Multiple sequence alignment - TraesCS1A01G385300

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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 TraesCS1A01G385300 chr1A 100.000 3764 0 0 1 3764 554527610 554523847 0.000000e+00 6951.0
1 TraesCS1A01G385300 chr1A 81.585 1211 204 14 1408 2605 554221882 554223086 0.000000e+00 983.0
2 TraesCS1A01G385300 chr1A 94.487 526 23 4 3245 3764 32863101 32862576 0.000000e+00 806.0
3 TraesCS1A01G385300 chr1A 94.872 507 21 3 3245 3746 462092859 462093365 0.000000e+00 787.0
4 TraesCS1A01G385300 chr1B 88.904 1424 130 8 1333 2729 637825416 637823994 0.000000e+00 1729.0
5 TraesCS1A01G385300 chr1B 90.025 1193 113 4 1568 2754 637820317 637819125 0.000000e+00 1539.0
6 TraesCS1A01G385300 chr1B 82.290 1214 198 8 1408 2606 637525035 637523824 0.000000e+00 1035.0
7 TraesCS1A01G385300 chr1B 81.758 1206 213 5 1408 2606 663611316 663610111 0.000000e+00 1002.0
8 TraesCS1A01G385300 chr1B 81.380 1203 212 10 1408 2605 637621906 637623101 0.000000e+00 970.0
9 TraesCS1A01G385300 chr1B 90.564 763 29 13 1 732 637826236 637825486 0.000000e+00 970.0
10 TraesCS1A01G385300 chr1B 89.262 298 23 4 2790 3086 637823970 637823681 7.680000e-97 364.0
11 TraesCS1A01G385300 chr1B 92.593 189 9 4 2906 3092 637819007 637818822 2.230000e-67 267.0
12 TraesCS1A01G385300 chr1D 92.066 1210 93 3 1520 2727 462730360 462729152 0.000000e+00 1700.0
13 TraesCS1A01G385300 chr1D 83.732 1838 204 40 1320 3092 462719017 462717210 0.000000e+00 1650.0
14 TraesCS1A01G385300 chr1D 89.224 928 38 17 1 879 462739599 462738685 0.000000e+00 1103.0
15 TraesCS1A01G385300 chr1D 81.229 1204 212 11 1408 2605 462487892 462489087 0.000000e+00 959.0
16 TraesCS1A01G385300 chr1D 84.542 731 107 4 1867 2594 462396184 462396911 0.000000e+00 719.0
17 TraesCS1A01G385300 chr1D 82.410 307 20 16 987 1260 462737212 462736907 1.750000e-58 237.0
18 TraesCS1A01G385300 chr1D 83.884 242 16 10 1306 1527 462736680 462736442 3.810000e-50 209.0
19 TraesCS1A01G385300 chr1D 90.000 110 10 1 3089 3197 9228657 9228766 1.410000e-29 141.0
20 TraesCS1A01G385300 chr1D 94.340 53 3 0 892 944 462737282 462737230 8.670000e-12 82.4
21 TraesCS1A01G385300 chr1D 97.059 34 1 0 3172 3205 462717213 462717180 1.460000e-04 58.4
22 TraesCS1A01G385300 chr7A 96.000 525 16 3 3245 3764 56505828 56506352 0.000000e+00 848.0
23 TraesCS1A01G385300 chr7A 86.765 136 12 6 3206 3339 56505735 56505866 3.030000e-31 147.0
24 TraesCS1A01G385300 chr7A 96.591 88 3 0 3089 3176 67676746 67676659 3.030000e-31 147.0
25 TraesCS1A01G385300 chr7A 85.816 141 13 7 3201 3339 684351037 684351172 3.920000e-30 143.0
26 TraesCS1A01G385300 chr7A 86.029 136 13 6 3206 3339 687163987 687163856 1.410000e-29 141.0
27 TraesCS1A01G385300 chr7A 86.029 136 13 6 3206 3339 687230613 687230482 1.410000e-29 141.0
28 TraesCS1A01G385300 chr2A 95.810 525 16 5 3245 3764 725584301 725584824 0.000000e+00 843.0
29 TraesCS1A01G385300 chr2A 95.611 524 16 5 3245 3764 658411355 658410835 0.000000e+00 833.0
30 TraesCS1A01G385300 chr2A 94.624 93 5 0 3088 3180 653372013 653371921 1.090000e-30 145.0
31 TraesCS1A01G385300 chr2A 85.816 141 14 6 3201 3339 658411453 658411317 1.090000e-30 145.0
32 TraesCS1A01G385300 chr3A 95.686 510 14 5 3245 3746 607287345 607286836 0.000000e+00 813.0
33 TraesCS1A01G385300 chr3A 87.591 137 11 6 3205 3339 745327152 745327284 1.810000e-33 154.0
34 TraesCS1A01G385300 chr6A 95.652 506 17 4 3246 3746 89091126 89090621 0.000000e+00 808.0
35 TraesCS1A01G385300 chr5A 95.276 508 17 5 3245 3746 7294480 7294986 0.000000e+00 798.0
36 TraesCS1A01G385300 chr5A 94.624 93 4 1 3081 3173 362170802 362170893 3.920000e-30 143.0
37 TraesCS1A01G385300 chr5A 86.885 122 9 7 3076 3192 706441057 706441176 3.050000e-26 130.0
38 TraesCS1A01G385300 chr4A 95.257 506 18 4 3247 3746 618651780 618652285 0.000000e+00 797.0
39 TraesCS1A01G385300 chr4A 85.417 144 13 8 3198 3339 519948585 519948722 3.920000e-30 143.0
40 TraesCS1A01G385300 chr4A 94.565 92 5 0 3089 3180 647219958 647219867 3.920000e-30 143.0
41 TraesCS1A01G385300 chr4A 86.029 136 13 6 3205 3338 158079210 158079079 1.410000e-29 141.0
42 TraesCS1A01G385300 chr5D 100.000 85 0 0 3089 3173 458893846 458893930 1.400000e-34 158.0
43 TraesCS1A01G385300 chr4B 94.565 92 5 0 3089 3180 592354518 592354427 3.920000e-30 143.0
44 TraesCS1A01G385300 chr3D 95.506 89 4 0 3088 3176 526827505 526827417 3.920000e-30 143.0
45 TraesCS1A01G385300 chr5B 94.565 92 4 1 3089 3180 432744706 432744616 1.410000e-29 141.0
46 TraesCS1A01G385300 chr7D 83.553 152 20 5 3189 3339 47296722 47296575 1.820000e-28 137.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1A01G385300 chr1A 554523847 554527610 3763 True 6951.00 6951 100.0000 1 3764 1 chr1A.!!$R2 3763
1 TraesCS1A01G385300 chr1A 554221882 554223086 1204 False 983.00 983 81.5850 1408 2605 1 chr1A.!!$F2 1197
2 TraesCS1A01G385300 chr1A 32862576 32863101 525 True 806.00 806 94.4870 3245 3764 1 chr1A.!!$R1 519
3 TraesCS1A01G385300 chr1A 462092859 462093365 506 False 787.00 787 94.8720 3245 3746 1 chr1A.!!$F1 501
4 TraesCS1A01G385300 chr1B 637523824 637525035 1211 True 1035.00 1035 82.2900 1408 2606 1 chr1B.!!$R1 1198
