Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002728.1 Hibiscus syriacus cultivar Beakdansim tig00005625_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: 72151
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:3162 original size:41 final size:40
Alignment explanation
Indices: 3105--3186 Score: 137
Period size: 41 Copynumber: 2.0 Consensus size: 40
3095 GTTATTATTC
*
3105 CGAATTAAAGAAGGGAAACAGTGGGGGTTTTTACATTTTAA
1 CGAATTAAAGAAGGGAAACAGT-GGGGATTTTACATTTTAA
*
3146 CGAATTGAAGAAGGGAAACAGTGGGGATTTTACATTTTAA
1 CGAATTAAAGAAGGGAAACAGTGGGGATTTTACATTTTAA
3186 C
1 C
3187 CATAAGATAG
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
40 18 0.46
41 21 0.54
ACGTcount: A:0.37, C:0.09, G:0.27, T:0.28
Consensus pattern (40 bp):
CGAATTAAAGAAGGGAAACAGTGGGGATTTTACATTTTAA
Found at i:11939 original size:21 final size:22
Alignment explanation
Indices: 11898--11939 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
11888 ATGAGGTAAA
*
11898 AACACCTAACTTTTGGAAATTG
1 AACACCAAACTTTTGGAAATTG
11920 AACACCAAACTTTT-GAAATT
1 AACACCAAACTTTTGGAAATT
11940 ACCCTTTTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.40, C:0.19, G:0.10, T:0.31
Consensus pattern (22 bp):
AACACCAAACTTTTGGAAATTG
Found at i:12773 original size:12 final size:12
Alignment explanation
Indices: 12756--12780 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
12746 CAAGAAATAG
12756 ACACACACACAT
1 ACACACACACAT
12768 ACACACACACAT
1 ACACACACACAT
12780 A
1 A
12781 TATATTATTC
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:0.52, C:0.40, G:0.00, T:0.08
Consensus pattern (12 bp):
ACACACACACAT
Found at i:17165 original size:17 final size:17
Alignment explanation
Indices: 17143--17175 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
17133 TATTGATTGA
*
17143 TGACACAGAGTTGTCAT
1 TGACACAGAGATGTCAT
17160 TGACACAGAGATGTCA
1 TGACACAGAGATGTCA
17176 AAATTAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.24
Consensus pattern (17 bp):
TGACACAGAGATGTCAT
Found at i:18168 original size:37 final size:37
Alignment explanation
Indices: 18111--18215 Score: 138
Period size: 37 Copynumber: 2.8 Consensus size: 37
18101 CCTTTTCGTC
*
18111 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
1 CTACTATGATTCAAACTCCTAAAAATAGGATAGAATT
* * * *
18148 TTGCTATGATTCAAACTCCTAAAAATATGATAGAGTT
1 CTACTATGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
18185 CTACTATTATTTAAACTCCTAAAGATAGGAT
1 CTACTATGATTCAAACTCCTAAAAATAGGAT
18216 CCACAAGCAT
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 57 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.32
Consensus pattern (37 bp):
CTACTATGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:18661 original size:23 final size:23
Alignment explanation
Indices: 18633--18679 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 23
18623 TATATGTATA
18633 TATTTAATTAT-ATTTTATTT-ATT
1 TATTT-ATTATAATTTT-TTTCATT
18656 TATTTATTATAATTTTTTTCATT
1 TATTTATTATAATTTTTTTCATT
18679 T
1 T
18680 TTCTTTGCGT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 8 0.36
23 14 0.64
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (23 bp):
TATTTATTATAATTTTTTTCATT
Found at i:18721 original size:2 final size:2
Alignment explanation
Indices: 18714--18743 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
18704 TTCCTATTAT
18714 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
18744 TATTTTATCT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:18806 original size:2 final size:2
