Multiple sequence alignment - TraesCS3D01G269200

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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 TraesCS3D01G269200 chr3D 100.000 2978 0 0 1 2978 373844973 373841996 0.000000e+00 5500.0
1 TraesCS3D01G269200 chr3D 98.039 51 1 0 1998 2048 65129680 65129730 4.090000e-14 89.8
2 TraesCS3D01G269200 chr3D 98.039 51 0 1 1998 2048 247039736 247039687 1.470000e-13 87.9
3 TraesCS3D01G269200 chr3D 98.039 51 0 1 1998 2048 438779089 438779138 1.470000e-13 87.9
4 TraesCS3D01G269200 chr3B 90.949 1845 127 16 573 2410 487558735 487556924 0.000000e+00 2446.0
5 TraesCS3D01G269200 chr3B 86.770 514 53 12 1 502 666617176 666616666 2.590000e-155 558.0
6 TraesCS3D01G269200 chr3B 91.709 398 23 3 2402 2793 487555287 487554894 7.260000e-151 544.0
7 TraesCS3D01G269200 chr3B 84.916 358 46 8 160 513 248577256 248577609 3.650000e-94 355.0
8 TraesCS3D01G269200 chr3B 84.637 358 47 8 160 513 248243157 248243510 1.700000e-92 350.0
9 TraesCS3D01G269200 chr3B 95.614 114 5 0 2865 2978 487554439 487554326 1.820000e-42 183.0
10 TraesCS3D01G269200 chr3B 98.039 51 1 0 1998 2048 563536538 563536488 4.090000e-14 89.8
11 TraesCS3D01G269200 chr3A 92.800 1500 88 9 651 2146 495569999 495568516 0.000000e+00 2154.0
12 TraesCS3D01G269200 chr3A 91.929 731 38 10 2138 2867 495555376 495554666 0.000000e+00 1003.0
13 TraesCS3D01G269200 chr3A 96.491 114 4 0 2865 2978 495554234 495554121 3.920000e-44 189.0
14 TraesCS3D01G269200 chr3A 87.261 157 17 2 2147 2300 500524980 500525136 3.050000e-40 176.0
15 TraesCS3D01G269200 chr3A 96.907 97 3 0 573 669 495570113 495570017 2.380000e-36 163.0
16 TraesCS3D01G269200 chr1D 82.877 438 48 19 67 498 242533315 242533731 4.690000e-98 368.0
17 TraesCS3D01G269200 chr1D 98.039 51 1 0 1998 2048 356186834 356186784 4.090000e-14 89.8
18 TraesCS3D01G269200 chr7D 85.393 178 22 3 2137 2311 264761831 264761655 6.560000e-42 182.0
19 TraesCS3D01G269200 chr7D 87.261 157 17 2 2147 2300 566026575 566026731 3.050000e-40 176.0
20 TraesCS3D01G269200 chr7D 98.039 51 1 0 1998 2048 287590805 287590855 4.090000e-14 89.8
21 TraesCS3D01G269200 chr6A 89.655 145 12 2 2147 2288 112005010 112005154 6.560000e-42 182.0
22 TraesCS3D01G269200 chr5D 87.898 157 16 2 2147 2300 461072763 461072607 6.560000e-42 182.0
23 TraesCS3D01G269200 chr2B 87.500 160 10 8 2147 2300 540431250 540431405 3.050000e-40 176.0
24 TraesCS3D01G269200 chr2B 79.904 209 25 11 22 217 734915176 734914972 1.440000e-28 137.0
25 TraesCS3D01G269200 chr2B 79.126 206 26 11 22 214 691768785 691768986 3.120000e-25 126.0
26 TraesCS3D01G269200 chr2B 83.333 114 17 2 2866 2978 20365066 20365178 1.460000e-18 104.0
27 TraesCS3D01G269200 chr4D 86.792 159 18 2 2147 2302 75266748 75266906 1.100000e-39 174.0