5 TraesCS1A01G385300 chr1B 663610111 663611316 1205 True 1002.00 1002 81.7580 1408 2606 1 chr1B.!!$R2 1198
6 TraesCS1A01G385300 chr1B 637818822 637826236 7414 True 973.80 1729 90.2696 1 3092 5 chr1B.!!$R3 3091
7 TraesCS1A01G385300 chr1B 637621906 637623101 1195 False 970.00 970 81.3800 1408 2605 1 chr1B.!!$F1 1197
8 TraesCS1A01G385300 chr1D 462729152 462730360 1208 True 1700.00 1700 92.0660 1520 2727 1 chr1D.!!$R1 1207
9 TraesCS1A01G385300 chr1D 462487892 462489087 1195 False 959.00 959 81.2290 1408 2605 1 chr1D.!!$F3 1197
10 TraesCS1A01G385300 chr1D 462717180 462719017 1837 True 854.20 1650 90.3955 1320 3205 2 chr1D.!!$R2 1885
11 TraesCS1A01G385300 chr1D 462396184 462396911 727 False 719.00 719 84.5420 1867 2594 1 chr1D.!!$F2 727
12 TraesCS1A01G385300 chr1D 462736442 462739599 3157 True 407.85 1103 87.4645 1 1527 4 chr1D.!!$R3 1526
13 TraesCS1A01G385300 chr7A 56505735 56506352 617 False 497.50 848 91.3825 3206 3764 2 chr7A.!!$F2 558
14 TraesCS1A01G385300 chr2A 725584301 725584824 523 False 843.00 843 95.8100 3245 3764 1 chr2A.!!$F1 519
15 TraesCS1A01G385300 chr2A 658410835 658411453 618 True 489.00 833 90.7135 3201 3764 2 chr2A.!!$R2 563
16 TraesCS1A01G385300 chr3A 607286836 607287345 509 True 813.00 813 95.6860 3245 3746 1 chr3A.!!$R1 501
17 TraesCS1A01G385300 chr6A 89090621 89091126 505 True 808.00 808 95.6520 3246 3746 1 chr6A.!!$R1 500
18 TraesCS1A01G385300 chr5A 7294480 7294986 506 False 798.00 798 95.2760 3245 3746 1 chr5A.!!$F1 501
19 TraesCS1A01G385300 chr4A 618651780 618652285 505 False 797.00 797 95.2570 3247 3746 1 chr4A.!!$F2 499

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
948 2396 0.446616 GGCGAAACCTCCAAATCGAC 59.553 55.0 0.0 0.0 37.48 4.20 F
1230 2713 0.100325 CAACTTGCTTGTTCGTGCCA 59.900 50.0 0.0 0.0 0.00 4.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2357 4075 0.836606 TCACAACCTGTTCCTCAGCA 59.163 50.0 0.0 0.0 42.38 4.41 R
3155 9766 0.115745 AGTACTCCCTCCGTCCCAAA 59.884 55.0 0.0 0.0 0.00 3.28 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
165 166 3.849911 TGTTTGGTGACATCGATCTCTC 58.150 45.455 0.00 0.00 42.32 3.20
167 168 1.403814 TGGTGACATCGATCTCTCCC 58.596 55.000 16.16 9.99 33.40 4.30
168 169 1.341976 TGGTGACATCGATCTCTCCCA 60.342 52.381 16.16 12.00 33.40 4.37
208 214 9.208022 CATATATAGCTGATTCTTTGTTTCCGA 57.792 33.333 0.00 0.00 0.00 4.55
300 311 3.523547 CTTGTGCTTGAGGATCTCTCTG 58.476 50.000 11.12 6.60 42.86 3.35
398 409 5.590818 AGTCCTCTTGTATCTTTGGTCCTA 58.409 41.667 0.00 0.00 0.00 2.94
399 410 6.206042 AGTCCTCTTGTATCTTTGGTCCTAT 58.794 40.000 0.00 0.00 0.00 2.57
401 412 8.013667 AGTCCTCTTGTATCTTTGGTCCTATAT 58.986 37.037 0.00 0.00 0.00 0.86
402 413 9.310449 GTCCTCTTGTATCTTTGGTCCTATATA 57.690 37.037 0.00 0.00 0.00 0.86
442 453 1.755179 AAGCTGGCACGCTCAAATAT 58.245 45.000 11.02 0.00 37.23 1.28
443 454 2.620251 AGCTGGCACGCTCAAATATA 57.380 45.000 5.75 0.00 33.48 0.86
470 491 2.448926 GCACCTTGCCGGTTTATTTT 57.551 45.000 1.90 0.00 46.37 1.82
522 543 3.959535 TTCCAATCAAAGGAATGTGCC 57.040 42.857 0.00 0.00 40.11 5.01
554 575 5.207768 CCTTTTGCACTATATTCGTGATGC 58.792 41.667 8.52 0.00 34.35 3.91
607 628 3.840666 TGCAGAGTTCTGGGATAGAGTTT 59.159 43.478 10.88 0.00 43.94 2.66
636 668 2.837498 TGTATGTAATGCATCGCAGCT 58.163 42.857 0.00 0.00 43.65 4.24
700 738 0.449388 GTGCCATTTCTTGAGCTCGG 59.551 55.000 9.64 4.66 0.00 4.63
732 770 0.459237 GGTCATCGACTCAGTGCCTG 60.459 60.000 0.00 0.00 32.47 4.85
783 841 4.759782 ACCAAGAGGAAATCTACGACATG 58.240 43.478 0.00 0.00 37.23 3.21
791 849 6.976088 AGGAAATCTACGACATGACTATCTG 58.024 40.000 0.00 0.00 0.00 2.90
801 859 5.047306 CGACATGACTATCTGCCCCTAATAA 60.047 44.000 0.00 0.00 0.00 1.40
848 906 1.041437 GGGCCTCTCGCTGTTATAGT 58.959 55.000 0.84 0.00 37.74 2.12
858 916 6.301486 TCTCGCTGTTATAGTCCCAGTAATA 58.699 40.000 0.00 0.00 0.00 0.98
860 918 6.978338 TCGCTGTTATAGTCCCAGTAATAAG 58.022 40.000 0.00 0.00 0.00 1.73
879 937 4.739046 AAGCAATCAACGAGAGACAAAG 57.261 40.909 0.00 0.00 0.00 2.77
881 939 3.743396 AGCAATCAACGAGAGACAAAGTC 59.257 43.478 0.00 0.00 0.00 3.01
883 941 4.212214 GCAATCAACGAGAGACAAAGTCTT 59.788 41.667 0.70 0.00 43.53 3.01
884 942 5.277538 GCAATCAACGAGAGACAAAGTCTTT 60.278 40.000 0.70 0.00 43.53 2.52
885 943 6.358762 CAATCAACGAGAGACAAAGTCTTTC 58.641 40.000 7.43 7.43 43.53 2.62
886 944 4.369182 TCAACGAGAGACAAAGTCTTTCC 58.631 43.478 10.83 0.00 43.53 3.13
889 947 4.120589 ACGAGAGACAAAGTCTTTCCAAC 58.879 43.478 10.83 0.00 43.53 3.77
890 948 3.495001 CGAGAGACAAAGTCTTTCCAACC 59.505 47.826 10.83 0.00 43.53 3.77
898 2346 5.163652 ACAAAGTCTTTCCAACCGAGAAAAG 60.164 40.000 0.00 0.00 33.06 2.27
904 2352 3.284793 TCCAACCGAGAAAAGGAACAA 57.715 42.857 0.00 0.00 0.00 2.83
909 2357 0.872388 CGAGAAAAGGAACAACCCGG 59.128 55.000 0.00 0.00 40.05 5.73
948 2396 0.446616 GGCGAAACCTCCAAATCGAC 59.553 55.000 0.00 0.00 37.48 4.20
949 2397 0.446616 GCGAAACCTCCAAATCGACC 59.553 55.000 0.00 0.00 37.48 4.79
950 2398 1.084289 CGAAACCTCCAAATCGACCC 58.916 55.000 0.00 0.00 37.48 4.46
951 2399 1.609580 CGAAACCTCCAAATCGACCCA 60.610 52.381 0.00 0.00 37.48 4.51
