Multiple sequence alignment - TraesCS7D01G389700

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 TraesCS7D01G389700 chr7D 100.000 2693 0 0 1 2693 504771154 504768462 0.000000e+00 4974
1 TraesCS7D01G389700 chr7A 94.683 1655 61 17 721 2357 572326857 572325212 0.000000e+00 2543
2 TraesCS7D01G389700 chr7A 91.812 574 30 11 507 1066 572327943 572327373 0.000000e+00 784
3 TraesCS7D01G389700 chr7A 89.189 518 52 3 1 517 572328688 572328174 0.000000e+00 643
4 TraesCS7D01G389700 chr7A 92.203 295 23 0 1161 1455 689896770 689896476 4.150000e-113 418
5 TraesCS7D01G389700 chr7A 93.309 269 16 2 2329 2597 572325205 572324939 1.940000e-106 396
6 TraesCS7D01G389700 chr7A 98.198 111 2 0 1482 1592 689896478 689896368 7.610000e-46 195
7 TraesCS7D01G389700 chr7B 92.958 1420 43 27 738 2123 532657469 532656073 0.000000e+00 2015
8 TraesCS7D01G389700 chr7B 88.636 748 70 10 4 747 532658509 532657773 0.000000e+00 896
9 TraesCS7D01G389700 chrUn 91.216 444 35 3 1014 1455 29286176 29285735 3.840000e-168 601
10 TraesCS7D01G389700 chrUn 96.396 111 4 0 1482 1592 29285737 29285627 1.650000e-42 183
11 TraesCS7D01G389700 chr6D 83.388 614 88 12 1088 1694 135113883 135114489 8.420000e-155 556
12 TraesCS7D01G389700 chr6D 99.020 102 1 0 2592 2693 82016688 82016587 1.650000e-42 183
13 TraesCS7D01G389700 chr6B 86.437 494 67 0 1200 1693 233694179 233694672 2.360000e-150 542
14 TraesCS7D01G389700 chr2D 92.177 294 23 0 1162 1455 29147782 29148075 1.490000e-112 416
15 TraesCS7D01G389700 chr2D 98.198 111 2 0 1482 1592 29148073 29148183 7.610000e-46 195
16 TraesCS7D01G389700 chr1D 92.832 279 20 0 1161 1439 493794518 493794796 3.230000e-109 405
17 TraesCS7D01G389700 chr1D 98.198 111 2 0 1482 1592 493812324 493812434 7.610000e-46 195
18 TraesCS7D01G389700 chr1D 92.029 138 9 2 1014 1149 493794412 493794549 2.740000e-45 193
19 TraesCS7D01G389700 chr1D 99.020 102 1 0 2592 2693 354011381 354011280 1.650000e-42 183
20 TraesCS7D01G389700 chr1D 95.455 110 3 2 2585 2693 469385675 469385567 9.910000e-40 174
21 TraesCS7D01G389700 chr4D 96.396 111 3 1 2583 2693 418889347 418889238 5.920000e-42 182
22 TraesCS7D01G389700 chr4B 98.077 104 2 0 2590 2693 395182643 395182746 5.920000e-42 182
23 TraesCS7D01G389700 chr4B 94.828 116 3 3 2578 2693 495310811 495310699 7.660000e-41 178
24 TraesCS7D01G389700 chr3B 98.077 104 2 0 2590 2693 114293765 114293662 5.920000e-42 182
25 TraesCS7D01G389700 chr3B 92.793 111 8 0 1482 1592 544847242 544847132 7.720000e-36 161
26 TraesCS7D01G389700 chr2B 95.575 113 5 0 2580 2692 679061008 679061120 5.920000e-42 182
27 TraesCS7D01G389700 chr5B 93.966 116 5 2 2577 2691 379254474 379254360 9.910000e-40 174


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 TraesCS7D01G389700 chr7D 504768462 504771154 2692 True 4974.0 4974 100.00000 1 2693 1 chr7D.!!$R1 2692
