Multiple sequence alignment - TraesCS2D01G167700

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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 TraesCS2D01G167700 chr2D 100.000 5430 0 0 1 5430 111336077 111330648 0.000000e+00 10028.0
1 TraesCS2D01G167700 chr2D 95.789 285 12 0 1312 1596 111334673 111334389 1.380000e-125 460.0
2 TraesCS2D01G167700 chr2D 95.789 285 12 0 1405 1689 111334766 111334482 1.380000e-125 460.0
3 TraesCS2D01G167700 chr2D 93.750 192 12 0 1312 1503 111334580 111334389 6.880000e-74 289.0
4 TraesCS2D01G167700 chr2D 93.750 192 12 0 1498 1689 111334766 111334575 6.880000e-74 289.0
5 TraesCS2D01G167700 chr2D 91.919 99 8 0 1312 1410 111334487 111334389 7.330000e-29 139.0
6 TraesCS2D01G167700 chr2D 91.919 99 8 0 1591 1689 111334766 111334668 7.330000e-29 139.0
7 TraesCS2D01G167700 chr2A 95.368 3238 95 18 1405 4613 111424154 111420943 0.000000e+00 5097.0
8 TraesCS2D01G167700 chr2A 93.614 1613 55 10 1 1596 111425451 111423870 0.000000e+00 2364.0
9 TraesCS2D01G167700 chr2A 91.892 629 36 7 4602 5225 111420914 111420296 0.000000e+00 865.0
10 TraesCS2D01G167700 chr2B 94.142 2851 88 26 1 2818 161419129 161416325 0.000000e+00 4266.0
11 TraesCS2D01G167700 chr2B 94.644 2222 71 17 2815 5003 161416223 161414017 0.000000e+00 3400.0
12 TraesCS2D01G167700 chr2B 96.140 285 11 0 1312 1596 161417745 161417461 2.960000e-127 466.0
13 TraesCS2D01G167700 chr2B 95.088 285 14 0 1405 1689 161417838 161417554 2.980000e-122 449.0
14 TraesCS2D01G167700 chr2B 94.271 192 11 0 1498 1689 161417838 161417647 1.480000e-75 294.0
15 TraesCS2D01G167700 chr2B 93.229 192 13 0 1312 1503 161417652 161417461 3.200000e-72 283.0
16 TraesCS2D01G167700 chr2B 93.939 99 6 0 1312 1410 161417559 161417461 3.390000e-32 150.0
17 TraesCS2D01G167700 chr3A 82.981 946 90 42 2317 3235 687993552 687992651 0.000000e+00 789.0
18 TraesCS2D01G167700 chr4A 86.387 191 24 2 3373 3563 255591598 255591410 1.980000e-49 207.0
19 TraesCS2D01G167700 chr4A 85.526 76 11 0 3248 3323 255591746 255591671 4.510000e-11 80.5
20 TraesCS2D01G167700 chr4D 89.441 161 17 0 3403 3563 274221106 274221266 2.560000e-48 204.0
21 TraesCS2D01G167700 chr4D 80.734 109 21 0 3215 3323 274220897 274221005 9.690000e-13 86.1
22 TraesCS2D01G167700 chr4B 85.864 191 25 2 3373 3563 240826723 240826911 9.220000e-48 202.0
23 TraesCS2D01G167700 chr4B 79.817 109 22 0 3215 3323 240826542 240826650 4.510000e-11 80.5
24 TraesCS2D01G167700 chr5D 84.545 110 17 0 5099 5208 384012527 384012636 5.750000e-20 110.0


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 TraesCS2D01G167700 chr2D 111330648 111336077 5429 True 1686.285714 10028 94.702286 1 5430 7 chr2D.!!$R1 5429
1 TraesCS2D01G167700 chr2A 111420296 111425451 5155 True 2775.333333 5097 93.624667 1 5225 3 chr2A.!!$R1 5224
2 TraesCS2D01G167700 chr2B 161414017 161419129 5112 True 1329.714286 4266 94.493286 1 5003 7 chr2B.!!$R1 5002
3 TraesCS2D01G167700 chr3A 687992651 687993552 901 True 789.000000 789 82.981000 2317 3235 1 chr3A.!!$R1 918

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
556 562 2.851263 TTCTGTGGTTTCGGTATGCT 57.149 45.000 0.0 0.0 0.00 3.79 F
1427 1455 1.066858 TGCGGAGGCTAGTGAGAAAAG 60.067 52.381 0.0 0.0 40.82 2.27 F
2022 2050 0.176680 CGCCTCCAGATGCTAGTGTT 59.823 55.000 0.0 0.0 0.00 3.32 F
2089 2117 1.815003 GACAAAATGCTGAGACCCTGG 59.185 52.381 0.0 0.0 0.00 4.45 F
3304 3493 1.071385 ACAGCAAGTGGAGGTTCTCAG 59.929 52.381 0.0 0.0 31.08 3.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1813 1841 1.065564 AGCTTGTGGAGATGCTTCCTC 60.066 52.381 0.00 0.00 38.12 3.71 R
2344 2372 1.117150 ATGGAGGGAATGTTGCATGC 58.883 50.000 11.82 11.82 0.00 4.06 R
3304 3493 1.757699 ACCTCACCTATCCGCTCTTTC 59.242 52.381 0.00 0.00 0.00 2.62 R
3486 3678 2.743636 TCCAGTTCTACCAAGAAGCG 57.256 50.000 0.00 0.00 42.40 4.68 R
4523 4717 0.028770 TGTTAACTGCTGCAACACGC 59.971 50.000 3.02 0.00 42.89 5.34 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
285 290 4.143333 ACCGTTGGGGATCTCGCG 62.143 66.667 0.00 0.00 39.97 5.87
449 455 4.020662 AGGTCTGTTCTGTGAGAGGAAATC 60.021 45.833 0.00 0.00 0.00 2.17
512 518 4.020928 TGGTTTCGTTATGCTCTGGAGTAA 60.021 41.667 0.00 0.00 0.00 2.24
513 519 4.933400 GGTTTCGTTATGCTCTGGAGTAAA 59.067 41.667 0.00 0.00 0.00 2.01
514 520 5.585047 GGTTTCGTTATGCTCTGGAGTAAAT 59.415 40.000 0.00 0.00 0.00 1.40
515 521 6.093633 GGTTTCGTTATGCTCTGGAGTAAATT 59.906 38.462 0.00 0.00 0.00 1.82
516 522 6.903883 TTCGTTATGCTCTGGAGTAAATTC 57.096 37.500 0.00 0.00 0.00 2.17
517 523 6.222038 TCGTTATGCTCTGGAGTAAATTCT 57.778 37.500 0.00 0.00 0.00 2.40
518 524 6.042777 TCGTTATGCTCTGGAGTAAATTCTG 58.957 40.000 0.00 0.00 0.00 3.02
519 525 5.812642 CGTTATGCTCTGGAGTAAATTCTGT 59.187 40.000 0.00 0.00 0.00 3.41
520 526 6.237942 CGTTATGCTCTGGAGTAAATTCTGTG 60.238 42.308 0.00 0.00 0.00 3.66
521 527 3.942829 TGCTCTGGAGTAAATTCTGTGG 58.057 45.455 0.00 0.00 0.00 4.17
522 528 3.327757 TGCTCTGGAGTAAATTCTGTGGT 59.672 43.478 0.00 0.00 0.00 4.16
523 529 4.202461 TGCTCTGGAGTAAATTCTGTGGTT 60.202 41.667 0.00 0.00 0.00 3.67
524 530 4.762251 GCTCTGGAGTAAATTCTGTGGTTT 59.238 41.667 0.00 0.00 0.00 3.27
525 531 5.241728 GCTCTGGAGTAAATTCTGTGGTTTT 59.758 40.000 0.00 0.00 0.00 2.43
526 532 6.633500 TCTGGAGTAAATTCTGTGGTTTTG 57.367 37.500 0.00 0.00 0.00 2.44
