Multiple sequence alignment - TraesCS1A01G192300

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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 TraesCS1A01G192300 chr1A 100.000 3566 0 0 1 3566 347636793 347633228 0.000000e+00 6586.0
1 TraesCS1A01G192300 chr1A 98.711 543 7 0 1 543 492997963 492997421 0.000000e+00 965.0
2 TraesCS1A01G192300 chr1A 86.469 606 42 4 1077 1682 239909152 239908587 2.340000e-176 628.0
3 TraesCS1A01G192300 chr1A 78.684 380 53 18 2657 3019 347627080 347626712 9.960000e-56 228.0
4 TraesCS1A01G192300 chr1B 93.668 2590 116 26 537 3102 374330762 374328197 0.000000e+00 3831.0
5 TraesCS1A01G192300 chr1B 98.711 543 7 0 1 543 60235223 60235765 0.000000e+00 965.0
6 TraesCS1A01G192300 chr1B 98.711 543 7 0 1 543 354985280 354985822 0.000000e+00 965.0
7 TraesCS1A01G192300 chr1B 79.404 369 44 18 2657 3006 374322794 374322439 7.700000e-57 231.0
8 TraesCS1A01G192300 chr1B 92.857 56 4 0 2440 2495 374322847 374322792 8.210000e-12 82.4
9 TraesCS1A01G192300 chr1D 96.346 2326 49 12 711 3013 275139831 275137519 0.000000e+00 3792.0
10 TraesCS1A01G192300 chr1D 91.534 189 14 2 538 725 275140039 275139852 3.530000e-65 259.0
11 TraesCS1A01G192300 chr1D 87.245 196 22 3 2909 3102 275137519 275137325 1.670000e-53 220.0
12 TraesCS1A01G192300 chr1D 90.756 119 6 1 2660 2773 274956962 274956844 1.710000e-33 154.0
13 TraesCS1A01G192300 chr1D 85.833 120 17 0 2674 2793 275135695 275135576 1.040000e-25 128.0
14 TraesCS1A01G192300 chr7B 98.711 543 7 0 1 543 181057266 181056724 0.000000e+00 965.0
15 TraesCS1A01G192300 chr7A 98.711 543 7 0 1 543 357348787 357349329 0.000000e+00 965.0
16 TraesCS1A01G192300 chr5A 98.711 543 7 0 1 543 483276044 483275502 0.000000e+00 965.0
17 TraesCS1A01G192300 chr4A 98.711 543 7 0 1 543 575699295 575698753 0.000000e+00 965.0
18 TraesCS1A01G192300 chr3B 98.711 543 7 0 1 543 123631339 123630797 0.000000e+00 965.0
19 TraesCS1A01G192300 chr3B 98.711 543 7 0 1 543 556044728 556045270 0.000000e+00 965.0
20 TraesCS1A01G192300 chr3B 89.796 392 39 1 1078 1469 426651566 426651956 5.310000e-138 501.0
21 TraesCS1A01G192300 chr3B 91.126 293 14 1 1174 1466 823473564 823473844 1.550000e-103 387.0
22 TraesCS1A01G192300 chr3B 89.130 276 30 0 1077 1352 522027735 522027460 9.480000e-91 344.0
23 TraesCS1A01G192300 chr3B 93.333 60 4 0 1074 1133 823473511 823473570 4.900000e-14 89.8
24 TraesCS1A01G192300 chrUn 89.752 605 51 7 1078 1682 239745056 239745649 0.000000e+00 763.0
25 TraesCS1A01G192300 chr6A 94.737 57 3 0 1261 1317 478310575 478310519 4.900000e-14 89.8
26 TraesCS1A01G192300 chr6D 96.078 51 2 0 1373 1423 337842842 337842792 2.280000e-12 84.2
27 TraesCS1A01G192300 chr6B 96.078 51 2 0 1373 1423 482470608 482470658 2.280000e-12 84.2


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 TraesCS1A01G192300 chr1A 347633228 347636793 3565 True 6586.00 6586 100.0000 1 3566 1 chr1A.!!$R3 3565
1 TraesCS1A01G192300 chr1A 492997421 492997963 542 True 965.00 965 98.7110 1 543 1 chr1A.!!$R4 542
2 TraesCS1A01G192300 chr1A 239908587 239909152 565 True 628.00 628 86.4690 1077 1682 1 chr1A.!!$R1 605
3 TraesCS1A01G192300 chr1B 374328197 374330762 2565 True 3831.00 3831 93.6680 537 3102 1 chr1B.!!$R1 2565
4 TraesCS1A01G192300 chr1B 60235223 60235765 542 False 965.00 965 98.7110 1 543 1 chr1B.!!$F1 542
5 TraesCS1A01G192300 chr1B 354985280 354985822 542 False 965.00 965 98.7110 1 543 1 chr1B.!!$F2 542
6 TraesCS1A01G192300 chr1D 275135576 275140039 4463 True 1099.75 3792 90.2395 538 3102 4 chr1D.!!$R2 2564
7 TraesCS1A01G192300 chr7B 181056724 181057266 542 True 965.00 965 98.7110 1 543 1 chr7B.!!$R1 542
8 TraesCS1A01G192300 chr7A 357348787 357349329 542 False 965.00 965 98.7110 1 543 1 chr7A.!!$F1 542
9 TraesCS1A01G192300 chr5A 483275502 483276044 542 True 965.00 965 98.7110 1 543 1 chr5A.!!$R1 542
10 TraesCS1A01G192300 chr4A 575698753 575699295 542 True 965.00 965 98.7110 1 543 1 chr4A.!!$R1 542
11 TraesCS1A01G192300 chr3B 123630797 123631339 542 True 965.00 965 98.7110 1 543 1 chr3B.!!$R1 542
12 TraesCS1A01G192300 chr3B 556044728 556045270 542 False 965.00 965 98.7110 1 543 1 chr3B.!!$F2 542
13 TraesCS1A01G192300 chrUn 239745056 239745649 593 False 763.00 763 89.7520 1078 1682 1 chrUn.!!$F1 604

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
775 808 0.961753 GGGCTGCTTTGCTTGTAAGT 59.038 50.000 0.00 0.00 0.00 2.24 F
985 1049 1.136502 GCCGATTCGATTCGATTCAGC 60.137 52.381 26.39 20.65 41.62 4.26 F
1881 1979 1.218854 GGTCACCAATGCCATTGCC 59.781 57.895 12.01 4.12 38.92 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2528 2626 0.043940 ATCTGCACCCTCTTCCTCCT 59.956 55.0 0.0 0.0 0.0 3.69 R
2529 2627 0.179936 CATCTGCACCCTCTTCCTCC 59.820 60.0 0.0 0.0 0.0 4.30 R
3405 3670 0.249699 CCCACTGCAACTACACACGA 60.250 55.0 0.0 0.0 0.0 4.35 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
