Multiple sequence alignment - TraesCS5B01G282600

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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 TraesCS5B01G282600 chr5B 100.000 5343 0 0 1 5343 467374143 467368801 0.000000e+00 9867.0
1 TraesCS5B01G282600 chr5B 93.706 1128 48 11 1828 2948 313961134 313960023 0.000000e+00 1668.0
2 TraesCS5B01G282600 chr5B 84.884 1032 136 13 3041 4066 517852967 517853984 0.000000e+00 1024.0
3 TraesCS5B01G282600 chr5B 87.417 453 45 4 1146 1586 517852452 517852904 1.330000e-140 510.0
4 TraesCS5B01G282600 chr5D 95.157 1755 55 16 2991 4717 388872710 388870958 0.000000e+00 2743.0
5 TraesCS5B01G282600 chr5D 90.813 947 57 18 4 948 388874385 388873467 0.000000e+00 1240.0
6 TraesCS5B01G282600 chr5D 84.884 1032 135 14 3043 4066 428700457 428701475 0.000000e+00 1022.0
7 TraesCS5B01G282600 chr5D 93.013 687 35 7 948 1626 388873389 388872708 0.000000e+00 990.0
8 TraesCS5B01G282600 chr5D 87.589 419 27 12 2576 2989 411174370 411174768 3.770000e-126 462.0
9 TraesCS5B01G282600 chr5D 80.593 371 62 8 4917 5281 313787597 313787963 1.470000e-70 278.0
10 TraesCS5B01G282600 chr5D 81.627 332 53 6 4964 5290 434699607 434699279 8.820000e-68 268.0
11 TraesCS5B01G282600 chr5D 91.623 191 16 0 4724 4914 388870887 388870697 1.140000e-66 265.0
12 TraesCS5B01G282600 chr2B 93.670 1327 54 17 1633 2948 753010338 753011645 0.000000e+00 1958.0
13 TraesCS5B01G282600 chr2B 95.826 1126 32 4 1826 2948 648644228 648643115 0.000000e+00 1805.0
14 TraesCS5B01G282600 chr2B 94.044 1125 45 10 1831 2948 774684322 774683213 0.000000e+00 1687.0
15 TraesCS5B01G282600 chr2B 91.419 1142 51 13 1814 2948 33532692 33533793 0.000000e+00 1522.0
16 TraesCS5B01G282600 chr2B 80.822 365 59 9 4929 5286 597733765 597734125 5.270000e-70 276.0
17 TraesCS5B01G282600 chr2B 94.595 37 1 1 676 712 16258675 16258710 7.480000e-04 56.5
18 TraesCS5B01G282600 chr6B 93.253 1334 56 8 1625 2948 88324815 88326124 0.000000e+00 1934.0
19 TraesCS5B01G282600 chr6B 93.531 1144 48 14 1813 2948 320985452 320986577 0.000000e+00 1679.0
20 TraesCS5B01G282600 chr3B 92.868 1332 60 19 1633 2948 741227015 741225703 0.000000e+00 1901.0
21 TraesCS5B01G282600 chr3B 92.250 671 31 9 2284 2948 170762426 170761771 0.000000e+00 931.0
22 TraesCS5B01G282600 chr3B 92.319 664 34 11 1631 2288 828646617 828645965 0.000000e+00 928.0
23 TraesCS5B01G282600 chr3B 100.000 29 0 0 4666 4694 802918294 802918266 3.000000e-03 54.7
24 TraesCS5B01G282600 chr3A 89.971 1366 72 26 1631 2948 571325783 571324435 0.000000e+00 1703.0
25 TraesCS5B01G282600 chrUn 94.133 1125 44 10 1831 2948 434245901 434244792 0.000000e+00 1692.0
26 TraesCS5B01G282600 chrUn 93.977 1046 41 10 1910 2948 445488012 445486982 0.000000e+00 1563.0
27 TraesCS5B01G282600 chrUn 84.072 609 65 19 2391 2990 164266405 164266990 4.670000e-155 558.0
28 TraesCS5B01G282600 chrUn 83.580 609 68 19 2391 2990 155204298 155203713 4.710000e-150 542.0
29 TraesCS5B01G282600 chrUn 83.180 327 45 8 4964 5284 71437661 71437983 1.880000e-74 291.0
30 TraesCS5B01G282600 chr7B 94.139 1092 49 4 1860 2948 559637758 559638837 0.000000e+00 1648.0
31 TraesCS5B01G282600 chr7B 83.234 1002 145 17 3043 4033 741226993 741227982 0.000000e+00 898.0
32 TraesCS5B01G282600 chr7B 82.546 762 105 15 3277 4027 741261807 741261063 0.000000e+00 645.0
33 TraesCS5B01G282600 chr7B 83.133 332 45 7 4964 5290 5313908 5313583 5.230000e-75 292.0
34 TraesCS5B01G282600 chr5A 84.429 1034 142 14 3043 4066 544534367 544535391 0.000000e+00 1000.0
35 TraesCS5B01G282600 chr7D 83.317 1037 139 20 3041 4059 634919955 634918935 0.000000e+00 926.0
36 TraesCS5B01G282600 chr7D 77.178 574 101 22 4725 5282 227285073 227285632 1.870000e-79 307.0
37 TraesCS5B01G282600 chr7D 83.483 333 44 8 4966 5290 567727676 567728005 3.130000e-77 300.0
38 TraesCS5B01G282600 chr7A 81.128 1028 143 23 3041 4054 730722658 730721668 0.000000e+00 776.0
39 TraesCS5B01G282600 chr7A 86.525 423 37 6 1170 1584 730723134 730722724 1.060000e-121 448.0
40 TraesCS5B01G282600 chr4A 81.565 933 123 34 2023 2939 610727556 610726657 0.000000e+00 725.0
41 TraesCS5B01G282600 chr4A 89.744 78 7 1 4539 4615 473289993 473290070 1.220000e-16 99.0
42 TraesCS5B01G282600 chr4A 92.308 65 1 4 2942 3005 603331697 603331636 7.370000e-14 89.8
43 TraesCS5B01G282600 chr2A 87.326 576 41 12 2429 2991 36195322 36194766 9.770000e-177 630.0
44 TraesCS5B01G282600 chr2A 81.818 330 49 8 4966 5290 704011724 704012047 3.170000e-67 267.0
45 TraesCS5B01G282600 chr2A 92.157 102 7 1 1636 1737 36196245 36196145 5.580000e-30 143.0
46 TraesCS5B01G282600 chr2A 90.541 74 4 2 4539 4611 69268922 69268993 1.580000e-15 95.3
47 TraesCS5B01G282600 chr1A 80.087 924 119 41 2023 2931 427952038 427951165 1.260000e-175 627.0
48 TraesCS5B01G282600 chr1A 88.235 85 6 4 4539 4620 514680903 514680820 1.220000e-16 99.0
49 TraesCS5B01G282600 chr1B 83.744 609 67 19 2391 2990 36157042 36156457 1.010000e-151 547.0
50 TraesCS5B01G282600 chr1B 82.594 609 68 21 2391 2992 28511050 28510473 2.220000e-138 503.0
51 TraesCS5B01G282600 chr4D 83.483 333 45 7 4964 5290 478220599 478220927 8.700000e-78 302.0
52 TraesCS5B01G282600 chr4D 97.500 40 1 0 4543 4582 375131930 375131891 9.600000e-08 69.4
53 TraesCS5B01G282600 chr6A 90.541 74 6 1 4539 4611 20901247 20901320 4.400000e-16 97.1
54 TraesCS5B01G282600 chr4B 97.500 40 1 0 4543 4582 462223448 462223409 9.600000e-08 69.4
