Multiple sequence alignment - TraesCS2A01G465500

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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 TraesCS2A01G465500 chr2A 100.000 4492 0 0 1 4492 710276627 710272136 0.000000e+00 8296.0
1 TraesCS2A01G465500 chr2A 89.379 885 45 15 2030 2910 710345145 710344306 0.000000e+00 1068.0
2 TraesCS2A01G465500 chr2A 94.382 267 11 1 2205 2471 710345538 710345276 1.500000e-109 407.0
3 TraesCS2A01G465500 chr2A 87.613 331 28 4 3420 3738 710343176 710342847 5.490000e-99 372.0
4 TraesCS2A01G465500 chr2A 84.800 250 12 3 3007 3231 710344256 710344008 1.260000e-55 228.0
5 TraesCS2A01G465500 chr2A 92.857 98 7 0 1889 1986 710345735 710345638 4.680000e-30 143.0
6 TraesCS2A01G465500 chr2A 97.619 42 1 0 1983 2024 53069338 53069297 6.230000e-09 73.1
7 TraesCS2A01G465500 chr2D 93.069 1991 116 10 1 1986 571663323 571661350 0.000000e+00 2892.0
8 TraesCS2A01G465500 chr2D 90.308 1589 103 17 422 1986 571550337 571548776 0.000000e+00 2034.0
9 TraesCS2A01G465500 chr2D 91.117 1092 49 10 2027 3105 571661365 571660309 0.000000e+00 1435.0
10 TraesCS2A01G465500 chr2D 93.476 935 47 8 3420 4345 571660041 571659112 0.000000e+00 1376.0
11 TraesCS2A01G465500 chr2D 95.916 759 26 2 3734 4492 571545619 571544866 0.000000e+00 1225.0
12 TraesCS2A01G465500 chr2D 90.372 779 52 11 2356 3131 571548585 571547827 0.000000e+00 1002.0
13 TraesCS2A01G465500 chr2D 99.361 313 2 0 3420 3732 571546046 571545734 6.520000e-158 568.0
14 TraesCS2A01G465500 chr2D 84.910 391 37 9 1 389 571550707 571550337 4.240000e-100 375.0
15 TraesCS2A01G465500 chr2D 97.849 186 4 0 3109 3294 571546227 571546042 5.610000e-84 322.0
16 TraesCS2A01G465500 chr2D 93.750 208 10 1 2027 2231 571548791 571548584 4.360000e-80 309.0
17 TraesCS2A01G465500 chr2D 94.643 168 8 1 4325 4492 571650215 571650049 4.460000e-65 259.0
18 TraesCS2A01G465500 chr2D 84.653 202 15 11 3109 3294 571660238 571660037 2.130000e-43 187.0
19 TraesCS2A01G465500 chr2D 95.455 44 2 0 3251 3294 571873952 571873909 2.240000e-08 71.3
20 TraesCS2A01G465500 chr2B 91.808 2002 126 14 3 1986 683275568 683273587 0.000000e+00 2754.0
21 TraesCS2A01G465500 chr2B 89.239 1998 146 25 3 1986 683488397 683486455 0.000000e+00 2435.0
22 TraesCS2A01G465500 chr2B 86.121 2003 155 41 1 1986 683690449 683688553 0.000000e+00 2045.0
23 TraesCS2A01G465500 chr2B 90.139 1298 77 25 2026 3294 683385367 683384092 0.000000e+00 1640.0
24 TraesCS2A01G465500 chr2B 88.822 1333 81 27 2026 3294 683273603 683272275 0.000000e+00 1574.0
25 TraesCS2A01G465500 chr2B 91.667 1140 68 16 855 1986 683310130 683309010 0.000000e+00 1554.0
26 TraesCS2A01G465500 chr2B 90.878 1173 64 19 843 1986 683386509 683385351 0.000000e+00 1533.0
27 TraesCS2A01G465500 chr2B 88.593 1166 81 21 850 1986 683592366 683591224 0.000000e+00 1369.0
28 TraesCS2A01G465500 chr2B 92.500 960 51 12 2026 2964 683688569 683687610 0.000000e+00 1354.0
29 TraesCS2A01G465500 chr2B 90.891 1010 50 18 3423 4423 683272273 683271297 0.000000e+00 1317.0
30 TraesCS2A01G465500 chr2B 92.072 946 56 11 2027 2964 683486470 683485536 0.000000e+00 1314.0
31 TraesCS2A01G465500 chr2B 91.143 971 67 15 2342 3294 683308532 683307563 0.000000e+00 1299.0
32 TraesCS2A01G465500 chr2B 90.125 800 70 4 3 793 683311123 683310324 0.000000e+00 1031.0
33 TraesCS2A01G465500 chr2B 91.341 716 45 9 2027 2738 683591239 683590537 0.000000e+00 963.0
34 TraesCS2A01G465500 chr2B 88.774 579 44 16 2736 3294 683590456 683589879 0.000000e+00 689.0
35 TraesCS2A01G465500 chr2B 87.587 572 68 3 4 573 683702742 683702172 0.000000e+00 660.0
36 TraesCS2A01G465500 chr2B 88.267 554 44 10 3422 3964 683483832 683483289 1.050000e-180 643.0
37 TraesCS2A01G465500 chr2B 87.906 554 46 10 3422 3964 683685903 683685360 2.280000e-177 632.0
38 TraesCS2A01G465500 chr2B 92.262 336 21 5 3420 3752 683307567 683307234 5.260000e-129 472.0
39 TraesCS2A01G465500 chr2B 91.964 336 22 5 3420 3752 683589883 683589550 2.450000e-127 466.0
40 TraesCS2A01G465500 chr2B 89.008 373 32 4 3420 3792 683384096 683383733 1.910000e-123 453.0
41 TraesCS2A01G465500 chr2B 91.901 284 17 2 2066 2343 683308975 683308692 4.210000e-105 392.0
42 TraesCS2A01G465500 chr2B 90.299 268 23 2 4102 4369 683383328 683383064 9.250000e-92 348.0
43 TraesCS2A01G465500 chr2B 86.755 302 16 8 2952 3231 683484208 683483909 9.380000e-82 315.0
44 TraesCS2A01G465500 chr2B 86.424 302 17 8 2952 3231 683686279 683685980 4.360000e-80 309.0
45 TraesCS2A01G465500 chr2B 91.189 227 17 3 569 793 683694156 683693931 5.650000e-79 305.0
46 TraesCS2A01G465500 chr2B 84.173 278 30 9 4214 4486 683589383 683589115 1.600000e-64 257.0
47 TraesCS2A01G465500 chr2B 89.385 179 15 4 3787 3963 683383640 683383464 5.850000e-54 222.0
48 TraesCS2A01G465500 chr2B 95.276 127 6 0 3295 3421 329140200 329140074 7.620000e-48 202.0
49 TraesCS2A01G465500 chr2B 95.276 127 6 0 3295 3421 653915260 653915386 7.620000e-48 202.0
