Multiple sequence alignment - TraesCS5A01G040500

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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 TraesCS5A01G040500 chr5A 100.000 3480 0 0 815 4294 36485036 36481557 0.000000e+00 6427.0
1 TraesCS5A01G040500 chr5A 100.000 571 0 0 1 571 36485850 36485280 0.000000e+00 1055.0
2 TraesCS5A01G040500 chr5B 88.580 3126 184 56 1286 4294 45845679 45842610 0.000000e+00 3635.0
3 TraesCS5A01G040500 chr5B 86.567 201 14 8 340 537 45865683 45865493 4.350000e-50 209.0
4 TraesCS5A01G040500 chr5B 83.163 196 10 6 376 571 45846371 45846199 1.600000e-34 158.0
5 TraesCS5A01G040500 chr5D 90.254 2637 122 37 1738 4294 45665322 45662741 0.000000e+00 3321.0
6 TraesCS5A01G040500 chr5D 84.486 535 41 23 19 530 45666706 45666191 1.390000e-134 490.0
7 TraesCS5A01G040500 chr5D 80.531 452 47 15 3712 4122 45648728 45648277 4.170000e-80 309.0
8 TraesCS5A01G040500 chr5D 96.721 183 5 1 4113 4294 45636934 45636752 1.940000e-78 303.0
9 TraesCS5A01G040500 chr2D 81.087 920 108 31 2375 3275 454716519 454717391 0.000000e+00 675.0
10 TraesCS5A01G040500 chr4D 86.069 524 54 12 3063 3582 48512010 48511502 2.920000e-151 545.0
11 TraesCS5A01G040500 chr4B 85.305 524 58 13 3062 3581 349114038 349113530 1.370000e-144 523.0
12 TraesCS5A01G040500 chr4B 92.063 63 5 0 4046 4108 384287922 384287984 5.910000e-14 89.8
13 TraesCS5A01G040500 chr6D 85.000 520 59 12 3068 3582 203752357 203751852 1.070000e-140 510.0
14 TraesCS5A01G040500 chr6B 84.866 522 59 14 3062 3578 480661390 480661896 3.830000e-140 508.0
15 TraesCS5A01G040500 chr6B 84.837 521 60 13 3062 3578 95584218 95584723 1.380000e-139 507.0
16 TraesCS5A01G040500 chr6B 81.572 369 32 11 2888 3255 208898540 208898207 5.470000e-69 272.0
17 TraesCS5A01G040500 chr2B 84.704 523 62 12 3063 3581 651320727 651320219 1.380000e-139 507.0
18 TraesCS5A01G040500 chr2B 84.615 520 62 12 3063 3578 480013922 480014427 6.410000e-138 501.0
19 TraesCS5A01G040500 chr2B 81.063 301 21 14 2888 3187 435343417 435343682 1.560000e-49 207.0
20 TraesCS5A01G040500 chr2B 78.931 318 49 9 2499 2813 514324776 514324474 2.620000e-47 200.0
21 TraesCS5A01G040500 chr2B 88.435 147 9 3 2839 2985 514324493 514324355 2.050000e-38 171.0
22 TraesCS5A01G040500 chr7A 80.277 649 84 13 3185 3805 2875490 2876122 2.360000e-122 449.0
23 TraesCS5A01G040500 chr1A 81.388 317 43 6 2499 2813 7296597 7296295 1.190000e-60 244.0
24 TraesCS5A01G040500 chr1A 87.755 147 10 3 2839 2985 7296314 7296176 9.550000e-37 165.0
25 TraesCS5A01G040500 chr2A 80.858 303 41 7 2510 2810 32761534 32761821 5.590000e-54 222.0
26 TraesCS5A01G040500 chr2A 87.143 140 12 2 2839 2978 32761805 32761938 2.070000e-33 154.0


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 TraesCS5A01G040500 chr5A 36481557 36485850 4293 True 3741.0 6427 100.0000 1 4294 2 chr5A.!!$R1 4293
1 TraesCS5A01G040500 chr5B 45842610 45846371 3761 True 1896.5 3635 85.8715 376 4294 2 chr5B.!!$R2 3918
2 TraesCS5A01G040500 chr5D 45662741 45666706 3965 True 1905.5 3321 87.3700 19 4294 2 chr5D.!!$R3 4275
3 TraesCS5A01G040500 chr2D 454716519 454717391 872 False 675.0 675 81.0870 2375 3275 1 chr2D.!!$F1 900
4 TraesCS5A01G040500 chr4D 48511502 48512010 508 True 545.0 545 86.0690 3063 3582 1 chr4D.!!$R1 519
5 TraesCS5A01G040500 chr4B 349113530 349114038 508 True 523.0 523 85.3050 3062 3581 1 chr4B.!!$R1 519
6 TraesCS5A01G040500 chr6D 203751852 203752357 505 True 510.0 510 85.0000 3068 3582 1 chr6D.!!$R1 514
7 TraesCS5A01G040500 chr6B 480661390 480661896 506 False 508.0 508 84.8660 3062 3578 1 chr6B.!!$F2 516
8 TraesCS5A01G040500 chr6B 95584218 95584723 505 False 507.0 507 84.8370 3062 3578 1 chr6B.!!$F1 516
9 TraesCS5A01G040500 chr2B 651320219 651320727 508 True 507.0 507 84.7040 3063 3581 1 chr2B.!!$R1 518
10 TraesCS5A01G040500 chr2B 480013922 480014427 505 False 501.0 501 84.6150 3063 3578 1 chr2B.!!$F2 515
11 TraesCS5A01G040500 chr7A 2875490 2876122 632 False 449.0 449 80.2770 3185 3805 1 chr7A.!!$F1 620

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
374 391 0.034380 TCTAGCCACGGAGTAGTGCT 60.034 55.0 0.00 0.0 41.61 4.40 F
1042 1142 0.540454 GGTCCAGGTAGTAGCAACCC 59.460 60.0 1.58 0.0 37.77 4.11 F
1281 1425 0.033503 CCGTTTATGGGGGAGGCTTT 60.034 55.0 0.00 0.0 0.00 3.51 F
1455 1631 0.108424 ATTCTCCGCAGTGACTGAGC 60.108 55.0 18.18 0.0 32.44 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1198 1308 0.178990 AAAGAGCCTTGACCCACACC 60.179 55.000 0.00 0.00 0.00 4.16 R
2161 2353 0.995024 AGAAGATGGGGTTGGAGTGG 59.005 55.000 0.00 0.00 0.00 4.00 R
2709 2924 1.139947 CGAGCTTCGAACTCCTCCC 59.860 63.158 16.79 0.36 43.74 4.30 R
3312 3570 0.172803 GGCTGCATTTCAGAGGCAAG 59.827 55.000 0.50 0.00 45.72 4.01 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
66 67 2.124570 AGCCGGAAATGCTGCGAT 60.125 55.556 5.05 0.00 42.35 4.58
72 73 1.643832 GAAATGCTGCGATCCGTCC 59.356 57.895 0.00 0.00 0.00 4.79
73 74 2.094126 GAAATGCTGCGATCCGTCCG 62.094 60.000 0.00 0.00 0.00 4.79
134 135 4.320456 CGGTGACACAGGCAGGCT 62.320 66.667 8.08 0.00 0.00 4.58
145 146 3.446570 GCAGGCTGCCGCAGAATT 61.447 61.111 28.87 5.26 37.42 2.17
