Multiple sequence alignment - TraesCS3D01G061600

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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 TraesCS3D01G061600 chr3D 100.000 2497 0 0 1 2497 26688196 26685700 0.000000e+00 4612.0
1 TraesCS3D01G061600 chr3D 93.728 1674 81 13 1 1666 27053173 27054830 0.000000e+00 2488.0
2 TraesCS3D01G061600 chr3D 82.901 1696 189 57 1 1666 26808761 26810385 0.000000e+00 1432.0
3 TraesCS3D01G061600 chr3D 89.474 418 32 9 1716 2127 27054990 27055401 3.680000e-143 518.0
4 TraesCS3D01G061600 chr3D 81.928 415 40 17 1718 2120 26810557 26810948 4.010000e-83 318.0
5 TraesCS3D01G061600 chr3D 83.721 86 9 3 2131 2212 600531184 600531100 2.660000e-10 76.8
6 TraesCS3D01G061600 chr3D 97.059 34 1 0 1931 1964 26810811 26810844 9.650000e-05 58.4
7 TraesCS3D01G061600 chr3D 100.000 28 0 0 1937 1964 26686208 26686181 4.000000e-03 52.8
8 TraesCS3D01G061600 chrUn 91.699 1566 105 11 9 1566 38655198 38656746 0.000000e+00 2148.0
9 TraesCS3D01G061600 chrUn 90.974 1119 73 11 522 1632 336342460 336343558 0.000000e+00 1482.0
10 TraesCS3D01G061600 chrUn 90.731 1122 76 11 522 1635 39212308 39211207 0.000000e+00 1471.0
11 TraesCS3D01G061600 chrUn 90.795 1119 75 11 522 1632 336353128 336354226 0.000000e+00 1471.0
12 TraesCS3D01G061600 chrUn 91.429 420 30 5 1746 2164 38657077 38657491 2.790000e-159 571.0
13 TraesCS3D01G061600 chrUn 88.333 420 37 9 1716 2130 39211038 39210626 6.200000e-136 494.0
14 TraesCS3D01G061600 chrUn 88.489 417 36 8 1716 2127 311241951 311242360 6.200000e-136 494.0
15 TraesCS3D01G061600 chrUn 88.489 417 36 8 1716 2127 336343730 336344139 6.200000e-136 494.0
16 TraesCS3D01G061600 chrUn 88.489 417 36 8 1716 2127 336354398 336354807 6.200000e-136 494.0
17 TraesCS3D01G061600 chrUn 85.270 482 43 8 58 536 39213398 39212942 2.910000e-129 472.0
18 TraesCS3D01G061600 chrUn 85.270 482 43 8 58 536 318356111 318355655 2.910000e-129 472.0
19 TraesCS3D01G061600 chrUn 92.337 261 13 6 2238 2497 38663876 38664130 5.080000e-97 364.0
20 TraesCS3D01G061600 chrUn 93.269 104 6 1 1564 1666 38656828 38656931 4.300000e-33 152.0
21 TraesCS3D01G061600 chrUn 84.000 100 14 1 1971 2070 307489999 307490096 7.350000e-16 95.3
22 TraesCS3D01G061600 chrUn 84.000 100 14 1 1971 2070 328830319 328830416 7.350000e-16 95.3
23 TraesCS3D01G061600 chr3A 93.599 1203 53 12 473 1666 36946255 36945068 0.000000e+00 1773.0
24 TraesCS3D01G061600 chr3A 93.942 1040 44 8 632 1666 37305749 37304724 0.000000e+00 1554.0
25 TraesCS3D01G061600 chr3A 94.844 931 38 5 736 1666 37242805 37241885 0.000000e+00 1445.0
26 TraesCS3D01G061600 chr3A 82.026 306 29 17 1718 2019 37304558 37304275 1.150000e-58 237.0
27 TraesCS3D01G061600 chr3A 75.446 448 69 27 52 486 741248057 741248476 1.970000e-41 180.0
28 TraesCS3D01G061600 chr3A 91.892 111 9 0 353 463 37266994 37266884 3.330000e-34 156.0
29 TraesCS3D01G061600 chr3A 83.516 91 13 2 2129 2219 545151488 545151576 1.590000e-12 84.2
30 TraesCS3D01G061600 chr3A 84.524 84 9 3 2136 2218 686547003 686546923 2.060000e-11 80.5
31 TraesCS3D01G061600 chr3B 84.827 1127 108 32 510 1616 45304673 45303590 0.000000e+00 1075.0
32 TraesCS3D01G061600 chr2D 77.172 495 104 8 1 486 14023419 14022925 1.890000e-71 279.0
33 TraesCS3D01G061600 chr1B 80.697 373 55 13 2136 2497 131287381 131287015 8.800000e-70 274.0
34 TraesCS3D01G061600 chr1B 80.726 358 53 14 2136 2481 130720751 130720398 5.300000e-67 265.0
35 TraesCS3D01G061600 chr1B 80.189 212 27 9 2297 2497 3045732 3045525 7.200000e-31 145.0
36 TraesCS3D01G061600 chr6B 76.837 449 86 15 53 488 715713935 715714378 1.150000e-58 237.0
37 TraesCS3D01G061600 chr1D 83.824 136 21 1 345 479 493753267 493753402 7.250000e-26 128.0
38 TraesCS3D01G061600 chr1A 82.270 141 23 2 347 486 592068411 592068550 1.210000e-23 121.0
39 TraesCS3D01G061600 chr5B 86.517 89 9 2 2131 2218 372169268 372169354 7.350000e-16 95.3
40 TraesCS3D01G061600 chr5D 83.505 97 14 2 2121 2217 344470352 344470258 3.420000e-14 89.8
41 TraesCS3D01G061600 chr7D 90.323 62 6 0 2123 2184 452688002 452688063 5.720000e-12 82.4
42 TraesCS3D01G061600 chr6D 84.337 83 11 2 2119 2201 24267078 24266998 2.060000e-11 80.5
43 TraesCS3D01G061600 chr6A 87.324 71 8 1 2131 2201 583293863 583293794 2.060000e-11 80.5
44 TraesCS3D01G061600 chr4A 79.381 97 17 3 2131 2226 36611271 36611365 5.760000e-07 65.8


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 TraesCS3D01G061600 chr3D 26685700 26688196 2496 True 2332.400000 4612 100.000000 1 2497 2 chr3D.!!$R2 2496
1 TraesCS3D01G061600 chr3D 27053173 27055401 2228 False 1503.000000 2488 91.601000 1 2127 2 chr3D.!!$F2 2126
