Multiple sequence alignment - TraesCS4A01G089500

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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 TraesCS4A01G089500 chr4A 100.000 6511 0 0 1 6511 95383261 95376751 0.000000e+00 12024
1 TraesCS4A01G089500 chr4A 85.065 154 14 8 315 460 309073437 309073589 1.460000e-31 148
2 TraesCS4A01G089500 chr4D 94.614 3082 89 30 577 3628 369112178 369115212 0.000000e+00 4700
3 TraesCS4A01G089500 chr4D 94.663 2773 87 19 3751 6511 369115210 369117933 0.000000e+00 4244
4 TraesCS4A01G089500 chr4D 87.361 451 35 12 40 469 369111673 369112122 1.260000e-136 497
5 TraesCS4A01G089500 chr4B 91.224 1937 86 35 575 2486 454513567 454515444 0.000000e+00 2558
6 TraesCS4A01G089500 chr4B 88.456 1334 84 22 3751 5065 454516732 454518014 0.000000e+00 1546
7 TraesCS4A01G089500 chr4B 92.442 860 60 4 2764 3619 454515871 454516729 0.000000e+00 1223
8 TraesCS4A01G089500 chr4B 90.013 791 37 15 4984 5744 454518010 454518788 0.000000e+00 985
9 TraesCS4A01G089500 chr4B 83.022 536 55 19 40 554 454513053 454513573 2.770000e-123 453
10 TraesCS4A01G089500 chr4B 90.000 270 22 3 6138 6405 454519340 454519606 1.740000e-90 344
11 TraesCS4A01G089500 chr4B 91.322 242 19 2 5869 6109 454518986 454519226 4.870000e-86 329
12 TraesCS4A01G089500 chr4B 96.403 139 4 1 3621 3759 99437048 99436911 1.830000e-55 228
13 TraesCS4A01G089500 chr5D 82.576 396 46 10 5936 6311 538669081 538668689 1.750000e-85 327
14 TraesCS4A01G089500 chr2B 81.658 398 47 10 5936 6309 780870042 780869647 2.280000e-79 307
15 TraesCS4A01G089500 chr2B 79.146 398 51 17 5943 6312 653795989 653795596 5.040000e-61 246
16 TraesCS4A01G089500 chr2B 78.607 402 56 17 5939 6312 601433038 601432639 8.440000e-59 239
17 TraesCS4A01G089500 chr2B 81.776 214 29 6 315 521 61455406 61455196 3.120000e-38 171
18 TraesCS4A01G089500 chr2B 80.952 231 30 12 315 534 236453829 236453602 3.120000e-38 171
19 TraesCS4A01G089500 chr5B 81.188 404 52 12 5936 6316 338490237 338490639 2.950000e-78 303
20 TraesCS4A01G089500 chr5B 92.053 151 10 2 3610 3759 703263550 703263401 1.840000e-50 211
21 TraesCS4A01G089500 chr5B 91.250 80 7 0 6230 6309 681208908 681208829 6.900000e-20 110
22 TraesCS4A01G089500 chr2A 80.100 402 50 13 5936 6312 690794983 690794587 8.320000e-69 272
23 TraesCS4A01G089500 chr2A 78.824 340 51 17 5987 6309 747279974 747279639 6.620000e-50 209
24 TraesCS4A01G089500 chr2D 79.644 393 54 14 5936 6309 382171978 382172363 6.480000e-65 259
25 TraesCS4A01G089500 chr2D 94.366 142 7 1 3614 3754 619720686 619720545 3.950000e-52 217
26 TraesCS4A01G089500 chr7A 79.188 394 58 17 5936 6309 652359912 652359523 1.080000e-62 252
27 TraesCS4A01G089500 chr3B 78.660 403 56 18 5936 6309 744599962 744600363 2.350000e-59 241
28 TraesCS4A01G089500 chr3B 81.107 307 42 12 5936 6228 260646576 260646272 1.410000e-56 231
29 TraesCS4A01G089500 chr7B 78.164 403 58 18 5932 6313 158916413 158916020 5.080000e-56 230
30 TraesCS4A01G089500 chr7B 94.964 139 7 0 3618 3756 140609396 140609534 1.100000e-52 219
31 TraesCS4A01G089500 chr3A 92.308 156 10 2 3600 3754 736073326 736073172 3.060000e-53 220
32 TraesCS4A01G089500 chr3A 91.613 155 10 3 3618 3769 287820790 287820944 1.840000e-50 211
33 TraesCS4A01G089500 chr3A 83.684 190 21 6 315 495 652711264 652711452 3.120000e-38 171
34 TraesCS4A01G089500 chr3A 83.246 191 21 7 315 495 652576718 652576907 1.450000e-36 165
35 TraesCS4A01G089500 chr3A 83.246 191 21 7 315 495 652664900 652665089 1.450000e-36 165
36 TraesCS4A01G089500 chr3A 87.970 133 15 1 315 447 43661624 43661493 8.740000e-34 156
37 TraesCS4A01G089500 chr3D 93.151 146 9 1 3610 3755 313287018 313286874 5.110000e-51 213
38 TraesCS4A01G089500 chr1B 94.286 140 6 2 3625 3762 567855573 567855434 5.110000e-51 213
39 TraesCS4A01G089500 chr6B 92.568 148 10 1 3608 3755 143826370 143826224 1.840000e-50 211
40 TraesCS4A01G089500 chr6B 82.819 227 26 8 315 529 48490611 48490836 2.400000e-44 191
41 TraesCS4A01G089500 chr6B 92.308 78 6 0 6232 6309 529248379 529248302 1.920000e-20 111
42 TraesCS4A01G089500 chr1D 79.130 230 34 8 315 533 391239889 391240115 5.260000e-31 147


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 TraesCS4A01G089500 chr4A 95376751 95383261 6510 True 12024.000000 12024 100.000000 1 6511 1 chr4A.!!$R1 6510
1 TraesCS4A01G089500 chr4D 369111673 369117933 6260 False 3147.000000 4700 92.212667 40 6511 3 chr4D.!!$F1 6471
2 TraesCS4A01G089500 chr4B 454513053 454519606 6553 False 1062.571429 2558 89.497000 40 6405 7 chr4B.!!$F1 6365

