Multiple sequence alignment - TraesCS5B01G191600

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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 TraesCS5B01G191600 chr5B 100.000 4265 0 0 1 4265 345050822 345055086 0.000000e+00 7877
1 TraesCS5B01G191600 chr5B 94.928 138 5 2 3353 3488 70794206 70794343 9.290000e-52 215
2 TraesCS5B01G191600 chr5D 90.367 2398 127 29 1 2337 302017955 302020309 0.000000e+00 3053
3 TraesCS5B01G191600 chr5D 93.574 1027 54 10 2335 3358 302020340 302021357 0.000000e+00 1520
4 TraesCS5B01G191600 chr5D 94.532 695 31 3 3568 4262 302021526 302022213 0.000000e+00 1066
5 TraesCS5B01G191600 chr5D 96.061 330 12 1 1534 1862 328392812 328392483 1.750000e-148 536
6 TraesCS5B01G191600 chr5D 93.548 93 5 1 3479 3570 302021353 302021445 2.070000e-28 137
7 TraesCS5B01G191600 chr5A 90.675 2327 130 27 81 2337 395836642 395834333 0.000000e+00 3014
8 TraesCS5B01G191600 chr5A 92.814 1002 53 13 2360 3358 395834245 395833260 0.000000e+00 1434
9 TraesCS5B01G191600 chr5A 85.145 276 21 1 3479 3754 395833264 395833009 9.090000e-67 265
10 TraesCS5B01G191600 chr6A 91.489 329 26 2 1534 1861 536911679 536912006 6.500000e-123 451
11 TraesCS5B01G191600 chr7D 94.545 165 9 0 1542 1706 55445958 55446122 5.470000e-64 255
12 TraesCS5B01G191600 chr3B 97.810 137 3 0 1570 1706 612294627 612294763 1.980000e-58 237
13 TraesCS5B01G191600 chr6B 95.683 139 5 1 3353 3491 207511030 207510893 5.550000e-54 222
14 TraesCS5B01G191600 chr6B 93.706 143 7 2 3341 3483 701355672 701355532 3.340000e-51 213
15 TraesCS5B01G191600 chr1A 96.970 132 4 0 3353 3484 486045770 486045901 5.550000e-54 222
16 TraesCS5B01G191600 chr2B 96.296 135 4 1 3350 3483 734000041 734000175 2.000000e-53 220
17 TraesCS5B01G191600 chr7A 94.964 139 7 0 3354 3492 504961061 504961199 7.180000e-53 219
18 TraesCS5B01G191600 chr7A 88.636 176 15 4 3314 3485 348209561 348209735 4.320000e-50 209
19 TraesCS5B01G191600 chr4B 91.772 158 8 5 3345 3501 55926040 55925887 9.290000e-52 215
20 TraesCS5B01G191600 chr3D 92.053 151 9 3 3340 3489 84562750 84562602 4.320000e-50 209


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 TraesCS5B01G191600 chr5B 345050822 345055086 4264 False 7877 7877 100.000000 1 4265 1 chr5B.!!$F2 4264
1 TraesCS5B01G191600 chr5D 302017955 302022213 4258 False 1444 3053 93.005250 1 4262 4 chr5D.!!$F1 4261
2 TraesCS5B01G191600 chr5A 395833009 395836642 3633 True 1571 3014 89.544667 81 3754 3 chr5A.!!$R1 3673

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
724 785 0.238289 CCATCGCCACACAACAACTC 59.762 55.0 0.00 0.0 0.0 3.01 F
1995 2098 0.097674 GCAAATCGACGCTGCTGAAT 59.902 50.0 7.72 0.0 33.2 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2355 2495 0.178813 AACTACCCCCTCCCAACCAT 60.179 55.0 0.00 0.00 0.00 3.55 R
3358 3531 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.0 13.64 4.95 46.06 4.20 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
28 30 5.138125 TGCATTCAGAGGTTCAATTTTCC 57.862 39.130 0.00 0.00 0.00 3.13
35 37 7.416964 TCAGAGGTTCAATTTTCCTTTTTGA 57.583 32.000 0.00 0.00 0.00 2.69
37 39 6.198966 CAGAGGTTCAATTTTCCTTTTTGACG 59.801 38.462 0.00 0.00 0.00 4.35
59 61 5.163824 ACGAAGTCACATGCAGTCATATTTG 60.164 40.000 0.00 0.00 29.74 2.32
60 62 5.571784 AAGTCACATGCAGTCATATTTGG 57.428 39.130 0.00 0.00 0.00 3.28
67 69 2.492881 TGCAGTCATATTTGGGCACAAG 59.507 45.455 0.00 0.00 37.97 3.16
76 78 2.813901 GGGCACAAGCTTTGCACA 59.186 55.556 24.87 0.00 43.35 4.57
77 79 1.368579 GGGCACAAGCTTTGCACAT 59.631 52.632 24.87 0.00 43.35 3.21
95 97 2.415168 ACATAACCGTGTGCAGAATTCG 59.585 45.455 0.00 0.00 0.00 3.34
193 202 0.810648 TGTCGCCAATGAATCAAGCC 59.189 50.000 0.00 0.00 0.00 4.35
285 294 7.330262 AGAATTTATACCAAACAGGCCAAATG 58.670 34.615 5.01 0.00 43.14 2.32
305 314 3.948126 TGGGGGATATGAATCTACACCA 58.052 45.455 0.00 0.00 32.29 4.17
306 315 4.512298 TGGGGGATATGAATCTACACCAT 58.488 43.478 0.00 0.00 32.29 3.55
307 316 5.670899 TGGGGGATATGAATCTACACCATA 58.329 41.667 0.00 0.00 32.29 2.74
308 317 6.279405 TGGGGGATATGAATCTACACCATAT 58.721 40.000 0.00 0.00 36.51 1.78
309 318 6.386927 TGGGGGATATGAATCTACACCATATC 59.613 42.308 0.00 0.00 43.92 1.63
401 441 5.665812 TGAATATAACAACCCTGAGCTACCT 59.334 40.000 0.00 0.00 0.00 3.08
402 442 5.810080 ATATAACAACCCTGAGCTACCTC 57.190 43.478 0.00 0.00 38.62 3.85
407 447 0.757188 ACCCTGAGCTACCTCGGATG 60.757 60.000 1.24 0.00 45.56 3.51
445 506 5.900425 TGTAATTTCACAAAGAGCAAAGCA 58.100 33.333 0.00 0.00 0.00 3.91
446 507 6.336566 TGTAATTTCACAAAGAGCAAAGCAA 58.663 32.000 0.00 0.00 0.00 3.91
