Multiple sequence alignment - TraesCS4B01G109800

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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 TraesCS4B01G109800 chr4B 100.000 5389 0 0 1 5389 122519521 122524909 0.000000e+00 9952.0
1 TraesCS4B01G109800 chr4D 92.327 3219 143 44 2103 5286 85580347 85583496 0.000000e+00 4481.0
2 TraesCS4B01G109800 chr4D 92.807 2141 98 35 1 2108 85578197 85580314 0.000000e+00 3049.0
3 TraesCS4B01G109800 chr4A 92.693 3038 124 41 2103 5092 499342670 499345657 0.000000e+00 4290.0
4 TraesCS4B01G109800 chr4A 92.767 2129 92 31 1 2108 499340550 499342637 0.000000e+00 3022.0
5 TraesCS4B01G109800 chr4A 79.167 384 74 6 1220 1600 466926167 466926547 1.490000e-65 261.0
6 TraesCS4B01G109800 chr4A 84.615 247 21 10 5146 5384 499345655 499345892 4.200000e-56 230.0
7 TraesCS4B01G109800 chr5D 90.625 544 47 2 1067 1606 177684261 177683718 0.000000e+00 719.0
8 TraesCS4B01G109800 chr5D 80.460 87 17 0 2843 2929 184874224 184874310 3.480000e-07 67.6
9 TraesCS4B01G109800 chr5A 90.257 544 49 2 1067 1606 191036298 191036841 0.000000e+00 708.0
10 TraesCS4B01G109800 chr5B 90.074 544 50 2 1067 1606 192383290 192382747 0.000000e+00 702.0
11 TraesCS4B01G109800 chr2D 79.839 496 86 11 1118 1606 564095494 564095006 3.090000e-92 350.0
12 TraesCS4B01G109800 chr2B 79.798 495 88 9 1118 1606 675356180 675355692 3.090000e-92 350.0
13 TraesCS4B01G109800 chr2A 79.234 496 89 11 1118 1606 704776749 704776261 3.110000e-87 333.0
14 TraesCS4B01G109800 chr6D 77.108 415 83 11 1133 1541 344207897 344208305 4.200000e-56 230.0
15 TraesCS4B01G109800 chr6B 76.627 415 85 11 1133 1541 519720425 519720833 9.090000e-53 219.0
16 TraesCS4B01G109800 chr7B 94.737 76 1 3 1186 1261 427834203 427834131 1.230000e-21 115.0
17 TraesCS4B01G109800 chr7B 98.039 51 0 1 1186 1236 14742759 14742808 2.670000e-13 87.9
18 TraesCS4B01G109800 chr7B 85.542 83 8 3 1186 1265 621800196 621800115 3.460000e-12 84.2


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 TraesCS4B01G109800 chr4B 122519521 122524909 5388 False 9952 9952 100.000 1 5389 1 chr4B.!!$F1 5388
1 TraesCS4B01G109800 chr4D 85578197 85583496 5299 False 3765 4481 92.567 1 5286 2 chr4D.!!$F1 5285
2 TraesCS4B01G109800 chr4A 499340550 499345892 5342 False 2514 4290 90.025 1 5384 3 chr4A.!!$F2 5383
3 TraesCS4B01G109800 chr5D 177683718 177684261 543 True 719 719 90.625 1067 1606 1 chr5D.!!$R1 539
4 TraesCS4B01G109800 chr5A 191036298 191036841 543 False 708 708 90.257 1067 1606 1 chr5A.!!$F1 539
5 TraesCS4B01G109800 chr5B 192382747 192383290 543 True 702 702 90.074 1067 1606 1 chr5B.!!$R1 539

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
433 467 0.033090 GATTACCATCGTCCCCGTCC 59.967 60.000 0.00 0.00 35.01 4.79 F
771 815 0.388649 CTCGTCGACAGGGTTGGAAG 60.389 60.000 17.16 0.00 0.00 3.46 F
1971 2022 0.318441 GAAACCTTGAAGGCTTGCCC 59.682 55.000 11.96 0.00 39.63 5.36 F
2730 2821 1.001406 CACCTCCTCCTTGTCACTCAC 59.999 57.143 0.00 0.00 0.00 3.51 F
4090 4195 0.107508 AGCTATCACAAGCATGCCGT 60.108 50.000 15.66 9.54 45.30 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1953 2004 0.398381 TGGGCAAGCCTTCAAGGTTT 60.398 50.000 11.40 1.65 39.54 3.27 R
2701 2792 1.270907 AGGAGGAGGTGCACTTACAG 58.729 55.000 17.98 0.00 0.00 2.74 R
2837 2928 1.153369 GCTTATCAGGCGCCACAGA 60.153 57.895 31.54 23.21 0.00 3.41 R
4181 4286 0.478072 TGTATGCATGGGGATGGGAC 59.522 55.000 10.16 0.00 0.00 4.46 R
4904 5018 0.310854 CAAACTCCCAAGGACAACGC 59.689 55.000 0.00 0.00 0.00 4.84 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
18 19 3.294079 ACAACCGATTCGACCGTTT 57.706 47.368 7.83 0.00 0.00 3.60
44 46 2.034939 CGGGTTTGGTTAGGGTTTGTTC 59.965 50.000 0.00 0.00 0.00 3.18
60 62 6.650390 GGGTTTGTTCTAAGGTTCGTGTTATA 59.350 38.462 0.00 0.00 0.00 0.98
61 63 7.360353 GGGTTTGTTCTAAGGTTCGTGTTATAC 60.360 40.741 0.00 0.00 0.00 1.47
65 67 5.002464 TCTAAGGTTCGTGTTATACAGGC 57.998 43.478 0.00 0.00 34.28 4.85
108 110 0.599060 AACGGGCCATTTTTACACCG 59.401 50.000 4.39 0.00 46.16 4.94
132 134 3.285215 CCTGATCGGGCTGCATGC 61.285 66.667 11.82 11.82 41.94 4.06
133 135 2.203167 CTGATCGGGCTGCATGCT 60.203 61.111 20.33 0.00 42.39 3.79
143 145 1.368209 CTGCATGCTGGCAACCAAA 59.632 52.632 20.33 0.00 44.40 3.28
148 150 0.104671 ATGCTGGCAACCAAACACAC 59.895 50.000 0.00 0.00 30.80 3.82
154 156 1.967779 GGCAACCAAACACACCCTTAT 59.032 47.619 0.00 0.00 0.00 1.73
155 157 2.029380 GGCAACCAAACACACCCTTATC 60.029 50.000 0.00 0.00 0.00 1.75
156 158 2.890945 GCAACCAAACACACCCTTATCT 59.109 45.455 0.00 0.00 0.00 1.98
157 159 3.305335 GCAACCAAACACACCCTTATCTG 60.305 47.826 0.00 0.00 0.00 2.90
159 161 4.657814 ACCAAACACACCCTTATCTGAT 57.342 40.909 0.00 0.00 0.00 2.90
160 162 4.998051 ACCAAACACACCCTTATCTGATT 58.002 39.130 0.00 0.00 0.00 2.57
161 163 4.766891 ACCAAACACACCCTTATCTGATTG 59.233 41.667 0.00 0.00 0.00 2.67
162 164 5.009631 CCAAACACACCCTTATCTGATTGA 58.990 41.667 0.00 0.00 0.00 2.57
