Multiple sequence alignment - TraesCS7B01G209700

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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 TraesCS7B01G209700 chr7B 100.000 6566 0 0 1 6566 382605239 382611804 0.000000e+00 12126.0
1 TraesCS7B01G209700 chr7B 81.818 330 53 6 6237 6563 604310864 604311189 3.020000e-68 270.0
2 TraesCS7B01G209700 chr7B 85.950 121 16 1 44 163 624470919 624471039 1.920000e-25 128.0
3 TraesCS7B01G209700 chr7B 97.561 41 1 0 1684 1724 382606879 382606919 3.280000e-08 71.3
4 TraesCS7B01G209700 chr7B 97.561 41 1 0 1641 1681 382606922 382606962 3.280000e-08 71.3
5 TraesCS7B01G209700 chr7B 100.000 29 0 0 5795 5823 382610999 382611027 3.000000e-03 54.7
6 TraesCS7B01G209700 chr7B 100.000 29 0 0 5761 5789 382611033 382611061 3.000000e-03 54.7
7 TraesCS7B01G209700 chr7A 96.032 3251 86 22 1682 4907 438141122 438144354 0.000000e+00 5249.0
8 TraesCS7B01G209700 chr7A 94.354 1169 48 9 519 1681 438140008 438141164 0.000000e+00 1777.0
9 TraesCS7B01G209700 chr7A 93.031 904 53 4 4914 5811 438144423 438145322 0.000000e+00 1312.0
10 TraesCS7B01G209700 chr7A 87.978 366 43 1 6195 6559 438145651 438146016 1.310000e-116 431.0
11 TraesCS7B01G209700 chr7A 89.888 267 7 9 232 484 438139750 438140010 6.350000e-85 326.0
12 TraesCS7B01G209700 chr7A 89.674 184 8 6 5863 6036 438145340 438145522 2.380000e-54 224.0
13 TraesCS7B01G209700 chr7A 83.459 133 19 3 44 174 286746955 286747086 3.220000e-23 121.0
14 TraesCS7B01G209700 chr7D 95.385 3142 62 28 1782 4909 387912261 387915333 0.000000e+00 4922.0
15 TraesCS7B01G209700 chr7D 89.028 1677 112 28 4914 6559 387915635 387917270 0.000000e+00 2012.0
16 TraesCS7B01G209700 chr7D 90.380 1237 64 22 44 1257 387910628 387911832 0.000000e+00 1574.0
17 TraesCS7B01G209700 chr7D 95.718 397 12 3 1290 1681 387911837 387912233 9.290000e-178 634.0
18 TraesCS7B01G209700 chr7D 79.077 325 62 4 6242 6563 226687040 226687361 1.110000e-52 219.0
19 TraesCS7B01G209700 chr7D 95.890 73 3 0 1682 1754 387912191 387912263 1.160000e-22 119.0
20 TraesCS7B01G209700 chr1D 84.551 356 50 5 6204 6557 401438390 401438038 1.360000e-91 348.0
21 TraesCS7B01G209700 chr1D 81.096 365 66 3 6204 6566 15617254 15616891 8.330000e-74 289.0
22 TraesCS7B01G209700 chr1D 80.420 143 25 3 44 183 475277832 475277974 9.000000e-19 106.0
23 TraesCS7B01G209700 chrUn 81.717 361 55 9 6204 6558 40899423 40899068 2.320000e-74 291.0
24 TraesCS7B01G209700 chrUn 81.717 361 55 9 6204 6558 333713438 333713793 2.320000e-74 291.0
25 TraesCS7B01G209700 chr6A 82.131 291 44 8 6278 6563 115337551 115337264 6.580000e-60 243.0
26 TraesCS7B01G209700 chr6A 88.235 136 15 1 2301 2435 169208083 169207948 1.890000e-35 161.0
27 TraesCS7B01G209700 chr1A 83.922 255 40 1 6300 6553 550899340 550899594 6.580000e-60 243.0
28 TraesCS7B01G209700 chr2D 89.655 174 17 1 2298 2471 147232818 147232646 3.080000e-53 220.0
29 TraesCS7B01G209700 chr2D 87.050 139 14 2 2324 2462 552199875 552199741 3.170000e-33 154.0
30 TraesCS7B01G209700 chr2D 87.500 120 15 0 44 163 7893657 7893538 8.880000e-29 139.0
31 TraesCS7B01G209700 chr2D 88.785 107 12 0 46 152 174246167 174246273 1.490000e-26 132.0
32 TraesCS7B01G209700 chr2D 85.833 120 16 1 44 163 431525314 431525196 6.910000e-25 126.0
33 TraesCS7B01G209700 chr2D 83.333 132 21 1 44 174 483172460 483172329 3.220000e-23 121.0
34 TraesCS7B01G209700 chr2A 89.326 178 14 2 2298 2471 155590906 155591082 1.110000e-52 219.0
35 TraesCS7B01G209700 chr3A 87.640 178 20 2 2298 2474 116533126 116532950 8.630000e-49 206.0
36 TraesCS7B01G209700 chr1B 84.000 175 23 4 2299 2471 309378434 309378263 5.270000e-36 163.0
37 TraesCS7B01G209700 chr3D 85.124 121 17 1 44 163 562514432 562514552 8.940000e-24 122.0
38 TraesCS7B01G209700 chr5D 85.470 117 16 1 2353 2469 127270358 127270243 3.220000e-23 121.0


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 TraesCS7B01G209700 chr7B 382605239 382611804 6565 False 12126.000000 12126 100.000000 1 6566 1 chr7B.!!$F1 6565
1 TraesCS7B01G209700 chr7A 438139750 438146016 6266 False 1553.166667 5249 91.826167 232 6559 6 chr7A.!!$F2 6327
2 TraesCS7B01G209700 chr7D 387910628 387917270 6642 False 1852.200000 4922 93.280200 44 6559 5 chr7D.!!$F2 6515

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
448 463 0.029989 ATTCCTACTCCCCCACCCTC 60.030 60.000 0.00 0.00 0.00 4.30 F
979 1001 0.469494 TCATGTAGTGCGGCATCCAT 59.531 50.000 5.72 6.07 0.00 3.41 F
1050 1072 0.610232 ATGTGTTCAGGAAGCAGGGC 60.610 55.000 0.00 0.00 0.00 5.19 F
1654 1682 1.005450 TCCTGGAAAATGGCACCTACC 59.995 52.381 0.00 0.00 0.00 3.18 F
2756 2802 0.107703 CACCCAAGCGAGGCTCAATA 60.108 55.000 15.95 0.00 38.25 1.90 F
4591 4646 2.816087 CTCCCTGTTTCCAATGACACAG 59.184 50.000 2.63 2.63 45.03 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1765 1793 1.188863 ATCCAGGACAGGCATTTTGC 58.811 50.000 0.00 0.0 44.08 3.68 R
2021 2050 2.502538 AGCTATAAGCCAACCGTAACCA 59.497 45.455 0.00 0.0 43.77 3.67 R
2022 2051 3.189618 AGCTATAAGCCAACCGTAACC 57.810 47.619 0.00 0.0 43.77 2.85 R
3541 3595 2.992124 TCAAATTTCCCTCGGCGATA 57.008 45.000 11.27 0.0 0.00 2.92 R
4706 4761 3.264193 ACAGAACAGCTATCCACCAATCA 59.736 43.478 0.00 0.0 0.00 2.57 R
