Multiple sequence alignment - TraesCS4B01G183900

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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 TraesCS4B01G183900 chr4B 100.000 2993 0 0 1 2993 403255329 403252337 0.000000e+00 5528
1 TraesCS4B01G183900 chr4B 91.367 139 10 2 2005 2142 360232872 360233009 3.940000e-44 189
2 TraesCS4B01G183900 chr4D 95.130 1540 44 15 477 2006 323098462 323096944 0.000000e+00 2399
3 TraesCS4B01G183900 chr4D 85.366 615 48 13 1 580 323099026 323098419 1.540000e-167 599
4 TraesCS4B01G183900 chr4D 90.545 275 12 11 2130 2402 323096946 323096684 4.750000e-93 351
5 TraesCS4B01G183900 chr4D 94.286 175 10 0 2391 2565 69494132 69494306 4.920000e-68 268
6 TraesCS4B01G183900 chr4D 92.105 190 12 3 2390 2578 238640341 238640154 6.360000e-67 265
7 TraesCS4B01G183900 chr4D 91.339 127 11 0 2753 2879 323096658 323096532 1.100000e-39 174
8 TraesCS4B01G183900 chr4A 92.963 1421 55 22 477 1891 149046291 149047672 0.000000e+00 2028
9 TraesCS4B01G183900 chr4A 87.857 280 12 6 2132 2401 149048919 149049186 2.900000e-80 309
10 TraesCS4B01G183900 chr4A 89.540 239 21 3 2758 2993 149049323 149049560 1.740000e-77 300
11 TraesCS4B01G183900 chr4A 96.471 170 6 0 1 170 149045646 149045815 6.320000e-72 281
12 TraesCS4B01G183900 chr4A 91.908 173 12 2 2574 2745 617923972 617923801 1.070000e-59 241
13 TraesCS4B01G183900 chr4A 93.421 152 10 0 166 317 149045837 149045988 3.000000e-55 226
14 TraesCS4B01G183900 chr6A 90.122 1316 85 18 708 2003 60973461 60972171 0.000000e+00 1668
15 TraesCS4B01G183900 chr6A 93.500 1000 65 0 997 1996 603249193 603250192 0.000000e+00 1487
16 TraesCS4B01G183900 chr6B 89.761 1299 94 19 710 2001 694258720 694259986 0.000000e+00 1626
17 TraesCS4B01G183900 chr6B 95.455 176 7 1 2398 2572 96958821 96958646 2.270000e-71 279
18 TraesCS4B01G183900 chr6B 92.593 135 9 1 1998 2132 184799058 184798925 3.040000e-45 193
19 TraesCS4B01G183900 chr6B 83.516 182 25 5 2224 2403 694260007 694260185 6.640000e-37 165
20 TraesCS4B01G183900 chr6D 94.500 1000 55 0 997 1996 456540530 456541529 0.000000e+00 1543
21 TraesCS4B01G183900 chr6D 85.356 239 24 8 708 944 456540289 456540518 1.390000e-58 237
22 TraesCS4B01G183900 chr3B 92.453 1007 70 4 996 1996 40773329 40774335 0.000000e+00 1434
23 TraesCS4B01G183900 chr2A 88.269 1219 109 16 790 1996 19164353 19163157 0.000000e+00 1428
24 TraesCS4B01G183900 chr2A 80.405 148 20 6 2150 2297 19163128 19162990 1.470000e-18 104
25 TraesCS4B01G183900 chr2D 87.256 1232 120 19 780 1996 18170159 18168950 0.000000e+00 1371
26 TraesCS4B01G183900 chr2D 95.349 172 7 1 2396 2566 560959655 560959484 3.800000e-69 272
27 TraesCS4B01G183900 chr2D 84.259 108 15 2 2150 2256 18168924 18168818 1.470000e-18 104
28 TraesCS4B01G183900 chr3D 95.858 169 7 0 2400 2568 7607559 7607391 1.060000e-69 274
29 TraesCS4B01G183900 chr5A 93.889 180 9 2 2401 2578 382566802 382566623 1.370000e-68 270
30 TraesCS4B01G183900 chr1B 95.322 171 7 1 2576 2745 48317906 48318076 1.370000e-68 270
31 TraesCS4B01G183900 chr1B 93.182 176 10 2 2574 2748 5724391 5724217 1.060000e-64 257
32 TraesCS4B01G183900 chrUn 94.253 174 8 2 2576 2748 361535345 361535173 6.360000e-67 265
33 TraesCS4B01G183900 chrUn 94.253 174 8 2 2576 2748 361537406 361537234 6.360000e-67 265
34 TraesCS4B01G183900 chr5D 92.473 186 13 1 2402 2586 458767356 458767171 6.360000e-67 265
35 TraesCS4B01G183900 chr5B 93.785 177 10 1 2573 2748 706583520 706583344 6.360000e-67 265
36 TraesCS4B01G183900 chr5B 92.593 135 9 1 1998 2132 330622291 330622424 3.040000e-45 193
37 TraesCS4B01G183900 chr3A 92.857 182 12 1 2396 2577 70479214 70479034 2.290000e-66 263
38 TraesCS4B01G183900 chr3A 91.379 174 12 2 2574 2745 710255575 710255403 4.990000e-58 235
39 TraesCS4B01G183900 chr3A 93.130 131 8 1 2004 2134 13008824 13008953 1.100000e-44 191
40 TraesCS4B01G183900 chr7D 92.432 185 10 2 2386 2570 175164115 175163935 8.230000e-66 261
41 TraesCS4B01G183900 chr7A 92.571 175 11 2 2572 2745 688841507 688841680 1.780000e-62 250
42 TraesCS4B01G183900 chr7A 92.593 135 9 1 1998 2132 621577600 621577467 3.040000e-45 193
43 TraesCS4B01G183900 chr7A 90.714 140 11 2 1993 2132 208247489 208247352 5.090000e-43 185
44 TraesCS4B01G183900 chr7B 91.477 176 14 1 2574 2748 529832061 529831886 1.070000e-59 241
45 TraesCS4B01G183900 chr2B 92.593 135 9 1 1998 2132 33815934 33816067 3.040000e-45 193
46 TraesCS4B01G183900 chr1A 92.593 135 8 2 2004 2137 415644528 415644661 3.040000e-45 193
47 TraesCS4B01G183900 chr1D 92.366 131 9 1 2004 2134 488630316 488630187 5.090000e-43 185