55 TraesCS5B01G282600 chr4B 93.182 44 3 0 4539 4582 619800087 619800044 1.240000e-06 65.8


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 TraesCS5B01G282600 chr5B 467368801 467374143 5342 True 9867.0 9867 100.0000 1 5343 1 chr5B.!!$R2 5342
1 TraesCS5B01G282600 chr5B 313960023 313961134 1111 True 1668.0 1668 93.7060 1828 2948 1 chr5B.!!$R1 1120
2 TraesCS5B01G282600 chr5B 517852452 517853984 1532 False 767.0 1024 86.1505 1146 4066 2 chr5B.!!$F1 2920
3 TraesCS5B01G282600 chr5D 388870697 388874385 3688 True 1309.5 2743 92.6515 4 4914 4 chr5D.!!$R2 4910
4 TraesCS5B01G282600 chr5D 428700457 428701475 1018 False 1022.0 1022 84.8840 3043 4066 1 chr5D.!!$F3 1023
5 TraesCS5B01G282600 chr2B 753010338 753011645 1307 False 1958.0 1958 93.6700 1633 2948 1 chr2B.!!$F4 1315
6 TraesCS5B01G282600 chr2B 648643115 648644228 1113 True 1805.0 1805 95.8260 1826 2948 1 chr2B.!!$R1 1122
7 TraesCS5B01G282600 chr2B 774683213 774684322 1109 True 1687.0 1687 94.0440 1831 2948 1 chr2B.!!$R2 1117
8 TraesCS5B01G282600 chr2B 33532692 33533793 1101 False 1522.0 1522 91.4190 1814 2948 1 chr2B.!!$F2 1134
9 TraesCS5B01G282600 chr6B 88324815 88326124 1309 False 1934.0 1934 93.2530 1625 2948 1 chr6B.!!$F1 1323
10 TraesCS5B01G282600 chr6B 320985452 320986577 1125 False 1679.0 1679 93.5310 1813 2948 1 chr6B.!!$F2 1135
11 TraesCS5B01G282600 chr3B 741225703 741227015 1312 True 1901.0 1901 92.8680 1633 2948 1 chr3B.!!$R2 1315
12 TraesCS5B01G282600 chr3B 170761771 170762426 655 True 931.0 931 92.2500 2284 2948 1 chr3B.!!$R1 664
13 TraesCS5B01G282600 chr3B 828645965 828646617 652 True 928.0 928 92.3190 1631 2288 1 chr3B.!!$R4 657
14 TraesCS5B01G282600 chr3A 571324435 571325783 1348 True 1703.0 1703 89.9710 1631 2948 1 chr3A.!!$R1 1317
15 TraesCS5B01G282600 chrUn 434244792 434245901 1109 True 1692.0 1692 94.1330 1831 2948 1 chrUn.!!$R2 1117
16 TraesCS5B01G282600 chrUn 445486982 445488012 1030 True 1563.0 1563 93.9770 1910 2948 1 chrUn.!!$R3 1038
17 TraesCS5B01G282600 chrUn 164266405 164266990 585 False 558.0 558 84.0720 2391 2990 1 chrUn.!!$F2 599
18 TraesCS5B01G282600 chrUn 155203713 155204298 585 True 542.0 542 83.5800 2391 2990 1 chrUn.!!$R1 599
19 TraesCS5B01G282600 chr7B 559637758 559638837 1079 False 1648.0 1648 94.1390 1860 2948 1 chr7B.!!$F1 1088
20 TraesCS5B01G282600 chr7B 741226993 741227982 989 False 898.0 898 83.2340 3043 4033 1 chr7B.!!$F2 990
21 TraesCS5B01G282600 chr7B 741261063 741261807 744 True 645.0 645 82.5460 3277 4027 1 chr7B.!!$R2 750
22 TraesCS5B01G282600 chr5A 544534367 544535391 1024 False 1000.0 1000 84.4290 3043 4066 1 chr5A.!!$F1 1023
23 TraesCS5B01G282600 chr7D 634918935 634919955 1020 True 926.0 926 83.3170 3041 4059 1 chr7D.!!$R1 1018
24 TraesCS5B01G282600 chr7D 227285073 227285632 559 False 307.0 307 77.1780 4725 5282 1 chr7D.!!$F1 557
25 TraesCS5B01G282600 chr7A 730721668 730723134 1466 True 612.0 776 83.8265 1170 4054 2 chr7A.!!$R1 2884
26 TraesCS5B01G282600 chr4A 610726657 610727556 899 True 725.0 725 81.5650 2023 2939 1 chr4A.!!$R2 916
27 TraesCS5B01G282600 chr2A 36194766 36196245 1479 True 386.5 630 89.7415 1636 2991 2 chr2A.!!$R1 1355
28 TraesCS5B01G282600 chr1A 427951165 427952038 873 True 627.0 627 80.0870 2023 2931 1 chr1A.!!$R1 908
29 TraesCS5B01G282600 chr1B 36156457 36157042 585 True 547.0 547 83.7440 2391 2990 1 chr1B.!!$R2 599
30 TraesCS5B01G282600 chr1B 28510473 28511050 577 True 503.0 503 82.5940 2391 2992 1 chr1B.!!$R1 601

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
284 287 0.672711 GAACAGCGTTGAGGGGGTAC 60.673 60.000 6.16 0.0 0.00 3.34 F
1091 1169 0.321298 GGCGACCTAGCTTGTTGGAA 60.321 55.000 0.00 0.0 37.29 3.53 F
1092 1170 1.079503 GCGACCTAGCTTGTTGGAAG 58.920 55.000 0.00 0.0 0.00 3.46 F
1791 1909 1.309102 CCCTTCCCCATCCCTTCCT 60.309 63.158 0.00 0.0 0.00 3.36 F
2293 2628 2.222445 CCGGTTGTAACTTTTCGTCCAG 59.778 50.000 0.00 0.0 0.00 3.86 F
2991 3441 0.391661 CGCCTAGCATCGCCCATTAT 60.392 55.000 0.00 0.0 0.00 1.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1689 1805 1.153745 GCTGCGATGAAGGAGACGT 60.154 57.895 0.00 0.00 0.00 4.34 R
2972 3422 0.391661 ATAATGGGCGATGCTAGGCG 60.392 55.000 0.00 0.00 34.74 5.52 R
2973 3423 1.826385 AATAATGGGCGATGCTAGGC 58.174 50.000 0.00 0.00 0.00 3.93 R
2981 3431 2.954989 TGCAGCATTAAATAATGGGCGA 59.045 40.909 13.47 0.00 42.46 5.54 R
4175 4683 0.945813 GGGGACATCGAGTAGAGTCG 59.054 60.000 0.15 0.15 41.51 4.18 R
4717 5248 0.175989 CGGAGAAGCCTAGGGTCAAC 59.824 60.000 15.24 9.11 0.00 3.18 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
63 64 2.612604 GGAAGGAGACGAGCTTTTCTC 58.387 52.381 14.40 14.40 38.04 2.87
96 97 7.694093 AGGAAAGAGATGGAAGAATTGTAGTT 58.306 34.615 0.00 0.00 0.00 2.24
103 104 8.115490 AGATGGAAGAATTGTAGTTCCTTTTG 57.885 34.615 2.26 0.00 40.49 2.44
116 117 7.719633 TGTAGTTCCTTTTGCTCTTTTCTATGT 59.280 33.333 0.00 0.00 0.00 2.29
159 160 9.238368 CCTGGTGTATCCTCATAAAAGTTTTTA 57.762 33.333 6.10 0.02 35.81 1.52
185 186 7.606858 AGTTAAATTTCGTAAAGCCTAGACC 57.393 36.000 0.00 0.00 0.00 3.85
284 287 0.672711 GAACAGCGTTGAGGGGGTAC 60.673 60.000 6.16 0.00 0.00 3.34
304 307 3.902150 ACTGCCTATATTGTGTCGATCG 58.098 45.455 9.36 9.36 0.00 3.69
307 310 3.509967 TGCCTATATTGTGTCGATCGGAT 59.490 43.478 16.41 4.89 0.00 4.18
321 324 4.778534 GATCGGATCGACCCATTAGTAA 57.221 45.455 0.00 0.00 39.18 2.24
329 332 2.223665 CGACCCATTAGTAACGGGAGTC 60.224 54.545 20.79 7.71 46.69 3.36