163 165 5.124457 CCAAACACACCCTTATCTGATTGAG 59.876 44.000 0.00 0.00 0.00 3.02
164 166 5.505181 AACACACCCTTATCTGATTGAGT 57.495 39.130 0.00 0.00 0.00 3.41
167 187 7.016153 ACACACCCTTATCTGATTGAGTAAA 57.984 36.000 0.00 0.00 0.00 2.01
170 190 8.960591 CACACCCTTATCTGATTGAGTAAAATT 58.039 33.333 0.00 0.00 0.00 1.82
174 194 9.359653 CCCTTATCTGATTGAGTAAAATTGGAT 57.640 33.333 0.00 0.00 0.00 3.41
182 202 9.177608 TGATTGAGTAAAATTGGATGACTTAGG 57.822 33.333 0.00 0.00 0.00 2.69
183 203 9.396022 GATTGAGTAAAATTGGATGACTTAGGA 57.604 33.333 0.00 0.00 0.00 2.94
185 205 8.146053 TGAGTAAAATTGGATGACTTAGGAGA 57.854 34.615 0.00 0.00 0.00 3.71
202 222 9.184523 ACTTAGGAGAGAATATCCGATAATGAG 57.815 37.037 0.00 0.00 42.02 2.90
203 223 6.463995 AGGAGAGAATATCCGATAATGAGC 57.536 41.667 0.00 0.00 42.02 4.26
204 224 6.194235 AGGAGAGAATATCCGATAATGAGCT 58.806 40.000 0.00 0.00 42.02 4.09
208 228 8.545229 AGAGAATATCCGATAATGAGCTTTTG 57.455 34.615 0.00 0.00 0.00 2.44
265 288 8.164057 AGTAAAATAATGGAGGAGAGGTTCTT 57.836 34.615 0.00 0.00 0.00 2.52
284 307 0.252742 TGGTTCCTTCCTCCCTCCTC 60.253 60.000 0.00 0.00 0.00 3.71
396 430 0.182775 CCCATCCTCCCCTTTTACCG 59.817 60.000 0.00 0.00 0.00 4.02
433 467 0.033090 GATTACCATCGTCCCCGTCC 59.967 60.000 0.00 0.00 35.01 4.79
434 468 1.405272 ATTACCATCGTCCCCGTCCC 61.405 60.000 0.00 0.00 35.01 4.46
447 481 3.139469 GTCCCCGTCCTCGTCCTC 61.139 72.222 0.00 0.00 35.01 3.71
457 491 1.740664 CTCGTCCTCGTCCTCGTCA 60.741 63.158 0.00 0.00 38.33 4.35
466 500 2.291741 CTCGTCCTCGTCATCATCATCA 59.708 50.000 0.00 0.00 38.33 3.07
479 513 0.773700 ATCATCACATCCCCTCCCCC 60.774 60.000 0.00 0.00 0.00 5.40
480 514 1.386485 CATCACATCCCCTCCCCCT 60.386 63.158 0.00 0.00 0.00 4.79
489 528 4.038804 CCTCCCCCTCCCCCAGAA 62.039 72.222 0.00 0.00 0.00 3.02
500 539 3.646637 CCTCCCCCAGAAAACTCGTATAT 59.353 47.826 0.00 0.00 0.00 0.86
508 547 7.717875 CCCCAGAAAACTCGTATATAAAATGGA 59.282 37.037 0.00 0.00 0.00 3.41
591 630 3.084786 GCAGGATAAAGAGGTTTGTGCT 58.915 45.455 0.00 0.00 36.13 4.40
613 652 1.441695 TCTTTTCCCCCGTTCTTCCT 58.558 50.000 0.00 0.00 0.00 3.36
616 655 2.759839 TTTCCCCCGTTCTTCCTTTT 57.240 45.000 0.00 0.00 0.00 2.27
617 656 2.281539 TTCCCCCGTTCTTCCTTTTC 57.718 50.000 0.00 0.00 0.00 2.29
682 722 5.704978 AGAAAGTGAGAGCAAGATTTCTTCC 59.295 40.000 0.00 0.00 33.40 3.46
743 787 3.378427 CCCATAAAGCTCCTTTTTCTCGG 59.622 47.826 0.00 0.00 35.21 4.63
747 791 0.687354 AGCTCCTTTTTCTCGGCTCA 59.313 50.000 0.00 0.00 0.00 4.26
748 792 0.799393 GCTCCTTTTTCTCGGCTCAC 59.201 55.000 0.00 0.00 0.00 3.51
771 815 0.388649 CTCGTCGACAGGGTTGGAAG 60.389 60.000 17.16 0.00 0.00 3.46
866 910 2.055042 ATCGGAGGTGAGCGAGCTT 61.055 57.895 0.00 0.00 30.42 3.74
871 915 4.475135 GGTGAGCGAGCTTCCCCC 62.475 72.222 0.00 0.00 0.00 5.40
926 970 4.043100 CCCGGTTTCCTGACCCCC 62.043 72.222 0.00 0.00 36.28 5.40
927 971 2.933834 CCGGTTTCCTGACCCCCT 60.934 66.667 0.00 0.00 36.28 4.79
928 972 1.614226 CCGGTTTCCTGACCCCCTA 60.614 63.158 0.00 0.00 36.28 3.53
1578 1629 3.522553 CCCACTCAAGACTACCGATTTC 58.477 50.000 0.00 0.00 0.00 2.17
1640 1691 9.534565 TGCTTCTATTGATTTACATGTCTACTC 57.465 33.333 0.00 0.00 0.00 2.59
1641 1692 8.983724 GCTTCTATTGATTTACATGTCTACTCC 58.016 37.037 0.00 0.00 0.00 3.85
1664 1715 8.918202 TCCAGTACTTTGTTCTTTCATATGTT 57.082 30.769 1.90 0.00 0.00 2.71
1676 1727 9.180678 GTTCTTTCATATGTTGTACTTTGTTGG 57.819 33.333 1.90 0.00 0.00 3.77
1687 1738 1.134220 ACTTTGTTGGCCAGTTCGAGA 60.134 47.619 5.11 0.00 0.00 4.04
1706 1757 9.419297 GTTCGAGATTTGTTGGTATAGCATATA 57.581 33.333 5.28 0.00 0.00 0.86
1883 1934 2.733956 AGTTGCCAACAAAAGGAGTGA 58.266 42.857 10.69 0.00 37.58 3.41
1953 2004 6.706716 TGTTATTGTGTGGTTTATCTCGTTGA 59.293 34.615 0.00 0.00 0.00 3.18
1964 2015 6.371389 GTTTATCTCGTTGAAACCTTGAAGG 58.629 40.000 10.24 10.24 42.49 3.46
1971 2022 0.318441 GAAACCTTGAAGGCTTGCCC 59.682 55.000 11.96 0.00 39.63 5.36
2121 2210 4.484236 ACAACACTGTTGTGAAATGTGTG 58.516 39.130 23.83 0.00 46.55 3.82
2127 2216 3.621558 TGTTGTGAAATGTGTGGTACCA 58.378 40.909 11.60 11.60 0.00 3.25
2162 2251 7.969536 ATATCATCAATCTAGTTGTTTCCGG 57.030 36.000 0.00 0.00 38.95 5.14
2223 2312 8.192774 TGCAGTCTTGATTTGATATTTTCATCC 58.807 33.333 0.00 0.00 33.34 3.51
2260 2349 7.959733 TGCTACGTTGTATATTTTGAGTCTTG 58.040 34.615 0.00 0.00 0.00 3.02
2452 2543 4.963276 TCTGTACATTTTGCTATGTGGC 57.037 40.909 0.00 0.00 39.06 5.01
2528 2619 3.416156 GCCTCCATATTCTCATGTTCCC 58.584 50.000 0.00 0.00 0.00 3.97
2531 2622 4.562347 CCTCCATATTCTCATGTTCCCTCG 60.562 50.000 0.00 0.00 0.00 4.63
2545 2636 2.151202 TCCCTCGTGCATGTTTTCTTC 58.849 47.619 5.68 0.00 0.00 2.87
2701 2792 2.760092 ACTCTCTGCTCATGAGGTTCTC 59.240 50.000 23.89 7.54 32.78 2.87
2722 2813 1.347707 TGTAAGTGCACCTCCTCCTTG 59.652 52.381 14.63 0.00 0.00 3.61
2730 2821 1.001406 CACCTCCTCCTTGTCACTCAC 59.999 57.143 0.00 0.00 0.00 3.51
2837 2928 4.403432 GTCACCCATGGATTGTTGATGATT 59.597 41.667 15.22 0.00 0.00 2.57
