Multiple sequence alignment - TraesCS5D01G161500

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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 TraesCS5D01G161500 chr5D 100.000 5910 0 0 1 5910 251963879 251957970 0.000000e+00 10914.0
1 TraesCS5D01G161500 chr5A 92.394 3905 207 40 1559 5396 334752344 334748463 0.000000e+00 5483.0
2 TraesCS5D01G161500 chr5A 90.964 830 39 16 740 1561 334753175 334752374 0.000000e+00 1085.0
3 TraesCS5D01G161500 chr5A 93.267 505 27 4 5408 5910 334748479 334747980 0.000000e+00 737.0
4 TraesCS5D01G161500 chr5B 93.275 2498 112 26 1559 4009 284371118 284368630 0.000000e+00 3631.0
5 TraesCS5D01G161500 chr5B 89.647 850 54 17 732 1561 284371983 284371148 0.000000e+00 1051.0
6 TraesCS5D01G161500 chr5B 88.816 760 56 15 4312 5058 284367523 284366780 0.000000e+00 905.0
7 TraesCS5D01G161500 chr5B 87.726 277 22 3 4062 4326 284367978 284367702 4.450000e-81 313.0
8 TraesCS5D01G161500 chr5B 84.444 90 8 5 5823 5908 317057842 317057929 3.800000e-12 84.2
9 TraesCS5D01G161500 chr1A 87.809 1173 94 25 3911 5050 566592052 566593208 0.000000e+00 1328.0
10 TraesCS5D01G161500 chr1A 97.333 75 2 0 2370 2444 554514146 554514220 1.730000e-25 128.0
11 TraesCS5D01G161500 chr1D 92.340 718 31 11 44 739 69092323 69093038 0.000000e+00 1000.0
12 TraesCS5D01G161500 chr1D 97.333 75 2 0 2370 2444 254396213 254396139 1.730000e-25 128.0
13 TraesCS5D01G161500 chr4A 89.481 751 45 13 1 729 738721740 738722478 0.000000e+00 918.0
14 TraesCS5D01G161500 chr2B 89.341 713 53 7 44 734 561389023 561388312 0.000000e+00 874.0
15 TraesCS5D01G161500 chr2B 81.098 164 24 6 5746 5905 508959619 508959459 2.240000e-24 124.0
16 TraesCS5D01G161500 chr7B 88.388 732 41 2 44 731 5015942 5015211 0.000000e+00 841.0
17 TraesCS5D01G161500 chr7A 82.597 362 36 12 1 338 500552246 500552604 1.610000e-75 294.0
18 TraesCS5D01G161500 chr7D 82.436 353 37 10 28 357 432750855 432751205 9.690000e-73 285.0
19 TraesCS5D01G161500 chr7D 83.333 96 11 3 366 461 432751281 432751371 3.800000e-12 84.2
20 TraesCS5D01G161500 chr7D 86.076 79 7 3 5833 5908 54233492 54233415 1.370000e-11 82.4
21 TraesCS5D01G161500 chr3B 80.780 359 44 10 28 363 771624839 771624483 2.110000e-64 257.0
22 TraesCS5D01G161500 chr6B 91.176 102 8 1 28 129 707708975 707708875 2.870000e-28 137.0
23 TraesCS5D01G161500 chr3A 89.320 103 11 0 379 481 102837473 102837575 4.810000e-26 130.0
24 TraesCS5D01G161500 chrUn 97.333 75 2 0 2370 2444 389361033 389361107 1.730000e-25 128.0
25 TraesCS5D01G161500 chrUn 97.333 75 2 0 2370 2444 436278258 436278184 1.730000e-25 128.0
26 TraesCS5D01G161500 chr6D 97.333 75 2 0 2370 2444 14944577 14944503 1.730000e-25 128.0
27 TraesCS5D01G161500 chr6D 97.333 75 2 0 2370 2444 168256824 168256898 1.730000e-25 128.0
28 TraesCS5D01G161500 chr6D 82.895 76 9 3 5835 5906 413057077 413057002 1.370000e-06 65.8
29 TraesCS5D01G161500 chr6A 97.333 75 2 0 2370 2444 73162723 73162797 1.730000e-25 128.0
30 TraesCS5D01G161500 chr6A 75.163 153 26 9 5760 5906 558598765 558598619 1.780000e-05 62.1
31 TraesCS5D01G161500 chr2A 86.869 99 10 2 31 126 327151602 327151700 2.250000e-19 108.0
32 TraesCS5D01G161500 chr3D 78.049 164 28 6 5746 5907 400694618 400694461 4.880000e-16 97.1


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 TraesCS5D01G161500 chr5D 251957970 251963879 5909 True 10914 10914 100.000000 1 5910 1 chr5D.!!$R1 5909
1 TraesCS5D01G161500 chr5A 334747980 334753175 5195 True 2435 5483 92.208333 740 5910 3 chr5A.!!$R1 5170
2 TraesCS5D01G161500 chr5B 284366780 284371983 5203 True 1475 3631 89.866000 732 5058 4 chr5B.!!$R1 4326
3 TraesCS5D01G161500 chr1A 566592052 566593208 1156 False 1328 1328 87.809000 3911 5050 1 chr1A.!!$F2 1139
4 TraesCS5D01G161500 chr1D 69092323 69093038 715 False 1000 1000 92.340000 44 739 1 chr1D.!!$F1 695
5 TraesCS5D01G161500 chr4A 738721740 738722478 738 False 918 918 89.481000 1 729 1 chr4A.!!$F1 728
6 TraesCS5D01G161500 chr2B 561388312 561389023 711 True 874 874 89.341000 44 734 1 chr2B.!!$R2 690
7 TraesCS5D01G161500 chr7B 5015211 5015942 731 True 841 841 88.388000 44 731 1 chr7B.!!$R1 687

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
708 753 0.037975 GGCTGAAGTTTCGACCGGTA 60.038 55.0 7.34 0.0 0.00 4.02 F
1512 1578 0.183492 TGCCCCTTCATCAGTATGCC 59.817 55.0 0.00 0.0 34.76 4.40 F
1513 1579 0.538287 GCCCCTTCATCAGTATGCCC 60.538 60.0 0.00 0.0 34.76 5.36 F
3228 3340 1.140312 AGGCTCTTGGTGGAAAGACA 58.860 50.0 0.00 0.0 32.75 3.41 F
4561 5524 0.606401 TCTTGGCTACTGCTTGCACC 60.606 55.0 0.00 0.0 39.59 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2183 2289 0.391661 GTGTCCACATCATCTGCGGT 60.392 55.000 0.00 0.00 0.00 5.68 R
3451 3564 0.737219 GCAGAGTTGCTTGGCTATGG 59.263 55.000 0.00 0.00 46.95 2.74 R
3505 3623 3.449737 GTCCATGTAGTAAGGTGCCTACA 59.550 47.826 2.36 2.36 45.40 2.74 R
