Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008521.1 Hibiscus syriacus cultivar Beakdansim tig00111388_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: 1601068
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 7
Found at i:1549399 original size:20 final size:18
Alignment explanation
Indices: 1549366--1549403 Score: 58
Period size: 20 Copynumber: 2.0 Consensus size: 18
1549356 TATTTTATAA
1549366 ATTTTAATATTTTTATTT
1 ATTTTAATATTTTTATTT
1549384 ATTTTAATAAATTTTTATTT
1 ATTTTAAT--ATTTTTATTT
1549404 TTAAATTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 8 0.44
20 10 0.56
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
ATTTTAATATTTTTATTT
Found at i:1552688 original size:175 final size:175
Alignment explanation
Indices: 1552397--1552747 Score: 639
Period size: 175 Copynumber: 2.0 Consensus size: 175
1552387 ACGAATTTGA
* * *
1552397 GATTACCACTTACTTATGCTTCCTCAACTCCCTCATCAATACAGCGGATGATGTTAAGGAGCTGT
1 GATTACCACTTACTTATGCTTCCTCAACTCCCTCATCAATACAGCGGACGATGTTAAGGAGCAGC
* *
1552462 GAGTTACGGGAATGCTTCACAACTACTTGGGCAGCGATGAAGATGTGGCTGATCTTTTCAATAAA
66 GAGTTACGGGAATGCTTCACAACTACTTGGGCAGCGACGAAGAGGTGGCTGATCTTTTCAATAAA
1552527 ATGAGCAGGGATTTGGTGCCTGACCAGCAGTGGTACTCTGATGTG
131 ATGAGCAGGGATTTGGTGCCTGACCAGCAGTGGTACTCTGATGTG
*
1552572 GATTACCACTTACTTATGCTTCCTCAACTCCCTCATCGATACAGCGGACGATGTTAAGGAGCAGC
1 GATTACCACTTACTTATGCTTCCTCAACTCCCTCATCAATACAGCGGACGATGTTAAGGAGCAGC
*
1552637 GAGTTACGGTAATGCTTCACAACTACTTGGGCAGCGACGAAGAGGTGGCTGATCTTTTCAATAAA
66 GAGTTACGGGAATGCTTCACAACTACTTGGGCAGCGACGAAGAGGTGGCTGATCTTTTCAATAAA
1552702 ATGAGCAGGGATTTGGTGCCTGACCAGCAGTGGTACTCTGATGTG
131 ATGAGCAGGGATTTGGTGCCTGACCAGCAGTGGTACTCTGATGTG
1552747 G
1 G
1552748 TAAAAGACAT
Statistics
Matches: 169, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
175 169 1.00
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.27
Consensus pattern (175 bp):
GATTACCACTTACTTATGCTTCCTCAACTCCCTCATCAATACAGCGGACGATGTTAAGGAGCAGC
GAGTTACGGGAATGCTTCACAACTACTTGGGCAGCGACGAAGAGGTGGCTGATCTTTTCAATAAA
ATGAGCAGGGATTTGGTGCCTGACCAGCAGTGGTACTCTGATGTG
Found at i:1557050 original size:77 final size:78
Alignment explanation
Indices: 1556898--1557042 Score: 188
Period size: 77 Copynumber: 1.9 Consensus size: 78
1556888 ATATAATAAG
** * *
1556898 TAAACATTAAATGAATGTAATTTTGATTATAACTCTTTAATTAATATTTATTTTGGAATAATTAA
1 TAAACATTAAATGAATGTAATTCAGATTATAACTATTTAATTAATATTTAATTTGGAATAATTAA
1556963 ATAAGATTTTAAA
66 ATAAGATTTTAAA
* * *
1556976 TAAACATTAAA-GATTTTAATTCAGATTATAAGTATTTAATGT-ATATTTAATTT-GAATTAATT
1 TAAACATTAAATGAATGTAATTCAGATTATAACTATTTAAT-TAATATTTAATTTGGAA-TAATT