447 508 6.985645 TGTAATTTCACAAAGAGCAAAGCAAT 59.014 30.769 0.00 0.00 0.00 3.56
448 509 6.535274 AATTTCACAAAGAGCAAAGCAATC 57.465 33.333 0.00 0.00 0.00 2.67
449 510 4.924305 TTCACAAAGAGCAAAGCAATCT 57.076 36.364 0.00 0.00 0.00 2.40
450 511 4.233123 TCACAAAGAGCAAAGCAATCTG 57.767 40.909 0.00 0.00 0.00 2.90
451 512 3.884693 TCACAAAGAGCAAAGCAATCTGA 59.115 39.130 0.00 0.00 0.00 3.27
452 513 4.521639 TCACAAAGAGCAAAGCAATCTGAT 59.478 37.500 0.00 0.00 0.00 2.90
453 514 5.706833 TCACAAAGAGCAAAGCAATCTGATA 59.293 36.000 0.00 0.00 0.00 2.15
454 515 5.798934 CACAAAGAGCAAAGCAATCTGATAC 59.201 40.000 0.00 0.00 0.00 2.24
455 516 5.709164 ACAAAGAGCAAAGCAATCTGATACT 59.291 36.000 0.00 0.00 0.00 2.12
456 517 6.881065 ACAAAGAGCAAAGCAATCTGATACTA 59.119 34.615 0.00 0.00 0.00 1.82
457 518 6.917217 AAGAGCAAAGCAATCTGATACTAC 57.083 37.500 0.00 0.00 0.00 2.73
458 519 6.232581 AGAGCAAAGCAATCTGATACTACT 57.767 37.500 0.00 0.00 0.00 2.57
459 520 7.353414 AGAGCAAAGCAATCTGATACTACTA 57.647 36.000 0.00 0.00 0.00 1.82
460 521 7.786030 AGAGCAAAGCAATCTGATACTACTAA 58.214 34.615 0.00 0.00 0.00 2.24
461 522 7.925483 AGAGCAAAGCAATCTGATACTACTAAG 59.075 37.037 0.00 0.00 0.00 2.18
481 542 7.822658 ACTAAGTAAGATCTAAGCCGATGATC 58.177 38.462 0.00 0.00 37.46 2.92
487 548 2.248248 TCTAAGCCGATGATCCCGATT 58.752 47.619 6.23 4.08 0.00 3.34
495 556 0.689623 ATGATCCCGATTCCTCCAGC 59.310 55.000 0.00 0.00 0.00 4.85
501 562 1.333636 CCGATTCCTCCAGCTCCACT 61.334 60.000 0.00 0.00 0.00 4.00
514 575 1.467734 GCTCCACTGCAATTGACTCAG 59.532 52.381 10.34 9.69 0.00 3.35
515 576 2.873245 GCTCCACTGCAATTGACTCAGA 60.873 50.000 10.34 0.00 0.00 3.27
517 578 2.634453 TCCACTGCAATTGACTCAGAGA 59.366 45.455 10.34 7.17 0.00 3.10
531 592 5.106515 TGACTCAGAGAACAATCGACTAGTG 60.107 44.000 3.79 0.00 0.00 2.74
713 774 3.834013 TTGGTCAACGCCATCGCCA 62.834 57.895 0.00 0.00 38.48 5.69
714 775 3.799755 GGTCAACGCCATCGCCAC 61.800 66.667 0.00 0.00 39.84 5.01
715 776 3.047280 GTCAACGCCATCGCCACA 61.047 61.111 0.00 0.00 39.84 4.17
716 777 3.047280 TCAACGCCATCGCCACAC 61.047 61.111 0.00 0.00 39.84 3.82
717 778 3.353029 CAACGCCATCGCCACACA 61.353 61.111 0.00 0.00 39.84 3.72
718 779 2.593148 AACGCCATCGCCACACAA 60.593 55.556 0.00 0.00 39.84 3.33
719 780 2.903547 AACGCCATCGCCACACAAC 61.904 57.895 0.00 0.00 39.84 3.32
720 781 3.353029 CGCCATCGCCACACAACA 61.353 61.111 0.00 0.00 0.00 3.33
721 782 2.902419 CGCCATCGCCACACAACAA 61.902 57.895 0.00 0.00 0.00 2.83
722 783 1.371635 GCCATCGCCACACAACAAC 60.372 57.895 0.00 0.00 0.00 3.32
723 784 1.795170 GCCATCGCCACACAACAACT 61.795 55.000 0.00 0.00 0.00 3.16
724 785 0.238289 CCATCGCCACACAACAACTC 59.762 55.000 0.00 0.00 0.00 3.01
745 806 0.393402 TCTGTAGAACCCTAGCGCGA 60.393 55.000 12.10 0.00 0.00 5.87
748 809 2.487532 TAGAACCCTAGCGCGAGGC 61.488 63.158 29.13 16.61 44.05 4.70
815 893 0.257328 TCGGAGCAGAGAGATGAGGT 59.743 55.000 0.00 0.00 0.00 3.85
816 894 1.110442 CGGAGCAGAGAGATGAGGTT 58.890 55.000 0.00 0.00 0.00 3.50
832 910 4.272489 TGAGGTTTTGAGATATGGGCTTG 58.728 43.478 0.00 0.00 0.00 4.01
841 919 2.687418 ATATGGGCTTGCCTGCTCGG 62.687 60.000 11.71 0.00 35.92 4.63
845 923 1.153168 GGCTTGCCTGCTCGGAATA 60.153 57.895 4.11 0.00 33.16 1.75
851 929 4.380531 CTTGCCTGCTCGGAATAATAAGA 58.619 43.478 0.00 0.00 33.16 2.10
853 931 4.318332 TGCCTGCTCGGAATAATAAGATG 58.682 43.478 0.00 0.00 33.16 2.90
854 932 3.686726 GCCTGCTCGGAATAATAAGATGG 59.313 47.826 0.00 0.00 33.16 3.51
855 933 4.256920 CCTGCTCGGAATAATAAGATGGG 58.743 47.826 0.00 0.00 33.16 4.00
856 934 4.256920 CTGCTCGGAATAATAAGATGGGG 58.743 47.826 0.00 0.00 0.00 4.96
861 939 3.092301 GGAATAATAAGATGGGGCCTGC 58.908 50.000 0.84 0.00 0.00 4.85
891 969 2.282603 GCCCGTTAAAGGCCCACA 60.283 61.111 0.00 0.00 45.16 4.17
898 976 1.749063 GTTAAAGGCCCACATGCTACC 59.251 52.381 0.00 0.00 0.00 3.18
930 1008 2.959465 AAGCCCAGCTTCTGTTAACT 57.041 45.000 7.22 0.00 46.77 2.24
931 1009 2.481289 AGCCCAGCTTCTGTTAACTC 57.519 50.000 7.22 0.00 33.89 3.01
1082 1173 1.304952 CCTCGTCTCCTCACCCTCT 59.695 63.158 0.00 0.00 0.00 3.69
1086 1177 1.324005 CGTCTCCTCACCCTCTTCCC 61.324 65.000 0.00 0.00 0.00 3.97
1089 1180 0.545309 CTCCTCACCCTCTTCCCACA 60.545 60.000 0.00 0.00 0.00 4.17
1102 1193 3.392947 TCTTCCCACACAACACATCCTAA 59.607 43.478 0.00 0.00 0.00 2.69
1106 1197 2.813754 CCACACAACACATCCTAACTGG 59.186 50.000 0.00 0.00 37.10 4.00
1653 1756 1.292541 GGACTTCGACGGCTCCTTT 59.707 57.895 0.00 0.00 0.00 3.11
1768 1871 1.367840 GTGGTCACCAAGCTCGACT 59.632 57.895 0.00 0.00 34.18 4.18
1992 2095 2.099062 GGCAAATCGACGCTGCTG 59.901 61.111 13.15 0.00 36.32 4.41
