Multiple sequence alignment - TraesCS6B01G130700

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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 TraesCS6B01G130700 chr6B 100.000 5696 0 0 1 5696 127321129 127326824 0.000000e+00 10519
1 TraesCS6B01G130700 chr6A 93.464 2953 182 9 2751 5696 71448989 71451937 0.000000e+00 4373
2 TraesCS6B01G130700 chr6A 88.833 2391 187 41 1 2355 71446248 71448594 0.000000e+00 2863
3 TraesCS6B01G130700 chr6A 93.684 380 21 3 2358 2736 71448628 71449005 2.980000e-157 566
4 TraesCS6B01G130700 chr6D 93.349 2962 174 17 2751 5696 56847894 56850848 0.000000e+00 4357
5 TraesCS6B01G130700 chr6D 90.562 2384 158 36 9 2355 56845146 56847499 0.000000e+00 3094
6 TraesCS6B01G130700 chr6D 93.684 380 21 3 2358 2736 56847533 56847910 2.980000e-157 566


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 TraesCS6B01G130700 chr6B 127321129 127326824 5695 False 10519.000000 10519 100.000000 1 5696 1 chr6B.!!$F1 5695
1 TraesCS6B01G130700 chr6A 71446248 71451937 5689 False 2600.666667 4373 91.993667 1 5696 3 chr6A.!!$F1 5695
2 TraesCS6B01G130700 chr6D 56845146 56850848 5702 False 2672.333333 4357 92.531667 9 5696 3 chr6D.!!$F1 5687

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
493 498 0.103208 CCACTCCGATTCCTCTTCCG 59.897 60.000 0.00 0.0 0.00 4.30 F
2096 2131 0.106719 CCACCAAACCACTGACCTGT 60.107 55.000 0.00 0.0 0.00 4.00 F
2619 2698 1.314730 TGTTTTCGTCTCCCCTTTGC 58.685 50.000 0.00 0.0 0.00 3.68 F
3383 3465 1.646447 AGGTAGGTCATGGGACTGAGA 59.354 52.381 0.00 0.0 43.77 3.27 F
4150 4238 1.113788 TTTGCTTTCCTGCAGCTGTT 58.886 45.000 16.64 0.0 44.27 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2166 2214 0.032515 TCTAGATGCGACCCTTCCCA 60.033 55.000 0.00 0.0 0.00 4.37 R
3084 3166 1.134189 TGGAGAGCCTCAATCATGCTG 60.134 52.381 0.00 0.0 34.99 4.41 R
3623 3706 1.293062 AGGATCATCACCACTGCCTT 58.707 50.000 0.00 0.0 0.00 4.35 R
4646 4736 0.105964 CAATCCCTCGCCGGTAATCA 59.894 55.000 1.90 0.0 0.00 2.57 R
5622 5715 0.252761 TGGATTGCTCATCGAAGCCA 59.747 50.000 6.64 0.0 41.77 4.75 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
31 32 9.841295 GTGGATTTGATAAAACATAGGGTAGTA 57.159 33.333 0.00 0.00 0.00 1.82
36 37 7.281040 TGATAAAACATAGGGTAGTACGGAG 57.719 40.000 0.00 0.00 0.00 4.63
38 39 4.996788 AAACATAGGGTAGTACGGAGTG 57.003 45.455 0.00 0.00 45.73 3.51
95 97 6.090898 GTGTATTACAAGTGTAACAGGAGCAG 59.909 42.308 6.05 0.00 42.55 4.24
97 99 1.160137 CAAGTGTAACAGGAGCAGCC 58.840 55.000 0.00 0.00 41.43 4.85
100 102 0.602905 GTGTAACAGGAGCAGCCGTT 60.603 55.000 0.00 9.43 43.43 4.44
107 109 0.465460 AGGAGCAGCCGTTGACAAAA 60.465 50.000 0.00 0.00 43.43 2.44
113 115 2.351641 GCAGCCGTTGACAAAATGATCA 60.352 45.455 0.00 0.00 0.00 2.92
114 116 3.236816 CAGCCGTTGACAAAATGATCAC 58.763 45.455 0.00 0.00 0.00 3.06
153 155 4.612943 TCATGGCTTACCGAAAACAAAAC 58.387 39.130 0.00 0.00 39.70 2.43
154 156 3.067721 TGGCTTACCGAAAACAAAACG 57.932 42.857 0.00 0.00 39.70 3.60
157 159 2.466205 GCTTACCGAAAACAAAACGCAG 59.534 45.455 0.00 0.00 0.00 5.18
182 185 8.356657 AGACAAATCAGATAGTCCTATTTCTCG 58.643 37.037 10.76 0.00 0.00 4.04
195 198 2.910688 TTTCTCGGTCTTGCTGACTT 57.089 45.000 9.56 0.00 44.74 3.01
196 199 4.537135 ATTTCTCGGTCTTGCTGACTTA 57.463 40.909 9.56 0.05 44.74 2.24
197 200 4.330944 TTTCTCGGTCTTGCTGACTTAA 57.669 40.909 9.56 0.00 44.74 1.85
217 220 1.172812 GCTTCCACCGAGCCAAGTTT 61.173 55.000 0.00 0.00 34.06 2.66
231 234 6.178607 AGCCAAGTTTGAAAGGATTGAAAT 57.821 33.333 0.00 0.00 0.00 2.17
247 250 8.584157 AGGATTGAAATTTGTAGCACATTGTTA 58.416 29.630 0.00 0.00 0.00 2.41
248 251 8.647226 GGATTGAAATTTGTAGCACATTGTTAC 58.353 33.333 0.00 0.00 35.09 2.50
251 254 7.367285 TGAAATTTGTAGCACATTGTTACTCC 58.633 34.615 0.00 0.00 35.47 3.85
252 255 5.897377 ATTTGTAGCACATTGTTACTCCC 57.103 39.130 2.48 0.00 35.47 4.30
254 257 4.202245 TGTAGCACATTGTTACTCCCTC 57.798 45.455 2.48 0.00 35.47 4.30
255 258 3.580895 TGTAGCACATTGTTACTCCCTCA 59.419 43.478 2.48 0.00 35.47 3.86
256 259 3.788227 AGCACATTGTTACTCCCTCAA 57.212 42.857 0.00 0.00 0.00 3.02
260 263 5.539955 AGCACATTGTTACTCCCTCAAAAAT 59.460 36.000 0.00 0.00 0.00 1.82
261 264 6.719370 AGCACATTGTTACTCCCTCAAAAATA 59.281 34.615 0.00 0.00 0.00 1.40
262 265 7.232534 AGCACATTGTTACTCCCTCAAAAATAA 59.767 33.333 0.00 0.00 0.00 1.40
263 266 7.870445 GCACATTGTTACTCCCTCAAAAATAAA 59.130 33.333 0.00 0.00 0.00 1.40
264 267 9.927668 CACATTGTTACTCCCTCAAAAATAAAT 57.072 29.630 0.00 0.00 0.00 1.40
292 296 3.119849 ACGATGGCCTGAAAATCGAAAAG 60.120 43.478 24.41 0.96 44.57 2.27
364 368 1.142748 CCCGCACAACAGCCAAAAA 59.857 52.632 0.00 0.00 0.00 1.94
