Multiple sequence alignment - TraesCS7A01G236400

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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 TraesCS7A01G236400 chr7A 100.000 4598 0 0 1 4598 209588849 209593446 0.000000e+00 8492.0
1 TraesCS7A01G236400 chr7B 88.962 2890 153 64 109 2911 164160541 164163351 0.000000e+00 3417.0
2 TraesCS7A01G236400 chr7B 96.336 655 24 0 2946 3600 164163605 164164259 0.000000e+00 1077.0
3 TraesCS7A01G236400 chr7B 91.273 550 25 12 3637 4172 164164253 164164793 0.000000e+00 728.0
4 TraesCS7A01G236400 chr7B 88.235 136 14 2 4378 4512 164499971 164500105 1.320000e-35 161.0
5 TraesCS7A01G236400 chr7B 87.288 118 5 4 1 108 164160392 164160509 4.830000e-25 126.0
6 TraesCS7A01G236400 chr7D 89.010 2111 113 50 442 2499 199560397 199562441 0.000000e+00 2503.0
7 TraesCS7A01G236400 chr7D 93.876 996 42 11 2912 3899 199562870 199563854 0.000000e+00 1483.0
8 TraesCS7A01G236400 chr7D 95.000 340 16 1 2559 2897 199562445 199562784 2.440000e-147 532.0
9 TraesCS7A01G236400 chr7D 91.316 380 13 6 1 363 199559495 199559871 6.870000e-138 501.0
10 TraesCS7A01G236400 chr7D 88.942 208 17 3 3967 4174 199564115 199564316 7.640000e-63 252.0
11 TraesCS7A01G236400 chr7D 90.370 135 13 0 4378 4512 199565884 199566018 1.310000e-40 178.0
12 TraesCS7A01G236400 chr5B 77.609 460 86 12 3077 3526 438017653 438017201 3.530000e-66 263.0
13 TraesCS7A01G236400 chr5B 91.860 86 7 0 4511 4596 637142938 637142853 2.250000e-23 121.0
14 TraesCS7A01G236400 chr5A 77.657 461 84 14 3077 3526 471724030 471723578 3.530000e-66 263.0
15 TraesCS7A01G236400 chr5A 90.805 87 6 1 4510 4596 546416152 546416068 1.050000e-21 115.0
16 TraesCS7A01G236400 chr5D 77.655 452 82 14 3086 3526 369308100 369307657 1.640000e-64 257.0
17 TraesCS7A01G236400 chr5D 77.654 358 71 8 3077 3428 369317934 369317580 4.660000e-50 209.0
18 TraesCS7A01G236400 chr5D 91.139 79 7 0 4518 4596 41363268 41363190 1.750000e-19 108.0
19 TraesCS7A01G236400 chr2B 96.774 93 1 1 4084 4174 538955361 538955269 2.220000e-33 154.0
20 TraesCS7A01G236400 chr2B 94.845 97 2 3 4075 4170 497799996 497799902 1.030000e-31 148.0
21 TraesCS7A01G236400 chr3B 96.739 92 1 2 4084 4173 805612354 805612445 7.970000e-33 152.0
22 TraesCS7A01G236400 chr3B 96.739 92 1 2 4084 4173 805619143 805619234 7.970000e-33 152.0
23 TraesCS7A01G236400 chr2D 98.837 86 0 1 4088 4173 423859912 423859828 7.970000e-33 152.0
24 TraesCS7A01G236400 chr2A 96.739 92 1 1 4084 4173 601338213 601338122 7.970000e-33 152.0
25 TraesCS7A01G236400 chr2A 93.269 104 3 4 4081 4182 564616394 564616495 2.870000e-32 150.0
26 TraesCS7A01G236400 chr2A 88.764 89 9 1 4510 4598 98127479 98127566 1.750000e-19 108.0
27 TraesCS7A01G236400 chr4D 91.026 78 7 0 4519 4596 58150006 58150083 6.290000e-19 106.0
28 TraesCS7A01G236400 chr4A 91.026 78 7 0 4519 4596 706262686 706262609 6.290000e-19 106.0
29 TraesCS7A01G236400 chr6A 89.610 77 8 0 4520 4596 563263343 563263419 1.050000e-16 99.0
30 TraesCS7A01G236400 chr6A 89.474 76 8 0 4520 4595 24835273 24835198 3.790000e-16 97.1
31 TraesCS7A01G236400 chr6A 88.158 76 9 0 4520 4595 50268535 50268460 1.760000e-14 91.6


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 TraesCS7A01G236400 chr7A 209588849 209593446 4597 False 8492.000000 8492 100.00000 1 4598 1 chr7A.!!$F1 4597
1 TraesCS7A01G236400 chr7B 164160392 164164793 4401 False 1337.000000 3417 90.96475 1 4172 4 chr7B.!!$F2 4171
2 TraesCS7A01G236400 chr7D 199559495 199566018 6523 False 908.166667 2503 91.41900 1 4512 6 chr7D.!!$F1 4511

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
447 944 0.035458 GTGGTTGAGGTGGAGTGGAG 59.965 60.000 0.00 0.0 0.00 3.86 F
682 1194 0.320771 CCATATAGCCGCCACTCCAC 60.321 60.000 0.00 0.0 0.00 4.02 F
815 1338 0.515919 CGTGAGTCGTCGTCGTACTG 60.516 60.000 10.53 0.0 38.33 2.74 F
1275 1816 0.583438 CTATGCGATCCTTGTTGCGG 59.417 55.000 0.00 0.0 0.00 5.69 F
1291 1832 1.590147 CGGCCGAGGTTCTTAGTGT 59.410 57.895 24.07 0.0 0.00 3.55 F
3123 3935 1.872234 CACGATCAACGCCGACGAT 60.872 57.895 0.00 0.0 46.94 3.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1275 1816 1.270678 ACCAACACTAAGAACCTCGGC 60.271 52.381 0.00 0.0 0.00 5.54 R
2267 2859 1.823797 TGTGCACTTGCTGATATGCA 58.176 45.000 19.41 0.0 45.45 3.96 R
2335 2927 1.876156 GTGTTTCAGAGGCTTGTCCAG 59.124 52.381 0.00 0.0 37.29 3.86 R
3174 3986 1.446099 GTGCGAGAACATGCTCCGA 60.446 57.895 10.05 0.0 0.00 4.55 R
3175 3987 2.792290 CGTGCGAGAACATGCTCCG 61.792 63.158 0.00 0.0 0.00 4.63 R
4513 6923 0.036388 GTGACCCTTCTGATCGGCAA 60.036 55.000 0.00 0.0 0.00 4.52 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
65 66 2.044946 GGCCCTGATTCGTTGCCT 60.045 61.111 0.00 0.00 39.05 4.75
66 67 1.223487 GGCCCTGATTCGTTGCCTA 59.777 57.895 0.00 0.00 39.05 3.93
67 68 0.393808 GGCCCTGATTCGTTGCCTAA 60.394 55.000 0.00 0.00 39.05 2.69
69 70 1.379527 CCCTGATTCGTTGCCTAACC 58.620 55.000 0.00 0.00 33.12 2.85
172 218 2.414824 CGCTGCCGTAAAAGCCAAAATA 60.415 45.455 0.00 0.00 35.98 1.40
179 225 5.220397 GCCGTAAAAGCCAAAATATTTGCTC 60.220 40.000 12.07 1.76 36.59 4.26
281 331 3.133691 GCAGAAGCGATATGAACCATCA 58.866 45.455 0.00 0.00 40.57 3.07
282 332 3.186001 GCAGAAGCGATATGAACCATCAG 59.814 47.826 0.00 0.00 39.39 2.90
318 460 0.179056 ATCCCCACTGATTAACCGCG 60.179 55.000 0.00 0.00 0.00 6.46