56 57 1.651987 TCCGTCTTTGATTCGATGGC 58.348 50.000 0.00 0.00 36.48 4.40
132 133 1.192428 GTGTCCTTCCGAGGTACCAT 58.808 55.000 15.94 0.00 43.97 3.55
209 210 6.348213 GCACATCATGTACTCGGTTTTAGTTT 60.348 38.462 0.00 0.00 0.00 2.66
295 296 2.606725 CGTCCGACTATCGTCAACTAGT 59.393 50.000 0.00 0.00 40.23 2.57
427 428 4.202223 TGCAGTCCTATCTTAATCGGGAAC 60.202 45.833 0.00 0.00 0.00 3.62
600 601 9.571804 GATTAATAATTTTGAAATGCACGATGC 57.428 29.630 0.00 0.00 45.29 3.91
693 697 2.186826 GCTGTGTGGGCGTTTCACT 61.187 57.895 0.00 0.00 36.21 3.41
697 701 1.527380 TGTGGGCGTTTCACTTCCC 60.527 57.895 0.00 0.00 39.22 3.97
703 707 1.153353 GCGTTTCACTTCCCATTCGA 58.847 50.000 0.00 0.00 0.00 3.71
773 806 2.436417 CTAGGGCTGCTTTGCTTGTAA 58.564 47.619 0.00 0.00 0.00 2.41
774 807 1.251251 AGGGCTGCTTTGCTTGTAAG 58.749 50.000 0.00 0.00 0.00 2.34
775 808 0.961753 GGGCTGCTTTGCTTGTAAGT 59.038 50.000 0.00 0.00 0.00 2.24
776 809 2.159382 GGGCTGCTTTGCTTGTAAGTA 58.841 47.619 0.00 0.00 0.00 2.24
808 854 1.341285 CCCATTCAGCATCCTGGTTGA 60.341 52.381 8.93 0.00 39.61 3.18
885 937 3.144193 CGCCGCCTCTCCTCTCTT 61.144 66.667 0.00 0.00 0.00 2.85
886 938 2.811799 GCCGCCTCTCCTCTCTTC 59.188 66.667 0.00 0.00 0.00 2.87
920 972 2.161012 GCCTACAAAACCCTAGCGAAAC 59.839 50.000 0.00 0.00 0.00 2.78
983 1047 2.127251 CAGCCGATTCGATTCGATTCA 58.873 47.619 26.39 6.59 41.62 2.57
984 1048 2.154580 CAGCCGATTCGATTCGATTCAG 59.845 50.000 26.39 16.41 41.62 3.02
985 1049 1.136502 GCCGATTCGATTCGATTCAGC 60.137 52.381 26.39 20.65 41.62 4.26
986 1050 1.457303 CCGATTCGATTCGATTCAGCC 59.543 52.381 26.39 5.10 41.62 4.85
988 1052 2.760374 GATTCGATTCGATTCAGCCCT 58.240 47.619 20.35 0.00 36.61 5.19
1881 1979 1.218854 GGTCACCAATGCCATTGCC 59.781 57.895 12.01 4.12 38.92 4.52
2002 2100 6.051074 CAGTACATGGTGCTTGATATTGAGA 58.949 40.000 0.00 0.00 0.00 3.27
2523 2621 2.496297 ACCCTTGGTGATGATGAGGAT 58.504 47.619 0.00 0.00 32.98 3.24
2524 2622 2.174210 ACCCTTGGTGATGATGAGGATG 59.826 50.000 0.00 0.00 32.98 3.51
2525 2623 2.440627 CCCTTGGTGATGATGAGGATGA 59.559 50.000 0.00 0.00 0.00 2.92
2526 2624 3.117776 CCCTTGGTGATGATGAGGATGAA 60.118 47.826 0.00 0.00 0.00 2.57
2527 2625 4.135306 CCTTGGTGATGATGAGGATGAAG 58.865 47.826 0.00 0.00 0.00 3.02
2528 2626 4.141551 CCTTGGTGATGATGAGGATGAAGA 60.142 45.833 0.00 0.00 0.00 2.87
2529 2627 4.684484 TGGTGATGATGAGGATGAAGAG 57.316 45.455 0.00 0.00 0.00 2.85
2530 2628 3.390311 TGGTGATGATGAGGATGAAGAGG 59.610 47.826 0.00 0.00 0.00 3.69
2531 2629 3.645212 GGTGATGATGAGGATGAAGAGGA 59.355 47.826 0.00 0.00 0.00 3.71
2628 2735 2.388735 CCACTGCAGGTCATAGGTCTA 58.611 52.381 19.93 0.00 0.00 2.59
2772 2879 8.786826 TGTTTGAAACCATATCTCGTATCTTT 57.213 30.769 5.50 0.00 0.00 2.52
2780 2887 6.916387 ACCATATCTCGTATCTTTGTGTAACG 59.084 38.462 0.00 0.00 42.39 3.18
2790 2897 8.804743 CGTATCTTTGTGTAACGATAATGTCTT 58.195 33.333 0.00 0.00 42.39 3.01
2833 2940 6.375945 TCATGTCATATGTTTGTGGTATGC 57.624 37.500 1.90 0.00 0.00 3.14
2835 2942 5.816449 TGTCATATGTTTGTGGTATGCTG 57.184 39.130 1.90 0.00 0.00 4.41
2842 2949 3.563808 TGTTTGTGGTATGCTGTTCAGTC 59.436 43.478 1.78 0.00 0.00 3.51
2848 2955 2.860735 GGTATGCTGTTCAGTCGTCATC 59.139 50.000 1.78 0.00 0.00 2.92
2849 2956 1.633561 ATGCTGTTCAGTCGTCATCG 58.366 50.000 1.78 0.00 38.55 3.84
2857 2964 5.224135 TGTTCAGTCGTCATCGTTTGATTA 58.776 37.500 0.00 0.00 36.54 1.75
2906 3013 7.647907 AAGATTTGATTCTTGAAACATGTGC 57.352 32.000 0.00 0.00 34.68 4.57
2907 3014 6.751157 AGATTTGATTCTTGAAACATGTGCA 58.249 32.000 0.00 0.00 0.00 4.57
2911 3018 9.661563 ATTTGATTCTTGAAACATGTGCATATT 57.338 25.926 0.00 0.00 0.00 1.28
2912 3019 8.468720 TTGATTCTTGAAACATGTGCATATTG 57.531 30.769 0.00 0.00 0.00 1.90
2950 3164 5.815233 TTATTGGATGTCTCTCAGGGATC 57.185 43.478 0.00 0.00 0.00 3.36
2952 3166 2.392662 TGGATGTCTCTCAGGGATCAC 58.607 52.381 0.00 0.00 0.00 3.06
2982 3196 7.311092 TGTTCTTTTCTAGAATGGTCACCTA 57.689 36.000 5.89 0.00 44.39 3.08
2987 3201 7.455008 TCTTTTCTAGAATGGTCACCTAAGAGT 59.545 37.037 5.89 0.00 0.00 3.24
2989 3203 6.777213 TCTAGAATGGTCACCTAAGAGTTC 57.223 41.667 0.00 0.00 0.00 3.01
3035 3250 6.796705 TGTATCTATGAATGCAGCTGAATG 57.203 37.500 20.43 0.00 0.00 2.67
3036 3251 6.527423 TGTATCTATGAATGCAGCTGAATGA 58.473 36.000 20.43 5.96 0.00 2.57
3037 3252 6.649557 TGTATCTATGAATGCAGCTGAATGAG 59.350 38.462 20.43 8.74 0.00 2.90
3038 3253 4.386711 TCTATGAATGCAGCTGAATGAGG 58.613 43.478 20.43 2.61 0.00 3.86
3039 3254 2.502142 TGAATGCAGCTGAATGAGGT 57.498 45.000 20.43 0.00 0.00 3.85
3040 3255 3.632643 TGAATGCAGCTGAATGAGGTA 57.367 42.857 20.43 0.00 0.00 3.08
3042 3257 4.529897 TGAATGCAGCTGAATGAGGTATT 58.470 39.130 20.43 0.00 0.00 1.89
3043 3258 4.337274 TGAATGCAGCTGAATGAGGTATTG 59.663 41.667 20.43 0.00 0.00 1.90
3044 3259 2.019249 TGCAGCTGAATGAGGTATTGC 58.981 47.619 20.43 0.00 0.00 3.56
3052 3267 5.449041 GCTGAATGAGGTATTGCGATTTTGA 60.449 40.000 0.00 0.00 0.00 2.69
