Multiple sequence alignment - TraesCS6B01G045400

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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 TraesCS6B01G045400 chr6B 100.000 3149 0 0 1 3149 27066953 27063805 0.000000e+00 5816.0
1 TraesCS6B01G045400 chr6B 93.726 2072 94 13 1086 3148 26688120 26686076 0.000000e+00 3073.0
2 TraesCS6B01G045400 chr6B 85.188 1303 168 18 1086 2369 26488715 26490011 0.000000e+00 1314.0
3 TraesCS6B01G045400 chr6B 80.661 1422 240 29 983 2378 26500510 26501922 0.000000e+00 1070.0
4 TraesCS6B01G045400 chr6B 84.146 82 11 2 3046 3126 164038670 164038750 9.360000e-11 78.7
5 TraesCS6B01G045400 chr6D 86.855 2191 231 25 972 3148 14792591 14790444 0.000000e+00 2398.0
6 TraesCS6B01G045400 chr6D 93.171 1479 71 17 959 2417 14503321 14504789 0.000000e+00 2145.0
7 TraesCS6B01G045400 chr6D 84.065 1732 221 35 972 2678 14727352 14725651 0.000000e+00 1618.0
8 TraesCS6B01G045400 chr6D 81.334 1859 269 53 834 2647 14941311 14939486 0.000000e+00 1439.0
9 TraesCS6B01G045400 chr6D 83.247 1552 208 33 1010 2528 15344826 15343294 0.000000e+00 1378.0
10 TraesCS6B01G045400 chr6D 84.218 1413 181 22 1277 2679 14442271 14443651 0.000000e+00 1336.0
11 TraesCS6B01G045400 chr6D 86.399 1022 105 17 1475 2470 15352522 15351509 0.000000e+00 1086.0
12 TraesCS6B01G045400 chr6D 87.267 911 87 24 1752 2647 15349398 15348502 0.000000e+00 1013.0
13 TraesCS6B01G045400 chr1B 85.255 1587 202 22 972 2528 48062374 48060790 0.000000e+00 1605.0
14 TraesCS6B01G045400 chr5D 85.354 1427 177 22 969 2369 27985513 27984093 0.000000e+00 1448.0
15 TraesCS6B01G045400 chr6A 85.249 1444 165 32 967 2369 15684828 15686264 0.000000e+00 1443.0
16 TraesCS6B01G045400 chr6A 87.377 1117 131 9 1086 2197 15914048 15912937 0.000000e+00 1273.0
17 TraesCS6B01G045400 chr6A 82.630 1399 201 20 834 2213 15925384 15924009 0.000000e+00 1199.0
18 TraesCS6B01G045400 chr6A 85.542 747 94 8 2408 3148 16599043 16599781 0.000000e+00 769.0
19 TraesCS6B01G045400 chr6A 86.562 640 60 13 812 1436 15934818 15934190 0.000000e+00 682.0
20 TraesCS6B01G045400 chr4B 85.490 765 98 8 2391 3148 575727475 575728233 0.000000e+00 785.0


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 TraesCS6B01G045400 chr6B 27063805 27066953 3148 True 5816 5816 100.000000 1 3149 1 chr6B.!!$R2 3148
1 TraesCS6B01G045400 chr6B 26686076 26688120 2044 True 3073 3073 93.726000 1086 3148 1 chr6B.!!$R1 2062
2 TraesCS6B01G045400 chr6B 26488715 26490011 1296 False 1314 1314 85.188000 1086 2369 1 chr6B.!!$F1 1283
3 TraesCS6B01G045400 chr6B 26500510 26501922 1412 False 1070 1070 80.661000 983 2378 1 chr6B.!!$F2 1395
4 TraesCS6B01G045400 chr6D 14790444 14792591 2147 True 2398 2398 86.855000 972 3148 1 chr6D.!!$R2 2176
5 TraesCS6B01G045400 chr6D 14503321 14504789 1468 False 2145 2145 93.171000 959 2417 1 chr6D.!!$F2 1458
6 TraesCS6B01G045400 chr6D 14725651 14727352 1701 True 1618 1618 84.065000 972 2678 1 chr6D.!!$R1 1706
7 TraesCS6B01G045400 chr6D 14939486 14941311 1825 True 1439 1439 81.334000 834 2647 1 chr6D.!!$R3 1813
8 TraesCS6B01G045400 chr6D 14442271 14443651 1380 False 1336 1336 84.218000 1277 2679 1 chr6D.!!$F1 1402
9 TraesCS6B01G045400 chr6D 15343294 15352522 9228 True 1159 1378 85.637667 1010 2647 3 chr6D.!!$R4 1637
10 TraesCS6B01G045400 chr1B 48060790 48062374 1584 True 1605 1605 85.255000 972 2528 1 chr1B.!!$R1 1556
11 TraesCS6B01G045400 chr5D 27984093 27985513 1420 True 1448 1448 85.354000 969 2369 1 chr5D.!!$R1 1400
12 TraesCS6B01G045400 chr6A 15684828 15686264 1436 False 1443 1443 85.249000 967 2369 1 chr6A.!!$F1 1402
13 TraesCS6B01G045400 chr6A 15912937 15914048 1111 True 1273 1273 87.377000 1086 2197 1 chr6A.!!$R1 1111
14 TraesCS6B01G045400 chr6A 15924009 15925384 1375 True 1199 1199 82.630000 834 2213 1 chr6A.!!$R2 1379
15 TraesCS6B01G045400 chr6A 16599043 16599781 738 False 769 769 85.542000 2408 3148 1 chr6A.!!$F2 740
16 TraesCS6B01G045400 chr6A 15934190 15934818 628 True 682 682 86.562000 812 1436 1 chr6A.!!$R3 624
17 TraesCS6B01G045400 chr4B 575727475 575728233 758 False 785 785 85.490000 2391 3148 1 chr4B.!!$F1 757

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
167 168 0.107654 GCTTCCCATACCGCACTCTT 60.108 55.0 0.0 0.0 0.00 2.85 F
807 808 0.251165 GAAGCACAAAGGTAGGCCCA 60.251 55.0 0.0 0.0 34.66 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1041 7729 0.255318 ATGCAGCTTTGGAGGGAGAG 59.745 55.0 0.0 0.0 0.00 3.20 R
2783 9604 0.033503 GGGATGGTTACCCCTGTTGG 60.034 60.0 0.0 0.0 41.38 3.77 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
