Multiple sequence alignment - TraesCS6B01G343700

Loading Multiple Alignment...

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 TraesCS6B01G343700 chr6B 100.000 4957 0 0 1 4957 605548530 605553486 0.000000e+00 9154
1 TraesCS6B01G343700 chr6B 80.275 218 38 4 167 381 621360606 621360821 5.140000e-35 159
2 TraesCS6B01G343700 chr6D 89.773 4312 273 70 1 4197 403794311 403798569 0.000000e+00 5365
3 TraesCS6B01G343700 chr6D 95.833 432 13 3 4527 4957 403802599 403803026 0.000000e+00 693
4 TraesCS6B01G343700 chr6D 94.175 103 6 0 4390 4492 403801665 403801767 1.850000e-34 158
5 TraesCS6B01G343700 chr6D 90.598 117 7 1 4281 4397 403798567 403798679 8.590000e-33 152
6 TraesCS6B01G343700 chr6A 92.948 1645 75 20 2583 4203 550281412 550283039 0.000000e+00 2357
7 TraesCS6B01G343700 chr6A 92.237 1636 96 16 841 2474 550279808 550281414 0.000000e+00 2289
8 TraesCS6B01G343700 chr6A 94.318 440 18 3 4518 4957 550283352 550283784 0.000000e+00 667
9 TraesCS6B01G343700 chr6A 90.045 221 22 0 4269 4489 550283043 550283263 2.260000e-73 287
10 TraesCS6B01G343700 chr1B 84.916 179 23 2 167 341 489542120 489541942 1.420000e-40 178
11 TraesCS6B01G343700 chr5B 84.659 176 26 1 167 341 255969286 255969461 1.830000e-39 174
12 TraesCS6B01G343700 chr4A 85.294 170 23 2 173 341 94756178 94756010 1.830000e-39 174
13 TraesCS6B01G343700 chr2A 86.842 152 18 2 192 341 703981384 703981233 8.530000e-38 169
14 TraesCS6B01G343700 chr1A 86.503 163 10 8 594 751 14983118 14983273 8.530000e-38 169
15 TraesCS6B01G343700 chr1A 86.420 162 10 8 595 751 14984071 14984225 3.070000e-37 167
16 TraesCS6B01G343700 chr2D 86.093 151 20 1 192 341 563947802 563947652 1.430000e-35 161
17 TraesCS6B01G343700 chr5A 80.184 217 37 5 167 381 276637584 276637796 1.850000e-34 158
18 TraesCS6B01G343700 chr7A 83.537 164 26 1 162 325 241802940 241802778 8.590000e-33 152


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 TraesCS6B01G343700 chr6B 605548530 605553486 4956 False 9154 9154 100.00000 1 4957 1 chr6B.!!$F1 4956
1 TraesCS6B01G343700 chr6D 403794311 403803026 8715 False 1592 5365 92.59475 1 4957 4 chr6D.!!$F1 4956
2 TraesCS6B01G343700 chr6A 550279808 550283784 3976 False 1400 2357 92.38700 841 4957 4 chr6A.!!$F1 4116

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
642 694 0.108898 CTCCAGTGTCCTCAAGCTCG 60.109 60.0 0.0 0.0 0.00 5.03 F
1543 1629 0.036765 TCCGTGGTATGTTGCTGTCC 60.037 55.0 0.0 0.0 0.00 4.02 F
2699 2793 0.317160 TTCTTGTCATCGCACTCCGT 59.683 50.0 0.0 0.0 38.35 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1966 2052 0.981183 AAGCCACCACTCGGTTATCA 59.019 50.0 0.00 0.0 46.31 2.15 R
3275 3378 0.113776 AAGGGAGTCCTGTGGTACGA 59.886 55.0 9.58 0.0 44.07 3.43 R
4159 4293 0.109153 AGTTCATGCAGCAGGTCACA 59.891 50.0 6.99 0.0 0.00 3.58 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
22 23 1.642762 AGAGGGGAAAAGATGGTGCAT 59.357 47.619 0.00 0.00 0.00 3.96
72 73 0.916358 CCACCTCCTCTTCCACCCAT 60.916 60.000 0.00 0.00 0.00 4.00
81 82 1.905894 TCTTCCACCCATCGTCATTCA 59.094 47.619 0.00 0.00 0.00 2.57
85 86 2.835156 TCCACCCATCGTCATTCAACTA 59.165 45.455 0.00 0.00 0.00 2.24
89 90 4.035558 CACCCATCGTCATTCAACTATTGG 59.964 45.833 0.00 0.00 0.00 3.16
114 121 4.768968 GGCCAATGATATGGTTGCTCTATT 59.231 41.667 0.00 0.00 42.75 1.73
150 157 2.206576 ACCTGCAATTCTGGTCTTCC 57.793 50.000 0.00 0.00 42.56 3.46
160 167 3.319137 TCTGGTCTTCCATTCTGTTCG 57.681 47.619 0.00 0.00 43.43 3.95
162 169 3.323691 TCTGGTCTTCCATTCTGTTCGAA 59.676 43.478 0.00 0.00 43.43 3.71
163 170 3.399330 TGGTCTTCCATTCTGTTCGAAC 58.601 45.455 21.42 21.42 39.03 3.95
165 172 3.813166 GGTCTTCCATTCTGTTCGAACAA 59.187 43.478 29.32 17.75 38.66 2.83
170 177 3.431912 TCCATTCTGTTCGAACAACATCG 59.568 43.478 29.32 18.29 44.04 3.84
171 178 3.186409 CCATTCTGTTCGAACAACATCGT 59.814 43.478 29.32 11.41 43.19 3.73
223 230 7.787028 ACTAACCTTTACATCTCCAAGATCTC 58.213 38.462 0.00 0.00 31.32 2.75
235 242 4.389374 TCCAAGATCTCAAAACACACCTC 58.611 43.478 0.00 0.00 0.00 3.85
241 248 3.691575 TCTCAAAACACACCTCCAACAA 58.308 40.909 0.00 0.00 0.00 2.83
248 255 1.946768 CACACCTCCAACAAATGACGT 59.053 47.619 0.00 0.00 0.00 4.34
322 329 6.925165 CACTTGAAGATGCAAATTTACACCTT 59.075 34.615 0.00 0.00 0.00 3.50
326 333 6.922957 TGAAGATGCAAATTTACACCTTCAAC 59.077 34.615 21.28 1.75 36.74 3.18
330 337 3.552068 GCAAATTTACACCTTCAACCGCT 60.552 43.478 0.00 0.00 0.00 5.52
343 350 1.066143 CAACCGCTGGAGATGTAACCT 60.066 52.381 1.50 0.00 0.00 3.50
