Multiple sequence alignment - TraesCS4B01G250200

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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 TraesCS4B01G250200 chr4B 100.000 5124 0 0 1 5124 516863723 516858600 0.000000e+00 9463.0
1 TraesCS4B01G250200 chr4D 96.321 4566 133 12 214 4753 419109958 419105402 0.000000e+00 7468.0
2 TraesCS4B01G250200 chr4D 96.021 377 15 0 4748 5124 419105365 419104989 9.430000e-172 614.0
3 TraesCS4B01G250200 chr4A 95.278 4172 165 18 214 4357 46046002 46050169 0.000000e+00 6584.0
4 TraesCS4B01G250200 chr4A 87.346 569 55 8 321 877 239788467 239789030 2.010000e-178 636.0
5 TraesCS4B01G250200 chr4A 85.940 569 64 10 321 877 355345080 355344516 1.230000e-165 593.0
6 TraesCS4B01G250200 chr4A 86.294 394 37 5 621 997 474673866 474673473 3.690000e-111 412.0
7 TraesCS4B01G250200 chr4A 89.109 101 11 0 4591 4691 612564741 612564641 5.390000e-25 126.0
8 TraesCS4B01G250200 chr5B 87.768 2003 151 42 2394 4357 526590675 526588728 0.000000e+00 2255.0
9 TraesCS4B01G250200 chr5B 84.656 756 85 16 913 1646 526592278 526591532 0.000000e+00 725.0
10 TraesCS4B01G250200 chr5B 81.135 652 90 18 1648 2276 526591370 526590729 4.610000e-135 492.0
11 TraesCS4B01G250200 chr5D 89.226 1485 117 22 2890 4357 433023479 433022021 0.000000e+00 1816.0
12 TraesCS4B01G250200 chr5D 82.528 1408 176 37 913 2276 433025465 433024084 0.000000e+00 1173.0
13 TraesCS4B01G250200 chr5D 88.307 573 47 8 321 877 41527380 41526812 0.000000e+00 669.0
14 TraesCS4B01G250200 chr5D 91.260 492 37 4 2394 2883 433024031 433023544 0.000000e+00 665.0
15 TraesCS4B01G250200 chr5A 90.105 1142 67 24 2396 3512 547648652 547647532 0.000000e+00 1441.0
16 TraesCS4B01G250200 chr5A 85.383 862 88 19 3510 4357 547647470 547646633 0.000000e+00 859.0
17 TraesCS4B01G250200 chr5A 83.711 927 120 18 913 1819 547650645 547649730 0.000000e+00 846.0
18 TraesCS4B01G250200 chr5A 94.615 260 12 1 4867 5124 613468948 613469207 7.990000e-108 401.0
19 TraesCS4B01G250200 chr5A 77.846 650 82 30 3378 4020 3309376 3308782 3.800000e-91 346.0
20 TraesCS4B01G250200 chr5A 84.419 353 48 5 1849 2197 547649216 547648867 1.770000e-89 340.0
21 TraesCS4B01G250200 chr3B 88.814 1037 86 13 774 1793 818294368 818293345 0.000000e+00 1245.0
22 TraesCS4B01G250200 chr3B 92.000 100 8 0 4590 4689 128063928 128063829 1.920000e-29 141.0
23 TraesCS4B01G250200 chr3B 97.297 37 0 1 240 275 818294973 818294937 1.540000e-05 62.1
24 TraesCS4B01G250200 chr3D 85.350 1099 97 36 263 1312 608387907 608388990 0.000000e+00 1079.0
25 TraesCS4B01G250200 chr3D 90.604 149 11 1 1375 1520 608388991 608389139 1.460000e-45 195.0
26 TraesCS4B01G250200 chr3D 84.043 94 14 1 1701 1793 608389140 608389233 7.070000e-14 89.8
27 TraesCS4B01G250200 chr2D 88.227 688 66 4 321 997 566786818 566786135 0.000000e+00 808.0
28 TraesCS4B01G250200 chr2D 87.695 577 47 6 321 877 581872984 581872412 0.000000e+00 651.0
