Multiple sequence alignment - TraesCS3D01G460700

Loading Multiple Alignment...

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 TraesCS3D01G460700 chr3D 100.000 3176 0 0 1 3176 565603203 565606378 0.000000e+00 5866.0
1 TraesCS3D01G460700 chr3D 78.500 1200 213 25 988 2175 565535511 565536677 0.000000e+00 745.0
2 TraesCS3D01G460700 chr3D 75.515 1552 289 60 994 2523 564308529 564307047 0.000000e+00 676.0
3 TraesCS3D01G460700 chr3D 76.423 615 115 19 1568 2172 564392615 564392021 3.980000e-79 305.0
4 TraesCS3D01G460700 chr3D 76.087 598 113 18 1568 2162 564486769 564486199 5.190000e-73 285.0
5 TraesCS3D01G460700 chr3D 85.317 252 22 12 2930 3176 565559341 565559582 2.450000e-61 246.0
6 TraesCS3D01G460700 chr3D 77.198 364 73 5 992 1353 565258642 565258997 1.490000e-48 204.0
7 TraesCS3D01G460700 chr3D 80.000 195 36 3 995 1186 569842827 569842633 1.190000e-29 141.0
8 TraesCS3D01G460700 chr3D 85.385 130 17 2 2391 2519 564485936 564485808 1.990000e-27 134.0
9 TraesCS3D01G460700 chr3D 83.158 95 16 0 2931 3025 564522189 564522095 1.570000e-13 87.9
10 TraesCS3D01G460700 chr3D 84.416 77 10 2 1716 1791 564904736 564904661 1.220000e-09 75.0
11 TraesCS3D01G460700 chr3A 94.857 2139 68 17 811 2926 699762757 699764876 0.000000e+00 3302.0
12 TraesCS3D01G460700 chr3A 75.740 1521 282 55 1024 2523 698858311 698856857 0.000000e+00 684.0
13 TraesCS3D01G460700 chr3A 78.225 969 165 27 1579 2517 699750895 699751847 2.120000e-161 579.0
14 TraesCS3D01G460700 chr3A 83.774 567 55 23 1 565 699761889 699762420 1.310000e-138 503.0
15 TraesCS3D01G460700 chr3A 97.189 249 3 2 2929 3176 699765020 699765265 4.900000e-113 418.0
16 TraesCS3D01G460700 chr3A 87.081 209 24 2 987 1192 655920283 655920491 1.900000e-57 233.0
17 TraesCS3D01G460700 chr3A 84.141 227 32 3 985 1208 699533367 699533592 1.920000e-52 217.0
18 TraesCS3D01G460700 chr3A 79.012 243 31 12 2939 3176 698856320 698856093 7.100000e-32 148.0
19 TraesCS3D01G460700 chr3B 95.171 2071 66 13 811 2862 753672560 753674615 0.000000e+00 3240.0
20 TraesCS3D01G460700 chr3B 75.775 1548 286 53 996 2523 752041289 752039811 0.000000e+00 699.0
21 TraesCS3D01G460700 chr3B 95.968 248 9 1 2930 3176 753674659 753674906 4.930000e-108 401.0
22 TraesCS3D01G460700 chr3B 76.190 609 122 14 1568 2172 752172798 752172209 1.850000e-77 300.0
23 TraesCS3D01G460700 chr3B 84.127 252 40 0 987 1238 752973262 752973011 8.800000e-61 244.0
24 TraesCS3D01G460700 chr3B 83.529 255 23 11 2930 3176 753577792 753578035 1.480000e-53 220.0
