Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005913.1 Hibiscus syriacus cultivar Beakdansim tig00013885_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: 67475
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.31
Found at i:4989 original size:25 final size:26
Alignment explanation
Indices: 4960--5008 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
4950 CTTTGGTAAA
4960 ATATAT-AATACTAAATTAAATTAGC
1 ATATATAAATACTAAATTAAATTAGC
4985 ATATATAAATACTAAATTAAATTA
1 ATATATAAATACTAAATTAAATTA
5009 ATTGACCCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 6 0.26
26 17 0.74
ACGTcount: A:0.55, C:0.06, G:0.02, T:0.37
Consensus pattern (26 bp):
ATATATAAATACTAAATTAAATTAGC
Found at i:11013 original size:123 final size:120
Alignment explanation
Indices: 10672--11024 Score: 552
Period size: 117 Copynumber: 2.9 Consensus size: 120
10662 TGTTAGATTT
* *
10672 TTAACTATAAAAATATATATTTTATTATTATTTCTTAATTTATC-AAATATATATTTTTTGGTTT
1 TTAACTATAAAAATAT-TATTTTATTATTTTTTCTTAATTTATCGATATATATA-TTTTTGGTTT
* *
10736 AAAGTAGGCCAAGTTTATTATTTGAGGTAAGAATATATATTTAAAATATTTAAATTC
64 AAAGTAGGCCAAGTTTATTATTTAAGTTAAGAATATATATTTAAAATATTTAAATTC
*
10793 TTAACTATAAAAATA-TATATT-TTATTTTTTCTTAATTTATCGA-ATATATATTTTTGGTTTAA
1 TTAACTATAAAAATATTATTTTATTATTTTTTCTTAATTTATCGATATATATATTTTTGGTTTAA
*
10855 AGTAGGCCAAGTTTATTATTTAAGTTAAGATTATATATTTAAAATATTTAAATTC
66 AGTAGGCCAAGTTTATTATTTAAGTTAAGAATATATATTTAAAATATTTAAATTC
*
10910 TTAACTATAAAAATATGTATTTTTATTATTTTTTCTTAATTTATTGTATATATATATTTTTGGTT
1 TTAACTATAAAAATAT-TA-TTTTATTATTTTTTCTTAATTTATCG-ATATATATATTTTTGGTT
* *
10975 TAAAGCATGCCAAGTTTATTATTTAAGTTAAGAATATATATTTAAAATAT
63 TAAAGTAGGCCAAGTTTATTATTTAAGTTAAGAATATATATTTAAAATAT
11025 ATATTTTTTG
Statistics
Matches: 215, Mismatches: 10, Indels: 12
0.91 0.04 0.05
Matches are distributed among these distances:
117 79 0.37
118 26 0.12
119 8 0.04
120 3 0.01
121 35 0.16
122 1 0.00
123 63 0.29
ACGTcount: A:0.38, C:0.05, G:0.08, T:0.50
Consensus pattern (120 bp):
TTAACTATAAAAATATTATTTTATTATTTTTTCTTAATTTATCGATATATATATTTTTGGTTTAA
AGTAGGCCAAGTTTATTATTTAAGTTAAGAATATATATTTAAAATATTTAAATTC
Found at i:11025 original size:13 final size:14
Alignment explanation
Indices: 11002--11030 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
10992 ATTATTTAAG
11002 TTAAGAATATATAT
1 TTAAGAATATATAT
11016 TTAA-AATATATAT
1 TTAAGAATATATAT
11029 TT
1 TT
11031 TTTGGTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (14 bp):
TTAAGAATATATAT
Found at i:11084 original size:123 final size:118
Alignment explanation
Indices: 10672--11088 Score: 513
Period size: 117 Copynumber: 3.5 Consensus size: 118
10662 TGTTAGATTT
* **
10672 TTAACTATAAAAATATATATTTTATTATTATTTCTTAATTTATCAAATATATAT-TTTTTGGTTT
1 TTAACTAT-AAAA-ATATATTTT-TTATTTTTTCTTAATTTATTGAATATATATATTTTTGGTTT
* *
10736 AAAGTAGGCCAAGTTTATTATTTGAGGTAAGAATATATATTTAAAATATTTAAATTC
63 AAAGTAGGCCAAGTTTATTATTTAAGTTAAGAATATATATTTAAAATA-TTAAATTC
* *
10793 TTAACTATAAAAATATATATTTTATTTTTTCTTAATTTATCG-A-ATATATATTTTTGGTTTAAA
1 TTAACTATAAAAATATATTTTTTATTTTTTCTTAATTTATTGAATATATATATTTTTGGTTTAAA
*
10856 GTAGGCCAAGTTTATTATTTAAGTTAAGATTATATATTTAAAATATTTAAATTC
66 GTAGGCCAAGTTTATTATTTAAGTTAAGAATATATATTTAAAATA-TTAAATTC
*
10910 TTAACTATAAAAATATGTATTTTTATTATTTTTTCTTAATTTATTGTATATATATATTTTTGGTT