401 405 5.679638 GCAAAAGATGAATAAATCCGTGGCT 60.680 40.000 0.00 0.00 0.00 4.75
435 439 4.993945 CGAAGCGCACGCACACAC 62.994 66.667 18.24 2.79 44.88 3.82
489 494 1.479709 CACTCCACTCCGATTCCTCT 58.520 55.000 0.00 0.00 0.00 3.69
493 498 0.103208 CCACTCCGATTCCTCTTCCG 59.897 60.000 0.00 0.00 0.00 4.30
499 504 3.083997 ATTCCTCTTCCGCCGCCT 61.084 61.111 0.00 0.00 0.00 5.52
569 581 0.109412 CGCGAGGTTCGTTTCTAGGT 60.109 55.000 0.00 0.00 42.81 3.08
590 603 2.024414 CTCCGCTTAATTTCCCCCAAG 58.976 52.381 0.00 0.00 0.00 3.61
668 682 3.303397 ATTTCCGCGTGCGTTTCCG 62.303 57.895 13.70 0.00 37.81 4.30
680 694 1.065109 GTTTCCGCGCTTGTTTGGT 59.935 52.632 5.56 0.00 0.00 3.67
765 779 3.088641 ACTGAGTCAGCCCACAGTATGT 61.089 50.000 20.31 0.00 43.13 2.29
795 815 2.294979 ACGAACAGTGAGGTTTTTCCC 58.705 47.619 0.00 0.00 36.75 3.97
838 858 1.528586 CTCCTTGCAGTTTCGTCAGTG 59.471 52.381 0.00 0.00 0.00 3.66
853 873 1.169577 CAGTGTAGGAGTCTGACGCT 58.830 55.000 11.27 5.52 34.32 5.07
860 880 1.211969 GAGTCTGACGCTGCGGTTA 59.788 57.895 26.95 10.73 0.00 2.85
873 893 2.930040 CTGCGGTTATCGAATGTGTTCT 59.070 45.455 0.00 0.00 42.43 3.01
874 894 2.670905 TGCGGTTATCGAATGTGTTCTG 59.329 45.455 0.00 0.00 42.43 3.02
875 895 2.536928 GCGGTTATCGAATGTGTTCTGC 60.537 50.000 0.00 0.00 42.43 4.26
876 896 2.285026 CGGTTATCGAATGTGTTCTGCG 60.285 50.000 0.00 0.00 42.43 5.18
883 903 0.511221 AATGTGTTCTGCGTGCGTAC 59.489 50.000 0.00 0.00 0.00 3.67
899 919 1.404449 CGTACATGAAGTTACCGGCCA 60.404 52.381 0.00 0.00 0.00 5.36
912 932 3.396951 CGGCCACCGGAGATTTATT 57.603 52.632 9.46 0.00 44.15 1.40
957 978 7.989741 AGTGGAAGATATACTGAATTTGACTGG 59.010 37.037 0.00 0.00 0.00 4.00
959 980 7.770433 TGGAAGATATACTGAATTTGACTGGTG 59.230 37.037 0.00 0.00 0.00 4.17
1024 1045 1.882912 ATGCTTGACTGCGAGTTTCA 58.117 45.000 0.00 0.00 35.36 2.69
1045 1066 2.105930 CGAGGTAGGCTCTGCTGC 59.894 66.667 0.00 0.00 0.00 5.25
1057 1078 2.124193 TGCTGCTGGTTGTGCACT 60.124 55.556 19.41 0.00 36.37 4.40
1059 1080 2.941333 CTGCTGGTTGTGCACTCG 59.059 61.111 19.41 2.92 36.37 4.18
1060 1081 3.245948 CTGCTGGTTGTGCACTCGC 62.246 63.158 19.41 12.93 36.37 5.03
1068 1089 0.380378 TTGTGCACTCGCCTTTTGTC 59.620 50.000 19.41 0.00 37.32 3.18
1107 1129 3.895041 AGGGAAATTCGACAAAATGTGGT 59.105 39.130 0.00 0.00 0.00 4.16
1113 1135 4.457834 TTCGACAAAATGTGGTGGTTTT 57.542 36.364 0.00 0.00 0.00 2.43
1125 1147 1.871676 GGTGGTTTTCGTTGTCTCTCC 59.128 52.381 0.00 0.00 0.00 3.71
1126 1148 1.871676 GTGGTTTTCGTTGTCTCTCCC 59.128 52.381 0.00 0.00 0.00 4.30
1127 1149 1.487142 TGGTTTTCGTTGTCTCTCCCA 59.513 47.619 0.00 0.00 0.00 4.37
1262 1286 6.237861 GGTTCTCTGCTATTTTACAGCTTACG 60.238 42.308 0.00 0.00 39.83 3.18
1348 1372 2.069273 CGTTCACGCTGGAGATCTTTT 58.931 47.619 0.00 0.00 0.00 2.27
1408 1432 4.336713 TCGAGTTCGACATCATCTTCATCT 59.663 41.667 0.00 0.00 44.22 2.90
1520 1544 2.177394 TGTGCCGCTTACTCATGAAA 57.823 45.000 0.00 0.00 0.00 2.69
1521 1545 2.076100 TGTGCCGCTTACTCATGAAAG 58.924 47.619 0.00 0.00 0.00 2.62
1522 1546 2.289382 TGTGCCGCTTACTCATGAAAGA 60.289 45.455 10.69 0.00 0.00 2.52
1523 1547 2.939103 GTGCCGCTTACTCATGAAAGAT 59.061 45.455 10.69 0.00 0.00 2.40
1524 1548 2.938451 TGCCGCTTACTCATGAAAGATG 59.062 45.455 10.69 3.04 0.00 2.90
1525 1549 3.198068 GCCGCTTACTCATGAAAGATGA 58.802 45.455 10.69 0.00 0.00 2.92
1526 1550 3.623060 GCCGCTTACTCATGAAAGATGAA 59.377 43.478 10.69 0.00 0.00 2.57
1577 1601 1.003116 CTGCAAGTTGACACACTCTGC 60.003 52.381 7.16 12.38 34.26 4.26
1605 1631 3.694072 TGAAATGGGGCTAGAATTGTTCG 59.306 43.478 0.00 0.00 34.02 3.95
1606 1632 3.366052 AATGGGGCTAGAATTGTTCGT 57.634 42.857 0.00 0.00 34.02 3.85
1622 1648 2.273370 TCGTGTACCTCTCGAAATGC 57.727 50.000 0.00 0.00 38.74 3.56
1634 1660 7.497595 ACCTCTCGAAATGCTTATACACATAA 58.502 34.615 0.00 0.00 0.00 1.90
1652 1685 7.918076 ACACATAATAGTCTTCTGAAAAGGGA 58.082 34.615 0.00 0.00 0.00 4.20
1661 1694 6.070824 AGTCTTCTGAAAAGGGAAAAAGCAAA 60.071 34.615 0.00 0.00 0.00 3.68
1682 1715 1.752498 CATGCTTGCATATGTGGGTGT 59.248 47.619 7.84 0.00 0.00 4.16
1747 1780 4.278170 TGTTAAAAGAGGCAGTGGTGATTG 59.722 41.667 0.00 0.00 0.00 2.67
1750 1783 2.414994 AGAGGCAGTGGTGATTGATG 57.585 50.000 0.00 0.00 0.00 3.07
1762 1795 6.156602 AGTGGTGATTGATGAATCTTCTCTCT 59.843 38.462 6.46 0.00 39.10 3.10
1763 1796 6.479660 GTGGTGATTGATGAATCTTCTCTCTC 59.520 42.308 6.46 0.00 39.10 3.20
1764 1797 6.383436 TGGTGATTGATGAATCTTCTCTCTCT 59.617 38.462 6.46 0.00 39.10 3.10
1765 1798 7.092979 TGGTGATTGATGAATCTTCTCTCTCTT 60.093 37.037 6.46 0.00 39.10 2.85
1845 1878 1.608590 GCTAAGTGAAGCAAACCAGCA 59.391 47.619 0.00 0.00 42.30 4.41