3054 3269 7.520453 GCTGAATGAGGTATTGCGATTTTGATA 60.520 37.037 0.00 0.00 0.00 2.15
3055 3270 7.864686 TGAATGAGGTATTGCGATTTTGATAG 58.135 34.615 0.00 0.00 0.00 2.08
3060 3275 4.083271 GGTATTGCGATTTTGATAGGGCTC 60.083 45.833 0.00 0.00 0.00 4.70
3061 3276 3.281727 TTGCGATTTTGATAGGGCTCT 57.718 42.857 0.00 0.00 0.00 4.09
3062 3277 2.564771 TGCGATTTTGATAGGGCTCTG 58.435 47.619 0.00 0.00 0.00 3.35
3078 3293 2.353208 GCTCTGTTACAGGTCTCACTGG 60.353 54.545 12.79 0.00 42.75 4.00
3087 3302 4.536765 ACAGGTCTCACTGGAAATTGTTT 58.463 39.130 0.00 0.00 42.75 2.83
3092 3318 5.335191 GGTCTCACTGGAAATTGTTTAGCTG 60.335 44.000 0.00 0.00 0.00 4.24
3095 3321 4.278170 TCACTGGAAATTGTTTAGCTGTGG 59.722 41.667 0.00 0.00 0.00 4.17
3096 3322 4.037923 CACTGGAAATTGTTTAGCTGTGGT 59.962 41.667 0.00 0.00 0.00 4.16
3098 3324 3.957497 TGGAAATTGTTTAGCTGTGGTGT 59.043 39.130 0.00 0.00 0.00 4.16
3099 3325 4.202101 TGGAAATTGTTTAGCTGTGGTGTG 60.202 41.667 0.00 0.00 0.00 3.82
3102 3328 2.051334 TGTTTAGCTGTGGTGTGCTT 57.949 45.000 0.00 0.00 40.35 3.91
3104 3330 3.546724 TGTTTAGCTGTGGTGTGCTTTA 58.453 40.909 0.00 0.00 40.35 1.85
3108 3334 1.140852 AGCTGTGGTGTGCTTTACTGA 59.859 47.619 0.00 0.00 35.86 3.41
3110 3336 3.007940 AGCTGTGGTGTGCTTTACTGATA 59.992 43.478 0.00 0.00 35.86 2.15
3111 3337 3.125316 GCTGTGGTGTGCTTTACTGATAC 59.875 47.826 0.00 0.00 0.00 2.24
3112 3338 4.314961 CTGTGGTGTGCTTTACTGATACA 58.685 43.478 0.00 0.00 0.00 2.29
3121 3347 8.131100 GTGTGCTTTACTGATACATAATGCATT 58.869 33.333 17.56 17.56 41.02 3.56
3122 3348 8.685427 TGTGCTTTACTGATACATAATGCATTT 58.315 29.630 18.75 1.86 41.02 2.32
3131 3357 9.486497 CTGATACATAATGCATTTAGACTCACT 57.514 33.333 18.75 0.00 0.00 3.41
3132 3358 9.836864 TGATACATAATGCATTTAGACTCACTT 57.163 29.630 18.75 0.00 0.00 3.16
3152 3378 9.915629 CTCACTTGTGACTAGTTTAGAAGTTAT 57.084 33.333 16.11 0.05 0.00 1.89
3170 3396 9.525409 AGAAGTTATTCATGAAAAATATGCAGC 57.475 29.630 13.09 0.00 37.94 5.25
3171 3397 8.652810 AAGTTATTCATGAAAAATATGCAGCC 57.347 30.769 13.09 0.00 0.00 4.85
3172 3398 7.212274 AGTTATTCATGAAAAATATGCAGCCC 58.788 34.615 13.09 0.00 0.00 5.19
3173 3399 5.881923 ATTCATGAAAAATATGCAGCCCT 57.118 34.783 13.09 0.00 0.00 5.19
3174 3400 4.659111 TCATGAAAAATATGCAGCCCTG 57.341 40.909 0.00 0.00 0.00 4.45
3175 3401 4.025360 TCATGAAAAATATGCAGCCCTGT 58.975 39.130 0.00 0.00 0.00 4.00
3176 3402 4.467082 TCATGAAAAATATGCAGCCCTGTT 59.533 37.500 0.00 0.00 0.00 3.16
3177 3403 4.454728 TGAAAAATATGCAGCCCTGTTC 57.545 40.909 0.00 0.00 0.00 3.18
3178 3404 3.195396 TGAAAAATATGCAGCCCTGTTCC 59.805 43.478 0.00 0.00 0.00 3.62
3179 3405 1.780503 AAATATGCAGCCCTGTTCCC 58.219 50.000 0.00 0.00 0.00 3.97
3180 3406 0.929244 AATATGCAGCCCTGTTCCCT 59.071 50.000 0.00 0.00 0.00 4.20
3181 3407 0.475906 ATATGCAGCCCTGTTCCCTC 59.524 55.000 0.00 0.00 0.00 4.30
3182 3408 1.635817 TATGCAGCCCTGTTCCCTCC 61.636 60.000 0.00 0.00 0.00 4.30
3183 3409 4.432741 GCAGCCCTGTTCCCTCCC 62.433 72.222 0.00 0.00 0.00 4.30
3184 3410 2.935481 CAGCCCTGTTCCCTCCCA 60.935 66.667 0.00 0.00 0.00 4.37
3185 3411 2.612115 AGCCCTGTTCCCTCCCAG 60.612 66.667 0.00 0.00 0.00 4.45
3186 3412 3.732849 GCCCTGTTCCCTCCCAGG 61.733 72.222 0.00 0.00 46.43 4.45
3199 3425 4.855298 CCTCCCAGGGTTAAATGACTTA 57.145 45.455 5.01 0.00 0.00 2.24
3206 3432 7.048512 CCCAGGGTTAAATGACTTAGTAAGAG 58.951 42.308 16.89 0.00 0.00 2.85
3216 3442 6.949352 TGACTTAGTAAGAGGGTTATACCG 57.051 41.667 16.89 0.00 39.83 4.02
3219 3445 8.052748 TGACTTAGTAAGAGGGTTATACCGTAA 58.947 37.037 16.89 0.00 39.83 3.18
3224 3488 8.082672 AGTAAGAGGGTTATACCGTAAAATGT 57.917 34.615 0.00 0.00 39.83 2.71
3225 3489 9.200817 AGTAAGAGGGTTATACCGTAAAATGTA 57.799 33.333 0.00 0.00 39.83 2.29
3226 3490 9.987272 GTAAGAGGGTTATACCGTAAAATGTAT 57.013 33.333 0.00 0.00 39.83 2.29
3240 3504 7.064134 CCGTAAAATGTATGAGCTGTTTGTAGA 59.936 37.037 0.00 0.00 0.00 2.59
3241 3505 7.898309 CGTAAAATGTATGAGCTGTTTGTAGAC 59.102 37.037 0.00 0.00 0.00 2.59
3242 3506 7.986085 AAAATGTATGAGCTGTTTGTAGACT 57.014 32.000 0.00 0.00 0.00 3.24
3243 3507 6.974932 AATGTATGAGCTGTTTGTAGACTG 57.025 37.500 0.00 0.00 0.00 3.51
3244 3508 5.468540 TGTATGAGCTGTTTGTAGACTGT 57.531 39.130 0.00 0.00 0.00 3.55
3245 3509 6.584185 TGTATGAGCTGTTTGTAGACTGTA 57.416 37.500 0.00 0.00 0.00 2.74
3246 3510 6.621613 TGTATGAGCTGTTTGTAGACTGTAG 58.378 40.000 0.00 0.00 0.00 2.74
3247 3511 5.730296 ATGAGCTGTTTGTAGACTGTAGT 57.270 39.130 0.00 0.00 0.00 2.73
3248 3512 6.835819 ATGAGCTGTTTGTAGACTGTAGTA 57.164 37.500 0.00 0.00 0.00 1.82
3249 3513 6.835819 TGAGCTGTTTGTAGACTGTAGTAT 57.164 37.500 0.00 0.00 0.00 2.12
3250 3514 7.933215 TGAGCTGTTTGTAGACTGTAGTATA 57.067 36.000 0.00 0.00 0.00 1.47
3293 3557 2.361757 TGAAAACAGGAATGCACCACAG 59.638 45.455 0.00 0.00 0.00 3.66
3294 3558 1.331214 AAACAGGAATGCACCACAGG 58.669 50.000 0.00 0.00 0.00 4.00
3295 3559 0.540365 AACAGGAATGCACCACAGGG 60.540 55.000 0.00 0.00 41.29 4.45