50 TraesCS2A01G465500 chr2B 78.063 351 38 17 3665 4007 683747337 683747018 7.670000e-43 185.0
51 TraesCS2A01G465500 chr2B 85.926 135 12 6 1 129 683322675 683322542 2.180000e-28 137.0
52 TraesCS2A01G465500 chr2B 88.136 59 7 0 4002 4060 709435679 709435737 2.240000e-08 71.3
53 TraesCS2A01G465500 chr2B 95.122 41 1 1 1984 2024 657842397 657842436 3.750000e-06 63.9
54 TraesCS2A01G465500 chr4D 83.889 540 70 9 131 667 465604960 465604435 2.410000e-137 499.0
55 TraesCS2A01G465500 chr4A 76.170 684 106 34 127 784 648745888 648745236 1.570000e-79 307.0
56 TraesCS2A01G465500 chr4B 82.445 319 52 4 1029 1345 82277253 82276937 4.430000e-70 276.0
57 TraesCS2A01G465500 chr4B 84.559 136 20 1 1034 1168 652859507 652859372 2.820000e-27 134.0
58 TraesCS2A01G465500 chr6B 96.063 127 5 0 3295 3421 117838592 117838466 1.640000e-49 207.0
59 TraesCS2A01G465500 chr6B 91.216 148 12 1 3287 3434 143751343 143751489 2.740000e-47 200.0
60 TraesCS2A01G465500 chr6B 97.436 39 1 0 1985 2023 27776601 27776563 2.900000e-07 67.6
61 TraesCS2A01G465500 chr3B 92.958 142 9 1 3285 3425 153653571 153653430 5.890000e-49 206.0
62 TraesCS2A01G465500 chr3B 95.312 128 6 0 3295 3422 809457966 809457839 2.120000e-48 204.0
63 TraesCS2A01G465500 chr3B 97.368 38 1 0 1988 2025 59705645 59705682 1.040000e-06 65.8
64 TraesCS2A01G465500 chr3B 95.000 40 2 0 1985 2024 118258958 118258997 3.750000e-06 63.9
65 TraesCS2A01G465500 chr5A 94.656 131 7 0 3295 3425 590920455 590920325 2.120000e-48 204.0
66 TraesCS2A01G465500 chr1D 95.276 127 6 0 3295 3421 407699524 407699398 7.620000e-48 202.0
67 TraesCS2A01G465500 chr1B 93.284 134 9 0 3289 3422 50990078 50990211 9.860000e-47 198.0
68 TraesCS2A01G465500 chr1A 87.302 63 4 4 660 718 549847605 549847543 8.060000e-08 69.4
69 TraesCS2A01G465500 chr1A 95.238 42 1 1 1985 2025 533214875 533214916 1.040000e-06 65.8
70 TraesCS2A01G465500 chr7B 100.000 36 0 0 1989 2024 65459829 65459794 2.900000e-07 67.6
71 TraesCS2A01G465500 chr7A 91.304 46 3 1 1978 2022 287852024 287851979 1.350000e-05 62.1
72 TraesCS2A01G465500 chr6A 93.023 43 1 2 1985 2025 77899550 77899508 1.350000e-05 62.1


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2A01G465500 chr2A 710272136 710276627 4491 True 8296.000000 8296 100.000000 1 4492 1 chr2A.!!$R2 4491
1 TraesCS2A01G465500 chr2A 710342847 710345735 2888 True 443.600000 1068 89.806200 1889 3738 5 chr2A.!!$R3 1849
2 TraesCS2A01G465500 chr2D 571659112 571663323 4211 True 1472.500000 2892 90.578750 1 4345 4 chr2D.!!$R4 4344
3 TraesCS2A01G465500 chr2D 571544866 571550707 5841 True 833.571429 2034 93.209429 1 4492 7 chr2D.!!$R3 4491
4 TraesCS2A01G465500 chr2B 683271297 683275568 4271 True 1881.666667 2754 90.507000 3 4423 3 chr2B.!!$R5 4420
5 TraesCS2A01G465500 chr2B 683483289 683488397 5108 True 1176.750000 2435 89.083250 3 3964 4 chr2B.!!$R8 3961
6 TraesCS2A01G465500 chr2B 683307234 683311123 3889 True 949.600000 1554 91.419600 3 3752 5 chr2B.!!$R6 3749
7 TraesCS2A01G465500 chr2B 683685360 683694156 8796 True 929.000000 2045 88.828000 1 3964 5 chr2B.!!$R10 3963
8 TraesCS2A01G465500 chr2B 683383064 683386509 3445 True 839.200000 1640 89.941800 843 4369 5 chr2B.!!$R7 3526
9 TraesCS2A01G465500 chr2B 683589115 683592366 3251 True 748.800000 1369 88.969000 850 4486 5 chr2B.!!$R9 3636
10 TraesCS2A01G465500 chr2B 683702172 683702742 570 True 660.000000 660 87.587000 4 573 1 chr2B.!!$R3 569
11 TraesCS2A01G465500 chr4D 465604435 465604960 525 True 499.000000 499 83.889000 131 667 1 chr4D.!!$R1 536
12 TraesCS2A01G465500 chr4A 648745236 648745888 652 True 307.000000 307 76.170000 127 784 1 chr4A.!!$R1 657

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
183 3901 0.037017 TCCGGAATTCGCCCTTTTCA 59.963 50.0 0.00 0.00 37.59 2.69 F
769 4512 0.462047 CGCCCATTTCGCTAAGGTCT 60.462 55.0 0.00 0.00 0.00 3.85 F
1858 5795 0.117140 TCTTTGGGGCCTCTCAGAGA 59.883 55.0 3.07 7.26 0.00 3.10 F
3303 11883 0.034059 ACAGACTTCAGCCCTGTTCG 59.966 55.0 0.00 0.00 37.86 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1779 5716 0.038744 AGACCTTGTCCAGCATTGGG 59.961 55.000 0.0 0.0 45.10 4.12 R
2627 7285 0.738762 CACCATCTGACAGCCTCACG 60.739 60.000 0.0 0.0 0.00 4.35 R
3342 11922 0.040067 CCAGCTTCGTGCCTTTTGAC 60.040 55.000 0.0 0.0 44.23 3.18 R
4407 13333 4.916983 TGCTAGATGTGCAAAAACAACT 57.083 36.364 0.0 0.0 37.51 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
61 3770 5.658634 GCTAGAAAAAGAAAGGGATCCCATT 59.341 40.000 32.69 27.08 38.92 3.16
121 3837 1.324383 TTTCTTCCTCCAAAACGGGC 58.676 50.000 0.00 0.00 34.36 6.13
123 3839 1.228429 CTTCCTCCAAAACGGGCCA 60.228 57.895 4.39 0.00 34.36 5.36
129 3847 1.978617 CCAAAACGGGCCAGAGCAT 60.979 57.895 10.86 0.00 42.56 3.79
183 3901 0.037017 TCCGGAATTCGCCCTTTTCA 59.963 50.000 0.00 0.00 37.59 2.69
208 3926 1.558233 GCCCGGTATGAGTATAGCCT 58.442 55.000 0.00 0.00 34.54 4.58
223 3941 9.511272 TGAGTATAGCCTAGTCAAATATTACGA 57.489 33.333 0.00 0.00 0.00 3.43
230 3948 6.759827 GCCTAGTCAAATATTACGACCTTTGA 59.240 38.462 12.18 0.00 35.78 2.69