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
631 651 0.598065 AAGCGGAACAAACCATCAGC 59.402 50.000 0.00 0.00 37.08 4.26 F
634 654 0.893270 CGGAACAAACCATCAGCCCA 60.893 55.000 0.00 0.00 0.00 5.36 F
1058 1090 1.198759 TGCTCCCTAACCCAGTCCAC 61.199 60.000 0.00 0.00 0.00 4.02 F
1533 1575 1.203063 TGCTGTCTAGGACTCCTGTGT 60.203 52.381 7.98 0.00 34.61 3.72 F
2748 2982 1.331756 GACGTTTGGAGGCATGCATAG 59.668 52.381 21.36 3.15 0.00 2.23 F
3295 3534 2.671396 CAGCATTTTTGCTCTCATTGCC 59.329 45.455 0.00 0.00 44.30 4.52 F
3645 3884 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17 F
3646 3885 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40 F
3648 3887 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2489 2542 1.483415 AGGGTGTACGAAACAGTGTGT 59.517 47.619 0.00 0.00 39.29 3.72 R
2674 2907 9.629878 TTTAGGGACTCTCTATAAGACAGTAAG 57.370 37.037 0.00 0.00 41.75 2.34 R
2731 2965 3.019564 ACTTCTATGCATGCCTCCAAAC 58.980 45.455 16.68 0.00 0.00 2.93 R
3295 3534 0.598065 CTTTTCTGCGGGTTTCCCAG 59.402 55.000 5.64 0.00 45.83 4.45 R
3629 3868 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20 R
4117 4366 1.537202 GTTGCCTTAGAGCTGTGTTGG 59.463 52.381 0.00 0.00 0.00 3.77 R
5376 5715 0.868406 GCCACAGAAAACGACCTCTG 59.132 55.000 9.72 9.72 43.90 3.35 R
5425 5764 4.759782 AGTCACAGTATACAAGACATGGC 58.240 43.478 18.44 0.00 0.00 4.40 R
5609 5966 5.522456 ACATTATAAACCAATGCAGATGCG 58.478 37.500 0.00 0.00 45.83 4.73 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
35 36 5.649782 GAATTCAAATTCTCTCCCTGCAA 57.350 39.130 0.00 0.00 41.18 4.08
36 37 6.029346 GAATTCAAATTCTCTCCCTGCAAA 57.971 37.500 0.00 0.00 41.18 3.68
37 38 6.423776 AATTCAAATTCTCTCCCTGCAAAA 57.576 33.333 0.00 0.00 0.00 2.44
38 39 5.867903 TTCAAATTCTCTCCCTGCAAAAA 57.132 34.783 0.00 0.00 0.00 1.94
76 77 2.094286 TCAAAGCATGCCATAAAACGGG 60.094 45.455 15.66 0.00 0.00 5.28
194 195 1.140052 ACACCGTTGTTGAGGACATGA 59.860 47.619 0.00 0.00 38.26 3.07
198 199 2.094258 CCGTTGTTGAGGACATGAATCG 59.906 50.000 0.00 0.00 38.26 3.34
247 248 6.672266 AACTTCTAGAGACAAATCAGTGGA 57.328 37.500 0.00 0.00 0.00 4.02
252 253 6.253758 TCTAGAGACAAATCAGTGGAAGGTA 58.746 40.000 0.00 0.00 0.00 3.08
277 281 7.107542 AGACTACAACTACCAAAAACTTGTCA 58.892 34.615 0.00 0.00 0.00 3.58
284 288 6.627243 ACTACCAAAAACTTGTCAAAACTCC 58.373 36.000 0.00 0.00 0.00 3.85
290 294 6.983474 AAAACTTGTCAAAACTCCAAATGG 57.017 33.333 0.00 0.00 0.00 3.16
296 300 4.201970 TGTCAAAACTCCAAATGGACGTTC 60.202 41.667 13.82 0.00 39.78 3.95
298 302 4.582656 TCAAAACTCCAAATGGACGTTCAT 59.417 37.500 2.59 2.59 39.78 2.57
299 303 4.503741 AAACTCCAAATGGACGTTCATG 57.496 40.909 10.86 0.00 39.78 3.07
356 372 7.757624 ACAAAAACAACGTTTGACACTATTCAT 59.242 29.630 0.00 0.00 38.05 2.57
361 377 8.948853 ACAACGTTTGACACTATTCATATTTG 57.051 30.769 0.00 0.00 0.00 2.32
418 435 6.768861 TCGAGTTTGGACCTGAAATTTTTAGA 59.231 34.615 2.68 0.00 0.00 2.10
424 441 6.369629 TGGACCTGAAATTTTTAGAGGTTGA 58.630 36.000 11.34 2.65 34.76 3.18
429 446 7.780271 ACCTGAAATTTTTAGAGGTTGAAGTCT 59.220 33.333 2.68 0.00 32.11 3.24
448 465 6.966534 AGTCTCATTCCTTGTGAACATTTT 57.033 33.333 0.00 0.00 35.31 1.82
506 523 9.823647 TTAAAATTAAGCATGAAGAAAACCACA 57.176 25.926 0.00 0.00 0.00 4.17
531 551 1.134220 TGGGAGCACGTGATATTTCCC 60.134 52.381 22.23 23.34 43.67 3.97
532 552 1.594331 GGAGCACGTGATATTTCCCC 58.406 55.000 22.23 5.33 0.00 4.81
533 553 1.217882 GAGCACGTGATATTTCCCCG 58.782 55.000 22.23 0.00 0.00 5.73
536 556 1.593196 CACGTGATATTTCCCCGCAT 58.407 50.000 10.90 0.00 0.00 4.73
537 557 1.264020 CACGTGATATTTCCCCGCATG 59.736 52.381 10.90 0.00 0.00 4.06
538 558 1.134220 ACGTGATATTTCCCCGCATGT 60.134 47.619 0.00 0.00 0.00 3.21
539 559 2.103432 ACGTGATATTTCCCCGCATGTA 59.897 45.455 0.00 0.00 0.00 2.29
540 560 3.244422 ACGTGATATTTCCCCGCATGTAT 60.244 43.478 0.00 0.00 0.00 2.29
559 579 7.999213 CATGTATGCATTTGGACATAAATTCG 58.001 34.615 3.54 0.00 31.99 3.34
560 580 7.094508 TGTATGCATTTGGACATAAATTCGT 57.905 32.000 3.54 0.00 30.89 3.85
561 581 7.542890 TGTATGCATTTGGACATAAATTCGTT 58.457 30.769 3.54 0.00 30.89 3.85
562 582 8.031864 TGTATGCATTTGGACATAAATTCGTTT 58.968 29.630 3.54 0.00 30.89 3.60
563 583 7.903995 ATGCATTTGGACATAAATTCGTTTT 57.096 28.000 0.00 0.00 0.00 2.43
564 584 7.721286 TGCATTTGGACATAAATTCGTTTTT 57.279 28.000 0.00 0.00 0.00 1.94
588 608 0.748450 TTAGGGGACATAGGTTCGCG 59.252 55.000 0.00 0.00 40.30 5.87
596 616 0.928229 CATAGGTTCGCGTACAAGCC 59.072 55.000 17.79 4.20 0.00 4.35
