Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008400.1 Hibiscus syriacus cultivar Beakdansim tig00111169_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: 142036
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2131 original size:31 final size:30
Alignment explanation
Indices: 2052--2160 Score: 98
Period size: 31 Copynumber: 3.6 Consensus size: 30
2042 TACTTTGATA
* *
2052 AAAT-GTCTAATATGTTACTTATATTTT-TA
1 AAATAGTC-AATATGATACTTATATTTTATG
* * * *
2081 AAATATTCGACATGGTACTTATATTTTATCG
1 AAATAGTCAATATGATACTTATATTTTAT-G
2112 AAATAGTCAATATGATACTTATATTTTATTG
1 AAATAGTCAATATGATACTTATATTTTA-TG
*
2143 AAATA-TCCAGTATGATAC
1 AAATAGT-CAATATGATAC
2161 ATAAACCGTT
Statistics
Matches: 65, Mismatches: 10, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
29 20 0.31
30 4 0.06
31 40 0.62
32 1 0.02
ACGTcount: A:0.37, C:0.10, G:0.10, T:0.43
Consensus pattern (30 bp):
AAATAGTCAATATGATACTTATATTTTATG
Found at i:2980 original size:2 final size:2
Alignment explanation
Indices: 2973--3013 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
2963 AAACGATAAA
2973 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3014 GCTGTTATGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:11500 original size:25 final size:25
Alignment explanation
Indices: 11471--11518 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 25
11461 AAATTATTAT
11471 ATATTATTATTATT-AT-ATATTTTAG
1 ATATT-TT-TTATTGATAATATTTTAG
11496 ATATTTTTTATTGATAATATTTT
1 ATATTTTTTATTGATAATATTTT
11519 TTTTCCACTA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 5 0.24
24 4 0.19
25 12 0.57
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.62
Consensus pattern (25 bp):
ATATTTTTTATTGATAATATTTTAG
Found at i:15121 original size:153 final size:153
Alignment explanation
Indices: 14843--15130 Score: 522
Period size: 153 Copynumber: 1.9 Consensus size: 153
14833 AAACTGGAAA
*
14843 AAAATCAAAATAGAATAGCAGGGAGCTGTAATACGCACTTAAAAGATGTGGGCCTCCAACCCACG
1 AAAATCAAAATAGAATAGCAGGGAGCCGTAATACGCACTTAAAAGATGTGGGCCTCCAACCCACG
* *
14908 TGGTTTATAATAAAGTACGCACTAGGATCGGAATGATATGACAATGCTAACATGCTACTGTTACA
66 TGGTTTATAATAAAGTACGCACTAGGATCGGAATGACATGACAATGCTAACACGCTACTGTTACA
14973 ATTAATATTTACACGATATAATT
131 ATTAATATTTACACGATATAATT
14996 AAAATCAAAATAGAATAGCAGGGAGCCGTAATACGCACTTAAAAGATGTGGGCCTCCAACCCACG
1 AAAATCAAAATAGAATAGCAGGGAGCCGTAATACGCACTTAAAAGATGTGGGCCTCCAACCCACG
* * *
15061 TGGTTTATAATAAAGTACGCGCTAGGATCGGAATGACATGACAATGCTAACACGGTACTGTTTCA
66 TGGTTTATAATAAAGTACGCACTAGGATCGGAATGACATGACAATGCTAACACGCTACTGTTACA
15126 ATTAA
131 ATTAA
15131 AATCAAAATA
Statistics
Matches: 129, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
153 129 1.00
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.24
Consensus pattern (153 bp):
AAAATCAAAATAGAATAGCAGGGAGCCGTAATACGCACTTAAAAGATGTGGGCCTCCAACCCACG
TGGTTTATAATAAAGTACGCACTAGGATCGGAATGACATGACAATGCTAACACGCTACTGTTACA
ATTAATATTTACACGATATAATT
Found at i:25767 original size:80 final size:80
Alignment explanation
Indices: 25634--25792 Score: 246
Period size: 80 Copynumber: 2.0 Consensus size: 80
25624 TCGAAGTATG
* *
25634 TATATCATGTAATCGTACTATCTCATATATATACAATGTAGTCATGCAATTCATATAAACTGACA
1 TATATCATGTAATCGTACTATCTCATATATATACAATGTAATCATGCAATTCATATAAACTAACA
**
25699 AACTTGTGATTTCTA
66 AAAATGTGATTTCTA
* * * *
