Multiple sequence alignment - TraesCS2A01G233100

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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 TraesCS2A01G233100 chr2A 100.000 5522 0 0 1 5522 277615353 277609832 0.000000e+00 10198.0
1 TraesCS2A01G233100 chr2D 94.548 1981 63 24 307 2280 205589098 205591040 0.000000e+00 3018.0
2 TraesCS2A01G233100 chr2D 95.379 1450 45 13 2349 3791 205591045 205592479 0.000000e+00 2287.0
3 TraesCS2A01G233100 chr2D 95.562 1014 31 12 3781 4787 205593633 205594639 0.000000e+00 1611.0
4 TraesCS2A01G233100 chr2D 86.967 399 35 10 5123 5519 205612663 205613046 3.060000e-117 433.0
5 TraesCS2A01G233100 chr2D 91.401 314 19 2 1 310 205588709 205589018 1.840000e-114 424.0
6 TraesCS2A01G233100 chr2D 88.186 237 18 4 4896 5123 205612398 205612633 1.960000e-69 274.0
7 TraesCS2A01G233100 chr2D 82.212 208 23 14 4334 4530 175291868 175292072 3.420000e-37 167.0
8 TraesCS2A01G233100 chr2D 92.000 50 4 0 2278 2327 286931441 286931490 2.760000e-08 71.3
9 TraesCS2A01G233100 chr2B 95.649 1586 43 7 3208 4788 259367000 259368564 0.000000e+00 2523.0
10 TraesCS2A01G233100 chr2B 90.514 1402 66 23 1 1390 259363951 259365297 0.000000e+00 1790.0
11 TraesCS2A01G233100 chr2B 93.714 875 43 8 2343 3210 259366071 259366940 0.000000e+00 1301.0
12 TraesCS2A01G233100 chr2B 88.989 445 36 8 5079 5522 259774690 259775122 6.290000e-149 538.0
13 TraesCS2A01G233100 chr2B 87.609 460 35 3 1376 1816 259365351 259365807 1.060000e-141 514.0
14 TraesCS2A01G233100 chr2B 83.849 291 17 13 1997 2284 259365811 259366074 3.300000e-62 250.0
15 TraesCS2A01G233100 chr7D 84.653 202 25 3 4334 4530 65532203 65532403 4.360000e-46 196.0
16 TraesCS2A01G233100 chr1D 79.062 320 36 12 4377 4691 2128029 2127736 2.030000e-44 191.0
17 TraesCS2A01G233100 chr1D 92.063 63 5 0 4629 4691 378103294 378103356 7.620000e-14 89.8
18 TraesCS2A01G233100 chr4B 82.723 191 25 7 4334 4517 559846174 559845985 4.430000e-36 163.0
19 TraesCS2A01G233100 chr5B 96.774 62 2 0 4630 4691 335520877 335520816 2.720000e-18 104.0


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 TraesCS2A01G233100 chr2A 277609832 277615353 5521 True 10198.0 10198 100.0000 1 5522 1 chr2A.!!$R1 5521
1 TraesCS2A01G233100 chr2D 205588709 205594639 5930 False 1835.0 3018 94.2225 1 4787 4 chr2D.!!$F3 4786
2 TraesCS2A01G233100 chr2D 205612398 205613046 648 False 353.5 433 87.5765 4896 5519 2 chr2D.!!$F4 623
3 TraesCS2A01G233100 chr2B 259363951 259368564 4613 False 1275.6 2523 90.2670 1 4788 5 chr2B.!!$F2 4787

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
389 478 0.531753 GTGTTTGCGGCCCATTTTGT 60.532 50.0 0.00 0.00 0.00 2.83 F
1171 1273 0.036388 AATGGCGGACGTGATTCACT 60.036 50.0 14.54 2.27 31.34 3.41 F
2004 2197 0.442310 ACGCCAAATCACGAATGTCG 59.558 50.0 0.00 0.00 46.93 4.35 F
3431 3699 0.118144 AGTTGGGAAGAGGAGGCTCT 59.882 55.0 15.23 0.00 34.76 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2328 2524 0.992695 AAGTAGGTTGAGGAAGGGCC 59.007 55.000 0.00 0.00 0.00 5.80 R
2329 2525 1.628846 TCAAGTAGGTTGAGGAAGGGC 59.371 52.381 0.00 0.00 40.45 5.19 R
3725 3998 0.039618 AAAATCCCGGGCATGTCACT 59.960 50.000 18.49 0.00 0.00 3.41 R
5305 6787 0.033699 AGCAGAGGGGAATGGCTTTC 60.034 55.000 4.63 4.63 0.00 2.62 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
80 81 3.248363 GCCTTTGCGCTTTCATTTTCTTT 59.752 39.130 9.73 0.00 0.00 2.52
159 160 3.951306 TCACGCTTCAGATGTTTTTGTG 58.049 40.909 0.00 0.00 0.00 3.33
160 161 2.468777 CACGCTTCAGATGTTTTTGTGC 59.531 45.455 0.00 0.00 0.00 4.57
161 162 2.098934 ACGCTTCAGATGTTTTTGTGCA 59.901 40.909 0.00 0.00 0.00 4.57
171 173 6.800408 CAGATGTTTTTGTGCAGTTCTGATAG 59.200 38.462 3.84 0.00 32.96 2.08
178 180 8.662781 TTTTGTGCAGTTCTGATAGTATATCC 57.337 34.615 3.84 0.00 0.00 2.59
180 182 4.859798 GTGCAGTTCTGATAGTATATCCGC 59.140 45.833 3.84 0.00 0.00 5.54
217 219 9.753674 TGAACCATATAAAACTCAGGAAAAGAT 57.246 29.630 0.00 0.00 0.00 2.40
389 478 0.531753 GTGTTTGCGGCCCATTTTGT 60.532 50.000 0.00 0.00 0.00 2.83
490 579 1.153489 CCAGAGTGGTCAGATGCCG 60.153 63.158 0.00 0.00 31.35 5.69
507 596 2.742053 TGCCGAGTTTGTCAAATAGAGC 59.258 45.455 0.40 4.19 0.00 4.09
511 600 3.060895 CGAGTTTGTCAAATAGAGCCGTC 59.939 47.826 0.40 0.00 0.00 4.79
573 670 9.403583 GGAATACTACTCCCAAATGTGAAATAA 57.596 33.333 0.00 0.00 0.00 1.40
575 672 9.975218 AATACTACTCCCAAATGTGAAATAAGT 57.025 29.630 0.00 0.00 0.00 2.24
577 674 8.788325 ACTACTCCCAAATGTGAAATAAGTAC 57.212 34.615 0.00 0.00 0.00 2.73
578 675 8.603304 ACTACTCCCAAATGTGAAATAAGTACT 58.397 33.333 0.00 0.00 0.00 2.73
667 764 1.227383 GCCCCACCCTACCAATCTG 59.773 63.158 0.00 0.00 0.00 2.90
679 776 1.276421 ACCAATCTGAGGTCAACCGAG 59.724 52.381 0.00 0.00 42.08 4.63
680 777 1.363744 CAATCTGAGGTCAACCGAGC 58.636 55.000 0.00 0.00 42.08 5.03
781 883 5.066593 CCCTCCCTCAATTATTACAAGCTC 58.933 45.833 0.00 0.00 0.00 4.09
925 1027 4.494091 ACCATATTCTTGTGCTGCTAGT 57.506 40.909 0.00 0.00 0.00 2.57
926 1028 4.194640 ACCATATTCTTGTGCTGCTAGTG 58.805 43.478 0.00 0.00 0.00 2.74
927 1029 3.003068 CCATATTCTTGTGCTGCTAGTGC 59.997 47.826 0.00 3.44 40.20 4.40
928 1030 2.486472 ATTCTTGTGCTGCTAGTGCT 57.514 45.000 0.00 0.00 40.48 4.40
929 1031 3.616956 ATTCTTGTGCTGCTAGTGCTA 57.383 42.857 0.00 0.00 40.48 3.49