4775 5739 1.188219 AACTCCTTGGAGCTCGCTGA 61.188 55.000 15.93 0.77 0.00 4.26 R
5512 6503 2.267188 TATGAAGACGCGGTGTACAC 57.733 50.000 18.01 18.01 0.00 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
26 27 8.917415 AGAAATTCAAGAAAAGTCAGTTGAAC 57.083 30.769 0.00 0.00 40.67 3.18
40 41 5.462068 GTCAGTTGAACCAAAAACATAAGCC 59.538 40.000 0.00 0.00 0.00 4.35
42 43 4.339814 AGTTGAACCAAAAACATAAGCCGA 59.660 37.500 0.00 0.00 0.00 5.54
170 171 0.247460 CTCAGAGGCGTGGTTCATCA 59.753 55.000 0.00 0.00 0.00 3.07
202 225 0.321919 GGCTTCCAGCATCTGACACA 60.322 55.000 0.00 0.00 44.75 3.72
375 420 1.742268 GCTCCTTCTACCGTTCTACGT 59.258 52.381 0.00 0.00 40.58 3.57
486 531 2.179767 CGACGTATCGTGGTGGCA 59.820 61.111 0.00 0.00 43.66 4.92
565 610 3.087638 CTCGAGCGAAAACGAGTGA 57.912 52.632 0.00 0.00 46.90 3.41
579 624 1.258676 GAGTGAAGGAGAAGACCCGT 58.741 55.000 0.00 0.00 0.00 5.28
581 626 0.966920 GTGAAGGAGAAGACCCGTGA 59.033 55.000 0.00 0.00 0.00 4.35
609 654 0.912006 AAGGAAGAGGGAGTGGGCTC 60.912 60.000 0.00 0.00 40.93 4.70
654 699 2.352817 ACGTGAGTGAAGGGAGGAC 58.647 57.895 0.00 0.00 46.97 3.85
655 700 0.178958 ACGTGAGTGAAGGGAGGACT 60.179 55.000 0.00 0.00 46.97 3.85
702 747 1.667830 CAGCCGGCTGAAGTTTCGA 60.668 57.895 46.72 0.00 46.30 3.71
708 753 0.037975 GGCTGAAGTTTCGACCGGTA 60.038 55.000 7.34 0.00 0.00 4.02
710 755 1.603678 GCTGAAGTTTCGACCGGTACA 60.604 52.381 7.34 0.00 0.00 2.90
753 798 3.842925 GAAAGGTGCCGGTCAGCCA 62.843 63.158 19.76 0.00 43.95 4.75
754 799 3.850098 AAAGGTGCCGGTCAGCCAG 62.850 63.158 19.76 0.00 43.95 4.85
756 801 4.101448 GGTGCCGGTCAGCCAGAT 62.101 66.667 14.63 0.00 37.22 2.90
757 802 2.821366 GTGCCGGTCAGCCAGATG 60.821 66.667 1.90 0.00 34.09 2.90
758 803 3.321648 TGCCGGTCAGCCAGATGT 61.322 61.111 1.90 0.00 34.09 3.06
759 804 1.987306 TGCCGGTCAGCCAGATGTA 60.987 57.895 1.90 0.00 34.09 2.29
768 813 5.184096 CGGTCAGCCAGATGTATATAGAGTT 59.816 44.000 0.00 0.00 34.09 3.01
822 874 3.518998 CGATCAGTCCGTCCGCCT 61.519 66.667 0.00 0.00 0.00 5.52
823 875 2.893398 GATCAGTCCGTCCGCCTT 59.107 61.111 0.00 0.00 0.00 4.35
825 877 1.668101 GATCAGTCCGTCCGCCTTCT 61.668 60.000 0.00 0.00 0.00 2.85
827 879 1.004918 CAGTCCGTCCGCCTTCTTT 60.005 57.895 0.00 0.00 0.00 2.52
859 922 2.480845 GTGGAGCGTAGTCAAACTTGT 58.519 47.619 0.00 0.00 0.00 3.16
867 930 6.091437 AGCGTAGTCAAACTTGTCATACTAC 58.909 40.000 0.00 0.00 37.18 2.73
968 1033 3.789756 GCGTCGAGAAGATATGAAAACGA 59.210 43.478 0.00 0.00 0.00 3.85
969 1034 4.441415 GCGTCGAGAAGATATGAAAACGAT 59.559 41.667 0.00 0.00 0.00 3.73
971 1036 6.305877 GCGTCGAGAAGATATGAAAACGATAT 59.694 38.462 0.00 0.00 0.00 1.63
1052 1118 5.584649 TCATATCAAAACCCTAAGCAAGTCG 59.415 40.000 0.00 0.00 0.00 4.18
1053 1119 2.500229 TCAAAACCCTAAGCAAGTCGG 58.500 47.619 0.00 0.00 0.00 4.79
1054 1120 1.068541 CAAAACCCTAAGCAAGTCGGC 60.069 52.381 0.00 0.00 0.00 5.54
1467 1533 8.758829 ACAGGGTAATAAAATCCATTCTTTTCC 58.241 33.333 0.00 0.00 0.00 3.13
1477 1543 8.512966 AAATCCATTCTTTTCCTACTTCTAGC 57.487 34.615 0.00 0.00 0.00 3.42
1478 1544 6.620877 TCCATTCTTTTCCTACTTCTAGCA 57.379 37.500 0.00 0.00 0.00 3.49
1503 1569 1.839424 GTGTTTAGCTGCCCCTTCAT 58.161 50.000 0.00 0.00 0.00 2.57
1504 1570 1.745653 GTGTTTAGCTGCCCCTTCATC 59.254 52.381 0.00 0.00 0.00 2.92
1506 1572 2.019984 GTTTAGCTGCCCCTTCATCAG 58.980 52.381 0.00 0.00 0.00 2.90
1507 1573 1.289160 TTAGCTGCCCCTTCATCAGT 58.711 50.000 0.00 0.00 0.00 3.41
1508 1574 2.174685 TAGCTGCCCCTTCATCAGTA 57.825 50.000 0.00 0.00 0.00 2.74
1510 1576 1.142465 AGCTGCCCCTTCATCAGTATG 59.858 52.381 0.00 0.00 37.54 2.39
1511 1577 1.602311 CTGCCCCTTCATCAGTATGC 58.398 55.000 0.00 0.00 34.76 3.14
1512 1578 0.183492 TGCCCCTTCATCAGTATGCC 59.817 55.000 0.00 0.00 34.76 4.40
1513 1579 0.538287 GCCCCTTCATCAGTATGCCC 60.538 60.000 0.00 0.00 34.76 5.36
1563 1661 6.493802 ACTTATTACTCCTCCGAGCATGATAA 59.506 38.462 0.00 0.00 40.03 1.75
1582 1680 2.851263 ACAGCTTATGAACGTCCCAA 57.149 45.000 0.00 0.00 0.00 4.12
1621 1719 9.171877 CTTGTCTTGCTCTAATTTCTAAATCCT 57.828 33.333 0.00 0.00 0.00 3.24
1628 1726 9.561069 TGCTCTAATTTCTAAATCCTAATGTCC 57.439 33.333 0.00 0.00 0.00 4.02
1629 1727 9.785982 GCTCTAATTTCTAAATCCTAATGTCCT 57.214 33.333 0.00 0.00 0.00 3.85
1633 1731 8.926092 AATTTCTAAATCCTAATGTCCTAGCC 57.074 34.615 0.00 0.00 0.00 3.93
1634 1732 5.723672 TCTAAATCCTAATGTCCTAGCCG 57.276 43.478 0.00 0.00 0.00 5.52
1635 1733 5.391256 TCTAAATCCTAATGTCCTAGCCGA 58.609 41.667 0.00 0.00 0.00 5.54
1636 1734 6.017192 TCTAAATCCTAATGTCCTAGCCGAT 58.983 40.000 0.00 0.00 0.00 4.18
1637 1735 5.568620 AAATCCTAATGTCCTAGCCGATT 57.431 39.130 0.00 0.00 0.00 3.34
1638 1736 4.543590 ATCCTAATGTCCTAGCCGATTG 57.456 45.455 0.00 0.00 0.00 2.67
1639 1737 2.037251 TCCTAATGTCCTAGCCGATTGC 59.963 50.000 0.00 0.00 41.71 3.56
1757 1857 6.786959 AGGAGATTTTGACTGATCCTAGCTAT 59.213 38.462 0.00 0.00 35.43 2.97
