Multiple sequence alignment - TraesCS3B01G247500

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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 TraesCS3B01G247500 chr3B 100.000 4992 0 0 1 4992 393335755 393340746 0.000000e+00 9219.0
1 TraesCS3B01G247500 chr3B 93.696 349 22 0 3638 3986 77841082 77840734 1.590000e-144 523.0
2 TraesCS3B01G247500 chr3B 84.650 443 45 12 2719 3141 77847415 77846976 2.150000e-113 420.0
3 TraesCS3B01G247500 chr3B 85.054 368 40 14 3139 3495 77841536 77841173 1.320000e-95 361.0
4 TraesCS3B01G247500 chr3B 92.641 231 13 2 2307 2533 77847781 77847551 3.730000e-86 329.0
5 TraesCS3B01G247500 chr3B 80.175 343 64 4 3640 3980 772465922 772465582 2.310000e-63 254.0
6 TraesCS3B01G247500 chr3B 77.099 262 52 8 1217 1474 772467253 772466996 1.450000e-30 145.0
7 TraesCS3B01G247500 chr3D 93.341 2463 81 25 1863 4304 298357754 298360154 0.000000e+00 3563.0
8 TraesCS3B01G247500 chr3D 91.251 903 31 18 977 1863 298356850 298357720 0.000000e+00 1186.0
9 TraesCS3B01G247500 chr3D 86.207 638 78 7 4362 4992 263795949 263796583 0.000000e+00 682.0
10 TraesCS3B01G247500 chr3D 85.803 641 84 5 4357 4992 241427945 241428583 0.000000e+00 673.0
11 TraesCS3B01G247500 chr3D 87.523 537 55 10 2970 3497 48837319 48836786 1.190000e-170 610.0
12 TraesCS3B01G247500 chr3D 93.478 368 22 1 3640 4005 48836680 48836313 3.400000e-151 545.0
13 TraesCS3B01G247500 chr3D 93.277 238 13 3 2307 2541 48837823 48837586 1.030000e-91 348.0
14 TraesCS3B01G247500 chr3D 80.117 342 66 2 3640 3980 578927363 578927703 2.310000e-63 254.0
15 TraesCS3B01G247500 chr3D 90.155 193 19 0 2719 2911 48837601 48837409 8.300000e-63 252.0
16 TraesCS3B01G247500 chr3D 78.244 262 49 8 1217 1474 578926041 578926298 1.440000e-35 161.0
17 TraesCS3B01G247500 chr3D 97.222 36 0 1 2197 2231 48837943 48837908 5.400000e-05 60.2
18 TraesCS3B01G247500 chr3D 87.500 48 6 0 1076 1123 578921696 578921743 6.980000e-04 56.5
19 TraesCS3B01G247500 chr3A 91.340 2171 74 39 1863 3996 396020125 396022218 0.000000e+00 2863.0
20 TraesCS3B01G247500 chr3A 90.032 933 29 22 963 1863 396019195 396020095 0.000000e+00 1149.0
21 TraesCS3B01G247500 chr3A 87.218 532 52 13 2976 3497 61312562 61312037 4.300000e-165 592.0
22 TraesCS3B01G247500 chr3A 94.958 357 18 0 3640 3996 61311930 61311574 1.210000e-155 560.0
23 TraesCS3B01G247500 chr3A 93.277 238 13 3 2307 2541 61313069 61312832 1.030000e-91 348.0
24 TraesCS3B01G247500 chr3A 91.623 191 16 0 2719 2909 61312847 61312657 1.070000e-66 265.0
25 TraesCS3B01G247500 chr3A 80.758 343 62 4 3640 3980 714290271 714289931 1.070000e-66 265.0
26 TraesCS3B01G247500 chr3A 91.946 149 12 0 4060 4208 396022562 396022710 5.060000e-50 209.0
27 TraesCS3B01G247500 chr3A 77.863 262 50 8 1217 1474 714291593 714291336 6.690000e-34 156.0
28 TraesCS3B01G247500 chr3A 92.553 94 7 0 4211 4304 396023083 396023176 8.720000e-28 135.0
29 TraesCS3B01G247500 chr3A 85.246 61 6 3 1059 1116 714297440 714297380 5.400000e-05 60.2
30 TraesCS3B01G247500 chr5B 98.345 967 14 1 1 965 658090691 658091657 0.000000e+00 1696.0
31 TraesCS3B01G247500 chr5B 96.891 965 29 1 1 965 528759504 528760467 0.000000e+00 1615.0
32 TraesCS3B01G247500 chr6B 98.246 969 13 2 1 965 650639995 650639027 0.000000e+00 1692.0
33 TraesCS3B01G247500 chr6B 86.321 636 79 6 4362 4992 327413192 327412560 0.000000e+00 686.0
34 TraesCS3B01G247500 chr7B 97.521 968 21 2 1 965 335933764 335934731 0.000000e+00 1652.0
35 TraesCS3B01G247500 chrUn 96.601 971 26 4 1 965 17588595 17589564 0.000000e+00 1604.0
36 TraesCS3B01G247500 chrUn 85.826 642 79 9 4359 4992 143325806 143325169 0.000000e+00 671.0
37 TraesCS3B01G247500 chrUn 87.850 535 52 11 2970 3495 39536083 39535553 2.550000e-172 616.0
38 TraesCS3B01G247500 chrUn 93.277 357 24 0 3640 3996 39535465 39535109 1.230000e-145 527.0
39 TraesCS3B01G247500 chrUn 94.714 227 12 0 2307 2533 39536712 39536486 2.210000e-93 353.0
40 TraesCS3B01G247500 chrUn 93.782 193 12 0 2719 2911 39536350 39536158 1.760000e-74 291.0
41 TraesCS3B01G247500 chr2B 96.384 968 32 2 1 965 29748034 29747067 0.000000e+00 1591.0
42 TraesCS3B01G247500 chr2B 96.091 972 30 6 1 966 155036186 155035217 0.000000e+00 1578.0
43 TraesCS3B01G247500 chr2B 94.948 970 40 8 1 965 178341246 178340281 0.000000e+00 1511.0
44 TraesCS3B01G247500 chr2B 86.028 637 82 5 4361 4992 337708170 337708804 0.000000e+00 676.0
45 TraesCS3B01G247500 chr2B 75.912 137 29 3 1258 1392 461127762 461127896 3.230000e-07 67.6
46 TraesCS3B01G247500 chr4A 95.975 969 32 3 1 965 660215536 660216501 0.000000e+00 1567.0
47 TraesCS3B01G247500 chr7A 86.207 638 76 8 4362 4992 366120448 366121080 0.000000e+00 680.0
