGAATTTCCCTTTTCTTATCGAACGA 59.907 38.462 3.89 0.00 0.00 3.85
2332 3986 7.361457 GGAATTTCCCTTTTCTTATCGAACGAA 60.361 37.037 3.89 0.00 0.00 3.85
2333 3987 6.864360 TTTCCCTTTTCTTATCGAACGAAA 57.136 33.333 0.12 0.00 0.00 3.46
2334 3988 6.864360 TTCCCTTTTCTTATCGAACGAAAA 57.136 33.333 14.82 14.82 35.87 2.29
2335 3989 6.864360 TCCCTTTTCTTATCGAACGAAAAA 57.136 33.333 15.79 3.23 36.54 1.94
2336 3990 7.443259 TCCCTTTTCTTATCGAACGAAAAAT 57.557 32.000 15.79 0.00 36.54 1.82
2337 3991 8.550710 TCCCTTTTCTTATCGAACGAAAAATA 57.449 30.769 15.79 6.54 36.54 1.40
2338 3992 9.169592 TCCCTTTTCTTATCGAACGAAAAATAT 57.830 29.630 15.79 0.00 36.54 1.28
2339 3993 9.434559 CCCTTTTCTTATCGAACGAAAAATATC 57.565 33.333 15.79 0.00 36.54 1.63
2340 3994 9.982291 CCTTTTCTTATCGAACGAAAAATATCA 57.018 29.630 15.79 0.65 36.54 2.15
2344 3998 8.987599 TCTTATCGAACGAAAAATATCATTGC 57.012 30.769 0.12 0.00 0.00 3.56
2345 3999 8.608317 TCTTATCGAACGAAAAATATCATTGCA 58.392 29.630 0.12 0.00 0.00 4.08
2346 4000 8.541733 TTATCGAACGAAAAATATCATTGCAC 57.458 30.769 0.12 0.00 0.00 4.57
2347 4001 5.328691 TCGAACGAAAAATATCATTGCACC 58.671 37.500 0.00 0.00 0.00 5.01
2348 4002 5.123186 TCGAACGAAAAATATCATTGCACCT 59.877 36.000 0.00 0.00 0.00 4.00
2349 4003 5.799936 CGAACGAAAAATATCATTGCACCTT 59.200 36.000 0.00 0.00 0.00 3.50
2350 4004 6.307800 CGAACGAAAAATATCATTGCACCTTT 59.692 34.615 0.00 0.00 0.00 3.11
2351 4005 7.148820 CGAACGAAAAATATCATTGCACCTTTT 60.149 33.333 0.00 0.00 0.00 2.27
2352 4006 7.581011 ACGAAAAATATCATTGCACCTTTTC 57.419 32.000 0.00 0.00 0.00 2.29
2353 4007 7.151308 ACGAAAAATATCATTGCACCTTTTCA 58.849 30.769 0.00 0.00 33.14 2.69
2354 4008 7.329226 ACGAAAAATATCATTGCACCTTTTCAG 59.671 33.333 0.00 0.00 33.14 3.02
2355 4009 7.541783 CGAAAAATATCATTGCACCTTTTCAGA 59.458 33.333 0.00 0.00 33.14 3.27
2356 4010 9.374838 GAAAAATATCATTGCACCTTTTCAGAT 57.625 29.630 0.00 0.00 33.55 2.90
2357 4011 8.712285 AAAATATCATTGCACCTTTTCAGATG 57.288 30.769 0.00 0.00 0.00 2.90
2358 4012 7.649533 AATATCATTGCACCTTTTCAGATGA 57.350 32.000 0.00 0.00 0.00 2.92
2359 4013 5.578005 ATCATTGCACCTTTTCAGATGAG 57.422 39.130 0.00 0.00 0.00 2.90
2360 4014 3.192001 TCATTGCACCTTTTCAGATGAGC 59.808 43.478 0.00 0.00 0.00 4.26
2361 4015 1.159285 TGCACCTTTTCAGATGAGCG 58.841 50.000 0.00 0.00 0.00 5.03
2362 4016 1.270785 TGCACCTTTTCAGATGAGCGA 60.271 47.619 0.00 0.00 0.00 4.93
2363 4017 1.806542 GCACCTTTTCAGATGAGCGAA 59.193 47.619 0.00 0.00 0.00 4.70
2364 4018 2.159599 GCACCTTTTCAGATGAGCGAAG 60.160 50.000 0.00 0.00 0.00 3.79
2365 4019 2.417933 CACCTTTTCAGATGAGCGAAGG 59.582 50.000 14.86 14.86 36.92 3.46
2366 4020 2.012673 CCTTTTCAGATGAGCGAAGGG 58.987 52.381 11.13 0.00 32.04 3.95
2367 4021 2.355108 CCTTTTCAGATGAGCGAAGGGA 60.355 50.000 11.13 0.00 32.04 4.20
2368 4022 2.680312 TTTCAGATGAGCGAAGGGAG 57.320 50.000 0.00 0.00 0.00 4.30
2369 4023 1.561643 TTCAGATGAGCGAAGGGAGT 58.438 50.000 0.00 0.00 0.00 3.85
2370 4024 2.437085 TCAGATGAGCGAAGGGAGTA 57.563 50.000 0.00 0.00 0.00 2.59
2371 4025 2.025155 TCAGATGAGCGAAGGGAGTAC 58.975 52.381 0.00 0.00 0.00 2.73
2372 4026 2.028130 CAGATGAGCGAAGGGAGTACT 58.972 52.381 0.00 0.00 0.00 2.73
2373 4027 2.034053 CAGATGAGCGAAGGGAGTACTC 59.966 54.545 14.87 14.87 0.00 2.59
2374 4028 2.025155 GATGAGCGAAGGGAGTACTCA 58.975 52.381 23.91 1.66 41.28 3.41
2375 4029 1.919240 TGAGCGAAGGGAGTACTCAA 58.081 50.000 23.91 0.00 34.59 3.02
2376 4030 1.819288 TGAGCGAAGGGAGTACTCAAG 59.181 52.381 23.91 10.73 34.59 3.02
