Multiple sequence alignment - TraesCS3A01G335100

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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 TraesCS3A01G335100 chr3A 100.000 3316 0 0 1 3316 581381376 581378061 0.000000e+00 6124.0
1 TraesCS3A01G335100 chr3A 86.853 753 85 7 1153 1901 581851877 581851135 0.000000e+00 830.0
2 TraesCS3A01G335100 chr3A 77.807 1514 215 64 517 1964 581391745 581390287 0.000000e+00 822.0
3 TraesCS3A01G335100 chr3A 77.468 1003 174 23 998 1967 581844228 581843245 1.340000e-153 553.0
4 TraesCS3A01G335100 chr3A 80.830 699 116 15 1261 1953 581624298 581623612 1.750000e-147 532.0
5 TraesCS3A01G335100 chr3A 83.959 586 48 29 1 570 581392293 581391738 1.360000e-143 520.0
6 TraesCS3A01G335100 chr3A 79.200 500 72 16 548 1035 581406634 581406155 5.340000e-83 318.0
7 TraesCS3A01G335100 chr3D 87.303 1142 72 33 1 1102 441172990 441171882 0.000000e+00 1238.0
8 TraesCS3A01G335100 chr3D 84.841 818 103 14 1153 1957 441264106 441263297 0.000000e+00 804.0
9 TraesCS3A01G335100 chr3D 83.961 717 98 14 1261 1973 441428975 441428272 0.000000e+00 671.0
10 TraesCS3A01G335100 chr3D 81.940 670 88 18 2022 2681 441428120 441427474 1.350000e-148 536.0
11 TraesCS3A01G335100 chr3D 83.025 595 95 4 1385 1977 441158803 441158213 4.870000e-148 534.0
12 TraesCS3A01G335100 chr3D 78.613 851 122 27 2103 2933 441156410 441155600 2.950000e-140 508.0
13 TraesCS3A01G335100 chr3D 81.967 122 13 3 1001 1116 441429985 441429867 9.790000e-16 95.3
14 TraesCS3A01G335100 chr3D 100.000 29 0 0 361 389 585683321 585683349 2.000000e-03 54.7
15 TraesCS3A01G335100 chr3B 94.219 813 40 6 2128 2933 578598288 578597476 0.000000e+00 1234.0
16 TraesCS3A01G335100 chr3B 84.559 816 109 7 1153 1957 578814241 578813432 0.000000e+00 793.0
17 TraesCS3A01G335100 chr3B 86.283 729 84 12 2021 2739 578776666 578775944 0.000000e+00 778.0
18 TraesCS3A01G335100 chr3B 86.460 709 93 2 1275 1982 578777497 578776791 0.000000e+00 774.0
19 TraesCS3A01G335100 chr3B 79.610 667 120 13 1301 1960 578765598 578764941 6.480000e-127 464.0
20 TraesCS3A01G335100 chr3B 81.569 510 51 20 562 1053 578600171 578599687 6.710000e-102 381.0
21 TraesCS3A01G335100 chr6B 78.321 1822 311 58 953 2739 696335911 696334139 0.000000e+00 1099.0
22 TraesCS3A01G335100 chr6B 98.228 395 4 1 2925 3316 151880116 151879722 0.000000e+00 688.0
23 TraesCS3A01G335100 chr6B 94.538 238 9 2 2932 3165 545204075 545204312 6.760000e-97 364.0
24 TraesCS3A01G335100 chr4A 98.964 386 2 2 2933 3316 626311600 626311985 0.000000e+00 689.0
25 TraesCS3A01G335100 chr4A 92.651 381 19 6 2933 3309 200093732 200094107 1.050000e-149 540.0
26 TraesCS3A01G335100 chr4B 98.446 386 4 2 2933 3316 271623934 271624319 0.000000e+00 678.0
27 TraesCS3A01G335100 chr2A 98.545 275 1 3 3044 3316 278462944 278462671 1.790000e-132 483.0
28 TraesCS3A01G335100 chr2A 94.215 242 8 2 2930 3165 148595205 148595446 6.760000e-97 364.0
29 TraesCS3A01G335100 chr2A 88.679 53 5 1 360 412 78949976 78950027 2.760000e-06 63.9
30 TraesCS3A01G335100 chr2A 88.679 53 5 1 360 412 78966270 78966321 2.760000e-06 63.9
31 TraesCS3A01G335100 chr7A 94.492 236 10 2 2933 3165 726415038 726414803 8.750000e-96 361.0
32 TraesCS3A01G335100 chr7A 93.361 241 11 2 2930 3165 19560549 19560789 5.260000e-93 351.0
33 TraesCS3A01G335100 chr6A 75.723 173 29 11 314 478 12506184 12506017 1.280000e-09 75.0
34 TraesCS3A01G335100 chr5B 86.567 67 8 1 328 393 227945966 227945900 4.590000e-09 73.1
35 TraesCS3A01G335100 chr7D 86.364 66 6 2 360 425 613632373 613632311 5.940000e-08 69.4


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3A01G335100 chr3A 581378061 581381376 3315 True 6124.0 6124 100.000000 1 3316 1 chr3A.!!$R1 3315
1 TraesCS3A01G335100 chr3A 581851135 581851877 742 True 830.0 830 86.853000 1153 1901 1 chr3A.!!$R5 748
2 TraesCS3A01G335100 chr3A 581390287 581392293 2006 True 671.0 822 80.883000 1 1964 2 chr3A.!!$R6 1963
3 TraesCS3A01G335100 chr3A 581843245 581844228 983 True 553.0 553 77.468000 998 1967 1 chr3A.!!$R4 969
4 TraesCS3A01G335100 chr3A 581623612 581624298 686 True 532.0 532 80.830000 1261 1953 1 chr3A.!!$R3 692
5 TraesCS3A01G335100 chr3D 441171882 441172990 1108 True 1238.0 1238 87.303000 1 1102 1 chr3D.!!$R1 1101
6 TraesCS3A01G335100 chr3D 441263297 441264106 809 True 804.0 804 84.841000 1153 1957 1 chr3D.!!$R2 804
7 TraesCS3A01G335100 chr3D 441155600 441158803 3203 True 521.0 534 80.819000 1385 2933 2 chr3D.!!$R3 1548
8 TraesCS3A01G335100 chr3D 441427474 441429985 2511 True 434.1 671 82.622667 1001 2681 3 chr3D.!!$R4 1680
9 TraesCS3A01G335100 chr3B 578597476 578600171 2695 True 807.5 1234 87.894000 562 2933 2 chr3B.!!$R3 2371
10 TraesCS3A01G335100 chr3B 578813432 578814241 809 True 793.0 793 84.559000 1153 1957 1 chr3B.!!$R2 804
11 TraesCS3A01G335100 chr3B 578775944 578777497 1553 True 776.0 778 86.371500 1275 2739 2 chr3B.!!$R4 1464
12 TraesCS3A01G335100 chr3B 578764941 578765598 657 True 464.0 464 79.610000 1301 1960 1 chr3B.!!$R1 659
13 TraesCS3A01G335100 chr6B 696334139 696335911 1772 True 1099.0 1099 78.321000 953 2739 1 chr6B.!!$R2 1786

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
61 63 0.107214 GGCCAGCCAATACTGTAGCA 60.107 55.0 3.12 0.0 35.83 3.49 F
1055 1164 0.107508 CCGACATGGATCTTGGCACT 60.108 55.0 0.00 0.0 42.00 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1240 2508 0.320697 AAACCTGTGCGACTAGGGAC 59.679 55.0 0.00 0.00 38.42 4.46 R
