Multiple sequence alignment - TraesCS5D01G347400

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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 TraesCS5D01G347400 chr5D 100.000 6061 0 0 1 6061 433027319 433021259 0.000000e+00 11193
1 TraesCS5D01G347400 chr5D 88.889 180 13 6 1411 1587 41527338 41527163 1.320000e-51 215
2 TraesCS5D01G347400 chr5D 87.293 181 16 6 1410 1587 123298718 123298542 3.700000e-47 200
3 TraesCS5D01G347400 chr5D 86.740 181 17 6 1410 1587 438348306 438348482 1.720000e-45 195
4 TraesCS5D01G347400 chr5B 94.228 1767 65 23 3818 5562 526590201 526588450 0.000000e+00 2663
5 TraesCS5D01G347400 chr5B 92.152 1478 51 26 1177 2601 526592993 526591528 0.000000e+00 2026
6 TraesCS5D01G347400 chr5B 92.447 1218 55 16 2595 3799 526591374 526590181 0.000000e+00 1705
7 TraesCS5D01G347400 chr5B 89.187 1045 94 10 1 1030 526609145 526608105 0.000000e+00 1286
8 TraesCS5D01G347400 chr5B 85.826 1150 124 19 1 1137 526594118 526592995 0.000000e+00 1184
9 TraesCS5D01G347400 chr5B 87.193 367 17 13 5356 5713 82564134 82563789 2.050000e-104 390
10 TraesCS5D01G347400 chr5B 86.777 363 18 13 5360 5713 432957415 432957074 1.590000e-100 377
11 TraesCS5D01G347400 chr5B 85.942 377 21 15 5347 5713 645657247 645657601 2.060000e-99 374
12 TraesCS5D01G347400 chr5B 86.501 363 19 13 5360 5713 614191212 614190871 7.420000e-99 372
13 TraesCS5D01G347400 chr5B 88.396 293 14 7 5421 5713 76672160 76672432 9.730000e-88 335
14 TraesCS5D01G347400 chr5B 81.902 326 33 11 5741 6061 526587799 526587495 1.010000e-62 252
15 TraesCS5D01G347400 chr5A 90.717 1702 97 36 1191 2852 547651330 547649650 0.000000e+00 2211
16 TraesCS5D01G347400 chr5A 93.323 1258 63 14 4456 5706 547647470 547646227 0.000000e+00 1838
17 TraesCS5D01G347400 chr5A 90.000 1070 90 11 1 1063 547652506 547651447 0.000000e+00 1367
18 TraesCS5D01G347400 chr5A 97.196 642 16 2 3818 4458 547648172 547647532 0.000000e+00 1085
19 TraesCS5D01G347400 chr5A 93.994 616 21 4 3188 3798 547648756 547648152 0.000000e+00 918
20 TraesCS5D01G347400 chr5A 93.120 407 25 2 2764 3169 547649271 547648867 1.450000e-165 593
21 TraesCS5D01G347400 chr5A 79.907 642 69 29 4329 4957 3309376 3308782 3.380000e-112 416
22 TraesCS5D01G347400 chr5A 91.852 270 16 3 1 270 547665633 547665370 7.420000e-99 372
23 TraesCS5D01G347400 chr5A 86.585 328 27 4 5738 6054 547645747 547645426 4.500000e-91 346
24 TraesCS5D01G347400 chr5A 96.703 91 3 0 2762 2852 547649411 547649321 1.050000e-32 152
25 TraesCS5D01G347400 chr5A 95.604 91 4 0 2762 2852 547649342 547649252 4.900000e-31 147
26 TraesCS5D01G347400 chr5A 95.833 72 3 0 2781 2852 547649461 547649390 3.840000e-22 117
27 TraesCS5D01G347400 chr4A 87.646 1627 142 33 3832 5421 46048690 46050294 0.000000e+00 1836
28 TraesCS5D01G347400 chr4A 83.642 1351 162 35 1853 3189 46046711 46048016 0.000000e+00 1216
29 TraesCS5D01G347400 chr4A 89.960 498 40 7 3289 3776 46048193 46048690 8.570000e-178 634
30 TraesCS5D01G347400 chr4A 88.205 195 16 6 1397 1587 46046136 46046327 6.110000e-55 226
31 TraesCS5D01G347400 chr4B 89.226 1485 117 22 3841 5299 516860834 516859367 0.000000e+00 1816
32 TraesCS5D01G347400 chr4B 82.528 1408 176 37 1855 3236 516862811 516861448 0.000000e+00 1173
33 TraesCS5D01G347400 chr4B 91.260 492 37 4 3289 3776 516861330 516860841 0.000000e+00 665
34 TraesCS5D01G347400 chr4B 90.104 192 11 7 1400 1587 516863373 516863186 6.070000e-60 243
35 TraesCS5D01G347400 chr4D 88.956 1485 123 21 3840 5299 419107265 419105797 0.000000e+00 1796
36 TraesCS5D01G347400 chr4D 83.038 1409 170 39 1853 3236 419109251 419107887 0.000000e+00 1214
37 TraesCS5D01G347400 chr4D 91.365 498 31 7 3289 3776 419107769 419107274 0.000000e+00 671
38 TraesCS5D01G347400 chr4D 86.667 195 13 9 1417 1604 419109806 419109618 2.860000e-48 204
39 TraesCS5D01G347400 chr3B 81.128 922 120 30 1853 2753 818294226 818293338 0.000000e+00 689
40 TraesCS5D01G347400 chr3A 85.000 620 71 15 2141 2754 740914043 740913440 1.440000e-170 610
41 TraesCS5D01G347400 chr3A 85.942 377 21 15 5347 5713 24623692 24624046 2.060000e-99 374
42 TraesCS5D01G347400 chr3A 94.030 67 2 1 5252 5318 24623639 24623703 3.870000e-17 100
43 TraesCS5D01G347400 chr1B 85.942 377 21 16 5347 5713 652544326 652544680 2.060000e-99 374
