Multiple sequence alignment - TraesCS5D01G135500

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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 TraesCS5D01G135500 chr5D 100.000 2799 0 0 1 2799 216058944 216061742 0.000000e+00 5169.0
1 TraesCS5D01G135500 chr5D 93.243 296 17 3 2506 2799 3039665 3039371 1.540000e-117 433.0
2 TraesCS5D01G135500 chr5D 91.694 301 22 3 2501 2799 10681931 10681632 5.580000e-112 414.0
3 TraesCS5D01G135500 chr5D 91.554 296 22 3 2506 2799 503735851 503735557 3.360000e-109 405.0
4 TraesCS5D01G135500 chr5D 95.556 90 4 0 2412 2501 369424160 369424249 8.080000e-31 145.0
5 TraesCS5D01G135500 chr5B 92.780 928 41 6 769 1686 231824829 231825740 0.000000e+00 1319.0
6 TraesCS5D01G135500 chr5B 90.438 251 18 5 2167 2411 231840318 231840568 2.690000e-85 326.0
7 TraesCS5D01G135500 chr5B 93.333 210 13 1 1679 1888 231838478 231838686 2.710000e-80 309.0
8 TraesCS5D01G135500 chr5B 90.385 208 17 1 1885 2092 231839884 231840088 1.280000e-68 270.0
9 TraesCS5D01G135500 chr5A 93.409 880 36 7 769 1634 284885829 284886700 0.000000e+00 1284.0
10 TraesCS5D01G135500 chr5A 89.495 495 42 8 110 600 536657900 536657412 3.960000e-173 617.0
11 TraesCS5D01G135500 chr5A 90.295 237 20 1 1885 2121 284900567 284900800 9.740000e-80 307.0
12 TraesCS5D01G135500 chr5A 91.429 210 14 3 1679 1888 284887327 284887532 4.560000e-73 285.0
13 TraesCS5D01G135500 chr5A 89.000 200 19 2 2156 2352 284901029 284901228 7.740000e-61 244.0
14 TraesCS5D01G135500 chr5A 82.941 170 14 3 1515 1684 284886656 284886810 3.760000e-29 139.0
15 TraesCS5D01G135500 chr5A 90.323 93 5 3 4 93 219372461 219372370 4.900000e-23 119.0
16 TraesCS5D01G135500 chr5A 90.000 90 5 3 7 93 536658064 536657976 2.280000e-21 113.0
17 TraesCS5D01G135500 chr5A 89.888 89 6 2 7 93 95775498 95775411 8.200000e-21 111.0
18 TraesCS5D01G135500 chr5A 100.000 31 0 0 82 112 536657816 536657786 1.080000e-04 58.4
19 TraesCS5D01G135500 chrUn 97.297 518 13 1 82 599 94076773 94076257 0.000000e+00 878.0
20 TraesCS5D01G135500 chrUn 95.152 165 8 0 595 759 94076198 94076034 7.690000e-66 261.0
21 TraesCS5D01G135500 chrUn 83.258 221 11 15 1 199 94076956 94076740 2.220000e-41 180.0
22 TraesCS5D01G135500 chrUn 94.681 94 3 2 2413 2504 104011272 104011179 8.080000e-31 145.0
23 TraesCS5D01G135500 chr2D 96.794 499 10 4 103 599 74140097 74140591 0.000000e+00 828.0
24 TraesCS5D01G135500 chr2D 91.892 296 21 3 2506 2799 364968816 364969110 7.220000e-111 411.0
25 TraesCS5D01G135500 chr2D 95.210 167 6 1 595 761 74140650 74140814 2.140000e-66 263.0
26 TraesCS5D01G135500 chr2D 87.981 208 15 6 1 201 74139893 74140097 1.300000e-58 237.0
27 TraesCS5D01G135500 chr6D 89.557 632 31 23 1 599 98131436 98132065 0.000000e+00 769.0
28 TraesCS5D01G135500 chr6D 90.323 496 38 8 110 600 348544858 348544368 2.350000e-180 641.0
29 TraesCS5D01G135500 chr6D 93.559 295 16 3 2507 2799 23078149 23078442 1.190000e-118 436.0
30 TraesCS5D01G135500 chr6D 95.122 82 3 1 4 84 348545087 348545006 8.140000e-26 128.0
31 TraesCS5D01G135500 chr6D 100.000 31 0 0 82 112 348544774 348544744 1.080000e-04 58.4
32 TraesCS5D01G135500 chr4D 94.468 470 22 3 82 548 12194794 12195262 0.000000e+00 721.0
33 TraesCS5D01G135500 chr4D 92.340 483 29 5 110 588 214984479 214984957 0.000000e+00 680.0
34 TraesCS5D01G135500 chr4D 91.030 301 23 4 2502 2799 389485313 389485612 1.210000e-108 403.0
35 TraesCS5D01G135500 chr4D 90.968 155 13 1 613 767 214997887 214998040 1.020000e-49 207.0
36 TraesCS5D01G135500 chr4D 90.132 152 13 2 621 772 460653736 460653885 2.200000e-46 196.0
37 TraesCS5D01G135500 chr4D 97.674 86 2 0 2412 2497 191234886 191234801 6.250000e-32 148.0
38 TraesCS5D01G135500 chr4D 94.048 84 5 0 1 84 214984248 214984331 8.140000e-26 128.0
39 TraesCS5D01G135500 chr4D 100.000 31 0 0 82 112 12194907 12194937 1.080000e-04 58.4
40 TraesCS5D01G135500 chr4D 100.000 31 0 0 82 112 214984566 214984596 1.080000e-04 58.4
41 TraesCS5D01G135500 chr7B 92.525 495 27 7 110 599 482299263 482299752 0.000000e+00 701.0
42 TraesCS5D01G135500 chr7B 94.624 93 4 1 2413 2504 418204659 418204567 2.910000e-30 143.0
43 TraesCS5D01G135500 chr7B 100.000 30 0 0 82 111 482299351 482299380 3.890000e-04 56.5
44 TraesCS5D01G135500 chr3A 92.668 491 26 7 110 599 459820107 459820588 0.000000e+00 699.0
45 TraesCS5D01G135500 chr2A 90.085 353 24 8 1 344 456290365 456290715 5.500000e-122 448.0
46 TraesCS5D01G135500 chr2A 100.000 31 0 0 82 112 456290564 456290594 1.080000e-04 58.4