1557038 AAATA
64 AAATA
1557043 TGTTTTTATT
Statistics
Matches: 58, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
76 3 0.05
77 43 0.74
78 12 0.21
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.45
Consensus pattern (78 bp):
TAAACATTAAATGAATGTAATTCAGATTATAACTATTTAATTAATATTTAATTTGGAATAATTAA
ATAAGATTTTAAA
Found at i:1562477 original size:114 final size:116
Alignment explanation
Indices: 1562263--1562477 Score: 251
Period size: 114 Copynumber: 1.9 Consensus size: 116
1562253 TTTAATTTTT
**
1562263 ATTTGAAATATAAATTAATTAGATTATTTATTTTTGATTTTACATATTAAATTGTATTCGAGTGG
1 ATTTGAAATATAAATTAATTAGATTATTTATTTTTGATTTTACATATTAAATTGTATTCGAGTAA
* * **
1562328 TTTAGTAAGTTTAATTTAAATTTTCGTGTAATTTTTAGTGTAATTTTTTTAA
66 TTTAGTAAGTGTAATTTAAATTATC-TACAATTTTTAGTGTAATTTTTTTAA
* * *
1562380 ATTT-AAATTTAAATT-ATTAGATTATTTA-TTTTGATTTTACATATTAAGTTGTATTTGAGTAA
1 ATTTGAAATATAAATTAATTAGATTATTTATTTTTGATTTTACATATTAAATTGTATTCGAGT-A
* * *
1562442 ATCTT-GATTAGTGTAGTTTAAATTAT-TACATTTTTT
65 AT-TTAG-TAAGTGTAATTTAAATTATCTACAATTTTT
1562478 TTTATTGAGT
Statistics
Matches: 83, Mismatches: 12, Indels: 9
0.80 0.12 0.09
Matches are distributed among these distances:
114 37 0.45
115 15 0.18
116 27 0.33
117 4 0.05
ACGTcount: A:0.33, C:0.03, G:0.11, T:0.53
Consensus pattern (116 bp):
ATTTGAAATATAAATTAATTAGATTATTTATTTTTGATTTTACATATTAAATTGTATTCGAGTAA
TTTAGTAAGTGTAATTTAAATTATCTACAATTTTTAGTGTAATTTTTTTAA
Found at i:1562634 original size:97 final size:98
Alignment explanation
Indices: 1562383--1562951 Score: 279
Period size: 102 Copynumber: 5.4 Consensus size: 98
1562373 TTTTTAAATT
* * *
1562383 TAAATTTAAATTATTAGATTATTTATTTTGATTTTACATATTAAGTTGTATTTGAGTAAATCTTG
1 TAAATATAAATTATTAGATTATTTATTTTG-TTTTACATATTAAATTGTATTTGAGT-AGT-TTG
* * * *
1562448 ATTAGTGTAGTTTAAATTATTACATTTTTTTTTATTG
63 GTAACTGTAGTTTAAATTATTA-ATTTATTTTTATTG
* * * * * *
1562485 -AGTAACATAAATTATTAGACTAATTATTTTTATTTTACATATTAAATCGTATTTGAGTTGTTTG
1 TA--AATATAAATTATTAGATTATTTA-TTTTGTTTTACATATTAAATTGTATTTGAGTAGTTTG
*
1562549 GTAACTTTAGTTTAACA-T-TT-ATTTATTTTTATTG
63 GTAACTGTAGTTTAA-ATTATTAATTTATTTTTATTG
* * * *
1562583 TAAATATAAATTAATTAGATTATTTATTTTGCTTTACACATTAAATTGTATTCGAGTGGTTTGGT
1 TAAATATAAATT-ATTAGATTATTTATTTTGTTTTACATATTAAATTGTATTTGAGTAGTTTGGT
* *** * * *
1562648 AAGT-TAAAAAATAATTTTTGTGTAATTTTTAGTATGTTTTTTG
65 AACTGT--AGTTTAA--ATTAT-TAA--TTTA-T-T-TTTATTG
* * * * *
1562691 TTTTTAATTTAAATTATAATTATTAGAATATTTATTTTGATTTCACATATTAAGTTGTATTTGAG
1 ---TAAATATAAA------TTATTAGATTATTTATTTTG-TTTTACATATTAAATTGTATTTGAG
** * *
1562756 TAGTTTGGTATGTTTAGTTTAAATTA-TATTTTTATCTTTTTATTG