2 TraesCS3D01G061600 chr3D 26808761 26810948 2187 False 602.800000 1432 87.296000 1 2120 3 chr3D.!!$F1 2119
3 TraesCS3D01G061600 chrUn 336342460 336344139 1679 False 988.000000 1482 89.731500 522 2127 2 chrUn.!!$F6 1605
4 TraesCS3D01G061600 chrUn 336353128 336354807 1679 False 982.500000 1471 89.642000 522 2127 2 chrUn.!!$F7 1605
5 TraesCS3D01G061600 chrUn 38655198 38657491 2293 False 957.000000 2148 92.132333 9 2164 3 chrUn.!!$F5 2155
6 TraesCS3D01G061600 chrUn 39210626 39213398 2772 True 812.333333 1471 88.111333 58 2130 3 chrUn.!!$R2 2072
7 TraesCS3D01G061600 chr3A 36945068 36946255 1187 True 1773.000000 1773 93.599000 473 1666 1 chr3A.!!$R1 1193
8 TraesCS3D01G061600 chr3A 37241885 37242805 920 True 1445.000000 1445 94.844000 736 1666 1 chr3A.!!$R2 930
9 TraesCS3D01G061600 chr3A 37304275 37305749 1474 True 895.500000 1554 87.984000 632 2019 2 chr3A.!!$R5 1387
10 TraesCS3D01G061600 chr3B 45303590 45304673 1083 True 1075.000000 1075 84.827000 510 1616 1 chr3B.!!$R1 1106

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
399 411 0.109735 CAGTGCTTCTAGTCGTCGCA 60.11 55.0 0.0 0.0 0.0 5.1 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2218 3152 0.101759 CCAGCCCAAATGAAGCGATG 59.898 55.0 0.0 0.0 0.0 3.84 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
37 38 6.097915 TCCTGTTTAGAAAGACGAGACAAT 57.902 37.500 0.00 0.00 0.00 2.71
49 50 3.104512 ACGAGACAATGATGGTTCCCTA 58.895 45.455 0.00 0.00 0.00 3.53
50 51 3.118738 ACGAGACAATGATGGTTCCCTAC 60.119 47.826 0.00 0.00 0.00 3.18
77 78 4.538490 TGGAATAAGGTTCTCCCTGCTTAA 59.462 41.667 0.00 0.00 45.47 1.85
84 89 1.298953 TCTCCCTGCTTAAGCCCAAT 58.701 50.000 24.30 0.00 41.18 3.16
154 159 3.305950 CGGTGGATCTCTCAGGATTCATC 60.306 52.174 0.00 0.00 34.22 2.92
181 186 3.279434 GTTATCTTTGGTGGATCCGCTT 58.721 45.455 24.15 6.06 39.52 4.68
205 210 6.703319 TGGATTTAGTCTTCATCCGTTTACA 58.297 36.000 5.80 0.00 39.64 2.41
226 234 6.620877 ACATAACTGTCTTCTGGTTGGATA 57.379 37.500 0.00 0.00 0.00 2.59
236 244 5.721480 TCTTCTGGTTGGATACTTCTGATCA 59.279 40.000 0.00 0.00 37.61 2.92
285 297 1.113517 TCCTGGTGCGTCCTATAGGC 61.114 60.000 14.50 8.38 39.48 3.93
299 311 1.041447 ATAGGCCCTTAGCACGACGT 61.041 55.000 0.00 0.00 46.50 4.34
333 345 4.156455 ACTACAATACATCTTGCCTGGG 57.844 45.455 0.00 0.00 0.00 4.45
359 371 1.151810 AGTGAGGGGTGGTGATGGT 60.152 57.895 0.00 0.00 0.00 3.55
399 411 0.109735 CAGTGCTTCTAGTCGTCGCA 60.110 55.000 0.00 0.00 0.00 5.10
502 515 5.629435 GGAAGTTTCCGCAAAGAAAAGTATG 59.371 40.000 0.00 0.00 37.49 2.39
503 516 5.767816 AGTTTCCGCAAAGAAAAGTATGT 57.232 34.783 0.00 0.00 37.49 2.29
510 523 1.904287 AAGAAAAGTATGTGCCGGCA 58.096 45.000 29.03 29.03 0.00 5.69
511 524 1.904287 AGAAAAGTATGTGCCGGCAA 58.096 45.000 34.66 21.87 0.00 4.52
551 1219 6.819146 AGTACTCTTTGCTGGCTCTATTTTAC 59.181 38.462 0.00 0.00 0.00 2.01
672 1349 3.188786 GTGTGAGGCGGATGCGAC 61.189 66.667 12.10 7.95 44.10 5.19
779 1459 4.032960 TGATATCACAGGTTTGCAAGGT 57.967 40.909 0.00 0.00 0.00 3.50
780 1460 5.172687 TGATATCACAGGTTTGCAAGGTA 57.827 39.130 0.00 0.00 0.00 3.08
781 1461 5.754782 TGATATCACAGGTTTGCAAGGTAT 58.245 37.500 0.00 0.00 0.00 2.73
782 1462 6.894682 TGATATCACAGGTTTGCAAGGTATA 58.105 36.000 0.00 0.00 0.00 1.47
943 1628 2.286872 CGGCAGAGAAAGATGCAGAAT 58.713 47.619 0.00 0.00 44.37 2.40
944 1629 3.461061 CGGCAGAGAAAGATGCAGAATA 58.539 45.455 0.00 0.00 44.37 1.75
945 1630 3.493877 CGGCAGAGAAAGATGCAGAATAG 59.506 47.826 0.00 0.00 44.37 1.73
946 1631 3.250521 GGCAGAGAAAGATGCAGAATAGC 59.749 47.826 0.00 0.00 44.37 2.97
1029 1731 3.493873 CCAAGATGATGAGGATCTTCGCA 60.494 47.826 0.00 1.80 41.75 5.10
1075 1777 5.104776 TGCAGCAGAGGTACTATTCAATTCT 60.105 40.000 0.00 0.00 41.55 2.40
1115 1820 5.984233 TCCAAATCGGACGAATCTAATTG 57.016 39.130 0.00 0.00 39.64 2.32
1156 1862 7.379529 TGATCGATTTCTTCTTCTTTTTGTTGC 59.620 33.333 0.00 0.00 0.00 4.17
1162 1868 3.163630 TCTTCTTTTTGTTGCTGGTGC 57.836 42.857 0.00 0.00 40.20 5.01
1338 2044 0.535335 CGGGTTCAAATCCTCCGAGA 59.465 55.000 0.00 0.00 42.94 4.04
1359 2065 1.448497 GTGGACCCCAACGTCTTCA 59.552 57.895 0.00 0.00 34.18 3.02
1553 2267 7.271223 CGATCAATAAGTTTGTGTTGGTTGATC 59.729 37.037 12.35 12.35 43.30 2.92
1666 2466 9.249053 TGTATCTTGCTACCATTGGAAAATTTA 57.751 29.630 10.37 0.00 0.00 1.40
1711 2572 6.150140 CCTCTGACCCAAAAAGTTTAGATCTG 59.850 42.308 5.18 0.00 0.00 2.90
1712 2573 6.003950 TCTGACCCAAAAAGTTTAGATCTGG 58.996 40.000 5.18 0.00 0.00 3.86
1714 2575 6.369629 TGACCCAAAAAGTTTAGATCTGGAA 58.630 36.000 5.18 0.00 0.00 3.53
1727 2651 4.473444 AGATCTGGAAACTTGCTGGAAAA 58.527 39.130 0.00 0.00 0.00 2.29
1758 2682 0.110056 GTCTGTTTGTCATGCTGCGG 60.110 55.000 0.00 0.00 0.00 5.69
