Multiple sequence alignment - TraesCS3D01G297400

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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 TraesCS3D01G297400 chr3D 100.000 4171 0 0 1 4171 410994437 410990267 0.000000e+00 7703.0
1 TraesCS3D01G297400 chr3D 94.969 159 7 1 3617 3774 610359389 610359231 8.950000e-62 248.0
2 TraesCS3D01G297400 chr3D 77.446 368 65 14 5 359 600582627 600582989 1.970000e-48 204.0
3 TraesCS3D01G297400 chr3B 95.011 2205 90 11 1294 3491 537435868 537433677 0.000000e+00 3445.0
4 TraesCS3D01G297400 chr3B 92.000 525 28 8 587 1104 537436383 537435866 0.000000e+00 725.0
5 TraesCS3D01G297400 chr3B 85.548 429 41 9 3758 4169 537430263 537429839 2.980000e-116 429.0
6 TraesCS3D01G297400 chr3B 78.025 405 75 10 1 392 131577600 131577197 4.170000e-60 243.0
7 TraesCS3D01G297400 chr3B 91.304 46 2 2 3561 3606 537430328 537430285 1.250000e-05 62.1
8 TraesCS3D01G297400 chr3A 93.653 1670 76 11 587 2246 540659011 540660660 0.000000e+00 2470.0
9 TraesCS3D01G297400 chr3A 94.374 1262 44 14 2231 3487 540660683 540661922 0.000000e+00 1912.0
10 TraesCS3D01G297400 chr3A 89.121 239 16 2 3769 4006 540662173 540662402 5.280000e-74 289.0
11 TraesCS3D01G297400 chr3A 96.970 165 5 0 4002 4166 540662671 540662835 1.140000e-70 278.0
12 TraesCS3D01G297400 chr3A 79.455 404 69 11 1 392 588535169 588535570 1.480000e-69 274.0
13 TraesCS3D01G297400 chr5B 77.632 608 108 20 1 598 493473595 493474184 1.110000e-90 344.0
14 TraesCS3D01G297400 chr5B 78.068 497 83 20 107 587 463153455 463153941 1.470000e-74 291.0
15 TraesCS3D01G297400 chr2D 92.683 164 6 2 3617 3775 405406317 405406155 9.020000e-57 231.0
16 TraesCS3D01G297400 chr2D 90.230 174 10 5 3606 3773 476917643 476917815 1.950000e-53 220.0
17 TraesCS3D01G297400 chr2D 88.701 177 13 4 3610 3780 78759848 78760023 4.230000e-50 209.0
18 TraesCS3D01G297400 chr6D 90.805 174 9 3 3606 3773 366999089 366999261 4.200000e-55 226.0
19 TraesCS3D01G297400 chr1D 91.667 168 5 4 3614 3772 128530470 128530637 1.510000e-54 224.0
20 TraesCS3D01G297400 chr4B 91.925 161 10 3 3617 3774 19746356 19746516 5.430000e-54 222.0
21 TraesCS3D01G297400 chr4B 89.474 171 14 2 3614 3780 113439984 113440154 3.270000e-51 213.0
22 TraesCS3D01G297400 chr2A 88.950 181 11 5 3611 3783 184561148 184561327 9.080000e-52 215.0
23 TraesCS3D01G297400 chr1B 77.212 373 68 14 5 364 131118021 131118389 7.070000e-48 202.0
24 TraesCS3D01G297400 chr1B 76.533 375 68 15 5 364 131543813 131544182 1.980000e-43 187.0
25 TraesCS3D01G297400 chr1B 76.267 375 71 13 5 364 130837273 130837644 2.560000e-42 183.0
26 TraesCS3D01G297400 chr1B 77.517 298 56 8 77 364 130778113 130778409 7.170000e-38 169.0
27 TraesCS3D01G297400 chr1A 76.152 369 68 13 3 359 548726226 548726586 4.290000e-40 176.0


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 TraesCS3D01G297400 chr3D 410990267 410994437 4170 True 7703.000 7703 100.00000 1 4171 1 chr3D.!!$R1 4170
1 TraesCS3D01G297400 chr3B 537429839 537436383 6544 True 1165.275 3445 90.96575 587 4169 4 chr3B.!!$R2 3582
2 TraesCS3D01G297400 chr3A 540659011 540662835 3824 False 1237.250 2470 93.52950 587 4166 4 chr3A.!!$F2 3579
3 TraesCS3D01G297400 chr5B 493473595 493474184 589 False 344.000 344 77.63200 1 598 1 chr5B.!!$F2 597

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
546 561 0.179234 TAAAATGATCGGCCGCTCCA 59.821 50.0 25.06 19.35 34.01 3.86 F
1571 1595 0.179121 CCATCGCGTGCCTAACAGTA 60.179 55.0 5.77 0.00 0.00 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1649 1673 0.652592 CGCTCAGCCATAGGAAAACG 59.347 55.0 0.0 0.0 0.0 3.60 R
3317 3390 0.673644 ACAGATTTCTTCCGTGCCCG 60.674 55.0 0.0 0.0 0.0 6.13 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
22 23 0.518636 CCGAAGTTGCACATCCACTG 59.481 55.000 0.00 0.00 0.00 3.66
29 30 1.078214 GCACATCCACTGCTAGGCA 60.078 57.895 0.00 0.00 36.92 4.75
43 44 0.476338 TAGGCAGTTGGTCAAGGCAA 59.524 50.000 8.76 0.00 0.00 4.52
44 45 1.109323 AGGCAGTTGGTCAAGGCAAC 61.109 55.000 0.00 0.00 0.00 4.17
50 51 2.094234 AGTTGGTCAAGGCAACAAACAC 60.094 45.455 0.00 0.00 33.73 3.32
52 53 2.175202 TGGTCAAGGCAACAAACACTT 58.825 42.857 0.00 0.00 41.41 3.16
57 58 5.815222 GGTCAAGGCAACAAACACTTAAAAT 59.185 36.000 0.00 0.00 41.41 1.82
58 59 6.238076 GGTCAAGGCAACAAACACTTAAAATG 60.238 38.462 0.00 0.00 41.41 2.32
60 61 4.702831 AGGCAACAAACACTTAAAATGGG 58.297 39.130 0.00 0.00 41.41 4.00
71 72 5.648092 ACACTTAAAATGGGCATCTACAGAC 59.352 40.000 0.00 0.00 0.00 3.51
73 74 6.319658 CACTTAAAATGGGCATCTACAGACAT 59.680 38.462 0.00 0.00 0.00 3.06
75 76 2.945080 ATGGGCATCTACAGACATGG 57.055 50.000 0.00 0.00 0.00 3.66
77 78 1.131638 GGGCATCTACAGACATGGGA 58.868 55.000 0.00 0.00 0.00 4.37
78 79 1.490490 GGGCATCTACAGACATGGGAA 59.510 52.381 0.00 0.00 0.00 3.97
82 83 4.265073 GCATCTACAGACATGGGAAAAGT 58.735 43.478 0.00 0.00 0.00 2.66
87 88 2.362077 ACAGACATGGGAAAAGTTGCAC 59.638 45.455 0.00 0.00 0.00 4.57
91 92 2.964464 ACATGGGAAAAGTTGCACATCA 59.036 40.909 0.00 0.00 0.00 3.07
149 150 1.759445 CACATCTCACTGGTAGGAGGG 59.241 57.143 0.00 0.00 0.00 4.30
155 156 2.234908 CTCACTGGTAGGAGGGAGTTTG 59.765 54.545 0.00 0.00 38.52 2.93
164 165 1.852626 AGGGAGTTTGGGGTGGAGG 60.853 63.158 0.00 0.00 0.00 4.30