29 TraesCS4B01G250200 chr3A 89.796 588 55 5 1210 1793 740914034 740913448 0.000000e+00 749.0
30 TraesCS4B01G250200 chr3A 86.712 587 57 11 605 1172 740914626 740914042 2.600000e-177 632.0
31 TraesCS4B01G250200 chr3A 94.118 255 13 1 4872 5124 57723184 57722930 2.240000e-103 387.0
32 TraesCS4B01G250200 chr1A 86.213 573 55 13 321 877 19277986 19277422 2.640000e-167 599.0
33 TraesCS4B01G250200 chr1A 86.038 573 56 13 321 877 19392134 19391570 1.230000e-165 593.0
34 TraesCS4B01G250200 chr7A 86.402 353 35 5 655 994 620155457 620155809 1.740000e-99 374.0
35 TraesCS4B01G250200 chr1B 86.645 307 32 3 700 997 553957965 553957659 1.060000e-86 331.0
36 TraesCS4B01G250200 chr2B 87.739 261 20 5 4867 5124 798843549 798843298 1.400000e-75 294.0


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 TraesCS4B01G250200 chr4B 516858600 516863723 5123 True 9463.000000 9463 100.000000 1 5124 1 chr4B.!!$R1 5123
1 TraesCS4B01G250200 chr4D 419104989 419109958 4969 True 4041.000000 7468 96.171000 214 5124 2 chr4D.!!$R1 4910
2 TraesCS4B01G250200 chr4A 46046002 46050169 4167 False 6584.000000 6584 95.278000 214 4357 1 chr4A.!!$F1 4143
3 TraesCS4B01G250200 chr4A 239788467 239789030 563 False 636.000000 636 87.346000 321 877 1 chr4A.!!$F2 556
4 TraesCS4B01G250200 chr4A 355344516 355345080 564 True 593.000000 593 85.940000 321 877 1 chr4A.!!$R1 556
5 TraesCS4B01G250200 chr5B 526588728 526592278 3550 True 1157.333333 2255 84.519667 913 4357 3 chr5B.!!$R1 3444
6 TraesCS4B01G250200 chr5D 433022021 433025465 3444 True 1218.000000 1816 87.671333 913 4357 3 chr5D.!!$R2 3444
7 TraesCS4B01G250200 chr5D 41526812 41527380 568 True 669.000000 669 88.307000 321 877 1 chr5D.!!$R1 556
8 TraesCS4B01G250200 chr5A 547646633 547650645 4012 True 871.500000 1441 85.904500 913 4357 4 chr5A.!!$R2 3444
9 TraesCS4B01G250200 chr5A 3308782 3309376 594 True 346.000000 346 77.846000 3378 4020 1 chr5A.!!$R1 642
10 TraesCS4B01G250200 chr3B 818293345 818294973 1628 True 653.550000 1245 93.055500 240 1793 2 chr3B.!!$R2 1553
11 TraesCS4B01G250200 chr3D 608387907 608389233 1326 False 454.600000 1079 86.665667 263 1793 3 chr3D.!!$F1 1530
12 TraesCS4B01G250200 chr2D 566786135 566786818 683 True 808.000000 808 88.227000 321 997 1 chr2D.!!$R1 676
13 TraesCS4B01G250200 chr2D 581872412 581872984 572 True 651.000000 651 87.695000 321 877 1 chr2D.!!$R2 556
14 TraesCS4B01G250200 chr3A 740913448 740914626 1178 True 690.500000 749 88.254000 605 1793 2 chr3A.!!$R2 1188
15 TraesCS4B01G250200 chr1A 19277422 19277986 564 True 599.000000 599 86.213000 321 877 1 chr1A.!!$R1 556
16 TraesCS4B01G250200 chr1A 19391570 19392134 564 True 593.000000 593 86.038000 321 877 1 chr1A.!!$R2 556

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
155 156 0.462759 GGCAGGCTGAAACTAGCGAT 60.463 55.000 20.86 0.00 44.60 4.58 F
1116 1413 0.308993 GCCAGCCATTCGAATGCTAC 59.691 55.000 28.90 20.30 35.08 3.58 F