631 651 0.598065 AAGCGGAACAAACCATCAGC 59.402 50.000 0.00 0.00 37.08 4.26
634 654 0.893270 CGGAACAAACCATCAGCCCA 60.893 55.000 0.00 0.00 0.00 5.36
762 787 7.054751 GGAGCCCTAGTTAAATCACAAATACT 58.945 38.462 0.00 0.00 0.00 2.12
763 788 7.226918 GGAGCCCTAGTTAAATCACAAATACTC 59.773 40.741 0.00 0.00 0.00 2.59
764 789 6.761714 AGCCCTAGTTAAATCACAAATACTCG 59.238 38.462 0.00 0.00 0.00 4.18
765 790 6.537660 GCCCTAGTTAAATCACAAATACTCGT 59.462 38.462 0.00 0.00 0.00 4.18
766 791 7.707893 GCCCTAGTTAAATCACAAATACTCGTA 59.292 37.037 0.00 0.00 0.00 3.43
767 792 9.028185 CCCTAGTTAAATCACAAATACTCGTAC 57.972 37.037 0.00 0.00 0.00 3.67
788 813 4.630111 ACGACCGGACACTTAAATAAACA 58.370 39.130 9.46 0.00 0.00 2.83
795 820 7.067251 ACCGGACACTTAAATAAACAAAAGACA 59.933 33.333 9.46 0.00 0.00 3.41
907 932 4.463879 CGTCCTGCTGCCCTCCTG 62.464 72.222 0.00 0.00 0.00 3.86
992 1020 2.743928 GGGAAGGAGCAGTGCGTG 60.744 66.667 10.00 0.00 0.00 5.34
1053 1085 2.592308 GCCTGCTCCCTAACCCAG 59.408 66.667 0.00 0.00 0.00 4.45
1058 1090 1.198759 TGCTCCCTAACCCAGTCCAC 61.199 60.000 0.00 0.00 0.00 4.02
1127 1161 4.767255 GCGGTGCTGCTGCTACCT 62.767 66.667 23.94 0.00 45.76 3.08
1128 1162 2.816958 CGGTGCTGCTGCTACCTG 60.817 66.667 23.94 17.30 37.84 4.00
1129 1163 3.130160 GGTGCTGCTGCTACCTGC 61.130 66.667 21.44 0.00 40.48 4.85
1130 1164 2.046507 GTGCTGCTGCTACCTGCT 60.047 61.111 17.00 0.00 43.37 4.24
1350 1389 2.065906 GAGATCTCTCGCCCCACGTC 62.066 65.000 15.80 0.00 44.19 4.34
1497 1536 3.125316 CCGAGTGGAAACTGCTCATTAAC 59.875 47.826 0.00 0.00 37.49 2.01
1533 1575 1.203063 TGCTGTCTAGGACTCCTGTGT 60.203 52.381 7.98 0.00 34.61 3.72
1539 1581 3.690628 GTCTAGGACTCCTGTGTCTGTAC 59.309 52.174 7.98 0.00 37.16 2.90
1632 1674 5.284864 ACTGTAGTGAGCATTATCATGTCG 58.715 41.667 0.00 0.00 32.28 4.35
1805 1847 3.324268 GTCTCAATAGGCCCCTAGGTTAC 59.676 52.174 8.29 0.00 34.57 2.50
1822 1864 8.211629 CCTAGGTTACCTCTGCTTTAATTATGT 58.788 37.037 7.39 0.00 34.61 2.29
1935 1977 3.503363 TCACATCTGATGTTTGGCTGTTC 59.497 43.478 20.13 0.00 42.70 3.18
2226 2276 1.610522 ACTGGTGTTGCATGAGCTTTC 59.389 47.619 0.00 0.00 42.74 2.62
2489 2542 7.058525 TGTATCCTCTCCTTCACGAGTATTAA 58.941 38.462 0.00 0.00 0.00 1.40
2500 2553 6.758593 TCACGAGTATTAACACACTGTTTC 57.241 37.500 0.00 0.00 41.45 2.78
2551 2688 6.308015 ACCATTATCTTGTACTGGCACTTA 57.692 37.500 0.00 0.00 0.00 2.24
2684 2917 5.939764 TGCATATGGTCTCTTACTGTCTT 57.060 39.130 4.56 0.00 0.00 3.01
2719 2953 8.548877 TCCCTAAACTCTATCTGCAATAACTTT 58.451 33.333 0.00 0.00 0.00 2.66
2731 2965 9.988350 ATCTGCAATAACTTTAAATAACTGACG 57.012 29.630 0.00 0.00 0.00 4.35
2748 2982 1.331756 GACGTTTGGAGGCATGCATAG 59.668 52.381 21.36 3.15 0.00 2.23
2892 3128 8.810990 TTAACCTTTACCAACTATAACCATGG 57.189 34.615 11.19 11.19 38.91 3.66
2984 3220 4.191544 CTCGCATGACCTTCCATTTAGAA 58.808 43.478 0.00 0.00 0.00 2.10
3021 3257 3.567585 TCATGATGCCGTTCTTTGTTTGA 59.432 39.130 0.00 0.00 0.00 2.69
3087 3325 3.125316 CACACAAAACAAATGGCTCAGG 58.875 45.455 0.00 0.00 0.00 3.86
3295 3534 2.671396 CAGCATTTTTGCTCTCATTGCC 59.329 45.455 0.00 0.00 44.30 4.52
3325 3564 2.727798 CCGCAGAAAAGATTTTGCTGTG 59.272 45.455 13.64 13.64 42.76 3.66
3429 3668 9.770097 TTAATTGTGTATTTTCTGGATTGCAAA 57.230 25.926 1.71 0.00 0.00 3.68
3635 3874 9.574516 AAACAAATATTATCATGTACTCCCTCC 57.425 33.333 0.00 0.00 0.00 4.30
3636 3875 7.386851 ACAAATATTATCATGTACTCCCTCCG 58.613 38.462 0.00 0.00 0.00 4.63
3637 3876 7.016268 ACAAATATTATCATGTACTCCCTCCGT 59.984 37.037 0.00 0.00 0.00 4.69
3638 3877 6.777213 ATATTATCATGTACTCCCTCCGTC 57.223 41.667 0.00 0.00 0.00 4.79
3639 3878 1.705873 ATCATGTACTCCCTCCGTCC 58.294 55.000 0.00 0.00 0.00 4.79
3640 3879 0.750546 TCATGTACTCCCTCCGTCCG 60.751 60.000 0.00 0.00 0.00 4.79
3641 3880 1.455217 ATGTACTCCCTCCGTCCGG 60.455 63.158 0.00 0.00 0.00 5.14
3642 3881 1.929860 ATGTACTCCCTCCGTCCGGA 61.930 60.000 0.00 0.00 42.90 5.14
3643 3882 1.379044 GTACTCCCTCCGTCCGGAA 60.379 63.158 5.23 0.00 44.66 4.30
3644 3883 0.967380 GTACTCCCTCCGTCCGGAAA 60.967 60.000 5.23 0.00 44.66 3.13
3645 3884 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
3646 3885 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
3647 3886 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
3648 3887 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
3649 3888 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
3650 3889 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
3651 3890 1.287425 CTCCGTCCGGAAATACTTGC 58.713 55.000 5.23 0.00 44.66 4.01