6137 6538 0.663568 CGTGGCGACCGAGGATAATC 60.664 60.000 0.00 0.0 0.00 1.75 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
19 20 2.276732 CACAGGATTCAGTTGGTGGT 57.723 50.000 0.00 0.00 0.00 4.16
20 21 1.881973 CACAGGATTCAGTTGGTGGTG 59.118 52.381 0.00 0.00 0.00 4.17
21 22 1.774254 ACAGGATTCAGTTGGTGGTGA 59.226 47.619 0.00 0.00 0.00 4.02
22 23 2.376518 ACAGGATTCAGTTGGTGGTGAT 59.623 45.455 0.00 0.00 0.00 3.06
23 24 3.012518 CAGGATTCAGTTGGTGGTGATC 58.987 50.000 0.00 0.00 0.00 2.92
24 25 2.915604 AGGATTCAGTTGGTGGTGATCT 59.084 45.455 0.00 0.00 0.00 2.75
25 26 3.331889 AGGATTCAGTTGGTGGTGATCTT 59.668 43.478 0.00 0.00 0.00 2.40
26 27 4.082125 GGATTCAGTTGGTGGTGATCTTT 58.918 43.478 0.00 0.00 0.00 2.52
27 28 4.082571 GGATTCAGTTGGTGGTGATCTTTG 60.083 45.833 0.00 0.00 0.00 2.77
28 29 2.862541 TCAGTTGGTGGTGATCTTTGG 58.137 47.619 0.00 0.00 0.00 3.28
29 30 2.174639 TCAGTTGGTGGTGATCTTTGGT 59.825 45.455 0.00 0.00 0.00 3.67
30 31 2.294233 CAGTTGGTGGTGATCTTTGGTG 59.706 50.000 0.00 0.00 0.00 4.17
31 32 1.613437 GTTGGTGGTGATCTTTGGTGG 59.387 52.381 0.00 0.00 0.00 4.61
32 33 1.144691 TGGTGGTGATCTTTGGTGGA 58.855 50.000 0.00 0.00 0.00 4.02
33 34 1.710244 TGGTGGTGATCTTTGGTGGAT 59.290 47.619 0.00 0.00 0.00 3.41
34 35 2.290896 TGGTGGTGATCTTTGGTGGATC 60.291 50.000 0.00 0.00 39.76 3.36
35 36 2.369394 GTGGTGATCTTTGGTGGATCC 58.631 52.381 4.20 4.20 38.89 3.36
36 37 1.065491 TGGTGATCTTTGGTGGATCCG 60.065 52.381 7.39 0.00 38.89 4.18
37 38 1.017387 GTGATCTTTGGTGGATCCGC 58.983 55.000 17.45 17.45 38.89 5.54
38 39 0.911769 TGATCTTTGGTGGATCCGCT 59.088 50.000 24.15 3.58 38.89 5.52
39 40 1.134401 TGATCTTTGGTGGATCCGCTC 60.134 52.381 24.15 14.79 38.89 5.03
40 41 0.179073 ATCTTTGGTGGATCCGCTCG 60.179 55.000 24.15 10.54 39.52 5.03
41 42 1.079127 CTTTGGTGGATCCGCTCGT 60.079 57.895 24.15 0.00 39.52 4.18
42 43 0.174845 CTTTGGTGGATCCGCTCGTA 59.825 55.000 24.15 6.63 39.52 3.43
47 48 1.472728 GGTGGATCCGCTCGTAACAAT 60.473 52.381 24.15 0.00 0.00 2.71
58 59 4.781528 CGCTCGTAACAATAAGTTTTGCTC 59.218 41.667 0.00 0.00 41.64 4.26
63 64 4.584327 AACAATAAGTTTTGCTCGGCTT 57.416 36.364 0.00 0.00 37.03 4.35
76 77 2.184579 GGCTTCGACGAGGAAGGG 59.815 66.667 11.60 0.00 42.88 3.95
78 79 2.647158 GCTTCGACGAGGAAGGGGT 61.647 63.158 11.60 0.00 42.88 4.95
79 80 1.215647 CTTCGACGAGGAAGGGGTG 59.784 63.158 0.00 0.00 39.76 4.61
80 81 1.228644 TTCGACGAGGAAGGGGTGA 60.229 57.895 0.00 0.00 0.00 4.02
81 82 0.613853 TTCGACGAGGAAGGGGTGAT 60.614 55.000 0.00 0.00 0.00 3.06
82 83 1.141881 CGACGAGGAAGGGGTGATG 59.858 63.158 0.00 0.00 0.00 3.07
83 84 1.320344 CGACGAGGAAGGGGTGATGA 61.320 60.000 0.00 0.00 0.00 2.92
84 85 0.175989 GACGAGGAAGGGGTGATGAC 59.824 60.000 0.00 0.00 0.00 3.06
85 86 1.141881 CGAGGAAGGGGTGATGACG 59.858 63.158 0.00 0.00 0.00 4.35
86 87 1.320344 CGAGGAAGGGGTGATGACGA 61.320 60.000 0.00 0.00 0.00 4.20
87 88 1.123928 GAGGAAGGGGTGATGACGAT 58.876 55.000 0.00 0.00 0.00 3.73
88 89 0.833287 AGGAAGGGGTGATGACGATG 59.167 55.000 0.00 0.00 0.00 3.84
89 90 0.179045 GGAAGGGGTGATGACGATGG 60.179 60.000 0.00 0.00 0.00 3.51
90 91 0.815615 GAAGGGGTGATGACGATGGC 60.816 60.000 0.00 0.00 0.00 4.40
91 92 1.561769 AAGGGGTGATGACGATGGCA 61.562 55.000 0.00 0.00 0.00 4.92
92 93 1.819632 GGGGTGATGACGATGGCAC 60.820 63.158 0.00 0.00 0.00 5.01
93 94 2.173669 GGGTGATGACGATGGCACG 61.174 63.158 7.71 7.71 39.31 5.34
96 97 3.272334 GATGACGATGGCACGCCC 61.272 66.667 5.42 0.00 36.70 6.13
119 120 2.349817 CGGTTTGCTTCAGTGCTTGTAG 60.350 50.000 0.00 0.00 0.00 2.74
123 124 1.068588 TGCTTCAGTGCTTGTAGTCGT 59.931 47.619 0.00 0.00 0.00 4.34
131 132 0.450983 GCTTGTAGTCGTCGCTAGGT 59.549 55.000 0.00 0.00 0.00 3.08
132 133 1.794437 GCTTGTAGTCGTCGCTAGGTG 60.794 57.143 0.00 0.00 0.00 4.00
138 139 1.089920 GTCGTCGCTAGGTGGTCTAA 58.910 55.000 0.00 0.00 0.00 2.10
140 141 1.093159 CGTCGCTAGGTGGTCTAAGT 58.907 55.000 0.00 0.00 0.00 2.24
152 153 6.071984 AGGTGGTCTAAGTATCTGGATGTAG 58.928 44.000 0.00 0.00 0.00 2.74
153 154 5.279056 GGTGGTCTAAGTATCTGGATGTAGC 60.279 48.000 0.00 0.00 0.00 3.58
170 171 8.202137 TGGATGTAGCTTTACTATTCCTTGTAC 58.798 37.037 0.00 0.00 37.12 2.90
171 172 8.422566 GGATGTAGCTTTACTATTCCTTGTACT 58.577 37.037 0.00 0.00 35.02 2.73
172 173 9.465985 GATGTAGCTTTACTATTCCTTGTACTC 57.534 37.037 0.00 0.00 32.15 2.59
173 174 7.478322 TGTAGCTTTACTATTCCTTGTACTCG 58.522 38.462 0.00 0.00 32.15 4.18
174 175 5.349809 AGCTTTACTATTCCTTGTACTCGC 58.650 41.667 0.00 0.00 0.00 5.03
175 176 5.105473 AGCTTTACTATTCCTTGTACTCGCA 60.105 40.000 0.00 0.00 0.00 5.10
176 177 5.753921 GCTTTACTATTCCTTGTACTCGCAT 59.246 40.000 0.00 0.00 0.00 4.73
198 199 7.041167 CGCATGATGAATAGATTGGAAGGTTTA 60.041 37.037 0.00 0.00 0.00 2.01
294 295 2.041265 TGCCTTCCTCCTCCTCCC 59.959 66.667 0.00 0.00 0.00 4.30
295 296 3.157949 GCCTTCCTCCTCCTCCCG 61.158 72.222 0.00 0.00 0.00 5.14
296 297 2.364961 CCTTCCTCCTCCTCCCGT 59.635 66.667 0.00 0.00 0.00 5.28
297 298 1.758906 CCTTCCTCCTCCTCCCGTC 60.759 68.421 0.00 0.00 0.00 4.79
298 299 1.308326 CTTCCTCCTCCTCCCGTCT 59.692 63.158 0.00 0.00 0.00 4.18
349 355 1.228245 GAAGCTGTGAAGCCCACCA 60.228 57.895 4.63 0.00 45.09 4.17
418 433 0.121197 TCTTGGATCCCCTTCCCTGT 59.879 55.000 9.90 0.00 34.67 4.00
448 463 0.029989 ATTCCTACTCCCCCACCCTC 60.030 60.000 0.00 0.00 0.00 4.30
