Multiple sequence alignment - TraesCS5D01G455700

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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 TraesCS5D01G455700 chr5D 100.000 2792 0 0 1 2792 502873075 502875866 0.000000e+00 5156.0
1 TraesCS5D01G455700 chr5B 82.235 1351 94 68 810 2090 631786337 631787611 0.000000e+00 1031.0
2 TraesCS5D01G455700 chr5B 90.909 484 22 13 233 697 631785605 631786085 5.070000e-177 630.0
3 TraesCS5D01G455700 chr5B 85.094 530 33 20 2091 2610 631787705 631788198 1.490000e-137 499.0
4 TraesCS5D01G455700 chr5B 93.697 238 12 2 1 236 631783154 631783390 1.230000e-93 353.0
5 TraesCS5D01G455700 chr5B 100.000 43 0 0 691 733 631786122 631786164 2.310000e-11 80.5
6 TraesCS5D01G455700 chr5A 84.135 624 42 23 1507 2090 631464190 631464796 4.060000e-153 551.0
7 TraesCS5D01G455700 chr5A 81.172 563 33 30 899 1446 631463580 631464084 4.360000e-103 385.0
8 TraesCS5D01G455700 chr5A 82.857 385 32 15 326 697 631463001 631463364 5.810000e-82 315.0
9 TraesCS5D01G455700 chr5A 89.147 258 17 6 2091 2339 631464891 631465146 7.510000e-81 311.0
10 TraesCS5D01G455700 chr5A 79.607 407 52 15 1543 1927 699208662 699209059 2.130000e-66 263.0
11 TraesCS5D01G455700 chr5A 87.387 111 3 5 755 856 631463462 631463570 1.760000e-22 117.0
12 TraesCS5D01G455700 chr5A 100.000 37 0 0 692 728 631463423 631463459 4.990000e-08 69.4
13 TraesCS5D01G455700 chr2B 85.279 197 18 6 3 191 250531915 250531722 2.840000e-45 193.0
14 TraesCS5D01G455700 chr2B 88.889 63 4 2 132 193 600714830 600714770 1.070000e-09 75.0
15 TraesCS5D01G455700 chr2D 91.765 85 7 0 1507 1591 38517078 38516994 4.890000e-23 119.0
16 TraesCS5D01G455700 chr6A 93.443 61 0 2 131 191 596204394 596204450 1.380000e-13 87.9
17 TraesCS5D01G455700 chr3D 91.667 60 3 1 132 191 45624029 45624086 6.410000e-12 82.4
18 TraesCS5D01G455700 chr3A 91.525 59 1 2 132 190 216647529 216647583 8.290000e-11 78.7


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 TraesCS5D01G455700 chr5D 502873075 502875866 2791 False 5156.0 5156 100.000000 1 2792 1 chr5D.!!$F1 2791
1 TraesCS5D01G455700 chr5B 631783154 631788198 5044 False 518.7 1031 90.387000 1 2610 5 chr5B.!!$F1 2609
2 TraesCS5D01G455700 chr5A 631463001 631465146 2145 False 291.4 551 87.449667 326 2339 6 chr5A.!!$F2 2013

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
766 3146 0.179163 GATTCGGCGGCCTTCTTTTG 60.179 55.0 18.34 0.0 0.0 2.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2519 5188 0.106708 TCCATCGCTATTGGCTGGAC 59.893 55.0 0.0 0.0 39.41 4.02 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
24 25 3.041946 AGAGTAAGGTTAGAGGGCATGG 58.958 50.000 0.00 0.00 0.00 3.66
76 77 6.096423 GGGAATGTAAACCCCTTCTTCATTAC 59.904 42.308 0.00 0.00 40.19 1.89
81 82 4.914177 AACCCCTTCTTCATTACGGTAA 57.086 40.909 2.62 2.62 0.00 2.85
140 141 7.623770 TGATGTACGTGTAAACTTTGTCTTTC 58.376 34.615 0.00 0.00 0.00 2.62
181 184 3.516681 GCACACTCATGCATATTCGAG 57.483 47.619 0.00 4.40 45.39 4.04
212 215 2.952273 CGATCGGTCGCATACAACA 58.048 52.632 4.56 0.00 41.49 3.33
218 221 2.165641 TCGGTCGCATACAACATCTCTT 59.834 45.455 0.00 0.00 0.00 2.85
238 241 5.865085 TCTTTAAAAGAGCTGCTCTAACCA 58.135 37.500 30.62 14.45 40.28 3.67
239 242 6.476378 TCTTTAAAAGAGCTGCTCTAACCAT 58.524 36.000 30.62 13.48 40.28 3.55
269 2492 1.614824 CCTCCCTGCTTCACCTCCT 60.615 63.158 0.00 0.00 0.00 3.69
308 2531 2.338984 GATACGAATCCGGCGGCT 59.661 61.111 23.83 9.44 40.78 5.52
426 2654 4.648626 GCACTGCTGGCCTGGTGA 62.649 66.667 18.80 0.00 32.12 4.02
524 2758 4.266070 GCAGCGATCGAGCCGGTA 62.266 66.667 21.57 0.00 38.01 4.02
595 2830 1.153353 GCGAAACGGAAGGATGACAA 58.847 50.000 0.00 0.00 0.00 3.18
599 2834 0.693049 AACGGAAGGATGACAAGGCT 59.307 50.000 0.00 0.00 0.00 4.58
734 3054 1.268184 GCAAAGCAAAGCAAAGCAACC 60.268 47.619 0.00 0.00 0.00 3.77
735 3055 1.331447 CAAAGCAAAGCAAAGCAACCC 59.669 47.619 0.00 0.00 0.00 4.11
736 3056 0.530431 AAGCAAAGCAAAGCAACCCG 60.530 50.000 0.00 0.00 0.00 5.28
737 3057 1.955663 GCAAAGCAAAGCAACCCGG 60.956 57.895 0.00 0.00 0.00 5.73
738 3058 1.441311 CAAAGCAAAGCAACCCGGT 59.559 52.632 0.00 0.00 0.00 5.28
739 3059 0.875474 CAAAGCAAAGCAACCCGGTG 60.875 55.000 0.00 0.00 0.00 4.94
740 3060 1.040339 AAAGCAAAGCAACCCGGTGA 61.040 50.000 0.00 0.00 0.00 4.02
741 3061 1.455383 AAGCAAAGCAACCCGGTGAG 61.455 55.000 0.00 0.00 0.00 3.51
760 3140 2.818274 GTTCGATTCGGCGGCCTT 60.818 61.111 18.34 1.14 0.00 4.35
761 3141 2.510691 TTCGATTCGGCGGCCTTC 60.511 61.111 18.34 10.11 0.00 3.46
765 3145 1.644786 CGATTCGGCGGCCTTCTTTT 61.645 55.000 18.34 0.00 0.00 2.27
766 3146 0.179163 GATTCGGCGGCCTTCTTTTG 60.179 55.000 18.34 0.00 0.00 2.44
767 3147 2.212900 ATTCGGCGGCCTTCTTTTGC 62.213 55.000 18.34 0.00 0.00 3.68
768 3148 4.759096 CGGCGGCCTTCTTTTGCG 62.759 66.667 18.34 0.00 0.00 4.85
772 3152 4.043200 GGCCTTCTTTTGCGCGCT 62.043 61.111 33.29 0.00 0.00 5.92
807 3187 1.079819 CACACCGGAGAAGCATCGT 60.080 57.895 9.46 0.00 0.00 3.73
915 3337 1.273455 GCCGGCTATAAGTACACGCG 61.273 60.000 22.15 3.53 0.00 6.01
