Multiple sequence alignment - TraesCS4D01G170700

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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 TraesCS4D01G170700 chr4D 100.000 2823 0 0 1 2823 297207800 297204978 0.000000e+00 5214.0
1 TraesCS4D01G170700 chr4D 100.000 207 0 0 3111 3317 297204690 297204484 1.870000e-102 383.0
2 TraesCS4D01G170700 chr4D 90.000 140 14 0 2586 2725 403719596 403719457 7.310000e-42 182.0
3 TraesCS4D01G170700 chr4D 93.162 117 7 1 3200 3315 334164386 334164502 1.580000e-38 171.0
4 TraesCS4D01G170700 chrUn 94.360 2553 93 23 17 2552 214476538 214474020 0.000000e+00 3869.0
5 TraesCS4D01G170700 chrUn 97.172 389 10 1 1111 1499 480243844 480243457 0.000000e+00 656.0
6 TraesCS4D01G170700 chrUn 92.308 117 8 1 3202 3317 100087308 100087192 7.360000e-37 165.0
7 TraesCS4D01G170700 chrUn 91.667 120 8 2 3198 3315 141680915 141680796 7.360000e-37 165.0
8 TraesCS4D01G170700 chrUn 97.561 41 1 0 3111 3151 385125568 385125608 1.650000e-08 71.3
9 TraesCS4D01G170700 chr4B 94.203 2553 97 23 17 2552 367928785 367926267 0.000000e+00 3847.0
10 TraesCS4D01G170700 chr4A 96.376 1959 62 3 469 2421 191119113 191121068 0.000000e+00 3216.0
11 TraesCS4D01G170700 chr4A 90.582 361 22 3 125 473 191118478 191118838 5.010000e-128 468.0
12 TraesCS4D01G170700 chr4A 88.276 145 12 4 2419 2561 191123680 191123821 5.690000e-38 169.0
13 TraesCS4D01G170700 chr4A 91.176 102 5 1 2564 2665 627383531 627383628 5.770000e-28 135.0
14 TraesCS4D01G170700 chr4A 84.545 110 17 0 2587 2696 153704258 153704367 3.500000e-20 110.0
15 TraesCS4D01G170700 chr4A 96.970 33 0 1 2561 2592 332646976 332646944 2.000000e-03 54.7
16 TraesCS4D01G170700 chr1D 83.262 233 24 10 2586 2817 275855335 275855553 2.020000e-47 200.0
17 TraesCS4D01G170700 chr1D 96.226 106 4 0 3210 3315 387944937 387944832 1.220000e-39 174.0
18 TraesCS4D01G170700 chr3A 91.935 124 10 0 2556 2679 12621168 12621291 1.220000e-39 174.0
19 TraesCS4D01G170700 chr3A 93.103 116 6 2 3202 3315 53566345 53566460 5.690000e-38 169.0
20 TraesCS4D01G170700 chr3A 82.390 159 27 1 2569 2726 358599108 358599266 1.600000e-28 137.0
21 TraesCS4D01G170700 chr3A 87.156 109 13 1 2578 2686 252917615 252917508 4.490000e-24 122.0
22 TraesCS4D01G170700 chr6B 94.643 112 5 1 3205 3315 481857851 481857962 4.400000e-39 172.0
23 TraesCS4D01G170700 chr2A 93.860 114 6 1 3203 3315 342647397 342647510 1.580000e-38 171.0
24 TraesCS4D01G170700 chr2A 90.476 126 9 3 3193 3315 184561329 184561204 2.650000e-36 163.0
25 TraesCS4D01G170700 chr7B 79.835 243 31 9 2578 2817 119796051 119795824 9.520000e-36 161.0
26 TraesCS4D01G170700 chr6A 86.184 152 13 8 3167 3315 499409607 499409753 1.230000e-34 158.0
27 TraesCS4D01G170700 chr1B 85.161 155 22 1 2569 2722 403770489 403770643 1.230000e-34 158.0
28 TraesCS4D01G170700 chr2B 83.221 149 21 1 2578 2722 444717189 444717041 2.080000e-27 134.0
29 TraesCS4D01G170700 chr3B 86.325 117 15 1 2569 2685 570742859 570742974 3.470000e-25 126.0
30 TraesCS4D01G170700 chr3B 97.674 43 1 0 3111 3153 315622178 315622220 1.280000e-09 75.0
31 TraesCS4D01G170700 chr6D 97.561 41 1 0 3111 3151 45770725 45770765 1.650000e-08 71.3
32 TraesCS4D01G170700 chr6D 97.561 41 1 0 3111 3151 62003880 62003920 1.650000e-08 71.3
33 TraesCS4D01G170700 chr6D 97.561 41 1 0 3111 3151 211921496 211921536 1.650000e-08 71.3
34 TraesCS4D01G170700 chr6D 97.561 41 1 0 3111 3151 228800239 228800279 1.650000e-08 71.3
35 TraesCS4D01G170700 chr6D 97.561 41 1 0 3111 3151 231906781 231906821 1.650000e-08 71.3
36 TraesCS4D01G170700 chr6D 97.561 41 1 0 3111 3151 236873637 236873677 1.650000e-08 71.3
37 TraesCS4D01G170700 chr6D 97.561 41 1 0 3111 3151 240821369 240821409 1.650000e-08 71.3


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 TraesCS4D01G170700 chr4D 297204484 297207800 3316 True 2798.500000 5214 100.000000 1 3317 2 chr4D.!!$R2 3316
1 TraesCS4D01G170700 chrUn 214474020 214476538 2518 True 3869.000000 3869 94.360000 17 2552 1 chrUn.!!$R3 2535
2 TraesCS4D01G170700 chr4B 367926267 367928785 2518 True 3847.000000 3847 94.203000 17 2552 1 chr4B.!!$R1 2535
3 TraesCS4D01G170700 chr4A 191118478 191123821 5343 False 1284.333333 3216 91.744667 125 2561 3 chr4A.!!$F3 2436

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