2518 5532 0.833949 TGTTCAGGGTGTACACTGCA 59.166 50.0 24.55 11.86 46.66 4.41 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
61 63 0.107214 GGCCAGCCAATACTGTAGCA 60.107 55.000 3.12 0.00 35.83 3.49
65 67 2.484417 CCAGCCAATACTGTAGCAGAGG 60.484 54.545 2.91 1.31 35.83 3.69
72 74 0.675837 ACTGTAGCAGAGGACGCGTA 60.676 55.000 13.97 0.00 35.18 4.42
131 135 2.621055 TCACTGTTTGCAGCGGTTTTAT 59.379 40.909 2.55 0.00 46.30 1.40
542 557 0.476338 TGGCCTTGCAAGTTGTCCTA 59.524 50.000 24.35 8.41 0.00 2.94
551 613 7.657336 CCTTGCAAGTTGTCCTATTCTTTTTA 58.343 34.615 24.35 0.00 0.00 1.52
556 618 9.346725 GCAAGTTGTCCTATTCTTTTTATCTTG 57.653 33.333 4.48 0.00 0.00 3.02
589 653 7.526608 TGAACTACACTTTGTCACTCTTTTTG 58.473 34.615 0.00 0.00 0.00 2.44
741 813 1.107114 AGTACGTCAGGGCAGAGATG 58.893 55.000 0.00 0.00 0.00 2.90
742 814 0.818296 GTACGTCAGGGCAGAGATGT 59.182 55.000 0.00 0.00 37.69 3.06
849 929 5.713025 CTCTGTTTCCCCACATTGTTAATG 58.287 41.667 0.28 0.28 44.48 1.90
859 939 3.378112 CACATTGTTAATGGAGTGCCGAT 59.622 43.478 6.51 0.00 43.21 4.18
877 957 3.489738 CCGATGCCAAGTCAATCCAAATC 60.490 47.826 0.00 0.00 0.00 2.17
878 958 3.489738 CGATGCCAAGTCAATCCAAATCC 60.490 47.826 0.00 0.00 0.00 3.01
880 960 2.827322 TGCCAAGTCAATCCAAATCCTG 59.173 45.455 0.00 0.00 0.00 3.86
882 962 4.016444 GCCAAGTCAATCCAAATCCTGTA 58.984 43.478 0.00 0.00 0.00 2.74
883 963 4.096984 GCCAAGTCAATCCAAATCCTGTAG 59.903 45.833 0.00 0.00 0.00 2.74
894 976 6.403878 TCCAAATCCTGTAGTACTAAACTGC 58.596 40.000 3.61 0.00 39.39 4.40
898 980 4.801891 TCCTGTAGTACTAAACTGCGTTG 58.198 43.478 3.61 0.00 43.24 4.10
908 990 1.948104 AACTGCGTTGCTTGTGTCTA 58.052 45.000 0.00 0.00 0.00 2.59
914 1000 1.394917 CGTTGCTTGTGTCTATCTGCC 59.605 52.381 0.00 0.00 0.00 4.85
916 1002 2.813754 GTTGCTTGTGTCTATCTGCCAA 59.186 45.455 0.00 0.00 0.00 4.52
944 1030 6.040878 ACTCGTACATAAGTCATTTGTAGCC 58.959 40.000 0.00 0.00 0.00 3.93
945 1031 6.127423 ACTCGTACATAAGTCATTTGTAGCCT 60.127 38.462 0.00 0.00 0.00 4.58
946 1032 6.270815 TCGTACATAAGTCATTTGTAGCCTC 58.729 40.000 0.00 0.00 0.00 4.70
948 1034 6.757010 CGTACATAAGTCATTTGTAGCCTCTT 59.243 38.462 0.00 0.00 0.00 2.85
949 1035 7.919091 CGTACATAAGTCATTTGTAGCCTCTTA 59.081 37.037 0.00 0.00 0.00 2.10
984 1082 3.570975 TGCTTCAGAACAGAACATTGCAT 59.429 39.130 0.00 0.00 0.00 3.96
1027 1127 4.090057 GCTTCGGTTGCTCGGCAC 62.090 66.667 0.00 0.00 38.71 5.01
1053 1162 1.451927 GCCGACATGGATCTTGGCA 60.452 57.895 7.31 0.00 42.03 4.92
1054 1163 1.718757 GCCGACATGGATCTTGGCAC 61.719 60.000 7.31 0.00 42.03 5.01
1055 1164 0.107508 CCGACATGGATCTTGGCACT 60.108 55.000 0.00 0.00 42.00 4.40
1072 1181 1.221021 CTGCTGCTGCTCATCCTGA 59.779 57.895 17.00 0.00 40.48 3.86
1119 1243 4.404073 CAGTCTTCTACCTCTGGTAATGCT 59.596 45.833 0.00 0.00 37.76 3.79
1124 1252 6.213600 TCTTCTACCTCTGGTAATGCTTTTCT 59.786 38.462 0.00 0.00 37.76 2.52
1140 1268 4.141733 GCTTTTCTCTTCTAGATCCCTGCT 60.142 45.833 0.00 0.00 33.05 4.24
1146 1274 2.673775 TCTAGATCCCTGCTCCTCTG 57.326 55.000 0.00 0.00 0.00 3.35
1148 1276 3.056832 TCTAGATCCCTGCTCCTCTGTA 58.943 50.000 0.00 0.00 0.00 2.74
1240 2508 9.507329 AACACTCACATATTATTAGCTATTGGG 57.493 33.333 0.00 0.00 0.00 4.12
1242 2510 9.155975 CACTCACATATTATTAGCTATTGGGTC 57.844 37.037 0.00 0.00 0.00 4.46
1255 2529 1.541310 TTGGGTCCCTAGTCGCACAG 61.541 60.000 10.00 0.00 0.00 3.66
1259 2533 0.320697 GTCCCTAGTCGCACAGGTTT 59.679 55.000 0.00 0.00 0.00 3.27
1345 2627 0.824109 TCATAAGCCTCGACTGTGGG 59.176 55.000 0.00 0.00 0.00 4.61
1376 2658 1.327690 TAGCCCCTACAAGGACAGCG 61.328 60.000 0.00 0.00 37.67 5.18
1423 2705 1.136305 GATGTTGGATTCGTCGAGGGA 59.864 52.381 5.12 0.00 0.00 4.20
1457 2739 3.693085 CCAAATAGCAGCAGAGTTCATGT 59.307 43.478 0.00 0.00 0.00 3.21
1579 2861 1.980036 AGGGCCTTGTTTACTTACGGA 59.020 47.619 0.00 0.00 0.00 4.69
1604 2886 1.270839 ACGATGGGTTGAACAGGACTG 60.271 52.381 0.00 0.00 0.00 3.51
1613 2895 1.458777 AACAGGACTGTGGACGGGA 60.459 57.895 5.63 0.00 44.13 5.14
1651 2933 2.290641 GCTCCATATCGGCGTCAATTTT 59.709 45.455 6.85 0.00 33.14 1.82
1661 2943 2.182014 GCGTCAATTTTTGGGATACGC 58.818 47.619 0.00 0.00 42.82 4.42
1694 2976 7.664552 ACAAATATGGATCCATCAAACACAT 57.335 32.000 30.61 13.87 37.82 3.21
1744 3026 1.006314 GCGACTCTGTGTCAGTCTGC 61.006 60.000 10.13 1.72 45.60 4.26
1761 3043 6.540982 CAGTCTGCCTGATAAACTTCGGTTT 61.541 44.000 0.00 0.00 45.40 3.27
1773 3055 2.500504 ACTTCGGTTTAGGGACTCCATC 59.499 50.000 0.00 0.00 41.75 3.51
1843 3125 6.961359 TTTGTGAATACTTCCGTATCAGTG 57.039 37.500 0.00 0.00 35.32 3.66
1867 3149 5.224135 GGCTACTTTAGACGGATCAGATTC 58.776 45.833 0.00 0.00 0.00 2.52
1880 3162 2.176045 TCAGATTCGGTGAAGCCACTA 58.824 47.619 0.00 0.00 42.77 2.74
1908 3195 2.965147 TCACAAGGTGAGACTGACATCA 59.035 45.455 0.00 0.00 37.67 3.07
1924 3211 9.674824 GACTGACATCAATCATATTTTTGGATC 57.325 33.333 0.00 0.00 0.00 3.36
1967 3254 5.994668 TCAATGGTTTTAAAATCTGTTGGCC 59.005 36.000 20.07 0.00 0.00 5.36
1970 3257 4.407296 TGGTTTTAAAATCTGTTGGCCTGT 59.593 37.500 12.28 0.00 0.00 4.00
1971 3258 4.988540 GGTTTTAAAATCTGTTGGCCTGTC 59.011 41.667 3.32 0.00 0.00 3.51
1972 3259 5.452636 GGTTTTAAAATCTGTTGGCCTGTCA 60.453 40.000 3.32 0.00 0.00 3.58
2001 3331 5.415701 TCTTATGCTTTCTGAATCCCACAAC 59.584 40.000 0.00 0.00 0.00 3.32
2018 3348 6.764560 TCCCACAACTACTTCTAACAGAAAAC 59.235 38.462 0.00 0.00 33.19 2.43