1868 2796 4.785346 AGTGATATGTTCTCCTTGGCAT 57.215 40.909 0.00 0.00 0.00 4.40
1871 2799 3.202818 TGATATGTTCTCCTTGGCATGGT 59.797 43.478 17.94 1.72 0.00 3.55
1914 2842 2.185004 ATTTCGGGTCTCACCACAAG 57.815 50.000 0.00 0.00 41.02 3.16
1918 2846 0.108138 CGGGTCTCACCACAAGATCC 60.108 60.000 0.00 0.00 41.02 3.36
1926 2854 3.399330 TCACCACAAGATCCGAACTTTC 58.601 45.455 0.00 0.00 0.00 2.62
1952 2885 9.368921 CGAAAAAGAAATTAGTTTGAATTTGGC 57.631 29.630 0.00 0.00 38.76 4.52
1955 2888 9.612066 AAAAGAAATTAGTTTGAATTTGGCTCA 57.388 25.926 0.00 0.00 38.76 4.26
1969 2902 7.501559 TGAATTTGGCTCAAAATTTCATTGGAA 59.498 29.630 10.24 0.00 39.31 3.53
2022 2956 8.552083 AATTTGGCTCAAAATTTCAGGATTAC 57.448 30.769 4.76 0.00 36.56 1.89
2103 3037 7.896383 TTTAATCCTGCTGCTTGGTATTATT 57.104 32.000 0.00 2.45 0.00 1.40
2234 3168 2.652941 TTTCATCGCTTCATTTGGGC 57.347 45.000 0.00 0.00 0.00 5.36
2235 3169 1.838112 TTCATCGCTTCATTTGGGCT 58.162 45.000 0.00 0.00 0.00 5.19
2236 3170 1.097232 TCATCGCTTCATTTGGGCTG 58.903 50.000 0.00 0.00 0.00 4.85
2237 3171 0.101759 CATCGCTTCATTTGGGCTGG 59.898 55.000 0.00 0.00 0.00 4.85
2238 3172 1.669999 ATCGCTTCATTTGGGCTGGC 61.670 55.000 0.00 0.00 0.00 4.85
2239 3173 2.580815 GCTTCATTTGGGCTGGCC 59.419 61.111 14.23 14.23 0.00 5.36
2240 3174 2.285024 GCTTCATTTGGGCTGGCCA 61.285 57.895 20.19 20.19 37.98 5.36
2241 3175 1.619807 GCTTCATTTGGGCTGGCCAT 61.620 55.000 24.56 7.21 37.98 4.40
2242 3176 0.177141 CTTCATTTGGGCTGGCCATG 59.823 55.000 24.56 19.52 37.98 3.66
2243 3177 0.252148 TTCATTTGGGCTGGCCATGA 60.252 50.000 24.56 21.50 37.98 3.07
2244 3178 0.252148 TCATTTGGGCTGGCCATGAA 60.252 50.000 24.56 16.39 37.98 2.57
2245 3179 0.108041 CATTTGGGCTGGCCATGAAC 60.108 55.000 24.56 0.00 37.98 3.18
2246 3180 1.266867 ATTTGGGCTGGCCATGAACC 61.267 55.000 24.56 7.07 37.98 3.62
2247 3181 3.903281 TTGGGCTGGCCATGAACCC 62.903 63.158 24.56 20.96 41.24 4.11
2248 3182 4.380945 GGGCTGGCCATGAACCCA 62.381 66.667 22.21 0.00 40.52 4.51
2249 3183 3.070576 GGCTGGCCATGAACCCAC 61.071 66.667 5.51 0.00 35.81 4.61
2250 3184 3.443045 GCTGGCCATGAACCCACG 61.443 66.667 5.51 0.00 0.00 4.94
2251 3185 3.443045 CTGGCCATGAACCCACGC 61.443 66.667 5.51 0.00 0.00 5.34
2264 3198 3.118454 CACGCCCGCACGAGATTT 61.118 61.111 2.15 0.00 36.70 2.17
2265 3199 3.118454 ACGCCCGCACGAGATTTG 61.118 61.111 2.15 0.00 36.70 2.32
2266 3200 4.520846 CGCCCGCACGAGATTTGC 62.521 66.667 0.00 0.00 36.57 3.68
2267 3201 3.127533 GCCCGCACGAGATTTGCT 61.128 61.111 0.00 0.00 37.87 3.91
2268 3202 2.690778 GCCCGCACGAGATTTGCTT 61.691 57.895 0.00 0.00 37.87 3.91
2269 3203 1.366111 GCCCGCACGAGATTTGCTTA 61.366 55.000 0.00 0.00 37.87 3.09
2270 3204 0.373716 CCCGCACGAGATTTGCTTAC 59.626 55.000 0.00 0.00 37.87 2.34
2271 3205 1.359848 CCGCACGAGATTTGCTTACT 58.640 50.000 0.00 0.00 37.87 2.24
2272 3206 1.324736 CCGCACGAGATTTGCTTACTC 59.675 52.381 0.00 0.00 37.87 2.59
2273 3207 1.992667 CGCACGAGATTTGCTTACTCA 59.007 47.619 0.00 0.00 37.87 3.41
2274 3208 2.222596 CGCACGAGATTTGCTTACTCAC 60.223 50.000 0.00 0.00 37.87 3.51
2275 3209 2.736721 GCACGAGATTTGCTTACTCACA 59.263 45.455 0.00 0.00 37.00 3.58
2276 3210 3.372206 GCACGAGATTTGCTTACTCACAT 59.628 43.478 0.00 0.00 37.00 3.21
2277 3211 4.726021 GCACGAGATTTGCTTACTCACATG 60.726 45.833 0.00 0.00 37.00 3.21
2278 3212 4.627035 CACGAGATTTGCTTACTCACATGA 59.373 41.667 0.00 0.00 0.00 3.07
2279 3213 8.561995 GCACGAGATTTGCTTACTCACATGAG 62.562 46.154 7.36 7.36 41.13 2.90
2294 3228 4.776795 ACATGAGTGTGTACGTGTATGA 57.223 40.909 0.00 0.00 37.14 2.15
2295 3229 4.733850 ACATGAGTGTGTACGTGTATGAG 58.266 43.478 0.00 0.00 37.14 2.90
2296 3230 4.457949 ACATGAGTGTGTACGTGTATGAGA 59.542 41.667 0.00 0.00 37.14 3.27
2297 3231 5.048294 ACATGAGTGTGTACGTGTATGAGAA 60.048 40.000 0.00 0.00 37.14 2.87
2298 3232 5.441709 TGAGTGTGTACGTGTATGAGAAA 57.558 39.130 0.00 0.00 0.00 2.52
2299 3233 5.834169 TGAGTGTGTACGTGTATGAGAAAA 58.166 37.500 0.00 0.00 0.00 2.29
2300 3234 6.274579 TGAGTGTGTACGTGTATGAGAAAAA 58.725 36.000 0.00 0.00 0.00 1.94
2301 3235 6.419710 TGAGTGTGTACGTGTATGAGAAAAAG 59.580 38.462 0.00 0.00 0.00 2.27
2302 3236 6.278363 AGTGTGTACGTGTATGAGAAAAAGT 58.722 36.000 0.00 0.00 0.00 2.66
2303 3237 7.428020 AGTGTGTACGTGTATGAGAAAAAGTA 58.572 34.615 0.00 0.00 0.00 2.24
2304 3238 7.380602 AGTGTGTACGTGTATGAGAAAAAGTAC 59.619 37.037 0.00 0.00 35.23 2.73
2305 3239 6.360414 TGTGTACGTGTATGAGAAAAAGTACG 59.640 38.462 0.00 0.00 36.84 3.67
2306 3240 6.578545 GTGTACGTGTATGAGAAAAAGTACGA 59.421 38.462 0.00 0.00 36.84 3.43
2307 3241 7.272084 GTGTACGTGTATGAGAAAAAGTACGAT 59.728 37.037 0.00 0.00 36.84 3.73
2308 3242 7.809331 TGTACGTGTATGAGAAAAAGTACGATT 59.191 33.333 0.00 0.00 36.84 3.34