44 TraesCS5D01G347400 chr1B 85.411 377 23 17 5347 5713 592416055 592416409 4.470000e-96 363
45 TraesCS5D01G347400 chr1B 94.030 67 2 1 5252 5318 592416002 592416066 3.870000e-17 100
46 TraesCS5D01G347400 chr1B 94.030 67 2 1 5252 5318 652544273 652544337 3.870000e-17 100
47 TraesCS5D01G347400 chrUn 85.870 368 20 11 5356 5713 244631641 244631296 4.470000e-96 363
48 TraesCS5D01G347400 chrUn 94.030 67 2 1 5252 5318 244631703 244631639 3.870000e-17 100
49 TraesCS5D01G347400 chr6B 92.035 226 17 1 5421 5646 673068297 673068521 3.530000e-82 316
50 TraesCS5D01G347400 chr3D 78.922 408 63 15 1853 2243 608388582 608388983 7.800000e-64 255
51 TraesCS5D01G347400 chr2D 87.293 181 16 6 1410 1587 29243012 29242836 3.700000e-47 200
52 TraesCS5D01G347400 chr7B 94.030 67 2 1 5252 5318 455249147 455249083 3.870000e-17 100
53 TraesCS5D01G347400 chr6A 94.030 67 2 1 5252 5318 578455992 578456056 3.870000e-17 100
54 TraesCS5D01G347400 chr2B 94.030 67 2 1 5252 5318 60386606 60386670 3.870000e-17 100


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 TraesCS5D01G347400 chr5D 433021259 433027319 6060 True 11193.00 11193 100.00000 1 6061 1 chr5D.!!$R3 6060
1 TraesCS5D01G347400 chr5B 526587495 526594118 6623 True 1566.00 2663 89.31100 1 6061 5 chr5B.!!$R5 6060
2 TraesCS5D01G347400 chr5B 526608105 526609145 1040 True 1286.00 1286 89.18700 1 1030 1 chr5B.!!$R3 1029
3 TraesCS5D01G347400 chr5A 547645426 547652506 7080 True 877.40 2211 93.30750 1 6054 10 chr5A.!!$R3 6053
4 TraesCS5D01G347400 chr5A 3308782 3309376 594 True 416.00 416 79.90700 4329 4957 1 chr5A.!!$R1 628
5 TraesCS5D01G347400 chr4A 46046136 46050294 4158 False 978.00 1836 87.36325 1397 5421 4 chr4A.!!$F1 4024
6 TraesCS5D01G347400 chr4B 516859367 516863373 4006 True 974.25 1816 88.27950 1400 5299 4 chr4B.!!$R1 3899
7 TraesCS5D01G347400 chr4D 419105797 419109806 4009 True 971.25 1796 87.50650 1417 5299 4 chr4D.!!$R1 3882
8 TraesCS5D01G347400 chr3B 818293338 818294226 888 True 689.00 689 81.12800 1853 2753 1 chr3B.!!$R1 900
9 TraesCS5D01G347400 chr3A 740913440 740914043 603 True 610.00 610 85.00000 2141 2754 1 chr3A.!!$R1 613

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
47 48 0.332972 ATCCAAGCTTGTCCTTCCCC 59.667 55.000 24.35 0.0 0.00 4.81 F
170 171 0.453793 CACCTCGACTAGCACTCCAG 59.546 60.000 0.00 0.0 0.00 3.86 F
1849 2055 0.460811 TGCAGAGGCTGTAGATTGCG 60.461 55.000 0.00 0.0 41.91 4.85 F
2256 2530 2.368439 TGGTGATGTTCATGCTAAGGC 58.632 47.619 0.00 0.0 39.26 4.35 F
3812 4916 0.179040 AACCTTTGCCTCCGTTTCGA 60.179 50.000 0.00 0.0 0.00 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1504 1589 0.324183 CCAGCCACAGAGAGAGAGGA 60.324 60.000 0.00 0.00 0.00 3.71 R
1964 2231 1.152567 CTTTTGGCCCCAGTGTGGA 60.153 57.895 0.00 0.00 40.96 4.02 R
2736 3182 0.324285 AGACTGAGGGAGCTGCTTTG 59.676 55.000 2.53 0.00 0.00 2.77 R
3878 4983 1.471676 CGGATACCAGTCTGCTTGGAC 60.472 57.143 0.00 1.48 36.56 4.02 R
5778 7638 0.391661 GGCATCTCACGTGGTGACAT 60.392 55.000 17.00 0.00 46.14 3.06 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
41 42 2.686915 CCATCTTCATCCAAGCTTGTCC 59.313 50.000 24.35 0.00 31.26 4.02
47 48 0.332972 ATCCAAGCTTGTCCTTCCCC 59.667 55.000 24.35 0.00 0.00 4.81
170 171 0.453793 CACCTCGACTAGCACTCCAG 59.546 60.000 0.00 0.00 0.00 3.86
177 178 2.747989 CGACTAGCACTCCAGTCACTAA 59.252 50.000 2.98 0.00 41.04 2.24
193 195 9.014297 CCAGTCACTAAAAATGACCTTCTTATT 57.986 33.333 1.62 0.00 46.38 1.40
313 328 8.662141 TCTCGTACTTAACTGGCATAAAAATTC 58.338 33.333 0.00 0.00 0.00 2.17
432 447 1.289160 ATGCCTTGCAACCTAGAGGA 58.711 50.000 1.60 0.00 43.62 3.71
451 466 4.999310 AGGATCGGAGTATCATCAACCTA 58.001 43.478 0.00 0.00 36.25 3.08
582 599 4.903049 TGACCTTGTTTTAGTCACCTAGGA 59.097 41.667 17.98 0.00 35.67 2.94
630 647 1.486310 CATCAACTTCCCCGATCTCCA 59.514 52.381 0.00 0.00 0.00 3.86
641 658 1.406219 CGATCTCCAGTTCGTGTGCG 61.406 60.000 0.00 0.00 39.92 5.34
670 687 8.887717 GTTCCATGCATATTTCATAGTATCCTC 58.112 37.037 0.00 0.00 0.00 3.71
679 696 9.896645 ATATTTCATAGTATCCTCGAATGCATT 57.103 29.630 12.83 12.83 0.00 3.56
716 733 1.454201 TCGTGTTCACCTTTGCAACA 58.546 45.000 0.00 0.00 0.00 3.33
744 761 4.344679 ACCATCTAGCAGATTTGGAGAGAG 59.655 45.833 10.78 0.00 31.32 3.20