449 464 2.040779 CCTACTCCCCCACCCTCC 60.041 72.222 0.00 0.00 0.00 4.30
450 465 2.647949 CCTACTCCCCCACCCTCCT 61.648 68.421 0.00 0.00 0.00 3.69
459 474 1.229658 CCACCCTCCTTCCAGTCCT 60.230 63.158 0.00 0.00 0.00 3.85
495 510 2.553247 CCAACAAACCTTCCTCCTCCTC 60.553 54.545 0.00 0.00 0.00 3.71
497 512 1.132365 ACAAACCTTCCTCCTCCTCCT 60.132 52.381 0.00 0.00 0.00 3.69
498 513 1.557371 CAAACCTTCCTCCTCCTCCTC 59.443 57.143 0.00 0.00 0.00 3.71
499 514 1.097722 AACCTTCCTCCTCCTCCTCT 58.902 55.000 0.00 0.00 0.00 3.69
500 515 1.097722 ACCTTCCTCCTCCTCCTCTT 58.902 55.000 0.00 0.00 0.00 2.85
598 619 4.547367 GTCGGGATCTTGGGCGGG 62.547 72.222 0.00 0.00 0.00 6.13
644 665 4.318332 GTGGGTTTAGTTAGGTACCACAC 58.682 47.826 15.94 10.04 44.63 3.82
646 667 5.245977 GTGGGTTTAGTTAGGTACCACACTA 59.754 44.000 15.94 15.89 44.63 2.74
656 677 3.014623 GGTACCACACTAATCCAAAGGC 58.985 50.000 7.15 0.00 0.00 4.35
795 816 3.181967 ATCGCAGCAACGTCTCGC 61.182 61.111 0.00 0.00 0.00 5.03
867 889 6.782082 AAAGTGCTTTCCTTTTCTCTCTTT 57.218 33.333 0.00 0.00 0.00 2.52
974 996 0.735978 CTCGTTCATGTAGTGCGGCA 60.736 55.000 0.00 0.00 0.00 5.69
979 1001 0.469494 TCATGTAGTGCGGCATCCAT 59.531 50.000 5.72 6.07 0.00 3.41
1050 1072 0.610232 ATGTGTTCAGGAAGCAGGGC 60.610 55.000 0.00 0.00 0.00 5.19
1077 1099 3.196685 ACTGGTATGAACAGCTTCTCTCC 59.803 47.826 0.00 0.00 39.55 3.71
1118 1140 3.713248 ACATGATCCTCTGCCATGTCTAA 59.287 43.478 0.00 0.00 45.25 2.10
1146 1168 4.628333 CACATTTCCTCATGGTTGCAAATC 59.372 41.667 0.00 0.00 34.23 2.17
1243 1267 3.805971 GCCATAATTACCACCGTAGACAC 59.194 47.826 0.00 0.00 0.00 3.67
1264 1288 3.118261 ACTGGAGTGTTTGTCTGTGTGAT 60.118 43.478 0.00 0.00 0.00 3.06
1313 1337 5.105063 GCCATTACTTCTTTCAGGAATTGC 58.895 41.667 0.00 0.00 30.69 3.56
1393 1417 3.733709 CAACCTCTTCCTGTTGGCT 57.266 52.632 0.00 0.00 38.50 4.75
1490 1514 3.267031 AGGCCAGCTAGGAAAACTACAAT 59.733 43.478 5.01 0.00 41.22 2.71
1493 1517 4.504858 CCAGCTAGGAAAACTACAATCGT 58.495 43.478 0.00 0.00 41.22 3.73
1545 1569 3.232662 GGAGGACTCCCTACCAGTTATC 58.767 54.545 7.13 0.00 44.53 1.75
1546 1570 3.232662 GAGGACTCCCTACCAGTTATCC 58.767 54.545 0.00 0.00 44.53 2.59
1547 1571 2.090663 AGGACTCCCTACCAGTTATCCC 60.091 54.545 0.00 0.00 42.15 3.85
1639 1667 2.093235 GGAGGACTTCATCTGTTCCTGG 60.093 54.545 0.00 0.00 0.00 4.45
1640 1668 2.834549 GAGGACTTCATCTGTTCCTGGA 59.165 50.000 0.00 0.00 0.00 3.86
1641 1669 3.251484 AGGACTTCATCTGTTCCTGGAA 58.749 45.455 4.68 4.68 0.00 3.53
1642 1670 3.652869 AGGACTTCATCTGTTCCTGGAAA 59.347 43.478 11.40 0.00 0.00 3.13
1643 1671 4.104738 AGGACTTCATCTGTTCCTGGAAAA 59.895 41.667 11.40 4.67 0.00 2.29
1644 1672 5.012893 GGACTTCATCTGTTCCTGGAAAAT 58.987 41.667 11.40 2.68 0.00 1.82
1645 1673 5.105997 GGACTTCATCTGTTCCTGGAAAATG 60.106 44.000 11.40 14.41 0.00 2.32
1646 1674 4.768968 ACTTCATCTGTTCCTGGAAAATGG 59.231 41.667 11.40 6.57 0.00 3.16
1647 1675 3.091545 TCATCTGTTCCTGGAAAATGGC 58.908 45.455 11.40 0.00 0.00 4.40
1648 1676 2.673775 TCTGTTCCTGGAAAATGGCA 57.326 45.000 11.40 3.63 0.00 4.92
1649 1677 2.238521 TCTGTTCCTGGAAAATGGCAC 58.761 47.619 11.40 0.00 0.00 5.01
1650 1678 1.273327 CTGTTCCTGGAAAATGGCACC 59.727 52.381 11.40 0.00 0.00 5.01
1651 1679 1.133199 TGTTCCTGGAAAATGGCACCT 60.133 47.619 11.40 0.00 0.00 4.00
1652 1680 2.109128 TGTTCCTGGAAAATGGCACCTA 59.891 45.455 11.40 0.00 0.00 3.08
1653 1681 2.492088 GTTCCTGGAAAATGGCACCTAC 59.508 50.000 11.40 0.00 0.00 3.18
1654 1682 1.005450 TCCTGGAAAATGGCACCTACC 59.995 52.381 0.00 0.00 0.00 3.18
1655 1683 1.005924 CCTGGAAAATGGCACCTACCT 59.994 52.381 0.00 0.00 0.00 3.08
1656 1684 2.557452 CCTGGAAAATGGCACCTACCTT 60.557 50.000 0.00 0.00 0.00 3.50
1657 1685 3.165071 CTGGAAAATGGCACCTACCTTT 58.835 45.455 0.00 0.00 0.00 3.11
1658 1686 3.578282 CTGGAAAATGGCACCTACCTTTT 59.422 43.478 0.00 0.00 38.36 2.27
1659 1687 4.742012 TGGAAAATGGCACCTACCTTTTA 58.258 39.130 0.00 0.00 36.38 1.52
1660 1688 5.337788 TGGAAAATGGCACCTACCTTTTAT 58.662 37.500 0.00 0.00 36.38 1.40
1661 1689 6.494952 TGGAAAATGGCACCTACCTTTTATA 58.505 36.000 0.00 0.00 36.38 0.98
1662 1690 6.605594 TGGAAAATGGCACCTACCTTTTATAG 59.394 38.462 0.00 0.00 36.38 1.31
1663 1691 6.605995 GGAAAATGGCACCTACCTTTTATAGT 59.394 38.462 0.00 0.00 36.38 2.12
1664 1692 7.776500 GGAAAATGGCACCTACCTTTTATAGTA 59.224 37.037 0.00 0.00 36.38 1.82
1665 1693 8.515695 AAAATGGCACCTACCTTTTATAGTAC 57.484 34.615 0.00 0.00 36.38 2.73
1666 1694 5.619132 TGGCACCTACCTTTTATAGTACC 57.381 43.478 0.00 0.00 0.00 3.34
1667 1695 5.031495 TGGCACCTACCTTTTATAGTACCA 58.969 41.667 0.00 0.00 0.00 3.25
1668 1696 5.668535 TGGCACCTACCTTTTATAGTACCAT 59.331 40.000 0.00 0.00 0.00 3.55
1669 1697 6.159046 TGGCACCTACCTTTTATAGTACCATT 59.841 38.462 0.00 0.00 0.00 3.16
1670 1698 7.058525 GGCACCTACCTTTTATAGTACCATTT 58.941 38.462 0.00 0.00 0.00 2.32
1671 1699 7.558807 GGCACCTACCTTTTATAGTACCATTTT 59.441 37.037 0.00 0.00 0.00 1.82
1672 1700 8.963725 GCACCTACCTTTTATAGTACCATTTTT 58.036 33.333 0.00 0.00 0.00 1.94
1674 1702 9.470399 ACCTACCTTTTATAGTACCATTTTTGG 57.530 33.333 0.00 0.00 0.00 3.28
1675 1703 8.909923 CCTACCTTTTATAGTACCATTTTTGGG 58.090 37.037 0.00 0.00 0.00 4.12
1676 1704 9.689501 CTACCTTTTATAGTACCATTTTTGGGA 57.310 33.333 0.00 0.00 0.00 4.37
