Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001340.1 Hibiscus syriacus cultivar Beakdansim tig00002614_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: 68631
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:2042 original size:36 final size:36
Alignment explanation
Indices: 1977--2086 Score: 109
Period size: 36 Copynumber: 3.1 Consensus size: 36
1967 ACTTGAGATT
**
1977 GTTTCCCTT-AAACATA--TTGTCTCTTTTGAGGCA
1 GTTTCCCTTGAAACATATTTTGTCTCGCTTGAGGCA
* * *
2010 TTTTCCCTTGAAACATATTTTGTCTCGCTTGAGTCC
1 GTTTCCCTTGAAACATATTTTGTCTCGCTTGAGGCA
* * * * *
2046 GTTTCTCTTGAAACAAATTTTGTCTCCCTCGAGACA
1 GTTTCCCTTGAAACATATTTTGTCTCGCTTGAGGCA
2082 GTTTC
1 GTTTC
2087 TTATGAAACA
Statistics
Matches: 62, Mismatches: 12, Indels: 3
0.81 0.16 0.04
Matches are distributed among these distances:
33 8 0.13
34 7 0.11
36 47 0.76
ACGTcount: A:0.20, C:0.24, G:0.15, T:0.42
Consensus pattern (36 bp):
GTTTCCCTTGAAACATATTTTGTCTCGCTTGAGGCA
Found at i:2087 original size:36 final size:36
Alignment explanation
Indices: 2011--2096 Score: 102
Period size: 36 Copynumber: 2.4 Consensus size: 36
2001 TTTGAGGCAT
* * * * * *
2011 TTTCCCTTGAAACATATTTTGTCTCGCTTGAGTCCG
1 TTTCTCTTGAAACAAATTTTGTCTCCCTCGAGACAG
2047 TTTCTCTTGAAACAAATTTTGTCTCCCTCGAGACAG
1 TTTCTCTTGAAACAAATTTTGTCTCCCTCGAGACAG
2083 TTTCT-TATGAAACA
1 TTTCTCT-TGAAACA
2097 CCAAACTTTG
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
35 1 0.02
36 42 0.98
ACGTcount: A:0.23, C:0.23, G:0.14, T:0.40
Consensus pattern (36 bp):
TTTCTCTTGAAACAAATTTTGTCTCCCTCGAGACAG
Found at i:2209 original size:66 final size:65
Alignment explanation
Indices: 1900--2225 Score: 191
Period size: 66 Copynumber: 4.9 Consensus size: 65
1890 AATATAATAC
* * * * * *
1900 CTTTGAGATTGTTTCTCTCGAAACAAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACATAA
1 CTTTGAGATCGTTTCCCTTGAAAC--AATTTTGTCTCTTTTGAGACAGTTTCTCATGAAACA-CA
1965 AAA
63 AAA
* * * * * * *
1968 C-TTGAGATTGTTTCCCTT-AAAC-ATATTGTCTCTTTTGAGGCATTTTCCCTTGAAACATATTT
1 CTTTGAGATCGTTTCCCTTGAAACAATTTTGTCTCTTTTGAGACAGTTTCTCATGAAACACA---
***
2030 TGT
63 AAA
* ** * *
2033 CTCGCTTGAG-TCCGTTTCTCTTGAAACAAATTTTGTCTCCCTCGAGACAGTTTCTTATGAAACA
1 CT---TTGAGAT-CGTTTCCCTTGAAAC-AATTTTGTCTCTTTTGAGACAGTTTCTCATGAAACA
*
2097 CCAAA
61 CAAAA
* * * *
2102 CTTTGAGATTGTTTCCCATGAAACAAGTTTTAT-TTTCTTTGAGATCA-TTTCTCATG-AACA-A
1 CTTTGAGATCGTTTCCCTTGAAACAA-TTTTGTCTCT-TTTGAGA-CAGTTTCTCATGAAACACA
2163 AATA
63 AA-A
* *
2167 TCTTTGAGATCGTTTCCCTTGAAACGAATTTTGTCTCTTTTGAGACAGCTTCTCTTGAA
1 -CTTTGAGATCGTTTCCCTTGAAAC-AATTTTGTCTCTTTTGAGACAGTTTCTCATGAA
2226 GCATCATCTA
Statistics
Matches: 194, Mismatches: 43, Indels: 43
0.69 0.15 0.15
Matches are distributed among these distances:
62 1 0.01
63 30 0.15
64 2 0.01
65 11 0.06
66 80 0.41
67 23 0.12
68 2 0.01
69 15 0.08
70 4 0.02
72 26 0.13
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.40
Consensus pattern (65 bp):
CTTTGAGATCGTTTCCCTTGAAACAATTTTGTCTCTTTTGAGACAGTTTCTCATGAAACACAAAA
Found at i:2566 original size:131 final size:131
Alignment explanation