793 811 7.856145 AAATATCATCAAGCTCTTCGTCTTT 57.144 32.000 0.00 0.00 0.00 2.52
814 832 2.760650 TCAGCTTCATCGCCTCTTCTAA 59.239 45.455 0.00 0.00 0.00 2.10
822 840 5.601662 TCATCGCCTCTTCTAAATCGATTT 58.398 37.500 25.48 25.48 34.91 2.17
855 874 2.694760 GCCTTTTCCTCCTGCTGCG 61.695 63.158 0.00 0.00 0.00 5.18
883 902 1.819288 GACTCCTTGAGGACGATGACA 59.181 52.381 0.00 0.00 39.78 3.58
929 949 0.769247 GCGGGGTGGGGACTATTATT 59.231 55.000 0.00 0.00 0.00 1.40
933 953 3.260128 CGGGGTGGGGACTATTATTAGAC 59.740 52.174 0.00 0.00 0.00 2.59
941 963 4.531339 GGGACTATTATTAGACCAGGGACC 59.469 50.000 12.92 0.00 40.68 4.46
950 972 0.605589 GACCAGGGACCGAAACAAGG 60.606 60.000 0.00 0.00 0.00 3.61
951 973 1.350310 ACCAGGGACCGAAACAAGGT 61.350 55.000 0.00 0.00 46.16 3.50
970 992 0.806868 TTGACTAACTCGACGCCGAT 59.193 50.000 0.00 0.00 44.62 4.18
1105 1182 9.474313 TTTGGATTGTAGTTTGCCTAATAATCT 57.526 29.630 0.00 0.00 34.74 2.40
1572 1665 0.830648 CCATACAGGAGAAGGGCGAA 59.169 55.000 0.00 0.00 41.22 4.70
1849 2055 0.460811 TGCAGAGGCTGTAGATTGCG 60.461 55.000 0.00 0.00 41.91 4.85
2014 2281 3.812053 GTGTGTGCTGTTCTCAGAGAAAT 59.188 43.478 14.77 0.00 43.76 2.17
2015 2282 3.811497 TGTGTGCTGTTCTCAGAGAAATG 59.189 43.478 14.77 11.10 43.76 2.32
2089 2363 3.763360 TCCCTTACATGATGCCTTGTTTG 59.237 43.478 0.00 0.00 33.44 2.93
2252 2526 3.070476 TGCTTGGTGATGTTCATGCTA 57.930 42.857 0.00 0.00 35.78 3.49
2256 2530 2.368439 TGGTGATGTTCATGCTAAGGC 58.632 47.619 0.00 0.00 39.26 4.35
2356 2638 6.887002 GGATGTTCTCCCTAATTGAAAGAAGT 59.113 38.462 0.00 0.00 38.19 3.01
2530 2812 6.662755 TGCAGGTAATCCTCATTTTAGACAT 58.337 36.000 0.00 0.00 43.07 3.06
2636 3081 8.938883 ACTGATTATTGGGTGAGTAATGATACT 58.061 33.333 0.00 0.00 45.10 2.12
2649 3094 8.745590 TGAGTAATGATACTACAGCAACACTTA 58.254 33.333 0.00 0.00 42.47 2.24
2652 3097 9.367444 GTAATGATACTACAGCAACACTTACTT 57.633 33.333 0.00 0.00 0.00 2.24
2654 3099 9.587772 AATGATACTACAGCAACACTTACTTAG 57.412 33.333 0.00 0.00 0.00 2.18
2656 3101 5.209818 ACTACAGCAACACTTACTTAGCA 57.790 39.130 0.00 0.00 0.00 3.49
2657 3102 5.230942 ACTACAGCAACACTTACTTAGCAG 58.769 41.667 0.00 0.00 0.00 4.24
2658 3103 4.073293 ACAGCAACACTTACTTAGCAGT 57.927 40.909 0.00 0.00 36.99 4.40
2659 3104 4.058817 ACAGCAACACTTACTTAGCAGTC 58.941 43.478 0.00 0.00 34.06 3.51
2690 3136 5.866092 TGTGAAGTCTGAAAATGAGATCTCG 59.134 40.000 17.76 1.90 0.00 4.04
2696 3142 5.121454 GTCTGAAAATGAGATCTCGTGCTTT 59.879 40.000 18.17 14.91 0.00 3.51
2704 3150 5.105063 TGAGATCTCGTGCTTTCATACTTG 58.895 41.667 17.76 0.00 0.00 3.16
2721 3167 9.658475 TTCATACTTGTGTTTTTGAATTAGTCG 57.342 29.630 0.00 0.00 0.00 4.18
2736 3182 9.982291 TTGAATTAGTCGTGCTTAAATGATTAC 57.018 29.630 0.00 0.00 0.00 1.89
2759 3205 0.396417 GCAGCTCCCTCAGTCTAGGA 60.396 60.000 0.00 0.00 39.15 2.94
2798 3244 5.163622 TGCCATTTTAGAAGCACAAGATAGC 60.164 40.000 0.00 0.00 0.00 2.97
2875 3788 4.333926 GTCAATGGAGAACTACAGCCATTC 59.666 45.833 0.00 0.00 45.35 2.67
2888 3801 3.003689 ACAGCCATTCGTTTTCTGTTCAG 59.996 43.478 0.00 0.00 34.69 3.02
2913 3828 8.392612 AGTTTCATGTTTGCTTTTCATTTCTTG 58.607 29.630 0.00 0.00 0.00 3.02
3010 3925 6.809869 AGAACTGTTTGCAAATCTTTAGCTT 58.190 32.000 16.21 6.54 0.00 3.74
3040 3955 7.667043 TTGGTTACATGTGAACATCTCTAAC 57.333 36.000 9.42 0.91 33.61 2.34
3061 3976 2.613977 CGCTTTGTCATCTCCCTGAACT 60.614 50.000 0.00 0.00 0.00 3.01
3062 3977 3.368427 CGCTTTGTCATCTCCCTGAACTA 60.368 47.826 0.00 0.00 0.00 2.24
3146 4061 6.879458 GGACAACAAAGATAATACAGGTCACT 59.121 38.462 0.00 0.00 0.00 3.41
3260 4331 5.544562 ACTTCCTGGAATAGCTTATAGGACC 59.455 44.000 10.03 0.00 34.30 4.46
3261 4332 5.355670 TCCTGGAATAGCTTATAGGACCT 57.644 43.478 0.00 0.00 29.86 3.85
3473 4568 8.578151 ACTACACTTAGTTCGAAAATTCTCTCT 58.422 33.333 0.00 0.00 34.66 3.10
3807 4911 4.494515 GGAAACCTTTGCCTCCGT 57.505 55.556 0.00 0.00 0.00 4.69
3808 4912 2.728397 GGAAACCTTTGCCTCCGTT 58.272 52.632 0.00 0.00 0.00 4.44
3809 4913 1.037493 GGAAACCTTTGCCTCCGTTT 58.963 50.000 0.00 0.00 0.00 3.60
3810 4914 1.000607 GGAAACCTTTGCCTCCGTTTC 60.001 52.381 0.00 0.00 42.05 2.78
3811 4915 0.666374 AAACCTTTGCCTCCGTTTCG 59.334 50.000 0.00 0.00 0.00 3.46
3812 4916 0.179040 AACCTTTGCCTCCGTTTCGA 60.179 50.000 0.00 0.00 0.00 3.71
