Multiple sequence alignment - TraesCS5B01G240300

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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 TraesCS5B01G240300 chr5B 100.000 4306 0 0 1 4306 420472692 420468387 0.000000e+00 7952.0
1 TraesCS5B01G240300 chr5B 76.214 412 89 9 265 672 72004849 72004443 4.360000e-50 209.0
2 TraesCS5B01G240300 chr5B 88.710 62 7 0 4116 4177 420459007 420458946 4.620000e-10 76.8
3 TraesCS5B01G240300 chr5B 100.000 33 0 0 3671 3703 420460585 420460553 1.290000e-05 62.1
4 TraesCS5B01G240300 chr5A 96.701 2728 76 10 854 3581 457519871 457522584 0.000000e+00 4527.0
5 TraesCS5B01G240300 chr5A 92.550 698 41 5 3613 4301 457522540 457523235 0.000000e+00 990.0
6 TraesCS5B01G240300 chr5A 80.873 664 117 9 17 672 444896040 444896701 8.260000e-142 514.0
7 TraesCS5B01G240300 chr5A 88.704 301 32 1 3671 3971 457526153 457526451 2.450000e-97 366.0
8 TraesCS5B01G240300 chr5A 79.459 370 73 1 44 410 17382501 17382870 4.270000e-65 259.0
9 TraesCS5B01G240300 chr5A 78.485 330 64 7 345 670 47655222 47655548 4.360000e-50 209.0
10 TraesCS5B01G240300 chr5A 92.982 57 4 0 672 728 457519723 457519779 2.760000e-12 84.2
11 TraesCS5B01G240300 chr5D 95.604 2775 87 13 824 3592 355739841 355737096 0.000000e+00 4416.0
12 TraesCS5B01G240300 chr5D 92.034 703 43 5 3613 4306 355737153 355736455 0.000000e+00 976.0
13 TraesCS5B01G240300 chr5D 81.203 665 113 9 17 672 346687981 346687320 3.810000e-145 525.0
14 TraesCS5B01G240300 chr5D 89.216 306 27 3 3671 3974 355735222 355734921 1.130000e-100 377.0
15 TraesCS5B01G240300 chr5D 100.000 43 0 0 766 808 355739867 355739825 3.570000e-11 80.5


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 TraesCS5B01G240300 chr5B 420468387 420472692 4305 True 7952.000 7952 100.00000 1 4306 1 chr5B.!!$R2 4305
1 TraesCS5B01G240300 chr5A 457519723 457526451 6728 False 1491.800 4527 92.73425 672 4301 4 chr5A.!!$F4 3629
2 TraesCS5B01G240300 chr5A 444896040 444896701 661 False 514.000 514 80.87300 17 672 1 chr5A.!!$F3 655
3 TraesCS5B01G240300 chr5D 355734921 355739867 4946 True 1462.375 4416 94.21350 766 4306 4 chr5D.!!$R2 3540
4 TraesCS5B01G240300 chr5D 346687320 346687981 661 True 525.000 525 81.20300 17 672 1 chr5D.!!$R1 655

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
846 853 0.161870 GAGCTCGTCAACAAACTCGC 59.838 55.0 0.00 0.0 0.0 5.03 F
1082 1090 0.726827 CAAACAGGTGACGCGCATAT 59.273 50.0 5.73 0.0 0.0 1.78 F
2849 2860 0.736325 GTGCTCGAGTGTATGCGGTT 60.736 55.0 15.13 0.0 0.0 4.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1868 1879 1.204062 CATCGGCGTGACAACACAC 59.796 57.895 6.85 0.0 46.20 3.82 R
2963 2974 2.768492 GCCTGCTCTTGCCAATCCG 61.768 63.158 0.00 0.0 38.71 4.18 R
3934 3948 0.179070 GAGAGGAGAAATGGGGACGC 60.179 60.000 0.00 0.0 0.00 5.19 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
31 32 6.548622 TGGCGTAAGTAGTAGGTGAATCTTAT 59.451 38.462 0.00 0.00 41.68 1.73
40 41 3.467803 AGGTGAATCTTATTGTAGCCGC 58.532 45.455 0.00 0.00 0.00 6.53
42 43 4.344102 AGGTGAATCTTATTGTAGCCGCTA 59.656 41.667 0.00 0.00 0.00 4.26
55 56 3.280920 CCGCTATGGCTGACTTCTC 57.719 57.895 0.00 0.00 36.09 2.87
58 59 0.249657 GCTATGGCTGACTTCTCCCG 60.250 60.000 0.00 0.00 35.22 5.14
64 65 1.900351 CTGACTTCTCCCGCATGGA 59.100 57.895 0.00 0.00 42.41 3.41
69 70 0.471617 CTTCTCCCGCATGGATCCTT 59.528 55.000 14.23 3.29 44.07 3.36
105 106 3.274288 CAAGGGCTAGTCATTCAACCTC 58.726 50.000 0.00 0.00 0.00 3.85
106 107 1.840635 AGGGCTAGTCATTCAACCTCC 59.159 52.381 0.00 0.00 0.00 4.30
107 108 1.559682 GGGCTAGTCATTCAACCTCCA 59.440 52.381 0.00 0.00 0.00 3.86
110 111 3.135530 GGCTAGTCATTCAACCTCCATCT 59.864 47.826 0.00 0.00 0.00 2.90
111 112 4.384647 GGCTAGTCATTCAACCTCCATCTT 60.385 45.833 0.00 0.00 0.00 2.40
112 113 4.813697 GCTAGTCATTCAACCTCCATCTTC 59.186 45.833 0.00 0.00 0.00 2.87
117 121 3.988976 TTCAACCTCCATCTTCCTGAG 57.011 47.619 0.00 0.00 0.00 3.35
123 127 1.836166 CTCCATCTTCCTGAGGCAGAA 59.164 52.381 4.65 0.00 32.44 3.02
139 143 0.538287 AGAAAGCAGTGTCCCTTGGC 60.538 55.000 0.00 0.00 0.00 4.52
141 145 0.178953 AAAGCAGTGTCCCTTGGCAT 60.179 50.000 0.00 0.00 0.00 4.40
182 186 1.920835 GCCAAGGTCCACTCCTCCT 60.921 63.158 0.00 0.00 36.74 3.69
183 187 0.617820 GCCAAGGTCCACTCCTCCTA 60.618 60.000 0.00 0.00 36.74 2.94
187 191 2.637872 CAAGGTCCACTCCTCCTAAACA 59.362 50.000 0.00 0.00 36.74 2.83
190 194 2.537143 GTCCACTCCTCCTAAACAGGA 58.463 52.381 0.00 0.00 37.75 3.86
193 197 3.173965 CCACTCCTCCTAAACAGGAAGA 58.826 50.000 0.00 0.00 39.69 2.87
194 198 3.583086 CCACTCCTCCTAAACAGGAAGAA 59.417 47.826 0.00 0.00 39.69 2.52
205 209 2.919228 ACAGGAAGAAGGTGTGTCAAC 58.081 47.619 0.00 0.00 0.00 3.18
242 246 4.489771 CCGCGAATGGCCTCCCTT 62.490 66.667 8.23 0.00 38.94 3.95
245 249 2.124151 CGAATGGCCTCCCTTGGG 60.124 66.667 3.32 0.00 0.00 4.12
250 254 2.612746 GGCCTCCCTTGGGTGGTA 60.613 66.667 23.12 0.00 0.00 3.25
255 259 2.224793 GCCTCCCTTGGGTGGTATATTC 60.225 54.545 23.12 6.42 0.00 1.75