1 TTAACTATAAAAATA--TA-TTTT-TTATTTTTTCTTAATTTATTGAATATATATATTTTTGGTT
* * * *
10975 TAAAGCATGCCAAGTTTATTATTTAAGTTAAGAATATATATTTAAAATA-TATATTT
62 TAAAGTAGGCCAAGTTTATTATTTAAGTTAAGAATATATATTTAAAATATTAAATTC
*** * *
11031 TTTGGTTTAAAATATATATTTTCTTATTTTTTTTCTTACTTTATTGAA-A-ATATATTTT
1 TTAACTATAAAA-ATATATTTT-TTA--TTTTTTCTTAATTTATTGAATATATATATTTT
11089 AAAATATTAT
Statistics
Matches: 266, Mismatches: 20, Indels: 22
0.86 0.06 0.07
Matches are distributed among these distances:
116 6 0.02
117 80 0.30
118 19 0.07
119 26 0.10
120 10 0.04
121 59 0.22
122 4 0.02
123 62 0.23
ACGTcount: A:0.36, C:0.05, G:0.07, T:0.52
Consensus pattern (118 bp):
TTAACTATAAAAATATATTTTTTATTTTTTCTTAATTTATTGAATATATATATTTTTGGTTTAAA
GTAGGCCAAGTTTATTATTTAAGTTAAGAATATATATTTAAAATATTAAATTC
Found at i:11723 original size:2 final size:2
Alignment explanation
Indices: 11716--11791 Score: 152
Period size: 2 Copynumber: 38.0 Consensus size: 2
11706 ACAACTCTTA
11716 AT AT AT 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 AT AT AT
11758 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
11792 CCATCTTTTA
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 74 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:15322 original size:2 final size:2
Alignment explanation
Indices: 15311--15343 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
15301 TTGCAAGGGT
15311 TA TA -A 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
15344 GGTTATTAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:16224 original size:31 final size:32
Alignment explanation
Indices: 16162--16225 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
16152 CATAACATTA
** *
16162 TAAATAATTGTATTTAATTTTAAATAGAAATT
1 TAAATAATCATATTTAATTTCAAATAGAAATT
*
16194 TAAATAATCATATTTAA-TTCAATTAGAAATT
1 TAAATAATCATATTTAATTTCAAATAGAAATT
16225 T
1 T
16226 TTAAACTCAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
31 13 0.46
32 15 0.54
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (32 bp):
TAAATAATCATATTTAATTTCAAATAGAAATT
Found at i:23214 original size:29 final size:30
Alignment explanation
Indices: 23152--23216 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
23142 GTGGCATATA
*
23152 ATAATATAAAATAATGTAAAATAGACAATC
1 ATAATATAAAATAATGTAAAATAGAAAATC
23182 ATAATATAAAAT-ATGTAATATATA-AAAAT-
1 ATAATATAAAATAATGTAA-A-ATAGAAAATC
23211 ATAATA
1 ATAATA
23217 AGATATAATA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
29 12 0.38
30 17 0.53
31 3 0.09
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.31
Consensus pattern (30 bp):
ATAATATAAAATAATGTAAAATAGAAAATC
Found at i:25899 original size:16 final size:17
Alignment explanation
Indices: 25878--25914 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
25868 AGCATGACCG
25878 GTTCGCT-ACCGATCCA
1 GTTCGCTAACCGATCCA
*
25894 GTTCGCTAACCGATCCG
1 GTTCGCTAACCGATCCA
25911 GTTC
1 GTTC
25915 TAAAAACCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.16, C:0.35, G:0.22, T:0.27
Consensus pattern (17 bp):
GTTCGCTAACCGATCCA
Found at i:26166 original size:25 final size:25
Alignment explanation
Indices: 26101--26175 Score: 68
Period size: 22 Copynumber: 3.0 Consensus size: 25
26091 GTGTTTACAA
*
26101 AAATTAAAATAGATAAATAATAATA-
1 AAATTAAAAT-GATAAAAAATAATAT
*
26126 ATATTAATAAT--T-AAAAATAATAT
