Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001612.1 Hibiscus syriacus cultivar Beakdansim tig00003202_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: 113668
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Found at i:1750 original size:32 final size:31
Alignment explanation
Indices: 1700--1776 Score: 73
Period size: 32 Copynumber: 2.4 Consensus size: 31
1690 TTTGGGTTTG
** * *
1700 GTTAAATTCTATTCGGGTTACTTTCGGATCGG
1 GTTAAATTCGGTT-GGGTTACATTCGGATCGA
* *
1732 GTTAAAATTCGGTTGGGTTTCATTCGGTTCGA
1 GTT-AAATTCGGTTGGGTTACATTCGGATCGA
*
1764 GTTAATTTCGGTT
1 GTTAAATTCGGTT
1777 TCGGTTTGGG
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
31 9 0.24
32 20 0.54
33 8 0.22
ACGTcount: A:0.18, C:0.13, G:0.26, T:0.43
Consensus pattern (31 bp):
GTTAAATTCGGTTGGGTTACATTCGGATCGA
Found at i:1782 original size:22 final size:22
Alignment explanation
Indices: 1754--1801 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
1744 TTGGGTTTCA
*
1754 TTCGGTTCGAGTTAATTTCGGT
1 TTCGGTTCGAGTTAATTTCGAT
* * *
1776 TTCGGTTTGGGTTGATTTCGAT
1 TTCGGTTCGAGTTAATTTCGAT
1798 TTCG
1 TTCG
1802 TTAAATTTTG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.10, C:0.12, G:0.29, T:0.48
Consensus pattern (22 bp):
TTCGGTTCGAGTTAATTTCGAT
Found at i:12496 original size:6 final size:6
Alignment explanation
Indices: 12485--12522 Score: 67
Period size: 6 Copynumber: 6.3 Consensus size: 6
12475 CTTATAATGC
*
12485 AATAGG AATAGG AATAGG AATAGG AATAGG AATTGG AA
1 AATAGG AATAGG AATAGG AATAGG AATAGG AATAGG AA
12523 CTGTAATTAC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.50, C:0.00, G:0.32, T:0.18
Consensus pattern (6 bp):
AATAGG
Found at i:16658 original size:21 final size:21
Alignment explanation
Indices: 16634--16687 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
16624 CACGCCGCCA
*
16634 ATGGAATAAACATTTTTAATG
1 ATGGAATAAACATATTTAATG
16655 ATGGAATAAACATATTTAATG
1 ATGGAATAAACATATTTAATG
16676 ATGGAATAAACA
1 ATGGAATAAACA
16688 AACCAACCGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.48, C:0.06, G:0.15, T:0.31
Consensus pattern (21 bp):
ATGGAATAAACATATTTAATG
Found at i:28309 original size:16 final size:16
Alignment explanation
Indices: 28283--28321 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
28273 ATTCATTACT
28283 ATTTACGTGAATAGTGA
1 ATTT-CGTGAATAGTGA
28300 ATTTCGTGAATAGTGA
1 ATTTCGTGAATAGTGA
*
28316 AATTCG
1 ATTTCG
28322 GTCGGCGATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 17 0.81
17 4 0.19
ACGTcount: A:0.33, C:0.08, G:0.23, T:0.36
Consensus pattern (16 bp):
ATTTCGTGAATAGTGA
Found at i:28319 original size:17 final size:17
Alignment explanation
Indices: 28283--28316 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
28273 ATTCATTACT
28283 ATTTACGTGAATAGTGA
1 ATTTACGTGAATAGTGA
28300 ATTT-CGTGAATAGTGA
1 ATTTACGTGAATAGTGA
28316 A
1 A
28317 ATTCGGTCGG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.35, C:0.06, G:0.24, T:0.35
Consensus pattern (17 bp):
ATTTACGTGAATAGTGA
Found at i:29089 original size:15 final size:16
Alignment explanation
Indices: 29071--29103 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
29061 GTGGCAAATC
29071 AAAATCCAG-ACGGGA
1 AAAATCCAGAACGGGA
29086 AAAATCCAGAACGGGA
1 AAAATCCAGAACGGGA
29102 AA
1 AA
29104 GAAAGATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.52, C:0.18, G:0.24, T:0.06
Consensus pattern (16 bp):
AAAATCCAGAACGGGA
Found at i:48765 original size:6 final size:6
Alignment explanation
Indices: 48754--48814 Score: 95
Period size: 6 Copynumber: 10.2 Consensus size: 6
48744 GACACGTATT
* * *
48754 ACCACG ACCACG ACCACG ACCACG ACCTCG ACCTCG ACCTCG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
48802 ACCACG ACCACG A
1 ACCACG ACCACG A
48815 GCCGAGCCGA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 53 1.00