1881 1914 7.338196 TCTCAAGAGACAGGTTCTATTACTGAG 59.662 40.741 0.00 0.00 33.25 3.35
2066 2101 2.399580 AGGACTCTAACCTGGGTATGC 58.600 52.381 0.00 0.00 36.30 3.14
2096 2131 0.106719 CCACCAAACCACTGACCTGT 60.107 55.000 0.00 0.00 0.00 4.00
2130 2178 6.903883 TCAAAATTAGCCGTCTATCTGAAC 57.096 37.500 0.00 0.00 0.00 3.18
2132 2180 7.778083 TCAAAATTAGCCGTCTATCTGAACTA 58.222 34.615 0.00 0.00 0.00 2.24
2134 2182 6.710597 AATTAGCCGTCTATCTGAACTACA 57.289 37.500 0.00 0.00 0.00 2.74
2154 2202 5.957771 ACAATGTAGGTCAGATATGGTGT 57.042 39.130 0.00 0.00 0.00 4.16
2162 2210 6.824305 AGGTCAGATATGGTGTTCTTTTTG 57.176 37.500 0.00 0.00 0.00 2.44
2166 2214 6.431234 GTCAGATATGGTGTTCTTTTTGACCT 59.569 38.462 0.00 0.00 0.00 3.85
2189 2237 2.168728 GGAAGGGTCGCATCTAGAACTT 59.831 50.000 0.00 0.00 0.00 2.66
2218 2266 6.148948 GCTACTTGCATGTTACAATTGTCAA 58.851 36.000 15.85 10.79 42.31 3.18
2224 2272 6.747125 TGCATGTTACAATTGTCAATTCACT 58.253 32.000 15.85 0.00 0.00 3.41
2362 2410 5.063204 CCAATGAGGTTTTGTGTAGACAGA 58.937 41.667 0.00 0.00 32.26 3.41
2363 2411 5.707298 CCAATGAGGTTTTGTGTAGACAGAT 59.293 40.000 0.00 0.00 32.26 2.90
2365 2413 7.255590 CCAATGAGGTTTTGTGTAGACAGATTT 60.256 37.037 0.00 0.00 32.26 2.17
2366 2414 6.861065 TGAGGTTTTGTGTAGACAGATTTC 57.139 37.500 0.00 0.00 32.26 2.17
2384 2463 9.325198 ACAGATTTCATATGTAAAAGTCGCATA 57.675 29.630 1.90 0.00 32.07 3.14
2467 2546 6.036300 CGCAAATAAAGGATGATGCAATTGTT 59.964 34.615 7.40 0.00 33.01 2.83
2521 2600 5.534654 ACTTGAACTGCAGGTTAGCATTTTA 59.465 36.000 19.93 0.00 44.68 1.52
2528 2607 7.441017 ACTGCAGGTTAGCATTTTATTTTTCA 58.559 30.769 19.93 0.00 44.68 2.69
2553 2632 9.708222 CAGATTGTTTAACTGTTATGCATAGTC 57.292 33.333 6.50 5.41 0.00 2.59
2560 2639 9.853555 TTTAACTGTTATGCATAGTCAATTTGG 57.146 29.630 6.50 2.15 0.00 3.28
2561 2640 7.701539 AACTGTTATGCATAGTCAATTTGGA 57.298 32.000 6.50 0.00 0.00 3.53
2563 2642 8.297470 ACTGTTATGCATAGTCAATTTGGATT 57.703 30.769 6.50 0.00 0.00 3.01
2565 2644 6.979817 TGTTATGCATAGTCAATTTGGATTGC 59.020 34.615 6.50 2.78 41.94 3.56
2606 2685 3.794564 GGTCACGTGTTCCAATTGTTTTC 59.205 43.478 16.51 0.00 0.00 2.29
2608 2687 3.127203 TCACGTGTTCCAATTGTTTTCGT 59.873 39.130 16.51 5.99 0.00 3.85
2610 2689 3.375922 ACGTGTTCCAATTGTTTTCGTCT 59.624 39.130 4.43 0.00 0.00 4.18
2614 2693 2.510613 TCCAATTGTTTTCGTCTCCCC 58.489 47.619 4.43 0.00 0.00 4.81
2619 2698 1.314730 TGTTTTCGTCTCCCCTTTGC 58.685 50.000 0.00 0.00 0.00 3.68
2623 2702 1.750341 TTCGTCTCCCCTTTGCGTCA 61.750 55.000 0.00 0.00 0.00 4.35
2642 2721 6.521477 TGCGTCATGTTTATCAACAAAATACG 59.479 34.615 0.00 6.02 46.17 3.06
2704 2783 6.704819 CACAGTTTTTAAGGTGATTGTTTGC 58.295 36.000 0.00 0.00 33.16 3.68
2711 2790 9.606631 TTTTTAAGGTGATTGTTTGCTAAATGT 57.393 25.926 0.00 0.00 0.00 2.71
2736 2815 3.756082 TTGCTGATCAACCCCCTTATT 57.244 42.857 0.00 0.00 0.00 1.40
2737 2816 3.756082 TGCTGATCAACCCCCTTATTT 57.244 42.857 0.00 0.00 0.00 1.40
2738 2817 4.059773 TGCTGATCAACCCCCTTATTTT 57.940 40.909 0.00 0.00 0.00 1.82
2739 2818 4.424842 TGCTGATCAACCCCCTTATTTTT 58.575 39.130 0.00 0.00 0.00 1.94
2821 2900 9.823647 TGTAAGCTCTTAGATTTATCTTCCTTG 57.176 33.333 0.00 0.00 38.32 3.61
2828 2907 8.705594 TCTTAGATTTATCTTCCTTGGTACTGG 58.294 37.037 0.00 0.00 38.32 4.00
2842 2921 9.305555 TCCTTGGTACTGGATGTATATAACTAC 57.694 37.037 0.00 0.00 33.23 2.73
2899 2978 3.181449 TGCACATGTAAGTAACCACCACT 60.181 43.478 0.00 0.00 0.00 4.00
2904 2983 4.904253 TGTAAGTAACCACCACTTTTGC 57.096 40.909 0.00 0.00 37.42 3.68
2909 2988 2.671130 AACCACCACTTTTGCTGTTG 57.329 45.000 0.00 0.00 0.00 3.33
2933 3014 3.740115 ACTGGAACTTTGTGCGTCTTAT 58.260 40.909 0.00 0.00 0.00 1.73
2936 3017 3.745975 TGGAACTTTGTGCGTCTTATCTG 59.254 43.478 0.00 0.00 0.00 2.90
2993 3074 8.743085 AGCTGAAGAGATTGCTAATTTTGATA 57.257 30.769 0.00 0.00 33.64 2.15
3022 3103 2.311841 AGGGTCAAGGAAGGTAAATGGG 59.688 50.000 0.00 0.00 0.00 4.00
3084 3166 6.477360 GGTAATTAGCAGAAAGAGCTACTGTC 59.523 42.308 9.77 4.18 43.71 3.51
3085 3167 5.667539 ATTAGCAGAAAGAGCTACTGTCA 57.332 39.130 10.03 0.00 43.71 3.58
3129 3211 9.859427 CATCATTACATTTGTCATTGTTACCTT 57.141 29.630 0.00 0.00 0.00 3.50
3170 3252 3.992260 ATAGTACGGCAGCTCACTTAG 57.008 47.619 0.00 0.00 0.00 2.18
3235 3317 2.165998 GAATGCCTATCCTTGATGCCC 58.834 52.381 0.00 0.00 0.00 5.36
3246 3328 4.703299 TCCTTGATGCCCTATCTCCATAT 58.297 43.478 0.00 0.00 36.71 1.78
3254 3336 5.809001 TGCCCTATCTCCATATGATTGAAC 58.191 41.667 3.65 0.00 0.00 3.18
3273 3355 5.348986 TGAACAGACAGTACTTGAGTTGAC 58.651 41.667 0.00 0.00 0.00 3.18
3276 3358 6.710597 ACAGACAGTACTTGAGTTGACTAA 57.289 37.500 0.00 0.00 0.00 2.24
3278 3360 7.727181 ACAGACAGTACTTGAGTTGACTAATT 58.273 34.615 0.00 0.00 0.00 1.40