56 TAGTTTGGTAACTGTAGTTTAAATTATTA-ATTTA--TTTTTATTG
* * * * *
1562801 -AGTAATATAAATTATTGGACTATTTATTTTTATTTTACATATTAAATCGAATTTGAGTAGTTTG
1 TA--AATATAAATTATTAGATTATTTA-TTTTGTTTTACATATTAAATTGTATTTGAGTAGTTTG
* * * *
1562865 GTAAGTTTAGTTTAAATTTTATTGTTTTATTTTTGTTTTTATTG
63 GTAACTGTAGTTTAAA--TTA-----TTA-ATTTATTTTTATTG
* *
1562909 TAAATATAAATTAATTAGACTATTTATTTTGATTTAACATATT
1 TAAATATAAATT-ATTAGATTATTTATTTTG-TTTTACATATT
1562952 TTTTGTTTAA
Statistics
Matches: 360, Mismatches: 62, Indels: 84
0.71 0.12 0.17
Matches are distributed among these distances:
96 1 0.00
97 45 0.12
98 28 0.08
99 1 0.00
100 3 0.01
101 17 0.05
102 59 0.16
103 48 0.13
104 7 0.02
105 4 0.01
106 1 0.00
107 15 0.04
108 44 0.12
109 1 0.00
110 13 0.04
111 13 0.04
112 3 0.01
114 2 0.01
116 21 0.06
117 33 0.09
118 1 0.00
ACGTcount: A:0.31, C:0.04, G:0.11, T:0.54
Consensus pattern (98 bp):
TAAATATAAATTATTAGATTATTTATTTTGTTTTACATATTAAATTGTATTTGAGTAGTTTGGTA
ACTGTAGTTTAAATTATTAATTTATTTTTATTG
Found at i:1562830 original size:316 final size:314
Alignment explanation
Indices: 1562249--1562948 Score: 907
Period size: 316 Copynumber: 2.2 Consensus size: 314
1562239 TTTATTGTTT
* *
1562249 CATTT-TTAATTTTTATT-TGAAATATAAATTAATTAGATTATTTATTTTTGATTTTACATATTA
1 CATTTATTTATTTTTATTGT-AAATATAAATTAATTAGATTATTTA-TTTTGA-TTTACACATTA
* **
1562312 AATTGTATTCGAGTGGTTTAGTAAGTTTAATTTAAATTTTCGTGTAATTTTTAGTGTAATTTTTT
63 AATTGTATTCGAGTGGTTTAGTAAGTTAAAAATAAATTTTCGTGTAATTTTTAGTGTAATTTTTT
* *
1562377 TAAATTTAAATTTAAATTATTAGATTATTTATTTTGATTTTACATATTAAGTTGTATTTGAGTAA
128 TAAATTTAAATTTAAATTATTAGAATATTTATTTTGATTTCACATATTAAGTTGTATTTGAGTAA
1562442 ATCTTGATTAGTGTAGTTTAAATTATTACATTTTTTTTTATTGAGTAACATAAATTATTAGACTA
193 ATCTTGATTAGTGTAGTTTAAATTATTACATTTTTTTTTATTGAGTAACATAAATTATTAGACTA
* *
1562507 ATTATTTTTATTTTACATATTAAATCGTATTTGAGTTGTTTGGTAACTTTAGTTTAA
258 ATTATTTTTATTTTACATATTAAATCGAATTTGAGTAGTTTGGTAACTTTAGTTTAA
*
1562564 CATTTATTTATTTTTATTGTAAATATAAATTAATTAGATTATTTATTTTGCTTTACACATTAAAT
1 CATTTATTTATTTTTATTGTAAATATAAATTAATTAGATTATTTATTTTGATTTACACATTAAAT
* * **
1562629 TGTATTCGAGTGGTTTGGTAAGTTAAAAA-ATAATTTTTGTGTAATTTTTAGTATGTTTTTTGTT
66 TGTATTCGAGTGGTTTAGTAAGTTAAAAATA-AATTTTCGTGTAATTTTTAG--TGTAATTT-TT
*
1562693 TTTAATTTAAA-TTATAATTATTAGAATATTTATTTTGATTTCACATATTAAGTTGTATTTGAGT
127 TTAAATTTAAATTTA-AATTATTAGAATATTTATTTTGATTTCACATATTAAGTTGTATTTGAGT
* * * ** * *
1562757 -AGT-TTG-GTATGTTTAGTTTAAATTA-TATTTTTATCTTTTTATTGAGTAATATAAATTATTG
191 AAATCTTGATTA-GTGTAGTTTAAATTATTACATTT-T-TTTTTATTGAGTAACATAAATTATTA
* *
1562818 GACTATTTATTTTTATTTTACATATTAAATCGAATTTGAGTAGTTTGGTAAGTTTAGTTTAA
