Multiple sequence alignment - TraesCS3A01G488000

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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 TraesCS3A01G488000 chr3A 100.000 3186 0 0 1 3186 715972777 715975962 0.000000e+00 5884.0
1 TraesCS3A01G488000 chr3A 97.297 222 5 1 2965 3186 451720299 451720079 3.000000e-100 375.0
2 TraesCS3A01G488000 chr3A 85.065 154 5 7 2965 3118 715977321 715977186 1.190000e-29 141.0
3 TraesCS3A01G488000 chr3A 91.304 69 6 0 2965 3033 451718702 451718770 9.410000e-16 95.3
4 TraesCS3A01G488000 chr3B 91.192 2123 132 28 466 2568 775735021 775737108 0.000000e+00 2833.0
5 TraesCS3A01G488000 chr3B 86.042 566 28 25 2418 2964 775736942 775737475 7.720000e-156 560.0
6 TraesCS3A01G488000 chr3D 95.062 1782 75 6 615 2391 580521385 580523158 0.000000e+00 2791.0
7 TraesCS3A01G488000 chr3D 92.358 458 15 7 2418 2859 580523157 580523610 4.480000e-178 634.0
8 TraesCS3A01G488000 chr3D 89.655 290 22 6 376 663 580521101 580521384 2.340000e-96 363.0
9 TraesCS3A01G488000 chr3D 86.774 310 38 2 1 310 580520794 580521100 3.040000e-90 342.0
10 TraesCS3A01G488000 chr6B 89.128 1536 113 19 871 2374 498544192 498542679 0.000000e+00 1862.0
11 TraesCS3A01G488000 chr6B 83.215 423 37 21 2558 2964 498542521 498542117 1.090000e-94 357.0
12 TraesCS3A01G488000 chr6B 84.038 213 27 6 1551 1758 498852254 498852464 6.970000e-47 198.0
13 TraesCS3A01G488000 chr6B 76.694 369 61 19 1116 1469 498851784 498852142 7.020000e-42 182.0
14 TraesCS3A01G488000 chr6B 78.879 232 43 6 648 874 39362977 39362747 5.500000e-33 152.0
15 TraesCS3A01G488000 chr6D 89.112 1497 116 16 871 2339 324783009 324784486 0.000000e+00 1818.0
16 TraesCS3A01G488000 chr6D 75.377 1259 202 67 982 2195 324599437 324598242 2.840000e-140 508.0
17 TraesCS3A01G488000 chr6D 80.977 389 38 19 2555 2920 324785012 324785387 3.130000e-70 276.0
18 TraesCS3A01G488000 chr6D 82.407 216 28 10 648 855 335360325 335360538 2.520000e-41 180.0
19 TraesCS3A01G488000 chr6A 88.467 1500 119 22 871 2339 462225715 462227191 0.000000e+00 1762.0
20 TraesCS3A01G488000 chr6A 79.066 664 108 24 1551 2195 461987185 461986534 8.170000e-116 427.0
21 TraesCS3A01G488000 chr6A 80.460 348 33 19 2556 2879 462227391 462227727 1.910000e-57 233.0
22 TraesCS3A01G488000 chr6A 75.299 502 74 32 982 1465 461987731 461987262 9.020000e-46 195.0
23 TraesCS3A01G488000 chr4A 98.655 223 2 1 2964 3186 436397784 436397563 8.280000e-106 394.0
24 TraesCS3A01G488000 chr7A 93.333 225 12 2 2964 3186 235691495 235691718 2.370000e-86 329.0
25 TraesCS3A01G488000 chr7A 90.909 154 13 1 2965 3118 235693087 235692935 4.170000e-49 206.0
26 TraesCS3A01G488000 chr7A 78.758 306 53 8 57 358 705698554 705698851 9.020000e-46 195.0
27 TraesCS3A01G488000 chr2B 90.541 222 14 4 2970 3186 718216390 718216609 1.450000e-73 287.0
28 TraesCS3A01G488000 chr2B 81.714 175 29 3 70 241 13368031 13367857 3.310000e-30 143.0
29 TraesCS3A01G488000 chr1A 82.562 281 39 10 88 363 522186316 522186041 4.110000e-59 239.0
30 TraesCS3A01G488000 chr5A 80.678 295 51 6 70 360 471460329 471460621 1.150000e-54 224.0
31 TraesCS3A01G488000 chr5A 80.435 230 37 6 648 871 205012886 205013113 5.470000e-38 169.0
32 TraesCS3A01G488000 chr5A 78.970 233 42 7 648 875 303188895 303189125 5.500000e-33 152.0
33 TraesCS3A01G488000 chr2D 83.099 213 33 3 113 323 172390555 172390766 1.170000e-44 191.0
34 TraesCS3A01G488000 chr4D 79.476 229 39 7 650 872 499679822 499680048 4.260000e-34 156.0
35 TraesCS3A01G488000 chr7D 78.947 228 43 4 648 871 568468249 568468023 1.980000e-32 150.0
36 TraesCS3A01G488000 chr5D 78.509 228 44 4 648 871 347680282 347680056 9.210000e-31 145.0


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 TraesCS3A01G488000 chr3A 715972777 715975962 3185 False 5884.0 5884 100.00000 1 3186 1 chr3A.!!$F2 3185
1 TraesCS3A01G488000 chr3B 775735021 775737475 2454 False 1696.5 2833 88.61700 466 2964 2 chr3B.!!$F1 2498
2 TraesCS3A01G488000 chr3D 580520794 580523610 2816 False 1032.5 2791 90.96225 1 2859 4 chr3D.!!$F1 2858
3 TraesCS3A01G488000 chr6B 498542117 498544192 2075 True 1109.5 1862 86.17150 871 2964 2 chr6B.!!$R2 2093
4 TraesCS3A01G488000 chr6D 324783009 324785387 2378 False 1047.0 1818 85.04450 871 2920 2 chr6D.!!$F2 2049
5 TraesCS3A01G488000 chr6D 324598242 324599437 1195 True 508.0 508 75.37700 982 2195 1 chr6D.!!$R1 1213
6 TraesCS3A01G488000 chr6A 462225715 462227727 2012 False 997.5 1762 84.46350 871 2879 2 chr6A.!!$F1 2008
7 TraesCS3A01G488000 chr6A 461986534 461987731 1197 True 311.0 427 77.18250 982 2195 2 chr6A.!!$R1 1213

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
180 181 0.323269 TGGGATGCGCTTTCAATGGA 60.323 50.0 9.73 0.0 0.00 3.41 F
1004 1076 0.454600 CTACAAGCAGCAGCAATGGG 59.545 55.0 3.17 0.0 45.49 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1054 1129 0.037975 CAAGCAATGGGGCTCACAAC 60.038 55.0 0.0 0.0 45.07 3.32 R
3000 3522 0.165944 GTGTGTCCGCATGTTACAGC 59.834 55.0 0.0 0.0 0.00 4.40 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
25 26 8.931385 TTTATAATAGGTACACGAACAGTTCC 57.069 34.615 7.76 0.00 0.00 3.62
27 28 2.814280 AGGTACACGAACAGTTCCAG 57.186 50.000 7.76 3.15 0.00 3.86
30 31 3.323979 AGGTACACGAACAGTTCCAGATT 59.676 43.478 7.76 0.00 0.00 2.40
44 45 7.285401 ACAGTTCCAGATTAAACTTCACAACAT 59.715 33.333 0.00 0.00 33.53 2.71
68 69 1.243902 GTTCTTCGCAAACCATCCCA 58.756 50.000 0.00 0.00 0.00 4.37
98 99 6.844388 TGGATGGTTATAGAGACAGTGGTATT 59.156 38.462 0.00 0.00 0.00 1.89
