Multiple sequence alignment - TraesCS6A01G409200

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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 TraesCS6A01G409200 chr6A 100.000 4786 0 0 1 4786 613331751 613336536 0.000000e+00 8839.0
1 TraesCS6A01G409200 chr6D 94.302 1246 62 3 2601 3837 467038394 467039639 0.000000e+00 1899.0
2 TraesCS6A01G409200 chr6D 86.977 1674 117 33 958 2593 467036715 467038325 0.000000e+00 1790.0
3 TraesCS6A01G409200 chr6D 92.874 856 38 10 3771 4605 467039754 467040607 0.000000e+00 1221.0
4 TraesCS6A01G409200 chr6D 96.491 171 6 0 1 171 467035747 467035917 2.820000e-72 283.0
5 TraesCS6A01G409200 chr6B 89.658 1112 72 12 3527 4605 712243343 712244444 0.000000e+00 1376.0
6 TraesCS6A01G409200 chr6B 93.579 841 44 5 2603 3433 712242514 712243354 0.000000e+00 1245.0
7 TraesCS6A01G409200 chr6B 82.132 985 64 49 1 934 712239925 712240848 0.000000e+00 741.0
8 TraesCS6A01G409200 chr6B 82.169 830 70 26 1785 2593 712241671 712242443 4.040000e-180 641.0
9 TraesCS6A01G409200 chr6B 88.554 332 23 12 948 1270 712241121 712241446 5.810000e-104 388.0
10 TraesCS6A01G409200 chr6B 86.893 206 12 4 996 1186 699123048 699123253 2.900000e-52 217.0
11 TraesCS6A01G409200 chr6B 91.667 84 1 4 4703 4786 712244568 712244645 1.410000e-20 111.0
12 TraesCS6A01G409200 chr1B 90.244 984 63 8 3508 4472 286299888 286298919 0.000000e+00 1254.0
13 TraesCS6A01G409200 chr1B 87.972 424 37 7 4049 4472 223862628 223863037 5.570000e-134 488.0
14 TraesCS6A01G409200 chr1B 93.182 88 6 0 996 1083 85713692 85713605 3.890000e-26 130.0
15 TraesCS6A01G409200 chr4D 87.851 996 55 19 2272 3234 51866554 51865592 0.000000e+00 1109.0
16 TraesCS6A01G409200 chr3A 91.528 720 50 7 3122 3836 648181990 648182703 0.000000e+00 981.0
17 TraesCS6A01G409200 chr7A 84.592 662 55 24 216 857 579219366 579218732 8.800000e-172 614.0
18 TraesCS6A01G409200 chr7A 89.671 213 12 7 216 427 541268495 541268698 3.670000e-66 263.0
19 TraesCS6A01G409200 chr7A 90.196 51 5 0 174 224 14183706 14183656 3.090000e-07 67.6
20 TraesCS6A01G409200 chr3B 85.467 289 25 5 996 1267 807586326 807586038 7.840000e-73 285.0
21 TraesCS6A01G409200 chr3B 90.196 51 5 0 174 224 517863251 517863201 3.090000e-07 67.6
22 TraesCS6A01G409200 chr2B 85.121 289 26 5 996 1267 780742705 780742993 3.650000e-71 279.0
23 TraesCS6A01G409200 chr2B 85.859 198 20 4 996 1186 73103139 73103335 2.260000e-48 204.0
24 TraesCS6A01G409200 chr4A 84.127 252 23 5 996 1231 111068289 111068039 1.340000e-55 228.0
25 TraesCS6A01G409200 chr4A 90.196 51 5 0 174 224 491513463 491513513 3.090000e-07 67.6
26 TraesCS6A01G409200 chr7B 85.437 206 15 5 996 1186 616528740 616528945 2.920000e-47 200.0
27 TraesCS6A01G409200 chr3D 83.415 205 20 6 2853 3055 608597975 608598167 1.370000e-40 178.0
28 TraesCS6A01G409200 chr3D 92.157 51 4 0 174 224 1591393 1591343 6.640000e-09 73.1
29 TraesCS6A01G409200 chr5A 92.308 52 2 2 174 224 514409444 514409494 6.640000e-09 73.1
30 TraesCS6A01G409200 chr5A 90.196 51 5 0 174 224 555334812 555334862 3.090000e-07 67.6
31 TraesCS6A01G409200 chrUn 90.196 51 5 0 174 224 88054057 88054107 3.090000e-07 67.6
32 TraesCS6A01G409200 chr5D 90.196 51 5 0 174 224 528409828 528409878 3.090000e-07 67.6


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6A01G409200 chr6A 613331751 613336536 4785 False 8839.000000 8839 100.000000 1 4786 1 chr6A.!!$F1 4785
1 TraesCS6A01G409200 chr6D 467035747 467040607 4860 False 1298.250000 1899 92.661000 1 4605 4 chr6D.!!$F1 4604
2 TraesCS6A01G409200 chr6B 712239925 712244645 4720 False 750.333333 1376 87.959833 1 4786 6 chr6B.!!$F2 4785
3 TraesCS6A01G409200 chr1B 286298919 286299888 969 True 1254.000000 1254 90.244000 3508 4472 1 chr1B.!!$R2 964
4 TraesCS6A01G409200 chr4D 51865592 51866554 962 True 1109.000000 1109 87.851000 2272 3234 1 chr4D.!!$R1 962
5 TraesCS6A01G409200 chr3A 648181990 648182703 713 False 981.000000 981 91.528000 3122 3836 1 chr3A.!!$F1 714
6 TraesCS6A01G409200 chr7A 579218732 579219366 634 True 614.000000 614 84.592000 216 857 1 chr7A.!!$R2 641

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
970 1644 0.384230 TTTTTGCTTCGCTTCGCTCG 60.384 50.0 0.00 0.0 0.0 5.03 F
1279 1966 0.037232 GTCCTGGTTAGCGCTCTTGT 60.037 55.0 16.34 0.0 0.0 3.16 F
1534 2236 0.098200 TGTCAGCGTTATCTCGACCG 59.902 55.0 0.00 0.0 0.0 4.79 F
1905 2660 0.237498 GCACCGTTTACTGCTCAACC 59.763 55.0 0.00 0.0 0.0 3.77 F
2823 3649 0.250295 TGTGGAAAAGTCGCTCCCTG 60.250 55.0 0.00 0.0 0.0 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2425 3190 0.037590 ATGCAAGTGGACGCCCTTTA 59.962 50.000 0.00 0.00 0.00 1.85 R