3652 3891 0.108041 TCCGTCCGGAAATACTTGCC 60.108 55.000 5.23 0.00 42.05 4.52
3653 3892 0.391927 CCGTCCGGAAATACTTGCCA 60.392 55.000 5.23 0.00 37.50 4.92
3654 3893 1.663695 CGTCCGGAAATACTTGCCAT 58.336 50.000 5.23 0.00 0.00 4.40
3655 3894 1.597663 CGTCCGGAAATACTTGCCATC 59.402 52.381 5.23 0.00 0.00 3.51
3656 3895 2.639065 GTCCGGAAATACTTGCCATCA 58.361 47.619 5.23 0.00 0.00 3.07
3657 3896 3.013921 GTCCGGAAATACTTGCCATCAA 58.986 45.455 5.23 0.00 0.00 2.57
3658 3897 3.442273 GTCCGGAAATACTTGCCATCAAA 59.558 43.478 5.23 0.00 0.00 2.69
3659 3898 4.082463 GTCCGGAAATACTTGCCATCAAAA 60.082 41.667 5.23 0.00 0.00 2.44
3660 3899 4.709397 TCCGGAAATACTTGCCATCAAAAT 59.291 37.500 0.00 0.00 0.00 1.82
3661 3900 4.805192 CCGGAAATACTTGCCATCAAAATG 59.195 41.667 0.00 0.00 0.00 2.32
3676 3915 7.128234 CATCAAAATGGATAAAAGGGGATGT 57.872 36.000 0.00 0.00 0.00 3.06
3677 3916 8.248904 CATCAAAATGGATAAAAGGGGATGTA 57.751 34.615 0.00 0.00 0.00 2.29
3678 3917 8.873144 CATCAAAATGGATAAAAGGGGATGTAT 58.127 33.333 0.00 0.00 0.00 2.29
3679 3918 8.477419 TCAAAATGGATAAAAGGGGATGTATC 57.523 34.615 0.00 0.00 0.00 2.24
3680 3919 8.288812 TCAAAATGGATAAAAGGGGATGTATCT 58.711 33.333 0.00 0.00 0.00 1.98
3681 3920 9.586732 CAAAATGGATAAAAGGGGATGTATCTA 57.413 33.333 0.00 0.00 0.00 1.98
3682 3921 9.813826 AAAATGGATAAAAGGGGATGTATCTAG 57.186 33.333 0.00 0.00 0.00 2.43
3683 3922 8.757307 AATGGATAAAAGGGGATGTATCTAGA 57.243 34.615 0.00 0.00 0.00 2.43
3684 3923 7.554959 TGGATAAAAGGGGATGTATCTAGAC 57.445 40.000 0.00 0.00 0.00 2.59
3685 3924 6.210784 TGGATAAAAGGGGATGTATCTAGACG 59.789 42.308 0.00 0.00 0.00 4.18
3686 3925 6.210984 GGATAAAAGGGGATGTATCTAGACGT 59.789 42.308 0.00 0.00 0.00 4.34
3687 3926 7.395489 GGATAAAAGGGGATGTATCTAGACGTA 59.605 40.741 0.00 0.00 0.00 3.57
3688 3927 8.896722 ATAAAAGGGGATGTATCTAGACGTAT 57.103 34.615 0.00 0.00 0.00 3.06
3689 3928 7.613551 AAAAGGGGATGTATCTAGACGTATT 57.386 36.000 0.00 0.00 0.00 1.89
3690 3929 7.613551 AAAGGGGATGTATCTAGACGTATTT 57.386 36.000 0.00 0.00 0.00 1.40
3691 3930 7.613551 AAGGGGATGTATCTAGACGTATTTT 57.386 36.000 0.00 0.00 0.00 1.82
3692 3931 8.716674 AAGGGGATGTATCTAGACGTATTTTA 57.283 34.615 0.00 0.00 0.00 1.52
3693 3932 8.350852 AGGGGATGTATCTAGACGTATTTTAG 57.649 38.462 0.00 0.00 0.00 1.85
3694 3933 7.949006 AGGGGATGTATCTAGACGTATTTTAGT 59.051 37.037 0.00 0.00 0.00 2.24
3695 3934 8.583296 GGGGATGTATCTAGACGTATTTTAGTT 58.417 37.037 0.00 0.00 0.00 2.24
3696 3935 9.623350 GGGATGTATCTAGACGTATTTTAGTTC 57.377 37.037 0.00 0.00 0.00 3.01
3739 3978 6.841119 TCCATTGTGATGACAAGTATTTTCG 58.159 36.000 3.63 0.00 45.29 3.46
3740 3979 6.029607 CCATTGTGATGACAAGTATTTTCGG 58.970 40.000 3.63 0.00 45.29 4.30
3741 3980 6.128035 CCATTGTGATGACAAGTATTTTCGGA 60.128 38.462 3.63 0.00 45.29 4.55
3742 3981 5.856126 TGTGATGACAAGTATTTTCGGAC 57.144 39.130 0.00 0.00 0.00 4.79
3743 3982 4.387559 TGTGATGACAAGTATTTTCGGACG 59.612 41.667 0.00 0.00 0.00 4.79
3744 3983 3.930229 TGATGACAAGTATTTTCGGACGG 59.070 43.478 0.00 0.00 0.00 4.79
3745 3984 3.663995 TGACAAGTATTTTCGGACGGA 57.336 42.857 0.00 0.00 0.00 4.69
3746 3985 3.581755 TGACAAGTATTTTCGGACGGAG 58.418 45.455 0.00 0.00 0.00 4.63
3747 3986 2.928116 GACAAGTATTTTCGGACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
3748 3987 2.277084 CAAGTATTTTCGGACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
3749 3988 1.856629 AGTATTTTCGGACGGAGGGA 58.143 50.000 0.00 0.00 0.00 4.20
3750 3989 1.755380 AGTATTTTCGGACGGAGGGAG 59.245 52.381 0.00 0.00 0.00 4.30
3751 3990 1.479730 GTATTTTCGGACGGAGGGAGT 59.520 52.381 0.00 0.00 0.00 3.85
3752 3991 1.856629 ATTTTCGGACGGAGGGAGTA 58.143 50.000 0.00 0.00 0.00 2.59
3760 3999 3.729966 GGACGGAGGGAGTATGAAAATC 58.270 50.000 0.00 0.00 0.00 2.17
4301 4550 1.774110 CTCTCTCTTGGCTCCTGCTA 58.226 55.000 0.00 0.00 39.59 3.49
4439 4688 0.393537 GCAATGCCAGCTACCAGTCT 60.394 55.000 0.00 0.00 0.00 3.24
4664 4913 6.762187 TCACTTGTTGTTTGATTTGCATTCAT 59.238 30.769 1.14 0.00 0.00 2.57
4683 4932 2.276732 TCCTTTTTCAGCCTGTCTGG 57.723 50.000 0.00 0.00 43.06 3.86
4684 4933 1.494721 TCCTTTTTCAGCCTGTCTGGT 59.505 47.619 0.00 0.00 43.06 4.00
4801 5059 5.335348 GCTTAACTTTGTCGGCAAATTCCTA 60.335 40.000 16.67 2.58 42.88 2.94
4845 5103 3.350219 TTCGAAATGAAAGGAGAGGGG 57.650 47.619 0.00 0.00 32.37 4.79
4980 5238 0.179056 AATGGTAACCGGCTCCGATG 60.179 55.000 10.28 0.00 42.83 3.84
4986 5244 3.957535 CCGGCTCCGATGCATTGC 61.958 66.667 10.28 0.46 42.83 3.56
5362 5701 6.573434 AGTTTTGGTTCATCTTTCCTTGTTC 58.427 36.000 0.00 0.00 0.00 3.18