48 TraesCS3B01G247500 chr4D 86.072 639 80 6 4361 4992 209340624 209339988 0.000000e+00 678.0
49 TraesCS3B01G247500 chr6A 85.938 640 79 9 4361 4992 285644960 285645596 0.000000e+00 673.0
50 TraesCS3B01G247500 chr5D 85.692 643 83 6 4357 4992 187890974 187891614 0.000000e+00 669.0
51 TraesCS3B01G247500 chr2A 75.912 137 29 3 1258 1392 526098321 526098455 3.230000e-07 67.6
52 TraesCS3B01G247500 chr2D 75.182 137 30 3 1258 1392 389287758 389287892 1.500000e-05 62.1


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 TraesCS3B01G247500 chr3B 393335755 393340746 4991 False 9219.00 9219 100.00000 1 4992 1 chr3B.!!$F1 4991
1 TraesCS3B01G247500 chr3B 77840734 77841536 802 True 442.00 523 89.37500 3139 3986 2 chr3B.!!$R1 847
2 TraesCS3B01G247500 chr3B 77846976 77847781 805 True 374.50 420 88.64550 2307 3141 2 chr3B.!!$R2 834
3 TraesCS3B01G247500 chr3D 298356850 298360154 3304 False 2374.50 3563 92.29600 977 4304 2 chr3D.!!$F4 3327
4 TraesCS3B01G247500 chr3D 263795949 263796583 634 False 682.00 682 86.20700 4362 4992 1 chr3D.!!$F2 630
5 TraesCS3B01G247500 chr3D 241427945 241428583 638 False 673.00 673 85.80300 4357 4992 1 chr3D.!!$F1 635
6 TraesCS3B01G247500 chr3D 48836313 48837943 1630 True 363.04 610 92.33100 2197 4005 5 chr3D.!!$R1 1808
7 TraesCS3B01G247500 chr3D 578926041 578927703 1662 False 207.50 254 79.18050 1217 3980 2 chr3D.!!$F5 2763
8 TraesCS3B01G247500 chr3A 396019195 396023176 3981 False 1089.00 2863 91.46775 963 4304 4 chr3A.!!$F1 3341
9 TraesCS3B01G247500 chr3A 61311574 61313069 1495 True 441.25 592 91.76900 2307 3996 4 chr3A.!!$R2 1689
10 TraesCS3B01G247500 chr3A 714289931 714291593 1662 True 210.50 265 79.31050 1217 3980 2 chr3A.!!$R3 2763
11 TraesCS3B01G247500 chr5B 658090691 658091657 966 False 1696.00 1696 98.34500 1 965 1 chr5B.!!$F2 964
12 TraesCS3B01G247500 chr5B 528759504 528760467 963 False 1615.00 1615 96.89100 1 965 1 chr5B.!!$F1 964
13 TraesCS3B01G247500 chr6B 650639027 650639995 968 True 1692.00 1692 98.24600 1 965 1 chr6B.!!$R2 964
14 TraesCS3B01G247500 chr6B 327412560 327413192 632 True 686.00 686 86.32100 4362 4992 1 chr6B.!!$R1 630
15 TraesCS3B01G247500 chr7B 335933764 335934731 967 False 1652.00 1652 97.52100 1 965 1 chr7B.!!$F1 964
16 TraesCS3B01G247500 chrUn 17588595 17589564 969 False 1604.00 1604 96.60100 1 965 1 chrUn.!!$F1 964
17 TraesCS3B01G247500 chrUn 143325169 143325806 637 True 671.00 671 85.82600 4359 4992 1 chrUn.!!$R1 633
18 TraesCS3B01G247500 chrUn 39535109 39536712 1603 True 446.75 616 92.40575 2307 3996 4 chrUn.!!$R2 1689
19 TraesCS3B01G247500 chr2B 29747067 29748034 967 True 1591.00 1591 96.38400 1 965 1 chr2B.!!$R1 964
20 TraesCS3B01G247500 chr2B 155035217 155036186 969 True 1578.00 1578 96.09100 1 966 1 chr2B.!!$R2 965
21 TraesCS3B01G247500 chr2B 178340281 178341246 965 True 1511.00 1511 94.94800 1 965 1 chr2B.!!$R3 964
22 TraesCS3B01G247500 chr2B 337708170 337708804 634 False 676.00 676 86.02800 4361 4992 1 chr2B.!!$F1 631
23 TraesCS3B01G247500 chr4A 660215536 660216501 965 False 1567.00 1567 95.97500 1 965 1 chr4A.!!$F1 964
24 TraesCS3B01G247500 chr7A 366120448 366121080 632 False 680.00 680 86.20700 4362 4992 1 chr7A.!!$F1 630
25 TraesCS3B01G247500 chr4D 209339988 209340624 636 True 678.00 678 86.07200 4361 4992 1 chr4D.!!$R1 631
26 TraesCS3B01G247500 chr6A 285644960 285645596 636 False 673.00 673 85.93800 4361 4992 1 chr6A.!!$F1 631
27 TraesCS3B01G247500 chr5D 187890974 187891614 640 False 669.00 669 85.69200 4357 4992 1 chr5D.!!$F1 635

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
979 988 1.003573 GTCCCCTGACCCCATCTCT 59.996 63.158 0.00 0.0 35.34 3.10 F
1142 1168 0.538057 TCGTACGTCACCACCCTTCT 60.538 55.000 16.05 0.0 0.00 2.85 F
1176 1202 1.226746 CCTTGGTTTCGTCGCTTCTT 58.773 50.000 0.00 0.0 0.00 2.52 F
3069 3370 1.053424 GGTCGGCTGGGGATACATAA 58.947 55.000 0.00 0.0 39.74 1.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2590 2698 0.169230 CAGTGCTCGCGAAGTAGAGT 59.831 55.0 11.33 0.00 36.93 3.24 R
3069 3370 0.107214 ACGGCAAATGTGATCCCGAT 60.107 50.0 10.69 0.00 41.34 4.18 R
3083 3384 0.907704 AGGGTATGTCCTTGACGGCA 60.908 55.0 0.00 0.00 34.95 5.69 R
4908 5916 0.392461 CCTCCAAATTCGCCCGAAGA 60.392 55.0 9.11 0.46 37.56 2.87 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
744 753 2.363795 CCTACCAGGGCCAGACGA 60.364 66.667 6.18 0.00 0.00 4.20
834 843 2.358737 CCAGACACCAGGGTTCGC 60.359 66.667 0.00 0.00 0.00 4.70
979 988 1.003573 GTCCCCTGACCCCATCTCT 59.996 63.158 0.00 0.00 35.34 3.10
1134 1155 1.652167 GGGACCTCTCGTACGTCACC 61.652 65.000 16.05 10.79 0.00 4.02
1135 1156 0.957395 GGACCTCTCGTACGTCACCA 60.957 60.000 16.05 0.00 0.00 4.17
