Multiple sequence alignment - TraesCS2D01G576300

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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 TraesCS2D01G576300 chr2D 100.000 3537 0 0 1 3537 639747905 639744369 0.000000e+00 6532.0
1 TraesCS2D01G576300 chr2D 84.111 2316 215 73 37 2272 639822980 639820738 0.000000e+00 2097.0
2 TraesCS2D01G576300 chr2D 84.610 1540 149 48 876 2372 639732942 639734436 0.000000e+00 1450.0
3 TraesCS2D01G576300 chr2D 86.503 326 25 7 2298 2612 639820745 639820428 1.220000e-89 340.0
4 TraesCS2D01G576300 chr2D 85.081 248 18 9 370 615 639732228 639732458 5.900000e-58 235.0
5 TraesCS2D01G576300 chr2D 89.655 87 9 0 3451 3537 181488733 181488647 1.040000e-20 111.0
6 TraesCS2D01G576300 chr2D 87.500 88 10 1 3451 3537 142418881 142418794 2.250000e-17 100.0
7 TraesCS2D01G576300 chr2D 91.781 73 5 1 677 749 639732568 639732639 2.250000e-17 100.0
8 TraesCS2D01G576300 chr2D 84.848 99 4 6 164 262 639732070 639732157 4.860000e-14 89.8
9 TraesCS2D01G576300 chr2D 78.947 152 11 4 536 682 639872787 639872652 2.260000e-12 84.2
10 TraesCS2D01G576300 chr2B 89.237 1626 123 24 1029 2612 799047706 799046091 0.000000e+00 1986.0
11 TraesCS2D01G576300 chr2B 81.982 1221 120 49 1410 2602 799029477 799030625 0.000000e+00 944.0
12 TraesCS2D01G576300 chr2B 83.971 836 84 25 1442 2258 798957997 798958801 0.000000e+00 756.0
13 TraesCS2D01G576300 chr2B 85.447 694 57 22 1118 1801 799107610 799106951 0.000000e+00 682.0
14 TraesCS2D01G576300 chr2B 83.880 732 49 26 677 1347 798957217 798957940 4.980000e-178 634.0
15 TraesCS2D01G576300 chr2B 87.110 481 46 9 205 676 799048522 799048049 6.720000e-147 531.0
16 TraesCS2D01G576300 chr2B 79.299 884 83 50 13 854 799028071 799028896 8.700000e-146 527.0
17 TraesCS2D01G576300 chr2B 84.830 501 46 10 872 1347 799028958 799029453 8.880000e-131 477.0
18 TraesCS2D01G576300 chr2B 89.418 378 28 9 2740 3111 799046094 799045723 1.920000e-127 466.0
19 TraesCS2D01G576300 chr2B 80.937 619 53 23 68 682 799108716 799108159 2.520000e-116 429.0
20 TraesCS2D01G576300 chr2B 86.688 308 19 13 2311 2599 798958821 798959125 4.400000e-84 322.0
21 TraesCS2D01G576300 chr2B 78.933 356 60 12 2709 3058 799030692 799031038 9.880000e-56 228.0
22 TraesCS2D01G576300 chr2B 82.772 267 25 10 351 615 798956865 798957112 5.940000e-53 219.0
23 TraesCS2D01G576300 chr2B 90.968 155 12 2 3115 3269 285854037 285853885 1.290000e-49 207.0
24 TraesCS2D01G576300 chr2B 86.932 176 9 3 3108 3269 414363650 414363475 6.030000e-43 185.0
25 TraesCS2D01G576300 chr2B 79.048 315 23 22 730 1005 799108085 799107775 3.630000e-40 176.0
26 TraesCS2D01G576300 chr2B 76.205 332 33 23 677 995 799048005 799047707 2.220000e-27 134.0
27 TraesCS2D01G576300 chr2B 86.441 118 6 2 37 144 799048663 799048546 1.720000e-23 121.0
28 TraesCS2D01G576300 chr2B 93.548 62 3 1 38 99 798956658 798956718 1.350000e-14 91.6
29 TraesCS2D01G576300 chr2B 83.178 107 7 6 164 270 798956748 798956843 1.750000e-13 87.9
30 TraesCS2D01G576300 chr2B 89.474 57 4 1 13 67 799115703 799115647 1.760000e-08 71.3
31 TraesCS2D01G576300 chr2A 87.680 1664 128 28 1035 2645 765393749 765392110 0.000000e+00 1866.0
32 TraesCS2D01G576300 chr2A 80.384 1769 155 82 677 2372 765373286 765374935 0.000000e+00 1168.0
33 TraesCS2D01G576300 chr2A 90.198 857 70 11 2684 3537 765392111 765391266 0.000000e+00 1105.0
34 TraesCS2D01G576300 chr2A 84.375 896 94 20 1409 2272 765441998 765441117 0.000000e+00 837.0
35 TraesCS2D01G576300 chr2A 87.582 612 42 11 94 682 765443323 765442723 0.000000e+00 678.0
36 TraesCS2D01G576300 chr2A 79.861 864 141 21 1429 2271 765516097 765515246 5.050000e-168 601.0
37 TraesCS2D01G576300 chr2A 83.119 699 58 29 2298 2981 765441124 765440471 1.830000e-162 582.0
38 TraesCS2D01G576300 chr2A 83.915 659 53 21 37 676 765394736 765394112 6.580000e-162 580.0
39 TraesCS2D01G576300 chr2A 78.744 908 121 30 1430 2287 765278093 765278978 3.110000e-150 542.0
40 TraesCS2D01G576300 chr2A 89.028 319 20 7 1055 1359 765442335 765442018 7.160000e-102 381.0
41 TraesCS2D01G576300 chr2A 81.461 356 41 17 677 1019 765442681 765442338 5.820000e-68 268.0
42 TraesCS2D01G576300 chr2A 89.503 181 17 2 3266 3445 102087143 102087322 9.880000e-56 228.0
43 TraesCS2D01G576300 chr2A 89.503 181 17 2 3272 3451 580047764 580047585 9.880000e-56 228.0
44 TraesCS2D01G576300 chr2A 84.080 201 12 7 677 873 765394068 765393884 3.630000e-40 176.0