238 3956 9.893305 CAAATATTACGACCTTTGAAGAACTTT 57.107 29.630 0.00 0.00 31.76 2.66
347 4078 4.699522 GTTCCCTTCTGCGGCGGT 62.700 66.667 9.78 0.00 0.00 5.68
372 4106 0.468226 TCAACACAACCTTCGCCTCT 59.532 50.000 0.00 0.00 0.00 3.69
718 4461 2.479275 GGTTTTCTCTTTTCGTCCGGAG 59.521 50.000 3.06 0.00 0.00 4.63
769 4512 0.462047 CGCCCATTTCGCTAAGGTCT 60.462 55.000 0.00 0.00 0.00 3.85
1032 4944 2.928116 GAGTAAAAGATCCCAACGTCCG 59.072 50.000 0.00 0.00 0.00 4.79
1181 5093 3.465403 CCTCACCCTCAGCCTCCG 61.465 72.222 0.00 0.00 0.00 4.63
1269 5190 2.507102 CTCAACATCCGCGTCGCT 60.507 61.111 16.36 0.00 0.00 4.93
1309 5230 2.362632 CCGGGACCTTCTCCTCGT 60.363 66.667 0.00 0.00 39.39 4.18
1311 5232 1.542187 CCGGGACCTTCTCCTCGTTT 61.542 60.000 0.00 0.00 39.39 3.60
1453 5383 3.095347 GCGAGGGCCCTCCACTTAG 62.095 68.421 40.37 27.73 39.77 2.18
1472 5402 1.442520 CCGTGTTCGCAAAGCCATG 60.443 57.895 0.00 0.00 35.54 3.66
1520 5453 1.433064 GCTCGCTGGAGAGACTCTG 59.567 63.158 10.44 0.00 43.27 3.35
1524 5457 1.603236 CGCTGGAGAGACTCTGCCTT 61.603 60.000 20.01 0.00 33.54 4.35
1686 5619 4.778143 AACAGATGGACCGGCCGC 62.778 66.667 22.85 6.98 40.66 6.53
1694 5627 4.250305 GACCGGCCGCACCCATAT 62.250 66.667 22.85 0.00 33.26 1.78
1695 5628 4.250305 ACCGGCCGCACCCATATC 62.250 66.667 22.85 0.00 33.26 1.63
1696 5629 4.248842 CCGGCCGCACCCATATCA 62.249 66.667 22.85 0.00 33.26 2.15
1697 5630 2.666190 CGGCCGCACCCATATCAG 60.666 66.667 14.67 0.00 33.26 2.90
1698 5631 2.980233 GGCCGCACCCATATCAGC 60.980 66.667 0.00 0.00 0.00 4.26
1699 5632 2.203195 GCCGCACCCATATCAGCA 60.203 61.111 0.00 0.00 0.00 4.41
1779 5716 2.043953 GGGGTGTCCATCTTGGCC 60.044 66.667 0.00 0.00 37.47 5.36
1858 5795 0.117140 TCTTTGGGGCCTCTCAGAGA 59.883 55.000 3.07 7.26 0.00 3.10
1905 5854 2.044555 CGGGAGAGACGCCTGTGTA 61.045 63.158 0.00 0.00 0.00 2.90
1986 5935 5.473504 GTCTCCTTTCCTGCTTGTTCAATTA 59.526 40.000 0.00 0.00 0.00 1.40
1987 5936 5.473504 TCTCCTTTCCTGCTTGTTCAATTAC 59.526 40.000 0.00 0.00 0.00 1.89
1989 5938 4.215399 CCTTTCCTGCTTGTTCAATTACGA 59.785 41.667 0.00 0.00 0.00 3.43
1990 5939 5.106157 CCTTTCCTGCTTGTTCAATTACGAT 60.106 40.000 0.00 0.00 0.00 3.73
1991 5940 6.093495 CCTTTCCTGCTTGTTCAATTACGATA 59.907 38.462 0.00 0.00 0.00 2.92
1992 5941 7.361713 CCTTTCCTGCTTGTTCAATTACGATAA 60.362 37.037 0.00 0.00 0.00 1.75
1993 5942 7.441890 TTCCTGCTTGTTCAATTACGATAAA 57.558 32.000 0.00 0.00 0.00 1.40
1994 5943 7.072177 TCCTGCTTGTTCAATTACGATAAAG 57.928 36.000 0.00 0.00 0.00 1.85
1995 5944 6.093495 TCCTGCTTGTTCAATTACGATAAAGG 59.907 38.462 0.00 0.00 0.00 3.11
1996 5945 6.189677 TGCTTGTTCAATTACGATAAAGGG 57.810 37.500 0.00 0.00 0.00 3.95
1997 5946 5.708230 TGCTTGTTCAATTACGATAAAGGGT 59.292 36.000 0.00 0.00 0.00 4.34
1998 5947 6.207810 TGCTTGTTCAATTACGATAAAGGGTT 59.792 34.615 0.00 0.00 0.00 4.11
1999 5948 7.088272 GCTTGTTCAATTACGATAAAGGGTTT 58.912 34.615 0.00 0.00 0.00 3.27
2000 5949 7.272731 GCTTGTTCAATTACGATAAAGGGTTTC 59.727 37.037 0.00 0.00 0.00 2.78
2001 5950 7.148355 TGTTCAATTACGATAAAGGGTTTCC 57.852 36.000 0.00 0.00 0.00 3.13
2002 5951 6.151480 TGTTCAATTACGATAAAGGGTTTCCC 59.849 38.462 0.00 0.00 45.90 3.97
2021 5970 8.582437 GGTTTCCCCCACTTTATATTATAAAGC 58.418 37.037 25.76 12.65 37.89 3.51
2022 5971 9.138596 GTTTCCCCCACTTTATATTATAAAGCA 57.861 33.333 25.76 8.96 37.89 3.91
2023 5972 9.716556 TTTCCCCCACTTTATATTATAAAGCAA 57.283 29.630 25.76 12.66 37.89 3.91
2024 5973 9.716556 TTCCCCCACTTTATATTATAAAGCAAA 57.283 29.630 25.76 13.84 37.89 3.68
2025 5974 9.890915 TCCCCCACTTTATATTATAAAGCAAAT 57.109 29.630 25.76 11.45 37.89 2.32
2042 5991 5.678132 GCAAATTCCTGCTTGTTCAATTT 57.322 34.783 0.00 0.00 39.34 1.82
2043 5992 6.783892 GCAAATTCCTGCTTGTTCAATTTA 57.216 33.333 0.00 0.00 39.34 1.40
2044 5993 7.368480 GCAAATTCCTGCTTGTTCAATTTAT 57.632 32.000 0.00 0.00 39.34 1.40
2045 5994 7.809665 GCAAATTCCTGCTTGTTCAATTTATT 58.190 30.769 0.00 0.00 39.34 1.40
2052 6001 8.093307 TCCTGCTTGTTCAATTTATTGCAATTA 58.907 29.630 18.75 5.47 37.68 1.40
2074 6034 1.787155 CGGCGAGATTGAACTTATCCG 59.213 52.381 0.00 0.00 0.00 4.18
2143 6614 2.195741 AATGCAGAGCTCAGCTTTGA 57.804 45.000 28.43 11.54 42.32 2.69
2254 6725 2.651382 CATCTCCTTGGGATGCATCA 57.349 50.000 27.25 6.50 34.97 3.07
2477 7134 2.101917 AGATGCATGCCCAGTAAATTGC 59.898 45.455 16.68 0.00 0.00 3.56
2627 7285 2.554893 TCCAATGCTTAAAACGGTGACC 59.445 45.455 0.00 0.00 0.00 4.02
2687 7345 4.867047 TGGTGCACAAAAGTAAACAACATG 59.133 37.500 20.43 0.00 0.00 3.21
2705 7363 5.057843 ACATGTTCATGGCATATCCTTCT 57.942 39.130 15.71 0.00 35.26 2.85
2706 7364 6.191657 ACATGTTCATGGCATATCCTTCTA 57.808 37.500 15.71 0.00 35.26 2.10
2740 7481 3.805108 GCTGATCTGGTAAGCAGGTATGG 60.805 52.174 1.46 0.00 36.91 2.74
2924 7669 3.229697 AGTTTTAGCTTGGTTCTGCCT 57.770 42.857 0.00 0.00 38.35 4.75
2965 9053 0.461870 GCACTGTGATGGTCCGCATA 60.462 55.000 12.86 0.00 0.00 3.14
3024 9117 7.727578 TTTTCTTAGGTTCAGTTTCCCTTTT 57.272 32.000 0.00 0.00 0.00 2.27
