Multiple sequence alignment - TraesCS5D01G111900

Loading Multiple Alignment...

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 TraesCS5D01G111900 chr5D 100.000 5334 0 0 1 5334 127253231 127258564 0.000000e+00 9851.0
1 TraesCS5D01G111900 chr5B 92.842 4317 196 41 607 4852 140730278 140734552 0.000000e+00 6156.0
2 TraesCS5D01G111900 chr5B 86.546 498 60 5 1 493 139572900 139572405 4.700000e-150 542.0
3 TraesCS5D01G111900 chr5B 92.744 317 15 5 5022 5334 140734591 140734903 8.150000e-123 451.0
4 TraesCS5D01G111900 chr5B 97.183 71 2 0 5071 5141 162772772 162772842 2.610000e-23 121.0
5 TraesCS5D01G111900 chr5B 87.156 109 10 1 4849 4957 603641103 603641207 2.610000e-23 121.0
6 TraesCS5D01G111900 chr5A 95.377 1990 66 9 1301 3280 142840427 142842400 0.000000e+00 3142.0
7 TraesCS5D01G111900 chr5A 89.515 1259 77 28 3930 5180 142843125 142844336 0.000000e+00 1543.0
8 TraesCS5D01G111900 chr5A 88.522 1150 63 31 173 1302 142839213 142840313 0.000000e+00 1328.0
9 TraesCS5D01G111900 chr5A 92.954 369 22 1 3263 3627 142842752 142843120 7.860000e-148 534.0
10 TraesCS5D01G111900 chr5A 93.567 171 10 1 5164 5334 142845476 142845645 2.470000e-63 254.0
11 TraesCS5D01G111900 chr5A 83.429 175 14 4 1 175 142806172 142806331 1.200000e-31 148.0
12 TraesCS5D01G111900 chr2B 86.655 562 54 12 1137 1689 735908066 735908615 2.130000e-168 603.0
13 TraesCS5D01G111900 chr6B 86.170 564 59 10 1135 1689 14170932 14170379 4.600000e-165 592.0
14 TraesCS5D01G111900 chr2A 84.832 567 63 15 1132 1689 730076649 730077201 2.810000e-152 549.0
15 TraesCS5D01G111900 chr7A 85.995 407 44 6 1283 1683 109534240 109534639 1.780000e-114 424.0
16 TraesCS5D01G111900 chr7A 87.685 203 20 2 1132 1333 620155864 620156062 1.160000e-56 231.0
17 TraesCS5D01G111900 chr7A 88.571 105 8 1 4853 4957 37108501 37108401 2.020000e-24 124.0
18 TraesCS5D01G111900 chr7A 95.890 73 3 0 5069 5141 686371308 686371380 9.380000e-23 119.0
19 TraesCS5D01G111900 chr1A 84.680 359 41 8 1339 1689 522940198 522940550 3.950000e-91 346.0
20 TraesCS5D01G111900 chr1A 84.401 359 41 8 1339 1689 522946362 522946713 6.620000e-89 339.0
21 TraesCS5D01G111900 chr1A 86.207 261 29 5 1432 1689 517122321 517122577 5.260000e-70 276.0
22 TraesCS5D01G111900 chr1A 86.341 205 18 6 1132 1333 517122134 517122331 1.160000e-51 215.0
23 TraesCS5D01G111900 chr1A 89.241 158 12 2 1139 1295 522946213 522946366 5.450000e-45 193.0
24 TraesCS5D01G111900 chr1A 88.608 158 13 2 1139 1295 522940049 522940202 2.540000e-43 187.0
25 TraesCS5D01G111900 chr1A 94.667 75 4 0 5071 5145 576371075 576371149 3.380000e-22 117.0
26 TraesCS5D01G111900 chr7D 91.071 112 6 2 4846 4957 433012432 433012539 1.200000e-31 148.0
27 TraesCS5D01G111900 chr7D 98.485 66 1 0 5076 5141 632404680 632404615 3.380000e-22 117.0
28 TraesCS5D01G111900 chr7D 83.962 106 13 3 4852 4957 395358596 395358495 1.220000e-16 99.0
29 TraesCS5D01G111900 chr2D 90.909 110 5 2 4849 4957 138808185 138808290 5.570000e-30 143.0
30 TraesCS5D01G111900 chr2D 92.683 82 6 0 5060 5141 117843024 117843105 9.380000e-23 119.0
31 TraesCS5D01G111900 chr3B 89.189 111 8 2 4847 4957 528494390 528494284 9.320000e-28 135.0
32 TraesCS5D01G111900 chr6A 87.719 114 8 3 4845 4957 2229147 2229039 1.560000e-25 128.0
33 TraesCS5D01G111900 chr4D 87.387 111 10 1 4847 4957 128777251 128777145 2.020000e-24 124.0
34 TraesCS5D01G111900 chr4B 90.426 94 4 5 5049 5141 640009183 640009094 9.380000e-23 119.0
35 TraesCS5D01G111900 chr7B 91.463 82 6 1 5072 5152 667453319 667453400 1.570000e-20 111.0
36 TraesCS5D01G111900 chr7B 81.319 91 13 3 4852 4942 39522886 39522800 2.670000e-08 71.3


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 TraesCS5D01G111900 chr5D 127253231 127258564 5333 False 9851.0 9851 100.000 1 5334 1 chr5D.!!$F1 5333
1 TraesCS5D01G111900 chr5B 140730278 140734903 4625 False 3303.5 6156 92.793 607 5334 2 chr5B.!!$F3 4727
2 TraesCS5D01G111900 chr5A 142839213 142845645 6432 False 1360.2 3142 91.987 173 5334 5 chr5A.!!$F2 5161
3 TraesCS5D01G111900 chr2B 735908066 735908615 549 False 603.0 603 86.655 1137 1689 1 chr2B.!!$F1 552
4 TraesCS5D01G111900 chr6B 14170379 14170932 553 True 592.0 592 86.170 1135 1689 1 chr6B.!!$R1 554
5 TraesCS5D01G111900 chr2A 730076649 730077201 552 False 549.0 549 84.832 1132 1689 1 chr2A.!!$F1 557
6 TraesCS5D01G111900 chr1A 522940049 522940550 501 False 266.5 346 86.644 1139 1689 2 chr1A.!!$F3 550
7 TraesCS5D01G111900 chr1A 522946213 522946713 500 False 266.0 339 86.821 1139 1689 2 chr1A.!!$F4 550

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
392 397 0.027979 CATCAAATCGCGCGTTGGAT 59.972 50.0 30.98 25.12 0.00 3.41 F
586 604 0.393402 TTACTGCTAGAGACGCCGGA 60.393 55.0 5.05 0.00 0.00 5.14 F
1212 1242 0.395862 GGAGGGAGATGGTCGAGTCA 60.396 60.0 0.00 0.00 0.00 3.41 F
1253 1283 0.898320 CTTCTCTTTCCCTCTCGCCA 59.102 55.0 0.00 0.00 0.00 5.69 F