344 351 0.537188 ACCGCTGGAGATGTAACCTG 59.463 55.000 1.50 0.00 0.00 4.00
361 368 1.666888 CCTGGATGCAAAACGACAAGC 60.667 52.381 0.00 0.00 0.00 4.01
365 372 3.091022 GCAAAACGACAAGCCGCG 61.091 61.111 0.00 0.00 0.00 6.46
399 406 2.540383 GCTTTGAAATTTCCCCTCCCT 58.460 47.619 15.48 0.00 0.00 4.20
401 408 3.055819 GCTTTGAAATTTCCCCTCCCTTC 60.056 47.826 15.48 0.00 0.00 3.46
418 425 3.827898 CCCTCGACTGGACGCCTC 61.828 72.222 0.00 0.00 0.00 4.70
422 429 3.827898 CGACTGGACGCCTCCCTC 61.828 72.222 0.00 0.00 35.34 4.30
434 455 4.458829 TCCCTCGATCCGCACCCT 62.459 66.667 0.00 0.00 0.00 4.34
502 523 0.733150 GCCCAACGCCTCTAAATCAC 59.267 55.000 0.00 0.00 0.00 3.06
503 524 1.679032 GCCCAACGCCTCTAAATCACT 60.679 52.381 0.00 0.00 0.00 3.41
509 530 1.920574 CGCCTCTAAATCACTGTCGTG 59.079 52.381 0.00 0.00 42.59 4.35
518 539 4.280494 ACTGTCGTGTCGCCGCTT 62.280 61.111 0.00 0.00 0.00 4.68
524 545 3.542742 GTGTCGCCGCTTCGCTAC 61.543 66.667 0.00 0.00 0.00 3.58
531 552 2.125912 CGCTTCGCTACTGCCACT 60.126 61.111 0.00 0.00 35.36 4.00
577 620 1.878953 CTCACTAGTTGCCCGTTGTT 58.121 50.000 0.00 0.00 0.00 2.83
584 627 0.878961 GTTGCCCGTTGTTCGTCTCT 60.879 55.000 0.00 0.00 37.94 3.10
586 629 0.892755 TGCCCGTTGTTCGTCTCTAT 59.107 50.000 0.00 0.00 37.94 1.98
594 637 1.400846 TGTTCGTCTCTATGCTCGGTC 59.599 52.381 0.00 0.00 0.00 4.79
613 664 2.262915 CCGCTCGTCCTCAAGCTT 59.737 61.111 0.00 0.00 36.35 3.74
615 666 2.097038 CGCTCGTCCTCAAGCTTGG 61.097 63.158 25.73 15.91 36.35 3.61
642 694 0.108898 CTCCAGTGTCCTCAAGCTCG 60.109 60.000 0.00 0.00 0.00 5.03
695 750 2.606065 GCCGCCGAACAAGTTTTACATT 60.606 45.455 0.00 0.00 0.00 2.71
741 796 5.008316 GGAGACAAGTTTTACGTCACCAAAT 59.992 40.000 0.00 0.00 39.40 2.32
743 798 7.094933 GGAGACAAGTTTTACGTCACCAAATAT 60.095 37.037 0.00 0.00 39.40 1.28
751 806 9.997482 GTTTTACGTCACCAAATATACATCATT 57.003 29.630 0.00 0.00 0.00 2.57
765 820 3.356290 ACATCATTAGTTGGAGTTGGCC 58.644 45.455 0.00 0.00 0.00 5.36
831 886 9.855021 AAATTATGCAACACCTACTTTTACATC 57.145 29.630 0.00 0.00 0.00 3.06
832 887 8.807948 ATTATGCAACACCTACTTTTACATCT 57.192 30.769 0.00 0.00 0.00 2.90
834 889 5.001232 TGCAACACCTACTTTTACATCTCC 58.999 41.667 0.00 0.00 0.00 3.71
835 890 5.001232 GCAACACCTACTTTTACATCTCCA 58.999 41.667 0.00 0.00 0.00 3.86
836 891 5.472137 GCAACACCTACTTTTACATCTCCAA 59.528 40.000 0.00 0.00 0.00 3.53
839 894 9.226606 CAACACCTACTTTTACATCTCCAAATA 57.773 33.333 0.00 0.00 0.00 1.40
923 1004 2.521991 GGGGGAAACGGAAACCCA 59.478 61.111 0.00 0.00 45.19 4.51
924 1005 1.904865 GGGGGAAACGGAAACCCAC 60.905 63.158 0.00 0.00 45.19 4.61
976 1059 2.409651 GTCGCTCGGCACTCTAGG 59.590 66.667 0.00 0.00 0.00 3.02
977 1060 3.518998 TCGCTCGGCACTCTAGGC 61.519 66.667 0.00 0.00 0.00 3.93
978 1061 3.826754 CGCTCGGCACTCTAGGCA 61.827 66.667 0.00 0.00 0.00 4.75
981 1064 1.517257 CTCGGCACTCTAGGCAACG 60.517 63.158 0.00 0.00 46.39 4.10
1065 1151 0.978146 AGAACATGGAGGACCTCGGG 60.978 60.000 15.46 9.44 37.04 5.14
1160 1246 4.716977 ACCCACTCCCCGTCCTCC 62.717 72.222 0.00 0.00 0.00 4.30
1196 1282 2.315038 CTGATCTTTCTTGCCCGCGC 62.315 60.000 0.00 0.00 0.00 6.86
1199 1285 3.499737 CTTTCTTGCCCGCGCGAT 61.500 61.111 34.63 0.00 38.08 4.58
1355 1441 0.463474 GGAGGATCTTGACAGGCTGC 60.463 60.000 15.89 8.22 33.73 5.25
1477 1563 2.349755 GCTTCGGCTGGGGTTACA 59.650 61.111 0.00 0.00 38.08 2.41
1486 1572 0.976641 CTGGGGTTACACAGCAGAGA 59.023 55.000 0.00 0.00 0.00 3.10
1543 1629 0.036765 TCCGTGGTATGTTGCTGTCC 60.037 55.000 0.00 0.00 0.00 4.02
1548 1634 0.391130 GGTATGTTGCTGTCCTCGCA 60.391 55.000 0.00 0.00 35.22 5.10
1562 1648 3.191371 GTCCTCGCAAATGTTCTTGGATT 59.809 43.478 0.00 0.00 0.00 3.01
1574 1660 3.652057 TCTTGGATTGGAGGATGTTCC 57.348 47.619 0.00 0.00 37.77 3.62
1585 1671 5.085920 TGGAGGATGTTCCATTGATTTTGT 58.914 37.500 0.00 0.00 42.24 2.83
1615 1701 6.516693 CGCAAAGGATACAGTATATGTGAGGA 60.517 42.308 0.00 0.00 43.80 3.71
1659 1745 5.516044 TCTAGTAGCCATCTACCAGAACAA 58.484 41.667 0.00 0.00 44.87 2.83
1686 1772 3.804036 TCTGGTCGTTGTCTGACATTTT 58.196 40.909 11.86 0.00 38.10 1.82
1786 1872 2.765689 TGAAAGGAGCCCTGGAAAAA 57.234 45.000 0.00 0.00 32.13 1.94
1789 1875 3.181418 TGAAAGGAGCCCTGGAAAAATCT 60.181 43.478 0.00 0.00 32.13 2.40
1816 1902 4.178956 ACTGGATGGTGGTTTTAGTGTT 57.821 40.909 0.00 0.00 0.00 3.32
1846 1932 1.202268 GCATCTGCTGGCAATGAAGTC 60.202 52.381 16.01 2.24 38.21 3.01
1966 2052 2.158957 ACGTGTTCTGTTGACACCTGAT 60.159 45.455 0.00 0.00 0.00 2.90
2110 2196 7.377398 TCGGTTTGAATTTGACAATCATGAAT 58.623 30.769 0.00 0.00 0.00 2.57