5376 5715 4.062991 TCCTTGTTCGTAGAAAAGGCTTC 58.937 43.478 0.00 0.00 45.90 3.86
5425 5764 4.462483 ACAGAGCTTAGAAACTCCTCTCTG 59.538 45.833 12.99 12.99 46.71 3.35
5586 5925 3.453424 ACTTTTTGACGGCATTGGTTTC 58.547 40.909 0.00 0.00 0.00 2.78
5609 5966 9.731819 TTTCTTTATCTATGTGTGACTACGATC 57.268 33.333 0.00 0.00 0.00 3.69
5653 6018 2.790433 ACATGGCCGTGTTGTTAAGAT 58.210 42.857 25.38 0.00 0.00 2.40
5665 6030 7.545965 CCGTGTTGTTAAGATAGTTCTGAGATT 59.454 37.037 0.00 0.00 30.72 2.40
5727 6092 2.682856 TGTCAAGCTTTGTTCTGGTGAC 59.317 45.455 0.00 0.00 0.00 3.67
5773 6138 4.272991 GCAGGATGTCTAGATGAGCAAAAG 59.727 45.833 0.00 0.00 39.31 2.27
5820 6185 7.639162 TTCTTCACTCTAACTTGATTTCGTC 57.361 36.000 0.00 0.00 0.00 4.20
5860 6225 5.309806 GGATCCCCTTGTAAGAAGGCTATAA 59.690 44.000 0.00 0.00 36.10 0.98
5954 6482 0.254747 TAGGGCATTTTGGAGACCGG 59.745 55.000 0.00 0.00 0.00 5.28
5955 6483 1.001393 GGGCATTTTGGAGACCGGA 60.001 57.895 9.46 0.00 0.00 5.14
5985 6513 6.747414 AGAGGCCTTAATTTTGGAAGTTTT 57.253 33.333 6.77 0.00 0.00 2.43
6077 6607 4.804108 TGTGCGTAAAATTTTGGGATGAG 58.196 39.130 13.76 0.00 0.00 2.90
6093 6623 3.499918 GGATGAGATACCTTGAATTGCGG 59.500 47.826 0.00 0.00 0.00 5.69
6188 6806 8.956426 TGTAGCTCTCATTTTAAGGTATTTTGG 58.044 33.333 0.00 0.00 0.00 3.28
6211 6829 5.127031 GGCCTGGAAATTTACACACATGTAT 59.873 40.000 0.00 0.00 41.02 2.29
6289 6907 1.298953 TTAAGGCCTCCATGGAGCTT 58.701 50.000 32.97 29.79 40.69 3.74
6309 6927 4.644498 CTTGGTCTCCATTTGGCATTTTT 58.356 39.130 0.00 0.00 31.53 1.94
6344 6964 6.996282 GGTGCTACATATATGTTACCAAACCT 59.004 38.462 22.90 0.00 41.97 3.50
6415 7035 9.178758 CCAAAGTTTAATAGTAGAGGCATCTTT 57.821 33.333 6.05 0.00 36.96 2.52
6467 7087 3.194542 ACTTCAGCAGAGTCACCATAGTC 59.805 47.826 0.00 0.00 0.00 2.59
6470 7090 1.103803 GCAGAGTCACCATAGTCGGA 58.896 55.000 0.00 0.00 0.00 4.55
6472 7092 2.101582 GCAGAGTCACCATAGTCGGATT 59.898 50.000 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 5.649782 TTGCAGGGAGAGAATTTGAATTC 57.350 39.130 8.11 8.11 43.96 2.17
14 15 6.423776 TTTTGCAGGGAGAGAATTTGAATT 57.576 33.333 0.00 0.00 0.00 2.17
15 16 6.423776 TTTTTGCAGGGAGAGAATTTGAAT 57.576 33.333 0.00 0.00 0.00 2.57
16 17 5.867903 TTTTTGCAGGGAGAGAATTTGAA 57.132 34.783 0.00 0.00 0.00 2.69
43 44 5.187381 TGGCATGCTTTGAGGATTTGAATTA 59.813 36.000 18.92 0.00 0.00 1.40
57 58 2.671130 CCCGTTTTATGGCATGCTTT 57.329 45.000 18.92 7.90 0.00 3.51
76 77 1.303309 CGGATCCATGTCTTCCTTGC 58.697 55.000 13.41 0.00 0.00 4.01
194 195 9.743057 TCATTTCTTAACATGTGAAAAACGATT 57.257 25.926 12.29 0.00 34.09 3.34
252 253 7.107542 TGACAAGTTTTTGGTAGTTGTAGTCT 58.892 34.615 0.00 0.00 38.81 3.24
265 266 7.118971 TCCATTTGGAGTTTTGACAAGTTTTTG 59.881 33.333 0.00 0.00 39.78 2.44
277 281 4.582656 TCATGAACGTCCATTTGGAGTTTT 59.417 37.500 0.00 0.00 46.49 2.43
327 343 5.151389 AGTGTCAAACGTTGTTTTTGTCTC 58.849 37.500 0.00 0.00 35.75 3.36
386 403 5.160607 TCAGGTCCAAACTCGAAATGTAT 57.839 39.130 0.00 0.00 0.00 2.29
418 435 4.103153 TCACAAGGAATGAGACTTCAACCT 59.897 41.667 0.00 0.00 42.15 3.50
424 441 6.966534 AAATGTTCACAAGGAATGAGACTT 57.033 33.333 0.00 0.00 37.93 3.01
485 502 6.267471 TCCTTGTGGTTTTCTTCATGCTTAAT 59.733 34.615 0.00 0.00 34.23 1.40
487 504 5.136828 TCCTTGTGGTTTTCTTCATGCTTA 58.863 37.500 0.00 0.00 34.23 3.09
491 508 4.322198 CCCATCCTTGTGGTTTTCTTCATG 60.322 45.833 0.00 0.00 37.57 3.07
500 517 0.251341 GTGCTCCCATCCTTGTGGTT 60.251 55.000 0.00 0.00 37.57 3.67
503 520 1.003355 ACGTGCTCCCATCCTTGTG 60.003 57.895 0.00 0.00 0.00 3.33
504 521 1.003355 CACGTGCTCCCATCCTTGT 60.003 57.895 0.82 0.00 0.00 3.16
505 522 0.107508 ATCACGTGCTCCCATCCTTG 60.108 55.000 11.67 0.00 0.00 3.61
506 523 1.496060 TATCACGTGCTCCCATCCTT 58.504 50.000 11.67 0.00 0.00 3.36
536 556 7.094508 ACGAATTTATGTCCAAATGCATACA 57.905 32.000 0.00 0.04 0.00 2.29
537 557 7.985634 AACGAATTTATGTCCAAATGCATAC 57.014 32.000 0.00 0.00 0.00 2.39
538 558 8.994429 AAAACGAATTTATGTCCAAATGCATA 57.006 26.923 0.00 0.00 0.00 3.14
539 559 7.903995 AAAACGAATTTATGTCCAAATGCAT 57.096 28.000 0.00 0.00 0.00 3.96
540 560 7.721286 AAAAACGAATTTATGTCCAAATGCA 57.279 28.000 0.00 0.00 0.00 3.96
561 581 6.431852 CGAACCTATGTCCCCTAAAAGAAAAA 59.568 38.462 0.00 0.00 0.00 1.94
562 582 5.941647 CGAACCTATGTCCCCTAAAAGAAAA 59.058 40.000 0.00 0.00 0.00 2.29
563 583 5.493809 CGAACCTATGTCCCCTAAAAGAAA 58.506 41.667 0.00 0.00 0.00 2.52
564 584 4.624604 GCGAACCTATGTCCCCTAAAAGAA 60.625 45.833 0.00 0.00 0.00 2.52
565 585 3.118519 GCGAACCTATGTCCCCTAAAAGA 60.119 47.826 0.00 0.00 0.00 2.52
