Multiple sequence alignment - TraesCS6A01G178500

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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 TraesCS6A01G178500 chr6A 100.000 8557 0 0 1 8557 200246534 200255090 0.000000e+00 15802.0
1 TraesCS6A01G178500 chr6D 95.368 5009 176 26 3268 8241 147154085 147149098 0.000000e+00 7914.0
2 TraesCS6A01G178500 chr6D 94.023 3346 106 38 1 3281 147157421 147154105 0.000000e+00 4985.0
3 TraesCS6A01G178500 chr6D 93.072 332 9 6 8231 8553 147149079 147148753 2.800000e-129 473.0
4 TraesCS6A01G178500 chr6B 96.259 2994 82 14 3268 6244 258008424 258011404 0.000000e+00 4881.0
5 TraesCS6A01G178500 chr6B 93.871 2953 118 25 363 3281 258005482 258008405 0.000000e+00 4392.0
6 TraesCS6A01G178500 chr6B 94.984 1535 66 7 6239 7764 258011427 258012959 0.000000e+00 2398.0
7 TraesCS6A01G178500 chr6B 90.807 805 37 16 7759 8553 258013042 258013819 0.000000e+00 1042.0
8 TraesCS6A01G178500 chr3A 75.172 290 54 12 1187 1460 399580087 399579800 4.200000e-23 121.0
9 TraesCS6A01G178500 chr3A 97.778 45 1 0 7955 7999 119479828 119479872 2.560000e-10 78.7
10 TraesCS6A01G178500 chr3D 75.175 286 54 10 1191 1460 323327721 323328005 1.510000e-22 119.0
11 TraesCS6A01G178500 chr3D 72.941 255 56 12 1214 1460 394195030 394194781 9.210000e-10 76.8
12 TraesCS6A01G178500 chr3B 75.547 274 50 11 1203 1460 395858788 395858516 1.510000e-22 119.0
13 TraesCS6A01G178500 chr3B 72.692 260 58 12 1209 1460 513814959 513814705 3.310000e-09 75.0
14 TraesCS6A01G178500 chr2A 73.354 319 78 6 85 400 767152458 767152772 2.530000e-20 111.0
15 TraesCS6A01G178500 chr2A 97.778 45 1 0 7955 7999 611104669 611104625 2.560000e-10 78.7
16 TraesCS6A01G178500 chr2A 100.000 28 0 0 7601 7628 547777121 547777094 1.600000e-02 52.8
17 TraesCS6A01G178500 chr2D 100.000 45 0 0 7955 7999 469737367 469737323 5.500000e-12 84.2
18 TraesCS6A01G178500 chr4A 78.689 122 21 3 341 462 2171944 2171828 9.210000e-10 76.8
19 TraesCS6A01G178500 chr7D 95.455 44 2 0 7956 7999 135361527 135361484 4.290000e-08 71.3
20 TraesCS6A01G178500 chr7D 93.617 47 3 0 7955 8001 452969839 452969885 4.290000e-08 71.3
21 TraesCS6A01G178500 chr7B 93.617 47 3 0 7955 8001 476199897 476199943 4.290000e-08 71.3
22 TraesCS6A01G178500 chr1A 89.286 56 5 1 7954 8009 347323161 347323107 1.540000e-07 69.4


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 TraesCS6A01G178500 chr6A 200246534 200255090 8556 False 15802.000000 15802 100.000000 1 8557 1 chr6A.!!$F1 8556
1 TraesCS6A01G178500 chr6D 147148753 147157421 8668 True 4457.333333 7914 94.154333 1 8553 3 chr6D.!!$R1 8552
2 TraesCS6A01G178500 chr6B 258005482 258013819 8337 False 3178.250000 4881 93.980250 363 8553 4 chr6B.!!$F1 8190

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
170 171 0.036388 ACATCAGTGGCCCACTTACG 60.036 55.000 15.33 0.58 42.59 3.18 F
575 605 1.497722 GACGTTTACCTGCAGCAGC 59.502 57.895 17.81 1.71 42.57 5.25 F
1744 1817 0.458260 AACCCAACAAAGTTCACGCC 59.542 50.000 0.00 0.00 0.00 5.68 F
2748 2823 0.311790 CCGCTGACACACTTGCATTT 59.688 50.000 0.00 0.00 0.00 2.32 F
3281 3390 0.320596 AAGAGCTCTCTGTGCTGCAC 60.321 55.000 25.15 25.15 41.30 4.57 F
3441 3550 0.899717 AAGCATTCCATGTTGGCCGT 60.900 50.000 0.00 0.00 37.47 5.68 F
4473 4585 1.000843 ACAGACAGCAATGACACGCTA 59.999 47.619 1.06 0.00 36.50 4.26 F
6038 6162 0.036010 ACAGAGCACCCGATTTCCAG 60.036 55.000 0.00 0.00 0.00 3.86 F
6338 6493 0.389948 GACCTAAGCACACCTCCACG 60.390 60.000 0.00 0.00 0.00 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1469 1533 0.108424 ACAGAAGCGAGGTGATGAGC 60.108 55.0 0.00 0.00 0.00 4.26 R
1894 1967 0.458260 AAAACAAACAGGCCCGTGAC 59.542 50.0 0.00 0.00 0.00 3.67 R
3074 3150 0.097674 GCTGAAGCAACGCGATCAAT 59.902 50.0 15.93 0.00 41.59 2.57 R
3987 4098 1.368641 CGATGTTTGGATCGAAGCCA 58.631 50.0 6.30 6.30 46.72 4.75 R
5153 5265 0.615331 CTGGCCTGAAAGCTCCACTA 59.385 55.0 3.32 0.00 32.77 2.74 R
5303 5415 0.388907 CAGCAATCCGGGCAAAAGTG 60.389 55.0 0.00 0.00 0.00 3.16 R
6338 6493 0.100146 GTACAGGTCCGTCGATCCAC 59.900 60.0 0.00 0.00 0.00 4.02 R
7064 7224 0.578683 CGACTATGGCAGCAATGTCG 59.421 55.0 15.77 15.77 40.55 4.35 R
8317 8612 0.391661 TGCAGAATCTGGCGGACTTC 60.392 55.0 12.66 4.38 31.21 3.01 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