99 100 7.015292 TGGATGGTTATAGAGACAGTGGTATTC 59.985 40.741 0.00 0.00 0.00 1.75
126 127 5.102953 CCATCAAGGTTCAAGTCCTGATA 57.897 43.478 0.00 0.00 35.27 2.15
141 142 5.305644 AGTCCTGATACTCGCATTATTCCTT 59.694 40.000 0.00 0.00 0.00 3.36
153 154 9.390795 CTCGCATTATTCCTTGATTTATTTCAG 57.609 33.333 0.00 0.00 0.00 3.02
156 157 9.688592 GCATTATTCCTTGATTTATTTCAGGAG 57.311 33.333 0.00 0.00 30.13 3.69
161 162 6.248433 TCCTTGATTTATTTCAGGAGTTGCT 58.752 36.000 0.00 0.00 0.00 3.91
162 163 6.151648 TCCTTGATTTATTTCAGGAGTTGCTG 59.848 38.462 0.00 0.00 0.00 4.41
163 164 5.902613 TGATTTATTTCAGGAGTTGCTGG 57.097 39.130 0.69 0.00 0.00 4.85
165 166 4.380843 TTTATTTCAGGAGTTGCTGGGA 57.619 40.909 0.69 0.00 0.00 4.37
176 177 1.177895 TTGCTGGGATGCGCTTTCAA 61.178 50.000 9.73 0.00 35.36 2.69
177 178 0.966875 TGCTGGGATGCGCTTTCAAT 60.967 50.000 9.73 0.00 35.36 2.57
180 181 0.323269 TGGGATGCGCTTTCAATGGA 60.323 50.000 9.73 0.00 0.00 3.41
183 184 1.202336 GGATGCGCTTTCAATGGAAGG 60.202 52.381 9.73 0.00 33.82 3.46
184 185 1.745087 GATGCGCTTTCAATGGAAGGA 59.255 47.619 9.73 0.00 32.18 3.36
185 186 1.167851 TGCGCTTTCAATGGAAGGAG 58.832 50.000 9.73 0.00 32.18 3.69
212 213 3.057548 TCAACGACGAGGCGCCTA 61.058 61.111 32.97 8.37 33.86 3.93
217 218 2.601398 CGACGAGGCGCCTACGATA 61.601 63.158 37.37 0.00 43.93 2.92
270 271 4.770531 TCGGTCTCTCAAAGGTCTTCATAA 59.229 41.667 0.00 0.00 0.00 1.90
272 273 5.105716 CGGTCTCTCAAAGGTCTTCATAAGA 60.106 44.000 0.00 0.00 34.51 2.10
273 274 6.572509 CGGTCTCTCAAAGGTCTTCATAAGAA 60.573 42.308 0.00 0.00 39.67 2.52
288 289 4.403113 TCATAAGAATAGGGTGTGCGTGTA 59.597 41.667 0.00 0.00 0.00 2.90
310 311 7.713507 GTGTATGCATTTATAAGGGTGAGTGTA 59.286 37.037 3.54 0.00 0.00 2.90
311 312 8.436778 TGTATGCATTTATAAGGGTGAGTGTAT 58.563 33.333 3.54 0.00 0.00 2.29
312 313 7.750229 ATGCATTTATAAGGGTGAGTGTATG 57.250 36.000 0.00 0.00 0.00 2.39
313 314 5.530915 TGCATTTATAAGGGTGAGTGTATGC 59.469 40.000 0.00 0.00 36.21 3.14
314 315 5.530915 GCATTTATAAGGGTGAGTGTATGCA 59.469 40.000 0.00 0.00 35.84 3.96
315 316 6.207417 GCATTTATAAGGGTGAGTGTATGCAT 59.793 38.462 3.79 3.79 35.84 3.96
316 317 7.587629 CATTTATAAGGGTGAGTGTATGCATG 58.412 38.462 10.16 0.00 0.00 4.06
317 318 4.778213 ATAAGGGTGAGTGTATGCATGT 57.222 40.909 10.16 0.00 0.00 3.21
318 319 2.408271 AGGGTGAGTGTATGCATGTG 57.592 50.000 10.16 0.00 0.00 3.21
319 320 1.630369 AGGGTGAGTGTATGCATGTGT 59.370 47.619 10.16 0.00 0.00 3.72
320 321 2.837591 AGGGTGAGTGTATGCATGTGTA 59.162 45.455 10.16 0.00 0.00 2.90
321 322 3.455910 AGGGTGAGTGTATGCATGTGTAT 59.544 43.478 10.16 0.00 0.00 2.29
322 323 4.653801 AGGGTGAGTGTATGCATGTGTATA 59.346 41.667 10.16 0.00 0.00 1.47
323 324 4.750098 GGGTGAGTGTATGCATGTGTATAC 59.250 45.833 10.16 12.49 41.83 1.47
324 325 5.356426 GGTGAGTGTATGCATGTGTATACA 58.644 41.667 16.55 16.55 46.35 2.29
332 333 3.405170 GCATGTGTATACAAGCGCTTT 57.595 42.857 22.51 14.46 41.03 3.51
333 334 3.100817 GCATGTGTATACAAGCGCTTTG 58.899 45.455 22.51 17.99 41.03 2.77
334 335 2.892373 TGTGTATACAAGCGCTTTGC 57.108 45.000 22.51 10.82 46.98 3.68
336 337 4.717310 ATGTGTATACAAGCGCTTTGCGT 61.717 43.478 22.51 18.04 46.66 5.24
337 338 6.472862 ATGTGTATACAAGCGCTTTGCGTC 62.473 45.833 22.51 11.75 46.66 5.19
347 348 1.636988 GCTTTGCGTCCGTATAGTGT 58.363 50.000 0.00 0.00 0.00 3.55
348 349 1.997606 GCTTTGCGTCCGTATAGTGTT 59.002 47.619 0.00 0.00 0.00 3.32
349 350 3.181397 GCTTTGCGTCCGTATAGTGTTA 58.819 45.455 0.00 0.00 0.00 2.41
350 351 3.613737 GCTTTGCGTCCGTATAGTGTTAA 59.386 43.478 0.00 0.00 0.00 2.01
351 352 4.091800 GCTTTGCGTCCGTATAGTGTTAAA 59.908 41.667 0.00 0.00 0.00 1.52
352 353 5.389725 GCTTTGCGTCCGTATAGTGTTAAAA 60.390 40.000 0.00 0.00 0.00 1.52
353 354 6.536731 TTTGCGTCCGTATAGTGTTAAAAA 57.463 33.333 0.00 0.00 0.00 1.94
373 374 5.705609 AAAAACATGTGCGTTCTCCTATT 57.294 34.783 0.00 0.00 0.00 1.73
374 375 4.685169 AAACATGTGCGTTCTCCTATTG 57.315 40.909 0.00 0.00 0.00 1.90
377 378 4.181578 ACATGTGCGTTCTCCTATTGTAC 58.818 43.478 0.00 0.00 0.00 2.90
387 388 9.783256 GCGTTCTCCTATTGTACAATTTATTTT 57.217 29.630 25.31 3.66 32.50 1.82
408 409 0.505655 GTTACACGACGTTGGCTCAC 59.494 55.000 7.90 0.00 0.00 3.51
409 410 0.598158 TTACACGACGTTGGCTCACC 60.598 55.000 7.90 0.00 0.00 4.02
410 411 1.457823 TACACGACGTTGGCTCACCT 61.458 55.000 7.90 0.00 36.63 4.00
460 461 7.095439 GCTCATATTTGTAGGTAGTGCAGATTC 60.095 40.741 0.00 0.00 0.00 2.52
548 549 9.965902 ACTCATCCTGTTGTTCTTAATAATTCT 57.034 29.630 0.00 0.00 0.00 2.40
554 555 7.361713 CCTGTTGTTCTTAATAATTCTCGCCAA 60.362 37.037 0.00 0.00 0.00 4.52
572 573 1.462283 CAAGTACTCCGTTCGTCTCGA 59.538 52.381 0.00 0.00 0.00 4.04
573 574 2.021355 AGTACTCCGTTCGTCTCGAT 57.979 50.000 0.00 0.00 35.23 3.59
579 580 2.729882 CTCCGTTCGTCTCGATGTTTTT 59.270 45.455 0.00 0.00 35.23 1.94
585 586 5.777386 CGTTCGTCTCGATGTTTTTCTTTAC 59.223 40.000 0.00 0.00 35.23 2.01
586 587 6.345565 CGTTCGTCTCGATGTTTTTCTTTACT 60.346 38.462 0.00 0.00 35.23 2.24
590 592 8.392612 TCGTCTCGATGTTTTTCTTTACTTTTT 58.607 29.630 0.00 0.00 0.00 1.94
720 775 8.213518 AGATCAATAACATTGTACACATGGTC 57.786 34.615 16.95 6.81 0.00 4.02
723 778 8.039603 TCAATAACATTGTACACATGGTCTTC 57.960 34.615 16.95 0.00 0.00 2.87
738 793 8.950210 CACATGGTCTTCTTAATTTCTACATGT 58.050 33.333 2.69 2.69 43.97 3.21
760 815 1.299541 TTAGCGCATTAAGGAGCAGC 58.700 50.000 17.81 10.93 35.93 5.25
765 820 1.004927 CGCATTAAGGAGCAGCGTAAC 60.005 52.381 0.00 0.00 43.08 2.50
801 856 3.190535 GTGATGGCTTACCGTTTCAATGT 59.809 43.478 0.00 0.00 39.70 2.71
