Multiple sequence alignment - TraesCS1B01G433600

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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 TraesCS1B01G433600 chr1B 100.000 3465 0 0 1 3465 658437644 658441108 0.000000e+00 6399.0
1 TraesCS1B01G433600 chr1B 97.395 883 23 0 2464 3346 556210737 556209855 0.000000e+00 1504.0
2 TraesCS1B01G433600 chr1B 91.385 325 25 2 266 589 31742387 31742709 3.170000e-120 442.0
3 TraesCS1B01G433600 chr1B 84.483 348 40 11 996 1335 658189395 658189736 7.170000e-87 331.0
4 TraesCS1B01G433600 chr1B 84.098 327 32 9 3033 3350 1772432 1772747 7.270000e-77 298.0
5 TraesCS1B01G433600 chr1B 84.308 325 23 10 266 589 2946933 2947230 3.380000e-75 292.0
6 TraesCS1B01G433600 chr1B 94.118 187 9 2 266 451 130021455 130021640 2.040000e-72 283.0
7 TraesCS1B01G433600 chr1B 81.595 326 38 13 3032 3346 278687102 278687416 2.060000e-62 250.0
8 TraesCS1B01G433600 chr1B 92.810 153 11 0 2460 2612 1771892 1772044 4.500000e-54 222.0
9 TraesCS1B01G433600 chr1B 91.772 158 13 0 2463 2620 278686564 278686721 1.620000e-53 220.0
10 TraesCS1B01G433600 chr1B 90.323 155 6 1 589 734 2947278 2947432 9.810000e-46 195.0
11 TraesCS1B01G433600 chr1B 98.148 108 2 0 39 146 559551459 559551352 4.570000e-44 189.0
12 TraesCS1B01G433600 chr1B 99.048 105 0 1 39 142 59884052 59884156 1.640000e-43 187.0
13 TraesCS1B01G433600 chr1B 87.821 156 9 2 589 734 130021778 130021933 1.280000e-39 174.0
14 TraesCS1B01G433600 chr1B 89.552 67 3 3 1 67 40174021 40173959 7.970000e-12 82.4
15 TraesCS1B01G433600 chr1B 91.525 59 4 1 3406 3464 449552736 449552793 2.870000e-11 80.5
16 TraesCS1B01G433600 chr1B 89.231 65 3 3 1 65 27367814 27367754 1.030000e-10 78.7
17 TraesCS1B01G433600 chr1B 89.231 65 3 3 1 65 426917333 426917393 1.030000e-10 78.7
18 TraesCS1B01G433600 chr1B 89.231 65 3 3 1 65 427222548 427222608 1.030000e-10 78.7
19 TraesCS1B01G433600 chr1B 94.737 38 2 0 1235 1272 660824566 660824603 3.730000e-05 60.2
20 TraesCS1B01G433600 chr1A 93.109 1727 94 11 750 2463 567598220 567599934 0.000000e+00 2507.0
21 TraesCS1B01G433600 chr1A 88.718 195 14 5 266 456 560304904 560305094 7.480000e-57 231.0
22 TraesCS1B01G433600 chr1A 83.966 237 22 6 3058 3283 8349192 8349423 2.710000e-51 213.0
23 TraesCS1B01G433600 chr1A 95.238 42 2 0 3346 3387 567599932 567599973 2.230000e-07 67.6
24 TraesCS1B01G433600 chr2B 97.523 888 22 0 2461 3348 425919090 425919977 0.000000e+00 1519.0
25 TraesCS1B01G433600 chr2B 98.165 109 1 1 39 146 186395847 186395955 4.570000e-44 189.0
26 TraesCS1B01G433600 chr2B 100.000 101 0 0 39 139 785236569 785236669 1.640000e-43 187.0
27 TraesCS1B01G433600 chr2B 89.157 83 6 3 3386 3465 47534028 47534110 2.200000e-17 100.0
28 TraesCS1B01G433600 chr6B 97.523 888 17 2 2463 3346 76273467 76274353 0.000000e+00 1513.0
29 TraesCS1B01G433600 chr6B 96.000 325 10 3 266 589 23280318 23280640 3.060000e-145 525.0
30 TraesCS1B01G433600 chr6B 84.830 501 61 10 1777 2275 76216741 76216254 1.120000e-134 490.0
31 TraesCS1B01G433600 chr6B 88.601 193 19 1 1124 1316 76217502 76217313 7.480000e-57 231.0
32 TraesCS1B01G433600 chr6B 95.798 119 3 2 616 734 23280705 23280821 1.270000e-44 191.0
33 TraesCS1B01G433600 chr6B 100.000 102 0 0 39 140 21930100 21930201 4.570000e-44 189.0
34 TraesCS1B01G433600 chr6B 100.000 102 0 0 39 140 111343901 111343800 4.570000e-44 189.0
35 TraesCS1B01G433600 chr5B 97.622 883 14 2 2463 3345 513319283 513320158 0.000000e+00 1507.0
36 TraesCS1B01G433600 chr5B 89.264 326 19 3 265 589 24680029 24679719 9.010000e-106 394.0
37 TraesCS1B01G433600 chr5B 89.744 156 5 3 589 734 24679671 24679517 4.570000e-44 189.0
38 TraesCS1B01G433600 chr5B 90.769 65 2 3 1 65 539848112 539848172 2.220000e-12 84.2
39 TraesCS1B01G433600 chr1D 94.609 946 43 3 1518 2463 473518464 473519401 0.000000e+00 1458.0
40 TraesCS1B01G433600 chr1D 92.715 906 35 7 2461 3354 338538490 338539376 0.000000e+00 1279.0
41 TraesCS1B01G433600 chr1D 93.449 748 39 4 743 1483 473517715 473518459 0.000000e+00 1101.0
42 TraesCS1B01G433600 chr1D 78.594 626 84 24 996 1582 473337516 473338130 5.460000e-98 368.0
43 TraesCS1B01G433600 chr1D 95.238 42 2 0 3346 3387 473519399 473519440 2.230000e-07 67.6
44 TraesCS1B01G433600 chr5D 95.039 887 44 0 2460 3346 540749309 540750195 0.000000e+00 1395.0
45 TraesCS1B01G433600 chr5D 93.964 845 49 2 2502 3346 540657996 540658838 0.000000e+00 1277.0
46 TraesCS1B01G433600 chr5D 84.286 140 9 6 2484 2620 556049286 556049415 1.310000e-24 124.0
47 TraesCS1B01G433600 chr5D 92.105 76 5 1 3390 3464 544719100 544719025 4.730000e-19 106.0
48 TraesCS1B01G433600 chr6A 84.496 516 59 13 1777 2284 40580689 40580187 1.120000e-134 490.0
49 TraesCS1B01G433600 chr6A 82.124 386 52 9 974 1354 40581589 40581216 7.220000e-82 315.0
50 TraesCS1B01G433600 chr6A 80.081 246 43 5 3107 3346 311862592 311862837 9.880000e-41 178.0
51 TraesCS1B01G433600 chr6A 93.421 76 5 0 2463 2538 608052080 608052155 2.830000e-21 113.0
52 TraesCS1B01G433600 chr6A 85.227 88 13 0 647 734 614198386 614198299 1.320000e-14 91.6
53 TraesCS1B01G433600 chr6A 89.231 65 3 3 1 65 580664613 580664673 1.030000e-10 78.7
54 TraesCS1B01G433600 chr2A 92.025 326 22 3 266 589 483942286 483941963 4.080000e-124 455.0
55 TraesCS1B01G433600 chr2A 82.792 308 41 11 266 568 757320488 757320188 7.370000e-67 265.0
56 TraesCS1B01G433600 chr2A 92.517 147 8 3 589 734 483941915 483941771 1.260000e-49 207.0
57 TraesCS1B01G433600 chr5A 85.037 401 44 10 2955 3348 201639697 201640088 9.010000e-106 394.0
58 TraesCS1B01G433600 chr5A 91.250 160 14 0 2461 2620 201639173 201639332 5.820000e-53 219.0