2111 2197 7.541783 TCGGTTTGAATTTGACAATCATGAATC 59.458 33.333 0.00 0.00 0.00 2.52
2140 2227 3.117888 CCGGAGATAAATCCATATGGGGG 60.118 52.174 21.78 0.00 39.53 5.40
2189 2276 4.818642 CTGTCTGTATGAGATGCATAGGG 58.181 47.826 0.00 0.00 40.04 3.53
2208 2295 7.173390 GCATAGGGAGCTAAATTAGGTGTTAAG 59.827 40.741 9.65 0.00 36.51 1.85
2260 2354 7.501559 ACTGCAATCTAGCATGATGTAGAAATT 59.498 33.333 0.00 0.00 44.68 1.82
2261 2355 8.229253 TGCAATCTAGCATGATGTAGAAATTT 57.771 30.769 0.00 0.00 40.11 1.82
2270 2364 5.975693 TGATGTAGAAATTTTGGTGGACC 57.024 39.130 0.00 0.00 0.00 4.46
2271 2365 4.770010 TGATGTAGAAATTTTGGTGGACCC 59.230 41.667 0.00 0.00 34.29 4.46
2279 2373 3.611025 TTTTGGTGGACCCTCTGAATT 57.389 42.857 0.00 0.00 34.29 2.17
2285 2379 4.010349 GGTGGACCCTCTGAATTTAGTTG 58.990 47.826 0.00 0.00 0.00 3.16
2301 2395 6.618287 TTTAGTTGGATTTCATATCCGCAG 57.382 37.500 0.00 0.00 41.03 5.18
2318 2412 6.698008 TCCGCAGAAAAATATTGACATGAT 57.302 33.333 0.00 0.00 0.00 2.45
2346 2440 9.593565 TTCTGGTGATGATTAGATACTAGACAT 57.406 33.333 0.00 0.00 30.24 3.06
2431 2525 3.817709 TCTCAATGTCATCGGCACATA 57.182 42.857 0.00 0.00 33.12 2.29
2475 2569 6.954944 TGCAAGTTGACACTGTAATTTACTC 58.045 36.000 7.16 0.00 31.60 2.59
2545 2639 5.464030 ACTTGGTCATAAAGTCGTGTACT 57.536 39.130 0.00 0.00 41.49 2.73
2579 2673 3.518303 TCTGTTAAGGAACTAGGCCTTCC 59.482 47.826 12.58 13.09 44.34 3.46
2584 2678 2.468915 AGGAACTAGGCCTTCCTGTAC 58.531 52.381 21.61 8.43 44.98 2.90
2669 2763 4.057432 CACGGAAATTTGCAGAAATTGGT 58.943 39.130 10.49 0.00 40.27 3.67
2699 2793 0.317160 TTCTTGTCATCGCACTCCGT 59.683 50.000 0.00 0.00 38.35 4.69
2998 3100 4.584327 TGCTCTTCCTTTTACTTTTGGC 57.416 40.909 0.00 0.00 0.00 4.52
3001 3103 3.236047 TCTTCCTTTTACTTTTGGCCCC 58.764 45.455 0.00 0.00 0.00 5.80
3107 3210 6.875726 TGAGAACATCACCATCTTTAGTTCTG 59.124 38.462 9.34 0.00 42.79 3.02
3273 3376 1.364901 GGCACAGCACTGCAACATT 59.635 52.632 3.30 0.00 39.08 2.71
3275 3378 1.203052 GGCACAGCACTGCAACATTAT 59.797 47.619 3.30 0.00 39.08 1.28
3276 3379 2.523015 GCACAGCACTGCAACATTATC 58.477 47.619 3.30 0.00 37.11 1.75
3288 3391 3.308866 GCAACATTATCGTACCACAGGAC 59.691 47.826 0.00 0.00 0.00 3.85
3549 3652 3.678072 TGTAACGAGCTAACTGAATGTGC 59.322 43.478 0.00 0.00 0.00 4.57
3602 3705 0.890542 GGTCACCAGAACATGCAGCA 60.891 55.000 0.00 0.00 0.00 4.41
3745 3848 4.927425 TGAAAACAGGTACGATGTAGAAGC 59.073 41.667 3.08 0.00 0.00 3.86
3764 3867 1.959042 CCACATCCCTCCGAAATCTG 58.041 55.000 0.00 0.00 0.00 2.90
3784 3887 4.661461 GCTGCAGCTGGTTTTTCC 57.339 55.556 31.33 0.00 38.21 3.13
3807 3925 6.212388 TCCTTCATGCTTCTACTTTCTTCTCT 59.788 38.462 0.00 0.00 0.00 3.10
3808 3926 6.313411 CCTTCATGCTTCTACTTTCTTCTCTG 59.687 42.308 0.00 0.00 0.00 3.35
3809 3927 6.596309 TCATGCTTCTACTTTCTTCTCTGA 57.404 37.500 0.00 0.00 0.00 3.27
4016 4135 7.065563 CCTGTCTGAGGATGTTTTAGAAGAATG 59.934 40.741 0.00 0.00 46.33 2.67
4028 4147 9.944663 TGTTTTAGAAGAATGTATGTTGTGTTC 57.055 29.630 0.00 0.00 0.00 3.18
4037 4156 3.500299 TGTATGTTGTGTTCGGGTTCATG 59.500 43.478 0.00 0.00 0.00 3.07
4181 4315 1.625315 TGACCTGCTGCATGAACTAGT 59.375 47.619 11.93 0.00 0.00 2.57
4183 4317 2.417933 GACCTGCTGCATGAACTAGTTG 59.582 50.000 14.14 0.00 0.00 3.16
4190 4324 5.010922 TGCTGCATGAACTAGTTGGAAAAAT 59.989 36.000 14.14 0.00 0.00 1.82
4193 4327 7.048629 TGCATGAACTAGTTGGAAAAATTCA 57.951 32.000 14.14 1.39 0.00 2.57
4203 4337 1.336795 GGAAAAATTCACCACCTGCCG 60.337 52.381 0.00 0.00 0.00 5.69
4204 4338 0.678950 AAAAATTCACCACCTGCCGG 59.321 50.000 0.00 0.00 0.00 6.13
4206 4340 0.469144 AAATTCACCACCTGCCGGTT 60.469 50.000 1.90 0.00 42.13 4.44
4207 4341 0.402504 AATTCACCACCTGCCGGTTA 59.597 50.000 1.90 0.00 42.13 2.85
4208 4342 0.322187 ATTCACCACCTGCCGGTTAC 60.322 55.000 1.90 0.00 42.13 2.50
4209 4343 1.697082 TTCACCACCTGCCGGTTACA 61.697 55.000 1.90 0.00 42.13 2.41
4210 4344 1.002624 CACCACCTGCCGGTTACAT 60.003 57.895 1.90 0.00 42.13 2.29
4211 4345 1.002624 ACCACCTGCCGGTTACATG 60.003 57.895 1.90 0.00 42.13 3.21
4212 4346 1.002624 CCACCTGCCGGTTACATGT 60.003 57.895 1.90 2.69 42.13 3.21
4213 4347 0.608035 CCACCTGCCGGTTACATGTT 60.608 55.000 2.30 0.00 42.13 2.71
4214 4348 0.802494 CACCTGCCGGTTACATGTTC 59.198 55.000 2.30 0.00 42.13 3.18
4215 4349 0.690762 ACCTGCCGGTTACATGTTCT 59.309 50.000 2.30 0.00 42.13 3.01
4216 4350 1.086696 CCTGCCGGTTACATGTTCTG 58.913 55.000 2.30 3.08 0.00 3.02
4217 4351 1.086696 CTGCCGGTTACATGTTCTGG 58.913 55.000 18.50 18.50 0.00 3.86