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 TraesCS4B01G183900 chr4B 403252337 403255329 2992 True 5528.00 5528 100.0000 1 2993 1 chr4B.!!$R1 2992
1 TraesCS4B01G183900 chr4D 323096532 323099026 2494 True 880.75 2399 90.5950 1 2879 4 chr4D.!!$R2 2878
2 TraesCS4B01G183900 chr4A 149045646 149049560 3914 False 628.80 2028 92.0504 1 2993 5 chr4A.!!$F1 2992
3 TraesCS4B01G183900 chr6A 60972171 60973461 1290 True 1668.00 1668 90.1220 708 2003 1 chr6A.!!$R1 1295
4 TraesCS4B01G183900 chr6A 603249193 603250192 999 False 1487.00 1487 93.5000 997 1996 1 chr6A.!!$F1 999
5 TraesCS4B01G183900 chr6B 694258720 694260185 1465 False 895.50 1626 86.6385 710 2403 2 chr6B.!!$F1 1693
6 TraesCS4B01G183900 chr6D 456540289 456541529 1240 False 890.00 1543 89.9280 708 1996 2 chr6D.!!$F1 1288
7 TraesCS4B01G183900 chr3B 40773329 40774335 1006 False 1434.00 1434 92.4530 996 1996 1 chr3B.!!$F1 1000
8 TraesCS4B01G183900 chr2A 19162990 19164353 1363 True 766.00 1428 84.3370 790 2297 2 chr2A.!!$R1 1507
9 TraesCS4B01G183900 chr2D 18168818 18170159 1341 True 737.50 1371 85.7575 780 2256 2 chr2D.!!$R2 1476
10 TraesCS4B01G183900 chrUn 361535173 361537406 2233 True 265.00 265 94.2530 2576 2748 2 chrUn.!!$R1 172

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
928 1153 0.394899 ATAGCTCACCAAAGCAGCCC 60.395 55.0 0.0 0.0 45.0 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2003 3386 0.890683 TTTTCGGACGGAGGGAGTAC 59.109 55.0 0.0 0.0 0.0 2.73 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
87 88 5.389935 GGCGTTTGAGATTACTGAACTGAAG 60.390 44.000 0.00 0.00 0.00 3.02
119 120 3.607741 AGTTCATGTCCTGCTCATTCTG 58.392 45.455 0.00 0.00 0.00 3.02
147 148 1.301716 GGTGAAGTTCTCGGCAGCA 60.302 57.895 4.17 0.00 0.00 4.41
210 237 9.021807 CCGAATTAATCTCTAGTACATAAGGGA 57.978 37.037 0.00 0.00 0.00 4.20
217 244 5.826737 TCTCTAGTACATAAGGGAAACTCCG 59.173 44.000 0.00 0.00 37.43 4.63
283 401 6.558775 TCTCTAGTACATAAGGGGCAATTCAT 59.441 38.462 0.00 0.00 0.00 2.57
340 477 1.342174 ACACTAAACGTCCACGGACAT 59.658 47.619 16.23 0.00 44.77 3.06
346 483 1.292223 CGTCCACGGACATGTTCCT 59.708 57.895 16.23 0.00 44.77 3.36
355 492 5.450688 CCACGGACATGTTCCTAAAACAAAA 60.451 40.000 0.00 0.00 43.25 2.44
356 493 5.457473 CACGGACATGTTCCTAAAACAAAAC 59.543 40.000 0.00 0.00 43.25 2.43
357 494 4.673311 CGGACATGTTCCTAAAACAAAACG 59.327 41.667 0.00 0.00 43.25 3.60
358 495 5.584442 GGACATGTTCCTAAAACAAAACGT 58.416 37.500 0.00 0.00 41.95 3.99
394 534 3.423123 CGTCCGCAGACACATCTAAAAAC 60.423 47.826 0.20 0.00 43.73 2.43
401 541 5.215160 CAGACACATCTAAAAACAGTTGGC 58.785 41.667 0.00 0.00 32.25 4.52
408 548 1.470051 AAAAACAGTTGGCGGACACT 58.530 45.000 0.00 0.00 0.00 3.55
430 570 2.365293 GTTCCAAAAACAGCTGGTGGAT 59.635 45.455 23.21 5.52 38.16 3.41
462 602 7.656707 ATTTTTCGGACGCTTAGTAACTAAA 57.343 32.000 0.00 0.00 0.00 1.85
463 603 7.656707 TTTTTCGGACGCTTAGTAACTAAAT 57.343 32.000 0.00 0.00 0.00 1.40
465 605 4.675510 TCGGACGCTTAGTAACTAAATGG 58.324 43.478 0.00 0.00 0.00 3.16
466 606 4.158394 TCGGACGCTTAGTAACTAAATGGT 59.842 41.667 0.00 0.00 0.00 3.55
467 607 5.356751 TCGGACGCTTAGTAACTAAATGGTA 59.643 40.000 0.00 0.00 0.00 3.25
468 608 5.456822 CGGACGCTTAGTAACTAAATGGTAC 59.543 44.000 0.00 0.00 39.08 3.34
469 609 5.456822 GGACGCTTAGTAACTAAATGGTACG 59.543 44.000 0.00 0.00 43.35 3.67
470 610 4.800471 ACGCTTAGTAACTAAATGGTACGC 59.200 41.667 0.00 0.00 43.35 4.42
471 611 5.039333 CGCTTAGTAACTAAATGGTACGCT 58.961 41.667 0.00 0.00 43.35 5.07
472 612 5.172771 CGCTTAGTAACTAAATGGTACGCTC 59.827 44.000 0.00 0.00 43.35 5.03
473 613 6.271566 GCTTAGTAACTAAATGGTACGCTCT 58.728 40.000 0.00 0.00 43.35 4.09
474 614 6.755607 GCTTAGTAACTAAATGGTACGCTCTT 59.244 38.462 0.00 0.00 43.35 2.85
556 750 1.748493 GTCAAAAACAGCTGGTGGACA 59.252 47.619 19.93 0.00 0.00 4.02
563 757 1.212935 ACAGCTGGTGGACACTCTTTT 59.787 47.619 19.93 0.00 0.00 2.27
568 762 5.010012 CAGCTGGTGGACACTCTTTTATTTT 59.990 40.000 5.57 0.00 0.00 1.82
576 770 7.222031 GTGGACACTCTTTTATTTTGGACAAAC 59.778 37.037 0.00 0.00 0.00 2.93
587 781 1.937278 TGGACAAACTAAACGTGCGA 58.063 45.000 0.00 0.00 0.00 5.10
597 791 1.647346 AAACGTGCGAGAACACTCAA 58.353 45.000 0.00 0.00 38.45 3.02
602 796 2.594654 CGTGCGAGAACACTCAATACTC 59.405 50.000 0.00 0.00 38.45 2.59
603 797 3.575630 GTGCGAGAACACTCAATACTCA 58.424 45.455 0.00 0.00 37.58 3.41
624 818 7.166167 ACTCACTCCGTCCAAAATTACTTTAT 58.834 34.615 0.00 0.00 0.00 1.40
663 861 5.758924 TGTATGCGCAGTAGTAGTAATCAG 58.241 41.667 18.32 0.00 0.00 2.90
701 899 1.061131 CTGGTGCACGCTCTTTATTCG 59.939 52.381 11.45 0.00 0.00 3.34
921 1146 2.354704 CCTCGTTCCATAGCTCACCAAA 60.355 50.000 0.00 0.00 0.00 3.28
922 1147 2.932614 CTCGTTCCATAGCTCACCAAAG 59.067 50.000 0.00 0.00 0.00 2.77
