Multiple sequence alignment - TraesCS2D01G369500

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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 TraesCS2D01G369500 chr2D 100.000 3335 0 0 1 3335 473701257 473697923 0.000000e+00 6159.0
1 TraesCS2D01G369500 chr2B 92.874 2119 101 20 374 2453 554291189 554289082 0.000000e+00 3031.0
2 TraesCS2D01G369500 chr2B 91.731 387 25 3 1 382 554291627 554291243 6.340000e-147 531.0
3 TraesCS2D01G369500 chr2B 90.244 205 11 6 2513 2717 554289059 554288864 3.300000e-65 259.0
4 TraesCS2D01G369500 chr2A 96.082 1608 51 4 858 2453 615702512 615700905 0.000000e+00 2610.0
5 TraesCS2D01G369500 chr2A 87.573 515 53 9 2825 3335 615689514 615689007 1.330000e-163 586.0
6 TraesCS2D01G369500 chr2A 89.474 323 29 5 31 349 615704987 615704666 1.440000e-108 403.0
7 TraesCS2D01G369500 chr2A 88.485 330 21 10 557 869 615704379 615704050 1.880000e-102 383.0
8 TraesCS2D01G369500 chr4B 89.412 85 7 2 2854 2938 584848428 584848346 4.550000e-19 106.0
9 TraesCS2D01G369500 chr4B 95.455 66 2 1 2873 2938 584873704 584873640 1.640000e-18 104.0
10 TraesCS2D01G369500 chr4B 95.455 66 2 1 2873 2938 584899084 584899020 1.640000e-18 104.0
11 TraesCS2D01G369500 chr6B 97.500 40 1 0 90 129 345204470 345204431 5.970000e-08 69.4
12 TraesCS2D01G369500 chr6B 96.970 33 0 1 2754 2785 668673187 668673155 2.000000e-03 54.7
13 TraesCS2D01G369500 chr7A 77.477 111 14 9 391 491 47939902 47939793 4.650000e-04 56.5
14 TraesCS2D01G369500 chr5A 96.970 33 0 1 2754 2785 7490737 7490769 2.000000e-03 54.7
15 TraesCS2D01G369500 chrUn 94.118 34 2 0 2752 2785 92809734 92809767 6.000000e-03 52.8


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 TraesCS2D01G369500 chr2D 473697923 473701257 3334 True 6159.000000 6159 100.000000 1 3335 1 chr2D.!!$R1 3334
1 TraesCS2D01G369500 chr2B 554288864 554291627 2763 True 1273.666667 3031 91.616333 1 2717 3 chr2B.!!$R1 2716
2 TraesCS2D01G369500 chr2A 615700905 615704987 4082 True 1132.000000 2610 91.347000 31 2453 3 chr2A.!!$R2 2422
3 TraesCS2D01G369500 chr2A 615689007 615689514 507 True 586.000000 586 87.573000 2825 3335 1 chr2A.!!$R1 510

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
443 514 0.683973 ATCGGCCAGAAGCTATGAGG 59.316 55.0 2.24 0.0 43.05 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2359 4128 0.466124 CCGATCTCCCACCTTCTTCC 59.534 60.0 0.0 0.0 0.0 3.46 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
120 124 9.729281 AGATTTTTAGGCATGACAAATTGAATT 57.271 25.926 0.00 0.00 0.00 2.17
182 186 1.537135 GGTTTGCAAAAACTAGCCGCA 60.537 47.619 14.67 0.00 33.37 5.69
183 187 1.786579 GTTTGCAAAAACTAGCCGCAG 59.213 47.619 14.67 0.00 33.48 5.18
237 246 6.457355 TGATCCAAGTTGAAATTCCACATTG 58.543 36.000 3.87 2.43 0.00 2.82
314 323 2.288395 CCCAAAATGCACAACTGGAGTC 60.288 50.000 7.37 0.00 0.00 3.36
351 360 5.699097 TTGAAGTAAACATACAAGGGCAC 57.301 39.130 0.00 0.00 0.00 5.01
352 361 3.749088 TGAAGTAAACATACAAGGGCACG 59.251 43.478 0.00 0.00 0.00 5.34
356 365 2.124320 CATACAAGGGCACGGGGG 60.124 66.667 0.00 0.00 0.00 5.40
357 366 2.285818 ATACAAGGGCACGGGGGA 60.286 61.111 0.00 0.00 0.00 4.81
379 450 7.871463 GGGGACACACACTTGTATATAGTATTC 59.129 40.741 0.00 0.00 33.30 1.75
405 476 7.121611 CCCTAATCAACGTTTTAAATAGTGGGT 59.878 37.037 0.00 0.00 0.00 4.51
443 514 0.683973 ATCGGCCAGAAGCTATGAGG 59.316 55.000 2.24 0.00 43.05 3.86
452 523 5.590259 GCCAGAAGCTATGAGGAACAAATAA 59.410 40.000 0.48 0.00 38.99 1.40
453 524 6.095440 GCCAGAAGCTATGAGGAACAAATAAA 59.905 38.462 0.48 0.00 38.99 1.40
454 525 7.475840 CCAGAAGCTATGAGGAACAAATAAAC 58.524 38.462 0.48 0.00 0.00 2.01
593 772 3.640967 TCCAGCCATAACAAAACAAAGCT 59.359 39.130 0.00 0.00 0.00 3.74
596 775 5.049167 CAGCCATAACAAAACAAAGCTTGA 58.951 37.500 0.00 0.00 0.00 3.02
610 789 3.589951 AGCTTGACATCCAGCCATAAT 57.410 42.857 1.52 0.00 0.00 1.28
622 801 4.038282 TCCAGCCATAATAATGCAAAGCTG 59.962 41.667 0.00 0.00 41.01 4.24
623 802 4.038282 CCAGCCATAATAATGCAAAGCTGA 59.962 41.667 10.06 0.00 42.53 4.26
624 803 4.980434 CAGCCATAATAATGCAAAGCTGAC 59.020 41.667 2.61 0.00 42.53 3.51
625 804 4.646040 AGCCATAATAATGCAAAGCTGACA 59.354 37.500 0.00 0.00 29.21 3.58
626 805 5.303589 AGCCATAATAATGCAAAGCTGACAT 59.696 36.000 0.00 0.00 29.21 3.06
627 806 6.491062 AGCCATAATAATGCAAAGCTGACATA 59.509 34.615 0.00 0.00 29.21 2.29
667 854 4.574599 AATGAGATCCAAATTTAGCGCC 57.425 40.909 2.29 0.00 0.00 6.53
