Multiple sequence alignment - TraesCS2A01G373600

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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 TraesCS2A01G373600 chr2A 100.000 5143 0 0 1 5143 616978816 616983958 0.000000e+00 9498
1 TraesCS2A01G373600 chr2D 91.825 4465 248 43 1 4422 474500962 474505352 0.000000e+00 6115
2 TraesCS2A01G373600 chr2D 95.582 498 17 3 4647 5139 474505345 474505842 0.000000e+00 793
3 TraesCS2A01G373600 chr2B 94.079 2449 106 13 2024 4450 555322173 555324604 0.000000e+00 3683
4 TraesCS2A01G373600 chr2B 94.103 1204 56 6 768 1970 555320994 555322183 0.000000e+00 1816
5 TraesCS2A01G373600 chr2B 95.052 667 30 2 4453 5118 555324636 555325300 0.000000e+00 1046
6 TraesCS2A01G373600 chr7B 90.580 138 12 1 4453 4589 332016376 332016513 1.140000e-41 182
7 TraesCS2A01G373600 chr1D 87.681 138 16 1 4453 4589 416682949 416683086 5.330000e-35 159
8 TraesCS2A01G373600 chr1B 87.879 132 15 1 4453 4583 563471077 563471208 2.480000e-33 154


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 TraesCS2A01G373600 chr2A 616978816 616983958 5142 False 9498.000000 9498 100.000000 1 5143 1 chr2A.!!$F1 5142
1 TraesCS2A01G373600 chr2D 474500962 474505842 4880 False 3454.000000 6115 93.703500 1 5139 2 chr2D.!!$F1 5138
2 TraesCS2A01G373600 chr2B 555320994 555325300 4306 False 2181.666667 3683 94.411333 768 5118 3 chr2B.!!$F1 4350

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
571 578 0.691078 CTAGGGCTCCTGGGCAGTTA 60.691 60.0 8.98 0.00 42.84 2.24 F
1278 1289 0.038744 CTGGAGGCCTTGGTGATGTT 59.961 55.0 6.77 0.00 0.00 2.71 F
2441 2463 0.251922 AGAATGCCAAGGTGCACCAT 60.252 50.0 36.39 24.14 45.48 3.55 F
2792 2816 0.841961 TGGATGAAGGCAGGGATCAG 59.158 55.0 0.00 0.00 0.00 2.90 F
3845 3879 0.363512 CAGTCGCTTCGAATGTCACG 59.636 55.0 0.00 0.00 44.94 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2000 2011 0.400213 TGATTTGAGGGGCTGAACGT 59.600 50.0 0.0 0.0 0.00 3.99 R
3056 3090 0.035881 TCTTGCTTCTGCCACCTGAG 59.964 55.0 0.0 0.0 38.71 3.35 R
3327 3361 0.035630 CTTCCCTGTGCCCTGAAGAG 60.036 60.0 0.0 0.0 37.07 2.85 R
3917 3951 0.038744 CAGTTCTGCCCACCTTCCAT 59.961 55.0 0.0 0.0 0.00 3.41 R
5122 5201 0.328258 AGGGTCACCAAGGCATGTAC 59.672 55.0 0.0 0.0 40.13 2.90 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
19 21 2.371910 GAAGCCACTAGTGACCAGTC 57.628 55.000 24.68 6.89 0.00 3.51
22 24 2.330216 AGCCACTAGTGACCAGTCTTT 58.670 47.619 24.68 0.00 0.00 2.52
28 30 6.231211 CCACTAGTGACCAGTCTTTATGTTT 58.769 40.000 24.68 0.00 0.00 2.83
32 34 9.436957 ACTAGTGACCAGTCTTTATGTTTTATG 57.563 33.333 0.00 0.00 0.00 1.90
37 39 8.296713 TGACCAGTCTTTATGTTTTATGCTTTC 58.703 33.333 0.00 0.00 0.00 2.62
40 42 7.271223 CCAGTCTTTATGTTTTATGCTTTCGTG 59.729 37.037 0.00 0.00 0.00 4.35
45 47 4.078363 TGTTTTATGCTTTCGTGCTAGC 57.922 40.909 8.10 8.10 37.89 3.42
69 71 4.837972 AGTCATTTAGGTTCTTCTGGAGC 58.162 43.478 0.00 0.00 0.00 4.70
83 85 5.296780 TCTTCTGGAGCAGTACAAGTTTTTG 59.703 40.000 0.00 0.00 35.26 2.44
86 89 4.992688 TGGAGCAGTACAAGTTTTTGTTG 58.007 39.130 0.00 0.00 45.01 3.33
92 95 6.543831 AGCAGTACAAGTTTTTGTTGATCTCT 59.456 34.615 0.00 0.00 45.01 3.10
93 96 6.634436 GCAGTACAAGTTTTTGTTGATCTCTG 59.366 38.462 0.00 0.00 45.01 3.35
115 118 1.483004 TCGGATGCCCTCGTGATTTTA 59.517 47.619 0.00 0.00 0.00 1.52
150 156 4.040339 TGTCAGGATGTTGTGATGTACTGT 59.960 41.667 0.00 0.00 37.40 3.55
154 160 5.349817 CAGGATGTTGTGATGTACTGTTCTC 59.650 44.000 0.00 0.00 0.00 2.87
160 166 3.582647 TGTGATGTACTGTTCTCCACCAT 59.417 43.478 0.00 0.00 0.00 3.55
180 186 4.397103 CCATGCAGATTTCTTGACTTAGCA 59.603 41.667 0.00 0.00 0.00 3.49
185 191 5.287992 GCAGATTTCTTGACTTAGCATTTGC 59.712 40.000 0.00 0.00 42.49 3.68
210 216 7.430502 GCATTTGAGTACACTGCTATTTGATTC 59.569 37.037 0.00 0.00 34.28 2.52
211 217 6.985188 TTGAGTACACTGCTATTTGATTCC 57.015 37.500 0.00 0.00 0.00 3.01
213 219 4.442706 AGTACACTGCTATTTGATTCCGG 58.557 43.478 0.00 0.00 0.00 5.14
232 238 2.100197 GGAAGGAAGAAAATTCCGGGG 58.900 52.381 0.00 0.00 43.23 5.73
235 241 1.427753 AGGAAGAAAATTCCGGGGTGT 59.572 47.619 0.00 0.00 43.23 4.16
237 243 3.074836 AGGAAGAAAATTCCGGGGTGTTA 59.925 43.478 0.00 0.00 43.23 2.41
238 244 3.827876 GGAAGAAAATTCCGGGGTGTTAA 59.172 43.478 0.00 0.00 0.00 2.01
245 251 2.785540 TCCGGGGTGTTAATGTTACC 57.214 50.000 0.00 0.00 0.00 2.85
247 253 1.338960 CCGGGGTGTTAATGTTACCGT 60.339 52.381 0.00 0.00 38.27 4.83
252 258 3.401182 GGTGTTAATGTTACCGTGTCCA 58.599 45.455 0.00 0.00 0.00 4.02