339 481 1.131126 CATTTGCGGCCAGTAGTTGAG 59.869 52.381 2.24 0.00 0.00 3.02
345 487 0.173708 GGCCAGTAGTTGAGACTCCG 59.826 60.000 0.00 0.00 37.33 4.63
394 540 4.510812 TCGTCGTCGAAAATGTTTTTCTG 58.489 39.130 1.37 5.24 43.34 3.02
395 541 3.657625 CGTCGTCGAAAATGTTTTTCTGG 59.342 43.478 0.00 1.57 39.71 3.86
398 544 3.649073 GTCGAAAATGTTTTTCTGGGGG 58.351 45.455 10.11 0.00 0.00 5.40
403 549 5.762711 CGAAAATGTTTTTCTGGGGGAAATT 59.237 36.000 10.11 0.00 42.63 1.82
406 552 4.953940 TGTTTTTCTGGGGGAAATTGAG 57.046 40.909 0.00 0.00 42.63 3.02
412 572 3.766545 TCTGGGGGAAATTGAGTGAAAG 58.233 45.455 0.00 0.00 0.00 2.62
424 584 3.045634 TGAGTGAAAGGAAGGGAACTGA 58.954 45.455 0.00 0.00 42.68 3.41
426 586 3.318313 AGTGAAAGGAAGGGAACTGAGA 58.682 45.455 0.00 0.00 42.68 3.27
439 599 1.051812 ACTGAGAGGTGGTTGAGGTG 58.948 55.000 0.00 0.00 0.00 4.00
447 944 0.035458 GTGGTTGAGGTGGAGTGGAG 59.965 60.000 0.00 0.00 0.00 3.86
451 948 1.483595 TTGAGGTGGAGTGGAGGCAG 61.484 60.000 0.00 0.00 0.00 4.85
483 982 9.574516 AATCTAATAAATCGGCTGGATAAAAGT 57.425 29.630 0.00 0.00 34.08 2.66
515 1018 0.815615 GGAGCATTCACCATCCGTCC 60.816 60.000 0.00 0.00 0.00 4.79
646 1158 1.150081 CCCATGTCCTCTGCCATCC 59.850 63.158 0.00 0.00 0.00 3.51
647 1159 1.150081 CCATGTCCTCTGCCATCCC 59.850 63.158 0.00 0.00 0.00 3.85
648 1160 1.638679 CCATGTCCTCTGCCATCCCA 61.639 60.000 0.00 0.00 0.00 4.37
649 1161 0.477204 CATGTCCTCTGCCATCCCAT 59.523 55.000 0.00 0.00 0.00 4.00
650 1162 0.769873 ATGTCCTCTGCCATCCCATC 59.230 55.000 0.00 0.00 0.00 3.51
651 1163 1.348008 TGTCCTCTGCCATCCCATCC 61.348 60.000 0.00 0.00 0.00 3.51
682 1194 0.320771 CCATATAGCCGCCACTCCAC 60.321 60.000 0.00 0.00 0.00 4.02
706 1228 3.339093 CCCCACCCCACCTCCTTC 61.339 72.222 0.00 0.00 0.00 3.46
810 1333 2.202146 GACCGTGAGTCGTCGTCG 60.202 66.667 0.00 0.00 35.30 5.12
811 1334 2.947890 GACCGTGAGTCGTCGTCGT 61.948 63.158 1.33 0.00 35.30 4.34
812 1335 1.617755 GACCGTGAGTCGTCGTCGTA 61.618 60.000 1.33 0.00 35.30 3.43
813 1336 1.225583 CCGTGAGTCGTCGTCGTAC 60.226 63.158 1.33 0.00 37.94 3.67
815 1338 0.515919 CGTGAGTCGTCGTCGTACTG 60.516 60.000 10.53 0.00 38.33 2.74
816 1339 0.786581 GTGAGTCGTCGTCGTACTGA 59.213 55.000 10.53 2.13 38.33 3.41
817 1340 1.392853 GTGAGTCGTCGTCGTACTGAT 59.607 52.381 10.53 0.00 38.33 2.90
818 1341 1.657594 TGAGTCGTCGTCGTACTGATC 59.342 52.381 10.53 0.00 38.33 2.92
819 1342 1.925847 GAGTCGTCGTCGTACTGATCT 59.074 52.381 10.53 0.00 38.33 2.75
820 1343 3.111838 GAGTCGTCGTCGTACTGATCTA 58.888 50.000 10.53 0.00 38.33 1.98
823 1346 1.260033 CGTCGTCGTACTGATCTACCC 59.740 57.143 0.00 0.00 0.00 3.69
824 1347 1.601430 GTCGTCGTACTGATCTACCCC 59.399 57.143 0.00 0.00 0.00 4.95
825 1348 0.585357 CGTCGTACTGATCTACCCCG 59.415 60.000 0.00 0.00 0.00 5.73
1164 1705 4.179599 CTCCCCTCCCCTCCCCTC 62.180 77.778 0.00 0.00 0.00 4.30
1168 1709 4.825679 CCTCCCCTCCCCTCCCAC 62.826 77.778 0.00 0.00 0.00 4.61
1173 1714 4.455137 CCTCCCCTCCCACCCCAT 62.455 72.222 0.00 0.00 0.00 4.00
1174 1715 2.774351 CTCCCCTCCCACCCCATC 60.774 72.222 0.00 0.00 0.00 3.51
1175 1716 4.448340 TCCCCTCCCACCCCATCC 62.448 72.222 0.00 0.00 0.00 3.51
1189 1730 1.678635 CATCCGCCCCTCTGCAAAA 60.679 57.895 0.00 0.00 0.00 2.44
1229 1770 7.255590 CCTGTTTGGTTTCTTGATTGACATACT 60.256 37.037 0.00 0.00 0.00 2.12
1266 1807 2.232452 AGTGTATCCTGCTATGCGATCC 59.768 50.000 0.00 0.00 0.00 3.36
1275 1816 0.583438 CTATGCGATCCTTGTTGCGG 59.417 55.000 0.00 0.00 0.00 5.69
1291 1832 1.590147 CGGCCGAGGTTCTTAGTGT 59.410 57.895 24.07 0.00 0.00 3.55
1333 1874 4.389374 TGGGTTTTCTTGTGATCAGTCTC 58.611 43.478 0.00 0.00 0.00 3.36
1336 1877 4.083590 GGTTTTCTTGTGATCAGTCTCAGC 60.084 45.833 0.00 0.00 0.00 4.26
1345 1886 4.754114 GTGATCAGTCTCAGCTTTTCAGTT 59.246 41.667 0.00 0.00 0.00 3.16
1350 1903 2.945668 GTCTCAGCTTTTCAGTTGTGGT 59.054 45.455 0.00 0.00 33.10 4.16
1408 1963 7.112452 AGGCTGTTTCTGTTAAAAATCTTGT 57.888 32.000 0.00 0.00 0.00 3.16
1427 1982 7.587037 TCTTGTTGGTTTGATTCTGAGAAAT 57.413 32.000 0.00 0.00 0.00 2.17
1431 1986 5.964958 TGGTTTGATTCTGAGAAATGGTC 57.035 39.130 0.00 0.00 0.00 4.02
1464 2025 5.763698 GGTAGTAGCAGTGAAGGTTTTCTTT 59.236 40.000 0.00 0.00 35.50 2.52
1466 2027 5.685728 AGTAGCAGTGAAGGTTTTCTTTCT 58.314 37.500 0.00 0.00 36.93 2.52
1468 2029 5.506686 AGCAGTGAAGGTTTTCTTTCTTC 57.493 39.130 0.00 0.00 36.93 2.87
1469 2030 5.196695 AGCAGTGAAGGTTTTCTTTCTTCT 58.803 37.500 0.00 0.00 38.10 2.85
1470 2031 5.298026 AGCAGTGAAGGTTTTCTTTCTTCTC 59.702 40.000 0.00 0.00 38.10 2.87
1471 2032 5.298026 GCAGTGAAGGTTTTCTTTCTTCTCT 59.702 40.000 0.00 0.00 40.05 3.10
1472 2033 6.483640 GCAGTGAAGGTTTTCTTTCTTCTCTA 59.516 38.462 0.00 0.00 38.49 2.43
1473 2034 7.012421 GCAGTGAAGGTTTTCTTTCTTCTCTAA 59.988 37.037 0.00 0.00 38.49 2.10
1474 2035 8.893727 CAGTGAAGGTTTTCTTTCTTCTCTAAA 58.106 33.333 0.00 0.00 38.49 1.85
1475 2036 9.114952 AGTGAAGGTTTTCTTTCTTCTCTAAAG 57.885 33.333 0.00 0.00 38.65 1.85
1476 2037 8.894731 GTGAAGGTTTTCTTTCTTCTCTAAAGT 58.105 33.333 0.00 0.00 38.10 2.66
1480 2041 9.767228 AGGTTTTCTTTCTTCTCTAAAGTACTC 57.233 33.333 0.00 0.00 35.79 2.59
1481 2042 8.991026 GGTTTTCTTTCTTCTCTAAAGTACTCC 58.009 37.037 0.00 0.00 35.79 3.85
1592 2156 5.661056 ATTATCAAGAGAGACGTGGAACA 57.339 39.130 0.00 0.00 35.74 3.18
1595 2159 3.717707 TCAAGAGAGACGTGGAACAAAG 58.282 45.455 0.00 0.00 44.16 2.77
1598 2162 2.297597 AGAGAGACGTGGAACAAAGGAG 59.702 50.000 0.00 0.00 44.16 3.69