2075 4760 2.028748 CCAGCTCCAATGGAACCAAAAG 60.029 50.000 2.61 0.00 40.51 2.27
2077 4762 1.338105 GCTCCAATGGAACCAAAAGGC 60.338 52.381 2.61 0.00 0.00 4.35
2172 5167 1.880819 TTACGACCGGTTCTGGGAGC 61.881 60.000 9.42 0.00 0.00 4.70
2173 5168 3.691342 CGACCGGTTCTGGGAGCA 61.691 66.667 9.42 0.00 0.00 4.26
2174 5169 2.266055 GACCGGTTCTGGGAGCAG 59.734 66.667 9.42 0.00 0.00 4.24
2178 5173 2.352805 GGTTCTGGGAGCAGTGGG 59.647 66.667 0.00 0.00 0.00 4.61
2341 5343 0.250727 CGTCACTGGGTCCCAATGTT 60.251 55.000 18.74 0.00 32.11 2.71
2518 5532 3.815401 GGCAGTTCTTGTATAATGGCGAT 59.185 43.478 0.00 0.00 0.00 4.58
2601 5615 1.891150 GGTGTACTCACTCCTTCGGAA 59.109 52.381 0.00 0.00 43.41 4.30
2732 5752 5.702209 ACATTCGCATTATCATCATGCAGTA 59.298 36.000 4.69 0.00 46.36 2.74
2758 5778 2.227388 CACCTGCTTAAACTGCCTGAAG 59.773 50.000 0.00 0.00 0.00 3.02
2807 5835 4.695455 ACAATCTAGCACAGTTATTTGCGT 59.305 37.500 0.00 0.00 43.87 5.24
2891 5923 3.698029 ATACATTTGAGATGCCAACGC 57.302 42.857 0.00 0.00 0.00 4.84
2893 5925 0.523968 CATTTGAGATGCCAACGCGG 60.524 55.000 12.47 0.00 38.08 6.46
2961 5993 8.943594 AAGGAGTATTAGTATTGGTCTAGGAG 57.056 38.462 0.00 0.00 0.00 3.69
2962 5994 8.059565 AGGAGTATTAGTATTGGTCTAGGAGT 57.940 38.462 0.00 0.00 0.00 3.85
2963 5995 8.165397 AGGAGTATTAGTATTGGTCTAGGAGTC 58.835 40.741 0.00 0.00 0.00 3.36
2964 5996 7.394077 GGAGTATTAGTATTGGTCTAGGAGTCC 59.606 44.444 0.00 0.00 0.00 3.85
2965 5997 8.059565 AGTATTAGTATTGGTCTAGGAGTCCT 57.940 38.462 17.78 17.78 37.71 3.85
2966 5998 8.512813 AGTATTAGTATTGGTCTAGGAGTCCTT 58.487 37.037 19.06 0.00 34.61 3.36
2967 5999 9.804977 GTATTAGTATTGGTCTAGGAGTCCTTA 57.195 37.037 19.06 3.09 34.61 2.69
2969 6001 9.900112 ATTAGTATTGGTCTAGGAGTCCTTATT 57.100 33.333 19.06 1.03 34.61 1.40
2971 6003 8.943594 AGTATTGGTCTAGGAGTCCTTATTAG 57.056 38.462 19.06 8.79 34.61 1.73
2972 6004 8.512813 AGTATTGGTCTAGGAGTCCTTATTAGT 58.487 37.037 19.06 1.58 34.61 2.24
2973 6005 7.842887 ATTGGTCTAGGAGTCCTTATTAGTC 57.157 40.000 19.06 6.20 34.61 2.59
2974 6006 6.593759 TGGTCTAGGAGTCCTTATTAGTCT 57.406 41.667 19.06 0.00 34.61 3.24
2975 6007 7.702807 TGGTCTAGGAGTCCTTATTAGTCTA 57.297 40.000 19.06 1.41 34.61 2.59
2976 6008 8.290463 TGGTCTAGGAGTCCTTATTAGTCTAT 57.710 38.462 19.06 0.00 34.61 1.98
2977 6009 8.164733 TGGTCTAGGAGTCCTTATTAGTCTATG 58.835 40.741 19.06 0.00 34.61 2.23
2978 6010 8.165397 GGTCTAGGAGTCCTTATTAGTCTATGT 58.835 40.741 19.06 0.00 34.61 2.29
2979 6011 9.577222 GTCTAGGAGTCCTTATTAGTCTATGTT 57.423 37.037 19.06 0.00 34.61 2.71
2983 6015 9.939424 AGGAGTCCTTATTAGTCTATGTTTAGT 57.061 33.333 5.62 0.00 0.00 2.24
2993 6025 6.803154 AGTCTATGTTTAGTTTCCTTGCAC 57.197 37.500 0.00 0.00 0.00 4.57
2994 6026 5.705905 AGTCTATGTTTAGTTTCCTTGCACC 59.294 40.000 0.00 0.00 0.00 5.01
2995 6027 5.705905 GTCTATGTTTAGTTTCCTTGCACCT 59.294 40.000 0.00 0.00 0.00 4.00
2996 6028 5.938125 TCTATGTTTAGTTTCCTTGCACCTC 59.062 40.000 0.00 0.00 0.00 3.85
2997 6029 3.892284 TGTTTAGTTTCCTTGCACCTCA 58.108 40.909 0.00 0.00 0.00 3.86
2998 6030 4.274147 TGTTTAGTTTCCTTGCACCTCAA 58.726 39.130 0.00 0.00 0.00 3.02
3006 6038 2.983402 CTTGCACCTCAAGTCATGTG 57.017 50.000 0.00 0.00 45.48 3.21
3007 6039 2.224606 CTTGCACCTCAAGTCATGTGT 58.775 47.619 0.00 0.00 45.48 3.72
3008 6040 3.402110 CTTGCACCTCAAGTCATGTGTA 58.598 45.455 0.00 0.00 45.48 2.90
3009 6041 3.483808 TGCACCTCAAGTCATGTGTAA 57.516 42.857 0.00 0.00 0.00 2.41
3010 6042 4.019792 TGCACCTCAAGTCATGTGTAAT 57.980 40.909 0.00 0.00 0.00 1.89
3011 6043 5.159273 TGCACCTCAAGTCATGTGTAATA 57.841 39.130 0.00 0.00 0.00 0.98
3012 6044 5.744171 TGCACCTCAAGTCATGTGTAATAT 58.256 37.500 0.00 0.00 0.00 1.28
3013 6045 6.883744 TGCACCTCAAGTCATGTGTAATATA 58.116 36.000 0.00 0.00 0.00 0.86
3014 6046 7.508687 TGCACCTCAAGTCATGTGTAATATAT 58.491 34.615 0.00 0.00 0.00 0.86
3015 6047 8.646900 TGCACCTCAAGTCATGTGTAATATATA 58.353 33.333 0.00 0.00 0.00 0.86
3016 6048 9.658799 GCACCTCAAGTCATGTGTAATATATAT 57.341 33.333 0.00 0.00 0.00 0.86
3041 6073 3.968265 CCTCTTGGGCCTTCAATAAAGA 58.032 45.455 4.53 2.34 37.12 2.52
3042 6074 4.540715 CCTCTTGGGCCTTCAATAAAGAT 58.459 43.478 4.53 0.00 37.12 2.40
3043 6075 5.694995 CCTCTTGGGCCTTCAATAAAGATA 58.305 41.667 4.53 0.00 37.12 1.98
3044 6076 6.129179 CCTCTTGGGCCTTCAATAAAGATAA 58.871 40.000 4.53 0.00 37.12 1.75
3045 6077 6.264067 CCTCTTGGGCCTTCAATAAAGATAAG 59.736 42.308 4.53 0.00 37.12 1.73
3046 6078 6.731467 TCTTGGGCCTTCAATAAAGATAAGT 58.269 36.000 4.53 0.00 37.12 2.24
3047 6079 7.182060 TCTTGGGCCTTCAATAAAGATAAGTT 58.818 34.615 4.53 0.00 37.12 2.66
3048 6080 6.773976 TGGGCCTTCAATAAAGATAAGTTG 57.226 37.500 4.53 0.00 37.12 3.16
3049 6081 5.127031 TGGGCCTTCAATAAAGATAAGTTGC 59.873 40.000 4.53 0.00 37.12 4.17
3050 6082 5.360999 GGGCCTTCAATAAAGATAAGTTGCT 59.639 40.000 0.84 0.00 37.12 3.91
3051 6083 6.127338 GGGCCTTCAATAAAGATAAGTTGCTT 60.127 38.462 0.84 0.00 37.12 3.91
3052 6084 7.323420 GGCCTTCAATAAAGATAAGTTGCTTT 58.677 34.615 0.00 9.55 37.12 3.51
3053 6085 7.489435 GGCCTTCAATAAAGATAAGTTGCTTTC 59.511 37.037 0.00 0.00 37.12 2.62
3054 6086 7.489435 GCCTTCAATAAAGATAAGTTGCTTTCC 59.511 37.037 8.32 0.00 37.12 3.13
3055 6087 8.743714 CCTTCAATAAAGATAAGTTGCTTTCCT 58.256 33.333 8.32 0.00 37.12 3.36
3062 6094 7.396540 AAGATAAGTTGCTTTCCTAACATGG 57.603 36.000 0.00 0.00 0.00 3.66
3063 6095 6.485171 AGATAAGTTGCTTTCCTAACATGGT 58.515 36.000 0.00 0.00 0.00 3.55
3064 6096 7.630082 AGATAAGTTGCTTTCCTAACATGGTA 58.370 34.615 0.00 0.00 0.00 3.25
