Multiple sequence alignment - TraesCS5B01G095200

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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 TraesCS5B01G095200 chr5B 100.000 5906 0 0 1 5906 125227328 125233233 0.000000e+00 10907.0
1 TraesCS5B01G095200 chr5B 93.814 97 6 0 3576 3672 417444289 417444385 4.770000e-31 147.0
2 TraesCS5B01G095200 chr5B 88.496 113 7 5 3556 3665 621231922 621232031 1.340000e-26 132.0
3 TraesCS5B01G095200 chr5D 93.043 2041 79 23 3916 5906 114352047 114354074 0.000000e+00 2924.0
4 TraesCS5B01G095200 chr5D 93.388 1346 51 15 1 1342 114348189 114349500 0.000000e+00 1958.0
5 TraesCS5B01G095200 chr5D 94.918 1161 52 5 1331 2491 114349540 114350693 0.000000e+00 1810.0
6 TraesCS5B01G095200 chr5D 89.846 975 70 11 2614 3569 114350691 114351655 0.000000e+00 1225.0
7 TraesCS5B01G095200 chr5A 96.203 1659 49 12 840 2491 119438777 119440428 0.000000e+00 2702.0
8 TraesCS5B01G095200 chr5A 93.209 1664 90 11 3662 5305 119441400 119443060 0.000000e+00 2425.0
9 TraesCS5B01G095200 chr5A 95.380 974 30 6 2611 3570 119440423 119441395 0.000000e+00 1535.0
10 TraesCS5B01G095200 chr5A 86.709 316 28 6 487 793 119437958 119438268 7.330000e-89 339.0
11 TraesCS5B01G095200 chr3A 80.556 324 57 6 4009 4329 189280282 189280602 1.640000e-60 244.0
12 TraesCS5B01G095200 chr3A 97.656 128 3 0 2490 2617 644809129 644809256 2.770000e-53 220.0
13 TraesCS5B01G095200 chr3A 94.776 134 7 0 1176 1309 189276072 189276205 6.000000e-50 209.0
14 TraesCS5B01G095200 chr3A 93.233 133 7 2 1177 1308 266451191 266451322 1.680000e-45 195.0
15 TraesCS5B01G095200 chr1A 97.080 137 3 1 2488 2623 481650973 481651109 4.600000e-56 230.0
16 TraesCS5B01G095200 chr1A 97.674 129 3 0 2488 2616 486045901 486045773 7.700000e-54 222.0
17 TraesCS5B01G095200 chr3D 79.630 324 60 6 4009 4329 160908837 160908517 1.660000e-55 228.0
18 TraesCS5B01G095200 chr3D 94.776 134 7 0 1176 1309 160912166 160912033 6.000000e-50 209.0
19 TraesCS5B01G095200 chr3D 93.985 133 6 2 1177 1308 193598104 193597973 3.610000e-47 200.0
20 TraesCS5B01G095200 chr6B 95.652 138 6 0 2490 2627 54403535 54403672 7.700000e-54 222.0
21 TraesCS5B01G095200 chr6B 97.674 129 3 0 2488 2616 207510899 207511027 7.700000e-54 222.0
22 TraesCS5B01G095200 chr6B 92.708 96 7 0 3579 3674 534906757 534906852 7.980000e-29 139.0
23 TraesCS5B01G095200 chr6B 83.951 81 11 1 5162 5242 594783148 594783070 6.350000e-10 76.8
24 TraesCS5B01G095200 chrUn 96.970 132 3 1 2486 2616 103517778 103517647 2.770000e-53 220.0
25 TraesCS5B01G095200 chr7D 79.751 321 52 10 452 764 596118319 596118634 2.770000e-53 220.0
26 TraesCS5B01G095200 chr7D 88.793 116 7 4 3552 3665 615461492 615461381 2.870000e-28 137.0
27 TraesCS5B01G095200 chr7A 79.751 321 50 11 454 764 689274819 689275134 9.970000e-53 219.0
28 TraesCS5B01G095200 chr4B 95.556 135 5 1 2488 2622 108417623 108417756 1.290000e-51 215.0
29 TraesCS5B01G095200 chr3B 94.776 134 7 0 1176 1309 237648052 237647919 6.000000e-50 209.0
30 TraesCS5B01G095200 chr3B 93.233 133 7 2 1177 1308 276849193 276849324 1.680000e-45 195.0
31 TraesCS5B01G095200 chr2B 90.506 158 11 2 2490 2647 129660213 129660060 7.760000e-49 206.0
32 TraesCS5B01G095200 chr2B 79.828 233 38 7 460 688 761576924 761576697 1.700000e-35 161.0
33 TraesCS5B01G095200 chr2B 79.654 231 38 7 462 688 761529324 761529099 2.200000e-34 158.0
34 TraesCS5B01G095200 chr2B 79.688 256 20 14 171 421 456028306 456028078 7.920000e-34 156.0
35 TraesCS5B01G095200 chr2B 79.399 233 39 7 460 688 761634291 761634064 7.920000e-34 156.0
36 TraesCS5B01G095200 chr2B 90.000 90 8 1 4 93 456028584 456028496 1.340000e-21 115.0
37 TraesCS5B01G095200 chr2B 76.757 185 27 11 2434 2616 385566773 385566943 8.150000e-14 89.8
38 TraesCS5B01G095200 chr1B 91.391 151 11 2 2489 2639 560493086 560493234 7.760000e-49 206.0
39 TraesCS5B01G095200 chr1B 88.182 110 11 2 3570 3678 344841074 344841182 4.800000e-26 130.0
40 TraesCS5B01G095200 chr6A 94.624 93 4 1 3578 3670 540320351 540320442 6.170000e-30 143.0
41 TraesCS5B01G095200 chr2D 93.684 95 5 1 3573 3666 7286173 7286079 2.220000e-29 141.0
42 TraesCS5B01G095200 chr2D 90.385 104 8 2 3571 3674 555221194 555221093 1.030000e-27 135.0
43 TraesCS5B01G095200 chr4A 90.291 103 8 2 3579 3680 661959875 661959774 3.710000e-27 134.0


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 TraesCS5B01G095200 chr5B 125227328 125233233 5905 False 10907.00 10907 100.00000 1 5906 1 chr5B.!!$F1 5905
1 TraesCS5B01G095200 chr5D 114348189 114354074 5885 False 1979.25 2924 92.79875 1 5906 4 chr5D.!!$F1 5905
2 TraesCS5B01G095200 chr5A 119437958 119443060 5102 False 1750.25 2702 92.87525 487 5305 4 chr5A.!!$F1 4818
3 TraesCS5B01G095200 chr3D 160908517 160912166 3649 True 218.50 228 87.20300 1176 4329 2 chr3D.!!$R2 3153

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
147 148 0.106708 CCGGGATTGATGACGATGGT 59.893 55.0 0.00 0.00 0.00 3.55 F
1813 2356 0.250295 TTTTGGTAGCTGAGCTGCGT 60.250 50.0 18.79 0.00 42.02 5.24 F
2508 4608 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.0 5.23 0.00 44.66 2.17 F
