Multiple sequence alignment - TraesCS5A01G479400

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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 TraesCS5A01G479400 chr5A 100.000 3659 0 0 1 3659 652645927 652649585 0.000000e+00 6758
1 TraesCS5A01G479400 chr5B 91.888 3390 116 65 1 3310 660587862 660591172 0.000000e+00 4590
2 TraesCS5A01G479400 chr5B 85.845 219 28 2 1638 1853 112194761 112194543 2.840000e-56 230
3 TraesCS5A01G479400 chr5D 90.919 3513 116 73 1 3408 525956295 525959709 0.000000e+00 4532
4 TraesCS5A01G479400 chr3D 89.952 209 19 2 1642 1849 610544049 610544256 6.020000e-68 268
5 TraesCS5A01G479400 chr3B 89.423 208 22 0 1642 1849 828111449 828111656 2.800000e-66 263
6 TraesCS5A01G479400 chr3B 88.038 209 22 3 1632 1839 675649880 675650086 1.010000e-60 244
7 TraesCS5A01G479400 chr3A 89.423 208 22 0 1642 1849 744879519 744879726 2.800000e-66 263
8 TraesCS5A01G479400 chr1A 86.222 225 28 1 1642 1863 18461761 18461537 1.310000e-59 241
9 TraesCS5A01G479400 chr1B 85.333 225 30 2 1642 1863 24933085 24932861 2.840000e-56 230


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 TraesCS5A01G479400 chr5A 652645927 652649585 3658 False 6758 6758 100.000 1 3659 1 chr5A.!!$F1 3658
1 TraesCS5A01G479400 chr5B 660587862 660591172 3310 False 4590 4590 91.888 1 3310 1 chr5B.!!$F1 3309
2 TraesCS5A01G479400 chr5D 525956295 525959709 3414 False 4532 4532 90.919 1 3408 1 chr5D.!!$F1 3407

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
261 272 0.038166 GATGAACCCCAGTTGCCAGA 59.962 55.0 0.00 0.0 35.94 3.86 F
717 738 0.536260 CCTCAGCTCCTTGTGAGAGG 59.464 60.0 0.86 0.0 44.42 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1435 1480 1.066257 GTTGCTGTTGCTGGTGGTG 59.934 57.895 0.00 0.00 40.48 4.17 R
2714 2768 1.680249 GGGCTACCTTTTGCAGAGAGG 60.680 57.143 9.72 9.72 36.62 3.69 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
78 81 1.743996 GGCAAGACCAAGATGAGACC 58.256 55.000 0.00 0.00 38.86 3.85
79 82 1.003580 GGCAAGACCAAGATGAGACCA 59.996 52.381 0.00 0.00 38.86 4.02
80 83 2.553028 GGCAAGACCAAGATGAGACCAA 60.553 50.000 0.00 0.00 38.86 3.67
81 84 2.746362 GCAAGACCAAGATGAGACCAAG 59.254 50.000 0.00 0.00 0.00 3.61
82 85 3.557898 GCAAGACCAAGATGAGACCAAGA 60.558 47.826 0.00 0.00 0.00 3.02
108 111 9.708092 ACTAGTAAGACCAACTTTTACTGATTC 57.292 33.333 0.00 0.00 37.95 2.52
161 164 2.055310 CTGCAGCCATACATGCACCG 62.055 60.000 0.00 0.00 46.97 4.94
174 178 2.833227 CACCGGAACACCCCAAGA 59.167 61.111 9.46 0.00 0.00 3.02
221 231 1.681327 CAGCCAGCCAGCTCCAATT 60.681 57.895 0.00 0.00 42.61 2.32
260 271 0.251297 TGATGAACCCCAGTTGCCAG 60.251 55.000 0.00 0.00 35.94 4.85
261 272 0.038166 GATGAACCCCAGTTGCCAGA 59.962 55.000 0.00 0.00 35.94 3.86
381 393 2.422377 CCCATGCATTCTCTCATCACCA 60.422 50.000 0.00 0.00 0.00 4.17
382 394 2.617308 CCATGCATTCTCTCATCACCAC 59.383 50.000 0.00 0.00 0.00 4.16
383 395 2.014335 TGCATTCTCTCATCACCACG 57.986 50.000 0.00 0.00 0.00 4.94
384 396 1.276138 TGCATTCTCTCATCACCACGT 59.724 47.619 0.00 0.00 0.00 4.49
406 418 1.132977 TCACTCCACCTGACCACCTAA 60.133 52.381 0.00 0.00 0.00 2.69
416 428 4.202760 ACCTGACCACCTAAGGTACTAACT 60.203 45.833 0.00 0.00 42.59 2.24
481 495 1.341383 ACATTCCCTTGCAGGCTAAGG 60.341 52.381 8.81 8.81 43.46 2.69
485 499 0.681243 CCCTTGCAGGCTAAGGAACC 60.681 60.000 16.14 0.00 46.08 3.62
515 536 2.044492 TCTCTCTAAGCTTCCTTCCCCA 59.956 50.000 0.00 0.00 32.47 4.96
558 579 8.352137 TCACATCCCAAATATATAATGCAAGG 57.648 34.615 0.00 0.00 0.00 3.61
717 738 0.536260 CCTCAGCTCCTTGTGAGAGG 59.464 60.000 0.86 0.00 44.42 3.69
718 739 1.554836 CTCAGCTCCTTGTGAGAGGA 58.445 55.000 0.00 0.00 44.42 3.71
840 876 1.530183 GCTTGCATGATCCCCTCCC 60.530 63.158 3.33 0.00 0.00 4.30
863 899 2.994957 AGCACCTATATACCCCTCGT 57.005 50.000 0.00 0.00 0.00 4.18
869 905 4.019141 CACCTATATACCCCTCGTCTCTCT 60.019 50.000 0.00 0.00 0.00 3.10
882 918 4.144727 TCTCTCCCGGCCCTCTCC 62.145 72.222 0.00 0.00 0.00 3.71
997 1033 3.814906 CCACCACCACCACCACCA 61.815 66.667 0.00 0.00 0.00 4.17
998 1034 2.518349 CACCACCACCACCACCAC 60.518 66.667 0.00 0.00 0.00 4.16
999 1035 3.816090 ACCACCACCACCACCACC 61.816 66.667 0.00 0.00 0.00 4.61
1058 1094 2.697751 CCAATTGGAACCAGAACCACAA 59.302 45.455 20.50 0.00 37.39 3.33
1222 1267 5.339530 CCCCTTCTTGAATATTCACACTCCT 60.340 44.000 17.76 0.00 36.83 3.69
1244 1289 5.300286 CCTATGGCTTTTTAGTTGCTATGCT 59.700 40.000 0.00 0.00 0.00 3.79
1304 1349 5.561725 GCTTTGATTCTCTTGCTTTTCGAGT 60.562 40.000 0.00 0.00 0.00 4.18
1353 1398 3.128188 CTCCAGCAGCAGCAGCAG 61.128 66.667 12.92 3.65 45.49 4.24
1435 1480 2.115052 TGGACATGCACCACCACC 59.885 61.111 7.95 0.00 32.03 4.61
1436 1481 2.115052 GGACATGCACCACCACCA 59.885 61.111 0.00 0.00 0.00 4.17
1437 1482 2.268076 GGACATGCACCACCACCAC 61.268 63.158 0.00 0.00 0.00 4.16
1455 1500 1.361271 CCACCAGCAACAGCAACAG 59.639 57.895 0.00 0.00 0.00 3.16
1464 1509 1.538512 CAACAGCAACAGCAGCAGTAT 59.461 47.619 0.00 0.00 31.17 2.12
1467 1512 1.397343 CAGCAACAGCAGCAGTATCAG 59.603 52.381 0.00 0.00 0.00 2.90
1478 1523 0.743345 CAGTATCAGCAGCAGCAGCA 60.743 55.000 12.92 0.00 45.49 4.41
1485 1530 3.738246 CAGCAGCAGCAGCACCAG 61.738 66.667 12.92 0.00 45.49 4.00