152 153 1.568612 CTGCCGCAGAATTCACACGT 61.569 55.000 15.74 0.00 32.44 4.49
153 154 1.163420 TGCCGCAGAATTCACACGTT 61.163 50.000 8.44 0.00 0.00 3.99
157 158 0.593128 GCAGAATTCACACGTTGGCT 59.407 50.000 8.44 0.00 0.00 4.75
158 159 1.400242 GCAGAATTCACACGTTGGCTC 60.400 52.381 8.44 0.00 0.00 4.70
160 161 0.521735 GAATTCACACGTTGGCTCCC 59.478 55.000 0.00 0.00 0.00 4.30
162 163 2.063015 ATTCACACGTTGGCTCCCCA 62.063 55.000 0.00 0.00 40.06 4.96
163 164 2.951475 TTCACACGTTGGCTCCCCAC 62.951 60.000 0.00 0.00 41.97 4.61
164 165 4.619227 ACACGTTGGCTCCCCACG 62.619 66.667 6.36 6.36 41.97 4.94
185 186 3.039588 CCGTTCCGTTCGTGGTGG 61.040 66.667 0.00 0.00 0.00 4.61
188 189 4.442018 TTCCGTTCGTGGTGGAAC 57.558 55.556 0.00 0.00 42.21 3.62
222 223 0.724785 GCGAGGGAAAAAGAAACGCG 60.725 55.000 3.53 3.53 35.78 6.01
230 231 4.087507 GGGAAAAAGAAACGCGAAATAACG 59.912 41.667 15.93 0.00 0.00 3.18
254 256 9.837525 ACGTTATAAAAACAAAAACACTGTACA 57.162 25.926 0.00 0.00 0.00 2.90
273 275 6.906659 TGTACACTAGTCGTAGAAAAGAAGG 58.093 40.000 0.00 0.00 39.69 3.46
275 277 4.174762 CACTAGTCGTAGAAAAGAAGGCC 58.825 47.826 0.00 0.00 39.69 5.19
276 278 2.365408 AGTCGTAGAAAAGAAGGCCG 57.635 50.000 0.00 0.00 39.69 6.13
279 281 1.619827 TCGTAGAAAAGAAGGCCGGAA 59.380 47.619 5.05 0.00 0.00 4.30
281 283 2.415512 CGTAGAAAAGAAGGCCGGAAAG 59.584 50.000 5.05 0.00 0.00 2.62
283 285 3.441500 AGAAAAGAAGGCCGGAAAGAT 57.558 42.857 5.05 0.00 0.00 2.40
336 353 1.949133 CGCGCGTGGCATACTGTAT 60.949 57.895 24.19 0.00 43.84 2.29
337 354 1.487452 CGCGCGTGGCATACTGTATT 61.487 55.000 24.19 0.00 43.84 1.89
338 355 0.232303 GCGCGTGGCATACTGTATTC 59.768 55.000 8.43 0.00 42.87 1.75
361 378 2.730672 CGTGCGTGCAAGTCTAGCC 61.731 63.158 0.59 0.00 0.00 3.93
365 382 2.094659 CGTGCAAGTCTAGCCACGG 61.095 63.158 10.36 0.00 34.92 4.94
366 383 1.292223 GTGCAAGTCTAGCCACGGA 59.708 57.895 0.00 0.00 0.00 4.69
367 384 0.737715 GTGCAAGTCTAGCCACGGAG 60.738 60.000 0.00 0.00 0.00 4.63
369 386 0.815734 GCAAGTCTAGCCACGGAGTA 59.184 55.000 0.00 0.00 41.61 2.59
370 387 1.202313 GCAAGTCTAGCCACGGAGTAG 60.202 57.143 0.00 0.00 41.61 2.57
374 391 0.034380 TCTAGCCACGGAGTAGTGCT 60.034 55.000 0.00 0.00 41.61 4.40
403 420 3.289834 CGTGCCCACTGCTTGCTT 61.290 61.111 0.00 0.00 42.00 3.91
551 571 4.109320 CCCCCTCCTCCGGTTATATAAAT 58.891 47.826 0.00 0.00 0.00 1.40
552 572 5.282946 CCCCCTCCTCCGGTTATATAAATA 58.717 45.833 0.00 0.00 0.00 1.40
553 573 5.727766 CCCCCTCCTCCGGTTATATAAATAA 59.272 44.000 0.00 0.00 0.00 1.40
554 574 6.216046 CCCCCTCCTCCGGTTATATAAATAAA 59.784 42.308 0.00 0.00 29.41 1.40
555 575 7.257126 CCCCCTCCTCCGGTTATATAAATAAAA 60.257 40.741 0.00 0.00 29.41 1.52
556 576 7.827729 CCCCTCCTCCGGTTATATAAATAAAAG 59.172 40.741 0.00 0.00 29.41 2.27
557 577 7.336176 CCCTCCTCCGGTTATATAAATAAAAGC 59.664 40.741 0.00 0.00 29.41 3.51
559 579 7.170277 TCCTCCGGTTATATAAATAAAAGCCC 58.830 38.462 0.00 0.00 29.41 5.19
560 580 6.093082 CCTCCGGTTATATAAATAAAAGCCCG 59.907 42.308 0.00 8.97 35.13 6.13
561 581 5.412286 TCCGGTTATATAAATAAAAGCCCGC 59.588 40.000 0.00 0.00 34.52 6.13
562 582 5.392272 CCGGTTATATAAATAAAAGCCCGCC 60.392 44.000 10.01 0.00 34.52 6.13
563 583 5.392272 CGGTTATATAAATAAAAGCCCGCCC 60.392 44.000 0.00 0.00 31.07 6.13
564 584 5.713389 GGTTATATAAATAAAAGCCCGCCCT 59.287 40.000 0.00 0.00 29.41 5.19
565 585 6.127814 GGTTATATAAATAAAAGCCCGCCCTC 60.128 42.308 0.00 0.00 29.41 4.30
566 586 2.061509 TAAATAAAAGCCCGCCCTCC 57.938 50.000 0.00 0.00 0.00 4.30
567 587 0.686441 AAATAAAAGCCCGCCCTCCC 60.686 55.000 0.00 0.00 0.00 4.30
568 588 1.580994 AATAAAAGCCCGCCCTCCCT 61.581 55.000 0.00 0.00 0.00 4.20
569 589 1.996070 ATAAAAGCCCGCCCTCCCTC 61.996 60.000 0.00 0.00 0.00 4.30
853 880 1.171308 CTGCTCCATCCAACAACCAG 58.829 55.000 0.00 0.00 0.00 4.00
889 924 2.073117 CCCCCACGCAATTAACAAAC 57.927 50.000 0.00 0.00 0.00 2.93
910 954 1.002544 CAATCTTATCGCCCTCCCTCC 59.997 57.143 0.00 0.00 0.00 4.30
911 955 0.545548 ATCTTATCGCCCTCCCTCCC 60.546 60.000 0.00 0.00 0.00 4.30
912 956 1.152226 CTTATCGCCCTCCCTCCCT 60.152 63.158 0.00 0.00 0.00 4.20
913 957 1.152312 TTATCGCCCTCCCTCCCTC 60.152 63.158 0.00 0.00 0.00 4.30
914 958 2.674672 TTATCGCCCTCCCTCCCTCC 62.675 65.000 0.00 0.00 0.00 4.30
927 971 2.341677 CCCTCCCTCCCTCCCCTTA 61.342 68.421 0.00 0.00 0.00 2.69
928 972 1.690148 CCCTCCCTCCCTCCCCTTAT 61.690 65.000 0.00 0.00 0.00 1.73
945 989 1.279496 TATCTCCACTTGCAGCACCT 58.721 50.000 0.00 0.00 0.00 4.00
958 1002 0.679002 AGCACCTGCATCACCATCAC 60.679 55.000 0.00 0.00 45.16 3.06
965 1009 0.666913 GCATCACCATCACCATCAGC 59.333 55.000 0.00 0.00 0.00 4.26
971 1015 0.952280 CCATCACCATCAGCATCAGC 59.048 55.000 0.00 0.00 42.56 4.26
972 1016 1.675552 CATCACCATCAGCATCAGCA 58.324 50.000 0.00 0.00 45.49 4.41
973 1017 2.230660 CATCACCATCAGCATCAGCAT 58.769 47.619 0.00 0.00 45.49 3.79
974 1018 1.963172 TCACCATCAGCATCAGCATC 58.037 50.000 0.00 0.00 45.49 3.91
987 1079 2.377073 TCAGCATCAGAGAGAGTGAGG 58.623 52.381 0.00 0.00 0.00 3.86
989 1081 0.752054 GCATCAGAGAGAGTGAGGGG 59.248 60.000 0.00 0.00 0.00 4.79
990 1082 0.752054 CATCAGAGAGAGTGAGGGGC 59.248 60.000 0.00 0.00 0.00 5.80
1008 1108 1.084370 GCGCTGTCACCATGGAGTAC 61.084 60.000 21.47 13.38 0.00 2.73