691 889 8.558973 CCAAATCACCTATTGGCAAAAATAAA 57.441 30.769 3.01 0.00 39.64 1.40
692 890 9.176460 CCAAATCACCTATTGGCAAAAATAAAT 57.824 29.630 3.01 0.00 39.64 1.40
847 1045 3.127030 CGGGAGAATTAGTTGGTGAAAGC 59.873 47.826 0.00 0.00 0.00 3.51
1089 2849 2.045045 CCTCGGAAGCCATTGCCA 60.045 61.111 0.00 0.00 38.69 4.92
1101 2861 1.481871 CATTGCCATTGCTCCTCCTT 58.518 50.000 0.00 0.00 38.71 3.36
1138 2898 2.242708 GTCCTCCTCCTACTCTTCTCCA 59.757 54.545 0.00 0.00 0.00 3.86
1226 2986 0.322816 AGGTCAGCAAATGCCACGAT 60.323 50.000 0.94 0.00 43.38 3.73
1232 2992 0.456653 GCAAATGCCACGATGACCAC 60.457 55.000 0.00 0.00 34.31 4.16
1235 2995 0.324614 AATGCCACGATGACCACTGA 59.675 50.000 0.00 0.00 0.00 3.41
1242 3002 0.461516 CGATGACCACTGATGCTGCT 60.462 55.000 0.00 0.00 0.00 4.24
1836 3605 2.126385 TACAAGTACGGCGGCGTG 60.126 61.111 42.22 29.08 0.00 5.34
2359 4128 2.857152 GAGAGTCTTAGAACTGCATGCG 59.143 50.000 14.09 10.50 0.00 4.73
2367 4136 0.449388 GAACTGCATGCGGAAGAAGG 59.551 55.000 32.80 7.70 0.00 3.46
2368 4137 0.250901 AACTGCATGCGGAAGAAGGT 60.251 50.000 32.80 9.54 0.00 3.50
2369 4138 0.957395 ACTGCATGCGGAAGAAGGTG 60.957 55.000 32.80 5.22 0.00 4.00
2370 4139 1.651240 CTGCATGCGGAAGAAGGTGG 61.651 60.000 22.55 0.00 0.00 4.61
2453 4224 9.778741 TTACAGGCAAGAAATAACATATAGAGG 57.221 33.333 0.00 0.00 0.00 3.69
2454 4225 8.034313 ACAGGCAAGAAATAACATATAGAGGA 57.966 34.615 0.00 0.00 0.00 3.71
2455 4226 8.494433 ACAGGCAAGAAATAACATATAGAGGAA 58.506 33.333 0.00 0.00 0.00 3.36
2456 4227 8.997323 CAGGCAAGAAATAACATATAGAGGAAG 58.003 37.037 0.00 0.00 0.00 3.46
2457 4228 8.718656 AGGCAAGAAATAACATATAGAGGAAGT 58.281 33.333 0.00 0.00 0.00 3.01
2458 4229 9.998106 GGCAAGAAATAACATATAGAGGAAGTA 57.002 33.333 0.00 0.00 0.00 2.24
2488 4259 1.610038 CAGTGATTTTGCTGCACCTGA 59.390 47.619 0.00 0.00 33.14 3.86
2489 4260 1.884579 AGTGATTTTGCTGCACCTGAG 59.115 47.619 0.00 0.00 33.14 3.35
2490 4261 1.881973 GTGATTTTGCTGCACCTGAGA 59.118 47.619 0.00 0.00 0.00 3.27
2491 4262 2.294233 GTGATTTTGCTGCACCTGAGAA 59.706 45.455 0.00 0.00 0.00 2.87
2492 4263 2.294233 TGATTTTGCTGCACCTGAGAAC 59.706 45.455 0.00 0.00 0.00 3.01
2493 4264 1.761449 TTTTGCTGCACCTGAGAACA 58.239 45.000 0.00 0.00 0.00 3.18
2494 4265 1.311859 TTTGCTGCACCTGAGAACAG 58.688 50.000 0.00 0.00 43.12 3.16
2509 4280 7.493743 CTGAGAACAGGGAGAATATTCAATG 57.506 40.000 17.56 11.64 40.14 2.82
2510 4281 7.199167 TGAGAACAGGGAGAATATTCAATGA 57.801 36.000 17.56 0.00 0.00 2.57
2511 4282 7.632861 TGAGAACAGGGAGAATATTCAATGAA 58.367 34.615 17.56 0.00 0.00 2.57
2536 4307 1.196012 GACTGGGAGGGTTACTCTGG 58.804 60.000 0.00 0.00 45.83 3.86
2544 4315 3.369576 GGAGGGTTACTCTGGCAAAGTAG 60.370 52.174 0.34 0.00 45.83 2.57
2564 4335 1.911269 TCCTCACCGCCACTGCTAA 60.911 57.895 0.00 0.00 34.43 3.09
2570 4341 0.902531 ACCGCCACTGCTAACATACT 59.097 50.000 0.00 0.00 34.43 2.12
2585 4356 1.030457 ATACTACTTGACGGCCCTCG 58.970 55.000 0.00 0.00 45.88 4.63
2645 4416 9.528489 TTGCTATTTCTTAGGTACCTGAAAATT 57.472 29.630 25.33 13.69 33.09 1.82
2654 4425 6.374417 AGGTACCTGAAAATTTCTCTAGCA 57.626 37.500 15.42 0.00 0.00 3.49
2666 4437 5.489792 TTTCTCTAGCATCAGTCACCTTT 57.510 39.130 0.00 0.00 0.00 3.11
2673 4444 4.218312 AGCATCAGTCACCTTTTTCCTTT 58.782 39.130 0.00 0.00 0.00 3.11
2674 4445 4.279420 AGCATCAGTCACCTTTTTCCTTTC 59.721 41.667 0.00 0.00 0.00 2.62
2676 4447 5.221322 GCATCAGTCACCTTTTTCCTTTCTT 60.221 40.000 0.00 0.00 0.00 2.52
2677 4448 6.442112 CATCAGTCACCTTTTTCCTTTCTTC 58.558 40.000 0.00 0.00 0.00 2.87
2678 4449 5.755849 TCAGTCACCTTTTTCCTTTCTTCT 58.244 37.500 0.00 0.00 0.00 2.85
2679 4450 5.590259 TCAGTCACCTTTTTCCTTTCTTCTG 59.410 40.000 0.00 0.00 0.00 3.02
2680 4451 4.889995 AGTCACCTTTTTCCTTTCTTCTGG 59.110 41.667 0.00 0.00 0.00 3.86
2681 4452 3.636764 TCACCTTTTTCCTTTCTTCTGGC 59.363 43.478 0.00 0.00 0.00 4.85
2682 4453 3.384467 CACCTTTTTCCTTTCTTCTGGCA 59.616 43.478 0.00 0.00 0.00 4.92
2683 4454 3.384789 ACCTTTTTCCTTTCTTCTGGCAC 59.615 43.478 0.00 0.00 0.00 5.01
2684 4455 3.243873 CCTTTTTCCTTTCTTCTGGCACC 60.244 47.826 0.00 0.00 0.00 5.01
2693 4464 1.291877 CTTCTGGCACCGAAACCTCG 61.292 60.000 0.00 0.00 45.02 4.63
2694 4465 2.030562 CTGGCACCGAAACCTCGT 59.969 61.111 0.00 0.00 43.87 4.18
2720 4491 2.095604 AGAGAGCCCCACTATCTTCC 57.904 55.000 0.00 0.00 44.69 3.46
2721 4492 1.052617 GAGAGCCCCACTATCTTCCC 58.947 60.000 0.00 0.00 33.63 3.97
2722 4493 0.644937 AGAGCCCCACTATCTTCCCT 59.355 55.000 0.00 0.00 0.00 4.20