806 861 5.945155 TGGCTTACCGTTTCAATGTATTTC 58.055 37.500 0.00 0.00 39.70 2.17
1004 1076 0.454600 CTACAAGCAGCAGCAATGGG 59.545 55.000 3.17 0.00 45.49 4.00
1015 1087 1.720781 AGCAATGGGGAAAACTTGCT 58.279 45.000 2.97 2.97 46.96 3.91
1020 1095 2.470057 TGGGGAAAACTTGCTCCTTT 57.530 45.000 0.00 0.00 31.88 3.11
1052 1127 1.447217 CACTGGTGGTGCTCTCACA 59.553 57.895 8.83 0.00 44.87 3.58
1053 1128 0.179048 CACTGGTGGTGCTCTCACAA 60.179 55.000 8.83 0.00 44.87 3.33
1054 1129 0.107456 ACTGGTGGTGCTCTCACAAG 59.893 55.000 9.09 9.09 44.87 3.16
1135 1210 1.108727 TGCAGTCAAGGGCCACAAAG 61.109 55.000 6.18 0.00 0.00 2.77
1263 1344 7.415229 GTTAGTGCTTTGCTTACTTTACTGTT 58.585 34.615 0.00 0.00 0.00 3.16
1267 1348 4.976116 GCTTTGCTTACTTTACTGTTGGTG 59.024 41.667 0.00 0.00 0.00 4.17
1373 1467 1.827399 CTACCAGACCGCTGTTGGGT 61.827 60.000 9.19 9.19 40.63 4.51
1402 1496 3.807077 CTCGTCGATGATCGCCGCA 62.807 63.158 13.73 2.15 41.26 5.69
1807 1945 3.504906 TCTTCAGTCTACAGTTACACGGG 59.495 47.826 0.00 0.00 0.00 5.28
1814 1952 4.209911 GTCTACAGTTACACGGGAAACAAC 59.790 45.833 0.00 0.00 0.00 3.32
1937 2079 3.277416 ACCCCTTCTACTTCAAGACCT 57.723 47.619 0.00 0.00 0.00 3.85
2092 2240 1.612462 CCATTCTGCCTCAAGCTCACA 60.612 52.381 0.00 0.00 44.23 3.58
2223 2376 2.290367 TCTGCTCCGTGTGTGAATTTTG 59.710 45.455 0.00 0.00 0.00 2.44
2339 2499 3.388024 TCTGCATTCCCCTAGTGATGTAC 59.612 47.826 0.00 0.00 0.00 2.90
2340 2500 2.102420 TGCATTCCCCTAGTGATGTACG 59.898 50.000 0.00 0.00 0.00 3.67
2341 2501 2.102588 GCATTCCCCTAGTGATGTACGT 59.897 50.000 0.00 0.00 0.00 3.57
2342 2502 3.319972 GCATTCCCCTAGTGATGTACGTA 59.680 47.826 0.00 0.00 0.00 3.57
2377 2540 6.989659 AGTCCGTCTGTCTGTATTTTTCTTA 58.010 36.000 0.00 0.00 0.00 2.10
2393 2556 8.981724 ATTTTTCTTAATAAGAGGAAAACGGC 57.018 30.769 12.25 0.00 39.03 5.68
2405 2666 2.159693 GGAAAACGGCGAGAGAAATGAC 60.160 50.000 16.62 0.00 0.00 3.06
2406 2667 1.439679 AAACGGCGAGAGAAATGACC 58.560 50.000 16.62 0.00 0.00 4.02
2413 2674 2.416893 GCGAGAGAAATGACCTTTCACC 59.583 50.000 6.07 0.00 44.82 4.02
2416 2677 4.331168 CGAGAGAAATGACCTTTCACCATC 59.669 45.833 6.07 0.00 44.82 3.51
2466 2727 6.102663 CACTCTCAAGTTCAATACTCCGAAT 58.897 40.000 0.00 0.00 35.54 3.34
2467 2728 6.035435 CACTCTCAAGTTCAATACTCCGAATG 59.965 42.308 0.00 0.00 35.54 2.67
2500 2777 0.945813 TAAAACTTGAACCGGTGGCG 59.054 50.000 8.52 0.00 0.00 5.69
2550 2827 7.992180 ATAAAATTTCCTCATCATGAAACGC 57.008 32.000 0.00 0.00 33.64 4.84
2663 3166 2.350895 CCCTGTCATGCCGTGGAA 59.649 61.111 0.00 0.00 0.00 3.53
2704 3207 3.746045 AAACGTAGTCAAAGGAGCAGA 57.254 42.857 0.00 0.00 45.00 4.26
2705 3208 3.305398 AACGTAGTCAAAGGAGCAGAG 57.695 47.619 0.00 0.00 45.00 3.35
2810 3324 8.496707 TTCAGTTCTACGTACACATGTATAGA 57.503 34.615 0.00 0.00 32.54 1.98
2862 3376 9.449719 AATCTTCGGTTGTGTCTTTTCTATAAT 57.550 29.630 0.00 0.00 0.00 1.28
2867 3381 6.816640 CGGTTGTGTCTTTTCTATAATCAGGA 59.183 38.462 0.00 0.00 0.00 3.86
2868 3382 7.495934 CGGTTGTGTCTTTTCTATAATCAGGAT 59.504 37.037 0.00 0.00 0.00 3.24
2872 3386 8.258007 TGTGTCTTTTCTATAATCAGGATTCGT 58.742 33.333 0.00 0.00 32.50 3.85
2873 3387 9.099454 GTGTCTTTTCTATAATCAGGATTCGTT 57.901 33.333 0.00 0.00 32.50 3.85
2874 3388 9.314321 TGTCTTTTCTATAATCAGGATTCGTTC 57.686 33.333 0.00 0.00 32.50 3.95
2875 3389 9.535878 GTCTTTTCTATAATCAGGATTCGTTCT 57.464 33.333 0.00 0.00 32.50 3.01
2910 3432 6.600822 ACACTAGTACTCGGCTTTATGAACTA 59.399 38.462 0.00 0.00 0.00 2.24
2964 3486 3.120199 CCACAAATTAAGACGCTCCACTG 60.120 47.826 0.00 0.00 0.00 3.66
2965 3487 3.074412 ACAAATTAAGACGCTCCACTGG 58.926 45.455 0.00 0.00 0.00 4.00
2966 3488 3.244422 ACAAATTAAGACGCTCCACTGGA 60.244 43.478 0.00 0.00 0.00 3.86
2967 3489 2.674796 ATTAAGACGCTCCACTGGAC 57.325 50.000 0.00 0.00 0.00 4.02
2968 3490 1.334160 TTAAGACGCTCCACTGGACA 58.666 50.000 0.00 0.00 0.00 4.02
2969 3491 0.888619 TAAGACGCTCCACTGGACAG 59.111 55.000 0.00 0.00 0.00 3.51
2970 3492 1.821061 AAGACGCTCCACTGGACAGG 61.821 60.000 4.14 0.00 0.00 4.00
2971 3493 3.302347 GACGCTCCACTGGACAGGG 62.302 68.421 4.14 0.00 0.00 4.45
2972 3494 2.997315 CGCTCCACTGGACAGGGA 60.997 66.667 2.51 6.29 32.29 4.20
2973 3495 2.362369 CGCTCCACTGGACAGGGAT 61.362 63.158 2.51 0.00 32.29 3.85
2974 3496 1.524482 GCTCCACTGGACAGGGATC 59.476 63.158 2.51 0.00 32.29 3.36
2975 3497 1.267574 GCTCCACTGGACAGGGATCA 61.268 60.000 2.51 0.00 32.29 2.92
2976 3498 0.829333 CTCCACTGGACAGGGATCAG 59.171 60.000 2.51 0.00 32.29 2.90
2977 3499 0.618680 TCCACTGGACAGGGATCAGG 60.619 60.000 2.51 0.00 32.29 3.86
2978 3500 0.911525 CCACTGGACAGGGATCAGGT 60.912 60.000 2.51 0.00 32.29 4.00
2979 3501 0.251354 CACTGGACAGGGATCAGGTG 59.749 60.000 4.14 0.00 32.29 4.00
2980 3502 0.117140 ACTGGACAGGGATCAGGTGA 59.883 55.000 4.14 0.00 33.19 4.02
2981 3503 0.539051 CTGGACAGGGATCAGGTGAC 59.461 60.000 0.00 0.00 0.00 3.67
2982 3504 0.117140 TGGACAGGGATCAGGTGACT 59.883 55.000 0.00 0.00 46.44 3.41
2983 3505 1.280457 GGACAGGGATCAGGTGACTT 58.720 55.000 0.00 0.00 40.21 3.01
2984 3506 1.065854 GGACAGGGATCAGGTGACTTG 60.066 57.143 0.00 0.00 40.21 3.16
2985 3507 0.326264 ACAGGGATCAGGTGACTTGC 59.674 55.000 0.00 0.00 40.21 4.01
2986 3508 0.393537 CAGGGATCAGGTGACTTGCC 60.394 60.000 0.00 0.00 40.21 4.52
2987 3509 0.548682 AGGGATCAGGTGACTTGCCT 60.549 55.000 0.00 0.00 40.21 4.75
2988 3510 0.329596 GGGATCAGGTGACTTGCCTT 59.670 55.000 0.00 0.00 40.21 4.35
2989 3511 1.680249 GGGATCAGGTGACTTGCCTTC 60.680 57.143 0.00 0.00 40.21 3.46
2990 3512 1.003580 GGATCAGGTGACTTGCCTTCA 59.996 52.381 0.00 0.00 40.21 3.02
2991 3513 2.354259 GATCAGGTGACTTGCCTTCAG 58.646 52.381 0.00 0.00 40.21 3.02