764 1062 0.518636 CGGAAGATGTGCTTGTGTGG 59.481 55.0 0.0 0.0 36.83 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2752 5679 0.036875 GAGTGGTTTCAGGGAGGGTG 59.963 60.0 0.0 0.0 0.0 4.61 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
108 109 3.834938 TGCATGCCTTGGATGATCATTA 58.165 40.909 16.68 0.00 33.15 1.90
109 110 4.412843 TGCATGCCTTGGATGATCATTAT 58.587 39.130 16.68 0.00 33.15 1.28
143 144 4.879545 GGACTAACTTTGTCTGTTGTTCCA 59.120 41.667 3.80 0.00 33.50 3.53
238 240 8.641541 TGGAGCTTTTCAGATATTTTTCTGTTT 58.358 29.630 0.00 0.00 43.02 2.83
246 248 7.587629 TCAGATATTTTTCTGTTTGTCTGCAG 58.412 34.615 7.63 7.63 43.02 4.41
253 255 3.867857 TCTGTTTGTCTGCAGTTGTACA 58.132 40.909 14.67 7.80 34.57 2.90
302 311 6.863126 AGTAACAAGATCATTTTCTTTTGCCG 59.137 34.615 0.00 0.00 33.69 5.69
396 405 3.916761 CAGCTCTCTCTGCCTTGATATC 58.083 50.000 0.00 0.00 0.00 1.63
629 921 4.966965 TTGCCTCGTTCAAGTGTTTTTA 57.033 36.364 0.00 0.00 0.00 1.52
705 1003 5.221843 TGTGTTTCCTCCTTGCAGTATTAGT 60.222 40.000 0.00 0.00 0.00 2.24
764 1062 0.518636 CGGAAGATGTGCTTGTGTGG 59.481 55.000 0.00 0.00 36.83 4.17
810 1108 5.293560 ACTGACAGTCTAGCTTTTGAAGAC 58.706 41.667 1.07 5.58 39.95 3.01
957 1267 2.910688 TCAGTTCTGACCACCTCAAC 57.089 50.000 0.00 0.00 0.00 3.18
1004 1314 3.010584 ACATAAGAACTGGCCAAGATGGT 59.989 43.478 7.01 0.00 40.46 3.55
1094 1407 8.470040 TTTGCTAAAGTTTACTATGGTCGTAG 57.530 34.615 0.00 0.00 0.00 3.51
1377 1690 3.067106 CAATAGTGCGGTTGACTTCTGT 58.933 45.455 0.00 0.00 0.00 3.41
1404 1717 0.248539 GAGGCGTCTATCACCGTGAC 60.249 60.000 2.57 0.00 0.00 3.67
1405 1718 1.226888 GGCGTCTATCACCGTGACC 60.227 63.158 2.57 0.00 0.00 4.02
1465 1778 7.752686 GCAATTTAAAGATCTCTGACTTTGGTC 59.247 37.037 0.00 0.00 42.42 4.02
1504 1817 1.339438 GCAAGAGACAAGATGGGCTGA 60.339 52.381 0.00 0.00 0.00 4.26
1755 2068 2.480845 CGTATTCTTGATCCGAACCCC 58.519 52.381 0.00 0.00 0.00 4.95
1788 2101 5.413309 TCTCCTTTTCAGAGATCTTGGAC 57.587 43.478 0.00 0.00 35.46 4.02
2347 2660 6.960431 GTGTGACTACTAAGTAAGCGTAGAAG 59.040 42.308 0.00 0.00 35.56 2.85
2389 2702 8.700722 TGTTTACATGTTGGAATCAATAATGC 57.299 30.769 2.30 0.00 35.23 3.56
2467 5394 5.580691 TGAAATGCTACTTCTGTATTGACCG 59.419 40.000 0.00 0.00 0.00 4.79
2529 5456 8.012957 ACTTGTTACTACTATGGATTGGAGAG 57.987 38.462 0.00 0.00 0.00 3.20
2552 5479 3.615224 ATTTGCATCATTGGTGGGTTC 57.385 42.857 0.00 0.00 0.00 3.62
2553 5480 2.307496 TTGCATCATTGGTGGGTTCT 57.693 45.000 0.00 0.00 0.00 3.01
2578 5505 7.396540 TTTTTCTCAGGAATGGCTAGAAATC 57.603 36.000 0.00 0.00 36.40 2.17
2579 5506 5.698741 TTCTCAGGAATGGCTAGAAATCA 57.301 39.130 0.00 0.00 0.00 2.57
2580 5507 5.287674 TCTCAGGAATGGCTAGAAATCAG 57.712 43.478 0.00 0.00 0.00 2.90
2581 5508 4.718774 TCTCAGGAATGGCTAGAAATCAGT 59.281 41.667 0.00 0.00 0.00 3.41
2582 5509 5.028549 TCAGGAATGGCTAGAAATCAGTC 57.971 43.478 0.00 0.00 0.00 3.51
2583 5510 4.471025 TCAGGAATGGCTAGAAATCAGTCA 59.529 41.667 0.00 0.00 31.00 3.41
2584 5511 4.815308 CAGGAATGGCTAGAAATCAGTCAG 59.185 45.833 0.00 0.00 29.71 3.51
2585 5512 3.563390 GGAATGGCTAGAAATCAGTCAGC 59.437 47.826 0.00 0.00 29.71 4.26
2586 5513 4.450053 GAATGGCTAGAAATCAGTCAGCT 58.550 43.478 0.00 0.00 29.71 4.24
2587 5514 3.257469 TGGCTAGAAATCAGTCAGCTG 57.743 47.619 7.63 7.63 43.87 4.24
2599 5526 4.965814 TCAGTCAGCTGAGTTTTTCATCT 58.034 39.130 21.67 6.60 45.94 2.90
2600 5527 4.993584 TCAGTCAGCTGAGTTTTTCATCTC 59.006 41.667 21.67 2.86 45.94 2.75
2601 5528 4.996122 CAGTCAGCTGAGTTTTTCATCTCT 59.004 41.667 21.67 5.30 45.28 3.10
2602 5529 4.996122 AGTCAGCTGAGTTTTTCATCTCTG 59.004 41.667 18.89 0.00 34.68 3.35
2603 5530 4.153835 GTCAGCTGAGTTTTTCATCTCTGG 59.846 45.833 18.89 0.00 34.68 3.86
2604 5531 3.439476 CAGCTGAGTTTTTCATCTCTGGG 59.561 47.826 8.42 0.00 34.68 4.45
2605 5532 2.163211 GCTGAGTTTTTCATCTCTGGGC 59.837 50.000 0.00 0.00 34.68 5.36
2606 5533 3.415212 CTGAGTTTTTCATCTCTGGGCA 58.585 45.455 0.00 0.00 34.68 5.36
2607 5534 3.415212 TGAGTTTTTCATCTCTGGGCAG 58.585 45.455 0.00 0.00 0.00 4.85
2608 5535 3.181440 TGAGTTTTTCATCTCTGGGCAGT 60.181 43.478 0.00 0.00 0.00 4.40
2609 5536 3.416156 AGTTTTTCATCTCTGGGCAGTC 58.584 45.455 0.00 0.00 0.00 3.51
2610 5537 2.099141 TTTTCATCTCTGGGCAGTCG 57.901 50.000 0.00 0.00 0.00 4.18
2611 5538 1.266178 TTTCATCTCTGGGCAGTCGA 58.734 50.000 0.00 0.00 0.00 4.20