45 TraesCS2D01G576300 chr2A 80.632 253 21 8 370 615 765372940 765373171 1.690000e-38 171.0
46 TraesCS2D01G576300 chr2A 88.489 139 13 3 2979 3115 765428772 765428635 7.860000e-37 165.0
47 TraesCS2D01G576300 chr2A 96.364 55 1 1 37 91 765549187 765549134 4.860000e-14 89.8
48 TraesCS2D01G576300 chr2A 91.525 59 3 2 770 826 765516642 765516584 2.930000e-11 80.5
49 TraesCS2D01G576300 chr2A 93.750 48 3 0 39 86 765372737 765372784 4.900000e-09 73.1
50 TraesCS2D01G576300 chr1B 95.322 171 7 1 3272 3442 606482172 606482003 1.620000e-68 270.0
51 TraesCS2D01G576300 chr7A 93.785 177 11 0 3272 3448 76185188 76185012 2.090000e-67 267.0
52 TraesCS2D01G576300 chr7A 93.125 160 11 0 3109 3268 706993394 706993235 5.900000e-58 235.0
53 TraesCS2D01G576300 chr6A 93.082 159 11 0 3111 3269 439059836 439059678 2.120000e-57 233.0
54 TraesCS2D01G576300 chr6A 89.326 178 17 2 3272 3448 191218649 191218825 4.600000e-54 222.0
55 TraesCS2D01G576300 chr6A 93.204 103 4 2 3112 3213 423384814 423384914 7.910000e-32 148.0
56 TraesCS2D01G576300 chr3B 89.831 177 17 1 3272 3448 513945843 513945668 3.550000e-55 226.0
57 TraesCS2D01G576300 chr3B 88.889 90 7 2 3451 3537 453884932 453885021 1.340000e-19 108.0
58 TraesCS2D01G576300 chr5A 88.764 178 18 2 3272 3448 666060444 666060620 2.140000e-52 217.0
59 TraesCS2D01G576300 chr7B 90.566 159 15 0 3112 3270 674107763 674107921 9.950000e-51 211.0
60 TraesCS2D01G576300 chr7B 90.260 154 14 1 3112 3264 226329537 226329690 2.150000e-47 200.0
61 TraesCS2D01G576300 chr3A 88.333 180 15 5 3272 3448 20233281 20233457 9.950000e-51 211.0
62 TraesCS2D01G576300 chr3A 88.889 153 16 1 3118 3270 75461825 75461674 1.680000e-43 187.0
63 TraesCS2D01G576300 chrUn 87.283 173 8 1 3112 3270 364057044 364057216 6.030000e-43 185.0
64 TraesCS2D01G576300 chr5B 92.308 117 6 2 3155 3270 425175338 425175224 2.830000e-36 163.0
65 TraesCS2D01G576300 chr5B 87.500 88 10 1 3451 3537 224327147 224327234 2.250000e-17 100.0
66 TraesCS2D01G576300 chr4D 90.909 88 7 1 3451 3537 444126889 444126802 2.230000e-22 117.0
67 TraesCS2D01G576300 chr4D 89.773 88 8 1 3451 3537 14055009 14054922 1.040000e-20 111.0
68 TraesCS2D01G576300 chr4D 89.773 88 8 1 3451 3537 21158022 21158109 1.040000e-20 111.0
69 TraesCS2D01G576300 chr4D 87.500 88 10 1 3451 3537 453361068 453361155 2.250000e-17 100.0


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 TraesCS2D01G576300 chr2D 639744369 639747905 3536 True 6532.00 6532 100.000000 1 3537 1 chr2D.!!$R3 3536
1 TraesCS2D01G576300 chr2D 639820428 639822980 2552 True 1218.50 2097 85.307000 37 2612 2 chr2D.!!$R5 2575
2 TraesCS2D01G576300 chr2D 639732070 639734436 2366 False 468.70 1450 86.580000 164 2372 4 chr2D.!!$F1 2208
3 TraesCS2D01G576300 chr2B 799045723 799048663 2940 True 647.60 1986 85.682200 37 3111 5 chr2B.!!$R4 3074
4 TraesCS2D01G576300 chr2B 799028071 799031038 2967 False 544.00 944 81.261000 13 3058 4 chr2B.!!$F2 3045
5 TraesCS2D01G576300 chr2B 799106951 799108716 1765 True 429.00 682 81.810667 68 1801 3 chr2B.!!$R5 1733
6 TraesCS2D01G576300 chr2B 798956658 798959125 2467 False 351.75 756 85.672833 38 2599 6 chr2B.!!$F1 2561
7 TraesCS2D01G576300 chr2A 765391266 765394736 3470 True 931.75 1866 86.468250 37 3537 4 chr2A.!!$R4 3500
8 TraesCS2D01G576300 chr2A 765440471 765443323 2852 True 549.20 837 85.113000 94 2981 5 chr2A.!!$R5 2887
9 TraesCS2D01G576300 chr2A 765278093 765278978 885 False 542.00 542 78.744000 1430 2287 1 chr2A.!!$F2 857
10 TraesCS2D01G576300 chr2A 765372737 765374935 2198 False 470.70 1168 84.922000 39 2372 3 chr2A.!!$F3 2333
11 TraesCS2D01G576300 chr2A 765515246 765516642 1396 True 340.75 601 85.693000 770 2271 2 chr2A.!!$R6 1501

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
276 324 0.318275 GTCCTGCTGGATCGATCGAC 60.318 60.0 22.06 14.0 45.29 4.20 F
1926 2707 0.032017 AGGCCGTCCTACATCTTCCT 60.032 55.0 0.00 0.0 42.06 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2274 3115 0.105039 GGCAGCCGTAGCAGAGTATT 59.895 55.000 0.0 0.0 43.56 1.89 R
3157 4088 1.065418 CGGTAGAGCCCCAAAAGTGAT 60.065 52.381 0.0 0.0 0.00 3.06 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
17 18 2.668550 AAGGCAACCCGCGAGTTC 60.669 61.111 8.23 0.60 43.84 3.01
22 23 0.947180 GCAACCCGCGAGTTCTGTAA 60.947 55.000 8.23 0.00 0.00 2.41
30 31 1.320852 GCGAGTTCTGTAAACGCTAGC 59.679 52.381 4.06 4.06 44.67 3.42
31 32 2.592194 CGAGTTCTGTAAACGCTAGCA 58.408 47.619 16.45 0.00 0.00 3.49
92 100 3.626670 ACCAGCTAGCTAGTACGTACTTG 59.373 47.826 31.58 28.70 37.73 3.16