253 GACTAATTATTTTTATTTTACATATTAAATCGAATTTGAGTAGTTTGGTAACTTTAGTTTAA
*
1562880 -ATTTTATTGTTTTATTTTTGTTTTTATTGTAAATATAAATTAATTAGACTATTTATTTTGATTT
1 CA-TTTA----TTTA------TTTTTATTGTAAATATAAATTAATTAGATTATTTATTTTGATTT
1562944 A-ACAT
55 ACACAT
1562949 ATTTTTTGTT
Statistics
Matches: 338, Mismatches: 26, Indels: 32
0.85 0.07 0.08
Matches are distributed among these distances:
313 1 0.00
314 64 0.19
315 29 0.09
316 133 0.39
317 60 0.18
320 4 0.01
325 4 0.01
326 43 0.13
ACGTcount: A:0.31, C:0.04, G:0.11, T:0.54
Consensus pattern (314 bp):
CATTTATTTATTTTTATTGTAAATATAAATTAATTAGATTATTTATTTTGATTTACACATTAAAT
TGTATTCGAGTGGTTTAGTAAGTTAAAAATAAATTTTCGTGTAATTTTTAGTGTAATTTTTTTAA
ATTTAAATTTAAATTATTAGAATATTTATTTTGATTTCACATATTAAGTTGTATTTGAGTAAATC
TTGATTAGTGTAGTTTAAATTATTACATTTTTTTTTATTGAGTAACATAAATTATTAGACTAATT
ATTTTTATTTTACATATTAAATCGAATTTGAGTAGTTTGGTAACTTTAGTTTAA
Found at i:1562866 original size:102 final size:106
Alignment explanation
Indices: 1562700--1562951 Score: 318
Period size: 102 Copynumber: 2.4 Consensus size: 106
1562690 GTTTTTAATT
* * * * *
1562700 TAAAT-TATAATTATTAGAATATTTATTTTGATTTCACATATTAAGTTGTATTTGAGTAGTTTGG
1 TAAATATA-AATTATTAGACTATTTATTTTGATTTAACATATTAAATCGAATTTGAGTAGTTTGG
*
1562764 TATGTTTAGTTTAAATTATA-T-TTTTATCTTTT-TATTGA-G
65 TAAGTTTAGTTTAAATTATATTGTTTTAT-TTTTGTATTGATG
* * *
1562803 T-AATATAAATTATTGGACTATTTATTTTTATTTTACATATTAAATCGAATTTGAGTAGTTTGGT
1 TAAATATAAATTATTAGACTATTTATTTTGATTTAACATATTAAATCGAATTTGAGTAGTTTGGT
* * *
1562867 AAGTTTAGTTTAAATTTTATTGTTTTATTTTTGTTTTTATTG
66 AAGTTTAGTTTAAATTATATTGTTTTATTTTTGTATTGA-TG
1562909 TAAATATAAATTAATTAGACTATTTATTTTGATTTAACATATT
1 TAAATATAAATT-ATTAGACTATTTATTTTGATTTAACATATT
1562952 TTTTGTTTAA
Statistics
Matches: 127, Mismatches: 14, Indels: 11
0.84 0.09 0.07
Matches are distributed among these distances:
102 70 0.55
103 8 0.06
104 10 0.08
106 2 0.02
107 10 0.08
108 27 0.21
ACGTcount: A:0.31, C:0.03, G:0.11, T:0.54
Consensus pattern (106 bp):
TAAATATAAATTATTAGACTATTTATTTTGATTTAACATATTAAATCGAATTTGAGTAGTTTGGT
AAGTTTAGTTTAAATTATATTGTTTTATTTTTGTATTGATG
Found at i:1570049 original size:32 final size:32
Alignment explanation
Indices: 1570011--1570071 Score: 122
Period size: 32 Copynumber: 1.9 Consensus size: 32
1570001 AAAATTTCAA
1570011 AAAAATGTAAATATATTAACAATATTTTTTAT
1 AAAAATGTAAATATATTAACAATATTTTTTAT
1570043 AAAAATGTAAATATATTAACAATATTTTT
1 AAAAATGTAAATATATTAACAATATTTTT
1570072 AACATTTTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (32 bp):
AAAAATGTAAATATATTAACAATATTTTTTAT
Found at i:1570159 original size:46 final size:46