3220 11011 8.400947 GCTGAATATGCTCAGATTTTCTTTGTA 58.599 33.333 8.35 0.00 44.82 2.41
3294 11874 7.378966 TCTGTATTTACAAGGACAGACTTCAG 58.621 38.462 0.00 0.00 42.51 3.02
3295 11875 5.932303 TGTATTTACAAGGACAGACTTCAGC 59.068 40.000 0.00 0.00 32.40 4.26
3296 11876 3.402628 TTACAAGGACAGACTTCAGCC 57.597 47.619 0.00 0.00 0.00 4.85
3297 11877 0.398318 ACAAGGACAGACTTCAGCCC 59.602 55.000 0.00 0.00 0.00 5.19
3298 11878 0.689623 CAAGGACAGACTTCAGCCCT 59.310 55.000 0.00 0.00 0.00 5.19
3299 11879 0.689623 AAGGACAGACTTCAGCCCTG 59.310 55.000 0.00 0.00 0.00 4.45
3300 11880 0.472734 AGGACAGACTTCAGCCCTGT 60.473 55.000 0.00 0.00 43.11 4.00
3301 11881 0.398318 GGACAGACTTCAGCCCTGTT 59.602 55.000 0.00 0.00 40.80 3.16
3302 11882 1.609320 GGACAGACTTCAGCCCTGTTC 60.609 57.143 0.00 0.00 40.80 3.18
3303 11883 0.034059 ACAGACTTCAGCCCTGTTCG 59.966 55.000 0.00 0.00 37.86 3.95
3304 11884 0.671781 CAGACTTCAGCCCTGTTCGG 60.672 60.000 0.00 0.00 0.00 4.30
3305 11885 0.832135 AGACTTCAGCCCTGTTCGGA 60.832 55.000 0.00 0.00 33.16 4.55
3306 11886 0.390472 GACTTCAGCCCTGTTCGGAG 60.390 60.000 0.00 0.00 33.16 4.63
3307 11887 0.832135 ACTTCAGCCCTGTTCGGAGA 60.832 55.000 0.00 0.00 33.16 3.71
3308 11888 0.390472 CTTCAGCCCTGTTCGGAGAC 60.390 60.000 0.00 0.00 34.32 3.36
3309 11889 1.827399 TTCAGCCCTGTTCGGAGACC 61.827 60.000 0.00 0.00 34.32 3.85
3310 11890 3.003763 AGCCCTGTTCGGAGACCC 61.004 66.667 0.00 0.00 34.32 4.46
3311 11891 3.319198 GCCCTGTTCGGAGACCCA 61.319 66.667 0.00 0.00 34.32 4.51
3312 11892 2.663196 CCCTGTTCGGAGACCCAC 59.337 66.667 0.00 0.00 34.32 4.61
3313 11893 2.663196 CCTGTTCGGAGACCCACC 59.337 66.667 0.00 0.00 34.32 4.61
3314 11894 2.214216 CCTGTTCGGAGACCCACCA 61.214 63.158 0.00 0.00 34.32 4.17
3315 11895 1.004918 CTGTTCGGAGACCCACCAC 60.005 63.158 0.00 0.00 34.32 4.16
3316 11896 1.458777 TGTTCGGAGACCCACCACT 60.459 57.895 0.00 0.00 34.32 4.00
3317 11897 1.292541 GTTCGGAGACCCACCACTC 59.707 63.158 0.00 0.00 34.32 3.51
3318 11898 1.911766 TTCGGAGACCCACCACTCC 60.912 63.158 0.00 0.00 46.31 3.85
3321 11901 3.069778 GAGACCCACCACTCCACC 58.930 66.667 0.00 0.00 0.00 4.61
3322 11902 1.841556 GAGACCCACCACTCCACCA 60.842 63.158 0.00 0.00 0.00 4.17
3323 11903 2.113243 GAGACCCACCACTCCACCAC 62.113 65.000 0.00 0.00 0.00 4.16
3324 11904 2.039831 ACCCACCACTCCACCACT 60.040 61.111 0.00 0.00 0.00 4.00
3325 11905 2.113243 GACCCACCACTCCACCACTC 62.113 65.000 0.00 0.00 0.00 3.51
3326 11906 1.843376 CCCACCACTCCACCACTCT 60.843 63.158 0.00 0.00 0.00 3.24
3327 11907 1.372683 CCACCACTCCACCACTCTG 59.627 63.158 0.00 0.00 0.00 3.35
3328 11908 1.302033 CACCACTCCACCACTCTGC 60.302 63.158 0.00 0.00 0.00 4.26
3329 11909 1.460305 ACCACTCCACCACTCTGCT 60.460 57.895 0.00 0.00 0.00 4.24
3330 11910 1.294780 CCACTCCACCACTCTGCTC 59.705 63.158 0.00 0.00 0.00 4.26
3331 11911 1.190833 CCACTCCACCACTCTGCTCT 61.191 60.000 0.00 0.00 0.00 4.09
3332 11912 0.246086 CACTCCACCACTCTGCTCTC 59.754 60.000 0.00 0.00 0.00 3.20
3333 11913 1.247419 ACTCCACCACTCTGCTCTCG 61.247 60.000 0.00 0.00 0.00 4.04
3334 11914 0.962855 CTCCACCACTCTGCTCTCGA 60.963 60.000 0.00 0.00 0.00 4.04
3335 11915 0.539669 TCCACCACTCTGCTCTCGAA 60.540 55.000 0.00 0.00 0.00 3.71
3336 11916 0.108898 CCACCACTCTGCTCTCGAAG 60.109 60.000 0.00 0.00 0.00 3.79
3347 11927 2.732412 CTCTCGAAGCTGGAGTCAAA 57.268 50.000 13.13 0.00 33.26 2.69
3348 11928 3.032017 CTCTCGAAGCTGGAGTCAAAA 57.968 47.619 13.13 0.00 33.26 2.44
3349 11929 2.992543 CTCTCGAAGCTGGAGTCAAAAG 59.007 50.000 13.13 1.96 33.26 2.27
3350 11930 2.072298 CTCGAAGCTGGAGTCAAAAGG 58.928 52.381 6.84 0.00 0.00 3.11
3351 11931 0.519077 CGAAGCTGGAGTCAAAAGGC 59.481 55.000 0.00 0.00 0.00 4.35
3352 11932 1.609208 GAAGCTGGAGTCAAAAGGCA 58.391 50.000 0.00 0.00 0.00 4.75
3353 11933 1.268079 GAAGCTGGAGTCAAAAGGCAC 59.732 52.381 0.00 0.00 0.00 5.01
3354 11934 0.886490 AGCTGGAGTCAAAAGGCACG 60.886 55.000 0.00 0.00 0.00 5.34
3355 11935 0.884704 GCTGGAGTCAAAAGGCACGA 60.885 55.000 0.00 0.00 0.00 4.35
3356 11936 1.593196 CTGGAGTCAAAAGGCACGAA 58.407 50.000 0.00 0.00 0.00 3.85
3357 11937 1.532868 CTGGAGTCAAAAGGCACGAAG 59.467 52.381 0.00 0.00 0.00 3.79
3358 11938 0.238553 GGAGTCAAAAGGCACGAAGC 59.761 55.000 0.00 0.00 44.65 3.86
3359 11939 1.230324 GAGTCAAAAGGCACGAAGCT 58.770 50.000 0.00 0.00 44.79 3.74
3360 11940 0.947244 AGTCAAAAGGCACGAAGCTG 59.053 50.000 0.00 0.00 44.79 4.24
3361 11941 0.040067 GTCAAAAGGCACGAAGCTGG 60.040 55.000 0.00 0.00 44.79 4.85
3362 11942 1.172180 TCAAAAGGCACGAAGCTGGG 61.172 55.000 0.00 0.00 44.79 4.45
3363 11943 1.150536 AAAAGGCACGAAGCTGGGA 59.849 52.632 0.00 0.00 44.79 4.37
3364 11944 0.467290 AAAAGGCACGAAGCTGGGAA 60.467 50.000 0.00 0.00 44.79 3.97
3365 11945 0.467290 AAAGGCACGAAGCTGGGAAA 60.467 50.000 0.00 0.00 44.79 3.13
3366 11946 0.890996 AAGGCACGAAGCTGGGAAAG 60.891 55.000 0.00 0.00 44.79 2.62
3367 11947 1.302511 GGCACGAAGCTGGGAAAGA 60.303 57.895 0.00 0.00 44.79 2.52
3368 11948 1.301677 GGCACGAAGCTGGGAAAGAG 61.302 60.000 0.00 0.00 44.79 2.85