Indices: 2258--2657 Score: 576
Period size: 131 Copynumber: 3.1 Consensus size: 131
2248 CTTGAAACTA
* * * *
2258 TGTTATCATCCCTAATGAT-GCATGTCATCCTCATCGCGTAGGAACCATGTCATCCCTCGACCAG
1 TGTTATCATCCCTAATGATGGCCTGCCATCCTCATCACGTAGGAACCGTGTCATCCCTCGACCAG
* *
2322 ATCTCCTCATCACGTAGGAGCCGTGTCAA--TTAAATAACCAGTCGTCCTCATCACGTA-GAACC
66 ATCTCCTCATCAAGTAGGAGCCGTGTCAACCTTAGATAACCAGTCGTCCTCATCACGTAGGAACC
2384 G
131 G
* * *
2385 TGTTATCACCCCTAATGATGGCCTACCATTCTCATCACGTAGGAACCGTGTCATCCCTCGACCAG
1 TGTTATCATCCCTAATGATGGCCTGCCATCCTCATCACGTAGGAACCGTGTCATCCCTCGACCAG
*
2450 ATCTCCTCATCAAGTAGGAGCCGTGTCAACCTTAGATAACCAGTCGTCCTCATCATGTAGGAACC
66 ATCTCCTCATCAAGTAGGAGCCGTGTCAACCTTAGATAACCAGTCGTCCTCATCACGTAGGAACC
2515 G
131 G
* * * *
2516 TGTTATCATCCCTAATGATGGCCTGCCATCCCCATCACGTAGGAATCGTGTCATCCTTCGACTAG
1 TGTTATCATCCCTAATGATGGCCTGCCATCCTCATCACGTAGGAACCGTGTCATCCCTCGACCAG
* ** * *
2581 ATCTCCTCATCACA-TAGAAGTTGTGTCAACCTTAGATAATCAGCCGTCCTCATCACGTAGGAAC
66 ATCTCCTCATCA-AGTAGGAGCCGTGTCAACCTTAGATAACCAGTCGTCCTCATCACGTAGGAAC
*
2645 TG
130 CG
2647 TGTTATCATCC
1 TGTTATCATCC
2658 TTAGACGATT
Statistics
Matches: 244, Mismatches: 24, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
127 18 0.07
128 67 0.27
130 26 0.11
131 132 0.54
132 1 0.00
ACGTcount: A:0.25, C:0.30, G:0.17, T:0.27
Consensus pattern (131 bp):
TGTTATCATCCCTAATGATGGCCTGCCATCCTCATCACGTAGGAACCGTGTCATCCCTCGACCAG
ATCTCCTCATCAAGTAGGAGCCGTGTCAACCTTAGATAACCAGTCGTCCTCATCACGTAGGAACC
G
Found at i:10913 original size:56 final size:57
Alignment explanation
Indices: 10807--10914 Score: 157
Period size: 56 Copynumber: 1.9 Consensus size: 57
10797 GAATGCATTT
* *
10807 CATGCATCGATGCACTGAGGATTTTATGAAAACATCGAATGCATTTGATGCACCAGC
1 CATGCATCGATGCACTCAGGATTTTATGAAAACATCGAATGCACTTGATGCACCAGC
* *
10864 CATGCATCGATGCACTCTGGCTATTT-TG-AAACATCGAATGCACTTGATGCA
1 CATGCATCGATGCACTCAGGAT-TTTATGAAAACATCGAATGCACTTGATGCA
10915 TCGATGCACT
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
56 22 0.48
57 21 0.46
58 3 0.07
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.28
Consensus pattern (57 bp):
CATGCATCGATGCACTCAGGATTTTATGAAAACATCGAATGCACTTGATGCACCAGC
Found at i:12367 original size:31 final size:31
Alignment explanation
Indices: 12329--12404 Score: 125
Period size: 31 Copynumber: 2.5 Consensus size: 31
12319 GAGTCGAGGG
**
12329 TTACCTATGTTCTTCGGGACATATGGACTGA
1 TTACCTATGTTCTTCGGGACATATGGACCAA
12360 TTACCTATGTTCTTCGGGACATATGGACCAA
1 TTACCTATGTTCTTCGGGACATATGGACCAA
*
12391 TTACCTAGGTTCTT
1 TTACCTATGTTCTT
12405 ATAGACCTAT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.22, C:0.21, G:0.20, T:0.37
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGACCAA
Found at i:12958 original size:19 final size:19
Alignment explanation
Indices: 12936--12986 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
12926 CAGTAGCAGT
*
12936 GTATCGGTACACTATAGTA
1 GTATCGATACACTATAGTA
12955 GTATCGATACACTATAGTA
1 GTATCGATACACTATAGTA
12974 GTATCGATACACT
1 GTATCGATACACT
12987 TTTTGTATTC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (19 bp):