256 260 3.327439 CCTCCCTTGGGTGGTATATTCT 58.673 50.000 16.49 0.00 0.00 2.40
264 268 6.409695 CCTTGGGTGGTATATTCTCATGTCTT 60.410 42.308 0.00 0.00 0.00 3.01
266 270 5.665360 TGGGTGGTATATTCTCATGTCTTGA 59.335 40.000 0.00 0.00 0.00 3.02
267 271 5.992217 GGGTGGTATATTCTCATGTCTTGAC 59.008 44.000 0.00 0.00 0.00 3.18
270 274 7.015292 GGTGGTATATTCTCATGTCTTGACCTA 59.985 40.741 0.00 0.00 0.00 3.08
273 277 8.807118 GGTATATTCTCATGTCTTGACCTATCA 58.193 37.037 0.00 0.00 0.00 2.15
276 280 4.614475 TCTCATGTCTTGACCTATCACCT 58.386 43.478 0.00 0.00 33.38 4.00
287 291 1.475403 CTATCACCTGACGACCCAGT 58.525 55.000 0.00 0.00 32.43 4.00
288 292 1.405821 CTATCACCTGACGACCCAGTC 59.594 57.143 0.00 0.00 41.30 3.51
314 318 1.298340 CAACGGGTGCATCAGGGTA 59.702 57.895 1.23 0.00 0.00 3.69
325 329 5.450965 GGTGCATCAGGGTATTCAAAAGATG 60.451 44.000 0.00 0.00 35.67 2.90
331 335 5.015178 TCAGGGTATTCAAAAGATGTTCCCT 59.985 40.000 0.00 0.00 42.75 4.20
348 352 5.433051 TGTTCCCTTGGATGGAGAAATATCT 59.567 40.000 0.00 0.00 39.10 1.98
359 363 6.911250 TGGAGAAATATCTATGCCTTCGTA 57.089 37.500 0.00 0.00 35.54 3.43
360 364 7.297936 TGGAGAAATATCTATGCCTTCGTAA 57.702 36.000 0.00 0.00 35.54 3.18
378 382 2.990066 AATCAAGGCTCCTCTTACCG 57.010 50.000 0.00 0.00 0.00 4.02
410 414 2.224597 ACCCTGGTTTTACTTACACCGG 60.225 50.000 0.00 0.00 36.79 5.28
441 446 1.373812 GCCTGTTACCCGTCTTGGT 59.626 57.895 0.00 0.00 42.62 3.67
446 451 0.609662 GTTACCCGTCTTGGTGGCTA 59.390 55.000 0.00 0.00 39.53 3.93
448 453 1.597797 TACCCGTCTTGGTGGCTACG 61.598 60.000 0.00 0.00 39.53 3.51
449 454 2.642254 CCCGTCTTGGTGGCTACGA 61.642 63.158 0.00 0.00 37.53 3.43
462 467 2.046988 TACGAGGCACGAGACGGA 60.047 61.111 12.15 0.00 45.77 4.69
499 505 0.176680 CTAGAGCCTTGACGCATGGT 59.823 55.000 11.45 0.00 32.20 3.55
500 506 1.409064 CTAGAGCCTTGACGCATGGTA 59.591 52.381 11.45 0.08 32.20 3.25
501 507 0.613260 AGAGCCTTGACGCATGGTAA 59.387 50.000 11.45 0.00 32.20 2.85
510 516 3.138128 GCATGGTAACCGGCCACC 61.138 66.667 16.44 16.44 39.03 4.61
527 533 3.387091 CCATGACGGGACCGGACA 61.387 66.667 9.46 14.35 44.69 4.02
528 534 2.125673 CATGACGGGACCGGACAC 60.126 66.667 9.46 0.37 44.69 3.67
531 537 4.065281 GACGGGACCGGACACTGG 62.065 72.222 9.46 0.00 44.69 4.00
540 546 1.070289 ACCGGACACTGGAGACTTTTC 59.930 52.381 9.46 0.00 0.00 2.29
541 547 1.344763 CCGGACACTGGAGACTTTTCT 59.655 52.381 0.00 0.00 33.37 2.52
542 548 2.408050 CGGACACTGGAGACTTTTCTG 58.592 52.381 0.00 0.00 29.47 3.02
543 549 2.224066 CGGACACTGGAGACTTTTCTGT 60.224 50.000 0.00 0.00 29.47 3.41
544 550 3.134458 GGACACTGGAGACTTTTCTGTG 58.866 50.000 0.00 0.00 29.47 3.66
545 551 3.432326 GGACACTGGAGACTTTTCTGTGT 60.432 47.826 12.95 12.95 37.40 3.72
547 553 3.941483 ACACTGGAGACTTTTCTGTGTTG 59.059 43.478 9.53 0.00 34.07 3.33
548 554 2.945668 ACTGGAGACTTTTCTGTGTTGC 59.054 45.455 0.00 0.00 29.47 4.17
549 555 2.945008 CTGGAGACTTTTCTGTGTTGCA 59.055 45.455 0.00 0.00 29.47 4.08
550 556 3.554934 TGGAGACTTTTCTGTGTTGCAT 58.445 40.909 0.00 0.00 29.47 3.96
553 559 5.592282 TGGAGACTTTTCTGTGTTGCATTTA 59.408 36.000 0.00 0.00 29.47 1.40
558 564 6.639563 ACTTTTCTGTGTTGCATTTAAAGGT 58.360 32.000 1.37 0.00 0.00 3.50
570 576 4.563374 GCATTTAAAGGTTGGCTTGATGGT 60.563 41.667 1.37 0.00 0.00 3.55
573 579 0.609131 AAGGTTGGCTTGATGGTCGG 60.609 55.000 0.00 0.00 0.00 4.79
574 580 2.700773 GGTTGGCTTGATGGTCGGC 61.701 63.158 0.00 0.00 0.00 5.54
588 594 0.798776 GTCGGCTTTGTCAGACCATG 59.201 55.000 0.00 0.00 0.00 3.66
589 595 0.684535 TCGGCTTTGTCAGACCATGA 59.315 50.000 0.00 0.00 34.79 3.07
590 596 1.071542 TCGGCTTTGTCAGACCATGAA 59.928 47.619 0.00 0.00 40.43 2.57
593 599 2.887152 GGCTTTGTCAGACCATGAAAGT 59.113 45.455 11.02 0.00 40.43 2.66
603 609 3.508793 AGACCATGAAAGTGCCTTGATTG 59.491 43.478 0.00 0.00 0.00 2.67
616 622 2.045926 GATTGCCACCCACGCTCT 60.046 61.111 0.00 0.00 0.00 4.09
620 626 4.148825 GCCACCCACGCTCTCGAT 62.149 66.667 0.00 0.00 39.41 3.59
648 654 2.342648 GAAGCGGAGAACGTGGGT 59.657 61.111 0.00 0.00 46.52 4.51
652 658 1.153881 GCGGAGAACGTGGGTAGTC 60.154 63.158 0.00 0.00 46.52 2.59
655 661 1.202268 CGGAGAACGTGGGTAGTCATC 60.202 57.143 0.00 0.00 37.93 2.92
682 689 0.460635 GCGGGCGGTATAACAAGTGA 60.461 55.000 0.00 0.00 0.00 3.41
711 718 2.029380 GGCAGTCCCAACCACAAATAAC 60.029 50.000 0.00 0.00 0.00 1.89
713 720 3.320826 GCAGTCCCAACCACAAATAACTT 59.679 43.478 0.00 0.00 0.00 2.66
718 725 3.901222 CCCAACCACAAATAACTTCCCTT 59.099 43.478 0.00 0.00 0.00 3.95
736 743 9.462606 ACTTCCCTTATTTAAAGAACATACCTG 57.537 33.333 0.00 0.00 0.00 4.00
737 744 8.817092 TTCCCTTATTTAAAGAACATACCTGG 57.183 34.615 0.00 0.00 0.00 4.45
738 745 7.935405 TCCCTTATTTAAAGAACATACCTGGT 58.065 34.615 4.05 4.05 0.00 4.00
739 746 8.395605 TCCCTTATTTAAAGAACATACCTGGTT 58.604 33.333 3.84 0.00 0.00 3.67
740 747 9.689501 CCCTTATTTAAAGAACATACCTGGTTA 57.310 33.333 3.84 0.00 0.00 2.85
805 812 1.542030 GAACTCTCCTGAGCTCGTCAA 59.458 52.381 9.64 0.00 43.85 3.18
806 813 0.885196 ACTCTCCTGAGCTCGTCAAC 59.115 55.000 9.64 0.00 43.85 3.18