25714 TATATCATGTAATCGTATTATCTCATCTATATACAATTTAATCATGCAATTCATATAAATTAACA
1 TATATCATGTAATCGTACTATCTCATATATATACAATGTAATCATGCAATTCATATAAACTAACA
25779 AAAATGTGATTTCT
66 AAAATGTGATTTCT
25793 TCAATCCATC
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
80 71 1.00
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.39
Consensus pattern (80 bp):
TATATCATGTAATCGTACTATCTCATATATATACAATGTAATCATGCAATTCATATAAACTAACA
AAAATGTGATTTCTA
Found at i:34592 original size:23 final size:23
Alignment explanation
Indices: 34566--34646 Score: 81
Period size: 23 Copynumber: 3.5 Consensus size: 23
34556 TCGAATCATA
*
34566 TAAACGAATATATTCGTAAATAT
1 TAAACGAATATATTAGTAAATAT
* * * **
34589 TAAATGAACATGTTAGTAAACGT
1 TAAACGAATATATTAGTAAATAT
*
34612 TAAACGAATATATTAATAAATAT
1 TAAACGAATATATTAGTAAATAT
*
34635 ATAAACAAATAT
1 -TAAACGAATAT
34647 GTTCACGATG
Statistics
Matches: 44, Mismatches: 13, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
23 34 0.77
24 10 0.23
ACGTcount: A:0.52, C:0.07, G:0.09, T:0.32
Consensus pattern (23 bp):
TAAACGAATATATTAGTAAATAT
Found at i:34727 original size:21 final size:21
Alignment explanation
Indices: 34703--34763 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
34693 AATTTTGAAA
34703 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
34724 AAAT-G-TTTC----TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
34738 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
34759 AAATG
1 AAATG
34764 TTTCTTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 4 0.13
16 4 0.13
19 4 0.13
20 4 0.13
21 10 0.32
ACGTcount: A:0.31, C:0.05, G:0.21, T:0.43
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:34794 original size:37 final size:37
Alignment explanation
Indices: 34696--34813 Score: 172
Period size: 35 Copynumber: 3.3 Consensus size: 37
34686 GGTAACCAAT
34696 TTTGAAAAA-ATGGTTTTCAAAGTTTGGTAAATGTTTC
1 TTTGAAAAATA-GGTTTTCAAAGTTTGGTAAATGTTTC
34733 TTTG-AAAAT-GGTTTTCAAAGTTTGGTAAATGTTTC
1 TTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTTC
* *
34768 TTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT-
1 TTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTTC
*
34804 GTTGAAAAAT
1 TTTGAAAAAT
34814 GATAATGGGA
Statistics
Matches: 75, Mismatches: 3, Indels: 7
0.88 0.04 0.08
Matches are distributed among these distances:
35 30 0.40
36 18 0.24
37 27 0.36
ACGTcount: A:0.32, C:0.04, G:0.19, T:0.44
Consensus pattern (37 bp):
TTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTTC
Found at i:39317 original size:36 final size:36
Alignment explanation
Indices: 39237--39348 Score: 113
Period size: 37 Copynumber: 3.1 Consensus size: 36
39227 TGAAATTATT
* ** **
39237 AAAATGGTTTTTC-AAGTTTGGTAACCAACT-TTGAA
1 AAAATAGTTTTTCAAAGTTTGGTAAATATTTCTTG-A
*
39272 AAAATAG-TTTTCAAAGTTTGGTAAATGTTTCTCTGA
1 AAAATAGTTTTTCAAAGTTTGGTAAATATTTCT-TGA
* *
39308 AAAATAGTTTTTCAAAGTTTGGTAGATATTTGTTGA
1 AAAATAGTTTTTCAAAGTTTGGTAAATATTTCTTGA
39344 AAAAT
1 AAAAT
39349 GATAATGGGA
Statistics
Matches: 64, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
34 5 0.08
35 18 0.28
36 17 0.27
37 24 0.38
ACGTcount: A:0.36, C:0.07, G:0.17, T:0.40
Consensus pattern (36 bp):
AAAATAGTTTTTCAAAGTTTGGTAAATATTTCTTGA
Found at i:40715 original size:56 final size:56
Alignment explanation
Indices: 40626--40738 Score: 199
Period size: 56 Copynumber: 2.0 Consensus size: 56