25 TraesCS3D01G460700 chr3B 81.452 248 32 10 2939 3176 752048190 752047947 1.160000e-44 191.0
26 TraesCS3D01G460700 chr3B 81.301 246 30 12 2939 3176 752078232 752077995 5.410000e-43 185.0
27 TraesCS3D01G460700 chr3B 79.424 243 30 13 2939 3176 752039099 752038872 1.530000e-33 154.0
28 TraesCS3D01G460700 chr3B 94.872 39 2 0 1753 1791 752376490 752376452 9.510000e-06 62.1
29 TraesCS3D01G460700 chr6D 91.083 942 69 8 1577 2503 380452260 380451319 0.000000e+00 1260.0
30 TraesCS3D01G460700 chr6D 88.503 748 50 24 811 1555 380453100 380452386 0.000000e+00 872.0
31 TraesCS3D01G460700 chr6D 92.308 390 22 4 2545 2929 380451322 380450936 5.990000e-152 547.0
32 TraesCS3D01G460700 chr6D 96.269 134 3 1 2936 3067 380450901 380450768 5.330000e-53 219.0
33 TraesCS3D01G460700 chr6B 91.908 828 49 5 2116 2926 565399797 565400623 0.000000e+00 1142.0
34 TraesCS3D01G460700 chr6B 89.946 746 50 15 811 1555 565398351 565399072 0.000000e+00 939.0
35 TraesCS3D01G460700 chr6B 89.608 587 54 4 1540 2119 565399099 565399685 0.000000e+00 739.0
36 TraesCS3D01G460700 chr6B 84.270 534 64 15 30 554 565397546 565398068 1.310000e-138 503.0
37 TraesCS3D01G460700 chr6B 94.118 136 7 1 2930 3064 565400655 565400790 4.150000e-49 206.0
38 TraesCS3D01G460700 chr1B 89.855 69 5 1 2860 2926 674821419 674821487 1.570000e-13 87.9
39 TraesCS3D01G460700 chr1B 91.525 59 5 0 2 60 510603218 510603160 7.300000e-12 82.4
40 TraesCS3D01G460700 chr1B 85.075 67 6 4 2869 2932 320105931 320105996 7.350000e-07 65.8
41 TraesCS3D01G460700 chr1D 90.769 65 4 2 2862 2926 484566474 484566536 5.640000e-13 86.1
42 TraesCS3D01G460700 chr7B 88.406 69 8 0 2860 2928 407941146 407941078 2.030000e-12 84.2
43 TraesCS3D01G460700 chr7D 87.931 58 3 3 3074 3129 575488447 575488392 7.350000e-07 65.8
44 TraesCS3D01G460700 chr5A 100.000 28 0 0 2900 2927 485201710 485201737 6.000000e-03 52.8


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3D01G460700 chr3D 565603203 565606378 3175 False 5866.000000 5866 100.00000 1 3176 1 chr3D.!!$F4 3175
1 TraesCS3D01G460700 chr3D 565535511 565536677 1166 False 745.000000 745 78.50000 988 2175 1 chr3D.!!$F2 1187
2 TraesCS3D01G460700 chr3D 564307047 564308529 1482 True 676.000000 676 75.51500 994 2523 1 chr3D.!!$R1 1529
3 TraesCS3D01G460700 chr3D 564392021 564392615 594 True 305.000000 305 76.42300 1568 2172 1 chr3D.!!$R2 604
4 TraesCS3D01G460700 chr3D 564485808 564486769 961 True 209.500000 285 80.73600 1568 2519 2 chr3D.!!$R6 951