167 168 1.603739 GAGTTTGGGGTGGAGGTGC 60.604 63.158 0.00 0.00 0.00 5.01
197 206 2.879103 AACCACACATCGGGAGAAAT 57.121 45.000 0.00 0.00 45.37 2.17
207 216 2.789213 TCGGGAGAAATTTGCACATCA 58.211 42.857 0.00 0.00 34.75 3.07
217 226 6.435277 AGAAATTTGCACATCAACTATCAGGT 59.565 34.615 0.00 0.00 33.73 4.00
218 227 7.611467 AGAAATTTGCACATCAACTATCAGGTA 59.389 33.333 0.00 0.00 33.73 3.08
219 228 6.932356 ATTTGCACATCAACTATCAGGTAG 57.068 37.500 0.00 0.00 33.73 3.18
220 229 5.420725 TTGCACATCAACTATCAGGTAGT 57.579 39.130 0.00 0.00 45.56 2.73
231 240 5.892568 ACTATCAGGTAGTTGAACATCGAC 58.107 41.667 0.00 0.00 40.80 4.20
232 241 5.652891 ACTATCAGGTAGTTGAACATCGACT 59.347 40.000 0.00 5.63 40.80 4.18
233 242 6.827251 ACTATCAGGTAGTTGAACATCGACTA 59.173 38.462 0.00 3.81 40.80 2.59
234 243 6.716934 ATCAGGTAGTTGAACATCGACTAT 57.283 37.500 9.96 0.00 43.22 2.12
235 244 6.132791 TCAGGTAGTTGAACATCGACTATC 57.867 41.667 9.96 9.56 43.22 2.08
236 245 5.650703 TCAGGTAGTTGAACATCGACTATCA 59.349 40.000 16.55 0.00 43.71 2.15
237 246 5.744345 CAGGTAGTTGAACATCGACTATCAC 59.256 44.000 16.55 5.94 43.71 3.06
238 247 5.417894 AGGTAGTTGAACATCGACTATCACA 59.582 40.000 16.55 0.00 43.71 3.58
239 248 5.515626 GGTAGTTGAACATCGACTATCACAC 59.484 44.000 11.49 2.44 43.22 3.82
252 261 4.315803 ACTATCACACAGTTGCACCTAAC 58.684 43.478 0.00 0.00 0.00 2.34
256 265 1.072505 ACAGTTGCACCTAACGGGG 59.927 57.895 0.00 0.00 40.03 5.73
268 277 0.321830 TAACGGGGCCTAAGTTGCAC 60.322 55.000 17.97 0.00 0.00 4.57
270 279 2.332654 CGGGGCCTAAGTTGCACAC 61.333 63.158 0.84 0.00 32.36 3.82
273 282 1.036707 GGGCCTAAGTTGCACACAAA 58.963 50.000 0.84 0.00 37.58 2.83
304 313 2.032894 CGAAACATACACATGCGGGATC 60.033 50.000 0.00 0.00 35.39 3.36
307 316 4.415881 AACATACACATGCGGGATCTAA 57.584 40.909 0.00 0.00 35.39 2.10
314 323 3.185188 CACATGCGGGATCTAATTTCGAG 59.815 47.826 0.00 0.00 0.00 4.04
321 330 3.053455 GGATCTAATTTCGAGGAGCACG 58.947 50.000 0.00 0.00 0.00 5.34
341 350 3.304382 GTCGCAACGATTCCAATAGTG 57.696 47.619 0.00 0.00 38.42 2.74
346 355 4.553429 CGCAACGATTCCAATAGTGAAAAC 59.447 41.667 0.00 0.00 0.00 2.43
347 356 4.553429 GCAACGATTCCAATAGTGAAAACG 59.447 41.667 0.00 0.00 34.36 3.60
350 359 4.998672 ACGATTCCAATAGTGAAAACGGAA 59.001 37.500 0.00 0.00 36.98 4.30
359 368 9.124807 CCAATAGTGAAAACGGAACTTAATTTC 57.875 33.333 0.00 0.00 0.00 2.17
371 380 5.163834 GGAACTTAATTTCGATGCACGGTTA 60.164 40.000 8.46 4.41 42.82 2.85
373 382 4.331717 ACTTAATTTCGATGCACGGTTAGG 59.668 41.667 8.46 8.39 42.82 2.69
374 383 1.663695 ATTTCGATGCACGGTTAGGG 58.336 50.000 8.46 0.00 42.82 3.53
379 388 1.135527 CGATGCACGGTTAGGGAGTTA 59.864 52.381 0.00 0.00 38.46 2.24
382 391 2.181125 TGCACGGTTAGGGAGTTATGA 58.819 47.619 0.00 0.00 0.00 2.15
388 397 5.704053 CACGGTTAGGGAGTTATGACTTTTT 59.296 40.000 0.00 0.00 35.88 1.94
389 398 5.704053 ACGGTTAGGGAGTTATGACTTTTTG 59.296 40.000 0.00 0.00 35.88 2.44
420 430 7.798596 AAAACCATGAATTAAATGCACAACA 57.201 28.000 0.00 0.00 0.00 3.33
424 434 6.646240 ACCATGAATTAAATGCACAACAGAAC 59.354 34.615 0.00 0.00 0.00 3.01
429 439 9.107177 TGAATTAAATGCACAACAGAACAAAAT 57.893 25.926 0.00 0.00 0.00 1.82
435 445 3.059461 GCACAACAGAACAAAATGCATGG 60.059 43.478 0.00 0.00 0.00 3.66
436 446 3.495377 CACAACAGAACAAAATGCATGGG 59.505 43.478 0.00 0.00 0.00 4.00
454 464 2.954684 GCAGTGGGATGACCGTGGA 61.955 63.158 0.00 0.00 44.64 4.02
455 465 1.907739 CAGTGGGATGACCGTGGAT 59.092 57.895 0.00 0.00 44.64 3.41
456 466 1.119684 CAGTGGGATGACCGTGGATA 58.880 55.000 0.00 0.00 44.64 2.59
459 469 1.416401 GTGGGATGACCGTGGATACAT 59.584 52.381 0.00 0.00 44.03 2.29
460 470 2.123589 TGGGATGACCGTGGATACATT 58.876 47.619 0.00 0.00 44.03 2.71
461 471 3.070446 GTGGGATGACCGTGGATACATTA 59.930 47.826 0.00 0.00 44.03 1.90
462 472 3.323691 TGGGATGACCGTGGATACATTAG 59.676 47.826 0.00 0.00 44.03 1.73
463 473 6.312064 TGGGATGACCGTGGATACATTAGC 62.312 50.000 0.00 0.00 44.03 3.09
471 481 3.452755 TGGATACATTAGCCAGTCGTG 57.547 47.619 0.00 0.00 46.17 4.35
472 482 3.028130 TGGATACATTAGCCAGTCGTGA 58.972 45.455 0.00 0.00 46.17 4.35
476 486 5.353123 GGATACATTAGCCAGTCGTGAAAAA 59.647 40.000 0.00 0.00 33.51 1.94
502 517 8.691661 AGTAATCAAGTGAAAAGCTTTCCTAA 57.308 30.769 13.10 2.32 0.00 2.69
541 556 6.885735 AAAAATTTCTAAAATGATCGGCCG 57.114 33.333 22.12 22.12 0.00 6.13
542 557 3.626028 ATTTCTAAAATGATCGGCCGC 57.374 42.857 23.51 8.29 0.00 6.53
544 559 1.865865 TCTAAAATGATCGGCCGCTC 58.134 50.000 23.51 22.55 0.00 5.03
546 561 0.179234 TAAAATGATCGGCCGCTCCA 59.821 50.000 25.06 19.35 34.01 3.86
547 562 0.466189 AAAATGATCGGCCGCTCCAT 60.466 50.000 25.06 20.60 34.01 3.41
548 563 1.168407 AAATGATCGGCCGCTCCATG 61.168 55.000 25.06 0.00 34.01 3.66
605 621 6.422223 CGTCCTTTAAAGTGATGATACATGC 58.578 40.000 14.03 0.00 0.00 4.06
644 660 6.586751 CGTTTTCACTATCAGCGTCTTTTTA 58.413 36.000 0.00 0.00 0.00 1.52
649 665 8.776680 TTCACTATCAGCGTCTTTTTAAAAAC 57.223 30.769 9.31 1.26 0.00 2.43
650 666 7.921787 TCACTATCAGCGTCTTTTTAAAAACA 58.078 30.769 9.31 0.00 0.00 2.83
652 668 8.469125 CACTATCAGCGTCTTTTTAAAAACAAC 58.531 33.333 9.31 9.59 0.00 3.32
738 756 6.884295 TCCTACCTTAAATGGAAGAATGTGTG 59.116 38.462 0.00 0.00 0.00 3.82
741 759 6.548321 ACCTTAAATGGAAGAATGTGTGGTA 58.452 36.000 0.00 0.00 0.00 3.25
