Multiple sequence alignment - TraesCS7D01G187900

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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 TraesCS7D01G187900 chr7D 100.000 3209 0 0 1 3209 140322590 140319382 0.000000e+00 5927.0
1 TraesCS7D01G187900 chr7D 77.592 1196 233 22 1042 2213 55012073 55013257 0.000000e+00 691.0
2 TraesCS7D01G187900 chr7D 77.321 1217 240 23 1022 2213 55007242 55008447 0.000000e+00 686.0
3 TraesCS7D01G187900 chr7D 77.250 1222 240 24 1017 2213 54997422 54998630 0.000000e+00 682.0
4 TraesCS7D01G187900 chr7D 77.341 1196 235 22 1042 2214 56235114 56236296 0.000000e+00 675.0
5 TraesCS7D01G187900 chr7D 78.782 542 103 11 1654 2191 55013533 55014066 1.420000e-93 353.0
6 TraesCS7D01G187900 chr7D 77.465 426 89 6 1771 2194 55015497 55015917 6.870000e-62 248.0
7 TraesCS7D01G187900 chr7D 77.910 421 57 18 2753 3141 106383088 106382672 2.490000e-56 230.0
8 TraesCS7D01G187900 chr7D 74.801 377 80 10 1778 2148 55530146 55530513 4.290000e-34 156.0
9 TraesCS7D01G187900 chr7B 90.476 2478 157 36 1 2448 105523829 105521401 0.000000e+00 3195.0
10 TraesCS7D01G187900 chr7B 76.180 466 73 20 2707 3141 64978065 64977607 9.020000e-51 211.0
11 TraesCS7D01G187900 chr7B 89.474 133 7 5 1604 1731 104558043 104558173 9.210000e-36 161.0
12 TraesCS7D01G187900 chr1A 88.732 710 63 6 2448 3155 278644318 278645012 0.000000e+00 852.0
13 TraesCS7D01G187900 chr6D 87.701 748 67 10 2448 3191 108773996 108774722 0.000000e+00 848.0
14 TraesCS7D01G187900 chr1D 90.995 633 52 4 2578 3209 213343941 213343313 0.000000e+00 848.0
15 TraesCS7D01G187900 chr4D 89.181 684 61 6 2448 3128 39609902 39610575 0.000000e+00 841.0
16 TraesCS7D01G187900 chr4A 77.014 1353 242 43 892 2214 673028992 673030305 0.000000e+00 712.0
17 TraesCS7D01G187900 chr4A 88.556 568 47 7 2437 3003 56721516 56720966 0.000000e+00 673.0
18 TraesCS7D01G187900 chr4A 76.486 1178 240 27 1042 2194 670985956 670984791 9.850000e-170 606.0
19 TraesCS7D01G187900 chr4A 72.958 1224 276 40 1042 2234 669921515 669920316 3.020000e-100 375.0
20 TraesCS7D01G187900 chr4A 72.296 1202 273 41 1042 2213 669993632 669992461 1.440000e-83 320.0
21 TraesCS7D01G187900 chr4A 73.529 442 95 15 1777 2212 672212924 672213349 7.170000e-32 148.0
22 TraesCS7D01G187900 chr4A 100.000 36 0 0 1777 1812 672180708 672180743 2.070000e-07 67.6
23 TraesCS7D01G187900 chr4A 100.000 36 0 0 1777 1812 672274398 672274433 2.070000e-07 67.6
24 TraesCS7D01G187900 chr7A 76.904 1234 242 31 1042 2249 60638540 60639756 0.000000e+00 660.0
25 TraesCS7D01G187900 chr7A 73.641 368 70 22 1774 2133 59434424 59434772 2.020000e-22 117.0
26 TraesCS7D01G187900 chr2A 88.783 526 51 4 2632 3154 169344631 169345151 3.490000e-179 638.0
27 TraesCS7D01G187900 chrUn 79.137 278 44 11 2750 3023 339894336 339894603 2.540000e-41 180.0
28 TraesCS7D01G187900 chrUn 73.529 442 95 15 1777 2212 284725379 284725804 7.170000e-32 148.0
29 TraesCS7D01G187900 chr1B 79.508 122 22 3 2447 2568 60067926 60067808 2.050000e-12 84.2


