Multiple sequence alignment - TraesCS7D01G233400

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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 TraesCS7D01G233400 chr7D 100.000 7381 0 0 1 7381 195306769 195314149 0.000000e+00 13631.0
1 TraesCS7D01G233400 chr7D 90.507 927 73 7 6459 7381 269045732 269044817 0.000000e+00 1210.0
2 TraesCS7D01G233400 chr7D 85.714 98 10 3 1504 1600 165657945 165657851 4.710000e-17 100.0
3 TraesCS7D01G233400 chr7B 96.501 2715 78 4 3761 6464 159139897 159142605 0.000000e+00 4471.0
4 TraesCS7D01G233400 chr7B 92.743 1874 76 17 1846 3715 159138076 159139893 0.000000e+00 2652.0
5 TraesCS7D01G233400 chr7B 92.410 1871 93 14 1 1847 159136073 159137918 0.000000e+00 2623.0
6 TraesCS7D01G233400 chr7B 91.812 574 45 2 6463 7034 114361269 114361842 0.000000e+00 798.0
7 TraesCS7D01G233400 chr7B 89.412 85 9 0 1504 1588 13801855 13801939 2.820000e-19 108.0
8 TraesCS7D01G233400 chr7A 96.247 2718 78 6 3761 6464 205169537 205172244 0.000000e+00 4433.0
9 TraesCS7D01G233400 chr7A 90.572 1697 120 16 2030 3715 205167866 205169533 0.000000e+00 2211.0
10 TraesCS7D01G233400 chr7A 89.469 1054 48 14 500 1512 205166655 205167686 0.000000e+00 1273.0
11 TraesCS7D01G233400 chr7A 91.342 924 73 5 6463 7381 205175169 205176090 0.000000e+00 1256.0
12 TraesCS7D01G233400 chr7A 89.479 922 93 4 6463 7381 296568043 296567123 0.000000e+00 1162.0
13 TraesCS7D01G233400 chr7A 91.667 576 44 3 6463 7034 493108666 493109241 0.000000e+00 795.0
14 TraesCS7D01G233400 chr7A 84.200 481 40 13 4 480 205166218 205166666 1.140000e-117 435.0
15 TraesCS7D01G233400 chr5A 91.957 920 68 5 6465 7379 40130228 40131146 0.000000e+00 1284.0
16 TraesCS7D01G233400 chr5A 89.435 814 59 6 6569 7381 40133458 40132671 0.000000e+00 1002.0
17 TraesCS7D01G233400 chr5A 89.888 89 8 1 1501 1588 11520500 11520412 6.050000e-21 113.0
18 TraesCS7D01G233400 chr5B 91.730 919 74 2 6465 7381 53694944 53695862 0.000000e+00 1275.0
19 TraesCS7D01G233400 chr5B 89.189 814 63 4 6569 7381 53697528 53696739 0.000000e+00 992.0
20 TraesCS7D01G233400 chr5B 89.888 89 8 1 1501 1588 13704495 13704407 6.050000e-21 113.0
21 TraesCS7D01G233400 chr5D 89.565 920 68 6 6465 7381 50807284 50808178 0.000000e+00 1142.0
22 TraesCS7D01G233400 chr5D 89.803 814 58 3 6569 7381 50809838 50809049 0.000000e+00 1020.0
23 TraesCS7D01G233400 chr5D 91.986 574 44 2 6463 7034 383174210 383173637 0.000000e+00 804.0
24 TraesCS7D01G233400 chr5D 87.234 94 12 0 1502 1595 294637758 294637665 2.820000e-19 108.0
25 TraesCS7D01G233400 chr5D 88.506 87 8 1 1504 1588 173751587 173751501 3.640000e-18 104.0
26 TraesCS7D01G233400 chr1D 91.638 574 46 2 6463 7034 340512123 340512696 0.000000e+00 793.0
27 TraesCS7D01G233400 chr2D 83.908 261 35 5 1 260 46902784 46903038 7.400000e-60 243.0
28 TraesCS7D01G233400 chr2D 84.865 185 27 1 79 262 46722466 46722282 1.260000e-42 185.0
29 TraesCS7D01G233400 chr2D 90.244 82 8 0 1505 1586 36689356 36689437 2.820000e-19 108.0
30 TraesCS7D01G233400 chr2B 86.977 215 23 2 48 262 74046764 74046555 3.440000e-58 237.0
31 TraesCS7D01G233400 chr2B 85.849 212 21 2 56 262 74207299 74207506 4.480000e-52 217.0
32 TraesCS7D01G233400 chr2A 84.932 219 29 1 48 262 50098731 50098513 1.250000e-52 219.0
33 TraesCS7D01G233400 chr2A 91.892 74 6 0 1504 1577 41006335 41006408 3.640000e-18 104.0
34 TraesCS7D01G233400 chr2A 97.143 35 1 0 3720 3754 59125918 59125952 8.000000e-05 60.2
35 TraesCS7D01G233400 chr4A 100.000 43 0 0 4154 4196 695036783 695036741 6.140000e-11 80.5


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 TraesCS7D01G233400 chr7D 195306769 195314149 7380 False 13631.000000 13631 100.000000 1 7381 1 chr7D.!!$F1 7380
1 TraesCS7D01G233400 chr7D 269044817 269045732 915 True 1210.000000 1210 90.507000 6459 7381 1 chr7D.!!$R2 922
2 TraesCS7D01G233400 chr7B 159136073 159142605 6532 False 3248.666667 4471 93.884667 1 6464 3 chr7B.!!$F3 6463
3 TraesCS7D01G233400 chr7B 114361269 114361842 573 False 798.000000 798 91.812000 6463 7034 1 chr7B.!!$F2 571
4 TraesCS7D01G233400 chr7A 205166218 205176090 9872 False 1921.600000 4433 90.366000 4 7381 5 chr7A.!!$F2 7377
5 TraesCS7D01G233400 chr7A 296567123 296568043 920 True 1162.000000 1162 89.479000 6463 7381 1 chr7A.!!$R1 918
6 TraesCS7D01G233400 chr7A 493108666 493109241 575 False 795.000000 795 91.667000 6463 7034 1 chr7A.!!$F1 571
7 TraesCS7D01G233400 chr5A 40130228 40131146 918 False 1284.000000 1284 91.957000 6465 7379 1 chr5A.!!$F1 914
8 TraesCS7D01G233400 chr5A 40132671 40133458 787 True 1002.000000 1002 89.435000 6569 7381 1 chr5A.!!$R2 812