1540 1585 4.467084 GGGCGTTGATGGCTCCGA 62.467 66.667 0.00 0.00 34.31 4.55
1570 1615 1.078426 ATGGGTAGTGCGGTTGCTC 60.078 57.895 0.00 0.00 43.34 4.26
1654 1705 2.494918 CAGGGTCGATGACGGACC 59.505 66.667 2.38 2.38 40.21 4.46
1655 1706 3.138798 AGGGTCGATGACGGACCG 61.139 66.667 13.61 13.61 39.07 4.79
2025 2079 4.195334 GCCGGGGCCATGATGTCT 62.195 66.667 4.39 0.00 34.56 3.41
2253 2307 0.538057 TGCAGCAGTTCCCCTTCTTG 60.538 55.000 0.00 0.00 0.00 3.02
2666 2720 2.548707 GCAACATCCTGTGACTGTGAGA 60.549 50.000 0.00 0.00 0.00 3.27
2714 2768 1.656652 CATGGTGGAATGGAGTCGAC 58.343 55.000 7.70 7.70 0.00 4.20
2733 2787 1.003696 ACCTCTCTGCAAAAGGTAGCC 59.996 52.381 11.56 0.00 41.61 3.93
2829 2883 1.376683 GGAGTTGTGGTGGCGCATA 60.377 57.895 10.83 0.00 0.00 3.14
2842 2897 1.335324 GGCGCATACAAGATCATTGCC 60.335 52.381 10.83 0.00 0.00 4.52
2844 2899 1.069703 CGCATACAAGATCATTGCCGG 60.070 52.381 0.00 0.00 0.00 6.13
2912 2971 2.362736 TCTCCATGCATGCTGTTCTTC 58.637 47.619 21.69 0.00 0.00 2.87
2943 3002 9.722184 GTCTTAATTAGGTTCTTTCTTGGTACT 57.278 33.333 0.00 0.00 0.00 2.73
2981 3040 6.015940 GGTGCTGGATTTTCTATATTCTTGGG 60.016 42.308 0.00 0.00 0.00 4.12
2997 3056 4.435137 TCTTGGGTCTCCTTAATTCTCCA 58.565 43.478 0.00 0.00 0.00 3.86
2998 3057 4.849810 TCTTGGGTCTCCTTAATTCTCCAA 59.150 41.667 0.00 0.00 0.00 3.53
3014 3073 5.565592 TCTCCAATGTCATTGTAATGCAC 57.434 39.130 21.32 1.32 38.59 4.57
3038 3097 8.437742 CACGTTAATTGGTACCAAGTTTACTAG 58.562 37.037 30.53 18.60 39.47 2.57
3039 3098 7.118245 ACGTTAATTGGTACCAAGTTTACTAGC 59.882 37.037 30.53 14.36 39.47 3.42
3040 3099 7.332678 CGTTAATTGGTACCAAGTTTACTAGCT 59.667 37.037 30.53 8.49 39.47 3.32
3041 3100 9.006839 GTTAATTGGTACCAAGTTTACTAGCTT 57.993 33.333 30.53 17.96 39.47 3.74
3042 3101 7.448748 AATTGGTACCAAGTTTACTAGCTTG 57.551 36.000 30.00 0.00 39.47 4.01
3145 3242 8.432013 TCAGTATATTGGTGCAATCTTCATACT 58.568 33.333 0.00 0.00 34.74 2.12
3171 3276 6.319658 CCATGTATGAGTAGCTTGGAATGTTT 59.680 38.462 0.00 0.00 31.49 2.83
3172 3277 6.985188 TGTATGAGTAGCTTGGAATGTTTC 57.015 37.500 0.00 0.00 0.00 2.78
3173 3278 6.711277 TGTATGAGTAGCTTGGAATGTTTCT 58.289 36.000 0.00 0.00 0.00 2.52
3174 3279 7.847096 TGTATGAGTAGCTTGGAATGTTTCTA 58.153 34.615 0.00 0.00 0.00 2.10
3175 3280 7.764443 TGTATGAGTAGCTTGGAATGTTTCTAC 59.236 37.037 0.00 0.00 0.00 2.59
3177 3282 6.398918 TGAGTAGCTTGGAATGTTTCTACTC 58.601 40.000 16.11 16.11 46.37 2.59
3178 3283 5.411781 AGTAGCTTGGAATGTTTCTACTCG 58.588 41.667 0.00 0.00 33.56 4.18
3180 3285 3.003480 GCTTGGAATGTTTCTACTCGCT 58.997 45.455 0.00 0.00 0.00 4.93
3181 3286 3.437049 GCTTGGAATGTTTCTACTCGCTT 59.563 43.478 0.00 0.00 0.00 4.68
3182 3287 4.630069 GCTTGGAATGTTTCTACTCGCTTA 59.370 41.667 0.00 0.00 0.00 3.09
3184 3289 6.183360 GCTTGGAATGTTTCTACTCGCTTATT 60.183 38.462 0.00 0.00 0.00 1.40
3185 3290 7.626452 GCTTGGAATGTTTCTACTCGCTTATTT 60.626 37.037 0.00 0.00 0.00 1.40
3186 3291 7.681939 TGGAATGTTTCTACTCGCTTATTTT 57.318 32.000 0.00 0.00 0.00 1.82
3373 3498 7.660617 AGGTTGATTGTCATTGCTATCATCTAG 59.339 37.037 0.00 0.00 32.51 2.43
3375 3500 9.481340 GTTGATTGTCATTGCTATCATCTAGTA 57.519 33.333 0.00 0.00 32.51 1.82
3381 3506 8.777413 TGTCATTGCTATCATCTAGTAATTTGC 58.223 33.333 0.00 0.00 29.50 3.68
3382 3507 8.777413 GTCATTGCTATCATCTAGTAATTTGCA 58.223 33.333 0.00 0.00 29.50 4.08
3414 3540 9.569122 TCCCTAGAAATTTAGTTTATATGTGCC 57.431 33.333 0.00 0.00 0.00 5.01
3415 3541 8.793592 CCCTAGAAATTTAGTTTATATGTGCCC 58.206 37.037 0.00 0.00 0.00 5.36
3416 3542 9.349713 CCTAGAAATTTAGTTTATATGTGCCCA 57.650 33.333 0.00 0.00 0.00 5.36
3432 3558 6.942532 TGTGCCCATTTATCAAATCTAGTC 57.057 37.500 0.00 0.00 0.00 2.59
3433 3559 6.662755 TGTGCCCATTTATCAAATCTAGTCT 58.337 36.000 0.00 0.00 0.00 3.24
3434 3560 7.118723 TGTGCCCATTTATCAAATCTAGTCTT 58.881 34.615 0.00 0.00 0.00 3.01
3435 3561 7.067372 TGTGCCCATTTATCAAATCTAGTCTTG 59.933 37.037 0.00 0.00 0.00 3.02
3436 3562 6.039717 TGCCCATTTATCAAATCTAGTCTTGC 59.960 38.462 0.00 0.00 0.00 4.01
3437 3563 6.264067 GCCCATTTATCAAATCTAGTCTTGCT 59.736 38.462 0.00 0.00 0.00 3.91
3438 3564 7.521261 GCCCATTTATCAAATCTAGTCTTGCTC 60.521 40.741 0.00 0.00 0.00 4.26
3439 3565 7.500227 CCCATTTATCAAATCTAGTCTTGCTCA 59.500 37.037 0.00 0.00 0.00 4.26
3440 3566 9.064706 CCATTTATCAAATCTAGTCTTGCTCAT 57.935 33.333 0.00 0.00 0.00 2.90
3441 3567 9.880064 CATTTATCAAATCTAGTCTTGCTCATG 57.120 33.333 0.00 0.00 0.00 3.07
3442 3568 8.442632 TTTATCAAATCTAGTCTTGCTCATGG 57.557 34.615 0.00 0.00 0.00 3.66
3443 3569 5.426689 TCAAATCTAGTCTTGCTCATGGT 57.573 39.130 0.00 0.00 0.00 3.55
3444 3570 6.544928 TCAAATCTAGTCTTGCTCATGGTA 57.455 37.500 0.00 0.00 0.00 3.25
3445 3571 6.341316 TCAAATCTAGTCTTGCTCATGGTAC 58.659 40.000 0.00 0.00 0.00 3.34
3446 3572 6.155221 TCAAATCTAGTCTTGCTCATGGTACT 59.845 38.462 0.00 0.00 0.00 2.73
3447 3573 5.782893 ATCTAGTCTTGCTCATGGTACTC 57.217 43.478 0.00 0.00 0.00 2.59
3448 3574 2.949451 AGTCTTGCTCATGGTACTCG 57.051 50.000 0.00 0.00 0.00 4.18
3449 3575 2.447443 AGTCTTGCTCATGGTACTCGA 58.553 47.619 0.00 0.00 0.00 4.04
3450 3576 2.826128 AGTCTTGCTCATGGTACTCGAA 59.174 45.455 0.00 0.00 0.00 3.71
3451 3577 3.449018 AGTCTTGCTCATGGTACTCGAAT 59.551 43.478 0.00 0.00 0.00 3.34