1820 1920 1.551883 ACCGGCGTTAACTCTGGTATT 59.448 47.619 24.43 3.51 38.47 1.89
1829 1931 7.201504 GGCGTTAACTCTGGTATTTAGTTTCTC 60.202 40.741 3.71 0.00 35.23 2.87
1938 2040 1.401905 GCTTCCTTGGTGGCTTAATCG 59.598 52.381 0.00 0.00 35.26 3.34
1943 2045 2.417651 CCTTGGTGGCTTAATCGTACGA 60.418 50.000 21.93 21.93 0.00 3.43
1945 2047 2.883574 TGGTGGCTTAATCGTACGAAG 58.116 47.619 23.56 16.18 0.00 3.79
1967 2070 9.570488 CGAAGCCTAAGTATATGGTAATACTTC 57.430 37.037 11.44 0.00 45.31 3.01
1988 2091 8.115490 ACTTCTTGTTTTGGATAGGATGAAAG 57.885 34.615 0.00 0.00 0.00 2.62
1989 2092 6.515272 TCTTGTTTTGGATAGGATGAAAGC 57.485 37.500 0.00 0.00 0.00 3.51
1992 2095 7.888021 TCTTGTTTTGGATAGGATGAAAGCTTA 59.112 33.333 0.00 0.00 0.00 3.09
1994 2097 8.055279 TGTTTTGGATAGGATGAAAGCTTAAG 57.945 34.615 0.00 0.00 0.00 1.85
1995 2098 7.669722 TGTTTTGGATAGGATGAAAGCTTAAGT 59.330 33.333 0.00 0.00 0.00 2.24
1997 2100 5.126067 TGGATAGGATGAAAGCTTAAGTGC 58.874 41.667 0.00 0.00 0.00 4.40
1998 2101 5.126067 GGATAGGATGAAAGCTTAAGTGCA 58.874 41.667 0.00 0.00 34.99 4.57
1999 2102 5.238214 GGATAGGATGAAAGCTTAAGTGCAG 59.762 44.000 0.00 0.00 34.99 4.41
2011 2117 6.903419 AGCTTAAGTGCAGTATTTTTCACTC 58.097 36.000 4.02 0.00 38.68 3.51
2017 2123 5.008019 AGTGCAGTATTTTTCACTCACACAG 59.992 40.000 0.00 0.00 35.05 3.66
2023 2129 4.678509 TTTTTCACTCACACAGTCACAC 57.321 40.909 0.00 0.00 30.26 3.82
2040 2146 6.018669 CAGTCACACTACTGTTTCTTTCTTCC 60.019 42.308 0.00 0.00 41.63 3.46
2127 2233 7.275183 TGGGCATATGTAAGTATAGCATCATC 58.725 38.462 4.29 0.00 0.00 2.92
2128 2234 7.092935 TGGGCATATGTAAGTATAGCATCATCA 60.093 37.037 4.29 0.00 0.00 3.07
2130 2236 9.166173 GGCATATGTAAGTATAGCATCATCAAA 57.834 33.333 4.29 0.00 0.00 2.69
2145 2251 8.475639 AGCATCATCAAATCTTGCTTCTAATTT 58.524 29.630 0.00 0.00 40.58 1.82
2146 2252 8.540492 GCATCATCAAATCTTGCTTCTAATTTG 58.460 33.333 0.00 0.00 39.38 2.32
2177 2283 4.215399 CCATTCACGGAAGCTGACTTTTTA 59.785 41.667 0.00 0.00 35.82 1.52
2183 2289 4.396790 ACGGAAGCTGACTTTTTAAACACA 59.603 37.500 0.00 0.00 35.82 3.72
2233 2339 3.027974 ACACGCAGGTTAAGAGAAGAC 57.972 47.619 0.00 0.00 0.00 3.01
2254 2360 1.808945 GGCAGTCTCATTGGTGTTCTG 59.191 52.381 0.00 0.00 0.00 3.02
3135 3247 1.676746 CAGCTGCAGTTCCATATGCT 58.323 50.000 16.64 0.00 42.98 3.79
3153 3265 5.679734 ATGCTGTGAAAACAGTACAAGAG 57.320 39.130 7.63 0.00 39.76 2.85
3204 3316 2.104111 CTGCATGGGCCATCAATTGATT 59.896 45.455 18.16 0.02 40.13 2.57
3228 3340 1.140312 AGGCTCTTGGTGGAAAGACA 58.860 50.000 0.00 0.00 32.75 3.41
3396 3508 5.483685 AGGTCATGTTACTTAGTGCTGAA 57.516 39.130 0.00 0.00 0.00 3.02
3411 3523 2.290008 TGCTGAATATGTGTCGTGGGTT 60.290 45.455 0.00 0.00 0.00 4.11
3417 3529 2.762535 ATGTGTCGTGGGTTTCCTAG 57.237 50.000 0.00 0.00 0.00 3.02
3418 3530 1.416243 TGTGTCGTGGGTTTCCTAGT 58.584 50.000 0.00 0.00 0.00 2.57
3426 3539 5.178252 GTCGTGGGTTTCCTAGTTTAACTTC 59.822 44.000 1.94 0.00 0.00 3.01
3431 3544 4.378149 GGTTTCCTAGTTTAACTTCAGCGC 60.378 45.833 1.94 0.00 0.00 5.92
3432 3545 3.671008 TCCTAGTTTAACTTCAGCGCA 57.329 42.857 11.47 0.00 0.00 6.09
3433 3546 3.323243 TCCTAGTTTAACTTCAGCGCAC 58.677 45.455 11.47 0.00 0.00 5.34
3439 3552 4.573201 AGTTTAACTTCAGCGCACACTAAA 59.427 37.500 11.47 2.82 0.00 1.85
3451 3564 4.031028 CGCACACTAAATTAGCTTCATGC 58.969 43.478 0.00 2.88 43.29 4.06
3505 3623 4.969359 TCTTTGGGCTTAGTATCTTAGGCT 59.031 41.667 8.66 0.00 36.25 4.58
3537 3658 7.492669 CACCTTACTACATGGACTAAGACATTG 59.507 40.741 6.04 0.00 0.00 2.82
3555 3676 3.906720 TTGAAGCTAGTACATGGGACC 57.093 47.619 0.00 0.00 0.00 4.46
3565 3688 1.447838 CATGGGACCGTGAAGACCG 60.448 63.158 4.52 0.00 35.09 4.79
3645 3769 3.696051 TCACAAGCAATCTTATTGGGCTC 59.304 43.478 2.11 0.00 32.84 4.70
3743 3867 1.818642 ATGACTTGTGCCTTCTCTGC 58.181 50.000 0.00 0.00 0.00 4.26
3754 3878 1.666054 CTTCTCTGCTTCATGAGGGC 58.334 55.000 6.99 10.83 0.00 5.19
3757 3881 1.632409 TCTCTGCTTCATGAGGGCTTT 59.368 47.619 18.83 0.00 0.00 3.51
3791 3915 9.995957 AATTTTTGTTGTTATTTTGTAGCAACC 57.004 25.926 10.75 0.00 37.69 3.77
3792 3916 8.547967 TTTTTGTTGTTATTTTGTAGCAACCA 57.452 26.923 10.75 0.20 37.69 3.67
3793 3917 8.547967 TTTTGTTGTTATTTTGTAGCAACCAA 57.452 26.923 10.75 5.27 37.69 3.67
3794 3918 8.723942 TTTGTTGTTATTTTGTAGCAACCAAT 57.276 26.923 10.75 0.00 37.69 3.16
3795 3919 9.817809 TTTGTTGTTATTTTGTAGCAACCAATA 57.182 25.926 10.75 0.00 37.69 1.90
3796 3920 9.817809 TTGTTGTTATTTTGTAGCAACCAATAA 57.182 25.926 10.75 0.00 37.69 1.40
3797 3921 9.817809 TGTTGTTATTTTGTAGCAACCAATAAA 57.182 25.926 10.75 0.00 37.69 1.40
3821 3945 7.578310 AATATTATGGACATATGCTCATGGC 57.422 36.000 16.88 0.00 42.22 4.40
3884 4031 9.120538 CTGTATAATATATGGGTGTAATTGGCC 57.879 37.037 0.00 0.00 0.00 5.36
3954 4101 6.500684 TTCCAAGCATAGATTGTCAGTTTC 57.499 37.500 0.00 0.00 0.00 2.78
4032 4294 9.919348 CTTGTATATTTTGCCAAATTGTAATGC 57.081 29.630 0.53 0.00 34.29 3.56