2988 3823 0.679505 GGGCAGCGGTACTCATCATA 59.320 55.000 0.00 0.00 0.00 2.15 R
3352 4190 0.040958 CCACGAACTTCAGCAACAGC 60.041 55.000 0.00 0.00 0.00 4.40 R
3399 4237 2.146342 GTTCATACCGATGATGCAGGG 58.854 52.381 0.00 0.00 41.77 4.45 R
4666 5726 1.191535 TCTAGACATTCACCGGGGTG 58.808 55.000 11.66 11.66 46.64 4.61 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
163 164 1.530771 CCCCCATCTCTGGCTCTTG 59.469 63.158 0.00 0.00 41.64 3.02
171 172 2.435586 CTGGCTCTTGTCTGGCGG 60.436 66.667 0.00 0.00 0.00 6.13
194 212 1.541147 GCTGTATTTGGTTGAGCTGCA 59.459 47.619 1.02 0.00 0.00 4.41
208 243 3.057736 TGAGCTGCAGATTCTGAAAAAGC 60.058 43.478 20.43 17.19 32.44 3.51
209 244 3.155501 AGCTGCAGATTCTGAAAAAGCT 58.844 40.909 20.43 18.85 33.83 3.74
211 246 3.673809 GCTGCAGATTCTGAAAAAGCTTG 59.326 43.478 20.43 0.00 32.44 4.01
241 276 5.567138 ATGCTAATTGACTGTAAAGCACC 57.433 39.130 0.00 0.00 42.23 5.01
326 364 5.571741 CAGTTATGAATGAAGCAGTGCAAAG 59.428 40.000 19.20 0.00 0.00 2.77
387 431 9.435570 AGATGGACCATACAAAATAGTACTACT 57.564 33.333 7.05 0.00 0.00 2.57
388 432 9.477484 GATGGACCATACAAAATAGTACTACTG 57.523 37.037 7.05 5.90 0.00 2.74
482 533 7.424803 TGGTTCATACAAAGAATTTCACACAG 58.575 34.615 0.00 0.00 35.03 3.66
560 614 2.615227 AATAAGGGAGGCCTGCAGCG 62.615 60.000 26.95 2.70 45.17 5.18
652 1001 3.256960 GTGGCACAAGGGGAGGGA 61.257 66.667 13.86 0.00 44.16 4.20
653 1002 2.935481 TGGCACAAGGGGAGGGAG 60.935 66.667 0.00 0.00 31.92 4.30
654 1003 3.732849 GGCACAAGGGGAGGGAGG 61.733 72.222 0.00 0.00 0.00 4.30
655 1004 3.732849 GCACAAGGGGAGGGAGGG 61.733 72.222 0.00 0.00 0.00 4.30
656 1005 2.124996 CACAAGGGGAGGGAGGGA 59.875 66.667 0.00 0.00 0.00 4.20
657 1006 1.997874 CACAAGGGGAGGGAGGGAG 60.998 68.421 0.00 0.00 0.00 4.30
658 1007 2.367512 CAAGGGGAGGGAGGGAGG 60.368 72.222 0.00 0.00 0.00 4.30
659 1008 3.711782 AAGGGGAGGGAGGGAGGG 61.712 72.222 0.00 0.00 0.00 4.30
660 1009 4.761304 AGGGGAGGGAGGGAGGGA 62.761 72.222 0.00 0.00 0.00 4.20
661 1010 4.179599 GGGGAGGGAGGGAGGGAG 62.180 77.778 0.00 0.00 0.00 4.30
662 1011 4.179599 GGGAGGGAGGGAGGGAGG 62.180 77.778 0.00 0.00 0.00 4.30
663 1012 4.179599 GGAGGGAGGGAGGGAGGG 62.180 77.778 0.00 0.00 0.00 4.30
707 1057 1.544703 GAGAGGGAGGTAGGAGGGG 59.455 68.421 0.00 0.00 0.00 4.79
851 1223 2.202676 GGCTTCGGACTCGCTGAG 60.203 66.667 4.36 4.36 36.13 3.35
858 1273 1.886585 GGACTCGCTGAGCTGAAGA 59.113 57.895 1.78 0.00 32.04 2.87
869 1284 2.701780 GCTGAAGAGGGACGAGCGA 61.702 63.158 0.00 0.00 0.00 4.93
870 1285 1.431440 CTGAAGAGGGACGAGCGAG 59.569 63.158 0.00 0.00 0.00 5.03
925 1340 6.294508 CGGCCTCTTTTTCCTGATTCTTTTTA 60.295 38.462 0.00 0.00 0.00 1.52
926 1341 6.868864 GGCCTCTTTTTCCTGATTCTTTTTAC 59.131 38.462 0.00 0.00 0.00 2.01
927 1342 7.255977 GGCCTCTTTTTCCTGATTCTTTTTACT 60.256 37.037 0.00 0.00 0.00 2.24
968 1642 3.552604 TTATTTTTGCTTCGCTTCGCT 57.447 38.095 0.00 0.00 0.00 4.93
969 1643 1.969103 ATTTTTGCTTCGCTTCGCTC 58.031 45.000 0.00 0.00 0.00 5.03
970 1644 0.384230 TTTTTGCTTCGCTTCGCTCG 60.384 50.000 0.00 0.00 0.00 5.03
971 1645 2.764251 TTTTGCTTCGCTTCGCTCGC 62.764 55.000 0.00 0.00 0.00 5.03
972 1646 4.724602 TGCTTCGCTTCGCTCGCT 62.725 61.111 0.00 0.00 0.00 4.93
973 1647 4.202196 GCTTCGCTTCGCTCGCTG 62.202 66.667 0.00 0.00 0.00 5.18
974 1648 3.549150 CTTCGCTTCGCTCGCTGG 61.549 66.667 0.00 0.00 0.00 4.85
975 1649 3.971453 CTTCGCTTCGCTCGCTGGA 62.971 63.158 0.00 0.00 0.00 3.86
976 1650 3.971453 TTCGCTTCGCTCGCTGGAG 62.971 63.158 0.00 0.00 43.46 3.86
1009 1689 1.821272 GCAGATCGGAGATGGAGAGGA 60.821 57.143 0.00 0.00 45.12 3.71
1244 1931 4.386100 AGGCCCCTCCCCATTCCA 62.386 66.667 0.00 0.00 34.51 3.53
1275 1962 2.202756 CCGTCCTGGTTAGCGCTC 60.203 66.667 16.34 0.00 0.00 5.03
1276 1963 2.711922 CCGTCCTGGTTAGCGCTCT 61.712 63.158 16.34 0.00 0.00 4.09
1279 1966 0.037232 GTCCTGGTTAGCGCTCTTGT 60.037 55.000 16.34 0.00 0.00 3.16
1281 1968 0.247736 CCTGGTTAGCGCTCTTGTCT 59.752 55.000 16.34 0.00 0.00 3.41
1284 1971 0.670546 GGTTAGCGCTCTTGTCTGCA 60.671 55.000 16.34 0.00 0.00 4.41
1288 1975 1.958205 GCGCTCTTGTCTGCACTGT 60.958 57.895 0.00 0.00 0.00 3.55
1295 1985 0.249447 TTGTCTGCACTGTCTGACCG 60.249 55.000 5.17 1.02 35.06 4.79
1312 2002 0.098728 CCGTGAATGGCATTTCGTCC 59.901 55.000 25.05 11.60 0.00 4.79
1323 2013 3.453424 GCATTTCGTCCAACACCTTTTT 58.547 40.909 0.00 0.00 0.00 1.94
1328 2018 0.317519 GTCCAACACCTTTTTCGCCG 60.318 55.000 0.00 0.00 0.00 6.46
1329 2019 1.007849 CCAACACCTTTTTCGCCGG 60.008 57.895 0.00 0.00 0.00 6.13