1026 1126 3.946558 AGTACGAGAGGATACACAAGGTC 59.053 47.826 0.00 0.00 41.41 3.85
1035 1135 4.016851 AGGATACACAAGGTCCAGGTAGTA 60.017 45.833 0.00 0.00 41.41 1.82
1037 1137 1.900486 ACACAAGGTCCAGGTAGTAGC 59.100 52.381 0.00 0.00 0.00 3.58
1040 1140 2.302157 ACAAGGTCCAGGTAGTAGCAAC 59.698 50.000 1.58 0.00 0.00 4.17
1041 1141 1.569653 AGGTCCAGGTAGTAGCAACC 58.430 55.000 1.58 6.34 37.27 3.77
1042 1142 0.540454 GGTCCAGGTAGTAGCAACCC 59.460 60.000 1.58 0.00 37.77 4.11
1043 1143 0.540454 GTCCAGGTAGTAGCAACCCC 59.460 60.000 1.58 0.00 37.77 4.95
1046 1146 1.209747 CCAGGTAGTAGCAACCCCTTC 59.790 57.143 1.58 0.00 37.77 3.46
1048 1148 0.545171 GGTAGTAGCAACCCCTTCCC 59.455 60.000 0.00 0.00 0.00 3.97
1050 1150 1.485480 GTAGTAGCAACCCCTTCCCTC 59.515 57.143 0.00 0.00 0.00 4.30
1052 1152 1.993391 TAGCAACCCCTTCCCTCGG 60.993 63.158 0.00 0.00 0.00 4.63
1054 1154 2.351276 CAACCCCTTCCCTCGGTG 59.649 66.667 0.00 0.00 0.00 4.94
1057 1157 1.196766 AACCCCTTCCCTCGGTGTAC 61.197 60.000 0.00 0.00 0.00 2.90
1062 1162 1.336125 CCTTCCCTCGGTGTACGTATC 59.664 57.143 0.00 0.00 44.69 2.24
1065 1165 2.838736 TCCCTCGGTGTACGTATCTAC 58.161 52.381 0.00 0.00 44.69 2.59
1082 1182 1.484653 CTACCCGTGTTCATCCATCCA 59.515 52.381 0.00 0.00 0.00 3.41
1105 1205 4.005032 GCGTCGAAGCCATCTCTC 57.995 61.111 12.67 0.00 0.00 3.20
1106 1206 1.590259 GCGTCGAAGCCATCTCTCC 60.590 63.158 12.67 0.00 0.00 3.71
1107 1207 1.298713 CGTCGAAGCCATCTCTCCG 60.299 63.158 0.00 0.00 0.00 4.63
1108 1208 1.066587 GTCGAAGCCATCTCTCCGG 59.933 63.158 0.00 0.00 0.00 5.14
1114 1214 2.827423 CCATCTCTCCGGCATGCT 59.173 61.111 18.92 0.00 0.00 3.79
1115 1215 1.597302 CCATCTCTCCGGCATGCTG 60.597 63.158 20.13 20.13 0.00 4.41
1116 1216 1.145598 CATCTCTCCGGCATGCTGT 59.854 57.895 24.56 2.29 0.00 4.40
1117 1217 1.145598 ATCTCTCCGGCATGCTGTG 59.854 57.895 24.56 16.51 0.00 3.66
1133 1240 2.514592 TGCCCGCTAGCAGCATTC 60.515 61.111 21.95 2.99 42.58 2.67
1136 1243 3.643978 CCGCTAGCAGCATTCGGC 61.644 66.667 16.45 0.00 42.58 5.54
1155 1262 1.474077 GCTAAAATCCACCCACAGCAG 59.526 52.381 0.00 0.00 0.00 4.24
1158 1265 0.610232 AAATCCACCCACAGCAGAGC 60.610 55.000 0.00 0.00 0.00 4.09
1173 1283 3.815856 CAGAGCTGCTAAATCCTCTCA 57.184 47.619 0.15 0.00 32.65 3.27
1174 1284 4.339872 CAGAGCTGCTAAATCCTCTCAT 57.660 45.455 0.15 0.00 32.65 2.90
1176 1286 3.324556 AGAGCTGCTAAATCCTCTCATCC 59.675 47.826 0.15 0.00 29.03 3.51
1178 1288 3.715834 AGCTGCTAAATCCTCTCATCCTT 59.284 43.478 0.00 0.00 0.00 3.36
1179 1289 4.165758 AGCTGCTAAATCCTCTCATCCTTT 59.834 41.667 0.00 0.00 0.00 3.11
1180 1290 4.886489 GCTGCTAAATCCTCTCATCCTTTT 59.114 41.667 0.00 0.00 0.00 2.27
1182 1292 6.017523 GCTGCTAAATCCTCTCATCCTTTTAC 60.018 42.308 0.00 0.00 0.00 2.01
1183 1293 6.357367 TGCTAAATCCTCTCATCCTTTTACC 58.643 40.000 0.00 0.00 0.00 2.85
1184 1294 6.069673 TGCTAAATCCTCTCATCCTTTTACCA 60.070 38.462 0.00 0.00 0.00 3.25
1187 1297 3.181329 TCCTCTCATCCTTTTACCAGCA 58.819 45.455 0.00 0.00 0.00 4.41
1188 1298 3.055094 TCCTCTCATCCTTTTACCAGCAC 60.055 47.826 0.00 0.00 0.00 4.40
1190 1300 3.937706 CTCTCATCCTTTTACCAGCACTG 59.062 47.826 0.00 0.00 0.00 3.66
1191 1301 3.327757 TCTCATCCTTTTACCAGCACTGT 59.672 43.478 0.00 0.00 0.00 3.55
1193 1303 3.149196 CATCCTTTTACCAGCACTGTGT 58.851 45.455 9.86 0.00 0.00 3.72
1195 1305 2.092646 TCCTTTTACCAGCACTGTGTGT 60.093 45.455 9.86 7.24 35.75 3.72
1210 1354 2.203139 TGTGCGGTGTGGGTCAAG 60.203 61.111 0.00 0.00 0.00 3.02
1214 1358 2.358737 CGGTGTGGGTCAAGGCTC 60.359 66.667 0.00 0.00 0.00 4.70
1221 1365 0.110486 TGGGTCAAGGCTCTTTCCAC 59.890 55.000 0.00 0.00 0.00 4.02
1222 1366 0.402121 GGGTCAAGGCTCTTTCCACT 59.598 55.000 0.00 0.00 0.00 4.00
1223 1367 1.202940 GGGTCAAGGCTCTTTCCACTT 60.203 52.381 0.00 0.00 0.00 3.16
1224 1368 2.587522 GGTCAAGGCTCTTTCCACTTT 58.412 47.619 0.00 0.00 0.00 2.66
1225 1369 2.959030 GGTCAAGGCTCTTTCCACTTTT 59.041 45.455 0.00 0.00 0.00 2.27
1226 1370 3.004839 GGTCAAGGCTCTTTCCACTTTTC 59.995 47.826 0.00 0.00 0.00 2.29
1227 1371 3.004839 GTCAAGGCTCTTTCCACTTTTCC 59.995 47.826 0.00 0.00 0.00 3.13
1228 1372 2.958355 CAAGGCTCTTTCCACTTTTCCA 59.042 45.455 0.00 0.00 0.00 3.53
1233 1377 3.366781 GCTCTTTCCACTTTTCCAGCATC 60.367 47.826 0.00 0.00 0.00 3.91
1236 1380 1.808411 TCCACTTTTCCAGCATCGAC 58.192 50.000 0.00 0.00 0.00 4.20
1243 1387 0.320683 TTCCAGCATCGACCACTGTG 60.321 55.000 0.00 0.00 0.00 3.66
1254 1398 3.256936 CACTGTGGTGGTGCATCG 58.743 61.111 0.00 0.00 39.59 3.84
1255 1399 2.669569 ACTGTGGTGGTGCATCGC 60.670 61.111 0.59 0.59 0.00 4.58
1279 1423 3.331293 CCGTTTATGGGGGAGGCT 58.669 61.111 0.00 0.00 0.00 4.58
1280 1424 1.613061 CCGTTTATGGGGGAGGCTT 59.387 57.895 0.00 0.00 0.00 4.35
1281 1425 0.033503 CCGTTTATGGGGGAGGCTTT 60.034 55.000 0.00 0.00 0.00 3.51
1282 1426 1.102978 CGTTTATGGGGGAGGCTTTG 58.897 55.000 0.00 0.00 0.00 2.77
1283 1427 1.485124 GTTTATGGGGGAGGCTTTGG 58.515 55.000 0.00 0.00 0.00 3.28
1284 1428 1.006639 GTTTATGGGGGAGGCTTTGGA 59.993 52.381 0.00 0.00 0.00 3.53
1292 1436 2.470990 GGGAGGCTTTGGATTGGATTT 58.529 47.619 0.00 0.00 0.00 2.17
1298 1442 5.737860 AGGCTTTGGATTGGATTTGATTTC 58.262 37.500 0.00 0.00 0.00 2.17
1327 1486 0.802494 GGGTAACATGGCACGAACAG 59.198 55.000 0.00 0.00 39.74 3.16