5 TraesCS3D01G460700 chr3A 699761889 699765265 3376 False 1407.666667 3302 91.94000 1 3176 3 chr3A.!!$F4 3175
6 TraesCS3D01G460700 chr3A 699750895 699751847 952 False 579.000000 579 78.22500 1579 2517 1 chr3A.!!$F3 938
7 TraesCS3D01G460700 chr3A 698856093 698858311 2218 True 416.000000 684 77.37600 1024 3176 2 chr3A.!!$R1 2152
8 TraesCS3D01G460700 chr3B 753672560 753674906 2346 False 1820.500000 3240 95.56950 811 3176 2 chr3B.!!$F2 2365
9 TraesCS3D01G460700 chr3B 752038872 752041289 2417 True 426.500000 699 77.59950 996 3176 2 chr3B.!!$R6 2180
10 TraesCS3D01G460700 chr3B 752172209 752172798 589 True 300.000000 300 76.19000 1568 2172 1 chr3B.!!$R3 604
11 TraesCS3D01G460700 chr6D 380450768 380453100 2332 True 724.500000 1260 92.04075 811 3067 4 chr6D.!!$R1 2256
12 TraesCS3D01G460700 chr6B 565397546 565400790 3244 False 705.800000 1142 89.97000 30 3064 5 chr6B.!!$F1 3034

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
804 1060 0.105964 TTCCTCACGACCACCACTTG 59.894 55.0 0.0 0.0 0.0 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2568 3608 3.998099 GGAAGCATAAATTCCTCCAGC 57.002 47.619 0.0 0.0 42.52 4.85 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
21 22 4.833478 ACTGAGACAAGTATGGAATGCT 57.167 40.909 0.00 0.00 42.77 3.79
22 23 4.511527 ACTGAGACAAGTATGGAATGCTG 58.488 43.478 0.00 0.00 38.77 4.41
78 79 3.007723 AGTGTATGCTATGCTCATCAGGG 59.992 47.826 0.00 0.00 0.00 4.45
97 98 2.489073 GGGTGGTCCTTGTTGATGTTCT 60.489 50.000 0.00 0.00 0.00 3.01
151 152 6.361481 CGACAACGTTATCTTCTTCAACTGTA 59.639 38.462 4.87 0.00 34.56 2.74
152 153 7.096353 CGACAACGTTATCTTCTTCAACTGTAA 60.096 37.037 4.87 0.00 34.56 2.41
154 155 6.707599 ACGTTATCTTCTTCAACTGTAAGC 57.292 37.500 0.00 0.00 37.60 3.09
155 156 6.220930 ACGTTATCTTCTTCAACTGTAAGCA 58.779 36.000 0.00 0.00 37.60 3.91
156 157 6.704493 ACGTTATCTTCTTCAACTGTAAGCAA 59.296 34.615 0.00 0.00 37.60 3.91
179 180 4.545929 TGCTCATCGGCATCTTGG 57.454 55.556 0.00 0.00 37.29 3.61
212 213 3.366374 GCAAGGTTGATAACTTGGTCTGC 60.366 47.826 5.22 0.00 43.21 4.26
213 214 3.073274 AGGTTGATAACTTGGTCTGCC 57.927 47.619 0.00 0.00 0.00 4.85
231 232 0.855349 CCGATGTTGACGCTGCTATC 59.145 55.000 0.00 0.00 0.00 2.08
334 363 0.314935 ACAAGGTTTGGCGCTTGATG 59.685 50.000 7.64 0.34 32.97 3.07
374 403 4.337274 TCGATGGCTCAATTTCTACGTCTA 59.663 41.667 0.00 0.00 0.00 2.59
375 404 5.041287 CGATGGCTCAATTTCTACGTCTAA 58.959 41.667 0.00 0.00 0.00 2.10