1118 1415 2.224606 CCAGCCATTCGAATGCTACAT 58.775 47.619 28.90 11.63 35.08 2.29 F
1874 2851 2.807967 GCAGTGCACTTCTGTGTTGATA 59.192 45.455 18.94 0.00 45.44 2.15 F
2810 3897 0.693049 AGGGTAGCACCAACTTGGAG 59.307 55.000 15.14 7.85 40.96 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1874 2851 1.745087 GTTGTCCATCGCCAACATGAT 59.255 47.619 0.0 0.0 40.46 2.45 R
2641 3718 2.102578 GACCAACTTCCCCCAATCATG 58.897 52.381 0.0 0.0 0.00 3.07 R
2676 3753 4.603131 ACTTCAAGCAACATCCCACATAT 58.397 39.130 0.0 0.0 0.00 1.78 R
3738 4954 1.538276 GTGAAAAGGCATCAATCGCG 58.462 50.000 0.0 0.0 0.00 5.87 R
4774 6062 0.251121 TTGGCACACCGATTCCACAT 60.251 50.000 0.0 0.0 39.29 3.21 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
28 29 7.148733 ACGTTTTTGACATTTCTTGAATTCG 57.851 32.000 0.04 0.00 0.00 3.34
29 30 6.750039 ACGTTTTTGACATTTCTTGAATTCGT 59.250 30.769 0.04 0.00 0.00 3.85
30 31 7.911205 ACGTTTTTGACATTTCTTGAATTCGTA 59.089 29.630 0.04 0.00 0.00 3.43
31 32 8.901748 CGTTTTTGACATTTCTTGAATTCGTAT 58.098 29.630 0.04 0.00 0.00 3.06
115 116 8.678593 AAGAGTAGTAAAAAGGGAAAACAGAG 57.321 34.615 0.00 0.00 0.00 3.35
116 117 6.711194 AGAGTAGTAAAAAGGGAAAACAGAGC 59.289 38.462 0.00 0.00 0.00 4.09
117 118 6.362248 AGTAGTAAAAAGGGAAAACAGAGCA 58.638 36.000 0.00 0.00 0.00 4.26
118 119 6.831868 AGTAGTAAAAAGGGAAAACAGAGCAA 59.168 34.615 0.00 0.00 0.00 3.91
119 120 6.538945 AGTAAAAAGGGAAAACAGAGCAAA 57.461 33.333 0.00 0.00 0.00 3.68
120 121 6.338146 AGTAAAAAGGGAAAACAGAGCAAAC 58.662 36.000 0.00 0.00 0.00 2.93
121 122 3.819564 AAAGGGAAAACAGAGCAAACC 57.180 42.857 0.00 0.00 0.00 3.27
122 123 2.755952 AGGGAAAACAGAGCAAACCT 57.244 45.000 0.00 0.00 0.00 3.50
123 124 2.310538 AGGGAAAACAGAGCAAACCTG 58.689 47.619 0.00 0.00 37.64 4.00
140 141 2.905880 GCATAGGCAGGCTGGCAG 60.906 66.667 37.80 27.68 46.46 4.85
141 142 2.203308 CATAGGCAGGCTGGCAGG 60.203 66.667 37.80 24.05 46.46 4.85
142 143 4.201122 ATAGGCAGGCTGGCAGGC 62.201 66.667 37.80 31.61 46.46 4.85
149 150 2.282745 GGCTGGCAGGCTGAAACT 60.283 61.111 31.42 0.00 37.85 2.66
150 151 1.002134 GGCTGGCAGGCTGAAACTA 60.002 57.895 31.42 0.00 37.85 2.24
151 152 1.028868 GGCTGGCAGGCTGAAACTAG 61.029 60.000 31.42 9.12 37.85 2.57
152 153 1.652167 GCTGGCAGGCTGAAACTAGC 61.652 60.000 20.86 15.43 42.94 3.42
153 154 1.364626 CTGGCAGGCTGAAACTAGCG 61.365 60.000 20.86 0.00 44.60 4.26
154 155 1.079127 GGCAGGCTGAAACTAGCGA 60.079 57.895 20.86 0.00 44.60 4.93
155 156 0.462759 GGCAGGCTGAAACTAGCGAT 60.463 55.000 20.86 0.00 44.60 4.58
156 157 0.654683 GCAGGCTGAAACTAGCGATG 59.345 55.000 20.86 0.00 44.60 3.84
157 158 1.293924 CAGGCTGAAACTAGCGATGG 58.706 55.000 9.42 0.00 44.60 3.51
158 159 0.905357 AGGCTGAAACTAGCGATGGT 59.095 50.000 0.00 0.00 44.60 3.55
159 160 1.279271 AGGCTGAAACTAGCGATGGTT 59.721 47.619 0.00 0.00 44.60 3.67
160 161 2.084546 GGCTGAAACTAGCGATGGTTT 58.915 47.619 15.25 15.25 44.60 3.27
161 162 2.488153 GGCTGAAACTAGCGATGGTTTT 59.512 45.455 16.36 0.71 44.60 2.43