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 TraesCS7D01G187900 chr7D 140319382 140322590 3208 True 5927.0 5927 100.000 1 3209 1 chr7D.!!$R2 3208
1 TraesCS7D01G187900 chr7D 54997422 54998630 1208 False 682.0 682 77.250 1017 2213 1 chr7D.!!$F1 1196
2 TraesCS7D01G187900 chr7D 56235114 56236296 1182 False 675.0 675 77.341 1042 2214 1 chr7D.!!$F3 1172
3 TraesCS7D01G187900 chr7D 55007242 55015917 8675 False 494.5 691 77.790 1022 2213 4 chr7D.!!$F4 1191
4 TraesCS7D01G187900 chr7B 105521401 105523829 2428 True 3195.0 3195 90.476 1 2448 1 chr7B.!!$R2 2447
5 TraesCS7D01G187900 chr1A 278644318 278645012 694 False 852.0 852 88.732 2448 3155 1 chr1A.!!$F1 707
6 TraesCS7D01G187900 chr6D 108773996 108774722 726 False 848.0 848 87.701 2448 3191 1 chr6D.!!$F1 743
7 TraesCS7D01G187900 chr1D 213343313 213343941 628 True 848.0 848 90.995 2578 3209 1 chr1D.!!$R1 631
8 TraesCS7D01G187900 chr4D 39609902 39610575 673 False 841.0 841 89.181 2448 3128 1 chr4D.!!$F1 680
9 TraesCS7D01G187900 chr4A 673028992 673030305 1313 False 712.0 712 77.014 892 2214 1 chr4A.!!$F4 1322
10 TraesCS7D01G187900 chr4A 56720966 56721516 550 True 673.0 673 88.556 2437 3003 1 chr4A.!!$R1 566
11 TraesCS7D01G187900 chr4A 670984791 670985956 1165 True 606.0 606 76.486 1042 2194 1 chr4A.!!$R4 1152
12 TraesCS7D01G187900 chr4A 669920316 669921515 1199 True 375.0 375 72.958 1042 2234 1 chr4A.!!$R2 1192
13 TraesCS7D01G187900 chr4A 669992461 669993632 1171 True 320.0 320 72.296 1042 2213 1 chr4A.!!$R3 1171
14 TraesCS7D01G187900 chr7A 60638540 60639756 1216 False 660.0 660 76.904 1042 2249 1 chr7A.!!$F2 1207
15 TraesCS7D01G187900 chr2A 169344631 169345151 520 False 638.0 638 88.783 2632 3154 1 chr2A.!!$F1 522

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
269 274 0.392595 CTCATGCTGCTGCTCTTGGA 60.393 55.0 17.0 6.18 40.48 3.53 F
450 463 0.520404 ACTGTGTACTACGCCGAGTG 59.480 55.0 0.0 0.00 0.00 3.51 F
1429 6276 0.622665 AGGTCCCTGCTCCAGATTTG 59.377 55.0 0.0 0.00 32.44 2.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1476 6323 0.322456 CAGCGACCAAGGAATTGGGA 60.322 55.0 11.47 0.0 46.23 4.37 R
1630 6477 1.190833 TTGCCAAATCCGCCCAATGT 61.191 50.0 0.00 0.0 0.00 2.71 R
3077 10086 0.999406 CGCACCTTATCACTTGGACG 59.001 55.0 0.00 0.0 0.00 4.79 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
37 38 7.982354 GGAACAGCAGATACTCAGTAATAAACT 59.018 37.037 0.00 0.00 39.81 2.66
49 50 7.108841 TCAGTAATAAACTTATCTCTGGCGT 57.891 36.000 10.88 0.00 35.76 5.68
50 51 6.978659 TCAGTAATAAACTTATCTCTGGCGTG 59.021 38.462 10.88 0.00 35.76 5.34
53 54 2.015736 AACTTATCTCTGGCGTGCAG 57.984 50.000 0.00 0.00 0.00 4.41
91 92 6.718454 CCTGTATTCCTTGAATAAGATGGCAT 59.282 38.462 0.00 0.00 36.46 4.40
93 94 6.491062 TGTATTCCTTGAATAAGATGGCATGG 59.509 38.462 3.81 0.00 36.46 3.66
113 114 5.689383 TGGCACTTCTTTTTCTACACATC 57.311 39.130 0.00 0.00 0.00 3.06
116 117 6.145535 GGCACTTCTTTTTCTACACATCTTG 58.854 40.000 0.00 0.00 0.00 3.02
117 118 6.238759 GGCACTTCTTTTTCTACACATCTTGT 60.239 38.462 0.00 0.00 42.84 3.16
118 119 7.041372 GGCACTTCTTTTTCTACACATCTTGTA 60.041 37.037 0.00 0.00 39.91 2.41