376 405 5.518847 CGATGGCTCAATTTCTACGTCTAAA 59.481 40.000 0.00 0.00 0.00 1.85
377 406 6.508088 CGATGGCTCAATTTCTACGTCTAAAC 60.508 42.308 0.00 0.00 0.00 2.01
378 407 5.543714 TGGCTCAATTTCTACGTCTAAACA 58.456 37.500 0.00 0.00 0.00 2.83
379 408 6.170506 TGGCTCAATTTCTACGTCTAAACAT 58.829 36.000 0.00 0.00 0.00 2.71
380 409 6.653320 TGGCTCAATTTCTACGTCTAAACATT 59.347 34.615 0.00 0.00 0.00 2.71
381 410 7.174253 TGGCTCAATTTCTACGTCTAAACATTT 59.826 33.333 0.00 0.00 0.00 2.32
382 411 8.021396 GGCTCAATTTCTACGTCTAAACATTTT 58.979 33.333 0.00 0.00 0.00 1.82
383 412 9.394477 GCTCAATTTCTACGTCTAAACATTTTT 57.606 29.630 0.00 0.00 0.00 1.94
413 442 6.666918 GCGACTTCTACGTCTAAACATTTCAC 60.667 42.308 0.00 0.00 0.00 3.18
455 489 2.421314 TCACAGGTGCCAGTGACG 59.579 61.111 11.63 0.00 37.50 4.35
495 529 2.169663 TATCGAACGACAGCGAGTTC 57.830 50.000 0.00 6.58 42.23 3.01
502 536 1.341802 GACAGCGAGTTCGATTGCG 59.658 57.895 5.60 0.00 43.02 4.85
521 555 2.092211 GCGTCTTTGACAAGATACACGG 59.908 50.000 0.00 0.00 41.26 4.94
566 600 3.802866 TGATTTGGAACCTTTTGTTGGC 58.197 40.909 0.00 0.00 37.29 4.52
568 602 2.977772 TTGGAACCTTTTGTTGGCAG 57.022 45.000 0.00 0.00 37.29 4.85
569 603 0.463620 TGGAACCTTTTGTTGGCAGC 59.536 50.000 0.00 0.00 37.29 5.25
570 604 0.752658 GGAACCTTTTGTTGGCAGCT 59.247 50.000 2.28 0.00 37.29 4.24
571 605 1.138859 GGAACCTTTTGTTGGCAGCTT 59.861 47.619 2.28 0.00 37.29 3.74
573 607 3.381045 GAACCTTTTGTTGGCAGCTTAC 58.619 45.455 2.28 0.00 37.29 2.34
574 608 1.686587 ACCTTTTGTTGGCAGCTTACC 59.313 47.619 2.28 0.00 0.00 2.85
575 609 1.686052 CCTTTTGTTGGCAGCTTACCA 59.314 47.619 2.28 0.86 34.65 3.25
576 610 2.102252 CCTTTTGTTGGCAGCTTACCAA 59.898 45.455 12.95 12.95 44.86 3.67
581 615 1.327303 TTGGCAGCTTACCAAACAGG 58.673 50.000 14.30 0.00 44.11 4.00
582 616 1.178534 TGGCAGCTTACCAAACAGGC 61.179 55.000 2.61 0.00 43.14 4.85
583 617 1.586541 GCAGCTTACCAAACAGGCC 59.413 57.895 0.00 0.00 43.14 5.19
584 618 1.875963 CAGCTTACCAAACAGGCCG 59.124 57.895 0.00 0.00 43.14 6.13
585 619 1.971695 AGCTTACCAAACAGGCCGC 60.972 57.895 0.00 0.00 43.14 6.53
587 621 1.524008 GCTTACCAAACAGGCCGCTT 61.524 55.000 0.00 0.00 43.14 4.68
588 622 0.240945 CTTACCAAACAGGCCGCTTG 59.759 55.000 0.04 0.04 43.14 4.01
590 624 2.912025 CCAAACAGGCCGCTTGGT 60.912 61.111 19.80 0.00 36.29 3.67
591 625 2.644992 CAAACAGGCCGCTTGGTC 59.355 61.111 7.48 0.00 37.78 4.02
609 681 6.237915 GCTTGGTCTTGTCTTTTTGATTTGTG 60.238 38.462 0.00 0.00 0.00 3.33
733 824 7.754851 AAAAACTATGGACTCGGTACATTTT 57.245 32.000 7.01 1.52 38.21 1.82