3065 6097 8.275040 AGATAAGTTGCTTTCCTAACATGGTAT 58.725 33.333 0.00 0.00 0.00 2.73
3066 6098 8.823220 ATAAGTTGCTTTCCTAACATGGTATT 57.177 30.769 0.00 0.00 0.00 1.89
3067 6099 9.914834 ATAAGTTGCTTTCCTAACATGGTATTA 57.085 29.630 0.00 0.00 0.00 0.98
3068 6100 7.865706 AGTTGCTTTCCTAACATGGTATTAG 57.134 36.000 0.00 0.00 0.00 1.73
3069 6101 7.630082 AGTTGCTTTCCTAACATGGTATTAGA 58.370 34.615 0.00 0.00 32.31 2.10
3070 6102 7.770897 AGTTGCTTTCCTAACATGGTATTAGAG 59.229 37.037 0.00 0.00 32.31 2.43
3071 6103 6.055588 TGCTTTCCTAACATGGTATTAGAGC 58.944 40.000 0.00 3.08 32.31 4.09
3072 6104 5.470437 GCTTTCCTAACATGGTATTAGAGCC 59.530 44.000 0.00 0.00 32.31 4.70
3073 6105 6.689177 GCTTTCCTAACATGGTATTAGAGCCT 60.689 42.308 0.00 0.00 32.31 4.58
3074 6106 7.472945 GCTTTCCTAACATGGTATTAGAGCCTA 60.473 40.741 0.00 0.00 32.31 3.93
3075 6107 7.540474 TTCCTAACATGGTATTAGAGCCTAG 57.460 40.000 0.00 0.00 32.31 3.02
3076 6108 6.017192 TCCTAACATGGTATTAGAGCCTAGG 58.983 44.000 3.67 3.67 32.31 3.02
3077 6109 5.780793 CCTAACATGGTATTAGAGCCTAGGT 59.219 44.000 11.31 0.00 32.31 3.08
3078 6110 6.270231 CCTAACATGGTATTAGAGCCTAGGTT 59.730 42.308 11.31 3.54 32.31 3.50
3079 6111 6.576778 AACATGGTATTAGAGCCTAGGTTT 57.423 37.500 11.31 0.00 0.00 3.27
3080 6112 7.685849 AACATGGTATTAGAGCCTAGGTTTA 57.314 36.000 11.31 0.00 0.00 2.01
3081 6113 7.304497 ACATGGTATTAGAGCCTAGGTTTAG 57.696 40.000 11.31 0.00 0.00 1.85
3083 6115 5.785123 TGGTATTAGAGCCTAGGTTTAGGT 58.215 41.667 11.31 0.00 46.96 3.08
3084 6116 5.837438 TGGTATTAGAGCCTAGGTTTAGGTC 59.163 44.000 11.31 0.00 46.96 3.85
3085 6117 6.076653 GGTATTAGAGCCTAGGTTTAGGTCT 58.923 44.000 11.31 6.76 46.96 3.85
3086 6118 6.209192 GGTATTAGAGCCTAGGTTTAGGTCTC 59.791 46.154 11.31 6.43 46.96 3.36
3087 6119 3.035055 AGAGCCTAGGTTTAGGTCTCC 57.965 52.381 11.31 0.00 46.96 3.71
3088 6120 1.682323 GAGCCTAGGTTTAGGTCTCCG 59.318 57.143 11.31 0.00 46.96 4.63
3089 6121 0.751452 GCCTAGGTTTAGGTCTCCGG 59.249 60.000 11.31 0.00 46.96 5.14
3090 6122 1.687368 GCCTAGGTTTAGGTCTCCGGA 60.687 57.143 11.31 2.93 46.96 5.14
3091 6123 2.030371 CCTAGGTTTAGGTCTCCGGAC 58.970 57.143 0.00 0.00 41.42 4.79
3092 6124 1.674962 CTAGGTTTAGGTCTCCGGACG 59.325 57.143 0.00 0.00 42.97 4.79
3093 6125 1.153686 GGTTTAGGTCTCCGGACGC 60.154 63.158 0.00 0.00 42.97 5.19
3094 6126 1.153686 GTTTAGGTCTCCGGACGCC 60.154 63.158 0.00 5.63 42.97 5.68
3106 6138 4.719369 GACGCCGCAACTCGTCCT 62.719 66.667 3.68 0.00 46.50 3.85
3107 6139 4.295119 ACGCCGCAACTCGTCCTT 62.295 61.111 0.00 0.00 33.09 3.36
3108 6140 3.777925 CGCCGCAACTCGTCCTTG 61.778 66.667 0.00 0.00 36.19 3.61
3109 6141 4.090057 GCCGCAACTCGTCCTTGC 62.090 66.667 4.91 4.91 40.61 4.01
3112 6144 3.876300 GCAACTCGTCCTTGCGAT 58.124 55.556 0.00 0.00 40.29 4.58
3113 6145 1.710339 GCAACTCGTCCTTGCGATC 59.290 57.895 0.00 0.00 40.29 3.69
3114 6146 1.696832 GCAACTCGTCCTTGCGATCC 61.697 60.000 0.00 0.00 40.29 3.36
3115 6147 0.389817 CAACTCGTCCTTGCGATCCA 60.390 55.000 0.00 0.00 40.29 3.41
3116 6148 0.537188 AACTCGTCCTTGCGATCCAT 59.463 50.000 0.00 0.00 40.29 3.41
3117 6149 0.537188 ACTCGTCCTTGCGATCCATT 59.463 50.000 0.00 0.00 40.29 3.16
3118 6150 1.066143 ACTCGTCCTTGCGATCCATTT 60.066 47.619 0.00 0.00 40.29 2.32
3119 6151 2.009774 CTCGTCCTTGCGATCCATTTT 58.990 47.619 0.00 0.00 40.29 1.82
3120 6152 2.420022 CTCGTCCTTGCGATCCATTTTT 59.580 45.455 0.00 0.00 40.29 1.94
3144 6176 7.421530 TTTTTCTCGATCGATCTGTTTTTCT 57.578 32.000 19.78 0.00 0.00 2.52
3145 6177 6.633668 TTTCTCGATCGATCTGTTTTTCTC 57.366 37.500 19.78 0.00 0.00 2.87
3146 6178 5.568685 TCTCGATCGATCTGTTTTTCTCT 57.431 39.130 19.78 0.00 0.00 3.10
3147 6179 5.335935 TCTCGATCGATCTGTTTTTCTCTG 58.664 41.667 19.78 1.43 0.00 3.35
3148 6180 4.424626 TCGATCGATCTGTTTTTCTCTGG 58.575 43.478 22.43 3.10 0.00 3.86
3149 6181 4.157840 TCGATCGATCTGTTTTTCTCTGGA 59.842 41.667 22.43 5.40 0.00 3.86
3150 6182 5.046529 CGATCGATCTGTTTTTCTCTGGAT 58.953 41.667 22.43 0.00 0.00 3.41
3151 6183 5.174761 CGATCGATCTGTTTTTCTCTGGATC 59.825 44.000 22.43 0.00 0.00 3.36
3152 6184 4.768659 CGATCTGTTTTTCTCTGGATCG 57.231 45.455 8.36 8.36 43.58 3.69
3155 6187 6.523676 GATCTGTTTTTCTCTGGATCGATC 57.476 41.667 17.36 17.36 0.00 3.69
3156 6188 5.667539 TCTGTTTTTCTCTGGATCGATCT 57.332 39.130 23.96 0.00 0.00 2.75
3157 6189 5.655488 TCTGTTTTTCTCTGGATCGATCTC 58.345 41.667 23.96 14.76 0.00 2.75
3158 6190 4.424626 TGTTTTTCTCTGGATCGATCTCG 58.575 43.478 23.96 15.11 41.45 4.04
3159 6191 4.082190 TGTTTTTCTCTGGATCGATCTCGT 60.082 41.667 23.96 0.00 40.80 4.18
3160 6192 3.972950 TTTCTCTGGATCGATCTCGTC 57.027 47.619 23.96 8.74 40.80 4.20
3161 6193 2.920724 TCTCTGGATCGATCTCGTCT 57.079 50.000 23.96 0.00 40.80 4.18
3162 6194 3.201353 TCTCTGGATCGATCTCGTCTT 57.799 47.619 23.96 0.00 40.80 3.01
3163 6195 3.135225 TCTCTGGATCGATCTCGTCTTC 58.865 50.000 23.96 6.97 40.80 2.87
3164 6196 2.222886 TCTGGATCGATCTCGTCTTCC 58.777 52.381 23.96 7.89 40.80 3.46
3165 6197 1.950216 CTGGATCGATCTCGTCTTCCA 59.050 52.381 23.96 12.15 39.56 3.53
3166 6198 2.556189 CTGGATCGATCTCGTCTTCCAT 59.444 50.000 23.96 0.00 40.30 3.41
3167 6199 2.294512 TGGATCGATCTCGTCTTCCATG 59.705 50.000 23.96 0.00 38.23 3.66
3168 6200 2.352225 GGATCGATCTCGTCTTCCATGG 60.352 54.545 23.96 4.97 40.80 3.66
3169 6201 0.385751 TCGATCTCGTCTTCCATGGC 59.614 55.000 6.96 0.00 40.80 4.40
3170 6202 0.103026 CGATCTCGTCTTCCATGGCA 59.897 55.000 6.96 0.00 34.11 4.92