2407 2565 1.056660 GTCACTCCTTCCCCAGAACA 58.943 55.0 0.00 0.00 0.00 3.18 F
3850 4422 0.471591 TTTTGCCCACAGCCCTGATT 60.472 50.0 1.69 0.00 42.71 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1235 1265 0.608640 GTGGCGAGAGGGAAAGAGAA 59.391 55.000 0.00 0.00 0.00 2.87 R
1630 1786 0.765510 AAAGACACACTCCCTCACCC 59.234 55.000 0.00 0.00 0.00 4.61 R
2243 2401 0.834612 ACTCACTTGGTTTCCCACGA 59.165 50.000 0.00 0.00 41.67 4.35 R
2509 2670 2.226437 TGAAGAACGCCATTTTCTGAGC 59.774 45.455 0.00 0.00 33.46 4.26 R
4226 4809 0.036577 CCAGTTCTCCTGCAGGTCAG 60.037 60.000 31.58 22.42 40.06 3.51 R
4876 5465 3.153676 TCAGTTGTCTGAAACGAACGA 57.846 42.857 0.14 0.00 46.17 3.85 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 4.388499 CGTTCCACGGAGGGGGTG 62.388 72.222 0.00 0.00 38.08 4.61
30 31 4.715130 CACGGAGGGGGTGGAGGA 62.715 72.222 0.00 0.00 0.00 3.71
31 32 4.400251 ACGGAGGGGGTGGAGGAG 62.400 72.222 0.00 0.00 0.00 3.69
40 41 4.131088 GTGGAGGAGGCGGTCGTC 62.131 72.222 0.03 0.03 39.05 4.20
46 47 3.878519 GAGGCGGTCGTCCTCGAG 61.879 72.222 5.13 5.13 46.96 4.04
68 69 3.574445 CGACCGCGACGAGAGGAT 61.574 66.667 8.23 0.00 43.02 3.24
69 70 2.799371 GACCGCGACGAGAGGATT 59.201 61.111 8.23 0.00 43.02 3.01
70 71 1.298488 GACCGCGACGAGAGGATTC 60.298 63.158 8.23 0.00 43.02 2.52
71 72 1.989966 GACCGCGACGAGAGGATTCA 61.990 60.000 8.23 0.00 43.02 2.57
72 73 1.586564 CCGCGACGAGAGGATTCAC 60.587 63.158 8.23 0.00 43.02 3.18
73 74 1.934956 CGCGACGAGAGGATTCACG 60.935 63.158 0.00 0.00 42.14 4.35
74 75 1.586564 GCGACGAGAGGATTCACGG 60.587 63.158 0.00 0.00 40.97 4.94
75 76 1.801332 CGACGAGAGGATTCACGGT 59.199 57.895 0.00 0.00 40.97 4.83
76 77 0.248134 CGACGAGAGGATTCACGGTC 60.248 60.000 0.00 0.00 40.97 4.79
77 78 0.248134 GACGAGAGGATTCACGGTCG 60.248 60.000 0.00 0.00 40.97 4.79
78 79 1.586564 CGAGAGGATTCACGGTCGC 60.587 63.158 0.00 0.00 34.38 5.19
79 80 1.586564 GAGAGGATTCACGGTCGCG 60.587 63.158 0.00 0.00 0.00 5.87
80 81 2.582498 GAGGATTCACGGTCGCGG 60.582 66.667 6.13 0.00 0.00 6.46
81 82 4.814294 AGGATTCACGGTCGCGGC 62.814 66.667 6.13 3.04 0.00 6.53
83 84 3.554692 GATTCACGGTCGCGGCAG 61.555 66.667 14.93 12.33 0.00 4.85
84 85 3.982372 GATTCACGGTCGCGGCAGA 62.982 63.158 19.74 6.77 0.00 4.26
85 86 3.583276 ATTCACGGTCGCGGCAGAA 62.583 57.895 19.74 16.01 0.00 3.02
86 87 4.717629 TCACGGTCGCGGCAGAAG 62.718 66.667 19.74 9.78 0.00 2.85
88 89 4.295119 ACGGTCGCGGCAGAAGTT 62.295 61.111 19.74 0.00 0.00 2.66
89 90 3.777925 CGGTCGCGGCAGAAGTTG 61.778 66.667 14.93 0.00 0.00 3.16
90 91 3.423154 GGTCGCGGCAGAAGTTGG 61.423 66.667 14.93 0.00 0.00 3.77
112 113 4.148825 GCGGCGACCACTCTCCAT 62.149 66.667 12.98 0.00 0.00 3.41
113 114 2.202797 CGGCGACCACTCTCCATG 60.203 66.667 0.00 0.00 0.00 3.66
114 115 2.187946 GGCGACCACTCTCCATGG 59.812 66.667 4.97 4.97 43.43 3.66
115 116 2.359169 GGCGACCACTCTCCATGGA 61.359 63.158 15.27 15.27 39.87 3.41
116 117 1.153549 GCGACCACTCTCCATGGAC 60.154 63.158 11.44 0.00 39.87 4.02
117 118 1.139734 CGACCACTCTCCATGGACG 59.860 63.158 11.44 7.35 45.97 4.79
118 119 2.579878 GACCACTCTCCATGGACGA 58.420 57.895 11.44 11.67 39.87 4.20
119 120 0.173708 GACCACTCTCCATGGACGAC 59.826 60.000 11.44 0.00 39.87 4.34
120 121 1.139734 CCACTCTCCATGGACGACG 59.860 63.158 11.44 0.56 39.87 5.12
121 122 1.595993 CCACTCTCCATGGACGACGT 61.596 60.000 11.44 0.00 39.87 4.34
122 123 0.456824 CACTCTCCATGGACGACGTG 60.457 60.000 11.44 16.15 35.80 4.49
127 128 3.490759 CATGGACGACGTGGCTGC 61.491 66.667 4.58 0.00 32.27 5.25
128 129 3.695606 ATGGACGACGTGGCTGCT 61.696 61.111 4.58 0.00 0.00 4.24
129 130 3.649277 ATGGACGACGTGGCTGCTC 62.649 63.158 4.58 0.00 0.00 4.26
130 131 4.057428 GGACGACGTGGCTGCTCT 62.057 66.667 4.58 0.00 0.00 4.09
131 132 2.807045 GACGACGTGGCTGCTCTG 60.807 66.667 4.58 0.00 0.00 3.35
139 140 2.359230 GGCTGCTCTGCCGTTTCT 60.359 61.111 0.00 0.00 43.74 2.52
140 141 2.684843 GGCTGCTCTGCCGTTTCTG 61.685 63.158 0.00 0.00 43.74 3.02
141 142 2.866028 CTGCTCTGCCGTTTCTGC 59.134 61.111 0.00 0.00 0.00 4.26
142 143 1.670406 CTGCTCTGCCGTTTCTGCT 60.670 57.895 0.00 0.00 0.00 4.24
143 144 1.227943 TGCTCTGCCGTTTCTGCTT 60.228 52.632 0.00 0.00 0.00 3.91
144 145 1.230635 TGCTCTGCCGTTTCTGCTTC 61.231 55.000 0.00 0.00 0.00 3.86
145 146 1.230635 GCTCTGCCGTTTCTGCTTCA 61.231 55.000 0.00 0.00 0.00 3.02
146 147 0.514691 CTCTGCCGTTTCTGCTTCAC 59.485 55.000 0.00 0.00 0.00 3.18
147 148 1.205064 CTGCCGTTTCTGCTTCACG 59.795 57.895 0.00 0.00 0.00 4.35
148 149 2.127232 GCCGTTTCTGCTTCACGC 60.127 61.111 0.00 0.00 39.77 5.34
149 150 2.556287 CCGTTTCTGCTTCACGCC 59.444 61.111 0.00 0.00 38.05 5.68
150 151 2.170985 CGTTTCTGCTTCACGCCG 59.829 61.111 0.00 0.00 38.05 6.46
151 152 2.556287 GTTTCTGCTTCACGCCGG 59.444 61.111 0.00 0.00 38.05 6.13
152 153 2.110213 TTTCTGCTTCACGCCGGT 59.890 55.556 1.90 0.00 38.05 5.28
153 154 2.250939 TTTCTGCTTCACGCCGGTG 61.251 57.895 14.93 14.93 45.78 4.94