3282 3364 7.497595 ACAGTACTTGAGTTGACTAATTGTGA 58.502 34.615 0.00 0.00 0.00 3.58
3300 3382 7.664552 ATTGTGATCCATGTACAATCCATTT 57.335 32.000 0.00 0.00 40.01 2.32
3306 3388 8.415553 TGATCCATGTACAATCCATTTGAAATC 58.584 33.333 0.00 0.16 38.76 2.17
3376 3458 3.158676 GCTACTCTAGGTAGGTCATGGG 58.841 54.545 15.79 0.00 45.83 4.00
3383 3465 1.646447 AGGTAGGTCATGGGACTGAGA 59.354 52.381 0.00 0.00 43.77 3.27
3391 3473 1.747355 CATGGGACTGAGATTTGGTGC 59.253 52.381 0.00 0.00 0.00 5.01
3427 3509 6.553100 TGGGATTGTTCCAGTTTGTTAAAGAT 59.447 34.615 0.00 0.00 44.60 2.40
3436 3518 5.586643 CCAGTTTGTTAAAGATCTCCCTAGC 59.413 44.000 0.00 0.00 0.00 3.42
3449 3531 4.219115 TCTCCCTAGCTATTGACCTGAAG 58.781 47.826 0.00 0.00 0.00 3.02
3457 3539 3.191371 GCTATTGACCTGAAGTTTGTGGG 59.809 47.826 0.00 0.00 0.00 4.61
3526 3609 9.241919 TGATCCTTGTTGTATTGATATGTTTGT 57.758 29.630 0.00 0.00 0.00 2.83
3560 3643 6.992063 AAGTCAACTATAAACTCCAGCATG 57.008 37.500 0.00 0.00 0.00 4.06
3564 3647 4.760530 ACTATAAACTCCAGCATGCTGA 57.239 40.909 42.21 27.94 46.30 4.26
3614 3697 4.552674 TGACTGGCATGGAATACCTAGTA 58.447 43.478 0.00 0.00 37.04 1.82
3615 3698 4.588951 TGACTGGCATGGAATACCTAGTAG 59.411 45.833 0.00 0.00 37.04 2.57
3623 3706 5.674799 TGGAATACCTAGTAGCCCTAAGA 57.325 43.478 0.00 0.00 37.04 2.10
3636 3719 1.561542 CCCTAAGAAGGCAGTGGTGAT 59.438 52.381 0.00 0.00 42.14 3.06
3659 3742 8.623903 TGATGATCCTTTGTCATTTATAACTGC 58.376 33.333 0.00 0.00 36.49 4.40
3670 3753 8.311109 TGTCATTTATAACTGCAGTTCTCACTA 58.689 33.333 34.29 17.21 39.31 2.74
3689 3772 5.696270 TCACTATCATGTTGTGAGTTGTGAC 59.304 40.000 11.81 0.00 40.92 3.67
3716 3800 7.977818 TGGATTCTGATATGCAAAGTAGGTAT 58.022 34.615 0.00 0.00 0.00 2.73
3783 3867 7.970614 TGTGATATAATATTCTGAGTGCTAGCG 59.029 37.037 10.77 0.00 0.00 4.26
3784 3868 8.184848 GTGATATAATATTCTGAGTGCTAGCGA 58.815 37.037 10.77 0.00 0.00 4.93
3787 3871 9.743057 ATATAATATTCTGAGTGCTAGCGATTC 57.257 33.333 10.77 8.02 0.00 2.52
3794 3878 4.053983 TGAGTGCTAGCGATTCATGATTC 58.946 43.478 10.77 7.42 0.00 2.52
3801 3885 4.412796 AGCGATTCATGATTCCTCAGAA 57.587 40.909 11.10 0.00 34.12 3.02
3818 3902 7.158697 TCCTCAGAACTAAATTTTGTCATCGA 58.841 34.615 5.74 0.00 0.00 3.59
3819 3903 7.824289 TCCTCAGAACTAAATTTTGTCATCGAT 59.176 33.333 5.74 0.00 0.00 3.59
3836 3920 8.398665 TGTCATCGATATATATTTCTGTCCTCG 58.601 37.037 0.00 0.00 0.00 4.63
3838 3922 6.132791 TCGATATATATTTCTGTCCTCGCC 57.867 41.667 0.00 0.00 0.00 5.54
3839 3923 4.970611 CGATATATATTTCTGTCCTCGCCG 59.029 45.833 0.00 0.00 0.00 6.46
3847 3931 4.395959 TTCTGTCCTCGCCGTAATAATT 57.604 40.909 0.00 0.00 0.00 1.40
3850 3934 5.180271 TCTGTCCTCGCCGTAATAATTTTT 58.820 37.500 0.00 0.00 0.00 1.94
3898 3982 6.115446 ACTTACAGCAGCTAAATATGCAGAA 58.885 36.000 0.00 0.00 45.01 3.02
3911 3995 6.428385 AATATGCAGAACAGTCTTTAGTGC 57.572 37.500 0.00 0.00 28.78 4.40
3922 4006 3.258372 AGTCTTTAGTGCGTTCTCATCCA 59.742 43.478 0.00 0.00 0.00 3.41
3981 4069 1.171308 ATGTGCTTAGCAGTGCCAAG 58.829 50.000 17.71 17.71 40.08 3.61
4006 4094 5.124617 TGCGAACAAATGCTTGTAATATCCA 59.875 36.000 0.00 0.00 45.25 3.41
4013 4101 9.086336 ACAAATGCTTGTAATATCCATTTTTCG 57.914 29.630 0.00 0.00 44.14 3.46
4049 4137 6.546034 TGCATAACAGTATCTAGAGCTGTGTA 59.454 38.462 24.51 19.40 41.94 2.90
4121 4209 6.673154 TTATGTGAAATCTGCTGACTGATG 57.327 37.500 0.00 0.00 34.95 3.07
4150 4238 1.113788 TTTGCTTTCCTGCAGCTGTT 58.886 45.000 16.64 0.00 44.27 3.16
4192 4280 9.615295 GTACAGATAAAGGATATCGAGTCTTTC 57.385 37.037 7.66 0.00 32.53 2.62
4299 4388 6.313519 TCTTGCACTCCTATATTTGTCCTT 57.686 37.500 0.00 0.00 0.00 3.36
4538 4628 2.032376 TTCTGCGATGCTGCCACA 59.968 55.556 0.00 0.00 0.00 4.17
4550 4640 2.006056 GCTGCCACACTCACTCTGATC 61.006 57.143 0.00 0.00 0.00 2.92
4646 4736 5.249393 AGTGGAAACTGTCATCAGAATACCT 59.751 40.000 2.17 0.00 43.76 3.08
4686 4776 6.671614 TTGACACAGAACAATAAACTCGTT 57.328 33.333 0.00 0.00 0.00 3.85
4731 4821 7.642082 TGTCTCTTAGAACTGTATTAGGACC 57.358 40.000 0.00 0.00 0.00 4.46
4821 4911 1.317431 TGATTGGGTCTGCATGCTGC 61.317 55.000 20.33 13.82 45.29 5.25
4835 4925 3.747529 GCATGCTGCCTTTGTAATTTTGT 59.252 39.130 11.37 0.00 37.42 2.83
4952 5042 7.810658 ACTGCATGTAAAATACTCTTCAAGTG 58.189 34.615 0.00 0.00 39.11 3.16
5037 5127 8.770828 CAAAGTGAATCTGCAGAATTTTGAAAT 58.229 29.630 22.50 0.00 0.00 2.17
5047 5137 6.151648 TGCAGAATTTTGAAATCTCTACCTGG 59.848 38.462 0.00 0.00 0.00 4.45
5049 5139 6.151648 CAGAATTTTGAAATCTCTACCTGGCA 59.848 38.462 0.00 0.00 0.00 4.92
5055 5145 0.324368 ATCTCTACCTGGCACCGACA 60.324 55.000 0.00 0.00 0.00 4.35
5150 5240 1.893786 AGCTACCACAAGAGCTCCG 59.106 57.895 10.93 4.45 46.08 4.63