4218 4352 0.398696 TGCCGGTTACATGTTCTGGT 59.601 50.000 21.58 0.00 0.00 4.00
4219 4353 1.202830 TGCCGGTTACATGTTCTGGTT 60.203 47.619 21.58 0.00 0.00 3.67
4220 4354 1.883926 GCCGGTTACATGTTCTGGTTT 59.116 47.619 21.58 0.00 0.00 3.27
4221 4355 2.351350 GCCGGTTACATGTTCTGGTTTG 60.351 50.000 21.58 5.41 0.00 2.93
4222 4356 2.227865 CCGGTTACATGTTCTGGTTTGG 59.772 50.000 2.30 0.00 0.00 3.28
4223 4357 2.882137 CGGTTACATGTTCTGGTTTGGT 59.118 45.455 2.30 0.00 0.00 3.67
4224 4358 4.066490 CGGTTACATGTTCTGGTTTGGTA 58.934 43.478 2.30 0.00 0.00 3.25
4225 4359 4.083696 CGGTTACATGTTCTGGTTTGGTAC 60.084 45.833 2.30 0.00 0.00 3.34
4226 4360 4.083696 GGTTACATGTTCTGGTTTGGTACG 60.084 45.833 2.30 0.00 0.00 3.67
4227 4361 3.202829 ACATGTTCTGGTTTGGTACGT 57.797 42.857 0.00 0.00 0.00 3.57
4228 4362 4.339872 ACATGTTCTGGTTTGGTACGTA 57.660 40.909 0.00 0.00 0.00 3.57
4229 4363 4.901868 ACATGTTCTGGTTTGGTACGTAT 58.098 39.130 0.00 0.00 0.00 3.06
4230 4364 4.693566 ACATGTTCTGGTTTGGTACGTATG 59.306 41.667 0.00 0.00 0.00 2.39
4231 4365 4.339872 TGTTCTGGTTTGGTACGTATGT 57.660 40.909 0.00 0.00 0.00 2.29
4232 4366 4.706035 TGTTCTGGTTTGGTACGTATGTT 58.294 39.130 0.00 0.00 0.00 2.71
4233 4367 4.751098 TGTTCTGGTTTGGTACGTATGTTC 59.249 41.667 0.00 0.00 0.00 3.18
4234 4368 4.603989 TCTGGTTTGGTACGTATGTTCA 57.396 40.909 0.00 0.00 0.00 3.18
4235 4369 4.958509 TCTGGTTTGGTACGTATGTTCAA 58.041 39.130 0.00 0.00 0.00 2.69
4236 4370 5.366460 TCTGGTTTGGTACGTATGTTCAAA 58.634 37.500 0.00 5.54 31.89 2.69
4237 4371 5.998981 TCTGGTTTGGTACGTATGTTCAAAT 59.001 36.000 14.92 0.00 34.72 2.32
4238 4372 6.487331 TCTGGTTTGGTACGTATGTTCAAATT 59.513 34.615 14.92 0.00 34.72 1.82
4239 4373 7.013464 TCTGGTTTGGTACGTATGTTCAAATTT 59.987 33.333 14.92 0.00 34.72 1.82
4240 4374 7.490000 TGGTTTGGTACGTATGTTCAAATTTT 58.510 30.769 14.92 0.00 34.72 1.82
4241 4375 8.627403 TGGTTTGGTACGTATGTTCAAATTTTA 58.373 29.630 14.92 4.90 34.72 1.52
4242 4376 9.628746 GGTTTGGTACGTATGTTCAAATTTTAT 57.371 29.630 14.92 0.00 34.72 1.40
4244 4378 9.627395 TTTGGTACGTATGTTCAAATTTTATGG 57.373 29.630 0.00 0.00 30.46 2.74
4245 4379 8.338072 TGGTACGTATGTTCAAATTTTATGGT 57.662 30.769 0.00 0.00 0.00 3.55
4246 4380 8.452534 TGGTACGTATGTTCAAATTTTATGGTC 58.547 33.333 0.00 0.00 0.00 4.02
4247 4381 8.671028 GGTACGTATGTTCAAATTTTATGGTCT 58.329 33.333 0.00 0.00 0.00 3.85
4248 4382 9.485591 GTACGTATGTTCAAATTTTATGGTCTG 57.514 33.333 0.00 0.00 0.00 3.51
4249 4383 7.535139 ACGTATGTTCAAATTTTATGGTCTGG 58.465 34.615 0.00 0.00 0.00 3.86
4250 4384 7.175990 ACGTATGTTCAAATTTTATGGTCTGGT 59.824 33.333 0.00 0.00 0.00 4.00
4251 4385 8.026607 CGTATGTTCAAATTTTATGGTCTGGTT 58.973 33.333 0.00 0.00 0.00 3.67
4254 4388 7.891561 TGTTCAAATTTTATGGTCTGGTTAGG 58.108 34.615 0.00 0.00 0.00 2.69
4255 4389 7.507616 TGTTCAAATTTTATGGTCTGGTTAGGT 59.492 33.333 0.00 0.00 0.00 3.08
4256 4390 9.016438 GTTCAAATTTTATGGTCTGGTTAGGTA 57.984 33.333 0.00 0.00 0.00 3.08
4257 4391 9.762381 TTCAAATTTTATGGTCTGGTTAGGTAT 57.238 29.630 0.00 0.00 0.00 2.73
4258 4392 9.184523 TCAAATTTTATGGTCTGGTTAGGTATG 57.815 33.333 0.00 0.00 0.00 2.39
4259 4393 8.966868 CAAATTTTATGGTCTGGTTAGGTATGT 58.033 33.333 0.00 0.00 0.00 2.29
4262 4396 9.793259 ATTTTATGGTCTGGTTAGGTATGTATG 57.207 33.333 0.00 0.00 0.00 2.39
4263 4397 7.924358 TTATGGTCTGGTTAGGTATGTATGT 57.076 36.000 0.00 0.00 0.00 2.29
4264 4398 6.824958 ATGGTCTGGTTAGGTATGTATGTT 57.175 37.500 0.00 0.00 0.00 2.71
4265 4399 6.229936 TGGTCTGGTTAGGTATGTATGTTC 57.770 41.667 0.00 0.00 0.00 3.18
4266 4400 5.722441 TGGTCTGGTTAGGTATGTATGTTCA 59.278 40.000 0.00 0.00 0.00 3.18
4267 4401 6.213802 TGGTCTGGTTAGGTATGTATGTTCAA 59.786 38.462 0.00 0.00 0.00 2.69
4290 4424 9.308000 TCAAATTTTATGTACTCCATCTGGTTT 57.692 29.630 0.00 0.00 34.86 3.27
4296 4430 6.575162 ATGTACTCCATCTGGTTTTTGAAC 57.425 37.500 0.00 0.00 36.34 3.18
4308 4442 3.115554 GTTTTTGAACTGCTGATGCGTT 58.884 40.909 0.00 0.00 43.34 4.84
4408 7535 4.955925 TTACGACAATGGCCAACTATTG 57.044 40.909 10.96 12.90 39.55 1.90
4420 7547 4.870991 GGCCAACTATTGTCTAGTCTGAAC 59.129 45.833 0.00 0.00 0.00 3.18
4448 7575 0.751643 GTGTGGCACCTCTGGTTGTT 60.752 55.000 16.26 0.00 31.02 2.83
4454 7581 2.365293 GGCACCTCTGGTTGTTGAATTT 59.635 45.455 0.00 0.00 31.02 1.82
4492 7619 8.193953 TCCTATCTGAATTATGCAGTGTCATA 57.806 34.615 0.00 3.93 34.98 2.15
4493 7620 8.090831 TCCTATCTGAATTATGCAGTGTCATAC 58.909 37.037 0.00 0.00 34.98 2.39
4494 7621 7.874528 CCTATCTGAATTATGCAGTGTCATACA 59.125 37.037 0.00 3.09 34.98 2.29