Alignment explanation
Indices: 1570068--1570160 Score: 127
Period size: 46 Copynumber: 2.0 Consensus size: 46
1570058 TTAACAATAT
* * *
1570068 TTTTAACATTTTTCTAGAAATACTAAATCAAATGTTGATCTAATTA
1 TTTTAACATTTTTCTACAAATACTAAATCAAATCTTGATCAAATTA
1570114 TTTTAACATTTTTACTACAAATACTAAATC-AATCTT-ATTCAAATTA
1 TTTTAACATTTTT-CTACAAATACTAAATCAAATCTTGA-TCAAATTA
1570160 T
1 T
1570161 ACTAATGATT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
45 1 0.02
46 26 0.62
47 15 0.36
ACGTcount: A:0.40, C:0.13, G:0.03, T:0.44
Consensus pattern (46 bp):
TTTTAACATTTTTCTACAAATACTAAATCAAATCTTGATCAAATTA
Found at i:1571174 original size:39 final size:39
Alignment explanation
Indices: 1571120--1571208 Score: 151
Period size: 39 Copynumber: 2.3 Consensus size: 39
1571110 CCGACCACCC
*
1571120 TGAAAACGCCAGGTAATCTTGGAGTCTTCTTATTTTGCA
1 TGAAAACGCCAGGTAATCTTAGAGTCTTCTTATTTTGCA
*
1571159 TGAAAACGCCAGGTAATCTTAGAGTCTTTTTATTTTGCA
1 TGAAAACGCCAGGTAATCTTAGAGTCTTCTTATTTTGCA
*
1571198 TGAAGACGCCA
1 TGAAAACGCCA
1571209 AATAAGCTTG
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 47 1.00
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (39 bp):
TGAAAACGCCAGGTAATCTTAGAGTCTTCTTATTTTGCA
Found at i:1573914 original size:78 final size:78
Alignment explanation
Indices: 1573780--1573935 Score: 294
Period size: 78 Copynumber: 2.0 Consensus size: 78
1573770 TTTATCGACA
* *
1573780 AGTCATTCATCGTTGTAGACATAAACAAGAAAAGGAAATTAGAGGCCGAGTTATTGGACTTGCCG
1 AGTCATTCATCGTTGTAGACATAAACAAGAAAAGGAAATTAGAGGACGAGTAATTGGACTTGCCG
1573845 TTATCGAAGCATC
66 TTATCGAAGCATC
1573858 AGTCATTCATCGTTGTAGACATAAACAAGAAAAGGAAATTAGAGGACGAGTAATTGGACTTGCCG
1 AGTCATTCATCGTTGTAGACATAAACAAGAAAAGGAAATTAGAGGACGAGTAATTGGACTTGCCG
1573923 TTATCGAAGCATC
66 TTATCGAAGCATC
1573936 GATATCGGAA
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
78 76 1.00
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25
Consensus pattern (78 bp):
AGTCATTCATCGTTGTAGACATAAACAAGAAAAGGAAATTAGAGGACGAGTAATTGGACTTGCCG
TTATCGAAGCATC
Found at i:1582378 original size:29 final size:29
Alignment explanation
Indices: 1582341--1582414 Score: 112
Period size: 29 Copynumber: 2.5 Consensus size: 29
1582331 TGTTCATGTA
1582341 CTCATGTCATTTCTCTTATGATCATATAG
1 CTCATGTCATTTCTCTTATGATCATATAG
* * *
1582370 CTCACGTCATTTCTCTTGTGATCATGTAG
1 CTCATGTCATTTCTCTTATGATCATATAG
1582399 CTCATGTCATGTTCTC
1 CTCATGTCAT-TTCTC
1582415 ATATCACATA
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
29 35 0.88
30 5 0.12
ACGTcount: A:0.19, C:0.24, G:0.14, T:0.43
Consensus pattern (29 bp):