1364 2066 0.179215 GCACTGCGAATGGTTTCTCG 60.179 55.000 0.00 0.00 38.11 4.04
1396 2098 3.200593 GCGCCTGCAGTCCATCTG 61.201 66.667 13.81 0.00 46.12 2.90
1437 2139 2.156343 GGCAAATCCGTAGCTAGAGG 57.844 55.000 8.52 8.52 0.00 3.69
1439 2141 1.202533 GCAAATCCGTAGCTAGAGGCA 60.203 52.381 9.71 1.52 44.79 4.75
1480 2182 5.822519 ACTGCTGTTGATTTACACTTCTTCA 59.177 36.000 0.00 0.00 0.00 3.02
1484 2186 4.024387 TGTTGATTTACACTTCTTCACGCC 60.024 41.667 0.00 0.00 0.00 5.68
1490 2192 0.601046 CACTTCTTCACGCCTCAGCA 60.601 55.000 0.00 0.00 39.83 4.41
1493 2195 3.123620 CTTCACGCCTCAGCAGCC 61.124 66.667 0.00 0.00 39.83 4.85
1499 2201 2.188994 GCCTCAGCAGCCCACTAG 59.811 66.667 0.00 0.00 39.53 2.57
1534 2236 0.098200 TGTCAGCGTTATCTCGACCG 59.902 55.000 0.00 0.00 0.00 4.79
1535 2237 1.063649 TCAGCGTTATCTCGACCGC 59.936 57.895 0.00 0.00 46.07 5.68
1537 2239 3.022914 GCGTTATCTCGACCGCGG 61.023 66.667 26.86 26.86 36.53 6.46
1538 2240 2.353145 CGTTATCTCGACCGCGGG 60.353 66.667 31.76 13.23 40.06 6.13
1540 2242 4.260355 TTATCTCGACCGCGGGCG 62.260 66.667 46.68 46.68 38.08 6.13
1563 2265 3.181967 CGGCTCAAGTTCTCGGCG 61.182 66.667 0.00 0.00 39.00 6.46
1570 2272 3.941657 AAGTTCTCGGCGCCTCTGC 62.942 63.158 26.68 10.72 0.00 4.26
1572 2274 2.754254 TTCTCGGCGCCTCTGCTA 60.754 61.111 26.68 1.43 34.43 3.49
1598 2313 3.833545 TTGCAAACAACGTTGTACAGT 57.166 38.095 32.47 15.63 41.31 3.55
1599 2314 4.941325 TTGCAAACAACGTTGTACAGTA 57.059 36.364 32.47 20.91 41.31 2.74
1600 2315 4.261736 TGCAAACAACGTTGTACAGTAC 57.738 40.909 32.47 18.78 41.31 2.73
1612 2327 2.093181 TGTACAGTACCATGGATGCCAC 60.093 50.000 21.47 14.60 35.80 5.01
1614 2329 1.354031 ACAGTACCATGGATGCCACAA 59.646 47.619 21.47 0.00 35.80 3.33
1615 2330 2.019249 CAGTACCATGGATGCCACAAG 58.981 52.381 21.47 1.81 35.80 3.16
1616 2331 0.740737 GTACCATGGATGCCACAAGC 59.259 55.000 21.47 0.00 44.14 4.01
1617 2332 0.625316 TACCATGGATGCCACAAGCT 59.375 50.000 21.47 0.00 44.23 3.74
1618 2333 0.968901 ACCATGGATGCCACAAGCTG 60.969 55.000 21.47 0.00 44.23 4.24
1626 2341 0.472044 TGCCACAAGCTGGTCAGTTA 59.528 50.000 0.00 0.00 42.99 2.24
1646 2364 1.818674 ACCATGAATTCGGTCTTTGCC 59.181 47.619 0.04 0.00 0.00 4.52
1651 2369 2.552315 TGAATTCGGTCTTTGCCAAGTC 59.448 45.455 0.04 0.00 0.00 3.01
1665 2383 2.870411 GCCAAGTCTGTAGAAACGTTGT 59.130 45.455 0.00 0.00 0.00 3.32
1679 2397 6.766429 AGAAACGTTGTCTTTAGGTTCCTAT 58.234 36.000 0.00 0.00 0.00 2.57
1680 2398 7.899973 AGAAACGTTGTCTTTAGGTTCCTATA 58.100 34.615 0.00 0.00 0.00 1.31
1682 2400 8.907222 AAACGTTGTCTTTAGGTTCCTATAAA 57.093 30.769 0.00 0.00 0.00 1.40
1686 2413 8.762426 CGTTGTCTTTAGGTTCCTATAAATAGC 58.238 37.037 0.00 0.00 0.00 2.97
1689 2416 9.209048 TGTCTTTAGGTTCCTATAAATAGCTGA 57.791 33.333 0.00 0.00 0.00 4.26
1742 2469 5.957798 CTGTGATGCAGGATTGTAATTTGT 58.042 37.500 0.00 0.00 41.42 2.83
1745 2472 6.127758 TGTGATGCAGGATTGTAATTTGTACC 60.128 38.462 0.00 0.00 0.00 3.34
1872 2610 3.490439 TTCTCTGCCAACAGTGATTCA 57.510 42.857 0.00 0.00 43.80 2.57
1896 2651 1.020333 TACATGCCCGCACCGTTTAC 61.020 55.000 0.00 0.00 0.00 2.01
1898 2653 2.038269 ATGCCCGCACCGTTTACTG 61.038 57.895 0.00 0.00 0.00 2.74
1905 2660 0.237498 GCACCGTTTACTGCTCAACC 59.763 55.000 0.00 0.00 0.00 3.77
1906 2661 1.588674 CACCGTTTACTGCTCAACCA 58.411 50.000 0.00 0.00 0.00 3.67
1907 2662 2.151202 CACCGTTTACTGCTCAACCAT 58.849 47.619 0.00 0.00 0.00 3.55
1915 2670 3.928005 ACTGCTCAACCATCATCAGAT 57.072 42.857 0.00 0.00 33.87 2.90
1955 2715 6.029607 TCATTTCTGTGCTCGCATAATTTTC 58.970 36.000 0.00 0.00 0.00 2.29
1957 2718 3.342719 TCTGTGCTCGCATAATTTTCCA 58.657 40.909 0.00 0.00 0.00 3.53
1963 2724 5.004726 GTGCTCGCATAATTTTCCATTGTTC 59.995 40.000 0.00 0.00 0.00 3.18
1985 2746 4.156556 TCCTTTCATACTTGAATGCAGTGC 59.843 41.667 8.58 8.58 41.38 4.40
2039 2804 0.904865 TCCAGTCTGGCAGAATCCGT 60.905 55.000 20.62 0.00 37.47 4.69
2055 2820 7.017645 CAGAATCCGTAACTGTTTCATCAAAG 58.982 38.462 0.00 0.00 0.00 2.77
2056 2821 6.934645 AGAATCCGTAACTGTTTCATCAAAGA 59.065 34.615 0.00 0.00 0.00 2.52
2057 2822 7.607991 AGAATCCGTAACTGTTTCATCAAAGAT 59.392 33.333 0.00 0.00 0.00 2.40
2058 2823 6.480524 TCCGTAACTGTTTCATCAAAGATG 57.519 37.500 0.00 0.62 0.00 2.90
2059 2824 6.227522 TCCGTAACTGTTTCATCAAAGATGA 58.772 36.000 5.63 5.63 40.57 2.92
2060 2825 6.708502 TCCGTAACTGTTTCATCAAAGATGAA 59.291 34.615 16.14 16.14 39.49 2.57
2061 2826 7.227711 TCCGTAACTGTTTCATCAAAGATGAAA 59.772 33.333 23.79 23.79 43.34 2.69
2136 2901 2.254152 TGCTGTCCTCTAACTGGGAT 57.746 50.000 0.00 0.00 33.89 3.85