32 33 4.710324 TGGAACAAAGTACCTGTTAGTGG 58.290 43.478 10.15 0.00 37.14 4.00
33 34 4.409574 TGGAACAAAGTACCTGTTAGTGGA 59.590 41.667 10.15 0.00 37.14 4.02
34 35 5.104444 TGGAACAAAGTACCTGTTAGTGGAA 60.104 40.000 10.15 0.00 37.14 3.53
35 36 5.824097 GGAACAAAGTACCTGTTAGTGGAAA 59.176 40.000 10.15 0.00 37.14 3.13
36 37 6.319405 GGAACAAAGTACCTGTTAGTGGAAAA 59.681 38.462 10.15 0.00 37.14 2.29
37 38 7.148035 GGAACAAAGTACCTGTTAGTGGAAAAA 60.148 37.037 10.15 0.00 37.14 1.94
66 67 9.706691 TCTCCACTTTTATAAGTAGTGTCAAAG 57.293 33.333 19.88 14.23 42.67 2.77
67 68 9.706691 CTCCACTTTTATAAGTAGTGTCAAAGA 57.293 33.333 19.88 12.71 42.67 2.52
77 78 9.793259 ATAAGTAGTGTCAAAGAAAAAGATCCA 57.207 29.630 0.00 0.00 0.00 3.41
79 80 5.444663 AGTGTCAAAGAAAAAGATCCAGC 57.555 39.130 0.00 0.00 0.00 4.85
80 81 5.136105 AGTGTCAAAGAAAAAGATCCAGCT 58.864 37.500 0.00 0.00 0.00 4.24
83 84 4.279420 GTCAAAGAAAAAGATCCAGCTGGT 59.721 41.667 31.58 19.20 36.34 4.00
84 85 4.895297 TCAAAGAAAAAGATCCAGCTGGTT 59.105 37.500 31.58 24.29 36.34 3.67
87 88 4.473444 AGAAAAAGATCCAGCTGGTTTGA 58.527 39.130 31.58 13.76 36.34 2.69
88 89 4.895297 AGAAAAAGATCCAGCTGGTTTGAA 59.105 37.500 31.58 13.35 36.34 2.69
90 91 3.515602 AAGATCCAGCTGGTTTGAAGT 57.484 42.857 31.58 9.61 36.34 3.01
92 93 2.087646 GATCCAGCTGGTTTGAAGTCC 58.912 52.381 31.58 6.65 36.34 3.85
93 94 1.140312 TCCAGCTGGTTTGAAGTCCT 58.860 50.000 31.58 0.00 36.34 3.85
94 95 1.072331 TCCAGCTGGTTTGAAGTCCTC 59.928 52.381 31.58 0.00 36.34 3.71
95 96 1.202806 CCAGCTGGTTTGAAGTCCTCA 60.203 52.381 25.53 0.00 0.00 3.86
96 97 1.876156 CAGCTGGTTTGAAGTCCTCAC 59.124 52.381 5.57 0.00 32.21 3.51
99 100 2.833794 CTGGTTTGAAGTCCTCACGAA 58.166 47.619 0.00 0.00 32.21 3.85
121 122 9.912634 ACGAATGTGAATTTGATTTCTTATTGT 57.087 25.926 0.00 0.00 0.00 2.71
149 150 4.514781 AAACAGAAATCGTTTTAGGGGC 57.485 40.909 0.00 0.00 32.76 5.80
150 151 3.434940 ACAGAAATCGTTTTAGGGGCT 57.565 42.857 0.00 0.00 0.00 5.19
151 152 3.763057 ACAGAAATCGTTTTAGGGGCTT 58.237 40.909 0.00 0.00 0.00 4.35
152 153 3.756963 ACAGAAATCGTTTTAGGGGCTTC 59.243 43.478 0.00 0.00 0.00 3.86
153 154 3.128764 CAGAAATCGTTTTAGGGGCTTCC 59.871 47.826 0.00 0.00 0.00 3.46
164 165 2.590092 GGCTTCCCATACCGCACT 59.410 61.111 0.00 0.00 0.00 4.40
165 166 1.523938 GGCTTCCCATACCGCACTC 60.524 63.158 0.00 0.00 0.00 3.51
166 167 1.522569 GCTTCCCATACCGCACTCT 59.477 57.895 0.00 0.00 0.00 3.24
167 168 0.107654 GCTTCCCATACCGCACTCTT 60.108 55.000 0.00 0.00 0.00 2.85
168 169 1.679032 GCTTCCCATACCGCACTCTTT 60.679 52.381 0.00 0.00 0.00 2.52
170 171 3.869065 CTTCCCATACCGCACTCTTTAA 58.131 45.455 0.00 0.00 0.00 1.52
171 172 3.985019 TCCCATACCGCACTCTTTAAA 57.015 42.857 0.00 0.00 0.00 1.52
172 173 4.289238 TCCCATACCGCACTCTTTAAAA 57.711 40.909 0.00 0.00 0.00 1.52
173 174 4.653868 TCCCATACCGCACTCTTTAAAAA 58.346 39.130 0.00 0.00 0.00 1.94
231 232 7.675161 ATAGAAAATGGACCAAAAATAGGGG 57.325 36.000 0.00 0.00 0.00 4.79
232 233 5.660533 AGAAAATGGACCAAAAATAGGGGA 58.339 37.500 0.00 0.00 0.00 4.81
234 235 6.560687 AGAAAATGGACCAAAAATAGGGGAAA 59.439 34.615 0.00 0.00 0.00 3.13
235 236 6.968400 AAATGGACCAAAAATAGGGGAAAT 57.032 33.333 0.00 0.00 0.00 2.17
236 237 8.456221 AAAATGGACCAAAAATAGGGGAAATA 57.544 30.769 0.00 0.00 0.00 1.40
237 238 8.456221 AAATGGACCAAAAATAGGGGAAATAA 57.544 30.769 0.00 0.00 0.00 1.40
238 239 8.637108 AATGGACCAAAAATAGGGGAAATAAT 57.363 30.769 0.00 0.00 0.00 1.28
239 240 9.736819 AATGGACCAAAAATAGGGGAAATAATA 57.263 29.630 0.00 0.00 0.00 0.98
240 241 9.736819 ATGGACCAAAAATAGGGGAAATAATAA 57.263 29.630 0.00 0.00 0.00 1.40
241 242 9.562226 TGGACCAAAAATAGGGGAAATAATAAA 57.438 29.630 0.00 0.00 0.00 1.40
377 378 8.525290 ACATAGAAAGATGGACCAAAATTAGG 57.475 34.615 0.00 0.00 0.00 2.69
378 379 8.336235 ACATAGAAAGATGGACCAAAATTAGGA 58.664 33.333 0.00 0.00 0.00 2.94
380 381 9.768215 ATAGAAAGATGGACCAAAATTAGGAAA 57.232 29.630 0.00 0.00 0.00 3.13
381 382 8.491045 AGAAAGATGGACCAAAATTAGGAAAA 57.509 30.769 0.00 0.00 0.00 2.29
409 410 9.871175 AATAAAAGGGTAACTAGGAAAGTGAAA 57.129 29.630 0.00 0.00 38.88 2.69
410 411 9.871175 ATAAAAGGGTAACTAGGAAAGTGAAAA 57.129 29.630 0.00 0.00 38.88 2.29
412 413 6.758806 AGGGTAACTAGGAAAGTGAAAAGA 57.241 37.500 0.00 0.00 38.88 2.52
415 416 8.057011 AGGGTAACTAGGAAAGTGAAAAGAAAA 58.943 33.333 0.00 0.00 38.88 2.29
416 417 8.350722 GGGTAACTAGGAAAGTGAAAAGAAAAG 58.649 37.037 0.00 0.00 38.88 2.27
417 418 9.117183 GGTAACTAGGAAAGTGAAAAGAAAAGA 57.883 33.333 0.00 0.00 38.88 2.52
420 421 9.634021 AACTAGGAAAGTGAAAAGAAAAGAGAT 57.366 29.630 0.00 0.00 38.88 2.75
421 422 9.061435 ACTAGGAAAGTGAAAAGAAAAGAGATG 57.939 33.333 0.00 0.00 36.93 2.90