59 TraesCS1B01G433600 chr7D 86.704 361 39 7 2992 3349 36460256 36460610 3.240000e-105 392.0
60 TraesCS1B01G433600 chr7D 81.275 251 44 3 266 514 5999370 5999121 2.110000e-47 200.0
61 TraesCS1B01G433600 chr7D 88.889 63 7 0 671 733 15684348 15684410 1.030000e-10 78.7
62 TraesCS1B01G433600 chr4B 87.195 328 26 8 3023 3343 418511739 418512057 3.290000e-95 359.0
63 TraesCS1B01G433600 chr4B 92.073 164 10 3 2460 2620 418511166 418511329 9.670000e-56 228.0
64 TraesCS1B01G433600 chr4B 89.231 65 3 3 1 65 556280188 556280128 1.030000e-10 78.7
65 TraesCS1B01G433600 chr4B 89.231 65 3 3 1 65 611504365 611504425 1.030000e-10 78.7
66 TraesCS1B01G433600 chr4A 94.660 206 10 1 265 469 709200929 709201134 5.580000e-83 318.0
67 TraesCS1B01G433600 chr4A 88.961 154 8 1 590 734 709201187 709201340 7.640000e-42 182.0
68 TraesCS1B01G433600 chr4A 88.608 79 8 1 3387 3464 190835285 190835363 1.020000e-15 95.3
69 TraesCS1B01G433600 chr4A 94.118 51 3 0 683 733 719818711 719818661 1.030000e-10 78.7
70 TraesCS1B01G433600 chr7A 84.422 199 26 3 266 461 19696975 19697171 1.270000e-44 191.0
71 TraesCS1B01G433600 chr7A 94.286 70 4 0 3396 3465 658890090 658890021 1.320000e-19 108.0
72 TraesCS1B01G433600 chr7A 92.857 70 5 0 3396 3465 576119963 576120032 6.120000e-18 102.0
73 TraesCS1B01G433600 chr7A 90.909 77 5 2 3390 3465 696046313 696046238 6.120000e-18 102.0
74 TraesCS1B01G433600 chr7A 91.803 61 5 0 674 734 668731264 668731204 6.160000e-13 86.1
75 TraesCS1B01G433600 chr3B 100.000 103 0 0 39 141 784030652 784030754 1.270000e-44 191.0
76 TraesCS1B01G433600 chrUn 100.000 102 0 0 39 140 158300882 158300983 4.570000e-44 189.0
77 TraesCS1B01G433600 chrUn 89.231 65 3 3 1 65 48526345 48526405 1.030000e-10 78.7
78 TraesCS1B01G433600 chr7B 99.048 105 1 0 39 143 711081551 711081447 4.570000e-44 189.0
79 TraesCS1B01G433600 chr7B 82.533 229 15 12 362 589 124546884 124546680 9.880000e-41 178.0
80 TraesCS1B01G433600 chr7B 89.781 137 4 2 608 734 124546612 124546476 2.140000e-37 167.0
81 TraesCS1B01G433600 chr7B 84.472 161 9 6 589 734 667386936 667387095 1.000000e-30 145.0
82 TraesCS1B01G433600 chr4D 92.208 77 5 1 3390 3465 29656646 29656570 1.320000e-19 108.0
83 TraesCS1B01G433600 chr4D 97.959 49 1 0 3416 3464 484726886 484726838 6.160000e-13 86.1
84 TraesCS1B01G433600 chr4D 96.078 51 2 0 3414 3464 439698224 439698274 2.220000e-12 84.2
85 TraesCS1B01G433600 chr2D 94.118 68 4 0 667 734 590082218 590082151 1.700000e-18 104.0
86 TraesCS1B01G433600 chr2D 90.000 80 7 1 3387 3465 110401901 110401980 6.120000e-18 102.0
87 TraesCS1B01G433600 chr2D 90.789 76 6 1 3390 3464 534482977 534482902 2.200000e-17 100.0
88 TraesCS1B01G433600 chr3D 90.000 80 7 1 3387 3465 104098852 104098931 6.120000e-18 102.0
89 TraesCS1B01G433600 chr3D 94.444 54 3 0 681 734 575414892 575414945 2.220000e-12 84.2
90 TraesCS1B01G433600 chr3D 93.750 48 1 1 3419 3464 5368443 5368396 1.730000e-08 71.3
91 TraesCS1B01G433600 chr6D 87.500 80 9 1 3387 3465 395525585 395525664 1.320000e-14 91.6


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 TraesCS1B01G433600 chr1B 658437644 658441108 3464 False 6399.000000 6399 100.0000 1 3465 1 chr1B.!!$F7 3464
1 TraesCS1B01G433600 chr1B 556209855 556210737 882 True 1504.000000 1504 97.3950 2464 3346 1 chr1B.!!$R3 882
2 TraesCS1B01G433600 chr1B 1771892 1772747 855 False 260.000000 298 88.4540 2460 3350 2 chr1B.!!$F9 890
3 TraesCS1B01G433600 chr1B 278686564 278687416 852 False 235.000000 250 86.6835 2463 3346 2 chr1B.!!$F12 883
4 TraesCS1B01G433600 chr1A 567598220 567599973 1753 False 1287.300000 2507 94.1735 750 3387 2 chr1A.!!$F3 2637
5 TraesCS1B01G433600 chr2B 425919090 425919977 887 False 1519.000000 1519 97.5230 2461 3348 1 chr2B.!!$F3 887
6 TraesCS1B01G433600 chr6B 76273467 76274353 886 False 1513.000000 1513 97.5230 2463 3346 1 chr6B.!!$F2 883
7 TraesCS1B01G433600 chr6B 76216254 76217502 1248 True 360.500000 490 86.7155 1124 2275 2 chr6B.!!$R2 1151
8 TraesCS1B01G433600 chr6B 23280318 23280821 503 False 358.000000 525 95.8990 266 734 2 chr6B.!!$F3 468
9 TraesCS1B01G433600 chr5B 513319283 513320158 875 False 1507.000000 1507 97.6220 2463 3345 1 chr5B.!!$F1 882
10 TraesCS1B01G433600 chr5B 24679517 24680029 512 True 291.500000 394 89.5040 265 734 2 chr5B.!!$R1 469
11 TraesCS1B01G433600 chr1D 338538490 338539376 886 False 1279.000000 1279 92.7150 2461 3354 1 chr1D.!!$F1 893
12 TraesCS1B01G433600 chr1D 473517715 473519440 1725 False 875.533333 1458 94.4320 743 3387 3 chr1D.!!$F3 2644
13 TraesCS1B01G433600 chr1D 473337516 473338130 614 False 368.000000 368 78.5940 996 1582 1 chr1D.!!$F2 586
14 TraesCS1B01G433600 chr5D 540749309 540750195 886 False 1395.000000 1395 95.0390 2460 3346 1 chr5D.!!$F2 886
15 TraesCS1B01G433600 chr5D 540657996 540658838 842 False 1277.000000 1277 93.9640 2502 3346 1 chr5D.!!$F1 844
16 TraesCS1B01G433600 chr6A 40580187 40581589 1402 True 402.500000 490 83.3100 974 2284 2 chr6A.!!$R2 1310
17 TraesCS1B01G433600 chr2A 483941771 483942286 515 True 331.000000 455 92.2710 266 734 2 chr2A.!!$R2 468
18 TraesCS1B01G433600 chr5A 201639173 201640088 915 False 306.500000 394 88.1435 2461 3348 2 chr5A.!!$F1 887
19 TraesCS1B01G433600 chr4B 418511166 418512057 891 False 293.500000 359 89.6340 2460 3343 2 chr4B.!!$F2 883

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
212 213 0.032678 CCTCCTGCGCATAGGTACAG 59.967 60.0 24.09 11.76 38.99 2.74 F
602 652 0.037790 GAACTCTCGCTGCCTGTTCT 60.038 55.0 11.63 0.00 35.51 3.01 F
