Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004760.1 Hibiscus syriacus cultivar Beakdansim tig00010739_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: 83102
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Found at i:3575 original size:30 final size:30
Alignment explanation
Indices: 3489--3587 Score: 98
Period size: 30 Copynumber: 3.4 Consensus size: 30
3479 GACATGTATT
*
3489 ATGTCATCACTT---ACGTGTACAAGTGTC
1 ATGTCATCACTTGAAACATGTACAAGTGTC
* * ** *
3516 ATGTCATCCCTTTAAACATGTGTATGTGTC
1 ATGTCATCACTTGAAACATGTACAAGTGTC
3546 ATGTCATCACTTGAACACATG-ACAAGTGTC
1 ATGTCATCACTTGAA-ACATGTACAAGTGTC
*
3576 ACGTCATCACTT
1 ATGTCATCACTT
3588 TTGACACATA
Statistics
Matches: 57, Mismatches: 11, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
27 11 0.19
30 41 0.72
31 5 0.09
ACGTcount: A:0.27, C:0.23, G:0.16, T:0.33
Consensus pattern (30 bp):
ATGTCATCACTTGAAACATGTACAAGTGTC
Found at i:4004 original size:5 final size:5
Alignment explanation
Indices: 3994--4019 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
3984 GAAGTTTTGA
3994 TTTCT TTTCT TTTCT TTTCT TTTCT T
1 TTTCT TTTCT TTTCT TTTCT TTTCT T
4020 ACTGTGAGAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTCT
Found at i:6916 original size:31 final size:31
Alignment explanation
Indices: 6873--6931 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
6863 AAATTACACA
*
6873 TTTGCTCCTAATTACTTACATTTTCTATTAT
1 TTTGCTCCTAATTACTTACATATTCTATTAT
* * *
6904 TTTGGTCCTAATTATTTATATATTCTAT
1 TTTGCTCCTAATTACTTACATATTCTAT
6932 CAAATTGATC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.24, C:0.15, G:0.05, T:0.56
Consensus pattern (31 bp):
TTTGCTCCTAATTACTTACATATTCTATTAT
Found at i:10000 original size:13 final size:14
Alignment explanation
Indices: 9982--10012 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
9972 TATTATATGT
9982 TTTAGA-TTTAAAA
1 TTTAGAGTTTAAAA
9995 TTTAGAGTTTAAAA
1 TTTAGAGTTTAAAA
10009 TTTA
1 TTTA
10013 AAATCATTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.35
14 11 0.65
ACGTcount: A:0.42, C:0.00, G:0.10, T:0.48
Consensus pattern (14 bp):
TTTAGAGTTTAAAA
Found at i:11037 original size:24 final size:24
Alignment explanation
Indices: 11004--11086 Score: 130
Period size: 24 Copynumber: 3.5 Consensus size: 24
10994 GTGTTTGTGT
11004 TGTTCGTTTATGTTCGTTCGTTTG
1 TGTTCGTTTATGTTCGTTCGTTTG
*
11028 TTTTCGTTTATGTTCGTTCGTTTG
1 TGTTCGTTTATGTTCGTTCGTTTG
* * *
11052 TGTTCGTTCATGTTCGTTTGTTTA
1 TGTTCGTTTATGTTCGTTCGTTTG
11076 TGTTCGTTTAT
1 TGTTCGTTTAT
11087 TTATTAAATG
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 53 1.00
ACGTcount: A:0.06, C:0.12, G:0.22, T:0.60
Consensus pattern (24 bp):
TGTTCGTTTATGTTCGTTCGTTTG
Found at i:11084 original size:14 final size:14
Alignment explanation
Indices: 10996--11083 Score: 86
Period size: 14 Copynumber: 6.9 Consensus size: 14
10986 TTTTTTGTGT
*
10996 GTTTGTGTT-GTTC
1 GTTTATGTTCGTTC
11009 GTTTATGTTCGTTC
1 GTTTATGTTCGTTC
11023 G-TT-TGTT--TTC
1 GTTTATGTTCGTTC
11033 GTTTATGTTCGTTC
1 GTTTATGTTCGTTC
11047 G-TT-TG-T-GTTC
1 GTTTATGTTCGTTC
* *
11057 GTTCATGTTCGTTT
1 GTTTATGTTCGTTC
11071 GTTTATGTTCGTT
1 GTTTATGTTCGTT