103 111 4.868067 AGTACGTACTTGCATGTATAGCC 58.132 43.478 22.45 2.57 31.13 3.93
245 266 5.029650 TGAATTGAGGTTGAAATTCGTCG 57.970 39.130 0.00 0.00 42.93 5.12
265 286 1.376543 CTGCAACCATAGTCCTGCTG 58.623 55.000 0.00 0.00 32.07 4.41
275 323 0.466372 AGTCCTGCTGGATCGATCGA 60.466 55.000 21.86 21.86 45.29 3.59
276 324 0.318275 GTCCTGCTGGATCGATCGAC 60.318 60.000 22.06 14.00 45.29 4.20
277 325 1.006805 CCTGCTGGATCGATCGACC 60.007 63.158 22.06 22.15 34.57 4.79
278 326 1.006805 CTGCTGGATCGATCGACCC 60.007 63.158 22.47 22.47 0.00 4.46
436 484 4.061131 TGACCAGAGACCCAATCTTCTA 57.939 45.455 0.00 0.00 38.00 2.10
455 504 8.016301 TCTTCTATCTCTAACCGTAGTGTAGA 57.984 38.462 0.00 0.00 0.00 2.59
459 508 8.026026 TCTATCTCTAACCGTAGTGTAGATACG 58.974 40.741 0.00 0.00 44.29 3.06
460 509 5.907207 TCTCTAACCGTAGTGTAGATACGT 58.093 41.667 0.00 0.00 43.42 3.57
461 510 5.750547 TCTCTAACCGTAGTGTAGATACGTG 59.249 44.000 0.00 0.18 43.42 4.49
462 511 5.419542 TCTAACCGTAGTGTAGATACGTGT 58.580 41.667 0.00 0.00 43.42 4.49
476 525 1.290955 CGTGTGTGTCCGGTACCAT 59.709 57.895 13.54 0.00 0.00 3.55
489 538 3.032667 TACCATTAGGCCGGCGCAA 62.033 57.895 22.54 17.19 39.06 4.85
507 556 4.795278 GCGCAAGAAAATGATGGAAACTAG 59.205 41.667 0.30 0.00 43.02 2.57
513 562 6.653989 AGAAAATGATGGAAACTAGACGGAT 58.346 36.000 0.00 0.00 0.00 4.18
573 639 5.239306 CCTGAAGTGCACTCAAAGAAACATA 59.761 40.000 21.95 0.00 0.00 2.29
615 687 4.503991 CCCTAAAAGCTTCACTCTCACAGT 60.504 45.833 0.00 0.00 34.67 3.55
645 732 5.221521 GCAGGACCTTTTCATTCCTCTTTTT 60.222 40.000 0.00 0.00 37.69 1.94
672 759 5.994250 TCTATCTTCTTCCATTCCCACTTG 58.006 41.667 0.00 0.00 0.00 3.16
689 827 2.490903 ACTTGACATTGCAATCAGCCTC 59.509 45.455 9.53 0.26 44.83 4.70
699 837 3.431922 CAATCAGCCTCGATTGCAATT 57.568 42.857 14.33 0.00 44.13 2.32
700 838 3.113322 CAATCAGCCTCGATTGCAATTG 58.887 45.455 19.13 19.13 44.13 2.32
701 839 1.825090 TCAGCCTCGATTGCAATTGT 58.175 45.000 23.14 4.34 0.00 2.71
702 840 2.984562 TCAGCCTCGATTGCAATTGTA 58.015 42.857 23.14 11.28 0.00 2.41
703 841 2.677836 TCAGCCTCGATTGCAATTGTAC 59.322 45.455 23.14 14.73 0.00 2.90
704 842 2.679837 CAGCCTCGATTGCAATTGTACT 59.320 45.455 23.14 16.38 0.00 2.73
705 843 3.127548 CAGCCTCGATTGCAATTGTACTT 59.872 43.478 23.14 8.19 0.00 2.24
706 844 3.758554 AGCCTCGATTGCAATTGTACTTT 59.241 39.130 23.14 6.99 0.00 2.66
707 845 3.853671 GCCTCGATTGCAATTGTACTTTG 59.146 43.478 23.14 9.82 0.00 2.77
708 846 4.615912 GCCTCGATTGCAATTGTACTTTGT 60.616 41.667 23.14 0.00 0.00 2.83
709 847 5.088739 CCTCGATTGCAATTGTACTTTGTC 58.911 41.667 23.14 3.23 0.00 3.18
710 848 5.041951 TCGATTGCAATTGTACTTTGTCC 57.958 39.130 23.14 1.95 0.00 4.02
711 849 4.759693 TCGATTGCAATTGTACTTTGTCCT 59.240 37.500 23.14 0.00 0.00 3.85
712 850 5.088739 CGATTGCAATTGTACTTTGTCCTC 58.911 41.667 14.33 0.00 0.00 3.71
713 851 5.334802 CGATTGCAATTGTACTTTGTCCTCA 60.335 40.000 14.33 0.00 0.00 3.86
714 852 5.437289 TTGCAATTGTACTTTGTCCTCAG 57.563 39.130 7.40 0.00 0.00 3.35
715 853 4.713553 TGCAATTGTACTTTGTCCTCAGA 58.286 39.130 7.40 0.00 0.00 3.27
716 854 5.129634 TGCAATTGTACTTTGTCCTCAGAA 58.870 37.500 7.40 0.00 0.00 3.02
717 855 5.592282 TGCAATTGTACTTTGTCCTCAGAAA 59.408 36.000 7.40 0.00 0.00 2.52
718 856 6.096141 TGCAATTGTACTTTGTCCTCAGAAAA 59.904 34.615 7.40 0.00 0.00 2.29
844 1162 4.432712 TCATATATATGAGCGTGCGCATT 58.567 39.130 19.44 1.72 37.76 3.56
850 1179 3.686392 GAGCGTGCGCATTCGTGTC 62.686 63.158 15.91 10.95 44.88 3.67
976 1526 7.597369 ACACGCATACAACATATATACACGATT 59.403 33.333 0.00 0.00 0.00 3.34
978 1528 7.062956 ACGCATACAACATATATACACGATTGG 59.937 37.037 0.00 0.00 0.00 3.16
1014 1564 0.178950 TTAGCACCATTGTTGCCCCA 60.179 50.000 2.20 0.00 0.00 4.96
1027 1577 1.588239 TGCCCCACTCTGAAGATCAT 58.412 50.000 0.00 0.00 0.00 2.45
1039 1589 0.842635 AAGATCATCTGTGGCCTCCC 59.157 55.000 3.32 0.00 0.00 4.30
1049 1599 4.740822 GGCCTCCCCACGTTGCAT 62.741 66.667 0.00 0.00 0.00 3.96
1053 1606 0.462047 CCTCCCCACGTTGCATCTAC 60.462 60.000 0.00 0.00 0.00 2.59
1059 1612 3.490419 CCCCACGTTGCATCTACTAGTAC 60.490 52.174 0.00 0.00 0.00 2.73
1106 1662 3.256879 TCAGTTCAGAAGACATCGAGCTT 59.743 43.478 0.00 0.00 0.00 3.74
1120 1758 1.661112 CGAGCTTGCTTGCTAAGGTAC 59.339 52.381 4.13 0.00 44.17 3.34
1129 1767 3.742640 GCTTGCTAAGGTACATGCTAGCT 60.743 47.826 17.23 0.00 45.55 3.32
1353 2001 8.223177 TCGTTTTGTAATTTTACTCTTTCCCA 57.777 30.769 2.45 0.00 34.77 4.37
1408 2065 3.021695 TGGAACTGAGGGAGTACATACG 58.978 50.000 0.00 0.00 33.09 3.06
