Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003622.1 Hibiscus syriacus cultivar Beakdansim tig00007662_pilon, 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: 104815
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:116 original size:16 final size:16
Alignment explanation
Indices: 79--120 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
69 GCAAGTGATA
* *
79 AAGAATT-AAAGCTTT
1 AAGAATTGAATGCTTG
*
94 AACAATTGAATGCTTG
1 AAGAATTGAATGCTTG
110 AAGAATTGAAT
1 AAGAATTGAAT
121 CTACCACTCT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
15 6 0.27
16 16 0.73
ACGTcount: A:0.45, C:0.07, G:0.17, T:0.31
Consensus pattern (16 bp):
AAGAATTGAATGCTTG
Found at i:3093 original size:6 final size:6
Alignment explanation
Indices: 3084--3280 Score: 122
Period size: 6 Copynumber: 31.5 Consensus size: 6
3074 CTATATACAT
*
3084 ACATGG ACATGG ACAT-G ACATGG ACATGG ACAATAG ACATGG ACATGG
1 ACATGG ACATGG ACATGG ACATGG ACATGG AC-ATGG ACATGG ACATGG
* * * *
3132 ACAATAG ACATAG ACATGG ACAATAG ACATGG ACAATAG -CATGG ACATAGG
1 AC-ATGG ACATGG ACATGG AC-ATGG ACATGG AC-ATGG ACATGG ACAT-GG
* *
3183 -CATGG ACAATAG -CATGG ACAATAGG -CATGG ACAATAGG -CATGG ACAATAG
1 ACATGG AC-ATGG ACATGG AC-AT-GG ACATGG AC-AT-GG ACATGG AC-ATGG
*
3233 ACATGG ACAATAG ACATGG ACAATAGG -CATGG ACAATAGG -CATGG ACA
1 ACATGG AC-ATGG ACATGG AC-AT-GG ACATGG AC-AT-GG ACATGG ACA
3281 AAAATGGACA
Statistics
Matches: 153, Mismatches: 14, Indels: 48
0.71 0.07 0.22
Matches are distributed among these distances:
5 21 0.14
6 79 0.52
7 45 0.29
8 8 0.05
ACGTcount: A:0.41, C:0.16, G:0.27, T:0.16
Consensus pattern (6 bp):
ACATGG
Found at i:3124 original size:13 final size:13
Alignment explanation
Indices: 3084--3320 Score: 298
Period size: 13 Copynumber: 19.0 Consensus size: 13
3074 CTATATACAT
*
3084 ACATGGAC-ATGG
1 ACATGGACAATAG
*
3096 ACAT-GAC-ATGG
1 ACATGGACAATAG
3107 ACATGGACAATAG
1 ACATGGACAATAG
*
3120 ACATGGAC-ATGG
1 ACATGGACAATAG
*
3132 ACAATAGAC-ATAG
1 AC-ATGGACAATAG
3145 ACATGGACAATAG
1 ACATGGACAATAG
3158 ACATGGACAATAG
1 ACATGGACAATAG
3171 -CATGGAC-ATAG
1 ACATGGACAATAG
*
3182 GCATGGACAATAG
1 ACATGGACAATAG
3195 -CATGGACAATAG
1 ACATGGACAATAG
*
3207 GCATGGACAATAG
1 ACATGGACAATAG
*
3220 GCATGGACAATAG
1 ACATGGACAATAG
3233 ACATGGACAATAG
1 ACATGGACAATAG
3246 ACATGGACAATAG
1 ACATGGACAATAG
*
3259 GCATGGACAATAG
1 ACATGGACAATAG
*
3272 GCATGGACAA-A-
1 ACATGGACAATAG
3283 A-ATGGACAATAG
1 ACATGGACAATAG
*
3295 GCATGGACAATAG
1 ACATGGACAATAG
3308 ACATGGACAATAG
1 ACATGGACAATAG
3321 GCATAGGCAT
Statistics
Matches: 205, Mismatches: 10, Indels: 19
0.88 0.04 0.08
Matches are distributed among these distances:
10 8 0.04
11 16 0.08
12 44 0.21
13 137 0.67
ACGTcount: A:0.42, C:0.16, G:0.27, T:0.16
Consensus pattern (13 bp):
ACATGGACAATAG
Found at i:3187 original size:62 final size:64
Alignment explanation
Indices: 3084--3324 Score: 295
Period size: 62 Copynumber: 3.9 Consensus size: 64
3074 CTATATACAT
* * *
3084 ACATGGAC-ATGGACAT-GAC-ATGGACATGGACAATAGACATGGAC-ATGGACAATAGAC-ATA
1 ACATGGACAATAGACATGGACAATAGACATGGACAATAGACATGGACAATGG-C-ATGGACAATA
3144 G
64 G
* *
3145 ACATGGACAATAGACATGGACAATAG-CATGGAC-ATAGGCATGGACAATAGCATGGACAATAG
1 ACATGGACAATAGACATGGACAATAGACATGGACAATAGACATGGACAATGGCATGGACAATAG
* *
3207 GCATGGACAATAGGCATGGACAATAGACATGGACAATAGACATGGACAATAGGCATGGACAATAG
1 ACATGGACAATAGACATGGACAATAGACATGGACAATAGACATGGACAAT-GGCATGGACAATAG
* *
3272 GCATGGACAA-A-A-ATGGACAATAGGCATGGACAATAGACATGGACAATAGGCAT
1 ACATGGACAATAGACATGGACAATAGACATGGACAATAGACATGGACAAT-GGCAT
3325 AGGCATAGGC
Statistics
Matches: 161, Mismatches: 11, Indels: 15
0.86 0.06 0.08
Matches are distributed among these distances:
61 13 0.08
62 87 0.54
63 20 0.12
64 18 0.11
65 23 0.14
ACGTcount: A:0.42, C:0.16, G:0.27, T:0.16
Consensus pattern (64 bp):
ACATGGACAATAGACATGGACAATAGACATGGACAATAGACATGGACAATGGCATGGACAATAG
Found at i:3225 original size:75 final size:75
Alignment explanation
Indices: 3100--3336 Score: 265
Period size: 75 Copynumber: 3.1 Consensus size: 75
3090 ACATGGACAT
* * * * *
3100 GACAT-GGACATGGACAATAGACATGGAC-ATGGACAATAGAC-ATAGACATGGACAATAGACAT
1 GACATAGG-CATGGACAATAGGCATGGACAATAGAC-ATGGACAATAGGCATGGAC-ATAGGCAT
3162 GGACAATAGCATG
63 GGACAATAGCATG
* *
3175 GACATAGGCATGGACAATA-GCATGGACAATAGGCATGGACAATAGGCATGGACAATAGACATGG
1 GACATAGGCATGGACAATAGGCATGGACAATAGACATGGACAATAGGCATGGAC-ATAGGCATGG
3239 ACAATAGACATG
65 ACAATAG-CATG
*
3251 GACAATAGGCATGGACAATAGGCATGGACAA-A-A-ATGGACAATAGGCATGGACAATAGACATG
1 GAC-ATAGGCATGGACAATAGGCATGGACAATAGACATGGACAATAGGCATGGAC-ATAGGCATG
3313 GACAATAGGCATAG
64 GACAATA-GCAT-G
3327 G-CATAGGCAT
1 GACATAGGCAT
3337 AGGCATCGGC
Statistics
Matches: 148, Mismatches: 6, Indels: 17
0.87 0.04 0.10
Matches are distributed among these distances:
74 20 0.14
75 89 0.60
76 12 0.08
77 17 0.11
78 10 0.07
ACGTcount: A:0.42, C:0.16, G:0.27, T:0.16
Consensus pattern (75 bp):
GACATAGGCATGGACAATAGGCATGGACAATAGACATGGACAATAGGCATGGACATAGGCATGGA
CAATAGCATG
Found at i:3326 original size:6 final size:6