3171 6203 1.576356 GATCTCGTCTTCCATGGCAC 58.424 55.000 6.96 2.42 0.00 5.01
3172 6204 0.179000 ATCTCGTCTTCCATGGCACC 59.821 55.000 6.96 0.00 0.00 5.01
3173 6205 1.191489 TCTCGTCTTCCATGGCACCA 61.191 55.000 6.96 0.00 0.00 4.17
3174 6206 1.003839 TCGTCTTCCATGGCACCAC 60.004 57.895 6.96 0.00 0.00 4.16
3175 6207 2.040544 CGTCTTCCATGGCACCACC 61.041 63.158 6.96 0.00 39.84 4.61
3207 6239 4.711949 CCTGGCGCCTTGACTGCT 62.712 66.667 29.70 0.00 0.00 4.24
3208 6240 3.123620 CTGGCGCCTTGACTGCTC 61.124 66.667 29.70 0.00 0.00 4.26
3213 6245 4.704833 GCCTTGACTGCTCGCCCA 62.705 66.667 0.00 0.00 0.00 5.36
3214 6246 2.435586 CCTTGACTGCTCGCCCAG 60.436 66.667 1.29 1.29 38.78 4.45
3247 6279 4.814294 CACCTCGTGGGCCGCTAC 62.814 72.222 16.24 0.00 39.10 3.58
3250 6282 4.514577 CTCGTGGGCCGCTACCTG 62.515 72.222 16.24 0.00 36.19 4.00
3259 6291 3.164269 CGCTACCTGCCCCTGGAT 61.164 66.667 0.00 0.00 38.78 3.41
3260 6292 2.832498 GCTACCTGCCCCTGGATC 59.168 66.667 0.00 0.00 35.15 3.36
3261 6293 3.142393 CTACCTGCCCCTGGATCG 58.858 66.667 0.00 0.00 0.00 3.69
3262 6294 1.457643 CTACCTGCCCCTGGATCGA 60.458 63.158 0.00 0.00 0.00 3.59
3263 6295 0.833834 CTACCTGCCCCTGGATCGAT 60.834 60.000 0.00 0.00 0.00 3.59
3264 6296 1.121407 TACCTGCCCCTGGATCGATG 61.121 60.000 0.54 0.00 0.00 3.84
3265 6297 2.429058 CTGCCCCTGGATCGATGG 59.571 66.667 0.54 0.00 0.00 3.51
3266 6298 3.839353 CTGCCCCTGGATCGATGGC 62.839 68.421 15.00 15.00 42.49 4.40
3267 6299 4.996434 GCCCCTGGATCGATGGCG 62.996 72.222 0.54 0.00 39.35 5.69
3268 6300 4.320456 CCCCTGGATCGATGGCGG 62.320 72.222 0.54 0.00 38.28 6.13
3269 6301 4.996434 CCCTGGATCGATGGCGGC 62.996 72.222 0.54 0.00 38.28 6.53
3270 6302 3.933722 CCTGGATCGATGGCGGCT 61.934 66.667 11.43 0.00 38.28 5.52
3271 6303 2.664185 CTGGATCGATGGCGGCTG 60.664 66.667 11.43 0.00 38.28 4.85
3272 6304 4.916293 TGGATCGATGGCGGCTGC 62.916 66.667 9.72 9.72 41.71 5.25
3283 6315 4.598894 CGGCTGCCTCAGATCGGG 62.599 72.222 17.92 0.00 32.44 5.14
3284 6316 3.157252 GGCTGCCTCAGATCGGGA 61.157 66.667 12.43 0.00 32.44 5.14
3285 6317 2.107953 GCTGCCTCAGATCGGGAC 59.892 66.667 6.60 0.37 32.44 4.46
3286 6318 2.818132 CTGCCTCAGATCGGGACC 59.182 66.667 6.60 0.00 32.44 4.46
3287 6319 2.038813 TGCCTCAGATCGGGACCA 59.961 61.111 6.60 0.00 0.00 4.02
3288 6320 1.383109 TGCCTCAGATCGGGACCAT 60.383 57.895 6.60 0.00 0.00 3.55
3289 6321 1.369321 GCCTCAGATCGGGACCATC 59.631 63.158 6.60 0.00 0.00 3.51
3290 6322 1.662608 CCTCAGATCGGGACCATCG 59.337 63.158 0.00 0.00 0.00 3.84
3291 6323 1.006805 CTCAGATCGGGACCATCGC 60.007 63.158 0.00 0.00 0.00 4.58
3292 6324 2.029666 CAGATCGGGACCATCGCC 59.970 66.667 0.00 0.00 0.00 5.54
3293 6325 2.123251 AGATCGGGACCATCGCCT 60.123 61.111 0.00 0.00 0.00 5.52
3294 6326 2.203771 AGATCGGGACCATCGCCTC 61.204 63.158 0.00 0.00 0.00 4.70
3295 6327 3.227792 GATCGGGACCATCGCCTCC 62.228 68.421 0.00 0.00 0.00 4.30
3296 6328 3.758133 ATCGGGACCATCGCCTCCT 62.758 63.158 0.00 0.00 0.00 3.69
3297 6329 4.227134 CGGGACCATCGCCTCCTG 62.227 72.222 0.00 0.00 0.00 3.86
3298 6330 3.083997 GGGACCATCGCCTCCTGT 61.084 66.667 0.00 0.00 0.00 4.00
3299 6331 2.187946 GGACCATCGCCTCCTGTG 59.812 66.667 0.00 0.00 0.00 3.66
3300 6332 2.512515 GACCATCGCCTCCTGTGC 60.513 66.667 0.00 0.00 0.00 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 0.839946 AGTATTGGCTGGCCCTGTAG 59.160 55.000 9.28 0.00 34.56 2.74
169 173 9.967451 AAAGGAAAAAGGAAAAACAAAGGATTA 57.033 25.926 0.00 0.00 0.00 1.75
170 174 8.877864 AAAGGAAAAAGGAAAAACAAAGGATT 57.122 26.923 0.00 0.00 0.00 3.01
551 613 7.469537 AAGTGTAGTTCAGTAGCTACAAGAT 57.530 36.000 25.28 11.10 45.94 2.40
556 618 6.362820 GTGACAAAGTGTAGTTCAGTAGCTAC 59.637 42.308 16.43 16.43 38.35 3.58
559 621 5.290386 AGTGACAAAGTGTAGTTCAGTAGC 58.710 41.667 0.00 0.00 0.00 3.58
589 653 6.426937 TGAACCAGTCTTCTGTGCTAAATTAC 59.573 38.462 0.00 0.00 39.82 1.89
638 710 1.104577 AGCTCGCTCCTACAGCCTAC 61.105 60.000 0.00 0.00 46.74 3.18
642 714 2.584694 GCAGCTCGCTCCTACAGC 60.585 66.667 1.48 0.00 45.85 4.40
741 813 7.360017 GCAACTTGCCATGGATTTTAGTTTAAC 60.360 37.037 18.40 5.13 37.42 2.01
742 814 6.648725 GCAACTTGCCATGGATTTTAGTTTAA 59.351 34.615 18.40 0.00 37.42 1.52
826 906 5.336690 CCATTAACAATGTGGGGAAACAGAG 60.337 44.000 0.00 0.00 37.18 3.35
849 929 2.045926 ACTTGGCATCGGCACTCC 60.046 61.111 0.00 0.00 43.71 3.85
859 939 2.827322 CAGGATTTGGATTGACTTGGCA 59.173 45.455 0.00 0.00 0.00 4.92
894 976 1.394917 GGCAGATAGACACAAGCAACG 59.605 52.381 0.00 0.00 0.00 4.10
898 980 5.355350 AGTTATTTGGCAGATAGACACAAGC 59.645 40.000 0.00 0.00 32.34 4.01
908 990 7.272978 ACTTATGTACGAGTTATTTGGCAGAT 58.727 34.615 0.00 0.00 0.00 2.90
969 1067 3.058293 TCGGTTCATGCAATGTTCTGTTC 60.058 43.478 0.00 0.00 46.80 3.18
970 1068 2.884012 TCGGTTCATGCAATGTTCTGTT 59.116 40.909 0.00 0.00 46.80 3.16
971 1069 2.485426 CTCGGTTCATGCAATGTTCTGT 59.515 45.455 0.00 0.00 46.80 3.41
972 1070 2.159476 CCTCGGTTCATGCAATGTTCTG 60.159 50.000 0.00 0.00 46.80 3.02
973 1071 2.086869 CCTCGGTTCATGCAATGTTCT 58.913 47.619 0.00 0.00 46.80 3.01
984 1082 2.093181 CACCATGGTATTCCTCGGTTCA 60.093 50.000 19.28 0.00 37.03 3.18
1027 1127 0.389391 ATCCATGTCGGCCTTCTACG 59.611 55.000 0.00 0.00 33.14 3.51
1053 1162 1.078356 CAGGATGAGCAGCAGCAGT 60.078 57.895 3.17 0.00 45.49 4.40
1054 1163 1.221021 TCAGGATGAGCAGCAGCAG 59.779 57.895 3.17 0.00 42.56 4.24
1055 1164 3.395630 TCAGGATGAGCAGCAGCA 58.604 55.556 3.17 0.00 42.56 4.41