952 2400 2.723273 GAAACCTCCAAATCGACCCAT 58.277 47.619 0.00 0.00 0.00 4.00
954 2402 1.584724 ACCTCCAAATCGACCCATCT 58.415 50.000 0.00 0.00 0.00 2.90
955 2403 1.916181 ACCTCCAAATCGACCCATCTT 59.084 47.619 0.00 0.00 0.00 2.40
956 2404 3.112263 ACCTCCAAATCGACCCATCTTA 58.888 45.455 0.00 0.00 0.00 2.10
958 2406 3.467803 CTCCAAATCGACCCATCTTACC 58.532 50.000 0.00 0.00 0.00 2.85
959 2407 2.159014 TCCAAATCGACCCATCTTACCG 60.159 50.000 0.00 0.00 0.00 4.02
960 2408 2.159014 CCAAATCGACCCATCTTACCGA 60.159 50.000 0.00 0.00 0.00 4.69
961 2409 3.494398 CCAAATCGACCCATCTTACCGAT 60.494 47.826 0.00 0.00 41.06 4.18
962 2410 4.262292 CCAAATCGACCCATCTTACCGATA 60.262 45.833 0.00 0.00 38.78 2.92
963 2411 5.479306 CAAATCGACCCATCTTACCGATAT 58.521 41.667 0.00 0.00 38.78 1.63
964 2412 5.740290 AATCGACCCATCTTACCGATATT 57.260 39.130 0.00 0.00 38.78 1.28
965 2413 4.778534 TCGACCCATCTTACCGATATTC 57.221 45.455 0.00 0.00 0.00 1.75
966 2414 4.404640 TCGACCCATCTTACCGATATTCT 58.595 43.478 0.00 0.00 0.00 2.40
967 2415 4.458295 TCGACCCATCTTACCGATATTCTC 59.542 45.833 0.00 0.00 0.00 2.87
968 2416 4.380655 CGACCCATCTTACCGATATTCTCC 60.381 50.000 0.00 0.00 0.00 3.71
969 2417 4.753186 ACCCATCTTACCGATATTCTCCT 58.247 43.478 0.00 0.00 0.00 3.69
970 2418 5.900437 ACCCATCTTACCGATATTCTCCTA 58.100 41.667 0.00 0.00 0.00 2.94
971 2419 6.503944 ACCCATCTTACCGATATTCTCCTAT 58.496 40.000 0.00 0.00 0.00 2.57
972 2420 7.649715 ACCCATCTTACCGATATTCTCCTATA 58.350 38.462 0.00 0.00 0.00 1.31
973 2421 8.290277 ACCCATCTTACCGATATTCTCCTATAT 58.710 37.037 0.00 0.00 0.00 0.86
974 2422 9.809395 CCCATCTTACCGATATTCTCCTATATA 57.191 37.037 0.00 0.00 0.00 0.86
978 2426 9.298250 TCTTACCGATATTCTCCTATATATGCC 57.702 37.037 0.00 0.00 0.00 4.40
979 2427 6.576662 ACCGATATTCTCCTATATATGCCG 57.423 41.667 0.00 0.00 0.00 5.69
980 2428 6.304624 ACCGATATTCTCCTATATATGCCGA 58.695 40.000 0.00 0.00 0.00 5.54
981 2429 6.776116 ACCGATATTCTCCTATATATGCCGAA 59.224 38.462 0.00 0.00 0.00 4.30
982 2430 7.287005 ACCGATATTCTCCTATATATGCCGAAA 59.713 37.037 0.00 0.00 0.00 3.46
983 2431 8.141909 CCGATATTCTCCTATATATGCCGAAAA 58.858 37.037 0.00 0.00 0.00 2.29
984 2432 9.529325 CGATATTCTCCTATATATGCCGAAAAA 57.471 33.333 0.00 0.00 0.00 1.94
1004 2452 0.677098 TCCGTCTCTCCCACGAGAAG 60.677 60.000 0.00 0.00 44.62 2.85
1063 2511 2.190578 CCACCTCCGCCAATCCTC 59.809 66.667 0.00 0.00 0.00 3.71
1064 2512 2.190578 CACCTCCGCCAATCCTCC 59.809 66.667 0.00 0.00 0.00 4.30
1065 2513 2.041265 ACCTCCGCCAATCCTCCT 59.959 61.111 0.00 0.00 0.00 3.69
1068 2516 0.322975 CCTCCGCCAATCCTCCTATG 59.677 60.000 0.00 0.00 0.00 2.23
1096 2564 4.202212 GCTTATGAGTTCCTTCTCTCCTCC 60.202 50.000 0.00 0.00 35.68 4.30
1145 2616 3.008049 GGAGTGAGCTCTTGGTAAGGAAA 59.992 47.826 16.19 0.00 41.38 3.13
1151 2622 3.519913 AGCTCTTGGTAAGGAAACCCTAG 59.480 47.826 0.00 0.00 38.90 3.02
1152 2623 3.263681 GCTCTTGGTAAGGAAACCCTAGT 59.736 47.826 0.00 0.00 38.90 2.57
1155 2626 6.270219 TCTTGGTAAGGAAACCCTAGTTTT 57.730 37.500 0.00 0.00 46.25 2.43
1165 2636 6.110033 GGAAACCCTAGTTTTCTCAGATCTC 58.890 44.000 11.77 0.00 46.25 2.75
1179 2653 4.583871 TCAGATCTCTTCTTCCTTTTGCC 58.416 43.478 0.00 0.00 29.93 4.52
1180 2654 4.042062 TCAGATCTCTTCTTCCTTTTGCCA 59.958 41.667 0.00 0.00 29.93 4.92
1191 2665 1.535462 CCTTTTGCCATCGTCGTTTCT 59.465 47.619 0.00 0.00 0.00 2.52
1194 2668 3.701532 TTTGCCATCGTCGTTTCTTTT 57.298 38.095 0.00 0.00 0.00 2.27
1195 2669 2.679355 TGCCATCGTCGTTTCTTTTG 57.321 45.000 0.00 0.00 0.00 2.44
1196 2670 1.327507 GCCATCGTCGTTTCTTTTGC 58.672 50.000 0.00 0.00 0.00 3.68
1197 2671 1.963747 CCATCGTCGTTTCTTTTGCC 58.036 50.000 0.00 0.00 0.00 4.52
1198 2672 1.265635 CCATCGTCGTTTCTTTTGCCA 59.734 47.619 0.00 0.00 0.00 4.92
1199 2673 2.287308 CCATCGTCGTTTCTTTTGCCAA 60.287 45.455 0.00 0.00 0.00 4.52
1200 2674 2.748461 TCGTCGTTTCTTTTGCCAAG 57.252 45.000 0.00 0.00 0.00 3.61
1201 2675 1.332375 TCGTCGTTTCTTTTGCCAAGG 59.668 47.619 0.00 0.00 0.00 3.61
1203 2677 2.223386 CGTCGTTTCTTTTGCCAAGGAA 60.223 45.455 0.00 0.00 0.00 3.36
1204 2678 3.550030 CGTCGTTTCTTTTGCCAAGGAAT 60.550 43.478 0.00 0.00 28.74 3.01
1205 2679 4.368315 GTCGTTTCTTTTGCCAAGGAATT 58.632 39.130 0.00 0.00 28.74 2.17
1206 2680 4.808895 GTCGTTTCTTTTGCCAAGGAATTT 59.191 37.500 0.00 0.00 28.74 1.82
1228 2711 1.846175 GTTCAACTTGCTTGTTCGTGC 59.154 47.619 0.00 0.00 0.00 5.34
1230 2713 0.100325 CAACTTGCTTGTTCGTGCCA 59.900 50.000 0.00 0.00 0.00 4.92
1246 2729 8.297426 TGTTCGTGCCAAAACAATACAAATATA 58.703 29.630 0.00 0.00 32.69 0.86
1248 2731 7.817641 TCGTGCCAAAACAATACAAATATACA 58.182 30.769 0.00 0.00 0.00 2.29
1249 2732 7.751348 TCGTGCCAAAACAATACAAATATACAC 59.249 33.333 0.00 0.00 0.00 2.90
1280 2763 9.130661 TCTACTACTACTACTACTAGTGTCCAG 57.869 40.741 5.39 0.00 34.79 3.86
1291 2774 1.220749 GTGTCCAGGATGCGGCTTA 59.779 57.895 0.00 0.00 31.97 3.09
1292 2775 0.392461 GTGTCCAGGATGCGGCTTAA 60.392 55.000 0.00 0.00 31.97 1.85
1293 2776 0.546122 TGTCCAGGATGCGGCTTAAT 59.454 50.000 0.00 0.00 31.97 1.40
1296 2779 1.070758 TCCAGGATGCGGCTTAATCTC 59.929 52.381 0.00 0.00 31.97 2.75
1297 2780 1.202687 CCAGGATGCGGCTTAATCTCA 60.203 52.381 0.00 0.00 31.97 3.27
1298 2781 2.551721 CCAGGATGCGGCTTAATCTCAT 60.552 50.000 0.00 0.00 31.97 2.90