3452 3578 4.081420 AGTCTTGCTCATGGTACTCGAATT 60.081 41.667 0.00 0.00 0.00 2.17
3453 3579 4.631813 GTCTTGCTCATGGTACTCGAATTT 59.368 41.667 0.00 0.00 0.00 1.82
3454 3580 5.122396 GTCTTGCTCATGGTACTCGAATTTT 59.878 40.000 0.00 0.00 0.00 1.82
3455 3581 5.351465 TCTTGCTCATGGTACTCGAATTTTC 59.649 40.000 0.00 0.00 0.00 2.29
3456 3582 4.832248 TGCTCATGGTACTCGAATTTTCT 58.168 39.130 0.00 0.00 0.00 2.52
3457 3583 5.245531 TGCTCATGGTACTCGAATTTTCTT 58.754 37.500 0.00 0.00 0.00 2.52
3458 3584 6.403049 TGCTCATGGTACTCGAATTTTCTTA 58.597 36.000 0.00 0.00 0.00 2.10
3459 3585 7.047891 TGCTCATGGTACTCGAATTTTCTTAT 58.952 34.615 0.00 0.00 0.00 1.73
3460 3586 8.201464 TGCTCATGGTACTCGAATTTTCTTATA 58.799 33.333 0.00 0.00 0.00 0.98
3461 3587 9.042008 GCTCATGGTACTCGAATTTTCTTATAA 57.958 33.333 0.00 0.00 0.00 0.98
3465 3591 8.644318 TGGTACTCGAATTTTCTTATAAGAGC 57.356 34.615 14.63 3.99 36.22 4.09
3466 3592 8.255206 TGGTACTCGAATTTTCTTATAAGAGCA 58.745 33.333 14.63 6.70 36.22 4.26
3467 3593 9.262358 GGTACTCGAATTTTCTTATAAGAGCAT 57.738 33.333 14.63 8.57 36.22 3.79
3469 3595 8.723942 ACTCGAATTTTCTTATAAGAGCATGT 57.276 30.769 14.63 2.09 36.22 3.21
3470 3596 8.607459 ACTCGAATTTTCTTATAAGAGCATGTG 58.393 33.333 14.63 6.42 36.22 3.21
3471 3597 8.492673 TCGAATTTTCTTATAAGAGCATGTGT 57.507 30.769 14.63 0.00 36.22 3.72
3472 3598 9.594478 TCGAATTTTCTTATAAGAGCATGTGTA 57.406 29.630 14.63 0.00 36.22 2.90
3473 3599 9.855361 CGAATTTTCTTATAAGAGCATGTGTAG 57.145 33.333 14.63 0.79 36.22 2.74
3477 3603 7.539712 TTCTTATAAGAGCATGTGTAGTTGC 57.460 36.000 14.63 0.00 36.22 4.17
3478 3604 6.639563 TCTTATAAGAGCATGTGTAGTTGCA 58.360 36.000 11.24 0.00 41.35 4.08
3479 3605 7.275183 TCTTATAAGAGCATGTGTAGTTGCAT 58.725 34.615 11.24 0.00 41.35 3.96
3480 3606 8.421002 TCTTATAAGAGCATGTGTAGTTGCATA 58.579 33.333 11.24 0.00 41.35 3.14
3481 3607 8.593492 TTATAAGAGCATGTGTAGTTGCATAG 57.407 34.615 0.00 0.00 41.35 2.23
3482 3608 4.743057 AGAGCATGTGTAGTTGCATAGA 57.257 40.909 0.00 0.00 41.35 1.98
3483 3609 4.437239 AGAGCATGTGTAGTTGCATAGAC 58.563 43.478 0.00 0.00 41.35 2.59
3484 3610 4.081476 AGAGCATGTGTAGTTGCATAGACA 60.081 41.667 0.34 0.34 41.35 3.41
3485 3611 4.186926 AGCATGTGTAGTTGCATAGACAG 58.813 43.478 3.99 0.00 41.35 3.51
3486 3612 3.310774 GCATGTGTAGTTGCATAGACAGG 59.689 47.826 5.24 5.24 38.72 4.00
3487 3613 2.972625 TGTGTAGTTGCATAGACAGGC 58.027 47.619 0.00 0.00 0.00 4.85
3488 3614 2.301583 TGTGTAGTTGCATAGACAGGCA 59.698 45.455 0.00 0.00 40.27 4.75
3489 3615 2.673368 GTGTAGTTGCATAGACAGGCAC 59.327 50.000 0.00 0.00 42.03 5.01
3490 3616 2.280628 GTAGTTGCATAGACAGGCACC 58.719 52.381 0.00 0.00 42.03 5.01
3491 3617 0.035056 AGTTGCATAGACAGGCACCC 60.035 55.000 0.00 0.00 42.03 4.61
3492 3618 0.035056 GTTGCATAGACAGGCACCCT 60.035 55.000 0.00 0.00 42.03 4.34
3493 3619 1.209504 GTTGCATAGACAGGCACCCTA 59.790 52.381 0.00 0.00 42.03 3.53
3494 3620 1.806496 TGCATAGACAGGCACCCTAT 58.194 50.000 0.00 0.00 36.34 2.57
3495 3621 2.126882 TGCATAGACAGGCACCCTATT 58.873 47.619 0.00 0.00 36.34 1.73
3496 3622 2.158769 TGCATAGACAGGCACCCTATTG 60.159 50.000 0.00 0.00 36.34 1.90
3497 3623 2.498167 CATAGACAGGCACCCTATTGC 58.502 52.381 0.00 0.00 42.18 3.56
3498 3624 1.879575 TAGACAGGCACCCTATTGCT 58.120 50.000 0.00 0.00 42.56 3.91
3499 3625 1.879575 AGACAGGCACCCTATTGCTA 58.120 50.000 0.00 0.00 42.56 3.49
3500 3626 2.196595 AGACAGGCACCCTATTGCTAA 58.803 47.619 0.00 0.00 42.56 3.09
3501 3627 2.576191 AGACAGGCACCCTATTGCTAAA 59.424 45.455 0.00 0.00 42.56 1.85
3502 3628 3.010138 AGACAGGCACCCTATTGCTAAAA 59.990 43.478 0.00 0.00 42.56 1.52
3503 3629 3.089284 ACAGGCACCCTATTGCTAAAAC 58.911 45.455 0.00 0.00 42.56 2.43
3504 3630 3.088532 CAGGCACCCTATTGCTAAAACA 58.911 45.455 0.00 0.00 42.56 2.83
3505 3631 3.129287 CAGGCACCCTATTGCTAAAACAG 59.871 47.826 0.00 0.00 42.56 3.16
3506 3632 3.010138 AGGCACCCTATTGCTAAAACAGA 59.990 43.478 0.00 0.00 42.56 3.41
3507 3633 3.954258 GGCACCCTATTGCTAAAACAGAT 59.046 43.478 0.00 0.00 42.56 2.90
3508 3634 4.402474 GGCACCCTATTGCTAAAACAGATT 59.598 41.667 0.00 0.00 42.56 2.40
3509 3635 5.592688 GGCACCCTATTGCTAAAACAGATTA 59.407 40.000 0.00 0.00 42.56 1.75
3510 3636 6.096282 GGCACCCTATTGCTAAAACAGATTAA 59.904 38.462 0.00 0.00 42.56 1.40
3511 3637 7.201911 GGCACCCTATTGCTAAAACAGATTAAT 60.202 37.037 0.00 0.00 42.56 1.40
3512 3638 8.197439 GCACCCTATTGCTAAAACAGATTAATT 58.803 33.333 0.00 0.00 39.59 1.40
3520 3646 9.681062 TTGCTAAAACAGATTAATTAGTAGGCT 57.319 29.630 0.00 0.00 0.00 4.58
3521 3647 9.681062 TGCTAAAACAGATTAATTAGTAGGCTT 57.319 29.630 0.00 0.00 0.00 4.35
3522 3648 9.937175 GCTAAAACAGATTAATTAGTAGGCTTG 57.063 33.333 0.00 0.00 0.00 4.01
3527 3653 8.644318 ACAGATTAATTAGTAGGCTTGTAACG 57.356 34.615 0.00 0.00 0.00 3.18
3528 3654 8.472413 ACAGATTAATTAGTAGGCTTGTAACGA 58.528 33.333 0.00 0.00 0.00 3.85
3529 3655 9.309516 CAGATTAATTAGTAGGCTTGTAACGAA 57.690 33.333 0.00 0.00 0.00 3.85
3530 3656 9.530633 AGATTAATTAGTAGGCTTGTAACGAAG 57.469 33.333 0.00 0.00 0.00 3.79
3531 3657 9.525409 GATTAATTAGTAGGCTTGTAACGAAGA 57.475 33.333 0.00 0.00 0.00 2.87
3535 3661 9.694137 AATTAGTAGGCTTGTAACGAAGATATC 57.306 33.333 0.00 0.00 0.00 1.63
3536 3662 6.086785 AGTAGGCTTGTAACGAAGATATCC 57.913 41.667 0.00 0.00 0.00 2.59
