Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015317.1 Kokia drynarioides strain JFW-HI SEQ_130362, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 666550
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 474 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:461465 original size:25 final size:26
Alignment explanation
Indices: 461431--461490 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
461421 TTCTCATCCA
* *
461431 AATTATACC-TCAGTAAAATTTTGAC
1 AATTTTACCTTCAATAAAATTTTGAC
*
461456 AATTTTACCTTTAATAAAATTTTGAC
1 AATTTTACCTTCAATAAAATTTTGAC
* *
461482 GATATTACC
1 AATTTTACC
461491 CCCTATAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
25 8 0.28
26 21 0.72
ACGTcount: A:0.38, C:0.15, G:0.07, T:0.40
Consensus pattern (26 bp):
AATTTTACCTTCAATAAAATTTTGAC
Found at i:461664 original size:6 final size:6
Alignment explanation
Indices: 461651--461697 Score: 58
Period size: 6 Copynumber: 7.8 Consensus size: 6
461641 AAAGTTTTCG
* ** *
461651 TTTCCA TTTTCA TTTTAA TTTTCA TTTCCA TTTCCA TTTCCA TTTCC
1 TTTCCA TTTCCA TTTCCA TTTCCA TTTCCA TTTCCA TTTCCA TTTCC
461698 GTTTTCGGAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.17, C:0.26, G:0.00, T:0.57
Consensus pattern (6 bp):
TTTCCA
Found at i:461683 original size:12 final size:12
Alignment explanation
Indices: 461645--461695 Score: 66
Period size: 12 Copynumber: 4.2 Consensus size: 12
461635 GGATTGAAAG
*
461645 TTTTCGTTTCCA
1 TTTTCATTTCCA
**
461657 TTTTCATTTTAA
1 TTTTCATTTCCA
461669 TTTTCATTTCCA
1 TTTTCATTTCCA
*
461681 TTTCCATTTCCA
1 TTTTCATTTCCA
461693 TTT
1 TTT
461696 CCGTTTTCGG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.16, C:0.22, G:0.02, T:0.61
Consensus pattern (12 bp):
TTTTCATTTCCA
Found at i:461689 original size:18 final size:18
Alignment explanation
Indices: 461645--461703 Score: 64
Period size: 18 Copynumber: 3.3 Consensus size: 18
461635 GGATTGAAAG
* *
461645 TTTTCGTTTCCATTTTCA
1 TTTTCATTTCCATTTCCA
* *
461663 TTTTAATTTTCATTTCCA
1 TTTTCATTTCCATTTCCA
* *
461681 TTTCCATTTCCATTTCCG
1 TTTTCATTTCCATTTCCA
461699 TTTTC
1 TTTTC
461704 GGAAACCTAC
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.14, C:0.24, G:0.03, T:0.59
Consensus pattern (18 bp):
TTTTCATTTCCATTTCCA
Found at i:465656 original size:19 final size:19
Alignment explanation
Indices: 465620--465658 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
465610 TATAACTAAC
* *
465620 TTAATTAATTAATTAAAAA
1 TTAATTAACTAATAAAAAA
*
465639 TTAATTAACTACTAAAAAA
1 TTAATTAACTAATAAAAAA
465658 T
1 T
465659 GGATGTGACA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (19 bp):
TTAATTAACTAATAAAAAA
Found at i:466007 original size:17 final size:18
Alignment explanation
Indices: 465980--466013 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
465970 ACCTTTGTAA
465980 GTATAGGTTTTAGATTCT
1 GTATAGGTTTTAGATTCT
*
465998 GTAT-GGTTTTCGATTC
1 GTATAGGTTTTAGATTC
466014 AGCTGTCGGC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.18, C:0.09, G:0.24, T:0.50
Consensus pattern (18 bp):
GTATAGGTTTTAGATTCT
Found at i:487320 original size:24 final size:24
Alignment explanation
Indices: 487291--487338 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
487281 TGTCATTGCA
*
487291 ATTTTTCTATTAATTT-TTGTCTTTT
1 ATTTTACT-TTAATTTGTT-TCTTTT
487316 ATTTTACTTTAATTTGTTTCTTT
1 ATTTTACTTTAATTTGTTTCTTT
487339 AGTTTTTGCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 12 0.57
25 9 0.43
ACGTcount: A:0.17, C:0.08, G:0.04, T:0.71
Consensus pattern (24 bp):
ATTTTACTTTAATTTGTTTCTTTT
Found at i:489601 original size:17 final size:17
Alignment explanation
Indices: 489554--489591 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
489544 TTTTCTCTAG
*
489554 TTGTCATTACATTTTAA
1 TTGTCACTACATTTTAA
*
489571 TTGTCACTGCATTTTAA
1 TTGTCACTACATTTTAA
489588 TTGT
1 TTGT