253 259 3.187022 GGTGTTAATGTTACCGTGTCCAC 59.813 47.826 0.00 0.00 0.00 4.02
268 274 3.059188 GTGTCCACGAAACATTGTACCTG 60.059 47.826 0.00 0.00 0.00 4.00
269 275 3.181464 TGTCCACGAAACATTGTACCTGA 60.181 43.478 0.00 0.00 0.00 3.86
270 276 3.185797 GTCCACGAAACATTGTACCTGAC 59.814 47.826 0.00 0.00 0.00 3.51
271 277 3.070446 TCCACGAAACATTGTACCTGACT 59.930 43.478 0.00 0.00 0.00 3.41
272 278 3.186409 CCACGAAACATTGTACCTGACTG 59.814 47.826 0.00 0.00 0.00 3.51
288 294 3.405831 TGACTGAGGCTTGAACATGAAG 58.594 45.455 0.00 0.00 0.00 3.02
294 300 1.336240 GGCTTGAACATGAAGGTGTGC 60.336 52.381 0.00 0.00 31.49 4.57
300 306 2.105006 ACATGAAGGTGTGCTGCTAG 57.895 50.000 0.00 0.00 0.00 3.42
332 338 9.679661 TGACATTTATCACTTACATTACATGGT 57.320 29.630 0.00 0.00 33.60 3.55
353 359 2.697431 TGCGCACCAAATTACTCAAC 57.303 45.000 5.66 0.00 0.00 3.18
354 360 2.226330 TGCGCACCAAATTACTCAACT 58.774 42.857 5.66 0.00 0.00 3.16
401 407 6.920817 TCTGTAATATCGGTTACTGCCTATG 58.079 40.000 7.45 0.00 35.94 2.23
404 410 2.240493 ATCGGTTACTGCCTATGTGC 57.760 50.000 0.00 0.00 0.00 4.57
406 412 1.484653 TCGGTTACTGCCTATGTGCAT 59.515 47.619 0.00 0.00 41.16 3.96
415 421 4.706476 ACTGCCTATGTGCATTGTATTTGT 59.294 37.500 0.00 0.00 41.16 2.83
420 426 6.457663 GCCTATGTGCATTGTATTTGTCGTAA 60.458 38.462 0.00 0.00 0.00 3.18
421 427 7.468441 CCTATGTGCATTGTATTTGTCGTAAA 58.532 34.615 0.00 0.00 0.00 2.01
427 433 8.484008 GTGCATTGTATTTGTCGTAAAACATTT 58.516 29.630 0.00 0.00 0.00 2.32
428 434 8.483218 TGCATTGTATTTGTCGTAAAACATTTG 58.517 29.630 0.00 0.00 0.00 2.32
440 447 8.800972 GTCGTAAAACATTTGTATCTGTCGATA 58.199 33.333 0.00 0.00 0.00 2.92
459 466 2.592102 ATGCACATTGGGAACAGACT 57.408 45.000 0.00 0.00 44.54 3.24
470 477 1.550976 GGAACAGACTAGTGTCCTGGG 59.449 57.143 0.00 0.00 43.91 4.45
475 482 4.534797 ACAGACTAGTGTCCTGGGTATAC 58.465 47.826 0.00 0.00 43.91 1.47
478 485 2.236766 CTAGTGTCCTGGGTATACGGG 58.763 57.143 0.00 0.00 38.29 5.28
479 486 1.047034 AGTGTCCTGGGTATACGGGC 61.047 60.000 0.00 0.00 36.80 6.13
488 495 1.473080 GGGTATACGGGCGCTGTTTAA 60.473 52.381 7.64 0.00 0.00 1.52
499 506 1.804748 CGCTGTTTAACCTCCCTGTTC 59.195 52.381 0.00 0.00 0.00 3.18
500 507 2.808933 CGCTGTTTAACCTCCCTGTTCA 60.809 50.000 0.00 0.00 0.00 3.18
501 508 2.552743 GCTGTTTAACCTCCCTGTTCAC 59.447 50.000 0.00 0.00 0.00 3.18
502 509 3.146847 CTGTTTAACCTCCCTGTTCACC 58.853 50.000 0.00 0.00 0.00 4.02
503 510 2.781174 TGTTTAACCTCCCTGTTCACCT 59.219 45.455 0.00 0.00 0.00 4.00
504 511 3.146847 GTTTAACCTCCCTGTTCACCTG 58.853 50.000 0.00 0.00 0.00 4.00
505 512 1.358152 TAACCTCCCTGTTCACCTGG 58.642 55.000 0.00 0.00 0.00 4.45
513 520 2.308866 CCCTGTTCACCTGGGTTCTATT 59.691 50.000 0.00 0.00 45.14 1.73
516 523 2.027561 TGTTCACCTGGGTTCTATTCCG 60.028 50.000 0.00 0.00 0.00 4.30
528 535 1.006832 CTATTCCGACGGCTGGTTTG 58.993 55.000 9.66 0.00 0.00 2.93
539 546 1.747774 CTGGTTTGGGTGCCCTTTG 59.252 57.895 8.91 0.00 36.94 2.77
555 562 3.445096 CCCTTTGGTTCCTTGAATGCTAG 59.555 47.826 0.00 0.00 0.00 3.42
565 572 1.348008 TGAATGCTAGGGCTCCTGGG 61.348 60.000 4.16 0.00 39.59 4.45
568 575 3.871395 GCTAGGGCTCCTGGGCAG 61.871 72.222 8.98 0.00 42.84 4.85
571 578 0.691078 CTAGGGCTCCTGGGCAGTTA 60.691 60.000 8.98 0.00 42.84 2.24
581 588 5.360999 GCTCCTGGGCAGTTAATAAGAAAAT 59.639 40.000 0.00 0.00 0.00 1.82
590 597 9.653287 GGCAGTTAATAAGAAAATTAAAAGCCT 57.347 29.630 17.40 1.38 42.75 4.58
603 610 2.806608 AAAGCCTGTGCATTGTCTTG 57.193 45.000 0.00 0.00 41.13 3.02
615 622 5.049198 GTGCATTGTCTTGAAGAACTCATCA 60.049 40.000 0.00 0.00 32.78 3.07
624 631 4.206375 TGAAGAACTCATCAACAAGGCAA 58.794 39.130 0.00 0.00 0.00 4.52
625 632 4.644234 TGAAGAACTCATCAACAAGGCAAA 59.356 37.500 0.00 0.00 0.00 3.68
626 633 5.126869 TGAAGAACTCATCAACAAGGCAAAA 59.873 36.000 0.00 0.00 0.00 2.44
627 634 5.796424 AGAACTCATCAACAAGGCAAAAT 57.204 34.783 0.00 0.00 0.00 1.82
628 635 5.535333 AGAACTCATCAACAAGGCAAAATG 58.465 37.500 0.00 0.00 0.00 2.32
629 636 4.942761 ACTCATCAACAAGGCAAAATGT 57.057 36.364 0.00 0.00 0.00 2.71
630 637 5.280654 ACTCATCAACAAGGCAAAATGTT 57.719 34.783 0.00 0.00 40.24 2.71
631 638 5.673514 ACTCATCAACAAGGCAAAATGTTT 58.326 33.333 0.00 0.00 37.66 2.83
632 639 6.114767 ACTCATCAACAAGGCAAAATGTTTT 58.885 32.000 0.00 0.00 37.66 2.43
664 671 7.915508 TCGAAAAAGCATGTACAATTATCGAT 58.084 30.769 2.16 2.16 30.52 3.59
665 672 9.036671 TCGAAAAAGCATGTACAATTATCGATA 57.963 29.630 0.00 0.00 30.52 2.92
702 709 2.365293 TGGAGCTTCCTTTTTGCCTTTC 59.635 45.455 0.00 0.00 37.46 2.62
712 719 3.340814 TTTTGCCTTTCAACCTTGCAA 57.659 38.095 0.00 0.00 39.92 4.08