402 405 9.244292 GGGAAGGTTCTAGAAAATGTTTATCTT 57.756 33.333 6.78 0.00 0.00 2.40
433 436 9.408648 TCCTTTTCTTTCTATTTGTTCTCACTT 57.591 29.630 0.00 0.00 0.00 3.16
434 437 9.670719 CCTTTTCTTTCTATTTGTTCTCACTTC 57.329 33.333 0.00 0.00 0.00 3.01
622 625 9.643693 AATTGGTGAACATTTATCTGAATTCAC 57.356 29.630 3.38 6.41 0.00 3.18
623 626 6.841119 TGGTGAACATTTATCTGAATTCACG 58.159 36.000 3.38 1.39 0.00 4.35
624 627 6.128035 TGGTGAACATTTATCTGAATTCACGG 60.128 38.462 3.38 0.00 0.00 4.94
625 628 6.093495 GGTGAACATTTATCTGAATTCACGGA 59.907 38.462 3.38 1.63 0.00 4.69
626 629 6.961554 GTGAACATTTATCTGAATTCACGGAC 59.038 38.462 3.38 0.00 0.00 4.79
627 630 6.652900 TGAACATTTATCTGAATTCACGGACA 59.347 34.615 3.38 0.00 0.00 4.02
628 631 7.336679 TGAACATTTATCTGAATTCACGGACAT 59.663 33.333 3.38 0.00 0.00 3.06
629 632 7.630242 ACATTTATCTGAATTCACGGACATT 57.370 32.000 3.38 0.00 0.00 2.71
630 633 7.697691 ACATTTATCTGAATTCACGGACATTC 58.302 34.615 3.38 0.00 0.00 2.67
651 654 6.917217 TTCTTTGAATCCGCAAACATTTTT 57.083 29.167 0.00 0.00 34.35 1.94
702 705 8.775527 TGATGAACATTTTCACAAATTTCATGG 58.224 29.630 15.26 0.00 44.66 3.66
797 800 0.889186 GAAAAAGGCGTGCTGGGAGA 60.889 55.000 0.00 0.00 0.00 3.71
798 801 1.172812 AAAAAGGCGTGCTGGGAGAC 61.173 55.000 0.00 0.00 0.00 3.36
877 880 4.233635 GAGCGATGCAGCGGCTTG 62.234 66.667 27.22 0.00 43.00 4.01
940 943 3.863407 GGTGCTACCCTCCTCTTTG 57.137 57.895 0.00 0.00 30.04 2.77
941 944 1.276622 GGTGCTACCCTCCTCTTTGA 58.723 55.000 0.00 0.00 30.04 2.69
942 945 1.628846 GGTGCTACCCTCCTCTTTGAA 59.371 52.381 0.00 0.00 30.04 2.69
944 947 3.497942 GGTGCTACCCTCCTCTTTGAAAA 60.498 47.826 0.00 0.00 30.04 2.29
945 948 3.753797 GTGCTACCCTCCTCTTTGAAAAG 59.246 47.826 0.00 0.00 37.36 2.27
946 949 3.394606 TGCTACCCTCCTCTTTGAAAAGT 59.605 43.478 2.88 0.00 37.31 2.66
947 950 4.595781 TGCTACCCTCCTCTTTGAAAAGTA 59.404 41.667 2.88 0.00 37.31 2.24
948 951 5.072600 TGCTACCCTCCTCTTTGAAAAGTAA 59.927 40.000 2.88 0.00 37.31 2.24
949 952 5.411977 GCTACCCTCCTCTTTGAAAAGTAAC 59.588 44.000 2.88 0.00 37.31 2.50
950 953 5.382664 ACCCTCCTCTTTGAAAAGTAACA 57.617 39.130 2.88 0.00 37.31 2.41
952 955 7.086685 ACCCTCCTCTTTGAAAAGTAACATA 57.913 36.000 2.88 0.00 37.31 2.29
953 956 7.168905 ACCCTCCTCTTTGAAAAGTAACATAG 58.831 38.462 2.88 0.00 37.31 2.23
956 1032 9.372369 CCTCCTCTTTGAAAAGTAACATAGTAG 57.628 37.037 2.88 0.00 37.31 2.57
1015 1091 4.115516 CGTCTGATCTGGATCGACATTTT 58.884 43.478 22.04 0.00 40.63 1.82
1016 1092 4.208047 CGTCTGATCTGGATCGACATTTTC 59.792 45.833 22.04 0.00 40.63 2.29
1019 1095 5.814188 TCTGATCTGGATCGACATTTTCTTG 59.186 40.000 6.17 0.00 40.63 3.02
1069 1147 1.600636 CAGGAGAAAGCGCCCACAA 60.601 57.895 2.29 0.00 34.01 3.33
1070 1148 0.962356 CAGGAGAAAGCGCCCACAAT 60.962 55.000 2.29 0.00 34.01 2.71
1088 1166 0.460284 ATCGGCGACCTAGCTTGTTG 60.460 55.000 13.76 0.00 37.29 3.33
1091 1169 0.321298 GGCGACCTAGCTTGTTGGAA 60.321 55.000 0.00 0.00 37.29 3.53
1092 1170 1.079503 GCGACCTAGCTTGTTGGAAG 58.920 55.000 0.00 0.00 0.00 3.46
1093 1171 1.608283 GCGACCTAGCTTGTTGGAAGT 60.608 52.381 0.00 0.00 0.00 3.01
1094 1172 2.353406 GCGACCTAGCTTGTTGGAAGTA 60.353 50.000 0.00 0.00 0.00 2.24
1095 1173 3.679083 GCGACCTAGCTTGTTGGAAGTAT 60.679 47.826 0.00 0.00 0.00 2.12
1097 1175 5.041940 CGACCTAGCTTGTTGGAAGTATAC 58.958 45.833 0.00 0.00 0.00 1.47
1098 1176 5.163540 CGACCTAGCTTGTTGGAAGTATACT 60.164 44.000 0.00 0.00 0.00 2.12
1099 1177 6.622427 ACCTAGCTTGTTGGAAGTATACTT 57.378 37.500 18.05 18.05 39.23 2.24
1101 1179 7.459234 ACCTAGCTTGTTGGAAGTATACTTTT 58.541 34.615 18.96 0.00 36.11 2.27
1102 1180 7.942894 ACCTAGCTTGTTGGAAGTATACTTTTT 59.057 33.333 18.96 0.00 36.11 1.94
1103 1181 9.444600 CCTAGCTTGTTGGAAGTATACTTTTTA 57.555 33.333 18.96 6.46 36.11 1.52
1105 1183 8.919777 AGCTTGTTGGAAGTATACTTTTTAGT 57.080 30.769 18.96 0.00 36.11 2.24
1106 1184 9.350951 AGCTTGTTGGAAGTATACTTTTTAGTT 57.649 29.630 18.96 6.99 36.11 2.24
1125 1209 1.722034 TCCAAGAAGTGAGAGCTGGT 58.278 50.000 0.00 0.00 0.00 4.00
1626 1742 2.953466 AGAAAGTACGCGCTCCATTA 57.047 45.000 5.73 0.00 0.00 1.90
1649 1765 1.770294 AAGGAAAACGTTTGGAGCCA 58.230 45.000 15.46 0.00 0.00 4.75
1689 1805 2.038975 CGGTCTCCCTCTTCCCCA 59.961 66.667 0.00 0.00 0.00 4.96
1760 1877 2.985456 CCGCCCTCTTCTTCTGCT 59.015 61.111 0.00 0.00 0.00 4.24
1763 1880 1.612395 CGCCCTCTTCTTCTGCTCCT 61.612 60.000 0.00 0.00 0.00 3.69
1791 1909 1.309102 CCCTTCCCCATCCCTTCCT 60.309 63.158 0.00 0.00 0.00 3.36
2293 2628 2.222445 CCGGTTGTAACTTTTCGTCCAG 59.778 50.000 0.00 0.00 0.00 3.86
2387 2810 3.133362 TCTCTGTCACCGGTTGTAACTTT 59.867 43.478 2.97 0.00 0.00 2.66
2388 2811 3.875134 CTCTGTCACCGGTTGTAACTTTT 59.125 43.478 2.97 0.00 0.00 2.27
2389 2812 3.872771 TCTGTCACCGGTTGTAACTTTTC 59.127 43.478 2.97 0.00 0.00 2.29
2395 2818 5.879223 TCACCGGTTGTAACTTTTCTTGTAA 59.121 36.000 2.97 0.00 0.00 2.41
2871 3315 3.196463 GTGAGAGGAAGACGACGATCTA 58.804 50.000 0.00 0.00 0.00 1.98
2872 3316 3.622163 GTGAGAGGAAGACGACGATCTAA 59.378 47.826 0.00 0.00 0.00 2.10
2957 3407 3.770424 CGACCGGCCGAAACGTTC 61.770 66.667 30.73 11.44 0.00 3.95
2989 3439 2.281070 CGCCTAGCATCGCCCATT 60.281 61.111 0.00 0.00 0.00 3.16
2990 3440 1.005037 CGCCTAGCATCGCCCATTA 60.005 57.895 0.00 0.00 0.00 1.90
2991 3441 0.391661 CGCCTAGCATCGCCCATTAT 60.392 55.000 0.00 0.00 0.00 1.28
2992 3442 1.826385 GCCTAGCATCGCCCATTATT 58.174 50.000 0.00 0.00 0.00 1.40
3085 3535 1.198094 TGTTCTCCATCTTCCCGGCA 61.198 55.000 0.00 0.00 0.00 5.69