930 1032 2.662006 TCTTGTGCTGCTAGTGCTAG 57.338 50.000 0.00 2.04 40.48 3.42
989 1091 2.361357 CGGTGGTCTCGAGGAGGT 60.361 66.667 13.56 0.00 0.00 3.85
1126 1228 3.181472 CCTTGGCCTTCCATTAAAGATGC 60.181 47.826 3.32 0.00 43.05 3.91
1171 1273 0.036388 AATGGCGGACGTGATTCACT 60.036 50.000 14.54 2.27 31.34 3.41
1184 1287 4.455124 GTGATTCACTTGTCGTGCTTAAC 58.545 43.478 9.59 0.00 43.46 2.01
1252 1355 6.514376 CGGTTAGTTTTGCTGGTCAACTATTT 60.514 38.462 0.00 0.00 33.92 1.40
1253 1356 7.207383 GGTTAGTTTTGCTGGTCAACTATTTT 58.793 34.615 0.00 0.00 33.92 1.82
1254 1357 7.709182 GGTTAGTTTTGCTGGTCAACTATTTTT 59.291 33.333 0.00 0.00 33.92 1.94
1255 1358 9.738832 GTTAGTTTTGCTGGTCAACTATTTTTA 57.261 29.630 0.00 0.00 33.92 1.52
1256 1359 9.738832 TTAGTTTTGCTGGTCAACTATTTTTAC 57.261 29.630 0.00 0.00 33.92 2.01
1257 1360 8.007405 AGTTTTGCTGGTCAACTATTTTTACT 57.993 30.769 0.00 0.00 33.73 2.24
1350 1456 8.000780 ACCATGGATCTTTGTATTAGCTTTTC 57.999 34.615 21.47 0.00 0.00 2.29
1355 1461 8.522830 TGGATCTTTGTATTAGCTTTTCTTTGG 58.477 33.333 0.00 0.00 0.00 3.28
1357 1463 9.346725 GATCTTTGTATTAGCTTTTCTTTGGTG 57.653 33.333 0.00 0.00 0.00 4.17
1358 1464 7.657336 TCTTTGTATTAGCTTTTCTTTGGTGG 58.343 34.615 0.00 0.00 0.00 4.61
1368 1474 3.036959 TTTGGTGGGGTGGGGGTT 61.037 61.111 0.00 0.00 0.00 4.11
1607 1800 5.985530 GCAATCAAGAACTACAAAAAGGCTT 59.014 36.000 0.00 0.00 0.00 4.35
1682 1875 3.120546 GGATGTCTCATGTGTTGTCGTTG 60.121 47.826 0.00 0.00 0.00 4.10
1735 1928 5.769835 TGATAGCCCTGGAATGAAGAAATT 58.230 37.500 0.00 0.00 0.00 1.82
1828 2021 7.124573 AGAGCACAATACAGTGGACAATATA 57.875 36.000 0.00 0.00 39.87 0.86
1892 2085 5.640732 CCATGTTTGCTGGTTTAGTATGAC 58.359 41.667 0.00 0.00 0.00 3.06
2004 2197 0.442310 ACGCCAAATCACGAATGTCG 59.558 50.000 0.00 0.00 46.93 4.35
2188 2381 5.071788 TGGAATTTATGAATAGCCGAGGAGT 59.928 40.000 0.00 0.00 0.00 3.85
2204 2398 5.450688 CCGAGGAGTAGAGGAACATAACTTG 60.451 48.000 0.00 0.00 0.00 3.16
2280 2476 5.945784 ACTGTAGCTGGAAAATGCTTGATAA 59.054 36.000 0.00 0.00 40.35 1.75
2281 2477 6.604795 ACTGTAGCTGGAAAATGCTTGATAAT 59.395 34.615 0.00 0.00 40.35 1.28
2284 2480 7.555914 TGTAGCTGGAAAATGCTTGATAATACA 59.444 33.333 0.00 0.00 40.35 2.29
2285 2481 7.592885 AGCTGGAAAATGCTTGATAATACAT 57.407 32.000 0.00 0.00 35.86 2.29
2286 2482 8.015185 AGCTGGAAAATGCTTGATAATACATT 57.985 30.769 0.00 0.00 35.86 2.71
2287 2483 8.480501 AGCTGGAAAATGCTTGATAATACATTT 58.519 29.630 0.00 0.00 42.81 2.32
2322 2518 9.581099 AATTTTCAGAAATATTACGCCGAAATT 57.419 25.926 0.00 0.00 34.44 1.82
2323 2519 8.609478 TTTTCAGAAATATTACGCCGAAATTC 57.391 30.769 0.00 0.00 0.00 2.17
2324 2520 7.548196 TTCAGAAATATTACGCCGAAATTCT 57.452 32.000 0.00 0.00 0.00 2.40
2325 2521 7.548196 TCAGAAATATTACGCCGAAATTCTT 57.452 32.000 0.00 0.00 0.00 2.52
2326 2522 7.981142 TCAGAAATATTACGCCGAAATTCTTT 58.019 30.769 0.00 0.00 0.00 2.52
2327 2523 9.100554 TCAGAAATATTACGCCGAAATTCTTTA 57.899 29.630 0.00 0.00 0.00 1.85
2328 2524 9.370126 CAGAAATATTACGCCGAAATTCTTTAG 57.630 33.333 0.00 0.00 0.00 1.85
2329 2525 8.557029 AGAAATATTACGCCGAAATTCTTTAGG 58.443 33.333 0.00 0.00 38.32 2.69
2336 2532 2.688446 CCGAAATTCTTTAGGCCCTTCC 59.312 50.000 0.00 0.00 0.00 3.46
2338 2534 3.628032 CGAAATTCTTTAGGCCCTTCCTC 59.372 47.826 0.00 0.00 43.20 3.71
2339 2535 4.600062 GAAATTCTTTAGGCCCTTCCTCA 58.400 43.478 0.00 0.00 43.20 3.86
2340 2536 4.675063 AATTCTTTAGGCCCTTCCTCAA 57.325 40.909 0.00 0.00 43.20 3.02
2341 2537 3.434940 TTCTTTAGGCCCTTCCTCAAC 57.565 47.619 0.00 0.00 43.20 3.18
2453 2652 7.604164 TCCAGACAGTTCTAGACAAATTCATTC 59.396 37.037 0.00 0.00 0.00 2.67
2945 3147 3.818210 TGCTTCGATTCCACTTGCTTTAA 59.182 39.130 0.00 0.00 0.00 1.52
3006 3208 7.202016 TGCCTATATGCTAAAATGTTACTGC 57.798 36.000 1.58 0.00 0.00 4.40
3024 3226 3.119173 ACTGCTGAGAGTGTTCTGCTATC 60.119 47.826 0.00 0.00 41.12 2.08
3078 3280 4.331968 TCGGCATAAGGTGAAAAAGATGT 58.668 39.130 0.00 0.00 0.00 3.06
3082 3284 7.040340 TCGGCATAAGGTGAAAAAGATGTAAAA 60.040 33.333 0.00 0.00 0.00 1.52
3091 3293 7.979537 GGTGAAAAAGATGTAAAAGGAAACACT 59.020 33.333 0.00 0.00 0.00 3.55
3134 3336 9.228949 TGGCAATACGTTTTAATAAGGTTAGAA 57.771 29.630 0.00 0.00 0.00 2.10
3200 3406 6.714810 TGTATGGTGTTTTTCTGCAATCTACT 59.285 34.615 0.00 0.00 0.00 2.57
3225 3493 7.182817 TGCAACTACCATACTAGAAACAGAT 57.817 36.000 0.00 0.00 0.00 2.90
3274 3542 3.002656 CACAGCTTATGCCTATTTGGACG 59.997 47.826 0.00 0.00 40.80 4.79
3296 3564 4.201589 CGTAGTCAACTGAATTTACAGCCG 60.202 45.833 0.00 0.00 41.06 5.52
3431 3699 0.118144 AGTTGGGAAGAGGAGGCTCT 59.882 55.000 15.23 0.00 34.76 4.09
3593 3861 5.516696 GCGAGAAATTATTGAGGAAAAAGGC 59.483 40.000 0.00 0.00 0.00 4.35
3684 3952 6.092670 TGCCTGAAAAAGTATCTTCATTCGAG 59.907 38.462 0.00 0.00 31.40 4.04
3725 3998 2.426431 TTCCCCCTGAACCTTGTCTA 57.574 50.000 0.00 0.00 0.00 2.59
3779 4052 0.952497 CAACTGACAGTGGCGCTCAT 60.952 55.000 9.33 0.00 0.00 2.90
3842 5279 8.356657 ACTGTCACAAGCTTATGATCTATACTC 58.643 37.037 11.22 0.00 0.00 2.59
4024 5461 6.683974 TTTCTAATTCTAGCAAGTGATGGC 57.316 37.500 0.00 0.00 0.00 4.40
4027 5464 7.124573 TCTAATTCTAGCAAGTGATGGCTTA 57.875 36.000 0.00 0.00 41.41 3.09
4058 5495 5.468072 GTGATGCCTATAAATCTCACACCAG 59.532 44.000 0.00 0.00 34.57 4.00
4065 5502 7.934120 GCCTATAAATCTCACACCAGTTATTCT 59.066 37.037 0.00 0.00 0.00 2.40