11084 TATTTATTAA
Statistics
Matches: 62, Mismatches: 4, Indels: 17
0.75 0.05 0.20
Matches are distributed among these distances:
10 9 0.15
11 4 0.06
12 12 0.19
13 13 0.21
14 24 0.39
ACGTcount: A:0.05, C:0.11, G:0.24, T:0.60
Consensus pattern (14 bp):
GTTTATGTTCGTTC
Found at i:11089 original size:14 final size:14
Alignment explanation
Indices: 11061--11090 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
11051 GTGTTCGTTC
*
11061 ATGTTCGTTTGTTT
1 ATGTTCGTTTATTT
11075 ATGTTCGTTTATTT
1 ATGTTCGTTTATTT
11089 AT
1 AT
11091 TAAATGAACG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.13, C:0.07, G:0.17, T:0.63
Consensus pattern (14 bp):
ATGTTCGTTTATTT
Found at i:13312 original size:17 final size:18
Alignment explanation
Indices: 13273--13316 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
13263 AAAAAAAAGA
13273 AGATT-ATTATTAATTAAT
1 AGATTAATT-TTAATTAAT
13291 A-ATTAATTTTAATT-AT
1 AGATTAATTTTAATTAAT
13307 AGATTAATTT
1 AGATTAATTT
13317 CCTAGGATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 3 0.12
17 17 0.71
18 4 0.17
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (18 bp):
AGATTAATTTTAATTAAT
Found at i:14748 original size:30 final size:29
Alignment explanation
Indices: 14714--14785 Score: 72
Period size: 30 Copynumber: 2.4 Consensus size: 29
14704 TCATAGAATT
*
14714 ACAATCAGCTCACTCAATTAATTGATTATA
1 ACAATCAG-TCACTCAATTAATTAATTATA
* ** *
14744 ACAATTAAGTCACTGGATTCATTAATTATA
1 ACAA-TCAGTCACTCAATTAATTAATTATA
14774 ACAATCAAGTCA
1 ACAATC-AGTCA
14786 TGTGTCATTG
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
29 1 0.03
30 30 0.88
31 3 0.09
ACGTcount: A:0.42, C:0.18, G:0.08, T:0.32
Consensus pattern (29 bp):
ACAATCAGTCACTCAATTAATTAATTATA
Found at i:15130 original size:31 final size:31
Alignment explanation
Indices: 15095--15166 Score: 74
Period size: 31 Copynumber: 2.3 Consensus size: 31
15085 GACTTTTTAA
* * *
15095 AATTGAATGA-TCCGTTTATAATCTTATTAGT
1 AATTGAATGACT-CATTTATAATCTTACTAAT
* *
15126 AATTGAGTGACTCATTTGTAATCTTACTAAT
1 AATTGAATGACTCATTTATAATCTTACTAAT
*
15157 AATTGGATGA
1 AATTGAATGA
15167 ATTATAATGC
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
31 32 0.97
32 1 0.03
ACGTcount: A:0.33, C:0.10, G:0.15, T:0.42
Consensus pattern (31 bp):
AATTGAATGACTCATTTATAATCTTACTAAT
Found at i:17950 original size:35 final size:35
Alignment explanation
Indices: 17904--17986 Score: 139
Period size: 35 Copynumber: 2.4 Consensus size: 35
17894 TGACGAATCT
*
17904 AGAAAAATTTTATAAATCGAACTAATATAAACTTA
1 AGAAAATTTTTATAAATCGAACTAATATAAACTTA
* *
17939 AGAAATTTTTTATAAATCGAGCTAATATAAACTTA
1 AGAAAATTTTTATAAATCGAACTAATATAAACTTA
17974 AGAAAATTTTTAT
1 AGAAAATTTTTAT
17987 TTAAAATAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 44 1.00
ACGTcount: A:0.49, C:0.07, G:0.07, T:0.36
Consensus pattern (35 bp):
AGAAAATTTTTATAAATCGAACTAATATAAACTTA
Found at i:19343 original size:17 final size:18
Alignment explanation
Indices: 19309--19349 Score: 66
Period size: 17 Copynumber: 2.3 Consensus size: 18
19299 TAACAATGAG
*
19309 TTATTATAAAATATATTT
1 TTATTATAAAACATATTT
19327 TTATTAT-AAACATATTT
1 TTATTATAAAACATATTT
19344 TTATTA
1 TTATTA