162 163 3.426292 GGCTGAAACTAGCGATGGTTTTC 60.426 47.826 16.36 10.10 44.60 2.29
163 164 3.437049 GCTGAAACTAGCGATGGTTTTCT 59.563 43.478 16.36 0.00 36.04 2.52
164 165 4.083271 GCTGAAACTAGCGATGGTTTTCTT 60.083 41.667 16.36 0.00 36.04 2.52
165 166 5.562890 GCTGAAACTAGCGATGGTTTTCTTT 60.563 40.000 16.36 0.00 36.04 2.52
166 167 6.385649 TGAAACTAGCGATGGTTTTCTTTT 57.614 33.333 16.36 0.00 36.04 2.27
167 168 6.801575 TGAAACTAGCGATGGTTTTCTTTTT 58.198 32.000 16.36 0.00 36.04 1.94
189 190 4.181010 CCGATCTGGGCCACTGGG 62.181 72.222 0.00 0.00 37.18 4.45
205 206 2.914097 GGCCTGGCCCATATGCAC 60.914 66.667 27.77 0.00 44.06 4.57
206 207 3.289834 GCCTGGCCCATATGCACG 61.290 66.667 7.66 0.00 0.00 5.34
207 208 3.289834 CCTGGCCCATATGCACGC 61.290 66.667 0.00 0.00 0.00 5.34
208 209 2.203252 CTGGCCCATATGCACGCT 60.203 61.111 0.00 0.00 0.00 5.07
209 210 1.825191 CTGGCCCATATGCACGCTT 60.825 57.895 0.00 0.00 0.00 4.68
210 211 2.067091 CTGGCCCATATGCACGCTTG 62.067 60.000 0.00 0.00 0.00 4.01
211 212 2.723746 GCCCATATGCACGCTTGG 59.276 61.111 0.00 0.00 0.00 3.61
212 213 2.723746 CCCATATGCACGCTTGGC 59.276 61.111 0.00 0.00 0.00 4.52
579 822 4.889409 TGATCTGCTTGTTTTCCTTCTTGT 59.111 37.500 0.00 0.00 0.00 3.16
603 846 2.802414 CGGGTCGGTTCGTTCGTC 60.802 66.667 0.00 0.00 0.00 4.20
734 994 2.806818 CAGCTTCGCGTAGTAGGATCTA 59.193 50.000 14.43 0.00 0.00 1.98
902 1190 6.417191 TTCAGTTCACTTATTTATGACGGC 57.583 37.500 0.00 0.00 0.00 5.68
911 1199 5.928264 ACTTATTTATGACGGCGGTAATACC 59.072 40.000 13.24 0.00 34.05 2.73
961 1250 7.639113 TGTTTATGTGGGGTTCTTATTCATC 57.361 36.000 0.00 0.00 0.00 2.92
973 1262 6.017852 GGTTCTTATTCATCTGATTTCGTCCC 60.018 42.308 0.00 0.00 0.00 4.46
1116 1413 0.308993 GCCAGCCATTCGAATGCTAC 59.691 55.000 28.90 20.30 35.08 3.58
1118 1415 2.224606 CCAGCCATTCGAATGCTACAT 58.775 47.619 28.90 11.63 35.08 2.29
1344 1650 4.397103 TGCTTGTTTCTAGATCTGGCAATG 59.603 41.667 5.18 0.00 0.00 2.82
1345 1651 4.732938 GCTTGTTTCTAGATCTGGCAATGC 60.733 45.833 5.18 0.00 0.00 3.56
1389 1695 5.893500 TGACCCCATTTGATTAGTTGGTTA 58.106 37.500 0.00 0.00 0.00 2.85
1572 1888 4.631131 TCCGATGACTATTATTGCAGGTG 58.369 43.478 0.00 0.00 0.00 4.00
1613 1929 6.974622 GCAGTTTATTCAACATGTTATCCCTG 59.025 38.462 11.53 11.41 37.93 4.45
1677 2166 7.703328 ACATGTTACTAAGTTTTTGGTGAGTG 58.297 34.615 0.00 0.00 0.00 3.51
1693 2182 8.806429 TTGGTGAGTGATGATACAATAACAAT 57.194 30.769 0.00 0.00 0.00 2.71
1717 2207 5.003692 TCTGCAGATCAGTAAGACATGTC 57.996 43.478 18.47 18.47 43.32 3.06
1826 2318 5.845985 GGCAACTTCTGGATTTTAAAAGC 57.154 39.130 7.67 7.67 0.00 3.51
1835 2327 6.738114 TCTGGATTTTAAAAGCAAGACAGTG 58.262 36.000 17.39 0.00 29.89 3.66
1874 2851 2.807967 GCAGTGCACTTCTGTGTTGATA 59.192 45.455 18.94 0.00 45.44 2.15
2075 3055 9.495754 GTTACATTTGAACATCTCTAATGCTTC 57.504 33.333 8.26 0.00 45.63 3.86
2173 3155 5.473504 GGACAACAAAGACAATACAGGTCAT 59.526 40.000 0.00 0.00 37.74 3.06
2311 3378 2.882761 GGCGGATACTTATTTTCCCCAC 59.117 50.000 0.00 0.00 0.00 4.61