1603 2167 4.461198 AGACGTGGAACAAAGGAGATTTT 58.539 39.130 0.00 0.00 44.16 1.82
1604 2168 4.515567 AGACGTGGAACAAAGGAGATTTTC 59.484 41.667 0.00 0.00 44.16 2.29
1605 2169 4.461198 ACGTGGAACAAAGGAGATTTTCT 58.539 39.130 0.00 0.00 44.16 2.52
1607 2171 5.701290 ACGTGGAACAAAGGAGATTTTCTAG 59.299 40.000 0.00 0.00 44.16 2.43
1609 2173 6.128526 CGTGGAACAAAGGAGATTTTCTAGAC 60.129 42.308 0.00 0.00 44.16 2.59
1610 2174 6.710744 GTGGAACAAAGGAGATTTTCTAGACA 59.289 38.462 0.00 0.00 44.16 3.41
1722 2286 9.745018 ACTTCTTCAAATCTCATCAGGATAAAA 57.255 29.630 0.00 0.00 0.00 1.52
1733 2297 9.456147 TCTCATCAGGATAAAATTTTCGGTTTA 57.544 29.630 6.72 0.00 0.00 2.01
1906 2470 6.069684 CTCTTTGCAGAGTTGTCAAATTCT 57.930 37.500 3.90 0.00 41.74 2.40
1924 2488 2.991540 GCCAAGAACACAGCCCCC 60.992 66.667 0.00 0.00 0.00 5.40
1973 2537 5.885449 ACTTCTGATATCCTTTCCTCCAG 57.115 43.478 0.00 0.00 0.00 3.86
2029 2593 9.305555 TGTCTTTTACTCCTTACTATGTACTGT 57.694 33.333 0.00 0.00 0.00 3.55
2121 2711 5.692204 GTGATGAGTTATCAGTTCATACGGG 59.308 44.000 0.00 0.00 46.09 5.28
2171 2761 5.122869 AGTGTCATGCAAAAGCAGTATACAG 59.877 40.000 5.50 0.00 0.00 2.74
2205 2797 2.957402 ACATTACATGATCGGGGCAT 57.043 45.000 0.00 0.00 0.00 4.40
2261 2853 8.519526 TGTTATTCCAAAATACCATGTTGAGTC 58.480 33.333 0.00 0.00 0.00 3.36
2267 2859 5.456921 AAATACCATGTTGAGTCCTCCAT 57.543 39.130 0.00 0.00 0.00 3.41
2335 2927 4.989279 ATTTGCATGAACACAGGTATCC 57.011 40.909 0.00 0.00 0.00 2.59
2427 3019 5.923733 TTGAGATAGAGTTTCTGGACCTC 57.076 43.478 0.00 0.00 0.00 3.85
2469 3061 3.059352 AGCACTGTTTCACCATCTACC 57.941 47.619 0.00 0.00 0.00 3.18
2471 3063 3.073062 AGCACTGTTTCACCATCTACCTT 59.927 43.478 0.00 0.00 0.00 3.50
2474 3066 4.821805 CACTGTTTCACCATCTACCTTTGT 59.178 41.667 0.00 0.00 0.00 2.83
2581 3173 4.220821 GGAGTGACATTCTTGACTCACCTA 59.779 45.833 0.00 0.00 37.22 3.08
2585 3177 5.866633 GTGACATTCTTGACTCACCTAGAAG 59.133 44.000 0.00 0.00 30.87 2.85
2933 3734 5.426504 TCCGGTTCAAACTTACAGTTAACA 58.573 37.500 8.61 0.00 37.47 2.41
2997 3809 4.524802 ATGTAATTCTGCATTCCAGGGA 57.475 40.909 0.00 0.00 42.05 4.20
3026 3838 2.415010 CTCGATCTGGGCCTCACG 59.585 66.667 4.53 5.88 0.00 4.35
3069 3881 3.706373 ACCGCGCTGTCATCCCTT 61.706 61.111 5.56 0.00 0.00 3.95
3123 3935 1.872234 CACGATCAACGCCGACGAT 60.872 57.895 0.00 0.00 46.94 3.73
3280 4092 2.730382 TCCTCAACTACATCTACGGCA 58.270 47.619 0.00 0.00 0.00 5.69
3606 4418 4.910585 GGCCGGTGAGCGTATGGG 62.911 72.222 1.90 0.00 0.00 4.00
3607 4419 4.910585 GCCGGTGAGCGTATGGGG 62.911 72.222 1.90 0.00 0.00 4.96
3627 4439 2.575993 CCTCTGCGTCTCTGGGTG 59.424 66.667 0.00 0.00 0.00 4.61
3628 4440 2.575993 CTCTGCGTCTCTGGGTGG 59.424 66.667 0.00 0.00 0.00 4.61
3629 4441 2.203640 TCTGCGTCTCTGGGTGGT 60.204 61.111 0.00 0.00 0.00 4.16
3726 4538 5.499139 CCATTGTTTGTTGGCGATATAGT 57.501 39.130 0.00 0.00 0.00 2.12
3742 4554 9.783425 GGCGATATAGTAAAATTTAACGTGTAC 57.217 33.333 0.00 0.00 0.00 2.90
3799 4611 7.661437 TGGTAATCCAATTCATGTAGATGTAGC 59.339 37.037 0.00 0.00 41.25 3.58
3862 4676 4.481930 TGACAGTTATTTTGTGAAGCCG 57.518 40.909 0.00 0.00 0.00 5.52
3864 4678 4.576873 TGACAGTTATTTTGTGAAGCCGAA 59.423 37.500 0.00 0.00 0.00 4.30
3889 4704 2.604686 TGCCTCCCTCTTCGTGCT 60.605 61.111 0.00 0.00 0.00 4.40
3904 4719 2.354510 TCGTGCTTCTTTGGTTCAGTTG 59.645 45.455 0.00 0.00 0.00 3.16
3918 4733 1.878088 TCAGTTGAGACTAACGCGAGT 59.122 47.619 15.93 6.65 39.55 4.18
3939 4754 6.678663 CGAGTTAGCACGTAAATCTTTTGATG 59.321 38.462 0.00 0.00 39.48 3.07
3940 4755 6.842163 AGTTAGCACGTAAATCTTTTGATGG 58.158 36.000 0.00 0.00 39.48 3.51
3959 4782 1.065636 GGTAAGTGGTAAGGGTCCAGC 60.066 57.143 0.00 0.00 35.49 4.85
3960 4783 1.626825 GTAAGTGGTAAGGGTCCAGCA 59.373 52.381 0.00 0.00 35.49 4.41
3961 4784 1.372501 AAGTGGTAAGGGTCCAGCAT 58.627 50.000 0.00 0.00 35.49 3.79
3962 4785 0.620556 AGTGGTAAGGGTCCAGCATG 59.379 55.000 0.00 0.00 35.49 4.06
4063 5071 7.413438 GGTGCTGTGAAGACTTGAATATGTAAG 60.413 40.741 0.00 0.00 0.00 2.34
4064 5072 7.331934 GTGCTGTGAAGACTTGAATATGTAAGA 59.668 37.037 0.00 0.00 0.00 2.10
4075 5083 9.477484 ACTTGAATATGTAAGACCTAAATAGCG 57.523 33.333 6.30 0.00 0.00 4.26
4199 5780 7.902920 AATCATTTCAGGCAATAGGTTACAT 57.097 32.000 0.00 0.00 0.00 2.29
4203 5784 6.509418 TTTCAGGCAATAGGTTACATGAAC 57.491 37.500 0.00 0.00 37.31 3.18
4217 5798 3.705604 ACATGAACGAGGCAAAAACTTG 58.294 40.909 0.00 0.00 0.00 3.16
4228 5809 6.509358 CGAGGCAAAAACTTGTTGGTAAAATG 60.509 38.462 0.00 0.00 0.00 2.32
4230 5811 6.315144 AGGCAAAAACTTGTTGGTAAAATGTC 59.685 34.615 0.00 0.00 0.00 3.06
4232 5813 7.398746 GCAAAAACTTGTTGGTAAAATGTCTC 58.601 34.615 0.00 0.00 0.00 3.36
4258 5839 2.159761 ACATGTATTTTTGTCGACGGCG 60.160 45.455 2.87 2.87 39.35 6.46
4272 5853 0.608640 ACGGCGAGAAAACAGGAGAT 59.391 50.000 16.62 0.00 0.00 2.75
4282 5863 7.201453 GCGAGAAAACAGGAGATTAAGACTTAC 60.201 40.741 0.00 0.00 0.00 2.34
4285 5866 8.871125 AGAAAACAGGAGATTAAGACTTACTGA 58.129 33.333 13.76 0.00 31.81 3.41
4287 5868 9.442047 AAAACAGGAGATTAAGACTTACTGATG 57.558 33.333 13.76 5.23 31.81 3.07
4288 5869 7.118496 ACAGGAGATTAAGACTTACTGATGG 57.882 40.000 13.76 0.00 31.81 3.51
4289 5870 6.670027 ACAGGAGATTAAGACTTACTGATGGT 59.330 38.462 13.76 0.00 31.81 3.55
4290 5871 7.181125 ACAGGAGATTAAGACTTACTGATGGTT 59.819 37.037 13.76 0.00 31.81 3.67
4291 5872 8.043710 CAGGAGATTAAGACTTACTGATGGTTT 58.956 37.037 0.00 0.00 0.00 3.27