489592 TCTCACATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.24, C:0.13, G:0.11, T:0.53
Consensus pattern (17 bp):
TTGTCACTACATTTTAA
Found at i:497993 original size:27 final size:28
Alignment explanation
Indices: 497963--498022 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 28
497953 CATAAGCATT
*
497963 TCATACT-TAGTTTTTATAATTTCCAAC
1 TCATACTAGAGTTTTTATAATTTCCAAC
*
497990 TCATTGCTAGAGTTTTTATAATTTCCAAC
1 TCA-TACTAGAGTTTTTATAATTTCCAAC
498019 TCAT
1 TCAT
498023 TGCTAGTTAG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 3 0.10
28 4 0.14
29 22 0.76
ACGTcount: A:0.28, C:0.18, G:0.07, T:0.47
Consensus pattern (28 bp):
TCATACTAGAGTTTTTATAATTTCCAAC
Found at i:498004 original size:29 final size:29
Alignment explanation
Indices: 497971--498028 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
497961 TTTCATACTT
497971 AGTTTTTATAATTTCCAACTCATTGCTAG
1 AGTTTTTATAATTTCCAACTCATTGCTAG
498000 AGTTTTTATAATTTCCAACTCATTGCTAG
1 AGTTTTTATAATTTCCAACTCATTGCTAG
498029 TTAGTTTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.28, C:0.17, G:0.10, T:0.45
Consensus pattern (29 bp):
AGTTTTTATAATTTCCAACTCATTGCTAG
Found at i:502554 original size:19 final size:20
Alignment explanation
Indices: 502507--502554 Score: 50
Period size: 19 Copynumber: 2.5 Consensus size: 20
502497 TTGATAATTC
502507 TTAA-TATTA-AATTATAAA
1 TTAATTATTATAATTATAAA
*
502525 TTAAATT-TTATAATT-TATA
1 TT-AATTATTATAATTATAAA
502544 TTAATTATTAT
1 TTAATTATTAT
502555 CAAAAGTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
18 6 0.24
19 14 0.56
20 5 0.20
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TTAATTATTATAATTATAAA
Found at i:503317 original size:26 final size:26
Alignment explanation
Indices: 503261--503317 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
503251 TCATCTTCTA
*
503261 ATTTTAATTTATTTAATTTATTAACT
1 ATTTTAATTTATTTAAATTATTAACT
*
503287 -CTTTAATTTATTTTAAATTATTAA-T
1 ATTTTAATTTA-TTTAAATTATTAACT
503312 ATTTTA
1 ATTTTA
503318 TGCTAATTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
25 10 0.38
26 16 0.62
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (26 bp):
ATTTTAATTTATTTAAATTATTAACT
Found at i:506743 original size:12 final size:12
Alignment explanation
Indices: 506726--506750 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
506716 TGTTGTTATG
506726 ATGAATGCTATT
1 ATGAATGCTATT
506738 ATGAATGCTATT
1 ATGAATGCTATT
506750 A
1 A
506751 ATTATTTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.08, G:0.16, T:0.40
Consensus pattern (12 bp):
ATGAATGCTATT
Found at i:508799 original size:26 final size:28
Alignment explanation
Indices: 508763--508814 Score: 81
Period size: 26 Copynumber: 1.9 Consensus size: 28
508753 GTCTAGCCAG
508763 AAAAAGAAAAAT-AG-AGAAAAAAAATC
1 AAAAAGAAAAATGAGTAGAAAAAAAATC
*
508789 AAAAAGAAAAATGAGTAGAAACAAAA
1 AAAAAGAAAAATGAGTAGAAAAAAAA
508815 GAAGTATAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 12 0.52
27 2 0.09
28 9 0.39
ACGTcount: A:0.75, C:0.04, G:0.13, T:0.08
Consensus pattern (28 bp):
AAAAAGAAAAATGAGTAGAAAAAAAATC
Found at i:531770 original size:14 final size:15
Alignment explanation
Indices: 531746--531778 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
531736 AATTAATAGT
*
531746 TTTTAATATATAATA
1 TTTTAATATATAACA
531761 TTTT-ATATATAACA
1 TTTTAATATATAACA
531775 TTTT
1 TTTT
531779 TTTAATATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (15 bp):
TTTTAATATATAACA
Found at i:540306 original size:21 final size:21
Alignment explanation
Indices: 540282--540322 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
540272 GTATCAATAT
540282 GACATAAAA-TATCGATACTTA
1 GACA-AAAAGTATCGATACTTA
540303 GACAAAAAGTATCGATACTT
1 GACAAAAAGTATCGATACTT
540323 TTTGTGTTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.46, C:0.15, G:0.12, T:0.27