3369 11949 0.320771 GCACGAAGCTGGGAAAGAGA 60.321 55.000 0.00 0.00 41.15 3.10
3370 11950 1.677217 GCACGAAGCTGGGAAAGAGAT 60.677 52.381 0.00 0.00 41.15 2.75
3371 11951 2.005451 CACGAAGCTGGGAAAGAGATG 58.995 52.381 0.00 0.00 0.00 2.90
3372 11952 1.012841 CGAAGCTGGGAAAGAGATGC 58.987 55.000 0.00 0.00 0.00 3.91
3373 11953 1.406614 CGAAGCTGGGAAAGAGATGCT 60.407 52.381 0.00 0.00 0.00 3.79
3374 11954 2.287769 GAAGCTGGGAAAGAGATGCTC 58.712 52.381 0.00 0.00 0.00 4.26
3375 11955 0.545646 AGCTGGGAAAGAGATGCTCC 59.454 55.000 0.00 0.00 0.00 4.70
3376 11956 0.254178 GCTGGGAAAGAGATGCTCCA 59.746 55.000 0.00 0.00 0.00 3.86
3377 11957 1.746516 GCTGGGAAAGAGATGCTCCAG 60.747 57.143 0.00 0.00 43.20 3.86
3378 11958 0.254178 TGGGAAAGAGATGCTCCAGC 59.746 55.000 0.00 0.00 42.50 4.85
3379 11959 0.545646 GGGAAAGAGATGCTCCAGCT 59.454 55.000 0.00 0.00 42.66 4.24
3380 11960 1.474855 GGGAAAGAGATGCTCCAGCTC 60.475 57.143 2.47 2.47 45.85 4.09
3381 11961 1.474855 GGAAAGAGATGCTCCAGCTCC 60.475 57.143 6.85 0.00 46.56 4.70
3382 11962 1.485895 GAAAGAGATGCTCCAGCTCCT 59.514 52.381 6.85 0.00 46.56 3.69
3383 11963 1.122227 AAGAGATGCTCCAGCTCCTC 58.878 55.000 6.85 10.76 46.56 3.71
3384 11964 1.108727 AGAGATGCTCCAGCTCCTCG 61.109 60.000 6.85 0.00 46.56 4.63
3385 11965 1.381056 AGATGCTCCAGCTCCTCGT 60.381 57.895 0.00 0.00 42.66 4.18
3386 11966 0.106469 AGATGCTCCAGCTCCTCGTA 60.106 55.000 0.00 0.00 42.66 3.43
3387 11967 0.965439 GATGCTCCAGCTCCTCGTAT 59.035 55.000 0.00 0.00 42.66 3.06
3388 11968 1.342819 GATGCTCCAGCTCCTCGTATT 59.657 52.381 0.00 0.00 42.66 1.89
3389 11969 1.195115 TGCTCCAGCTCCTCGTATTT 58.805 50.000 0.00 0.00 42.66 1.40
3390 11970 1.555075 TGCTCCAGCTCCTCGTATTTT 59.445 47.619 0.00 0.00 42.66 1.82
3391 11971 2.027192 TGCTCCAGCTCCTCGTATTTTT 60.027 45.455 0.00 0.00 42.66 1.94
3392 11972 3.196901 TGCTCCAGCTCCTCGTATTTTTA 59.803 43.478 0.00 0.00 42.66 1.52
3393 11973 3.804873 GCTCCAGCTCCTCGTATTTTTAG 59.195 47.826 0.00 0.00 38.21 1.85
3394 11974 4.372656 CTCCAGCTCCTCGTATTTTTAGG 58.627 47.826 0.00 0.00 0.00 2.69
3395 11975 4.028131 TCCAGCTCCTCGTATTTTTAGGA 58.972 43.478 0.00 0.00 37.07 2.94
3402 11982 5.974108 TCCTCGTATTTTTAGGAGTTGGAG 58.026 41.667 0.00 0.00 34.46 3.86
3403 11983 5.482878 TCCTCGTATTTTTAGGAGTTGGAGT 59.517 40.000 0.00 0.00 34.46 3.85
3404 11984 5.581085 CCTCGTATTTTTAGGAGTTGGAGTG 59.419 44.000 0.00 0.00 31.94 3.51
3405 11985 6.349243 TCGTATTTTTAGGAGTTGGAGTGA 57.651 37.500 0.00 0.00 0.00 3.41
3406 11986 6.161381 TCGTATTTTTAGGAGTTGGAGTGAC 58.839 40.000 0.00 0.00 0.00 3.67
3407 11987 6.014840 TCGTATTTTTAGGAGTTGGAGTGACT 60.015 38.462 0.00 0.00 0.00 3.41
3408 11988 6.310711 CGTATTTTTAGGAGTTGGAGTGACTC 59.689 42.308 3.47 3.47 42.16 3.36
3417 11997 1.592223 GGAGTGACTCCGAACAGGG 59.408 63.158 16.95 0.00 41.08 4.45
3418 11998 1.079750 GAGTGACTCCGAACAGGGC 60.080 63.158 0.00 0.00 41.52 5.19
3419 11999 2.047179 GTGACTCCGAACAGGGCC 60.047 66.667 0.00 0.00 41.52 5.80
3420 12000 2.203788 TGACTCCGAACAGGGCCT 60.204 61.111 0.00 0.00 41.52 5.19
3421 12001 1.841556 TGACTCCGAACAGGGCCTT 60.842 57.895 1.32 0.00 41.52 4.35
3422 12002 1.079057 GACTCCGAACAGGGCCTTC 60.079 63.158 1.32 0.00 41.52 3.46
3423 12003 1.827399 GACTCCGAACAGGGCCTTCA 61.827 60.000 1.32 0.00 41.52 3.02
3563 12155 0.530870 GCCGACCAACTCCTATCTGC 60.531 60.000 0.00 0.00 0.00 4.26
3732 12454 3.452990 TGGTCGGCTGGTCTGAATATTAA 59.547 43.478 0.00 0.00 0.00 1.40
3865 12687 9.627123 CTGGTCAAAATTAAGATGGACCTAATA 57.373 33.333 14.72 0.00 43.94 0.98
3989 12905 7.929941 TGTTAAGCCACATATATGTTGAACA 57.070 32.000 18.56 15.11 39.39 3.18
4007 12923 6.357579 TGAACATGCACCCTTTTCAAATAT 57.642 33.333 0.00 0.00 0.00 1.28
4009 12925 6.873076 TGAACATGCACCCTTTTCAAATATTC 59.127 34.615 0.00 0.00 0.00 1.75
4025 12941 0.180406 ATTCCCTCCGTCCGGAATTG 59.820 55.000 5.23 0.00 44.75 2.32
4051 12967 3.673809 GTCGCGGAAATGGATGTATCTAC 59.326 47.826 6.13 0.00 0.00 2.59
4054 12970 5.184287 TCGCGGAAATGGATGTATCTACATA 59.816 40.000 6.13 0.00 46.20 2.29
4090 13006 6.462073 TTTTCTCGACAAGTAATTCCGAAG 57.538 37.500 0.00 0.00 0.00 3.79
4382 13308 8.390921 AGAAAGAAAAGGGTTGATATAGGACAA 58.609 33.333 0.00 0.00 0.00 3.18
4423 13349 7.096065 GGTCTGAATTAGTTGTTTTTGCACATC 60.096 37.037 0.00 0.00 0.00 3.06
4477 13406 4.735985 TGCAGTTTCACATGATATTGCAC 58.264 39.130 15.15 0.00 41.15 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 3732 5.533154 TCTTTTTCTAGCAACATTTTCCGGA 59.467 36.000 0.00 0.00 0.00 5.14
123 3839 3.157087 ACGAAATCCAAAACCATGCTCT 58.843 40.909 0.00 0.00 0.00 4.09
183 3901 2.859525 TACTCATACCGGGCCGTGGT 62.860 60.000 26.32 20.75 43.62 4.16
208 3926 9.932207 TTCTTCAAAGGTCGTAATATTTGACTA 57.068 29.630 15.83 0.00 40.36 2.59
220 3938 3.312697 GCTCAAAGTTCTTCAAAGGTCGT 59.687 43.478 0.00 0.00 0.00 4.34
223 3941 2.959030 GGGCTCAAAGTTCTTCAAAGGT 59.041 45.455 0.00 0.00 0.00 3.50
230 3948 1.603739 GGCCGGGCTCAAAGTTCTT 60.604 57.895 22.87 0.00 0.00 2.52
238 3956 2.931105 TACTTTGGGCCGGGCTCA 60.931 61.111 28.80 19.86 37.19 4.26