1677 1705 8.589701 ACCTTTTATAGTACCATTTTTGGGAG 57.410 34.615 0.00 0.00 0.00 4.30
1678 1706 8.174757 ACCTTTTATAGTACCATTTTTGGGAGT 58.825 33.333 0.00 0.00 0.00 3.85
1679 1707 9.031537 CCTTTTATAGTACCATTTTTGGGAGTT 57.968 33.333 0.00 0.00 0.00 3.01
1755 1783 1.271926 GCAGTGGTGGGTAAATGGAGT 60.272 52.381 0.00 0.00 0.00 3.85
1756 1784 2.436417 CAGTGGTGGGTAAATGGAGTG 58.564 52.381 0.00 0.00 0.00 3.51
1758 1786 1.074889 GTGGTGGGTAAATGGAGTGGT 59.925 52.381 0.00 0.00 0.00 4.16
1759 1787 1.353022 TGGTGGGTAAATGGAGTGGTC 59.647 52.381 0.00 0.00 0.00 4.02
1760 1788 1.353022 GGTGGGTAAATGGAGTGGTCA 59.647 52.381 0.00 0.00 0.00 4.02
1761 1789 2.433436 GTGGGTAAATGGAGTGGTCAC 58.567 52.381 0.00 0.00 0.00 3.67
1762 1790 2.058705 TGGGTAAATGGAGTGGTCACA 58.941 47.619 3.82 0.00 0.00 3.58
1763 1791 2.039746 TGGGTAAATGGAGTGGTCACAG 59.960 50.000 3.82 0.00 0.00 3.66
1764 1792 2.039879 GGGTAAATGGAGTGGTCACAGT 59.960 50.000 3.82 0.00 0.00 3.55
1765 1793 3.074412 GGTAAATGGAGTGGTCACAGTG 58.926 50.000 3.82 0.00 0.00 3.66
1766 1794 1.609208 AAATGGAGTGGTCACAGTGC 58.391 50.000 3.82 0.00 38.70 4.40
1767 1795 3.640761 TGGAGTGGTCACAGTGCA 58.359 55.556 3.82 0.00 44.72 4.57
1768 1796 1.911471 TGGAGTGGTCACAGTGCAA 59.089 52.632 3.82 0.00 44.09 4.08
1826 1855 6.405278 TCCATGAGAAATATTGTCTCGCTA 57.595 37.500 16.22 6.17 43.80 4.26
1960 1989 1.518572 CGCCGAGCATTACTCCGTT 60.519 57.895 0.00 0.00 43.01 4.44
1980 2009 4.320788 CGTTAGATACCGGTCCTGGAATAC 60.321 50.000 12.40 0.00 0.00 1.89
1984 2013 1.396653 ACCGGTCCTGGAATACGTAG 58.603 55.000 0.00 0.00 0.00 3.51
2232 2274 7.777440 TGACCATGGATATTTAAGTGCATGTTA 59.223 33.333 21.47 0.00 41.02 2.41
2592 2638 8.148351 TGTAGTGCATTAAGTTTAGTTCACTCT 58.852 33.333 3.73 0.00 35.48 3.24
2718 2764 3.210074 AGGGATAGACATGGAGGGTAGTT 59.790 47.826 0.00 0.00 0.00 2.24
2756 2802 0.107703 CACCCAAGCGAGGCTCAATA 60.108 55.000 15.95 0.00 38.25 1.90
2783 2829 6.882610 ACATTGAGCTCATGTTCACTTTAA 57.117 33.333 19.04 0.00 33.21 1.52
2917 2963 6.481976 CCACTTATATTCATGTACTTCCGCAA 59.518 38.462 0.00 0.00 0.00 4.85
3224 3278 3.377172 CGTCCATCCCAAAATAAGTGTCC 59.623 47.826 0.00 0.00 0.00 4.02
3228 3282 4.381932 CCATCCCAAAATAAGTGTCCTTGC 60.382 45.833 0.00 0.00 31.89 4.01
3643 3697 2.874701 GGCACTTCATACTTGCGATGAT 59.125 45.455 0.00 0.00 37.11 2.45
4591 4646 2.816087 CTCCCTGTTTCCAATGACACAG 59.184 50.000 2.63 2.63 45.03 3.66
4601 4656 3.118223 TCCAATGACACAGTAACACACCA 60.118 43.478 0.00 0.00 0.00 4.17
4639 4694 4.854173 TGCATATCCTCAGTAAGGCAAAA 58.146 39.130 0.00 0.00 45.78 2.44
4652 4707 8.748412 TCAGTAAGGCAAAACATTATTAGCATT 58.252 29.630 0.00 0.00 0.00 3.56
4752 4807 4.893424 TCAGTTCCAAAACCTTTTCTCG 57.107 40.909 0.00 0.00 35.92 4.04
4873 4928 3.965379 TTAGGTTGCACGAAGATGGTA 57.035 42.857 0.00 0.00 0.00 3.25
4880 4935 5.404946 GTTGCACGAAGATGGTACTTACTA 58.595 41.667 0.00 0.00 0.00 1.82
4957 5314 1.160137 AAGTTCGCCTTGCTGATGTC 58.840 50.000 0.00 0.00 30.18 3.06
4984 5342 3.781079 TGTTTTGTTTCTGCTCCTGTG 57.219 42.857 0.00 0.00 0.00 3.66
5127 5485 0.976641 TCATCGTGCAGGTCCTCTTT 59.023 50.000 6.26 0.00 0.00 2.52
5139 5497 1.729517 GTCCTCTTTTTCGAGCAGCTC 59.270 52.381 12.94 12.94 0.00 4.09
5187 5545 2.697751 CCTGATGATCTCCGAGAACCTT 59.302 50.000 1.27 0.00 0.00 3.50
5196 5554 2.436824 GAGAACCTTGAGGGCGGC 60.437 66.667 0.00 0.00 40.27 6.53
5409 5767 1.220477 GAGCAGGCTGTTCTCCCTC 59.780 63.158 22.25 12.14 0.00 4.30
5457 5815 2.690881 AAGGATGCTACCCCCGCA 60.691 61.111 0.00 0.00 42.25 5.69
5472 5830 2.650196 GCAAAGGCGACAATGGCA 59.350 55.556 0.00 0.00 36.77 4.92
5514 5872 1.236616 TGGTGAAAGCTGATGCCACG 61.237 55.000 0.00 0.00 40.80 4.94
5567 5925 0.600557 CTGTCCATAGAGGCCTAGCG 59.399 60.000 4.42 0.00 37.29 4.26
5568 5926 0.827925 TGTCCATAGAGGCCTAGCGG 60.828 60.000 4.42 4.15 37.29 5.52
5596 5954 5.762825 TCGTTTGTGTTACTCTGTACTCT 57.237 39.130 0.00 0.00 0.00 3.24
5613 5972 3.019564 ACTCTTGAGTTGCTGTTTTGCT 58.980 40.909 0.00 0.00 0.00 3.91
5667 6026 1.226746 CCACCTGTGAACGAAGAACC 58.773 55.000 0.00 0.00 0.00 3.62
5715 6074 7.509546 AGACCTCATTCTAAGTTTTTGACAGA 58.490 34.615 0.00 0.00 0.00 3.41
5769 6128 3.451540 TGGCACCGGTAACATCTTGTATA 59.548 43.478 6.87 0.00 0.00 1.47
5793 6157 4.600062 TGTGTCTCTAGGATTGCTAGTCA 58.400 43.478 11.44 7.46 0.00 3.41
5811 6175 8.478066 TGCTAGTCAATCTTGTATAATGTGTCT 58.522 33.333 0.00 0.00 0.00 3.41
5817 6181 9.421399 TCAATCTTGTATAATGTGTCTCTAGGA 57.579 33.333 0.00 0.00 0.00 2.94
5876 6240 2.427245 CCCAGGTAGGCAGTCCTCG 61.427 68.421 0.00 0.00 43.06 4.63
5925 6300 5.918011 CACTTTTATTTTACGAGCAAGGCAA 59.082 36.000 0.00 0.00 0.00 4.52
5951 6326 6.347696 AGCTCTGTGGATTTCATTAAGAGAG 58.652 40.000 0.00 0.00 34.74 3.20
5955 6330 8.553459 TCTGTGGATTTCATTAAGAGAGAAAC 57.447 34.615 0.00 0.00 34.47 2.78
5988 6363 7.333672 ACAGAGCTACCGGTTTATAAGAAAAAG 59.666 37.037 15.04 0.00 0.00 2.27
6008 6383 3.088532 AGCAAGGCCGAAAATCAACATA 58.911 40.909 0.00 0.00 0.00 2.29
6026 6418 0.463295 TAAACCAACACCGACGCCAA 60.463 50.000 0.00 0.00 0.00 4.52
6029 6421 2.326550 CAACACCGACGCCAACAC 59.673 61.111 0.00 0.00 0.00 3.32
6031 6423 3.683966 AACACCGACGCCAACACCA 62.684 57.895 0.00 0.00 0.00 4.17
6049 6449 3.323403 CACCAAAGGGCATTTCTAACCAA 59.677 43.478 0.00 0.00 37.90 3.67
6050 6450 4.020307 CACCAAAGGGCATTTCTAACCAAT 60.020 41.667 0.00 0.00 37.90 3.16