2992 3514 0.397941 TCAGGTGACTTGCCTTCAGG 59.602 55.000 0.00 0.00 40.21 3.86
3002 3524 2.345244 CCTTCAGGCAGTCACGCT 59.655 61.111 0.00 0.00 0.00 5.07
3004 3526 1.301244 CTTCAGGCAGTCACGCTGT 60.301 57.895 0.00 0.00 46.64 4.40
3005 3527 0.038251 CTTCAGGCAGTCACGCTGTA 60.038 55.000 0.00 0.00 46.64 2.74
3006 3528 0.391228 TTCAGGCAGTCACGCTGTAA 59.609 50.000 0.00 0.00 46.64 2.41
3007 3529 0.319555 TCAGGCAGTCACGCTGTAAC 60.320 55.000 0.00 0.00 46.64 2.50
3008 3530 0.599991 CAGGCAGTCACGCTGTAACA 60.600 55.000 0.00 0.00 46.64 2.41
3009 3531 0.321671 AGGCAGTCACGCTGTAACAT 59.678 50.000 0.00 0.00 46.64 2.71
3010 3532 0.443869 GGCAGTCACGCTGTAACATG 59.556 55.000 0.00 0.00 46.64 3.21
3011 3533 0.179215 GCAGTCACGCTGTAACATGC 60.179 55.000 0.00 0.00 46.64 4.06
3018 3540 2.539003 GCTGTAACATGCGGACACA 58.461 52.632 0.00 0.00 0.00 3.72
3019 3541 0.165944 GCTGTAACATGCGGACACAC 59.834 55.000 0.00 0.00 0.00 3.82
3020 3542 1.507562 CTGTAACATGCGGACACACA 58.492 50.000 0.00 0.00 0.00 3.72
3021 3543 2.076100 CTGTAACATGCGGACACACAT 58.924 47.619 0.00 0.00 0.00 3.21
3022 3544 2.073056 TGTAACATGCGGACACACATC 58.927 47.619 0.00 0.00 0.00 3.06
3023 3545 1.396996 GTAACATGCGGACACACATCC 59.603 52.381 0.00 0.00 35.16 3.51
3024 3546 0.250684 AACATGCGGACACACATCCA 60.251 50.000 0.00 0.00 38.87 3.41
3025 3547 0.674581 ACATGCGGACACACATCCAG 60.675 55.000 0.00 0.00 38.87 3.86
3026 3548 1.746615 ATGCGGACACACATCCAGC 60.747 57.895 0.00 0.00 38.87 4.85
3027 3549 3.490759 GCGGACACACATCCAGCG 61.491 66.667 0.00 0.00 38.87 5.18
3028 3550 2.048222 CGGACACACATCCAGCGT 60.048 61.111 0.00 0.00 38.87 5.07
3029 3551 2.094659 CGGACACACATCCAGCGTC 61.095 63.158 0.00 0.00 38.87 5.19
3030 3552 1.741770 GGACACACATCCAGCGTCC 60.742 63.158 0.00 0.00 38.77 4.79
3031 3553 1.005037 GACACACATCCAGCGTCCA 60.005 57.895 0.00 0.00 0.00 4.02
3032 3554 0.391661 GACACACATCCAGCGTCCAT 60.392 55.000 0.00 0.00 0.00 3.41
3033 3555 0.036732 ACACACATCCAGCGTCCATT 59.963 50.000 0.00 0.00 0.00 3.16
3034 3556 1.277842 ACACACATCCAGCGTCCATTA 59.722 47.619 0.00 0.00 0.00 1.90
3035 3557 1.665679 CACACATCCAGCGTCCATTAC 59.334 52.381 0.00 0.00 0.00 1.89
3036 3558 1.277842 ACACATCCAGCGTCCATTACA 59.722 47.619 0.00 0.00 0.00 2.41
3037 3559 1.665679 CACATCCAGCGTCCATTACAC 59.334 52.381 0.00 0.00 0.00 2.90
3038 3560 1.277842 ACATCCAGCGTCCATTACACA 59.722 47.619 0.00 0.00 0.00 3.72
3039 3561 2.092968 ACATCCAGCGTCCATTACACAT 60.093 45.455 0.00 0.00 0.00 3.21
3040 3562 2.779755 TCCAGCGTCCATTACACATT 57.220 45.000 0.00 0.00 0.00 2.71
3041 3563 2.627945 TCCAGCGTCCATTACACATTC 58.372 47.619 0.00 0.00 0.00 2.67
3042 3564 2.027653 TCCAGCGTCCATTACACATTCA 60.028 45.455 0.00 0.00 0.00 2.57
3043 3565 2.746904 CCAGCGTCCATTACACATTCAA 59.253 45.455 0.00 0.00 0.00 2.69
3044 3566 3.426159 CCAGCGTCCATTACACATTCAAC 60.426 47.826 0.00 0.00 0.00 3.18
3045 3567 2.415168 AGCGTCCATTACACATTCAACG 59.585 45.455 0.00 0.00 0.00 4.10
3046 3568 2.475519 GCGTCCATTACACATTCAACGG 60.476 50.000 0.00 0.00 0.00 4.44
3047 3569 2.475519 CGTCCATTACACATTCAACGGC 60.476 50.000 0.00 0.00 0.00 5.68
3048 3570 2.088423 TCCATTACACATTCAACGGCC 58.912 47.619 0.00 0.00 0.00 6.13
3049 3571 1.815613 CCATTACACATTCAACGGCCA 59.184 47.619 2.24 0.00 0.00 5.36
3050 3572 2.426738 CCATTACACATTCAACGGCCAT 59.573 45.455 2.24 0.00 0.00 4.40
3051 3573 3.119173 CCATTACACATTCAACGGCCATT 60.119 43.478 2.24 0.00 0.00 3.16
3052 3574 4.097135 CCATTACACATTCAACGGCCATTA 59.903 41.667 2.24 0.00 0.00 1.90
3053 3575 4.955925 TTACACATTCAACGGCCATTAG 57.044 40.909 2.24 0.00 0.00 1.73
3054 3576 1.472480 ACACATTCAACGGCCATTAGC 59.528 47.619 2.24 0.00 42.60 3.09
3055 3577 1.472082 CACATTCAACGGCCATTAGCA 59.528 47.619 2.24 0.00 46.50 3.49
3056 3578 2.094803 CACATTCAACGGCCATTAGCAA 60.095 45.455 2.24 0.00 46.50 3.91
3057 3579 2.760092 ACATTCAACGGCCATTAGCAAT 59.240 40.909 2.24 0.00 46.50 3.56
3058 3580 3.181487 ACATTCAACGGCCATTAGCAATC 60.181 43.478 2.24 0.00 46.50 2.67
3059 3581 2.121291 TCAACGGCCATTAGCAATCA 57.879 45.000 2.24 0.00 46.50 2.57
3060 3582 2.441410 TCAACGGCCATTAGCAATCAA 58.559 42.857 2.24 0.00 46.50 2.57
3061 3583 3.023119 TCAACGGCCATTAGCAATCAAT 58.977 40.909 2.24 0.00 46.50 2.57
3062 3584 3.117794 CAACGGCCATTAGCAATCAATG 58.882 45.455 2.24 0.00 46.50 2.82
3063 3585 2.378038 ACGGCCATTAGCAATCAATGT 58.622 42.857 2.24 0.00 46.50 2.71
3064 3586 2.099592 ACGGCCATTAGCAATCAATGTG 59.900 45.455 2.24 0.00 46.50 3.21
3065 3587 2.358582 CGGCCATTAGCAATCAATGTGA 59.641 45.455 2.24 0.00 46.50 3.58
3066 3588 3.181488 CGGCCATTAGCAATCAATGTGAA 60.181 43.478 2.24 0.00 46.50 3.18
3067 3589 4.677514 CGGCCATTAGCAATCAATGTGAAA 60.678 41.667 2.24 0.00 46.50 2.69
3068 3590 5.177326 GGCCATTAGCAATCAATGTGAAAA 58.823 37.500 0.00 0.00 46.50 2.29
3069 3591 5.642919 GGCCATTAGCAATCAATGTGAAAAA 59.357 36.000 0.00 0.00 46.50 1.94
3088 3610 3.988976 AAAAGCTCCAGATCTAGCACA 57.011 42.857 17.69 0.00 41.32 4.57
3089 3611 2.977772 AAGCTCCAGATCTAGCACAC 57.022 50.000 17.69 0.00 41.32 3.82
3090 3612 0.743688 AGCTCCAGATCTAGCACACG 59.256 55.000 17.69 0.00 41.32 4.49
3091 3613 0.873743 GCTCCAGATCTAGCACACGC 60.874 60.000 11.84 0.00 38.63 5.34
3092 3614 0.457443 CTCCAGATCTAGCACACGCA 59.543 55.000 0.00 0.00 42.27 5.24
3093 3615 0.173481 TCCAGATCTAGCACACGCAC 59.827 55.000 0.00 0.00 42.27 5.34
3094 3616 0.108662 CCAGATCTAGCACACGCACA 60.109 55.000 0.00 0.00 42.27 4.57
3095 3617 0.994995 CAGATCTAGCACACGCACAC 59.005 55.000 0.00 0.00 42.27 3.82
3096 3618 0.603065 AGATCTAGCACACGCACACA 59.397 50.000 0.00 0.00 42.27 3.72