3813 4917 0.179040 ACCTTTGCCTCCGTTTCGAA 60.179 50.000 0.00 0.00 0.00 3.71
3814 4918 0.948678 CCTTTGCCTCCGTTTCGAAA 59.051 50.000 6.47 6.47 0.00 3.46
3815 4919 1.335496 CCTTTGCCTCCGTTTCGAAAA 59.665 47.619 13.10 0.00 0.00 2.29
3816 4920 2.604614 CCTTTGCCTCCGTTTCGAAAAG 60.605 50.000 13.10 14.60 0.00 2.27
3817 4921 1.956297 TTGCCTCCGTTTCGAAAAGA 58.044 45.000 22.90 16.30 0.00 2.52
3818 4922 1.956297 TGCCTCCGTTTCGAAAAGAA 58.044 45.000 22.90 3.90 37.01 2.52
3819 4923 2.290464 TGCCTCCGTTTCGAAAAGAAA 58.710 42.857 22.90 10.97 45.76 2.52
4216 5321 1.975363 GCATCCTCGCAGTTGAGCAC 61.975 60.000 0.00 0.00 34.56 4.40
4685 5867 2.091994 CCCTGGGAAGAAATCTCATGCT 60.092 50.000 7.01 0.00 38.06 3.79
5078 6278 1.899814 TGAGATACCCACGAGCTGTTT 59.100 47.619 0.00 0.00 0.00 2.83
5079 6279 2.301870 TGAGATACCCACGAGCTGTTTT 59.698 45.455 0.00 0.00 0.00 2.43
5080 6280 2.673368 GAGATACCCACGAGCTGTTTTG 59.327 50.000 0.00 0.00 0.00 2.44
5081 6281 2.301870 AGATACCCACGAGCTGTTTTGA 59.698 45.455 0.00 0.00 0.00 2.69
5241 6449 1.404315 CGTTCTGTAGGGAGTGGCTTC 60.404 57.143 0.00 0.00 0.00 3.86
5242 6450 1.623811 GTTCTGTAGGGAGTGGCTTCA 59.376 52.381 0.00 0.00 0.00 3.02
5400 6616 2.998670 CTGCTGTACTCTGTTGGACATG 59.001 50.000 0.00 0.00 0.00 3.21
5421 6637 1.527034 ACCATTGCTAGCAGTGTGTG 58.473 50.000 30.98 21.22 32.72 3.82
5422 6638 1.202806 ACCATTGCTAGCAGTGTGTGT 60.203 47.619 30.98 21.77 32.72 3.72
5424 6640 1.466167 CATTGCTAGCAGTGTGTGTCC 59.534 52.381 27.10 0.00 0.00 4.02
5425 6641 0.758734 TTGCTAGCAGTGTGTGTCCT 59.241 50.000 18.45 0.00 0.00 3.85
5426 6642 0.033920 TGCTAGCAGTGTGTGTCCTG 59.966 55.000 14.93 0.00 0.00 3.86
5440 6665 2.237392 GTGTCCTGCCAAGGTAAGAGAT 59.763 50.000 0.00 0.00 44.82 2.75
5558 6794 3.432186 GGATGAAGTATGTAGTGCTGGCA 60.432 47.826 0.00 0.00 0.00 4.92
5579 6815 4.280677 GCACCTGAGAATGAGTAGAGCTAT 59.719 45.833 0.00 0.00 0.00 2.97
5610 6947 0.969149 AAGCAACTTAAAGCCCCAGC 59.031 50.000 0.00 0.00 40.32 4.85
5641 6978 1.571460 GTCTGTTTGAGCAGTGCCG 59.429 57.895 12.58 0.00 37.70 5.69
5660 6997 3.998341 GCCGTCTTATTGTCAACAGGTTA 59.002 43.478 0.00 0.00 0.00 2.85
5663 7000 5.107220 CCGTCTTATTGTCAACAGGTTACAC 60.107 44.000 0.00 0.00 0.00 2.90
5706 7043 0.534412 GAGCAGCTGCCTCTACTGAA 59.466 55.000 34.39 0.00 43.38 3.02
5713 7050 2.168521 GCTGCCTCTACTGAACCACATA 59.831 50.000 0.00 0.00 0.00 2.29
5714 7051 3.739519 GCTGCCTCTACTGAACCACATAG 60.740 52.174 0.00 0.00 0.00 2.23
5715 7052 2.766263 TGCCTCTACTGAACCACATAGG 59.234 50.000 0.00 0.00 45.67 2.57
5716 7053 2.483889 GCCTCTACTGAACCACATAGGC 60.484 54.545 0.00 0.00 43.14 3.93
5717 7054 3.034635 CCTCTACTGAACCACATAGGCT 58.965 50.000 0.00 0.00 43.14 4.58
5720 7057 5.452077 CCTCTACTGAACCACATAGGCTTAC 60.452 48.000 0.00 0.00 43.14 2.34
5721 7058 5.020795 TCTACTGAACCACATAGGCTTACA 58.979 41.667 0.00 0.00 43.14 2.41
5726 7063 6.126768 ACTGAACCACATAGGCTTACATATGT 60.127 38.462 13.93 13.93 42.03 2.29
5729 7066 6.996180 ACCACATAGGCTTACATATGTACT 57.004 37.500 15.20 11.56 39.91 2.73
5730 7067 6.994221 ACCACATAGGCTTACATATGTACTC 58.006 40.000 15.20 9.54 39.91 2.59
5731 7068 6.553476 ACCACATAGGCTTACATATGTACTCA 59.447 38.462 15.20 0.44 39.91 3.41
5732 7069 7.235606 ACCACATAGGCTTACATATGTACTCAT 59.764 37.037 15.20 9.86 39.91 2.90
5733 7070 7.547019 CCACATAGGCTTACATATGTACTCATG 59.453 40.741 15.20 14.76 39.91 3.07
5734 7071 8.090831 CACATAGGCTTACATATGTACTCATGT 58.909 37.037 15.20 15.28 39.91 3.21
5735 7072 8.307483 ACATAGGCTTACATATGTACTCATGTC 58.693 37.037 15.20 5.52 40.07 3.06
5753 7613 6.068010 TCATGTCAACAAGATAGGTTTGGTT 58.932 36.000 0.00 0.00 0.00 3.67
5762 7622 7.238710 ACAAGATAGGTTTGGTTTGGTTCTAT 58.761 34.615 0.00 0.00 0.00 1.98
5773 7633 8.877864 TTGGTTTGGTTCTATTCAAGATATGT 57.122 30.769 0.00 0.00 33.05 2.29
5821 7681 6.361114 CGAATATCAAACAGATCATGTGCTC 58.639 40.000 0.00 0.00 43.00 4.26
5832 7703 1.069973 TCATGTGCTCGCTTTTCAACG 60.070 47.619 0.00 0.00 0.00 4.10
5841 7712 1.136197 CGCTTTTCAACGCCAACGATA 60.136 47.619 0.00 0.00 43.93 2.92
5844 7715 3.425404 CTTTTCAACGCCAACGATATGG 58.575 45.455 0.00 0.00 43.93 2.74
5845 7716 2.388310 TTCAACGCCAACGATATGGA 57.612 45.000 10.15 0.00 43.54 3.41
5846 7717 2.388310 TCAACGCCAACGATATGGAA 57.612 45.000 10.15 0.00 43.54 3.53