3159 3609 3.379445 GGCGGAGGACTTCACGGA 61.379 66.667 0.00 0.00 0.00 4.69
3184 3634 3.395702 CCGTGGATCCCGTTCCCA 61.396 66.667 9.90 0.00 34.67 4.37
3437 3902 2.954753 GAAGCTGTTGCCGACCGTG 61.955 63.158 0.00 0.00 40.80 4.94
3988 4489 2.117206 AATGCCAGGGCGTTCCAA 59.883 55.556 11.90 0.00 46.07 3.53
4036 4537 1.391485 GACAAGTACGTCGACGAGCTA 59.609 52.381 41.52 22.41 43.02 3.32
4106 4614 6.372937 TGCCTGTCGAAATGTGTAATCAATAA 59.627 34.615 0.00 0.00 0.00 1.40
4118 4626 7.534282 TGTGTAATCAATAATCGTGCATGTTT 58.466 30.769 5.68 6.64 0.00 2.83
4128 4636 4.200838 TCGTGCATGTTTCCTCAATCTA 57.799 40.909 5.68 0.00 0.00 1.98
4140 4648 2.297597 CCTCAATCTACTCGATGTCCCC 59.702 54.545 0.00 0.00 31.20 4.81
4156 4664 6.565811 CGATGTCCCCGAAATATGTAAATGTG 60.566 42.308 0.00 0.00 0.00 3.21
4175 4683 5.856126 TGTGATAATCGTGTCTGTTTTCC 57.144 39.130 0.00 0.00 0.00 3.13
4178 4686 4.624024 TGATAATCGTGTCTGTTTTCCGAC 59.376 41.667 0.00 0.00 35.18 4.79
4213 4721 6.951198 TGTCCCCTGAAATGTGTAAATGTAAT 59.049 34.615 0.00 0.00 0.00 1.89
4214 4722 8.110271 TGTCCCCTGAAATGTGTAAATGTAATA 58.890 33.333 0.00 0.00 0.00 0.98
4264 4776 5.123820 CGATGTCCCTGAAATGTGTAAATGT 59.876 40.000 0.00 0.00 0.00 2.71
4299 4814 2.341846 TTTCCCAATCTACCCGATGC 57.658 50.000 0.00 0.00 31.20 3.91
4316 4831 3.423123 CGATGCTCCTGAAACGTGTAAAC 60.423 47.826 0.00 0.00 0.00 2.01
4317 4832 2.907634 TGCTCCTGAAACGTGTAAACA 58.092 42.857 0.00 0.00 0.00 2.83
4324 4839 7.691050 GCTCCTGAAACGTGTAAACATAATAAC 59.309 37.037 0.00 0.00 0.00 1.89
4325 4840 7.731720 TCCTGAAACGTGTAAACATAATAACG 58.268 34.615 0.00 0.00 37.09 3.18
4326 4841 7.384660 TCCTGAAACGTGTAAACATAATAACGT 59.615 33.333 0.00 0.00 45.26 3.99
4327 4842 8.646356 CCTGAAACGTGTAAACATAATAACGTA 58.354 33.333 0.00 0.00 42.82 3.57
4330 4845 9.623687 GAAACGTGTAAACATAATAACGTATCC 57.376 33.333 0.00 0.00 42.82 2.59
4331 4846 8.700722 AACGTGTAAACATAATAACGTATCCA 57.299 30.769 0.00 0.00 42.82 3.41
4332 4847 8.118893 ACGTGTAAACATAATAACGTATCCAC 57.881 34.615 0.00 0.00 41.94 4.02
4346 4872 2.054232 ATCCACGAGACTATCCACGT 57.946 50.000 0.00 0.00 39.53 4.49
4366 4892 5.171337 CACGTATTAATTCTGCATTTTCCGC 59.829 40.000 0.00 0.00 0.00 5.54
4496 5023 4.405358 TGCTACCTCATCACATATGTCACA 59.595 41.667 5.07 0.00 0.00 3.58
4500 5027 6.183810 ACCTCATCACATATGTCACATCAT 57.816 37.500 5.07 0.00 0.00 2.45
4504 5031 7.390718 CCTCATCACATATGTCACATCATCATT 59.609 37.037 5.07 0.00 0.00 2.57
4567 5094 1.228245 ACATGCCACCTCACCACAC 60.228 57.895 0.00 0.00 0.00 3.82
4647 5174 0.250295 ACATCCCAACTCACCACACG 60.250 55.000 0.00 0.00 0.00 4.49
4653 5180 1.302511 AACTCACCACACGCCATCC 60.303 57.895 0.00 0.00 0.00 3.51
4698 5229 5.012239 AGATGCACACAACCATGTATTTCT 58.988 37.500 0.00 0.00 37.82 2.52
4717 5248 1.079543 CTCACCTGAGGCAGAACCG 60.080 63.158 0.00 0.00 46.52 4.44
4718 5249 1.821061 CTCACCTGAGGCAGAACCGT 61.821 60.000 0.00 0.00 46.52 4.83
4719 5250 1.071471 CACCTGAGGCAGAACCGTT 59.929 57.895 0.00 0.00 46.52 4.44
4720 5251 1.071471 ACCTGAGGCAGAACCGTTG 59.929 57.895 0.00 0.00 46.52 4.10
4721 5252 1.371183 CCTGAGGCAGAACCGTTGA 59.629 57.895 0.00 0.00 46.52 3.18
4722 5253 0.951040 CCTGAGGCAGAACCGTTGAC 60.951 60.000 0.00 0.00 46.52 3.18
4839 5434 1.154413 GTTGTTGCGCTCGATGGTG 60.154 57.895 9.73 0.00 0.00 4.17
4857 5452 2.515071 GGGCGCCTGGATCAGATCT 61.515 63.158 28.56 0.00 32.44 2.75
4875 5470 2.113774 GCATGATCCATCCGGCCA 59.886 61.111 2.24 0.00 0.00 5.36
4879 5474 1.135698 ATGATCCATCCGGCCATCCA 61.136 55.000 2.24 0.00 0.00 3.41
4892 5487 3.222855 ATCCAGAGGAGCTCCGCG 61.223 66.667 27.99 21.92 40.98 6.46
4924 5535 2.366167 AGCGGGCCAGATCCTTCT 60.366 61.111 7.23 0.00 0.00 2.85
4942 5553 4.309950 GGCCGTTCGGGACACTGT 62.310 66.667 13.16 0.00 46.58 3.55
4943 5554 3.041940 GCCGTTCGGGACACTGTG 61.042 66.667 13.16 6.19 38.47 3.66
4944 5555 2.357034 CCGTTCGGGACACTGTGG 60.357 66.667 13.09 0.00 38.47 4.17
4945 5556 2.357034 CGTTCGGGACACTGTGGG 60.357 66.667 13.09 0.00 0.00 4.61
4946 5557 2.826702 GTTCGGGACACTGTGGGT 59.173 61.111 13.09 0.00 0.00 4.51
4968 5579 4.078516 GGCAGTCGGTTACGCCCT 62.079 66.667 0.00 0.00 40.02 5.19
4969 5580 2.813908 GCAGTCGGTTACGCCCTG 60.814 66.667 0.00 0.00 39.89 4.45
4970 5581 2.967397 CAGTCGGTTACGCCCTGA 59.033 61.111 0.00 0.00 39.54 3.86
4972 5583 2.183555 GTCGGTTACGCCCTGAGG 59.816 66.667 0.00 0.00 40.69 3.86
4983 5594 1.424638 GCCCTGAGGTGCCTAATCTA 58.575 55.000 0.00 0.00 34.57 1.98
4987 5598 3.513515 CCCTGAGGTGCCTAATCTAGATC 59.486 52.174 5.51 0.00 0.00 2.75
4988 5599 3.192422 CCTGAGGTGCCTAATCTAGATCG 59.808 52.174 5.51 0.38 0.00 3.69
4994 5605 1.751924 GCCTAATCTAGATCGCGGGAT 59.248 52.381 15.66 15.66 34.96 3.85
4999 5610 0.037734 TCTAGATCGCGGGATGCCTA 59.962 55.000 20.80 14.07 42.08 3.93
5000 5611 0.171455 CTAGATCGCGGGATGCCTAC 59.829 60.000 20.80 4.83 42.08 3.18
5001 5612 0.538746 TAGATCGCGGGATGCCTACA 60.539 55.000 20.80 0.00 42.08 2.74
5014 5625 1.221021 CCTACAAGCCTTCGTCCCC 59.779 63.158 0.00 0.00 0.00 4.81
5019 5630 2.960688 AAGCCTTCGTCCCCTGCTC 61.961 63.158 0.00 0.00 0.00 4.26
5020 5631 4.821589 GCCTTCGTCCCCTGCTCG 62.822 72.222 0.00 0.00 0.00 5.03
5022 5633 4.821589 CTTCGTCCCCTGCTCGGC 62.822 72.222 0.00 0.00 0.00 5.54
5033 5644 3.782244 GCTCGGCGTGCTTGTCTG 61.782 66.667 24.86 0.00 0.00 3.51
5035 5646 2.661537 TCGGCGTGCTTGTCTGTG 60.662 61.111 6.85 0.00 0.00 3.66
5044 5655 0.390340 GCTTGTCTGTGCGGATCTGA 60.390 55.000 5.48 0.00 0.00 3.27
5046 5657 0.390340 TTGTCTGTGCGGATCTGAGC 60.390 55.000 5.48 3.55 0.00 4.26