3306 3570 2.805897 CCACAGGGTGCTTCAAACA 58.194 52.632 0.00 0.00 31.34 2.83
3308 3572 2.513753 CCACAGGGTGCTTCAAACATA 58.486 47.619 0.00 0.00 31.34 2.29
3309 3573 2.489329 CCACAGGGTGCTTCAAACATAG 59.511 50.000 0.00 0.00 31.34 2.23
3311 3575 2.375174 ACAGGGTGCTTCAAACATAGGA 59.625 45.455 0.00 0.00 0.00 2.94
3313 3577 2.912956 AGGGTGCTTCAAACATAGGAGA 59.087 45.455 0.00 0.00 0.00 3.71
3314 3578 3.054802 AGGGTGCTTCAAACATAGGAGAG 60.055 47.826 0.00 0.00 0.00 3.20
3315 3579 3.307762 GGGTGCTTCAAACATAGGAGAGT 60.308 47.826 0.00 0.00 0.00 3.24
3317 3581 5.396884 GGGTGCTTCAAACATAGGAGAGTAT 60.397 44.000 0.00 0.00 0.00 2.12
3318 3582 6.116126 GGTGCTTCAAACATAGGAGAGTATT 58.884 40.000 0.00 0.00 0.00 1.89
3319 3583 6.037610 GGTGCTTCAAACATAGGAGAGTATTG 59.962 42.308 0.00 0.00 0.00 1.90
3320 3584 5.586243 TGCTTCAAACATAGGAGAGTATTGC 59.414 40.000 0.00 0.00 0.00 3.56
3321 3585 5.819901 GCTTCAAACATAGGAGAGTATTGCT 59.180 40.000 0.00 0.00 0.00 3.91
3322 3586 6.238320 GCTTCAAACATAGGAGAGTATTGCTG 60.238 42.308 0.00 0.00 0.00 4.41
3323 3587 6.299805 TCAAACATAGGAGAGTATTGCTGT 57.700 37.500 0.00 0.00 0.00 4.40
3324 3588 6.711277 TCAAACATAGGAGAGTATTGCTGTT 58.289 36.000 0.00 0.00 0.00 3.16
3325 3589 7.168219 TCAAACATAGGAGAGTATTGCTGTTT 58.832 34.615 0.00 0.00 36.36 2.83
3326 3590 7.334421 TCAAACATAGGAGAGTATTGCTGTTTC 59.666 37.037 0.00 0.00 34.39 2.78
3327 3591 6.552445 ACATAGGAGAGTATTGCTGTTTCT 57.448 37.500 0.00 0.00 0.00 2.52
3328 3592 6.344500 ACATAGGAGAGTATTGCTGTTTCTG 58.656 40.000 0.00 0.00 0.00 3.02
3329 3593 4.899352 AGGAGAGTATTGCTGTTTCTGT 57.101 40.909 0.00 0.00 0.00 3.41
3330 3594 4.573900 AGGAGAGTATTGCTGTTTCTGTG 58.426 43.478 0.00 0.00 0.00 3.66
3331 3595 4.040952 AGGAGAGTATTGCTGTTTCTGTGT 59.959 41.667 0.00 0.00 0.00 3.72
3332 3596 5.246203 AGGAGAGTATTGCTGTTTCTGTGTA 59.754 40.000 0.00 0.00 0.00 2.90
3333 3597 5.348997 GGAGAGTATTGCTGTTTCTGTGTAC 59.651 44.000 0.00 0.00 0.00 2.90
3334 3598 5.853936 AGAGTATTGCTGTTTCTGTGTACA 58.146 37.500 0.00 0.00 0.00 2.90
3335 3599 6.288294 AGAGTATTGCTGTTTCTGTGTACAA 58.712 36.000 0.00 0.00 0.00 2.41
3336 3600 6.936900 AGAGTATTGCTGTTTCTGTGTACAAT 59.063 34.615 0.00 0.00 0.00 2.71
3337 3601 7.445402 AGAGTATTGCTGTTTCTGTGTACAATT 59.555 33.333 0.00 0.00 0.00 2.32
3338 3602 8.615878 AGTATTGCTGTTTCTGTGTACAATTA 57.384 30.769 0.00 0.00 0.00 1.40
3339 3603 9.231297 AGTATTGCTGTTTCTGTGTACAATTAT 57.769 29.630 0.00 0.00 0.00 1.28
3342 3606 8.615878 TTGCTGTTTCTGTGTACAATTATAGT 57.384 30.769 0.00 0.00 0.00 2.12
3343 3607 8.615878 TGCTGTTTCTGTGTACAATTATAGTT 57.384 30.769 0.00 0.00 0.00 2.24
3344 3608 8.503196 TGCTGTTTCTGTGTACAATTATAGTTG 58.497 33.333 6.44 6.44 35.25 3.16
3345 3609 7.481798 GCTGTTTCTGTGTACAATTATAGTTGC 59.518 37.037 7.82 0.00 32.32 4.17
3346 3610 8.384607 TGTTTCTGTGTACAATTATAGTTGCA 57.615 30.769 7.82 0.00 32.32 4.08
3347 3611 8.286800 TGTTTCTGTGTACAATTATAGTTGCAC 58.713 33.333 7.82 6.19 32.32 4.57
3348 3612 7.971183 TTCTGTGTACAATTATAGTTGCACA 57.029 32.000 15.53 15.53 34.02 4.57
3349 3613 8.560355 TTCTGTGTACAATTATAGTTGCACAT 57.440 30.769 14.85 0.00 37.60 3.21
3350 3614 7.973601 TCTGTGTACAATTATAGTTGCACATG 58.026 34.615 14.85 11.64 37.60 3.21
3351 3615 7.065683 TCTGTGTACAATTATAGTTGCACATGG 59.934 37.037 14.85 11.35 37.60 3.66
3352 3616 6.094742 TGTGTACAATTATAGTTGCACATGGG 59.905 38.462 14.85 0.00 37.60 4.00
3353 3617 6.094881 GTGTACAATTATAGTTGCACATGGGT 59.905 38.462 14.85 0.00 37.60 4.51
3354 3618 7.281324 GTGTACAATTATAGTTGCACATGGGTA 59.719 37.037 14.85 0.00 37.60 3.69
3355 3619 7.829706 TGTACAATTATAGTTGCACATGGGTAA 59.170 33.333 9.34 0.00 32.06 2.85
3356 3620 7.710676 ACAATTATAGTTGCACATGGGTAAA 57.289 32.000 0.00 0.00 32.32 2.01
3357 3621 8.305046 ACAATTATAGTTGCACATGGGTAAAT 57.695 30.769 3.79 3.79 32.32 1.40
3358 3622 8.196771 ACAATTATAGTTGCACATGGGTAAATG 58.803 33.333 9.08 0.00 32.32 2.32
3359 3623 7.896383 ATTATAGTTGCACATGGGTAAATGT 57.104 32.000 9.08 4.85 41.50 2.71
3360 3624 7.710676 TTATAGTTGCACATGGGTAAATGTT 57.289 32.000 9.08 0.00 38.75 2.71
3361 3625 4.953940 AGTTGCACATGGGTAAATGTTT 57.046 36.364 0.00 0.00 38.75 2.83
3362 3626 5.289083 AGTTGCACATGGGTAAATGTTTT 57.711 34.783 0.00 0.00 38.75 2.43
3363 3627 5.296748 AGTTGCACATGGGTAAATGTTTTC 58.703 37.500 0.00 0.00 38.75 2.29
3364 3628 4.264460 TGCACATGGGTAAATGTTTTCC 57.736 40.909 0.00 0.00 38.75 3.13
3365 3629 3.900601 TGCACATGGGTAAATGTTTTCCT 59.099 39.130 0.00 0.00 38.75 3.36
3366 3630 4.346418 TGCACATGGGTAAATGTTTTCCTT 59.654 37.500 0.00 0.00 38.75 3.36
3367 3631 4.929211 GCACATGGGTAAATGTTTTCCTTC 59.071 41.667 0.00 0.00 38.75 3.46
3368 3632 5.478407 CACATGGGTAAATGTTTTCCTTCC 58.522 41.667 0.00 0.00 38.75 3.46
3369 3633 5.245977 CACATGGGTAAATGTTTTCCTTCCT 59.754 40.000 0.00 0.00 38.75 3.36
3370 3634 5.843969 ACATGGGTAAATGTTTTCCTTCCTT 59.156 36.000 0.00 0.00 37.50 3.36