9 TraesCS7D01G233400 chr5B 53694944 53695862 918 False 1275.000000 1275 91.730000 6465 7381 1 chr5B.!!$F1 916
10 TraesCS7D01G233400 chr5B 53696739 53697528 789 True 992.000000 992 89.189000 6569 7381 1 chr5B.!!$R2 812
11 TraesCS7D01G233400 chr5D 50807284 50808178 894 False 1142.000000 1142 89.565000 6465 7381 1 chr5D.!!$F1 916
12 TraesCS7D01G233400 chr5D 50809049 50809838 789 True 1020.000000 1020 89.803000 6569 7381 1 chr5D.!!$R1 812
13 TraesCS7D01G233400 chr5D 383173637 383174210 573 True 804.000000 804 91.986000 6463 7034 1 chr5D.!!$R4 571
14 TraesCS7D01G233400 chr1D 340512123 340512696 573 False 793.000000 793 91.638000 6463 7034 1 chr1D.!!$F1 571

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
551 566 0.614979 GACAGCTGGGAGGGAGTGTA 60.615 60.000 19.93 0.0 0.00 2.90 F
614 629 0.977395 GTGGGCTCTCTGTAGTGGTT 59.023 55.000 0.00 0.0 0.00 3.67 F
711 726 1.524621 CGCCCATGACAGATGACCC 60.525 63.158 0.00 0.0 0.00 4.46 F
1783 1839 0.183492 AGTGCCTTCAACTGCTTCCA 59.817 50.000 0.00 0.0 0.00 3.53 F
3342 3669 0.912486 AAGCGGGCATAGAGGAACTT 59.088 50.000 0.00 0.0 41.55 2.66 F
3560 3888 2.362397 TCAGGCTATTACAGGAGAAGCG 59.638 50.000 0.00 0.0 33.96 4.68 F
4861 5189 0.613260 CCAGTCAGGGAAACGGATGA 59.387 55.000 0.00 0.0 0.00 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1422 1478 0.103876 ACCTCCTCCCCTTGTTTCCT 60.104 55.000 0.00 0.00 0.00 3.36 R
1423 1479 0.778083 AACCTCCTCCCCTTGTTTCC 59.222 55.000 0.00 0.00 0.00 3.13 R
1960 2175 2.358247 GTCGCATCCACCGTGGTT 60.358 61.111 17.32 6.37 39.03 3.67 R
3560 3888 0.179192 TTTCGCATCGCATTGCTGTC 60.179 50.000 7.12 0.00 40.54 3.51 R
4411 4739 0.322975 CCCAGTCCCAGAGTTCACAG 59.677 60.000 0.00 0.00 0.00 3.66 R
5379 5718 2.568509 AGGCCTTTGTGCAAAAGCATAT 59.431 40.909 16.83 3.42 38.98 1.78 R
6520 9788 0.036164 TCCGTGGAGTTGGTTGATGG 59.964 55.000 0.00 0.00 0.00 3.51 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 2.235016 CCAACCCAGAAAATTGGTCGA 58.765 47.619 0.00 0.00 38.47 4.20
149 153 2.290705 ACCACCTTTATCCCTTCAACCG 60.291 50.000 0.00 0.00 0.00 4.44
199 203 6.202516 TCTTAACCAAACACCAAAACTGAG 57.797 37.500 0.00 0.00 0.00 3.35
200 204 5.712917 TCTTAACCAAACACCAAAACTGAGT 59.287 36.000 0.00 0.00 0.00 3.41
246 250 2.972713 GTCCCAGCCCACTCATATCTAA 59.027 50.000 0.00 0.00 0.00 2.10
263 267 5.982890 ATCTAACCCTTCAACCAAACATG 57.017 39.130 0.00 0.00 0.00 3.21
268 272 2.558359 CCCTTCAACCAAACATGGTCTC 59.442 50.000 0.20 0.00 42.20 3.36
271 279 4.082571 CCTTCAACCAAACATGGTCTCATC 60.083 45.833 0.20 0.00 42.20 2.92
445 458 8.967218 CAGTAATTTAACATTTGTGAACTGTGG 58.033 33.333 0.00 0.00 0.00 4.17
449 464 2.586425 ACATTTGTGAACTGTGGGAGG 58.414 47.619 0.00 0.00 0.00 4.30
476 491 3.933332 GCTAATGAAGTGTTAAGACGGCT 59.067 43.478 0.00 0.00 0.00 5.52
551 566 0.614979 GACAGCTGGGAGGGAGTGTA 60.615 60.000 19.93 0.00 0.00 2.90
614 629 0.977395 GTGGGCTCTCTGTAGTGGTT 59.023 55.000 0.00 0.00 0.00 3.67
711 726 1.524621 CGCCCATGACAGATGACCC 60.525 63.158 0.00 0.00 0.00 4.46
725 740 2.534042 TGACCCCGAGATCTTCTCTT 57.466 50.000 0.00 0.00 41.26 2.85
726 741 3.664551 TGACCCCGAGATCTTCTCTTA 57.335 47.619 0.00 0.00 41.26 2.10
727 742 3.977312 TGACCCCGAGATCTTCTCTTAA 58.023 45.455 0.00 0.00 41.26 1.85
747 762 7.179269 TCTTAATAACCAAACTAAGCCACCAT 58.821 34.615 0.00 0.00 0.00 3.55
766 793 1.937278 TCTCACACGTAAAAACCGCA 58.063 45.000 0.00 0.00 0.00 5.69
878 905 2.740055 CAGCGCACTCCACAGTCC 60.740 66.667 11.47 0.00 0.00 3.85
1077 1119 3.327404 GGCCTCCTTCCCGGAACA 61.327 66.667 0.73 0.00 42.53 3.18
1121 1163 3.504134 GGGTTTCCTCTGAAGAAAAGAGC 59.496 47.826 3.15 0.00 39.94 4.09
1153 1195 2.576615 AGGAGGTTCTTGTTGCTTGAC 58.423 47.619 0.00 0.00 0.00 3.18
1188 1230 4.283467 TCGGACTCTCCTTTCATCTTTTCA 59.717 41.667 0.00 0.00 33.30 2.69
1208 1250 5.138125 TCACTTTCCTGATTTTGATTGGC 57.862 39.130 0.00 0.00 0.00 4.52
1294 1336 3.131400 TGGTTTTAGCCCACAAGTTTCAC 59.869 43.478 0.00 0.00 0.00 3.18
1295 1337 3.368495 GTTTTAGCCCACAAGTTTCACG 58.632 45.455 0.00 0.00 0.00 4.35
1394 1450 2.223044 GCTCCGTTTGATCCAACGAATC 60.223 50.000 28.01 14.66 0.00 2.52
1405 1461 6.645306 TGATCCAACGAATCAATACAGGTTA 58.355 36.000 0.00 0.00 0.00 2.85
1406 1462 6.537301 TGATCCAACGAATCAATACAGGTTAC 59.463 38.462 0.00 0.00 0.00 2.50
1410 1466 6.183360 CCAACGAATCAATACAGGTTACCTTC 60.183 42.308 0.00 0.00 0.00 3.46
1411 1467 5.425630 ACGAATCAATACAGGTTACCTTCC 58.574 41.667 0.00 0.00 0.00 3.46
1412 1468 5.189145 ACGAATCAATACAGGTTACCTTCCT 59.811 40.000 0.00 0.00 35.45 3.36
1413 1469 5.753921 CGAATCAATACAGGTTACCTTCCTC 59.246 44.000 0.00 0.00 32.37 3.71
1414 1470 6.407074 CGAATCAATACAGGTTACCTTCCTCT 60.407 42.308 0.00 0.00 32.37 3.69
1415 1471 6.893020 ATCAATACAGGTTACCTTCCTCTT 57.107 37.500 0.00 0.00 32.37 2.85