749 767 6.406370 TGGAAGAATGTGTGGTATCTTGTAG 58.594 40.000 0.00 0.00 32.54 2.74
789 811 1.140312 TCACCTATCCCATTCCTGGC 58.860 55.000 0.00 0.00 41.64 4.85
837 859 2.165998 GCAGGAGCATGTTCTTTCCTT 58.834 47.619 9.57 0.00 37.97 3.36
919 941 1.577328 CTCGGCAAGCAACAACGGAT 61.577 55.000 0.00 0.00 0.00 4.18
1101 1123 4.878439 TGCCGTTCATCATAGGTATGTAC 58.122 43.478 0.00 0.00 35.26 2.90
1102 1124 4.587262 TGCCGTTCATCATAGGTATGTACT 59.413 41.667 0.00 0.00 35.26 2.73
1103 1125 5.771165 TGCCGTTCATCATAGGTATGTACTA 59.229 40.000 0.00 0.00 35.26 1.82
1148 1172 0.745845 CATGGACTGGTAGGTGCAGC 60.746 60.000 8.11 8.11 40.58 5.25
1149 1173 1.200760 ATGGACTGGTAGGTGCAGCA 61.201 55.000 19.63 0.00 40.58 4.41
1150 1174 1.376037 GGACTGGTAGGTGCAGCAC 60.376 63.158 17.97 17.97 0.00 4.40
1151 1175 1.674057 GACTGGTAGGTGCAGCACT 59.326 57.895 24.75 13.23 34.40 4.40
1152 1176 0.671781 GACTGGTAGGTGCAGCACTG 60.672 60.000 24.75 13.43 34.40 3.66
1186 1210 3.307691 GGACACCCAACTGAGAATGATCA 60.308 47.826 0.00 0.00 0.00 2.92
1188 1212 4.927049 ACACCCAACTGAGAATGATCATT 58.073 39.130 20.85 20.85 0.00 2.57
1191 1215 5.593095 CACCCAACTGAGAATGATCATTGAT 59.407 40.000 25.37 13.46 0.00 2.57
1199 1223 7.496263 ACTGAGAATGATCATTGATGAGACAAG 59.504 37.037 25.37 12.11 40.64 3.16
1203 1227 8.894731 AGAATGATCATTGATGAGACAAGAAAG 58.105 33.333 25.37 0.00 40.64 2.62
1205 1229 7.606858 TGATCATTGATGAGACAAGAAAGTC 57.393 36.000 3.32 0.00 40.64 3.01
1214 1238 3.775316 GAGACAAGAAAGTCCCCTGGATA 59.225 47.826 0.00 0.00 39.34 2.59
1229 1253 5.302823 CCCCTGGATAAACATGATTTCCTTC 59.697 44.000 0.00 0.00 0.00 3.46
1312 1336 8.768397 ACTGACTATACATCCCTTCAATTTGTA 58.232 33.333 0.00 0.00 0.00 2.41
1319 1343 7.404671 ACATCCCTTCAATTTGTAATGGTAC 57.595 36.000 0.00 0.00 0.00 3.34
1529 1553 1.214325 CGACATGTACACAGGCCGA 59.786 57.895 0.00 0.00 0.00 5.54
1559 1583 3.888079 CTCGCTAGGCTCCATCGCG 62.888 68.421 0.00 0.00 44.63 5.87
1571 1595 0.179121 CCATCGCGTGCCTAACAGTA 60.179 55.000 5.77 0.00 0.00 2.74
1576 1600 1.012486 GCGTGCCTAACAGTAAGCGT 61.012 55.000 0.00 0.00 0.00 5.07
1581 1605 4.433805 CGTGCCTAACAGTAAGCGTAAAAG 60.434 45.833 0.00 0.00 0.00 2.27
1595 1619 5.806366 GCGTAAAAGCTACTCCCAAATAA 57.194 39.130 0.00 0.00 0.00 1.40
1598 1622 6.456584 GCGTAAAAGCTACTCCCAAATAAGAC 60.457 42.308 0.00 0.00 0.00 3.01
1605 1629 2.635915 ACTCCCAAATAAGACCGTGTCA 59.364 45.455 6.78 0.00 34.60 3.58
1629 1653 3.004210 TGCTTCACTTGCGCTAAATTTGA 59.996 39.130 9.73 0.00 0.00 2.69
1647 1671 0.322546 GAACCACTTACTGCAGGGGG 60.323 60.000 19.93 13.51 42.47 5.40
1649 1673 1.299976 CCACTTACTGCAGGGGGTC 59.700 63.158 19.93 0.00 33.00 4.46
1685 1709 2.828868 GCCATGATACCCGGAGCA 59.171 61.111 0.73 0.00 0.00 4.26
2246 2277 6.343703 TGATCGACTCAATGATTGTTCATCT 58.656 36.000 4.93 0.00 41.83 2.90
2247 2278 6.257193 TGATCGACTCAATGATTGTTCATCTG 59.743 38.462 4.93 0.00 41.83 2.90
2306 2373 0.322816 TCCTGAACAAGGCCTGCATC 60.323 55.000 5.69 5.40 46.92 3.91
2318 2385 1.734707 GCCTGCATCATCAGCAACAAC 60.735 52.381 0.00 0.00 42.17 3.32
2374 2444 2.029288 CAGAGCGTGATGGCAACGT 61.029 57.895 12.72 0.93 42.51 3.99
2450 2520 2.427540 GGATCCTGCCGATCTGGTCG 62.428 65.000 3.84 2.72 45.90 4.79
2465 2535 1.663702 GTCGTCCACCGTGTTCCTG 60.664 63.158 0.00 0.00 37.94 3.86
3266 3339 2.114411 TTGCGGGGTTGGTTCTCC 59.886 61.111 0.00 0.00 0.00 3.71
3317 3390 5.163395 TGTGGTTAATGTTTCAAAGTTCCCC 60.163 40.000 0.00 0.00 0.00 4.81
3340 3413 2.840974 ACGGAAGAAATCTGTGCGG 58.159 52.632 9.72 0.00 46.12 5.69
3362 3435 1.659622 CGCCTTGCCATTCATCAGCA 61.660 55.000 0.00 0.00 33.97 4.41
3373 3446 0.901827 TCATCAGCAAAGCCGGAGTA 59.098 50.000 5.05 0.00 0.00 2.59
3387 3460 3.442100 CCGGAGTATACACGGTTCTTTC 58.558 50.000 23.24 3.37 42.53 2.62
3432 3505 3.505386 TCTTCTTCTCAACAGAGAGGCT 58.495 45.455 0.00 0.00 39.43 4.58
3477 3551 7.669722 ACCTTCAGCCATCTAATTTCAACTAAA 59.330 33.333 0.00 0.00 0.00 1.85
3478 3552 7.970614 CCTTCAGCCATCTAATTTCAACTAAAC 59.029 37.037 0.00 0.00 0.00 2.01
3480 3554 8.044060 TCAGCCATCTAATTTCAACTAAACAG 57.956 34.615 0.00 0.00 0.00 3.16
3481 3555 6.749118 CAGCCATCTAATTTCAACTAAACAGC 59.251 38.462 0.00 0.00 0.00 4.40
3482 3556 6.434028 AGCCATCTAATTTCAACTAAACAGCA 59.566 34.615 0.00 0.00 0.00 4.41
3483 3557 6.528072 GCCATCTAATTTCAACTAAACAGCAC 59.472 38.462 0.00 0.00 0.00 4.40
3484 3558 7.592938 CCATCTAATTTCAACTAAACAGCACA 58.407 34.615 0.00 0.00 0.00 4.57
3485 3559 7.538678 CCATCTAATTTCAACTAAACAGCACAC 59.461 37.037 0.00 0.00 0.00 3.82
3499 3573 9.956797 CTAAACAGCACACAAAAATATTTATGC 57.043 29.630 0.01 7.06 0.00 3.14
3500 3574 8.606040 AAACAGCACACAAAAATATTTATGCT 57.394 26.923 13.65 13.65 42.69 3.79
3501 3575 8.606040 AACAGCACACAAAAATATTTATGCTT 57.394 26.923 15.51 0.74 40.06 3.91
3502 3576 9.703892 AACAGCACACAAAAATATTTATGCTTA 57.296 25.926 15.51 0.00 40.06 3.09
3518 3592 8.537728 TTTATGCTTATGATTTTCCCTCATGT 57.462 30.769 0.00 0.00 35.12 3.21
3519 3593 8.537728 TTATGCTTATGATTTTCCCTCATGTT 57.462 30.769 0.00 0.00 35.12 2.71
3520 3594 6.855763 TGCTTATGATTTTCCCTCATGTTT 57.144 33.333 0.00 0.00 35.12 2.83
3524 3598 8.686334 GCTTATGATTTTCCCTCATGTTTTAGA 58.314 33.333 0.00 0.00 35.12 2.10
3530 5787 6.817765 TTTCCCTCATGTTTTAGACATCAC 57.182 37.500 0.00 0.00 45.88 3.06