1 TraesCS7D01G389700 chr7A 572324939 572328688 3749 True 1091.5 2543 92.24825 1 2597 4 chr7A.!!$R1 2596
2 TraesCS7D01G389700 chr7B 532656073 532658509 2436 True 1455.5 2015 90.79700 4 2123 2 chr7B.!!$R1 2119
3 TraesCS7D01G389700 chrUn 29285627 29286176 549 True 392.0 601 93.80600 1014 1592 2 chrUn.!!$R1 578
4 TraesCS7D01G389700 chr6D 135113883 135114489 606 False 556.0 556 83.38800 1088 1694 1 chr6D.!!$F1 606

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
618 866 0.253207 CCCTACAACCTTCCCCTCCT 60.253 60.0 0.0 0.0 0.0 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2427 3943 0.100682 CGCTCGTATGTGTACCTGCT 59.899 55.0 0.0 0.0 0.0 4.24 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
18 19 2.268920 GCTCGAGCCCAATCCACA 59.731 61.111 27.22 0.00 34.31 4.17
82 83 1.761244 TTGATATCACGCTTGCGCCG 61.761 55.000 15.21 3.44 0.00 6.46
83 84 2.943345 GATATCACGCTTGCGCCGG 61.943 63.158 15.21 0.00 0.00 6.13
121 122 2.159338 GCTCATTGATGGCATTGACGTT 60.159 45.455 0.00 0.00 32.64 3.99
131 132 1.222300 CATTGACGTTGGTTGGACGA 58.778 50.000 3.48 0.00 42.82 4.20
146 147 1.223187 GACGAAGCTCAAACGGGAAA 58.777 50.000 0.00 0.00 0.00 3.13
161 162 3.087906 AAAGGGACCCGCCGCTAT 61.088 61.111 4.40 0.00 37.63 2.97
174 175 0.962489 CCGCTATGGTCCTCGAAGAT 59.038 55.000 0.00 0.00 33.89 2.40
175 176 1.341531 CCGCTATGGTCCTCGAAGATT 59.658 52.381 0.00 0.00 33.89 2.40
218 219 1.048160 TCACAGACCCAGTGCTCACA 61.048 55.000 2.63 0.00 36.93 3.58
233 234 1.152984 CACACAACCTGGGTGCTGA 60.153 57.895 12.68 0.00 45.59 4.26
259 260 0.882474 CGAAGACGACCAAGGAGTCT 59.118 55.000 13.29 13.29 46.01 3.24
300 304 4.541482 CACATCGCCGCCACATGC 62.541 66.667 0.00 0.00 0.00 4.06
301 305 4.783621 ACATCGCCGCCACATGCT 62.784 61.111 0.00 0.00 38.05 3.79
417 423 1.272490 ACGACATCGACATCAACTGGT 59.728 47.619 8.54 0.00 43.02 4.00
425 431 1.002087 GACATCAACTGGTCGGAGGTT 59.998 52.381 0.00 0.00 0.00 3.50
429 435 1.768888 AACTGGTCGGAGGTTGGGT 60.769 57.895 0.00 0.00 0.00 4.51
452 458 4.100084 TAGGACCCGTCGCTCCGA 62.100 66.667 0.00 0.00 0.00 4.55
486 492 2.163818 ATCCGAGTTCGAGCAACAAA 57.836 45.000 1.01 0.00 43.02 2.83
503 509 3.664107 ACAAATCTGACTAGCGCTTCAA 58.336 40.909 18.68 5.86 0.00 2.69
517 764 1.497991 CTTCAAAACTCGGTGCTCGA 58.502 50.000 3.07 3.07 46.77 4.04
523 770 2.811317 CTCGGTGCTCGACCAAGC 60.811 66.667 0.00 0.00 46.55 4.01
583 831 0.609957 CACCCCATCAAGCAAGAGCA 60.610 55.000 0.00 0.00 45.49 4.26
589 837 2.413765 CCATCAAGCAAGAGCAAGAACG 60.414 50.000 0.00 0.00 45.49 3.95
618 866 0.253207 CCCTACAACCTTCCCCTCCT 60.253 60.000 0.00 0.00 0.00 3.69
643 892 0.888736 CGTCCACCTGATGTTTGCCA 60.889 55.000 0.00 0.00 0.00 4.92
715 964 8.870160 TCTACAATTTTGAACAAACAATCCTG 57.130 30.769 0.00 0.00 0.00 3.86
866 1436 1.693640 CCCTGCTTTCTCCACCCAT 59.306 57.895 0.00 0.00 0.00 4.00
1095 2539 4.150454 CCCGCCTCCTCCCTCTCT 62.150 72.222 0.00 0.00 0.00 3.10