Consensus pattern (21 bp):
GACAAAAAGTATCGATACTTA
Found at i:542849 original size:23 final size:23
Alignment explanation
Indices: 542823--542867 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
542813 NNNNNNNNTA
542823 TTAAAACATAAT-TTATTATTATT
1 TTAAAA-ATAATATTATTATTATT
*
542846 TTAAAAATATTATTATTATTAT
1 TTAAAAATAATATTATTATTAT
542868 CAATATATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (23 bp):
TTAAAAATAATATTATTATTATT
Found at i:542875 original size:20 final size:20
Alignment explanation
Indices: 542835--542887 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
542825 AAAACATAAT
*
542835 TTATTATTATTTTAAAAATA
1 TTATTATTATTATAAAAATA
* *
542855 TTATTATTATTATCAATATA
1 TTATTATTATTATAAAAATA
*
542875 TTCATTGTTATTA
1 TT-ATTATTATTA
542888 AATAATCATT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 19 0.68
21 9 0.32
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.57
Consensus pattern (20 bp):
TTATTATTATTATAAAAATA
Found at i:542885 original size:18 final size:18
Alignment explanation
Indices: 542836--542873 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
542826 AAACATAATT
**
542836 TATTATTATT-TTAAAAA
1 TATTATTATTATTATCAA
542853 TATTATTATTATTATCAA
1 TATTATTATTATTATCAA
542871 TAT
1 TAT
542874 ATTCATTGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (18 bp):
TATTATTATTATTATCAA
Found at i:544858 original size:205 final size:206
Alignment explanation
Indices: 544506--544984 Score: 777
Period size: 205 Copynumber: 2.3 Consensus size: 206
544496 NNNNNNNNNN
* * *
544506 AGATTTGTTTACATCGAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGA
1 AGATTTGTTCACATCGAGCATGGGTTTAATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGA
*
544571 CCGCGTCGTTTGTTTCAATACGCTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTC
66 CCGCGTCGTTTGTTTCAATACGCTTCTCTGTATCTCATCAGGAAGACAAATTTGGTCCACTTCTC
*
544636 AGTATCTCATCAGGAAGCTAACC-TTTTATTGCTTCGACCTG-TCTCTCAGTGTCTCATCAGGAA
131 AGTATCTCATCAGGAAGCTAACCGTTTTATTGCTTCGACCTGCT-TCTCAGTGTCACATCAGGAA
544699 GCTGTGGTTCGA
195 GCTGTGGTTCGA
* *
544711 AGATTTGTTCACATCGAGCATGGATTTTATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGA
1 AGATTTGTTCACATCGAGCATGGGTTTAATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGA
*
544776 CCGCGTCGTTTGTTTCAATTCGCTTCTCTGTATCTCATCAGGAAGACAAATTTGGTCCA-TATCT
66 CCGCGTCGTTTGTTTCAATACGCTTCTCTGTATCTCATCAGGAAGACAAATTTGGTCCACT-TCT
* * *
544840 CTGTATCTCATCAGGAAGCTAACCGTTTTATTGCTTCGACTTGCTTCTCGGTGTCACATCAGGAA
130 CAGTATCTCATCAGGAAGCTAACCGTTTTATTGCTTCGACCTGCTTCTCAGTGTCACATCAGGAA
544905 GCTGTGGTTCGA
195 GCTGTGGTTCGA
* * *
544917 AGATTTATTCACATCGAGCATGGGTTTAATTTAGTCTTCTTCTCAGTATCTCATCTGGCAA-ATG
1 AGATTTGTTCACATCGAGCATGGGTTTAATTTGGTCTTCTTCTCAGTATCTCATCAGG-AAGATG
544981 ACCG
65 ACCG
544985 TTTTGTTGTT
Statistics
Matches: 255, Mismatches: 15, Indels: 7
0.92 0.05 0.03
Matches are distributed among these distances:
204 1 0.00
205 144 0.56
206 107 0.42
207 3 0.01
ACGTcount: A:0.22, C:0.22, G:0.20, T:0.36
Consensus pattern (206 bp):
AGATTTGTTCACATCGAGCATGGGTTTAATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGA
CCGCGTCGTTTGTTTCAATACGCTTCTCTGTATCTCATCAGGAAGACAAATTTGGTCCACTTCTC
AGTATCTCATCAGGAAGCTAACCGTTTTATTGCTTCGACCTGCTTCTCAGTGTCACATCAGGAAG
CTGTGGTTCGA
Found at i:555606 original size:29 final size:28
Alignment explanation
Indices: 555573--555919 Score: 277
Period size: 29 Copynumber: 11.8 Consensus size: 28
555563 CGAGGTTAAT
*
555573 AATGGGATTTTTGGAAGTTAGGGAGTAAA
1 AATGGAATTTTTGGAAGTTAGGG-GTAAA
*
555602 AATGGAATTTTTGGAAGTTTTA-GGGTTAA
1 AATGGAATTTTTGGAAG--TTAGGGGTAAA
* *
555631 AATGGGATTTTTGGAAGTTCGAGGGTAAA
1 AATGGAATTTTTGGAAGTTAG-GGGTAAA
* * *
555660 AATGAAATTTTTGGAAGTTTCGAGGTCAAA
1 AATGGAATTTTTGGAAG-TTAGGGGT-AAA
* * *
555690 AATGGGATTTTCGGAAGTTCA-AGGTAAA
1 AATGGAATTTTTGGAAGTT-AGGGGTAAA