2509 4609 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.0 5.23 0.00 44.66 1.40 F
2511 4611 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.0 5.23 0.00 44.66 2.12 F
2612 5442 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.0 13.64 4.95 46.06 4.20 F
4156 7199 0.891373 AGATCGACATCCCCTATGCG 59.109 55.0 0.00 0.00 39.39 4.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1995 2539 0.947244 GATCTAACTTGCATGCCCCG 59.053 55.000 16.68 5.81 0.00 5.73 R
3507 6426 1.415200 AGCCGTTCTTATCTCCCTCC 58.585 55.000 0.00 0.00 0.00 4.30 R
4000 7020 1.133823 ACTGCATCAACCTGACCACAA 60.134 47.619 0.00 0.00 0.00 3.33 R
4156 7199 1.685355 GGAGCTCTTCCTCTGAGGCC 61.685 65.000 19.08 8.55 43.16 5.19 R
4182 7225 2.162408 GTGAAGTTGCTAAGACCCATGC 59.838 50.000 0.00 0.00 0.00 4.06 R
4582 7637 2.697654 GAGGCTGCTATGACCATCATC 58.302 52.381 0.00 0.00 38.26 2.92 R
5767 8878 0.179020 TGTTGGGTGTGCTTCTCCAG 60.179 55.000 0.00 0.00 0.00 3.86 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
20 21 2.858644 TGTACATCTTCCCTTCCCCAT 58.141 47.619 0.00 0.00 0.00 4.00
54 55 2.022195 CACCTCCAGGCAAGATGAATG 58.978 52.381 0.00 0.00 39.32 2.67
56 57 1.030457 CTCCAGGCAAGATGAATGGC 58.970 55.000 0.00 0.00 43.17 4.40
140 141 2.918248 CCTGGCCGGGATTGATGA 59.082 61.111 28.28 0.00 0.00 2.92
144 145 1.071471 GGCCGGGATTGATGACGAT 59.929 57.895 2.18 0.00 0.00 3.73
147 148 0.106708 CCGGGATTGATGACGATGGT 59.893 55.000 0.00 0.00 0.00 3.55
222 223 0.479589 TGGAAGGATGGGAAAGGGGT 60.480 55.000 0.00 0.00 0.00 4.95
287 288 3.201726 AGGTTGATTTTTCATCGTGCG 57.798 42.857 0.00 0.00 0.00 5.34
351 353 4.394712 GGATAGCGATGGGGGCGG 62.395 72.222 0.00 0.00 35.00 6.13
352 354 3.311110 GATAGCGATGGGGGCGGA 61.311 66.667 0.00 0.00 35.00 5.54
353 355 2.607750 ATAGCGATGGGGGCGGAT 60.608 61.111 0.00 0.00 35.00 4.18
369 371 0.744771 GGATGAAGGACGGGCAGAAC 60.745 60.000 0.00 0.00 0.00 3.01
401 403 6.655930 TGTGGTAGGAAAAAGAACACTACTT 58.344 36.000 0.00 0.00 35.54 2.24
495 497 5.262455 AGAATAGCCTTCCTTTTCCTGTT 57.738 39.130 0.00 0.00 33.53 3.16
517 519 1.523758 ACGGAGTGCTTCATTCAACC 58.476 50.000 0.00 0.00 42.51 3.77
519 521 2.154462 CGGAGTGCTTCATTCAACCTT 58.846 47.619 0.00 0.00 0.00 3.50
521 523 2.489722 GGAGTGCTTCATTCAACCTTCC 59.510 50.000 0.00 0.00 0.00 3.46
567 569 2.823154 CCTTGAAACCCGCCTTAATTGA 59.177 45.455 0.00 0.00 0.00 2.57
625 627 9.447040 GTTTTCTTTGGTAAGACAATAAGTGAC 57.553 33.333 0.00 0.00 40.04 3.67
656 658 8.797436 AATAAAATCCTAAAATATGGGCAGGT 57.203 30.769 0.00 0.00 0.00 4.00
657 659 9.890915 AATAAAATCCTAAAATATGGGCAGGTA 57.109 29.630 0.00 0.00 0.00 3.08
658 660 9.890915 ATAAAATCCTAAAATATGGGCAGGTAA 57.109 29.630 0.00 0.00 0.00 2.85
659 661 8.616799 AAAATCCTAAAATATGGGCAGGTAAA 57.383 30.769 0.00 0.00 0.00 2.01
660 662 8.797436 AAATCCTAAAATATGGGCAGGTAAAT 57.203 30.769 0.00 0.00 0.00 1.40
661 663 9.890915 AAATCCTAAAATATGGGCAGGTAAATA 57.109 29.630 0.00 0.00 0.00 1.40
662 664 9.890915 AATCCTAAAATATGGGCAGGTAAATAA 57.109 29.630 0.00 0.00 0.00 1.40
763 780 1.894756 GTACCCCTTGCAACGCACA 60.895 57.895 0.00 0.00 38.71 4.57
770 787 1.469917 CTTGCAACGCACAGACAAAG 58.530 50.000 0.00 0.00 38.71 2.77
838 889 9.398170 CTTCAGAAAATACATGGTGTAACTTTG 57.602 33.333 0.00 0.00 36.31 2.77
1015 1505 2.419297 GCTGTCCCAGGTGTCATTCTAG 60.419 54.545 0.00 0.00 31.21 2.43
1422 1965 4.044065 AGGTTTGGAGGAATTGTGATGGTA 59.956 41.667 0.00 0.00 0.00 3.25
1585 2128 4.737946 GCCAGTAGATGTTCATCTTAGCGT 60.738 45.833 18.43 0.00 32.36 5.07
1813 2356 0.250295 TTTTGGTAGCTGAGCTGCGT 60.250 50.000 18.79 0.00 42.02 5.24
1872 2415 4.822350 GGAAAACTCCCATATAGCACCTTC 59.178 45.833 0.00 0.00 0.00 3.46
1913 2457 5.732647 CAGTAATCCGTGCGTAAAAAGATTG 59.267 40.000 0.00 0.00 0.00 2.67
1995 2539 5.306160 TGGGTACTAGCTACCATGTAATTCC 59.694 44.000 17.76 3.82 46.53 3.01
2029 2573 2.941453 AGATCTGCTGCAAATGCTTG 57.059 45.000 3.02 1.22 42.66 4.01
2032 2576 2.894763 TCTGCTGCAAATGCTTGTTT 57.105 40.000 3.02 0.00 42.66 2.83
2080 2624 9.463443 AAATTCAGTAAGTTTGCACACTTAATC 57.537 29.630 23.39 14.04 40.24 1.75
2081 2625 6.223138 TCAGTAAGTTTGCACACTTAATCG 57.777 37.500 23.39 17.00 40.24 3.34
2082 2626 5.986741 TCAGTAAGTTTGCACACTTAATCGA 59.013 36.000 23.39 18.53 40.24 3.59
2083 2627 6.649141 TCAGTAAGTTTGCACACTTAATCGAT 59.351 34.615 23.39 8.00 40.24 3.59
2086 2630 8.995220 AGTAAGTTTGCACACTTAATCGATAAA 58.005 29.630 23.39 1.54 40.24 1.40
2090 2635 5.092554 TGCACACTTAATCGATAAAGGGA 57.907 39.130 0.00 0.00 30.45 4.20
2186 2731 7.611467 AGCTGGACATAATCAAGTTCAACATAA 59.389 33.333 0.00 0.00 29.81 1.90
2419 2964 8.522830 CAAGGTCTCATCTTCCTCTATCTTATC 58.477 40.741 0.00 0.00 0.00 1.75
2488 4588 2.507484 TGCATTTCTTCTCCTGTGGTG 58.493 47.619 0.00 0.00 0.00 4.17
2489 4589 2.158623 TGCATTTCTTCTCCTGTGGTGT 60.159 45.455 0.00 0.00 0.00 4.16
2490 4590 3.072330 TGCATTTCTTCTCCTGTGGTGTA 59.928 43.478 0.00 0.00 0.00 2.90
2491 4591 3.437049 GCATTTCTTCTCCTGTGGTGTAC 59.563 47.826 0.00 0.00 0.00 2.90
2492 4592 4.804261 GCATTTCTTCTCCTGTGGTGTACT 60.804 45.833 0.00 0.00 0.00 2.73
2493 4593 4.602340 TTTCTTCTCCTGTGGTGTACTC 57.398 45.455 0.00 0.00 0.00 2.59