119 120 7.798982 GCACTTCTTTTTCTACACATCTTGTAC 59.201 37.037 0.00 0.00 39.91 2.90
120 121 9.046296 CACTTCTTTTTCTACACATCTTGTACT 57.954 33.333 0.00 0.00 39.91 2.73
121 122 9.614792 ACTTCTTTTTCTACACATCTTGTACTT 57.385 29.630 0.00 0.00 39.91 2.24
155 158 4.397417 CCTCTGGCCTTTCATCTAAACAAG 59.603 45.833 3.32 0.00 0.00 3.16
156 159 5.241403 TCTGGCCTTTCATCTAAACAAGA 57.759 39.130 3.32 0.00 39.02 3.02
188 193 1.405821 GACTGCGTGCTATCACTAGGT 59.594 52.381 0.00 0.00 40.99 3.08
202 207 4.523083 TCACTAGGTGATTTACATTGGCC 58.477 43.478 0.00 0.00 37.67 5.36
203 208 4.018870 TCACTAGGTGATTTACATTGGCCA 60.019 41.667 0.00 0.00 37.67 5.36
215 220 7.415592 TTTACATTGGCCATTTCACATGATA 57.584 32.000 17.69 5.73 0.00 2.15
239 244 2.880268 CTGACAGCACAATTCCTTCACA 59.120 45.455 0.00 0.00 0.00 3.58
240 245 3.286353 TGACAGCACAATTCCTTCACAA 58.714 40.909 0.00 0.00 0.00 3.33
243 248 4.874970 ACAGCACAATTCCTTCACAATTC 58.125 39.130 0.00 0.00 0.00 2.17
245 250 3.896888 AGCACAATTCCTTCACAATTCCA 59.103 39.130 0.00 0.00 0.00 3.53
256 261 5.449588 CCTTCACAATTCCACATACTCATGC 60.450 44.000 0.00 0.00 35.39 4.06
261 266 2.320745 TCCACATACTCATGCTGCTG 57.679 50.000 0.00 0.00 35.39 4.41
262 267 0.661552 CCACATACTCATGCTGCTGC 59.338 55.000 8.89 8.89 35.39 5.25
263 268 1.664873 CACATACTCATGCTGCTGCT 58.335 50.000 17.00 0.00 40.48 4.24
264 269 1.598132 CACATACTCATGCTGCTGCTC 59.402 52.381 17.00 0.00 40.48 4.26
269 274 0.392595 CTCATGCTGCTGCTCTTGGA 60.393 55.000 17.00 6.18 40.48 3.53
281 286 5.877012 TGCTGCTCTTGGAATTTCTAGTTAG 59.123 40.000 0.00 0.00 0.00 2.34
292 297 8.101419 TGGAATTTCTAGTTAGAGGAAAGGAAC 58.899 37.037 0.00 0.00 33.41 3.62
298 303 5.167303 AGTTAGAGGAAAGGAACCACATC 57.833 43.478 0.00 0.00 0.00 3.06
299 304 4.846940 AGTTAGAGGAAAGGAACCACATCT 59.153 41.667 0.00 0.00 0.00 2.90
320 328 7.229306 ACATCTTCTTTCAGTTTTAGTCATGCA 59.771 33.333 0.00 0.00 0.00 3.96
333 344 4.240881 AGTCATGCACCACTTTATCCAT 57.759 40.909 0.00 0.00 0.00 3.41
378 391 6.875948 TCAGTTCTAAAACAAGCATAAGCA 57.124 33.333 0.00 0.00 39.63 3.91
382 395 7.430502 CAGTTCTAAAACAAGCATAAGCATAGC 59.569 37.037 0.00 0.00 39.63 2.97
384 397 3.698029 AAACAAGCATAAGCATAGCCG 57.302 42.857 0.00 0.00 45.49 5.52
413 426 9.124807 GTTGTTACTTTACCATGACAAATAAGC 57.875 33.333 0.00 0.00 0.00 3.09
415 428 7.388224 TGTTACTTTACCATGACAAATAAGCGA 59.612 33.333 0.00 0.00 0.00 4.93
416 429 8.395633 GTTACTTTACCATGACAAATAAGCGAT 58.604 33.333 0.00 0.00 0.00 4.58
418 431 5.651172 TTACCATGACAAATAAGCGATCG 57.349 39.130 11.69 11.69 0.00 3.69
441 454 3.319689 TGCAGCTGTTGTACTGTGTACTA 59.680 43.478 16.64 0.00 36.26 1.82
445 458 3.240069 CTGTTGTACTGTGTACTACGCC 58.760 50.000 14.11 0.00 0.00 5.68
450 463 0.520404 ACTGTGTACTACGCCGAGTG 59.480 55.000 0.00 0.00 0.00 3.51
460 473 1.153842 CGCCGAGTGCATGACTACA 60.154 57.895 0.00 0.00 41.33 2.74
504 517 9.817809 TTGTACTAGTTATAGCCTCTTTGATTG 57.182 33.333 0.00 0.00 31.66 2.67
521 534 7.971722 TCTTTGATTGACATAATTCTGCACATG 59.028 33.333 0.00 0.00 0.00 3.21
535 548 2.840038 TGCACATGTGGAGATAGGAACT 59.160 45.455 26.55 0.00 46.37 3.01