Alignment explanation
Indices: 3317--3374 Score: 98
Period size: 6 Copynumber: 9.7 Consensus size: 6
3307 GACATGGACA
* *
3317 ATAGGC ATAGGC ATAGGC ATAGGC ATCGGC ATAGGC ATCGGC ATAGGC
1 ATAGGC ATAGGC ATAGGC ATAGGC ATAGGC ATAGGC ATAGGC ATAGGC
3365 ATAGGC ATAG
1 ATAGGC ATAG
3375 ATACACATAC
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 48 1.00
ACGTcount: A:0.31, C:0.19, G:0.33, T:0.17
Consensus pattern (6 bp):
ATAGGC
Found at i:9974 original size:21 final size:20
Alignment explanation
Indices: 9932--9976 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
9922 TATTAAATAA
*
9932 ATTTAAAAAATTTCGCTCTT
1 ATTTAAAAAATTTAGCTCTT
9952 ATTTAAATAAATTTAG-TCATT
1 ATTTAAA-AAATTTAGCTC-TT
9973 ATTT
1 ATTT
9977 GAGATTTTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 9 0.41
21 13 0.59
ACGTcount: A:0.38, C:0.09, G:0.04, T:0.49
Consensus pattern (20 bp):
ATTTAAAAAATTTAGCTCTT
Found at i:20016 original size:14 final size:14
Alignment explanation
Indices: 19997--20029 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
19987 GACTCGGTCA
*
19997 ACCCGGTTGACTCG
1 ACCCGGTTGACCCG
20011 ACCCGGTTGACCCG
1 ACCCGGTTGACCCG
20025 ACCCG
1 ACCCG
20030 CCGACCCGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.15, C:0.42, G:0.27, T:0.15
Consensus pattern (14 bp):
ACCCGGTTGACCCG
Found at i:20023 original size:23 final size:23
Alignment explanation
Indices: 19971--20024 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
19961 GCAAAACTAT
*
19971 TCGACCCGGTTGACTCGACTCGG
1 TCGACCCGGTTGACTCGACCCGG
*
19994 TCAACCCGGTTGACTCGACCCGG
1 TCGACCCGGTTGACTCGACCCGG
*
20017 TTGACCCG
1 TCGACCCG
20025 ACCCGCCGAC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.15, C:0.37, G:0.28, T:0.20
Consensus pattern (23 bp):
TCGACCCGGTTGACTCGACCCGG
Found at i:21612 original size:23 final size:23
Alignment explanation
Indices: 21582--21644 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
21572 ACTTATGTGT
21582 TGAATCATTCAGCACTGTTTTGC
1 TGAATCATTCAGCACTGTTTTGC
* *
21605 TGAATCATTCAACACTGTTTTGT
1 TGAATCATTCAGCACTGTTTTGC
*
21628 TGAATCAGTCAGCACTG
1 TGAATCATTCAGCACTG
21645 AATAATTCAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.25, C:0.21, G:0.17, T:0.37
Consensus pattern (23 bp):
TGAATCATTCAGCACTGTTTTGC
Found at i:24001 original size:31 final size:31
Alignment explanation
Indices: 23966--24033 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
23956 TCAAAAAATA
*
23966 TAAGATA-TAGTCACTTTCGTTTTTATTTAAT
1 TAAGATATTA-TCACTTTCATTTTTATTTAAT
* *
23997 TAAGATATTATCACTTTTATTTTTATTTATT
1 TAAGATATTATCACTTTCATTTTTATTTAAT
24028 TAAGAT
1 TAAGAT
24034 GTAACTCTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
31 31 0.94
32 2 0.06
ACGTcount: A:0.31, C:0.07, G:0.07, T:0.54
Consensus pattern (31 bp):
TAAGATATTATCACTTTCATTTTTATTTAAT
Found at i:27815 original size:19 final size:16
Alignment explanation
Indices: 27792--27834 Score: 50
Period size: 19 Copynumber: 2.5 Consensus size: 16
27782 TATAATGTAA
27792 AATTATTTTTATTATATT
1 AATTATTTTTA-TAT-TT
*
27810 ATATTAATTTTATATTT
1 A-ATTATTTTTATATTT
27827 AATTATTT
1 AATTATTT
27835 GGCCAAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
16 6 0.27
17 3 0.14
18 4 0.18
19 9 0.41
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
AATTATTTTTATATTT
Found at i:28572 original size:13 final size:13
Alignment explanation
Indices: 28554--28579 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
28544 AATAACAACA
28554 ATTAAATAGAAAC
1 ATTAAATAGAAAC
28567 ATTAAATAGAAAC
1 ATTAAATAGAAAC
28580 GATACAATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.08, G:0.08, T:0.23
Consensus pattern (13 bp):
ATTAAATAGAAAC
Found at i:33052 original size:23 final size:23
Alignment explanation
Indices: 33018--33110 Score: 141
Period size: 23 Copynumber: 4.0 Consensus size: 23
33008 GAGTCGAGGG
* *
33018 TTCTACGCGGTCCTTCGGGATAA
1 TTCTACGCGGTCCTTCGGGACAT
*
33041 TTCTACGTGGTCCTTCGGGACAT
1 TTCTACGCGGTCCTTCGGGACAT
*
33064 TTCTACGTGGTCCTTCGGGACAT
1 TTCTACGCGGTCCTTCGGGACAT
*
33087 TTCTACGCGGTCCTTCAGGACAT
1 TTCTACGCGGTCCTTCGGGACAT
33110 T
1 T
33111 CTATGTGACA
Statistics
Matches: 65, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 65 1.00
ACGTcount: A:0.15, C:0.27, G:0.25, T:0.33
Consensus pattern (23 bp):
TTCTACGCGGTCCTTCGGGACAT
Found at i:33135 original size:45 final size:46
Alignment explanation
Indices: 33018--33147 Score: 122
Period size: 46 Copynumber: 2.8 Consensus size: 46
33008 GAGTCGAGGG
* * * * * * *
33018 TTCTACGCGGTCCTTCGGGATAATTCTACGTGGTCCTTCGGGACAT
1 TTCTACGTGGACCTTCGCGACATTTCTACGCGGTCCTTCAGGACAT
* *
33064 TTCTACGTGGTCCTTCGGGACATTTCTACGCGGTCCTTCAGGACA-
1 TTCTACGTGGACCTTCGCGACATTTCTACGCGGTCCTTCAGGACAT
* *
33109 TTCTATGT-GACACTTCAGCG-CATTTCTACGCGGTACTTC
1 TTCTACGTGGAC-CTTC-GCGACATTTCTACGCGGTCCTTC
33148 GGTACAATTT
Statistics
Matches: 73, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
44 2 0.03
45 29 0.40
46 42 0.58
ACGTcount: A:0.16, C:0.28, G:0.23, T:0.33