2309 3243 7.647907 ACGTGTATGAGAAAAAGTACGATTT 57.352 32.000 0.00 0.00 34.71 2.17
2310 3244 7.507304 ACGTGTATGAGAAAAAGTACGATTTG 58.493 34.615 0.00 0.00 34.71 2.32
2311 3245 6.461698 CGTGTATGAGAAAAAGTACGATTTGC 59.538 38.462 4.02 1.24 32.58 3.68
2312 3246 7.519002 GTGTATGAGAAAAAGTACGATTTGCT 58.481 34.615 7.23 7.23 0.00 3.91
2313 3247 8.015658 GTGTATGAGAAAAAGTACGATTTGCTT 58.984 33.333 8.53 0.00 0.00 3.91
2314 3248 9.210329 TGTATGAGAAAAAGTACGATTTGCTTA 57.790 29.630 8.53 5.87 28.53 3.09
2315 3249 9.474249 GTATGAGAAAAAGTACGATTTGCTTAC 57.526 33.333 8.53 5.65 28.53 2.34
2316 3250 7.724305 TGAGAAAAAGTACGATTTGCTTACT 57.276 32.000 8.53 0.00 33.41 2.24
2317 3251 7.793902 TGAGAAAAAGTACGATTTGCTTACTC 58.206 34.615 8.53 6.95 31.04 2.59
2318 3252 7.439955 TGAGAAAAAGTACGATTTGCTTACTCA 59.560 33.333 8.53 8.79 35.08 3.41
2319 3253 7.573627 AGAAAAAGTACGATTTGCTTACTCAC 58.426 34.615 4.02 0.00 31.04 3.51
2320 3254 6.854496 AAAAGTACGATTTGCTTACTCACA 57.146 33.333 0.00 0.00 31.04 3.58
2321 3255 5.840940 AAGTACGATTTGCTTACTCACAC 57.159 39.130 0.00 0.00 31.04 3.82
2322 3256 3.918591 AGTACGATTTGCTTACTCACACG 59.081 43.478 0.00 0.00 26.02 4.49
2323 3257 3.021269 ACGATTTGCTTACTCACACGA 57.979 42.857 0.00 0.00 0.00 4.35
2324 3258 2.987149 ACGATTTGCTTACTCACACGAG 59.013 45.455 0.00 0.00 45.49 4.18
2337 3271 2.717485 ACGAGTGTGTACGTGCGT 59.283 55.556 0.00 2.05 41.17 5.24
2338 3272 1.064621 ACGAGTGTGTACGTGCGTT 59.935 52.632 1.66 0.00 41.17 4.84
2339 3273 1.204228 ACGAGTGTGTACGTGCGTTG 61.204 55.000 1.66 0.00 41.17 4.10
2340 3274 1.204228 CGAGTGTGTACGTGCGTTGT 61.204 55.000 1.66 0.00 0.00 3.32
2341 3275 0.228742 GAGTGTGTACGTGCGTTGTG 59.771 55.000 1.66 0.00 0.00 3.33
2342 3276 0.458889 AGTGTGTACGTGCGTTGTGT 60.459 50.000 1.66 0.00 0.00 3.72
2343 3277 0.314738 GTGTGTACGTGCGTTGTGTG 60.315 55.000 1.66 0.00 0.00 3.82
2344 3278 1.367195 GTGTACGTGCGTTGTGTGC 60.367 57.895 1.66 0.00 0.00 4.57
2345 3279 1.810030 TGTACGTGCGTTGTGTGCA 60.810 52.632 1.66 0.00 40.70 4.57
2351 3285 3.605013 TGCGTTGTGTGCACTAGAT 57.395 47.368 19.41 0.00 37.44 1.98
2352 3286 1.877637 TGCGTTGTGTGCACTAGATT 58.122 45.000 19.41 0.00 37.44 2.40
2353 3287 1.530720 TGCGTTGTGTGCACTAGATTG 59.469 47.619 19.41 4.87 37.44 2.67
2354 3288 1.531149 GCGTTGTGTGCACTAGATTGT 59.469 47.619 19.41 0.00 0.00 2.71
2355 3289 2.662791 GCGTTGTGTGCACTAGATTGTG 60.663 50.000 19.41 1.72 40.62 3.33
2356 3290 2.543848 CGTTGTGTGCACTAGATTGTGT 59.456 45.455 19.41 0.00 39.89 3.72
2357 3291 3.002246 CGTTGTGTGCACTAGATTGTGTT 59.998 43.478 19.41 0.00 39.89 3.32
2358 3292 4.527564 GTTGTGTGCACTAGATTGTGTTC 58.472 43.478 19.41 0.00 39.89 3.18
2359 3293 4.071961 TGTGTGCACTAGATTGTGTTCT 57.928 40.909 19.41 0.00 39.89 3.01
2360 3294 4.450976 TGTGTGCACTAGATTGTGTTCTT 58.549 39.130 19.41 0.00 39.89 2.52
2361 3295 5.606505 TGTGTGCACTAGATTGTGTTCTTA 58.393 37.500 19.41 0.00 39.89 2.10
2362 3296 6.052360 TGTGTGCACTAGATTGTGTTCTTAA 58.948 36.000 19.41 0.00 39.89 1.85
2363 3297 6.540551 TGTGTGCACTAGATTGTGTTCTTAAA 59.459 34.615 19.41 0.00 39.89 1.52
2364 3298 7.066404 TGTGTGCACTAGATTGTGTTCTTAAAA 59.934 33.333 19.41 0.00 39.89 1.52
2365 3299 7.913297 GTGTGCACTAGATTGTGTTCTTAAAAA 59.087 33.333 19.41 0.00 39.89 1.94
2390 3324 8.635765 AAAAATAAGAGTATGCTGGTTCAAGA 57.364 30.769 0.00 0.00 0.00 3.02
2391 3325 8.635765 AAAATAAGAGTATGCTGGTTCAAGAA 57.364 30.769 0.00 0.00 0.00 2.52
2392 3326 8.635765 AAATAAGAGTATGCTGGTTCAAGAAA 57.364 30.769 0.00 0.00 0.00 2.52
2393 3327 7.856145 ATAAGAGTATGCTGGTTCAAGAAAG 57.144 36.000 0.00 0.00 0.00 2.62
2394 3328 4.006319 AGAGTATGCTGGTTCAAGAAAGC 58.994 43.478 0.00 0.66 36.18 3.51
2395 3329 4.006319 GAGTATGCTGGTTCAAGAAAGCT 58.994 43.478 7.70 0.00 36.60 3.74
2396 3330 5.046304 AGAGTATGCTGGTTCAAGAAAGCTA 60.046 40.000 7.70 0.00 36.60 3.32
2397 3331 5.181748 AGTATGCTGGTTCAAGAAAGCTAG 58.818 41.667 7.70 0.00 36.60 3.42
2398 3332 3.492102 TGCTGGTTCAAGAAAGCTAGT 57.508 42.857 7.70 0.00 36.60 2.57
2399 3333 4.617253 TGCTGGTTCAAGAAAGCTAGTA 57.383 40.909 7.70 0.00 36.60 1.82
2400 3334 5.165961 TGCTGGTTCAAGAAAGCTAGTAT 57.834 39.130 7.70 0.00 36.60 2.12
2401 3335 5.178797 TGCTGGTTCAAGAAAGCTAGTATC 58.821 41.667 7.70 0.00 36.60 2.24
2402 3336 5.046304 TGCTGGTTCAAGAAAGCTAGTATCT 60.046 40.000 7.70 0.00 36.60 1.98
2403 3337 5.877564 GCTGGTTCAAGAAAGCTAGTATCTT 59.122 40.000 0.00 0.00 36.31 2.40
2404 3338 6.372937 GCTGGTTCAAGAAAGCTAGTATCTTT 59.627 38.462 0.00 0.00 36.31 2.52
2405 3339 7.094592 GCTGGTTCAAGAAAGCTAGTATCTTTT 60.095 37.037 0.76 0.00 36.31 2.27
2406 3340 9.436957 CTGGTTCAAGAAAGCTAGTATCTTTTA 57.563 33.333 0.76 0.00 36.31 1.52
2407 3341 9.959721 TGGTTCAAGAAAGCTAGTATCTTTTAT 57.040 29.630 0.76 0.00 36.31 1.40