422 423 7.282332 AGGAAAGTGAAAAGAAAAGAGATGG 57.718 36.000 0.00 0.00 0.00 3.51
423 424 7.062957 AGGAAAGTGAAAAGAAAAGAGATGGA 58.937 34.615 0.00 0.00 0.00 3.41
424 425 7.727634 AGGAAAGTGAAAAGAAAAGAGATGGAT 59.272 33.333 0.00 0.00 0.00 3.41
425 426 9.014297 GGAAAGTGAAAAGAAAAGAGATGGATA 57.986 33.333 0.00 0.00 0.00 2.59
429 430 9.354673 AGTGAAAAGAAAAGAGATGGATAAACA 57.645 29.630 0.00 0.00 0.00 2.83
430 431 9.617975 GTGAAAAGAAAAGAGATGGATAAACAG 57.382 33.333 0.00 0.00 0.00 3.16
431 432 9.354673 TGAAAAGAAAAGAGATGGATAAACAGT 57.645 29.630 0.00 0.00 0.00 3.55
489 490 7.856145 AACTGGAAAACAAATTTATTGCACA 57.144 28.000 0.00 0.00 0.00 4.57
491 492 8.273780 ACTGGAAAACAAATTTATTGCACAAA 57.726 26.923 0.00 0.00 0.00 2.83
492 493 8.734386 ACTGGAAAACAAATTTATTGCACAAAA 58.266 25.926 0.00 0.00 0.00 2.44
493 494 9.224058 CTGGAAAACAAATTTATTGCACAAAAG 57.776 29.630 0.00 0.00 0.00 2.27
494 495 8.734386 TGGAAAACAAATTTATTGCACAAAAGT 58.266 25.926 0.00 0.00 0.00 2.66
559 560 8.528044 AAATGGTAACTAGGAAAGTGAAAACA 57.472 30.769 0.00 0.00 38.88 2.83
561 562 7.941431 TGGTAACTAGGAAAGTGAAAACAAA 57.059 32.000 0.00 0.00 38.88 2.83
641 642 8.940952 TGAATGAAAAACAAAACAAAAGTAGGG 58.059 29.630 0.00 0.00 0.00 3.53
643 644 9.508642 AATGAAAAACAAAACAAAAGTAGGGAA 57.491 25.926 0.00 0.00 0.00 3.97
644 645 8.904099 TGAAAAACAAAACAAAAGTAGGGAAA 57.096 26.923 0.00 0.00 0.00 3.13
645 646 9.338622 TGAAAAACAAAACAAAAGTAGGGAAAA 57.661 25.926 0.00 0.00 0.00 2.29
649 650 9.562408 AAACAAAACAAAAGTAGGGAAAAAGAA 57.438 25.926 0.00 0.00 0.00 2.52
650 651 9.562408 AACAAAACAAAAGTAGGGAAAAAGAAA 57.438 25.926 0.00 0.00 0.00 2.52
651 652 9.562408 ACAAAACAAAAGTAGGGAAAAAGAAAA 57.438 25.926 0.00 0.00 0.00 2.29
654 655 7.490657 ACAAAAGTAGGGAAAAAGAAAACCT 57.509 32.000 0.00 0.00 35.37 3.50
655 656 7.553334 ACAAAAGTAGGGAAAAAGAAAACCTC 58.447 34.615 0.00 0.00 32.87 3.85
656 657 7.179516 ACAAAAGTAGGGAAAAAGAAAACCTCA 59.820 33.333 0.00 0.00 32.87 3.86
658 659 6.901081 AGTAGGGAAAAAGAAAACCTCATG 57.099 37.500 0.00 0.00 32.87 3.07
659 660 4.607293 AGGGAAAAAGAAAACCTCATGC 57.393 40.909 0.00 0.00 0.00 4.06
661 662 5.393866 AGGGAAAAAGAAAACCTCATGCTA 58.606 37.500 0.00 0.00 0.00 3.49
662 663 5.838521 AGGGAAAAAGAAAACCTCATGCTAA 59.161 36.000 0.00 0.00 0.00 3.09
664 665 6.239317 GGGAAAAAGAAAACCTCATGCTAACT 60.239 38.462 0.00 0.00 0.00 2.24
665 666 7.039993 GGGAAAAAGAAAACCTCATGCTAACTA 60.040 37.037 0.00 0.00 0.00 2.24
667 668 9.744468 GAAAAAGAAAACCTCATGCTAACTAAA 57.256 29.630 0.00 0.00 0.00 1.85
668 669 9.529325 AAAAAGAAAACCTCATGCTAACTAAAC 57.471 29.630 0.00 0.00 0.00 2.01
670 671 7.440523 AGAAAACCTCATGCTAACTAAACTG 57.559 36.000 0.00 0.00 0.00 3.16
671 672 6.431234 AGAAAACCTCATGCTAACTAAACTGG 59.569 38.462 0.00 0.00 0.00 4.00
673 674 4.833390 ACCTCATGCTAACTAAACTGGAC 58.167 43.478 0.00 0.00 0.00 4.02
674 675 4.192317 CCTCATGCTAACTAAACTGGACC 58.808 47.826 0.00 0.00 0.00 4.46
675 676 3.857052 TCATGCTAACTAAACTGGACCG 58.143 45.455 0.00 0.00 0.00 4.79
677 678 4.020928 TCATGCTAACTAAACTGGACCGAA 60.021 41.667 0.00 0.00 0.00 4.30
678 679 3.656559 TGCTAACTAAACTGGACCGAAC 58.343 45.455 0.00 0.00 0.00 3.95
680 681 3.431233 GCTAACTAAACTGGACCGAACAC 59.569 47.826 0.00 0.00 0.00 3.32
683 684 4.081322 ACTAAACTGGACCGAACACAAT 57.919 40.909 0.00 0.00 0.00 2.71
684 685 5.217978 ACTAAACTGGACCGAACACAATA 57.782 39.130 0.00 0.00 0.00 1.90
685 686 4.992951 ACTAAACTGGACCGAACACAATAC 59.007 41.667 0.00 0.00 0.00 1.89
686 687 3.478857 AACTGGACCGAACACAATACA 57.521 42.857 0.00 0.00 0.00 2.29
687 688 3.478857 ACTGGACCGAACACAATACAA 57.521 42.857 0.00 0.00 0.00 2.41
688 689 3.135994 ACTGGACCGAACACAATACAAC 58.864 45.455 0.00 0.00 0.00 3.32
690 691 3.542648 TGGACCGAACACAATACAACAA 58.457 40.909 0.00 0.00 0.00 2.83
691 692 3.945921 TGGACCGAACACAATACAACAAA 59.054 39.130 0.00 0.00 0.00 2.83
692 693 4.398358 TGGACCGAACACAATACAACAAAA 59.602 37.500 0.00 0.00 0.00 2.44
693 694 4.973663 GGACCGAACACAATACAACAAAAG 59.026 41.667 0.00 0.00 0.00 2.27
694 695 5.449451 GGACCGAACACAATACAACAAAAGT 60.449 40.000 0.00 0.00 0.00 2.66
695 696 5.336744 ACCGAACACAATACAACAAAAGTG 58.663 37.500 0.00 0.00 0.00 3.16
696 697 5.124138 ACCGAACACAATACAACAAAAGTGA 59.876 36.000 0.00 0.00 0.00 3.41
697 698 6.030849 CCGAACACAATACAACAAAAGTGAA 58.969 36.000 0.00 0.00 0.00 3.18
698 699 6.695278 CCGAACACAATACAACAAAAGTGAAT 59.305 34.615 0.00 0.00 0.00 2.57
701 702 7.754069 ACACAATACAACAAAAGTGAATGTG 57.246 32.000 0.00 0.00 40.05 3.21
702 703 6.756074 ACACAATACAACAAAAGTGAATGTGG 59.244 34.615 0.00 0.00 38.89 4.17
703 704 6.977502 CACAATACAACAAAAGTGAATGTGGA 59.022 34.615 0.00 0.00 32.91 4.02