1334 1493 3.521560 ACATGGCACGAACAGTATAGTG 58.478 45.455 6.00 6.00 37.63 2.74
1356 1515 1.897560 GGGTCACCTTCCTCTGTTTG 58.102 55.000 0.00 0.00 0.00 2.93
1357 1516 1.143073 GGGTCACCTTCCTCTGTTTGT 59.857 52.381 0.00 0.00 0.00 2.83
1358 1517 2.495084 GGTCACCTTCCTCTGTTTGTC 58.505 52.381 0.00 0.00 0.00 3.18
1359 1518 2.104963 GGTCACCTTCCTCTGTTTGTCT 59.895 50.000 0.00 0.00 0.00 3.41
1360 1519 3.433740 GGTCACCTTCCTCTGTTTGTCTT 60.434 47.826 0.00 0.00 0.00 3.01
1361 1520 3.561725 GTCACCTTCCTCTGTTTGTCTTG 59.438 47.826 0.00 0.00 0.00 3.02
1362 1521 3.199946 TCACCTTCCTCTGTTTGTCTTGT 59.800 43.478 0.00 0.00 0.00 3.16
1363 1522 3.947834 CACCTTCCTCTGTTTGTCTTGTT 59.052 43.478 0.00 0.00 0.00 2.83
1374 1533 7.881142 TCTGTTTGTCTTGTTTTCTTCTTTCA 58.119 30.769 0.00 0.00 0.00 2.69
1380 1539 7.021196 TGTCTTGTTTTCTTCTTTCACTTTCG 58.979 34.615 0.00 0.00 0.00 3.46
1406 1582 2.488355 CCATGCTTTGCTGCTCCG 59.512 61.111 0.00 0.00 0.00 4.63
1412 1588 3.020026 CTTTGCTGCTCCGTGCTCG 62.020 63.158 0.00 0.14 43.37 5.03
1443 1619 1.521681 GGGCTCGGTTCATTCTCCG 60.522 63.158 0.00 0.00 46.93 4.63
1449 1625 0.389817 CGGTTCATTCTCCGCAGTGA 60.390 55.000 0.00 0.00 40.28 3.41
1450 1626 1.079503 GGTTCATTCTCCGCAGTGAC 58.920 55.000 0.00 0.00 0.00 3.67
1451 1627 1.338200 GGTTCATTCTCCGCAGTGACT 60.338 52.381 0.00 0.00 0.00 3.41
1455 1631 0.108424 ATTCTCCGCAGTGACTGAGC 60.108 55.000 18.18 0.00 32.44 4.26
1471 1647 2.433318 GCGGGTGAGTGAGTGAGC 60.433 66.667 0.00 0.00 0.00 4.26
1475 1651 1.445238 GGTGAGTGAGTGAGCGAGC 60.445 63.158 0.00 0.00 0.00 5.03
1486 1662 4.127040 AGCGAGCGAGCTCAGTGG 62.127 66.667 22.81 9.17 45.67 4.00
1494 1670 1.761174 GAGCTCAGTGGGGTTTGGA 59.239 57.895 9.40 0.00 0.00 3.53
1496 1672 1.973812 GCTCAGTGGGGTTTGGAGC 60.974 63.158 0.00 0.00 43.41 4.70
1510 1686 2.270527 GAGCTGGTGGGAAGAGGC 59.729 66.667 0.00 0.00 0.00 4.70
1513 1689 2.581354 CTGGTGGGAAGAGGCTCG 59.419 66.667 9.22 0.00 0.00 5.03
1518 1694 1.610673 TGGGAAGAGGCTCGCTCTT 60.611 57.895 9.22 3.67 43.09 2.85
1519 1695 1.153469 GGGAAGAGGCTCGCTCTTG 60.153 63.158 9.22 0.00 40.79 3.02
1530 1709 2.442999 CGCTCTTGCTCTGCTCACG 61.443 63.158 0.00 0.00 36.97 4.35
1561 1740 3.035173 AATGGCAGCCTCGCTAGCA 62.035 57.895 16.45 0.92 36.40 3.49
1562 1741 2.937379 AATGGCAGCCTCGCTAGCAG 62.937 60.000 16.45 10.99 36.40 4.24
1563 1742 4.906792 GGCAGCCTCGCTAGCAGG 62.907 72.222 21.94 21.94 36.40 4.85
1624 1803 0.169672 CCAAGGCACTGATTTCTGCG 59.830 55.000 0.00 0.00 40.86 5.18
1651 1830 1.209127 GTCGCCACAAATTCCCACG 59.791 57.895 0.00 0.00 0.00 4.94
1657 1836 1.616620 CACAAATTCCCACGCATTCG 58.383 50.000 0.00 0.00 42.43 3.34
1688 1867 6.426980 TTTAGCACTGAGATTAACAGCATG 57.573 37.500 0.00 0.00 46.00 4.06
1706 1885 7.153478 CAGCATGTTTACTTCTGTTTTGAAC 57.847 36.000 0.00 0.00 0.00 3.18
1707 1886 6.974622 CAGCATGTTTACTTCTGTTTTGAACT 59.025 34.615 0.00 0.00 0.00 3.01
1708 1887 7.489113 CAGCATGTTTACTTCTGTTTTGAACTT 59.511 33.333 0.00 0.00 0.00 2.66
1709 1888 7.702348 AGCATGTTTACTTCTGTTTTGAACTTC 59.298 33.333 0.00 0.00 0.00 3.01
1710 1889 7.702348 GCATGTTTACTTCTGTTTTGAACTTCT 59.298 33.333 0.00 0.00 0.00 2.85
1711 1890 9.573133 CATGTTTACTTCTGTTTTGAACTTCTT 57.427 29.630 0.00 0.00 0.00 2.52
1712 1891 9.788960 ATGTTTACTTCTGTTTTGAACTTCTTC 57.211 29.630 0.00 0.00 0.00 2.87
1713 1892 8.241367 TGTTTACTTCTGTTTTGAACTTCTTCC 58.759 33.333 0.00 0.00 0.00 3.46
1714 1893 8.459635 GTTTACTTCTGTTTTGAACTTCTTCCT 58.540 33.333 0.00 0.00 0.00 3.36
1715 1894 6.442513 ACTTCTGTTTTGAACTTCTTCCTG 57.557 37.500 0.00 0.00 0.00 3.86
1716 1895 6.180472 ACTTCTGTTTTGAACTTCTTCCTGA 58.820 36.000 0.00 0.00 0.00 3.86
1717 1896 6.830838 ACTTCTGTTTTGAACTTCTTCCTGAT 59.169 34.615 0.00 0.00 0.00 2.90
1718 1897 7.340487 ACTTCTGTTTTGAACTTCTTCCTGATT 59.660 33.333 0.00 0.00 0.00 2.57
1719 1898 8.746052 TTCTGTTTTGAACTTCTTCCTGATTA 57.254 30.769 0.00 0.00 0.00 1.75
1720 1899 8.924511 TCTGTTTTGAACTTCTTCCTGATTAT 57.075 30.769 0.00 0.00 0.00 1.28
1731 1910 9.520515 ACTTCTTCCTGATTATAATGTGTTTGT 57.479 29.630 1.78 0.00 0.00 2.83
1735 1914 5.065859 TCCTGATTATAATGTGTTTGTGCCG 59.934 40.000 1.78 0.00 0.00 5.69
1756 1939 2.738314 GCTGATTTTGATTTGTGTGGGC 59.262 45.455 0.00 0.00 0.00 5.36
1757 1940 2.988493 CTGATTTTGATTTGTGTGGGCG 59.012 45.455 0.00 0.00 0.00 6.13
1758 1941 2.363680 TGATTTTGATTTGTGTGGGCGT 59.636 40.909 0.00 0.00 0.00 5.68
1759 1942 2.215907 TTTTGATTTGTGTGGGCGTG 57.784 45.000 0.00 0.00 0.00 5.34
1760 1943 0.249238 TTTGATTTGTGTGGGCGTGC 60.249 50.000 0.00 0.00 0.00 5.34
1761 1944 1.387295 TTGATTTGTGTGGGCGTGCA 61.387 50.000 0.00 0.00 0.00 4.57
1822 2005 0.911045 TGAGGATGAAGCTGCTGGGA 60.911 55.000 1.35 0.00 0.00 4.37
1875 2058 4.379243 CGCCAGCAAGGACGAGGT 62.379 66.667 0.00 0.00 41.22 3.85
1978 2161 0.616679 CCTCGGAGTACCCCAAGGAA 60.617 60.000 0.00 0.00 36.80 3.36
1982 2165 1.675219 GAGTACCCCAAGGAACGCA 59.325 57.895 0.00 0.00 36.73 5.24
1987 2170 3.047877 CCCAAGGAACGCACGGAC 61.048 66.667 0.00 0.00 0.00 4.79
2347 2545 4.081030 TCGTCGCTGTCGTCGGTC 62.081 66.667 9.85 0.00 44.74 4.79
2709 2924 1.734047 CGAAGAAGACGAAGCCAGGAG 60.734 57.143 0.00 0.00 0.00 3.69