2413 3485 4.098914 TGACCTGGCAGTAATTTTCAGT 57.901 40.909 14.43 0.00 0.00 3.41
2414 3486 4.072131 TGACCTGGCAGTAATTTTCAGTC 58.928 43.478 14.43 10.34 0.00 3.51
2641 3718 4.254492 CTGTCCTCAGGCTTAAGGTAAAC 58.746 47.826 11.47 4.86 37.97 2.01
2665 3742 3.335183 TGATTGGGGGAAGTTGGTCATAA 59.665 43.478 0.00 0.00 0.00 1.90
2666 3743 4.016666 TGATTGGGGGAAGTTGGTCATAAT 60.017 41.667 0.00 0.00 0.00 1.28
2668 3745 5.538082 TTGGGGGAAGTTGGTCATAATAA 57.462 39.130 0.00 0.00 0.00 1.40
2669 3746 4.862371 TGGGGGAAGTTGGTCATAATAAC 58.138 43.478 0.00 0.00 0.00 1.89
2671 3748 5.015817 TGGGGGAAGTTGGTCATAATAACTT 59.984 40.000 0.00 0.00 44.67 2.66
2674 3751 7.363530 GGGGGAAGTTGGTCATAATAACTTTTC 60.364 40.741 0.00 0.00 42.75 2.29
2676 3753 9.457436 GGGAAGTTGGTCATAATAACTTTTCTA 57.543 33.333 0.00 0.00 42.75 2.10
2810 3897 0.693049 AGGGTAGCACCAACTTGGAG 59.307 55.000 15.14 7.85 40.96 3.86
3541 4753 4.284234 AGGCATTCTGTTTTATTTGGCTGT 59.716 37.500 0.00 0.00 38.39 4.40
3554 4766 5.880054 ATTTGGCTGTACACTGAATACAC 57.120 39.130 0.00 0.00 0.00 2.90
3738 4954 1.636003 ACCCCTGGGAAGAAATCTCAC 59.364 52.381 16.20 0.00 32.01 3.51
4148 5388 4.559229 CTCGATGCGGCGCTCTCA 62.559 66.667 33.26 13.41 0.00 3.27
4276 5517 2.900546 ACTGGAACTTGTAGCTGCTAGT 59.099 45.455 12.70 12.70 0.00 2.57
4575 5821 9.842775 TCTTTATATCTTTGTCAGATGAGCATT 57.157 29.630 0.00 0.00 42.76 3.56
4736 5982 5.565455 ACCCAACATGAATGGATTTGTTT 57.435 34.783 19.54 0.00 40.56 2.83
4742 5988 8.875803 CCAACATGAATGGATTTGTTTATTCTG 58.124 33.333 14.63 0.00 40.56 3.02
4774 6062 0.887247 CGGGTGGATGTTTGCAATCA 59.113 50.000 12.39 12.39 0.00 2.57
4791 6079 0.676466 TCATGTGGAATCGGTGTGCC 60.676 55.000 0.00 0.00 0.00 5.01
4807 6095 4.038642 GGTGTGCCAACTGAAATTTTCCTA 59.961 41.667 6.68 0.00 34.09 2.94
4879 6167 0.732571 CCATATGCTGCGTTCGGTTT 59.267 50.000 0.00 0.00 0.00 3.27
4942 6230 1.680207 GAAAGATTCCCTGATGCAGCC 59.320 52.381 0.00 0.00 0.00 4.85
4945 6233 1.133853 AGATTCCCTGATGCAGCCTTC 60.134 52.381 0.00 0.00 0.00 3.46
4946 6234 0.106318 ATTCCCTGATGCAGCCTTCC 60.106 55.000 0.00 0.00 0.00 3.46
4968 6256 3.130516 CGTCTGCAGGGATGAAGTACTAA 59.869 47.826 15.13 0.00 0.00 2.24
4979 6267 8.440771 AGGGATGAAGTACTAAAATTCCATAGG 58.559 37.037 10.74 0.00 0.00 2.57
4996 6284 4.878397 CCATAGGAAAGTTTCTGTAGCCTG 59.122 45.833 15.05 3.96 0.00 4.85
5004 6292 2.878406 GTTTCTGTAGCCTGCAGTTTCA 59.122 45.455 13.81 3.96 35.60 2.69
5023 6311 3.491342 TCACGGGAAATCAAACATCCAA 58.509 40.909 0.00 0.00 34.82 3.53
5040 6328 1.603802 CCAACGAGCTCTTTTTCTGCA 59.396 47.619 12.85 0.00 0.00 4.41
5089 6377 1.308998 CAAGTTGAGACCCACACCAC 58.691 55.000 0.00 0.00 0.00 4.16
5093 6381 0.757561 TTGAGACCCACACCACGAGA 60.758 55.000 0.00 0.00 0.00 4.04
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 7.274686 ACGAATTCAAGAAATGTCAAAAACGTT 59.725 29.630 6.22 0.00 38.80 3.99
4 5 6.750039 ACGAATTCAAGAAATGTCAAAAACGT 59.250 30.769 6.22 0.00 0.00 3.99