2137 2902 3.398318 TGCTGTCCTCTAACTGGGATA 57.602 47.619 0.00 0.00 33.89 2.59
2258 3023 2.708216 TGTGCCTTCTTCACTTGTCA 57.292 45.000 0.00 0.00 35.58 3.58
2270 3035 3.213506 TCACTTGTCAATTGGTCACTGG 58.786 45.455 5.42 2.38 0.00 4.00
2296 3061 3.003480 CGGGAATGACAGGACTCTTTTC 58.997 50.000 0.00 0.00 0.00 2.29
2334 3099 5.126222 CAGATCAAGGTAGAGCACTCTTGTA 59.874 44.000 5.33 1.94 40.93 2.41
2376 3141 5.919755 TCGTACTGTTATATTTGGCATCCA 58.080 37.500 0.00 0.00 0.00 3.41
2379 3144 3.882888 ACTGTTATATTTGGCATCCACCG 59.117 43.478 0.00 0.00 30.78 4.94
2380 3145 4.133820 CTGTTATATTTGGCATCCACCGA 58.866 43.478 0.00 0.00 30.78 4.69
2383 3148 5.009510 TGTTATATTTGGCATCCACCGATTG 59.990 40.000 0.00 0.00 30.78 2.67
2384 3149 0.461135 ATTTGGCATCCACCGATTGC 59.539 50.000 0.00 0.00 30.78 3.56
2418 3183 2.033141 AGCATGCGTCCACTTGCT 59.967 55.556 13.01 0.00 43.83 3.91
2422 3187 1.869342 GCATGCGTCCACTTGCTTTTT 60.869 47.619 0.00 0.00 37.64 1.94
2441 3206 3.719173 TTTTTAAAGGGCGTCCACTTG 57.281 42.857 9.71 0.00 34.83 3.16
2579 3345 5.814705 GCTGATTGCCTGATCCATAGTATAC 59.185 44.000 0.00 0.00 35.15 1.47
2580 3346 5.965922 TGATTGCCTGATCCATAGTATACG 58.034 41.667 0.00 0.00 0.00 3.06
2581 3347 5.480422 TGATTGCCTGATCCATAGTATACGT 59.520 40.000 0.00 0.00 0.00 3.57
2582 3348 6.661805 TGATTGCCTGATCCATAGTATACGTA 59.338 38.462 0.00 0.00 0.00 3.57
2660 3486 6.126863 ACAGTTTATGAGGGAGTGAAATCA 57.873 37.500 0.00 0.00 0.00 2.57
2774 3600 3.626670 GCTATGCAATCTTGAGAAGCAGT 59.373 43.478 14.09 7.66 40.62 4.40
2823 3649 0.250295 TGTGGAAAAGTCGCTCCCTG 60.250 55.000 0.00 0.00 0.00 4.45
3088 3923 7.885297 TCAGGTATGAAAAAGGTGAATTCAAG 58.115 34.615 10.35 0.00 36.72 3.02
3105 3940 8.869109 TGAATTCAAGGTGATTTTATGGAGTTT 58.131 29.630 5.45 0.00 0.00 2.66
3108 3943 7.938140 TCAAGGTGATTTTATGGAGTTTAGG 57.062 36.000 0.00 0.00 0.00 2.69
3176 4011 7.833786 TGAAATCTGCTCTTTCTAAAATGCAT 58.166 30.769 0.00 0.00 34.43 3.96
3179 4014 6.822667 TCTGCTCTTTCTAAAATGCATTCA 57.177 33.333 13.38 2.90 0.00 2.57
3180 4015 6.849502 TCTGCTCTTTCTAAAATGCATTCAG 58.150 36.000 13.38 12.92 0.00 3.02
3269 4107 4.488126 TCAATTGCACTGACACTAAAGC 57.512 40.909 0.00 0.00 0.00 3.51
3274 4112 3.213506 TGCACTGACACTAAAGCACATT 58.786 40.909 0.00 0.00 0.00 2.71
3352 4190 0.252479 AAGACTGCAGATGGCTGAGG 59.748 55.000 23.35 0.00 45.17 3.86
3399 4237 6.595772 AGCAAGTCGATAATCAAATCTGTC 57.404 37.500 0.00 0.00 0.00 3.51
3873 4897 5.382664 TCTTTTACCTGACAAAGAACCCT 57.617 39.130 0.00 0.00 36.33 4.34
4045 5069 2.234908 GTCTGTACTTCTGGTCTGCCAT 59.765 50.000 0.00 0.00 45.05 4.40
4080 5124 7.627298 ATGAAGAATCTTTTCACTCTGATGG 57.373 36.000 0.00 0.00 37.38 3.51
4187 5234 0.106708 TGACCCTGTTCTGTGTGAGC 59.893 55.000 0.00 0.00 0.00 4.26
4311 5366 1.241165 CAAGCAGACAGTGGATGCAA 58.759 50.000 19.99 0.00 42.45 4.08
4404 5459 1.228245 TTGTCTTGCAGAGTGGCCC 60.228 57.895 0.00 0.00 0.00 5.80
4405 5460 1.993701 TTGTCTTGCAGAGTGGCCCA 61.994 55.000 0.00 0.00 0.00 5.36
4419 5474 0.323451 GGCCCAGGGACAAAGGTAAG 60.323 60.000 10.89 0.00 0.00 2.34
4513 5573 4.080919 TGTTACTGAAGGCTGTAGCATGAT 60.081 41.667 6.18 0.00 44.36 2.45
4554 5614 1.679139 CTTTTGACCACACTGCAGGA 58.321 50.000 19.93 0.00 0.00 3.86
4560 5620 0.767375 ACCACACTGCAGGAGAACAT 59.233 50.000 19.93 0.00 0.00 2.71
4576 5636 1.825105 ACATAGATGGCATGGGTCCT 58.175 50.000 3.81 0.00 0.00 3.85
4596 5656 1.566018 GCCACGCAGGTAACACTCAC 61.566 60.000 0.00 0.00 40.61 3.51
4605 5665 3.195610 CAGGTAACACTCACATGCTCCTA 59.804 47.826 0.00 0.00 41.41 2.94
4606 5666 4.033709 AGGTAACACTCACATGCTCCTAT 58.966 43.478 0.00 0.00 41.41 2.57
4609 5669 6.156256 AGGTAACACTCACATGCTCCTATAAA 59.844 38.462 0.00 0.00 41.41 1.40
4610 5670 6.258068 GGTAACACTCACATGCTCCTATAAAC 59.742 42.308 0.00 0.00 0.00 2.01
4612 5672 4.130118 CACTCACATGCTCCTATAAACCC 58.870 47.826 0.00 0.00 0.00 4.11
4613 5673 4.040755 ACTCACATGCTCCTATAAACCCT 58.959 43.478 0.00 0.00 0.00 4.34
4614 5674 4.475016 ACTCACATGCTCCTATAAACCCTT 59.525 41.667 0.00 0.00 0.00 3.95
4615 5675 5.044846 ACTCACATGCTCCTATAAACCCTTT 60.045 40.000 0.00 0.00 0.00 3.11
4616 5676 5.437060 TCACATGCTCCTATAAACCCTTTC 58.563 41.667 0.00 0.00 0.00 2.62
4617 5677 5.045213 TCACATGCTCCTATAAACCCTTTCA 60.045 40.000 0.00 0.00 0.00 2.69
4618 5678 5.652014 CACATGCTCCTATAAACCCTTTCAA 59.348 40.000 0.00 0.00 0.00 2.69
4620 5680 6.152831 ACATGCTCCTATAAACCCTTTCAAAC 59.847 38.462 0.00 0.00 0.00 2.93
4621 5681 5.887754 TGCTCCTATAAACCCTTTCAAACT 58.112 37.500 0.00 0.00 0.00 2.66
4622 5682 5.710099 TGCTCCTATAAACCCTTTCAAACTG 59.290 40.000 0.00 0.00 0.00 3.16