Alignment explanation
Indices: 18799--18823 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
18789 TTCCTAACGT
18799 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
18824 TCTTACTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:18964 original size:22 final size:22
Alignment explanation
Indices: 18928--18981 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
18918 CTATTTAGTA
*
18928 TTTTATTATAT-TATACATACAT
1 TTTTATTATTTGTATACATA-AT
* *
18950 TTTTA-TATTTGTATATATATT
1 TTTTATTATTTGTATACATAAT
18971 TTTTATTATTT
1 TTTTATTATTT
18982 TATTTATACT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 10 0.37
22 17 0.63
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.65
Consensus pattern (22 bp):
TTTTATTATTTGTATACATAAT
Found at i:19142 original size:20 final size:19
Alignment explanation
Indices: 19102--19156 Score: 51
Period size: 19 Copynumber: 2.8 Consensus size: 19
19092 TTTTATCTTC
*
19102 ATTTATTTTATTTTATTCA
1 ATTTATTTTATTTTATCCA
19121 ATTTCATTTT-TTTTCATCCA
1 ATTT-ATTTTATTTT-ATCCA
*
19141 A-TTGTTTTATGTTTAT
1 ATTTATTTTAT-TTTAT
19157 TATTATTGGT
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
18 4 0.13
19 13 0.43
20 13 0.43
ACGTcount: A:0.22, C:0.09, G:0.04, T:0.65
Consensus pattern (19 bp):
ATTTATTTTATTTTATCCA
Found at i:23466 original size:17 final size:16
Alignment explanation
Indices: 23446--23503 Score: 73
Period size: 16 Copynumber: 3.6 Consensus size: 16
23436 GGGAAAACAT
*
23446 AAAAAAGAA-AAGAAAC
1 AAAAAAGAACAA-AAAA
23462 AAAAAAGAACAAAATAA
1 AAAAAAGAACAAAA-AA
*
23479 AAAAAAGAACAAAAAG
1 AAAAAAGAACAAAAAA
23495 AAAAAAGAA
1 AAAAAAGAA
23504 AAAGGGACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
16 21 0.55
17 17 0.45
ACGTcount: A:0.83, C:0.05, G:0.10, T:0.02
Consensus pattern (16 bp):
AAAAAAGAACAAAAAA
Found at i:23482 original size:26 final size:25
Alignment explanation
Indices: 23448--23506 Score: 73
Period size: 25 Copynumber: 2.2 Consensus size: 25
23438 GAAAACATAA
*
23448 AAAAGAAAAGAAACAAAAAAGAACAAAAT
1 AAAA-AAAAG-AAC-AAAAAGAA-AAAAG
23477 AAAAAAAAGAACAAAAAGAAAAAAG
1 AAAAAAAAGAACAAAAAGAAAAAAG
23502 AAAAA
1 AAAAA
23507 GGGACAAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
25 9 0.31
26 8 0.28
27 3 0.10
28 5 0.17
29 4 0.14
ACGTcount: A:0.83, C:0.05, G:0.10, T:0.02
Consensus pattern (25 bp):
AAAAAAAAGAACAAAAAGAAAAAAG
Found at i:26663 original size:106 final size:106
Alignment explanation
Indices: 24976--26662 Score: 2654
Period size: 106 Copynumber: 15.9 Consensus size: 106
24966 CAAGAAAACA
* * * * *
24976 CAAGTTCAACTTCACAACAAAGGGACAGATGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
25041 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
66 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
* * * * *
25082 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTATCAATAAATAATTTCTCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
25147 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
66 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
* *
25188 CAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
*
25253 ATTTCAACTTCACAACGAAGGATATTGGACTCTAGACAACG
66 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
* * * * *
25294 CAAGTTCAACTTCACAACGAATGGACCGCTGGTTGTCAATAAATAATTTCCCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
* *
25359 ATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACG
66 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