5847 7718 2.276201 TCAACGCCAACGATATGGAAG 58.724 47.619 10.15 6.11 43.54 3.46
5848 7719 1.014352 AACGCCAACGATATGGAAGC 58.986 50.000 10.15 0.00 43.54 3.86
5849 7720 0.107897 ACGCCAACGATATGGAAGCA 60.108 50.000 10.15 0.00 43.54 3.91
5850 7721 1.013596 CGCCAACGATATGGAAGCAA 58.986 50.000 10.15 0.00 43.54 3.91
5851 7722 1.400142 CGCCAACGATATGGAAGCAAA 59.600 47.619 10.15 0.00 43.54 3.68
5852 7723 2.033299 CGCCAACGATATGGAAGCAAAT 59.967 45.455 10.15 0.00 43.54 2.32
5853 7724 3.374745 GCCAACGATATGGAAGCAAATG 58.625 45.455 10.15 0.00 43.54 2.32
5854 7725 3.066621 GCCAACGATATGGAAGCAAATGA 59.933 43.478 10.15 0.00 43.54 2.57
5855 7726 4.261741 GCCAACGATATGGAAGCAAATGAT 60.262 41.667 10.15 0.00 43.54 2.45
5856 7727 5.048782 GCCAACGATATGGAAGCAAATGATA 60.049 40.000 10.15 0.00 43.54 2.15
5857 7728 6.373779 CCAACGATATGGAAGCAAATGATAC 58.626 40.000 0.00 0.00 43.54 2.24
5858 7729 6.017192 CCAACGATATGGAAGCAAATGATACA 60.017 38.462 0.00 0.00 43.54 2.29
5859 7730 6.791887 ACGATATGGAAGCAAATGATACAG 57.208 37.500 0.00 0.00 0.00 2.74
5860 7731 6.524734 ACGATATGGAAGCAAATGATACAGA 58.475 36.000 0.00 0.00 0.00 3.41
5861 7732 7.164122 ACGATATGGAAGCAAATGATACAGAT 58.836 34.615 0.00 0.00 0.00 2.90
5862 7733 8.314021 ACGATATGGAAGCAAATGATACAGATA 58.686 33.333 0.00 0.00 0.00 1.98
5863 7734 8.598924 CGATATGGAAGCAAATGATACAGATAC 58.401 37.037 0.00 0.00 0.00 2.24
5864 7735 9.440773 GATATGGAAGCAAATGATACAGATACA 57.559 33.333 0.00 0.00 0.00 2.29
5865 7736 9.797642 ATATGGAAGCAAATGATACAGATACAA 57.202 29.630 0.00 0.00 0.00 2.41
5866 7737 7.320443 TGGAAGCAAATGATACAGATACAAC 57.680 36.000 0.00 0.00 0.00 3.32
5867 7738 6.883756 TGGAAGCAAATGATACAGATACAACA 59.116 34.615 0.00 0.00 0.00 3.33
5868 7739 7.066163 TGGAAGCAAATGATACAGATACAACAG 59.934 37.037 0.00 0.00 0.00 3.16
5869 7740 7.280876 GGAAGCAAATGATACAGATACAACAGA 59.719 37.037 0.00 0.00 0.00 3.41
5870 7741 7.545362 AGCAAATGATACAGATACAACAGAC 57.455 36.000 0.00 0.00 0.00 3.51
5871 7742 7.105588 AGCAAATGATACAGATACAACAGACA 58.894 34.615 0.00 0.00 0.00 3.41
5872 7743 7.772292 AGCAAATGATACAGATACAACAGACAT 59.228 33.333 0.00 0.00 0.00 3.06
5873 7744 8.400947 GCAAATGATACAGATACAACAGACATT 58.599 33.333 0.00 0.00 0.00 2.71
5899 7796 1.825285 CGCCGCGATCTGATCCAAAG 61.825 60.000 8.23 0.00 0.00 2.77
5906 7803 4.687948 CGCGATCTGATCCAAAGTAATCAT 59.312 41.667 11.84 0.00 31.79 2.45
5995 7897 2.689646 GTCTCGCCTATAAATCCAGCC 58.310 52.381 0.00 0.00 0.00 4.85
6027 7929 1.012086 CAACAGCATCACCTGATCGG 58.988 55.000 0.00 0.00 36.67 4.18
6036 7938 1.134818 TCACCTGATCGGCACACATAC 60.135 52.381 0.00 0.00 35.61 2.39
6043 7945 1.077787 CGGCACACATACCCACCAT 60.078 57.895 0.00 0.00 0.00 3.55
6055 7957 0.818445 CCCACCATCAGCTGAGCATC 60.818 60.000 22.96 0.00 0.00 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 0.036294 GGAAGTGACCTTCGGGGAAG 60.036 60.000 2.52 0.00 46.72 3.46
47 48 1.376037 GCCCTGGAAGTGACCTTCG 60.376 63.158 0.00 0.00 46.72 3.79
59 60 0.108520 GCACATGAAACATGCCCTGG 60.109 55.000 0.00 0.00 33.06 4.45
170 171 8.793592 ACCAATAAGAAGGTCATTTTTAGTGAC 58.206 33.333 8.87 0.00 44.01 3.67
177 178 7.416326 GGCGATAACCAATAAGAAGGTCATTTT 60.416 37.037 0.00 0.00 37.07 1.82
193 195 5.023452 AGGACTATATGATGGCGATAACCA 58.977 41.667 0.00 0.00 45.82 3.67
199 201 5.510430 AGTATGAGGACTATATGATGGCGA 58.490 41.667 0.00 0.00 0.00 5.54
259 261 2.160417 GCTTCTTTGACATCCTTGGTCG 59.840 50.000 0.00 0.00 38.10 4.79
432 447 4.081420 GGCATAGGTTGATGATACTCCGAT 60.081 45.833 0.00 0.00 0.00 4.18
451 466 2.351276 GGGTCAACGTCTGGGCAT 59.649 61.111 0.00 0.00 0.00 4.40
582 599 7.934855 ATCTCTTCATGATACAGTGCTTTTT 57.065 32.000 0.00 0.00 0.00 1.94
679 696 2.490115 ACGAACAAGTTCTTTGGTGCAA 59.510 40.909 10.83 0.00 36.66 4.08
716 733 3.285484 CAAATCTGCTAGATGGTTGGCT 58.715 45.455 0.00 0.00 34.65 4.75
744 761 1.154814 GGCGAAGAGGAAATCTCGGC 61.155 60.000 1.11 1.11 46.82 5.54
793 811 1.189752 AGAAGAGGCGATGAAGCTGA 58.810 50.000 0.00 0.00 37.29 4.26
814 832 1.474330 GGCAGGGTTGGAAATCGATT 58.526 50.000 4.39 4.39 0.00 3.34
822 840 4.299796 GGCAAGGGCAGGGTTGGA 62.300 66.667 0.00 0.00 43.71 3.53
855 874 3.672295 CTCAAGGAGTCCAGGCGGC 62.672 68.421 12.86 0.00 0.00 6.53
859 878 0.612174 TCGTCCTCAAGGAGTCCAGG 60.612 60.000 12.86 9.88 46.49 4.45
896 915 4.406173 CCGCGACTGCACTCGTCT 62.406 66.667 8.23 0.00 42.97 4.18