4623 5683 5.393135 GCTCCTATAAACCCTTTCAAACTGC 60.393 44.000 0.00 0.00 0.00 4.40
4627 5687 6.152661 CCTATAAACCCTTTCAAACTGCATGA 59.847 38.462 0.00 0.00 0.00 3.07
4628 5688 4.961438 AAACCCTTTCAAACTGCATGAT 57.039 36.364 0.00 0.00 0.00 2.45
4629 5689 4.525912 AACCCTTTCAAACTGCATGATC 57.474 40.909 0.00 0.00 0.00 2.92
4630 5690 3.499338 ACCCTTTCAAACTGCATGATCA 58.501 40.909 0.00 0.00 0.00 2.92
4631 5691 4.091549 ACCCTTTCAAACTGCATGATCAT 58.908 39.130 1.18 1.18 0.00 2.45
4632 5692 5.263599 ACCCTTTCAAACTGCATGATCATA 58.736 37.500 8.15 0.00 0.00 2.15
4633 5693 5.895534 ACCCTTTCAAACTGCATGATCATAT 59.104 36.000 8.15 0.00 0.00 1.78
4634 5694 6.381994 ACCCTTTCAAACTGCATGATCATATT 59.618 34.615 8.15 0.00 0.00 1.28
4635 5695 7.560991 ACCCTTTCAAACTGCATGATCATATTA 59.439 33.333 8.15 0.00 0.00 0.98
4636 5696 8.582437 CCCTTTCAAACTGCATGATCATATTAT 58.418 33.333 8.15 0.00 0.00 1.28
4637 5697 9.406828 CCTTTCAAACTGCATGATCATATTATG 57.593 33.333 8.15 0.00 0.00 1.90
4646 5706 8.263940 TGCATGATCATATTATGTCACTCATG 57.736 34.615 8.15 21.09 40.89 3.07
4648 5708 6.956299 TGATCATATTATGTCACTCATGCG 57.044 37.500 3.67 0.00 37.91 4.73
4657 5717 1.256376 GTCACTCATGCGTATGAAGCG 59.744 52.381 17.11 8.46 42.48 4.68
4658 5718 0.578683 CACTCATGCGTATGAAGCGG 59.421 55.000 17.11 8.12 42.48 5.52
4660 5720 1.135046 CTCATGCGTATGAAGCGGAG 58.865 55.000 17.11 0.95 42.48 4.63
4665 5725 2.627945 TGCGTATGAAGCGGAGAAAAT 58.372 42.857 0.00 0.00 37.44 1.82
4666 5726 2.607635 TGCGTATGAAGCGGAGAAAATC 59.392 45.455 0.00 0.00 37.44 2.17
4668 5728 3.544244 GCGTATGAAGCGGAGAAAATCAC 60.544 47.826 0.00 0.00 0.00 3.06
4669 5729 3.001330 CGTATGAAGCGGAGAAAATCACC 59.999 47.826 0.00 0.00 0.00 4.02
4670 5730 1.821216 TGAAGCGGAGAAAATCACCC 58.179 50.000 0.00 0.00 0.00 4.61
4671 5731 1.095600 GAAGCGGAGAAAATCACCCC 58.904 55.000 0.00 0.00 0.00 4.95
4672 5732 0.676782 AAGCGGAGAAAATCACCCCG 60.677 55.000 0.00 0.00 42.74 5.73
4689 5759 2.434336 CCCCGGTGAATGTCTAGATTCA 59.566 50.000 0.00 4.92 39.52 2.57
4692 5762 5.221641 CCCCGGTGAATGTCTAGATTCATAA 60.222 44.000 11.06 0.00 42.78 1.90
4693 5763 6.467677 CCCGGTGAATGTCTAGATTCATAAT 58.532 40.000 11.06 0.00 42.78 1.28
4694 5764 6.936900 CCCGGTGAATGTCTAGATTCATAATT 59.063 38.462 11.06 0.00 42.78 1.40
4695 5765 7.118390 CCCGGTGAATGTCTAGATTCATAATTC 59.882 40.741 11.06 7.70 42.78 2.17
4696 5766 7.118390 CCGGTGAATGTCTAGATTCATAATTCC 59.882 40.741 11.06 7.13 42.78 3.01
4697 5767 7.657354 CGGTGAATGTCTAGATTCATAATTCCA 59.343 37.037 11.06 0.00 42.78 3.53
4699 5769 9.770097 GTGAATGTCTAGATTCATAATTCCAGA 57.230 33.333 11.06 0.00 42.78 3.86
4734 5829 1.505353 GCAATCTGTGTGAGGCAGC 59.495 57.895 0.00 0.00 34.21 5.25
4764 5859 3.225548 CGTTCATTCATTGTCAACACCG 58.774 45.455 0.00 0.00 0.00 4.94
4767 5862 2.483877 TCATTCATTGTCAACACCGAGC 59.516 45.455 0.00 0.00 0.00 5.03
4768 5863 1.960417 TTCATTGTCAACACCGAGCA 58.040 45.000 0.00 0.00 0.00 4.26
4769 5864 1.511850 TCATTGTCAACACCGAGCAG 58.488 50.000 0.00 0.00 0.00 4.24
4770 5865 0.110056 CATTGTCAACACCGAGCAGC 60.110 55.000 0.00 0.00 0.00 5.25
4771 5866 0.534877 ATTGTCAACACCGAGCAGCA 60.535 50.000 0.00 0.00 0.00 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
163 164 4.530857 ATACAGCCGCCGCCAGAC 62.531 66.667 0.00 0.00 34.57 3.51
171 172 0.179163 GCTCAACCAAATACAGCCGC 60.179 55.000 0.00 0.00 0.00 6.53
194 212 6.455360 TTCACACAAGCTTTTTCAGAATCT 57.545 33.333 0.00 0.00 0.00 2.40
208 243 6.919662 ACAGTCAATTAGCATTTTCACACAAG 59.080 34.615 0.00 0.00 0.00 3.16
209 244 6.804677 ACAGTCAATTAGCATTTTCACACAA 58.195 32.000 0.00 0.00 0.00 3.33
211 246 8.795786 TTTACAGTCAATTAGCATTTTCACAC 57.204 30.769 0.00 0.00 0.00 3.82
241 276 2.724690 GGCAATGTAGTAGTACGCATCG 59.275 50.000 11.83 4.80 30.95 3.84
246 281 1.406539 ACCGGGCAATGTAGTAGTACG 59.593 52.381 6.32 0.00 30.95 3.67
326 364 7.335171 TGAAGCTGTATGTATGATGCCATTATC 59.665 37.037 0.00 0.00 34.31 1.75
414 458 4.333372 TGCTTGTATGCATGACATGTACAG 59.667 41.667 16.62 11.87 40.06 2.74
416 460 4.880886 TGCTTGTATGCATGACATGTAC 57.119 40.909 16.62 12.10 40.06 2.90
417 461 4.201940 GCTTGCTTGTATGCATGACATGTA 60.202 41.667 16.62 12.88 42.96 2.29
418 462 3.428452 GCTTGCTTGTATGCATGACATGT 60.428 43.478 16.62 0.00 42.96 3.21
482 533 2.373540 TGTATTGGTCAGTACGTGGC 57.626 50.000 0.00 0.00 0.00 5.01
542 596 2.922234 GCTGCAGGCCTCCCTTAT 59.078 61.111 17.12 0.00 40.33 1.73
626 702 1.152984 CTTGTGCCACTGTCACCCA 60.153 57.895 0.00 0.00 33.71 4.51
652 1001 3.039526 CTCCCTCCCTCCCTCCCT 61.040 72.222 0.00 0.00 0.00 4.20
653 1002 4.179599 CCTCCCTCCCTCCCTCCC 62.180 77.778 0.00 0.00 0.00 4.30