2873 2964 7.382110 TGATAAGCCTATAGATTCTGCTGTTC 58.618 38.462 0.00 3.11 31.55 3.18
2941 3032 6.384886 AGATGGCATTGAGGGTATGAATTTTT 59.615 34.615 0.00 0.00 0.00 1.94
2954 3045 9.883142 GGGTATGAATTTTTAATTGTCCATTCA 57.117 29.630 7.15 7.15 35.64 2.57
2982 3074 4.082300 TGCACAACTTCTTTTTGAGCAGAA 60.082 37.500 3.52 0.00 42.99 3.02
3077 3169 3.745458 GCACTAGCTAATTCTCCAGATGC 59.255 47.826 0.00 0.00 37.91 3.91
3117 3209 8.354426 GTGGTTAATTGCTAAGTTACCTCAAAA 58.646 33.333 0.00 0.00 0.00 2.44
3138 3230 9.134734 TCAAAATTTAATGCTTCGTTCCATTAC 57.865 29.630 0.00 0.00 34.62 1.89
3187 3279 4.439700 GCATCATATACCAATGCATGCCTC 60.440 45.833 16.68 0.00 44.07 4.70
3188 3280 4.645863 TCATATACCAATGCATGCCTCT 57.354 40.909 16.68 0.00 0.00 3.69
3189 3281 4.989277 TCATATACCAATGCATGCCTCTT 58.011 39.130 16.68 3.18 0.00 2.85
3190 3282 6.125589 TCATATACCAATGCATGCCTCTTA 57.874 37.500 16.68 0.00 0.00 2.10
3191 3283 6.175471 TCATATACCAATGCATGCCTCTTAG 58.825 40.000 16.68 2.06 0.00 2.18
3192 3284 4.712051 ATACCAATGCATGCCTCTTAGA 57.288 40.909 16.68 0.00 0.00 2.10
3193 3285 3.370840 ACCAATGCATGCCTCTTAGAA 57.629 42.857 16.68 0.00 0.00 2.10
3194 3286 3.907221 ACCAATGCATGCCTCTTAGAAT 58.093 40.909 16.68 0.00 0.00 2.40
3195 3287 3.887716 ACCAATGCATGCCTCTTAGAATC 59.112 43.478 16.68 0.00 0.00 2.52
3196 3288 3.255149 CCAATGCATGCCTCTTAGAATCC 59.745 47.826 16.68 0.00 0.00 3.01
3197 3289 2.645838 TGCATGCCTCTTAGAATCCC 57.354 50.000 16.68 0.00 0.00 3.85
3198 3290 1.845791 TGCATGCCTCTTAGAATCCCA 59.154 47.619 16.68 0.00 0.00 4.37
3199 3291 2.225467 GCATGCCTCTTAGAATCCCAC 58.775 52.381 6.36 0.00 0.00 4.61
3200 3292 2.158696 GCATGCCTCTTAGAATCCCACT 60.159 50.000 6.36 0.00 0.00 4.00
3201 3293 3.686691 GCATGCCTCTTAGAATCCCACTT 60.687 47.826 6.36 0.00 0.00 3.16
3202 3294 4.530875 CATGCCTCTTAGAATCCCACTTT 58.469 43.478 0.00 0.00 0.00 2.66
3203 3295 4.657814 TGCCTCTTAGAATCCCACTTTT 57.342 40.909 0.00 0.00 0.00 2.27
3204 3296 5.772393 TGCCTCTTAGAATCCCACTTTTA 57.228 39.130 0.00 0.00 0.00 1.52
3205 3297 6.134535 TGCCTCTTAGAATCCCACTTTTAA 57.865 37.500 0.00 0.00 0.00 1.52
3206 3298 5.944007 TGCCTCTTAGAATCCCACTTTTAAC 59.056 40.000 0.00 0.00 0.00 2.01
3207 3299 5.357314 GCCTCTTAGAATCCCACTTTTAACC 59.643 44.000 0.00 0.00 0.00 2.85
3208 3300 5.886474 CCTCTTAGAATCCCACTTTTAACCC 59.114 44.000 0.00 0.00 0.00 4.11
3209 3301 6.297068 CCTCTTAGAATCCCACTTTTAACCCT 60.297 42.308 0.00 0.00 0.00 4.34
3210 3302 7.092578 CCTCTTAGAATCCCACTTTTAACCCTA 60.093 40.741 0.00 0.00 0.00 3.53
3211 3303 7.858498 TCTTAGAATCCCACTTTTAACCCTAG 58.142 38.462 0.00 0.00 0.00 3.02
3212 3304 7.460082 TCTTAGAATCCCACTTTTAACCCTAGT 59.540 37.037 0.00 0.00 0.00 2.57
3220 3312 6.127253 CCCACTTTTAACCCTAGTATCGAAGA 60.127 42.308 0.00 0.00 45.75 2.87
3234 3326 1.895798 TCGAAGACCAAGCATCTCTGT 59.104 47.619 0.00 0.00 0.00 3.41
3246 3338 4.797743 AGCATCTCTGTCTACCATCAGTA 58.202 43.478 0.00 0.00 33.89 2.74
3255 3347 6.595326 TCTGTCTACCATCAGTATTGCTTTTG 59.405 38.462 0.00 0.00 33.89 2.44
3303 3395 5.643421 AGGAAATAGTGGAGCATCTTGAT 57.357 39.130 0.00 0.00 33.73 2.57
3334 3426 9.113838 CTGCCTAATTTTCTCTATTTTGCTAGA 57.886 33.333 0.00 0.00 0.00 2.43
3335 3427 9.113838 TGCCTAATTTTCTCTATTTTGCTAGAG 57.886 33.333 0.00 2.10 44.06 2.43
3353 3445 2.952310 AGAGTCTTGGCCAACTTTGTTC 59.048 45.455 16.05 6.80 0.00 3.18
3432 3524 9.371136 CCATAGCAGATTATTGTTATACGACAT 57.629 33.333 0.00 0.00 0.00 3.06
3447 3539 9.383462 GTTATACGACATGAGTTAGTGTATCAG 57.617 37.037 0.00 0.00 0.00 2.90
3456 3548 6.387465 TGAGTTAGTGTATCAGTGCTGTTAC 58.613 40.000 11.46 11.46 36.69 2.50
3459 3551 8.118976 AGTTAGTGTATCAGTGCTGTTACTAA 57.881 34.615 16.58 13.97 36.94 2.24
3461 3553 5.967088 AGTGTATCAGTGCTGTTACTAAGG 58.033 41.667 16.58 0.00 36.94 2.69
3462 3554 5.715279 AGTGTATCAGTGCTGTTACTAAGGA 59.285 40.000 16.58 0.24 36.94 3.36
3463 3555 6.210784 AGTGTATCAGTGCTGTTACTAAGGAA 59.789 38.462 16.58 0.00 36.94 3.36
3467 3559 3.997021 CAGTGCTGTTACTAAGGAACCAG 59.003 47.826 0.00 0.00 0.00 4.00
3468 3560 3.646637 AGTGCTGTTACTAAGGAACCAGT 59.353 43.478 0.00 0.00 0.00 4.00
3469 3561 3.995048 GTGCTGTTACTAAGGAACCAGTC 59.005 47.826 0.00 0.00 0.00 3.51
3472 3573 5.163237 TGCTGTTACTAAGGAACCAGTCTTT 60.163 40.000 0.00 0.00 0.00 2.52
3522 3625 3.526899 TGGAGTCTTGAGGGTTTATGGA 58.473 45.455 0.00 0.00 0.00 3.41
3523 3626 3.263425 TGGAGTCTTGAGGGTTTATGGAC 59.737 47.826 0.00 0.00 0.00 4.02
3524 3627 3.519913 GGAGTCTTGAGGGTTTATGGACT 59.480 47.826 0.00 0.00 35.63 3.85
3525 3628 4.508662 GAGTCTTGAGGGTTTATGGACTG 58.491 47.826 0.00 0.00 33.53 3.51
3527 3630 4.351111 AGTCTTGAGGGTTTATGGACTGTT 59.649 41.667 0.00 0.00 32.39 3.16
3528 3631 4.455877 GTCTTGAGGGTTTATGGACTGTTG 59.544 45.833 0.00 0.00 0.00 3.33
3529 3632 3.433306 TGAGGGTTTATGGACTGTTGG 57.567 47.619 0.00 0.00 0.00 3.77
3557 3660 9.909644 GCATTATGAAGATTGCATAATTTCTCT 57.090 29.630 0.00 0.00 42.99 3.10
3614 3717 5.434408 TCATCTTGAGCTGCTTATTCACAT 58.566 37.500 2.53 0.00 0.00 3.21