28 TraesCS3D01G269200 chr4D 98.077 52 0 1 1998 2048 347844272 347844323 4.090000e-14 89.8
29 TraesCS3D01G269200 chr7A 80.349 229 31 9 1 217 8230639 8230413 8.540000e-36 161.0
30 TraesCS3D01G269200 chr7B 81.188 202 22 11 24 213 693394644 693394841 6.650000e-32 148.0
31 TraesCS3D01G269200 chr7B 81.188 202 22 11 24 213 698931327 698931524 6.650000e-32 148.0
32 TraesCS3D01G269200 chr7B 78.191 188 29 11 67 248 693394650 693394831 3.140000e-20 110.0
33 TraesCS3D01G269200 chr1B 79.310 203 24 14 95 283 483140099 483139901 3.120000e-25 126.0
34 TraesCS3D01G269200 chr2A 84.348 115 14 4 2866 2978 14471108 14470996 3.140000e-20 110.0
35 TraesCS3D01G269200 chr6D 98.039 51 1 0 1998 2048 40569710 40569760 4.090000e-14 89.8
36 TraesCS3D01G269200 chr5A 97.561 41 1 0 898 938 493398757 493398797 1.480000e-08 71.3


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 TraesCS3D01G269200 chr3D 373841996 373844973 2977 True 5500.000000 5500 100.000000 1 2978 1 chr3D.!!$R2 2977
1 TraesCS3D01G269200 chr3B 487554326 487558735 4409 True 1057.666667 2446 92.757333 573 2978 3 chr3B.!!$R3 2405
2 TraesCS3D01G269200 chr3B 666616666 666617176 510 True 558.000000 558 86.770000 1 502 1 chr3B.!!$R2 501
3 TraesCS3D01G269200 chr3A 495568516 495570113 1597 True 1158.500000 2154 94.853500 573 2146 2 chr3A.!!$R2 1573
4 TraesCS3D01G269200 chr3A 495554121 495555376 1255 True 596.000000 1003 94.210000 2138 2978 2 chr3A.!!$R1 840

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
541 554 0.247736 CTGACGCTTAAGGCTCTGGT 59.752 55.0 4.29 0.0 39.13 4.00 F
1027 1078 0.463654 GTCATGCCCAGTATCCGCAA 60.464 55.0 0.00 0.0 35.85 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1492 1543 0.44899 GCATGCGCAGTTGAAGATGA 59.551 50.0 18.32 0.0 38.36 2.92 R
2544 4251 1.08992 CGCATTCAAGGGAAGTCTGG 58.910 55.0 0.00 0.0 36.25 3.86 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
194 204 1.981256 ACACGGTGAGCATTTCCTTT 58.019 45.000 16.29 0.00 0.00 3.11
195 205 3.134574 ACACGGTGAGCATTTCCTTTA 57.865 42.857 16.29 0.00 0.00 1.85
196 206 3.686016 ACACGGTGAGCATTTCCTTTAT 58.314 40.909 16.29 0.00 0.00 1.40
197 207 4.839121 ACACGGTGAGCATTTCCTTTATA 58.161 39.130 16.29 0.00 0.00 0.98
198 208 5.437060 ACACGGTGAGCATTTCCTTTATAT 58.563 37.500 16.29 0.00 0.00 0.86
199 209 6.588204 ACACGGTGAGCATTTCCTTTATATA 58.412 36.000 16.29 0.00 0.00 0.86
200 210 6.482308 ACACGGTGAGCATTTCCTTTATATAC 59.518 38.462 16.29 0.00 0.00 1.47
359 371 4.956075 ACCTGAAACACAAAACTGGAAGAT 59.044 37.500 0.00 0.00 37.43 2.40
380 393 2.282180 GGGAAAACCCGAGCAGCA 60.282 61.111 0.00 0.00 35.07 4.41
385 398 0.886490 AAAACCCGAGCAGCAGACAG 60.886 55.000 0.00 0.00 0.00 3.51
446 459 3.077519 GCCTACGTCACTCCGCCAT 62.078 63.158 0.00 0.00 0.00 4.40
461 474 1.672881 CGCCATGGAGGAAATCTTCAC 59.327 52.381 18.40 0.00 41.22 3.18
502 515 2.288025 ACACGGGCGTCCAATAGGT 61.288 57.895 6.96 0.00 35.89 3.08