4101 5538 8.887717 GGATCTAACTCATTGCATTATGTATCC 58.112 37.037 0.00 0.00 0.00 2.59
4133 5570 0.394565 AACCAGTCTGTGTCCTCTGC 59.605 55.000 0.00 0.00 0.00 4.26
4143 5580 3.385384 TCCTCTGCCCTCTGTGCG 61.385 66.667 0.00 0.00 0.00 5.34
4172 5609 1.270785 TGGGGATATGCACGCACTATG 60.271 52.381 0.00 0.00 0.00 2.23
4336 5774 3.077359 GCTAAGTTGCATCTGGTGAGTT 58.923 45.455 0.00 0.00 0.00 3.01
4352 5790 5.009110 TGGTGAGTTTACGATTTGCAAATGA 59.991 36.000 28.67 11.19 0.00 2.57
4598 6036 2.753452 TGGTTTTACGGTTTGCTGTTGA 59.247 40.909 0.00 0.00 35.51 3.18
4762 6204 1.593196 TGCGACTTCCTTGGTTTCTG 58.407 50.000 0.00 0.00 0.00 3.02
4788 6230 1.602605 CAGTTGGGTTTCGGGGTCC 60.603 63.158 0.00 0.00 0.00 4.46
4789 6231 2.079911 AGTTGGGTTTCGGGGTCCA 61.080 57.895 0.00 0.00 0.00 4.02
4790 6232 1.900016 GTTGGGTTTCGGGGTCCAC 60.900 63.158 0.00 0.00 0.00 4.02
4791 6233 3.136043 TTGGGTTTCGGGGTCCACC 62.136 63.158 0.00 0.00 39.11 4.61
4792 6234 3.254617 GGGTTTCGGGGTCCACCT 61.255 66.667 0.00 0.00 40.03 4.00
4793 6235 1.919816 GGGTTTCGGGGTCCACCTA 60.920 63.158 0.00 0.00 40.03 3.08
4794 6236 1.297689 GGTTTCGGGGTCCACCTAC 59.702 63.158 0.00 0.00 40.03 3.18
4795 6237 1.297689 GTTTCGGGGTCCACCTACC 59.702 63.158 0.00 0.00 40.03 3.18
4801 6243 4.573261 GGTCCACCTACCCTTCCA 57.427 61.111 0.00 0.00 33.02 3.53
4802 6244 2.297937 GGTCCACCTACCCTTCCAG 58.702 63.158 0.00 0.00 33.02 3.86
4803 6245 1.602771 GTCCACCTACCCTTCCAGC 59.397 63.158 0.00 0.00 0.00 4.85
4804 6246 0.910088 GTCCACCTACCCTTCCAGCT 60.910 60.000 0.00 0.00 0.00 4.24
4805 6247 0.909610 TCCACCTACCCTTCCAGCTG 60.910 60.000 6.78 6.78 0.00 4.24
4806 6248 1.078143 CACCTACCCTTCCAGCTGC 60.078 63.158 8.66 0.00 0.00 5.25
4807 6249 2.187946 CCTACCCTTCCAGCTGCG 59.812 66.667 8.66 1.56 0.00 5.18
4808 6250 2.660064 CCTACCCTTCCAGCTGCGT 61.660 63.158 8.66 1.12 0.00 5.24
4809 6251 1.153549 CTACCCTTCCAGCTGCGTC 60.154 63.158 8.66 0.00 0.00 5.19
4810 6252 1.608717 CTACCCTTCCAGCTGCGTCT 61.609 60.000 8.66 0.00 0.00 4.18
4811 6253 0.323999 TACCCTTCCAGCTGCGTCTA 60.324 55.000 8.66 0.00 0.00 2.59
4812 6254 0.978146 ACCCTTCCAGCTGCGTCTAT 60.978 55.000 8.66 0.00 0.00 1.98
4813 6255 0.531532 CCCTTCCAGCTGCGTCTATG 60.532 60.000 8.66 0.00 0.00 2.23
4814 6256 0.176680 CCTTCCAGCTGCGTCTATGT 59.823 55.000 8.66 0.00 0.00 2.29
4815 6257 1.409064 CCTTCCAGCTGCGTCTATGTA 59.591 52.381 8.66 0.00 0.00 2.29
4816 6258 2.544694 CCTTCCAGCTGCGTCTATGTAG 60.545 54.545 8.66 0.00 0.00 2.74
4817 6259 1.763968 TCCAGCTGCGTCTATGTAGT 58.236 50.000 8.66 0.00 0.00 2.73
4818 6260 1.676529 TCCAGCTGCGTCTATGTAGTC 59.323 52.381 8.66 0.00 0.00 2.59
4819 6261 1.405463 CCAGCTGCGTCTATGTAGTCA 59.595 52.381 8.66 0.00 0.00 3.41
4820 6262 2.035193 CCAGCTGCGTCTATGTAGTCAT 59.965 50.000 8.66 0.00 38.00 3.06
4821 6263 3.491619 CCAGCTGCGTCTATGTAGTCATT 60.492 47.826 8.66 0.00 35.70 2.57
4822 6264 4.115516 CAGCTGCGTCTATGTAGTCATTT 58.884 43.478 0.00 0.00 35.70 2.32
4823 6265 4.568359 CAGCTGCGTCTATGTAGTCATTTT 59.432 41.667 0.00 0.00 35.70 1.82
4824 6266 4.568359 AGCTGCGTCTATGTAGTCATTTTG 59.432 41.667 0.00 0.00 35.70 2.44
4825 6267 4.330074 GCTGCGTCTATGTAGTCATTTTGT 59.670 41.667 0.00 0.00 35.70 2.83
4826 6268 5.500931 GCTGCGTCTATGTAGTCATTTTGTC 60.501 44.000 0.00 0.00 35.70 3.18
4827 6269 5.720202 TGCGTCTATGTAGTCATTTTGTCT 58.280 37.500 0.00 0.00 35.70 3.41
4828 6270 5.576774 TGCGTCTATGTAGTCATTTTGTCTG 59.423 40.000 0.00 0.00 35.70 3.51
4829 6271 5.500931 GCGTCTATGTAGTCATTTTGTCTGC 60.501 44.000 0.00 0.00 35.70 4.26
4830 6272 5.576774 CGTCTATGTAGTCATTTTGTCTGCA 59.423 40.000 0.00 0.00 33.68 4.41
4831 6273 6.454318 CGTCTATGTAGTCATTTTGTCTGCAC 60.454 42.308 0.00 0.00 32.33 4.57
4832 6274 5.874810 TCTATGTAGTCATTTTGTCTGCACC 59.125 40.000 0.00 0.00 32.33 5.01
4833 6275 2.805671 TGTAGTCATTTTGTCTGCACCG 59.194 45.455 0.00 0.00 0.00 4.94
4834 6276 0.593128 AGTCATTTTGTCTGCACCGC 59.407 50.000 0.00 0.00 0.00 5.68
4835 6277 0.725784 GTCATTTTGTCTGCACCGCG 60.726 55.000 0.00 0.00 0.00 6.46
4836 6278 2.082366 CATTTTGTCTGCACCGCGC 61.082 57.895 0.00 0.00 42.89 6.86
4846 6288 4.465512 CACCGCGCAGGCATCAAC 62.466 66.667 16.48 0.00 46.52 3.18
4847 6289 4.704833 ACCGCGCAGGCATCAACT 62.705 61.111 16.48 0.00 46.52 3.16
4848 6290 3.869272 CCGCGCAGGCATCAACTC 61.869 66.667 8.75 0.00 39.92 3.01
4849 6291 3.120385 CGCGCAGGCATCAACTCA 61.120 61.111 8.75 0.00 39.92 3.41
4850 6292 2.679934 CGCGCAGGCATCAACTCAA 61.680 57.895 8.75 0.00 39.92 3.02
4851 6293 1.136147 GCGCAGGCATCAACTCAAG 59.864 57.895 0.30 0.00 39.62 3.02
4852 6294 1.300971 GCGCAGGCATCAACTCAAGA 61.301 55.000 0.30 0.00 39.62 3.02
4853 6295 0.445436 CGCAGGCATCAACTCAAGAC 59.555 55.000 0.00 0.00 0.00 3.01
4854 6296 1.527034 GCAGGCATCAACTCAAGACA 58.473 50.000 0.00 0.00 0.00 3.41
4855 6297 1.881973 GCAGGCATCAACTCAAGACAA 59.118 47.619 0.00 0.00 0.00 3.18
4856 6298 2.490903 GCAGGCATCAACTCAAGACAAT 59.509 45.455 0.00 0.00 0.00 2.71
4857 6299 3.672511 GCAGGCATCAACTCAAGACAATG 60.673 47.826 0.00 0.00 0.00 2.82
4858 6300 2.490903 AGGCATCAACTCAAGACAATGC 59.509 45.455 0.00 0.00 38.95 3.56
4859 6301 2.229543 GGCATCAACTCAAGACAATGCA 59.770 45.455 7.36 0.00 40.89 3.96
4860 6302 3.240069 GCATCAACTCAAGACAATGCAC 58.760 45.455 0.00 0.00 39.36 4.57