**
555718 AATGGAATTTTTGGAAGTTTCAGGGACAAA
1 AATGGAATTTTTGGAAG-TT-AGGGGTAAA
* * * *
555748 ATTGGGATTTTTAGAAGTTTGGGGGTAAA
1 AATGGAATTTTTGGAAG-TTAGGGGTAAA
* *
555777 AATGGAATTTTTGGAAGTTTTGAGGTTAAA
1 AATGGAATTTTTGGAAG-TTAG-GGGTAAA
* *
555807 AATGGGATTTTTGGAAGTTTGGGGCTAAA
1 AATGGAATTTTTGGAAGTTAGGGG-TAAA
* * *
555836 AATGGAATTTTTTGAAGTTTCGAGGTTAAA
1 AATGGAATTTTTGGAAG-TTAG-GGGTAAA
*
555866 AAT-GAGATTTTTGGAAGTTCGGGGGTAAA
1 AATGGA-ATTTTTGGAAGTT-AGGGGTAAA
*
555895 AATAGAATTTTTGGATAGTTTAGGG
1 AATGGAATTTTTGGA-AG-TTAGGG
555920 ACCTCCGGAG
Statistics
Matches: 262, Mismatches: 38, Indels: 35
0.78 0.11 0.10
Matches are distributed among these distances:
27 2 0.01
28 20 0.08
29 139 0.53
30 94 0.36
31 7 0.03
ACGTcount: A:0.33, C:0.03, G:0.30, T:0.35
Consensus pattern (28 bp):
AATGGAATTTTTGGAAGTTAGGGGTAAA
Found at i:555647 original size:58 final size:57
Alignment explanation
Indices: 555540--555917 Score: 420
Period size: 59 Copynumber: 6.4 Consensus size: 57
555530 CATCCAGGGG
* * *
555540 AAAATGGTAATTTTAGGGAGTTTCGAGGTTAATAATGGGATTTTTGGAAGTTAGGGAGTA
1 AAAATGG-AATTTTTGGAAGTTTAGAGGTTAA-AATGGGATTTTTGGAAGTTAGGG-GTA
*
555600 AAAATGGAATTTTTGGAAGTTTTAG-GGTTAAAATGGGATTTTTGGAAGTTCGAGGGTA
1 AAAATGGAATTTTTGGAAG-TTTAGAGGTTAAAATGGGATTTTTGGAAGTTAG-GGGTA
* * * * *
555658 AAAATGAAATTTTTGGAAGTTTCGAGGTCAAAAATGGGATTTTCGGAAGTTCA-AGGTA
1 AAAATGGAATTTTTGGAAGTTTAGAGGT-TAAAATGGGATTTTTGGAAGTT-AGGGGTA
** * *
555716 AAAATGGAATTTTTGGAAGTTTCAG-GGACAAAATTGGGATTTTTAGAAGTTTGGGGGTA
1 AAAATGGAATTTTTGGAAGTTT-AGAGGTTAAAA-TGGGATTTTTGGAAG-TTAGGGGTA
* *
555775 AAAATGGAATTTTTGGAAGTTTTGAGGTTAAAAATGGGATTTTTGGAAGTTTGGGGCTA
1 AAAATGGAATTTTTGGAAGTTTAGAGGTT-AAAATGGGATTTTTGGAAGTTAGGGG-TA
* * * *
555834 AAAATGGAATTTTTTGAAGTTTCGAGGTTAAAAATGAGATTTTTGGAAGTTCGGGGGTA
1 AAAATGGAATTTTTGGAAGTTTAGAGGTT-AAAATGGGATTTTTGGAAGTT-AGGGGTA
*
555893 AAAATAGAATTTTTGGATAGTTTAG
1 AAAATGGAATTTTTGGA-AGTTTAG
555918 GGACCTCCGG
Statistics
Matches: 274, Mismatches: 30, Indels: 28
0.83 0.09 0.08
Matches are distributed among these distances:
57 8 0.03
58 91 0.33
59 150 0.55
60 25 0.09
ACGTcount: A:0.33, C:0.03, G:0.29, T:0.35
Consensus pattern (57 bp):
AAAATGGAATTTTTGGAAGTTTAGAGGTTAAAATGGGATTTTTGGAAGTTAGGGGTA
Found at i:566891 original size:29 final size:28
Alignment explanation
Indices: 566858--567204 Score: 277
Period size: 29 Copynumber: 11.8 Consensus size: 28
566848 CGAGGTTAAT
*
566858 AATGGGATTTTTGGAAGTTAGGGAGTAAA
1 AATGGAATTTTTGGAAGTTAGGG-GTAAA
*
566887 AATGGAATTTTTGGAAGTTTTA-GGGTTAA
1 AATGGAATTTTTGGAAG--TTAGGGGTAAA
* *
566916 AATGGGATTTTTGGAAGTTCGAGGGTAAA
1 AATGGAATTTTTGGAAGTTAG-GGGTAAA
* * *
566945 AATGAAATTTTTGGAAGTTTCGAGGTCAAA
1 AATGGAATTTTTGGAAG-TTAGGGGT-AAA
* * *
566975 AATGGGATTTTCGGAAGTTCA-AGGTAAA
1 AATGGAATTTTTGGAAGTT-AGGGGTAAA
**
567003 AATGGAATTTTTGGAAGTTTCAGGGACAAA
1 AATGGAATTTTTGGAAG-TT-AGGGGTAAA
* * * *
567033 ATTGGGATTTTTAGAAGTTTGGGGGTAAA
1 AATGGAATTTTTGGAAG-TTAGGGGTAAA
* *
567062 AATGGAATTTTTGGAAGTTTTGAGGTTAAA
1 AATGGAATTTTTGGAAG-TTAG-GGGTAAA
* *
567092 AATGGGATTTTTGGAAGTTTGGGGCTAAA
1 AATGGAATTTTTGGAAGTTAGGGG-TAAA
* * *
567121 AATGGAATTTTTTGAAGTTTCGAGGTTAAA
1 AATGGAATTTTTGGAAG-TTAG-GGGTAAA
*
567151 AAT-GAGATTTTTGGAAGTTCGGGGGTAAA
1 AATGGA-ATTTTTGGAAGTT-AGGGGTAAA
*
567180 AATAGAATTTTTGGATAGTTTAGGG
1 AATGGAATTTTTGGA-AG-TTAGGG
567205 ACCTCCGGAG
Statistics
Matches: 262, Mismatches: 38, Indels: 35
0.78 0.11 0.10
Matches are distributed among these distances:
27 2 0.01
28 20 0.08
29 139 0.53
30 94 0.36
31 7 0.03
ACGTcount: A:0.33, C:0.03, G:0.30, T:0.35
Consensus pattern (28 bp):
AATGGAATTTTTGGAAGTTAGGGGTAAA
Found at i:566932 original size:58 final size:57
Alignment explanation
Indices: 566825--567202 Score: 420
Period size: 59 Copynumber: 6.4 Consensus size: 57
566815 CATCCAGGGG
* * *
566825 AAAATGGTAATTTTAGGGAGTTTCGAGGTTAATAATGGGATTTTTGGAAGTTAGGGAGTA