503 516 0.971959 ACACGGGCGTCCAATAGGTA 60.972 55.000 6.96 0.00 35.89 3.08
504 517 0.249322 CACGGGCGTCCAATAGGTAG 60.249 60.000 6.96 0.00 35.89 3.18
505 518 1.366366 CGGGCGTCCAATAGGTAGG 59.634 63.158 6.96 0.00 35.89 3.18
506 519 1.111116 CGGGCGTCCAATAGGTAGGA 61.111 60.000 6.96 0.00 35.89 2.94
507 520 1.349067 GGGCGTCCAATAGGTAGGAT 58.651 55.000 0.00 0.00 36.11 3.24
508 521 1.697982 GGGCGTCCAATAGGTAGGATT 59.302 52.381 0.00 0.00 36.11 3.01
509 522 2.289506 GGGCGTCCAATAGGTAGGATTC 60.290 54.545 0.00 0.00 36.11 2.52
510 523 2.609737 GGCGTCCAATAGGTAGGATTCG 60.610 54.545 0.00 0.00 36.11 3.34
511 524 2.673833 CGTCCAATAGGTAGGATTCGC 58.326 52.381 0.00 0.00 36.11 4.70
512 525 2.609737 CGTCCAATAGGTAGGATTCGCC 60.610 54.545 0.00 0.00 36.11 5.54
513 526 1.975680 TCCAATAGGTAGGATTCGCCC 59.024 52.381 0.00 0.00 34.70 6.13
514 527 1.978580 CCAATAGGTAGGATTCGCCCT 59.021 52.381 0.00 0.00 40.29 5.19
515 528 2.028020 CCAATAGGTAGGATTCGCCCTC 60.028 54.545 0.00 0.00 37.74 4.30
516 529 1.939980 ATAGGTAGGATTCGCCCTCC 58.060 55.000 0.00 0.00 37.74 4.30
517 530 0.858369 TAGGTAGGATTCGCCCTCCT 59.142 55.000 5.71 5.71 45.22 3.69
518 531 0.470268 AGGTAGGATTCGCCCTCCTC 60.470 60.000 3.86 0.00 42.25 3.71
519 532 0.470268 GGTAGGATTCGCCCTCCTCT 60.470 60.000 3.86 0.00 42.25 3.69
520 533 0.676736 GTAGGATTCGCCCTCCTCTG 59.323 60.000 3.86 0.00 42.25 3.35
521 534 1.115930 TAGGATTCGCCCTCCTCTGC 61.116 60.000 3.86 0.00 42.25 4.26
522 535 2.110006 GATTCGCCCTCCTCTGCC 59.890 66.667 0.00 0.00 0.00 4.85
523 536 2.366167 ATTCGCCCTCCTCTGCCT 60.366 61.111 0.00 0.00 0.00 4.75
524 537 2.657102 GATTCGCCCTCCTCTGCCTG 62.657 65.000 0.00 0.00 0.00 4.85
525 538 3.905153 TTCGCCCTCCTCTGCCTGA 62.905 63.158 0.00 0.00 0.00 3.86
526 539 4.154347 CGCCCTCCTCTGCCTGAC 62.154 72.222 0.00 0.00 0.00 3.51
527 540 4.154347 GCCCTCCTCTGCCTGACG 62.154 72.222 0.00 0.00 0.00 4.35
528 541 4.154347 CCCTCCTCTGCCTGACGC 62.154 72.222 0.00 0.00 38.31 5.19
529 542 3.073735 CCTCCTCTGCCTGACGCT 61.074 66.667 0.00 0.00 38.78 5.07
530 543 2.654079 CCTCCTCTGCCTGACGCTT 61.654 63.158 0.00 0.00 38.78 4.68
531 544 1.323271 CCTCCTCTGCCTGACGCTTA 61.323 60.000 0.00 0.00 38.78 3.09
532 545 0.532573 CTCCTCTGCCTGACGCTTAA 59.467 55.000 0.00 0.00 38.78 1.85
533 546 0.532573 TCCTCTGCCTGACGCTTAAG 59.467 55.000 0.00 0.00 38.78 1.85
534 547 0.460987 CCTCTGCCTGACGCTTAAGG 60.461 60.000 4.29 0.00 38.78 2.69
539 552 3.056628 CCTGACGCTTAAGGCTCTG 57.943 57.895 4.29 2.03 39.13 3.35
540 553 0.460987 CCTGACGCTTAAGGCTCTGG 60.461 60.000 4.29 6.35 39.13 3.86
541 554 0.247736 CTGACGCTTAAGGCTCTGGT 59.752 55.000 4.29 0.00 39.13 4.00
542 555 1.476891 CTGACGCTTAAGGCTCTGGTA 59.523 52.381 4.29 0.00 39.13 3.25
543 556 1.897133 TGACGCTTAAGGCTCTGGTAA 59.103 47.619 4.29 0.00 39.13 2.85