807 814 0.884514 CTCTCCTGAGCTCGTCAACA 59.115 55.000 9.64 0.00 33.60 3.33
809 816 1.895798 TCTCCTGAGCTCGTCAACATT 59.104 47.619 9.64 0.00 33.60 2.71
810 817 2.300152 TCTCCTGAGCTCGTCAACATTT 59.700 45.455 9.64 0.00 33.60 2.32
811 818 2.414481 CTCCTGAGCTCGTCAACATTTG 59.586 50.000 9.64 0.00 33.60 2.32
814 821 3.003689 CCTGAGCTCGTCAACATTTGTTT 59.996 43.478 9.64 0.00 35.83 2.83
817 824 6.125327 TGAGCTCGTCAACATTTGTTTTTA 57.875 33.333 9.64 0.00 35.83 1.52
818 825 6.198687 TGAGCTCGTCAACATTTGTTTTTAG 58.801 36.000 9.64 0.00 35.83 1.85
819 826 6.037720 TGAGCTCGTCAACATTTGTTTTTAGA 59.962 34.615 9.64 0.00 35.83 2.10
822 829 6.687081 TCGTCAACATTTGTTTTTAGAGGT 57.313 33.333 0.00 0.00 35.83 3.85
824 831 7.190871 TCGTCAACATTTGTTTTTAGAGGTTC 58.809 34.615 0.00 0.00 35.83 3.62
825 832 6.416750 CGTCAACATTTGTTTTTAGAGGTTCC 59.583 38.462 0.00 0.00 35.83 3.62
826 833 7.489160 GTCAACATTTGTTTTTAGAGGTTCCT 58.511 34.615 0.00 0.00 35.83 3.36
827 834 7.435192 GTCAACATTTGTTTTTAGAGGTTCCTG 59.565 37.037 0.00 0.00 35.83 3.86
828 835 7.340743 TCAACATTTGTTTTTAGAGGTTCCTGA 59.659 33.333 0.00 0.00 35.83 3.86
829 836 7.277174 ACATTTGTTTTTAGAGGTTCCTGAG 57.723 36.000 0.00 0.00 0.00 3.35
830 837 5.767816 TTTGTTTTTAGAGGTTCCTGAGC 57.232 39.130 0.00 0.00 0.00 4.26
831 838 4.706842 TGTTTTTAGAGGTTCCTGAGCT 57.293 40.909 0.00 0.00 39.22 4.09
836 843 2.268022 GAGGTTCCTGAGCTCGTCA 58.732 57.895 9.64 0.00 42.45 4.35
846 853 0.161870 GAGCTCGTCAACAAACTCGC 59.838 55.000 0.00 0.00 0.00 5.03
895 903 2.398554 CCACGGCCCAAATCTGACG 61.399 63.158 0.00 0.00 0.00 4.35
1075 1083 2.946990 AGGGTAAAACAAACAGGTGACG 59.053 45.455 0.00 0.00 0.00 4.35
1077 1085 2.368685 GTAAAACAAACAGGTGACGCG 58.631 47.619 3.53 3.53 0.00 6.01
1082 1090 0.726827 CAAACAGGTGACGCGCATAT 59.273 50.000 5.73 0.00 0.00 1.78
1083 1091 1.930503 CAAACAGGTGACGCGCATATA 59.069 47.619 5.73 0.00 0.00 0.86
1088 1096 1.666872 GTGACGCGCATATACCCCC 60.667 63.158 5.73 0.00 0.00 5.40
1143 1151 4.320023 TCGGTTTGCTAAGAATGTGCTAA 58.680 39.130 0.00 0.00 0.00 3.09
1166 1174 2.353704 CGTGGGCTCTGTCATAAGTTCA 60.354 50.000 0.00 0.00 0.00 3.18
1179 1187 6.876789 TGTCATAAGTTCAAGCGGAAATTAGA 59.123 34.615 15.52 11.49 45.79 2.10
1190 1198 5.016831 AGCGGAAATTAGAAAGGGTTTCAT 58.983 37.500 2.44 0.00 42.10 2.57
1210 1218 4.338118 TCATGAACCTGACCTTTGTTGTTC 59.662 41.667 0.00 0.00 32.72 3.18
1227 1235 7.177498 TGTTGTTCGTTGCTATGATATCATC 57.823 36.000 21.42 9.25 37.76 2.92
1312 1320 3.885901 TGCAGCCATTTGTAACAGTTACA 59.114 39.130 20.32 20.32 43.92 2.41
1319 1327 7.120726 AGCCATTTGTAACAGTTACATTAGTCC 59.879 37.037 23.85 12.50 44.85 3.85
1384 1392 7.326063 GTGTGCTGGATTAGATTGTTGTTTTAC 59.674 37.037 0.00 0.00 0.00 2.01
1385 1393 7.013750 TGTGCTGGATTAGATTGTTGTTTTACA 59.986 33.333 0.00 0.00 0.00 2.41
1481 1490 6.847956 TGTTTGAAAATCTTGAATTGCTGG 57.152 33.333 0.00 0.00 0.00 4.85
1482 1491 6.347696 TGTTTGAAAATCTTGAATTGCTGGT 58.652 32.000 0.00 0.00 0.00 4.00
1502 1513 2.417933 GTGCGCAGAGAATGAGATTGTT 59.582 45.455 12.22 0.00 0.00 2.83
1520 1531 1.139498 TTCAGATGTTCCAGCCCCCA 61.139 55.000 0.00 0.00 0.00 4.96
1528 1539 4.760047 CCAGCCCCCAGTTCGTCG 62.760 72.222 0.00 0.00 0.00 5.12
1763 1774 3.560105 GGCAGCAAGGAAGAGGAATTAT 58.440 45.455 0.00 0.00 0.00 1.28
1778 1789 5.734720 AGGAATTATGAACACGACACATCT 58.265 37.500 0.00 0.00 0.00 2.90
1781 1792 6.018994 GGAATTATGAACACGACACATCTACC 60.019 42.308 0.00 0.00 0.00 3.18
1868 1879 5.064707 CCAAGAAATGGTACGTAATCCTGTG 59.935 44.000 0.00 0.00 44.85 3.66
2564 2575 5.102313 GCACTTTTTGAATCTAAATCCCGG 58.898 41.667 0.00 0.00 0.00 5.73
2804 2815 1.929836 GCACACGAGCTATTTCAGGAG 59.070 52.381 0.00 0.00 0.00 3.69
2849 2860 0.736325 GTGCTCGAGTGTATGCGGTT 60.736 55.000 15.13 0.00 0.00 4.44
2963 2974 1.369625 CTTACAACGCCCTCATGTCC 58.630 55.000 0.00 0.00 0.00 4.02
3290 3301 5.984725 TCTATACTTGAGGCGATTGGAAAA 58.015 37.500 0.00 0.00 0.00 2.29
3302 3313 5.460646 GCGATTGGAAAAGTTGATCAAGAA 58.539 37.500 8.80 0.00 0.00 2.52
3309 3320 8.690203 TGGAAAAGTTGATCAAGAATGAACTA 57.310 30.769 8.80 0.00 40.43 2.24
3337 3348 4.080919 TGGTCAGTAGGAACAGGATTCATG 60.081 45.833 0.00 0.00 38.63 3.07
3349 3360 3.026694 AGGATTCATGCCTTTTGGTAGC 58.973 45.455 0.00 0.00 42.99 3.58
3356 3367 3.128852 TGCCTTTTGGTAGCGTTCTAA 57.871 42.857 0.00 0.00 42.99 2.10
3357 3368 3.071479 TGCCTTTTGGTAGCGTTCTAAG 58.929 45.455 0.00 0.00 42.99 2.18
3417 3428 1.035139 CTCCCAGTTTTTGTGCAGCT 58.965 50.000 0.00 0.00 0.00 4.24
3498 3511 3.446442 AAAATCATGGAGGACAGCAGT 57.554 42.857 0.00 0.00 0.00 4.40
3499 3512 2.414994 AATCATGGAGGACAGCAGTG 57.585 50.000 0.00 0.00 0.00 3.66
3506 3519 1.606737 GGAGGACAGCAGTGAGTCAAC 60.607 57.143 15.30 9.49 36.50 3.18
3540 3553 8.635877 GTGTGTATTTCACCATTTTGTTAACA 57.364 30.769 3.59 3.59 45.61 2.41
3541 3554 8.536407 GTGTGTATTTCACCATTTTGTTAACAC 58.464 33.333 8.07 0.00 45.61 3.32
3542 3555 8.251026 TGTGTATTTCACCATTTTGTTAACACA 58.749 29.630 8.07 0.00 45.61 3.72
3543 3556 9.255304 GTGTATTTCACCATTTTGTTAACACAT 57.745 29.630 8.07 0.46 40.84 3.21