Consensus pattern (46 bp):
TTCTACGTGGACCTTCGCGACATTTCTACGCGGTCCTTCAGGACAT
Found at i:33146 original size:23 final size:23
Alignment explanation
Indices: 33018--33147 Score: 102
Period size: 23 Copynumber: 5.7 Consensus size: 23
33008 GAGTCGAGGG
* * * *
33018 TTCTACGCGGTCCTTCGGGATAA
1 TTCTACGCGGTACTTCAGGACAT
* * *
33041 TTCTACGTGGTCCTTCGGGACAT
1 TTCTACGCGGTACTTCAGGACAT
* * *
33064 TTCTACGTGGTCCTTCGGGACAT
1 TTCTACGCGGTACTTCAGGACAT
*
33087 TTCTACGCGGTCCTTCAGGACA-
1 TTCTACGCGGTACTTCAGGACAT
* * **
33109 TTCTATGTGACACTTCAGCG-CAT
1 TTCTACGCGGTACTTCAG-GACAT
33132 TTCTACGCGGTACTTC
1 TTCTACGCGGTACTTC
33148 GGTACAATTT
Statistics
Matches: 91, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
22 15 0.16
23 76 0.84
ACGTcount: A:0.16, C:0.28, G:0.23, T:0.33
Consensus pattern (23 bp):
TTCTACGCGGTACTTCAGGACAT
Found at i:34078 original size:2 final size:2
Alignment explanation
Indices: 34071--34106 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
34061 AATAAAGTTG
34071 AT AT 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
34107 TGCATTTAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:42681 original size:7 final size:7
Alignment explanation
Indices: 42669--42694 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
42659 GATCAATGAT
42669 GCATTTG
1 GCATTTG
42676 GCATTTG
1 GCATTTG
42683 GCATTTG
1 GCATTTG
42690 GCATT
1 GCATT
42695 GGCTGATTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.15, G:0.27, T:0.42
Consensus pattern (7 bp):
GCATTTG
Found at i:45987 original size:13 final size:13
Alignment explanation
Indices: 45969--45994 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
45959 CAGCCTACAA
45969 GCATTATTAACAC
1 GCATTATTAACAC
45982 GCATTATTAACAC
1 GCATTATTAACAC
45995 CCGGAATTAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.23, G:0.08, T:0.31
Consensus pattern (13 bp):
GCATTATTAACAC
Found at i:49847 original size:70 final size:71
Alignment explanation
Indices: 49713--49851 Score: 208
Period size: 70 Copynumber: 2.0 Consensus size: 71
49703 GGCCATGTAG
* * *
49713 AAGACCCCGAGATTACTAAATTTTGATGTGATGTAATAAAATTATAATAATTAGGAATGATCAAA
1 AAGACCCCAAGATTACTAAATTTTGATGTAATGAAATAAAATTATAATAATTAGGAATGATCAAA
49778 TTTCAA
66 TTTCAA
* * * *
49784 AAGACTCCAAGATTACTAAATTTTGATGTAAT-AAATAAGATTATAATAATTGGGAATGGTCAAA
1 AAGACCCCAAGATTACTAAATTTTGATGTAATGAAATAAAATTATAATAATTAGGAATGATCAAA
49848 TTTC
66 TTTC
49852 TAAATTTTTA
Statistics
Matches: 61, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
70 32 0.52
71 29 0.48
ACGTcount: A:0.43, C:0.09, G:0.14, T:0.33
Consensus pattern (71 bp):
AAGACCCCAAGATTACTAAATTTTGATGTAATGAAATAAAATTATAATAATTAGGAATGATCAAA
TTTCAA
Found at i:50060 original size:34 final size:37
Alignment explanation
Indices: 50020--50100 Score: 96
Period size: 38 Copynumber: 2.2 Consensus size: 37
50010 AAAACAATTA
* * * *
50020 ATATATATTTA-AA-AATTATTATTATA-ATATCTTT
1 ATATATATTTAGAATAATTACTAATATATATATATAT
50054 ATATATATTTAGGAATAATTACTAATATATATATATAT
1 ATATATATTTA-GAATAATTACTAATATATATATATAT
50092 ATATATATT
1 ATATATATT
50101 AAATTATCTC
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
34 11 0.28
36 2 0.05
37 11 0.28
38 15 0.38
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.49
Consensus pattern (37 bp):
ATATATATTTAGAATAATTACTAATATATATATATAT
Found at i:50447 original size:60 final size:60
Alignment explanation
Indices: 50379--50579 Score: 198
Period size: 60 Copynumber: 3.3 Consensus size: 60
50369 TTTTTAGTTA
* *
50379 AAAATAAGTCCT-TAAACTATTATATATGACCACTTTAAGTACCTCAATTATCTTTTCATC
1 AAAATAAGT-CTATAAACTATTATATATGACCACTTTAAGTACCTAAACTATCTTTTCATC
* * * * * * *
50439 AAAATAAGTATATATATA-TATATATATAT-A-TATTTTAAATATCTAAACTAT-TTTTTAGTTA
1 AAAATAAGTCTATA-A-ACTAT-TATATATGACCACTTTAAGTACCTAAACTATCTTTTCA--TC
*
50500 AAAATAAGTCCT-TAAACTATTATATATGACCACTTTAAGTACCTTAACTATCTTTTCATC
1 AAAATAAGT-CTATAAACTATTATATATGACCACTTTAAGTACCTAAACTATCTTTTCATC
*
50560 AAAATAAGTCTCTAAACTAT
1 AAAATAAGTCTATAAACTAT
50580 ATTTTTTTTT
Statistics
Matches: 112, Mismatches: 17, Indels: 24
0.73 0.11 0.16
Matches are distributed among these distances:
59 16 0.14
60 49 0.44
61 33 0.29
62 14 0.12
ACGTcount: A:0.41, C:0.14, G:0.04, T:0.40
Consensus pattern (60 bp):
AAAATAAGTCTATAAACTATTATATATGACCACTTTAAGTACCTAAACTATCTTTTCATC
Found at i:50454 original size:2 final size:2
Alignment explanation
Indices: 50447--50471 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
50437 TCAAAATAAG
50447 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
50472 TTTAAATATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:50524 original size:61 final size:61
Alignment explanation
Indices: 50351--50579 Score: 195
Period size: 60 Copynumber: 3.8 Consensus size: 61
50341 AATACTTAAA
*
50351 TTTAAATATCTAAACTATTTTTTAGTTAAAAATAAGTCCTTAAACTATTATATATGACCAC
1 TTTAAATATCTAAACTATTTTTTAGTTAAAAATAAGTCCTTAAACTATTATATATGAACAC
* * * * * * * * * *
50412 TTTAAGTACCTCAATTATCTTTTCA--TCAAAATAAGT-ATATATA-TATATATATAT-ATATAT