544 557 2.094182 TGACGCTTAAGGCTCTGGTAAG 60.094 50.000 4.29 0.00 39.13 2.34
545 558 1.207329 ACGCTTAAGGCTCTGGTAAGG 59.793 52.381 4.29 0.43 39.13 2.69
546 559 1.480954 CGCTTAAGGCTCTGGTAAGGA 59.519 52.381 4.29 0.00 39.13 3.36
547 560 2.482142 CGCTTAAGGCTCTGGTAAGGAG 60.482 54.545 4.29 0.00 39.13 3.69
548 561 2.158885 GCTTAAGGCTCTGGTAAGGAGG 60.159 54.545 4.29 0.00 38.06 4.30
549 562 2.942604 TAAGGCTCTGGTAAGGAGGT 57.057 50.000 0.00 0.00 0.00 3.85
550 563 1.574263 AAGGCTCTGGTAAGGAGGTC 58.426 55.000 0.00 0.00 0.00 3.85
551 564 0.713579 AGGCTCTGGTAAGGAGGTCT 59.286 55.000 0.00 0.00 0.00 3.85
552 565 1.116308 GGCTCTGGTAAGGAGGTCTC 58.884 60.000 0.00 0.00 0.00 3.36
553 566 1.619977 GGCTCTGGTAAGGAGGTCTCA 60.620 57.143 0.14 0.00 0.00 3.27
554 567 1.478916 GCTCTGGTAAGGAGGTCTCAC 59.521 57.143 0.14 0.00 0.00 3.51
555 568 2.808919 CTCTGGTAAGGAGGTCTCACA 58.191 52.381 0.14 0.00 0.00 3.58
556 569 3.370104 CTCTGGTAAGGAGGTCTCACAT 58.630 50.000 0.14 0.00 0.00 3.21
557 570 4.537751 CTCTGGTAAGGAGGTCTCACATA 58.462 47.826 0.14 0.00 0.00 2.29
558 571 5.144100 CTCTGGTAAGGAGGTCTCACATAT 58.856 45.833 0.14 0.00 0.00 1.78
559 572 5.529289 TCTGGTAAGGAGGTCTCACATATT 58.471 41.667 0.14 0.00 0.00 1.28
560 573 6.679542 TCTGGTAAGGAGGTCTCACATATTA 58.320 40.000 0.14 0.00 0.00 0.98
561 574 6.778069 TCTGGTAAGGAGGTCTCACATATTAG 59.222 42.308 0.14 0.00 0.00 1.73
562 575 5.839063 TGGTAAGGAGGTCTCACATATTAGG 59.161 44.000 0.14 0.00 0.00 2.69
563 576 5.246429 GGTAAGGAGGTCTCACATATTAGGG 59.754 48.000 0.14 0.00 0.00 3.53
564 577 3.863086 AGGAGGTCTCACATATTAGGGG 58.137 50.000 0.14 0.00 0.00 4.79
565 578 2.303311 GGAGGTCTCACATATTAGGGGC 59.697 54.545 0.14 0.00 0.00 5.80
566 579 2.303311 GAGGTCTCACATATTAGGGGCC 59.697 54.545 0.00 0.00 0.00 5.80
567 580 2.054799 GGTCTCACATATTAGGGGCCA 58.945 52.381 4.39 0.00 0.00 5.36
568 581 2.644798 GGTCTCACATATTAGGGGCCAT 59.355 50.000 4.39 0.00 0.00 4.40
569 582 3.844211 GGTCTCACATATTAGGGGCCATA 59.156 47.826 4.39 0.00 0.00 2.74
570 583 4.288626 GGTCTCACATATTAGGGGCCATAA 59.711 45.833 13.68 13.68 0.00 1.90
571 584 5.044846 GGTCTCACATATTAGGGGCCATAAT 60.045 44.000 24.96 24.96 0.00 1.28
675 724 4.473477 AAAGTGTGGCAGATAGGAGTAC 57.527 45.455 0.00 0.00 0.00 2.73
694 745 3.409026 ACAGAGGTGACTGATTTGGAC 57.591 47.619 0.00 0.00 44.43 4.02
756 807 5.822519 CCATTTGGATTCTAACTCCGAATCA 59.177 40.000 12.96 0.16 45.32 2.57
783 834 3.423154 GAAACCTGACCGCCAGCG 61.423 66.667 4.75 4.75 41.57 5.18
825 876 1.084370 GTGGAGCCAGAACCGATTCG 61.084 60.000 0.00 0.00 40.04 3.34
843 894 2.076803 GGGAGCCCGGGACCTATTT 61.077 63.158 29.31 0.00 0.00 1.40
850 901 2.583143 CCCGGGACCTATTTTGATTCC 58.417 52.381 18.48 0.00 0.00 3.01
944 995 2.907910 ACAATTTCGCTCATGTGCTC 57.092 45.000 16.99 0.00 0.00 4.26
994 1045 4.353437 GCCAGTCGTCGTCGGGTT 62.353 66.667 9.94 0.00 37.69 4.11