2494 4594 2.526432 TCTTCTCCTGTGGTGTACTCC 58.474 52.381 7.03 7.03 0.00 3.85
2495 4595 1.550976 CTTCTCCTGTGGTGTACTCCC 59.449 57.143 11.36 3.51 0.00 4.30
2496 4596 0.784495 TCTCCTGTGGTGTACTCCCT 59.216 55.000 11.36 0.00 0.00 4.20
2498 4598 0.252103 TCCTGTGGTGTACTCCCTCC 60.252 60.000 11.36 0.72 0.00 4.30
2499 4599 1.605058 CCTGTGGTGTACTCCCTCCG 61.605 65.000 11.36 2.08 0.00 4.63
2500 4600 0.898789 CTGTGGTGTACTCCCTCCGT 60.899 60.000 11.36 0.00 0.00 4.69
2502 4602 1.304713 TGGTGTACTCCCTCCGTCC 60.305 63.158 11.36 0.00 0.00 4.79
2503 4603 2.413142 GGTGTACTCCCTCCGTCCG 61.413 68.421 2.33 0.00 0.00 4.79
2505 4605 2.273449 GTACTCCCTCCGTCCGGA 59.727 66.667 0.00 0.00 42.90 5.14
2506 4606 1.379044 GTACTCCCTCCGTCCGGAA 60.379 63.158 5.23 0.00 44.66 4.30
2507 4607 0.967380 GTACTCCCTCCGTCCGGAAA 60.967 60.000 5.23 0.00 44.66 3.13
2508 4608 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
2509 4609 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
2510 4610 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
2511 4611 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
2512 4612 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
2514 4614 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
2515 4615 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
2516 4616 1.894466 TCCGTCCGGAAATACTTGTCA 59.106 47.619 5.23 0.00 42.05 3.58
2518 4618 2.864343 CCGTCCGGAAATACTTGTCATC 59.136 50.000 5.23 0.00 37.50 2.92
2522 4622 5.106869 CGTCCGGAAATACTTGTCATCAAAA 60.107 40.000 5.23 0.00 32.87 2.44
2523 4623 6.403200 CGTCCGGAAATACTTGTCATCAAAAT 60.403 38.462 5.23 0.00 32.87 1.82
2539 4770 8.248945 GTCATCAAAATGGATCAAAAGAGATGT 58.751 33.333 11.55 0.00 33.42 3.06
2543 4774 9.690913 TCAAAATGGATCAAAAGAGATGTATCT 57.309 29.630 0.00 0.00 40.50 1.98
2548 4779 9.995003 ATGGATCAAAAGAGATGTATCTAGAAC 57.005 33.333 0.00 0.00 37.25 3.01
2549 4780 9.206690 TGGATCAAAAGAGATGTATCTAGAACT 57.793 33.333 0.00 0.00 37.25 3.01
2589 5419 7.128234 ACATCCCCTTTTATCCATTTTGATG 57.872 36.000 0.00 0.00 33.80 3.07
2590 5420 6.902416 ACATCCCCTTTTATCCATTTTGATGA 59.098 34.615 0.00 0.00 32.39 2.92
2593 5423 6.728164 TCCCCTTTTATCCATTTTGATGACAA 59.272 34.615 0.00 0.00 0.00 3.18
2594 5424 7.043565 CCCCTTTTATCCATTTTGATGACAAG 58.956 38.462 0.00 0.00 37.32 3.16
2595 5425 7.310609 CCCCTTTTATCCATTTTGATGACAAGT 60.311 37.037 0.00 0.00 37.32 3.16
2596 5426 8.748412 CCCTTTTATCCATTTTGATGACAAGTA 58.252 33.333 0.00 0.00 37.32 2.24
2602 5432 6.851609 TCCATTTTGATGACAAGTATTTCCG 58.148 36.000 0.00 0.00 37.32 4.30
2603 5433 6.035843 CCATTTTGATGACAAGTATTTCCGG 58.964 40.000 0.00 0.00 37.32 5.14
2604 5434 6.127758 CCATTTTGATGACAAGTATTTCCGGA 60.128 38.462 0.00 0.00 37.32 5.14
2605 5435 5.873179 TTTGATGACAAGTATTTCCGGAC 57.127 39.130 1.83 0.00 37.32 4.79
2606 5436 3.517602 TGATGACAAGTATTTCCGGACG 58.482 45.455 1.83 0.00 0.00 4.79
2607 5437 2.373540 TGACAAGTATTTCCGGACGG 57.626 50.000 1.83 3.96 0.00 4.79
2609 5439 2.094390 TGACAAGTATTTCCGGACGGAG 60.094 50.000 13.64 3.15 46.06 4.63
2610 5440 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
2611 5441 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
2612 5442 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
2855 5770 3.636300 TGCATTTTGAACCACAAGTAGCT 59.364 39.130 0.00 0.00 39.77 3.32
2986 5901 7.107542 ACGTAAAGTAGGGAATATGCTTTCAA 58.892 34.615 0.00 0.00 34.87 2.69
2987 5902 7.773690 ACGTAAAGTAGGGAATATGCTTTCAAT 59.226 33.333 0.00 0.00 34.87 2.57
3414 6333 1.051556 TTTGGTGGAACAAAGGGGGC 61.052 55.000 0.00 0.00 44.16 5.80
3445 6364 2.115910 CTGGTGCTGGCAAAGGGA 59.884 61.111 0.00 0.00 0.00 4.20
3471 6390 5.126061 CAGATCCAGAAGGGTTAAATTGGTG 59.874 44.000 0.00 0.00 38.11 4.17
3507 6426 4.974645 TGGATAGGGGTGCAATTACTAG 57.025 45.455 0.00 0.00 0.00 2.57
3586 6506 8.079211 TGGATACATTAGATTATAGTGCTCCC 57.921 38.462 0.00 0.00 46.17 4.30
3589 6509 6.613153 ACATTAGATTATAGTGCTCCCTCC 57.387 41.667 0.00 0.00 0.00 4.30
3590 6510 5.186021 ACATTAGATTATAGTGCTCCCTCCG 59.814 44.000 0.00 0.00 0.00 4.63
3591 6511 3.246416 AGATTATAGTGCTCCCTCCGT 57.754 47.619 0.00 0.00 0.00 4.69
3595 6515 4.660789 TTATAGTGCTCCCTCCGTAAAC 57.339 45.455 0.00 0.00 0.00 2.01
3596 6516 2.226962 TAGTGCTCCCTCCGTAAACT 57.773 50.000 0.00 0.00 0.00 2.66
3597 6517 2.226962 AGTGCTCCCTCCGTAAACTA 57.773 50.000 0.00 0.00 0.00 2.24
3598 6518 2.532843 AGTGCTCCCTCCGTAAACTAA 58.467 47.619 0.00 0.00 0.00 2.24
3603 6523 6.552350 AGTGCTCCCTCCGTAAACTAATATAA 59.448 38.462 0.00 0.00 0.00 0.98
3604 6524 6.867293 GTGCTCCCTCCGTAAACTAATATAAG 59.133 42.308 0.00 0.00 0.00 1.73
3605 6525 6.779049 TGCTCCCTCCGTAAACTAATATAAGA 59.221 38.462 0.00 0.00 0.00 2.10
3606 6526 7.039923 TGCTCCCTCCGTAAACTAATATAAGAG 60.040 40.741 0.00 0.00 0.00 2.85
3607 6527 7.224522 TCCCTCCGTAAACTAATATAAGAGC 57.775 40.000 0.00 0.00 0.00 4.09
3608 6528 6.072286 TCCCTCCGTAAACTAATATAAGAGCG 60.072 42.308 0.00 0.00 0.00 5.03
3609 6529 6.294397 CCCTCCGTAAACTAATATAAGAGCGT 60.294 42.308 0.00 0.00 0.00 5.07
3610 6530 7.144000 CCTCCGTAAACTAATATAAGAGCGTT 58.856 38.462 0.00 0.00 0.00 4.84