154 155 4.680237 TCTGCTTCACGCCGGTGG 62.680 66.667 21.14 8.58 44.50 4.61
175 176 1.295423 GGAGGAGTAGGCGCAACAA 59.705 57.895 10.83 0.00 0.00 2.83
250 251 0.724453 CGACGCATGGAAAACGTTGG 60.724 55.000 0.00 0.00 40.69 3.77
252 253 1.732683 CGCATGGAAAACGTTGGCC 60.733 57.895 0.00 7.18 0.00 5.36
257 258 2.570284 GGAAAACGTTGGCCAGGGG 61.570 63.158 5.11 1.32 0.00 4.79
259 260 1.382009 AAAACGTTGGCCAGGGGTT 60.382 52.632 5.11 8.96 0.00 4.11
260 261 1.681486 AAAACGTTGGCCAGGGGTTG 61.681 55.000 15.98 3.36 0.00 3.77
261 262 2.864770 AAACGTTGGCCAGGGGTTGT 62.865 55.000 15.98 3.91 0.00 3.32
279 284 3.814268 CTCCATGGCGGCGTTTGG 61.814 66.667 6.96 16.31 33.14 3.28
303 308 2.491621 CGATGAGGCGAGACAGCA 59.508 61.111 0.00 0.00 39.27 4.41
304 309 1.067084 CGATGAGGCGAGACAGCAT 59.933 57.895 0.00 0.00 39.27 3.79
321 326 1.309013 ATGGGGCTGGAGGGATTGA 60.309 57.895 0.00 0.00 0.00 2.57
364 369 2.124942 CGCAGAAGGGGAGGAAGC 60.125 66.667 0.00 0.00 0.00 3.86
367 372 0.393673 GCAGAAGGGGAGGAAGCTTC 60.394 60.000 18.54 18.54 0.00 3.86
384 389 0.463654 TTCCCTCCCATCAAATCGCG 60.464 55.000 0.00 0.00 0.00 5.87
392 397 0.027979 CATCAAATCGCGCGTTGGAT 59.972 50.000 30.98 25.12 0.00 3.41
401 406 1.300233 CGCGTTGGATAGAGGGAGC 60.300 63.158 0.00 0.00 0.00 4.70
423 428 1.975660 CAAAACGGAAAGGAGGGACA 58.024 50.000 0.00 0.00 0.00 4.02
424 429 1.880027 CAAAACGGAAAGGAGGGACAG 59.120 52.381 0.00 0.00 0.00 3.51
425 430 0.400594 AAACGGAAAGGAGGGACAGG 59.599 55.000 0.00 0.00 0.00 4.00
426 431 0.473117 AACGGAAAGGAGGGACAGGA 60.473 55.000 0.00 0.00 0.00 3.86
427 432 0.905337 ACGGAAAGGAGGGACAGGAG 60.905 60.000 0.00 0.00 0.00 3.69
428 433 0.614979 CGGAAAGGAGGGACAGGAGA 60.615 60.000 0.00 0.00 0.00 3.71
429 434 1.886422 GGAAAGGAGGGACAGGAGAT 58.114 55.000 0.00 0.00 0.00 2.75
430 435 2.200955 GGAAAGGAGGGACAGGAGATT 58.799 52.381 0.00 0.00 0.00 2.40
431 436 2.578480 GGAAAGGAGGGACAGGAGATTT 59.422 50.000 0.00 0.00 0.00 2.17
432 437 3.615155 GAAAGGAGGGACAGGAGATTTG 58.385 50.000 0.00 0.00 0.00 2.32
433 438 1.589414 AGGAGGGACAGGAGATTTGG 58.411 55.000 0.00 0.00 0.00 3.28
438 443 0.744771 GGACAGGAGATTTGGCGGAC 60.745 60.000 0.00 0.00 0.00 4.79
440 445 1.079127 CAGGAGATTTGGCGGACGT 60.079 57.895 0.00 0.00 0.00 4.34
441 446 1.079127 AGGAGATTTGGCGGACGTG 60.079 57.895 0.00 0.00 0.00 4.49
452 457 1.381165 GCGGACGTGGGCCAAAATAT 61.381 55.000 8.40 0.00 0.00 1.28
465 470 2.752354 CCAAAATATGAAGGTCACCGCA 59.248 45.455 0.00 0.00 0.00 5.69
524 539 2.754946 TTATTCCGGTCCCGCATATC 57.245 50.000 0.00 0.00 38.24 1.63
526 541 1.183030 ATTCCGGTCCCGCATATCGA 61.183 55.000 0.00 0.00 41.67 3.59
538 553 3.246699 CCGCATATCGACGGTTATTTTGT 59.753 43.478 4.14 0.00 44.46 2.83
540 555 4.523813 GCATATCGACGGTTATTTTGTGG 58.476 43.478 0.00 0.00 0.00 4.17
542 557 1.810959 TCGACGGTTATTTTGTGGGG 58.189 50.000 0.00 0.00 0.00 4.96
543 558 1.347050 TCGACGGTTATTTTGTGGGGA 59.653 47.619 0.00 0.00 0.00 4.81
544 559 2.027007 TCGACGGTTATTTTGTGGGGAT 60.027 45.455 0.00 0.00 0.00 3.85
545 560 3.197333 TCGACGGTTATTTTGTGGGGATA 59.803 43.478 0.00 0.00 0.00 2.59
546 561 4.131596 CGACGGTTATTTTGTGGGGATAT 58.868 43.478 0.00 0.00 0.00 1.63
549 564 5.067954 ACGGTTATTTTGTGGGGATATAGC 58.932 41.667 0.00 0.00 0.00 2.97
550 565 5.067273 CGGTTATTTTGTGGGGATATAGCA 58.933 41.667 0.00 0.00 0.00 3.49
552 567 6.039941 CGGTTATTTTGTGGGGATATAGCAAA 59.960 38.462 0.00 0.00 0.00 3.68
553 568 7.255801 CGGTTATTTTGTGGGGATATAGCAAAT 60.256 37.037 0.00 0.00 0.00 2.32
554 569 8.088365 GGTTATTTTGTGGGGATATAGCAAATC 58.912 37.037 0.00 0.00 0.00 2.17
557 572 8.641498 ATTTTGTGGGGATATAGCAAATCTAG 57.359 34.615 0.00 0.00 0.00 2.43
559 574 7.574021 TTGTGGGGATATAGCAAATCTAGAT 57.426 36.000 0.00 0.00 32.24 1.98
561 576 7.988937 TGTGGGGATATAGCAAATCTAGATTT 58.011 34.615 22.43 22.43 41.33 2.17
562 577 8.448008 TGTGGGGATATAGCAAATCTAGATTTT 58.552 33.333 24.94 15.72 38.84 1.82
586 604 0.393402 TTACTGCTAGAGACGCCGGA 60.393 55.000 5.05 0.00 0.00 5.14
613 631 1.611491 CTAGGACGAGGATTGAGGAGC 59.389 57.143 0.00 0.00 0.00 4.70
614 632 1.066587 GGACGAGGATTGAGGAGCG 59.933 63.158 0.00 0.00 0.00 5.03
769 787 1.668751 CGCGCTAGGGCTTATCAAAAA 59.331 47.619 26.90 0.00 36.09 1.94
795 823 2.034999 TGACACCCCCGCCATTTC 59.965 61.111 0.00 0.00 0.00 2.17
1107 1137 0.794981 CGTCGTCTTCTGCTTCCTCG 60.795 60.000 0.00 0.00 0.00 4.63
1110 1140 1.448717 GTCTTCTGCTTCCTCGGGC 60.449 63.158 0.00 0.00 0.00 6.13
1212 1242 0.395862 GGAGGGAGATGGTCGAGTCA 60.396 60.000 0.00 0.00 0.00 3.41
1235 1265 3.379445 CGACACGTACTGCCCCCT 61.379 66.667 0.00 0.00 0.00 4.79
1253 1283 0.898320 CTTCTCTTTCCCTCTCGCCA 59.102 55.000 0.00 0.00 0.00 5.69
1304 1449 2.954318 TGTAGGCCTGTACCGTCTAATC 59.046 50.000 17.99 0.00 33.69 1.75
1333 1478 4.330250 CTCATCCTTCTGATTGTTGGTGT 58.670 43.478 0.00 0.00 0.00 4.16
1368 1513 4.041075 TGCCAGTAGGATTTAGTTCACACA 59.959 41.667 0.00 0.00 36.89 3.72
1379 1524 9.559958 GGATTTAGTTCACACATTTGTTCTATG 57.440 33.333 0.00 0.00 31.66 2.23