1138 1159 1.505353 CTCTCGTACGTCACCACCC 59.495 63.158 16.05 0.00 0.00 4.61
1139 1160 0.959372 CTCTCGTACGTCACCACCCT 60.959 60.000 16.05 0.00 0.00 4.34
1142 1168 0.538057 TCGTACGTCACCACCCTTCT 60.538 55.000 16.05 0.00 0.00 2.85
1176 1202 1.226746 CCTTGGTTTCGTCGCTTCTT 58.773 50.000 0.00 0.00 0.00 2.52
1177 1203 2.409975 CCTTGGTTTCGTCGCTTCTTA 58.590 47.619 0.00 0.00 0.00 2.10
1178 1204 2.803956 CCTTGGTTTCGTCGCTTCTTAA 59.196 45.455 0.00 0.00 0.00 1.85
1181 1207 2.798283 TGGTTTCGTCGCTTCTTAACTG 59.202 45.455 0.00 0.00 0.00 3.16
1182 1208 3.054878 GGTTTCGTCGCTTCTTAACTGA 58.945 45.455 0.00 0.00 0.00 3.41
1184 1210 4.151867 GGTTTCGTCGCTTCTTAACTGATT 59.848 41.667 0.00 0.00 0.00 2.57
1185 1211 4.903638 TTCGTCGCTTCTTAACTGATTG 57.096 40.909 0.00 0.00 0.00 2.67
1186 1212 4.168922 TCGTCGCTTCTTAACTGATTGA 57.831 40.909 0.00 0.00 0.00 2.57
1187 1213 4.744570 TCGTCGCTTCTTAACTGATTGAT 58.255 39.130 0.00 0.00 0.00 2.57
1475 1503 5.431178 CCTCATGGATCACCGGATGGTAC 62.431 56.522 9.46 0.00 40.80 3.34
1487 1515 2.034179 CGGATGGTACGCTACTCAATCA 59.966 50.000 0.00 0.00 0.00 2.57
1488 1516 3.381949 GGATGGTACGCTACTCAATCAC 58.618 50.000 0.00 0.00 0.00 3.06
1529 1559 6.809630 ATCTTTCTTGTCTTTTGCTACCTC 57.190 37.500 0.00 0.00 0.00 3.85
1534 1564 5.869579 TCTTGTCTTTTGCTACCTCTCAAT 58.130 37.500 0.00 0.00 0.00 2.57
1546 1576 4.543590 ACCTCTCAATGTTCTCGAATGT 57.456 40.909 0.00 0.00 0.00 2.71
1547 1577 5.661056 ACCTCTCAATGTTCTCGAATGTA 57.339 39.130 0.00 0.00 0.00 2.29
1611 1646 2.223923 CGGAAGGAGAGGATCATGTCAC 60.224 54.545 6.85 0.00 37.82 3.67
1634 1669 1.329599 GTGAACGAACCGCTTTCTGTT 59.670 47.619 0.00 5.49 35.22 3.16
1636 1671 2.223157 TGAACGAACCGCTTTCTGTTTG 60.223 45.455 0.00 0.00 33.75 2.93
1637 1672 1.375551 ACGAACCGCTTTCTGTTTGT 58.624 45.000 0.00 0.00 34.90 2.83
1638 1673 1.741145 ACGAACCGCTTTCTGTTTGTT 59.259 42.857 0.00 0.00 35.98 2.83
1639 1674 2.162809 ACGAACCGCTTTCTGTTTGTTT 59.837 40.909 0.00 0.00 35.98 2.83
1640 1675 3.175929 CGAACCGCTTTCTGTTTGTTTT 58.824 40.909 0.00 0.00 31.20 2.43
1641 1676 3.239712 CGAACCGCTTTCTGTTTGTTTTC 59.760 43.478 0.00 0.00 31.20 2.29
1651 1686 7.952101 GCTTTCTGTTTGTTTTCTTTTTGTCTC 59.048 33.333 0.00 0.00 0.00 3.36
1697 1736 5.048504 TGCGAAATTTCTGCATCTCTTTCTT 60.049 36.000 24.08 0.00 33.93 2.52
1698 1737 5.511025 GCGAAATTTCTGCATCTCTTTCTTC 59.489 40.000 21.83 0.00 0.00 2.87
1699 1738 6.622462 GCGAAATTTCTGCATCTCTTTCTTCT 60.622 38.462 21.83 0.00 0.00 2.85
1700 1739 6.741811 CGAAATTTCTGCATCTCTTTCTTCTG 59.258 38.462 15.92 0.00 0.00 3.02
1701 1740 7.521871 AAATTTCTGCATCTCTTTCTTCTGT 57.478 32.000 0.00 0.00 0.00 3.41
1702 1741 5.936686 TTTCTGCATCTCTTTCTTCTGTG 57.063 39.130 0.00 0.00 0.00 3.66
1703 1742 4.613925 TCTGCATCTCTTTCTTCTGTGT 57.386 40.909 0.00 0.00 0.00 3.72
1704 1743 4.965814 TCTGCATCTCTTTCTTCTGTGTT 58.034 39.130 0.00 0.00 0.00 3.32
1781 1821 7.592885 ACTCATTTATTCCCTTTGATCCATG 57.407 36.000 0.00 0.00 0.00 3.66
1782 1822 6.041296 ACTCATTTATTCCCTTTGATCCATGC 59.959 38.462 0.00 0.00 0.00 4.06
1783 1823 4.916983 TTTATTCCCTTTGATCCATGCG 57.083 40.909 0.00 0.00 0.00 4.73
1784 1824 2.442236 ATTCCCTTTGATCCATGCGT 57.558 45.000 0.00 0.00 0.00 5.24
1796 1836 7.624360 TTGATCCATGCGTATTAATTATCCC 57.376 36.000 0.00 0.00 0.00 3.85
1887 1972 2.228138 TGTTTAACGACGTGCTCCTT 57.772 45.000 0.00 0.00 0.00 3.36
2039 2130 2.362077 GACCTGTGGTTGAAAATGTGCT 59.638 45.455 0.00 0.00 35.25 4.40
2040 2131 3.561143 ACCTGTGGTTGAAAATGTGCTA 58.439 40.909 0.00 0.00 27.29 3.49
2041 2132 3.569701 ACCTGTGGTTGAAAATGTGCTAG 59.430 43.478 0.00 0.00 27.29 3.42
2085 2176 1.940613 AGACAAAGACGTCCTTGCAAC 59.059 47.619 23.53 15.81 36.52 4.17
2131 2222 9.998106 GCCCATTTTTCTTACTGTAGATAGATA 57.002 33.333 0.00 0.00 0.00 1.98
2149 2240 8.907885 AGATAGATATACGCTATTGATTGCTCA 58.092 33.333 0.00 0.00 0.00 4.26
2181 2276 1.420138 TCCAATTATTCCCGGCCTCTC 59.580 52.381 0.00 0.00 0.00 3.20
2188 2283 4.227134 CCCGGCCTCTCATGACGG 62.227 72.222 13.30 13.30 43.89 4.79
2257 2352 1.615392 AGTGGCTCAACTTTGAATGCC 59.385 47.619 13.00 13.00 44.40 4.40
2258 2353 1.615392 GTGGCTCAACTTTGAATGCCT 59.385 47.619 18.17 0.00 44.43 4.75
2260 2355 2.297033 TGGCTCAACTTTGAATGCCTTC 59.703 45.455 18.17 0.00 44.43 3.46
2545 2653 5.381757 ACATGCTAGGTTCTCTCCTACTAG 58.618 45.833 0.00 0.00 38.86 2.57
2546 2654 5.103855 ACATGCTAGGTTCTCTCCTACTAGT 60.104 44.000 0.00 0.00 38.86 2.57
2547 2655 6.101442 ACATGCTAGGTTCTCTCCTACTAGTA 59.899 42.308 1.89 1.89 38.86 1.82
2548 2656 5.927819 TGCTAGGTTCTCTCCTACTAGTAC 58.072 45.833 0.00 0.00 38.86 2.73
2549 2657 5.666718 TGCTAGGTTCTCTCCTACTAGTACT 59.333 44.000 0.00 0.00 38.86 2.73
2550 2658 6.843333 TGCTAGGTTCTCTCCTACTAGTACTA 59.157 42.308 1.89 1.89 38.86 1.82