3097 3619 1.205655 AGATCTAGCACACGCACACAT 59.794 47.619 0.00 0.00 42.27 3.21
3098 3620 1.325640 GATCTAGCACACGCACACATG 59.674 52.381 0.00 0.00 42.27 3.21
3099 3621 0.670239 TCTAGCACACGCACACATGG 60.670 55.000 0.00 0.00 42.27 3.66
3100 3622 0.670239 CTAGCACACGCACACATGGA 60.670 55.000 0.00 0.00 42.27 3.41
3101 3623 0.670239 TAGCACACGCACACATGGAG 60.670 55.000 0.00 0.00 42.27 3.86
3102 3624 1.960763 GCACACGCACACATGGAGA 60.961 57.895 0.00 0.00 38.36 3.71
3103 3625 1.862123 CACACGCACACATGGAGAC 59.138 57.895 0.00 0.00 0.00 3.36
3104 3626 1.664649 ACACGCACACATGGAGACG 60.665 57.895 0.00 0.00 0.00 4.18
3105 3627 2.738521 ACGCACACATGGAGACGC 60.739 61.111 0.00 0.00 0.00 5.19
3106 3628 3.490759 CGCACACATGGAGACGCC 61.491 66.667 0.00 0.00 37.10 5.68
3107 3629 3.127533 GCACACATGGAGACGCCC 61.128 66.667 0.00 0.00 34.97 6.13
3108 3630 2.347114 CACACATGGAGACGCCCA 59.653 61.111 0.00 0.00 41.05 5.36
3109 3631 2.034879 CACACATGGAGACGCCCAC 61.035 63.158 0.00 0.00 39.34 4.61
3110 3632 2.347114 CACATGGAGACGCCCACA 59.653 61.111 0.00 0.00 39.34 4.17
3111 3633 2.034879 CACATGGAGACGCCCACAC 61.035 63.158 0.00 0.00 39.34 3.82
3112 3634 2.217038 ACATGGAGACGCCCACACT 61.217 57.895 0.00 0.00 39.34 3.55
3113 3635 1.003355 CATGGAGACGCCCACACTT 60.003 57.895 0.00 0.00 39.34 3.16
3114 3636 1.003355 ATGGAGACGCCCACACTTG 60.003 57.895 0.00 0.00 39.34 3.16
3115 3637 1.768684 ATGGAGACGCCCACACTTGT 61.769 55.000 0.00 0.00 39.34 3.16
3116 3638 1.116536 TGGAGACGCCCACACTTGTA 61.117 55.000 0.00 0.00 34.97 2.41
3117 3639 0.389948 GGAGACGCCCACACTTGTAG 60.390 60.000 0.00 0.00 0.00 2.74
3118 3640 1.004918 AGACGCCCACACTTGTAGC 60.005 57.895 0.00 0.00 0.00 3.58
3119 3641 1.301401 GACGCCCACACTTGTAGCA 60.301 57.895 4.88 0.00 0.00 3.49
3120 3642 0.882927 GACGCCCACACTTGTAGCAA 60.883 55.000 4.88 0.00 0.00 3.91
3121 3643 0.884704 ACGCCCACACTTGTAGCAAG 60.885 55.000 7.27 7.27 0.00 4.01
3122 3644 0.884704 CGCCCACACTTGTAGCAAGT 60.885 55.000 8.53 8.53 0.00 3.16
3123 3645 1.606994 CGCCCACACTTGTAGCAAGTA 60.607 52.381 13.27 0.00 0.00 2.24
3124 3646 2.076863 GCCCACACTTGTAGCAAGTAG 58.923 52.381 13.27 10.59 0.00 2.57
3125 3647 2.289444 GCCCACACTTGTAGCAAGTAGA 60.289 50.000 13.27 0.00 0.00 2.59
3126 3648 3.619979 GCCCACACTTGTAGCAAGTAGAT 60.620 47.826 13.27 1.57 0.00 1.98
3127 3649 4.579869 CCCACACTTGTAGCAAGTAGATT 58.420 43.478 13.27 0.00 0.00 2.40
3128 3650 5.003804 CCCACACTTGTAGCAAGTAGATTT 58.996 41.667 13.27 0.00 0.00 2.17
3129 3651 5.473504 CCCACACTTGTAGCAAGTAGATTTT 59.526 40.000 13.27 0.00 0.00 1.82
3130 3652 6.016276 CCCACACTTGTAGCAAGTAGATTTTT 60.016 38.462 13.27 0.00 0.00 1.94
3131 3653 7.174253 CCCACACTTGTAGCAAGTAGATTTTTA 59.826 37.037 13.27 0.00 0.00 1.52
3132 3654 8.230486 CCACACTTGTAGCAAGTAGATTTTTAG 58.770 37.037 13.27 2.45 0.00 1.85
3133 3655 8.988934 CACACTTGTAGCAAGTAGATTTTTAGA 58.011 33.333 13.27 0.00 0.00 2.10
3134 3656 9.555727 ACACTTGTAGCAAGTAGATTTTTAGAA 57.444 29.630 13.27 0.00 0.00 2.10
3136 3658 9.780186 ACTTGTAGCAAGTAGATTTTTAGAAGT 57.220 29.630 12.20 0.00 0.00 3.01
3168 3690 8.966069 AATTAAGAGCAGATTTTAGTAGGACC 57.034 34.615 0.00 0.00 0.00 4.46
3169 3691 4.657436 AGAGCAGATTTTAGTAGGACCG 57.343 45.455 0.00 0.00 0.00 4.79
3170 3692 4.024670 AGAGCAGATTTTAGTAGGACCGT 58.975 43.478 0.00 0.00 0.00 4.83
3171 3693 4.466726 AGAGCAGATTTTAGTAGGACCGTT 59.533 41.667 0.00 0.00 0.00 4.44
3172 3694 4.756502 AGCAGATTTTAGTAGGACCGTTC 58.243 43.478 0.00 0.00 0.00 3.95
3173 3695 4.222145 AGCAGATTTTAGTAGGACCGTTCA 59.778 41.667 0.00 0.00 0.00 3.18
3174 3696 4.329256 GCAGATTTTAGTAGGACCGTTCAC 59.671 45.833 0.00 0.00 0.00 3.18
3175 3697 5.475719 CAGATTTTAGTAGGACCGTTCACA 58.524 41.667 0.00 0.00 0.00 3.58
3176 3698 5.929992 CAGATTTTAGTAGGACCGTTCACAA 59.070 40.000 0.00 0.00 0.00 3.33
3177 3699 6.425721 CAGATTTTAGTAGGACCGTTCACAAA 59.574 38.462 0.00 0.00 0.00 2.83
3178 3700 6.993902 AGATTTTAGTAGGACCGTTCACAAAA 59.006 34.615 0.00 0.00 0.00 2.44
3179 3701 6.998968 TTTTAGTAGGACCGTTCACAAAAA 57.001 33.333 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 3.489355 TCTGGAACTGTTCGTGTACCTA 58.511 45.455 13.89 0.00 0.00 3.08
19 20 7.026631 TGTTGTGAAGTTTAATCTGGAACTG 57.973 36.000 0.00 0.00 36.31 3.16
22 23 7.581213 ACATGTTGTGAAGTTTAATCTGGAA 57.419 32.000 0.00 0.00 0.00 3.53
44 45 1.454201 TGGTTTGCGAAGAACACACA 58.546 45.000 0.00 0.00 0.00 3.72
54 55 4.335214 CCATGGGATGGTTTGCGA 57.665 55.556 2.85 0.00 45.54 5.10
68 69 5.667626 ACTGTCTCTATAACCATCCAACCAT 59.332 40.000 0.00 0.00 0.00 3.55
103 104 9.420682 GAGTATCAGGACTTGAACCTTGATGGT 62.421 44.444 0.00 0.00 43.73 3.55
104 105 3.423539 TCAGGACTTGAACCTTGATGG 57.576 47.619 0.00 0.00 42.93 3.51
107 108 4.082190 CGAGTATCAGGACTTGAACCTTGA 60.082 45.833 0.00 0.00 39.77 3.02
110 111 2.166664 GCGAGTATCAGGACTTGAACCT 59.833 50.000 0.00 0.00 39.77 3.50
126 127 8.902806 TGAAATAAATCAAGGAATAATGCGAGT 58.097 29.630 0.00 0.00 0.00 4.18
141 142 4.706476 CCCAGCAACTCCTGAAATAAATCA 59.294 41.667 0.00 0.00 34.77 2.57
153 154 3.512516 GCGCATCCCAGCAACTCC 61.513 66.667 0.30 0.00 0.00 3.85
156 157 1.153958 GAAAGCGCATCCCAGCAAC 60.154 57.895 11.47 0.00 35.48 4.17
161 162 0.323269 TCCATTGAAAGCGCATCCCA 60.323 50.000 11.47 0.00 0.00 4.37
162 163 0.817013 TTCCATTGAAAGCGCATCCC 59.183 50.000 11.47 0.00 0.00 3.85
163 164 1.202336 CCTTCCATTGAAAGCGCATCC 60.202 52.381 11.47 0.00 0.00 3.51
165 166 1.747355 CTCCTTCCATTGAAAGCGCAT 59.253 47.619 11.47 0.00 0.00 4.73
176 177 1.486726 GACCGGAACATCTCCTTCCAT 59.513 52.381 9.46 0.00 42.85 3.41