4292 5873 8.043710 AGGAGATTAAGACTTACTGATGGTTTG 58.956 37.037 0.00 0.00 0.00 2.93
4293 5874 7.281100 GGAGATTAAGACTTACTGATGGTTTGG 59.719 40.741 0.00 0.00 0.00 3.28
4294 5875 6.599638 AGATTAAGACTTACTGATGGTTTGGC 59.400 38.462 0.00 0.00 0.00 4.52
4295 5876 2.699954 AGACTTACTGATGGTTTGGCG 58.300 47.619 0.00 0.00 0.00 5.69
4319 6729 2.305635 TCATGGGAAGCAGCTCTGTTTA 59.694 45.455 0.00 0.00 34.15 2.01
4335 6745 2.569853 TGTTTATGTGTGGGGATCTCGT 59.430 45.455 0.00 0.00 0.00 4.18
4339 6749 2.758327 TGTGGGGATCTCGTCGGG 60.758 66.667 0.00 0.00 0.00 5.14
4341 6751 4.458829 TGGGGATCTCGTCGGGCT 62.459 66.667 0.00 0.00 0.00 5.19
4342 6752 3.917760 GGGGATCTCGTCGGGCTG 61.918 72.222 0.00 0.00 0.00 4.85
4343 6753 2.833582 GGGATCTCGTCGGGCTGA 60.834 66.667 0.00 0.00 0.00 4.26
4344 6754 2.413765 GGATCTCGTCGGGCTGAC 59.586 66.667 16.63 16.63 44.53 3.51
4345 6755 2.122167 GGATCTCGTCGGGCTGACT 61.122 63.158 23.18 5.25 45.87 3.41
4346 6756 1.064946 GATCTCGTCGGGCTGACTG 59.935 63.158 23.18 16.39 45.87 3.51
4347 6757 1.658686 GATCTCGTCGGGCTGACTGT 61.659 60.000 23.18 7.12 45.87 3.55
4348 6758 0.393944 ATCTCGTCGGGCTGACTGTA 60.394 55.000 23.18 9.11 45.87 2.74
4349 6759 0.607217 TCTCGTCGGGCTGACTGTAA 60.607 55.000 23.18 6.27 45.87 2.41
4350 6760 0.456221 CTCGTCGGGCTGACTGTAAT 59.544 55.000 23.18 0.00 45.87 1.89
4351 6761 0.892755 TCGTCGGGCTGACTGTAATT 59.107 50.000 23.18 0.00 45.87 1.40
4352 6762 1.274167 TCGTCGGGCTGACTGTAATTT 59.726 47.619 23.18 0.00 45.87 1.82
4353 6763 2.073816 CGTCGGGCTGACTGTAATTTT 58.926 47.619 23.18 0.00 45.87 1.82
4354 6764 2.482721 CGTCGGGCTGACTGTAATTTTT 59.517 45.455 23.18 0.00 45.87 1.94
4396 6806 5.938125 GGGCTGACTGTAATTCTCTTTTACA 59.062 40.000 0.00 0.00 37.25 2.41
4397 6807 6.430000 GGGCTGACTGTAATTCTCTTTTACAA 59.570 38.462 0.00 0.00 38.65 2.41
4404 6814 9.143155 ACTGTAATTCTCTTTTACAAATTGGGT 57.857 29.630 0.00 0.00 38.65 4.51
4418 6828 6.600388 ACAAATTGGGTTCCTTGCTTATTTT 58.400 32.000 0.00 0.00 0.00 1.82
4419 6829 6.486320 ACAAATTGGGTTCCTTGCTTATTTTG 59.514 34.615 0.00 0.00 0.00 2.44
4477 6887 5.193099 AGTTTTATGGAGGCATGTACCTT 57.807 39.130 0.00 0.00 41.32 3.50
4478 6888 6.321821 AGTTTTATGGAGGCATGTACCTTA 57.678 37.500 0.00 0.00 41.32 2.69
4483 6893 4.623932 TGGAGGCATGTACCTTATCATC 57.376 45.455 0.00 0.00 41.32 2.92
4488 6898 5.371526 AGGCATGTACCTTATCATCTTGTG 58.628 41.667 0.00 0.00 36.28 3.33
4512 6922 7.013834 TGTAATACAAACCTTTGGGATCCTTT 58.986 34.615 12.58 0.00 42.34 3.11
4513 6923 7.511028 TGTAATACAAACCTTTGGGATCCTTTT 59.489 33.333 12.58 0.00 42.34 2.27
4514 6924 7.387265 AATACAAACCTTTGGGATCCTTTTT 57.613 32.000 12.58 0.00 42.34 1.94
4515 6925 5.034852 ACAAACCTTTGGGATCCTTTTTG 57.965 39.130 12.58 13.33 42.34 2.44
4516 6926 3.769739 AACCTTTGGGATCCTTTTTGC 57.230 42.857 12.58 0.00 36.25 3.68
4517 6927 1.977854 ACCTTTGGGATCCTTTTTGCC 59.022 47.619 12.58 0.00 36.25 4.52
4518 6928 1.066929 CCTTTGGGATCCTTTTTGCCG 60.067 52.381 12.58 0.00 33.58 5.69
4519 6929 1.892474 CTTTGGGATCCTTTTTGCCGA 59.108 47.619 12.58 0.00 0.00 5.54
4520 6930 2.230130 TTGGGATCCTTTTTGCCGAT 57.770 45.000 12.58 0.00 0.00 4.18
4521 6931 1.762708 TGGGATCCTTTTTGCCGATC 58.237 50.000 12.58 0.00 33.17 3.69
4522 6932 1.005332 TGGGATCCTTTTTGCCGATCA 59.995 47.619 12.58 0.00 35.19 2.92
4523 6933 1.678101 GGGATCCTTTTTGCCGATCAG 59.322 52.381 12.58 0.00 35.19 2.90
4524 6934 2.643551 GGATCCTTTTTGCCGATCAGA 58.356 47.619 3.84 0.00 35.19 3.27
4525 6935 3.016736 GGATCCTTTTTGCCGATCAGAA 58.983 45.455 3.84 0.00 35.19 3.02
4526 6936 3.065925 GGATCCTTTTTGCCGATCAGAAG 59.934 47.826 3.84 0.00 35.19 2.85
4527 6937 2.436417 TCCTTTTTGCCGATCAGAAGG 58.564 47.619 0.00 11.78 39.35 3.46
4528 6938 1.474077 CCTTTTTGCCGATCAGAAGGG 59.526 52.381 0.00 5.10 36.75 3.95
4529 6939 2.162681 CTTTTTGCCGATCAGAAGGGT 58.837 47.619 0.00 0.00 0.00 4.34
4530 6940 1.821216 TTTTGCCGATCAGAAGGGTC 58.179 50.000 0.00 0.00 0.00 4.46
4531 6941 0.690192 TTTGCCGATCAGAAGGGTCA 59.310 50.000 0.00 0.00 0.00 4.02
4532 6942 0.036388 TTGCCGATCAGAAGGGTCAC 60.036 55.000 0.00 0.00 0.00 3.67
4533 6943 1.191489 TGCCGATCAGAAGGGTCACA 61.191 55.000 0.00 0.00 0.00 3.58
4534 6944 0.741221 GCCGATCAGAAGGGTCACAC 60.741 60.000 0.00 0.00 0.00 3.82
4535 6945 0.458543 CCGATCAGAAGGGTCACACG 60.459 60.000 0.00 0.00 0.00 4.49
4536 6946 0.458543 CGATCAGAAGGGTCACACGG 60.459 60.000 0.00 0.00 0.00 4.94
4537 6947 0.741221 GATCAGAAGGGTCACACGGC 60.741 60.000 0.00 0.00 0.00 5.68
4538 6948 2.185310 ATCAGAAGGGTCACACGGCC 62.185 60.000 0.00 0.00 0.00 6.13
4539 6949 3.637273 AGAAGGGTCACACGGCCC 61.637 66.667 0.00 0.00 45.16 5.80
4540 6950 4.717313 GAAGGGTCACACGGCCCC 62.717 72.222 0.00 0.00 45.95 5.80
4544 6954 4.360405 GGTCACACGGCCCCCATT 62.360 66.667 0.00 0.00 0.00 3.16
4545 6955 2.282887 GTCACACGGCCCCCATTT 60.283 61.111 0.00 0.00 0.00 2.32
4546 6956 1.906333 GTCACACGGCCCCCATTTT 60.906 57.895 0.00 0.00 0.00 1.82
4547 6957 1.605165 TCACACGGCCCCCATTTTC 60.605 57.895 0.00 0.00 0.00 2.29
4548 6958 1.905843 CACACGGCCCCCATTTTCA 60.906 57.895 0.00 0.00 0.00 2.69
4549 6959 1.078347 ACACGGCCCCCATTTTCAT 59.922 52.632 0.00 0.00 0.00 2.57
4550 6960 0.544120 ACACGGCCCCCATTTTCATT 60.544 50.000 0.00 0.00 0.00 2.57
4551 6961 1.272760 ACACGGCCCCCATTTTCATTA 60.273 47.619 0.00 0.00 0.00 1.90
4552 6962 1.136110 CACGGCCCCCATTTTCATTAC 59.864 52.381 0.00 0.00 0.00 1.89