527 533 6.361433 TCTGGAGTAAATTCTGTGGTTTTGA 58.639 36.000 0.00 0.00 0.00 2.69
528 534 7.004086 TCTGGAGTAAATTCTGTGGTTTTGAT 58.996 34.615 0.00 0.00 0.00 2.57
529 535 8.160765 TCTGGAGTAAATTCTGTGGTTTTGATA 58.839 33.333 0.00 0.00 0.00 2.15
530 536 8.877864 TGGAGTAAATTCTGTGGTTTTGATAT 57.122 30.769 0.00 0.00 0.00 1.63
556 562 2.851263 TTCTGTGGTTTCGGTATGCT 57.149 45.000 0.00 0.00 0.00 3.79
599 605 6.183360 GCCTATGCAATTTTGTTTTATGGTGG 60.183 38.462 0.00 0.00 37.47 4.61
681 692 7.226128 CACTTATGACTTATCACACAGATGCAT 59.774 37.037 0.00 0.00 37.79 3.96
697 708 6.088824 CAGATGCATAGTGTGAAACCTTTTC 58.911 40.000 0.00 0.00 34.36 2.29
716 727 6.655003 CCTTTTCTTTCTACATGGAGCACTTA 59.345 38.462 0.00 0.00 0.00 2.24
745 756 6.261381 TGACTATAATTTTACCCACCAATCGC 59.739 38.462 0.00 0.00 0.00 4.58
807 818 7.126726 GCATGTAAATTGCTACTCTATCAGG 57.873 40.000 0.00 0.00 37.14 3.86
880 904 4.276926 AGTTTGCAGCAACTTAAGAAGGAG 59.723 41.667 7.54 0.00 0.00 3.69
972 997 9.023962 TCATGTTTAATGGTTTAGCTGATTTCT 57.976 29.630 0.00 0.00 0.00 2.52
1153 1178 7.130099 TGAGGAACTTCAGGGTGATATACTTA 58.870 38.462 0.00 0.00 41.55 2.24
1376 1404 6.583562 AGGTTATTCAGGATGCTGTAGTTAC 58.416 40.000 14.43 7.28 34.76 2.50
1394 1422 6.175712 AGTTACTACCGAAGAAGTTAGTCG 57.824 41.667 1.56 1.56 34.58 4.18
1427 1455 1.066858 TGCGGAGGCTAGTGAGAAAAG 60.067 52.381 0.00 0.00 40.82 2.27
1431 1459 2.027653 GGAGGCTAGTGAGAAAAGTGCT 60.028 50.000 0.00 0.00 0.00 4.40
1677 1705 5.687828 AGTAACGAAGAAGTTAGTCAGACG 58.312 41.667 0.00 0.00 35.92 4.18
1812 1840 4.579869 CTCCAAGTGGCAGTAATGTAGTT 58.420 43.478 0.00 0.00 34.44 2.24
1813 1841 4.323417 TCCAAGTGGCAGTAATGTAGTTG 58.677 43.478 0.00 8.97 34.44 3.16
1917 1945 8.499162 GTGATTGCTAATTATCTACCATGTGAC 58.501 37.037 0.00 0.00 0.00 3.67
2021 2049 0.684479 TCGCCTCCAGATGCTAGTGT 60.684 55.000 0.00 0.00 0.00 3.55
2022 2050 0.176680 CGCCTCCAGATGCTAGTGTT 59.823 55.000 0.00 0.00 0.00 3.32
2089 2117 1.815003 GACAAAATGCTGAGACCCTGG 59.185 52.381 0.00 0.00 0.00 4.45
2205 2233 2.107726 AGGGACAAAAGACCAGGTAACC 59.892 50.000 0.00 0.00 37.17 2.85
2576 2636 7.290948 TGTTGATACCATTATCAGATCTGGAGT 59.709 37.037 22.42 11.39 44.03 3.85
2836 3000 7.894376 AAAGTATTTCATTTTCTGTGGCATG 57.106 32.000 0.00 0.00 27.08 4.06
2886 3073 7.503521 TGTGTAAAGTTCATTGTCTGCATTA 57.496 32.000 0.00 0.00 0.00 1.90
2951 3138 3.563808 TGCATGAAACAGTTGTACCTCAC 59.436 43.478 0.00 0.00 0.00 3.51
3304 3493 1.071385 ACAGCAAGTGGAGGTTCTCAG 59.929 52.381 0.00 0.00 31.08 3.35
3331 3520 2.022195 CGGATAGGTGAGGTTTCTCGA 58.978 52.381 0.00 0.00 42.79 4.04
3701 3893 8.647226 GTGTTACAGCTAAAATTTGCTAAATGG 58.353 33.333 2.95 0.00 37.15 3.16
3799 3993 8.289544 AGGGATTAATTTTTGGCTAGGTATTCT 58.710 33.333 0.00 0.00 0.00 2.40
3809 4003 7.618019 TTGGCTAGGTATTCTTCTGTATGAT 57.382 36.000 0.00 0.00 0.00 2.45
3858 4052 2.811431 TCGTGCCTTATTGTTGGTTCAG 59.189 45.455 0.00 0.00 0.00 3.02
4012 4206 2.243810 GTTTACAACCTCCAATGGCCA 58.756 47.619 8.56 8.56 0.00 5.36
4083 4277 3.251004 GTGAAGCTCAAAATCGAACACCT 59.749 43.478 0.00 0.00 0.00 4.00
4193 4387 2.611505 CCCCATGGCACTGGTACCA 61.612 63.158 15.39 15.39 41.06 3.25
4342 4536 0.471780 TCTTCAGGAGGACACAGGCA 60.472 55.000 0.00 0.00 0.00 4.75
4396 4590 1.073897 GGAGGTGTCAGCCAAGCTT 59.926 57.895 0.00 0.00 36.40 3.74
4429 4623 1.276989 AGGCGAAATTGGAGACGGTAA 59.723 47.619 0.00 0.00 0.00 2.85
4496 4690 5.426504 CTCATCTCTTATTCAGGCACAACT 58.573 41.667 0.00 0.00 0.00 3.16
4523 4717 0.179062 CCAGCGGATTCTCTTCCCAG 60.179 60.000 0.00 0.00 31.61 4.45
4524 4718 0.813210 CAGCGGATTCTCTTCCCAGC 60.813 60.000 0.00 0.00 31.61 4.85
4555 4761 2.095059 CAGTTAACATGAAGGCTGTGGC 60.095 50.000 8.61 0.00 37.82 5.01
4590 4796 4.075682 TGGTTGGTGATATTTTGCGAAGA 58.924 39.130 0.00 0.00 0.00 2.87
4591 4797 4.520874 TGGTTGGTGATATTTTGCGAAGAA 59.479 37.500 0.00 0.00 0.00 2.52
4592 4798 5.095490 GGTTGGTGATATTTTGCGAAGAAG 58.905 41.667 0.00 0.00 0.00 2.85
4613 4862 1.264288 CTTTGCACGGTCTTGGTCTTC 59.736 52.381 0.00 0.00 0.00 2.87
4664 4913 4.683832 TCTAGCTCTATTTTCGCTTGTCC 58.316 43.478 0.00 0.00 35.33 4.02
4669 4918 1.062587 CTATTTTCGCTTGTCCGCCTG 59.937 52.381 0.00 0.00 0.00 4.85
4729 4978 4.286808 TCAGTCATCCTTTGGATCAGTTGA 59.713 41.667 0.00 0.00 40.98 3.18
4738 4987 3.144657 TGGATCAGTTGAGCAATGTGT 57.855 42.857 0.00 0.00 30.87 3.72
4767 5016 3.159213 TGTTGATGAACCCTTGATGCT 57.841 42.857 0.00 0.00 0.00 3.79
4768 5017 3.499338 TGTTGATGAACCCTTGATGCTT 58.501 40.909 0.00 0.00 0.00 3.91
4769 5018 4.661222 TGTTGATGAACCCTTGATGCTTA 58.339 39.130 0.00 0.00 0.00 3.09
4770 5019 4.701651 TGTTGATGAACCCTTGATGCTTAG 59.298 41.667 0.00 0.00 0.00 2.18
4771 5020 3.889815 TGATGAACCCTTGATGCTTAGG 58.110 45.455 0.00 0.00 0.00 2.69
4772 5021 3.523157 TGATGAACCCTTGATGCTTAGGA 59.477 43.478 0.00 0.00 33.13 2.94
4773 5022 4.018506 TGATGAACCCTTGATGCTTAGGAA 60.019 41.667 0.00 0.00 33.13 3.36
4774 5023 3.955471 TGAACCCTTGATGCTTAGGAAG 58.045 45.455 0.00 0.00 33.13 3.46
4893 5142 6.200878 TGAGGGAACTTGGTCTCTTTATTT 57.799 37.500 0.00 0.00 44.43 1.40
5032 5291 6.599356 TTTTGAGGGGGTAAGCTAAATTTC 57.401 37.500 0.00 0.00 0.00 2.17
5068 5327 6.769822 AGTAGCATGGAGAGGAATACAAATTG 59.230 38.462 0.00 0.00 0.00 2.32
5077 5336 4.207165 AGGAATACAAATTGGATCGTGGG 58.793 43.478 0.00 0.00 0.00 4.61