1015 1085 0.181350 AGGAATCACGCCCTGAATCC 59.819 55.0 5.35 5.35 46.21 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1029 1099 0.670162 AGGTGCAATGCAATATCGGC 59.330 50.000 10.44 0.0 41.47 5.54 R
2246 2508 0.601558 GCCGCCGTCTATATCTTGGA 59.398 55.000 0.00 0.0 0.00 3.53 R
2814 3237 1.602237 CGTGCCTGATGGGTTAGGT 59.398 57.895 0.00 0.0 36.44 3.08 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
35 36 3.851098 CTGACACAGCCTCTTTAGTACC 58.149 50.000 0.00 0.00 0.00 3.34
36 37 2.230508 TGACACAGCCTCTTTAGTACCG 59.769 50.000 0.00 0.00 0.00 4.02
37 38 1.549170 ACACAGCCTCTTTAGTACCGG 59.451 52.381 0.00 0.00 0.00 5.28
38 39 1.549170 CACAGCCTCTTTAGTACCGGT 59.451 52.381 13.98 13.98 0.00 5.28
39 40 2.028385 CACAGCCTCTTTAGTACCGGTT 60.028 50.000 15.04 0.00 0.00 4.44
40 41 2.028385 ACAGCCTCTTTAGTACCGGTTG 60.028 50.000 15.04 2.00 32.99 3.77
41 42 2.232941 CAGCCTCTTTAGTACCGGTTGA 59.767 50.000 15.04 0.00 0.00 3.18
42 43 3.105283 AGCCTCTTTAGTACCGGTTGAT 58.895 45.455 15.04 0.95 0.00 2.57
43 44 3.132467 AGCCTCTTTAGTACCGGTTGATC 59.868 47.826 15.04 1.07 0.00 2.92
44 45 3.703420 CCTCTTTAGTACCGGTTGATCG 58.297 50.000 15.04 0.00 0.00 3.69
45 46 3.114065 CTCTTTAGTACCGGTTGATCGC 58.886 50.000 15.04 0.00 0.00 4.58
46 47 2.159198 TCTTTAGTACCGGTTGATCGCC 60.159 50.000 15.04 0.00 0.00 5.54
54 55 3.115892 GTTGATCGCCGCCACGAA 61.116 61.111 0.00 0.00 46.59 3.85
55 56 3.115892 TTGATCGCCGCCACGAAC 61.116 61.111 0.00 0.00 46.59 3.95
65 66 4.609995 CCACGAACCGGCACTAAT 57.390 55.556 0.00 0.00 0.00 1.73
66 67 2.086510 CCACGAACCGGCACTAATG 58.913 57.895 0.00 0.00 0.00 1.90
67 68 0.672401 CCACGAACCGGCACTAATGT 60.672 55.000 0.00 0.00 0.00 2.71
68 69 1.404449 CCACGAACCGGCACTAATGTA 60.404 52.381 0.00 0.00 0.00 2.29
69 70 1.657094 CACGAACCGGCACTAATGTAC 59.343 52.381 0.00 0.00 0.00 2.90
70 71 1.273048 ACGAACCGGCACTAATGTACA 59.727 47.619 0.00 0.00 0.00 2.90
71 72 1.657094 CGAACCGGCACTAATGTACAC 59.343 52.381 0.00 0.00 0.00 2.90
72 73 2.690786 GAACCGGCACTAATGTACACA 58.309 47.619 0.00 0.00 0.00 3.72
73 74 3.267483 GAACCGGCACTAATGTACACAT 58.733 45.455 0.00 0.00 38.41 3.21
75 76 4.475051 ACCGGCACTAATGTACACATTA 57.525 40.909 0.00 12.86 44.09 1.90
86 87 4.615901 CACATTAGTGCCGGCTGA 57.384 55.556 29.70 9.94 39.21 4.26
87 88 2.853159 CACATTAGTGCCGGCTGAA 58.147 52.632 29.70 18.66 39.21 3.02
88 89 1.164411 CACATTAGTGCCGGCTGAAA 58.836 50.000 29.70 18.42 39.21 2.69
89 90 1.745087 CACATTAGTGCCGGCTGAAAT 59.255 47.619 29.70 19.83 39.21 2.17
90 91 2.164219 CACATTAGTGCCGGCTGAAATT 59.836 45.455 29.70 6.34 39.21 1.82
91 92 2.423538 ACATTAGTGCCGGCTGAAATTC 59.576 45.455 29.70 8.96 0.00 2.17
92 93 2.192664 TTAGTGCCGGCTGAAATTCA 57.807 45.000 29.70 0.07 0.00 2.57
93 94 2.192664 TAGTGCCGGCTGAAATTCAA 57.807 45.000 29.70 0.00 0.00 2.69
94 95 1.327303 AGTGCCGGCTGAAATTCAAA 58.673 45.000 29.70 0.00 0.00 2.69
95 96 1.000274 AGTGCCGGCTGAAATTCAAAC 60.000 47.619 29.70 13.21 0.00 2.93
96 97 0.316841 TGCCGGCTGAAATTCAAACC 59.683 50.000 29.70 0.98 0.00 3.27
97 98 0.732538 GCCGGCTGAAATTCAAACCG 60.733 55.000 22.15 22.68 42.47 4.44
98 99 3.399879 CGGCTGAAATTCAAACCGG 57.600 52.632 22.18 0.00 40.46 5.28
99 100 0.732538 CGGCTGAAATTCAAACCGGC 60.733 55.000 22.18 11.17 40.46 6.13
100 101 0.316841 GGCTGAAATTCAAACCGGCA 59.683 50.000 0.00 0.00 32.85 5.69
101 102 1.418373 GCTGAAATTCAAACCGGCAC 58.582 50.000 0.00 0.00 0.00 5.01
102 103 1.000274 GCTGAAATTCAAACCGGCACT 60.000 47.619 0.00 0.00 0.00 4.40
103 104 2.227865 GCTGAAATTCAAACCGGCACTA 59.772 45.455 0.00 0.00 0.00 2.74
104 105 3.119495 GCTGAAATTCAAACCGGCACTAT 60.119 43.478 0.00 0.00 0.00 2.12
105 106 4.618227 GCTGAAATTCAAACCGGCACTATT 60.618 41.667 0.00 0.00 0.00 1.73
106 107 4.804108 TGAAATTCAAACCGGCACTATTG 58.196 39.130 0.00 0.00 0.00 1.90
107 108 4.279671 TGAAATTCAAACCGGCACTATTGT 59.720 37.500 0.00 0.00 0.00 2.71
108 109 3.848272 ATTCAAACCGGCACTATTGTG 57.152 42.857 0.00 2.65 46.37 3.33
122 123 5.156355 CACTATTGTGCTTCACATTTGACC 58.844 41.667 0.11 0.00 44.16 4.02
123 124 3.665745 ATTGTGCTTCACATTTGACCC 57.334 42.857 0.11 0.00 44.16 4.46
124 125 2.363306 TGTGCTTCACATTTGACCCT 57.637 45.000 0.00 0.00 39.62 4.34
125 126 2.665165 TGTGCTTCACATTTGACCCTT 58.335 42.857 0.00 0.00 39.62 3.95
126 127 3.030291 TGTGCTTCACATTTGACCCTTT 58.970 40.909 0.00 0.00 39.62 3.11
127 128 3.450457 TGTGCTTCACATTTGACCCTTTT 59.550 39.130 0.00 0.00 39.62 2.27
128 129 4.081198 TGTGCTTCACATTTGACCCTTTTT 60.081 37.500 0.00 0.00 39.62 1.94
129 130 4.507756 GTGCTTCACATTTGACCCTTTTTC 59.492 41.667 0.00 0.00 34.08 2.29
130 131 4.405358 TGCTTCACATTTGACCCTTTTTCT 59.595 37.500 0.00 0.00 0.00 2.52
131 132 5.596361 TGCTTCACATTTGACCCTTTTTCTA 59.404 36.000 0.00 0.00 0.00 2.10
132 133 5.920840 GCTTCACATTTGACCCTTTTTCTAC 59.079 40.000 0.00 0.00 0.00 2.59
133 134 6.239036 GCTTCACATTTGACCCTTTTTCTACT 60.239 38.462 0.00 0.00 0.00 2.57
134 135 7.040686 GCTTCACATTTGACCCTTTTTCTACTA 60.041 37.037 0.00 0.00 0.00 1.82
135 136 7.979444 TCACATTTGACCCTTTTTCTACTAG 57.021 36.000 0.00 0.00 0.00 2.57
136 137 7.514721 TCACATTTGACCCTTTTTCTACTAGT 58.485 34.615 0.00 0.00 0.00 2.57
137 138 7.444183 TCACATTTGACCCTTTTTCTACTAGTG 59.556 37.037 5.39 0.00 0.00 2.74
138 139 7.228706 CACATTTGACCCTTTTTCTACTAGTGT 59.771 37.037 5.39 0.00 0.00 3.55
139 140 7.228706 ACATTTGACCCTTTTTCTACTAGTGTG 59.771 37.037 5.39 0.00 0.00 3.82
140 141 6.488769 TTGACCCTTTTTCTACTAGTGTGA 57.511 37.500 5.39 0.71 0.00 3.58
141 142 5.850614 TGACCCTTTTTCTACTAGTGTGAC 58.149 41.667 5.39 0.00 0.00 3.67
142 143 5.601313 TGACCCTTTTTCTACTAGTGTGACT 59.399 40.000 5.39 0.00 0.00 3.41
143 144 6.779049 TGACCCTTTTTCTACTAGTGTGACTA 59.221 38.462 5.39 0.00 0.00 2.59
153 154 2.999507 AGTGTGACTAGCGAGTTGAG 57.000 50.000 0.00 0.00 35.45 3.02