1650 2314 1.079819 CAAGCCGGTGATGTCGTCT 60.080 57.895 1.90 0.00 0.00 4.18
1659 2323 2.750637 ATGTCGTCTCGGAGCCGT 60.751 61.111 8.39 0.00 40.74 5.68
1752 2440 0.968901 TCATCCACGAGTACCGCCTT 60.969 55.000 0.00 0.00 43.32 4.35
1782 2470 2.361610 CATGCCCCCACACAGGTC 60.362 66.667 0.00 0.00 34.66 3.85
1786 2474 3.566210 CCCCCACACAGGTCCGTT 61.566 66.667 0.00 0.00 34.66 4.44
1790 2478 1.555992 CCCCACACAGGTCCGTTATTA 59.444 52.381 0.00 0.00 34.66 0.98
1821 2548 6.284459 TCTTCAGTTCTTCTTCTGTTCTTCC 58.716 40.000 0.00 0.00 33.89 3.46
1823 2553 6.978674 TCAGTTCTTCTTCTGTTCTTCCTA 57.021 37.500 0.00 0.00 33.89 2.94
1879 2660 1.932156 AAGGTTGGGTGGTGTGCAGA 61.932 55.000 0.00 0.00 0.00 4.26
1926 2707 0.032017 AGGCCGTCCTACATCTTCCT 60.032 55.000 0.00 0.00 42.06 3.36
1927 2708 0.105039 GGCCGTCCTACATCTTCCTG 59.895 60.000 0.00 0.00 0.00 3.86
1928 2709 0.530870 GCCGTCCTACATCTTCCTGC 60.531 60.000 0.00 0.00 0.00 4.85
1931 2712 0.530870 GTCCTACATCTTCCTGCCGC 60.531 60.000 0.00 0.00 0.00 6.53
1970 2751 2.436469 TCGGCGGCTACTACGACA 60.436 61.111 7.21 0.00 39.94 4.35
2239 3047 1.813513 CTGGCATCGACTGGAACTTT 58.186 50.000 0.00 0.00 0.00 2.66
2270 3111 4.357947 TGTCCACGACGCAGCTCC 62.358 66.667 0.00 0.00 34.95 4.70
2271 3112 4.357947 GTCCACGACGCAGCTCCA 62.358 66.667 0.00 0.00 0.00 3.86
2272 3113 3.381983 TCCACGACGCAGCTCCAT 61.382 61.111 0.00 0.00 0.00 3.41
2273 3114 3.190849 CCACGACGCAGCTCCATG 61.191 66.667 0.00 0.00 0.00 3.66
2274 3115 2.125952 CACGACGCAGCTCCATGA 60.126 61.111 0.00 0.00 0.00 3.07
2275 3116 1.737735 CACGACGCAGCTCCATGAA 60.738 57.895 0.00 0.00 0.00 2.57
2276 3117 1.086067 CACGACGCAGCTCCATGAAT 61.086 55.000 0.00 0.00 0.00 2.57
2277 3118 0.459899 ACGACGCAGCTCCATGAATA 59.540 50.000 0.00 0.00 0.00 1.75
2278 3119 0.855349 CGACGCAGCTCCATGAATAC 59.145 55.000 0.00 0.00 0.00 1.89
2279 3120 1.536922 CGACGCAGCTCCATGAATACT 60.537 52.381 0.00 0.00 0.00 2.12
2280 3121 2.131183 GACGCAGCTCCATGAATACTC 58.869 52.381 0.00 0.00 0.00 2.59
2281 3122 1.759445 ACGCAGCTCCATGAATACTCT 59.241 47.619 0.00 0.00 0.00 3.24
2282 3123 2.133553 CGCAGCTCCATGAATACTCTG 58.866 52.381 0.00 0.00 0.00 3.35
2283 3124 1.872313 GCAGCTCCATGAATACTCTGC 59.128 52.381 0.00 0.61 38.62 4.26
2284 3125 2.485124 GCAGCTCCATGAATACTCTGCT 60.485 50.000 0.00 0.00 41.37 4.24
2285 3126 3.244009 GCAGCTCCATGAATACTCTGCTA 60.244 47.826 0.00 0.00 41.37 3.49
2286 3127 4.305769 CAGCTCCATGAATACTCTGCTAC 58.694 47.826 0.00 0.00 0.00 3.58
2287 3128 3.005261 AGCTCCATGAATACTCTGCTACG 59.995 47.826 0.00 0.00 0.00 3.51
2288 3129 3.858877 GCTCCATGAATACTCTGCTACGG 60.859 52.174 0.00 0.00 0.00 4.02
2289 3130 2.035961 TCCATGAATACTCTGCTACGGC 59.964 50.000 0.00 0.00 39.26 5.68
2290 3131 2.036475 CCATGAATACTCTGCTACGGCT 59.964 50.000 0.00 0.00 39.59 5.52
2291 3132 2.871182 TGAATACTCTGCTACGGCTG 57.129 50.000 0.00 0.00 39.59 4.85
2292 3133 1.202417 TGAATACTCTGCTACGGCTGC 60.202 52.381 0.00 0.00 39.59 5.25
2293 3134 0.105039 AATACTCTGCTACGGCTGCC 59.895 55.000 9.11 9.11 39.59 4.85
2294 3135 0.757188 ATACTCTGCTACGGCTGCCT 60.757 55.000 17.92 6.50 39.59 4.75
2295 3136 1.384989 TACTCTGCTACGGCTGCCTC 61.385 60.000 17.92 3.76 39.59 4.70
2296 3137 2.679996 TCTGCTACGGCTGCCTCA 60.680 61.111 17.92 8.19 39.59 3.86
2297 3138 2.510238 CTGCTACGGCTGCCTCAC 60.510 66.667 17.92 4.06 39.59 3.51
2298 3139 3.300934 CTGCTACGGCTGCCTCACA 62.301 63.158 17.92 8.58 39.59 3.58
2308 3182 0.954449 CTGCCTCACAGCTTCACCTG 60.954 60.000 0.00 0.00 40.19 4.00
2338 3220 6.887545 AGTGAAGTAGAGTTAGCAGACATACT 59.112 38.462 0.00 0.00 0.00 2.12
2455 3370 7.556996 ACACTTGGTTGTACCTAGATAGACTAG 59.443 40.741 13.04 0.00 42.55 2.57
2456 3371 6.546772 ACTTGGTTGTACCTAGATAGACTAGC 59.453 42.308 13.04 0.00 42.55 3.42
2457 3372 6.263412 TGGTTGTACCTAGATAGACTAGCT 57.737 41.667 5.44 5.44 45.09 3.32
2458 3373 7.384524 TGGTTGTACCTAGATAGACTAGCTA 57.615 40.000 7.24 7.24 45.09 3.32
2577 3496 4.141135 TGGTAAATTTCAGGGACAGTTGGA 60.141 41.667 0.00 0.00 0.00 3.53
2614 3534 6.984474 TGATTTGCTAATAGTACACCACTAGC 59.016 38.462 0.00 0.96 43.01 3.42
2638 3558 0.387202 AGCACAGGCAGTATAGAGCG 59.613 55.000 0.00 0.00 44.61 5.03
2705 3627 5.324784 TGACACTTGTACCTAGCATAGTG 57.675 43.478 0.00 0.00 36.82 2.74
2722 3644 2.914059 AGTGGCGTGTGTTCTAGTTTT 58.086 42.857 0.00 0.00 0.00 2.43
2725 3647 3.064271 GTGGCGTGTGTTCTAGTTTTCAA 59.936 43.478 0.00 0.00 0.00 2.69
2730 3652 5.277345 GCGTGTGTTCTAGTTTTCAACAGAT 60.277 40.000 0.00 0.00 30.72 2.90