559 575 9.770097 ACTACTACATATGAATTGACAGGAATG 57.230 33.333 10.38 0.00 0.00 2.67
560 576 9.770097 CTACTACATATGAATTGACAGGAATGT 57.230 33.333 10.38 0.00 0.00 2.71
561 577 8.442632 ACTACATATGAATTGACAGGAATGTG 57.557 34.615 10.38 0.00 0.00 3.21
571 587 3.384146 TGACAGGAATGTGTGCACAAAAT 59.616 39.130 23.59 15.62 45.41 1.82
591 607 2.206576 AGAGGATTGGGAAACACTGC 57.793 50.000 0.00 0.00 0.00 4.40
593 609 1.815003 GAGGATTGGGAAACACTGCAG 59.185 52.381 13.48 13.48 0.00 4.41
598 614 3.518634 TTGGGAAACACTGCAGTTTTC 57.481 42.857 28.03 28.03 41.48 2.29
623 639 2.357637 ACTTGGGTGTTTGATTCACACG 59.642 45.455 0.00 0.00 44.76 4.49
626 642 2.356382 TGGGTGTTTGATTCACACGTTC 59.644 45.455 0.00 0.00 44.76 3.95
666 682 8.539770 AACAGAAACATAATACACTCAGTCAG 57.460 34.615 0.00 0.00 0.00 3.51
679 695 9.761504 ATACACTCAGTCAGATCATAGAAATTG 57.238 33.333 0.00 0.00 0.00 2.32
689 705 9.671279 TCAGATCATAGAAATTGTAGCAAAGAA 57.329 29.630 0.00 0.00 0.00 2.52
769 785 6.575162 TTTCCTCTATTTCTGTTTTGCTCC 57.425 37.500 0.00 0.00 0.00 4.70
811 827 4.219115 TGAATAGTGCCACCAAAGGAAAA 58.781 39.130 0.00 0.00 0.00 2.29
1012 1032 8.950210 ACTGTGTTTTTACTATGAATCTGATGG 58.050 33.333 0.00 0.00 0.00 3.51
1013 1033 7.761409 TGTGTTTTTACTATGAATCTGATGGC 58.239 34.615 0.00 0.00 0.00 4.40
1014 1034 7.392953 TGTGTTTTTACTATGAATCTGATGGCA 59.607 33.333 0.00 0.00 0.00 4.92
1015 1035 8.408601 GTGTTTTTACTATGAATCTGATGGCAT 58.591 33.333 0.00 0.00 0.00 4.40
1016 1036 8.970020 TGTTTTTACTATGAATCTGATGGCATT 58.030 29.630 0.00 0.00 0.00 3.56
1017 1037 9.807649 GTTTTTACTATGAATCTGATGGCATTT 57.192 29.630 0.00 0.00 0.00 2.32
1029 1049 9.584008 AATCTGATGGCATTTTACTATGAATCT 57.416 29.630 0.00 0.00 0.00 2.40
1030 1050 8.387190 TCTGATGGCATTTTACTATGAATCTG 57.613 34.615 0.00 0.00 0.00 2.90
1034 1054 7.514784 TGGCATTTTACTATGAATCTGATGG 57.485 36.000 0.00 0.00 0.00 3.51
1072 5904 4.648007 TGGAGGCTCCACAGTCTT 57.352 55.556 32.01 0.00 42.67 3.01
1254 6086 2.307686 TGGTACCTTCCTCAACATTCCC 59.692 50.000 14.36 0.00 0.00 3.97
1286 6130 4.054825 CCGCATGCCCGCTTGTTT 62.055 61.111 13.15 0.00 0.00 2.83
1429 6276 0.622665 AGGTCCCTGCTCCAGATTTG 59.377 55.000 0.00 0.00 32.44 2.32
1440 6287 4.861102 CTCCAGATTTGAGCCAGTTTTT 57.139 40.909 0.00 0.00 0.00 1.94
1476 6323 1.674764 CCTCAGCGCTGGACTCATCT 61.675 60.000 35.36 0.00 0.00 2.90
1505 6352 1.394917 CTTGGTCGCTGCACTAATCAC 59.605 52.381 0.00 0.00 0.00 3.06
1510 6357 1.679153 TCGCTGCACTAATCACGGATA 59.321 47.619 0.00 0.00 0.00 2.59
1522 6369 8.773645 CACTAATCACGGATAATTCTAATTGCA 58.226 33.333 0.00 0.00 0.00 4.08
1630 6477 6.040278 TGCATTCTTTGATGGAAAGTTGTACA 59.960 34.615 0.00 0.00 41.75 2.90
1655 6502 0.737367 GGCGGATTTGGCAAGCTTTC 60.737 55.000 0.00 0.00 0.00 2.62
1719 6569 4.339530 GGGAAGATAATTGACTCTTTGGGC 59.660 45.833 0.00 0.00 31.99 5.36
1734 6584 0.251916 TGGGCGATTTAGGTGGAGTG 59.748 55.000 0.00 0.00 0.00 3.51
1750 6600 3.185203 TGCCTCAACCCTTGGCCT 61.185 61.111 3.32 0.00 45.56 5.19
1879 6732 1.385528 TGAAGATAGACGCACGGCTA 58.614 50.000 8.27 8.27 40.42 3.93