4553 6963 0.383949 CGGCCCCCATTTTCATTACG 59.616 55.000 0.00 0.00 0.00 3.18
4554 6964 1.770294 GGCCCCCATTTTCATTACGA 58.230 50.000 0.00 0.00 0.00 3.43
4555 6965 2.104170 GGCCCCCATTTTCATTACGAA 58.896 47.619 0.00 0.00 0.00 3.85
4556 6966 2.498078 GGCCCCCATTTTCATTACGAAA 59.502 45.455 0.00 0.00 41.95 3.46
4569 6979 8.996988 TTTCATTACGAAAATGTAGTCACAAC 57.003 30.769 12.64 0.00 40.70 3.32
4570 6980 7.716768 TCATTACGAAAATGTAGTCACAACA 57.283 32.000 12.64 0.00 38.42 3.33
4571 6981 8.317891 TCATTACGAAAATGTAGTCACAACAT 57.682 30.769 12.64 0.00 38.42 2.71
4572 6982 9.425577 TCATTACGAAAATGTAGTCACAACATA 57.574 29.630 12.64 0.00 38.42 2.29
4573 6983 9.472995 CATTACGAAAATGTAGTCACAACATAC 57.527 33.333 0.00 0.00 38.42 2.39
4574 6984 8.590719 TTACGAAAATGTAGTCACAACATACA 57.409 30.769 0.00 0.00 38.42 2.29
4575 6985 7.485418 ACGAAAATGTAGTCACAACATACAA 57.515 32.000 0.00 0.00 38.42 2.41
4576 6986 7.921787 ACGAAAATGTAGTCACAACATACAAA 58.078 30.769 0.00 0.00 38.42 2.83
4577 6987 7.853929 ACGAAAATGTAGTCACAACATACAAAC 59.146 33.333 0.00 0.00 38.42 2.93
4578 6988 7.322699 CGAAAATGTAGTCACAACATACAAACC 59.677 37.037 0.00 0.00 38.42 3.27
4579 6989 7.575414 AAATGTAGTCACAACATACAAACCA 57.425 32.000 0.00 0.00 38.42 3.67
4580 6990 7.575414 AATGTAGTCACAACATACAAACCAA 57.425 32.000 0.00 0.00 38.42 3.67
4581 6991 6.612247 TGTAGTCACAACATACAAACCAAG 57.388 37.500 0.00 0.00 0.00 3.61
4582 6992 6.116806 TGTAGTCACAACATACAAACCAAGT 58.883 36.000 0.00 0.00 0.00 3.16
4583 6993 6.600032 TGTAGTCACAACATACAAACCAAGTT 59.400 34.615 0.00 0.00 0.00 2.66
4584 6994 6.524101 AGTCACAACATACAAACCAAGTTT 57.476 33.333 0.00 0.00 36.05 2.66
4585 6995 6.560711 AGTCACAACATACAAACCAAGTTTC 58.439 36.000 0.00 0.00 33.10 2.78
4586 6996 6.151985 AGTCACAACATACAAACCAAGTTTCA 59.848 34.615 0.00 0.00 33.10 2.69
4587 6997 6.978080 GTCACAACATACAAACCAAGTTTCAT 59.022 34.615 0.00 0.00 33.10 2.57
4588 6998 8.132362 GTCACAACATACAAACCAAGTTTCATA 58.868 33.333 0.00 0.00 33.10 2.15
4589 6999 8.132362 TCACAACATACAAACCAAGTTTCATAC 58.868 33.333 0.00 0.00 33.10 2.39
4590 7000 7.918033 CACAACATACAAACCAAGTTTCATACA 59.082 33.333 0.00 0.00 33.10 2.29
4591 7001 8.134895 ACAACATACAAACCAAGTTTCATACAG 58.865 33.333 0.00 0.00 33.10 2.74
4592 7002 8.349245 CAACATACAAACCAAGTTTCATACAGA 58.651 33.333 0.00 0.00 33.10 3.41
4593 7003 7.871853 ACATACAAACCAAGTTTCATACAGAC 58.128 34.615 0.00 0.00 33.10 3.51
4594 7004 7.719633 ACATACAAACCAAGTTTCATACAGACT 59.280 33.333 0.00 0.00 33.10 3.24
4595 7005 8.567948 CATACAAACCAAGTTTCATACAGACTT 58.432 33.333 0.00 0.00 33.10 3.01
4596 7006 7.027778 ACAAACCAAGTTTCATACAGACTTC 57.972 36.000 0.00 0.00 33.10 3.01
4597 7007 6.601613 ACAAACCAAGTTTCATACAGACTTCA 59.398 34.615 0.00 0.00 33.10 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
179 225 1.936880 CTTGCTCTCGTCGCTAGCG 60.937 63.158 30.91 30.91 39.14 4.26
194 240 2.352617 GCTCCATATCTCCGCTCTCTTG 60.353 54.545 0.00 0.00 0.00 3.02
281 331 4.079558 GGGGATCATTGGCCATATCATACT 60.080 45.833 6.09 0.00 0.00 2.12
282 332 4.210331 GGGGATCATTGGCCATATCATAC 58.790 47.826 6.09 0.00 0.00 2.39
318 460 0.456653 CAACTACTGGCCGCAAATGC 60.457 55.000 0.00 0.00 37.78 3.56
334 476 2.405172 GGTTCTTCACGGAGTCTCAAC 58.595 52.381 1.47 0.00 41.61 3.18
339 481 1.726853 CATGGGTTCTTCACGGAGTC 58.273 55.000 0.00 0.00 41.61 3.36
345 487 0.819582 CCATGGCATGGGTTCTTCAC 59.180 55.000 34.26 0.00 46.86 3.18
394 540 3.169512 TCCTTTCACTCAATTTCCCCC 57.830 47.619 0.00 0.00 0.00 5.40
395 541 3.511540 CCTTCCTTTCACTCAATTTCCCC 59.488 47.826 0.00 0.00 0.00 4.81
398 544 5.536538 AGTTCCCTTCCTTTCACTCAATTTC 59.463 40.000 0.00 0.00 0.00 2.17
403 549 3.045634 TCAGTTCCCTTCCTTTCACTCA 58.954 45.455 0.00 0.00 0.00 3.41
406 552 3.558109 CCTCTCAGTTCCCTTCCTTTCAC 60.558 52.174 0.00 0.00 0.00 3.18
412 572 0.615850 CCACCTCTCAGTTCCCTTCC 59.384 60.000 0.00 0.00 0.00 3.46
424 584 0.104934 ACTCCACCTCAACCACCTCT 60.105 55.000 0.00 0.00 0.00 3.69
426 586 1.418908 CCACTCCACCTCAACCACCT 61.419 60.000 0.00 0.00 0.00 4.00
439 599 0.617820 TTACTCCCTGCCTCCACTCC 60.618 60.000 0.00 0.00 0.00 3.85
447 944 5.875359 CCGATTTATTAGATTACTCCCTGCC 59.125 44.000 0.00 0.00 0.00 4.85
451 948 5.875359 CCAGCCGATTTATTAGATTACTCCC 59.125 44.000 0.00 0.00 0.00 4.30
482 981 6.371389 GTGAATGCTCCGGCTTATTAATTAC 58.629 40.000 0.00 0.00 39.59 1.89
483 982 5.472137 GGTGAATGCTCCGGCTTATTAATTA 59.528 40.000 0.00 0.00 39.59 1.40
484 983 4.278419 GGTGAATGCTCCGGCTTATTAATT 59.722 41.667 0.00 0.00 39.59 1.40
486 985 3.211045 GGTGAATGCTCCGGCTTATTAA 58.789 45.455 0.00 0.00 39.59 1.40
488 987 1.064758 TGGTGAATGCTCCGGCTTATT 60.065 47.619 0.00 0.00 39.59 1.40
489 988 0.546122 TGGTGAATGCTCCGGCTTAT 59.454 50.000 0.00 0.00 39.59 1.73
646 1158 2.603008 GTGGTGGGATGGGGATGG 59.397 66.667 0.00 0.00 0.00 3.51
647 1159 1.658053 ATGGTGGTGGGATGGGGATG 61.658 60.000 0.00 0.00 0.00 3.51
648 1160 0.028118 TATGGTGGTGGGATGGGGAT 60.028 55.000 0.00 0.00 0.00 3.85
649 1161 0.028118 ATATGGTGGTGGGATGGGGA 60.028 55.000 0.00 0.00 0.00 4.81
650 1162 1.635487 CTATATGGTGGTGGGATGGGG 59.365 57.143 0.00 0.00 0.00 4.96
651 1163 1.004745 GCTATATGGTGGTGGGATGGG 59.995 57.143 0.00 0.00 0.00 4.00
692 1204 4.410400 GCGGAAGGAGGTGGGGTG 62.410 72.222 0.00 0.00 0.00 4.61
740 1263 4.824515 AGTCGCGGAGGGCTAGCT 62.825 66.667 15.72 0.00 41.64 3.32
741 1264 4.273257 GAGTCGCGGAGGGCTAGC 62.273 72.222 6.04 6.04 41.64 3.42