3534 5791 7.331026 TCCCTCATGTTTTAGACATCACTAAG 58.669 38.462 0.00 0.00 45.88 2.18
3541 5798 7.159372 TGTTTTAGACATCACTAAGTCTTCCC 58.841 38.462 0.02 0.00 42.12 3.97
3558 6942 8.056407 AGTCTTCCCTTATTATGAGCAAAAAC 57.944 34.615 0.00 0.00 0.00 2.43
3559 6943 7.890655 AGTCTTCCCTTATTATGAGCAAAAACT 59.109 33.333 0.00 0.00 0.00 2.66
3619 7037 4.439289 GGACGGCGACACTAAATAAGTACT 60.439 45.833 16.62 0.00 35.76 2.73
3621 7039 4.040376 CGGCGACACTAAATAAGTACTCC 58.960 47.826 0.00 0.00 35.76 3.85
3622 7040 4.366586 GGCGACACTAAATAAGTACTCCC 58.633 47.826 0.00 0.00 35.76 4.30
3623 7041 4.099113 GGCGACACTAAATAAGTACTCCCT 59.901 45.833 0.00 0.00 35.76 4.20
3624 7042 5.280164 GCGACACTAAATAAGTACTCCCTC 58.720 45.833 0.00 0.00 35.76 4.30
3625 7043 5.735638 GCGACACTAAATAAGTACTCCCTCC 60.736 48.000 0.00 0.00 35.76 4.30
3626 7044 5.505324 CGACACTAAATAAGTACTCCCTCCG 60.505 48.000 0.00 0.00 35.76 4.63
3627 7045 5.267587 ACACTAAATAAGTACTCCCTCCGT 58.732 41.667 0.00 0.00 35.76 4.69
3628 7046 5.718607 ACACTAAATAAGTACTCCCTCCGTT 59.281 40.000 0.00 0.00 35.76 4.44
3629 7047 6.127507 ACACTAAATAAGTACTCCCTCCGTTC 60.128 42.308 0.00 0.00 35.76 3.95
3630 7048 4.750021 AAATAAGTACTCCCTCCGTTCC 57.250 45.455 0.00 0.00 0.00 3.62
3631 7049 3.684408 ATAAGTACTCCCTCCGTTCCT 57.316 47.619 0.00 0.00 0.00 3.36
3632 7050 4.803329 ATAAGTACTCCCTCCGTTCCTA 57.197 45.455 0.00 0.00 0.00 2.94
3633 7051 3.463048 AAGTACTCCCTCCGTTCCTAA 57.537 47.619 0.00 0.00 0.00 2.69
3634 7052 3.463048 AGTACTCCCTCCGTTCCTAAA 57.537 47.619 0.00 0.00 0.00 1.85
3635 7053 3.991683 AGTACTCCCTCCGTTCCTAAAT 58.008 45.455 0.00 0.00 0.00 1.40
3636 7054 5.134725 AGTACTCCCTCCGTTCCTAAATA 57.865 43.478 0.00 0.00 0.00 1.40
3637 7055 5.713807 AGTACTCCCTCCGTTCCTAAATAT 58.286 41.667 0.00 0.00 0.00 1.28
3638 7056 6.856757 AGTACTCCCTCCGTTCCTAAATATA 58.143 40.000 0.00 0.00 0.00 0.86
3639 7057 7.300658 AGTACTCCCTCCGTTCCTAAATATAA 58.699 38.462 0.00 0.00 0.00 0.98
3640 7058 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
3641 7059 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
3642 7060 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
3643 7061 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
3644 7062 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
3645 7063 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
3646 7064 7.991460 CCCTCCGTTCCTAAATATAAGTCTTTT 59.009 37.037 0.00 0.00 0.00 2.27
3647 7065 9.392259 CCTCCGTTCCTAAATATAAGTCTTTTT 57.608 33.333 0.00 0.00 0.00 1.94
3671 7089 9.701098 TTTAGACATTTCAAATAGACTACACGT 57.299 29.630 0.00 0.00 0.00 4.49
3674 7092 9.302345 AGACATTTCAAATAGACTACACGTATG 57.698 33.333 0.00 0.00 0.00 2.39
3675 7093 8.997621 ACATTTCAAATAGACTACACGTATGT 57.002 30.769 0.00 0.00 43.30 2.29
3710 7128 9.677567 TTTAAAGTGTAGATTCACTCATTTTGC 57.322 29.630 0.00 0.00 46.25 3.68
3711 7129 7.516198 AAAGTGTAGATTCACTCATTTTGCT 57.484 32.000 0.00 0.00 46.25 3.91
3712 7130 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26
3713 7131 5.645497 AGTGTAGATTCACTCATTTTGCTCC 59.355 40.000 0.00 0.00 44.07 4.70
3714 7132 4.631377 TGTAGATTCACTCATTTTGCTCCG 59.369 41.667 0.00 0.00 0.00 4.63
3715 7133 3.679389 AGATTCACTCATTTTGCTCCGT 58.321 40.909 0.00 0.00 0.00 4.69
3716 7134 4.832248 AGATTCACTCATTTTGCTCCGTA 58.168 39.130 0.00 0.00 0.00 4.02
3717 7135 5.431765 AGATTCACTCATTTTGCTCCGTAT 58.568 37.500 0.00 0.00 0.00 3.06
3718 7136 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
3719 7137 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
3720 7138 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
3721 7139 5.109210 TCACTCATTTTGCTCCGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
3722 7140 4.870426 CACTCATTTTGCTCCGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
3723 7141 5.005779 CACTCATTTTGCTCCGTATGTAGTC 59.994 44.000 0.00 0.00 0.00 2.59
3724 7142 5.079689 TCATTTTGCTCCGTATGTAGTCA 57.920 39.130 0.00 0.00 0.00 3.41
3725 7143 4.868171 TCATTTTGCTCCGTATGTAGTCAC 59.132 41.667 0.00 0.00 0.00 3.67
3726 7144 4.530710 TTTTGCTCCGTATGTAGTCACT 57.469 40.909 0.00 0.00 0.00 3.41
3727 7145 4.530710 TTTGCTCCGTATGTAGTCACTT 57.469 40.909 0.00 0.00 0.00 3.16
3728 7146 3.503827 TGCTCCGTATGTAGTCACTTG 57.496 47.619 0.00 0.00 0.00 3.16
3729 7147 2.823747 TGCTCCGTATGTAGTCACTTGT 59.176 45.455 0.00 0.00 0.00 3.16
3730 7148 3.257375 TGCTCCGTATGTAGTCACTTGTT 59.743 43.478 0.00 0.00 0.00 2.83
3731 7149 3.612860 GCTCCGTATGTAGTCACTTGTTG 59.387 47.826 0.00 0.00 0.00 3.33
3732 7150 4.617530 GCTCCGTATGTAGTCACTTGTTGA 60.618 45.833 0.00 0.00 0.00 3.18
3733 7151 5.456548 TCCGTATGTAGTCACTTGTTGAA 57.543 39.130 0.00 0.00 35.39 2.69
3734 7152 5.845103 TCCGTATGTAGTCACTTGTTGAAA 58.155 37.500 0.00 0.00 35.39 2.69
3735 7153 6.460781 TCCGTATGTAGTCACTTGTTGAAAT 58.539 36.000 0.00 0.00 35.39 2.17
3736 7154 6.588756 TCCGTATGTAGTCACTTGTTGAAATC 59.411 38.462 0.00 0.00 35.39 2.17
3737 7155 6.590292 CCGTATGTAGTCACTTGTTGAAATCT 59.410 38.462 0.00 0.00 35.39 2.40
3738 7156 7.201444 CCGTATGTAGTCACTTGTTGAAATCTC 60.201 40.741 0.00 0.00 35.39 2.75
3739 7157 7.542477 CGTATGTAGTCACTTGTTGAAATCTCT 59.458 37.037 0.00 0.00 35.39 3.10
3740 7158 9.856488 GTATGTAGTCACTTGTTGAAATCTCTA 57.144 33.333 0.00 0.00 35.39 2.43
3742 7160 9.778741 ATGTAGTCACTTGTTGAAATCTCTAAA 57.221 29.630 0.00 0.00 35.39 1.85