3537 3663 5.834204 AGTAGGCTTGTAACGAAGATATCCT 59.166 40.000 0.00 0.00 0.00 3.24
3538 3664 5.203060 AGGCTTGTAACGAAGATATCCTC 57.797 43.478 0.00 0.00 0.00 3.71
3539 3665 4.896482 AGGCTTGTAACGAAGATATCCTCT 59.104 41.667 0.00 0.00 34.96 3.69
3540 3666 4.985409 GGCTTGTAACGAAGATATCCTCTG 59.015 45.833 0.00 0.00 33.29 3.35
3541 3667 5.452077 GGCTTGTAACGAAGATATCCTCTGT 60.452 44.000 0.00 0.00 33.29 3.41
3542 3668 6.043411 GCTTGTAACGAAGATATCCTCTGTT 58.957 40.000 12.76 12.76 33.29 3.16
3543 3669 7.201145 GCTTGTAACGAAGATATCCTCTGTTA 58.799 38.462 0.00 6.83 33.29 2.41
3544 3670 7.705325 GCTTGTAACGAAGATATCCTCTGTTAA 59.295 37.037 14.65 6.96 33.29 2.01
3545 3671 8.922058 TTGTAACGAAGATATCCTCTGTTAAC 57.078 34.615 14.65 0.00 33.29 2.01
3546 3672 7.486647 TGTAACGAAGATATCCTCTGTTAACC 58.513 38.462 14.65 8.52 33.29 2.85
3547 3673 6.540438 AACGAAGATATCCTCTGTTAACCA 57.460 37.500 2.48 0.00 33.29 3.67
3548 3674 6.732896 ACGAAGATATCCTCTGTTAACCAT 57.267 37.500 2.48 0.00 33.29 3.55
3549 3675 6.750148 ACGAAGATATCCTCTGTTAACCATC 58.250 40.000 2.48 0.00 33.29 3.51
3550 3676 6.551601 ACGAAGATATCCTCTGTTAACCATCT 59.448 38.462 2.48 0.00 33.29 2.90
3551 3677 7.070074 ACGAAGATATCCTCTGTTAACCATCTT 59.930 37.037 2.48 6.01 34.95 2.40
3552 3678 7.596995 CGAAGATATCCTCTGTTAACCATCTTC 59.403 40.741 2.48 12.30 41.54 2.87
3553 3679 8.560124 AAGATATCCTCTGTTAACCATCTTCT 57.440 34.615 2.48 0.00 33.29 2.85
3554 3680 8.560124 AGATATCCTCTGTTAACCATCTTCTT 57.440 34.615 2.48 0.00 31.12 2.52
3555 3681 8.428063 AGATATCCTCTGTTAACCATCTTCTTG 58.572 37.037 2.48 0.00 31.12 3.02
3556 3682 5.825593 TCCTCTGTTAACCATCTTCTTGT 57.174 39.130 2.48 0.00 0.00 3.16
3557 3683 6.928348 TCCTCTGTTAACCATCTTCTTGTA 57.072 37.500 2.48 0.00 0.00 2.41
3558 3684 7.496346 TCCTCTGTTAACCATCTTCTTGTAT 57.504 36.000 2.48 0.00 0.00 2.29
3559 3685 8.603898 TCCTCTGTTAACCATCTTCTTGTATA 57.396 34.615 2.48 0.00 0.00 1.47
3560 3686 8.696374 TCCTCTGTTAACCATCTTCTTGTATAG 58.304 37.037 2.48 0.00 0.00 1.31
3561 3687 8.478877 CCTCTGTTAACCATCTTCTTGTATAGT 58.521 37.037 2.48 0.00 0.00 2.12
3562 3688 9.877178 CTCTGTTAACCATCTTCTTGTATAGTT 57.123 33.333 2.48 0.00 0.00 2.24
3563 3689 9.653287 TCTGTTAACCATCTTCTTGTATAGTTG 57.347 33.333 2.48 0.00 0.00 3.16
3564 3690 8.263940 TGTTAACCATCTTCTTGTATAGTTGC 57.736 34.615 2.48 0.00 0.00 4.17
3565 3691 7.880713 TGTTAACCATCTTCTTGTATAGTTGCA 59.119 33.333 2.48 0.00 0.00 4.08
3566 3692 8.893727 GTTAACCATCTTCTTGTATAGTTGCAT 58.106 33.333 0.00 0.00 0.00 3.96
3567 3693 6.932356 ACCATCTTCTTGTATAGTTGCATG 57.068 37.500 0.00 0.00 0.00 4.06
3568 3694 6.418101 ACCATCTTCTTGTATAGTTGCATGT 58.582 36.000 0.00 0.00 0.00 3.21
3569 3695 7.564793 ACCATCTTCTTGTATAGTTGCATGTA 58.435 34.615 0.00 0.00 0.00 2.29
3570 3696 7.712639 ACCATCTTCTTGTATAGTTGCATGTAG 59.287 37.037 0.00 0.00 0.00 2.74
3571 3697 7.928167 CCATCTTCTTGTATAGTTGCATGTAGA 59.072 37.037 0.00 0.00 0.00 2.59
3572 3698 8.759641 CATCTTCTTGTATAGTTGCATGTAGAC 58.240 37.037 0.00 0.00 28.17 2.59
3573 3699 7.836842 TCTTCTTGTATAGTTGCATGTAGACA 58.163 34.615 0.00 0.00 0.00 3.41
3574 3700 8.478066 TCTTCTTGTATAGTTGCATGTAGACAT 58.522 33.333 4.63 0.00 36.96 3.06
3620 3746 9.874205 AAACATTATATACAAATTGCAAGCACT 57.126 25.926 4.94 0.00 0.00 4.40
3621 3747 8.861033 ACATTATATACAAATTGCAAGCACTG 57.139 30.769 4.94 1.88 0.00 3.66
3622 3748 8.685427 ACATTATATACAAATTGCAAGCACTGA 58.315 29.630 4.94 0.00 0.00 3.41
3623 3749 9.518906 CATTATATACAAATTGCAAGCACTGAA 57.481 29.630 4.94 0.00 0.00 3.02
3627 3753 5.199024 ACAAATTGCAAGCACTGAATACA 57.801 34.783 4.94 0.00 0.00 2.29
3628 3754 5.599732 ACAAATTGCAAGCACTGAATACAA 58.400 33.333 4.94 0.00 0.00 2.41
3629 3755 5.693104 ACAAATTGCAAGCACTGAATACAAG 59.307 36.000 4.94 0.00 0.00 3.16
3630 3756 5.710513 AATTGCAAGCACTGAATACAAGA 57.289 34.783 4.94 0.00 0.00 3.02
3631 3757 4.488126 TTGCAAGCACTGAATACAAGAC 57.512 40.909 0.00 0.00 0.00 3.01
3632 3758 3.475575 TGCAAGCACTGAATACAAGACA 58.524 40.909 0.00 0.00 0.00 3.41
3633 3759 4.074259 TGCAAGCACTGAATACAAGACAT 58.926 39.130 0.00 0.00 0.00 3.06
3634 3760 4.520111 TGCAAGCACTGAATACAAGACATT 59.480 37.500 0.00 0.00 0.00 2.71
3635 3761 5.704978 TGCAAGCACTGAATACAAGACATTA 59.295 36.000 0.00 0.00 0.00 1.90
3636 3762 6.128200 TGCAAGCACTGAATACAAGACATTAG 60.128 38.462 0.00 0.00 0.00 1.73
3637 3763 6.253746 CAAGCACTGAATACAAGACATTAGC 58.746 40.000 0.00 0.00 0.00 3.09
3638 3764 4.878397 AGCACTGAATACAAGACATTAGCC 59.122 41.667 0.00 0.00 0.00 3.93
3639 3765 4.635765 GCACTGAATACAAGACATTAGCCA 59.364 41.667 0.00 0.00 0.00 4.75
3640 3766 5.447818 GCACTGAATACAAGACATTAGCCAC 60.448 44.000 0.00 0.00 0.00 5.01
3641 3767 5.065218 CACTGAATACAAGACATTAGCCACC 59.935 44.000 0.00 0.00 0.00 4.61
3642 3768 5.045578 ACTGAATACAAGACATTAGCCACCT 60.046 40.000 0.00 0.00 0.00 4.00
3643 3769 6.156256 ACTGAATACAAGACATTAGCCACCTA 59.844 38.462 0.00 0.00 0.00 3.08
3644 3770 6.582636 TGAATACAAGACATTAGCCACCTAG 58.417 40.000 0.00 0.00 0.00 3.02
3645 3771 3.914426 ACAAGACATTAGCCACCTAGG 57.086 47.619 7.41 7.41 41.84 3.02
3646 3772 3.182152 ACAAGACATTAGCCACCTAGGT 58.818 45.455 9.21 9.21 40.61 3.08
3647 3773 3.587506 ACAAGACATTAGCCACCTAGGTT 59.412 43.478 13.15 0.00 40.61 3.50