3371 3635 6.014584 ACATGGGTAAATGTTTTCCTTCCTTC 60.015 38.462 0.00 0.00 37.50 3.46
3372 3636 5.459505 TGGGTAAATGTTTTCCTTCCTTCA 58.540 37.500 1.94 0.00 0.00 3.02
3373 3637 5.538433 TGGGTAAATGTTTTCCTTCCTTCAG 59.462 40.000 1.94 0.00 0.00 3.02
3374 3638 5.538813 GGGTAAATGTTTTCCTTCCTTCAGT 59.461 40.000 1.94 0.00 0.00 3.41
3375 3639 6.717997 GGGTAAATGTTTTCCTTCCTTCAGTA 59.282 38.462 1.94 0.00 0.00 2.74
3376 3640 7.396339 GGGTAAATGTTTTCCTTCCTTCAGTAT 59.604 37.037 1.94 0.00 0.00 2.12
3377 3641 9.457436 GGTAAATGTTTTCCTTCCTTCAGTATA 57.543 33.333 0.00 0.00 0.00 1.47
3394 3658 7.101652 TCAGTATACTCCAGTGAACTGATTC 57.898 40.000 12.05 0.00 46.59 2.52
3396 3660 2.751166 ACTCCAGTGAACTGATTCGG 57.249 50.000 12.05 0.00 46.59 4.30
3405 3670 3.562973 GTGAACTGATTCGGATGATGCAT 59.437 43.478 0.00 0.00 37.69 3.96
3406 3671 3.811497 TGAACTGATTCGGATGATGCATC 59.189 43.478 20.14 20.14 37.69 3.91
3420 3685 1.147473 TGCATCGTGTGTAGTTGCAG 58.853 50.000 0.00 0.00 38.79 4.41
3423 3688 1.460743 CATCGTGTGTAGTTGCAGTGG 59.539 52.381 0.00 0.00 0.00 4.00
3424 3689 0.249699 TCGTGTGTAGTTGCAGTGGG 60.250 55.000 0.00 0.00 0.00 4.61
3425 3690 1.841663 CGTGTGTAGTTGCAGTGGGC 61.842 60.000 0.00 0.00 45.13 5.36
3450 3715 6.642707 CCTAGTGTAGGGATAAGTTGAGAG 57.357 45.833 0.00 0.00 42.42 3.20
3496 3765 7.865706 TCTTTAGTAAGAAATCATTCCAGGC 57.134 36.000 0.00 0.00 37.45 4.85
3506 3775 1.004277 TCATTCCAGGCGGCTACTTTT 59.996 47.619 12.74 0.00 0.00 2.27
3516 3785 2.427506 CGGCTACTTTTTCCAAGCTCT 58.572 47.619 0.00 0.00 35.30 4.09
3518 3787 3.253432 CGGCTACTTTTTCCAAGCTCTTT 59.747 43.478 0.00 0.00 35.30 2.52
3519 3788 4.261614 CGGCTACTTTTTCCAAGCTCTTTT 60.262 41.667 0.00 0.00 35.30 2.27
3520 3789 4.984785 GGCTACTTTTTCCAAGCTCTTTTG 59.015 41.667 0.00 0.00 35.30 2.44
3521 3790 5.451937 GGCTACTTTTTCCAAGCTCTTTTGT 60.452 40.000 0.00 0.00 35.30 2.83
3522 3791 6.042777 GCTACTTTTTCCAAGCTCTTTTGTT 58.957 36.000 0.00 0.00 32.18 2.83
3525 3794 6.101997 ACTTTTTCCAAGCTCTTTTGTTCTG 58.898 36.000 0.00 0.00 0.00 3.02
3533 3802 3.135530 AGCTCTTTTGTTCTGTGGTCTCT 59.864 43.478 0.00 0.00 0.00 3.10
3546 3815 3.259374 TGTGGTCTCTCATGTTCCTCTTC 59.741 47.826 0.00 0.00 0.00 2.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
56 57 4.141413 TGGGGGTATTGATGAAGATGTGAG 60.141 45.833 0.00 0.00 0.00 3.51
209 210 5.743636 TCGAAAGGGTTTAGGCTTAGTAA 57.256 39.130 0.00 0.00 0.00 2.24
295 296 2.905075 CTCTTTGCGGATGATGTGGTA 58.095 47.619 0.00 0.00 0.00 3.25
693 697 1.735571 GCTTAAAGCGTCGAATGGGAA 59.264 47.619 0.00 0.00 0.00 3.97
725 729 2.527951 AATGGCGGTCTCTGGAGTGC 62.528 60.000 0.00 1.63 0.00 4.40
731 735 2.202932 CGGGAATGGCGGTCTCTG 60.203 66.667 0.00 0.00 0.00 3.35
734 738 4.143333 CGACGGGAATGGCGGTCT 62.143 66.667 0.00 0.00 0.00 3.85
773 806 3.181423 TGAATGGGCCTTTTGGTTCTACT 60.181 43.478 4.53 0.00 42.99 2.57
774 807 3.161866 TGAATGGGCCTTTTGGTTCTAC 58.838 45.455 4.53 0.00 42.99 2.59
775 808 3.430453 CTGAATGGGCCTTTTGGTTCTA 58.570 45.455 4.53 0.00 42.99 2.10
776 809 2.250924 CTGAATGGGCCTTTTGGTTCT 58.749 47.619 4.53 0.00 42.99 3.01
808 854 3.061848 CCGCGTGGGCTTTTGGAT 61.062 61.111 7.26 0.00 36.88 3.41
882 934 0.696501 GGCTTTGTAGGTGGGGAAGA 59.303 55.000 0.00 0.00 0.00 2.87
883 935 0.698818 AGGCTTTGTAGGTGGGGAAG 59.301 55.000 0.00 0.00 0.00 3.46
884 936 1.631898 GTAGGCTTTGTAGGTGGGGAA 59.368 52.381 0.00 0.00 0.00 3.97
885 937 1.282382 GTAGGCTTTGTAGGTGGGGA 58.718 55.000 0.00 0.00 0.00 4.81
886 938 0.988832 TGTAGGCTTTGTAGGTGGGG 59.011 55.000 0.00 0.00 0.00 4.96
920 972 0.108898 GGCTCGATCGGATGGAGATG 60.109 60.000 27.57 8.38 37.30 2.90
986 1050 3.466791 ATCATCTTGCGCGGGGAGG 62.467 63.158 8.83 0.00 0.00 4.30
988 1052 2.203056 CATCATCTTGCGCGGGGA 60.203 61.111 8.83 0.38 0.00 4.81
1776 1874 1.407656 GGTCCTCACGGCATATGGGA 61.408 60.000 4.56 0.00 0.00 4.37
1881 1979 2.190488 GAGTGAGGGGGTCAAGCAGG 62.190 65.000 0.00 0.00 36.74 4.85
2002 2100 2.175202 GGTGATCTCAGGTGACTCTGT 58.825 52.381 0.00 0.00 40.21 3.41
2040 2138 1.890510 CTGCGCATATGCCAGCTGA 60.891 57.895 24.08 9.31 37.91 4.26
2064 2162 1.750193 TCCCAAAATCAGACATCCGC 58.250 50.000 0.00 0.00 0.00 5.54
2523 2621 1.944177 CACCCTCTTCCTCCTCTTCA 58.056 55.000 0.00 0.00 0.00 3.02
2524 2622 0.539518 GCACCCTCTTCCTCCTCTTC 59.460 60.000 0.00 0.00 0.00 2.87
2525 2623 0.178891 TGCACCCTCTTCCTCCTCTT 60.179 55.000 0.00 0.00 0.00 2.85
2526 2624 0.617249 CTGCACCCTCTTCCTCCTCT 60.617 60.000 0.00 0.00 0.00 3.69
2527 2625 0.616111 TCTGCACCCTCTTCCTCCTC 60.616 60.000 0.00 0.00 0.00 3.71
2528 2626 0.043940 ATCTGCACCCTCTTCCTCCT 59.956 55.000 0.00 0.00 0.00 3.69
2529 2627 0.179936 CATCTGCACCCTCTTCCTCC 59.820 60.000 0.00 0.00 0.00 4.30
2530 2628 0.463474 GCATCTGCACCCTCTTCCTC 60.463 60.000 0.00 0.00 41.59 3.71
2531 2629 0.913451 AGCATCTGCACCCTCTTCCT 60.913 55.000 4.79 0.00 45.16 3.36
2833 2940 3.049912 TCAAACGATGACGACTGAACAG 58.950 45.455 0.00 0.00 42.66 3.16