2426 3360 9.146984 TCTTTTATGTAACTCTGTTATGAACGG 57.853 33.333 0.00 0.00 39.17 4.44
2427 3361 8.836268 TTTTATGTAACTCTGTTATGAACGGT 57.164 30.769 0.00 0.00 38.89 4.83
2428 3362 8.836268 TTTATGTAACTCTGTTATGAACGGTT 57.164 30.769 0.00 0.00 38.89 4.44
2429 3363 8.836268 TTATGTAACTCTGTTATGAACGGTTT 57.164 30.769 0.00 0.00 38.89 3.27
2430 3364 7.739498 ATGTAACTCTGTTATGAACGGTTTT 57.261 32.000 0.00 0.00 38.89 2.43
2431 3365 7.556733 TGTAACTCTGTTATGAACGGTTTTT 57.443 32.000 0.00 0.00 38.89 1.94
2432 3366 7.632721 TGTAACTCTGTTATGAACGGTTTTTC 58.367 34.615 0.00 0.00 38.89 2.29
2433 3367 6.937436 AACTCTGTTATGAACGGTTTTTCT 57.063 33.333 0.00 0.00 38.89 2.52
2434 3368 6.937436 ACTCTGTTATGAACGGTTTTTCTT 57.063 33.333 0.00 0.00 38.89 2.52
2435 3369 7.329588 ACTCTGTTATGAACGGTTTTTCTTT 57.670 32.000 0.00 0.00 38.89 2.52
2436 3370 7.415229 ACTCTGTTATGAACGGTTTTTCTTTC 58.585 34.615 0.00 0.00 38.89 2.62
2437 3371 6.731164 TCTGTTATGAACGGTTTTTCTTTCC 58.269 36.000 0.00 0.00 38.89 3.13
2438 3372 6.319152 TCTGTTATGAACGGTTTTTCTTTCCA 59.681 34.615 0.00 0.00 38.89 3.53
2439 3373 6.267070 TGTTATGAACGGTTTTTCTTTCCAC 58.733 36.000 0.00 0.00 0.00 4.02
2440 3374 3.786516 TGAACGGTTTTTCTTTCCACC 57.213 42.857 0.00 0.00 0.00 4.61
2441 3375 3.090037 TGAACGGTTTTTCTTTCCACCA 58.910 40.909 0.00 0.00 0.00 4.17
2442 3376 3.702045 TGAACGGTTTTTCTTTCCACCAT 59.298 39.130 0.00 0.00 0.00 3.55
2443 3377 4.202070 TGAACGGTTTTTCTTTCCACCATC 60.202 41.667 0.00 0.00 0.00 3.51
2444 3378 2.626266 ACGGTTTTTCTTTCCACCATCC 59.374 45.455 0.00 0.00 0.00 3.51
2445 3379 2.351350 CGGTTTTTCTTTCCACCATCCG 60.351 50.000 0.00 0.00 0.00 4.18
2446 3380 2.626266 GGTTTTTCTTTCCACCATCCGT 59.374 45.455 0.00 0.00 0.00 4.69
2447 3381 3.069016 GGTTTTTCTTTCCACCATCCGTT 59.931 43.478 0.00 0.00 0.00 4.44
2448 3382 4.442332 GGTTTTTCTTTCCACCATCCGTTT 60.442 41.667 0.00 0.00 0.00 3.60
2449 3383 5.113383 GTTTTTCTTTCCACCATCCGTTTT 58.887 37.500 0.00 0.00 0.00 2.43
2450 3384 5.346181 TTTTCTTTCCACCATCCGTTTTT 57.654 34.783 0.00 0.00 0.00 1.94
2451 3385 6.466885 TTTTCTTTCCACCATCCGTTTTTA 57.533 33.333 0.00 0.00 0.00 1.52
2452 3386 6.658188 TTTCTTTCCACCATCCGTTTTTAT 57.342 33.333 0.00 0.00 0.00 1.40
2453 3387 6.658188 TTCTTTCCACCATCCGTTTTTATT 57.342 33.333 0.00 0.00 0.00 1.40
2454 3388 6.658188 TCTTTCCACCATCCGTTTTTATTT 57.342 33.333 0.00 0.00 0.00 1.40
2455 3389 7.762588 TCTTTCCACCATCCGTTTTTATTTA 57.237 32.000 0.00 0.00 0.00 1.40
2456 3390 8.179509 TCTTTCCACCATCCGTTTTTATTTAA 57.820 30.769 0.00 0.00 0.00 1.52
2457 3391 8.639761 TCTTTCCACCATCCGTTTTTATTTAAA 58.360 29.630 0.00 0.00 0.00 1.52
2458 3392 9.262358 CTTTCCACCATCCGTTTTTATTTAAAA 57.738 29.630 0.00 0.00 33.41 1.52
2459 3393 9.780186 TTTCCACCATCCGTTTTTATTTAAAAT 57.220 25.926 0.00 0.00 37.98 1.82
2460 3394 8.764524 TCCACCATCCGTTTTTATTTAAAATG 57.235 30.769 0.00 0.00 40.76 2.32
2461 3395 8.368668 TCCACCATCCGTTTTTATTTAAAATGT 58.631 29.630 0.00 0.00 39.88 2.71
2462 3396 8.439286 CCACCATCCGTTTTTATTTAAAATGTG 58.561 33.333 0.00 0.00 39.88 3.21
2463 3397 9.197694 CACCATCCGTTTTTATTTAAAATGTGA 57.802 29.630 0.00 0.00 39.88 3.58
2464 3398 9.198837 ACCATCCGTTTTTATTTAAAATGTGAC 57.801 29.630 0.00 0.00 39.88 3.67
2465 3399 9.418045 CCATCCGTTTTTATTTAAAATGTGACT 57.582 29.630 0.00 0.00 39.88 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 8.311836 TCTCGTCTTTCTAAACAGGATACAAAT 58.688 33.333 0.00 0.00 41.41 2.32
21 22 5.661056 ACCATCATTGTCTCGTCTTTCTA 57.339 39.130 0.00 0.00 0.00 2.10
24 25 4.003648 GGAACCATCATTGTCTCGTCTTT 58.996 43.478 0.00 0.00 0.00 2.52
49 50 4.779993 GGGAGAACCTTATTCCATCTGT 57.220 45.455 0.00 0.00 35.85 3.41
77 78 2.036256 GCACCACTGGATTGGGCT 59.964 61.111 0.71 0.00 41.49 5.19
84 89 1.906333 TGCTAGACGCACCACTGGA 60.906 57.895 0.71 0.00 45.47 3.86
135 140 2.896044 CGGATGAATCCTGAGAGATCCA 59.104 50.000 7.71 0.00 44.93 3.41
154 159 1.003812 TCCACCAAAGATAACCACCGG 59.996 52.381 0.00 0.00 0.00 5.28
163 168 1.683011 CCAAGCGGATCCACCAAAGAT 60.683 52.381 13.41 0.00 38.90 2.40
181 186 6.703319 TGTAAACGGATGAAGACTAAATCCA 58.297 36.000 13.92 0.00 39.98 3.41
205 210 6.875972 AGTATCCAACCAGAAGACAGTTAT 57.124 37.500 0.00 0.00 0.00 1.89
209 214 5.047021 TCAGAAGTATCCAACCAGAAGACAG 60.047 44.000 0.00 0.00 0.00 3.51
226 234 2.072298 GCAGAAGCGTTGATCAGAAGT 58.928 47.619 0.00 0.00 0.00 3.01
285 297 1.459592 CAGAAAACGTCGTGCTAAGGG 59.540 52.381 0.00 0.00 0.00 3.95
299 311 9.787435 AGATGTATTGTAGTAAACACCAGAAAA 57.213 29.630 0.00 0.00 38.00 2.29
374 386 1.401670 CGACTAGAAGCACTGAAGCGT 60.402 52.381 0.00 0.00 40.15 5.07
399 411 1.489481 TCAGATCGGCAGACCATCTT 58.511 50.000 0.00 0.00 33.90 2.40
529 1197 5.645497 CAGTAAAATAGAGCCAGCAAAGAGT 59.355 40.000 0.00 0.00 0.00 3.24