3544 3557 9.254133 TGTATTTCACCATTTTGTTAACACATG 57.746 29.630 8.07 12.99 31.06 3.21
3545 3558 7.727331 ATTTCACCATTTTGTTAACACATGG 57.273 32.000 29.15 29.15 40.41 3.66
3546 3559 5.860941 TCACCATTTTGTTAACACATGGT 57.139 34.783 30.07 30.07 44.81 3.55
3547 3560 5.837437 TCACCATTTTGTTAACACATGGTC 58.163 37.500 31.61 0.00 43.33 4.02
3548 3561 5.360999 TCACCATTTTGTTAACACATGGTCA 59.639 36.000 31.61 24.16 43.33 4.02
3549 3562 6.045318 CACCATTTTGTTAACACATGGTCAA 58.955 36.000 31.61 13.36 43.33 3.18
3550 3563 6.536582 CACCATTTTGTTAACACATGGTCAAA 59.463 34.615 31.61 19.36 43.33 2.69
3551 3564 7.065085 CACCATTTTGTTAACACATGGTCAAAA 59.935 33.333 31.61 18.81 43.33 2.44
3552 3565 7.772757 ACCATTTTGTTAACACATGGTCAAAAT 59.227 29.630 30.07 18.95 42.36 1.82
3553 3566 8.281893 CCATTTTGTTAACACATGGTCAAAATC 58.718 33.333 25.59 0.00 40.80 2.17
3554 3567 7.778470 TTTTGTTAACACATGGTCAAAATCC 57.222 32.000 8.07 0.00 32.45 3.01
3555 3568 6.723298 TTGTTAACACATGGTCAAAATCCT 57.277 33.333 8.07 0.00 31.06 3.24
3556 3569 6.083098 TGTTAACACATGGTCAAAATCCTG 57.917 37.500 3.59 0.00 0.00 3.86
3557 3570 5.596361 TGTTAACACATGGTCAAAATCCTGT 59.404 36.000 3.59 0.00 0.00 4.00
3558 3571 6.097554 TGTTAACACATGGTCAAAATCCTGTT 59.902 34.615 3.59 0.00 0.00 3.16
3559 3572 7.285629 TGTTAACACATGGTCAAAATCCTGTTA 59.714 33.333 3.59 0.00 0.00 2.41
3560 3573 6.916360 AACACATGGTCAAAATCCTGTTAT 57.084 33.333 0.00 0.00 0.00 1.89
3561 3574 6.271488 ACACATGGTCAAAATCCTGTTATG 57.729 37.500 0.00 0.00 0.00 1.90
3562 3575 5.774690 ACACATGGTCAAAATCCTGTTATGT 59.225 36.000 0.00 0.00 0.00 2.29
3563 3576 6.267471 ACACATGGTCAAAATCCTGTTATGTT 59.733 34.615 0.00 0.00 0.00 2.71
3564 3577 6.808212 CACATGGTCAAAATCCTGTTATGTTC 59.192 38.462 0.00 0.00 0.00 3.18
3565 3578 5.975693 TGGTCAAAATCCTGTTATGTTCC 57.024 39.130 0.00 0.00 0.00 3.62
3566 3579 4.457603 TGGTCAAAATCCTGTTATGTTCCG 59.542 41.667 0.00 0.00 0.00 4.30
3567 3580 4.457949 GGTCAAAATCCTGTTATGTTCCGT 59.542 41.667 0.00 0.00 0.00 4.69
3568 3581 5.391629 GGTCAAAATCCTGTTATGTTCCGTC 60.392 44.000 0.00 0.00 0.00 4.79
3569 3582 4.698304 TCAAAATCCTGTTATGTTCCGTCC 59.302 41.667 0.00 0.00 0.00 4.79
3570 3583 4.569719 AAATCCTGTTATGTTCCGTCCT 57.430 40.909 0.00 0.00 0.00 3.85
3571 3584 3.821421 ATCCTGTTATGTTCCGTCCTC 57.179 47.619 0.00 0.00 0.00 3.71
3572 3585 2.816411 TCCTGTTATGTTCCGTCCTCT 58.184 47.619 0.00 0.00 0.00 3.69
3573 3586 3.170717 TCCTGTTATGTTCCGTCCTCTT 58.829 45.455 0.00 0.00 0.00 2.85
3574 3587 3.581332 TCCTGTTATGTTCCGTCCTCTTT 59.419 43.478 0.00 0.00 0.00 2.52
3575 3588 4.773674 TCCTGTTATGTTCCGTCCTCTTTA 59.226 41.667 0.00 0.00 0.00 1.85
3576 3589 5.246656 TCCTGTTATGTTCCGTCCTCTTTAA 59.753 40.000 0.00 0.00 0.00 1.52
3577 3590 5.935789 CCTGTTATGTTCCGTCCTCTTTAAA 59.064 40.000 0.00 0.00 0.00 1.52
3578 3591 6.598064 CCTGTTATGTTCCGTCCTCTTTAAAT 59.402 38.462 0.00 0.00 0.00 1.40
3579 3592 7.120726 CCTGTTATGTTCCGTCCTCTTTAAATT 59.879 37.037 0.00 0.00 0.00 1.82
3580 3593 8.398878 TGTTATGTTCCGTCCTCTTTAAATTT 57.601 30.769 0.00 0.00 0.00 1.82
3581 3594 8.293867 TGTTATGTTCCGTCCTCTTTAAATTTG 58.706 33.333 0.00 0.00 0.00 2.32
3582 3595 8.508875 GTTATGTTCCGTCCTCTTTAAATTTGA 58.491 33.333 0.00 0.00 0.00 2.69
3583 3596 7.703058 ATGTTCCGTCCTCTTTAAATTTGAT 57.297 32.000 0.00 0.00 0.00 2.57
3584 3597 8.801882 ATGTTCCGTCCTCTTTAAATTTGATA 57.198 30.769 0.00 0.00 0.00 2.15
3585 3598 8.624367 TGTTCCGTCCTCTTTAAATTTGATAA 57.376 30.769 0.00 0.00 0.00 1.75
3586 3599 9.238368 TGTTCCGTCCTCTTTAAATTTGATAAT 57.762 29.630 0.00 0.00 0.00 1.28
3587 3600 9.717892 GTTCCGTCCTCTTTAAATTTGATAATC 57.282 33.333 0.00 0.00 0.00 1.75
3588 3601 9.681062 TTCCGTCCTCTTTAAATTTGATAATCT 57.319 29.630 0.00 0.00 0.00 2.40
3604 3617 7.997107 TGATAATCTACACGTGTATTTCACC 57.003 36.000 27.50 15.93 43.51 4.02
3605 3618 7.778083 TGATAATCTACACGTGTATTTCACCT 58.222 34.615 27.50 10.30 43.51 4.00
3606 3619 8.255206 TGATAATCTACACGTGTATTTCACCTT 58.745 33.333 27.50 14.82 43.51 3.50
3607 3620 9.095065 GATAATCTACACGTGTATTTCACCTTT 57.905 33.333 27.50 14.09 43.51 3.11
3608 3621 7.739498 AATCTACACGTGTATTTCACCTTTT 57.261 32.000 27.50 8.94 43.51 2.27
3609 3622 7.739498 ATCTACACGTGTATTTCACCTTTTT 57.261 32.000 27.50 0.00 43.51 1.94
3610 3623 6.950545 TCTACACGTGTATTTCACCTTTTTG 58.049 36.000 27.50 11.86 43.51 2.44
3611 3624 5.570234 ACACGTGTATTTCACCTTTTTGT 57.430 34.783 21.98 0.00 43.51 2.83
3616 3629 5.338559 CGTGTATTTCACCTTTTTGTTAGCG 59.661 40.000 0.00 0.00 43.51 4.26
3642 3655 3.444388 GGCCAAAATACCGTTATGTTCCA 59.556 43.478 0.00 0.00 0.00 3.53
3645 3658 5.067283 GCCAAAATACCGTTATGTTCCATCT 59.933 40.000 0.00 0.00 0.00 2.90
3685 3698 3.955471 TCTGCAGCTGCCTAAATACTTT 58.045 40.909 34.64 0.00 41.18 2.66
3724 3737 8.954350 CAGAATCACTTTTCTCCATTAAGATGT 58.046 33.333 0.00 0.00 33.69 3.06
3752 3765 2.354510 TGTTGCTGAAAAGTTGAGACCG 59.645 45.455 0.00 0.00 0.00 4.79
3756 3769 3.181501 TGCTGAAAAGTTGAGACCGTTTG 60.182 43.478 0.00 0.00 0.00 2.93
3788 3802 9.694137 AAGTTAACTACTGTATGTTGAGAGTTC 57.306 33.333 8.92 0.00 37.12 3.01