923 1148 1.398390 CGTTCCATAGCTCACCAAAGC 59.602 52.381 0.00 0.00 42.82 3.51
927 1152 0.737219 CATAGCTCACCAAAGCAGCC 59.263 55.000 0.00 0.00 45.00 4.85
928 1153 0.394899 ATAGCTCACCAAAGCAGCCC 60.395 55.000 0.00 0.00 45.00 5.19
929 1154 2.803155 TAGCTCACCAAAGCAGCCCG 62.803 60.000 0.00 0.00 45.00 6.13
930 1155 2.032528 CTCACCAAAGCAGCCCGA 59.967 61.111 0.00 0.00 0.00 5.14
933 1158 4.660938 ACCAAAGCAGCCCGACCC 62.661 66.667 0.00 0.00 0.00 4.46
934 1159 4.659172 CCAAAGCAGCCCGACCCA 62.659 66.667 0.00 0.00 0.00 4.51
1279 1524 2.434359 CCTTCGACAACCCGCTCC 60.434 66.667 0.00 0.00 0.00 4.70
1557 1802 1.667830 CATGTCGTTCCACACCGCT 60.668 57.895 0.00 0.00 0.00 5.52
1953 3336 4.612412 GTGGCGGACGTGACCCAA 62.612 66.667 0.00 0.00 0.00 4.12
1974 3357 1.859302 AGAGAGAGGAGTTCGCCAAT 58.141 50.000 0.00 0.00 0.00 3.16
2012 3395 1.513586 CGTTGCGACGTACTCCCTC 60.514 63.158 18.62 0.00 44.08 4.30
2013 3396 1.153881 GTTGCGACGTACTCCCTCC 60.154 63.158 0.00 0.00 0.00 4.30
2015 3398 3.130160 GCGACGTACTCCCTCCGT 61.130 66.667 0.00 0.00 37.56 4.69
2016 3399 3.096791 CGACGTACTCCCTCCGTC 58.903 66.667 0.00 0.00 45.49 4.79
2017 3400 2.467826 CGACGTACTCCCTCCGTCC 61.468 68.421 5.91 0.00 46.03 4.79
2018 3401 2.437359 ACGTACTCCCTCCGTCCG 60.437 66.667 0.00 0.00 0.00 4.79
2020 3403 1.746615 CGTACTCCCTCCGTCCGAA 60.747 63.158 0.00 0.00 0.00 4.30
2022 3405 0.890683 GTACTCCCTCCGTCCGAAAA 59.109 55.000 0.00 0.00 0.00 2.29
2023 3406 1.479730 GTACTCCCTCCGTCCGAAAAT 59.520 52.381 0.00 0.00 0.00 1.82
2024 3407 1.856629 ACTCCCTCCGTCCGAAAATA 58.143 50.000 0.00 0.00 0.00 1.40
2025 3408 1.479730 ACTCCCTCCGTCCGAAAATAC 59.520 52.381 0.00 0.00 0.00 1.89
2026 3409 1.755380 CTCCCTCCGTCCGAAAATACT 59.245 52.381 0.00 0.00 0.00 2.12
2027 3410 2.167900 CTCCCTCCGTCCGAAAATACTT 59.832 50.000 0.00 0.00 0.00 2.24
2028 3411 2.093869 TCCCTCCGTCCGAAAATACTTG 60.094 50.000 0.00 0.00 0.00 3.16
2029 3412 2.354403 CCCTCCGTCCGAAAATACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
2030 3413 2.928116 CCTCCGTCCGAAAATACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
2031 3414 3.581755 CTCCGTCCGAAAATACTTGTCA 58.418 45.455 0.00 0.00 0.00 3.58
2032 3415 4.181578 CTCCGTCCGAAAATACTTGTCAT 58.818 43.478 0.00 0.00 0.00 3.06
2033 3416 4.178540 TCCGTCCGAAAATACTTGTCATC 58.821 43.478 0.00 0.00 0.00 2.92
2034 3417 3.930229 CCGTCCGAAAATACTTGTCATCA 59.070 43.478 0.00 0.00 0.00 3.07
2035 3418 4.390603 CCGTCCGAAAATACTTGTCATCAA 59.609 41.667 0.00 0.00 0.00 2.57
2036 3419 5.106869 CCGTCCGAAAATACTTGTCATCAAA 60.107 40.000 0.00 0.00 32.87 2.69
2037 3420 6.367421 CGTCCGAAAATACTTGTCATCAAAA 58.633 36.000 0.00 0.00 32.87 2.44
2038 3421 7.021196 CGTCCGAAAATACTTGTCATCAAAAT 58.979 34.615 0.00 0.00 32.87 1.82
2039 3422 7.007367 CGTCCGAAAATACTTGTCATCAAAATG 59.993 37.037 0.00 0.00 32.87 2.32
2040 3423 7.273381 GTCCGAAAATACTTGTCATCAAAATGG 59.727 37.037 0.00 0.00 33.42 3.16
2041 3424 7.175816 TCCGAAAATACTTGTCATCAAAATGGA 59.824 33.333 0.00 0.00 33.42 3.41
2042 3425 7.273381 CCGAAAATACTTGTCATCAAAATGGAC 59.727 37.037 0.00 0.00 33.42 4.02
2043 3426 7.807433 CGAAAATACTTGTCATCAAAATGGACA 59.193 33.333 0.00 0.00 33.42 4.02
2044 3427 9.474920 GAAAATACTTGTCATCAAAATGGACAA 57.525 29.630 0.00 0.00 34.59 3.18
2045 3428 9.829507 AAAATACTTGTCATCAAAATGGACAAA 57.170 25.926 7.70 0.00 34.98 2.83
2046 3429 9.829507 AAATACTTGTCATCAAAATGGACAAAA 57.170 25.926 7.70 0.84 34.98 2.44
2047 3430 9.480053 AATACTTGTCATCAAAATGGACAAAAG 57.520 29.630 7.70 0.73 34.98 2.27
2048 3431 7.111247 ACTTGTCATCAAAATGGACAAAAGA 57.889 32.000 7.70 0.00 34.98 2.52
2049 3432 7.205297 ACTTGTCATCAAAATGGACAAAAGAG 58.795 34.615 7.70 0.00 34.98 2.85
2050 3433 6.088016 TGTCATCAAAATGGACAAAAGAGG 57.912 37.500 0.00 0.00 33.42 3.69
2051 3434 5.832595 TGTCATCAAAATGGACAAAAGAGGA 59.167 36.000 0.00 0.00 33.42 3.71
2052 3435 6.494491 TGTCATCAAAATGGACAAAAGAGGAT 59.506 34.615 0.00 0.00 33.42 3.24
2053 3436 6.810182 GTCATCAAAATGGACAAAAGAGGATG 59.190 38.462 0.00 0.00 33.42 3.51
2054 3437 6.494491 TCATCAAAATGGACAAAAGAGGATGT 59.506 34.615 0.00 0.00 33.42 3.06
2055 3438 7.669304 TCATCAAAATGGACAAAAGAGGATGTA 59.331 33.333 0.00 0.00 33.42 2.29
2056 3439 8.472413 CATCAAAATGGACAAAAGAGGATGTAT 58.528 33.333 0.00 0.00 0.00 2.29
2057 3440 8.055279 TCAAAATGGACAAAAGAGGATGTATC 57.945 34.615 0.00 0.00 0.00 2.24
2058 3441 7.890127 TCAAAATGGACAAAAGAGGATGTATCT 59.110 33.333 0.00 0.00 0.00 1.98
2059 3442 9.177608 CAAAATGGACAAAAGAGGATGTATCTA 57.822 33.333 0.00 0.00 0.00 1.98
2060 3443 8.970859 AAATGGACAAAAGAGGATGTATCTAG 57.029 34.615 0.00 0.00 0.00 2.43
2061 3444 7.921041 ATGGACAAAAGAGGATGTATCTAGA 57.079 36.000 0.00 0.00 0.00 2.43