1299 2782 2.483106 CAGGATGCGGCTTAATCTCATG 59.517 50.000 0.00 0.00 0.00 3.07
1300 2783 2.369860 AGGATGCGGCTTAATCTCATGA 59.630 45.455 0.00 0.00 0.00 3.07
1301 2784 3.141398 GGATGCGGCTTAATCTCATGAA 58.859 45.455 0.00 0.00 0.00 2.57
1302 2785 3.565482 GGATGCGGCTTAATCTCATGAAA 59.435 43.478 0.00 0.00 0.00 2.69
1303 2786 4.531332 GATGCGGCTTAATCTCATGAAAC 58.469 43.478 0.00 0.00 0.00 2.78
1304 2787 3.342719 TGCGGCTTAATCTCATGAAACA 58.657 40.909 0.00 0.00 0.00 2.83
1309 2988 5.220739 CGGCTTAATCTCATGAAACAAGGAG 60.221 44.000 0.00 0.00 0.00 3.69
1312 2991 6.038050 GCTTAATCTCATGAAACAAGGAGGAG 59.962 42.308 0.00 0.00 0.00 3.69
1316 2995 1.815003 CATGAAACAAGGAGGAGTGCC 59.185 52.381 0.00 0.00 0.00 5.01
1317 2996 0.843309 TGAAACAAGGAGGAGTGCCA 59.157 50.000 0.00 0.00 36.29 4.92
1404 3089 2.441001 AGGAAGAGGGCCATTGTATCTG 59.559 50.000 6.18 0.00 0.00 2.90
1405 3090 2.173569 GGAAGAGGGCCATTGTATCTGT 59.826 50.000 6.18 0.00 0.00 3.41
1406 3091 3.372025 GGAAGAGGGCCATTGTATCTGTT 60.372 47.826 6.18 0.00 0.00 3.16
1426 3131 4.877823 TGTTTGATGACATGATACTGGAGC 59.122 41.667 0.00 0.00 0.00 4.70
1456 3161 0.740737 GCTCCCGGTCAAATCCATTG 59.259 55.000 0.00 0.00 40.58 2.82
1548 3253 0.179034 CCACCTCTAAGATGCTGCCC 60.179 60.000 0.00 0.00 0.00 5.36
1550 3255 1.070445 CCTCTAAGATGCTGCCCCG 59.930 63.158 0.00 0.00 0.00 5.73
1551 3256 1.596477 CTCTAAGATGCTGCCCCGC 60.596 63.158 0.00 0.00 0.00 6.13
1571 3276 1.227383 CCCCCAATCTACTGGTGCC 59.773 63.158 0.00 0.00 34.33 5.01
1611 3316 2.356553 TCCGTTGCAGTGTACGCC 60.357 61.111 12.56 0.00 36.49 5.68
1692 3409 1.234615 CCGTTGAAATGGTGACGCCT 61.235 55.000 6.60 0.00 38.35 5.52
1769 3486 2.046285 GCAATGCGGCTACAAGGGT 61.046 57.895 0.00 0.00 0.00 4.34
1902 3619 2.604373 CGATGAGAAGGAGACGATCAGC 60.604 54.545 0.00 0.00 0.00 4.26
1915 3632 0.372679 GATCAGCTGTGATGTGTGCG 59.627 55.000 14.67 0.00 43.92 5.34
1978 3695 3.773560 CCCTTCAAATGGTCCCAGTTTA 58.226 45.455 0.00 0.00 31.54 2.01
1995 3712 6.272318 CCAGTTTACAAATTCTGCAGTTCAA 58.728 36.000 14.67 0.48 0.00 2.69
2081 3798 5.033589 CCTTCACTTATCATCAGAAGGCT 57.966 43.478 6.58 0.00 46.00 4.58
2337 4054 5.315118 TGAATCATCGAATCGATTTGTCG 57.685 39.130 21.98 16.58 44.59 4.35
2349 4067 2.159572 CGATTTGTCGGGCAGGTAAAAG 60.160 50.000 0.00 0.00 0.00 2.27
2357 4075 2.560981 CGGGCAGGTAAAAGGTGAATTT 59.439 45.455 0.00 0.00 0.00 1.82
2364 4082 4.524328 AGGTAAAAGGTGAATTTGCTGAGG 59.476 41.667 0.00 0.00 0.00 3.86
2365 4083 4.522789 GGTAAAAGGTGAATTTGCTGAGGA 59.477 41.667 0.00 0.00 0.00 3.71
2514 4238 3.381908 TCGAGTTCTAGAGGGCATTCTTC 59.618 47.826 0.00 0.00 0.00 2.87
2610 4334 3.691118 TGCTCCAGTGCATAAAACTCATC 59.309 43.478 0.00 0.00 38.12 2.92
2621 4348 2.957402 AAACTCATCAAGACCTGGCA 57.043 45.000 0.00 0.00 0.00 4.92
2668 4395 3.225940 GGCTCCATGCTAAAAGGCTAAT 58.774 45.455 0.00 0.00 42.39 1.73
2676 4403 6.073548 CCATGCTAAAAGGCTAATAGACGAAG 60.074 42.308 9.88 0.00 0.00 3.79
2704 4431 7.640240 GTCACTGTTGTTGAAATCTTCTGTAAC 59.360 37.037 0.00 0.00 0.00 2.50
2722 4449 9.847224 TTCTGTAACTGAAGGACTTTAAGATTT 57.153 29.630 0.00 0.00 0.00 2.17
2729 4456 9.301897 ACTGAAGGACTTTAAGATTTTTGCTAT 57.698 29.630 0.00 0.00 0.00 2.97
2730 4457 9.565213 CTGAAGGACTTTAAGATTTTTGCTATG 57.435 33.333 0.00 0.00 0.00 2.23
2792 9391 5.086727 GCGCAACCTTTAAGTATGAAGAAC 58.913 41.667 0.30 0.00 0.00 3.01
2808 9416 4.813697 TGAAGAACATGTTTGATGTCGTCA 59.186 37.500 13.36 9.73 34.25 4.35
2840 9448 4.810191 TTTTTGTGGTTTGGCTTGTAGT 57.190 36.364 0.00 0.00 0.00 2.73
2841 9449 5.916661 TTTTTGTGGTTTGGCTTGTAGTA 57.083 34.783 0.00 0.00 0.00 1.82
2842 9450 4.904253 TTTGTGGTTTGGCTTGTAGTAC 57.096 40.909 0.00 0.00 0.00 2.73
2846 9454 4.345837 TGTGGTTTGGCTTGTAGTACTAGT 59.654 41.667 1.87 0.00 0.00 2.57
2893 9501 5.750650 GAGTAGTCGAGCACTAAGGATAAC 58.249 45.833 0.00 0.00 39.44 1.89
2904 9514 7.952671 AGCACTAAGGATAACGAAGATATGAA 58.047 34.615 0.00 0.00 0.00 2.57
2914 9524 9.784824 GATAACGAAGATATGAATTTCTTGACG 57.215 33.333 1.38 3.07 32.46 4.35
2925 9535 7.722795 TGAATTTCTTGACGTTCTTGTGATA 57.277 32.000 0.00 0.00 0.00 2.15
2926 9536 8.322906 TGAATTTCTTGACGTTCTTGTGATAT 57.677 30.769 0.00 0.00 0.00 1.63
2930 9540 5.705902 TCTTGACGTTCTTGTGATATCGAA 58.294 37.500 0.00 0.00 0.00 3.71
2993 9604 8.746922 ACAGTTAATTGTGCATTGTTATGAAG 57.253 30.769 2.38 0.00 33.37 3.02
3037 9648 3.008157 TCCAAGCAAGTTACCCGACATAA 59.992 43.478 0.00 0.00 0.00 1.90
3086 9697 6.927933 TCGATGTACGATATGCATAAACAG 57.072 37.500 11.13 5.16 46.45 3.16
3088 9699 7.312899 TCGATGTACGATATGCATAAACAGAT 58.687 34.615 11.13 0.85 46.45 2.90
3089 9700 8.455682 TCGATGTACGATATGCATAAACAGATA 58.544 33.333 11.13 0.00 46.45 1.98
3090 9701 8.524267 CGATGTACGATATGCATAAACAGATAC 58.476 37.037 11.13 8.34 45.77 2.24
3091 9702 9.574458 GATGTACGATATGCATAAACAGATACT 57.426 33.333 11.13 0.00 33.14 2.12
3093 9704 9.836076 TGTACGATATGCATAAACAGATACTAC 57.164 33.333 11.13 1.96 0.00 2.73
3094 9705 9.286946 GTACGATATGCATAAACAGATACTACC 57.713 37.037 11.13 0.00 0.00 3.18
3095 9706 8.123639 ACGATATGCATAAACAGATACTACCT 57.876 34.615 11.13 0.00 0.00 3.08
3096 9707 8.244802 ACGATATGCATAAACAGATACTACCTC 58.755 37.037 11.13 0.00 0.00 3.85