89 90 9.774413 CTCTGTTTTCCCTTTTTACTACTCTTA 57.226 33.333 0.00 0.00 0.00 2.10
90 91 7.228906 GCTCTGTTTTCCCTTTTTACTACTCTT 59.771 37.037 0.00 0.00 0.00 2.85
91 92 6.711194 GCTCTGTTTTCCCTTTTTACTACTCT 59.289 38.462 0.00 0.00 0.00 3.24
92 93 6.485648 TGCTCTGTTTTCCCTTTTTACTACTC 59.514 38.462 0.00 0.00 0.00 2.59
93 94 6.362248 TGCTCTGTTTTCCCTTTTTACTACT 58.638 36.000 0.00 0.00 0.00 2.57
94 95 6.628919 TGCTCTGTTTTCCCTTTTTACTAC 57.371 37.500 0.00 0.00 0.00 2.73
95 96 7.417003 GGTTTGCTCTGTTTTCCCTTTTTACTA 60.417 37.037 0.00 0.00 0.00 1.82
96 97 6.338146 GTTTGCTCTGTTTTCCCTTTTTACT 58.662 36.000 0.00 0.00 0.00 2.24
97 98 5.522460 GGTTTGCTCTGTTTTCCCTTTTTAC 59.478 40.000 0.00 0.00 0.00 2.01
98 99 5.423931 AGGTTTGCTCTGTTTTCCCTTTTTA 59.576 36.000 0.00 0.00 0.00 1.52
99 100 4.225042 AGGTTTGCTCTGTTTTCCCTTTTT 59.775 37.500 0.00 0.00 0.00 1.94
100 101 3.774766 AGGTTTGCTCTGTTTTCCCTTTT 59.225 39.130 0.00 0.00 0.00 2.27
101 102 3.132824 CAGGTTTGCTCTGTTTTCCCTTT 59.867 43.478 0.00 0.00 0.00 3.11
102 103 2.695147 CAGGTTTGCTCTGTTTTCCCTT 59.305 45.455 0.00 0.00 0.00 3.95
103 104 2.310538 CAGGTTTGCTCTGTTTTCCCT 58.689 47.619 0.00 0.00 0.00 4.20
104 105 1.269778 GCAGGTTTGCTCTGTTTTCCC 60.270 52.381 0.00 0.00 46.95 3.97
105 106 2.140065 GCAGGTTTGCTCTGTTTTCC 57.860 50.000 0.00 0.00 46.95 3.13
123 124 2.905880 CTGCCAGCCTGCCTATGC 60.906 66.667 0.00 0.00 38.26 3.14
124 125 2.203308 CCTGCCAGCCTGCCTATG 60.203 66.667 0.00 0.00 0.00 2.23
125 126 4.201122 GCCTGCCAGCCTGCCTAT 62.201 66.667 0.00 0.00 0.00 2.57
130 131 2.282674 TTTCAGCCTGCCAGCCTG 60.283 61.111 0.00 0.00 0.00 4.85
131 132 1.492133 TAGTTTCAGCCTGCCAGCCT 61.492 55.000 0.00 0.00 0.00 4.58
132 133 1.002134 TAGTTTCAGCCTGCCAGCC 60.002 57.895 0.00 0.00 0.00 4.85
133 134 1.652167 GCTAGTTTCAGCCTGCCAGC 61.652 60.000 0.00 0.00 35.40 4.85
134 135 1.364626 CGCTAGTTTCAGCCTGCCAG 61.365 60.000 0.00 0.00 38.37 4.85
135 136 1.375908 CGCTAGTTTCAGCCTGCCA 60.376 57.895 0.00 0.00 38.37 4.92
136 137 0.462759 ATCGCTAGTTTCAGCCTGCC 60.463 55.000 0.00 0.00 38.37 4.85
137 138 0.654683 CATCGCTAGTTTCAGCCTGC 59.345 55.000 0.00 0.00 38.37 4.85
138 139 1.293924 CCATCGCTAGTTTCAGCCTG 58.706 55.000 0.00 0.00 38.37 4.85
139 140 0.905357 ACCATCGCTAGTTTCAGCCT 59.095 50.000 0.00 0.00 38.37 4.58
140 141 1.739067 AACCATCGCTAGTTTCAGCC 58.261 50.000 0.00 0.00 38.37 4.85
141 142 3.437049 AGAAAACCATCGCTAGTTTCAGC 59.563 43.478 0.00 0.00 35.19 4.26
142 143 5.613358 AAGAAAACCATCGCTAGTTTCAG 57.387 39.130 0.00 0.00 35.19 3.02
143 144 6.385649 AAAAGAAAACCATCGCTAGTTTCA 57.614 33.333 0.00 0.00 35.19 2.69
172 173 4.181010 CCCAGTGGCCCAGATCGG 62.181 72.222 2.61 0.00 0.00 4.18
189 190 3.289834 CGTGCATATGGGCCAGGC 61.290 66.667 13.78 16.18 0.00 4.85
190 191 3.289834 GCGTGCATATGGGCCAGG 61.290 66.667 13.78 5.22 0.00 4.45
191 192 1.825191 AAGCGTGCATATGGGCCAG 60.825 57.895 13.78 0.00 0.00 4.85
192 193 2.120282 CAAGCGTGCATATGGGCCA 61.120 57.895 9.61 9.61 0.00 5.36