40616 CGTAGTCTAC
* *
40626 TAGACTTTACTGCAATCGATCAATTCATTCCTTTTCTTGCAGCATATATTAATAGG
1 TAGACTTTACTGCAATCGATCAATTCATCCCTTTTCTTGCAACATATATTAATAGG
*
40682 TAGACTTTACTGCAATCGATCAATTCATCCCTTTTCTTGTAACATATATTAATAGG
1 TAGACTTTACTGCAATCGATCAATTCATCCCTTTTCTTGCAACATATATTAATAGG
40738 T
1 T
40739 TTTGCGGGTT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 54 1.00
ACGTcount: A:0.29, C:0.19, G:0.12, T:0.40
Consensus pattern (56 bp):
TAGACTTTACTGCAATCGATCAATTCATCCCTTTTCTTGCAACATATATTAATAGG
Found at i:43825 original size:2 final size:2
Alignment explanation
Indices: 43820--43862 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
43810 TAATTCTCTC
*
43820 AT AT AT AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
43861 AT
1 AT
43863 CTGTTCTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:47504 original size:24 final size:24
Alignment explanation
Indices: 47476--47584 Score: 123
Period size: 24 Copynumber: 4.5 Consensus size: 24
47466 GAATGTTTTA
*
47476 TCTGATTTCCGATTTGAATTCTGT
1 TCTGATTTCTGATTTGAATTCTGT
* *
47500 TCTGATTTCTGATATGAATTCTAT
1 TCTGATTTCTGATTTGAATTCTGT
*
47524 TCTGATTTCTGATTT-AGATTTTGT
1 TCTGATTTCTGATTTGA-ATTCTGT
*
47548 TCTGATATT-TGATCTGAATTCTGT
1 TCTGAT-TTCTGATTTGAATTCTGT
* *
47572 TTTGATTTTTGAT
1 TCTGATTTCTGAT
47585 ATCTCCATTT
Statistics
Matches: 72, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
23 3 0.04
24 66 0.92
25 3 0.04
ACGTcount: A:0.19, C:0.11, G:0.16, T:0.54
Consensus pattern (24 bp):
TCTGATTTCTGATTTGAATTCTGT
Found at i:67590 original size:2 final size:2
Alignment explanation
Indices: 67585--67613 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
67575 TATATATATC
67585 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
67614 GTGCATTCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:67984 original size:22 final size:21
Alignment explanation
Indices: 67941--68001 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
67931 CTTATTTAAT
* *
67941 GTTAGAGTTTAAAAATCT-AGG
1 GTTAGAATTT-AAAATTTAAGG
67962 GTTTAGAATTTAAAATTTAAGG
1 G-TTAGAATTTAAAATTTAAGG
* *
67984 GTTAAAATTTATAATTTA
1 GTTAGAATTTAAAATTTA
68002 GAATTAGAGT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
21 22 0.65
22 12 0.35
ACGTcount: A:0.41, C:0.02, G:0.16, T:0.41
Consensus pattern (21 bp):
GTTAGAATTTAAAATTTAAGG
Found at i:68726 original size:29 final size:29
Alignment explanation
Indices: 68691--68777 Score: 120
Period size: 29 Copynumber: 3.0 Consensus size: 29
68681 AAACTAAATT
*
68691 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
* *
68720 GATGTCATTGCTTACATCATTTAAGTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
* *
68749 GATGTCATTGTTTACATCAATTTAGTTAA
1 GATGTCATTGCTTACATC-ATTTAATTAA
68778 GTGAGAGTTA
Statistics
Matches: 51, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
29 43 0.84
30 8 0.16
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:71237 original size:32 final size:30
Alignment explanation
Indices: 71190--71277 Score: 99
Period size: 32 Copynumber: 2.9 Consensus size: 30
71180 AAACACAACC
*
71190 TCAATATT-CTAAGCTTTGCTAAGCTTT-AC
1 TCAA-ATTCCTAAGCTTTGCTAAGCTTTCAA
*
71219 TCAAATTCTCTCATAGCTTTTCTAAGCTTTCAA
1 TCAAATTC-CT-A-AGCTTTGCTAAGCTTTCAA
*
71252 TCATATTCCTAAGCTTTGCTAAGCTT
1 TCAAATTCCTAAGCTTTGCTAAGCTT
71278 CACCCTCTCT
Statistics
Matches: 50, Mismatches: 4, Indels: 9