* * *
25400 CAAGTTCAACTTCATGACGAAGGGACCGCTGGTTGCCAATAAACAACTTCCCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
**
25465 ATTTCAACTTCACAGTGAAGGATATTGGACTCCAGACAACG
66 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
*
25506 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
25571 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
66 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
25612 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
* *
25677 ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACG
66 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
*
25718 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTTTCAACAAACAACTTCCCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
* *
25783 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACT
66 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
** * *
25824 CAAGTTCAACTTCACGACGAAGGGATTGTTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
*
25889 ATTTCAACTTCACAATGAAGGATATTGGACTCCAGACAACG
66 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
25930 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
* * * *
25995 ATTTCAATTTCATAGCGAAGGATATTGGACTCGAGACAACG
66 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
* * *
26036 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTTTCAACAAACAATTTCCCAATTTCGGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
* * * *
26101 ATTTCAACTCCGCAGCGAAAGATATTGGACTCCAGACAACG
66 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
* *
26142 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCGGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
* * * * *
26207 ATTTCAACTTCACGACAAAGGATATTGGACTCGAGAGAACA
66 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
* * * * *
26248 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAATTCCAGAGCTA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
* *
26313 ATTTCAACTTCACGACGGAGGATATTGGACTCCAGACAACG
66 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
* *
26354 CAAGTTCAACTTCACGACGAAGGGACCGATGGCTGTCAACAAACAACTTCCCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
* *
26419 ATTTCAACTTCACAACGAAGGATATTAGACTCGAGACAACG
66 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
* *
26460 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCGGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
* * * * *
26525 ATTTCAACTTCACGACAAAGGATATTGGACTCGAGAGAACA
66 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
* * * * * *
26566 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCGATTCCAGAGCTA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
* *
26631 ATTTCAACTTCACGACGGAGGATATTGGACTC
66 ATTTCAACTTCACAACGAAGGATATTGGACTC
26663 GGAACAATGC
Statistics
Matches: 1466, Mismatches: 115, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
106 1466 1.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.22
Consensus pattern (106 bp):
CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
Found at i:27381 original size:37 final size:37
Alignment explanation
Indices: 27328--27432 Score: 140
Period size: 37 Copynumber: 2.8 Consensus size: 37
27318 CATTTTCGTC
27328 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT-AAAGTT
* *
27366 -TGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAGTT
** * *
27402 CTACTATTATTTAAACTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
27433 CCACAAGCAT
Statistics
Matches: 59, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