1995 2098 0.097674 GCAAATCGACGCTGCTGAAT 59.902 50.000 7.72 0.00 33.20 2.57
2106 2209 2.328099 CGTTCTTGGTGCTCAGGCC 61.328 63.158 0.00 0.00 37.74 5.19
2128 2231 1.095807 GCTGTTTGATACTCCGGGCC 61.096 60.000 0.00 0.00 0.00 5.80
2358 2498 8.537049 TCTTTTCATTAAGCAATTGTGAATGG 57.463 30.769 19.81 11.94 0.00 3.16
2359 2499 8.149647 TCTTTTCATTAAGCAATTGTGAATGGT 58.850 29.630 19.81 0.00 0.00 3.55
2362 2502 6.164876 TCATTAAGCAATTGTGAATGGTTGG 58.835 36.000 19.81 4.43 37.76 3.77
2363 2503 3.405823 AAGCAATTGTGAATGGTTGGG 57.594 42.857 7.40 0.00 36.05 4.12
2364 2504 2.607499 AGCAATTGTGAATGGTTGGGA 58.393 42.857 7.40 0.00 0.00 4.37
2365 2505 2.564062 AGCAATTGTGAATGGTTGGGAG 59.436 45.455 7.40 0.00 0.00 4.30
2376 2546 1.132135 TGGTTGGGAGGGGGTAGTTAA 60.132 52.381 0.00 0.00 0.00 2.01
2401 2571 9.541884 AATTCACCCTTTAAACAGTAACCATAT 57.458 29.630 0.00 0.00 0.00 1.78
2403 2573 8.943594 TCACCCTTTAAACAGTAACCATATTT 57.056 30.769 0.00 0.00 0.00 1.40
2455 2626 5.221904 TGTGTGATGATATACTGGATTGGGG 60.222 44.000 0.00 0.00 0.00 4.96
2460 2631 8.328758 GTGATGATATACTGGATTGGGGAATTA 58.671 37.037 0.00 0.00 0.00 1.40
2498 2670 7.654116 GTGCTTAGAAAGTTCAGTTCTTAGACT 59.346 37.037 4.79 0.00 34.96 3.24
2554 2726 7.539712 TCCGAAATGACATGAATAGTCTTTC 57.460 36.000 0.00 0.00 36.94 2.62
2567 2739 8.873215 TGAATAGTCTTTCGATAAGAATCACC 57.127 34.615 11.61 5.56 38.86 4.02
2645 2817 3.452627 GGCAGTCCATACATATAGGAGGG 59.547 52.174 0.00 0.00 30.78 4.30
2648 2820 5.519808 CAGTCCATACATATAGGAGGGCTA 58.480 45.833 0.00 0.00 28.48 3.93
2696 2868 8.533569 TGACTGTAGGATCAATCTATGTTACA 57.466 34.615 0.00 0.00 0.00 2.41
2777 2949 8.267183 TCTATGATGAAAGATCACTTTGGCTTA 58.733 33.333 0.00 0.00 44.97 3.09
2790 2962 3.433306 TTGGCTTACAACTGCAGGTAT 57.567 42.857 19.93 2.07 33.18 2.73
2791 2963 2.985896 TGGCTTACAACTGCAGGTATC 58.014 47.619 19.93 6.53 0.00 2.24
2792 2964 2.571653 TGGCTTACAACTGCAGGTATCT 59.428 45.455 19.93 0.00 0.00 1.98
2800 2972 6.155475 ACAACTGCAGGTATCTTCTATCTC 57.845 41.667 19.93 0.00 0.00 2.75
2880 3053 0.394216 TGGTGTGATATGTGCAGCCC 60.394 55.000 0.00 0.00 0.00 5.19
3006 3179 1.339727 GGTCTTGGCTGGTACGGAATT 60.340 52.381 0.00 0.00 36.31 2.17
3045 3218 6.735704 AGGCAGTATTAGGGTTATGGACATAT 59.264 38.462 0.00 0.00 0.00 1.78
3093 3266 1.565390 CCCTTGTCCATGAGAGGGCA 61.565 60.000 8.94 0.00 42.18 5.36
3185 3358 6.218746 AGCTGAAAGGCAATAAGAAAACAAG 58.781 36.000 0.00 0.00 34.17 3.16
3205 3378 1.399791 GCAAGAAGGAGATGAAAGCCG 59.600 52.381 0.00 0.00 0.00 5.52
3226 3399 5.178797 CCGGTTCACATTCTTCTGAAGTAT 58.821 41.667 16.43 10.18 35.44 2.12
3228 3401 5.004821 CGGTTCACATTCTTCTGAAGTATCG 59.995 44.000 16.43 7.89 35.44 2.92
3233 3406 6.071334 TCACATTCTTCTGAAGTATCGGAACT 60.071 38.462 16.43 0.00 44.22 3.01
3242 3415 6.015350 TCTGAAGTATCGGAACTTTCAGAACT 60.015 38.462 19.90 0.29 39.78 3.01
3339 3512 2.024414 ACTGTTGGCTGAGGTTTGAAC 58.976 47.619 0.00 0.00 0.00 3.18
3358 3531 6.791867 TGAACCACATAGAAGCATAGTACT 57.208 37.500 0.00 0.00 0.00 2.73
3359 3532 6.806751 TGAACCACATAGAAGCATAGTACTC 58.193 40.000 0.00 0.00 0.00 2.59
3360 3533 5.793030 ACCACATAGAAGCATAGTACTCC 57.207 43.478 0.00 0.00 0.00 3.85
3361 3534 4.589374 ACCACATAGAAGCATAGTACTCCC 59.411 45.833 0.00 0.00 0.00 4.30
3362 3535 4.835615 CCACATAGAAGCATAGTACTCCCT 59.164 45.833 0.00 0.00 0.00 4.20
3363 3536 5.047660 CCACATAGAAGCATAGTACTCCCTC 60.048 48.000 0.00 0.00 0.00 4.30
3364 3537 5.047660 CACATAGAAGCATAGTACTCCCTCC 60.048 48.000 0.00 0.00 0.00 4.30
3365 3538 2.588620 AGAAGCATAGTACTCCCTCCG 58.411 52.381 0.00 0.00 0.00 4.63
3366 3539 2.091775 AGAAGCATAGTACTCCCTCCGT 60.092 50.000 0.00 0.00 0.00 4.69
3367 3540 1.984066 AGCATAGTACTCCCTCCGTC 58.016 55.000 0.00 0.00 0.00 4.79
3368 3541 0.960286 GCATAGTACTCCCTCCGTCC 59.040 60.000 0.00 0.00 0.00 4.79
3369 3542 1.236628 CATAGTACTCCCTCCGTCCG 58.763 60.000 0.00 0.00 0.00 4.79
3370 3543 0.110104 ATAGTACTCCCTCCGTCCGG 59.890 60.000 0.00 0.00 0.00 5.14
3371 3544 0.982852 TAGTACTCCCTCCGTCCGGA 60.983 60.000 0.00 0.00 42.90 5.14
3372 3545 1.379044 GTACTCCCTCCGTCCGGAA 60.379 63.158 5.23 0.00 44.66 4.30
3373 3546 0.967380 GTACTCCCTCCGTCCGGAAA 60.967 60.000 5.23 0.00 44.66 3.13
3374 3547 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
3375 3548 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
3376 3549 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
3377 3550 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
3378 3551 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
3379 3552 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
