Multiple sequence alignment - TraesCS4D01G185100

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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 TraesCS4D01G185100 chr4D 100.000 4165 0 0 1 4165 323111537 323107373 0.000000e+00 7692.0
1 TraesCS4D01G185100 chr4A 89.768 2111 115 36 1 2065 149034979 149037034 0.000000e+00 2608.0
2 TraesCS4D01G185100 chr4A 93.960 1010 57 2 2072 3081 149037097 149038102 0.000000e+00 1524.0
3 TraesCS4D01G185100 chr4A 83.949 785 70 27 3043 3815 149038115 149038855 0.000000e+00 701.0
4 TraesCS4D01G185100 chr4A 94.156 154 6 1 4015 4165 149039055 149039208 9.000000e-57 231.0
5 TraesCS4D01G185100 chr4A 96.226 53 2 0 3606 3658 37058778 37058830 2.060000e-13 87.9
6 TraesCS4D01G185100 chr4A 94.231 52 3 0 3606 3657 450788323 450788272 3.450000e-11 80.5
7 TraesCS4D01G185100 chr4B 94.511 1257 49 5 2072 3325 403263872 403262633 0.000000e+00 1921.0
8 TraesCS4D01G185100 chr4B 87.088 1394 103 48 705 2065 403265284 403263935 0.000000e+00 1506.0
9 TraesCS4D01G185100 chr4B 87.251 502 24 15 3677 4165 403262327 403261853 1.700000e-148 536.0
10 TraesCS4D01G185100 chr4B 80.363 662 80 22 36 679 403265911 403265282 1.360000e-124 457.0
11 TraesCS4D01G185100 chr4B 96.111 180 6 1 3394 3573 403262611 403262433 4.070000e-75 292.0
12 TraesCS4D01G185100 chr4B 83.730 252 34 4 13 263 403268256 403268011 9.000000e-57 231.0
13 TraesCS4D01G185100 chr4B 80.892 157 24 6 286 438 481800176 481800330 7.310000e-23 119.0
14 TraesCS4D01G185100 chr4B 81.013 158 21 8 286 438 183798225 183798072 2.630000e-22 117.0
15 TraesCS4D01G185100 chr7D 79.061 277 41 15 5 273 117544544 117544811 1.540000e-39 174.0
16 TraesCS4D01G185100 chr7D 88.710 124 12 1 13 134 117544679 117544802 2.590000e-32 150.0
17 TraesCS4D01G185100 chr7D 83.200 125 18 2 13 135 605155230 605155107 1.220000e-20 111.0
18 TraesCS4D01G185100 chr7D 79.054 148 25 5 292 437 133669067 133668924 3.430000e-16 97.1
19 TraesCS4D01G185100 chr7A 78.723 282 44 9 5 280 700066680 700066951 1.540000e-39 174.0
20 TraesCS4D01G185100 chr7A 92.453 53 4 0 3606 3658 10845748 10845696 4.460000e-10 76.8
21 TraesCS4D01G185100 chr5A 78.755 273 40 13 5 270 466571120 466570859 2.580000e-37 167.0
22 TraesCS4D01G185100 chr5B 78.571 266 43 10 10 269 78736359 78736102 3.330000e-36 163.0
23 TraesCS4D01G185100 chr1D 78.113 265 43 13 10 262 22185495 22185234 2.010000e-33 154.0
24 TraesCS4D01G185100 chr1D 81.699 153 27 1 286 437 5415158 5415310 4.370000e-25 126.0
25 TraesCS4D01G185100 chr2D 85.612 139 18 1 13 149 560398334 560398472 1.210000e-30 145.0
26 TraesCS4D01G185100 chr2D 82.927 123 19 1 15 135 621848944 621848822 4.400000e-20 110.0
27 TraesCS4D01G185100 chr2D 94.231 52 3 0 3606 3657 612720246 612720297 3.450000e-11 80.5
28 TraesCS4D01G185100 chr3B 82.803 157 23 4 281 435 172959927 172959773 2.020000e-28 137.0
29 TraesCS4D01G185100 chr3B 76.580 269 46 12 10 270 652963310 652963051 9.400000e-27 132.0
30 TraesCS4D01G185100 chr3B 94.340 53 2 1 3606 3657 67411131 67411079 3.450000e-11 80.5
31 TraesCS4D01G185100 chr3A 81.410 156 27 2 281 435 42217048 42216894 4.370000e-25 126.0
32 TraesCS4D01G185100 chr1B 87.037 108 14 0 28 135 378941986 378942093 5.650000e-24 122.0
33 TraesCS4D01G185100 chr1B 84.906 106 15 1 159 263 378941987 378942092 5.690000e-19 106.0
34 TraesCS4D01G185100 chr2B 80.357 168 24 8 281 444 672525729 672525567 7.310000e-23 119.0
35 TraesCS4D01G185100 chr2B 79.739 153 26 5 286 435 789530111 789530261 5.690000e-19 106.0
36 TraesCS4D01G185100 chr2A 82.927 123 19 2 15 135 753543361 753543239 4.400000e-20 110.0
37 TraesCS4D01G185100 chr2A 97.872 47 1 0 3611 3657 52577548 52577502 9.600000e-12 82.4
38 TraesCS4D01G185100 chr2A 92.982 57 3 1 3606 3662 195359164 195359219 9.600000e-12 82.4
39 TraesCS4D01G185100 chr6B 75.000 272 47 14 11 273 144850120 144849861 5.690000e-19 106.0
40 TraesCS4D01G185100 chr6D 94.340 53 3 0 3606 3658 325713102 325713154 9.600000e-12 82.4
41 TraesCS4D01G185100 chr7B 91.228 57 5 0 3605 3661 69537731 69537675 1.240000e-10 78.7


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 TraesCS4D01G185100 chr4D 323107373 323111537 4164 True 7692.000000 7692 100.000000 1 4165 1 chr4D.!!$R1 4164
1 TraesCS4D01G185100 chr4A 149034979 149039208 4229 False 1266.000000 2608 90.458250 1 4165 4 chr4A.!!$F2 4164
2 TraesCS4D01G185100 chr4B 403261853 403268256 6403 True 823.833333 1921 88.175667 13 4165 6 chr4B.!!$R2 4152