36 5 0.08
37 54 0.92
ACGTcount: A:0.41, C:0.15, G:0.14, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAAAGTT
Found at i:28162 original size:22 final size:23
Alignment explanation
Indices: 28137--28182 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
28127 TTTTATTATA
28137 TTATACATACATTTTT-ATATTT
1 TTATACATACATTTTTAATATTT
* **
28159 TTATATATATTTTTTTAATATTT
1 TTATACATACATTTTTAATATTT
28182 T
1 T
28183 ATTTATACTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.65
Consensus pattern (23 bp):
TTATACATACATTTTTAATATTT
Found at i:28179 original size:13 final size:12
Alignment explanation
Indices: 28147--28201 Score: 51
Period size: 12 Copynumber: 4.5 Consensus size: 12
28137 TTATACATAC
*
28147 ATTTTTATATTT
1 ATTTATATATTT
28159 -TTATATATATTT
1 ATT-TATATATTT
*
28171 TTTTA-ATATTTT
1 ATTTATATA-TTT
28183 ATTTATACTATTT
1 ATTTATA-TATTT
28196 ATTTAT
1 ATTTAT
28202 TTTCATTATA
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
11 5 0.14
12 17 0.47
13 12 0.33
14 2 0.06
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (12 bp):
ATTTATATATTT
Found at i:28183 original size:22 final size:22
Alignment explanation
Indices: 28148--28216 Score: 63
Period size: 22 Copynumber: 3.1 Consensus size: 22
28138 TATACATACA
28148 TTTTTATATTTTTATATATATT
1 TTTTTATATTTTTATATATATT
*
28170 TTTTTA-ATATTTTATTTATACTAT
1 TTTTTATAT-TTTTATATATA-T-T
* *
28194 TTATT-TATTTTCAT-TATATT
1 TTTTTATATTTTTATATATATT
28214 TTT
1 TTT
28217 AGTTTCTTTG
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
20 3 0.08
21 3 0.08
22 20 0.51
23 6 0.15
24 7 0.18
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (22 bp):
TTTTTATATTTTTATATATATT
Found at i:31499 original size:29 final size:28
Alignment explanation
Indices: 31431--31594 Score: 107
Period size: 29 Copynumber: 5.7 Consensus size: 28
31421 TCCGAAGAGT
* *
31431 ATCCCAAATAGAAACAGGACGGGATATA
1 ATCCCATACAGAAACAGGACGGGATATA
** *
31459 ATCTTATGCAGAAACAGGACAGGGATATA
1 ATCCCATACAGAAACAGGAC-GGGATATA
* **
31488 ATCCCATACAGAATCAAAACGGAGATATA
1 ATCCCATACAGAAACAGGACGG-GATATA
* * *
31517 ATCTCC-TGCA-AAATCAGGATGGGGATACA
1 ATC-CCATACAGAAA-CAGGA-CGGGATATA
** * *
31546 ATCCCATGTAGAATCAGGACGGTGGTATA
1 ATCCCATACAGAAACAGGACGG-GATATA
* *
31575 ATCTCATACAGAATCAGGAC
1 ATCCCATACAGAAACAGGAC
31595 ACATCAGTAT
Statistics
Matches: 103, Mismatches: 25, Indels: 15
0.72 0.17 0.10
Matches are distributed among these distances:
28 23 0.22
29 74 0.72
30 6 0.06
ACGTcount: A:0.40, C:0.19, G:0.21, T:0.20
Consensus pattern (28 bp):
ATCCCATACAGAAACAGGACGGGATATA
Found at i:31535 original size:58 final size:57
Alignment explanation
Indices: 31449--31595 Score: 152
Period size: 58 Copynumber: 2.5 Consensus size: 57
31439 TAGAAACAGG
* *
31449 ACGGGATATAATCTTATGCAGAAA-CAGGACAGGGATATAATCCCATACAGAATCAAA
1 ACGGGATATAATCTCATGCA-AAATCAGGACAGGGATACAATCCCATACAGAATCAAA
* ** ** **
31506 ACGGAGATATAATCTCCTGCAAAATCAGGATGGGGATACAATCCCATGTAGAATCAGG
1 ACGG-GATATAATCTCATGCAAAATCAGGACAGGGATACAATCCCATACAGAATCAAA
* * *
31564 ACGGTGGTATAATCTCATACAGAATCAGGACA
1 ACGG-GATATAATCTCATGCAAAATCAGGACA
31596 CATCAGTATA
Statistics
Matches: 72, Mismatches: 16, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
57 7 0.10
58 65 0.90
ACGTcount: A:0.39, C:0.18, G:0.22, T:0.20
Consensus pattern (57 bp):
ACGGGATATAATCTCATGCAAAATCAGGACAGGGATACAATCCCATACAGAATCAAA
Found at i:35366 original size:25 final size:26
Alignment explanation