2723 4494 0.761802 GAGCCCCACTATCTTCCCTG 59.238 60.000 0.00 0.00 0.00 4.45
2724 4495 0.695803 AGCCCCACTATCTTCCCTGG 60.696 60.000 0.00 0.00 0.00 4.45
2725 4496 0.988678 GCCCCACTATCTTCCCTGGT 60.989 60.000 0.00 0.00 0.00 4.00
2726 4497 0.839946 CCCCACTATCTTCCCTGGTG 59.160 60.000 0.00 0.00 0.00 4.17
2727 4498 0.181350 CCCACTATCTTCCCTGGTGC 59.819 60.000 0.00 0.00 0.00 5.01
2728 4499 0.911769 CCACTATCTTCCCTGGTGCA 59.088 55.000 0.00 0.00 0.00 4.57
2729 4500 1.134280 CCACTATCTTCCCTGGTGCAG 60.134 57.143 0.00 0.00 0.00 4.41
2730 4501 0.543749 ACTATCTTCCCTGGTGCAGC 59.456 55.000 9.47 9.47 0.00 5.25
2731 4502 0.543277 CTATCTTCCCTGGTGCAGCA 59.457 55.000 19.03 19.03 0.00 4.41
2732 4503 0.543277 TATCTTCCCTGGTGCAGCAG 59.457 55.000 33.77 33.77 0.00 4.24
2733 4504 2.207501 ATCTTCCCTGGTGCAGCAGG 62.208 60.000 44.26 44.26 38.29 4.85
2734 4505 4.666253 TTCCCTGGTGCAGCAGGC 62.666 66.667 45.30 11.12 45.13 4.85
2743 4514 4.643795 GCAGCAGGCATACAAGGA 57.356 55.556 0.00 0.00 43.97 3.36
2744 4515 3.106738 GCAGCAGGCATACAAGGAT 57.893 52.632 0.00 0.00 43.97 3.24
2745 4516 0.666913 GCAGCAGGCATACAAGGATG 59.333 55.000 0.00 0.00 43.97 3.51
2746 4517 1.315690 CAGCAGGCATACAAGGATGG 58.684 55.000 0.00 0.00 0.00 3.51
2747 4518 0.921896 AGCAGGCATACAAGGATGGT 59.078 50.000 0.00 0.00 0.00 3.55
2748 4519 1.285962 AGCAGGCATACAAGGATGGTT 59.714 47.619 0.00 0.00 0.00 3.67
2749 4520 1.406539 GCAGGCATACAAGGATGGTTG 59.593 52.381 0.00 0.00 0.00 3.77
2750 4521 2.726821 CAGGCATACAAGGATGGTTGT 58.273 47.619 0.00 0.00 43.22 3.32
2751 4522 2.424601 CAGGCATACAAGGATGGTTGTG 59.575 50.000 0.00 0.00 40.89 3.33
2752 4523 1.750778 GGCATACAAGGATGGTTGTGG 59.249 52.381 0.00 0.00 40.89 4.17
2753 4524 1.134946 GCATACAAGGATGGTTGTGGC 59.865 52.381 0.00 0.51 40.89 5.01
2754 4525 1.401552 CATACAAGGATGGTTGTGGCG 59.598 52.381 0.00 0.00 40.89 5.69
2755 4526 0.322098 TACAAGGATGGTTGTGGCGG 60.322 55.000 0.00 0.00 40.89 6.13
2756 4527 1.603455 CAAGGATGGTTGTGGCGGT 60.603 57.895 0.00 0.00 0.00 5.68
2757 4528 1.603455 AAGGATGGTTGTGGCGGTG 60.603 57.895 0.00 0.00 0.00 4.94
2758 4529 3.061848 GGATGGTTGTGGCGGTGG 61.062 66.667 0.00 0.00 0.00 4.61
2759 4530 3.061848 GATGGTTGTGGCGGTGGG 61.062 66.667 0.00 0.00 0.00 4.61
2760 4531 4.676951 ATGGTTGTGGCGGTGGGG 62.677 66.667 0.00 0.00 0.00 4.96
2769 4540 4.410400 GCGGTGGGGGAGGTTGAG 62.410 72.222 0.00 0.00 0.00 3.02
2770 4541 3.717294 CGGTGGGGGAGGTTGAGG 61.717 72.222 0.00 0.00 0.00 3.86
2771 4542 3.339093 GGTGGGGGAGGTTGAGGG 61.339 72.222 0.00 0.00 0.00 4.30
2772 4543 3.339093 GTGGGGGAGGTTGAGGGG 61.339 72.222 0.00 0.00 0.00 4.79
2773 4544 3.547737 TGGGGGAGGTTGAGGGGA 61.548 66.667 0.00 0.00 0.00 4.81
2774 4545 2.692741 GGGGGAGGTTGAGGGGAG 60.693 72.222 0.00 0.00 0.00 4.30
2775 4546 2.692741 GGGGAGGTTGAGGGGAGG 60.693 72.222 0.00 0.00 0.00 4.30
2776 4547 2.692741 GGGAGGTTGAGGGGAGGG 60.693 72.222 0.00 0.00 0.00 4.30
2777 4548 2.125225 GGAGGTTGAGGGGAGGGT 59.875 66.667 0.00 0.00 0.00 4.34
2778 4549 2.301738 GGAGGTTGAGGGGAGGGTG 61.302 68.421 0.00 0.00 0.00 4.61
2779 4550 2.204151 AGGTTGAGGGGAGGGTGG 60.204 66.667 0.00 0.00 0.00 4.61
2780 4551 3.339093 GGTTGAGGGGAGGGTGGG 61.339 72.222 0.00 0.00 0.00 4.61
2781 4552 3.339093 GTTGAGGGGAGGGTGGGG 61.339 72.222 0.00 0.00 0.00 4.96
2801 4572 4.840005 GGGTAGCGCCTGCCAGTC 62.840 72.222 2.29 0.00 44.31 3.51
2802 4573 4.082523 GGTAGCGCCTGCCAGTCA 62.083 66.667 2.29 0.00 44.31 3.41
2803 4574 2.815647 GTAGCGCCTGCCAGTCAC 60.816 66.667 2.29 0.00 44.31 3.67
2804 4575 4.435436 TAGCGCCTGCCAGTCACG 62.435 66.667 2.29 0.00 44.31 4.35
2809 4580 4.704833 CCTGCCAGTCACGGGTGG 62.705 72.222 0.00 0.00 36.85 4.61
2810 4581 3.941188 CTGCCAGTCACGGGTGGT 61.941 66.667 0.00 0.00 36.10 4.16
2819 4590 3.953775 ACGGGTGGTGAAGGCTGG 61.954 66.667 0.00 0.00 0.00 4.85
2820 4591 3.953775 CGGGTGGTGAAGGCTGGT 61.954 66.667 0.00 0.00 0.00 4.00
2821 4592 2.282462 GGGTGGTGAAGGCTGGTG 60.282 66.667 0.00 0.00 0.00 4.17
2822 4593 2.282462 GGTGGTGAAGGCTGGTGG 60.282 66.667 0.00 0.00 0.00 4.61
2823 4594 2.515901 GTGGTGAAGGCTGGTGGT 59.484 61.111 0.00 0.00 0.00 4.16
2839 4610 4.426313 GTTAGGGCGGGGCAAGCT 62.426 66.667 3.58 0.00 34.52 3.74
2840 4611 4.424711 TTAGGGCGGGGCAAGCTG 62.425 66.667 0.00 0.00 34.52 4.24
2850 4621 4.487412 GCAAGCTGGCGGCATCAC 62.487 66.667 22.28 5.30 44.79 3.06
2853 4624 4.827087 AGCTGGCGGCATCACGAG 62.827 66.667 22.28 0.00 44.79 4.18
2859 4630 1.447838 GCGGCATCACGAGGAAGAA 60.448 57.895 0.00 0.00 35.47 2.52