3097 9708 8.462811 CGATATGCATAAACAGATACTACCTCT 58.537 37.037 11.13 0.00 0.00 3.69
3098 9709 9.579768 GATATGCATAAACAGATACTACCTCTG 57.420 37.037 11.13 0.00 44.60 3.35
3106 9717 5.677319 CAGATACTACCTCTGTCCCAAAA 57.323 43.478 0.00 0.00 36.26 2.44
3107 9718 6.240549 CAGATACTACCTCTGTCCCAAAAT 57.759 41.667 0.00 0.00 36.26 1.82
3108 9719 7.361457 CAGATACTACCTCTGTCCCAAAATA 57.639 40.000 0.00 0.00 36.26 1.40
3109 9720 7.967908 CAGATACTACCTCTGTCCCAAAATAT 58.032 38.462 0.00 0.00 36.26 1.28
3110 9721 9.090103 CAGATACTACCTCTGTCCCAAAATATA 57.910 37.037 0.00 0.00 36.26 0.86
3111 9722 9.670442 AGATACTACCTCTGTCCCAAAATATAA 57.330 33.333 0.00 0.00 0.00 0.98
3112 9723 9.930693 GATACTACCTCTGTCCCAAAATATAAG 57.069 37.037 0.00 0.00 0.00 1.73
3113 9724 7.989947 ACTACCTCTGTCCCAAAATATAAGA 57.010 36.000 0.00 0.00 0.00 2.10
3114 9725 8.388656 ACTACCTCTGTCCCAAAATATAAGAA 57.611 34.615 0.00 0.00 0.00 2.52
3115 9726 8.265764 ACTACCTCTGTCCCAAAATATAAGAAC 58.734 37.037 0.00 0.00 0.00 3.01
3116 9727 6.113411 ACCTCTGTCCCAAAATATAAGAACG 58.887 40.000 0.00 0.00 0.00 3.95
3117 9728 6.113411 CCTCTGTCCCAAAATATAAGAACGT 58.887 40.000 0.00 0.00 0.00 3.99
3118 9729 6.598064 CCTCTGTCCCAAAATATAAGAACGTT 59.402 38.462 0.00 0.00 0.00 3.99
3119 9730 7.120726 CCTCTGTCCCAAAATATAAGAACGTTT 59.879 37.037 0.46 0.00 0.00 3.60
3120 9731 8.398878 TCTGTCCCAAAATATAAGAACGTTTT 57.601 30.769 0.46 0.00 0.00 2.43
3121 9732 8.852135 TCTGTCCCAAAATATAAGAACGTTTTT 58.148 29.630 9.22 9.22 0.00 1.94
3122 9733 8.804688 TGTCCCAAAATATAAGAACGTTTTTG 57.195 30.769 13.87 12.16 37.14 2.44
3123 9734 8.630917 TGTCCCAAAATATAAGAACGTTTTTGA 58.369 29.630 13.87 2.81 38.79 2.69
3124 9735 9.634163 GTCCCAAAATATAAGAACGTTTTTGAT 57.366 29.630 13.87 4.93 38.79 2.57
3135 9746 8.773404 AAGAACGTTTTTGATACTATGCTAGT 57.227 30.769 0.46 2.19 42.68 2.57
3136 9747 8.186178 AGAACGTTTTTGATACTATGCTAGTG 57.814 34.615 0.46 0.00 39.81 2.74
3137 9748 7.817962 AGAACGTTTTTGATACTATGCTAGTGT 59.182 33.333 0.46 0.61 39.81 3.55
3138 9749 8.991243 AACGTTTTTGATACTATGCTAGTGTA 57.009 30.769 0.00 0.00 39.81 2.90
3139 9750 8.991243 ACGTTTTTGATACTATGCTAGTGTAA 57.009 30.769 6.21 0.00 39.81 2.41
3140 9751 9.426837 ACGTTTTTGATACTATGCTAGTGTAAA 57.573 29.630 6.21 0.00 39.81 2.01
3164 9775 5.806366 AACGTTCTTATATTTTGGGACGG 57.194 39.130 0.00 0.00 0.00 4.79
3165 9776 5.088680 ACGTTCTTATATTTTGGGACGGA 57.911 39.130 0.00 0.00 0.00 4.69
3166 9777 5.114081 ACGTTCTTATATTTTGGGACGGAG 58.886 41.667 0.00 0.00 0.00 4.63
3167 9778 4.510340 CGTTCTTATATTTTGGGACGGAGG 59.490 45.833 0.00 0.00 0.00 4.30
3168 9779 4.699925 TCTTATATTTTGGGACGGAGGG 57.300 45.455 0.00 0.00 0.00 4.30
3169 9780 4.300345 TCTTATATTTTGGGACGGAGGGA 58.700 43.478 0.00 0.00 0.00 4.20
3170 9781 4.347000 TCTTATATTTTGGGACGGAGGGAG 59.653 45.833 0.00 0.00 0.00 4.30
3176 9787 0.324091 TGGGACGGAGGGAGTACTTC 60.324 60.000 0.00 0.00 0.00 3.01
3213 9824 4.325028 TTTTCCTGTCACGCACTAGTAA 57.675 40.909 0.00 0.00 0.00 2.24
3261 9926 1.381463 GCCCCTTTAGTCCCGGTTT 59.619 57.895 0.00 0.00 0.00 3.27
3339 10008 4.322953 GGTAACATCAACCGGGACTAAAGA 60.323 45.833 6.32 0.00 0.00 2.52
3421 10094 1.351017 AGTGTGTAATCACCACCCCTG 59.649 52.381 0.00 0.00 43.26 4.45
3477 10150 8.910944 CCTCATCATTCCAAATCATCTAACTTT 58.089 33.333 0.00 0.00 0.00 2.66
3497 10170 1.295423 CGAACGGTCACCCATCCTT 59.705 57.895 0.00 0.00 0.00 3.36
3501 10174 0.914417 ACGGTCACCCATCCTTCCAT 60.914 55.000 0.00 0.00 0.00 3.41
3511 10184 0.628668 ATCCTTCCATTCCCCCAGCT 60.629 55.000 0.00 0.00 0.00 4.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
243 249 0.250467 ACATGACACACCTCACAGCC 60.250 55.000 0.00 0.00 0.00 4.85
300 311 1.066071 GCAGAAAGGTGTCCCCTAGAC 60.066 57.143 0.00 0.00 45.47 2.59
398 409 8.896320 TTGGCGTCAAATTGTGTACTATATAT 57.104 30.769 0.00 0.00 0.00 0.86
399 410 8.719560 TTTGGCGTCAAATTGTGTACTATATA 57.280 30.769 11.91 0.00 37.89 0.86
401 412 6.402766 GCTTTGGCGTCAAATTGTGTACTATA 60.403 38.462 16.67 0.00 41.45 1.31
402 413 5.619086 GCTTTGGCGTCAAATTGTGTACTAT 60.619 40.000 16.67 0.00 41.45 2.12
403 414 4.319911 GCTTTGGCGTCAAATTGTGTACTA 60.320 41.667 16.67 0.00 41.45 1.82
404 415 3.550030 GCTTTGGCGTCAAATTGTGTACT 60.550 43.478 16.67 0.00 41.45 2.73
405 416 2.724174 GCTTTGGCGTCAAATTGTGTAC 59.276 45.455 16.67 0.00 41.45 2.90
406 417 2.621055 AGCTTTGGCGTCAAATTGTGTA 59.379 40.909 16.67 0.00 41.45 2.90
407 418 1.408702 AGCTTTGGCGTCAAATTGTGT 59.591 42.857 16.67 0.00 41.45 3.72
408 419 1.788308 CAGCTTTGGCGTCAAATTGTG 59.212 47.619 16.67 9.76 41.45 3.33
409 420 1.269726 CCAGCTTTGGCGTCAAATTGT 60.270 47.619 16.67 0.40 41.45 2.71
410 421 1.421382 CCAGCTTTGGCGTCAAATTG 58.579 50.000 16.67 16.29 41.45 2.32
411 422 0.319813 GCCAGCTTTGGCGTCAAATT 60.320 50.000 16.67 4.70 45.79 1.82
442 453 2.047274 GCAAGGTGCCAGAGCGTA 60.047 61.111 0.00 0.00 44.31 4.42
470 491 2.682856 GGTTCTGACTTGTTGCTTGACA 59.317 45.455 0.00 0.00 0.00 3.58
521 542 2.681421 GCAAAAGGGGCCCTCTGG 60.681 66.667 28.97 11.87 30.89 3.86
522 543 2.118076 TGCAAAAGGGGCCCTCTG 59.882 61.111 28.97 25.93 30.89 3.35
554 575 8.537049 TGAAGCATTTATTCCATTTTGTCAAG 57.463 30.769 0.00 0.00 0.00 3.02
607 628 6.915300 GCGATGCATTACATACAAATTTGGTA 59.085 34.615 21.74 11.53 39.84 3.25