47 TraesCS5D01G135500 chr3D 92.542 295 19 3 2507 2799 283322513 283322806 1.200000e-113 420.0
48 TraesCS5D01G135500 chr3D 83.003 353 24 8 447 767 598111820 598112168 1.270000e-73 287.0
49 TraesCS5D01G135500 chr7D 91.837 294 21 3 2506 2797 590075760 590076052 9.330000e-110 407.0
50 TraesCS5D01G135500 chr7D 93.182 176 11 1 595 770 584454602 584454776 9.950000e-65 257.0
51 TraesCS5D01G135500 chr7D 92.655 177 11 2 595 770 245261339 245261514 1.290000e-63 254.0
52 TraesCS5D01G135500 chr7D 91.329 173 13 2 598 770 612261403 612261233 4.660000e-58 235.0
53 TraesCS5D01G135500 chr7D 94.737 95 5 0 2410 2504 621487681 621487587 6.250000e-32 148.0
54 TraesCS5D01G135500 chr7D 97.647 85 2 0 2413 2497 4902285 4902201 2.250000e-31 147.0
55 TraesCS5D01G135500 chr7D 93.750 96 5 1 2409 2504 6009662 6009568 2.910000e-30 143.0
56 TraesCS5D01G135500 chr6A 90.728 302 26 2 2500 2799 550290307 550290006 4.340000e-108 401.0
57 TraesCS5D01G135500 chr7A 92.667 150 9 2 621 770 53972977 53972830 6.070000e-52 215.0
58 TraesCS5D01G135500 chr4A 93.878 98 4 2 2409 2505 680395127 680395031 2.250000e-31 147.0
59 TraesCS5D01G135500 chr1D 96.552 87 3 0 2411 2497 509219 509305 8.080000e-31 145.0
60 TraesCS5D01G135500 chr4B 92.941 85 5 1 1 84 599081451 599081535 3.790000e-24 122.0


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 TraesCS5D01G135500 chr5D 216058944 216061742 2798 False 5169.000000 5169 100.000000 1 2799 1 chr5D.!!$F1 2798
1 TraesCS5D01G135500 chr5B 231824829 231825740 911 False 1319.000000 1319 92.780000 769 1686 1 chr5B.!!$F1 917
2 TraesCS5D01G135500 chr5B 231838478 231840568 2090 False 301.666667 326 91.385333 1679 2411 3 chr5B.!!$F2 732
3 TraesCS5D01G135500 chr5A 284885829 284887532 1703 False 569.333333 1284 89.259667 769 1888 3 chr5A.!!$F1 1119
4 TraesCS5D01G135500 chr5A 284900567 284901228 661 False 275.500000 307 89.647500 1885 2352 2 chr5A.!!$F2 467
5 TraesCS5D01G135500 chr5A 536657412 536658064 652 True 262.800000 617 93.165000 7 600 3 chr5A.!!$R3 593
6 TraesCS5D01G135500 chrUn 94076034 94076956 922 True 439.666667 878 91.902333 1 759 3 chrUn.!!$R2 758
7 TraesCS5D01G135500 chr2D 74139893 74140814 921 False 442.666667 828 93.328333 1 761 3 chr2D.!!$F2 760
8 TraesCS5D01G135500 chr6D 98131436 98132065 629 False 769.000000 769 89.557000 1 599 1 chr6D.!!$F2 598
9 TraesCS5D01G135500 chr6D 348544368 348545087 719 True 275.800000 641 95.148333 4 600 3 chr6D.!!$R1 596
10 TraesCS5D01G135500 chr4D 214984248 214984957 709 False 288.800000 680 95.462667 1 588 3 chr4D.!!$F5 587

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
847 1235 0.251077 CCGTACCCCCTAGCTCGTAT 60.251 60.0 0.0 0.0 0.0 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2583 4971 0.036671 ATTCCAGAAACGGTCCGGAC 60.037 55.0 27.04 27.04 0.0 4.79 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
88 92 8.986929 CCAAATATGGTTTCTCCTTATTCTCT 57.013 34.615 5.80 0.00 42.17 3.10
90 94 9.618890 CAAATATGGTTTCTCCTTATTCTCTCA 57.381 33.333 5.80 0.00 42.17 3.27
93 97 9.790344 ATATGGTTTCTCCTTATTCTCTCAATG 57.210 33.333 0.00 0.00 34.24 2.82
95 99 5.298026 GGTTTCTCCTTATTCTCTCAATGCC 59.702 44.000 0.00 0.00 0.00 4.40
104 178 4.647564 TTCTCTCAATGCCTCTTTCCTT 57.352 40.909 0.00 0.00 0.00 3.36
108 182 3.331889 TCTCAATGCCTCTTTCCTTCCTT 59.668 43.478 0.00 0.00 0.00 3.36
111 185 5.831103 TCAATGCCTCTTTCCTTCCTTATT 58.169 37.500 0.00 0.00 0.00 1.40
189 403 5.786121 ATCTCAATCCCTCTTTCTTTCCA 57.214 39.130 0.00 0.00 0.00 3.53
257 571 5.822519 TGATTTTCTCCGTAATGATTCCTGG 59.177 40.000 0.00 0.00 0.00 4.45
445 761 1.021202 TGACAGGCGTGAAACCTTTG 58.979 50.000 14.38 0.00 34.42 2.77
588 906 0.255890 GGCTGACTTGGGCCAGATAA 59.744 55.000 6.23 0.00 46.84 1.75
601 981 2.224784 GCCAGATAAACGTTTTGACGGT 59.775 45.455 20.19 0.00 37.45 4.83
611 991 3.058501 ACGTTTTGACGGTGGATGAAATC 60.059 43.478 3.90 0.00 39.09 2.17
614 994 8.697846 ACGTTTTGACGGTGGATGAAATCATG 62.698 42.308 0.00 0.00 40.65 3.07
731 1111 3.460103 AAACGTATTGTGACGGTGAACT 58.540 40.909 0.00 0.00 43.33 3.01
799 1179 6.530019 AGTACCCAGCAAAAGGAAAATATG 57.470 37.500 0.00 0.00 0.00 1.78
843 1231 1.683418 CCAACCGTACCCCCTAGCTC 61.683 65.000 0.00 0.00 0.00 4.09
847 1235 0.251077 CCGTACCCCCTAGCTCGTAT 60.251 60.000 0.00 0.00 0.00 3.06
862 1250 3.467803 CTCGTATTCTTCCCAACCATCC 58.532 50.000 0.00 0.00 0.00 3.51
863 1251 2.841266 TCGTATTCTTCCCAACCATCCA 59.159 45.455 0.00 0.00 0.00 3.41