2062 3445 7.921041 TGGACAAAAGAGGATGTATCTAGAT 57.079 36.000 10.73 10.73 0.00 1.98
2063 3446 7.730084 TGGACAAAAGAGGATGTATCTAGATG 58.270 38.462 15.79 0.00 0.00 2.90
2064 3447 7.345653 TGGACAAAAGAGGATGTATCTAGATGT 59.654 37.037 15.79 0.92 0.00 3.06
2065 3448 8.861086 GGACAAAAGAGGATGTATCTAGATGTA 58.139 37.037 15.79 4.44 0.00 2.29
2117 3500 9.872757 TTGTCTATTTTGACGACAAGTATTTTC 57.127 29.630 0.00 0.00 41.27 2.29
2118 3501 8.218441 TGTCTATTTTGACGACAAGTATTTTCG 58.782 33.333 0.00 0.00 39.64 3.46
2119 3502 7.686938 GTCTATTTTGACGACAAGTATTTTCGG 59.313 37.037 0.00 0.00 37.32 4.30
2120 3503 5.987777 TTTTGACGACAAGTATTTTCGGA 57.012 34.783 0.00 0.00 37.32 4.55
2121 3504 4.977741 TTGACGACAAGTATTTTCGGAC 57.022 40.909 0.00 0.00 37.07 4.79
2122 3505 2.981805 TGACGACAAGTATTTTCGGACG 59.018 45.455 0.00 0.00 37.07 4.79
2123 3506 3.236816 GACGACAAGTATTTTCGGACGA 58.763 45.455 0.00 0.00 37.07 4.20
2124 3507 3.641648 ACGACAAGTATTTTCGGACGAA 58.358 40.909 2.62 2.62 37.07 3.85
2125 3508 3.671928 ACGACAAGTATTTTCGGACGAAG 59.328 43.478 7.25 0.00 37.07 3.79
2126 3509 3.060363 CGACAAGTATTTTCGGACGAAGG 59.940 47.826 7.25 0.00 35.38 3.46
2127 3510 3.332034 ACAAGTATTTTCGGACGAAGGG 58.668 45.455 7.25 0.00 35.38 3.95
2128 3511 3.007182 ACAAGTATTTTCGGACGAAGGGA 59.993 43.478 7.25 0.00 35.38 4.20
2142 3525 5.294552 GGACGAAGGGAGTAATGAAAATGAG 59.705 44.000 0.00 0.00 0.00 2.90
2143 3526 4.636206 ACGAAGGGAGTAATGAAAATGAGC 59.364 41.667 0.00 0.00 0.00 4.26
2161 3544 3.118454 GGGCGTGTGTGGTCATCG 61.118 66.667 0.00 0.00 0.00 3.84
2292 3687 2.161410 TGATGTTTACAAGCGCATGTCC 59.839 45.455 22.97 11.79 34.75 4.02
2331 3727 1.062121 AGGCAGGCTAGACCAGGATAA 60.062 52.381 0.00 0.00 43.14 1.75
2405 3836 7.162082 AGACGATTTTCCTTCACAAATACTCT 58.838 34.615 0.00 0.00 0.00 3.24
2414 3845 4.451629 TCACAAATACTCTCTCCGTTCC 57.548 45.455 0.00 0.00 0.00 3.62
2415 3846 3.830178 TCACAAATACTCTCTCCGTTCCA 59.170 43.478 0.00 0.00 0.00 3.53
2418 3849 5.468746 CACAAATACTCTCTCCGTTCCAAAA 59.531 40.000 0.00 0.00 0.00 2.44
2421 3852 8.047310 ACAAATACTCTCTCCGTTCCAAAATAT 58.953 33.333 0.00 0.00 0.00 1.28
2427 3858 6.472887 TCTCTCCGTTCCAAAATATTTGTCT 58.527 36.000 0.39 0.00 0.00 3.41
2429 3860 7.447238 TCTCTCCGTTCCAAAATATTTGTCTTT 59.553 33.333 0.39 0.00 0.00 2.52
2430 3861 7.590279 TCTCCGTTCCAAAATATTTGTCTTTC 58.410 34.615 0.39 0.00 0.00 2.62
2431 3862 7.447238 TCTCCGTTCCAAAATATTTGTCTTTCT 59.553 33.333 0.39 0.00 0.00 2.52
2433 3864 8.726988 TCCGTTCCAAAATATTTGTCTTTCTAG 58.273 33.333 0.39 0.00 0.00 2.43
2434 3865 8.726988 CCGTTCCAAAATATTTGTCTTTCTAGA 58.273 33.333 0.39 0.00 0.00 2.43
2447 3878 8.964476 TTGTCTTTCTAGAGATTTCAACAAGT 57.036 30.769 0.00 0.00 0.00 3.16
2448 3879 8.370493 TGTCTTTCTAGAGATTTCAACAAGTG 57.630 34.615 0.00 0.00 0.00 3.16
2449 3880 8.204160 TGTCTTTCTAGAGATTTCAACAAGTGA 58.796 33.333 0.00 0.00 0.00 3.41
2450 3881 8.491950 GTCTTTCTAGAGATTTCAACAAGTGAC 58.508 37.037 0.00 0.00 35.39 3.67
2451 3882 8.424918 TCTTTCTAGAGATTTCAACAAGTGACT 58.575 33.333 0.00 0.00 35.39 3.41
2452 3883 9.698309 CTTTCTAGAGATTTCAACAAGTGACTA 57.302 33.333 0.00 0.00 35.39 2.59
2462 3893 8.662781 TTTCAACAAGTGACTATATATGGAGC 57.337 34.615 2.68 0.00 35.39 4.70
2463 3894 7.360113 TCAACAAGTGACTATATATGGAGCA 57.640 36.000 2.68 0.00 0.00 4.26
2464 3895 7.791029 TCAACAAGTGACTATATATGGAGCAA 58.209 34.615 2.68 0.00 0.00 3.91
2465 3896 8.264347 TCAACAAGTGACTATATATGGAGCAAA 58.736 33.333 2.68 0.00 0.00 3.68
2466 3897 8.554528 CAACAAGTGACTATATATGGAGCAAAG 58.445 37.037 2.68 0.00 0.00 2.77
2467 3898 7.796054 ACAAGTGACTATATATGGAGCAAAGT 58.204 34.615 2.68 0.00 0.00 2.66
2468 3899 7.712639 ACAAGTGACTATATATGGAGCAAAGTG 59.287 37.037 2.68 3.27 0.00 3.16
2469 3900 7.603180 AGTGACTATATATGGAGCAAAGTGA 57.397 36.000 2.68 0.00 0.00 3.41
2470 3901 7.665690 AGTGACTATATATGGAGCAAAGTGAG 58.334 38.462 2.68 0.00 0.00 3.51
2471 3902 7.288852 AGTGACTATATATGGAGCAAAGTGAGT 59.711 37.037 2.68 0.00 0.00 3.41
2472 3903 7.383572 GTGACTATATATGGAGCAAAGTGAGTG 59.616 40.741 2.68 0.00 0.00 3.51
2473 3904 7.287696 TGACTATATATGGAGCAAAGTGAGTGA 59.712 37.037 2.68 0.00 0.00 3.41
2474 3905 8.023021 ACTATATATGGAGCAAAGTGAGTGAA 57.977 34.615 2.68 0.00 0.00 3.18
2475 3906 8.654997 ACTATATATGGAGCAAAGTGAGTGAAT 58.345 33.333 2.68 0.00 0.00 2.57
2476 3907 7.976135 ATATATGGAGCAAAGTGAGTGAATC 57.024 36.000 0.00 0.00 0.00 2.52
2477 3908 3.777106 TGGAGCAAAGTGAGTGAATCT 57.223 42.857 0.00 0.00 0.00 2.40
2478 3909 3.405831 TGGAGCAAAGTGAGTGAATCTG 58.594 45.455 0.00 0.00 0.00 2.90
2479 3910 2.161211 GGAGCAAAGTGAGTGAATCTGC 59.839 50.000 0.00 0.00 0.00 4.26
2480 3911 2.810274 GAGCAAAGTGAGTGAATCTGCA 59.190 45.455 0.00 0.00 0.00 4.41