3611 6531 7.650903 CCTCCGTAAACTAATATAAGAGCGTTT 59.349 37.037 0.00 0.00 0.00 3.60
3612 6532 9.669353 CTCCGTAAACTAATATAAGAGCGTTTA 57.331 33.333 0.00 0.00 0.00 2.01
3613 6533 9.669353 TCCGTAAACTAATATAAGAGCGTTTAG 57.331 33.333 0.00 0.00 30.36 1.85
3614 6534 9.669353 CCGTAAACTAATATAAGAGCGTTTAGA 57.331 33.333 0.00 0.00 30.36 2.10
3628 6548 9.570488 AAGAGCGTTTAGATTACTAAAGTAGTG 57.430 33.333 0.00 0.00 45.42 2.74
3629 6549 8.954350 AGAGCGTTTAGATTACTAAAGTAGTGA 58.046 33.333 0.00 0.00 45.42 3.41
3630 6550 9.733219 GAGCGTTTAGATTACTAAAGTAGTGAT 57.267 33.333 0.00 0.00 45.42 3.06
3631 6551 9.733219 AGCGTTTAGATTACTAAAGTAGTGATC 57.267 33.333 10.62 10.62 46.38 2.92
3638 6558 7.988904 ATTACTAAAGTAGTGATCTGAACGC 57.011 36.000 0.00 0.00 39.81 4.84
3639 6559 5.646577 ACTAAAGTAGTGATCTGAACGCT 57.353 39.130 6.26 6.26 37.69 5.07
3640 6560 5.642686 ACTAAAGTAGTGATCTGAACGCTC 58.357 41.667 4.17 0.00 37.69 5.03
3641 6561 4.792521 AAAGTAGTGATCTGAACGCTCT 57.207 40.909 4.17 0.55 0.00 4.09
3642 6562 4.792521 AAGTAGTGATCTGAACGCTCTT 57.207 40.909 4.17 5.99 0.00 2.85
3643 6563 5.899120 AAGTAGTGATCTGAACGCTCTTA 57.101 39.130 4.17 0.00 0.00 2.10
3644 6564 5.238006 AGTAGTGATCTGAACGCTCTTAC 57.762 43.478 4.17 0.00 0.00 2.34
3645 6565 4.700692 AGTAGTGATCTGAACGCTCTTACA 59.299 41.667 4.17 0.00 0.00 2.41
3646 6566 4.727507 AGTGATCTGAACGCTCTTACAT 57.272 40.909 0.00 0.00 0.00 2.29
3647 6567 5.078411 AGTGATCTGAACGCTCTTACATT 57.922 39.130 0.00 0.00 0.00 2.71
3648 6568 6.208988 AGTGATCTGAACGCTCTTACATTA 57.791 37.500 0.00 0.00 0.00 1.90
3649 6569 6.269315 AGTGATCTGAACGCTCTTACATTAG 58.731 40.000 0.00 0.00 0.00 1.73
3650 6570 6.037098 GTGATCTGAACGCTCTTACATTAGT 58.963 40.000 0.00 0.00 0.00 2.24
3651 6571 6.531948 GTGATCTGAACGCTCTTACATTAGTT 59.468 38.462 0.00 0.00 0.00 2.24
3652 6572 7.063544 GTGATCTGAACGCTCTTACATTAGTTT 59.936 37.037 0.00 0.00 0.00 2.66
3653 6573 8.248253 TGATCTGAACGCTCTTACATTAGTTTA 58.752 33.333 0.00 0.00 0.00 2.01
3654 6574 7.807687 TCTGAACGCTCTTACATTAGTTTAC 57.192 36.000 0.00 0.00 0.00 2.01
3655 6575 7.372714 TCTGAACGCTCTTACATTAGTTTACA 58.627 34.615 0.00 0.00 0.00 2.41
3656 6576 7.868922 TCTGAACGCTCTTACATTAGTTTACAA 59.131 33.333 0.00 0.00 0.00 2.41
3657 6577 8.367943 TGAACGCTCTTACATTAGTTTACAAA 57.632 30.769 0.00 0.00 0.00 2.83
3658 6578 8.492748 TGAACGCTCTTACATTAGTTTACAAAG 58.507 33.333 0.00 0.00 0.00 2.77
3659 6579 7.360575 ACGCTCTTACATTAGTTTACAAAGG 57.639 36.000 0.00 0.00 0.00 3.11
3660 6580 6.370718 ACGCTCTTACATTAGTTTACAAAGGG 59.629 38.462 0.00 0.00 0.00 3.95
3695 6615 1.980772 AGCAATCAACCTGGCTGGC 60.981 57.895 10.71 0.00 40.22 4.85
3696 6616 2.277591 GCAATCAACCTGGCTGGCA 61.278 57.895 10.71 3.18 40.22 4.92
3719 6639 7.358830 GCAAAGACTTTAGCAGGAATATCATC 58.641 38.462 13.89 0.00 0.00 2.92
3726 6646 6.753913 TTAGCAGGAATATCATCAGGAACT 57.246 37.500 0.00 0.00 43.88 3.01
3730 6650 3.580458 AGGAATATCATCAGGAACTCCCG 59.420 47.826 0.00 0.00 40.87 5.14
3909 6848 7.884877 TCTCTGTTATTCCTGATGATGTTGTTT 59.115 33.333 0.00 0.00 0.00 2.83
3920 6859 8.950210 CCTGATGATGTTGTTTTGACTTAGTAT 58.050 33.333 0.00 0.00 0.00 2.12
3981 7001 4.036027 CGATCCTGGATTTCATCTGTTTGG 59.964 45.833 11.17 0.00 0.00 3.28
4000 7020 2.306805 TGGTGCCATCTTCTGATTGTCT 59.693 45.455 0.00 0.00 0.00 3.41
4156 7199 0.891373 AGATCGACATCCCCTATGCG 59.109 55.000 0.00 0.00 39.39 4.73
4182 7225 2.413765 GGAAGAGCTCCGCTACCG 59.586 66.667 10.93 0.00 39.88 4.02
4398 7444 7.865706 AGTCATGGTGATAATCCTGTTTTAC 57.134 36.000 0.00 0.00 0.00 2.01
4399 7445 6.828785 AGTCATGGTGATAATCCTGTTTTACC 59.171 38.462 0.00 0.00 0.00 2.85
4400 7446 6.828785 GTCATGGTGATAATCCTGTTTTACCT 59.171 38.462 0.00 0.00 0.00 3.08
4401 7447 7.339466 GTCATGGTGATAATCCTGTTTTACCTT 59.661 37.037 0.00 0.00 0.00 3.50
4402 7448 8.553153 TCATGGTGATAATCCTGTTTTACCTTA 58.447 33.333 0.00 0.00 0.00 2.69
4481 7532 7.552687 TGATGTAATGGATGTAGTTCAAAGTCC 59.447 37.037 0.00 0.00 0.00 3.85
4582 7637 1.212688 TGGTGCTCCATGGTATTCTGG 59.787 52.381 12.58 0.00 39.03 3.86
4819 7881 0.881118 TCGCCAGCATCTTTGAAACC 59.119 50.000 0.00 0.00 0.00 3.27
4820 7882 0.883833 CGCCAGCATCTTTGAAACCT 59.116 50.000 0.00 0.00 0.00 3.50
4822 7884 2.680577 GCCAGCATCTTTGAAACCTTG 58.319 47.619 0.00 0.00 0.00 3.61
4823 7885 2.036346 GCCAGCATCTTTGAAACCTTGT 59.964 45.455 0.00 0.00 0.00 3.16
4878 7940 5.816258 TCATGAATTCTGATTCTGCTGAGAC 59.184 40.000 7.05 0.00 41.80 3.36
4918 7981 7.348956 CAATTTTGTCCCGTTTAAAATCCAAC 58.651 34.615 0.00 0.00 34.07 3.77
4924 7987 3.976306 CCCGTTTAAAATCCAACGTTGAC 59.024 43.478 29.35 15.06 43.43 3.18
5022 8086 4.793520 TCTCAAGGATAAAATGGGGGAAGA 59.206 41.667 0.00 0.00 0.00 2.87
5046 8110 1.424302 TGGTCCTAGACTCTATCCCCG 59.576 57.143 0.00 0.00 32.47 5.73
5085 8149 8.228035 AGGTCTTGAAGACATAGTGATAGTAC 57.772 38.462 24.95 4.73 46.79 2.73
5119 8183 9.796120 TCAGTTTTTCAACATTATTTTTCGTCT 57.204 25.926 0.00 0.00 35.05 4.18
5157 8221 5.808366 AGAATGGAGGCGAAGTATATCAA 57.192 39.130 0.00 0.00 0.00 2.57
5160 8224 7.907389 AGAATGGAGGCGAAGTATATCAATAA 58.093 34.615 0.00 0.00 0.00 1.40
5162 8226 5.466819 TGGAGGCGAAGTATATCAATAACG 58.533 41.667 0.00 0.00 0.00 3.18