878 1266 4.023291 ACCATCCACAACAAGTTTGAACT 58.977 39.130 0.00 0.00 42.04 3.01
893 1281 5.998363 AGTTTGAACTAACTCAACCATCCTC 59.002 40.000 0.00 0.00 37.52 3.71
993 1384 4.954970 CCCTGCACCGCACCTGTT 62.955 66.667 0.00 0.00 33.79 3.16
1081 1472 1.678970 GCCATCGGCCAAGAAACCT 60.679 57.895 2.24 0.00 44.06 3.50
1086 1477 1.599797 CGGCCAAGAAACCTTCGGT 60.600 57.895 2.24 0.00 37.65 4.69
1241 1635 2.742372 CAACGAGGACGGCCAAGG 60.742 66.667 11.69 0.00 44.46 3.61
1350 1744 2.268076 GGTCACGGGCAGCAACATT 61.268 57.895 0.00 0.00 0.00 2.71
1555 1949 1.470979 GCGCGAAGGAAAGGTCAGATA 60.471 52.381 12.10 0.00 0.00 1.98
1556 1950 2.194271 CGCGAAGGAAAGGTCAGATAC 58.806 52.381 0.00 0.00 0.00 2.24
1581 2037 7.003939 TCAGATGTAAATGTGAAATAGCACG 57.996 36.000 0.00 0.00 41.63 5.34
1587 2043 2.552599 TGTGAAATAGCACGGACCAA 57.447 45.000 0.00 0.00 41.63 3.67
1602 2058 5.468746 CACGGACCAAGTGAAGAAATAGAAA 59.531 40.000 0.00 0.00 41.83 2.52
1604 2060 5.468746 CGGACCAAGTGAAGAAATAGAAACA 59.531 40.000 0.00 0.00 0.00 2.83
1605 2061 6.347725 CGGACCAAGTGAAGAAATAGAAACAG 60.348 42.308 0.00 0.00 0.00 3.16
1606 2062 6.710744 GGACCAAGTGAAGAAATAGAAACAGA 59.289 38.462 0.00 0.00 0.00 3.41
1607 2063 7.391833 GGACCAAGTGAAGAAATAGAAACAGAT 59.608 37.037 0.00 0.00 0.00 2.90
1608 2064 8.697507 ACCAAGTGAAGAAATAGAAACAGATT 57.302 30.769 0.00 0.00 0.00 2.40
1609 2065 9.136323 ACCAAGTGAAGAAATAGAAACAGATTT 57.864 29.630 0.00 0.00 0.00 2.17
1610 2066 9.971922 CCAAGTGAAGAAATAGAAACAGATTTT 57.028 29.630 0.00 0.00 0.00 1.82
1630 2086 9.525826 AGATTTTTCAGATGTAAAGGTCAGATT 57.474 29.630 0.00 0.00 0.00 2.40
1636 2092 9.436957 TTCAGATGTAAAGGTCAGATTTAACTC 57.563 33.333 0.00 0.00 0.00 3.01
1671 2127 7.860872 AGATTTCAGAAACGTGATTGTAAAACC 59.139 33.333 0.00 0.00 0.00 3.27
1695 2673 0.539438 GCACCATTGGAACCAGGACA 60.539 55.000 10.37 0.00 0.00 4.02
1725 2703 1.411074 GGAAACTGGGAACTTGTGGGT 60.411 52.381 0.00 0.00 0.00 4.51
1735 2713 0.037303 ACTTGTGGGTCAGCTCATGG 59.963 55.000 0.00 0.00 0.00 3.66
1778 2756 4.911390 AGGTGAAGATGAACCCTTAACTG 58.089 43.478 0.00 0.00 37.13 3.16
1781 2759 4.938226 GTGAAGATGAACCCTTAACTGGAG 59.062 45.833 0.00 0.00 0.00 3.86
1871 2849 5.852738 ACTCTGAGATGTTTTCAACGATG 57.147 39.130 12.44 0.00 0.00 3.84
1879 2857 5.765182 AGATGTTTTCAACGATGACTTTCCT 59.235 36.000 0.00 0.00 34.61 3.36
1954 4132 1.270625 GGTGAACCTTGTGGATCGTGA 60.271 52.381 0.00 0.00 37.89 4.35
1957 4135 2.288825 TGAACCTTGTGGATCGTGAGAC 60.289 50.000 0.00 0.00 37.89 3.36
1965 4143 1.471287 TGGATCGTGAGACGGTTGTAG 59.529 52.381 0.00 0.00 46.97 2.74
1968 4146 0.039798 TCGTGAGACGGTTGTAGCAC 60.040 55.000 0.00 0.00 42.81 4.40
2011 4189 8.824756 TGAATAGATGGAGATATACACCCTAC 57.175 38.462 0.00 0.00 0.00 3.18
2014 4192 9.615660 AATAGATGGAGATATACACCCTACAAA 57.384 33.333 0.00 0.00 0.00 2.83
2039 4217 4.582869 TGACTGGATCATCTTCAAACCTG 58.417 43.478 0.00 0.00 29.99 4.00
2160 4536 9.959749 CATGGACTACTAGAAATAAAGTCTCTC 57.040 37.037 0.00 0.00 37.36 3.20
2168 4544 9.041354 ACTAGAAATAAAGTCTCTCAACCATCT 57.959 33.333 0.00 0.00 0.00 2.90
2197 4579 7.755591 TGACATCATCTACAAATTGCTTTCTC 58.244 34.615 0.00 0.00 0.00 2.87
2222 4605 1.376553 GGCTCTGGAGACTGTTGCC 60.377 63.158 1.35 0.00 40.28 4.52
2225 4608 1.612726 GCTCTGGAGACTGTTGCCAAT 60.613 52.381 1.35 0.00 0.00 3.16
2227 4610 3.265791 CTCTGGAGACTGTTGCCAATAC 58.734 50.000 4.50 0.00 0.00 1.89
2229 4612 3.264193 TCTGGAGACTGTTGCCAATACAT 59.736 43.478 4.50 0.00 0.00 2.29
2230 4613 3.346315 TGGAGACTGTTGCCAATACATG 58.654 45.455 0.00 0.00 0.00 3.21
2247 4632 3.441101 ACATGGGAGCTACAGTCACTTA 58.559 45.455 0.00 0.00 0.00 2.24
2400 4788 0.808755 GGTTGTATTGGGTCCTTGCG 59.191 55.000 0.00 0.00 0.00 4.85
2411 4799 1.026182 GTCCTTGCGACCATGCATCA 61.026 55.000 0.00 0.00 45.78 3.07
2412 4800 0.107066 TCCTTGCGACCATGCATCAT 60.107 50.000 0.00 0.00 45.78 2.45
2413 4801 1.140652 TCCTTGCGACCATGCATCATA 59.859 47.619 0.00 0.00 45.78 2.15
2414 4802 1.265095 CCTTGCGACCATGCATCATAC 59.735 52.381 0.00 0.00 45.78 2.39
2415 4803 2.216046 CTTGCGACCATGCATCATACT 58.784 47.619 0.00 0.00 45.78 2.12
2416 4804 1.869774 TGCGACCATGCATCATACTC 58.130 50.000 0.00 0.00 40.62 2.59
2417 4805 1.151668 GCGACCATGCATCATACTCC 58.848 55.000 0.00 0.00 34.15 3.85
2418 4806 1.800805 CGACCATGCATCATACTCCC 58.199 55.000 0.00 0.00 0.00 4.30
2419 4807 1.345741 CGACCATGCATCATACTCCCT 59.654 52.381 0.00 0.00 0.00 4.20
2420 4808 2.611473 CGACCATGCATCATACTCCCTC 60.611 54.545 0.00 0.00 0.00 4.30
2421 4809 2.636893 GACCATGCATCATACTCCCTCT 59.363 50.000 0.00 0.00 0.00 3.69