2766 3688 9.288576 ACTCTGTTCAACTCAATGATGAATTTA 57.711 29.630 3.03 0.00 39.17 1.40
2798 3726 6.207221 AGCTGATCATCATCACTCAGTAGTAG 59.793 42.308 0.00 0.00 37.90 2.57
2816 3744 9.376075 CAGTAGTAGATGTTTCACTCAATCAAT 57.624 33.333 0.00 0.00 0.00 2.57
2878 3806 1.291877 CTTTCTGGGCCGTTCACGAG 61.292 60.000 0.00 0.00 43.02 4.18
2915 3843 0.884704 GATGTGCCCACGCGGATTAT 60.885 55.000 12.47 0.00 38.08 1.28
2916 3844 0.394938 ATGTGCCCACGCGGATTATA 59.605 50.000 12.47 0.00 38.08 0.98
2917 3845 0.249699 TGTGCCCACGCGGATTATAG 60.250 55.000 12.47 0.00 38.08 1.31
2918 3846 0.249741 GTGCCCACGCGGATTATAGT 60.250 55.000 12.47 0.00 38.08 2.12
2919 3847 0.466543 TGCCCACGCGGATTATAGTT 59.533 50.000 12.47 0.00 38.08 2.24
2920 3848 1.687660 TGCCCACGCGGATTATAGTTA 59.312 47.619 12.47 0.00 38.08 2.24
2922 3850 2.477754 GCCCACGCGGATTATAGTTAAC 59.522 50.000 12.47 0.00 0.00 2.01
2923 3851 3.719924 CCCACGCGGATTATAGTTAACA 58.280 45.455 12.47 0.00 0.00 2.41
2924 3852 4.312443 CCCACGCGGATTATAGTTAACAT 58.688 43.478 12.47 2.37 0.00 2.71
2957 3885 6.980978 CGTGATAGTGAGTGGATTAATTGAGT 59.019 38.462 0.00 0.00 0.00 3.41
3131 4062 5.296780 TGATCAAGCTTTTAAATCTAGGCCG 59.703 40.000 0.00 0.00 0.00 6.13
3135 4066 6.482308 TCAAGCTTTTAAATCTAGGCCGATAC 59.518 38.462 0.00 0.00 0.00 2.24
3137 4068 4.986659 GCTTTTAAATCTAGGCCGATACGA 59.013 41.667 0.00 0.00 0.00 3.43
3138 4069 5.107568 GCTTTTAAATCTAGGCCGATACGAC 60.108 44.000 0.00 0.00 0.00 4.34
3139 4070 5.779529 TTTAAATCTAGGCCGATACGACT 57.220 39.130 0.00 0.00 0.00 4.18
3140 4071 3.644884 AAATCTAGGCCGATACGACTG 57.355 47.619 0.00 0.00 0.00 3.51
3141 4072 2.563261 ATCTAGGCCGATACGACTGA 57.437 50.000 0.00 0.00 0.00 3.41
3142 4073 2.563261 TCTAGGCCGATACGACTGAT 57.437 50.000 0.00 0.00 0.00 2.90
3143 4074 3.690475 TCTAGGCCGATACGACTGATA 57.310 47.619 0.00 0.00 0.00 2.15
3144 4075 4.217836 TCTAGGCCGATACGACTGATAT 57.782 45.455 0.00 0.00 0.00 1.63
3145 4076 5.349061 TCTAGGCCGATACGACTGATATA 57.651 43.478 0.00 0.00 0.00 0.86
3146 4077 5.926663 TCTAGGCCGATACGACTGATATAT 58.073 41.667 0.00 0.00 0.00 0.86
3147 4078 7.059202 TCTAGGCCGATACGACTGATATATA 57.941 40.000 0.00 0.00 0.00 0.86
3148 4079 7.153315 TCTAGGCCGATACGACTGATATATAG 58.847 42.308 0.00 0.00 0.00 1.31
3149 4080 5.064558 AGGCCGATACGACTGATATATAGG 58.935 45.833 0.00 0.00 0.00 2.57
3150 4081 4.320348 GGCCGATACGACTGATATATAGGC 60.320 50.000 6.17 6.17 42.89 3.93
3151 4082 4.320348 GCCGATACGACTGATATATAGGCC 60.320 50.000 0.00 0.00 39.72 5.19
3152 4083 4.820173 CCGATACGACTGATATATAGGCCA 59.180 45.833 5.01 0.00 0.00 5.36
3153 4084 5.049336 CCGATACGACTGATATATAGGCCAG 60.049 48.000 5.01 0.00 0.00 4.85
3154 4085 5.527951 CGATACGACTGATATATAGGCCAGT 59.472 44.000 5.01 12.33 41.96 4.00
3155 4086 6.704937 CGATACGACTGATATATAGGCCAGTA 59.295 42.308 5.01 0.00 39.67 2.74
3156 4087 7.388224 CGATACGACTGATATATAGGCCAGTAT 59.612 40.741 5.01 5.26 39.67 2.12
3157 4088 9.722184 GATACGACTGATATATAGGCCAGTATA 57.278 37.037 5.01 7.56 39.67 1.47
3177 4108 0.323629 TCACTTTTGGGGCTCTACCG 59.676 55.000 0.00 0.00 40.62 4.02
3217 4162 6.918892 TCATTTTCAAACGTATCATCCGAT 57.081 33.333 0.00 0.00 35.50 4.18
3268 4213 4.261238 CGATATCTAGCCCGATATGTCCAC 60.261 50.000 9.39 0.00 36.88 4.02
3274 4219 1.000955 GCCCGATATGTCCACCTAGTG 59.999 57.143 0.00 0.00 0.00 2.74
3329 4274 4.681978 ACGGCGTTCCTGTCTGCC 62.682 66.667 6.77 0.00 44.09 4.85
3332 4277 2.031163 GCGTTCCTGTCTGCCAGT 59.969 61.111 0.00 0.00 39.74 4.00
3470 4415 8.136165 ACTGTTTCCACTGATATAGAACGATAC 58.864 37.037 0.00 0.00 0.00 2.24
3477 4422 8.117370 CCACTGATATAGAACGATACGTAGATG 58.883 40.741 0.08 0.00 39.99 2.90
3479 4424 8.871862 ACTGATATAGAACGATACGTAGATGAC 58.128 37.037 0.08 0.00 39.99 3.06
3510 4455 8.617290 TTCTTACTGGAAAGGAGTGAAATAAC 57.383 34.615 0.00 0.00 0.00 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.668550 GAACTCGCGGGTTGCCTT 60.669 61.111 32.17 3.86 42.08 4.35
2 3 2.775032 TACAGAACTCGCGGGTTGCC 62.775 60.000 32.17 16.33 42.08 4.52
4 5 1.193874 GTTTACAGAACTCGCGGGTTG 59.806 52.381 32.17 19.90 0.00 3.77
6 7 0.665369 CGTTTACAGAACTCGCGGGT 60.665 55.000 5.36 5.36 0.00 5.28
7 8 1.952266 GCGTTTACAGAACTCGCGGG 61.952 60.000 3.27 3.27 37.74 6.13
8 9 1.414897 GCGTTTACAGAACTCGCGG 59.585 57.895 6.13 0.00 37.74 6.46
9 10 4.999550 GCGTTTACAGAACTCGCG 57.000 55.556 0.00 0.00 37.74 5.87
10 11 1.320852 GCTAGCGTTTACAGAACTCGC 59.679 52.381 0.00 0.00 45.82 5.03
11 12 2.592194 TGCTAGCGTTTACAGAACTCG 58.408 47.619 10.77 0.00 0.00 4.18
17 18 3.926527 TCATGACTTGCTAGCGTTTACAG 59.073 43.478 10.77 1.58 0.00 2.74