Indices: 35332--35382 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
35322 ATTGGGAATT
* *
35332 AAGTTTAAAGTT-GATTCGATTCGAA
1 AAGTTTAAAGTTAGAATCGAATCGAA
35357 AAGTTTAAAGTTAGAATCGAATCGAA
1 AAGTTTAAAGTTAGAATCGAATCGAA
35383 TCGAATCGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 12 0.52
26 11 0.48
ACGTcount: A:0.41, C:0.08, G:0.20, T:0.31
Consensus pattern (26 bp):
AAGTTTAAAGTTAGAATCGAATCGAA
Found at i:41978 original size:15 final size:16
Alignment explanation
Indices: 41950--41981 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
41940 AAAATCTTTC
41950 TTTCCCGTTCTGGATT
1 TTTCCCGTTCTGGATT
41966 TTTCCCG-TCTGGATT
1 TTTCCCGTTCTGGATT
41981 T
1 T
41982 GGATCTGCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.06, C:0.25, G:0.19, T:0.50
Consensus pattern (16 bp):
TTTCCCGTTCTGGATT
Found at i:42756 original size:16 final size:16
Alignment explanation
Indices: 42732--42765 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
42722 TATCGCCGAC
*
42732 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
42748 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
42764 CG
1 CG
42766 TGAATAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.26, G:0.09, T:0.32
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:43392 original size:20 final size:20
Alignment explanation
Indices: 43353--43392 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
43343 TGGTAGTTAG
*
43353 ATTTATTTAATAAAATAAAT
1 ATTTATTTAAGAAAATAAAT
43373 ATTTATTTTAAGAAAA-AAAT
1 ATTTA-TTTAAGAAAATAAAT
43393 CTTATAGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (20 bp):
ATTTATTTAAGAAAATAAAT
Found at i:45318 original size:13 final size:12
Alignment explanation
Indices: 45300--45393 Score: 62
Period size: 12 Copynumber: 7.5 Consensus size: 12
45290 TTTTTATAAC
45300 CATATATGATATA
1 CATATAT-ATATA
*
45313 CATATATATATTT
1 CATATATATA-TA
** * *
45326 TGTGATATTTTTA
1 CAT-ATATATATA
*
45339 CATATGTGATATA
1 CATATAT-ATATA
*
45352 TATATATATATA
1 CATATATATATA
*
45364 TATATATATATA
1 CATATATATATA
*
45376 TATATATATATA
1 CATATATATATA
*
45388 TATATA
1 CATATA
45394 GAGTTGAGAG
Statistics
Matches: 65, Mismatches: 13, Indels: 7
0.76 0.15 0.08
Matches are distributed among these distances:
12 41 0.63
13 19 0.29
14 5 0.08
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.49
Consensus pattern (12 bp):
CATATATATATA
Found at i:45354 original size:2 final size:2
Alignment explanation
Indices: 45347--45393 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
45337 TACATATGTG
45347 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
45389 AT AT A
1 AT AT A
45394 GAGTTGAGAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:48826 original size:19 final size:19
Alignment explanation
Indices: 48790--48826 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
48780 TTGAAAAATA
**
48790 ATTTTTTTAATTTGATTTC
1 ATTTTTTTAATTCAATTTC
48809 ATTTTTTTAATTCAATTT
1 ATTTTTTTAATTCAATTT
48827 GAAACTAACC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.24, C:0.05, G:0.03, T:0.68
Consensus pattern (19 bp):
ATTTTTTTAATTCAATTTC
Found at i:49070 original size:27 final size:27
Alignment explanation
Indices: 49040--49128 Score: 169
Period size: 27 Copynumber: 3.3 Consensus size: 27
49030 CATGTTGTTC
49040 CAAGGTTCAGTCATTTGGGTTTGATGG
1 CAAGGTTCAGTCATTTGGGTTTGATGG
49067 CAAGGTTCAGTCATTTGGGTTTGATGG
1 CAAGGTTCAGTCATTTGGGTTTGATGG
49094 CAAGGTTCAGTCATTTGGGTTTGATGG
1 CAAGGTTCAGTCATTTGGGTTTGATGG
*
49121 TAAGGTTC
1 CAAGGTTC