3615 3718 6.585416 TCATCTTGAGCTGCTTATTCACATA 58.415 36.000 2.53 0.00 0.00 2.29
3616 3719 6.481313 TCATCTTGAGCTGCTTATTCACATAC 59.519 38.462 2.53 0.00 0.00 2.39
3617 3720 5.118990 TCTTGAGCTGCTTATTCACATACC 58.881 41.667 2.53 0.00 0.00 2.73
3620 3723 4.818005 TGAGCTGCTTATTCACATACCATG 59.182 41.667 2.53 0.00 0.00 3.66
3782 3886 0.850100 TGAAAAGGGTGGGCTCAGAA 59.150 50.000 0.00 0.00 0.00 3.02
3830 3934 1.264749 TGGATGCGGTAGGTGCTTCT 61.265 55.000 1.72 0.00 36.89 2.85
3835 3939 1.338389 TGCGGTAGGTGCTTCTTTACC 60.338 52.381 0.00 0.00 37.23 2.85
3878 3982 9.994432 CCTTCATTCAGAAAATGAGTATAACAC 57.006 33.333 1.24 0.00 39.68 3.32
3991 4096 2.523015 GCAGCTACATTGCACATGAAC 58.477 47.619 13.53 0.00 41.17 3.18
4057 4162 4.387026 TGACAAGGATGGAAGTGGATTT 57.613 40.909 0.00 0.00 0.00 2.17
4081 4186 3.384467 TCACCATCGATGAGCTATCACAA 59.616 43.478 26.86 0.00 38.57 3.33
4090 4195 0.107508 AGCTATCACAAGCATGCCGT 60.108 50.000 15.66 9.54 45.30 5.68
4091 4196 0.305922 GCTATCACAAGCATGCCGTC 59.694 55.000 15.66 0.00 42.30 4.79
4108 4213 1.133025 CGTCAATTTGGCCTGGATGAC 59.867 52.381 17.09 17.09 35.13 3.06
4173 4278 8.344831 CAATGTCAGTGTTTCTTCATACTTGAA 58.655 33.333 0.00 0.00 39.54 2.69
4174 4279 7.246674 TGTCAGTGTTTCTTCATACTTGAAC 57.753 36.000 0.00 0.00 36.94 3.18
4177 4282 7.012421 GTCAGTGTTTCTTCATACTTGAACCTT 59.988 37.037 0.00 0.00 36.94 3.50
4178 4283 7.556275 TCAGTGTTTCTTCATACTTGAACCTTT 59.444 33.333 0.00 0.00 36.94 3.11
4180 4285 7.775561 AGTGTTTCTTCATACTTGAACCTTTCT 59.224 33.333 0.00 0.00 36.94 2.52
4181 4286 7.857885 GTGTTTCTTCATACTTGAACCTTTCTG 59.142 37.037 0.00 0.00 36.94 3.02
4182 4287 7.556275 TGTTTCTTCATACTTGAACCTTTCTGT 59.444 33.333 0.00 0.00 36.94 3.41
4183 4288 7.730364 TTCTTCATACTTGAACCTTTCTGTC 57.270 36.000 0.00 0.00 36.94 3.51
4186 4291 4.349636 TCATACTTGAACCTTTCTGTCCCA 59.650 41.667 0.00 0.00 0.00 4.37
4187 4292 3.884037 ACTTGAACCTTTCTGTCCCAT 57.116 42.857 0.00 0.00 0.00 4.00
4188 4293 3.756117 ACTTGAACCTTTCTGTCCCATC 58.244 45.455 0.00 0.00 0.00 3.51
4199 4304 0.478072 TGTCCCATCCCCATGCATAC 59.522 55.000 0.00 0.00 0.00 2.39
4224 4329 5.108517 TGTTTTGTTTGATTCCTGACTTGC 58.891 37.500 0.00 0.00 0.00 4.01
4231 4336 3.565307 TGATTCCTGACTTGCCTGTTTT 58.435 40.909 0.00 0.00 0.00 2.43
4235 4340 2.158475 TCCTGACTTGCCTGTTTTCCAT 60.158 45.455 0.00 0.00 0.00 3.41
4236 4341 2.229784 CCTGACTTGCCTGTTTTCCATC 59.770 50.000 0.00 0.00 0.00 3.51
4240 4345 5.136828 TGACTTGCCTGTTTTCCATCTAAA 58.863 37.500 0.00 0.00 0.00 1.85
4247 4353 5.644644 CCTGTTTTCCATCTAAATCTGTGC 58.355 41.667 0.00 0.00 0.00 4.57
4361 4467 3.055530 ACAGCTTGAATCTGAATCTCGGT 60.056 43.478 2.71 0.00 35.61 4.69
4485 4594 7.147707 GCTGGACTACTAATCTAAGAGGGAAAA 60.148 40.741 0.00 0.00 0.00 2.29
4517 4626 4.669206 TGGAGTCTCCTAGTAGTACTCG 57.331 50.000 19.82 0.00 37.93 4.18
4740 4854 0.886490 CTGCTGGTCACCTTGTGTCC 60.886 60.000 0.00 3.93 40.97 4.02
4771 4885 5.192923 TCTTGTATAATGGGGCTACCTTGTT 59.807 40.000 0.00 0.00 41.11 2.83
4789 4903 5.803967 CCTTGTTTATACAGTGACGAGGTAC 59.196 44.000 0.00 0.00 38.39 3.34
4854 4968 6.628919 TGCACAGATTGAATCCATTATCAG 57.371 37.500 0.75 0.00 0.00 2.90
4897 5011 8.904834 CCCGTTAACTGCACTATCTATCTATAT 58.095 37.037 3.71 0.00 0.00 0.86
4915 5030 7.889589 TCTATATTCATATGCGTTGTCCTTG 57.110 36.000 0.00 0.00 0.00 3.61
4946 5061 8.436046 TTGGACCTTTGATTTTCTGAAAAATG 57.564 30.769 18.43 5.97 43.48 2.32
4947 5062 7.790027 TGGACCTTTGATTTTCTGAAAAATGA 58.210 30.769 18.43 5.68 43.48 2.57
4949 5064 9.108284 GGACCTTTGATTTTCTGAAAAATGAAA 57.892 29.630 18.43 14.90 43.48 2.69
4958 5073 9.934190 ATTTTCTGAAAAATGAAAAATTGGTCG 57.066 25.926 18.43 0.00 42.21 4.79
4959 5074 8.709386 TTTCTGAAAAATGAAAAATTGGTCGA 57.291 26.923 0.00 0.00 30.41 4.20
4960 5075 8.709386 TTCTGAAAAATGAAAAATTGGTCGAA 57.291 26.923 0.00 0.00 0.00 3.71
4990 5105 6.455647 TCTCTTCGTATCACAGAAAACATGT 58.544 36.000 0.00 0.00 0.00 3.21
4995 5110 5.755861 TCGTATCACAGAAAACATGTGTCAA 59.244 36.000 0.00 0.00 46.49 3.18
5000 5123 6.041511 TCACAGAAAACATGTGTCAATTTGG 58.958 36.000 0.00 0.00 46.49 3.28
5001 5124 5.811613 CACAGAAAACATGTGTCAATTTGGT 59.188 36.000 0.00 0.00 42.47 3.67
5002 5125 6.019640 CACAGAAAACATGTGTCAATTTGGTC 60.020 38.462 0.00 0.00 42.47 4.02
5065 5203 0.454600 ACGCGACGTGTATGAAGGAT 59.545 50.000 15.93 0.00 39.18 3.24
5089 5227 1.277842 TCAGGCGATTTTGACCTAGCA 59.722 47.619 0.00 0.00 30.84 3.49
5095 5233 3.788797 GCGATTTTGACCTAGCAATTCCG 60.789 47.826 0.00 0.00 0.00 4.30
5099 5237 5.523438 TTTTGACCTAGCAATTCCGTTTT 57.477 34.783 0.00 0.00 0.00 2.43
5107 5245 6.090783 CCTAGCAATTCCGTTTTCTTAAACC 58.909 40.000 0.00 0.00 40.42 3.27
5113 5251 7.570507 GCAATTCCGTTTTCTTAAACCAATTCC 60.571 37.037 0.00 0.00 40.42 3.01
5119 5257 7.169140 CCGTTTTCTTAAACCAATTCCTTCAAG 59.831 37.037 0.00 0.00 40.42 3.02
5175 5313 9.743057 TGTACTGAAATTCTGTTTGGTTATTTG 57.257 29.630 10.65 0.00 31.00 2.32
5187 5325 9.500864 CTGTTTGGTTATTTGATTTTGTTTTGG 57.499 29.630 0.00 0.00 0.00 3.28