2481 3912 2.551459 AGCAAAGTGAGTGAATCTGCAC 59.449 45.455 0.00 0.00 39.05 4.57
2514 3945 7.956328 ATGTCTATATACATCCGTATGTGGT 57.044 36.000 3.56 0.00 45.99 4.16
2516 3947 8.502105 TGTCTATATACATCCGTATGTGGTAG 57.498 38.462 3.56 3.93 45.99 3.18
2517 3948 8.105197 TGTCTATATACATCCGTATGTGGTAGT 58.895 37.037 3.56 0.00 45.99 2.73
2518 3949 8.610896 GTCTATATACATCCGTATGTGGTAGTC 58.389 40.741 3.56 0.00 45.99 2.59
2519 3950 6.770746 ATATACATCCGTATGTGGTAGTCC 57.229 41.667 3.56 0.00 45.99 3.85
2520 3951 2.742348 ACATCCGTATGTGGTAGTCCA 58.258 47.619 0.00 0.00 44.79 4.02
2521 3952 3.305720 ACATCCGTATGTGGTAGTCCAT 58.694 45.455 0.00 0.00 44.79 3.41
2522 3953 3.709653 ACATCCGTATGTGGTAGTCCATT 59.290 43.478 0.00 0.00 44.79 3.16
2523 3954 4.163458 ACATCCGTATGTGGTAGTCCATTT 59.837 41.667 0.00 0.00 44.79 2.32
2524 3955 4.131649 TCCGTATGTGGTAGTCCATTTG 57.868 45.455 0.00 0.00 46.20 2.32
2525 3956 3.516300 TCCGTATGTGGTAGTCCATTTGT 59.484 43.478 0.00 0.00 46.20 2.83
2526 3957 4.710865 TCCGTATGTGGTAGTCCATTTGTA 59.289 41.667 0.00 0.00 46.20 2.41
2527 3958 5.187381 TCCGTATGTGGTAGTCCATTTGTAA 59.813 40.000 0.00 0.00 46.20 2.41
2528 3959 6.053005 CCGTATGTGGTAGTCCATTTGTAAT 58.947 40.000 0.00 0.00 46.20 1.89
2529 3960 6.202188 CCGTATGTGGTAGTCCATTTGTAATC 59.798 42.308 0.00 0.00 46.20 1.75
2530 3961 6.984474 CGTATGTGGTAGTCCATTTGTAATCT 59.016 38.462 0.00 0.00 46.20 2.40
2531 3962 7.169308 CGTATGTGGTAGTCCATTTGTAATCTC 59.831 40.741 0.00 0.00 46.20 2.75
2532 3963 6.620877 TGTGGTAGTCCATTTGTAATCTCT 57.379 37.500 0.00 0.00 46.20 3.10
2533 3964 7.727578 TGTGGTAGTCCATTTGTAATCTCTA 57.272 36.000 0.00 0.00 46.20 2.43
2534 3965 8.141298 TGTGGTAGTCCATTTGTAATCTCTAA 57.859 34.615 0.00 0.00 46.20 2.10
2535 3966 8.598916 TGTGGTAGTCCATTTGTAATCTCTAAA 58.401 33.333 0.00 0.00 46.20 1.85
2536 3967 9.444600 GTGGTAGTCCATTTGTAATCTCTAAAA 57.555 33.333 0.00 0.00 46.20 1.52
2560 3991 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
2561 3992 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
2562 3993 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
2563 3994 5.191124 ACAAATATTTAGGAACGGAGGGAGT 59.809 40.000 0.00 0.00 0.00 3.85
2564 3995 6.384886 ACAAATATTTAGGAACGGAGGGAGTA 59.615 38.462 0.00 0.00 0.00 2.59
2565 3996 6.667558 AATATTTAGGAACGGAGGGAGTAG 57.332 41.667 0.00 0.00 0.00 2.57
2566 3997 3.463048 TTTAGGAACGGAGGGAGTAGT 57.537 47.619 0.00 0.00 0.00 2.73
2567 3998 4.591321 TTTAGGAACGGAGGGAGTAGTA 57.409 45.455 0.00 0.00 0.00 1.82
2568 3999 2.433662 AGGAACGGAGGGAGTAGTAC 57.566 55.000 0.00 0.00 0.00 2.73
2569 4000 1.020437 GGAACGGAGGGAGTAGTACG 58.980 60.000 0.00 0.00 0.00 3.67
2570 4001 1.407437 GGAACGGAGGGAGTAGTACGA 60.407 57.143 0.00 0.00 0.00 3.43
2571 4002 2.570135 GAACGGAGGGAGTAGTACGAT 58.430 52.381 0.00 0.00 0.00 3.73
2572 4003 1.964552 ACGGAGGGAGTAGTACGATG 58.035 55.000 0.00 0.00 0.00 3.84
2573 4004 1.211457 ACGGAGGGAGTAGTACGATGT 59.789 52.381 0.00 0.00 0.00 3.06
2574 4005 2.295885 CGGAGGGAGTAGTACGATGTT 58.704 52.381 0.00 0.00 0.00 2.71
2615 6106 1.198094 TCCCCGTCCTCTGCATCAAA 61.198 55.000 0.00 0.00 0.00 2.69
2641 6132 5.586243 GTGATGCATACGGCCATCTTATTAT 59.414 40.000 2.24 0.00 43.89 1.28
2660 6151 2.859526 TCGAAGCAACAAAATGTGCA 57.140 40.000 0.00 0.00 30.52 4.57
2690 6182 5.998363 AGTCCATAGTCTCAAACTGAAAACC 59.002 40.000 0.00 0.00 39.11 3.27
2712 6204 1.035139 AAAAAGCAGCCCACACAGAG 58.965 50.000 0.00 0.00 0.00 3.35
2713 6205 0.106519 AAAAGCAGCCCACACAGAGT 60.107 50.000 0.00 0.00 0.00 3.24
2748 6240 9.601217 CTAGAAACACTAACTAGCCAATACAAT 57.399 33.333 0.00 0.00 0.00 2.71
2749 6241 8.268850 AGAAACACTAACTAGCCAATACAATG 57.731 34.615 0.00 0.00 0.00 2.82
2750 6242 7.883311 AGAAACACTAACTAGCCAATACAATGT 59.117 33.333 0.00 0.00 0.00 2.71
2751 6243 9.158233 GAAACACTAACTAGCCAATACAATGTA 57.842 33.333 0.00 0.00 0.00 2.29
2799 6291 3.319137 AGTTGCTCGCTAATTCTGACA 57.681 42.857 0.00 0.00 0.00 3.58
2802 6294 3.592898 TGCTCGCTAATTCTGACAGAA 57.407 42.857 19.85 19.85 38.78 3.02
2826 6318 2.364970 CCCATGTTTGCTTTTGACCTCA 59.635 45.455 0.00 0.00 0.00 3.86
2833 6328 3.507162 TGCTTTTGACCTCAGAATCCA 57.493 42.857 0.00 0.00 0.00 3.41
2856 6351 4.899239 GGCTCGACGGGCCTCATG 62.899 72.222 31.54 0.00 45.57 3.07
2883 6378 5.335976 GGGATCAACTTCATGGTTTCTGTTC 60.336 44.000 0.00 0.00 0.00 3.18
2891 6386 1.808411 TGGTTTCTGTTCGAGCCATC 58.192 50.000 0.00 0.00 0.00 3.51
2899 6394 0.442699 GTTCGAGCCATCACCGTTTC 59.557 55.000 0.00 0.00 0.00 2.78
2902 6397 1.413767 CGAGCCATCACCGTTTCTCG 61.414 60.000 0.00 0.00 37.65 4.04
2940 6435 5.982516 TGTAAATTGGAGTGTTTGATGTTGC 59.017 36.000 0.00 0.00 0.00 4.17
2945 6440 0.311790 AGTGTTTGATGTTGCAGCCG 59.688 50.000 0.00 0.00 0.00 5.52