2043 6899 3.881688 AGGATTGCATCTACTTCATGTGC 59.118 43.478 0.00 0.00 36.39 4.57
2202 7058 2.864114 GGTTTTCCCTTCGGTAGCC 58.136 57.895 0.00 0.00 0.00 3.93
2352 7214 5.006941 AGTTGGTATGTTTGTGTGTACGTTC 59.993 40.000 0.00 0.00 0.00 3.95
2497 7930 3.326747 ACTTGCACTCGAGGTACAAATC 58.673 45.455 18.41 0.00 31.61 2.17
2569 8002 5.403166 TCCGAGTACGTTTCAGTACATTTTG 59.597 40.000 0.00 0.00 46.85 2.44
2580 8013 8.837389 GTTTCAGTACATTTTGGTTAACTCTCT 58.163 33.333 5.42 0.00 0.00 3.10
2743 8177 6.590292 TGTTTTCTTCTCAATGTCGGTATCTC 59.410 38.462 0.00 0.00 0.00 2.75
2820 8758 3.461982 GTCGCACGCGTCAGACAG 61.462 66.667 28.17 12.17 40.74 3.51
2824 8762 1.081376 GCACGCGTCAGACAGTAGT 60.081 57.895 9.86 0.00 0.00 2.73
2929 9017 2.485266 GTGTGTTGCACAGGGTTTAC 57.515 50.000 1.86 0.00 45.43 2.01
2966 9973 4.721132 TCTCAACACTATTTTTCCCGGTT 58.279 39.130 0.00 0.00 0.00 4.44
2969 9976 3.232720 ACACTATTTTTCCCGGTTGGT 57.767 42.857 0.00 0.00 34.77 3.67
3023 10032 7.858052 ATGCTTTTGACATCGTTAAAGAAAG 57.142 32.000 0.00 0.00 30.97 2.62
3038 10047 8.850452 CGTTAAAGAAAGTAGAATTCAAATGGC 58.150 33.333 8.44 0.00 0.00 4.40
3077 10086 4.917415 ACATGTTTTCGCATAACAGCTTTC 59.083 37.500 0.00 0.00 38.74 2.62
3093 10102 3.008049 AGCTTTCGTCCAAGTGATAAGGT 59.992 43.478 0.00 0.00 0.00 3.50
3115 10124 4.988540 GTGCGAACCATAACAGCTCATATA 59.011 41.667 0.00 0.00 0.00 0.86
3129 10139 5.812642 CAGCTCATATACGAAAACTGGACTT 59.187 40.000 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 7.168302 CACGCCAGAGATAAGTTTATTACTGAG 59.832 40.741 14.69 11.97 37.12 3.35
37 38 4.521075 GCTGCACGCCAGAGATAA 57.479 55.556 7.77 0.00 44.64 1.75
46 47 1.005294 CTGAAACAATGGCTGCACGC 61.005 55.000 0.50 0.11 38.13 5.34
47 48 1.005294 GCTGAAACAATGGCTGCACG 61.005 55.000 0.50 0.00 0.00 5.34
49 50 0.828762 AGGCTGAAACAATGGCTGCA 60.829 50.000 0.50 0.00 35.27 4.41
50 51 0.389426 CAGGCTGAAACAATGGCTGC 60.389 55.000 9.42 0.00 44.87 5.25
53 54 3.429410 GGAATACAGGCTGAAACAATGGC 60.429 47.826 23.66 0.29 0.00 4.40
56 57 5.324409 TCAAGGAATACAGGCTGAAACAAT 58.676 37.500 23.66 0.00 0.00 2.71
57 58 4.724399 TCAAGGAATACAGGCTGAAACAA 58.276 39.130 23.66 1.05 0.00 2.83
58 59 4.365514 TCAAGGAATACAGGCTGAAACA 57.634 40.909 23.66 3.34 0.00 2.83
91 92 5.376625 AGATGTGTAGAAAAAGAAGTGCCA 58.623 37.500 0.00 0.00 0.00 4.92
93 94 6.729187 ACAAGATGTGTAGAAAAAGAAGTGC 58.271 36.000 0.00 0.00 39.29 4.40
113 114 6.708054 CCAGAGGGCATTCTATTAAGTACAAG 59.292 42.308 0.00 0.00 0.00 3.16
147 150 8.821894 GCAGTCCACTCTAATTATCTTGTTTAG 58.178 37.037 0.00 0.00 0.00 1.85
155 158 3.491267 GCACGCAGTCCACTCTAATTATC 59.509 47.826 0.00 0.00 41.61 1.75
156 159 3.133003 AGCACGCAGTCCACTCTAATTAT 59.867 43.478 0.00 0.00 41.61 1.28
163 168 0.173481 TGATAGCACGCAGTCCACTC 59.827 55.000 0.00 0.00 41.61 3.51
188 193 5.735285 TGTGAAATGGCCAATGTAAATCA 57.265 34.783 10.96 0.00 0.00 2.57
192 197 5.936187 ATCATGTGAAATGGCCAATGTAA 57.064 34.783 10.96 0.00 0.00 2.41
195 200 6.256975 CAGTTTATCATGTGAAATGGCCAATG 59.743 38.462 10.96 8.19 0.00 2.82
196 201 6.154877 TCAGTTTATCATGTGAAATGGCCAAT 59.845 34.615 10.96 0.00 0.00 3.16