2551 2659 7.154656 GCTAGGTTCTCTCCTACTAGTACTAC 58.845 46.154 0.00 0.00 38.86 2.73
2590 2698 3.429822 GCACTTGCCCTACACGATTACTA 60.430 47.826 0.00 0.00 34.31 1.82
2591 2699 4.110482 CACTTGCCCTACACGATTACTAC 58.890 47.826 0.00 0.00 0.00 2.73
2592 2700 4.021916 ACTTGCCCTACACGATTACTACT 58.978 43.478 0.00 0.00 0.00 2.57
2599 2707 6.293353 GCCCTACACGATTACTACTCTACTTC 60.293 46.154 0.00 0.00 0.00 3.01
2618 2726 1.416813 CGCGAGCACTGATTCTCACC 61.417 60.000 0.00 0.00 0.00 4.02
2655 2764 9.874205 GCTAGAGAATAAATAATCAGAGAGCAT 57.126 33.333 0.00 0.00 0.00 3.79
2657 2766 8.550710 AGAGAATAAATAATCAGAGAGCATGC 57.449 34.615 10.51 10.51 0.00 4.06
2658 2767 8.155510 AGAGAATAAATAATCAGAGAGCATGCA 58.844 33.333 21.98 0.00 0.00 3.96
2682 2791 4.223556 TGGCATCCACTTTATTAACGGA 57.776 40.909 0.00 0.00 0.00 4.69
2683 2792 4.787551 TGGCATCCACTTTATTAACGGAT 58.212 39.130 0.00 0.00 36.92 4.18
2968 3269 5.072040 TGTCAGTGTTGATATGATCGTGT 57.928 39.130 0.00 0.00 35.39 4.49
3069 3370 1.053424 GGTCGGCTGGGGATACATAA 58.947 55.000 0.00 0.00 39.74 1.90
3080 3381 3.517901 GGGGATACATAATCGGGATCACA 59.482 47.826 0.00 0.00 35.21 3.58
3083 3384 6.180472 GGGATACATAATCGGGATCACATTT 58.820 40.000 0.00 0.00 35.21 2.32
3263 3564 1.460504 TGAGCTCCGTGACGAGTAAT 58.539 50.000 12.15 0.00 32.11 1.89
3351 3660 3.242772 TGAGATCACTCGCTCGTTGTATC 60.243 47.826 0.00 0.00 45.25 2.24
3352 3661 2.683362 AGATCACTCGCTCGTTGTATCA 59.317 45.455 0.00 0.00 0.00 2.15
3509 3821 2.548904 CCGGTAAACCATTGTTCGACAA 59.451 45.455 0.00 3.49 42.95 3.18
3539 3873 6.313905 GCATTTCACTGCAACTACTACTACAT 59.686 38.462 0.00 0.00 41.87 2.29
3540 3874 7.491372 GCATTTCACTGCAACTACTACTACATA 59.509 37.037 0.00 0.00 41.87 2.29
3541 3875 8.808529 CATTTCACTGCAACTACTACTACATAC 58.191 37.037 0.00 0.00 0.00 2.39
3543 3877 8.797350 TTCACTGCAACTACTACTACATACTA 57.203 34.615 0.00 0.00 0.00 1.82
3544 3878 8.206325 TCACTGCAACTACTACTACATACTAC 57.794 38.462 0.00 0.00 0.00 2.73
3545 3879 8.045507 TCACTGCAACTACTACTACATACTACT 58.954 37.037 0.00 0.00 0.00 2.57
3546 3880 8.123575 CACTGCAACTACTACTACATACTACTG 58.876 40.741 0.00 0.00 0.00 2.74
3574 3914 5.360591 AGTATTTCATTTCCGGCAGAGTAG 58.639 41.667 0.00 0.00 0.00 2.57
3575 3915 2.691409 TTCATTTCCGGCAGAGTAGG 57.309 50.000 0.00 0.00 0.00 3.18
3576 3916 1.860641 TCATTTCCGGCAGAGTAGGA 58.139 50.000 0.00 0.00 0.00 2.94
3578 3918 1.482593 CATTTCCGGCAGAGTAGGAGT 59.517 52.381 0.00 0.00 35.23 3.85
3579 3919 2.519771 TTTCCGGCAGAGTAGGAGTA 57.480 50.000 0.00 0.00 35.23 2.59
3580 3920 1.760192 TTCCGGCAGAGTAGGAGTAC 58.240 55.000 0.00 0.00 35.23 2.73
3581 3921 0.106819 TCCGGCAGAGTAGGAGTACC 60.107 60.000 0.00 0.00 0.00 3.34
3583 3923 1.310904 CGGCAGAGTAGGAGTACCTC 58.689 60.000 0.00 0.00 46.43 3.85
3630 3979 7.835682 TGATAATCCTGGTCTGTGATTGAAAAT 59.164 33.333 0.00 0.00 31.55 1.82
3631 3980 9.342308 GATAATCCTGGTCTGTGATTGAAAATA 57.658 33.333 0.00 0.00 31.55 1.40
3632 3981 9.699410 ATAATCCTGGTCTGTGATTGAAAATAA 57.301 29.630 0.00 0.00 31.55 1.40
3633 3982 8.421249 AATCCTGGTCTGTGATTGAAAATAAA 57.579 30.769 0.00 0.00 0.00 1.40
4010 4359 0.164217 GTTTCGCGCGTGTGGAATTA 59.836 50.000 30.98 3.31 0.00 1.40
4015 4364 1.810197 GCGCGTGTGGAATTATTGTC 58.190 50.000 8.43 0.00 0.00 3.18
4080 4709 2.866762 CGCTTTAGGCTGGTTGTATCTC 59.133 50.000 0.00 0.00 39.13 2.75
4134 4763 9.878599 CGTTGTAATTACTTTCTTCAACAAGAT 57.121 29.630 16.33 0.00 38.50 2.40
4167 4797 6.821665 TGGACTAATTCATACTGCCAGTTAAC 59.178 38.462 1.02 0.00 0.00 2.01
4192 4822 4.084589 CGGCAAAATGTTTGGCTAAGAAAC 60.085 41.667 20.61 0.00 42.06 2.78
4208 4838 7.361127 GCTAAGAAACTTCTTTGAACTTACCC 58.639 38.462 15.03 0.00 44.70 3.69
4209 4839 7.012989 GCTAAGAAACTTCTTTGAACTTACCCA 59.987 37.037 15.03 0.00 44.70 4.51
4210 4840 7.898014 AAGAAACTTCTTTGAACTTACCCAT 57.102 32.000 0.00 0.00 44.70 4.00
4212 4842 8.990163 AGAAACTTCTTTGAACTTACCCATTA 57.010 30.769 0.00 0.00 32.55 1.90
4234 5234 2.345641 CCGTGCTTGTATCGTTTCTCAG 59.654 50.000 0.00 0.00 0.00 3.35
4282 5282 7.451566 GCCTTGGATTATATACCCAAAGTTGAT 59.548 37.037 13.72 0.00 39.22 2.57
4304 5304 0.824759 GCCTTGGATACTCACGGACT 59.175 55.000 0.00 0.00 37.61 3.85
4305 5305 1.471676 GCCTTGGATACTCACGGACTG 60.472 57.143 0.00 0.00 37.61 3.51
4306 5306 1.137086 CCTTGGATACTCACGGACTGG 59.863 57.143 0.00 0.00 37.61 4.00
4307 5307 1.825474 CTTGGATACTCACGGACTGGT 59.175 52.381 0.00 0.00 37.61 4.00
4308 5308 1.182667 TGGATACTCACGGACTGGTG 58.817 55.000 0.00 0.00 39.29 4.17
4309 5309 1.183549 GGATACTCACGGACTGGTGT 58.816 55.000 0.00 0.00 39.00 4.16
4310 5310 1.135083 GGATACTCACGGACTGGTGTG 60.135 57.143 0.00 0.00 39.00 3.82
4311 5311 0.895530 ATACTCACGGACTGGTGTGG 59.104 55.000 0.00 0.00 39.00 4.17
4312 5312 0.468585 TACTCACGGACTGGTGTGGT 60.469 55.000 0.00 1.24 39.00 4.16