738 745 8.902540 TTGTAGCACTAACAATAATATCCCTG 57.097 34.615 0.00 0.00 32.07 4.45
745 752 4.689612 ACAATAATATCCCTGACACGCT 57.310 40.909 0.00 0.00 0.00 5.07
746 753 4.632153 ACAATAATATCCCTGACACGCTC 58.368 43.478 0.00 0.00 0.00 5.03
753 760 0.803768 CCCTGACACGCTCGAATGAG 60.804 60.000 0.00 0.00 45.49 2.90
765 775 3.181506 GCTCGAATGAGAATTGGGTTCAC 60.182 47.826 0.00 0.00 45.57 3.18
766 776 4.002982 CTCGAATGAGAATTGGGTTCACA 58.997 43.478 0.00 0.00 45.57 3.58
786 796 4.712239 ACAGTATGCAAGCAGTTAGCACG 61.712 47.826 0.00 0.00 44.29 5.34
819 829 7.277098 TGCCACATCGTAGTACTCTTTTATTTC 59.723 37.037 0.00 0.00 0.00 2.17
888 898 5.742446 GCATAGTAGTGCTGCTTTACATTC 58.258 41.667 13.69 1.52 41.82 2.67
899 909 8.616076 GTGCTGCTTTACATTCAGAATATAAGT 58.384 33.333 0.00 0.00 0.00 2.24
951 961 2.575279 AGCAGAAGTTCATCATGACCCT 59.425 45.455 5.50 0.00 0.00 4.34
952 962 3.009916 AGCAGAAGTTCATCATGACCCTT 59.990 43.478 5.50 0.00 0.00 3.95
954 964 4.219288 GCAGAAGTTCATCATGACCCTTTT 59.781 41.667 5.50 0.00 0.00 2.27
997 1007 1.086634 GTCGTCATTGAGAGGCTGCC 61.087 60.000 11.65 11.65 32.24 4.85
998 1008 1.078918 CGTCATTGAGAGGCTGCCA 60.079 57.895 22.65 0.00 0.00 4.92
1008 1019 0.899717 GAGGCTGCCAAATGGGTTCA 60.900 55.000 22.65 0.00 39.65 3.18
1077 1088 7.629157 TGAAACTATCACCTCACATCCAATTA 58.371 34.615 0.00 0.00 31.50 1.40
1080 1091 6.957631 ACTATCACCTCACATCCAATTACAA 58.042 36.000 0.00 0.00 0.00 2.41
1180 1191 9.915629 ATTATGGAACTCATCGTAATTCTAGTC 57.084 33.333 0.00 0.00 37.30 2.59
1278 1289 0.038744 CTGGAGGCCTTGGTGATGTT 59.961 55.000 6.77 0.00 0.00 2.71
1341 1352 7.042321 CCTTGTCACGTACTGTTAATTCTGAAA 60.042 37.037 0.00 0.00 0.00 2.69
1381 1392 2.673368 GACTGCACTTTTATCACCCTCG 59.327 50.000 0.00 0.00 0.00 4.63
1419 1430 1.832883 GGTGTGATGCACAACCCATA 58.167 50.000 4.30 0.00 45.29 2.74
1421 1432 2.760092 GGTGTGATGCACAACCCATATT 59.240 45.455 4.30 0.00 45.29 1.28
1517 1528 8.055279 ACAAATGTTCTTGTTGAGGTATATGG 57.945 34.615 0.00 0.00 36.05 2.74
1538 1549 7.604657 ATGGTTTTAGTTGATTTGTTGGGTA 57.395 32.000 0.00 0.00 0.00 3.69
1541 1552 9.144298 TGGTTTTAGTTGATTTGTTGGGTATTA 57.856 29.630 0.00 0.00 0.00 0.98
1542 1553 9.414295 GGTTTTAGTTGATTTGTTGGGTATTAC 57.586 33.333 0.00 0.00 0.00 1.89
1545 1556 8.927675 TTAGTTGATTTGTTGGGTATTACTGT 57.072 30.769 0.00 0.00 0.00 3.55
1577 1588 6.113411 AGCTCGCATTTAACTTATACCAGTT 58.887 36.000 0.00 0.00 40.28 3.16
1578 1589 7.270047 AGCTCGCATTTAACTTATACCAGTTA 58.730 34.615 0.00 0.00 38.07 2.24
1620 1631 7.595311 AAAAACAGTTTTGCTTCTTTAGGTG 57.405 32.000 12.13 0.00 35.58 4.00
1682 1693 3.073798 TGCTACAAAAGGGGAGTTGATCA 59.926 43.478 0.00 0.00 0.00 2.92
1855 1866 5.140454 GGATCAAAATTGTATGGGCCTACT 58.860 41.667 4.53 0.00 0.00 2.57
1967 1978 8.630054 AGCACCTCACTTATGTAATTTACAAA 57.370 30.769 12.96 8.16 42.76 2.83
1990 2001 2.284754 TTTCAATGCTGTGGCCTGTA 57.715 45.000 3.32 0.00 37.74 2.74
2018 2029 2.280628 CTACGTTCAGCCCCTCAAATC 58.719 52.381 0.00 0.00 0.00 2.17
2045 2057 4.776795 ATTACCAACCCTTGTTTTAGCG 57.223 40.909 0.00 0.00 30.42 4.26
2057 2069 6.095720 CCCTTGTTTTAGCGGAATTAATGGTA 59.904 38.462 0.00 0.00 0.00 3.25
2348 2370 5.200483 TCACCAGGAGAAAATGTTGTCTTT 58.800 37.500 0.00 0.00 0.00 2.52
2435 2457 5.127519 TGGAATTTATGAGAATGCCAAGGTG 59.872 40.000 0.00 0.00 40.93 4.00
2441 2463 0.251922 AGAATGCCAAGGTGCACCAT 60.252 50.000 36.39 24.14 45.48 3.55
2471 2493 5.534654 TCCTTTTGTTGACAAGTAGGGAATG 59.465 40.000 18.80 2.12 38.72 2.67
2492 2514 6.720112 ATGTGCATCATAGGTTTTATGCTT 57.280 33.333 7.56 0.00 43.98 3.91
2502 2524 8.677300 TCATAGGTTTTATGCTTCACAGATTTC 58.323 33.333 0.00 0.00 0.00 2.17
2503 2525 6.272822 AGGTTTTATGCTTCACAGATTTCC 57.727 37.500 0.00 0.00 0.00 3.13
2507 2530 6.455360 TTTATGCTTCACAGATTTCCCATC 57.545 37.500 0.00 0.00 0.00 3.51
2511 2534 4.018506 TGCTTCACAGATTTCCCATCCTTA 60.019 41.667 0.00 0.00 0.00 2.69
2520 2543 7.013655 ACAGATTTCCCATCCTTATTTTGATCG 59.986 37.037 0.00 0.00 0.00 3.69
2532 2555 8.044309 TCCTTATTTTGATCGGTGAATAGTTGA 58.956 33.333 0.00 0.00 0.00 3.18
2624 2647 9.946165 AACTTCTTAATTTACCTGAAAGTTTCG 57.054 29.630 10.92 5.92 0.00 3.46
2629 2652 2.922740 TACCTGAAAGTTTCGTGCCT 57.077 45.000 10.92 0.00 0.00 4.75
2660 2683 6.496565 TGATTTTGTTGATGGGTATGAACCTT 59.503 34.615 0.00 0.00 45.95 3.50
2667 2690 4.949238 TGATGGGTATGAACCTTCATGTTG 59.051 41.667 10.28 0.00 46.68 3.33
2669 2692 4.078537 TGGGTATGAACCTTCATGTTGTG 58.921 43.478 10.28 0.00 46.68 3.33
2677 2700 5.636965 TGAACCTTCATGTTGTGTTGTTTTG 59.363 36.000 0.00 0.00 31.01 2.44