4512 7660 1.535462 ACAGTCATTGCACGTAAAGGC 59.465 47.619 0.00 0.00 0.00 4.35
4513 7661 1.806542 CAGTCATTGCACGTAAAGGCT 59.193 47.619 0.00 0.00 0.00 4.58
4514 7701 2.076863 AGTCATTGCACGTAAAGGCTC 58.923 47.619 0.00 0.00 0.00 4.70
4586 8549 2.818921 TGGGCCAAGTGCAAAGATAAT 58.181 42.857 2.13 0.00 43.89 1.28
4587 8550 3.974719 TGGGCCAAGTGCAAAGATAATA 58.025 40.909 2.13 0.00 43.89 0.98
4589 8552 4.402155 TGGGCCAAGTGCAAAGATAATAAG 59.598 41.667 2.13 0.00 43.89 1.73
4590 8553 4.363138 GGCCAAGTGCAAAGATAATAAGC 58.637 43.478 0.00 0.00 43.89 3.09
4591 8554 4.142182 GGCCAAGTGCAAAGATAATAAGCA 60.142 41.667 0.00 0.00 43.89 3.91
4592 8555 5.410067 GCCAAGTGCAAAGATAATAAGCAA 58.590 37.500 0.00 0.00 40.77 3.91
4593 8556 5.868801 GCCAAGTGCAAAGATAATAAGCAAA 59.131 36.000 0.00 0.00 40.77 3.68
4594 8557 6.183360 GCCAAGTGCAAAGATAATAAGCAAAC 60.183 38.462 0.00 0.00 40.77 2.93
4596 8559 7.062605 CCAAGTGCAAAGATAATAAGCAAACAG 59.937 37.037 0.00 0.00 36.91 3.16
4597 8560 7.452880 AGTGCAAAGATAATAAGCAAACAGA 57.547 32.000 0.00 0.00 36.91 3.41
4598 8561 7.885297 AGTGCAAAGATAATAAGCAAACAGAA 58.115 30.769 0.00 0.00 36.91 3.02
4599 8562 8.526147 AGTGCAAAGATAATAAGCAAACAGAAT 58.474 29.630 0.00 0.00 36.91 2.40
4600 8563 8.589629 GTGCAAAGATAATAAGCAAACAGAATG 58.410 33.333 0.00 0.00 38.58 2.67
4691 8654 5.655488 AGTTGTCGAGATATCCAAGAGTTG 58.345 41.667 0.00 0.00 0.00 3.16
4732 8696 1.725641 TTCGACAGCATTGCTACCAG 58.274 50.000 11.55 1.24 36.40 4.00
4883 8847 1.597663 CTACAAGCCCGGCGAAATAAG 59.402 52.381 9.30 0.00 0.00 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 5.163364 TGTTTGGTTACATGCACCATCTTTT 60.163 36.000 16.26 0.00 44.05 2.27
13 14 3.574614 GTGTTTGGTTACATGCACCATC 58.425 45.455 16.26 13.05 44.05 3.51
22 23 0.395311 TTGGGGCGTGTTTGGTTACA 60.395 50.000 0.00 0.00 0.00 2.41
72 73 3.006940 GCCACCAATAGTTGAATGACGA 58.993 45.455 0.00 0.00 0.00 4.20
89 90 2.034124 AGCAACCATATCATTGGCCAC 58.966 47.619 3.88 0.00 40.68 5.01
101 108 7.550551 CGACCATCATAATAATAGAGCAACCAT 59.449 37.037 0.00 0.00 0.00 3.55
138 145 9.789759 TGTTCGAACAGAATGGAAGACCAGAAT 62.790 40.741 26.53 0.00 43.62 2.40
150 157 4.084589 TGACGATGTTGTTCGAACAGAATG 60.085 41.667 28.21 20.16 41.62 2.67
204 211 8.233190 GTGTTTTGAGATCTTGGAGATGTAAAG 58.767 37.037 0.00 0.00 34.53 1.85
219 226 3.897239 TGTTGGAGGTGTGTTTTGAGAT 58.103 40.909 0.00 0.00 0.00 2.75
221 228 4.448537 TTTGTTGGAGGTGTGTTTTGAG 57.551 40.909 0.00 0.00 0.00 3.02
223 230 4.566360 GTCATTTGTTGGAGGTGTGTTTTG 59.434 41.667 0.00 0.00 0.00 2.44
303 310 6.223120 GGTTGAAGGTGTAAATTTGCATCTT 58.777 36.000 28.11 28.11 45.03 2.40
322 329 1.066430 GGTTACATCTCCAGCGGTTGA 60.066 52.381 0.00 0.00 0.00 3.18
326 333 0.179073 CCAGGTTACATCTCCAGCGG 60.179 60.000 0.00 0.00 0.00 5.52
330 337 2.195727 TGCATCCAGGTTACATCTCCA 58.804 47.619 0.00 0.00 0.00 3.86
343 350 0.313672 GGCTTGTCGTTTTGCATCCA 59.686 50.000 0.00 0.00 0.00 3.41
344 351 0.729140 CGGCTTGTCGTTTTGCATCC 60.729 55.000 0.00 0.00 0.00 3.51
375 382 1.893137 AGGGGAAATTTCAAAGCGGTC 59.107 47.619 19.49 0.00 0.00 4.79
399 406 3.379445 GGCGTCCAGTCGAGGGAA 61.379 66.667 7.30 0.00 35.88 3.97
401 408 3.827898 GAGGCGTCCAGTCGAGGG 61.828 72.222 0.00 0.00 0.00 4.30
418 425 4.227134 CAGGGTGCGGATCGAGGG 62.227 72.222 0.00 0.00 0.00 4.30
502 523 3.470567 GAAGCGGCGACACGACAG 61.471 66.667 12.98 0.00 32.52 3.51
518 539 4.129737 GCGGAGTGGCAGTAGCGA 62.130 66.667 0.00 0.00 43.41 4.93
546 589 2.088423 ACTAGTGAGCTTGGAGACGAG 58.912 52.381 0.00 0.00 45.38 4.18
577 620 1.773054 GCGACCGAGCATAGAGACGA 61.773 60.000 0.00 0.00 37.05 4.20
621 672 0.472734 AGCTTGAGGACACTGGAGGT 60.473 55.000 0.00 0.00 0.00 3.85
624 675 1.536073 CCGAGCTTGAGGACACTGGA 61.536 60.000 1.22 0.00 0.00 3.86
626 677 1.739562 GCCGAGCTTGAGGACACTG 60.740 63.158 1.22 0.00 0.00 3.66
627 678 2.659610 GCCGAGCTTGAGGACACT 59.340 61.111 1.22 0.00 0.00 3.55
628 679 2.435059 GGCCGAGCTTGAGGACAC 60.435 66.667 1.22 0.00 35.06 3.67
629 680 4.069232 CGGCCGAGCTTGAGGACA 62.069 66.667 24.07 0.00 34.45 4.02
671 726 1.240256 AAAACTTGTTCGGCGGCATA 58.760 45.000 10.53 0.00 0.00 3.14
719 774 7.739498 ATATTTGGTGACGTAAAACTTGTCT 57.261 32.000 0.00 0.00 33.81 3.41
732 787 9.337396 TCCAACTAATGATGTATATTTGGTGAC 57.663 33.333 0.00 0.00 32.25 3.67
733 788 9.559732 CTCCAACTAATGATGTATATTTGGTGA 57.440 33.333 0.00 0.00 32.25 4.02
741 796 6.296026 GGCCAACTCCAACTAATGATGTATA 58.704 40.000 0.00 0.00 0.00 1.47
743 798 4.523083 GGCCAACTCCAACTAATGATGTA 58.477 43.478 0.00 0.00 0.00 2.29
751 806 3.322191 AAAAAGGGCCAACTCCAACTA 57.678 42.857 6.18 0.00 0.00 2.24