ACGTcount: A:0.30, C:0.49, G:0.16, T:0.05
Consensus pattern (6 bp):
ACCACG
Found at i:48822 original size:5 final size:5
Alignment explanation
Indices: 48812--48860 Score: 62
Period size: 5 Copynumber: 9.8 Consensus size: 5
48802 ACCACGACCA
* * * *
48812 CGAGC CGAGC CGAGC CGAGC CGTGC CGTGC CGTGC CGAGC CGAGA CGAG
1 CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAG
48861 ACGGACGGAC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 41 1.00
ACGTcount: A:0.16, C:0.37, G:0.41, T:0.06
Consensus pattern (5 bp):
CGAGC
Found at i:54622 original size:6 final size:6
Alignment explanation
Indices: 54611--54708 Score: 196
Period size: 6 Copynumber: 16.3 Consensus size: 6
54601 AGACACGTAT
54611 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC
1 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC
54659 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC
1 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC
54707 GA
1 GA
54709 GCCGAGCCGA
Statistics
Matches: 92, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 92 1.00
ACGTcount: A:0.34, C:0.49, G:0.17, T:0.00
Consensus pattern (6 bp):
GACCAC
Found at i:75141 original size:26 final size:26
Alignment explanation
Indices: 75105--75157 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
75095 TTAATGATAT
75105 GATATATGGTAGTTGGCAAGGGATTC
1 GATATATGGTAGTTGGCAAGGGATTC
75131 GATATATGGTAGTTGGCAAGGGATTC
1 GATATATGGTAGTTGGCAAGGGATTC
75157 G
1 G
75158 CTACCAAATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.26, C:0.08, G:0.36, T:0.30
Consensus pattern (26 bp):
GATATATGGTAGTTGGCAAGGGATTC
Found at i:75646 original size:15 final size:15
Alignment explanation
Indices: 75626--75655 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
75616 AGGTTTTTTT
75626 TTTATATCCCAACAA
1 TTTATATCCCAACAA
75641 TTTATATCCCAACAA
1 TTTATATCCCAACAA
75656 CTTGTCCATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.27, G:0.00, T:0.33
Consensus pattern (15 bp):
TTTATATCCCAACAA
Found at i:77849 original size:23 final size:23
Alignment explanation
Indices: 77823--77867 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
77813 CACCACAGCT
* *
77823 CGTATAATTGCACTGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
*
77846 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
77868 ATATAAAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.24
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:78085 original size:149 final size:149
Alignment explanation
Indices: 77843--78149 Score: 560
Period size: 149 Copynumber: 2.1 Consensus size: 149
77833 CACTGAAGTG
77843 CCGCGTAGAATTGCACCGTAGTGCCATATAAAAATGTCCATAAGGACCACATATTATTCCTTAAG
1 CCGCGTAGAATTGCACCGTAGTGCCATATAAAAATGTCCATAAGGACCACATATTATTCCTTAAG
*
77908 AATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCACAGAAT
66 AATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAAT
*
77973 ATATATATATCCCGAAGGA
131 ATACATATATCCCGAAGGA
* **
77992 CCGCGTAGAATTGCACCGTAGTGCTATATAATGATGTCCATAAGGACCACATATTATTCCTTAAG
1 CCGCGTAGAATTGCACCGTAGTGCCATATAAAAATGTCCATAAGGACCACATATTATTCCTTAAG
78057 AATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAAT
66 AATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAAT
*
78122 ATACATATGTCCCGAAGGA
131 ATACATATATCCCGAAGGA
78141 CCGCGTAGA
1 CCGCGTAGA
78150 CCCTCGACTC
Statistics
Matches: 152, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
149 152 1.00
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.28
Consensus pattern (149 bp):
CCGCGTAGAATTGCACCGTAGTGCCATATAAAAATGTCCATAAGGACCACATATTATTCCTTAAG
AATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAAT
ATACATATATCCCGAAGGA
Found at i:78269 original size:14 final size:14
Alignment explanation
Indices: 78250--78277 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
78240 AACTTGTAAT
78250 TCACGTATCACATA