2678 2701 5.398603 ACCTTCATGTTGTGTTGTTTTGA 57.601 34.783 0.00 0.00 0.00 2.69
2679 2702 5.976458 ACCTTCATGTTGTGTTGTTTTGAT 58.024 33.333 0.00 0.00 0.00 2.57
2680 2703 7.106439 ACCTTCATGTTGTGTTGTTTTGATA 57.894 32.000 0.00 0.00 0.00 2.15
2681 2704 7.202526 ACCTTCATGTTGTGTTGTTTTGATAG 58.797 34.615 0.00 0.00 0.00 2.08
2682 2705 7.068103 ACCTTCATGTTGTGTTGTTTTGATAGA 59.932 33.333 0.00 0.00 0.00 1.98
2683 2706 7.592533 CCTTCATGTTGTGTTGTTTTGATAGAG 59.407 37.037 0.00 0.00 0.00 2.43
2684 2707 7.800155 TCATGTTGTGTTGTTTTGATAGAGA 57.200 32.000 0.00 0.00 0.00 3.10
2685 2708 8.394971 TCATGTTGTGTTGTTTTGATAGAGAT 57.605 30.769 0.00 0.00 0.00 2.75
2686 2709 9.500785 TCATGTTGTGTTGTTTTGATAGAGATA 57.499 29.630 0.00 0.00 0.00 1.98
2792 2816 0.841961 TGGATGAAGGCAGGGATCAG 59.158 55.000 0.00 0.00 0.00 2.90
2832 2856 7.822822 GTCCTTACAGTTAGTCCACATTATGTT 59.177 37.037 0.00 0.00 0.00 2.71
2850 2874 9.003658 CATTATGTTAAAGAACTCACTTCTGGT 57.996 33.333 0.00 0.00 39.36 4.00
2877 2901 3.117512 AGAAAGGTGTTGAGTTGGATGGT 60.118 43.478 0.00 0.00 0.00 3.55
2943 2967 3.443329 TGGATGTTGTTGATTGGAATCCG 59.557 43.478 0.00 0.00 35.84 4.18
2992 3016 3.412237 ACAATGCAACTACGGTAAGGT 57.588 42.857 0.00 0.00 0.00 3.50
3007 3038 4.325119 GGTAAGGTTTCAGTTTCTCCTCC 58.675 47.826 0.00 0.00 0.00 4.30
3011 3042 5.906772 AGGTTTCAGTTTCTCCTCCTTTA 57.093 39.130 0.00 0.00 0.00 1.85
3021 3055 3.094572 TCTCCTCCTTTACCAGTTACCG 58.905 50.000 0.00 0.00 0.00 4.02
3037 3071 6.429692 CCAGTTACCGCATATGGATAATTCAA 59.570 38.462 4.56 0.00 32.55 2.69
3056 3090 7.573968 ATTCAATACTTACAGAGGGCATTTC 57.426 36.000 0.00 0.00 0.00 2.17
3117 3151 0.883833 AAGCTGAAGTTGGATTGCCG 59.116 50.000 0.00 0.00 36.79 5.69
3153 3187 7.834181 AGCATACCTGTTATAGTTTTCATTGGT 59.166 33.333 0.00 0.00 0.00 3.67
3198 3232 5.297776 GTCAGACATACTAATTGCAGCCATT 59.702 40.000 0.00 0.00 0.00 3.16
3208 3242 1.243342 TGCAGCCATTCCGGAGTTTG 61.243 55.000 3.34 4.12 36.56 2.93
3286 3320 1.375853 GCACTCATACGGCATGGCAA 61.376 55.000 20.37 6.93 35.16 4.52
3302 3336 5.352016 GCATGGCAAGAGATAGAAGATGATC 59.648 44.000 0.00 0.00 0.00 2.92
3312 3346 6.155827 AGATAGAAGATGATCGTTGCTTAGC 58.844 40.000 0.00 0.00 0.00 3.09
3320 3354 4.908736 TGATCGTTGCTTAGCTAAATTGC 58.091 39.130 7.74 8.34 0.00 3.56
3327 3361 2.594214 GCTTAGCTAAATTGCGTTGTGC 59.406 45.455 7.74 0.00 46.70 4.57
3329 3363 2.619013 AGCTAAATTGCGTTGTGCTC 57.381 45.000 0.00 0.00 46.63 4.26
3427 3461 3.798337 GCATAGCAAAATTCAATGTCCCG 59.202 43.478 0.00 0.00 0.00 5.14
3537 3571 3.961408 AGATATGGAGTGGTAAGCGTTCT 59.039 43.478 0.00 0.00 0.00 3.01
3596 3630 7.687941 AAGTATTGATTGTCCCAGTTAACAG 57.312 36.000 8.61 0.00 0.00 3.16
3601 3635 4.346709 TGATTGTCCCAGTTAACAGAGTCA 59.653 41.667 8.61 4.27 0.00 3.41
3610 3644 7.770433 TCCCAGTTAACAGAGTCATTGATATTG 59.230 37.037 8.61 0.00 0.00 1.90
3626 3660 9.976511 CATTGATATTGCATTTTACAGATTCCT 57.023 29.630 0.00 0.00 0.00 3.36
3674 3708 2.122547 ACGGTGAGGGAGGGTGTT 60.123 61.111 0.00 0.00 0.00 3.32
3704 3738 3.078097 CCACATGGGTTCGTTCAATGTA 58.922 45.455 0.00 0.00 0.00 2.29
3745 3779 4.019321 AGGCTTGGTCTAAGTATTTGCTCA 60.019 41.667 0.00 0.00 38.70 4.26
3845 3879 0.363512 CAGTCGCTTCGAATGTCACG 59.636 55.000 0.00 0.00 44.94 4.35
3871 3905 5.186198 AGCTCTGAAACAGTACAAAACACT 58.814 37.500 0.00 0.00 32.61 3.55
3917 3951 1.447217 CATGGCGCAGGACCTATCA 59.553 57.895 10.83 0.00 0.00 2.15
3959 3993 6.252995 TGTCAATTAAGTTCCTATTTGCCCT 58.747 36.000 0.00 0.00 0.00 5.19
3980 4014 6.808704 GCCCTTTAACATGAATGAGTTTCTTC 59.191 38.462 0.00 0.00 35.23 2.87
4061 4095 1.631071 GGGAGGAGGCTCTTCTTGGG 61.631 65.000 23.68 0.00 0.00 4.12
4118 4152 4.919653 GAGATCGCTCCAGTTGCA 57.080 55.556 0.00 0.00 35.01 4.08
4195 4229 9.922305 CTAAGATTCGACAAAATAATGAGGTTC 57.078 33.333 0.00 0.00 0.00 3.62
4229 4263 3.879295 GCTGTATTCATCTAGGCTTTGCA 59.121 43.478 0.00 0.00 0.00 4.08
4251 4285 5.007136 GCAATTTCTCTACTACTCCATGTGC 59.993 44.000 0.00 0.00 0.00 4.57
4376 4420 4.589374 GCTTGTAGTATCTGGGGTGATAGT 59.411 45.833 0.00 0.00 36.74 2.12
4401 4445 3.310727 GCTTTGTGCCATTTGCCTT 57.689 47.368 0.00 0.00 40.16 4.35
4426 4471 2.376518 TCTGCCAAATCAAGAACTCCCT 59.623 45.455 0.00 0.00 0.00 4.20
4450 4495 8.527810 CCTCACCAAAATTGCCTAATAAGTTTA 58.472 33.333 0.00 0.00 0.00 2.01
4451 4496 9.353999 CTCACCAAAATTGCCTAATAAGTTTAC 57.646 33.333 0.00 0.00 0.00 2.01
4482 4556 3.875134 AGAAATAGAATAAACCGGCACCG 59.125 43.478 0.00 1.02 39.44 4.94
4506 4580 3.814625 TGTGCAACAGATTTCACCAGTA 58.185 40.909 0.00 0.00 45.67 2.74