5095 5354 0.471022 GGGGGTGAACCAAACATGGT 60.471 55.000 1.16 0.00 45.55 3.55
5102 5361 0.399806 AACCAAACATGGTGCCCCTT 60.400 50.000 0.47 0.00 42.20 3.95
5103 5362 1.120795 ACCAAACATGGTGCCCCTTG 61.121 55.000 0.00 0.00 41.33 3.61
5111 5370 1.152546 GGTGCCCCTTGTCCAAAGT 60.153 57.895 0.00 0.00 0.00 2.66
5112 5371 0.759060 GGTGCCCCTTGTCCAAAGTT 60.759 55.000 0.00 0.00 0.00 2.66
5137 5396 9.554724 TTTTCGCAAATTTAGCTAAACTATCTG 57.445 29.630 20.85 13.67 0.00 2.90
5141 5400 7.322222 CGCAAATTTAGCTAAACTATCTGCATC 59.678 37.037 20.85 2.53 0.00 3.91
5169 5428 0.519077 CAGCTCGCCCTTCAAAGTTC 59.481 55.000 0.00 0.00 0.00 3.01
5173 5432 2.029918 GCTCGCCCTTCAAAGTTCAATT 60.030 45.455 0.00 0.00 0.00 2.32
5176 5435 5.116069 TCGCCCTTCAAAGTTCAATTTAC 57.884 39.130 0.00 0.00 0.00 2.01
5194 5453 7.913297 TCAATTTACAGTTGTAGTTTGTTGCTC 59.087 33.333 12.20 0.00 31.68 4.26
5201 5460 1.069906 GTAGTTTGTTGCTCGGTGCTG 60.070 52.381 3.53 0.00 43.37 4.41
5215 5474 4.196193 TCGGTGCTGTATTTCCTTAATGG 58.804 43.478 0.00 0.00 37.10 3.16
5220 5479 6.438763 GTGCTGTATTTCCTTAATGGTATGC 58.561 40.000 0.00 0.00 37.07 3.14
5232 5491 2.865119 TGGTATGCCCATATCTGCTG 57.135 50.000 0.00 0.00 38.72 4.41
5233 5492 2.057140 TGGTATGCCCATATCTGCTGT 58.943 47.619 0.00 0.00 38.72 4.40
5234 5493 2.038952 TGGTATGCCCATATCTGCTGTC 59.961 50.000 0.00 0.00 38.72 3.51
5235 5494 2.616510 GGTATGCCCATATCTGCTGTCC 60.617 54.545 0.00 0.00 0.00 4.02
5236 5495 0.035881 ATGCCCATATCTGCTGTCCG 59.964 55.000 0.00 0.00 0.00 4.79
5237 5496 1.337384 TGCCCATATCTGCTGTCCGT 61.337 55.000 0.00 0.00 0.00 4.69
5238 5497 0.179045 GCCCATATCTGCTGTCCGTT 60.179 55.000 0.00 0.00 0.00 4.44
5239 5498 1.871080 CCCATATCTGCTGTCCGTTC 58.129 55.000 0.00 0.00 0.00 3.95
5240 5499 1.491670 CCATATCTGCTGTCCGTTCG 58.508 55.000 0.00 0.00 0.00 3.95
5241 5500 0.855349 CATATCTGCTGTCCGTTCGC 59.145 55.000 0.00 0.00 0.00 4.70
5242 5501 0.747255 ATATCTGCTGTCCGTTCGCT 59.253 50.000 0.00 0.00 0.00 4.93
5243 5502 0.530744 TATCTGCTGTCCGTTCGCTT 59.469 50.000 0.00 0.00 0.00 4.68
5244 5503 0.737715 ATCTGCTGTCCGTTCGCTTC 60.738 55.000 0.00 0.00 0.00 3.86
5245 5504 1.373497 CTGCTGTCCGTTCGCTTCT 60.373 57.895 0.00 0.00 0.00 2.85
5246 5505 1.347817 CTGCTGTCCGTTCGCTTCTC 61.348 60.000 0.00 0.00 0.00 2.87
5247 5506 1.372997 GCTGTCCGTTCGCTTCTCA 60.373 57.895 0.00 0.00 0.00 3.27
5248 5507 0.944311 GCTGTCCGTTCGCTTCTCAA 60.944 55.000 0.00 0.00 0.00 3.02
5249 5508 1.714794 CTGTCCGTTCGCTTCTCAAT 58.285 50.000 0.00 0.00 0.00 2.57
5250 5509 2.876091 CTGTCCGTTCGCTTCTCAATA 58.124 47.619 0.00 0.00 0.00 1.90
5251 5510 3.448686 CTGTCCGTTCGCTTCTCAATAT 58.551 45.455 0.00 0.00 0.00 1.28
5252 5511 3.444916 TGTCCGTTCGCTTCTCAATATC 58.555 45.455 0.00 0.00 0.00 1.63
5253 5512 2.468040 GTCCGTTCGCTTCTCAATATCG 59.532 50.000 0.00 0.00 0.00 2.92
5254 5513 1.190323 CCGTTCGCTTCTCAATATCGC 59.810 52.381 0.00 0.00 0.00 4.58
5255 5514 2.120232 CGTTCGCTTCTCAATATCGCT 58.880 47.619 0.00 0.00 0.00 4.93
5256 5515 3.297472 CGTTCGCTTCTCAATATCGCTA 58.703 45.455 0.00 0.00 0.00 4.26
5257 5516 3.729217 CGTTCGCTTCTCAATATCGCTAA 59.271 43.478 0.00 0.00 0.00 3.09
5258 5517 4.374112 CGTTCGCTTCTCAATATCGCTAAC 60.374 45.833 0.00 0.00 0.00 2.34
5259 5518 3.639538 TCGCTTCTCAATATCGCTAACC 58.360 45.455 0.00 0.00 0.00 2.85
5260 5519 3.067601 TCGCTTCTCAATATCGCTAACCA 59.932 43.478 0.00 0.00 0.00 3.67
5261 5520 3.182572 CGCTTCTCAATATCGCTAACCAC 59.817 47.826 0.00 0.00 0.00 4.16
5262 5521 3.495001 GCTTCTCAATATCGCTAACCACC 59.505 47.826 0.00 0.00 0.00 4.61
5263 5522 4.740934 GCTTCTCAATATCGCTAACCACCT 60.741 45.833 0.00 0.00 0.00 4.00
5264 5523 4.322080 TCTCAATATCGCTAACCACCTG 57.678 45.455 0.00 0.00 0.00 4.00
5265 5524 2.802816 CTCAATATCGCTAACCACCTGC 59.197 50.000 0.00 0.00 0.00 4.85
5266 5525 2.434336 TCAATATCGCTAACCACCTGCT 59.566 45.455 0.00 0.00 0.00 4.24
5267 5526 3.118408 TCAATATCGCTAACCACCTGCTT 60.118 43.478 0.00 0.00 0.00 3.91
5268 5527 2.596904 TATCGCTAACCACCTGCTTC 57.403 50.000 0.00 0.00 0.00 3.86
5269 5528 0.460284 ATCGCTAACCACCTGCTTCG 60.460 55.000 0.00 0.00 0.00 3.79
5270 5529 1.080093 CGCTAACCACCTGCTTCGA 60.080 57.895 0.00 0.00 0.00 3.71
5271 5530 1.078759 CGCTAACCACCTGCTTCGAG 61.079 60.000 0.00 0.00 0.00 4.04
5272 5531 0.037232 GCTAACCACCTGCTTCGAGT 60.037 55.000 0.00 0.00 0.00 4.18
5273 5532 1.997669 CTAACCACCTGCTTCGAGTC 58.002 55.000 0.00 0.00 0.00 3.36
5274 5533 0.606604 TAACCACCTGCTTCGAGTCC 59.393 55.000 0.00 0.00 0.00 3.85
5275 5534 2.125912 CCACCTGCTTCGAGTCCG 60.126 66.667 0.00 0.00 37.07 4.79
5276 5535 2.636412 CCACCTGCTTCGAGTCCGA 61.636 63.158 0.00 0.00 43.96 4.55
5277 5536 1.513158 CACCTGCTTCGAGTCCGAT 59.487 57.895 0.00 0.00 45.10 4.18
5278 5537 0.803768 CACCTGCTTCGAGTCCGATG 60.804 60.000 0.00 0.00 45.10 3.84
5283 5542 3.122150 CTTCGAGTCCGATGCAACA 57.878 52.632 0.00 0.00 45.10 3.33
5284 5543 1.428448 CTTCGAGTCCGATGCAACAA 58.572 50.000 0.00 0.00 45.10 2.83
5285 5544 2.002586 CTTCGAGTCCGATGCAACAAT 58.997 47.619 0.00 0.00 45.10 2.71
5286 5545 1.358877 TCGAGTCCGATGCAACAATG 58.641 50.000 0.00 0.00 40.30 2.82
5287 5546 1.067213 TCGAGTCCGATGCAACAATGA 60.067 47.619 0.00 0.00 40.30 2.57
5288 5547 1.731709 CGAGTCCGATGCAACAATGAA 59.268 47.619 0.00 0.00 38.22 2.57
5289 5548 2.159430 CGAGTCCGATGCAACAATGAAA 59.841 45.455 0.00 0.00 38.22 2.69