654 1003 4.179599 CCCTCCCTCCCTCCCTCC 62.180 77.778 0.00 0.00 0.00 4.30
655 1004 1.979389 ATTCCCTCCCTCCCTCCCTC 61.979 65.000 0.00 0.00 0.00 4.30
656 1005 1.954994 ATTCCCTCCCTCCCTCCCT 60.955 63.158 0.00 0.00 0.00 4.20
657 1006 1.772156 CATTCCCTCCCTCCCTCCC 60.772 68.421 0.00 0.00 0.00 4.30
658 1007 1.772156 CCATTCCCTCCCTCCCTCC 60.772 68.421 0.00 0.00 0.00 4.30
659 1008 1.772156 CCCATTCCCTCCCTCCCTC 60.772 68.421 0.00 0.00 0.00 4.30
660 1009 2.378522 CCCATTCCCTCCCTCCCT 59.621 66.667 0.00 0.00 0.00 4.20
661 1010 2.778717 CCCCATTCCCTCCCTCCC 60.779 72.222 0.00 0.00 0.00 4.30
662 1011 1.772156 CTCCCCATTCCCTCCCTCC 60.772 68.421 0.00 0.00 0.00 4.30
663 1012 1.772156 CCTCCCCATTCCCTCCCTC 60.772 68.421 0.00 0.00 0.00 4.30
851 1223 2.202676 CGCTCGTCCCTCTTCAGC 60.203 66.667 0.00 0.00 0.00 4.26
899 1314 1.133216 GAATCAGGAAAAAGAGGCCGC 59.867 52.381 0.00 0.00 0.00 6.53
900 1315 2.716217 AGAATCAGGAAAAAGAGGCCG 58.284 47.619 0.00 0.00 0.00 6.13
901 1316 5.474578 AAAAGAATCAGGAAAAAGAGGCC 57.525 39.130 0.00 0.00 0.00 5.19
902 1317 7.661968 AGTAAAAAGAATCAGGAAAAAGAGGC 58.338 34.615 0.00 0.00 0.00 4.70
971 1645 3.114616 CAACTGCCGACGCTCCAG 61.115 66.667 6.79 6.79 35.36 3.86
972 1646 4.680237 CCAACTGCCGACGCTCCA 62.680 66.667 0.00 0.00 35.36 3.86
1275 1962 1.506493 GGTCAGACAGTGCAGACAAG 58.494 55.000 2.17 0.00 32.79 3.16
1276 1963 0.249447 CGGTCAGACAGTGCAGACAA 60.249 55.000 2.17 0.00 32.79 3.18
1279 1966 1.106944 TCACGGTCAGACAGTGCAGA 61.107 55.000 24.49 8.88 42.66 4.26
1281 1968 0.392706 ATTCACGGTCAGACAGTGCA 59.607 50.000 24.49 17.00 42.66 4.57
1284 1971 0.320771 GCCATTCACGGTCAGACAGT 60.321 55.000 2.17 0.89 0.00 3.55
1288 1975 2.083774 GAAATGCCATTCACGGTCAGA 58.916 47.619 0.00 0.00 0.00 3.27
1295 1985 2.030363 TGTTGGACGAAATGCCATTCAC 60.030 45.455 0.00 0.00 33.46 3.18
1312 2002 0.040425 CTCCGGCGAAAAAGGTGTTG 60.040 55.000 9.30 0.00 0.00 3.33
1389 2091 0.621280 TCTGGGCATGGACAGATGGA 60.621 55.000 0.00 0.00 38.71 3.41
1390 2092 0.465097 GTCTGGGCATGGACAGATGG 60.465 60.000 0.00 0.00 44.65 3.51
1391 2093 0.812811 CGTCTGGGCATGGACAGATG 60.813 60.000 0.00 0.00 44.65 2.90
1392 2094 1.524002 CGTCTGGGCATGGACAGAT 59.476 57.895 0.00 0.00 44.65 2.90
1393 2095 2.659063 CCGTCTGGGCATGGACAGA 61.659 63.158 0.00 0.00 41.13 3.41
1394 2096 2.124983 CCGTCTGGGCATGGACAG 60.125 66.667 0.00 0.00 36.07 3.51
1418 2120 1.874320 GCCTCTAGCTACGGATTTGCC 60.874 57.143 8.23 0.00 38.99 4.52
1454 2156 5.368145 AGAAGTGTAAATCAACAGCAGTGA 58.632 37.500 0.00 0.00 0.00 3.41
1469 2171 1.336887 GCTGAGGCGTGAAGAAGTGTA 60.337 52.381 0.00 0.00 0.00 2.90
1484 2186 0.107312 AATGCTAGTGGGCTGCTGAG 60.107 55.000 0.00 0.00 0.00 3.35
1490 2192 1.209019 CAGACTGAATGCTAGTGGGCT 59.791 52.381 0.00 0.00 0.00 5.19
1493 2195 1.065926 TGCCAGACTGAATGCTAGTGG 60.066 52.381 3.32 0.00 0.00 4.00
1563 2265 1.746991 GCAACCCTGTAGCAGAGGC 60.747 63.158 0.00 0.00 41.61 4.70
1596 2311 1.683011 GCTTGTGGCATCCATGGTACT 60.683 52.381 12.58 0.00 41.35 2.73
1597 2312 0.740737 GCTTGTGGCATCCATGGTAC 59.259 55.000 12.58 2.11 41.35 3.34
1598 2313 0.625316 AGCTTGTGGCATCCATGGTA 59.375 50.000 12.58 0.00 44.79 3.25
1599 2314 0.968901 CAGCTTGTGGCATCCATGGT 60.969 55.000 12.58 0.00 44.79 3.55
1600 2315 1.672854 CCAGCTTGTGGCATCCATGG 61.673 60.000 4.97 4.97 44.79 3.66
1626 2341 1.818674 GGCAAAGACCGAATTCATGGT 59.181 47.619 6.22 5.47 42.42 3.55
1646 2364 5.968387 AAGACAACGTTTCTACAGACTTG 57.032 39.130 0.00 0.00 0.00 3.16
1651 2369 6.073927 GGAACCTAAAGACAACGTTTCTACAG 60.074 42.308 0.00 6.26 0.00 2.74
1665 2383 9.435570 AGTCAGCTATTTATAGGAACCTAAAGA 57.564 33.333 4.63 0.00 31.73 2.52
1682 2400 5.366768 TCCCAGCTACAAAATAGTCAGCTAT 59.633 40.000 0.00 0.00 40.50 2.97
1686 2413 5.344743 TCTCCCAGCTACAAAATAGTCAG 57.655 43.478 0.00 0.00 0.00 3.51
1689 2416 4.935808 CGTTTCTCCCAGCTACAAAATAGT 59.064 41.667 0.00 0.00 0.00 2.12
1695 2422 1.053424 ACCGTTTCTCCCAGCTACAA 58.947 50.000 0.00 0.00 0.00 2.41
1735 2462 4.250464 CTCAGGCGAAGTGGTACAAATTA 58.750 43.478 0.00 0.00 44.16 1.40
1742 2469 2.103432 TGAAAACTCAGGCGAAGTGGTA 59.897 45.455 0.00 0.00 0.00 3.25
1745 2472 1.070577 CGTGAAAACTCAGGCGAAGTG 60.071 52.381 0.00 0.00 0.00 3.16
1872 2610 1.095228 CGGTGCGGGCATGTAAGAAT 61.095 55.000 0.00 0.00 0.00 2.40
1896 2651 2.801111 CGATCTGATGATGGTTGAGCAG 59.199 50.000 0.00 0.00 32.19 4.24
1898 2653 2.831333 ACGATCTGATGATGGTTGAGC 58.169 47.619 0.00 0.00 38.23 4.26
1905 2660 6.038714 TCTCCGGATATTACGATCTGATGATG 59.961 42.308 3.57 0.00 34.59 3.07
1906 2661 6.122964 TCTCCGGATATTACGATCTGATGAT 58.877 40.000 3.57 0.00 34.59 2.45