6054 6454 1.681264 GGGCATTTCTAACCAATCCCG 59.319 52.381 0.00 0.00 0.00 5.14
6058 6458 4.455877 GGCATTTCTAACCAATCCCGATAG 59.544 45.833 0.00 0.00 0.00 2.08
6080 6480 5.557866 AGCCGGTTAAAGAAGTACAAATCT 58.442 37.500 1.90 0.00 0.00 2.40
6082 6482 5.410439 GCCGGTTAAAGAAGTACAAATCTGA 59.590 40.000 1.90 0.00 0.00 3.27
6126 6527 2.202932 CGGTCCTCATCGGCCTTG 60.203 66.667 0.00 0.00 0.00 3.61
6137 6538 0.470080 TCGGCCTTGGAGGAGGATAG 60.470 60.000 0.00 0.00 37.67 2.08
6154 6555 2.281539 TAGATTATCCTCGGTCGCCA 57.718 50.000 0.00 0.00 0.00 5.69
6157 6558 1.105167 ATTATCCTCGGTCGCCACGA 61.105 55.000 0.00 0.00 38.79 4.35
6170 6571 1.603172 CGCCACGATTCTCCCTGTATC 60.603 57.143 0.00 0.00 0.00 2.24
6177 6578 3.437395 CGATTCTCCCTGTATCTACTCCG 59.563 52.174 0.00 0.00 0.00 4.63
6179 6580 1.202903 TCTCCCTGTATCTACTCCGCC 60.203 57.143 0.00 0.00 0.00 6.13
6182 6583 1.173444 CCTGTATCTACTCCGCCGCT 61.173 60.000 0.00 0.00 0.00 5.52
6183 6584 0.238817 CTGTATCTACTCCGCCGCTC 59.761 60.000 0.00 0.00 0.00 5.03
6184 6585 0.179026 TGTATCTACTCCGCCGCTCT 60.179 55.000 0.00 0.00 0.00 4.09
6185 6586 0.238817 GTATCTACTCCGCCGCTCTG 59.761 60.000 0.00 0.00 0.00 3.35
6186 6587 1.516365 TATCTACTCCGCCGCTCTGC 61.516 60.000 0.00 0.00 0.00 4.26
6187 6588 4.577246 CTACTCCGCCGCTCTGCC 62.577 72.222 0.00 0.00 0.00 4.85
6241 6642 3.637273 GCCCCCGTCTGGTTCACT 61.637 66.667 0.00 0.00 0.00 3.41
6249 6650 1.605712 CGTCTGGTTCACTGACTTCCC 60.606 57.143 0.00 0.00 43.53 3.97
6258 6659 1.305381 CTGACTTCCCGGACCTCCT 60.305 63.158 0.73 0.00 0.00 3.69
6320 6721 4.028490 GCGTGTGGGGGACATGGA 62.028 66.667 0.00 0.00 41.35 3.41
6340 6741 2.415608 GGCGGAGATCACTGACCGA 61.416 63.158 10.05 0.00 46.94 4.69
6417 6818 0.663153 GAATATGACCGGTGGCAAGC 59.337 55.000 14.63 0.00 0.00 4.01
6430 6831 2.035626 CAAGCCCGGTTCCATGGT 59.964 61.111 12.58 0.00 0.00 3.55
6454 6855 1.371183 CACGAGGCTCAACTTCCCA 59.629 57.895 15.95 0.00 0.00 4.37
6537 6939 1.682684 GGAGGACCAAGAGGCGAGA 60.683 63.158 0.00 0.00 39.06 4.04
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.881973 CACCACCAACTGAATCCTGTG 59.118 52.381 0.00 0.00 0.00 3.66
1 2 1.774254 TCACCACCAACTGAATCCTGT 59.226 47.619 0.00 0.00 0.00 4.00
2 3 2.566833 TCACCACCAACTGAATCCTG 57.433 50.000 0.00 0.00 0.00 3.86
3 4 2.915604 AGATCACCACCAACTGAATCCT 59.084 45.455 0.00 0.00 0.00 3.24
4 5 3.356529 AGATCACCACCAACTGAATCC 57.643 47.619 0.00 0.00 0.00 3.01
5 6 4.082571 CCAAAGATCACCACCAACTGAATC 60.083 45.833 0.00 0.00 0.00 2.52
6 7 3.828451 CCAAAGATCACCACCAACTGAAT 59.172 43.478 0.00 0.00 0.00 2.57
7 8 3.221771 CCAAAGATCACCACCAACTGAA 58.778 45.455 0.00 0.00 0.00 3.02
8 9 2.174639 ACCAAAGATCACCACCAACTGA 59.825 45.455 0.00 0.00 0.00 3.41
9 10 2.294233 CACCAAAGATCACCACCAACTG 59.706 50.000 0.00 0.00 0.00 3.16
10 11 2.586425 CACCAAAGATCACCACCAACT 58.414 47.619 0.00 0.00 0.00 3.16
11 12 1.613437 CCACCAAAGATCACCACCAAC 59.387 52.381 0.00 0.00 0.00 3.77
12 13 1.496857 TCCACCAAAGATCACCACCAA 59.503 47.619 0.00 0.00 0.00 3.67
13 14 1.144691 TCCACCAAAGATCACCACCA 58.855 50.000 0.00 0.00 0.00 4.17
14 15 2.369394 GATCCACCAAAGATCACCACC 58.631 52.381 0.00 0.00 39.97 4.61
15 16 2.369394 GGATCCACCAAAGATCACCAC 58.631 52.381 6.95 0.00 41.64 4.16
16 17 1.065491 CGGATCCACCAAAGATCACCA 60.065 52.381 13.41 0.00 41.64 4.17
17 18 1.668419 CGGATCCACCAAAGATCACC 58.332 55.000 13.41 0.00 41.64 4.02
18 19 1.017387 GCGGATCCACCAAAGATCAC 58.983 55.000 13.41 0.00 41.64 3.06
19 20 0.911769 AGCGGATCCACCAAAGATCA 59.088 50.000 13.41 0.00 41.64 2.92
20 21 1.587547 GAGCGGATCCACCAAAGATC 58.412 55.000 13.41 0.00 39.57 2.75
21 22 0.179073 CGAGCGGATCCACCAAAGAT 60.179 55.000 13.41 0.00 38.90 2.40
22 23 1.218047 CGAGCGGATCCACCAAAGA 59.782 57.895 13.41 0.00 38.90 2.52
23 24 0.174845 TACGAGCGGATCCACCAAAG 59.825 55.000 13.41 0.00 38.90 2.77
24 25 0.609151 TTACGAGCGGATCCACCAAA 59.391 50.000 13.41 0.00 38.90 3.28
25 26 0.108520 GTTACGAGCGGATCCACCAA 60.109 55.000 13.41 0.00 38.90 3.67
26 27 1.252215 TGTTACGAGCGGATCCACCA 61.252 55.000 13.41 0.00 38.90 4.17
27 28 0.108520 TTGTTACGAGCGGATCCACC 60.109 55.000 13.41 1.51 0.00 4.61
28 29 1.935933 ATTGTTACGAGCGGATCCAC 58.064 50.000 13.41 0.99 0.00 4.02
29 30 3.131577 ACTTATTGTTACGAGCGGATCCA 59.868 43.478 13.41 0.00 0.00 3.41
30 31 3.714391 ACTTATTGTTACGAGCGGATCC 58.286 45.455 0.00 0.00 0.00 3.36
31 32 5.713822 AAACTTATTGTTACGAGCGGATC 57.286 39.130 0.00 0.00 38.03 3.36
32 33 5.672819 GCAAAACTTATTGTTACGAGCGGAT 60.673 40.000 0.00 0.00 38.03 4.18
33 34 4.377635 GCAAAACTTATTGTTACGAGCGGA 60.378 41.667 0.00 0.00 38.03 5.54
34 35 3.844099 GCAAAACTTATTGTTACGAGCGG 59.156 43.478 0.00 0.00 38.03 5.52
35 36 4.708601 AGCAAAACTTATTGTTACGAGCG 58.291 39.130 0.00 0.00 38.03 5.03
36 37 4.781528 CGAGCAAAACTTATTGTTACGAGC 59.218 41.667 0.00 0.00 38.03 5.03
37 38 5.313623 CCGAGCAAAACTTATTGTTACGAG 58.686 41.667 0.00 0.00 38.03 4.18
38 39 4.377635 GCCGAGCAAAACTTATTGTTACGA 60.378 41.667 0.00 0.00 38.03 3.43
39 40 3.844099 GCCGAGCAAAACTTATTGTTACG 59.156 43.478 0.00 0.00 38.03 3.18
40 41 5.043189 AGCCGAGCAAAACTTATTGTTAC 57.957 39.130 0.00 0.00 38.03 2.50
41 42 5.615984 CGAAGCCGAGCAAAACTTATTGTTA 60.616 40.000 0.00 0.00 36.42 2.41
42 43 4.546570 GAAGCCGAGCAAAACTTATTGTT 58.453 39.130 0.00 0.00 41.29 2.83