1 TCACGTATCACATA
78264 TCACGTATCACATA
1 TCACGTATCACATA
78278 GCTTCTTTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.29, G:0.07, T:0.29
Consensus pattern (14 bp):
TCACGTATCACATA
Found at i:78796 original size:2 final size:2
Alignment explanation
Indices: 78784--78817 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
78774 ATTTCATTTC
*
78784 AT AT CT 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
78818 TCTCAAGATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:79703 original size:21 final size:21
Alignment explanation
Indices: 79679--79723 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
79669 TGTTGTTCGT
* *
79679 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
79700 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
79721 TTG
1 TTG
79724 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:83360 original size:2 final size:2
Alignment explanation
Indices: 83350--83379 Score: 51
Period size: 2 Copynumber: 14.5 Consensus size: 2
83340 CTCTCCTTAA
83350 TC TC ATC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC -TC TC TC TC TC TC TC TC TC TC TC TC T
83380 AGATATATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 25 0.93
3 2 0.07
ACGTcount: A:0.03, C:0.47, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:83387 original size:2 final size:2
Alignment explanation
Indices: 83382--83447 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
83372 CTCTCTCTAG
83382 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
83424 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
83448 CCTTTTGGCT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:84999 original size:5 final size:5
Alignment explanation
Indices: 84989--85020 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
84979 GACCACGACC
84989 CGAGA CGAGA CGAGA CGAGA CGAGA CGAGA CG
1 CGAGA CGAGA CGAGA CGAGA CGAGA CGAGA CG
85021 GCGGCGGCGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.38, C:0.22, G:0.41, T:0.00
Consensus pattern (5 bp):
CGAGA
Found at i:85774 original size:6 final size:6
Alignment explanation
Indices: 85763--85801 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
85753 TCTCGTCTCG
85763 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
85802 AATACGTGTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.00, C:0.15, G:0.51, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:85916 original size:20 final size:20
Alignment explanation
Indices: 85891--86000 Score: 116
Period size: 20 Copynumber: 5.4 Consensus size: 20
85881 TTTTGCCGTT
85891 TTGCGATTCTTGGAATCGCG
1 TTGCGATTCTTGGAATCGCG
** *
85911 TTGCGATT-TTCTCAATCGCA
1 TTGCGATTCTT-GGAATCGCG
*
85931 TTGCGATTCCTGGAATCGCG
1 TTGCGATTCTTGGAATCGCG
**
85951 TTGCGATT-TTCTCAATCGCG
1 TTGCGATTCTT-GGAATCGCG
85971 TTGCGATTCTTGGAAGATCGCG
1 TTGCGATTCTTGG-A-ATCGCG
85993 TTGCGATT
1 TTGCGATT
86001 TTCTTTTGAC
Statistics
Matches: 72, Mismatches: 12, Indels: 10
0.77 0.13 0.11
Matches are distributed among these distances:
19 3 0.04
20 51 0.71
21 4 0.06
22 14 0.19
ACGTcount: A:0.16, C:0.22, G:0.25, T:0.36
Consensus pattern (20 bp):
TTGCGATTCTTGGAATCGCG
Found at i:86016 original size:20 final size:20
Alignment explanation
Indices: 85991--86045 Score: 74
Period size: 21 Copynumber: 2.7 Consensus size: 20
85981 TGGAAGATCG
* *
85991 CGTTGCGATTTTCTTTTGAC
1 CGTTGCGATTTTCTTTTCAA
86011 CGTTGCGATTTTTCTTTTCAA
1 CGTTGCGA-TTTTCTTTTCAA
*
86032 CATTGCGATTTTCT
1 CGTTGCGATTTTCT
86046 AAATCGCGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
20 14 0.45
21 17 0.55
ACGTcount: A:0.13, C:0.20, G:0.16, T:0.51
Consensus pattern (20 bp):
CGTTGCGATTTTCTTTTCAA
Found at i:86020 original size:42 final size:40
Alignment explanation
Indices: 85891--86004 Score: 192
Period size: 40 Copynumber: 2.8 Consensus size: 40
85881 TTTTGCCGTT
*