700 738 0.107945 GATGACCAGCACCCTGAGAC 60.108 60.000 0.00 0.00 41.77 3.36
732 770 5.294552 GTGAGAGTTTATTATGTGGGTGCTC 59.705 44.000 0.00 0.00 0.00 4.26
743 801 6.751157 TCTTGGTTCACGTGAGAGTTTATTA 58.249 36.000 19.11 0.00 0.00 0.98
783 841 4.141914 CGGGATTATTAGGGGCAGATAGTC 60.142 50.000 0.00 0.00 0.00 2.59
791 849 1.418637 TCACACGGGATTATTAGGGGC 59.581 52.381 0.00 0.00 0.00 5.80
801 859 0.914417 ACCCCAAGATCACACGGGAT 60.914 55.000 12.61 0.00 41.62 3.85
848 906 5.092554 TCGTTGATTGCTTATTACTGGGA 57.907 39.130 0.00 0.00 0.00 4.37
858 916 4.130118 ACTTTGTCTCTCGTTGATTGCTT 58.870 39.130 0.00 0.00 0.00 3.91
860 918 3.743396 AGACTTTGTCTCTCGTTGATTGC 59.257 43.478 0.00 0.00 38.71 3.56
879 937 3.473625 TCCTTTTCTCGGTTGGAAAGAC 58.526 45.455 6.41 0.00 34.73 3.01
881 939 3.630312 TGTTCCTTTTCTCGGTTGGAAAG 59.370 43.478 0.00 0.00 38.35 2.62
883 941 3.284793 TGTTCCTTTTCTCGGTTGGAA 57.715 42.857 0.00 0.00 34.81 3.53
884 942 2.946990 GTTGTTCCTTTTCTCGGTTGGA 59.053 45.455 0.00 0.00 0.00 3.53
885 943 2.034179 GGTTGTTCCTTTTCTCGGTTGG 59.966 50.000 0.00 0.00 0.00 3.77
886 944 2.034179 GGGTTGTTCCTTTTCTCGGTTG 59.966 50.000 0.00 0.00 36.25 3.77
889 947 0.872388 CGGGTTGTTCCTTTTCTCGG 59.128 55.000 0.00 0.00 36.25 4.63
890 948 0.872388 CCGGGTTGTTCCTTTTCTCG 59.128 55.000 0.00 0.00 36.25 4.04
909 2357 0.108041 TTACCAGCGGAAACCGATCC 60.108 55.000 14.43 0.00 44.45 3.36
944 2392 4.404640 AGAATATCGGTAAGATGGGTCGA 58.595 43.478 0.00 0.00 40.40 4.20
945 2393 4.380655 GGAGAATATCGGTAAGATGGGTCG 60.381 50.000 0.00 0.00 40.40 4.79
946 2394 4.773149 AGGAGAATATCGGTAAGATGGGTC 59.227 45.833 0.00 0.00 40.40 4.46
948 2396 8.713708 ATATAGGAGAATATCGGTAAGATGGG 57.286 38.462 0.00 0.00 40.40 4.00
952 2400 9.298250 GGCATATATAGGAGAATATCGGTAAGA 57.702 37.037 0.00 0.00 0.00 2.10
954 2402 7.940688 TCGGCATATATAGGAGAATATCGGTAA 59.059 37.037 0.00 0.00 0.00 2.85
955 2403 7.455891 TCGGCATATATAGGAGAATATCGGTA 58.544 38.462 0.00 0.00 0.00 4.02
956 2404 6.304624 TCGGCATATATAGGAGAATATCGGT 58.695 40.000 0.00 0.00 0.00 4.69
958 2406 9.529325 TTTTTCGGCATATATAGGAGAATATCG 57.471 33.333 0.00 0.00 0.00 2.92
961 2409 9.832445 GGATTTTTCGGCATATATAGGAGAATA 57.168 33.333 0.00 0.00 0.00 1.75
962 2410 7.495934 CGGATTTTTCGGCATATATAGGAGAAT 59.504 37.037 0.00 0.00 0.00 2.40
963 2411 6.816640 CGGATTTTTCGGCATATATAGGAGAA 59.183 38.462 0.00 0.61 0.00 2.87
964 2412 6.070995 ACGGATTTTTCGGCATATATAGGAGA 60.071 38.462 0.00 0.00 0.00 3.71
965 2413 6.106673 ACGGATTTTTCGGCATATATAGGAG 58.893 40.000 0.00 0.00 0.00 3.69
966 2414 6.045072 ACGGATTTTTCGGCATATATAGGA 57.955 37.500 0.00 0.00 0.00 2.94
967 2415 6.106673 AGACGGATTTTTCGGCATATATAGG 58.893 40.000 0.00 0.00 38.26 2.57
968 2416 7.036220 AGAGACGGATTTTTCGGCATATATAG 58.964 38.462 0.00 0.00 38.26 1.31
969 2417 6.931838 AGAGACGGATTTTTCGGCATATATA 58.068 36.000 0.00 0.00 38.26 0.86
970 2418 5.794894 AGAGACGGATTTTTCGGCATATAT 58.205 37.500 0.00 0.00 38.26 0.86
971 2419 5.209818 AGAGACGGATTTTTCGGCATATA 57.790 39.130 0.00 0.00 38.26 0.86
972 2420 4.058817 GAGAGACGGATTTTTCGGCATAT 58.941 43.478 0.00 0.00 38.26 1.78
973 2421 3.454375 GAGAGACGGATTTTTCGGCATA 58.546 45.455 0.00 0.00 38.26 3.14
974 2422 2.280628 GAGAGACGGATTTTTCGGCAT 58.719 47.619 0.00 0.00 38.26 4.40
975 2423 1.674817 GGAGAGACGGATTTTTCGGCA 60.675 52.381 0.00 0.00 38.26 5.69
976 2424 1.007580 GGAGAGACGGATTTTTCGGC 58.992 55.000 0.00 0.00 35.58 5.54
977 2425 1.066430 TGGGAGAGACGGATTTTTCGG 60.066 52.381 0.00 0.00 0.00 4.30
978 2426 2.000447 GTGGGAGAGACGGATTTTTCG 59.000 52.381 0.00 0.00 0.00 3.46
979 2427 2.000447 CGTGGGAGAGACGGATTTTTC 59.000 52.381 0.00 0.00 33.08 2.29
980 2428 1.621814 TCGTGGGAGAGACGGATTTTT 59.378 47.619 0.00 0.00 37.43 1.94
981 2429 1.204941 CTCGTGGGAGAGACGGATTTT 59.795 52.381 0.00 0.00 43.27 1.82
982 2430 0.818296 CTCGTGGGAGAGACGGATTT 59.182 55.000 0.00 0.00 43.27 2.17
983 2431 0.034380 TCTCGTGGGAGAGACGGATT 60.034 55.000 0.00 0.00 44.28 3.01
984 2432 1.608154 TCTCGTGGGAGAGACGGAT 59.392 57.895 0.00 0.00 44.28 4.18
985 2433 3.075186 TCTCGTGGGAGAGACGGA 58.925 61.111 0.00 0.00 44.28 4.69
1004 2452 1.268234 CGCCCAAAGAAAGATGCGATC 60.268 52.381 0.00 0.00 44.32 3.69
1063 2511 4.530161 AGGAACTCATAAGCTAGGCATAGG 59.470 45.833 7.62 0.00 0.00 2.57
1064 2512 5.736951 AGGAACTCATAAGCTAGGCATAG 57.263 43.478 0.00 0.00 0.00 2.23
1065 2513 5.841237 AGAAGGAACTCATAAGCTAGGCATA 59.159 40.000 0.00 0.00 38.49 3.14
1068 2516 4.343814 AGAGAAGGAACTCATAAGCTAGGC 59.656 45.833 0.00 0.00 38.49 3.93
1096 2564 1.572085 GCGAATCCATCCATCCGCTG 61.572 60.000 0.00 0.00 39.57 5.18
1145 2616 6.260663 AGAAGAGATCTGAGAAAACTAGGGT 58.739 40.000 0.00 0.00 36.88 4.34
1151 2622 7.977789 AAAGGAAGAAGAGATCTGAGAAAAC 57.022 36.000 0.00 0.00 38.79 2.43
1152 2623 7.040823 GCAAAAGGAAGAAGAGATCTGAGAAAA 60.041 37.037 0.00 0.00 38.79 2.29
1155 2626 5.486526 GCAAAAGGAAGAAGAGATCTGAGA 58.513 41.667 0.00 0.00 38.79 3.27
1165 2636 2.159653 CGACGATGGCAAAAGGAAGAAG 60.160 50.000 0.00 0.00 0.00 2.85
1179 2653 2.679355 TGGCAAAAGAAACGACGATG 57.321 45.000 0.00 0.00 0.00 3.84
1180 2654 2.031157 CCTTGGCAAAAGAAACGACGAT 60.031 45.455 0.00 0.00 0.00 3.73