2422 4810 2.371179 ACCATGCATCATACTCCCTCTG 59.629 50.000 0.00 0.00 0.00 3.35
2423 4811 2.371179 CCATGCATCATACTCCCTCTGT 59.629 50.000 0.00 0.00 0.00 3.41
2424 4812 3.580022 CCATGCATCATACTCCCTCTGTA 59.420 47.826 0.00 0.00 0.00 2.74
2425 4813 4.040829 CCATGCATCATACTCCCTCTGTAA 59.959 45.833 0.00 0.00 0.00 2.41
2426 4814 5.455183 CCATGCATCATACTCCCTCTGTAAA 60.455 44.000 0.00 0.00 0.00 2.01
2427 4815 5.023533 TGCATCATACTCCCTCTGTAAAC 57.976 43.478 0.00 0.00 0.00 2.01
2428 4816 4.716784 TGCATCATACTCCCTCTGTAAACT 59.283 41.667 0.00 0.00 0.00 2.66
2429 4817 5.897250 TGCATCATACTCCCTCTGTAAACTA 59.103 40.000 0.00 0.00 0.00 2.24
2430 4818 6.382859 TGCATCATACTCCCTCTGTAAACTAA 59.617 38.462 0.00 0.00 0.00 2.24
2431 4819 7.071196 TGCATCATACTCCCTCTGTAAACTAAT 59.929 37.037 0.00 0.00 0.00 1.73
2432 4820 8.585881 GCATCATACTCCCTCTGTAAACTAATA 58.414 37.037 0.00 0.00 0.00 0.98
2439 4827 8.862085 ACTCCCTCTGTAAACTAATATAAGAGC 58.138 37.037 0.00 0.00 0.00 4.09
2440 4828 8.777578 TCCCTCTGTAAACTAATATAAGAGCA 57.222 34.615 0.00 0.00 0.00 4.26
2441 4829 9.381038 TCCCTCTGTAAACTAATATAAGAGCAT 57.619 33.333 0.00 0.00 0.00 3.79
2492 4880 8.617290 ATGCTTTTATATTAGTTTACGGAGGG 57.383 34.615 0.00 0.00 0.00 4.30
2493 4881 7.794041 TGCTTTTATATTAGTTTACGGAGGGA 58.206 34.615 0.00 0.00 0.00 4.20
2494 4882 7.929785 TGCTTTTATATTAGTTTACGGAGGGAG 59.070 37.037 0.00 0.00 0.00 4.30
2495 4883 7.930325 GCTTTTATATTAGTTTACGGAGGGAGT 59.070 37.037 0.00 0.00 0.00 3.85
2517 4905 0.945813 TTTTTACGCCAACTCCACCG 59.054 50.000 0.00 0.00 0.00 4.94
2518 4906 1.508808 TTTTACGCCAACTCCACCGC 61.509 55.000 0.00 0.00 0.00 5.68
2536 4924 4.404098 GCGACCCCAACCGGATGT 62.404 66.667 9.46 0.00 0.00 3.06
2537 4925 2.125269 CGACCCCAACCGGATGTC 60.125 66.667 9.46 5.99 33.10 3.06
2538 4926 2.271173 GACCCCAACCGGATGTCC 59.729 66.667 9.46 0.00 31.29 4.02
2548 4936 2.874751 GGATGTCCGTTTTGCCCG 59.125 61.111 0.00 0.00 0.00 6.13
2549 4937 2.696759 GGATGTCCGTTTTGCCCGG 61.697 63.158 0.00 0.00 46.83 5.73
2556 4944 2.253513 CGTTTTGCCCGGATTCTGT 58.746 52.632 0.73 0.00 0.00 3.41
2557 4945 0.168128 CGTTTTGCCCGGATTCTGTC 59.832 55.000 0.73 0.00 0.00 3.51
2558 4946 0.526211 GTTTTGCCCGGATTCTGTCC 59.474 55.000 0.73 0.00 44.10 4.02
2566 4954 3.644861 GGATTCTGTCCGTTTGGGT 57.355 52.632 0.00 0.00 37.23 4.51
2567 4955 2.773993 GGATTCTGTCCGTTTGGGTA 57.226 50.000 0.00 0.00 37.23 3.69
2568 4956 2.629051 GGATTCTGTCCGTTTGGGTAG 58.371 52.381 0.00 0.00 37.23 3.18
2569 4957 2.629051 GATTCTGTCCGTTTGGGTAGG 58.371 52.381 0.00 0.00 37.00 3.18
2570 4958 0.688487 TTCTGTCCGTTTGGGTAGGG 59.312 55.000 0.00 0.00 37.00 3.53
2571 4959 1.376812 CTGTCCGTTTGGGTAGGGC 60.377 63.158 0.00 0.00 37.00 5.19
2572 4960 2.119484 CTGTCCGTTTGGGTAGGGCA 62.119 60.000 0.00 0.00 37.30 5.36
2573 4961 1.073548 GTCCGTTTGGGTAGGGCAA 59.926 57.895 0.00 0.00 37.00 4.52
2574 4962 0.323087 GTCCGTTTGGGTAGGGCAAT 60.323 55.000 0.00 0.00 37.00 3.56
2575 4963 1.065272 GTCCGTTTGGGTAGGGCAATA 60.065 52.381 0.00 0.00 37.00 1.90
2576 4964 1.210967 TCCGTTTGGGTAGGGCAATAG 59.789 52.381 0.00 0.00 37.00 1.73
2577 4965 1.675552 CGTTTGGGTAGGGCAATAGG 58.324 55.000 0.00 0.00 0.00 2.57
2578 4966 1.749286 CGTTTGGGTAGGGCAATAGGG 60.749 57.143 0.00 0.00 0.00 3.53
2579 4967 1.286849 GTTTGGGTAGGGCAATAGGGT 59.713 52.381 0.00 0.00 0.00 4.34
2580 4968 1.218844 TTGGGTAGGGCAATAGGGTC 58.781 55.000 0.00 0.00 0.00 4.46
2581 4969 1.052124 TGGGTAGGGCAATAGGGTCG 61.052 60.000 0.00 0.00 0.00 4.79
2582 4970 1.052694 GGGTAGGGCAATAGGGTCGT 61.053 60.000 0.00 0.00 0.00 4.34
2583 4971 0.106149 GGTAGGGCAATAGGGTCGTG 59.894 60.000 0.00 0.00 0.00 4.35
2584 4972 0.828677 GTAGGGCAATAGGGTCGTGT 59.171 55.000 0.00 0.00 0.00 4.49
2585 4973 1.117150 TAGGGCAATAGGGTCGTGTC 58.883 55.000 0.00 0.00 0.00 3.67
2586 4974 1.153229 GGGCAATAGGGTCGTGTCC 60.153 63.158 0.00 0.00 0.00 4.02
2587 4975 1.520787 GGCAATAGGGTCGTGTCCG 60.521 63.158 0.00 0.00 0.00 4.79
2588 4976 1.520787 GCAATAGGGTCGTGTCCGG 60.521 63.158 0.00 0.00 33.95 5.14
2589 4977 1.952102 GCAATAGGGTCGTGTCCGGA 61.952 60.000 0.00 0.00 33.95 5.14
2590 4978 0.179119 CAATAGGGTCGTGTCCGGAC 60.179 60.000 28.17 28.17 33.95 4.79
2591 4979 1.325476 AATAGGGTCGTGTCCGGACC 61.325 60.000 31.19 20.60 35.12 4.46
2594 4982 3.982241 GGTCGTGTCCGGACCGTT 61.982 66.667 31.11 0.00 33.95 4.44
2595 4983 2.028043 GTCGTGTCCGGACCGTTT 59.972 61.111 31.11 0.00 33.95 3.60
2596 4984 2.018324 GTCGTGTCCGGACCGTTTC 61.018 63.158 31.11 22.44 33.95 2.78