0.79 0.06 0.14
Matches are distributed among these distances:
28 3 0.06
29 4 0.08
30 16 0.32
31 2 0.04
32 17 0.34
33 8 0.16
ACGTcount: A:0.26, C:0.23, G:0.09, T:0.42
Consensus pattern (30 bp):
TCAAATTCCTAAGCTTTGCTAAGCTTTCAA
Found at i:72410 original size:32 final size:30
Alignment explanation
Indices: 72369--72446 Score: 86
Period size: 32 Copynumber: 2.5 Consensus size: 30
72359 AATCTCAATA
*
72369 TTCTAAGCTTTGCTAAACTTT-ACTCAAAT
1 TTCTAAGCTTTGCTAAACTTTCAATCAAAT
* * *
72398 TCTCTCATAGCTTTTCTAAGCTTTCAATCATAT
1 T-TCT-A-AGCTTTGCTAAACTTTCAATCAAAT
72431 TTCTAAGCTTTGCTAA
1 TTCTAAGCTTTGCTAA
72447 GCTTCACCCT
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
29 1 0.03
30 13 0.32
31 2 0.05
32 17 0.43
33 7 0.17
ACGTcount: A:0.27, C:0.22, G:0.08, T:0.44
Consensus pattern (30 bp):
TTCTAAGCTTTGCTAAACTTTCAATCAAAT
Found at i:75009 original size:22 final size:21
Alignment explanation
Indices: 74967--75010 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
74957 TAATAACATT
* *
74967 ATTAATTCAATTTATAAATGA
1 ATTAATTCAAATTAAAAATGA
*
74988 ATTAATTTAAATTAAAAGATGA
1 ATTAATTCAAATTAAAA-ATGA
75010 A
1 A
75011 GTGTTATAAC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.52, C:0.02, G:0.07, T:0.39
Consensus pattern (21 bp):
ATTAATTCAAATTAAAAATGA
Found at i:78034 original size:5 final size:6
Alignment explanation
Indices: 78017--78041 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
78007 CCATCTCTGA
78017 TATTTT TATTTT TATTTT TATTTT T
1 TATTTT TATTTT TATTTT TATTTT T
78042 GATATATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TATTTT
Found at i:84994 original size:4 final size:4
Alignment explanation
Indices: 84985--85014 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
84975 AAAATACTCA
84985 ATTT ATTT ATTT ATTT ATTT ATTT ATTT AT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT AT
85015 CTCAACTCCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (4 bp):
ATTT
Found at i:87173 original size:2 final size:2
Alignment explanation
Indices: 87168--87197 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
87158 GGTGAAGAAT
87168 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
87198 CATTAAAAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:87485 original size:2 final size:2
Alignment explanation
Indices: 87478--87504 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
87468 AGGTTAAAGA
87478 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
87505 CACATTAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:91741 original size:32 final size:29
Alignment explanation
Indices: 91649--91742 Score: 84
Period size: 29 Copynumber: 3.1 Consensus size: 29
91639 TAATTTATTG
* * * *
91649 AATACTATTTATGTCAATATTAT-TATTAA
1 AATATTATTTATAT-AATATTATAAATAAA
*
91678 AATATTATTTATATAATTTTATAAATAAA
1 AATATTATTTATATAATATTATAAATAAA
91707 AATATTAATTCTAGTATATATATTA-AAATAAA
1 AATATT-ATT-TA-TATA-ATATTATAAATAAA
91739 AATA
1 AATA
91743 AGATAAATTA
Statistics
Matches: 54, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
28 7 0.13
29 22 0.41
30 3 0.06
31 2 0.04
32 15 0.28
33 5 0.09
ACGTcount: A:0.50, C:0.03, G:0.02, T:0.45
Consensus pattern (29 bp):
AATATTATTTATATAATATTATAAATAAA
Found at i:92067 original size:23 final size:23
Alignment explanation
Indices: 92025--92080 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 23