1382 1527 6.560253 AGTTCACACATTTGTTCTATGTCC 57.440 37.500 0.00 0.00 34.11 4.02
1412 1557 3.007614 TGCCCTCTGTTTGTTACTAGGAC 59.992 47.826 0.00 0.00 34.41 3.85
1630 1786 4.576053 TGGTTTATCTGATTGGAATGCGAG 59.424 41.667 0.00 0.00 0.00 5.03
1655 1811 3.711704 TGAGGGAGTGTGTCTTTCTCTTT 59.288 43.478 0.00 0.00 31.62 2.52
1658 1814 5.148502 AGGGAGTGTGTCTTTCTCTTTAGA 58.851 41.667 0.00 0.00 0.00 2.10
1753 1911 4.350346 CTTTGTGCATGTCGAGTTTTTCA 58.650 39.130 0.00 0.00 0.00 2.69
1784 1942 1.134946 GTAATCCAATTGGCGCTGCTT 59.865 47.619 20.33 8.20 34.44 3.91
2131 2289 3.664107 TCATCAGCACTCAACAGTTACC 58.336 45.455 0.00 0.00 0.00 2.85
2174 2332 5.940470 GGAATCTGGTATTCTGAACAGTGTT 59.060 40.000 8.61 8.61 32.92 3.32
2243 2401 3.541632 TGAGAAACAAGACGAAGCCTTT 58.458 40.909 0.00 0.00 0.00 3.11
2395 2553 2.935201 GCATCACTGATGAAGTCACTCC 59.065 50.000 21.20 0.00 42.09 3.85
2407 2565 1.056660 GTCACTCCTTCCCCAGAACA 58.943 55.000 0.00 0.00 0.00 3.18
2470 2631 2.298729 TGACATCACCTGACGATTGTGA 59.701 45.455 0.00 0.00 42.65 3.58
2509 2670 4.082625 TGCTGTTGATGAGGCTATTGTTTG 60.083 41.667 0.00 0.00 0.00 2.93
2607 2771 7.814264 ATCAAGACAGAAGTTGTTCAGATTT 57.186 32.000 0.00 0.00 41.05 2.17
2618 2782 3.084039 TGTTCAGATTTCAGATGGCCAC 58.916 45.455 8.16 1.58 0.00 5.01
2682 2846 2.480037 TCGAATACAAGTGCAGCAACAG 59.520 45.455 0.00 0.00 0.00 3.16
2758 2922 0.887387 GCCAGCCCTAACGAACAACA 60.887 55.000 0.00 0.00 0.00 3.33
2777 2941 5.591877 ACAACAAAAGTCAGAAGATCTTGCT 59.408 36.000 14.00 7.13 0.00 3.91
2844 3008 4.119136 AGGTTTTTGCAAGAATTTGACCG 58.881 39.130 5.62 0.00 36.36 4.79
3022 3208 4.739587 TTGTTTACTTTTGGTTGGACCC 57.260 40.909 0.00 0.00 37.50 4.46
3202 3389 2.643551 GTGAGGCAAGCAAGGCTAATA 58.356 47.619 4.49 0.00 45.32 0.98
3529 4090 3.623510 GCTTTGGAACAGCTATAGGTGAC 59.376 47.826 32.85 24.45 45.66 3.67
3616 4177 4.282950 CACATGATGCAGTGGTTATGTC 57.717 45.455 0.00 0.00 32.24 3.06
3678 4239 6.892658 ACATTTTCATGGTACTGCACTTTA 57.107 33.333 0.00 0.00 34.27 1.85
3679 4240 7.466746 ACATTTTCATGGTACTGCACTTTAT 57.533 32.000 0.00 0.00 34.27 1.40
3740 4312 5.494632 AAGCCAAACTTTGTAGTACACAC 57.505 39.130 1.43 0.00 36.69 3.82
3756 4328 7.587037 AGTACACACTACACAGTAAAACCTA 57.413 36.000 0.00 0.00 32.21 3.08
3850 4422 0.471591 TTTTGCCCACAGCCCTGATT 60.472 50.000 1.69 0.00 42.71 2.57
3868 4440 9.449550 GCCCTGATTTGAATTTTAAAAGTTTTG 57.550 29.630 11.18 0.00 0.00 2.44
3901 4473 9.710900 CTATTTCCTTTTCTGGTTGCTTAAATT 57.289 29.630 0.00 0.00 0.00 1.82
3905 4477 6.765512 TCCTTTTCTGGTTGCTTAAATTTTGG 59.234 34.615 0.00 0.00 0.00 3.28
3907 4479 7.713073 CCTTTTCTGGTTGCTTAAATTTTGGTA 59.287 33.333 0.00 0.00 0.00 3.25
3920 4492 9.717942 CTTAAATTTTGGTATGGTTCATTGGAA 57.282 29.630 0.00 0.00 0.00 3.53
3927 4499 5.593909 TGGTATGGTTCATTGGAATGTGATC 59.406 40.000 0.00 0.00 37.65 2.92
3938 4510 1.478105 GAATGTGATCCTTTGTGGGGC 59.522 52.381 0.00 0.00 36.20 5.80
4167 4740 4.165779 CCATGGCAAACGTTTGATAACTC 58.834 43.478 38.04 21.63 40.55 3.01
4216 4799 3.668447 TGACCTTTTGTCTCTCTCATGC 58.332 45.455 0.00 0.00 44.75 4.06
4226 4809 4.111916 GTCTCTCTCATGCTCTGCTTTAC 58.888 47.826 0.00 0.00 0.00 2.01
4406 4989 0.108756 ACTAGGAAACGAGAAGCGCC 60.109 55.000 2.29 0.00 46.04 6.53
4407 4990 0.806492 CTAGGAAACGAGAAGCGCCC 60.806 60.000 2.29 0.00 46.04 6.13
4533 5118 5.637810 TCAGATGTATCGTTTGGTCAACTTC 59.362 40.000 0.00 0.00 32.53 3.01
4534 5119 4.625742 AGATGTATCGTTTGGTCAACTTCG 59.374 41.667 0.00 0.00 32.53 3.79
4674 5259 4.843220 AATCGAGCATGAATGATTTCCC 57.157 40.909 0.00 0.00 0.00 3.97
4692 5279 4.759516 TCCCGTTAACTTTTCTGCAATC 57.240 40.909 3.71 0.00 0.00 2.67
4860 5449 7.939784 AATGAACAAATTTAGTACTCCCTCC 57.060 36.000 0.00 0.00 0.00 4.30
4872 5461 3.397849 ACTCCCTCCGTTCACTTTTAC 57.602 47.619 0.00 0.00 0.00 2.01
4876 5465 3.135167 TCCCTCCGTTCACTTTTACAAGT 59.865 43.478 0.00 0.00 44.72 3.16
4878 5467 3.183775 CCTCCGTTCACTTTTACAAGTCG 59.816 47.826 0.00 0.00 41.69 4.18
4881 5470 4.268405 TCCGTTCACTTTTACAAGTCGTTC 59.732 41.667 0.00 0.00 41.69 3.95
4882 5471 4.191161 CGTTCACTTTTACAAGTCGTTCG 58.809 43.478 0.00 0.00 41.69 3.95
4883 5472 4.259530 CGTTCACTTTTACAAGTCGTTCGT 60.260 41.667 0.00 0.00 41.69 3.85
4884 5473 5.553721 GTTCACTTTTACAAGTCGTTCGTT 58.446 37.500 0.00 0.00 41.69 3.85
4885 5474 5.783100 TCACTTTTACAAGTCGTTCGTTT 57.217 34.783 0.00 0.00 41.69 3.60
4889 5478 5.577945 ACTTTTACAAGTCGTTCGTTTCAGA 59.422 36.000 0.00 0.00 39.15 3.27
4890 5479 5.379757 TTTACAAGTCGTTCGTTTCAGAC 57.620 39.130 0.00 0.00 0.00 3.51
4891 5480 2.883574 ACAAGTCGTTCGTTTCAGACA 58.116 42.857 0.00 0.00 36.18 3.41
4893 5482 3.061697 ACAAGTCGTTCGTTTCAGACAAC 59.938 43.478 0.00 0.00 36.18 3.32
4894 5483 3.160777 AGTCGTTCGTTTCAGACAACT 57.839 42.857 0.00 0.00 36.18 3.16
4895 5484 2.858344 AGTCGTTCGTTTCAGACAACTG 59.142 45.455 0.00 0.00 44.66 3.16
4913 5502 6.406093 CAACTGAAATTGAGTTGTTTTGCA 57.594 33.333 15.51 0.00 43.55 4.08