3648 3774 3.914426 AGACATTAGCCACCTAGGTTG 57.086 47.619 13.15 10.65 40.61 3.77
3649 3775 3.450904 AGACATTAGCCACCTAGGTTGA 58.549 45.455 17.04 0.00 40.61 3.18
3650 3776 4.040755 AGACATTAGCCACCTAGGTTGAT 58.959 43.478 17.04 13.02 40.61 2.57
3651 3777 4.130118 GACATTAGCCACCTAGGTTGATG 58.870 47.826 17.04 14.65 46.03 3.07
3652 3778 4.156455 CATTAGCCACCTAGGTTGATGT 57.844 45.455 17.04 1.47 39.01 3.06
3653 3779 3.627395 TTAGCCACCTAGGTTGATGTG 57.373 47.619 17.04 2.48 40.61 3.21
3657 3783 2.698855 CACCTAGGTTGATGTGGAGG 57.301 55.000 13.15 0.00 0.00 4.30
3658 3784 1.210478 CACCTAGGTTGATGTGGAGGG 59.790 57.143 13.15 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 4.871822 TCTCTCTCTCTCTCTCTCTCTCA 58.128 47.826 0.00 0.00 0.00 3.27
72 75 4.994282 TGGTCTTACTAGTCTTGGTCTCA 58.006 43.478 0.00 0.00 0.00 3.27
73 76 5.477637 AGTTGGTCTTACTAGTCTTGGTCTC 59.522 44.000 0.00 0.00 0.00 3.36
74 77 5.395611 AGTTGGTCTTACTAGTCTTGGTCT 58.604 41.667 0.00 0.00 0.00 3.85
75 78 5.725325 AGTTGGTCTTACTAGTCTTGGTC 57.275 43.478 0.00 0.00 0.00 4.02
76 79 6.496144 AAAGTTGGTCTTACTAGTCTTGGT 57.504 37.500 0.00 0.00 35.02 3.67
77 80 8.148999 AGTAAAAGTTGGTCTTACTAGTCTTGG 58.851 37.037 0.00 0.00 34.81 3.61
78 81 8.979574 CAGTAAAAGTTGGTCTTACTAGTCTTG 58.020 37.037 0.00 0.00 34.81 3.02
79 82 8.921205 TCAGTAAAAGTTGGTCTTACTAGTCTT 58.079 33.333 0.00 0.00 34.81 3.01
80 83 8.474710 TCAGTAAAAGTTGGTCTTACTAGTCT 57.525 34.615 0.00 0.00 34.81 3.24
81 84 9.708092 AATCAGTAAAAGTTGGTCTTACTAGTC 57.292 33.333 0.00 0.00 34.81 2.59
82 85 9.708092 GAATCAGTAAAAGTTGGTCTTACTAGT 57.292 33.333 0.00 0.00 34.81 2.57
161 164 1.318576 CTTGTGTCTTGGGGTGTTCC 58.681 55.000 0.00 0.00 0.00 3.62
174 178 4.717233 TCAAAATGAGCAACACTTGTGT 57.283 36.364 0.00 0.00 0.00 3.72
221 231 3.256879 TCAGCAACCAAACAAAACAGTGA 59.743 39.130 0.00 0.00 0.00 3.41
260 271 3.062042 CTGTTTGGAAGGCTTGCATTTC 58.938 45.455 22.35 14.89 0.00 2.17
261 272 2.435437 ACTGTTTGGAAGGCTTGCATTT 59.565 40.909 22.35 2.59 0.00 2.32
381 393 1.179814 GGTCAGGTGGAGTGAGACGT 61.180 60.000 0.00 0.00 0.00 4.34
382 394 1.179174 TGGTCAGGTGGAGTGAGACG 61.179 60.000 0.00 0.00 0.00 4.18
383 395 0.318762 GTGGTCAGGTGGAGTGAGAC 59.681 60.000 0.00 0.00 0.00 3.36
384 396 0.832135 GGTGGTCAGGTGGAGTGAGA 60.832 60.000 0.00 0.00 0.00 3.27
406 418 4.650131 CCTAGCTTGGCTTAGTTAGTACCT 59.350 45.833 0.00 0.00 40.44 3.08
481 495 4.338400 GCTTAGAGAGAAGAGAGAGGGTTC 59.662 50.000 0.00 0.00 0.00 3.62
485 499 4.580580 GGAAGCTTAGAGAGAAGAGAGAGG 59.419 50.000 0.00 0.00 0.00 3.69
515 536 3.134623 TGTGAAACATATGGAGAGGCGAT 59.865 43.478 7.80 0.00 45.67 4.58
558 579 8.556213 TTATATTTTGTCTTAGTGGTGGTGTC 57.444 34.615 0.00 0.00 0.00 3.67
722 743 1.736681 GCACACAAGAATGGAGCTCTC 59.263 52.381 14.64 3.27 0.00 3.20
723 744 1.072806 TGCACACAAGAATGGAGCTCT 59.927 47.619 14.64 0.00 0.00 4.09
840 876 4.771054 ACGAGGGGTATATAGGTGCTTTAG 59.229 45.833 0.00 0.00 0.00 1.85
863 899 3.024356 AGAGGGCCGGGAGAGAGA 61.024 66.667 2.18 0.00 0.00 3.10
882 918 0.606401 TCCTCCTTGCTTCTTTGCGG 60.606 55.000 0.00 0.00 35.36 5.69
997 1033 2.951229 ACCGAAGAAAAGACCATGGT 57.049 45.000 19.89 19.89 0.00 3.55
998 1034 2.488153 GGAACCGAAGAAAAGACCATGG 59.512 50.000 11.19 11.19 0.00 3.66
999 1035 2.488153 GGGAACCGAAGAAAAGACCATG 59.512 50.000 0.00 0.00 40.86 3.66
1078 1123 4.077822 AGAGAGAAAAGGCAATTCACCTG 58.922 43.478 0.00 0.00 37.67 4.00
1079 1124 4.379302 AGAGAGAAAAGGCAATTCACCT 57.621 40.909 5.30 0.00 40.02 4.00
1080 1125 6.765915 ATAAGAGAGAAAAGGCAATTCACC 57.234 37.500 5.30 0.00 0.00 4.02
1222 1267 6.773976 AAGCATAGCAACTAAAAAGCCATA 57.226 33.333 0.00 0.00 0.00 2.74
1244 1289 6.625362 TCACAATCACACAAAACTAGCAAAA 58.375 32.000 0.00 0.00 0.00 2.44
1304 1349 6.045318 CACCATGGTTTACAATCAAAACACA 58.955 36.000 16.84 0.00 37.90 3.72
1354 1399 2.188849 CTCAGTTGCTGCTGCTGCTG 62.189 60.000 27.67 23.22 40.29 4.41
1410 1455 4.408821 TGCATGTCCACTCCGCCC 62.409 66.667 0.00 0.00 0.00 6.13
1422 1467 2.203466 TGGTGGTGGTGGTGCATG 60.203 61.111 0.00 0.00 0.00 4.06
1435 1480 1.066257 GTTGCTGTTGCTGGTGGTG 59.934 57.895 0.00 0.00 40.48 4.17
1436 1481 1.379710 TGTTGCTGTTGCTGGTGGT 60.380 52.632 0.00 0.00 40.48 4.16
1437 1482 1.361271 CTGTTGCTGTTGCTGGTGG 59.639 57.895 0.00 0.00 40.48 4.61
1455 1500 2.015382 CTGCTGCTGATACTGCTGC 58.985 57.895 19.07 19.07 46.82 5.25
1478 1523 4.962836 GGTGCTGGTGCTGGTGCT 62.963 66.667 0.00 0.00 40.48 4.40
1519 1564 4.431131 AGCCATCAACGCCCCAGG 62.431 66.667 0.00 0.00 0.00 4.45
1521 1566 4.424711 GGAGCCATCAACGCCCCA 62.425 66.667 0.00 0.00 0.00 4.96
1952 2006 4.973360 CGTTGCCGTTGCCGTTGG 62.973 66.667 0.00 0.00 36.33 3.77
2544 2598 2.082231 CTGCTGTGACTTCCTCCATTG 58.918 52.381 0.00 0.00 0.00 2.82
2714 2768 1.680249 GGGCTACCTTTTGCAGAGAGG 60.680 57.143 9.72 9.72 36.62 3.69
2733 2787 9.307121 CTTCAATTCGGAGCTTGTATATATAGG 57.693 37.037 0.00 0.00 0.00 2.57
2829 2883 0.249120 TCGACCGGCAATGATCTTGT 59.751 50.000 0.00 0.00 0.00 3.16
2842 2897 7.838498 AGAATAAAACTAATTTCGATCGACCG 58.162 34.615 19.26 7.00 32.27 4.79
2912 2971 8.870879 CAAGAAAGAACCTAATTAAGACGGTAG 58.129 37.037 0.00 0.00 0.00 3.18
2943 3002 4.919774 TCCAGCACCTTAAACAATAGGA 57.080 40.909 0.00 0.00 35.45 2.94
2981 3040 7.337942 ACAATGACATTGGAGAATTAAGGAGAC 59.662 37.037 27.46 0.00 44.42 3.36