197 202 5.479724 TCAGTTTATCATGTGAAATGGCCAA 59.520 36.000 10.96 0.00 0.00 4.52
198 203 5.015515 TCAGTTTATCATGTGAAATGGCCA 58.984 37.500 8.56 8.56 0.00 5.36
199 204 5.105797 TGTCAGTTTATCATGTGAAATGGCC 60.106 40.000 0.00 0.00 26.51 5.36
200 205 5.953183 TGTCAGTTTATCATGTGAAATGGC 58.047 37.500 0.00 0.00 0.00 4.40
201 206 6.032094 GCTGTCAGTTTATCATGTGAAATGG 58.968 40.000 0.93 0.00 0.00 3.16
202 207 6.525628 GTGCTGTCAGTTTATCATGTGAAATG 59.474 38.462 0.93 0.00 0.00 2.32
203 208 6.207221 TGTGCTGTCAGTTTATCATGTGAAAT 59.793 34.615 0.93 0.00 0.00 2.17
215 220 3.953612 TGAAGGAATTGTGCTGTCAGTTT 59.046 39.130 0.93 0.00 0.00 2.66
239 244 3.630769 CAGCAGCATGAGTATGTGGAATT 59.369 43.478 0.00 0.00 39.69 2.17
240 245 3.211865 CAGCAGCATGAGTATGTGGAAT 58.788 45.455 0.00 0.00 39.69 3.01
243 248 0.661552 GCAGCAGCATGAGTATGTGG 59.338 55.000 0.00 0.00 39.69 4.17
245 250 1.485480 AGAGCAGCAGCATGAGTATGT 59.515 47.619 3.17 0.00 45.49 2.29
256 261 4.260170 ACTAGAAATTCCAAGAGCAGCAG 58.740 43.478 0.00 0.00 0.00 4.24
261 266 6.879400 TCCTCTAACTAGAAATTCCAAGAGC 58.121 40.000 0.00 0.00 0.00 4.09
262 267 9.377312 CTTTCCTCTAACTAGAAATTCCAAGAG 57.623 37.037 0.00 0.00 0.00 2.85
263 268 8.322091 CCTTTCCTCTAACTAGAAATTCCAAGA 58.678 37.037 0.00 0.00 0.00 3.02
264 269 8.322091 TCCTTTCCTCTAACTAGAAATTCCAAG 58.678 37.037 0.00 0.00 0.00 3.61
269 274 7.883833 GTGGTTCCTTTCCTCTAACTAGAAATT 59.116 37.037 0.00 0.00 0.00 1.82
281 286 4.293662 AGAAGATGTGGTTCCTTTCCTC 57.706 45.455 0.00 0.00 0.00 3.71
292 297 7.496529 TGACTAAAACTGAAAGAAGATGTGG 57.503 36.000 0.00 0.00 37.43 4.17
298 303 6.145535 GGTGCATGACTAAAACTGAAAGAAG 58.854 40.000 0.00 0.00 37.43 2.85
299 304 5.592282 TGGTGCATGACTAAAACTGAAAGAA 59.408 36.000 0.00 0.00 37.43 2.52
351 364 7.522236 GCTTATGCTTGTTTTAGAACTGAAGGT 60.522 37.037 0.00 0.00 35.05 3.50
352 365 6.803807 GCTTATGCTTGTTTTAGAACTGAAGG 59.196 38.462 0.00 0.00 35.05 3.46
353 366 7.362662 TGCTTATGCTTGTTTTAGAACTGAAG 58.637 34.615 1.96 0.00 40.48 3.02
354 367 7.270757 TGCTTATGCTTGTTTTAGAACTGAA 57.729 32.000 1.96 0.00 40.48 3.02
355 368 6.875948 TGCTTATGCTTGTTTTAGAACTGA 57.124 33.333 1.96 0.00 40.48 3.41
356 369 7.430502 GCTATGCTTATGCTTGTTTTAGAACTG 59.569 37.037 1.96 0.00 40.48 3.16
357 370 7.415653 GGCTATGCTTATGCTTGTTTTAGAACT 60.416 37.037 1.96 0.00 40.48 3.01
358 371 6.693113 GGCTATGCTTATGCTTGTTTTAGAAC 59.307 38.462 1.96 0.00 40.48 3.01
359 372 6.458206 CGGCTATGCTTATGCTTGTTTTAGAA 60.458 38.462 1.96 0.00 40.48 2.10
378 391 3.937079 GGTAAAGTAACAACTGCGGCTAT 59.063 43.478 0.00 0.00 0.00 2.97
382 395 3.749088 TCATGGTAAAGTAACAACTGCGG 59.251 43.478 0.00 0.00 0.00 5.69
384 397 5.682943 TGTCATGGTAAAGTAACAACTGC 57.317 39.130 0.00 0.00 0.00 4.40
411 424 2.047844 AACAGCTGCACGATCGCT 60.048 55.556 16.60 0.00 0.00 4.93
413 426 0.366871 GTACAACAGCTGCACGATCG 59.633 55.000 15.27 14.88 0.00 3.69
415 428 1.270305 ACAGTACAACAGCTGCACGAT 60.270 47.619 15.27 0.00 36.26 3.73
416 429 0.104120 ACAGTACAACAGCTGCACGA 59.896 50.000 15.27 0.00 36.26 4.35
418 431 1.299541 ACACAGTACAACAGCTGCAC 58.700 50.000 15.27 6.94 36.26 4.57