3795 3809 9.482627 CTACTGTATGTTGAGAGTTCTTTCTTT 57.517 33.333 0.00 0.00 0.00 2.52
3805 3819 6.992123 TGAGAGTTCTTTCTTTAGCAATCACA 59.008 34.615 0.00 0.00 0.00 3.58
3815 3829 2.645838 AGCAATCACAAGTGGAGTGT 57.354 45.000 0.00 0.00 38.16 3.55
3870 3884 2.419324 TGTCGTGTTTGTGTGGGTAAAC 59.581 45.455 0.00 0.00 37.32 2.01
3934 3948 9.135189 TGAATCCAAAATCAAAGATATGGTAGG 57.865 33.333 9.97 0.00 0.00 3.18
3959 3973 5.148502 GTCCCCATTTCTCCTCTCTGTATA 58.851 45.833 0.00 0.00 0.00 1.47
3984 3998 1.540267 GCTTTCCGAACTTCCTTTCCC 59.460 52.381 0.00 0.00 0.00 3.97
4022 4036 3.558418 GCTTTTCCAGATTTATACGGCGA 59.442 43.478 16.62 0.00 0.00 5.54
4092 4106 7.464577 GCATTTTTCACACTTTTCTCTTTCACC 60.465 37.037 0.00 0.00 0.00 4.02
4172 4193 4.568072 TGTGCCTAATCTTTCCAGCTAA 57.432 40.909 0.00 0.00 0.00 3.09
4218 4239 1.674817 GCTGCCATTGCTTCATTGCTT 60.675 47.619 0.00 0.00 38.71 3.91
4258 4279 1.040339 ACCAGCAAAGAACCGGCAAA 61.040 50.000 0.00 0.00 0.00 3.68
4297 4320 4.241681 GCCAAGTCCAGAATCGAGATATC 58.758 47.826 0.00 0.00 0.00 1.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.994054 TCACCTACTACTTACGCCACTATAG 59.006 44.000 0.00 0.00 0.00 1.31
1 2 5.928976 TCACCTACTACTTACGCCACTATA 58.071 41.667 0.00 0.00 0.00 1.31
2 3 4.785301 TCACCTACTACTTACGCCACTAT 58.215 43.478 0.00 0.00 0.00 2.12
3 4 4.220693 TCACCTACTACTTACGCCACTA 57.779 45.455 0.00 0.00 0.00 2.74
4 5 3.077484 TCACCTACTACTTACGCCACT 57.923 47.619 0.00 0.00 0.00 4.00
5 6 3.855689 TTCACCTACTACTTACGCCAC 57.144 47.619 0.00 0.00 0.00 5.01
6 7 4.275810 AGATTCACCTACTACTTACGCCA 58.724 43.478 0.00 0.00 0.00 5.69
7 8 4.915158 AGATTCACCTACTACTTACGCC 57.085 45.455 0.00 0.00 0.00 5.68
8 9 7.919621 ACAATAAGATTCACCTACTACTTACGC 59.080 37.037 0.00 0.00 0.00 4.42
12 13 8.422566 GGCTACAATAAGATTCACCTACTACTT 58.577 37.037 0.00 0.00 0.00 2.24
13 14 7.255520 CGGCTACAATAAGATTCACCTACTACT 60.256 40.741 0.00 0.00 0.00 2.57
14 15 6.862090 CGGCTACAATAAGATTCACCTACTAC 59.138 42.308 0.00 0.00 0.00 2.73
15 16 6.516194 GCGGCTACAATAAGATTCACCTACTA 60.516 42.308 0.00 0.00 0.00 1.82
19 20 3.134804 AGCGGCTACAATAAGATTCACCT 59.865 43.478 0.00 0.00 0.00 4.00
40 41 0.249657 GCGGGAGAAGTCAGCCATAG 60.250 60.000 0.00 0.00 0.00 2.23
42 43 1.630126 ATGCGGGAGAAGTCAGCCAT 61.630 55.000 0.00 0.00 0.00 4.40
46 47 1.900351 TCCATGCGGGAGAAGTCAG 59.100 57.895 0.00 0.00 42.15 3.51
55 56 2.281070 CGGAAGGATCCATGCGGG 60.281 66.667 21.48 0.00 46.97 6.13
105 106 2.641305 CTTTCTGCCTCAGGAAGATGG 58.359 52.381 0.56 0.00 46.86 3.51
106 107 2.015587 GCTTTCTGCCTCAGGAAGATG 58.984 52.381 16.74 0.00 46.86 2.90
107 108 1.632409 TGCTTTCTGCCTCAGGAAGAT 59.368 47.619 16.74 0.00 46.86 2.40
110 111 0.767375 ACTGCTTTCTGCCTCAGGAA 59.233 50.000 0.00 0.00 42.00 3.36
111 112 0.035881 CACTGCTTTCTGCCTCAGGA 59.964 55.000 0.00 0.00 42.00 3.86
112 113 0.250640 ACACTGCTTTCTGCCTCAGG 60.251 55.000 0.00 0.00 42.00 3.86
117 121 0.538287 AAGGGACACTGCTTTCTGCC 60.538 55.000 0.00 0.00 42.00 4.85
123 127 0.896940 CATGCCAAGGGACACTGCTT 60.897 55.000 0.00 0.00 0.00 3.91
139 143 1.597797 AAGCCGTGCAATGTCCCATG 61.598 55.000 0.00 0.00 0.00 3.66
141 145 1.971167 GAAGCCGTGCAATGTCCCA 60.971 57.895 0.00 0.00 0.00 4.37
145 149 3.055719 CCGGAAGCCGTGCAATGT 61.056 61.111 0.00 0.00 46.80 2.71
157 161 2.528127 TGGACCTTGGCTCCGGAA 60.528 61.111 5.23 0.00 0.00 4.30
162 166 1.599576 GAGGAGTGGACCTTGGCTC 59.400 63.158 0.00 0.00 40.73 4.70
165 169 1.952621 TTAGGAGGAGTGGACCTTGG 58.047 55.000 0.00 0.00 40.73 3.61
182 186 4.764050 TGACACACCTTCTTCCTGTTTA 57.236 40.909 0.00 0.00 0.00 2.01
183 187 3.644966 TGACACACCTTCTTCCTGTTT 57.355 42.857 0.00 0.00 0.00 2.83
187 191 1.810412 GCGTTGACACACCTTCTTCCT 60.810 52.381 0.00 0.00 0.00 3.36
190 194 1.157870 CCGCGTTGACACACCTTCTT 61.158 55.000 4.92 0.00 0.00 2.52
193 197 3.276846 GCCGCGTTGACACACCTT 61.277 61.111 4.92 0.00 0.00 3.50
236 240 3.973973 TGAGAATATACCACCCAAGGGAG 59.026 47.826 13.15 3.47 38.96 4.30
237 241 4.015617 TGAGAATATACCACCCAAGGGA 57.984 45.455 13.15 0.00 38.96 4.20
242 246 5.665360 TCAAGACATGAGAATATACCACCCA 59.335 40.000 0.00 0.00 33.04 4.51
245 249 6.821388 AGGTCAAGACATGAGAATATACCAC 58.179 40.000 0.00 0.00 39.19 4.16
250 254 7.512058 AGGTGATAGGTCAAGACATGAGAATAT 59.488 37.037 0.00 0.00 39.19 1.28
255 259 4.403752 TCAGGTGATAGGTCAAGACATGAG 59.596 45.833 0.00 0.00 39.19 2.90
256 260 4.160439 GTCAGGTGATAGGTCAAGACATGA 59.840 45.833 0.00 0.00 35.80 3.07
264 268 1.471119 GGTCGTCAGGTGATAGGTCA 58.529 55.000 0.00 0.00 0.00 4.02
266 270 0.040646 TGGGTCGTCAGGTGATAGGT 59.959 55.000 0.00 0.00 0.00 3.08
267 271 0.747255 CTGGGTCGTCAGGTGATAGG 59.253 60.000 0.00 0.00 0.00 2.57
270 274 1.258445 GGACTGGGTCGTCAGGTGAT 61.258 60.000 7.74 0.00 38.98 3.06
273 277 1.229209 ATGGACTGGGTCGTCAGGT 60.229 57.895 7.74 0.00 38.98 4.00
276 280 3.387716 CCATGGACTGGGTCGTCA 58.612 61.111 5.56 0.00 41.82 4.35
287 291 2.753701 CACCCGTTGGACCATGGA 59.246 61.111 21.47 0.00 34.81 3.41