GTATCGATACACTATAGTA
Found at i:13058 original size:20 final size:20
Alignment explanation
Indices: 13033--13073 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
13023 ATTATTGTTC
13033 ACACAGAATCGATACTATTT
1 ACACAGAATCGATACTATTT
* **
13053 ACACAGTATTTATACTATTT
1 ACACAGAATCGATACTATTT
13073 A
1 A
13074 TACAATACTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.39, C:0.17, G:0.07, T:0.37
Consensus pattern (20 bp):
ACACAGAATCGATACTATTT
Found at i:16595 original size:14 final size:14
Alignment explanation
Indices: 16576--16613 Score: 76
Period size: 14 Copynumber: 2.7 Consensus size: 14
16566 TCAAAGCATG
16576 AAGGAAGAAGAAGA
1 AAGGAAGAAGAAGA
16590 AAGGAAGAAGAAGA
1 AAGGAAGAAGAAGA
16604 AAGGAAGAAG
1 AAGGAAGAAG
16614 GAAAATTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (14 bp):
AAGGAAGAAGAAGA
Found at i:19307 original size:31 final size:31
Alignment explanation
Indices: 19241--19308 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
19231 GGTTATCTAT
* *
19241 GTTCTTTGGGACATATAAACTGATTACATAT
1 GTTCTTCGGGACATATAAACTGATTACATAG
** * *
19272 GTTCTTCGGGACATATGGATTGATTACTTAG
1 GTTCTTCGGGACATATAAACTGATTACATAG
19303 GTTCTT
1 GTTCTT
19309 ATGGACCTAT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.25, C:0.13, G:0.21, T:0.41
Consensus pattern (31 bp):
GTTCTTCGGGACATATAAACTGATTACATAG
Found at i:19320 original size:31 final size:31
Alignment explanation
Indices: 19241--19321 Score: 81
Period size: 31 Copynumber: 2.6 Consensus size: 31
19231 GGTTATCTAT
* ** * *
19241 GTTCTTTGGGACATATAAACTGATTACATAT
1 GTTCTTAGGGACATATGGATTGATTACATAG
* *
19272 GTTCTTCGGGACATATGGATTGATTACTTAG
1 GTTCTTAGGGACATATGGATTGATTACATAG
* *
19303 GTTCTTATGGACCTATGGA
1 GTTCTTAGGGACATATGGA
19322 CTGGTCATTC
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.26, C:0.14, G:0.22, T:0.38
Consensus pattern (31 bp):
GTTCTTAGGGACATATGGATTGATTACATAG
Found at i:19947 original size:20 final size:20
Alignment explanation
Indices: 19917--19967 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
19907 TTCATTATTG
*
19917 TTCAGACAGTATCGGTAATA
1 TTCATACAGTATCGGTAATA
* *
19937 TTTATACAGTATCGGTACTA
1 TTCATACAGTATCGGTAATA
19957 TTCATACAGTA
1 TTCATACAGTA
19968 CAATACTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (20 bp):
TTCATACAGTATCGGTAATA
Found at i:21157 original size:2 final size:2
Alignment explanation
Indices: 21150--21242 Score: 114
Period size: 2 Copynumber: 45.0 Consensus size: 2
21140 CTCTATAATA
21150 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
* * * * *
21192 AT AT AT AT AT AT CAT AT AT GAA AA AT AT AA AA AT AT AT AT GT AT
1 AT AT AT AT AT AT -AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT
21236 CAT AT AT
1 -AT AT AT
21243 GACTATAAAA
Statistics
Matches: 82, Mismatches: 6, Indels: 6
0.87 0.06 0.06
Matches are distributed among these distances:
2 77 0.94
3 5 0.06
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (2 bp):
AT
Found at i:25506 original size:8 final size:8