734 825 6.980051 AAACTATGGACTCGGTACATTTTC 57.020 37.500 7.01 0.00 38.21 2.29
735 826 5.934402 ACTATGGACTCGGTACATTTTCT 57.066 39.130 7.01 0.00 38.21 2.52
738 829 4.610605 TGGACTCGGTACATTTTCTCAA 57.389 40.909 0.00 0.00 0.00 3.02
739 830 5.160607 TGGACTCGGTACATTTTCTCAAT 57.839 39.130 0.00 0.00 0.00 2.57
741 832 6.703319 TGGACTCGGTACATTTTCTCAATAA 58.297 36.000 0.00 0.00 0.00 1.40
743 834 7.662258 TGGACTCGGTACATTTTCTCAATAAAA 59.338 33.333 0.00 0.00 33.15 1.52
744 835 7.961283 GGACTCGGTACATTTTCTCAATAAAAC 59.039 37.037 0.00 0.00 31.50 2.43
745 836 8.617290 ACTCGGTACATTTTCTCAATAAAACT 57.383 30.769 0.00 0.00 31.50 2.66
788 1044 8.424274 AACATGTTTTTGAAAGTCTCATTTCC 57.576 30.769 4.92 0.00 38.21 3.13
789 1045 7.785033 ACATGTTTTTGAAAGTCTCATTTCCT 58.215 30.769 0.00 0.00 38.21 3.36
790 1046 7.922811 ACATGTTTTTGAAAGTCTCATTTCCTC 59.077 33.333 0.00 0.00 38.21 3.71
791 1047 7.403312 TGTTTTTGAAAGTCTCATTTCCTCA 57.597 32.000 0.00 0.00 38.21 3.86
792 1048 7.257722 TGTTTTTGAAAGTCTCATTTCCTCAC 58.742 34.615 0.00 0.00 38.21 3.51
793 1049 5.673337 TTTGAAAGTCTCATTTCCTCACG 57.327 39.130 0.00 0.00 38.21 4.35
794 1050 4.600692 TGAAAGTCTCATTTCCTCACGA 57.399 40.909 0.00 0.00 38.21 4.35
795 1051 4.307432 TGAAAGTCTCATTTCCTCACGAC 58.693 43.478 0.00 0.00 38.21 4.34
796 1052 3.320673 AAGTCTCATTTCCTCACGACC 57.679 47.619 0.00 0.00 0.00 4.79
797 1053 2.248248 AGTCTCATTTCCTCACGACCA 58.752 47.619 0.00 0.00 0.00 4.02
798 1054 2.028930 AGTCTCATTTCCTCACGACCAC 60.029 50.000 0.00 0.00 0.00 4.16
799 1055 1.275291 TCTCATTTCCTCACGACCACC 59.725 52.381 0.00 0.00 0.00 4.61
800 1056 1.001974 CTCATTTCCTCACGACCACCA 59.998 52.381 0.00 0.00 0.00 4.17
801 1057 1.156736 CATTTCCTCACGACCACCAC 58.843 55.000 0.00 0.00 0.00 4.16
802 1058 1.056660 ATTTCCTCACGACCACCACT 58.943 50.000 0.00 0.00 0.00 4.00
803 1059 0.834612 TTTCCTCACGACCACCACTT 59.165 50.000 0.00 0.00 0.00 3.16
804 1060 0.105964 TTCCTCACGACCACCACTTG 59.894 55.000 0.00 0.00 0.00 3.16
916 1174 1.136500 CCGTTCCTGGTTACTAGGAGC 59.864 57.143 18.74 18.74 44.65 4.70
1456 1740 1.371558 GACTCCAAGGTCCGTTGCT 59.628 57.895 0.00 0.00 0.00 3.91
1532 1819 6.748658 GTGTATGGTAAAAATAAGGAAACCGC 59.251 38.462 0.00 0.00 0.00 5.68
1557 1883 2.159043 TCGTCATGAGGAGGAAATCTGC 60.159 50.000 13.94 0.00 37.46 4.26
1563 1889 5.882557 TCATGAGGAGGAAATCTGCTTTTAC 59.117 40.000 0.00 0.00 44.53 2.01
1749 2198 5.592104 ACATGATAGTGGTATTCGACACA 57.408 39.130 0.00 0.00 39.99 3.72
2866 3918 6.017605 CCTTCTCATCATTTGAATTACTCCCG 60.018 42.308 0.00 0.00 32.78 5.14