5225 5318 1.675310 CTCCGCCAGCCATTGTTGA 60.675 57.895 0.00 0.00 0.00 3.18
5232 5325 0.957395 CAGCCATTGTTGAGGACGCT 60.957 55.000 0.00 0.00 0.00 5.07
5330 5423 1.538950 GAGGTACTTGACGTCGAAGGT 59.461 52.381 22.82 14.68 41.55 3.50
5334 5427 1.300620 CTTGACGTCGAAGGTGCCA 60.301 57.895 11.62 0.00 0.00 4.92
5622 5715 2.225467 GTGGAAGAAGAAGCAGCAGTT 58.775 47.619 0.00 0.00 0.00 3.16
5670 5763 2.203126 GCCCTGATCTTGCCGAGG 60.203 66.667 0.00 0.00 0.00 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 8.985805 CGTACTACCCTATGTTTTATCAAATCC 58.014 37.037 0.00 0.00 0.00 3.01
10 11 8.076910 TCCGTACTACCCTATGTTTTATCAAA 57.923 34.615 0.00 0.00 0.00 2.69
31 32 4.894784 TGAAATTCTAGCTTTCACTCCGT 58.105 39.130 13.26 0.00 37.61 4.69
66 67 8.640063 TCCTGTTACACTTGTAATACACTCTA 57.360 34.615 5.16 0.00 41.85 2.43
74 76 4.003648 GCTGCTCCTGTTACACTTGTAAT 58.996 43.478 5.16 0.00 41.85 1.89
87 89 1.165907 TTTGTCAACGGCTGCTCCTG 61.166 55.000 0.00 0.00 0.00 3.86
95 97 2.595386 GGTGATCATTTTGTCAACGGC 58.405 47.619 0.00 0.00 0.00 5.68
97 99 3.913548 TGGGTGATCATTTTGTCAACG 57.086 42.857 0.00 0.00 32.85 4.10
100 102 6.267242 TCATCTTTTGGGTGATCATTTTGTCA 59.733 34.615 0.00 0.00 0.00 3.58
153 155 4.052159 AGGACTATCTGATTTGTCTGCG 57.948 45.455 17.03 0.00 0.00 5.18
154 156 7.930865 AGAAATAGGACTATCTGATTTGTCTGC 59.069 37.037 17.03 7.19 0.00 4.26
157 159 7.596995 CCGAGAAATAGGACTATCTGATTTGTC 59.403 40.741 12.21 12.21 0.00 3.18
195 198 0.036388 CTTGGCTCGGTGGAAGCTTA 60.036 55.000 0.00 0.00 0.00 3.09
196 199 1.302832 CTTGGCTCGGTGGAAGCTT 60.303 57.895 0.00 0.00 0.00 3.74
197 200 2.056906 AACTTGGCTCGGTGGAAGCT 62.057 55.000 0.00 0.00 0.00 3.74
217 220 7.048629 TGTGCTACAAATTTCAATCCTTTCA 57.951 32.000 0.00 0.00 0.00 2.69
231 234 4.980573 AGGGAGTAACAATGTGCTACAAA 58.019 39.130 3.50 0.00 0.00 2.83
260 263 9.959749 GATTTTCAGGCCATCGTAATTTATTTA 57.040 29.630 5.01 0.00 0.00 1.40
261 264 7.647715 CGATTTTCAGGCCATCGTAATTTATTT 59.352 33.333 5.01 0.00 36.00 1.40
262 265 7.012894 TCGATTTTCAGGCCATCGTAATTTATT 59.987 33.333 18.62 0.00 40.57 1.40
263 266 6.485313 TCGATTTTCAGGCCATCGTAATTTAT 59.515 34.615 18.62 0.00 40.57 1.40
264 267 5.818336 TCGATTTTCAGGCCATCGTAATTTA 59.182 36.000 18.62 0.02 40.57 1.40
265 268 4.638421 TCGATTTTCAGGCCATCGTAATTT 59.362 37.500 18.62 0.00 40.57 1.82
266 269 4.196193 TCGATTTTCAGGCCATCGTAATT 58.804 39.130 18.62 0.00 40.57 1.40
267 270 3.804036 TCGATTTTCAGGCCATCGTAAT 58.196 40.909 18.62 6.16 40.57 1.89
268 271 3.254470 TCGATTTTCAGGCCATCGTAA 57.746 42.857 18.62 1.90 40.57 3.18
269 272 2.971660 TCGATTTTCAGGCCATCGTA 57.028 45.000 18.62 6.44 40.57 3.43
301 305 0.692419 AAGATGAGGTCCCAGCCGAT 60.692 55.000 0.00 0.00 0.00 4.18
347 351 0.459237 TGTTTTTGGCTGTTGTGCGG 60.459 50.000 0.00 0.00 0.00 5.69
364 368 7.475771 TTCATCTTTTGCGCTTTATTTTTGT 57.524 28.000 9.73 0.00 0.00 2.83
435 439 3.246619 GAGGAGCTCGTAGTTCTGTTTG 58.753 50.000 9.29 0.00 0.00 2.93
499 504 3.060020 GAGATCGAACGGCGGTGGA 62.060 63.158 13.06 13.06 41.33 4.02
502 507 4.189188 CGGAGATCGAACGGCGGT 62.189 66.667 13.24 3.35 42.43 5.68
569 581 1.291109 TGGGGGAAATTAAGCGGAGA 58.709 50.000 0.00 0.00 0.00 3.71
607 621 1.153765 CAATCGCGACAGGAGCTCA 60.154 57.895 12.93 0.00 0.00 4.26
637 651 2.038269 GGAAATCGGAACAGGCGCA 61.038 57.895 10.83 0.00 0.00 6.09
640 654 2.791927 GCGGAAATCGGAACAGGC 59.208 61.111 0.00 0.00 39.69 4.85
641 655 1.740296 ACGCGGAAATCGGAACAGG 60.740 57.895 12.47 0.00 39.69 4.00
668 682 0.451783 CCTATCCACCAAACAAGCGC 59.548 55.000 0.00 0.00 0.00 5.92
680 694 2.039418 CCACGGATCAACTCCTATCCA 58.961 52.381 0.00 0.00 41.57 3.41
795 815 2.592308 GCCCCTTGCCCTACTGAG 59.408 66.667 0.00 0.00 0.00 3.35
818 838 1.528586 CACTGACGAAACTGCAAGGAG 59.471 52.381 0.00 0.00 39.30 3.69
838 858 1.226435 CGCAGCGTCAGACTCCTAC 60.226 63.158 6.65 0.00 0.00 3.18
850 870 0.043053 CACATTCGATAACCGCAGCG 60.043 55.000 8.18 8.18 38.37 5.18
853 873 2.670905 CAGAACACATTCGATAACCGCA 59.329 45.455 0.00 0.00 40.04 5.69
860 880 0.443869 GCACGCAGAACACATTCGAT 59.556 50.000 0.00 0.00 40.04 3.59
873 893 1.722464 GTAACTTCATGTACGCACGCA 59.278 47.619 0.00 0.00 0.00 5.24
874 894 1.060122 GGTAACTTCATGTACGCACGC 59.940 52.381 0.00 0.00 0.00 5.34
875 895 1.319374 CGGTAACTTCATGTACGCACG 59.681 52.381 0.00 0.00 0.00 5.34
876 896 1.657094 CCGGTAACTTCATGTACGCAC 59.343 52.381 0.00 0.00 0.00 5.34
883 903 1.366111 CGGTGGCCGGTAACTTCATG 61.366 60.000 1.90 0.00 44.15 3.07
899 919 5.875359 GTGAACAGAAGAATAAATCTCCGGT 59.125 40.000 0.00 0.00 37.42 5.28
910 930 6.183360 CCACTCAAAACTGTGAACAGAAGAAT 60.183 38.462 17.11 0.00 46.59 2.40