2997 3056 7.275341 CCAATTAACGTGCATTACAATGACATT 59.725 33.333 6.13 0.00 38.70 2.71
2998 3057 6.751425 CCAATTAACGTGCATTACAATGACAT 59.249 34.615 6.13 0.00 38.70 3.06
3014 3073 7.332678 AGCTAGTAAACTTGGTACCAATTAACG 59.667 37.037 27.24 17.25 35.20 3.18
3038 3097 4.305769 TGAACACATTAATTGCACCAAGC 58.694 39.130 0.00 0.00 45.96 4.01
3039 3098 5.349270 CCATGAACACATTAATTGCACCAAG 59.651 40.000 0.00 0.00 0.00 3.61
3040 3099 5.221601 ACCATGAACACATTAATTGCACCAA 60.222 36.000 0.00 0.00 0.00 3.67
3041 3100 4.282957 ACCATGAACACATTAATTGCACCA 59.717 37.500 0.00 0.00 0.00 4.17
3042 3101 4.626604 CACCATGAACACATTAATTGCACC 59.373 41.667 0.00 0.00 0.00 5.01
3043 3102 4.626604 CCACCATGAACACATTAATTGCAC 59.373 41.667 0.00 0.00 0.00 4.57
3044 3103 4.525874 TCCACCATGAACACATTAATTGCA 59.474 37.500 0.00 0.00 0.00 4.08
3096 3157 7.394016 TGAAACCAACTCAATATTCTAGCTCA 58.606 34.615 0.00 0.00 0.00 4.26
3097 3158 7.550906 ACTGAAACCAACTCAATATTCTAGCTC 59.449 37.037 0.00 0.00 0.00 4.09
3105 3166 9.920946 ACCAATATACTGAAACCAACTCAATAT 57.079 29.630 0.00 0.00 0.00 1.28
3107 3168 7.362920 GCACCAATATACTGAAACCAACTCAAT 60.363 37.037 0.00 0.00 0.00 2.57
3145 3242 5.130975 ACATTCCAAGCTACTCATACATGGA 59.869 40.000 0.00 0.00 33.88 3.41
3342 3467 9.625747 TGATAGCAATGACAATCAACCTAATTA 57.374 29.630 0.00 0.00 0.00 1.40
3343 3468 8.523915 TGATAGCAATGACAATCAACCTAATT 57.476 30.769 0.00 0.00 0.00 1.40
3344 3469 8.701908 ATGATAGCAATGACAATCAACCTAAT 57.298 30.769 0.00 0.00 32.47 1.73
3345 3470 7.994911 AGATGATAGCAATGACAATCAACCTAA 59.005 33.333 0.00 0.00 32.47 2.69
3346 3471 7.512130 AGATGATAGCAATGACAATCAACCTA 58.488 34.615 0.00 0.00 32.47 3.08
3347 3472 6.363065 AGATGATAGCAATGACAATCAACCT 58.637 36.000 0.00 0.00 32.47 3.50
3348 3473 6.630444 AGATGATAGCAATGACAATCAACC 57.370 37.500 0.00 0.00 32.47 3.77
3349 3474 8.375608 ACTAGATGATAGCAATGACAATCAAC 57.624 34.615 0.00 0.00 32.47 3.18
3357 3482 8.907222 TGCAAATTACTAGATGATAGCAATGA 57.093 30.769 0.00 0.00 0.00 2.57
3366 3491 9.866655 AGGGAATAATTGCAAATTACTAGATGA 57.133 29.630 1.71 0.00 0.00 2.92
3408 3534 7.293073 AGACTAGATTTGATAAATGGGCACAT 58.707 34.615 0.00 0.00 39.54 3.21
3409 3535 6.662755 AGACTAGATTTGATAAATGGGCACA 58.337 36.000 0.00 0.00 0.00 4.57
3410 3536 7.420800 CAAGACTAGATTTGATAAATGGGCAC 58.579 38.462 0.00 0.00 0.00 5.01
3411 3537 6.039717 GCAAGACTAGATTTGATAAATGGGCA 59.960 38.462 12.87 0.00 0.00 5.36
3412 3538 6.264067 AGCAAGACTAGATTTGATAAATGGGC 59.736 38.462 12.87 0.00 0.00 5.36
3413 3539 7.500227 TGAGCAAGACTAGATTTGATAAATGGG 59.500 37.037 12.87 0.00 0.00 4.00
3414 3540 8.442632 TGAGCAAGACTAGATTTGATAAATGG 57.557 34.615 12.87 0.00 0.00 3.16
3415 3541 9.880064 CATGAGCAAGACTAGATTTGATAAATG 57.120 33.333 12.87 10.36 0.00 2.32
3416 3542 9.064706 CCATGAGCAAGACTAGATTTGATAAAT 57.935 33.333 12.87 0.00 0.00 1.40
3417 3543 8.049117 ACCATGAGCAAGACTAGATTTGATAAA 58.951 33.333 12.87 2.52 0.00 1.40
3418 3544 7.568349 ACCATGAGCAAGACTAGATTTGATAA 58.432 34.615 12.87 2.97 0.00 1.75
3419 3545 7.129457 ACCATGAGCAAGACTAGATTTGATA 57.871 36.000 12.87 1.99 0.00 2.15
3420 3546 5.999044 ACCATGAGCAAGACTAGATTTGAT 58.001 37.500 12.87 7.93 0.00 2.57
3421 3547 5.426689 ACCATGAGCAAGACTAGATTTGA 57.573 39.130 12.87 0.00 0.00 2.69
3422 3548 6.344500 AGTACCATGAGCAAGACTAGATTTG 58.656 40.000 0.00 1.59 0.00 2.32
3423 3549 6.552445 AGTACCATGAGCAAGACTAGATTT 57.448 37.500 0.00 0.00 0.00 2.17
3424 3550 5.221145 CGAGTACCATGAGCAAGACTAGATT 60.221 44.000 0.00 0.00 0.00 2.40
3425 3551 4.277174 CGAGTACCATGAGCAAGACTAGAT 59.723 45.833 0.00 0.00 0.00 1.98
3426 3552 3.628032 CGAGTACCATGAGCAAGACTAGA 59.372 47.826 0.00 0.00 0.00 2.43
3427 3553 3.628032 TCGAGTACCATGAGCAAGACTAG 59.372 47.826 0.00 0.00 0.00 2.57
3428 3554 3.617284 TCGAGTACCATGAGCAAGACTA 58.383 45.455 0.00 0.00 0.00 2.59
3429 3555 2.447443 TCGAGTACCATGAGCAAGACT 58.553 47.619 0.00 0.00 0.00 3.24
3430 3556 2.941453 TCGAGTACCATGAGCAAGAC 57.059 50.000 0.00 0.00 0.00 3.01
3431 3557 4.471904 AATTCGAGTACCATGAGCAAGA 57.528 40.909 0.00 0.00 0.00 3.02
3432 3558 5.352569 AGAAAATTCGAGTACCATGAGCAAG 59.647 40.000 0.00 0.00 0.00 4.01
3433 3559 5.245531 AGAAAATTCGAGTACCATGAGCAA 58.754 37.500 0.00 0.00 0.00 3.91
3434 3560 4.832248 AGAAAATTCGAGTACCATGAGCA 58.168 39.130 0.00 0.00 0.00 4.26
3435 3561 5.803020 AAGAAAATTCGAGTACCATGAGC 57.197 39.130 0.00 0.00 0.00 4.26
3439 3565 9.262358 GCTCTTATAAGAAAATTCGAGTACCAT 57.738 33.333 15.85 0.00 34.03 3.55
3440 3566 8.255206 TGCTCTTATAAGAAAATTCGAGTACCA 58.745 33.333 15.85 0.00 34.03 3.25
3441 3567 8.644318 TGCTCTTATAAGAAAATTCGAGTACC 57.356 34.615 15.85 0.00 34.03 3.34
3443 3569 9.817809 ACATGCTCTTATAAGAAAATTCGAGTA 57.182 29.630 15.85 2.58 34.03 2.59
3444 3570 8.607459 CACATGCTCTTATAAGAAAATTCGAGT 58.393 33.333 15.85 4.85 34.03 4.18
3445 3571 8.607459 ACACATGCTCTTATAAGAAAATTCGAG 58.393 33.333 15.85 3.61 34.03 4.04
3446 3572 8.492673 ACACATGCTCTTATAAGAAAATTCGA 57.507 30.769 15.85 0.00 34.03 3.71
3447 3573 9.855361 CTACACATGCTCTTATAAGAAAATTCG 57.145 33.333 15.85 4.94 34.03 3.34
3451 3577 8.450964 GCAACTACACATGCTCTTATAAGAAAA 58.549 33.333 15.85 7.76 39.46 2.29
3452 3578 7.606073 TGCAACTACACATGCTCTTATAAGAAA 59.394 33.333 15.85 8.09 42.97 2.52