3067 4262 6.615264 TTGTACTTCTACCGAGCTAGTATG 57.385 41.667 0.00 0.00 0.00 2.39
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 2.025981 TGCCAGCATTCCATACTTGTCT 60.026 45.455 0.00 0.00 0.00 3.41
15 16 5.919141 GTCATCTCAAATATTGCCAGCATTC 59.081 40.000 0.00 0.00 0.00 2.67
19 20 4.906065 TGTCATCTCAAATATTGCCAGC 57.094 40.909 0.00 0.00 0.00 4.85
21 22 5.015515 TGGTTGTCATCTCAAATATTGCCA 58.984 37.500 0.00 0.00 0.00 4.92
22 23 5.581126 TGGTTGTCATCTCAAATATTGCC 57.419 39.130 0.00 0.00 0.00 4.52
78 79 4.396166 CCATAGAACATCAACAAGGACCAC 59.604 45.833 0.00 0.00 0.00 4.16
197 198 2.236146 ACATCGGCAGACCAAGTTATCA 59.764 45.455 0.00 0.00 34.57 2.15
212 213 0.855349 GATAGCAGCGTCAACATCGG 59.145 55.000 0.00 0.00 0.00 4.18
213 214 1.845266 AGATAGCAGCGTCAACATCG 58.155 50.000 4.02 0.00 0.00 3.84
231 232 3.360867 AGCATCACCCCGATCTAGATAG 58.639 50.000 4.89 5.46 29.21 2.08
357 386 8.950403 AAAATGTTTAGACGTAGAAATTGAGC 57.050 30.769 0.00 0.00 0.00 4.26
383 412 5.519566 TGTTTAGACGTAGAAGTCGCAAAAA 59.480 36.000 0.00 0.00 45.26 1.94
384 413 5.042593 TGTTTAGACGTAGAAGTCGCAAAA 58.957 37.500 0.00 0.00 45.26 2.44
385 414 4.609947 TGTTTAGACGTAGAAGTCGCAAA 58.390 39.130 0.00 0.00 45.26 3.68
386 415 4.227512 TGTTTAGACGTAGAAGTCGCAA 57.772 40.909 0.00 0.00 45.26 4.85
387 416 3.902261 TGTTTAGACGTAGAAGTCGCA 57.098 42.857 0.00 0.00 45.26 5.10
388 417 5.344128 TGAAATGTTTAGACGTAGAAGTCGC 59.656 40.000 0.00 0.00 45.26 5.19
389 418 6.581542 AGTGAAATGTTTAGACGTAGAAGTCG 59.418 38.462 0.00 0.00 45.26 4.18
390 419 7.594015 TCAGTGAAATGTTTAGACGTAGAAGTC 59.406 37.037 0.00 0.00 41.23 3.01
391 420 7.431249 TCAGTGAAATGTTTAGACGTAGAAGT 58.569 34.615 0.00 0.00 0.00 3.01
392 421 7.410942 GCTCAGTGAAATGTTTAGACGTAGAAG 60.411 40.741 0.00 0.00 0.00 2.85
393 422 6.365247 GCTCAGTGAAATGTTTAGACGTAGAA 59.635 38.462 0.00 0.00 0.00 2.10
394 423 5.862323 GCTCAGTGAAATGTTTAGACGTAGA 59.138 40.000 0.00 0.00 0.00 2.59
395 424 5.062308 GGCTCAGTGAAATGTTTAGACGTAG 59.938 44.000 0.00 0.00 0.00 3.51
396 425 4.927425 GGCTCAGTGAAATGTTTAGACGTA 59.073 41.667 0.00 0.00 0.00 3.57
397 426 3.746492 GGCTCAGTGAAATGTTTAGACGT 59.254 43.478 0.00 0.00 0.00 4.34
398 427 3.745975 TGGCTCAGTGAAATGTTTAGACG 59.254 43.478 0.00 0.00 0.00 4.18
399 428 5.470098 TCTTGGCTCAGTGAAATGTTTAGAC 59.530 40.000 0.00 0.00 0.00 2.59
400 429 5.620206 TCTTGGCTCAGTGAAATGTTTAGA 58.380 37.500 0.00 0.00 0.00 2.10
401 430 5.106396 CCTCTTGGCTCAGTGAAATGTTTAG 60.106 44.000 0.00 0.00 0.00 1.85