2950 6445 0.522626 TTGATGTTGCAGCCGTGATG 59.477 50.000 0.00 0.00 0.00 3.07
2974 6469 2.096496 CCTCATCGGCATTGTTCACTTC 59.904 50.000 0.00 0.00 0.00 3.01
2975 6470 2.743664 CTCATCGGCATTGTTCACTTCA 59.256 45.455 0.00 0.00 0.00 3.02
2977 6472 3.127376 TCATCGGCATTGTTCACTTCATG 59.873 43.478 0.00 0.00 0.00 3.07
2987 6482 7.462856 GCATTGTTCACTTCATGTACTAGTACG 60.463 40.741 24.36 13.54 38.85 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
87 88 3.755378 AGGACATGAACTTCACTGATTGC 59.245 43.478 0.00 0.00 0.00 3.56
119 120 2.476997 GAGAACTTCACCGAAGAACAGC 59.523 50.000 10.58 0.00 41.71 4.40
147 148 5.475220 TGGTGATTACGTTTCATTTGGACAT 59.525 36.000 0.00 0.00 0.00 3.06
217 244 3.616821 TGTTCGATTTGATGATCCACGTC 59.383 43.478 0.00 0.00 35.29 4.34
283 401 2.715749 ATCAGATTTGGTGATCCGCA 57.284 45.000 0.00 0.00 36.30 5.69
340 477 3.937706 TCCGACGTTTTGTTTTAGGAACA 59.062 39.130 0.00 0.00 0.00 3.18
346 483 7.706281 TTAGTATGTCCGACGTTTTGTTTTA 57.294 32.000 0.00 0.00 0.00 1.52
355 492 3.122937 GACGTTTAGTATGTCCGACGT 57.877 47.619 0.00 0.00 45.10 4.34
394 534 1.507141 GGAACAGTGTCCGCCAACTG 61.507 60.000 0.00 7.74 36.39 3.16
401 541 2.794631 GCTGTTTTTGGAACAGTGTCCG 60.795 50.000 17.26 0.00 46.89 4.79
408 548 1.480137 CCACCAGCTGTTTTTGGAACA 59.520 47.619 13.81 0.00 37.89 3.18
430 570 3.071479 AGCGTCCGAAAAATAAAGAGCA 58.929 40.909 0.00 0.00 0.00 4.26
469 609 5.607119 TCAACTATTTTTGGACGAAGAGC 57.393 39.130 0.00 0.00 0.00 4.09
470 610 6.403636 CCCATCAACTATTTTTGGACGAAGAG 60.404 42.308 0.00 0.00 0.00 2.85
471 611 5.414454 CCCATCAACTATTTTTGGACGAAGA 59.586 40.000 0.00 0.00 0.00 2.87
472 612 5.640732 CCCATCAACTATTTTTGGACGAAG 58.359 41.667 0.00 0.00 0.00 3.79
473 613 4.082463 GCCCATCAACTATTTTTGGACGAA 60.082 41.667 0.00 0.00 0.00 3.85
474 614 3.442273 GCCCATCAACTATTTTTGGACGA 59.558 43.478 0.00 0.00 0.00 4.20
479 619 2.923020 GCGTGCCCATCAACTATTTTTG 59.077 45.455 0.00 0.00 0.00 2.44
556 750 9.511144 CGTTTAGTTTGTCCAAAATAAAAGAGT 57.489 29.630 22.30 0.00 45.85 3.24
563 757 5.007430 TCGCACGTTTAGTTTGTCCAAAATA 59.993 36.000 0.00 0.00 30.75 1.40
568 762 1.862201 CTCGCACGTTTAGTTTGTCCA 59.138 47.619 0.00 0.00 0.00 4.02
576 770 2.390938 TGAGTGTTCTCGCACGTTTAG 58.609 47.619 0.00 0.00 43.61 1.85
587 781 3.827302 ACGGAGTGAGTATTGAGTGTTCT 59.173 43.478 0.00 0.00 42.51 3.01
624 818 8.384607 TGCGCATACATCCATTTTAGTATAAA 57.615 30.769 5.66 0.00 0.00 1.40
645 839 2.223735 TGGCTGATTACTACTACTGCGC 60.224 50.000 0.00 0.00 0.00 6.09
673 871 1.226945 GCGTGCACCAGCTGTTTTT 60.227 52.632 13.81 0.00 42.74 1.94
674 872 2.063541 GAGCGTGCACCAGCTGTTTT 62.064 55.000 21.79 0.00 44.69 2.43
675 873 2.516930 AGCGTGCACCAGCTGTTT 60.517 55.556 17.08 0.00 42.82 2.83
676 874 2.947938 AAGAGCGTGCACCAGCTGTT 62.948 55.000 21.79 20.27 44.69 3.16
677 875 2.947938 AAAGAGCGTGCACCAGCTGT 62.948 55.000 21.79 15.88 44.69 4.40
923 1148 4.394712 GAGTGGTGGGTCGGGCTG 62.395 72.222 0.00 0.00 0.00 4.85
927 1152 2.923035 AGTGGAGTGGTGGGTCGG 60.923 66.667 0.00 0.00 0.00 4.79
928 1153 2.657237 GAGTGGAGTGGTGGGTCG 59.343 66.667 0.00 0.00 0.00 4.79
929 1154 1.841556 TGGAGTGGAGTGGTGGGTC 60.842 63.158 0.00 0.00 0.00 4.46
930 1155 2.147387 GTGGAGTGGAGTGGTGGGT 61.147 63.158 0.00 0.00 0.00 4.51
933 1158 0.833834 AGGAGTGGAGTGGAGTGGTG 60.834 60.000 0.00 0.00 0.00 4.17
934 1159 0.833834 CAGGAGTGGAGTGGAGTGGT 60.834 60.000 0.00 0.00 0.00 4.16
978 1211 3.719268 TTACCTGGTACCTGACGAGTA 57.281 47.619 19.66 10.25 32.20 2.59
979 1212 2.592102 TTACCTGGTACCTGACGAGT 57.408 50.000 19.66 11.17 32.20 4.18
981 1214 3.055675 CCATTTTACCTGGTACCTGACGA 60.056 47.826 19.66 2.17 0.00 4.20
1279 1524 1.450312 GGAAGATGGCGAGGTGGTG 60.450 63.158 0.00 0.00 0.00 4.17
1289 1534 2.398588 TGCTGTAGTAGGGGAAGATGG 58.601 52.381 0.00 0.00 0.00 3.51
1953 3336 1.633774 TGGCGAACTCCTCTCTCTTT 58.366 50.000 0.00 0.00 0.00 2.52
2003 3386 0.890683 TTTTCGGACGGAGGGAGTAC 59.109 55.000 0.00 0.00 0.00 2.73
2004 3387 1.856629 ATTTTCGGACGGAGGGAGTA 58.143 50.000 0.00 0.00 0.00 2.59
2010 3393 3.581755 TGACAAGTATTTTCGGACGGAG 58.418 45.455 0.00 0.00 0.00 4.63
2012 3395 3.930229 TGATGACAAGTATTTTCGGACGG 59.070 43.478 0.00 0.00 0.00 4.79
2013 3396 5.524511 TTGATGACAAGTATTTTCGGACG 57.475 39.130 0.00 0.00 0.00 4.79
2015 3398 7.175816 TCCATTTTGATGACAAGTATTTTCGGA 59.824 33.333 0.00 0.00 37.32 4.55
2016 3399 7.273381 GTCCATTTTGATGACAAGTATTTTCGG 59.727 37.037 0.00 0.00 37.32 4.30
2017 3400 7.807433 TGTCCATTTTGATGACAAGTATTTTCG 59.193 33.333 0.00 0.00 37.32 3.46
2018 3401 9.474920 TTGTCCATTTTGATGACAAGTATTTTC 57.525 29.630 0.00 0.00 37.32 2.29
2020 3403 9.829507 TTTTGTCCATTTTGATGACAAGTATTT 57.170 25.926 0.00 0.00 37.13 1.40