2860 4631 1.424493 GCGGCATCACGAGGAAGAAG 61.424 60.000 0.00 0.00 35.47 2.85
2861 4632 0.173481 CGGCATCACGAGGAAGAAGA 59.827 55.000 0.00 0.00 35.47 2.87
2862 4633 1.202463 CGGCATCACGAGGAAGAAGAT 60.202 52.381 0.00 0.00 35.47 2.40
2863 4634 2.478831 GGCATCACGAGGAAGAAGATC 58.521 52.381 0.00 0.00 0.00 2.75
2864 4635 2.102252 GGCATCACGAGGAAGAAGATCT 59.898 50.000 0.00 0.00 0.00 2.75
2865 4636 3.319405 GGCATCACGAGGAAGAAGATCTA 59.681 47.826 0.00 0.00 0.00 1.98
2866 4637 4.202161 GGCATCACGAGGAAGAAGATCTAA 60.202 45.833 0.00 0.00 0.00 2.10
2868 4639 4.617808 TCACGAGGAAGAAGATCTAACG 57.382 45.455 0.00 0.00 0.00 3.18
2869 4640 4.259356 TCACGAGGAAGAAGATCTAACGA 58.741 43.478 0.00 0.00 0.00 3.85
2870 4641 4.882427 TCACGAGGAAGAAGATCTAACGAT 59.118 41.667 0.00 0.00 0.00 3.73
2871 4642 5.357314 TCACGAGGAAGAAGATCTAACGATT 59.643 40.000 0.00 0.00 0.00 3.34
2880 4651 6.109359 AGAAGATCTAACGATTTCTGGTTGG 58.891 40.000 0.00 0.00 31.68 3.77
2893 4664 2.038952 TCTGGTTGGAAGTGACTGATGG 59.961 50.000 0.00 0.00 0.00 3.51
2904 4675 7.505585 TGGAAGTGACTGATGGACTTTTATTTT 59.494 33.333 0.00 0.00 30.01 1.82
2909 4680 6.071952 TGACTGATGGACTTTTATTTTCAGGC 60.072 38.462 0.00 0.00 38.08 4.85
2924 4695 9.969001 TTATTTTCAGGCACCTAACTTATAGTT 57.031 29.630 0.00 0.00 41.97 2.24
2928 4699 5.249852 TCAGGCACCTAACTTATAGTTGGTT 59.750 40.000 2.45 0.00 39.11 3.67
2930 4701 4.880120 GGCACCTAACTTATAGTTGGTTCC 59.120 45.833 11.04 11.04 39.11 3.62
2939 4710 5.944007 ACTTATAGTTGGTTCCGAGCAAATT 59.056 36.000 0.00 0.00 44.11 1.82
2957 4728 5.619981 GCAAATTAGACAAGATCACCCACAC 60.620 44.000 0.00 0.00 0.00 3.82
2961 4733 2.705658 AGACAAGATCACCCACACTTCA 59.294 45.455 0.00 0.00 0.00 3.02
3003 4775 2.363680 AGATCATACGTCTTGAGGGCAG 59.636 50.000 0.00 0.00 0.00 4.85
3023 4795 5.508320 GGCAGTCTTTGGTTAATCGGAAAAA 60.508 40.000 0.00 0.00 0.00 1.94
3024 4796 5.401376 GCAGTCTTTGGTTAATCGGAAAAAC 59.599 40.000 0.00 0.00 0.00 2.43
3025 4797 6.500041 CAGTCTTTGGTTAATCGGAAAAACA 58.500 36.000 7.76 0.38 0.00 2.83
3026 4798 6.636850 CAGTCTTTGGTTAATCGGAAAAACAG 59.363 38.462 7.76 0.00 0.00 3.16
3027 4799 6.320418 AGTCTTTGGTTAATCGGAAAAACAGT 59.680 34.615 7.76 0.00 0.00 3.55
3028 4800 6.416750 GTCTTTGGTTAATCGGAAAAACAGTG 59.583 38.462 7.76 0.00 0.00 3.66
3030 4802 3.570550 TGGTTAATCGGAAAAACAGTGGG 59.429 43.478 0.00 0.00 0.00 4.61
3031 4803 3.571571 GTTAATCGGAAAAACAGTGGGC 58.428 45.455 0.00 0.00 0.00 5.36
3032 4804 1.995376 AATCGGAAAAACAGTGGGCT 58.005 45.000 0.00 0.00 0.00 5.19
3033 4805 1.534729 ATCGGAAAAACAGTGGGCTC 58.465 50.000 0.00 0.00 0.00 4.70
3034 4806 0.181587 TCGGAAAAACAGTGGGCTCA 59.818 50.000 0.00 0.00 0.00 4.26
3036 4808 0.673985 GGAAAAACAGTGGGCTCACC 59.326 55.000 14.62 0.00 44.64 4.02
3058 4830 2.203480 GCACTTGGGTGGCCTTGA 60.203 61.111 3.32 0.00 43.18 3.02
3060 4832 1.187567 GCACTTGGGTGGCCTTGATT 61.188 55.000 3.32 0.00 43.18 2.57
3070 4842 2.034053 GTGGCCTTGATTTTGTCGACAA 59.966 45.455 26.53 26.53 0.00 3.18
3075 4847 4.560035 GCCTTGATTTTGTCGACAATGATG 59.440 41.667 30.10 17.39 35.55 3.07
3082 4855 4.700268 TTGTCGACAATGATGATTTGGG 57.300 40.909 26.53 0.00 0.00 4.12
3083 4856 3.684908 TGTCGACAATGATGATTTGGGT 58.315 40.909 17.62 0.00 0.00 4.51
3092 4865 2.288948 TGATGATTTGGGTGTGCTTTGC 60.289 45.455 0.00 0.00 0.00 3.68
3099 4872 1.891919 GGTGTGCTTTGCGTCTCCA 60.892 57.895 0.00 0.00 0.00 3.86
3102 4875 1.804151 GTGTGCTTTGCGTCTCCATTA 59.196 47.619 0.00 0.00 0.00 1.90
3106 4879 1.017387 CTTTGCGTCTCCATTAGCCC 58.983 55.000 0.00 0.00 0.00 5.19
3128 4901 1.746615 CTGCAATGGACCGACCCTG 60.747 63.158 0.00 0.00 38.00 4.45
3136 4909 2.603776 ACCGACCCTGACAGACCC 60.604 66.667 3.32 0.00 0.00 4.46
3144 4917 1.617947 CCTGACAGACCCTAGGTGGC 61.618 65.000 8.29 1.95 35.25 5.01
3150 4923 0.339859 AGACCCTAGGTGGCATCTCA 59.660 55.000 2.02 0.00 35.25 3.27
3156 4929 0.833287 TAGGTGGCATCTCAGCTTCC 59.167 55.000 2.02 0.00 42.05 3.46
3164 4937 1.599606 ATCTCAGCTTCCGTGCGACT 61.600 55.000 0.00 0.00 38.13 4.18
3169 4942 0.669625 AGCTTCCGTGCGACTAAACC 60.670 55.000 0.00 0.00 38.13 3.27
3185 4960 6.507456 CGACTAAACCGACATAGAATTTTCCG 60.507 42.308 0.00 0.00 0.00 4.30
3197 4972 0.041090 ATTTTCCGGGCCTTCACCAT 59.959 50.000 0.84 0.00 0.00 3.55
3201 4976 1.526917 CCGGGCCTTCACCATCATC 60.527 63.158 0.84 0.00 0.00 2.92
3208 4983 1.004628 CCTTCACCATCATCACCACCA 59.995 52.381 0.00 0.00 0.00 4.17
3225 5000 3.077484 ACCAAAGATGTCCATGGTGAG 57.923 47.619 12.58 0.00 44.25 3.51