79 80 6.704056 TTCTTCTTCTGGAGATTAAACCCT 57.296 37.500 0.00 0.00 33.49 4.34
82 83 7.621796 TCTTCTTCTGGAGATTAAACCCTAAC 58.378 38.462 0.00 0.00 33.49 2.34
83 84 6.945636 TCTTCTGGAGATTAAACCCTAACA 57.054 37.500 0.00 0.00 0.00 2.41
104 105 6.932356 ACAAGCAAGATGGTACTTATGATG 57.068 37.500 0.00 0.00 0.00 3.07
114 115 5.704354 TGGTACTTATGATGATTGCCCAAT 58.296 37.500 0.00 0.00 0.00 3.16
121 122 1.487558 GATGATTGCCCAATTTGCCCT 59.512 47.619 0.00 0.00 0.00 5.19
134 135 5.653769 CCAATTTGCCCTAGAAGAAATGAGA 59.346 40.000 0.00 0.00 0.00 3.27
151 152 4.639078 TGAGACATTTGGGAAGTGATGA 57.361 40.909 0.00 0.00 0.00 2.92
157 158 4.703575 ACATTTGGGAAGTGATGACATCAG 59.296 41.667 18.49 5.54 40.53 2.90
170 171 0.036388 ACATCAGTGGCCCACTTACG 60.036 55.000 15.33 0.58 42.59 3.18
220 221 2.936498 GGAATACTAGCAATGCACGTGT 59.064 45.455 18.38 2.94 0.00 4.49
241 242 3.069300 GTCGAGGAGGATAAGTTTACCCC 59.931 52.174 0.00 0.00 0.00 4.95
393 398 4.097286 GCCAAGTTGACAACAGAAAACCTA 59.903 41.667 20.08 0.00 0.00 3.08
401 411 4.682787 ACAACAGAAAACCTAAGCAAAGC 58.317 39.130 0.00 0.00 0.00 3.51
402 412 4.159506 ACAACAGAAAACCTAAGCAAAGCA 59.840 37.500 0.00 0.00 0.00 3.91
403 413 5.108517 CAACAGAAAACCTAAGCAAAGCAA 58.891 37.500 0.00 0.00 0.00 3.91
440 450 9.485206 CATCATCATCTACATGAATAGTGTGAA 57.515 33.333 0.00 0.00 42.53 3.18
471 481 9.665719 ACTTTTGTGAAAATTAACTTTGGTGAT 57.334 25.926 0.00 0.00 0.00 3.06
573 603 1.666553 CCGACGTTTACCTGCAGCA 60.667 57.895 8.66 0.00 0.00 4.41
574 604 1.626654 CCGACGTTTACCTGCAGCAG 61.627 60.000 16.23 16.23 0.00 4.24
575 605 1.497722 GACGTTTACCTGCAGCAGC 59.502 57.895 17.81 1.71 42.57 5.25
1469 1533 2.505777 CGGTGCGTCTCAGCTCAG 60.506 66.667 0.00 0.00 40.87 3.35
1470 1534 2.813042 GGTGCGTCTCAGCTCAGC 60.813 66.667 0.00 0.00 39.95 4.26
1686 1758 0.514255 CATGGTATGCATCTTCGGCG 59.486 55.000 0.19 0.00 0.00 6.46
1708 1780 2.614520 CAGCAGCTTCATGATCCTTCAG 59.385 50.000 0.00 0.00 34.73 3.02
1709 1781 2.239150 AGCAGCTTCATGATCCTTCAGT 59.761 45.455 0.00 0.00 34.73 3.41
1744 1817 0.458260 AACCCAACAAAGTTCACGCC 59.542 50.000 0.00 0.00 0.00 5.68
1894 1967 4.504916 CGGCAGGTGAGCGAGAGG 62.505 72.222 0.00 0.00 34.64 3.69
1947 2020 7.359595 TCACAGTTCTTTCCATGTTTTAATCG 58.640 34.615 0.00 0.00 0.00 3.34
1964 2037 4.336889 AATCGTGTGGAGTTTCTTCAGA 57.663 40.909 0.00 0.00 0.00 3.27
2054 2127 2.234168 GGACTCAACTCTCAAGGTACCC 59.766 54.545 8.74 0.00 0.00 3.69
2078 2151 5.220739 CCATCTTCACATCCTTTCGTGATTC 60.221 44.000 0.00 0.00 41.55 2.52
2095 2168 6.641314 TCGTGATTCTGAGTACTCTGTTTTTC 59.359 38.462 23.01 16.39 0.00 2.29
2096 2169 6.399039 CGTGATTCTGAGTACTCTGTTTTTCG 60.399 42.308 23.01 18.94 0.00 3.46
2097 2170 6.421202 GTGATTCTGAGTACTCTGTTTTTCGT 59.579 38.462 23.01 6.29 0.00 3.85
2099 2172 6.823678 TTCTGAGTACTCTGTTTTTCGTTC 57.176 37.500 23.01 0.00 0.00 3.95
2146 2221 9.474313 GATCAGGGAAGATATAGAGATGTAAGT 57.526 37.037 0.00 0.00 0.00 2.24
2298 2373 1.275291 GAAATGACGGTGAGGGAGACA 59.725 52.381 0.00 0.00 0.00 3.41
2376 2451 4.386873 GGGAGCTGGAAAAAGGGATATCTT 60.387 45.833 2.05 0.00 0.00 2.40
2392 2467 6.865205 GGGATATCTTGCTATTCACAAATTGC 59.135 38.462 2.05 0.00 41.95 3.56
2508 2583 3.515104 TGATGTCTACATGAAGGTGAGCA 59.485 43.478 0.00 0.00 36.57 4.26
2515 2590 6.036517 GTCTACATGAAGGTGAGCAGTTATTG 59.963 42.308 0.00 0.00 0.00 1.90
2533 2608 8.829612 CAGTTATTGCATATACACTGTGAATCA 58.170 33.333 15.86 0.89 0.00 2.57
2536 2611 9.612066 TTATTGCATATACACTGTGAATCAAGA 57.388 29.630 15.86 4.45 0.00 3.02
2537 2612 7.920160 TTGCATATACACTGTGAATCAAGAA 57.080 32.000 15.86 0.00 0.00 2.52
2538 2613 7.307493 TGCATATACACTGTGAATCAAGAAC 57.693 36.000 15.86 0.00 0.00 3.01
2539 2614 6.316140 TGCATATACACTGTGAATCAAGAACC 59.684 38.462 15.86 0.00 0.00 3.62
2540 2615 6.540189 GCATATACACTGTGAATCAAGAACCT 59.460 38.462 15.86 0.00 0.00 3.50
2541 2616 7.066284 GCATATACACTGTGAATCAAGAACCTT 59.934 37.037 15.86 0.00 0.00 3.50
2542 2617 9.599866 CATATACACTGTGAATCAAGAACCTTA 57.400 33.333 15.86 0.00 0.00 2.69
2572 2647 5.874895 AGAAGTAAACGGTATTGCCTTTC 57.125 39.130 0.00 0.00 34.25 2.62
2578 2653 3.418684 ACGGTATTGCCTTTCTGAAGT 57.581 42.857 0.00 0.00 34.25 3.01
2579 2654 4.546829 ACGGTATTGCCTTTCTGAAGTA 57.453 40.909 0.00 0.00 34.25 2.24