1 AAAATGG-AATTTTTGGAAGTTTAGAGGTTAA-AATGGGATTTTTGGAAGTTAGGG-GTA
*
566885 AAAATGGAATTTTTGGAAGTTTTAG-GGTTAAAATGGGATTTTTGGAAGTTCGAGGGTA
1 AAAATGGAATTTTTGGAAG-TTTAGAGGTTAAAATGGGATTTTTGGAAGTTAG-GGGTA
* * * * *
566943 AAAATGAAATTTTTGGAAGTTTCGAGGTCAAAAATGGGATTTTCGGAAGTTCA-AGGTA
1 AAAATGGAATTTTTGGAAGTTTAGAGGT-TAAAATGGGATTTTTGGAAGTT-AGGGGTA
** * *
567001 AAAATGGAATTTTTGGAAGTTTCAG-GGACAAAATTGGGATTTTTAGAAGTTTGGGGGTA
1 AAAATGGAATTTTTGGAAGTTT-AGAGGTTAAAA-TGGGATTTTTGGAAG-TTAGGGGTA
* *
567060 AAAATGGAATTTTTGGAAGTTTTGAGGTTAAAAATGGGATTTTTGGAAGTTTGGGGCTA
1 AAAATGGAATTTTTGGAAGTTTAGAGGTT-AAAATGGGATTTTTGGAAGTTAGGGG-TA
* * * *
567119 AAAATGGAATTTTTTGAAGTTTCGAGGTTAAAAATGAGATTTTTGGAAGTTCGGGGGTA
1 AAAATGGAATTTTTGGAAGTTTAGAGGTT-AAAATGGGATTTTTGGAAGTT-AGGGGTA
*
567178 AAAATAGAATTTTTGGATAGTTTAG
1 AAAATGGAATTTTTGGA-AGTTTAG
567203 GGACCTCCGG
Statistics
Matches: 274, Mismatches: 30, Indels: 28
0.83 0.09 0.08
Matches are distributed among these distances:
57 8 0.03
58 91 0.33
59 150 0.55
60 25 0.09
ACGTcount: A:0.33, C:0.03, G:0.29, T:0.35
Consensus pattern (57 bp):
AAAATGGAATTTTTGGAAGTTTAGAGGTTAAAATGGGATTTTTGGAAGTTAGGGGTA
Found at i:568252 original size:22 final size:24
Alignment explanation
Indices: 568206--568255 Score: 68
Period size: 22 Copynumber: 2.2 Consensus size: 24
568196 TTTCCCTTTT
* *
568206 TTATTATTAAAACATTATTTATTA
1 TTATTATTAAAAAAATATTTATTA
568230 TTATT-TTAAAAAAATA-TTATTA
1 TTATTATTAAAAAAATATTTATTA
568252 TTAT
1 TTAT
568256 CAATATATTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 10 0.42
23 9 0.38
24 5 0.21
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (24 bp):
TTATTATTAAAAAAATATTTATTA
Found at i:568417 original size:29 final size:29
Alignment explanation
Indices: 568384--568609 Score: 280
Period size: 29 Copynumber: 7.7 Consensus size: 29
568374 TTTAAAAACT
568384 AAATGGAATTTTTGGAAGTTTCGGGGTAA
1 AAATGGAATTTTTGGAAGTTTCGGGGTAA
*
568413 AAATGAAATTTTTGGAAGTTTCGGGG-ACA
1 AAATGGAATTTTTGGAAGTTTCGGGGTA-A
*
568442 AAATGGGATTTTTGGAAG-TTCGGGGATAA
1 AAATGGAATTTTTGGAAGTTTCGGGG-TAA
* **
568471 AAATGAAATTTTTGGAAGTTTCGTGGACAA
1 AAATGGAATTTTTGGAAGTTTCG-GGGTAA
*
568501 AAATGGGATTTTTGGAAG-TTCGGGGGTAA
1 AAATGGAATTTTTGGAAGTTTC-GGGGTAA
* *
568530 AAATAGAATTTTTGGAAGTTTCGGGGTCA
1 AAATGGAATTTTTGGAAGTTTCGGGGTAA
*
568559 AAATGGGATTTTTGGAAG-TTCGGGGGTAA
1 AAATGGAATTTTTGGAAGTTTC-GGGGTAA
*
568588 AAATGGAATTTTTTGATAGTTT
1 AAATGGAATTTTTGGA-AGTTT
568610 AGGGACCTTC
Statistics
Matches: 168, Mismatches: 19, Indels: 18
0.82 0.09 0.09
Matches are distributed among these distances:
28 11 0.07
29 124 0.74
30 29 0.17
31 4 0.02
ACGTcount: A:0.31, C:0.04, G:0.30, T:0.34
Consensus pattern (29 bp):
AAATGGAATTTTTGGAAGTTTCGGGGTAA
Found at i:568472 original size:58 final size:58
Alignment explanation
Indices: 568384--568609 Score: 348
Period size: 58 Copynumber: 3.9 Consensus size: 58
568374 TTTAAAAACT
*
568384 AAATGGAATTTTTGGAAGTTTC-GGGGTAAAAATGAAATTTTTGGAAGTTTCGGGGACA
1 AAATGGGATTTTTGGAAG-TTCGGGGGTAAAAATGAAATTTTTGGAAGTTTCGGGGACA
* *
568442 AAATGGGATTTTTGGAAGTTCGGGGATAAAAATGAAATTTTTGGAAGTTTCGTGGACAA
1 AAATGGGATTTTTGGAAGTTCGGGGGTAAAAATGAAATTTTTGGAAGTTTCGGGGAC-A
*
568501 AAATGGGATTTTTGGAAGTTCGGGGGTAAAAAT-AGAATTTTTGGAAGTTTCGGGGTCA
1 AAATGGGATTTTTGGAAGTTCGGGGGTAAAAATGA-AATTTTTGGAAGTTTCGGGGACA
* *
568559 AAATGGGATTTTTGGAAGTTCGGGGGTAAAAATGGAATTTTTTGATAGTTT
1 AAATGGGATTTTTGGAAGTTCGGGGGTAAAAATGAAATTTTTGGA-AGTTT
568610 AGGGACCTTC
Statistics
Matches: 155, Mismatches: 8, Indels: 9
0.90 0.05 0.05
Matches are distributed among these distances:
57 3 0.02
58 94 0.61
59 58 0.37
ACGTcount: A:0.31, C:0.04, G:0.30, T:0.34
Consensus pattern (58 bp):
AAATGGGATTTTTGGAAGTTCGGGGGTAAAAATGAAATTTTTGGAAGTTTCGGGGACA
Found at i:568527 original size:117 final size:118
Alignment explanation
Indices: 568384--568609 Score: 368