1119 1243 4.407296 GGAGCAGGGATCTAGAAGAGAAAA 59.593 45.833 0.00 0.00 37.85 2.29
1124 1252 2.788807 AGAGGAGCAGGGATCTAGAAGA 59.211 50.000 0.00 0.00 0.00 2.87
1140 1268 1.134580 GCATGCAGAGCTTACAGAGGA 60.135 52.381 14.21 0.00 0.00 3.71
1146 1274 1.446907 ACTGTGCATGCAGAGCTTAC 58.553 50.000 36.89 18.26 40.48 2.34
1148 1276 0.879765 GAACTGTGCATGCAGAGCTT 59.120 50.000 36.89 29.21 40.48 3.74
1240 2508 0.320697 AAACCTGTGCGACTAGGGAC 59.679 55.000 0.00 0.00 38.42 4.46
1242 2510 1.156736 CAAAACCTGTGCGACTAGGG 58.843 55.000 0.00 0.00 38.42 3.53
1285 2566 8.501580 AGAATATGTATCGATTTCATGTGCTTG 58.498 33.333 19.21 0.00 0.00 4.01
1288 2569 7.459486 GGAGAATATGTATCGATTTCATGTGC 58.541 38.462 19.21 14.01 0.00 4.57
1298 2579 6.262193 TGCATAACGGAGAATATGTATCGA 57.738 37.500 0.00 0.00 34.89 3.59
1345 2627 3.512724 TGTAGGGGCTAGTGTTTCTGTAC 59.487 47.826 0.00 0.00 0.00 2.90
1376 2658 3.570550 AGGAGCTGTATTCCTCGTATGAC 59.429 47.826 0.00 0.00 41.18 3.06
1423 2705 2.158385 TGCTATTTGGTGGGTCAAACCT 60.158 45.455 0.00 0.00 39.13 3.50
1457 2739 1.613925 GCTCTCATATACCGCACCAGA 59.386 52.381 0.00 0.00 0.00 3.86
1579 2861 2.233922 CCTGTTCAACCCATCGTAGTCT 59.766 50.000 0.00 0.00 0.00 3.24
1604 2886 1.602377 CAGAAACAAAGTCCCGTCCAC 59.398 52.381 0.00 0.00 0.00 4.02
1613 2895 2.430694 GGAGCCCAAACAGAAACAAAGT 59.569 45.455 0.00 0.00 0.00 2.66
1651 2933 4.274602 TGTTAAGTTCAGCGTATCCCAA 57.725 40.909 0.00 0.00 0.00 4.12
1661 2943 9.123902 TGATGGATCCATATTTGTTAAGTTCAG 57.876 33.333 27.38 0.00 36.70 3.02
1744 3026 4.874396 GTCCCTAAACCGAAGTTTATCAGG 59.126 45.833 0.00 0.15 45.16 3.86
1761 3043 0.629596 AGACACGGATGGAGTCCCTA 59.370 55.000 6.74 0.00 44.77 3.53
1773 3055 3.414700 GCTCCAACGCAGACACGG 61.415 66.667 0.00 0.00 37.37 4.94
1843 3125 2.957006 TCTGATCCGTCTAAAGTAGCCC 59.043 50.000 0.00 0.00 0.00 5.19
1867 3149 4.092968 GTGATAAAGTTAGTGGCTTCACCG 59.907 45.833 0.00 0.00 43.94 4.94
1880 3162 5.992217 GTCAGTCTCACCTTGTGATAAAGTT 59.008 40.000 0.00 0.00 41.94 2.66
1926 3213 6.186957 ACCATTGACAGGCATAATTCAGTTA 58.813 36.000 0.00 0.00 0.00 2.24
1967 3254 5.353400 TCAGAAAGCATAAGAGCATTGACAG 59.647 40.000 0.00 0.00 36.85 3.51
1970 3257 6.039047 GGATTCAGAAAGCATAAGAGCATTGA 59.961 38.462 0.00 0.00 36.85 2.57
1971 3258 6.207213 GGATTCAGAAAGCATAAGAGCATTG 58.793 40.000 0.00 0.00 36.85 2.82
1972 3259 5.301298 GGGATTCAGAAAGCATAAGAGCATT 59.699 40.000 0.00 0.00 36.85 3.56
2018 3348 5.239306 TCTTGGCAAGTTGAGATGTACTTTG 59.761 40.000 25.39 0.00 32.50 2.77
2075 4760 0.876342 GCTAGCACGATACCACTGCC 60.876 60.000 10.63 0.00 0.00 4.85
2077 4762 3.275400 CTAGCTAGCACGATACCACTG 57.725 52.381 18.83 0.00 0.00 3.66
2124 5119 1.138661 TGGATATCTGCATCGCACACA 59.861 47.619 2.05 0.00 33.79 3.72
2172 5167 2.749621 GGTAAGAATTGAGTGCCCACTG 59.250 50.000 5.53 0.00 42.66 3.66
2173 5168 2.290960 GGGTAAGAATTGAGTGCCCACT 60.291 50.000 0.00 0.00 45.84 4.00
2174 5169 2.092323 GGGTAAGAATTGAGTGCCCAC 58.908 52.381 0.00 0.00 34.95 4.61
2178 5173 2.026262 TCCAGGGGTAAGAATTGAGTGC 60.026 50.000 0.00 0.00 0.00 4.40
2180 5175 4.111577 TGATCCAGGGGTAAGAATTGAGT 58.888 43.478 0.00 0.00 0.00 3.41
2181 5176 4.778213 TGATCCAGGGGTAAGAATTGAG 57.222 45.455 0.00 0.00 0.00 3.02
2184 5179 3.858638 AGGTTGATCCAGGGGTAAGAATT 59.141 43.478 0.00 0.00 39.02 2.17
2186 5181 2.576191 CAGGTTGATCCAGGGGTAAGAA 59.424 50.000 0.00 0.00 39.02 2.52
2188 5183 2.196595 TCAGGTTGATCCAGGGGTAAG 58.803 52.381 0.00 0.00 39.02 2.34
2237 5238 1.271379 ACATTGAAGTAGTCGTCGCCA 59.729 47.619 0.00 0.00 0.00 5.69
2341 5343 3.744719 CGGACGCTCTCGGGAACA 61.745 66.667 0.00 0.00 40.69 3.18
2518 5532 0.833949 TGTTCAGGGTGTACACTGCA 59.166 50.000 24.55 11.86 46.66 4.41
2601 5615 3.433740 GGAGTCAGTGGTGAAGTTTTCCT 60.434 47.826 0.00 0.00 33.27 3.36
2732 5752 4.641989 CAGGCAGTTTAAGCAGGTGAATAT 59.358 41.667 0.00 0.00 0.00 1.28
2758 5778 9.601217 TTTAAAAGCAGGAATCTGTAGATACTC 57.399 33.333 0.00 0.00 42.78 2.59
2772 5792 5.767665 TGTGCTAGATTGTTTAAAAGCAGGA 59.232 36.000 9.65 0.00 40.36 3.86
2807 5835 2.170607 GAGGTGACTAAAGCATAGCCCA 59.829 50.000 0.00 0.00 44.43 5.36
2879 5911 1.134694 GAAACCGCGTTGGCATCTC 59.865 57.895 4.92 0.00 43.94 2.75
2891 5923 2.266554 TGCAACAAAAGCAAGAAACCG 58.733 42.857 0.00 0.00 39.39 4.44
2936 5968 8.512813 ACTCCTAGACCAATACTAATACTCCTT 58.487 37.037 0.00 0.00 0.00 3.36
2937 5969 8.059565 ACTCCTAGACCAATACTAATACTCCT 57.940 38.462 0.00 0.00 0.00 3.69
2938 5970 7.394077 GGACTCCTAGACCAATACTAATACTCC 59.606 44.444 0.00 0.00 30.29 3.85
2939 5971 8.165397 AGGACTCCTAGACCAATACTAATACTC 58.835 40.741 0.00 0.00 32.35 2.59
2940 5972 8.059565 AGGACTCCTAGACCAATACTAATACT 57.940 38.462 0.00 0.00 32.35 2.12
2941 5973 8.709272 AAGGACTCCTAGACCAATACTAATAC 57.291 38.462 0.00 0.00 32.35 1.89
2943 5975 9.900112 AATAAGGACTCCTAGACCAATACTAAT 57.100 33.333 0.00 0.00 32.35 1.73
2946 5978 8.512813 ACTAATAAGGACTCCTAGACCAATACT 58.487 37.037 0.00 0.00 32.35 2.12
2947 5979 8.709272 ACTAATAAGGACTCCTAGACCAATAC 57.291 38.462 0.00 0.00 32.35 1.89
2948 5980 8.734763 AGACTAATAAGGACTCCTAGACCAATA 58.265 37.037 0.00 0.00 32.35 1.90
2949 5981 7.597327 AGACTAATAAGGACTCCTAGACCAAT 58.403 38.462 0.00 0.00 32.35 3.16
2950 5982 6.982899 AGACTAATAAGGACTCCTAGACCAA 58.017 40.000 0.00 0.00 32.35 3.67
2951 5983 6.593759 AGACTAATAAGGACTCCTAGACCA 57.406 41.667 0.00 0.00 32.35 4.02
2952 5984 8.165397 ACATAGACTAATAAGGACTCCTAGACC 58.835 40.741 0.00 0.00 31.13 3.85