916 3338 0.662374 CCGGCTATAAGTACACGCGG 60.662 60.000 12.47 1.27 0.00 6.46
945 3367 0.679960 AGAAACGCCATTAGCCACCC 60.680 55.000 0.00 0.00 38.78 4.61
946 3368 0.963355 GAAACGCCATTAGCCACCCA 60.963 55.000 0.00 0.00 38.78 4.51
947 3369 1.248101 AAACGCCATTAGCCACCCAC 61.248 55.000 0.00 0.00 38.78 4.61
949 3371 1.378514 CGCCATTAGCCACCCACTT 60.379 57.895 0.00 0.00 38.78 3.16
950 3372 1.376609 CGCCATTAGCCACCCACTTC 61.377 60.000 0.00 0.00 38.78 3.01
951 3373 0.323360 GCCATTAGCCACCCACTTCA 60.323 55.000 0.00 0.00 34.35 3.02
952 3374 1.686115 GCCATTAGCCACCCACTTCAT 60.686 52.381 0.00 0.00 34.35 2.57
981 3403 0.611200 CCACTGTTACCCGTCCATCA 59.389 55.000 0.00 0.00 0.00 3.07
1029 3451 4.039357 CCGGCGTCACTGTCGACT 62.039 66.667 17.92 0.00 39.90 4.18
1031 3453 2.502080 GGCGTCACTGTCGACTCG 60.502 66.667 17.92 13.63 33.54 4.18
1032 3454 2.251667 GCGTCACTGTCGACTCGT 59.748 61.111 17.92 11.00 33.54 4.18
1060 3489 2.202453 GAGTTCGTCGTCTCGGGC 60.202 66.667 0.00 0.00 0.00 6.13
1121 3556 3.617538 CGCAAGGTACGCTAGCGC 61.618 66.667 35.63 20.71 44.19 5.92
1122 3557 2.202756 GCAAGGTACGCTAGCGCT 60.203 61.111 35.63 22.18 44.19 5.92
1123 3558 2.231618 GCAAGGTACGCTAGCGCTC 61.232 63.158 35.63 26.47 44.19 5.03
1124 3559 1.138883 CAAGGTACGCTAGCGCTCA 59.861 57.895 35.63 19.04 44.19 4.26
1125 3560 0.867753 CAAGGTACGCTAGCGCTCAG 60.868 60.000 35.63 17.38 44.19 3.35
1138 3573 1.903294 GCTCAGCTCACCCTCATCA 59.097 57.895 0.00 0.00 0.00 3.07
1140 3575 1.540797 GCTCAGCTCACCCTCATCATC 60.541 57.143 0.00 0.00 0.00 2.92
1141 3576 2.040939 CTCAGCTCACCCTCATCATCT 58.959 52.381 0.00 0.00 0.00 2.90
1143 3578 2.040939 CAGCTCACCCTCATCATCTCT 58.959 52.381 0.00 0.00 0.00 3.10
1145 3580 3.113824 AGCTCACCCTCATCATCTCTTT 58.886 45.455 0.00 0.00 0.00 2.52
1146 3581 4.100653 CAGCTCACCCTCATCATCTCTTTA 59.899 45.833 0.00 0.00 0.00 1.85
1147 3582 4.344679 AGCTCACCCTCATCATCTCTTTAG 59.655 45.833 0.00 0.00 0.00 1.85
1148 3583 4.100808 GCTCACCCTCATCATCTCTTTAGT 59.899 45.833 0.00 0.00 0.00 2.24
1149 3584 5.738783 GCTCACCCTCATCATCTCTTTAGTC 60.739 48.000 0.00 0.00 0.00 2.59
1150 3585 5.523588 TCACCCTCATCATCTCTTTAGTCT 58.476 41.667 0.00 0.00 0.00 3.24
1151 3586 5.362143 TCACCCTCATCATCTCTTTAGTCTG 59.638 44.000 0.00 0.00 0.00 3.51
1152 3587 4.100808 ACCCTCATCATCTCTTTAGTCTGC 59.899 45.833 0.00 0.00 0.00 4.26
1153 3588 4.100653 CCCTCATCATCTCTTTAGTCTGCA 59.899 45.833 0.00 0.00 0.00 4.41
1162 3597 6.019779 TCTCTTTAGTCTGCAGAGAAGAAC 57.980 41.667 25.28 13.36 40.10 3.01
1163 3598 5.047660 TCTCTTTAGTCTGCAGAGAAGAACC 60.048 44.000 25.28 12.34 40.10 3.62
1193 3628 2.282887 AAGATGCGGCCGGGTTTT 60.283 55.556 29.38 0.00 0.00 2.43
1206 3641 3.735820 GCCGGGTTTTCTTTTCGTTTCTT 60.736 43.478 2.18 0.00 0.00 2.52
1230 3665 7.186570 TGATCTTGATCTTGATGGTCTGTTA 57.813 36.000 11.31 0.00 0.00 2.41
1231 3666 7.799081 TGATCTTGATCTTGATGGTCTGTTAT 58.201 34.615 11.31 0.00 0.00 1.89
1236 3671 6.115446 TGATCTTGATGGTCTGTTATTGGTC 58.885 40.000 0.00 0.00 0.00 4.02
1237 3672 5.497464 TCTTGATGGTCTGTTATTGGTCA 57.503 39.130 0.00 0.00 0.00 4.02
1238 3673 6.065976 TCTTGATGGTCTGTTATTGGTCAT 57.934 37.500 0.00 0.00 0.00 3.06
1240 3675 6.947733 TCTTGATGGTCTGTTATTGGTCATTT 59.052 34.615 0.00 0.00 0.00 2.32
1381 3824 1.063764 CTCGAAGGCTGGTACGTACTC 59.936 57.143 24.07 14.94 0.00 2.59
1383 3826 1.200716 CGAAGGCTGGTACGTACTCAA 59.799 52.381 24.07 10.27 0.00 3.02
1388 3831 3.131755 AGGCTGGTACGTACTCAATTACC 59.868 47.826 24.07 16.67 35.47 2.85
1390 3833 4.357996 GCTGGTACGTACTCAATTACCTC 58.642 47.826 24.07 5.15 35.86 3.85
1411 3858 0.958091 TGCACGGCTAATTGCTTGTT 59.042 45.000 0.00 0.00 42.39 2.83
1438 3885 4.142381 GGCCGCTACTTTTTCTCATGATTT 60.142 41.667 0.00 0.00 0.00 2.17
1446 3893 3.454719 TTTCTCATGATTTGGCTCCCA 57.545 42.857 0.00 0.00 0.00 4.37
1448 3895 1.019673 CTCATGATTTGGCTCCCACG 58.980 55.000 0.00 0.00 30.78 4.94
1451 3898 0.546122 ATGATTTGGCTCCCACGCTA 59.454 50.000 0.00 0.00 30.78 4.26
1452 3899 0.107703 TGATTTGGCTCCCACGCTAG 60.108 55.000 0.00 0.00 30.78 3.42
1461 3930 0.898326 TCCCACGCTAGCTCAACTCA 60.898 55.000 13.93 0.00 0.00 3.41
1471 3940 3.518634 AGCTCAACTCACTAGCTTAGC 57.481 47.619 0.00 0.00 43.97 3.09
1474 3943 4.707448 AGCTCAACTCACTAGCTTAGCTAA 59.293 41.667 15.23 5.94 43.97 3.09
1477 3946 6.536941 GCTCAACTCACTAGCTTAGCTAATTT 59.463 38.462 15.23 0.96 40.82 1.82
1483 3952 8.631797 ACTCACTAGCTTAGCTAATTTACCTAC 58.368 37.037 15.23 0.00 40.82 3.18
1485 3954 7.783596 TCACTAGCTTAGCTAATTTACCTACCT 59.216 37.037 15.23 0.00 40.82 3.08
1490 3959 9.076781 AGCTTAGCTAATTTACCTACCTAGTAC 57.923 37.037 4.30 0.00 36.99 2.73
1496 3965 8.911965 GCTAATTTACCTACCTAGTACTCAACT 58.088 37.037 0.00 0.00 42.62 3.16
1498 3967 8.890410 AATTTACCTACCTAGTACTCAACTGA 57.110 34.615 0.00 0.00 39.39 3.41
1499 3968 7.693969 TTTACCTACCTAGTACTCAACTGAC 57.306 40.000 0.00 0.00 39.39 3.51
1501 3970 5.499313 ACCTACCTAGTACTCAACTGACTC 58.501 45.833 0.00 0.00 39.39 3.36
1502 3971 5.251237 ACCTACCTAGTACTCAACTGACTCT 59.749 44.000 0.00 0.00 39.39 3.24