3233 5008 3.228188 TGTCCATGGTGAGCTTTTCTT 57.772 42.857 12.58 0.00 0.00 2.52
3240 5015 2.159254 TGGTGAGCTTTTCTTGCACAAC 60.159 45.455 0.00 0.00 38.77 3.32
3241 5016 2.463876 GTGAGCTTTTCTTGCACAACC 58.536 47.619 0.00 0.00 33.32 3.77
3254 5029 1.229177 ACAACCATTGGAAGCCCCC 60.229 57.895 10.37 0.00 34.12 5.40
3322 5097 0.950836 CAAAACGGTGCACCATGAGA 59.049 50.000 34.16 0.00 35.14 3.27
3327 5102 0.729116 CGGTGCACCATGAGATGAAC 59.271 55.000 34.16 3.97 35.14 3.18
3328 5103 1.825090 GGTGCACCATGAGATGAACA 58.175 50.000 31.23 0.00 35.64 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
143 147 6.457257 GCAAACCAAATTTACCATCATCATGC 60.457 38.462 0.00 0.00 0.00 4.06
145 149 6.709281 TGCAAACCAAATTTACCATCATCAT 58.291 32.000 0.00 0.00 0.00 2.45
237 246 0.179108 GAGGACGAGCACATGGTACC 60.179 60.000 4.43 4.43 0.00 3.34
293 302 1.688197 ACTCCAGTTGTGCATTTTGGG 59.312 47.619 0.00 0.00 0.00 4.12
299 308 0.320771 GGACGACTCCAGTTGTGCAT 60.321 55.000 12.48 0.00 46.24 3.96
314 323 7.813148 TGTTTACTTCAATCTAGAGAAAGGACG 59.187 37.037 13.21 0.00 0.00 4.79
351 360 0.323629 ATACAAGTGTGTGTCCCCCG 59.676 55.000 0.00 0.00 38.82 5.73
352 361 3.926058 ATATACAAGTGTGTGTCCCCC 57.074 47.619 0.00 0.00 38.82 5.40
356 365 8.639761 AGGGAATACTATATACAAGTGTGTGTC 58.360 37.037 0.00 0.00 38.82 3.67
357 366 8.548880 AGGGAATACTATATACAAGTGTGTGT 57.451 34.615 0.00 0.00 38.82 3.72
379 450 7.121611 ACCCACTATTTAAAACGTTGATTAGGG 59.878 37.037 0.00 6.29 0.00 3.53
386 457 6.528774 GGCATAACCCACTATTTAAAACGTTG 59.471 38.462 0.00 0.00 0.00 4.10
389 460 6.197364 TGGCATAACCCACTATTTAAAACG 57.803 37.500 0.00 0.00 37.83 3.60
422 493 1.617850 CTCATAGCTTCTGGCCGATCT 59.382 52.381 0.00 2.19 43.05 2.75
452 523 8.539117 AAATGCTAAATAGGGCTTAGATTGTT 57.461 30.769 0.00 0.00 0.00 2.83
453 524 8.539117 AAAATGCTAAATAGGGCTTAGATTGT 57.461 30.769 0.00 0.00 0.00 2.71
498 569 7.094549 TGCCTAATACTGTACGCTTTTCAAAAT 60.095 33.333 0.00 0.00 0.00 1.82
503 574 5.522460 TGATGCCTAATACTGTACGCTTTTC 59.478 40.000 0.00 0.00 0.00 2.29
510 582 9.658799 ATGTGATATTGATGCCTAATACTGTAC 57.341 33.333 0.00 0.00 0.00 2.90
551 708 0.918258 TGCCAGGTCCATTGATGCTA 59.082 50.000 0.00 0.00 0.00 3.49
552 709 0.260816 ATGCCAGGTCCATTGATGCT 59.739 50.000 0.00 0.00 0.00 3.79
553 710 0.672342 GATGCCAGGTCCATTGATGC 59.328 55.000 0.00 0.00 0.00 3.91
554 711 1.325355 GGATGCCAGGTCCATTGATG 58.675 55.000 0.00 0.00 35.76 3.07
581 760 4.685924 CTGGATGTCAAGCTTTGTTTTGT 58.314 39.130 0.00 0.00 0.00 2.83
593 772 5.139001 TGCATTATTATGGCTGGATGTCAA 58.861 37.500 0.00 0.00 32.16 3.18
596 775 5.510179 GCTTTGCATTATTATGGCTGGATGT 60.510 40.000 0.00 0.00 32.15 3.06
647 834 3.554934 TGGCGCTAAATTTGGATCTCAT 58.445 40.909 7.64 0.00 0.00 2.90
652 839 4.432712 GTGATTTGGCGCTAAATTTGGAT 58.567 39.130 29.01 10.14 30.78 3.41
691 889 7.115663 ACGTTTGTTTTGCGCTAAATGATTTAT 59.884 29.630 19.41 1.92 0.00 1.40
692 890 6.418226 ACGTTTGTTTTGCGCTAAATGATTTA 59.582 30.769 19.41 0.00 0.00 1.40
693 891 5.233263 ACGTTTGTTTTGCGCTAAATGATTT 59.767 32.000 19.41 0.00 0.00 2.17
694 892 4.742659 ACGTTTGTTTTGCGCTAAATGATT 59.257 33.333 19.41 1.14 0.00 2.57
695 893 4.295051 ACGTTTGTTTTGCGCTAAATGAT 58.705 34.783 19.41 1.35 0.00 2.45
696 894 3.696898 ACGTTTGTTTTGCGCTAAATGA 58.303 36.364 19.41 9.00 0.00 2.57
771 969 3.489059 CGTTTACTTGCCATGCATTAGGG 60.489 47.826 0.00 0.00 38.76 3.53
847 1045 8.349983 ACAGGTTAAAATTAAGTACACTTGCTG 58.650 33.333 4.86 0.00 37.40 4.41
915 2666 0.808755 GCGGTCTTTGTAACATGGGG 59.191 55.000 0.00 0.00 0.00 4.96
1029 2789 1.404851 GGAGGGAAGAAGAGCGAAGTG 60.405 57.143 0.00 0.00 0.00 3.16
1089 2849 2.240921 GGAGAAGGAAAGGAGGAGCAAT 59.759 50.000 0.00 0.00 0.00 3.56
1101 2861 0.908180 GGACGGGGAAGGAGAAGGAA 60.908 60.000 0.00 0.00 0.00 3.36
1138 2898 0.394488 TGCGAGAGGAGGAAGACGAT 60.394 55.000 0.00 0.00 0.00 3.73
1226 2986 1.673337 GCAGCAGCATCAGTGGTCA 60.673 57.895 0.00 0.00 41.58 4.02
2297 4066 1.870055 ATTGCAGAACAAGCAGCCGG 61.870 55.000 0.00 0.00 42.87 6.13
2359 4128 0.466124 CCGATCTCCCACCTTCTTCC 59.534 60.000 0.00 0.00 0.00 3.46
2367 4136 2.107141 CCGAAGCCGATCTCCCAC 59.893 66.667 0.00 0.00 38.22 4.61
2368 4137 1.987855 AACCGAAGCCGATCTCCCA 60.988 57.895 0.00 0.00 38.22 4.37
2369 4138 1.521681 CAACCGAAGCCGATCTCCC 60.522 63.158 0.00 0.00 38.22 4.30
2370 4139 1.521681 CCAACCGAAGCCGATCTCC 60.522 63.158 0.00 0.00 38.22 3.71
2450 4221 4.815308 TCACTGCTCTATACGTACTTCCTC 59.185 45.833 0.00 0.00 0.00 3.71
2451 4222 4.778579 TCACTGCTCTATACGTACTTCCT 58.221 43.478 0.00 0.00 0.00 3.36