2953 5985 9.577222 AACATAGACTAATAAGGACTCCTAGAC 57.423 37.037 0.00 0.00 31.13 2.59
2957 5989 9.939424 ACTAAACATAGACTAATAAGGACTCCT 57.061 33.333 0.00 0.00 33.87 3.69
2967 5999 8.947115 GTGCAAGGAAACTAAACATAGACTAAT 58.053 33.333 0.00 0.00 42.68 1.73
2968 6000 7.389607 GGTGCAAGGAAACTAAACATAGACTAA 59.610 37.037 0.00 0.00 42.68 2.24
2969 6001 6.877322 GGTGCAAGGAAACTAAACATAGACTA 59.123 38.462 0.00 0.00 42.68 2.59
2970 6002 5.705905 GGTGCAAGGAAACTAAACATAGACT 59.294 40.000 0.00 0.00 42.68 3.24
2971 6003 5.705905 AGGTGCAAGGAAACTAAACATAGAC 59.294 40.000 0.00 0.00 42.68 2.59
2972 6004 5.876357 AGGTGCAAGGAAACTAAACATAGA 58.124 37.500 0.00 0.00 42.68 1.98
2973 6005 5.705441 TGAGGTGCAAGGAAACTAAACATAG 59.295 40.000 0.00 0.00 42.68 2.23
2974 6006 5.626142 TGAGGTGCAAGGAAACTAAACATA 58.374 37.500 0.00 0.00 42.68 2.29
2975 6007 4.469657 TGAGGTGCAAGGAAACTAAACAT 58.530 39.130 0.00 0.00 42.68 2.71
2976 6008 3.892284 TGAGGTGCAAGGAAACTAAACA 58.108 40.909 0.00 0.00 42.68 2.83
2977 6009 4.911514 TTGAGGTGCAAGGAAACTAAAC 57.088 40.909 0.00 0.00 42.68 2.01
2988 6020 2.346766 ACACATGACTTGAGGTGCAA 57.653 45.000 0.00 0.00 34.69 4.08
2989 6021 3.483808 TTACACATGACTTGAGGTGCA 57.516 42.857 0.00 0.00 34.69 4.57
2990 6022 7.969536 ATATATTACACATGACTTGAGGTGC 57.030 36.000 0.00 0.00 34.69 5.01
3020 6052 3.968265 TCTTTATTGAAGGCCCAAGAGG 58.032 45.455 0.00 0.00 35.98 3.69
3021 6053 6.830838 ACTTATCTTTATTGAAGGCCCAAGAG 59.169 38.462 0.00 0.00 35.98 2.85
3022 6054 6.731467 ACTTATCTTTATTGAAGGCCCAAGA 58.269 36.000 0.00 0.00 35.98 3.02
3023 6055 7.260603 CAACTTATCTTTATTGAAGGCCCAAG 58.739 38.462 0.00 0.00 35.98 3.61
3024 6056 6.350949 GCAACTTATCTTTATTGAAGGCCCAA 60.351 38.462 0.00 0.00 35.98 4.12
3025 6057 5.127031 GCAACTTATCTTTATTGAAGGCCCA 59.873 40.000 0.00 0.00 35.98 5.36
3026 6058 5.360999 AGCAACTTATCTTTATTGAAGGCCC 59.639 40.000 0.00 0.00 35.98 5.80
3027 6059 6.456795 AGCAACTTATCTTTATTGAAGGCC 57.543 37.500 0.00 0.00 35.98 5.19
3028 6060 7.489435 GGAAAGCAACTTATCTTTATTGAAGGC 59.511 37.037 0.00 0.00 35.98 4.35
3029 6061 8.743714 AGGAAAGCAACTTATCTTTATTGAAGG 58.256 33.333 0.00 0.00 35.98 3.46
3036 6068 8.956426 CCATGTTAGGAAAGCAACTTATCTTTA 58.044 33.333 0.00 0.00 33.14 1.85
3037 6069 7.451566 ACCATGTTAGGAAAGCAACTTATCTTT 59.548 33.333 0.00 0.00 35.44 2.52
3038 6070 6.948309 ACCATGTTAGGAAAGCAACTTATCTT 59.052 34.615 0.00 0.00 0.00 2.40
3039 6071 6.485171 ACCATGTTAGGAAAGCAACTTATCT 58.515 36.000 0.00 0.00 0.00 1.98
3040 6072 6.759497 ACCATGTTAGGAAAGCAACTTATC 57.241 37.500 0.00 0.00 0.00 1.75
3041 6073 8.823220 AATACCATGTTAGGAAAGCAACTTAT 57.177 30.769 0.00 0.00 0.00 1.73
3042 6074 9.391006 CTAATACCATGTTAGGAAAGCAACTTA 57.609 33.333 0.00 0.00 0.00 2.24
3043 6075 8.107095 TCTAATACCATGTTAGGAAAGCAACTT 58.893 33.333 0.00 0.00 31.59 2.66
3044 6076 7.630082 TCTAATACCATGTTAGGAAAGCAACT 58.370 34.615 0.00 0.00 31.59 3.16
3045 6077 7.467403 GCTCTAATACCATGTTAGGAAAGCAAC 60.467 40.741 8.00 0.00 31.59 4.17
3046 6078 6.542370 GCTCTAATACCATGTTAGGAAAGCAA 59.458 38.462 8.00 0.00 31.59 3.91
3047 6079 6.055588 GCTCTAATACCATGTTAGGAAAGCA 58.944 40.000 8.00 0.00 31.59 3.91
3048 6080 5.470437 GGCTCTAATACCATGTTAGGAAAGC 59.530 44.000 0.00 0.00 31.59 3.51
3049 6081 6.831976 AGGCTCTAATACCATGTTAGGAAAG 58.168 40.000 0.00 0.00 31.59 2.62
3050 6082 6.824958 AGGCTCTAATACCATGTTAGGAAA 57.175 37.500 0.00 0.00 31.59 3.13
3051 6083 6.497259 CCTAGGCTCTAATACCATGTTAGGAA 59.503 42.308 0.00 0.00 31.59 3.36
3052 6084 6.017192 CCTAGGCTCTAATACCATGTTAGGA 58.983 44.000 0.00 0.00 31.59 2.94
3053 6085 5.780793 ACCTAGGCTCTAATACCATGTTAGG 59.219 44.000 9.30 0.00 31.59 2.69
3054 6086 6.919775 ACCTAGGCTCTAATACCATGTTAG 57.080 41.667 9.30 0.00 0.00 2.34
3055 6087 7.685849 AAACCTAGGCTCTAATACCATGTTA 57.314 36.000 9.30 0.00 0.00 2.41
3056 6088 6.576778 AAACCTAGGCTCTAATACCATGTT 57.423 37.500 9.30 0.00 0.00 2.71
3057 6089 6.270231 CCTAAACCTAGGCTCTAATACCATGT 59.730 42.308 9.30 0.00 38.50 3.21
3058 6090 6.702329 CCTAAACCTAGGCTCTAATACCATG 58.298 44.000 9.30 0.00 38.50 3.66
3059 6091 6.936968 CCTAAACCTAGGCTCTAATACCAT 57.063 41.667 9.30 0.00 38.50 3.55
3072 6104 1.674962 CGTCCGGAGACCTAAACCTAG 59.325 57.143 3.06 0.00 40.12 3.02
3073 6105 1.755179 CGTCCGGAGACCTAAACCTA 58.245 55.000 3.06 0.00 40.12 3.08
3074 6106 1.602327 GCGTCCGGAGACCTAAACCT 61.602 60.000 3.06 0.00 40.12 3.50
3075 6107 1.153686 GCGTCCGGAGACCTAAACC 60.154 63.158 3.06 0.00 40.12 3.27
3076 6108 1.153686 GGCGTCCGGAGACCTAAAC 60.154 63.158 3.06 0.00 40.12 2.01
3077 6109 2.703798 CGGCGTCCGGAGACCTAAA 61.704 63.158 18.24 0.00 44.15 1.85
3078 6110 3.136123 CGGCGTCCGGAGACCTAA 61.136 66.667 18.24 0.00 44.15 2.69
3095 6127 1.696832 GGATCGCAAGGACGAGTTGC 61.697 60.000 9.96 9.96 46.69 4.17
3096 6128 0.389817 TGGATCGCAAGGACGAGTTG 60.390 55.000 0.00 0.00 46.69 3.16
3097 6129 0.537188 ATGGATCGCAAGGACGAGTT 59.463 50.000 0.00 0.00 46.69 3.01
3098 6130 0.537188 AATGGATCGCAAGGACGAGT 59.463 50.000 0.00 0.00 46.69 4.18
3099 6131 1.656652 AAATGGATCGCAAGGACGAG 58.343 50.000 0.00 0.00 46.69 4.18
3101 6133 2.919666 AAAAATGGATCGCAAGGACG 57.080 45.000 0.00 0.00 38.47 4.79
3120 6152 7.385205 AGAGAAAAACAGATCGATCGAGAAAAA 59.615 33.333 23.84 0.00 0.00 1.94
3121 6153 6.868864 AGAGAAAAACAGATCGATCGAGAAAA 59.131 34.615 23.84 0.00 0.00 2.29
3122 6154 6.309009 CAGAGAAAAACAGATCGATCGAGAAA 59.691 38.462 23.84 0.00 0.00 2.52
3123 6155 5.802451 CAGAGAAAAACAGATCGATCGAGAA 59.198 40.000 23.84 0.00 0.00 2.87