3380 3553 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
3381 3554 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
3382 3555 1.894466 TCCGTCCGGAAATACTTGTCA 59.106 47.619 5.23 0.00 42.05 3.58
3383 3556 2.498481 TCCGTCCGGAAATACTTGTCAT 59.502 45.455 5.23 0.00 42.05 3.06
3384 3557 2.864343 CCGTCCGGAAATACTTGTCATC 59.136 50.000 5.23 0.00 37.50 2.92
3385 3558 3.517602 CGTCCGGAAATACTTGTCATCA 58.482 45.455 5.23 0.00 0.00 3.07
3386 3559 3.930229 CGTCCGGAAATACTTGTCATCAA 59.070 43.478 5.23 0.00 0.00 2.57
3387 3560 4.390603 CGTCCGGAAATACTTGTCATCAAA 59.609 41.667 5.23 0.00 32.87 2.69
3388 3561 5.106869 CGTCCGGAAATACTTGTCATCAAAA 60.107 40.000 5.23 0.00 32.87 2.44
3389 3562 6.403200 CGTCCGGAAATACTTGTCATCAAAAT 60.403 38.462 5.23 0.00 32.87 1.82
3390 3563 6.747280 GTCCGGAAATACTTGTCATCAAAATG 59.253 38.462 5.23 0.00 32.87 2.32
3391 3564 6.035843 CCGGAAATACTTGTCATCAAAATGG 58.964 40.000 0.00 0.00 33.42 3.16
3392 3565 6.127758 CCGGAAATACTTGTCATCAAAATGGA 60.128 38.462 0.00 0.00 33.42 3.41
3393 3566 7.416664 CCGGAAATACTTGTCATCAAAATGGAT 60.417 37.037 0.00 0.00 33.42 3.41
3394 3567 8.620416 CGGAAATACTTGTCATCAAAATGGATA 58.380 33.333 0.00 0.00 33.42 2.59
3401 3574 8.096414 ACTTGTCATCAAAATGGATAAAAAGGG 58.904 33.333 0.00 0.00 33.42 3.95
3402 3575 7.789202 TGTCATCAAAATGGATAAAAAGGGA 57.211 32.000 0.00 0.00 33.42 4.20
3403 3576 8.378115 TGTCATCAAAATGGATAAAAAGGGAT 57.622 30.769 0.00 0.00 33.42 3.85
3404 3577 8.259411 TGTCATCAAAATGGATAAAAAGGGATG 58.741 33.333 0.00 0.00 33.42 3.51
3405 3578 7.712205 GTCATCAAAATGGATAAAAAGGGATGG 59.288 37.037 0.00 0.00 33.42 3.51
3406 3579 7.622878 TCATCAAAATGGATAAAAAGGGATGGA 59.377 33.333 0.00 0.00 33.42 3.41
3407 3580 7.993349 TCAAAATGGATAAAAAGGGATGGAT 57.007 32.000 0.00 0.00 0.00 3.41
3408 3581 8.021898 TCAAAATGGATAAAAAGGGATGGATC 57.978 34.615 0.00 0.00 0.00 3.36
3409 3582 7.845800 TCAAAATGGATAAAAAGGGATGGATCT 59.154 33.333 0.00 0.00 0.00 2.75
3410 3583 9.146586 CAAAATGGATAAAAAGGGATGGATCTA 57.853 33.333 0.00 0.00 0.00 1.98
3411 3584 8.946797 AAATGGATAAAAAGGGATGGATCTAG 57.053 34.615 0.00 0.00 0.00 2.43
3412 3585 7.895144 ATGGATAAAAAGGGATGGATCTAGA 57.105 36.000 0.00 0.00 0.00 2.43
3413 3586 7.079451 TGGATAAAAAGGGATGGATCTAGAC 57.921 40.000 0.00 0.00 0.00 2.59
3414 3587 6.166982 GGATAAAAAGGGATGGATCTAGACG 58.833 44.000 0.00 0.00 0.00 4.18
3415 3588 6.239629 GGATAAAAAGGGATGGATCTAGACGT 60.240 42.308 0.00 0.00 0.00 4.34
3416 3589 7.039223 GGATAAAAAGGGATGGATCTAGACGTA 60.039 40.741 0.00 0.00 0.00 3.57
3417 3590 6.749036 AAAAAGGGATGGATCTAGACGTAT 57.251 37.500 0.00 0.00 0.00 3.06
3418 3591 6.749036 AAAAGGGATGGATCTAGACGTATT 57.251 37.500 0.00 0.00 0.00 1.89
3419 3592 6.749036 AAAGGGATGGATCTAGACGTATTT 57.251 37.500 0.00 0.00 0.00 1.40
3420 3593 6.749036 AAGGGATGGATCTAGACGTATTTT 57.251 37.500 0.00 0.00 0.00 1.82
3421 3594 7.850935 AAGGGATGGATCTAGACGTATTTTA 57.149 36.000 0.00 0.00 0.00 1.52
3422 3595 7.469537 AGGGATGGATCTAGACGTATTTTAG 57.530 40.000 0.00 0.00 0.00 1.85
3423 3596 7.011382 AGGGATGGATCTAGACGTATTTTAGT 58.989 38.462 0.00 0.00 0.00 2.24
3424 3597 7.509659 AGGGATGGATCTAGACGTATTTTAGTT 59.490 37.037 0.00 0.00 0.00 2.24
3425 3598 7.813627 GGGATGGATCTAGACGTATTTTAGTTC 59.186 40.741 0.00 0.00 0.00 3.01
3426 3599 8.578151 GGATGGATCTAGACGTATTTTAGTTCT 58.422 37.037 0.00 0.00 0.00 3.01
3429 3602 9.842775 TGGATCTAGACGTATTTTAGTTCTAGA 57.157 33.333 8.64 8.64 38.94 2.43
3472 3645 7.922505 TTTTGATGACAAGTATTTTTGGACG 57.077 32.000 0.00 0.00 37.32 4.79
3473 3646 5.621197 TGATGACAAGTATTTTTGGACGG 57.379 39.130 0.00 0.00 32.32 4.79
3474 3647 5.309638 TGATGACAAGTATTTTTGGACGGA 58.690 37.500 0.00 0.00 32.32 4.69
3475 3648 5.411361 TGATGACAAGTATTTTTGGACGGAG 59.589 40.000 0.00 0.00 32.32 4.63
3476 3649 4.069304 TGACAAGTATTTTTGGACGGAGG 58.931 43.478 0.00 0.00 32.32 4.30
3477 3650 3.418047 ACAAGTATTTTTGGACGGAGGG 58.582 45.455 0.00 0.00 32.32 4.30
3478 3651 3.073356 ACAAGTATTTTTGGACGGAGGGA 59.927 43.478 0.00 0.00 32.32 4.20
3479 3652 3.629142 AGTATTTTTGGACGGAGGGAG 57.371 47.619 0.00 0.00 0.00 4.30
3480 3653 2.910977 AGTATTTTTGGACGGAGGGAGT 59.089 45.455 0.00 0.00 0.00 3.85
3481 3654 4.098894 AGTATTTTTGGACGGAGGGAGTA 58.901 43.478 0.00 0.00 0.00 2.59
3482 3655 2.845363 TTTTTGGACGGAGGGAGTAC 57.155 50.000 0.00 0.00 0.00 2.73
3497 3670 5.325239 AGGGAGTACAATTTAAGCTTGCTT 58.675 37.500 9.86 12.65 0.00 3.91
3619 3876 7.334421 TGAATCTTTGTTAGTATGCTTGACTCC 59.666 37.037 0.00 0.00 0.00 3.85
3621 3878 6.769512 TCTTTGTTAGTATGCTTGACTCCTT 58.230 36.000 0.00 0.00 0.00 3.36
3754 4011 7.752239 GTCAGTTTTTACATCTGAATCATGTGG 59.248 37.037 0.14 0.00 39.42 4.17