49129 TTTAGGTTAA
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 61 1.00
ACGTcount: A:0.19, C:0.11, G:0.33, T:0.37
Consensus pattern (27 bp):
CAAGGTTCAGTCATTTGGGTTTGATGG
Found at i:53124 original size:24 final size:24
Alignment explanation
Indices: 53097--53168 Score: 101
Period size: 24 Copynumber: 3.0 Consensus size: 24
53087 GTAAACGGAG
*
53097 ATATCAGAAATCAAAACAGAATTC
1 ATATCAGAAATCAGAACAGAATTC
* *
53121 ATATCAGATATCAGAACAGAATCC
1 ATATCAGAAATCAGAACAGAATTC
*
53145 AGATCAG-AATCAGAACAGAATTC
1 ATATCAGAAATCAGAACAGAATTC
53168 A
1 A
53169 GGTAACGTAT
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
23 15 0.36
24 27 0.64
ACGTcount: A:0.50, C:0.18, G:0.12, T:0.19
Consensus pattern (24 bp):
ATATCAGAAATCAGAACAGAATTC
Found at i:53128 original size:12 final size:12
Alignment explanation
Indices: 53101--53169 Score: 61
Period size: 12 Copynumber: 5.8 Consensus size: 12
53091 ACGGAGATAT
* *
53101 CAGAAATCAAAA
1 CAGAATTCAGAA
* *
53113 CAGAATTCATAT
1 CAGAATTCAGAA
53125 CAG-ATATCAGAA
1 CAGAAT-TCAGAA
* *
53137 CAGAATCCAGAT
1 CAGAATTCAGAA
53149 CAGAA-TCAGAA
1 CAGAATTCAGAA
53160 CAGAATTCAG
1 CAGAATTCAG
53170 GTAACGTATC
Statistics
Matches: 45, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
11 11 0.24
12 32 0.71
13 2 0.04
ACGTcount: A:0.49, C:0.19, G:0.14, T:0.17
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:53185 original size:24 final size:23
Alignment explanation
Indices: 53106--53192 Score: 84
Period size: 24 Copynumber: 3.7 Consensus size: 23
53096 GATATCAGAA
* * *
53106 ATCAAAACAGAATTCATATCAGAT
1 ATCAGAACAGAATTCAGATAAG-T
* * *
53130 ATCAGAACAGAATCCAGATCAGA
1 ATCAGAACAGAATTCAGATAAGT
*
53153 ATCAGAACAGAATTCAGGTAACGT
1 ATCAGAACAGAATTCAGATAA-GT
*
53177 ATCAGAACAAAATTCA
1 ATCAGAACAGAATTCA
53193 ATTCGGAAAT
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
23 18 0.34
24 35 0.66
ACGTcount: A:0.48, C:0.18, G:0.14, T:0.20
Consensus pattern (23 bp):
ATCAGAACAGAATTCAGATAAGT
Found at i:54178 original size:18 final size:18
Alignment explanation
Indices: 54157--54191 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
54147 TGCCATCCGG
*
54157 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
54175 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
54192 GTCATTTTGA
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:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:55521 original size:13 final size:13
Alignment explanation
Indices: 55503--55566 Score: 65
Period size: 13 Copynumber: 4.5 Consensus size: 13
55493 CAATGGTCAA
55503 CGGGTCAACGGGT
1 CGGGTCAACGGGT
55516 CGGGTCAACAGGTTGGGT
1 CGGGTCAAC-----GGGT
55534 CGGGTCAACGGGT
1 CGGGTCAACGGGT
* *
55547 CGGGTAAATGGGT
1 CGGGTCAACGGGT
55560 CGGGTCA
1 CGGGTCA
55567 GGTTGTGACC
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
13 30 0.70
18 13 0.30
ACGTcount: A:0.17, C:0.19, G:0.45, T:0.19
Consensus pattern (13 bp):
CGGGTCAACGGGT
Found at i:55551 original size:18 final size:18
Alignment explanation
Indices: 55497--55551 Score: 65
Period size: 18 Copynumber: 2.9 Consensus size: 18
55487 AGTGGTCAAT
55497 GGTCAACGGGTCAACGGGTCG
1 GGTCAACGGGT---CGGGTCG
* *
55518 GGTCAACAGGTTGGGTCG
1 GGTCAACGGGTCGGGTCG
55536 GGTCAACGGGTCGGGT
1 GGTCAACGGGTCGGGT
55552 AAATGGGTCG
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
18 20 0.67
21 10 0.33
ACGTcount: A:0.16, C:0.20, G:0.45, T:0.18
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCG
Found at i:55565 original size:31 final size:31