2022 3405 8.859090 TCTTTTGTCCATTTTGATGACAAGTAT 58.141 29.630 0.00 0.00 37.13 2.12
2023 3406 8.231692 TCTTTTGTCCATTTTGATGACAAGTA 57.768 30.769 0.00 0.00 37.13 2.24
2024 3407 7.111247 TCTTTTGTCCATTTTGATGACAAGT 57.889 32.000 0.00 0.00 37.13 3.16
2025 3408 6.643770 CCTCTTTTGTCCATTTTGATGACAAG 59.356 38.462 0.00 0.00 37.13 3.16
2026 3409 6.323482 TCCTCTTTTGTCCATTTTGATGACAA 59.677 34.615 0.00 0.00 34.47 3.18
2027 3410 5.832595 TCCTCTTTTGTCCATTTTGATGACA 59.167 36.000 0.00 0.00 0.00 3.58
2028 3411 6.331369 TCCTCTTTTGTCCATTTTGATGAC 57.669 37.500 0.00 0.00 0.00 3.06
2029 3412 6.494491 ACATCCTCTTTTGTCCATTTTGATGA 59.506 34.615 0.00 0.00 32.39 2.92
2030 3413 6.694447 ACATCCTCTTTTGTCCATTTTGATG 58.306 36.000 0.00 0.00 33.80 3.07
2031 3414 6.923199 ACATCCTCTTTTGTCCATTTTGAT 57.077 33.333 0.00 0.00 0.00 2.57
2032 3415 7.890127 AGATACATCCTCTTTTGTCCATTTTGA 59.110 33.333 0.00 0.00 0.00 2.69
2033 3416 8.059798 AGATACATCCTCTTTTGTCCATTTTG 57.940 34.615 0.00 0.00 0.00 2.44
2034 3417 9.401058 CTAGATACATCCTCTTTTGTCCATTTT 57.599 33.333 0.00 0.00 0.00 1.82
2035 3418 8.772250 TCTAGATACATCCTCTTTTGTCCATTT 58.228 33.333 0.00 0.00 0.00 2.32
2036 3419 8.324191 TCTAGATACATCCTCTTTTGTCCATT 57.676 34.615 0.00 0.00 0.00 3.16
2037 3420 7.921041 TCTAGATACATCCTCTTTTGTCCAT 57.079 36.000 0.00 0.00 0.00 3.41
2038 3421 7.345653 ACATCTAGATACATCCTCTTTTGTCCA 59.654 37.037 4.54 0.00 0.00 4.02
2039 3422 7.731054 ACATCTAGATACATCCTCTTTTGTCC 58.269 38.462 4.54 0.00 0.00 4.02
2092 3475 8.218441 CGAAAATACTTGTCGTCAAAATAGACA 58.782 33.333 0.00 0.00 42.36 3.41
2093 3476 7.686938 CCGAAAATACTTGTCGTCAAAATAGAC 59.313 37.037 0.00 0.00 32.87 2.59
2094 3477 7.599621 TCCGAAAATACTTGTCGTCAAAATAGA 59.400 33.333 0.00 0.00 32.87 1.98
2095 3478 7.686938 GTCCGAAAATACTTGTCGTCAAAATAG 59.313 37.037 0.00 0.00 32.87 1.73
2096 3479 7.512297 GTCCGAAAATACTTGTCGTCAAAATA 58.488 34.615 0.00 0.00 32.87 1.40
2097 3480 6.368213 GTCCGAAAATACTTGTCGTCAAAAT 58.632 36.000 0.00 0.00 32.87 1.82
2098 3481 5.556758 CGTCCGAAAATACTTGTCGTCAAAA 60.557 40.000 0.00 0.00 32.87 2.44
2099 3482 4.084952 CGTCCGAAAATACTTGTCGTCAAA 60.085 41.667 0.00 0.00 32.87 2.69
2100 3483 3.426191 CGTCCGAAAATACTTGTCGTCAA 59.574 43.478 0.00 0.00 32.93 3.18
2101 3484 2.981805 CGTCCGAAAATACTTGTCGTCA 59.018 45.455 0.00 0.00 32.93 4.35
2102 3485 3.236816 TCGTCCGAAAATACTTGTCGTC 58.763 45.455 0.00 0.00 32.93 4.20
2103 3486 3.287312 TCGTCCGAAAATACTTGTCGT 57.713 42.857 0.00 0.00 32.93 4.34
2104 3487 3.060363 CCTTCGTCCGAAAATACTTGTCG 59.940 47.826 3.52 0.00 33.34 4.35
2105 3488 3.370061 CCCTTCGTCCGAAAATACTTGTC 59.630 47.826 3.52 0.00 33.34 3.18
2106 3489 3.007182 TCCCTTCGTCCGAAAATACTTGT 59.993 43.478 3.52 0.00 33.34 3.16
2107 3490 3.592059 TCCCTTCGTCCGAAAATACTTG 58.408 45.455 3.52 0.00 33.34 3.16
2108 3491 3.260128 ACTCCCTTCGTCCGAAAATACTT 59.740 43.478 3.52 0.00 33.34 2.24
2109 3492 2.830321 ACTCCCTTCGTCCGAAAATACT 59.170 45.455 3.52 0.00 33.34 2.12
2110 3493 3.242549 ACTCCCTTCGTCCGAAAATAC 57.757 47.619 3.52 0.00 33.34 1.89
2111 3494 5.127519 TCATTACTCCCTTCGTCCGAAAATA 59.872 40.000 3.52 0.00 33.34 1.40
2112 3495 3.967332 TTACTCCCTTCGTCCGAAAAT 57.033 42.857 3.52 0.00 33.34 1.82
2113 3496 3.258872 TCATTACTCCCTTCGTCCGAAAA 59.741 43.478 3.52 0.00 33.34 2.29
2114 3497 2.827322 TCATTACTCCCTTCGTCCGAAA 59.173 45.455 3.52 0.00 33.34 3.46
2115 3498 2.449464 TCATTACTCCCTTCGTCCGAA 58.551 47.619 1.81 1.81 0.00 4.30
2116 3499 2.133281 TCATTACTCCCTTCGTCCGA 57.867 50.000 0.00 0.00 0.00 4.55
2117 3500 2.953466 TTCATTACTCCCTTCGTCCG 57.047 50.000 0.00 0.00 0.00 4.79
2118 3501 5.183228 TCATTTTCATTACTCCCTTCGTCC 58.817 41.667 0.00 0.00 0.00 4.79
2119 3502 5.220681 GCTCATTTTCATTACTCCCTTCGTC 60.221 44.000 0.00 0.00 0.00 4.20
2120 3503 4.636206 GCTCATTTTCATTACTCCCTTCGT 59.364 41.667 0.00 0.00 0.00 3.85
2121 3504 4.260375 CGCTCATTTTCATTACTCCCTTCG 60.260 45.833 0.00 0.00 0.00 3.79
2122 3505 4.035675 CCGCTCATTTTCATTACTCCCTTC 59.964 45.833 0.00 0.00 0.00 3.46
2123 3506 3.947834 CCGCTCATTTTCATTACTCCCTT 59.052 43.478 0.00 0.00 0.00 3.95
2124 3507 3.545703 CCGCTCATTTTCATTACTCCCT 58.454 45.455 0.00 0.00 0.00 4.20
2125 3508 2.618709 CCCGCTCATTTTCATTACTCCC 59.381 50.000 0.00 0.00 0.00 4.30
2126 3509 2.033424 GCCCGCTCATTTTCATTACTCC 59.967 50.000 0.00 0.00 0.00 3.85
2127 3510 2.286418 CGCCCGCTCATTTTCATTACTC 60.286 50.000 0.00 0.00 0.00 2.59
2128 3511 1.670811 CGCCCGCTCATTTTCATTACT 59.329 47.619 0.00 0.00 0.00 2.24
2143 3526 3.118454 GATGACCACACACGCCCG 61.118 66.667 0.00 0.00 0.00 6.13
2161 3544 2.048503 AAGCAGCCACGTACGGAC 60.049 61.111 21.06 8.27 0.00 4.79
2292 3687 5.724328 TGCCTTTCATAGACAAGTCTACAG 58.276 41.667 11.81 8.27 44.11 2.74