1503 3972 5.587043 CCTACCTAGTACTCAACTGACTCTG 59.413 48.000 0.00 0.00 39.39 3.35
1505 3974 2.999507 AGTACTCAACTGACTCTGCG 57.000 50.000 0.00 0.00 36.93 5.18
1509 4001 1.683917 ACTCAACTGACTCTGCGTTCT 59.316 47.619 0.00 0.00 0.00 3.01
1643 4151 3.327757 ACTGTACAAAGAGATGGCCTCAA 59.672 43.478 3.32 0.00 44.40 3.02
1644 4152 3.937706 CTGTACAAAGAGATGGCCTCAAG 59.062 47.826 3.32 0.00 44.40 3.02
1645 4153 2.503895 ACAAAGAGATGGCCTCAAGG 57.496 50.000 3.32 0.00 44.40 3.61
1647 4155 2.579860 ACAAAGAGATGGCCTCAAGGAT 59.420 45.455 3.32 0.00 44.40 3.24
1648 4156 3.782523 ACAAAGAGATGGCCTCAAGGATA 59.217 43.478 3.32 0.00 44.40 2.59
1649 4157 4.414846 ACAAAGAGATGGCCTCAAGGATAT 59.585 41.667 3.32 0.00 44.40 1.63
1747 4284 0.323087 TCTCACTACGGTGCTGCCTA 60.323 55.000 0.00 0.00 42.72 3.93
1807 4348 2.910688 TCTTACCATCTTCCATCCGC 57.089 50.000 0.00 0.00 0.00 5.54
1808 4349 2.115427 TCTTACCATCTTCCATCCGCA 58.885 47.619 0.00 0.00 0.00 5.69
1810 4351 2.839486 TACCATCTTCCATCCGCATC 57.161 50.000 0.00 0.00 0.00 3.91
1813 4354 0.399454 CATCTTCCATCCGCATCCCT 59.601 55.000 0.00 0.00 0.00 4.20
1828 4369 3.160269 CATCCCTTTTCCTCTGCTTGTT 58.840 45.455 0.00 0.00 0.00 2.83
1829 4370 2.586425 TCCCTTTTCCTCTGCTTGTTG 58.414 47.619 0.00 0.00 0.00 3.33
1832 4373 3.888930 CCCTTTTCCTCTGCTTGTTGTTA 59.111 43.478 0.00 0.00 0.00 2.41
1833 4374 4.022849 CCCTTTTCCTCTGCTTGTTGTTAG 60.023 45.833 0.00 0.00 0.00 2.34
1836 4377 5.499139 TTTCCTCTGCTTGTTGTTAGTTG 57.501 39.130 0.00 0.00 0.00 3.16
1840 4381 4.213482 CCTCTGCTTGTTGTTAGTTGTACC 59.787 45.833 0.00 0.00 0.00 3.34
1889 4431 5.814188 TGCTCAGTAGTGATGATTTGTGATC 59.186 40.000 0.00 0.00 30.18 2.92
1896 4438 8.890718 AGTAGTGATGATTTGTGATCAATTCTG 58.109 33.333 0.00 0.00 35.92 3.02
1897 4439 7.096884 AGTGATGATTTGTGATCAATTCTGG 57.903 36.000 0.00 0.00 35.92 3.86
1958 4512 0.242286 TCTCTGCACTGAACGAGAGC 59.758 55.000 0.00 0.00 38.67 4.09
2113 4766 4.041075 TGAGATAGCTCTGATAGAGACGGT 59.959 45.833 9.79 0.00 45.07 4.83
2114 4767 5.246429 TGAGATAGCTCTGATAGAGACGGTA 59.754 44.000 9.79 0.00 45.07 4.02
2167 4820 1.852942 CGGTGGATAATCAGGTGTCG 58.147 55.000 0.00 0.00 0.00 4.35
2204 4857 1.597663 CAGTTGACAGACGGTTGGAAC 59.402 52.381 0.00 0.00 0.00 3.62
2240 4893 4.566987 AGGACGTTTACTGGATCACTTTC 58.433 43.478 0.00 0.00 0.00 2.62
2320 4982 7.713764 AAACTTGCAAATTATTCCACTCAAC 57.286 32.000 0.00 0.00 0.00 3.18
2328 4990 7.571059 GCAAATTATTCCACTCAACGCAAAAAT 60.571 33.333 0.00 0.00 0.00 1.82
2332 4994 8.873215 TTATTCCACTCAACGCAAAAATAAAA 57.127 26.923 0.00 0.00 0.00 1.52
2333 4995 7.778470 ATTCCACTCAACGCAAAAATAAAAA 57.222 28.000 0.00 0.00 0.00 1.94
2334 4996 7.778470 TTCCACTCAACGCAAAAATAAAAAT 57.222 28.000 0.00 0.00 0.00 1.82
2335 4997 8.873215 TTCCACTCAACGCAAAAATAAAAATA 57.127 26.923 0.00 0.00 0.00 1.40
2404 5073 3.225235 GCCCTCAGCCCTACAGAG 58.775 66.667 0.00 0.00 34.35 3.35
2405 5074 1.687493 GCCCTCAGCCCTACAGAGT 60.687 63.158 0.00 0.00 34.35 3.24
2406 5075 0.397254 GCCCTCAGCCCTACAGAGTA 60.397 60.000 0.00 0.00 34.35 2.59
2407 5076 1.404843 CCCTCAGCCCTACAGAGTAC 58.595 60.000 0.00 0.00 30.12 2.73
2408 5077 1.342076 CCCTCAGCCCTACAGAGTACA 60.342 57.143 0.00 0.00 30.12 2.90
2409 5078 2.672098 CCTCAGCCCTACAGAGTACAT 58.328 52.381 0.00 0.00 30.12 2.29
2410 5079 2.625790 CCTCAGCCCTACAGAGTACATC 59.374 54.545 0.00 0.00 30.12 3.06
2411 5080 3.291584 CTCAGCCCTACAGAGTACATCA 58.708 50.000 0.00 0.00 0.00 3.07
2412 5081 3.894427 CTCAGCCCTACAGAGTACATCAT 59.106 47.826 0.00 0.00 0.00 2.45
2443 5112 2.086869 CAGCCATCGTTCAGTTGGAAT 58.913 47.619 0.00 0.00 41.23 3.01
2444 5113 2.096496 CAGCCATCGTTCAGTTGGAATC 59.904 50.000 0.00 0.00 41.23 2.52
2445 5114 2.083774 GCCATCGTTCAGTTGGAATCA 58.916 47.619 0.00 0.00 41.23 2.57
2446 5115 2.487762 GCCATCGTTCAGTTGGAATCAA 59.512 45.455 0.00 0.00 41.23 2.57
2447 5116 3.426695 GCCATCGTTCAGTTGGAATCAAG 60.427 47.826 0.00 0.00 41.23 3.02
2448 5117 3.753272 CCATCGTTCAGTTGGAATCAAGT 59.247 43.478 0.00 0.00 41.23 3.16
2449 5118 4.216257 CCATCGTTCAGTTGGAATCAAGTT 59.784 41.667 0.00 0.00 41.23 2.66
2450 5119 4.811555 TCGTTCAGTTGGAATCAAGTTG 57.188 40.909 0.00 0.00 37.93 3.16
2451 5120 3.563808 TCGTTCAGTTGGAATCAAGTTGG 59.436 43.478 2.34 0.00 37.93 3.77
2452 5121 3.563808 CGTTCAGTTGGAATCAAGTTGGA 59.436 43.478 2.34 0.00 37.93 3.53
2453 5122 4.036262 CGTTCAGTTGGAATCAAGTTGGAA 59.964 41.667 2.34 0.00 37.93 3.53
2454 5123 5.278463 CGTTCAGTTGGAATCAAGTTGGAAT 60.278 40.000 2.34 0.00 37.93 3.01
2491 5160 5.748152 ACATGAAACACATTTTCCTTGTTCG 59.252 36.000 0.00 0.00 37.07 3.95
2518 5187 7.497925 AAAGAACTTCAAGTTGATGACTACC 57.502 36.000 21.87 8.36 38.80 3.18
2519 5188 5.230942 AGAACTTCAAGTTGATGACTACCG 58.769 41.667 21.87 1.56 38.80 4.02
2548 5219 4.081476 CCAATAGCGATGGATGTATGGAGA 60.081 45.833 0.00 0.00 40.56 3.71
2561 5232 5.255397 TGTATGGAGAACTGGAAATTGGT 57.745 39.130 0.00 0.00 0.00 3.67
2564 5235 7.410174 TGTATGGAGAACTGGAAATTGGTAAT 58.590 34.615 0.00 0.00 0.00 1.89
2605 5276 5.685954 GGGACTCGAAATTTGAAAAACTCAC 59.314 40.000 0.00 0.00 32.21 3.51
2610 5281 8.455682 ACTCGAAATTTGAAAAACTCACAACTA 58.544 29.630 0.00 0.00 32.21 2.24