1416 1472 6.697641 TCAATACAGGTTACCTTCCTCTTT 57.302 37.500 0.00 0.00 32.37 2.52
1417 1473 7.086685 TCAATACAGGTTACCTTCCTCTTTT 57.913 36.000 0.00 0.00 32.37 2.27
1418 1474 6.940298 TCAATACAGGTTACCTTCCTCTTTTG 59.060 38.462 0.00 0.00 32.37 2.44
1419 1475 3.487372 ACAGGTTACCTTCCTCTTTTGC 58.513 45.455 0.00 0.00 32.37 3.68
1420 1476 3.138468 ACAGGTTACCTTCCTCTTTTGCT 59.862 43.478 0.00 0.00 32.37 3.91
1421 1477 3.753797 CAGGTTACCTTCCTCTTTTGCTC 59.246 47.826 0.00 0.00 32.37 4.26
1422 1478 3.394606 AGGTTACCTTCCTCTTTTGCTCA 59.605 43.478 0.00 0.00 0.00 4.26
1423 1479 3.753797 GGTTACCTTCCTCTTTTGCTCAG 59.246 47.826 0.00 0.00 0.00 3.35
1424 1480 2.575805 ACCTTCCTCTTTTGCTCAGG 57.424 50.000 0.00 0.00 0.00 3.86
1425 1481 2.057922 ACCTTCCTCTTTTGCTCAGGA 58.942 47.619 0.00 0.00 34.31 3.86
1426 1482 2.443255 ACCTTCCTCTTTTGCTCAGGAA 59.557 45.455 0.00 0.00 42.87 3.36
1427 1483 3.117512 ACCTTCCTCTTTTGCTCAGGAAA 60.118 43.478 1.49 0.00 44.11 3.13
1442 1498 0.778083 GGAAACAAGGGGAGGAGGTT 59.222 55.000 0.00 0.00 0.00 3.50
1446 1502 1.657804 ACAAGGGGAGGAGGTTACAG 58.342 55.000 0.00 0.00 0.00 2.74
1517 1573 4.959596 TCGCTACTACTACCTCTGTTTG 57.040 45.455 0.00 0.00 0.00 2.93
1693 1749 4.667519 ACTTGTCTTTCTAGTCCAACGT 57.332 40.909 0.00 0.00 0.00 3.99
1694 1750 5.019785 ACTTGTCTTTCTAGTCCAACGTT 57.980 39.130 0.00 0.00 0.00 3.99
1695 1751 6.152932 ACTTGTCTTTCTAGTCCAACGTTA 57.847 37.500 0.00 0.00 0.00 3.18
1696 1752 6.576185 ACTTGTCTTTCTAGTCCAACGTTAA 58.424 36.000 0.00 0.00 0.00 2.01
1723 1779 2.026356 CACCTGGGAATGATACACACCA 60.026 50.000 0.00 0.00 0.00 4.17
1783 1839 0.183492 AGTGCCTTCAACTGCTTCCA 59.817 50.000 0.00 0.00 0.00 3.53
1802 1858 7.093727 TGCTTCCATACTCCAGCTAATATAGAC 60.094 40.741 0.00 0.00 33.15 2.59
1804 1860 9.688091 CTTCCATACTCCAGCTAATATAGACTA 57.312 37.037 0.00 0.00 0.00 2.59
1868 2083 7.179694 ACCTAGTAAATAGTAACAAGTGCCTGA 59.820 37.037 0.00 0.00 0.00 3.86
1910 2125 4.214437 GAGCAATGTGAAAACAGTCTTCG 58.786 43.478 0.00 0.00 0.00 3.79
1913 2128 4.024893 GCAATGTGAAAACAGTCTTCGAGA 60.025 41.667 0.00 0.00 0.00 4.04
1914 2129 5.504010 GCAATGTGAAAACAGTCTTCGAGAA 60.504 40.000 0.00 0.00 0.00 2.87
1915 2130 6.486248 CAATGTGAAAACAGTCTTCGAGAAA 58.514 36.000 0.00 0.00 0.00 2.52
1916 2131 6.677781 ATGTGAAAACAGTCTTCGAGAAAA 57.322 33.333 0.00 0.00 0.00 2.29
1917 2132 6.489127 TGTGAAAACAGTCTTCGAGAAAAA 57.511 33.333 0.00 0.00 0.00 1.94
1918 2133 7.083875 TGTGAAAACAGTCTTCGAGAAAAAT 57.916 32.000 0.00 0.00 0.00 1.82
1919 2134 6.966632 TGTGAAAACAGTCTTCGAGAAAAATG 59.033 34.615 0.00 0.00 0.00 2.32
1920 2135 5.971202 TGAAAACAGTCTTCGAGAAAAATGC 59.029 36.000 0.00 0.00 0.00 3.56
1921 2136 5.757850 AAACAGTCTTCGAGAAAAATGCT 57.242 34.783 0.00 0.00 0.00 3.79
1922 2137 6.861065 AAACAGTCTTCGAGAAAAATGCTA 57.139 33.333 0.00 0.00 0.00 3.49
1923 2138 7.440523 AAACAGTCTTCGAGAAAAATGCTAT 57.559 32.000 0.00 0.00 0.00 2.97
1924 2139 7.440523 AACAGTCTTCGAGAAAAATGCTATT 57.559 32.000 0.00 0.00 0.00 1.73
1925 2140 7.066374 ACAGTCTTCGAGAAAAATGCTATTC 57.934 36.000 0.00 0.00 0.00 1.75
1926 2141 6.092807 ACAGTCTTCGAGAAAAATGCTATTCC 59.907 38.462 0.00 0.00 0.00 3.01
1927 2142 6.092670 CAGTCTTCGAGAAAAATGCTATTCCA 59.907 38.462 0.00 0.00 0.00 3.53
1928 2143 6.825721 AGTCTTCGAGAAAAATGCTATTCCAT 59.174 34.615 0.00 0.00 0.00 3.41
1929 2144 7.987458 AGTCTTCGAGAAAAATGCTATTCCATA 59.013 33.333 0.00 0.00 0.00 2.74
1930 2145 8.778358 GTCTTCGAGAAAAATGCTATTCCATAT 58.222 33.333 0.00 0.00 0.00 1.78
1931 2146 8.777413 TCTTCGAGAAAAATGCTATTCCATATG 58.223 33.333 0.00 0.00 0.00 1.78
1932 2147 8.675705 TTCGAGAAAAATGCTATTCCATATGA 57.324 30.769 3.65 0.00 0.00 2.15
1933 2148 8.853077 TCGAGAAAAATGCTATTCCATATGAT 57.147 30.769 3.65 0.00 0.00 2.45
1934 2149 9.942850 TCGAGAAAAATGCTATTCCATATGATA 57.057 29.630 3.65 0.00 0.00 2.15
2090 2403 8.837099 ATGGTCAAAGGGATATTGTATTCAAA 57.163 30.769 0.00 0.00 37.11 2.69
2232 2550 6.238484 GCATTTCACCATGTATGAACTCTACC 60.238 42.308 8.71 0.00 35.82 3.18
2238 2556 5.248477 ACCATGTATGAACTCTACCAGTTGT 59.752 40.000 0.00 0.00 46.10 3.32
2297 2615 4.565564 CACTCGTGCTAATGTTAGGTTACC 59.434 45.833 0.00 0.00 0.00 2.85
2489 2811 6.773638 TCTCCTTTCTTTTGCTGAAGATACT 58.226 36.000 3.70 0.00 35.70 2.12
2490 2812 6.652481 TCTCCTTTCTTTTGCTGAAGATACTG 59.348 38.462 3.70 0.00 35.70 2.74
2491 2813 6.533730 TCCTTTCTTTTGCTGAAGATACTGA 58.466 36.000 3.70 0.00 35.70 3.41
2492 2814 7.170965 TCCTTTCTTTTGCTGAAGATACTGAT 58.829 34.615 3.70 0.00 35.70 2.90
2493 2815 7.667219 TCCTTTCTTTTGCTGAAGATACTGATT 59.333 33.333 3.70 0.00 35.70 2.57
2494 2816 7.754027 CCTTTCTTTTGCTGAAGATACTGATTG 59.246 37.037 3.70 0.00 35.70 2.67