912 932 4.635765 CCACTCAAAACTGTGAACAGAAGA 59.364 41.667 17.11 7.77 46.59 2.87
1024 1045 3.141488 CAGAGCCTACCTCGCGGT 61.141 66.667 6.13 1.16 45.54 5.68
1045 1066 1.447317 AAAGGCGAGTGCACAACCAG 61.447 55.000 21.04 6.16 45.35 4.00
1057 1078 4.811969 TTAGTATCTGGACAAAAGGCGA 57.188 40.909 0.00 0.00 0.00 5.54
1059 1080 7.391148 TTGAATTAGTATCTGGACAAAAGGC 57.609 36.000 0.00 0.00 0.00 4.35
1060 1081 9.846248 CTTTTGAATTAGTATCTGGACAAAAGG 57.154 33.333 4.43 0.00 43.76 3.11
1107 1129 1.487142 TGGGAGAGACAACGAAAACCA 59.513 47.619 0.00 0.00 0.00 3.67
1113 1135 4.884668 ATTAACTTGGGAGAGACAACGA 57.115 40.909 0.00 0.00 0.00 3.85
1348 1372 7.041916 CCATTTTCTAAATTCAAACTTGCTGCA 60.042 33.333 0.00 0.00 0.00 4.41
1399 1423 3.387374 CACTAGTCTGCCCAGATGAAGAT 59.613 47.826 0.77 0.00 39.97 2.40
1408 1432 1.892819 GCTGCTCACTAGTCTGCCCA 61.893 60.000 12.42 0.00 0.00 5.36
1507 1531 7.983307 ACTGATTTCATCTTTCATGAGTAAGC 58.017 34.615 0.00 0.00 0.00 3.09
1520 1544 5.106791 CGCAGAAGAACAACTGATTTCATCT 60.107 40.000 0.00 0.00 36.38 2.90
1521 1545 5.084722 CGCAGAAGAACAACTGATTTCATC 58.915 41.667 0.00 0.00 36.38 2.92
1522 1546 4.516698 ACGCAGAAGAACAACTGATTTCAT 59.483 37.500 0.00 0.00 36.38 2.57
1523 1547 3.876914 ACGCAGAAGAACAACTGATTTCA 59.123 39.130 0.00 0.00 36.38 2.69
1524 1548 4.474226 ACGCAGAAGAACAACTGATTTC 57.526 40.909 0.00 0.00 36.38 2.17
1525 1549 4.900635 AACGCAGAAGAACAACTGATTT 57.099 36.364 0.00 0.00 36.38 2.17
1526 1550 4.900635 AAACGCAGAAGAACAACTGATT 57.099 36.364 0.00 0.00 36.38 2.57
1532 1556 6.184580 TCTTTTGTAAACGCAGAAGAACAA 57.815 33.333 0.00 0.00 36.89 2.83
1543 1567 5.797934 TCAACTTGCAGTTCTTTTGTAAACG 59.202 36.000 0.00 0.00 36.03 3.60
1577 1601 6.324770 ACAATTCTAGCCCCATTTCATTTAGG 59.675 38.462 0.00 0.00 0.00 2.69
1605 1631 6.198591 GTGTATAAGCATTTCGAGAGGTACAC 59.801 42.308 0.00 4.36 33.82 2.90
1606 1632 6.127563 TGTGTATAAGCATTTCGAGAGGTACA 60.128 38.462 0.00 0.00 0.00 2.90
1634 1660 6.777580 TGCTTTTTCCCTTTTCAGAAGACTAT 59.222 34.615 0.00 0.00 0.00 2.12
1639 1665 5.874261 TGTTTGCTTTTTCCCTTTTCAGAAG 59.126 36.000 0.00 0.00 0.00 2.85
1640 1666 5.799213 TGTTTGCTTTTTCCCTTTTCAGAA 58.201 33.333 0.00 0.00 0.00 3.02
1641 1667 5.413309 TGTTTGCTTTTTCCCTTTTCAGA 57.587 34.783 0.00 0.00 0.00 3.27
1642 1668 5.504501 GCATGTTTGCTTTTTCCCTTTTCAG 60.505 40.000 0.00 0.00 45.77 3.02
1643 1669 4.335037 GCATGTTTGCTTTTTCCCTTTTCA 59.665 37.500 0.00 0.00 45.77 2.69
1644 1670 4.847633 GCATGTTTGCTTTTTCCCTTTTC 58.152 39.130 0.00 0.00 45.77 2.29
1645 1671 4.898829 GCATGTTTGCTTTTTCCCTTTT 57.101 36.364 0.00 0.00 45.77 2.27
1661 1694 1.752498 CACCCACATATGCAAGCATGT 59.248 47.619 17.26 8.14 37.82 3.21
1682 1715 5.712446 TGTGGCCAACATTACATAGCTTAAA 59.288 36.000 7.24 0.00 32.36 1.52
1750 1783 8.725148 TGCAAAATAACAAGAGAGAGAAGATTC 58.275 33.333 0.00 0.00 0.00 2.52
1762 1795 8.632679 AGAGATTTCAACTGCAAAATAACAAGA 58.367 29.630 0.00 0.00 0.00 3.02
1763 1796 8.807667 AGAGATTTCAACTGCAAAATAACAAG 57.192 30.769 0.00 0.00 0.00 3.16
1764 1797 9.598517 AAAGAGATTTCAACTGCAAAATAACAA 57.401 25.926 0.00 0.00 0.00 2.83
1765 1798 9.598517 AAAAGAGATTTCAACTGCAAAATAACA 57.401 25.926 0.00 0.00 0.00 2.41
1914 1947 8.227791 CAGTCATACAACACCACATTTTACTAC 58.772 37.037 0.00 0.00 0.00 2.73
1922 1955 2.436417 GCCAGTCATACAACACCACAT 58.564 47.619 0.00 0.00 0.00 3.21
2066 2101 0.391263 GTTTGGTGGTAGCCTCCTCG 60.391 60.000 7.64 0.00 37.97 4.63
2096 2131 7.610305 AGACGGCTAATTTTGAATCTAAAGGAA 59.390 33.333 0.00 0.00 0.00 3.36
2130 2178 7.055667 ACACCATATCTGACCTACATTGTAG 57.944 40.000 15.58 15.58 0.00 2.74
2132 2180 5.957771 ACACCATATCTGACCTACATTGT 57.042 39.130 0.00 0.00 0.00 2.71
2134 2182 6.814954 AGAACACCATATCTGACCTACATT 57.185 37.500 0.00 0.00 0.00 2.71
2149 2197 2.024846 TCCCAGGTCAAAAAGAACACCA 60.025 45.455 0.00 0.00 35.97 4.17
2154 2202 2.246327 ACCCTTCCCAGGTCAAAAAGAA 59.754 45.455 0.00 0.00 38.79 2.52
2166 2214 0.032515 TCTAGATGCGACCCTTCCCA 60.033 55.000 0.00 0.00 0.00 4.37
2218 2266 3.482156 AGCAGACAGTGTCAAGTGAAT 57.518 42.857 24.73 4.96 34.60 2.57
2224 2272 3.982475 CTGAGTTAGCAGACAGTGTCAA 58.018 45.455 24.73 7.80 38.14 3.18
2292 2340 1.942657 AGTTATGCCGCTGCTAACATG 59.057 47.619 17.67 0.00 38.71 3.21
2300 2348 1.539388 TGGAAAACAGTTATGCCGCTG 59.461 47.619 0.00 0.00 38.58 5.18
2355 2403 9.031360 GCGACTTTTACATATGAAATCTGTCTA 57.969 33.333 10.38 0.00 35.16 2.59
2356 2404 7.549134 TGCGACTTTTACATATGAAATCTGTCT 59.451 33.333 10.38 0.00 35.16 3.41
2357 2405 7.684670 TGCGACTTTTACATATGAAATCTGTC 58.315 34.615 10.38 9.04 35.16 3.51
2365 2413 9.719355 ATGGTATTATGCGACTTTTACATATGA 57.281 29.630 10.38 0.00 0.00 2.15