566 586 3.203716 GCGAACCTATGTCCCCTAAAAG 58.796 50.000 0.00 0.00 0.00 2.27
567 587 2.419021 CGCGAACCTATGTCCCCTAAAA 60.419 50.000 0.00 0.00 0.00 1.52
568 588 1.137479 CGCGAACCTATGTCCCCTAAA 59.863 52.381 0.00 0.00 0.00 1.85
569 589 0.748450 CGCGAACCTATGTCCCCTAA 59.252 55.000 0.00 0.00 0.00 2.69
570 590 0.396139 ACGCGAACCTATGTCCCCTA 60.396 55.000 15.93 0.00 0.00 3.53
571 591 0.396139 TACGCGAACCTATGTCCCCT 60.396 55.000 15.93 0.00 0.00 4.79
572 592 0.249197 GTACGCGAACCTATGTCCCC 60.249 60.000 15.93 0.00 0.00 4.81
573 593 0.457035 TGTACGCGAACCTATGTCCC 59.543 55.000 15.93 0.00 0.00 4.46
588 608 0.322546 CACCCCTCCTTGGCTTGTAC 60.323 60.000 0.00 0.00 0.00 2.90
596 616 1.675641 CTTTCGCCACCCCTCCTTG 60.676 63.158 0.00 0.00 0.00 3.61
631 651 3.256631 CACCTCTCCAAAGAATGTTTGGG 59.743 47.826 19.83 11.71 46.71 4.12
634 654 4.792068 TGACACCTCTCCAAAGAATGTTT 58.208 39.130 0.00 0.00 33.27 2.83
762 787 1.518325 TTAAGTGTCCGGTCGTACGA 58.482 50.000 15.28 15.28 35.47 3.43
763 788 2.330231 TTTAAGTGTCCGGTCGTACG 57.670 50.000 9.53 9.53 0.00 3.67
764 789 5.633182 TGTTTATTTAAGTGTCCGGTCGTAC 59.367 40.000 0.00 0.00 0.00 3.67
765 790 5.777802 TGTTTATTTAAGTGTCCGGTCGTA 58.222 37.500 0.00 0.00 0.00 3.43
766 791 4.630111 TGTTTATTTAAGTGTCCGGTCGT 58.370 39.130 0.00 0.00 0.00 4.34
767 792 5.594724 TTGTTTATTTAAGTGTCCGGTCG 57.405 39.130 0.00 0.00 0.00 4.79
788 813 6.059484 TCACCCTAGAATTTCGTTGTCTTTT 58.941 36.000 0.00 0.00 0.00 2.27
795 820 3.260884 TCTGCTCACCCTAGAATTTCGTT 59.739 43.478 0.00 0.00 0.00 3.85
960 988 5.452636 GCTCCTTCCCTCTGTATTTCTACTG 60.453 48.000 0.00 0.00 0.00 2.74
961 989 4.651962 GCTCCTTCCCTCTGTATTTCTACT 59.348 45.833 0.00 0.00 0.00 2.57
962 990 4.406003 TGCTCCTTCCCTCTGTATTTCTAC 59.594 45.833 0.00 0.00 0.00 2.59
1027 1059 4.785453 GGAGCAGGCGGTTGAGGG 62.785 72.222 0.00 0.00 0.00 4.30
1053 1085 2.422945 GGATAATGTGAAGGGGGTGGAC 60.423 54.545 0.00 0.00 0.00 4.02
1058 1090 0.884704 CGCGGATAATGTGAAGGGGG 60.885 60.000 0.00 0.00 0.00 5.40
1129 1163 4.034258 CACCAGCAACAGCGGCAG 62.034 66.667 1.45 0.00 0.00 4.85
1301 1338 2.897350 GCGAATCTGGCGGGAAGG 60.897 66.667 0.00 0.00 0.00 3.46
1479 1518 3.366374 GGCAGTTAATGAGCAGTTTCCAC 60.366 47.826 0.00 0.00 0.00 4.02
1497 1536 2.219458 CAGCATCCATCAGTAAGGCAG 58.781 52.381 0.00 0.00 0.00 4.85
1533 1575 8.404000 GCTTAATAACTGCAGTAGTAGTACAGA 58.596 37.037 22.01 0.00 39.97 3.41
1539 1581 6.419413 GCTCAGCTTAATAACTGCAGTAGTAG 59.581 42.308 22.01 13.82 39.18 2.57
1632 1674 7.551262 TGTATCATGTAGGAATTGTTGGTACAC 59.449 37.037 0.00 0.00 39.29 2.90
1822 1864 7.489160 ACAGAAGCGAATGAACATATACTGTA 58.511 34.615 0.00 0.00 36.98 2.74
1823 1865 6.341316 ACAGAAGCGAATGAACATATACTGT 58.659 36.000 0.00 0.00 40.84 3.55
1835 1877 5.344128 CAGAAAATTTGGACAGAAGCGAATG 59.656 40.000 0.00 0.00 0.00 2.67
1935 1977 4.318760 CCAACGGCTGAAATGACATATACG 60.319 45.833 0.00 0.00 0.00 3.06
2123 2168 2.016318 CCAGCCATCGAAGTATTGCAA 58.984 47.619 0.00 0.00 0.00 4.08
2226 2276 2.045524 AGAGACCATGTATCAGGGCAG 58.954 52.381 0.24 0.00 39.09 4.85
2271 2321 9.956720 AATGTATTGCAATAACAATAAGCTCTC 57.043 29.630 20.46 4.57 42.53 3.20
2398 2451 4.202245 AGCAAGGTAAGCGAGTTTATGA 57.798 40.909 0.00 0.00 37.01 2.15
2489 2542 1.483415 AGGGTGTACGAAACAGTGTGT 59.517 47.619 0.00 0.00 39.29 3.72
2674 2907 9.629878 TTTAGGGACTCTCTATAAGACAGTAAG 57.370 37.037 0.00 0.00 41.75 2.34
2719 2953 4.643463 TGCCTCCAAACGTCAGTTATTTA 58.357 39.130 0.00 0.00 40.18 1.40
2731 2965 3.019564 ACTTCTATGCATGCCTCCAAAC 58.980 45.455 16.68 0.00 0.00 2.93
2748 2982 7.358830 GCTGGATAATAGATCTTTGCAACTTC 58.641 38.462 0.00 0.00 0.00 3.01
2892 3128 8.753497 AGAAGGATGGGAGAACAATAATTTAC 57.247 34.615 0.00 0.00 0.00 2.01
2984 3220 4.907809 CATCATGAGTATGCATCTTCCCT 58.092 43.478 0.19 0.00 34.21 4.20
3021 3257 3.314357 CCGAGCATCATGTCATCAAACAT 59.686 43.478 0.00 0.00 40.49 2.71
3120 3358 0.693622 TATGCCCGGGAGTGTTTCAA 59.306 50.000 29.31 0.00 0.00 2.69
3295 3534 0.598065 CTTTTCTGCGGGTTTCCCAG 59.402 55.000 5.64 0.00 45.83 4.45
3429 3668 3.263425 ACAGAAGTCCGTTCCCATACAAT 59.737 43.478 0.00 0.00 35.51 2.71
3619 3858 2.812983 CGGACGGAGGGAGTACATGATA 60.813 54.545 0.00 0.00 0.00 2.15
3628 3867 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
3629 3868 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
3630 3869 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
3631 3870 1.935933 CAAGTATTTCCGGACGGAGG 58.064 55.000 13.64 0.00 46.06 4.30
3632 3871 1.287425 GCAAGTATTTCCGGACGGAG 58.713 55.000 13.64 1.75 46.06 4.63