2377 4031 2.093106 GAGCGAAGGGAGTACTCAAGA 58.907 52.381 23.91 0.00 0.00 3.02
2378 4032 2.691011 GAGCGAAGGGAGTACTCAAGAT 59.309 50.000 23.91 8.70 0.00 2.40
2379 4033 3.884091 GAGCGAAGGGAGTACTCAAGATA 59.116 47.826 23.91 0.00 0.00 1.98
2380 4034 3.633065 AGCGAAGGGAGTACTCAAGATAC 59.367 47.826 23.91 9.24 0.00 2.24
2381 4035 3.380637 GCGAAGGGAGTACTCAAGATACA 59.619 47.826 23.91 0.00 0.00 2.29
2382 4036 4.734108 GCGAAGGGAGTACTCAAGATACAC 60.734 50.000 23.91 4.23 0.00 2.90
2383 4037 4.398358 CGAAGGGAGTACTCAAGATACACA 59.602 45.833 23.91 0.00 0.00 3.72
2384 4038 5.067936 CGAAGGGAGTACTCAAGATACACAT 59.932 44.000 23.91 0.00 0.00 3.21
2385 4039 6.472686 AAGGGAGTACTCAAGATACACATC 57.527 41.667 23.91 2.31 0.00 3.06
2386 4040 4.896482 AGGGAGTACTCAAGATACACATCC 59.104 45.833 23.91 11.07 0.00 3.51
2387 4041 4.261656 GGGAGTACTCAAGATACACATCCG 60.262 50.000 23.91 0.00 0.00 4.18
2388 4042 4.261656 GGAGTACTCAAGATACACATCCGG 60.262 50.000 23.91 0.00 0.00 5.14
2389 4043 3.637229 AGTACTCAAGATACACATCCGGG 59.363 47.826 0.00 0.00 0.00 5.73
2390 4044 1.762957 ACTCAAGATACACATCCGGGG 59.237 52.381 0.00 0.00 0.00 5.73
2391 4045 2.039418 CTCAAGATACACATCCGGGGA 58.961 52.381 0.00 0.00 0.00 4.81
2392 4046 2.036475 CTCAAGATACACATCCGGGGAG 59.964 54.545 0.00 0.00 0.00 4.30
2393 4047 0.759346 AAGATACACATCCGGGGAGC 59.241 55.000 0.00 0.00 0.00 4.70
2394 4048 0.105453 AGATACACATCCGGGGAGCT 60.105 55.000 0.00 0.00 0.00 4.09
2395 4049 0.318762 GATACACATCCGGGGAGCTC 59.681 60.000 4.71 4.71 0.00 4.09
2396 4050 1.122019 ATACACATCCGGGGAGCTCC 61.122 60.000 25.59 25.59 0.00 4.70
2397 4051 2.238319 TACACATCCGGGGAGCTCCT 62.238 60.000 31.36 9.35 35.95 3.69
2398 4052 2.444895 ACATCCGGGGAGCTCCTC 60.445 66.667 31.36 27.90 35.95 3.71
2407 4061 3.560534 GGAGCTCCTCCCTGTTTTC 57.439 57.895 26.25 0.00 44.36 2.29
2408 4062 0.988063 GGAGCTCCTCCCTGTTTTCT 59.012 55.000 26.25 0.00 44.36 2.52
2409 4063 1.352687 GGAGCTCCTCCCTGTTTTCTT 59.647 52.381 26.25 0.00 44.36 2.52
2410 4064 2.616765 GGAGCTCCTCCCTGTTTTCTTC 60.617 54.545 26.25 0.00 44.36 2.87
2411 4065 2.039084 GAGCTCCTCCCTGTTTTCTTCA 59.961 50.000 0.87 0.00 0.00 3.02
2412 4066 2.039613 AGCTCCTCCCTGTTTTCTTCAG 59.960 50.000 0.00 0.00 0.00 3.02
2413 4067 2.039084 GCTCCTCCCTGTTTTCTTCAGA 59.961 50.000 0.00 0.00 35.20 3.27
2414 4068 3.496870 GCTCCTCCCTGTTTTCTTCAGAA 60.497 47.826 0.00 0.00 35.20 3.02
2415 4069 4.718961 CTCCTCCCTGTTTTCTTCAGAAA 58.281 43.478 0.00 0.00 41.77 2.52
2442 4096 9.958234 AAAGAAAGAAAGAAAGAAATACTGAGC 57.042 29.630 0.00 0.00 0.00 4.26
2443 4097 8.682936 AGAAAGAAAGAAAGAAATACTGAGCA 57.317 30.769 0.00 0.00 0.00 4.26
2444 4098 9.294614 AGAAAGAAAGAAAGAAATACTGAGCAT 57.705 29.630 0.00 0.00 0.00 3.79
2447 4101 9.507329 AAGAAAGAAAGAAATACTGAGCATACA 57.493 29.630 0.00 0.00 0.00 2.29
2448 4102 8.940952 AGAAAGAAAGAAATACTGAGCATACAC 58.059 33.333 0.00 0.00 0.00 2.90
2449 4103 8.621532 AAAGAAAGAAATACTGAGCATACACA 57.378 30.769 0.00 0.00 0.00 3.72
2450 4104 8.621532 AAGAAAGAAATACTGAGCATACACAA 57.378 30.769 0.00 0.00 0.00 3.33
2451 4105 8.798859 AGAAAGAAATACTGAGCATACACAAT 57.201 30.769 0.00 0.00 0.00 2.71
2452 4106 9.890629 AGAAAGAAATACTGAGCATACACAATA 57.109 29.630 0.00 0.00 0.00 1.90
2453 4107 9.922305 GAAAGAAATACTGAGCATACACAATAC 57.078 33.333 0.00 0.00 0.00 1.89
2454 4108 9.448438 AAAGAAATACTGAGCATACACAATACA 57.552 29.630 0.00 0.00 0.00 2.29
2455 4109 8.654230 AGAAATACTGAGCATACACAATACAG 57.346 34.615 0.00 0.00 0.00 2.74
2456 4110 7.712639 AGAAATACTGAGCATACACAATACAGG 59.287 37.037 0.00 0.00 0.00 4.00