4313 5313 1.006102 CTCACGGACTGGTGTGGTC 60.006 63.158 0.00 0.00 39.00 4.02
4314 5314 2.355837 CACGGACTGGTGTGGTCG 60.356 66.667 0.00 0.00 34.82 4.79
4315 5315 2.520020 ACGGACTGGTGTGGTCGA 60.520 61.111 0.00 0.00 34.82 4.20
4316 5316 2.258591 CGGACTGGTGTGGTCGAG 59.741 66.667 0.00 0.00 34.82 4.04
4317 5317 2.657237 GGACTGGTGTGGTCGAGG 59.343 66.667 0.00 0.00 34.82 4.63
4318 5318 2.657237 GACTGGTGTGGTCGAGGG 59.343 66.667 0.00 0.00 0.00 4.30
4319 5319 3.591254 GACTGGTGTGGTCGAGGGC 62.591 68.421 0.00 0.00 0.00 5.19
4320 5320 4.742201 CTGGTGTGGTCGAGGGCG 62.742 72.222 0.00 0.00 39.35 6.13
4331 5331 3.081409 GAGGGCGGGGCTCTGTTA 61.081 66.667 0.00 0.00 40.72 2.41
4332 5332 3.083997 AGGGCGGGGCTCTGTTAG 61.084 66.667 0.00 0.00 38.31 2.34
4333 5333 4.176752 GGGCGGGGCTCTGTTAGG 62.177 72.222 0.00 0.00 0.00 2.69
4334 5334 3.081409 GGCGGGGCTCTGTTAGGA 61.081 66.667 0.00 0.00 0.00 2.94
4335 5335 2.187163 GCGGGGCTCTGTTAGGAC 59.813 66.667 0.00 0.00 0.00 3.85
4336 5336 2.901042 CGGGGCTCTGTTAGGACC 59.099 66.667 0.00 0.00 0.00 4.46
4337 5337 2.732619 CGGGGCTCTGTTAGGACCC 61.733 68.421 0.00 0.00 40.05 4.46
4338 5338 1.307084 GGGGCTCTGTTAGGACCCT 60.307 63.158 0.00 0.00 40.64 4.34
4339 5339 1.627297 GGGGCTCTGTTAGGACCCTG 61.627 65.000 0.00 0.00 40.64 4.45
4340 5340 0.617820 GGGCTCTGTTAGGACCCTGA 60.618 60.000 0.00 0.00 37.59 3.86
4341 5341 1.276622 GGCTCTGTTAGGACCCTGAA 58.723 55.000 0.00 0.00 0.00 3.02
4342 5342 1.840635 GGCTCTGTTAGGACCCTGAAT 59.159 52.381 0.00 0.00 0.00 2.57
4343 5343 2.158885 GGCTCTGTTAGGACCCTGAATC 60.159 54.545 0.00 0.00 0.00 2.52
4344 5344 2.769095 GCTCTGTTAGGACCCTGAATCT 59.231 50.000 0.00 0.00 0.00 2.40
4345 5345 3.198853 GCTCTGTTAGGACCCTGAATCTT 59.801 47.826 0.00 0.00 0.00 2.40
4346 5346 4.682050 GCTCTGTTAGGACCCTGAATCTTC 60.682 50.000 0.00 0.00 0.00 2.87
4347 5347 3.775316 TCTGTTAGGACCCTGAATCTTCC 59.225 47.826 0.00 0.00 0.00 3.46
4348 5348 3.519510 CTGTTAGGACCCTGAATCTTCCA 59.480 47.826 0.00 0.00 0.00 3.53
4349 5349 3.913799 TGTTAGGACCCTGAATCTTCCAA 59.086 43.478 0.00 0.00 0.00 3.53
4350 5350 4.262617 GTTAGGACCCTGAATCTTCCAAC 58.737 47.826 0.00 0.00 0.00 3.77
4351 5351 2.637165 AGGACCCTGAATCTTCCAACT 58.363 47.619 0.00 0.00 0.00 3.16
4352 5352 3.803340 AGGACCCTGAATCTTCCAACTA 58.197 45.455 0.00 0.00 0.00 2.24
4353 5353 4.375313 AGGACCCTGAATCTTCCAACTAT 58.625 43.478 0.00 0.00 0.00 2.12
4354 5354 5.538877 AGGACCCTGAATCTTCCAACTATA 58.461 41.667 0.00 0.00 0.00 1.31
4355 5355 6.153924 AGGACCCTGAATCTTCCAACTATAT 58.846 40.000 0.00 0.00 0.00 0.86
4378 5380 1.680651 CTGACAGAGGCGAGGGTCT 60.681 63.158 0.00 0.00 0.00 3.85
4401 5403 9.421806 GTCTCGATCTTTGAATGAGATGATAAT 57.578 33.333 0.00 0.00 37.93 1.28
4435 5437 3.907474 TGGAGAACTACTTGGACAATCCA 59.093 43.478 0.00 0.00 46.61 3.41
4451 5453 4.826733 ACAATCCAACTAGAAATGTGCACA 59.173 37.500 24.08 24.08 0.00 4.57
4457 5459 5.277586 CCAACTAGAAATGTGCACAACGTTA 60.278 40.000 25.72 13.07 36.99 3.18
4458 5460 6.370593 CAACTAGAAATGTGCACAACGTTAT 58.629 36.000 25.72 17.01 36.99 1.89
4463 5465 0.871722 TGTGCACAACGTTATGCCTC 59.128 50.000 27.26 19.91 41.33 4.70
4472 5474 4.037446 ACAACGTTATGCCTCAACAATTGT 59.963 37.500 4.92 4.92 33.41 2.71
4542 5547 2.158900 CCACGAAGGTCTATTCCTGCAT 60.159 50.000 0.00 0.00 37.93 3.96
4642 5648 1.966451 CGAAAGCGGCCTTGGTCTT 60.966 57.895 0.00 0.00 0.00 3.01
4646 5652 2.281484 GCGGCCTTGGTCTTGTCA 60.281 61.111 0.00 0.00 0.00 3.58
4650 5656 0.244721 GGCCTTGGTCTTGTCATTGC 59.755 55.000 0.00 0.00 0.00 3.56
4710 5716 7.926018 ACTTTTAACTAAACAAATCCCAAGCAG 59.074 33.333 0.00 0.00 0.00 4.24
4712 5719 7.775053 TTAACTAAACAAATCCCAAGCAGAT 57.225 32.000 0.00 0.00 0.00 2.90
4714 5721 6.759497 ACTAAACAAATCCCAAGCAGATAC 57.241 37.500 0.00 0.00 0.00 2.24
4718 5725 5.653255 ACAAATCCCAAGCAGATACCTAT 57.347 39.130 0.00 0.00 0.00 2.57
4721 5728 7.582719 ACAAATCCCAAGCAGATACCTATTAA 58.417 34.615 0.00 0.00 0.00 1.40
4724 5731 9.660544 AAATCCCAAGCAGATACCTATTAAATT 57.339 29.630 0.00 0.00 0.00 1.82
4771 5778 2.610859 GGCCAAGGAGGTGGGAGA 60.611 66.667 0.00 0.00 39.26 3.71
4777 5784 0.178929 AAGGAGGTGGGAGAACGTCT 60.179 55.000 0.00 0.00 35.71 4.18
4809 5816 5.069648 GCCTAAAACTAACCCTAGGTCGTAT 59.930 44.000 8.29 0.00 33.12 3.06
4832 5839 2.362889 CCATGGGCCCAAGTGGAC 60.363 66.667 33.17 1.20 44.14 4.02
4837 5844 2.358737 GGCCCAAGTGGACGTGAG 60.359 66.667 0.00 0.00 37.39 3.51
4838 5845 2.741092 GCCCAAGTGGACGTGAGA 59.259 61.111 0.00 0.00 37.39 3.27
4846 5853 0.179094 GTGGACGTGAGACAACACCA 60.179 55.000 0.00 0.00 37.48 4.17
4850 5857 2.479837 GACGTGAGACAACACCATTGA 58.520 47.619 0.00 0.00 37.48 2.57
4862 5869 7.554835 AGACAACACCATTGAACTTGTAGTTTA 59.445 33.333 0.00 0.00 38.80 2.01