4097 4847 6.732896 TTGAACCTATTTGCTTGGGTTTTA 57.267 33.333 0.00 0.00 41.44 1.52
4099 4849 5.245075 TGAACCTATTTGCTTGGGTTTTAGG 59.755 40.000 0.00 0.00 41.44 2.69
4228 4995 4.162592 TGGTGTTTGAGCAGCAGG 57.837 55.556 0.00 0.00 41.24 4.85
4251 5018 9.877178 CAGGGATAGTAAGTTATGCTTATAAGG 57.123 37.037 14.28 0.00 41.25 2.69
4333 5296 8.863049 GTTTTTGAATTACTGGTGCATATGAAG 58.137 33.333 6.97 0.42 0.00 3.02
4334 5297 7.936496 TTTGAATTACTGGTGCATATGAAGA 57.064 32.000 6.97 0.00 0.00 2.87
4335 5298 7.936496 TTGAATTACTGGTGCATATGAAGAA 57.064 32.000 6.97 0.00 0.00 2.52
4336 5299 8.523915 TTGAATTACTGGTGCATATGAAGAAT 57.476 30.769 6.97 0.00 0.00 2.40
4337 5300 8.158169 TGAATTACTGGTGCATATGAAGAATC 57.842 34.615 6.97 0.00 0.00 2.52
4338 5301 7.774625 TGAATTACTGGTGCATATGAAGAATCA 59.225 33.333 6.97 0.00 40.57 2.57
4343 5306 6.139048 TGGTGCATATGAAGAATCATTGTG 57.861 37.500 6.97 0.00 43.89 3.33
4387 5350 2.172505 CCATAACTATGCTGTGGACCCA 59.827 50.000 0.00 0.00 32.40 4.51
4495 5458 2.160721 TGTCTCTCCAGTACCATCCC 57.839 55.000 0.00 0.00 0.00 3.85
4504 5467 0.927767 AGTACCATCCCGAGTCCTCT 59.072 55.000 0.00 0.00 0.00 3.69
4507 5470 2.196925 CCATCCCGAGTCCTCTCCG 61.197 68.421 0.00 0.00 37.40 4.63
4510 5473 4.444081 CCCGAGTCCTCTCCGGGT 62.444 72.222 10.62 0.00 43.13 5.28
4513 5476 2.359404 GAGTCCTCTCCGGGTCCA 59.641 66.667 0.00 0.00 34.87 4.02
4555 5518 5.677319 TGTATAACTTCTTGGCTACTGCT 57.323 39.130 0.00 0.00 39.59 4.24
4561 5524 0.606401 TCTTGGCTACTGCTTGCACC 60.606 55.000 0.00 0.00 39.59 5.01
4578 5541 2.675603 GCACCCAAAACAGTTTTTCGGT 60.676 45.455 16.80 16.80 44.41 4.69
4618 5581 6.230472 TCCATTATTAATCTGGTCGTGGATG 58.770 40.000 13.80 0.00 0.00 3.51
4775 5739 1.385528 GGTTTGTTGTTGGACCGACT 58.614 50.000 13.25 0.00 0.00 4.18
4831 5795 5.188555 TGTTGATTTCTCCTATCAGCTGACT 59.811 40.000 20.97 11.03 35.18 3.41
4978 5963 4.516698 TCTCCTTTGCTTTGCAGTAGAAAG 59.483 41.667 2.38 8.21 40.61 2.62
4989 5974 6.959639 TTGCAGTAGAAAGGAAGAAAACAT 57.040 33.333 0.00 0.00 0.00 2.71
5003 5988 7.036863 AGGAAGAAAACATAATTCCCTAGGACA 60.037 37.037 11.48 0.00 41.81 4.02
5131 6121 9.573166 TGATTTTACAGATTCAAGGAAAGAAGA 57.427 29.630 0.00 0.00 0.00 2.87
5138 6128 9.171877 ACAGATTCAAGGAAAGAAGATGATAAC 57.828 33.333 0.00 0.00 0.00 1.89
5160 6150 3.435186 GAAGGGCAGCAGGCGAAC 61.435 66.667 0.00 0.00 46.16 3.95
5177 6167 4.434520 GCGAACTGAGCTTATAGGTCTTT 58.565 43.478 7.33 1.46 42.83 2.52
5178 6168 4.870991 GCGAACTGAGCTTATAGGTCTTTT 59.129 41.667 7.33 1.16 42.83 2.27
5179 6169 6.040878 GCGAACTGAGCTTATAGGTCTTTTA 58.959 40.000 7.33 0.00 42.83 1.52
5216 6206 5.124776 CGGAGGTGCACTATTGGATTTTTAA 59.875 40.000 17.98 0.00 0.00 1.52
5279 6269 3.128349 TCTACTGACTTGCGGAACAAAC 58.872 45.455 0.00 0.00 37.96 2.93
5290 6280 1.539827 CGGAACAAACCATCCAACTCC 59.460 52.381 0.00 0.00 35.34 3.85
5295 6285 3.222603 ACAAACCATCCAACTCCTTGAC 58.777 45.455 0.00 0.00 0.00 3.18
5300 6291 3.146066 CCATCCAACTCCTTGACGAAAA 58.854 45.455 0.00 0.00 0.00 2.29
5317 6308 5.934921 ACGAAAATTTAACTTCGATGTCCC 58.065 37.500 15.00 0.00 45.65 4.46
5318 6309 5.019498 CGAAAATTTAACTTCGATGTCCCG 58.981 41.667 4.21 0.00 45.65 5.14
5319 6310 5.163933 CGAAAATTTAACTTCGATGTCCCGA 60.164 40.000 4.21 0.00 45.65 5.14
5320 6311 6.563222 AAAATTTAACTTCGATGTCCCGAA 57.437 33.333 4.21 0.00 45.01 4.30
5335 6326 2.569853 TCCCGAAGACATTGAGGCTAAA 59.430 45.455 0.00 0.00 30.53 1.85
5340 6331 6.073003 CCCGAAGACATTGAGGCTAAATAATC 60.073 42.308 0.00 0.00 30.53 1.75
5359 6350 1.134098 TCCGCCTGGAATGAGATTTCC 60.134 52.381 0.00 0.00 42.85 3.13
5361 6352 1.473257 CGCCTGGAATGAGATTTCCGA 60.473 52.381 0.00 0.00 46.85 4.55
5368 6359 6.767902 CCTGGAATGAGATTTCCGAATTCTTA 59.232 38.462 3.52 4.09 46.85 2.10
5376 6367 4.921470 TTTCCGAATTCTTAACTCGCAG 57.079 40.909 3.52 0.00 0.00 5.18
5389 6380 7.159372 TCTTAACTCGCAGAAGAAATAGGTTT 58.841 34.615 0.00 0.00 34.09 3.27
5391 6382 4.894784 ACTCGCAGAAGAAATAGGTTTGA 58.105 39.130 0.00 0.00 34.09 2.69
5392 6383 5.491982 ACTCGCAGAAGAAATAGGTTTGAT 58.508 37.500 0.00 0.00 34.09 2.57
5393 6384 5.940470 ACTCGCAGAAGAAATAGGTTTGATT 59.060 36.000 0.00 0.00 34.09 2.57
5394 6385 6.128172 ACTCGCAGAAGAAATAGGTTTGATTG 60.128 38.462 0.00 0.00 34.09 2.67
5395 6386 5.937540 TCGCAGAAGAAATAGGTTTGATTGA 59.062 36.000 0.00 0.00 0.00 2.57
5396 6387 6.599244 TCGCAGAAGAAATAGGTTTGATTGAT 59.401 34.615 0.00 0.00 0.00 2.57
5397 6388 7.121168 TCGCAGAAGAAATAGGTTTGATTGATT 59.879 33.333 0.00 0.00 0.00 2.57
5398 6389 7.430502 CGCAGAAGAAATAGGTTTGATTGATTC 59.569 37.037 0.00 0.00 0.00 2.52
5399 6390 8.465201 GCAGAAGAAATAGGTTTGATTGATTCT 58.535 33.333 0.00 0.00 0.00 2.40
5404 6395 9.525826 AGAAATAGGTTTGATTGATTCTTCACT 57.474 29.630 0.00 0.00 0.00 3.41
5405 6396 9.780413 GAAATAGGTTTGATTGATTCTTCACTC 57.220 33.333 0.00 0.00 33.38 3.51
5406 6397 5.869753 AGGTTTGATTGATTCTTCACTCG 57.130 39.130 0.00 0.00 35.01 4.18