3743 7161 9.607988 TGTAGTCACTTGTTGAAATCTCTAAAA 57.392 29.630 0.00 0.00 35.39 1.52
3746 7164 9.396022 AGTCACTTGTTGAAATCTCTAAAAAGA 57.604 29.630 0.00 0.00 35.39 2.52
3747 7165 9.439537 GTCACTTGTTGAAATCTCTAAAAAGAC 57.560 33.333 0.00 0.00 35.39 3.01
3748 7166 9.396022 TCACTTGTTGAAATCTCTAAAAAGACT 57.604 29.630 0.00 0.00 0.00 3.24
3766 7184 8.959705 AAAAGACTTATATTTAGGAACGGAGG 57.040 34.615 0.00 0.00 0.00 4.30
3767 7185 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
3768 7186 6.379579 AGACTTATATTTAGGAACGGAGGGA 58.620 40.000 0.00 0.00 0.00 4.20
3769 7187 6.494146 AGACTTATATTTAGGAACGGAGGGAG 59.506 42.308 0.00 0.00 0.00 4.30
3770 7188 6.141790 ACTTATATTTAGGAACGGAGGGAGT 58.858 40.000 0.00 0.00 0.00 3.85
3771 7189 7.300658 ACTTATATTTAGGAACGGAGGGAGTA 58.699 38.462 0.00 0.00 0.00 2.59
3772 7190 7.232330 ACTTATATTTAGGAACGGAGGGAGTAC 59.768 40.741 0.00 0.00 0.00 2.73
3773 7191 2.905415 TTAGGAACGGAGGGAGTACA 57.095 50.000 0.00 0.00 0.00 2.90
3774 7192 3.393426 TTAGGAACGGAGGGAGTACAT 57.607 47.619 0.00 0.00 0.00 2.29
3792 7211 7.351414 AGTACATAACATGTATGCTTATGCG 57.649 36.000 12.39 0.00 46.39 4.73
3940 7365 7.593825 ACAGAACAAAATTATTAGCTGACACC 58.406 34.615 0.00 0.00 0.00 4.16
3941 7366 7.230510 ACAGAACAAAATTATTAGCTGACACCA 59.769 33.333 0.00 0.00 0.00 4.17
3958 7383 1.341531 ACCACTATATGTCTGCCTCGC 59.658 52.381 0.00 0.00 0.00 5.03
3968 7393 4.704833 TGCCTCGCAGAAGGGTGC 62.705 66.667 0.00 0.00 40.29 5.01
4080 7784 6.882610 TGAAATCAGTAGCAAACTCAACAT 57.117 33.333 0.00 0.00 35.76 2.71
4148 7856 0.826715 TGGCATTCCGAGGAAGAGAG 59.173 55.000 10.56 2.18 37.56 3.20
4156 7864 1.957877 CCGAGGAAGAGAGTCCCATAC 59.042 57.143 0.00 0.00 38.59 2.39
4169 7877 1.202371 TCCCATACGTGCAATCTCGTC 60.202 52.381 3.12 0.00 41.78 4.20
4170 7878 0.846401 CCATACGTGCAATCTCGTCG 59.154 55.000 3.12 0.00 41.78 5.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 0.518636 CAGTGGATGTGCAACTTCGG 59.481 55.000 0.00 0.00 41.51 4.30
5 6 1.242076 AGCAGTGGATGTGCAACTTC 58.758 50.000 0.00 0.00 43.82 3.01
22 23 1.308783 GCCTTGACCAACTGCCTAGC 61.309 60.000 0.00 0.00 0.00 3.42
29 30 2.094234 GTGTTTGTTGCCTTGACCAACT 60.094 45.455 5.94 0.00 42.25 3.16
35 36 5.814705 CCATTTTAAGTGTTTGTTGCCTTGA 59.185 36.000 0.00 0.00 0.00 3.02
43 44 5.806654 AGATGCCCATTTTAAGTGTTTGT 57.193 34.783 0.00 0.00 0.00 2.83
44 45 6.686630 TGTAGATGCCCATTTTAAGTGTTTG 58.313 36.000 0.00 0.00 0.00 2.93
50 51 6.238842 CCATGTCTGTAGATGCCCATTTTAAG 60.239 42.308 0.00 0.00 0.00 1.85
52 53 5.132502 CCATGTCTGTAGATGCCCATTTTA 58.867 41.667 0.00 0.00 0.00 1.52
57 58 0.839277 CCCATGTCTGTAGATGCCCA 59.161 55.000 0.00 0.00 0.00 5.36
58 59 1.131638 TCCCATGTCTGTAGATGCCC 58.868 55.000 0.00 0.00 0.00 5.36
60 61 4.265073 ACTTTTCCCATGTCTGTAGATGC 58.735 43.478 0.00 0.00 0.00 3.91
71 72 3.663995 TGATGTGCAACTTTTCCCATG 57.336 42.857 0.00 0.00 38.04 3.66
82 83 5.483685 ACTTCCTAGTAGTTGATGTGCAA 57.516 39.130 0.00 0.00 31.21 4.08
91 92 2.496470 CTCGGCCAACTTCCTAGTAGTT 59.504 50.000 2.24 2.53 36.31 2.24
109 110 1.373497 AACTTCGTCTGCTGCCTCG 60.373 57.895 0.00 0.00 0.00 4.63
149 150 1.603739 GCACCTCCACCCCAAACTC 60.604 63.158 0.00 0.00 0.00 3.01
164 165 1.680735 TGTGGTTTTCACTGATGGCAC 59.319 47.619 0.00 0.00 46.20 5.01
167 168 3.365264 CGATGTGTGGTTTTCACTGATGG 60.365 47.826 0.00 0.00 46.20 3.51
171 172 1.266718 CCCGATGTGTGGTTTTCACTG 59.733 52.381 0.00 0.00 46.20 3.66
188 197 3.057315 AGTTGATGTGCAAATTTCTCCCG 60.057 43.478 0.00 0.00 38.44 5.14
191 200 6.971184 CCTGATAGTTGATGTGCAAATTTCTC 59.029 38.462 0.00 0.00 38.44 2.87
197 206 5.804639 ACTACCTGATAGTTGATGTGCAAA 58.195 37.500 0.00 0.00 41.71 3.68
217 226 6.072119 ACTGTGTGATAGTCGATGTTCAACTA 60.072 38.462 0.00 0.00 0.00 2.24
218 227 5.134202 TGTGTGATAGTCGATGTTCAACT 57.866 39.130 0.00 0.00 0.00 3.16
219 228 4.923871 ACTGTGTGATAGTCGATGTTCAAC 59.076 41.667 0.00 0.00 0.00 3.18
220 229 5.134202 ACTGTGTGATAGTCGATGTTCAA 57.866 39.130 0.00 0.00 0.00 2.69
221 230 4.783764 ACTGTGTGATAGTCGATGTTCA 57.216 40.909 0.00 0.00 0.00 3.18
222 231 4.201628 GCAACTGTGTGATAGTCGATGTTC 60.202 45.833 0.00 0.00 0.00 3.18
223 232 3.679980 GCAACTGTGTGATAGTCGATGTT 59.320 43.478 0.00 0.00 0.00 2.71
224 233 3.254060 GCAACTGTGTGATAGTCGATGT 58.746 45.455 0.00 0.00 0.00 3.06
225 234 3.061295 GTGCAACTGTGTGATAGTCGATG 59.939 47.826 0.00 0.00 0.00 3.84
226 235 3.254060 GTGCAACTGTGTGATAGTCGAT 58.746 45.455 0.00 0.00 0.00 3.59
227 236 2.609491 GGTGCAACTGTGTGATAGTCGA 60.609 50.000 0.00 0.00 36.74 4.20
228 237 1.726791 GGTGCAACTGTGTGATAGTCG 59.273 52.381 0.00 0.00 36.74 4.18
229 238 3.045601 AGGTGCAACTGTGTGATAGTC 57.954 47.619 1.66 0.00 36.74 2.59
230 239 4.315803 GTTAGGTGCAACTGTGTGATAGT 58.684 43.478 16.44 0.00 36.74 2.12
231 240 3.367932 CGTTAGGTGCAACTGTGTGATAG 59.632 47.826 16.44 0.00 36.74 2.08
232 241 3.322369 CGTTAGGTGCAACTGTGTGATA 58.678 45.455 16.44 0.00 36.74 2.15
233 242 2.143122 CGTTAGGTGCAACTGTGTGAT 58.857 47.619 16.44 0.00 36.74 3.06
234 243 1.577468 CGTTAGGTGCAACTGTGTGA 58.423 50.000 16.44 0.00 36.74 3.58
235 244 0.586319 CCGTTAGGTGCAACTGTGTG 59.414 55.000 16.44 0.99 36.74 3.82
236 245 0.534203 CCCGTTAGGTGCAACTGTGT 60.534 55.000 16.44 0.00 36.74 3.72
237 246 1.234615 CCCCGTTAGGTGCAACTGTG 61.235 60.000 16.44 3.41 36.74 3.66