1668 3118 2.203195 TTCACCAACAGCAGCGCT 60.203 55.556 2.64 2.64 40.77 5.92
1768 3219 1.872653 GCTCGGTTCGTCCTCTGTTTT 60.873 52.381 0.00 0.00 0.00 2.43
1769 3220 2.608752 GCTCGGTTCGTCCTCTGTTTTA 60.609 50.000 0.00 0.00 0.00 1.52
1770 3221 2.985139 CTCGGTTCGTCCTCTGTTTTAC 59.015 50.000 0.00 0.00 0.00 2.01
1771 3222 2.624838 TCGGTTCGTCCTCTGTTTTACT 59.375 45.455 0.00 0.00 0.00 2.24
1772 3223 2.729882 CGGTTCGTCCTCTGTTTTACTG 59.270 50.000 0.00 0.00 0.00 2.74
1774 3225 4.374399 GGTTCGTCCTCTGTTTTACTGAA 58.626 43.478 0.00 0.00 0.00 3.02
1776 3227 4.252971 TCGTCCTCTGTTTTACTGAAGG 57.747 45.455 0.00 0.00 0.00 3.46
1778 3229 3.075148 GTCCTCTGTTTTACTGAAGGCC 58.925 50.000 0.00 0.00 0.00 5.19
1854 3311 1.008079 GGTCTGTGTTTGCTGCTGC 60.008 57.895 8.89 8.89 40.20 5.25
1855 3312 1.450531 GGTCTGTGTTTGCTGCTGCT 61.451 55.000 17.00 0.00 40.48 4.24
1856 3313 0.317603 GTCTGTGTTTGCTGCTGCTG 60.318 55.000 17.00 0.77 40.48 4.41
1873 3330 0.520404 CTGCTGTCACCTTGATGTGC 59.480 55.000 0.00 0.00 36.17 4.57
1897 3354 1.201647 GGCGAGTACTGAGTAGTGCAA 59.798 52.381 4.39 0.00 41.40 4.08
1916 3394 3.482110 GCAACGTAGCTTTGTGAAGTTTG 59.518 43.478 0.00 0.00 35.25 2.93
1996 3474 1.280066 ACTTTTGCTTGCTGTTTGCG 58.720 45.000 0.00 0.00 46.63 4.85
2041 3523 3.122150 CACATCCGTGTCGTGATGT 57.878 52.632 15.01 15.01 43.09 3.06
2042 3524 1.428448 CACATCCGTGTCGTGATGTT 58.572 50.000 16.82 6.67 41.71 2.71
2083 3565 0.733150 GGCTCCGTTTATGCAGGAAC 59.267 55.000 0.00 0.00 33.10 3.62
2133 3615 4.048504 GGTAACAGGTTGTGAATTTGTGC 58.951 43.478 0.00 0.00 0.00 4.57
2138 3620 4.099881 ACAGGTTGTGAATTTGTGCTGATT 59.900 37.500 0.00 0.00 0.00 2.57
2139 3621 5.301551 ACAGGTTGTGAATTTGTGCTGATTA 59.698 36.000 0.00 0.00 0.00 1.75
2172 3654 4.466370 TGGGACATGTAGTAGTTCCTTCAG 59.534 45.833 0.00 0.00 34.32 3.02
2194 3676 8.296211 TCAGCATGATCCAATAAAGAATTTCA 57.704 30.769 0.00 0.00 42.56 2.69
2320 3802 7.806014 TCAAACCTTATTAAATTTCGACAGTGC 59.194 33.333 0.00 0.00 0.00 4.40
2328 3810 3.963383 ATTTCGACAGTGCGTTCTTTT 57.037 38.095 6.81 0.00 0.00 2.27
2329 3811 5.412526 AATTTCGACAGTGCGTTCTTTTA 57.587 34.783 6.81 0.00 0.00 1.52
2330 3812 5.607119 ATTTCGACAGTGCGTTCTTTTAT 57.393 34.783 6.81 0.00 0.00 1.40
2331 3813 6.715344 ATTTCGACAGTGCGTTCTTTTATA 57.285 33.333 6.81 0.00 0.00 0.98
2332 3814 5.756950 TTCGACAGTGCGTTCTTTTATAG 57.243 39.130 6.81 0.00 0.00 1.31
2427 3943 2.416162 GCCGAACAAACAACCTGAAACA 60.416 45.455 0.00 0.00 0.00 2.83
2443 3959 3.006003 TGAAACAGCAGGTACACATACGA 59.994 43.478 0.00 0.00 31.40 3.43
2447 3963 0.179145 GCAGGTACACATACGAGCGT 60.179 55.000 0.00 0.00 31.40 5.07
2508 4024 8.385111 CGTAGTTTTGTCTAAAGAACAACAGAA 58.615 33.333 0.00 0.00 0.00 3.02
2533 4049 3.369892 CCCCTGAAGATGGTGACTTACAG 60.370 52.174 0.00 0.00 0.00 2.74
2541 4057 3.474798 TGGTGACTTACAGAGGATCCT 57.525 47.619 16.13 16.13 33.66 3.24