5407 6398 4.697352 AGGTTTGATTGATTCTTCACTCGG 59.303 41.667 0.00 0.00 35.01 4.63
5408 6399 4.695455 GGTTTGATTGATTCTTCACTCGGA 59.305 41.667 0.00 0.00 35.01 4.55
5409 6400 5.181245 GGTTTGATTGATTCTTCACTCGGAA 59.819 40.000 0.00 0.00 35.01 4.30
5410 6401 6.293955 GGTTTGATTGATTCTTCACTCGGAAA 60.294 38.462 0.00 0.00 35.01 3.13
5411 6402 7.308435 GTTTGATTGATTCTTCACTCGGAAAT 58.692 34.615 0.00 0.00 35.01 2.17
5412 6403 8.450964 GTTTGATTGATTCTTCACTCGGAAATA 58.549 33.333 0.00 0.00 35.01 1.40
5413 6404 7.776933 TGATTGATTCTTCACTCGGAAATAG 57.223 36.000 0.00 0.00 35.01 1.73
5414 6405 6.763135 TGATTGATTCTTCACTCGGAAATAGG 59.237 38.462 0.00 0.00 35.01 2.57
5415 6406 5.677319 TGATTCTTCACTCGGAAATAGGT 57.323 39.130 0.00 0.00 34.44 3.08
5416 6407 6.049955 TGATTCTTCACTCGGAAATAGGTT 57.950 37.500 0.00 0.00 34.44 3.50
5417 6408 6.472887 TGATTCTTCACTCGGAAATAGGTTT 58.527 36.000 0.00 0.00 34.44 3.27
5418 6409 6.594159 TGATTCTTCACTCGGAAATAGGTTTC 59.406 38.462 0.00 0.00 42.39 2.78
5450 6441 9.953697 GTATAGACACGAAGACTTCAATCTTAT 57.046 33.333 15.36 9.08 39.08 1.73
5561 6552 3.191371 ACGGGCATTCTGAATTCTTCAAC 59.809 43.478 7.05 0.00 39.58 3.18
5566 6557 5.860716 GGCATTCTGAATTCTTCAACTGTTC 59.139 40.000 7.05 0.00 39.58 3.18
5588 6579 6.031964 TCCACATAATTTTTAGGGGCCATA 57.968 37.500 4.39 0.00 0.00 2.74
5727 6718 9.667107 TTACAAAACCCACAAAATGAACAATAA 57.333 25.926 0.00 0.00 0.00 1.40
5736 6727 9.097257 CCACAAAATGAACAATAACATATTCCC 57.903 33.333 0.00 0.00 0.00 3.97
5844 6835 6.237901 TGACATCTACTGCACCAAATTAGTT 58.762 36.000 0.00 0.00 0.00 2.24
5853 6844 7.820648 ACTGCACCAAATTAGTTTCATTAGAG 58.179 34.615 0.00 0.00 0.00 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 7.170658 TGTTTTTGGTTCAACTGACTTTTCTTG 59.829 33.333 0.00 0.00 0.00 3.02
9 10 7.213678 TGTTTTTGGTTCAACTGACTTTTCTT 58.786 30.769 0.00 0.00 0.00 2.52
16 17 5.462068 GGCTTATGTTTTTGGTTCAACTGAC 59.538 40.000 0.00 0.00 0.00 3.51
17 18 5.596845 GGCTTATGTTTTTGGTTCAACTGA 58.403 37.500 0.00 0.00 0.00 3.41
26 27 4.423732 CTGGAATCGGCTTATGTTTTTGG 58.576 43.478 0.00 0.00 0.00 3.28
40 41 3.574284 TCCATGTTTTTGCTGGAATCG 57.426 42.857 0.00 0.00 36.15 3.34
42 43 3.511146 ACGATCCATGTTTTTGCTGGAAT 59.489 39.130 0.00 0.00 42.12 3.01
202 225 4.800554 CTGGAAGCTGGAACCGTT 57.199 55.556 0.00 0.00 0.00 4.44
375 420 2.039084 GAGAGGAAAAGCTGGAACCTCA 59.961 50.000 22.43 0.00 46.43 3.86
461 506 4.012554 CGATACGTCGCCAGCAAT 57.987 55.556 0.00 0.00 41.49 3.56
471 516 1.080093 CACTGCCACCACGATACGT 60.080 57.895 0.00 0.00 42.36 3.57
555 600 3.494573 GGGTCTTCTCCTTCACTCGTTTT 60.495 47.826 0.00 0.00 0.00 2.43
565 610 3.197983 CCTATTTCACGGGTCTTCTCCTT 59.802 47.826 0.00 0.00 0.00 3.36
579 624 6.327626 CACTCCCTCTTCCTTATCCTATTTCA 59.672 42.308 0.00 0.00 0.00 2.69
581 626 5.608860 CCACTCCCTCTTCCTTATCCTATTT 59.391 44.000 0.00 0.00 0.00 1.40
609 654 1.799258 GCAGAGTTGTTGGCCCACAG 61.799 60.000 9.94 0.00 0.00 3.66
641 686 1.479709 CGATCAGTCCTCCCTTCACT 58.520 55.000 0.00 0.00 0.00 3.41
655 700 0.029433 CGTTCGATCTGAGGCGATCA 59.971 55.000 6.30 0.00 39.78 2.92
692 737 1.269726 GGTGTACCGGTCGAAACTTCA 60.270 52.381 12.40 0.00 0.00 3.02
708 753 2.212652 GGAAACGTTTAGAACCGGTGT 58.787 47.619 14.65 0.11 0.00 4.16
710 755 1.417517 AGGGAAACGTTTAGAACCGGT 59.582 47.619 14.65 0.00 0.00 5.28
768 813 3.709653 ACCCAGCCGTATCTTTCTTATCA 59.290 43.478 0.00 0.00 0.00 2.15
834 895 1.541310 TTGACTACGCTCCACCCCTG 61.541 60.000 0.00 0.00 0.00 4.45
845 906 7.082602 ACAGTAGTATGACAAGTTTGACTACG 58.917 38.462 12.22 10.62 42.52 3.51
859 922 1.669265 CAGACGCGGACAGTAGTATGA 59.331 52.381 12.47 0.00 0.00 2.15
867 930 0.039074 AGAGAAACAGACGCGGACAG 60.039 55.000 12.47 3.57 0.00 3.51
969 1034 9.850628 GTAAAAGTGAGGACGCATATATGTATA 57.149 33.333 14.14 0.00 0.00 1.47
971 1036 7.948357 AGTAAAAGTGAGGACGCATATATGTA 58.052 34.615 14.14 0.00 0.00 2.29
1467 1533 6.198591 GCTAAACACGGTATTGCTAGAAGTAG 59.801 42.308 0.00 0.00 0.00 2.57
1475 1541 1.737793 GCAGCTAAACACGGTATTGCT 59.262 47.619 0.00 0.00 0.00 3.91
1476 1542 1.202143 GGCAGCTAAACACGGTATTGC 60.202 52.381 0.00 0.00 0.00 3.56
1477 1543 1.400494 GGGCAGCTAAACACGGTATTG 59.600 52.381 0.00 0.00 0.00 1.90
1478 1544 1.680860 GGGGCAGCTAAACACGGTATT 60.681 52.381 0.00 0.00 0.00 1.89
1503 1569 5.892686 TGATTTGATTTCATGGGCATACTGA 59.107 36.000 0.00 0.00 0.00 3.41
1504 1570 5.981315 GTGATTTGATTTCATGGGCATACTG 59.019 40.000 0.00 0.00 0.00 2.74
1506 1572 6.152932 AGTGATTTGATTTCATGGGCATAC 57.847 37.500 0.00 0.00 0.00 2.39
1507 1573 8.481492 AATAGTGATTTGATTTCATGGGCATA 57.519 30.769 0.00 0.00 0.00 3.14
1508 1574 6.989155 ATAGTGATTTGATTTCATGGGCAT 57.011 33.333 0.00 0.00 0.00 4.40
1510 1576 9.768662 AATAAATAGTGATTTGATTTCATGGGC 57.231 29.630 0.00 0.00 35.96 5.36
1563 1661 2.851263 TTGGGACGTTCATAAGCTGT 57.149 45.000 0.00 0.00 0.00 4.40
1582 1680 8.804912 AGAGCAAGACAAGAAAGATAAATCAT 57.195 30.769 0.00 0.00 0.00 2.45