92015 ATTATTGTAT
92025 TATATTATTAAAAATATTAATAAA
1 TATATT-TTAAAAATATTAATAAA
* * *
92049 TATATTTTAAATATGTTAATAAT
1 TATATTTTAAAAATATTAATAAA
92072 TAATATTTT
1 T-ATATTTT
92081 TATTAAAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 15 0.54
24 13 0.46
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (23 bp):
TATATTTTAAAAATATTAATAAA
Found at i:97456 original size:10 final size:9
Alignment explanation
Indices: 97421--97513 Score: 87
Period size: 10 Copynumber: 9.7 Consensus size: 9
97411 GCTGCTGGAA
*
97421 ACCGGTTTA
1 ACCGGTTTG
*
97430 ACCGGTTTTCA
1 ACCGG-TTT-G
97441 ACCGGTTCTG
1 ACCGGTT-TG
97451 ACCGGTTTG
1 ACCGGTTTG
*
97460 ACCGGTTTCA
1 ACCGGTTT-G
*
97470 ACCGGTTCG
1 ACCGGTTTG
97479 AACCGGTTTG
1 -ACCGGTTTG
*
97489 ACCGGTCTG
1 ACCGGTTTG
97498 AACCGGTTTG
1 -ACCGGTTTG
97508 ACCGGT
1 ACCGGT
97514 CAGACCCGAC
Statistics
Matches: 71, Mismatches: 7, Indels: 12
0.79 0.08 0.13
Matches are distributed among these distances:
9 29 0.41
10 35 0.49
11 7 0.10
ACGTcount: A:0.16, C:0.27, G:0.28, T:0.29
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:97465 original size:19 final size:20
Alignment explanation
Indices: 97421--97513 Score: 104
Period size: 19 Copynumber: 4.8 Consensus size: 20
97411 GCTGCTGGAA
* * *
97421 ACCGGTTTAACCGGTTTTCA
1 ACCGGTTTGACCGGTTCTGA
97441 ACCGGTTCTGACCGGTT-TG-
1 ACCGGTT-TGACCGGTTCTGA
*
97460 ACCGGTTTCAACCGGTTC-GA
1 ACCGGTTT-GACCGGTTCTGA
97480 ACCGGTTTGACCGG-TCTGA
1 ACCGGTTTGACCGGTTCTGA
97499 ACCGGTTTGACCGGT
1 ACCGGTTTGACCGGT
97514 CAGACCCGAC
Statistics
Matches: 63, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
18 3 0.05
19 36 0.57
20 16 0.25
21 8 0.13
ACGTcount: A:0.16, C:0.27, G:0.28, T:0.29
Consensus pattern (20 bp):
ACCGGTTTGACCGGTTCTGA
Found at i:97483 original size:29 final size:28
Alignment explanation
Indices: 97421--97513 Score: 123
Period size: 29 Copynumber: 3.2 Consensus size: 28
97411 GCTGCTGGAA
*
97421 ACCGGTTTAACCGGTTTTCAACCGGTTCTG
1 ACCGGTTTGACCGG-TTTCAACCGGTTC-G
97451 ACCGGTTTGACCGGTTTCAACCGGTTCG
1 ACCGGTTTGACCGGTTTCAACCGGTTCG
* * *
97479 AACCGGTTTGACCGGTCTGAACCGGTTTG
1 -ACCGGTTTGACCGGTTTCAACCGGTTCG
97508 ACCGGT
1 ACCGGT
97514 CAGACCCGAC
Statistics
Matches: 58, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
28 7 0.12
29 38 0.66
30 13 0.22
ACGTcount: A:0.16, C:0.27, G:0.28, T:0.29
Consensus pattern (28 bp):
ACCGGTTTGACCGGTTTCAACCGGTTCG
Found at i:97519 original size:9 final size:9
Alignment explanation
Indices: 97441--97519 Score: 52
Period size: 9 Copynumber: 8.3 Consensus size: 9
97431 CCGGTTTTCA
97441 ACCGGTTCTG
1 ACCGG-TCTG
*
97451 ACCGGTTTG
1 ACCGGTCTG
* *
97460 ACCGGTTTCA
1 ACCGGTCT-G
97470 ACCGGT-TCG
1 ACCGGTCT-G
*
97479 AACCGGTTTG
1 -ACCGGTCTG
97489 ACCGGTCTG
1 ACCGGTCTG
*
97498 AACCGGTTTG
1 -ACCGGTCTG
*
97508 ACCGGTCAG
1 ACCGGTCTG
97517 ACC
1 ACC
97520 CGACCCGACC
Statistics
Matches: 58, Mismatches: 7, Indels: 9
0.78 0.09 0.12
Matches are distributed among these distances:
9 31 0.53
10 26 0.45
11 1 0.02
ACGTcount: A:0.16, C:0.29, G:0.29, T:0.25
Consensus pattern (9 bp):
ACCGGTCTG
Found at i:97526 original size:5 final size:5
Alignment explanation
Indices: 97516--97573 Score: 62
Period size: 5 Copynumber: 10.8 Consensus size: 5
97506 TGACCGGTCA
* *
97516 GACCC GACCC GACCGTT GACCC GACCC GACCC GACCGTT GACCC GACCC