3633 3872 0.108041 GGCAAGTATTTCCGGACGGA 60.108 55.000 1.83 9.76 43.52 4.69
3634 3873 0.391927 TGGCAAGTATTTCCGGACGG 60.392 55.000 1.83 3.96 0.00 4.79
3635 3874 1.597663 GATGGCAAGTATTTCCGGACG 59.402 52.381 1.83 0.00 0.00 4.79
3636 3875 2.639065 TGATGGCAAGTATTTCCGGAC 58.361 47.619 1.83 0.00 0.00 4.79
3637 3876 3.358111 TTGATGGCAAGTATTTCCGGA 57.642 42.857 0.00 0.00 0.00 5.14
3638 3877 4.448537 TTTTGATGGCAAGTATTTCCGG 57.551 40.909 0.00 0.00 35.04 5.14
3639 3878 4.805192 CCATTTTGATGGCAAGTATTTCCG 59.195 41.667 0.00 0.00 35.04 4.30
3640 3879 5.976458 TCCATTTTGATGGCAAGTATTTCC 58.024 37.500 0.00 0.00 41.43 3.13
3641 3880 9.598517 TTTATCCATTTTGATGGCAAGTATTTC 57.401 29.630 0.00 0.00 41.43 2.17
3642 3881 9.956640 TTTTATCCATTTTGATGGCAAGTATTT 57.043 25.926 0.00 0.00 41.43 1.40
3643 3882 9.603921 CTTTTATCCATTTTGATGGCAAGTATT 57.396 29.630 0.00 0.00 41.43 1.89
3644 3883 8.206189 CCTTTTATCCATTTTGATGGCAAGTAT 58.794 33.333 0.00 0.00 41.43 2.12
3645 3884 7.364585 CCCTTTTATCCATTTTGATGGCAAGTA 60.365 37.037 0.00 0.00 41.43 2.24
3646 3885 6.408869 CCTTTTATCCATTTTGATGGCAAGT 58.591 36.000 0.00 0.00 41.43 3.16
3647 3886 5.818857 CCCTTTTATCCATTTTGATGGCAAG 59.181 40.000 0.00 1.59 41.43 4.01
3648 3887 5.339035 CCCCTTTTATCCATTTTGATGGCAA 60.339 40.000 0.00 0.00 41.43 4.52
3649 3888 4.163839 CCCCTTTTATCCATTTTGATGGCA 59.836 41.667 0.00 0.00 41.43 4.92
3650 3889 4.408596 TCCCCTTTTATCCATTTTGATGGC 59.591 41.667 0.52 0.00 41.43 4.40
3651 3890 6.100134 ACATCCCCTTTTATCCATTTTGATGG 59.900 38.462 0.00 0.00 43.01 3.51
3652 3891 7.128234 ACATCCCCTTTTATCCATTTTGATG 57.872 36.000 0.00 0.00 33.80 3.07
3653 3892 9.093458 GATACATCCCCTTTTATCCATTTTGAT 57.907 33.333 0.00 0.00 0.00 2.57
3654 3893 8.288812 AGATACATCCCCTTTTATCCATTTTGA 58.711 33.333 0.00 0.00 0.00 2.69
3655 3894 8.482852 AGATACATCCCCTTTTATCCATTTTG 57.517 34.615 0.00 0.00 0.00 2.44
3656 3895 9.813826 CTAGATACATCCCCTTTTATCCATTTT 57.186 33.333 0.00 0.00 0.00 1.82
3657 3896 9.182642 TCTAGATACATCCCCTTTTATCCATTT 57.817 33.333 0.00 0.00 0.00 2.32
3658 3897 8.606830 GTCTAGATACATCCCCTTTTATCCATT 58.393 37.037 0.00 0.00 0.00 3.16
3659 3898 7.093289 CGTCTAGATACATCCCCTTTTATCCAT 60.093 40.741 0.00 0.00 0.00 3.41
3660 3899 6.210784 CGTCTAGATACATCCCCTTTTATCCA 59.789 42.308 0.00 0.00 0.00 3.41
3661 3900 6.210984 ACGTCTAGATACATCCCCTTTTATCC 59.789 42.308 0.00 0.00 0.00 2.59
3662 3901 7.229581 ACGTCTAGATACATCCCCTTTTATC 57.770 40.000 0.00 0.00 0.00 1.75
3663 3902 8.896722 ATACGTCTAGATACATCCCCTTTTAT 57.103 34.615 0.00 0.00 0.00 1.40
3664 3903 8.716674 AATACGTCTAGATACATCCCCTTTTA 57.283 34.615 0.00 0.00 0.00 1.52
3665 3904 7.613551 AATACGTCTAGATACATCCCCTTTT 57.386 36.000 0.00 0.00 0.00 2.27
3666 3905 7.613551 AAATACGTCTAGATACATCCCCTTT 57.386 36.000 0.00 0.00 0.00 3.11
3667 3906 7.613551 AAAATACGTCTAGATACATCCCCTT 57.386 36.000 0.00 0.00 0.00 3.95
3668 3907 7.949006 ACTAAAATACGTCTAGATACATCCCCT 59.051 37.037 0.00 0.00 0.00 4.79
3669 3908 8.120140 ACTAAAATACGTCTAGATACATCCCC 57.880 38.462 0.00 0.00 0.00 4.81
3670 3909 9.623350 GAACTAAAATACGTCTAGATACATCCC 57.377 37.037 0.00 0.00 0.00 3.85
3713 3952 8.611757 CGAAAATACTTGTCATCACAATGGATA 58.388 33.333 0.00 0.00 41.82 2.59
3714 3953 7.415541 CCGAAAATACTTGTCATCACAATGGAT 60.416 37.037 0.00 0.00 41.82 3.41
3715 3954 6.128035 CCGAAAATACTTGTCATCACAATGGA 60.128 38.462 0.00 0.00 41.82 3.41
3716 3955 6.029607 CCGAAAATACTTGTCATCACAATGG 58.970 40.000 0.00 0.00 41.82 3.16
3717 3956 6.742718 GTCCGAAAATACTTGTCATCACAATG 59.257 38.462 0.00 0.00 41.82 2.82
3718 3957 6.402118 CGTCCGAAAATACTTGTCATCACAAT 60.402 38.462 0.00 0.00 41.82 2.71
3719 3958 5.107259 CGTCCGAAAATACTTGTCATCACAA 60.107 40.000 0.00 0.00 40.40 3.33
3720 3959 4.387559 CGTCCGAAAATACTTGTCATCACA 59.612 41.667 0.00 0.00 0.00 3.58
3721 3960 4.201685 CCGTCCGAAAATACTTGTCATCAC 60.202 45.833 0.00 0.00 0.00 3.06
3722 3961 3.930229 CCGTCCGAAAATACTTGTCATCA 59.070 43.478 0.00 0.00 0.00 3.07
3723 3962 4.178540 TCCGTCCGAAAATACTTGTCATC 58.821 43.478 0.00 0.00 0.00 2.92
3724 3963 4.181578 CTCCGTCCGAAAATACTTGTCAT 58.818 43.478 0.00 0.00 0.00 3.06
3725 3964 3.581755 CTCCGTCCGAAAATACTTGTCA 58.418 45.455 0.00 0.00 0.00 3.58
3726 3965 2.928116 CCTCCGTCCGAAAATACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
3727 3966 2.354403 CCCTCCGTCCGAAAATACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
3728 3967 2.093869 TCCCTCCGTCCGAAAATACTTG 60.094 50.000 0.00 0.00 0.00 3.16
3729 3968 2.167900 CTCCCTCCGTCCGAAAATACTT 59.832 50.000 0.00 0.00 0.00 2.24