1027 1078 0.463654 GTCATGCCCAGTATCCGCAA 60.464 55.000 0.00 0.00 35.85 4.85
1030 1081 2.516225 GCCCAGTATCCGCAACCC 60.516 66.667 0.00 0.00 0.00 4.11
1165 1216 1.528129 CCTCACTGGCAAGTTTCTCC 58.472 55.000 0.00 0.00 32.98 3.71
1184 1235 2.355837 GGCAAGCGACGACAGTGA 60.356 61.111 0.00 0.00 0.00 3.41
1373 1424 1.860676 GTCTACAAGCACAACGGTCA 58.139 50.000 0.00 0.00 0.00 4.02
1538 1589 0.388659 GAGGCTGCTGATGACGAGAT 59.611 55.000 0.00 0.00 0.00 2.75
1561 1612 2.991866 GGAGGTAAAAGGAAGAACGACG 59.008 50.000 0.00 0.00 0.00 5.12
1578 1629 2.330372 CGACCAGAGTCCCGACGAA 61.330 63.158 0.00 0.00 40.12 3.85
1618 1669 2.942376 CGTTGTTGCCATAATCTGCCTA 59.058 45.455 0.00 0.00 0.00 3.93
1708 1759 1.289066 CCGTCGACTTCAGCTCCAA 59.711 57.895 14.70 0.00 0.00 3.53
1720 1771 1.443872 GCTCCAACGTCGTCGATGT 60.444 57.895 14.33 14.33 37.99 3.06
1730 1781 2.391821 GTCGATGTTGCAGTCGCG 59.608 61.111 0.00 0.00 42.97 5.87
1748 1799 1.749033 GGCGGGAGAGGTTATCCTG 59.251 63.158 0.00 0.00 45.24 3.86
1990 2041 3.445857 GTCGCCTGATTTGTACTACCTC 58.554 50.000 0.00 0.00 0.00 3.85
1991 2042 3.130693 GTCGCCTGATTTGTACTACCTCT 59.869 47.826 0.00 0.00 0.00 3.69
1992 2043 4.337555 GTCGCCTGATTTGTACTACCTCTA 59.662 45.833 0.00 0.00 0.00 2.43
1995 2046 6.071221 TCGCCTGATTTGTACTACCTCTAAAA 60.071 38.462 0.00 0.00 0.00 1.52
1996 2047 6.035758 CGCCTGATTTGTACTACCTCTAAAAC 59.964 42.308 0.00 0.00 0.00 2.43
2044 2105 2.327200 GCTACCCGCTTATTCCAAGT 57.673 50.000 0.00 0.00 35.14 3.16
2056 2117 6.178324 GCTTATTCCAAGTGGTTACTACCTT 58.822 40.000 0.00 0.00 45.27 3.50
2089 2150 1.896220 AGATGTTTCGCTTTCTGCCA 58.104 45.000 0.00 0.00 38.78 4.92
2133 2194 4.384098 CCCTCTTTTGGGTTTTTGCTTCTT 60.384 41.667 0.00 0.00 42.25 2.52
2146 2207 7.304735 GTTTTTGCTTCTTGGTTTTTGTCATT 58.695 30.769 0.00 0.00 0.00 2.57
2165 2226 5.579904 GTCATTACTCCCTCCGTTTCTAAAC 59.420 44.000 0.00 0.00 35.59 2.01
2203 2265 8.367660 AGAGATTTCAACAAGGACTACTATGA 57.632 34.615 0.00 0.00 0.00 2.15
2206 2268 9.965902 AGATTTCAACAAGGACTACTATGAATT 57.034 29.630 0.00 0.00 31.04 2.17
2435 4142 1.561643 CTAGACCCAGCTCCAACTGA 58.438 55.000 0.00 0.00 40.25 3.41
2470 4177 3.441496 AACTGCAACTGACAAACATGG 57.559 42.857 0.00 0.00 0.00 3.66
2518 4225 7.138736 CCGAACATTACAACTGAGTTCAAATT 58.861 34.615 0.00 0.00 38.71 1.82
2544 4251 3.978718 GCCATAAGCATCCTGAAAGAC 57.021 47.619 0.00 0.00 42.97 3.01
2562 4269 2.087646 GACCAGACTTCCCTTGAATGC 58.912 52.381 0.00 0.00 0.00 3.56
2585 4292 5.111293 CGCCTTCATTGGATTTGCTATTTT 58.889 37.500 0.00 0.00 0.00 1.82
2618 4325 3.601443 AAGGAACATCTTCACTCCGAG 57.399 47.619 0.00 0.00 32.91 4.63
2675 4382 2.203280 TGGTCCAGCCAAACCACG 60.203 61.111 0.00 0.00 45.94 4.94
2696 4403 4.222114 CGAGACAGTCTTGGAAATTTTGC 58.778 43.478 9.81 0.00 0.00 3.68
2793 4506 5.131067 ACCTCTCTCCAGTAAACCAAAAAC 58.869 41.667 0.00 0.00 0.00 2.43
2824 4537 6.421892 ACCCCTACCTATATAATCCCGTAA 57.578 41.667 0.00 0.00 0.00 3.18