288 292 3.061848 GCACCCGTTGGACCATGG 61.062 66.667 11.19 11.19 34.81 3.66
314 318 5.188359 CCATCCAAGGGAACATCTTTTGAAT 59.812 40.000 0.00 0.00 34.34 2.57
325 329 5.946486 AGATATTTCTCCATCCAAGGGAAC 58.054 41.667 0.00 0.00 34.34 3.62
331 335 6.708885 AGGCATAGATATTTCTCCATCCAA 57.291 37.500 0.00 0.00 33.17 3.53
359 363 1.486726 CCGGTAAGAGGAGCCTTGATT 59.513 52.381 0.00 0.00 0.00 2.57
360 364 1.123928 CCGGTAAGAGGAGCCTTGAT 58.876 55.000 0.00 0.00 0.00 2.57
367 371 5.242615 GGTATTACTAACCCGGTAAGAGGAG 59.757 48.000 0.00 0.00 33.50 3.69
421 425 1.677552 CAAGACGGGTAACAGGCCT 59.322 57.895 0.00 0.00 43.16 5.19
426 431 1.071814 GCCACCAAGACGGGTAACA 59.928 57.895 0.00 0.00 39.79 2.41
441 446 2.360726 TCTCGTGCCTCGTAGCCA 60.361 61.111 0.00 0.00 40.80 4.75
446 451 3.432588 CTCCGTCTCGTGCCTCGT 61.433 66.667 0.00 0.00 40.80 4.18
448 453 2.750637 TCCTCCGTCTCGTGCCTC 60.751 66.667 0.00 0.00 0.00 4.70
449 454 3.063084 GTCCTCCGTCTCGTGCCT 61.063 66.667 0.00 0.00 0.00 4.75
481 487 1.480789 TACCATGCGTCAAGGCTCTA 58.519 50.000 0.00 0.00 0.00 2.43
483 489 0.727398 GTTACCATGCGTCAAGGCTC 59.273 55.000 0.00 0.00 0.00 4.70
499 505 2.672295 GTCATGGGTGGCCGGTTA 59.328 61.111 1.90 0.00 0.00 2.85
500 506 4.715523 CGTCATGGGTGGCCGGTT 62.716 66.667 1.90 0.00 0.00 4.44
510 516 3.387091 TGTCCGGTCCCGTCATGG 61.387 66.667 0.00 0.00 37.81 3.66
525 531 3.914426 ACACAGAAAAGTCTCCAGTGT 57.086 42.857 0.00 0.00 35.04 3.55
526 532 3.242870 GCAACACAGAAAAGTCTCCAGTG 60.243 47.826 0.00 0.00 33.55 3.66
527 533 2.945668 GCAACACAGAAAAGTCTCCAGT 59.054 45.455 0.00 0.00 28.78 4.00
528 534 2.945008 TGCAACACAGAAAAGTCTCCAG 59.055 45.455 0.00 0.00 28.78 3.86
531 537 7.168135 CCTTTAAATGCAACACAGAAAAGTCTC 59.832 37.037 0.00 0.00 28.78 3.36
540 546 3.494251 GCCAACCTTTAAATGCAACACAG 59.506 43.478 0.00 0.00 0.00 3.66
541 547 3.133721 AGCCAACCTTTAAATGCAACACA 59.866 39.130 0.00 0.00 0.00 3.72
542 548 3.727726 AGCCAACCTTTAAATGCAACAC 58.272 40.909 0.00 0.00 0.00 3.32
543 549 4.125703 CAAGCCAACCTTTAAATGCAACA 58.874 39.130 0.00 0.00 0.00 3.33
544 550 4.376146 TCAAGCCAACCTTTAAATGCAAC 58.624 39.130 0.00 0.00 0.00 4.17
545 551 4.679373 TCAAGCCAACCTTTAAATGCAA 57.321 36.364 0.00 0.00 0.00 4.08
547 553 3.934579 CCATCAAGCCAACCTTTAAATGC 59.065 43.478 0.00 0.00 0.00 3.56
548 554 5.151297 ACCATCAAGCCAACCTTTAAATG 57.849 39.130 0.00 0.00 0.00 2.32
549 555 4.082245 CGACCATCAAGCCAACCTTTAAAT 60.082 41.667 0.00 0.00 0.00 1.40
550 556 3.254657 CGACCATCAAGCCAACCTTTAAA 59.745 43.478 0.00 0.00 0.00 1.52
553 559 1.247567 CGACCATCAAGCCAACCTTT 58.752 50.000 0.00 0.00 0.00 3.11
558 564 0.539438 AAAGCCGACCATCAAGCCAA 60.539 50.000 0.00 0.00 0.00 4.52
570 576 0.684535 TCATGGTCTGACAAAGCCGA 59.315 50.000 10.38 0.00 0.00 5.54
573 579 3.854784 GCACTTTCATGGTCTGACAAAGC 60.855 47.826 10.38 0.00 32.17 3.51
574 580 3.304928 GGCACTTTCATGGTCTGACAAAG 60.305 47.826 10.38 12.35 32.17 2.77
593 599 1.907807 GTGGGTGGCAATCAAGGCA 60.908 57.895 0.00 0.00 42.25 4.75
603 609 4.148825 ATCGAGAGCGTGGGTGGC 62.149 66.667 0.00 0.00 38.98 5.01
616 622 1.218047 CTTCCCAAGGACGCATCGA 59.782 57.895 0.00 0.00 0.00 3.59
619 625 2.436646 CGCTTCCCAAGGACGCAT 60.437 61.111 12.01 0.00 45.57 4.73
620 626 4.697756 CCGCTTCCCAAGGACGCA 62.698 66.667 12.01 0.00 45.57 5.24
682 689 2.311542 TGGTTGGGACTGCCTAATGATT 59.688 45.455 0.00 0.00 36.98 2.57
711 718 8.903820 CCAGGTATGTTCTTTAAATAAGGGAAG 58.096 37.037 0.00 0.00 0.00 3.46
713 720 7.935405 ACCAGGTATGTTCTTTAAATAAGGGA 58.065 34.615 0.00 0.00 0.00 4.20
760 767 8.580720 TCACAATTTAACTAGGCATGCTAAAAA 58.419 29.630 18.92 10.05 0.00 1.94
761 768 8.116651 TCACAATTTAACTAGGCATGCTAAAA 57.883 30.769 18.92 9.39 0.00 1.52
762 769 7.695480 TCACAATTTAACTAGGCATGCTAAA 57.305 32.000 18.92 13.90 0.00 1.85
763 770 7.393234 AGTTCACAATTTAACTAGGCATGCTAA 59.607 33.333 18.92 4.89 34.23 3.09
764 771 6.884295 AGTTCACAATTTAACTAGGCATGCTA 59.116 34.615 18.92 7.14 34.23 3.49
805 812 6.239036 GCTCAGGAACCTCTAAAAACAAATGT 60.239 38.462 0.00 0.00 0.00 2.71
806 813 6.015940 AGCTCAGGAACCTCTAAAAACAAATG 60.016 38.462 0.00 0.00 0.00 2.32
807 814 6.071320 AGCTCAGGAACCTCTAAAAACAAAT 58.929 36.000 0.00 0.00 0.00 2.32
809 816 5.048846 AGCTCAGGAACCTCTAAAAACAA 57.951 39.130 0.00 0.00 0.00 2.83
810 817 4.642429 GAGCTCAGGAACCTCTAAAAACA 58.358 43.478 9.40 0.00 0.00 2.83
811 818 3.680458 CGAGCTCAGGAACCTCTAAAAAC 59.320 47.826 15.40 0.00 0.00 2.43
814 821 2.492484 GACGAGCTCAGGAACCTCTAAA 59.508 50.000 15.40 0.00 0.00 1.85
817 824 0.251386 TGACGAGCTCAGGAACCTCT 60.251 55.000 15.40 0.00 0.00 3.69
818 825 0.603569 TTGACGAGCTCAGGAACCTC 59.396 55.000 15.40 1.06 0.00 3.85
819 826 0.318762 GTTGACGAGCTCAGGAACCT 59.681 55.000 15.40 0.00 0.00 3.50
822 829 2.158957 AGTTTGTTGACGAGCTCAGGAA 60.159 45.455 15.40 0.00 0.00 3.36
824 831 1.795286 GAGTTTGTTGACGAGCTCAGG 59.205 52.381 15.40 0.13 37.49 3.86
825 832 1.453524 CGAGTTTGTTGACGAGCTCAG 59.546 52.381 15.40 9.21 37.42 3.35
826 833 1.487482 CGAGTTTGTTGACGAGCTCA 58.513 50.000 15.40 0.00 37.42 4.26