4507 4581 4.397420 TGTGCAACAGATTTCACCAGTAT 58.603 39.130 0.00 0.00 45.67 2.12
4516 4590 6.127026 ACAGATTTCACCAGTATCTCCTTACC 60.127 42.308 0.00 0.00 0.00 2.85
4517 4591 6.098982 CAGATTTCACCAGTATCTCCTTACCT 59.901 42.308 0.00 0.00 0.00 3.08
4519 4593 4.332683 TCACCAGTATCTCCTTACCTGT 57.667 45.455 0.00 0.00 0.00 4.00
4520 4594 4.023980 TCACCAGTATCTCCTTACCTGTG 58.976 47.826 0.00 0.00 0.00 3.66
4521 4595 4.023980 CACCAGTATCTCCTTACCTGTGA 58.976 47.826 0.00 0.00 31.07 3.58
4541 4616 7.129109 TGTGACGATAAAGTTTTCTCAATCC 57.871 36.000 0.00 0.00 0.00 3.01
4551 4626 5.012893 AGTTTTCTCAATCCATCCCTTCAC 58.987 41.667 0.00 0.00 0.00 3.18
4558 4633 3.941704 ATCCATCCCTTCACCTTTCTC 57.058 47.619 0.00 0.00 0.00 2.87
4602 4677 7.521509 ACTTGAATGCTTACTATTACGTGTC 57.478 36.000 0.00 0.00 0.00 3.67
4603 4678 7.321153 ACTTGAATGCTTACTATTACGTGTCT 58.679 34.615 0.00 0.00 0.00 3.41
4604 4679 7.817962 ACTTGAATGCTTACTATTACGTGTCTT 59.182 33.333 0.00 0.00 0.00 3.01
4633 4708 2.239654 TGTGAATCAAAGAGGGCCCTAG 59.760 50.000 28.78 15.59 0.00 3.02
4853 4931 3.564264 TCAGCTAGACTGCATCATCTCT 58.436 45.455 8.72 0.00 46.76 3.10
4870 4948 0.982852 TCTGCCACCCCCTATCACTG 60.983 60.000 0.00 0.00 0.00 3.66
4916 4994 3.058983 CACATAAGAAGACACGCAAAGCA 60.059 43.478 0.00 0.00 0.00 3.91
5041 5120 7.926705 AGAAATATAAGCCTAGATTCCAGCAT 58.073 34.615 0.00 0.00 0.00 3.79
5046 5125 1.143684 GCCTAGATTCCAGCATCCCAA 59.856 52.381 0.00 0.00 0.00 4.12
5051 5130 4.803329 AGATTCCAGCATCCCAACTAAT 57.197 40.909 0.00 0.00 0.00 1.73
5053 5132 4.166725 AGATTCCAGCATCCCAACTAATGA 59.833 41.667 0.00 0.00 0.00 2.57
5122 5201 5.751680 CCAAATGTGGCGATAACTCTATTG 58.248 41.667 0.00 0.00 38.35 1.90
5139 5218 1.904287 TTGTACATGCCTTGGTGACC 58.096 50.000 0.00 0.00 0.00 4.02
5140 5219 0.037590 TGTACATGCCTTGGTGACCC 59.962 55.000 0.00 0.00 0.00 4.46
5141 5220 0.328258 GTACATGCCTTGGTGACCCT 59.672 55.000 0.00 0.00 0.00 4.34
5142 5221 1.072266 TACATGCCTTGGTGACCCTT 58.928 50.000 0.00 0.00 0.00 3.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 21 7.044706 GCTAGCACGAAAGCATAAAACATAAAG 60.045 37.037 10.63 0.00 38.63 1.85
22 24 5.352846 TGCTAGCACGAAAGCATAAAACATA 59.647 36.000 14.93 0.00 43.56 2.29
32 34 1.148310 TGACTTGCTAGCACGAAAGC 58.852 50.000 26.29 13.10 39.25 3.51
37 39 3.262420 ACCTAAATGACTTGCTAGCACG 58.738 45.455 19.17 19.00 0.00 5.34
40 42 5.877564 AGAAGAACCTAAATGACTTGCTAGC 59.122 40.000 8.10 8.10 0.00 3.42
45 47 5.123027 GCTCCAGAAGAACCTAAATGACTTG 59.877 44.000 0.00 0.00 0.00 3.16
46 48 5.221925 TGCTCCAGAAGAACCTAAATGACTT 60.222 40.000 0.00 0.00 0.00 3.01
69 71 6.634436 GCAGAGATCAACAAAAACTTGTACTG 59.366 38.462 0.00 0.00 34.24 2.74
83 85 1.216122 GCATCCGAGCAGAGATCAAC 58.784 55.000 0.00 0.00 0.00 3.18
86 89 1.005156 GGGCATCCGAGCAGAGATC 60.005 63.158 0.00 0.00 35.83 2.75
92 95 4.147449 CACGAGGGCATCCGAGCA 62.147 66.667 0.00 0.00 38.33 4.26
93 96 2.650813 AATCACGAGGGCATCCGAGC 62.651 60.000 0.00 0.00 38.33 5.03
115 118 8.469200 CACAACATCCTGACATGGTAAAAATAT 58.531 33.333 0.00 0.00 0.00 1.28
154 160 3.087031 AGTCAAGAAATCTGCATGGTGG 58.913 45.455 0.00 0.00 0.00 4.61
160 166 6.384224 CAAATGCTAAGTCAAGAAATCTGCA 58.616 36.000 0.00 0.00 0.00 4.41
180 186 6.764308 ATAGCAGTGTACTCAAATGCAAAT 57.236 33.333 6.84 0.00 39.49 2.32
185 191 7.912250 GGAATCAAATAGCAGTGTACTCAAATG 59.088 37.037 0.00 0.00 0.00 2.32
213 219 2.492088 CACCCCGGAATTTTCTTCCTTC 59.508 50.000 0.73 0.00 36.45 3.46
220 226 4.794278 ACATTAACACCCCGGAATTTTC 57.206 40.909 0.73 0.00 0.00 2.29
225 231 2.614987 CGGTAACATTAACACCCCGGAA 60.615 50.000 0.73 0.00 0.00 4.30
232 238 4.394099 GTGGACACGGTAACATTAACAC 57.606 45.455 0.00 0.00 0.00 3.32
247 253 3.135225 CAGGTACAATGTTTCGTGGACA 58.865 45.455 0.00 0.00 29.42 4.02
252 258 4.307432 CTCAGTCAGGTACAATGTTTCGT 58.693 43.478 0.00 0.00 0.00 3.85
253 259 3.679980 CCTCAGTCAGGTACAATGTTTCG 59.320 47.826 0.00 0.00 37.53 3.46
268 274 2.746362 CCTTCATGTTCAAGCCTCAGTC 59.254 50.000 0.00 0.00 0.00 3.51
269 275 2.107204 ACCTTCATGTTCAAGCCTCAGT 59.893 45.455 0.00 0.00 0.00 3.41
270 276 2.486982 CACCTTCATGTTCAAGCCTCAG 59.513 50.000 0.00 0.00 0.00 3.35
271 277 2.158623 ACACCTTCATGTTCAAGCCTCA 60.159 45.455 0.00 0.00 0.00 3.86
272 278 2.227388 CACACCTTCATGTTCAAGCCTC 59.773 50.000 0.00 0.00 0.00 4.70
280 286 2.430465 CTAGCAGCACACCTTCATGTT 58.570 47.619 0.00 0.00 0.00 2.71
288 294 1.757118 TCAGTATCCTAGCAGCACACC 59.243 52.381 0.00 0.00 0.00 4.16
294 300 7.665690 AGTGATAAATGTCAGTATCCTAGCAG 58.334 38.462 0.00 0.00 30.19 4.24
306 312 9.679661 ACCATGTAATGTAAGTGATAAATGTCA 57.320 29.630 0.00 0.00 44.81 3.58