742 1265 3.597728 GGAGTCGCGGAGGGCTAG 61.598 72.222 6.13 0.00 41.64 3.42
809 1332 1.105167 TGGCGGGGTAGATCAGTACG 61.105 60.000 0.00 0.00 0.00 3.67
810 1333 1.000955 CATGGCGGGGTAGATCAGTAC 59.999 57.143 0.00 0.00 0.00 2.73
811 1334 1.338107 CATGGCGGGGTAGATCAGTA 58.662 55.000 0.00 0.00 0.00 2.74
812 1335 0.691078 ACATGGCGGGGTAGATCAGT 60.691 55.000 0.00 0.00 0.00 3.41
813 1336 0.034059 GACATGGCGGGGTAGATCAG 59.966 60.000 0.00 0.00 0.00 2.90
815 1338 1.006102 CGACATGGCGGGGTAGATC 60.006 63.158 14.85 0.00 0.00 2.75
816 1339 1.745320 GACGACATGGCGGGGTAGAT 61.745 60.000 27.41 0.66 35.12 1.98
817 1340 2.363276 ACGACATGGCGGGGTAGA 60.363 61.111 27.41 0.00 35.12 2.59
818 1341 2.106332 GACGACATGGCGGGGTAG 59.894 66.667 27.41 0.00 35.12 3.18
819 1342 3.829044 CGACGACATGGCGGGGTA 61.829 66.667 27.41 0.00 35.12 3.69
824 1347 3.842126 CAGCACGACGACATGGCG 61.842 66.667 21.98 21.98 37.29 5.69
825 1348 2.432456 TCAGCACGACGACATGGC 60.432 61.111 0.00 0.00 0.00 4.40
1062 1600 1.049289 GGTAGGTGTAGCAGGGGAGG 61.049 65.000 0.00 0.00 0.00 4.30
1151 1692 4.825679 GTGGGAGGGGAGGGGAGG 62.826 77.778 0.00 0.00 0.00 4.30
1170 1711 3.643595 TTTGCAGAGGGGCGGATGG 62.644 63.158 0.00 0.00 36.28 3.51
1171 1712 1.039233 ATTTTGCAGAGGGGCGGATG 61.039 55.000 0.00 0.00 36.28 3.51
1172 1713 0.324645 AATTTTGCAGAGGGGCGGAT 60.325 50.000 0.00 0.00 36.28 4.18
1173 1714 1.076549 AATTTTGCAGAGGGGCGGA 59.923 52.632 0.00 0.00 36.28 5.54
1174 1715 1.216178 CAATTTTGCAGAGGGGCGG 59.784 57.895 0.00 0.00 36.28 6.13
1175 1716 0.318120 AACAATTTTGCAGAGGGGCG 59.682 50.000 0.00 0.00 36.28 6.13
1176 1717 1.799544 CAACAATTTTGCAGAGGGGC 58.200 50.000 0.00 0.00 0.00 5.80
1189 1730 2.185004 AACAGGTAGCGAGCAACAAT 57.815 45.000 0.00 0.00 0.00 2.71
1229 1770 1.311859 CACTCTGCTTTGCTGGACAA 58.688 50.000 0.00 0.00 36.13 3.18
1258 1799 2.764314 GCCGCAACAAGGATCGCAT 61.764 57.895 0.00 0.00 0.00 4.73
1266 1807 2.966309 GAACCTCGGCCGCAACAAG 61.966 63.158 23.51 12.55 0.00 3.16
1275 1816 1.270678 ACCAACACTAAGAACCTCGGC 60.271 52.381 0.00 0.00 0.00 5.54
1291 1832 5.009631 CCCATGACTGAACTCATAAACCAA 58.990 41.667 0.00 0.00 29.28 3.67
1333 1874 4.108699 TCAAACCACAACTGAAAAGCTG 57.891 40.909 0.00 0.00 0.00 4.24
1336 1877 6.332630 ACAGAATCAAACCACAACTGAAAAG 58.667 36.000 0.00 0.00 0.00 2.27
1345 1886 4.698201 TGGTAGACAGAATCAAACCACA 57.302 40.909 0.00 0.00 39.48 4.17
1408 1963 5.243730 GGACCATTTCTCAGAATCAAACCAA 59.756 40.000 0.00 0.00 0.00 3.67
1443 2004 5.685728 AGAAAGAAAACCTTCACTGCTACT 58.314 37.500 0.00 0.00 33.02 2.57
1444 2005 6.261158 AGAAGAAAGAAAACCTTCACTGCTAC 59.739 38.462 0.00 0.00 38.89 3.58
1445 2006 6.357367 AGAAGAAAGAAAACCTTCACTGCTA 58.643 36.000 0.00 0.00 38.89 3.49
1575 2139 2.802816 CCTTTGTTCCACGTCTCTCTTG 59.197 50.000 0.00 0.00 0.00 3.02
1595 2159 9.452065 GTGAAAACTTTTGTCTAGAAAATCTCC 57.548 33.333 0.00 0.00 0.00 3.71
1603 2167 7.827236 TGGAGAAAGTGAAAACTTTTGTCTAGA 59.173 33.333 5.40 0.00 39.74 2.43
1604 2168 7.985476 TGGAGAAAGTGAAAACTTTTGTCTAG 58.015 34.615 5.40 0.00 39.74 2.43
1605 2169 7.931578 TGGAGAAAGTGAAAACTTTTGTCTA 57.068 32.000 5.40 2.21 39.74 2.59
1607 2171 6.866248 TGTTGGAGAAAGTGAAAACTTTTGTC 59.134 34.615 5.40 5.92 39.74 3.18
1609 2173 6.868339 AGTGTTGGAGAAAGTGAAAACTTTTG 59.132 34.615 5.40 0.00 39.74 2.44
1610 2174 6.993079 AGTGTTGGAGAAAGTGAAAACTTTT 58.007 32.000 5.40 0.00 39.74 2.27
1738 2302 9.640952 CCCCATCCTTTATGATTTTAGAACTTA 57.359 33.333 0.00 0.00 37.86 2.24
1743 2307 8.108378 TGTACCCCATCCTTTATGATTTTAGA 57.892 34.615 0.00 0.00 37.86 2.10
1744 2308 8.760980 TTGTACCCCATCCTTTATGATTTTAG 57.239 34.615 0.00 0.00 37.86 1.85
1745 2309 8.561769 TCTTGTACCCCATCCTTTATGATTTTA 58.438 33.333 0.00 0.00 37.86 1.52
1761 2325 4.906060 ACCCTCATAACTATCTTGTACCCC 59.094 45.833 0.00 0.00 0.00 4.95
1906 2470 2.203480 GGGGCTGTGTTCTTGGCA 60.203 61.111 0.00 0.00 0.00 4.92
1939 2503 6.369065 AGGATATCAGAAGTTTCGTGACAAAC 59.631 38.462 4.83 3.52 36.64 2.93
1973 2537 6.283544 TGGATGCTCTATGATCTTCTGATC 57.716 41.667 0.00 0.00 46.89 2.92
2121 2711 8.906636 TGATCTCTACACAAATTAACTCGTAC 57.093 34.615 0.00 0.00 0.00 3.67
2205 2797 3.627395 AGAATTTCAGACCGGCATGTA 57.373 42.857 0.00 0.00 0.00 2.29
2261 2853 2.552743 CACTTGCTGATATGCATGGAGG 59.447 50.000 10.16 0.00 42.96 4.30
2267 2859 1.823797 TGTGCACTTGCTGATATGCA 58.176 45.000 19.41 0.00 45.45 3.96
2335 2927 1.876156 GTGTTTCAGAGGCTTGTCCAG 59.124 52.381 0.00 0.00 37.29 3.86
2469 3061 8.023050 TGTACCAAACATTGACAAAAACAAAG 57.977 30.769 0.00 0.00 31.43 2.77
2471 3063 7.441157 TGTTGTACCAAACATTGACAAAAACAA 59.559 29.630 0.00 0.00 38.10 2.83
2474 3066 7.441157 TGTTGTTGTACCAAACATTGACAAAAA 59.559 29.630 0.10 0.00 37.81 1.94
2581 3173 5.356470 GCTGTCTAAAATCAGATTGGCTTCT 59.644 40.000 0.00 0.00 34.02 2.85
2585 3177 4.732938 GCAGCTGTCTAAAATCAGATTGGC 60.733 45.833 16.64 0.00 34.02 4.52
2748 3340 3.803555 CTTTGCACGTCTCTGATCAAAC 58.196 45.455 0.00 0.00 0.00 2.93
2893 3486 7.942990 TGAACCGGAATTTACAGTGTTTATTT 58.057 30.769 9.46 0.00 0.00 1.40
2895 3488 7.513371 TTGAACCGGAATTTACAGTGTTTAT 57.487 32.000 9.46 0.00 0.00 1.40
3026 3838 2.816087 TCTGAAGACTGCTTGATTTGGC 59.184 45.455 0.00 0.00 33.61 4.52
3174 3986 1.446099 GTGCGAGAACATGCTCCGA 60.446 57.895 10.05 0.00 0.00 4.55
3175 3987 2.792290 CGTGCGAGAACATGCTCCG 61.792 63.158 0.00 0.00 0.00 4.63
3280 4092 4.749310 CTCCTCGCTGCGCAGGTT 62.749 66.667 36.47 0.00 31.92 3.50