2612 5539 1.489481 TTCATCTCTGGGCAGTCGAT 58.511 50.000 0.00 0.00 0.00 3.59
2613 5540 1.489481 TCATCTCTGGGCAGTCGATT 58.511 50.000 0.00 0.00 0.00 3.34
2614 5541 1.833630 TCATCTCTGGGCAGTCGATTT 59.166 47.619 0.00 0.00 0.00 2.17
2615 5542 2.237143 TCATCTCTGGGCAGTCGATTTT 59.763 45.455 0.00 0.00 0.00 1.82
2616 5543 2.386661 TCTCTGGGCAGTCGATTTTC 57.613 50.000 0.00 0.00 0.00 2.29
2617 5544 1.066143 TCTCTGGGCAGTCGATTTTCC 60.066 52.381 0.00 0.00 0.00 3.13
2618 5545 0.690192 TCTGGGCAGTCGATTTTCCA 59.310 50.000 0.00 0.00 0.00 3.53
2619 5546 1.089920 CTGGGCAGTCGATTTTCCAG 58.910 55.000 10.51 10.51 36.28 3.86
2620 5547 0.960364 TGGGCAGTCGATTTTCCAGC 60.960 55.000 0.00 0.00 0.00 4.85
2621 5548 1.657751 GGGCAGTCGATTTTCCAGCC 61.658 60.000 0.00 0.00 39.86 4.85
2622 5549 1.425428 GCAGTCGATTTTCCAGCCG 59.575 57.895 0.00 0.00 0.00 5.52
2623 5550 1.298859 GCAGTCGATTTTCCAGCCGT 61.299 55.000 0.00 0.00 0.00 5.68
2624 5551 1.156736 CAGTCGATTTTCCAGCCGTT 58.843 50.000 0.00 0.00 0.00 4.44
2625 5552 1.135972 CAGTCGATTTTCCAGCCGTTG 60.136 52.381 0.00 0.00 0.00 4.10
2634 5561 3.262936 CAGCCGTTGGATGCGAAA 58.737 55.556 0.00 0.00 30.51 3.46
2635 5562 1.802636 CAGCCGTTGGATGCGAAAT 59.197 52.632 0.00 0.00 30.51 2.17
2636 5563 0.248215 CAGCCGTTGGATGCGAAATC 60.248 55.000 0.00 0.00 30.51 2.17
2637 5564 0.676466 AGCCGTTGGATGCGAAATCA 60.676 50.000 0.00 0.00 0.00 2.57
2638 5565 0.170116 GCCGTTGGATGCGAAATCAA 59.830 50.000 0.00 0.00 0.00 2.57
2639 5566 1.402194 GCCGTTGGATGCGAAATCAAA 60.402 47.619 0.00 0.00 0.00 2.69
2640 5567 2.518949 CCGTTGGATGCGAAATCAAAG 58.481 47.619 0.00 0.00 0.00 2.77
2641 5568 2.518949 CGTTGGATGCGAAATCAAAGG 58.481 47.619 0.00 0.00 0.00 3.11
2642 5569 2.262211 GTTGGATGCGAAATCAAAGGC 58.738 47.619 0.00 0.00 0.00 4.35
2643 5570 0.817013 TGGATGCGAAATCAAAGGCC 59.183 50.000 0.00 0.00 0.00 5.19
2644 5571 1.106285 GGATGCGAAATCAAAGGCCT 58.894 50.000 0.00 0.00 0.00 5.19
2645 5572 1.202336 GGATGCGAAATCAAAGGCCTG 60.202 52.381 5.69 0.00 0.00 4.85
2646 5573 0.174162 ATGCGAAATCAAAGGCCTGC 59.826 50.000 5.69 2.56 0.00 4.85
2647 5574 1.177895 TGCGAAATCAAAGGCCTGCA 61.178 50.000 5.69 5.92 0.00 4.41
2648 5575 0.457337 GCGAAATCAAAGGCCTGCAG 60.457 55.000 5.69 6.78 0.00 4.41
2649 5576 0.883833 CGAAATCAAAGGCCTGCAGT 59.116 50.000 5.69 0.00 0.00 4.40
2650 5577 1.270550 CGAAATCAAAGGCCTGCAGTT 59.729 47.619 5.69 0.00 0.00 3.16
2651 5578 2.669391 CGAAATCAAAGGCCTGCAGTTC 60.669 50.000 5.69 7.50 0.00 3.01
2652 5579 1.999648 AATCAAAGGCCTGCAGTTCA 58.000 45.000 5.69 0.00 0.00 3.18
2653 5580 2.226962 ATCAAAGGCCTGCAGTTCAT 57.773 45.000 5.69 0.00 0.00 2.57
2654 5581 1.538047 TCAAAGGCCTGCAGTTCATC 58.462 50.000 5.69 0.00 0.00 2.92
2655 5582 1.074405 TCAAAGGCCTGCAGTTCATCT 59.926 47.619 5.69 0.00 0.00 2.90
2656 5583 1.891150 CAAAGGCCTGCAGTTCATCTT 59.109 47.619 5.69 5.79 0.00 2.40
2657 5584 2.298163 CAAAGGCCTGCAGTTCATCTTT 59.702 45.455 5.69 11.13 0.00 2.52
2658 5585 3.439857 AAGGCCTGCAGTTCATCTTTA 57.560 42.857 5.69 0.00 0.00 1.85
2659 5586 2.996631 AGGCCTGCAGTTCATCTTTAG 58.003 47.619 13.81 0.00 0.00 1.85
2660 5587 1.403323 GGCCTGCAGTTCATCTTTAGC 59.597 52.381 13.81 4.32 0.00 3.09
2661 5588 1.403323 GCCTGCAGTTCATCTTTAGCC 59.597 52.381 13.81 0.00 0.00 3.93
2662 5589 2.943199 GCCTGCAGTTCATCTTTAGCCT 60.943 50.000 13.81 0.00 0.00 4.58
2663 5590 2.941720 CCTGCAGTTCATCTTTAGCCTC 59.058 50.000 13.81 0.00 0.00 4.70
2664 5591 2.941720 CTGCAGTTCATCTTTAGCCTCC 59.058 50.000 5.25 0.00 0.00 4.30
2665 5592 1.936547 GCAGTTCATCTTTAGCCTCCG 59.063 52.381 0.00 0.00 0.00 4.63
2666 5593 1.936547 CAGTTCATCTTTAGCCTCCGC 59.063 52.381 0.00 0.00 0.00 5.54
2667 5594 1.134371 AGTTCATCTTTAGCCTCCGCC 60.134 52.381 0.00 0.00 34.57 6.13
2668 5595 0.180406 TTCATCTTTAGCCTCCGCCC 59.820 55.000 0.00 0.00 34.57 6.13
2669 5596 1.227973 CATCTTTAGCCTCCGCCCC 60.228 63.158 0.00 0.00 34.57 5.80
2670 5597 2.452937 ATCTTTAGCCTCCGCCCCC 61.453 63.158 0.00 0.00 34.57 5.40
2671 5598 2.916553 ATCTTTAGCCTCCGCCCCCT 62.917 60.000 0.00 0.00 34.57 4.79
2672 5599 2.612746 TTTAGCCTCCGCCCCCTT 60.613 61.111 0.00 0.00 34.57 3.95
2673 5600 2.893682 CTTTAGCCTCCGCCCCCTTG 62.894 65.000 0.00 0.00 34.57 3.61
2674 5601 3.935456 TTAGCCTCCGCCCCCTTGA 62.935 63.158 0.00 0.00 34.57 3.02
2697 5624 4.308458 CAGCCACCACCGACCGAA 62.308 66.667 0.00 0.00 0.00 4.30