2583 2658 7.107542 ACGGTATTGCCTTTCTGAAGTAAATA 58.892 34.615 0.00 0.00 34.25 1.40
2621 2696 8.904834 CAGTTACTAAGTTATTCTGCTCCTCTA 58.095 37.037 0.00 0.00 0.00 2.43
2745 2820 3.279116 GCCGCTGACACACTTGCA 61.279 61.111 0.00 0.00 0.00 4.08
2747 2822 1.951510 CCGCTGACACACTTGCATT 59.048 52.632 0.00 0.00 0.00 3.56
2748 2823 0.311790 CCGCTGACACACTTGCATTT 59.688 50.000 0.00 0.00 0.00 2.32
2749 2824 1.269206 CCGCTGACACACTTGCATTTT 60.269 47.619 0.00 0.00 0.00 1.82
2754 2829 4.103365 TGACACACTTGCATTTTTCGTT 57.897 36.364 0.00 0.00 0.00 3.85
2796 2871 2.424601 CTGTGCAGATACAATGGTTGGG 59.575 50.000 0.00 0.00 34.12 4.12
2927 3003 7.978414 TCATGACAGTGAAATCAGATCTCTAAC 59.022 37.037 0.00 0.00 0.00 2.34
3003 3079 1.633432 TGGATGAAATCTCCACCGGTT 59.367 47.619 2.97 0.00 44.71 4.44
3176 3252 1.219393 CCAGGGTCCTCGAGAAAGC 59.781 63.158 15.71 11.05 0.00 3.51
3224 3300 1.493861 TCAGATGCCCTGAGAGGAAG 58.506 55.000 2.19 0.00 46.38 3.46
3263 3339 6.934083 TCTTGCAAGAAGTATGTGATACACAA 59.066 34.615 26.61 0.00 38.85 3.33
3281 3390 0.320596 AAGAGCTCTCTGTGCTGCAC 60.321 55.000 25.15 25.15 41.30 4.57
3285 3394 1.858041 CTCTCTGTGCTGCACGTTG 59.142 57.895 25.88 18.31 37.14 4.10
3302 3411 3.135167 ACGTTGGGACTAGGAACTCAAAA 59.865 43.478 0.00 0.00 41.75 2.44
3305 3414 5.240844 CGTTGGGACTAGGAACTCAAAATTT 59.759 40.000 0.00 0.00 41.75 1.82
3306 3415 6.447162 GTTGGGACTAGGAACTCAAAATTTG 58.553 40.000 0.00 0.00 41.75 2.32
3307 3416 5.947663 TGGGACTAGGAACTCAAAATTTGA 58.052 37.500 8.25 8.25 41.75 2.69
3308 3417 5.768164 TGGGACTAGGAACTCAAAATTTGAC 59.232 40.000 4.03 0.00 41.75 3.18
3309 3418 5.183331 GGGACTAGGAACTCAAAATTTGACC 59.817 44.000 4.03 5.12 41.75 4.02
3310 3419 5.106673 GGACTAGGAACTCAAAATTTGACCG 60.107 44.000 4.03 0.00 41.75 4.79
3312 3421 4.568152 AGGAACTCAAAATTTGACCGTG 57.432 40.909 4.03 0.00 35.46 4.94
3314 3423 4.401202 AGGAACTCAAAATTTGACCGTGTT 59.599 37.500 4.03 7.46 35.46 3.32
3315 3424 5.105513 AGGAACTCAAAATTTGACCGTGTTT 60.106 36.000 4.03 0.00 35.46 2.83
3316 3425 6.095720 AGGAACTCAAAATTTGACCGTGTTTA 59.904 34.615 4.03 0.00 35.46 2.01
3318 3427 7.114388 GGAACTCAAAATTTGACCGTGTTTATC 59.886 37.037 4.03 0.00 35.46 1.75
3319 3428 7.033530 ACTCAAAATTTGACCGTGTTTATCA 57.966 32.000 4.03 0.00 35.46 2.15
3371 3480 4.598257 CCAGTACTGGTGCCGAAG 57.402 61.111 30.57 5.48 45.53 3.79
3441 3550 0.899717 AAGCATTCCATGTTGGCCGT 60.900 50.000 0.00 0.00 37.47 5.68
3540 3649 2.398252 TCAGCAAGATGGAGCTTCTG 57.602 50.000 0.00 0.00 39.50 3.02
3603 3712 8.895737 AGGAACTCGTTTGTTTACATCTTTAAA 58.104 29.630 0.00 0.00 0.00 1.52
3636 3745 1.617850 TGCATCCCGCTTGTTGAAATT 59.382 42.857 0.00 0.00 43.06 1.82
3647 3756 6.346838 CCGCTTGTTGAAATTTTCCTCAATTC 60.347 38.462 6.68 6.34 34.26 2.17
3652 3761 9.835389 TTGTTGAAATTTTCCTCAATTCTGAAT 57.165 25.926 6.68 0.00 34.26 2.57
3664 3773 6.933521 CCTCAATTCTGAATTCGGATAGTGAT 59.066 38.462 17.62 5.28 0.00 3.06
3680 3789 7.816513 CGGATAGTGATGTCTGATGAATGTTAT 59.183 37.037 0.00 0.00 0.00 1.89
3945 4056 4.825422 TGCTCAAGATCCCGATATCATTC 58.175 43.478 3.12 0.00 0.00 2.67
3951 4062 4.429505 AGATCCCGATATCATTCCTGGAA 58.570 43.478 12.26 12.26 0.00 3.53
4152 4263 1.801178 CTTGTTCTTCTGGTTCTCGGC 59.199 52.381 0.00 0.00 0.00 5.54
4198 4309 1.542108 CGAATCTCCCTCCATTCAGCC 60.542 57.143 0.00 0.00 0.00 4.85
4209 4320 1.404391 CCATTCAGCCTCTGTTCATGC 59.596 52.381 0.00 0.00 32.61 4.06
4236 4347 4.903054 TCAACTGTCAAGAAGATCATGCT 58.097 39.130 0.00 0.00 0.00 3.79
4239 4350 4.505808 ACTGTCAAGAAGATCATGCTGAG 58.494 43.478 0.00 0.00 0.00 3.35
4240 4351 4.020396 ACTGTCAAGAAGATCATGCTGAGT 60.020 41.667 0.00 0.00 0.00 3.41
4241 4352 4.903054 TGTCAAGAAGATCATGCTGAGTT 58.097 39.130 0.00 0.00 0.00 3.01
4242 4353 4.694037 TGTCAAGAAGATCATGCTGAGTTG 59.306 41.667 0.00 0.00 0.00 3.16
4243 4354 4.694509 GTCAAGAAGATCATGCTGAGTTGT 59.305 41.667 0.00 0.00 0.00 3.32
4244 4355 4.694037 TCAAGAAGATCATGCTGAGTTGTG 59.306 41.667 0.00 0.00 0.00 3.33
4245 4356 4.548451 AGAAGATCATGCTGAGTTGTGA 57.452 40.909 0.00 0.00 0.00 3.58
4400 4511 1.550524 CTGGACCCTTGATCAGTCGAA 59.449 52.381 7.31 0.00 0.00 3.71
4416 4527 9.684448 GATCAGTCGAATTTCAGACAGATAATA 57.316 33.333 19.03 3.80 41.51 0.98
4473 4585 1.000843 ACAGACAGCAATGACACGCTA 59.999 47.619 1.06 0.00 36.50 4.26