193 194 2.723746 CAAGCGTGCATATGGGCC 59.276 61.111 4.56 0.00 0.00 5.80
194 195 2.723746 CCAAGCGTGCATATGGGC 59.276 61.111 4.56 0.00 0.00 5.36
195 196 1.825191 AGCCAAGCGTGCATATGGG 60.825 57.895 4.56 0.00 33.45 4.00
196 197 1.357690 CAGCCAAGCGTGCATATGG 59.642 57.895 4.56 0.00 36.00 2.74
197 198 1.298863 GCAGCCAAGCGTGCATATG 60.299 57.895 0.00 0.00 39.62 1.78
198 199 2.484062 GGCAGCCAAGCGTGCATAT 61.484 57.895 6.55 0.00 41.75 1.78
199 200 3.133464 GGCAGCCAAGCGTGCATA 61.133 61.111 6.55 0.00 41.75 3.14
202 203 4.487412 GATGGCAGCCAAGCGTGC 62.487 66.667 20.84 0.00 36.95 5.34
203 204 4.170062 CGATGGCAGCCAAGCGTG 62.170 66.667 20.84 2.61 36.95 5.34
546 783 2.575279 ACAAGCAGATCAGATGGGAAGT 59.425 45.455 0.00 0.00 0.00 3.01
647 890 8.484641 TTTGCAGTCTAAATGAGATCAGTAAG 57.515 34.615 0.00 0.00 36.29 2.34
734 994 1.324740 TGTCTGCCGCGGTAACCTAT 61.325 55.000 28.70 0.00 0.00 2.57
810 1095 0.890683 TCGAAGGAGACCGGTAAACC 59.109 55.000 7.34 11.77 0.00 3.27
902 1190 8.433421 AACAATGATTCTACAAGGTATTACCG 57.567 34.615 7.21 0.00 44.90 4.02
911 1199 5.879223 AGAGGCTGAACAATGATTCTACAAG 59.121 40.000 0.00 0.00 0.00 3.16
961 1250 1.452108 GCCAGGGGGACGAAATCAG 60.452 63.158 0.00 0.00 35.59 2.90
973 1262 0.829182 ACAAAAGAAGCCTGCCAGGG 60.829 55.000 13.78 0.00 35.37 4.45
984 1273 1.892474 GCCATGGCACCTACAAAAGAA 59.108 47.619 32.08 0.00 41.49 2.52
1116 1413 9.439500 AACATGTAAATTCCAAGGAAAATCATG 57.561 29.630 22.47 22.47 37.69 3.07
1118 1415 9.921637 GTAACATGTAAATTCCAAGGAAAATCA 57.078 29.630 5.52 4.18 37.69 2.57
1298 1600 6.348622 GCATCATCTCAGCAGGAAAATCATAG 60.349 42.308 0.00 0.00 0.00 2.23
1299 1601 5.472478 GCATCATCTCAGCAGGAAAATCATA 59.528 40.000 0.00 0.00 0.00 2.15
1344 1650 3.070878 AGGAGAAGCTATAAGAAGCCTGC 59.929 47.826 0.00 0.00 43.86 4.85
1345 1651 4.343526 TCAGGAGAAGCTATAAGAAGCCTG 59.656 45.833 0.00 0.00 43.86 4.85
1433 1746 6.861065 TGGACTTTTGAGATGTCTAACAAC 57.139 37.500 0.00 0.00 33.96 3.32
1496 1812 1.876156 CTCAACAGTTCTCCAGCCAAC 59.124 52.381 0.00 0.00 0.00 3.77
1572 1888 5.803020 AAACTGCGTCTAAAATGAGGATC 57.197 39.130 0.00 0.00 0.00 3.36
1613 1929 9.463443 ACTAAGAGTTGCACAATTTTAAATGTC 57.537 29.630 0.00 0.00 0.00 3.06
1717 2207 6.090358 GCATGAGATGTCATTTTCCAAACTTG 59.910 38.462 1.88 0.00 40.84 3.16
1874 2851 1.745087 GTTGTCCATCGCCAACATGAT 59.255 47.619 0.00 0.00 40.46 2.45
1951 2929 4.906065 TCTGCATTAATAAGCAAGCCAG 57.094 40.909 2.50 0.00 40.73 4.85
2311 3378 9.727627 GGAAGTGATGCTCATTAAAAGATAAAG 57.272 33.333 0.00 0.00 0.00 1.85
2320 3387 8.928448 AGTATTCTAGGAAGTGATGCTCATTAA 58.072 33.333 0.00 0.00 0.00 1.40
2339 3406 4.290942 ACCAGGTGCTAAGCTAGTATTCT 58.709 43.478 0.00 0.00 31.35 2.40
2413 3485 9.066892 ACTGCAATAAACTTTAAACATCTGAGA 57.933 29.630 0.00 0.00 0.00 3.27
2414 3486 9.334693 GACTGCAATAAACTTTAAACATCTGAG 57.665 33.333 0.00 0.00 0.00 3.35
2471 3548 2.503356 AGAAGACTATTCCTGGTGGCAG 59.497 50.000 0.00 0.00 0.00 4.85
2641 3718 2.102578 GACCAACTTCCCCCAATCATG 58.897 52.381 0.00 0.00 0.00 3.07