CTCATGTCATTTCTCTTATGATCATATAG
Found at i:1582430 original size:12 final size:12
Alignment explanation
Indices: 1582413--1582437 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1582403 TGTCATGTTC
1582413 TCATATCACATA
1 TCATATCACATA
1582425 TCATATCACATA
1 TCATATCACATA
1582437 T
1 T
1582438 GTATTTGAAG
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:0.40, C:0.24, G:0.00, T:0.36
Consensus pattern (12 bp):
TCATATCACATA
Found at i:1582860 original size:64 final size:63
Alignment explanation
Indices: 1582791--1582947 Score: 167
Period size: 64 Copynumber: 2.5 Consensus size: 63
1582781 TAATGAAGGT
* **
1582791 ATGCATCGATGCACTACTTGTGCATCGGTGCA-TAAAATGCATTCGAT-GTTTTATTATTAATGG
1 ATGCATCGATGCACTACTTGTGCATCGATGCACT-AAATGCATTCGATCGTTTTATT-TTAA-AA
1582854 G
63 G
* * * * *
1582855 ATGCATCGATGCA-TGCCTTATACATCGATGCACTAATTGCATTCGATCTTTTTATTTTAAAAG
1 ATGCATCGATGCACT-ACTTGTGCATCGATGCACTAAATGCATTCGATCGTTTTATTTTAAAAG
*
1582918 AGTGCATCGATGCACTACCTGTGCATCGAT
1 A-TGCATCGATGCACTACTTGTGCATCGAT
1582948 ACACCTTCAA
Statistics
Matches: 76, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
63 3 0.04
64 64 0.84
65 9 0.12
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (63 bp):
ATGCATCGATGCACTACTTGTGCATCGATGCACTAAATGCATTCGATCGTTTTATTTTAAAAG
Found at i:1594528 original size:23 final size:22
Alignment explanation
Indices: 1594470--1594533 Score: 65
Period size: 23 Copynumber: 2.9 Consensus size: 22
1594460 TATTTGATCT
*
1594470 AATAATTTTTAAATTATTTAAA
1 AATAATTTTTATATTATTTAAA
* * **
1594492 AATTATATCAATATTCATTTAAA
1 AATAATTTTTATATT-ATTTAAA
*
1594515 TATAATTTTTATATTATTT
1 AATAATTTTTATATTATTT
1594534 TTTAAATTCA
Statistics
Matches: 31, Mismatches: 10, Indels: 2
0.72 0.23 0.05
Matches are distributed among these distances:
22 14 0.45
23 17 0.55
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (22 bp):
AATAATTTTTATATTATTTAAA
Found at i:1597157 original size:6 final size:6
Alignment explanation
Indices: 1597146--1598013 Score: 1431
Period size: 6 Copynumber: 148.7 Consensus size: 6
1597136 CAGTTCGTGC
1597146 TTATAT TTATAT TTATAT TTATAT TTATAT TTATA- TT-TAT TTATAT
1 TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT
1597192 TTATAT TTATAT TTATAT TTATA- TTATA- TTATAT TTATAT TTATAT
1 TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT
1597238 TTATAT TTATA- TTATAT TTATA- TTATAT TTATAT TTATAT TTATAT
1 TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT
1597284 TTATAT TTATAT TTAT-T TTATAT TTATAT TTATTTAT TTAT-T TTATAT
1 TTATAT TTATAT TTATAT TTATAT TTATAT TTA--TAT TTATAT TTATAT