Alignment explanation
Indices: 25493--25533 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
25483 CTCATTTTCA
25493 GAGAATTT
1 GAGAATTT
25501 GAGAATTT
1 GAGAATTT
*
25509 -AGAGTTT
1 GAGAATTT
*
25516 GGGAATTT
1 GAGAATTT
25524 GAGAATTT
1 GAGAATTT
25532 GA
1 GA
25534 AAGATTGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:25834 original size:128 final size:128
Alignment explanation
Indices: 25604--26104 Score: 939
Period size: 128 Copynumber: 3.9 Consensus size: 128
25594 TAATCGGAGT
* *
25604 ACTATTCATATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTAT
*
25669 CATTGCCCTATTATGTCACTCATGTCCCTCGTGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
*
25732 ACTATTCACATGAAGGCGCGTTCCCGGGGGCACGCCTTCCATTATTTCATCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTAT
* * *
25797 CATTACCCTATTATGTCACTCATGTCCCTCGGAGACACTAGATATATCAATACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
25860 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTAT
25925 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
25988 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTAT
26053 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
26105 AATCAGGTAA
Statistics
Matches: 362, Mismatches: 11, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
128 362 1.00
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.32
Consensus pattern (128 bp):
ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTAT
CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
Found at i:26600 original size:33 final size:32
Alignment explanation
Indices: 26497--26601 Score: 131
Period size: 33 Copynumber: 3.2 Consensus size: 32
26487 TAAGTTGAAA
*
26497 TTTAATGTTAAATTTCGAATACTATAATTTATAT
1 TTTAAT-TTAAATTTCGAATAATATAATTT-TAT
*
26531 TTTAAATTTAAATTT-GAATAATATTATTTTATT
1 TTT-AATTTAAATTTCGAATAATATAATTTTA-T
*
26564 TTTATTTTAAATTTCGAATAATATAATTTGTAT
1 TTTAATTTAAATTTCGAATAATATAATTT-TAT
26597 TTTAA
1 TTTAA
26602 AAACATTTAT
Statistics
Matches: 62, Mismatches: 5, Indels: 9
0.82 0.07 0.12
Matches are distributed among these distances:
32 12 0.19
33 34 0.55
34 13 0.21
35 3 0.05
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.54
Consensus pattern (32 bp):
TTTAATTTAAATTTCGAATAATATAATTTTAT
Found at i:27152 original size:21 final size:20
Alignment explanation
Indices: 27125--27194 Score: 95
Period size: 21 Copynumber: 3.4 Consensus size: 20
27115 GGTATAAAAC
*
27125 CCTGCGGGCTAGGCATGTAA
1 CCTGCGGGCTAGGAATGTAA
27145 CCTGGCGGGCTAGGAATGTAA
1 CCT-GCGGGCTAGGAATGTAA
*
27166 CCCTGCGGGCTCGGAATGTAA
1 -CCTGCGGGCTAGGAATGTAA
27187 CCCTGCGG
1 -CCTGCGG
27195 AGATGGCATA
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
20 3 0.07
21 40 0.87
22 3 0.07
ACGTcount: A:0.19, C:0.27, G:0.36, T:0.19
Consensus pattern (20 bp):
CCTGCGGGCTAGGAATGTAA
Found at i:27800 original size:31 final size:31
Alignment explanation
Indices: 27733--27792 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
27723 TAATTTAAGG
*
27733 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTATTTGGACTTGAATTGAATTTA
27764 CAAAAT-GTATTTGGACTT-AATTGAATTTA
1 CAAAATGGTATTTGGACTTGAATTGAATTTA
27793 TTCAAAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.35, C:0.07, G:0.17, T:0.42
Consensus pattern (31 bp):
CAAAATGGTATTTGGACTTGAATTGAATTTA
Found at i:27891 original size:18 final size:18
Alignment explanation
Indices: 27857--27922 Score: 78
Period size: 19 Copynumber: 3.6 Consensus size: 18
27847 AATGTTTTTA
*
27857 TGAATAGTAATTTACTATT
1 TGAACAGTAA-TTACTATT
*
27876 TGAACAGTAATTACTATG
1 TGAACAGTAATTACTATT
* *
27894 TGAACAGTAAATCACTGTT
1 TGAACAGT-AATTACTATT
27913 TGAACAGTAA
1 TGAACAGTAA
27923 CCCGAGGCTC
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
18 17 0.41
19 24 0.59
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.35
Consensus pattern (18 bp):
TGAACAGTAATTACTATT
Found at i:28131 original size:21 final size:21
Alignment explanation
Indices: 28098--28137 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
28088 TTTTTGCAGA
*
28098 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
28120 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
28138 AGATATGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:31276 original size:31 final size:31
Alignment explanation
Indices: 31209--31268 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
31199 TAATTTAAGG
*
31209 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTATTTGGACTTGAATTGAATTTA
31240 CAAAAT-GTATTTGGACTT-AATTGAATTTA
1 CAAAATGGTATTTGGACTTGAATTGAATTTA
31269 TTCAAAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.35, C:0.07, G:0.17, T:0.42
Consensus pattern (31 bp):
CAAAATGGTATTTGGACTTGAATTGAATTTA
Found at i:31360 original size:19 final size:19
Alignment explanation
Indices: 31333--31399 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
31323 AATGTTTTTA
* *
31333 TGAATAGTAATTTACTATT
1 TGAACAGTAAATTACTATT
*
31352 TGAACAGTAAATTACTATG
1 TGAACAGTAAATTACTATT
* *
31371 TGAACAGTAAATCACTGTT
1 TGAACAGTAAATTACTATT
31390 TGAACAGTAA
1 TGAACAGTAA
31400 CCCGAGGCTC
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 42 1.00
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.34
Consensus pattern (19 bp):
TGAACAGTAAATTACTATT
Found at i:31608 original size:21 final size:21
Alignment explanation
Indices: 31575--31614 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
31565 TTTTTGCAGA
*
31575 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
31597 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
31615 AGATATGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:33243 original size:31 final size:33
Alignment explanation
Indices: 33201--33275 Score: 84
Period size: 31 Copynumber: 2.4 Consensus size: 33
33191 ATAATTCTAA
* * *
33201 ATAAATAATAATTATATAAAT-ATTATTTTAAT
1 ATAAAAAATAATTATATAAATAAATATATTAAT
* *
33233 A-AAAAAATAA-TATTTACATAAATATATTAAT
1 ATAAAAAATAATTATATAAATAAATATATTAAT
33264 ATAAAAAATAAT
1 ATAAAAAATAAT
33276 AACTATTTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
30 7 0.20
31 18 0.51