2698 5625 4.309950 AGCCACCACCGACCGAAC 62.310 66.667 0.00 0.00 0.00 3.95
2765 5692 3.264845 GCCCCACCCTCCCTGAAA 61.265 66.667 0.00 0.00 0.00 2.69
2766 5693 2.763902 CCCCACCCTCCCTGAAAC 59.236 66.667 0.00 0.00 0.00 2.78
2767 5694 2.763902 CCCACCCTCCCTGAAACC 59.236 66.667 0.00 0.00 0.00 3.27
2768 5695 2.160171 CCCACCCTCCCTGAAACCA 61.160 63.158 0.00 0.00 0.00 3.67
2769 5696 1.074951 CCACCCTCCCTGAAACCAC 59.925 63.158 0.00 0.00 0.00 4.16
2770 5697 1.427072 CCACCCTCCCTGAAACCACT 61.427 60.000 0.00 0.00 0.00 4.00
2771 5698 0.036875 CACCCTCCCTGAAACCACTC 59.963 60.000 0.00 0.00 0.00 3.51
2772 5699 1.134438 ACCCTCCCTGAAACCACTCC 61.134 60.000 0.00 0.00 0.00 3.85
2773 5700 0.842467 CCCTCCCTGAAACCACTCCT 60.842 60.000 0.00 0.00 0.00 3.69
2774 5701 0.615850 CCTCCCTGAAACCACTCCTC 59.384 60.000 0.00 0.00 0.00 3.71
2775 5702 1.352083 CTCCCTGAAACCACTCCTCA 58.648 55.000 0.00 0.00 0.00 3.86
2776 5703 1.002544 CTCCCTGAAACCACTCCTCAC 59.997 57.143 0.00 0.00 0.00 3.51
2777 5704 0.036875 CCCTGAAACCACTCCTCACC 59.963 60.000 0.00 0.00 0.00 4.02
2778 5705 0.320771 CCTGAAACCACTCCTCACCG 60.321 60.000 0.00 0.00 0.00 4.94
2779 5706 0.951040 CTGAAACCACTCCTCACCGC 60.951 60.000 0.00 0.00 0.00 5.68
2780 5707 1.671379 GAAACCACTCCTCACCGCC 60.671 63.158 0.00 0.00 0.00 6.13
2781 5708 3.530910 AAACCACTCCTCACCGCCG 62.531 63.158 0.00 0.00 0.00 6.46
2784 5711 4.436998 CACTCCTCACCGCCGGTC 62.437 72.222 5.41 0.00 31.02 4.79
2809 5736 2.122989 GCCCCGACCATCCCTCTA 60.123 66.667 0.00 0.00 0.00 2.43
2810 5737 2.210711 GCCCCGACCATCCCTCTAG 61.211 68.421 0.00 0.00 0.00 2.43
2811 5738 2.210711 CCCCGACCATCCCTCTAGC 61.211 68.421 0.00 0.00 0.00 3.42
2812 5739 2.210711 CCCGACCATCCCTCTAGCC 61.211 68.421 0.00 0.00 0.00 3.93
2813 5740 2.210711 CCGACCATCCCTCTAGCCC 61.211 68.421 0.00 0.00 0.00 5.19
2814 5741 2.210711 CGACCATCCCTCTAGCCCC 61.211 68.421 0.00 0.00 0.00 5.80
2815 5742 1.843832 GACCATCCCTCTAGCCCCC 60.844 68.421 0.00 0.00 0.00 5.40
3130 6057 2.676748 TGACCCAAAAGCCAATTCAGT 58.323 42.857 0.00 0.00 0.00 3.41
3131 6058 2.627699 TGACCCAAAAGCCAATTCAGTC 59.372 45.455 0.00 0.00 0.00 3.51
3132 6059 1.613437 ACCCAAAAGCCAATTCAGTCG 59.387 47.619 0.00 0.00 0.00 4.18
3133 6060 1.885887 CCCAAAAGCCAATTCAGTCGA 59.114 47.619 0.00 0.00 0.00 4.20
3134 6061 2.351738 CCCAAAAGCCAATTCAGTCGAC 60.352 50.000 7.70 7.70 0.00 4.20
3135 6062 2.554032 CCAAAAGCCAATTCAGTCGACT 59.446 45.455 13.58 13.58 0.00 4.18
3136 6063 3.558505 CAAAAGCCAATTCAGTCGACTG 58.441 45.455 34.76 34.76 45.08 3.51
3146 6073 2.999507 CAGTCGACTGAAGTGTAGCT 57.000 50.000 36.73 0.00 46.59 3.32
3148 6075 4.421033 CAGTCGACTGAAGTGTAGCTAA 57.579 45.455 36.73 0.00 46.59 3.09
3149 6076 4.795268 CAGTCGACTGAAGTGTAGCTAAA 58.205 43.478 36.73 0.00 46.59 1.85
3150 6077 5.403246 CAGTCGACTGAAGTGTAGCTAAAT 58.597 41.667 36.73 0.00 46.59 1.40
3151 6078 6.552629 CAGTCGACTGAAGTGTAGCTAAATA 58.447 40.000 36.73 0.00 46.59 1.40
3152 6079 6.689241 CAGTCGACTGAAGTGTAGCTAAATAG 59.311 42.308 36.73 6.10 46.59 1.73
3153 6080 6.374894 AGTCGACTGAAGTGTAGCTAAATAGT 59.625 38.462 19.30 0.00 0.00 2.12
3154 6081 7.028361 GTCGACTGAAGTGTAGCTAAATAGTT 58.972 38.462 8.70 0.00 0.00 2.24
3155 6082 7.541437 GTCGACTGAAGTGTAGCTAAATAGTTT 59.459 37.037 8.70 0.00 0.00 2.66
3156 6083 8.086522 TCGACTGAAGTGTAGCTAAATAGTTTT 58.913 33.333 0.00 0.00 0.00 2.43
3157 6084 8.373992 CGACTGAAGTGTAGCTAAATAGTTTTC 58.626 37.037 0.00 0.00 0.00 2.29
3158 6085 9.425577 GACTGAAGTGTAGCTAAATAGTTTTCT 57.574 33.333 0.00 0.00 0.00 2.52
3159 6086 9.425577 ACTGAAGTGTAGCTAAATAGTTTTCTC 57.574 33.333 0.00 0.00 0.00 2.87
3160 6087 9.646427 CTGAAGTGTAGCTAAATAGTTTTCTCT 57.354 33.333 0.00 0.00 0.00 3.10
3161 6088 9.640963 TGAAGTGTAGCTAAATAGTTTTCTCTC 57.359 33.333 0.00 0.00 0.00 3.20
3162 6089 9.863845 GAAGTGTAGCTAAATAGTTTTCTCTCT 57.136 33.333 0.00 0.00 0.00 3.10
3163 6090 9.863845 AAGTGTAGCTAAATAGTTTTCTCTCTC 57.136 33.333 0.00 0.00 0.00 3.20
3164 6091 9.250246 AGTGTAGCTAAATAGTTTTCTCTCTCT 57.750 33.333 0.00 0.00 0.00 3.10
3165 6092 9.863845 GTGTAGCTAAATAGTTTTCTCTCTCTT 57.136 33.333 0.00 0.00 0.00 2.85
3215 6142 8.745149 TCTCTACTATCTATTACTCCCTCTGT 57.255 38.462 0.00 0.00 0.00 3.41
3216 6143 9.173231 TCTCTACTATCTATTACTCCCTCTGTT 57.827 37.037 0.00 0.00 0.00 3.16