1 AAATTAA-AATGATAAAAAATAATAT
*
26149 AAATTAAAATGATAAAAAGAAAATAT
1 AAATTAAAATGATAAAAA-ATAATAT
26175 A
1 A
26176 TAAACAAAAG
Statistics
Matches: 40, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
22 12 0.30
23 7 0.17
24 1 0.03
25 10 0.25
26 10 0.25
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (25 bp):
AAATTAAAATGATAAAAAATAATAT
Found at i:35601 original size:27 final size:27
Alignment explanation
Indices: 35556--35615 Score: 86
Period size: 26 Copynumber: 2.2 Consensus size: 27
35546 ATTAACAAAG
*
35556 TAAAATTTTTAAATAAAATAAATATAAA
1 TAAAATTTTAAAATAAAAT-AATATAAA
*
35584 TAAAATTTTAAAAT-AAATAATATCAA
1 TAAAATTTTAAAATAAAATAATATAAA
35610 TAAAAT
1 TAAAAT
35616 AATTAATTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 13 0.43
27 4 0.13
28 13 0.43
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (27 bp):
TAAAATTTTAAAATAAAATAATATAAA
Found at i:35613 original size:18 final size:16
Alignment explanation
Indices: 35592--35634 Score: 52
Period size: 18 Copynumber: 2.6 Consensus size: 16
35582 AATAAAATTT
35592 TAAAATAAATAATATCAA
1 TAAAATAAATAAT-T-AA
*
35610 TAAAATAATTAATTAA
1 TAAAATAAATAATTAA
35626 TAAAA-AAAT
1 TAAAATAAAT
35635 TCATATTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 3 0.13
16 7 0.30
17 1 0.04
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (16 bp):
TAAAATAAATAATTAA
Found at i:35629 original size:16 final size:18
Alignment explanation
Indices: 35592--35640 Score: 57
Period size: 16 Copynumber: 2.8 Consensus size: 18
35582 AATAAAATTT
*
35592 TAAAATAAATAATATCAA
1 TAAAATAATTAATATCAA
35610 TAAAATAATTAAT-T-AA
1 TAAAATAATTAATATCAA
* *
35626 TAAAAAAATTCATAT
1 TAAAATAATTAATAT
35641 TTTAAGATAG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 13 0.48
17 2 0.07
18 12 0.44
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (18 bp):
TAAAATAATTAATATCAA
Found at i:36764 original size:18 final size:18
Alignment explanation
Indices: 36730--36764 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
36720 GACTCCATCA
* *
36730 ATTTAAATTTAATATATG
1 ATTTAAATATAAAATATG
36748 ATTTAAATATAAAATAT
1 ATTTAAATATAAAATAT
36765 TAATATTTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (18 bp):
ATTTAAATATAAAATATG
Found at i:36880 original size:29 final size:29
Alignment explanation
Indices: 36814--36881 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
36804 TCAAACTTGT
**
36814 AATAATAAAAAAAATAAATTTTAAATCTA
1 AATAATAATTAAAATAAATTTTAAATCTA
*
36843 AATAATAATTAAATTAAATTTTAAAT-TGA
1 AATAATAATTAAAATAAATTTTAAATCT-A
36872 AATAATAATT
1 AATAATAATT
36882 TGAATCAATC
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
28 1 0.03
29 34 0.97
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.37
Consensus pattern (29 bp):
AATAATAATTAAAATAAATTTTAAATCTA
Found at i:39056 original size:22 final size:22
Alignment explanation
Indices: 39031--39079 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
39021 ATATATTTAT
39031 TAATATTTGTAATAATATAATA
1 TAATATTTGTAATAATATAATA
* *
39053 TAATATTTTTAATATTATAATA
1 TAATATTTGTAATAATATAATA
*
39075 AAATA
1 TAATA
39080 ATCAATTATA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (22 bp):
TAATATTTGTAATAATATAATA
Found at i:39368 original size:27 final size:27
Alignment explanation
Indices: 39333--39386 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