929 949 1.621814 CTTGTTTCGGTCCCTGGTCTA 59.378 52.381 0.00 0.00 0.00 2.59
933 953 0.179001 AACCTTGTTTCGGTCCCTGG 60.179 55.000 0.00 0.00 32.46 4.45
941 963 4.046462 TCGAGTTAGTCAACCTTGTTTCG 58.954 43.478 0.00 0.00 35.05 3.46
950 972 0.110056 TCGGCGTCGAGTTAGTCAAC 60.110 55.000 8.66 0.00 40.88 3.18
951 973 2.246841 TCGGCGTCGAGTTAGTCAA 58.753 52.632 8.66 0.00 40.88 3.18
970 992 1.377725 GTACTCCGTCGTCTCCCCA 60.378 63.158 0.00 0.00 0.00 4.96
1081 1107 9.778741 CTAGATTATTAGGCAAACTACAATCCA 57.221 33.333 0.00 0.00 35.69 3.41
1082 1108 9.998106 TCTAGATTATTAGGCAAACTACAATCC 57.002 33.333 0.00 0.00 35.69 3.01
1105 1182 6.161855 TGTGCAAAAGAGTTCTCTTCTCTA 57.838 37.500 14.28 1.82 40.79 2.43
1163 1240 7.736881 AAAAACCTACCCCTGTTTCTAAAAA 57.263 32.000 0.00 0.00 33.76 1.94
1200 1277 4.821589 GGACTCGGCCCGCTTCTG 62.822 72.222 0.00 0.00 0.00 3.02
1241 1318 4.397090 TTTTGATGTGCGGCCGCG 62.397 61.111 41.73 12.29 45.51 6.46
1242 1319 2.504681 CTTTTGATGTGCGGCCGC 60.505 61.111 42.35 42.35 42.35 6.53
1459 1544 3.621225 CTGATCCAGCCACGGAGA 58.379 61.111 0.00 0.00 38.83 3.71
1501 1586 1.357420 AGCCACAGAGAGAGAGGAAGA 59.643 52.381 0.00 0.00 0.00 2.87
1502 1587 1.477700 CAGCCACAGAGAGAGAGGAAG 59.522 57.143 0.00 0.00 0.00 3.46
1504 1589 0.324183 CCAGCCACAGAGAGAGAGGA 60.324 60.000 0.00 0.00 0.00 3.71
1505 1590 1.329171 CCCAGCCACAGAGAGAGAGG 61.329 65.000 0.00 0.00 0.00 3.69
1572 1665 4.457496 CTCACCATCCTGGCGCGT 62.457 66.667 8.43 0.00 42.67 6.01
1617 1710 1.300620 CAACAGTGGAACCGAGCGA 60.301 57.895 0.00 0.00 37.80 4.93
1690 1783 4.457496 ATCTGGTGCTCCGCGGTG 62.457 66.667 27.15 24.66 36.30 4.94
1691 1784 4.148825 GATCTGGTGCTCCGCGGT 62.149 66.667 27.15 0.78 36.30 5.68
1819 2019 5.165961 ACAGCCTCTGCAGTCTAAATAAA 57.834 39.130 14.67 0.00 41.13 1.40
1820 2020 4.826274 ACAGCCTCTGCAGTCTAAATAA 57.174 40.909 14.67 0.00 41.13 1.40
1821 2021 5.201243 TCTACAGCCTCTGCAGTCTAAATA 58.799 41.667 14.67 0.83 38.31 1.40
1822 2022 4.026744 TCTACAGCCTCTGCAGTCTAAAT 58.973 43.478 14.67 0.00 38.31 1.40
1964 2231 1.152567 CTTTTGGCCCCAGTGTGGA 60.153 57.895 0.00 0.00 40.96 4.02
2014 2281 3.244146 CCATCTTTTGTCCAAATGCACCA 60.244 43.478 0.00 0.00 0.00 4.17
2015 2282 3.328505 CCATCTTTTGTCCAAATGCACC 58.671 45.455 0.00 0.00 0.00 5.01
2252 2526 3.334583 TCTAGAAACAAGCATCGCCTT 57.665 42.857 0.00 0.00 0.00 4.35
2256 2530 3.247173 GCCAGATCTAGAAACAAGCATCG 59.753 47.826 0.00 0.00 0.00 3.84
2530 2812 9.181061 GTTAGGGCTAACATTTTAGATAAACCA 57.819 33.333 2.74 0.00 43.55 3.67
2615 3060 8.148351 GCTGTAGTATCATTACTCACCCAATAA 58.852 37.037 0.00 0.00 39.42 1.40
2617 3062 6.099701 TGCTGTAGTATCATTACTCACCCAAT 59.900 38.462 0.00 0.00 39.42 3.16
2636 3081 5.209818 ACTGCTAAGTAAGTGTTGCTGTA 57.790 39.130 0.00 0.00 33.79 2.74
2649 3094 2.899900 TCACATGTCCTGACTGCTAAGT 59.100 45.455 0.00 0.00 40.21 2.24
2652 3097 2.899900 ACTTCACATGTCCTGACTGCTA 59.100 45.455 0.00 0.00 0.00 3.49
2653 3098 1.696336 ACTTCACATGTCCTGACTGCT 59.304 47.619 0.00 0.00 0.00 4.24
2654 3099 2.072298 GACTTCACATGTCCTGACTGC 58.928 52.381 0.00 0.00 0.00 4.40
2656 3101 3.234353 TCAGACTTCACATGTCCTGACT 58.766 45.455 0.00 0.00 35.21 3.41
2657 3102 3.667497 TCAGACTTCACATGTCCTGAC 57.333 47.619 0.00 0.00 35.21 3.51
2658 3103 4.687901 TTTCAGACTTCACATGTCCTGA 57.312 40.909 0.00 1.54 35.21 3.86
2659 3104 5.471116 TCATTTTCAGACTTCACATGTCCTG 59.529 40.000 0.00 0.00 35.21 3.86
2690 3136 7.518731 TTCAAAAACACAAGTATGAAAGCAC 57.481 32.000 0.00 0.00 0.00 4.40
2696 3142 8.832521 ACGACTAATTCAAAAACACAAGTATGA 58.167 29.630 0.00 0.00 0.00 2.15
2704 3150 7.901874 TTAAGCACGACTAATTCAAAAACAC 57.098 32.000 0.00 0.00 0.00 3.32
2721 3167 6.095377 AGCTGCTTTGTAATCATTTAAGCAC 58.905 36.000 0.00 7.52 44.30 4.40
2736 3182 0.324285 AGACTGAGGGAGCTGCTTTG 59.676 55.000 2.53 0.00 0.00 2.77
2798 3244 7.641020 GCTTTCACATTTTGGTTTTTCAAGATG 59.359 33.333 6.57 6.57 41.85 2.90
2868 3781 3.214328 ACTGAACAGAAAACGAATGGCT 58.786 40.909 8.87 0.00 0.00 4.75
2869 3782 3.626028 ACTGAACAGAAAACGAATGGC 57.374 42.857 8.87 0.00 0.00 4.40
2875 3788 6.685767 CAAACATGAAACTGAACAGAAAACG 58.314 36.000 8.87 0.00 0.00 3.60
2888 3801 8.177013 ACAAGAAATGAAAAGCAAACATGAAAC 58.823 29.630 0.00 0.00 0.00 2.78
3010 3925 8.806429 AGATGTTCACATGTAACCAAATGATA 57.194 30.769 0.00 0.00 36.57 2.15