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
332 2655 0.555769 TTCTCCCAAACACCTGCCTT 59.444 50.0 0.00 0.00 0.0 4.35 F
1359 3718 0.032403 ACGACGGGTTCAATTGACGA 59.968 50.0 19.97 0.04 0.0 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1376 3735 0.037326 CAACGCAGACCTAGGAAGCA 60.037 55.0 17.98 0.0 0.0 3.91 R
3333 5851 0.399833 TGTAGACCATGCAGCCACAA 59.600 50.0 0.00 0.0 0.0 3.33 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
87 201 6.095440 CGAGTGACCCAATTCCAATTAAAGAT 59.905 38.462 0.00 0.00 0.00 2.40
88 202 7.174107 AGTGACCCAATTCCAATTAAAGATG 57.826 36.000 0.00 0.00 0.00 2.90
119 233 7.001674 TGAATGTTGGCTCTTTAAAACTAGGA 58.998 34.615 0.00 0.00 0.00 2.94
180 296 5.760253 ACGAGAGTGTTGAGAAATTGTTGAT 59.240 36.000 0.00 0.00 46.97 2.57
197 313 2.785562 TGATTCGGTCAAAATCGGGTT 58.214 42.857 0.00 0.00 36.18 4.11
209 325 7.704899 GGTCAAAATCGGGTTATCCAATTTTAG 59.295 37.037 11.73 8.65 37.93 1.85
248 364 7.589958 TGAATGTTGGCTTTTAAAACTAGGA 57.410 32.000 0.00 0.00 0.00 2.94
306 2628 4.857871 TTCAGCTTTTTACATCCGATCG 57.142 40.909 8.51 8.51 0.00 3.69
322 2645 2.225491 CGATCGCACTTTTTCTCCCAAA 59.775 45.455 0.26 0.00 0.00 3.28
332 2655 0.555769 TTCTCCCAAACACCTGCCTT 59.444 50.000 0.00 0.00 0.00 4.35
344 2667 1.272147 ACCTGCCTTTTGTGGAGGATC 60.272 52.381 4.76 0.00 36.33 3.36
374 2697 6.748969 TCCCTATCCAAACCTACTTTCTCTA 58.251 40.000 0.00 0.00 0.00 2.43
395 2718 4.963318 AACATCCGATCCTACATGACAT 57.037 40.909 0.00 0.00 0.00 3.06
413 2736 2.292126 ACATGTGGGGCATCACCATAAA 60.292 45.455 0.00 0.00 40.70 1.40
681 3027 4.921470 TTCATTGACGCAGCTTTAGTAC 57.079 40.909 0.00 0.00 0.00 2.73
682 3028 2.921121 TCATTGACGCAGCTTTAGTACG 59.079 45.455 0.00 0.00 0.00 3.67
683 3029 2.427232 TTGACGCAGCTTTAGTACGT 57.573 45.000 0.00 0.00 40.11 3.57
684 3030 3.557577 TTGACGCAGCTTTAGTACGTA 57.442 42.857 0.00 0.00 37.05 3.57
685 3031 3.770263 TGACGCAGCTTTAGTACGTAT 57.230 42.857 0.00 0.00 37.05 3.06
686 3032 4.100707 TGACGCAGCTTTAGTACGTATT 57.899 40.909 0.00 0.00 37.05 1.89
687 3033 4.487948 TGACGCAGCTTTAGTACGTATTT 58.512 39.130 0.00 0.00 37.05 1.40
688 3034 4.325204 TGACGCAGCTTTAGTACGTATTTG 59.675 41.667 0.00 0.00 37.05 2.32
689 3035 3.615496 ACGCAGCTTTAGTACGTATTTGG 59.385 43.478 0.00 0.00 34.79 3.28
690 3036 3.861113 CGCAGCTTTAGTACGTATTTGGA 59.139 43.478 0.00 0.00 0.00 3.53
691 3037 4.506654 CGCAGCTTTAGTACGTATTTGGAT 59.493 41.667 0.00 0.00 0.00 3.41
692 3038 5.688621 CGCAGCTTTAGTACGTATTTGGATA 59.311 40.000 0.00 0.00 0.00 2.59
693 3039 6.365247 CGCAGCTTTAGTACGTATTTGGATAT 59.635 38.462 0.00 0.00 0.00 1.63
694 3040 7.539710 CGCAGCTTTAGTACGTATTTGGATATA 59.460 37.037 0.00 0.00 0.00 0.86
695 3041 8.645487 GCAGCTTTAGTACGTATTTGGATATAC 58.355 37.037 0.00 0.00 0.00 1.47
717 3063 6.786967 ACGTACAATTTAGATGACCTACCT 57.213 37.500 0.00 0.00 0.00 3.08
718 3064 7.886629 ACGTACAATTTAGATGACCTACCTA 57.113 36.000 0.00 0.00 0.00 3.08
736 3082 8.657712 ACCTACCTACTAGAGTTTTGTGAATTT 58.342 33.333 0.00 0.00 0.00 1.82
860 3208 2.561373 CCTGCGGCCGTTCTTTTC 59.439 61.111 28.70 8.52 0.00 2.29
893 3241 1.675641 CTTCCCAAGGAACCTGCCG 60.676 63.158 0.00 0.00 36.71 5.69
968 3322 1.198713 GGAGAGATCCTTGGTCTGCA 58.801 55.000 0.00 0.00 0.00 4.41
1209 3565 1.310216 GGTTTATGGCGCCTTTCGGT 61.310 55.000 29.70 8.99 38.94 4.69
1229 3585 3.365969 GGTCTTTGATTCGGCGATTTTGT 60.366 43.478 11.76 0.00 0.00 2.83
1289 3648 2.359975 GGCTGGTTTCGAGTGGGG 60.360 66.667 0.00 0.00 0.00 4.96
1303 3662 0.249657 GTGGGGATGCGTCTGATCTC 60.250 60.000 5.77 0.00 0.00 2.75
1312 3671 1.914634 CGTCTGATCTCGGGTTTCTG 58.085 55.000 0.00 0.00 0.00 3.02
1332 3691 0.593263 GACGACGGTAATGGCTACGG 60.593 60.000 0.00 0.00 36.99 4.02
1341 3700 0.179108 AATGGCTACGGAGAGCGAAC 60.179 55.000 0.00 0.00 43.83 3.95
1345 3704 1.296722 CTACGGAGAGCGAACGACG 60.297 63.158 0.00 0.00 45.66 5.12
1346 3705 2.628697 CTACGGAGAGCGAACGACGG 62.629 65.000 0.00 0.00 42.83 4.79
1348 3707 3.745803 GGAGAGCGAACGACGGGT 61.746 66.667 0.00 0.00 42.83 5.28
1359 3718 0.032403 ACGACGGGTTCAATTGACGA 59.968 50.000 19.97 0.04 0.00 4.20
1361 3720 1.060553 CGACGGGTTCAATTGACGATG 59.939 52.381 19.97 9.03 0.00 3.84
1362 3721 1.396996 GACGGGTTCAATTGACGATGG 59.603 52.381 19.97 7.35 0.00 3.51
1363 3722 1.271163 ACGGGTTCAATTGACGATGGT 60.271 47.619 19.97 7.89 0.00 3.55
1364 3723 2.027929 ACGGGTTCAATTGACGATGGTA 60.028 45.455 19.97 0.00 0.00 3.25
1365 3724 3.202906 CGGGTTCAATTGACGATGGTAT 58.797 45.455 7.89 0.00 0.00 2.73