Period size: 117 Copynumber: 1.9 Consensus size: 118
568374 TTTAAAAACT
568384 AAATGGAATTTTTGGAAGTTTCGGGGTAAAAAT-GAAATTTTTGGAAGTTTCGGGGACAAAATGG
1 AAATGGAATTTTTGGAAGTTTCGGGGTAAAAATAG-AATTTTTGGAAGTTTCGGGGACAAAATGG
568448 GATTTTTGGAAGTTCGGGGATAAAAATGAAATTTTTGGA-AGTTTCGTGGACAA
65 GATTTTTGGAAGTTCGGGGATAAAAATGAAATTTTTGGATAGTTTCGTGGACAA
* *
568501 AAATGGGATTTTTGGAAG-TTCGGGGGTAAAAATAGAATTTTTGGAAGTTTCGGGGTCAAAATGG
1 AAATGGAATTTTTGGAAGTTTC-GGGGTAAAAATAGAATTTTTGGAAGTTTCGGGGACAAAATGG
* * *
568565 GATTTTTGGAAGTTCGGGGGTAAAAATGGAATTTTTTGATAGTTT
65 GATTTTTGGAAGTTCGGGGATAAAAATGAAATTTTTGGATAGTTT
568610 AGGGACCTTC
Statistics
Matches: 101, Mismatches: 5, Indels: 5
0.91 0.05 0.05
Matches are distributed among these distances:
116 3 0.03
117 92 0.91
118 6 0.06
ACGTcount: A:0.31, C:0.04, G:0.30, T:0.34
Consensus pattern (118 bp):
AAATGGAATTTTTGGAAGTTTCGGGGTAAAAATAGAATTTTTGGAAGTTTCGGGGACAAAATGGG
ATTTTTGGAAGTTCGGGGATAAAAATGAAATTTTTGGATAGTTTCGTGGACAA
Found at i:569664 original size:22 final size:24
Alignment explanation
Indices: 569618--569667 Score: 77
Period size: 22 Copynumber: 2.2 Consensus size: 24
569608 TTTCCCTTTT
*
569618 TTATTATTAAAACATTATTTATTA
1 TTATTATTAAAAAATTATTTATTA
569642 TTATT-TTAAAAAATTA-TTATTA
1 TTATTATTAAAAAATTATTTATTA
569664 TTAT
1 TTAT
569668 CAATATATTC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 10 0.40
23 10 0.40
24 5 0.20
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (24 bp):
TTATTATTAAAAAATTATTTATTA
Found at i:570415 original size:17 final size:17
Alignment explanation
Indices: 570395--570486 Score: 114
Period size: 17 Copynumber: 5.2 Consensus size: 17
570385 ATTTAAATCC
*
570395 ATTTAAATTCT-AATTAA
1 ATTTAAATT-TAAAATAA
**
570412 ATTTAAATTTAAAGCAA
1 ATTTAAATTTAAAATAA
570429 ATTTAAATTTAAAAGATAA
1 ATTTAAATTT-AAA-ATAA
570448 ATTTAAATTTAAAATAA
1 ATTTAAATTTAAAATAA
570465 ATTTAAATTTAAAAATAA
1 ATTTAAATTT-AAAATAA
570483 ATTT
1 ATTT
570487 GAATCAATTT
Statistics
Matches: 67, Mismatches: 4, Indels: 7
0.86 0.05 0.09
Matches are distributed among these distances:
16 1 0.01
17 37 0.55
18 17 0.25
19 12 0.18
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.41
Consensus pattern (17 bp):
ATTTAAATTTAAAATAA
Found at i:570417 original size:6 final size:6
Alignment explanation
Indices: 570395--570477 Score: 75
Period size: 6 Copynumber: 14.2 Consensus size: 6
570385 ATTTAAATCC
**
570395 ATTTAA ATTCT-A A-TTAA ATTTAA ATTTAA A-GCAA ATTTAA ATTTAAA
1 ATTTAA ATT-TAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTT-AA
** *
570442 AGATAA ATTTAA ATTTAA A-ATAA ATTTAA ATTTAA A
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA A
570478 AATAAATTTG
Statistics
Matches: 61, Mismatches: 10, Indels: 12
0.73 0.12 0.14
Matches are distributed among these distances:
4 1 0.02
5 10 0.16
6 45 0.74
7 5 0.08
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.41
Consensus pattern (6 bp):
ATTTAA
Found at i:570456 original size:36 final size:35
Alignment explanation
Indices: 570409--570486 Score: 129
Period size: 36 Copynumber: 2.2 Consensus size: 35
570399 AAATTCTAAT
*
570409 TAAATTTAAATTTAAAGCAAATTTAAATTTAAAAGA
1 TAAATTTAAATTTAAAACAAATTTAAATTTAAAA-A
*
570445 TAAATTTAAATTTAAAATAAATTTAAATTTAAAAA
1 TAAATTTAAATTTAAAACAAATTTAAATTTAAAAA
570480 TAAATTT
1 TAAATTT
570487 GAATCAATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
35 8 0.20
36 32 0.80
ACGTcount: A:0.56, C:0.01, G:0.03, T:0.40
Consensus pattern (35 bp):
TAAATTTAAATTTAAAACAAATTTAAATTTAAAAA
Found at i:573521 original size:29 final size:29
Alignment explanation
Indices: 573467--573545 Score: 72
Period size: 29 Copynumber: 2.7 Consensus size: 29
573457 GCATCAACAG
573467 TTAATTAATTTTTTAAATTTTAAAAA-ATATT
1 TTAA-TAA-TTTTTAAATTTTAAAAATA-ATT
* *
573498 TTTATAATTTTTATACTTTT-AAAATAATT
1 TTAATAATTTTTA-AATTTTAAAAATAATT
* *