2835 2942 4.647291 AATCAAACGATGACGACTGAAC 57.353 40.909 0.00 0.00 41.93 3.18
2842 2949 5.509605 TTGTGACTAATCAAACGATGACG 57.490 39.130 0.00 0.00 41.93 4.35
2848 2955 8.141835 TCCATGATATTGTGACTAATCAAACG 57.858 34.615 0.00 0.00 36.31 3.60
2849 2956 9.113838 ACTCCATGATATTGTGACTAATCAAAC 57.886 33.333 0.00 0.00 36.31 2.93
2857 2964 6.042437 TGCATCTACTCCATGATATTGTGACT 59.958 38.462 0.00 0.00 0.00 3.41
2911 3018 6.716284 TCCAATAATCAGTAATCACACCACA 58.284 36.000 0.00 0.00 0.00 4.17
2912 3019 7.283127 ACATCCAATAATCAGTAATCACACCAC 59.717 37.037 0.00 0.00 0.00 4.16
2950 3164 7.175641 ACCATTCTAGAAAAGAACATTCAGGTG 59.824 37.037 9.71 0.00 46.90 4.00
2952 3166 7.391554 TGACCATTCTAGAAAAGAACATTCAGG 59.608 37.037 9.71 0.74 46.90 3.86
2966 3180 6.494952 AGAACTCTTAGGTGACCATTCTAGA 58.505 40.000 3.63 0.00 0.00 2.43
2987 3201 0.693049 GACAGGCAAGAGGGGAAGAA 59.307 55.000 0.00 0.00 0.00 2.52
2989 3203 1.301293 GGACAGGCAAGAGGGGAAG 59.699 63.158 0.00 0.00 0.00 3.46
3035 3250 4.083271 GCCCTATCAAAATCGCAATACCTC 60.083 45.833 0.00 0.00 0.00 3.85
3036 3251 3.821033 GCCCTATCAAAATCGCAATACCT 59.179 43.478 0.00 0.00 0.00 3.08
3037 3252 3.821033 AGCCCTATCAAAATCGCAATACC 59.179 43.478 0.00 0.00 0.00 2.73
3038 3253 4.757149 AGAGCCCTATCAAAATCGCAATAC 59.243 41.667 0.00 0.00 0.00 1.89
3039 3254 4.756642 CAGAGCCCTATCAAAATCGCAATA 59.243 41.667 0.00 0.00 0.00 1.90
3040 3255 3.567164 CAGAGCCCTATCAAAATCGCAAT 59.433 43.478 0.00 0.00 0.00 3.56
3042 3257 2.092968 ACAGAGCCCTATCAAAATCGCA 60.093 45.455 0.00 0.00 0.00 5.10
3043 3258 2.565841 ACAGAGCCCTATCAAAATCGC 58.434 47.619 0.00 0.00 0.00 4.58
3044 3259 5.116180 TGTAACAGAGCCCTATCAAAATCG 58.884 41.667 0.00 0.00 0.00 3.34
3052 3267 3.301274 GAGACCTGTAACAGAGCCCTAT 58.699 50.000 0.00 0.00 32.44 2.57
3054 3269 1.203187 TGAGACCTGTAACAGAGCCCT 60.203 52.381 0.00 0.00 32.44 5.19
3055 3270 1.066787 GTGAGACCTGTAACAGAGCCC 60.067 57.143 0.00 0.00 32.44 5.19
3060 3275 4.336889 TTTCCAGTGAGACCTGTAACAG 57.663 45.455 0.00 0.00 0.00 3.16
3061 3276 4.974645 ATTTCCAGTGAGACCTGTAACA 57.025 40.909 0.00 0.00 0.00 2.41
3062 3277 5.063880 ACAATTTCCAGTGAGACCTGTAAC 58.936 41.667 0.00 0.00 0.00 2.50
3078 3293 3.735746 GCACACCACAGCTAAACAATTTC 59.264 43.478 0.00 0.00 0.00 2.17
3087 3302 2.367241 TCAGTAAAGCACACCACAGCTA 59.633 45.455 0.00 0.00 40.90 3.32
3092 3318 6.978343 TTATGTATCAGTAAAGCACACCAC 57.022 37.500 0.00 0.00 0.00 4.16
3095 3321 7.015226 TGCATTATGTATCAGTAAAGCACAC 57.985 36.000 0.00 0.00 31.85 3.82
3096 3322 7.806409 ATGCATTATGTATCAGTAAAGCACA 57.194 32.000 0.00 0.00 37.34 4.57
3104 3330 9.265901 GTGAGTCTAAATGCATTATGTATCAGT 57.734 33.333 13.39 0.00 0.00 3.41
3108 3334 9.618890 ACAAGTGAGTCTAAATGCATTATGTAT 57.381 29.630 13.39 0.00 0.00 2.29
3110 3336 7.607607 TCACAAGTGAGTCTAAATGCATTATGT 59.392 33.333 13.39 0.00 34.14 2.29
3111 3337 7.907045 GTCACAAGTGAGTCTAAATGCATTATG 59.093 37.037 13.39 8.71 40.75 1.90
3112 3338 7.826252 AGTCACAAGTGAGTCTAAATGCATTAT 59.174 33.333 13.39 5.90 38.84 1.28
3121 3347 8.687292 TCTAAACTAGTCACAAGTGAGTCTAA 57.313 34.615 13.42 0.00 41.92 2.10
3122 3348 8.687292 TTCTAAACTAGTCACAAGTGAGTCTA 57.313 34.615 13.42 7.01 41.92 2.59
3123 3349 7.285858 ACTTCTAAACTAGTCACAAGTGAGTCT 59.714 37.037 13.42 6.25 41.92 3.24
3152 3378 4.467082 ACAGGGCTGCATATTTTTCATGAA 59.533 37.500 3.38 3.38 0.00 2.57
3153 3379 4.025360 ACAGGGCTGCATATTTTTCATGA 58.975 39.130 0.50 0.00 0.00 3.07
3156 3382 3.195396 GGAACAGGGCTGCATATTTTTCA 59.805 43.478 0.50 0.00 0.00 2.69
3157 3383 3.430790 GGGAACAGGGCTGCATATTTTTC 60.431 47.826 0.50 0.00 0.00 2.29
3158 3384 2.501316 GGGAACAGGGCTGCATATTTTT 59.499 45.455 0.50 0.00 0.00 1.94
3159 3385 2.110578 GGGAACAGGGCTGCATATTTT 58.889 47.619 0.50 0.00 0.00 1.82
3160 3386 1.288932 AGGGAACAGGGCTGCATATTT 59.711 47.619 0.50 0.00 0.00 1.40
3161 3387 0.929244 AGGGAACAGGGCTGCATATT 59.071 50.000 0.50 0.00 0.00 1.28
3162 3388 0.475906 GAGGGAACAGGGCTGCATAT 59.524 55.000 0.50 0.00 0.00 1.78
3163 3389 1.635817 GGAGGGAACAGGGCTGCATA 61.636 60.000 0.50 0.00 0.00 3.14
3164 3390 2.679716 GAGGGAACAGGGCTGCAT 59.320 61.111 0.50 0.00 0.00 3.96
3165 3391 3.650950 GGAGGGAACAGGGCTGCA 61.651 66.667 0.50 0.00 0.00 4.41
3166 3392 4.432741 GGGAGGGAACAGGGCTGC 62.433 72.222 0.00 0.00 0.00 5.25
3167 3393 2.935481 TGGGAGGGAACAGGGCTG 60.935 66.667 0.00 0.00 0.00 4.85
3168 3394 2.612115 CTGGGAGGGAACAGGGCT 60.612 66.667 0.00 0.00 0.00 5.19
3178 3404 3.739401 AAGTCATTTAACCCTGGGAGG 57.261 47.619 22.23 0.00 34.30 4.30
3179 3405 5.437191 ACTAAGTCATTTAACCCTGGGAG 57.563 43.478 22.23 3.78 0.00 4.30
3180 3406 6.731919 TCTTACTAAGTCATTTAACCCTGGGA 59.268 38.462 22.23 0.00 0.00 4.37
3181 3407 6.954232 TCTTACTAAGTCATTTAACCCTGGG 58.046 40.000 12.28 12.28 0.00 4.45
3182 3408 7.048512 CCTCTTACTAAGTCATTTAACCCTGG 58.951 42.308 0.00 0.00 0.00 4.45
3183 3409 7.048512 CCCTCTTACTAAGTCATTTAACCCTG 58.951 42.308 0.00 0.00 0.00 4.45