22 23 1.363744 GCTCATGACTTGCTAGCGTT 58.636 50.000 10.77 0.00 0.00 4.84
30 31 0.811616 GTAGCCGGGCTCATGACTTG 60.812 60.000 27.65 0.00 40.44 3.16
31 32 0.978146 AGTAGCCGGGCTCATGACTT 60.978 55.000 27.65 0.79 40.44 3.01
92 100 3.687572 GCATATGCTGGCTATACATGC 57.312 47.619 20.64 0.00 38.21 4.06
245 266 0.393537 AGCAGGACTATGGTTGCAGC 60.394 55.000 8.38 0.00 38.97 5.25
265 286 1.067776 GGTACATGGGTCGATCGATCC 60.068 57.143 35.56 35.56 45.36 3.36
275 323 0.616891 GGTTTCGGAGGTACATGGGT 59.383 55.000 0.00 0.00 0.00 4.51
276 324 0.616371 TGGTTTCGGAGGTACATGGG 59.384 55.000 0.00 0.00 0.00 4.00
277 325 2.710096 ATGGTTTCGGAGGTACATGG 57.290 50.000 0.00 0.00 0.00 3.66
278 326 4.755123 GGAATATGGTTTCGGAGGTACATG 59.245 45.833 0.00 0.00 0.00 3.21
324 372 3.957497 CAGGCTCTGAACTACAGGTATCT 59.043 47.826 0.00 0.00 45.76 1.98
328 376 2.310779 TCAGGCTCTGAACTACAGGT 57.689 50.000 2.78 0.00 45.76 4.00
356 404 1.729470 CGTACAGCTCCCGCAGAGAT 61.729 60.000 4.96 0.00 46.50 2.75
368 416 7.194607 TGAACTACAGGTATATACGTACAGC 57.805 40.000 7.72 0.00 0.00 4.40
436 484 6.423302 CACGTATCTACACTACGGTTAGAGAT 59.577 42.308 7.65 0.00 44.70 2.75
455 504 0.527565 GGTACCGGACACACACGTAT 59.472 55.000 9.46 0.00 0.00 3.06
459 508 2.613691 CTAATGGTACCGGACACACAC 58.386 52.381 9.46 0.00 0.00 3.82
460 509 1.551430 CCTAATGGTACCGGACACACA 59.449 52.381 9.46 6.53 0.00 3.72
461 510 1.741394 GCCTAATGGTACCGGACACAC 60.741 57.143 9.46 0.00 35.27 3.82
462 511 0.538118 GCCTAATGGTACCGGACACA 59.462 55.000 9.46 3.39 35.27 3.72
476 525 0.963355 ATTTTCTTGCGCCGGCCTAA 60.963 50.000 23.46 15.31 38.85 2.69
489 538 6.049955 TCCGTCTAGTTTCCATCATTTTCT 57.950 37.500 0.00 0.00 0.00 2.52
507 556 2.291043 ACCACCACCTCCATCCGTC 61.291 63.158 0.00 0.00 0.00 4.79
513 562 1.463214 ACATCCACCACCACCTCCA 60.463 57.895 0.00 0.00 0.00 3.86
615 687 6.672593 AGGAATGAAAAGGTCCTGCATATAA 58.327 36.000 0.00 0.00 40.37 0.98
645 732 6.445139 AGTGGGAATGGAAGAAGATAGAAGAA 59.555 38.462 0.00 0.00 0.00 2.52
672 759 1.372582 TCGAGGCTGATTGCAATGTC 58.627 50.000 18.59 4.80 45.15 3.06
689 827 5.046910 AGGACAAAGTACAATTGCAATCG 57.953 39.130 13.38 3.59 0.00 3.34
694 832 5.689383 TTCTGAGGACAAAGTACAATTGC 57.311 39.130 5.05 4.96 0.00 3.56
697 835 7.505585 TCCATTTTTCTGAGGACAAAGTACAAT 59.494 33.333 0.00 0.00 0.00 2.71
698 836 6.831353 TCCATTTTTCTGAGGACAAAGTACAA 59.169 34.615 0.00 0.00 0.00 2.41
699 837 6.361433 TCCATTTTTCTGAGGACAAAGTACA 58.639 36.000 0.00 0.00 0.00 2.90
700 838 6.877611 TCCATTTTTCTGAGGACAAAGTAC 57.122 37.500 0.00 0.00 0.00 2.73
701 839 6.659242 GGATCCATTTTTCTGAGGACAAAGTA 59.341 38.462 6.95 0.00 32.04 2.24
702 840 5.478332 GGATCCATTTTTCTGAGGACAAAGT 59.522 40.000 6.95 0.00 32.04 2.66
703 841 5.477984 TGGATCCATTTTTCTGAGGACAAAG 59.522 40.000 11.44 0.00 32.04 2.77
704 842 5.392995 TGGATCCATTTTTCTGAGGACAAA 58.607 37.500 11.44 0.00 32.04 2.83
705 843 4.996793 TGGATCCATTTTTCTGAGGACAA 58.003 39.130 11.44 0.00 32.04 3.18
706 844 4.568380 CCTGGATCCATTTTTCTGAGGACA 60.568 45.833 16.63 0.00 32.04 4.02
707 845 3.950395 CCTGGATCCATTTTTCTGAGGAC 59.050 47.826 16.63 0.00 32.04 3.85
708 846 3.851976 TCCTGGATCCATTTTTCTGAGGA 59.148 43.478 16.63 12.11 34.12 3.71
709 847 3.950395 GTCCTGGATCCATTTTTCTGAGG 59.050 47.826 16.63 9.74 0.00 3.86
710 848 4.592942 TGTCCTGGATCCATTTTTCTGAG 58.407 43.478 16.63 0.00 0.00 3.35
711 849 4.656100 TGTCCTGGATCCATTTTTCTGA 57.344 40.909 16.63 0.90 0.00 3.27
712 850 4.951715 TCATGTCCTGGATCCATTTTTCTG 59.048 41.667 16.63 9.19 0.00 3.02
713 851 5.197224 TCATGTCCTGGATCCATTTTTCT 57.803 39.130 16.63 0.00 0.00 2.52
714 852 6.278363 CAATCATGTCCTGGATCCATTTTTC 58.722 40.000 16.63 5.35 0.00 2.29
715 853 5.395990 GCAATCATGTCCTGGATCCATTTTT 60.396 40.000 16.63 0.00 0.00 1.94
716 854 4.100498 GCAATCATGTCCTGGATCCATTTT 59.900 41.667 16.63 0.00 0.00 1.82
717 855 3.640029 GCAATCATGTCCTGGATCCATTT 59.360 43.478 16.63 0.00 0.00 2.32
718 856 3.228453 GCAATCATGTCCTGGATCCATT 58.772 45.455 16.63 0.36 0.00 3.16
759 922 2.684881 GCCCACACCAAATCTGTCTATG 59.315 50.000 0.00 0.00 0.00 2.23
828 1146 0.875908 ACGAATGCGCACGCTCATAT 60.876 50.000 14.90 0.00 42.48 1.78
829 1147 1.518352 ACGAATGCGCACGCTCATA 60.518 52.632 14.90 0.00 42.48 2.15
831 1149 3.776849 CACGAATGCGCACGCTCA 61.777 61.111 14.90 0.00 42.48 4.26
844 1162 1.796190 AAGCAGAGCAGACGACACGA 61.796 55.000 0.00 0.00 0.00 4.35
850 1179 1.624865 GACAGCAAGCAGAGCAGACG 61.625 60.000 0.00 0.00 0.00 4.18