2452 4223 5.692613 ATCACTGCTCTATACGTACTTCC 57.307 43.478 0.00 0.00 0.00 3.46
2453 4224 7.515371 GCAAAATCACTGCTCTATACGTACTTC 60.515 40.741 0.00 0.00 36.84 3.01
2454 4225 6.255887 GCAAAATCACTGCTCTATACGTACTT 59.744 38.462 0.00 0.00 36.84 2.24
2455 4226 5.749109 GCAAAATCACTGCTCTATACGTACT 59.251 40.000 0.00 0.00 36.84 2.73
2456 4227 5.964070 GCAAAATCACTGCTCTATACGTAC 58.036 41.667 0.00 0.00 36.84 3.67
2485 4256 7.278135 TCATTGAATATTCTCCCTGTTCTCAG 58.722 38.462 16.24 0.00 41.01 3.35
2488 4259 8.743714 GTTTTCATTGAATATTCTCCCTGTTCT 58.256 33.333 16.24 0.00 0.00 3.01
2489 4260 8.522830 TGTTTTCATTGAATATTCTCCCTGTTC 58.477 33.333 16.24 3.43 0.00 3.18
2490 4261 8.421249 TGTTTTCATTGAATATTCTCCCTGTT 57.579 30.769 16.24 0.00 0.00 3.16
2491 4262 8.472413 CATGTTTTCATTGAATATTCTCCCTGT 58.528 33.333 16.24 0.00 38.64 4.00
2492 4263 8.689061 TCATGTTTTCATTGAATATTCTCCCTG 58.311 33.333 16.24 8.41 38.64 4.45
2493 4264 8.689972 GTCATGTTTTCATTGAATATTCTCCCT 58.310 33.333 16.24 0.00 38.64 4.20
2494 4265 8.689972 AGTCATGTTTTCATTGAATATTCTCCC 58.310 33.333 16.24 0.00 38.64 4.30
2495 4266 9.512435 CAGTCATGTTTTCATTGAATATTCTCC 57.488 33.333 16.24 0.00 38.64 3.71
2496 4267 9.512435 CCAGTCATGTTTTCATTGAATATTCTC 57.488 33.333 16.24 0.00 38.64 2.87
2497 4268 8.472413 CCCAGTCATGTTTTCATTGAATATTCT 58.528 33.333 16.24 0.00 38.64 2.40
2498 4269 8.469200 TCCCAGTCATGTTTTCATTGAATATTC 58.531 33.333 8.60 8.60 38.64 1.75
2499 4270 8.365060 TCCCAGTCATGTTTTCATTGAATATT 57.635 30.769 0.00 0.00 38.64 1.28
2500 4271 7.069085 CCTCCCAGTCATGTTTTCATTGAATAT 59.931 37.037 0.00 0.00 38.64 1.28
2501 4272 6.377996 CCTCCCAGTCATGTTTTCATTGAATA 59.622 38.462 0.00 0.00 38.64 1.75
2502 4273 5.186409 CCTCCCAGTCATGTTTTCATTGAAT 59.814 40.000 0.00 0.00 38.64 2.57
2503 4274 4.523943 CCTCCCAGTCATGTTTTCATTGAA 59.476 41.667 0.00 0.00 38.64 2.69
2504 4275 4.081406 CCTCCCAGTCATGTTTTCATTGA 58.919 43.478 0.00 0.00 38.64 2.57
2505 4276 3.194116 CCCTCCCAGTCATGTTTTCATTG 59.806 47.826 0.00 0.00 38.64 2.82
2506 4277 3.181418 ACCCTCCCAGTCATGTTTTCATT 60.181 43.478 0.00 0.00 38.64 2.57
2507 4278 2.379907 ACCCTCCCAGTCATGTTTTCAT 59.620 45.455 0.00 0.00 41.78 2.57
2508 4279 1.780309 ACCCTCCCAGTCATGTTTTCA 59.220 47.619 0.00 0.00 0.00 2.69
2509 4280 2.586648 ACCCTCCCAGTCATGTTTTC 57.413 50.000 0.00 0.00 0.00 2.29
2510 4281 3.397955 AGTAACCCTCCCAGTCATGTTTT 59.602 43.478 0.00 0.00 0.00 2.43
2511 4282 2.986728 AGTAACCCTCCCAGTCATGTTT 59.013 45.455 0.00 0.00 0.00 2.83
2536 4307 1.019805 GCGGTGAGGACCTACTTTGC 61.020 60.000 0.00 0.00 40.58 3.68
2564 4335 1.755380 GAGGGCCGTCAAGTAGTATGT 59.245 52.381 20.47 0.00 0.00 2.29
2585 4356 1.002087 CAGGATACAATACGGAGGGGC 59.998 57.143 0.00 0.00 41.41 5.80
2630 4401 7.490657 TGCTAGAGAAATTTTCAGGTACCTA 57.509 36.000 15.80 0.00 0.00 3.08
2632 4403 6.823689 TGATGCTAGAGAAATTTTCAGGTACC 59.176 38.462 2.73 2.73 0.00 3.34
2645 4416 5.489792 AAAAGGTGACTGATGCTAGAGAA 57.510 39.130 0.00 0.00 42.68 2.87
2654 4425 6.264067 CAGAAGAAAGGAAAAAGGTGACTGAT 59.736 38.462 0.00 0.00 42.68 2.90
2666 4437 1.142060 TCGGTGCCAGAAGAAAGGAAA 59.858 47.619 0.00 0.00 0.00 3.13
2673 4444 0.034896 GAGGTTTCGGTGCCAGAAGA 59.965 55.000 0.00 0.00 0.00 2.87
2674 4445 1.291877 CGAGGTTTCGGTGCCAGAAG 61.292 60.000 0.00 0.00 43.05 2.85
2676 4447 2.342279 CGAGGTTTCGGTGCCAGA 59.658 61.111 0.00 0.00 43.05 3.86
2693 4464 1.682684 TGGGGCTCTCTTCTCCGAC 60.683 63.158 0.00 0.00 0.00 4.79
2694 4465 1.682684 GTGGGGCTCTCTTCTCCGA 60.683 63.158 0.00 0.00 0.00 4.55
2697 4468 2.957474 AGATAGTGGGGCTCTCTTCTC 58.043 52.381 0.00 0.00 27.57 2.87
2726 4497 0.666913 CATCCTTGTATGCCTGCTGC 59.333 55.000 0.00 0.00 41.77 5.25
2727 4498 1.315690 CCATCCTTGTATGCCTGCTG 58.684 55.000 0.00 0.00 0.00 4.41
2728 4499 0.921896 ACCATCCTTGTATGCCTGCT 59.078 50.000 0.00 0.00 0.00 4.24
2729 4500 1.406539 CAACCATCCTTGTATGCCTGC 59.593 52.381 0.00 0.00 0.00 4.85
2730 4501 2.424601 CACAACCATCCTTGTATGCCTG 59.575 50.000 0.00 0.00 32.90 4.85
2731 4502 2.621407 CCACAACCATCCTTGTATGCCT 60.621 50.000 0.00 0.00 32.90 4.75
2732 4503 1.750778 CCACAACCATCCTTGTATGCC 59.249 52.381 0.00 0.00 32.90 4.40
2733 4504 1.134946 GCCACAACCATCCTTGTATGC 59.865 52.381 0.00 0.00 32.90 3.14
2734 4505 1.401552 CGCCACAACCATCCTTGTATG 59.598 52.381 0.00 0.00 32.90 2.39
2735 4506 1.681780 CCGCCACAACCATCCTTGTAT 60.682 52.381 0.00 0.00 32.90 2.29
2736 4507 0.322098 CCGCCACAACCATCCTTGTA 60.322 55.000 0.00 0.00 32.90 2.41