32 10 0.29
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (33 bp):
ATAAAAAATAATTATATAAATAAATATATTAAT
Found at i:33243 original size:34 final size:31
Alignment explanation
Indices: 33198--33286 Score: 97
Period size: 34 Copynumber: 2.7 Consensus size: 31
33188 TTAATAATTC
*
33198 TAAATAAATAATAATTATATAAATATTATTTTAA
1 TAAAAAAATAATAATTATATAAATA-TA--TTAA
* *
33232 TAAAAAAATAATATTTACATAAATATATTAA
1 TAAAAAAATAATAATTATATAAATATATTAA
* *
33263 TATAAAAAATAATAACTATTTAAA
1 TA-AAAAAATAATAATTATATAAA
33287 AAAATACTAA
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
31 6 0.13
32 17 0.36
33 2 0.04
34 22 0.47
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (31 bp):
TAAAAAAATAATAATTATATAAATATATTAA
Found at i:48176 original size:25 final size:26
Alignment explanation
Indices: 48121--48190 Score: 63
Period size: 25 Copynumber: 2.8 Consensus size: 26
48111 CCAATTATTT
* *
48121 AAATATAAAATATTT-TTTATAATAA
1 AAATTTAATATATTTATTTATAATAA
** *
48146 TTATTTTATATATTTATTTAT-ATAA
1 AAATTTAATATATTTATTTATAATAA
* *
48171 AAATTTAATTTATTAATTTA
1 AAATTTAATATATTTATTTA
48191 GATTAAATAT
Statistics
Matches: 34, Mismatches: 10, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
25 29 0.85
26 5 0.15
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (26 bp):
AAATTTAATATATTTATTTATAATAA
Found at i:48850 original size:37 final size:36
Alignment explanation
Indices: 48777--48850 Score: 89
Period size: 37 Copynumber: 2.0 Consensus size: 36
48767 AGTTGAAAAT
* *
48777 ATTTATATATTTTCTTTAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAATTAAAAATCATAAA
48813 ATTTATATAATTGTT-TTTACAAAATTAAAAAT-ATAAA
1 ATTTATAT-ATT-TTCTTTA-AAAATTAAAAATCATAAA
48850 A
1 A
48851 AGTTTAACGA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
36 8 0.24
37 13 0.39
38 12 0.36
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.46
Consensus pattern (36 bp):
ATTTATATATTTTCTTTAAAAATTAAAAATCATAAA
Found at i:49555 original size:16 final size:17
Alignment explanation
Indices: 49530--49564 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
49520 CATTACAAGT
49530 TATAACAATA-TAGTTA
1 TATAACAATATTAGTTA
*
49546 TATAATAATATTAGTTA
1 TATAACAATATTAGTTA
49563 TA
1 TA
49565 AAATTTGAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.49, C:0.03, G:0.06, T:0.43
Consensus pattern (17 bp):
TATAACAATATTAGTTA
Found at i:52846 original size:19 final size:19
Alignment explanation
Indices: 52822--52872 Score: 86
Period size: 19 Copynumber: 2.7 Consensus size: 19
52812 AATCTAATTT
52822 GGGTATC-GATACCTAGAGG
1 GGGTATCAG-TACCTAGAGG
52841 GGGTATCAGTACCTAGAGG
1 GGGTATCAGTACCTAGAGG
52860 GGGTATCAGTACC
1 GGGTATCAGTACC
52873 ATAGCAAAGG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
19 30 0.97
20 1 0.03
ACGTcount: A:0.25, C:0.18, G:0.35, T:0.22
Consensus pattern (19 bp):
GGGTATCAGTACCTAGAGG
Found at i:52887 original size:22 final size:20
Alignment explanation
Indices: 52822--52888 Score: 68
Period size: 19 Copynumber: 3.4 Consensus size: 20
52812 AATCTAATTT
*
52822 GGGTATC-GATACC-TAGAGG