3217 6144 9.444600 CTCTACTATCTATTACTCCCTCTGTTC 57.555 40.741 0.00 0.00 0.00 3.18
3218 6145 8.384718 TCTACTATCTATTACTCCCTCTGTTCC 58.615 40.741 0.00 0.00 0.00 3.62
3219 6146 7.169287 ACTATCTATTACTCCCTCTGTTCCT 57.831 40.000 0.00 0.00 0.00 3.36
3220 6147 8.290463 ACTATCTATTACTCCCTCTGTTCCTA 57.710 38.462 0.00 0.00 0.00 2.94
3221 6148 8.734763 ACTATCTATTACTCCCTCTGTTCCTAA 58.265 37.037 0.00 0.00 0.00 2.69
3222 6149 9.589461 CTATCTATTACTCCCTCTGTTCCTAAA 57.411 37.037 0.00 0.00 0.00 1.85
3229 6156 9.725206 TTACTCCCTCTGTTCCTAAATATAAGT 57.275 33.333 0.00 0.00 0.00 2.24
3230 6157 8.625467 ACTCCCTCTGTTCCTAAATATAAGTT 57.375 34.615 0.00 0.00 0.00 2.66
3231 6158 9.059023 ACTCCCTCTGTTCCTAAATATAAGTTT 57.941 33.333 0.00 0.00 0.00 2.66
3232 6159 9.907229 CTCCCTCTGTTCCTAAATATAAGTTTT 57.093 33.333 0.00 0.00 0.00 2.43
3266 6193 9.682465 ATTCTAATATAGACTACATACGGAGCA 57.318 33.333 0.00 0.00 33.84 4.26
3267 6194 9.511272 TTCTAATATAGACTACATACGGAGCAA 57.489 33.333 0.00 0.00 33.84 3.91
3268 6195 9.511272 TCTAATATAGACTACATACGGAGCAAA 57.489 33.333 0.00 0.00 0.00 3.68
3271 6198 8.988064 ATATAGACTACATACGGAGCAAAATG 57.012 34.615 0.00 0.00 0.00 2.32
3272 6199 5.339008 AGACTACATACGGAGCAAAATGA 57.661 39.130 0.00 0.00 0.00 2.57
3273 6200 5.352284 AGACTACATACGGAGCAAAATGAG 58.648 41.667 0.00 0.00 0.00 2.90
3274 6201 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
3275 6202 4.870426 ACTACATACGGAGCAAAATGAGTG 59.130 41.667 0.00 0.00 0.00 3.51
3276 6203 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
3277 6204 4.323417 ACATACGGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
3278 6205 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
3279 6206 5.065218 ACATACGGAGCAAAATGAGTGAATC 59.935 40.000 0.00 0.00 0.00 2.52
3280 6207 3.679389 ACGGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
3281 6208 4.832248 ACGGAGCAAAATGAGTGAATCTA 58.168 39.130 0.00 0.00 0.00 1.98
3282 6209 4.631813 ACGGAGCAAAATGAGTGAATCTAC 59.368 41.667 0.00 0.00 0.00 2.59
3283 6210 4.631377 CGGAGCAAAATGAGTGAATCTACA 59.369 41.667 0.00 0.00 0.00 2.74
3284 6211 5.446473 CGGAGCAAAATGAGTGAATCTACAC 60.446 44.000 0.00 0.00 40.60 2.90
3298 6225 9.121658 AGTGAATCTACACTCTAAATATGTCGA 57.878 33.333 0.00 0.00 46.36 4.20
3299 6226 9.900710 GTGAATCTACACTCTAAATATGTCGAT 57.099 33.333 0.00 0.00 37.73 3.59
3308 6235 9.439537 CACTCTAAATATGTCGATATACATCCG 57.560 37.037 3.79 0.00 40.52 4.18
3309 6236 9.175312 ACTCTAAATATGTCGATATACATCCGT 57.825 33.333 3.79 0.00 40.52 4.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.537135 ATCACTAGTATTATGGGCACGG 57.463 45.455 0.00 0.00 0.00 4.94
1 2 6.365247 GTGTAATCACTAGTATTATGGGCACG 59.635 42.308 0.00 0.00 40.98 5.34
2 3 7.214381 TGTGTAATCACTAGTATTATGGGCAC 58.786 38.462 0.00 6.04 44.14 5.01
3 4 7.368198 TGTGTAATCACTAGTATTATGGGCA 57.632 36.000 0.00 0.00 44.14 5.36
4 5 8.848474 ATTGTGTAATCACTAGTATTATGGGC 57.152 34.615 0.00 0.00 44.14 5.36
5 6 9.140286 CGATTGTGTAATCACTAGTATTATGGG 57.860 37.037 0.00 0.00 42.27 4.00
6 7 8.648097 GCGATTGTGTAATCACTAGTATTATGG 58.352 37.037 0.00 0.00 42.27 2.74
7 8 8.365938 CGCGATTGTGTAATCACTAGTATTATG 58.634 37.037 0.00 0.00 42.27 1.90
8 9 7.541091 CCGCGATTGTGTAATCACTAGTATTAT 59.459 37.037 8.23 0.00 42.27 1.28
9 10 6.859508 CCGCGATTGTGTAATCACTAGTATTA 59.140 38.462 8.23 0.00 42.27 0.98
10 11 5.690409 CCGCGATTGTGTAATCACTAGTATT 59.310 40.000 8.23 0.00 42.27 1.89
11 12 5.009310 TCCGCGATTGTGTAATCACTAGTAT 59.991 40.000 8.23 0.00 42.27 2.12
12 13 4.336153 TCCGCGATTGTGTAATCACTAGTA 59.664 41.667 8.23 0.00 42.27 1.82
13 14 3.129813 TCCGCGATTGTGTAATCACTAGT 59.870 43.478 8.23 0.00 42.27 2.57
14 15 3.702330 TCCGCGATTGTGTAATCACTAG 58.298 45.455 8.23 0.00 42.27 2.57
15 16 3.786516 TCCGCGATTGTGTAATCACTA 57.213 42.857 8.23 0.00 42.27 2.74
29 30 4.978083 ATTCTAAAGAGTACTTCCGCGA 57.022 40.909 8.23 0.00 35.05 5.87
31 32 4.503370 CGGAATTCTAAAGAGTACTTCCGC 59.497 45.833 12.43 0.00 44.63 5.54
33 34 7.095270 TCAACGGAATTCTAAAGAGTACTTCC 58.905 38.462 5.23 0.00 35.05 3.46
108 109 4.741928 AAGTTAGTCCCAACTCCCAAAT 57.258 40.909 0.00 0.00 37.78 2.32
109 110 4.211920 CAAAGTTAGTCCCAACTCCCAAA 58.788 43.478 0.00 0.00 37.78 3.28
143 144 9.010029 ACCAAACAAATCGTTCAGATATTTAGT 57.990 29.630 0.00 0.00 38.98 2.24
238 240 6.564328 CATCTAGTATGTACAACTGCAGACA 58.436 40.000 23.35 14.81 30.13 3.41