573527 TTAATACTTTTTAAGTTTT
1 TTAATAATTTTTAAATTTT
573546 TTAAATATAT
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
28 5 0.12
29 24 0.59
30 9 0.22
31 3 0.07
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.58
Consensus pattern (29 bp):
TTAATAATTTTTAAATTTTAAAAATAATT
Found at i:583521 original size:30 final size:30
Alignment explanation
Indices: 583480--583540 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
583470 GCATAATAAA
*
583480 GTGCGGTTGTAAGGTATGGCTGTTATCATT
1 GTGCAGTTGTAAGGTATGGCTGTTATCATT
*
583510 GTGCAGTTGTAAGGTATGGTTGTTATCATT
1 GTGCAGTTGTAAGGTATGGCTGTTATCATT
583540 G
1 G
583541 CTTGTATGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.18, C:0.08, G:0.33, T:0.41
Consensus pattern (30 bp):
GTGCAGTTGTAAGGTATGGCTGTTATCATT
Found at i:593976 original size:9 final size:9
Alignment explanation
Indices: 593962--594014 Score: 50
Period size: 9 Copynumber: 6.8 Consensus size: 9
593952 ATTTTAAAAA
593962 AATAATTTT
1 AATAATTTT
593971 AATAATTTT
1 AATAATTTT
593980 -AT-ATTTT
1 AATAATTTT
593987 AA-AA----
1 AATAATTTT
593991 AATAATTTT
1 AATAATTTT
594000 AATAATTTT
1 AATAATTTT
594009 AA-AATT
1 AATAATT
594015 ATTTGTTGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 15
0.71 0.00 0.29
Matches are distributed among these distances:
4 2 0.05
5 2 0.05
7 5 0.14
8 8 0.22
9 20 0.54
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (9 bp):
AATAATTTT
Found at i:593996 original size:20 final size:22
Alignment explanation
Indices: 593971--594012 Score: 70
Period size: 20 Copynumber: 2.0 Consensus size: 22
593961 AAATAATTTT
593971 AATAATTTT-AT-ATTTTAAAA
1 AATAATTTTAATAATTTTAAAA
593991 AATAATTTTAATAATTTTAAAA
1 AATAATTTTAATAATTTTAAAA
594013 TTATTTGTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 9 0.45
21 2 0.10
22 9 0.45
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
AATAATTTTAATAATTTTAAAA
Found at i:594000 original size:29 final size:31
Alignment explanation
Indices: 593937--594009 Score: 132
Period size: 29 Copynumber: 2.4 Consensus size: 31
593927 ATTAAAATTA
593937 TTTAATAATTTTATTATTTTAAAAAAATAAT
1 TTTAATAATTTTATTATTTTAAAAAAATAAT
593968 TTTAATAATTTTA-TATTTT-AAAAAATAAT
1 TTTAATAATTTTATTATTTTAAAAAAATAAT
593997 TTTAATAATTTTA
1 TTTAATAATTTTA
594010 AAATTATTTG
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
29 23 0.55
30 6 0.14
31 13 0.31
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (31 bp):
TTTAATAATTTTATTATTTTAAAAAAATAAT
Found at i:594013 original size:20 final size:20
Alignment explanation
Indices: 593962--594018 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
593952 ATTTTAAAAA
593962 AATAATTTT--AATAATTTT
1 AATAATTTTAAAATAATTTT
593980 -AT-ATTTTAAAAAATAATTTT
1 AATAATTTT--AAAATAATTTT
*
594000 AATAATTTTAAAATTATTT
1 AATAATTTTAAAATAATTT
594019 GTTGAAGTGG
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
16 5 0.16
17 2 0.06
20 18 0.56
21 2 0.06
22 5 0.16
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
AATAATTTTAAAATAATTTT
Found at i:621284 original size:16 final size:16
Alignment explanation
Indices: 621244--621282 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
621234 ATAGTAAAAA
621244 TATAATTTATTATTTT
1 TATAATTTATTATTTT
* *
621260 AATAGTTTA-TATTTT
1 TATAATTTATTATTTT
621275 TATAATTT
1 TATAATTT
621283 TAAACGATTA
Statistics
Matches: 19, Mismatches: 4, Indels: 1
0.79 0.17 0.04
Matches are distributed among these distances:
15 12 0.63
16 7 0.37
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (16 bp):
TATAATTTATTATTTT
Found at i:621321 original size:29 final size:30
Alignment explanation
Indices: 621270--621351 Score: 78
Period size: 29 Copynumber: 2.6 Consensus size: 30
621260 AATAGTTTAT
* * *
621270 ATTTTTA-TAATTTTAAACGATTAAATTA-A
1 ATTTTTATTATTTTTAAA-AATTAAAATATA
621299 ATTTTTATTATTTTTAAAAATTAAAATATA