705 706 8.203485 ACAATACAACAAAAGTGAATGTGGAAT 58.797 29.630 0.00 0.00 32.91 3.01
706 707 9.689976 CAATACAACAAAAGTGAATGTGGAATA 57.310 29.630 0.00 0.00 32.91 1.75
711 712 9.426837 CAACAAAAGTGAATGTGGAATATCATT 57.573 29.630 0.00 0.00 37.04 2.57
758 759 6.912203 TTTTGTCTAAACATTCGACTCACA 57.088 33.333 0.00 0.00 34.73 3.58
759 760 6.912203 TTTGTCTAAACATTCGACTCACAA 57.088 33.333 0.00 0.00 34.73 3.33
760 761 6.912203 TTGTCTAAACATTCGACTCACAAA 57.088 33.333 0.00 0.00 34.73 2.83
761 762 6.912203 TGTCTAAACATTCGACTCACAAAA 57.088 33.333 0.00 0.00 0.00 2.44
762 763 7.310072 TGTCTAAACATTCGACTCACAAAAA 57.690 32.000 0.00 0.00 0.00 1.94
779 780 3.391506 AAAAAGCAAGACATGAAGGCC 57.608 42.857 0.00 0.00 0.00 5.19
780 781 1.999648 AAAGCAAGACATGAAGGCCA 58.000 45.000 5.01 0.00 0.00 5.36
781 782 1.999648 AAGCAAGACATGAAGGCCAA 58.000 45.000 5.01 0.00 0.00 4.52
782 783 1.251251 AGCAAGACATGAAGGCCAAC 58.749 50.000 5.01 0.00 0.00 3.77
783 784 1.202976 AGCAAGACATGAAGGCCAACT 60.203 47.619 5.01 0.00 0.00 3.16
784 785 1.068055 GCAAGACATGAAGGCCAACTG 60.068 52.381 5.01 0.00 0.00 3.16
785 786 1.542915 CAAGACATGAAGGCCAACTGG 59.457 52.381 5.01 0.00 38.53 4.00
795 796 2.594303 CCAACTGGCCGAAGCACA 60.594 61.111 0.00 0.00 42.56 4.57
797 798 1.732917 CAACTGGCCGAAGCACAAA 59.267 52.632 0.00 0.00 42.56 2.83
798 799 0.318107 CAACTGGCCGAAGCACAAAG 60.318 55.000 0.00 0.00 42.56 2.77
799 800 1.455383 AACTGGCCGAAGCACAAAGG 61.455 55.000 0.00 0.00 42.56 3.11
801 802 0.605319 CTGGCCGAAGCACAAAGGTA 60.605 55.000 0.00 0.00 42.56 3.08
802 803 0.605319 TGGCCGAAGCACAAAGGTAG 60.605 55.000 0.00 0.00 42.56 3.18
803 804 1.305930 GGCCGAAGCACAAAGGTAGG 61.306 60.000 0.00 0.00 42.56 3.18
804 805 1.923227 GCCGAAGCACAAAGGTAGGC 61.923 60.000 0.00 0.00 41.89 3.93
805 806 1.305930 CCGAAGCACAAAGGTAGGCC 61.306 60.000 0.00 0.00 0.00 5.19
806 807 1.305930 CGAAGCACAAAGGTAGGCCC 61.306 60.000 0.00 0.00 34.57 5.80
807 808 0.251165 GAAGCACAAAGGTAGGCCCA 60.251 55.000 0.00 0.00 34.66 5.36
808 809 0.409484 AAGCACAAAGGTAGGCCCAT 59.591 50.000 0.00 0.00 34.66 4.00
809 810 0.409484 AGCACAAAGGTAGGCCCATT 59.591 50.000 0.00 0.00 34.66 3.16
811 812 2.042433 AGCACAAAGGTAGGCCCATTAA 59.958 45.455 0.00 0.00 34.66 1.40
812 813 2.829120 GCACAAAGGTAGGCCCATTAAA 59.171 45.455 0.00 0.00 34.66 1.52
814 815 3.829601 CACAAAGGTAGGCCCATTAAACA 59.170 43.478 0.00 0.00 34.66 2.83
815 816 4.466015 CACAAAGGTAGGCCCATTAAACAT 59.534 41.667 0.00 0.00 34.66 2.71
817 818 4.601406 AAGGTAGGCCCATTAAACATCA 57.399 40.909 0.00 0.00 34.66 3.07
819 820 5.922960 AGGTAGGCCCATTAAACATCATA 57.077 39.130 0.00 0.00 34.66 2.15
820 821 5.880901 AGGTAGGCCCATTAAACATCATAG 58.119 41.667 0.00 0.00 34.66 2.23
822 823 6.068670 GGTAGGCCCATTAAACATCATAGTT 58.931 40.000 0.00 0.00 0.00 2.24
1041 7729 3.265479 CCATCCTTTCCCATATCCTCTCC 59.735 52.174 0.00 0.00 0.00 3.71
1072 7766 0.694771 AGCTGCATTCTTCCCACTCA 59.305 50.000 1.02 0.00 0.00 3.41
1080 7774 3.249189 TTCCCACTCAGCCGCCTT 61.249 61.111 0.00 0.00 0.00 4.35
1918 8643 2.971660 TGCTCATCGACCGGAAATAA 57.028 45.000 9.46 0.00 0.00 1.40
2302 9058 5.335976 GCTTGTTGCTAAATGCTAACTCCTT 60.336 40.000 0.00 0.00 43.37 3.36
2303 9059 6.128007 GCTTGTTGCTAAATGCTAACTCCTTA 60.128 38.462 0.00 0.00 43.37 2.69
2440 9221 5.128919 AGATCTTGGAAACTGGATATGTGC 58.871 41.667 0.00 0.00 0.00 4.57
2480 9262 4.734398 TGAACCAAGCATTCACAAAACT 57.266 36.364 0.00 0.00 31.11 2.66
2504 9286 6.635030 AGAAACCAAAAGAGTAATGTGGTC 57.365 37.500 0.00 0.00 41.74 4.02
2532 9314 7.696453 CGTTTTCCACCAAAATGTATCAGTATC 59.304 37.037 0.00 0.00 36.35 2.24
2535 9317 8.821686 TTCCACCAAAATGTATCAGTATCATT 57.178 30.769 0.00 0.00 33.94 2.57
2559 9341 6.497785 TGCTTCCATGCCAAAATTTATTTG 57.502 33.333 0.00 0.00 0.00 2.32
2570 9352 6.743627 GCCAAAATTTATTTGTCATGCATGTG 59.256 34.615 25.43 11.61 0.00 3.21
2607 9396 9.209048 TCCTTATCTTTTAGCTTCCACTGTATA 57.791 33.333 0.00 0.00 0.00 1.47
2691 9481 2.039216 TGTTGTCCACCCGTTACATGAT 59.961 45.455 0.00 0.00 0.00 2.45
2704 9494 5.067936 CCGTTACATGATACTGAGACCTTCT 59.932 44.000 0.00 0.00 0.00 2.85
2707 9526 3.133721 ACATGATACTGAGACCTTCTGCC 59.866 47.826 0.00 0.00 0.00 4.85
2708 9527 1.751351 TGATACTGAGACCTTCTGCCG 59.249 52.381 0.00 0.00 0.00 5.69
2709 9528 1.067821 GATACTGAGACCTTCTGCCGG 59.932 57.143 0.00 0.00 0.00 6.13
2712 9531 0.671781 CTGAGACCTTCTGCCGGTTG 60.672 60.000 1.90 0.00 34.19 3.77
2713 9532 1.371558 GAGACCTTCTGCCGGTTGT 59.628 57.895 1.90 0.00 34.19 3.32
2714 9533 0.670854 GAGACCTTCTGCCGGTTGTC 60.671 60.000 1.90 1.23 34.19 3.18
2715 9534 1.671379 GACCTTCTGCCGGTTGTCC 60.671 63.158 1.90 0.00 34.19 4.02
2716 9535 2.391724 GACCTTCTGCCGGTTGTCCA 62.392 60.000 1.90 0.00 34.19 4.02