2597 4985 2.195567 TCGTGTCCGGACCGTTTCT 61.196 57.895 31.11 0.00 33.95 2.52
2598 4986 2.019951 CGTGTCCGGACCGTTTCTG 61.020 63.158 31.19 9.44 0.00 3.02
2604 4992 1.794222 CGGACCGTTTCTGGAATGC 59.206 57.895 5.48 0.00 0.00 3.56
2605 4993 1.794222 GGACCGTTTCTGGAATGCG 59.206 57.895 0.00 0.00 0.00 4.73
2606 4994 1.644786 GGACCGTTTCTGGAATGCGG 61.645 60.000 18.13 18.13 41.58 5.69
2607 4995 0.953960 GACCGTTTCTGGAATGCGGT 60.954 55.000 22.32 22.32 46.83 5.68
2608 4996 1.234615 ACCGTTTCTGGAATGCGGTG 61.235 55.000 21.85 6.93 44.53 4.94
2609 4997 1.501741 CGTTTCTGGAATGCGGTGG 59.498 57.895 0.00 0.00 0.00 4.61
2610 4998 1.212751 GTTTCTGGAATGCGGTGGC 59.787 57.895 0.00 0.00 40.52 5.01
2611 4999 1.976474 TTTCTGGAATGCGGTGGCC 60.976 57.895 0.00 0.00 38.85 5.36
2648 5036 4.034258 GCATCCGGCCGCATCATG 62.034 66.667 22.85 18.56 36.11 3.07
2649 5037 2.592574 CATCCGGCCGCATCATGT 60.593 61.111 22.85 0.00 0.00 3.21
2650 5038 2.281070 ATCCGGCCGCATCATGTC 60.281 61.111 22.85 0.00 0.00 3.06
2651 5039 3.832237 ATCCGGCCGCATCATGTCC 62.832 63.158 22.85 0.00 0.00 4.02
2657 5045 4.580044 CGCATCATGTCCGCGCAC 62.580 66.667 8.75 0.00 42.79 5.34
2658 5046 3.197790 GCATCATGTCCGCGCACT 61.198 61.111 8.75 0.00 0.00 4.40
2659 5047 2.753966 GCATCATGTCCGCGCACTT 61.754 57.895 8.75 0.00 0.00 3.16
2660 5048 1.796151 CATCATGTCCGCGCACTTT 59.204 52.632 8.75 0.00 0.00 2.66
2661 5049 0.168788 CATCATGTCCGCGCACTTTT 59.831 50.000 8.75 0.00 0.00 2.27
2662 5050 0.881118 ATCATGTCCGCGCACTTTTT 59.119 45.000 8.75 0.00 0.00 1.94
2682 5070 6.429791 TTTTTCTTTGCAAGCCTTTAAACC 57.570 33.333 0.00 0.00 0.00 3.27
2683 5071 5.351948 TTTCTTTGCAAGCCTTTAAACCT 57.648 34.783 0.00 0.00 0.00 3.50
2684 5072 5.351948 TTCTTTGCAAGCCTTTAAACCTT 57.648 34.783 0.00 0.00 0.00 3.50
2685 5073 5.351948 TCTTTGCAAGCCTTTAAACCTTT 57.648 34.783 0.00 0.00 0.00 3.11
2686 5074 5.739959 TCTTTGCAAGCCTTTAAACCTTTT 58.260 33.333 0.00 0.00 0.00 2.27
2687 5075 6.176896 TCTTTGCAAGCCTTTAAACCTTTTT 58.823 32.000 0.00 0.00 0.00 1.94
2710 5098 9.642327 TTTTTCATCATTCATTCTTGGTACATG 57.358 29.630 0.00 0.00 39.30 3.21
2711 5099 6.947644 TCATCATTCATTCTTGGTACATGG 57.052 37.500 0.00 0.00 39.30 3.66
2712 5100 6.661777 TCATCATTCATTCTTGGTACATGGA 58.338 36.000 0.00 0.00 39.30 3.41
2713 5101 7.118060 TCATCATTCATTCTTGGTACATGGAA 58.882 34.615 0.00 0.00 39.30 3.53
2714 5102 7.614974 TCATCATTCATTCTTGGTACATGGAAA 59.385 33.333 0.00 0.00 39.30 3.13
2715 5103 7.959658 TCATTCATTCTTGGTACATGGAAAT 57.040 32.000 0.00 0.00 39.30 2.17
2716 5104 9.645128 ATCATTCATTCTTGGTACATGGAAATA 57.355 29.630 0.00 0.00 39.30 1.40
2717 5105 8.902806 TCATTCATTCTTGGTACATGGAAATAC 58.097 33.333 0.00 0.00 39.30 1.89
2718 5106 8.685427 CATTCATTCTTGGTACATGGAAATACA 58.315 33.333 0.00 0.00 39.30 2.29
2719 5107 8.821686 TTCATTCTTGGTACATGGAAATACAT 57.178 30.769 0.00 0.00 39.30 2.29
2720 5108 8.450578 TCATTCTTGGTACATGGAAATACATC 57.549 34.615 0.00 0.00 39.30 3.06
2721 5109 8.052141 TCATTCTTGGTACATGGAAATACATCA 58.948 33.333 0.00 0.00 39.30 3.07
2722 5110 8.853126 CATTCTTGGTACATGGAAATACATCAT 58.147 33.333 0.00 0.00 39.30 2.45
2723 5111 8.450578 TTCTTGGTACATGGAAATACATCATC 57.549 34.615 0.00 0.00 39.30 2.92
2724 5112 7.572814 TCTTGGTACATGGAAATACATCATCA 58.427 34.615 0.00 0.00 39.30 3.07
2725 5113 8.052141 TCTTGGTACATGGAAATACATCATCAA 58.948 33.333 0.00 0.00 39.30 2.57
2726 5114 8.586879 TTGGTACATGGAAATACATCATCAAA 57.413 30.769 0.00 0.00 39.30 2.69
2727 5115 8.765488 TGGTACATGGAAATACATCATCAAAT 57.235 30.769 0.00 0.00 0.00 2.32
2728 5116 9.199645 TGGTACATGGAAATACATCATCAAATT 57.800 29.630 0.00 0.00 0.00 1.82
2798 5186 9.927081 ACATTTTAGAAGATATCCAACTTCCAT 57.073 29.630 0.00 0.00 42.09 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
80 84 6.319048 AGGAAAGAGGCATTGAGAGAATAA 57.681 37.500 0.00 0.00 0.00 1.40
84 88 3.054802 GGAAGGAAAGAGGCATTGAGAGA 60.055 47.826 0.00 0.00 0.00 3.10
86 90 2.915604 AGGAAGGAAAGAGGCATTGAGA 59.084 45.455 0.00 0.00 0.00 3.27
87 91 3.362870 AGGAAGGAAAGAGGCATTGAG 57.637 47.619 0.00 0.00 0.00 3.02
88 92 3.814504 AAGGAAGGAAAGAGGCATTGA 57.185 42.857 0.00 0.00 0.00 2.57
90 94 6.084749 AGAATAAGGAAGGAAAGAGGCATT 57.915 37.500 0.00 0.00 0.00 3.56
91 95 5.192522 TGAGAATAAGGAAGGAAAGAGGCAT 59.807 40.000 0.00 0.00 0.00 4.40
92 96 4.536090 TGAGAATAAGGAAGGAAAGAGGCA 59.464 41.667 0.00 0.00 0.00 4.75
93 97 5.104259 TGAGAATAAGGAAGGAAAGAGGC 57.896 43.478 0.00 0.00 0.00 4.70
95 99 7.572814 AGGAATGAGAATAAGGAAGGAAAGAG 58.427 38.462 0.00 0.00 0.00 2.85