2457 4111 6.731292 ATACTGAGCATACACAATACAGGA 57.269 37.500 0.00 0.00 0.00 3.86
2458 4112 5.016051 ACTGAGCATACACAATACAGGAG 57.984 43.478 0.00 0.00 0.00 3.69
2459 4113 4.467795 ACTGAGCATACACAATACAGGAGT 59.532 41.667 0.00 0.00 0.00 3.85
2460 4114 5.046304 ACTGAGCATACACAATACAGGAGTT 60.046 40.000 0.00 0.00 0.00 3.01
2461 4115 5.178061 TGAGCATACACAATACAGGAGTTG 58.822 41.667 0.00 0.00 0.00 3.16
2462 4116 4.517285 AGCATACACAATACAGGAGTTGG 58.483 43.478 0.00 0.00 0.00 3.77
2463 4117 3.065371 GCATACACAATACAGGAGTTGGC 59.935 47.826 0.00 0.00 0.00 4.52
2464 4118 2.949177 ACACAATACAGGAGTTGGCA 57.051 45.000 0.00 0.00 0.00 4.92
2465 4119 3.439857 ACACAATACAGGAGTTGGCAT 57.560 42.857 0.00 0.00 0.00 4.40
2466 4120 3.084039 ACACAATACAGGAGTTGGCATG 58.916 45.455 0.00 0.00 0.00 4.06
2467 4121 3.244875 ACACAATACAGGAGTTGGCATGA 60.245 43.478 0.00 0.00 0.00 3.07
2468 4122 3.376234 CACAATACAGGAGTTGGCATGAG 59.624 47.826 0.00 0.00 0.00 2.90
2469 4123 3.009473 ACAATACAGGAGTTGGCATGAGT 59.991 43.478 0.00 0.00 0.00 3.41
2470 4124 4.225042 ACAATACAGGAGTTGGCATGAGTA 59.775 41.667 0.00 0.00 0.00 2.59
2471 4125 4.679373 ATACAGGAGTTGGCATGAGTAG 57.321 45.455 0.00 0.00 0.00 2.57
2472 4126 1.556911 ACAGGAGTTGGCATGAGTAGG 59.443 52.381 0.00 0.00 0.00 3.18
2473 4127 0.543749 AGGAGTTGGCATGAGTAGGC 59.456 55.000 0.00 0.00 0.00 3.93
2474 4128 0.253044 GGAGTTGGCATGAGTAGGCA 59.747 55.000 0.00 0.00 40.01 4.75
2475 4129 1.373570 GAGTTGGCATGAGTAGGCAC 58.626 55.000 0.00 0.00 41.56 5.01
2476 4130 0.987294 AGTTGGCATGAGTAGGCACT 59.013 50.000 0.00 0.00 41.56 4.40
2489 4143 2.647297 GCACTCAGCAACCAAGGC 59.353 61.111 0.00 0.00 44.79 4.35
2490 4144 2.924105 GCACTCAGCAACCAAGGCC 61.924 63.158 0.00 0.00 44.79 5.19
2491 4145 1.228367 CACTCAGCAACCAAGGCCT 60.228 57.895 0.00 0.00 0.00 5.19
2492 4146 0.825010 CACTCAGCAACCAAGGCCTT 60.825 55.000 13.78 13.78 0.00 4.35
2493 4147 0.106015 ACTCAGCAACCAAGGCCTTT 60.106 50.000 17.61 0.00 0.00 3.11
2494 4148 1.043022 CTCAGCAACCAAGGCCTTTT 58.957 50.000 17.61 5.82 0.00 2.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.285756 TCTTTCGTTGGTAAGTGTTGCG 59.714 45.455 0.00 0.00 0.00 4.85
1 2 3.558418 TCTCTTTCGTTGGTAAGTGTTGC 59.442 43.478 0.00 0.00 0.00 4.17
2 3 4.317839 CGTCTCTTTCGTTGGTAAGTGTTG 60.318 45.833 0.00 0.00 0.00 3.33
4 5 3.378339 CGTCTCTTTCGTTGGTAAGTGT 58.622 45.455 0.00 0.00 0.00 3.55
5 6 2.729882 CCGTCTCTTTCGTTGGTAAGTG 59.270 50.000 0.00 0.00 0.00 3.16
6 7 2.865276 GCCGTCTCTTTCGTTGGTAAGT 60.865 50.000 0.00 0.00 0.00 2.24
7 8 1.725164 GCCGTCTCTTTCGTTGGTAAG 59.275 52.381 0.00 0.00 0.00 2.34
8 9 1.606224 GGCCGTCTCTTTCGTTGGTAA 60.606 52.381 0.00 0.00 0.00 2.85
9 10 0.037975 GGCCGTCTCTTTCGTTGGTA 60.038 55.000 0.00 0.00 0.00 3.25
10 11 1.301479 GGCCGTCTCTTTCGTTGGT 60.301 57.895 0.00 0.00 0.00 3.67
11 12 1.301401 TGGCCGTCTCTTTCGTTGG 60.301 57.895 0.00 0.00 0.00 3.77
12 13 1.860078 GTGGCCGTCTCTTTCGTTG 59.140 57.895 0.00 0.00 0.00 4.10
13 14 1.663702 CGTGGCCGTCTCTTTCGTT 60.664 57.895 0.00 0.00 0.00 3.85
69 70 2.586079 CCAGTACGGCTCCGCATG 60.586 66.667 8.41 4.80 44.19 4.06
79 80 0.735978 TGATCGCTGTTGCCAGTACG 60.736 55.000 0.00 0.00 41.02 3.67
90 91 4.177165 AGATGCTCTAATCTGATCGCTG 57.823 45.455 0.00 0.00 35.54 5.18
97 98 3.856521 CCGCGATAAGATGCTCTAATCTG 59.143 47.826 8.23 0.00 36.99 2.90
102 103 0.109735 CGCCGCGATAAGATGCTCTA 60.110 55.000 8.23 0.00 0.00 2.43
103 104 1.372251 CGCCGCGATAAGATGCTCT 60.372 57.895 8.23 0.00 0.00 4.09
151 152 4.166011 GGGAAGCATCGCACGCAC 62.166 66.667 0.60 0.00 38.34 5.34