2776 2991 3.828451 AGTGTAAACTTGCATCAAGGCAT 59.172 39.130 10.80 0.42 44.81 4.40
2823 3038 5.415701 TCCTGATTCTTGTGCCTAATTGTTC 59.584 40.000 0.00 0.00 0.00 3.18
2872 3093 7.774134 TGAATCTTATGATGTTTTGGTCATGG 58.226 34.615 0.00 0.00 36.53 3.66
2994 3215 5.352846 GCTTCCATCTGAACTCCTAAACTTC 59.647 44.000 0.00 0.00 0.00 3.01
2995 3216 6.688073 TTCCATCTGAACTCCTAAACTTCT 57.312 37.500 0.00 0.00 0.00 2.85
3066 3304 7.756272 TCAACAAATTCTGATCATGCATTGTAC 59.244 33.333 13.89 0.00 0.00 2.90
3312 3570 5.086888 CTGAAAACCAAGCAAAATTCAGC 57.913 39.130 0.00 0.00 37.87 4.26
3368 3629 0.957888 GAAGGTCTCAGTGCAAGCCC 60.958 60.000 0.00 0.00 0.00 5.19
3378 3640 2.037847 GCAAGCCCCTGGGACAAT 59.962 61.111 16.20 0.00 38.70 2.71
3393 3655 7.428020 CCTGGGACAATATGTACATGAAATTG 58.572 38.462 20.77 20.77 38.70 2.32
3642 3935 3.675348 TCCATGATGGAATCTGGCTTT 57.325 42.857 12.63 0.00 45.00 3.51
3655 3948 0.390124 TGGCTTTCTTGCTGCTTTGG 59.610 50.000 0.00 0.00 0.00 3.28
3680 3973 1.906574 AGCCATTTTGGTCTCGGACTA 59.093 47.619 4.41 0.00 40.46 2.59
3768 4062 4.657814 ACCCACCACAATATTCAGACTT 57.342 40.909 0.00 0.00 0.00 3.01
3769 4063 4.589908 ACCCACCACAATATTCAGACTTC 58.410 43.478 0.00 0.00 0.00 3.01
3798 4100 7.038659 TCGAACTTGTGAATTTTCCACATTTT 58.961 30.769 0.00 0.00 43.17 1.82
3826 4138 7.182089 GCTGTTTCCAAATTTCTTGTGAAAAG 58.818 34.615 0.00 0.00 44.22 2.27
3828 4140 8.839310 TGTTTCCAAATTTCTTGTGAAAAGAA 57.161 26.923 0.00 0.00 44.22 2.52
3832 4144 9.664332 TTCCAAATTTCTTGTGAAAAGAATCAA 57.336 25.926 0.00 0.00 44.22 2.57
3839 4151 3.157087 TGTGAAAAGAATCAAGGCCTCC 58.843 45.455 5.23 0.00 0.00 4.30
3874 4186 7.446625 CAGGATTCTCAAAATGTAGGAATAGGG 59.553 40.741 0.00 0.00 0.00 3.53
3877 4190 8.753497 ATTCTCAAAATGTAGGAATAGGGAAC 57.247 34.615 0.00 0.00 0.00 3.62
3934 4247 8.388656 TCCTGTAGAATTAGAAAACCATAGGT 57.611 34.615 0.00 0.00 37.65 3.08
3952 4265 8.828751 ACCATAGGTATTTTAGACCAAACAGTA 58.171 33.333 0.00 0.00 39.65 2.74
3953 4266 9.326413 CCATAGGTATTTTAGACCAAACAGTAG 57.674 37.037 0.00 0.00 39.65 2.57
3980 4314 7.785033 TGATATAACATGAGAGCTTTCAGTGA 58.215 34.615 12.98 5.01 0.00 3.41
4011 4345 8.907222 AAATTTCTTCCAAAATAGTGTGCAAT 57.093 26.923 0.00 0.00 0.00 3.56
4022 4356 6.720112 AATAGTGTGCAATGCAATCCTTAT 57.280 33.333 10.44 1.57 41.47 1.73
4023 4357 4.380841 AGTGTGCAATGCAATCCTTATG 57.619 40.909 10.44 0.00 41.47 1.90
4025 4359 4.647853 AGTGTGCAATGCAATCCTTATGAT 59.352 37.500 10.44 0.00 41.47 2.45
4026 4360 5.128171 AGTGTGCAATGCAATCCTTATGATT 59.872 36.000 10.44 0.00 44.67 2.57
4106 4440 3.524095 TTTGAATCAAAGGAGCCCTCA 57.476 42.857 4.03 0.00 30.89 3.86
4125 4459 4.322801 CCTCAGTATTCCGAACAAGGTCTT 60.323 45.833 0.00 0.00 0.00 3.01
4260 4595 3.627237 CCCTTCAATAGCCTGCCCTTTTA 60.627 47.826 0.00 0.00 0.00 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 4.087892 ACGCCCAGCAGCTACCTG 62.088 66.667 0.00 6.59 42.13 4.00
14 15 4.087892 CACGCCCAGCAGCTACCT 62.088 66.667 0.00 0.00 0.00 3.08
42 43 2.509336 CATTTCCGGCTCGAGCGT 60.509 61.111 29.81 9.46 43.26 5.07
119 120 3.360340 GCAGCCTGCCTGTGTCAC 61.360 66.667 5.06 0.00 43.71 3.67
128 129 3.407046 GAATTCTGCGGCAGCCTGC 62.407 63.158 24.78 18.13 44.33 4.85
134 135 1.163420 AACGTGTGAATTCTGCGGCA 61.163 50.000 7.05 1.29 0.00 5.69
145 146 3.164977 TGGGGAGCCAACGTGTGA 61.165 61.111 0.00 0.00 0.00 3.58
173 174 1.503818 CCTTGTTCCACCACGAACGG 61.504 60.000 0.00 0.00 44.22 4.44
182 183 0.868406 CAGCTTCGTCCTTGTTCCAC 59.132 55.000 0.00 0.00 0.00 4.02
185 186 1.578206 GCCCAGCTTCGTCCTTGTTC 61.578 60.000 0.00 0.00 0.00 3.18
188 189 3.121030 CGCCCAGCTTCGTCCTTG 61.121 66.667 0.00 0.00 0.00 3.61
238 240 5.870978 ACGACTAGTGTACAGTGTTTTTGTT 59.129 36.000 13.66 0.00 0.00 2.83
240 242 5.961395 ACGACTAGTGTACAGTGTTTTTG 57.039 39.130 13.66 1.40 0.00 2.44
246 248 6.895898 TCTTTTCTACGACTAGTGTACAGTG 58.104 40.000 13.66 6.09 0.00 3.66
249 251 6.569226 GCCTTCTTTTCTACGACTAGTGTACA 60.569 42.308 0.00 0.00 0.00 2.90
253 255 4.174762 GGCCTTCTTTTCTACGACTAGTG 58.825 47.826 0.00 0.00 0.00 2.74
254 256 3.119566 CGGCCTTCTTTTCTACGACTAGT 60.120 47.826 0.00 0.00 0.00 2.57
256 258 2.165030 CCGGCCTTCTTTTCTACGACTA 59.835 50.000 0.00 0.00 0.00 2.59
258 260 1.067354 TCCGGCCTTCTTTTCTACGAC 60.067 52.381 0.00 0.00 0.00 4.34
295 310 0.376152 CGTCGCTCCTTTCTACGCTA 59.624 55.000 0.00 0.00 0.00 4.26
336 353 2.876879 CTTGCACGCACGAACGGAA 61.877 57.895 0.00 0.00 37.37 4.30
337 354 3.334751 CTTGCACGCACGAACGGA 61.335 61.111 0.00 0.00 37.37 4.69
338 355 3.558282 GACTTGCACGCACGAACGG 62.558 63.158 2.18 0.00 37.37 4.44
361 378 1.515088 CGAGCAGCACTACTCCGTG 60.515 63.158 0.00 0.00 37.94 4.94
365 382 0.798771 CGAACCGAGCAGCACTACTC 60.799 60.000 0.00 0.00 0.00 2.59
366 383 1.213013 CGAACCGAGCAGCACTACT 59.787 57.895 0.00 0.00 0.00 2.57
367 384 1.805945 CCGAACCGAGCAGCACTAC 60.806 63.158 0.00 0.00 0.00 2.73
368 385 2.571757 CCGAACCGAGCAGCACTA 59.428 61.111 0.00 0.00 0.00 2.74
391 408 2.677875 GGGGGAAGCAAGCAGTGG 60.678 66.667 0.00 0.00 0.00 4.00
490 509 4.452733 GGTTGGCGACGAGGAGGG 62.453 72.222 0.00 0.00 0.00 4.30
551 571 2.612746 AGGGAGGGCGGGCTTTTA 60.613 61.111 0.26 0.00 0.00 1.52
552 572 4.048470 GAGGGAGGGCGGGCTTTT 62.048 66.667 0.26 0.00 0.00 2.27