3184 3410 6.734281 ACCCTCTTACTAAGTCATTTAACCCT 59.266 38.462 0.00 0.00 0.00 4.34
3185 3411 6.955364 ACCCTCTTACTAAGTCATTTAACCC 58.045 40.000 0.00 0.00 0.00 4.11
3190 3416 8.419442 CGGTATAACCCTCTTACTAAGTCATTT 58.581 37.037 0.00 0.00 33.75 2.32
3191 3417 7.562821 ACGGTATAACCCTCTTACTAAGTCATT 59.437 37.037 0.00 0.00 33.75 2.57
3192 3418 7.065504 ACGGTATAACCCTCTTACTAAGTCAT 58.934 38.462 0.00 0.00 33.75 3.06
3193 3419 6.426587 ACGGTATAACCCTCTTACTAAGTCA 58.573 40.000 0.00 0.00 33.75 3.41
3194 3420 6.951062 ACGGTATAACCCTCTTACTAAGTC 57.049 41.667 0.00 0.00 33.75 3.01
3199 3425 8.082672 ACATTTTACGGTATAACCCTCTTACT 57.917 34.615 0.00 0.00 33.75 2.24
3206 3432 6.932960 AGCTCATACATTTTACGGTATAACCC 59.067 38.462 0.00 0.00 33.75 4.11
3213 3439 5.472137 ACAAACAGCTCATACATTTTACGGT 59.528 36.000 0.00 0.00 0.00 4.83
3214 3440 5.938322 ACAAACAGCTCATACATTTTACGG 58.062 37.500 0.00 0.00 0.00 4.02
3216 3442 8.936864 AGTCTACAAACAGCTCATACATTTTAC 58.063 33.333 0.00 0.00 0.00 2.01
3219 3445 6.936900 ACAGTCTACAAACAGCTCATACATTT 59.063 34.615 0.00 0.00 0.00 2.32
3224 3488 6.835819 ACTACAGTCTACAAACAGCTCATA 57.164 37.500 0.00 0.00 0.00 2.15
3225 3489 5.730296 ACTACAGTCTACAAACAGCTCAT 57.270 39.130 0.00 0.00 0.00 2.90
3226 3490 6.835819 ATACTACAGTCTACAAACAGCTCA 57.164 37.500 0.00 0.00 0.00 4.26
3257 3521 9.695526 TTCCTGTTTTCAACATCTCAATTAATG 57.304 29.630 0.00 0.00 41.26 1.90
3260 3524 7.814107 GCATTCCTGTTTTCAACATCTCAATTA 59.186 33.333 0.00 0.00 41.26 1.40
3264 3528 4.583907 TGCATTCCTGTTTTCAACATCTCA 59.416 37.500 0.00 0.00 41.26 3.27
3266 3530 4.262164 GGTGCATTCCTGTTTTCAACATCT 60.262 41.667 0.00 0.00 41.26 2.90
3273 3537 2.288395 CCTGTGGTGCATTCCTGTTTTC 60.288 50.000 0.00 0.00 0.00 2.29
3275 3539 1.331214 CCTGTGGTGCATTCCTGTTT 58.669 50.000 0.00 0.00 0.00 2.83
3293 3557 3.274288 CTCTCCTATGTTTGAAGCACCC 58.726 50.000 0.00 0.00 0.00 4.61
3294 3558 3.944087 ACTCTCCTATGTTTGAAGCACC 58.056 45.455 0.00 0.00 0.00 5.01
3295 3559 6.457528 GCAATACTCTCCTATGTTTGAAGCAC 60.458 42.308 0.00 0.00 0.00 4.40
3298 3562 6.820656 ACAGCAATACTCTCCTATGTTTGAAG 59.179 38.462 0.00 0.00 0.00 3.02
3299 3563 6.711277 ACAGCAATACTCTCCTATGTTTGAA 58.289 36.000 0.00 0.00 0.00 2.69
3302 3566 7.335422 CAGAAACAGCAATACTCTCCTATGTTT 59.665 37.037 0.00 0.00 41.03 2.83
3303 3567 6.820656 CAGAAACAGCAATACTCTCCTATGTT 59.179 38.462 0.00 0.00 0.00 2.71
3305 3569 6.257411 CACAGAAACAGCAATACTCTCCTATG 59.743 42.308 0.00 0.00 0.00 2.23
3306 3570 6.070538 ACACAGAAACAGCAATACTCTCCTAT 60.071 38.462 0.00 0.00 0.00 2.57
3308 3572 4.040952 ACACAGAAACAGCAATACTCTCCT 59.959 41.667 0.00 0.00 0.00 3.69
3309 3573 4.319177 ACACAGAAACAGCAATACTCTCC 58.681 43.478 0.00 0.00 0.00 3.71
3311 3575 5.853936 TGTACACAGAAACAGCAATACTCT 58.146 37.500 0.00 0.00 0.00 3.24
3313 3577 7.510549 AATTGTACACAGAAACAGCAATACT 57.489 32.000 0.00 0.00 0.00 2.12
3317 3581 8.615878 ACTATAATTGTACACAGAAACAGCAA 57.384 30.769 0.00 0.00 0.00 3.91
3318 3582 8.503196 CAACTATAATTGTACACAGAAACAGCA 58.497 33.333 0.00 0.00 0.00 4.41
3319 3583 7.481798 GCAACTATAATTGTACACAGAAACAGC 59.518 37.037 0.00 0.00 31.83 4.40
3320 3584 8.503196 TGCAACTATAATTGTACACAGAAACAG 58.497 33.333 0.00 0.00 31.83 3.16
3321 3585 8.286800 GTGCAACTATAATTGTACACAGAAACA 58.713 33.333 9.80 0.00 42.68 2.83
3322 3586 8.286800 TGTGCAACTATAATTGTACACAGAAAC 58.713 33.333 12.83 0.00 46.19 2.78
3323 3587 8.384607 TGTGCAACTATAATTGTACACAGAAA 57.615 30.769 12.83 0.00 46.19 2.52
3324 3588 7.971183 TGTGCAACTATAATTGTACACAGAA 57.029 32.000 12.83 0.00 46.19 3.02
3330 3594 6.693315 ACCCATGTGCAACTATAATTGTAC 57.307 37.500 8.02 8.02 43.23 2.90
3331 3595 8.809468 TTTACCCATGTGCAACTATAATTGTA 57.191 30.769 0.00 0.00 38.04 2.41
3332 3596 7.710676 TTTACCCATGTGCAACTATAATTGT 57.289 32.000 0.00 0.00 38.04 2.71
3333 3597 8.196771 ACATTTACCCATGTGCAACTATAATTG 58.803 33.333 0.00 0.00 35.97 2.32
3334 3598 8.305046 ACATTTACCCATGTGCAACTATAATT 57.695 30.769 0.00 0.00 35.97 1.40
3335 3599 7.896383 ACATTTACCCATGTGCAACTATAAT 57.104 32.000 0.00 0.00 35.97 1.28
3336 3600 7.710676 AACATTTACCCATGTGCAACTATAA 57.289 32.000 0.00 0.00 37.46 0.98
3337 3601 7.710676 AAACATTTACCCATGTGCAACTATA 57.289 32.000 0.00 0.00 37.46 1.31
3338 3602 6.603940 AAACATTTACCCATGTGCAACTAT 57.396 33.333 0.00 0.00 37.46 2.12
3339 3603 6.412362 AAAACATTTACCCATGTGCAACTA 57.588 33.333 0.00 0.00 37.46 2.24
3340 3604 4.953940 AAACATTTACCCATGTGCAACT 57.046 36.364 0.00 0.00 37.46 3.16
3341 3605 4.450757 GGAAAACATTTACCCATGTGCAAC 59.549 41.667 0.00 0.00 37.46 4.17
3342 3606 4.346418 AGGAAAACATTTACCCATGTGCAA 59.654 37.500 0.00 0.00 37.46 4.08
3343 3607 3.900601 AGGAAAACATTTACCCATGTGCA 59.099 39.130 0.00 0.00 37.46 4.57
3344 3608 4.535526 AGGAAAACATTTACCCATGTGC 57.464 40.909 0.00 0.00 37.46 4.57
3345 3609 5.245977 AGGAAGGAAAACATTTACCCATGTG 59.754 40.000 0.00 0.00 37.46 3.21
3346 3610 5.402630 AGGAAGGAAAACATTTACCCATGT 58.597 37.500 0.00 0.00 39.17 3.21