1366 3725 4.141892 ACGGGTTCAATTGACGATGGTATA 60.142 41.667 19.97 0.00 0.00 1.47
1367 3726 4.447724 CGGGTTCAATTGACGATGGTATAG 59.552 45.833 7.89 0.00 0.00 1.31
1368 3727 5.365619 GGGTTCAATTGACGATGGTATAGT 58.634 41.667 7.89 0.00 0.00 2.12
1369 3728 5.236478 GGGTTCAATTGACGATGGTATAGTG 59.764 44.000 7.89 0.00 0.00 2.74
1370 3729 5.277345 GGTTCAATTGACGATGGTATAGTGC 60.277 44.000 7.89 0.00 0.00 4.40
1371 3730 5.276461 TCAATTGACGATGGTATAGTGCT 57.724 39.130 3.38 0.00 0.00 4.40
1372 3731 6.399639 TCAATTGACGATGGTATAGTGCTA 57.600 37.500 3.38 0.00 0.00 3.49
1373 3732 6.213677 TCAATTGACGATGGTATAGTGCTAC 58.786 40.000 3.38 0.00 0.00 3.58
1374 3733 5.784578 ATTGACGATGGTATAGTGCTACA 57.215 39.130 0.00 0.00 0.00 2.74
1375 3734 5.585820 TTGACGATGGTATAGTGCTACAA 57.414 39.130 0.00 0.00 0.00 2.41
1376 3735 5.784578 TGACGATGGTATAGTGCTACAAT 57.215 39.130 0.00 0.00 0.00 2.71
1377 3736 5.528870 TGACGATGGTATAGTGCTACAATG 58.471 41.667 0.00 0.00 0.00 2.82
1382 3741 4.703897 TGGTATAGTGCTACAATGCTTCC 58.296 43.478 0.00 0.00 0.00 3.46
1391 3750 2.409948 ACAATGCTTCCTAGGTCTGC 57.590 50.000 9.08 11.94 0.00 4.26
1476 3860 5.602628 AGTGAAGTCAGACTTGTTAAGGAC 58.397 41.667 21.00 4.13 38.80 3.85
1573 3961 3.262420 CACTGTCTAGCATGGTTGGTAC 58.738 50.000 1.12 0.00 34.79 3.34
1651 4053 3.958860 AGGGCTTGAAGGCAGCGT 61.959 61.111 20.63 0.00 43.44 5.07
1652 4054 3.435186 GGGCTTGAAGGCAGCGTC 61.435 66.667 20.63 0.00 43.44 5.19
1653 4055 2.669569 GGCTTGAAGGCAGCGTCA 60.670 61.111 14.34 0.00 40.97 4.35
1681 4083 5.183014 TCGCATACTGTTATGACGAAGAT 57.817 39.130 0.00 0.00 39.30 2.40
1824 4227 1.021968 GCATACTGTTTAAGGGGGCG 58.978 55.000 0.00 0.00 0.00 6.13
1848 4251 3.391965 GCAAATGTTTGGAGTGCATTGA 58.608 40.909 7.51 0.00 38.57 2.57
1869 4272 1.226974 GCTGAAGCCATGCATGCAG 60.227 57.895 26.69 21.35 34.31 4.41
1902 4309 3.891049 AGTTTGTTGGGATGGATAGAGC 58.109 45.455 0.00 0.00 0.00 4.09
1920 4327 1.335132 GCCACCCTGGAGACCGATTA 61.335 60.000 0.00 0.00 40.96 1.75
2035 4446 4.937620 GCTTCCATTCAGTAACTGTGATGA 59.062 41.667 0.00 0.00 32.44 2.92
2051 4462 8.521170 ACTGTGATGATGATTTGATTTCATCT 57.479 30.769 13.15 1.81 46.28 2.90
2067 4478 9.725019 TGATTTCATCTCACAATAGTGTAAAGT 57.275 29.630 0.00 0.00 46.01 2.66
2069 4480 6.968131 TCATCTCACAATAGTGTAAAGTGC 57.032 37.500 0.00 0.00 46.01 4.40
2097 4564 2.936498 CCAGTTTTCCTGCTGGTATACG 59.064 50.000 9.73 3.03 45.28 3.06
2109 4576 3.740141 GCTGGTATACGTTGTGTGGCTAT 60.740 47.826 0.00 0.00 0.00 2.97
2114 4581 2.465860 ACGTTGTGTGGCTATTAGCA 57.534 45.000 17.11 1.36 44.75 3.49
2122 4589 3.865164 GTGTGGCTATTAGCATTTTTGCC 59.135 43.478 17.11 0.00 44.75 4.52
2151 4618 3.008266 TCATGCTGATGTGTTCCTCTCAA 59.992 43.478 0.00 0.00 0.00 3.02
2206 4673 8.718158 ATCTTCAATCACTGGATCTATGAGTA 57.282 34.615 0.00 0.00 31.88 2.59
2254 4721 1.266989 GCCCTGTTGCTAAGTTGACAC 59.733 52.381 0.00 0.00 0.00 3.67
2273 4740 3.319972 ACACATTGGCAAGCCATGATATC 59.680 43.478 15.49 0.00 46.64 1.63
2355 4824 7.654568 TGCTATTGAATTGATATTGCTCTTGG 58.345 34.615 0.00 0.00 0.00 3.61
2410 4879 8.166422 ACGATTTCATTTTGGAGAAGTAAACT 57.834 30.769 0.00 0.00 0.00 2.66
2420 4889 5.428253 TGGAGAAGTAAACTGGATGTATGC 58.572 41.667 0.00 0.00 0.00 3.14
2425 4894 6.948309 AGAAGTAAACTGGATGTATGCCTTTT 59.052 34.615 0.00 0.00 0.00 2.27
2507 4976 0.394080 AGGAGGCTGCATCAAAGAGC 60.394 55.000 16.67 0.00 0.00 4.09
2588 5057 0.910088 AGGAGGGGGTGAAGCTGTAC 60.910 60.000 0.00 0.00 0.00 2.90
2705 5174 1.377725 GGCAGCCAAGCTAGCTCAA 60.378 57.895 19.65 0.00 38.95 3.02
2807 5276 4.246458 ACTTCTTCGAGGCAATGTACTTC 58.754 43.478 0.00 0.00 0.00 3.01
3090 5607 1.546476 ACTACAGAAGTGGCGAAGGAG 59.454 52.381 0.00 0.00 36.93 3.69
3103 5620 2.636830 CGAAGGAGATGAGCCAACATT 58.363 47.619 0.00 0.00 0.00 2.71
3104 5621 3.012518 CGAAGGAGATGAGCCAACATTT 58.987 45.455 0.00 0.00 0.00 2.32
3115 5632 2.076863 GCCAACATTTAGTGAGACGCT 58.923 47.619 0.00 0.00 0.00 5.07
3234 5751 2.029649 CAGCAAGCAAGCACCACTTATT 60.030 45.455 3.19 0.00 36.04 1.40
3327 5845 8.187480 TGTATAATAGAAACGTTTGCATGCAAT 58.813 29.630 32.27 18.17 35.70 3.56
3330 5848 3.916761 AGAAACGTTTGCATGCAATCAT 58.083 36.364 32.27 18.54 35.70 2.45
3351 5869 0.804989 GTTGTGGCTGCATGGTCTAC 59.195 55.000 0.50 0.00 0.00 2.59
3358 5876 1.937278 CTGCATGGTCTACAGCAGAG 58.063 55.000 7.44 0.00 45.77 3.35
3359 5877 0.538584 TGCATGGTCTACAGCAGAGG 59.461 55.000 0.00 0.00 32.51 3.69
3360 5878 0.539051 GCATGGTCTACAGCAGAGGT 59.461 55.000 0.00 0.00 32.51 3.85
3361 5879 1.757118 GCATGGTCTACAGCAGAGGTA 59.243 52.381 0.00 0.00 32.51 3.08