154 155 2.231529 AGTGTGACTAGCGAGTTGAGT 58.768 47.619 0.00 0.00 35.45 3.41
155 156 2.623889 AGTGTGACTAGCGAGTTGAGTT 59.376 45.455 0.00 0.00 35.45 3.01
156 157 2.726760 GTGTGACTAGCGAGTTGAGTTG 59.273 50.000 0.00 0.00 35.45 3.16
157 158 1.721926 GTGACTAGCGAGTTGAGTTGC 59.278 52.381 0.00 0.00 35.45 4.17
158 159 1.336887 TGACTAGCGAGTTGAGTTGCC 60.337 52.381 0.00 0.00 35.45 4.52
159 160 0.969894 ACTAGCGAGTTGAGTTGCCT 59.030 50.000 0.00 0.00 28.61 4.75
160 161 1.344763 ACTAGCGAGTTGAGTTGCCTT 59.655 47.619 0.00 0.00 28.61 4.35
161 162 2.561419 ACTAGCGAGTTGAGTTGCCTTA 59.439 45.455 0.00 0.00 28.61 2.69
162 163 1.797025 AGCGAGTTGAGTTGCCTTAC 58.203 50.000 0.00 0.00 0.00 2.34
163 164 0.438830 GCGAGTTGAGTTGCCTTACG 59.561 55.000 0.00 0.00 0.00 3.18
164 165 1.068474 CGAGTTGAGTTGCCTTACGG 58.932 55.000 0.00 0.00 0.00 4.02
165 166 1.439679 GAGTTGAGTTGCCTTACGGG 58.560 55.000 0.00 0.00 38.36 5.28
166 167 1.001633 GAGTTGAGTTGCCTTACGGGA 59.998 52.381 0.00 0.00 37.23 5.14
167 168 1.628846 AGTTGAGTTGCCTTACGGGAT 59.371 47.619 0.00 0.00 37.23 3.85
168 169 1.737793 GTTGAGTTGCCTTACGGGATG 59.262 52.381 0.00 0.00 37.23 3.51
169 170 0.981183 TGAGTTGCCTTACGGGATGT 59.019 50.000 0.00 0.00 37.23 3.06
170 171 1.338674 TGAGTTGCCTTACGGGATGTG 60.339 52.381 0.00 0.00 37.23 3.21
171 172 0.035439 AGTTGCCTTACGGGATGTGG 60.035 55.000 0.00 0.00 37.23 4.17
172 173 0.322187 GTTGCCTTACGGGATGTGGT 60.322 55.000 0.00 0.00 37.23 4.16
173 174 0.035820 TTGCCTTACGGGATGTGGTC 60.036 55.000 0.00 0.00 37.23 4.02
174 175 0.907704 TGCCTTACGGGATGTGGTCT 60.908 55.000 0.00 0.00 37.23 3.85
175 176 1.117150 GCCTTACGGGATGTGGTCTA 58.883 55.000 0.00 0.00 37.23 2.59
176 177 1.202498 GCCTTACGGGATGTGGTCTAC 60.202 57.143 0.00 0.00 37.23 2.59
177 178 2.104967 CCTTACGGGATGTGGTCTACA 58.895 52.381 0.00 0.00 44.87 2.74
187 188 2.104967 TGTGGTCTACATTACCCTCCG 58.895 52.381 0.00 0.00 36.06 4.63
188 189 1.117150 TGGTCTACATTACCCTCCGC 58.883 55.000 0.00 0.00 36.06 5.54
189 190 0.391966 GGTCTACATTACCCTCCGCC 59.608 60.000 0.00 0.00 0.00 6.13
190 191 1.117150 GTCTACATTACCCTCCGCCA 58.883 55.000 0.00 0.00 0.00 5.69
191 192 1.117150 TCTACATTACCCTCCGCCAC 58.883 55.000 0.00 0.00 0.00 5.01
192 193 0.828022 CTACATTACCCTCCGCCACA 59.172 55.000 0.00 0.00 0.00 4.17
193 194 0.538118 TACATTACCCTCCGCCACAC 59.462 55.000 0.00 0.00 0.00 3.82
194 195 1.451387 CATTACCCTCCGCCACACC 60.451 63.158 0.00 0.00 0.00 4.16
195 196 1.615424 ATTACCCTCCGCCACACCT 60.615 57.895 0.00 0.00 0.00 4.00
196 197 1.623542 ATTACCCTCCGCCACACCTC 61.624 60.000 0.00 0.00 0.00 3.85
199 200 4.087892 CCTCCGCCACACCTCCTG 62.088 72.222 0.00 0.00 0.00 3.86
200 201 4.767255 CTCCGCCACACCTCCTGC 62.767 72.222 0.00 0.00 0.00 4.85
205 206 2.584064 CCACACCTCCTGCGCATA 59.416 61.111 12.24 0.46 0.00 3.14
206 207 1.522355 CCACACCTCCTGCGCATAG 60.522 63.158 12.24 11.99 0.00 2.23
207 208 1.522355 CACACCTCCTGCGCATAGG 60.522 63.158 28.34 28.34 39.29 2.57
208 209 1.990060 ACACCTCCTGCGCATAGGT 60.990 57.895 29.43 29.43 44.54 3.08
209 210 0.686441 ACACCTCCTGCGCATAGGTA 60.686 55.000 32.42 13.48 41.75 3.08
210 211 0.249489 CACCTCCTGCGCATAGGTAC 60.249 60.000 32.42 0.00 41.75 3.34
211 212 0.686441 ACCTCCTGCGCATAGGTACA 60.686 55.000 32.18 8.67 41.86 2.90
212 213 0.032678 CCTCCTGCGCATAGGTACAG 59.967 60.000 24.09 11.76 38.99 2.74
213 214 0.747255 CTCCTGCGCATAGGTACAGT 59.253 55.000 12.24 0.00 38.99 3.55
214 215 1.137086 CTCCTGCGCATAGGTACAGTT 59.863 52.381 12.24 0.00 38.99 3.16
215 216 1.136305 TCCTGCGCATAGGTACAGTTC 59.864 52.381 12.24 0.00 38.99 3.01
216 217 1.200483 CTGCGCATAGGTACAGTTCG 58.800 55.000 12.24 0.00 0.00 3.95
217 218 0.804544 TGCGCATAGGTACAGTTCGC 60.805 55.000 5.66 10.39 41.22 4.70
218 219 1.488261 GCGCATAGGTACAGTTCGCC 61.488 60.000 0.30 0.00 35.71 5.54
219 220 0.179121 CGCATAGGTACAGTTCGCCA 60.179 55.000 0.00 0.00 0.00 5.69
220 221 1.571919 GCATAGGTACAGTTCGCCAG 58.428 55.000 0.00 0.00 0.00 4.85
221 222 1.806623 GCATAGGTACAGTTCGCCAGG 60.807 57.143 0.00 0.00 0.00 4.45
222 223 1.754803 CATAGGTACAGTTCGCCAGGA 59.245 52.381 0.00 0.00 0.00 3.86
223 224 2.154567 TAGGTACAGTTCGCCAGGAT 57.845 50.000 0.00 0.00 0.00 3.24
224 225 0.537188 AGGTACAGTTCGCCAGGATG 59.463 55.000 0.00 0.00 0.00 3.51
225 226 0.249398 GGTACAGTTCGCCAGGATGT 59.751 55.000 0.00 0.00 0.00 3.06
226 227 1.359848 GTACAGTTCGCCAGGATGTG 58.640 55.000 0.00 0.00 0.00 3.21
243 244 2.104967 TGTGGTCTACATTACCCTCCG 58.895 52.381 0.00 0.00 36.06 4.63
244 245 1.117150 TGGTCTACATTACCCTCCGC 58.883 55.000 0.00 0.00 36.06 5.54
245 246 0.391966 GGTCTACATTACCCTCCGCC 59.608 60.000 0.00 0.00 0.00 6.13
246 247 1.411041 GTCTACATTACCCTCCGCCT 58.589 55.000 0.00 0.00 0.00 5.52
247 248 1.068741 GTCTACATTACCCTCCGCCTG 59.931 57.143 0.00 0.00 0.00 4.85
248 249 0.249911 CTACATTACCCTCCGCCTGC 60.250 60.000 0.00 0.00 0.00 4.85
249 250 0.978667 TACATTACCCTCCGCCTGCA 60.979 55.000 0.00 0.00 0.00 4.41
250 251 1.149174 CATTACCCTCCGCCTGCAT 59.851 57.895 0.00 0.00 0.00 3.96
251 252 1.149174 ATTACCCTCCGCCTGCATG 59.851 57.895 0.00 0.00 0.00 4.06
252 253 2.965716 ATTACCCTCCGCCTGCATGC 62.966 60.000 11.82 11.82 0.00 4.06
259 260 3.117812 CGCCTGCATGCACGTGTA 61.118 61.111 18.46 14.09 0.00 2.90
260 261 2.787249 GCCTGCATGCACGTGTAG 59.213 61.111 18.46 5.77 0.00 2.74
261 262 2.787249 CCTGCATGCACGTGTAGC 59.213 61.111 18.46 18.09 31.43 3.58
263 264 1.422662 CTGCATGCACGTGTAGCAG 59.577 57.895 29.89 29.89 46.36 4.24
434 436 3.054728 TCTGGACTCAAGTTTGTCACCAA 60.055 43.478 7.73 0.00 35.11 3.67
496 498 2.859165 TTCCTCGAGGTTGCAAGATT 57.141 45.000 30.17 0.00 36.34 2.40
595 645 1.148759 GGGATTCGAACTCTCGCTGC 61.149 60.000 0.00 0.00 45.04 5.25