851 1180 0.602106 TGACAGCAAGCAGAGCAGAC 60.602 55.000 0.00 0.00 0.00 3.51
887 1357 9.806448 TCTAGAGAAGAATAATGACTGCTAGAT 57.194 33.333 0.00 0.00 0.00 1.98
888 1358 9.806448 ATCTAGAGAAGAATAATGACTGCTAGA 57.194 33.333 0.00 0.00 37.89 2.43
890 1360 9.806448 AGATCTAGAGAAGAATAATGACTGCTA 57.194 33.333 0.00 0.00 37.89 3.49
941 1421 1.231221 TGTATGCGTGTGGACCAAAC 58.769 50.000 4.51 4.51 0.00 2.93
978 1528 2.735762 GCTAACTGGTCCACTGATCGAC 60.736 54.545 0.00 0.00 0.00 4.20
985 1535 1.362224 ATGGTGCTAACTGGTCCACT 58.638 50.000 0.00 0.00 0.00 4.00
992 1542 1.067635 GGGCAACAATGGTGCTAACTG 60.068 52.381 23.36 0.00 39.74 3.16
995 1545 0.178950 TGGGGCAACAATGGTGCTAA 60.179 50.000 23.36 6.11 39.74 3.09
1014 1564 2.170187 GGCCACAGATGATCTTCAGAGT 59.830 50.000 10.90 4.02 0.00 3.24
1027 1577 4.954118 ACGTGGGGAGGCCACAGA 62.954 66.667 5.01 0.00 37.75 3.41
1039 1589 3.181503 ACGTACTAGTAGATGCAACGTGG 60.182 47.826 14.95 0.00 40.23 4.94
1043 1593 6.939551 TTTCAACGTACTAGTAGATGCAAC 57.060 37.500 1.87 0.00 0.00 4.17
1045 1595 6.097356 CCTTTTCAACGTACTAGTAGATGCA 58.903 40.000 1.87 0.00 0.00 3.96
1046 1596 6.098017 ACCTTTTCAACGTACTAGTAGATGC 58.902 40.000 1.87 0.00 0.00 3.91
1047 1597 7.597743 ACAACCTTTTCAACGTACTAGTAGATG 59.402 37.037 1.87 3.22 0.00 2.90
1048 1598 7.597743 CACAACCTTTTCAACGTACTAGTAGAT 59.402 37.037 1.87 0.00 0.00 1.98
1049 1599 6.919662 CACAACCTTTTCAACGTACTAGTAGA 59.080 38.462 1.87 0.00 0.00 2.59
1053 1606 4.607557 CGCACAACCTTTTCAACGTACTAG 60.608 45.833 0.00 0.00 0.00 2.57
1059 1612 0.248458 AGCGCACAACCTTTTCAACG 60.248 50.000 11.47 0.00 0.00 4.10
1106 1662 2.787473 AGCATGTACCTTAGCAAGCA 57.213 45.000 0.00 0.00 32.52 3.91
1129 1767 0.471191 CCTCATGGTGCTGCTCCATA 59.529 55.000 29.51 18.76 42.92 2.74
1145 1789 0.244178 GGAACACACGACTCCTCCTC 59.756 60.000 0.00 0.00 0.00 3.71
1353 2001 6.930722 GTCATGGTTTCAGTTCAAAATTGGAT 59.069 34.615 0.00 0.00 0.00 3.41
1408 2065 3.825014 TCACCACCTCACTAGAACACTAC 59.175 47.826 0.00 0.00 0.00 2.73
1453 2114 0.325933 CACCTCTCTGCACCATCCAA 59.674 55.000 0.00 0.00 0.00 3.53
1629 2293 1.079819 CGACATCACCGGCTTGTCT 60.080 57.895 22.26 0.00 38.06 3.41
1659 2323 2.202919 CTCATGCCGATCACGCCA 60.203 61.111 0.00 0.00 38.29 5.69
1752 2440 2.125391 GCATGCTCGCTGGTCTGA 60.125 61.111 11.37 0.00 0.00 3.27
1790 2478 8.688747 ACAGAAGAAGAACTGAAGAATTGAAT 57.311 30.769 0.00 0.00 37.54 2.57
1814 2506 9.922305 CAACGATAAATTCTCAATAGGAAGAAC 57.078 33.333 0.00 0.00 0.00 3.01
1821 2548 9.045223 TCACCATCAACGATAAATTCTCAATAG 57.955 33.333 0.00 0.00 0.00 1.73
1823 2553 7.864108 TCACCATCAACGATAAATTCTCAAT 57.136 32.000 0.00 0.00 0.00 2.57
2007 2794 2.042831 GCGCTCTGCAGGAAATGGT 61.043 57.895 15.13 0.00 45.45 3.55
2218 3023 1.375908 GTTCCAGTCGATGCCAGCA 60.376 57.895 0.00 0.00 0.00 4.41
2261 3069 1.759445 AGAGTATTCATGGAGCTGCGT 59.241 47.619 0.00 0.00 0.00 5.24
2270 3111 3.055591 CAGCCGTAGCAGAGTATTCATG 58.944 50.000 0.00 0.00 43.56 3.07
2271 3112 2.546795 GCAGCCGTAGCAGAGTATTCAT 60.547 50.000 0.00 0.00 43.56 2.57
2272 3113 1.202417 GCAGCCGTAGCAGAGTATTCA 60.202 52.381 0.00 0.00 43.56 2.57
2273 3114 1.492720 GCAGCCGTAGCAGAGTATTC 58.507 55.000 0.00 0.00 43.56 1.75
2274 3115 0.105039 GGCAGCCGTAGCAGAGTATT 59.895 55.000 0.00 0.00 43.56 1.89
2275 3116 0.757188 AGGCAGCCGTAGCAGAGTAT 60.757 55.000 5.55 0.00 43.56 2.12
2276 3117 1.379977 AGGCAGCCGTAGCAGAGTA 60.380 57.895 5.55 0.00 43.56 2.59
2277 3118 2.681778 AGGCAGCCGTAGCAGAGT 60.682 61.111 5.55 0.00 43.56 3.24
2278 3119 2.105930 GAGGCAGCCGTAGCAGAG 59.894 66.667 5.55 0.00 43.56 3.35
2279 3120 2.679996 TGAGGCAGCCGTAGCAGA 60.680 61.111 5.55 0.00 43.56 4.26
2280 3121 2.510238 GTGAGGCAGCCGTAGCAG 60.510 66.667 5.55 0.00 43.56 4.24
2281 3122 3.300934 CTGTGAGGCAGCCGTAGCA 62.301 63.158 5.55 3.38 43.56 3.49
2282 3123 2.510238 CTGTGAGGCAGCCGTAGC 60.510 66.667 5.55 0.00 38.52 3.58
2290 3131 1.071987 CAGGTGAAGCTGTGAGGCA 59.928 57.895 1.30 0.00 34.17 4.75
2291 3132 2.331132 GCAGGTGAAGCTGTGAGGC 61.331 63.158 10.90 0.00 0.00 4.70
2292 3133 0.954449 CTGCAGGTGAAGCTGTGAGG 60.954 60.000 5.57 0.00 0.00 3.86
2293 3134 1.575576 GCTGCAGGTGAAGCTGTGAG 61.576 60.000 17.12 8.36 43.48 3.51
2294 3135 1.598962 GCTGCAGGTGAAGCTGTGA 60.599 57.895 17.12 0.00 43.48 3.58
2295 3136 1.853114 CTGCTGCAGGTGAAGCTGTG 61.853 60.000 21.71 5.98 46.98 3.66
2296 3137 1.600076 CTGCTGCAGGTGAAGCTGT 60.600 57.895 21.71 0.00 46.98 4.40
2297 3138 1.600076 ACTGCTGCAGGTGAAGCTG 60.600 57.895 31.00 13.78 46.98 4.24
2298 3139 1.600076 CACTGCTGCAGGTGAAGCT 60.600 57.895 31.00 7.70 46.98 3.74