4880 5887 2.988010 TAACTCGGATTCTGCTGCAT 57.012 45.000 1.31 0.00 0.00 3.96
4887 5895 0.574454 GATTCTGCTGCATCGTCGAC 59.426 55.000 5.18 5.18 0.00 4.20
4908 5916 5.420409 GACTGTTTCGGAAATATCTCCACT 58.580 41.667 6.43 0.00 34.91 4.00
4915 5923 3.553096 CGGAAATATCTCCACTCTTCGGG 60.553 52.174 0.00 0.00 34.91 5.14
4924 5932 0.447801 CACTCTTCGGGCGAATTTGG 59.552 55.000 0.00 0.00 33.28 3.28
4945 5953 3.430453 GAGGTGAATCCAATTGGGTTGA 58.570 45.455 27.72 17.15 38.97 3.18
4948 5956 4.284234 AGGTGAATCCAATTGGGTTGAAAG 59.716 41.667 27.72 0.00 38.97 2.62
4949 5957 4.040339 GGTGAATCCAATTGGGTTGAAAGT 59.960 41.667 27.72 4.35 38.97 2.66
4951 5959 6.156519 GTGAATCCAATTGGGTTGAAAGTAC 58.843 40.000 27.72 11.49 38.97 2.73
4952 5960 5.835819 TGAATCCAATTGGGTTGAAAGTACA 59.164 36.000 27.72 13.95 38.97 2.90
4953 5961 5.982890 ATCCAATTGGGTTGAAAGTACAG 57.017 39.130 24.29 0.00 40.37 2.74
4955 5963 3.320541 CCAATTGGGTTGAAAGTACAGCA 59.679 43.478 17.36 0.00 40.37 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
272 278 7.048629 TGGTTGTATGTGACATGATTTGTTT 57.951 32.000 8.61 0.00 39.18 2.83
557 566 0.712380 ATCTGAGGCCCCCAAACATT 59.288 50.000 0.00 0.00 0.00 2.71
744 753 2.526873 AGACGCCAAGGACCCTGT 60.527 61.111 0.00 0.00 0.00 4.00
772 781 3.712881 GTTGACCCGCTGACGTGC 61.713 66.667 0.00 0.00 37.70 5.34
1084 1105 2.583593 CTTGTAGCCGAGCTCGCC 60.584 66.667 30.49 20.93 40.44 5.54
1134 1155 2.107366 GAGGAGAGGAGAAGAAGGGTG 58.893 57.143 0.00 0.00 0.00 4.61
1135 1156 2.007636 AGAGGAGAGGAGAAGAAGGGT 58.992 52.381 0.00 0.00 0.00 4.34
1138 1159 2.244769 AGGGAGAGGAGAGGAGAAGAAG 59.755 54.545 0.00 0.00 0.00 2.85
1139 1160 2.293246 AGGGAGAGGAGAGGAGAAGAA 58.707 52.381 0.00 0.00 0.00 2.52
1142 1168 1.007721 CCAAGGGAGAGGAGAGGAGAA 59.992 57.143 0.00 0.00 0.00 2.87
1176 1202 7.201848 GCCCTCAATCAATCAATCAATCAGTTA 60.202 37.037 0.00 0.00 0.00 2.24
1177 1203 6.406624 GCCCTCAATCAATCAATCAATCAGTT 60.407 38.462 0.00 0.00 0.00 3.16
1178 1204 5.068723 GCCCTCAATCAATCAATCAATCAGT 59.931 40.000 0.00 0.00 0.00 3.41
1181 1207 4.037208 ACGCCCTCAATCAATCAATCAATC 59.963 41.667 0.00 0.00 0.00 2.67
1182 1208 3.956199 ACGCCCTCAATCAATCAATCAAT 59.044 39.130 0.00 0.00 0.00 2.57
1184 1210 2.684374 CACGCCCTCAATCAATCAATCA 59.316 45.455 0.00 0.00 0.00 2.57
1185 1211 2.684881 ACACGCCCTCAATCAATCAATC 59.315 45.455 0.00 0.00 0.00 2.67
1186 1212 2.424601 CACACGCCCTCAATCAATCAAT 59.575 45.455 0.00 0.00 0.00 2.57
1187 1213 1.811965 CACACGCCCTCAATCAATCAA 59.188 47.619 0.00 0.00 0.00 2.57
1475 1503 0.366871 GCGTGTGTGATTGAGTAGCG 59.633 55.000 0.00 0.00 0.00 4.26
1487 1515 0.107897 TTTGAGTGGAGTGCGTGTGT 60.108 50.000 0.00 0.00 0.00 3.72
1488 1516 1.195448 GATTTGAGTGGAGTGCGTGTG 59.805 52.381 0.00 0.00 0.00 3.82
1546 1576 6.553476 TCCCAACCAGAGAAGAAATCGATATA 59.447 38.462 0.00 0.00 0.00 0.86
1547 1577 5.366768 TCCCAACCAGAGAAGAAATCGATAT 59.633 40.000 0.00 0.00 0.00 1.63
1634 1669 5.854338 GTCACACGAGACAAAAAGAAAACAA 59.146 36.000 0.00 0.00 38.40 2.83
1636 1671 5.387279 TGTCACACGAGACAAAAAGAAAAC 58.613 37.500 7.45 0.00 44.92 2.43
1637 1672 5.614923 TGTCACACGAGACAAAAAGAAAA 57.385 34.783 7.45 0.00 44.92 2.29
1651 1686 2.318578 GCACCAATTTGATGTCACACG 58.681 47.619 0.00 0.00 0.00 4.49
1766 1806 3.576078 ATACGCATGGATCAAAGGGAA 57.424 42.857 0.00 0.00 0.00 3.97
1827 1875 0.320771 GCATCCCCGATGATAACGCT 60.321 55.000 5.82 0.00 42.09 5.07
1828 1876 0.602638 TGCATCCCCGATGATAACGC 60.603 55.000 5.82 0.00 42.09 4.84
1887 1972 5.047164 ACAAATATTCTGTTCTGCATTGCCA 60.047 36.000 6.12 0.00 0.00 4.92
1996 2087 6.348540 GGTCGCTGTCAAAATCAGACTTTATT 60.349 38.462 0.00 0.00 36.94 1.40
2039 2130 6.791867 ACTACAAGAACCATGCTGATACTA 57.208 37.500 0.00 0.00 0.00 1.82
2040 2131 5.683876 ACTACAAGAACCATGCTGATACT 57.316 39.130 0.00 0.00 0.00 2.12
2041 2132 5.874810 TCAACTACAAGAACCATGCTGATAC 59.125 40.000 0.00 0.00 0.00 2.24
2085 2176 2.638673 CCATGCGTATATGTGCGTTTG 58.361 47.619 1.54 0.37 35.76 2.93
2131 2222 4.675190 GCATGAGCAATCAATAGCGTAT 57.325 40.909 0.00 0.00 41.58 3.06
2149 2240 4.533311 GGAATAATTGGAATGGGGATGCAT 59.467 41.667 0.00 0.00 0.00 3.96
2181 2276 1.730121 GCAGCACAACAATCCGTCATG 60.730 52.381 0.00 0.00 0.00 3.07
2461 2569 1.002069 ATGGGGAGGCTGTTGATGAA 58.998 50.000 0.00 0.00 0.00 2.57
2546 2654 4.272018 GCGAATGAAGAGAGGTACGTAGTA 59.728 45.833 0.00 0.00 45.11 1.82
2548 2656 3.064958 TGCGAATGAAGAGAGGTACGTAG 59.935 47.826 0.00 0.00 0.00 3.51
2549 2657 3.011818 TGCGAATGAAGAGAGGTACGTA 58.988 45.455 0.00 0.00 0.00 3.57
2550 2658 1.816835 TGCGAATGAAGAGAGGTACGT 59.183 47.619 0.00 0.00 0.00 3.57
2551 2659 2.159366 AGTGCGAATGAAGAGAGGTACG 60.159 50.000 0.00 0.00 0.00 3.67
2590 2698 0.169230 CAGTGCTCGCGAAGTAGAGT 59.831 55.000 11.33 0.00 36.93 3.24