601 651 1.347817 CGAACTCTCGCTGCCTGTTC 61.348 60.000 0.00 3.24 38.45 3.18
602 652 0.037790 GAACTCTCGCTGCCTGTTCT 60.038 55.000 11.63 0.00 35.51 3.01
604 654 2.047844 TCTCGCTGCCTGTTCTGC 60.048 61.111 0.00 0.00 0.00 4.26
738 797 4.683832 GGAGGTATCCGAATATTCATCCG 58.316 47.826 15.57 2.00 35.37 4.18
739 798 4.401519 GGAGGTATCCGAATATTCATCCGA 59.598 45.833 15.57 5.35 35.37 4.55
740 799 5.326200 AGGTATCCGAATATTCATCCGAC 57.674 43.478 15.57 6.20 0.00 4.79
741 800 4.103357 GGTATCCGAATATTCATCCGACG 58.897 47.826 15.57 0.23 0.00 5.12
787 846 2.435120 AAACCCTCCCCCGCGAAAAT 62.435 55.000 8.23 0.00 0.00 1.82
838 897 2.806856 CTTCTCGCATGCAGGACGC 61.807 63.158 19.57 0.00 42.89 5.19
934 1004 2.413112 CACGGATCGATGGCATATCAAC 59.587 50.000 0.54 0.00 0.00 3.18
1015 1085 0.181350 AGGAATCACGCCCTGAATCC 59.819 55.000 5.35 5.35 46.21 3.01
1029 1099 0.600255 GAATCCACATACGGAGGCGG 60.600 60.000 0.00 0.00 38.83 6.13
1322 1410 0.392336 GGATGAGGATGAAGCGAGCT 59.608 55.000 0.00 0.00 0.00 4.09
1328 1416 1.590259 GATGAAGCGAGCTCCGTCC 60.590 63.158 8.47 0.00 41.15 4.79
1363 1496 3.501548 GGCGCGGCGGAAACAATA 61.502 61.111 25.03 0.00 0.00 1.90
1364 1497 2.481464 GCGCGGCGGAAACAATAA 59.519 55.556 25.03 0.00 0.00 1.40
1365 1498 1.063488 GCGCGGCGGAAACAATAAT 59.937 52.632 25.03 0.00 0.00 1.28
1740 1963 2.661866 GCCGCGCCGATACATTCT 60.662 61.111 0.00 0.00 0.00 2.40
1826 2082 1.449070 CTGCGGCTCAGCTTCATCA 60.449 57.895 0.00 0.00 35.78 3.07
2168 2430 2.504244 GGAGCTTCGTCGACGTGG 60.504 66.667 34.40 27.02 40.80 4.94
2246 2508 3.072915 TGGTCTCATGTGTTTGGTGATCT 59.927 43.478 0.00 0.00 0.00 2.75
2268 2530 0.956633 AAGATATAGACGGCGGCGAA 59.043 50.000 38.93 22.11 0.00 4.70
2330 2592 0.905337 AGCAAGTCGCCTCTAGGGTT 60.905 55.000 0.00 0.00 44.04 4.11
2357 2619 4.665451 TGGATGTCTGGATGTGATTGTTT 58.335 39.130 0.00 0.00 0.00 2.83
2384 2646 7.947890 AGTTTTTGTTTAGACATGGAGGGATAA 59.052 33.333 0.00 0.00 35.29 1.75
2385 2647 7.696992 TTTTGTTTAGACATGGAGGGATAAC 57.303 36.000 0.00 0.00 35.29 1.89
2386 2648 6.381498 TTGTTTAGACATGGAGGGATAACA 57.619 37.500 0.00 0.00 35.29 2.41
2387 2649 6.575244 TGTTTAGACATGGAGGGATAACAT 57.425 37.500 0.00 0.00 0.00 2.71
2388 2650 7.684317 TGTTTAGACATGGAGGGATAACATA 57.316 36.000 0.00 0.00 0.00 2.29
2457 2721 4.514441 TCCTTTTCGTTATTAAACACGGCA 59.486 37.500 9.26 0.00 37.02 5.69
2702 3124 2.751259 ACACACACAATCATCCATGAGC 59.249 45.455 0.00 0.00 40.64 4.26
2814 3237 1.679977 GCCATCAAGCCAGCCTCAA 60.680 57.895 0.00 0.00 0.00 3.02
2950 3407 1.031571 GCAGATCCGCCCAAATCACA 61.032 55.000 0.00 0.00 0.00 3.58
3219 3705 1.270826 GCTCTTCCCAACCAGCTTTTC 59.729 52.381 0.00 0.00 0.00 2.29
3326 3816 2.308866 CCTGTCCAACCAAGGGATAACT 59.691 50.000 0.00 0.00 36.67 2.24
3353 3843 3.805207 ACCAAACGCCACCTTATAGATC 58.195 45.455 0.00 0.00 0.00 2.75
3358 3848 5.552870 AACGCCACCTTATAGATCAAGAT 57.447 39.130 0.00 0.00 0.00 2.40
3388 3878 9.922305 CTCGAAACACAATAGATAAAGATTTCC 57.078 33.333 0.00 0.00 0.00 3.13
3389 3879 8.600625 TCGAAACACAATAGATAAAGATTTCCG 58.399 33.333 0.00 0.00 0.00 4.30
3390 3880 8.388103 CGAAACACAATAGATAAAGATTTCCGT 58.612 33.333 0.00 0.00 0.00 4.69
3391 3881 9.704098 GAAACACAATAGATAAAGATTTCCGTC 57.296 33.333 0.00 0.00 0.00 4.79
3392 3882 9.449719 AAACACAATAGATAAAGATTTCCGTCT 57.550 29.630 0.00 0.00 0.00 4.18
3401 3891 9.099454 AGATAAAGATTTCCGTCTAAACACATC 57.901 33.333 0.00 0.00 0.00 3.06
3402 3892 5.779806 AAGATTTCCGTCTAAACACATCG 57.220 39.130 0.00 0.00 0.00 3.84
3403 3893 5.068234 AGATTTCCGTCTAAACACATCGA 57.932 39.130 0.00 0.00 0.00 3.59
3404 3894 5.103000 AGATTTCCGTCTAAACACATCGAG 58.897 41.667 0.00 0.00 0.00 4.04
3405 3895 4.508461 TTTCCGTCTAAACACATCGAGA 57.492 40.909 0.00 0.00 0.00 4.04
3406 3896 4.713824 TTCCGTCTAAACACATCGAGAT 57.286 40.909 0.00 0.00 0.00 2.75
3407 3897 4.028852 TCCGTCTAAACACATCGAGATG 57.971 45.455 11.19 11.19 44.15 2.90
3422 3912 7.110179 CATCGAGATGTTACATGGTTATGTC 57.890 40.000 1.24 0.00 39.69 3.06
3423 3913 6.215495 TCGAGATGTTACATGGTTATGTCA 57.785 37.500 1.24 0.00 44.00 3.58
3424 3914 6.040247 TCGAGATGTTACATGGTTATGTCAC 58.960 40.000 1.24 0.00 44.00 3.67
3432 3922 9.900710 TGTTACATGGTTATGTCACATTTAAAC 57.099 29.630 0.00 0.00 44.00 2.01
3435 3925 8.402798 ACATGGTTATGTCACATTTAAACTGA 57.597 30.769 0.00 0.00 44.00 3.41
3436 3926 9.023962 ACATGGTTATGTCACATTTAAACTGAT 57.976 29.630 0.00 0.00 44.00 2.90
3437 3927 9.292846 CATGGTTATGTCACATTTAAACTGATG 57.707 33.333 0.00 0.00 0.00 3.07
3438 3928 8.402798 TGGTTATGTCACATTTAAACTGATGT 57.597 30.769 0.00 0.00 36.97 3.06
3439 3929 8.511321 TGGTTATGTCACATTTAAACTGATGTC 58.489 33.333 0.00 0.00 34.42 3.06
3440 3930 7.968405 GGTTATGTCACATTTAAACTGATGTCC 59.032 37.037 0.00 0.00 34.42 4.02
3441 3931 8.511321 GTTATGTCACATTTAAACTGATGTCCA 58.489 33.333 0.00 0.00 34.42 4.02
3442 3932 6.312399 TGTCACATTTAAACTGATGTCCAC 57.688 37.500 0.00 0.00 34.42 4.02
3443 3933 6.061441 TGTCACATTTAAACTGATGTCCACT 58.939 36.000 0.00 0.00 34.42 4.00
3444 3934 6.204688 TGTCACATTTAAACTGATGTCCACTC 59.795 38.462 0.00 0.00 34.42 3.51
3445 3935 6.428159 GTCACATTTAAACTGATGTCCACTCT 59.572 38.462 0.00 0.00 34.42 3.24
3446 3936 6.427853 TCACATTTAAACTGATGTCCACTCTG 59.572 38.462 0.00 0.00 34.42 3.35
3447 3937 6.205464 CACATTTAAACTGATGTCCACTCTGT 59.795 38.462 0.00 0.00 34.42 3.41
3448 3938 6.772716 ACATTTAAACTGATGTCCACTCTGTT 59.227 34.615 0.00 0.00 36.66 3.16
3449 3939 7.285401 ACATTTAAACTGATGTCCACTCTGTTT 59.715 33.333 11.33 11.33 43.11 2.83
3450 3940 6.618287 TTAAACTGATGTCCACTCTGTTTG 57.382 37.500 14.59 0.00 41.71 2.93
3451 3941 3.845781 ACTGATGTCCACTCTGTTTGT 57.154 42.857 0.00 0.00 0.00 2.83