3380 5898 6.708054 AGAGGTACTGAACATCAACAAAGAAG 59.292 38.462 0.00 0.00 41.42 2.85
3382 5900 7.054124 AGGTACTGAACATCAACAAAGAAGAA 58.946 34.615 0.00 0.00 37.18 2.52
3384 5902 7.644157 GGTACTGAACATCAACAAAGAAGAAAC 59.356 37.037 0.00 0.00 0.00 2.78
3385 5903 7.156876 ACTGAACATCAACAAAGAAGAAACA 57.843 32.000 0.00 0.00 0.00 2.83
3386 5904 7.029563 ACTGAACATCAACAAAGAAGAAACAC 58.970 34.615 0.00 0.00 0.00 3.32
3387 5905 6.918626 TGAACATCAACAAAGAAGAAACACA 58.081 32.000 0.00 0.00 0.00 3.72
3388 5906 7.546358 TGAACATCAACAAAGAAGAAACACAT 58.454 30.769 0.00 0.00 0.00 3.21
3389 5907 7.701924 TGAACATCAACAAAGAAGAAACACATC 59.298 33.333 0.00 0.00 0.00 3.06
3390 5908 7.338800 ACATCAACAAAGAAGAAACACATCT 57.661 32.000 0.00 0.00 0.00 2.90
3391 5909 7.198390 ACATCAACAAAGAAGAAACACATCTG 58.802 34.615 0.00 0.00 0.00 2.90
3392 5910 6.135290 TCAACAAAGAAGAAACACATCTGG 57.865 37.500 0.00 0.00 0.00 3.86
3526 6045 3.448301 TGCCCCTTCATTTAGCAAGAATG 59.552 43.478 0.00 0.00 36.15 2.67
3554 6073 4.869297 CAGAATGAGCTCCTTTCTACTGTG 59.131 45.833 21.87 11.27 39.69 3.66
3587 6139 5.647589 TGTTGCACGTTAACCTATCTCTAG 58.352 41.667 9.29 0.00 0.00 2.43
3598 6150 5.231702 ACCTATCTCTAGTACTCCTTCCG 57.768 47.826 0.00 0.00 0.00 4.30
3599 6151 4.659835 ACCTATCTCTAGTACTCCTTCCGT 59.340 45.833 0.00 0.00 0.00 4.69
3607 6159 5.826737 TCTAGTACTCCTTCCGTTTCCATAG 59.173 44.000 0.00 0.00 0.00 2.23
3621 6173 7.980662 TCCGTTTCCATAGTTCGTATTGAAATA 59.019 33.333 0.00 0.00 40.98 1.40
3651 6206 6.954487 AGGGCTTATATTTAAAAACGGAGG 57.046 37.500 0.00 0.00 0.00 4.30
3652 6207 5.831525 AGGGCTTATATTTAAAAACGGAGGG 59.168 40.000 0.00 0.00 0.00 4.30
3653 6208 5.829391 GGGCTTATATTTAAAAACGGAGGGA 59.171 40.000 0.00 0.00 0.00 4.20
3654 6209 6.016527 GGGCTTATATTTAAAAACGGAGGGAG 60.017 42.308 0.00 0.00 0.00 4.30
3655 6210 6.544931 GGCTTATATTTAAAAACGGAGGGAGT 59.455 38.462 0.00 0.00 0.00 3.85
3656 6211 7.716560 GGCTTATATTTAAAAACGGAGGGAGTA 59.283 37.037 0.00 0.00 0.00 2.59
3657 6212 9.281371 GCTTATATTTAAAAACGGAGGGAGTAT 57.719 33.333 0.00 0.00 0.00 2.12
3662 6217 8.959705 ATTTAAAAACGGAGGGAGTATTAGAG 57.040 34.615 0.00 0.00 0.00 2.43
3663 6218 5.354842 AAAAACGGAGGGAGTATTAGAGG 57.645 43.478 0.00 0.00 0.00 3.69
3664 6219 3.967467 AACGGAGGGAGTATTAGAGGA 57.033 47.619 0.00 0.00 0.00 3.71
3665 6220 3.512219 ACGGAGGGAGTATTAGAGGAG 57.488 52.381 0.00 0.00 0.00 3.69
3666 6221 3.054576 ACGGAGGGAGTATTAGAGGAGA 58.945 50.000 0.00 0.00 0.00 3.71
3667 6222 3.073356 ACGGAGGGAGTATTAGAGGAGAG 59.927 52.174 0.00 0.00 0.00 3.20
3668 6223 3.073356 CGGAGGGAGTATTAGAGGAGAGT 59.927 52.174 0.00 0.00 0.00 3.24
3669 6224 4.286549 CGGAGGGAGTATTAGAGGAGAGTA 59.713 50.000 0.00 0.00 0.00 2.59
3670 6225 5.045432 CGGAGGGAGTATTAGAGGAGAGTAT 60.045 48.000 0.00 0.00 0.00 2.12
3671 6226 6.156602 CGGAGGGAGTATTAGAGGAGAGTATA 59.843 46.154 0.00 0.00 0.00 1.47
3672 6227 7.311171 CGGAGGGAGTATTAGAGGAGAGTATAA 60.311 44.444 0.00 0.00 0.00 0.98
3673 6228 8.050930 GGAGGGAGTATTAGAGGAGAGTATAAG 58.949 44.444 0.00 0.00 0.00 1.73
3674 6229 7.407729 AGGGAGTATTAGAGGAGAGTATAAGC 58.592 42.308 0.00 0.00 0.00 3.09
3675 6230 7.241039 AGGGAGTATTAGAGGAGAGTATAAGCT 59.759 40.741 0.00 0.00 0.00 3.74
3692 6247 1.533711 CTGGAATCCCGGAGCCAAT 59.466 57.895 0.73 0.00 41.53 3.16
3693 6248 0.536006 CTGGAATCCCGGAGCCAATC 60.536 60.000 0.73 0.00 41.53 2.67
3694 6249 1.278302 TGGAATCCCGGAGCCAATCA 61.278 55.000 0.73 0.00 34.29 2.57
3695 6250 0.111253 GGAATCCCGGAGCCAATCAT 59.889 55.000 0.73 0.00 0.00 2.45
3696 6251 1.479389 GGAATCCCGGAGCCAATCATT 60.479 52.381 0.73 0.00 0.00 2.57
3697 6252 2.224769 GGAATCCCGGAGCCAATCATTA 60.225 50.000 0.73 0.00 0.00 1.90
3753 6308 2.126071 CAAGCGACCCGACATCGT 60.126 61.111 0.00 0.00 41.68 3.73
3765 6320 3.682858 CCCGACATCGTCACATAAACTTT 59.317 43.478 0.00 0.00 37.74 2.66
3792 6347 8.166066 CACAAAAGTTTCGTGATATGTCGATAA 58.834 33.333 0.04 0.00 36.01 1.75
3816 6371 5.647658 ACATGACTCCATTGCGATTAAAGAA 59.352 36.000 0.00 0.00 0.00 2.52
3825 6380 9.119418 TCCATTGCGATTAAAGAAGATGATTTA 57.881 29.630 0.00 0.00 0.00 1.40
3849 6404 1.649664 CTCGGAGCAGATTCCAGTTG 58.350 55.000 0.00 0.00 37.05 3.16
3864 6419 1.594331 AGTTGGCGACTGGAGTTTTC 58.406 50.000 6.59 0.00 37.17 2.29
3865 6420 1.134220 AGTTGGCGACTGGAGTTTTCA 60.134 47.619 6.59 0.00 37.17 2.69
3866 6421 1.880027 GTTGGCGACTGGAGTTTTCAT 59.120 47.619 0.00 0.00 0.00 2.57
3867 6422 1.808411 TGGCGACTGGAGTTTTCATC 58.192 50.000 0.00 0.00 0.00 2.92