5190 8254 9.638239 GAAATTAAACTGATGAGCCATACAAAA 57.362 29.630 0.00 0.00 0.00 2.44
5230 8294 4.213482 ACATTGAGCACCGTTTAAGAAGAC 59.787 41.667 0.00 0.00 0.00 3.01
5283 8354 8.519526 TGCCTAATACAACAACTTATGAAAAGG 58.480 33.333 0.00 0.00 0.00 3.11
5305 8376 6.526526 AGGTAGAGGAAAAGAAGAACTTCAC 58.473 40.000 15.43 3.26 41.84 3.18
5349 8420 6.846350 AGGAAAAGAAGAACTTCAATATGCG 58.154 36.000 15.43 0.00 41.84 4.73
5369 8449 2.788233 CGACTGCTCTCGAGATCAAATG 59.212 50.000 17.03 8.89 35.58 2.32
5377 8457 3.571828 TCTCGAGATCAAATGCTCCTAGG 59.428 47.826 12.08 0.82 0.00 3.02
5503 8614 7.277539 TCAGTGTTTCAAAAATGCTAGTTTTGG 59.722 33.333 16.19 2.95 43.22 3.28
5510 8621 8.364129 TCAAAAATGCTAGTTTTGGAAACATC 57.636 30.769 16.19 0.00 43.22 3.06
5552 8663 2.217750 CACACCTTCCACGAATGTCAA 58.782 47.619 0.00 0.00 0.00 3.18
5554 8665 3.253188 CACACCTTCCACGAATGTCAATT 59.747 43.478 0.00 0.00 0.00 2.32
5555 8666 3.888930 ACACCTTCCACGAATGTCAATTT 59.111 39.130 0.00 0.00 0.00 1.82
5556 8667 4.023193 ACACCTTCCACGAATGTCAATTTC 60.023 41.667 0.00 0.00 0.00 2.17
5557 8668 4.216257 CACCTTCCACGAATGTCAATTTCT 59.784 41.667 0.00 0.00 0.00 2.52
5597 8708 9.044150 CAATCATACAAAACATTTGTGAAGGTT 57.956 29.630 16.47 7.45 41.12 3.50
5598 8709 8.816640 ATCATACAAAACATTTGTGAAGGTTC 57.183 30.769 16.47 0.00 38.69 3.62
5662 8773 3.396260 TCAACTTTACTGTTCCTCGGG 57.604 47.619 0.00 0.00 0.00 5.14
5696 8807 5.586643 AGCTCGGGATCAGAATAAAACTTTC 59.413 40.000 0.00 0.00 0.00 2.62
5697 8808 5.354234 GCTCGGGATCAGAATAAAACTTTCA 59.646 40.000 0.00 0.00 0.00 2.69
5767 8878 2.143876 AAATGTCATGTGGTAGGCCC 57.856 50.000 0.00 0.00 0.00 5.80
5798 8909 4.133820 CACACCCAACATAACAGACTTGA 58.866 43.478 0.00 0.00 0.00 3.02
5805 8916 6.151691 CCAACATAACAGACTTGACCAAATG 58.848 40.000 0.00 0.00 0.00 2.32
5807 8918 5.630121 ACATAACAGACTTGACCAAATGGA 58.370 37.500 6.42 0.00 38.94 3.41
5839 8950 1.805120 CGGCTCAACCTGGGTTATACG 60.805 57.143 4.58 4.60 36.46 3.06
5840 8951 1.474498 GGCTCAACCTGGGTTATACGG 60.474 57.143 4.58 0.00 36.46 4.02
5850 8962 1.139520 GTTATACGGGCCGACACGT 59.860 57.895 35.78 12.77 46.17 4.49
5859 8971 2.261361 CCGACACGTCATGGCTCA 59.739 61.111 0.00 0.00 31.94 4.26
5860 8972 1.807165 CCGACACGTCATGGCTCAG 60.807 63.158 0.00 0.00 31.94 3.35
5880 8992 1.332552 GCCAAACACGACAAGTACACG 60.333 52.381 0.00 0.00 0.00 4.49
5889 9001 0.321298 ACAAGTACACGGGTCATGCC 60.321 55.000 0.00 0.00 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 1.438651 GAGGTGCGTGCTGACAATTA 58.561 50.000 0.00 0.00 0.00 1.40
54 55 2.291605 ACCATCTTTCCCCTACAAAGCC 60.292 50.000 0.00 0.00 31.85 4.35
56 57 4.200092 GCTACCATCTTTCCCCTACAAAG 58.800 47.826 0.00 0.00 32.89 2.77
58 59 2.169769 CGCTACCATCTTTCCCCTACAA 59.830 50.000 0.00 0.00 0.00 2.41
61 62 1.420430 CCGCTACCATCTTTCCCCTA 58.580 55.000 0.00 0.00 0.00 3.53
93 94 3.697747 CCGTCGCCACCAACCCTA 61.698 66.667 0.00 0.00 0.00 3.53
124 125 1.889105 CGTCATCAATCCCGGCCAG 60.889 63.158 2.24 0.00 0.00 4.85
222 223 3.566351 TCTCCTTAGATCCAGATTGCGA 58.434 45.455 0.00 0.00 0.00 5.10
287 288 2.428925 TTCGACCTCCCGCATACCC 61.429 63.158 0.00 0.00 0.00 3.69
325 327 2.574955 ATCGCTATCCCTCCCGCAC 61.575 63.158 0.00 0.00 0.00 5.34
351 353 1.084370 CGTTCTGCCCGTCCTTCATC 61.084 60.000 0.00 0.00 0.00 2.92
352 354 1.079127 CGTTCTGCCCGTCCTTCAT 60.079 57.895 0.00 0.00 0.00 2.57
353 355 2.342279 CGTTCTGCCCGTCCTTCA 59.658 61.111 0.00 0.00 0.00 3.02
425 427 9.495382 AGGTAAGGAGTGAAATCTCTACTATTT 57.505 33.333 0.00 0.00 30.96 1.40
426 428 9.138596 GAGGTAAGGAGTGAAATCTCTACTATT 57.861 37.037 0.00 0.00 30.96 1.73
427 429 8.507761 AGAGGTAAGGAGTGAAATCTCTACTAT 58.492 37.037 0.00 0.00 30.96 2.12
428 430 7.874252 AGAGGTAAGGAGTGAAATCTCTACTA 58.126 38.462 0.00 0.00 30.96 1.82
481 483 4.246458 CTCCGTCTAACAGGAAAAGGAAG 58.754 47.826 0.00 0.00 35.90 3.46
490 492 1.272490 TGAAGCACTCCGTCTAACAGG 59.728 52.381 0.00 0.00 0.00 4.00
495 497 3.585862 GTTGAATGAAGCACTCCGTCTA 58.414 45.455 0.00 0.00 0.00 2.59
648 650 1.289231 TGCCCATTATTTACCTGCCCA 59.711 47.619 0.00 0.00 0.00 5.36
649 651 1.963515 CTGCCCATTATTTACCTGCCC 59.036 52.381 0.00 0.00 0.00 5.36
650 652 1.963515 CCTGCCCATTATTTACCTGCC 59.036 52.381 0.00 0.00 0.00 4.85
651 653 2.944129 TCCTGCCCATTATTTACCTGC 58.056 47.619 0.00 0.00 0.00 4.85
652 654 5.221501 CCAAATCCTGCCCATTATTTACCTG 60.222 44.000 0.00 0.00 0.00 4.00
653 655 4.901250 CCAAATCCTGCCCATTATTTACCT 59.099 41.667 0.00 0.00 0.00 3.08
654 656 4.653801 ACCAAATCCTGCCCATTATTTACC 59.346 41.667 0.00 0.00 0.00 2.85
655 657 5.869649 ACCAAATCCTGCCCATTATTTAC 57.130 39.130 0.00 0.00 0.00 2.01
656 658 6.041523 GCTTACCAAATCCTGCCCATTATTTA 59.958 38.462 0.00 0.00 0.00 1.40
657 659 5.163311 GCTTACCAAATCCTGCCCATTATTT 60.163 40.000 0.00 0.00 0.00 1.40
658 660 4.344968 GCTTACCAAATCCTGCCCATTATT 59.655 41.667 0.00 0.00 0.00 1.40
659 661 3.897505 GCTTACCAAATCCTGCCCATTAT 59.102 43.478 0.00 0.00 0.00 1.28
660 662 3.295973 GCTTACCAAATCCTGCCCATTA 58.704 45.455 0.00 0.00 0.00 1.90
661 663 2.110578 GCTTACCAAATCCTGCCCATT 58.889 47.619 0.00 0.00 0.00 3.16
662 664 1.006998 TGCTTACCAAATCCTGCCCAT 59.993 47.619 0.00 0.00 0.00 4.00