19350 GTAATTTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 15 0.68
18 7 0.32
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.56
Consensus pattern (18 bp):
TTATTATAAAACATATTT
Found at i:19614 original size:24 final size:25
Alignment explanation
Indices: 19583--19641 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 25
19573 AAAATAAAAC
* *
19583 TAAAAATATAATGTTCAAAA-TATT
1 TAAAAATATAATATTAAAAACTATT
*
19607 TAAAAATAAAATATTAAAAACTATT
1 TAAAAATATAATATTAAAAACTATT
* *
19632 TGAAACTATA
1 TAAAAATATA
19642 TTGAATCATT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
24 17 0.61
25 11 0.39
ACGTcount: A:0.58, C:0.05, G:0.03, T:0.34
Consensus pattern (25 bp):
TAAAAATATAATATTAAAAACTATT
Found at i:19950 original size:11 final size:10
Alignment explanation
Indices: 19864--19983 Score: 64
Period size: 11 Copynumber: 11.4 Consensus size: 10
19854 CTGGATTTTT
19864 ATATTATTAAA
1 ATATTATT-AA
*
19875 ATAGTCATTAA
1 ATA-TTATTAA
*
19886 AT-TTATAAA
1 ATATTATTAA
19895 ATGATTATTAA
1 AT-ATTATTAA
**
19906 ATGAGCATTAA
1 AT-ATTATTAA
* *
19917 ATTTTATCAA
1 ATATTATTAA
**
19927 ATTATTAGAAA
1 A-TATTATTAA
19938 ATAGTTATTAA
1 ATA-TTATTAA
19949 AT-TTATTAA
1 ATATTATTAA
*
19958 GATATTATAAA
1 -ATATTATTAA
*
19969 ATAATAATTAA
1 AT-ATTATTAA
19980 ATAT
1 ATAT
19984 GTCATTCTTT
Statistics
Matches: 83, Mismatches: 18, Indels: 17
0.70 0.15 0.14
Matches are distributed among these distances:
9 14 0.17
10 13 0.16
11 52 0.63
12 4 0.05
ACGTcount: A:0.50, C:0.03, G:0.06, T:0.42
Consensus pattern (10 bp):
ATATTATTAA
Found at i:19964 original size:31 final size:30
Alignment explanation
Indices: 19864--19981 Score: 112
Period size: 31 Copynumber: 3.8 Consensus size: 30
19854 CTGGATTTTT
*
19864 ATATTATTAAAATAGTCATTAAATTTATAAA
1 ATATTA-TAAAATAGTCATTAAATTTATTAA
* *
19895 ATGATTATTAAATGAG-CATTAAATTTTATCAA
1 AT-ATTATAAAAT-AGTCATTAAA-TTTATTAA
* *
19927 ATTATTAGAAAATAGTTATTAAATTTATTAA
1 A-TATTATAAAATAGTCATTAAATTTATTAA
* *
19958 GATATTATAAAATAATAATTAAAT
1 -ATATTATAAAATAGTCATTAAAT
19982 ATGTCATTCT
Statistics
Matches: 72, Mismatches: 9, Indels: 12
0.77 0.10 0.13
Matches are distributed among these distances:
31 42 0.58
32 29 0.40
33 1 0.01
ACGTcount: A:0.50, C:0.03, G:0.06, T:0.42
Consensus pattern (30 bp):
ATATTATAAAATAGTCATTAAATTTATTAA
Found at i:24695 original size:120 final size:120
Alignment explanation
Indices: 24445--24727 Score: 356
Period size: 120 Copynumber: 2.3 Consensus size: 120
24435 TGATTGGAAT
* *
24445 TTGGAACTTTGAAACCTTCTTTGAGATTATGGATTCATTGGCTTGATATTCGCATCGCACCTAAT
1 TTGGAACTTTGAAACCTT-TTTGAGATTAGGGATTCATTGGCTCGATA-T--CATCGCACCTAAT
* * * * *
24510 AACATAGATATTTTGAGTATATTCTTATATCCGATACTCGTATCGAATAATTTAGATAA
62 AACATAGATATTTCGAGCATATTCTTATATCCAACACTCGTATCGAATAATGTAGATAA
* * *
24569 TCGGAACTTTGAAACCTTTTTACAGATTAGGGATTCATTGGCTCGATA-C-TCGCACCTAGTAAC
1 TTGGAACTTTGAAACCTTTTT-GAGATTAGGGATTCATTGGCTCGATATCATCGCACCTAATAAC
* *
24632 AATAGATATTTCGAGCGTATTCTTATATCCAACACTC-TCATTGAATAATGTAGATAA
65 -ATAGATATTTCGAGCATATTCTTATATCCAACACTCGT-ATCGAATAATGTAGATAA
*
24689 TTGGAACTTTGAAACCTTTTTTGAGATTAGAGATTCATT
1 TTGGAACTTTGAAACC-TTTTTGAGATTAGGGATTCATT