104 178 6.552008 ACCAAACAAGGAATGAGAATAAGGA 58.448 36.000 0.00 0.00 0.00 3.36
111 185 8.700051 TGATTAAAAACCAAACAAGGAATGAGA 58.300 29.630 0.00 0.00 0.00 3.27
189 403 6.791969 AGGAAAGAGGCCTTGAGAGAATATAT 59.208 38.462 6.77 0.00 31.91 0.86
203 517 7.227711 GTCTCATAATAAGAAAGGAAAGAGGCC 59.772 40.741 0.00 0.00 0.00 5.19
239 553 3.040655 TCCCAGGAATCATTACGGAGA 57.959 47.619 0.00 0.00 0.00 3.71
433 749 3.839293 TGTTTGAACCAAAGGTTTCACG 58.161 40.909 2.55 0.00 46.95 4.35
445 761 5.863935 GCTAGGATGTTTTCATGTTTGAACC 59.136 40.000 0.00 0.00 41.50 3.62
588 906 8.175392 ATGATTTCATCCACCGTCAAAACGTT 62.175 38.462 0.00 0.00 38.55 3.99
601 981 4.821260 CCGTCATTACCATGATTTCATCCA 59.179 41.667 0.00 0.00 41.64 3.41
611 991 3.259064 AGTTTCGTCCGTCATTACCATG 58.741 45.455 0.00 0.00 0.00 3.66
614 994 3.836949 TGTAGTTTCGTCCGTCATTACC 58.163 45.455 0.00 0.00 0.00 2.85
731 1111 8.786826 AATAAAGTATGGATTGACTTTGTCGA 57.213 30.769 9.65 0.00 43.84 4.20
761 1141 4.072131 TGGGTACTTTGCACATCTTTCTC 58.928 43.478 0.00 0.00 0.00 2.87
762 1142 4.074970 CTGGGTACTTTGCACATCTTTCT 58.925 43.478 0.00 0.00 0.00 2.52
763 1143 3.366374 GCTGGGTACTTTGCACATCTTTC 60.366 47.826 0.00 0.00 0.00 2.62
764 1144 2.558359 GCTGGGTACTTTGCACATCTTT 59.442 45.455 0.00 0.00 0.00 2.52
765 1145 2.162681 GCTGGGTACTTTGCACATCTT 58.837 47.619 0.00 0.00 0.00 2.40
766 1146 1.073763 TGCTGGGTACTTTGCACATCT 59.926 47.619 0.00 0.00 0.00 2.90
767 1147 1.533625 TGCTGGGTACTTTGCACATC 58.466 50.000 0.00 0.00 0.00 3.06
843 1231 2.943033 GTGGATGGTTGGGAAGAATACG 59.057 50.000 0.00 0.00 0.00 3.06
847 1235 2.091610 TGTTGTGGATGGTTGGGAAGAA 60.092 45.455 0.00 0.00 0.00 2.52
862 1250 6.526674 GGTTGAGTTAGTTCAAACTTGTTGTG 59.473 38.462 0.00 0.00 40.74 3.33
863 1251 6.207810 TGGTTGAGTTAGTTCAAACTTGTTGT 59.792 34.615 0.00 0.00 43.56 3.32
878 1266 2.838202 GTCAGGGAGGATGGTTGAGTTA 59.162 50.000 0.00 0.00 0.00 2.24
893 1281 3.129502 CTGCATGCGGTGTCAGGG 61.130 66.667 18.84 0.00 32.10 4.45
993 1384 2.826128 ACTTGTGGCTACTTGAGATCGA 59.174 45.455 0.64 0.00 0.00 3.59
1081 1472 1.933181 GATCATCGTGATTGCACCGAA 59.067 47.619 0.00 0.00 42.09 4.30
1086 1477 1.408702 TCCTCGATCATCGTGATTGCA 59.591 47.619 10.68 0.00 41.35 4.08
1241 1635 2.505337 TGTGCGTATCGTGTCGGC 60.505 61.111 0.00 0.00 0.00 5.54
1340 1734 2.089980 AGGATGAGACAATGTTGCTGC 58.910 47.619 0.00 0.00 0.00 5.25
1350 1744 4.809193 AGAAGGCATAGTAGGATGAGACA 58.191 43.478 0.00 0.00 0.00 3.41
1455 1849 0.955919 GAAACCTCGCCCAAGTGGAG 60.956 60.000 0.00 0.00 37.39 3.86
1555 1949 7.201556 CGTGCTATTTCACATTTACATCTGAGT 60.202 37.037 0.00 0.00 36.80 3.41
1556 1950 7.121911 CGTGCTATTTCACATTTACATCTGAG 58.878 38.462 0.00 0.00 36.80 3.35
1581 2037 6.710744 TCTGTTTCTATTTCTTCACTTGGTCC 59.289 38.462 0.00 0.00 0.00 4.46
1602 2058 7.939039 TCTGACCTTTACATCTGAAAAATCTGT 59.061 33.333 0.00 0.00 0.00 3.41
1604 2060 9.525826 AATCTGACCTTTACATCTGAAAAATCT 57.474 29.630 0.00 0.00 0.00 2.40
1609 2065 9.793259 AGTTAAATCTGACCTTTACATCTGAAA 57.207 29.630 0.00 0.00 0.00 2.69
1610 2066 9.436957 GAGTTAAATCTGACCTTTACATCTGAA 57.563 33.333 0.00 0.00 0.00 3.02
1630 2086 8.731275 TTCTGAAATCTGAACACAAGAGTTAA 57.269 30.769 0.00 0.00 0.00 2.01
1636 2092 5.678483 CACGTTTCTGAAATCTGAACACAAG 59.322 40.000 6.06 0.00 34.31 3.16
1671 2127 2.046285 GGTTCCAATGGTGCCCTCG 61.046 63.158 0.00 0.00 0.00 4.63
1695 2673 2.408565 TCCCAGTTTCCTGTGAGTCTT 58.591 47.619 0.00 0.00 36.95 3.01
1712 2690 0.606673 GAGCTGACCCACAAGTTCCC 60.607 60.000 0.00 0.00 0.00 3.97
1722 2700 1.690633 TCCCTCCATGAGCTGACCC 60.691 63.158 0.00 0.00 0.00 4.46
1725 2703 1.383664 CCCTCCCTCCATGAGCTGA 60.384 63.158 0.00 0.00 0.00 4.26
1735 2713 2.040412 TCTTCAAGAAAAGCCCTCCCTC 59.960 50.000 0.00 0.00 0.00 4.30
1778 2756 4.574013 GTGATCACATGAACTTCATCCTCC 59.426 45.833 21.07 0.00 34.28 4.30
1897 4075 2.455032 CACGTTCAAAACATTCGGCAA 58.545 42.857 0.00 0.00 0.00 4.52
1900 4078 1.604755 TCCCACGTTCAAAACATTCGG 59.395 47.619 0.00 0.00 0.00 4.30
1901 4079 2.032302 TGTCCCACGTTCAAAACATTCG 59.968 45.455 0.00 0.00 0.00 3.34
1933 4111 0.762418 ACGATCCACAAGGTTCACCA 59.238 50.000 0.00 0.00 38.89 4.17
1954 4132 1.751349 AACCCGTGCTACAACCGTCT 61.751 55.000 0.00 0.00 0.00 4.18
1957 4135 1.864176 GAAACCCGTGCTACAACCG 59.136 57.895 0.00 0.00 0.00 4.44
1965 4143 7.276256 ATTCATTTAGAAAACGAAACCCGTGC 61.276 38.462 0.00 0.00 44.53 5.34
1968 4146 7.745015 TCTATTCATTTAGAAAACGAAACCCG 58.255 34.615 0.00 0.00 40.22 5.28
2010 4188 4.042062 TGAAGATGATCCAGTCAGGTTTGT 59.958 41.667 0.00 0.00 40.92 2.83