3453 3579 7.102993 TGCAACTACACATGCTCTTATAAGAA 58.897 34.615 15.85 3.13 42.97 2.52
3454 3580 6.639563 TGCAACTACACATGCTCTTATAAGA 58.360 36.000 14.42 14.42 42.97 2.10
3455 3581 6.908870 TGCAACTACACATGCTCTTATAAG 57.091 37.500 6.11 6.11 42.97 1.73
3456 3582 8.421002 TCTATGCAACTACACATGCTCTTATAA 58.579 33.333 0.00 0.00 42.97 0.98
3457 3583 7.867909 GTCTATGCAACTACACATGCTCTTATA 59.132 37.037 0.00 0.00 42.97 0.98
3458 3584 6.703607 GTCTATGCAACTACACATGCTCTTAT 59.296 38.462 0.00 0.00 42.97 1.73
3459 3585 6.042777 GTCTATGCAACTACACATGCTCTTA 58.957 40.000 0.00 0.00 42.97 2.10
3460 3586 4.872691 GTCTATGCAACTACACATGCTCTT 59.127 41.667 0.00 0.00 42.97 2.85
3461 3587 4.081476 TGTCTATGCAACTACACATGCTCT 60.081 41.667 0.00 0.00 42.97 4.09
3462 3588 4.183865 TGTCTATGCAACTACACATGCTC 58.816 43.478 0.00 0.00 42.97 4.26
3463 3589 4.186926 CTGTCTATGCAACTACACATGCT 58.813 43.478 0.00 0.00 42.97 3.79
3464 3590 3.310774 CCTGTCTATGCAACTACACATGC 59.689 47.826 0.00 0.00 42.86 4.06
3465 3591 3.310774 GCCTGTCTATGCAACTACACATG 59.689 47.826 0.00 0.00 0.00 3.21
3466 3592 3.055167 TGCCTGTCTATGCAACTACACAT 60.055 43.478 0.00 0.00 33.87 3.21
3467 3593 2.301583 TGCCTGTCTATGCAACTACACA 59.698 45.455 0.00 0.00 33.87 3.72
3468 3594 2.673368 GTGCCTGTCTATGCAACTACAC 59.327 50.000 0.00 0.00 39.57 2.90
3469 3595 2.354704 GGTGCCTGTCTATGCAACTACA 60.355 50.000 0.00 0.00 41.93 2.74
3470 3596 2.280628 GGTGCCTGTCTATGCAACTAC 58.719 52.381 0.00 0.00 41.93 2.73
3471 3597 1.209504 GGGTGCCTGTCTATGCAACTA 59.790 52.381 0.00 0.00 44.57 2.24
3472 3598 0.035056 GGGTGCCTGTCTATGCAACT 60.035 55.000 0.00 0.00 44.57 3.16
3473 3599 0.035056 AGGGTGCCTGTCTATGCAAC 60.035 55.000 0.00 0.00 44.44 4.17
3474 3600 1.578897 TAGGGTGCCTGTCTATGCAA 58.421 50.000 0.00 0.00 39.57 4.08
3475 3601 1.806496 ATAGGGTGCCTGTCTATGCA 58.194 50.000 0.00 0.00 34.61 3.96
3476 3602 2.498167 CAATAGGGTGCCTGTCTATGC 58.502 52.381 0.00 0.00 34.61 3.14
3477 3603 2.105477 AGCAATAGGGTGCCTGTCTATG 59.895 50.000 0.00 0.00 46.14 2.23
3478 3604 2.412591 AGCAATAGGGTGCCTGTCTAT 58.587 47.619 0.00 0.00 46.14 1.98
3479 3605 1.879575 AGCAATAGGGTGCCTGTCTA 58.120 50.000 0.00 0.00 46.14 2.59
3480 3606 1.879575 TAGCAATAGGGTGCCTGTCT 58.120 50.000 0.00 0.00 46.14 3.41
3481 3607 2.710096 TTAGCAATAGGGTGCCTGTC 57.290 50.000 0.00 0.00 46.14 3.51
3482 3608 3.089284 GTTTTAGCAATAGGGTGCCTGT 58.911 45.455 0.00 0.00 46.14 4.00
3483 3609 3.088532 TGTTTTAGCAATAGGGTGCCTG 58.911 45.455 0.00 0.00 46.14 4.85
3484 3610 3.010138 TCTGTTTTAGCAATAGGGTGCCT 59.990 43.478 0.00 0.00 46.14 4.75
3485 3611 3.352648 TCTGTTTTAGCAATAGGGTGCC 58.647 45.455 0.00 0.00 46.14 5.01
3486 3612 5.582689 AATCTGTTTTAGCAATAGGGTGC 57.417 39.130 0.00 0.00 45.28 5.01
3494 3620 9.681062 AGCCTACTAATTAATCTGTTTTAGCAA 57.319 29.630 0.00 0.00 0.00 3.91
3495 3621 9.681062 AAGCCTACTAATTAATCTGTTTTAGCA 57.319 29.630 0.00 0.00 0.00 3.49
3496 3622 9.937175 CAAGCCTACTAATTAATCTGTTTTAGC 57.063 33.333 0.00 0.00 0.00 3.09
3501 3627 9.095065 CGTTACAAGCCTACTAATTAATCTGTT 57.905 33.333 0.00 0.00 0.00 3.16
3502 3628 8.472413 TCGTTACAAGCCTACTAATTAATCTGT 58.528 33.333 0.00 0.00 0.00 3.41
3503 3629 8.867112 TCGTTACAAGCCTACTAATTAATCTG 57.133 34.615 0.00 0.00 0.00 2.90
3504 3630 9.530633 CTTCGTTACAAGCCTACTAATTAATCT 57.469 33.333 0.00 0.00 0.00 2.40
3505 3631 9.525409 TCTTCGTTACAAGCCTACTAATTAATC 57.475 33.333 0.00 0.00 0.00 1.75
3509 3635 9.694137 GATATCTTCGTTACAAGCCTACTAATT 57.306 33.333 0.00 0.00 0.00 1.40
3510 3636 8.305317 GGATATCTTCGTTACAAGCCTACTAAT 58.695 37.037 2.05 0.00 0.00 1.73
3511 3637 7.504911 AGGATATCTTCGTTACAAGCCTACTAA 59.495 37.037 2.05 0.00 0.00 2.24
3512 3638 7.002879 AGGATATCTTCGTTACAAGCCTACTA 58.997 38.462 2.05 0.00 0.00 1.82
3513 3639 5.834204 AGGATATCTTCGTTACAAGCCTACT 59.166 40.000 2.05 0.00 0.00 2.57
3514 3640 6.016108 AGAGGATATCTTCGTTACAAGCCTAC 60.016 42.308 9.01 0.00 32.99 3.18
3515 3641 6.016192 CAGAGGATATCTTCGTTACAAGCCTA 60.016 42.308 9.01 0.00 35.47 3.93
3516 3642 4.896482 AGAGGATATCTTCGTTACAAGCCT 59.104 41.667 9.01 0.00 32.99 4.58
3517 3643 4.985409 CAGAGGATATCTTCGTTACAAGCC 59.015 45.833 9.01 0.00 35.47 4.35
3518 3644 5.593010 ACAGAGGATATCTTCGTTACAAGC 58.407 41.667 9.01 0.00 35.47 4.01
3519 3645 9.021863 GTTAACAGAGGATATCTTCGTTACAAG 57.978 37.037 20.76 7.74 35.47 3.16
3520 3646 7.977853 GGTTAACAGAGGATATCTTCGTTACAA 59.022 37.037 20.76 12.93 35.47 2.41
3521 3647 7.123098 TGGTTAACAGAGGATATCTTCGTTACA 59.877 37.037 20.76 16.52 35.47 2.41
3522 3648 7.486647 TGGTTAACAGAGGATATCTTCGTTAC 58.513 38.462 20.76 17.16 35.47 2.50
3523 3649 7.649533 TGGTTAACAGAGGATATCTTCGTTA 57.350 36.000 18.84 18.84 35.47 3.18
3524 3650 6.540438 TGGTTAACAGAGGATATCTTCGTT 57.460 37.500 20.16 20.16 35.47 3.85
3525 3651 6.551601 AGATGGTTAACAGAGGATATCTTCGT 59.448 38.462 8.10 7.62 35.47 3.85
3526 3652 6.987386 AGATGGTTAACAGAGGATATCTTCG 58.013 40.000 8.10 7.06 35.47 3.79
3527 3653 8.646900 AGAAGATGGTTAACAGAGGATATCTTC 58.353 37.037 19.54 19.54 44.60 2.87
3528 3654 8.560124 AGAAGATGGTTAACAGAGGATATCTT 57.440 34.615 8.10 9.70 35.47 2.40
3529 3655 8.428063 CAAGAAGATGGTTAACAGAGGATATCT 58.572 37.037 8.10 2.37 39.56 1.98