39323 TATTAATATT
*
39333 TTTATTAATAAA-ATTATAAAAATAATA
1 TTTAATAATAAATATT-TAAAAATAATA
*
39360 TTTAATAATAAATATTTTAAAATAATA
1 TTTAATAATAAATATTTAAAAATAATA
39387 ATAGTAAGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 21 0.88
28 3 0.12
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (27 bp):
TTTAATAATAAATATTTAAAAATAATA
Found at i:39548 original size:20 final size:20
Alignment explanation
Indices: 39510--39549 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
39500 ATCATAAAAT
**
39510 ATTTTCCAGAAATGTAATTC
1 ATTTTCCAGAAATCAAATTC
*
39530 ATTTTCCAGAATTCAAATTC
1 ATTTTCCAGAAATCAAATTC
39550 CAGTAATTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.35, C:0.17, G:0.07, T:0.40
Consensus pattern (20 bp):
ATTTTCCAGAAATCAAATTC
Found at i:39565 original size:15 final size:15
Alignment explanation
Indices: 39523--39582 Score: 86
Period size: 15 Copynumber: 4.1 Consensus size: 15
39513 TTCCAGAAAT
39523 GTAATTCATTTTCCA
1 GTAATTCATTTTCCA
**
39538 G-AATTCAAATTCCA
1 GTAATTCATTTTCCA
*
39552 GTAATTTATTTTCCA
1 GTAATTCATTTTCCA
39567 GTAATTCATTTTCCA
1 GTAATTCATTTTCCA
39582 G
1 G
39583 AAAACCAATT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
14 12 0.32
15 26 0.68
ACGTcount: A:0.30, C:0.18, G:0.08, T:0.43
Consensus pattern (15 bp):
GTAATTCATTTTCCA
Found at i:41644 original size:31 final size:30
Alignment explanation
Indices: 41568--41664 Score: 92
Period size: 30 Copynumber: 3.2 Consensus size: 30
41558 GATTATTATA
* * *
41568 TTATAATAAAAT-ATATAATTTAATAATTATT
1 TTATAATAAATTAATA-AAATTAATAAATA-T
*
41599 TTATAA-CAATTAATAAAATTAATAAATAT
1 TTATAATAAATTAATAAAATTAATAAATAT
*
41628 TATATAATAAATTAAT-AAATCTAATAACTAT
1 T-TATAATAAATTAATAAAAT-TAATAAATAT
41659 TTATAA
1 TTATAA
41665 CTGAAATATT
Statistics
Matches: 56, Mismatches: 6, Indels: 9
0.79 0.08 0.13
Matches are distributed among these distances:
29 2 0.04
30 28 0.50
31 26 0.46
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (30 bp):
TTATAATAAATTAATAAAATTAATAAATAT
Found at i:44363 original size:136 final size:138
Alignment explanation
Indices: 44119--44675 Score: 944
Period size: 137 Copynumber: 4.0 Consensus size: 138
44109 ACTAGGACGG
*
44119 TGAGTATTATGGATCCACATACTGTTTGGTGTACGCATAAATAATAATACTTGAAACTAGTGATG
1 TGAGTATTATGGATCCACATACTGTTTGGTGTACGCATAAATAATAATACTTGAAACTAGTGATC
* *
44184 ATCATCAACTTAAGTTGTGAAGTTGTACGATGTAGTTTGAGATTTT-G-GTGTGCATTTGCAGTG
66 AACATCAACTTAAGTTGTGAAGTTATACGATGTAGTTTGAGATTTTGGTGTGTGCATTTGCAGTG
44247 TTGTGCAC
131 TTGTGCAC
44255 TGAGTATTATGGATCCACATACTGTTTGGTGTACGCATAAATAATAATACTTGAAACTAGTGATC
1 TGAGTATTATGGATCCACATACTGTTTGGTGTACGCATAAATAATAATACTTGAAACTAGTGATC
44320 AACATCAACTTAAGTTGTGAAGTTATACGATGTAGTTTGAGATTTTGGTGTGTGCATTTGCAGTG
66 AACATCAACTTAAGTTGTGAAGTTATACGATGTAGTTTGAGATTTTGGTGTGTGCATTTGCAGTG
44385 TTGTGCAC
131 TTGTGCAC
*
44393 CGAGTATTATGGATCCACATACTG-TT--TGTACGCATAAATAATAATATACTTGAAACTAGTGA
1 TGAGTATTATGGATCCACATACTGTTTGGTGTACGCATAAATAAT-A-ATACTTGAAACTAGTGA
*
44455 TCAACATCAACTTAAGTTGTGAAGTTATACGATGTAGTTTGAGATTTTGGTGTGTGCATTTGAAG
64 TCAACATCAACTTAAGTTGTGAAGTTATACGATGTAGTTTGAGATTTTGGTGTGTGCATTTGCAG
44520 TGTTGTGCAC
129 TGTTGTGCAC
*
44530 TGAGTATTATGGATCCACATACTGTTTGGTGTACGCATAAATAATAATACTTGAAACTAGTGATG
1 TGAGTATTATGGATCCACATACTGTTTGGTGTACGCATAAATAATAATACTTGAAACTAGTGATC