2495 2817 7.984422 TTCTTTTGCTGAAGATACTGATTGA 57.016 32.000 3.70 0.00 35.70 2.57
2496 2818 7.606858 TCTTTTGCTGAAGATACTGATTGAG 57.393 36.000 0.00 0.00 30.98 3.02
2623 2946 8.000709 TGGCTTTTGACAGATGGAGAATAATAT 58.999 33.333 0.00 0.00 31.06 1.28
2891 3217 7.831193 GCATTAATCCAGTACTTCCCATCATAT 59.169 37.037 0.00 0.00 0.00 1.78
2898 3224 5.699915 CAGTACTTCCCATCATATGCAAGAG 59.300 44.000 0.00 0.00 0.00 2.85
2901 3227 5.862845 ACTTCCCATCATATGCAAGAGTAG 58.137 41.667 0.00 0.00 0.00 2.57
2918 3244 9.158233 GCAAGAGTAGTTGTGTATGGTTAATAA 57.842 33.333 0.00 0.00 0.00 1.40
2975 3301 4.058124 TGCTGTATCCAACTATGATTCGC 58.942 43.478 0.00 0.00 0.00 4.70
2985 3311 6.936335 TCCAACTATGATTCGCATCACAATAT 59.064 34.615 0.00 0.00 42.46 1.28
2988 3314 7.356641 ACTATGATTCGCATCACAATATCAC 57.643 36.000 0.00 0.00 42.46 3.06
2999 3325 7.478322 GCATCACAATATCACTGTCTCAAATT 58.522 34.615 0.00 0.00 0.00 1.82
3058 3384 5.023920 CACATACTGCATTTAGCTTTCGTG 58.976 41.667 0.00 0.00 45.94 4.35
3095 3421 5.559417 TGTAGTAACAACTTAAAAGCGCAGC 60.559 40.000 11.47 0.00 44.38 5.25
3162 3489 8.514330 TTGTTATATCATTTTCACCAGGTACC 57.486 34.615 2.73 2.73 0.00 3.34
3166 3493 4.015872 TCATTTTCACCAGGTACCTGTC 57.984 45.455 34.49 0.00 42.15 3.51
3177 3504 1.271217 GGTACCTGTCCAAACCCTCAC 60.271 57.143 4.06 0.00 0.00 3.51
3181 3508 2.091333 ACCTGTCCAAACCCTCACATTT 60.091 45.455 0.00 0.00 0.00 2.32
3182 3509 2.965147 CCTGTCCAAACCCTCACATTTT 59.035 45.455 0.00 0.00 0.00 1.82
3327 3654 1.398390 GCTCAACCAGGATGTAAAGCG 59.602 52.381 0.00 0.00 0.00 4.68
3342 3669 0.912486 AAGCGGGCATAGAGGAACTT 59.088 50.000 0.00 0.00 41.55 2.66
3387 3714 8.581578 GTTGACAAAGGGAAACTTATAATCCAA 58.418 33.333 6.05 0.00 38.85 3.53
3423 3750 6.316390 AGTGCAGTAGTCTTTATTTGGTATGC 59.684 38.462 0.00 0.00 0.00 3.14
3443 3770 2.420547 GCCACTCTGCATTCAGGATGTA 60.421 50.000 0.00 0.00 40.69 2.29
3453 3780 7.395772 TCTGCATTCAGGATGTAAAACCATTTA 59.604 33.333 0.00 0.00 40.69 1.40
3507 3835 6.423776 AAATGATTTTCCTTGGCTTCTCAA 57.576 33.333 0.00 0.00 0.00 3.02
3560 3888 2.362397 TCAGGCTATTACAGGAGAAGCG 59.638 50.000 0.00 0.00 33.96 4.68
3665 3993 5.363939 GCTGATCAGGCTAGTTTACTCAAT 58.636 41.667 23.89 0.00 0.00 2.57
3668 3996 7.615582 TGATCAGGCTAGTTTACTCAATTTG 57.384 36.000 0.00 0.00 0.00 2.32
3693 4021 4.789807 AGATCACTCAATAGCAGGCAAAT 58.210 39.130 0.00 0.00 0.00 2.32
3720 4048 8.862325 TTTTTCTAGGCTGATCATTAACTCAA 57.138 30.769 0.00 0.00 0.00 3.02
3721 4049 9.466497 TTTTTCTAGGCTGATCATTAACTCAAT 57.534 29.630 0.00 0.00 0.00 2.57
3722 4050 9.466497 TTTTCTAGGCTGATCATTAACTCAATT 57.534 29.630 0.00 0.00 0.00 2.32
3723 4051 9.466497 TTTCTAGGCTGATCATTAACTCAATTT 57.534 29.630 0.00 0.00 0.00 1.82
3724 4052 8.442632 TCTAGGCTGATCATTAACTCAATTTG 57.557 34.615 0.00 0.00 0.00 2.32
3725 4053 8.267183 TCTAGGCTGATCATTAACTCAATTTGA 58.733 33.333 0.00 0.00 0.00 2.69
3726 4054 7.707624 AGGCTGATCATTAACTCAATTTGAA 57.292 32.000 0.00 0.00 0.00 2.69
3727 4055 7.542025 AGGCTGATCATTAACTCAATTTGAAC 58.458 34.615 0.00 0.00 0.00 3.18
3728 4056 7.395489 AGGCTGATCATTAACTCAATTTGAACT 59.605 33.333 0.00 0.00 0.00 3.01
3729 4057 8.677300 GGCTGATCATTAACTCAATTTGAACTA 58.323 33.333 0.00 0.00 0.00 2.24
3737 4065 8.844441 TTAACTCAATTTGAACTAAAACCACG 57.156 30.769 0.01 0.00 0.00 4.94
3738 4066 6.445357 ACTCAATTTGAACTAAAACCACGT 57.555 33.333 0.01 0.00 0.00 4.49
3739 4067 6.859017 ACTCAATTTGAACTAAAACCACGTT 58.141 32.000 0.01 0.00 0.00 3.99
3740 4068 7.987649 ACTCAATTTGAACTAAAACCACGTTA 58.012 30.769 0.01 0.00 0.00 3.18
3741 4069 8.460428 ACTCAATTTGAACTAAAACCACGTTAA 58.540 29.630 0.01 0.00 0.00 2.01
3742 4070 8.844441 TCAATTTGAACTAAAACCACGTTAAG 57.156 30.769 0.00 0.00 0.00 1.85
3743 4071 8.460428 TCAATTTGAACTAAAACCACGTTAAGT 58.540 29.630 0.00 0.00 0.00 2.24
3744 4072 9.719279 CAATTTGAACTAAAACCACGTTAAGTA 57.281 29.630 0.00 0.00 0.00 2.24
3749 4077 9.719279 TGAACTAAAACCACGTTAAGTATTTTG 57.281 29.630 0.00 0.00 34.30 2.44
3750 4078 9.172820 GAACTAAAACCACGTTAAGTATTTTGG 57.827 33.333 0.00 0.00 36.03 3.28
3751 4079 8.449251 ACTAAAACCACGTTAAGTATTTTGGA 57.551 30.769 8.98 0.00 34.80 3.53
3752 4080 8.901793 ACTAAAACCACGTTAAGTATTTTGGAA 58.098 29.630 8.98 0.00 34.80 3.53
3753 4081 7.990541 AAAACCACGTTAAGTATTTTGGAAC 57.009 32.000 0.00 0.00 32.41 3.62
3754 4082 6.696441 AACCACGTTAAGTATTTTGGAACA 57.304 33.333 0.00 0.00 0.00 3.18
3776 4104 4.634012 AAGGTAGTACATGGTTTGCTCA 57.366 40.909 2.06 0.00 0.00 4.26
3781 4109 4.891992 AGTACATGGTTTGCTCACTAGT 57.108 40.909 0.00 0.00 0.00 2.57
3789 4117 6.761099 TGGTTTGCTCACTAGTTGTAAAAA 57.239 33.333 9.38 0.00 0.00 1.94
3838 4166 8.806429 TTCTTGGAATATCAATCAAAGTAGCA 57.194 30.769 0.00 0.00 31.11 3.49
3840 4168 9.060347 TCTTGGAATATCAATCAAAGTAGCATC 57.940 33.333 0.00 0.00 31.11 3.91