5055 5670 1.519719 GGATCTGAGCCGACTTGCT 59.480 57.895 0.00 0.00 46.37 3.91
5062 5677 0.107945 GAGCCGACTTGCTGATCCTT 60.108 55.000 0.00 0.00 42.95 3.36
5063 5678 0.392193 AGCCGACTTGCTGATCCTTG 60.392 55.000 0.00 0.00 40.90 3.61
5067 5682 1.329906 CGACTTGCTGATCCTTGATGC 59.670 52.381 0.00 0.00 0.00 3.91
5070 5685 0.035152 TTGCTGATCCTTGATGCGGT 60.035 50.000 0.00 0.00 0.00 5.68
5071 5686 0.035152 TGCTGATCCTTGATGCGGTT 60.035 50.000 0.00 0.00 0.00 4.44
5078 5693 1.651240 CCTTGATGCGGTTGGAGCTG 61.651 60.000 0.00 0.00 35.28 4.24
5081 5696 2.045926 ATGCGGTTGGAGCTGGAC 60.046 61.111 0.00 0.00 35.28 4.02
5083 5698 4.373116 GCGGTTGGAGCTGGACGA 62.373 66.667 0.00 0.00 0.00 4.20
5094 5710 0.537188 GCTGGACGAGGGATTCAGAA 59.463 55.000 0.00 0.00 0.00 3.02
5120 5736 2.576648 AGAAATCCCTAGACGGCCTTTT 59.423 45.455 0.00 0.00 0.00 2.27
5153 5769 4.778143 GACAACCGAGGGCGCCAT 62.778 66.667 30.85 24.69 35.83 4.40
5185 5801 0.736053 GGAGACGCTCGTCAGATCTT 59.264 55.000 22.18 2.57 46.76 2.40
5202 5818 5.047021 CAGATCTTCTTCTACTTCCACCACA 60.047 44.000 0.00 0.00 0.00 4.17
5203 5819 4.602340 TCTTCTTCTACTTCCACCACAC 57.398 45.455 0.00 0.00 0.00 3.82
5240 5856 1.774894 AAAGCCCTAACTGCGGTGGA 61.775 55.000 0.00 0.00 0.00 4.02
5241 5857 2.436115 GCCCTAACTGCGGTGGAC 60.436 66.667 0.00 0.00 0.00 4.02
5261 5877 2.745884 CAATGGCGTCTTCGGGCA 60.746 61.111 0.00 0.00 44.49 5.36
5282 5898 1.876664 GTTCCCTTCTTGAAGGCGC 59.123 57.895 20.71 0.00 38.63 6.53
5283 5899 1.303317 TTCCCTTCTTGAAGGCGCC 60.303 57.895 21.89 21.89 38.63 6.53
5284 5900 3.127533 CCCTTCTTGAAGGCGCCG 61.128 66.667 23.20 6.32 38.63 6.46
5285 5901 3.804193 CCTTCTTGAAGGCGCCGC 61.804 66.667 23.20 18.21 32.43 6.53
5286 5902 2.743928 CTTCTTGAAGGCGCCGCT 60.744 61.111 23.20 13.07 0.00 5.52
5287 5903 2.281484 TTCTTGAAGGCGCCGCTT 60.281 55.556 23.20 11.40 0.00 4.68
5288 5904 1.856265 CTTCTTGAAGGCGCCGCTTT 61.856 55.000 23.20 6.02 0.00 3.51
5289 5905 2.126734 CTTGAAGGCGCCGCTTTG 60.127 61.111 23.20 9.16 0.00 2.77
5290 5906 4.341502 TTGAAGGCGCCGCTTTGC 62.342 61.111 23.20 1.74 0.00 3.68
5301 5917 3.838795 GCTTTGCGCGTCGACGAT 61.839 61.111 39.74 0.00 43.02 3.73
5302 5918 2.018670 CTTTGCGCGTCGACGATG 59.981 61.111 39.74 29.77 43.02 3.84
5303 5919 2.429404 TTTGCGCGTCGACGATGA 60.429 55.556 39.74 19.49 43.02 2.92
5304 5920 2.583141 CTTTGCGCGTCGACGATGAC 62.583 60.000 39.74 24.03 43.02 3.06
5310 5926 2.792599 GTCGACGATGACGGCTCT 59.207 61.111 0.00 0.00 46.46 4.09
5311 5927 1.136984 GTCGACGATGACGGCTCTT 59.863 57.895 0.00 0.00 46.46 2.85
5312 5928 1.134530 GTCGACGATGACGGCTCTTG 61.135 60.000 0.00 0.00 46.46 3.02
5313 5929 1.874019 CGACGATGACGGCTCTTGG 60.874 63.158 0.00 0.00 46.46 3.61
5314 5930 1.215647 GACGATGACGGCTCTTGGT 59.784 57.895 0.00 0.00 45.04 3.67
5315 5931 1.078759 GACGATGACGGCTCTTGGTG 61.079 60.000 0.00 0.00 45.04 4.17
5316 5932 1.811266 CGATGACGGCTCTTGGTGG 60.811 63.158 0.00 0.00 35.72 4.61
5317 5933 2.045926 ATGACGGCTCTTGGTGGC 60.046 61.111 0.00 0.00 0.00 5.01
5318 5934 2.803155 GATGACGGCTCTTGGTGGCA 62.803 60.000 0.00 0.00 0.00 4.92
5319 5935 2.045926 GACGGCTCTTGGTGGCAT 60.046 61.111 0.00 0.00 0.00 4.40
5320 5936 2.360350 ACGGCTCTTGGTGGCATG 60.360 61.111 0.00 0.00 0.00 4.06
5321 5937 3.136123 CGGCTCTTGGTGGCATGG 61.136 66.667 0.00 0.00 0.00 3.66
5322 5938 2.036256 GGCTCTTGGTGGCATGGT 59.964 61.111 0.00 0.00 0.00 3.55
5323 5939 1.302949 GGCTCTTGGTGGCATGGTA 59.697 57.895 0.00 0.00 0.00 3.25
5324 5940 1.032114 GGCTCTTGGTGGCATGGTAC 61.032 60.000 0.00 0.00 0.00 3.34
5337 5953 2.957060 TGGTACAGTGGAGTCTCGG 58.043 57.895 0.00 0.00 0.00 4.63
5338 5954 1.248785 TGGTACAGTGGAGTCTCGGC 61.249 60.000 0.00 0.00 0.00 5.54
5339 5955 1.136984 GTACAGTGGAGTCTCGGCG 59.863 63.158 0.00 0.00 0.00 6.46
5340 5956 2.044555 TACAGTGGAGTCTCGGCGG 61.045 63.158 7.21 0.00 0.00 6.13
5341 5957 4.803426 CAGTGGAGTCTCGGCGGC 62.803 72.222 7.21 0.00 0.00 6.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.466922 CCATCTTCCATGGCCTCCAC 60.467 60.000 6.96 0.00 35.80 4.02
1 2 1.648302 CCCATCTTCCATGGCCTCCA 61.648 60.000 6.96 0.00 37.85 3.86
2 3 1.152368 CCCATCTTCCATGGCCTCC 59.848 63.158 6.96 0.00 37.85 4.30
11 12 1.522569 CCGGTCTGTCCCATCTTCC 59.477 63.158 0.00 0.00 0.00 3.46
13 14 2.990479 GCCGGTCTGTCCCATCTT 59.010 61.111 1.90 0.00 0.00 2.40
36 37 4.831307 CGTCTCCTTCCGTCGGCG 62.831 72.222 6.34 0.29 37.95 6.46
63 64 3.556999 TCCATCTCTTTCCTCCTCTACG 58.443 50.000 0.00 0.00 0.00 3.51
64 65 5.205056 TCTTCCATCTCTTTCCTCCTCTAC 58.795 45.833 0.00 0.00 0.00 2.59
96 97 6.299141 AGTGACATAGAAAAGAGCAAAAGGA 58.701 36.000 0.00 0.00 0.00 3.36
103 104 6.256757 GGTGTATGAGTGACATAGAAAAGAGC 59.743 42.308 0.00 0.00 41.41 4.09
116 117 2.624293 CCAGGGAGAGGTGTATGAGTGA 60.624 54.545 0.00 0.00 0.00 3.41
159 160 9.322773 GGTCTAGGCTTTACGAAATTTAACTAT 57.677 33.333 0.00 0.00 0.00 2.12
172 173 5.686834 CAACTTTTTCGGTCTAGGCTTTAC 58.313 41.667 0.00 0.00 0.00 2.01
184 185 5.957910 TTAATTGTGTGCAACTTTTTCGG 57.042 34.783 0.00 0.00 37.44 4.30
185 186 7.042791 AGGAATTAATTGTGTGCAACTTTTTCG 60.043 33.333 5.17 0.00 37.44 3.46
230 231 2.778299 TCTTTTGCGCTACATCAACCT 58.222 42.857 9.73 0.00 0.00 3.50
270 271 2.436115 GCAGTACCCCCTCAACGC 60.436 66.667 0.00 0.00 0.00 4.84
271 272 0.974010 TAGGCAGTACCCCCTCAACG 60.974 60.000 5.26 0.00 40.58 4.10
277 278 2.709397 ACACAATATAGGCAGTACCCCC 59.291 50.000 0.00 0.00 40.58 5.40
284 287 3.057526 TCCGATCGACACAATATAGGCAG 60.058 47.826 18.66 0.00 0.00 4.85