3124 6156 5.335935 CAGAGAAAAACAGATCGATCGAGA 58.664 41.667 23.84 0.68 0.00 4.04
3125 6157 4.502282 CCAGAGAAAAACAGATCGATCGAG 59.498 45.833 23.84 17.57 0.00 4.04
3126 6158 4.157840 TCCAGAGAAAAACAGATCGATCGA 59.842 41.667 21.86 21.86 0.00 3.59
3127 6159 4.424626 TCCAGAGAAAAACAGATCGATCG 58.575 43.478 19.33 9.36 0.00 3.69
3128 6160 6.523676 GATCCAGAGAAAAACAGATCGATC 57.476 41.667 17.91 17.91 0.00 3.69
3131 6163 4.768659 CGATCCAGAGAAAAACAGATCG 57.231 45.455 5.90 5.90 44.63 3.69
3132 6164 6.279882 AGATCGATCCAGAGAAAAACAGATC 58.720 40.000 21.66 0.00 0.00 2.75
3133 6165 6.232581 AGATCGATCCAGAGAAAAACAGAT 57.767 37.500 21.66 0.00 0.00 2.90
3134 6166 5.655488 GAGATCGATCCAGAGAAAAACAGA 58.345 41.667 21.66 0.00 0.00 3.41
3135 6167 4.502282 CGAGATCGATCCAGAGAAAAACAG 59.498 45.833 21.66 0.00 43.02 3.16
3136 6168 4.082190 ACGAGATCGATCCAGAGAAAAACA 60.082 41.667 21.66 0.00 43.02 2.83
3137 6169 4.425520 ACGAGATCGATCCAGAGAAAAAC 58.574 43.478 21.66 0.00 43.02 2.43
3138 6170 4.399618 AGACGAGATCGATCCAGAGAAAAA 59.600 41.667 21.66 0.00 43.02 1.94
3139 6171 3.948473 AGACGAGATCGATCCAGAGAAAA 59.052 43.478 21.66 0.00 43.02 2.29
3140 6172 3.546724 AGACGAGATCGATCCAGAGAAA 58.453 45.455 21.66 0.00 43.02 2.52
3141 6173 3.201353 AGACGAGATCGATCCAGAGAA 57.799 47.619 21.66 0.00 43.02 2.87
3142 6174 2.920724 AGACGAGATCGATCCAGAGA 57.079 50.000 21.66 0.00 43.02 3.10
3143 6175 2.225491 GGAAGACGAGATCGATCCAGAG 59.775 54.545 21.66 12.61 43.02 3.35
3144 6176 2.222886 GGAAGACGAGATCGATCCAGA 58.777 52.381 21.66 0.00 43.02 3.86
3145 6177 1.950216 TGGAAGACGAGATCGATCCAG 59.050 52.381 21.66 17.36 41.30 3.86
3146 6178 2.052782 TGGAAGACGAGATCGATCCA 57.947 50.000 21.66 18.20 42.62 3.41
3147 6179 2.352225 CCATGGAAGACGAGATCGATCC 60.352 54.545 21.66 12.11 43.02 3.36
3148 6180 2.924454 GCCATGGAAGACGAGATCGATC 60.924 54.545 18.40 17.91 43.02 3.69
3149 6181 1.000283 GCCATGGAAGACGAGATCGAT 60.000 52.381 18.40 0.00 43.02 3.59
3150 6182 0.385751 GCCATGGAAGACGAGATCGA 59.614 55.000 18.40 0.00 43.02 3.59
3151 6183 0.103026 TGCCATGGAAGACGAGATCG 59.897 55.000 18.40 0.00 46.33 3.69
3152 6184 1.576356 GTGCCATGGAAGACGAGATC 58.424 55.000 18.40 0.00 0.00 2.75
3153 6185 0.179000 GGTGCCATGGAAGACGAGAT 59.821 55.000 18.40 0.00 0.00 2.75
3154 6186 1.191489 TGGTGCCATGGAAGACGAGA 61.191 55.000 18.40 0.00 0.00 4.04
3155 6187 1.021390 GTGGTGCCATGGAAGACGAG 61.021 60.000 18.40 0.00 0.00 4.18
3156 6188 1.003839 GTGGTGCCATGGAAGACGA 60.004 57.895 18.40 2.58 0.00 4.20
3157 6189 2.040544 GGTGGTGCCATGGAAGACG 61.041 63.158 18.40 0.00 37.17 4.18
3158 6190 1.074775 TGGTGGTGCCATGGAAGAC 59.925 57.895 18.40 8.22 43.61 3.01
3159 6191 3.586543 TGGTGGTGCCATGGAAGA 58.413 55.556 18.40 0.00 43.61 2.87
3190 6222 4.711949 AGCAGTCAAGGCGCCAGG 62.712 66.667 31.54 20.41 36.08 4.45
3191 6223 3.123620 GAGCAGTCAAGGCGCCAG 61.124 66.667 31.54 21.15 36.08 4.85
3196 6228 4.704833 TGGGCGAGCAGTCAAGGC 62.705 66.667 0.00 0.00 0.00 4.35
3197 6229 2.435586 CTGGGCGAGCAGTCAAGG 60.436 66.667 0.00 0.00 0.00 3.61
3243 6275 2.832498 GATCCAGGGGCAGGTAGC 59.168 66.667 0.00 0.00 44.65 3.58
3244 6276 0.833834 ATCGATCCAGGGGCAGGTAG 60.834 60.000 0.00 0.00 0.00 3.18
3245 6277 1.121407 CATCGATCCAGGGGCAGGTA 61.121 60.000 0.00 0.00 0.00 3.08
3246 6278 2.040464 ATCGATCCAGGGGCAGGT 60.040 61.111 0.00 0.00 0.00 4.00
3247 6279 2.429058 CATCGATCCAGGGGCAGG 59.571 66.667 0.00 0.00 0.00 4.85
3248 6280 2.429058 CCATCGATCCAGGGGCAG 59.571 66.667 0.00 0.00 0.00 4.85
3249 6281 3.877450 GCCATCGATCCAGGGGCA 61.877 66.667 16.53 0.00 44.01 5.36
3250 6282 4.996434 CGCCATCGATCCAGGGGC 62.996 72.222 12.50 12.50 41.20 5.80
3251 6283 4.320456 CCGCCATCGATCCAGGGG 62.320 72.222 9.60 9.60 38.10 4.79
3252 6284 4.996434 GCCGCCATCGATCCAGGG 62.996 72.222 0.00 0.00 38.10 4.45
3253 6285 3.933722 AGCCGCCATCGATCCAGG 61.934 66.667 0.00 0.00 38.10 4.45
3254 6286 2.664185 CAGCCGCCATCGATCCAG 60.664 66.667 0.00 0.00 38.10 3.86
3255 6287 4.916293 GCAGCCGCCATCGATCCA 62.916 66.667 0.00 0.00 38.10 3.41
3266 6298 4.598894 CCCGATCTGAGGCAGCCG 62.599 72.222 5.55 0.00 0.00 5.52
3267 6299 3.157252 TCCCGATCTGAGGCAGCC 61.157 66.667 1.84 1.84 0.00 4.85
3268 6300 2.107953 GTCCCGATCTGAGGCAGC 59.892 66.667 0.00 0.00 0.00 5.25
3269 6301 1.406065 ATGGTCCCGATCTGAGGCAG 61.406 60.000 0.00 0.00 0.00 4.85
3270 6302 1.383109 ATGGTCCCGATCTGAGGCA 60.383 57.895 0.00 0.00 0.00 4.75
3271 6303 1.369321 GATGGTCCCGATCTGAGGC 59.631 63.158 0.00 0.00 0.00 4.70
3272 6304 1.662608 CGATGGTCCCGATCTGAGG 59.337 63.158 0.00 0.00 0.00 3.86
3273 6305 1.006805 GCGATGGTCCCGATCTGAG 60.007 63.158 0.00 0.00 0.00 3.35
3274 6306 2.498941 GGCGATGGTCCCGATCTGA 61.499 63.158 0.00 0.00 0.00 3.27
3275 6307 2.029666 GGCGATGGTCCCGATCTG 59.970 66.667 0.00 0.00 0.00 2.90
3276 6308 2.123251 AGGCGATGGTCCCGATCT 60.123 61.111 0.00 0.00 0.00 2.75
3277 6309 2.340443 GAGGCGATGGTCCCGATC 59.660 66.667 0.00 0.00 0.00 3.69
3278 6310 3.234730 GGAGGCGATGGTCCCGAT 61.235 66.667 0.00 0.00 0.00 4.18
3279 6311 4.458829 AGGAGGCGATGGTCCCGA 62.459 66.667 0.00 0.00 32.70 5.14
3280 6312 4.227134 CAGGAGGCGATGGTCCCG 62.227 72.222 0.00 0.00 32.70 5.14
3281 6313 3.083997 ACAGGAGGCGATGGTCCC 61.084 66.667 0.00 0.00 32.70 4.46
3282 6314 2.187946 CACAGGAGGCGATGGTCC 59.812 66.667 0.00 0.00 0.00 4.46
3283 6315 2.512515 GCACAGGAGGCGATGGTC 60.513 66.667 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.