3530 3656 8.207545 ACAAGAAGATGGTTAACAGAGGATATC 58.792 37.037 8.10 0.00 0.00 1.63
3531 3657 8.095452 ACAAGAAGATGGTTAACAGAGGATAT 57.905 34.615 8.10 0.00 0.00 1.63
3532 3658 7.496346 ACAAGAAGATGGTTAACAGAGGATA 57.504 36.000 8.10 0.00 0.00 2.59
3533 3659 6.380079 ACAAGAAGATGGTTAACAGAGGAT 57.620 37.500 8.10 0.00 0.00 3.24
3534 3660 5.825593 ACAAGAAGATGGTTAACAGAGGA 57.174 39.130 8.10 0.00 0.00 3.71
3535 3661 8.478877 ACTATACAAGAAGATGGTTAACAGAGG 58.521 37.037 8.10 0.00 0.00 3.69
3536 3662 9.877178 AACTATACAAGAAGATGGTTAACAGAG 57.123 33.333 8.10 0.00 0.00 3.35
3537 3663 9.653287 CAACTATACAAGAAGATGGTTAACAGA 57.347 33.333 8.10 0.00 0.00 3.41
3538 3664 8.391106 GCAACTATACAAGAAGATGGTTAACAG 58.609 37.037 8.10 0.00 0.00 3.16
3539 3665 7.880713 TGCAACTATACAAGAAGATGGTTAACA 59.119 33.333 8.10 0.00 0.00 2.41
3540 3666 8.263940 TGCAACTATACAAGAAGATGGTTAAC 57.736 34.615 0.00 0.00 0.00 2.01
3541 3667 8.892723 CATGCAACTATACAAGAAGATGGTTAA 58.107 33.333 0.00 0.00 0.00 2.01
3542 3668 8.046708 ACATGCAACTATACAAGAAGATGGTTA 58.953 33.333 0.00 0.00 0.00 2.85
3543 3669 6.886459 ACATGCAACTATACAAGAAGATGGTT 59.114 34.615 0.00 0.00 0.00 3.67
3544 3670 6.418101 ACATGCAACTATACAAGAAGATGGT 58.582 36.000 0.00 0.00 0.00 3.55
3545 3671 6.932356 ACATGCAACTATACAAGAAGATGG 57.068 37.500 0.00 0.00 0.00 3.51
3546 3672 8.759641 GTCTACATGCAACTATACAAGAAGATG 58.240 37.037 0.00 0.00 0.00 2.90
3547 3673 8.478066 TGTCTACATGCAACTATACAAGAAGAT 58.522 33.333 0.00 0.00 0.00 2.40
3548 3674 7.836842 TGTCTACATGCAACTATACAAGAAGA 58.163 34.615 0.00 0.00 0.00 2.87
3549 3675 8.546244 CATGTCTACATGCAACTATACAAGAAG 58.454 37.037 9.98 0.00 45.92 2.85
3550 3676 8.424274 CATGTCTACATGCAACTATACAAGAA 57.576 34.615 9.98 0.00 45.92 2.52
3594 3720 9.874205 AGTGCTTGCAATTTGTATATAATGTTT 57.126 25.926 0.00 0.00 0.00 2.83
3595 3721 9.304731 CAGTGCTTGCAATTTGTATATAATGTT 57.695 29.630 0.00 0.00 0.00 2.71
3596 3722 8.685427 TCAGTGCTTGCAATTTGTATATAATGT 58.315 29.630 0.00 0.00 0.00 2.71
3597 3723 9.518906 TTCAGTGCTTGCAATTTGTATATAATG 57.481 29.630 0.00 0.00 0.00 1.90
3601 3727 8.685427 TGTATTCAGTGCTTGCAATTTGTATAT 58.315 29.630 0.00 0.00 0.00 0.86
3602 3728 8.049655 TGTATTCAGTGCTTGCAATTTGTATA 57.950 30.769 0.00 0.00 0.00 1.47
3603 3729 6.923012 TGTATTCAGTGCTTGCAATTTGTAT 58.077 32.000 0.00 0.00 0.00 2.29
3604 3730 6.324561 TGTATTCAGTGCTTGCAATTTGTA 57.675 33.333 0.00 0.00 0.00 2.41
3605 3731 5.199024 TGTATTCAGTGCTTGCAATTTGT 57.801 34.783 0.00 0.00 0.00 2.83
3606 3732 5.921976 TCTTGTATTCAGTGCTTGCAATTTG 59.078 36.000 0.00 0.00 0.00 2.32
3607 3733 5.922544 GTCTTGTATTCAGTGCTTGCAATTT 59.077 36.000 0.00 0.00 0.00 1.82
3608 3734 5.009911 TGTCTTGTATTCAGTGCTTGCAATT 59.990 36.000 0.00 0.00 0.00 2.32
3609 3735 4.520111 TGTCTTGTATTCAGTGCTTGCAAT 59.480 37.500 0.00 0.00 0.00 3.56
3610 3736 3.882288 TGTCTTGTATTCAGTGCTTGCAA 59.118 39.130 0.00 0.00 0.00 4.08
3611 3737 3.475575 TGTCTTGTATTCAGTGCTTGCA 58.524 40.909 0.00 0.00 0.00 4.08
3612 3738 4.691860 ATGTCTTGTATTCAGTGCTTGC 57.308 40.909 0.00 0.00 0.00 4.01
3613 3739 6.253746 GCTAATGTCTTGTATTCAGTGCTTG 58.746 40.000 0.00 0.00 0.00 4.01
3614 3740 5.355350 GGCTAATGTCTTGTATTCAGTGCTT 59.645 40.000 0.00 0.00 0.00 3.91
3615 3741 4.878397 GGCTAATGTCTTGTATTCAGTGCT 59.122 41.667 0.00 0.00 0.00 4.40
3616 3742 4.635765 TGGCTAATGTCTTGTATTCAGTGC 59.364 41.667 0.00 0.00 0.00 4.40
3617 3743 5.065218 GGTGGCTAATGTCTTGTATTCAGTG 59.935 44.000 0.00 0.00 0.00 3.66
3618 3744 5.045578 AGGTGGCTAATGTCTTGTATTCAGT 60.046 40.000 0.00 0.00 0.00 3.41
3619 3745 5.431765 AGGTGGCTAATGTCTTGTATTCAG 58.568 41.667 0.00 0.00 0.00 3.02
3620 3746 5.435686 AGGTGGCTAATGTCTTGTATTCA 57.564 39.130 0.00 0.00 0.00 2.57
3621 3747 5.992217 CCTAGGTGGCTAATGTCTTGTATTC 59.008 44.000 0.00 0.00 0.00 1.75
3622 3748 5.428783 ACCTAGGTGGCTAATGTCTTGTATT 59.571 40.000 15.42 0.00 40.22 1.89
3623 3749 4.969359 ACCTAGGTGGCTAATGTCTTGTAT 59.031 41.667 15.42 0.00 40.22 2.29
3624 3750 4.359105 ACCTAGGTGGCTAATGTCTTGTA 58.641 43.478 15.42 0.00 40.22 2.41
3625 3751 3.182152 ACCTAGGTGGCTAATGTCTTGT 58.818 45.455 15.42 0.00 40.22 3.16
3626 3752 3.914426 ACCTAGGTGGCTAATGTCTTG 57.086 47.619 15.42 0.00 40.22 3.02
3627 3753 3.844211 TCAACCTAGGTGGCTAATGTCTT 59.156 43.478 17.14 0.00 40.22 3.01
3628 3754 3.450904 TCAACCTAGGTGGCTAATGTCT 58.549 45.455 17.14 0.00 40.22 3.41
3629 3755 3.906720 TCAACCTAGGTGGCTAATGTC 57.093 47.619 17.14 0.00 40.22 3.06
3630 3756 3.523564 ACATCAACCTAGGTGGCTAATGT 59.476 43.478 17.14 15.11 40.22 2.71
3631 3757 3.879295 CACATCAACCTAGGTGGCTAATG 59.121 47.826 17.14 14.45 40.22 1.90
3632 3758 3.117888 CCACATCAACCTAGGTGGCTAAT 60.118 47.826 17.14 0.00 43.61 1.73
3633 3759 2.238646 CCACATCAACCTAGGTGGCTAA 59.761 50.000 17.14 0.00 43.61 3.09
3634 3760 1.837439 CCACATCAACCTAGGTGGCTA 59.163 52.381 17.14 0.00 43.61 3.93
3635 3761 0.620556 CCACATCAACCTAGGTGGCT 59.379 55.000 17.14 0.00 43.61 4.75
3636 3762 3.175133 CCACATCAACCTAGGTGGC 57.825 57.895 17.14 0.00 43.61 5.01
3638 3764 1.210478 CCCTCCACATCAACCTAGGTG 59.790 57.143 17.14 10.04 0.00 4.00
3639 3765 1.584724 CCCTCCACATCAACCTAGGT 58.415 55.000 9.21 9.21 0.00 3.08


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

AutoCloner maintained by Alex Coulton.