752 807 2.174685 AAAAAGGGCCAACTCCAACT 57.825 45.000 6.18 0.00 0.00 3.16
773 828 8.749354 ACCAGAAAGTGAGTTTTTACATCTTTT 58.251 29.630 0.00 0.00 0.00 2.27
774 829 8.190784 CACCAGAAAGTGAGTTTTTACATCTTT 58.809 33.333 0.00 0.00 40.34 2.52
775 830 7.556275 TCACCAGAAAGTGAGTTTTTACATCTT 59.444 33.333 0.00 0.00 41.78 2.40
789 844 7.537715 TGCATAATTTACATCACCAGAAAGTG 58.462 34.615 0.00 0.00 39.20 3.16
790 845 7.701539 TGCATAATTTACATCACCAGAAAGT 57.298 32.000 0.00 0.00 0.00 2.66
791 846 8.028354 TGTTGCATAATTTACATCACCAGAAAG 58.972 33.333 0.00 0.00 0.00 2.62
798 853 7.985476 AGTAGGTGTTGCATAATTTACATCAC 58.015 34.615 0.43 0.00 34.68 3.06
821 876 9.449719 AGAACGATTATTTGGAGATGTAAAAGT 57.550 29.630 0.00 0.00 0.00 2.66
822 877 9.708222 CAGAACGATTATTTGGAGATGTAAAAG 57.292 33.333 0.00 0.00 0.00 2.27
831 886 6.024049 GCTCAAACAGAACGATTATTTGGAG 58.976 40.000 0.00 0.00 32.36 3.86
832 887 5.471797 TGCTCAAACAGAACGATTATTTGGA 59.528 36.000 0.00 0.00 32.36 3.53
834 889 6.193410 CGATGCTCAAACAGAACGATTATTTG 59.807 38.462 0.00 0.00 0.00 2.32
835 890 6.128282 ACGATGCTCAAACAGAACGATTATTT 60.128 34.615 0.00 0.00 0.00 1.40
836 891 5.351465 ACGATGCTCAAACAGAACGATTATT 59.649 36.000 0.00 0.00 0.00 1.40
839 894 3.067106 ACGATGCTCAAACAGAACGATT 58.933 40.909 0.00 0.00 0.00 3.34
923 1004 0.476611 AGAAGGGGAGAAGGCTTGGT 60.477 55.000 3.46 0.00 0.00 3.67
924 1005 0.701147 AAGAAGGGGAGAAGGCTTGG 59.299 55.000 3.46 0.00 0.00 3.61
971 1054 0.669318 CCGCTTGTTCGTTGCCTAGA 60.669 55.000 0.00 0.00 0.00 2.43
976 1059 4.700365 GCCCCGCTTGTTCGTTGC 62.700 66.667 0.00 0.00 0.00 4.17
977 1060 2.731587 CTTGCCCCGCTTGTTCGTTG 62.732 60.000 0.00 0.00 0.00 4.10
978 1061 2.517402 TTGCCCCGCTTGTTCGTT 60.517 55.556 0.00 0.00 0.00 3.85
981 1064 1.285950 GTTCTTGCCCCGCTTGTTC 59.714 57.895 0.00 0.00 0.00 3.18
1065 1151 4.222847 GCCTCGTCGGGGTCCATC 62.223 72.222 13.92 0.00 0.00 3.51
1160 1246 0.469070 CAGAGATCTGAAGCCCTGGG 59.531 60.000 8.86 8.86 46.59 4.45
1199 1285 4.980805 GTTCAGCCCACCGCGTGA 62.981 66.667 4.92 0.00 44.76 4.35
1210 1296 2.435059 GGTGGCGAGAGGTTCAGC 60.435 66.667 0.00 0.00 0.00 4.26
1355 1441 1.982223 CAACTCGTCGAGCAAAGAGAG 59.018 52.381 22.00 0.00 34.98 3.20
1481 1567 1.018226 CCCGAAGCAAGCAGTCTCTG 61.018 60.000 0.00 0.00 34.12 3.35
1484 1570 2.359230 GCCCGAAGCAAGCAGTCT 60.359 61.111 0.00 0.00 42.97 3.24
1543 1629 3.191162 TCCAATCCAAGAACATTTGCGAG 59.809 43.478 0.00 0.00 0.00 5.03
1548 1634 5.336102 ACATCCTCCAATCCAAGAACATTT 58.664 37.500 0.00 0.00 0.00 2.32
1574 1660 4.084433 CCTTTGCGGAACACAAAATCAATG 60.084 41.667 0.00 0.00 39.98 2.82
1585 1671 8.375455 CACATATACTGTATCCTTTGCGGAACA 61.375 40.741 3.09 0.00 40.06 3.18
1621 1707 7.671302 TGGCTACTAGATCATATGGAGAAAAC 58.329 38.462 2.13 0.00 0.00 2.43
1639 1725 3.838317 TGTTGTTCTGGTAGATGGCTACT 59.162 43.478 0.00 0.00 45.10 2.57
1640 1726 4.202245 TGTTGTTCTGGTAGATGGCTAC 57.798 45.455 0.00 0.00 45.04 3.58
1659 1745 2.628178 TCAGACAACGACCAGAGAATGT 59.372 45.455 0.00 0.00 0.00 2.71
1686 1772 2.573009 TCTGCAGATTGAGTTCATCCCA 59.427 45.455 13.74 0.00 0.00 4.37
1745 1831 8.592529 TTCAAGATATCCATGACAATTTTGGA 57.407 30.769 8.02 0.00 43.37 3.53
1786 1872 6.770286 AAACCACCATCCAGTATATCAGAT 57.230 37.500 0.00 0.00 0.00 2.90
1789 1875 7.092623 ACACTAAAACCACCATCCAGTATATCA 60.093 37.037 0.00 0.00 0.00 2.15
1816 1902 3.364441 GCAGATGCCGTTGCCACA 61.364 61.111 0.00 0.00 36.33 4.17
1966 2052 0.981183 AAGCCACCACTCGGTTATCA 59.019 50.000 0.00 0.00 46.31 2.15
2110 2196 5.943349 TGGATTTATCTCCGGTAAACTGA 57.057 39.130 0.00 0.00 38.21 3.41
2111 2197 7.334421 CCATATGGATTTATCTCCGGTAAACTG 59.666 40.741 17.49 0.00 38.21 3.16
2260 2354 3.611025 AAATTCAGAGGGTCCACCAAA 57.389 42.857 0.00 0.00 43.89 3.28
2261 2355 3.655777 ACTAAATTCAGAGGGTCCACCAA 59.344 43.478 0.00 0.00 43.89 3.67
2279 2373 5.924356 TCTGCGGATATGAAATCCAACTAA 58.076 37.500 4.98 0.00 38.08 2.24
2285 2379 9.132521 CAATATTTTTCTGCGGATATGAAATCC 57.867 33.333 0.00 0.00 34.90 3.01
2301 2395 9.512435 CACCAGAAGATCATGTCAATATTTTTC 57.488 33.333 0.00 0.00 0.00 2.29
2318 2412 9.290988 GTCTAGTATCTAATCATCACCAGAAGA 57.709 37.037 0.00 0.00 0.00 2.87
2396 2490 4.763793 ACATTGAGAAACCAGGATGTTCAG 59.236 41.667 0.00 0.00 0.00 3.02
2404 2498 2.679837 CCGATGACATTGAGAAACCAGG 59.320 50.000 4.07 0.00 0.00 4.45
2568 2662 2.226962 TTCGTACAGGAAGGCCTAGT 57.773 50.000 5.16 5.42 44.80 2.57
2569 2663 2.693591 TCATTCGTACAGGAAGGCCTAG 59.306 50.000 5.16 0.00 44.80 3.02