47 48 1.796459 GTCGAAGCCGAGCAAAACTTA 59.204 47.619 0.00 0.00 46.52 2.24
58 59 2.202623 CCTTCCTCGTCGAAGCCG 60.203 66.667 0.00 0.00 38.35 5.52
63 64 1.000019 ATCACCCCTTCCTCGTCGA 60.000 57.895 0.00 0.00 0.00 4.20
70 71 0.179045 CCATCGTCATCACCCCTTCC 60.179 60.000 0.00 0.00 0.00 3.46
71 72 0.815615 GCCATCGTCATCACCCCTTC 60.816 60.000 0.00 0.00 0.00 3.46
72 73 1.224592 GCCATCGTCATCACCCCTT 59.775 57.895 0.00 0.00 0.00 3.95
76 77 2.813179 GCGTGCCATCGTCATCACC 61.813 63.158 0.00 0.00 0.00 4.02
78 79 2.511373 GGCGTGCCATCGTCATCA 60.511 61.111 5.89 0.00 35.41 3.07
79 80 3.272334 GGGCGTGCCATCGTCATC 61.272 66.667 13.76 0.00 37.15 2.92
80 81 3.740128 GAGGGCGTGCCATCGTCAT 62.740 63.158 13.76 0.00 37.15 3.06
81 82 4.451150 GAGGGCGTGCCATCGTCA 62.451 66.667 13.76 0.00 37.15 4.35
85 86 4.778143 AACCGAGGGCGTGCCATC 62.778 66.667 15.20 15.20 42.83 3.51
86 87 4.344865 AAACCGAGGGCGTGCCAT 62.345 61.111 13.76 5.22 37.98 4.40
90 91 2.966309 GAAGCAAACCGAGGGCGTG 61.966 63.158 0.00 0.00 35.23 5.34
91 92 2.668550 GAAGCAAACCGAGGGCGT 60.669 61.111 0.00 0.00 35.23 5.68
92 93 2.668212 TGAAGCAAACCGAGGGCG 60.668 61.111 0.00 0.00 37.24 6.13
93 94 1.600916 ACTGAAGCAAACCGAGGGC 60.601 57.895 0.00 0.00 0.00 5.19
96 97 0.947244 AAGCACTGAAGCAAACCGAG 59.053 50.000 0.00 0.00 36.85 4.63
101 102 2.543848 CGACTACAAGCACTGAAGCAAA 59.456 45.455 0.00 0.00 36.85 3.68
119 120 1.063764 CTTAGACCACCTAGCGACGAC 59.936 57.143 0.00 0.00 0.00 4.34
123 124 4.135306 CAGATACTTAGACCACCTAGCGA 58.865 47.826 0.00 0.00 0.00 4.93
131 132 5.706447 AGCTACATCCAGATACTTAGACCA 58.294 41.667 0.00 0.00 0.00 4.02
132 133 6.658188 AAGCTACATCCAGATACTTAGACC 57.342 41.667 0.00 0.00 0.00 3.85
138 139 8.808092 GGAATAGTAAAGCTACATCCAGATACT 58.192 37.037 0.00 0.00 38.20 2.12
140 141 8.958060 AGGAATAGTAAAGCTACATCCAGATA 57.042 34.615 0.00 0.00 39.59 1.98
152 153 5.107133 TGCGAGTACAAGGAATAGTAAAGC 58.893 41.667 0.00 0.00 0.00 3.51
153 154 6.978659 TCATGCGAGTACAAGGAATAGTAAAG 59.021 38.462 0.00 0.00 0.00 1.85
160 161 4.406648 TCATCATGCGAGTACAAGGAAT 57.593 40.909 0.00 0.00 0.00 3.01
170 171 5.121925 CCTTCCAATCTATTCATCATGCGAG 59.878 44.000 0.00 0.00 0.00 5.03
171 172 4.999311 CCTTCCAATCTATTCATCATGCGA 59.001 41.667 0.00 0.00 0.00 5.10
172 173 4.758674 ACCTTCCAATCTATTCATCATGCG 59.241 41.667 0.00 0.00 0.00 4.73
173 174 6.645790 AACCTTCCAATCTATTCATCATGC 57.354 37.500 0.00 0.00 0.00 4.06
174 175 9.347240 ACTAAACCTTCCAATCTATTCATCATG 57.653 33.333 0.00 0.00 0.00 3.07
207 208 9.899661 GGCCCCTTTGTTTATTATTATTTTCTT 57.100 29.630 0.00 0.00 0.00 2.52
209 210 9.674068 TTGGCCCCTTTGTTTATTATTATTTTC 57.326 29.630 0.00 0.00 0.00 2.29
212 213 8.831738 ACTTTGGCCCCTTTGTTTATTATTATT 58.168 29.630 0.00 0.00 0.00 1.40
214 215 7.310734 CCACTTTGGCCCCTTTGTTTATTATTA 60.311 37.037 0.00 0.00 0.00 0.98
216 217 5.045942 CCACTTTGGCCCCTTTGTTTATTAT 60.046 40.000 0.00 0.00 0.00 1.28
217 218 4.284746 CCACTTTGGCCCCTTTGTTTATTA 59.715 41.667 0.00 0.00 0.00 0.98
218 219 3.072330 CCACTTTGGCCCCTTTGTTTATT 59.928 43.478 0.00 0.00 0.00 1.40
219 220 2.637382 CCACTTTGGCCCCTTTGTTTAT 59.363 45.455 0.00 0.00 0.00 1.40
220 221 2.043227 CCACTTTGGCCCCTTTGTTTA 58.957 47.619 0.00 0.00 0.00 2.01
221 222 0.836606 CCACTTTGGCCCCTTTGTTT 59.163 50.000 0.00 0.00 0.00 2.83
224 225 1.276138 GAATCCACTTTGGCCCCTTTG 59.724 52.381 0.00 0.00 37.47 2.77
225 226 1.149923 AGAATCCACTTTGGCCCCTTT 59.850 47.619 0.00 0.00 37.47 3.11
226 227 0.786435 AGAATCCACTTTGGCCCCTT 59.214 50.000 0.00 0.00 37.47 3.95
228 229 0.972471 CCAGAATCCACTTTGGCCCC 60.972 60.000 0.00 0.00 37.47 5.80
229 230 0.972471 CCCAGAATCCACTTTGGCCC 60.972 60.000 0.00 0.00 37.47 5.80
230 231 1.607801 GCCCAGAATCCACTTTGGCC 61.608 60.000 0.00 0.00 37.47 5.36
294 295 0.953960 CCAAACGGAAAGGGGAGACG 60.954 60.000 0.00 0.00 0.00 4.18
295 296 0.109913 ACCAAACGGAAAGGGGAGAC 59.890 55.000 0.00 0.00 0.00 3.36
296 297 0.109723 CACCAAACGGAAAGGGGAGA 59.890 55.000 0.00 0.00 0.00 3.71
297 298 0.179001 ACACCAAACGGAAAGGGGAG 60.179 55.000 0.00 0.00 0.00 4.30
298 299 0.179012 GACACCAAACGGAAAGGGGA 60.179 55.000 0.00 0.00 0.00 4.81
349 355 2.071778 ACTGCTGTGGTGTGGATTTT 57.928 45.000 0.00 0.00 0.00 1.82
418 433 2.027192 GGAGTAGGAATGTTGTGGCAGA 60.027 50.000 0.00 0.00 0.00 4.26
448 463 5.070001 TGTTTGTTTATGAGGACTGGAAGG 58.930 41.667 0.00 0.00 39.30 3.46
449 464 6.633500 TTGTTTGTTTATGAGGACTGGAAG 57.367 37.500 0.00 0.00 42.29 3.46
450 465 6.183360 GGTTTGTTTGTTTATGAGGACTGGAA 60.183 38.462 0.00 0.00 0.00 3.53
459 474 7.162082 AGGTTTGTTGGTTTGTTTGTTTATGA 58.838 30.769 0.00 0.00 0.00 2.15
495 510 4.268720 CGGAGGAGGAGGAAGAGG 57.731 66.667 0.00 0.00 0.00 3.69
598 619 3.394719 GGCGAATTACTCCTGGATTCTC 58.605 50.000 0.00 0.00 0.00 2.87
618 639 0.986527 ACCTAACTAAACCCACCCGG 59.013 55.000 0.00 0.00 37.81 5.73
644 665 2.186826 CGGCGGGCCTTTGGATTAG 61.187 63.158 0.84 0.00 0.00 1.73
795 816 2.880890 CTCAATCTAGCCCAAAATCCCG 59.119 50.000 0.00 0.00 0.00 5.14
867 889 1.899534 CGCGGAACCAAGGGGAAAA 60.900 57.895 0.00 0.00 38.05 2.29
871 893 4.778143 CCTCGCGGAACCAAGGGG 62.778 72.222 6.13 0.00 41.29 4.79
881 903 1.369091 CCAGAACCAAATCCTCGCGG 61.369 60.000 6.13 0.00 0.00 6.46
883 905 0.804989 CACCAGAACCAAATCCTCGC 59.195 55.000 0.00 0.00 0.00 5.03