177 178 0.902531 GACCGGAACATCTCCTTCCA 59.097 55.000 9.46 0.00 42.85 3.53
180 181 1.337823 CGTTGACCGGAACATCTCCTT 60.338 52.381 9.46 0.00 42.85 3.36
183 184 1.347320 GTCGTTGACCGGAACATCTC 58.653 55.000 9.46 0.00 37.11 2.75
184 185 0.388134 CGTCGTTGACCGGAACATCT 60.388 55.000 9.46 0.00 37.11 2.90
185 186 0.387622 TCGTCGTTGACCGGAACATC 60.388 55.000 9.46 6.43 37.11 3.06
241 242 1.480137 CCTTTGAGAGACCGAGCTGAT 59.520 52.381 0.00 0.00 0.00 2.90
244 245 0.892063 GACCTTTGAGAGACCGAGCT 59.108 55.000 0.00 0.00 0.00 4.09
247 248 2.594131 TGAAGACCTTTGAGAGACCGA 58.406 47.619 0.00 0.00 0.00 4.69
254 255 7.497249 CACCCTATTCTTATGAAGACCTTTGAG 59.503 40.741 0.00 0.00 37.23 3.02
270 271 2.741878 GCATACACGCACACCCTATTCT 60.742 50.000 0.00 0.00 0.00 2.40
272 273 1.065782 TGCATACACGCACACCCTATT 60.066 47.619 0.00 0.00 36.86 1.73
273 274 0.539518 TGCATACACGCACACCCTAT 59.460 50.000 0.00 0.00 36.86 2.57
288 289 6.207417 GCATACACTCACCCTTATAAATGCAT 59.793 38.462 0.00 0.00 36.79 3.96
312 313 3.100817 CAAAGCGCTTGTATACACATGC 58.899 45.455 25.80 9.45 46.88 4.06
313 314 3.100817 GCAAAGCGCTTGTATACACATG 58.899 45.455 25.80 15.52 37.36 3.21
314 315 3.405170 GCAAAGCGCTTGTATACACAT 57.595 42.857 25.80 0.49 37.36 3.21
315 316 2.892373 GCAAAGCGCTTGTATACACA 57.108 45.000 25.80 0.00 37.36 3.72
328 329 1.636988 ACACTATACGGACGCAAAGC 58.363 50.000 0.00 0.00 0.00 3.51
329 330 5.766702 TTTAACACTATACGGACGCAAAG 57.233 39.130 0.00 0.00 0.00 2.77
330 331 6.536731 TTTTTAACACTATACGGACGCAAA 57.463 33.333 0.00 0.00 0.00 3.68
351 352 5.009610 ACAATAGGAGAACGCACATGTTTTT 59.990 36.000 0.00 0.00 30.75 1.94
352 353 4.518970 ACAATAGGAGAACGCACATGTTTT 59.481 37.500 0.00 0.00 30.75 2.43
353 354 4.072131 ACAATAGGAGAACGCACATGTTT 58.928 39.130 0.00 0.00 30.75 2.83
354 355 3.674997 ACAATAGGAGAACGCACATGTT 58.325 40.909 0.00 0.00 34.02 2.71
355 356 3.334583 ACAATAGGAGAACGCACATGT 57.665 42.857 0.00 0.00 0.00 3.21
356 357 4.180817 TGTACAATAGGAGAACGCACATG 58.819 43.478 0.00 0.00 0.00 3.21
357 358 4.465632 TGTACAATAGGAGAACGCACAT 57.534 40.909 0.00 0.00 0.00 3.21
358 359 3.945981 TGTACAATAGGAGAACGCACA 57.054 42.857 0.00 0.00 0.00 4.57
359 360 5.796350 AATTGTACAATAGGAGAACGCAC 57.204 39.130 21.07 0.00 0.00 5.34
360 361 8.500753 AATAAATTGTACAATAGGAGAACGCA 57.499 30.769 21.07 0.00 0.00 5.24
361 362 9.783256 AAAATAAATTGTACAATAGGAGAACGC 57.217 29.630 21.07 0.00 0.00 4.84
373 374 9.156156 CGTCGTGTAACAAAAATAAATTGTACA 57.844 29.630 0.00 0.00 39.98 2.90
374 375 9.157259 ACGTCGTGTAACAAAAATAAATTGTAC 57.843 29.630 0.00 0.00 39.98 2.90
377 378 7.993792 CCAACGTCGTGTAACAAAAATAAATTG 59.006 33.333 0.00 0.00 35.74 2.32
387 388 1.210870 GAGCCAACGTCGTGTAACAA 58.789 50.000 0.00 0.00 35.74 2.83
389 390 0.505655 GTGAGCCAACGTCGTGTAAC 59.494 55.000 0.00 0.00 0.00 2.50
416 417 0.442699 GCCAAAGTCGAGCCGTAAAG 59.557 55.000 0.00 0.00 0.00 1.85
485 486 2.099592 ACGTGACGAGTTGGTGTAGAAA 59.900 45.455 13.70 0.00 0.00 2.52
529 530 7.072177 TGGCGAGAATTATTAAGAACAACAG 57.928 36.000 0.00 0.00 0.00 3.16
534 535 8.421673 AGTACTTGGCGAGAATTATTAAGAAC 57.578 34.615 9.20 0.00 0.00 3.01
548 549 1.210931 CGAACGGAGTACTTGGCGA 59.789 57.895 0.00 0.00 45.00 5.54
549 550 1.069378 GACGAACGGAGTACTTGGCG 61.069 60.000 0.00 4.69 45.00 5.69
554 555 1.664659 CATCGAGACGAACGGAGTACT 59.335 52.381 0.00 0.00 45.00 2.73
668 722 7.721842 TGATTACTGTGTTATGAGGGAAAAACA 59.278 33.333 0.00 0.00 0.00 2.83
669 723 8.106247 TGATTACTGTGTTATGAGGGAAAAAC 57.894 34.615 0.00 0.00 0.00 2.43
670 724 8.698973 TTGATTACTGTGTTATGAGGGAAAAA 57.301 30.769 0.00 0.00 0.00 1.94
738 793 3.498397 GCTGCTCCTTAATGCGCTAAATA 59.502 43.478 9.73 0.00 0.00 1.40
740 795 1.670811 GCTGCTCCTTAATGCGCTAAA 59.329 47.619 9.73 0.00 0.00 1.85
752 807 3.447586 TCATCTTTAGTTACGCTGCTCCT 59.552 43.478 0.00 0.00 0.00 3.69
760 815 6.915300 CCATCACTCTCTCATCTTTAGTTACG 59.085 42.308 0.00 0.00 0.00 3.18
765 820 5.534207 AGCCATCACTCTCTCATCTTTAG 57.466 43.478 0.00 0.00 0.00 1.85
851 906 9.607333 TTTATAGTACTTCCTCCATCTGATGAT 57.393 33.333 18.92 2.77 0.00 2.45
947 1002 7.119387 AGGAATGGGAACTCGAAAATTTAGAT 58.881 34.615 0.00 0.00 0.00 1.98
1004 1076 2.101415 AGCACAAAGGAGCAAGTTTTCC 59.899 45.455 0.00 0.00 32.55 3.13
1015 1087 2.554636 CGCCAAGCAGCACAAAGGA 61.555 57.895 0.00 0.00 0.00 3.36
1052 1127 0.178953 AGCAATGGGGCTCACAACTT 60.179 50.000 0.00 0.00 41.05 2.66
1053 1128 0.178953 AAGCAATGGGGCTCACAACT 60.179 50.000 0.00 0.00 45.07 3.16
1054 1129 0.037975 CAAGCAATGGGGCTCACAAC 60.038 55.000 0.00 0.00 45.07 3.32
1135 1210 0.323957 GGGTTAGTGGTGGTCTGGTC 59.676 60.000 0.00 0.00 0.00 4.02
1263 1344 3.293714 CCCATGCGTGCAACACCA 61.294 61.111 0.00 0.00 35.74 4.17
1267 1348 2.672996 AGGTCCCATGCGTGCAAC 60.673 61.111 0.00 0.26 0.00 4.17
1373 1467 3.803082 CGACGAGAACGGCCGGTA 61.803 66.667 31.76 0.00 45.81 4.02
1402 1496 0.105964 TGAATAGAGGCGAGCTCCCT 60.106 55.000 20.01 20.01 34.77 4.20
1533 1653 1.941294 ACGCCACATGAACACGTTTTA 59.059 42.857 0.00 0.00 32.09 1.52
1807 1945 5.469084 AGGAGACATTTACTTCCGTTGTTTC 59.531 40.000 0.00 0.00 0.00 2.78
1814 1952 5.269505 AGATCAGGAGACATTTACTTCCG 57.730 43.478 0.00 0.00 0.00 4.30
1829 1971 2.867109 ACAGGAACACCAAGATCAGG 57.133 50.000 0.00 0.00 0.00 3.86
1937 2079 1.445410 CGCCCACGAACTCGATCAA 60.445 57.895 6.05 0.00 43.93 2.57
1963 2105 4.329545 GCCACGGCCTTGAGGTCA 62.330 66.667 11.54 0.00 40.62 4.02
2223 2376 5.383130 GCACATTCTTTCTTTTCGAGGTAC 58.617 41.667 0.00 0.00 0.00 3.34
2339 2499 3.064958 AGACGGACTACACACATGATACG 59.935 47.826 0.00 0.00 0.00 3.06