2611 5282 8.835467 TCGAAATTTGAAAAACTCACAACTAG 57.165 30.769 0.00 0.00 32.21 2.57
2612 5283 7.913297 TCGAAATTTGAAAAACTCACAACTAGG 59.087 33.333 0.00 0.00 32.21 3.02
2613 5284 7.305993 CGAAATTTGAAAAACTCACAACTAGGC 60.306 37.037 0.00 0.00 32.21 3.93
2614 5285 4.911514 TTGAAAAACTCACAACTAGGCC 57.088 40.909 0.00 0.00 32.21 5.19
2615 5286 3.219281 TGAAAAACTCACAACTAGGCCC 58.781 45.455 0.00 0.00 0.00 5.80
2616 5287 3.117663 TGAAAAACTCACAACTAGGCCCT 60.118 43.478 0.00 0.00 0.00 5.19
2617 5288 2.568623 AAACTCACAACTAGGCCCTG 57.431 50.000 0.00 0.00 0.00 4.45
2618 5289 0.693049 AACTCACAACTAGGCCCTGG 59.307 55.000 0.00 0.00 0.00 4.45
2619 5290 1.078143 CTCACAACTAGGCCCTGGC 60.078 63.158 0.00 0.00 41.06 4.85
2620 5291 1.538876 TCACAACTAGGCCCTGGCT 60.539 57.895 8.29 0.00 42.39 4.75
2621 5292 1.377725 CACAACTAGGCCCTGGCTG 60.378 63.158 8.29 0.00 39.30 4.85
2622 5293 2.439156 CAACTAGGCCCTGGCTGC 60.439 66.667 8.29 0.00 39.30 5.25
2686 5357 8.831715 AAAACTCACAACTCAAATTTTGAAGT 57.168 26.923 12.62 9.10 39.58 3.01
2687 5358 8.831715 AAACTCACAACTCAAATTTTGAAGTT 57.168 26.923 12.62 13.71 39.58 2.66
2688 5359 8.466086 AACTCACAACTCAAATTTTGAAGTTC 57.534 30.769 12.62 0.00 39.58 3.01
2689 5360 7.035612 ACTCACAACTCAAATTTTGAAGTTCC 58.964 34.615 12.62 0.00 39.58 3.62
2690 5361 6.033341 TCACAACTCAAATTTTGAAGTTCCG 58.967 36.000 12.62 10.92 39.58 4.30
2691 5362 6.033341 CACAACTCAAATTTTGAAGTTCCGA 58.967 36.000 12.62 0.00 39.58 4.55
2692 5363 6.197096 CACAACTCAAATTTTGAAGTTCCGAG 59.803 38.462 12.62 9.27 39.58 4.63
2693 5364 6.094881 ACAACTCAAATTTTGAAGTTCCGAGA 59.905 34.615 12.62 0.00 39.58 4.04
2694 5365 6.693315 ACTCAAATTTTGAAGTTCCGAGAA 57.307 33.333 12.62 0.00 39.58 2.87
2695 5366 7.095695 ACTCAAATTTTGAAGTTCCGAGAAA 57.904 32.000 12.62 0.00 39.58 2.52
2696 5367 7.716612 ACTCAAATTTTGAAGTTCCGAGAAAT 58.283 30.769 12.62 0.01 39.58 2.17
2697 5368 8.197439 ACTCAAATTTTGAAGTTCCGAGAAATT 58.803 29.630 12.62 5.69 39.58 1.82
2698 5369 8.574196 TCAAATTTTGAAGTTCCGAGAAATTC 57.426 30.769 9.36 15.36 36.59 2.17
2699 5370 8.413229 TCAAATTTTGAAGTTCCGAGAAATTCT 58.587 29.630 19.86 0.00 36.59 2.40
2700 5371 8.482429 CAAATTTTGAAGTTCCGAGAAATTCTG 58.518 33.333 19.86 10.35 0.00 3.02
2701 5372 6.935741 TTTTGAAGTTCCGAGAAATTCTGA 57.064 33.333 19.86 11.00 0.00 3.27
2702 5373 6.935741 TTTGAAGTTCCGAGAAATTCTGAA 57.064 33.333 19.86 14.39 0.00 3.02
2703 5374 6.935741 TTGAAGTTCCGAGAAATTCTGAAA 57.064 33.333 19.86 9.46 31.91 2.69
2704 5375 6.935741 TGAAGTTCCGAGAAATTCTGAAAA 57.064 33.333 19.86 4.91 31.91 2.29
2705 5376 7.328277 TGAAGTTCCGAGAAATTCTGAAAAA 57.672 32.000 19.86 4.41 31.91 1.94
2706 5377 7.940850 TGAAGTTCCGAGAAATTCTGAAAAAT 58.059 30.769 19.86 0.00 31.91 1.82
2707 5378 9.062524 TGAAGTTCCGAGAAATTCTGAAAAATA 57.937 29.630 19.86 3.41 31.91 1.40
2708 5379 9.331106 GAAGTTCCGAGAAATTCTGAAAAATAC 57.669 33.333 15.11 0.00 31.91 1.89
2709 5380 8.391075 AGTTCCGAGAAATTCTGAAAAATACA 57.609 30.769 0.00 0.00 31.91 2.29
2710 5381 8.290325 AGTTCCGAGAAATTCTGAAAAATACAC 58.710 33.333 0.00 0.00 31.91 2.90
2711 5382 7.737972 TCCGAGAAATTCTGAAAAATACACA 57.262 32.000 0.00 0.00 0.00 3.72
2712 5383 8.335532 TCCGAGAAATTCTGAAAAATACACAT 57.664 30.769 0.00 0.00 0.00 3.21
2713 5384 8.236586 TCCGAGAAATTCTGAAAAATACACATG 58.763 33.333 0.00 0.00 0.00 3.21
2714 5385 8.023128 CCGAGAAATTCTGAAAAATACACATGT 58.977 33.333 0.00 0.00 0.00 3.21
2722 5393 9.689976 TTCTGAAAAATACACATGTACATTTGG 57.310 29.630 22.52 10.78 32.72 3.28
2723 5394 8.303156 TCTGAAAAATACACATGTACATTTGGG 58.697 33.333 22.52 11.45 32.72 4.12
2724 5395 8.183104 TGAAAAATACACATGTACATTTGGGA 57.817 30.769 22.52 12.49 32.72 4.37
2725 5396 8.811017 TGAAAAATACACATGTACATTTGGGAT 58.189 29.630 22.52 13.93 32.72 3.85
2729 5400 8.408043 AATACACATGTACATTTGGGATATGG 57.592 34.615 22.52 4.33 32.72 2.74
2730 5401 5.765510 ACACATGTACATTTGGGATATGGT 58.234 37.500 22.52 4.91 0.00 3.55
2731 5402 5.827797 ACACATGTACATTTGGGATATGGTC 59.172 40.000 22.52 0.00 0.00 4.02
2732 5403 6.064060 CACATGTACATTTGGGATATGGTCT 58.936 40.000 13.22 0.00 0.00 3.85
2733 5404 7.147391 ACACATGTACATTTGGGATATGGTCTA 60.147 37.037 22.52 0.00 0.00 2.59
2734 5405 7.173218 CACATGTACATTTGGGATATGGTCTAC 59.827 40.741 13.22 0.00 0.00 2.59
2735 5406 6.816616 TGTACATTTGGGATATGGTCTACA 57.183 37.500 0.00 0.00 0.00 2.74
2736 5407 7.201702 TGTACATTTGGGATATGGTCTACAA 57.798 36.000 0.00 0.00 0.00 2.41
2737 5408 7.279615 TGTACATTTGGGATATGGTCTACAAG 58.720 38.462 0.00 0.00 0.00 3.16
2738 5409 6.327386 ACATTTGGGATATGGTCTACAAGT 57.673 37.500 0.00 0.00 0.00 3.16
2739 5410 6.122277 ACATTTGGGATATGGTCTACAAGTG 58.878 40.000 0.00 0.00 37.39 3.16
2740 5411 5.772393 TTTGGGATATGGTCTACAAGTGT 57.228 39.130 0.00 0.00 0.00 3.55
2741 5412 4.753516 TGGGATATGGTCTACAAGTGTG 57.246 45.455 0.00 0.00 0.00 3.82
2742 5413 4.358214 TGGGATATGGTCTACAAGTGTGA 58.642 43.478 0.00 0.00 0.00 3.58
2743 5414 4.780554 TGGGATATGGTCTACAAGTGTGAA 59.219 41.667 0.00 0.00 0.00 3.18
2744 5415 5.249622 TGGGATATGGTCTACAAGTGTGAAA 59.750 40.000 0.00 0.00 0.00 2.69