4618 4730 1.542492 TGACCGTGAGTACCTTCTCC 58.458 55.000 0.00 0.00 33.93 3.71
4814 4926 3.154827 TCCCAGAATTCACCTTCCAAC 57.845 47.619 8.44 0.00 0.00 3.77
4865 4977 1.953686 CAAGGAACACATTTCCACCGT 59.046 47.619 5.85 0.00 41.00 4.83
4973 5085 3.884037 ACTCCCTTGTCAATCACCTTT 57.116 42.857 0.00 0.00 0.00 3.11
5303 5415 2.235402 TGGATACCCGAAGAACCAAGAC 59.765 50.000 0.00 0.00 34.29 3.01
5336 5448 2.340210 TTGCTGGTTACTGTGAGCAA 57.660 45.000 5.95 9.35 46.49 3.91
5432 5544 4.937201 TGTAGACTCAGAAGCAAGACAA 57.063 40.909 0.00 0.00 0.00 3.18
5451 5563 8.836413 CAAGACAAGTAAGTTGAATGACCTTTA 58.164 33.333 0.00 0.00 38.60 1.85
5515 5639 4.751767 ACTGATCTCTGGAGTCCATTTC 57.248 45.455 13.56 7.94 30.82 2.17
5960 6084 2.218115 TTTATGTCGGCCCCTTGGGG 62.218 60.000 20.18 20.18 44.57 4.96
6014 6138 2.102252 GGTGAGGCTCCTTACTGATCTG 59.898 54.545 12.86 0.00 33.70 2.90
6015 6139 2.102252 GTGAGGCTCCTTACTGATCTGG 59.898 54.545 12.86 0.00 31.00 3.86
6038 6162 0.036010 ACAGAGCACCCGATTTCCAG 60.036 55.000 0.00 0.00 0.00 3.86
6039 6163 1.078143 AGAGCACCCGATTTCCAGC 60.078 57.895 0.00 0.00 0.00 4.85
6076 6201 2.736531 CTTGCTTGGTGCCCCAAC 59.263 61.111 0.00 0.00 45.93 3.77
6292 6447 7.491048 TCATTTCACTGATTCAAATGCATCATG 59.509 33.333 0.00 2.55 37.41 3.07
6293 6448 5.907866 TCACTGATTCAAATGCATCATGT 57.092 34.783 0.00 0.00 28.06 3.21
6338 6493 0.389948 GACCTAAGCACACCTCCACG 60.390 60.000 0.00 0.00 0.00 4.94
6361 6516 1.065251 GATCGACGGACCTGTACTTCC 59.935 57.143 0.00 0.00 0.00 3.46
6372 6527 5.514310 GGACCTGTACTTCCCAAAACAGTAT 60.514 44.000 0.00 0.00 38.10 2.12
6375 6530 4.720046 TGTACTTCCCAAAACAGTATGCA 58.280 39.130 0.00 0.00 42.53 3.96
6396 6551 2.880890 ACAGTCCTTCTTCACACAATGC 59.119 45.455 0.00 0.00 0.00 3.56
6397 6552 2.880268 CAGTCCTTCTTCACACAATGCA 59.120 45.455 0.00 0.00 0.00 3.96
6420 6575 1.228644 TTGCCTGTGGAAGCAGCAT 60.229 52.632 0.00 0.00 40.73 3.79
6426 6581 2.012673 CTGTGGAAGCAGCATAAGTCC 58.987 52.381 0.00 0.00 0.00 3.85
6462 6617 7.360113 TCCATCATACACTGCAACTAGAATA 57.640 36.000 0.00 0.00 0.00 1.75
6483 6638 2.736144 TCTTCACGACGGTTATTGCT 57.264 45.000 0.00 0.00 0.00 3.91
6523 6678 7.014230 CCATCTTTTTGAACCTAGGACAGAAAA 59.986 37.037 17.98 18.47 0.00 2.29
6551 6706 1.079503 CCTTCGCTAACAACTCCAGC 58.920 55.000 0.00 0.00 0.00 4.85
6562 6719 2.289320 ACAACTCCAGCTGACACTGATC 60.289 50.000 17.39 0.00 40.25 2.92
6594 6751 6.220930 ACACAGCGTGAGAAAGAAACTTATA 58.779 36.000 14.18 0.00 36.96 0.98
6626 6783 1.808411 TTACTTTCAGCGGCAAGAGG 58.192 50.000 2.99 0.09 0.00 3.69
6755 6912 1.211190 CCGAGAAAAAGCTGCTGGC 59.789 57.895 1.35 0.00 42.19 4.85
6800 6957 2.264005 TTGCACAGGTAATGGTCGTT 57.736 45.000 0.00 0.00 0.00 3.85
6807 6964 3.009723 CAGGTAATGGTCGTTGCAGAAT 58.990 45.455 0.00 0.00 0.00 2.40
6816 6973 5.457140 TGGTCGTTGCAGAATATTTGAAAC 58.543 37.500 9.64 9.64 31.89 2.78
6827 6984 9.128107 GCAGAATATTTGAAACGAAAAGATTGA 57.872 29.630 0.00 0.00 30.71 2.57
6834 6991 9.971744 ATTTGAAACGAAAAGATTGAACTTTTG 57.028 25.926 10.42 6.52 45.91 2.44
6835 6992 6.988329 TGAAACGAAAAGATTGAACTTTTGC 58.012 32.000 10.42 3.48 45.91 3.68
6845 7002 5.595952 AGATTGAACTTTTGCTCCTTCAACT 59.404 36.000 0.00 0.00 35.89 3.16
6905 7065 4.708421 CAGGTTTTCATTGAGATCCCACAT 59.292 41.667 1.65 0.00 0.00 3.21
6914 7074 3.994317 TGAGATCCCACATGTCTTCCTA 58.006 45.455 0.00 0.00 0.00 2.94
6974 7134 1.683385 GGCTTGGACTGGGCATTTATC 59.317 52.381 0.00 0.00 0.00 1.75
7064 7224 2.126346 GCCATGACGCCAAACAGC 60.126 61.111 0.00 0.00 0.00 4.40
7082 7242 0.305922 GCGACATTGCTGCCATAGTC 59.694 55.000 0.00 2.24 0.00 2.59
7121 7281 4.389374 CAGTATGGAATATCTTTGCCGGT 58.611 43.478 1.90 0.00 0.00 5.28
7137 7297 1.903294 GGTTTCCTAGTCCCCCGAC 59.097 63.158 0.00 0.00 39.50 4.79
7181 7341 6.039941 TGGTTTATTTGTAGTGAACCAACCTG 59.960 38.462 3.95 0.00 44.75 4.00
7200 7360 5.186198 ACCTGTACATTTTCTCCATACTGC 58.814 41.667 0.00 0.00 0.00 4.40
7326 7486 4.641989 GTTGCCTCACAATATGGAGACATT 59.358 41.667 0.00 0.00 44.94 2.71
7337 7497 2.683968 TGGAGACATTGCAGACGTTAC 58.316 47.619 0.00 0.00 33.40 2.50
7418 7578 4.573201 TGATTACGTAGGTTTTATGGCTGC 59.427 41.667 0.00 0.00 0.00 5.25
7467 7627 2.394708 GCTTTCGTTTTTGCCTTCTCC 58.605 47.619 0.00 0.00 0.00 3.71
7588 7748 7.215085 GGAACACAGGAAAGTAAGTTTAGAGA 58.785 38.462 0.00 0.00 0.00 3.10