3609 4421 3.386237 ACCCAGAGACGCAGAGGC 61.386 66.667 0.00 0.00 0.00 4.70
3610 4422 2.575993 CACCCAGAGACGCAGAGG 59.424 66.667 0.00 0.00 0.00 3.69
3611 4423 2.279069 ACCACCCAGAGACGCAGAG 61.279 63.158 0.00 0.00 0.00 3.35
3613 4425 2.047844 CACCACCCAGAGACGCAG 60.048 66.667 0.00 0.00 0.00 5.18
3614 4426 3.625897 CCACCACCCAGAGACGCA 61.626 66.667 0.00 0.00 0.00 5.24
3615 4427 3.626924 ACCACCACCCAGAGACGC 61.627 66.667 0.00 0.00 0.00 5.19
3616 4428 2.343758 CACCACCACCCAGAGACG 59.656 66.667 0.00 0.00 0.00 4.18
3624 4436 1.826487 GAACACCACCACCACCACC 60.826 63.158 0.00 0.00 0.00 4.61
3627 4439 2.598467 TGGAACACCACCACCACC 59.402 61.111 0.00 0.00 32.03 4.61
3725 4537 7.104326 TCGAGGTGTACACGTTAAATTTTAC 57.896 36.000 21.20 5.59 0.00 2.01
3726 4538 7.887996 ATCGAGGTGTACACGTTAAATTTTA 57.112 32.000 21.20 3.47 0.00 1.52
3742 4554 4.764679 TGAACAAAATCCAATCGAGGTG 57.235 40.909 0.00 0.00 0.00 4.00
3799 4611 0.172578 TACAGGATCACCAAGACGCG 59.827 55.000 3.53 3.53 38.94 6.01
3862 4676 0.463474 GAGGGAGGCAGCTCACATTC 60.463 60.000 0.00 0.00 0.00 2.67
3864 4678 0.913451 AAGAGGGAGGCAGCTCACAT 60.913 55.000 0.00 0.00 0.00 3.21
3889 4704 5.522460 CGTTAGTCTCAACTGAACCAAAGAA 59.478 40.000 0.00 0.00 36.92 2.52
3918 4733 6.811253 ACCATCAAAAGATTTACGTGCTAA 57.189 33.333 0.00 0.00 0.00 3.09
3939 4754 1.065636 GCTGGACCCTTACCACTTACC 60.066 57.143 0.00 0.00 33.57 2.85
3940 4755 1.626825 TGCTGGACCCTTACCACTTAC 59.373 52.381 0.00 0.00 33.57 2.34
3951 4774 0.111061 TATGCCATCATGCTGGACCC 59.889 55.000 19.76 2.38 38.69 4.46
3959 4782 7.012610 TCTGTTGTGAGTTATTATGCCATCATG 59.987 37.037 0.00 0.00 34.22 3.07
3960 4783 7.056006 TCTGTTGTGAGTTATTATGCCATCAT 58.944 34.615 0.00 0.00 36.73 2.45
3961 4784 6.413892 TCTGTTGTGAGTTATTATGCCATCA 58.586 36.000 0.00 0.00 0.00 3.07
3962 4785 6.540189 ACTCTGTTGTGAGTTATTATGCCATC 59.460 38.462 0.00 0.00 44.01 3.51
4026 5034 4.402155 TCTTCACAGCACCTGTTTTCAAAT 59.598 37.500 0.00 0.00 42.59 2.32
4027 5035 3.761218 TCTTCACAGCACCTGTTTTCAAA 59.239 39.130 0.00 0.00 42.59 2.69
4028 5036 3.128589 GTCTTCACAGCACCTGTTTTCAA 59.871 43.478 0.00 0.00 42.59 2.69
4029 5037 2.682856 GTCTTCACAGCACCTGTTTTCA 59.317 45.455 0.00 0.00 42.59 2.69
4041 5049 8.037758 AGGTCTTACATATTCAAGTCTTCACAG 58.962 37.037 0.00 0.00 0.00 3.66
4063 5071 5.276270 TGATGTACGTTCGCTATTTAGGTC 58.724 41.667 0.00 0.00 0.00 3.85
4064 5072 5.252969 TGATGTACGTTCGCTATTTAGGT 57.747 39.130 0.00 0.00 0.00 3.08
4074 5082 1.722011 AGGCCTTTGATGTACGTTCG 58.278 50.000 0.00 0.00 0.00 3.95
4075 5083 5.050295 GCTAATAGGCCTTTGATGTACGTTC 60.050 44.000 12.58 0.00 0.00 3.95
4174 5184 7.716799 TGTAACCTATTGCCTGAAATGATTT 57.283 32.000 0.00 0.00 0.00 2.17
4179 5235 6.183360 CGTTCATGTAACCTATTGCCTGAAAT 60.183 38.462 0.00 0.00 37.02 2.17
4187 5243 4.188462 TGCCTCGTTCATGTAACCTATTG 58.812 43.478 0.00 0.00 34.33 1.90
4199 5780 3.506810 CAACAAGTTTTTGCCTCGTTCA 58.493 40.909 0.00 0.00 37.85 3.18
4203 5784 2.577449 ACCAACAAGTTTTTGCCTCG 57.423 45.000 0.00 0.00 37.85 4.63
4217 5798 7.871853 ACATGTGTAAGAGACATTTTACCAAC 58.128 34.615 0.00 0.00 41.14 3.77
4228 5809 7.950496 GTCGACAAAAATACATGTGTAAGAGAC 59.050 37.037 11.55 3.82 33.76 3.36
4230 5811 6.948228 CGTCGACAAAAATACATGTGTAAGAG 59.052 38.462 17.16 0.00 33.76 2.85
4232 5813 6.013085 CCGTCGACAAAAATACATGTGTAAG 58.987 40.000 17.16 0.00 33.76 2.34
4258 5839 9.145865 CAGTAAGTCTTAATCTCCTGTTTTCTC 57.854 37.037 0.00 0.00 0.00 2.87
4272 5853 4.693566 CGCCAAACCATCAGTAAGTCTTAA 59.306 41.667 0.00 0.00 0.00 1.85
4282 5863 1.033746 ATGAGGCGCCAAACCATCAG 61.034 55.000 31.54 0.00 0.00 2.90
4285 5866 2.053865 CCATGAGGCGCCAAACCAT 61.054 57.895 31.54 21.61 0.00 3.55
4287 5868 3.451894 CCCATGAGGCGCCAAACC 61.452 66.667 31.54 14.98 0.00 3.27
4288 5869 1.937546 CTTCCCATGAGGCGCCAAAC 61.938 60.000 31.54 19.58 34.51 2.93
4289 5870 1.678635 CTTCCCATGAGGCGCCAAA 60.679 57.895 31.54 17.23 34.51 3.28
4290 5871 2.045045 CTTCCCATGAGGCGCCAA 60.045 61.111 31.54 17.66 34.51 4.52
4291 5872 4.802051 GCTTCCCATGAGGCGCCA 62.802 66.667 31.54 9.64 33.61 5.69
4292 5873 4.802051 TGCTTCCCATGAGGCGCC 62.802 66.667 21.89 21.89 45.99 6.53
4293 5874 3.207669 CTGCTTCCCATGAGGCGC 61.208 66.667 0.00 0.00 45.99 6.53
4294 5875 3.207669 GCTGCTTCCCATGAGGCG 61.208 66.667 0.00 0.00 45.99 5.52
4295 5876 1.823041 GAGCTGCTTCCCATGAGGC 60.823 63.158 2.53 0.00 43.49 4.70
4319 6729 1.676678 CCGACGAGATCCCCACACAT 61.677 60.000 0.00 0.00 0.00 3.21
4360 6770 2.487762 CAGTCAGCCCTATTCGCAAAAA 59.512 45.455 0.00 0.00 0.00 1.94
4361 6771 2.083774 CAGTCAGCCCTATTCGCAAAA 58.916 47.619 0.00 0.00 0.00 2.44
4362 6772 1.003118 ACAGTCAGCCCTATTCGCAAA 59.997 47.619 0.00 0.00 0.00 3.68
4363 6773 0.613260 ACAGTCAGCCCTATTCGCAA 59.387 50.000 0.00 0.00 0.00 4.85
4364 6774 1.480789 TACAGTCAGCCCTATTCGCA 58.519 50.000 0.00 0.00 0.00 5.10
4365 6775 2.596904 TTACAGTCAGCCCTATTCGC 57.403 50.000 0.00 0.00 0.00 4.70
4366 6776 4.950050 AGAATTACAGTCAGCCCTATTCG 58.050 43.478 0.00 0.00 0.00 3.34
4367 6777 6.168270 AGAGAATTACAGTCAGCCCTATTC 57.832 41.667 0.00 0.00 0.00 1.75
4368 6778 6.567602 AAGAGAATTACAGTCAGCCCTATT 57.432 37.500 0.00 0.00 0.00 1.73
4369 6779 6.567602 AAAGAGAATTACAGTCAGCCCTAT 57.432 37.500 0.00 0.00 0.00 2.57
4370 6780 6.374417 AAAAGAGAATTACAGTCAGCCCTA 57.626 37.500 0.00 0.00 0.00 3.53
4371 6781 4.917906 AAAGAGAATTACAGTCAGCCCT 57.082 40.909 0.00 0.00 0.00 5.19