1 TTTAAATATCTAAACTAT-TTTTTAGTTAAAAATAAGTCCT-TAAACTAT-TATATATGA-ACAC
*
50472 TTTAAATATCTAAACTATTTTTTAGTTAAAAATAAGTCCTTAAACTATTATATATGACCAC
1 TTTAAATATCTAAACTATTTTTTAGTTAAAAATAAGTCCTTAAACTATTATATATGAACAC
* * * * *
50533 TTTAAGTACCTTAACTATCTTTTCA--TCAAAATAAGT-CTCTAAACTAT
1 TTTAAATATCTAAACTAT-TTTTTAGTTAAAAATAAGTCCT-TAAACTAT
50580 ATTTTTTTTT
Statistics
Matches: 130, Mismatches: 27, Indels: 23
0.72 0.15 0.13
Matches are distributed among these distances:
59 12 0.09
60 53 0.41
61 50 0.38
62 15 0.12
ACGTcount: A:0.40, C:0.14, G:0.04, T:0.42
Consensus pattern (61 bp):
TTTAAATATCTAAACTATTTTTTAGTTAAAAATAAGTCCTTAAACTATTATATATGAACAC
Found at i:50565 original size:121 final size:121
Alignment explanation
Indices: 50351--50568 Score: 418
Period size: 121 Copynumber: 1.8 Consensus size: 121
50341 AATACTTAAA
50351 TTTAAATATCTAAACTATTTTTTAGTTAAAAATAAGTCCTTAAACTATTATATATGACCACTTTA
1 TTTAAATATCTAAACTATTTTTTAGTTAAAAATAAGTCCTTAAACTATTATATATGACCACTTTA
*
50416 AGTACCTCAATTATCTTTTCATCAAAATAAGTATATATATATATATATATATATAT
66 AGTACCTCAACTATCTTTTCATCAAAATAAGTATATATATATATATATATATATAT
50472 TTTAAATATCTAAACTATTTTTTAGTTAAAAATAAGTCCTTAAACTATTATATATGACCACTTTA
1 TTTAAATATCTAAACTATTTTTTAGTTAAAAATAAGTCCTTAAACTATTATATATGACCACTTTA
*
50537 AGTACCTTAACTATCTTTTCATCAAAATAAGT
66 AGTACCTCAACTATCTTTTCATCAAAATAAGT
50569 CTCTAAACTA
Statistics
Matches: 95, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
121 95 1.00
ACGTcount: A:0.40, C:0.13, G:0.05, T:0.42
Consensus pattern (121 bp):
TTTAAATATCTAAACTATTTTTTAGTTAAAAATAAGTCCTTAAACTATTATATATGACCACTTTA
AGTACCTCAACTATCTTTTCATCAAAATAAGTATATATATATATATATATATATAT
Found at i:56102 original size:11 final size:10
Alignment explanation
Indices: 56076--56108 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
56066 CTGAAAATCA
56076 GGAAAAACCG
1 GGAAAAACCG
56086 GGAAAAACCG
1 GGAAAAACCG
*
56096 GGAAAAATCG
1 GGAAAAACCG
56106 GGA
1 GGA
56109 TTTTTGTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.48, C:0.15, G:0.33, T:0.03
Consensus pattern (10 bp):
GGAAAAACCG
Found at i:56627 original size:14 final size:14
Alignment explanation
Indices: 56608--56634 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
56598 ATTTATTTTT
56608 TAATTATAGTTATA
1 TAATTATAGTTATA
56622 TAATTATAGTTAT
1 TAATTATAGTTAT
56635 TATTTAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (14 bp):
TAATTATAGTTATA
Found at i:59580 original size:22 final size:22
Alignment explanation
Indices: 59546--59594 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
59536 ATAATTATTT
59546 AAAAA-ATTAAAT-AAAAATACA
1 AAAAATATTAAATAAAAAATA-A
*
59567 AAAAATATTTAATAAAAAATAA
1 AAAAATATTAAATAAAAAATAA
59589 AAAAAT
1 AAAAAT
59595 TAGGTTGAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 5 0.20
22 13 0.52
23 7 0.28
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (22 bp):
AAAAATATTAAATAAAAAATAA
Found at i:60901 original size:24 final size:24
Alignment explanation
Indices: 60870--60944 Score: 79
Period size: 24 Copynumber: 3.3 Consensus size: 24
60860 TAATATATAA
60870 AAAATATTATTAATGAGTTATCTT
1 AAAATATTATTAATGAGTTATCTT
* * * *
60894 AAAGTATT-TT--TTA--TATATA
1 AAAATATTATTAATGAGTTATCTT
60913 AAAATATTATTAATGAGTTATCTT
1 AAAATATTATTAATGAGTTATCTT
60937 AAAATATT
1 AAAATATT
60945 TTTTATATTT
Statistics
Matches: 38, Mismatches: 8, Indels: 10
0.68 0.14 0.18
Matches are distributed among these distances:
19 11 0.29
20 2 0.05
21 2 0.05
22 2 0.05
23 2 0.05
24 19 0.50
ACGTcount: A:0.44, C:0.03, G:0.07, T:0.47
Consensus pattern (24 bp):
AAAATATTATTAATGAGTTATCTT
Found at i:60916 original size:44 final size:43
Alignment explanation
Indices: 60851--60952 Score: 170
Period size: 43 Copynumber: 2.4 Consensus size: 43
60841 TTTTTCTTAA
**
60851 TAAAATATTTAATATATA-AAAAATATTATTAATGAGTTATCT
1 TAAAATATTTTTTATATATAAAAATATTATTAATGAGTTATCT
*
60893 TAAAGTATTTTTTATATATAAAAATATTATTAATGAGTTATCT
1 TAAAATATTTTTTATATATAAAAATATTATTAATGAGTTATCT
60936 TAAAATATTTTTTATAT
1 TAAAATATTTTTTATAT
60953 TTTTATTATA
Statistics
Matches: 55, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
42 15 0.27
43 40 0.73
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (43 bp):
TAAAATATTTTTTATATATAAAAATATTATTAATGAGTTATCT
Found at i:63623 original size:21 final size:21
Alignment explanation
Indices: 63599--63772 Score: 105
Period size: 21 Copynumber: 8.4 Consensus size: 21
63589 CATATTCGCA
63599 TTGCGA-TAGTCCAAGTTCGCG
1 TTGCGATTAGTCCAAGTTC-CG
* * *
63620 TTGCGATTTATTACAAGTT-CA
1 TTGCGA-TTAGTCCAAGTTCCG
*
63641 TTGCGA-TAGTCGAAGTTCGCG
1 TTGCGATTAGTCCAAGTTC-CG
* * *
63662 TTGCGATTTATTCCAAATT-CA
1 TTGCGA-TTAGTCCAAGTTCCG
* * *
63683 TTTCGATTTATTCCAAATT-CG
1 TTGCGA-TTAGTCCAAGTTCCG
63704 TTGCGA-TAGTCCAAGTTCACG
1 TTGCGATTAGTCCAAGTTC-CG
* *
63725 TTGCGATTTATTCCAAATT-CG
1 TTGCGA-TTAGTCCAAGTTCCG
*
63746 TTGCGA-TAGTCCAAGTT-CA
1 TTGCGATTAGTCCAAGTTCCG
63765 TTGCGATT
1 TTGCGATT
63773 TATTTAGTTT
Statistics
Matches: 121, Mismatches: 21, Indels: 23
0.73 0.13 0.14
Matches are distributed among these distances:
19 33 0.27
20 1 0.01
21 61 0.50
23 26 0.21
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.37
Consensus pattern (21 bp):
TTGCGATTAGTCCAAGTTCCG
Found at i:63648 original size:42 final size:42
Alignment explanation
Indices: 63597--63689 Score: 150
Period size: 42 Copynumber: 2.2 Consensus size: 42
63587 TACATATTCG
*
63597 CATTGCGATAGTCCAAGTTCGCGTTGCGATTTATTACAAGTT
1 CATTGCGATAGTCCAAGTTCGCGTTGCGATTTATTACAAATT
* *
63639 CATTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
1 CATTGCGATAGTCCAAGTTCGCGTTGCGATTTATTACAAATT
*
63681 CATTTCGAT
1 CATTGCGAT
63690 TTATTCCAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.24, C:0.19, G:0.20, T:0.37
Consensus pattern (42 bp):
CATTGCGATAGTCCAAGTTCGCGTTGCGATTTATTACAAATT
Found at i:63690 original size:63 final size:63
Alignment explanation
Indices: 63620--63771 Score: 218
Period size: 63 Copynumber: 2.4 Consensus size: 63
63610 CAAGTTCGCG
* * *
63620 TTGCGATTTATTACAAGTTCATTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCA
1 TTGCGATTTATTCCAAGTTCATTGCGATAGTCCAAGTTCACGTTGCGATTTATTCCAAATTCA
* * * *
63683 TTTCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCACGTTGCGATTTATTCCAAATTCG
1 TTGCGATTTATTCCAAGTTCATTGCGATAGTCCAAGTTCACGTTGCGATTTATTCCAAATTCA
*
63746 TTGCGA--TAGTCCAAGTTCATTGCGAT
1 TTGCGATTTATTCCAAGTTCATTGCGAT
63772 TTATTTAGTT
Statistics
Matches: 78, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
61 17 0.22
63 61 0.78
ACGTcount: A:0.24, C:0.19, G:0.18, T:0.38
Consensus pattern (63 bp):
TTGCGATTTATTCCAAGTTCATTGCGATAGTCCAAGTTCACGTTGCGATTTATTCCAAATTCA
Found at i:63706 original size:42 final size:40
Alignment explanation
Indices: 63673--63776 Score: 172
Period size: 42 Copynumber: 2.5 Consensus size: 40
63663 TGCGATTTAT
* *
63673 TCCAAATTCATTTCGATTTATTCCAAATTCGTTGCGATAG
1 TCCAAGTTCATTGCGATTTATTCCAAATTCGTTGCGATAG
63713 TCCAAGTTCACGTTGCGATTTATTCCAAATTCGTTGCGATAG
1 TCCAAGTTCA--TTGCGATTTATTCCAAATTCGTTGCGATAG
63755 TCCAAGTTCATTGCGATTTATT
1 TCCAAGTTCATTGCGATTTATT
63777 TAGTTTTAAA
Statistics
Matches: 60, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
40 21 0.35
42 39 0.65
ACGTcount: A:0.25, C:0.20, G:0.15, T:0.39
Consensus pattern (40 bp):
TCCAAGTTCATTGCGATTTATTCCAAATTCGTTGCGATAG
Found at i:64738 original size:333 final size:333
Alignment explanation
Indices: 64132--65118 Score: 1700
Period size: 333 Copynumber: 3.0 Consensus size: 333
64122 ACGTTAAATC
64132 TTGAACGGGTACTAAAAT-AGAACAAAAACTAGAATTTTTAAATGCGAGGTACTAAAATAAAACA
1 TTGAACGGGTACTAAAATGA-AACAAAAACTAGAATTTTTAAATGCGAGGTACTAAAATAAAACA
*
64196 AAAGCTAAACTTTATGTATGATTTTGAAAGAATTGAAAGTTTAGGTGCTAAAACGAACCAAACTG
65 AAAGCTAAACTTTAGGTATGATTTTGAAAGAATTGAAAGTTTAGGTGCTAAAACGAACCAAACTG
*
64261 ATAGTTTAGGTACTAAATACGTAGTTTACCCTTAAAAATATTTAATATCAACCGATACCAATACC
130 ATAGTTTAGGTACTAAATACGTAGTTTATCCTTAAAAATATTTAATATCAACCGATACCAATACC
64326 ATATCAATTATTTTTTTGAATAGTCTAGGCGATTACAAGGTACGTAGTATCTGTTCAGAATTTTT
195 ATATCAATTATTTTTTTGAATAGTCTAGGCGATTACAAGGTACGTAGTATCTGTTCAGAATTTTT
64391 CTTAATCAATAACACCACATACACATTCTAACGACGTAATTGCTCAAACCCAAGATCTTAAGAGA
260 CTTAATCAATAACACCACATACACATTCTAACGACGTAATTGCTCAAACCCAAGATCTTAAGAGA
64456 GAACAATAA
325 GAACAATAA
64465 TTGAACGGGTACTAAAATGAAACAAAAACTAGAATTTTTAAATGCGAGGTACTAAAATAAAACAA
1 TTGAACGGGTACTAAAATGAAACAAAAACTAGAATTTTTAAATGCGAGGTACTAAAATAAAACAA
* *
64530 AAGCTAAACTTTAGGTATGATTTTGAAAGAATTGAAAGTTTAGGTGCTAAAATGAAGCAAACTGA
66 AAGCTAAACTTTAGGTATGATTTTGAAAGAATTGAAAGTTTAGGTGCTAAAACGAACCAAACTGA
*
64595 TAGTTTAGGTACTAAATACATAGTTTATCCTTAAAAATATTTAATATCAACCGATACCAATACCA
131 TAGTTTAGGTACTAAATACGTAGTTTATCCTTAAAAATATTTAATATCAACCGATACCAATACCA
* *
64660 TATCAATTATTTTTTTGAATAGTCTAAGCGATTACAAGGTACGTAGTATCTGTTCGGAATTTTTC
196 TATCAATTATTTTTTTGAATAGTCTAGGCGATTACAAGGTACGTAGTATCTGTTCAGAATTTTTC
*
64725 TTAATCAAT-A-A-CAC---CACA---T-AC-ACGTAATTGCTCAAACCCAAAATCTT-A-AGAG
261 TTAATCAATAACACCACATACACATTCTAACGACGTAATTGCTCAAACCCAAGATCTTAAGAGAG
64777 AACAATAA
326 AACAATAA
* *
64785 TTGAACGGGTACTAAAATGGAAA-GAAAACTAGAATTTTTAAATGCGAGGTACTAAAATAAAATA
1 TTGAACGGGTACTAAAAT-GAAACAAAAACTAGAATTTTTAAATGCGAGGTACTAAAATAAAACA
*
64849 AAAGCTAAACTTTAGGTATGATTTTGAAAGAATTGAAAGTTTATGTGCTAAAACGAACCAAACTG
65 AAAGCTAAACTTTAGGTATGATTTTGAAAGAATTGAAAGTTTAGGTGCTAAAACGAACCAAACTG
* * *
64914 ATAGTTTAGATACTAAATACGTAGTTTATCCTTAAAAATATTTAATATTAACCGATACTAATACC
130 ATAGTTTAGGTACTAAATACGTAGTTTATCCTTAAAAATATTTAATATCAACCGATACCAATACC
64979 ATATCAATTATTTTTTT-AATAGTCTAGGCGATTACAAGGTACGTAGTATCTGTTCAGAATTTTT
195 ATATCAATTATTTTTTTGAATAGTCTAGGCGATTACAAGGTACGTAGTATCTGTTCAGAATTTTT
*
65043 CTTAATCAATAACACCACATATACATTCTAACGACGTAATTGCTCAAACCCAAGATCTTAAGAGA
260 CTTAATCAATAACACCACATACACATTCTAACGACGTAATTGCTCAAACCCAAGATCTTAAGAGA
*
65108 GAATAATAA
325 GAACAATAA
65117 TT
1 TT
65119 ACTTTAGCCA
Statistics
Matches: 617, Mismatches: 22, Indels: 31
0.92 0.03 0.05
Matches are distributed among these distances:
319 55 0.09
320 210 0.34
321 6 0.01
322 28 0.05
323 2 0.00
324 1 0.00
325 3 0.00
327 4 0.01
328 1 0.00
329 2 0.00