* * *
44595 AACATCAACTTAATTTGTTAAGTTATACGATGTAGCTTGAGATTTTGGTGTGCGTGCGCATTTGC
66 AACATCAACTTAAGTTGTGAAGTTATACGATGTAGTTTGAGATTTTGGTGT--GT--GCATTTGC
44660 AGTGTTGTGCAC
127 AGTGTTGTGCAC
44672 TGAG
1 TGAG
44676 CACTGAATAT
Statistics
Matches: 399, Mismatches: 11, Indels: 16
0.94 0.03 0.04
Matches are distributed among these distances:
135 16 0.04
136 109 0.27
137 117 0.29
138 115 0.29
139 1 0.00
140 18 0.05
142 23 0.06
ACGTcount: A:0.29, C:0.12, G:0.23, T:0.36
Consensus pattern (138 bp):
TGAGTATTATGGATCCACATACTGTTTGGTGTACGCATAAATAATAATACTTGAAACTAGTGATC
AACATCAACTTAAGTTGTGAAGTTATACGATGTAGTTTGAGATTTTGGTGTGTGCATTTGCAGTG
TTGTGCAC
Found at i:44620 original size:275 final size:275
Alignment explanation
Indices: 44120--44671 Score: 941
Period size: 275 Copynumber: 2.0 Consensus size: 275
44110 CTAGGACGGT
*
44120 GAGTATTATGGATCCACATACTGTTTGGTGTACGCATAAATAATAATACTTGAAACTAGTGATGA
1 GAGTATTATGGATCCACATACTGTTT-GTGTACGCATAAATAATAATACTTGAAACTAGTGATCA
* * *
44185 TCATCAACTTAAGTTGTGAAGTTGTACGATGTAGTTTGAGATTTTGGTGTGCATTTGCAGTGTTG
65 ACATCAACTTAAGTTGTGAAGTTATACGATGTAGTTTGAGATTTTGGTGTGCATTTGAAGTGTTG
44250 TGCACTGAGTATTATGGATCCACATACTGTTTGGTGTACGCATAAATAATAATACTTGAAACTAG
130 TGCACTGAGTATTATGGATCCACATACTGTTTGGTGTACGCATAAATAATAATACTTGAAACTAG
*
44315 TGATCAACATCAACTTAAGTTGTGAAGTTATACGATGTAGTTTGAGATTTTGGTGT-GT-GCATT
195 TGATCAACATCAACTTAAGTTGTGAAGTTATACGATGTAGCTTGAGATTTTGGTGTCGTCGCATT
44378 TGCAGTGTTGTGCACC
260 TGCAGTGTTGTGCACC
44394 GAGTATTATGGATCCACATACTG-TT-TGTACGCATAAATAATAATATACTTGAAACTAGTGATC
1 GAGTATTATGGATCCACATACTGTTTGTGTACGCATAAATAAT-A-ATACTTGAAACTAGTGATC
44457 AACATCAACTTAAGTTGTGAAGTTATACGATGTAGTTTGAGATTTTGGTGTGTGCATTTGAAGTG
64 AACATCAACTTAAGTTGTGAAGTTATACGATGTAGTTTGAGATTTT-G-GTGTGCATTTGAAGTG
44522 TTGTGCACTGAGTATTATGGATCCACATACTGTTTGGTGTACGCATAAATAATAATACTTGAAAC
127 TTGTGCACTGAGTATTATGGATCCACATACTGTTTGGTGTACGCATAAATAATAATACTTGAAAC
* * *
44587 TAGTGATGAACATCAACTTAATTTGTTAAGTTATACGATGTAGCTTGAGATTTTGGTGTGCGTGC
192 TAGTGATCAACATCAACTTAAGTTGTGAAGTTATACGATGTAGCTTGAGATTTTGGTGT-CGT-C
44652 GCATTTGCAGTGTTGTGCAC
255 GCATTTGCAGTGTTGTGCAC
44672 TGAGCACTGA
Statistics
Matches: 262, Mismatches: 8, Indels: 11
0.93 0.03 0.04
Matches are distributed among these distances:
271 16 0.06
272 1 0.00
273 64 0.24
274 24 0.09
275 135 0.52
277 2 0.01
279 20 0.08
ACGTcount: A:0.29, C:0.12, G:0.22, T:0.36
Consensus pattern (275 bp):
GAGTATTATGGATCCACATACTGTTTGTGTACGCATAAATAATAATACTTGAAACTAGTGATCAA
CATCAACTTAAGTTGTGAAGTTATACGATGTAGTTTGAGATTTTGGTGTGCATTTGAAGTGTTGT
GCACTGAGTATTATGGATCCACATACTGTTTGGTGTACGCATAAATAATAATACTTGAAACTAGT
GATCAACATCAACTTAAGTTGTGAAGTTATACGATGTAGCTTGAGATTTTGGTGTCGTCGCATTT
GCAGTGTTGTGCACC
Found at i:45057 original size:190 final size:189
Alignment explanation
Indices: 44696--45069 Score: 592
Period size: 190 Copynumber: 2.0 Consensus size: 189
44686 CGTAGTTCCG
44696 ACATGATCTTATTTGTTATAGGAGCTCAAAGAAACGATGAGAAAATCAATGCAAGTGTATCCAAA
1 ACATGATCTTATTTGTTATAGGAGCTCAAAGAAACGATGAGAAAATCAATGCAAGTGTATCCAAA
* * *
44761 GTTCTTGTTTTAATCTAGATAAACATTGATTATGCTTTTGTAGACAAACTCATGATCTGGCAGGT
66 GATCTTGTTTTAATCTAGATAAACATTGATTATGCTTCTGTAGACAAAC-CATGATCTAGCAGGT
44826 TGGCCTAATGATGCCTTAGAAAATGGGGGGAAAAGAACCAATTGAGTGCAAACATTTCAT
130 TGGCCTAATGATGCCTTAGAAAATGGGGGGAAAAGAACCAATTGAGTGCAAACATTTCAT