1197 2671 4.696455 AGCAAGTTGAACCAAATTCCTTG 58.304 39.130 7.16 0.00 38.57 3.61
1198 2672 5.118286 CAAGCAAGTTGAACCAAATTCCTT 58.882 37.500 7.16 0.00 38.60 3.36
1199 2673 4.162131 ACAAGCAAGTTGAACCAAATTCCT 59.838 37.500 7.16 0.00 38.60 3.36
1200 2674 4.441792 ACAAGCAAGTTGAACCAAATTCC 58.558 39.130 7.16 0.00 38.60 3.01
1201 2675 5.276348 CGAACAAGCAAGTTGAACCAAATTC 60.276 40.000 7.16 0.08 38.60 2.17
1203 2677 4.111916 CGAACAAGCAAGTTGAACCAAAT 58.888 39.130 7.16 0.00 38.60 2.32
1204 2678 3.057174 ACGAACAAGCAAGTTGAACCAAA 60.057 39.130 7.16 0.00 38.60 3.28
1205 2679 2.490115 ACGAACAAGCAAGTTGAACCAA 59.510 40.909 7.16 0.00 38.60 3.67
1206 2680 2.088423 ACGAACAAGCAAGTTGAACCA 58.912 42.857 7.16 0.00 38.60 3.67
1210 2693 0.380378 GGCACGAACAAGCAAGTTGA 59.620 50.000 7.16 0.00 38.60 3.18
1255 2738 8.359642 CCTGGACACTAGTAGTAGTAGTAGTAG 58.640 44.444 20.10 19.25 41.62 2.57
1256 2739 8.061920 TCCTGGACACTAGTAGTAGTAGTAGTA 58.938 40.741 20.10 8.14 41.62 1.82
1257 2740 6.900186 TCCTGGACACTAGTAGTAGTAGTAGT 59.100 42.308 15.79 16.38 43.52 2.73
1258 2741 7.358770 TCCTGGACACTAGTAGTAGTAGTAG 57.641 44.000 15.79 15.27 37.40 2.57
1259 2742 7.688820 GCATCCTGGACACTAGTAGTAGTAGTA 60.689 44.444 15.79 2.11 37.40 1.82
1260 2743 6.593807 CATCCTGGACACTAGTAGTAGTAGT 58.406 44.000 9.94 11.28 37.40 2.73
1261 2744 5.470777 GCATCCTGGACACTAGTAGTAGTAG 59.529 48.000 9.94 10.04 37.40 2.57
1262 2745 5.374921 GCATCCTGGACACTAGTAGTAGTA 58.625 45.833 9.94 0.00 37.40 1.82
1263 2746 4.208746 GCATCCTGGACACTAGTAGTAGT 58.791 47.826 1.57 4.29 40.38 2.73
1264 2747 3.251245 CGCATCCTGGACACTAGTAGTAG 59.749 52.174 1.57 2.87 0.00 2.57
1265 2748 3.211865 CGCATCCTGGACACTAGTAGTA 58.788 50.000 1.57 0.00 0.00 1.82
1266 2749 2.025155 CGCATCCTGGACACTAGTAGT 58.975 52.381 0.00 0.00 0.00 2.73
1267 2750 1.338337 CCGCATCCTGGACACTAGTAG 59.662 57.143 0.00 0.00 0.00 2.57
1268 2751 1.399714 CCGCATCCTGGACACTAGTA 58.600 55.000 0.00 0.00 0.00 1.82
1269 2752 1.961180 GCCGCATCCTGGACACTAGT 61.961 60.000 0.00 0.00 0.00 2.57
1270 2753 1.227380 GCCGCATCCTGGACACTAG 60.227 63.158 0.00 0.00 0.00 2.57
1273 2756 0.392461 TTAAGCCGCATCCTGGACAC 60.392 55.000 0.00 0.00 0.00 3.67
1280 2763 2.771089 TCATGAGATTAAGCCGCATCC 58.229 47.619 0.00 0.00 0.00 3.51
1291 2774 5.251764 CACTCCTCCTTGTTTCATGAGATT 58.748 41.667 0.00 0.00 0.00 2.40
1292 2775 4.841422 CACTCCTCCTTGTTTCATGAGAT 58.159 43.478 0.00 0.00 0.00 2.75
1293 2776 3.557898 GCACTCCTCCTTGTTTCATGAGA 60.558 47.826 0.00 0.00 0.00 3.27
1296 2779 1.815003 GGCACTCCTCCTTGTTTCATG 59.185 52.381 0.00 0.00 0.00 3.07
1297 2780 1.425066 TGGCACTCCTCCTTGTTTCAT 59.575 47.619 0.00 0.00 0.00 2.57
1298 2781 0.843309 TGGCACTCCTCCTTGTTTCA 59.157 50.000 0.00 0.00 0.00 2.69
1299 2782 1.202818 AGTGGCACTCCTCCTTGTTTC 60.203 52.381 15.88 0.00 0.00 2.78
1300 2783 0.846693 AGTGGCACTCCTCCTTGTTT 59.153 50.000 15.88 0.00 0.00 2.83
1301 2784 0.109342 CAGTGGCACTCCTCCTTGTT 59.891 55.000 19.13 0.00 0.00 2.83
1302 2785 1.757306 CAGTGGCACTCCTCCTTGT 59.243 57.895 19.13 0.00 0.00 3.16
1303 2786 1.673665 GCAGTGGCACTCCTCCTTG 60.674 63.158 19.13 6.81 40.72 3.61
1304 2787 2.753029 GCAGTGGCACTCCTCCTT 59.247 61.111 19.13 0.00 40.72 3.36
1309 2988 3.446570 GCATGGCAGTGGCACTCC 61.447 66.667 23.12 20.84 41.84 3.85
1316 2995 3.214123 CGGGATGGCATGGCAGTG 61.214 66.667 27.02 12.51 0.00 3.66
1339 3018 3.127533 CCTTCTTCTTGGCGGCCG 61.128 66.667 24.05 24.05 0.00 6.13
1344 3023 3.804193 CGCCGCCTTCTTCTTGGC 61.804 66.667 0.00 0.00 45.25 4.52
1373 3058 1.948144 GCCCTCTTCCTCTTGTTGCTC 60.948 57.143 0.00 0.00 0.00 4.26
1404 3089 5.121811 AGCTCCAGTATCATGTCATCAAAC 58.878 41.667 0.00 0.00 0.00 2.93
1405 3090 5.363562 AGCTCCAGTATCATGTCATCAAA 57.636 39.130 0.00 0.00 0.00 2.69
1406 3091 5.129980 AGAAGCTCCAGTATCATGTCATCAA 59.870 40.000 0.00 0.00 0.00 2.57
1426 3131 3.121019 CGGGAGCCGGAGTAGAAG 58.879 66.667 5.05 0.00 44.15 2.85
1498 3203 1.760192 CTGCAGAAATCCTTGGAGGG 58.240 55.000 8.42 0.00 35.59 4.30
1548 3253 3.861797 AGTAGATTGGGGGCGCGG 61.862 66.667 8.83 0.00 0.00 6.46
1550 3255 2.203209 CCAGTAGATTGGGGGCGC 60.203 66.667 0.00 0.00 34.46 6.53
1551 3256 1.153168 CACCAGTAGATTGGGGGCG 60.153 63.158 0.00 0.00 42.76 6.13
1611 3316 2.125350 GGGCTTGACGGAGAGCAG 60.125 66.667 8.15 0.00 40.63 4.24
1617 3322 2.036098 TCTACGGGGCTTGACGGA 59.964 61.111 0.00 0.00 0.00 4.69
1713 3430 2.962253 GCGGCGTCATACAGGAGC 60.962 66.667 9.37 0.00 0.00 4.70
1769 3486 2.358615 GTGGCAGGCGTGTGATCA 60.359 61.111 8.40 0.00 0.00 2.92
1978 3695 4.053295 GCATGTTGAACTGCAGAATTTGT 58.947 39.130 23.35 0.00 38.28 2.83
1995 3712 1.729470 TTTTGTTCACCGCCGCATGT 61.729 50.000 0.00 0.00 0.00 3.21
2081 3798 6.040504 TGAAAAGGATACGATAGCAGCTCTTA 59.959 38.462 0.00 0.00 46.39 2.10
2337 4054 3.864540 GCAAATTCACCTTTTACCTGCCC 60.865 47.826 0.00 0.00 0.00 5.36
2349 4067 2.229784 CCTGTTCCTCAGCAAATTCACC 59.770 50.000 0.00 0.00 42.38 4.02
2357 4075 0.836606 TCACAACCTGTTCCTCAGCA 59.163 50.000 0.00 0.00 42.38 4.41
2364 4082 3.506067 CCAATAACCCTCACAACCTGTTC 59.494 47.826 0.00 0.00 0.00 3.18
2365 4083 3.117284 ACCAATAACCCTCACAACCTGTT 60.117 43.478 0.00 0.00 0.00 3.16
2398 4116 0.875059 CTTCTTCCCCGACTTGCAAC 59.125 55.000 0.00 0.00 0.00 4.17