4914 5503 6.242829 CAACTGAAATTGAGTTGTTTTGCAC 58.757 36.000 15.51 0.00 43.55 4.57
4915 5504 4.562394 ACTGAAATTGAGTTGTTTTGCACG 59.438 37.500 0.00 0.00 0.00 5.34
4916 5505 4.489810 TGAAATTGAGTTGTTTTGCACGT 58.510 34.783 0.00 0.00 0.00 4.49
4917 5506 4.926238 TGAAATTGAGTTGTTTTGCACGTT 59.074 33.333 0.00 0.00 0.00 3.99
4918 5507 6.093404 TGAAATTGAGTTGTTTTGCACGTTA 58.907 32.000 0.00 0.00 0.00 3.18
4919 5508 6.754209 TGAAATTGAGTTGTTTTGCACGTTAT 59.246 30.769 0.00 0.00 0.00 1.89
4920 5509 6.747659 AATTGAGTTGTTTTGCACGTTATC 57.252 33.333 0.00 0.00 0.00 1.75
4921 5510 5.493133 TTGAGTTGTTTTGCACGTTATCT 57.507 34.783 0.00 0.00 0.00 1.98
4922 5511 4.843147 TGAGTTGTTTTGCACGTTATCTG 58.157 39.130 0.00 0.00 0.00 2.90
4923 5512 4.572795 TGAGTTGTTTTGCACGTTATCTGA 59.427 37.500 0.00 0.00 0.00 3.27
4925 5514 5.885881 AGTTGTTTTGCACGTTATCTGAAA 58.114 33.333 0.00 0.00 0.00 2.69
4926 5515 6.503524 AGTTGTTTTGCACGTTATCTGAAAT 58.496 32.000 0.00 0.00 0.00 2.17
4927 5516 6.417635 AGTTGTTTTGCACGTTATCTGAAATG 59.582 34.615 0.00 0.00 0.00 2.32
4928 5517 5.826586 TGTTTTGCACGTTATCTGAAATGT 58.173 33.333 0.00 0.00 0.00 2.71
4929 5518 5.912396 TGTTTTGCACGTTATCTGAAATGTC 59.088 36.000 0.00 0.00 0.00 3.06
4930 5519 5.940192 TTTGCACGTTATCTGAAATGTCT 57.060 34.783 0.00 0.00 0.00 3.41
4931 5520 7.041712 TGTTTTGCACGTTATCTGAAATGTCTA 60.042 33.333 0.00 0.00 0.00 2.59
4932 5521 6.403333 TTGCACGTTATCTGAAATGTCTAC 57.597 37.500 0.00 0.00 0.00 2.59
4933 5522 5.474825 TGCACGTTATCTGAAATGTCTACA 58.525 37.500 0.00 0.00 0.00 2.74
4934 5523 5.929415 TGCACGTTATCTGAAATGTCTACAA 59.071 36.000 0.00 0.00 0.00 2.41
4935 5524 6.128661 TGCACGTTATCTGAAATGTCTACAAC 60.129 38.462 0.00 0.00 0.00 3.32
4936 5525 6.128661 GCACGTTATCTGAAATGTCTACAACA 60.129 38.462 0.00 0.00 43.51 3.33
4937 5526 7.227461 CACGTTATCTGAAATGTCTACAACAC 58.773 38.462 0.00 0.00 41.75 3.32
4952 5541 9.048446 TGTCTACAACACCTTATAAAAGTGAAC 57.952 33.333 17.79 8.94 31.20 3.18
4957 5546 7.773690 ACAACACCTTATAAAAGTGAACAGAGT 59.226 33.333 17.79 7.33 0.00 3.24
4958 5547 8.621286 CAACACCTTATAAAAGTGAACAGAGTT 58.379 33.333 17.79 2.46 0.00 3.01
4959 5548 8.154649 ACACCTTATAAAAGTGAACAGAGTTG 57.845 34.615 17.79 0.00 0.00 3.16
5143 5736 8.537016 AGTAGTGATCTAGACGCTCTTATAGAT 58.463 37.037 10.41 0.00 37.62 1.98
5160 5753 9.381033 TCTTATAGATGGAGTACTTCGCTATAC 57.619 37.037 17.08 0.00 0.00 1.47
5176 5769 5.009710 TCGCTATACCTAAAGGATGACACAG 59.990 44.000 2.23 0.00 38.94 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 4.715130 TCCTCCACCCCCTCCGTG 62.715 72.222 0.00 0.00 0.00 4.94
14 15 4.400251 CTCCTCCACCCCCTCCGT 62.400 72.222 0.00 0.00 0.00 4.69
23 24 4.131088 GACGACCGCCTCCTCCAC 62.131 72.222 0.00 0.00 0.00 4.02
26 27 3.519930 GAGGACGACCGCCTCCTC 61.520 72.222 16.50 14.17 44.96 3.71
29 30 3.878519 CTCGAGGACGACCGCCTC 61.879 72.222 3.91 17.03 46.74 4.70
51 52 2.968330 GAATCCTCTCGTCGCGGTCG 62.968 65.000 6.13 12.36 0.00 4.79
52 53 1.298488 GAATCCTCTCGTCGCGGTC 60.298 63.158 6.13 0.00 0.00 4.79
53 54 2.044555 TGAATCCTCTCGTCGCGGT 61.045 57.895 6.13 0.00 0.00 5.68
54 55 1.586564 GTGAATCCTCTCGTCGCGG 60.587 63.158 6.13 0.00 0.00 6.46
55 56 1.934956 CGTGAATCCTCTCGTCGCG 60.935 63.158 0.00 0.00 38.71 5.87
56 57 1.586564 CCGTGAATCCTCTCGTCGC 60.587 63.158 0.00 0.00 36.95 5.19
57 58 0.248134 GACCGTGAATCCTCTCGTCG 60.248 60.000 0.00 0.00 36.95 5.12
58 59 0.248134 CGACCGTGAATCCTCTCGTC 60.248 60.000 0.00 0.00 36.95 4.20
59 60 1.801332 CGACCGTGAATCCTCTCGT 59.199 57.895 0.00 0.00 36.95 4.18
60 61 1.586564 GCGACCGTGAATCCTCTCG 60.587 63.158 0.00 0.00 38.10 4.04
61 62 1.586564 CGCGACCGTGAATCCTCTC 60.587 63.158 0.00 0.00 0.00 3.20
62 63 2.490217 CGCGACCGTGAATCCTCT 59.510 61.111 0.00 0.00 0.00 3.69
63 64 2.582498 CCGCGACCGTGAATCCTC 60.582 66.667 8.23 0.00 0.00 3.71
64 65 4.814294 GCCGCGACCGTGAATCCT 62.814 66.667 8.23 0.00 0.00 3.24
66 67 3.554692 CTGCCGCGACCGTGAATC 61.555 66.667 8.23 0.00 0.00 2.52
67 68 3.583276 TTCTGCCGCGACCGTGAAT 62.583 57.895 8.23 0.00 0.00 2.57
68 69 4.287781 TTCTGCCGCGACCGTGAA 62.288 61.111 8.23 4.43 0.00 3.18
69 70 4.717629 CTTCTGCCGCGACCGTGA 62.718 66.667 8.23 0.00 0.00 4.35
71 72 4.295119 AACTTCTGCCGCGACCGT 62.295 61.111 8.23 0.00 0.00 4.83
72 73 3.777925 CAACTTCTGCCGCGACCG 61.778 66.667 8.23 0.00 0.00 4.79
73 74 3.423154 CCAACTTCTGCCGCGACC 61.423 66.667 8.23 0.00 0.00 4.79
74 75 4.090057 GCCAACTTCTGCCGCGAC 62.090 66.667 8.23 0.00 0.00 5.19
95 96 4.148825 ATGGAGAGTGGTCGCCGC 62.149 66.667 1.74 1.74 45.40 6.53
96 97 2.202797 CATGGAGAGTGGTCGCCG 60.203 66.667 0.00 0.00 45.40 6.46
97 98 2.187946 CCATGGAGAGTGGTCGCC 59.812 66.667 5.56 0.00 42.85 5.54
98 99 1.153549 GTCCATGGAGAGTGGTCGC 60.154 63.158 16.81 0.00 37.96 5.19
99 100 1.139734 CGTCCATGGAGAGTGGTCG 59.860 63.158 16.81 9.62 40.65 4.79
100 101 0.173708 GTCGTCCATGGAGAGTGGTC 59.826 60.000 16.81 0.00 37.96 4.02