3870 6425 1.671850 GCGACTGGAGTTTTCATCCGA 60.672 52.381 0.00 0.00 39.91 4.55
3871 6426 2.263077 CGACTGGAGTTTTCATCCGAG 58.737 52.381 0.00 0.00 39.91 4.63
3872 6427 2.622436 GACTGGAGTTTTCATCCGAGG 58.378 52.381 0.00 0.00 39.91 4.63
3873 6428 1.339151 ACTGGAGTTTTCATCCGAGGC 60.339 52.381 0.00 0.00 39.91 4.70
3880 6435 0.881118 TTTCATCCGAGGCTTGTTGC 59.119 50.000 0.12 0.00 41.94 4.17
3883 6438 0.169672 CATCCGAGGCTTGTTGCTTG 59.830 55.000 0.12 0.00 42.39 4.01
3885 6440 1.165907 TCCGAGGCTTGTTGCTTGTG 61.166 55.000 0.12 0.00 42.39 3.33
3886 6441 1.447317 CCGAGGCTTGTTGCTTGTGT 61.447 55.000 0.12 0.00 42.39 3.72
3887 6442 0.040958 CGAGGCTTGTTGCTTGTGTC 60.041 55.000 0.00 0.00 42.39 3.67
3910 6521 8.138712 TGTCAAAATCAACCCAAATTGTACTAC 58.861 33.333 0.00 0.00 0.00 2.73
3961 6572 7.500629 AAAAAGCCAGGATCCTCAAATTATT 57.499 32.000 12.69 0.00 0.00 1.40
3962 6573 8.608185 AAAAAGCCAGGATCCTCAAATTATTA 57.392 30.769 12.69 0.00 0.00 0.98
4108 6730 9.173021 CTGCACTATTCTATGCTATCTACTACT 57.827 37.037 0.00 0.00 42.55 2.57
4109 6736 9.168451 TGCACTATTCTATGCTATCTACTACTC 57.832 37.037 0.00 0.00 42.55 2.59
4114 6741 7.809226 TTCTATGCTATCTACTACTCGTACG 57.191 40.000 9.53 9.53 0.00 3.67
4124 6751 7.916128 TCTACTACTCGTACGTGTATAGAAC 57.084 40.000 25.26 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 8.455903 TTCTCAACACTCTCATTCAATTCTTT 57.544 30.769 0.00 0.00 0.00 2.52
64 178 6.725834 ACATCTTTAATTGGAATTGGGTCACT 59.274 34.615 0.00 0.00 0.00 3.41
87 201 5.534207 AAAGAGCCAACATTCAATTGACA 57.466 34.783 7.89 0.11 0.00 3.58
88 202 7.945033 TTTAAAGAGCCAACATTCAATTGAC 57.055 32.000 7.89 0.00 0.00 3.18
180 296 3.272581 GGATAACCCGATTTTGACCGAA 58.727 45.455 0.00 0.00 0.00 4.30
209 325 5.464168 CAACATTCAATTGAGGTCTCCAAC 58.536 41.667 8.41 0.00 0.00 3.77
306 2628 2.430694 AGGTGTTTGGGAGAAAAAGTGC 59.569 45.455 0.00 0.00 0.00 4.40
322 2645 0.468029 CCTCCACAAAAGGCAGGTGT 60.468 55.000 0.00 0.00 0.00 4.16
332 2655 1.004745 GGAAGCAGGATCCTCCACAAA 59.995 52.381 12.69 0.00 39.61 2.83
344 2667 1.566231 AGGTTTGGATAGGGAAGCAGG 59.434 52.381 0.00 0.00 0.00 4.85
374 2697 4.101585 ACATGTCATGTAGGATCGGATGTT 59.898 41.667 16.99 0.00 42.78 2.71
395 2718 2.175202 GTTTTATGGTGATGCCCCACA 58.825 47.619 7.69 0.00 38.74 4.17
497 2843 8.522003 TCCCACTTTTAAAACGACTTTACTTTT 58.478 29.630 0.00 0.00 0.00 2.27
498 2844 8.054152 TCCCACTTTTAAAACGACTTTACTTT 57.946 30.769 0.00 0.00 0.00 2.66
499 2845 7.337689 ACTCCCACTTTTAAAACGACTTTACTT 59.662 33.333 0.00 0.00 0.00 2.24
500 2846 6.825213 ACTCCCACTTTTAAAACGACTTTACT 59.175 34.615 0.00 0.00 0.00 2.24
501 2847 7.019774 ACTCCCACTTTTAAAACGACTTTAC 57.980 36.000 0.00 0.00 0.00 2.01
502 2848 7.986889 ACTACTCCCACTTTTAAAACGACTTTA 59.013 33.333 0.00 0.00 0.00 1.85
503 2849 6.825213 ACTACTCCCACTTTTAAAACGACTTT 59.175 34.615 0.00 0.00 0.00 2.66
504 2850 6.259387 CACTACTCCCACTTTTAAAACGACTT 59.741 38.462 0.00 0.00 0.00 3.01
505 2851 5.756833 CACTACTCCCACTTTTAAAACGACT 59.243 40.000 0.00 0.00 0.00 4.18
506 2852 5.525012 ACACTACTCCCACTTTTAAAACGAC 59.475 40.000 0.00 0.00 0.00 4.34
507 2853 5.673514 ACACTACTCCCACTTTTAAAACGA 58.326 37.500 0.00 0.00 0.00 3.85
508 2854 5.524646 TGACACTACTCCCACTTTTAAAACG 59.475 40.000 0.00 0.00 0.00 3.60
509 2855 6.930667 TGACACTACTCCCACTTTTAAAAC 57.069 37.500 0.00 0.00 0.00 2.43
510 2856 7.941431 TTTGACACTACTCCCACTTTTAAAA 57.059 32.000 0.00 0.00 0.00 1.52
511 2857 7.941431 TTTTGACACTACTCCCACTTTTAAA 57.059 32.000 0.00 0.00 0.00 1.52
512 2858 7.612633 ACTTTTTGACACTACTCCCACTTTTAA 59.387 33.333 0.00 0.00 0.00 1.52
513 2859 7.114095 ACTTTTTGACACTACTCCCACTTTTA 58.886 34.615 0.00 0.00 0.00 1.52
514 2860 5.949952 ACTTTTTGACACTACTCCCACTTTT 59.050 36.000 0.00 0.00 0.00 2.27
515 2861 5.506708 ACTTTTTGACACTACTCCCACTTT 58.493 37.500 0.00 0.00 0.00 2.66
516 2862 5.112129 ACTTTTTGACACTACTCCCACTT 57.888 39.130 0.00 0.00 0.00 3.16
517 2863 4.772886 ACTTTTTGACACTACTCCCACT 57.227 40.909 0.00 0.00 0.00 4.00
518 2864 4.879545 TGAACTTTTTGACACTACTCCCAC 59.120 41.667 0.00 0.00 0.00 4.61
519 2865 5.104693 TCTGAACTTTTTGACACTACTCCCA 60.105 40.000 0.00 0.00 0.00 4.37
520 2866 5.365619 TCTGAACTTTTTGACACTACTCCC 58.634 41.667 0.00 0.00 0.00 4.30
521 2867 6.073003 CCATCTGAACTTTTTGACACTACTCC 60.073 42.308 0.00 0.00 0.00 3.85
606 2952 6.822667 TTTTGAGCTCATATTTCAGAAGCA 57.177 33.333 19.04 0.00 0.00 3.91
686 3032 9.701098 GGTCATCTAAATTGTACGTATATCCAA 57.299 33.333 0.00 0.00 0.00 3.53
687 3033 9.085645 AGGTCATCTAAATTGTACGTATATCCA 57.914 33.333 0.00 0.00 0.00 3.41