3347 3611 6.014669 TGAAGGAAGGAAAACATTTACCCATG 60.015 38.462 0.00 0.00 0.00 3.66
3348 3612 6.081356 TGAAGGAAGGAAAACATTTACCCAT 58.919 36.000 0.00 0.00 0.00 4.00
3349 3613 5.459505 TGAAGGAAGGAAAACATTTACCCA 58.540 37.500 0.00 0.00 0.00 4.51
3350 3614 5.538813 ACTGAAGGAAGGAAAACATTTACCC 59.461 40.000 0.00 0.00 0.00 3.69
3351 3615 6.650427 ACTGAAGGAAGGAAAACATTTACC 57.350 37.500 0.00 0.00 0.00 2.85
3354 3618 9.232473 GAGTATACTGAAGGAAGGAAAACATTT 57.768 33.333 10.90 0.00 0.00 2.32
3355 3619 7.829706 GGAGTATACTGAAGGAAGGAAAACATT 59.170 37.037 10.90 0.00 0.00 2.71
3356 3620 7.037586 TGGAGTATACTGAAGGAAGGAAAACAT 60.038 37.037 10.90 0.00 0.00 2.71
3357 3621 6.271391 TGGAGTATACTGAAGGAAGGAAAACA 59.729 38.462 10.90 0.00 0.00 2.83
3358 3622 6.708285 TGGAGTATACTGAAGGAAGGAAAAC 58.292 40.000 10.90 0.00 0.00 2.43
3359 3623 6.500751 ACTGGAGTATACTGAAGGAAGGAAAA 59.499 38.462 10.90 0.00 0.00 2.29
3360 3624 6.023603 ACTGGAGTATACTGAAGGAAGGAAA 58.976 40.000 10.90 0.00 0.00 3.13
3361 3625 5.422331 CACTGGAGTATACTGAAGGAAGGAA 59.578 44.000 10.90 0.00 0.00 3.36
3362 3626 4.956700 CACTGGAGTATACTGAAGGAAGGA 59.043 45.833 10.90 0.00 0.00 3.36
3363 3627 4.956700 TCACTGGAGTATACTGAAGGAAGG 59.043 45.833 10.90 0.49 0.00 3.46
3364 3628 6.153680 AGTTCACTGGAGTATACTGAAGGAAG 59.846 42.308 10.90 1.39 0.00 3.46
3365 3629 6.017192 AGTTCACTGGAGTATACTGAAGGAA 58.983 40.000 10.90 9.71 0.00 3.36
3366 3630 5.419155 CAGTTCACTGGAGTATACTGAAGGA 59.581 44.000 10.90 4.71 39.21 3.36
3367 3631 5.419155 TCAGTTCACTGGAGTATACTGAAGG 59.581 44.000 10.90 4.07 40.98 3.46
3368 3632 6.516739 TCAGTTCACTGGAGTATACTGAAG 57.483 41.667 10.90 9.75 40.98 3.02
3369 3633 7.482169 AATCAGTTCACTGGAGTATACTGAA 57.518 36.000 10.90 5.28 43.90 3.02
3370 3634 6.183360 CGAATCAGTTCACTGGAGTATACTGA 60.183 42.308 10.90 18.22 44.34 3.41
3371 3635 5.974158 CGAATCAGTTCACTGGAGTATACTG 59.026 44.000 10.90 11.52 43.91 2.74
3372 3636 5.067936 CCGAATCAGTTCACTGGAGTATACT 59.932 44.000 4.68 4.68 43.91 2.12
3373 3637 5.067413 TCCGAATCAGTTCACTGGAGTATAC 59.933 44.000 7.11 0.00 43.91 1.47
3374 3638 5.198207 TCCGAATCAGTTCACTGGAGTATA 58.802 41.667 7.11 0.00 43.91 1.47
3375 3639 4.023980 TCCGAATCAGTTCACTGGAGTAT 58.976 43.478 7.11 0.00 43.91 2.12
3376 3640 3.427573 TCCGAATCAGTTCACTGGAGTA 58.572 45.455 7.11 0.00 43.91 2.59
3377 3641 2.248248 TCCGAATCAGTTCACTGGAGT 58.752 47.619 7.11 0.00 43.91 3.85
3378 3642 3.118992 TCATCCGAATCAGTTCACTGGAG 60.119 47.826 7.11 0.00 43.91 3.86
3379 3643 2.831526 TCATCCGAATCAGTTCACTGGA 59.168 45.455 7.11 0.00 43.91 3.86
3394 3658 1.788886 CTACACACGATGCATCATCCG 59.211 52.381 25.70 15.02 37.57 4.18
3396 3660 3.544834 GCAACTACACACGATGCATCATC 60.545 47.826 25.70 1.19 37.50 2.92
3405 3670 0.249699 CCCACTGCAACTACACACGA 60.250 55.000 0.00 0.00 0.00 4.35
3406 3671 1.841663 GCCCACTGCAACTACACACG 61.842 60.000 0.00 0.00 40.77 4.49
3420 3685 0.616679 TCCCTACACTAGGTGCCCAC 60.617 60.000 0.00 0.00 44.73 4.61
3423 3688 3.306613 ACTTATCCCTACACTAGGTGCC 58.693 50.000 0.00 0.00 44.73 5.01
3424 3689 4.404715 TCAACTTATCCCTACACTAGGTGC 59.595 45.833 0.00 0.00 44.73 5.01
3425 3690 5.892119 TCTCAACTTATCCCTACACTAGGTG 59.108 44.000 0.00 0.00 44.73 4.00
3426 3691 6.068971 TCTCTCAACTTATCCCTACACTAGGT 60.069 42.308 0.00 0.00 44.73 3.08
3427 3692 6.366340 TCTCTCAACTTATCCCTACACTAGG 58.634 44.000 0.00 0.00 45.81 3.02
3428 3693 9.005777 GTATCTCTCAACTTATCCCTACACTAG 57.994 40.741 0.00 0.00 0.00 2.57
3430 3695 6.778559 GGTATCTCTCAACTTATCCCTACACT 59.221 42.308 0.00 0.00 0.00 3.55
3431 3696 6.778559 AGGTATCTCTCAACTTATCCCTACAC 59.221 42.308 0.00 0.00 0.00 2.90
3436 3701 9.930158 AGATATAGGTATCTCTCAACTTATCCC 57.070 37.037 0.00 0.00 42.67 3.85
3476 3741 4.703897 CCGCCTGGAATGATTTCTTACTA 58.296 43.478 0.00 0.00 37.49 1.82
3480 3745 1.106285 GCCGCCTGGAATGATTTCTT 58.894 50.000 0.00 0.00 37.49 2.52
3487 3752 1.463674 AAAAGTAGCCGCCTGGAATG 58.536 50.000 0.00 0.00 37.49 2.67
3492 3757 1.200020 CTTGGAAAAAGTAGCCGCCTG 59.800 52.381 0.00 0.00 0.00 4.85
3496 3765 2.427506 AGAGCTTGGAAAAAGTAGCCG 58.572 47.619 0.00 0.00 0.00 5.52
3506 3775 3.381272 CCACAGAACAAAAGAGCTTGGAA 59.619 43.478 0.00 0.00 0.00 3.53
3516 3785 4.780815 ACATGAGAGACCACAGAACAAAA 58.219 39.130 0.00 0.00 0.00 2.44
3518 3787 4.380531 GAACATGAGAGACCACAGAACAA 58.619 43.478 0.00 0.00 0.00 2.83
3519 3788 3.244215 GGAACATGAGAGACCACAGAACA 60.244 47.826 0.00 0.00 0.00 3.18
3520 3789 3.007398 AGGAACATGAGAGACCACAGAAC 59.993 47.826 0.00 0.00 0.00 3.01
3521 3790 3.242867 AGGAACATGAGAGACCACAGAA 58.757 45.455 0.00 0.00 0.00 3.02
3522 3791 2.828520 GAGGAACATGAGAGACCACAGA 59.171 50.000 0.00 0.00 0.00 3.41
3525 3794 3.513515 AGAAGAGGAACATGAGAGACCAC 59.486 47.826 0.00 0.00 0.00 4.16
3533 3802 3.394274 TGGGTTCAAGAAGAGGAACATGA 59.606 43.478 0.00 0.00 43.96 3.07


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

AutoCloner maintained by Alex Coulton.