2340 2500 4.142447 ACAGACGGACTACACACATGATAC 60.142 45.833 0.00 0.00 0.00 2.24
2341 2501 4.014406 ACAGACGGACTACACACATGATA 58.986 43.478 0.00 0.00 0.00 2.15
2342 2502 2.826128 ACAGACGGACTACACACATGAT 59.174 45.455 0.00 0.00 0.00 2.45
2377 2540 3.194968 TCTCTCGCCGTTTTCCTCTTATT 59.805 43.478 0.00 0.00 0.00 1.40
2389 2552 0.608640 AAGGTCATTTCTCTCGCCGT 59.391 50.000 0.00 0.00 0.00 5.68
2391 2554 2.416893 GTGAAAGGTCATTTCTCTCGCC 59.583 50.000 11.00 0.00 46.34 5.54
2392 2555 2.416893 GGTGAAAGGTCATTTCTCTCGC 59.583 50.000 11.00 0.00 46.34 5.03
2393 2556 3.664107 TGGTGAAAGGTCATTTCTCTCG 58.336 45.455 11.00 0.00 46.34 4.04
2405 2666 2.229784 GGAAGCAAGTGATGGTGAAAGG 59.770 50.000 0.00 0.00 40.33 3.11
2406 2667 3.152341 AGGAAGCAAGTGATGGTGAAAG 58.848 45.455 0.00 0.00 40.33 2.62
2413 2674 7.672983 TTTTAGTAAGAGGAAGCAAGTGATG 57.327 36.000 0.00 0.00 0.00 3.07
2416 2677 7.327032 GCAAATTTTAGTAAGAGGAAGCAAGTG 59.673 37.037 0.00 0.00 0.00 3.16
2500 2777 5.402270 GTCCAAAGAATTGTTGTGCATACAC 59.598 40.000 4.32 0.00 39.92 2.90
2550 2827 6.641314 AGAGTAACGGTAATTTGCATCTATCG 59.359 38.462 0.00 0.00 0.00 2.92
2663 3166 1.278985 TCGGGAGAATTGCATGTGTCT 59.721 47.619 0.00 0.00 34.75 3.41
2719 3222 5.692115 TGAGTAGGGCAATCAGTATTTGA 57.308 39.130 0.00 0.00 40.85 2.69
2810 3324 9.658799 TTTGTACGTAGACTTATAGAGTAGTGT 57.341 33.333 0.00 0.00 39.19 3.55
2862 3376 6.656270 TGTAGTACAAGTAGAACGAATCCTGA 59.344 38.462 0.00 0.00 0.00 3.86
2867 3381 8.558973 ACTAGTGTAGTACAAGTAGAACGAAT 57.441 34.615 20.43 2.60 37.23 3.34
2868 3382 7.969536 ACTAGTGTAGTACAAGTAGAACGAA 57.030 36.000 20.43 0.00 37.23 3.85
2910 3432 0.696501 AAACCGGTTGGCCACTATCT 59.303 50.000 23.08 0.00 39.70 1.98
2945 3467 3.125316 GTCCAGTGGAGCGTCTTAATTTG 59.875 47.826 13.61 0.00 29.39 2.32
2964 3486 1.065854 CAAGTCACCTGATCCCTGTCC 60.066 57.143 0.00 0.00 0.00 4.02
2965 3487 1.677217 GCAAGTCACCTGATCCCTGTC 60.677 57.143 0.00 0.00 0.00 3.51
2966 3488 0.326264 GCAAGTCACCTGATCCCTGT 59.674 55.000 0.00 0.00 0.00 4.00
2967 3489 0.393537 GGCAAGTCACCTGATCCCTG 60.394 60.000 0.00 0.00 0.00 4.45
2968 3490 0.548682 AGGCAAGTCACCTGATCCCT 60.549 55.000 0.00 0.00 35.72 4.20
2969 3491 0.329596 AAGGCAAGTCACCTGATCCC 59.670 55.000 0.00 0.00 37.67 3.85
2970 3492 1.003580 TGAAGGCAAGTCACCTGATCC 59.996 52.381 0.00 0.00 37.67 3.36
2971 3493 2.354259 CTGAAGGCAAGTCACCTGATC 58.646 52.381 0.00 0.00 37.67 2.92
2972 3494 1.004044 CCTGAAGGCAAGTCACCTGAT 59.996 52.381 0.00 0.00 37.67 2.90
2973 3495 0.397941 CCTGAAGGCAAGTCACCTGA 59.602 55.000 0.00 0.00 37.67 3.86
2974 3496 2.938354 CCTGAAGGCAAGTCACCTG 58.062 57.895 0.00 0.00 37.67 4.00
2985 3507 2.031516 CAGCGTGACTGCCTGAAGG 61.032 63.158 0.00 0.00 40.19 3.46
2986 3508 3.559024 CAGCGTGACTGCCTGAAG 58.441 61.111 0.00 0.00 40.19 3.02
3000 3522 0.165944 GTGTGTCCGCATGTTACAGC 59.834 55.000 0.00 0.00 0.00 4.40
3001 3523 1.507562 TGTGTGTCCGCATGTTACAG 58.492 50.000 0.00 0.00 0.00 2.74
3002 3524 2.073056 GATGTGTGTCCGCATGTTACA 58.927 47.619 0.00 0.00 41.77 2.41
3003 3525 1.396996 GGATGTGTGTCCGCATGTTAC 59.603 52.381 0.00 0.00 41.77 2.50
3004 3526 1.002544 TGGATGTGTGTCCGCATGTTA 59.997 47.619 0.00 0.00 41.77 2.41
3005 3527 0.250684 TGGATGTGTGTCCGCATGTT 60.251 50.000 0.00 0.00 41.77 2.71
3006 3528 0.674581 CTGGATGTGTGTCCGCATGT 60.675 55.000 0.00 0.00 41.77 3.21
3007 3529 1.985447 GCTGGATGTGTGTCCGCATG 61.985 60.000 0.00 0.00 41.77 4.06
3008 3530 1.746615 GCTGGATGTGTGTCCGCAT 60.747 57.895 0.00 0.00 44.32 4.73
3009 3531 2.358615 GCTGGATGTGTGTCCGCA 60.359 61.111 0.00 0.00 41.35 5.69
3010 3532 3.490759 CGCTGGATGTGTGTCCGC 61.491 66.667 0.00 0.00 41.35 5.54
3011 3533 2.048222 ACGCTGGATGTGTGTCCG 60.048 61.111 0.00 0.00 41.35 4.79
3012 3534 3.876300 GACGCTGGATGTGTGTCC 58.124 61.111 0.00 0.00 39.84 4.02
3013 3535 0.391661 ATGGACGCTGGATGTGTGTC 60.392 55.000 0.00 0.00 42.30 3.67
3014 3536 0.036732 AATGGACGCTGGATGTGTGT 59.963 50.000 0.00 0.00 39.84 3.72
3015 3537 1.665679 GTAATGGACGCTGGATGTGTG 59.334 52.381 0.00 0.00 39.84 3.82
3016 3538 1.277842 TGTAATGGACGCTGGATGTGT 59.722 47.619 0.00 0.00 42.84 3.72
3017 3539 1.665679 GTGTAATGGACGCTGGATGTG 59.334 52.381 0.00 0.00 35.54 3.21
3018 3540 1.277842 TGTGTAATGGACGCTGGATGT 59.722 47.619 0.00 0.00 39.46 3.06
3019 3541 2.022764 TGTGTAATGGACGCTGGATG 57.977 50.000 0.00 0.00 39.46 3.51
3020 3542 3.206150 GAATGTGTAATGGACGCTGGAT 58.794 45.455 0.00 0.00 39.46 3.41
3021 3543 2.027653 TGAATGTGTAATGGACGCTGGA 60.028 45.455 0.00 0.00 39.46 3.86
3022 3544 2.355197 TGAATGTGTAATGGACGCTGG 58.645 47.619 0.00 0.00 39.46 4.85
3023 3545 3.724716 CGTTGAATGTGTAATGGACGCTG 60.725 47.826 0.00 0.00 39.46 5.18
3024 3546 2.415168 CGTTGAATGTGTAATGGACGCT 59.585 45.455 0.00 0.00 39.46 5.07
3025 3547 2.475519 CCGTTGAATGTGTAATGGACGC 60.476 50.000 0.00 0.00 35.44 5.19
3026 3548 2.475519 GCCGTTGAATGTGTAATGGACG 60.476 50.000 0.00 0.00 35.44 4.79
3027 3549 2.159435 GGCCGTTGAATGTGTAATGGAC 60.159 50.000 0.00 0.00 35.44 4.02
3028 3550 2.088423 GGCCGTTGAATGTGTAATGGA 58.912 47.619 0.00 0.00 35.44 3.41
3029 3551 1.815613 TGGCCGTTGAATGTGTAATGG 59.184 47.619 0.00 0.00 36.31 3.16
3030 3552 3.781079 ATGGCCGTTGAATGTGTAATG 57.219 42.857 0.00 0.00 0.00 1.90
3031 3553 4.202010 GCTAATGGCCGTTGAATGTGTAAT 60.202 41.667 20.91 0.00 34.27 1.89
3032 3554 3.127895 GCTAATGGCCGTTGAATGTGTAA 59.872 43.478 20.91 0.00 34.27 2.41
3033 3555 2.680841 GCTAATGGCCGTTGAATGTGTA 59.319 45.455 20.91 0.00 34.27 2.90
3034 3556 1.472480 GCTAATGGCCGTTGAATGTGT 59.528 47.619 20.91 0.00 34.27 3.72