3730 3969 1.755380 CTCCCTCCGTCCGAAAATACT 59.245 52.381 0.00 0.00 0.00 2.12
3731 3970 1.479730 ACTCCCTCCGTCCGAAAATAC 59.520 52.381 0.00 0.00 0.00 1.89
3732 3971 1.856629 ACTCCCTCCGTCCGAAAATA 58.143 50.000 0.00 0.00 0.00 1.40
3733 3972 1.856629 TACTCCCTCCGTCCGAAAAT 58.143 50.000 0.00 0.00 0.00 1.82
3734 3973 1.479323 CATACTCCCTCCGTCCGAAAA 59.521 52.381 0.00 0.00 0.00 2.29
3735 3974 1.108776 CATACTCCCTCCGTCCGAAA 58.891 55.000 0.00 0.00 0.00 3.46
3736 3975 0.256752 TCATACTCCCTCCGTCCGAA 59.743 55.000 0.00 0.00 0.00 4.30
3737 3976 0.256752 TTCATACTCCCTCCGTCCGA 59.743 55.000 0.00 0.00 0.00 4.55
3738 3977 1.108776 TTTCATACTCCCTCCGTCCG 58.891 55.000 0.00 0.00 0.00 4.79
3739 3978 3.388350 AGATTTTCATACTCCCTCCGTCC 59.612 47.826 0.00 0.00 0.00 4.79
3740 3979 4.674281 AGATTTTCATACTCCCTCCGTC 57.326 45.455 0.00 0.00 0.00 4.79
3741 3980 7.850935 TTATAGATTTTCATACTCCCTCCGT 57.149 36.000 0.00 0.00 0.00 4.69
3742 3981 9.726438 AATTTATAGATTTTCATACTCCCTCCG 57.274 33.333 0.00 0.00 0.00 4.63
3859 4098 1.250328 CATGCTGCAGGGACAAAAGA 58.750 50.000 17.12 0.00 0.00 2.52
4013 4260 8.250143 TGCCTCTATAGTACAATGATTTCAGA 57.750 34.615 0.00 0.00 0.00 3.27
4014 4261 9.499479 AATGCCTCTATAGTACAATGATTTCAG 57.501 33.333 0.00 0.00 0.00 3.02
4015 4262 9.494271 GAATGCCTCTATAGTACAATGATTTCA 57.506 33.333 0.00 0.00 0.00 2.69
4016 4263 9.494271 TGAATGCCTCTATAGTACAATGATTTC 57.506 33.333 0.00 0.00 0.00 2.17
4107 4356 5.796424 AGAGCTGTGTTGGAATTTTGATT 57.204 34.783 0.00 0.00 0.00 2.57
4117 4366 1.537202 GTTGCCTTAGAGCTGTGTTGG 59.463 52.381 0.00 0.00 0.00 3.77
4301 4550 5.183140 CCAAAATGGGAAGTAAATCAGACGT 59.817 40.000 0.00 0.00 32.67 4.34
4399 4648 4.458989 TGCAAGAACAAGAACAGTGAGTTT 59.541 37.500 0.00 0.00 41.51 2.66
4439 4688 5.406163 TCCAGCTTCCTCAAGGATATGATA 58.594 41.667 0.00 0.00 44.98 2.15
4735 4991 3.610040 GGGGGAATCCAAATTTCACAC 57.390 47.619 0.09 0.00 37.22 3.82
4814 5072 5.463061 CCTTTCATTTCGAAATGCACAGTTT 59.537 36.000 35.42 7.44 42.69 2.66
4816 5074 4.278170 TCCTTTCATTTCGAAATGCACAGT 59.722 37.500 35.42 8.85 42.69 3.55
4818 5076 4.518590 TCTCCTTTCATTTCGAAATGCACA 59.481 37.500 35.42 22.97 42.69 4.57
4980 5238 3.608432 GGGTCTCCCAAGCAATGC 58.392 61.111 0.00 0.00 44.65 3.56
5031 5366 3.126343 GGGTTAATACAGTTTCTGGTGCG 59.874 47.826 1.90 0.00 35.51 5.34
5339 5678 5.458779 CGAACAAGGAAAGATGAACCAAAAC 59.541 40.000 0.00 0.00 0.00 2.43
5362 5701 3.254892 GACCTCTGAAGCCTTTTCTACG 58.745 50.000 0.00 0.00 0.00 3.51
5376 5715 0.868406 GCCACAGAAAACGACCTCTG 59.132 55.000 9.72 9.72 43.90 3.35
5425 5764 4.759782 AGTCACAGTATACAAGACATGGC 58.240 43.478 18.44 0.00 0.00 4.40
5586 5925 6.303496 GCGATCGTAGTCACACATAGATAAAG 59.697 42.308 17.81 0.00 0.00 1.85
5609 5966 5.522456 ACATTATAAACCAATGCAGATGCG 58.478 37.500 0.00 0.00 45.83 4.73
5727 6092 3.427638 CCTGTCAGCATCTGAAATTGCAG 60.428 47.826 7.16 7.16 42.46 4.41
5773 6138 0.609662 TAGCAAACCCACCCGTAGAC 59.390 55.000 0.00 0.00 0.00 2.59
5820 6185 2.673368 GGATCCGTCTTACAAGCACTTG 59.327 50.000 8.82 8.82 45.58 3.16
5860 6225 9.877178 CTTCAACACAGTTTAGACCTAGATAAT 57.123 33.333 0.00 0.00 0.00 1.28
5954 6482 5.532779 CCAAAATTAAGGCCTCTATGGAGTC 59.467 44.000 5.23 0.00 37.86 3.36
5955 6483 5.193728 TCCAAAATTAAGGCCTCTATGGAGT 59.806 40.000 5.23 0.00 37.86 3.85
5962 6490 6.747414 AAAACTTCCAAAATTAAGGCCTCT 57.253 33.333 5.23 0.00 0.00 3.69
6077 6607 2.479560 GCAACCCGCAATTCAAGGTATC 60.480 50.000 0.00 0.00 41.79 2.24
6093 6623 7.671495 AGTCCATGAATTTTTATTTGCAACC 57.329 32.000 0.00 0.00 0.00 3.77
6162 6778 8.956426 CCAAAATACCTTAAAATGAGAGCTACA 58.044 33.333 0.00 0.00 0.00 2.74
6163 6779 7.915923 GCCAAAATACCTTAAAATGAGAGCTAC 59.084 37.037 0.00 0.00 0.00 3.58
6164 6780 7.068226 GGCCAAAATACCTTAAAATGAGAGCTA 59.932 37.037 0.00 0.00 0.00 3.32
6179 6797 5.872617 GTGTAAATTTCCAGGCCAAAATACC 59.127 40.000 5.01 1.08 0.00 2.73
6188 6806 4.519540 ACATGTGTGTAAATTTCCAGGC 57.480 40.909 0.00 0.00 36.63 4.85
6289 6907 3.244491 CCAAAAATGCCAAATGGAGACCA 60.244 43.478 2.98 0.00 38.19 4.02
6309 6927 2.949177 ATGTAGCACCAAGTTGTCCA 57.051 45.000 1.45 0.00 0.00 4.02
6344 6964 4.584874 ACACAACCGACCATGAAATATCA 58.415 39.130 0.00 0.00 40.57 2.15
6437 7057 3.056962 TGACTCTGCTGAAGTTGCTCTAG 60.057 47.826 0.00 0.00 0.00 2.43
6449 7069 1.202348 CCGACTATGGTGACTCTGCTG 60.202 57.143 0.00 0.00 0.00 4.41
6480 7100 4.841813 TCCAATAGCCTCCAAATCCGTATA 59.158 41.667 0.00 0.00 0.00 1.47


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

AutoCloner maintained by Alex Coulton.