4861 6303 3.057736 GCATCAACTCAAGACAATGCACT 60.058 43.478 0.00 0.00 39.36 4.40
4862 6304 4.720090 CATCAACTCAAGACAATGCACTC 58.280 43.478 0.00 0.00 0.00 3.51
4863 6305 3.141398 TCAACTCAAGACAATGCACTCC 58.859 45.455 0.00 0.00 0.00 3.85
4864 6306 3.144506 CAACTCAAGACAATGCACTCCT 58.855 45.455 0.00 0.00 0.00 3.69
4865 6307 3.051081 ACTCAAGACAATGCACTCCTC 57.949 47.619 0.00 0.00 0.00 3.71
4866 6308 2.636893 ACTCAAGACAATGCACTCCTCT 59.363 45.455 0.00 0.00 0.00 3.69
4867 6309 3.260740 CTCAAGACAATGCACTCCTCTC 58.739 50.000 0.00 0.00 0.00 3.20
4868 6310 2.634453 TCAAGACAATGCACTCCTCTCA 59.366 45.455 0.00 0.00 0.00 3.27
4869 6311 3.071457 TCAAGACAATGCACTCCTCTCAA 59.929 43.478 0.00 0.00 0.00 3.02
4870 6312 3.051081 AGACAATGCACTCCTCTCAAC 57.949 47.619 0.00 0.00 0.00 3.18
4871 6313 2.636893 AGACAATGCACTCCTCTCAACT 59.363 45.455 0.00 0.00 0.00 3.16
4872 6314 2.740981 GACAATGCACTCCTCTCAACTG 59.259 50.000 0.00 0.00 0.00 3.16
4873 6315 2.369860 ACAATGCACTCCTCTCAACTGA 59.630 45.455 0.00 0.00 0.00 3.41
4874 6316 2.740981 CAATGCACTCCTCTCAACTGAC 59.259 50.000 0.00 0.00 0.00 3.51
4875 6317 0.315251 TGCACTCCTCTCAACTGACG 59.685 55.000 0.00 0.00 0.00 4.35
4876 6318 1.011451 GCACTCCTCTCAACTGACGC 61.011 60.000 0.00 0.00 0.00 5.19
4877 6319 0.730834 CACTCCTCTCAACTGACGCG 60.731 60.000 3.53 3.53 0.00 6.01
4878 6320 1.153939 CTCCTCTCAACTGACGCGG 60.154 63.158 12.47 0.00 0.00 6.46
4879 6321 2.125912 CCTCTCAACTGACGCGGG 60.126 66.667 12.47 0.00 0.00 6.13
4880 6322 2.651361 CTCTCAACTGACGCGGGT 59.349 61.111 12.47 4.12 0.00 5.28
4881 6323 1.734477 CTCTCAACTGACGCGGGTG 60.734 63.158 10.96 0.81 0.00 4.61
4882 6324 3.414700 CTCAACTGACGCGGGTGC 61.415 66.667 10.96 2.32 37.91 5.01
4883 6325 4.228567 TCAACTGACGCGGGTGCA 62.229 61.111 10.96 7.20 42.97 4.57
4884 6326 3.716006 CAACTGACGCGGGTGCAG 61.716 66.667 21.65 21.65 42.97 4.41
4885 6327 4.988598 AACTGACGCGGGTGCAGG 62.989 66.667 24.66 13.63 42.97 4.85
4897 6339 2.203480 TGCAGGCACCCCTTTGTC 60.203 61.111 0.00 0.00 40.33 3.18
4905 6347 2.125269 CCCCTTTGTCGGCTACGG 60.125 66.667 0.00 0.00 41.39 4.02
4906 6348 2.660802 CCCTTTGTCGGCTACGGT 59.339 61.111 0.00 0.00 41.39 4.83
4911 6353 2.752322 TTTGTCGGCTACGGTGGTCG 62.752 60.000 12.50 12.50 45.88 4.79
4968 6410 4.841617 TCCTCCTCGGCAGGCGAT 62.842 66.667 20.75 0.00 40.12 4.58
4969 6411 2.715181 ATCCTCCTCGGCAGGCGATA 62.715 60.000 20.75 10.29 40.12 2.92
4987 6438 4.183539 GATACCGCAAATCGACTCAAAG 57.816 45.455 0.00 0.00 41.67 2.77
5050 6501 4.846779 TGAGAAAGGGTTTCGAAATTGG 57.153 40.909 14.69 0.00 44.29 3.16
5056 6507 5.560722 AAGGGTTTCGAAATTGGGAAAAT 57.439 34.783 14.69 0.00 34.26 1.82
5057 6508 5.147330 AGGGTTTCGAAATTGGGAAAATC 57.853 39.130 14.69 0.00 34.26 2.17
5061 6512 5.216648 GTTTCGAAATTGGGAAAATCGACA 58.783 37.500 14.69 0.00 41.65 4.35
5066 6517 6.373216 TCGAAATTGGGAAAATCGACATTAGT 59.627 34.615 0.00 0.00 37.59 2.24
5080 6531 9.840427 AATCGACATTAGTCTTTTTACCAAATG 57.160 29.630 0.00 0.00 42.73 2.32
5082 6533 8.286800 TCGACATTAGTCTTTTTACCAAATGTG 58.713 33.333 2.79 0.00 42.73 3.21
5088 6539 9.743057 TTAGTCTTTTTACCAAATGTGTTGATG 57.257 29.630 0.00 0.00 0.00 3.07
5089 6540 6.701400 AGTCTTTTTACCAAATGTGTTGATGC 59.299 34.615 0.00 0.00 0.00 3.91
5103 6554 3.947196 TGTTGATGCTGAACTCTTTGTGT 59.053 39.130 0.00 0.00 0.00 3.72
5137 6618 5.698832 TGTGTTGATTAGCAAAGAATTCGG 58.301 37.500 0.00 0.00 38.44 4.30
5140 6621 7.041030 TGTGTTGATTAGCAAAGAATTCGGTAA 60.041 33.333 0.00 3.18 38.44 2.85
5183 6664 8.529424 TCGAGAGGATTACTACCTTTCATTTA 57.471 34.615 0.00 0.00 38.17 1.40
5236 6718 1.740025 GTCTTGAGGAAAATGGCTCCG 59.260 52.381 0.00 0.00 38.08 4.63
5246 6728 3.561120 ATGGCTCCGAAAACCCGCA 62.561 57.895 0.00 0.00 0.00 5.69
5247 6729 2.750237 GGCTCCGAAAACCCGCAT 60.750 61.111 0.00 0.00 0.00 4.73
5251 6733 1.404035 GCTCCGAAAACCCGCATAAAT 59.596 47.619 0.00 0.00 0.00 1.40
5253 6735 3.303791 GCTCCGAAAACCCGCATAAATAG 60.304 47.826 0.00 0.00 0.00 1.73
5254 6736 4.124238 CTCCGAAAACCCGCATAAATAGA 58.876 43.478 0.00 0.00 0.00 1.98
5256 6738 4.942483 TCCGAAAACCCGCATAAATAGAAA 59.058 37.500 0.00 0.00 0.00 2.52
5257 6739 5.415077 TCCGAAAACCCGCATAAATAGAAAA 59.585 36.000 0.00 0.00 0.00 2.29
5258 6740 5.513849 CCGAAAACCCGCATAAATAGAAAAC 59.486 40.000 0.00 0.00 0.00 2.43
5259 6741 6.087522 CGAAAACCCGCATAAATAGAAAACA 58.912 36.000 0.00 0.00 0.00 2.83
5260 6742 6.583050 CGAAAACCCGCATAAATAGAAAACAA 59.417 34.615 0.00 0.00 0.00 2.83
5261 6743 7.115095 CGAAAACCCGCATAAATAGAAAACAAA 59.885 33.333 0.00 0.00 0.00 2.83
5262 6744 8.664211 AAAACCCGCATAAATAGAAAACAAAA 57.336 26.923 0.00 0.00 0.00 2.44
5263 6745 8.664211 AAACCCGCATAAATAGAAAACAAAAA 57.336 26.923 0.00 0.00 0.00 1.94
5264 6746 8.840833 AACCCGCATAAATAGAAAACAAAAAT 57.159 26.923 0.00 0.00 0.00 1.82
5265 6747 8.250538 ACCCGCATAAATAGAAAACAAAAATG 57.749 30.769 0.00 0.00 0.00 2.32
5293 6775 2.052104 GCGAATCCCCTTTGGTGGG 61.052 63.158 0.00 0.00 46.68 4.61
5347 6829 1.995626 GTCCTCAAGGGCCAGCCTA 60.996 63.158 6.18 0.00 32.49 3.93
5350 6832 2.285668 TCAAGGGCCAGCCTAGCT 60.286 61.111 6.18 0.00 40.77 3.32
5358 6840 2.034607 CCAGCCTAGCTACCTCGAC 58.965 63.158 0.00 0.00 36.40 4.20
5387 6869 4.870426 TCATACGAGTTCCTTTGAAGATGC 59.130 41.667 0.00 0.00 0.00 3.91
5396 6878 3.118261 TCCTTTGAAGATGCGCCTATTCT 60.118 43.478 18.56 7.39 0.00 2.40