304 307 3.022607 CCGTTACTAATGGGTCGATCC 57.977 52.381 8.12 8.12 33.75 3.36
600 603 6.093495 TCCGTGAATTCAGATAAATGTTCACC 59.907 38.462 8.80 0.00 41.23 4.02
615 618 6.030228 GGATTCAAAGAATGTCCGTGAATTC 58.970 40.000 0.00 0.00 38.65 2.17
616 619 5.391950 CGGATTCAAAGAATGTCCGTGAATT 60.392 40.000 11.62 0.00 40.80 2.17
617 620 4.094887 CGGATTCAAAGAATGTCCGTGAAT 59.905 41.667 11.62 0.00 40.80 2.57
618 621 3.435327 CGGATTCAAAGAATGTCCGTGAA 59.565 43.478 11.62 0.00 40.80 3.18
619 622 3.000041 CGGATTCAAAGAATGTCCGTGA 59.000 45.455 11.62 0.00 40.80 4.35
620 623 2.476185 GCGGATTCAAAGAATGTCCGTG 60.476 50.000 17.82 0.00 45.02 4.94
621 624 1.737793 GCGGATTCAAAGAATGTCCGT 59.262 47.619 17.82 0.00 45.02 4.69
622 625 1.737236 TGCGGATTCAAAGAATGTCCG 59.263 47.619 14.29 14.29 45.64 4.79
623 626 3.848272 TTGCGGATTCAAAGAATGTCC 57.152 42.857 0.00 0.00 0.00 4.02
624 627 4.545610 TGTTTGCGGATTCAAAGAATGTC 58.454 39.130 0.00 0.00 36.71 3.06
625 628 4.582701 TGTTTGCGGATTCAAAGAATGT 57.417 36.364 0.00 0.00 36.71 2.71
626 629 6.470557 AAATGTTTGCGGATTCAAAGAATG 57.529 33.333 0.00 0.00 36.71 2.67
627 630 7.495135 AAAAATGTTTGCGGATTCAAAGAAT 57.505 28.000 0.00 0.00 36.71 2.40
628 631 6.917217 AAAAATGTTTGCGGATTCAAAGAA 57.083 29.167 0.00 0.00 36.71 2.52
797 800 4.293626 GCAACAACACGCGCGAGT 62.294 61.111 39.36 32.89 0.00 4.18
827 830 0.461516 ATGAGACATGCAGCACGAGG 60.462 55.000 0.00 0.00 0.00 4.63
831 834 1.938577 CCTACATGAGACATGCAGCAC 59.061 52.381 0.00 0.00 0.00 4.40
832 835 1.832998 TCCTACATGAGACATGCAGCA 59.167 47.619 0.00 0.00 0.00 4.41
833 836 2.609427 TCCTACATGAGACATGCAGC 57.391 50.000 0.00 0.00 0.00 5.25
834 837 2.871022 GCTTCCTACATGAGACATGCAG 59.129 50.000 0.00 8.02 0.00 4.41
891 894 2.383527 GGGCGCTGCTATATGTCGC 61.384 63.158 7.64 0.00 44.39 5.19
931 934 9.930693 ACTACTATGTTACTTTTCAAAGAGGAG 57.069 33.333 6.29 1.10 39.31 3.69
1015 1091 3.938334 CGAGAGAGATGAGACAGACAAGA 59.062 47.826 0.00 0.00 0.00 3.02
1016 1092 3.487376 GCGAGAGAGATGAGACAGACAAG 60.487 52.174 0.00 0.00 0.00 3.16
1019 1095 1.333619 GGCGAGAGAGATGAGACAGAC 59.666 57.143 0.00 0.00 0.00 3.51
1069 1147 0.460284 CAACAAGCTAGGTCGCCGAT 60.460 55.000 0.00 0.00 0.00 4.18
1070 1148 1.080093 CAACAAGCTAGGTCGCCGA 60.080 57.895 0.00 0.00 0.00 5.54
1094 1172 9.495572 CTCTCACTTCTTGGAACTAAAAAGTAT 57.504 33.333 0.00 0.00 0.00 2.12
1095 1173 7.441458 GCTCTCACTTCTTGGAACTAAAAAGTA 59.559 37.037 0.00 0.00 0.00 2.24
1097 1175 6.484977 AGCTCTCACTTCTTGGAACTAAAAAG 59.515 38.462 0.00 0.00 0.00 2.27
1098 1176 6.260936 CAGCTCTCACTTCTTGGAACTAAAAA 59.739 38.462 0.00 0.00 0.00 1.94
1099 1177 5.760253 CAGCTCTCACTTCTTGGAACTAAAA 59.240 40.000 0.00 0.00 0.00 1.52
1101 1179 4.262635 CCAGCTCTCACTTCTTGGAACTAA 60.263 45.833 0.00 0.00 0.00 2.24
1102 1180 3.259374 CCAGCTCTCACTTCTTGGAACTA 59.741 47.826 0.00 0.00 0.00 2.24
1103 1181 2.038295 CCAGCTCTCACTTCTTGGAACT 59.962 50.000 0.00 0.00 0.00 3.01
1104 1182 2.224402 ACCAGCTCTCACTTCTTGGAAC 60.224 50.000 0.00 0.00 0.00 3.62
1105 1183 2.050144 ACCAGCTCTCACTTCTTGGAA 58.950 47.619 0.00 0.00 0.00 3.53
1106 1184 1.722034 ACCAGCTCTCACTTCTTGGA 58.278 50.000 0.00 0.00 0.00 3.53
1109 1187 3.620966 GCCATAACCAGCTCTCACTTCTT 60.621 47.826 0.00 0.00 0.00 2.52
1110 1188 2.093235 GCCATAACCAGCTCTCACTTCT 60.093 50.000 0.00 0.00 0.00 2.85
1111 1189 2.284190 GCCATAACCAGCTCTCACTTC 58.716 52.381 0.00 0.00 0.00 3.01
1113 1191 1.279496 TGCCATAACCAGCTCTCACT 58.721 50.000 0.00 0.00 0.00 3.41
1116 1194 2.159324 GCTTTTGCCATAACCAGCTCTC 60.159 50.000 0.00 0.00 40.15 3.20
1117 1195 1.821136 GCTTTTGCCATAACCAGCTCT 59.179 47.619 0.00 0.00 40.15 4.09
1118 1196 2.284263 GCTTTTGCCATAACCAGCTC 57.716 50.000 0.00 0.00 40.15 4.09
1141 1225 3.056328 GACCTTGCGGTGGCTTCC 61.056 66.667 0.00 0.00 45.73 3.46
1372 1468 4.465512 GTCGACTCGGCGCCGTAA 62.466 66.667 44.16 28.13 40.74 3.18
1462 1566 2.048603 GCAGGCTCCGGCAAGAAAT 61.049 57.895 6.17 0.00 40.87 2.17
1522 1638 3.807622 GTGTGAAGTCAACGAAGATCCAA 59.192 43.478 0.00 0.00 0.00 3.53
1602 1718 4.374843 TGGAGCGCGTACTTTCTTTATA 57.625 40.909 8.43 0.00 0.00 0.98
1626 1742 4.342665 TGGCTCCAAACGTTTTCCTTAAAT 59.657 37.500 11.66 0.00 0.00 1.40
1649 1765 2.231380 AATGTTCCTCCGGTGCCCT 61.231 57.895 0.00 0.00 0.00 5.19
1659 1775 2.198304 GAGACCGGCCCAATGTTCCT 62.198 60.000 0.00 0.00 0.00 3.36
1689 1805 1.153745 GCTGCGATGAAGGAGACGT 60.154 57.895 0.00 0.00 0.00 4.34
1760 1877 1.229853 GAAGGGTGGGGAGGAAGGA 60.230 63.158 0.00 0.00 0.00 3.36
1763 1880 2.204244 GGGAAGGGTGGGGAGGAA 60.204 66.667 0.00 0.00 0.00 3.36
2112 2444 5.753721 AGCTTCAAACTCCTTATCTCAGT 57.246 39.130 0.00 0.00 0.00 3.41
2293 2628 0.462375 AACCGTGGAAACAAAAGCCC 59.538 50.000 0.00 0.00 46.06 5.19
2387 2810 6.831353 TGGATGACCAAGAAAAGTTACAAGAA 59.169 34.615 0.00 0.00 43.91 2.52
2388 2811 6.361433 TGGATGACCAAGAAAAGTTACAAGA 58.639 36.000 0.00 0.00 43.91 3.02
2389 2812 6.633500 TGGATGACCAAGAAAAGTTACAAG 57.367 37.500 0.00 0.00 43.91 3.16
2492 2916 1.005037 TCAGTGCTGCAACCTACGG 60.005 57.895 2.77 0.00 0.00 4.02
2596 3024 3.680786 CTCTGGTGGCGACGACCA 61.681 66.667 11.40 11.40 38.59 4.02
2851 3295 2.404923 AGATCGTCGTCTTCCTCTCA 57.595 50.000 0.00 0.00 0.00 3.27
2972 3422 0.391661 ATAATGGGCGATGCTAGGCG 60.392 55.000 0.00 0.00 34.74 5.52
2973 3423 1.826385 AATAATGGGCGATGCTAGGC 58.174 50.000 0.00 0.00 0.00 3.93
2974 3424 5.677091 GCATTAAATAATGGGCGATGCTAGG 60.677 44.000 13.47 0.00 42.46 3.02
2975 3425 5.124457 AGCATTAAATAATGGGCGATGCTAG 59.876 40.000 13.47 0.00 44.73 3.42