974 996 1.566231 GAGTCCCAGGTTCCAATGGAT 59.434 52.381 1.39 0.00 39.02 3.41
979 1001 1.982958 GTTAGGAGTCCCAGGTTCCAA 59.017 52.381 5.25 3.41 33.32 3.53
1050 1072 3.686726 GAAGCTGTTCATACCAGTCTTGG 59.313 47.826 0.00 0.00 40.34 3.61
1077 1099 3.238597 TGTTGGGGGAAATGAAGAAAGG 58.761 45.455 0.00 0.00 0.00 3.11
1118 1140 1.076024 ACCATGAGGAAATGTGCAGGT 59.924 47.619 0.00 0.00 38.69 4.00
1169 1191 4.618227 GCACGGATTAAAAGGTGAAGCAAT 60.618 41.667 7.17 0.00 32.23 3.56
1211 1233 5.278957 GGTGGTAATTATGGCAGCAAATAGG 60.279 44.000 0.00 0.00 0.00 2.57
1243 1267 2.905075 TCACACAGACAAACACTCCAG 58.095 47.619 0.00 0.00 0.00 3.86
1264 1288 2.290641 ACATTTCCTATCGTGCCCAACA 60.291 45.455 0.00 0.00 0.00 3.33
1545 1569 3.071874 TGATTAACAGGCTGTCTTGGG 57.928 47.619 22.31 0.00 0.00 4.12
1546 1570 6.543465 TGATATTGATTAACAGGCTGTCTTGG 59.457 38.462 22.31 0.00 0.00 3.61
1547 1571 7.558161 TGATATTGATTAACAGGCTGTCTTG 57.442 36.000 22.31 0.00 0.00 3.02
1639 1667 7.640597 ACTATAAAAGGTAGGTGCCATTTTC 57.359 36.000 0.00 0.00 32.54 2.29
1640 1668 7.558807 GGTACTATAAAAGGTAGGTGCCATTTT 59.441 37.037 0.00 0.00 32.54 1.82
1641 1669 7.058525 GGTACTATAAAAGGTAGGTGCCATTT 58.941 38.462 0.00 0.00 34.37 2.32
1642 1670 6.159046 TGGTACTATAAAAGGTAGGTGCCATT 59.841 38.462 0.00 0.00 0.00 3.16
1643 1671 5.668535 TGGTACTATAAAAGGTAGGTGCCAT 59.331 40.000 0.00 0.00 0.00 4.40
1644 1672 5.031495 TGGTACTATAAAAGGTAGGTGCCA 58.969 41.667 0.00 0.00 0.00 4.92
1645 1673 5.619132 TGGTACTATAAAAGGTAGGTGCC 57.381 43.478 0.00 0.00 0.00 5.01
1646 1674 8.515695 AAAATGGTACTATAAAAGGTAGGTGC 57.484 34.615 0.00 0.00 0.00 5.01
1648 1676 9.470399 CCAAAAATGGTACTATAAAAGGTAGGT 57.530 33.333 0.00 0.00 0.00 3.08
1649 1677 8.909923 CCCAAAAATGGTACTATAAAAGGTAGG 58.090 37.037 0.00 0.00 0.00 3.18
1650 1678 9.689501 TCCCAAAAATGGTACTATAAAAGGTAG 57.310 33.333 0.00 0.00 0.00 3.18
1651 1679 9.689501 CTCCCAAAAATGGTACTATAAAAGGTA 57.310 33.333 0.00 0.00 0.00 3.08
1652 1680 8.174757 ACTCCCAAAAATGGTACTATAAAAGGT 58.825 33.333 0.00 0.00 0.00 3.50
1653 1681 8.589701 ACTCCCAAAAATGGTACTATAAAAGG 57.410 34.615 0.00 0.00 0.00 3.11
1659 1687 9.816787 TTTTCTAACTCCCAAAAATGGTACTAT 57.183 29.630 0.00 0.00 0.00 2.12
1660 1688 9.643735 TTTTTCTAACTCCCAAAAATGGTACTA 57.356 29.630 0.00 0.00 0.00 1.82
1661 1689 8.541899 TTTTTCTAACTCCCAAAAATGGTACT 57.458 30.769 0.00 0.00 0.00 2.73
1662 1690 9.203421 CATTTTTCTAACTCCCAAAAATGGTAC 57.797 33.333 16.22 0.00 45.46 3.34
1667 1695 7.936847 GGTTCCATTTTTCTAACTCCCAAAAAT 59.063 33.333 0.00 0.00 39.29 1.82
1668 1696 7.126573 AGGTTCCATTTTTCTAACTCCCAAAAA 59.873 33.333 0.00 0.00 34.41 1.94
1669 1697 6.613679 AGGTTCCATTTTTCTAACTCCCAAAA 59.386 34.615 0.00 0.00 0.00 2.44
1670 1698 6.140377 AGGTTCCATTTTTCTAACTCCCAAA 58.860 36.000 0.00 0.00 0.00 3.28
1671 1699 5.711698 AGGTTCCATTTTTCTAACTCCCAA 58.288 37.500 0.00 0.00 0.00 4.12
1672 1700 5.333566 AGGTTCCATTTTTCTAACTCCCA 57.666 39.130 0.00 0.00 0.00 4.37
1673 1701 5.651139 GGTAGGTTCCATTTTTCTAACTCCC 59.349 44.000 0.00 0.00 0.00 4.30
1674 1702 6.482524 AGGTAGGTTCCATTTTTCTAACTCC 58.517 40.000 0.00 0.00 0.00 3.85
1675 1703 7.997773 AAGGTAGGTTCCATTTTTCTAACTC 57.002 36.000 0.00 0.00 28.87 3.01
1676 1704 8.777578 AAAAGGTAGGTTCCATTTTTCTAACT 57.222 30.769 0.00 0.00 30.14 2.24
1755 1783 3.963676 GCATTTTGCACTGTGACCA 57.036 47.368 12.86 0.00 44.26 4.02
1756 1784 4.167818 ACAGGCATTTTGCACTGTGACC 62.168 50.000 12.86 0.00 45.92 4.02
1758 1786 1.337703 GACAGGCATTTTGCACTGTGA 59.662 47.619 20.62 0.00 46.85 3.58
1759 1787 1.603678 GGACAGGCATTTTGCACTGTG 60.604 52.381 20.62 2.76 46.85 3.66
1765 1793 1.188863 ATCCAGGACAGGCATTTTGC 58.811 50.000 0.00 0.00 44.08 3.68
1766 1794 3.181483 GCTAATCCAGGACAGGCATTTTG 60.181 47.826 0.00 0.00 0.00 2.44
1767 1795 3.026694 GCTAATCCAGGACAGGCATTTT 58.973 45.455 0.00 0.00 0.00 1.82
1768 1796 2.025037 TGCTAATCCAGGACAGGCATTT 60.025 45.455 7.69 0.00 0.00 2.32
1826 1855 4.002797 GCCCAAAAGTCAGGCGAT 57.997 55.556 0.00 0.00 36.84 4.58
1960 1989 3.181440 ACGTATTCCAGGACCGGTATCTA 60.181 47.826 7.34 0.00 0.00 1.98
1980 2009 7.576750 TTCAGATTTGTAGCAGTTTACTACG 57.423 36.000 0.00 0.00 42.41 3.51
1984 2013 8.342634 TCAAGTTTCAGATTTGTAGCAGTTTAC 58.657 33.333 0.00 0.00 0.00 2.01
2021 2050 2.502538 AGCTATAAGCCAACCGTAACCA 59.497 45.455 0.00 0.00 43.77 3.67
2022 2051 3.189618 AGCTATAAGCCAACCGTAACC 57.810 47.619 0.00 0.00 43.77 2.85
2023 2052 8.033626 AGATATTAGCTATAAGCCAACCGTAAC 58.966 37.037 0.00 0.00 43.77 2.50
2026 2055 6.437793 AGAGATATTAGCTATAAGCCAACCGT 59.562 38.462 0.00 0.00 43.77 4.83
2027 2056 6.868622 AGAGATATTAGCTATAAGCCAACCG 58.131 40.000 0.00 0.00 43.77 4.44
2232 2274 5.667539 ACTTCTAGACTGTATGCACACAT 57.332 39.130 0.00 0.00 40.49 3.21
2617 2663 6.491745 TGCTTCTTGGAAAAACATGGTATACA 59.508 34.615 5.01 0.00 0.00 2.29
2718 2764 3.776417 GGTGGGGGTAGATGTACAAACTA 59.224 47.826 0.00 4.36 0.00 2.24
2783 2829 6.204882 GCTGTATTTAGTTCGGCCATCTATTT 59.795 38.462 2.24 0.00 0.00 1.40
2872 2918 5.309282 AGTGGGAAAATTATTCCAGCCAAAA 59.691 36.000 16.32 0.00 40.32 2.44
3155 3209 7.974504 ACTAGAAGTTTCCCAGAATCAAAGTA 58.025 34.615 0.00 0.00 0.00 2.24
3224 3278 9.651718 CTCTAAACAAAGTTGTACTAAAGCAAG 57.348 33.333 0.00 0.00 41.31 4.01