402 431 4.761739 CCTCTTGGCTCAGTGAAATGTTTA 59.238 41.667 0.00 0.00 0.00 2.01
403 432 3.571401 CCTCTTGGCTCAGTGAAATGTTT 59.429 43.478 0.00 0.00 0.00 2.83
434 463 0.471022 TCACTGGCACCTGTGACCTA 60.471 55.000 21.38 4.00 45.43 3.08
475 509 2.717530 GAACTCGCTGTCGTTCGATAT 58.282 47.619 0.00 0.00 36.96 1.63
476 510 2.169663 GAACTCGCTGTCGTTCGATA 57.830 50.000 0.00 0.00 36.96 2.92
495 529 3.729526 ATCTTGTCAAAGACGCAATCG 57.270 42.857 0.00 0.00 45.12 3.34
502 536 3.000727 CCCCGTGTATCTTGTCAAAGAC 58.999 50.000 0.00 0.00 45.12 3.01
521 555 2.320587 CGCAAGATCGGCTATGCCC 61.321 63.158 10.10 0.00 43.91 5.36
566 600 1.875963 CGGCCTGTTTGGTAAGCTG 59.124 57.895 0.00 0.00 38.35 4.24
568 602 1.524008 AAGCGGCCTGTTTGGTAAGC 61.524 55.000 0.00 0.00 38.35 3.09
569 603 0.240945 CAAGCGGCCTGTTTGGTAAG 59.759 55.000 13.55 0.00 35.36 2.34
570 604 2.336341 CAAGCGGCCTGTTTGGTAA 58.664 52.632 13.55 0.00 35.36 2.85
571 605 4.073052 CAAGCGGCCTGTTTGGTA 57.927 55.556 13.55 0.00 35.36 3.25
574 608 1.455383 AAGACCAAGCGGCCTGTTTG 61.455 55.000 14.15 14.15 38.41 2.93
575 609 1.152756 AAGACCAAGCGGCCTGTTT 60.153 52.632 0.00 0.00 34.57 2.83
576 610 1.898574 CAAGACCAAGCGGCCTGTT 60.899 57.895 0.00 0.00 34.57 3.16
578 612 2.281761 ACAAGACCAAGCGGCCTG 60.282 61.111 0.00 0.00 34.57 4.85
580 614 1.172812 AAAGACAAGACCAAGCGGCC 61.173 55.000 0.00 0.00 34.57 6.13
581 615 0.668535 AAAAGACAAGACCAAGCGGC 59.331 50.000 0.00 0.00 34.57 6.53
582 616 2.357637 TCAAAAAGACAAGACCAAGCGG 59.642 45.455 0.00 0.00 38.77 5.52
583 617 3.691049 TCAAAAAGACAAGACCAAGCG 57.309 42.857 0.00 0.00 0.00 4.68
584 618 5.812127 ACAAATCAAAAAGACAAGACCAAGC 59.188 36.000 0.00 0.00 0.00 4.01
585 619 7.035004 TCACAAATCAAAAAGACAAGACCAAG 58.965 34.615 0.00 0.00 0.00 3.61
587 621 6.522625 TCACAAATCAAAAAGACAAGACCA 57.477 33.333 0.00 0.00 0.00 4.02
588 622 9.696917 AATATCACAAATCAAAAAGACAAGACC 57.303 29.630 0.00 0.00 0.00 3.85
641 721 5.132502 CACCATGGCTACCTTTATTGATCA 58.867 41.667 13.04 0.00 0.00 2.92
709 800 7.664318 AGAAAATGTACCGAGTCCATAGTTTTT 59.336 33.333 0.00 0.00 0.00 1.94
710 801 7.166167 AGAAAATGTACCGAGTCCATAGTTTT 58.834 34.615 0.00 0.00 0.00 2.43
712 803 6.070995 TGAGAAAATGTACCGAGTCCATAGTT 60.071 38.462 0.00 0.00 0.00 2.24
718 809 7.605410 TTTATTGAGAAAATGTACCGAGTCC 57.395 36.000 0.00 0.00 0.00 3.85
731 822 8.664798 CCACGTGATCATAGTTTTATTGAGAAA 58.335 33.333 19.30 0.00 0.00 2.52
732 823 8.038351 TCCACGTGATCATAGTTTTATTGAGAA 58.962 33.333 19.30 0.00 0.00 2.87
733 824 7.552459 TCCACGTGATCATAGTTTTATTGAGA 58.448 34.615 19.30 0.00 0.00 3.27