24728 TACAACATTT
Statistics
Matches: 140, Mismatches: 15, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
119 14 0.10
120 78 0.56
121 5 0.04
123 3 0.02
124 40 0.29
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Consensus pattern (120 bp):
TTGGAACTTTGAAACCTTTTTGAGATTAGGGATTCATTGGCTCGATATCATCGCACCTAATAACA
TAGATATTTCGAGCATATTCTTATATCCAACACTCGTATCGAATAATGTAGATAA
Found at i:32540 original size:81 final size:80
Alignment explanation
Indices: 32405--32644 Score: 271
Period size: 81 Copynumber: 3.0 Consensus size: 80
32395 AAAAACGTTA
* * *
32405 GATCATATGAATTATACCTAAGATATTGAAGAACACGCAGAATAAAGCAATTATTAAAGGAAGAA
1 GATCATATGAATTATACCTAGGATA-TGAATAACATGCAGAATAAAGCAATTATTAAAGGAAGAA
*
32470 GAAGAAGAAGATG-AT
65 GAAGAAGAAGAAGAAT
32485 GGATCATATGAATTATACCTAGGATATCGAATAACATGCAGAATAAAGCAATTATTAAAGGTGGA
1 -GATCATATGAATTATACCTAGGATAT-GAATAACATGCAGAATAAAGCAATTATTAAA---GG-
32550 AGCAGAAGAAGAAGAAGAAGAAT
60 A--AGAAGAAGAAGAAGAAGAAT
* * *
32573 GATCATATGAATTAAACCTAGG--AT--AT---ATGCAGACTAAAGCAATTATTAAAAGAAGAAG
1 GATCATATGAATTATACCTAGGATATGAATAACATGCAGAATAAAGCAATTATTAAAGGAAGAAG
*
32631 ACGAAGAAGAAGAA
66 AAGAAGAAGAAGAA
32645 GCTTACAGTT
Statistics
Matches: 143, Mismatches: 8, Indels: 24
0.82 0.05 0.14
Matches are distributed among these distances:
73 18 0.13
75 1 0.01
76 1 0.01
79 23 0.16
80 1 0.01
81 53 0.37
82 2 0.01
84 2 0.01
85 3 0.02
87 37 0.26
88 2 0.01
ACGTcount: A:0.50, C:0.09, G:0.21, T:0.20
Consensus pattern (80 bp):
GATCATATGAATTATACCTAGGATATGAATAACATGCAGAATAAAGCAATTATTAAAGGAAGAAG
AAGAAGAAGAAGAAT
Found at i:34038 original size:4 final size:4
Alignment explanation
Indices: 34031--34364 Score: 551
Period size: 4 Copynumber: 83.5 Consensus size: 4
34021 ACACACACAA
34031 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
34079 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
34127 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
34175 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
34223 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
* * * * *
34271 ATGT ATGT ATGT ATAT ACGT ATGT ATGT ATGT ATGT ACGT ATGT ACGC
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
* * * * ** **
34319 GTAT ACGT ATGT ACGT ATGT ACAT ACAT ATGT ATGT ATGT ATGT AT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT
34365 TTGAGATTTA
Statistics
Matches: 308, Mismatches: 22, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 308 1.00
ACGTcount: A:0.26, C:0.02, G:0.24, T:0.48
Consensus pattern (4 bp):
ATGT
Found at i:35001 original size:22 final size:22
Alignment explanation
Indices: 34976--35029 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
34966 ATTGATAACC
34976 CTAAACCATAGCCCTGTAGCCT
1 CTAAACCATAGCCCTGTAGCCT
*
34998 CTAAACCATAGCCCTGTAGTCT
1 CTAAACCATAGCCCTGTAGCCT
35020 CTAAACCATA
1 CTAAACCATA
35030 AAACCTAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.31, C:0.33, G:0.11, T:0.24
Consensus pattern (22 bp):
CTAAACCATAGCCCTGTAGCCT
Found at i:35814 original size:14 final size:14
Alignment explanation
Indices: 35797--35838 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
35787 TTAAATAGTT
35797 AAATATTTATATTA