2384 2463 7.721399 CCTGGCACTATTAAGAGAAATGGTATT 59.279 37.037 3.65 0.00 30.35 1.89
2407 2486 8.855110 ACATAAGATCTAGTCAGTAATGACCTG 58.145 37.037 19.08 12.29 39.50 4.00
2437 2516 4.285292 CATCATCCTTTATTTGCGACTGC 58.715 43.478 0.00 0.00 43.20 4.40
2528 2607 9.448438 TGACTATGCATAACAGTTAAACAATCT 57.552 29.630 8.00 0.00 0.00 2.40
2553 2632 5.080969 ACATCTTGAGGCAATCCAAATTG 57.919 39.130 0.00 0.00 44.31 2.32
2558 2637 3.084039 GACAACATCTTGAGGCAATCCA 58.916 45.455 0.00 0.00 33.74 3.41
2560 2639 2.096496 CGGACAACATCTTGAGGCAATC 59.904 50.000 0.00 0.00 0.00 2.67
2561 2640 2.086869 CGGACAACATCTTGAGGCAAT 58.913 47.619 0.00 0.00 0.00 3.56
2563 2642 0.321564 CCGGACAACATCTTGAGGCA 60.322 55.000 0.00 0.00 0.00 4.75
2565 2644 1.442769 CACCGGACAACATCTTGAGG 58.557 55.000 9.46 0.00 0.00 3.86
2606 2685 1.079127 ATGACGCAAAGGGGAGACG 60.079 57.895 0.00 0.00 0.00 4.18
2608 2687 0.400213 AACATGACGCAAAGGGGAGA 59.600 50.000 0.00 0.00 0.00 3.71
2610 2689 2.570415 TAAACATGACGCAAAGGGGA 57.430 45.000 0.00 0.00 0.00 4.81
2614 2693 6.746104 TTTGTTGATAAACATGACGCAAAG 57.254 33.333 0.00 0.00 32.01 2.77
2619 2698 7.532546 ACACGTATTTTGTTGATAAACATGACG 59.467 33.333 0.00 13.64 32.01 4.35
2623 2702 8.973378 CCAAACACGTATTTTGTTGATAAACAT 58.027 29.630 16.51 0.00 37.26 2.71
2642 2721 3.882888 TGATCACAGAAAGGACCAAACAC 59.117 43.478 0.00 0.00 0.00 3.32
2697 2776 6.369890 TCAGCAACAAAACATTTAGCAAACAA 59.630 30.769 0.00 0.00 0.00 2.83
2740 2819 2.028567 GGGGGTTGATCATTCGCAAAAA 60.029 45.455 0.00 0.00 0.00 1.94
2741 2820 1.548269 GGGGGTTGATCATTCGCAAAA 59.452 47.619 0.00 0.00 0.00 2.44
2742 2821 1.181786 GGGGGTTGATCATTCGCAAA 58.818 50.000 0.00 0.00 0.00 3.68
2743 2822 0.331278 AGGGGGTTGATCATTCGCAA 59.669 50.000 0.00 0.00 0.00 4.85
2744 2823 0.331278 AAGGGGGTTGATCATTCGCA 59.669 50.000 0.00 0.00 0.00 5.10
2745 2824 2.341846 TAAGGGGGTTGATCATTCGC 57.658 50.000 0.00 1.61 0.00 4.70
2746 2825 8.677300 CATAATTATAAGGGGGTTGATCATTCG 58.323 37.037 0.00 0.00 0.00 3.34
2747 2826 8.470002 GCATAATTATAAGGGGGTTGATCATTC 58.530 37.037 0.00 0.00 0.00 2.67
2748 2827 8.179487 AGCATAATTATAAGGGGGTTGATCATT 58.821 33.333 0.00 0.00 0.00 2.57
2749 2828 7.616935 CAGCATAATTATAAGGGGGTTGATCAT 59.383 37.037 0.00 0.00 0.00 2.45
2750 2829 6.947733 CAGCATAATTATAAGGGGGTTGATCA 59.052 38.462 0.00 0.00 0.00 2.92
2751 2830 7.175104 TCAGCATAATTATAAGGGGGTTGATC 58.825 38.462 0.00 0.00 0.00 2.92
2752 2831 7.102518 TCAGCATAATTATAAGGGGGTTGAT 57.897 36.000 0.00 0.00 0.00 2.57
2753 2832 6.523035 TCAGCATAATTATAAGGGGGTTGA 57.477 37.500 0.00 0.00 0.00 3.18
2754 2833 7.781324 AATCAGCATAATTATAAGGGGGTTG 57.219 36.000 0.00 0.00 0.00 3.77
2755 2834 8.010105 TGAAATCAGCATAATTATAAGGGGGTT 58.990 33.333 0.00 0.00 0.00 4.11
2756 2835 7.451566 GTGAAATCAGCATAATTATAAGGGGGT 59.548 37.037 0.00 0.00 0.00 4.95
2757 2836 7.671398 AGTGAAATCAGCATAATTATAAGGGGG 59.329 37.037 0.00 0.00 0.00 5.40
2758 2837 8.641498 AGTGAAATCAGCATAATTATAAGGGG 57.359 34.615 0.00 0.00 0.00 4.79
2812 2891 9.615660 TTATATACATCCAGTACCAAGGAAGAT 57.384 33.333 8.33 3.90 37.48 2.40
2861 2940 7.375106 ACATGTGCAAAAGACAAAATTGAAA 57.625 28.000 0.00 0.00 0.00 2.69
2868 2947 6.975772 GGTTACTTACATGTGCAAAAGACAAA 59.024 34.615 9.11 0.00 0.00 2.83
2870 2949 5.590663 TGGTTACTTACATGTGCAAAAGACA 59.409 36.000 9.11 1.92 0.00 3.41
2880 2959 5.221165 GCAAAAGTGGTGGTTACTTACATGT 60.221 40.000 2.69 2.69 37.39 3.21
2899 2978 3.626930 AGTTCCAGTACCAACAGCAAAA 58.373 40.909 0.00 0.00 0.00 2.44
2904 2983 3.243068 GCACAAAGTTCCAGTACCAACAG 60.243 47.826 0.00 0.00 0.00 3.16
2909 2988 1.529865 GACGCACAAAGTTCCAGTACC 59.470 52.381 0.00 0.00 0.00 3.34
2933 3014 4.072131 GCCTGTGGACATAAAGAAACAGA 58.928 43.478 2.32 0.00 37.76 3.41
2936 3017 5.222631 CAAAGCCTGTGGACATAAAGAAAC 58.777 41.667 0.00 0.00 0.00 2.78
2993 3074 2.243221 CCTTCCTTGACCCTGATGGAAT 59.757 50.000 0.00 0.00 36.39 3.01
3084 3166 1.134189 TGGAGAGCCTCAATCATGCTG 60.134 52.381 0.00 0.00 34.99 4.41
3085 3167 1.210538 TGGAGAGCCTCAATCATGCT 58.789 50.000 0.00 0.00 38.24 3.79
3096 3178 4.883585 TGACAAATGTAATGATGGAGAGCC 59.116 41.667 0.00 0.00 0.00 4.70
3129 3211 8.715191 ACTATTGTCAAATGTCTTTGCAAAAA 57.285 26.923 13.84 0.00 41.29 1.94
3235 3317 8.366401 ACTGTCTGTTCAATCATATGGAGATAG 58.634 37.037 2.13 0.00 0.00 2.08
3246 3328 6.161855 ACTCAAGTACTGTCTGTTCAATCA 57.838 37.500 0.00 0.00 0.00 2.57
3254 3336 7.653713 ACAATTAGTCAACTCAAGTACTGTCTG 59.346 37.037 0.00 0.00 0.00 3.51
3273 3355 7.806409 TGGATTGTACATGGATCACAATTAG 57.194 36.000 14.45 0.00 41.65 1.73
3276 3358 7.342541 TCAAATGGATTGTACATGGATCACAAT 59.657 33.333 13.63 13.63 43.65 2.71
3278 3360 6.186234 TCAAATGGATTGTACATGGATCACA 58.814 36.000 0.00 0.00 40.11 3.58