3452 3942 3.470709 ACTGATGTCCACTCTGTTTGTG 58.529 45.455 0.00 0.00 35.39 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 2.740055 GTGTCAGCCTGCGGTCAG 60.740 66.667 0.00 0.00 40.02 3.51
4 5 3.519973 CTGTGTCAGCCTGCGGTCA 62.520 63.158 0.00 0.00 0.00 4.02
5 6 2.740055 CTGTGTCAGCCTGCGGTC 60.740 66.667 0.00 0.00 0.00 4.79
14 15 3.673594 CGGTACTAAAGAGGCTGTGTCAG 60.674 52.174 0.00 0.00 34.12 3.51
15 16 2.230508 CGGTACTAAAGAGGCTGTGTCA 59.769 50.000 0.00 0.00 0.00 3.58
16 17 2.416972 CCGGTACTAAAGAGGCTGTGTC 60.417 54.545 0.00 0.00 0.00 3.67
17 18 1.549170 CCGGTACTAAAGAGGCTGTGT 59.451 52.381 0.00 0.00 0.00 3.72
18 19 1.549170 ACCGGTACTAAAGAGGCTGTG 59.451 52.381 4.49 0.00 0.00 3.66
19 20 1.934410 ACCGGTACTAAAGAGGCTGT 58.066 50.000 4.49 0.00 0.00 4.40
20 21 2.232941 TCAACCGGTACTAAAGAGGCTG 59.767 50.000 8.00 0.00 0.00 4.85
21 22 2.532843 TCAACCGGTACTAAAGAGGCT 58.467 47.619 8.00 0.00 0.00 4.58
22 23 3.455327 GATCAACCGGTACTAAAGAGGC 58.545 50.000 8.00 0.00 0.00 4.70
23 24 3.703420 CGATCAACCGGTACTAAAGAGG 58.297 50.000 8.00 0.00 0.00 3.69
24 25 3.114065 GCGATCAACCGGTACTAAAGAG 58.886 50.000 8.00 0.00 0.00 2.85
25 26 2.159198 GGCGATCAACCGGTACTAAAGA 60.159 50.000 8.00 0.00 0.00 2.52
26 27 2.199236 GGCGATCAACCGGTACTAAAG 58.801 52.381 8.00 0.00 0.00 1.85
27 28 2.298411 GGCGATCAACCGGTACTAAA 57.702 50.000 8.00 0.00 0.00 1.85
37 38 3.115892 TTCGTGGCGGCGATCAAC 61.116 61.111 12.98 0.87 40.76 3.18
38 39 3.115892 GTTCGTGGCGGCGATCAA 61.116 61.111 12.98 0.00 40.76 2.57
48 49 0.672401 ACATTAGTGCCGGTTCGTGG 60.672 55.000 1.90 0.00 0.00 4.94
49 50 1.657094 GTACATTAGTGCCGGTTCGTG 59.343 52.381 1.90 0.00 0.00 4.35
50 51 1.273048 TGTACATTAGTGCCGGTTCGT 59.727 47.619 1.90 0.00 0.00 3.85
51 52 1.657094 GTGTACATTAGTGCCGGTTCG 59.343 52.381 1.90 0.00 0.00 3.95
52 53 2.690786 TGTGTACATTAGTGCCGGTTC 58.309 47.619 1.90 0.00 0.00 3.62
53 54 2.843401 TGTGTACATTAGTGCCGGTT 57.157 45.000 1.90 0.00 0.00 4.44
54 55 3.343941 AATGTGTACATTAGTGCCGGT 57.656 42.857 8.40 0.00 44.09 5.28
62 63 3.118555 AGCCGGCACTAATGTGTACATTA 60.119 43.478 31.54 14.68 44.09 1.90
64 65 1.209504 AGCCGGCACTAATGTGTACAT 59.790 47.619 31.54 0.00 45.44 2.29
65 66 0.611200 AGCCGGCACTAATGTGTACA 59.389 50.000 31.54 0.00 45.44 2.90
66 67 1.006832 CAGCCGGCACTAATGTGTAC 58.993 55.000 31.54 0.00 45.44 2.90
67 68 0.899019 TCAGCCGGCACTAATGTGTA 59.101 50.000 31.54 3.54 45.44 2.90
68 69 0.036164 TTCAGCCGGCACTAATGTGT 59.964 50.000 31.54 0.00 45.44 3.72
69 70 1.164411 TTTCAGCCGGCACTAATGTG 58.836 50.000 31.54 16.59 46.37 3.21
70 71 2.128771 ATTTCAGCCGGCACTAATGT 57.871 45.000 31.54 1.71 0.00 2.71
71 72 2.423185 TGAATTTCAGCCGGCACTAATG 59.577 45.455 31.54 18.23 0.00 1.90
72 73 2.722094 TGAATTTCAGCCGGCACTAAT 58.278 42.857 31.54 20.32 0.00 1.73
73 74 2.192664 TGAATTTCAGCCGGCACTAA 57.807 45.000 31.54 18.90 0.00 2.24
74 75 2.192664 TTGAATTTCAGCCGGCACTA 57.807 45.000 31.54 10.66 0.00 2.74
75 76 1.000274 GTTTGAATTTCAGCCGGCACT 60.000 47.619 31.54 5.56 0.00 4.40
76 77 1.418373 GTTTGAATTTCAGCCGGCAC 58.582 50.000 31.54 10.10 0.00 5.01
77 78 0.316841 GGTTTGAATTTCAGCCGGCA 59.683 50.000 31.54 8.23 0.00 5.69
78 79 0.732538 CGGTTTGAATTTCAGCCGGC 60.733 55.000 21.89 21.89 40.49 6.13
79 80 3.399879 CGGTTTGAATTTCAGCCGG 57.600 52.632 24.52 0.00 40.49 6.13
80 81 0.732538 GCCGGTTTGAATTTCAGCCG 60.733 55.000 24.94 24.94 42.31 5.52
81 82 0.316841 TGCCGGTTTGAATTTCAGCC 59.683 50.000 1.90 10.35 0.00 4.85
82 83 1.000274 AGTGCCGGTTTGAATTTCAGC 60.000 47.619 1.90 0.34 0.00 4.26
83 84 4.701956 ATAGTGCCGGTTTGAATTTCAG 57.298 40.909 1.90 0.00 0.00 3.02
84 85 4.279671 ACAATAGTGCCGGTTTGAATTTCA 59.720 37.500 1.90 0.00 0.00 2.69
85 86 4.621034 CACAATAGTGCCGGTTTGAATTTC 59.379 41.667 1.90 0.00 39.21 2.17
86 87 4.555262 CACAATAGTGCCGGTTTGAATTT 58.445 39.130 1.90 0.00 39.21 1.82
87 88 4.173036 CACAATAGTGCCGGTTTGAATT 57.827 40.909 1.90 0.00 39.21 2.17
88 89 3.848272 CACAATAGTGCCGGTTTGAAT 57.152 42.857 1.90 0.00 39.21 2.57
106 107 3.733443 AAAGGGTCAAATGTGAAGCAC 57.267 42.857 0.00 0.00 34.87 4.40
107 108 4.405358 AGAAAAAGGGTCAAATGTGAAGCA 59.595 37.500 0.00 0.00 34.87 3.91
108 109 4.948847 AGAAAAAGGGTCAAATGTGAAGC 58.051 39.130 0.00 0.00 34.87 3.86
109 110 7.277174 AGTAGAAAAAGGGTCAAATGTGAAG 57.723 36.000 0.00 0.00 34.87 3.02
110 111 7.996644 ACTAGTAGAAAAAGGGTCAAATGTGAA 59.003 33.333 3.59 0.00 34.87 3.18
111 112 7.444183 CACTAGTAGAAAAAGGGTCAAATGTGA 59.556 37.037 3.59 0.00 0.00 3.58
112 113 7.228706 ACACTAGTAGAAAAAGGGTCAAATGTG 59.771 37.037 3.59 0.00 0.00 3.21
113 114 7.228706 CACACTAGTAGAAAAAGGGTCAAATGT 59.771 37.037 3.59 0.00 0.00 2.71
114 115 7.444183 TCACACTAGTAGAAAAAGGGTCAAATG 59.556 37.037 3.59 0.00 0.00 2.32
115 116 7.444487 GTCACACTAGTAGAAAAAGGGTCAAAT 59.556 37.037 3.59 0.00 0.00 2.32
116 117 6.764560 GTCACACTAGTAGAAAAAGGGTCAAA 59.235 38.462 3.59 0.00 0.00 2.69
117 118 6.099269 AGTCACACTAGTAGAAAAAGGGTCAA 59.901 38.462 3.59 0.00 0.00 3.18
118 119 5.601313 AGTCACACTAGTAGAAAAAGGGTCA 59.399 40.000 3.59 0.00 0.00 4.02
119 120 6.099159 AGTCACACTAGTAGAAAAAGGGTC 57.901 41.667 3.59 0.00 0.00 4.46
120 121 7.229581 CTAGTCACACTAGTAGAAAAAGGGT 57.770 40.000 3.59 0.00 42.41 4.34
133 134 3.409570 ACTCAACTCGCTAGTCACACTA 58.590 45.455 0.00 0.00 33.75 2.74
134 135 2.231529 ACTCAACTCGCTAGTCACACT 58.768 47.619 0.00 0.00 33.75 3.55
135 136 2.708386 ACTCAACTCGCTAGTCACAC 57.292 50.000 0.00 0.00 33.75 3.82
136 137 2.862530 GCAACTCAACTCGCTAGTCACA 60.863 50.000 0.00 0.00 33.75 3.58
137 138 1.721926 GCAACTCAACTCGCTAGTCAC 59.278 52.381 0.00 0.00 33.75 3.67
138 139 1.336887 GGCAACTCAACTCGCTAGTCA 60.337 52.381 0.00 0.00 33.75 3.41
139 140 1.351153 GGCAACTCAACTCGCTAGTC 58.649 55.000 0.00 0.00 33.75 2.59