246 248 6.074302 CCGTTCATGCATCTAGTATGTACAAC 60.074 42.308 0.00 0.00 39.43 3.32
253 255 3.898123 AGTCCCGTTCATGCATCTAGTAT 59.102 43.478 0.00 0.00 0.00 2.12
705 1003 6.173339 AGATATTTTCCTTCGCACTGAAAGA 58.827 36.000 0.00 0.00 35.79 2.52
764 1062 2.500504 CCCAACCAAGGTAGTCCTCTAC 59.499 54.545 0.00 0.00 44.35 2.59
810 1108 4.756642 TGGAGCAACTCTTGTATTTCAGTG 59.243 41.667 0.00 0.00 0.00 3.66
851 1149 1.417890 GATGGTAGGTGGTCCATGGAG 59.582 57.143 16.81 0.00 43.45 3.86
957 1267 4.977963 CACAAAAGGCAGTGATGTTGTAAG 59.022 41.667 0.00 0.00 37.97 2.34
1004 1314 8.654997 CCATCAAGATATTTCCCTTCTTCTCTA 58.345 37.037 0.00 0.00 0.00 2.43
1094 1407 2.287909 ACGCTCTGTGAAGTCTTGAGAC 60.288 50.000 2.93 2.93 45.08 3.36
1404 1717 5.008980 AGAAGAAGATTTTCAGGCTTCAGG 58.991 41.667 0.00 0.00 40.26 3.86
1405 1718 6.206243 TCAAGAAGAAGATTTTCAGGCTTCAG 59.794 38.462 0.00 0.00 40.26 3.02
1734 2047 1.865340 GGGTTCGGATCAAGAATACGC 59.135 52.381 6.21 1.38 41.80 4.42
1755 2068 2.094390 TGAAAAGGAGATCCGTGTACCG 60.094 50.000 0.00 0.00 42.08 4.02
1788 2101 1.812571 CCTGTCCGGAACCAAGAATTG 59.187 52.381 5.23 0.00 39.93 2.32
2019 2332 5.048504 AGCTGTGTTGGTAGATGTGAATTTG 60.049 40.000 0.00 0.00 0.00 2.32
2417 2730 7.985634 AATAAAAACATGACAGTGAACACAC 57.014 32.000 0.00 0.00 35.07 3.82
2509 5436 8.798975 AATTCCTCTCCAATCCATAGTAGTAA 57.201 34.615 0.00 0.00 0.00 2.24
2510 5437 8.651389 CAAATTCCTCTCCAATCCATAGTAGTA 58.349 37.037 0.00 0.00 0.00 1.82
2511 5438 7.512992 CAAATTCCTCTCCAATCCATAGTAGT 58.487 38.462 0.00 0.00 0.00 2.73
2529 5456 2.236893 ACCCACCAATGATGCAAATTCC 59.763 45.455 0.00 0.00 0.00 3.01
2562 5489 4.685575 GCTGACTGATTTCTAGCCATTCCT 60.686 45.833 0.00 0.00 0.00 3.36
2563 5490 3.563390 GCTGACTGATTTCTAGCCATTCC 59.437 47.826 0.00 0.00 0.00 3.01
2564 5491 4.450053 AGCTGACTGATTTCTAGCCATTC 58.550 43.478 0.00 0.00 35.05 2.67
2565 5492 4.500499 AGCTGACTGATTTCTAGCCATT 57.500 40.909 0.00 0.00 35.05 3.16
2584 5511 2.163211 GCCCAGAGATGAAAAACTCAGC 59.837 50.000 0.00 0.00 40.99 4.26
2585 5512 3.415212 TGCCCAGAGATGAAAAACTCAG 58.585 45.455 0.00 0.00 37.52 3.35
2586 5513 3.181440 ACTGCCCAGAGATGAAAAACTCA 60.181 43.478 1.69 0.00 38.81 3.41
2587 5514 3.416156 ACTGCCCAGAGATGAAAAACTC 58.584 45.455 1.69 0.00 0.00 3.01
2588 5515 3.416156 GACTGCCCAGAGATGAAAAACT 58.584 45.455 1.69 0.00 0.00 2.66
2589 5516 2.160417 CGACTGCCCAGAGATGAAAAAC 59.840 50.000 1.69 0.00 0.00 2.43
2590 5517 2.038426 TCGACTGCCCAGAGATGAAAAA 59.962 45.455 1.69 0.00 0.00 1.94
2591 5518 1.623311 TCGACTGCCCAGAGATGAAAA 59.377 47.619 1.69 0.00 0.00 2.29
2592 5519 1.266178 TCGACTGCCCAGAGATGAAA 58.734 50.000 1.69 0.00 0.00 2.69
2593 5520 1.489481 ATCGACTGCCCAGAGATGAA 58.511 50.000 1.69 0.00 31.96 2.57
2594 5521 1.489481 AATCGACTGCCCAGAGATGA 58.511 50.000 1.69 0.00 32.87 2.92
2595 5522 2.322355 AAATCGACTGCCCAGAGATG 57.678 50.000 1.69 0.00 32.87 2.90
2596 5523 2.420687 GGAAAATCGACTGCCCAGAGAT 60.421 50.000 1.69 4.14 33.49 2.75
2597 5524 1.066143 GGAAAATCGACTGCCCAGAGA 60.066 52.381 1.69 1.96 0.00 3.10
2598 5525 1.339055 TGGAAAATCGACTGCCCAGAG 60.339 52.381 1.69 0.00 0.00 3.35
2599 5526 0.690192 TGGAAAATCGACTGCCCAGA 59.310 50.000 1.69 0.00 0.00 3.86
2600 5527 1.089920 CTGGAAAATCGACTGCCCAG 58.910 55.000 10.18 10.18 35.75 4.45
2601 5528 0.960364 GCTGGAAAATCGACTGCCCA 60.960 55.000 0.00 0.00 0.00 5.36
2602 5529 1.657751 GGCTGGAAAATCGACTGCCC 61.658 60.000 9.01 0.21 41.61 5.36
2603 5530 1.803289 GGCTGGAAAATCGACTGCC 59.197 57.895 5.36 5.36 41.01 4.85
2604 5531 1.298859 ACGGCTGGAAAATCGACTGC 61.299 55.000 0.00 0.00 0.00 4.40
2605 5532 1.135972 CAACGGCTGGAAAATCGACTG 60.136 52.381 0.00 0.00 0.00 3.51
2606 5533 1.156736 CAACGGCTGGAAAATCGACT 58.843 50.000 0.00 0.00 0.00 4.18
2607 5534 3.676091 CAACGGCTGGAAAATCGAC 57.324 52.632 0.00 0.00 0.00 4.20
2617 5544 0.248215 GATTTCGCATCCAACGGCTG 60.248 55.000 0.00 0.00 0.00 4.85
2618 5545 0.676466 TGATTTCGCATCCAACGGCT 60.676 50.000 0.00 0.00 0.00 5.52
2619 5546 0.170116 TTGATTTCGCATCCAACGGC 59.830 50.000 0.00 0.00 0.00 5.68
2620 5547 2.518949 CTTTGATTTCGCATCCAACGG 58.481 47.619 0.00 0.00 0.00 4.44
2621 5548 2.518949 CCTTTGATTTCGCATCCAACG 58.481 47.619 0.00 0.00 0.00 4.10
2622 5549 2.262211 GCCTTTGATTTCGCATCCAAC 58.738 47.619 0.00 0.00 0.00 3.77