238 247 1.072505 CCCCGTTAGGTGCAACTGT 59.927 57.895 16.44 0.00 36.74 3.55
239 248 2.332654 GCCCCGTTAGGTGCAACTG 61.333 63.158 16.44 0.00 36.74 3.16
252 261 2.033448 TGTGCAACTTAGGCCCCG 59.967 61.111 0.00 0.00 38.04 5.73
273 282 4.861210 TGTGTATGTTTCGGCGAAATTTT 58.139 34.783 34.14 23.58 33.97 1.82
277 286 2.413502 GCATGTGTATGTTTCGGCGAAA 60.414 45.455 29.31 29.31 36.65 3.46
281 290 0.248054 CCGCATGTGTATGTTTCGGC 60.248 55.000 5.38 0.00 36.65 5.54
282 291 0.376852 CCCGCATGTGTATGTTTCGG 59.623 55.000 5.38 0.55 37.27 4.30
292 301 3.130633 TCGAAATTAGATCCCGCATGTG 58.869 45.455 0.00 0.00 0.00 3.21
293 302 3.393800 CTCGAAATTAGATCCCGCATGT 58.606 45.455 0.00 0.00 0.00 3.21
304 313 1.846782 CGACGTGCTCCTCGAAATTAG 59.153 52.381 0.00 0.00 31.24 1.73
307 316 1.805945 GCGACGTGCTCCTCGAAAT 60.806 57.895 10.63 0.00 41.73 2.17
321 330 2.927477 TCACTATTGGAATCGTTGCGAC 59.073 45.455 0.00 0.00 39.18 5.19
325 334 5.086058 CCGTTTTCACTATTGGAATCGTTG 58.914 41.667 4.47 0.00 33.26 4.10
326 335 4.998672 TCCGTTTTCACTATTGGAATCGTT 59.001 37.500 4.47 0.00 33.26 3.85
337 346 7.712264 TCGAAATTAAGTTCCGTTTTCACTA 57.288 32.000 9.88 0.00 0.00 2.74
341 350 5.854338 TGCATCGAAATTAAGTTCCGTTTTC 59.146 36.000 9.88 0.00 0.00 2.29
346 355 3.342269 CGTGCATCGAAATTAAGTTCCG 58.658 45.455 9.88 5.78 42.86 4.30
347 356 3.126343 ACCGTGCATCGAAATTAAGTTCC 59.874 43.478 9.88 0.00 42.86 3.62
350 359 4.331717 CCTAACCGTGCATCGAAATTAAGT 59.668 41.667 9.75 0.00 42.86 2.24
359 368 0.108329 AACTCCCTAACCGTGCATCG 60.108 55.000 0.00 0.00 39.52 3.84
400 410 6.645827 TGTTCTGTTGTGCATTTAATTCATGG 59.354 34.615 0.00 0.00 0.00 3.66
435 445 2.436646 CACGGTCATCCCACTGCC 60.437 66.667 0.00 0.00 0.00 4.85
436 446 2.257409 ATCCACGGTCATCCCACTGC 62.257 60.000 0.00 0.00 0.00 4.40
438 448 1.120530 GTATCCACGGTCATCCCACT 58.879 55.000 0.00 0.00 0.00 4.00
439 449 0.828022 TGTATCCACGGTCATCCCAC 59.172 55.000 0.00 0.00 0.00 4.61
441 451 2.930826 AATGTATCCACGGTCATCCC 57.069 50.000 0.00 0.00 0.00 3.85
476 486 7.588497 AGGAAAGCTTTTCACTTGATTACTT 57.412 32.000 19.71 0.00 0.00 2.24
478 488 9.914131 AATTAGGAAAGCTTTTCACTTGATTAC 57.086 29.630 19.71 0.00 0.00 1.89
479 489 9.912634 CAATTAGGAAAGCTTTTCACTTGATTA 57.087 29.630 19.71 0.00 0.00 1.75
481 491 8.181904 TCAATTAGGAAAGCTTTTCACTTGAT 57.818 30.769 19.71 9.97 0.00 2.57
482 492 7.581213 TCAATTAGGAAAGCTTTTCACTTGA 57.419 32.000 19.71 18.79 0.00 3.02
483 493 7.864307 CTCAATTAGGAAAGCTTTTCACTTG 57.136 36.000 19.71 17.10 0.00 3.16
518 533 5.290885 GCGGCCGATCATTTTAGAAATTTTT 59.709 36.000 33.48 0.00 0.00 1.94
521 536 3.632145 AGCGGCCGATCATTTTAGAAATT 59.368 39.130 33.48 0.00 0.00 1.82
522 537 3.214328 AGCGGCCGATCATTTTAGAAAT 58.786 40.909 33.48 0.00 0.00 2.17
525 540 1.540363 GGAGCGGCCGATCATTTTAGA 60.540 52.381 40.53 0.00 31.28 2.10
527 542 0.179234 TGGAGCGGCCGATCATTTTA 59.821 50.000 40.53 20.24 40.66 1.52
528 543 0.466189 ATGGAGCGGCCGATCATTTT 60.466 50.000 40.53 21.13 40.66 1.82
532 547 4.240103 CCATGGAGCGGCCGATCA 62.240 66.667 40.53 27.76 40.66 2.92
542 557 4.976925 CCCGCTAGCGCCATGGAG 62.977 72.222 31.35 14.87 38.24 3.86
574 590 3.829948 TCACTTTAAAGGACGCGTCTAG 58.170 45.455 35.50 23.38 0.00 2.43
582 598 7.320443 TGCATGTATCATCACTTTAAAGGAC 57.680 36.000 19.14 6.15 0.00 3.85
605 621 2.576287 AAACGCGCGGTGCATGTATG 62.576 55.000 35.22 1.22 46.97 2.39
644 660 5.011635 ACACACAGGAGGAAAAGTTGTTTTT 59.988 36.000 0.00 0.00 41.59 1.94
649 665 3.181487 CCAACACACAGGAGGAAAAGTTG 60.181 47.826 0.00 0.00 35.97 3.16
650 666 3.023832 CCAACACACAGGAGGAAAAGTT 58.976 45.455 0.00 0.00 0.00 2.66
652 668 2.654863 ACCAACACACAGGAGGAAAAG 58.345 47.619 0.00 0.00 0.00 2.27
738 756 1.340568 GAGGGGCGTCTACAAGATACC 59.659 57.143 0.00 0.00 0.00 2.73
741 759 2.116383 CGAGGGGCGTCTACAAGAT 58.884 57.895 0.00 0.00 34.64 2.40
789 811 1.643310 TGGAAATTGGCAGAAAGGGG 58.357 50.000 0.00 0.00 0.00 4.79
837 859 1.139734 GCAACTCTGAGATCGCCGA 59.860 57.895 12.44 0.00 0.00 5.54
919 941 2.782222 GCTCCCGTGCTGGATCGTA 61.782 63.158 0.00 0.00 42.00 3.43
952 974 2.040779 AGGTAGGTAGCTGGGGGC 60.041 66.667 4.27 0.00 42.19 5.80
958 980 2.427245 CGGCAGCAGGTAGGTAGCT 61.427 63.158 0.00 0.00 39.63 3.32
1029 1051 0.179111 TGTGAGCATCGGATTCGGAC 60.179 55.000 0.00 0.00 38.61 4.79
1032 1054 2.002586 ACTTTGTGAGCATCGGATTCG 58.997 47.619 0.00 0.00 38.61 3.34
1101 1123 6.004574 GGGCAGAGTAAGGGGAAAATATTAG 58.995 44.000 0.00 0.00 0.00 1.73
1102 1124 5.163023 GGGGCAGAGTAAGGGGAAAATATTA 60.163 44.000 0.00 0.00 0.00 0.98
1103 1125 4.387550 GGGGCAGAGTAAGGGGAAAATATT 60.388 45.833 0.00 0.00 0.00 1.28
1148 1172 1.754803 TGTCCTATTCCTACGGCAGTG 59.245 52.381 0.00 0.00 0.00 3.66
1149 1173 1.755380 GTGTCCTATTCCTACGGCAGT 59.245 52.381 0.00 0.00 0.00 4.40
1150 1174 1.068741 GGTGTCCTATTCCTACGGCAG 59.931 57.143 0.00 0.00 0.00 4.85
1151 1175 1.117150 GGTGTCCTATTCCTACGGCA 58.883 55.000 0.00 0.00 0.00 5.69
1152 1176 0.391966 GGGTGTCCTATTCCTACGGC 59.608 60.000 0.00 0.00 0.00 5.68
1153 1177 1.784358 TGGGTGTCCTATTCCTACGG 58.216 55.000 0.00 0.00 0.00 4.02
1154 1178 2.764572 AGTTGGGTGTCCTATTCCTACG 59.235 50.000 0.00 0.00 31.97 3.51
1155 1179 3.773119 TCAGTTGGGTGTCCTATTCCTAC 59.227 47.826 0.00 0.00 0.00 3.18