2331 3727 5.619757 CGACACATATTGTTTCTTGGCACAT 60.620 40.000 0.00 0.00 39.17 3.21
2405 3836 7.447238 AGAAAGACAAATATTTTGGAACGGAGA 59.553 33.333 0.00 0.00 0.00 3.71
2421 3852 9.396022 ACTTGTTGAAATCTCTAGAAAGACAAA 57.604 29.630 0.00 0.00 0.00 2.83
2437 3868 8.264347 TGCTCCATATATAGTCACTTGTTGAAA 58.736 33.333 0.00 0.00 35.39 2.69
2439 3870 7.360113 TGCTCCATATATAGTCACTTGTTGA 57.640 36.000 0.00 0.00 0.00 3.18
2440 3871 8.437360 TTTGCTCCATATATAGTCACTTGTTG 57.563 34.615 0.00 0.00 0.00 3.33
2442 3873 7.712639 CACTTTGCTCCATATATAGTCACTTGT 59.287 37.037 0.00 0.00 0.00 3.16
2444 3875 8.023021 TCACTTTGCTCCATATATAGTCACTT 57.977 34.615 0.00 0.00 0.00 3.16
2447 3878 7.287696 TCACTCACTTTGCTCCATATATAGTCA 59.712 37.037 0.00 0.00 0.00 3.41
2448 3879 7.661968 TCACTCACTTTGCTCCATATATAGTC 58.338 38.462 0.00 0.00 0.00 2.59
2449 3880 7.603180 TCACTCACTTTGCTCCATATATAGT 57.397 36.000 0.00 0.00 0.00 2.12
2450 3881 9.149225 GATTCACTCACTTTGCTCCATATATAG 57.851 37.037 0.00 0.00 0.00 1.31
2451 3882 8.874156 AGATTCACTCACTTTGCTCCATATATA 58.126 33.333 0.00 0.00 0.00 0.86
2452 3883 7.660617 CAGATTCACTCACTTTGCTCCATATAT 59.339 37.037 0.00 0.00 0.00 0.86
2454 3885 5.821470 CAGATTCACTCACTTTGCTCCATAT 59.179 40.000 0.00 0.00 0.00 1.78
2457 3888 3.405831 CAGATTCACTCACTTTGCTCCA 58.594 45.455 0.00 0.00 0.00 3.86
2458 3889 2.161211 GCAGATTCACTCACTTTGCTCC 59.839 50.000 0.00 0.00 0.00 4.70
2459 3890 2.810274 TGCAGATTCACTCACTTTGCTC 59.190 45.455 0.00 0.00 0.00 4.26
2460 3891 2.551459 GTGCAGATTCACTCACTTTGCT 59.449 45.455 0.00 0.00 34.29 3.91
2461 3892 2.551459 AGTGCAGATTCACTCACTTTGC 59.449 45.455 0.00 0.00 43.28 3.68
2470 3901 8.430801 AGACATATTTTAGAGTGCAGATTCAC 57.569 34.615 0.00 0.00 37.24 3.18
2488 3919 9.642343 ACCACATACGGATGTATATAGACATAT 57.358 33.333 14.23 5.08 44.82 1.78
2490 3921 7.956328 ACCACATACGGATGTATATAGACAT 57.044 36.000 14.23 12.70 44.82 3.06
2491 3922 8.105197 ACTACCACATACGGATGTATATAGACA 58.895 37.037 22.62 2.07 44.82 3.41
2492 3923 8.503458 ACTACCACATACGGATGTATATAGAC 57.497 38.462 22.62 0.00 44.82 2.59
2497 3928 5.633117 TGGACTACCACATACGGATGTATA 58.367 41.667 14.23 8.27 44.82 1.47
2515 3946 9.793259 TGTCTTTTTAGAGATTACAAATGGACT 57.207 29.630 0.00 0.00 0.00 3.85
2533 3964 8.520351 CCTCCGTTCCTAAATATTTGTCTTTTT 58.480 33.333 11.05 0.00 0.00 1.94
2534 3965 7.122204 CCCTCCGTTCCTAAATATTTGTCTTTT 59.878 37.037 11.05 0.00 0.00 2.27
2535 3966 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
2536 3967 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
2543 3974 5.713807 ACTACTCCCTCCGTTCCTAAATAT 58.286 41.667 0.00 0.00 0.00 1.28
2546 3977 3.463048 ACTACTCCCTCCGTTCCTAAA 57.537 47.619 0.00 0.00 0.00 1.85
2549 3980 1.407989 CGTACTACTCCCTCCGTTCCT 60.408 57.143 0.00 0.00 0.00 3.36
2550 3981 1.020437 CGTACTACTCCCTCCGTTCC 58.980 60.000 0.00 0.00 0.00 3.62
2615 6106 1.141657 AGATGGCCGTATGCATCACTT 59.858 47.619 0.19 0.00 43.89 3.16
2641 6132 2.859526 TGCACATTTTGTTGCTTCGA 57.140 40.000 0.00 0.00 0.00 3.71
2660 6151 7.907389 TCAGTTTGAGACTATGGACTTTGTAT 58.093 34.615 0.00 0.00 36.65 2.29
2690 6182 2.557924 TCTGTGTGGGCTGCTTTTTATG 59.442 45.455 0.00 0.00 0.00 1.90
2712 6204 2.772287 AGTGTTTCTAGCCTTCTGCAC 58.228 47.619 0.00 0.00 44.83 4.57
2713 6205 4.040461 AGTTAGTGTTTCTAGCCTTCTGCA 59.960 41.667 0.00 0.00 44.83 4.41
2745 6237 6.455113 GCACAAATGTACTCGGTACTACATTG 60.455 42.308 15.19 12.40 40.92 2.82
2748 6240 4.022155 TGCACAAATGTACTCGGTACTACA 60.022 41.667 13.14 0.00 39.49 2.74
2749 6241 4.487948 TGCACAAATGTACTCGGTACTAC 58.512 43.478 13.14 0.00 39.49 2.73
2750 6242 4.219070 ACTGCACAAATGTACTCGGTACTA 59.781 41.667 13.14 3.59 39.49 1.82
2751 6243 3.006537 ACTGCACAAATGTACTCGGTACT 59.993 43.478 13.14 0.47 39.49 2.73
2799 6291 3.960102 TCAAAAGCAAACATGGGTCTTCT 59.040 39.130 0.00 0.00 0.00 2.85
2802 6294 2.365293 GGTCAAAAGCAAACATGGGTCT 59.635 45.455 0.00 0.00 0.00 3.85
2833 6328 4.241555 GCCCGTCGAGCCATGGAT 62.242 66.667 18.40 10.08 0.00 3.41
2854 6349 2.854967 ACCATGAAGTTGATCCCCTCAT 59.145 45.455 0.00 0.00 32.72 2.90
2856 6351 3.372440 AACCATGAAGTTGATCCCCTC 57.628 47.619 0.00 0.00 0.00 4.30
2883 6378 1.413767 CGAGAAACGGTGATGGCTCG 61.414 60.000 0.00 0.00 39.12 5.03
2899 6394 7.361201 CCAATTTACATAATCATAGTGCCCGAG 60.361 40.741 0.00 0.00 0.00 4.63
2902 6397 7.448469 ACTCCAATTTACATAATCATAGTGCCC 59.552 37.037 0.00 0.00 0.00 5.36
2940 6435 3.465990 ATGAGGTTCATCACGGCTG 57.534 52.632 0.00 0.00 29.59 4.85
2950 6445 2.083774 TGAACAATGCCGATGAGGTTC 58.916 47.619 0.00 0.00 43.70 3.62
2961 6456 6.727824 ACTAGTACATGAAGTGAACAATGC 57.272 37.500 0.00 0.00 0.00 3.56


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

AutoCloner maintained by Alex Coulton.