734 825 7.770801 TCCACGTGATCATAGTTTTATTGAG 57.229 36.000 19.30 0.00 0.00 3.02
735 826 9.825109 TTATCCACGTGATCATAGTTTTATTGA 57.175 29.630 19.30 0.00 34.76 2.57
741 832 8.330466 TGTTTTTATCCACGTGATCATAGTTT 57.670 30.769 19.30 0.00 34.76 2.66
743 834 7.552687 ACATGTTTTTATCCACGTGATCATAGT 59.447 33.333 19.30 0.00 34.52 2.12
744 835 7.919690 ACATGTTTTTATCCACGTGATCATAG 58.080 34.615 19.30 0.00 34.52 2.23
745 836 7.857734 ACATGTTTTTATCCACGTGATCATA 57.142 32.000 19.30 7.40 34.52 2.15
783 1039 1.056660 AGTGGTGGTCGTGAGGAAAT 58.943 50.000 0.00 0.00 0.00 2.17
784 1040 0.834612 AAGTGGTGGTCGTGAGGAAA 59.165 50.000 0.00 0.00 0.00 3.13
785 1041 0.105964 CAAGTGGTGGTCGTGAGGAA 59.894 55.000 0.00 0.00 0.00 3.36
786 1042 1.745890 CAAGTGGTGGTCGTGAGGA 59.254 57.895 0.00 0.00 0.00 3.71
787 1043 1.301716 CCAAGTGGTGGTCGTGAGG 60.302 63.158 0.00 0.00 43.20 3.86
788 1044 4.361253 CCAAGTGGTGGTCGTGAG 57.639 61.111 0.00 0.00 43.20 3.51
796 1052 5.990996 ACAAAATGCTTTTATCCAAGTGGTG 59.009 36.000 0.00 0.00 36.34 4.17
797 1053 6.173427 ACAAAATGCTTTTATCCAAGTGGT 57.827 33.333 0.00 0.00 36.34 4.16
798 1054 7.226325 TCAAACAAAATGCTTTTATCCAAGTGG 59.774 33.333 0.00 0.00 0.00 4.00
799 1055 8.140677 TCAAACAAAATGCTTTTATCCAAGTG 57.859 30.769 0.00 0.00 0.00 3.16
800 1056 8.729805 TTCAAACAAAATGCTTTTATCCAAGT 57.270 26.923 0.00 0.00 0.00 3.16
916 1174 2.009774 GTGGTCGTGAGGAAATGGATG 58.990 52.381 0.00 0.00 0.00 3.51
1236 1511 0.745468 GGTCGTAGGTGATGAGGTCC 59.255 60.000 0.00 0.00 0.00 4.46
1456 1740 1.037493 CGATACATCCCCAAGACCGA 58.963 55.000 0.00 0.00 0.00 4.69
1532 1819 5.925397 CAGATTTCCTCCTCATGACGATAAG 59.075 44.000 0.00 0.00 0.00 1.73
1557 1883 3.871006 TGTAGCAGGCATCATCGTAAAAG 59.129 43.478 0.00 0.00 0.00 2.27
1563 1889 2.452295 AGATGTAGCAGGCATCATCG 57.548 50.000 16.63 0.00 43.66 3.84
2194 2767 4.437239 CAGTTCACTCAACAGTCTTCAGT 58.563 43.478 0.00 0.00 37.48 3.41
2420 3060 6.698107 CACACATTTCAAACACACATCAAAG 58.302 36.000 0.00 0.00 0.00 2.77
2504 3146 8.451908 AATATTATACCAAGAAGACCACAAGC 57.548 34.615 0.00 0.00 0.00 4.01
2568 3608 3.998099 GGAAGCATAAATTCCTCCAGC 57.002 47.619 0.00 0.00 42.52 4.85
2866 3918 4.727235 ACGTCTTGTAAAAAGCTACAGC 57.273 40.909 0.00 0.00 42.49 4.40
2926 3978 8.882736 CATATGCAGTAACAAGTGATCAGTTTA 58.117 33.333 13.25 2.01 0.00 2.01
3067 4262 1.244816 GCTGGTTTACCCTTGTGTCC 58.755 55.000 0.00 0.00 34.29 4.02


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

AutoCloner maintained by Alex Coulton.