3040 3955 1.734465 GTTCAGGGAGATGACAAAGCG 59.266 52.381 0.00 0.00 0.00 4.68
3061 3976 7.016170 TCAGCAGCCATTCTGTAACCTAATATA 59.984 37.037 0.00 0.00 44.66 0.86
3062 3977 6.000219 CAGCAGCCATTCTGTAACCTAATAT 59.000 40.000 0.00 0.00 44.66 1.28
3260 4331 4.494091 AGGACAACCAATGATACCAGAG 57.506 45.455 0.00 0.00 38.94 3.35
3261 4332 5.030147 ACTAGGACAACCAATGATACCAGA 58.970 41.667 0.00 0.00 38.94 3.86
3352 4447 4.843728 TCCTGGTGGTGAAATCTTGATAC 58.156 43.478 0.00 0.00 34.23 2.24
3361 4456 5.945784 CAGAAGAATATTCCTGGTGGTGAAA 59.054 40.000 11.92 0.00 34.23 2.69
3473 4568 4.041567 TCAGCAAAATACTCCTTGTCCTGA 59.958 41.667 0.00 0.00 0.00 3.86
3798 4902 1.956297 TCTTTTCGAAACGGAGGCAA 58.044 45.000 10.79 0.00 0.00 4.52
3799 4903 1.956297 TTCTTTTCGAAACGGAGGCA 58.044 45.000 10.79 0.00 0.00 4.75
3800 4904 3.554259 ATTTCTTTTCGAAACGGAGGC 57.446 42.857 10.79 0.00 43.90 4.70
3804 4908 9.607285 CCCATAATATATTTCTTTTCGAAACGG 57.393 33.333 10.79 6.89 43.90 4.44
3810 4914 9.607285 CGGTTTCCCATAATATATTTCTTTTCG 57.393 33.333 2.68 0.00 0.00 3.46
3818 4922 9.939802 GAGAACTACGGTTTCCCATAATATATT 57.060 33.333 2.97 2.97 35.58 1.28
3819 4923 9.322769 AGAGAACTACGGTTTCCCATAATATAT 57.677 33.333 0.00 0.00 35.58 0.86
3820 4924 8.716674 AGAGAACTACGGTTTCCCATAATATA 57.283 34.615 0.00 0.00 35.58 0.86
3821 4925 7.613551 AGAGAACTACGGTTTCCCATAATAT 57.386 36.000 0.00 0.00 35.58 1.28
3822 4926 7.427989 AAGAGAACTACGGTTTCCCATAATA 57.572 36.000 0.00 0.00 35.58 0.98
3823 4927 5.952347 AGAGAACTACGGTTTCCCATAAT 57.048 39.130 0.00 0.00 35.58 1.28
3824 4928 5.750352 AAGAGAACTACGGTTTCCCATAA 57.250 39.130 0.00 0.00 35.58 1.90
3825 4929 5.750352 AAAGAGAACTACGGTTTCCCATA 57.250 39.130 0.00 0.00 35.58 2.74
3826 4930 4.635699 AAAGAGAACTACGGTTTCCCAT 57.364 40.909 0.00 0.00 35.58 4.00
3827 4931 4.426736 AAAAGAGAACTACGGTTTCCCA 57.573 40.909 0.00 0.00 35.58 4.37
3828 4932 5.583854 GGATAAAAGAGAACTACGGTTTCCC 59.416 44.000 0.00 0.00 35.58 3.97
3829 4933 5.583854 GGGATAAAAGAGAACTACGGTTTCC 59.416 44.000 0.00 0.00 35.58 3.13
3830 4934 6.168389 TGGGATAAAAGAGAACTACGGTTTC 58.832 40.000 0.00 0.00 35.58 2.78
3831 4935 6.117975 TGGGATAAAAGAGAACTACGGTTT 57.882 37.500 0.00 0.00 35.58 3.27
3832 4936 5.247792 ACTGGGATAAAAGAGAACTACGGTT 59.752 40.000 0.00 0.00 38.52 4.44
3833 4937 4.776308 ACTGGGATAAAAGAGAACTACGGT 59.224 41.667 0.00 0.00 0.00 4.83
3834 4938 5.340439 ACTGGGATAAAAGAGAACTACGG 57.660 43.478 0.00 0.00 0.00 4.02
3878 4983 1.471676 CGGATACCAGTCTGCTTGGAC 60.472 57.143 0.00 1.48 36.56 4.02
4216 5321 1.699656 CGATGCCCTCAAAGTCAGCG 61.700 60.000 0.00 0.00 32.18 5.18
4502 5680 3.111853 TGCTCACTGTAGACAACAAGG 57.888 47.619 0.00 0.00 37.74 3.61
4685 5867 2.514902 GCACGCGAAAAAGCATCAATA 58.485 42.857 15.93 0.00 36.85 1.90
5012 6211 1.536072 GCGCAGGTTATGATCTCGTCA 60.536 52.381 0.30 0.00 42.06 4.35
5078 6278 3.870538 AGATAGCCCAGCATCAATCAA 57.129 42.857 0.00 0.00 0.00 2.57
5079 6279 4.287845 ACATAGATAGCCCAGCATCAATCA 59.712 41.667 0.00 0.00 0.00 2.57
5080 6280 4.841422 ACATAGATAGCCCAGCATCAATC 58.159 43.478 0.00 0.00 0.00 2.67
5081 6281 4.923516 ACATAGATAGCCCAGCATCAAT 57.076 40.909 0.00 0.00 0.00 2.57
5241 6449 7.190920 AGTGGAAAATAACTCGAGAAAACTG 57.809 36.000 21.68 0.00 0.00 3.16
5242 6450 8.365647 TCTAGTGGAAAATAACTCGAGAAAACT 58.634 33.333 21.68 10.78 0.00 2.66
5400 6616 2.095567 CACACACTGCTAGCAATGGTTC 60.096 50.000 28.01 0.00 0.00 3.62
5421 6637 4.101741 ACATATCTCTTACCTTGGCAGGAC 59.898 45.833 9.53 0.00 44.19 3.85
5422 6638 4.298626 ACATATCTCTTACCTTGGCAGGA 58.701 43.478 9.53 0.00 44.19 3.86
5424 6640 6.870965 GTCATACATATCTCTTACCTTGGCAG 59.129 42.308 0.00 0.00 0.00 4.85
5425 6641 6.554982 AGTCATACATATCTCTTACCTTGGCA 59.445 38.462 0.00 0.00 0.00 4.92
5426 6642 6.870965 CAGTCATACATATCTCTTACCTTGGC 59.129 42.308 0.00 0.00 0.00 4.52
5440 6665 6.806668 TGGATCCAGTTTCAGTCATACATA 57.193 37.500 11.44 0.00 0.00 2.29
5500 6731 4.887748 ACTGGGATATAATCAAGAGCACG 58.112 43.478 0.00 0.00 0.00 5.34
5540 6776 2.093447 AGGTGCCAGCACTACATACTTC 60.093 50.000 21.19 2.63 45.52 3.01
5558 6794 5.952387 AGATAGCTCTACTCATTCTCAGGT 58.048 41.667 0.00 0.00 0.00 4.00
5579 6815 5.468540 TTAAGTTGCTTGCAGAGACTAGA 57.531 39.130 0.00 0.00 0.00 2.43