2976 3426 5.009631 AGCATTAAATAATGGGCGATGCTA 58.990 37.500 13.47 0.00 44.73 3.49
2977 3427 3.828451 AGCATTAAATAATGGGCGATGCT 59.172 39.130 13.47 2.38 42.46 3.79
2978 3428 3.922240 CAGCATTAAATAATGGGCGATGC 59.078 43.478 13.47 0.00 42.46 3.91
2979 3429 3.922240 GCAGCATTAAATAATGGGCGATG 59.078 43.478 13.47 0.29 42.46 3.84
2980 3430 3.573538 TGCAGCATTAAATAATGGGCGAT 59.426 39.130 13.47 0.00 42.46 4.58
2981 3431 2.954989 TGCAGCATTAAATAATGGGCGA 59.045 40.909 13.47 0.00 42.46 5.54
2982 3432 3.367992 TGCAGCATTAAATAATGGGCG 57.632 42.857 13.47 0.00 42.46 6.13
2983 3433 5.865552 CAGTATGCAGCATTAAATAATGGGC 59.134 40.000 14.58 2.29 42.46 5.36
3138 3588 3.379445 TGAAGTCCTCCGCCGTCC 61.379 66.667 0.00 0.00 0.00 4.79
4019 4520 1.719600 ACTAGCTCGTCGACGTACTT 58.280 50.000 34.40 21.08 40.80 2.24
4051 4555 1.097547 CCTTGCCCTATTGCAGTCGG 61.098 60.000 0.00 0.00 43.21 4.79
4106 4614 3.614092 AGATTGAGGAAACATGCACGAT 58.386 40.909 0.00 0.00 0.00 3.73
4118 4626 3.223435 GGGACATCGAGTAGATTGAGGA 58.777 50.000 0.00 0.00 37.52 3.71
4128 4636 2.698797 ACATATTTCGGGGACATCGAGT 59.301 45.455 0.00 0.00 37.93 4.18
4156 4664 4.863131 AGTCGGAAAACAGACACGATTATC 59.137 41.667 0.00 0.00 39.67 1.75
4175 4683 0.945813 GGGGACATCGAGTAGAGTCG 59.054 60.000 0.15 0.15 41.51 4.18
4178 4686 2.350057 TCAGGGGACATCGAGTAGAG 57.650 55.000 0.00 0.00 0.00 2.43
4213 4721 2.952978 ACTGGGAAAACATGCACGTTTA 59.047 40.909 11.79 0.00 38.13 2.01
4214 4722 1.754226 ACTGGGAAAACATGCACGTTT 59.246 42.857 4.81 4.81 40.79 3.60
4264 4776 4.590918 TGGGAAAACAGGCACGATTATTA 58.409 39.130 0.00 0.00 0.00 0.98
4299 4814 7.896274 CGTTATTATGTTTACACGTTTCAGGAG 59.104 37.037 0.00 0.00 0.00 3.69
4325 4840 2.877168 ACGTGGATAGTCTCGTGGATAC 59.123 50.000 0.00 0.00 35.24 2.24
4326 4841 3.204306 ACGTGGATAGTCTCGTGGATA 57.796 47.619 0.00 0.00 35.24 2.59
4327 4842 2.054232 ACGTGGATAGTCTCGTGGAT 57.946 50.000 0.00 0.00 35.24 3.41
4328 4843 2.696989 TACGTGGATAGTCTCGTGGA 57.303 50.000 0.00 0.00 37.66 4.02
4330 4845 7.323895 CAGAATTAATACGTGGATAGTCTCGTG 59.676 40.741 0.00 0.00 37.66 4.35
4331 4846 7.361127 CAGAATTAATACGTGGATAGTCTCGT 58.639 38.462 0.00 0.00 39.74 4.18
4332 4847 6.305877 GCAGAATTAATACGTGGATAGTCTCG 59.694 42.308 0.00 0.00 0.00 4.04
4333 4848 7.145985 TGCAGAATTAATACGTGGATAGTCTC 58.854 38.462 0.00 0.00 0.00 3.36
4334 4849 7.050970 TGCAGAATTAATACGTGGATAGTCT 57.949 36.000 0.00 0.00 0.00 3.24
4335 4850 7.891183 ATGCAGAATTAATACGTGGATAGTC 57.109 36.000 0.00 0.00 0.00 2.59
4336 4851 8.677148 AAATGCAGAATTAATACGTGGATAGT 57.323 30.769 0.00 0.00 0.00 2.12
4338 4853 8.564574 GGAAAATGCAGAATTAATACGTGGATA 58.435 33.333 0.00 0.00 0.00 2.59
4339 4854 7.425606 GGAAAATGCAGAATTAATACGTGGAT 58.574 34.615 0.00 0.00 0.00 3.41
4340 4855 6.457663 CGGAAAATGCAGAATTAATACGTGGA 60.458 38.462 0.00 0.00 0.00 4.02
4341 4856 5.681105 CGGAAAATGCAGAATTAATACGTGG 59.319 40.000 0.00 0.00 0.00 4.94
4342 4857 5.171337 GCGGAAAATGCAGAATTAATACGTG 59.829 40.000 0.00 0.00 0.00 4.49
4343 4858 5.163703 TGCGGAAAATGCAGAATTAATACGT 60.164 36.000 0.00 0.00 37.44 3.57
4346 4872 6.201226 TGTGCGGAAAATGCAGAATTAATA 57.799 33.333 0.00 0.00 44.21 0.98
4366 4892 2.154854 ATCACGTGGACAGTCTTGTG 57.845 50.000 17.00 7.19 37.76 3.33
4483 5010 7.277396 AGTGAATGATGATGTGACATATGTGA 58.723 34.615 14.43 0.68 0.00 3.58
4567 5094 3.555527 AGTGGATGATGAGGTGACATG 57.444 47.619 0.00 0.00 0.00 3.21
4608 5135 9.328845 GGGATGTGTGCATATTAAAATTTTCAT 57.671 29.630 6.72 4.73 35.07 2.57
4647 5174 3.130869 TGCAATTAGTGTGATTGGATGGC 59.869 43.478 0.00 0.00 35.54 4.40
4653 5180 6.614160 TCTTGTGATGCAATTAGTGTGATTG 58.386 36.000 0.00 0.00 36.36 2.67
4686 5217 4.163078 CCTCAGGTGAGAGAAATACATGGT 59.837 45.833 8.64 0.00 44.74 3.55
4698 5229 1.536073 CGGTTCTGCCTCAGGTGAGA 61.536 60.000 8.64 0.00 44.74 3.27
4717 5248 0.175989 CGGAGAAGCCTAGGGTCAAC 59.824 60.000 15.24 9.11 0.00 3.18
4718 5249 1.614241 GCGGAGAAGCCTAGGGTCAA 61.614 60.000 15.24 0.00 0.00 3.18
4719 5250 2.058595 GCGGAGAAGCCTAGGGTCA 61.059 63.158 15.24 0.00 0.00 4.02
4720 5251 1.331399 AAGCGGAGAAGCCTAGGGTC 61.331 60.000 15.24 8.06 38.01 4.46
4721 5252 1.306226 AAGCGGAGAAGCCTAGGGT 60.306 57.895 7.93 7.93 38.01 4.34
4722 5253 1.443828 GAAGCGGAGAAGCCTAGGG 59.556 63.158 11.72 0.00 38.01 3.53
4795 5390 2.382305 TCCTAGTCTCCACCTTCCTTGA 59.618 50.000 0.00 0.00 0.00 3.02
4833 5428 4.195334 ATCCAGGCGCCCACCATC 62.195 66.667 26.15 0.00 0.00 3.51
4839 5434 2.031768 GATCTGATCCAGGCGCCC 59.968 66.667 26.15 7.94 31.51 6.13
4857 5452 2.071636 ATGGCCGGATGGATCATGCA 62.072 55.000 5.05 0.00 37.49 3.96
4924 5535 4.308458 CAGTGTCCCGAACGGCCA 62.308 66.667 2.24 3.95 0.00 5.36
4954 5565 2.348888 CCTCAGGGCGTAACCGACT 61.349 63.158 0.00 0.00 43.49 4.18
4957 5568 2.125673 CACCTCAGGGCGTAACCG 60.126 66.667 0.00 0.00 40.62 4.44
4960 5571 0.905809 TTAGGCACCTCAGGGCGTAA 60.906 55.000 12.63 12.63 37.84 3.18
4961 5572 0.689745 ATTAGGCACCTCAGGGCGTA 60.690 55.000 0.00 0.00 35.63 4.42
4962 5573 1.972660 GATTAGGCACCTCAGGGCGT 61.973 60.000 0.00 0.00 35.63 5.68
4968 5579 2.558795 GCGATCTAGATTAGGCACCTCA 59.441 50.000 6.70 0.00 0.00 3.86
4969 5580 2.414824 CGCGATCTAGATTAGGCACCTC 60.415 54.545 18.49 1.06 0.00 3.85
4970 5581 1.542030 CGCGATCTAGATTAGGCACCT 59.458 52.381 18.49 0.00 0.00 4.00
4972 5583 1.402984 CCCGCGATCTAGATTAGGCAC 60.403 57.143 8.23 2.16 0.00 5.01
4978 5589 0.247736 GGCATCCCGCGATCTAGATT 59.752 55.000 8.23 0.00 43.84 2.40