101 102 1.595993 CGTCGTCCATGGAGAGTGGT 61.596 60.000 16.81 0.00 37.96 4.16
102 103 1.139734 CGTCGTCCATGGAGAGTGG 59.860 63.158 16.81 2.46 38.11 4.00
103 104 0.456824 CACGTCGTCCATGGAGAGTG 60.457 60.000 16.81 17.82 0.00 3.51
104 105 1.595993 CCACGTCGTCCATGGAGAGT 61.596 60.000 16.81 10.01 35.33 3.24
105 106 1.139734 CCACGTCGTCCATGGAGAG 59.860 63.158 16.81 12.85 35.33 3.20
106 107 3.001902 GCCACGTCGTCCATGGAGA 62.002 63.158 16.81 12.10 35.33 3.71
107 108 2.509336 GCCACGTCGTCCATGGAG 60.509 66.667 16.81 9.76 35.33 3.86
108 109 2.994995 AGCCACGTCGTCCATGGA 60.995 61.111 11.44 11.44 35.33 3.41
109 110 2.815211 CAGCCACGTCGTCCATGG 60.815 66.667 4.97 4.97 36.51 3.66
110 111 3.490759 GCAGCCACGTCGTCCATG 61.491 66.667 0.00 0.00 0.00 3.66
111 112 3.649277 GAGCAGCCACGTCGTCCAT 62.649 63.158 0.00 0.00 0.00 3.41
112 113 4.357947 GAGCAGCCACGTCGTCCA 62.358 66.667 0.00 0.00 0.00 4.02
113 114 4.057428 AGAGCAGCCACGTCGTCC 62.057 66.667 0.00 0.00 0.00 4.79
114 115 2.807045 CAGAGCAGCCACGTCGTC 60.807 66.667 0.00 0.00 0.00 4.20
123 124 2.866028 CAGAAACGGCAGAGCAGC 59.134 61.111 0.00 0.00 0.00 5.25
124 125 1.233285 AAGCAGAAACGGCAGAGCAG 61.233 55.000 0.00 0.00 0.00 4.24
125 126 1.227943 AAGCAGAAACGGCAGAGCA 60.228 52.632 0.00 0.00 0.00 4.26
126 127 1.230635 TGAAGCAGAAACGGCAGAGC 61.231 55.000 0.00 0.00 0.00 4.09
127 128 0.514691 GTGAAGCAGAAACGGCAGAG 59.485 55.000 0.00 0.00 0.00 3.35
128 129 1.221466 CGTGAAGCAGAAACGGCAGA 61.221 55.000 0.00 0.00 33.77 4.26
129 130 1.205064 CGTGAAGCAGAAACGGCAG 59.795 57.895 0.00 0.00 33.77 4.85
130 131 3.329231 CGTGAAGCAGAAACGGCA 58.671 55.556 0.00 0.00 33.77 5.69
155 156 3.081409 TTGCGCCTACTCCTCCCC 61.081 66.667 4.18 0.00 0.00 4.81
156 157 2.180159 TTGTTGCGCCTACTCCTCCC 62.180 60.000 4.18 0.00 0.00 4.30
157 158 1.019805 GTTGTTGCGCCTACTCCTCC 61.020 60.000 4.18 0.00 0.00 4.30
158 159 1.352156 CGTTGTTGCGCCTACTCCTC 61.352 60.000 4.18 0.00 0.00 3.71
159 160 1.374252 CGTTGTTGCGCCTACTCCT 60.374 57.895 4.18 0.00 0.00 3.69
160 161 1.352156 CTCGTTGTTGCGCCTACTCC 61.352 60.000 4.18 0.00 0.00 3.85
161 162 1.352156 CCTCGTTGTTGCGCCTACTC 61.352 60.000 4.18 0.67 0.00 2.59
162 163 1.374252 CCTCGTTGTTGCGCCTACT 60.374 57.895 4.18 0.00 0.00 2.57
163 164 0.947180 TTCCTCGTTGTTGCGCCTAC 60.947 55.000 4.18 3.49 0.00 3.18
164 165 0.947180 GTTCCTCGTTGTTGCGCCTA 60.947 55.000 4.18 0.00 0.00 3.93
165 166 2.110213 TTCCTCGTTGTTGCGCCT 59.890 55.556 4.18 0.00 0.00 5.52
166 167 1.852067 ATGTTCCTCGTTGTTGCGCC 61.852 55.000 4.18 0.00 0.00 6.53
167 168 0.725784 CATGTTCCTCGTTGTTGCGC 60.726 55.000 0.00 0.00 0.00 6.09
168 169 0.865111 TCATGTTCCTCGTTGTTGCG 59.135 50.000 0.00 0.00 0.00 4.85
169 170 1.873591 AGTCATGTTCCTCGTTGTTGC 59.126 47.619 0.00 0.00 0.00 4.17
170 171 2.349817 GCAGTCATGTTCCTCGTTGTTG 60.350 50.000 0.00 0.00 0.00 3.33
171 172 1.873591 GCAGTCATGTTCCTCGTTGTT 59.126 47.619 0.00 0.00 0.00 2.83
175 176 0.109086 CTCGCAGTCATGTTCCTCGT 60.109 55.000 0.00 0.00 0.00 4.18
227 228 2.281831 TTTTCCATGCGTCGGCCA 60.282 55.556 2.24 0.00 38.85 5.36
260 261 2.746277 AAACGCCGCCATGGAGAC 60.746 61.111 18.40 3.07 40.56 3.36
261 262 2.745884 CAAACGCCGCCATGGAGA 60.746 61.111 18.40 0.00 40.56 3.71
287 292 0.879400 CCATGCTGTCTCGCCTCATC 60.879 60.000 0.00 0.00 0.00 2.92
303 308 1.309013 TCAATCCCTCCAGCCCCAT 60.309 57.895 0.00 0.00 0.00 4.00
304 309 2.127065 TCAATCCCTCCAGCCCCA 59.873 61.111 0.00 0.00 0.00 4.96
309 314 2.202932 CGCCGTCAATCCCTCCAG 60.203 66.667 0.00 0.00 0.00 3.86
345 350 4.082523 TTCCTCCCCTTCTGCGCG 62.083 66.667 0.00 0.00 0.00 6.86
364 369 1.312815 GCGATTTGATGGGAGGGAAG 58.687 55.000 0.00 0.00 0.00 3.46
367 372 2.546494 GCGCGATTTGATGGGAGGG 61.546 63.158 12.10 0.00 0.00 4.30
374 379 1.526887 CTATCCAACGCGCGATTTGAT 59.473 47.619 39.36 29.15 0.00 2.57
384 389 1.300233 CGCTCCCTCTATCCAACGC 60.300 63.158 0.00 0.00 0.00 4.84
392 397 1.079405 CGTTTTGCCGCTCCCTCTA 60.079 57.895 0.00 0.00 0.00 2.43
401 406 1.579429 CCTCCTTTCCGTTTTGCCG 59.421 57.895 0.00 0.00 0.00 5.69
423 428 1.079127 CACGTCCGCCAAATCTCCT 60.079 57.895 0.00 0.00 0.00 3.69
424 429 2.106683 CCACGTCCGCCAAATCTCC 61.107 63.158 0.00 0.00 0.00 3.71
425 430 2.106683 CCCACGTCCGCCAAATCTC 61.107 63.158 0.00 0.00 0.00 2.75
426 431 2.046314 CCCACGTCCGCCAAATCT 60.046 61.111 0.00 0.00 0.00 2.40
427 432 3.810896 GCCCACGTCCGCCAAATC 61.811 66.667 0.00 0.00 0.00 2.17
433 438 1.381165 ATATTTTGGCCCACGTCCGC 61.381 55.000 0.00 0.00 0.00 5.54
438 443 2.099098 GACCTTCATATTTTGGCCCACG 59.901 50.000 0.00 0.00 0.00 4.94
440 445 3.096092 GTGACCTTCATATTTTGGCCCA 58.904 45.455 0.00 0.00 0.00 5.36
441 446 2.430694 GGTGACCTTCATATTTTGGCCC 59.569 50.000 0.00 0.00 0.00 5.80
473 478 2.344500 CAGGGCCCGACACGTAAA 59.656 61.111 18.44 0.00 0.00 2.01
474 479 3.697747 CCAGGGCCCGACACGTAA 61.698 66.667 18.44 0.00 0.00 3.18
480 485 3.282374 AATCCAACCAGGGCCCGAC 62.282 63.158 18.44 0.00 38.24 4.79
481 486 2.938798 AATCCAACCAGGGCCCGA 60.939 61.111 18.44 6.71 38.24 5.14