330 28 0.05
331 2 0.00
332 14 0.02
333 260 0.42
334 1 0.00
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.31
Consensus pattern (333 bp):
TTGAACGGGTACTAAAATGAAACAAAAACTAGAATTTTTAAATGCGAGGTACTAAAATAAAACAA
AAGCTAAACTTTAGGTATGATTTTGAAAGAATTGAAAGTTTAGGTGCTAAAACGAACCAAACTGA
TAGTTTAGGTACTAAATACGTAGTTTATCCTTAAAAATATTTAATATCAACCGATACCAATACCA
TATCAATTATTTTTTTGAATAGTCTAGGCGATTACAAGGTACGTAGTATCTGTTCAGAATTTTTC
TTAATCAATAACACCACATACACATTCTAACGACGTAATTGCTCAAACCCAAGATCTTAAGAGAG
AACAATAA
Found at i:68097 original size:10 final size:10
Alignment explanation
Indices: 68082--68138 Score: 51
Period size: 10 Copynumber: 5.4 Consensus size: 10
68072 CCGAGCTATG
68082 CGAGGGCATC
1 CGAGGGCATC
*
68092 CGAGGGCAAC
1 CGAGGGCATC
*
68102 CGAGCGAGCTATG
1 CGAG-G-GC-ATC
*
68115 CGAGGGAATC
1 CGAGGGCATC
*
68125 CGAGGGCAAC
1 CGAGGGCATC
68135 CGAG
1 CGAG
68139 CGAGGGTAGG
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
10 27 0.73
11 2 0.05
12 3 0.08
13 5 0.14
ACGTcount: A:0.26, C:0.26, G:0.40, T:0.07
Consensus pattern (10 bp):
CGAGGGCATC
Found at i:68112 original size:33 final size:33
Alignment explanation
Indices: 68068--68142 Score: 132
Period size: 33 Copynumber: 2.3 Consensus size: 33
68058 CTGAGGCCAT
* *
68068 CCGACCGAGCTATGCGAGGGCATCCGAGGGCAA
1 CCGAGCGAGCTATGCGAGGGAATCCGAGGGCAA
68101 CCGAGCGAGCTATGCGAGGGAATCCGAGGGCAA
1 CCGAGCGAGCTATGCGAGGGAATCCGAGGGCAA
68134 CCGAGCGAG
1 CCGAGCGAG
68143 GGTAGGTCGC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.25, C:0.28, G:0.39, T:0.08
Consensus pattern (33 bp):
CCGAGCGAGCTATGCGAGGGAATCCGAGGGCAA
Found at i:68211 original size:30 final size:30
Alignment explanation
Indices: 68144--68212 Score: 113
Period size: 29 Copynumber: 2.3 Consensus size: 30
68134 CCGAGCGAGG
*
68144 GTAGGTCGCCTGGAGTGCATGGCGACCTAC
1 GTAGGTCGCCCGGAGTGCATGGCGACCTAC
*
68174 -AAGGTCGCCCGGAGTGCATGGCGACCTAC
1 GTAGGTCGCCCGGAGTGCATGGCGACCTAC
68203 GTAGGTCGCC
1 GTAGGTCGCC
68213 ATGCACTCCG
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
29 27 0.77
30 8 0.23
ACGTcount: A:0.17, C:0.29, G:0.36, T:0.17
Consensus pattern (30 bp):
GTAGGTCGCCCGGAGTGCATGGCGACCTAC
Found at i:68288 original size:10 final size:10
Alignment explanation
Indices: 68269--68340 Score: 54
Period size: 10 Copynumber: 6.9 Consensus size: 10
68259 GCATAGCTCG
*
68269 CTCGGTTGCC
1 CTCGGATGCC
68279 CTCGGATGCC
1 CTCGGATGCC
*
68289 CTCGCATAGCTC
1 CTCGGAT-GC-C
* * *
68301 GTTCGAATGGC
1 -CTCGGATGCC
*
68312 CTCGGATGCT
1 CTCGGATGCC
*
68322 CTCGGATGGC
1 CTCGGATGCC
68332 CTCGGATGC
1 CTCGGATGC
68341 TTTCGGATGG
Statistics
Matches: 47, Mismatches: 12, Indels: 6
0.72 0.18 0.09
Matches are distributed among these distances:
10 37 0.79
11 3 0.06
12 2 0.04
13 5 0.11
ACGTcount: A:0.11, C:0.33, G:0.31, T:0.25
Consensus pattern (10 bp):
CTCGGATGCC
Found at i:68292 original size:33 final size:32
Alignment explanation
Indices: 68234--68325 Score: 105
Period size: 33 Copynumber: 2.8 Consensus size: 32
68224 GCGACCTACC
**
68234 CTCGCTCGGTTG-CTCGGATTTCCTCGCATAG
1 CTCGCTCGGTTGCCTCGGATGCCCTCGCATAG
68265 CTCGCTCGGTTGCCCTCGGATGCCCTCGCATAG
1 CTCGCTCGGTTG-CCTCGGATGCCCTCGCATAG
* * * *
68298 CTCGTTCGAATGGCCTCGGATGCTCTCG
1 CTCGCTCG-GTTGCCTCGGATGCCCTCG
68326 GATGGCCTCG
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
31 12 0.23
33 38 0.73
34 2 0.04
ACGTcount: A:0.10, C:0.35, G:0.27, T:0.28
Consensus pattern (32 bp):
CTCGCTCGGTTGCCTCGGATGCCCTCGCATAG
Found at i:68332 original size:20 final size:20
Alignment explanation
Indices: 68269--68353 Score: 89
Period size: 20 Copynumber: 4.1 Consensus size: 20
68259 GCATAGCTCG
* * *
68269 CTCGGTTGCCCTCGGATGCC
1 CTCGGATGCTCTCGGATGGC
* *
68289 CTCGCATAGCTCGTTCGAATGGC
1 CTCGGAT-GCTC--TCGGATGGC
68312 CTCGGATGCTCTCGGATGGC
1 CTCGGATGCTCTCGGATGGC
*
68332 CTCGGATGCTTTCGGATGGC
1 CTCGGATGCTCTCGGATGGC
68352 CT
1 CT
68354 TGGTCGAATG
Statistics
Matches: 54, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
20 34 0.63
21 3 0.06
22 4 0.07
23 13 0.24
ACGTcount: A:0.11, C:0.32, G:0.31, T:0.27
Consensus pattern (20 bp):
CTCGGATGCTCTCGGATGGC
Found at i:68346 original size:10 final size:10
Alignment explanation
Indices: 68312--68349 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
68302 TTCGAATGGC
68312 CTCGGATGCT
1 CTCGGATGCT
68322 CTCGGATGGC-
1 CTCGGAT-GCT
68332 CTCGGATGCT
1 CTCGGATGCT
*
68342 TTCGGATG
1 CTCGGATG
68350 GCCTTGGTCG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 2 0.08
10 21 0.84
11 2 0.08
ACGTcount: A:0.11, C:0.26, G:0.34, T:0.29
Consensus pattern (10 bp):
CTCGGATGCT
Found at i:68478 original size:29 final size:30
Alignment explanation
Indices: 68421--68493 Score: 121
Period size: 29 Copynumber: 2.5 Consensus size: 30
68411 CTGCATGGAT
68421 TGCATGGCGACCTACCTAGGTCGCTGGGCG
1 TGCATGGCGACCTACCTAGGTCGCTGGGCG
**
68451 TGCATGGCGACCT-GGTAGGTCGCTGGGCG
1 TGCATGGCGACCTACCTAGGTCGCTGGGCG
68480 TGCATGGCGACCTA
1 TGCATGGCGACCTA
68494 TATGGGGACT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
29 27 0.68
30 13 0.32