2442 4160 2.933906 TCTGAAACTTGTCGTGAACCAC 59.066 45.455 0.00 0.00 0.00 4.16
2610 4334 4.449743 CACATTTTTGAATGCCAGGTCTTG 59.550 41.667 0.00 0.00 33.57 3.02
2621 4348 9.180678 CGTAGTTTCTTTAGCACATTTTTGAAT 57.819 29.630 0.00 0.00 0.00 2.57
2668 4395 4.337274 TCAACAACAGTGACTCTTCGTCTA 59.663 41.667 0.00 0.00 43.25 2.59
2676 4403 6.037610 ACAGAAGATTTCAACAACAGTGACTC 59.962 38.462 0.00 0.00 0.00 3.36
2704 4431 9.565213 CATAGCAAAAATCTTAAAGTCCTTCAG 57.435 33.333 0.00 0.00 0.00 3.02
2722 4449 4.142924 CGTGCATGACAACTACATAGCAAA 60.143 41.667 0.00 0.00 35.47 3.68
2729 4456 2.517650 TCACGTGCATGACAACTACA 57.482 45.000 14.17 0.00 0.00 2.74
2730 4457 5.492854 CATAATCACGTGCATGACAACTAC 58.507 41.667 14.17 0.00 0.00 2.73
2792 9391 3.173599 GGCAATGACGACATCAAACATG 58.826 45.455 0.00 0.00 41.93 3.21
2893 9501 7.899974 AGAACGTCAAGAAATTCATATCTTCG 58.100 34.615 0.00 0.00 33.73 3.79
2904 9514 6.811665 TCGATATCACAAGAACGTCAAGAAAT 59.188 34.615 3.12 0.00 0.00 2.17
2925 9535 7.012704 ACACAATGCAGCTATTTATCTTTCGAT 59.987 33.333 0.00 0.00 0.00 3.59
2926 9536 6.316140 ACACAATGCAGCTATTTATCTTTCGA 59.684 34.615 0.00 0.00 0.00 3.71
2930 9540 7.395190 TTCACACAATGCAGCTATTTATCTT 57.605 32.000 0.00 0.00 0.00 2.40
2937 9547 3.623703 TCCATTCACACAATGCAGCTAT 58.376 40.909 0.00 0.00 0.00 2.97
2993 9604 8.561738 TGGATTCTTACCTGATTTTGAGTTAC 57.438 34.615 0.00 0.00 0.00 2.50
3086 9697 9.930693 CTTATATTTTGGGACAGAGGTAGTATC 57.069 37.037 0.00 0.00 42.39 2.24
3088 9699 9.496710 TTCTTATATTTTGGGACAGAGGTAGTA 57.503 33.333 0.00 0.00 42.39 1.82
3089 9700 7.989947 TCTTATATTTTGGGACAGAGGTAGT 57.010 36.000 0.00 0.00 42.39 2.73
3090 9701 7.438459 CGTTCTTATATTTTGGGACAGAGGTAG 59.562 40.741 0.00 0.00 42.39 3.18
3091 9702 7.093201 ACGTTCTTATATTTTGGGACAGAGGTA 60.093 37.037 0.00 0.00 42.39 3.08
3092 9703 6.113411 CGTTCTTATATTTTGGGACAGAGGT 58.887 40.000 0.00 0.00 42.39 3.85
3093 9704 6.113411 ACGTTCTTATATTTTGGGACAGAGG 58.887 40.000 0.00 0.00 42.39 3.69
3094 9705 7.611213 AACGTTCTTATATTTTGGGACAGAG 57.389 36.000 0.00 0.00 42.39 3.35
3095 9706 7.989416 AAACGTTCTTATATTTTGGGACAGA 57.011 32.000 0.00 0.00 42.39 3.41
3096 9707 8.911662 CAAAAACGTTCTTATATTTTGGGACAG 58.088 33.333 0.00 0.00 42.39 3.51
3097 9708 8.630917 TCAAAAACGTTCTTATATTTTGGGACA 58.369 29.630 15.53 0.00 39.94 4.02
3098 9709 9.634163 ATCAAAAACGTTCTTATATTTTGGGAC 57.366 29.630 15.53 0.00 39.94 4.46
3139 9750 7.040548 TCCGTCCCAAAATATAAGAACGTTTTT 60.041 33.333 9.22 9.22 0.00 1.94
3140 9751 6.430616 TCCGTCCCAAAATATAAGAACGTTTT 59.569 34.615 0.46 0.00 0.00 2.43
3141 9752 5.939296 TCCGTCCCAAAATATAAGAACGTTT 59.061 36.000 0.46 0.00 0.00 3.60
3142 9753 5.490159 TCCGTCCCAAAATATAAGAACGTT 58.510 37.500 0.00 0.00 0.00 3.99
3143 9754 5.088680 TCCGTCCCAAAATATAAGAACGT 57.911 39.130 0.00 0.00 0.00 3.99
3144 9755 4.510340 CCTCCGTCCCAAAATATAAGAACG 59.490 45.833 0.00 0.00 0.00 3.95
3145 9756 4.820173 CCCTCCGTCCCAAAATATAAGAAC 59.180 45.833 0.00 0.00 0.00 3.01
3146 9757 4.722781 TCCCTCCGTCCCAAAATATAAGAA 59.277 41.667 0.00 0.00 0.00 2.52
3147 9758 4.300345 TCCCTCCGTCCCAAAATATAAGA 58.700 43.478 0.00 0.00 0.00 2.10
3148 9759 4.102681 ACTCCCTCCGTCCCAAAATATAAG 59.897 45.833 0.00 0.00 0.00 1.73
3149 9760 4.042174 ACTCCCTCCGTCCCAAAATATAA 58.958 43.478 0.00 0.00 0.00 0.98
3150 9761 3.660959 ACTCCCTCCGTCCCAAAATATA 58.339 45.455 0.00 0.00 0.00 0.86
3151 9762 2.488836 ACTCCCTCCGTCCCAAAATAT 58.511 47.619 0.00 0.00 0.00 1.28
3152 9763 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
3153 9764 1.558294 GTACTCCCTCCGTCCCAAAAT 59.442 52.381 0.00 0.00 0.00 1.82
3154 9765 0.978907 GTACTCCCTCCGTCCCAAAA 59.021 55.000 0.00 0.00 0.00 2.44
3155 9766 0.115745 AGTACTCCCTCCGTCCCAAA 59.884 55.000 0.00 0.00 0.00 3.28
3156 9767 0.115745 AAGTACTCCCTCCGTCCCAA 59.884 55.000 0.00 0.00 0.00 4.12
3157 9768 0.324091 GAAGTACTCCCTCCGTCCCA 60.324 60.000 0.00 0.00 0.00 4.37
3158 9769 0.324091 TGAAGTACTCCCTCCGTCCC 60.324 60.000 0.00 0.00 0.00 4.46
3159 9770 1.777941 ATGAAGTACTCCCTCCGTCC 58.222 55.000 0.00 0.00 0.00 4.79
3160 9771 5.532664 AATTATGAAGTACTCCCTCCGTC 57.467 43.478 0.00 0.00 0.00 4.79
3161 9772 7.289317 TGAATAATTATGAAGTACTCCCTCCGT 59.711 37.037 0.00 0.00 0.00 4.69
3162 9773 7.667557 TGAATAATTATGAAGTACTCCCTCCG 58.332 38.462 0.00 0.00 0.00 4.63
3163 9774 9.660180 GATGAATAATTATGAAGTACTCCCTCC 57.340 37.037 0.00 0.00 0.00 4.30
3164 9775 9.660180 GGATGAATAATTATGAAGTACTCCCTC 57.340 37.037 0.00 0.00 0.00 4.30
3165 9776 9.170890 TGGATGAATAATTATGAAGTACTCCCT 57.829 33.333 0.00 0.00 0.00 4.20
3166 9777 9.965902 ATGGATGAATAATTATGAAGTACTCCC 57.034 33.333 0.00 0.00 0.00 4.30
3261 9926 0.609662 CCCTTTAGTCCCGGTTCGAA 59.390 55.000 0.00 0.00 0.00 3.71
3298 9967 0.688487 CCAACCGGGACTAAAGGTGA 59.312 55.000 6.32 0.00 40.01 4.02
3323 9992 6.718522 AAAATTTTCTTTAGTCCCGGTTGA 57.281 33.333 0.00 0.00 0.00 3.18
3421 10094 8.845413 ATTAGAGGATAAATTGAGCAGTGATC 57.155 34.615 0.17 0.17 0.00 2.92
3497 10170 2.001803 CTCAAGCTGGGGGAATGGA 58.998 57.895 0.00 0.00 0.00 3.41
3501 10174 2.436109 GTGCTCAAGCTGGGGGAA 59.564 61.111 3.32 0.00 42.66 3.97
3511 10184 1.144969 CGGAAGTTAAGCGTGCTCAA 58.855 50.000 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.