5290 5549 3.181507 CGAGTCCGATGCAACAATGAAAT 60.182 43.478 0.00 0.00 38.22 2.17
5291 5550 4.672542 CGAGTCCGATGCAACAATGAAATT 60.673 41.667 0.00 0.00 35.41 1.82
5292 5551 5.138125 AGTCCGATGCAACAATGAAATTT 57.862 34.783 0.00 0.00 31.22 1.82
5293 5552 5.540911 AGTCCGATGCAACAATGAAATTTT 58.459 33.333 0.00 0.00 31.22 1.82
5294 5553 5.406175 AGTCCGATGCAACAATGAAATTTTG 59.594 36.000 0.00 0.00 31.22 2.44
5295 5554 5.404968 GTCCGATGCAACAATGAAATTTTGA 59.595 36.000 0.00 0.00 31.22 2.69
5296 5555 5.987953 TCCGATGCAACAATGAAATTTTGAA 59.012 32.000 0.00 0.00 31.22 2.69
5297 5556 6.145858 TCCGATGCAACAATGAAATTTTGAAG 59.854 34.615 0.00 0.00 31.22 3.02
5298 5557 6.301108 CGATGCAACAATGAAATTTTGAAGG 58.699 36.000 0.00 0.00 31.22 3.46
5299 5558 6.145858 CGATGCAACAATGAAATTTTGAAGGA 59.854 34.615 0.00 0.00 31.22 3.36
5300 5559 6.847956 TGCAACAATGAAATTTTGAAGGAG 57.152 33.333 0.00 0.00 31.22 3.69
5301 5560 5.236911 TGCAACAATGAAATTTTGAAGGAGC 59.763 36.000 0.00 0.00 31.22 4.70
5302 5561 5.236911 GCAACAATGAAATTTTGAAGGAGCA 59.763 36.000 0.00 0.00 31.22 4.26
5303 5562 6.238429 GCAACAATGAAATTTTGAAGGAGCAA 60.238 34.615 0.00 0.00 31.22 3.91
5304 5563 7.349711 CAACAATGAAATTTTGAAGGAGCAAG 58.650 34.615 0.00 0.00 31.22 4.01
5305 5564 6.585416 ACAATGAAATTTTGAAGGAGCAAGT 58.415 32.000 0.00 0.00 31.22 3.16
5306 5565 6.703165 ACAATGAAATTTTGAAGGAGCAAGTC 59.297 34.615 0.00 0.00 31.22 3.01
5307 5566 5.850557 TGAAATTTTGAAGGAGCAAGTCA 57.149 34.783 0.00 0.00 0.00 3.41
5308 5567 6.409524 TGAAATTTTGAAGGAGCAAGTCAT 57.590 33.333 0.00 0.00 0.00 3.06
5309 5568 6.449698 TGAAATTTTGAAGGAGCAAGTCATC 58.550 36.000 0.00 0.00 0.00 2.92
5310 5569 4.691860 ATTTTGAAGGAGCAAGTCATCG 57.308 40.909 0.00 0.00 0.00 3.84
5311 5570 2.099141 TTGAAGGAGCAAGTCATCGG 57.901 50.000 0.00 0.00 0.00 4.18
5312 5571 0.391661 TGAAGGAGCAAGTCATCGGC 60.392 55.000 0.00 0.00 0.00 5.54
5313 5572 0.391661 GAAGGAGCAAGTCATCGGCA 60.392 55.000 0.00 0.00 0.00 5.69
5314 5573 0.036732 AAGGAGCAAGTCATCGGCAA 59.963 50.000 0.00 0.00 0.00 4.52
5315 5574 0.392193 AGGAGCAAGTCATCGGCAAG 60.392 55.000 0.00 0.00 0.00 4.01
5316 5575 1.372087 GGAGCAAGTCATCGGCAAGG 61.372 60.000 0.00 0.00 0.00 3.61
5317 5576 1.986575 GAGCAAGTCATCGGCAAGGC 61.987 60.000 0.00 0.00 0.00 4.35
5318 5577 2.334946 GCAAGTCATCGGCAAGGCA 61.335 57.895 0.00 0.00 0.00 4.75
5319 5578 1.503542 CAAGTCATCGGCAAGGCAC 59.496 57.895 0.00 0.00 0.00 5.01
5320 5579 1.073025 AAGTCATCGGCAAGGCACA 59.927 52.632 0.00 0.00 0.00 4.57
5321 5580 0.537143 AAGTCATCGGCAAGGCACAA 60.537 50.000 0.00 0.00 0.00 3.33
5322 5581 0.957395 AGTCATCGGCAAGGCACAAG 60.957 55.000 0.00 0.00 0.00 3.16
5323 5582 1.675310 TCATCGGCAAGGCACAAGG 60.675 57.895 0.00 0.00 0.00 3.61
5324 5583 2.361610 ATCGGCAAGGCACAAGGG 60.362 61.111 0.00 0.00 0.00 3.95
5325 5584 3.210012 ATCGGCAAGGCACAAGGGT 62.210 57.895 0.00 0.00 0.00 4.34
5326 5585 2.713531 ATCGGCAAGGCACAAGGGTT 62.714 55.000 0.00 0.00 0.00 4.11
5327 5586 2.919494 CGGCAAGGCACAAGGGTTC 61.919 63.158 0.00 0.00 0.00 3.62
5328 5587 1.832167 GGCAAGGCACAAGGGTTCA 60.832 57.895 0.00 0.00 0.00 3.18
5329 5588 1.363807 GCAAGGCACAAGGGTTCAC 59.636 57.895 0.00 0.00 0.00 3.18
5330 5589 1.391157 GCAAGGCACAAGGGTTCACA 61.391 55.000 0.00 0.00 0.00 3.58
5331 5590 1.110442 CAAGGCACAAGGGTTCACAA 58.890 50.000 0.00 0.00 0.00 3.33
5332 5591 1.111277 AAGGCACAAGGGTTCACAAC 58.889 50.000 0.00 0.00 0.00 3.32
5333 5592 0.033601 AGGCACAAGGGTTCACAACA 60.034 50.000 0.00 0.00 0.00 3.33
5334 5593 0.385390 GGCACAAGGGTTCACAACAG 59.615 55.000 0.00 0.00 0.00 3.16
5335 5594 0.385390 GCACAAGGGTTCACAACAGG 59.615 55.000 0.00 0.00 0.00 4.00
5336 5595 0.385390 CACAAGGGTTCACAACAGGC 59.615 55.000 0.00 0.00 0.00 4.85
5337 5596 0.258774 ACAAGGGTTCACAACAGGCT 59.741 50.000 0.00 0.00 0.00 4.58
5338 5597 1.493022 ACAAGGGTTCACAACAGGCTA 59.507 47.619 0.00 0.00 0.00 3.93
5339 5598 2.108250 ACAAGGGTTCACAACAGGCTAT 59.892 45.455 0.00 0.00 0.00 2.97
5340 5599 2.749621 CAAGGGTTCACAACAGGCTATC 59.250 50.000 0.00 0.00 0.00 2.08
5341 5600 1.066143 AGGGTTCACAACAGGCTATCG 60.066 52.381 0.00 0.00 0.00 2.92
5342 5601 0.727398 GGTTCACAACAGGCTATCGC 59.273 55.000 0.00 0.00 0.00 4.58
5343 5602 1.676014 GGTTCACAACAGGCTATCGCT 60.676 52.381 0.00 0.00 36.09 4.93
5344 5603 2.076863 GTTCACAACAGGCTATCGCTT 58.923 47.619 0.00 0.00 36.09 4.68
5345 5604 2.010145 TCACAACAGGCTATCGCTTC 57.990 50.000 0.00 0.00 36.09 3.86
5346 5605 1.009829 CACAACAGGCTATCGCTTCC 58.990 55.000 0.00 0.00 36.09 3.46
5347 5606 0.460284 ACAACAGGCTATCGCTTCCG 60.460 55.000 0.00 0.00 36.09 4.30
5348 5607 1.144057 AACAGGCTATCGCTTCCGG 59.856 57.895 0.00 0.00 36.09 5.14
5349 5608 1.614241 AACAGGCTATCGCTTCCGGT 61.614 55.000 0.00 0.00 36.09 5.28
5350 5609 1.592669 CAGGCTATCGCTTCCGGTG 60.593 63.158 0.00 0.00 36.09 4.94
5351 5610 2.967615 GGCTATCGCTTCCGGTGC 60.968 66.667 0.00 6.75 36.09 5.01
5352 5611 2.107141 GCTATCGCTTCCGGTGCT 59.893 61.111 17.12 5.29 34.56 4.40
5353 5612 2.240500 GCTATCGCTTCCGGTGCTG 61.241 63.158 17.12 11.86 34.56 4.41
5354 5613 2.202878 TATCGCTTCCGGTGCTGC 60.203 61.111 17.12 9.74 34.56 5.25
5355 5614 2.906182 CTATCGCTTCCGGTGCTGCA 62.906 60.000 17.12 0.00 34.56 4.41
5356 5615 2.514510 TATCGCTTCCGGTGCTGCAA 62.515 55.000 2.77 0.00 34.56 4.08
5357 5616 4.389576 CGCTTCCGGTGCTGCAAC 62.390 66.667 7.83 7.83 0.00 4.17