2737 4508 1.603455 CCGCCACAACCATCCTTGT 60.603 57.895 0.00 0.00 34.56 3.16
2738 4509 1.603455 ACCGCCACAACCATCCTTG 60.603 57.895 0.00 0.00 0.00 3.61
2739 4510 1.603455 CACCGCCACAACCATCCTT 60.603 57.895 0.00 0.00 0.00 3.36
2740 4511 2.034066 CACCGCCACAACCATCCT 59.966 61.111 0.00 0.00 0.00 3.24
2741 4512 3.061848 CCACCGCCACAACCATCC 61.062 66.667 0.00 0.00 0.00 3.51
2742 4513 3.061848 CCCACCGCCACAACCATC 61.062 66.667 0.00 0.00 0.00 3.51
2743 4514 4.676951 CCCCACCGCCACAACCAT 62.677 66.667 0.00 0.00 0.00 3.55
2752 4523 4.410400 CTCAACCTCCCCCACCGC 62.410 72.222 0.00 0.00 0.00 5.68
2753 4524 3.717294 CCTCAACCTCCCCCACCG 61.717 72.222 0.00 0.00 0.00 4.94
2754 4525 3.339093 CCCTCAACCTCCCCCACC 61.339 72.222 0.00 0.00 0.00 4.61
2755 4526 3.339093 CCCCTCAACCTCCCCCAC 61.339 72.222 0.00 0.00 0.00 4.61
2756 4527 3.547737 TCCCCTCAACCTCCCCCA 61.548 66.667 0.00 0.00 0.00 4.96
2757 4528 2.692741 CTCCCCTCAACCTCCCCC 60.693 72.222 0.00 0.00 0.00 5.40
2758 4529 2.692741 CCTCCCCTCAACCTCCCC 60.693 72.222 0.00 0.00 0.00 4.81
2759 4530 2.692741 CCCTCCCCTCAACCTCCC 60.693 72.222 0.00 0.00 0.00 4.30
2760 4531 2.125225 ACCCTCCCCTCAACCTCC 59.875 66.667 0.00 0.00 0.00 4.30
2761 4532 2.301738 CCACCCTCCCCTCAACCTC 61.302 68.421 0.00 0.00 0.00 3.85
2762 4533 2.204151 CCACCCTCCCCTCAACCT 60.204 66.667 0.00 0.00 0.00 3.50
2763 4534 3.339093 CCCACCCTCCCCTCAACC 61.339 72.222 0.00 0.00 0.00 3.77
2764 4535 3.339093 CCCCACCCTCCCCTCAAC 61.339 72.222 0.00 0.00 0.00 3.18
2784 4555 4.840005 GACTGGCAGGCGCTACCC 62.840 72.222 20.34 5.53 40.58 3.69
2785 4556 4.082523 TGACTGGCAGGCGCTACC 62.083 66.667 20.34 7.19 38.60 3.18
2786 4557 2.815647 GTGACTGGCAGGCGCTAC 60.816 66.667 26.28 10.23 38.60 3.58
2787 4558 4.435436 CGTGACTGGCAGGCGCTA 62.435 66.667 29.59 3.17 38.60 4.26
2792 4563 4.704833 CCACCCGTGACTGGCAGG 62.705 72.222 20.34 2.68 0.00 4.85
2793 4564 3.941188 ACCACCCGTGACTGGCAG 61.941 66.667 14.16 14.16 0.00 4.85
2794 4565 4.248842 CACCACCCGTGACTGGCA 62.249 66.667 0.00 0.00 46.20 4.92
2795 4566 3.936203 TCACCACCCGTGACTGGC 61.936 66.667 0.00 0.00 46.80 4.85
2801 4572 2.669569 CAGCCTTCACCACCCGTG 60.670 66.667 0.00 0.00 44.50 4.94
2802 4573 3.953775 CCAGCCTTCACCACCCGT 61.954 66.667 0.00 0.00 0.00 5.28
2803 4574 3.953775 ACCAGCCTTCACCACCCG 61.954 66.667 0.00 0.00 0.00 5.28
2804 4575 2.282462 CACCAGCCTTCACCACCC 60.282 66.667 0.00 0.00 0.00 4.61
2805 4576 2.282462 CCACCAGCCTTCACCACC 60.282 66.667 0.00 0.00 0.00 4.61
2806 4577 0.109723 TAACCACCAGCCTTCACCAC 59.890 55.000 0.00 0.00 0.00 4.16
2807 4578 0.400213 CTAACCACCAGCCTTCACCA 59.600 55.000 0.00 0.00 0.00 4.17
2808 4579 0.322546 CCTAACCACCAGCCTTCACC 60.323 60.000 0.00 0.00 0.00 4.02
2809 4580 0.322546 CCCTAACCACCAGCCTTCAC 60.323 60.000 0.00 0.00 0.00 3.18
2810 4581 2.074967 CCCTAACCACCAGCCTTCA 58.925 57.895 0.00 0.00 0.00 3.02
2811 4582 1.378646 GCCCTAACCACCAGCCTTC 60.379 63.158 0.00 0.00 0.00 3.46
2812 4583 2.763902 GCCCTAACCACCAGCCTT 59.236 61.111 0.00 0.00 0.00 4.35
2813 4584 3.717294 CGCCCTAACCACCAGCCT 61.717 66.667 0.00 0.00 0.00 4.58
2814 4585 4.796495 CCGCCCTAACCACCAGCC 62.796 72.222 0.00 0.00 0.00 4.85
2815 4586 4.796495 CCCGCCCTAACCACCAGC 62.796 72.222 0.00 0.00 0.00 4.85
2816 4587 4.109675 CCCCGCCCTAACCACCAG 62.110 72.222 0.00 0.00 0.00 4.00
2819 4590 4.354162 TTGCCCCGCCCTAACCAC 62.354 66.667 0.00 0.00 0.00 4.16
2820 4591 4.041762 CTTGCCCCGCCCTAACCA 62.042 66.667 0.00 0.00 0.00 3.67
2822 4593 4.426313 AGCTTGCCCCGCCCTAAC 62.426 66.667 0.00 0.00 0.00 2.34
2823 4594 4.424711 CAGCTTGCCCCGCCCTAA 62.425 66.667 0.00 0.00 0.00 2.69
2839 4610 3.664025 CTTCCTCGTGATGCCGCCA 62.664 63.158 0.00 0.00 0.00 5.69
2840 4611 2.852495 TTCTTCCTCGTGATGCCGCC 62.852 60.000 0.00 0.00 0.00 6.13
2844 4615 3.451141 AGATCTTCTTCCTCGTGATGC 57.549 47.619 0.00 0.00 0.00 3.91
2848 4619 4.617808 TCGTTAGATCTTCTTCCTCGTG 57.382 45.455 0.00 0.00 0.00 4.35
2849 4620 5.838531 AATCGTTAGATCTTCTTCCTCGT 57.161 39.130 0.00 0.00 35.74 4.18
2850 4621 6.416455 CAGAAATCGTTAGATCTTCTTCCTCG 59.584 42.308 0.00 0.00 35.74 4.63
2853 4624 6.342111 ACCAGAAATCGTTAGATCTTCTTCC 58.658 40.000 0.00 0.00 35.74 3.46
2859 4630 5.677319 TCCAACCAGAAATCGTTAGATCT 57.323 39.130 0.00 0.00 35.74 2.75
2860 4631 5.875359 ACTTCCAACCAGAAATCGTTAGATC 59.125 40.000 0.00 0.00 35.74 2.75
2861 4632 5.643777 CACTTCCAACCAGAAATCGTTAGAT 59.356 40.000 0.00 0.00 39.12 1.98
2862 4633 4.994852 CACTTCCAACCAGAAATCGTTAGA 59.005 41.667 0.00 0.00 0.00 2.10