1 AAATATTTATATTA
**
35811 AAATACATATAGTT-
1 AAATATTTATA-TTA
35825 AAATATTTATATTA
1 AAATATTTATATTA
35839 TTAAAGTATA
Statistics
Matches: 22, Mismatches: 4, Indels: 4
0.73 0.13 0.13
Matches are distributed among these distances:
13 2 0.09
14 18 0.82
15 2 0.09
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (14 bp):
AAATATTTATATTA
Found at i:39508 original size:159 final size:158
Alignment explanation
Indices: 39219--39551 Score: 639
Period size: 159 Copynumber: 2.1 Consensus size: 158
39209 CGTTCAGCTT
39219 AGTTTTATTCGGATTAAGCACGAGCTTCATTTACTTTATTTGAATCCTGAGATTTTGGTTCTGAA
1 AGTTTTATTCGGATTAAGCACGAGCTTCATTTACTTTATTTGAATCCTGAGATTTTGGTTCTGAA
39284 AATTTTGATATTTCAACTCCTTGCCACAATCGGTGTAACATTCATTCTTTGTATTTTATGTTTGT
66 AATTTTGATATTTCAACTCCTTGCCACAATCGGTGTAACATTCATTCTTTGTATTTTATGTTTGT
39349 TTAAAGCATCTTTGGGTTTCCTTCGATTC
131 TT-AAGCATCTTTGGGTTTCCTTCGATTC
39378 AGTTTTATTCGGATTAAGCACGAGCTTCATTTACTTTATTTGAATCCTGAGATTTTGGTTCTGAA
1 AGTTTTATTCGGATTAAGCACGAGCTTCATTTACTTTATTTGAATCCTGAGATTTTGGTTCTGAA
39443 AATTTTGATATTTCAACTCCTTGCCACAATCGGTGTAACATTCATTCTTTGTATTTTATGTTTGT
66 AATTTTGATATTTCAACTCCTTGCCACAATCGGTGTAACATTCATTCTTTGTATTTTATGTTTGT
*
39508 TTAGGCATCTTTGGGTTTCCTTCGATTC
131 TTAAGCATCTTTGGGTTTCCTTCGATTC
*
39536 AGTTTTATCCGGATTA
1 AGTTTTATTCGGATTA
39552 TGTAAGAGTT
Statistics
Matches: 172, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
158 40 0.23
159 132 0.77
ACGTcount: A:0.22, C:0.16, G:0.16, T:0.45
Consensus pattern (158 bp):
AGTTTTATTCGGATTAAGCACGAGCTTCATTTACTTTATTTGAATCCTGAGATTTTGGTTCTGAA
AATTTTGATATTTCAACTCCTTGCCACAATCGGTGTAACATTCATTCTTTGTATTTTATGTTTGT
TTAAGCATCTTTGGGTTTCCTTCGATTC
Found at i:43799 original size:2 final size:2
Alignment explanation
Indices: 43792--43827 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
43782 TTAAACGAGT
43792 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
43828 GGATATAGCC
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):
TA
Found at i:47452 original size:13 final size:15
Alignment explanation
Indices: 47421--47455 Score: 56
Period size: 13 Copynumber: 2.5 Consensus size: 15
47411 ATTAATTTCT
47421 TATTTATTTAAATAA
1 TATTTATTTAAATAA
47436 TATTT-TTTAAA-AA
1 TATTTATTTAAATAA
47449 TATTTAT
1 TATTTAT
47456 AAAAAACTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 7 0.37
14 7 0.37
15 5 0.26
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TATTTATTTAAATAA
Found at i:48357 original size:16 final size:15
Alignment explanation
Indices: 48325--48357 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
48315 TTATTTTACT
48325 AAAATAAAATATAAA
1 AAAATAAAATATAAA
48340 AAAATAAAA-ATAAGA
1 AAAATAAAATATAA-A
48355 AAA
1 AAA
48358 CTGGAGTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (15 bp):
AAAATAAAATATAAA
Found at i:48996 original size:22 final size:21
Alignment explanation
Indices: 48970--49013 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
48960 AATAATAAAA
48970 TTTT-AGATTATTTTATTTTATT
1 TTTTAAGATTA-TTTA-TTTATT
*
48992 TTTTAATATTATTTATTTATT
1 TTTTAAGATTATTTATTTATT
49013 T
1 T
49014 GATGTAATCG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 7 0.35
22 8 0.40