4372 6782 5.938125 TGTAAAAGAGAATTACAGTCAGCCC 59.062 40.000 0.00 0.00 38.10 5.19
4373 6783 7.435068 TTGTAAAAGAGAATTACAGTCAGCC 57.565 36.000 0.00 0.00 42.40 4.85
4374 6784 9.899226 AATTTGTAAAAGAGAATTACAGTCAGC 57.101 29.630 0.00 0.00 42.40 4.26
4396 6806 6.003326 CCAAAATAAGCAAGGAACCCAATTT 58.997 36.000 0.00 0.00 0.00 1.82
4397 6807 5.514659 CCCAAAATAAGCAAGGAACCCAATT 60.515 40.000 0.00 0.00 0.00 2.32
4404 6814 6.379988 GTCTAATCCCCAAAATAAGCAAGGAA 59.620 38.462 0.00 0.00 0.00 3.36
4418 6828 9.403583 GAAAACATAAATACAGTCTAATCCCCA 57.596 33.333 0.00 0.00 0.00 4.96
4419 6829 8.847196 GGAAAACATAAATACAGTCTAATCCCC 58.153 37.037 0.00 0.00 0.00 4.81
4459 6869 6.501805 AGATGATAAGGTACATGCCTCCATAA 59.498 38.462 0.00 0.00 38.03 1.90
4488 6898 7.476540 AAAGGATCCCAAAGGTTTGTATTAC 57.523 36.000 8.55 0.00 36.45 1.89
4494 6904 3.814842 GCAAAAAGGATCCCAAAGGTTTG 59.185 43.478 8.55 10.79 37.90 2.93
4503 6913 1.678101 CTGATCGGCAAAAAGGATCCC 59.322 52.381 8.55 0.00 36.58 3.85
4506 6916 3.019564 CCTTCTGATCGGCAAAAAGGAT 58.980 45.455 12.43 0.00 36.24 3.24
4512 6922 0.690192 TGACCCTTCTGATCGGCAAA 59.310 50.000 0.00 0.00 0.00 3.68
4513 6923 0.036388 GTGACCCTTCTGATCGGCAA 60.036 55.000 0.00 0.00 0.00 4.52
4514 6924 1.191489 TGTGACCCTTCTGATCGGCA 61.191 55.000 0.00 0.00 0.00 5.69
4515 6925 0.741221 GTGTGACCCTTCTGATCGGC 60.741 60.000 0.00 0.00 0.00 5.54
4516 6926 0.458543 CGTGTGACCCTTCTGATCGG 60.459 60.000 0.00 0.00 0.00 4.18
4517 6927 0.458543 CCGTGTGACCCTTCTGATCG 60.459 60.000 0.00 0.00 0.00 3.69
4518 6928 0.741221 GCCGTGTGACCCTTCTGATC 60.741 60.000 0.00 0.00 0.00 2.92
4519 6929 1.296715 GCCGTGTGACCCTTCTGAT 59.703 57.895 0.00 0.00 0.00 2.90
4520 6930 2.741092 GCCGTGTGACCCTTCTGA 59.259 61.111 0.00 0.00 0.00 3.27
4521 6931 2.358737 GGCCGTGTGACCCTTCTG 60.359 66.667 0.00 0.00 0.00 3.02
4522 6932 3.637273 GGGCCGTGTGACCCTTCT 61.637 66.667 0.00 0.00 43.36 2.85
4523 6933 4.717313 GGGGCCGTGTGACCCTTC 62.717 72.222 0.00 0.00 46.19 3.46
4527 6937 3.879180 AAATGGGGGCCGTGTGACC 62.879 63.158 0.00 0.00 0.00 4.02
4528 6938 1.873270 GAAAATGGGGGCCGTGTGAC 61.873 60.000 0.00 0.00 0.00 3.67
4529 6939 1.605165 GAAAATGGGGGCCGTGTGA 60.605 57.895 0.00 0.00 0.00 3.58
4530 6940 1.257055 ATGAAAATGGGGGCCGTGTG 61.257 55.000 0.00 0.00 0.00 3.82
4531 6941 0.544120 AATGAAAATGGGGGCCGTGT 60.544 50.000 0.00 0.00 0.00 4.49
4532 6942 1.136110 GTAATGAAAATGGGGGCCGTG 59.864 52.381 0.00 0.00 0.00 4.94
4533 6943 1.480789 GTAATGAAAATGGGGGCCGT 58.519 50.000 0.00 0.00 0.00 5.68
4534 6944 0.383949 CGTAATGAAAATGGGGGCCG 59.616 55.000 0.00 0.00 0.00 6.13
4535 6945 1.770294 TCGTAATGAAAATGGGGGCC 58.230 50.000 0.00 0.00 0.00 5.80
4536 6946 3.878160 TTTCGTAATGAAAATGGGGGC 57.122 42.857 0.00 0.00 43.46 5.80
4544 6954 8.613482 TGTTGTGACTACATTTTCGTAATGAAA 58.387 29.630 16.19 0.00 39.29 2.69
4545 6955 8.144155 TGTTGTGACTACATTTTCGTAATGAA 57.856 30.769 16.19 0.00 36.53 2.57
4546 6956 7.716768 TGTTGTGACTACATTTTCGTAATGA 57.283 32.000 16.19 3.85 36.53 2.57
4547 6957 9.472995 GTATGTTGTGACTACATTTTCGTAATG 57.527 33.333 17.01 10.17 37.42 1.90
4548 6958 9.210329 TGTATGTTGTGACTACATTTTCGTAAT 57.790 29.630 17.01 0.00 37.42 1.89
4549 6959 8.590719 TGTATGTTGTGACTACATTTTCGTAA 57.409 30.769 17.01 0.00 37.42 3.18
4550 6960 8.590719 TTGTATGTTGTGACTACATTTTCGTA 57.409 30.769 17.01 0.00 37.42 3.43
4551 6961 7.485418 TTGTATGTTGTGACTACATTTTCGT 57.515 32.000 17.01 0.00 37.42 3.85
4552 6962 7.322699 GGTTTGTATGTTGTGACTACATTTTCG 59.677 37.037 17.01 0.00 37.42 3.46
4553 6963 8.132362 TGGTTTGTATGTTGTGACTACATTTTC 58.868 33.333 17.01 9.43 37.42 2.29
4554 6964 8.001881 TGGTTTGTATGTTGTGACTACATTTT 57.998 30.769 17.01 0.00 37.42 1.82
4555 6965 7.575414 TGGTTTGTATGTTGTGACTACATTT 57.425 32.000 17.01 0.00 37.42 2.32
4556 6966 7.284489 ACTTGGTTTGTATGTTGTGACTACATT 59.716 33.333 17.01 3.29 37.42 2.71
4557 6967 6.770785 ACTTGGTTTGTATGTTGTGACTACAT 59.229 34.615 16.17 16.17 39.44 2.29
4558 6968 6.116806 ACTTGGTTTGTATGTTGTGACTACA 58.883 36.000 1.83 1.83 34.31 2.74
4559 6969 6.613755 ACTTGGTTTGTATGTTGTGACTAC 57.386 37.500 0.00 0.00 0.00 2.73
4560 6970 7.337184 TGAAACTTGGTTTGTATGTTGTGACTA 59.663 33.333 0.17 0.00 35.77 2.59
4561 6971 6.151985 TGAAACTTGGTTTGTATGTTGTGACT 59.848 34.615 0.17 0.00 35.77 3.41
4562 6972 6.326375 TGAAACTTGGTTTGTATGTTGTGAC 58.674 36.000 0.17 0.00 35.77 3.67
4563 6973 6.516739 TGAAACTTGGTTTGTATGTTGTGA 57.483 33.333 0.17 0.00 35.77 3.58
4564 6974 7.918033 TGTATGAAACTTGGTTTGTATGTTGTG 59.082 33.333 0.17 0.00 35.77 3.33
4565 6975 8.001881 TGTATGAAACTTGGTTTGTATGTTGT 57.998 30.769 0.17 0.00 35.77 3.32
4566 6976 8.349245 TCTGTATGAAACTTGGTTTGTATGTTG 58.651 33.333 0.17 0.00 35.77 3.33
4567 6977 8.349983 GTCTGTATGAAACTTGGTTTGTATGTT 58.650 33.333 0.17 0.00 35.77 2.71
4568 6978 7.719633 AGTCTGTATGAAACTTGGTTTGTATGT 59.280 33.333 0.17 0.00 35.77 2.29
4569 6979 8.099364 AGTCTGTATGAAACTTGGTTTGTATG 57.901 34.615 0.17 0.00 35.77 2.39
4570 6980 8.691661 AAGTCTGTATGAAACTTGGTTTGTAT 57.308 30.769 0.17 0.00 35.77 2.29
4571 6981 7.771361 TGAAGTCTGTATGAAACTTGGTTTGTA 59.229 33.333 0.17 0.00 35.77 2.41
4572 6982 6.601613 TGAAGTCTGTATGAAACTTGGTTTGT 59.398 34.615 0.17 0.00 35.77 2.83
4573 6983 7.026631 TGAAGTCTGTATGAAACTTGGTTTG 57.973 36.000 0.17 0.00 35.77 2.93


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

AutoCloner maintained by Alex Coulton.