5358 5617 4.043200 GCTTCCGGTGCTGCAACC 62.043 66.667 12.81 11.21 36.82 3.77
5359 5618 2.281761 CTTCCGGTGCTGCAACCT 60.282 61.111 12.81 0.00 38.14 3.50
5360 5619 2.281484 TTCCGGTGCTGCAACCTC 60.281 61.111 12.81 0.00 38.14 3.85
5361 5620 4.680237 TCCGGTGCTGCAACCTCG 62.680 66.667 12.81 10.07 38.14 4.63
5362 5621 4.988598 CCGGTGCTGCAACCTCGT 62.989 66.667 12.81 0.00 38.14 4.18
5363 5622 2.972505 CGGTGCTGCAACCTCGTT 60.973 61.111 12.81 0.00 38.14 3.85
5364 5623 1.666553 CGGTGCTGCAACCTCGTTA 60.667 57.895 12.81 0.00 38.14 3.18
5365 5624 1.225376 CGGTGCTGCAACCTCGTTAA 61.225 55.000 12.81 0.00 38.14 2.01
5366 5625 1.165270 GGTGCTGCAACCTCGTTAAT 58.835 50.000 6.36 0.00 37.24 1.40
5367 5626 1.539827 GGTGCTGCAACCTCGTTAATT 59.460 47.619 6.36 0.00 37.24 1.40
5368 5627 2.414161 GGTGCTGCAACCTCGTTAATTC 60.414 50.000 6.36 0.00 37.24 2.17
5369 5628 1.810151 TGCTGCAACCTCGTTAATTCC 59.190 47.619 0.00 0.00 0.00 3.01
5370 5629 1.810151 GCTGCAACCTCGTTAATTCCA 59.190 47.619 0.00 0.00 0.00 3.53
5371 5630 2.423538 GCTGCAACCTCGTTAATTCCAT 59.576 45.455 0.00 0.00 0.00 3.41
5372 5631 3.731867 GCTGCAACCTCGTTAATTCCATG 60.732 47.826 0.00 0.00 0.00 3.66
5373 5632 2.752354 TGCAACCTCGTTAATTCCATGG 59.248 45.455 4.97 4.97 0.00 3.66
5374 5633 2.099098 GCAACCTCGTTAATTCCATGGG 59.901 50.000 13.02 0.00 0.00 4.00
5375 5634 3.352648 CAACCTCGTTAATTCCATGGGT 58.647 45.455 13.02 0.00 0.00 4.51
5376 5635 2.999331 ACCTCGTTAATTCCATGGGTG 58.001 47.619 13.02 0.00 0.00 4.61
5378 5637 2.356741 CCTCGTTAATTCCATGGGTGGT 60.357 50.000 13.02 0.00 46.16 4.16
5379 5638 3.118186 CCTCGTTAATTCCATGGGTGGTA 60.118 47.826 13.02 0.00 46.16 3.25
5380 5639 4.519213 CTCGTTAATTCCATGGGTGGTAA 58.481 43.478 13.02 0.00 46.16 2.85
5381 5640 4.519213 TCGTTAATTCCATGGGTGGTAAG 58.481 43.478 13.02 0.00 46.16 2.34
5382 5641 3.630312 CGTTAATTCCATGGGTGGTAAGG 59.370 47.826 13.02 7.61 46.16 2.69
5383 5642 2.846665 AATTCCATGGGTGGTAAGGG 57.153 50.000 13.02 0.00 46.16 3.95
5384 5643 0.261696 ATTCCATGGGTGGTAAGGGC 59.738 55.000 13.02 0.00 46.16 5.19
5385 5644 1.869824 TTCCATGGGTGGTAAGGGCC 61.870 60.000 13.02 0.00 46.16 5.80
5386 5645 2.124320 CATGGGTGGTAAGGGCCG 60.124 66.667 0.00 0.00 0.00 6.13
5387 5646 3.416880 ATGGGTGGTAAGGGCCGG 61.417 66.667 0.00 0.00 0.00 6.13
5388 5647 3.954740 ATGGGTGGTAAGGGCCGGA 62.955 63.158 5.05 0.00 0.00 5.14
5389 5648 4.105553 GGGTGGTAAGGGCCGGAC 62.106 72.222 5.05 0.00 0.00 4.79
5390 5649 3.007323 GGTGGTAAGGGCCGGACT 61.007 66.667 7.57 0.00 0.00 3.85
5391 5650 2.267961 GTGGTAAGGGCCGGACTG 59.732 66.667 7.57 0.00 0.00 3.51
5392 5651 3.712907 TGGTAAGGGCCGGACTGC 61.713 66.667 7.57 0.00 0.00 4.40
5400 5659 2.282180 GCCGGACTGCCAAGGAAA 60.282 61.111 5.05 0.00 0.00 3.13
5401 5660 1.901464 GCCGGACTGCCAAGGAAAA 60.901 57.895 5.05 0.00 0.00 2.29
5402 5661 1.866853 GCCGGACTGCCAAGGAAAAG 61.867 60.000 5.05 0.00 0.00 2.27
5403 5662 1.244019 CCGGACTGCCAAGGAAAAGG 61.244 60.000 0.00 0.00 0.00 3.11
5408 5667 4.198087 GCCAAGGAAAAGGCCAGT 57.802 55.556 5.01 0.00 45.18 4.00
5409 5668 2.440946 GCCAAGGAAAAGGCCAGTT 58.559 52.632 5.01 0.00 45.18 3.16
5410 5669 0.033920 GCCAAGGAAAAGGCCAGTTG 59.966 55.000 5.01 0.00 45.18 3.16
5411 5670 0.033920 CCAAGGAAAAGGCCAGTTGC 59.966 55.000 5.01 3.27 40.16 4.17
5412 5671 0.752054 CAAGGAAAAGGCCAGTTGCA 59.248 50.000 5.01 0.00 43.89 4.08
5413 5672 1.345415 CAAGGAAAAGGCCAGTTGCAT 59.655 47.619 5.01 0.00 43.89 3.96
5414 5673 1.260544 AGGAAAAGGCCAGTTGCATC 58.739 50.000 5.01 0.00 43.89 3.91
5415 5674 0.247460 GGAAAAGGCCAGTTGCATCC 59.753 55.000 5.01 0.00 43.89 3.51
5416 5675 0.247460 GAAAAGGCCAGTTGCATCCC 59.753 55.000 5.01 0.00 43.89 3.85
5417 5676 0.178924 AAAAGGCCAGTTGCATCCCT 60.179 50.000 5.01 0.00 43.89 4.20
5418 5677 0.901580 AAAGGCCAGTTGCATCCCTG 60.902 55.000 5.01 0.00 43.89 4.45
5428 5687 3.587095 CATCCCTGCACACTGCTG 58.413 61.111 0.00 0.00 45.31 4.41
5429 5688 2.360852 ATCCCTGCACACTGCTGC 60.361 61.111 0.00 0.00 45.31 5.25
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
77 78 4.090723 CGGAAGGAAACAACCCCC 57.909 61.111 0.00 0.00 0.00 5.40
357 362 3.623060 CCTAACCATCTGAACAATGTCCG 59.377 47.826 0.00 0.00 0.00 4.79
449 455 3.848272 AAAACGACAATGGCCACTATG 57.152 42.857 8.16 10.85 0.00 2.23
497 503 6.115446 CCACAGAATTTACTCCAGAGCATAA 58.885 40.000 0.00 0.00 0.00 1.90
525 531 9.621629 ACCGAAACCACAGAATTTATTATATCA 57.378 29.630 0.00 0.00 0.00 2.15
529 535 8.349983 GCATACCGAAACCACAGAATTTATTAT 58.650 33.333 0.00 0.00 0.00 1.28
530 536 7.554835 AGCATACCGAAACCACAGAATTTATTA 59.445 33.333 0.00 0.00 0.00 0.98
556 562 0.317799 GCCATTCATGCACACAACCA 59.682 50.000 0.00 0.00 0.00 3.67
599 605 8.455903 TGAAAATTCTGGATAGGACATTCATC 57.544 34.615 0.00 0.00 0.00 2.92
681 692 8.836413 CATGTAGAAAGAAAAGGTTTCACACTA 58.164 33.333 3.74 1.71 36.53 2.74
697 708 6.650807 TCAAGTTAAGTGCTCCATGTAGAAAG 59.349 38.462 0.00 0.00 0.00 2.62
716 727 8.943594 TTGGTGGGTAAAATTATAGTCAAGTT 57.056 30.769 0.00 0.00 0.00 2.66
745 756 6.007076 TCTTCAGAGACATATAGCTACCAGG 58.993 44.000 0.00 0.00 0.00 4.45
807 818 2.504175 TGCATTGTAGGGAGTAGGAACC 59.496 50.000 0.00 0.00 0.00 3.62
880 904 7.790707 TCAATTTATGAAGTAGGCAAAACTGCC 60.791 37.037 8.11 8.11 44.64 4.85
991 1016 0.599060 TACGTCGACATTGTGGCTGA 59.401 50.000 17.16 0.00 0.00 4.26