751 768 1.469917 CTTTGTCTGTGCGTTGCAAG 58.530 50.000 0.00 0.00 41.47 4.01
838 889 3.898741 TGAAAAATGTAACCCTTGGGTCC 59.101 43.478 12.27 6.65 0.00 4.46
1015 1505 3.526534 GGATTAATAGGAGGAGATGCGC 58.473 50.000 0.00 0.00 0.00 6.09
1372 1915 5.594725 TCAAACTACCAAACCTTATTGCACA 59.405 36.000 0.00 0.00 0.00 4.57
1585 2128 3.583086 AGAAAATCCCCAAGAACTCTCGA 59.417 43.478 0.00 0.00 0.00 4.04
1663 2206 9.726438 CTACCCGAATCTAAAGAATATGGATTT 57.274 33.333 0.00 0.00 0.00 2.17
1664 2207 7.824779 GCTACCCGAATCTAAAGAATATGGATT 59.175 37.037 0.00 0.00 0.00 3.01
1665 2208 7.181125 AGCTACCCGAATCTAAAGAATATGGAT 59.819 37.037 0.00 0.00 0.00 3.41
1688 2231 4.380841 TTTACCACATACGATCGAAGCT 57.619 40.909 24.34 0.83 0.00 3.74
1813 2356 5.737063 GCAATCCAGTGCTCAAAGAAAGAAA 60.737 40.000 0.00 0.00 41.51 2.52
1872 2415 7.698130 CGGATTACTGGAAGAAGCAAAATTTAG 59.302 37.037 0.00 0.00 37.43 1.85
1963 2507 1.757340 GCTAGTACCCAGGACGGCT 60.757 63.158 0.00 0.00 0.00 5.52
1995 2539 0.947244 GATCTAACTTGCATGCCCCG 59.053 55.000 16.68 5.81 0.00 5.73
2078 2622 8.035448 AGTAAAAAGATCCTCCCTTTATCGAT 57.965 34.615 2.16 2.16 33.85 3.59
2079 2623 7.433537 AGTAAAAAGATCCTCCCTTTATCGA 57.566 36.000 0.00 0.00 33.85 3.59
2080 2624 9.425577 GATAGTAAAAAGATCCTCCCTTTATCG 57.574 37.037 0.00 0.00 33.85 2.92
2081 2625 9.727859 GGATAGTAAAAAGATCCTCCCTTTATC 57.272 37.037 0.00 0.00 36.89 1.75
2082 2626 8.376270 CGGATAGTAAAAAGATCCTCCCTTTAT 58.624 37.037 0.00 0.00 37.57 1.40
2083 2627 7.566138 TCGGATAGTAAAAAGATCCTCCCTTTA 59.434 37.037 0.00 0.00 37.57 1.85
2086 2630 5.304871 GTCGGATAGTAAAAAGATCCTCCCT 59.695 44.000 0.00 0.00 37.57 4.20
2090 2635 6.156429 ACCAAGTCGGATAGTAAAAAGATCCT 59.844 38.462 0.00 0.00 37.57 3.24
2186 2731 1.270199 TGTGATTTGGCATGCGCTTTT 60.270 42.857 12.44 0.00 38.60 2.27
2488 4588 0.967380 TTTCCGGACGGAGGGAGTAC 60.967 60.000 13.64 0.00 46.06 2.73
2489 4589 0.032813 ATTTCCGGACGGAGGGAGTA 60.033 55.000 13.64 0.00 46.06 2.59
2490 4590 0.032813 TATTTCCGGACGGAGGGAGT 60.033 55.000 13.64 0.00 46.06 3.85
2491 4591 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
2492 4592 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
2493 4593 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
2494 4594 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
2495 4595 2.094390 TGACAAGTATTTCCGGACGGAG 60.094 50.000 13.64 3.15 46.06 4.63
2496 4596 1.894466 TGACAAGTATTTCCGGACGGA 59.106 47.619 1.83 9.76 43.52 4.69
2498 4598 3.517602 TGATGACAAGTATTTCCGGACG 58.482 45.455 1.83 0.00 0.00 4.79
2499 4599 5.873179 TTTGATGACAAGTATTTCCGGAC 57.127 39.130 1.83 0.00 37.32 4.79
2500 4600 6.127758 CCATTTTGATGACAAGTATTTCCGGA 60.128 38.462 0.00 0.00 37.32 5.14
2502 4602 6.851609 TCCATTTTGATGACAAGTATTTCCG 58.148 36.000 0.00 0.00 37.32 4.30
2503 4603 8.469200 TGATCCATTTTGATGACAAGTATTTCC 58.531 33.333 0.00 0.00 37.32 3.13
2507 4607 9.865321 CTTTTGATCCATTTTGATGACAAGTAT 57.135 29.630 0.00 0.00 37.32 2.12
2508 4608 9.076781 TCTTTTGATCCATTTTGATGACAAGTA 57.923 29.630 0.00 0.00 37.32 2.24
2509 4609 7.954835 TCTTTTGATCCATTTTGATGACAAGT 58.045 30.769 0.00 0.00 37.32 3.16
2510 4610 8.301720 TCTCTTTTGATCCATTTTGATGACAAG 58.698 33.333 0.00 0.00 37.32 3.16
2511 4611 8.180706 TCTCTTTTGATCCATTTTGATGACAA 57.819 30.769 0.00 0.00 0.00 3.18
2512 4612 7.764141 TCTCTTTTGATCCATTTTGATGACA 57.236 32.000 0.00 0.00 0.00 3.58
2514 4614 8.357290 ACATCTCTTTTGATCCATTTTGATGA 57.643 30.769 15.03 0.00 33.85 2.92
2522 4622 9.995003 GTTCTAGATACATCTCTTTTGATCCAT 57.005 33.333 0.00 0.00 38.32 3.41
2523 4623 9.206690 AGTTCTAGATACATCTCTTTTGATCCA 57.793 33.333 0.00 0.00 38.32 3.41
2548 4779 9.774413 AAGGGGATGTATTTAGACGTATTTTAG 57.226 33.333 0.00 0.00 0.00 1.85
2553 4784 9.939802 GATAAAAGGGGATGTATTTAGACGTAT 57.060 33.333 0.00 0.00 0.00 3.06
2554 4785 8.370182 GGATAAAAGGGGATGTATTTAGACGTA 58.630 37.037 0.00 0.00 0.00 3.57
2555 4786 7.147444 TGGATAAAAGGGGATGTATTTAGACGT 60.147 37.037 0.00 0.00 0.00 4.34
2556 4787 7.221450 TGGATAAAAGGGGATGTATTTAGACG 58.779 38.462 0.00 0.00 0.00 4.18
2557 4788 9.588096 AATGGATAAAAGGGGATGTATTTAGAC 57.412 33.333 0.00 0.00 0.00 2.59
2561 4792 9.278011 TCAAAATGGATAAAAGGGGATGTATTT 57.722 29.630 0.00 0.00 0.00 1.40
2565 5395 6.902416 TCATCAAAATGGATAAAAGGGGATGT 59.098 34.615 0.00 0.00 33.42 3.06
2569 5399 6.543430 TGTCATCAAAATGGATAAAAGGGG 57.457 37.500 0.00 0.00 33.42 4.79
2578 5408 6.127758 CCGGAAATACTTGTCATCAAAATGGA 60.128 38.462 0.00 0.00 33.42 3.41
2585 5415 3.517602 CGTCCGGAAATACTTGTCATCA 58.482 45.455 5.23 0.00 0.00 3.07
2589 5419 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
2590 5420 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
2593 5423 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
2594 5424 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
2595 5425 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
2596 5426 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
2598 5428 1.077212 CTACTCCCTCCGTCCGGAA 60.077 63.158 5.23 0.00 44.66 4.30
2599 5429 1.856539 AACTACTCCCTCCGTCCGGA 61.857 60.000 0.00 0.00 42.90 5.14
2600 5430 0.969409 AAACTACTCCCTCCGTCCGG 60.969 60.000 0.00 0.00 0.00 5.14