347 4078 2.610374 GCGAAGGTTGTGTTGACTACAA 59.390 45.455 0.00 0.00 38.80 2.41
603 4344 9.965902 ATTGAAATCAGGTAGAACAAGACTATT 57.034 29.630 0.00 0.00 0.00 1.73
646 4387 5.328691 GCCGAAATTTGAACGATAATGACA 58.671 37.500 0.00 0.00 0.00 3.58
702 4445 2.228343 GAGAACTCCGGACGAAAAGAGA 59.772 50.000 0.00 0.00 0.00 3.10
718 4461 7.270579 CGTCATTTCGGAAAATTTTAGGAGAAC 59.729 37.037 7.33 1.72 32.69 3.01
817 4561 1.620739 ATGAGCTGCTCGTGGTGGAT 61.621 55.000 22.75 7.05 32.35 3.41
1181 5093 4.162690 AGCCGAATGGGAGGTCGC 62.163 66.667 0.00 0.00 38.47 5.19
1191 5103 2.423446 GCCTGGATCGAGCCGAAT 59.577 61.111 16.16 0.00 39.99 3.34
1298 5219 0.173708 CCGGAGAAACGAGGAGAAGG 59.826 60.000 0.00 0.00 35.47 3.46
1309 5230 4.735132 CGCAGCGTCCCGGAGAAA 62.735 66.667 6.65 0.00 0.00 2.52
1391 5312 2.743928 GGAAGCTGGGCAGTGTCG 60.744 66.667 0.00 0.00 0.00 4.35
1438 5360 2.692741 GGCTAAGTGGAGGGCCCT 60.693 66.667 29.18 29.18 38.77 5.19
1453 5383 3.267597 ATGGCTTTGCGAACACGGC 62.268 57.895 0.00 0.00 0.00 5.68
1481 5414 0.107165 GAAGGGGACATACCAGCCAC 60.107 60.000 0.00 0.00 41.20 5.01
1488 5421 1.067582 CGAGCGGAAGGGGACATAC 59.932 63.158 0.00 0.00 0.00 2.39
1524 5457 0.249868 GATCGATGTGGCATCCCGAA 60.250 55.000 0.54 0.00 32.84 4.30
1686 5619 1.154197 CGCTGATGCTGATATGGGTG 58.846 55.000 0.00 0.00 36.97 4.61
1694 5627 1.137614 GAGTCGACGCTGATGCTGA 59.862 57.895 12.41 0.00 36.97 4.26
1695 5628 1.875813 GGAGTCGACGCTGATGCTG 60.876 63.158 18.88 0.00 36.97 4.41
1696 5629 2.492090 GGAGTCGACGCTGATGCT 59.508 61.111 18.88 0.00 36.97 3.79
1697 5630 2.583593 GGGAGTCGACGCTGATGC 60.584 66.667 18.88 1.87 0.00 3.91
1698 5631 2.105128 GGGGAGTCGACGCTGATG 59.895 66.667 18.88 0.00 0.00 3.07
1699 5632 2.043852 AGGGGAGTCGACGCTGAT 60.044 61.111 18.88 2.31 0.00 2.90
1779 5716 0.038744 AGACCTTGTCCAGCATTGGG 59.961 55.000 0.00 0.00 45.10 4.12
1995 5944 8.582437 GCTTTATAATATAAAGTGGGGGAAACC 58.418 37.037 25.08 8.44 41.88 3.27
1996 5945 9.138596 TGCTTTATAATATAAAGTGGGGGAAAC 57.861 33.333 25.08 11.77 37.00 2.78
1997 5946 9.716556 TTGCTTTATAATATAAAGTGGGGGAAA 57.283 29.630 25.08 11.64 37.00 3.13
1998 5947 9.716556 TTTGCTTTATAATATAAAGTGGGGGAA 57.283 29.630 25.08 11.16 37.00 3.97
1999 5948 9.890915 ATTTGCTTTATAATATAAAGTGGGGGA 57.109 29.630 25.08 12.02 37.00 4.81
2020 5969 5.678132 AAATTGAACAAGCAGGAATTTGC 57.322 34.783 0.00 0.00 44.41 3.68
2021 5970 7.747357 GCAATAAATTGAACAAGCAGGAATTTG 59.253 33.333 6.87 0.00 40.14 2.32
2022 5971 7.444792 TGCAATAAATTGAACAAGCAGGAATTT 59.555 29.630 6.87 0.00 40.14 1.82
2023 5972 6.935771 TGCAATAAATTGAACAAGCAGGAATT 59.064 30.769 6.87 0.00 40.14 2.17
2024 5973 6.465948 TGCAATAAATTGAACAAGCAGGAAT 58.534 32.000 6.87 0.00 40.14 3.01
2025 5974 5.851720 TGCAATAAATTGAACAAGCAGGAA 58.148 33.333 6.87 0.00 40.14 3.36
2026 5975 5.465532 TGCAATAAATTGAACAAGCAGGA 57.534 34.783 6.87 0.00 40.14 3.86
2027 5976 6.730960 ATTGCAATAAATTGAACAAGCAGG 57.269 33.333 11.02 0.00 40.14 4.85
2028 5977 8.170553 GGTAATTGCAATAAATTGAACAAGCAG 58.829 33.333 13.39 0.00 40.14 4.24
2029 5978 7.148672 CGGTAATTGCAATAAATTGAACAAGCA 60.149 33.333 13.39 0.00 40.14 3.91
2030 5979 7.172757 CGGTAATTGCAATAAATTGAACAAGC 58.827 34.615 13.39 0.00 40.14 4.01
2031 5980 7.673776 GCCGGTAATTGCAATAAATTGAACAAG 60.674 37.037 13.39 2.02 40.14 3.16
2032 5981 6.091441 GCCGGTAATTGCAATAAATTGAACAA 59.909 34.615 13.39 3.13 40.14 2.83
2033 5982 5.578727 GCCGGTAATTGCAATAAATTGAACA 59.421 36.000 13.39 0.00 40.14 3.18
2034 5983 5.276161 CGCCGGTAATTGCAATAAATTGAAC 60.276 40.000 13.39 2.99 40.14 3.18
2035 5984 4.800993 CGCCGGTAATTGCAATAAATTGAA 59.199 37.500 13.39 0.00 40.14 2.69
2036 5985 4.096532 TCGCCGGTAATTGCAATAAATTGA 59.903 37.500 13.39 2.74 40.14 2.57
2037 5986 4.355437 TCGCCGGTAATTGCAATAAATTG 58.645 39.130 13.39 3.23 40.66 2.32
2038 5987 4.336993 TCTCGCCGGTAATTGCAATAAATT 59.663 37.500 13.39 0.00 34.24 1.82
2039 5988 3.880490 TCTCGCCGGTAATTGCAATAAAT 59.120 39.130 13.39 0.00 0.00 1.40
2040 5989 3.271729 TCTCGCCGGTAATTGCAATAAA 58.728 40.909 13.39 0.91 0.00 1.40
2041 5990 2.907634 TCTCGCCGGTAATTGCAATAA 58.092 42.857 13.39 0.00 0.00 1.40
2042 5991 2.605837 TCTCGCCGGTAATTGCAATA 57.394 45.000 13.39 0.00 0.00 1.90
2043 5992 1.967319 ATCTCGCCGGTAATTGCAAT 58.033 45.000 5.99 5.99 0.00 3.56
2044 5993 1.400142 CAATCTCGCCGGTAATTGCAA 59.600 47.619 0.00 0.00 0.00 4.08
2045 5994 1.013596 CAATCTCGCCGGTAATTGCA 58.986 50.000 1.90 0.00 0.00 4.08
2052 6001 2.483188 GGATAAGTTCAATCTCGCCGGT 60.483 50.000 1.90 0.00 0.00 5.28
2074 6034 2.457366 ACAGTTCGACAAGACATCCC 57.543 50.000 0.00 0.00 0.00 3.85
2143 6614 5.247110 ACCATATGTTTATCGATCTCTGCCT 59.753 40.000 0.00 0.00 0.00 4.75
2343 6815 7.936301 TGGCTGAACATGTACTGCATATAAATA 59.064 33.333 15.44 0.00 35.74 1.40
2344 6816 6.772233 TGGCTGAACATGTACTGCATATAAAT 59.228 34.615 15.44 0.00 35.74 1.40
2345 6817 6.118852 TGGCTGAACATGTACTGCATATAAA 58.881 36.000 15.44 0.00 35.74 1.40
2346 6818 5.679601 TGGCTGAACATGTACTGCATATAA 58.320 37.500 15.44 0.00 35.74 0.98