5198 5336 7.082700 TGATTTTGTTTTGGAAGAAAAAGGC 57.917 32.000 0.00 0.00 40.16 4.35
5200 5338 6.493449 TTTTGTTTTGGAAGAAAAAGGCAG 57.507 33.333 0.00 0.00 35.74 4.85
5201 5339 5.413309 TTGTTTTGGAAGAAAAAGGCAGA 57.587 34.783 0.00 0.00 29.93 4.26
5202 5340 4.754322 TGTTTTGGAAGAAAAAGGCAGAC 58.246 39.130 0.00 0.00 29.93 3.51
5203 5341 4.119862 GTTTTGGAAGAAAAAGGCAGACC 58.880 43.478 0.00 0.00 29.93 3.85
5204 5342 1.604604 TGGAAGAAAAAGGCAGACCG 58.395 50.000 0.00 0.00 42.76 4.79
5205 5343 1.133915 TGGAAGAAAAAGGCAGACCGT 60.134 47.619 0.00 0.00 42.76 4.83
5206 5344 1.266989 GGAAGAAAAAGGCAGACCGTG 59.733 52.381 0.00 0.00 42.76 4.94
5207 5345 1.947456 GAAGAAAAAGGCAGACCGTGT 59.053 47.619 0.00 0.00 42.76 4.49
5208 5346 2.052782 AGAAAAAGGCAGACCGTGTT 57.947 45.000 0.00 0.00 42.76 3.32
5209 5347 1.676006 AGAAAAAGGCAGACCGTGTTG 59.324 47.619 0.00 0.00 42.76 3.33
5210 5348 1.404035 GAAAAAGGCAGACCGTGTTGT 59.596 47.619 0.00 0.00 42.76 3.32
5211 5349 2.335316 AAAAGGCAGACCGTGTTGTA 57.665 45.000 0.00 0.00 42.76 2.41
5212 5350 1.589803 AAAGGCAGACCGTGTTGTAC 58.410 50.000 0.00 0.00 42.76 2.90
5213 5351 0.250166 AAGGCAGACCGTGTTGTACC 60.250 55.000 0.00 0.00 42.76 3.34
5286 5431 5.036117 AGTTTGGTGAAACAGAGAGCTTA 57.964 39.130 0.00 0.00 43.51 3.09
5288 5433 3.026630 TGGTGAAACAGAGAGCTTACG 57.973 47.619 0.00 0.00 39.98 3.18
5303 5448 2.298300 CTTACGCGCACAACTTTGAAG 58.702 47.619 5.73 0.00 0.00 3.02
5319 5466 4.837093 TTGAAGATAGTTACAGGGGTGG 57.163 45.455 0.00 0.00 0.00 4.61
5321 5468 3.773119 TGAAGATAGTTACAGGGGTGGTC 59.227 47.826 0.00 0.00 0.00 4.02
5324 5471 4.805744 AGATAGTTACAGGGGTGGTCTAG 58.194 47.826 0.00 0.00 0.00 2.43
5349 5496 5.127682 AGAAGTGAAACACAAGGCAGAAAAT 59.872 36.000 4.75 0.00 41.43 1.82
5350 5497 5.343307 AGTGAAACACAAGGCAGAAAATT 57.657 34.783 4.75 0.00 41.43 1.82
5358 5505 5.534654 ACACAAGGCAGAAAATTTAGTAGCA 59.465 36.000 0.00 0.00 0.00 3.49
5366 5513 7.922811 GGCAGAAAATTTAGTAGCATAAGCAAT 59.077 33.333 0.00 0.00 45.49 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 5.010314 CCTTAGAACAAACCCTAACCAAACC 59.990 44.000 0.00 0.00 0.00 3.27
28 29 5.391577 ACCTTAGAACAAACCCTAACCAA 57.608 39.130 0.00 0.00 0.00 3.67
32 33 5.058490 CACGAACCTTAGAACAAACCCTAA 58.942 41.667 0.00 0.00 0.00 2.69
34 35 3.118149 ACACGAACCTTAGAACAAACCCT 60.118 43.478 0.00 0.00 0.00 4.34
44 46 4.117685 GGCCTGTATAACACGAACCTTAG 58.882 47.826 0.00 0.00 0.00 2.18
60 62 2.649831 CATTCACTGCTTGGCCTGT 58.350 52.632 3.32 0.00 0.00 4.00
85 87 3.054166 GTGTAAAAATGGCCCGTTTGAC 58.946 45.455 0.71 4.47 0.00 3.18
87 89 2.409012 GGTGTAAAAATGGCCCGTTTG 58.591 47.619 0.71 0.00 0.00 2.93
95 97 1.513160 CCGCGCGGTGTAAAAATGG 60.513 57.895 39.71 10.47 0.00 3.16
132 134 1.042559 AGGGTGTGTTTGGTTGCCAG 61.043 55.000 0.00 0.00 33.81 4.85
133 135 0.616111 AAGGGTGTGTTTGGTTGCCA 60.616 50.000 0.00 0.00 0.00 4.92
138 140 4.657814 ATCAGATAAGGGTGTGTTTGGT 57.342 40.909 0.00 0.00 0.00 3.67
143 145 6.620877 TTACTCAATCAGATAAGGGTGTGT 57.379 37.500 0.00 0.00 0.00 3.72
148 150 8.752005 TCCAATTTTACTCAATCAGATAAGGG 57.248 34.615 0.00 0.00 0.00 3.95
154 156 8.868522 AAGTCATCCAATTTTACTCAATCAGA 57.131 30.769 0.00 0.00 0.00 3.27
156 158 9.177608 CCTAAGTCATCCAATTTTACTCAATCA 57.822 33.333 0.00 0.00 0.00 2.57
157 159 9.396022 TCCTAAGTCATCCAATTTTACTCAATC 57.604 33.333 0.00 0.00 0.00 2.67
159 161 8.602424 TCTCCTAAGTCATCCAATTTTACTCAA 58.398 33.333 0.00 0.00 0.00 3.02
160 162 8.146053 TCTCCTAAGTCATCCAATTTTACTCA 57.854 34.615 0.00 0.00 0.00 3.41
161 163 8.478877 TCTCTCCTAAGTCATCCAATTTTACTC 58.521 37.037 0.00 0.00 0.00 2.59
162 164 8.380742 TCTCTCCTAAGTCATCCAATTTTACT 57.619 34.615 0.00 0.00 0.00 2.24
163 165 9.620259 ATTCTCTCCTAAGTCATCCAATTTTAC 57.380 33.333 0.00 0.00 0.00 2.01
167 187 8.601546 GGATATTCTCTCCTAAGTCATCCAATT 58.398 37.037 0.00 0.00 31.67 2.32
170 190 5.712446 CGGATATTCTCTCCTAAGTCATCCA 59.288 44.000 0.00 0.00 31.67 3.41
174 194 8.961634 CATTATCGGATATTCTCTCCTAAGTCA 58.038 37.037 0.00 0.00 0.00 3.41
175 195 9.179909 TCATTATCGGATATTCTCTCCTAAGTC 57.820 37.037 0.00 0.00 0.00 3.01
176 196 9.184523 CTCATTATCGGATATTCTCTCCTAAGT 57.815 37.037 0.00 0.00 0.00 2.24
177 197 8.134895 GCTCATTATCGGATATTCTCTCCTAAG 58.865 40.741 0.00 0.00 0.00 2.18
182 202 8.655092 CAAAAGCTCATTATCGGATATTCTCTC 58.345 37.037 0.00 0.00 0.00 3.20
183 203 7.118971 GCAAAAGCTCATTATCGGATATTCTCT 59.881 37.037 0.00 0.00 0.00 3.10
185 205 6.150140 GGCAAAAGCTCATTATCGGATATTCT 59.850 38.462 0.00 0.00 0.00 2.40
236 259 7.797062 ACCTCTCCTCCATTATTTTACTTCTC 58.203 38.462 0.00 0.00 0.00 2.87
239 262 8.164057 AGAACCTCTCCTCCATTATTTTACTT 57.836 34.615 0.00 0.00 0.00 2.24
265 288 0.252742 GAGGAGGGAGGAAGGAACCA 60.253 60.000 0.00 0.00 0.00 3.67
284 307 1.303317 CTCCACGGGGTTTTCAGGG 60.303 63.158 2.12 0.00 34.93 4.45
433 467 3.507009 GACGAGGACGAGGACGGG 61.507 72.222 0.00 0.00 44.46 5.28
434 468 3.507009 GGACGAGGACGAGGACGG 61.507 72.222 0.00 0.00 44.46 4.79
435 469 2.436292 AGGACGAGGACGAGGACG 60.436 66.667 0.00 0.00 42.66 4.79