2557 4073 3.371285 GGATCCTTAGTTTGACTGTTCGC 59.629 47.826 3.84 0.00 0.00 4.70
2599 4115 9.490379 TTTCTTTCAAGAAATGAGTACTACTCC 57.510 33.333 12.79 0.00 46.80 3.85
2600 4116 7.612677 TCTTTCAAGAAATGAGTACTACTCCC 58.387 38.462 12.79 1.67 39.77 4.30
2601 4117 7.455008 TCTTTCAAGAAATGAGTACTACTCCCT 59.545 37.037 12.79 3.60 39.77 4.20
2602 4118 6.777213 TCAAGAAATGAGTACTACTCCCTC 57.223 41.667 12.79 7.26 44.44 4.30
2603 4119 5.657302 TCAAGAAATGAGTACTACTCCCTCC 59.343 44.000 12.79 1.96 44.44 4.30
2604 4120 5.475398 AGAAATGAGTACTACTCCCTCCT 57.525 43.478 12.79 3.90 44.44 3.69
2605 4121 5.844601 AGAAATGAGTACTACTCCCTCCTT 58.155 41.667 12.79 0.93 44.44 3.36
2606 4122 6.265304 AGAAATGAGTACTACTCCCTCCTTT 58.735 40.000 12.79 5.90 44.44 3.11
2607 4123 6.381707 AGAAATGAGTACTACTCCCTCCTTTC 59.618 42.308 12.79 12.37 44.44 2.62
2608 4124 3.978610 TGAGTACTACTCCCTCCTTTCC 58.021 50.000 12.79 0.00 44.44 3.13
2609 4125 2.950975 GAGTACTACTCCCTCCTTTCCG 59.049 54.545 5.01 0.00 39.28 4.30
2610 4126 2.030371 GTACTACTCCCTCCTTTCCGG 58.970 57.143 0.00 0.00 0.00 5.14
2611 4127 0.412640 ACTACTCCCTCCTTTCCGGT 59.587 55.000 0.00 0.00 0.00 5.28
2612 4128 1.203275 ACTACTCCCTCCTTTCCGGTT 60.203 52.381 0.00 0.00 0.00 4.44
2613 4129 1.907255 CTACTCCCTCCTTTCCGGTTT 59.093 52.381 0.00 0.00 0.00 3.27
2614 4130 2.034436 ACTCCCTCCTTTCCGGTTTA 57.966 50.000 0.00 0.00 0.00 2.01
2615 4131 2.558974 ACTCCCTCCTTTCCGGTTTAT 58.441 47.619 0.00 0.00 0.00 1.40
2616 4132 3.727948 ACTCCCTCCTTTCCGGTTTATA 58.272 45.455 0.00 0.00 0.00 0.98
2617 4133 3.710165 ACTCCCTCCTTTCCGGTTTATAG 59.290 47.826 0.00 0.00 0.00 1.31
2618 4134 3.043418 TCCCTCCTTTCCGGTTTATAGG 58.957 50.000 0.00 4.62 0.00 2.57
2619 4135 2.105993 CCCTCCTTTCCGGTTTATAGGG 59.894 54.545 16.03 16.03 36.05 3.53
2620 4136 2.486727 CCTCCTTTCCGGTTTATAGGGC 60.487 54.545 0.00 0.00 0.00 5.19
2621 4137 2.438392 CTCCTTTCCGGTTTATAGGGCT 59.562 50.000 0.00 0.00 0.00 5.19
2622 4138 2.848071 TCCTTTCCGGTTTATAGGGCTT 59.152 45.455 0.00 0.00 0.00 4.35
2623 4139 4.039339 TCCTTTCCGGTTTATAGGGCTTA 58.961 43.478 0.00 0.00 0.00 3.09
2624 4140 4.661709 TCCTTTCCGGTTTATAGGGCTTAT 59.338 41.667 0.00 0.00 0.00 1.73
2625 4141 5.001874 CCTTTCCGGTTTATAGGGCTTATC 58.998 45.833 0.00 0.00 0.00 1.75
2626 4142 5.221864 CCTTTCCGGTTTATAGGGCTTATCT 60.222 44.000 0.00 0.00 0.00 1.98
2627 4143 5.479124 TTCCGGTTTATAGGGCTTATCTC 57.521 43.478 0.00 0.00 0.00 2.75
2628 4144 4.485875 TCCGGTTTATAGGGCTTATCTCA 58.514 43.478 0.00 0.00 0.00 3.27
2629 4145 4.903049 TCCGGTTTATAGGGCTTATCTCAA 59.097 41.667 0.00 0.00 0.00 3.02
2630 4146 5.367352 TCCGGTTTATAGGGCTTATCTCAAA 59.633 40.000 0.00 0.00 0.00 2.69
2631 4147 6.059484 CCGGTTTATAGGGCTTATCTCAAAA 58.941 40.000 0.00 0.00 0.00 2.44
2632 4148 6.715264 CCGGTTTATAGGGCTTATCTCAAAAT 59.285 38.462 0.00 0.00 0.00 1.82
2633 4149 7.230712 CCGGTTTATAGGGCTTATCTCAAAATT 59.769 37.037 0.00 0.00 0.00 1.82