506 521 0.528924 CGATATGCGGGACCGGAATA 59.471 55.000 9.46 5.70 43.97 1.75
510 525 2.049433 GTCGATATGCGGGACCGG 60.049 66.667 13.21 0.00 41.33 5.28
517 532 4.200827 CACAAAATAACCGTCGATATGCG 58.799 43.478 0.00 0.00 42.69 4.73
519 534 4.024387 CCCCACAAAATAACCGTCGATATG 60.024 45.833 0.00 0.00 0.00 1.78
524 539 1.810959 TCCCCACAAAATAACCGTCG 58.189 50.000 0.00 0.00 0.00 5.12
526 541 5.067954 GCTATATCCCCACAAAATAACCGT 58.932 41.667 0.00 0.00 0.00 4.83
557 572 7.851472 GGCGTCTCTAGCAGTAAAAATAAAATC 59.149 37.037 0.00 0.00 36.08 2.17
559 574 6.183360 CGGCGTCTCTAGCAGTAAAAATAAAA 60.183 38.462 0.00 0.00 36.08 1.52
561 576 4.802039 CGGCGTCTCTAGCAGTAAAAATAA 59.198 41.667 0.00 0.00 36.08 1.40
562 577 4.357142 CGGCGTCTCTAGCAGTAAAAATA 58.643 43.478 0.00 0.00 36.08 1.40
586 604 4.094476 TCAATCCTCGTCCTAGGTTTTCT 58.906 43.478 9.08 0.00 37.91 2.52
613 631 4.271816 CGCGGTCCAGGATCTCCG 62.272 72.222 11.86 11.86 44.86 4.63
614 632 2.833582 TCGCGGTCCAGGATCTCC 60.834 66.667 6.13 0.00 0.00 3.71
795 823 2.736826 GGAGAAAGGAGGGAGGCGG 61.737 68.421 0.00 0.00 0.00 6.13
848 876 2.581354 CCCACCCAGAGAAGCGAG 59.419 66.667 0.00 0.00 0.00 5.03
1017 1047 3.299977 CCGACGACCCAGGTCACA 61.300 66.667 16.78 0.00 44.77 3.58
1235 1265 0.608640 GTGGCGAGAGGGAAAGAGAA 59.391 55.000 0.00 0.00 0.00 2.87
1253 1283 9.174166 ACAGAATTCAAAACTACAAGTAACTGT 57.826 29.630 8.44 0.00 0.00 3.55
1304 1449 4.398358 ACAATCAGAAGGATGAGCATGTTG 59.602 41.667 0.00 0.00 36.02 3.33
1333 1478 7.775053 AATCCTACTGGCAACTTCATTTTAA 57.225 32.000 0.00 0.00 37.61 1.52
1368 1513 5.183904 GCACCAAGAAGGACATAGAACAAAT 59.816 40.000 0.00 0.00 41.22 2.32
1630 1786 0.765510 AAAGACACACTCCCTCACCC 59.234 55.000 0.00 0.00 0.00 4.61
1655 1811 6.371809 AAATCTTTGTGCAAAACGAGTCTA 57.628 33.333 1.97 0.00 0.00 2.59
1658 1814 8.564574 TCTATAAAATCTTTGTGCAAAACGAGT 58.435 29.630 1.97 0.00 0.00 4.18
1753 1911 6.183360 CGCCAATTGGATTACTACAAGGAAAT 60.183 38.462 29.02 0.00 37.39 2.17
1784 1942 3.181479 CCCGATACCTGAAATGAGACGAA 60.181 47.826 0.00 0.00 0.00 3.85
2131 2289 5.459536 TTCCAAGATATCAGATGAGGTCG 57.540 43.478 5.32 0.00 0.00 4.79
2174 2332 4.018506 TCTGCTACATTCCCATTTTGGAGA 60.019 41.667 0.00 0.00 40.96 3.71
2243 2401 0.834612 ACTCACTTGGTTTCCCACGA 59.165 50.000 0.00 0.00 41.67 4.35
2258 2416 7.625469 TCTCAGAACTATTAGTCTGAGACTCA 58.375 38.462 28.88 8.90 44.61 3.41
2395 2553 4.911390 AGAAACACTATGTTCTGGGGAAG 58.089 43.478 0.00 0.00 40.14 3.46
2470 2631 6.230472 TCAACAGCAGTATTAGTTGTGACAT 58.770 36.000 0.00 0.00 41.43 3.06
2509 2670 2.226437 TGAAGAACGCCATTTTCTGAGC 59.774 45.455 0.00 0.00 33.46 4.26
2607 2771 3.432749 GCAGATCTAAAGTGGCCATCTGA 60.433 47.826 26.89 14.51 42.05 3.27
2682 2846 4.507710 TCAATGGACACAGCTGATTCTAC 58.492 43.478 23.35 5.86 0.00 2.59
2777 2941 2.499693 TGTATCCATTGCTGGTCGAGAA 59.500 45.455 0.00 0.00 43.61 2.87
2814 2978 9.643693 CAAATTCTTGCAAAAACCTACATAGAT 57.356 29.630 0.00 0.00 0.00 1.98
2821 2985 5.163499 ACGGTCAAATTCTTGCAAAAACCTA 60.163 36.000 0.00 0.00 32.14 3.08
2844 3008 9.708222 CATGATTATGCACAGTTTAGTAAAGAC 57.292 33.333 0.00 0.00 0.00 3.01
2991 3175 6.118852 ACCAAAAGTAAACAATGTGCCATTT 58.881 32.000 0.00 0.00 0.00 2.32
3001 3185 4.354662 AGGGTCCAACCAAAAGTAAACAA 58.645 39.130 0.00 0.00 41.02 2.83
3038 3224 7.601886 TGGACATACCAAAATTTGCAGTAAATG 59.398 33.333 0.00 0.00 46.75 2.32
3066 3253 8.295288 CCCTGAAAAGATGCAGAATAATATGAC 58.705 37.037 0.00 0.00 34.06 3.06
3174 3361 2.394563 GCTTGCCTCACGCTCTTCC 61.395 63.158 0.00 0.00 38.78 3.46
3202 3389 3.627577 GTCGCACTTATCCCATGTTCATT 59.372 43.478 0.00 0.00 0.00 2.57
3511 4072 2.827755 TGGTCACCTATAGCTGTTCCA 58.172 47.619 0.00 3.00 0.00 3.53
3529 4090 2.292569 AGCATGCTATTTCGCAGATTGG 59.707 45.455 21.21 0.00 44.10 3.16
3641 4202 3.055819 TGAAAATGTTCGGAGGGAGAGAG 60.056 47.826 0.00 0.00 36.46 3.20
3678 4239 7.803189 CACGCTAAAAGTGAAATGTTACTTGAT 59.197 33.333 0.00 0.00 41.83 2.57
3679 4240 7.129622 CACGCTAAAAGTGAAATGTTACTTGA 58.870 34.615 0.00 0.00 41.83 3.02
3734 4306 7.147932 TGTGTAGGTTTTACTGTGTAGTGTGTA 60.148 37.037 0.00 0.00 37.78 2.90
3735 4307 6.044682 GTGTAGGTTTTACTGTGTAGTGTGT 58.955 40.000 0.00 0.00 37.78 3.72
3736 4308 6.044046 TGTGTAGGTTTTACTGTGTAGTGTG 58.956 40.000 0.00 0.00 37.78 3.82
3737 4309 6.097270 TCTGTGTAGGTTTTACTGTGTAGTGT 59.903 38.462 0.00 0.00 37.78 3.55
3738 4310 6.509656 TCTGTGTAGGTTTTACTGTGTAGTG 58.490 40.000 0.00 0.00 37.78 2.74
3739 4311 6.720112 TCTGTGTAGGTTTTACTGTGTAGT 57.280 37.500 0.00 0.00 40.99 2.73
3740 4312 7.169308 CAGTTCTGTGTAGGTTTTACTGTGTAG 59.831 40.741 0.00 0.00 0.00 2.74
3756 4328 7.493320 TCGTCTTAAAAATGTACAGTTCTGTGT 59.507 33.333 9.28 0.00 34.21 3.72
3795 4367 2.034124 ACATTGTTGAGCAGCCAGTTT 58.966 42.857 0.00 0.00 0.00 2.66
3850 4422 9.237187 AGAAAGGGCAAAACTTTTAAAATTCAA 57.763 25.926 0.09 0.00 38.21 2.69
3868 4440 4.772624 ACCAGAAAAGGAAATAGAAAGGGC 59.227 41.667 0.00 0.00 0.00 5.19