5610 6947 5.335191 GCTCAAACAGACCATCAACTAAAGG 60.335 44.000 0.00 0.00 0.00 3.11
5641 6978 6.854496 TGTGTAACCTGTTGACAATAAGAC 57.146 37.500 0.00 0.00 34.36 3.01
5660 6997 6.042437 TCTGATAATGATCACCAGCTATGTGT 59.958 38.462 13.50 3.78 37.15 3.72
5663 7000 7.328737 TCATCTGATAATGATCACCAGCTATG 58.671 38.462 0.00 4.95 37.15 2.23
5706 7043 6.553476 TGAGTACATATGTAAGCCTATGTGGT 59.447 38.462 17.07 0.00 37.15 4.16
5713 7050 6.731292 TGACATGAGTACATATGTAAGCCT 57.269 37.500 17.07 10.29 37.63 4.58
5714 7051 6.761242 TGTTGACATGAGTACATATGTAAGCC 59.239 38.462 17.07 9.65 37.63 4.35
5715 7052 7.770801 TGTTGACATGAGTACATATGTAAGC 57.229 36.000 17.07 12.14 37.63 3.09
5716 7053 9.586435 TCTTGTTGACATGAGTACATATGTAAG 57.414 33.333 17.07 8.22 37.63 2.34
5720 7057 9.201127 CCTATCTTGTTGACATGAGTACATATG 57.799 37.037 0.00 0.00 35.09 1.78
5721 7058 8.928448 ACCTATCTTGTTGACATGAGTACATAT 58.072 33.333 0.00 0.73 35.09 1.78
5726 7063 6.878923 CCAAACCTATCTTGTTGACATGAGTA 59.121 38.462 0.00 0.00 34.23 2.59
5729 7066 5.630121 ACCAAACCTATCTTGTTGACATGA 58.370 37.500 0.00 2.71 35.04 3.07
5730 7067 5.964958 ACCAAACCTATCTTGTTGACATG 57.035 39.130 0.00 0.00 0.00 3.21
5731 7068 6.239289 CCAAACCAAACCTATCTTGTTGACAT 60.239 38.462 0.00 0.00 0.00 3.06
5732 7069 5.068460 CCAAACCAAACCTATCTTGTTGACA 59.932 40.000 0.00 0.00 0.00 3.58
5733 7070 5.068591 ACCAAACCAAACCTATCTTGTTGAC 59.931 40.000 0.00 0.00 0.00 3.18
5734 7071 5.205056 ACCAAACCAAACCTATCTTGTTGA 58.795 37.500 0.00 0.00 0.00 3.18
5735 7072 5.529581 ACCAAACCAAACCTATCTTGTTG 57.470 39.130 0.00 0.00 0.00 3.33
5744 7604 6.133356 TCTTGAATAGAACCAAACCAAACCT 58.867 36.000 0.00 0.00 0.00 3.50
5762 7622 7.041721 GTGGTGACATGAGTACATATCTTGAA 58.958 38.462 0.00 0.00 46.14 2.69
5778 7638 0.391661 GGCATCTCACGTGGTGACAT 60.392 55.000 17.00 0.00 46.14 3.06
5821 7681 0.385473 ATCGTTGGCGTTGAAAAGCG 60.385 50.000 0.00 0.00 39.49 4.68
5832 7703 3.066621 TCATTTGCTTCCATATCGTTGGC 59.933 43.478 0.00 0.00 36.66 4.52
5838 7709 9.440773 TGTATCTGTATCATTTGCTTCCATATC 57.559 33.333 0.00 0.00 0.00 1.63
5841 7712 7.557358 TGTTGTATCTGTATCATTTGCTTCCAT 59.443 33.333 0.00 0.00 0.00 3.41
5844 7715 8.119226 GTCTGTTGTATCTGTATCATTTGCTTC 58.881 37.037 0.00 0.00 0.00 3.86
5845 7716 7.607607 TGTCTGTTGTATCTGTATCATTTGCTT 59.392 33.333 0.00 0.00 0.00 3.91
5846 7717 7.105588 TGTCTGTTGTATCTGTATCATTTGCT 58.894 34.615 0.00 0.00 0.00 3.91
5847 7718 7.307493 TGTCTGTTGTATCTGTATCATTTGC 57.693 36.000 0.00 0.00 0.00 3.68
5850 7721 8.896744 CCAAATGTCTGTTGTATCTGTATCATT 58.103 33.333 0.00 0.00 0.00 2.57
5851 7722 7.012704 GCCAAATGTCTGTTGTATCTGTATCAT 59.987 37.037 0.00 0.00 0.00 2.45
5852 7723 6.316140 GCCAAATGTCTGTTGTATCTGTATCA 59.684 38.462 0.00 0.00 0.00 2.15
5853 7724 6.238484 GGCCAAATGTCTGTTGTATCTGTATC 60.238 42.308 0.00 0.00 0.00 2.24
5854 7725 5.590259 GGCCAAATGTCTGTTGTATCTGTAT 59.410 40.000 0.00 0.00 0.00 2.29
5855 7726 4.941263 GGCCAAATGTCTGTTGTATCTGTA 59.059 41.667 0.00 0.00 0.00 2.74
5856 7727 3.758554 GGCCAAATGTCTGTTGTATCTGT 59.241 43.478 0.00 0.00 0.00 3.41
5857 7728 3.129287 GGGCCAAATGTCTGTTGTATCTG 59.871 47.826 4.39 0.00 0.00 2.90
5858 7729 3.356290 GGGCCAAATGTCTGTTGTATCT 58.644 45.455 4.39 0.00 0.00 1.98
5859 7730 2.427095 GGGGCCAAATGTCTGTTGTATC 59.573 50.000 4.39 0.00 0.00 2.24
5860 7731 2.456577 GGGGCCAAATGTCTGTTGTAT 58.543 47.619 4.39 0.00 0.00 2.29
5861 7732 1.884497 CGGGGCCAAATGTCTGTTGTA 60.884 52.381 4.39 0.00 0.00 2.41
5862 7733 1.178534 CGGGGCCAAATGTCTGTTGT 61.179 55.000 4.39 0.00 0.00 3.32
5863 7734 1.586028 CGGGGCCAAATGTCTGTTG 59.414 57.895 4.39 0.00 0.00 3.33
5864 7735 2.275380 GCGGGGCCAAATGTCTGTT 61.275 57.895 4.39 0.00 0.00 3.16
5865 7736 2.676471 GCGGGGCCAAATGTCTGT 60.676 61.111 4.39 0.00 0.00 3.41
5891 7788 5.295787 TGTTGCGGTATGATTACTTTGGATC 59.704 40.000 0.00 0.00 0.00 3.36
5953 7855 2.189499 GGGAAGGGCATCATCGTGC 61.189 63.158 0.00 0.00 44.31 5.34
5995 7897 2.594303 TGTTGAGCTGGGCCGTTG 60.594 61.111 0.00 0.00 0.00 4.10
6002 7904 0.322277 AGGTGATGCTGTTGAGCTGG 60.322 55.000 0.00 0.00 46.39 4.85
6027 7929 1.382522 CTGATGGTGGGTATGTGTGC 58.617 55.000 0.00 0.00 0.00 4.57
6036 7938 0.818445 GATGCTCAGCTGATGGTGGG 60.818 60.000 18.63 5.37 44.43 4.61


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

AutoCloner maintained by Alex Coulton.