2634 4150 8.630037 CGGTTTATAGGGCTTATCTCAAAATTT 58.370 33.333 0.00 0.00 0.00 1.82
2665 4181 9.447157 TTTTCCATTTTATAAGGCTCAATTTGG 57.553 29.630 0.00 0.00 0.00 3.28
2666 4182 7.732222 TCCATTTTATAAGGCTCAATTTGGT 57.268 32.000 0.00 0.00 0.00 3.67
2667 4183 8.144862 TCCATTTTATAAGGCTCAATTTGGTT 57.855 30.769 0.00 0.00 0.00 3.67
2668 4184 8.040132 TCCATTTTATAAGGCTCAATTTGGTTG 58.960 33.333 0.00 0.00 39.25 3.77
2669 4185 7.823799 CCATTTTATAAGGCTCAATTTGGTTGT 59.176 33.333 0.00 0.00 38.95 3.32
2670 4186 9.218440 CATTTTATAAGGCTCAATTTGGTTGTT 57.782 29.630 0.00 0.00 38.95 2.83
2671 4187 8.825667 TTTTATAAGGCTCAATTTGGTTGTTC 57.174 30.769 0.00 0.00 38.95 3.18
2672 4188 3.751479 AAGGCTCAATTTGGTTGTTCC 57.249 42.857 0.00 0.00 38.95 3.62
2673 4189 1.970640 AGGCTCAATTTGGTTGTTCCC 59.029 47.619 0.00 0.00 38.95 3.97
2674 4190 1.001974 GGCTCAATTTGGTTGTTCCCC 59.998 52.381 0.00 0.00 38.95 4.81
2675 4191 1.336795 GCTCAATTTGGTTGTTCCCCG 60.337 52.381 0.00 0.00 38.95 5.73
2676 4192 1.960689 CTCAATTTGGTTGTTCCCCGT 59.039 47.619 0.00 0.00 38.95 5.28
2677 4193 1.957877 TCAATTTGGTTGTTCCCCGTC 59.042 47.619 0.00 0.00 38.95 4.79
2678 4194 1.683917 CAATTTGGTTGTTCCCCGTCA 59.316 47.619 0.00 0.00 33.01 4.35
2679 4195 1.324383 ATTTGGTTGTTCCCCGTCAC 58.676 50.000 0.00 0.00 34.77 3.67
2680 4196 0.034380 TTTGGTTGTTCCCCGTCACA 60.034 50.000 0.00 0.00 34.77 3.58
2681 4197 0.183971 TTGGTTGTTCCCCGTCACAT 59.816 50.000 0.00 0.00 34.77 3.21
2682 4198 0.536233 TGGTTGTTCCCCGTCACATG 60.536 55.000 0.00 0.00 34.77 3.21
2683 4199 0.536460 GGTTGTTCCCCGTCACATGT 60.536 55.000 0.00 0.00 0.00 3.21
2684 4200 1.314730 GTTGTTCCCCGTCACATGTT 58.685 50.000 0.00 0.00 0.00 2.71
2685 4201 1.265905 GTTGTTCCCCGTCACATGTTC 59.734 52.381 0.00 0.00 0.00 3.18
2686 4202 0.470341 TGTTCCCCGTCACATGTTCA 59.530 50.000 0.00 0.00 0.00 3.18
2687 4203 1.156736 GTTCCCCGTCACATGTTCAG 58.843 55.000 0.00 0.00 0.00 3.02
2688 4204 1.052617 TTCCCCGTCACATGTTCAGA 58.947 50.000 0.00 0.00 0.00 3.27
2689 4205 1.275666 TCCCCGTCACATGTTCAGAT 58.724 50.000 0.00 0.00 0.00 2.90
2690 4206 1.628340 TCCCCGTCACATGTTCAGATT 59.372 47.619 0.00 0.00 0.00 2.40
2691 4207 2.009774 CCCCGTCACATGTTCAGATTC 58.990 52.381 0.00 0.00 0.00 2.52
2692 4208 2.009774 CCCGTCACATGTTCAGATTCC 58.990 52.381 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 1.473965 GCGATGTGTCTCCATGATGGT 60.474 52.381 11.87 0.00 39.03 3.55
82 83 1.219393 CTCCTCCTTGAAGACGGCC 59.781 63.158 0.00 0.00 0.00 6.13
83 84 1.448717 GCTCCTCCTTGAAGACGGC 60.449 63.158 0.00 0.00 0.00 5.68
121 122 1.305201 GTTTGAGCTTCGTCCAACCA 58.695 50.000 0.00 0.00 0.00 3.67
131 132 0.476771 TCCCTTTCCCGTTTGAGCTT 59.523 50.000 0.00 0.00 0.00 3.74
161 162 0.250234 CCTGCAATCTTCGAGGACCA 59.750 55.000 0.00 0.00 0.00 4.02
163 164 1.363744 CACCTGCAATCTTCGAGGAC 58.636 55.000 0.00 0.00 0.00 3.85
164 165 0.250234 CCACCTGCAATCTTCGAGGA 59.750 55.000 0.00 0.00 0.00 3.71