3897 4154 3.321497 CCTTCACACAGTAACAGCTCTC 58.679 50.000 0.00 0.00 0.00 3.20
3898 4155 3.243873 CCTTCACACAGTAACAGCTCTCA 60.244 47.826 0.00 0.00 0.00 3.27
3931 4188 6.814506 AGAACATCTCACTGAATCCTTTTG 57.185 37.500 0.00 0.00 0.00 2.44
3939 4196 2.227388 ACTGAATCCTTTTGCTGCTTCG 59.773 45.455 0.00 0.00 0.00 3.79
3946 4203 1.737355 TTTTGCTGCTTCGGCTTGCT 61.737 50.000 0.00 0.00 42.37 3.91
3959 4216 1.613437 GGCTTGCTTTTTGCTGGACTA 59.387 47.619 0.00 0.00 43.37 2.59
3978 4235 8.611654 TGGACTAGTTATGTAAGGTTTTTGTC 57.388 34.615 0.00 0.00 0.00 3.18
4016 4273 5.168526 TGTGACCTTCGTTTCTTGAAATG 57.831 39.130 8.55 8.55 0.00 2.32
4025 4282 6.249035 TCGTTTCTTGAAATGGTACCATTC 57.751 37.500 34.67 26.84 44.86 2.67
4070 4327 6.315891 CCAAAAACACAACATGATGTTCCTTT 59.684 34.615 8.03 3.57 38.77 3.11
4093 4350 5.705609 TGCATAAAAACTGGAGAGGTTTC 57.294 39.130 0.00 0.00 38.21 2.78
4101 4358 6.396829 AAACTGGAGAGGTTTCAAGAAATG 57.603 37.500 0.00 0.00 32.26 2.32
4107 4364 5.130292 AGAGGTTTCAAGAAATGTGCATG 57.870 39.130 0.00 0.00 32.36 4.06
4135 4392 2.486472 AATGGTCTCACAGAAGCAGG 57.514 50.000 0.00 0.00 0.00 4.85
4139 4396 0.250038 GTCTCACAGAAGCAGGCACA 60.250 55.000 0.00 0.00 0.00 4.57
4178 4435 9.918630 ATTGACAAGTTTTCTGGATGATTAAAG 57.081 29.630 0.00 0.00 0.00 1.85
4205 4462 1.511850 TGTGAACATCTGTGAAGCCG 58.488 50.000 0.00 0.00 0.00 5.52
4209 4466 3.003275 GTGAACATCTGTGAAGCCGAAAA 59.997 43.478 0.00 0.00 0.00 2.29
4216 4473 5.255710 TCTGTGAAGCCGAAAATTTCAAA 57.744 34.783 6.53 0.00 33.10 2.69
4217 4474 5.655488 TCTGTGAAGCCGAAAATTTCAAAA 58.345 33.333 6.53 0.00 33.10 2.44
4218 4475 6.102663 TCTGTGAAGCCGAAAATTTCAAAAA 58.897 32.000 6.53 0.00 33.10 1.94
4262 4519 2.015587 CCAAAGCATCTCTGAAGCCTC 58.984 52.381 0.00 0.00 0.00 4.70
4263 4520 2.617276 CCAAAGCATCTCTGAAGCCTCA 60.617 50.000 0.00 0.00 0.00 3.86
4264 4521 3.079578 CAAAGCATCTCTGAAGCCTCAA 58.920 45.455 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 24 6.202516 TGTGACTTCGTCAAAAAGGAAAAT 57.797 33.333 0.00 0.00 44.49 1.82
28 30 3.951306 TGCATGTGACTTCGTCAAAAAG 58.049 40.909 0.00 0.00 44.49 2.27
35 37 2.462456 ATGACTGCATGTGACTTCGT 57.538 45.000 0.00 0.00 32.31 3.85
37 39 5.449588 CCCAAATATGACTGCATGTGACTTC 60.450 44.000 0.00 0.00 35.94 3.01
51 53 3.617045 GCAAAGCTTGTGCCCAAATATGA 60.617 43.478 17.56 0.00 40.80 2.15
59 61 0.602562 TATGTGCAAAGCTTGTGCCC 59.397 50.000 22.41 15.71 41.49 5.36
60 62 2.061028 GTTATGTGCAAAGCTTGTGCC 58.939 47.619 22.41 16.55 41.49 5.01
67 69 1.685302 CACACGGTTATGTGCAAAGC 58.315 50.000 0.00 0.00 43.29 3.51
76 78 2.006888 CCGAATTCTGCACACGGTTAT 58.993 47.619 3.52 0.00 38.97 1.89
77 79 1.434555 CCGAATTCTGCACACGGTTA 58.565 50.000 3.52 0.00 38.97 2.85
95 97 6.342111 CAGTCTCAACTTTTATAGAGGACCC 58.658 44.000 0.00 0.00 31.71 4.46
221 230 8.642432 TCTAGTACTGGAAATTATCATCAGTGG 58.358 37.037 6.45 0.00 38.84 4.00
275 284 1.147608 TCATATCCCCCATTTGGCCTG 59.852 52.381 3.32 0.00 0.00 4.85
280 289 5.711976 GGTGTAGATTCATATCCCCCATTTG 59.288 44.000 0.00 0.00 0.00 2.32
285 294 6.617371 AGATATGGTGTAGATTCATATCCCCC 59.383 42.308 14.95 0.00 45.13 5.40
305 314 3.243035 GCATCGCAGCGAGAGATAGATAT 60.243 47.826 24.08 0.00 39.91 1.63
306 315 2.096657 GCATCGCAGCGAGAGATAGATA 59.903 50.000 24.08 0.00 39.91 1.98
307 316 1.135431 GCATCGCAGCGAGAGATAGAT 60.135 52.381 24.08 0.00 39.91 1.98
308 317 0.239613 GCATCGCAGCGAGAGATAGA 59.760 55.000 24.08 0.00 39.91 1.98
309 318 0.039708 TGCATCGCAGCGAGAGATAG 60.040 55.000 24.08 9.35 39.91 2.08
350 374 7.926555 ACGGATTGAAAAATCATAGATCTACGT 59.073 33.333 4.10 2.20 0.00 3.57
351 375 8.299262 ACGGATTGAAAAATCATAGATCTACG 57.701 34.615 4.10 0.00 0.00 3.51
352 376 9.869844 CAACGGATTGAAAAATCATAGATCTAC 57.130 33.333 4.10 0.00 38.15 2.59
354 378 8.737168 TCAACGGATTGAAAAATCATAGATCT 57.263 30.769 0.00 0.00 41.99 2.75
373 409 4.035208 GCTCAGGGTTGTTATATTCAACGG 59.965 45.833 13.46 8.48 43.93 4.44
389 425 0.468214 TCATCCGAGGTAGCTCAGGG 60.468 60.000 21.17 14.80 0.00 4.45
401 441 5.917462 ACAATATGATGTGTTCTCATCCGA 58.083 37.500 10.84 2.09 42.24 4.55
402 442 7.713764 TTACAATATGATGTGTTCTCATCCG 57.286 36.000 10.84 0.00 42.24 4.18
449 510 9.217278 CGGCTTAGATCTTACTTAGTAGTATCA 57.783 37.037 0.00 3.38 36.76 2.15
450 511 9.434420 TCGGCTTAGATCTTACTTAGTAGTATC 57.566 37.037 0.00 7.53 36.76 2.24
451 512 9.962809 ATCGGCTTAGATCTTACTTAGTAGTAT 57.037 33.333 0.00 0.00 36.76 2.12
452 513 9.217278 CATCGGCTTAGATCTTACTTAGTAGTA 57.783 37.037 0.00 0.00 35.78 1.82
453 514 7.937942 TCATCGGCTTAGATCTTACTTAGTAGT 59.062 37.037 0.00 0.00 38.44 2.73