1597332 TTATAT TTATAT TTA-AT TTATAT TTATAT TTATAT TTATAT TTATAT
1 TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT
1597379 TTATAT TTATA- TTATAT TTATA- TTATAT TTATAT TTATA- TT-TAT
1 TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT
*
1597423 TT-TAT TTATAT TTATAT TTATAT TTATATT TTATAT TTATAT TATTTAT
1 TTATAT TTATAT TTATAT TTATAT TTATA-T TTATAT TTATAT T-TATAT
1597472 TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATA- TTATAT
1 TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT
1597519 TTATAT TTATA- TT-TAT TTATAT TTATAT TTATAT TTATA- TT-TAT
1 TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT
1597563 TTATAT TTATAT TTATA- TT-TAT TTATAT TTATAT TTATAT TTATAT
1 TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT
1597609 TTATAT TTATAT TTATAT TTATA- TTATAT TTATAT TTATAT TTATAT
1 TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT
1597656 TTATAT TTATAT TTATA- TTATAT TTATAT TTATA- TT-TAT TTATAT
1 TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT
1597701 TTATAT TTAT-T TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT
1 TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT
1597748 TTATAT TTATAT TTATAT TTATAT TTATAT TTATA- TTATA- TT-TAT
1 TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT
1597793 TTATATT TTATAT TTATAT ATTATAT TTATAT TTATAT TTATAT TTATAT
1 TTATA-T TTATAT TTATAT -TTATAT TTATAT TTATAT TTATAT TTATAT
1597843 TTATAT TTATAT TTATA- TTATAT TTATAT TTATAT TTATTAT ATTATAT
1 TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTA-TAT -TTATAT
1597892 TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT
1 TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT
1597940 TTATA- TT-TAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT
1 TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT
1597986 TTATAT TTATAT TTATAT TTATAT TTAT
1 TTATAT TTATAT TTATAT TTATAT TTAT
1598014 TGATTAATAT
Statistics
Matches: 823, Mismatches: 2, Indels: 74
0.92 0.00 0.08
Matches are distributed among these distances:
4 16 0.02
5 112 0.14
6 657 0.80
7 29 0.04
8 9 0.01
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
TTATAT
Found at i:1601050 original size:18 final size:18
Alignment explanation
Indices: 1601023--1601058 Score: 56
Period size: 17 Copynumber: 2.0 Consensus size: 18
1601013 TAAAAATAAA
1601023 AATTTAAATAATCAAAAAT
1 AATTTAAATAAT-AAAAAT
1601042 AATTT-AATAATAAAAAT
1 AATTTAAATAATAAAAAT
1601059 TATTATTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.35
18 6 0.35
19 5 0.29
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (18 bp):
AATTTAAATAATAAAAAT
Done.