189 190 0.037326 GGGTCTGTGAGATCGTGCAA 60.037 55.000 0.00 0.00 0.00 4.08
196 197 0.901124 GAGCACTGGGTCTGTGAGAT 59.099 55.000 8.71 0.00 38.50 2.75
218 219 1.152756 GGTTCAGCACCCAGGTTGT 60.153 57.895 0.00 0.00 40.19 3.32
219 220 2.260869 CGGTTCAGCACCCAGGTTG 61.261 63.158 0.00 0.00 43.83 3.77
221 222 3.953775 CCGGTTCAGCACCCAGGT 61.954 66.667 0.00 0.00 43.83 4.00
278 279 4.451150 TGGCGGCGATGTGTCTCC 62.451 66.667 12.98 0.00 0.00 3.71
367 373 4.785453 CGGTGGGCTCCTCCTTGC 62.785 72.222 9.67 0.00 35.24 4.01
417 423 2.096707 TACTCCCACCCAACCTCCGA 62.097 60.000 0.00 0.00 0.00 4.55
429 435 2.044650 CGACGGGTCCTACTCCCA 60.045 66.667 1.91 0.00 44.81 4.37
452 458 1.146263 GGATTTCGTCATCGGGGCT 59.854 57.895 0.00 0.00 37.69 5.19
486 492 3.929610 GAGTTTTGAAGCGCTAGTCAGAT 59.070 43.478 12.05 0.00 0.00 2.90
523 770 2.180017 GACAATGCTTGCTGCGGG 59.820 61.111 0.00 0.00 46.63 6.13
535 783 2.311688 GATGAGGCGACGGGGACAAT 62.312 60.000 0.00 0.00 0.00 2.71
537 785 3.458163 GATGAGGCGACGGGGACA 61.458 66.667 0.00 0.00 0.00 4.02
570 818 1.808945 CCGTTCTTGCTCTTGCTTGAT 59.191 47.619 0.00 0.00 40.48 2.57
618 866 2.284625 ATCAGGTGGACGCCCAGA 60.285 61.111 0.00 0.00 44.55 3.86
629 878 2.198827 TCGAATGGCAAACATCAGGT 57.801 45.000 0.00 0.00 39.40 4.00
643 892 1.474330 GGGGTGAAGGCATTTCGAAT 58.526 50.000 0.00 0.00 38.71 3.34
796 1366 2.124529 GGGCTGGGCAAGAGCTAC 60.125 66.667 0.00 0.00 41.70 3.58
803 1373 3.233231 GTTGCTTGGGCTGGGCAA 61.233 61.111 7.25 7.25 42.54 4.52
850 1420 0.394899 GGGATGGGTGGAGAAAGCAG 60.395 60.000 0.00 0.00 0.00 4.24
866 1436 2.043772 CCTATGTGGGGGTGGGGA 59.956 66.667 0.00 0.00 0.00 4.81
1081 2522 1.819905 CGAAAGAGAGGGAGGAGGC 59.180 63.158 0.00 0.00 0.00 4.70
1082 2523 1.681486 GGCGAAAGAGAGGGAGGAGG 61.681 65.000 0.00 0.00 0.00 4.30
1083 2524 0.686112 AGGCGAAAGAGAGGGAGGAG 60.686 60.000 0.00 0.00 0.00 3.69
1668 3118 1.078918 CGCCTTGAGCATGTCCTCA 60.079 57.895 0.00 0.00 44.04 3.86
1737 3188 2.453773 GAACCGAGCTGACGACGTCA 62.454 60.000 27.61 27.61 40.50 4.35
1739 3190 2.254651 GAACCGAGCTGACGACGT 59.745 61.111 0.00 0.00 35.09 4.34
1747 3198 1.179814 AACAGAGGACGAACCGAGCT 61.180 55.000 0.00 0.00 44.74 4.09
1838 3295 2.027325 CAGCAGCAGCAAACACAGA 58.973 52.632 3.17 0.00 45.49 3.41
1854 3311 0.520404 GCACATCAAGGTGACAGCAG 59.480 55.000 7.50 0.00 41.32 4.24
1855 3312 1.229975 CGCACATCAAGGTGACAGCA 61.230 55.000 7.50 0.00 41.32 4.41
1856 3313 1.499056 CGCACATCAAGGTGACAGC 59.501 57.895 0.00 0.00 41.32 4.40
1873 3330 0.377554 CTACTCAGTACTCGCCACCG 59.622 60.000 0.00 0.00 0.00 4.94
1897 3354 3.064820 CCACAAACTTCACAAAGCTACGT 59.935 43.478 0.00 0.00 35.81 3.57
1916 3394 2.735762 GCCACGACTCATAGTTCTCCAC 60.736 54.545 0.00 0.00 0.00 4.02
2041 3523 1.180029 GTACTCCACTCCAGCCGTAA 58.820 55.000 0.00 0.00 0.00 3.18
2042 3524 0.682209 GGTACTCCACTCCAGCCGTA 60.682 60.000 0.00 0.00 0.00 4.02