23 5 0.25
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (21 bp):
TTTTAAGATTATTTATTTATT
Found at i:53582 original size:17 final size:17
Alignment explanation
Indices: 53560--53593 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
53550 TCCAATGGAT
*
53560 TTAATTATTATTATTTA
1 TTAATTATTAGTATTTA
53577 TTAATTATTAGTATTTA
1 TTAATTATTAGTATTTA
53594 ATTCATCAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (17 bp):
TTAATTATTAGTATTTA
Found at i:60272 original size:32 final size:33
Alignment explanation
Indices: 60226--60289 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
60216 CTACCTCGAG
*
60226 TATCACTAAACATAAAC-AAAATCTCCCACTTA
1 TATCACTAAACATAAACAAAAATATCCCACTTA
*
60258 TATCACTAAGCATAAACAAAAATATCCCACTT
1 TATCACTAAACATAAACAAAAATATCCCACTT
60290 GGAATTAAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 16 0.55
33 13 0.45
ACGTcount: A:0.47, C:0.27, G:0.02, T:0.25
Consensus pattern (33 bp):
TATCACTAAACATAAACAAAAATATCCCACTTA
Found at i:65998 original size:21 final size:21
Alignment explanation
Indices: 65972--66033 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
65962 CGCAACTCAG
65972 TTTCCAAATTCGCGTTGCGAT
1 TTTCCAAATTCGCGTTGCGAT
*
65993 TTTCC-ATTTCGCGTTGCGAT
1 TTTCCAAATTCGCGTTGCGAT
** *
66013 AGTCCAAATTCGCATTGCGAT
1 TTTCCAAATTCGCGTTGCGAT
66034 ATCGCAACGC
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
20 17 0.49
21 18 0.51
ACGTcount: A:0.19, C:0.24, G:0.19, T:0.37
Consensus pattern (21 bp):
TTTCCAAATTCGCGTTGCGAT
Found at i:66034 original size:21 final size:21
Alignment explanation
Indices: 65974--66034 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 21
65964 CAACTCAGTT
**
65974 TCCAAATTCGCGTTGCGATTT
1 TCCAAATTCGCGTTGCGATAG
*
65995 TCC-ATTTCGCGTTGCGATAG
1 TCCAAATTCGCGTTGCGATAG
*
66015 TCCAAATTCGCATTGCGATA
1 TCCAAATTCGCGTTGCGATA
66035 TCGCAACGCG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
20 17 0.50
21 17 0.50
ACGTcount: A:0.21, C:0.25, G:0.20, T:0.34
Consensus pattern (21 bp):
TCCAAATTCGCGTTGCGATAG
Found at i:66361 original size:20 final size:20
Alignment explanation
Indices: 66336--66378 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
66326 ATCGTTGGAG
*
66336 TTGGAGTTGGAGTTGCGAAT
1 TTGGAGTTCGAGTTGCGAAT
* *
66356 TTGGAGTTCGCGTTGCGATT
1 TTGGAGTTCGAGTTGCGAAT
66376 TTG
1 TTG
66379 TTGGTCATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.14, C:0.09, G:0.37, T:0.40
Consensus pattern (20 bp):
TTGGAGTTCGAGTTGCGAAT
Found at i:67751 original size:20 final size:20
Alignment explanation
Indices: 67723--67763 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
67713 TGGATTTTGA
* *
67723 AAATTTATTTTTGAAATTAT
1 AAATATATTTTTAAAATTAT
67743 AAATATATTTTTAAAATTAT
1 AAATATATTTTTAAAATTAT
67763 A
1 A
67764 TTTAAAACTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (20 bp):
AAATATATTTTTAAAATTAT
Found at i:68012 original size:20 final size:20
Alignment explanation
Indices: 67987--68024 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
67977 TTAATTATAA
67987 ATTTATAATTTAAAAAATAC
1 ATTTATAATTTAAAAAATAC
*
68007 ATTTATAATTTTAAAAAT
1 ATTTATAATTTAAAAAAT