85891 TTGCGATTCTTGGAATCGCGTTGCGATTTTCTCAATCGCA
1 TTGCGATTCTTGGAATCGCGTTGCGATTTTCTCAATCGCG
*
85931 TTGCGATTCCTGGAATCGCGTTGCGATTTTCTCAATCGCG
1 TTGCGATTCTTGGAATCGCGTTGCGATTTTCTCAATCGCG
85971 TTGCGATTCTTGGAAGATCGCGTTGCGATTTTCT
1 TTGCGATTCTTGG-A-ATCGCGTTGCGATTTTCT
86005 TTTGACCGTT
Statistics
Matches: 69, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
40 50 0.72
41 1 0.01
42 18 0.26
ACGTcount: A:0.16, C:0.22, G:0.25, T:0.38
Consensus pattern (40 bp):
TTGCGATTCTTGGAATCGCGTTGCGATTTTCTCAATCGCG
Found at i:87554 original size:28 final size:28
Alignment explanation
Indices: 87514--87578 Score: 121
Period size: 28 Copynumber: 2.3 Consensus size: 28
87504 TTGATTGTCG
87514 GGATTACTATTCTCATTAGTATTATATA
1 GGATTACTATTCTCATTAGTATTATATA
87542 GGATTACTATTCTCATTAGTATTATATA
1 GGATTACTATTCTCATTAGTATTATATA
*
87570 AGATTACTA
1 GGATTACTA
87579 ATGTAATCGA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.45
Consensus pattern (28 bp):
GGATTACTATTCTCATTAGTATTATATA
Found at i:94230 original size:27 final size:29
Alignment explanation
Indices: 94176--94233 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 29
94166 AAATTACTAT
94176 TTTAATGAATAAAAATAAAATTACATTTTC
1 TTTAATGAATAAAAATAAAATTA-ATTTTC
* *
94206 TTTAATGAATAAAAA-AATATTATTTTTC
1 TTTAATGAATAAAAATAAAATTAATTTTC
94234 ATCATCCATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 5 0.19
29 6 0.23
30 15 0.58
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.43
Consensus pattern (29 bp):
TTTAATGAATAAAAATAAAATTAATTTTC
Found at i:95469 original size:65 final size:65
Alignment explanation
Indices: 95061--95453 Score: 567
Period size: 65 Copynumber: 6.1 Consensus size: 65
95051 AAAGGTAGAG
* * * * ** *
95061 TGAATA-AGTACAAATCACTC--ATGACTCATGCACATTTGTGGTTAATGAGGTGGATTGATAAT
1 TGAATACAATACAGATCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAAT
95123 TGAATACAATACAGATCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAAT
1 TGAATACAATACAGATCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAAT
* * **
95188 TGAATACAATACAAATCACTCATATGACTTATGTACCTTTGTGGTGCATGATATGGAGTGATAAT
1 TGAATACAATACAGATCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAAT
* * ** *
95253 TGAATACAGTACTGATCACTCATATGACTGTTGTACCTTTGTGGTGCATGAGGTAGAGTGATAAT
1 TGAATACAATACAGATCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAAT
* * *
95318 TGTATACAATACAGATCACTCATATGACTCATGTACCTTTGTAGTGCATAAGGTGGAGTGATAAT
1 TGAATACAATACAGATCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAAT
* * *
95383 TGAATACAGTACAGATCACTCATATGACTCGTGTACTTTTGTGGTGCATGAGGTGGAGTGATAAT
1 TGAATACAATACAGATCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAAT
95448 TGAATA
1 TGAATA
95454 TTGCAAAGAC
Statistics
Matches: 295, Mismatches: 33, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
62 6 0.02
63 12 0.04
65 277 0.94
ACGTcount: A:0.31, C:0.14, G:0.22, T:0.33
Consensus pattern (65 bp):
TGAATACAATACAGATCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAAT
Found at i:98564 original size:18 final size:18
Alignment explanation
Indices: 98538--98572 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
98528 GAAATGAAAA
98538 AAAAATAATAATAATAAG
1 AAAAATAATAATAATAAG
* *
98556 AAAAGTAATACTAATAA
1 AAAAATAATAATAATAA
98573 TTAATGTGCA
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:0.69, C:0.03, G:0.06, T:0.23
Consensus pattern (18 bp):
AAAAATAATAATAATAAG
Found at i:104274 original size:9 final size:9
Alignment explanation
Indices: 104260--104293 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
104250 CCTGCTACAA
104260 AAAACAAAC
1 AAAACAAAC
104269 AAAACAAAAC
1 AAAAC-AAAC
104279 AAAACAAAC
1 AAAACAAAC
*
104288 GAAACA
1 AAAACA
104294 CAGCAGCCCT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 14 0.61
10 9 0.39
ACGTcount: A:0.76, C:0.21, G:0.03, T:0.00
Consensus pattern (9 bp):
AAAACAAAC
Done.