2083 3565 0.734309 TGCGCATCACAGCCTTAATG 59.266 50.000 5.66 0.00 0.00 1.90
2112 3594 4.739716 CAGCACAAATTCACAACCTGTTAC 59.260 41.667 0.00 0.00 0.00 2.50
2128 3610 7.282224 GTCCCATTAACATAGTAATCAGCACAA 59.718 37.037 0.00 0.00 0.00 3.33
2133 3615 8.908786 ACATGTCCCATTAACATAGTAATCAG 57.091 34.615 0.00 0.00 35.62 2.90
2138 3620 9.650714 ACTACTACATGTCCCATTAACATAGTA 57.349 33.333 0.00 0.00 35.62 1.82
2139 3621 8.548880 ACTACTACATGTCCCATTAACATAGT 57.451 34.615 0.00 0.00 35.62 2.12
2158 3640 4.962362 TGGATCATGCTGAAGGAACTACTA 59.038 41.667 0.00 0.00 38.49 1.82
2166 3648 6.704289 TTCTTTATTGGATCATGCTGAAGG 57.296 37.500 0.00 0.00 0.00 3.46
2172 3654 9.193133 CTGATGAAATTCTTTATTGGATCATGC 57.807 33.333 0.00 0.00 30.29 4.06
2190 3672 6.409524 AGCTTCATGGAAAAACTGATGAAA 57.590 33.333 0.00 0.00 35.08 2.69
2194 3676 5.105997 GCTGTAGCTTCATGGAAAAACTGAT 60.106 40.000 0.00 0.00 38.21 2.90
2203 3685 0.107508 GCTGGCTGTAGCTTCATGGA 60.108 55.000 3.63 0.00 40.52 3.41
2352 3868 7.446769 TCTCTGCTTCTCTAGTCGAGTTATAT 58.553 38.462 0.00 0.00 40.75 0.86
2360 3876 3.127589 TCGATCTCTGCTTCTCTAGTCG 58.872 50.000 0.00 0.00 0.00 4.18
2363 3879 4.319766 GCTTCTCGATCTCTGCTTCTCTAG 60.320 50.000 0.00 0.00 0.00 2.43
2371 3887 0.176680 TTGGGCTTCTCGATCTCTGC 59.823 55.000 0.00 0.00 0.00 4.26
2372 3888 2.481854 CATTGGGCTTCTCGATCTCTG 58.518 52.381 0.00 0.00 0.00 3.35
2427 3943 0.100682 CGCTCGTATGTGTACCTGCT 59.899 55.000 0.00 0.00 0.00 4.24
2438 3954 3.615496 GTGTTTATGTTGGACGCTCGTAT 59.385 43.478 0.00 0.00 0.00 3.06
2439 3955 2.988493 GTGTTTATGTTGGACGCTCGTA 59.012 45.455 0.00 0.00 0.00 3.43
2443 3959 2.846193 AGTGTGTTTATGTTGGACGCT 58.154 42.857 0.00 0.00 0.00 5.07
2447 3963 6.058833 TCAGCTTTAGTGTGTTTATGTTGGA 58.941 36.000 0.00 0.00 0.00 3.53
2482 3998 7.902032 TCTGTTGTTCTTTAGACAAAACTACG 58.098 34.615 0.00 0.00 32.47 3.51
2508 4024 1.918293 TCACCATCTTCAGGGGCGT 60.918 57.895 0.00 0.00 0.00 5.68
2533 4049 4.865365 CGAACAGTCAAACTAAGGATCCTC 59.135 45.833 16.52 0.00 0.00 3.71
2541 4057 1.573026 TGCGCGAACAGTCAAACTAA 58.427 45.000 12.10 0.00 0.00 2.24
2597 4113 3.043418 CCTATAAACCGGAAAGGAGGGA 58.957 50.000 9.46 0.00 45.00 4.20
2598 4114 2.105993 CCCTATAAACCGGAAAGGAGGG 59.894 54.545 9.46 14.71 45.00 4.30
2599 4115 2.486727 GCCCTATAAACCGGAAAGGAGG 60.487 54.545 9.46 9.03 45.00 4.30
2600 4116 2.438392 AGCCCTATAAACCGGAAAGGAG 59.562 50.000 9.46 0.00 45.00 3.69
2601 4117 2.484602 AGCCCTATAAACCGGAAAGGA 58.515 47.619 9.46 0.00 45.00 3.36
2603 4119 5.866207 AGATAAGCCCTATAAACCGGAAAG 58.134 41.667 9.46 0.00 0.00 2.62
2604 4120 5.367352 TGAGATAAGCCCTATAAACCGGAAA 59.633 40.000 9.46 0.00 0.00 3.13
2605 4121 4.903049 TGAGATAAGCCCTATAAACCGGAA 59.097 41.667 9.46 0.00 0.00 4.30
2606 4122 4.485875 TGAGATAAGCCCTATAAACCGGA 58.514 43.478 9.46 0.00 0.00 5.14
2607 4123 4.884668 TGAGATAAGCCCTATAAACCGG 57.115 45.455 0.00 0.00 0.00 5.28