460 473 4.445452 ACAACTACATTCGACGTACCAT 57.555 40.909 0.00 0.00 0.00 3.55
467 480 9.379811 GCTATAACTAGTACAACTACATTCGAC 57.620 37.037 0.00 0.00 0.00 4.20
504 517 4.877823 TCTCCACATGTGCAGAATTATGTC 59.122 41.667 17.25 0.00 31.84 3.06
521 534 8.865420 TCATATGTAGTAGTTCCTATCTCCAC 57.135 38.462 1.90 0.00 0.00 4.02
535 548 9.546428 CACATTCCTGTCAATTCATATGTAGTA 57.454 33.333 1.90 0.00 31.62 1.82
538 551 7.201723 GCACACATTCCTGTCAATTCATATGTA 60.202 37.037 1.90 0.00 31.62 2.29
539 552 6.405065 GCACACATTCCTGTCAATTCATATGT 60.405 38.462 1.90 0.00 31.62 2.29
540 553 5.975344 GCACACATTCCTGTCAATTCATATG 59.025 40.000 0.00 0.00 31.62 1.78
541 554 5.653330 TGCACACATTCCTGTCAATTCATAT 59.347 36.000 0.00 0.00 31.62 1.78
542 555 5.008980 TGCACACATTCCTGTCAATTCATA 58.991 37.500 0.00 0.00 31.62 2.15
544 557 3.004629 GTGCACACATTCCTGTCAATTCA 59.995 43.478 13.17 0.00 31.62 2.57
545 558 3.004629 TGTGCACACATTCCTGTCAATTC 59.995 43.478 17.42 0.00 36.21 2.17
559 575 4.380867 CCCAATCCTCTATTTTGTGCACAC 60.381 45.833 21.56 0.00 0.00 3.82
560 576 3.763360 CCCAATCCTCTATTTTGTGCACA 59.237 43.478 17.42 17.42 0.00 4.57
561 577 4.016444 TCCCAATCCTCTATTTTGTGCAC 58.984 43.478 10.75 10.75 0.00 4.57
571 587 2.642311 TGCAGTGTTTCCCAATCCTCTA 59.358 45.455 0.00 0.00 0.00 2.43
591 607 4.718940 AACACCCAAGTTCAGAAAACTG 57.281 40.909 0.00 0.00 0.00 3.16
593 609 5.066968 TCAAACACCCAAGTTCAGAAAAC 57.933 39.130 0.00 0.00 0.00 2.43
598 614 4.097741 TGTGAATCAAACACCCAAGTTCAG 59.902 41.667 0.00 0.00 37.45 3.02
639 655 9.337396 TGACTGAGTGTATTATGTTTCTGTTTT 57.663 29.630 0.00 0.00 0.00 2.43
641 657 8.367911 TCTGACTGAGTGTATTATGTTTCTGTT 58.632 33.333 0.00 0.00 0.00 3.16
659 675 7.785033 TGCTACAATTTCTATGATCTGACTGA 58.215 34.615 0.00 0.00 0.00 3.41
679 695 5.886960 ATCCACACAGATTTCTTTGCTAC 57.113 39.130 0.00 0.00 0.00 3.58
689 705 8.208224 TCGGTAATATTACAATCCACACAGATT 58.792 33.333 23.59 0.00 36.92 2.40
695 711 9.887629 TTAAACTCGGTAATATTACAATCCACA 57.112 29.630 23.59 4.71 35.37 4.17
740 756 9.260002 GCAAAACAGAAATAGAGGAAAATTTCA 57.740 29.630 8.09 0.00 42.14 2.69
788 804 3.737559 TCCTTTGGTGGCACTATTCAT 57.262 42.857 18.45 0.00 0.00 2.57
811 827 2.434702 GGAACCCGTTGAGATAGGACAT 59.565 50.000 0.00 0.00 0.00 3.06
820 836 1.247567 AAATGCAGGAACCCGTTGAG 58.752 50.000 0.00 0.00 0.00 3.02
873 889 2.877097 TTCCTTTGCTGGCACTATCA 57.123 45.000 0.00 0.00 0.00 2.15
874 890 3.248602 CGTATTCCTTTGCTGGCACTATC 59.751 47.826 0.00 0.00 0.00 2.08
877 893 1.271379 ACGTATTCCTTTGCTGGCACT 60.271 47.619 0.00 0.00 0.00 4.40
878 894 1.165270 ACGTATTCCTTTGCTGGCAC 58.835 50.000 0.00 0.00 0.00 5.01
880 896 1.810151 TCAACGTATTCCTTTGCTGGC 59.190 47.619 0.00 0.00 0.00 4.85
884 900 4.473199 GGAAGTTCAACGTATTCCTTTGC 58.527 43.478 5.01 0.00 38.53 3.68
1004 1024 9.011095 CAGATTCATAGTAAAATGCCATCAGAT 57.989 33.333 0.00 0.00 0.00 2.90
1012 1032 6.973843 TGCCATCAGATTCATAGTAAAATGC 58.026 36.000 0.00 0.00 0.00 3.56
1013 1033 9.976511 AAATGCCATCAGATTCATAGTAAAATG 57.023 29.630 0.00 0.00 0.00 2.32
1015 1035 9.412460 AGAAATGCCATCAGATTCATAGTAAAA 57.588 29.630 0.00 0.00 0.00 1.52