1907 2662 5.497474 TCTCCGGATATTACGATCTGATGA 58.503 41.667 3.57 0.00 34.59 2.92
1915 2670 6.208797 ACAGAAATGATCTCCGGATATTACGA 59.791 38.462 3.57 0.00 35.73 3.43
2055 2820 8.723942 AGATGAGTAATACACAAGGTTTCATC 57.276 34.615 6.81 6.81 0.00 2.92
2056 2821 8.543774 AGAGATGAGTAATACACAAGGTTTCAT 58.456 33.333 0.00 0.00 0.00 2.57
2057 2822 7.907389 AGAGATGAGTAATACACAAGGTTTCA 58.093 34.615 0.00 0.00 0.00 2.69
2058 2823 8.660373 CAAGAGATGAGTAATACACAAGGTTTC 58.340 37.037 0.00 0.00 0.00 2.78
2059 2824 7.119846 GCAAGAGATGAGTAATACACAAGGTTT 59.880 37.037 0.00 0.00 0.00 3.27
2060 2825 6.595716 GCAAGAGATGAGTAATACACAAGGTT 59.404 38.462 0.00 0.00 0.00 3.50
2061 2826 6.070538 AGCAAGAGATGAGTAATACACAAGGT 60.071 38.462 0.00 0.00 0.00 3.50
2062 2827 6.344500 AGCAAGAGATGAGTAATACACAAGG 58.656 40.000 0.00 0.00 0.00 3.61
2136 2901 4.695455 GCTGAACAGGACAAGCATTAACTA 59.305 41.667 3.99 0.00 0.00 2.24
2137 2902 3.503748 GCTGAACAGGACAAGCATTAACT 59.496 43.478 3.99 0.00 0.00 2.24
2258 3023 0.609131 CCGAAGCCCAGTGACCAATT 60.609 55.000 0.00 0.00 0.00 2.32
2270 3035 0.744771 GTCCTGTCATTCCCGAAGCC 60.745 60.000 0.00 0.00 0.00 4.35
2296 3061 5.057819 CCTTGATCTGTGGAGAGATGAATG 58.942 45.833 0.00 0.00 32.57 2.67
2376 3141 1.340211 TGTAAATTCGGGGCAATCGGT 60.340 47.619 0.00 0.00 0.00 4.69
2379 3144 2.165437 TGCTTGTAAATTCGGGGCAATC 59.835 45.455 0.00 0.00 0.00 2.67
2380 3145 2.175202 TGCTTGTAAATTCGGGGCAAT 58.825 42.857 0.00 0.00 0.00 3.56
2383 3148 1.735700 GCTTGCTTGTAAATTCGGGGC 60.736 52.381 0.00 0.00 0.00 5.80
2384 3149 1.543802 TGCTTGCTTGTAAATTCGGGG 59.456 47.619 0.00 0.00 0.00 5.73
2422 3187 1.338655 GCAAGTGGACGCCCTTTAAAA 59.661 47.619 0.00 0.00 0.00 1.52
2423 3188 0.955905 GCAAGTGGACGCCCTTTAAA 59.044 50.000 0.00 0.00 0.00 1.52
2424 3189 0.179015 TGCAAGTGGACGCCCTTTAA 60.179 50.000 0.00 0.00 0.00 1.52
2425 3190 0.037590 ATGCAAGTGGACGCCCTTTA 59.962 50.000 0.00 0.00 0.00 1.85
2426 3191 0.827507 AATGCAAGTGGACGCCCTTT 60.828 50.000 0.00 0.00 0.00 3.11
2427 3192 0.827507 AAATGCAAGTGGACGCCCTT 60.828 50.000 0.00 0.00 0.00 3.95
2428 3193 0.037590 TAAATGCAAGTGGACGCCCT 59.962 50.000 0.00 0.00 0.00 5.19
2429 3194 1.102978 ATAAATGCAAGTGGACGCCC 58.897 50.000 0.00 0.00 0.00 6.13
2430 3195 4.568152 AATATAAATGCAAGTGGACGCC 57.432 40.909 0.00 0.00 0.00 5.68
2431 3196 5.339990 ACAAATATAAATGCAAGTGGACGC 58.660 37.500 0.00 0.00 0.00 5.19
2432 3197 6.253298 CCAACAAATATAAATGCAAGTGGACG 59.747 38.462 0.00 0.00 0.00 4.79
2433 3198 7.096551 ACCAACAAATATAAATGCAAGTGGAC 58.903 34.615 0.00 0.00 0.00 4.02
2434 3199 7.238486 ACCAACAAATATAAATGCAAGTGGA 57.762 32.000 0.00 0.00 0.00 4.02
2435 3200 8.994429 TTACCAACAAATATAAATGCAAGTGG 57.006 30.769 0.00 0.00 0.00 4.00
2530 3296 6.638021 AGGTATAACTTTGGTAAGCTCCTT 57.362 37.500 0.00 0.00 34.60 3.36
2660 3486 5.960811 TGTCTCATCCTCCTCTTTGTAGAAT 59.039 40.000 0.00 0.00 0.00 2.40
2752 3578 3.626670 ACTGCTTCTCAAGATTGCATAGC 59.373 43.478 8.11 0.00 34.90 2.97
2774 3600 8.546083 AGATTGTTTGTGGCCCATAAATAATA 57.454 30.769 21.84 2.99 36.81 0.98
2823 3649 5.990668 AGTGATTGGTTATCTTACCTGGAC 58.009 41.667 0.00 0.00 39.04 4.02
2988 3823 0.679505 GGGCAGCGGTACTCATCATA 59.320 55.000 0.00 0.00 0.00 2.15
3088 3923 6.715347 ATGCCTAAACTCCATAAAATCACC 57.285 37.500 0.00 0.00 0.00 4.02
3200 4036 6.595716 ACCACTTAAGATGCAGAGAACAATAC 59.404 38.462 10.09 0.00 0.00 1.89
3251 4089 3.213506 TGTGCTTTAGTGTCAGTGCAAT 58.786 40.909 0.00 0.00 32.10 3.56
3312 4150 1.913419 GAAACCCTATCTGGTCCACCA 59.087 52.381 0.00 0.00 45.30 4.17
3352 4190 0.040958 CCACGAACTTCAGCAACAGC 60.041 55.000 0.00 0.00 0.00 4.40
3399 4237 2.146342 GTTCATACCGATGATGCAGGG 58.854 52.381 0.00 0.00 41.77 4.45
3587 4427 5.641209 GGGTCATATGACTACATGATGCTTC 59.359 44.000 29.87 12.16 44.20 3.86
3595 4435 8.370940 CACTGATAAAGGGTCATATGACTACAT 58.629 37.037 29.87 18.40 44.20 2.29
3873 4897 3.327626 TGCGATTTCGGCAAACTAGTAA 58.672 40.909 0.00 0.00 40.23 2.24
4003 5027 3.181451 ACTTCTGAAGAGCACACATGGAA 60.181 43.478 23.36 0.00 0.00 3.53
4139 5184 6.432472 AGACATCCTCCAGAGAAACAAAATTC 59.568 38.462 0.00 0.00 0.00 2.17
4187 5234 5.163794 ACCGAGACTGCAAAATAAAATACCG 60.164 40.000 0.00 0.00 0.00 4.02
4311 5366 3.989698 CTCGTGGCCGCGTGAATCT 62.990 63.158 35.52 0.00 0.00 2.40
4404 5459 3.983044 ACTAGCTTACCTTTGTCCCTG 57.017 47.619 0.00 0.00 0.00 4.45
4405 5460 4.466726 CAGTACTAGCTTACCTTTGTCCCT 59.533 45.833 0.00 0.00 0.00 4.20
4419 5474 2.025155 TGGAGCAGTAGCAGTACTAGC 58.975 52.381 0.00 1.88 45.49 3.42
4513 5573 4.229582 AGCAACAGGGATTAGGGATAACAA 59.770 41.667 0.00 0.00 0.00 2.83