5402 6884 2.042464 AGATGCGCCTATTCTTCTCCA 58.958 47.619 4.18 0.00 0.00 3.86
5409 6891 4.199310 CGCCTATTCTTCTCCATCCAAAA 58.801 43.478 0.00 0.00 0.00 2.44
5410 6892 4.640201 CGCCTATTCTTCTCCATCCAAAAA 59.360 41.667 0.00 0.00 0.00 1.94
5434 6916 1.666872 GTACCACTGTGCCGACACC 60.667 63.158 1.29 0.00 46.86 4.16
5435 6917 3.215597 TACCACTGTGCCGACACCG 62.216 63.158 1.29 0.00 46.86 4.94
5454 6936 0.809241 GCTCCTCGCATGAGAACCAG 60.809 60.000 0.00 0.00 45.57 4.00
5468 6950 1.478105 GAACCAGGAAATCATGCCACC 59.522 52.381 0.00 0.00 0.00 4.61
5469 6951 0.324645 ACCAGGAAATCATGCCACCC 60.325 55.000 0.00 0.00 0.00 4.61
5479 6961 3.315952 ATGCCACCCCACCATTCCC 62.316 63.158 0.00 0.00 0.00 3.97
5482 6964 2.857889 CACCCCACCATTCCCCAA 59.142 61.111 0.00 0.00 0.00 4.12
5485 6967 2.065789 CCCCACCATTCCCCAATGC 61.066 63.158 0.00 0.00 38.53 3.56
5489 6971 0.324552 CACCATTCCCCAATGCCAGA 60.325 55.000 0.00 0.00 38.53 3.86
5490 6972 0.032813 ACCATTCCCCAATGCCAGAG 60.033 55.000 0.00 0.00 38.53 3.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
80 81 8.934507 AAAAAGGAAACGACAAAATGTATTCA 57.065 26.923 0.00 0.00 0.00 2.57
110 111 9.040939 ACTGAAATTCGGTTTATTTCAAAAAGG 57.959 29.630 0.85 3.84 45.93 3.11
114 115 8.625651 TGAGACTGAAATTCGGTTTATTTCAAA 58.374 29.630 9.04 0.00 45.93 2.69
115 116 8.073768 GTGAGACTGAAATTCGGTTTATTTCAA 58.926 33.333 9.04 0.00 45.93 2.69
116 117 7.570507 CGTGAGACTGAAATTCGGTTTATTTCA 60.571 37.037 9.04 9.77 45.06 2.69
117 118 6.736853 CGTGAGACTGAAATTCGGTTTATTTC 59.263 38.462 9.04 0.00 40.66 2.17
159 160 5.060662 TGCGGATATACTATCAGAACTGC 57.939 43.478 0.00 0.00 0.00 4.40
160 161 8.539770 AATTTGCGGATATACTATCAGAACTG 57.460 34.615 0.00 0.00 0.00 3.16
171 173 7.116662 TGGTTCACGTATAATTTGCGGATATAC 59.883 37.037 0.00 0.00 37.81 1.47
178 180 9.653067 TTTTATATGGTTCACGTATAATTTGCG 57.347 29.630 0.00 0.00 41.06 4.85
187 189 7.172868 TCCTGAGTTTTATATGGTTCACGTA 57.827 36.000 0.00 0.00 0.00 3.57
189 191 6.978343 TTCCTGAGTTTTATATGGTTCACG 57.022 37.500 0.00 0.00 0.00 4.35
217 219 5.196695 TGGTATGGCTTTGTATGCAACATA 58.803 37.500 0.00 0.00 38.10 2.29
256 262 5.751680 CCACTAAATCATTGGTATGCTTCG 58.248 41.667 0.00 0.00 0.00 3.79
266 272 3.514645 GCCACTTGCCACTAAATCATTG 58.485 45.455 0.00 0.00 0.00 2.82
440 529 6.486248 TGACAAGCTATCGATAAAAACATGC 58.514 36.000 6.58 4.64 0.00 4.06
452 541 2.614057 GGGGTTTCATGACAAGCTATCG 59.386 50.000 14.87 0.00 0.00 2.92
490 579 3.994392 TGACGGCTCTATTTGACAAACTC 59.006 43.478 1.94 0.00 0.00 3.01
507 596 1.506262 CGGGGCAAAAATCTGACGG 59.494 57.895 0.00 0.00 0.00 4.79
511 600 0.611896 AGGACCGGGGCAAAAATCTG 60.612 55.000 6.32 0.00 0.00 2.90
546 636 5.018539 TCACATTTGGGAGTAGTATTCCG 57.981 43.478 5.68 0.00 35.48 4.30
551 641 9.880157 GTACTTATTTCACATTTGGGAGTAGTA 57.120 33.333 0.00 0.00 0.00 1.82
552 642 8.603304 AGTACTTATTTCACATTTGGGAGTAGT 58.397 33.333 0.00 0.00 0.00 2.73
553 643 9.449719 AAGTACTTATTTCACATTTGGGAGTAG 57.550 33.333 6.26 0.00 0.00 2.57
573 670 5.280521 CCCTGTCCTTTTCATACCAAGTACT 60.281 44.000 0.00 0.00 0.00 2.73
574 671 4.941873 CCCTGTCCTTTTCATACCAAGTAC 59.058 45.833 0.00 0.00 0.00 2.73
575 672 4.018779 CCCCTGTCCTTTTCATACCAAGTA 60.019 45.833 0.00 0.00 0.00 2.24
576 673 3.245264 CCCCTGTCCTTTTCATACCAAGT 60.245 47.826 0.00 0.00 0.00 3.16
577 674 3.356290 CCCCTGTCCTTTTCATACCAAG 58.644 50.000 0.00 0.00 0.00 3.61
578 675 2.042433 CCCCCTGTCCTTTTCATACCAA 59.958 50.000 0.00 0.00 0.00 3.67
667 764 0.389757 GGATAGGCTCGGTTGACCTC 59.610 60.000 0.00 0.00 34.92 3.85
679 776 1.881498 GCTGGATCTTGCTGGATAGGC 60.881 57.143 0.00 0.00 0.00 3.93
680 777 1.271271 GGCTGGATCTTGCTGGATAGG 60.271 57.143 9.56 0.00 0.00 2.57
738 836 2.204090 GGAGGAGGGGTTGGTGGA 60.204 66.667 0.00 0.00 0.00 4.02
781 883 7.467623 GGTCTGAAGTGATTAACAATGCTAAG 58.532 38.462 0.00 0.00 0.00 2.18
927 1029 1.245376 GGTCGCCCCTAGCTAGCTAG 61.245 65.000 35.39 35.39 44.07 3.42
928 1030 1.228490 GGTCGCCCCTAGCTAGCTA 60.228 63.158 22.85 22.85 40.39 3.32
929 1031 2.522193 GGTCGCCCCTAGCTAGCT 60.522 66.667 23.12 23.12 40.39 3.32
930 1032 3.979739 CGGTCGCCCCTAGCTAGC 61.980 72.222 15.74 6.62 40.39 3.42
989 1091 3.238497 CGGCCATGGGATCGGGTA 61.238 66.667 15.13 0.00 0.00 3.69
1136 1238 2.350522 CCATTTCACGGGTCTCTCAAG 58.649 52.381 0.00 0.00 0.00 3.02
1171 1273 1.933500 GCTCGGAGTTAAGCACGACAA 60.934 52.381 6.90 0.00 38.42 3.18
1184 1287 0.179089 CTCCCAAGACATGCTCGGAG 60.179 60.000 0.00 0.00 36.98 4.63
1252 1355 5.938125 GCATCACTGGAGAAGGTAAAGTAAA 59.062 40.000 0.00 0.00 0.00 2.01
1253 1356 5.012664 TGCATCACTGGAGAAGGTAAAGTAA 59.987 40.000 0.00 0.00 0.00 2.24
1254 1357 4.530553 TGCATCACTGGAGAAGGTAAAGTA 59.469 41.667 0.00 0.00 0.00 2.24
1255 1358 3.327757 TGCATCACTGGAGAAGGTAAAGT 59.672 43.478 0.00 0.00 0.00 2.66
1256 1359 3.937706 CTGCATCACTGGAGAAGGTAAAG 59.062 47.826 0.00 0.00 43.06 1.85
1257 1360 3.582647 TCTGCATCACTGGAGAAGGTAAA 59.417 43.478 0.00 0.00 45.62 2.01
1350 1456 3.094751 AACCCCCACCCCACCAAAG 62.095 63.158 0.00 0.00 0.00 2.77
1419 1593 9.555727 TTAATACATCCAGCTATTGAAACCTAC 57.444 33.333 0.00 0.00 0.00 3.18
1607 1800 6.899089 TGAGGGACATATAGATTTTGCTTCA 58.101 36.000 0.00 0.00 0.00 3.02
1682 1875 5.767816 ACAGGGAATTTATATTGTTCGCC 57.232 39.130 0.00 0.00 35.98 5.54
1735 1928 2.470057 AAAGGGTTTGCTTCCTCCAA 57.530 45.000 0.00 0.00 32.02 3.53