2608 4124 7.745620 ATTTTGAGATAAGCCCTATAAACCG 57.254 36.000 0.00 0.00 0.00 4.44
2639 4155 9.447157 CCAAATTGAGCCTTATAAAATGGAAAA 57.553 29.630 0.00 0.00 0.00 2.29
2640 4156 8.601546 ACCAAATTGAGCCTTATAAAATGGAAA 58.398 29.630 0.00 0.00 0.00 3.13
2641 4157 8.144862 ACCAAATTGAGCCTTATAAAATGGAA 57.855 30.769 0.00 0.00 0.00 3.53
2642 4158 7.732222 ACCAAATTGAGCCTTATAAAATGGA 57.268 32.000 0.00 0.00 0.00 3.41
2643 4159 7.823799 ACAACCAAATTGAGCCTTATAAAATGG 59.176 33.333 0.00 0.00 41.23 3.16
2644 4160 8.776376 ACAACCAAATTGAGCCTTATAAAATG 57.224 30.769 0.00 0.00 41.23 2.32
2645 4161 9.435688 GAACAACCAAATTGAGCCTTATAAAAT 57.564 29.630 0.00 0.00 41.23 1.82
2646 4162 7.875554 GGAACAACCAAATTGAGCCTTATAAAA 59.124 33.333 0.00 0.00 41.23 1.52
2647 4163 7.382898 GGAACAACCAAATTGAGCCTTATAAA 58.617 34.615 0.00 0.00 41.23 1.40
2648 4164 6.071051 GGGAACAACCAAATTGAGCCTTATAA 60.071 38.462 0.00 0.00 41.23 0.98
2649 4165 5.420739 GGGAACAACCAAATTGAGCCTTATA 59.579 40.000 0.00 0.00 41.23 0.98
2650 4166 4.222810 GGGAACAACCAAATTGAGCCTTAT 59.777 41.667 0.00 0.00 41.23 1.73
2651 4167 3.576550 GGGAACAACCAAATTGAGCCTTA 59.423 43.478 0.00 0.00 41.23 2.69
2652 4168 2.368548 GGGAACAACCAAATTGAGCCTT 59.631 45.455 0.00 0.00 41.23 4.35
2653 4169 1.970640 GGGAACAACCAAATTGAGCCT 59.029 47.619 0.00 0.00 41.23 4.58
2654 4170 1.001974 GGGGAACAACCAAATTGAGCC 59.998 52.381 0.00 0.00 41.23 4.70
2655 4171 1.336795 CGGGGAACAACCAAATTGAGC 60.337 52.381 0.00 0.00 41.23 4.26
2656 4172 1.960689 ACGGGGAACAACCAAATTGAG 59.039 47.619 0.00 0.00 41.23 3.02
2657 4173 1.957877 GACGGGGAACAACCAAATTGA 59.042 47.619 0.00 0.00 41.23 2.57
2658 4174 1.683917 TGACGGGGAACAACCAAATTG 59.316 47.619 0.00 0.00 44.60 2.32
2659 4175 1.684450 GTGACGGGGAACAACCAAATT 59.316 47.619 0.00 0.00 41.20 1.82
2660 4176 1.324383 GTGACGGGGAACAACCAAAT 58.676 50.000 0.00 0.00 41.20 2.32
2661 4177 0.034380 TGTGACGGGGAACAACCAAA 60.034 50.000 0.00 0.00 41.20 3.28
2662 4178 0.183971 ATGTGACGGGGAACAACCAA 59.816 50.000 0.00 0.00 41.20 3.67
2663 4179 0.536233 CATGTGACGGGGAACAACCA 60.536 55.000 0.00 0.00 41.20 3.67
2664 4180 0.536460 ACATGTGACGGGGAACAACC 60.536 55.000 0.00 0.00 38.08 3.77
2665 4181 1.265905 GAACATGTGACGGGGAACAAC 59.734 52.381 0.00 0.00 0.00 3.32
2666 4182 1.134068 TGAACATGTGACGGGGAACAA 60.134 47.619 0.00 0.00 0.00 2.83
2667 4183 0.470341 TGAACATGTGACGGGGAACA 59.530 50.000 0.00 0.00 0.00 3.18
2668 4184 1.156736 CTGAACATGTGACGGGGAAC 58.843 55.000 0.00 0.00 0.00 3.62
2669 4185 1.052617 TCTGAACATGTGACGGGGAA 58.947 50.000 0.00 0.00 0.00 3.97
2670 4186 1.275666 ATCTGAACATGTGACGGGGA 58.724 50.000 0.00 0.00 0.00 4.81
2671 4187 2.009774 GAATCTGAACATGTGACGGGG 58.990 52.381 0.00 0.00 0.00 5.73
2672 4188 2.009774 GGAATCTGAACATGTGACGGG 58.990 52.381 0.00 0.00 0.00 5.28


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

AutoCloner maintained by Alex Coulton.