2623 5550 1.204467 GGCCTTTGATTTCGCATCCAA 59.796 47.619 0.00 0.00 0.00 3.53
2624 5551 0.817013 GGCCTTTGATTTCGCATCCA 59.183 50.000 0.00 0.00 0.00 3.41
2625 5552 1.106285 AGGCCTTTGATTTCGCATCC 58.894 50.000 0.00 0.00 0.00 3.51
2626 5553 1.800286 GCAGGCCTTTGATTTCGCATC 60.800 52.381 0.00 0.00 0.00 3.91
2627 5554 0.174162 GCAGGCCTTTGATTTCGCAT 59.826 50.000 0.00 0.00 0.00 4.73
2628 5555 1.177895 TGCAGGCCTTTGATTTCGCA 61.178 50.000 0.00 3.77 0.00 5.10
2629 5556 0.457337 CTGCAGGCCTTTGATTTCGC 60.457 55.000 0.00 0.30 0.00 4.70
2630 5557 0.883833 ACTGCAGGCCTTTGATTTCG 59.116 50.000 19.93 0.00 0.00 3.46
2631 5558 2.297033 TGAACTGCAGGCCTTTGATTTC 59.703 45.455 19.93 9.62 0.00 2.17
2632 5559 2.318908 TGAACTGCAGGCCTTTGATTT 58.681 42.857 19.93 0.00 0.00 2.17
2633 5560 1.999648 TGAACTGCAGGCCTTTGATT 58.000 45.000 19.93 0.00 0.00 2.57
2634 5561 2.097825 GATGAACTGCAGGCCTTTGAT 58.902 47.619 19.93 2.29 0.00 2.57
2635 5562 1.074405 AGATGAACTGCAGGCCTTTGA 59.926 47.619 19.93 0.00 0.00 2.69
2636 5563 1.542492 AGATGAACTGCAGGCCTTTG 58.458 50.000 19.93 0.00 0.00 2.77
2637 5564 2.299326 AAGATGAACTGCAGGCCTTT 57.701 45.000 19.93 2.30 0.00 3.11
2638 5565 2.299326 AAAGATGAACTGCAGGCCTT 57.701 45.000 19.93 10.13 0.00 4.35
2639 5566 2.943199 GCTAAAGATGAACTGCAGGCCT 60.943 50.000 19.93 0.00 0.00 5.19
2640 5567 1.403323 GCTAAAGATGAACTGCAGGCC 59.597 52.381 19.93 9.66 0.00 5.19
2641 5568 1.403323 GGCTAAAGATGAACTGCAGGC 59.597 52.381 19.93 10.32 0.00 4.85
2642 5569 2.941720 GAGGCTAAAGATGAACTGCAGG 59.058 50.000 19.93 0.00 0.00 4.85
2643 5570 2.941720 GGAGGCTAAAGATGAACTGCAG 59.058 50.000 13.48 13.48 0.00 4.41
2644 5571 2.677902 CGGAGGCTAAAGATGAACTGCA 60.678 50.000 0.00 0.00 0.00 4.41
2645 5572 1.936547 CGGAGGCTAAAGATGAACTGC 59.063 52.381 0.00 0.00 0.00 4.40
2646 5573 1.936547 GCGGAGGCTAAAGATGAACTG 59.063 52.381 0.00 0.00 35.83 3.16
2647 5574 2.317530 GCGGAGGCTAAAGATGAACT 57.682 50.000 0.00 0.00 35.83 3.01
2680 5607 4.308458 TTCGGTCGGTGGTGGCTG 62.308 66.667 0.00 0.00 0.00 4.85
2681 5608 4.309950 GTTCGGTCGGTGGTGGCT 62.310 66.667 0.00 0.00 0.00 4.75
2748 5675 3.264845 TTTCAGGGAGGGTGGGGC 61.265 66.667 0.00 0.00 0.00 5.80
2749 5676 2.763902 GTTTCAGGGAGGGTGGGG 59.236 66.667 0.00 0.00 0.00 4.96
2750 5677 2.160171 TGGTTTCAGGGAGGGTGGG 61.160 63.158 0.00 0.00 0.00 4.61
2751 5678 1.074951 GTGGTTTCAGGGAGGGTGG 59.925 63.158 0.00 0.00 0.00 4.61
2752 5679 0.036875 GAGTGGTTTCAGGGAGGGTG 59.963 60.000 0.00 0.00 0.00 4.61
2753 5680 1.134438 GGAGTGGTTTCAGGGAGGGT 61.134 60.000 0.00 0.00 0.00 4.34
2754 5681 0.842467 AGGAGTGGTTTCAGGGAGGG 60.842 60.000 0.00 0.00 0.00 4.30
2755 5682 0.615850 GAGGAGTGGTTTCAGGGAGG 59.384 60.000 0.00 0.00 0.00 4.30
2756 5683 1.002544 GTGAGGAGTGGTTTCAGGGAG 59.997 57.143 0.00 0.00 0.00 4.30
2757 5684 1.056660 GTGAGGAGTGGTTTCAGGGA 58.943 55.000 0.00 0.00 0.00 4.20
2758 5685 0.036875 GGTGAGGAGTGGTTTCAGGG 59.963 60.000 0.00 0.00 0.00 4.45
2759 5686 0.320771 CGGTGAGGAGTGGTTTCAGG 60.321 60.000 0.00 0.00 0.00 3.86
2760 5687 0.951040 GCGGTGAGGAGTGGTTTCAG 60.951 60.000 0.00 0.00 0.00 3.02
2761 5688 1.070786 GCGGTGAGGAGTGGTTTCA 59.929 57.895 0.00 0.00 0.00 2.69
2762 5689 1.671379 GGCGGTGAGGAGTGGTTTC 60.671 63.158 0.00 0.00 0.00 2.78
2763 5690 2.430367 GGCGGTGAGGAGTGGTTT 59.570 61.111 0.00 0.00 0.00 3.27
2764 5691 4.003788 CGGCGGTGAGGAGTGGTT 62.004 66.667 0.00 0.00 0.00 3.67
2767 5694 4.436998 GACCGGCGGTGAGGAGTG 62.437 72.222 39.41 4.02 35.25 3.51
2792 5719 2.122989 TAGAGGGATGGTCGGGGC 60.123 66.667 0.00 0.00 0.00 5.80
2793 5720 2.210711 GCTAGAGGGATGGTCGGGG 61.211 68.421 0.00 0.00 0.00 5.73
2794 5721 2.210711 GGCTAGAGGGATGGTCGGG 61.211 68.421 0.00 0.00 0.00 5.14
2795 5722 2.210711 GGGCTAGAGGGATGGTCGG 61.211 68.421 0.00 0.00 0.00 4.79
2796 5723 2.210711 GGGGCTAGAGGGATGGTCG 61.211 68.421 0.00 0.00 0.00 4.79
2797 5724 1.843832 GGGGGCTAGAGGGATGGTC 60.844 68.421 0.00 0.00 0.00 4.02
2798 5725 2.290745 GGGGGCTAGAGGGATGGT 59.709 66.667 0.00 0.00 0.00 3.55
3110 6037 2.627699 GACTGAATTGGCTTTTGGGTCA 59.372 45.455 0.00 0.00 0.00 4.02
3111 6038 2.351738 CGACTGAATTGGCTTTTGGGTC 60.352 50.000 0.00 0.00 0.00 4.46
3112 6039 1.613437 CGACTGAATTGGCTTTTGGGT 59.387 47.619 0.00 0.00 0.00 4.51
3113 6040 1.885887 TCGACTGAATTGGCTTTTGGG 59.114 47.619 0.00 0.00 0.00 4.12