1619 1717 2.417719 GCAATCGGCTAGGACATTAGG 58.582 52.381 0.00 0.00 40.25 2.69
1631 1729 2.945668 AGACAAATCCTAAGCAATCGGC 59.054 45.455 0.00 0.00 45.30 5.54
1632 1730 4.191544 TGAGACAAATCCTAAGCAATCGG 58.808 43.478 0.00 0.00 0.00 4.18
1633 1731 4.872691 ACTGAGACAAATCCTAAGCAATCG 59.127 41.667 0.00 0.00 0.00 3.34
1634 1732 7.519649 GCATACTGAGACAAATCCTAAGCAATC 60.520 40.741 0.00 0.00 0.00 2.67
1635 1733 6.261826 GCATACTGAGACAAATCCTAAGCAAT 59.738 38.462 0.00 0.00 0.00 3.56
1636 1734 5.586243 GCATACTGAGACAAATCCTAAGCAA 59.414 40.000 0.00 0.00 0.00 3.91
1637 1735 5.104776 AGCATACTGAGACAAATCCTAAGCA 60.105 40.000 0.00 0.00 0.00 3.91
1638 1736 5.363939 AGCATACTGAGACAAATCCTAAGC 58.636 41.667 0.00 0.00 0.00 3.09
1639 1737 6.815089 AGAGCATACTGAGACAAATCCTAAG 58.185 40.000 0.00 0.00 0.00 2.18
1757 1857 3.698539 TCATCAAAACAAACTGACCAGCA 59.301 39.130 0.00 0.00 0.00 4.41
1832 1934 8.146053 TGGAGTATTAGATTCTGTTTCTTGGA 57.854 34.615 0.00 0.00 0.00 3.53
1882 1984 1.473278 CGTCACCTACAAGAGAGTCCC 59.527 57.143 0.00 0.00 0.00 4.46
1938 2040 9.780413 GTATTACCATATACTTAGGCTTCGTAC 57.220 37.037 0.00 0.00 0.00 3.67
1967 2070 6.521151 AGCTTTCATCCTATCCAAAACAAG 57.479 37.500 0.00 0.00 0.00 3.16
1988 2091 6.578919 GTGAGTGAAAAATACTGCACTTAAGC 59.421 38.462 1.29 0.00 41.30 3.09
1989 2092 7.587757 GTGTGAGTGAAAAATACTGCACTTAAG 59.412 37.037 0.00 0.00 41.30 1.85
1992 2095 5.356751 TGTGTGAGTGAAAAATACTGCACTT 59.643 36.000 0.00 0.00 41.30 3.16
1994 2097 5.168526 TGTGTGAGTGAAAAATACTGCAC 57.831 39.130 0.00 0.00 34.24 4.57
1995 2098 4.881273 ACTGTGTGAGTGAAAAATACTGCA 59.119 37.500 0.00 0.00 31.75 4.41
1997 2100 6.037062 TGTGACTGTGTGAGTGAAAAATACTG 59.963 38.462 0.00 0.00 33.83 2.74
1998 2101 6.037172 GTGTGACTGTGTGAGTGAAAAATACT 59.963 38.462 0.00 0.00 33.83 2.12
1999 2102 6.037172 AGTGTGACTGTGTGAGTGAAAAATAC 59.963 38.462 0.00 0.00 33.83 1.89
2017 2123 5.815740 TGGAAGAAAGAAACAGTAGTGTGAC 59.184 40.000 3.39 1.81 36.84 3.67
2023 2129 7.385478 GGAAGTACTGGAAGAAAGAAACAGTAG 59.615 40.741 0.00 0.00 43.06 2.57
2040 2146 2.872038 GCACCTCCAGTTGGAAGTACTG 60.872 54.545 0.00 0.00 44.91 2.74
2130 2236 9.466497 TGGAGTAATTCAAATTAGAAGCAAGAT 57.534 29.630 0.00 0.00 31.94 2.40
2145 2251 3.938963 GCTTCCGTGAATGGAGTAATTCA 59.061 43.478 0.00 0.00 42.78 2.57
2146 2252 4.034510 CAGCTTCCGTGAATGGAGTAATTC 59.965 45.833 0.00 0.00 39.72 2.17
2177 2283 1.536766 CACATCATCTGCGGTGTGTTT 59.463 47.619 5.96 0.00 37.70 2.83
2183 2289 0.391661 GTGTCCACATCATCTGCGGT 60.392 55.000 0.00 0.00 0.00 5.68
2212 2318 3.365666 CGTCTTCTCTTAACCTGCGTGTA 60.366 47.826 0.00 0.00 0.00 2.90
2233 2339 0.798776 GAACACCAATGAGACTGCCG 59.201 55.000 0.00 0.00 0.00 5.69
2254 2360 2.110901 TGAGAGACTGGTCGGTACTC 57.889 55.000 0.00 0.00 34.09 2.59
2279 2385 2.978278 TGGCCATTTCCAACAATTCCTT 59.022 40.909 0.00 0.00 32.18 3.36
2835 2945 1.741028 TGAACTCCCATCCTGAACCA 58.259 50.000 0.00 0.00 0.00 3.67
3060 3172 7.284034 CCATCAGGCTTCAAATTAAGTACATCT 59.716 37.037 0.00 0.00 0.00 2.90
3135 3247 8.304596 CCTACTATCTCTTGTACTGTTTTCACA 58.695 37.037 0.00 0.00 0.00 3.58
3204 3316 3.970410 CCACCAAGAGCCTGCCCA 61.970 66.667 0.00 0.00 0.00 5.36
3228 3340 8.934825 CCGTGATGACCAAATTTCATTTTAAAT 58.065 29.630 0.00 0.00 33.70 1.40
3361 3473 4.431416 ACATGACCTACCAGAAAACACA 57.569 40.909 0.00 0.00 0.00 3.72
3396 3508 3.773119 ACTAGGAAACCCACGACACATAT 59.227 43.478 0.00 0.00 0.00 1.78
3411 3523 3.744426 GTGCGCTGAAGTTAAACTAGGAA 59.256 43.478 9.73 0.00 0.00 3.36
3417 3529 4.461992 TTAGTGTGCGCTGAAGTTAAAC 57.538 40.909 9.73 0.00 0.00 2.01
3418 3530 5.682943 ATTTAGTGTGCGCTGAAGTTAAA 57.317 34.783 9.73 6.88 0.00 1.52
3426 3539 3.125146 TGAAGCTAATTTAGTGTGCGCTG 59.875 43.478 9.73 0.00 0.00 5.18
3431 3544 5.565592 TGGCATGAAGCTAATTTAGTGTG 57.434 39.130 0.00 0.19 44.79 3.82
3432 3545 6.016777 GCTATGGCATGAAGCTAATTTAGTGT 60.017 38.462 10.98 0.00 44.79 3.55
3433 3546 6.376978 GCTATGGCATGAAGCTAATTTAGTG 58.623 40.000 10.98 0.00 44.79 2.74
3439 3552 3.513909 TGGCTATGGCATGAAGCTAAT 57.486 42.857 18.85 0.00 44.79 1.73
3451 3564 0.737219 GCAGAGTTGCTTGGCTATGG 59.263 55.000 0.00 0.00 46.95 2.74
3478 3591 7.509546 CCTAAGATACTAAGCCCAAAGATGAA 58.490 38.462 0.00 0.00 0.00 2.57
3505 3623 3.449737 GTCCATGTAGTAAGGTGCCTACA 59.550 47.826 2.36 2.36 45.40 2.74
3537 3658 1.755380 ACGGTCCCATGTACTAGCTTC 59.245 52.381 0.00 0.00 0.00 3.86
3555 3676 3.117794 TCACAAAACTACGGTCTTCACG 58.882 45.455 0.00 0.00 37.36 4.35
3565 3688 6.729187 AGTCTTTCAGCATTCACAAAACTAC 58.271 36.000 0.00 0.00 0.00 2.73
3617 3741 6.293081 CCCAATAAGATTGCTTGTGAGATACG 60.293 42.308 0.00 0.00 35.56 3.06
3618 3742 6.514048 GCCCAATAAGATTGCTTGTGAGATAC 60.514 42.308 0.00 0.00 35.56 2.24
3620 3744 4.340381 GCCCAATAAGATTGCTTGTGAGAT 59.660 41.667 0.00 0.00 35.56 2.75
3624 3748 3.444742 TGAGCCCAATAAGATTGCTTGTG 59.555 43.478 0.00 0.00 35.56 3.33