831 851 0.524862 GTTGTTGGATGGAGCAGCAG 59.475 55.000 0.00 0.00 0.00 4.24
839 866 0.540365 AGGTGCTGGTTGTTGGATGG 60.540 55.000 0.00 0.00 0.00 3.51
840 867 0.599558 CAGGTGCTGGTTGTTGGATG 59.400 55.000 0.00 0.00 0.00 3.51
841 868 1.181098 GCAGGTGCTGGTTGTTGGAT 61.181 55.000 0.00 0.00 38.21 3.41
842 869 1.827789 GCAGGTGCTGGTTGTTGGA 60.828 57.895 0.00 0.00 38.21 3.53
843 870 2.730094 GCAGGTGCTGGTTGTTGG 59.270 61.111 0.00 0.00 38.21 3.77
853 880 4.416738 GGTGGGAGGAGCAGGTGC 62.417 72.222 0.00 0.00 42.49 5.01
877 912 6.019881 GGCGATAAGATTGGTTTGTTAATTGC 60.020 38.462 0.00 0.00 0.00 3.56
878 913 6.475402 GGGCGATAAGATTGGTTTGTTAATTG 59.525 38.462 0.00 0.00 0.00 2.32
889 924 1.002544 GAGGGAGGGCGATAAGATTGG 59.997 57.143 0.00 0.00 0.00 3.16
910 954 0.178888 GATAAGGGGAGGGAGGGAGG 60.179 65.000 0.00 0.00 0.00 4.30
911 955 0.871024 AGATAAGGGGAGGGAGGGAG 59.129 60.000 0.00 0.00 0.00 4.30
912 956 0.868186 GAGATAAGGGGAGGGAGGGA 59.132 60.000 0.00 0.00 0.00 4.20
913 957 0.178888 GGAGATAAGGGGAGGGAGGG 60.179 65.000 0.00 0.00 0.00 4.30
914 958 0.568192 TGGAGATAAGGGGAGGGAGG 59.432 60.000 0.00 0.00 0.00 4.30
915 959 1.221781 AGTGGAGATAAGGGGAGGGAG 59.778 57.143 0.00 0.00 0.00 4.30
916 960 1.330155 AGTGGAGATAAGGGGAGGGA 58.670 55.000 0.00 0.00 0.00 4.20
927 971 0.322277 CAGGTGCTGCAAGTGGAGAT 60.322 55.000 2.77 0.00 35.31 2.75
928 972 1.071987 CAGGTGCTGCAAGTGGAGA 59.928 57.895 2.77 0.00 35.31 3.71
945 989 2.020181 GCTGATGGTGATGGTGATGCA 61.020 52.381 0.00 0.00 0.00 3.96
952 996 0.952280 GCTGATGCTGATGGTGATGG 59.048 55.000 0.00 0.00 36.03 3.51
958 1002 2.147150 CTCTGATGCTGATGCTGATGG 58.853 52.381 0.00 0.00 40.48 3.51
965 1009 3.243602 CCTCACTCTCTCTGATGCTGATG 60.244 52.174 0.00 0.00 0.00 3.07
971 1015 0.752054 GCCCCTCACTCTCTCTGATG 59.248 60.000 0.00 0.00 0.00 3.07
972 1016 0.754957 CGCCCCTCACTCTCTCTGAT 60.755 60.000 0.00 0.00 0.00 2.90
973 1017 1.379176 CGCCCCTCACTCTCTCTGA 60.379 63.158 0.00 0.00 0.00 3.27
974 1018 3.074999 GCGCCCCTCACTCTCTCTG 62.075 68.421 0.00 0.00 0.00 3.35
1008 1108 2.099921 CTGGACCTTGTGTATCCTCTCG 59.900 54.545 0.00 0.00 33.34 4.04
1026 1126 1.209747 GAAGGGGTTGCTACTACCTGG 59.790 57.143 13.53 0.00 35.92 4.45
1035 1135 3.330720 CCGAGGGAAGGGGTTGCT 61.331 66.667 0.00 0.00 0.00 3.91
1037 1137 1.196104 TACACCGAGGGAAGGGGTTG 61.196 60.000 0.00 0.00 44.24 3.77
1040 1140 2.718073 CGTACACCGAGGGAAGGGG 61.718 68.421 0.00 0.00 39.56 4.79
1041 1141 0.680921 TACGTACACCGAGGGAAGGG 60.681 60.000 0.00 0.00 40.70 3.95
1042 1142 1.336125 GATACGTACACCGAGGGAAGG 59.664 57.143 0.00 0.00 40.70 3.46
1043 1143 2.295885 AGATACGTACACCGAGGGAAG 58.704 52.381 0.00 0.00 40.70 3.46
1046 1146 1.876156 GGTAGATACGTACACCGAGGG 59.124 57.143 0.00 0.00 40.70 4.30
1048 1148 1.528586 CGGGTAGATACGTACACCGAG 59.471 57.143 15.71 9.55 38.22 4.63
1050 1150 1.003545 CACGGGTAGATACGTACACCG 60.004 57.143 17.87 17.87 42.04 4.94
1052 1152 3.126858 TGAACACGGGTAGATACGTACAC 59.873 47.826 0.00 0.00 42.04 2.90
1054 1154 4.531332 GATGAACACGGGTAGATACGTAC 58.469 47.826 0.00 0.00 42.04 3.67
1057 1157 2.359848 TGGATGAACACGGGTAGATACG 59.640 50.000 0.00 0.00 0.00 3.06
1062 1162 1.484653 TGGATGGATGAACACGGGTAG 59.515 52.381 0.00 0.00 0.00 3.18
1065 1165 1.311859 CATGGATGGATGAACACGGG 58.688 55.000 0.00 0.00 0.00 5.28
1089 1189 1.298713 CGGAGAGATGGCTTCGACG 60.299 63.158 0.00 0.00 0.00 5.12
1097 1197 1.597302 CAGCATGCCGGAGAGATGG 60.597 63.158 15.66 0.00 0.00 3.51
1114 1214 3.626996 AATGCTGCTAGCGGGCACA 62.627 57.895 28.77 18.09 46.26 4.57
1115 1215 2.825836 AATGCTGCTAGCGGGCAC 60.826 61.111 28.77 13.52 46.26 5.01
1116 1216 2.514592 GAATGCTGCTAGCGGGCA 60.515 61.111 28.49 28.49 46.26 5.36
1117 1217 3.643978 CGAATGCTGCTAGCGGGC 61.644 66.667 24.73 22.55 46.26 6.13
1118 1218 2.969238 CCGAATGCTGCTAGCGGG 60.969 66.667 24.73 13.79 46.26 6.13
1133 1240 1.094785 CTGTGGGTGGATTTTAGCCG 58.905 55.000 0.00 0.00 38.52 5.52
1136 1243 3.012518 CTCTGCTGTGGGTGGATTTTAG 58.987 50.000 0.00 0.00 0.00 1.85
1138 1245 1.915141 CTCTGCTGTGGGTGGATTTT 58.085 50.000 0.00 0.00 0.00 1.82
1139 1246 0.610232 GCTCTGCTGTGGGTGGATTT 60.610 55.000 0.00 0.00 0.00 2.17
1140 1247 1.001641 GCTCTGCTGTGGGTGGATT 60.002 57.895 0.00 0.00 0.00 3.01
1141 1248 1.922369 AGCTCTGCTGTGGGTGGAT 60.922 57.895 0.00 0.00 37.57 3.41
1155 1262 3.324556 AGGATGAGAGGATTTAGCAGCTC 59.675 47.826 0.00 0.00 0.00 4.09
1158 1265 6.484977 GGTAAAAGGATGAGAGGATTTAGCAG 59.515 42.308 0.00 0.00 33.38 4.24
1170 1280 3.438087 CACAGTGCTGGTAAAAGGATGAG 59.562 47.826 4.11 0.00 34.19 2.90
1172 1282 3.058016 CACACAGTGCTGGTAAAAGGATG 60.058 47.826 0.00 0.00 34.19 3.51
1173 1283 3.149196 CACACAGTGCTGGTAAAAGGAT 58.851 45.455 0.00 0.00 34.19 3.24
1174 1284 2.092646 ACACACAGTGCTGGTAAAAGGA 60.093 45.455 0.00 0.00 36.98 3.36
1176 1286 3.338818 CACACACAGTGCTGGTAAAAG 57.661 47.619 0.00 0.00 42.15 2.27
1187 1297 2.513666 CCACACCGCACACACAGT 60.514 61.111 0.00 0.00 0.00 3.55
1188 1298 3.279116 CCCACACCGCACACACAG 61.279 66.667 0.00 0.00 0.00 3.66
1190 1300 3.276846 GACCCACACCGCACACAC 61.277 66.667 0.00 0.00 0.00 3.82
1191 1301 3.330992 TTGACCCACACCGCACACA 62.331 57.895 0.00 0.00 0.00 3.72
1193 1303 2.203139 CTTGACCCACACCGCACA 60.203 61.111 0.00 0.00 0.00 4.57