3270 3324 4.696479 ATTTACTTCATCCTCCGCAGAT 57.304 40.909 0.00 0.00 0.00 2.90
3541 3595 2.992124 TCAAATTTCCCTCGGCGATA 57.008 45.000 11.27 0.00 0.00 2.92
3643 3697 6.146510 GCAATTTTTCAGCAAGATCAATGACA 59.853 34.615 0.00 0.00 0.00 3.58
4652 4707 8.822805 ACAAGGATAGGAACAACTAAGTTATGA 58.177 33.333 0.00 0.00 0.00 2.15
4665 4720 7.159372 TGACAAGAAGTTACAAGGATAGGAAC 58.841 38.462 0.00 0.00 0.00 3.62
4706 4761 3.264193 ACAGAACAGCTATCCACCAATCA 59.736 43.478 0.00 0.00 0.00 2.57
4889 4949 9.729281 TTATTTACGGAAGATAAAAGGAACAGT 57.271 29.630 0.00 0.00 0.00 3.55
4924 5281 3.254166 GGCGAACTTATGATTGATGCCAT 59.746 43.478 0.00 0.00 39.70 4.40
4957 5314 6.418819 CAGGAGCAGAAACAAAACATAAACAG 59.581 38.462 0.00 0.00 0.00 3.16
4984 5342 0.990374 AGATGGGGATGAGCCTATGC 59.010 55.000 0.00 0.00 36.66 3.14
5286 5644 3.410628 ATGCCGTCCATGCCCTCA 61.411 61.111 0.00 0.00 31.48 3.86
5421 5779 2.435586 GCGGTGCTGCAGATCTGT 60.436 61.111 23.38 0.00 34.15 3.41
5457 5815 1.290009 GCTTGCCATTGTCGCCTTT 59.710 52.632 0.00 0.00 0.00 3.11
5468 5826 3.776659 TTGTCGTCGTCGCTTGCCA 62.777 57.895 0.00 0.00 36.96 4.92
5472 5830 2.016704 CAGCTTGTCGTCGTCGCTT 61.017 57.895 0.00 0.00 36.96 4.68
5567 5925 2.415512 GAGTAACACAAACGATGGAGCC 59.584 50.000 0.00 0.00 0.00 4.70
5568 5926 3.123621 CAGAGTAACACAAACGATGGAGC 59.876 47.826 0.00 0.00 0.00 4.70
5569 5927 4.307432 ACAGAGTAACACAAACGATGGAG 58.693 43.478 0.00 0.00 0.00 3.86
5596 5954 1.824230 ACCAGCAAAACAGCAACTCAA 59.176 42.857 0.00 0.00 36.85 3.02
5613 5972 6.463995 AAAAAGCATCTAACAAGTTCACCA 57.536 33.333 0.00 0.00 0.00 4.17
5667 6026 6.017934 TCTCAACAACTCATTTTCTTCTTCCG 60.018 38.462 0.00 0.00 0.00 4.30
5715 6074 2.800629 GCGCGTGTAATATACAGGGTGT 60.801 50.000 8.43 0.00 42.91 4.16
5752 6111 6.984474 AGACACATTATACAAGATGTTACCGG 59.016 38.462 0.00 0.00 34.42 5.28
5769 6128 5.658634 TGACTAGCAATCCTAGAGACACATT 59.341 40.000 4.50 0.00 45.30 2.71
5811 6175 5.605534 GCTAGTCATTTCAGCAATCCTAGA 58.394 41.667 0.00 0.00 35.35 2.43
5817 6181 2.092968 TCCCGCTAGTCATTTCAGCAAT 60.093 45.455 0.00 0.00 34.94 3.56
5876 6240 4.331168 GCAAATATCCCGATCACATCTAGC 59.669 45.833 0.00 0.00 0.00 3.42
5925 6300 6.155910 TCTCTTAATGAAATCCACAGAGCTCT 59.844 38.462 11.45 11.45 31.55 4.09
5951 6326 3.546670 CGGTAGCTCTGTATTCACGTTTC 59.453 47.826 0.00 0.00 0.00 2.78
5955 6330 1.404391 ACCGGTAGCTCTGTATTCACG 59.596 52.381 4.49 0.00 0.00 4.35
5988 6363 2.368655 ATGTTGATTTTCGGCCTTGC 57.631 45.000 0.00 0.00 0.00 4.01
6008 6383 1.749638 TTGGCGTCGGTGTTGGTTT 60.750 52.632 0.00 0.00 0.00 3.27
6026 6418 2.897326 GGTTAGAAATGCCCTTTGGTGT 59.103 45.455 0.00 0.00 0.00 4.16
6029 6421 4.383010 GGATTGGTTAGAAATGCCCTTTGG 60.383 45.833 0.00 0.00 0.00 3.28
6031 6423 3.774766 GGGATTGGTTAGAAATGCCCTTT 59.225 43.478 0.00 0.00 39.04 3.11
6054 6454 6.973229 TTTGTACTTCTTTAACCGGCTATC 57.027 37.500 0.00 0.00 0.00 2.08
6058 6458 5.410439 TCAGATTTGTACTTCTTTAACCGGC 59.590 40.000 0.00 0.00 0.00 6.13
6066 6466 8.170730 AGGGGTAAAATCAGATTTGTACTTCTT 58.829 33.333 9.24 5.57 31.77 2.52
6069 6469 7.699878 AGAGGGGTAAAATCAGATTTGTACTT 58.300 34.615 9.24 0.00 31.77 2.24
6074 6474 6.038271 CGGTTAGAGGGGTAAAATCAGATTTG 59.962 42.308 9.24 0.00 31.77 2.32
6080 6480 2.092807 GCCGGTTAGAGGGGTAAAATCA 60.093 50.000 1.90 0.00 0.00 2.57
6082 6482 1.917568 TGCCGGTTAGAGGGGTAAAAT 59.082 47.619 1.90 0.00 0.00 1.82
6089 6489 2.029307 GCTAGGTGCCGGTTAGAGGG 62.029 65.000 1.90 0.00 35.15 4.30
6115 6515 2.066393 CCTCCTCCAAGGCCGATGA 61.066 63.158 12.59 2.32 34.61 2.92
6137 6538 0.663568 CGTGGCGACCGAGGATAATC 60.664 60.000 0.00 0.00 0.00 1.75
6147 6548 2.202892 GGGAGAATCGTGGCGACC 60.203 66.667 0.00 0.00 39.18 4.79
6149 6550 0.681887 TACAGGGAGAATCGTGGCGA 60.682 55.000 0.00 0.00 41.13 5.54
6154 6555 4.400120 GGAGTAGATACAGGGAGAATCGT 58.600 47.826 0.00 0.00 34.37 3.73
6157 6558 3.158676 GCGGAGTAGATACAGGGAGAAT 58.841 50.000 0.00 0.00 0.00 2.40
6170 6571 4.577246 GGCAGAGCGGCGGAGTAG 62.577 72.222 9.78 0.00 33.57 2.57
6187 6588 3.406361 GCATGGATCCGCGCTACG 61.406 66.667 16.03 0.00 43.15 3.51
6188 6589 3.044305 GGCATGGATCCGCGCTAC 61.044 66.667 20.92 5.65 0.00 3.58
6189 6590 4.662961 CGGCATGGATCCGCGCTA 62.663 66.667 20.92 0.00 40.46 4.26
6231 6632 0.679505 CGGGAAGTCAGTGAACCAGA 59.320 55.000 12.29 0.00 0.00 3.86
6233 6634 0.761323 TCCGGGAAGTCAGTGAACCA 60.761 55.000 0.00 0.00 0.00 3.67
6239 6640 1.609794 GGAGGTCCGGGAAGTCAGT 60.610 63.158 0.00 0.00 0.00 3.41
6241 6642 0.903454 GAAGGAGGTCCGGGAAGTCA 60.903 60.000 0.00 0.00 42.08 3.41
6268 6669 1.257750 TGTATGTCCTCTGCGGCACT 61.258 55.000 0.00 0.00 0.00 4.40
6306 6707 2.995077 GCCATCCATGTCCCCCACA 61.995 63.158 0.00 0.00 40.18 4.17
6320 6721 1.826024 GGTCAGTGATCTCCGCCAT 59.174 57.895 0.00 0.00 0.00 4.40
6340 6741 1.062488 ACTTCCTTGTGTGGGCCTCT 61.062 55.000 4.53 0.00 0.00 3.69
6352 6753 2.580601 CGACCCGACCCACTTCCTT 61.581 63.158 0.00 0.00 0.00 3.36
6394 6795 1.214175 TGCCACCGGTCATATTCCATT 59.786 47.619 2.59 0.00 0.00 3.16
6417 6818 2.751436 CAGCACCATGGAACCGGG 60.751 66.667 21.47 0.00 0.00 5.73
6437 6838 0.693049 AATGGGAAGTTGAGCCTCGT 59.307 50.000 0.00 0.00 0.00 4.18
6454 6855 3.912745 GACCGGCACCGTCCCAAAT 62.913 63.158 0.00 0.00 37.81 2.32


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

AutoCloner maintained by Alex Coulton.