2717 9536 1.002134 CCTTCTGCCGGTTGTCCAT 60.002 57.895 1.90 0.00 0.00 3.41
2718 9537 0.609131 CCTTCTGCCGGTTGTCCATT 60.609 55.000 1.90 0.00 0.00 3.16
2719 9538 0.804989 CTTCTGCCGGTTGTCCATTC 59.195 55.000 1.90 0.00 0.00 2.67
2720 9539 0.400213 TTCTGCCGGTTGTCCATTCT 59.600 50.000 1.90 0.00 0.00 2.40
2721 9540 1.271856 TCTGCCGGTTGTCCATTCTA 58.728 50.000 1.90 0.00 0.00 2.10
2722 9541 1.626321 TCTGCCGGTTGTCCATTCTAA 59.374 47.619 1.90 0.00 0.00 2.10
2723 9542 1.737793 CTGCCGGTTGTCCATTCTAAC 59.262 52.381 1.90 0.00 0.00 2.34
2724 9543 1.072489 TGCCGGTTGTCCATTCTAACA 59.928 47.619 1.90 0.00 0.00 2.41
2725 9544 2.290641 TGCCGGTTGTCCATTCTAACAT 60.291 45.455 1.90 0.00 0.00 2.71
2726 9545 3.055021 TGCCGGTTGTCCATTCTAACATA 60.055 43.478 1.90 0.00 0.00 2.29
2727 9546 3.942748 GCCGGTTGTCCATTCTAACATAA 59.057 43.478 1.90 0.00 0.00 1.90
2728 9547 4.396790 GCCGGTTGTCCATTCTAACATAAA 59.603 41.667 1.90 0.00 0.00 1.40
2729 9548 5.448632 GCCGGTTGTCCATTCTAACATAAAG 60.449 44.000 1.90 0.00 0.00 1.85
2730 9549 5.878116 CCGGTTGTCCATTCTAACATAAAGA 59.122 40.000 0.00 0.00 0.00 2.52
2731 9550 6.037172 CCGGTTGTCCATTCTAACATAAAGAG 59.963 42.308 0.00 0.00 0.00 2.85
2732 9551 6.594159 CGGTTGTCCATTCTAACATAAAGAGT 59.406 38.462 0.00 0.00 0.00 3.24
2733 9552 7.413000 CGGTTGTCCATTCTAACATAAAGAGTG 60.413 40.741 0.00 0.00 32.22 3.51
2734 9553 7.148239 GGTTGTCCATTCTAACATAAAGAGTGG 60.148 40.741 8.00 8.00 46.75 4.00
2735 9554 5.880332 TGTCCATTCTAACATAAAGAGTGGC 59.120 40.000 9.15 6.13 45.63 5.01
2736 9555 5.880332 GTCCATTCTAACATAAAGAGTGGCA 59.120 40.000 9.15 0.00 45.63 4.92
2737 9556 6.374333 GTCCATTCTAACATAAAGAGTGGCAA 59.626 38.462 9.15 0.00 45.63 4.52
2783 9604 5.897050 TGTTTCCTGGTTGTGTTTAATGAC 58.103 37.500 0.00 0.00 0.00 3.06
2816 9637 0.179100 CATCCCTGCTACTGTCACCG 60.179 60.000 0.00 0.00 0.00 4.94
2914 9736 7.661040 AGAAAATTGCAGCAACTAGTTGTATT 58.339 30.769 30.90 20.12 42.31 1.89
3148 9979 1.136828 AGAGTGTTGTGCCTGGGTTA 58.863 50.000 0.00 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 8.983702 AACAGGTACTTTGTTCCAAATAGTAA 57.016 30.769 9.52 0.00 34.60 2.24
5 6 8.504005 CACTAACAGGTACTTTGTTCCAAATAG 58.496 37.037 16.06 11.11 39.36 1.73
10 11 4.409574 TCCACTAACAGGTACTTTGTTCCA 59.590 41.667 16.06 3.89 39.36 3.53
11 12 4.964593 TCCACTAACAGGTACTTTGTTCC 58.035 43.478 16.06 0.00 39.36 3.62
12 13 6.930667 TTTCCACTAACAGGTACTTTGTTC 57.069 37.500 16.06 0.00 39.36 3.18
40 41 9.706691 CTTTGACACTACTTATAAAAGTGGAGA 57.293 33.333 22.33 10.94 44.62 3.71
41 42 9.706691 TCTTTGACACTACTTATAAAAGTGGAG 57.293 33.333 22.33 16.34 44.62 3.86
51 52 9.793259 TGGATCTTTTTCTTTGACACTACTTAT 57.207 29.630 0.00 0.00 0.00 1.73
52 53 9.273016 CTGGATCTTTTTCTTTGACACTACTTA 57.727 33.333 0.00 0.00 0.00 2.24
53 54 7.255277 GCTGGATCTTTTTCTTTGACACTACTT 60.255 37.037 0.00 0.00 0.00 2.24
54 55 6.205658 GCTGGATCTTTTTCTTTGACACTACT 59.794 38.462 0.00 0.00 0.00 2.57
57 58 5.009410 CAGCTGGATCTTTTTCTTTGACACT 59.991 40.000 5.57 0.00 0.00 3.55
58 59 5.218139 CAGCTGGATCTTTTTCTTTGACAC 58.782 41.667 5.57 0.00 0.00 3.67
59 60 4.279169 CCAGCTGGATCTTTTTCTTTGACA 59.721 41.667 29.88 0.00 37.39 3.58
61 62 4.473444 ACCAGCTGGATCTTTTTCTTTGA 58.527 39.130 39.19 0.00 38.94 2.69
63 64 5.363580 TCAAACCAGCTGGATCTTTTTCTTT 59.636 36.000 39.19 21.27 38.94 2.52
66 67 4.853924 TCAAACCAGCTGGATCTTTTTC 57.146 40.909 39.19 0.00 38.94 2.29
67 68 4.651045 ACTTCAAACCAGCTGGATCTTTTT 59.349 37.500 39.19 24.15 38.94 1.94
68 69 4.218312 ACTTCAAACCAGCTGGATCTTTT 58.782 39.130 39.19 24.53 38.94 2.27
69 70 3.823304 GACTTCAAACCAGCTGGATCTTT 59.177 43.478 39.19 24.89 38.94 2.52
70 71 3.416156 GACTTCAAACCAGCTGGATCTT 58.584 45.455 39.19 23.82 38.94 2.40
71 72 2.290577 GGACTTCAAACCAGCTGGATCT 60.291 50.000 39.19 19.43 38.94 2.75
73 74 1.707427 AGGACTTCAAACCAGCTGGAT 59.293 47.619 39.19 25.96 38.94 3.41
75 76 1.202806 TGAGGACTTCAAACCAGCTGG 60.203 52.381 31.60 31.60 35.30 4.85
77 78 1.541233 CGTGAGGACTTCAAACCAGCT 60.541 52.381 0.00 0.00 37.61 4.24
79 80 2.526304 TCGTGAGGACTTCAAACCAG 57.474 50.000 0.00 0.00 37.61 4.00
80 81 2.992124 TTCGTGAGGACTTCAAACCA 57.008 45.000 0.00 0.00 37.61 3.67
95 96 9.912634 ACAATAAGAAATCAAATTCACATTCGT 57.087 25.926 0.00 0.00 0.00 3.85
126 127 5.069914 AGCCCCTAAAACGATTTCTGTTTTT 59.930 36.000 8.85 0.00 44.69 1.94
128 129 4.149598 AGCCCCTAAAACGATTTCTGTTT 58.850 39.130 0.00 0.00 41.07 2.83
129 130 3.763057 AGCCCCTAAAACGATTTCTGTT 58.237 40.909 0.00 0.00 0.00 3.16
130 131 3.434940 AGCCCCTAAAACGATTTCTGT 57.565 42.857 0.00 0.00 0.00 3.41
132 133 3.353557 GGAAGCCCCTAAAACGATTTCT 58.646 45.455 0.00 0.00 0.00 2.52