2591 2699 0.448197 TCAGTGCTCGCGAAGTAGAG 59.552 55.000 11.33 0.00 37.44 2.43
2592 2700 1.095600 ATCAGTGCTCGCGAAGTAGA 58.904 50.000 11.33 5.30 0.00 2.59
2599 2707 4.483711 TGAGAATCAGTGCTCGCG 57.516 55.556 0.00 0.00 42.56 5.87
2656 2765 3.874392 AATAAAGTGGATGCCAACTGC 57.126 42.857 0.00 0.00 34.18 4.40
2657 2766 5.331902 CGTTAATAAAGTGGATGCCAACTG 58.668 41.667 0.00 0.00 34.18 3.16
2658 2767 4.398044 CCGTTAATAAAGTGGATGCCAACT 59.602 41.667 0.00 0.00 34.18 3.16
2682 2791 2.113807 TGGAGAGCCATCCATCTCAT 57.886 50.000 3.38 0.00 44.56 2.90
2683 2792 3.641003 TGGAGAGCCATCCATCTCA 57.359 52.632 3.38 0.00 44.56 3.27
2932 3192 4.887748 ACACTGACAACGAGATGAGATTT 58.112 39.130 0.00 0.00 0.00 2.17
2968 3269 0.390492 CTCCTCCGTCTGCATGCATA 59.610 55.000 22.97 11.96 0.00 3.14
3069 3370 0.107214 ACGGCAAATGTGATCCCGAT 60.107 50.000 10.69 0.00 41.34 4.18
3080 3381 2.365582 GGTATGTCCTTGACGGCAAAT 58.634 47.619 4.62 0.00 34.95 2.32
3083 3384 0.907704 AGGGTATGTCCTTGACGGCA 60.908 55.000 0.00 0.00 34.95 5.69
3137 3438 1.377202 GAAGACTTGGGCGATGGCA 60.377 57.895 1.01 0.00 42.47 4.92
3351 3660 4.965814 AGCATACACCATCCTAGTCATTG 58.034 43.478 0.00 0.00 0.00 2.82
3352 3661 5.636903 AAGCATACACCATCCTAGTCATT 57.363 39.130 0.00 0.00 0.00 2.57
3543 3877 6.047231 GCCGGAAATGAAATACTACTACAGT 58.953 40.000 5.05 0.00 41.62 3.55
3544 3878 6.046593 TGCCGGAAATGAAATACTACTACAG 58.953 40.000 5.05 0.00 0.00 2.74
3545 3879 5.979993 TGCCGGAAATGAAATACTACTACA 58.020 37.500 5.05 0.00 0.00 2.74
3546 3880 6.278363 TCTGCCGGAAATGAAATACTACTAC 58.722 40.000 5.05 0.00 0.00 2.73
3576 3916 6.547510 GCAGGATCAATTTATTTGGAGGTACT 59.452 38.462 0.00 0.00 35.93 2.73
3578 3918 6.672593 AGCAGGATCAATTTATTTGGAGGTA 58.327 36.000 0.00 0.00 35.92 3.08
3579 3919 5.522641 AGCAGGATCAATTTATTTGGAGGT 58.477 37.500 0.00 0.00 35.92 3.85
3580 3920 5.832060 AGAGCAGGATCAATTTATTTGGAGG 59.168 40.000 0.00 0.00 35.92 4.30
3581 3921 6.544931 TCAGAGCAGGATCAATTTATTTGGAG 59.455 38.462 0.00 0.00 35.92 3.86
3582 3922 6.425735 TCAGAGCAGGATCAATTTATTTGGA 58.574 36.000 0.00 0.00 35.92 3.53
3583 3923 6.704289 TCAGAGCAGGATCAATTTATTTGG 57.296 37.500 0.00 0.00 35.92 3.28
3586 3926 9.240734 GGATTATCAGAGCAGGATCAATTTATT 57.759 33.333 0.00 0.00 0.00 1.40
3587 3927 8.613034 AGGATTATCAGAGCAGGATCAATTTAT 58.387 33.333 0.00 0.00 0.00 1.40
3588 3928 7.881751 CAGGATTATCAGAGCAGGATCAATTTA 59.118 37.037 0.00 0.00 0.00 1.40
3589 3929 6.715718 CAGGATTATCAGAGCAGGATCAATTT 59.284 38.462 0.00 0.00 0.00 1.82
3630 3979 2.423185 CCCAGCGACTGCAATCAATTTA 59.577 45.455 0.00 0.00 46.23 1.40
3631 3980 1.203052 CCCAGCGACTGCAATCAATTT 59.797 47.619 0.00 0.00 46.23 1.82
3632 3981 0.813184 CCCAGCGACTGCAATCAATT 59.187 50.000 0.00 0.00 46.23 2.32
3633 3982 0.322816 ACCCAGCGACTGCAATCAAT 60.323 50.000 0.00 0.00 46.23 2.57
3762 4111 3.330720 CGAGGTTGAAGGGCCCCT 61.331 66.667 21.43 4.78 33.87 4.79
4080 4709 1.947678 GCCTCCACCTCATGTCTTGTG 60.948 57.143 0.00 0.00 0.00 3.33
4093 4722 3.264866 AACGTCTCGTCGCCTCCAC 62.265 63.158 0.00 0.00 39.99 4.02
4134 4763 7.217200 GCAGTATGAATTAGTCCATGTTCCTA 58.783 38.462 0.00 0.00 39.69 2.94
4167 4797 0.605589 TAGCCAAACATTTTGCCGGG 59.394 50.000 2.18 0.00 29.82 5.73
4192 4822 5.704053 ACGGTAATGGGTAAGTTCAAAGAAG 59.296 40.000 0.00 0.00 0.00 2.85
4208 4838 4.328983 AGAAACGATACAAGCACGGTAATG 59.671 41.667 0.00 0.00 0.00 1.90
4209 4839 4.501071 AGAAACGATACAAGCACGGTAAT 58.499 39.130 0.00 0.00 0.00 1.89
4210 4840 3.916761 AGAAACGATACAAGCACGGTAA 58.083 40.909 0.00 0.00 0.00 2.85
4212 4842 2.288579 TGAGAAACGATACAAGCACGGT 60.289 45.455 0.00 0.00 0.00 4.83
4234 5234 5.064834 GGCTAGTCAACTTGCTGGTAAATAC 59.935 44.000 14.54 0.00 42.80 1.89
4282 5282 2.429610 GTCCGTGAGTATCCAAGGCTAA 59.570 50.000 0.00 0.00 35.96 3.09
4314 5314 3.081409 TAACAGAGCCCCGCCCTC 61.081 66.667 0.00 0.00 0.00 4.30
4315 5315 3.083997 CTAACAGAGCCCCGCCCT 61.084 66.667 0.00 0.00 0.00 5.19
4316 5316 4.176752 CCTAACAGAGCCCCGCCC 62.177 72.222 0.00 0.00 0.00 6.13
4317 5317 3.081409 TCCTAACAGAGCCCCGCC 61.081 66.667 0.00 0.00 0.00 6.13
4318 5318 2.187163 GTCCTAACAGAGCCCCGC 59.813 66.667 0.00 0.00 0.00 6.13
4319 5319 2.732619 GGGTCCTAACAGAGCCCCG 61.733 68.421 0.00 0.00 46.64 5.73
4320 5320 3.321445 GGGTCCTAACAGAGCCCC 58.679 66.667 0.00 0.00 46.64 5.80
4323 5323 2.769095 AGATTCAGGGTCCTAACAGAGC 59.231 50.000 0.00 0.00 0.00 4.09
4324 5324 4.141824 GGAAGATTCAGGGTCCTAACAGAG 60.142 50.000 0.00 0.00 0.00 3.35
4325 5325 3.775316 GGAAGATTCAGGGTCCTAACAGA 59.225 47.826 0.00 0.00 0.00 3.41
4326 5326 3.519510 TGGAAGATTCAGGGTCCTAACAG 59.480 47.826 0.00 0.00 0.00 3.16
4327 5327 3.526899 TGGAAGATTCAGGGTCCTAACA 58.473 45.455 0.00 0.00 0.00 2.41