454 515 8.325421 TCATCGGCTTAGATCTTACTTAGTAG 57.675 38.462 0.00 0.00 0.00 2.57
455 516 8.865420 ATCATCGGCTTAGATCTTACTTAGTA 57.135 34.615 0.00 0.00 0.00 1.82
456 517 7.094118 GGATCATCGGCTTAGATCTTACTTAGT 60.094 40.741 0.00 0.00 38.51 2.24
457 518 7.254852 GGATCATCGGCTTAGATCTTACTTAG 58.745 42.308 0.00 0.00 38.51 2.18
458 519 6.153000 GGGATCATCGGCTTAGATCTTACTTA 59.847 42.308 0.00 0.00 38.51 2.24
459 520 5.046950 GGGATCATCGGCTTAGATCTTACTT 60.047 44.000 0.00 0.00 38.51 2.24
460 521 4.464597 GGGATCATCGGCTTAGATCTTACT 59.535 45.833 0.00 0.00 38.51 2.24
461 522 4.675671 CGGGATCATCGGCTTAGATCTTAC 60.676 50.000 0.00 0.00 38.51 2.34
481 542 2.066393 TGGAGCTGGAGGAATCGGG 61.066 63.158 0.00 0.00 0.00 5.14
487 548 1.203441 ATTGCAGTGGAGCTGGAGGA 61.203 55.000 0.00 0.00 46.16 3.71
495 556 3.001414 CTCTGAGTCAATTGCAGTGGAG 58.999 50.000 0.00 2.34 0.00 3.86
501 562 4.152938 CGATTGTTCTCTGAGTCAATTGCA 59.847 41.667 21.32 0.00 31.87 4.08
514 575 3.061429 GCTTGCACTAGTCGATTGTTCTC 59.939 47.826 0.00 0.00 0.00 2.87
515 576 2.996621 GCTTGCACTAGTCGATTGTTCT 59.003 45.455 0.00 0.00 0.00 3.01
517 578 2.766313 TGCTTGCACTAGTCGATTGTT 58.234 42.857 0.00 0.00 0.00 2.83
548 609 2.202440 CACCACGTACGCTCTCCG 60.202 66.667 16.72 0.00 44.21 4.63
570 631 2.043852 GGCTCGAGGAGGAGTCCA 60.044 66.667 15.58 0.00 46.80 4.02
713 774 4.443034 GGTTCTACAGAGGAGTTGTTGTGT 60.443 45.833 0.00 0.00 0.00 3.72
714 775 4.058817 GGTTCTACAGAGGAGTTGTTGTG 58.941 47.826 0.00 0.00 0.00 3.33
715 776 3.071167 GGGTTCTACAGAGGAGTTGTTGT 59.929 47.826 0.00 0.00 0.00 3.32
716 777 3.325135 AGGGTTCTACAGAGGAGTTGTTG 59.675 47.826 0.00 0.00 0.00 3.33
717 778 3.588569 AGGGTTCTACAGAGGAGTTGTT 58.411 45.455 0.00 0.00 0.00 2.83
718 779 3.261818 AGGGTTCTACAGAGGAGTTGT 57.738 47.619 0.00 0.00 0.00 3.32
719 780 3.131400 GCTAGGGTTCTACAGAGGAGTTG 59.869 52.174 0.00 0.00 0.00 3.16
720 781 3.367321 GCTAGGGTTCTACAGAGGAGTT 58.633 50.000 0.00 0.00 0.00 3.01
721 782 2.684334 CGCTAGGGTTCTACAGAGGAGT 60.684 54.545 0.00 0.00 0.00 3.85
722 783 1.950909 CGCTAGGGTTCTACAGAGGAG 59.049 57.143 0.00 0.00 0.00 3.69
723 784 2.022754 GCGCTAGGGTTCTACAGAGGA 61.023 57.143 8.77 0.00 0.00 3.71
724 785 0.386113 GCGCTAGGGTTCTACAGAGG 59.614 60.000 8.77 0.00 0.00 3.69
815 893 3.025978 CAGGCAAGCCCATATCTCAAAA 58.974 45.455 7.62 0.00 36.58 2.44
816 894 2.658285 CAGGCAAGCCCATATCTCAAA 58.342 47.619 7.62 0.00 36.58 2.69
832 910 3.686726 CCATCTTATTATTCCGAGCAGGC 59.313 47.826 0.00 0.00 40.77 4.85
841 919 2.749621 CGCAGGCCCCATCTTATTATTC 59.250 50.000 0.00 0.00 0.00 1.75
842 920 2.795329 CGCAGGCCCCATCTTATTATT 58.205 47.619 0.00 0.00 0.00 1.40
845 923 1.529244 GCGCAGGCCCCATCTTATT 60.529 57.895 0.30 0.00 0.00 1.40
891 969 1.279496 TCAGCCTTGTGAGGTAGCAT 58.721 50.000 0.00 0.00 45.44 3.79
929 1007 3.522731 CGTCTCAGCGGGGAGGAG 61.523 72.222 0.00 0.00 35.58 3.69
930 1008 4.361971 ACGTCTCAGCGGGGAGGA 62.362 66.667 13.47 0.00 35.58 3.71
931 1009 3.827898 GACGTCTCAGCGGGGAGG 61.828 72.222 8.70 4.81 35.58 4.30
1032 1123 4.598894 CGGAGGAGGCAGCGGATG 62.599 72.222 0.00 0.00 0.00 3.51
1064 1155 0.323908 AAGAGGGTGAGGAGACGAGG 60.324 60.000 0.00 0.00 0.00 4.63
1071 1162 0.836400 GTGTGGGAAGAGGGTGAGGA 60.836 60.000 0.00 0.00 0.00 3.71
1082 1173 3.137544 AGTTAGGATGTGTTGTGTGGGAA 59.862 43.478 0.00 0.00 0.00 3.97
1086 1177 2.226437 GCCAGTTAGGATGTGTTGTGTG 59.774 50.000 0.00 0.00 41.22 3.82
1089 1180 2.290323 GGAGCCAGTTAGGATGTGTTGT 60.290 50.000 0.00 0.00 41.22 3.32
1102 1193 1.681229 TTAGGGATTTGGGAGCCAGT 58.319 50.000 0.00 0.00 33.81 4.00
1106 1197 1.288037 AGGGTTTAGGGATTTGGGAGC 59.712 52.381 0.00 0.00 0.00 4.70
1275 1378 0.035056 ATGGGAGGTTGAAGAAGCCG 60.035 55.000 0.00 0.00 0.00 5.52
1365 1468 1.746991 GAGGAGCCCGCTTTTCAGG 60.747 63.158 0.00 0.00 0.00 3.86
1992 2095 1.226773 GCACCGAGCAATGGCATTC 60.227 57.895 10.36 5.70 44.61 2.67
2085 2188 1.597854 CTGAGCACCAAGAACGCCA 60.598 57.895 0.00 0.00 0.00 5.69
2106 2209 2.009774 CCCGGAGTATCAAACAGCTTG 58.990 52.381 0.73 0.00 36.25 4.01
2128 2231 0.322277 AGCTGGTGTCCATGAAGCAG 60.322 55.000 14.25 14.25 30.82 4.24
2293 2396 1.229428 TGAGGAAACAAGCAGCGAAG 58.771 50.000 0.00 0.00 0.00 3.79
2296 2399 1.398390 GGTATGAGGAAACAAGCAGCG 59.602 52.381 0.00 0.00 0.00 5.18
2297 2400 1.745653 GGGTATGAGGAAACAAGCAGC 59.254 52.381 0.00 0.00 0.00 5.25
2355 2495 0.178813 AACTACCCCCTCCCAACCAT 60.179 55.000 0.00 0.00 0.00 3.55
2357 2497 1.672529 TTAACTACCCCCTCCCAACC 58.327 55.000 0.00 0.00 0.00 3.77
2358 2498 3.267551 TGAATTAACTACCCCCTCCCAAC 59.732 47.826 0.00 0.00 0.00 3.77
2359 2499 3.267551 GTGAATTAACTACCCCCTCCCAA 59.732 47.826 0.00 0.00 0.00 4.12