1153 1178 1.763770 CAACTGGCCCTTCTCCACT 59.236 57.895 0.00 0.00 0.00 4.00
1427 1455 2.428890 ACCTCTGTAGTAGCATCAGCAC 59.571 50.000 0.00 0.00 45.49 4.40
1431 1459 6.040955 CCTGAATAACCTCTGTAGTAGCATCA 59.959 42.308 0.00 0.00 0.00 3.07
1503 1531 2.027653 GGCACTTTTCTCACTAGCCTCT 60.028 50.000 0.00 0.00 37.67 3.69
1508 1536 2.349886 GCATCGGCACTTTTCTCACTAG 59.650 50.000 0.00 0.00 40.72 2.57
1677 1705 1.067283 TCAGTAGCAGCAGCAAGAGTC 60.067 52.381 3.17 0.00 45.49 3.36
1685 1713 4.179926 TCACTAACTTCAGTAGCAGCAG 57.820 45.455 0.00 0.00 0.00 4.24
1812 1840 1.339438 GCTTGTGGAGATGCTTCCTCA 60.339 52.381 0.00 0.19 38.56 3.86
1813 1841 1.065564 AGCTTGTGGAGATGCTTCCTC 60.066 52.381 0.00 0.00 38.12 3.71
1917 1945 2.078849 TGACATCAGTACTGGCAACG 57.921 50.000 22.48 9.22 42.51 4.10
2004 2032 2.284190 GAAACACTAGCATCTGGAGGC 58.716 52.381 0.00 0.00 38.58 4.70
2021 2049 5.481122 ACATCCAATGGATCAACATGTGAAA 59.519 36.000 12.63 0.00 40.98 2.69
2022 2050 5.018149 ACATCCAATGGATCAACATGTGAA 58.982 37.500 12.63 0.00 40.98 3.18
2089 2117 8.948631 TTATCACTCAAATCTATCACAGGAAC 57.051 34.615 0.00 0.00 0.00 3.62
2183 2211 3.436035 GGTTACCTGGTCTTTTGTCCCTT 60.436 47.826 0.63 0.00 0.00 3.95
2205 2233 1.202580 CCTAGAACAGGATTGGCCTCG 60.203 57.143 3.32 0.00 46.97 4.63
2344 2372 1.117150 ATGGAGGGAATGTTGCATGC 58.883 50.000 11.82 11.82 0.00 4.06
2576 2636 3.587797 CTGAGGTAACCGCAGTCTTTA 57.412 47.619 0.00 0.00 44.47 1.85
2819 2983 7.215789 ACATAAAACATGCCACAGAAAATGAA 58.784 30.769 0.00 0.00 0.00 2.57
2836 3000 7.747888 TGCACACACATACTGATACATAAAAC 58.252 34.615 0.00 0.00 0.00 2.43
2886 3073 6.817765 AATCCACAATGACAAAGATTACGT 57.182 33.333 0.00 0.00 0.00 3.57
2951 3138 6.250819 CAAAACCGTACAAGAGCAGAATATG 58.749 40.000 0.00 0.00 0.00 1.78
2998 3186 6.214819 AGGCCACAAATCTTACTAAAGGACTA 59.785 38.462 5.01 0.00 33.22 2.59
3304 3493 1.757699 ACCTCACCTATCCGCTCTTTC 59.242 52.381 0.00 0.00 0.00 2.62
3486 3678 2.743636 TCCAGTTCTACCAAGAAGCG 57.256 50.000 0.00 0.00 42.40 4.68
3575 3767 5.856126 TTCTGCACAGGTAAAATAAGACG 57.144 39.130 0.00 0.00 0.00 4.18
3629 3821 3.600388 CTGAAAAGGTCATAGAAGGCGT 58.400 45.455 0.00 0.00 35.07 5.68
3799 3993 4.641541 CAGGTTTGCATCCATCATACAGAA 59.358 41.667 10.40 0.00 0.00 3.02
3809 4003 2.885135 ACATCTCAGGTTTGCATCCA 57.115 45.000 10.40 0.00 0.00 3.41
3858 4052 5.521735 ACAAGTAATGCATCACGAGATTCTC 59.478 40.000 0.00 3.43 30.20 2.87
4012 4206 6.149474 CAGCTAAGTAACTGCCATTGTTTAGT 59.851 38.462 0.00 0.00 0.00 2.24
4184 4378 0.178873 AGACCCCATGTGGTACCAGT 60.179 55.000 16.93 8.55 39.24 4.00
4342 4536 4.461081 GGCAAGTAGTAGATCATCGGAGAT 59.539 45.833 0.00 0.00 45.12 2.75
4429 4623 1.073897 GCAGCAGGTTTGAGTCCCT 59.926 57.895 0.00 0.00 0.00 4.20
4523 4717 0.028770 TGTTAACTGCTGCAACACGC 59.971 50.000 3.02 0.00 42.89 5.34
4524 4718 2.032117 TCATGTTAACTGCTGCAACACG 60.032 45.455 3.02 0.00 35.17 4.49
4555 4761 4.323417 TCACCAACCATTACAAGCAGTAG 58.677 43.478 0.00 0.00 33.43 2.57
4590 4796 0.751643 ACCAAGACCGTGCAAAGCTT 60.752 50.000 0.00 0.00 0.00 3.74
4591 4797 1.152963 ACCAAGACCGTGCAAAGCT 60.153 52.632 0.00 0.00 0.00 3.74
4592 4798 1.166531 AGACCAAGACCGTGCAAAGC 61.167 55.000 0.00 0.00 0.00 3.51
4642 4891 4.683832 GGACAAGCGAAAATAGAGCTAGA 58.316 43.478 0.00 0.00 40.78 2.43
4664 4913 1.137404 GCATGTTAACAGCCAGGCG 59.863 57.895 14.65 3.56 0.00 5.52
4669 4918 0.591170 ACGTGTGCATGTTAACAGCC 59.409 50.000 14.65 7.78 0.00 4.85
4738 4987 2.486203 GGGTTCATCAACATACACGCAA 59.514 45.455 0.00 0.00 33.70 4.85
4767 5016 4.162320 CCAGCAGGACTCATAACTTCCTAA 59.838 45.833 0.00 0.00 37.69 2.69
4768 5017 3.706594 CCAGCAGGACTCATAACTTCCTA 59.293 47.826 0.00 0.00 37.69 2.94
4769 5018 2.503356 CCAGCAGGACTCATAACTTCCT 59.497 50.000 0.00 0.00 40.63 3.36
4770 5019 2.237392 ACCAGCAGGACTCATAACTTCC 59.763 50.000 0.35 0.00 38.69 3.46
4771 5020 3.618690 ACCAGCAGGACTCATAACTTC 57.381 47.619 0.35 0.00 38.69 3.01
4772 5021 3.679389 CAACCAGCAGGACTCATAACTT 58.321 45.455 0.35 0.00 38.69 2.66
4773 5022 2.616510 GCAACCAGCAGGACTCATAACT 60.617 50.000 0.35 0.00 44.79 2.24
4774 5023 1.740025 GCAACCAGCAGGACTCATAAC 59.260 52.381 0.35 0.00 44.79 1.89
4980 5237 6.202202 AGTGCTACAGTAGTCATATCCCTA 57.798 41.667 9.42 0.00 0.00 3.53
5013 5270 5.891551 TCAATGAAATTTAGCTTACCCCCTC 59.108 40.000 0.00 0.00 31.22 4.30
5031 5290 6.417258 TCTCCATGCTACTTTTGATCAATGA 58.583 36.000 9.40 0.39 0.00 2.57
5032 5291 6.238676 CCTCTCCATGCTACTTTTGATCAATG 60.239 42.308 9.40 8.09 0.00 2.82
5051 5310 5.237344 CACGATCCAATTTGTATTCCTCTCC 59.763 44.000 0.00 0.00 0.00 3.71
5095 5354 1.760029 GAAAACTTTGGACAAGGGGCA 59.240 47.619 0.00 0.00 0.00 5.36
5102 5361 5.233263 GCTAAATTTGCGAAAACTTTGGACA 59.767 36.000 0.00 0.00 0.00 4.02
5103 5362 5.462068 AGCTAAATTTGCGAAAACTTTGGAC 59.538 36.000 0.00 0.00 35.28 4.02
5111 5370 9.554724 CAGATAGTTTAGCTAAATTTGCGAAAA 57.445 29.630 21.28 12.81 36.94 2.29
5112 5371 7.696453 GCAGATAGTTTAGCTAAATTTGCGAAA 59.304 33.333 21.28 8.49 33.86 3.46
5169 5428 7.097047 CGAGCAACAAACTACAACTGTAAATTG 60.097 37.037 10.49 10.49 34.75 2.32
5173 5432 4.271533 CCGAGCAACAAACTACAACTGTAA 59.728 41.667 0.00 0.00 0.00 2.41
5176 5435 2.612212 ACCGAGCAACAAACTACAACTG 59.388 45.455 0.00 0.00 0.00 3.16
5194 5453 3.945285 ACCATTAAGGAAATACAGCACCG 59.055 43.478 0.00 0.00 41.22 4.94