1 GGGTATCAG-TACCATAGAAG
*
52841 GGGTATCAGTACC-TAGAGG
1 GGGTATCAGTACCATAGAAG
52860 GGGTATCAGTACCATAGCAAAG
1 GGGTATCAGTACCATAG--AAG
52882 GGGTATC
1 GGGTATC
52889 GATACCATGG
Statistics
Matches: 43, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
19 30 0.70
20 4 0.09
22 9 0.21
ACGTcount: A:0.28, C:0.16, G:0.34, T:0.21
Consensus pattern (20 bp):
GGGTATCAGTACCATAGAAG
Found at i:53608 original size:45 final size:45
Alignment explanation
Indices: 53555--54043 Score: 654
Period size: 45 Copynumber: 10.9 Consensus size: 45
53545 AAAGGATGCC
* **
53555 ATAGTTGAAATATATATGGGTACATTATCAACAGAAAAACATACT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
* * * * *
53600 TTAATTGAAATGTATATAGGTACATTATCAACATAAAAGTATGCT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
* * * *
53645 AGAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTAAACT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
* *
53690 ATGGTTGAAATGTATATGGGTACATTATCAACAGAAAAATATACT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
* **
53735 ATGGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTACGCT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
* * * * *
53780 AGAGTTTAAATGCATATGGGTGCATTATCAACAGAAAAGTATATT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
* * * *
53825 ATGGTTGAAATGTATATGGGAACATTATCAACAAAAAAGTATGCT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
* * *
53870 AGAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATACT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
*
53915 ATGGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
* *
53960 ATGGTTGAAATGTATATGGGTACATTATCAAAAGAAAAGTATACT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
* ** *
54005 ATAGTTGAAATGCATATGGGTGTATTATCAACAAAAAAG
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAG
54044 ATGTTATACT
Statistics
Matches: 383, Mismatches: 61, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 383 1.00
ACGTcount: A:0.42, C:0.09, G:0.19, T:0.30
Consensus pattern (45 bp):
ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
Found at i:65368 original size:22 final size:22
Alignment explanation
Indices: 65288--65369 Score: 58
Period size: 22 Copynumber: 3.7 Consensus size: 22
65278 TTCTTCTATT
65288 AGTGCTAA-GACACTTTAGTATC
1 AGTGCTAAGGA-ACTTTAGTATC
* * * ** *
65310 AGTGCGAACGCACTTCCGTACC
1 AGTGCTAAGGAACTTTAGTATC
* * * *
65332 AGTGTTGAGGCACTTTAGTATT
1 AGTGCTAAGGAACTTTAGTATC
65354 AGTGCTAAGGAACTTT
1 AGTGCTAAGGAACTTT
65370 CGCTATCCGA
Statistics
Matches: 43, Mismatches: 16, Indels: 2
0.70 0.26 0.03
Matches are distributed among these distances:
22 42 0.98
23 1 0.02
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (22 bp):
AGTGCTAAGGAACTTTAGTATC
Found at i:66602 original size:3 final size:3
Alignment explanation
Indices: 66594--66625 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
66584 AATAGTAAAT
66594 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
66626 TAATCTTTAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Done.