691 3037 9.578576 AGGTAGGTCATCTAAATTGTACGTATA 57.421 33.333 0.00 0.00 0.00 1.47
692 3038 8.474710 AGGTAGGTCATCTAAATTGTACGTAT 57.525 34.615 0.00 0.00 0.00 3.06
693 3039 7.886629 AGGTAGGTCATCTAAATTGTACGTA 57.113 36.000 0.00 0.00 0.00 3.57
694 3040 6.786967 AGGTAGGTCATCTAAATTGTACGT 57.213 37.500 0.00 0.00 0.00 3.57
695 3041 7.938715 AGTAGGTAGGTCATCTAAATTGTACG 58.061 38.462 0.00 0.00 0.00 3.67
698 3044 9.357161 CTCTAGTAGGTAGGTCATCTAAATTGT 57.643 37.037 0.00 0.00 0.00 2.71
736 3082 0.871722 CGCCCGACTTGTTTGAATGA 59.128 50.000 0.00 0.00 0.00 2.57
860 3208 5.337491 CCTTGGGAAGAAAAGAGAGAGAGAG 60.337 48.000 0.00 0.00 0.00 3.20
990 3346 3.826754 TCGAGCATCTTCGCGGCT 61.827 61.111 6.13 6.35 40.29 5.52
1209 3565 3.252215 ACACAAAATCGCCGAATCAAAGA 59.748 39.130 0.00 0.00 0.00 2.52
1229 3585 2.197324 GAAACAGCCCCCACCACA 59.803 61.111 0.00 0.00 0.00 4.17
1289 3648 0.103208 AACCCGAGATCAGACGCATC 59.897 55.000 0.00 0.00 0.00 3.91
1303 3662 1.865788 TACCGTCGTCCAGAAACCCG 61.866 60.000 0.00 0.00 0.00 5.28
1312 3671 0.593263 CGTAGCCATTACCGTCGTCC 60.593 60.000 0.00 0.00 0.00 4.79
1332 3691 1.800713 GAACCCGTCGTTCGCTCTC 60.801 63.158 0.00 0.00 41.51 3.20
1341 3700 1.060553 CATCGTCAATTGAACCCGTCG 59.939 52.381 10.35 8.58 0.00 5.12
1345 3704 5.236478 CACTATACCATCGTCAATTGAACCC 59.764 44.000 10.35 0.00 0.00 4.11
1346 3705 5.277345 GCACTATACCATCGTCAATTGAACC 60.277 44.000 10.35 0.00 0.00 3.62
1348 3707 5.670485 AGCACTATACCATCGTCAATTGAA 58.330 37.500 10.35 0.00 0.00 2.69
1356 3715 4.039245 AGCATTGTAGCACTATACCATCGT 59.961 41.667 0.00 0.00 36.85 3.73
1357 3716 4.560128 AGCATTGTAGCACTATACCATCG 58.440 43.478 0.00 0.00 36.85 3.84
1359 3718 5.072329 AGGAAGCATTGTAGCACTATACCAT 59.928 40.000 0.00 0.00 36.85 3.55
1361 3720 4.962155 AGGAAGCATTGTAGCACTATACC 58.038 43.478 0.00 0.00 36.85 2.73
1362 3721 6.159988 CCTAGGAAGCATTGTAGCACTATAC 58.840 44.000 1.05 0.00 36.85 1.47
1363 3722 5.839063 ACCTAGGAAGCATTGTAGCACTATA 59.161 40.000 17.98 0.00 36.85 1.31
1364 3723 4.656112 ACCTAGGAAGCATTGTAGCACTAT 59.344 41.667 17.98 0.00 36.85 2.12
1365 3724 4.030913 ACCTAGGAAGCATTGTAGCACTA 58.969 43.478 17.98 0.00 36.85 2.74
1366 3725 2.840651 ACCTAGGAAGCATTGTAGCACT 59.159 45.455 17.98 0.00 36.85 4.40
1367 3726 3.118592 AGACCTAGGAAGCATTGTAGCAC 60.119 47.826 17.98 0.00 36.85 4.40
1368 3727 3.107601 AGACCTAGGAAGCATTGTAGCA 58.892 45.455 17.98 0.00 36.85 3.49
1369 3728 3.462021 CAGACCTAGGAAGCATTGTAGC 58.538 50.000 17.98 0.00 0.00 3.58
1370 3729 3.462021 GCAGACCTAGGAAGCATTGTAG 58.538 50.000 17.98 0.00 0.00 2.74
1371 3730 2.159099 CGCAGACCTAGGAAGCATTGTA 60.159 50.000 17.98 0.00 0.00 2.41
1372 3731 1.406069 CGCAGACCTAGGAAGCATTGT 60.406 52.381 17.98 0.00 0.00 2.71
1373 3732 1.293924 CGCAGACCTAGGAAGCATTG 58.706 55.000 17.98 5.29 0.00 2.82
1374 3733 0.905357 ACGCAGACCTAGGAAGCATT 59.095 50.000 17.98 3.23 0.00 3.56
1375 3734 0.905357 AACGCAGACCTAGGAAGCAT 59.095 50.000 17.98 1.28 0.00 3.79
1376 3735 0.037326 CAACGCAGACCTAGGAAGCA 60.037 55.000 17.98 0.00 0.00 3.91
1377 3736 0.246635 TCAACGCAGACCTAGGAAGC 59.753 55.000 17.98 14.67 0.00 3.86
1382 3741 1.645034 CCACATCAACGCAGACCTAG 58.355 55.000 0.00 0.00 0.00 3.02
1391 3750 3.430862 CCACCGCCCACATCAACG 61.431 66.667 0.00 0.00 0.00 4.10
1622 4024 0.673022 CAAGCCCTGAGACAGACAGC 60.673 60.000 0.00 0.00 32.44 4.40
1651 4053 2.385013 AACAGTATGCGAGCATGTGA 57.615 45.000 19.64 0.00 42.53 3.58
1652 4054 3.803778 TCATAACAGTATGCGAGCATGTG 59.196 43.478 19.64 17.53 42.53 3.21
1653 4055 3.804325 GTCATAACAGTATGCGAGCATGT 59.196 43.478 19.64 8.72 42.53 3.21
1663 4065 7.068839 ACTCCAAGATCTTCGTCATAACAGTAT 59.931 37.037 4.57 0.00 0.00 2.12
1824 4227 1.202510 TGCACTCCAAACATTTGCCAC 60.203 47.619 0.00 0.00 36.86 5.01
1869 4272 6.325919 TCCCAACAAACTTACATGATGAAC 57.674 37.500 0.00 0.00 0.00 3.18
1902 4309 0.464452 GTAATCGGTCTCCAGGGTGG 59.536 60.000 0.00 0.00 39.43 4.61
1944 4351 3.489398 CGACAGGTCCAGAGTATTGCTAC 60.489 52.174 0.00 0.00 0.00 3.58
1952 4359 0.112606 TTCTCCGACAGGTCCAGAGT 59.887 55.000 11.63 0.00 39.05 3.24
2022 4433 9.234827 TGAAATCAAATCATCATCACAGTTACT 57.765 29.630 0.00 0.00 0.00 2.24
2051 4462 5.606505 TGTCTGCACTTTACACTATTGTGA 58.393 37.500 14.37 0.00 46.55 3.58
2065 4476 2.107204 AGGAAAACTGGATGTCTGCACT 59.893 45.455 0.00 0.00 0.00 4.40
2066 4477 2.227388 CAGGAAAACTGGATGTCTGCAC 59.773 50.000 0.00 0.00 43.70 4.57
2067 4478 2.507484 CAGGAAAACTGGATGTCTGCA 58.493 47.619 0.00 0.00 43.70 4.41