1 GACCC GACCC GACC--C GACCC GACCC GACCC GACC--C GACCC GACCC
97565 GACCC GACC
1 GACCC GACC
97574 GTTGACCGTT
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
5 37 0.82
7 8 0.18
ACGTcount: A:0.19, C:0.52, G:0.22, T:0.07
Consensus pattern (5 bp):
GACCC
Found at i:97542 original size:22 final size:22
Alignment explanation
Indices: 97516--97580 Score: 130
Period size: 22 Copynumber: 3.0 Consensus size: 22
97506 TGACCGGTCA
97516 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
97538 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
97560 GACCCGACCCGACCGTTGACC
1 GACCCGACCCGACCGTTGACC
97581 GTTGACCGTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.18, C:0.49, G:0.23, T:0.09
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:104757 original size:9 final size:9
Alignment explanation
Indices: 104743--104845 Score: 80
Period size: 9 Copynumber: 10.8 Consensus size: 9
104733 GGCTGCTGGA
104743 AACCGGTTT
1 AACCGGTTT
104752 AACCGGTTTT
1 AACCGG-TTT
104762 CAACCGGTTCT
1 -AACCGGTT-T
*
104773 GACCGGTTT
1 AACCGGTTT
* *
104782 GACCGGTTCG
1 AACCGGTT-T
104792 AACCGGTTT
1 AACCGGTTT
* *
104801 GACCGGTTCG
1 AACCGGTT-T
104811 AACCGGTTT
1 AACCGGTTT
* *
104820 GACCGGTCTG
1 AACCGGT-TT
104830 AACCGGTTT
1 AACCGGTTT
*
104839 GACCGGT
1 AACCGGT
104846 CAGACCCGAC
Statistics
Matches: 75, Mismatches: 13, Indels: 12
0.75 0.13 0.12
Matches are distributed among these distances:
9 35 0.47
10 33 0.44
11 7 0.09
ACGTcount: A:0.17, C:0.26, G:0.29, T:0.28
Consensus pattern (9 bp):
AACCGGTTT
Found at i:104768 original size:11 final size:10
Alignment explanation
Indices: 104743--104838 Score: 56
Period size: 10 Copynumber: 9.9 Consensus size: 10
104733 GGCTGCTGGA
104743 AACCGG-TTT
1 AACCGGTTTT
104752 AACCGGTTTT
1 AACCGGTTTT
*
104762 CAACCGGTTCT
1 -AACCGGTTTT
*
104773 GACCGG-TTT
1 AACCGGTTTT
* **
104782 GACCGGTTCG
1 AACCGGTTTT
104792 AACCGG-TTT
1 AACCGGTTTT
* **
104801 GACCGGTTCG
1 AACCGGTTTT
104811 AACCGG-TTT
1 AACCGGTTTT
* * *
104820 GACCGGTCTG
1 AACCGGTTTT
104830 AACCGGTTT
1 AACCGGTTT
104839 GACCGGTCAG
Statistics
Matches: 63, Mismatches: 19, Indels: 9
0.69 0.21 0.10
Matches are distributed among these distances:
9 26 0.41
10 28 0.44
11 9 0.14
ACGTcount: A:0.17, C:0.26, G:0.28, T:0.29
Consensus pattern (10 bp):
AACCGGTTTT
Found at i:104768 original size:20 final size:21
Alignment explanation
Indices: 104743--104819 Score: 74
Period size: 19 Copynumber: 3.9 Consensus size: 21
104733 GGCTGCTGGA
104743 AACCGGTT-TAACCGGTTTTC
1 AACCGGTTCTAACCGGTTTTC
*
104763 AACCGGTTCTGACCGG-TTT-
1 AACCGGTTCTAACCGGTTTTC
* *
104782 GACCGGTTCGAACCGG-TTT-
1 AACCGGTTCTAACCGGTTTTC
* *
104801 GACCGGTTCGAACCGGTTT
1 AACCGGTTCTAACCGGTTT
104820 GACCGGTCTG
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
19 32 0.63
20 13 0.25
21 6 0.12
ACGTcount: A:0.17, C:0.26, G:0.27, T:0.30
Consensus pattern (21 bp):
AACCGGTTCTAACCGGTTTTC
Found at i:104788 original size:19 final size:19
Alignment explanation
Indices: 104764--104845 Score: 132
Period size: 19 Copynumber: 4.3 Consensus size: 19
104754 CCGGTTTTCA
104764 ACCGGTTCTG-ACCGGTTTG
1 ACCGGTTC-GAACCGGTTTG
104783 ACCGGTTCGAACCGGTTTG
1 ACCGGTTCGAACCGGTTTG
104802 ACCGGTTCGAACCGGTTTG
1 ACCGGTTCGAACCGGTTTG
104821 ACCGG-TCTGAACCGGTTTG
1 ACCGGTTC-GAACCGGTTTG
104840 ACCGGT
1 ACCGGT
104846 CAGACCCGAC