5215 5474 2.704572 GGACAGCAGATATGGGCATAC 58.295 52.381 0.00 0.00 0.00 2.39
5220 5479 1.869754 CGAACGGACAGCAGATATGGG 60.870 57.143 0.00 0.00 0.00 4.00
5225 5484 0.737715 GAAGCGAACGGACAGCAGAT 60.738 55.000 0.00 0.00 0.00 2.90
5226 5485 1.372997 GAAGCGAACGGACAGCAGA 60.373 57.895 0.00 0.00 0.00 4.26
5227 5486 1.347817 GAGAAGCGAACGGACAGCAG 61.348 60.000 0.00 0.00 0.00 4.24
5228 5487 1.372997 GAGAAGCGAACGGACAGCA 60.373 57.895 0.00 0.00 0.00 4.41
5229 5488 0.944311 TTGAGAAGCGAACGGACAGC 60.944 55.000 0.00 0.00 0.00 4.40
5230 5489 1.714794 ATTGAGAAGCGAACGGACAG 58.285 50.000 0.00 0.00 0.00 3.51
5231 5490 3.444916 GATATTGAGAAGCGAACGGACA 58.555 45.455 0.00 0.00 0.00 4.02
5232 5491 2.468040 CGATATTGAGAAGCGAACGGAC 59.532 50.000 0.00 0.00 0.00 4.79
5233 5492 2.727777 CGATATTGAGAAGCGAACGGA 58.272 47.619 0.00 0.00 0.00 4.69
5234 5493 1.190323 GCGATATTGAGAAGCGAACGG 59.810 52.381 0.00 0.00 0.00 4.44
5235 5494 2.120232 AGCGATATTGAGAAGCGAACG 58.880 47.619 0.00 0.00 0.00 3.95
5236 5495 4.085004 GGTTAGCGATATTGAGAAGCGAAC 60.085 45.833 0.00 3.75 40.78 3.95
5237 5496 4.049186 GGTTAGCGATATTGAGAAGCGAA 58.951 43.478 0.00 0.00 0.00 4.70
5238 5497 3.067601 TGGTTAGCGATATTGAGAAGCGA 59.932 43.478 0.00 0.00 0.00 4.93
5239 5498 3.182572 GTGGTTAGCGATATTGAGAAGCG 59.817 47.826 0.00 0.00 0.00 4.68
5240 5499 3.495001 GGTGGTTAGCGATATTGAGAAGC 59.505 47.826 0.00 0.00 0.00 3.86
5241 5500 4.747108 CAGGTGGTTAGCGATATTGAGAAG 59.253 45.833 0.00 0.00 0.00 2.85
5242 5501 4.693283 CAGGTGGTTAGCGATATTGAGAA 58.307 43.478 0.00 0.00 0.00 2.87
5243 5502 3.492656 GCAGGTGGTTAGCGATATTGAGA 60.493 47.826 0.00 0.00 0.00 3.27
5244 5503 2.802816 GCAGGTGGTTAGCGATATTGAG 59.197 50.000 0.00 0.00 0.00 3.02
5245 5504 2.434336 AGCAGGTGGTTAGCGATATTGA 59.566 45.455 0.00 0.00 0.00 2.57
5246 5505 2.838736 AGCAGGTGGTTAGCGATATTG 58.161 47.619 0.00 0.00 0.00 1.90
5247 5506 3.467803 GAAGCAGGTGGTTAGCGATATT 58.532 45.455 0.00 0.00 35.69 1.28
5248 5507 2.545952 CGAAGCAGGTGGTTAGCGATAT 60.546 50.000 0.00 0.00 35.69 1.63
5249 5508 1.202371 CGAAGCAGGTGGTTAGCGATA 60.202 52.381 0.00 0.00 35.69 2.92
5250 5509 0.460284 CGAAGCAGGTGGTTAGCGAT 60.460 55.000 0.00 0.00 35.69 4.58
5251 5510 1.080093 CGAAGCAGGTGGTTAGCGA 60.080 57.895 0.00 0.00 35.69 4.93
5252 5511 1.078759 CTCGAAGCAGGTGGTTAGCG 61.079 60.000 0.00 0.00 35.69 4.26
5253 5512 0.037232 ACTCGAAGCAGGTGGTTAGC 60.037 55.000 0.00 0.00 35.69 3.09
5254 5513 1.404315 GGACTCGAAGCAGGTGGTTAG 60.404 57.143 0.00 0.00 35.69 2.34
5255 5514 0.606604 GGACTCGAAGCAGGTGGTTA 59.393 55.000 0.00 0.00 35.69 2.85
5256 5515 1.371558 GGACTCGAAGCAGGTGGTT 59.628 57.895 0.00 0.00 38.61 3.67
5257 5516 2.932234 CGGACTCGAAGCAGGTGGT 61.932 63.158 0.00 0.00 39.00 4.16
5258 5517 2.125912 CGGACTCGAAGCAGGTGG 60.126 66.667 0.00 0.00 39.00 4.61
5259 5518 2.962569 TCGGACTCGAAGCAGGTG 59.037 61.111 0.00 0.00 43.03 4.00
5268 5527 1.358877 TCATTGTTGCATCGGACTCG 58.641 50.000 0.00 0.00 37.82 4.18
5269 5528 3.829886 TTTCATTGTTGCATCGGACTC 57.170 42.857 0.00 0.00 0.00 3.36
5270 5529 4.789012 AATTTCATTGTTGCATCGGACT 57.211 36.364 0.00 0.00 0.00 3.85
5271 5530 5.404968 TCAAAATTTCATTGTTGCATCGGAC 59.595 36.000 0.00 0.00 0.00 4.79
5272 5531 5.536260 TCAAAATTTCATTGTTGCATCGGA 58.464 33.333 0.00 0.00 0.00 4.55
5273 5532 5.842619 TCAAAATTTCATTGTTGCATCGG 57.157 34.783 0.00 0.00 0.00 4.18
5274 5533 6.145858 TCCTTCAAAATTTCATTGTTGCATCG 59.854 34.615 0.00 0.00 0.00 3.84
5275 5534 7.424227 TCCTTCAAAATTTCATTGTTGCATC 57.576 32.000 0.00 0.00 0.00 3.91
5276 5535 6.072893 GCTCCTTCAAAATTTCATTGTTGCAT 60.073 34.615 0.00 0.00 0.00 3.96
5277 5536 5.236911 GCTCCTTCAAAATTTCATTGTTGCA 59.763 36.000 0.00 0.00 0.00 4.08
5278 5537 5.236911 TGCTCCTTCAAAATTTCATTGTTGC 59.763 36.000 0.00 0.00 0.00 4.17
5279 5538 6.847956 TGCTCCTTCAAAATTTCATTGTTG 57.152 33.333 0.00 0.00 0.00 3.33
5280 5539 7.049754 ACTTGCTCCTTCAAAATTTCATTGTT 58.950 30.769 0.00 0.00 0.00 2.83
5281 5540 6.585416 ACTTGCTCCTTCAAAATTTCATTGT 58.415 32.000 0.00 0.00 0.00 2.71
5282 5541 6.702723 TGACTTGCTCCTTCAAAATTTCATTG 59.297 34.615 0.00 0.00 0.00 2.82
5283 5542 6.819284 TGACTTGCTCCTTCAAAATTTCATT 58.181 32.000 0.00 0.00 0.00 2.57
5284 5543 6.409524 TGACTTGCTCCTTCAAAATTTCAT 57.590 33.333 0.00 0.00 0.00 2.57
5285 5544 5.850557 TGACTTGCTCCTTCAAAATTTCA 57.149 34.783 0.00 0.00 0.00 2.69
5286 5545 5.570589 CGATGACTTGCTCCTTCAAAATTTC 59.429 40.000 0.00 0.00 0.00 2.17
5287 5546 5.464168 CGATGACTTGCTCCTTCAAAATTT 58.536 37.500 0.00 0.00 0.00 1.82
5288 5547 4.082571 CCGATGACTTGCTCCTTCAAAATT 60.083 41.667 0.00 0.00 0.00 1.82
5289 5548 3.441572 CCGATGACTTGCTCCTTCAAAAT 59.558 43.478 0.00 0.00 0.00 1.82
5290 5549 2.813754 CCGATGACTTGCTCCTTCAAAA 59.186 45.455 0.00 0.00 0.00 2.44
5291 5550 2.426522 CCGATGACTTGCTCCTTCAAA 58.573 47.619 0.00 0.00 0.00 2.69
5292 5551 1.945819 GCCGATGACTTGCTCCTTCAA 60.946 52.381 0.00 0.00 0.00 2.69
5293 5552 0.391661 GCCGATGACTTGCTCCTTCA 60.392 55.000 0.00 0.00 0.00 3.02
5294 5553 0.391661 TGCCGATGACTTGCTCCTTC 60.392 55.000 0.00 0.00 0.00 3.46
5295 5554 0.036732 TTGCCGATGACTTGCTCCTT 59.963 50.000 0.00 0.00 0.00 3.36
5296 5555 0.392193 CTTGCCGATGACTTGCTCCT 60.392 55.000 0.00 0.00 0.00 3.69
5297 5556 1.372087 CCTTGCCGATGACTTGCTCC 61.372 60.000 0.00 0.00 0.00 4.70
5298 5557 1.986575 GCCTTGCCGATGACTTGCTC 61.987 60.000 0.00 0.00 0.00 4.26