827 834 0.161870 GCGAGTTTGTTGACGAGCTC 59.838 55.000 2.73 2.73 35.15 4.09
828 835 0.529773 TGCGAGTTTGTTGACGAGCT 60.530 50.000 0.00 0.00 0.00 4.09
829 836 0.512952 ATGCGAGTTTGTTGACGAGC 59.487 50.000 0.00 0.00 0.00 5.03
830 837 1.792367 TGATGCGAGTTTGTTGACGAG 59.208 47.619 0.00 0.00 0.00 4.18
831 838 1.792367 CTGATGCGAGTTTGTTGACGA 59.208 47.619 0.00 0.00 0.00 4.20
832 839 1.526887 ACTGATGCGAGTTTGTTGACG 59.473 47.619 0.00 0.00 0.00 4.35
833 840 2.543848 TCACTGATGCGAGTTTGTTGAC 59.456 45.455 0.00 0.00 0.00 3.18
835 842 3.485633 CATCACTGATGCGAGTTTGTTG 58.514 45.455 6.08 0.00 33.17 3.33
836 843 3.818961 CATCACTGATGCGAGTTTGTT 57.181 42.857 6.08 0.00 33.17 2.83
846 853 1.077501 AACCCGGGCATCACTGATG 60.078 57.895 24.08 13.90 42.37 3.07
895 903 4.547859 CTGCAGGATGTAGGTGGC 57.452 61.111 5.57 0.00 45.67 5.01
1062 1070 0.601576 TATGCGCGTCACCTGTTTGT 60.602 50.000 4.79 0.00 0.00 2.83
1094 1102 4.506255 GAAGGGTGGGCGGATGGG 62.506 72.222 0.00 0.00 0.00 4.00
1100 1108 1.933307 ATAAAGGGGAAGGGTGGGCG 61.933 60.000 0.00 0.00 0.00 6.13
1101 1109 0.338467 AATAAAGGGGAAGGGTGGGC 59.662 55.000 0.00 0.00 0.00 5.36
1102 1110 2.747177 GAAATAAAGGGGAAGGGTGGG 58.253 52.381 0.00 0.00 0.00 4.61
1107 1115 3.368013 GCAAACCGAAATAAAGGGGAAGG 60.368 47.826 0.00 0.00 0.00 3.46
1166 1174 4.830600 TGAAACCCTTTCTAATTTCCGCTT 59.169 37.500 0.00 0.00 40.32 4.68
1190 1198 2.680841 CGAACAACAAAGGTCAGGTTCA 59.319 45.455 0.00 0.00 34.66 3.18
1210 1218 7.511809 AATACGTGATGATATCATAGCAACG 57.488 36.000 25.55 25.55 42.04 4.10
1227 1235 4.504461 GCTGATCTGACCTTGTAATACGTG 59.496 45.833 0.00 0.00 0.00 4.49
1312 1320 9.993454 GGAAGTAATTTATTCTACCGGACTAAT 57.007 33.333 9.46 6.81 0.00 1.73
1319 1327 9.250624 CTCAGAAGGAAGTAATTTATTCTACCG 57.749 37.037 4.04 0.00 0.00 4.02
1388 1396 8.213518 ACACAGATCGTATGCTCAAAAATAAT 57.786 30.769 0.00 0.00 0.00 1.28
1389 1397 7.609760 ACACAGATCGTATGCTCAAAAATAA 57.390 32.000 0.00 0.00 0.00 1.40
1391 1399 6.317088 CAACACAGATCGTATGCTCAAAAAT 58.683 36.000 0.00 0.00 0.00 1.82
1454 1463 9.002080 CAGCAATTCAAGATTTTCAAACAAAAC 57.998 29.630 0.00 0.00 0.00 2.43
1481 1490 2.005451 ACAATCTCATTCTCTGCGCAC 58.995 47.619 5.66 0.00 0.00 5.34
1482 1491 2.391616 ACAATCTCATTCTCTGCGCA 57.608 45.000 10.98 10.98 0.00 6.09
1502 1513 1.541118 TGGGGGCTGGAACATCTGA 60.541 57.895 0.00 0.00 38.20 3.27
1520 1531 0.961358 CCTCCTCACTCCGACGAACT 60.961 60.000 0.00 0.00 0.00 3.01
1528 1539 0.972983 TGCTACTGCCTCCTCACTCC 60.973 60.000 0.00 0.00 38.71 3.85
1763 1774 3.822167 TGTAGGTAGATGTGTCGTGTTCA 59.178 43.478 0.00 0.00 0.00 3.18
1778 1789 4.948341 ACGTATCAATGCCATGTAGGTA 57.052 40.909 0.00 0.00 40.61 3.08
1781 1792 5.484173 AACAACGTATCAATGCCATGTAG 57.516 39.130 0.00 0.00 0.00 2.74
1859 1870 3.127589 CGTGACAACACACACAGGATTA 58.872 45.455 0.00 0.00 46.20 1.75
1868 1879 1.204062 CATCGGCGTGACAACACAC 59.796 57.895 6.85 0.00 46.20 3.82
2561 2572 5.048921 CCATGATGAAATCTCAGAAATCCGG 60.049 44.000 0.00 0.00 45.81 5.14
2564 2575 7.011763 TCGAACCATGATGAAATCTCAGAAATC 59.988 37.037 0.00 0.00 45.81 2.17
2804 2815 5.047731 AGAGGAGCCACAATTTTCTTTTAGC 60.048 40.000 0.00 0.00 0.00 3.09
2849 2860 7.054124 CAGCCTTCCCTAAGTGTTTTATCATA 58.946 38.462 0.00 0.00 0.00 2.15
2963 2974 2.768492 GCCTGCTCTTGCCAATCCG 61.768 63.158 0.00 0.00 38.71 4.18
3290 3301 8.517878 CCATGTTTAGTTCATTCTTGATCAACT 58.482 33.333 3.38 1.44 0.00 3.16
3302 3313 6.620877 TCCTACTGACCATGTTTAGTTCAT 57.379 37.500 0.00 0.00 0.00 2.57
3309 3320 3.650942 TCCTGTTCCTACTGACCATGTTT 59.349 43.478 0.00 0.00 0.00 2.83
3312 3323 4.080919 TGAATCCTGTTCCTACTGACCATG 60.081 45.833 0.00 0.00 0.00 3.66
3333 3344 1.810151 GAACGCTACCAAAAGGCATGA 59.190 47.619 0.00 0.00 0.00 3.07
3337 3348 3.072211 ACTTAGAACGCTACCAAAAGGC 58.928 45.455 0.00 0.00 0.00 4.35
3349 3360 8.251750 TGGATCAAGATGTTTTACTTAGAACG 57.748 34.615 0.00 0.00 0.00 3.95
3397 3408 0.746659 GCTGCACAAAAACTGGGAGT 59.253 50.000 0.00 0.00 0.00 3.85
3417 3428 6.818644 AGCTTTTTATATCGAAGAGTTGCAGA 59.181 34.615 0.00 0.00 43.63 4.26
3426 3437 9.065871 CACAAAAGGAAGCTTTTTATATCGAAG 57.934 33.333 0.00 0.00 34.68 3.79
3498 3511 2.035449 CACACCTTCTACGGTTGACTCA 59.965 50.000 0.00 0.00 34.29 3.41
3499 3512 2.035576 ACACACCTTCTACGGTTGACTC 59.964 50.000 0.00 0.00 34.29 3.36
3529 3542 8.210265 AGGATTTTGACCATGTGTTAACAAAAT 58.790 29.630 10.51 9.77 44.66 1.82
3530 3543 7.493971 CAGGATTTTGACCATGTGTTAACAAAA 59.506 33.333 10.51 5.14 40.46 2.44
3531 3544 6.983307 CAGGATTTTGACCATGTGTTAACAAA 59.017 34.615 10.51 5.16 40.46 2.83
3532 3545 6.097554 ACAGGATTTTGACCATGTGTTAACAA 59.902 34.615 10.51 1.41 40.46 2.83
3533 3546 5.596361 ACAGGATTTTGACCATGTGTTAACA 59.404 36.000 3.59 3.59 41.58 2.41
3534 3547 6.084326 ACAGGATTTTGACCATGTGTTAAC 57.916 37.500 0.00 0.00 0.00 2.01
3535 3548 6.723298 AACAGGATTTTGACCATGTGTTAA 57.277 33.333 0.00 0.00 0.00 2.01
3536 3549 7.450014 ACATAACAGGATTTTGACCATGTGTTA 59.550 33.333 0.00 0.00 33.46 2.41
3537 3550 6.267471 ACATAACAGGATTTTGACCATGTGTT 59.733 34.615 0.00 0.00 31.58 3.32