2011 4189 4.582869 TGAAGATGATCCAGTCAGGTTTG 58.417 43.478 0.00 0.00 40.92 2.93
2014 4192 4.566488 GGTTTGAAGATGATCCAGTCAGGT 60.566 45.833 0.00 0.00 40.92 4.00
2039 4217 0.938008 GGAAATCGGCGAATCCAGTC 59.062 55.000 29.24 11.81 34.01 3.51
2160 4536 3.945921 AGATGATGTCAGCAAGATGGTTG 59.054 43.478 0.00 0.00 34.14 3.77
2168 4544 5.416639 AGCAATTTGTAGATGATGTCAGCAA 59.583 36.000 0.00 0.00 34.14 3.91
2197 4579 2.028930 ACAGTCTCCAGAGCCGTAAAAG 60.029 50.000 0.00 0.00 0.00 2.27
2222 4605 4.122776 GTGACTGTAGCTCCCATGTATTG 58.877 47.826 0.00 0.00 0.00 1.90
2225 4608 3.101643 AGTGACTGTAGCTCCCATGTA 57.898 47.619 0.00 0.00 0.00 2.29
2227 4610 4.184629 GTTAAGTGACTGTAGCTCCCATG 58.815 47.826 0.00 0.00 0.00 3.66
2229 4612 2.565834 GGTTAAGTGACTGTAGCTCCCA 59.434 50.000 0.00 0.00 0.00 4.37
2230 4613 2.416972 CGGTTAAGTGACTGTAGCTCCC 60.417 54.545 0.00 0.00 0.00 4.30
2233 4616 1.549170 CCCGGTTAAGTGACTGTAGCT 59.451 52.381 0.00 0.00 0.00 3.32
2234 4617 1.274447 ACCCGGTTAAGTGACTGTAGC 59.726 52.381 0.00 0.00 0.00 3.58
2235 4618 2.094338 GGACCCGGTTAAGTGACTGTAG 60.094 54.545 0.00 0.00 0.00 2.74
2280 4665 2.359850 TGCCCTCCGTGATGTTGC 60.360 61.111 0.00 0.00 0.00 4.17
2300 4685 2.231215 AGGCTATCTTGTCATGACGC 57.769 50.000 20.54 15.56 0.00 5.19
2382 4770 1.467342 GTCGCAAGGACCCAATACAAC 59.533 52.381 0.00 0.00 39.90 3.32
2400 4788 2.636893 AGAGGGAGTATGATGCATGGTC 59.363 50.000 2.46 0.00 0.00 4.02
2413 4801 8.862085 GCTCTTATATTAGTTTACAGAGGGAGT 58.138 37.037 0.00 0.00 0.00 3.85
2414 4802 8.861086 TGCTCTTATATTAGTTTACAGAGGGAG 58.139 37.037 0.00 0.00 0.00 4.30
2415 4803 8.777578 TGCTCTTATATTAGTTTACAGAGGGA 57.222 34.615 0.00 0.00 0.00 4.20
2466 4854 9.063615 CCCTCCGTAAACTAATATAAAAGCATT 57.936 33.333 0.00 0.00 0.00 3.56
2467 4855 8.434392 TCCCTCCGTAAACTAATATAAAAGCAT 58.566 33.333 0.00 0.00 0.00 3.79
2468 4856 7.794041 TCCCTCCGTAAACTAATATAAAAGCA 58.206 34.615 0.00 0.00 0.00 3.91
2469 4857 7.930325 ACTCCCTCCGTAAACTAATATAAAAGC 59.070 37.037 0.00 0.00 0.00 3.51
2498 4886 0.945813 CGGTGGAGTTGGCGTAAAAA 59.054 50.000 0.00 0.00 0.00 1.94
2499 4887 1.508808 GCGGTGGAGTTGGCGTAAAA 61.509 55.000 0.00 0.00 0.00 1.52
2500 4888 1.962306 GCGGTGGAGTTGGCGTAAA 60.962 57.895 0.00 0.00 0.00 2.01
2501 4889 2.357760 GCGGTGGAGTTGGCGTAA 60.358 61.111 0.00 0.00 0.00 3.18
2502 4890 4.728102 CGCGGTGGAGTTGGCGTA 62.728 66.667 0.00 0.00 43.36 4.42
2519 4907 4.404098 ACATCCGGTTGGGGTCGC 62.404 66.667 16.70 0.00 36.01 5.19
2520 4908 2.125269 GACATCCGGTTGGGGTCG 60.125 66.667 16.70 0.00 36.01 4.79
2521 4909 2.271173 GGACATCCGGTTGGGGTC 59.729 66.667 16.70 10.46 38.48 4.46
2531 4919 2.874751 CGGGCAAAACGGACATCC 59.125 61.111 0.00 0.00 0.00 3.51
2538 4926 0.168128 GACAGAATCCGGGCAAAACG 59.832 55.000 0.00 0.00 0.00 3.60
2539 4927 0.526211 GGACAGAATCCGGGCAAAAC 59.474 55.000 0.00 0.00 37.88 2.43
2540 4928 2.955609 GGACAGAATCCGGGCAAAA 58.044 52.632 0.00 0.00 37.88 2.44
2541 4929 4.734652 GGACAGAATCCGGGCAAA 57.265 55.556 0.00 0.00 37.88 3.68
2548 4936 2.629051 CTACCCAAACGGACAGAATCC 58.371 52.381 0.00 0.00 45.20 3.01
2549 4937 2.629051 CCTACCCAAACGGACAGAATC 58.371 52.381 0.00 0.00 34.64 2.52
2550 4938 1.280998 CCCTACCCAAACGGACAGAAT 59.719 52.381 0.00 0.00 34.64 2.40
2551 4939 0.688487 CCCTACCCAAACGGACAGAA 59.312 55.000 0.00 0.00 34.64 3.02
2552 4940 1.833787 GCCCTACCCAAACGGACAGA 61.834 60.000 0.00 0.00 34.64 3.41
2553 4941 1.376812 GCCCTACCCAAACGGACAG 60.377 63.158 0.00 0.00 34.64 3.51
2554 4942 1.706995 TTGCCCTACCCAAACGGACA 61.707 55.000 0.00 0.00 34.64 4.02
2555 4943 0.323087 ATTGCCCTACCCAAACGGAC 60.323 55.000 0.00 0.00 34.64 4.79
2556 4944 1.210967 CTATTGCCCTACCCAAACGGA 59.789 52.381 0.00 0.00 34.64 4.69
2557 4945 1.675552 CTATTGCCCTACCCAAACGG 58.324 55.000 0.00 0.00 37.81 4.44
2558 4946 1.675552 CCTATTGCCCTACCCAAACG 58.324 55.000 0.00 0.00 0.00 3.60
2559 4947 1.286849 ACCCTATTGCCCTACCCAAAC 59.713 52.381 0.00 0.00 0.00 2.93
2560 4948 1.567175 GACCCTATTGCCCTACCCAAA 59.433 52.381 0.00 0.00 0.00 3.28
2561 4949 1.218844 GACCCTATTGCCCTACCCAA 58.781 55.000 0.00 0.00 0.00 4.12
2562 4950 1.052124 CGACCCTATTGCCCTACCCA 61.052 60.000 0.00 0.00 0.00 4.51
2563 4951 1.052694 ACGACCCTATTGCCCTACCC 61.053 60.000 0.00 0.00 0.00 3.69
2564 4952 0.106149 CACGACCCTATTGCCCTACC 59.894 60.000 0.00 0.00 0.00 3.18
2565 4953 0.828677 ACACGACCCTATTGCCCTAC 59.171 55.000 0.00 0.00 0.00 3.18
2566 4954 1.117150 GACACGACCCTATTGCCCTA 58.883 55.000 0.00 0.00 0.00 3.53