2362 2502 2.174210 GGGTGAATTAACTACCCCCTCC 59.826 54.545 11.00 0.00 46.74 4.30
2363 2503 3.572632 GGGTGAATTAACTACCCCCTC 57.427 52.381 11.00 0.00 46.74 4.30
2376 2546 9.541884 AATATGGTTACTGTTTAAAGGGTGAAT 57.458 29.630 0.00 0.00 0.00 2.57
2401 2571 8.234546 GTCAACTTCAGTTTCAGACTAACAAAA 58.765 33.333 0.00 0.00 36.65 2.44
2403 2573 6.876789 TGTCAACTTCAGTTTCAGACTAACAA 59.123 34.615 9.04 0.00 36.65 2.83
2567 2739 9.653287 TTAGAAATATAAGAACCTGTCACACAG 57.347 33.333 0.00 0.00 45.53 3.66
2605 2777 1.821666 GCCCTGCCTGAAAAGGTTGTA 60.822 52.381 0.00 0.00 0.00 2.41
2645 2817 2.176273 CACATCCAGGCGCACTAGC 61.176 63.158 10.83 0.00 37.42 3.42
2648 2820 2.809861 CTTCCACATCCAGGCGCACT 62.810 60.000 10.83 0.02 0.00 4.40
2696 2868 1.331214 CAAGTGGTGATGCCCAAACT 58.669 50.000 0.00 0.00 35.92 2.66
2777 2949 5.658634 TGAGATAGAAGATACCTGCAGTTGT 59.341 40.000 13.81 6.92 0.00 3.32
2836 3009 9.013490 CAAGCAGCAAGTTATTTTATGATGTAC 57.987 33.333 0.00 0.00 32.13 2.90
2880 3053 2.040178 ACTCGTTTCTGGCCTATAGGG 58.960 52.381 20.58 4.07 35.18 3.53
3006 3179 1.845627 CTGCCTCTCCTTTCAGCCCA 61.846 60.000 0.00 0.00 0.00 5.36
3045 3218 2.513753 GGGACAACATCAACACCATCA 58.486 47.619 0.00 0.00 0.00 3.07
3093 3266 6.660949 AGAATCCTGTTTCCTCAAAAATCGAT 59.339 34.615 0.00 0.00 0.00 3.59
3185 3358 1.399791 CGGCTTTCATCTCCTTCTTGC 59.600 52.381 0.00 0.00 0.00 4.01
3205 3378 5.292101 CCGATACTTCAGAAGAATGTGAACC 59.708 44.000 17.56 0.00 34.22 3.62
3226 3399 3.194005 AGCAAGTTCTGAAAGTTCCGA 57.806 42.857 0.00 0.00 33.76 4.55
3228 3401 3.186613 CCGTAGCAAGTTCTGAAAGTTCC 59.813 47.826 0.00 0.00 33.76 3.62
3233 3406 3.462483 TGACCGTAGCAAGTTCTGAAA 57.538 42.857 0.00 0.00 0.00 2.69
3242 3415 3.132111 TCAAGCATCTATGACCGTAGCAA 59.868 43.478 0.00 0.00 0.00 3.91
3339 3512 4.835615 AGGGAGTACTATGCTTCTATGTGG 59.164 45.833 0.00 0.00 0.00 4.17
3358 3531 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
3359 3532 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
3360 3533 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
3361 3534 2.094390 TGACAAGTATTTCCGGACGGAG 60.094 50.000 13.64 3.15 46.06 4.63
3362 3535 1.894466 TGACAAGTATTTCCGGACGGA 59.106 47.619 1.83 9.76 43.52 4.69
3363 3536 2.373540 TGACAAGTATTTCCGGACGG 57.626 50.000 1.83 3.96 0.00 4.79
3364 3537 3.517602 TGATGACAAGTATTTCCGGACG 58.482 45.455 1.83 0.00 0.00 4.79
3365 3538 5.873179 TTTGATGACAAGTATTTCCGGAC 57.127 39.130 1.83 0.00 37.32 4.79
3366 3539 6.127758 CCATTTTGATGACAAGTATTTCCGGA 60.128 38.462 0.00 0.00 37.32 5.14
3367 3540 6.035843 CCATTTTGATGACAAGTATTTCCGG 58.964 40.000 0.00 0.00 37.32 5.14
3368 3541 6.851609 TCCATTTTGATGACAAGTATTTCCG 58.148 36.000 0.00 0.00 37.32 4.30
3375 3548 8.096414 CCCTTTTTATCCATTTTGATGACAAGT 58.904 33.333 0.00 0.00 37.32 3.16
3376 3549 8.313292 TCCCTTTTTATCCATTTTGATGACAAG 58.687 33.333 0.00 0.00 37.32 3.16
3377 3550 8.200024 TCCCTTTTTATCCATTTTGATGACAA 57.800 30.769 0.00 0.00 0.00 3.18
3378 3551 7.789202 TCCCTTTTTATCCATTTTGATGACA 57.211 32.000 0.00 0.00 0.00 3.58
3379 3552 7.712205 CCATCCCTTTTTATCCATTTTGATGAC 59.288 37.037 0.00 0.00 0.00 3.06
3380 3553 7.622878 TCCATCCCTTTTTATCCATTTTGATGA 59.377 33.333 0.00 0.00 0.00 2.92
3381 3554 7.794041 TCCATCCCTTTTTATCCATTTTGATG 58.206 34.615 0.00 0.00 0.00 3.07
3382 3555 7.993349 TCCATCCCTTTTTATCCATTTTGAT 57.007 32.000 0.00 0.00 0.00 2.57
3383 3556 7.845800 AGATCCATCCCTTTTTATCCATTTTGA 59.154 33.333 0.00 0.00 0.00 2.69
3384 3557 8.026396 AGATCCATCCCTTTTTATCCATTTTG 57.974 34.615 0.00 0.00 0.00 2.44
3385 3558 9.372189 CTAGATCCATCCCTTTTTATCCATTTT 57.628 33.333 0.00 0.00 0.00 1.82
3386 3559 8.736675 TCTAGATCCATCCCTTTTTATCCATTT 58.263 33.333 0.00 0.00 0.00 2.32
3387 3560 8.166726 GTCTAGATCCATCCCTTTTTATCCATT 58.833 37.037 0.00 0.00 0.00 3.16
3388 3561 7.527868 CGTCTAGATCCATCCCTTTTTATCCAT 60.528 40.741 0.00 0.00 0.00 3.41
3389 3562 6.239600 CGTCTAGATCCATCCCTTTTTATCCA 60.240 42.308 0.00 0.00 0.00 3.41
3390 3563 6.166982 CGTCTAGATCCATCCCTTTTTATCC 58.833 44.000 0.00 0.00 0.00 2.59
3391 3564 6.760291 ACGTCTAGATCCATCCCTTTTTATC 58.240 40.000 0.00 0.00 0.00 1.75
3392 3565 6.749036 ACGTCTAGATCCATCCCTTTTTAT 57.251 37.500 0.00 0.00 0.00 1.40
3393 3566 7.850935 ATACGTCTAGATCCATCCCTTTTTA 57.149 36.000 0.00 0.00 0.00 1.52
3394 3567 6.749036 ATACGTCTAGATCCATCCCTTTTT 57.251 37.500 0.00 0.00 0.00 1.94
3395 3568 6.749036 AATACGTCTAGATCCATCCCTTTT 57.251 37.500 0.00 0.00 0.00 2.27
3396 3569 6.749036 AAATACGTCTAGATCCATCCCTTT 57.251 37.500 0.00 0.00 0.00 3.11
3397 3570 6.749036 AAAATACGTCTAGATCCATCCCTT 57.251 37.500 0.00 0.00 0.00 3.95