1195 1305 4.947147 GCCTTGACCCACACCGCA 62.947 66.667 0.00 0.00 0.00 5.69
1197 1307 2.358737 GAGCCTTGACCCACACCG 60.359 66.667 0.00 0.00 0.00 4.94
1198 1308 0.178990 AAAGAGCCTTGACCCACACC 60.179 55.000 0.00 0.00 0.00 4.16
1210 1354 1.270826 GCTGGAAAAGTGGAAAGAGCC 59.729 52.381 0.00 0.00 0.00 4.70
1214 1358 2.813754 TCGATGCTGGAAAAGTGGAAAG 59.186 45.455 0.00 0.00 0.00 2.62
1221 1365 1.466167 CAGTGGTCGATGCTGGAAAAG 59.534 52.381 0.00 0.00 0.00 2.27
1222 1366 1.202758 ACAGTGGTCGATGCTGGAAAA 60.203 47.619 15.01 0.00 34.79 2.29
1223 1367 0.396435 ACAGTGGTCGATGCTGGAAA 59.604 50.000 15.01 0.00 34.79 3.13
1224 1368 0.320683 CACAGTGGTCGATGCTGGAA 60.321 55.000 15.01 0.00 34.79 3.53
1225 1369 1.293179 CACAGTGGTCGATGCTGGA 59.707 57.895 15.01 0.00 34.79 3.86
1226 1370 1.742880 CCACAGTGGTCGATGCTGG 60.743 63.158 11.99 5.37 34.79 4.85
1227 1371 3.880591 CCACAGTGGTCGATGCTG 58.119 61.111 11.99 10.81 36.41 4.41
1243 1387 3.576356 CGATGGCGATGCACCACC 61.576 66.667 0.00 0.00 40.82 4.61
1250 1394 1.227999 ATAAACGGGCGATGGCGATG 61.228 55.000 0.00 0.00 41.24 3.84
1251 1395 1.070786 ATAAACGGGCGATGGCGAT 59.929 52.632 0.00 0.00 41.24 4.58
1252 1396 1.885388 CATAAACGGGCGATGGCGA 60.885 57.895 0.00 0.00 41.24 5.54
1253 1397 2.631428 CATAAACGGGCGATGGCG 59.369 61.111 0.00 0.00 41.24 5.69
1254 1398 2.551912 CCCATAAACGGGCGATGGC 61.552 63.158 0.00 0.00 40.07 4.40
1255 1399 1.896660 CCCCATAAACGGGCGATGG 60.897 63.158 0.00 0.00 45.90 3.51
1274 1418 5.349061 AATCAAATCCAATCCAAAGCCTC 57.651 39.130 0.00 0.00 0.00 4.70
1275 1419 5.486419 AGAAATCAAATCCAATCCAAAGCCT 59.514 36.000 0.00 0.00 0.00 4.58
1276 1420 5.737860 AGAAATCAAATCCAATCCAAAGCC 58.262 37.500 0.00 0.00 0.00 4.35
1277 1421 6.652062 ACAAGAAATCAAATCCAATCCAAAGC 59.348 34.615 0.00 0.00 0.00 3.51
1278 1422 7.332678 GGACAAGAAATCAAATCCAATCCAAAG 59.667 37.037 0.00 0.00 0.00 2.77
1279 1423 7.160726 GGACAAGAAATCAAATCCAATCCAAA 58.839 34.615 0.00 0.00 0.00 3.28
1280 1424 6.295802 GGGACAAGAAATCAAATCCAATCCAA 60.296 38.462 0.00 0.00 0.00 3.53
1281 1425 5.187576 GGGACAAGAAATCAAATCCAATCCA 59.812 40.000 0.00 0.00 0.00 3.41
1282 1426 5.187576 TGGGACAAGAAATCAAATCCAATCC 59.812 40.000 0.00 0.00 31.92 3.01
1283 1427 6.284891 TGGGACAAGAAATCAAATCCAATC 57.715 37.500 0.00 0.00 31.92 2.67
1321 1471 4.201990 GGTGACCCTACACTATACTGTTCG 60.202 50.000 0.00 0.00 40.22 3.95
1327 1486 4.544683 AGGAAGGTGACCCTACACTATAC 58.455 47.826 0.00 0.00 41.56 1.47
1334 1493 1.939980 ACAGAGGAAGGTGACCCTAC 58.060 55.000 0.00 0.00 41.56 3.18
1348 1507 8.023128 TGAAAGAAGAAAACAAGACAAACAGAG 58.977 33.333 0.00 0.00 0.00 3.35
1350 1509 7.809806 AGTGAAAGAAGAAAACAAGACAAACAG 59.190 33.333 0.00 0.00 0.00 3.16
1356 1515 6.021390 GCGAAAGTGAAAGAAGAAAACAAGAC 60.021 38.462 0.00 0.00 0.00 3.01
1357 1516 6.027749 GCGAAAGTGAAAGAAGAAAACAAGA 58.972 36.000 0.00 0.00 0.00 3.02
1358 1517 6.021153 CAGCGAAAGTGAAAGAAGAAAACAAG 60.021 38.462 0.00 0.00 0.00 3.16
1359 1518 5.799936 CAGCGAAAGTGAAAGAAGAAAACAA 59.200 36.000 0.00 0.00 0.00 2.83
1360 1519 5.106317 ACAGCGAAAGTGAAAGAAGAAAACA 60.106 36.000 0.00 0.00 0.00 2.83
1361 1520 5.332707 ACAGCGAAAGTGAAAGAAGAAAAC 58.667 37.500 0.00 0.00 0.00 2.43
1362 1521 5.560966 ACAGCGAAAGTGAAAGAAGAAAA 57.439 34.783 0.00 0.00 0.00 2.29
1363 1522 6.293407 CCATACAGCGAAAGTGAAAGAAGAAA 60.293 38.462 0.00 0.00 0.00 2.52
1374 1533 1.382522 CATGGCCATACAGCGAAAGT 58.617 50.000 20.30 0.00 0.00 2.66
1380 1539 0.529119 GCAAAGCATGGCCATACAGC 60.529 55.000 20.30 18.23 0.00 4.40
1419 1595 2.764637 AATGAACCGAGCCCCCACAC 62.765 60.000 0.00 0.00 0.00 3.82
1420 1596 2.478335 GAATGAACCGAGCCCCCACA 62.478 60.000 0.00 0.00 0.00 4.17
1443 1619 2.740055 CACCCGCTCAGTCACTGC 60.740 66.667 0.00 0.00 0.00 4.40
1449 1625 1.531840 ACTCACTCACCCGCTCAGT 60.532 57.895 0.00 0.00 0.00 3.41
1450 1626 1.080230 CACTCACTCACCCGCTCAG 60.080 63.158 0.00 0.00 0.00 3.35
1451 1627 1.527433 CTCACTCACTCACCCGCTCA 61.527 60.000 0.00 0.00 0.00 4.26
1455 1631 2.126307 CGCTCACTCACTCACCCG 60.126 66.667 0.00 0.00 0.00 5.28
1457 1633 1.445238 GCTCGCTCACTCACTCACC 60.445 63.158 0.00 0.00 0.00 4.02
1471 1647 4.504916 CCCCACTGAGCTCGCTCG 62.505 72.222 9.64 10.76 45.48 5.03
1475 1651 1.672356 CCAAACCCCACTGAGCTCG 60.672 63.158 9.64 6.63 0.00 5.03
1486 1662 2.283173 CCCACCAGCTCCAAACCC 60.283 66.667 0.00 0.00 0.00 4.11
1494 1670 2.204059 AGCCTCTTCCCACCAGCT 60.204 61.111 0.00 0.00 0.00 4.24
1496 1672 2.581354 CGAGCCTCTTCCCACCAG 59.419 66.667 0.00 0.00 0.00 4.00
1513 1689 3.472533 CGTGAGCAGAGCAAGAGC 58.527 61.111 0.00 0.00 42.56 4.09
1530 1709 3.957535 CCATTGGAGCGCGATGGC 61.958 66.667 12.10 0.00 34.47 4.40
1538 1717 3.207669 CGAGGCTGCCATTGGAGC 61.208 66.667 22.65 12.10 34.23 4.70
1592 1771 2.747855 CTTGGTTCCCTCCGCAGC 60.748 66.667 0.00 0.00 0.00 5.25
1602 1781 2.352127 GCAGAAATCAGTGCCTTGGTTC 60.352 50.000 0.00 0.00 33.29 3.62
1614 1793 2.492418 GGATTGGCCGCAGAAATCA 58.508 52.632 13.16 0.00 32.96 2.57
1633 1812 1.209127 CGTGGGAATTTGTGGCGAC 59.791 57.895 0.00 0.00 0.00 5.19
1651 1830 5.470845 AGTGCTAAAACTGATACGAATGC 57.529 39.130 0.00 0.00 0.00 3.56
1676 1855 9.463443 AAAACAGAAGTAAACATGCTGTTAATC 57.537 29.630 11.43 3.20 45.84 1.75