2868 5015 8.963725 GGGTTGCTATTACTTTTAAATACTGGT 58.036 33.333 0.00 0.00 0.00 4.00
2931 5078 1.226407 CGATGCAAGAGTCGAGCGA 60.226 57.895 1.16 0.00 40.11 4.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
157 166 9.995957 TCACCGTGTATTAATAAATGTTCAATG 57.004 29.630 0.00 0.00 0.00 2.82
169 178 5.437060 AGGAAATGCTCACCGTGTATTAAT 58.563 37.500 0.00 0.00 0.00 1.40
176 186 6.346598 CGTATATAAAGGAAATGCTCACCGTG 60.347 42.308 0.00 0.00 0.00 4.94
179 189 7.602644 TCATCGTATATAAAGGAAATGCTCACC 59.397 37.037 0.00 0.00 0.00 4.02
180 190 8.534333 TCATCGTATATAAAGGAAATGCTCAC 57.466 34.615 0.00 0.00 0.00 3.51
213 224 2.315925 AGAGTTCACCGTGCCATATG 57.684 50.000 0.00 0.00 0.00 1.78
214 225 3.009723 CAAAGAGTTCACCGTGCCATAT 58.990 45.455 0.00 0.00 0.00 1.78
217 228 0.107410 ACAAAGAGTTCACCGTGCCA 60.107 50.000 0.00 0.00 0.00 4.92
219 230 5.796350 ATTATACAAAGAGTTCACCGTGC 57.204 39.130 0.00 0.00 0.00 5.34
271 282 6.434018 TTTTTCTTCCGGTTTTTCGTTCTA 57.566 33.333 0.00 0.00 0.00 2.10
339 351 6.040391 CCCTTATCTTCCAGTTTTGTGTTTCA 59.960 38.462 0.00 0.00 0.00 2.69
340 352 6.447162 CCCTTATCTTCCAGTTTTGTGTTTC 58.553 40.000 0.00 0.00 0.00 2.78
380 393 3.531538 TGTTCTTTTTCAGTCGCTGTCT 58.468 40.909 6.72 0.00 32.61 3.41
385 398 3.038710 CTGCTTGTTCTTTTTCAGTCGC 58.961 45.455 0.00 0.00 0.00 5.19
426 439 4.849329 GCGGAGTGACGTAGGCCG 62.849 72.222 12.52 12.52 44.47 6.13
429 442 1.226974 CATGGCGGAGTGACGTAGG 60.227 63.158 0.00 0.00 35.98 3.18
431 444 1.679641 TCCATGGCGGAGTGACGTA 60.680 57.895 6.96 0.00 39.64 3.57
446 459 2.615493 GCTTCGGTGAAGATTTCCTCCA 60.615 50.000 10.58 0.00 41.71 3.86
504 517 2.110006 GCAGAGGAGGGCGAATCC 59.890 66.667 0.00 0.00 37.07 3.01
505 518 2.110006 GGCAGAGGAGGGCGAATC 59.890 66.667 0.00 0.00 0.00 2.52
506 519 2.366167 AGGCAGAGGAGGGCGAAT 60.366 61.111 0.00 0.00 35.71 3.34
507 520 3.393970 CAGGCAGAGGAGGGCGAA 61.394 66.667 0.00 0.00 35.71 4.70
508 521 4.382541 TCAGGCAGAGGAGGGCGA 62.383 66.667 0.00 0.00 35.71 5.54
509 522 4.154347 GTCAGGCAGAGGAGGGCG 62.154 72.222 0.00 0.00 35.71 6.13
510 523 4.154347 CGTCAGGCAGAGGAGGGC 62.154 72.222 0.00 0.00 34.03 5.19
511 524 4.154347 GCGTCAGGCAGAGGAGGG 62.154 72.222 3.64 0.00 42.87 4.30
527 540 2.158885 CCTCCTTACCAGAGCCTTAAGC 60.159 54.545 0.00 0.00 44.25 3.09
528 541 3.108376 ACCTCCTTACCAGAGCCTTAAG 58.892 50.000 0.00 0.00 0.00 1.85
529 542 3.105283 GACCTCCTTACCAGAGCCTTAA 58.895 50.000 0.00 0.00 0.00 1.85
530 543 2.315155 AGACCTCCTTACCAGAGCCTTA 59.685 50.000 0.00 0.00 0.00 2.69
531 544 1.079658 AGACCTCCTTACCAGAGCCTT 59.920 52.381 0.00 0.00 0.00 4.35
532 545 0.713579 AGACCTCCTTACCAGAGCCT 59.286 55.000 0.00 0.00 0.00 4.58
533 546 1.116308 GAGACCTCCTTACCAGAGCC 58.884 60.000 0.00 0.00 0.00 4.70
534 547 1.478916 GTGAGACCTCCTTACCAGAGC 59.521 57.143 0.00 0.00 0.00 4.09