316 322 3.851403 GCGCAAACCATGTAATGTAAGTG 59.149 43.478 0.30 0.00 44.81 3.16
332 338 3.067461 AGTTGAGTAATTTGGTGCGCAAA 59.933 39.130 14.00 2.71 0.00 3.68
387 393 3.451793 TGCACATAGGCAGTAACCG 57.548 52.632 0.00 0.00 39.25 4.44
395 401 4.201910 ACGACAAATACAATGCACATAGGC 60.202 41.667 0.00 0.00 0.00 3.93
401 407 6.978024 TGTTTTACGACAAATACAATGCAC 57.022 33.333 0.00 0.00 0.00 4.57
415 421 7.821595 ATCGACAGATACAAATGTTTTACGA 57.178 32.000 0.00 0.00 34.85 3.43
420 426 7.065683 TGTGCATATCGACAGATACAAATGTTT 59.934 33.333 0.00 0.00 41.66 2.83
421 427 6.538381 TGTGCATATCGACAGATACAAATGTT 59.462 34.615 0.00 0.00 41.66 2.71
427 433 4.990426 CCAATGTGCATATCGACAGATACA 59.010 41.667 0.00 0.00 41.66 2.29
428 434 4.389992 CCCAATGTGCATATCGACAGATAC 59.610 45.833 0.00 0.00 41.66 2.24
431 437 2.433970 TCCCAATGTGCATATCGACAGA 59.566 45.455 0.00 0.00 0.00 3.41
432 438 2.837498 TCCCAATGTGCATATCGACAG 58.163 47.619 0.00 0.00 0.00 3.51
433 439 2.942376 GTTCCCAATGTGCATATCGACA 59.058 45.455 0.00 0.00 0.00 4.35
434 440 2.942376 TGTTCCCAATGTGCATATCGAC 59.058 45.455 0.00 0.00 0.00 4.20
440 447 2.592102 AGTCTGTTCCCAATGTGCAT 57.408 45.000 0.00 0.00 0.00 3.96
459 466 1.755265 GCCCGTATACCCAGGACACTA 60.755 57.143 5.62 0.00 0.00 2.74
470 477 1.594397 GGTTAAACAGCGCCCGTATAC 59.406 52.381 2.29 1.20 0.00 1.47
475 482 2.396157 GGAGGTTAAACAGCGCCCG 61.396 63.158 2.29 0.00 36.88 6.13
478 485 0.605589 ACAGGGAGGTTAAACAGCGC 60.606 55.000 0.00 0.00 0.00 5.92
479 486 1.804748 GAACAGGGAGGTTAAACAGCG 59.195 52.381 0.00 0.00 0.00 5.18
488 495 1.847968 CCCAGGTGAACAGGGAGGT 60.848 63.158 0.00 0.00 45.80 3.85
499 506 1.470979 CGTCGGAATAGAACCCAGGTG 60.471 57.143 0.00 0.00 0.00 4.00
500 507 0.822164 CGTCGGAATAGAACCCAGGT 59.178 55.000 0.00 0.00 0.00 4.00
501 508 0.104304 CCGTCGGAATAGAACCCAGG 59.896 60.000 4.91 0.00 0.00 4.45
502 509 0.529992 GCCGTCGGAATAGAACCCAG 60.530 60.000 17.49 0.00 0.00 4.45
503 510 0.974010 AGCCGTCGGAATAGAACCCA 60.974 55.000 17.49 0.00 0.00 4.51
504 511 0.529992 CAGCCGTCGGAATAGAACCC 60.530 60.000 17.49 0.00 0.00 4.11
505 512 0.529992 CCAGCCGTCGGAATAGAACC 60.530 60.000 17.49 0.00 0.00 3.62
513 520 4.323477 CCCAAACCAGCCGTCGGA 62.323 66.667 17.49 0.00 0.00 4.55
516 523 3.670377 GCACCCAAACCAGCCGTC 61.670 66.667 0.00 0.00 0.00 4.79
539 546 1.064389 AGCCCTAGCATTCAAGGAACC 60.064 52.381 0.00 0.00 43.56 3.62
555 562 0.843984 TATTAACTGCCCAGGAGCCC 59.156 55.000 0.00 0.00 0.00 5.19
571 578 9.506018 AATGCACAGGCTTTTAATTTTCTTATT 57.494 25.926 0.00 0.00 41.91 1.40
581 588 4.340666 TCAAGACAATGCACAGGCTTTTAA 59.659 37.500 5.61 0.00 41.91 1.52
590 597 4.198530 TGAGTTCTTCAAGACAATGCACA 58.801 39.130 0.00 0.00 31.34 4.57
592 599 5.065235 TGATGAGTTCTTCAAGACAATGCA 58.935 37.500 0.00 0.00 39.77 3.96
593 600 5.618056 TGATGAGTTCTTCAAGACAATGC 57.382 39.130 0.00 0.00 39.77 3.56
603 610 4.836125 TTGCCTTGTTGATGAGTTCTTC 57.164 40.909 0.00 0.00 0.00 2.87
645 652 9.325198 TGTTCTTATCGATAATTGTACATGCTT 57.675 29.630 17.84 0.00 0.00 3.91
664 671 8.150945 GGAAGCTCCATTACAGATATGTTCTTA 58.849 37.037 0.00 0.00 36.28 2.10
665 672 6.995091 GGAAGCTCCATTACAGATATGTTCTT 59.005 38.462 0.00 0.00 36.28 2.52
676 683 3.258123 GGCAAAAAGGAAGCTCCATTACA 59.742 43.478 5.21 0.00 39.61 2.41
677 684 3.511540 AGGCAAAAAGGAAGCTCCATTAC 59.488 43.478 5.21 0.00 39.61 1.89
685 692 2.872245 GGTTGAAAGGCAAAAAGGAAGC 59.128 45.455 0.00 0.00 38.44 3.86
702 709 3.648339 AGTGCTACAATTGCAAGGTTG 57.352 42.857 4.94 8.28 42.41 3.77
712 719 9.507329 CAGGGATATTATTGTTAGTGCTACAAT 57.493 33.333 0.00 0.00 45.45 2.71
737 744 2.654749 ATTCTCATTCGAGCGTGTCA 57.345 45.000 0.00 0.00 39.30 3.58
738 745 2.029728 CCAATTCTCATTCGAGCGTGTC 59.970 50.000 0.00 0.00 39.30 3.67
745 752 4.002982 CTGTGAACCCAATTCTCATTCGA 58.997 43.478 0.00 0.00 39.46 3.71
746 753 3.753272 ACTGTGAACCCAATTCTCATTCG 59.247 43.478 0.00 0.00 39.46 3.34
753 760 4.737054 CTTGCATACTGTGAACCCAATTC 58.263 43.478 0.00 0.00 37.88 2.17
765 775 2.222886 CGTGCTAACTGCTTGCATACTG 60.223 50.000 0.00 0.00 43.37 2.74
766 776 2.002586 CGTGCTAACTGCTTGCATACT 58.997 47.619 0.00 0.00 43.37 2.12
786 796 2.346803 ACTACGATGTGGCACATGAAC 58.653 47.619 35.82 20.76 44.52 3.18
819 829 7.975058 TGCCACAAATATACATGTCATTTTCTG 59.025 33.333 0.00 7.29 0.00 3.02
907 917 9.412460 TGCTTCAGAGAAACATGGAAATATATT 57.588 29.630 0.00 0.00 0.00 1.28
908 918 8.985315 TGCTTCAGAGAAACATGGAAATATAT 57.015 30.769 0.00 0.00 0.00 0.86
909 919 8.267183 TCTGCTTCAGAGAAACATGGAAATATA 58.733 33.333 0.00 0.00 35.39 0.86