4554 5614 2.107204 GGACCCATGCCATCTATGTTCT 59.893 50.000 0.00 0.00 0.00 3.01
4560 5620 1.839191 GCAGGACCCATGCCATCTA 59.161 57.895 0.00 0.00 37.73 1.98
4576 5636 1.301401 GAGTGTTACCTGCGTGGCA 60.301 57.895 0.00 0.00 40.22 4.92
4580 5640 1.795768 CATGTGAGTGTTACCTGCGT 58.204 50.000 0.00 0.00 0.00 5.24
4582 5642 1.734465 GAGCATGTGAGTGTTACCTGC 59.266 52.381 0.00 0.00 39.14 4.85
4596 5656 6.378280 AGTTTGAAAGGGTTTATAGGAGCATG 59.622 38.462 0.00 0.00 0.00 4.06
4605 5665 6.211184 TGATCATGCAGTTTGAAAGGGTTTAT 59.789 34.615 0.00 0.00 0.00 1.40
4606 5666 5.538053 TGATCATGCAGTTTGAAAGGGTTTA 59.462 36.000 0.00 0.00 0.00 2.01
4609 5669 3.499338 TGATCATGCAGTTTGAAAGGGT 58.501 40.909 0.00 0.00 0.00 4.34
4610 5670 4.730949 ATGATCATGCAGTTTGAAAGGG 57.269 40.909 7.59 0.00 0.00 3.95
4612 5672 9.961265 ACATAATATGATCATGCAGTTTGAAAG 57.039 29.630 18.72 0.00 0.00 2.62
4613 5673 9.955208 GACATAATATGATCATGCAGTTTGAAA 57.045 29.630 18.72 0.00 0.00 2.69
4614 5674 9.122779 TGACATAATATGATCATGCAGTTTGAA 57.877 29.630 18.72 0.00 0.00 2.69
4615 5675 8.562052 GTGACATAATATGATCATGCAGTTTGA 58.438 33.333 18.72 0.00 0.00 2.69
4616 5676 8.565416 AGTGACATAATATGATCATGCAGTTTG 58.435 33.333 18.72 6.64 0.00 2.93
4617 5677 8.687292 AGTGACATAATATGATCATGCAGTTT 57.313 30.769 18.72 6.67 0.00 2.66
4618 5678 7.935210 TGAGTGACATAATATGATCATGCAGTT 59.065 33.333 18.72 9.88 0.00 3.16
4620 5680 7.900782 TGAGTGACATAATATGATCATGCAG 57.099 36.000 18.72 6.24 0.00 4.41
4621 5681 8.263940 CATGAGTGACATAATATGATCATGCA 57.736 34.615 18.72 0.00 37.46 3.96
4622 5682 7.187480 GCATGAGTGACATAATATGATCATGC 58.813 38.462 28.21 28.21 45.85 4.06
4623 5683 7.064253 ACGCATGAGTGACATAATATGATCATG 59.936 37.037 18.72 22.42 39.89 3.07
4627 5687 8.253113 TCATACGCATGAGTGACATAATATGAT 58.747 33.333 12.80 0.00 36.22 2.45
4628 5688 7.601856 TCATACGCATGAGTGACATAATATGA 58.398 34.615 12.80 7.71 36.22 2.15
4629 5689 7.816945 TCATACGCATGAGTGACATAATATG 57.183 36.000 12.80 5.46 36.22 1.78
4630 5690 7.063898 GCTTCATACGCATGAGTGACATAATAT 59.936 37.037 12.80 0.00 42.11 1.28
4631 5691 6.366061 GCTTCATACGCATGAGTGACATAATA 59.634 38.462 12.80 0.00 42.11 0.98
4632 5692 5.178252 GCTTCATACGCATGAGTGACATAAT 59.822 40.000 12.80 0.00 42.11 1.28
4633 5693 4.507756 GCTTCATACGCATGAGTGACATAA 59.492 41.667 12.80 0.00 42.11 1.90
4634 5694 4.051237 GCTTCATACGCATGAGTGACATA 58.949 43.478 12.80 0.00 42.11 2.29
4635 5695 2.868583 GCTTCATACGCATGAGTGACAT 59.131 45.455 12.80 0.00 42.11 3.06
4636 5696 2.270923 GCTTCATACGCATGAGTGACA 58.729 47.619 12.80 0.00 42.11 3.58
4637 5697 1.256376 CGCTTCATACGCATGAGTGAC 59.744 52.381 12.80 0.00 42.11 3.67
4646 5706 2.607635 TGATTTTCTCCGCTTCATACGC 59.392 45.455 0.00 0.00 0.00 4.42
4648 5708 3.312697 GGGTGATTTTCTCCGCTTCATAC 59.687 47.826 0.00 0.00 31.07 2.39
4666 5726 1.191535 TCTAGACATTCACCGGGGTG 58.808 55.000 11.66 11.66 46.64 4.61
4668 5728 2.434336 TGAATCTAGACATTCACCGGGG 59.566 50.000 6.32 0.00 37.77 5.73
4669 5729 3.819564 TGAATCTAGACATTCACCGGG 57.180 47.619 6.32 0.00 37.77 5.73
4670 5730 7.118390 GGAATTATGAATCTAGACATTCACCGG 59.882 40.741 10.28 0.00 43.88 5.28
4671 5731 7.657354 TGGAATTATGAATCTAGACATTCACCG 59.343 37.037 10.28 0.00 43.88 4.94
4672 5732 8.908786 TGGAATTATGAATCTAGACATTCACC 57.091 34.615 10.28 7.88 43.88 4.02
4683 5753 6.239396 CAGGCTGATCTGGAATTATGAATCT 58.761 40.000 9.42 0.00 0.00 2.40
4684 5754 5.106237 GCAGGCTGATCTGGAATTATGAATC 60.106 44.000 20.86 0.00 35.43 2.52
4689 5759 2.224967 GGGCAGGCTGATCTGGAATTAT 60.225 50.000 20.86 0.00 35.43 1.28
4692 5762 1.535685 GGGCAGGCTGATCTGGAAT 59.464 57.895 20.86 0.00 35.43 3.01
4693 5763 2.683465 GGGGCAGGCTGATCTGGAA 61.683 63.158 20.86 0.00 35.43 3.53
4694 5764 3.092511 GGGGCAGGCTGATCTGGA 61.093 66.667 20.86 0.00 35.43 3.86
4695 5765 3.095163 AGGGGCAGGCTGATCTGG 61.095 66.667 20.86 0.00 35.43 3.86
4696 5766 2.192443 CAGGGGCAGGCTGATCTG 59.808 66.667 20.86 16.82 37.79 2.90
4697 5767 2.285969 ACAGGGGCAGGCTGATCT 60.286 61.111 20.86 8.75 0.00 2.75
4699 5769 3.736224 CCACAGGGGCAGGCTGAT 61.736 66.667 20.86 0.00 0.00 2.90
4718 5813 2.073232 AGGCTGCCTCACACAGATT 58.927 52.632 17.22 0.00 37.32 2.40
4734 5829 1.683943 ATGAATGAACGCCCATGAGG 58.316 50.000 0.00 0.00 39.47 3.86
4764 5859 2.623915 CCAGTGGTGCTTGCTGCTC 61.624 63.158 0.00 0.73 43.37 4.26
4767 5862 1.880894 CATCCAGTGGTGCTTGCTG 59.119 57.895 9.54 0.00 0.00 4.41
4768 5863 4.410225 CATCCAGTGGTGCTTGCT 57.590 55.556 9.54 0.00 0.00 3.91


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

AutoCloner maintained by Alex Coulton.