436 470 2.462782 CGAGGACGAGGACGAGGAC 61.463 68.421 0.00 0.00 42.66 3.85
437 471 2.125229 CGAGGACGAGGACGAGGA 60.125 66.667 0.00 0.00 42.66 3.71
438 472 2.436292 ACGAGGACGAGGACGAGG 60.436 66.667 0.00 0.00 42.66 4.63
439 473 1.090625 ATGACGAGGACGAGGACGAG 61.091 60.000 0.00 0.00 42.66 4.18
440 474 1.078637 ATGACGAGGACGAGGACGA 60.079 57.895 0.00 0.00 42.66 4.20
441 475 1.352404 GATGACGAGGACGAGGACG 59.648 63.158 0.00 0.00 42.66 4.79
442 476 1.002251 GATGATGACGAGGACGAGGAC 60.002 57.143 0.00 0.00 42.66 3.85
443 477 1.309950 GATGATGACGAGGACGAGGA 58.690 55.000 0.00 0.00 42.66 3.71
444 478 1.025041 TGATGATGACGAGGACGAGG 58.975 55.000 0.00 0.00 42.66 4.63
445 479 2.291741 TGATGATGATGACGAGGACGAG 59.708 50.000 0.00 0.00 42.66 4.18
446 480 2.033424 GTGATGATGATGACGAGGACGA 59.967 50.000 0.00 0.00 42.66 4.20
447 481 2.223572 TGTGATGATGATGACGAGGACG 60.224 50.000 0.00 0.00 45.75 4.79
457 491 1.991070 GGGAGGGGATGTGATGATGAT 59.009 52.381 0.00 0.00 0.00 2.45
466 500 4.124126 GGGAGGGGGAGGGGATGT 62.124 72.222 0.00 0.00 0.00 3.06
479 513 4.957684 ATATACGAGTTTTCTGGGGGAG 57.042 45.455 0.00 0.00 0.00 4.30
480 514 6.811634 TTTATATACGAGTTTTCTGGGGGA 57.188 37.500 0.00 0.00 0.00 4.81
508 547 1.194781 ACAGGATCTTGGTGGCTCGT 61.195 55.000 9.90 0.00 0.00 4.18
591 630 3.590182 AGGAAGAACGGGGGAAAAGATTA 59.410 43.478 0.00 0.00 0.00 1.75
743 787 1.263776 CTGTCGACGAGATTGTGAGC 58.736 55.000 11.62 0.00 0.00 4.26
747 791 0.966920 AACCCTGTCGACGAGATTGT 59.033 50.000 11.62 5.34 0.00 2.71
748 792 1.350193 CAACCCTGTCGACGAGATTG 58.650 55.000 11.62 9.27 0.00 2.67
771 815 1.228510 CTCTGGGGATTCTTGGGCC 59.771 63.158 0.00 0.00 0.00 5.80
866 910 1.063654 AGAACCGGTCAAAAGGGGGA 61.064 55.000 8.04 0.00 0.00 4.81
871 915 3.243367 TGCAATCAAGAACCGGTCAAAAG 60.243 43.478 8.04 0.00 0.00 2.27
909 953 4.043100 GGGGGTCAGGAAACCGGG 62.043 72.222 6.32 0.00 40.46 5.73
926 970 6.400091 CGAACCTTGAATCAAGAAACGAGTAG 60.400 42.308 23.32 6.57 43.42 2.57
927 971 5.404366 CGAACCTTGAATCAAGAAACGAGTA 59.596 40.000 23.32 0.00 43.42 2.59
928 972 4.211374 CGAACCTTGAATCAAGAAACGAGT 59.789 41.667 23.32 9.21 43.42 4.18
964 1009 0.036010 CGCACCCTGGATCAAGAACT 60.036 55.000 0.00 0.00 0.00 3.01
1578 1629 3.560068 GCTTGTAGAACATGGATAACCCG 59.440 47.826 0.00 0.00 37.93 5.28
1582 1633 3.433031 CCGGGCTTGTAGAACATGGATAA 60.433 47.826 0.00 0.00 0.00 1.75
1638 1689 8.553459 ACATATGAAAGAACAAAGTACTGGAG 57.447 34.615 10.38 0.00 0.00 3.86
1639 1690 8.783093 CAACATATGAAAGAACAAAGTACTGGA 58.217 33.333 10.38 0.00 0.00 3.86
1640 1691 8.567948 ACAACATATGAAAGAACAAAGTACTGG 58.432 33.333 10.38 0.00 0.00 4.00
1664 1715 1.944024 CGAACTGGCCAACAAAGTACA 59.056 47.619 7.01 0.00 0.00 2.90
1676 1727 1.880027 ACCAACAAATCTCGAACTGGC 59.120 47.619 0.00 0.00 0.00 4.85
1706 1757 7.864108 TCGACATTTAAATCAACCTGATCAT 57.136 32.000 0.00 0.00 35.76 2.45
1953 2004 0.398381 TGGGCAAGCCTTCAAGGTTT 60.398 50.000 11.40 1.65 39.54 3.27
1964 2015 1.683385 AGAAGACAAGTTTGGGCAAGC 59.317 47.619 0.00 0.00 0.00 4.01
2056 2108 3.053619 GTCTTCCCACCCATATGAGGTTT 60.054 47.826 3.65 0.00 34.56 3.27
2121 2210 9.502091 TTGATGATATTGCTAGTAATTGGTACC 57.498 33.333 11.50 4.43 32.58 3.34
2179 2268 4.997395 ACTGCACACTGGAATAACAACTAG 59.003 41.667 0.00 0.00 0.00 2.57
2192 2281 4.761235 ATCAAATCAAGACTGCACACTG 57.239 40.909 0.00 0.00 0.00 3.66
2223 2312 1.296867 CGTAGCATTTGAAGCGCCG 60.297 57.895 2.29 0.00 37.01 6.46
2280 2371 4.116747 ACAAATCTAGTCTGGCTCGAAG 57.883 45.455 0.00 0.00 0.00 3.79
2528 2619 3.742882 TCTGAGAAGAAAACATGCACGAG 59.257 43.478 0.00 0.00 0.00 4.18
2531 2622 5.684626 CAGTTTCTGAGAAGAAAACATGCAC 59.315 40.000 2.63 0.00 39.20 4.57
2545 2636 4.577875 AGATTCCTGCTTCAGTTTCTGAG 58.422 43.478 0.00 0.00 41.75 3.35
2701 2792 1.270907 AGGAGGAGGTGCACTTACAG 58.729 55.000 17.98 0.00 0.00 2.74
2730 2821 1.737793 GCACCAAATCTACCACTTCCG 59.262 52.381 0.00 0.00 0.00 4.30
2777 2868 2.286294 GGCAATGACAGTATGAGAAGCG 59.714 50.000 0.00 0.00 39.69 4.68
2837 2928 1.153369 GCTTATCAGGCGCCACAGA 60.153 57.895 31.54 23.21 0.00 3.41
2860 2951 4.040217 AGTCTTGACAGAACAGCAGAATCT 59.960 41.667 3.49 0.00 0.00 2.40
2873 2964 5.913514 CAGAAAAATGCTTCAGTCTTGACAG 59.086 40.000 3.49 0.00 31.71 3.51
2954 3045 6.985645 TGCTCAAAAAGAAGTTGTGCATTTAT 59.014 30.769 9.17 0.00 45.46 1.40
3030 3122 7.429340 GCATTTACTAGCACATTCATGTAACAC 59.571 37.037 0.00 0.00 39.39 3.32
3117 3209 7.391148 ACAGTAATGGAACGAAGCATTAAAT 57.609 32.000 0.00 0.00 0.00 1.40
3187 3279 7.631007 ACTAGGGTTAAAAGTGGGATTCTAAG 58.369 38.462 0.00 0.00 0.00 2.18
3188 3280 7.578458 ACTAGGGTTAAAAGTGGGATTCTAA 57.422 36.000 0.00 0.00 0.00 2.10
3189 3281 8.865244 ATACTAGGGTTAAAAGTGGGATTCTA 57.135 34.615 0.00 0.00 0.00 2.10
3190 3282 7.418712 CGATACTAGGGTTAAAAGTGGGATTCT 60.419 40.741 0.00 0.00 0.00 2.40
3191 3283 6.704937 CGATACTAGGGTTAAAAGTGGGATTC 59.295 42.308 0.00 0.00 0.00 2.52
3192 3284 6.384886 TCGATACTAGGGTTAAAAGTGGGATT 59.615 38.462 0.00 0.00 0.00 3.01