163 164 3.127533 CGCGCCAAGGAAGGGAAG 61.128 66.667 0.00 0.00 0.00 3.46
194 250 2.171725 GCCGAACATGTAGGCGACC 61.172 63.158 23.79 9.05 41.53 4.79
272 334 2.200337 GCTTGAAACCCGGCCAACT 61.200 57.895 2.24 0.00 0.00 3.16
361 429 4.439057 GTCAGGTTGGCACGATTAGATAA 58.561 43.478 0.00 0.00 0.00 1.75
362 430 3.181469 GGTCAGGTTGGCACGATTAGATA 60.181 47.826 0.00 0.00 0.00 1.98
363 431 2.420129 GGTCAGGTTGGCACGATTAGAT 60.420 50.000 0.00 0.00 0.00 1.98
364 432 1.066430 GGTCAGGTTGGCACGATTAGA 60.066 52.381 0.00 0.00 0.00 2.10
368 436 0.392998 GATGGTCAGGTTGGCACGAT 60.393 55.000 0.00 0.00 0.00 3.73
406 474 1.391485 CAAAAGTCATCCTCGAGTGCG 59.609 52.381 12.31 0.00 39.35 5.34
407 475 2.417719 ACAAAAGTCATCCTCGAGTGC 58.582 47.619 12.31 1.06 0.00 4.40
408 476 3.187227 CCAACAAAAGTCATCCTCGAGTG 59.813 47.826 12.31 4.04 0.00 3.51
410 478 2.744202 CCCAACAAAAGTCATCCTCGAG 59.256 50.000 5.13 5.13 0.00 4.04
426 506 1.304464 CTGGAAGGAAGGCCCCAAC 60.304 63.158 0.00 0.00 34.66 3.77
573 936 0.667487 ATGTCTCCGTGTGAACTGCG 60.667 55.000 0.00 0.00 0.00 5.18
639 1002 5.032220 TCGCTATTGTTCATACAGTACGTG 58.968 41.667 0.00 0.00 35.28 4.49
688 1539 2.151202 TCAGCGTCAAAATTCTGGTCC 58.849 47.619 0.00 0.00 0.00 4.46
762 1636 1.933021 TGGATTCAGGACACGTAGGT 58.067 50.000 0.00 0.00 0.00 3.08
846 1744 2.009774 CTGGTAACTTGAGCGAATGGG 58.990 52.381 0.00 0.00 37.61 4.00
878 1814 3.260884 CCTAGCCGGAATTTATAGAGCCA 59.739 47.826 5.05 0.00 33.16 4.75
938 1895 3.982241 GCTGTGGTTGCCTGGTGC 61.982 66.667 0.00 0.00 41.77 5.01
958 1915 1.606531 GGAAGCAGAGCAGGGATGT 59.393 57.895 0.00 0.00 0.00 3.06
977 1945 2.841988 ATCAGAGAGCGGGAGGCC 60.842 66.667 0.00 0.00 45.17 5.19
978 1946 1.805428 GAGATCAGAGAGCGGGAGGC 61.805 65.000 0.00 0.00 44.05 4.70
979 1947 0.467106 TGAGATCAGAGAGCGGGAGG 60.467 60.000 0.00 0.00 0.00 4.30
980 1948 0.667993 GTGAGATCAGAGAGCGGGAG 59.332 60.000 0.00 0.00 0.00 4.30
981 1949 0.034089 TGTGAGATCAGAGAGCGGGA 60.034 55.000 0.00 0.00 0.00 5.14
1188 2179 3.628982 GGGTGGTTCGTCGGGGAA 61.629 66.667 0.00 0.00 0.00 3.97
1527 2541 4.379302 GGAATTTCCCTCCTATGCTCAT 57.621 45.455 3.89 0.00 0.00 2.90
1608 3079 1.794116 CAATTTTCTGCAGCAAACGGG 59.206 47.619 13.82 3.14 0.00 5.28
1675 3158 1.475280 GACACTCCAGGCGTATACACA 59.525 52.381 3.32 0.00 0.00 3.72
1687 3170 9.573166 CCATATATTATCCAAAAAGACACTCCA 57.427 33.333 0.00 0.00 0.00 3.86
1710 3193 7.462571 TTGCTACTCATGTACGTATATCCAT 57.537 36.000 1.31 0.00 0.00 3.41
1711 3194 6.887626 TTGCTACTCATGTACGTATATCCA 57.112 37.500 1.31 0.00 0.00 3.41
1712 3195 8.648097 CAATTTGCTACTCATGTACGTATATCC 58.352 37.037 1.31 0.00 0.00 2.59
1713 3196 8.648097 CCAATTTGCTACTCATGTACGTATATC 58.352 37.037 1.31 0.00 0.00 1.63
1720 3203 5.874810 TGTCTCCAATTTGCTACTCATGTAC 59.125 40.000 0.00 0.00 0.00 2.90
1762 3378 1.079543 CTCTTGTCACGGGGCAGAG 60.080 63.158 0.00 0.00 0.00 3.35
1776 3393 2.782341 AGGATGGATAAGCAAGCCTCTT 59.218 45.455 0.00 0.00 0.00 2.85
1835 3467 4.667262 CGAGATGTACTCCAGAAACAGAG 58.333 47.826 0.00 0.00 42.18 3.35
1850 3486 1.072331 ACCAAAACAGAGGCGAGATGT 59.928 47.619 0.00 0.00 0.00 3.06
1860 3498 4.394729 AGCTTATCCGAAACCAAAACAGA 58.605 39.130 0.00 0.00 0.00 3.41
1888 3527 2.027007 ACGCTACTGAGTACTGACCTCT 60.027 50.000 0.00 0.00 0.00 3.69
1889 3528 2.352342 GACGCTACTGAGTACTGACCTC 59.648 54.545 0.00 0.00 0.00 3.85
1890 3529 2.027007 AGACGCTACTGAGTACTGACCT 60.027 50.000 0.00 0.00 0.00 3.85
1891 3530 2.352342 GAGACGCTACTGAGTACTGACC 59.648 54.545 0.00 0.00 0.00 4.02