* *
44886 ACATGATCTTATTTGTTATAGGAGCTCAAAGAAATGATGAGAAAATCAATGCAAGTTTATCCAAA
1 ACATGATCTTATTTGTTATAGGAGCTCAAAGAAACGATGAGAAAATCAATGCAAGTGTATCCAAA
* *
44951 GCAT-TTGTTTTTATCTAGATAAACATTGATTATGCTTCTGTAGACGAA-C-TGATCTAGCAGGT
66 G-ATCTTGTTTTAATCTAGATAAACATTGATTATGCTTCTGTAGACAAACCATGATCTAGCAGGT
** *
45013 TGGCCTAATGATGCCTTAGAAAATGGGGGGGGGGCAATAACCAATTGAGTGCAAACA
130 TGGCCTAATGATGCCTTAGAAAAT---GGGGGGAAAAGAACCAATTGAGTGCAAACA
45070 ATTATCAACC
Statistics
Matches: 170, Mismatches: 10, Indels: 8
0.90 0.05 0.04
Matches are distributed among these distances:
187 36 0.21
188 1 0.01
190 132 0.78
191 1 0.01
ACGTcount: A:0.35, C:0.14, G:0.21, T:0.30
Consensus pattern (189 bp):
ACATGATCTTATTTGTTATAGGAGCTCAAAGAAACGATGAGAAAATCAATGCAAGTGTATCCAAA
GATCTTGTTTTAATCTAGATAAACATTGATTATGCTTCTGTAGACAAACCATGATCTAGCAGGTT
GGCCTAATGATGCCTTAGAAAATGGGGGGAAAAGAACCAATTGAGTGCAAACATTTCAT
Found at i:59902 original size:12 final size:12
Alignment explanation
Indices: 59885--59909 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
59875 TAATATATAG
59885 TTTTTGAAAACA
1 TTTTTGAAAACA
59897 TTTTTGAAAACA
1 TTTTTGAAAACA
59909 T
1 T
59910 ATATATTATA
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:0.08, G:0.08, T:0.44
Consensus pattern (12 bp):
TTTTTGAAAACA
Found at i:59912 original size:38 final size:38
Alignment explanation
Indices: 59795--59977 Score: 147
Period size: 38 Copynumber: 4.9 Consensus size: 38
59785 ATTTATATAT
* *
59795 ATATATATTATATAG--TTTGAAATCA-TTTTGAAAAC
1 ATATATAATATATAGTTTTTGAAAACATTTTTGAAAAC
* *
59830 -TATATAATATATGGTTTTTTTTTAAAAAAACA-TTTTG-AAA-
1 ATATATAATATATAG----TTTTT--GAAAACATTTTTGAAAAC
59870 ATATATAATATATAGTTTTTGAAAACATTTTTGAAAAC
1 ATATATAATATATAGTTTTTGAAAACATTTTTGAAAAC
* **
59908 ATATATATTATATAGTTTTTGAAGTCATTTTTGAAAAC
1 ATATATAATATATAGTTTTTGAAAACATTTTTGAAAAC
*
59946 ATATA-ACATATA-A---TTTCAAAACATTTTTGAAA
1 ATATATA-ATATATAGTTTTTGAAAACATTTTTGAAA
59978 CTATGAGTTT
Statistics
Matches: 122, Mismatches: 13, Indels: 27
0.75 0.08 0.17
Matches are distributed among these distances:
34 28 0.23
35 6 0.05
36 5 0.04
37 10 0.08
38 44 0.36
40 3 0.02
41 16 0.13
42 10 0.08
ACGTcount: A:0.43, C:0.05, G:0.08, T:0.44
Consensus pattern (38 bp):
ATATATAATATATAGTTTTTGAAAACATTTTTGAAAAC
Found at i:62409 original size:19 final size:19
Alignment explanation
Indices: 62375--62419 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
62365 ATTTAGACAT
62375 TTTGCA-TTTCTTATTTTC
1 TTTGCATTTTCTTATTTTC
*
62393 TTTGCATTTTGTTATTTTC
1 TTTGCATTTTCTTATTTTC
62412 TTTGCATT
1 TTTGCATT
62420 CACATTAACT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 6 0.24
19 19 0.76
ACGTcount: A:0.11, C:0.13, G:0.09, T:0.67
Consensus pattern (19 bp):
TTTGCATTTTCTTATTTTC
Found at i:66111 original size:80 final size:81
Alignment explanation
Indices: 65735--66586 Score: 781
Period size: 85 Copynumber: 10.4 Consensus size: 81
65725 AAACAAAACT
* * * * ***
65735 ATTTGCAGCTTAGCTCAAGGCCAGAAGGGCTATCTGCCCACCAAGACCTTTGAGTTCGACTACGC
1 ATTTGCAGCATAACTTAAGGCTAGAAGGGCTATCTG-CCA--AAGACCCCCGAGTTCGACTACGC
* *
65800 TCAGC-TCCAAGGCACATC
63 TCAGCTTCGAGGGCACATC
* * * *
65818 ATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGACTACGCTCA
1 ATTTGCAGCATAACTTAAGGCTAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGACTACGCTCA
65883 GCTTCGAGGGCACATC
66 GCTTCGAGGGCACATC
* * * * *
65899 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAGAAGACCCCCAAGTTCGA-TACA
1 ATTTGCAGCATAACTTAAGGCTAGAAGGGCTATCTG---CCA-AAGACCCCCGAGTTCGACTACG
65963 CTCAGCTTCGAGGGCACATC
62 CTCAGCTTCGAGGGCACATC
* * **
65983 ATTTGCAGAATAGCTT-A----AGAAGGGCTATCTGCCAAAGACCTTCGAGTTCGACTACGCTCA
1 ATTTGCAGCATAACTTAAGGCTAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGACTACGCTCA
* *
66043 GC-TCCAAGGCACATC
66 GCTTCGAGGGCACATC
* * * * * * *
66058 ATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCAAGTTCGATTACACTCA
1 ATTTGCAGCATAACTTAAGGCTAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGACTACGCTCA
66123 GCTTCGAGGGCACATC
66 GCTTCGAGGGCACATC
* * * * ***
66139 ATTTGCAGTATAACTTAAGTCAAGAAGGGTTATCTGCTAACAAAAGACCTTTGAGTTCGACTACG
1 ATTTGCAGCATAACTTAAGGCTAGAAGGGCTATCTGC---C-AAAGACCCCCGAGTTCGACTACG
66204 CTCAGCTTCGAGGGCACATC
62 CTCAGCTTCGAGGGCACATC
* * * ** * *
66224 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGATTACA
1 ATTTGCAGCATAACTTAAGGCTAGAAGGGCTATCTG---CC-AAAGACCCCCGAGTTCGACTACG
*
66289 CTCAGCTTCGAGGGCACATT
62 CTCAGCTTCGAGGGCACATC
* * * * ***
66309 ATTTACAGCATAACTCAAGGCTAGAAGGG-TTTCTGTCACAAAAACCTTTGAGTTCGACTACGCT
1 ATTTGCAGCATAACTTAAGGCTAGAAGGGCTATCTG-C-CAAAGACCCCCGAGTTCGACTACGCT
* *
66373 CAGC-TCCAAGGCACATC
64 CAGCTTCGAGGGCACATC
* * * *
66390 ATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGA-CCCCGAGTTCGACTACGCTCA
1 ATTTGCAGCATAACTTAAGGCTAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGACTACGCTCA
66454 GCTTCGAGGGCACATC
66 GCTTCGAGGGCACATC
* * * * ** *
66470 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCCGTCAACAAAGACCCCCGAGTTCGGTTACAC
1 ATTTGCAGCATAACTTAAGGCTAGAAGGGCTATCTG-C--CAAAGACCCCCGAGTTCGACTACGC
* * *
66535 TCAACTTCGAGGTCATATC
63 TCAGCTTCGAGGGCACATC
* * * * *
66554 ATTTACAACATAGCTCAAGGCAAGAAGGGCTAT
1 ATTTGCAGCATAACTTAAGGCTAGAAGGGCTAT
66587 TTTTCAATAA
Statistics
Matches: 647, Mismatches: 96, Indels: 51
0.81 0.12 0.06
Matches are distributed among these distances:
75 41 0.06
76 13 0.02
79 33 0.05
80 109 0.17
81 119 0.18
82 34 0.05
83 39 0.06
84 104 0.16
85 154 0.24
88 1 0.00
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.23
Consensus pattern (81 bp):
ATTTGCAGCATAACTTAAGGCTAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGACTACGCTCA
GCTTCGAGGGCACATC
Found at i:66610 original size:246 final size:250
Alignment explanation
Indices: 65865--66613 Score: 721
Period size: 246 Copynumber: 3.0 Consensus size: 250
65855 CAAAGACCCC
* * * * * * * * *
65865 CGAGTTCGACTACGCTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTT
1 CGAGTTCGACTACACTCAGCTTCCAAGGCACATCATTTGCAGTATAACTTAAGTCAAGAAGGGCT
* * * * * *
65930 ATCTGTCACCAGAAGACCCCCAAGTTCGA-TACACTCAGCTTCGAGGGCACATCATTTGCAGAAT
66 ATCTG-CA-CAAAAGACCTCCGAGTTCGACTACGCTCAGCTTCGAGGGCACATCATTTACAGCAT
* * * * ** * * * *
65994 AGCT-TA----AGAAGGGCTATCTG-C--C-AAAGACCTTCGAGTTCGACTACGCTCAGC-TCCA
129 AACTCAAGGCTAGAAGGGTTATCCGTCAACAAAAGACCCCCGAGTTCGATTACACTCAACTTCGA
* * * * * * * * **
66049 AGGCACATCATTTGCAGA-ATAGCTTAAGTCGAGAAGGGCTATCTG-C-CAAAGACCCC
194 GGGCACATCATTTACA-ACATAACTCAAGGCAAGAAGGG-TTTCTGTCACAAAAACCAT
* * * * *
66105 CAAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGTATAACTTAAGTCAAGAAGGGTT