535 548 2.808919 TGTGAGACCTCCTTACCAGAG 58.191 52.381 0.00 0.00 30.96 3.35
536 549 2.992847 TGTGAGACCTCCTTACCAGA 57.007 50.000 0.00 0.00 30.96 3.86
537 550 5.878406 AATATGTGAGACCTCCTTACCAG 57.122 43.478 0.00 0.00 30.96 4.00
538 551 5.839063 CCTAATATGTGAGACCTCCTTACCA 59.161 44.000 0.00 0.00 30.96 3.25
539 552 5.246429 CCCTAATATGTGAGACCTCCTTACC 59.754 48.000 0.00 0.00 30.96 2.85
540 553 5.246429 CCCCTAATATGTGAGACCTCCTTAC 59.754 48.000 0.00 0.00 32.50 2.34
541 554 5.403512 CCCCTAATATGTGAGACCTCCTTA 58.596 45.833 0.00 0.00 0.00 2.69
542 555 4.235372 CCCCTAATATGTGAGACCTCCTT 58.765 47.826 0.00 0.00 0.00 3.36
543 556 3.863086 CCCCTAATATGTGAGACCTCCT 58.137 50.000 0.00 0.00 0.00 3.69
544 557 2.303311 GCCCCTAATATGTGAGACCTCC 59.697 54.545 0.00 0.00 0.00 4.30
545 558 2.303311 GGCCCCTAATATGTGAGACCTC 59.697 54.545 0.00 0.00 0.00 3.85
546 559 2.339769 GGCCCCTAATATGTGAGACCT 58.660 52.381 0.00 0.00 0.00 3.85
547 560 2.054799 TGGCCCCTAATATGTGAGACC 58.945 52.381 0.00 0.00 0.00 3.85
548 561 5.499004 TTATGGCCCCTAATATGTGAGAC 57.501 43.478 0.00 0.00 0.00 3.36
549 562 9.514093 TTATATTATGGCCCCTAATATGTGAGA 57.486 33.333 24.57 11.26 34.88 3.27
551 564 9.914834 GTTTATATTATGGCCCCTAATATGTGA 57.085 33.333 24.57 14.52 34.88 3.58
552 565 9.920946 AGTTTATATTATGGCCCCTAATATGTG 57.079 33.333 24.57 0.00 34.88 3.21
556 569 8.272173 GCTGAGTTTATATTATGGCCCCTAATA 58.728 37.037 14.11 14.11 0.00 0.98
557 570 7.119387 GCTGAGTTTATATTATGGCCCCTAAT 58.881 38.462 0.00 6.60 0.00 1.73
558 571 6.044989 TGCTGAGTTTATATTATGGCCCCTAA 59.955 38.462 0.00 0.00 0.00 2.69
559 572 5.550011 TGCTGAGTTTATATTATGGCCCCTA 59.450 40.000 0.00 0.00 0.00 3.53
560 573 4.353788 TGCTGAGTTTATATTATGGCCCCT 59.646 41.667 0.00 0.00 0.00 4.79
561 574 4.662278 TGCTGAGTTTATATTATGGCCCC 58.338 43.478 0.00 0.00 0.00 5.80
562 575 5.335976 GCTTGCTGAGTTTATATTATGGCCC 60.336 44.000 0.00 0.00 0.00 5.80
563 576 5.241506 TGCTTGCTGAGTTTATATTATGGCC 59.758 40.000 0.00 0.00 0.00 5.36
564 577 6.205464 TCTGCTTGCTGAGTTTATATTATGGC 59.795 38.462 0.00 0.00 0.00 4.40
565 578 7.443575 AGTCTGCTTGCTGAGTTTATATTATGG 59.556 37.037 2.48 0.00 0.00 2.74
566 579 8.375608 AGTCTGCTTGCTGAGTTTATATTATG 57.624 34.615 2.48 0.00 0.00 1.90
567 580 8.206867 TGAGTCTGCTTGCTGAGTTTATATTAT 58.793 33.333 10.37 0.00 0.00 1.28
568 581 7.555965 TGAGTCTGCTTGCTGAGTTTATATTA 58.444 34.615 10.37 0.00 0.00 0.98
569 582 6.409704 TGAGTCTGCTTGCTGAGTTTATATT 58.590 36.000 10.37 0.00 0.00 1.28
570 583 5.982356 TGAGTCTGCTTGCTGAGTTTATAT 58.018 37.500 10.37 0.00 0.00 0.86
571 584 5.405935 TGAGTCTGCTTGCTGAGTTTATA 57.594 39.130 10.37 0.00 0.00 0.98
675 724 3.594134 GAGTCCAAATCAGTCACCTCTG 58.406 50.000 0.00 0.00 36.85 3.35
694 745 0.807667 CAAGGTTCGCATCGGAGGAG 60.808 60.000 0.00 0.00 0.00 3.69
756 807 2.978010 CAGGTTTCCGTTGCCGCT 60.978 61.111 0.00 0.00 0.00 5.52