2395 7052 1.133513 TGCTCCACTGTTGGGACATTT 60.134 47.619 0.00 0.00 44.11 2.32
2477 7134 3.450457 AGTTCTTAGGCTCATCACAGAGG 59.550 47.826 0.00 0.00 36.15 3.69
2627 7285 0.738762 CACCATCTGACAGCCTCACG 60.739 60.000 0.00 0.00 0.00 4.35
2687 7345 5.724328 TCGATAGAAGGATATGCCATGAAC 58.276 41.667 0.00 0.00 46.15 3.18
2705 7363 3.749609 CCAGATCAGCATTGCATTCGATA 59.250 43.478 11.91 0.00 0.00 2.92
2706 7364 2.552743 CCAGATCAGCATTGCATTCGAT 59.447 45.455 11.91 6.97 0.00 3.59
2740 7481 5.760253 ACTATTGAGTATGCTAACCATGCAC 59.240 40.000 0.00 0.00 43.59 4.57
2888 7632 8.451908 AGCTAAAACTAAGTCAACTTGAACAT 57.548 30.769 5.66 0.00 37.40 2.71
2924 7669 4.269844 GCCGATTTTTCAGCAAACAAAGAA 59.730 37.500 0.00 0.00 0.00 2.52
2965 9053 2.604046 ACGAAGAACACTGCTGAAGT 57.396 45.000 0.00 0.00 40.93 3.01
3220 11011 3.230134 TGGAGTGCAGGCTAAAATGTTT 58.770 40.909 0.00 0.00 0.00 2.83
3224 11015 2.887151 ACTGGAGTGCAGGCTAAAAT 57.113 45.000 16.69 0.00 0.00 1.82
3294 11874 3.319198 TGGGTCTCCGAACAGGGC 61.319 66.667 0.00 0.00 41.52 5.19
3295 11875 2.663196 GTGGGTCTCCGAACAGGG 59.337 66.667 0.00 0.00 41.52 4.45
3296 11876 2.214216 TGGTGGGTCTCCGAACAGG 61.214 63.158 0.00 0.00 42.97 4.00
3297 11877 1.004918 GTGGTGGGTCTCCGAACAG 60.005 63.158 0.00 0.00 35.24 3.16
3298 11878 1.458777 AGTGGTGGGTCTCCGAACA 60.459 57.895 0.00 0.00 35.24 3.18
3299 11879 1.292541 GAGTGGTGGGTCTCCGAAC 59.707 63.158 0.00 0.00 35.24 3.95
3300 11880 1.911766 GGAGTGGTGGGTCTCCGAA 60.912 63.158 0.00 0.00 40.36 4.30
3301 11881 2.283676 GGAGTGGTGGGTCTCCGA 60.284 66.667 0.00 0.00 40.36 4.55
3304 11884 1.841556 TGGTGGAGTGGTGGGTCTC 60.842 63.158 0.00 0.00 0.00 3.36
3305 11885 2.147387 GTGGTGGAGTGGTGGGTCT 61.147 63.158 0.00 0.00 0.00 3.85
3306 11886 2.113243 GAGTGGTGGAGTGGTGGGTC 62.113 65.000 0.00 0.00 0.00 4.46
3307 11887 2.039831 AGTGGTGGAGTGGTGGGT 60.040 61.111 0.00 0.00 0.00 4.51
3308 11888 1.843376 AGAGTGGTGGAGTGGTGGG 60.843 63.158 0.00 0.00 0.00 4.61
3309 11889 1.372683 CAGAGTGGTGGAGTGGTGG 59.627 63.158 0.00 0.00 0.00 4.61
3310 11890 1.302033 GCAGAGTGGTGGAGTGGTG 60.302 63.158 0.00 0.00 0.00 4.17
3311 11891 1.460305 AGCAGAGTGGTGGAGTGGT 60.460 57.895 0.00 0.00 0.00 4.16
3312 11892 1.190833 AGAGCAGAGTGGTGGAGTGG 61.191 60.000 0.00 0.00 0.00 4.00
3313 11893 0.246086 GAGAGCAGAGTGGTGGAGTG 59.754 60.000 0.00 0.00 0.00 3.51
3314 11894 1.247419 CGAGAGCAGAGTGGTGGAGT 61.247 60.000 0.00 0.00 0.00 3.85
3315 11895 0.962855 TCGAGAGCAGAGTGGTGGAG 60.963 60.000 0.00 0.00 0.00 3.86
3316 11896 0.539669 TTCGAGAGCAGAGTGGTGGA 60.540 55.000 0.00 0.00 0.00 4.02
3317 11897 0.108898 CTTCGAGAGCAGAGTGGTGG 60.109 60.000 0.00 0.00 0.00 4.61
3318 11898 3.415237 CTTCGAGAGCAGAGTGGTG 57.585 57.895 0.00 0.00 0.00 4.17
3328 11908 2.732412 TTTGACTCCAGCTTCGAGAG 57.268 50.000 13.38 6.46 0.00 3.20
3329 11909 2.289072 CCTTTTGACTCCAGCTTCGAGA 60.289 50.000 13.38 0.00 0.00 4.04
3330 11910 2.072298 CCTTTTGACTCCAGCTTCGAG 58.928 52.381 6.10 6.10 0.00 4.04
3331 11911 1.878102 GCCTTTTGACTCCAGCTTCGA 60.878 52.381 0.00 0.00 0.00 3.71
3332 11912 0.519077 GCCTTTTGACTCCAGCTTCG 59.481 55.000 0.00 0.00 0.00 3.79
3333 11913 1.268079 GTGCCTTTTGACTCCAGCTTC 59.732 52.381 0.00 0.00 0.00 3.86
3334 11914 1.322442 GTGCCTTTTGACTCCAGCTT 58.678 50.000 0.00 0.00 0.00 3.74
3335 11915 0.886490 CGTGCCTTTTGACTCCAGCT 60.886 55.000 0.00 0.00 0.00 4.24
3336 11916 0.884704 TCGTGCCTTTTGACTCCAGC 60.885 55.000 0.00 0.00 0.00 4.85
3337 11917 1.532868 CTTCGTGCCTTTTGACTCCAG 59.467 52.381 0.00 0.00 0.00 3.86
3338 11918 1.593196 CTTCGTGCCTTTTGACTCCA 58.407 50.000 0.00 0.00 0.00 3.86
3339 11919 0.238553 GCTTCGTGCCTTTTGACTCC 59.761 55.000 0.00 0.00 35.15 3.85
3340 11920 1.069636 CAGCTTCGTGCCTTTTGACTC 60.070 52.381 0.00 0.00 44.23 3.36
3341 11921 0.947244 CAGCTTCGTGCCTTTTGACT 59.053 50.000 0.00 0.00 44.23 3.41
3342 11922 0.040067 CCAGCTTCGTGCCTTTTGAC 60.040 55.000 0.00 0.00 44.23 3.18
3343 11923 1.172180 CCCAGCTTCGTGCCTTTTGA 61.172 55.000 0.00 0.00 44.23 2.69
3344 11924 1.172180 TCCCAGCTTCGTGCCTTTTG 61.172 55.000 0.00 0.00 44.23 2.44
3345 11925 0.467290 TTCCCAGCTTCGTGCCTTTT 60.467 50.000 0.00 0.00 44.23 2.27
3346 11926 0.467290 TTTCCCAGCTTCGTGCCTTT 60.467 50.000 0.00 0.00 44.23 3.11
3347 11927 0.890996 CTTTCCCAGCTTCGTGCCTT 60.891 55.000 0.00 0.00 44.23 4.35
3348 11928 1.302832 CTTTCCCAGCTTCGTGCCT 60.303 57.895 0.00 0.00 44.23 4.75
3349 11929 1.301677 CTCTTTCCCAGCTTCGTGCC 61.302 60.000 0.00 0.00 44.23 5.01
3350 11930 0.320771 TCTCTTTCCCAGCTTCGTGC 60.321 55.000 0.00 0.00 43.29 5.34
3351 11931 2.005451 CATCTCTTTCCCAGCTTCGTG 58.995 52.381 0.00 0.00 0.00 4.35
3352 11932 1.677217 GCATCTCTTTCCCAGCTTCGT 60.677 52.381 0.00 0.00 0.00 3.85
3353 11933 1.012841 GCATCTCTTTCCCAGCTTCG 58.987 55.000 0.00 0.00 0.00 3.79
3354 11934 2.287769 GAGCATCTCTTTCCCAGCTTC 58.712 52.381 0.00 0.00 31.61 3.86
3355 11935 1.064832 GGAGCATCTCTTTCCCAGCTT 60.065 52.381 0.00 0.00 33.73 3.74
3356 11936 0.545646 GGAGCATCTCTTTCCCAGCT 59.454 55.000 0.00 0.00 33.73 4.24