3193 3285 5.901276 TCGATACTAGGGTTAAAAGTGGGAT 59.099 40.000 0.00 0.00 0.00 3.85
3194 3286 5.271598 TCGATACTAGGGTTAAAAGTGGGA 58.728 41.667 0.00 0.00 0.00 4.37
3195 3287 5.603170 TCGATACTAGGGTTAAAAGTGGG 57.397 43.478 0.00 0.00 0.00 4.61
3196 3288 6.755607 GTCTTCGATACTAGGGTTAAAAGTGG 59.244 42.308 0.00 0.00 0.00 4.00
3197 3289 6.755607 GGTCTTCGATACTAGGGTTAAAAGTG 59.244 42.308 0.00 0.00 0.00 3.16
3198 3290 6.438425 TGGTCTTCGATACTAGGGTTAAAAGT 59.562 38.462 0.00 0.00 0.00 2.66
3199 3291 6.870769 TGGTCTTCGATACTAGGGTTAAAAG 58.129 40.000 0.00 0.00 0.00 2.27
3200 3292 6.855763 TGGTCTTCGATACTAGGGTTAAAA 57.144 37.500 0.00 0.00 0.00 1.52
3201 3293 6.628844 GCTTGGTCTTCGATACTAGGGTTAAA 60.629 42.308 0.00 0.00 0.00 1.52
3202 3294 5.163478 GCTTGGTCTTCGATACTAGGGTTAA 60.163 44.000 0.00 0.00 0.00 2.01
3203 3295 4.340381 GCTTGGTCTTCGATACTAGGGTTA 59.660 45.833 0.00 0.00 0.00 2.85
3204 3296 3.132467 GCTTGGTCTTCGATACTAGGGTT 59.868 47.826 0.00 0.00 0.00 4.11
3205 3297 2.694109 GCTTGGTCTTCGATACTAGGGT 59.306 50.000 0.00 0.00 0.00 4.34
3206 3298 2.693591 TGCTTGGTCTTCGATACTAGGG 59.306 50.000 0.00 0.00 0.00 3.53
3207 3299 4.279671 AGATGCTTGGTCTTCGATACTAGG 59.720 45.833 0.00 0.00 0.00 3.02
3208 3300 5.240623 AGAGATGCTTGGTCTTCGATACTAG 59.759 44.000 0.00 0.00 0.00 2.57
3209 3301 5.009110 CAGAGATGCTTGGTCTTCGATACTA 59.991 44.000 0.00 0.00 0.00 1.82
3210 3302 3.957497 AGAGATGCTTGGTCTTCGATACT 59.043 43.478 0.00 0.00 0.00 2.12
3211 3303 4.047822 CAGAGATGCTTGGTCTTCGATAC 58.952 47.826 0.00 0.00 0.00 2.24
3212 3304 3.701542 ACAGAGATGCTTGGTCTTCGATA 59.298 43.478 0.00 0.00 0.00 2.92
3220 3312 2.540383 TGGTAGACAGAGATGCTTGGT 58.460 47.619 0.00 0.00 0.00 3.67
3234 3326 7.119699 CAGAACAAAAGCAATACTGATGGTAGA 59.880 37.037 0.00 0.00 33.51 2.59
3303 3395 3.439857 AGAGAAAATTAGGCAGGCACA 57.560 42.857 0.00 0.00 0.00 4.57
3334 3426 3.018423 AGAACAAAGTTGGCCAAGACT 57.982 42.857 21.21 12.01 0.00 3.24
3335 3427 4.082733 GGATAGAACAAAGTTGGCCAAGAC 60.083 45.833 21.21 9.33 0.00 3.01
3353 3445 7.278875 AGAAAGCTAGAAAACCATCTGGATAG 58.721 38.462 2.55 0.00 38.94 2.08
3390 3482 8.384693 TCTGCTATGGTAATATGGATCTGAAT 57.615 34.615 0.00 0.00 0.00 2.57
3406 3498 8.757164 TGTCGTATAACAATAATCTGCTATGG 57.243 34.615 0.00 0.00 0.00 2.74
3432 3524 5.468540 AACAGCACTGATACACTAACTCA 57.531 39.130 4.31 0.00 0.00 3.41
3433 3525 6.622549 AGTAACAGCACTGATACACTAACTC 58.377 40.000 17.15 0.00 40.10 3.01
3447 3539 3.995048 GACTGGTTCCTTAGTAACAGCAC 59.005 47.826 0.00 0.00 0.00 4.40
3522 3625 5.622914 GCAATCTTCATAATGCACCAACAGT 60.623 40.000 0.00 0.00 38.63 3.55
3523 3626 4.802039 GCAATCTTCATAATGCACCAACAG 59.198 41.667 0.00 0.00 38.63 3.16
3524 3627 4.220163 TGCAATCTTCATAATGCACCAACA 59.780 37.500 0.00 0.00 43.32 3.33
3525 3628 4.746729 TGCAATCTTCATAATGCACCAAC 58.253 39.130 0.00 0.00 43.32 3.77
3557 3660 9.979578 AAGTTGCAAAATGTTTATCAAGTATCA 57.020 25.926 0.00 0.00 0.00 2.15
3646 3749 2.041620 AGGCTTTCAGCAATAACCTGGA 59.958 45.455 0.00 0.00 44.75 3.86
3647 3750 2.165030 CAGGCTTTCAGCAATAACCTGG 59.835 50.000 0.00 0.00 44.75 4.45
3782 3886 4.261801 CCTGGATTTCATGTTCGGTTAGT 58.738 43.478 0.00 0.00 0.00 2.24
3830 3934 8.570068 AAGGAATCGTTTATTTAGCTGGTAAA 57.430 30.769 13.70 13.70 35.03 2.01
3835 3939 8.397906 TGAATGAAGGAATCGTTTATTTAGCTG 58.602 33.333 7.04 0.00 37.40 4.24
3867 3971 8.862325 AAAATCCACAGATTGTGTTATACTCA 57.138 30.769 8.25 0.00 46.45 3.41
3991 4096 4.349365 AGTTCTCCTCCCTCTCTAGTTTG 58.651 47.826 0.00 0.00 0.00 2.93
4057 4162 4.766891 TGTGATAGCTCATCGATGGTGATA 59.233 41.667 24.61 19.33 36.33 2.15
4090 4195 1.271871 ACGTCATCCAGGCCAAATTGA 60.272 47.619 5.01 0.00 0.00 2.57
4091 4196 1.176527 ACGTCATCCAGGCCAAATTG 58.823 50.000 5.01 0.00 0.00 2.32
4099 4204 1.001974 TCAAGGTGAACGTCATCCAGG 59.998 52.381 0.00 0.00 0.00 4.45
4108 4213 4.948847 TGATCATATCCTCAAGGTGAACG 58.051 43.478 0.00 0.00 36.34 3.95
4180 4285 3.574768 ATGTATGCATGGGGATGGGACA 61.575 50.000 10.16 2.23 36.89 4.02
4181 4286 0.478072 TGTATGCATGGGGATGGGAC 59.522 55.000 10.16 0.00 0.00 4.46
4182 4287 1.075861 CATGTATGCATGGGGATGGGA 59.924 52.381 15.36 0.00 46.47 4.37
4183 4288 1.552578 CATGTATGCATGGGGATGGG 58.447 55.000 15.36 0.00 46.47 4.00
4199 4304 6.292488 GCAAGTCAGGAATCAAACAAAACATG 60.292 38.462 0.00 0.00 0.00 3.21
4210 4315 2.957402 AACAGGCAAGTCAGGAATCA 57.043 45.000 0.00 0.00 0.00 2.57
4224 4329 5.416952 AGCACAGATTTAGATGGAAAACAGG 59.583 40.000 0.00 0.00 0.00 4.00
4231 4336 6.003326 TGAAAACAGCACAGATTTAGATGGA 58.997 36.000 0.00 0.00 0.00 3.41
4235 4340 5.620206 TCCTGAAAACAGCACAGATTTAGA 58.380 37.500 0.00 0.00 34.07 2.10
4236 4341 5.947228 TCCTGAAAACAGCACAGATTTAG 57.053 39.130 0.00 0.00 34.07 1.85
4240 4345 3.087031 CCATCCTGAAAACAGCACAGAT 58.913 45.455 0.00 0.00 34.07 2.90
4247 4353 3.674138 CGATTTGCCCATCCTGAAAACAG 60.674 47.826 0.00 0.00 0.00 3.16
4259 4365 3.270027 CTCACTGTAATCGATTTGCCCA 58.730 45.455 17.19 7.52 0.00 5.36
4361 4467 3.084039 GTTGCTGGGATTCAAGATGTCA 58.916 45.455 0.00 0.00 0.00 3.58