Statistics
Matches: 60, Mismatches: 0, Indels: 5
0.92 0.00 0.08
Matches are distributed among these distances:
18 3 0.05
19 57 0.95
ACGTcount: A:0.15, C:0.27, G:0.32, T:0.27
Consensus pattern (19 bp):
ACCGGTTCGAACCGGTTTG
Found at i:104858 original size:5 final size:5
Alignment explanation
Indices: 104848--104904 Score: 53
Period size: 5 Copynumber: 10.8 Consensus size: 5
104838 TGACCGGTCA
* *
104848 GACCC GACCC GACCGTT GACCC GACCC GACCC GACCGTT GA-CC GACCC
1 GACCC GACCC GACC--C GACCC GACCC GACCC GACC--C GACCC GACCC
104896 GACCC GACC
1 GACCC GACC
104905 GTTGACCGTT
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
4 2 0.05
5 34 0.79
6 1 0.02
7 6 0.14
ACGTcount: A:0.19, C:0.51, G:0.23, T:0.07
Consensus pattern (5 bp):
GACCC
Found at i:104894 original size:21 final size:21
Alignment explanation
Indices: 104848--104912 Score: 121
Period size: 21 Copynumber: 3.0 Consensus size: 21
104838 TGACCGGTCA
104848 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGA-CC
104870 GACCCGACCCGACCGTTGACC
1 GACCCGACCCGACCGTTGACC
104891 GACCCGACCCGACCGTTGACC
1 GACCCGACCCGACCGTTGACC
104912 G
1 G
104913 TTGACCGTTG
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
21 24 0.56
22 19 0.44
ACGTcount: A:0.18, C:0.48, G:0.25, T:0.09
Consensus pattern (21 bp):
GACCCGACCCGACCGTTGACC
Found at i:104899 original size:26 final size:27
Alignment explanation
Indices: 104865--104919 Score: 85
Period size: 26 Copynumber: 2.0 Consensus size: 27
104855 CCCGACCGTT
104865 GACCCGACCCGACC-CGACCGTTGACC
1 GACCCGACCCGACCGCGACCGTTGACC
*
104891 GACCCGACCCGACCGTTGACCGTTGACC
1 GACCCGACCCGACCG-CGACCGTTGACC
104919 G
1 G
104920 TTGACTTTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 14 0.54
28 12 0.46
ACGTcount: A:0.18, C:0.45, G:0.25, T:0.11
Consensus pattern (27 bp):
GACCCGACCCGACCGCGACCGTTGACC
Found at i:109313 original size:37 final size:37
Alignment explanation
Indices: 109240--109314 Score: 91
Period size: 37 Copynumber: 2.0 Consensus size: 37
109230 GTTAGAAAAT
* *
109240 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
*
109277 ATTTATATAAATTTT-TTTACAAAATTGAAAAT-ATAAA
1 ATTTATAT--ATTTTCTTTAAAAAATTGAAAATCATAAA
109314 A
1 A
109315 AGGTTTAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
37 14 0.42
38 14 0.42
39 5 0.15
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.45
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
Found at i:114954 original size:14 final size:17
Alignment explanation
Indices: 114931--114971 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 17
114921 AACATAACCT
114931 ATAC-AAAGAAA-CA-A
1 ATACAAAAGAAACCATA
114945 AT-CAAAAGAAACCATA
1 ATACAAAAGAAACCATA
114961 ATACAAAAGAA
1 ATACAAAAGAA
114972 TTAAATACGA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
13 1 0.04
14 9 0.39
15 2 0.09
16 3 0.13
17 8 0.35
ACGTcount: A:0.68, C:0.15, G:0.07, T:0.10
Consensus pattern (17 bp):
ATACAAAAGAAACCATA
Found at i:123232 original size:4 final size:4
Alignment explanation
Indices: 123223--124686 Score: 2403
Period size: 4 Copynumber: 366.0 Consensus size: 4
123213 TATTTTGCTT
123223 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
123271 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
123319 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
123367 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