133 134 3.777465 GGAAGCCCCTAAAACGATTTC 57.223 47.619 0.00 0.00 0.00 2.17
146 147 2.516225 GTGCGGTATGGGAAGCCC 60.516 66.667 0.00 0.00 45.71 5.19
147 148 1.523938 GAGTGCGGTATGGGAAGCC 60.524 63.158 0.00 0.00 0.00 4.35
148 149 0.107654 AAGAGTGCGGTATGGGAAGC 60.108 55.000 0.00 0.00 0.00 3.86
149 150 2.403252 AAAGAGTGCGGTATGGGAAG 57.597 50.000 0.00 0.00 0.00 3.46
150 151 3.985019 TTAAAGAGTGCGGTATGGGAA 57.015 42.857 0.00 0.00 0.00 3.97
151 152 3.985019 TTTAAAGAGTGCGGTATGGGA 57.015 42.857 0.00 0.00 0.00 4.37
205 206 9.379770 CCCCTATTTTTGGTCCATTTTCTATAT 57.620 33.333 0.00 0.00 0.00 0.86
206 207 8.570470 TCCCCTATTTTTGGTCCATTTTCTATA 58.430 33.333 0.00 0.00 0.00 1.31
207 208 7.426667 TCCCCTATTTTTGGTCCATTTTCTAT 58.573 34.615 0.00 0.00 0.00 1.98
209 210 5.660533 TCCCCTATTTTTGGTCCATTTTCT 58.339 37.500 0.00 0.00 0.00 2.52
210 211 6.367374 TTCCCCTATTTTTGGTCCATTTTC 57.633 37.500 0.00 0.00 0.00 2.29
211 212 6.771934 TTTCCCCTATTTTTGGTCCATTTT 57.228 33.333 0.00 0.00 0.00 1.82
212 213 6.968400 ATTTCCCCTATTTTTGGTCCATTT 57.032 33.333 0.00 0.00 0.00 2.32
213 214 8.637108 ATTATTTCCCCTATTTTTGGTCCATT 57.363 30.769 0.00 0.00 0.00 3.16
321 322 9.593134 ACTTTTGTGCAATATGTTAGTTTTTCA 57.407 25.926 0.00 0.00 0.00 2.69
351 352 9.627123 CCTAATTTTGGTCCATCTTTCTATGTA 57.373 33.333 0.00 0.00 0.00 2.29
353 354 8.752005 TCCTAATTTTGGTCCATCTTTCTATG 57.248 34.615 0.00 0.00 0.00 2.23
354 355 9.768215 TTTCCTAATTTTGGTCCATCTTTCTAT 57.232 29.630 0.00 0.00 0.00 1.98
355 356 9.594936 TTTTCCTAATTTTGGTCCATCTTTCTA 57.405 29.630 0.00 0.00 0.00 2.10
383 384 9.871175 TTTCACTTTCCTAGTTACCCTTTTATT 57.129 29.630 0.00 0.00 33.85 1.40
384 385 9.871175 TTTTCACTTTCCTAGTTACCCTTTTAT 57.129 29.630 0.00 0.00 33.85 1.40
385 386 9.346005 CTTTTCACTTTCCTAGTTACCCTTTTA 57.654 33.333 0.00 0.00 33.85 1.52
387 388 7.580007 TCTTTTCACTTTCCTAGTTACCCTTT 58.420 34.615 0.00 0.00 33.85 3.11
388 389 7.145474 TCTTTTCACTTTCCTAGTTACCCTT 57.855 36.000 0.00 0.00 33.85 3.95
389 390 6.758806 TCTTTTCACTTTCCTAGTTACCCT 57.241 37.500 0.00 0.00 33.85 4.34
390 391 7.812690 TTTCTTTTCACTTTCCTAGTTACCC 57.187 36.000 0.00 0.00 33.85 3.69
391 392 9.117183 TCTTTTCTTTTCACTTTCCTAGTTACC 57.883 33.333 0.00 0.00 33.85 2.85
394 395 9.634021 ATCTCTTTTCTTTTCACTTTCCTAGTT 57.366 29.630 0.00 0.00 33.85 2.24
395 396 9.061435 CATCTCTTTTCTTTTCACTTTCCTAGT 57.939 33.333 0.00 0.00 37.68 2.57
398 399 7.062957 TCCATCTCTTTTCTTTTCACTTTCCT 58.937 34.615 0.00 0.00 0.00 3.36
399 400 7.277174 TCCATCTCTTTTCTTTTCACTTTCC 57.723 36.000 0.00 0.00 0.00 3.13
403 404 9.354673 TGTTTATCCATCTCTTTTCTTTTCACT 57.645 29.630 0.00 0.00 0.00 3.41
404 405 9.617975 CTGTTTATCCATCTCTTTTCTTTTCAC 57.382 33.333 0.00 0.00 0.00 3.18
405 406 9.354673 ACTGTTTATCCATCTCTTTTCTTTTCA 57.645 29.630 0.00 0.00 0.00 2.69
463 464 8.734386 TGTGCAATAAATTTGTTTTCCAGTTTT 58.266 25.926 0.00 0.00 0.00 2.43
464 465 8.273780 TGTGCAATAAATTTGTTTTCCAGTTT 57.726 26.923 0.00 0.00 0.00 2.66
465 466 7.856145 TGTGCAATAAATTTGTTTTCCAGTT 57.144 28.000 0.00 0.00 0.00 3.16
466 467 7.856145 TTGTGCAATAAATTTGTTTTCCAGT 57.144 28.000 0.00 0.00 0.00 4.00
467 468 9.224058 CTTTTGTGCAATAAATTTGTTTTCCAG 57.776 29.630 0.00 0.00 0.00 3.86
468 469 8.734386 ACTTTTGTGCAATAAATTTGTTTTCCA 58.266 25.926 0.00 0.00 0.00 3.53
533 534 8.973182 TGTTTTCACTTTCCTAGTTACCATTTT 58.027 29.630 0.00 0.00 33.85 1.82
534 535 8.528044 TGTTTTCACTTTCCTAGTTACCATTT 57.472 30.769 0.00 0.00 33.85 2.32
535 536 8.528044 TTGTTTTCACTTTCCTAGTTACCATT 57.472 30.769 0.00 0.00 33.85 3.16
536 537 8.528044 TTTGTTTTCACTTTCCTAGTTACCAT 57.472 30.769 0.00 0.00 33.85 3.55
537 538 7.941431 TTTGTTTTCACTTTCCTAGTTACCA 57.059 32.000 0.00 0.00 33.85 3.25
615 616 8.940952 CCCTACTTTTGTTTTGTTTTTCATTCA 58.059 29.630 0.00 0.00 0.00 2.57
617 618 9.508642 TTCCCTACTTTTGTTTTGTTTTTCATT 57.491 25.926 0.00 0.00 0.00 2.57
618 619 9.508642 TTTCCCTACTTTTGTTTTGTTTTTCAT 57.491 25.926 0.00 0.00 0.00 2.57
619 620 8.904099 TTTCCCTACTTTTGTTTTGTTTTTCA 57.096 26.923 0.00 0.00 0.00 2.69
622 623 9.562408 TCTTTTTCCCTACTTTTGTTTTGTTTT 57.438 25.926 0.00 0.00 0.00 2.43
624 625 9.562408 TTTCTTTTTCCCTACTTTTGTTTTGTT 57.438 25.926 0.00 0.00 0.00 2.83
625 626 9.562408 TTTTCTTTTTCCCTACTTTTGTTTTGT 57.438 25.926 0.00 0.00 0.00 2.83
626 627 9.820229 GTTTTCTTTTTCCCTACTTTTGTTTTG 57.180 29.630 0.00 0.00 0.00 2.44
627 628 9.005777 GGTTTTCTTTTTCCCTACTTTTGTTTT 57.994 29.630 0.00 0.00 0.00 2.43
628 629 8.380099 AGGTTTTCTTTTTCCCTACTTTTGTTT 58.620 29.630 0.00 0.00 0.00 2.83
629 630 7.913789 AGGTTTTCTTTTTCCCTACTTTTGTT 58.086 30.769 0.00 0.00 0.00 2.83
631 632 7.552459 TGAGGTTTTCTTTTTCCCTACTTTTG 58.448 34.615 0.00 0.00 0.00 2.44