3645 3769 9.403110 CAACTGGATTTTAACTTCAAGAATCTG 57.597 33.333 0.00 0.00 0.00 2.90
3710 3834 6.238320 GGCACAAGTCATAGAATGAAGATCAC 60.238 42.308 0.00 0.00 41.69 3.06
3743 3867 2.787994 ACTGTGAAAGCCCTCATGAAG 58.212 47.619 0.00 0.00 0.00 3.02
3795 3919 8.472413 GCCATGAGCATATGTCCATAATATTTT 58.528 33.333 4.29 0.00 42.97 1.82
3796 3920 7.069085 GGCCATGAGCATATGTCCATAATATTT 59.931 37.037 0.00 0.00 46.50 1.40
3797 3921 6.548622 GGCCATGAGCATATGTCCATAATATT 59.451 38.462 0.00 0.00 46.50 1.28
3798 3922 6.066690 GGCCATGAGCATATGTCCATAATAT 58.933 40.000 0.00 0.00 46.50 1.28
3799 3923 5.044993 TGGCCATGAGCATATGTCCATAATA 60.045 40.000 0.00 0.00 46.50 0.98
3800 3924 4.264038 TGGCCATGAGCATATGTCCATAAT 60.264 41.667 0.00 0.00 46.50 1.28
3801 3925 3.074242 TGGCCATGAGCATATGTCCATAA 59.926 43.478 0.00 0.00 46.50 1.90
3802 3926 2.643801 TGGCCATGAGCATATGTCCATA 59.356 45.455 0.00 0.00 46.50 2.74
3803 3927 1.426215 TGGCCATGAGCATATGTCCAT 59.574 47.619 0.00 5.48 46.50 3.41
3804 3928 0.845337 TGGCCATGAGCATATGTCCA 59.155 50.000 0.00 3.25 46.50 4.02
3805 3929 1.985473 TTGGCCATGAGCATATGTCC 58.015 50.000 6.09 0.00 46.50 4.02
3806 3930 3.151554 TGATTGGCCATGAGCATATGTC 58.848 45.455 6.09 1.80 46.50 3.06
3808 3932 3.761752 TCATGATTGGCCATGAGCATATG 59.238 43.478 6.09 5.34 45.54 1.78
3810 3934 3.512219 TCATGATTGGCCATGAGCATA 57.488 42.857 6.09 0.00 45.54 3.14
3811 3935 2.375014 TCATGATTGGCCATGAGCAT 57.625 45.000 6.09 3.78 45.54 3.79
3812 3936 3.907458 TCATGATTGGCCATGAGCA 57.093 47.368 6.09 0.59 45.54 4.26
3817 3941 6.381994 ACTTCAAAACTATCATGATTGGCCAT 59.618 34.615 14.65 0.00 0.00 4.40
3819 3943 6.212888 ACTTCAAAACTATCATGATTGGCC 57.787 37.500 14.65 0.00 0.00 5.36
3820 3944 9.455847 GATAACTTCAAAACTATCATGATTGGC 57.544 33.333 14.65 0.00 0.00 4.52
3857 3983 9.681062 GCCAATTACACCCATATATTATACAGT 57.319 33.333 0.00 0.00 0.00 3.55
3903 4050 9.467258 CTGACAATGATAGTTTCAACATTTTGT 57.533 29.630 0.00 0.84 38.03 2.83
3933 4080 4.096984 GGGAAACTGACAATCTATGCTTGG 59.903 45.833 0.00 0.00 0.00 3.61
3954 4101 1.048160 ATAAGCAAAATGGGCGGGGG 61.048 55.000 0.00 0.00 36.08 5.40
4029 4291 3.637229 AGTTACGCATACCTGACTAGCAT 59.363 43.478 0.00 0.00 0.00 3.79
4032 4294 4.804139 CCAAAGTTACGCATACCTGACTAG 59.196 45.833 0.00 0.00 0.00 2.57
4097 4847 4.019321 TGACCTTATGCTGAAAGTAAGCCT 60.019 41.667 0.00 0.00 40.06 4.58
4099 4849 5.819901 AGATGACCTTATGCTGAAAGTAAGC 59.180 40.000 0.00 0.00 41.22 3.09
4219 4986 3.828875 AACTTACTATCCCTGCTGCTC 57.171 47.619 0.00 0.00 0.00 4.26
4333 5296 7.894376 ACCAAATCAAATGTCACAATGATTC 57.106 32.000 17.80 0.00 40.58 2.52
4334 5297 9.373603 CATACCAAATCAAATGTCACAATGATT 57.626 29.630 13.71 13.71 42.61 2.57
4335 5298 7.493320 GCATACCAAATCAAATGTCACAATGAT 59.507 33.333 4.08 4.08 34.11 2.45
4336 5299 6.812656 GCATACCAAATCAAATGTCACAATGA 59.187 34.615 0.00 0.00 0.00 2.57
4337 5300 6.590677 TGCATACCAAATCAAATGTCACAATG 59.409 34.615 0.00 0.00 0.00 2.82
4338 5301 6.699366 TGCATACCAAATCAAATGTCACAAT 58.301 32.000 0.00 0.00 0.00 2.71
4339 5302 6.015603 TCTGCATACCAAATCAAATGTCACAA 60.016 34.615 0.00 0.00 0.00 3.33
4343 5306 5.807011 GGTTCTGCATACCAAATCAAATGTC 59.193 40.000 12.06 0.00 35.67 3.06
4387 5350 1.381327 TCCTTCCGGGAGCGATTCT 60.381 57.895 3.32 0.00 39.58 2.40
4408 5371 5.682943 TTAGGTTGATGTGTGTAACTTGC 57.317 39.130 0.00 0.00 38.04 4.01
4414 5377 5.870706 TGGTCATTTAGGTTGATGTGTGTA 58.129 37.500 0.00 0.00 0.00 2.90
4495 5458 2.829458 GGACCCGGAGAGGACTCG 60.829 72.222 0.73 0.00 45.00 4.18
4510 5473 1.625315 CCCAAGTCTGAGTCATGTGGA 59.375 52.381 11.25 0.00 0.00 4.02
4513 5476 3.840666 ACATACCCAAGTCTGAGTCATGT 59.159 43.478 0.00 0.00 0.00 3.21
4555 5518 2.996621 CGAAAAACTGTTTTGGGTGCAA 59.003 40.909 18.33 0.00 37.07 4.08
4561 5524 5.238006 TGTCTACCGAAAAACTGTTTTGG 57.762 39.130 18.33 17.29 37.07 3.28
4607 5570 2.029380 CAGTAAGTCACATCCACGACCA 60.029 50.000 0.00 0.00 32.33 4.02
4611 5574 6.202188 AGTTAAAACAGTAAGTCACATCCACG 59.798 38.462 0.00 0.00 0.00 4.94
4618 5581 7.431376 GCCAAAAGAGTTAAAACAGTAAGTCAC 59.569 37.037 0.00 0.00 36.34 3.67
4730 5694 1.719780 GAGTACAAGTTTCGCCACTCG 59.280 52.381 0.00 0.00 40.15 4.18
4735 5699 1.193874 CAACCGAGTACAAGTTTCGCC 59.806 52.381 0.00 0.00 33.25 5.54
4775 5739 1.188219 AACTCCTTGGAGCTCGCTGA 61.188 55.000 15.93 0.77 0.00 4.26
4804 5768 6.070596 TCAGCTGATAGGAGAAATCAACAAGA 60.071 38.462 13.74 0.00 33.13 3.02
4978 5963 7.116736 TGTCCTAGGGAATTATGTTTTCTTCC 58.883 38.462 9.46 0.00 37.11 3.46
4989 5974 5.550403 ACTGGAAACTTGTCCTAGGGAATTA 59.450 40.000 9.46 0.00 38.62 1.40
5003 5988 2.439507 TCAGGAGCTCAACTGGAAACTT 59.560 45.455 17.19 0.00 35.47 2.66
5131 6121 2.684927 GCTGCCCTTCCACTGTTATCAT 60.685 50.000 0.00 0.00 0.00 2.45
5138 6128 2.360852 CCTGCTGCCCTTCCACTG 60.361 66.667 0.00 0.00 0.00 3.66
5160 6150 6.183360 TGCCTCTAAAAGACCTATAAGCTCAG 60.183 42.308 0.00 0.00 0.00 3.35
5177 6167 1.304962 TCCGACCAGCTGCCTCTAA 60.305 57.895 8.66 0.00 0.00 2.10