123415 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
123463 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
123511 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
123559 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* *
123607 CATA CATA CATA CATA CATA CATA CATA CATA CATA C-TG CATG CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
123654 CATA CATA CATA CATA CATA CATA CAT- -ATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
123700 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
123748 CATA CATA CATA CATA CATA CATG CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * * * * * * *
123796 CATA CATG CATG CATG CATG CATG CATG CATG CATG CATA CATG CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * * *
123844 CATA CATA CATA CATG CATG CATG CATG CATG CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * *
123892 CATG CATG CATG CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
123940 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
123988 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* *
124036 CATA CATA CATA CATA CATA CATA CATA CATG CATA CATG CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
124084 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
124132 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
124180 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * * * * * *
124228 CATG CATA CATG CATG CATG CATA CATG CATG CATG CATA CATG CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * * * *
124276 CATG CATA CATG CATA CATG CATA CATG CATA CATG CATA CATG CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * * * *
124324 CATG CATA CATG CATA CATG CATA CATG CATA CATG CATA CATG CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * * * * *
124372 CATG CATA CATA CATG CATA CATG CATA CATC CATG CATA CATC CATG
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * *
124420 CATA CATC CATG CATA CATA CATG CATA CATA CATG CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
124468 CATA CATGCA CATA CCATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CAT--A CATA -CATA CATA CATA CATA CATA CATA CATA CATA CATA
124519 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
124567 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
124615 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
124663 CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA
124687 TAAACTAACT
Statistics
Matches: 1387, Mismatches: 67, Indels: 12
0.95 0.05 0.01
Matches are distributed among these distances:
2 2 0.00
3 2 0.00
4 1375 0.99
5 4 0.00
6 4 0.00
ACGTcount: A:0.46, C:0.25, G:0.03, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:138570 original size:2 final size:2
Alignment explanation
Indices: 138563--138592 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
138553 ATTATAACAT
138563 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
138593 GGGGTTCTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:141488 original size:2 final size:2
Alignment explanation
Indices: 141481--141511 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
141471 AATATGTTTT
141481 TA TA TA TA TA TA TA TA TA TA TA -A TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
141512 AAATACTTGC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Done.