2745 5416 6.177610 GGGATATGGTCTACAAGTGTGAAAA 58.822 40.000 0.00 0.00 0.00 2.29
2746 5417 6.316390 GGGATATGGTCTACAAGTGTGAAAAG 59.684 42.308 0.00 0.00 0.00 2.27
2747 5418 6.879458 GGATATGGTCTACAAGTGTGAAAAGT 59.121 38.462 0.00 0.00 0.00 2.66
2748 5419 7.390718 GGATATGGTCTACAAGTGTGAAAAGTT 59.609 37.037 0.00 0.00 0.00 2.66
2749 5420 6.619801 ATGGTCTACAAGTGTGAAAAGTTC 57.380 37.500 0.00 0.00 0.00 3.01
2750 5421 4.879545 TGGTCTACAAGTGTGAAAAGTTCC 59.120 41.667 0.00 0.00 0.00 3.62
2751 5422 4.879545 GGTCTACAAGTGTGAAAAGTTCCA 59.120 41.667 0.00 0.00 0.00 3.53
2752 5423 5.531287 GGTCTACAAGTGTGAAAAGTTCCAT 59.469 40.000 0.00 0.00 0.00 3.41
2753 5424 6.430451 GTCTACAAGTGTGAAAAGTTCCATG 58.570 40.000 0.00 0.00 0.00 3.66
2754 5425 6.260050 GTCTACAAGTGTGAAAAGTTCCATGA 59.740 38.462 0.00 0.00 0.00 3.07
2755 5426 6.998074 TCTACAAGTGTGAAAAGTTCCATGAT 59.002 34.615 0.00 0.00 0.00 2.45
2756 5427 5.835257 ACAAGTGTGAAAAGTTCCATGATG 58.165 37.500 0.00 0.00 0.00 3.07
2757 5428 5.360714 ACAAGTGTGAAAAGTTCCATGATGT 59.639 36.000 0.00 0.00 0.00 3.06
2758 5429 5.443185 AGTGTGAAAAGTTCCATGATGTG 57.557 39.130 0.00 0.00 0.00 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
76 77 1.226323 CGCTCTCACCTCGTTACCG 60.226 63.158 0.00 0.00 0.00 4.02
81 82 0.321387 TCACTACGCTCTCACCTCGT 60.321 55.000 0.00 0.00 39.88 4.18
83 84 0.736053 CCTCACTACGCTCTCACCTC 59.264 60.000 0.00 0.00 0.00 3.85
164 167 3.391506 TCCCTCGAATATGCATGAGTG 57.608 47.619 10.16 0.00 0.00 3.51
200 203 7.739295 TCTTTTAAAGAGATGTTGTATGCGAC 58.261 34.615 2.94 0.00 32.71 5.19
218 221 6.149474 GTCAATGGTTAGAGCAGCTCTTTTAA 59.851 38.462 29.97 15.63 41.50 1.52
236 239 1.065126 GGGAGGAGACCTTGTCAATGG 60.065 57.143 0.00 0.00 34.60 3.16
237 240 1.912043 AGGGAGGAGACCTTGTCAATG 59.088 52.381 0.00 0.00 33.64 2.82
238 241 1.912043 CAGGGAGGAGACCTTGTCAAT 59.088 52.381 0.00 0.00 35.78 2.57
239 242 1.352083 CAGGGAGGAGACCTTGTCAA 58.648 55.000 0.00 0.00 35.78 3.18
288 2511 2.048503 CGCCGGATTCGTATCCCC 60.049 66.667 14.72 6.01 46.53 4.81
308 2531 9.839817 TGGTCCATGATTTTATTTATTACTCGA 57.160 29.630 0.00 0.00 0.00 4.04
415 2643 1.669115 CACGTCTTCACCAGGCCAG 60.669 63.158 5.01 0.00 0.00 4.85
421 2649 0.179094 AGTTTCGCACGTCTTCACCA 60.179 50.000 0.00 0.00 0.00 4.17
426 2654 0.319641 GGAGGAGTTTCGCACGTCTT 60.320 55.000 0.00 0.00 0.00 3.01
523 2757 1.378762 GGCTGGCTTGGTTCTGGTA 59.621 57.895 0.00 0.00 0.00 3.25
524 2758 2.116125 GGCTGGCTTGGTTCTGGT 59.884 61.111 0.00 0.00 0.00 4.00
666 2922 3.276846 GCCGTGCGTTGTGTTCCT 61.277 61.111 0.00 0.00 0.00 3.36
734 3054 1.518572 CGAATCGAACCCTCACCGG 60.519 63.158 0.00 0.00 0.00 5.28
735 3055 1.518572 CCGAATCGAACCCTCACCG 60.519 63.158 3.36 0.00 0.00 4.94
736 3056 1.814169 GCCGAATCGAACCCTCACC 60.814 63.158 3.36 0.00 0.00 4.02
737 3057 2.165301 CGCCGAATCGAACCCTCAC 61.165 63.158 3.36 0.00 0.00 3.51
738 3058 2.183300 CGCCGAATCGAACCCTCA 59.817 61.111 3.36 0.00 0.00 3.86
739 3059 2.585247 CCGCCGAATCGAACCCTC 60.585 66.667 3.36 0.00 0.00 4.30
740 3060 4.832608 GCCGCCGAATCGAACCCT 62.833 66.667 3.36 0.00 0.00 4.34
760 3140 0.317770 CTGGAAAAGCGCGCAAAAGA 60.318 50.000 35.10 11.20 0.00 2.52
761 3141 0.317770 TCTGGAAAAGCGCGCAAAAG 60.318 50.000 35.10 20.07 0.00 2.27
765 3145 2.869646 CATCTGGAAAAGCGCGCA 59.130 55.556 35.10 10.38 0.00 6.09
766 3146 2.577911 GCATCTGGAAAAGCGCGC 60.578 61.111 26.66 26.66 0.00 6.86
767 3147 2.100991 GGCATCTGGAAAAGCGCG 59.899 61.111 0.00 0.00 0.00 6.86
768 3148 1.431036 GAGGCATCTGGAAAAGCGC 59.569 57.895 0.00 0.00 0.00 5.92
769 3149 1.717937 CGAGGCATCTGGAAAAGCG 59.282 57.895 0.00 0.00 0.00 4.68
770 3150 1.431036 GCGAGGCATCTGGAAAAGC 59.569 57.895 0.00 0.00 0.00 3.51
771 3151 0.677731 TGGCGAGGCATCTGGAAAAG 60.678 55.000 0.00 0.00 0.00 2.27
772 3152 0.960364 GTGGCGAGGCATCTGGAAAA 60.960 55.000 1.94 0.00 0.00 2.29
807 3187 3.039588 GTGTCGGCCGAAGCGAAA 61.040 61.111 32.93 8.66 41.24 3.46
945 3367 3.438087 CAGTGGAGCAGGTAAATGAAGTG 59.562 47.826 0.00 0.00 0.00 3.16
946 3368 3.073062 ACAGTGGAGCAGGTAAATGAAGT 59.927 43.478 0.00 0.00 0.00 3.01
947 3369 3.679389 ACAGTGGAGCAGGTAAATGAAG 58.321 45.455 0.00 0.00 0.00 3.02
949 3371 3.788227 AACAGTGGAGCAGGTAAATGA 57.212 42.857 0.00 0.00 0.00 2.57
950 3372 3.689649 GGTAACAGTGGAGCAGGTAAATG 59.310 47.826 0.00 0.00 0.00 2.32
951 3373 3.308188 GGGTAACAGTGGAGCAGGTAAAT 60.308 47.826 0.00 0.00 39.74 1.40
952 3374 2.039348 GGGTAACAGTGGAGCAGGTAAA 59.961 50.000 0.00 0.00 39.74 2.01
981 3403 2.470938 GAAGGAAGCGGCTGGAAGGT 62.471 60.000 1.81 0.00 0.00 3.50
1029 3451 1.657594 CGAACTCGCTACTCTGTACGA 59.342 52.381 0.00 0.00 0.00 3.43
1031 3453 2.534544 CGACGAACTCGCTACTCTGTAC 60.535 54.545 0.00 0.00 44.43 2.90
1032 3454 1.657594 CGACGAACTCGCTACTCTGTA 59.342 52.381 0.00 0.00 44.43 2.74
1046 3475 3.796443 CTCGCCCGAGACGACGAA 61.796 66.667 12.04 0.00 44.53 3.85
1054 3483 1.175347 TCATCCTGATCTCGCCCGAG 61.175 60.000 11.24 11.24 43.21 4.63
1055 3484 1.152756 TCATCCTGATCTCGCCCGA 60.153 57.895 0.00 0.00 0.00 5.14
1060 3489 0.039617 GGTCGCTCATCCTGATCTCG 60.040 60.000 0.00 0.00 0.00 4.04