3035 3557 1.472082 TGCTAATGGCCGTTGAATGTG 59.528 47.619 20.91 4.67 40.92 3.21
3036 3558 1.832883 TGCTAATGGCCGTTGAATGT 58.167 45.000 20.91 0.00 40.92 2.71
3037 3559 2.937469 TTGCTAATGGCCGTTGAATG 57.063 45.000 20.91 8.67 40.92 2.67
3038 3560 3.023119 TGATTGCTAATGGCCGTTGAAT 58.977 40.909 20.91 14.41 40.92 2.57
3039 3561 2.441410 TGATTGCTAATGGCCGTTGAA 58.559 42.857 20.91 10.35 40.92 2.69
3040 3562 2.121291 TGATTGCTAATGGCCGTTGA 57.879 45.000 20.91 4.05 40.92 3.18
3041 3563 2.937469 TTGATTGCTAATGGCCGTTG 57.063 45.000 20.91 11.12 40.92 4.10
3042 3564 2.760092 ACATTGATTGCTAATGGCCGTT 59.240 40.909 16.02 16.02 39.30 4.44
3043 3565 2.099592 CACATTGATTGCTAATGGCCGT 59.900 45.455 0.00 0.00 39.30 5.68
3044 3566 2.358582 TCACATTGATTGCTAATGGCCG 59.641 45.455 0.00 0.00 39.30 6.13
3045 3567 4.389890 TTCACATTGATTGCTAATGGCC 57.610 40.909 0.00 0.00 39.30 5.36
3046 3568 6.724694 TTTTTCACATTGATTGCTAATGGC 57.275 33.333 0.00 0.00 39.30 4.40
3067 3589 4.006319 GTGTGCTAGATCTGGAGCTTTTT 58.994 43.478 16.54 0.00 39.54 1.94
3068 3590 3.604582 GTGTGCTAGATCTGGAGCTTTT 58.395 45.455 16.54 0.00 39.54 2.27
3069 3591 2.417924 CGTGTGCTAGATCTGGAGCTTT 60.418 50.000 16.54 0.00 39.54 3.51
3070 3592 1.135915 CGTGTGCTAGATCTGGAGCTT 59.864 52.381 16.54 0.00 39.54 3.74
3071 3593 0.743688 CGTGTGCTAGATCTGGAGCT 59.256 55.000 16.54 0.00 39.54 4.09
3072 3594 0.873743 GCGTGTGCTAGATCTGGAGC 60.874 60.000 10.75 10.39 39.25 4.70
3073 3595 0.457443 TGCGTGTGCTAGATCTGGAG 59.543 55.000 10.75 0.00 43.34 3.86
3074 3596 0.173481 GTGCGTGTGCTAGATCTGGA 59.827 55.000 10.75 0.00 43.34 3.86
3075 3597 0.108662 TGTGCGTGTGCTAGATCTGG 60.109 55.000 5.18 2.94 43.34 3.86
3076 3598 0.994995 GTGTGCGTGTGCTAGATCTG 59.005 55.000 5.18 0.00 43.34 2.90
3077 3599 0.603065 TGTGTGCGTGTGCTAGATCT 59.397 50.000 0.00 0.00 43.34 2.75
3078 3600 1.325640 CATGTGTGCGTGTGCTAGATC 59.674 52.381 0.00 0.00 43.34 2.75
3079 3601 1.362768 CATGTGTGCGTGTGCTAGAT 58.637 50.000 0.00 0.00 43.34 1.98
3080 3602 0.670239 CCATGTGTGCGTGTGCTAGA 60.670 55.000 0.00 0.00 43.34 2.43
3081 3603 0.670239 TCCATGTGTGCGTGTGCTAG 60.670 55.000 0.00 0.00 43.34 3.42
3082 3604 0.670239 CTCCATGTGTGCGTGTGCTA 60.670 55.000 0.00 0.00 43.34 3.49
3083 3605 1.962822 CTCCATGTGTGCGTGTGCT 60.963 57.895 0.00 0.00 43.34 4.40
3084 3606 1.960763 TCTCCATGTGTGCGTGTGC 60.961 57.895 0.00 0.00 43.20 4.57
3085 3607 1.862123 GTCTCCATGTGTGCGTGTG 59.138 57.895 0.00 0.00 0.00 3.82
3086 3608 1.664649 CGTCTCCATGTGTGCGTGT 60.665 57.895 0.00 0.00 0.00 4.49
3087 3609 3.015293 GCGTCTCCATGTGTGCGTG 62.015 63.158 0.00 0.00 0.00 5.34
3088 3610 2.738521 GCGTCTCCATGTGTGCGT 60.739 61.111 0.00 0.00 0.00 5.24
3089 3611 3.490759 GGCGTCTCCATGTGTGCG 61.491 66.667 0.00 0.00 34.01 5.34
3090 3612 3.127533 GGGCGTCTCCATGTGTGC 61.128 66.667 0.00 0.00 36.21 4.57
3091 3613 2.034879 GTGGGCGTCTCCATGTGTG 61.035 63.158 0.00 0.00 39.26 3.82
3092 3614 2.347490 GTGGGCGTCTCCATGTGT 59.653 61.111 0.00 0.00 39.26 3.72
3093 3615 2.034879 GTGTGGGCGTCTCCATGTG 61.035 63.158 0.00 0.00 39.26 3.21
3094 3616 1.768684 AAGTGTGGGCGTCTCCATGT 61.769 55.000 0.00 0.00 39.26 3.21
3095 3617 1.003355 AAGTGTGGGCGTCTCCATG 60.003 57.895 0.00 0.00 39.26 3.66
3096 3618 1.003355 CAAGTGTGGGCGTCTCCAT 60.003 57.895 0.00 0.00 39.26 3.41
3097 3619 1.116536 TACAAGTGTGGGCGTCTCCA 61.117 55.000 0.00 0.00 36.21 3.86
3098 3620 0.389948 CTACAAGTGTGGGCGTCTCC 60.390 60.000 0.00 0.00 0.00 3.71
3099 3621 1.014564 GCTACAAGTGTGGGCGTCTC 61.015 60.000 0.00 0.00 0.00 3.36
3100 3622 1.004918 GCTACAAGTGTGGGCGTCT 60.005 57.895 0.00 0.00 0.00 4.18
3101 3623 0.882927 TTGCTACAAGTGTGGGCGTC 60.883 55.000 0.00 0.00 33.25 5.19
3102 3624 0.884704 CTTGCTACAAGTGTGGGCGT 60.885 55.000 0.00 0.00 33.25 5.68
3103 3625 0.884704 ACTTGCTACAAGTGTGGGCG 60.885 55.000 11.95 0.00 33.25 6.13
3104 3626 2.076863 CTACTTGCTACAAGTGTGGGC 58.923 52.381 20.32 0.00 0.00 5.36
3105 3627 3.678056 TCTACTTGCTACAAGTGTGGG 57.322 47.619 20.32 9.59 0.00 4.61
3106 3628 6.560253 AAAATCTACTTGCTACAAGTGTGG 57.440 37.500 20.32 11.56 0.00 4.17
3107 3629 8.988934 TCTAAAAATCTACTTGCTACAAGTGTG 58.011 33.333 20.32 13.61 0.00 3.82
3108 3630 9.555727 TTCTAAAAATCTACTTGCTACAAGTGT 57.444 29.630 20.32 6.23 0.00 3.55
3110 3632 9.780186 ACTTCTAAAAATCTACTTGCTACAAGT 57.220 29.630 16.42 16.42 0.00 3.16
3143 3665 7.711339 CGGTCCTACTAAAATCTGCTCTTAATT 59.289 37.037 0.00 0.00 0.00 1.40
3144 3666 7.147707 ACGGTCCTACTAAAATCTGCTCTTAAT 60.148 37.037 0.00 0.00 0.00 1.40
3145 3667 6.154021 ACGGTCCTACTAAAATCTGCTCTTAA 59.846 38.462 0.00 0.00 0.00 1.85
3146 3668 5.655532 ACGGTCCTACTAAAATCTGCTCTTA 59.344 40.000 0.00 0.00 0.00 2.10
3147 3669 4.466726 ACGGTCCTACTAAAATCTGCTCTT 59.533 41.667 0.00 0.00 0.00 2.85
3148 3670 4.024670 ACGGTCCTACTAAAATCTGCTCT 58.975 43.478 0.00 0.00 0.00 4.09
3149 3671 4.388378 ACGGTCCTACTAAAATCTGCTC 57.612 45.455 0.00 0.00 0.00 4.26
3150 3672 4.222145 TGAACGGTCCTACTAAAATCTGCT 59.778 41.667 0.00 0.00 0.00 4.24
3151 3673 4.329256 GTGAACGGTCCTACTAAAATCTGC 59.671 45.833 0.00 0.00 0.00 4.26
3152 3674 5.475719 TGTGAACGGTCCTACTAAAATCTG 58.524 41.667 0.00 0.00 0.00 2.90
3153 3675 5.733620 TGTGAACGGTCCTACTAAAATCT 57.266 39.130 0.00 0.00 0.00 2.40
3154 3676 6.790285 TTTGTGAACGGTCCTACTAAAATC 57.210 37.500 0.00 0.00 0.00 2.17
3155 3677 7.571080 TTTTTGTGAACGGTCCTACTAAAAT 57.429 32.000 0.00 0.00 0.00 1.82
3156 3678 6.998968 TTTTTGTGAACGGTCCTACTAAAA 57.001 33.333 0.00 3.67 0.00 1.52


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

AutoCloner maintained by Alex Coulton.