632 633 7.727578 TGAGGTTTTCTTTTTCCCTACTTTT 57.272 32.000 0.00 0.00 0.00 2.27
634 635 6.239317 GCATGAGGTTTTCTTTTTCCCTACTT 60.239 38.462 0.00 0.00 0.00 2.24
635 636 5.243954 GCATGAGGTTTTCTTTTTCCCTACT 59.756 40.000 0.00 0.00 0.00 2.57
636 637 5.243954 AGCATGAGGTTTTCTTTTTCCCTAC 59.756 40.000 0.00 0.00 0.00 3.18
638 639 4.226384 AGCATGAGGTTTTCTTTTTCCCT 58.774 39.130 0.00 0.00 0.00 4.20
639 640 4.607293 AGCATGAGGTTTTCTTTTTCCC 57.393 40.909 0.00 0.00 0.00 3.97
640 641 6.749139 AGTTAGCATGAGGTTTTCTTTTTCC 58.251 36.000 0.00 0.00 0.00 3.13
641 642 9.744468 TTTAGTTAGCATGAGGTTTTCTTTTTC 57.256 29.630 0.00 0.00 0.00 2.29
643 644 8.914011 AGTTTAGTTAGCATGAGGTTTTCTTTT 58.086 29.630 0.00 0.00 0.00 2.27
644 645 8.352942 CAGTTTAGTTAGCATGAGGTTTTCTTT 58.647 33.333 0.00 0.00 0.00 2.52
645 646 7.040409 CCAGTTTAGTTAGCATGAGGTTTTCTT 60.040 37.037 0.00 0.00 0.00 2.52
646 647 6.431234 CCAGTTTAGTTAGCATGAGGTTTTCT 59.569 38.462 0.00 0.00 0.00 2.52
647 648 6.430000 TCCAGTTTAGTTAGCATGAGGTTTTC 59.570 38.462 0.00 0.00 0.00 2.29
649 650 5.705905 GTCCAGTTTAGTTAGCATGAGGTTT 59.294 40.000 0.00 0.00 0.00 3.27
650 651 5.246307 GTCCAGTTTAGTTAGCATGAGGTT 58.754 41.667 0.00 0.00 0.00 3.50
651 652 4.323562 GGTCCAGTTTAGTTAGCATGAGGT 60.324 45.833 0.00 0.00 0.00 3.85
654 655 3.512329 TCGGTCCAGTTTAGTTAGCATGA 59.488 43.478 0.00 0.00 0.00 3.07
655 656 3.857052 TCGGTCCAGTTTAGTTAGCATG 58.143 45.455 0.00 0.00 0.00 4.06
656 657 4.251268 GTTCGGTCCAGTTTAGTTAGCAT 58.749 43.478 0.00 0.00 0.00 3.79
658 659 3.431233 GTGTTCGGTCCAGTTTAGTTAGC 59.569 47.826 0.00 0.00 0.00 3.09
659 660 4.624015 TGTGTTCGGTCCAGTTTAGTTAG 58.376 43.478 0.00 0.00 0.00 2.34
661 662 3.547054 TGTGTTCGGTCCAGTTTAGTT 57.453 42.857 0.00 0.00 0.00 2.24
662 663 3.547054 TTGTGTTCGGTCCAGTTTAGT 57.453 42.857 0.00 0.00 0.00 2.24
664 665 4.958509 TGTATTGTGTTCGGTCCAGTTTA 58.041 39.130 0.00 0.00 0.00 2.01
665 666 3.811083 TGTATTGTGTTCGGTCCAGTTT 58.189 40.909 0.00 0.00 0.00 2.66
667 668 3.135994 GTTGTATTGTGTTCGGTCCAGT 58.864 45.455 0.00 0.00 0.00 4.00
668 669 3.135225 TGTTGTATTGTGTTCGGTCCAG 58.865 45.455 0.00 0.00 0.00 3.86
670 671 4.555348 TTTGTTGTATTGTGTTCGGTCC 57.445 40.909 0.00 0.00 0.00 4.46
671 672 5.454232 CACTTTTGTTGTATTGTGTTCGGTC 59.546 40.000 0.00 0.00 0.00 4.79
673 674 5.574082 TCACTTTTGTTGTATTGTGTTCGG 58.426 37.500 0.00 0.00 0.00 4.30
674 675 7.219917 ACATTCACTTTTGTTGTATTGTGTTCG 59.780 33.333 0.00 0.00 0.00 3.95
675 676 8.320295 CACATTCACTTTTGTTGTATTGTGTTC 58.680 33.333 0.00 0.00 0.00 3.18
677 678 6.756074 CCACATTCACTTTTGTTGTATTGTGT 59.244 34.615 0.00 0.00 0.00 3.72
678 679 6.977502 TCCACATTCACTTTTGTTGTATTGTG 59.022 34.615 0.00 0.00 0.00 3.33
680 681 8.592105 ATTCCACATTCACTTTTGTTGTATTG 57.408 30.769 0.00 0.00 0.00 1.90
683 684 9.072375 TGATATTCCACATTCACTTTTGTTGTA 57.928 29.630 0.00 0.00 0.00 2.41
684 685 7.950512 TGATATTCCACATTCACTTTTGTTGT 58.049 30.769 0.00 0.00 0.00 3.32
685 686 8.991243 ATGATATTCCACATTCACTTTTGTTG 57.009 30.769 0.00 0.00 0.00 3.33
734 735 7.310072 TGTGAGTCGAATGTTTAGACAAAAA 57.690 32.000 0.00 0.00 39.66 1.94
735 736 6.912203 TGTGAGTCGAATGTTTAGACAAAA 57.088 33.333 0.00 0.00 39.66 2.44
737 738 6.912203 TTTGTGAGTCGAATGTTTAGACAA 57.088 33.333 0.00 0.00 39.66 3.18
759 760 2.699846 TGGCCTTCATGTCTTGCTTTTT 59.300 40.909 3.32 0.00 0.00 1.94
760 761 2.318908 TGGCCTTCATGTCTTGCTTTT 58.681 42.857 3.32 0.00 0.00 2.27
761 762 1.999648 TGGCCTTCATGTCTTGCTTT 58.000 45.000 3.32 0.00 0.00 3.51
762 763 1.615392 GTTGGCCTTCATGTCTTGCTT 59.385 47.619 3.32 0.00 0.00 3.91
763 764 1.202976 AGTTGGCCTTCATGTCTTGCT 60.203 47.619 3.32 0.00 0.00 3.91
764 765 1.068055 CAGTTGGCCTTCATGTCTTGC 60.068 52.381 3.32 0.00 0.00 4.01
765 766 1.542915 CCAGTTGGCCTTCATGTCTTG 59.457 52.381 3.32 0.00 0.00 3.02
766 767 1.915141 CCAGTTGGCCTTCATGTCTT 58.085 50.000 3.32 0.00 0.00 3.01
767 768 3.658398 CCAGTTGGCCTTCATGTCT 57.342 52.632 3.32 0.00 0.00 3.41
778 779 1.733402 TTTGTGCTTCGGCCAGTTGG 61.733 55.000 2.24 0.00 40.91 3.77
779 780 0.318107 CTTTGTGCTTCGGCCAGTTG 60.318 55.000 2.24 0.00 40.91 3.16
780 781 1.455383 CCTTTGTGCTTCGGCCAGTT 61.455 55.000 2.24 0.00 40.91 3.16
781 782 1.898574 CCTTTGTGCTTCGGCCAGT 60.899 57.895 2.24 0.00 40.91 4.00
782 783 0.605319 TACCTTTGTGCTTCGGCCAG 60.605 55.000 2.24 0.00 40.91 4.85
783 784 0.605319 CTACCTTTGTGCTTCGGCCA 60.605 55.000 2.24 0.00 40.91 5.36
784 785 1.305930 CCTACCTTTGTGCTTCGGCC 61.306 60.000 0.00 0.00 40.91 6.13
785 786 1.923227 GCCTACCTTTGTGCTTCGGC 61.923 60.000 0.00 0.00 42.19 5.54
786 787 1.305930 GGCCTACCTTTGTGCTTCGG 61.306 60.000 0.00 0.00 0.00 4.30
787 788 1.305930 GGGCCTACCTTTGTGCTTCG 61.306 60.000 0.84 0.00 35.85 3.79