68025 GAATCATGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (20 bp):
ATTTATAATTTAAAAAATAC
Found at i:68461 original size:9 final size:10
Alignment explanation
Indices: 68447--68479 Score: 52
Period size: 9 Copynumber: 3.5 Consensus size: 10
68437 TTTTATGAGG
68447 TTATTA-TTA
1 TTATTATTTA
68456 TTATTATTTA
1 TTATTATTTA
68466 TTA-TATTTA
1 TTATTATTTA
68475 TTATT
1 TTATT
68480 TATCAGGTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 15 0.68
10 7 0.32
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (10 bp):
TTATTATTTA
Found at i:68468 original size:16 final size:16
Alignment explanation
Indices: 68447--68482 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
68437 TTTTATGAGG
68447 TTATTAT-TATTATTAT
1 TTATTATAT-TTATTAT
68463 TTATTATATTTATTAT
1 TTATTATATTTATTAT
68479 TTAT
1 TTAT
68483 CAGGTTTGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 18 0.95
17 1 0.05
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (16 bp):
TTATTATATTTATTAT
Found at i:76112 original size:3 final size:3
Alignment explanation
Indices: 76104--76162 Score: 75
Period size: 3 Copynumber: 19.7 Consensus size: 3
76094 CCCCCTCCCC
*
76104 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT ATT CGTT -TT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C-TT CTT CTT
**
76149 CTT CAA CTT CTT CT
1 CTT CTT CTT CTT CT
76163 CCCATTCACT
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
2 2 0.04
3 44 0.92
4 2 0.04
ACGTcount: A:0.05, C:0.31, G:0.02, T:0.63
Consensus pattern (3 bp):
CTT
Found at i:76655 original size:6 final size:6
Alignment explanation
Indices: 76644--76708 Score: 100
Period size: 6 Copynumber: 11.3 Consensus size: 6
76634 ATAAGAAGGT
*
76644 GGAGAA GGAGAA GGAGAA GGAGAA GGAG-A --AGAA GGAGAA GGATAA
1 GGAGAA GGAGAA GGAGAA GGAGAA GGAGAA GGAGAA GGAGAA GGAGAA
76689 GGAGAA GGAGAA GGAGAA GG
1 GGAGAA GGAGAA GGAGAA GG
76709 GGGTTAACGA
Statistics
Matches: 54, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
3 2 0.04
4 1 0.02
5 1 0.02
6 50 0.93
ACGTcount: A:0.49, C:0.00, G:0.49, T:0.02
Consensus pattern (6 bp):
GGAGAA
Found at i:76674 original size:33 final size:33
Alignment explanation
Indices: 76616--76708 Score: 118
Period size: 33 Copynumber: 2.8 Consensus size: 33
76606 GCGGATGAAG
* *
76616 AGGAGAAGAAGAAGGAAGATA--AGAAGGTGGAGA
1 AGGAGAAGGAGAAGG-AGA-AGGAGAAGGAGGAGA
*
76649 AGGAGAAGGAGAAGGAGAAGGAGAAGAAGGAGA
1 AGGAGAAGGAGAAGGAGAAGGAGAAGGAGGAGA
*
76682 AGGATAAGGAGAAGGAGAAGGAGAAGG
1 AGGAGAAGGAGAAGGAGAAGGAGAAGG
76709 GGGTTAACGA
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
31 1 0.02
32 3 0.06
33 49 0.92
ACGTcount: A:0.51, C:0.00, G:0.46, T:0.03
Consensus pattern (33 bp):
AGGAGAAGGAGAAGGAGAAGGAGAAGGAGGAGA
Found at i:77890 original size:21 final size:21
Alignment explanation
Indices: 77856--77895 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
77846 TGTTGTATAT
*
77856 AGCCGTTGGGGATG-TTTTGG
1 AGCCGTTGGAGATGATTTTGG
77876 AGCCGTTTGGAGATGATTTT
1 AGCCG-TTGGAGATGATTTT
77896 TCTACTCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 8 0.47
22 4 0.24
ACGTcount: A:0.15, C:0.10, G:0.38, T:0.38
Consensus pattern (21 bp):
AGCCGTTGGAGATGATTTTGG
Done.