2601 5431 0.455005 GAAACTACTCCCTCCGTCCG 59.545 60.000 0.00 0.00 0.00 4.79
2602 5432 1.849977 AGAAACTACTCCCTCCGTCC 58.150 55.000 0.00 0.00 0.00 4.79
2603 5433 3.883669 TCTAGAAACTACTCCCTCCGTC 58.116 50.000 0.00 0.00 0.00 4.79
2604 5434 4.313020 TTCTAGAAACTACTCCCTCCGT 57.687 45.455 1.68 0.00 0.00 4.69
2605 5435 5.855740 ATTTCTAGAAACTACTCCCTCCG 57.144 43.478 19.94 0.00 32.51 4.63
2606 5436 8.706521 ACAATATTTCTAGAAACTACTCCCTCC 58.293 37.037 19.94 0.00 32.51 4.30
2607 5437 9.535878 CACAATATTTCTAGAAACTACTCCCTC 57.464 37.037 19.94 0.00 32.51 4.30
2609 5439 7.988028 AGCACAATATTTCTAGAAACTACTCCC 59.012 37.037 19.94 7.40 32.51 4.30
2610 5440 8.821894 CAGCACAATATTTCTAGAAACTACTCC 58.178 37.037 19.94 6.70 32.51 3.85
2611 5441 9.372369 ACAGCACAATATTTCTAGAAACTACTC 57.628 33.333 19.94 6.80 32.51 2.59
2612 5442 9.726438 AACAGCACAATATTTCTAGAAACTACT 57.274 29.630 19.94 7.14 32.51 2.57
2855 5770 5.073428 CAGCATATAGGAGTACTGGAGTCA 58.927 45.833 0.00 0.00 0.00 3.41
2970 5885 7.836183 ACAGACTAAATTGAAAGCATATTCCCT 59.164 33.333 0.00 0.00 0.00 4.20
2987 5902 8.892723 CCAATAGATTATTGTGCACAGACTAAA 58.107 33.333 20.59 11.10 43.05 1.85
3013 5930 5.186409 GGTAAAAGGAAAACCCCTGGTATTC 59.814 44.000 0.00 0.00 36.49 1.75
3206 6123 3.259064 CCAAATTGATCCTGCTGCAAAG 58.741 45.455 3.02 0.00 0.00 2.77
3207 6124 2.633967 ACCAAATTGATCCTGCTGCAAA 59.366 40.909 3.02 0.00 0.00 3.68
3362 6281 9.737844 ATTTCATGGTTTGGCAAATTTAGTTAT 57.262 25.926 16.74 3.45 0.00 1.89
3445 6364 5.264395 CAATTTAACCCTTCTGGATCTGGT 58.736 41.667 0.00 0.00 38.00 4.00
3471 6390 4.881850 CCCTATCCAAGTGTCCATTGTAAC 59.118 45.833 0.00 0.00 0.00 2.50
3507 6426 1.415200 AGCCGTTCTTATCTCCCTCC 58.585 55.000 0.00 0.00 0.00 4.30
3570 6490 4.383931 ACGGAGGGAGCACTATAATCTA 57.616 45.455 0.00 0.00 0.00 1.98
3572 6492 5.010820 AGTTTACGGAGGGAGCACTATAATC 59.989 44.000 0.00 0.00 0.00 1.75
3574 6494 4.284178 AGTTTACGGAGGGAGCACTATAA 58.716 43.478 0.00 0.00 0.00 0.98
3575 6495 3.907221 AGTTTACGGAGGGAGCACTATA 58.093 45.455 0.00 0.00 0.00 1.31
3576 6496 2.748388 AGTTTACGGAGGGAGCACTAT 58.252 47.619 0.00 0.00 0.00 2.12
3577 6497 2.226962 AGTTTACGGAGGGAGCACTA 57.773 50.000 0.00 0.00 0.00 2.74
3578 6498 2.226962 TAGTTTACGGAGGGAGCACT 57.773 50.000 0.00 0.00 0.00 4.40
3579 6499 3.538634 ATTAGTTTACGGAGGGAGCAC 57.461 47.619 0.00 0.00 0.00 4.40
3583 6503 6.072286 CGCTCTTATATTAGTTTACGGAGGGA 60.072 42.308 0.00 0.00 34.63 4.20
3584 6504 6.091437 CGCTCTTATATTAGTTTACGGAGGG 58.909 44.000 0.00 0.00 0.00 4.30
3585 6505 6.675987 ACGCTCTTATATTAGTTTACGGAGG 58.324 40.000 0.00 0.00 0.00 4.30
3586 6506 8.571461 AAACGCTCTTATATTAGTTTACGGAG 57.429 34.615 0.00 0.00 31.14 4.63
3603 6523 8.954350 TCACTACTTTAGTAATCTAAACGCTCT 58.046 33.333 0.00 0.00 40.05 4.09
3604 6524 9.733219 ATCACTACTTTAGTAATCTAAACGCTC 57.267 33.333 0.00 0.00 40.05 5.03
3605 6525 9.733219 GATCACTACTTTAGTAATCTAAACGCT 57.267 33.333 0.00 0.00 40.05 5.07
3606 6526 9.733219 AGATCACTACTTTAGTAATCTAAACGC 57.267 33.333 0.00 0.00 40.05 4.84
3612 6532 7.916450 GCGTTCAGATCACTACTTTAGTAATCT 59.084 37.037 0.00 0.00 37.23 2.40
3613 6533 7.916450 AGCGTTCAGATCACTACTTTAGTAATC 59.084 37.037 0.00 0.00 37.23 1.75
3614 6534 7.773149 AGCGTTCAGATCACTACTTTAGTAAT 58.227 34.615 0.00 0.00 37.23 1.89
3615 6535 7.120873 AGAGCGTTCAGATCACTACTTTAGTAA 59.879 37.037 1.01 0.00 37.82 2.24
3616 6536 6.598457 AGAGCGTTCAGATCACTACTTTAGTA 59.402 38.462 1.01 0.00 37.82 1.82
3617 6537 5.416326 AGAGCGTTCAGATCACTACTTTAGT 59.584 40.000 1.01 0.00 37.82 2.24
3618 6538 5.885881 AGAGCGTTCAGATCACTACTTTAG 58.114 41.667 1.01 0.00 37.82 1.85
3619 6539 5.899120 AGAGCGTTCAGATCACTACTTTA 57.101 39.130 1.01 0.00 37.82 1.85
3620 6540 4.792521 AGAGCGTTCAGATCACTACTTT 57.207 40.909 1.01 0.00 37.82 2.66
3621 6541 4.792521 AAGAGCGTTCAGATCACTACTT 57.207 40.909 1.01 0.00 37.82 2.24
3622 6542 4.700692 TGTAAGAGCGTTCAGATCACTACT 59.299 41.667 1.01 0.00 37.82 2.57
3623 6543 4.982999 TGTAAGAGCGTTCAGATCACTAC 58.017 43.478 1.01 0.00 37.82 2.73
3624 6544 5.836821 ATGTAAGAGCGTTCAGATCACTA 57.163 39.130 1.01 0.00 37.82 2.74
3625 6545 4.727507 ATGTAAGAGCGTTCAGATCACT 57.272 40.909 1.01 0.00 37.82 3.41
3626 6546 6.037098 ACTAATGTAAGAGCGTTCAGATCAC 58.963 40.000 1.01 0.00 37.82 3.06
3627 6547 6.208988 ACTAATGTAAGAGCGTTCAGATCA 57.791 37.500 1.01 0.00 37.82 2.92
3628 6548 7.527084 AAACTAATGTAAGAGCGTTCAGATC 57.473 36.000 1.01 0.00 35.01 2.75
3629 6549 8.033038 TGTAAACTAATGTAAGAGCGTTCAGAT 58.967 33.333 1.01 0.00 0.00 2.90
3630 6550 7.372714 TGTAAACTAATGTAAGAGCGTTCAGA 58.627 34.615 1.01 0.00 0.00 3.27
3631 6551 7.576750 TGTAAACTAATGTAAGAGCGTTCAG 57.423 36.000 1.01 0.00 0.00 3.02
3632 6552 7.949903 TTGTAAACTAATGTAAGAGCGTTCA 57.050 32.000 1.01 0.00 0.00 3.18
3633 6553 7.955864 CCTTTGTAAACTAATGTAAGAGCGTTC 59.044 37.037 0.00 0.00 0.00 3.95
3634 6554 7.094933 CCCTTTGTAAACTAATGTAAGAGCGTT 60.095 37.037 0.00 0.00 0.00 4.84
3635 6555 6.370718 CCCTTTGTAAACTAATGTAAGAGCGT 59.629 38.462 0.00 0.00 0.00 5.07
3636 6556 6.592607 TCCCTTTGTAAACTAATGTAAGAGCG 59.407 38.462 0.00 0.00 0.00 5.03