1892 3531 2.029486 CGAGACGCTACTGAGTACTGAC 59.971 54.545 0.00 0.00 0.00 3.51
1893 3532 2.269172 CGAGACGCTACTGAGTACTGA 58.731 52.381 0.00 0.00 0.00 3.41
1894 3533 2.722936 CGAGACGCTACTGAGTACTG 57.277 55.000 0.00 0.00 0.00 2.74
1917 3556 2.202570 CGTGACCGGAGTAAGCGG 60.203 66.667 9.46 0.00 0.00 5.52
1982 3629 0.465705 TCCCGTGCTCAATCTCCATC 59.534 55.000 0.00 0.00 0.00 3.51
1984 3631 0.614697 TCTCCCGTGCTCAATCTCCA 60.615 55.000 0.00 0.00 0.00 3.86
1985 3632 0.537188 TTCTCCCGTGCTCAATCTCC 59.463 55.000 0.00 0.00 0.00 3.71
1986 3633 2.386661 TTTCTCCCGTGCTCAATCTC 57.613 50.000 0.00 0.00 0.00 2.75
1987 3634 2.420687 GGATTTCTCCCGTGCTCAATCT 60.421 50.000 0.00 0.00 35.28 2.40
1988 3635 1.943340 GGATTTCTCCCGTGCTCAATC 59.057 52.381 0.00 0.00 35.28 2.67
1989 3636 2.044123 GGATTTCTCCCGTGCTCAAT 57.956 50.000 0.00 0.00 35.28 2.57
1990 3637 3.551259 GGATTTCTCCCGTGCTCAA 57.449 52.632 0.00 0.00 35.28 3.02
2025 3672 1.208642 TTCATCATCAGTAGCGCGCG 61.209 55.000 28.44 28.44 0.00 6.86
2029 3676 3.067320 TCCTCAGTTCATCATCAGTAGCG 59.933 47.826 0.00 0.00 0.00 4.26
2032 3679 6.611613 AAAGTCCTCAGTTCATCATCAGTA 57.388 37.500 0.00 0.00 0.00 2.74
2065 3712 4.854399 AGAGAGAAGAAATATCACGAGCG 58.146 43.478 0.00 0.00 0.00 5.03
2101 3748 3.733024 TCGCGCCAACAGTAAAAATAG 57.267 42.857 0.00 0.00 0.00 1.73
2149 3796 1.630244 CGCAAGTTCAAGAGCGGGAG 61.630 60.000 0.00 0.00 45.83 4.30
2154 3801 0.029300 TGTTGCGCAAGTTCAAGAGC 59.971 50.000 25.78 8.94 41.68 4.09
2172 3819 3.668447 CCCACCGATCTCCAATATCTTG 58.332 50.000 0.00 0.00 0.00 3.02
2177 3824 1.745890 CGCCCACCGATCTCCAATA 59.254 57.895 0.00 0.00 40.02 1.90
2178 3825 2.505982 CGCCCACCGATCTCCAAT 59.494 61.111 0.00 0.00 40.02 3.16
2179 3826 4.467084 GCGCCCACCGATCTCCAA 62.467 66.667 0.00 0.00 40.02 3.53
2182 3829 4.451150 TGTGCGCCCACCGATCTC 62.451 66.667 4.18 0.00 41.35 2.75
2205 3859 2.511452 AAGAGCCAGCTGTGTCCGT 61.511 57.895 13.81 0.00 0.00 4.69
2231 3885 1.036707 TTCCGGCCAAGAACCAAAAG 58.963 50.000 2.24 0.00 0.00 2.27
2234 3888 0.965439 CATTTCCGGCCAAGAACCAA 59.035 50.000 2.24 0.00 0.00 3.67
2237 3891 0.958822 ACACATTTCCGGCCAAGAAC 59.041 50.000 2.24 0.00 0.00 3.01
2253 3907 2.279186 GCCAACCCAACGCAACAC 60.279 61.111 0.00 0.00 0.00 3.32
2254 3908 3.893763 CGCCAACCCAACGCAACA 61.894 61.111 0.00 0.00 0.00 3.33
2269 3923 1.269102 ACTATCTGACGTACATGGCGC 60.269 52.381 0.00 0.00 0.00 6.53
2285 3939 0.457853 CGCGGTGTGCAGTGTACTAT 60.458 55.000 12.78 0.00 46.97 2.12
2286 3940 1.081041 CGCGGTGTGCAGTGTACTA 60.081 57.895 12.78 0.00 46.97 1.82
2287 3941 2.355837 CGCGGTGTGCAGTGTACT 60.356 61.111 12.78 0.00 46.97 2.73
2288 3942 2.660552 ACGCGGTGTGCAGTGTAC 60.661 61.111 12.47 4.15 46.97 2.90
2289 3943 2.660224 CACGCGGTGTGCAGTGTA 60.660 61.111 12.47 0.00 46.97 2.90
2297 3951 1.969589 GGGAAATTCCACGCGGTGT 60.970 57.895 14.68 0.00 38.64 4.16
2298 3952 1.241315 AAGGGAAATTCCACGCGGTG 61.241 55.000 14.68 6.37 38.64 4.94
2299 3953 0.538746 AAAGGGAAATTCCACGCGGT 60.539 50.000 14.68 0.00 38.64 5.68
2300 3954 0.601057 AAAAGGGAAATTCCACGCGG 59.399 50.000 14.68 0.00 38.64 6.46
2301 3955 1.539827 AGAAAAGGGAAATTCCACGCG 59.460 47.619 14.68 3.53 38.64 6.01
2302 3956 3.660501 AAGAAAAGGGAAATTCCACGC 57.339 42.857 14.68 0.00 38.64 5.34
2303 3957 5.353123 TCGATAAGAAAAGGGAAATTCCACG 59.647 40.000 14.68 3.90 38.64 4.94
2304 3958 6.753107 TCGATAAGAAAAGGGAAATTCCAC 57.247 37.500 14.68 3.46 38.64 4.02
2305 3959 6.128117 CGTTCGATAAGAAAAGGGAAATTCCA 60.128 38.462 14.68 0.00 41.10 3.53