1791 1984 4.471904 TTGTGCTCTCCTACCATACTTG 57.528 45.455 0.00 0.00 0.00 3.16
1828 2021 7.448469 AGTGTCAATTAAAATCTAAGCCTGTGT 59.552 33.333 0.00 0.00 0.00 3.72
1922 2115 5.754782 ACAATATAATCCACTCCAGTGCAA 58.245 37.500 0.76 0.00 44.34 4.08
2004 2197 4.374399 TCCACGTTTTTCTGTAGGAGAAC 58.626 43.478 0.00 0.00 40.60 3.01
2006 2199 4.675976 TTCCACGTTTTTCTGTAGGAGA 57.324 40.909 0.00 0.00 0.00 3.71
2007 2200 5.689819 CAATTCCACGTTTTTCTGTAGGAG 58.310 41.667 0.00 0.00 0.00 3.69
2296 2492 9.581099 AATTTCGGCGTAATATTTCTGAAAATT 57.419 25.926 12.14 6.71 37.36 1.82
2297 2493 9.233232 GAATTTCGGCGTAATATTTCTGAAAAT 57.767 29.630 12.14 11.53 37.36 1.82
2298 2494 8.455682 AGAATTTCGGCGTAATATTTCTGAAAA 58.544 29.630 12.14 0.00 37.36 2.29
2299 2495 7.981142 AGAATTTCGGCGTAATATTTCTGAAA 58.019 30.769 12.14 5.15 37.95 2.69
2300 2496 7.548196 AGAATTTCGGCGTAATATTTCTGAA 57.452 32.000 12.14 0.00 0.00 3.02
2301 2497 7.548196 AAGAATTTCGGCGTAATATTTCTGA 57.452 32.000 12.14 0.00 0.00 3.27
2302 2498 9.370126 CTAAAGAATTTCGGCGTAATATTTCTG 57.630 33.333 18.58 12.57 40.09 3.02
2303 2499 8.557029 CCTAAAGAATTTCGGCGTAATATTTCT 58.443 33.333 18.58 13.55 40.09 2.52
2304 2500 8.709496 CCTAAAGAATTTCGGCGTAATATTTC 57.291 34.615 18.58 11.97 40.09 2.17
2315 2511 2.688446 GGAAGGGCCTAAAGAATTTCGG 59.312 50.000 6.41 0.00 43.25 4.30
2328 2524 0.992695 AAGTAGGTTGAGGAAGGGCC 59.007 55.000 0.00 0.00 0.00 5.80
2329 2525 1.628846 TCAAGTAGGTTGAGGAAGGGC 59.371 52.381 0.00 0.00 40.45 5.19
2330 2526 2.637872 TGTCAAGTAGGTTGAGGAAGGG 59.362 50.000 0.00 0.00 46.18 3.95
2331 2527 4.256920 CATGTCAAGTAGGTTGAGGAAGG 58.743 47.826 0.00 0.00 46.18 3.46
2332 2528 3.686726 GCATGTCAAGTAGGTTGAGGAAG 59.313 47.826 0.00 0.00 46.18 3.46
2333 2529 3.327757 AGCATGTCAAGTAGGTTGAGGAA 59.672 43.478 0.00 0.00 46.18 3.36
2334 2530 2.906389 AGCATGTCAAGTAGGTTGAGGA 59.094 45.455 0.00 0.00 46.18 3.71
2335 2531 3.340814 AGCATGTCAAGTAGGTTGAGG 57.659 47.619 0.00 0.00 46.18 3.86
2336 2532 4.067896 ACAAGCATGTCAAGTAGGTTGAG 58.932 43.478 9.76 0.00 46.18 3.02
2337 2533 3.814842 CACAAGCATGTCAAGTAGGTTGA 59.185 43.478 9.76 0.00 43.26 3.18
2338 2534 3.814842 TCACAAGCATGTCAAGTAGGTTG 59.185 43.478 0.00 0.00 43.07 3.77
2339 2535 4.067896 CTCACAAGCATGTCAAGTAGGTT 58.932 43.478 0.00 0.00 37.82 3.50
2340 2536 3.071602 ACTCACAAGCATGTCAAGTAGGT 59.928 43.478 5.15 0.00 37.82 3.08
2341 2537 3.668447 ACTCACAAGCATGTCAAGTAGG 58.332 45.455 5.15 0.00 37.82 3.18
2397 2596 4.445452 AGTGCATAACATTTCAAGGCAG 57.555 40.909 0.00 0.00 0.00 4.85
2446 2645 7.872138 TGTCTAAATAGTTCCCCAGAATGAAT 58.128 34.615 0.00 0.00 39.69 2.57
2453 2652 3.456277 AGCCTGTCTAAATAGTTCCCCAG 59.544 47.826 0.00 0.00 0.00 4.45
2953 3155 4.558697 GCAATTACTGAACTTTGACCCCAC 60.559 45.833 0.00 0.00 0.00 4.61
2954 3156 3.572255 GCAATTACTGAACTTTGACCCCA 59.428 43.478 0.00 0.00 0.00 4.96
3006 3208 7.040548 TGAGATATGATAGCAGAACACTCTCAG 60.041 40.741 3.25 0.00 34.18 3.35
3091 3293 5.798125 TTGCCAACATTACTGATTGGAAA 57.202 34.783 14.37 9.63 44.84 3.13
3146 3351 2.203800 TATGCACTTCTTAGCCGACG 57.796 50.000 0.00 0.00 0.00 5.12
3200 3406 6.999950 TCTGTTTCTAGTATGGTAGTTGCAA 58.000 36.000 0.00 0.00 0.00 4.08
3225 3493 7.991084 TTAAGTCGCTACCTATATTGCTCTA 57.009 36.000 0.00 0.00 0.00 2.43
3274 3542 4.689345 ACGGCTGTAAATTCAGTTGACTAC 59.311 41.667 0.00 0.00 37.70 2.73
3593 3861 3.068560 TGGTAGGTTCGAAACAAATCCG 58.931 45.455 16.95 0.00 0.00 4.18
3710 3983 3.320673 GTCACTAGACAAGGTTCAGGG 57.679 52.381 0.00 0.00 44.34 4.45
3725 3998 0.039618 AAAATCCCGGGCATGTCACT 59.960 50.000 18.49 0.00 0.00 3.41
3779 4052 6.881065 AGAAAACTGCTATTAGCTGAATCACA 59.119 34.615 24.20 0.00 41.94 3.58
3817 5254 8.575589 AGAGTATAGATCATAAGCTTGTGACAG 58.424 37.037 25.81 0.00 31.01 3.51
3842 5279 6.094048 ACATGTTCGGAATTGAACCTCAATAG 59.906 38.462 2.45 0.00 45.57 1.73
4054 5491 6.078456 TCCAATCCATCAAGAATAACTGGT 57.922 37.500 0.00 0.00 0.00 4.00
4058 5495 9.566432 AGTTAGATCCAATCCATCAAGAATAAC 57.434 33.333 0.00 0.00 0.00 1.89
4065 5502 6.263842 GCAATGAGTTAGATCCAATCCATCAA 59.736 38.462 0.00 0.00 0.00 2.57
4101 5538 5.349817 CACAGACTGGTTTATACTGAGCTTG 59.650 44.000 7.51 0.00 33.53 4.01
4133 5570 1.043816 ATAGATGACCGCACAGAGGG 58.956 55.000 0.00 0.00 0.00 4.30
4143 5580 3.679917 CGTGCATATCCCCATAGATGACC 60.680 52.174 0.00 0.00 0.00 4.02
4336 5774 6.526325 GCATTAGTGTCATTTGCAAATCGTAA 59.474 34.615 21.70 13.92 33.58 3.18
4352 5790 5.512753 TTGTGTCATGTTTGCATTAGTGT 57.487 34.783 0.00 0.00 31.99 3.55
4365 5803 5.396484 GTCATCACCTGAATTTGTGTCATG 58.604 41.667 0.00 0.00 35.07 3.07
4443 5881 0.392193 CCTGCTCCGTCAGATGCTTT 60.392 55.000 0.00 0.00 36.19 3.51
4545 5983 8.519526 ACACAAAAGAAATTGTACACTTGAGAA 58.480 29.630 0.00 0.00 41.44 2.87
4598 6036 8.519799 AAAGATTAAACACAATATCCGACCAT 57.480 30.769 0.00 0.00 0.00 3.55
4741 6183 2.357637 CAGAAACCAAGGAAGTCGCAAA 59.642 45.455 0.00 0.00 0.00 3.68
4788 6230 1.078143 GCAGCTGGAAGGGTAGGTG 60.078 63.158 17.12 0.00 43.34 4.00
4789 6231 2.660064 CGCAGCTGGAAGGGTAGGT 61.660 63.158 17.12 0.00 0.00 3.08
4790 6232 2.187946 CGCAGCTGGAAGGGTAGG 59.812 66.667 17.12 0.00 0.00 3.18
4791 6233 1.153549 GACGCAGCTGGAAGGGTAG 60.154 63.158 17.12 0.00 0.00 3.18
4792 6234 0.323999 TAGACGCAGCTGGAAGGGTA 60.324 55.000 17.12 0.00 0.00 3.69