2665 3742 8.850156 GCAACATCCCACATATAGAAAAGTTAT 58.150 33.333 0.00 0.00 0.00 1.89
2666 3743 8.052748 AGCAACATCCCACATATAGAAAAGTTA 58.947 33.333 0.00 0.00 0.00 2.24
2668 3745 6.426587 AGCAACATCCCACATATAGAAAAGT 58.573 36.000 0.00 0.00 0.00 2.66
2669 3746 6.949352 AGCAACATCCCACATATAGAAAAG 57.051 37.500 0.00 0.00 0.00 2.27
2671 3748 6.422333 TCAAGCAACATCCCACATATAGAAA 58.578 36.000 0.00 0.00 0.00 2.52
2674 3751 5.824624 ACTTCAAGCAACATCCCACATATAG 59.175 40.000 0.00 0.00 0.00 1.31
2676 3753 4.603131 ACTTCAAGCAACATCCCACATAT 58.397 39.130 0.00 0.00 0.00 1.78
2741 3822 9.666626 CATACCAAATCAACGTTTTACTAACAA 57.333 29.630 0.00 0.00 0.00 2.83
2810 3897 5.858581 CGGTTTCTTCAGAATTTGGATTGAC 59.141 40.000 0.00 0.00 33.54 3.18
3472 4618 5.698545 GCATGATAAGGAGCTACACCTAAAG 59.301 44.000 0.00 0.00 36.67 1.85
3476 4624 3.041211 TGCATGATAAGGAGCTACACCT 58.959 45.455 0.00 0.00 39.69 4.00
3554 4766 3.702330 TCACTGTAGACAACAAGACACG 58.298 45.455 0.00 0.00 37.74 4.49
3738 4954 1.538276 GTGAAAAGGCATCAATCGCG 58.462 50.000 0.00 0.00 0.00 5.87
3800 5016 2.030371 TCAGCTCAGCACTATCCAGAG 58.970 52.381 0.00 0.00 0.00 3.35
4148 5388 4.973168 ACTCGGCAAACCATCATACATAT 58.027 39.130 0.00 0.00 34.57 1.78
4276 5517 1.071699 GCCACTCCCTACAGAACAACA 59.928 52.381 0.00 0.00 0.00 3.33
4414 5660 1.265095 CCGATTCTGCCATACATGTGC 59.735 52.381 9.11 3.92 0.00 4.57
4473 5719 2.109126 GCTCCAATCGCACAGGTCC 61.109 63.158 0.00 0.00 0.00 4.46
4575 5821 2.357050 CCCTGAATGTGGTCCAGCATAA 60.357 50.000 0.00 0.00 0.00 1.90
4656 5902 2.763249 AAGTTTTGCAGCTGTCTTCG 57.237 45.000 16.64 0.00 0.00 3.79
4736 5982 3.895656 CCCGGAGTTCATAGACCAGAATA 59.104 47.826 0.73 0.00 0.00 1.75
4742 5988 0.464452 CCACCCGGAGTTCATAGACC 59.536 60.000 0.73 0.00 0.00 3.85
4774 6062 0.251121 TTGGCACACCGATTCCACAT 60.251 50.000 0.00 0.00 39.29 3.21
4791 6079 9.793252 CAGTATTCCATAGGAAAATTTCAGTTG 57.207 33.333 8.09 1.76 45.41 3.16
4807 6095 5.121380 AGGAAGCATGAACAGTATTCCAT 57.879 39.130 0.00 0.00 38.92 3.41
4879 6167 5.796502 ACTTTTCCTCCATAAATCCTCCA 57.203 39.130 0.00 0.00 0.00 3.86
4942 6230 0.250234 TTCATCCCTGCAGACGGAAG 59.750 55.000 17.39 11.49 0.00 3.46
4945 6233 0.824109 TACTTCATCCCTGCAGACGG 59.176 55.000 17.39 9.21 0.00 4.79
4946 6234 1.478510 AGTACTTCATCCCTGCAGACG 59.521 52.381 17.39 4.69 0.00 4.18
4968 6256 7.122799 GGCTACAGAAACTTTCCTATGGAATTT 59.877 37.037 0.00 0.00 41.71 1.82
4979 6267 3.142174 ACTGCAGGCTACAGAAACTTTC 58.858 45.455 21.34 0.00 38.55 2.62
4996 6284 3.049912 GTTTGATTTCCCGTGAAACTGC 58.950 45.455 0.00 0.00 42.97 4.40
5004 6292 2.227865 CGTTGGATGTTTGATTTCCCGT 59.772 45.455 0.00 0.00 0.00 5.28
5023 6311 0.861837 CGTGCAGAAAAAGAGCTCGT 59.138 50.000 8.37 1.01 39.52 4.18
5089 6377 0.037882 TGCAAGACTGAAGCCTCTCG 60.038 55.000 0.00 0.00 0.00 4.04
5093 6381 0.964358 GCCATGCAAGACTGAAGCCT 60.964 55.000 0.00 0.00 0.00 4.58


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

AutoCloner maintained by Alex Coulton.