910 920 7.114754 TCTGCTTCAGAGAAACATGGAAATAT 58.885 34.615 0.00 0.00 35.39 1.28
911 921 6.475504 TCTGCTTCAGAGAAACATGGAAATA 58.524 36.000 0.00 0.00 35.39 1.40
920 930 5.468072 TGATGAACTTCTGCTTCAGAGAAAC 59.532 40.000 0.00 0.00 41.75 2.78
932 942 5.972107 AAAAGGGTCATGATGAACTTCTG 57.028 39.130 10.69 0.00 33.75 3.02
997 1007 8.531146 ACAATAAGTAGGAATTGAACCCATTTG 58.469 33.333 2.30 0.00 36.73 2.32
998 1008 8.664669 ACAATAAGTAGGAATTGAACCCATTT 57.335 30.769 2.30 0.00 36.73 2.32
1059 1070 5.569355 TGTTGTAATTGGATGTGAGGTGAT 58.431 37.500 0.00 0.00 0.00 3.06
1077 1088 6.959639 ACTCCATTGTTACAAGATTGTTGT 57.040 33.333 3.63 4.48 42.35 3.32
1080 1091 8.635765 ACATAACTCCATTGTTACAAGATTGT 57.364 30.769 3.63 3.37 44.86 2.71
1107 1118 5.620206 TGTGTCTTATTCCGCATGGATAAT 58.380 37.500 0.00 0.00 45.91 1.28
1108 1119 5.029807 TGTGTCTTATTCCGCATGGATAA 57.970 39.130 0.00 0.00 45.91 1.75
1188 1199 3.555956 CAGTTGAACATACGATAGGTGCC 59.444 47.826 0.00 0.00 43.77 5.01
1356 1367 4.072131 GGGTGATAAAAGTGCAGTCTCAA 58.928 43.478 0.00 0.00 0.00 3.02
1381 1392 5.408604 CACACCAAAGATAGTACAACAGACC 59.591 44.000 0.00 0.00 0.00 3.85
1415 1426 5.539574 TGTCCCATTGCCTATGAAAATATGG 59.460 40.000 0.00 0.00 36.26 2.74
1419 1430 3.706086 GGTGTCCCATTGCCTATGAAAAT 59.294 43.478 0.00 0.00 36.26 1.82
1421 1432 2.733956 GGTGTCCCATTGCCTATGAAA 58.266 47.619 0.00 0.00 36.26 2.69
1437 1448 1.068127 GCTATCGTCATAACCCGGTGT 59.932 52.381 0.00 0.00 0.00 4.16
1541 1552 9.326413 AGTTAAATGCGAGCTAAATAATACAGT 57.674 29.630 0.00 0.00 0.00 3.55
1578 1589 9.681062 ACTGTTTTTAGCATATATAACACCAGT 57.319 29.630 0.00 0.00 0.00 4.00
1620 1631 5.163663 TGTTTCTGTTCTGTCACCAACAATC 60.164 40.000 0.00 0.00 37.45 2.67
1682 1693 9.643693 GAAACATAGGATGATCAACAAAAACAT 57.356 29.630 0.00 0.00 0.00 2.71
1745 1756 8.710749 AATGTATATATTGTTCAGTGGGCATT 57.289 30.769 0.00 0.00 0.00 3.56
1855 1866 3.150458 TCTCGGAAGTCTGTTCCAGTA 57.850 47.619 4.73 0.00 38.49 2.74
2000 2011 0.400213 TGATTTGAGGGGCTGAACGT 59.600 50.000 0.00 0.00 0.00 3.99
2018 2029 8.931775 GCTAAAACAAGGGTTGGTAATTTTATG 58.068 33.333 0.00 0.00 37.30 1.90
2045 2057 6.320164 TGCTACCAACACATACCATTAATTCC 59.680 38.462 0.00 0.00 0.00 3.01
2057 2069 3.057315 GCACTTCAATGCTACCAACACAT 60.057 43.478 0.00 0.00 42.62 3.21
2348 2370 1.109609 TGTGCCAGTCATTTGCAACA 58.890 45.000 0.00 0.00 36.65 3.33
2435 2457 3.751479 ACAAAAGGAAGGAAATGGTGC 57.249 42.857 0.00 0.00 0.00 5.01
2441 2463 5.993748 ACTTGTCAACAAAAGGAAGGAAA 57.006 34.783 0.00 0.00 35.15 3.13
2471 2493 5.973565 GTGAAGCATAAAACCTATGATGCAC 59.026 40.000 5.59 5.59 45.72 4.57
2492 2514 7.181361 TCAAAATAAGGATGGGAAATCTGTGA 58.819 34.615 0.00 0.00 0.00 3.58
2502 2524 4.460263 TCACCGATCAAAATAAGGATGGG 58.540 43.478 0.00 0.00 42.89 4.00
2503 2525 6.639632 ATTCACCGATCAAAATAAGGATGG 57.360 37.500 0.00 0.00 0.00 3.51
2507 2530 8.122952 GTCAACTATTCACCGATCAAAATAAGG 58.877 37.037 0.00 0.00 0.00 2.69
2511 2534 6.094048 CAGGTCAACTATTCACCGATCAAAAT 59.906 38.462 0.00 0.00 35.13 1.82
2624 2647 6.347888 CCATCAACAAAATCAAATGAAGGCAC 60.348 38.462 0.00 0.00 0.00 5.01
2629 2652 8.591940 TCATACCCATCAACAAAATCAAATGAA 58.408 29.630 0.00 0.00 0.00 2.57
2660 2683 7.800155 TCTCTATCAAAACAACACAACATGA 57.200 32.000 0.00 0.00 0.00 3.07
2720 2743 2.026356 TGCCTGCACACATTATGGTACT 60.026 45.455 0.00 0.00 0.00 2.73
2721 2744 2.364632 TGCCTGCACACATTATGGTAC 58.635 47.619 0.00 0.00 0.00 3.34
2757 2781 6.387192 TTCATCCAGTTAATCTTTCTCCCA 57.613 37.500 0.00 0.00 0.00 4.37
2792 2816 2.550830 AAGGACCACATCACACTCAC 57.449 50.000 0.00 0.00 0.00 3.51
2832 2856 4.899457 TCTGGACCAGAAGTGAGTTCTTTA 59.101 41.667 22.30 0.00 43.54 1.85
2850 2874 3.433598 CCAACTCAACACCTTTCTCTGGA 60.434 47.826 0.00 0.00 0.00 3.86
2877 2901 0.884704 GAGGCTTTGCACGAAGGACA 60.885 55.000 0.52 0.00 0.00 4.02
2943 2967 5.178797 ACACTGATGTACTTATCTGTTGCC 58.821 41.667 0.00 0.00 37.26 4.52
2982 3006 4.590222 AGGAGAAACTGAAACCTTACCGTA 59.410 41.667 0.00 0.00 0.00 4.02
2992 3016 5.132144 ACTGGTAAAGGAGGAGAAACTGAAA 59.868 40.000 0.00 0.00 0.00 2.69
3007 3038 4.699637 TCCATATGCGGTAACTGGTAAAG 58.300 43.478 0.00 0.00 0.00 1.85
3011 3042 4.967084 TTATCCATATGCGGTAACTGGT 57.033 40.909 0.00 0.00 0.00 4.00
3037 3071 5.163258 CCTGAGAAATGCCCTCTGTAAGTAT 60.163 44.000 0.00 0.00 33.76 2.12
3049 3083 0.322816 TCTGCCACCTGAGAAATGCC 60.323 55.000 0.00 0.00 0.00 4.40
3056 3090 0.035881 TCTTGCTTCTGCCACCTGAG 59.964 55.000 0.00 0.00 38.71 3.35
3117 3151 2.389715 ACAGGTATGCTAGAGTCCACC 58.610 52.381 0.00 0.00 0.00 4.61