2567 4955 1.623542 GGACACGACCCTATTGCCCT 61.624 60.000 0.00 0.00 0.00 5.19
2568 4956 1.153229 GGACACGACCCTATTGCCC 60.153 63.158 0.00 0.00 0.00 5.36
2569 4957 1.520787 CGGACACGACCCTATTGCC 60.521 63.158 0.00 0.00 44.60 4.52
2570 4958 1.520787 CCGGACACGACCCTATTGC 60.521 63.158 0.00 0.00 44.60 3.56
2571 4959 0.179119 GTCCGGACACGACCCTATTG 60.179 60.000 29.75 0.00 44.60 1.90
2572 4960 1.325476 GGTCCGGACACGACCCTATT 61.325 60.000 34.40 0.00 44.60 1.73
2573 4961 1.755783 GGTCCGGACACGACCCTAT 60.756 63.158 34.40 0.00 44.60 2.57
2574 4962 2.361610 GGTCCGGACACGACCCTA 60.362 66.667 34.40 0.00 44.60 3.53
2577 4965 3.504524 AAACGGTCCGGACACGACC 62.505 63.158 36.08 21.79 44.60 4.79
2578 4966 2.018324 GAAACGGTCCGGACACGAC 61.018 63.158 36.08 25.69 44.60 4.34
2579 4967 2.195567 AGAAACGGTCCGGACACGA 61.196 57.895 36.08 4.09 44.60 4.35
2580 4968 2.019951 CAGAAACGGTCCGGACACG 61.020 63.158 34.40 32.48 40.55 4.49
2581 4969 1.666872 CCAGAAACGGTCCGGACAC 60.667 63.158 34.40 22.34 0.00 3.67
2582 4970 1.401318 TTCCAGAAACGGTCCGGACA 61.401 55.000 34.40 9.22 0.00 4.02
2583 4971 0.036671 ATTCCAGAAACGGTCCGGAC 60.037 55.000 27.04 27.04 0.00 4.79
2584 4972 0.036765 CATTCCAGAAACGGTCCGGA 60.037 55.000 17.28 0.00 0.00 5.14
2585 4973 1.644786 GCATTCCAGAAACGGTCCGG 61.645 60.000 17.28 0.00 0.00 5.14
2586 4974 1.794222 GCATTCCAGAAACGGTCCG 59.206 57.895 10.48 10.48 0.00 4.79
2587 4975 1.644786 CCGCATTCCAGAAACGGTCC 61.645 60.000 13.98 0.00 38.49 4.46
2588 4976 1.794222 CCGCATTCCAGAAACGGTC 59.206 57.895 13.98 0.00 38.49 4.79
2589 4977 1.072505 ACCGCATTCCAGAAACGGT 59.927 52.632 19.39 19.39 45.95 4.83
2590 4978 1.501741 CACCGCATTCCAGAAACGG 59.498 57.895 18.37 18.37 44.56 4.44
2591 4979 1.501741 CCACCGCATTCCAGAAACG 59.498 57.895 0.00 0.63 0.00 3.60
2592 4980 1.212751 GCCACCGCATTCCAGAAAC 59.787 57.895 0.00 0.00 34.03 2.78
2593 4981 1.976474 GGCCACCGCATTCCAGAAA 60.976 57.895 0.00 0.00 36.38 2.52
2594 4982 2.361104 GGCCACCGCATTCCAGAA 60.361 61.111 0.00 0.00 36.38 3.02
2595 4983 4.776322 CGGCCACCGCATTCCAGA 62.776 66.667 2.24 0.00 41.17 3.86
2631 5019 4.034258 CATGATGCGGCCGGATGC 62.034 66.667 37.91 25.95 40.16 3.91
2632 5020 2.592574 ACATGATGCGGCCGGATG 60.593 61.111 37.91 26.19 0.00 3.51
2633 5021 2.281070 GACATGATGCGGCCGGAT 60.281 61.111 33.56 33.56 0.00 4.18
2634 5022 4.545706 GGACATGATGCGGCCGGA 62.546 66.667 29.38 27.51 0.00 5.14
2641 5029 2.257286 AAAGTGCGCGGACATGATGC 62.257 55.000 32.28 3.48 0.00 3.91
2642 5030 0.168788 AAAAGTGCGCGGACATGATG 59.831 50.000 32.28 0.00 0.00 3.07
2643 5031 0.881118 AAAAAGTGCGCGGACATGAT 59.119 45.000 32.28 13.07 0.00 2.45
2644 5032 2.326222 AAAAAGTGCGCGGACATGA 58.674 47.368 32.28 0.00 0.00 3.07
2645 5033 4.942090 AAAAAGTGCGCGGACATG 57.058 50.000 32.28 0.00 0.00 3.21
2684 5072 9.642327 CATGTACCAAGAATGAATGATGAAAAA 57.358 29.630 0.00 0.00 0.00 1.94
2685 5073 8.252417 CCATGTACCAAGAATGAATGATGAAAA 58.748 33.333 0.00 0.00 0.00 2.29
2686 5074 7.614974 TCCATGTACCAAGAATGAATGATGAAA 59.385 33.333 0.00 0.00 0.00 2.69
2687 5075 7.118060 TCCATGTACCAAGAATGAATGATGAA 58.882 34.615 0.00 0.00 0.00 2.57
2688 5076 6.661777 TCCATGTACCAAGAATGAATGATGA 58.338 36.000 0.00 0.00 0.00 2.92
2689 5077 6.947644 TCCATGTACCAAGAATGAATGATG 57.052 37.500 0.00 0.00 0.00 3.07
2690 5078 7.959658 TTTCCATGTACCAAGAATGAATGAT 57.040 32.000 0.00 0.00 0.00 2.45
2691 5079 7.959658 ATTTCCATGTACCAAGAATGAATGA 57.040 32.000 0.00 0.00 0.00 2.57
2692 5080 8.685427 TGTATTTCCATGTACCAAGAATGAATG 58.315 33.333 0.00 0.00 0.00 2.67
2693 5081 8.821686 TGTATTTCCATGTACCAAGAATGAAT 57.178 30.769 0.00 0.00 0.00 2.57
2694 5082 8.821686 ATGTATTTCCATGTACCAAGAATGAA 57.178 30.769 0.00 0.00 0.00 2.57
2695 5083 8.052141 TGATGTATTTCCATGTACCAAGAATGA 58.948 33.333 0.00 0.00 0.00 2.57
2696 5084 8.224389 TGATGTATTTCCATGTACCAAGAATG 57.776 34.615 0.00 0.00 0.00 2.67
2697 5085 9.071276 GATGATGTATTTCCATGTACCAAGAAT 57.929 33.333 0.00 0.00 0.00 2.40
2698 5086 8.052141 TGATGATGTATTTCCATGTACCAAGAA 58.948 33.333 0.00 0.00 0.00 2.52
2699 5087 7.572814 TGATGATGTATTTCCATGTACCAAGA 58.427 34.615 0.00 0.00 0.00 3.02
2700 5088 7.806409 TGATGATGTATTTCCATGTACCAAG 57.194 36.000 0.00 0.00 0.00 3.61
2701 5089 8.586879 TTTGATGATGTATTTCCATGTACCAA 57.413 30.769 0.00 0.00 0.00 3.67
2702 5090 8.765488 ATTTGATGATGTATTTCCATGTACCA 57.235 30.769 0.00 0.00 0.00 3.25
2772 5160 9.927081 ATGGAAGTTGGATATCTTCTAAAATGT 57.073 29.630 2.05 0.00 39.67 2.71


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

AutoCloner maintained by Alex Coulton.