5299 5558 2.042831 GCCTTGCCGATGACTTGCT 61.043 57.895 0.00 0.00 0.00 3.91
5300 5559 2.334946 TGCCTTGCCGATGACTTGC 61.335 57.895 0.00 0.00 0.00 4.01
5301 5560 1.236616 TGTGCCTTGCCGATGACTTG 61.237 55.000 0.00 0.00 0.00 3.16
5302 5561 0.537143 TTGTGCCTTGCCGATGACTT 60.537 50.000 0.00 0.00 0.00 3.01
5303 5562 0.957395 CTTGTGCCTTGCCGATGACT 60.957 55.000 0.00 0.00 0.00 3.41
5304 5563 1.503542 CTTGTGCCTTGCCGATGAC 59.496 57.895 0.00 0.00 0.00 3.06
5305 5564 1.675310 CCTTGTGCCTTGCCGATGA 60.675 57.895 0.00 0.00 0.00 2.92
5306 5565 2.703798 CCCTTGTGCCTTGCCGATG 61.704 63.158 0.00 0.00 0.00 3.84
5307 5566 2.361610 CCCTTGTGCCTTGCCGAT 60.362 61.111 0.00 0.00 0.00 4.18
5308 5567 3.429372 AACCCTTGTGCCTTGCCGA 62.429 57.895 0.00 0.00 0.00 5.54
5309 5568 2.912025 AACCCTTGTGCCTTGCCG 60.912 61.111 0.00 0.00 0.00 5.69
5310 5569 1.832167 TGAACCCTTGTGCCTTGCC 60.832 57.895 0.00 0.00 0.00 4.52
5311 5570 1.363807 GTGAACCCTTGTGCCTTGC 59.636 57.895 0.00 0.00 0.00 4.01
5312 5571 1.110442 TTGTGAACCCTTGTGCCTTG 58.890 50.000 0.00 0.00 0.00 3.61
5313 5572 1.111277 GTTGTGAACCCTTGTGCCTT 58.889 50.000 0.00 0.00 0.00 4.35
5314 5573 0.033601 TGTTGTGAACCCTTGTGCCT 60.034 50.000 0.00 0.00 0.00 4.75
5315 5574 0.385390 CTGTTGTGAACCCTTGTGCC 59.615 55.000 0.00 0.00 0.00 5.01
5316 5575 0.385390 CCTGTTGTGAACCCTTGTGC 59.615 55.000 0.00 0.00 0.00 4.57
5317 5576 0.385390 GCCTGTTGTGAACCCTTGTG 59.615 55.000 0.00 0.00 0.00 3.33
5318 5577 0.258774 AGCCTGTTGTGAACCCTTGT 59.741 50.000 0.00 0.00 0.00 3.16
5319 5578 2.270352 TAGCCTGTTGTGAACCCTTG 57.730 50.000 0.00 0.00 0.00 3.61
5320 5579 2.615493 CGATAGCCTGTTGTGAACCCTT 60.615 50.000 0.00 0.00 0.00 3.95
5321 5580 1.066143 CGATAGCCTGTTGTGAACCCT 60.066 52.381 0.00 0.00 0.00 4.34
5322 5581 1.369625 CGATAGCCTGTTGTGAACCC 58.630 55.000 0.00 0.00 0.00 4.11
5336 5595 2.240500 GCAGCACCGGAAGCGATAG 61.241 63.158 9.46 6.30 37.01 2.08
5337 5596 2.202878 GCAGCACCGGAAGCGATA 60.203 61.111 9.46 0.00 37.01 2.92
5338 5597 3.899981 TTGCAGCACCGGAAGCGAT 62.900 57.895 9.46 0.00 37.01 4.58
5339 5598 4.617520 TTGCAGCACCGGAAGCGA 62.618 61.111 9.46 2.96 37.01 4.93
5340 5599 4.389576 GTTGCAGCACCGGAAGCG 62.390 66.667 9.46 9.53 37.01 4.68
5341 5600 4.043200 GGTTGCAGCACCGGAAGC 62.043 66.667 9.46 12.61 0.00 3.86
5342 5601 2.281761 AGGTTGCAGCACCGGAAG 60.282 61.111 9.46 0.15 42.33 3.46
5343 5602 2.281484 GAGGTTGCAGCACCGGAA 60.281 61.111 9.46 0.00 42.33 4.30
5344 5603 4.680237 CGAGGTTGCAGCACCGGA 62.680 66.667 9.46 0.00 42.33 5.14
5345 5604 4.988598 ACGAGGTTGCAGCACCGG 62.989 66.667 15.54 0.00 42.33 5.28
5346 5605 1.225376 TTAACGAGGTTGCAGCACCG 61.225 55.000 2.05 7.54 42.33 4.94
5347 5606 1.165270 ATTAACGAGGTTGCAGCACC 58.835 50.000 2.05 0.29 37.04 5.01
5348 5607 2.414161 GGAATTAACGAGGTTGCAGCAC 60.414 50.000 2.05 0.00 0.00 4.40
5349 5608 1.810151 GGAATTAACGAGGTTGCAGCA 59.190 47.619 2.05 0.00 0.00 4.41
5350 5609 1.810151 TGGAATTAACGAGGTTGCAGC 59.190 47.619 0.00 0.00 0.00 5.25
5351 5610 3.181497 CCATGGAATTAACGAGGTTGCAG 60.181 47.826 5.56 0.00 0.00 4.41
5352 5611 2.752354 CCATGGAATTAACGAGGTTGCA 59.248 45.455 5.56 0.00 0.00 4.08
5353 5612 2.099098 CCCATGGAATTAACGAGGTTGC 59.901 50.000 15.22 0.00 0.00 4.17
5354 5613 3.128589 CACCCATGGAATTAACGAGGTTG 59.871 47.826 15.22 0.00 0.00 3.77
5355 5614 3.352648 CACCCATGGAATTAACGAGGTT 58.647 45.455 15.22 0.00 0.00 3.50
5356 5615 2.999331 CACCCATGGAATTAACGAGGT 58.001 47.619 15.22 0.00 0.00 3.85
5369 5628 2.124320 CGGCCCTTACCACCCATG 60.124 66.667 0.00 0.00 0.00 3.66
5370 5629 3.416880 CCGGCCCTTACCACCCAT 61.417 66.667 0.00 0.00 0.00 4.00
5371 5630 4.660611 TCCGGCCCTTACCACCCA 62.661 66.667 0.00 0.00 0.00 4.51
5372 5631 4.105553 GTCCGGCCCTTACCACCC 62.106 72.222 0.00 0.00 0.00 4.61
5373 5632 3.007323 AGTCCGGCCCTTACCACC 61.007 66.667 0.00 0.00 0.00 4.61
5374 5633 2.267961 CAGTCCGGCCCTTACCAC 59.732 66.667 0.00 0.00 0.00 4.16
5375 5634 3.712907 GCAGTCCGGCCCTTACCA 61.713 66.667 0.00 0.00 0.00 3.25
5383 5642 1.866853 CTTTTCCTTGGCAGTCCGGC 61.867 60.000 0.00 0.00 41.67 6.13
5384 5643 1.244019 CCTTTTCCTTGGCAGTCCGG 61.244 60.000 0.00 0.00 34.14 5.14
5385 5644 2.257353 CCTTTTCCTTGGCAGTCCG 58.743 57.895 0.00 0.00 34.14 4.79
5392 5651 0.033920 GCAACTGGCCTTTTCCTTGG 59.966 55.000 3.32 0.00 36.11 3.61
5393 5652 0.752054 TGCAACTGGCCTTTTCCTTG 59.248 50.000 3.32 0.00 43.89 3.61
5394 5653 1.620323 GATGCAACTGGCCTTTTCCTT 59.380 47.619 3.32 0.00 43.89 3.36
5395 5654 1.260544 GATGCAACTGGCCTTTTCCT 58.739 50.000 3.32 0.00 43.89 3.36
5396 5655 0.247460 GGATGCAACTGGCCTTTTCC 59.753 55.000 3.32 0.00 43.89 3.13
5397 5656 0.247460 GGGATGCAACTGGCCTTTTC 59.753 55.000 3.32 0.00 43.89 2.29
5398 5657 0.178924 AGGGATGCAACTGGCCTTTT 60.179 50.000 3.32 0.00 43.89 2.27
5399 5658 0.901580 CAGGGATGCAACTGGCCTTT 60.902 55.000 3.32 0.00 43.89 3.11
5400 5659 1.304713 CAGGGATGCAACTGGCCTT 60.305 57.895 3.32 0.00 43.89 4.35
5401 5660 2.357836 CAGGGATGCAACTGGCCT 59.642 61.111 3.32 0.00 43.89 5.19
5402 5661 3.455469 GCAGGGATGCAACTGGCC 61.455 66.667 15.39 0.00 43.89 5.36
5403 5662 2.677524 TGCAGGGATGCAACTGGC 60.678 61.111 15.39 7.93 42.40 4.85
5409 5668 2.674033 GCAGTGTGCAGGGATGCA 60.674 61.111 0.00 0.00 44.26 3.96


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

AutoCloner maintained by Alex Coulton.