1688 1867 8.459635 AGGAAGAAGTTCAAAACAGAAGTAAAC 58.540 33.333 5.50 0.00 33.93 2.01
1702 1881 9.739276 AACACATTATAATCAGGAAGAAGTTCA 57.261 29.630 5.50 0.00 33.93 3.18
1705 1884 9.520515 ACAAACACATTATAATCAGGAAGAAGT 57.479 29.630 0.00 0.00 0.00 3.01
1706 1885 9.778993 CACAAACACATTATAATCAGGAAGAAG 57.221 33.333 0.00 0.00 0.00 2.85
1707 1886 8.243426 GCACAAACACATTATAATCAGGAAGAA 58.757 33.333 0.00 0.00 0.00 2.52
1708 1887 7.148086 GGCACAAACACATTATAATCAGGAAGA 60.148 37.037 0.00 0.00 0.00 2.87
1709 1888 6.974622 GGCACAAACACATTATAATCAGGAAG 59.025 38.462 0.00 0.00 0.00 3.46
1710 1889 6.404184 CGGCACAAACACATTATAATCAGGAA 60.404 38.462 0.00 0.00 0.00 3.36
1711 1890 5.065859 CGGCACAAACACATTATAATCAGGA 59.934 40.000 0.00 0.00 0.00 3.86
1712 1891 5.273170 CGGCACAAACACATTATAATCAGG 58.727 41.667 0.00 0.00 0.00 3.86
1713 1892 4.734854 GCGGCACAAACACATTATAATCAG 59.265 41.667 0.00 0.00 0.00 2.90
1714 1893 4.397730 AGCGGCACAAACACATTATAATCA 59.602 37.500 1.45 0.00 0.00 2.57
1715 1894 4.734854 CAGCGGCACAAACACATTATAATC 59.265 41.667 1.45 0.00 0.00 1.75
1716 1895 4.397730 TCAGCGGCACAAACACATTATAAT 59.602 37.500 1.45 0.00 0.00 1.28
1717 1896 3.753797 TCAGCGGCACAAACACATTATAA 59.246 39.130 1.45 0.00 0.00 0.98
1718 1897 3.339141 TCAGCGGCACAAACACATTATA 58.661 40.909 1.45 0.00 0.00 0.98
1719 1898 2.158559 TCAGCGGCACAAACACATTAT 58.841 42.857 1.45 0.00 0.00 1.28
1720 1899 1.598882 TCAGCGGCACAAACACATTA 58.401 45.000 1.45 0.00 0.00 1.90
1729 1908 2.035704 ACAAATCAAAATCAGCGGCACA 59.964 40.909 1.45 0.00 0.00 4.57
1731 1910 2.035704 ACACAAATCAAAATCAGCGGCA 59.964 40.909 1.45 0.00 0.00 5.69
1735 1914 2.738314 GCCCACACAAATCAAAATCAGC 59.262 45.455 0.00 0.00 0.00 4.26
1756 1939 0.248743 GCATCCCAATCACATGCACG 60.249 55.000 0.00 0.00 42.18 5.34
1757 1940 0.818938 TGCATCCCAATCACATGCAC 59.181 50.000 1.71 0.00 46.22 4.57
1759 1942 1.395635 TCTGCATCCCAATCACATGC 58.604 50.000 0.00 0.00 42.81 4.06
1760 1943 2.296190 CCATCTGCATCCCAATCACATG 59.704 50.000 0.00 0.00 0.00 3.21
1761 1944 2.594131 CCATCTGCATCCCAATCACAT 58.406 47.619 0.00 0.00 0.00 3.21
1978 2161 2.637383 GGAAGAGGAGTCCGTGCGT 61.637 63.158 2.76 0.00 0.00 5.24
1982 2165 2.362632 CCGGGAAGAGGAGTCCGT 60.363 66.667 2.76 0.00 40.78 4.69
1987 2170 4.194720 CGCGACCGGGAAGAGGAG 62.195 72.222 6.32 0.00 0.00 3.69
2161 2353 0.995024 AGAAGATGGGGTTGGAGTGG 59.005 55.000 0.00 0.00 0.00 4.00
2666 2880 4.882396 GCTCTTCTCCGGCGAGGC 62.882 72.222 9.30 0.00 40.77 4.70
2709 2924 1.139947 CGAGCTTCGAACTCCTCCC 59.860 63.158 16.79 0.36 43.74 4.30
2743 2958 4.023963 GCAAGTTTACACTTCTTGGACTCC 60.024 45.833 0.00 0.00 41.69 3.85
2776 2991 7.890127 AGGATTAAAATGTGGAGATTCTGTTCA 59.110 33.333 0.00 0.00 0.00 3.18
2823 3038 7.495279 TCAGAAGAAAATGGTGTTTTTGAATGG 59.505 33.333 0.00 0.00 0.00 3.16
2872 3093 3.706594 TCCTCTGATATCTGAACCACCAC 59.293 47.826 12.72 0.00 0.00 4.16
2994 3215 7.012327 TCACAGTTTTGTCAGGAGAATGTAAAG 59.988 37.037 0.00 0.00 34.62 1.85
2995 3216 6.826231 TCACAGTTTTGTCAGGAGAATGTAAA 59.174 34.615 0.00 0.00 34.62 2.01
3031 3252 3.565482 TCAGAATTTGTTGACAGACAGCC 59.435 43.478 0.00 0.00 0.00 4.85
3066 3304 4.505191 CACCTGAAATGAAGTTTGCACAAG 59.495 41.667 0.00 0.00 0.00 3.16
3312 3570 0.172803 GGCTGCATTTCAGAGGCAAG 59.827 55.000 0.50 0.00 45.72 4.01
3368 3629 7.068593 ACAATTTCATGTACATATTGTCCCAGG 59.931 37.037 21.74 3.67 35.20 4.45
3393 3655 5.156355 CACCTACAGCACATTGATTCAAAC 58.844 41.667 2.68 0.00 0.00 2.93
3570 3863 9.881773 TCCTAGATAAAATGCCATATTTTTCCT 57.118 29.630 3.32 4.43 33.73 3.36
3626 3919 2.756760 GCAAGAAAGCCAGATTCCATCA 59.243 45.455 0.00 0.00 0.00 3.07
3655 3948 2.223572 CCGAGACCAAAATGGCTTATGC 60.224 50.000 0.00 0.00 42.67 3.14
3724 4018 9.406828 GGGTTCTTGAAAGTTTATATTTGTGTC 57.593 33.333 0.00 0.00 0.00 3.67
3732 4026 6.366340 TGTGGTGGGTTCTTGAAAGTTTATA 58.634 36.000 0.00 0.00 0.00 0.98
3739 4033 5.835819 TGAATATTGTGGTGGGTTCTTGAAA 59.164 36.000 0.00 0.00 0.00 2.69
3768 4062 5.820423 TGGAAAATTCACAAGTTCGAGAAGA 59.180 36.000 0.00 0.00 0.00 2.87
3769 4063 5.909610 GTGGAAAATTCACAAGTTCGAGAAG 59.090 40.000 0.00 0.00 35.39 2.85
3798 4100 4.874966 CACAAGAAATTTGGAAACAGCCAA 59.125 37.500 0.00 0.00 45.77 4.52
3832 4144 1.222936 CTGCGATTCAAGGAGGCCT 59.777 57.895 3.86 3.86 33.87 5.19
3874 4186 9.229784 GACATGTCATTTCAATCATGTATGTTC 57.770 33.333 21.07 0.00 46.77 3.18
3877 4190 7.937649 AGGACATGTCATTTCAATCATGTATG 58.062 34.615 26.47 0.00 46.77 2.39
3952 4265 8.263640 ACTGAAAGCTCTCATGTTATATCAACT 58.736 33.333 0.00 0.00 37.60 3.16
3953 4266 8.333908 CACTGAAAGCTCTCATGTTATATCAAC 58.666 37.037 0.00 0.00 37.60 3.18
3960 4273 5.645067 CCATTCACTGAAAGCTCTCATGTTA 59.355 40.000 0.00 0.00 37.60 2.41
4032 4366 5.093849 TCCTTAGGAACGGAAACATTAGG 57.906 43.478 0.00 0.00 0.00 2.69
4085 4419 3.828451 CTGAGGGCTCCTTTGATTCAAAA 59.172 43.478 12.62 0.00 32.75 2.44
4106 4440 5.997384 ACTAAGACCTTGTTCGGAATACT 57.003 39.130 0.00 0.00 0.00 2.12
4172 4506 5.359009 GTGGTGGTACTACTAATGCTGTCTA 59.641 44.000 9.41 0.00 0.00 2.59
4260 4595 2.082140 ATCATGGTTCCATGCATGCT 57.918 45.000 21.69 1.07 42.38 3.79


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

AutoCloner maintained by Alex Coulton.