3896 4224 3.780294 TGGAGGTGTATCCAGTATTTGCT 59.220 43.478 0.00 0.00 44.56 3.91
3897 4225 4.130118 GGAGGTGTATCCAGTATTTGCTG 58.870 47.826 0.00 0.00 39.34 4.41
3898 4226 3.545703 AGGTGTATCCAGTATTTGCTGC 58.454 45.455 0.00 0.00 39.02 5.25
4028 4356 5.468746 TCACTATTTGTAACAGGTTGCTGAC 59.531 40.000 2.11 0.00 0.00 3.51
4335 4663 2.938354 CCTGAGACAGGTGCAAAGG 58.062 57.895 9.36 0.00 45.82 3.11
4514 4842 5.123502 CCCAATATCTATGAAGCTGATGCAC 59.876 44.000 0.00 0.00 42.74 4.57
4778 5106 4.301628 CCCTGATTGCTCACAAAAACTTC 58.698 43.478 0.00 0.00 39.77 3.01
4861 5189 0.613260 CCAGTCAGGGAAACGGATGA 59.387 55.000 0.00 0.00 0.00 2.92
4882 5210 5.202004 TGAGCCAAAAACTAGTTTTACCCA 58.798 37.500 28.97 19.72 41.45 4.51
5111 5439 9.500864 GAATTTCTTAAGAATGACAATCTCAGC 57.499 33.333 18.37 0.00 33.54 4.26
5379 5718 5.473504 GCTCCAAAAGTTAGGAATTCTGTCA 59.526 40.000 5.23 0.00 32.57 3.58
5523 5862 0.175760 AGTGCGGCTGATTGTATCGT 59.824 50.000 0.00 0.00 0.00 3.73
5525 5864 1.004927 GTGCGGCTGATTGTATCGTTC 60.005 52.381 0.00 0.00 0.00 3.95
5534 5873 5.277538 GCTGATTGTATCGTTCCTTGATTCC 60.278 44.000 0.00 0.00 0.00 3.01
5657 5996 3.387962 TGGAGCTTTGGATACTGGAGAT 58.612 45.455 0.00 0.00 37.61 2.75
5675 6014 3.618351 AGATAATGAGTGCTTGCAGCTT 58.382 40.909 9.12 0.00 42.97 3.74
5726 6065 9.123902 TCATCCAGTAATGATGTAAAATCCTTG 57.876 33.333 0.00 0.00 40.38 3.61
5730 6069 7.198390 CAGTAATGATGTAAAATCCTTGCTGG 58.802 38.462 11.06 0.00 34.97 4.85
5808 6147 4.442052 CCGAGTATTGCCTGAAGATTCTGA 60.442 45.833 1.44 0.00 0.00 3.27
6068 6407 6.615088 GTCTTCAATCAAGCTGCTTCAAATA 58.385 36.000 12.82 0.00 31.26 1.40
6206 6548 1.310904 TTTTCTCAAAACCCCGGTCG 58.689 50.000 0.00 0.00 0.00 4.79
6213 6555 3.753806 AAACCCCGGTCGCGAAACA 62.754 57.895 12.06 0.00 0.00 2.83
6324 6666 4.181578 CGGGTAGTAGTGTCCAAATGAAG 58.818 47.826 0.00 0.00 0.00 3.02
6337 6679 5.048083 GTCCAAATGAAGTGCTTAATGTGGA 60.048 40.000 14.50 14.50 42.84 4.02
6373 6715 8.617290 ACCGAAATGTATTTGACTAGAGTTTT 57.383 30.769 0.00 0.00 0.00 2.43
6395 6737 9.209297 GTTTTTATTTGCACATGTTTTTGTCTC 57.791 29.630 0.00 0.00 0.00 3.36
6431 6773 4.022413 AGAAAAGGGAGGTTTAGCTCAC 57.978 45.455 10.73 7.15 0.00 3.51
6436 6778 1.351350 GGGAGGTTTAGCTCACAGGTT 59.649 52.381 10.73 0.00 0.00 3.50
6507 9775 4.387598 ACTCCTCTATGAATGAATGCAGC 58.612 43.478 0.00 0.00 0.00 5.25
6537 9805 2.113860 ATCCATCAACCAACTCCACG 57.886 50.000 0.00 0.00 0.00 4.94
6538 9806 0.036164 TCCATCAACCAACTCCACGG 59.964 55.000 0.00 0.00 0.00 4.94
6666 9942 7.282585 TGAATGTCCTTCCAATACTTATCAGG 58.717 38.462 0.00 0.00 32.49 3.86
6671 9947 8.044908 TGTCCTTCCAATACTTATCAGGTTTAC 58.955 37.037 0.00 0.00 0.00 2.01
6907 10184 7.538334 TCATATTGTTTCTCAACTTGATTTGCG 59.462 33.333 0.00 0.00 38.97 4.85
6920 10197 2.280183 TGATTTGCGCGTTTGAAAACAC 59.720 40.909 8.43 0.00 38.81 3.32
7034 10314 7.448748 TTTTTAAACTTAGCCATCTCCTCAC 57.551 36.000 0.00 0.00 0.00 3.51
7035 10315 6.374417 TTTAAACTTAGCCATCTCCTCACT 57.626 37.500 0.00 0.00 0.00 3.41
7036 10316 4.917906 AAACTTAGCCATCTCCTCACTT 57.082 40.909 0.00 0.00 0.00 3.16
7076 10356 1.555075 CCAATCTCGAGGAAAGGGACA 59.445 52.381 13.56 0.00 0.00 4.02
7085 10365 1.026718 GGAAAGGGACATGGCGTCTG 61.027 60.000 0.00 0.00 44.70 3.51
7097 10377 4.686091 ACATGGCGTCTGTATATTGAATCG 59.314 41.667 0.00 0.00 0.00 3.34
7098 10378 4.316205 TGGCGTCTGTATATTGAATCGT 57.684 40.909 0.00 0.00 0.00 3.73
7145 10425 3.127548 AGGCAAGAATAGCAACAACATCG 59.872 43.478 0.00 0.00 0.00 3.84
7151 10431 2.987413 TAGCAACAACATCGGCAAAG 57.013 45.000 0.00 0.00 0.00 2.77
7157 10437 4.324402 GCAACAACATCGGCAAAGATTTAG 59.676 41.667 0.00 0.00 0.00 1.85
7182 10463 7.703058 TCAGAATGAGACACTGAGTTGTATA 57.297 36.000 0.00 0.00 42.56 1.47
7231 10512 1.016627 GATGCGCCAGTGATGCTTTA 58.983 50.000 4.18 0.00 0.00 1.85
7242 10523 1.828595 TGATGCTTTAGTCCCGTAGCA 59.171 47.619 0.00 0.00 46.47 3.49
7246 10527 2.094182 TGCTTTAGTCCCGTAGCAAGAG 60.094 50.000 0.00 0.00 40.39 2.85
7311 10592 0.170339 TATCCTATGCGCCGACATCG 59.830 55.000 4.18 0.00 39.44 3.84
7333 10614 4.261909 CGTAACCTCGGTCCTAGCATTTAT 60.262 45.833 0.00 0.00 0.00 1.40
7343 10624 5.239525 GGTCCTAGCATTTATTGTGATGACC 59.760 44.000 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 2.235891 GGTTCGACCAATTTTCTGGGT 58.764 47.619 0.00 0.00 41.16 4.51
14 15 2.567067 CGTTCGGTTCGACCAATTTTC 58.433 47.619 5.15 0.00 38.47 2.29
37 38 5.569355 TGTGAGGAGCCAAATAGAAATTGA 58.431 37.500 0.00 0.00 0.00 2.57
43 44 5.378230 AATCATGTGAGGAGCCAAATAGA 57.622 39.130 0.00 0.00 0.00 1.98
93 95 8.416329 GGTCCTTGCATAAAATAATCACAAGAT 58.584 33.333 0.00 0.00 36.08 2.40
161 165 5.875224 TGGTTAAGATGAGTGGAATGAACA 58.125 37.500 0.00 0.00 0.00 3.18