1118 3553 3.382803 ATGAGGGTGAGCTGAGCGC 62.383 63.158 0.00 0.00 39.57 5.92
1119 3554 1.227205 GATGAGGGTGAGCTGAGCG 60.227 63.158 0.00 0.00 0.00 5.03
1120 3555 0.469070 ATGATGAGGGTGAGCTGAGC 59.531 55.000 0.00 0.00 0.00 4.26
1121 3556 2.036217 GAGATGATGAGGGTGAGCTGAG 59.964 54.545 0.00 0.00 0.00 3.35
1122 3557 2.037901 GAGATGATGAGGGTGAGCTGA 58.962 52.381 0.00 0.00 0.00 4.26
1123 3558 2.040939 AGAGATGATGAGGGTGAGCTG 58.959 52.381 0.00 0.00 0.00 4.24
1124 3559 2.475339 AGAGATGATGAGGGTGAGCT 57.525 50.000 0.00 0.00 0.00 4.09
1125 3560 3.557228 AAAGAGATGATGAGGGTGAGC 57.443 47.619 0.00 0.00 0.00 4.26
1126 3561 5.598005 AGACTAAAGAGATGATGAGGGTGAG 59.402 44.000 0.00 0.00 0.00 3.51
1127 3562 5.362143 CAGACTAAAGAGATGATGAGGGTGA 59.638 44.000 0.00 0.00 0.00 4.02
1138 3573 6.350949 GGTTCTTCTCTGCAGACTAAAGAGAT 60.351 42.308 13.74 0.00 44.39 2.75
1140 3575 5.167845 GGTTCTTCTCTGCAGACTAAAGAG 58.832 45.833 13.74 0.85 39.05 2.85
1141 3576 4.588951 TGGTTCTTCTCTGCAGACTAAAGA 59.411 41.667 13.74 17.84 0.00 2.52
1143 3578 4.588951 TCTGGTTCTTCTCTGCAGACTAAA 59.411 41.667 13.74 6.78 0.00 1.85
1145 3580 3.767711 TCTGGTTCTTCTCTGCAGACTA 58.232 45.455 13.74 0.37 0.00 2.59
1146 3581 2.603021 TCTGGTTCTTCTCTGCAGACT 58.397 47.619 13.74 0.00 0.00 3.24
1147 3582 3.006323 TCTTCTGGTTCTTCTCTGCAGAC 59.994 47.826 13.74 1.89 0.00 3.51
1148 3583 3.234353 TCTTCTGGTTCTTCTCTGCAGA 58.766 45.455 17.19 17.19 0.00 4.26
1149 3584 3.587923 CTCTTCTGGTTCTTCTCTGCAG 58.412 50.000 7.63 7.63 0.00 4.41
1150 3585 2.301296 CCTCTTCTGGTTCTTCTCTGCA 59.699 50.000 0.00 0.00 0.00 4.41
1151 3586 2.564947 TCCTCTTCTGGTTCTTCTCTGC 59.435 50.000 0.00 0.00 0.00 4.26
1152 3587 4.141959 GGATCCTCTTCTGGTTCTTCTCTG 60.142 50.000 3.84 0.00 0.00 3.35
1153 3588 4.030216 GGATCCTCTTCTGGTTCTTCTCT 58.970 47.826 3.84 0.00 0.00 3.10
1162 3597 2.806019 CGCATCTTGGATCCTCTTCTGG 60.806 54.545 14.23 0.00 0.00 3.86
1163 3598 2.481854 CGCATCTTGGATCCTCTTCTG 58.518 52.381 14.23 5.52 0.00 3.02
1193 3628 7.969536 AGATCAAGATCAAGAAACGAAAAGA 57.030 32.000 12.21 0.00 40.22 2.52
1206 3641 5.688814 ACAGACCATCAAGATCAAGATCA 57.311 39.130 12.21 0.00 40.22 2.92
1230 3665 7.779798 AGTAACCTGCATACATAAATGACCAAT 59.220 33.333 0.00 0.00 0.00 3.16
1231 3666 7.116075 AGTAACCTGCATACATAAATGACCAA 58.884 34.615 0.00 0.00 0.00 3.67
1236 3671 7.173218 CCTGGTAGTAACCTGCATACATAAATG 59.827 40.741 0.00 0.00 46.91 2.32
1237 3672 7.224297 CCTGGTAGTAACCTGCATACATAAAT 58.776 38.462 0.00 0.00 46.91 1.40
1238 3673 6.408776 CCCTGGTAGTAACCTGCATACATAAA 60.409 42.308 0.00 0.00 46.91 1.40
1240 3675 4.591498 CCCTGGTAGTAACCTGCATACATA 59.409 45.833 0.00 0.00 46.91 2.29
1381 3824 0.392998 AGCCGTGCAGGAGGTAATTG 60.393 55.000 8.24 0.00 45.00 2.32
1383 3826 1.200519 TTAGCCGTGCAGGAGGTAAT 58.799 50.000 8.24 0.00 45.00 1.89
1388 3831 1.723870 GCAATTAGCCGTGCAGGAG 59.276 57.895 8.24 0.00 45.00 3.69
1411 3858 1.376295 GAAAAAGTAGCGGCCGGGA 60.376 57.895 29.38 0.00 0.00 5.14
1438 3885 3.461773 GAGCTAGCGTGGGAGCCA 61.462 66.667 9.55 0.00 39.65 4.75
1446 3893 1.133407 GCTAGTGAGTTGAGCTAGCGT 59.867 52.381 9.55 0.00 45.13 5.07
1452 3899 3.518634 AGCTAAGCTAGTGAGTTGAGC 57.481 47.619 0.00 0.00 36.99 4.26
1461 3930 9.299465 CTAGGTAGGTAAATTAGCTAAGCTAGT 57.701 37.037 22.18 1.89 42.34 2.57
1470 3939 8.911965 AGTTGAGTACTAGGTAGGTAAATTAGC 58.088 37.037 0.00 0.00 34.56 3.09
1474 3943 8.114743 AGTCAGTTGAGTACTAGGTAGGTAAAT 58.885 37.037 0.00 0.00 34.56 1.40
1477 3946 6.443206 AGAGTCAGTTGAGTACTAGGTAGGTA 59.557 42.308 0.00 0.00 34.56 3.08
1483 3952 3.181505 CGCAGAGTCAGTTGAGTACTAGG 60.182 52.174 0.00 0.00 34.56 3.02
1485 3954 3.409570 ACGCAGAGTCAGTTGAGTACTA 58.590 45.455 0.00 0.00 34.56 1.82
1489 3958 1.683917 AGAACGCAGAGTCAGTTGAGT 59.316 47.619 3.86 0.00 0.00 3.41
1490 3959 2.430546 AGAACGCAGAGTCAGTTGAG 57.569 50.000 3.86 0.00 0.00 3.02
1494 3963 0.390860 AGCAAGAACGCAGAGTCAGT 59.609 50.000 0.00 0.00 0.00 3.41
1496 3965 0.104855 ACAGCAAGAACGCAGAGTCA 59.895 50.000 0.00 0.00 0.00 3.41
1498 3967 1.502163 GCACAGCAAGAACGCAGAGT 61.502 55.000 0.00 0.00 0.00 3.24
1499 3968 1.206072 GCACAGCAAGAACGCAGAG 59.794 57.895 0.00 0.00 0.00 3.35
1501 3970 1.082300 CTGCACAGCAAGAACGCAG 60.082 57.895 0.00 0.00 43.55 5.18
1502 3971 1.375853 AACTGCACAGCAAGAACGCA 61.376 50.000 0.00 0.00 38.41 5.24
1503 3972 0.248621 AAACTGCACAGCAAGAACGC 60.249 50.000 0.00 0.00 38.41 4.84
1505 3974 1.843992 CCAAACTGCACAGCAAGAAC 58.156 50.000 0.00 0.00 38.41 3.01
1509 4001 1.438399 CAGCCAAACTGCACAGCAA 59.562 52.632 0.00 0.00 40.19 3.91
1609 4103 1.288419 TGTACAGTTGACGCATGCCG 61.288 55.000 13.15 10.04 44.21 5.69
1612 4106 3.740832 TCTCTTTGTACAGTTGACGCATG 59.259 43.478 0.00 0.00 0.00 4.06
1613 4107 3.990092 TCTCTTTGTACAGTTGACGCAT 58.010 40.909 0.00 0.00 0.00 4.73
1614 4108 3.446310 TCTCTTTGTACAGTTGACGCA 57.554 42.857 0.00 0.00 0.00 5.24
1615 4109 3.123621 CCATCTCTTTGTACAGTTGACGC 59.876 47.826 0.00 0.00 0.00 5.19
1643 4151 6.038936 GGCAACAACGTGGTAAATAATATCCT 59.961 38.462 0.00 0.00 0.00 3.24