1156 1180 4.030913 CTCAGTTGGGTGTCCTATTCCTA 58.969 47.826 0.00 0.00 0.00 2.94
1157 1181 2.840651 CTCAGTTGGGTGTCCTATTCCT 59.159 50.000 0.00 0.00 0.00 3.36
1158 1182 2.838202 TCTCAGTTGGGTGTCCTATTCC 59.162 50.000 0.00 0.00 0.00 3.01
1164 1188 2.859165 TCATTCTCAGTTGGGTGTCC 57.141 50.000 0.00 0.00 0.00 4.02
1186 1210 4.290722 AGGGGACTTTCTTGTCTCATCAAT 59.709 41.667 0.00 0.00 39.10 2.57
1188 1212 3.008375 CAGGGGACTTTCTTGTCTCATCA 59.992 47.826 0.00 0.00 39.10 3.07
1191 1215 1.699634 CCAGGGGACTTTCTTGTCTCA 59.300 52.381 0.00 0.00 39.10 3.27
1199 1223 4.855340 TCATGTTTATCCAGGGGACTTTC 58.145 43.478 0.00 0.00 40.21 2.62
1203 1227 4.584743 GGAAATCATGTTTATCCAGGGGAC 59.415 45.833 0.00 0.00 32.98 4.46
1205 1229 4.808042 AGGAAATCATGTTTATCCAGGGG 58.192 43.478 14.68 0.00 32.47 4.79
1214 1238 7.248743 ACATGGATTGAAGGAAATCATGTTT 57.751 32.000 0.00 0.00 36.26 2.83
1312 1336 6.127310 GGTCAGAGAGAACACTATGTACCATT 60.127 42.308 0.00 0.00 33.73 3.16
1319 1343 4.629200 GCAAAGGTCAGAGAGAACACTATG 59.371 45.833 0.00 0.00 35.97 2.23
1529 1553 1.002888 CCTAGCGAGATGGCCATGAAT 59.997 52.381 26.56 8.91 0.00 2.57
1559 1583 4.668431 GCTTTTACGCTTACTGTTAGGCAC 60.668 45.833 0.00 0.00 30.61 5.01
1571 1595 3.412237 TTGGGAGTAGCTTTTACGCTT 57.588 42.857 0.00 0.00 41.30 4.68
1576 1600 6.110707 CGGTCTTATTTGGGAGTAGCTTTTA 58.889 40.000 0.00 0.00 0.00 1.52
1581 1605 3.195661 CACGGTCTTATTTGGGAGTAGC 58.804 50.000 0.00 0.00 0.00 3.58
1583 1607 3.833650 TGACACGGTCTTATTTGGGAGTA 59.166 43.478 5.77 0.00 33.15 2.59
1584 1608 2.635915 TGACACGGTCTTATTTGGGAGT 59.364 45.455 5.77 0.00 33.15 3.85
1585 1609 3.328382 TGACACGGTCTTATTTGGGAG 57.672 47.619 5.77 0.00 33.15 4.30
1586 1610 3.773418 TTGACACGGTCTTATTTGGGA 57.227 42.857 5.77 0.00 33.15 4.37
1587 1611 3.427503 GCATTGACACGGTCTTATTTGGG 60.428 47.826 5.77 0.00 33.15 4.12
1595 1619 1.070758 AGTGAAGCATTGACACGGTCT 59.929 47.619 5.77 0.00 33.40 3.85
1598 1622 1.664016 GCAAGTGAAGCATTGACACGG 60.664 52.381 0.00 0.00 33.40 4.94
1605 1629 3.855689 ATTTAGCGCAAGTGAAGCATT 57.144 38.095 11.47 0.00 41.68 3.56
1629 1653 1.065997 ACCCCCTGCAGTAAGTGGTT 61.066 55.000 13.81 0.00 0.00 3.67
1647 1671 1.666189 GCTCAGCCATAGGAAAACGAC 59.334 52.381 0.00 0.00 0.00 4.34
1649 1673 0.652592 CGCTCAGCCATAGGAAAACG 59.347 55.000 0.00 0.00 0.00 3.60
2246 2277 5.363939 TCAAACATCGCCATATATGTCACA 58.636 37.500 11.73 0.00 35.30 3.58
2247 2278 5.922739 TCAAACATCGCCATATATGTCAC 57.077 39.130 11.73 0.46 35.30 3.67
2306 2373 2.993471 GCCCCCGTTGTTGCTGATG 61.993 63.158 0.00 0.00 0.00 3.07
2318 2385 4.462280 GGTAAGTCCACGCCCCCG 62.462 72.222 0.00 0.00 41.14 5.73
2450 2520 2.668550 GCCAGGAACACGGTGGAC 60.669 66.667 13.48 5.74 32.60 4.02
2654 2724 1.751927 CTGCTTCATGGTGAGCCCC 60.752 63.158 12.11 0.00 0.00 5.80
3057 3127 2.975799 GAAGTTGACGGCGCCCAA 60.976 61.111 23.46 17.74 0.00 4.12
3266 3339 2.810852 GAGCAGTTTGGTTCAGAGAAGG 59.189 50.000 0.00 0.00 0.00 3.46
3279 3352 2.717639 ACCACAGTTCAGAGCAGTTT 57.282 45.000 0.00 0.00 0.00 2.66
3317 3390 0.673644 ACAGATTTCTTCCGTGCCCG 60.674 55.000 0.00 0.00 0.00 6.13
3340 3413 1.358046 GATGAATGGCAAGGCGAGC 59.642 57.895 0.00 0.00 0.00 5.03
3362 3435 1.188863 ACCGTGTATACTCCGGCTTT 58.811 50.000 25.00 10.66 45.49 3.51
3395 3468 8.786898 TGAGAAGAAGAATGAGGTAAACATTTG 58.213 33.333 0.00 0.00 37.96 2.32
3452 3526 7.630242 TTAGTTGAAATTAGATGGCTGAAGG 57.370 36.000 0.00 0.00 0.00 3.46
3457 3531 6.434028 TGCTGTTTAGTTGAAATTAGATGGCT 59.566 34.615 0.00 0.00 0.00 4.75
3459 3533 7.538678 GTGTGCTGTTTAGTTGAAATTAGATGG 59.461 37.037 0.00 0.00 0.00 3.51
3477 3551 9.874205 ATAAGCATAAATATTTTTGTGTGCTGT 57.126 25.926 16.72 12.10 38.36 4.40
3496 3570 7.427989 AAACATGAGGGAAAATCATAAGCAT 57.572 32.000 0.00 0.00 35.64 3.79
3500 3574 9.527157 TGTCTAAAACATGAGGGAAAATCATAA 57.473 29.630 0.00 0.00 35.64 1.90
3501 3575 9.699410 ATGTCTAAAACATGAGGGAAAATCATA 57.301 29.630 0.00 0.00 47.00 2.15
3502 3576 8.599624 ATGTCTAAAACATGAGGGAAAATCAT 57.400 30.769 0.00 0.00 47.00 2.45
3516 3590 7.016268 AGGGAAGACTTAGTGATGTCTAAAACA 59.984 37.037 0.00 0.00 42.02 2.83
3517 3591 7.387643 AGGGAAGACTTAGTGATGTCTAAAAC 58.612 38.462 0.00 0.00 42.02 2.43
3518 3592 7.554959 AGGGAAGACTTAGTGATGTCTAAAA 57.445 36.000 0.00 0.00 42.02 1.52
3519 3593 7.554959 AAGGGAAGACTTAGTGATGTCTAAA 57.445 36.000 0.00 0.00 42.02 1.85
3520 3594 8.840200 ATAAGGGAAGACTTAGTGATGTCTAA 57.160 34.615 0.00 0.00 42.02 2.10
3524 3598 9.213777 TCATAATAAGGGAAGACTTAGTGATGT 57.786 33.333 0.00 0.00 36.47 3.06
3530 5787 8.964476 TTTGCTCATAATAAGGGAAGACTTAG 57.036 34.615 0.00 0.00 36.47 2.18
3534 5791 8.056407 AGTTTTTGCTCATAATAAGGGAAGAC 57.944 34.615 0.00 0.00 0.00 3.01
3590 6984 0.683828 TAGTGTCGCCGTCCCCATTA 60.684 55.000 0.00 0.00 0.00 1.90
3592 6986 1.546589 TTTAGTGTCGCCGTCCCCAT 61.547 55.000 0.00 0.00 0.00 4.00
3593 6987 1.546589 ATTTAGTGTCGCCGTCCCCA 61.547 55.000 0.00 0.00 0.00 4.96
3619 7037 6.379579 AGACTTATATTTAGGAACGGAGGGA 58.620 40.000 0.00 0.00 0.00 4.20
3621 7039 8.959705 AAAAGACTTATATTTAGGAACGGAGG 57.040 34.615 0.00 0.00 0.00 4.30
3645 7063 9.701098 ACGTGTAGTCTATTTGAAATGTCTAAA 57.299 29.630 0.00 0.00 0.00 1.85
3648 7066 9.302345 CATACGTGTAGTCTATTTGAAATGTCT 57.698 33.333 0.00 0.00 0.00 3.41
3649 7067 9.084164 ACATACGTGTAGTCTATTTGAAATGTC 57.916 33.333 0.00 0.00 36.63 3.06