ACGTcount: A:0.14, C:0.27, G:0.38, T:0.21
Consensus pattern (30 bp):
TGCATGGCGACCTACCTAGGTCGCTGGGCG
Found at i:77513 original size:7 final size:7
Alignment explanation
Indices: 77501--77527 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
77491 AATTAACTGA
77501 AAATATT
1 AAATATT
77508 AAATATT
1 AAATATT
77515 AAATATT
1 AAATATT
77522 AAATAT
1 AAATAT
77528 ATAATATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (7 bp):
AAATATT
Found at i:78747 original size:26 final size:26
Alignment explanation
Indices: 78718--78775 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
78708 AATTTTCATT
78718 GAAAAACCG-ATGAACCGAACAGAACC
1 GAAAAACCGCAT-AACCGAACAGAACC
* * * *
78744 GAAAAATCGCATTATCGAACCGAACC
1 GAAAAACCGCATAACCGAACAGAACC
78770 GAAAAA
1 GAAAAA
78776 ATCGTTTTCA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 25 0.93
27 2 0.07
ACGTcount: A:0.50, C:0.24, G:0.17, T:0.09
Consensus pattern (26 bp):
GAAAAACCGCATAACCGAACAGAACC
Found at i:79160 original size:18 final size:18
Alignment explanation
Indices: 79137--79174 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
79127 GACCCGACCC
79137 AAAATAATATATTTATTA
1 AAAATAATATATTTATTA
* *
79155 AAAATATTATTTTTATTA
1 AAAATAATATATTTATTA
79173 AA
1 AA
79175 TAAAAATAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
AAAATAATATATTTATTA
Found at i:80442 original size:42 final size:42
Alignment explanation
Indices: 80388--80503 Score: 214
Period size: 42 Copynumber: 2.8 Consensus size: 42
80378 CCCGAATTTT
* *
80388 CGTGTTTTTTTCACGTAATTCGTTTTCCGGAAAATGTTTTCC
1 CGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTTTTCC
80430 CGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTTTTCC
1 CGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTTTTCC
80472 CGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
1 CGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
80504 TGTAATTCAT
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 72 1.00
ACGTcount: A:0.16, C:0.20, G:0.19, T:0.45
Consensus pattern (42 bp):
CGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTTTTCC
Found at i:80750 original size:19 final size:20
Alignment explanation
Indices: 80692--80750 Score: 66
Period size: 19 Copynumber: 3.0 Consensus size: 20
80682 TAATTATTAA
* *
80692 AATATTTAAAATATATTTATT
1 AATATTTATAATAT-TATATT
*
80713 AATATTTATAATATAATATT
1 AATATTTATAATATTATATT
*
80733 -ATATTTTTAATATTATAT
1 AATATTTATAATATTATAT
80751 AAAATAATCA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
19 16 0.48
20 4 0.12
21 13 0.39
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
AATATTTATAATATTATATT
Found at i:80768 original size:31 final size:29
Alignment explanation
Indices: 80703--80775 Score: 89
Period size: 29 Copynumber: 2.5 Consensus size: 29
80693 ATATTTAAAA
*
80703 TATATTTATTAATATTTATAATATAATAT
1 TATATTTATTAATATTTATAAAATAATAT
80732 TATATTT-TTAATATTATATAAAATAATCAAT
1 TATATTTATTAATATT-TATAAAATAAT--AT
80763 TATA-TTA-TAATAT
1 TATATTTATTAATAT
80776 AAGATATTAT
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
28 8 0.21
29 17 0.44
30 8 0.21
31 6 0.15
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (29 bp):
TATATTTATTAATATTTATAAAATAATAT
Found at i:80809 original size:51 final size:49
Alignment explanation
Indices: 80718--80814 Score: 117
Period size: 51 Copynumber: 1.9 Consensus size: 49
80708 TTATTAATAT
* *
80718 TTATAATATAATATTATATTTTTAATATTATATAAAATAATCAATTATA
1 TTATAATATAATATTATATTTTTAATATTATAAAAAATAATAAATTATA
*
80767 TTATAATATAAGATATTATATTTTT-ATTTTA-AAAATATATAATAAATT
1 TTATAATAT-A-ATATTATATTTTTAATATTATAAAA-A-ATAATAAATT
80815 TTTTATATAT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
49 12 0.29
50 7 0.17
51 22 0.54
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (49 bp):
TTATAATATAATATTATATTTTTAATATTATAAAAAATAATAAATTATA
Found at i:80839 original size:30 final size:28
Alignment explanation
Indices: 80763--80862 Score: 89
Period size: 28 Copynumber: 3.5 Consensus size: 28
80753 AATAATCAAT
* *
80763 TATATTATAAT-ATAAGATATTATATTTT-
1 TATATT-TAATAATAA-ATAATATTTTTTA
* *
80791 TAT-TTTAAAAATATATAATAAATTTTTTA
1 TATATTTAATAATAAATAAT--ATTTTTTA
*
80820 TATATTTAATAATAAATAATATTATTTA
1 TATATTTAATAATAAATAATATTTTTTA
80848 TATATTTCAATAATA
1 TATATTT-AATAATA
80863 TTTTAGTAAA
Statistics
Matches: 59, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
26 7 0.12
27 5 0.08
28 23 0.39
29 10 0.17
30 14 0.24
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (28 bp):
TATATTTAATAATAAATAATATTTTTTA
Found at i:81107 original size:20 final size:20
Alignment explanation
Indices: 81029--81098 Score: 104
Period size: 20 Copynumber: 3.5 Consensus size: 20
81019 TTTCCAGATG
* * *
81029 TTTTTCAGAAATATAATTCA
1 TTTTCCAGAAATGTAATTTA
81049 TTTTCCAGAAATGTAATTTA
1 TTTTCCAGAAATGTAATTTA
*
81069 TTTTACAGAAATGTAATTTA
1 TTTTCCAGAAATGTAATTTA
81089 TTTTCCAGAA
1 TTTTCCAGAA
81099 TTTAAATTTC
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.37, C:0.10, G:0.09, T:0.44