3881 4453 6.542005 ACCAAAATTTAAGCAACCAGAAAAGG 59.458 34.615 0.00 0.00 0.00 3.11
3901 4473 5.777223 TCACATTCCAATGAACCATACCAAA 59.223 36.000 6.29 0.00 39.67 3.28
3905 4477 5.829924 AGGATCACATTCCAATGAACCATAC 59.170 40.000 6.29 0.00 39.58 2.39
3907 4479 4.875389 AGGATCACATTCCAATGAACCAT 58.125 39.130 6.29 0.00 39.58 3.55
3920 4492 0.680921 CGCCCCACAAAGGATCACAT 60.681 55.000 0.00 0.00 41.22 3.21
3927 4499 0.325602 TAACTACCGCCCCACAAAGG 59.674 55.000 0.00 0.00 37.03 3.11
3938 4510 6.033619 GCGATATAGCATTTCACTAACTACCG 59.966 42.308 2.59 0.00 37.05 4.02
4150 4723 4.844267 AGTGTGAGTTATCAAACGTTTGC 58.156 39.130 31.42 19.37 46.71 3.68
4216 4799 2.462456 TGCAGGTCAGTAAAGCAGAG 57.538 50.000 0.00 0.00 0.00 3.35
4226 4809 0.036577 CCAGTTCTCCTGCAGGTCAG 60.037 60.000 31.58 22.42 40.06 3.51
4421 5004 6.324512 AGACATCTATATGCATCAGGGAGATC 59.675 42.308 0.19 0.69 36.50 2.75
4533 5118 1.258982 GTCAACTTGACACAGCAGACG 59.741 52.381 15.77 0.00 46.22 4.18
4674 5259 7.967854 TCCATAATGATTGCAGAAAAGTTAACG 59.032 33.333 0.00 0.00 0.00 3.18
4692 5279 4.201950 CGGAAGGAACAAGCTTCCATAATG 60.202 45.833 2.71 0.00 44.95 1.90
4860 5449 4.191161 CGAACGACTTGTAAAAGTGAACG 58.809 43.478 2.08 3.44 32.22 3.95
4872 5461 3.306166 AGTTGTCTGAAACGAACGACTTG 59.694 43.478 0.14 0.00 35.13 3.16
4876 5465 3.153676 TCAGTTGTCTGAAACGAACGA 57.846 42.857 0.14 0.00 46.17 3.85
4891 5480 5.062058 CGTGCAAAACAACTCAATTTCAGTT 59.938 36.000 0.00 0.00 34.24 3.16
4893 5482 4.562394 ACGTGCAAAACAACTCAATTTCAG 59.438 37.500 0.00 0.00 0.00 3.02
4894 5483 4.489810 ACGTGCAAAACAACTCAATTTCA 58.510 34.783 0.00 0.00 0.00 2.69
4895 5484 5.448926 AACGTGCAAAACAACTCAATTTC 57.551 34.783 0.00 0.00 0.00 2.17
4898 5487 5.914635 CAGATAACGTGCAAAACAACTCAAT 59.085 36.000 0.00 0.00 0.00 2.57
4899 5488 5.065346 TCAGATAACGTGCAAAACAACTCAA 59.935 36.000 0.00 0.00 0.00 3.02
4900 5489 4.572795 TCAGATAACGTGCAAAACAACTCA 59.427 37.500 0.00 0.00 0.00 3.41
4901 5490 5.090652 TCAGATAACGTGCAAAACAACTC 57.909 39.130 0.00 0.00 0.00 3.01
4902 5491 5.493133 TTCAGATAACGTGCAAAACAACT 57.507 34.783 0.00 0.00 0.00 3.16
4903 5492 6.198216 ACATTTCAGATAACGTGCAAAACAAC 59.802 34.615 0.00 0.00 0.00 3.32
4904 5493 6.269315 ACATTTCAGATAACGTGCAAAACAA 58.731 32.000 0.00 0.00 0.00 2.83
4905 5494 5.826586 ACATTTCAGATAACGTGCAAAACA 58.173 33.333 0.00 0.00 0.00 2.83
4906 5495 6.142817 AGACATTTCAGATAACGTGCAAAAC 58.857 36.000 0.00 0.00 0.00 2.43
4909 5498 5.929415 TGTAGACATTTCAGATAACGTGCAA 59.071 36.000 0.00 0.00 0.00 4.08
4910 5499 5.474825 TGTAGACATTTCAGATAACGTGCA 58.525 37.500 0.00 0.00 0.00 4.57
4913 5502 6.367969 GGTGTTGTAGACATTTCAGATAACGT 59.632 38.462 0.00 0.00 41.10 3.99
4914 5503 6.590292 AGGTGTTGTAGACATTTCAGATAACG 59.410 38.462 0.00 0.00 41.10 3.18
4915 5504 7.907214 AGGTGTTGTAGACATTTCAGATAAC 57.093 36.000 0.00 0.00 41.10 1.89
4925 5514 9.787435 TTCACTTTTATAAGGTGTTGTAGACAT 57.213 29.630 15.45 0.00 36.37 3.06
4926 5515 9.048446 GTTCACTTTTATAAGGTGTTGTAGACA 57.952 33.333 15.45 0.00 35.61 3.41
4927 5516 9.048446 TGTTCACTTTTATAAGGTGTTGTAGAC 57.952 33.333 15.45 9.43 35.61 2.59
4928 5517 9.268268 CTGTTCACTTTTATAAGGTGTTGTAGA 57.732 33.333 15.45 0.04 35.61 2.59
4929 5518 9.268268 TCTGTTCACTTTTATAAGGTGTTGTAG 57.732 33.333 15.45 11.55 35.61 2.74
4930 5519 9.268268 CTCTGTTCACTTTTATAAGGTGTTGTA 57.732 33.333 15.45 0.80 35.61 2.41
4931 5520 7.773690 ACTCTGTTCACTTTTATAAGGTGTTGT 59.226 33.333 15.45 7.86 35.61 3.32
4932 5521 8.154649 ACTCTGTTCACTTTTATAAGGTGTTG 57.845 34.615 15.45 8.31 35.61 3.33
4933 5522 8.621286 CAACTCTGTTCACTTTTATAAGGTGTT 58.379 33.333 15.45 4.03 35.61 3.32
4934 5523 7.228706 CCAACTCTGTTCACTTTTATAAGGTGT 59.771 37.037 15.45 2.38 35.61 4.16
4935 5524 7.228706 ACCAACTCTGTTCACTTTTATAAGGTG 59.771 37.037 11.87 11.87 35.61 4.00
4936 5525 7.287810 ACCAACTCTGTTCACTTTTATAAGGT 58.712 34.615 0.00 0.00 35.61 3.50
4937 5526 7.745620 ACCAACTCTGTTCACTTTTATAAGG 57.254 36.000 0.00 0.00 35.61 2.69
4942 5531 9.101655 GTAAAGTACCAACTCTGTTCACTTTTA 57.898 33.333 14.09 2.32 36.47 1.52
4952 5541 7.226720 ACATTCAAGTGTAAAGTACCAACTCTG 59.773 37.037 0.00 0.00 33.75 3.35
4957 5546 7.446013 CCCTTACATTCAAGTGTAAAGTACCAA 59.554 37.037 1.75 0.00 42.25 3.67
4958 5547 6.938030 CCCTTACATTCAAGTGTAAAGTACCA 59.062 38.462 1.75 0.00 42.25 3.25
4959 5548 6.938596 ACCCTTACATTCAAGTGTAAAGTACC 59.061 38.462 1.75 0.00 42.25 3.34
5074 5665 9.425248 TCTTATATTTCTTTACGGAGGGAGTAA 57.575 33.333 0.00 0.00 32.84 2.24
5118 5711 8.600625 CATCTATAAGAGCGTCTAGATCACTAC 58.399 40.741 0.00 0.00 37.82 2.73
5129 5722 6.563222 AAGTACTCCATCTATAAGAGCGTC 57.437 41.667 0.00 0.00 0.00 5.19
5143 5736 5.533903 CCTTTAGGTATAGCGAAGTACTCCA 59.466 44.000 15.29 0.00 0.00 3.86
5160 5753 4.709397 AGTCTCTCTGTGTCATCCTTTAGG 59.291 45.833 0.00 0.00 0.00 2.69
5289 7038 4.074259 TCCAGGATGTGATGTTTGTTGAG 58.926 43.478 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.