2579 2673 4.935205 TGGATCCAAACTTCATTCGTACAG 59.065 41.667 13.46 0.00 0.00 2.74
2584 2678 5.412594 TCTCTTTGGATCCAAACTTCATTCG 59.587 40.000 31.75 20.49 40.51 3.34
2669 2763 2.595124 TGACAAGAACTTCTGCGACA 57.405 45.000 0.00 0.00 0.00 4.35
2817 2911 7.118496 ACAGTGGAAATTCAAACCATAACAA 57.882 32.000 0.00 0.00 36.09 2.83
2829 2923 3.935828 GAGCCTCACTACAGTGGAAATTC 59.064 47.826 9.41 0.00 45.65 2.17
2837 2938 4.373156 AAAAATGGAGCCTCACTACAGT 57.627 40.909 0.00 0.00 44.60 3.55
2914 3015 2.237643 TGCTTAGTTGCCTGCAATTCA 58.762 42.857 7.94 0.00 38.28 2.57
2931 3032 5.909621 ACATCAAGCTTTTCATGTATGCT 57.090 34.783 11.94 0.00 35.30 3.79
2932 3033 6.094719 TGAACATCAAGCTTTTCATGTATGC 58.905 36.000 13.37 8.55 0.00 3.14
2933 3034 9.791820 TTATGAACATCAAGCTTTTCATGTATG 57.208 29.630 24.60 11.38 38.75 2.39
2998 3100 6.152154 AGGAAATAAGTTTTTGATACACGGGG 59.848 38.462 0.00 0.00 0.00 5.73
3273 3376 1.567649 AGGGAGTCCTGTGGTACGATA 59.432 52.381 9.58 0.00 42.98 2.92
3275 3378 0.113776 AAGGGAGTCCTGTGGTACGA 59.886 55.000 9.58 0.00 44.07 3.43
3276 3379 0.531200 GAAGGGAGTCCTGTGGTACG 59.469 60.000 9.58 0.00 44.07 3.67
3288 3391 7.510549 TTGTTCTCATACAAAAAGAAGGGAG 57.489 36.000 0.00 0.00 35.22 4.30
3549 3652 4.433615 ACTTGCACGATAGACATTACCTG 58.566 43.478 0.00 0.00 41.38 4.00
3602 3705 4.778415 CCTAGCGCGACTGCACGT 62.778 66.667 12.10 0.00 42.97 4.49
3641 3744 3.161866 GGAGGGGAACTTTTGCATTGTA 58.838 45.455 0.00 0.00 0.00 2.41
3745 3848 1.959042 CAGATTTCGGAGGGATGTGG 58.041 55.000 0.00 0.00 0.00 4.17
3783 3886 6.313411 CAGAGAAGAAAGTAGAAGCATGAAGG 59.687 42.308 0.00 0.00 0.00 3.46
3784 3887 7.095910 TCAGAGAAGAAAGTAGAAGCATGAAG 58.904 38.462 0.00 0.00 0.00 3.02
3807 3925 3.731264 CGGTGGTAAAAACAAGCGTTTCA 60.731 43.478 0.00 0.00 44.65 2.69
3808 3926 2.784928 CGGTGGTAAAAACAAGCGTTTC 59.215 45.455 0.00 0.00 44.65 2.78
3960 4079 2.029623 CACACGGTAGGCTATGTAGGT 58.970 52.381 0.00 0.00 0.00 3.08
3961 4080 2.029623 ACACACGGTAGGCTATGTAGG 58.970 52.381 0.00 0.00 0.00 3.18
3962 4081 4.906065 TTACACACGGTAGGCTATGTAG 57.094 45.455 0.00 0.00 32.49 2.74
3963 4082 4.706476 ACTTTACACACGGTAGGCTATGTA 59.294 41.667 0.00 0.00 32.49 2.29
3964 4083 3.512724 ACTTTACACACGGTAGGCTATGT 59.487 43.478 0.00 0.00 32.49 2.29
3965 4084 4.119442 ACTTTACACACGGTAGGCTATG 57.881 45.455 0.00 0.00 32.49 2.23
4016 4135 3.119990 CCATGAACCCGAACACAACATAC 60.120 47.826 0.00 0.00 0.00 2.39
4028 4147 2.046285 GCCCAGTTCCATGAACCCG 61.046 63.158 0.00 0.00 42.85 5.28
4159 4293 0.109153 AGTTCATGCAGCAGGTCACA 59.891 50.000 6.99 0.00 0.00 3.58
4181 4315 2.103941 GGCAGGTGGTGAATTTTTCCAA 59.896 45.455 0.00 0.00 32.82 3.53
4183 4317 1.336795 CGGCAGGTGGTGAATTTTTCC 60.337 52.381 0.00 0.00 0.00 3.13
4203 4337 4.083696 CGTACCAAACCAGAACATGTAACC 60.084 45.833 0.00 0.00 0.00 2.85
4204 4338 4.512571 ACGTACCAAACCAGAACATGTAAC 59.487 41.667 0.00 0.00 0.00 2.50
4205 4339 4.706035 ACGTACCAAACCAGAACATGTAA 58.294 39.130 0.00 0.00 0.00 2.41
4206 4340 4.339872 ACGTACCAAACCAGAACATGTA 57.660 40.909 0.00 0.00 0.00 2.29
4207 4341 3.202829 ACGTACCAAACCAGAACATGT 57.797 42.857 0.00 0.00 0.00 3.21
4208 4342 4.693566 ACATACGTACCAAACCAGAACATG 59.306 41.667 0.00 0.00 0.00 3.21
4209 4343 4.901868 ACATACGTACCAAACCAGAACAT 58.098 39.130 0.00 0.00 0.00 2.71
4210 4344 4.339872 ACATACGTACCAAACCAGAACA 57.660 40.909 0.00 0.00 0.00 3.18
4211 4345 4.751098 TGAACATACGTACCAAACCAGAAC 59.249 41.667 0.00 0.00 0.00 3.01
4212 4346 4.958509 TGAACATACGTACCAAACCAGAA 58.041 39.130 0.00 0.00 0.00 3.02
4213 4347 4.603989 TGAACATACGTACCAAACCAGA 57.396 40.909 0.00 0.00 0.00 3.86
4214 4348 5.676532 TTTGAACATACGTACCAAACCAG 57.323 39.130 0.00 0.00 0.00 4.00
4215 4349 6.636562 AATTTGAACATACGTACCAAACCA 57.363 33.333 0.00 0.00 33.46 3.67
4216 4350 7.933728 AAAATTTGAACATACGTACCAAACC 57.066 32.000 0.00 0.00 33.46 3.27
4218 4352 9.627395 CCATAAAATTTGAACATACGTACCAAA 57.373 29.630 0.00 7.03 34.44 3.28
4219 4353 8.794553 ACCATAAAATTTGAACATACGTACCAA 58.205 29.630 0.00 0.00 0.00 3.67
4220 4354 8.338072 ACCATAAAATTTGAACATACGTACCA 57.662 30.769 0.00 0.00 0.00 3.25
4221 4355 8.671028 AGACCATAAAATTTGAACATACGTACC 58.329 33.333 0.00 0.00 0.00 3.34
4222 4356 9.485591 CAGACCATAAAATTTGAACATACGTAC 57.514 33.333 0.00 0.00 0.00 3.67
4223 4357 8.670135 CCAGACCATAAAATTTGAACATACGTA 58.330 33.333 0.00 0.00 0.00 3.57
4224 4358 7.175990 ACCAGACCATAAAATTTGAACATACGT 59.824 33.333 0.00 0.00 0.00 3.57
4225 4359 7.535139 ACCAGACCATAAAATTTGAACATACG 58.465 34.615 0.00 0.00 0.00 3.06