1 CGAGTTCGACTACACTCAGCTTCCAAGGCACATCATTTGCAGTATAACTTAAGTCAAGAAGGGCT
**
66170 ATCTGCTAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTTCGAGGGCACATCATTTACAGCAT
66 ATCTGC--ACAAAAGACCTCCGAGTTCGACTACGCTCAGCTTCGAGGGCACATCATTTACAGCAT
* * ** *
66235 AACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGATTACACTCAGCTTCGA
129 AACTCAAGGCTAGAAGGGTTATCCGTCAACAAAAGACCCCCGAGTTCGATTACACTCAACTTCGA
* * * *
66300 GGGCACATTATTTACAGCATAACTCAAGGCTAGAAGGGTTTCTGTCACAAAAACCTT
194 GGGCACATCATTTACAACATAACTCAAGGCAAGAAGGGTTTCTGTCACAAAAACCAT
* * * *
66357 TGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTGCAGTATAGCTTAAGTCGAGAAGGGCT
1 CGAGTTCGACTACACTCAGCTTCCAAGGCACATCATTTGCAGTATAACTTAAGTCAAGAAGGGCT
66421 ATCTGC-C-AAAGACC-CCGAGTTCGACTACGCTCAGCTTCGAGGGCACATCATTTACAGCATAA
66 ATCTGCACAAAAGACCTCCGAGTTCGACTACGCTCAGCTTCGAGGGCACATCATTTACAGCATAA
*
66483 CTCAAGGCTAGAAGGGTTATCCGTCAAC-AAAGACCCCCGAGTTCGGTTACACTCAACTTCGAGG
131 CTCAAGGCTAGAAGGGTTATCCGTCAACAAAAGACCCCCGAGTTCGATTACACTCAACTTCGAGG
* * * * *
66547 TCATATCATTTACAACATAGCTCAAGGCAAGAAGGGCTATT-TTTCA-ATAAAATCAT
196 GCACATCATTTACAACATAACTCAAGGCAAGAAGGG-T-TTCTGTCACA-AAAACCAT
66603 CGAGTTCGACT
1 CGAGTTCGACT
66614 CTATTCAGCT
Statistics
Matches: 429, Mismatches: 61, Indels: 32
0.82 0.12 0.06
Matches are distributed among these distances:
239 1 0.00
240 77 0.18
241 36 0.08
242 1 0.00
245 63 0.15
246 106 0.25
247 10 0.02
248 1 0.00
249 1 0.00
250 32 0.07
251 78 0.18
252 23 0.05
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.24
Consensus pattern (250 bp):
CGAGTTCGACTACACTCAGCTTCCAAGGCACATCATTTGCAGTATAACTTAAGTCAAGAAGGGCT
ATCTGCACAAAAGACCTCCGAGTTCGACTACGCTCAGCTTCGAGGGCACATCATTTACAGCATAA
CTCAAGGCTAGAAGGGTTATCCGTCAACAAAAGACCCCCGAGTTCGATTACACTCAACTTCGAGG
GCACATCATTTACAACATAACTCAAGGCAAGAAGGGTTTCTGTCACAAAAACCAT
Found at i:67240 original size:34 final size:34
Alignment explanation
Indices: 67134--67275 Score: 148
Period size: 34 Copynumber: 4.1 Consensus size: 34
67124 TATATATATA
*
67134 ATATATATATAG--TTTGAAATCATTTTGAAAAC
1 ATATATATATAGTTTTTGAAAACATTTTGAAAAC
* ** *
67166 TATATAATATGTTTTTTTTAAAAAAACATTTTG-AAA-
1 -ATAT-ATATATAGTTTTT--GAAAACATTTTGAAAAC
67202 ATATATATATAGTTTTTGAAAACATTTTGAAAAC
1 ATATATATATAGTTTTTGAAAACATTTTGAAAAC
**
67236 ATATATATATAGTTTTTGAAGTCATTTTTGAAAAC
1 ATATATATATAGTTTTTGAAAACA-TTTTGAAAAC
67271 ATATA
1 ATATA
67276 ACATATAATT
Statistics
Matches: 90, Mismatches: 11, Indels: 14
0.78 0.10 0.12
Matches are distributed among these distances:
32 11 0.12
33 7 0.08
34 37 0.41
35 19 0.21
36 3 0.03
37 3 0.03
38 10 0.11
ACGTcount: A:0.43, C:0.05, G:0.08, T:0.44
Consensus pattern (34 bp):
ATATATATATAGTTTTTGAAAACATTTTGAAAAC
Found at i:67388 original size:35 final size:35
Alignment explanation
Indices: 67310--67394 Score: 100
Period size: 35 Copynumber: 2.4 Consensus size: 35
67300 AAACTATGAG
* *
67310 TTTGAAAATATTTTAAAAAAATATATAATATATAAT
1 TTTGAAAATATTTT-TAAAAATATATAATATAGAAT
* * **
67346 TTT-AAAATATTTTTGAAAATATATATTATAGGTT
1 TTTGAAAATATTTTTAAAAATATATAATATAGAAT
67380 TTTGAAAATATTTTT
1 TTTGAAAATATTTTT
67395 TATTATTATA
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
34 18 0.43
35 21 0.50
36 3 0.07
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.48
Consensus pattern (35 bp):
TTTGAAAATATTTTTAAAAATATATAATATAGAAT
Done.