2306 3960 6.093082 TCGTTCGATAAGAAAAGGGAAATTCC 59.907 38.462 2.79 2.79 41.10 3.01
2307 3961 7.068692 TCGTTCGATAAGAAAAGGGAAATTC 57.931 36.000 0.00 0.00 41.10 2.17
2308 3962 7.443259 TTCGTTCGATAAGAAAAGGGAAATT 57.557 32.000 0.00 0.00 41.10 1.82
2309 3963 7.443259 TTTCGTTCGATAAGAAAAGGGAAAT 57.557 32.000 7.65 0.00 41.10 2.17
2310 3964 6.864360 TTTCGTTCGATAAGAAAAGGGAAA 57.136 33.333 7.65 0.00 41.10 3.13
2311 3965 6.864360 TTTTCGTTCGATAAGAAAAGGGAA 57.136 33.333 14.86 0.00 41.10 3.97
2312 3966 6.864360 TTTTTCGTTCGATAAGAAAAGGGA 57.136 33.333 16.85 6.40 42.44 4.20
2313 3967 9.434559 GATATTTTTCGTTCGATAAGAAAAGGG 57.565 33.333 16.85 0.00 42.44 3.95
2314 3968 9.982291 TGATATTTTTCGTTCGATAAGAAAAGG 57.018 29.630 16.85 0.00 42.44 3.11
2318 3972 9.433317 GCAATGATATTTTTCGTTCGATAAGAA 57.567 29.630 0.00 0.00 36.31 2.52
2319 3973 8.608317 TGCAATGATATTTTTCGTTCGATAAGA 58.392 29.630 0.00 0.00 0.00 2.10
2320 3974 8.673275 GTGCAATGATATTTTTCGTTCGATAAG 58.327 33.333 0.00 0.00 0.00 1.73
2321 3975 7.642194 GGTGCAATGATATTTTTCGTTCGATAA 59.358 33.333 0.00 0.00 0.00 1.75
2322 3976 7.011950 AGGTGCAATGATATTTTTCGTTCGATA 59.988 33.333 0.00 0.00 0.00 2.92
2323 3977 5.971202 GGTGCAATGATATTTTTCGTTCGAT 59.029 36.000 0.00 0.00 0.00 3.59
2324 3978 5.123186 AGGTGCAATGATATTTTTCGTTCGA 59.877 36.000 0.00 0.00 0.00 3.71
2325 3979 5.331902 AGGTGCAATGATATTTTTCGTTCG 58.668 37.500 0.00 0.00 0.00 3.95
2326 3980 7.581011 AAAGGTGCAATGATATTTTTCGTTC 57.419 32.000 0.00 0.00 0.00 3.95
2327 3981 7.655328 TGAAAAGGTGCAATGATATTTTTCGTT 59.345 29.630 0.00 0.00 36.41 3.85
2328 3982 7.151308 TGAAAAGGTGCAATGATATTTTTCGT 58.849 30.769 0.00 0.00 36.41 3.85
2329 3983 7.541783 TCTGAAAAGGTGCAATGATATTTTTCG 59.458 33.333 0.00 0.00 36.41 3.46
2330 3984 8.761575 TCTGAAAAGGTGCAATGATATTTTTC 57.238 30.769 0.00 0.00 35.02 2.29
2331 3985 9.158233 CATCTGAAAAGGTGCAATGATATTTTT 57.842 29.630 0.00 0.00 0.00 1.94
2332 3986 8.533657 TCATCTGAAAAGGTGCAATGATATTTT 58.466 29.630 0.00 0.00 0.00 1.82
2333 3987 8.070034 TCATCTGAAAAGGTGCAATGATATTT 57.930 30.769 0.00 0.00 0.00 1.40
2334 3988 7.649533 TCATCTGAAAAGGTGCAATGATATT 57.350 32.000 0.00 0.00 0.00 1.28
2335 3989 6.238953 GCTCATCTGAAAAGGTGCAATGATAT 60.239 38.462 0.00 0.00 0.00 1.63
2336 3990 5.066893 GCTCATCTGAAAAGGTGCAATGATA 59.933 40.000 0.00 0.00 0.00 2.15
2337 3991 4.142227 GCTCATCTGAAAAGGTGCAATGAT 60.142 41.667 0.00 0.00 0.00 2.45
2338 3992 3.192001 GCTCATCTGAAAAGGTGCAATGA 59.808 43.478 0.00 0.00 0.00 2.57
2339 3993 3.508762 GCTCATCTGAAAAGGTGCAATG 58.491 45.455 0.00 0.00 0.00 2.82
2340 3994 2.163010 CGCTCATCTGAAAAGGTGCAAT 59.837 45.455 0.00 0.00 0.00 3.56
2341 3995 1.536766 CGCTCATCTGAAAAGGTGCAA 59.463 47.619 0.00 0.00 0.00 4.08
2342 3996 1.159285 CGCTCATCTGAAAAGGTGCA 58.841 50.000 0.00 0.00 0.00 4.57
2343 3997 1.442769 TCGCTCATCTGAAAAGGTGC 58.557 50.000 0.00 0.00 0.00 5.01
2344 3998 2.417933 CCTTCGCTCATCTGAAAAGGTG 59.582 50.000 7.19 0.00 0.00 4.00
2345 3999 2.616510 CCCTTCGCTCATCTGAAAAGGT 60.617 50.000 11.63 0.00 33.05 3.50
2346 4000 2.012673 CCCTTCGCTCATCTGAAAAGG 58.987 52.381 7.96 7.96 34.38 3.11
2347 4001 2.935201 CTCCCTTCGCTCATCTGAAAAG 59.065 50.000 0.00 0.00 0.00 2.27
2348 4002 2.303022 ACTCCCTTCGCTCATCTGAAAA 59.697 45.455 0.00 0.00 0.00 2.29
2349 4003 1.902508 ACTCCCTTCGCTCATCTGAAA 59.097 47.619 0.00 0.00 0.00 2.69
2350 4004 1.561643 ACTCCCTTCGCTCATCTGAA 58.438 50.000 0.00 0.00 0.00 3.02
2351 4005 2.025155 GTACTCCCTTCGCTCATCTGA 58.975 52.381 0.00 0.00 0.00 3.27