3538 3551 5.774690 ACATAACAGGATTTTGACCATGTGT 59.225 36.000 0.00 0.00 0.00 3.72
3539 3552 6.271488 ACATAACAGGATTTTGACCATGTG 57.729 37.500 0.00 0.00 0.00 3.21
3540 3553 6.071391 GGAACATAACAGGATTTTGACCATGT 60.071 38.462 0.00 0.00 0.00 3.21
3541 3554 6.332630 GGAACATAACAGGATTTTGACCATG 58.667 40.000 0.00 0.00 0.00 3.66
3542 3555 5.125417 CGGAACATAACAGGATTTTGACCAT 59.875 40.000 0.00 0.00 0.00 3.55
3543 3556 4.457603 CGGAACATAACAGGATTTTGACCA 59.542 41.667 0.00 0.00 0.00 4.02
3544 3557 4.457949 ACGGAACATAACAGGATTTTGACC 59.542 41.667 0.00 0.00 0.00 4.02
3545 3558 5.391629 GGACGGAACATAACAGGATTTTGAC 60.392 44.000 0.00 0.00 0.00 3.18
3546 3559 4.698304 GGACGGAACATAACAGGATTTTGA 59.302 41.667 0.00 0.00 0.00 2.69
3547 3560 4.700213 AGGACGGAACATAACAGGATTTTG 59.300 41.667 0.00 0.00 0.00 2.44
3548 3561 4.918588 AGGACGGAACATAACAGGATTTT 58.081 39.130 0.00 0.00 0.00 1.82
3549 3562 4.225267 AGAGGACGGAACATAACAGGATTT 59.775 41.667 0.00 0.00 0.00 2.17
3550 3563 3.775316 AGAGGACGGAACATAACAGGATT 59.225 43.478 0.00 0.00 0.00 3.01
3551 3564 3.375699 AGAGGACGGAACATAACAGGAT 58.624 45.455 0.00 0.00 0.00 3.24
3552 3565 2.816411 AGAGGACGGAACATAACAGGA 58.184 47.619 0.00 0.00 0.00 3.86
3553 3566 3.611766 AAGAGGACGGAACATAACAGG 57.388 47.619 0.00 0.00 0.00 4.00
3554 3567 7.611213 ATTTAAAGAGGACGGAACATAACAG 57.389 36.000 0.00 0.00 0.00 3.16
3555 3568 7.989416 AATTTAAAGAGGACGGAACATAACA 57.011 32.000 0.00 0.00 0.00 2.41
3556 3569 8.508875 TCAAATTTAAAGAGGACGGAACATAAC 58.491 33.333 0.00 0.00 0.00 1.89
3557 3570 8.624367 TCAAATTTAAAGAGGACGGAACATAA 57.376 30.769 0.00 0.00 0.00 1.90
3558 3571 8.801882 ATCAAATTTAAAGAGGACGGAACATA 57.198 30.769 0.00 0.00 0.00 2.29
3559 3572 7.703058 ATCAAATTTAAAGAGGACGGAACAT 57.297 32.000 0.00 0.00 0.00 2.71
3560 3573 8.624367 TTATCAAATTTAAAGAGGACGGAACA 57.376 30.769 0.00 0.00 0.00 3.18
3561 3574 9.717892 GATTATCAAATTTAAAGAGGACGGAAC 57.282 33.333 0.00 0.00 0.00 3.62
3562 3575 9.681062 AGATTATCAAATTTAAAGAGGACGGAA 57.319 29.630 0.00 0.00 0.00 4.30
3594 3607 6.621316 TCGCTAACAAAAAGGTGAAATACA 57.379 33.333 0.00 0.00 0.00 2.29
3595 3608 7.061789 CCATTCGCTAACAAAAAGGTGAAATAC 59.938 37.037 0.00 0.00 33.07 1.89
3596 3609 7.087639 CCATTCGCTAACAAAAAGGTGAAATA 58.912 34.615 0.00 0.00 33.07 1.40
3597 3610 5.925969 CCATTCGCTAACAAAAAGGTGAAAT 59.074 36.000 0.00 0.00 33.07 2.17
3598 3611 5.285651 CCATTCGCTAACAAAAAGGTGAAA 58.714 37.500 0.00 0.00 33.07 2.69
3599 3612 4.794655 GCCATTCGCTAACAAAAAGGTGAA 60.795 41.667 0.00 0.00 33.69 3.18
3600 3613 3.305064 GCCATTCGCTAACAAAAAGGTGA 60.305 43.478 0.00 0.00 0.00 4.02
3601 3614 2.986479 GCCATTCGCTAACAAAAAGGTG 59.014 45.455 0.00 0.00 0.00 4.00
3602 3615 2.029380 GGCCATTCGCTAACAAAAAGGT 60.029 45.455 0.00 0.00 37.74 3.50
3603 3616 2.029470 TGGCCATTCGCTAACAAAAAGG 60.029 45.455 0.00 0.00 37.74 3.11
3604 3617 3.296322 TGGCCATTCGCTAACAAAAAG 57.704 42.857 0.00 0.00 37.74 2.27
3605 3618 3.735237 TTGGCCATTCGCTAACAAAAA 57.265 38.095 6.09 0.00 32.20 1.94
3606 3619 3.735237 TTTGGCCATTCGCTAACAAAA 57.265 38.095 6.09 0.00 37.73 2.44
3607 3620 3.735237 TTTTGGCCATTCGCTAACAAA 57.265 38.095 6.09 0.00 37.73 2.83
3608 3621 3.951775 ATTTTGGCCATTCGCTAACAA 57.048 38.095 6.09 0.00 37.73 2.83
3609 3622 3.129638 GGTATTTTGGCCATTCGCTAACA 59.870 43.478 6.09 0.00 37.73 2.41
3610 3623 3.702330 GGTATTTTGGCCATTCGCTAAC 58.298 45.455 6.09 0.00 37.73 2.34
3611 3624 2.356382 CGGTATTTTGGCCATTCGCTAA 59.644 45.455 6.09 0.00 35.94 3.09
3616 3629 5.257082 ACATAACGGTATTTTGGCCATTC 57.743 39.130 6.09 0.00 0.00 2.67
3710 3723 3.135348 CAGCCCTCACATCTTAATGGAGA 59.865 47.826 0.00 0.00 37.19 3.71
3724 3737 1.321474 CTTTTCAGCAACAGCCCTCA 58.679 50.000 0.00 0.00 0.00 3.86
3752 3765 9.659830 CATACAGTAGTTAACTTTTCACCAAAC 57.340 33.333 14.49 2.33 35.76 2.93
3756 3769 9.048446 TCAACATACAGTAGTTAACTTTTCACC 57.952 33.333 14.49 0.00 35.76 4.02
3788 3802 6.016777 ACTCCACTTGTGATTGCTAAAGAAAG 60.017 38.462 1.89 0.00 0.00 2.62
3795 3809 3.402110 CACACTCCACTTGTGATTGCTA 58.598 45.455 1.89 0.00 46.18 3.49
3805 3819 1.072173 TGTAGCATGCACACTCCACTT 59.928 47.619 21.98 0.00 0.00 3.16
3815 3829 3.689347 ACTTCAGGAATTGTAGCATGCA 58.311 40.909 21.98 2.77 0.00 3.96
3851 3865 2.015587 GGTTTACCCACACAAACACGA 58.984 47.619 0.00 0.00 36.56 4.35
3908 3922 9.135189 CCTACCATATCTTTGATTTTGGATTCA 57.865 33.333 12.86 0.00 0.00 2.57
3934 3948 0.179070 GAGAGGAGAAATGGGGACGC 60.179 60.000 0.00 0.00 0.00 5.19
3959 3973 1.617357 AGGAAGTTCGGAAAGCTACGT 59.383 47.619 0.00 0.00 0.00 3.57
3984 3998 9.912634 TCTGGAAAAGCTATATTTTTCAACAAG 57.087 29.630 17.46 11.81 43.14 3.16
4045 4059 1.746220 TGCCAAACTACAACACACACC 59.254 47.619 0.00 0.00 0.00 4.16
4092 4106 2.029020 TGTCAGAATCCACAGAGTTCCG 60.029 50.000 0.00 0.00 0.00 4.30
4172 4193 0.609131 GTAAGCCCCTGTGCACACAT 60.609 55.000 17.42 1.44 41.01 3.21
4218 4239 3.478857 TTCGGAAGGCTTCAAACACTA 57.521 42.857 27.17 0.36 0.00 2.74


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

AutoCloner maintained by Alex Coulton.