1644 4152 6.203647 GGCAACAACGTGGTAAATAATATCC 58.796 40.000 0.00 0.00 0.00 2.59
1747 4284 3.513912 TGATGGATTCGAGTTACACAGGT 59.486 43.478 0.00 0.00 0.00 4.00
1807 4348 2.800250 ACAAGCAGAGGAAAAGGGATG 58.200 47.619 0.00 0.00 0.00 3.51
1808 4349 3.160269 CAACAAGCAGAGGAAAAGGGAT 58.840 45.455 0.00 0.00 0.00 3.85
1810 4351 2.310538 ACAACAAGCAGAGGAAAAGGG 58.689 47.619 0.00 0.00 0.00 3.95
1813 4354 5.417580 ACAACTAACAACAAGCAGAGGAAAA 59.582 36.000 0.00 0.00 0.00 2.29
1828 4369 2.158928 ACGTGCAAGGGTACAACTAACA 60.159 45.455 4.26 0.00 0.00 2.41
1829 4370 2.222445 CACGTGCAAGGGTACAACTAAC 59.778 50.000 0.82 0.00 0.00 2.34
1832 4373 0.179468 ACACGTGCAAGGGTACAACT 59.821 50.000 17.22 0.00 0.00 3.16
1833 4374 1.018910 AACACGTGCAAGGGTACAAC 58.981 50.000 17.22 0.00 0.00 3.32
1857 4398 5.737860 TCATCACTACTGAGCACAATGAAT 58.262 37.500 0.00 0.00 0.00 2.57
1889 4431 5.187576 ACCCAACCACAATAATCCAGAATTG 59.812 40.000 0.00 0.00 38.71 2.32
1896 4438 3.094484 TCCACCCAACCACAATAATCC 57.906 47.619 0.00 0.00 0.00 3.01
1897 4439 4.466015 ACATTCCACCCAACCACAATAATC 59.534 41.667 0.00 0.00 0.00 1.75
1958 4512 4.283678 TCGCAAATTGTTGTTACCTTTCG 58.716 39.130 0.00 0.00 37.06 3.46
2090 4648 4.041075 ACCGTCTCTATCAGAGCTATCTCA 59.959 45.833 0.00 0.00 42.04 3.27
2091 4649 4.575885 ACCGTCTCTATCAGAGCTATCTC 58.424 47.826 0.00 0.00 42.04 2.75
2092 4650 4.634012 ACCGTCTCTATCAGAGCTATCT 57.366 45.455 0.00 0.00 42.04 1.98
2094 4652 5.482526 TCTCTACCGTCTCTATCAGAGCTAT 59.517 44.000 0.00 0.00 42.04 2.97
2113 4766 2.031870 CCACGGTGATGGTCATCTCTA 58.968 52.381 10.28 0.00 38.60 2.43
2114 4767 0.826715 CCACGGTGATGGTCATCTCT 59.173 55.000 10.28 0.00 38.60 3.10
2167 4820 0.251634 CTGCTCCCTCAGTCCCTTTC 59.748 60.000 0.00 0.00 0.00 2.62
2176 4829 0.681733 GTCTGTCAACTGCTCCCTCA 59.318 55.000 0.00 0.00 0.00 3.86
2204 4857 2.069273 ACGTCCTTTTCTGCAAGATCG 58.931 47.619 0.00 0.00 46.36 3.69
2240 4893 7.906160 TCGTAGACTCTTTTCTTGTTTTTGAG 58.094 34.615 0.00 0.00 0.00 3.02
2368 5030 5.993055 AGGGCCCAATTAAATGATTTTCAG 58.007 37.500 27.56 0.00 0.00 3.02
2375 5037 2.387757 GCTGAGGGCCCAATTAAATGA 58.612 47.619 27.56 0.00 34.27 2.57
2376 5038 2.896745 GCTGAGGGCCCAATTAAATG 57.103 50.000 27.56 5.87 34.27 2.32
2397 5066 7.935520 ACAGACATGTATGATGTACTCTGTAG 58.064 38.462 26.38 0.00 38.09 2.74
2404 5073 4.747108 GGCTGACAGACATGTATGATGTAC 59.253 45.833 26.38 11.14 40.68 2.90
2405 5074 4.405358 TGGCTGACAGACATGTATGATGTA 59.595 41.667 26.38 8.61 40.68 2.29
2406 5075 3.198417 TGGCTGACAGACATGTATGATGT 59.802 43.478 26.38 15.09 40.68 3.06
2407 5076 3.800531 TGGCTGACAGACATGTATGATG 58.199 45.455 26.38 15.39 40.68 3.07
2408 5077 4.639334 GATGGCTGACAGACATGTATGAT 58.361 43.478 28.66 10.95 45.82 2.45
2409 5078 3.491447 CGATGGCTGACAGACATGTATGA 60.491 47.826 28.66 4.59 45.82 2.15
2410 5079 2.798847 CGATGGCTGACAGACATGTATG 59.201 50.000 28.66 18.66 45.82 2.39
2411 5080 2.432146 ACGATGGCTGACAGACATGTAT 59.568 45.455 28.66 10.39 45.82 2.29
2412 5081 1.824852 ACGATGGCTGACAGACATGTA 59.175 47.619 28.66 0.00 45.82 2.29
2443 5112 4.163441 TGTGGTTCTGATTCCAACTTGA 57.837 40.909 4.15 0.00 35.38 3.02
2444 5113 4.580167 TCTTGTGGTTCTGATTCCAACTTG 59.420 41.667 4.15 0.00 35.38 3.16
2445 5114 4.580580 GTCTTGTGGTTCTGATTCCAACTT 59.419 41.667 4.15 0.00 35.38 2.66
2446 5115 4.137543 GTCTTGTGGTTCTGATTCCAACT 58.862 43.478 4.15 0.00 35.38 3.16
2447 5116 3.882888 TGTCTTGTGGTTCTGATTCCAAC 59.117 43.478 4.15 1.22 35.38 3.77
2448 5117 4.163441 TGTCTTGTGGTTCTGATTCCAA 57.837 40.909 4.15 0.00 35.38 3.53
2449 5118 3.855255 TGTCTTGTGGTTCTGATTCCA 57.145 42.857 0.00 0.00 0.00 3.53
2450 5119 4.326826 TCATGTCTTGTGGTTCTGATTCC 58.673 43.478 0.00 0.00 0.00 3.01
2451 5120 5.947228 TTCATGTCTTGTGGTTCTGATTC 57.053 39.130 0.00 0.00 0.00 2.52
2452 5121 5.593909 TGTTTCATGTCTTGTGGTTCTGATT 59.406 36.000 0.00 0.00 0.00 2.57
2453 5122 5.009010 GTGTTTCATGTCTTGTGGTTCTGAT 59.991 40.000 0.00 0.00 0.00 2.90
2454 5123 4.335315 GTGTTTCATGTCTTGTGGTTCTGA 59.665 41.667 0.00 0.00 0.00 3.27
2517 5186 1.069765 ATCGCTATTGGCTGGACGG 59.930 57.895 0.00 0.00 39.13 4.79
2518 5187 1.224069 CCATCGCTATTGGCTGGACG 61.224 60.000 0.00 0.00 38.19 4.79
2519 5188 0.106708 TCCATCGCTATTGGCTGGAC 59.893 55.000 0.00 0.00 39.41 4.02
2548 5219 4.677182 AGCTCCATTACCAATTTCCAGTT 58.323 39.130 0.00 0.00 0.00 3.16
2605 5276 2.439156 GCAGCCAGGGCCTAGTTG 60.439 66.667 5.28 8.94 43.17 3.16
2660 5331 9.271828 ACTTCAAAATTTGAGTTGTGAGTTTTT 57.728 25.926 8.51 0.00 41.38 1.94
2661 5332 8.831715 ACTTCAAAATTTGAGTTGTGAGTTTT 57.168 26.923 8.51 0.00 41.38 2.43
2662 5333 8.831715 AACTTCAAAATTTGAGTTGTGAGTTT 57.168 26.923 16.71 4.83 41.38 2.66
2663 5334 7.545615 GGAACTTCAAAATTTGAGTTGTGAGTT 59.454 33.333 20.05 18.34 41.38 3.01
2664 5335 7.035612 GGAACTTCAAAATTTGAGTTGTGAGT 58.964 34.615 20.05 12.80 41.38 3.41
2665 5336 6.197096 CGGAACTTCAAAATTTGAGTTGTGAG 59.803 38.462 20.05 12.31 41.38 3.51
2666 5337 6.033341 CGGAACTTCAAAATTTGAGTTGTGA 58.967 36.000 20.05 2.61 41.38 3.58
2667 5338 6.033341 TCGGAACTTCAAAATTTGAGTTGTG 58.967 36.000 20.05 14.49 41.38 3.33