3114 6041 2.554032 AGTCGACTGAATTGGCTTTTGG 59.446 45.455 19.30 0.00 0.00 3.28
3115 6042 3.558505 CAGTCGACTGAATTGGCTTTTG 58.441 45.455 36.73 8.90 46.59 2.44
3116 6043 3.904136 CAGTCGACTGAATTGGCTTTT 57.096 42.857 36.73 0.00 46.59 2.27
3127 6054 2.999507 AGCTACACTTCAGTCGACTG 57.000 50.000 34.76 34.76 45.08 3.51
3128 6055 5.646577 ATTTAGCTACACTTCAGTCGACT 57.353 39.130 13.58 13.58 0.00 4.18
3129 6056 6.553524 ACTATTTAGCTACACTTCAGTCGAC 58.446 40.000 7.70 7.70 0.00 4.20
3130 6057 6.754702 ACTATTTAGCTACACTTCAGTCGA 57.245 37.500 0.00 0.00 0.00 4.20
3131 6058 7.813852 AAACTATTTAGCTACACTTCAGTCG 57.186 36.000 0.00 0.00 0.00 4.18
3132 6059 9.425577 AGAAAACTATTTAGCTACACTTCAGTC 57.574 33.333 0.00 0.00 0.00 3.51
3133 6060 9.425577 GAGAAAACTATTTAGCTACACTTCAGT 57.574 33.333 0.00 0.00 0.00 3.41
3134 6061 9.646427 AGAGAAAACTATTTAGCTACACTTCAG 57.354 33.333 0.00 0.00 0.00 3.02
3135 6062 9.640963 GAGAGAAAACTATTTAGCTACACTTCA 57.359 33.333 0.00 0.00 0.00 3.02
3136 6063 9.863845 AGAGAGAAAACTATTTAGCTACACTTC 57.136 33.333 0.00 0.00 0.00 3.01
3137 6064 9.863845 GAGAGAGAAAACTATTTAGCTACACTT 57.136 33.333 0.00 0.00 0.00 3.16
3138 6065 9.250246 AGAGAGAGAAAACTATTTAGCTACACT 57.750 33.333 0.00 0.00 0.00 3.55
3139 6066 9.863845 AAGAGAGAGAAAACTATTTAGCTACAC 57.136 33.333 0.00 0.00 0.00 2.90
3189 6116 9.173231 ACAGAGGGAGTAATAGATAGTAGAGAA 57.827 37.037 0.00 0.00 0.00 2.87
3190 6117 8.745149 ACAGAGGGAGTAATAGATAGTAGAGA 57.255 38.462 0.00 0.00 0.00 3.10
3191 6118 9.444600 GAACAGAGGGAGTAATAGATAGTAGAG 57.555 40.741 0.00 0.00 0.00 2.43
3192 6119 8.384718 GGAACAGAGGGAGTAATAGATAGTAGA 58.615 40.741 0.00 0.00 0.00 2.59
3193 6120 8.387813 AGGAACAGAGGGAGTAATAGATAGTAG 58.612 40.741 0.00 0.00 0.00 2.57
3194 6121 8.290463 AGGAACAGAGGGAGTAATAGATAGTA 57.710 38.462 0.00 0.00 0.00 1.82
3195 6122 7.169287 AGGAACAGAGGGAGTAATAGATAGT 57.831 40.000 0.00 0.00 0.00 2.12
3196 6123 9.589461 TTTAGGAACAGAGGGAGTAATAGATAG 57.411 37.037 0.00 0.00 0.00 2.08
3203 6130 9.725206 ACTTATATTTAGGAACAGAGGGAGTAA 57.275 33.333 0.00 0.00 0.00 2.24
3204 6131 9.725206 AACTTATATTTAGGAACAGAGGGAGTA 57.275 33.333 0.00 0.00 0.00 2.59
3205 6132 8.625467 AACTTATATTTAGGAACAGAGGGAGT 57.375 34.615 0.00 0.00 0.00 3.85
3206 6133 9.907229 AAAACTTATATTTAGGAACAGAGGGAG 57.093 33.333 0.00 0.00 0.00 4.30
3240 6167 9.682465 TGCTCCGTATGTAGTCTATATTAGAAT 57.318 33.333 0.00 0.00 36.40 2.40
3241 6168 9.511272 TTGCTCCGTATGTAGTCTATATTAGAA 57.489 33.333 0.00 0.00 36.40 2.10
3242 6169 9.511272 TTTGCTCCGTATGTAGTCTATATTAGA 57.489 33.333 0.00 0.00 0.00 2.10
3245 6172 9.424319 CATTTTGCTCCGTATGTAGTCTATATT 57.576 33.333 0.00 0.00 0.00 1.28
3246 6173 8.803235 TCATTTTGCTCCGTATGTAGTCTATAT 58.197 33.333 0.00 0.00 0.00 0.86
3247 6174 8.173542 TCATTTTGCTCCGTATGTAGTCTATA 57.826 34.615 0.00 0.00 0.00 1.31
3248 6175 7.050970 TCATTTTGCTCCGTATGTAGTCTAT 57.949 36.000 0.00 0.00 0.00 1.98
3249 6176 6.096423 ACTCATTTTGCTCCGTATGTAGTCTA 59.904 38.462 0.00 0.00 0.00 2.59
3250 6177 5.105310 ACTCATTTTGCTCCGTATGTAGTCT 60.105 40.000 0.00 0.00 0.00 3.24
3251 6178 5.005779 CACTCATTTTGCTCCGTATGTAGTC 59.994 44.000 0.00 0.00 0.00 2.59
3252 6179 4.870426 CACTCATTTTGCTCCGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
3253 6180 5.109210 TCACTCATTTTGCTCCGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
3254 6181 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
3255 6182 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
3256 6183 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
3257 6184 5.431765 AGATTCACTCATTTTGCTCCGTAT 58.568 37.500 0.00 0.00 0.00 3.06
3258 6185 4.832248 AGATTCACTCATTTTGCTCCGTA 58.168 39.130 0.00 0.00 0.00 4.02
3259 6186 3.679389 AGATTCACTCATTTTGCTCCGT 58.321 40.909 0.00 0.00 0.00 4.69
3260 6187 4.631377 TGTAGATTCACTCATTTTGCTCCG 59.369 41.667 0.00 0.00 0.00 4.63
3261 6188 5.645497 AGTGTAGATTCACTCATTTTGCTCC 59.355 40.000 0.00 0.00 44.07 4.70
3262 6189 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26
3273 6200 9.900710 ATCGACATATTTAGAGTGTAGATTCAC 57.099 33.333 0.00 0.00 35.58 3.18
3282 6209 9.439537 CGGATGTATATCGACATATTTAGAGTG 57.560 37.037 0.00 0.00 40.18 3.51
3283 6210 9.175312 ACGGATGTATATCGACATATTTAGAGT 57.825 33.333 0.00 0.00 40.18 3.24


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

AutoCloner maintained by Alex Coulton.