2352 4006 2.028130 AGTACTCCCTTCGCTCATCTG 58.972 52.381 0.00 0.00 0.00 2.90
2353 4007 2.303175 GAGTACTCCCTTCGCTCATCT 58.697 52.381 12.13 0.00 0.00 2.90
2354 4008 2.025155 TGAGTACTCCCTTCGCTCATC 58.975 52.381 20.11 0.00 32.09 2.92
2355 4009 2.145397 TGAGTACTCCCTTCGCTCAT 57.855 50.000 20.11 0.00 32.09 2.90
2356 4010 1.819288 CTTGAGTACTCCCTTCGCTCA 59.181 52.381 20.11 0.00 34.80 4.26
2357 4011 2.093106 TCTTGAGTACTCCCTTCGCTC 58.907 52.381 20.11 0.00 0.00 5.03
2358 4012 2.217510 TCTTGAGTACTCCCTTCGCT 57.782 50.000 20.11 0.00 0.00 4.93
2359 4013 3.380637 TGTATCTTGAGTACTCCCTTCGC 59.619 47.826 20.11 7.38 0.00 4.70
2360 4014 4.398358 TGTGTATCTTGAGTACTCCCTTCG 59.602 45.833 20.11 4.34 0.00 3.79
2361 4015 5.916661 TGTGTATCTTGAGTACTCCCTTC 57.083 43.478 20.11 6.67 0.00 3.46
2362 4016 5.364157 GGATGTGTATCTTGAGTACTCCCTT 59.636 44.000 20.11 5.34 33.68 3.95
2363 4017 4.896482 GGATGTGTATCTTGAGTACTCCCT 59.104 45.833 20.11 4.84 33.68 4.20
2364 4018 4.261656 CGGATGTGTATCTTGAGTACTCCC 60.262 50.000 20.11 8.16 33.68 4.30
2365 4019 4.261656 CCGGATGTGTATCTTGAGTACTCC 60.262 50.000 20.11 4.12 33.68 3.85
2366 4020 4.261656 CCCGGATGTGTATCTTGAGTACTC 60.262 50.000 16.32 16.32 33.68 2.59
2367 4021 3.637229 CCCGGATGTGTATCTTGAGTACT 59.363 47.826 0.73 0.00 33.68 2.73
2368 4022 3.243771 CCCCGGATGTGTATCTTGAGTAC 60.244 52.174 0.73 0.00 33.68 2.73
2369 4023 2.963101 CCCCGGATGTGTATCTTGAGTA 59.037 50.000 0.73 0.00 33.68 2.59
2370 4024 1.762957 CCCCGGATGTGTATCTTGAGT 59.237 52.381 0.73 0.00 33.68 3.41
2371 4025 2.036475 CTCCCCGGATGTGTATCTTGAG 59.964 54.545 0.73 0.00 33.68 3.02
2372 4026 2.039418 CTCCCCGGATGTGTATCTTGA 58.961 52.381 0.73 0.00 33.68 3.02
2373 4027 1.541233 GCTCCCCGGATGTGTATCTTG 60.541 57.143 0.73 0.00 33.68 3.02
2374 4028 0.759346 GCTCCCCGGATGTGTATCTT 59.241 55.000 0.73 0.00 33.68 2.40
2375 4029 0.105453 AGCTCCCCGGATGTGTATCT 60.105 55.000 0.73 0.00 33.68 1.98
2376 4030 0.318762 GAGCTCCCCGGATGTGTATC 59.681 60.000 0.73 0.00 0.00 2.24
2377 4031 1.122019 GGAGCTCCCCGGATGTGTAT 61.122 60.000 23.19 0.00 0.00 2.29
2378 4032 1.760875 GGAGCTCCCCGGATGTGTA 60.761 63.158 23.19 0.00 0.00 2.90
2379 4033 3.083997 GGAGCTCCCCGGATGTGT 61.084 66.667 23.19 0.00 0.00 3.72
2380 4034 2.765807 AGGAGCTCCCCGGATGTG 60.766 66.667 29.54 0.00 36.42 3.21
2381 4035 2.444895 GAGGAGCTCCCCGGATGT 60.445 66.667 29.54 8.83 36.42 3.06
2382 4036 3.237741 GGAGGAGCTCCCCGGATG 61.238 72.222 29.54 0.00 44.36 3.51
2390 4044 2.039084 TGAAGAAAACAGGGAGGAGCTC 59.961 50.000 4.71 4.71 0.00 4.09
2391 4045 2.039613 CTGAAGAAAACAGGGAGGAGCT 59.960 50.000 0.00 0.00 0.00 4.09
2392 4046 2.039084 TCTGAAGAAAACAGGGAGGAGC 59.961 50.000 0.00 0.00 36.22 4.70
2393 4047 4.357918 TTCTGAAGAAAACAGGGAGGAG 57.642 45.455 0.00 0.00 36.22 3.69
2394 4048 4.788925 TTTCTGAAGAAAACAGGGAGGA 57.211 40.909 3.00 0.00 40.68 3.71
2416 4070 9.958234 GCTCAGTATTTCTTTCTTTCTTTCTTT 57.042 29.630 0.00 0.00 0.00 2.52
2417 4071 9.125026 TGCTCAGTATTTCTTTCTTTCTTTCTT 57.875 29.630 0.00 0.00 0.00 2.52
2418 4072 8.682936 TGCTCAGTATTTCTTTCTTTCTTTCT 57.317 30.769 0.00 0.00 0.00 2.52
2421 4075 9.507329 TGTATGCTCAGTATTTCTTTCTTTCTT 57.493 29.630 0.00 0.00 0.00 2.52
2422 4076 8.940952 GTGTATGCTCAGTATTTCTTTCTTTCT 58.059 33.333 0.00 0.00 0.00 2.52
2423 4077 8.721478 TGTGTATGCTCAGTATTTCTTTCTTTC 58.279 33.333 0.00 0.00 0.00 2.62
2424 4078 8.621532 TGTGTATGCTCAGTATTTCTTTCTTT 57.378 30.769 0.00 0.00 0.00 2.52
2425 4079 8.621532 TTGTGTATGCTCAGTATTTCTTTCTT 57.378 30.769 0.00 0.00 0.00 2.52