4983 5594 1.399744 TTGTAGGCATCCCGCGATCT 61.400 55.000 8.23 0.00 43.84 2.75
4987 5598 3.272334 GCTTGTAGGCATCCCGCG 61.272 66.667 0.00 0.00 43.84 6.46
4988 5599 2.893682 AAGGCTTGTAGGCATCCCGC 62.894 60.000 0.00 0.00 44.19 6.13
4994 5605 1.295423 GGACGAAGGCTTGTAGGCA 59.705 57.895 3.46 0.00 44.19 4.75
4999 5610 2.750350 CAGGGGACGAAGGCTTGT 59.250 61.111 3.46 2.94 0.00 3.16
5000 5611 2.747855 GCAGGGGACGAAGGCTTG 60.748 66.667 3.46 0.00 0.00 4.01
5001 5612 2.930562 AGCAGGGGACGAAGGCTT 60.931 61.111 0.00 0.00 0.00 4.35
5014 5625 3.782244 GACAAGCACGCCGAGCAG 61.782 66.667 9.58 3.38 0.00 4.24
5019 5630 4.374702 GCACAGACAAGCACGCCG 62.375 66.667 0.00 0.00 0.00 6.46
5020 5631 4.374702 CGCACAGACAAGCACGCC 62.375 66.667 0.00 0.00 0.00 5.68
5022 5633 1.959899 GATCCGCACAGACAAGCACG 61.960 60.000 0.00 0.00 0.00 5.34
5029 5640 1.520342 GGCTCAGATCCGCACAGAC 60.520 63.158 0.00 0.00 0.00 3.51
5033 5644 2.564553 AAGTCGGCTCAGATCCGCAC 62.565 60.000 7.89 7.36 46.05 5.34
5035 5646 1.880340 CAAGTCGGCTCAGATCCGC 60.880 63.158 7.89 3.69 46.05 5.54
5046 5657 1.938577 CATCAAGGATCAGCAAGTCGG 59.061 52.381 0.00 0.00 0.00 4.79
5055 5670 0.617935 TCCAACCGCATCAAGGATCA 59.382 50.000 0.00 0.00 0.00 2.92
5062 5677 2.046023 CCAGCTCCAACCGCATCA 60.046 61.111 0.00 0.00 0.00 3.07
5063 5678 2.109126 GTCCAGCTCCAACCGCATC 61.109 63.158 0.00 0.00 0.00 3.91
5067 5682 2.125912 CTCGTCCAGCTCCAACCG 60.126 66.667 0.00 0.00 0.00 4.44
5070 5685 0.909610 AATCCCTCGTCCAGCTCCAA 60.910 55.000 0.00 0.00 0.00 3.53
5071 5686 1.306141 AATCCCTCGTCCAGCTCCA 60.306 57.895 0.00 0.00 0.00 3.86
5078 5693 0.179108 CCGTTCTGAATCCCTCGTCC 60.179 60.000 0.00 0.00 0.00 4.79
5081 5696 0.103208 CTCCCGTTCTGAATCCCTCG 59.897 60.000 0.00 0.00 0.00 4.63
5083 5698 1.952621 TTCTCCCGTTCTGAATCCCT 58.047 50.000 0.00 0.00 0.00 4.20
5139 5755 2.282887 AAAATGGCGCCCTCGGTT 60.283 55.556 26.77 8.09 35.95 4.44
5140 5756 2.750237 GAAAATGGCGCCCTCGGT 60.750 61.111 26.77 5.01 35.95 4.69
5185 5801 2.684943 TGGTGTGGTGGAAGTAGAAGA 58.315 47.619 0.00 0.00 0.00 2.87
5202 5818 1.131303 TCACCCGGGAGACAAATGGT 61.131 55.000 32.02 0.00 0.00 3.55
5203 5819 0.037590 TTCACCCGGGAGACAAATGG 59.962 55.000 32.02 4.55 0.00 3.16
5240 5856 3.118454 CGAAGACGCCATTGCCGT 61.118 61.111 0.00 0.00 42.31 5.68
5241 5857 3.864686 CCGAAGACGCCATTGCCG 61.865 66.667 0.00 0.00 38.29 5.69
5245 5861 1.819632 GATGCCCGAAGACGCCATT 60.820 57.895 0.00 0.00 38.29 3.16
5247 5863 4.812476 CGATGCCCGAAGACGCCA 62.812 66.667 0.00 0.00 41.76 5.69
5252 5868 2.582436 GGGAACGATGCCCGAAGA 59.418 61.111 2.54 0.00 41.76 2.87
5257 5873 0.035439 TCAAGAAGGGAACGATGCCC 60.035 55.000 0.00 1.59 46.40 5.36
5284 5900 3.838795 ATCGTCGACGCGCAAAGC 61.839 61.111 32.19 0.00 43.95 3.51
5285 5901 2.018670 CATCGTCGACGCGCAAAG 59.981 61.111 32.19 13.73 39.60 2.77
5286 5902 2.429404 TCATCGTCGACGCGCAAA 60.429 55.556 32.19 15.92 39.60 3.68
5287 5903 3.169924 GTCATCGTCGACGCGCAA 61.170 61.111 32.19 16.33 39.60 4.85
5293 5909 1.134530 CAAGAGCCGTCATCGTCGAC 61.135 60.000 5.18 5.18 35.01 4.20
5294 5910 1.136774 CAAGAGCCGTCATCGTCGA 59.863 57.895 0.00 0.00 35.01 4.20
5295 5911 1.874019 CCAAGAGCCGTCATCGTCG 60.874 63.158 0.00 0.00 35.01 5.12
5296 5912 1.078759 CACCAAGAGCCGTCATCGTC 61.079 60.000 0.00 0.00 35.01 4.20
5297 5913 1.079819 CACCAAGAGCCGTCATCGT 60.080 57.895 0.00 0.00 35.01 3.73
5298 5914 1.811266 CCACCAAGAGCCGTCATCG 60.811 63.158 0.00 0.00 0.00 3.84
5299 5915 2.109126 GCCACCAAGAGCCGTCATC 61.109 63.158 0.00 0.00 0.00 2.92
5300 5916 2.045926 GCCACCAAGAGCCGTCAT 60.046 61.111 0.00 0.00 0.00 3.06
5301 5917 2.894257 ATGCCACCAAGAGCCGTCA 61.894 57.895 0.00 0.00 0.00 4.35
5302 5918 2.045926 ATGCCACCAAGAGCCGTC 60.046 61.111 0.00 0.00 0.00 4.79
5303 5919 2.360350 CATGCCACCAAGAGCCGT 60.360 61.111 0.00 0.00 0.00 5.68
5304 5920 2.535485 TACCATGCCACCAAGAGCCG 62.535 60.000 0.00 0.00 0.00 5.52
5305 5921 1.032114 GTACCATGCCACCAAGAGCC 61.032 60.000 0.00 0.00 0.00 4.70
5306 5922 0.322456 TGTACCATGCCACCAAGAGC 60.322 55.000 0.00 0.00 0.00 4.09
5307 5923 1.003580 ACTGTACCATGCCACCAAGAG 59.996 52.381 0.00 0.00 0.00 2.85
5308 5924 1.064003 ACTGTACCATGCCACCAAGA 58.936 50.000 0.00 0.00 0.00 3.02
5309 5925 1.167851 CACTGTACCATGCCACCAAG 58.832 55.000 0.00 0.00 0.00 3.61
5310 5926 0.251121 CCACTGTACCATGCCACCAA 60.251 55.000 0.00 0.00 0.00 3.67
5311 5927 1.130678 TCCACTGTACCATGCCACCA 61.131 55.000 0.00 0.00 0.00 4.17
5312 5928 0.392998 CTCCACTGTACCATGCCACC 60.393 60.000 0.00 0.00 0.00 4.61
5313 5929 0.324943 ACTCCACTGTACCATGCCAC 59.675 55.000 0.00 0.00 0.00 5.01
5314 5930 0.613260 GACTCCACTGTACCATGCCA 59.387 55.000 0.00 0.00 0.00 4.92
5315 5931 0.905357 AGACTCCACTGTACCATGCC 59.095 55.000 0.00 0.00 0.00 4.40
5316 5932 1.469940 CGAGACTCCACTGTACCATGC 60.470 57.143 0.00 0.00 0.00 4.06
5317 5933 1.135139 CCGAGACTCCACTGTACCATG 59.865 57.143 0.00 0.00 0.00 3.66
5318 5934 1.475403 CCGAGACTCCACTGTACCAT 58.525 55.000 0.00 0.00 0.00 3.55
5319 5935 1.248785 GCCGAGACTCCACTGTACCA 61.249 60.000 0.00 0.00 0.00 3.25
5320 5936 1.511768 GCCGAGACTCCACTGTACC 59.488 63.158 0.00 0.00 0.00 3.34
5321 5937 1.136984 CGCCGAGACTCCACTGTAC 59.863 63.158 0.00 0.00 0.00 2.90
5322 5938 2.044555 CCGCCGAGACTCCACTGTA 61.045 63.158 0.00 0.00 0.00 2.74
5323 5939 3.374402 CCGCCGAGACTCCACTGT 61.374 66.667 0.00 0.00 0.00 3.55
5324 5940 4.803426 GCCGCCGAGACTCCACTG 62.803 72.222 0.00 0.00 0.00 3.66


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

AutoCloner maintained by Alex Coulton.