3650 7068 8.997621 ACATACGTGTAGTCTATTTGAAATGT 57.002 30.769 0.00 0.00 36.63 2.71
3690 7108 5.446473 CGGAGCAAAATGAGTGAATCTACAC 60.446 44.000 0.00 0.00 40.60 2.90
3691 7109 4.631377 CGGAGCAAAATGAGTGAATCTACA 59.369 41.667 0.00 0.00 0.00 2.74
3692 7110 4.631813 ACGGAGCAAAATGAGTGAATCTAC 59.368 41.667 0.00 0.00 0.00 2.59
3693 7111 4.832248 ACGGAGCAAAATGAGTGAATCTA 58.168 39.130 0.00 0.00 0.00 1.98
3694 7112 3.679389 ACGGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
3695 7113 5.065218 ACATACGGAGCAAAATGAGTGAATC 59.935 40.000 0.00 0.00 0.00 2.52
3696 7114 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
3697 7115 4.323417 ACATACGGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
3698 7116 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
3699 7117 4.870426 ACTACATACGGAGCAAAATGAGTG 59.130 41.667 0.00 0.00 0.00 3.51
3700 7118 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
3701 7119 5.005779 GTGACTACATACGGAGCAAAATGAG 59.994 44.000 0.00 0.00 0.00 2.90
3702 7120 4.868171 GTGACTACATACGGAGCAAAATGA 59.132 41.667 0.00 0.00 0.00 2.57
3703 7121 4.870426 AGTGACTACATACGGAGCAAAATG 59.130 41.667 0.00 0.00 0.00 2.32
3704 7122 5.086104 AGTGACTACATACGGAGCAAAAT 57.914 39.130 0.00 0.00 0.00 1.82
3705 7123 4.530710 AGTGACTACATACGGAGCAAAA 57.469 40.909 0.00 0.00 0.00 2.44
3706 7124 4.242475 CAAGTGACTACATACGGAGCAAA 58.758 43.478 0.00 0.00 0.00 3.68
3707 7125 3.257375 ACAAGTGACTACATACGGAGCAA 59.743 43.478 0.00 0.00 0.00 3.91
3708 7126 2.823747 ACAAGTGACTACATACGGAGCA 59.176 45.455 0.00 0.00 0.00 4.26
3709 7127 3.505464 ACAAGTGACTACATACGGAGC 57.495 47.619 0.00 0.00 0.00 4.70
3710 7128 5.055642 TCAACAAGTGACTACATACGGAG 57.944 43.478 0.00 0.00 0.00 4.63
3711 7129 5.456548 TTCAACAAGTGACTACATACGGA 57.543 39.130 0.00 0.00 35.39 4.69
3712 7130 6.590292 AGATTTCAACAAGTGACTACATACGG 59.410 38.462 0.00 0.00 35.39 4.02
3713 7131 7.542477 AGAGATTTCAACAAGTGACTACATACG 59.458 37.037 0.00 0.00 35.39 3.06
3714 7132 8.764524 AGAGATTTCAACAAGTGACTACATAC 57.235 34.615 0.00 0.00 35.39 2.39
3716 7134 9.778741 TTTAGAGATTTCAACAAGTGACTACAT 57.221 29.630 0.00 0.00 35.39 2.29
3717 7135 9.607988 TTTTAGAGATTTCAACAAGTGACTACA 57.392 29.630 0.00 0.00 35.39 2.74
3720 7138 9.396022 TCTTTTTAGAGATTTCAACAAGTGACT 57.604 29.630 0.00 0.00 35.39 3.41
3721 7139 9.439537 GTCTTTTTAGAGATTTCAACAAGTGAC 57.560 33.333 0.00 0.00 35.39 3.67
3722 7140 9.396022 AGTCTTTTTAGAGATTTCAACAAGTGA 57.604 29.630 0.00 0.00 0.00 3.41
3740 7158 9.392259 CCTCCGTTCCTAAATATAAGTCTTTTT 57.608 33.333 0.00 0.00 0.00 1.94
3741 7159 7.991460 CCCTCCGTTCCTAAATATAAGTCTTTT 59.009 37.037 0.00 0.00 0.00 2.27
3742 7160 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
3743 7161 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
3744 7162 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
3745 7163 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
3746 7164 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
3747 7165 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
3748 7166 7.068702 TGTACTCCCTCCGTTCCTAAATATAA 58.931 38.462 0.00 0.00 0.00 0.98
3749 7167 6.613699 TGTACTCCCTCCGTTCCTAAATATA 58.386 40.000 0.00 0.00 0.00 0.86
3750 7168 5.461327 TGTACTCCCTCCGTTCCTAAATAT 58.539 41.667 0.00 0.00 0.00 1.28
3751 7169 4.870636 TGTACTCCCTCCGTTCCTAAATA 58.129 43.478 0.00 0.00 0.00 1.40
3752 7170 3.716431 TGTACTCCCTCCGTTCCTAAAT 58.284 45.455 0.00 0.00 0.00 1.40
3753 7171 3.173953 TGTACTCCCTCCGTTCCTAAA 57.826 47.619 0.00 0.00 0.00 1.85
3754 7172 2.905415 TGTACTCCCTCCGTTCCTAA 57.095 50.000 0.00 0.00 0.00 2.69
3755 7173 4.210331 GTTATGTACTCCCTCCGTTCCTA 58.790 47.826 0.00 0.00 0.00 2.94
3756 7174 3.029570 GTTATGTACTCCCTCCGTTCCT 58.970 50.000 0.00 0.00 0.00 3.36
3757 7175 2.762327 TGTTATGTACTCCCTCCGTTCC 59.238 50.000 0.00 0.00 0.00 3.62
3758 7176 4.142004 ACATGTTATGTACTCCCTCCGTTC 60.142 45.833 0.00 0.00 42.78 3.95
3759 7177 3.773119 ACATGTTATGTACTCCCTCCGTT 59.227 43.478 0.00 0.00 42.78 4.44
3760 7178 3.371965 ACATGTTATGTACTCCCTCCGT 58.628 45.455 0.00 0.00 42.78 4.69
3766 7184 7.411912 CGCATAAGCATACATGTTATGTACTCC 60.412 40.741 2.30 0.00 42.03 3.85
3767 7185 7.116376 ACGCATAAGCATACATGTTATGTACTC 59.884 37.037 2.30 0.48 42.03 2.59
3768 7186 6.929049 ACGCATAAGCATACATGTTATGTACT 59.071 34.615 2.30 0.00 42.03 2.73
3769 7187 7.117241 ACGCATAAGCATACATGTTATGTAC 57.883 36.000 2.30 0.00 42.03 2.90
3770 7188 7.722795 AACGCATAAGCATACATGTTATGTA 57.277 32.000 2.30 4.33 42.03 2.29
3771 7189 6.618287 AACGCATAAGCATACATGTTATGT 57.382 33.333 2.30 0.00 43.56 2.29
3772 7190 6.578545 GGAAACGCATAAGCATACATGTTATG 59.421 38.462 2.30 6.89 42.27 1.90
3773 7191 6.293955 GGGAAACGCATAAGCATACATGTTAT 60.294 38.462 2.30 0.00 42.27 1.89
3774 7192 5.008217 GGGAAACGCATAAGCATACATGTTA 59.992 40.000 2.30 0.00 42.27 2.41
3792 7211 2.427095 GTTCCATGTGCCATAGGGAAAC 59.573 50.000 9.20 1.19 39.18 2.78
3940 7365 2.800881 TGCGAGGCAGACATATAGTG 57.199 50.000 0.00 0.00 33.32 2.74
3958 7383 3.641437 TTTTTCAATCGCACCCTTCTG 57.359 42.857 0.00 0.00 0.00 3.02
4148 7856 1.209128 CGAGATTGCACGTATGGGAC 58.791 55.000 0.00 0.00 0.00 4.46


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

AutoCloner maintained by Alex Coulton.