551 1219 4.090090 TCTACCAAGGAGAAGAGGAACAG 58.910 47.826 0.00 0.00 0.00 3.16
607 1278 5.516696 CGTCGCTTGATCTTTCTGATTCTAA 59.483 40.000 0.00 0.00 35.14 2.10
672 1349 4.159266 TCGACAGCGATCCTAGGG 57.841 61.111 9.46 0.00 42.51 3.53
779 1459 8.880244 GGGTATATGCCATGTCAAGGATATATA 58.120 37.037 12.29 3.49 0.00 0.86
780 1460 7.202223 GGGGTATATGCCATGTCAAGGATATAT 60.202 40.741 12.29 4.35 0.00 0.86
781 1461 6.101150 GGGGTATATGCCATGTCAAGGATATA 59.899 42.308 12.29 1.47 0.00 0.86
782 1462 5.103940 GGGGTATATGCCATGTCAAGGATAT 60.104 44.000 12.29 2.38 0.00 1.63
848 1531 5.302313 CGCCCTCCCTATTTACCTCTATATC 59.698 48.000 0.00 0.00 0.00 1.63
852 1535 2.178544 ACGCCCTCCCTATTTACCTCTA 59.821 50.000 0.00 0.00 0.00 2.43
943 1628 6.261158 TGTTGTGTTTGTTGTAATGCTAGCTA 59.739 34.615 17.23 2.58 0.00 3.32
944 1629 5.067153 TGTTGTGTTTGTTGTAATGCTAGCT 59.933 36.000 17.23 0.00 0.00 3.32
945 1630 5.173131 GTGTTGTGTTTGTTGTAATGCTAGC 59.827 40.000 8.10 8.10 0.00 3.42
946 1631 6.196353 GTGTGTTGTGTTTGTTGTAATGCTAG 59.804 38.462 0.00 0.00 0.00 3.42
1066 1768 8.014217 TTCGGAGAGTGGATCAAAGAATTGAAT 61.014 37.037 0.00 0.00 43.51 2.57
1067 1769 6.744056 TTCGGAGAGTGGATCAAAGAATTGAA 60.744 38.462 0.00 0.00 43.51 2.69
1075 1777 2.837591 TGGATTCGGAGAGTGGATCAAA 59.162 45.455 0.00 0.00 38.43 2.69
1156 1862 1.203052 CATTGCCTTTACCAGCACCAG 59.797 52.381 0.00 0.00 39.10 4.00
1162 1868 0.734889 CTCCGCATTGCCTTTACCAG 59.265 55.000 2.41 0.00 0.00 4.00
1338 2044 3.932483 GACGTTGGGGTCCACGGT 61.932 66.667 5.34 0.00 34.29 4.83
1531 2245 6.434596 TCGATCAACCAACACAAACTTATTG 58.565 36.000 0.00 0.00 0.00 1.90
1570 2368 4.340666 TCATGCATGTGCGGGTTAATTTAT 59.659 37.500 25.43 0.00 45.83 1.40
1579 2377 1.514657 CGTTTCATGCATGTGCGGG 60.515 57.895 25.43 9.40 45.83 6.13
1676 2523 0.108138 GGGTCAGAGGACATGAACGG 60.108 60.000 0.00 0.00 46.17 4.44
1678 2532 2.859165 TTGGGTCAGAGGACATGAAC 57.141 50.000 0.00 0.00 46.17 3.18
1689 2550 6.003950 TCCAGATCTAAACTTTTTGGGTCAG 58.996 40.000 0.00 0.00 0.00 3.51
1711 2572 7.728847 AATTACAATTTTCCAGCAAGTTTCC 57.271 32.000 0.00 0.00 0.00 3.13
1712 2573 9.476202 ACTAATTACAATTTTCCAGCAAGTTTC 57.524 29.630 0.00 0.00 0.00 2.78
1714 2575 8.421002 ACACTAATTACAATTTTCCAGCAAGTT 58.579 29.630 0.00 0.00 0.00 2.66
1727 2651 8.023128 GCATGACAAACAGACACTAATTACAAT 58.977 33.333 0.00 0.00 0.00 2.71
1881 2809 4.996344 ACCCGAAATTGTTTTGTTTACGT 58.004 34.783 0.00 0.00 0.00 3.57
1926 2854 9.368921 GCCAAATTCAAACTAATTTCTTTTTCG 57.631 29.630 0.00 0.00 37.03 3.46
1941 2874 8.136165 CCAATGAAATTTTGAGCCAAATTCAAA 58.864 29.630 14.84 7.17 41.40 2.69
1944 2877 7.437793 TCCAATGAAATTTTGAGCCAAATTC 57.562 32.000 0.00 4.81 31.22 2.17
1945 2878 7.820578 TTCCAATGAAATTTTGAGCCAAATT 57.179 28.000 0.00 0.00 31.22 1.82
1947 2880 7.820578 AATTCCAATGAAATTTTGAGCCAAA 57.179 28.000 0.00 0.00 31.22 3.28
1948 2881 8.782144 GTTAATTCCAATGAAATTTTGAGCCAA 58.218 29.630 0.00 0.00 31.22 4.52
1949 2882 7.390162 GGTTAATTCCAATGAAATTTTGAGCCA 59.610 33.333 0.00 0.00 31.22 4.75
1950 2883 7.607607 AGGTTAATTCCAATGAAATTTTGAGCC 59.392 33.333 0.00 0.00 31.22 4.70
1951 2884 8.552083 AGGTTAATTCCAATGAAATTTTGAGC 57.448 30.769 0.00 0.00 31.22 4.26
1986 2920 9.558396 AATTTTGAGCCAAATTCAAACTAATGA 57.442 25.926 0.31 0.00 42.44 2.57
2022 2956 8.491331 AATTTTGTTGGGGATCGAAATATTTG 57.509 30.769 5.17 0.00 30.41 2.32
2213 3147 3.006752 AGCCCAAATGAAGCGATGAAAAA 59.993 39.130 0.00 0.00 0.00 1.94
2214 3148 2.562298 AGCCCAAATGAAGCGATGAAAA 59.438 40.909 0.00 0.00 0.00 2.29
2215 3149 2.094597 CAGCCCAAATGAAGCGATGAAA 60.095 45.455 0.00 0.00 0.00 2.69
2216 3150 1.473677 CAGCCCAAATGAAGCGATGAA 59.526 47.619 0.00 0.00 0.00 2.57
2217 3151 1.097232 CAGCCCAAATGAAGCGATGA 58.903 50.000 0.00 0.00 0.00 2.92
2218 3152 0.101759 CCAGCCCAAATGAAGCGATG 59.898 55.000 0.00 0.00 0.00 3.84
2219 3153 1.669999 GCCAGCCCAAATGAAGCGAT 61.670 55.000 0.00 0.00 0.00 4.58
2220 3154 2.342650 GCCAGCCCAAATGAAGCGA 61.343 57.895 0.00 0.00 0.00 4.93
2221 3155 2.182537 GCCAGCCCAAATGAAGCG 59.817 61.111 0.00 0.00 0.00 4.68
2222 3156 2.285024 TGGCCAGCCCAAATGAAGC 61.285 57.895 0.00 0.00 41.82 3.86
2223 3157 4.116926 TGGCCAGCCCAAATGAAG 57.883 55.556 0.00 0.00 41.82 3.02
2231 3165 4.380945 TGGGTTCATGGCCAGCCC 62.381 66.667 23.13 23.13 39.73 5.19
2232 3166 3.070576 GTGGGTTCATGGCCAGCC 61.071 66.667 13.05 10.69 0.00 4.85
2233 3167 3.443045 CGTGGGTTCATGGCCAGC 61.443 66.667 13.05 0.77 0.00 4.85
2234 3168 3.443045 GCGTGGGTTCATGGCCAG 61.443 66.667 13.05 3.43 0.00 4.85
2247 3181 3.118454 AAATCTCGTGCGGGCGTG 61.118 61.111 0.00 0.00 0.00 5.34
2248 3182 3.118454 CAAATCTCGTGCGGGCGT 61.118 61.111 0.00 0.00 0.00 5.68
2249 3183 4.520846 GCAAATCTCGTGCGGGCG 62.521 66.667 0.00 0.00 31.20 6.13