Consensus pattern (20 bp):
TTTTCCAGAAATGTAATTTA
Found at i:84549 original size:18 final size:18
Alignment explanation
Indices: 84528--84568 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
84518 ATTTCTTAAA
84528 ATTTTAAAATTATTATAT
1 ATTTTAAAATTATTATAT
* * *
84546 ATTTTAGAGTTTTTATAT
1 ATTTTAAAATTATTATAT
84564 ATTTT
1 ATTTT
84569 TTATTAGAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (18 bp):
ATTTTAAAATTATTATAT
Found at i:91514 original size:39 final size:39
Alignment explanation
Indices: 91410--91515 Score: 101
Period size: 39 Copynumber: 2.7 Consensus size: 39
91400 CATAATCCAC
* * *
91410 AAATTATTTCAC-TCTAATATTCTAAAATCTCAATTTCTT
1 AAATTATTACACAT-TAATGTTCTAAATTCTCAATTTCTT
* *
91449 AAATT-TTGACACCA-TAACGTTCTAAATTCTTAATTTCTT
1 AAATTATT-ACA-CATTAATGTTCTAAATTCTCAATTTCTT
* *
91488 AAATTATTCCACATTAATGTTGTAAATT
1 AAATTATTACACATTAATGTTCTAAATT
91516 ATTTTTTAAA
Statistics
Matches: 54, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
38 4 0.07
39 47 0.87
40 3 0.06
ACGTcount: A:0.36, C:0.16, G:0.04, T:0.44
Consensus pattern (39 bp):
AAATTATTACACATTAATGTTCTAAATTCTCAATTTCTT
Found at i:91686 original size:193 final size:193
Alignment explanation
Indices: 91462--91823 Score: 634
Period size: 193 Copynumber: 1.9 Consensus size: 193
91452 TTTTGACACC
* * ** *
91462 ATAACGTTCTAAATTCTTAATTTCTTAAATTATTCCACATTAATGTTGTAAATTATTTTTTAAAA
1 ATAACATTCTAAATTCTTAATTTCATAAATTATTCCACATTAACATTCTAAATTATTTTTTAAAA
*
91527 TATTTATTTTAACTTTAAAACATTTGAAATTTAATTATATTTCTTTATTTCAAATTTTAATAAAT
66 TATTTATTTTAACTTTAAAACATTTGAAATTTAATTATATTTCTTTATTTCAAATGTTAATAAAT
* *
91592 TTTATTTCAATTATGTATTTTTAATTTTTAAAACTTTTAAATTTTAACTTTTAGATTTTTTTA
131 TTTATTTCAATTATGTATTGTGAATTTTTAAAACTTTTAAATTTTAACTTTTAGATTTTTTTA
* *
91655 ATAACATTTTAAATTCTTAATTTCATAAATTATTTCACATTAACATTCTAAATTATTTTTTAAAA
1 ATAACATTCTAAATTCTTAATTTCATAAATTATTCCACATTAACATTCTAAATTATTTTTTAAAA
91720 TATTTATTTTAACTTTAAAACATTTGAAATTTAATTATATTTCTTTATTTCAAATGTTAATAAAT
66 TATTTATTTTAACTTTAAAACATTTGAAATTTAATTATATTTCTTTATTTCAAATGTTAATAAAT
91785 TTTATTTCAATTATGTATTGTGAATTTTTAAAACTTTTA
131 TTTATTTCAATTATGTATTGTGAATTTTTAAAACTTTTA
91824 TACATATTAA
Statistics
Matches: 159, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
193 159 1.00
ACGTcount: A:0.36, C:0.07, G:0.03, T:0.53
Consensus pattern (193 bp):
ATAACATTCTAAATTCTTAATTTCATAAATTATTCCACATTAACATTCTAAATTATTTTTTAAAA
TATTTATTTTAACTTTAAAACATTTGAAATTTAATTATATTTCTTTATTTCAAATGTTAATAAAT
TTTATTTCAATTATGTATTGTGAATTTTTAAAACTTTTAAATTTTAACTTTTAGATTTTTTTA
Found at i:91866 original size:23 final size:25
Alignment explanation
Indices: 91838--91883 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
91828 TATTAACTTA
91838 AAATAT-TTTTATT-TCAACTTATG
1 AAATATATTTTATTATCAACTTATG
*
91861 AAATATATTTTATTATTAACTTA
1 AAATATATTTTATTATCAACTTA
91884 ATTTAAAGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.39, C:0.07, G:0.02, T:0.52
Consensus pattern (25 bp):
AAATATATTTTATTATCAACTTATG
Found at i:91881 original size:25 final size:22
Alignment explanation
Indices: 91828--91884 Score: 71
Period size: 21 Copynumber: 2.5 Consensus size: 22
91818 CTTTTATACA
91828 TATTAACTTAAAATATTTTTAT
1 TATTAACTTAAAATATTTTTAT
*
91850 T-TCAACTTATGAAATATATTTTAT
1 TATTAACTTA--AAATAT-TTTTAT
91874 TATTAACTTAA
1 TATTAACTTAA
91885 TTTAAAGATG
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
21 7 0.24
22 1 0.03
23 7 0.24
24 7 0.24
25 7 0.24
ACGTcount: A:0.40, C:0.07, G:0.02, T:0.51
Consensus pattern (22 bp):
TATTAACTTAAAATATTTTTAT
Found at i:97682 original size:131 final size:130
Alignment explanation
Indices: 97415--97807 Score: 680
Period size: 131 Copynumber: 3.0 Consensus size: 130
97405 AAAGCAAACC
97415 CCGTATCTTCGATGCAATCACCGCATAGATTCTACAGCTGCGTCTTAGAGTCCAACCACTAAGA-
1 CCGTATCTTCGATGCAATCACCGCATAGATTCTACAGCTGCGTCTTAGAGTCCAA-CACTAAGAC
* *
97479 CTTGTTTGAACAAAGAAGGTTTCAAGTTTGCAATAAACAACTACATGGACCACGTGCAACAGATT
65 CTTGTTCGAACAAAGAAGGTTTCAAGTTTGCAATAAACAACTACATGGACCAAGTGCAACAGATT
97544 A
130 A
* *
97545 CTGTATCTTCGATGCAATCACCACATAGATTCTACAGCTGCGTCTTAGAGTCCAAGCACTAAGAC
1 CCGTATCTTCGATGCAATCACCGCATAGATTCTACAGCTGCGTCTTAGAGTCCAA-CACTAAGAC
* *
97610 CTTGTTCGAACAAAGAAGGTTTCAAGTTTGCAATAAACAACTACAAGGACCAAGTGAAACAGATT
65 CTTGTTCGAACAAAGAAGGTTTCAAGTTTGCAATAAACAACTACATGGACCAAGTGCAACAGATT
97675 A
130 A
*
97676 CCGTATCTTCGATGCAATCACCGCATAGATTCTACAGCTGCGTCTTAGAGTCCGACAACTAAGAC
1 CCGTATCTTCGATGCAATCACCGCATAGATTCTACAGCTGCGTCTTAGAGTCCAAC-ACTAAGAC
*
97741 CTTGTTCGAACAAAGGAGGTTTCAAGTTTGCAATAAACAACTACATGGACCAAGTGCAACAGATT
65 CTTGTTCGAACAAAGAAGGTTTCAAGTTTGCAATAAACAACTACATGGACCAAGTGCAACAGATT
97806 A
130 A
97807 C
1 C
97808 ACTAATTTAT
Statistics
Matches: 248, Mismatches: 13, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
130 62 0.25
131 186 0.75
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.25
Consensus pattern (130 bp):
CCGTATCTTCGATGCAATCACCGCATAGATTCTACAGCTGCGTCTTAGAGTCCAACACTAAGACC
TTGTTCGAACAAAGAAGGTTTCAAGTTTGCAATAAACAACTACATGGACCAAGTGCAACAGATTA
Done.