783 834 1.229975 GCAAGGTTGGCAATTGCACC 61.230 55.000 30.32 27.54 46.64 5.01
825 876 1.642513 AAAATAGGTCCCGGGCTCCC 61.643 60.000 24.48 19.58 0.00 4.30
843 894 3.938963 GCTGATCCGTAGTTTGGAATCAA 59.061 43.478 0.00 0.00 39.39 2.57
850 901 0.739462 TGCCGCTGATCCGTAGTTTG 60.739 55.000 0.00 0.00 0.00 2.93
994 1045 0.880441 CATGACGTGGCCATGACAAA 59.120 50.000 31.74 10.84 42.89 2.83
1027 1078 2.058595 CGGAAGGATGACGAGGGGT 61.059 63.158 0.00 0.00 0.00 4.95
1030 1081 0.179108 GGTTCGGAAGGATGACGAGG 60.179 60.000 0.00 0.00 37.95 4.63
1152 1203 2.282180 GCCGGGAGAAACTTGCCA 60.282 61.111 2.18 0.00 0.00 4.92
1373 1424 2.284405 ACCCAGTCCGGATCCGTT 60.284 61.111 31.22 14.67 36.56 4.44
1455 1506 6.096141 TGAAGTAAATTTTGCACAAGACCAGA 59.904 34.615 0.00 0.00 0.00 3.86
1492 1543 0.448990 GCATGCGCAGTTGAAGATGA 59.551 50.000 18.32 0.00 38.36 2.92
1517 1568 0.528033 CTCGTCATCAGCAGCCTCTG 60.528 60.000 0.00 0.00 35.46 3.35
1520 1571 0.829333 AATCTCGTCATCAGCAGCCT 59.171 50.000 0.00 0.00 0.00 4.58
1533 1584 5.086104 TCTTCCTTTTACCTCCAATCTCG 57.914 43.478 0.00 0.00 0.00 4.04
1538 1589 4.383173 GTCGTTCTTCCTTTTACCTCCAA 58.617 43.478 0.00 0.00 0.00 3.53
1561 1612 1.507174 CTTCGTCGGGACTCTGGTC 59.493 63.158 0.00 0.00 41.43 4.02
1578 1629 0.610687 GCTGTCTTACTGGAGGTGCT 59.389 55.000 0.00 0.00 0.00 4.40
1708 1759 1.002250 GACTGCAACATCGACGACGT 61.002 55.000 0.00 0.00 40.69 4.34
1730 1781 1.049289 ACAGGATAACCTCTCCCGCC 61.049 60.000 0.00 0.00 45.94 6.13
1822 1873 1.303091 ACGAAATAAGGTGGCGCCAC 61.303 55.000 44.64 44.64 45.49 5.01
2030 2091 3.606687 AGTAACCACTTGGAATAAGCGG 58.393 45.455 1.14 0.00 38.94 5.52
2056 2117 5.396484 CGAAACATCTTCGTCCTAGTTACA 58.604 41.667 0.00 0.00 37.18 2.41
2133 2194 4.403734 GGAGGGAGTAATGACAAAAACCA 58.596 43.478 0.00 0.00 0.00 3.67
2146 2207 6.608405 TCATATGTTTAGAAACGGAGGGAGTA 59.392 38.462 1.90 0.00 41.74 2.59
2294 2356 4.684724 ACACCTGTCTAGTATTTCCTCCA 58.315 43.478 0.00 0.00 0.00 3.86
2518 4225 3.966979 TCAGGATGCTTATGGCTTTCAA 58.033 40.909 0.00 0.00 42.39 2.69
2544 4251 1.089920 CGCATTCAAGGGAAGTCTGG 58.910 55.000 0.00 0.00 36.25 3.86
2562 4269 3.996150 ATAGCAAATCCAATGAAGGCG 57.004 42.857 0.00 0.00 0.00 5.52
2597 4304 3.325135 ACTCGGAGTGAAGATGTTCCTTT 59.675 43.478 10.41 0.00 0.00 3.11
2598 4305 2.900546 ACTCGGAGTGAAGATGTTCCTT 59.099 45.455 10.41 0.00 0.00 3.36
2618 4325 4.454504 TCTTTTCGAATCAGTTGGCCTAAC 59.545 41.667 3.32 7.14 39.65 2.34
2675 4382 5.009010 TGAGCAAAATTTCCAAGACTGTCTC 59.991 40.000 11.31 0.00 0.00 3.36
2815 4528 4.872124 GTGGAATTTACTCGTTACGGGATT 59.128 41.667 12.99 0.00 0.00 3.01
2824 4537 4.028993 ACCCATTGTGGAATTTACTCGT 57.971 40.909 0.00 0.00 40.96 4.18
2868 5015 2.614331 TTCCCAATACCCCCGGCA 60.614 61.111 0.00 0.00 0.00 5.69


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

AutoCloner maintained by Alex Coulton.