3153 3187 3.134081 ACCCTTTCTGTTCTTCAAGACGA 59.866 43.478 0.00 0.00 0.00 4.20
3198 3232 0.251033 TCTCCTCGACAAACTCCGGA 60.251 55.000 2.93 2.93 0.00 5.14
3208 3242 6.758886 ACAATTATCTGAACATTCTCCTCGAC 59.241 38.462 0.00 0.00 0.00 4.20
3286 3320 6.403866 AAGCAACGATCATCTTCTATCTCT 57.596 37.500 0.00 0.00 0.00 3.10
3302 3336 3.117434 ACGCAATTTAGCTAAGCAACG 57.883 42.857 14.41 14.84 0.00 4.10
3312 3346 4.145876 TGAAGAGCACAACGCAATTTAG 57.854 40.909 0.00 0.00 46.13 1.85
3320 3354 1.597854 TGCCCTGAAGAGCACAACG 60.598 57.895 0.00 0.00 33.08 4.10
3327 3361 0.035630 CTTCCCTGTGCCCTGAAGAG 60.036 60.000 0.00 0.00 37.07 2.85
3329 3363 0.401738 TTCTTCCCTGTGCCCTGAAG 59.598 55.000 0.00 0.00 36.42 3.02
3383 3417 1.555075 TCTGGCATTCTGTGGGTACTC 59.445 52.381 0.00 0.00 0.00 2.59
3427 3461 0.794229 CGAACATCATGTGCGCCAAC 60.794 55.000 4.89 0.00 43.10 3.77
3537 3571 8.697846 AATTTAACGTCTAATTGATCGAGTCA 57.302 30.769 6.94 0.00 34.25 3.41
3582 3616 4.346709 TCAATGACTCTGTTAACTGGGACA 59.653 41.667 18.25 17.54 0.00 4.02
3592 3626 9.793252 GTAAAATGCAATATCAATGACTCTGTT 57.207 29.630 0.00 0.00 0.00 3.16
3626 3660 2.039418 CCTCCGGTGGATGAACAGATA 58.961 52.381 17.99 0.00 0.00 1.98
3674 3708 1.210967 GAACCCATGTGGAATCCGGTA 59.789 52.381 0.00 0.00 37.39 4.02
3704 3738 7.092399 ACCAAGCCTATATTGTTCTTTACCTCT 60.092 37.037 0.00 0.00 0.00 3.69
3745 3779 4.968812 TCATCAATGCATCGACATTTGT 57.031 36.364 0.00 0.00 38.19 2.83
3845 3879 2.065993 TGTACTGTTTCAGAGCTCGC 57.934 50.000 8.37 0.00 35.18 5.03
3917 3951 0.038744 CAGTTCTGCCCACCTTCCAT 59.961 55.000 0.00 0.00 0.00 3.41
3955 3989 6.272822 AGAAACTCATTCATGTTAAAGGGC 57.727 37.500 0.00 0.00 40.72 5.19
3959 3993 9.342308 ACAGAGAAGAAACTCATTCATGTTAAA 57.658 29.630 0.00 0.00 40.72 1.52
3980 4014 6.333416 TCAATTTATCCTTGTCTCGACAGAG 58.667 40.000 0.00 2.10 42.94 3.35
4061 4095 1.026584 GACTTCCCTCGACTCCTAGC 58.973 60.000 0.00 0.00 0.00 3.42
4113 4147 1.866601 GGCCACATTCTGTTTTGCAAC 59.133 47.619 0.00 0.00 0.00 4.17
4118 4152 1.963515 GGAGTGGCCACATTCTGTTTT 59.036 47.619 36.39 13.63 34.13 2.43
4229 4263 6.299805 TGCACATGGAGTAGTAGAGAAATT 57.700 37.500 0.00 0.00 0.00 1.82
4251 4285 9.311916 TCTTGTTGAAATTCAGGTATTTTGTTG 57.688 29.630 0.00 0.00 0.00 3.33
4256 4290 8.695456 ACTTGTCTTGTTGAAATTCAGGTATTT 58.305 29.630 0.00 0.00 0.00 1.40
4258 4292 7.823745 ACTTGTCTTGTTGAAATTCAGGTAT 57.176 32.000 0.00 0.00 0.00 2.73
4401 4445 3.476552 AGTTCTTGATTTGGCAGAACGA 58.523 40.909 8.74 0.00 42.36 3.85
4426 4471 9.084533 AGTAAACTTATTAGGCAATTTTGGTGA 57.915 29.630 0.00 0.00 0.00 4.02
4451 4496 9.503427 CCGGTTTATTCTATTTCTTGCTTTAAG 57.497 33.333 0.00 0.00 37.76 1.85
4463 4537 1.944709 GCGGTGCCGGTTTATTCTATT 59.055 47.619 12.82 0.00 40.19 1.73
4482 4556 2.223782 TGGTGAAATCTGTTGCACAAGC 60.224 45.455 2.05 0.00 44.40 4.01
4488 4562 4.333926 GGAGATACTGGTGAAATCTGTTGC 59.666 45.833 0.00 0.00 30.19 4.17
4506 4580 5.657302 ACTTTATCGTCACAGGTAAGGAGAT 59.343 40.000 0.00 0.00 0.00 2.75
4507 4581 5.014858 ACTTTATCGTCACAGGTAAGGAGA 58.985 41.667 0.00 0.00 0.00 3.71
4516 4590 7.095229 TGGATTGAGAAAACTTTATCGTCACAG 60.095 37.037 5.15 0.00 31.34 3.66
4517 4591 6.708502 TGGATTGAGAAAACTTTATCGTCACA 59.291 34.615 5.15 0.00 31.34 3.58
4519 4593 7.065803 GGATGGATTGAGAAAACTTTATCGTCA 59.934 37.037 5.15 0.00 31.34 4.35
4520 4594 7.410485 GGATGGATTGAGAAAACTTTATCGTC 58.590 38.462 0.00 0.00 31.34 4.20
4521 4595 6.318900 GGGATGGATTGAGAAAACTTTATCGT 59.681 38.462 0.00 0.00 31.34 3.73
4541 4616 2.040278 TGTGGAGAAAGGTGAAGGGATG 59.960 50.000 0.00 0.00 0.00 3.51
4558 4633 5.676079 CAAGTACTTGAAACACAGGTTGTGG 60.676 44.000 28.17 0.00 46.23 4.17
4602 4677 6.349115 CCCTCTTTGATTCACACATTCTCAAG 60.349 42.308 0.00 0.00 0.00 3.02
4603 4678 5.474532 CCCTCTTTGATTCACACATTCTCAA 59.525 40.000 0.00 0.00 0.00 3.02
4604 4679 5.005740 CCCTCTTTGATTCACACATTCTCA 58.994 41.667 0.00 0.00 0.00 3.27
4706 4781 6.472486 TGCATCTTTTCGTAGTAGATTCTTCG 59.528 38.462 0.00 0.00 0.00 3.79
4853 4931 2.000701 CCAGTGATAGGGGGTGGCA 61.001 63.158 0.00 0.00 0.00 4.92
4870 4948 5.169295 AGTCGTTGTCATTTCTAGCTAACC 58.831 41.667 0.00 0.00 0.00 2.85
4966 5045 0.820891 ATGGTTCATGCCAGCGGATC 60.821 55.000 0.00 0.00 42.47 3.36
5027 5106 2.441001 AGTTGGGATGCTGGAATCTAGG 59.559 50.000 0.00 0.00 0.00 3.02
5041 5120 3.264193 ACAGCTGACATCATTAGTTGGGA 59.736 43.478 23.35 0.00 0.00 4.37
5122 5201 0.328258 AGGGTCACCAAGGCATGTAC 59.672 55.000 0.00 0.00 40.13 2.90


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

AutoCloner maintained by Alex Coulton.