7590 7750 6.214399 ACACAGGAAAGTAAGTTTAGAGACG 58.786 40.000 0.00 0.00 0.00 4.18
7591 7751 5.634020 CACAGGAAAGTAAGTTTAGAGACGG 59.366 44.000 0.00 0.00 0.00 4.79
7624 7785 4.932268 TCCGTTTCTTAGGCAATTAACG 57.068 40.909 0.00 0.00 38.36 3.18
7640 7801 8.827677 GGCAATTAACGTATTTCTTAGATCAGT 58.172 33.333 0.00 0.00 0.00 3.41
7707 7868 4.021807 AGGGCCCGTTGTAATTTTGTAAAG 60.022 41.667 18.44 0.00 0.00 1.85
7713 7876 7.515528 GCCCGTTGTAATTTTGTAAAGTTCAAC 60.516 37.037 10.16 10.16 31.16 3.18
7771 8023 5.249622 TGGTTCAGTTGATACATGTTCCCTA 59.750 40.000 2.30 0.00 0.00 3.53
7849 8101 6.302535 TCCGAAGAATATTGTGGGAAACTA 57.697 37.500 0.00 0.00 0.00 2.24
7876 8128 7.203218 ACAAATTTCCAGTGAAAACTAGCTTC 58.797 34.615 0.00 0.00 43.37 3.86
7885 8138 3.250040 TGAAAACTAGCTTCGGAAACTGC 59.750 43.478 3.97 0.00 0.00 4.40
7887 8140 2.086054 ACTAGCTTCGGAAACTGCTG 57.914 50.000 11.83 6.03 37.02 4.41
7918 8171 2.424601 AGATTTGTGAATGGTGATGCGG 59.575 45.455 0.00 0.00 0.00 5.69
8007 8260 7.598278 ACGTTTTGGCAGTTTAAATATCATCA 58.402 30.769 0.00 0.00 0.00 3.07
8144 8402 8.043710 AGGTTCTCAAATCCAGTTACTATCTTG 58.956 37.037 0.00 0.00 0.00 3.02
8149 8407 8.251750 TCAAATCCAGTTACTATCTTGTTTCG 57.748 34.615 0.00 0.00 0.00 3.46
8190 8456 9.651913 ATTGTGTCTCAAATTGTTTTGTTTACT 57.348 25.926 0.00 0.00 42.37 2.24
8288 8583 2.688446 TGCTGGTAGAATCGACACTAGG 59.312 50.000 0.00 0.00 0.00 3.02
8293 8588 6.630444 TGGTAGAATCGACACTAGGTAATC 57.370 41.667 0.00 0.00 0.00 1.75
8317 8612 1.277273 TCTGAGAACAGGCATCCACTG 59.723 52.381 0.00 0.00 43.60 3.66
8318 8613 1.277273 CTGAGAACAGGCATCCACTGA 59.723 52.381 0.00 0.00 40.14 3.41
8553 8857 3.564027 CCTTGGAATCCGCGCGAC 61.564 66.667 34.63 18.54 0.00 5.19
8554 8858 2.509336 CTTGGAATCCGCGCGACT 60.509 61.111 34.63 15.51 0.00 4.18
8555 8859 2.508439 TTGGAATCCGCGCGACTC 60.508 61.111 34.63 22.77 0.00 3.36
8556 8860 4.508128 TGGAATCCGCGCGACTCC 62.508 66.667 34.63 30.07 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
60 61 6.945636 TGTTAGGGTTTAATCTCCAGAAGA 57.054 37.500 0.00 0.00 38.72 2.87
61 62 6.094186 GCTTGTTAGGGTTTAATCTCCAGAAG 59.906 42.308 0.00 0.00 0.00 2.85
62 63 5.944007 GCTTGTTAGGGTTTAATCTCCAGAA 59.056 40.000 0.00 0.00 0.00 3.02
63 64 5.013704 TGCTTGTTAGGGTTTAATCTCCAGA 59.986 40.000 0.00 0.00 0.00 3.86
64 65 5.253330 TGCTTGTTAGGGTTTAATCTCCAG 58.747 41.667 0.00 0.00 0.00 3.86
65 66 5.249780 TGCTTGTTAGGGTTTAATCTCCA 57.750 39.130 0.00 0.00 0.00 3.86
79 80 8.264347 TCATCATAAGTACCATCTTGCTTGTTA 58.736 33.333 0.00 0.00 0.00 2.41
82 83 7.741027 ATCATCATAAGTACCATCTTGCTTG 57.259 36.000 0.00 0.00 0.00 4.01
83 84 7.255381 GCAATCATCATAAGTACCATCTTGCTT 60.255 37.037 0.00 0.00 33.28 3.91
104 105 2.387757 TCTAGGGCAAATTGGGCAATC 58.612 47.619 8.88 0.00 34.52 2.67
114 115 5.241403 TGTCTCATTTCTTCTAGGGCAAA 57.759 39.130 0.00 0.00 0.00 3.68
121 122 7.391554 CACTTCCCAAATGTCTCATTTCTTCTA 59.608 37.037 4.97 0.00 0.00 2.10
134 135 4.665451 TGATGTCATCACTTCCCAAATGT 58.335 39.130 11.62 0.00 33.59 2.71
151 152 0.036388 CGTAAGTGGGCCACTGATGT 60.036 55.000 38.18 24.98 44.62 3.06
157 158 1.534163 GAAGTTTCGTAAGTGGGCCAC 59.466 52.381 29.32 29.32 39.48 5.01
220 221 3.052338 AGGGGTAAACTTATCCTCCTCGA 60.052 47.826 0.00 0.00 34.26 4.04
255 256 3.261897 ACATCTCTGGTTGGTTAGACAGG 59.738 47.826 0.00 0.00 0.00 4.00
393 398 4.894784 TGTAGCTACTAGTTGCTTTGCTT 58.105 39.130 31.62 13.16 41.56 3.91
401 411 8.787852 TGTAGATGATGATGTAGCTACTAGTTG 58.212 37.037 23.84 0.00 31.86 3.16
402 412 8.926092 TGTAGATGATGATGTAGCTACTAGTT 57.074 34.615 23.84 7.46 31.86 2.24
403 413 8.955388 CATGTAGATGATGATGTAGCTACTAGT 58.045 37.037 23.84 10.59 31.86 2.57
440 450 9.150348 CAAAGTTAATTTTCACAAAAGTGACCT 57.850 29.630 0.00 0.00 36.14 3.85
475 505 7.771927 AGAAGGAAATGATTCTCAAACATGT 57.228 32.000 0.00 0.00 35.79 3.21
495 525 9.868277 ACTCTCTTGATTTCACATTACTAGAAG 57.132 33.333 0.00 0.00 0.00 2.85
790 828 0.809385 TCCTTGTCGTTCGGCTCTAG 59.191 55.000 0.00 0.00 0.00 2.43
917 958 0.876342 GAGCTATATATGCCCGCGCC 60.876 60.000 0.00 0.00 0.00 6.53
1469 1533 0.108424 ACAGAAGCGAGGTGATGAGC 60.108 55.000 0.00 0.00 0.00 4.26
1470 1534 2.797792 GCTACAGAAGCGAGGTGATGAG 60.798 54.545 0.00 0.00 42.53 2.90
1497 1561 1.139654 TGCCGAGAGAGAAATGGATGG 59.860 52.381 0.00 0.00 0.00 3.51