3637 6557 7.606839 ACTCCCTTTGTAAACTAATGTAAGAGC 59.393 37.037 0.00 0.00 0.00 4.09
3653 6573 7.934120 GCTGAGTTTATATGATACTCCCTTTGT 59.066 37.037 0.00 0.00 37.97 2.83
3654 6574 7.933577 TGCTGAGTTTATATGATACTCCCTTTG 59.066 37.037 0.00 0.00 37.97 2.77
3655 6575 8.034313 TGCTGAGTTTATATGATACTCCCTTT 57.966 34.615 0.00 0.00 37.97 3.11
3656 6576 7.618019 TGCTGAGTTTATATGATACTCCCTT 57.382 36.000 0.00 0.00 37.97 3.95
3657 6577 7.618019 TTGCTGAGTTTATATGATACTCCCT 57.382 36.000 0.00 0.00 37.97 4.20
3658 6578 8.097038 TGATTGCTGAGTTTATATGATACTCCC 58.903 37.037 0.00 0.00 37.97 4.30
3659 6579 9.494271 TTGATTGCTGAGTTTATATGATACTCC 57.506 33.333 0.00 0.00 37.97 3.85
3668 6588 4.640201 GCCAGGTTGATTGCTGAGTTTATA 59.360 41.667 0.00 0.00 0.00 0.98
3695 6615 8.442632 TGATGATATTCCTGCTAAAGTCTTTG 57.557 34.615 8.14 0.00 0.00 2.77
3696 6616 7.718753 CCTGATGATATTCCTGCTAAAGTCTTT 59.281 37.037 2.81 2.81 0.00 2.52
3719 6639 4.347000 TCCTTATTATTCCGGGAGTTCCTG 59.653 45.833 0.00 0.00 42.13 3.86
3920 6859 8.421784 AGTACTCAGAATGACAGAAAAGTACAA 58.578 33.333 14.89 0.00 42.56 2.41
3981 7001 3.755378 ACAAGACAATCAGAAGATGGCAC 59.245 43.478 0.00 0.00 33.90 5.01
4000 7020 1.133823 ACTGCATCAACCTGACCACAA 60.134 47.619 0.00 0.00 0.00 3.33
4156 7199 1.685355 GGAGCTCTTCCTCTGAGGCC 61.685 65.000 19.08 8.55 43.16 5.19
4182 7225 2.162408 GTGAAGTTGCTAAGACCCATGC 59.838 50.000 0.00 0.00 0.00 4.06
4398 7444 4.073293 ACACTCTTGTGACAAGGTAAGG 57.927 45.455 23.65 12.16 46.55 2.69
4399 7445 5.696724 CCTAACACTCTTGTGACAAGGTAAG 59.303 44.000 23.65 16.34 46.55 2.34
4400 7446 5.454187 CCCTAACACTCTTGTGACAAGGTAA 60.454 44.000 23.65 5.33 46.55 2.85
4401 7447 4.039973 CCCTAACACTCTTGTGACAAGGTA 59.960 45.833 23.65 6.05 46.55 3.08
4402 7448 3.181454 CCCTAACACTCTTGTGACAAGGT 60.181 47.826 23.65 17.19 46.55 3.50
4505 7556 8.044060 ACATCACATTGTAATAACTCAACCAG 57.956 34.615 0.00 0.00 0.00 4.00
4582 7637 2.697654 GAGGCTGCTATGACCATCATC 58.302 52.381 0.00 0.00 38.26 2.92
4674 7729 6.295249 TGAATACTGATGAAAGGTGTGTCAA 58.705 36.000 0.00 0.00 0.00 3.18
4822 7884 8.836413 TCCAAGAATAAAACCATCGAATATGAC 58.164 33.333 0.00 0.00 0.00 3.06
4823 7885 8.836413 GTCCAAGAATAAAACCATCGAATATGA 58.164 33.333 0.00 0.00 0.00 2.15
4878 7940 8.450180 GGGACAAAATTGGTTTATTGCAATTAG 58.550 33.333 18.75 0.00 0.00 1.73
4918 7981 0.457851 TTTGGTTGCAAGGGTCAACG 59.542 50.000 0.00 0.00 43.37 4.10
4924 7987 2.038659 TCCTTCTTTTGGTTGCAAGGG 58.961 47.619 0.00 0.00 35.29 3.95
5022 8086 3.244981 GGGATAGAGTCTAGGACCATCGT 60.245 52.174 17.01 0.00 32.18 3.73
5046 8110 1.128188 AGACCTCCCCACACCTCAAC 61.128 60.000 0.00 0.00 0.00 3.18
5085 8149 4.545823 TGTTGAAAAACTGAGTTAGCCG 57.454 40.909 0.00 0.00 0.00 5.52
5119 8183 6.550854 CCTCCATTCTTTGGGCATCTTATTTA 59.449 38.462 0.00 0.00 46.45 1.40
5157 8221 7.120579 TGGCTCATCAGTTTAATTTCACGTTAT 59.879 33.333 0.00 0.00 0.00 1.89
5160 8224 4.759693 TGGCTCATCAGTTTAATTTCACGT 59.240 37.500 0.00 0.00 0.00 4.49
5162 8226 7.761409 TGTATGGCTCATCAGTTTAATTTCAC 58.239 34.615 0.00 0.00 0.00 3.18
5190 8254 8.891720 TGCTCAATGTTTATTTTTCAAAGCTTT 58.108 25.926 5.69 5.69 0.00 3.51
5196 8260 6.276847 ACGGTGCTCAATGTTTATTTTTCAA 58.723 32.000 0.00 0.00 0.00 2.69
5230 8294 0.940126 AAACTGAGCACGCTTGTCAG 59.060 50.000 15.98 15.98 42.91 3.51
5283 8354 7.971183 ATGTGAAGTTCTTCTTTTCCTCTAC 57.029 36.000 12.74 1.88 36.40 2.59
5285 8356 8.214364 AGTTATGTGAAGTTCTTCTTTTCCTCT 58.786 33.333 12.74 2.94 36.40 3.69
5286 8357 8.384607 AGTTATGTGAAGTTCTTCTTTTCCTC 57.615 34.615 12.74 1.16 36.40 3.71
5349 8420 2.539274 GCATTTGATCTCGAGAGCAGTC 59.461 50.000 29.88 18.34 41.80 3.51
5421 8509 3.813166 GGTGCTGACTGTTAAAGCTTACA 59.187 43.478 0.00 0.00 37.82 2.41
5426 8514 3.708563 TTTGGTGCTGACTGTTAAAGC 57.291 42.857 4.66 4.66 37.46 3.51
5435 8523 5.104374 CCACAAATATCATTTGGTGCTGAC 58.896 41.667 14.31 0.00 33.92 3.51
5480 8591 7.532682 TCCAAAACTAGCATTTTTGAAACAC 57.467 32.000 15.15 0.00 43.67 3.32
5503 8614 7.872113 ATAAATCAGGACTCCAAGATGTTTC 57.128 36.000 0.00 0.00 0.00 2.78
5507 8618 6.460676 GGCAAATAAATCAGGACTCCAAGATG 60.461 42.308 0.00 0.00 0.00 2.90
5510 8621 4.706476 TGGCAAATAAATCAGGACTCCAAG 59.294 41.667 0.00 0.00 0.00 3.61
5653 8764 2.742204 GCTCAAATACTCCCCGAGGAAC 60.742 54.545 0.00 0.00 43.40 3.62
5657 8768 1.269309 CGAGCTCAAATACTCCCCGAG 60.269 57.143 15.40 0.00 35.52 4.63
5662 8773 2.365617 TGATCCCGAGCTCAAATACTCC 59.634 50.000 15.40 0.00 0.00 3.85
5721 8832 6.206829 GTGGTATTATATTGTGGGCCTTCTTC 59.793 42.308 4.53 0.00 0.00 2.87
5767 8878 0.179020 TGTTGGGTGTGCTTCTCCAG 60.179 55.000 0.00 0.00 0.00 3.86
5798 8909 4.733542 CGGGCCGGTCCATTTGGT 62.734 66.667 27.89 0.00 36.21 3.67
5825 8936 1.917495 GGCCCGTATAACCCAGGTT 59.083 57.895 7.34 7.34 41.65 3.50
5840 8951 4.760047 AGCCATGACGTGTCGGCC 62.760 66.667 13.54 0.00 46.08 6.13
5859 8971 1.937899 GTGTACTTGTCGTGTTTGGCT 59.062 47.619 0.00 0.00 0.00 4.75
5860 8972 1.332552 CGTGTACTTGTCGTGTTTGGC 60.333 52.381 0.00 0.00 0.00 4.52
5864 8976 0.461135 ACCCGTGTACTTGTCGTGTT 59.539 50.000 0.00 0.00 0.00 3.32
5869 8981 1.076332 GCATGACCCGTGTACTTGTC 58.924 55.000 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.