3282 3364 8.308851 TGATTTCAAATGGATTGTACATGGAT 57.691 30.769 0.00 0.00 40.11 3.41
3318 3400 7.639113 AGAAATTTAACAACAGGACAACAGA 57.361 32.000 0.00 0.00 0.00 3.41
3360 3442 2.856864 TCAGTCCCATGACCTACCTAGA 59.143 50.000 0.00 0.00 42.81 2.43
3376 3458 3.274288 CCTAAGGCACCAAATCTCAGTC 58.726 50.000 0.00 0.00 0.00 3.51
3391 3473 1.152963 CAATCCCACCGGCCTAAGG 60.153 63.158 0.00 0.00 0.00 2.69
3427 3509 3.973472 TCAGGTCAATAGCTAGGGAGA 57.027 47.619 0.00 0.00 0.00 3.71
3436 3518 3.191371 GCCCACAAACTTCAGGTCAATAG 59.809 47.826 0.00 0.00 0.00 1.73
3486 3568 7.710475 ACAACAAGGATCAATTTGTTTAAGTGG 59.290 33.333 15.38 8.88 43.00 4.00
3519 3602 9.120538 AGTTGACTTACTATGACAAACAAACAT 57.879 29.630 0.00 0.00 0.00 2.71
3535 3618 7.466050 GCATGCTGGAGTTTATAGTTGACTTAC 60.466 40.741 11.37 0.00 0.00 2.34
3551 3634 1.467734 GTGACTTTCAGCATGCTGGAG 59.532 52.381 39.72 35.44 43.75 3.86
3560 3643 1.537202 AGCGGAATTGTGACTTTCAGC 59.463 47.619 12.92 12.92 41.45 4.26
3564 3647 2.778299 TGCTAGCGGAATTGTGACTTT 58.222 42.857 10.77 0.00 0.00 2.66
3623 3706 1.293062 AGGATCATCACCACTGCCTT 58.707 50.000 0.00 0.00 0.00 4.35
3629 3712 5.649782 AAATGACAAAGGATCATCACCAC 57.350 39.130 0.00 0.00 35.72 4.16
3636 3719 7.611467 ACTGCAGTTATAAATGACAAAGGATCA 59.389 33.333 15.25 1.29 0.00 2.92
3670 3753 4.216902 CCATGTCACAACTCACAACATGAT 59.783 41.667 13.71 0.00 46.36 2.45
3689 3772 6.713903 ACCTACTTTGCATATCAGAATCCATG 59.286 38.462 0.00 0.00 0.00 3.66
3716 3800 3.732212 CACTTGGATCTCACTGTCAACA 58.268 45.455 0.00 0.00 0.00 3.33
3763 3847 7.606349 TGAATCGCTAGCACTCAGAATATTAT 58.394 34.615 16.45 0.00 0.00 1.28
3765 3849 5.847304 TGAATCGCTAGCACTCAGAATATT 58.153 37.500 16.45 0.00 0.00 1.28
3787 3871 9.565213 GACAAAATTTAGTTCTGAGGAATCATG 57.435 33.333 0.00 0.00 33.71 3.07
3794 3878 7.364522 TCGATGACAAAATTTAGTTCTGAGG 57.635 36.000 0.00 0.00 0.00 3.86
3810 3894 8.398665 CGAGGACAGAAATATATATCGATGACA 58.601 37.037 8.54 0.00 0.00 3.58
3818 3902 5.916661 ACGGCGAGGACAGAAATATATAT 57.083 39.130 16.62 0.00 0.00 0.86
3819 3903 6.822667 TTACGGCGAGGACAGAAATATATA 57.177 37.500 16.62 0.00 0.00 0.86
3836 3920 8.736751 TGAAGTTTCTCAAAAATTATTACGGC 57.263 30.769 0.00 0.00 33.15 5.68
3847 3931 7.642071 GCAATAAGCATGAAGTTTCTCAAAA 57.358 32.000 0.00 0.00 44.79 2.44
3874 3958 5.674525 TCTGCATATTTAGCTGCTGTAAGT 58.325 37.500 13.43 0.00 39.16 2.24
3898 3982 3.728076 TGAGAACGCACTAAAGACTGT 57.272 42.857 0.00 0.00 0.00 3.55
3922 4006 6.418057 TGCCAATTTTACTTCACCAAAGAT 57.582 33.333 0.00 0.00 38.44 2.40
3981 4069 5.455525 GGATATTACAAGCATTTGTTCGCAC 59.544 40.000 0.00 0.00 45.01 5.34
4006 4094 7.120579 TGTTATGCAACTAGATGTCCGAAAAAT 59.879 33.333 0.00 0.00 35.56 1.82
4012 4100 4.433615 ACTGTTATGCAACTAGATGTCCG 58.566 43.478 0.00 0.00 35.56 4.79
4013 4101 7.437748 AGATACTGTTATGCAACTAGATGTCC 58.562 38.462 0.00 0.00 35.56 4.02
4075 4163 5.413309 AGTCTAACTTAGAGCATTGCACT 57.587 39.130 13.17 13.17 35.04 4.40
4110 4198 5.921962 AACACTAGTATCATCAGTCAGCA 57.078 39.130 0.00 0.00 0.00 4.41
4121 4209 4.695455 TGCAGGAAAGCAAACACTAGTATC 59.305 41.667 0.00 0.00 42.46 2.24
4150 4238 6.560003 ATCTGTACCATAACCTTGTCATGA 57.440 37.500 0.00 0.00 0.00 3.07
4646 4736 0.105964 CAATCCCTCGCCGGTAATCA 59.894 55.000 1.90 0.00 0.00 2.57
4709 4799 6.421485 ACGGTCCTAATACAGTTCTAAGAGA 58.579 40.000 0.00 0.00 0.00 3.10
4711 4801 6.543831 GGTACGGTCCTAATACAGTTCTAAGA 59.456 42.308 0.00 0.00 0.00 2.10
4731 4821 3.640029 ACCCATGGTAGTAATCTGGTACG 59.360 47.826 11.73 0.00 32.11 3.67
4761 4851 3.362281 TCATACAACACGAATTTCGCG 57.638 42.857 18.24 11.77 45.12 5.87
4835 4925 5.952347 TGGCTTCAGTAGATCAGTTAAGAGA 59.048 40.000 0.00 0.00 0.00 3.10
4925 5015 9.155975 ACTTGAAGAGTATTTTACATGCAGTAG 57.844 33.333 0.00 0.00 36.65 2.57
5003 5093 6.054941 TCTGCAGATTCACTTTGTAACTTCA 58.945 36.000 13.74 0.00 0.00 3.02
5004 5094 6.545504 TCTGCAGATTCACTTTGTAACTTC 57.454 37.500 13.74 0.00 0.00 3.01
5037 5127 1.076014 TGTCGGTGCCAGGTAGAGA 59.924 57.895 0.00 0.00 0.00 3.10
5150 5240 3.556004 GCAGGAGGTAGCTGATAACCATC 60.556 52.174 0.00 1.36 38.30 3.51
5220 5313 2.031012 CTGCCAGCGTCCTCAACA 59.969 61.111 0.00 0.00 0.00 3.33
5244 5337 1.078848 GGAGTGCCTTGATGTCGCT 60.079 57.895 0.00 0.00 0.00 4.93
5247 5340 0.615331 TCCAGGAGTGCCTTGATGTC 59.385 55.000 0.00 0.00 43.90 3.06
5388 5481 3.241530 TTCAGGGTGCCGTGCTCT 61.242 61.111 6.08 0.00 0.00 4.09
5622 5715 0.252761 TGGATTGCTCATCGAAGCCA 59.747 50.000 6.64 0.00 41.77 4.75
5630 5723 1.138859 TCGAATCGGTGGATTGCTCAT 59.861 47.619 1.76 0.00 42.86 2.90


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

AutoCloner maintained by Alex Coulton.