2668 5339 6.094881 TCTCGGAACTTCAAAATTTGAGTTGT 59.905 34.615 20.05 13.32 41.38 3.32
2669 5340 6.494842 TCTCGGAACTTCAAAATTTGAGTTG 58.505 36.000 20.05 12.85 41.38 3.16
2670 5341 6.693315 TCTCGGAACTTCAAAATTTGAGTT 57.307 33.333 17.13 17.13 41.38 3.01
2671 5342 6.693315 TTCTCGGAACTTCAAAATTTGAGT 57.307 33.333 8.51 6.73 41.38 3.41
2672 5343 8.579682 AATTTCTCGGAACTTCAAAATTTGAG 57.420 30.769 8.51 6.16 41.38 3.02
2673 5344 8.413229 AGAATTTCTCGGAACTTCAAAATTTGA 58.587 29.630 4.03 4.03 38.04 2.69
2674 5345 8.482429 CAGAATTTCTCGGAACTTCAAAATTTG 58.518 33.333 14.49 0.00 0.00 2.32
2675 5346 8.413229 TCAGAATTTCTCGGAACTTCAAAATTT 58.587 29.630 14.49 0.00 0.00 1.82
2676 5347 7.940850 TCAGAATTTCTCGGAACTTCAAAATT 58.059 30.769 14.49 0.00 0.00 1.82
2677 5348 7.510549 TCAGAATTTCTCGGAACTTCAAAAT 57.489 32.000 14.49 0.00 0.00 1.82
2678 5349 6.935741 TCAGAATTTCTCGGAACTTCAAAA 57.064 33.333 14.49 0.00 0.00 2.44
2679 5350 6.935741 TTCAGAATTTCTCGGAACTTCAAA 57.064 33.333 14.49 8.58 33.87 2.69
2680 5351 6.935741 TTTCAGAATTTCTCGGAACTTCAA 57.064 33.333 14.49 4.01 37.88 2.69
2681 5352 6.935741 TTTTCAGAATTTCTCGGAACTTCA 57.064 33.333 14.49 0.00 37.88 3.02
2682 5353 9.331106 GTATTTTTCAGAATTTCTCGGAACTTC 57.669 33.333 0.00 7.95 37.88 3.01
2683 5354 8.846211 TGTATTTTTCAGAATTTCTCGGAACTT 58.154 29.630 0.00 0.00 37.88 2.66
2684 5355 8.290325 GTGTATTTTTCAGAATTTCTCGGAACT 58.710 33.333 0.00 0.00 37.88 3.01
2685 5356 8.073768 TGTGTATTTTTCAGAATTTCTCGGAAC 58.926 33.333 0.00 0.00 37.88 3.62
2686 5357 8.160521 TGTGTATTTTTCAGAATTTCTCGGAA 57.839 30.769 0.00 0.00 36.59 4.30
2687 5358 7.737972 TGTGTATTTTTCAGAATTTCTCGGA 57.262 32.000 0.00 0.00 0.00 4.55
2688 5359 8.023128 ACATGTGTATTTTTCAGAATTTCTCGG 58.977 33.333 0.00 0.00 0.00 4.63
2689 5360 8.955061 ACATGTGTATTTTTCAGAATTTCTCG 57.045 30.769 0.00 0.00 0.00 4.04
2696 5367 9.689976 CCAAATGTACATGTGTATTTTTCAGAA 57.310 29.630 21.90 0.00 32.54 3.02
2697 5368 8.303156 CCCAAATGTACATGTGTATTTTTCAGA 58.697 33.333 21.90 0.00 32.54 3.27
2698 5369 8.303156 TCCCAAATGTACATGTGTATTTTTCAG 58.697 33.333 21.90 5.88 32.54 3.02
2699 5370 8.183104 TCCCAAATGTACATGTGTATTTTTCA 57.817 30.769 21.90 0.00 32.54 2.69
2703 5374 8.859090 CCATATCCCAAATGTACATGTGTATTT 58.141 33.333 21.90 11.81 32.54 1.40
2704 5375 8.004215 ACCATATCCCAAATGTACATGTGTATT 58.996 33.333 21.90 10.14 32.54 1.89
2705 5376 7.526041 ACCATATCCCAAATGTACATGTGTAT 58.474 34.615 21.90 17.00 32.54 2.29
2706 5377 6.905736 ACCATATCCCAAATGTACATGTGTA 58.094 36.000 21.90 11.85 0.00 2.90
2707 5378 5.765510 ACCATATCCCAAATGTACATGTGT 58.234 37.500 21.90 8.69 0.00 3.72
2708 5379 6.064060 AGACCATATCCCAAATGTACATGTG 58.936 40.000 17.82 17.82 0.00 3.21
2709 5380 6.266131 AGACCATATCCCAAATGTACATGT 57.734 37.500 9.63 2.69 0.00 3.21
2710 5381 7.223584 TGTAGACCATATCCCAAATGTACATG 58.776 38.462 9.63 0.00 0.00 3.21
2711 5382 7.387265 TGTAGACCATATCCCAAATGTACAT 57.613 36.000 1.41 1.41 0.00 2.29
2712 5383 6.816616 TGTAGACCATATCCCAAATGTACA 57.183 37.500 0.00 0.00 0.00 2.90
2713 5384 7.226720 CACTTGTAGACCATATCCCAAATGTAC 59.773 40.741 0.00 0.00 0.00 2.90
2714 5385 7.092623 ACACTTGTAGACCATATCCCAAATGTA 60.093 37.037 0.00 0.00 31.25 2.29
2715 5386 6.122277 CACTTGTAGACCATATCCCAAATGT 58.878 40.000 0.00 0.00 0.00 2.71
2716 5387 6.038603 CACACTTGTAGACCATATCCCAAATG 59.961 42.308 0.00 0.00 0.00 2.32
2717 5388 6.069673 TCACACTTGTAGACCATATCCCAAAT 60.070 38.462 0.00 0.00 0.00 2.32
2718 5389 5.249622 TCACACTTGTAGACCATATCCCAAA 59.750 40.000 0.00 0.00 0.00 3.28
2719 5390 4.780554 TCACACTTGTAGACCATATCCCAA 59.219 41.667 0.00 0.00 0.00 4.12
2720 5391 4.358214 TCACACTTGTAGACCATATCCCA 58.642 43.478 0.00 0.00 0.00 4.37
2721 5392 5.353394 TTCACACTTGTAGACCATATCCC 57.647 43.478 0.00 0.00 0.00 3.85
2722 5393 6.879458 ACTTTTCACACTTGTAGACCATATCC 59.121 38.462 0.00 0.00 0.00 2.59
2723 5394 7.907214 ACTTTTCACACTTGTAGACCATATC 57.093 36.000 0.00 0.00 0.00 1.63
2724 5395 7.390718 GGAACTTTTCACACTTGTAGACCATAT 59.609 37.037 0.00 0.00 0.00 1.78
2725 5396 6.708949 GGAACTTTTCACACTTGTAGACCATA 59.291 38.462 0.00 0.00 0.00 2.74
2726 5397 5.531287 GGAACTTTTCACACTTGTAGACCAT 59.469 40.000 0.00 0.00 0.00 3.55
2727 5398 4.879545 GGAACTTTTCACACTTGTAGACCA 59.120 41.667 0.00 0.00 0.00 4.02
2728 5399 4.879545 TGGAACTTTTCACACTTGTAGACC 59.120 41.667 0.00 0.00 0.00 3.85
2729 5400 6.260050 TCATGGAACTTTTCACACTTGTAGAC 59.740 38.462 0.00 0.00 0.00 2.59
2730 5401 6.353323 TCATGGAACTTTTCACACTTGTAGA 58.647 36.000 0.00 0.00 0.00 2.59
2731 5402 6.618287 TCATGGAACTTTTCACACTTGTAG 57.382 37.500 0.00 0.00 0.00 2.74
2732 5403 6.545666 ACATCATGGAACTTTTCACACTTGTA 59.454 34.615 0.00 0.00 0.00 2.41
2733 5404 5.360714 ACATCATGGAACTTTTCACACTTGT 59.639 36.000 0.00 0.00 0.00 3.16
2734 5405 5.688621 CACATCATGGAACTTTTCACACTTG 59.311 40.000 0.00 0.00 0.00 3.16
2735 5406 5.835257 CACATCATGGAACTTTTCACACTT 58.165 37.500 0.00 0.00 0.00 3.16
2736 5407 5.443185 CACATCATGGAACTTTTCACACT 57.557 39.130 0.00 0.00 0.00 3.55


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

AutoCloner maintained by Alex Coulton.