4517 4626 2.252714 CATTCCCTCCCTCTAGCTACC 58.747 57.143 0.00 0.00 0.00 3.18
4561 4670 4.142271 CCTCCATATCCAGCGTCTAAGATC 60.142 50.000 0.00 0.00 0.00 2.75
4749 4863 5.459982 AACAAGGTAGCCCCATTATACAA 57.540 39.130 0.00 0.00 34.66 2.41
4751 4865 8.158789 TGTATAAACAAGGTAGCCCCATTATAC 58.841 37.037 14.79 14.79 35.90 1.47
4799 4913 9.788960 GTTTGAAAATAGTTTCTCTTGTTCAGT 57.211 29.630 15.90 0.00 43.13 3.41
4854 4968 5.632244 AACGGGACATGTTTATGGTAAAC 57.368 39.130 0.00 5.81 38.66 2.01
4897 5011 2.026729 TCCCAAGGACAACGCATATGAA 60.027 45.455 6.97 0.00 0.00 2.57
4898 5012 1.557371 TCCCAAGGACAACGCATATGA 59.443 47.619 6.97 0.00 0.00 2.15
4904 5018 0.310854 CAAACTCCCAAGGACAACGC 59.689 55.000 0.00 0.00 0.00 4.84
4915 5030 4.588951 AGAAAATCAAAGGTCCAAACTCCC 59.411 41.667 0.00 0.00 0.00 4.30
4946 5061 9.278734 GAAGAGAACATATTCGACCAATTTTTC 57.721 33.333 0.00 0.00 40.04 2.29
4947 5062 7.962918 CGAAGAGAACATATTCGACCAATTTTT 59.037 33.333 0.51 0.00 46.57 1.94
4949 5064 6.594159 ACGAAGAGAACATATTCGACCAATTT 59.406 34.615 12.87 0.00 46.57 1.82
4950 5065 6.106673 ACGAAGAGAACATATTCGACCAATT 58.893 36.000 12.87 0.00 46.57 2.32
4951 5066 5.661458 ACGAAGAGAACATATTCGACCAAT 58.339 37.500 12.87 0.00 46.57 3.16
4953 5068 4.713824 ACGAAGAGAACATATTCGACCA 57.286 40.909 12.87 0.00 46.57 4.02
4954 5069 6.360148 GTGATACGAAGAGAACATATTCGACC 59.640 42.308 12.87 3.13 46.57 4.79
4955 5070 6.910972 TGTGATACGAAGAGAACATATTCGAC 59.089 38.462 12.87 2.22 46.57 4.20
4956 5071 7.012044 TCTGTGATACGAAGAGAACATATTCGA 59.988 37.037 12.87 0.00 46.57 3.71
4958 5073 8.858003 TTCTGTGATACGAAGAGAACATATTC 57.142 34.615 0.00 0.00 34.78 1.75
4959 5074 9.653287 TTTTCTGTGATACGAAGAGAACATATT 57.347 29.630 0.00 0.00 27.64 1.28
4960 5075 9.088512 GTTTTCTGTGATACGAAGAGAACATAT 57.911 33.333 0.00 0.00 35.93 1.78
4990 5105 3.433306 AGGGATTCGACCAAATTGACA 57.567 42.857 0.00 0.00 0.00 3.58
4995 5110 3.610911 GACTCAAGGGATTCGACCAAAT 58.389 45.455 0.00 0.00 0.00 2.32
5002 5125 2.860735 GTTGATCGACTCAAGGGATTCG 59.139 50.000 5.79 0.00 44.44 3.34
5080 5218 4.015872 AGAAAACGGAATTGCTAGGTCA 57.984 40.909 0.00 0.00 0.00 4.02
5089 5227 7.732025 AGGAATTGGTTTAAGAAAACGGAATT 58.268 30.769 8.29 8.29 44.97 2.17
5095 5233 9.764363 ATCTTGAAGGAATTGGTTTAAGAAAAC 57.236 29.630 7.35 0.00 43.58 2.43
5099 5237 6.721208 AGCATCTTGAAGGAATTGGTTTAAGA 59.279 34.615 6.22 6.22 0.00 2.10
5107 5245 5.291128 GCAATCAAGCATCTTGAAGGAATTG 59.709 40.000 12.53 12.28 31.55 2.32
5113 5251 3.168963 CACGCAATCAAGCATCTTGAAG 58.831 45.455 12.53 9.70 31.55 3.02
5119 5257 2.645411 GCACACGCAATCAAGCATC 58.355 52.632 0.00 0.00 38.36 3.91
5175 5313 7.065683 TCTGCCTTTTTCTTCCAAAACAAAATC 59.934 33.333 0.00 0.00 0.00 2.17
5181 5319 4.119862 GGTCTGCCTTTTTCTTCCAAAAC 58.880 43.478 0.00 0.00 0.00 2.43
5187 5325 1.947456 ACACGGTCTGCCTTTTTCTTC 59.053 47.619 0.00 0.00 0.00 2.87
5193 5331 1.589803 GTACAACACGGTCTGCCTTT 58.410 50.000 0.00 0.00 0.00 3.11
5195 5333 1.119574 AGGTACAACACGGTCTGCCT 61.120 55.000 0.00 0.00 0.00 4.75
5196 5334 0.604578 TAGGTACAACACGGTCTGCC 59.395 55.000 0.00 0.00 0.00 4.85
5197 5335 2.268298 CATAGGTACAACACGGTCTGC 58.732 52.381 0.00 0.00 0.00 4.26
5198 5336 2.268298 GCATAGGTACAACACGGTCTG 58.732 52.381 0.00 0.00 0.00 3.51
5200 5338 2.373540 TGCATAGGTACAACACGGTC 57.626 50.000 0.00 0.00 0.00 4.79
5201 5339 3.267483 GAATGCATAGGTACAACACGGT 58.733 45.455 0.00 0.00 0.00 4.83
5202 5340 3.266636 TGAATGCATAGGTACAACACGG 58.733 45.455 0.00 0.00 0.00 4.94
5203 5341 4.937696 TTGAATGCATAGGTACAACACG 57.062 40.909 0.00 0.00 0.00 4.49
5204 5342 5.567534 CGTTTTGAATGCATAGGTACAACAC 59.432 40.000 0.00 4.99 0.00 3.32
5205 5343 5.470437 TCGTTTTGAATGCATAGGTACAACA 59.530 36.000 0.00 0.00 0.00 3.33
5206 5344 5.933790 TCGTTTTGAATGCATAGGTACAAC 58.066 37.500 0.00 0.00 0.00 3.32
5207 5345 5.391523 GCTCGTTTTGAATGCATAGGTACAA 60.392 40.000 0.00 0.00 0.00 2.41
5208 5346 4.094294 GCTCGTTTTGAATGCATAGGTACA 59.906 41.667 0.00 0.00 0.00 2.90
5209 5347 4.495844 GGCTCGTTTTGAATGCATAGGTAC 60.496 45.833 0.00 0.00 0.00 3.34
5210 5348 3.625764 GGCTCGTTTTGAATGCATAGGTA 59.374 43.478 0.00 0.00 0.00 3.08
5211 5349 2.423538 GGCTCGTTTTGAATGCATAGGT 59.576 45.455 0.00 0.00 0.00 3.08
5212 5350 2.539547 CGGCTCGTTTTGAATGCATAGG 60.540 50.000 0.00 0.00 0.00 2.57
5213 5351 2.095853 ACGGCTCGTTTTGAATGCATAG 59.904 45.455 0.00 0.00 36.35 2.23
5286 5431 0.944386 ATCTTCAAAGTTGTGCGCGT 59.056 45.000 8.43 0.00 0.00 6.01
5288 5433 3.813529 ACTATCTTCAAAGTTGTGCGC 57.186 42.857 0.00 0.00 0.00 6.09
5303 5448 4.801164 TCTAGACCACCCCTGTAACTATC 58.199 47.826 0.00 0.00 0.00 2.08
5319 5466 4.449405 GCCTTGTGTTTCACTTCTCTAGAC 59.551 45.833 0.00 0.00 35.11 2.59
5321 5468 4.380531 TGCCTTGTGTTTCACTTCTCTAG 58.619 43.478 1.72 0.00 35.11 2.43
5324 5471 3.206150 TCTGCCTTGTGTTTCACTTCTC 58.794 45.455 1.72 0.00 35.11 2.87


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

AutoCloner maintained by Alex Coulton.