2863 4634 4.994852 TCACTTCCAACCAGAAATCGTTAG 59.005 41.667 0.00 0.00 0.00 2.34
2864 4635 4.753107 GTCACTTCCAACCAGAAATCGTTA 59.247 41.667 0.00 0.00 0.00 3.18
2865 4636 3.564225 GTCACTTCCAACCAGAAATCGTT 59.436 43.478 0.00 0.00 0.00 3.85
2866 4637 3.139077 GTCACTTCCAACCAGAAATCGT 58.861 45.455 0.00 0.00 0.00 3.73
2868 4639 4.389374 TCAGTCACTTCCAACCAGAAATC 58.611 43.478 0.00 0.00 0.00 2.17
2869 4640 4.437682 TCAGTCACTTCCAACCAGAAAT 57.562 40.909 0.00 0.00 0.00 2.17
2870 4641 3.924114 TCAGTCACTTCCAACCAGAAA 57.076 42.857 0.00 0.00 0.00 2.52
2871 4642 3.496692 CCATCAGTCACTTCCAACCAGAA 60.497 47.826 0.00 0.00 0.00 3.02
2880 4651 8.567948 TGAAAATAAAAGTCCATCAGTCACTTC 58.432 33.333 0.00 0.00 29.85 3.01
2893 4664 7.215719 AGTTAGGTGCCTGAAAATAAAAGTC 57.784 36.000 0.12 0.00 0.00 3.01
2904 4675 4.781087 ACCAACTATAAGTTAGGTGCCTGA 59.219 41.667 0.12 0.00 37.83 3.86
2909 4680 5.969423 TCGGAACCAACTATAAGTTAGGTG 58.031 41.667 11.87 0.00 38.60 4.00
2924 4695 3.410631 TGTCTAATTTGCTCGGAACCA 57.589 42.857 0.00 0.00 0.00 3.67
2928 4699 4.870426 GTGATCTTGTCTAATTTGCTCGGA 59.130 41.667 0.00 0.00 0.00 4.55
2930 4701 4.034510 GGGTGATCTTGTCTAATTTGCTCG 59.965 45.833 0.00 0.00 0.00 5.03
2939 4710 3.901222 TGAAGTGTGGGTGATCTTGTCTA 59.099 43.478 0.00 0.00 0.00 2.59
2982 4754 2.363680 CTGCCCTCAAGACGTATGATCT 59.636 50.000 4.19 0.00 0.00 2.75
2995 4767 3.686016 GATTAACCAAAGACTGCCCTCA 58.314 45.455 0.00 0.00 0.00 3.86
3003 4775 6.416750 CACTGTTTTTCCGATTAACCAAAGAC 59.583 38.462 0.00 0.00 0.00 3.01
3023 4795 1.109323 GCTTTTGGTGAGCCCACTGT 61.109 55.000 0.00 0.00 45.19 3.55
3024 4796 1.108727 TGCTTTTGGTGAGCCCACTG 61.109 55.000 0.00 0.00 45.19 3.66
3025 4797 1.109323 GTGCTTTTGGTGAGCCCACT 61.109 55.000 0.00 0.00 45.19 4.00
3026 4798 1.109323 AGTGCTTTTGGTGAGCCCAC 61.109 55.000 0.00 0.00 45.19 4.61
3027 4799 0.396974 AAGTGCTTTTGGTGAGCCCA 60.397 50.000 0.00 0.00 43.27 5.36
3028 4800 0.032540 CAAGTGCTTTTGGTGAGCCC 59.967 55.000 0.00 0.00 39.38 5.19
3030 4802 0.032540 CCCAAGTGCTTTTGGTGAGC 59.967 55.000 15.57 0.00 44.98 4.26
3031 4803 1.067516 CACCCAAGTGCTTTTGGTGAG 59.932 52.381 18.39 6.16 44.98 3.51
3032 4804 1.110442 CACCCAAGTGCTTTTGGTGA 58.890 50.000 18.39 0.00 44.98 4.02
3033 4805 0.104671 CCACCCAAGTGCTTTTGGTG 59.895 55.000 17.14 17.14 44.98 4.17
3034 4806 1.685355 GCCACCCAAGTGCTTTTGGT 61.685 55.000 15.57 5.54 44.98 3.67
3036 4808 1.069596 GGCCACCCAAGTGCTTTTG 59.930 57.895 0.00 0.00 43.09 2.44
3037 4809 0.690744 AAGGCCACCCAAGTGCTTTT 60.691 50.000 5.01 0.00 43.09 2.27
3058 4830 6.101332 CCCAAATCATCATTGTCGACAAAAT 58.899 36.000 32.69 24.73 39.55 1.82
3060 4832 4.522405 ACCCAAATCATCATTGTCGACAAA 59.478 37.500 32.69 19.21 39.55 2.83
3070 4842 3.618019 GCAAAGCACACCCAAATCATCAT 60.618 43.478 0.00 0.00 0.00 2.45
3075 4847 0.031994 ACGCAAAGCACACCCAAATC 59.968 50.000 0.00 0.00 0.00 2.17
3082 4855 0.593128 AATGGAGACGCAAAGCACAC 59.407 50.000 0.00 0.00 0.00 3.82
3083 4856 2.076100 CTAATGGAGACGCAAAGCACA 58.924 47.619 0.00 0.00 0.00 4.57
3092 4865 1.227674 GCCAGGGCTAATGGAGACG 60.228 63.158 2.30 0.00 40.51 4.18
3106 4879 2.046023 TCGGTCCATTGCAGCCAG 60.046 61.111 0.00 0.00 0.00 4.85
3128 4901 0.466124 GATGCCACCTAGGGTCTGTC 59.534 60.000 14.81 1.87 38.09 3.51
3136 4909 1.202627 GGAAGCTGAGATGCCACCTAG 60.203 57.143 0.00 0.00 0.00 3.02
3144 4917 1.153765 TCGCACGGAAGCTGAGATG 60.154 57.895 0.00 0.00 0.00 2.90
3150 4923 0.669625 GGTTTAGTCGCACGGAAGCT 60.670 55.000 0.00 0.00 0.00 3.74
3156 4929 1.844357 CTATGTCGGTTTAGTCGCACG 59.156 52.381 0.00 0.00 0.00 5.34
3164 4937 4.877251 CCCGGAAAATTCTATGTCGGTTTA 59.123 41.667 0.73 0.00 34.87 2.01
3169 4942 1.602377 GGCCCGGAAAATTCTATGTCG 59.398 52.381 0.73 0.00 0.00 4.35
3185 4960 0.753111 GGTGATGATGGTGAAGGCCC 60.753 60.000 0.00 0.00 0.00 5.80
3197 4972 2.374839 TGGACATCTTTGGTGGTGATGA 59.625 45.455 8.86 0.00 39.72 2.92
3201 4976 1.820519 CCATGGACATCTTTGGTGGTG 59.179 52.381 5.56 0.00 0.00 4.17
3208 4983 3.446442 AAGCTCACCATGGACATCTTT 57.554 42.857 21.47 2.55 0.00 2.52
3225 5000 2.545106 CCAATGGTTGTGCAAGAAAAGC 59.455 45.455 0.00 0.00 0.00 3.51
3233 5008 1.470996 GGGCTTCCAATGGTTGTGCA 61.471 55.000 0.00 0.00 0.00 4.57
3254 5029 0.321564 TGATGCCAACGAGTTGAGGG 60.322 55.000 16.66 2.34 42.93 4.30
3264 5039 0.322816 TGAAGAGCCCTGATGCCAAC 60.323 55.000 0.00 0.00 0.00 3.77


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

AutoCloner maintained by Alex Coulton.