2300 3141 0.873054 CTTCACTGCTGCAGGTGAAG 59.127 55.000 33.85 33.85 39.96 3.02
2301 3142 0.181114 ACTTCACTGCTGCAGGTGAA 59.819 50.000 31.00 29.59 35.51 3.18
2302 3143 1.001293 CTACTTCACTGCTGCAGGTGA 59.999 52.381 31.00 25.99 35.51 4.02
2308 3182 2.926838 GCTAACTCTACTTCACTGCTGC 59.073 50.000 0.00 0.00 0.00 5.25
2338 3220 2.401583 ATGAAATCGGTGCTGCTACA 57.598 45.000 0.00 0.00 0.00 2.74
2455 3370 5.774630 ACTCAGTAAGTGAAACAGAGTAGC 58.225 41.667 0.14 0.00 40.59 3.58
2456 3371 6.016192 TGGACTCAGTAAGTGAAACAGAGTAG 60.016 42.308 1.89 0.00 41.90 2.57
2457 3372 5.831525 TGGACTCAGTAAGTGAAACAGAGTA 59.168 40.000 1.89 0.00 41.90 2.59
2458 3373 4.649674 TGGACTCAGTAAGTGAAACAGAGT 59.350 41.667 1.53 1.53 43.74 3.24
2606 3526 0.319728 CTGTGCTCTGTGCTAGTGGT 59.680 55.000 3.20 0.00 43.37 4.16
2614 3534 2.428530 TCTATACTGCCTGTGCTCTGTG 59.571 50.000 0.00 0.00 38.71 3.66
2705 3627 3.614588 GTTGAAAACTAGAACACACGCC 58.385 45.455 0.00 0.00 45.32 5.68
2722 3644 3.829026 AGAGTGCTCTGTGTATCTGTTGA 59.171 43.478 0.28 0.00 38.75 3.18
2766 3688 3.815962 GTGATGATGATCAGCTGCTCAAT 59.184 43.478 22.96 13.51 39.36 2.57
2798 3726 9.346725 GAAAGGTTATTGATTGAGTGAAACATC 57.653 33.333 0.00 0.00 41.43 3.06
2816 3744 3.064271 GCGTATGGCGAAATGAAAGGTTA 59.936 43.478 0.00 0.00 44.77 2.85
2878 3806 6.362283 GGCACATCATACATTTAATTAACCGC 59.638 38.462 0.00 0.00 0.00 5.68
2915 3843 4.625972 TCACGCTCGATCATGTTAACTA 57.374 40.909 7.22 0.00 0.00 2.24
2916 3844 3.503827 TCACGCTCGATCATGTTAACT 57.496 42.857 7.22 0.00 0.00 2.24
2917 3845 4.976731 ACTATCACGCTCGATCATGTTAAC 59.023 41.667 0.00 0.00 0.00 2.01
2918 3846 4.976116 CACTATCACGCTCGATCATGTTAA 59.024 41.667 0.00 0.00 0.00 2.01
2919 3847 4.274950 TCACTATCACGCTCGATCATGTTA 59.725 41.667 0.00 0.00 0.00 2.41
2920 3848 3.066760 TCACTATCACGCTCGATCATGTT 59.933 43.478 0.00 0.00 0.00 2.71
2922 3850 3.232771 CTCACTATCACGCTCGATCATG 58.767 50.000 0.00 0.00 0.00 3.07
2923 3851 2.881513 ACTCACTATCACGCTCGATCAT 59.118 45.455 0.00 0.00 0.00 2.45
2924 3852 2.032178 CACTCACTATCACGCTCGATCA 59.968 50.000 0.00 0.00 0.00 2.92
2957 3885 6.015180 CCAGAAAAGATGATTGACAGGGAAAA 60.015 38.462 0.00 0.00 0.00 2.29
3131 4062 6.945938 ACTGGCCTATATATCAGTCGTATC 57.054 41.667 3.32 0.00 35.83 2.24
3135 4066 8.508062 GTGATATACTGGCCTATATATCAGTCG 58.492 40.741 30.36 1.51 45.13 4.18
3137 4068 9.944079 AAGTGATATACTGGCCTATATATCAGT 57.056 33.333 30.36 29.84 46.72 3.41
3142 4073 8.768397 CCCAAAAGTGATATACTGGCCTATATA 58.232 37.037 3.32 6.65 40.26 0.86
3143 4074 7.311929 CCCCAAAAGTGATATACTGGCCTATAT 60.312 40.741 3.32 4.10 40.26 0.86
3144 4075 6.012858 CCCCAAAAGTGATATACTGGCCTATA 60.013 42.308 3.32 0.00 40.26 1.31
3145 4076 5.222130 CCCCAAAAGTGATATACTGGCCTAT 60.222 44.000 3.32 0.00 40.26 2.57
3146 4077 4.104102 CCCCAAAAGTGATATACTGGCCTA 59.896 45.833 3.32 0.00 40.26 3.93
3147 4078 3.117512 CCCCAAAAGTGATATACTGGCCT 60.118 47.826 3.32 0.00 40.26 5.19
3148 4079 3.222603 CCCCAAAAGTGATATACTGGCC 58.777 50.000 0.00 0.00 40.26 5.36
3149 4080 2.623416 GCCCCAAAAGTGATATACTGGC 59.377 50.000 0.00 0.00 40.26 4.85
3150 4081 4.137543 GAGCCCCAAAAGTGATATACTGG 58.862 47.826 0.00 0.00 40.26 4.00
3151 4082 5.041191 AGAGCCCCAAAAGTGATATACTG 57.959 43.478 0.00 0.00 40.26 2.74
3152 4083 5.071923 GGTAGAGCCCCAAAAGTGATATACT 59.928 44.000 0.00 0.00 42.89 2.12
3153 4084 5.306394 GGTAGAGCCCCAAAAGTGATATAC 58.694 45.833 0.00 0.00 0.00 1.47
3154 4085 4.039973 CGGTAGAGCCCCAAAAGTGATATA 59.960 45.833 0.00 0.00 0.00 0.86
3155 4086 3.181454 CGGTAGAGCCCCAAAAGTGATAT 60.181 47.826 0.00 0.00 0.00 1.63
3156 4087 2.169769 CGGTAGAGCCCCAAAAGTGATA 59.830 50.000 0.00 0.00 0.00 2.15
3157 4088 1.065418 CGGTAGAGCCCCAAAAGTGAT 60.065 52.381 0.00 0.00 0.00 3.06
3217 4162 1.264020 CGGTCGATATTTCGGTCCGTA 59.736 52.381 22.86 0.00 46.81 4.02
3219 4164 2.792374 CGGTCGATATTTCGGTCCG 58.208 57.895 20.15 20.15 46.84 4.79
3235 4180 2.029828 GGCTAGATATCGGCCATATCGG 60.030 54.545 26.66 18.32 45.90 4.18
3245 4190 3.883489 TGGACATATCGGGCTAGATATCG 59.117 47.826 11.23 10.03 40.68 2.92
3445 4390 7.323895 CGTATCGTTCTATATCAGTGGAAACAG 59.676 40.741 0.00 0.00 44.46 3.16
3470 4415 6.811665 TCCAGTAAGAATTGTTGTCATCTACG 59.188 38.462 0.00 0.00 0.00 3.51
3477 4422 6.486993 ACTCCTTTCCAGTAAGAATTGTTGTC 59.513 38.462 0.00 0.00 0.00 3.18
3479 4424 6.486657 TCACTCCTTTCCAGTAAGAATTGTTG 59.513 38.462 0.00 0.00 0.00 3.33


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

AutoCloner maintained by Alex Coulton.