1 ATTTTTATTATTTTTAAAAATTAAAATATA
621329 ATTTTATCATTATTAATTTAAAA
1 ATTTT-T-ATTATT--TTTAAAA
621352 TTTTATAAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
29 15 0.34
30 15 0.34
31 1 0.02
32 6 0.14
34 7 0.16
ACGTcount: A:0.45, C:0.02, G:0.01, T:0.51
Consensus pattern (30 bp):
ATTTTTATTATTTTTAAAAATTAAAATATA
Found at i:631996 original size:2 final size:2
Alignment explanation
Indices: 631983--632029 Score: 80
Period size: 2 Copynumber: 24.5 Consensus size: 2
631973 ACTCGATCAA
631983 AT AT AT -T A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
632023 AT AT AT A
1 AT AT AT A
632030 ATTAATGTAA
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 41 0.95
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:632637 original size:17 final size:19
Alignment explanation
Indices: 632615--632655 Score: 52
Period size: 17 Copynumber: 2.3 Consensus size: 19
632605 TTGTTTAGAC
*
632615 TAAATAATTAAAAT-ATG-
1 TAAATAATAAAAATAATGA
632632 TAAAT-ATAAAAATAATGA
1 TAAATAATAAAAATAATGA
632650 TAAATA
1 TAAATA
632656 TTTCAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
16 7 0.35
17 8 0.40
18 5 0.25
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (19 bp):
TAAATAATAAAAATAATGA
Found at i:637675 original size:19 final size:20
Alignment explanation
Indices: 637643--637680 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
637633 TTTTTTAATA
637643 TTAAATAAATAAA-TAAAAT
1 TTAAATAAATAAATTAAAAT
637662 TTAAAT-AATGAAATTAAAA
1 TTAAATAAAT-AAATTAAAA
637681 AAAATATTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 3 0.18
19 9 0.53
20 5 0.29
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.32
Consensus pattern (20 bp):
TTAAATAAATAAATTAAAAT
Found at i:637964 original size:14 final size:14
Alignment explanation
Indices: 637928--637970 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
637918 TTAATTTTAA
637928 TTTTTGTATTATATT
1 TTTTTGTATTAT-TT
** *
637943 TTGGTGTATAATTT
1 TTTTTGTATTATTT
637957 TTTTTGTATTATTT
1 TTTTTGTATTATTT
637971 ATGTCAAAAA
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
14 13 0.59
15 9 0.41
ACGTcount: A:0.19, C:0.00, G:0.12, T:0.70
Consensus pattern (14 bp):
TTTTTGTATTATTT
Found at i:639321 original size:12 final size:12
Alignment explanation
Indices: 639304--639330 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
639294 TATCTGCTGT
639304 TTCTTGTTCCTC
1 TTCTTGTTCCTC
639316 TTCTTGTTCCTC
1 TTCTTGTTCCTC
639328 TTC
1 TTC
639331 CTGAATCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.00, C:0.33, G:0.07, T:0.59
Consensus pattern (12 bp):
TTCTTGTTCCTC
Found at i:641851 original size:17 final size:18
Alignment explanation
Indices: 641825--641859 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
641815 GGGAGAAGAA
641825 GAGAAAAAAAT-GAAAGG
1 GAGAAAAAAATAGAAAGG
*
641842 GAGAAGAAAATAGAAAGG
1 GAGAAAAAAATAGAAAGG
641860 AAAATAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.63, C:0.00, G:0.31, T:0.06
Consensus pattern (18 bp):
GAGAAAAAAATAGAAAGG
Found at i:645846 original size:3 final size:3
Alignment explanation
Indices: 645838--645872 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
645828 TTTAACCTGT
645838 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
645873 CATCAAGATC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:646060 original size:34 final size:34
Alignment explanation
Indices: 646022--646087 Score: 98
Period size: 34 Copynumber: 1.9 Consensus size: 34
646012 TCAAATCCAT
*
646022 GAAATTTCATGAACC-AATCATTCTAAAAAGAACA
1 GAAATTTCATG-ACCTAATCATTCCAAAAAGAACA
*
646056 GAAATTTCATGACCTAATCATTCCGAAAAGAA
1 GAAATTTCATGACCTAATCATTCCAAAAAGAA
646088 TAAAAACTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 3 0.10
34 26 0.90
ACGTcount: A:0.47, C:0.18, G:0.11, T:0.24
Consensus pattern (34 bp):
GAAATTTCATGACCTAATCATTCCAAAAAGAACA
Done.