4793 6235 0.978146 ATAGACGCAGCTGGAAGGGT 60.978 55.000 17.12 3.17 0.00 4.34
4794 6236 0.531532 CATAGACGCAGCTGGAAGGG 60.532 60.000 17.12 0.00 0.00 3.95
4795 6237 0.176680 ACATAGACGCAGCTGGAAGG 59.823 55.000 17.12 2.28 0.00 3.46
4796 6238 2.099921 ACTACATAGACGCAGCTGGAAG 59.900 50.000 17.12 0.00 0.00 3.46
4797 6239 2.099263 GACTACATAGACGCAGCTGGAA 59.901 50.000 17.12 0.00 0.00 3.53
4798 6240 1.676529 GACTACATAGACGCAGCTGGA 59.323 52.381 17.12 0.00 0.00 3.86
4799 6241 1.405463 TGACTACATAGACGCAGCTGG 59.595 52.381 17.12 8.27 0.00 4.85
4800 6242 2.851805 TGACTACATAGACGCAGCTG 57.148 50.000 10.11 10.11 0.00 4.24
4801 6243 4.392921 AAATGACTACATAGACGCAGCT 57.607 40.909 0.00 0.00 35.50 4.24
4802 6244 4.330074 ACAAAATGACTACATAGACGCAGC 59.670 41.667 0.00 0.00 35.50 5.25
4803 6245 5.807520 AGACAAAATGACTACATAGACGCAG 59.192 40.000 0.00 0.00 35.50 5.18
4804 6246 5.576774 CAGACAAAATGACTACATAGACGCA 59.423 40.000 0.00 0.00 35.50 5.24
4805 6247 5.500931 GCAGACAAAATGACTACATAGACGC 60.501 44.000 0.00 0.00 35.50 5.19
4806 6248 5.576774 TGCAGACAAAATGACTACATAGACG 59.423 40.000 0.00 0.00 35.50 4.18
4807 6249 6.183360 GGTGCAGACAAAATGACTACATAGAC 60.183 42.308 0.00 0.00 35.50 2.59
4808 6250 5.874810 GGTGCAGACAAAATGACTACATAGA 59.125 40.000 0.00 0.00 35.50 1.98
4809 6251 5.220472 CGGTGCAGACAAAATGACTACATAG 60.220 44.000 0.00 0.00 35.50 2.23
4810 6252 4.629634 CGGTGCAGACAAAATGACTACATA 59.370 41.667 0.00 0.00 35.50 2.29
4811 6253 3.436704 CGGTGCAGACAAAATGACTACAT 59.563 43.478 0.00 0.00 38.50 2.29
4812 6254 2.805671 CGGTGCAGACAAAATGACTACA 59.194 45.455 0.00 0.00 0.00 2.74
4813 6255 2.412847 GCGGTGCAGACAAAATGACTAC 60.413 50.000 0.00 0.00 0.00 2.73
4814 6256 1.804151 GCGGTGCAGACAAAATGACTA 59.196 47.619 0.00 0.00 0.00 2.59
4815 6257 0.593128 GCGGTGCAGACAAAATGACT 59.407 50.000 0.00 0.00 0.00 3.41
4816 6258 0.725784 CGCGGTGCAGACAAAATGAC 60.726 55.000 0.00 0.00 0.00 3.06
4817 6259 1.573932 CGCGGTGCAGACAAAATGA 59.426 52.632 0.00 0.00 0.00 2.57
4818 6260 2.082366 GCGCGGTGCAGACAAAATG 61.082 57.895 8.83 0.00 45.45 2.32
4819 6261 2.255252 GCGCGGTGCAGACAAAAT 59.745 55.556 8.83 0.00 45.45 1.82
4829 6271 4.465512 GTTGATGCCTGCGCGGTG 62.466 66.667 16.49 7.92 38.08 4.94
4830 6272 4.704833 AGTTGATGCCTGCGCGGT 62.705 61.111 16.49 0.00 38.08 5.68
4831 6273 3.869272 GAGTTGATGCCTGCGCGG 61.869 66.667 9.96 9.96 38.08 6.46
4832 6274 2.573341 CTTGAGTTGATGCCTGCGCG 62.573 60.000 0.00 0.00 38.08 6.86
4833 6275 1.136147 CTTGAGTTGATGCCTGCGC 59.864 57.895 0.00 0.00 0.00 6.09
4834 6276 0.445436 GTCTTGAGTTGATGCCTGCG 59.555 55.000 0.00 0.00 0.00 5.18
4835 6277 1.527034 TGTCTTGAGTTGATGCCTGC 58.473 50.000 0.00 0.00 0.00 4.85
4836 6278 3.672511 GCATTGTCTTGAGTTGATGCCTG 60.673 47.826 0.00 0.00 35.16 4.85
4837 6279 2.490903 GCATTGTCTTGAGTTGATGCCT 59.509 45.455 0.00 0.00 35.16 4.75
4838 6280 2.229543 TGCATTGTCTTGAGTTGATGCC 59.770 45.455 0.00 0.00 39.18 4.40
4839 6281 3.057736 AGTGCATTGTCTTGAGTTGATGC 60.058 43.478 0.00 0.00 40.07 3.91
4840 6282 4.379186 GGAGTGCATTGTCTTGAGTTGATG 60.379 45.833 0.00 0.00 0.00 3.07
4841 6283 3.755378 GGAGTGCATTGTCTTGAGTTGAT 59.245 43.478 0.00 0.00 0.00 2.57
4842 6284 3.141398 GGAGTGCATTGTCTTGAGTTGA 58.859 45.455 0.00 0.00 0.00 3.18
4843 6285 3.144506 AGGAGTGCATTGTCTTGAGTTG 58.855 45.455 0.00 0.00 0.00 3.16
4844 6286 3.072184 AGAGGAGTGCATTGTCTTGAGTT 59.928 43.478 0.00 0.00 0.00 3.01
4845 6287 2.636893 AGAGGAGTGCATTGTCTTGAGT 59.363 45.455 0.00 0.00 0.00 3.41
4846 6288 3.260740 GAGAGGAGTGCATTGTCTTGAG 58.739 50.000 0.00 0.00 0.00 3.02
4847 6289 2.634453 TGAGAGGAGTGCATTGTCTTGA 59.366 45.455 0.00 0.00 0.00 3.02
4848 6290 3.049708 TGAGAGGAGTGCATTGTCTTG 57.950 47.619 0.00 0.00 0.00 3.02
4849 6291 3.072184 AGTTGAGAGGAGTGCATTGTCTT 59.928 43.478 0.00 0.00 0.00 3.01
4850 6292 2.636893 AGTTGAGAGGAGTGCATTGTCT 59.363 45.455 0.00 0.00 0.00 3.41
4851 6293 2.740981 CAGTTGAGAGGAGTGCATTGTC 59.259 50.000 0.00 0.00 0.00 3.18
4852 6294 2.369860 TCAGTTGAGAGGAGTGCATTGT 59.630 45.455 0.00 0.00 0.00 2.71
4853 6295 2.740981 GTCAGTTGAGAGGAGTGCATTG 59.259 50.000 0.00 0.00 0.00 2.82
4854 6296 2.611473 CGTCAGTTGAGAGGAGTGCATT 60.611 50.000 0.00 0.00 0.00 3.56
4855 6297 1.067283 CGTCAGTTGAGAGGAGTGCAT 60.067 52.381 0.00 0.00 0.00 3.96
4856 6298 0.315251 CGTCAGTTGAGAGGAGTGCA 59.685 55.000 0.00 0.00 0.00 4.57
4857 6299 1.011451 GCGTCAGTTGAGAGGAGTGC 61.011 60.000 0.00 0.00 0.00 4.40
4858 6300 0.730834 CGCGTCAGTTGAGAGGAGTG 60.731 60.000 0.00 0.00 0.00 3.51
4859 6301 1.581954 CGCGTCAGTTGAGAGGAGT 59.418 57.895 0.00 0.00 0.00 3.85
4860 6302 1.153939 CCGCGTCAGTTGAGAGGAG 60.154 63.158 4.92 0.00 0.00 3.69
4861 6303 2.636412 CCCGCGTCAGTTGAGAGGA 61.636 63.158 4.92 0.00 0.00 3.71
4862 6304 2.125912 CCCGCGTCAGTTGAGAGG 60.126 66.667 4.92 0.00 0.00 3.69
4863 6305 1.734477 CACCCGCGTCAGTTGAGAG 60.734 63.158 4.92 0.00 0.00 3.20
4864 6306 2.338620 CACCCGCGTCAGTTGAGA 59.661 61.111 4.92 0.00 0.00 3.27
4865 6307 3.414700 GCACCCGCGTCAGTTGAG 61.415 66.667 4.92 0.00 0.00 3.02
4866 6308 4.228567 TGCACCCGCGTCAGTTGA 62.229 61.111 4.92 0.00 42.97 3.18
4867 6309 3.716006 CTGCACCCGCGTCAGTTG 61.716 66.667 4.92 0.00 42.97 3.16
4868 6310 4.988598 CCTGCACCCGCGTCAGTT 62.989 66.667 4.92 0.00 42.97 3.16
4879 6321 2.521708 ACAAAGGGGTGCCTGCAC 60.522 61.111 13.75 13.75 45.49 4.57