140 141 3.516578 GGCAACTCAACTCGCTAGT 57.483 52.632 0.00 0.00 37.65 2.57
156 157 3.795022 TGTAGACCACATCCCGTAAGGC 61.795 54.545 0.00 0.00 45.12 4.35
157 158 2.104967 TGTAGACCACATCCCGTAAGG 58.895 52.381 0.00 0.00 45.77 2.69
167 168 2.104967 CGGAGGGTAATGTAGACCACA 58.895 52.381 0.00 0.00 42.69 4.17
168 169 1.202498 GCGGAGGGTAATGTAGACCAC 60.202 57.143 0.00 0.00 38.86 4.16
169 170 1.117150 GCGGAGGGTAATGTAGACCA 58.883 55.000 0.00 0.00 38.86 4.02
170 171 0.391966 GGCGGAGGGTAATGTAGACC 59.608 60.000 0.00 0.00 36.12 3.85
171 172 1.117150 TGGCGGAGGGTAATGTAGAC 58.883 55.000 0.00 0.00 0.00 2.59
172 173 1.117150 GTGGCGGAGGGTAATGTAGA 58.883 55.000 0.00 0.00 0.00 2.59
173 174 0.828022 TGTGGCGGAGGGTAATGTAG 59.172 55.000 0.00 0.00 0.00 2.74
174 175 0.538118 GTGTGGCGGAGGGTAATGTA 59.462 55.000 0.00 0.00 0.00 2.29
175 176 1.298667 GTGTGGCGGAGGGTAATGT 59.701 57.895 0.00 0.00 0.00 2.71
176 177 1.451387 GGTGTGGCGGAGGGTAATG 60.451 63.158 0.00 0.00 0.00 1.90
177 178 1.615424 AGGTGTGGCGGAGGGTAAT 60.615 57.895 0.00 0.00 0.00 1.89
178 179 2.203877 AGGTGTGGCGGAGGGTAA 60.204 61.111 0.00 0.00 0.00 2.85
179 180 2.682494 GAGGTGTGGCGGAGGGTA 60.682 66.667 0.00 0.00 0.00 3.69
182 183 4.087892 CAGGAGGTGTGGCGGAGG 62.088 72.222 0.00 0.00 0.00 4.30
183 184 4.767255 GCAGGAGGTGTGGCGGAG 62.767 72.222 0.00 0.00 0.00 4.63
187 188 3.680620 TATGCGCAGGAGGTGTGGC 62.681 63.158 18.32 0.00 37.13 5.01
188 189 1.522355 CTATGCGCAGGAGGTGTGG 60.522 63.158 18.32 0.00 37.13 4.17
189 190 1.522355 CCTATGCGCAGGAGGTGTG 60.522 63.158 25.91 7.18 38.00 3.82
190 191 0.686441 TACCTATGCGCAGGAGGTGT 60.686 55.000 38.29 24.48 43.55 4.16
191 192 0.249489 GTACCTATGCGCAGGAGGTG 60.249 60.000 38.29 20.61 43.55 4.00
192 193 0.686441 TGTACCTATGCGCAGGAGGT 60.686 55.000 35.69 35.69 45.63 3.85
193 194 0.032678 CTGTACCTATGCGCAGGAGG 59.967 60.000 30.17 30.17 39.18 4.30
194 195 0.747255 ACTGTACCTATGCGCAGGAG 59.253 55.000 21.44 17.43 39.18 3.69
195 196 1.136305 GAACTGTACCTATGCGCAGGA 59.864 52.381 21.44 8.62 39.18 3.86
196 197 1.571919 GAACTGTACCTATGCGCAGG 58.428 55.000 18.32 15.77 41.87 4.85
197 198 1.200483 CGAACTGTACCTATGCGCAG 58.800 55.000 18.32 4.62 35.31 5.18
198 199 0.804544 GCGAACTGTACCTATGCGCA 60.805 55.000 14.96 14.96 42.21 6.09
199 200 1.488261 GGCGAACTGTACCTATGCGC 61.488 60.000 0.00 0.00 41.95 6.09
200 201 0.179121 TGGCGAACTGTACCTATGCG 60.179 55.000 0.00 0.00 0.00 4.73
201 202 1.571919 CTGGCGAACTGTACCTATGC 58.428 55.000 0.00 0.00 0.00 3.14
202 203 1.754803 TCCTGGCGAACTGTACCTATG 59.245 52.381 0.00 0.00 0.00 2.23
203 204 2.154567 TCCTGGCGAACTGTACCTAT 57.845 50.000 0.00 0.00 0.00 2.57
204 205 1.754803 CATCCTGGCGAACTGTACCTA 59.245 52.381 0.00 0.00 0.00 3.08
205 206 0.537188 CATCCTGGCGAACTGTACCT 59.463 55.000 0.00 0.00 0.00 3.08
206 207 0.249398 ACATCCTGGCGAACTGTACC 59.751 55.000 0.00 0.00 0.00 3.34
207 208 1.359848 CACATCCTGGCGAACTGTAC 58.640 55.000 0.00 0.00 0.00 2.90
208 209 0.249120 CCACATCCTGGCGAACTGTA 59.751 55.000 0.00 0.00 31.36 2.74
209 210 1.003355 CCACATCCTGGCGAACTGT 60.003 57.895 0.00 0.00 31.36 3.55
210 211 1.003355 ACCACATCCTGGCGAACTG 60.003 57.895 0.00 0.00 45.32 3.16
211 212 1.194781 AGACCACATCCTGGCGAACT 61.195 55.000 0.00 0.00 45.32 3.01
212 213 0.535335 TAGACCACATCCTGGCGAAC 59.465 55.000 0.00 0.00 45.32 3.95
213 214 0.535335 GTAGACCACATCCTGGCGAA 59.465 55.000 0.00 0.00 45.32 4.70
214 215 0.613572 TGTAGACCACATCCTGGCGA 60.614 55.000 0.00 0.00 45.32 5.54
215 216 0.465705 ATGTAGACCACATCCTGGCG 59.534 55.000 0.00 0.00 44.99 5.69
223 224 2.104967 CGGAGGGTAATGTAGACCACA 58.895 52.381 0.00 0.00 42.69 4.17
224 225 1.202498 GCGGAGGGTAATGTAGACCAC 60.202 57.143 0.00 0.00 38.86 4.16
225 226 1.117150 GCGGAGGGTAATGTAGACCA 58.883 55.000 0.00 0.00 38.86 4.02
226 227 0.391966 GGCGGAGGGTAATGTAGACC 59.608 60.000 0.00 0.00 36.12 3.85
227 228 1.068741 CAGGCGGAGGGTAATGTAGAC 59.931 57.143 0.00 0.00 0.00 2.59
228 229 1.410004 CAGGCGGAGGGTAATGTAGA 58.590 55.000 0.00 0.00 0.00 2.59
229 230 0.249911 GCAGGCGGAGGGTAATGTAG 60.250 60.000 0.00 0.00 0.00 2.74
230 231 0.978667 TGCAGGCGGAGGGTAATGTA 60.979 55.000 0.00 0.00 0.00 2.29
231 232 1.635817 ATGCAGGCGGAGGGTAATGT 61.636 55.000 0.00 0.00 0.00 2.71
232 233 1.149174 ATGCAGGCGGAGGGTAATG 59.851 57.895 0.00 0.00 0.00 1.90
233 234 1.149174 CATGCAGGCGGAGGGTAAT 59.851 57.895 0.00 0.00 0.00 1.89
234 235 2.589540 CATGCAGGCGGAGGGTAA 59.410 61.111 0.00 0.00 0.00 2.85
235 236 4.175337 GCATGCAGGCGGAGGGTA 62.175 66.667 14.21 0.00 0.00 3.69
242 243 3.087273 CTACACGTGCATGCAGGCG 62.087 63.158 33.85 28.93 35.48 5.52
243 244 2.787249 CTACACGTGCATGCAGGC 59.213 61.111 33.85 18.05 35.48 4.85
244 245 1.974249 CTGCTACACGTGCATGCAGG 61.974 60.000 32.15 32.69 44.95 4.85
245 246 1.422662 CTGCTACACGTGCATGCAG 59.577 57.895 29.62 29.62 43.71 4.41
246 247 2.034317 CCTGCTACACGTGCATGCA 61.034 57.895 18.46 18.46 39.86 3.96
247 248 2.787249 CCTGCTACACGTGCATGC 59.213 61.111 17.22 17.31 39.86 4.06
248 249 1.576451 TTGCCTGCTACACGTGCATG 61.576 55.000 17.22 3.82 39.86 4.06
249 250 1.300971 CTTGCCTGCTACACGTGCAT 61.301 55.000 17.22 0.00 39.86 3.96
250 251 1.960763 CTTGCCTGCTACACGTGCA 60.961 57.895 17.22 7.23 38.81 4.57
251 252 2.680913 CCTTGCCTGCTACACGTGC 61.681 63.158 17.22 1.66 0.00 5.34
252 253 0.391661 ATCCTTGCCTGCTACACGTG 60.392 55.000 15.48 15.48 0.00 4.49
253 254 0.324943 AATCCTTGCCTGCTACACGT 59.675 50.000 0.00 0.00 0.00 4.49
254 255 1.131126 CAAATCCTTGCCTGCTACACG 59.869 52.381 0.00 0.00 0.00 4.49
255 256 1.474077 CCAAATCCTTGCCTGCTACAC 59.526 52.381 0.00 0.00 0.00 2.90
256 257 1.354031 TCCAAATCCTTGCCTGCTACA 59.646 47.619 0.00 0.00 0.00 2.74