168 172 4.141367 TGGTGTTTGGTTAAGATGAGTGGA 60.141 41.667 0.00 0.00 0.00 4.02
199 203 5.511234 CCAGATTTTGGGAATGAGATGAC 57.489 43.478 0.00 0.00 43.75 3.06
263 267 4.582701 AATCTGAGACATCGATGAGACC 57.417 45.455 31.33 16.35 0.00 3.85
268 272 3.006217 TGGCCTAATCTGAGACATCGATG 59.994 47.826 23.68 23.68 0.00 3.84
271 279 3.459232 TTGGCCTAATCTGAGACATCG 57.541 47.619 3.32 0.00 0.00 3.84
317 326 7.767261 TGTGCAACACCCTTTTTATATATGTC 58.233 34.615 0.00 0.00 45.67 3.06
445 458 0.831307 ACTTCATTAGCCGTCCCTCC 59.169 55.000 0.00 0.00 0.00 4.30
449 464 4.329256 GTCTTAACACTTCATTAGCCGTCC 59.671 45.833 0.00 0.00 0.00 4.79
476 491 2.092861 TCACCTTTTTCGTTCACAGGGA 60.093 45.455 0.00 0.00 0.00 4.20
561 576 3.214250 GAGATGCCGGCTCGTAGGG 62.214 68.421 29.70 0.00 0.00 3.53
614 629 0.970640 TTGTAGCCGCCTGTTCTACA 59.029 50.000 0.00 0.00 40.37 2.74
725 740 6.727394 AGATGGTGGCTTAGTTTGGTTATTA 58.273 36.000 0.00 0.00 0.00 0.98
726 741 5.580022 AGATGGTGGCTTAGTTTGGTTATT 58.420 37.500 0.00 0.00 0.00 1.40
727 742 5.193099 AGATGGTGGCTTAGTTTGGTTAT 57.807 39.130 0.00 0.00 0.00 1.89
740 755 1.803334 TTTACGTGTGAGATGGTGGC 58.197 50.000 0.00 0.00 0.00 5.01
747 762 1.937278 TGCGGTTTTTACGTGTGAGA 58.063 45.000 0.00 0.00 0.00 3.27
766 793 2.591715 GCGCACCGGGATTAGCAT 60.592 61.111 6.32 0.00 0.00 3.79
804 831 0.391661 ATGTTCAATGCGCTCTCGGT 60.392 50.000 9.73 0.00 35.95 4.69
1121 1163 1.488393 GAACCTCCTTCTGATCCCCAG 59.512 57.143 0.00 0.00 44.27 4.45
1153 1195 1.145803 GAGTCCGAAAACCGAACCTG 58.854 55.000 0.00 0.00 41.76 4.00
1188 1230 3.056607 CCGCCAATCAAAATCAGGAAAGT 60.057 43.478 0.00 0.00 0.00 2.66
1312 1354 7.768120 AGATTAAGCAAAAACAATGAACAACCA 59.232 29.630 0.00 0.00 0.00 3.67
1394 1450 6.349363 GCAAAAGAGGAAGGTAACCTGTATTG 60.349 42.308 0.00 0.00 37.93 1.90
1405 1461 2.057922 TCCTGAGCAAAAGAGGAAGGT 58.942 47.619 0.00 0.00 32.74 3.50
1406 1462 2.867109 TCCTGAGCAAAAGAGGAAGG 57.133 50.000 0.00 0.00 32.74 3.46
1410 1466 3.005155 CCTTGTTTCCTGAGCAAAAGAGG 59.995 47.826 0.00 0.00 0.00 3.69
1411 1467 3.005155 CCCTTGTTTCCTGAGCAAAAGAG 59.995 47.826 0.00 0.00 0.00 2.85
1412 1468 2.958355 CCCTTGTTTCCTGAGCAAAAGA 59.042 45.455 0.00 0.00 0.00 2.52
1413 1469 2.036346 CCCCTTGTTTCCTGAGCAAAAG 59.964 50.000 0.00 0.00 0.00 2.27
1414 1470 2.038659 CCCCTTGTTTCCTGAGCAAAA 58.961 47.619 0.00 0.00 0.00 2.44
1415 1471 1.216678 TCCCCTTGTTTCCTGAGCAAA 59.783 47.619 0.00 0.00 0.00 3.68
1416 1472 0.850100 TCCCCTTGTTTCCTGAGCAA 59.150 50.000 0.00 0.00 0.00 3.91
1417 1473 0.401738 CTCCCCTTGTTTCCTGAGCA 59.598 55.000 0.00 0.00 0.00 4.26
1418 1474 0.322906 CCTCCCCTTGTTTCCTGAGC 60.323 60.000 0.00 0.00 0.00 4.26
1419 1475 1.280421 CTCCTCCCCTTGTTTCCTGAG 59.720 57.143 0.00 0.00 0.00 3.35
1420 1476 1.362224 CTCCTCCCCTTGTTTCCTGA 58.638 55.000 0.00 0.00 0.00 3.86
1421 1477 0.329596 CCTCCTCCCCTTGTTTCCTG 59.670 60.000 0.00 0.00 0.00 3.86
1422 1478 0.103876 ACCTCCTCCCCTTGTTTCCT 60.104 55.000 0.00 0.00 0.00 3.36
1423 1479 0.778083 AACCTCCTCCCCTTGTTTCC 59.222 55.000 0.00 0.00 0.00 3.13
1424 1480 2.374170 TGTAACCTCCTCCCCTTGTTTC 59.626 50.000 0.00 0.00 0.00 2.78
1425 1481 2.375509 CTGTAACCTCCTCCCCTTGTTT 59.624 50.000 0.00 0.00 0.00 2.83
1426 1482 1.985895 CTGTAACCTCCTCCCCTTGTT 59.014 52.381 0.00 0.00 0.00 2.83
1427 1483 1.151413 TCTGTAACCTCCTCCCCTTGT 59.849 52.381 0.00 0.00 0.00 3.16
1442 1498 2.563179 GAGGAAGCAACTCACCTCTGTA 59.437 50.000 0.00 0.00 43.64 2.74
1446 1502 2.224402 ACTTGAGGAAGCAACTCACCTC 60.224 50.000 0.00 0.00 44.07 3.85
1493 1549 3.277715 ACAGAGGTAGTAGTAGCGAACC 58.722 50.000 1.22 0.00 0.00 3.62
1498 1554 8.033626 ACATTTACAAACAGAGGTAGTAGTAGC 58.966 37.037 0.00 0.00 0.00 3.58
1517 1573 7.865385 TGAACTGCCAAAACATCTTACATTTAC 59.135 33.333 0.00 0.00 0.00 2.01
1654 1710 8.842358 AGACAAGTATAATTCAGAAAAACCGA 57.158 30.769 0.00 0.00 0.00 4.69
1677 1733 7.711772 TGACAAATTAACGTTGGACTAGAAAGA 59.288 33.333 11.99 0.00 0.00 2.52
1693 1749 7.122055 GTGTATCATTCCCAGGTGACAAATTAA 59.878 37.037 0.00 0.00 0.00 1.40
1694 1750 6.601613 GTGTATCATTCCCAGGTGACAAATTA 59.398 38.462 0.00 0.00 0.00 1.40
1695 1751 5.418840 GTGTATCATTCCCAGGTGACAAATT 59.581 40.000 0.00 0.00 0.00 1.82
1696 1752 4.949856 GTGTATCATTCCCAGGTGACAAAT 59.050 41.667 0.00 0.00 0.00 2.32
1723 1779 9.500785 CAAAAACAAATTTGACCCCATAAGTAT 57.499 29.630 24.64 0.00 41.73 2.12
1783 1839 9.456147 CAGTGTAGTCTATATTAGCTGGAGTAT 57.544 37.037 0.00 0.00 0.00 2.12
1868 2083 5.125097 TGCTCCAAAAACATGTGCAATTTTT 59.875 32.000 0.00 0.00 36.26 1.94
1960 2175 2.358247 GTCGCATCCACCGTGGTT 60.358 61.111 17.32 6.37 39.03 3.67
2232 2550 7.651304 TGAAAACAATTAGTTATGCCACAACTG 59.349 33.333 0.00 0.00 40.26 3.16