4328 5328 4.019231 AGTTGGAAGATTCAGGGTCCTAAC 60.019 45.833 0.00 0.00 0.00 2.34
4329 5329 4.175962 AGTTGGAAGATTCAGGGTCCTAA 58.824 43.478 0.00 0.00 0.00 2.69
4330 5330 3.803340 AGTTGGAAGATTCAGGGTCCTA 58.197 45.455 0.00 0.00 0.00 2.94
4331 5331 2.637165 AGTTGGAAGATTCAGGGTCCT 58.363 47.619 0.00 0.00 0.00 3.85
4332 5332 4.779993 ATAGTTGGAAGATTCAGGGTCC 57.220 45.455 0.00 0.00 0.00 4.46
4333 5333 7.963532 TGTATATAGTTGGAAGATTCAGGGTC 58.036 38.462 0.00 0.00 0.00 4.46
4334 5334 7.931015 TGTATATAGTTGGAAGATTCAGGGT 57.069 36.000 0.00 0.00 0.00 4.34
4335 5335 8.820831 AGATGTATATAGTTGGAAGATTCAGGG 58.179 37.037 0.00 0.00 0.00 4.45
4336 5336 9.650539 CAGATGTATATAGTTGGAAGATTCAGG 57.349 37.037 0.00 0.00 0.00 3.86
4341 5341 9.593565 TCTGTCAGATGTATATAGTTGGAAGAT 57.406 33.333 0.00 0.00 0.00 2.40
4342 5342 8.996651 TCTGTCAGATGTATATAGTTGGAAGA 57.003 34.615 0.00 0.00 0.00 2.87
4343 5343 8.303156 CCTCTGTCAGATGTATATAGTTGGAAG 58.697 40.741 2.22 0.00 0.00 3.46
4344 5344 7.255977 GCCTCTGTCAGATGTATATAGTTGGAA 60.256 40.741 2.22 0.00 0.00 3.53
4345 5345 6.209589 GCCTCTGTCAGATGTATATAGTTGGA 59.790 42.308 2.22 0.00 0.00 3.53
4346 5346 6.393990 GCCTCTGTCAGATGTATATAGTTGG 58.606 44.000 2.22 0.00 0.00 3.77
4347 5347 6.072452 TCGCCTCTGTCAGATGTATATAGTTG 60.072 42.308 2.22 0.00 0.00 3.16
4348 5348 6.004574 TCGCCTCTGTCAGATGTATATAGTT 58.995 40.000 2.22 0.00 0.00 2.24
4349 5349 5.561679 TCGCCTCTGTCAGATGTATATAGT 58.438 41.667 2.22 0.00 0.00 2.12
4350 5350 5.065859 CCTCGCCTCTGTCAGATGTATATAG 59.934 48.000 2.22 0.00 0.00 1.31
4351 5351 4.944317 CCTCGCCTCTGTCAGATGTATATA 59.056 45.833 2.22 0.00 0.00 0.86
4352 5352 3.761218 CCTCGCCTCTGTCAGATGTATAT 59.239 47.826 2.22 0.00 0.00 0.86
4353 5353 3.149981 CCTCGCCTCTGTCAGATGTATA 58.850 50.000 2.22 0.00 0.00 1.47
4354 5354 1.959985 CCTCGCCTCTGTCAGATGTAT 59.040 52.381 2.22 0.00 0.00 2.29
4355 5355 1.393603 CCTCGCCTCTGTCAGATGTA 58.606 55.000 2.22 0.00 0.00 2.29
4405 5407 6.013379 TGTCCAAGTAGTTCTCCATCAAATCT 60.013 38.462 0.00 0.00 0.00 2.40
4412 5414 4.536090 TGGATTGTCCAAGTAGTTCTCCAT 59.464 41.667 0.00 0.00 45.00 3.41
4426 5428 4.458989 TGCACATTTCTAGTTGGATTGTCC 59.541 41.667 0.00 0.00 36.96 4.02
4435 5437 4.893424 AACGTTGTGCACATTTCTAGTT 57.107 36.364 22.39 16.24 0.00 2.24
4440 5442 2.661195 GGCATAACGTTGTGCACATTTC 59.339 45.455 38.88 23.28 45.65 2.17
4451 5453 4.846779 ACAATTGTTGAGGCATAACGTT 57.153 36.364 4.92 5.88 0.00 3.99
4457 5459 5.543507 TGGTTTAACAATTGTTGAGGCAT 57.456 34.783 29.72 7.91 38.90 4.40
4458 5460 5.344743 TTGGTTTAACAATTGTTGAGGCA 57.655 34.783 29.72 10.09 38.90 4.75
4463 5465 7.432869 TCAGGAGATTGGTTTAACAATTGTTG 58.567 34.615 29.72 11.58 40.92 3.33
4472 5474 6.271391 TCAGTAACCTCAGGAGATTGGTTTAA 59.729 38.462 0.00 0.00 42.14 1.52
4542 5547 2.877786 TCTTGCTTGTTCTTCGATTGCA 59.122 40.909 0.00 0.00 0.00 4.08
4614 5620 2.584608 CGCTTTCGGATCCCCACT 59.415 61.111 6.06 0.00 0.00 4.00
4633 5639 1.955778 TGTGCAATGACAAGACCAAGG 59.044 47.619 0.00 0.00 0.00 3.61
4642 5648 4.185467 ACTTTGTTTGTGTGCAATGACA 57.815 36.364 0.00 0.00 34.18 3.58
4646 5652 4.101942 CGTGTACTTTGTTTGTGTGCAAT 58.898 39.130 0.00 0.00 34.18 3.56
4650 5656 4.965062 ACTTCGTGTACTTTGTTTGTGTG 58.035 39.130 0.00 0.00 0.00 3.82
4731 5738 6.513180 CCGTCACTCTTTGCTCCTATATAAA 58.487 40.000 0.00 0.00 0.00 1.40
4746 5753 2.286523 CCTCCTTGGCCGTCACTCT 61.287 63.158 0.00 0.00 0.00 3.24
4748 5755 2.526873 ACCTCCTTGGCCGTCACT 60.527 61.111 0.00 0.00 40.22 3.41
4771 5778 0.685097 TTAGGCTGCCTTGAGACGTT 59.315 50.000 28.55 0.88 34.61 3.99
4777 5784 3.418047 GGTTAGTTTTAGGCTGCCTTGA 58.582 45.455 28.55 13.46 34.61 3.02
4832 5839 2.872245 AGTTCAATGGTGTTGTCTCACG 59.128 45.455 0.00 0.00 39.00 4.35
4837 5844 5.751243 ACTACAAGTTCAATGGTGTTGTC 57.249 39.130 0.00 0.00 33.50 3.18
4838 5845 6.524101 AAACTACAAGTTCAATGGTGTTGT 57.476 33.333 0.00 0.00 37.47 3.32
4846 5853 8.617290 AATCCGAGTTAAACTACAAGTTCAAT 57.383 30.769 0.00 0.00 37.47 2.57
4850 5857 6.147328 GCAGAATCCGAGTTAAACTACAAGTT 59.853 38.462 0.00 0.00 40.80 2.66
4862 5869 1.661341 GATGCAGCAGAATCCGAGTT 58.339 50.000 0.00 0.00 0.00 3.01
4887 5895 5.665459 AGAGTGGAGATATTTCCGAAACAG 58.335 41.667 7.73 0.00 40.27 3.16
4895 5903 3.394719 GCCCGAAGAGTGGAGATATTTC 58.605 50.000 0.00 0.00 0.00 2.17
4896 5904 2.224066 CGCCCGAAGAGTGGAGATATTT 60.224 50.000 0.00 0.00 0.00 1.40
4897 5905 1.341531 CGCCCGAAGAGTGGAGATATT 59.658 52.381 0.00 0.00 0.00 1.28
4908 5916 0.392461 CCTCCAAATTCGCCCGAAGA 60.392 55.000 9.11 0.46 37.56 2.87
4915 5923 2.091541 TGGATTCACCTCCAAATTCGC 58.908 47.619 0.00 0.00 42.36 4.70
4924 5932 3.430453 TCAACCCAATTGGATTCACCTC 58.570 45.455 26.60 0.00 38.98 3.85


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

AutoCloner maintained by Alex Coulton.