3357 11937 0.254178 TGGAGCATCTCTTTCCCAGC 59.746 55.000 0.00 0.00 33.73 4.85
3358 11938 1.746516 GCTGGAGCATCTCTTTCCCAG 60.747 57.143 0.00 0.00 42.88 4.45
3359 11939 0.254178 GCTGGAGCATCTCTTTCCCA 59.746 55.000 0.00 0.00 41.59 4.37
3360 11940 0.545646 AGCTGGAGCATCTCTTTCCC 59.454 55.000 0.65 0.00 45.16 3.97
3361 11941 1.474855 GGAGCTGGAGCATCTCTTTCC 60.475 57.143 0.00 0.00 45.16 3.13
3362 11942 1.485895 AGGAGCTGGAGCATCTCTTTC 59.514 52.381 0.00 0.00 45.16 2.62
3363 11943 1.485895 GAGGAGCTGGAGCATCTCTTT 59.514 52.381 0.00 0.00 45.16 2.52
3364 11944 1.122227 GAGGAGCTGGAGCATCTCTT 58.878 55.000 0.00 0.00 45.16 2.85
3365 11945 1.108727 CGAGGAGCTGGAGCATCTCT 61.109 60.000 14.87 2.67 45.16 3.10
3366 11946 1.363443 CGAGGAGCTGGAGCATCTC 59.637 63.158 0.00 6.34 45.16 2.75
3367 11947 0.106469 TACGAGGAGCTGGAGCATCT 60.106 55.000 0.00 0.00 45.16 2.90
3368 11948 0.965439 ATACGAGGAGCTGGAGCATC 59.035 55.000 0.00 0.00 45.16 3.91
3369 11949 1.418334 AATACGAGGAGCTGGAGCAT 58.582 50.000 0.00 0.00 45.16 3.79
3370 11950 1.195115 AAATACGAGGAGCTGGAGCA 58.805 50.000 0.00 0.00 45.16 4.26
3371 11951 2.317530 AAAATACGAGGAGCTGGAGC 57.682 50.000 0.00 0.00 42.49 4.70
3372 11952 4.099573 TCCTAAAAATACGAGGAGCTGGAG 59.900 45.833 0.00 0.00 34.36 3.86
3373 11953 4.028131 TCCTAAAAATACGAGGAGCTGGA 58.972 43.478 0.00 0.00 34.36 3.86
3374 11954 4.402056 TCCTAAAAATACGAGGAGCTGG 57.598 45.455 0.00 0.00 34.36 4.85
3379 11959 5.482878 ACTCCAACTCCTAAAAATACGAGGA 59.517 40.000 0.00 0.00 37.02 3.71
3380 11960 5.581085 CACTCCAACTCCTAAAAATACGAGG 59.419 44.000 0.00 0.00 0.00 4.63
3381 11961 6.310711 GTCACTCCAACTCCTAAAAATACGAG 59.689 42.308 0.00 0.00 0.00 4.18
3382 11962 6.014840 AGTCACTCCAACTCCTAAAAATACGA 60.015 38.462 0.00 0.00 0.00 3.43
3383 11963 6.164176 AGTCACTCCAACTCCTAAAAATACG 58.836 40.000 0.00 0.00 0.00 3.06
3384 11964 7.598189 GAGTCACTCCAACTCCTAAAAATAC 57.402 40.000 0.00 0.00 37.72 1.89
3399 11979 1.592223 CCCTGTTCGGAGTCACTCC 59.408 63.158 14.67 14.67 46.44 3.85
3400 11980 1.079750 GCCCTGTTCGGAGTCACTC 60.080 63.158 0.00 0.00 33.16 3.51
3401 11981 2.584391 GGCCCTGTTCGGAGTCACT 61.584 63.158 0.00 0.00 33.16 3.41
3402 11982 2.047179 GGCCCTGTTCGGAGTCAC 60.047 66.667 0.00 0.00 33.16 3.67
3403 11983 1.827399 GAAGGCCCTGTTCGGAGTCA 61.827 60.000 0.00 0.00 33.16 3.41
3404 11984 1.079057 GAAGGCCCTGTTCGGAGTC 60.079 63.158 0.00 0.00 33.16 3.36
3405 11985 1.201429 ATGAAGGCCCTGTTCGGAGT 61.201 55.000 0.00 0.00 33.16 3.85
3406 11986 0.830648 TATGAAGGCCCTGTTCGGAG 59.169 55.000 0.00 0.00 33.16 4.63
3407 11987 1.416401 GATATGAAGGCCCTGTTCGGA 59.584 52.381 0.00 0.00 33.16 4.55
3408 11988 1.417890 AGATATGAAGGCCCTGTTCGG 59.582 52.381 0.00 0.00 0.00 4.30
3409 11989 2.158900 ACAGATATGAAGGCCCTGTTCG 60.159 50.000 0.00 0.00 34.79 3.95
3410 11990 3.567478 ACAGATATGAAGGCCCTGTTC 57.433 47.619 0.00 0.00 34.79 3.18
3411 11991 5.450818 TTTACAGATATGAAGGCCCTGTT 57.549 39.130 12.85 0.00 38.76 3.16
3412 11992 5.132648 TCATTTACAGATATGAAGGCCCTGT 59.867 40.000 12.35 12.35 40.66 4.00
3413 11993 5.471456 GTCATTTACAGATATGAAGGCCCTG 59.529 44.000 0.00 0.00 32.94 4.45
3414 11994 5.370880 AGTCATTTACAGATATGAAGGCCCT 59.629 40.000 0.00 0.00 32.94 5.19
3415 11995 5.471456 CAGTCATTTACAGATATGAAGGCCC 59.529 44.000 0.00 0.00 32.94 5.80
3416 11996 6.291377 TCAGTCATTTACAGATATGAAGGCC 58.709 40.000 0.00 0.00 32.94 5.19
3417 11997 7.792374 TTCAGTCATTTACAGATATGAAGGC 57.208 36.000 0.00 0.00 32.94 4.35
3418 11998 9.388506 AGTTTCAGTCATTTACAGATATGAAGG 57.611 33.333 0.00 0.00 32.94 3.46
3420 12000 9.166173 CCAGTTTCAGTCATTTACAGATATGAA 57.834 33.333 0.00 0.00 32.94 2.57
3421 12001 8.321353 ACCAGTTTCAGTCATTTACAGATATGA 58.679 33.333 0.00 0.00 0.00 2.15
3422 12002 8.498054 ACCAGTTTCAGTCATTTACAGATATG 57.502 34.615 0.00 0.00 0.00 1.78
3423 12003 8.321353 TGACCAGTTTCAGTCATTTACAGATAT 58.679 33.333 0.00 0.00 38.07 1.63
3563 12155 4.643784 AGCCATTAAGCAAGATCCTGAAAG 59.356 41.667 0.00 0.00 34.23 2.62
3865 12687 6.127366 TGGAGAAAAGAAGAAGCACAAACATT 60.127 34.615 0.00 0.00 0.00 2.71
3985 12901 6.313658 GGAATATTTGAAAAGGGTGCATGTTC 59.686 38.462 0.00 0.00 0.00 3.18
3989 12905 5.032170 AGGGAATATTTGAAAAGGGTGCAT 58.968 37.500 0.00 0.00 0.00 3.96
4007 12923 1.600107 CAATTCCGGACGGAGGGAA 59.400 57.895 13.64 5.91 46.06 3.97
4009 12925 2.513897 GCAATTCCGGACGGAGGG 60.514 66.667 13.64 8.49 46.06 4.30
4025 12941 0.248215 CATCCATTTCCGCGACAAGC 60.248 55.000 8.23 0.00 43.95 4.01
4054 12970 9.838339 ACTTGTCGAGAAAATGGATAGAAATAT 57.162 29.630 0.00 0.00 0.00 1.28
4071 12987 4.106029 TCCTTCGGAATTACTTGTCGAG 57.894 45.455 0.00 0.00 0.00 4.04
4090 13006 5.685728 AGAAGCAAATGTAATACTCCCTCC 58.314 41.667 0.00 0.00 0.00 4.30
4123 13040 5.106712 CCGTAAAAATAACTCTTGCTCTGCA 60.107 40.000 0.00 0.00 36.47 4.41
4407 13333 4.916983 TGCTAGATGTGCAAAAACAACT 57.083 36.364 0.00 0.00 37.51 3.16
4438 13367 8.772705 TGAAACTGCAAAATTTCATTGGAATAC 58.227 29.630 13.62 0.00 39.34 1.89


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

AutoCloner maintained by Alex Coulton.