1686 1758 1.334243 GAAGGATCATGAAGCTGCTGC 59.666 52.381 1.35 7.62 40.05 5.25
1708 1780 2.369394 GGTTCTCCCATTCCATGACAC 58.631 52.381 0.00 0.00 0.00 3.67
1709 1781 2.806945 GGTTCTCCCATTCCATGACA 57.193 50.000 0.00 0.00 0.00 3.58
1729 1802 0.655733 ACTCGGCGTGAACTTTGTTG 59.344 50.000 16.57 0.00 0.00 3.33
1744 1817 1.009389 GCTGAAGTCGGAACCACTCG 61.009 60.000 0.00 0.00 0.00 4.18
1894 1967 0.458260 AAAACAAACAGGCCCGTGAC 59.542 50.000 0.00 0.00 0.00 3.67
1901 1974 3.656559 AGATGATGCAAAACAAACAGGC 58.343 40.909 0.00 0.00 0.00 4.85
1947 2020 4.214332 GGACATTCTGAAGAAACTCCACAC 59.786 45.833 11.76 0.00 37.61 3.82
1964 2037 0.681175 GGCCAAGCAACAAGGACATT 59.319 50.000 0.00 0.00 0.00 2.71
1994 2067 4.745649 CCAGGAGTAGACTAGTTTTTCCG 58.254 47.826 0.00 0.51 0.00 4.30
2054 2127 3.599343 TCACGAAAGGATGTGAAGATGG 58.401 45.455 0.00 0.00 41.82 3.51
2078 2151 4.974275 TCGAACGAAAAACAGAGTACTCAG 59.026 41.667 24.44 18.88 0.00 3.35
2095 2168 7.850492 TCATATTGCAAATTTCTGTATCGAACG 59.150 33.333 1.71 0.00 0.00 3.95
2096 2169 9.669353 ATCATATTGCAAATTTCTGTATCGAAC 57.331 29.630 1.71 0.00 0.00 3.95
2097 2170 9.882996 GATCATATTGCAAATTTCTGTATCGAA 57.117 29.630 1.71 0.00 0.00 3.71
2099 2172 9.326339 CTGATCATATTGCAAATTTCTGTATCG 57.674 33.333 1.71 0.00 0.00 2.92
2265 2340 1.062587 GTCATTTCGCCGATGTGAAGG 59.937 52.381 3.90 0.00 41.68 3.46
2345 2420 1.067295 TTTCCAGCTCCCATGTCACT 58.933 50.000 0.00 0.00 0.00 3.41
2376 2451 5.840715 TCACTTTGCAATTTGTGAATAGCA 58.159 33.333 20.56 0.00 36.64 3.49
2392 2467 6.898041 TGAAACCACGATAAGAATCACTTTG 58.102 36.000 0.00 0.00 39.72 2.77
2508 2583 8.962884 TGATTCACAGTGTATATGCAATAACT 57.037 30.769 0.00 0.00 29.06 2.24
2515 2590 6.540189 AGGTTCTTGATTCACAGTGTATATGC 59.460 38.462 0.00 0.00 0.00 3.14
2521 2596 7.823745 AAATAAGGTTCTTGATTCACAGTGT 57.176 32.000 0.00 0.00 0.00 3.55
2543 2618 9.452287 AGGCAATACCGTTTACTTCTAAATAAA 57.548 29.630 0.00 0.00 46.52 1.40
2558 2633 3.418684 ACTTCAGAAAGGCAATACCGT 57.581 42.857 0.00 0.00 46.52 4.83
2559 2634 5.873179 TTTACTTCAGAAAGGCAATACCG 57.127 39.130 0.00 0.00 46.52 4.02
2560 2635 8.732746 TCTATTTACTTCAGAAAGGCAATACC 57.267 34.615 0.00 0.00 36.78 2.73
2563 2638 9.077885 TGTTTCTATTTACTTCAGAAAGGCAAT 57.922 29.630 0.00 0.00 38.57 3.56
2595 2670 7.777095 AGAGGAGCAGAATAACTTAGTAACTG 58.223 38.462 0.00 0.00 0.00 3.16
2597 2672 9.902196 GATAGAGGAGCAGAATAACTTAGTAAC 57.098 37.037 0.00 0.00 0.00 2.50
2621 2696 1.637553 ACAGAGATGGCCTGTTTGGAT 59.362 47.619 3.32 0.00 41.68 3.41
2717 2792 1.750206 TGTCAGCGGCATATGCATTTT 59.250 42.857 28.07 8.54 44.36 1.82
2731 2806 2.468777 CGAAAAATGCAAGTGTGTCAGC 59.531 45.455 0.00 0.00 0.00 4.26
2745 2820 6.215845 CAGACCCAAAATCTGAACGAAAAAT 58.784 36.000 0.00 0.00 45.46 1.82
2747 2822 4.037446 CCAGACCCAAAATCTGAACGAAAA 59.963 41.667 3.58 0.00 45.46 2.29
2748 2823 3.568007 CCAGACCCAAAATCTGAACGAAA 59.432 43.478 3.58 0.00 45.46 3.46
2749 2824 3.146066 CCAGACCCAAAATCTGAACGAA 58.854 45.455 3.58 0.00 45.46 3.85
2754 2829 5.261040 AGATTTCCAGACCCAAAATCTGA 57.739 39.130 8.36 0.00 45.46 3.27
2796 2871 1.040646 TGCCTCTGATCATACCGTCC 58.959 55.000 0.00 0.00 0.00 4.79
2927 3003 9.903682 ATCTCGCCTATTTAAATTTCAATGATG 57.096 29.630 5.91 0.00 0.00 3.07
3074 3150 0.097674 GCTGAAGCAACGCGATCAAT 59.902 50.000 15.93 0.00 41.59 2.57
3176 3252 1.801178 GCCTCAAAGAACTCAAGGACG 59.199 52.381 0.00 0.00 0.00 4.79
3224 3300 0.312102 GCAAGAAGTCTGCAACACCC 59.688 55.000 0.00 0.00 0.00 4.61
3227 3303 2.642427 TCTTGCAAGAAGTCTGCAACA 58.358 42.857 26.61 0.00 42.65 3.33
3263 3339 1.292860 GTGCAGCACAGAGAGCTCT 59.707 57.895 18.28 18.28 41.14 4.09
3267 3343 1.563435 CCAACGTGCAGCACAGAGAG 61.563 60.000 25.19 10.82 33.40 3.20
3281 3390 3.396260 TTTGAGTTCCTAGTCCCAACG 57.604 47.619 0.00 0.00 0.00 4.10
3285 3394 5.183331 GGTCAAATTTTGAGTTCCTAGTCCC 59.817 44.000 12.02 2.78 41.01 4.46
3302 3411 7.754924 GTGAATTCATGATAAACACGGTCAAAT 59.245 33.333 12.12 0.00 0.00 2.32
3305 3414 5.703130 TGTGAATTCATGATAAACACGGTCA 59.297 36.000 12.12 0.00 0.00 4.02
3306 3415 6.176975 TGTGAATTCATGATAAACACGGTC 57.823 37.500 12.12 0.00 0.00 4.79
3307 3416 5.123820 CCTGTGAATTCATGATAAACACGGT 59.876 40.000 12.12 0.00 33.20 4.83
3308 3417 5.123820 ACCTGTGAATTCATGATAAACACGG 59.876 40.000 12.12 17.14 34.33 4.94