3398 3571 7.011382 ACTAAAATACGTCTAGATCCATCCCT 58.989 38.462 0.00 0.00 0.00 4.20
3399 3572 7.229581 ACTAAAATACGTCTAGATCCATCCC 57.770 40.000 0.00 0.00 0.00 3.85
3400 3573 8.578151 AGAACTAAAATACGTCTAGATCCATCC 58.422 37.037 0.00 0.00 0.00 3.51
3403 3576 9.842775 TCTAGAACTAAAATACGTCTAGATCCA 57.157 33.333 0.00 0.00 32.48 3.41
3446 3619 9.619316 CGTCCAAAAATACTTGTCATCAAAATA 57.381 29.630 0.00 0.00 32.87 1.40
3447 3620 7.598493 CCGTCCAAAAATACTTGTCATCAAAAT 59.402 33.333 0.00 0.00 32.87 1.82
3448 3621 6.920758 CCGTCCAAAAATACTTGTCATCAAAA 59.079 34.615 0.00 0.00 32.87 2.44
3449 3622 6.263392 TCCGTCCAAAAATACTTGTCATCAAA 59.737 34.615 0.00 0.00 32.87 2.69
3450 3623 5.765677 TCCGTCCAAAAATACTTGTCATCAA 59.234 36.000 0.00 0.00 0.00 2.57
3451 3624 5.309638 TCCGTCCAAAAATACTTGTCATCA 58.690 37.500 0.00 0.00 0.00 3.07
3452 3625 5.163754 CCTCCGTCCAAAAATACTTGTCATC 60.164 44.000 0.00 0.00 0.00 2.92
3453 3626 4.700213 CCTCCGTCCAAAAATACTTGTCAT 59.300 41.667 0.00 0.00 0.00 3.06
3454 3627 4.069304 CCTCCGTCCAAAAATACTTGTCA 58.931 43.478 0.00 0.00 0.00 3.58
3455 3628 3.439129 CCCTCCGTCCAAAAATACTTGTC 59.561 47.826 0.00 0.00 0.00 3.18
3456 3629 3.073356 TCCCTCCGTCCAAAAATACTTGT 59.927 43.478 0.00 0.00 0.00 3.16
3457 3630 3.681593 TCCCTCCGTCCAAAAATACTTG 58.318 45.455 0.00 0.00 0.00 3.16
3458 3631 3.329814 ACTCCCTCCGTCCAAAAATACTT 59.670 43.478 0.00 0.00 0.00 2.24
3459 3632 2.910977 ACTCCCTCCGTCCAAAAATACT 59.089 45.455 0.00 0.00 0.00 2.12
3460 3633 3.345508 ACTCCCTCCGTCCAAAAATAC 57.654 47.619 0.00 0.00 0.00 1.89
3461 3634 3.839490 TGTACTCCCTCCGTCCAAAAATA 59.161 43.478 0.00 0.00 0.00 1.40
3462 3635 2.640826 TGTACTCCCTCCGTCCAAAAAT 59.359 45.455 0.00 0.00 0.00 1.82
3463 3636 2.048601 TGTACTCCCTCCGTCCAAAAA 58.951 47.619 0.00 0.00 0.00 1.94
3464 3637 1.719529 TGTACTCCCTCCGTCCAAAA 58.280 50.000 0.00 0.00 0.00 2.44
3465 3638 1.719529 TTGTACTCCCTCCGTCCAAA 58.280 50.000 0.00 0.00 0.00 3.28
3466 3639 1.946984 ATTGTACTCCCTCCGTCCAA 58.053 50.000 0.00 0.00 0.00 3.53
3467 3640 1.946984 AATTGTACTCCCTCCGTCCA 58.053 50.000 0.00 0.00 0.00 4.02
3468 3641 4.439968 CTTAAATTGTACTCCCTCCGTCC 58.560 47.826 0.00 0.00 0.00 4.79
3469 3642 3.869832 GCTTAAATTGTACTCCCTCCGTC 59.130 47.826 0.00 0.00 0.00 4.79
3470 3643 3.518303 AGCTTAAATTGTACTCCCTCCGT 59.482 43.478 0.00 0.00 0.00 4.69
3471 3644 4.138487 AGCTTAAATTGTACTCCCTCCG 57.862 45.455 0.00 0.00 0.00 4.63
3472 3645 4.096532 GCAAGCTTAAATTGTACTCCCTCC 59.903 45.833 0.00 0.00 0.00 4.30
3473 3646 4.944317 AGCAAGCTTAAATTGTACTCCCTC 59.056 41.667 0.00 0.00 0.00 4.30
3474 3647 4.923415 AGCAAGCTTAAATTGTACTCCCT 58.077 39.130 0.00 0.00 0.00 4.20
3475 3648 5.402398 CAAGCAAGCTTAAATTGTACTCCC 58.598 41.667 7.03 0.00 34.50 4.30
3476 3649 5.183140 TCCAAGCAAGCTTAAATTGTACTCC 59.817 40.000 7.03 0.00 34.50 3.85
3477 3650 6.254281 TCCAAGCAAGCTTAAATTGTACTC 57.746 37.500 7.03 0.00 34.50 2.59
3478 3651 5.183904 CCTCCAAGCAAGCTTAAATTGTACT 59.816 40.000 7.03 0.00 34.50 2.73
3479 3652 5.402398 CCTCCAAGCAAGCTTAAATTGTAC 58.598 41.667 7.03 0.00 34.50 2.90
3480 3653 4.462483 CCCTCCAAGCAAGCTTAAATTGTA 59.538 41.667 7.03 0.00 34.50 2.41
3481 3654 3.259123 CCCTCCAAGCAAGCTTAAATTGT 59.741 43.478 7.03 0.00 34.50 2.71
3482 3655 3.368739 CCCCTCCAAGCAAGCTTAAATTG 60.369 47.826 7.03 4.60 34.50 2.32
3497 3670 1.748732 TGAACAACCATACCCCTCCA 58.251 50.000 0.00 0.00 0.00 3.86
3619 3876 5.382618 AGGCATTCTCTTGCTGTTTTAAG 57.617 39.130 0.00 0.00 42.38 1.85
3897 4154 5.404366 CAGTGAGATGTTCTTTGGCAAAATG 59.596 40.000 14.43 3.47 0.00 2.32
3898 4155 5.302568 TCAGTGAGATGTTCTTTGGCAAAAT 59.697 36.000 14.43 4.31 0.00 1.82
3931 4188 0.598419 AAAAAGCAAGCCGAAGCAGC 60.598 50.000 0.00 0.00 43.56 5.25
3946 4203 7.228590 ACCTTACATAACTAGTCCAGCAAAAA 58.771 34.615 0.00 0.00 0.00 1.94
3978 4235 4.456911 AGGTCACAGTCAATGCAAATGTAG 59.543 41.667 0.00 0.00 0.00 2.74
3986 4243 1.512926 ACGAAGGTCACAGTCAATGC 58.487 50.000 0.00 0.00 0.00 3.56
4016 4273 9.420551 GCATTAGTAGTACATAAGAATGGTACC 57.579 37.037 4.43 4.43 37.43 3.34
4070 4327 5.596361 TGAAACCTCTCCAGTTTTTATGCAA 59.404 36.000 0.00 0.00 37.55 4.08
4093 4350 4.857799 TGTACACACATGCACATTTCTTG 58.142 39.130 0.00 0.00 26.41 3.02
4101 4358 3.253188 AGACCATTTGTACACACATGCAC 59.747 43.478 0.00 0.92 33.83 4.57
4107 4364 4.377021 TCTGTGAGACCATTTGTACACAC 58.623 43.478 0.00 0.00 38.51 3.82
4178 4435 3.499537 TCACAGATGTTCACATGCTGTTC 59.500 43.478 16.15 0.00 39.91 3.18
4241 4498 1.353694 AGGCTTCAGAGATGCTTTGGT 59.646 47.619 5.12 0.00 33.95 3.67


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

AutoCloner maintained by Alex Coulton.