2250 3184 1.366111 TAAGCAAATCTCGTGCGGGC 61.366 55.000 0.00 0.00 46.86 6.13
2251 3185 0.373716 GTAAGCAAATCTCGTGCGGG 59.626 55.000 0.00 0.00 46.86 6.13
2252 3186 1.324736 GAGTAAGCAAATCTCGTGCGG 59.675 52.381 0.00 0.00 46.86 5.69
2253 3187 1.992667 TGAGTAAGCAAATCTCGTGCG 59.007 47.619 0.00 0.00 46.86 5.34
2254 3188 2.736721 TGTGAGTAAGCAAATCTCGTGC 59.263 45.455 0.00 0.00 42.55 5.34
2255 3189 4.627035 TCATGTGAGTAAGCAAATCTCGTG 59.373 41.667 0.00 5.12 0.00 4.35
2256 3190 4.820897 TCATGTGAGTAAGCAAATCTCGT 58.179 39.130 0.00 0.00 0.00 4.18
2257 3191 5.386810 CTCATGTGAGTAAGCAAATCTCG 57.613 43.478 1.84 0.00 37.40 4.04
2273 3207 4.457949 TCTCATACACGTACACACTCATGT 59.542 41.667 0.00 0.00 40.80 3.21
2274 3208 4.981794 TCTCATACACGTACACACTCATG 58.018 43.478 0.00 0.00 0.00 3.07
2275 3209 5.638596 TTCTCATACACGTACACACTCAT 57.361 39.130 0.00 0.00 0.00 2.90
2276 3210 5.441709 TTTCTCATACACGTACACACTCA 57.558 39.130 0.00 0.00 0.00 3.41
2277 3211 6.420008 ACTTTTTCTCATACACGTACACACTC 59.580 38.462 0.00 0.00 0.00 3.51
2278 3212 6.278363 ACTTTTTCTCATACACGTACACACT 58.722 36.000 0.00 0.00 0.00 3.55
2279 3213 6.520792 ACTTTTTCTCATACACGTACACAC 57.479 37.500 0.00 0.00 0.00 3.82
2280 3214 6.360414 CGTACTTTTTCTCATACACGTACACA 59.640 38.462 0.00 0.00 0.00 3.72
2281 3215 6.578545 TCGTACTTTTTCTCATACACGTACAC 59.421 38.462 0.00 0.00 0.00 2.90
2282 3216 6.667370 TCGTACTTTTTCTCATACACGTACA 58.333 36.000 0.00 0.00 0.00 2.90
2283 3217 7.731556 ATCGTACTTTTTCTCATACACGTAC 57.268 36.000 0.00 0.00 0.00 3.67
2284 3218 8.641155 CAAATCGTACTTTTTCTCATACACGTA 58.359 33.333 0.00 0.00 0.00 3.57
2285 3219 7.507304 CAAATCGTACTTTTTCTCATACACGT 58.493 34.615 0.00 0.00 0.00 4.49
2286 3220 6.461698 GCAAATCGTACTTTTTCTCATACACG 59.538 38.462 0.00 0.00 0.00 4.49
2287 3221 7.519002 AGCAAATCGTACTTTTTCTCATACAC 58.481 34.615 0.00 0.00 0.00 2.90
2288 3222 7.667043 AGCAAATCGTACTTTTTCTCATACA 57.333 32.000 0.00 0.00 0.00 2.29
2289 3223 9.474249 GTAAGCAAATCGTACTTTTTCTCATAC 57.526 33.333 0.00 0.00 0.00 2.39
2290 3224 9.431887 AGTAAGCAAATCGTACTTTTTCTCATA 57.568 29.630 0.00 0.00 36.76 2.15
2291 3225 8.324163 AGTAAGCAAATCGTACTTTTTCTCAT 57.676 30.769 0.00 0.00 36.76 2.90
2292 3226 7.439955 TGAGTAAGCAAATCGTACTTTTTCTCA 59.560 33.333 0.00 0.00 39.53 3.27
2293 3227 7.740781 GTGAGTAAGCAAATCGTACTTTTTCTC 59.259 37.037 0.00 0.00 39.53 2.87
2294 3228 7.225931 TGTGAGTAAGCAAATCGTACTTTTTCT 59.774 33.333 0.00 0.00 39.53 2.52
2295 3229 7.320560 GTGTGAGTAAGCAAATCGTACTTTTTC 59.679 37.037 0.00 0.00 39.53 2.29
2296 3230 7.130269 GTGTGAGTAAGCAAATCGTACTTTTT 58.870 34.615 0.00 0.00 39.53 1.94
2297 3231 6.563381 CGTGTGAGTAAGCAAATCGTACTTTT 60.563 38.462 0.00 0.00 39.53 2.27
2298 3232 5.107607 CGTGTGAGTAAGCAAATCGTACTTT 60.108 40.000 0.00 0.00 39.53 2.66
2299 3233 4.384846 CGTGTGAGTAAGCAAATCGTACTT 59.615 41.667 0.00 0.00 39.53 2.24
2300 3234 3.918591 CGTGTGAGTAAGCAAATCGTACT 59.081 43.478 0.00 0.00 41.59 2.73
2301 3235 3.916172 TCGTGTGAGTAAGCAAATCGTAC 59.084 43.478 0.00 0.00 0.00 3.67
2302 3236 4.163458 TCGTGTGAGTAAGCAAATCGTA 57.837 40.909 0.00 0.00 0.00 3.43
2303 3237 2.987149 CTCGTGTGAGTAAGCAAATCGT 59.013 45.455 0.00 0.00 37.46 3.73
2304 3238 3.624726 CTCGTGTGAGTAAGCAAATCG 57.375 47.619 0.00 0.00 37.46 3.34
2320 3254 1.064621 AACGCACGTACACACTCGT 59.935 52.632 0.00 0.00 40.99 4.18
2321 3255 1.204228 ACAACGCACGTACACACTCG 61.204 55.000 0.00 0.00 0.00 4.18
2322 3256 0.228742 CACAACGCACGTACACACTC 59.771 55.000 0.00 0.00 0.00 3.51
2323 3257 0.458889 ACACAACGCACGTACACACT 60.459 50.000 0.00 0.00 0.00 3.55
2324 3258 0.314738 CACACAACGCACGTACACAC 60.315 55.000 0.00 0.00 0.00 3.82
2325 3259 1.999819 CACACAACGCACGTACACA 59.000 52.632 0.00 0.00 0.00 3.72
2326 3260 1.367195 GCACACAACGCACGTACAC 60.367 57.895 0.00 0.00 0.00 2.90
2327 3261 1.810030 TGCACACAACGCACGTACA 60.810 52.632 0.00 0.00 33.55 2.90
2328 3262 3.007516 TGCACACAACGCACGTAC 58.992 55.556 0.00 0.00 33.55 3.67
2333 3267 1.530720 CAATCTAGTGCACACAACGCA 59.469 47.619 21.04 0.00 36.94 5.24
2334 3268 1.531149 ACAATCTAGTGCACACAACGC 59.469 47.619 21.04 0.00 0.00 4.84
2335 3269 2.543848 ACACAATCTAGTGCACACAACG 59.456 45.455 21.04 5.14 43.23 4.10
2336 3270 4.273480 AGAACACAATCTAGTGCACACAAC 59.727 41.667 21.04 0.00 43.23 3.32
2337 3271 4.450976 AGAACACAATCTAGTGCACACAA 58.549 39.130 21.04 3.34 43.23 3.33
2338 3272 4.071961 AGAACACAATCTAGTGCACACA 57.928 40.909 21.04 5.21 43.23 3.72
2339 3273 6.539649 TTAAGAACACAATCTAGTGCACAC 57.460 37.500 21.04 0.00 43.23 3.82
2340 3274 7.561021 TTTTAAGAACACAATCTAGTGCACA 57.439 32.000 21.04 4.13 43.23 4.57
2365 3299 8.635765 TCTTGAACCAGCATACTCTTATTTTT 57.364 30.769 0.00 0.00 0.00 1.94