2091 4558 5.045215 TGCTAATAGCCACACAACGTATAC 58.955 41.667 10.06 0.00 41.51 1.47
2096 4563 4.355543 AAATGCTAATAGCCACACAACG 57.644 40.909 10.06 0.00 41.51 4.10
2097 4564 5.163963 GCAAAAATGCTAATAGCCACACAAC 60.164 40.000 10.06 0.00 41.51 3.32
2109 4576 3.006644 TGAGCACATGGCAAAAATGCTAA 59.993 39.130 15.29 7.98 46.33 3.09
2254 4721 2.555325 ACGATATCATGGCTTGCCAATG 59.445 45.455 18.76 15.76 0.00 2.82
2273 4740 3.848272 ACAATGTGGCCATTTTCTACG 57.152 42.857 9.72 0.00 39.28 3.51
2355 4824 9.732130 ATACTATCTAGGAGAAAATTTGGATGC 57.268 33.333 0.00 0.00 0.00 3.91
2386 4855 7.538678 CCAGTTTACTTCTCCAAAATGAAATCG 59.461 37.037 0.00 0.00 32.90 3.34
2410 4879 8.254508 GGTTAATTTACAAAAGGCATACATCCA 58.745 33.333 0.00 0.00 0.00 3.41
2507 4976 1.452110 TCATGAATGTGAACTGCCCG 58.548 50.000 0.00 0.00 0.00 6.13
2588 5057 1.860078 GCTTCGGAGGTTGTTCACG 59.140 57.895 0.00 0.00 0.00 4.35
2648 5117 3.851458 TCTATCACAGCATCAGCCAAT 57.149 42.857 0.00 0.00 43.56 3.16
2698 5167 1.298667 GCCCCGACCTTTTGAGCTA 59.701 57.895 0.00 0.00 0.00 3.32
2705 5174 2.561037 CGCTTTTGCCCCGACCTTT 61.561 57.895 0.00 0.00 43.93 3.11
2741 5210 1.876156 CCCAATATCCTCTTCGCTTGC 59.124 52.381 0.00 0.00 0.00 4.01
2807 5276 1.699656 CTTCAGTCATGCTTCCGCCG 61.700 60.000 0.00 0.00 34.43 6.46
3090 5607 4.033358 CGTCTCACTAAATGTTGGCTCATC 59.967 45.833 0.00 0.00 0.00 2.92
3103 5620 2.683867 GCCTCTTCTAGCGTCTCACTAA 59.316 50.000 0.00 0.00 0.00 2.24
3104 5621 2.290464 GCCTCTTCTAGCGTCTCACTA 58.710 52.381 0.00 0.00 0.00 2.74
3115 5632 1.670949 CTCCTGCTGCGCCTCTTCTA 61.671 60.000 4.18 0.00 0.00 2.10
3129 5646 2.143419 CCCCCGATTCCTCCTCCTG 61.143 68.421 0.00 0.00 0.00 3.86
3130 5647 2.287251 CCCCCGATTCCTCCTCCT 59.713 66.667 0.00 0.00 0.00 3.69
3234 5751 5.581126 AGACATGCAAAAACAAGTTCAGA 57.419 34.783 0.00 0.00 0.00 3.27
3282 5800 8.532186 TTATACACAATGGCCATACAAGAATT 57.468 30.769 21.15 0.00 0.00 2.17
3327 5845 1.252215 CCATGCAGCCACAACCATGA 61.252 55.000 0.00 0.00 37.78 3.07
3330 5848 1.902918 GACCATGCAGCCACAACCA 60.903 57.895 0.00 0.00 0.00 3.67
3333 5851 0.399833 TGTAGACCATGCAGCCACAA 59.600 50.000 0.00 0.00 0.00 3.33
3335 5853 2.772739 CTGTAGACCATGCAGCCAC 58.227 57.895 0.00 0.00 34.70 5.01
3351 5869 3.599730 TGATGTTCAGTACCTCTGCTG 57.400 47.619 0.00 0.00 43.32 4.41
3354 5872 5.991606 TCTTTGTTGATGTTCAGTACCTCTG 59.008 40.000 0.00 0.00 44.85 3.35
3355 5873 6.174720 TCTTTGTTGATGTTCAGTACCTCT 57.825 37.500 0.00 0.00 0.00 3.69
3356 5874 6.706270 TCTTCTTTGTTGATGTTCAGTACCTC 59.294 38.462 0.00 0.00 0.00 3.85
3357 5875 6.591935 TCTTCTTTGTTGATGTTCAGTACCT 58.408 36.000 0.00 0.00 0.00 3.08
3358 5876 6.861065 TCTTCTTTGTTGATGTTCAGTACC 57.139 37.500 0.00 0.00 0.00 3.34
3359 5877 8.181573 TGTTTCTTCTTTGTTGATGTTCAGTAC 58.818 33.333 0.00 0.00 0.00 2.73
3360 5878 8.181573 GTGTTTCTTCTTTGTTGATGTTCAGTA 58.818 33.333 0.00 0.00 0.00 2.74
3361 5879 7.029563 GTGTTTCTTCTTTGTTGATGTTCAGT 58.970 34.615 0.00 0.00 0.00 3.41
3380 5898 2.039084 ACTCCCAGACCAGATGTGTTTC 59.961 50.000 0.00 0.00 0.00 2.78
3382 5900 1.734655 ACTCCCAGACCAGATGTGTT 58.265 50.000 0.00 0.00 0.00 3.32
3384 5902 3.303938 AGATACTCCCAGACCAGATGTG 58.696 50.000 0.00 0.00 0.00 3.21
3385 5903 3.697190 AGATACTCCCAGACCAGATGT 57.303 47.619 0.00 0.00 0.00 3.06
3386 5904 4.653341 AGAAAGATACTCCCAGACCAGATG 59.347 45.833 0.00 0.00 0.00 2.90
3387 5905 4.889780 AGAAAGATACTCCCAGACCAGAT 58.110 43.478 0.00 0.00 0.00 2.90
3388 5906 4.338795 AGAAAGATACTCCCAGACCAGA 57.661 45.455 0.00 0.00 0.00 3.86
3389 5907 4.223923 ACAAGAAAGATACTCCCAGACCAG 59.776 45.833 0.00 0.00 0.00 4.00
3390 5908 4.168101 ACAAGAAAGATACTCCCAGACCA 58.832 43.478 0.00 0.00 0.00 4.02
3391 5909 4.828072 ACAAGAAAGATACTCCCAGACC 57.172 45.455 0.00 0.00 0.00 3.85
3392 5910 5.105310 TGCTACAAGAAAGATACTCCCAGAC 60.105 44.000 0.00 0.00 0.00 3.51
3526 6045 4.831107 AGAAAGGAGCTCATTCTGAAGAC 58.169 43.478 24.92 8.86 32.42 3.01
3587 6139 4.732672 ACTATGGAAACGGAAGGAGTAC 57.267 45.455 0.00 0.00 0.00 2.73
3607 6159 8.837389 AGCCCTTTTAGATATTTCAATACGAAC 58.163 33.333 0.00 0.00 31.73 3.95
3626 6178 7.147794 CCCTCCGTTTTTAAATATAAGCCCTTT 60.148 37.037 0.00 0.00 0.00 3.11
3642 6197 4.617593 TCCTCTAATACTCCCTCCGTTTT 58.382 43.478 0.00 0.00 0.00 2.43
3648 6203 7.555195 GCTTATACTCTCCTCTAATACTCCCTC 59.445 44.444 0.00 0.00 0.00 4.30
3649 6204 7.241039 AGCTTATACTCTCCTCTAATACTCCCT 59.759 40.741 0.00 0.00 0.00 4.20
3650 6205 7.338449 CAGCTTATACTCTCCTCTAATACTCCC 59.662 44.444 0.00 0.00 0.00 4.30
3651 6206 7.338449 CCAGCTTATACTCTCCTCTAATACTCC 59.662 44.444 0.00 0.00 0.00 3.85