4880 6322 2.203480 GACAAAGGGGTGCCTGCA 60.203 61.111 0.00 0.00 0.00 4.41
4881 6323 3.365265 CGACAAAGGGGTGCCTGC 61.365 66.667 0.00 0.00 0.00 4.85
4882 6324 2.672996 CCGACAAAGGGGTGCCTG 60.673 66.667 0.00 0.00 0.00 4.85
4883 6325 4.660938 GCCGACAAAGGGGTGCCT 62.661 66.667 0.00 0.00 0.00 4.75
4884 6326 3.262448 TAGCCGACAAAGGGGTGCC 62.262 63.158 0.00 0.00 36.51 5.01
4885 6327 2.038837 GTAGCCGACAAAGGGGTGC 61.039 63.158 0.00 0.00 36.51 5.01
4886 6328 1.740296 CGTAGCCGACAAAGGGGTG 60.740 63.158 0.00 0.00 36.51 4.61
4887 6329 2.660802 CGTAGCCGACAAAGGGGT 59.339 61.111 0.00 0.00 39.02 4.95
4888 6330 2.125269 CCGTAGCCGACAAAGGGG 60.125 66.667 0.00 0.00 35.63 4.79
4889 6331 1.740296 CACCGTAGCCGACAAAGGG 60.740 63.158 0.00 0.00 35.63 3.95
4890 6332 1.740296 CCACCGTAGCCGACAAAGG 60.740 63.158 0.00 0.00 35.63 3.11
4891 6333 1.005394 ACCACCGTAGCCGACAAAG 60.005 57.895 0.00 0.00 35.63 2.77
4892 6334 1.005867 GACCACCGTAGCCGACAAA 60.006 57.895 0.00 0.00 35.63 2.83
4893 6335 2.652530 GACCACCGTAGCCGACAA 59.347 61.111 0.00 0.00 35.63 3.18
4894 6336 3.740397 CGACCACCGTAGCCGACA 61.740 66.667 0.00 0.00 35.63 4.35
4911 6353 2.218603 AGGTTGTGACATGAACGGAAC 58.781 47.619 0.00 0.00 0.00 3.62
4914 6356 2.069273 GAGAGGTTGTGACATGAACGG 58.931 52.381 0.00 0.00 0.00 4.44
4968 6410 3.306917 TCTTTGAGTCGATTTGCGGTA 57.693 42.857 0.00 0.00 41.33 4.02
4969 6411 2.163818 TCTTTGAGTCGATTTGCGGT 57.836 45.000 0.00 0.00 41.33 5.68
5000 6451 2.564771 TCTTCAAGCACTCACACCAAG 58.435 47.619 0.00 0.00 0.00 3.61
5043 6494 7.971004 GACTAATGTCGATTTTCCCAATTTC 57.029 36.000 0.00 0.00 33.15 2.17
5066 6517 6.700960 CAGCATCAACACATTTGGTAAAAAGA 59.299 34.615 0.00 0.00 0.00 2.52
5080 6531 4.201950 ACACAAAGAGTTCAGCATCAACAC 60.202 41.667 0.00 0.00 0.00 3.32
5082 6533 4.558538 ACACAAAGAGTTCAGCATCAAC 57.441 40.909 0.00 0.00 0.00 3.18
5088 6539 7.861630 TGAATTTAGTACACAAAGAGTTCAGC 58.138 34.615 0.00 0.00 0.00 4.26
5089 6540 9.817365 CATGAATTTAGTACACAAAGAGTTCAG 57.183 33.333 0.00 0.00 0.00 3.02
5150 6631 3.150767 AGTAATCCTCTCGATTCCTCGG 58.849 50.000 0.00 0.00 45.10 4.63
5183 6664 6.262273 CCTCTTGTTAATATGCATTTACCCGT 59.738 38.462 3.54 0.00 0.00 5.28
5193 6675 4.508124 CGAGTCCACCTCTTGTTAATATGC 59.492 45.833 0.00 0.00 38.11 3.14
5200 6682 1.705873 AGACGAGTCCACCTCTTGTT 58.294 50.000 0.00 0.00 38.11 2.83
5218 6700 2.113860 TCGGAGCCATTTTCCTCAAG 57.886 50.000 0.00 0.00 32.34 3.02
5224 6706 1.402325 CGGGTTTTCGGAGCCATTTTC 60.402 52.381 4.08 0.00 37.01 2.29
5230 6712 1.027792 TTATGCGGGTTTTCGGAGCC 61.028 55.000 0.00 0.00 33.32 4.70
5236 6718 7.876896 TTGTTTTCTATTTATGCGGGTTTTC 57.123 32.000 0.00 0.00 0.00 2.29
5251 6733 7.145323 GCTAGTTGGCTCATTTTTGTTTTCTA 58.855 34.615 0.00 0.00 0.00 2.10
5253 6735 5.107875 CGCTAGTTGGCTCATTTTTGTTTTC 60.108 40.000 0.00 0.00 0.00 2.29
5254 6736 4.744631 CGCTAGTTGGCTCATTTTTGTTTT 59.255 37.500 0.00 0.00 0.00 2.43
5256 6738 3.568007 TCGCTAGTTGGCTCATTTTTGTT 59.432 39.130 0.00 0.00 0.00 2.83
5257 6739 3.146066 TCGCTAGTTGGCTCATTTTTGT 58.854 40.909 0.00 0.00 0.00 2.83
5258 6740 3.829886 TCGCTAGTTGGCTCATTTTTG 57.170 42.857 0.00 0.00 0.00 2.44
5259 6741 4.142381 GGATTCGCTAGTTGGCTCATTTTT 60.142 41.667 0.00 0.00 0.00 1.94
5260 6742 3.378427 GGATTCGCTAGTTGGCTCATTTT 59.622 43.478 0.00 0.00 0.00 1.82
5261 6743 2.945668 GGATTCGCTAGTTGGCTCATTT 59.054 45.455 0.00 0.00 0.00 2.32
5262 6744 2.565841 GGATTCGCTAGTTGGCTCATT 58.434 47.619 0.00 0.00 0.00 2.57
5263 6745 1.202698 GGGATTCGCTAGTTGGCTCAT 60.203 52.381 0.00 0.00 0.00 2.90
5264 6746 0.178068 GGGATTCGCTAGTTGGCTCA 59.822 55.000 0.00 0.00 0.00 4.26
5265 6747 0.533085 GGGGATTCGCTAGTTGGCTC 60.533 60.000 0.40 0.00 0.00 4.70
5271 6753 1.065418 CACCAAAGGGGATTCGCTAGT 60.065 52.381 0.00 0.00 41.15 2.57
5293 6775 2.460757 TGGCTTTCGGTAACTACCAC 57.539 50.000 6.71 0.00 46.80 4.16
5305 6787 0.033699 AGCAGAGGGGAATGGCTTTC 60.034 55.000 4.63 4.63 0.00 2.62
5376 6858 4.842029 GAAGAATAGGCGCATCTTCAAAG 58.158 43.478 26.03 0.00 45.30 2.77
5387 6869 3.475566 TTGGATGGAGAAGAATAGGCG 57.524 47.619 0.00 0.00 0.00 5.52
5409 6891 1.533731 CGGCACAGTGGTACGAAATTT 59.466 47.619 1.84 0.00 0.00 1.82
5410 6892 1.153353 CGGCACAGTGGTACGAAATT 58.847 50.000 1.84 0.00 0.00 1.82
5411 6893 0.319083 TCGGCACAGTGGTACGAAAT 59.681 50.000 1.84 0.00 34.16 2.17
5413 6895 1.007038 GTCGGCACAGTGGTACGAA 60.007 57.895 1.84 0.00 37.34 3.85
5415 6897 2.019951 GTGTCGGCACAGTGGTACG 61.020 63.158 16.80 0.00 44.64 3.67
5434 6916 2.563050 TGGTTCTCATGCGAGGAGCG 62.563 60.000 0.00 0.00 46.66 5.03
5435 6917 0.809241 CTGGTTCTCATGCGAGGAGC 60.809 60.000 0.00 0.00 44.35 4.70
5444 6926 3.294214 GGCATGATTTCCTGGTTCTCAT 58.706 45.455 0.00 0.00 0.00 2.90
5454 6936 1.329913 GGTGGGGTGGCATGATTTCC 61.330 60.000 0.00 0.00 0.00 3.13
5468 6950 2.065789 GGCATTGGGGAATGGTGGG 61.066 63.158 0.00 0.00 0.00 4.61
5469 6951 1.305971 TGGCATTGGGGAATGGTGG 60.306 57.895 0.00 0.00 0.00 4.61
5485 6967 1.077285 TCATGTGGCATGCCTCTGG 60.077 57.895 35.53 25.61 36.94 3.86
5489 6971 1.450848 CTCGTCATGTGGCATGCCT 60.451 57.895 35.53 15.05 36.94 4.75
5490 6972 1.026182 TTCTCGTCATGTGGCATGCC 61.026 55.000 30.54 30.54 0.00 4.40


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

AutoCloner maintained by Alex Coulton.