2366 3300 8.635765 TTCTTGAACCAGCATACTCTTATTTT 57.364 30.769 0.00 0.00 0.00 1.82
2367 3301 8.635765 TTTCTTGAACCAGCATACTCTTATTT 57.364 30.769 0.00 0.00 0.00 1.40
2368 3302 7.148171 GCTTTCTTGAACCAGCATACTCTTATT 60.148 37.037 3.10 0.00 32.17 1.40
2369 3303 6.317391 GCTTTCTTGAACCAGCATACTCTTAT 59.683 38.462 3.10 0.00 32.17 1.73
2370 3304 5.643777 GCTTTCTTGAACCAGCATACTCTTA 59.356 40.000 3.10 0.00 32.17 2.10
2371 3305 4.457257 GCTTTCTTGAACCAGCATACTCTT 59.543 41.667 3.10 0.00 32.17 2.85
2372 3306 4.006319 GCTTTCTTGAACCAGCATACTCT 58.994 43.478 3.10 0.00 32.17 3.24
2373 3307 4.006319 AGCTTTCTTGAACCAGCATACTC 58.994 43.478 8.99 0.00 34.49 2.59
2374 3308 4.026356 AGCTTTCTTGAACCAGCATACT 57.974 40.909 8.99 0.00 34.49 2.12
2375 3309 4.938226 ACTAGCTTTCTTGAACCAGCATAC 59.062 41.667 0.00 0.00 34.49 2.39
2376 3310 5.165961 ACTAGCTTTCTTGAACCAGCATA 57.834 39.130 0.00 0.83 34.49 3.14
2377 3311 4.026356 ACTAGCTTTCTTGAACCAGCAT 57.974 40.909 0.00 0.00 34.49 3.79
2378 3312 3.492102 ACTAGCTTTCTTGAACCAGCA 57.508 42.857 0.00 0.00 34.49 4.41
2379 3313 5.423886 AGATACTAGCTTTCTTGAACCAGC 58.576 41.667 0.00 0.26 0.00 4.85
2380 3314 7.913674 AAAGATACTAGCTTTCTTGAACCAG 57.086 36.000 0.00 0.00 30.11 4.00
2381 3315 9.959721 ATAAAAGATACTAGCTTTCTTGAACCA 57.040 29.630 0.00 0.00 34.68 3.67
2400 3334 9.146984 CCGTTCATAACAGAGTTACATAAAAGA 57.853 33.333 0.00 0.00 0.00 2.52
2401 3335 8.932791 ACCGTTCATAACAGAGTTACATAAAAG 58.067 33.333 0.00 0.00 0.00 2.27
2402 3336 8.836268 ACCGTTCATAACAGAGTTACATAAAA 57.164 30.769 0.00 0.00 0.00 1.52
2403 3337 8.836268 AACCGTTCATAACAGAGTTACATAAA 57.164 30.769 0.00 0.00 0.00 1.40
2404 3338 8.836268 AAACCGTTCATAACAGAGTTACATAA 57.164 30.769 0.00 0.00 0.00 1.90
2405 3339 8.836268 AAAACCGTTCATAACAGAGTTACATA 57.164 30.769 0.00 0.00 0.00 2.29
2406 3340 7.739498 AAAACCGTTCATAACAGAGTTACAT 57.261 32.000 0.00 0.00 0.00 2.29
2407 3341 7.496591 AGAAAAACCGTTCATAACAGAGTTACA 59.503 33.333 0.00 0.00 0.00 2.41
2408 3342 7.858583 AGAAAAACCGTTCATAACAGAGTTAC 58.141 34.615 0.00 0.00 0.00 2.50
2409 3343 8.441312 AAGAAAAACCGTTCATAACAGAGTTA 57.559 30.769 0.00 0.00 0.00 2.24
2410 3344 6.937436 AGAAAAACCGTTCATAACAGAGTT 57.063 33.333 0.00 0.00 0.00 3.01
2411 3345 6.937436 AAGAAAAACCGTTCATAACAGAGT 57.063 33.333 0.00 0.00 0.00 3.24
2412 3346 6.856426 GGAAAGAAAAACCGTTCATAACAGAG 59.144 38.462 0.00 0.00 0.00 3.35
2413 3347 6.319152 TGGAAAGAAAAACCGTTCATAACAGA 59.681 34.615 0.00 0.00 0.00 3.41
2414 3348 6.416750 GTGGAAAGAAAAACCGTTCATAACAG 59.583 38.462 0.00 0.00 0.00 3.16
2415 3349 6.267070 GTGGAAAGAAAAACCGTTCATAACA 58.733 36.000 0.00 0.00 0.00 2.41
2416 3350 5.688621 GGTGGAAAGAAAAACCGTTCATAAC 59.311 40.000 0.00 0.00 0.00 1.89
2417 3351 5.360144 TGGTGGAAAGAAAAACCGTTCATAA 59.640 36.000 0.00 0.00 35.33 1.90
2418 3352 4.888239 TGGTGGAAAGAAAAACCGTTCATA 59.112 37.500 0.00 0.00 35.33 2.15
2419 3353 3.702045 TGGTGGAAAGAAAAACCGTTCAT 59.298 39.130 0.00 0.00 35.33 2.57
2420 3354 3.090037 TGGTGGAAAGAAAAACCGTTCA 58.910 40.909 0.00 0.00 35.33 3.18
2421 3355 3.786516 TGGTGGAAAGAAAAACCGTTC 57.213 42.857 0.00 0.00 35.33 3.95
2422 3356 3.069016 GGATGGTGGAAAGAAAAACCGTT 59.931 43.478 0.00 0.00 35.33 4.44
2423 3357 2.626266 GGATGGTGGAAAGAAAAACCGT 59.374 45.455 0.00 0.00 35.33 4.83
2424 3358 2.351350 CGGATGGTGGAAAGAAAAACCG 60.351 50.000 0.00 0.00 35.33 4.44
2425 3359 2.626266 ACGGATGGTGGAAAGAAAAACC 59.374 45.455 0.00 0.00 0.00 3.27
2426 3360 4.316205 AACGGATGGTGGAAAGAAAAAC 57.684 40.909 0.00 0.00 0.00 2.43
2427 3361 5.346181 AAAACGGATGGTGGAAAGAAAAA 57.654 34.783 0.00 0.00 0.00 1.94
2428 3362 5.346181 AAAAACGGATGGTGGAAAGAAAA 57.654 34.783 0.00 0.00 0.00 2.29
2429 3363 6.658188 ATAAAAACGGATGGTGGAAAGAAA 57.342 33.333 0.00 0.00 0.00 2.52
2430 3364 6.658188 AATAAAAACGGATGGTGGAAAGAA 57.342 33.333 0.00 0.00 0.00 2.52
2431 3365 6.658188 AAATAAAAACGGATGGTGGAAAGA 57.342 33.333 0.00 0.00 0.00 2.52
2432 3366 8.819643 TTTAAATAAAAACGGATGGTGGAAAG 57.180 30.769 0.00 0.00 0.00 2.62
2433 3367 9.780186 ATTTTAAATAAAAACGGATGGTGGAAA 57.220 25.926 2.74 0.00 39.82 3.13
2434 3368 9.209175 CATTTTAAATAAAAACGGATGGTGGAA 57.791 29.630 2.74 0.00 39.82 3.53
2435 3369 8.368668 ACATTTTAAATAAAAACGGATGGTGGA 58.631 29.630 2.74 0.00 39.82 4.02
2436 3370 8.439286 CACATTTTAAATAAAAACGGATGGTGG 58.561 33.333 2.74 0.00 39.82 4.61
2437 3371 9.197694 TCACATTTTAAATAAAAACGGATGGTG 57.802 29.630 2.74 0.00 39.82 4.17
2438 3372 9.198837 GTCACATTTTAAATAAAAACGGATGGT 57.801 29.630 2.74 0.00 39.82 3.55
2439 3373 9.418045 AGTCACATTTTAAATAAAAACGGATGG 57.582 29.630 2.74 0.00 39.82 3.51


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

AutoCloner maintained by Alex Coulton.