2426 4080 8.798859 ATTGTGTATGCTCAGTATTTCTTTCT 57.201 30.769 0.00 0.00 0.00 2.52
2427 4081 9.922305 GTATTGTGTATGCTCAGTATTTCTTTC 57.078 33.333 0.00 0.00 0.00 2.62
2428 4082 9.448438 TGTATTGTGTATGCTCAGTATTTCTTT 57.552 29.630 0.00 0.00 0.00 2.52
2429 4083 9.102757 CTGTATTGTGTATGCTCAGTATTTCTT 57.897 33.333 0.00 0.00 0.00 2.52
2430 4084 7.712639 CCTGTATTGTGTATGCTCAGTATTTCT 59.287 37.037 0.00 0.00 0.00 2.52
2431 4085 7.710907 TCCTGTATTGTGTATGCTCAGTATTTC 59.289 37.037 0.00 0.00 0.00 2.17
2432 4086 7.564793 TCCTGTATTGTGTATGCTCAGTATTT 58.435 34.615 0.00 0.00 0.00 1.40
2433 4087 7.124573 TCCTGTATTGTGTATGCTCAGTATT 57.875 36.000 0.00 0.00 0.00 1.89
2434 4088 6.325028 ACTCCTGTATTGTGTATGCTCAGTAT 59.675 38.462 0.00 0.00 0.00 2.12
2435 4089 5.656859 ACTCCTGTATTGTGTATGCTCAGTA 59.343 40.000 0.00 0.00 0.00 2.74
2436 4090 4.467795 ACTCCTGTATTGTGTATGCTCAGT 59.532 41.667 0.00 0.00 0.00 3.41
2437 4091 5.016051 ACTCCTGTATTGTGTATGCTCAG 57.984 43.478 0.00 0.00 0.00 3.35
2438 4092 5.178061 CAACTCCTGTATTGTGTATGCTCA 58.822 41.667 0.00 0.00 0.00 4.26
2439 4093 4.572389 CCAACTCCTGTATTGTGTATGCTC 59.428 45.833 0.00 0.00 0.00 4.26
2440 4094 4.517285 CCAACTCCTGTATTGTGTATGCT 58.483 43.478 0.00 0.00 0.00 3.79
2441 4095 3.065371 GCCAACTCCTGTATTGTGTATGC 59.935 47.826 0.00 0.00 0.00 3.14
2442 4096 4.260985 TGCCAACTCCTGTATTGTGTATG 58.739 43.478 0.00 0.00 0.00 2.39
2443 4097 4.568072 TGCCAACTCCTGTATTGTGTAT 57.432 40.909 0.00 0.00 0.00 2.29
2444 4098 4.019771 TCATGCCAACTCCTGTATTGTGTA 60.020 41.667 0.00 0.00 0.00 2.90
2445 4099 2.949177 TGCCAACTCCTGTATTGTGT 57.051 45.000 0.00 0.00 0.00 3.72
2446 4100 3.346315 TCATGCCAACTCCTGTATTGTG 58.654 45.455 0.00 0.00 0.00 3.33
2447 4101 3.009473 ACTCATGCCAACTCCTGTATTGT 59.991 43.478 0.00 0.00 0.00 2.71
2448 4102 3.614092 ACTCATGCCAACTCCTGTATTG 58.386 45.455 0.00 0.00 0.00 1.90
2449 4103 4.141620 CCTACTCATGCCAACTCCTGTATT 60.142 45.833 0.00 0.00 0.00 1.89
2450 4104 3.389329 CCTACTCATGCCAACTCCTGTAT 59.611 47.826 0.00 0.00 0.00 2.29
2451 4105 2.766263 CCTACTCATGCCAACTCCTGTA 59.234 50.000 0.00 0.00 0.00 2.74
2452 4106 1.556911 CCTACTCATGCCAACTCCTGT 59.443 52.381 0.00 0.00 0.00 4.00
2453 4107 1.745141 GCCTACTCATGCCAACTCCTG 60.745 57.143 0.00 0.00 0.00 3.86
2454 4108 0.543749 GCCTACTCATGCCAACTCCT 59.456 55.000 0.00 0.00 0.00 3.69
2455 4109 0.253044 TGCCTACTCATGCCAACTCC 59.747 55.000 0.00 0.00 0.00 3.85
2456 4110 1.065854 AGTGCCTACTCATGCCAACTC 60.066 52.381 0.00 0.00 28.79 3.01
2457 4111 0.987294 AGTGCCTACTCATGCCAACT 59.013 50.000 0.00 0.00 28.79 3.16
2458 4112 3.558674 AGTGCCTACTCATGCCAAC 57.441 52.632 0.00 0.00 28.79 3.77
2467 4121 0.764890 TTGGTTGCTGAGTGCCTACT 59.235 50.000 0.00 0.00 42.00 2.57
2468 4122 1.160137 CTTGGTTGCTGAGTGCCTAC 58.840 55.000 0.00 0.00 42.00 3.18
2469 4123 0.036732 CCTTGGTTGCTGAGTGCCTA 59.963 55.000 0.00 0.00 42.00 3.93
2470 4124 1.228367 CCTTGGTTGCTGAGTGCCT 60.228 57.895 0.00 0.00 42.00 4.75
2471 4125 2.924105 GCCTTGGTTGCTGAGTGCC 61.924 63.158 0.00 0.00 42.00 5.01
2472 4126 2.647297 GCCTTGGTTGCTGAGTGC 59.353 61.111 0.00 0.00 43.25 4.40
2473 4127 0.825010 AAGGCCTTGGTTGCTGAGTG 60.825 55.000 19.73 0.00 0.00 3.51
2474 4128 0.106015 AAAGGCCTTGGTTGCTGAGT 60.106 50.000 21.33 0.00 0.00 3.41
2475 4129 1.043022 AAAAGGCCTTGGTTGCTGAG 58.957 50.000 21.33 0.00 0.00 3.35
2476 4130 3.222287 AAAAGGCCTTGGTTGCTGA 57.778 47.368 21.33 0.00 0.00 4.26


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

AutoCloner maintained by Alex Coulton.