2238 2556 6.934056 AGCATGAAAACAATTAGTTATGCCA 58.066 32.000 15.59 0.00 44.85 4.92
2297 2615 3.916172 CACCATTGTCTTGCAATTCGAAG 59.084 43.478 3.35 0.00 44.82 3.79
2489 2811 9.891828 GTTATTTGTAACACAATCACTCAATCA 57.108 29.630 0.00 0.00 38.00 2.57
2490 2812 9.891828 TGTTATTTGTAACACAATCACTCAATC 57.108 29.630 0.00 0.00 38.00 2.67
2495 2817 9.862371 TGTTTTGTTATTTGTAACACAATCACT 57.138 25.926 0.83 0.00 38.00 3.41
2623 2946 4.522405 CAGGTGTACCAAACATTCCATCAA 59.478 41.667 3.56 0.00 41.10 2.57
2720 3043 8.889849 ACAACAAAATACGAACAGTTATATGC 57.110 30.769 0.00 0.00 0.00 3.14
2891 3217 4.617253 ACCATACACAACTACTCTTGCA 57.383 40.909 0.00 0.00 0.00 4.08
2985 3311 7.394016 TCAGGCTTAATAATTTGAGACAGTGA 58.606 34.615 0.00 0.00 28.84 3.41
2999 3325 9.920946 AGAAATTCCACTATTTCAGGCTTAATA 57.079 29.630 10.61 0.00 43.67 0.98
3058 3384 3.259902 GTTACTACACCTGCCAACTAGC 58.740 50.000 0.00 0.00 0.00 3.42
3090 3416 5.861251 TGAAATGGTAGTTTAAAATGCTGCG 59.139 36.000 3.83 0.00 0.00 5.18
3162 3489 3.799917 GCAAAATGTGAGGGTTTGGACAG 60.800 47.826 0.00 0.00 33.72 3.51
3166 3493 3.573967 ACTAGCAAAATGTGAGGGTTTGG 59.426 43.478 0.00 0.00 33.72 3.28
3306 3633 2.436417 GCTTTACATCCTGGTTGAGCA 58.564 47.619 11.60 0.00 31.67 4.26
3327 3654 2.128771 TGCAAAGTTCCTCTATGCCC 57.871 50.000 0.00 0.00 36.20 5.36
3342 3669 5.122239 GTCAACTATGCTGTACAGATTGCAA 59.878 40.000 27.08 0.00 38.96 4.08
3423 3750 2.414994 ACATCCTGAATGCAGAGTGG 57.585 50.000 0.74 0.00 45.17 4.00
3480 3808 8.036575 TGAGAAGCCAAGGAAAATCATTTTATG 58.963 33.333 0.00 0.00 31.94 1.90
3489 3817 6.494835 ACAATACTTGAGAAGCCAAGGAAAAT 59.505 34.615 8.29 0.00 45.76 1.82
3507 3835 8.454106 GTGTGCTCAATATCAAAAGACAATACT 58.546 33.333 0.00 0.00 0.00 2.12
3560 3888 0.179192 TTTCGCATCGCATTGCTGTC 60.179 50.000 7.12 0.00 40.54 3.51
3662 3990 8.504815 CCTGCTATTGAGTGATCTATCAAATTG 58.495 37.037 14.45 9.91 38.80 2.32
3665 3993 5.994054 GCCTGCTATTGAGTGATCTATCAAA 59.006 40.000 14.45 6.35 38.80 2.69
3668 3996 5.144692 TGCCTGCTATTGAGTGATCTATC 57.855 43.478 0.00 0.00 0.00 2.08
3703 4031 7.542025 AGTTCAAATTGAGTTAATGATCAGCC 58.458 34.615 0.09 0.00 0.00 4.85
3715 4043 6.445357 ACGTGGTTTTAGTTCAAATTGAGT 57.555 33.333 0.00 0.00 0.00 3.41
3716 4044 8.844441 TTAACGTGGTTTTAGTTCAAATTGAG 57.156 30.769 0.00 0.00 0.00 3.02
3717 4045 8.460428 ACTTAACGTGGTTTTAGTTCAAATTGA 58.540 29.630 0.00 0.00 0.00 2.57
3718 4046 8.623310 ACTTAACGTGGTTTTAGTTCAAATTG 57.377 30.769 0.00 0.00 0.00 2.32
3723 4051 9.719279 CAAAATACTTAACGTGGTTTTAGTTCA 57.281 29.630 0.00 0.00 0.00 3.18
3724 4052 9.172820 CCAAAATACTTAACGTGGTTTTAGTTC 57.827 33.333 0.00 0.00 0.00 3.01
3725 4053 8.901793 TCCAAAATACTTAACGTGGTTTTAGTT 58.098 29.630 0.00 0.00 0.00 2.24
3726 4054 8.449251 TCCAAAATACTTAACGTGGTTTTAGT 57.551 30.769 0.00 0.00 0.00 2.24
3727 4055 9.172820 GTTCCAAAATACTTAACGTGGTTTTAG 57.827 33.333 0.00 0.00 0.00 1.85
3728 4056 8.680903 TGTTCCAAAATACTTAACGTGGTTTTA 58.319 29.630 0.00 0.00 0.00 1.52
3729 4057 7.545489 TGTTCCAAAATACTTAACGTGGTTTT 58.455 30.769 0.00 0.00 0.00 2.43
3730 4058 7.098074 TGTTCCAAAATACTTAACGTGGTTT 57.902 32.000 0.00 0.00 0.00 3.27
3731 4059 6.696441 TGTTCCAAAATACTTAACGTGGTT 57.304 33.333 0.00 0.00 0.00 3.67
3732 4060 6.696441 TTGTTCCAAAATACTTAACGTGGT 57.304 33.333 0.00 0.00 0.00 4.16
3733 4061 6.639279 CCTTTGTTCCAAAATACTTAACGTGG 59.361 38.462 0.00 0.00 0.00 4.94
3734 4062 7.197703 ACCTTTGTTCCAAAATACTTAACGTG 58.802 34.615 0.00 0.00 0.00 4.49
3735 4063 7.337480 ACCTTTGTTCCAAAATACTTAACGT 57.663 32.000 0.00 0.00 0.00 3.99
3736 4064 8.562052 ACTACCTTTGTTCCAAAATACTTAACG 58.438 33.333 0.00 0.00 0.00 3.18
3740 4068 8.983702 TGTACTACCTTTGTTCCAAAATACTT 57.016 30.769 0.00 0.00 0.00 2.24
3741 4069 9.010029 CATGTACTACCTTTGTTCCAAAATACT 57.990 33.333 0.00 0.00 0.00 2.12
3742 4070 8.241367 CCATGTACTACCTTTGTTCCAAAATAC 58.759 37.037 0.00 0.00 0.00 1.89
3743 4071 7.945664 ACCATGTACTACCTTTGTTCCAAAATA 59.054 33.333 0.00 0.00 0.00 1.40
3744 4072 6.780522 ACCATGTACTACCTTTGTTCCAAAAT 59.219 34.615 0.00 0.00 0.00 1.82
3745 4073 6.130569 ACCATGTACTACCTTTGTTCCAAAA 58.869 36.000 0.00 0.00 0.00 2.44
3746 4074 5.697067 ACCATGTACTACCTTTGTTCCAAA 58.303 37.500 0.00 0.00 0.00 3.28
3747 4075 5.313280 ACCATGTACTACCTTTGTTCCAA 57.687 39.130 0.00 0.00 0.00 3.53
3748 4076 4.986054 ACCATGTACTACCTTTGTTCCA 57.014 40.909 0.00 0.00 0.00 3.53
3749 4077 5.564063 GCAAACCATGTACTACCTTTGTTCC 60.564 44.000 0.00 0.00 0.00 3.62
3750 4078 5.240844 AGCAAACCATGTACTACCTTTGTTC 59.759 40.000 0.00 0.00 0.00 3.18
3751 4079 5.137551 AGCAAACCATGTACTACCTTTGTT 58.862 37.500 0.00 0.00 0.00 2.83
3752 4080 4.725490 AGCAAACCATGTACTACCTTTGT 58.275 39.130 0.00 0.00 0.00 2.83