5178 6168 1.754621 CTCCGACCAGCTGCCTCTA 60.755 63.158 8.66 0.00 0.00 2.43
5179 6169 3.073735 CTCCGACCAGCTGCCTCT 61.074 66.667 8.66 0.00 0.00 3.69
5233 6223 6.024049 GTGCTCTGAGTTAAAAATCCAATCG 58.976 40.000 6.53 0.00 0.00 3.34
5279 6269 2.472695 TTCGTCAAGGAGTTGGATGG 57.527 50.000 0.00 0.00 34.09 3.51
5290 6280 7.268447 GGACATCGAAGTTAAATTTTCGTCAAG 59.732 37.037 14.03 8.05 44.68 3.02
5295 6285 5.019498 CGGGACATCGAAGTTAAATTTTCG 58.981 41.667 0.00 0.00 45.49 3.46
5317 6308 6.346919 CGGATTATTTAGCCTCAATGTCTTCG 60.347 42.308 0.00 0.00 0.00 3.79
5318 6309 6.566753 GCGGATTATTTAGCCTCAATGTCTTC 60.567 42.308 0.00 0.00 0.00 2.87
5319 6310 5.239525 GCGGATTATTTAGCCTCAATGTCTT 59.760 40.000 0.00 0.00 0.00 3.01
5320 6311 4.757149 GCGGATTATTTAGCCTCAATGTCT 59.243 41.667 0.00 0.00 0.00 3.41
5335 6326 4.647564 AATCTCATTCCAGGCGGATTAT 57.352 40.909 0.00 0.00 42.41 1.28
5340 6331 1.312815 GGAAATCTCATTCCAGGCGG 58.687 55.000 1.30 0.00 46.70 6.13
5359 6350 5.763444 TTCTTCTGCGAGTTAAGAATTCG 57.237 39.130 0.00 0.32 42.62 3.34
5361 6352 7.824779 ACCTATTTCTTCTGCGAGTTAAGAATT 59.175 33.333 0.00 0.00 38.61 2.17
5368 6359 5.305585 TCAAACCTATTTCTTCTGCGAGTT 58.694 37.500 0.00 0.00 0.00 3.01
5391 6382 6.653989 ACCTATTTCCGAGTGAAGAATCAAT 58.346 36.000 0.00 0.00 37.30 2.57
5392 6383 6.049955 ACCTATTTCCGAGTGAAGAATCAA 57.950 37.500 0.00 0.00 37.30 2.57
5393 6384 5.677319 ACCTATTTCCGAGTGAAGAATCA 57.323 39.130 0.00 0.00 33.63 2.57
5394 6385 6.594159 TGAAACCTATTTCCGAGTGAAGAATC 59.406 38.462 0.00 0.00 43.18 2.52
5395 6386 6.472887 TGAAACCTATTTCCGAGTGAAGAAT 58.527 36.000 0.00 0.00 43.18 2.40
5396 6387 5.860611 TGAAACCTATTTCCGAGTGAAGAA 58.139 37.500 0.00 0.00 43.18 2.52
5397 6388 5.477607 TGAAACCTATTTCCGAGTGAAGA 57.522 39.130 0.00 0.00 43.18 2.87
5398 6389 6.371548 TCAATGAAACCTATTTCCGAGTGAAG 59.628 38.462 0.00 0.00 43.18 3.02
5399 6390 6.234920 TCAATGAAACCTATTTCCGAGTGAA 58.765 36.000 0.00 0.00 43.18 3.18
5400 6391 5.800296 TCAATGAAACCTATTTCCGAGTGA 58.200 37.500 0.00 0.00 43.18 3.41
5401 6392 5.643777 ACTCAATGAAACCTATTTCCGAGTG 59.356 40.000 12.21 0.95 43.18 3.51
5402 6393 5.805728 ACTCAATGAAACCTATTTCCGAGT 58.194 37.500 9.19 9.19 43.18 4.18
5403 6394 9.197694 CTATACTCAATGAAACCTATTTCCGAG 57.802 37.037 0.00 4.16 43.18 4.63
5404 6395 8.920174 TCTATACTCAATGAAACCTATTTCCGA 58.080 33.333 0.00 0.00 43.18 4.55
5405 6396 8.979574 GTCTATACTCAATGAAACCTATTTCCG 58.020 37.037 0.00 0.00 43.18 4.30
5406 6397 9.832445 TGTCTATACTCAATGAAACCTATTTCC 57.168 33.333 0.00 0.00 43.18 3.13
5408 6399 9.314321 CGTGTCTATACTCAATGAAACCTATTT 57.686 33.333 0.00 0.00 0.00 1.40
5409 6400 8.692710 TCGTGTCTATACTCAATGAAACCTATT 58.307 33.333 0.00 0.00 0.00 1.73
5410 6401 8.234136 TCGTGTCTATACTCAATGAAACCTAT 57.766 34.615 0.00 0.00 0.00 2.57
5411 6402 7.634671 TCGTGTCTATACTCAATGAAACCTA 57.365 36.000 0.00 0.00 0.00 3.08
5412 6403 6.525578 TCGTGTCTATACTCAATGAAACCT 57.474 37.500 0.00 0.00 0.00 3.50
5413 6404 7.009357 GTCTTCGTGTCTATACTCAATGAAACC 59.991 40.741 0.00 0.00 0.00 3.27
5414 6405 7.755822 AGTCTTCGTGTCTATACTCAATGAAAC 59.244 37.037 0.00 0.00 0.00 2.78
5415 6406 7.827701 AGTCTTCGTGTCTATACTCAATGAAA 58.172 34.615 0.00 0.00 0.00 2.69
5416 6407 7.392494 AGTCTTCGTGTCTATACTCAATGAA 57.608 36.000 0.00 0.00 0.00 2.57
5417 6408 7.120726 TGAAGTCTTCGTGTCTATACTCAATGA 59.879 37.037 8.06 0.00 0.00 2.57
5418 6409 7.251281 TGAAGTCTTCGTGTCTATACTCAATG 58.749 38.462 8.06 0.00 0.00 2.82
5450 6441 8.472413 ACATCAAACCGTACTATTAAGAGCTAA 58.528 33.333 0.00 0.00 0.00 3.09
5451 6442 7.919091 CACATCAAACCGTACTATTAAGAGCTA 59.081 37.037 0.00 0.00 0.00 3.32
5452 6443 6.757010 CACATCAAACCGTACTATTAAGAGCT 59.243 38.462 0.00 0.00 0.00 4.09
5502 6493 3.242381 ACGCGGTGTACACTTTTGTTTAC 60.242 43.478 24.55 4.65 37.15 2.01
5512 6503 2.267188 TATGAAGACGCGGTGTACAC 57.733 50.000 18.01 18.01 0.00 2.90
5514 6505 2.793232 GGAATATGAAGACGCGGTGTAC 59.207 50.000 12.47 0.00 0.00 2.90
5566 6557 6.326323 AGTTATGGCCCCTAAAAATTATGTGG 59.674 38.462 0.00 0.00 0.00 4.17
5588 6579 5.382616 AGGATTTGGTTTAACCGAAGAGTT 58.617 37.500 20.04 5.44 44.41 3.01
5627 6618 7.147915 GGAACCCATGTGTTTGTGAATATACAT 60.148 37.037 0.00 0.00 0.00 2.29
5634 6625 3.025322 AGGAACCCATGTGTTTGTGAA 57.975 42.857 0.00 0.00 0.00 3.18
5682 6673 8.870160 TTTGTAAATGTTTTGATGTTCTGGAG 57.130 30.769 0.00 0.00 0.00 3.86
5736 6727 8.361592 AGAGCTTCAAATGTTTTCAATCAAAG 57.638 30.769 0.00 0.00 0.00 2.77
5739 6730 7.448161 TCCTAGAGCTTCAAATGTTTTCAATCA 59.552 33.333 0.00 0.00 0.00 2.57
5744 6735 7.597386 ACAATCCTAGAGCTTCAAATGTTTTC 58.403 34.615 0.00 0.00 0.00 2.29
5815 6806 6.403866 TTTGGTGCAGTAGATGTCAATTTT 57.596 33.333 0.00 0.00 0.00 1.82
5817 6808 6.594788 AATTTGGTGCAGTAGATGTCAATT 57.405 33.333 0.00 0.00 0.00 2.32
5821 6812 6.743575 AACTAATTTGGTGCAGTAGATGTC 57.256 37.500 0.00 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.