4228 4362 8.531146 CCTAACCAGACCATAAAATTTGAACAT 58.469 33.333 0.00 0.00 0.00 2.71
4229 4363 7.507616 ACCTAACCAGACCATAAAATTTGAACA 59.492 33.333 0.00 0.00 0.00 3.18
4230 4364 7.892609 ACCTAACCAGACCATAAAATTTGAAC 58.107 34.615 0.00 0.00 0.00 3.18
4231 4365 9.762381 ATACCTAACCAGACCATAAAATTTGAA 57.238 29.630 0.00 0.00 0.00 2.69
4232 4366 9.184523 CATACCTAACCAGACCATAAAATTTGA 57.815 33.333 0.00 0.00 0.00 2.69
4233 4367 8.966868 ACATACCTAACCAGACCATAAAATTTG 58.033 33.333 0.00 0.00 0.00 2.32
4236 4370 9.793259 CATACATACCTAACCAGACCATAAAAT 57.207 33.333 0.00 0.00 0.00 1.82
4237 4371 8.774183 ACATACATACCTAACCAGACCATAAAA 58.226 33.333 0.00 0.00 0.00 1.52
4238 4372 8.326765 ACATACATACCTAACCAGACCATAAA 57.673 34.615 0.00 0.00 0.00 1.40
4239 4373 7.924358 ACATACATACCTAACCAGACCATAA 57.076 36.000 0.00 0.00 0.00 1.90
4240 4374 7.565768 TGAACATACATACCTAACCAGACCATA 59.434 37.037 0.00 0.00 0.00 2.74
4241 4375 6.385759 TGAACATACATACCTAACCAGACCAT 59.614 38.462 0.00 0.00 0.00 3.55
4242 4376 5.722441 TGAACATACATACCTAACCAGACCA 59.278 40.000 0.00 0.00 0.00 4.02
4243 4377 6.229936 TGAACATACATACCTAACCAGACC 57.770 41.667 0.00 0.00 0.00 3.85
4244 4378 8.732746 ATTTGAACATACATACCTAACCAGAC 57.267 34.615 0.00 0.00 0.00 3.51
4245 4379 9.747898 AAATTTGAACATACATACCTAACCAGA 57.252 29.630 0.00 0.00 0.00 3.86
4261 4395 8.739039 CCAGATGGAGTACATAAAATTTGAACA 58.261 33.333 0.00 0.00 40.72 3.18
4262 4396 8.739972 ACCAGATGGAGTACATAAAATTTGAAC 58.260 33.333 5.72 0.00 40.72 3.18
4263 4397 8.877864 ACCAGATGGAGTACATAAAATTTGAA 57.122 30.769 5.72 0.00 40.72 2.69
4264 4398 8.877864 AACCAGATGGAGTACATAAAATTTGA 57.122 30.769 5.72 0.00 40.72 2.69
4265 4399 9.927668 AAAACCAGATGGAGTACATAAAATTTG 57.072 29.630 5.72 0.00 40.72 2.32
4267 4401 9.927668 CAAAAACCAGATGGAGTACATAAAATT 57.072 29.630 5.72 0.00 40.72 1.82
4285 4419 2.543445 CGCATCAGCAGTTCAAAAACCA 60.543 45.455 0.00 0.00 42.27 3.67
4290 4424 1.600164 GCAACGCATCAGCAGTTCAAA 60.600 47.619 0.00 0.00 42.27 2.69
4308 4442 5.445069 ACAAGTTAGTTATGCCCATATGCA 58.555 37.500 0.00 0.00 46.94 3.96
4408 7535 2.094649 CCGTTCAGGGTTCAGACTAGAC 60.095 54.545 0.00 0.00 35.97 2.59
4420 7547 2.978010 GTGCCACACCGTTCAGGG 60.978 66.667 0.00 0.00 46.96 4.45
4448 7575 7.830697 AGATAGGAATGACACATGACAAATTCA 59.169 33.333 0.00 0.00 39.11 2.57
4454 7581 5.937975 TCAGATAGGAATGACACATGACA 57.062 39.130 0.00 0.00 0.00 3.58
4492 7619 1.535462 GCCTTTACGTGCAATGACTGT 59.465 47.619 0.00 0.00 0.00 3.55
4493 7620 1.806542 AGCCTTTACGTGCAATGACTG 59.193 47.619 0.00 0.00 0.00 3.51
4494 7621 2.076863 GAGCCTTTACGTGCAATGACT 58.923 47.619 0.00 0.00 0.00 3.41
4512 7660 0.606401 ACCCAGTTGAATGGTGCGAG 60.606 55.000 0.00 0.00 38.81 5.03
4513 7661 0.888736 CACCCAGTTGAATGGTGCGA 60.889 55.000 0.00 0.00 42.71 5.10
4514 7701 1.580942 CACCCAGTTGAATGGTGCG 59.419 57.895 0.00 0.00 42.71 5.34
4586 8549 8.001881 TGTCCTTTTTACATTCTGTTTGCTTA 57.998 30.769 0.00 0.00 0.00 3.09
4587 8550 6.872920 TGTCCTTTTTACATTCTGTTTGCTT 58.127 32.000 0.00 0.00 0.00 3.91
4589 8552 6.701400 ACATGTCCTTTTTACATTCTGTTTGC 59.299 34.615 0.00 0.00 35.39 3.68
4590 8553 7.920151 TGACATGTCCTTTTTACATTCTGTTTG 59.080 33.333 22.85 0.00 35.39 2.93
4591 8554 8.006298 TGACATGTCCTTTTTACATTCTGTTT 57.994 30.769 22.85 0.00 35.39 2.83
4592 8555 7.581213 TGACATGTCCTTTTTACATTCTGTT 57.419 32.000 22.85 0.00 35.39 3.16
4593 8556 7.231317 ACATGACATGTCCTTTTTACATTCTGT 59.769 33.333 22.85 1.77 39.92 3.41
4594 8557 7.596494 ACATGACATGTCCTTTTTACATTCTG 58.404 34.615 22.85 1.18 39.92 3.02
4596 8559 7.867403 ACAACATGACATGTCCTTTTTACATTC 59.133 33.333 22.85 0.00 44.07 2.67
4597 8560 7.725251 ACAACATGACATGTCCTTTTTACATT 58.275 30.769 22.85 0.00 44.07 2.71
4598 8561 7.288810 ACAACATGACATGTCCTTTTTACAT 57.711 32.000 22.85 5.03 44.07 2.29
4599 8562 6.512578 CGACAACATGACATGTCCTTTTTACA 60.513 38.462 22.85 2.63 44.07 2.41
4600 8563 5.851177 CGACAACATGACATGTCCTTTTTAC 59.149 40.000 22.85 8.99 44.07 2.01
4601 8564 5.760743 TCGACAACATGACATGTCCTTTTTA 59.239 36.000 22.85 3.48 44.07 1.52
4602 8565 4.578516 TCGACAACATGACATGTCCTTTTT 59.421 37.500 22.85 8.14 44.07 1.94
4607 8570 2.412870 TGTCGACAACATGACATGTCC 58.587 47.619 22.85 12.22 44.07 4.02
4732 8696 8.718734 CCTGAACCTTTTGTGTTAGTATAGAAC 58.281 37.037 0.00 0.00 0.00 3.01
4841 8805 8.289618 TGTAGTTTGTCTATGCATTTTGACTTC 58.710 33.333 20.16 13.43 0.00 3.01
4883 8847 6.905544 GGTTATTCTTAGAACCTACTGCAC 57.094 41.667 0.00 0.00 41.45 4.57


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

AutoCloner maintained by Alex Coulton.