3652 6207 8.104566 TCCAGCTTATACTCTCCTCTAATACTC 58.895 40.741 0.00 0.00 0.00 2.59
3653 6208 7.991174 TCCAGCTTATACTCTCCTCTAATACT 58.009 38.462 0.00 0.00 0.00 2.12
3654 6209 8.638629 TTCCAGCTTATACTCTCCTCTAATAC 57.361 38.462 0.00 0.00 0.00 1.89
3655 6210 9.469097 GATTCCAGCTTATACTCTCCTCTAATA 57.531 37.037 0.00 0.00 0.00 0.98
3656 6211 7.398904 GGATTCCAGCTTATACTCTCCTCTAAT 59.601 40.741 0.00 0.00 0.00 1.73
3657 6212 6.722129 GGATTCCAGCTTATACTCTCCTCTAA 59.278 42.308 0.00 0.00 0.00 2.10
3658 6213 6.249951 GGATTCCAGCTTATACTCTCCTCTA 58.750 44.000 0.00 0.00 0.00 2.43
3659 6214 5.083821 GGATTCCAGCTTATACTCTCCTCT 58.916 45.833 0.00 0.00 0.00 3.69
3660 6215 4.221924 GGGATTCCAGCTTATACTCTCCTC 59.778 50.000 4.80 0.00 0.00 3.71
3661 6216 4.164204 GGGATTCCAGCTTATACTCTCCT 58.836 47.826 4.80 0.00 0.00 3.69
3662 6217 3.056465 CGGGATTCCAGCTTATACTCTCC 60.056 52.174 4.80 0.00 0.00 3.71
3663 6218 3.056465 CCGGGATTCCAGCTTATACTCTC 60.056 52.174 4.80 0.00 0.00 3.20
3664 6219 2.900546 CCGGGATTCCAGCTTATACTCT 59.099 50.000 4.80 0.00 0.00 3.24
3665 6220 2.897969 TCCGGGATTCCAGCTTATACTC 59.102 50.000 0.00 0.00 0.00 2.59
3666 6221 2.900546 CTCCGGGATTCCAGCTTATACT 59.099 50.000 0.00 0.00 0.00 2.12
3667 6222 2.613223 GCTCCGGGATTCCAGCTTATAC 60.613 54.545 0.00 0.00 31.49 1.47
3668 6223 1.623811 GCTCCGGGATTCCAGCTTATA 59.376 52.381 0.00 0.00 31.49 0.98
3669 6224 0.398318 GCTCCGGGATTCCAGCTTAT 59.602 55.000 0.00 0.00 31.49 1.73
3670 6225 1.696097 GGCTCCGGGATTCCAGCTTA 61.696 60.000 0.00 0.00 33.83 3.09
3671 6226 2.592308 GCTCCGGGATTCCAGCTT 59.408 61.111 0.00 0.00 31.49 3.74
3672 6227 3.483869 GGCTCCGGGATTCCAGCT 61.484 66.667 0.00 0.00 33.83 4.24
3673 6228 2.631012 ATTGGCTCCGGGATTCCAGC 62.631 60.000 15.08 0.83 32.90 4.85
3674 6229 0.536006 GATTGGCTCCGGGATTCCAG 60.536 60.000 15.08 0.00 0.00 3.86
3675 6230 1.278302 TGATTGGCTCCGGGATTCCA 61.278 55.000 12.53 12.53 0.00 3.53
3692 6247 4.332543 GCGACAGTGGACAAATGATAATGA 59.667 41.667 0.00 0.00 0.00 2.57
3693 6248 4.496341 GGCGACAGTGGACAAATGATAATG 60.496 45.833 0.00 0.00 0.00 1.90
3694 6249 3.627577 GGCGACAGTGGACAAATGATAAT 59.372 43.478 0.00 0.00 0.00 1.28
3695 6250 3.006940 GGCGACAGTGGACAAATGATAA 58.993 45.455 0.00 0.00 0.00 1.75
3696 6251 2.627945 GGCGACAGTGGACAAATGATA 58.372 47.619 0.00 0.00 0.00 2.15
3697 6252 1.453155 GGCGACAGTGGACAAATGAT 58.547 50.000 0.00 0.00 0.00 2.45
3741 6296 2.572191 TTATGTGACGATGTCGGGTC 57.428 50.000 7.38 0.00 44.95 4.46
3765 6320 5.692654 TCGACATATCACGAAACTTTTGTGA 59.307 36.000 21.77 21.77 45.71 3.58
3792 6347 5.185454 TCTTTAATCGCAATGGAGTCATGT 58.815 37.500 0.00 0.00 33.18 3.21
3805 6360 8.436200 AGCGTATAAATCATCTTCTTTAATCGC 58.564 33.333 13.68 13.68 39.83 4.58
3816 6371 3.255888 TGCTCCGAGCGTATAAATCATCT 59.744 43.478 15.58 0.00 46.26 2.90
3825 6380 0.315568 GGAATCTGCTCCGAGCGTAT 59.684 55.000 15.58 8.47 46.26 3.06
3829 6384 0.107945 AACTGGAATCTGCTCCGAGC 60.108 55.000 13.81 13.81 42.82 5.03
3849 6404 1.087501 GGATGAAAACTCCAGTCGCC 58.912 55.000 0.00 0.00 32.72 5.54
3871 6426 8.567796 GTTGATTTTGACACAAGCAACAAGCC 62.568 42.308 23.57 3.24 45.61 4.35
3872 6427 3.864583 TGATTTTGACACAAGCAACAAGC 59.135 39.130 0.00 0.00 46.19 4.01
3873 6428 5.788467 GTTGATTTTGACACAAGCAACAAG 58.212 37.500 23.57 0.00 45.61 3.16
3880 6435 6.315891 ACAATTTGGGTTGATTTTGACACAAG 59.684 34.615 0.78 0.00 40.00 3.16
3883 6438 6.983890 AGTACAATTTGGGTTGATTTTGACAC 59.016 34.615 0.78 0.00 33.37 3.67
3885 6440 7.597369 GGTAGTACAATTTGGGTTGATTTTGAC 59.403 37.037 2.06 0.00 33.37 3.18
3886 6441 7.287927 TGGTAGTACAATTTGGGTTGATTTTGA 59.712 33.333 2.06 0.00 33.37 2.69
3887 6442 7.437748 TGGTAGTACAATTTGGGTTGATTTTG 58.562 34.615 2.06 0.00 33.37 2.44
3910 6521 7.148255 TGTCGGTTTGATAATTTGAGAATCTGG 60.148 37.037 0.00 0.00 34.92 3.86
3941 6552 9.692325 GATAATAATAATTTGAGGATCCTGGCT 57.308 33.333 22.02 0.00 0.00 4.75
3962 6573 9.491675 TTGAATTGATTGTTGTGCTTTGATAAT 57.508 25.926 0.00 0.00 0.00 1.28
4008 6619 7.171508 GCCCCTTTTGAAAAATGTTTCTCTTAG 59.828 37.037 9.75 2.66 43.13 2.18
4108 6730 4.260985 TCCCTTGTTCTATACACGTACGA 58.739 43.478 24.41 0.00 36.21 3.43
4109 6736 4.497006 CCTCCCTTGTTCTATACACGTACG 60.497 50.000 15.01 15.01 36.21 3.67
4114 6741 3.388350 CCTCCCTCCCTTGTTCTATACAC 59.612 52.174 0.00 0.00 36.21 2.90
4124 6751 3.474570 CTCGGCCTCCCTCCCTTG 61.475 72.222 0.00 0.00 0.00 3.61


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

AutoCloner maintained by Alex Coulton.