3309 3418 6.182039 ACCTGTGAATTCATGATAAACACG 57.818 37.500 12.12 0.13 0.00 4.49
3310 3419 8.511321 TGTTACCTGTGAATTCATGATAAACAC 58.489 33.333 12.12 6.11 0.00 3.32
3312 3421 9.722056 GATGTTACCTGTGAATTCATGATAAAC 57.278 33.333 12.12 13.47 0.00 2.01
3315 3424 9.987272 CTAGATGTTACCTGTGAATTCATGATA 57.013 33.333 12.12 0.00 0.00 2.15
3316 3425 7.935755 CCTAGATGTTACCTGTGAATTCATGAT 59.064 37.037 12.12 0.00 0.00 2.45
3318 3427 7.275183 TCCTAGATGTTACCTGTGAATTCATG 58.725 38.462 12.12 7.83 0.00 3.07
3319 3428 7.437713 TCCTAGATGTTACCTGTGAATTCAT 57.562 36.000 12.12 0.00 0.00 2.57
3371 3480 1.335810 TGTATCGGTATGGCTCGTCAC 59.664 52.381 0.00 0.00 0.00 3.67
3441 3550 0.397114 TGAGCTCCGAGCCCATCTTA 60.397 55.000 16.99 0.00 43.77 2.10
3540 3649 0.249657 CCCTAGAGACGCATGCCTTC 60.250 60.000 13.15 9.04 0.00 3.46
3603 3712 3.807209 GCGGGATGCATACCTGAACTATT 60.807 47.826 25.72 0.00 45.45 1.73
3636 3745 7.280876 CACTATCCGAATTCAGAATTGAGGAAA 59.719 37.037 23.44 10.34 37.63 3.13
3647 3756 5.836347 TCAGACATCACTATCCGAATTCAG 58.164 41.667 6.22 0.00 0.00 3.02
3652 3761 5.852282 TTCATCAGACATCACTATCCGAA 57.148 39.130 0.00 0.00 0.00 4.30
3664 3773 7.509141 ACAAACACATAACATTCATCAGACA 57.491 32.000 0.00 0.00 0.00 3.41
3680 3789 4.941263 GGATTATGAGCTGGTACAAACACA 59.059 41.667 0.00 0.00 38.70 3.72
3858 3969 5.540337 CAGGTCCCTCTGCTTGTAGAATATA 59.460 44.000 0.00 0.00 0.00 0.86
3945 4056 2.334946 CCACACGGCACATTCCAGG 61.335 63.158 0.00 0.00 0.00 4.45
3951 4062 1.746615 GCAGATCCACACGGCACAT 60.747 57.895 0.00 0.00 0.00 3.21
3987 4098 1.368641 CGATGTTTGGATCGAAGCCA 58.631 50.000 6.30 6.30 46.72 4.75
4152 4263 2.625790 ACCTCTAGCTATCAAGAAGCCG 59.374 50.000 0.00 0.00 41.02 5.52
4198 4309 4.825546 AGTTGAAACTGCATGAACAGAG 57.174 40.909 7.27 0.00 40.25 3.35
4236 4347 3.565482 GCAGAAATGGAACTCACAACTCA 59.435 43.478 0.00 0.00 0.00 3.41
4239 4350 3.565482 TCTGCAGAAATGGAACTCACAAC 59.435 43.478 15.67 0.00 0.00 3.32
4240 4351 3.819368 TCTGCAGAAATGGAACTCACAA 58.181 40.909 15.67 0.00 0.00 3.33
4241 4352 3.490439 TCTGCAGAAATGGAACTCACA 57.510 42.857 15.67 0.00 0.00 3.58
4242 4353 5.412594 TGTTATCTGCAGAAATGGAACTCAC 59.587 40.000 22.50 3.83 0.00 3.51
4243 4354 5.559770 TGTTATCTGCAGAAATGGAACTCA 58.440 37.500 22.50 7.21 0.00 3.41
4244 4355 6.317140 TGATGTTATCTGCAGAAATGGAACTC 59.683 38.462 22.50 16.18 0.00 3.01
4245 4356 6.182627 TGATGTTATCTGCAGAAATGGAACT 58.817 36.000 22.50 3.74 0.00 3.01
4473 4585 2.607282 CGACTTCAAGACTTGTACGCCT 60.607 50.000 14.75 0.00 0.00 5.52
4512 4624 1.553248 CCGATCCAGTACCAGTTTGGA 59.447 52.381 1.40 3.48 44.52 3.53
4618 4730 1.476085 TCAATGCATTTTACGGCTGGG 59.524 47.619 9.83 0.00 0.00 4.45
4814 4926 6.019479 GTCTATGCAAGAATTTCTACTGACCG 60.019 42.308 0.00 0.00 35.47 4.79
4853 4965 1.614996 TGATGCAACGGTGGAAATGT 58.385 45.000 0.00 0.00 0.00 2.71
4865 4977 5.067023 TGTTACACTTGTCACAATGATGCAA 59.933 36.000 0.00 0.00 30.14 4.08
5153 5265 0.615331 CTGGCCTGAAAGCTCCACTA 59.385 55.000 3.32 0.00 32.77 2.74
5303 5415 0.388907 CAGCAATCCGGGCAAAAGTG 60.389 55.000 0.00 0.00 0.00 3.16
5336 5448 7.230108 GTGACATGTGGAGAATGGATATCATTT 59.770 37.037 1.15 0.00 45.36 2.32
5399 5511 2.832129 TGAGTCTACATCAGGGGACAAC 59.168 50.000 0.00 0.00 0.00 3.32
5432 5544 7.885399 AGCAGAATAAAGGTCATTCAACTTACT 59.115 33.333 0.00 0.00 35.30 2.24
5451 5563 7.353414 TGAGCTACTTATGAACTAGCAGAAT 57.647 36.000 0.00 0.00 36.18 2.40
5484 5597 1.463831 CAGAGATCAGTTGCAGTGTGC 59.536 52.381 0.00 0.00 45.29 4.57
5515 5639 6.448852 TGTTCCACAAACATCTGAATTCATG 58.551 36.000 8.96 8.04 42.95 3.07
5960 6084 1.456296 TCAGATGGCATGAGTTGTGC 58.544 50.000 3.81 0.00 41.78 4.57
6015 6139 1.464997 GAAATCGGGTGCTCTGTTCAC 59.535 52.381 0.00 0.00 0.00 3.18
6038 6162 3.508793 AGGTTATCATGCATGCCATAAGC 59.491 43.478 26.99 26.99 44.14 3.09
6039 6163 5.466819 CAAGGTTATCATGCATGCCATAAG 58.533 41.667 22.25 6.33 31.47 1.73
6076 6201 4.819105 TCACACCTTGTATTCCCTACAG 57.181 45.455 0.00 0.00 41.30 2.74
6084 6209 7.505585 TCCTTGATTTTCTTCACACCTTGTATT 59.494 33.333 0.00 0.00 0.00 1.89
6292 6447 3.214328 TCAAAGCTTTGTTCCTCCTGAC 58.786 45.455 32.46 0.00 39.18 3.51
6293 6448 3.576078 TCAAAGCTTTGTTCCTCCTGA 57.424 42.857 32.46 12.59 39.18 3.86
6338 6493 0.100146 GTACAGGTCCGTCGATCCAC 59.900 60.000 0.00 0.00 0.00 4.02