788 789 0.251165 TGGGCCTACCTTTGTGCTTC 60.251 55.000 4.53 0.00 41.11 3.86
789 790 0.409484 ATGGGCCTACCTTTGTGCTT 59.591 50.000 4.53 0.00 41.11 3.91
790 791 0.409484 AATGGGCCTACCTTTGTGCT 59.591 50.000 4.53 0.00 41.11 4.40
791 792 2.137810 TAATGGGCCTACCTTTGTGC 57.862 50.000 4.53 0.00 41.11 4.57
793 794 4.120946 TGTTTAATGGGCCTACCTTTGT 57.879 40.909 4.53 0.00 41.11 2.83
794 795 4.709397 TGATGTTTAATGGGCCTACCTTTG 59.291 41.667 4.53 0.00 41.11 2.77
795 796 4.941713 TGATGTTTAATGGGCCTACCTTT 58.058 39.130 4.53 0.00 41.11 3.11
797 798 4.814224 ATGATGTTTAATGGGCCTACCT 57.186 40.909 4.53 0.00 41.11 3.08
798 799 5.631119 ACTATGATGTTTAATGGGCCTACC 58.369 41.667 4.53 0.00 40.81 3.18
799 800 7.582667 AAACTATGATGTTTAATGGGCCTAC 57.417 36.000 4.53 0.00 38.25 3.18
801 802 7.494922 AAAAACTATGATGTTTAATGGGCCT 57.505 32.000 4.53 0.00 38.98 5.19
822 823 9.745880 TTTGTGTTAACACTGTTCTAACAAAAA 57.254 25.926 32.58 19.51 46.55 1.94
827 828 7.080353 ACCTTTGTGTTAACACTGTTCTAAC 57.920 36.000 32.58 9.69 46.55 2.34
1041 7729 0.255318 ATGCAGCTTTGGAGGGAGAG 59.745 55.000 0.00 0.00 0.00 3.20
1080 7774 3.387947 GAAACGGGGGCGGAGAGA 61.388 66.667 0.00 0.00 0.00 3.10
1918 8643 3.560025 CGGCCCTCCATGCTATAAGAAAT 60.560 47.826 0.00 0.00 0.00 2.17
2440 9221 5.339990 GTTCATCATAAAATTGGACCACCG 58.660 41.667 0.00 0.00 39.42 4.94
2480 9262 7.514721 AGACCACATTACTCTTTTGGTTTCTA 58.485 34.615 0.00 0.00 40.75 2.10
2504 9286 6.007936 TGATACATTTTGGTGGAAAACGAG 57.992 37.500 0.00 0.00 36.35 4.18
2532 9314 5.379732 AAATTTTGGCATGGAAGCAAATG 57.620 34.783 0.00 0.00 35.83 2.32
2535 9317 6.489361 ACAAATAAATTTTGGCATGGAAGCAA 59.511 30.769 0.00 0.00 35.83 3.91
2574 9357 9.479549 TGGAAGCTAAAAGATAAGGAAATGAAT 57.520 29.630 0.00 0.00 0.00 2.57
2626 9415 9.635520 TCTCGAAGTCTAACCTAAACATTAAAG 57.364 33.333 0.00 0.00 0.00 1.85
2691 9481 0.251653 ACCGGCAGAAGGTCTCAGTA 60.252 55.000 0.00 0.00 37.44 2.74
2704 9494 1.072489 TGTTAGAATGGACAACCGGCA 59.928 47.619 0.00 0.00 39.42 5.69
2707 9526 6.594159 ACTCTTTATGTTAGAATGGACAACCG 59.406 38.462 0.00 0.00 39.42 4.44
2708 9527 7.148239 CCACTCTTTATGTTAGAATGGACAACC 60.148 40.741 0.00 0.00 40.56 3.77
2709 9528 7.626452 GCCACTCTTTATGTTAGAATGGACAAC 60.626 40.741 4.68 0.00 40.56 3.32
2712 9531 5.880332 TGCCACTCTTTATGTTAGAATGGAC 59.120 40.000 4.68 0.00 40.56 4.02
2713 9532 6.061022 TGCCACTCTTTATGTTAGAATGGA 57.939 37.500 4.68 0.00 40.56 3.41
2714 9533 6.375455 ACTTGCCACTCTTTATGTTAGAATGG 59.625 38.462 0.00 0.00 40.94 3.16
2715 9534 7.383102 ACTTGCCACTCTTTATGTTAGAATG 57.617 36.000 0.00 0.00 0.00 2.67
2716 9535 7.448469 ACAACTTGCCACTCTTTATGTTAGAAT 59.552 33.333 0.00 0.00 0.00 2.40
2717 9536 6.770785 ACAACTTGCCACTCTTTATGTTAGAA 59.229 34.615 0.00 0.00 0.00 2.10
2718 9537 6.204688 CACAACTTGCCACTCTTTATGTTAGA 59.795 38.462 0.00 0.00 0.00 2.10
2719 9538 6.017109 ACACAACTTGCCACTCTTTATGTTAG 60.017 38.462 0.00 0.00 0.00 2.34
2720 9539 5.825679 ACACAACTTGCCACTCTTTATGTTA 59.174 36.000 0.00 0.00 0.00 2.41
2721 9540 4.644685 ACACAACTTGCCACTCTTTATGTT 59.355 37.500 0.00 0.00 0.00 2.71
2722 9541 4.207165 ACACAACTTGCCACTCTTTATGT 58.793 39.130 0.00 0.00 0.00 2.29
2723 9542 4.836125 ACACAACTTGCCACTCTTTATG 57.164 40.909 0.00 0.00 0.00 1.90
2724 9543 5.852282 AAACACAACTTGCCACTCTTTAT 57.148 34.783 0.00 0.00 0.00 1.40
2725 9544 5.047660 ACAAAACACAACTTGCCACTCTTTA 60.048 36.000 0.00 0.00 0.00 1.85
2726 9545 4.244862 CAAAACACAACTTGCCACTCTTT 58.755 39.130 0.00 0.00 0.00 2.52
2727 9546 3.258123 ACAAAACACAACTTGCCACTCTT 59.742 39.130 0.00 0.00 0.00 2.85
2728 9547 2.825532 ACAAAACACAACTTGCCACTCT 59.174 40.909 0.00 0.00 0.00 3.24
2729 9548 2.923020 CACAAAACACAACTTGCCACTC 59.077 45.455 0.00 0.00 0.00 3.51
2730 9549 2.560542 TCACAAAACACAACTTGCCACT 59.439 40.909 0.00 0.00 0.00 4.00
2731 9550 2.953020 TCACAAAACACAACTTGCCAC 58.047 42.857 0.00 0.00 0.00 5.01
2732 9551 3.056250 ACATCACAAAACACAACTTGCCA 60.056 39.130 0.00 0.00 0.00 4.92
2733 9552 3.520569 ACATCACAAAACACAACTTGCC 58.479 40.909 0.00 0.00 0.00 4.52
2734 9553 6.826893 ATTACATCACAAAACACAACTTGC 57.173 33.333 0.00 0.00 0.00 4.01
2783 9604 0.033503 GGGATGGTTACCCCTGTTGG 60.034 60.000 0.00 0.00 41.38 3.77
2816 9637 8.421002 AGGGAAAATGTTTGTATATAATGGCAC 58.579 33.333 0.00 0.00 0.00 5.01
2904 9726 5.049474 TGCAGCTTTCACACAATACAACTAG 60.049 40.000 0.00 0.00 0.00 2.57
2914 9736 1.538634 GCCATTTGCAGCTTTCACACA 60.539 47.619 0.00 0.00 40.77 3.72
3019 9849 1.377202 GGCGCTTCATCACCTTGGA 60.377 57.895 7.64 0.00 0.00 3.53
3126 9957 0.179020 CCCAGGCACAACACTCTTCA 60.179 55.000 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.