1016 1036 8.843262 CAGAAATGCCATCAGATTCATAGTAAA 58.157 33.333 0.00 0.00 0.00 2.01
1017 1037 7.994911 ACAGAAATGCCATCAGATTCATAGTAA 59.005 33.333 0.00 0.00 0.00 2.24
1018 1038 7.512130 ACAGAAATGCCATCAGATTCATAGTA 58.488 34.615 0.00 0.00 0.00 1.82
1019 1039 6.363065 ACAGAAATGCCATCAGATTCATAGT 58.637 36.000 0.00 0.00 0.00 2.12
1020 1040 6.879276 ACAGAAATGCCATCAGATTCATAG 57.121 37.500 0.00 0.00 0.00 2.23
1029 1049 3.273434 GCAGTCTACAGAAATGCCATCA 58.727 45.455 6.47 0.00 34.67 3.07
1030 1050 3.273434 TGCAGTCTACAGAAATGCCATC 58.727 45.455 12.62 0.00 37.90 3.51
1034 1054 4.261072 CCATGATGCAGTCTACAGAAATGC 60.261 45.833 9.62 9.62 38.66 3.56
1072 5904 1.280133 CTGAAGATCTGACCAAGGCCA 59.720 52.381 5.01 0.00 0.00 5.36
1286 6130 1.425066 AGTTGTCAATGGAGCCTTGGA 59.575 47.619 0.00 0.00 0.00 3.53
1476 6323 0.322456 CAGCGACCAAGGAATTGGGA 60.322 55.000 11.47 0.00 46.23 4.37
1505 6352 5.008019 AGTGTGCTGCAATTAGAATTATCCG 59.992 40.000 2.77 0.00 0.00 4.18
1630 6477 1.190833 TTGCCAAATCCGCCCAATGT 61.191 50.000 0.00 0.00 0.00 2.71
1655 6502 4.332819 GGTCCTTGTCCAACTCAAATATCG 59.667 45.833 0.00 0.00 0.00 2.92
1700 6550 4.487714 TCGCCCAAAGAGTCAATTATCT 57.512 40.909 0.00 0.00 0.00 1.98
1701 6551 5.757850 AATCGCCCAAAGAGTCAATTATC 57.242 39.130 0.00 0.00 0.00 1.75
1750 6600 5.175859 CCTTGTAATAAACGGCTTCTCTGA 58.824 41.667 0.00 0.00 0.00 3.27
1836 6689 4.820897 AGACATCGTCACTTGCAGAAATA 58.179 39.130 0.00 0.00 34.60 1.40
1879 6732 1.490490 TGCCTCAAAGACCTCAAGTGT 59.510 47.619 0.00 0.00 0.00 3.55
1914 6767 4.570663 CTCCATCGACGACGGGGC 62.571 72.222 10.49 0.00 40.21 5.80
2043 6899 3.043419 CTCGGCCAGGGATAGTCG 58.957 66.667 2.24 0.00 0.00 4.18
2198 7054 2.279741 GCTTCGTTGATCACATGGCTA 58.720 47.619 0.00 0.00 0.00 3.93
2202 7058 4.087510 ACATTGCTTCGTTGATCACATG 57.912 40.909 0.00 0.00 0.00 3.21
2234 7090 2.787473 ACGCATGAGGATTCCAAGAA 57.213 45.000 5.29 0.00 0.00 2.52
2235 7091 2.766263 AGTACGCATGAGGATTCCAAGA 59.234 45.455 5.29 0.00 0.00 3.02
2469 7902 7.337480 TGTACCTCGAGTGCAAGTTTATATA 57.663 36.000 12.31 0.00 38.23 0.86
2471 7904 5.648178 TGTACCTCGAGTGCAAGTTTATA 57.352 39.130 12.31 0.00 38.23 0.98
2522 7955 6.426937 GGAATGCAAGTTATAGGCTCGATTTA 59.573 38.462 0.00 0.00 0.00 1.40
2530 7963 3.467803 ACTCGGAATGCAAGTTATAGGC 58.532 45.455 0.00 0.00 0.00 3.93
2580 8013 3.247411 CAGCTCACGTGTCATGTTTAACA 59.753 43.478 16.51 0.00 0.00 2.41
2784 8722 3.050619 GACACAACGTCTCGAGTTTGAT 58.949 45.455 22.40 13.88 41.81 2.57
2793 8731 2.837280 CGTGCGACACAACGTCTC 59.163 61.111 9.95 0.00 42.98 3.36
2966 9973 3.541632 GGAAATTTCAGATAGCCGACCA 58.458 45.455 19.49 0.00 0.00 4.02
2969 9976 3.118920 TCACGGAAATTTCAGATAGCCGA 60.119 43.478 22.71 7.85 40.39 5.54
3023 10032 4.340381 AGCATCTGGCCATTTGAATTCTAC 59.660 41.667 5.51 0.00 46.50 2.59
3077 10086 0.999406 CGCACCTTATCACTTGGACG 59.001 55.000 0.00 0.00 0.00 4.79
3093 10102 2.401583 ATGAGCTGTTATGGTTCGCA 57.598 45.000 0.00 0.00 0.00 5.10


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

AutoCloner maintained by Alex Coulton.