3753 4081 4.759693 TGAGCAAACCATGTACTACCTTTG 59.240 41.667 0.00 0.00 0.00 2.77
3754 4082 4.760204 GTGAGCAAACCATGTACTACCTTT 59.240 41.667 0.00 0.00 0.00 3.11
3755 4083 4.041691 AGTGAGCAAACCATGTACTACCTT 59.958 41.667 0.00 0.00 0.00 3.50
3756 4084 3.583086 AGTGAGCAAACCATGTACTACCT 59.417 43.478 0.00 0.00 0.00 3.08
3757 4085 3.939066 AGTGAGCAAACCATGTACTACC 58.061 45.455 0.00 0.00 0.00 3.18
3758 4086 5.721232 ACTAGTGAGCAAACCATGTACTAC 58.279 41.667 0.00 0.00 0.00 2.73
3759 4087 5.995565 ACTAGTGAGCAAACCATGTACTA 57.004 39.130 0.00 0.00 0.00 1.82
3815 4143 8.843262 TGATGCTACTTTGATTGATATTCCAAG 58.157 33.333 0.00 0.00 0.00 3.61
3838 4166 3.845781 ATGCGAGTTTCCCATACTGAT 57.154 42.857 0.00 0.00 0.00 2.90
3840 4168 3.063997 GTGAATGCGAGTTTCCCATACTG 59.936 47.826 0.00 0.00 0.00 2.74
3898 4226 2.096069 GCAGACAACGCATGCCTATATG 60.096 50.000 13.15 6.69 33.81 1.78
4005 4333 5.614668 CGTCAGCAACCTGTTACAAATAGTG 60.615 44.000 0.00 0.00 40.09 2.74
4028 4356 8.911247 TCATATTTCGGAGATCATTATGTACG 57.089 34.615 0.00 0.00 34.05 3.67
4335 4663 4.391830 TGTAGTTTCATTCGCAGTTCCATC 59.608 41.667 0.00 0.00 0.00 3.51
4410 4738 1.051812 CCAGTCCCAGAGTTCACAGT 58.948 55.000 0.00 0.00 0.00 3.55
4411 4739 0.322975 CCCAGTCCCAGAGTTCACAG 59.677 60.000 0.00 0.00 0.00 3.66
4514 4842 4.381398 CCAGAGGCTATTATCACAGGATCG 60.381 50.000 0.00 0.00 34.89 3.69
4778 5106 2.663602 GCTATGCTCGACCATGTAATCG 59.336 50.000 3.39 5.21 39.72 3.34
4861 5189 5.205821 ACTGGGTAAAACTAGTTTTTGGCT 58.794 37.500 32.37 15.18 42.22 4.75
4882 5210 7.933033 ACTGGCAATTGACATTTGAATAAAACT 59.067 29.630 15.95 0.00 29.25 2.66
5111 5439 4.754372 TTTCTGAGCTTGTAATGTGCTG 57.246 40.909 0.00 0.00 37.16 4.41
5379 5718 2.568509 AGGCCTTTGTGCAAAAGCATAT 59.431 40.909 16.83 3.42 38.98 1.78
5523 5862 4.695455 CAGCTTTAACTCGGAATCAAGGAA 59.305 41.667 0.00 0.00 0.00 3.36
5525 5864 3.375299 CCAGCTTTAACTCGGAATCAAGG 59.625 47.826 0.00 0.00 0.00 3.61
5675 6014 4.115516 GTTCGCAGATCATCTTTAGAGCA 58.884 43.478 0.00 0.00 35.04 4.26
5808 6147 4.385825 TGTTTCACTTCGCATAAGTTCCT 58.614 39.130 0.00 0.00 0.00 3.36
6088 6427 0.460811 TCCAGCATCGACAGCATGAC 60.461 55.000 13.43 0.00 39.69 3.06
6206 6548 2.966050 AGTTCTCAGAGGATGTTTCGC 58.034 47.619 0.00 0.00 0.00 4.70
6248 6590 9.119418 TGTCAAATTCACAAAGTTCTGATTCTA 57.881 29.630 0.00 0.00 0.00 2.10
6373 6715 7.715657 AGAGAGACAAAAACATGTGCAAATAA 58.284 30.769 0.00 0.00 32.57 1.40
6395 6737 4.944317 CCCTTTTCTTACCCTAGCAAAGAG 59.056 45.833 0.00 0.00 32.38 2.85
6431 6773 3.860641 AGCCTTTTTGACACAAAACCTG 58.139 40.909 8.79 3.32 0.00 4.00
6436 6778 2.999355 GTGCAAGCCTTTTTGACACAAA 59.001 40.909 0.00 0.00 36.26 2.83
6507 9775 4.780815 TGGTTGATGGATTAGTTGCTAGG 58.219 43.478 0.00 0.00 0.00 3.02
6520 9788 0.036164 TCCGTGGAGTTGGTTGATGG 59.964 55.000 0.00 0.00 0.00 3.51
6537 9805 6.484977 GGAATTGACCATCTTCTTATGAGTCC 59.515 42.308 0.00 0.00 31.47 3.85
6538 9806 7.050377 TGGAATTGACCATCTTCTTATGAGTC 58.950 38.462 0.00 0.00 34.77 3.36
6611 9884 2.642311 TGGGATGGCTACACTTCTTGAA 59.358 45.455 0.00 0.00 0.00 2.69
6666 9942 7.832769 ACTCTCTGAGGAAATGACTAGTAAAC 58.167 38.462 4.59 0.00 33.35 2.01
6701 9977 1.745653 GGCCACTTCTAGCAATCCAAC 59.254 52.381 0.00 0.00 0.00 3.77
6776 10052 5.360591 GTTCTCGGGAACTGATTATGTGAT 58.639 41.667 21.05 0.00 45.89 3.06
6907 10184 2.844122 ACAGAGGTGTTTTCAAACGC 57.156 45.000 7.34 7.34 45.94 4.84
6920 10197 3.550437 AGCAGCTTTACCATACAGAGG 57.450 47.619 0.00 0.00 0.00 3.69
7035 10315 7.804843 TTGGACTAATGAACTTTCGGTAAAA 57.195 32.000 0.00 0.00 0.00 1.52
7036 10316 7.881232 AGATTGGACTAATGAACTTTCGGTAAA 59.119 33.333 0.00 0.00 0.00 2.01
7076 10356 4.883083 ACGATTCAATATACAGACGCCAT 58.117 39.130 0.00 0.00 0.00 4.40
7097 10377 6.530534 ACGTTGCTAAGATACAACATCAGTAC 59.469 38.462 6.67 0.00 45.08 2.73
7098 10378 6.627243 ACGTTGCTAAGATACAACATCAGTA 58.373 36.000 6.67 0.00 45.08 2.74
7145 10425 6.372659 TGTCTCATTCTGACTAAATCTTTGCC 59.627 38.462 0.00 0.00 35.63 4.52
7151 10431 7.319646 ACTCAGTGTCTCATTCTGACTAAATC 58.680 38.462 0.00 0.00 34.97 2.17
7157 10437 4.626042 ACAACTCAGTGTCTCATTCTGAC 58.374 43.478 0.00 0.00 34.97 3.51
7231 10512 2.032620 CCATACTCTTGCTACGGGACT 58.967 52.381 0.00 0.00 0.00 3.85
7242 10523 1.710809 ACAGTTTGGGGCCATACTCTT 59.289 47.619 4.39 0.00 36.38 2.85
7246 10527 2.578683 CCACAGTTTGGGGCCATAC 58.421 57.895 4.39 0.00 42.54 2.39
7311 10592 3.538634 AAATGCTAGGACCGAGGTTAC 57.461 47.619 3.58 0.00 0.00 2.50
7333 10614 2.794103 CCATGGAGTTGGTCATCACAA 58.206 47.619 5.56 0.00 31.74 3.33
7343 10624 3.643320 TCTGGTATCTAGCCATGGAGTTG 59.357 47.826 18.40 2.56 35.19 3.16


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

AutoCloner maintained by Alex Coulton.