257 258 2.128771 TCCAAATCCTTGCCTGCTAC 57.871 50.000 0.00 0.00 0.00 3.58
258 259 2.423373 GGATCCAAATCCTTGCCTGCTA 60.423 50.000 6.95 0.00 46.97 3.49
259 260 1.687368 GGATCCAAATCCTTGCCTGCT 60.687 52.381 6.95 0.00 46.97 4.24
260 261 0.749049 GGATCCAAATCCTTGCCTGC 59.251 55.000 6.95 0.00 46.97 4.85
496 498 1.246649 ATTGTTGCTGTGGCGATTCA 58.753 45.000 0.00 0.00 42.25 2.57
564 566 0.813184 CGAATCCCATTGCTGCTGTT 59.187 50.000 0.00 0.00 0.00 3.16
566 568 1.097232 TTCGAATCCCATTGCTGCTG 58.903 50.000 0.00 0.00 0.00 4.41
595 645 2.557920 AGGAACTCTTGCAGAACAGG 57.442 50.000 0.00 0.00 0.00 4.00
601 651 7.492994 GGTTAGATACTTTAGGAACTCTTGCAG 59.507 40.741 0.00 0.00 41.75 4.41
602 652 7.180408 AGGTTAGATACTTTAGGAACTCTTGCA 59.820 37.037 0.00 0.00 41.75 4.08
734 793 1.475403 ACTCCAGATTGACGTCGGAT 58.525 50.000 11.62 7.52 0.00 4.18
735 794 1.067846 CAACTCCAGATTGACGTCGGA 60.068 52.381 11.62 9.87 0.00 4.55
736 795 1.336887 ACAACTCCAGATTGACGTCGG 60.337 52.381 11.62 5.55 0.00 4.79
737 796 1.721389 CACAACTCCAGATTGACGTCG 59.279 52.381 11.62 0.00 0.00 5.12
738 797 1.461127 GCACAACTCCAGATTGACGTC 59.539 52.381 9.11 9.11 0.00 4.34
739 798 1.202639 TGCACAACTCCAGATTGACGT 60.203 47.619 0.00 0.00 0.00 4.34
740 799 1.511850 TGCACAACTCCAGATTGACG 58.488 50.000 0.00 0.00 0.00 4.35
741 800 2.618241 TGTTGCACAACTCCAGATTGAC 59.382 45.455 14.16 0.00 41.67 3.18
787 846 3.744426 GCTGGACTCGTAAAGCAGTAAAA 59.256 43.478 0.00 0.00 35.69 1.52
838 897 0.937699 TCCGTCTTCAAGTGTTCGCG 60.938 55.000 0.00 0.00 0.00 5.87
875 945 5.457799 CAGATTCACATTTGGATTCGCATTC 59.542 40.000 0.00 0.00 0.00 2.67
1029 1099 0.670162 AGGTGCAATGCAATATCGGC 59.330 50.000 10.44 0.00 41.47 5.54
1688 1911 3.512516 GGCGTCAATGGGCTCAGC 61.513 66.667 0.00 0.00 0.00 4.26
1826 2082 2.185350 CTCGATGCGCTTCTGGGT 59.815 61.111 19.63 0.00 0.00 4.51
2032 2294 4.643387 AGCCCGCCGTGCTTCTTT 62.643 61.111 0.00 0.00 34.87 2.52
2168 2430 2.871096 TCCATCACTTGTAACCCACC 57.129 50.000 0.00 0.00 0.00 4.61
2246 2508 0.601558 GCCGCCGTCTATATCTTGGA 59.398 55.000 0.00 0.00 0.00 3.53
2330 2592 2.845586 TCACATCCAGACATCCAATCCA 59.154 45.455 0.00 0.00 0.00 3.41
2357 2619 6.843752 TCCCTCCATGTCTAAACAAAAACTA 58.156 36.000 0.00 0.00 39.30 2.24
2384 2646 7.362401 GGTTTCATGATCTCAGTTTTGCTATGT 60.362 37.037 0.00 0.00 0.00 2.29
2385 2647 6.971184 GGTTTCATGATCTCAGTTTTGCTATG 59.029 38.462 0.00 0.00 0.00 2.23
2386 2648 6.660521 TGGTTTCATGATCTCAGTTTTGCTAT 59.339 34.615 0.00 0.00 0.00 2.97
2387 2649 6.003326 TGGTTTCATGATCTCAGTTTTGCTA 58.997 36.000 0.00 0.00 0.00 3.49
2388 2650 4.828939 TGGTTTCATGATCTCAGTTTTGCT 59.171 37.500 0.00 0.00 0.00 3.91
2457 2721 2.959707 TGAACCAAACGCCACCTAAAAT 59.040 40.909 0.00 0.00 0.00 1.82
2702 3124 5.061853 ACTGCAGCCTGATCAGTTATTATG 58.938 41.667 21.11 10.78 37.78 1.90
2814 3237 1.602237 CGTGCCTGATGGGTTAGGT 59.398 57.895 0.00 0.00 36.44 3.08
3077 3541 0.977395 CACCTTTCCTCGTCCTCCTT 59.023 55.000 0.00 0.00 0.00 3.36
3219 3705 4.689812 CCAAGATGCTGAGAATATTCCTCG 59.310 45.833 11.92 1.95 33.51 4.63
3326 3816 0.179004 AGGTGGCGTTTGGTTCATCA 60.179 50.000 0.00 0.00 0.00 3.07
3395 3885 7.847878 ACATAACCATGTAACATCTCGATGTGT 60.848 37.037 12.84 3.50 45.31 3.72
3396 3886 6.479990 ACATAACCATGTAACATCTCGATGTG 59.520 38.462 12.84 2.92 45.31 3.21
3397 3887 6.582636 ACATAACCATGTAACATCTCGATGT 58.417 36.000 6.72 6.72 44.37 3.06
3398 3888 6.701400 TGACATAACCATGTAACATCTCGATG 59.299 38.462 5.40 5.40 45.58 3.84
3399 3889 6.701841 GTGACATAACCATGTAACATCTCGAT 59.298 38.462 1.14 0.00 45.58 3.59
3400 3890 6.040247 GTGACATAACCATGTAACATCTCGA 58.960 40.000 1.14 0.00 45.58 4.04
3401 3891 6.274001 GTGACATAACCATGTAACATCTCG 57.726 41.667 1.14 0.00 45.58 4.04
3409 3899 9.508642 TCAGTTTAAATGTGACATAACCATGTA 57.491 29.630 0.00 0.00 45.58 2.29
3411 3901 9.292846 CATCAGTTTAAATGTGACATAACCATG 57.707 33.333 0.00 2.39 38.21 3.66
3412 3902 9.023962 ACATCAGTTTAAATGTGACATAACCAT 57.976 29.630 0.00 0.00 34.88 3.55
3413 3903 8.402798 ACATCAGTTTAAATGTGACATAACCA 57.597 30.769 0.00 0.00 34.88 3.67
3414 3904 7.968405 GGACATCAGTTTAAATGTGACATAACC 59.032 37.037 0.00 0.00 36.28 2.85
3415 3905 8.511321 TGGACATCAGTTTAAATGTGACATAAC 58.489 33.333 0.00 0.00 36.28 1.89
3416 3906 8.511321 GTGGACATCAGTTTAAATGTGACATAA 58.489 33.333 0.00 0.00 36.28 1.90
3417 3907 7.882791 AGTGGACATCAGTTTAAATGTGACATA 59.117 33.333 0.00 0.00 36.28 2.29
3418 3908 6.716628 AGTGGACATCAGTTTAAATGTGACAT 59.283 34.615 0.00 0.00 36.28 3.06
3419 3909 6.061441 AGTGGACATCAGTTTAAATGTGACA 58.939 36.000 5.59 0.00 36.28 3.58
3420 3910 6.428159 AGAGTGGACATCAGTTTAAATGTGAC 59.572 38.462 5.59 0.05 36.28 3.67
3421 3911 6.427853 CAGAGTGGACATCAGTTTAAATGTGA 59.572 38.462 5.87 5.87 36.28 3.58
3422 3912 6.205464 ACAGAGTGGACATCAGTTTAAATGTG 59.795 38.462 0.00 0.00 36.28 3.21
3423 3913 6.299141 ACAGAGTGGACATCAGTTTAAATGT 58.701 36.000 0.00 0.00 38.78 2.71
3424 3914 6.808008 ACAGAGTGGACATCAGTTTAAATG 57.192 37.500 0.00 0.00 0.00 2.32
3425 3915 7.285401 ACAAACAGAGTGGACATCAGTTTAAAT 59.715 33.333 0.00 0.00 35.12 1.40
3426 3916 6.601613 ACAAACAGAGTGGACATCAGTTTAAA 59.398 34.615 0.00 0.00 35.12 1.52
3427 3917 6.038161 CACAAACAGAGTGGACATCAGTTTAA 59.962 38.462 0.00 0.00 35.12 1.52
3428 3918 5.527214 CACAAACAGAGTGGACATCAGTTTA 59.473 40.000 0.00 0.00 35.12 2.01
3429 3919 4.336433 CACAAACAGAGTGGACATCAGTTT 59.664 41.667 0.00 0.00 37.00 2.66
3430 3920 3.879295 CACAAACAGAGTGGACATCAGTT 59.121 43.478 0.00 0.00 33.43 3.16
3431 3921 3.470709 CACAAACAGAGTGGACATCAGT 58.529 45.455 0.00 0.00 33.43 3.41


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

AutoCloner maintained by Alex Coulton.