6361 6516 3.149196 AGGACTGTGCATACTGTTTTGG 58.851 45.455 1.24 0.00 38.83 3.28
6372 6527 1.209261 TGTGTGAAGAAGGACTGTGCA 59.791 47.619 1.24 0.00 0.00 4.57
6375 6530 2.880890 GCATTGTGTGAAGAAGGACTGT 59.119 45.455 0.00 0.00 0.00 3.55
6396 6551 0.389426 GCTTCCACAGGCAAGCAATG 60.389 55.000 12.29 0.00 43.87 2.82
6397 6552 1.969862 GCTTCCACAGGCAAGCAAT 59.030 52.632 12.29 0.00 43.87 3.56
6462 6617 3.596214 AGCAATAACCGTCGTGAAGAAT 58.404 40.909 0.00 0.00 0.00 2.40
6483 6638 3.726557 AAGATGGTGCCAAAGATGAGA 57.273 42.857 0.00 0.00 0.00 3.27
6551 6706 5.422145 TGTGTCATTATGGATCAGTGTCAG 58.578 41.667 0.00 0.00 0.00 3.51
6562 6719 2.892374 TCTCACGCTGTGTCATTATGG 58.108 47.619 8.22 0.00 34.79 2.74
6594 6751 6.313905 CCGCTGAAAGTAAAGATGAAGTACAT 59.686 38.462 0.00 0.00 37.99 2.29
6609 6766 1.968540 GCCTCTTGCCGCTGAAAGT 60.969 57.895 0.00 0.00 35.30 2.66
6626 6783 3.305608 CCAAAGAATTGAACAGGTCCTGC 60.306 47.826 19.40 4.13 38.94 4.85
6629 6786 3.230976 ACCCAAAGAATTGAACAGGTCC 58.769 45.455 0.00 0.00 38.94 4.46
6746 6903 0.107800 CAGAGTACATGCCAGCAGCT 60.108 55.000 0.00 0.00 44.23 4.24
6755 6912 4.321601 GCATAGGGTAGAGCAGAGTACATG 60.322 50.000 0.00 0.00 0.00 3.21
6792 6949 5.895636 TTCAAATATTCTGCAACGACCAT 57.104 34.783 0.00 0.00 0.00 3.55
6795 6952 5.379003 TCGTTTCAAATATTCTGCAACGAC 58.621 37.500 21.43 3.60 43.86 4.34
6800 6957 8.914654 CAATCTTTTCGTTTCAAATATTCTGCA 58.085 29.630 0.00 0.00 0.00 4.41
6816 6973 5.523369 AGGAGCAAAAGTTCAATCTTTTCG 58.477 37.500 2.11 1.27 43.09 3.46
6861 7021 8.055279 ACCTGTTGAATGGTTAACATCATTAG 57.945 34.615 8.10 9.17 39.40 1.73
6869 7029 7.708752 TCAATGAAAACCTGTTGAATGGTTAAC 59.291 33.333 0.00 0.00 44.83 2.01
6974 7134 9.918630 ATGAAGAAGATGTACCAAAAGAATTTG 57.081 29.630 0.00 0.00 44.50 2.32
6992 7152 6.261826 ACAGGAAAGTGAAGAACATGAAGAAG 59.738 38.462 0.00 0.00 0.00 2.85
7064 7224 0.578683 CGACTATGGCAGCAATGTCG 59.421 55.000 15.77 15.77 40.55 4.35
7100 7260 4.706842 ACCGGCAAAGATATTCCATACT 57.293 40.909 0.00 0.00 0.00 2.12
7121 7281 0.616679 CTGGTCGGGGGACTAGGAAA 60.617 60.000 0.00 0.00 31.19 3.13
7137 7297 3.769844 ACCAGTCATAGGACACTTACTGG 59.230 47.826 15.80 15.80 46.80 4.00
7181 7341 4.439057 TCGGCAGTATGGAGAAAATGTAC 58.561 43.478 0.00 0.00 35.86 2.90
7200 7360 6.701841 ACAAGACACATATAGTTTAGCATCGG 59.298 38.462 0.00 0.00 0.00 4.18
7326 7486 1.080772 CTCCAGCGTAACGTCTGCA 60.081 57.895 8.96 0.00 32.73 4.41
7337 7497 2.190578 GTTCCCCATCCTCCAGCG 59.809 66.667 0.00 0.00 0.00 5.18
7418 7578 2.289444 ACAGTGAATCCTACAACACCGG 60.289 50.000 0.00 0.00 34.33 5.28
7771 8023 1.002773 AGTCGGTAATGGGCTTTTCGT 59.997 47.619 0.00 0.00 0.00 3.85
7849 8101 7.555965 AGCTAGTTTTCACTGGAAATTTGTTT 58.444 30.769 0.00 0.00 42.31 2.83
7876 8128 5.116180 TCTTGATTATACCAGCAGTTTCCG 58.884 41.667 0.00 0.00 0.00 4.30
7885 8138 8.906867 ACCATTCACAAATCTTGATTATACCAG 58.093 33.333 0.00 0.00 0.00 4.00
7887 8140 8.902806 TCACCATTCACAAATCTTGATTATACC 58.097 33.333 0.00 0.00 0.00 2.73
7918 8171 4.285807 TGTATGCTGAACACAAACACAC 57.714 40.909 0.00 0.00 0.00 3.82
8050 8307 4.271533 TGTTAGTCGTTGAAATGCGAGTTT 59.728 37.500 0.00 0.00 40.63 2.66
8130 8388 6.645415 AGTTGTCGAAACAAGATAGTAACTGG 59.355 38.462 11.33 0.00 45.78 4.00
8144 8402 5.178809 ACAATAGCCTGTTAGTTGTCGAAAC 59.821 40.000 0.00 0.00 0.00 2.78
8149 8407 5.238583 AGACACAATAGCCTGTTAGTTGTC 58.761 41.667 0.00 0.00 31.19 3.18
8189 8455 6.688813 GCTGCTCCAAAATTATCGAGTTTTAG 59.311 38.462 0.00 0.00 0.00 1.85
8190 8456 6.150307 TGCTGCTCCAAAATTATCGAGTTTTA 59.850 34.615 0.00 0.00 0.00 1.52
8193 8459 4.009675 TGCTGCTCCAAAATTATCGAGTT 58.990 39.130 0.00 0.00 0.00 3.01
8194 8460 3.609853 TGCTGCTCCAAAATTATCGAGT 58.390 40.909 0.00 0.00 0.00 4.18
8195 8461 4.621068 TTGCTGCTCCAAAATTATCGAG 57.379 40.909 0.00 0.00 0.00 4.04
8196 8462 4.217334 TGTTTGCTGCTCCAAAATTATCGA 59.783 37.500 0.00 0.00 36.55 3.59
8288 8583 4.569943 TGCCTGTTCTCAGAGTTGATTAC 58.430 43.478 0.00 0.00 43.76 1.89
8293 8588 2.289882 TGGATGCCTGTTCTCAGAGTTG 60.290 50.000 0.00 0.00 43.76 3.16
8317 8612 0.391661 TGCAGAATCTGGCGGACTTC 60.392 55.000 12.66 4.38 31.21 3.01
8318 8613 0.392193 CTGCAGAATCTGGCGGACTT 60.392 55.000 8.42 0.00 38.70 3.01


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

AutoCloner maintained by Alex Coulton.