Alignment explanation
Indices: 55503--55565 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
55493 CAATGGTCAA
* *
55503 CGGGTCAACGGGTCGGGTCAACAGGTTGGGT
1 CGGGTCAACGGGTCGGGTAAACAGGTCGGGT
**
55534 CGGGTCAACGGGTCGGGTAAATGGGTCGGGT
1 CGGGTCAACGGGTCGGGTAAACAGGTCGGGT
55565 C
1 C
55566 AGGTTGTGAC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.16, C:0.19, G:0.46, T:0.19
Consensus pattern (31 bp):
CGGGTCAACGGGTCGGGTAAACAGGTCGGGT
Found at i:57127 original size:15 final size:15
Alignment explanation
Indices: 57109--57137 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
57099 TTTATCATTT
57109 TATTTTTTAACGAAG
1 TATTTTTTAACGAAG
57124 TATTTTTTAACGAA
1 TATTTTTTAACGAA
57138 ACTATCTGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.07, G:0.10, T:0.48
Consensus pattern (15 bp):
TATTTTTTAACGAAG
Found at i:62530 original size:14 final size:14
Alignment explanation
Indices: 62511--62539 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
62501 GGAATTACTT
62511 AATTAGTTAGATTC
1 AATTAGTTAGATTC
62525 AATTAGTTAGATTC
1 AATTAGTTAGATTC
62539 A
1 A
62540 GATCTGAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.07, G:0.14, T:0.41
Consensus pattern (14 bp):
AATTAGTTAGATTC
Found at i:67180 original size:22 final size:20
Alignment explanation
Indices: 67140--67219 Score: 74
Period size: 22 Copynumber: 3.9 Consensus size: 20
67130 AAATAAAAAT
*
67140 AATTAT-TTATATATTTAAA
1 AATTATATTAAATATTTAAA
67159 AATTATATTAAATAATTCTAAA
1 AATTATATTAAAT-ATT-TAAA
* *
67181 TATTATATTAATATTTTTTAAA
1 AATTATATTAA-A-TATTTAAA
*
67203 AA-TATTTTAAATATTTA
1 AATTATATTAAATATTTA
67220 TTTAATTTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
19 11 0.22
20 6 0.12
21 10 0.20
22 19 0.38
23 3 0.06
24 1 0.02
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.51
Consensus pattern (20 bp):
AATTATATTAAATATTTAAA
Found at i:67215 original size:33 final size:31
Alignment explanation
Indices: 67168--67233 Score: 80
Period size: 30 Copynumber: 2.1 Consensus size: 31
67158 AAATTATATT
*
67168 AAATAATTCTAAATATTATATTAATATTTTTTAA
1 AAATAATTCTAAATATT-TATT--TAATTTTTAA
*
67202 AAAT-ATTTTAAATATTTATTTAATTTTTAA
1 AAATAATTCTAAATATTTATTTAATTTTTAA
67232 AA
1 AA
67234 TCATATTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
30 11 0.37
32 4 0.13
33 11 0.37
34 4 0.13
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (31 bp):
AAATAATTCTAAATATTTATTTAATTTTTAA
Found at i:67263 original size:17 final size:18
Alignment explanation
Indices: 67221--67266 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 18
67211 AAATATTTAT
67221 TTAATT-TTTAAAATCATA
1 TTAATTATTTAAAA-CATA
* *
67239 TTATTTATTTAAAA-ATG
1 TTAATTATTTAAAACATA
67256 TTAATTATTTA
1 TTAATTATTTA
67267 TTTTAAATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
17 12 0.50
18 5 0.21
19 7 0.29
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.54
Consensus pattern (18 bp):
TTAATTATTTAAAACATA
Found at i:67438 original size:22 final size:20
Alignment explanation
Indices: 67413--67460 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
67403 TAATATTAAT
*
67413 TTAATAATTAATTAATATGATG
1 TTAATAATTAAATAA-AT-ATG
*
67435 TTAA-AATTAAATAAATATT
1 TTAATAATTAAATAAATATG
67454 TTAATAA
1 TTAATAA
67461 ATTATAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 6 0.26
20 4 0.17
21 9 0.39
22 4 0.17
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (20 bp):
TTAATAATTAAATAAATATG
Found at i:67765 original size:15 final size:16
Alignment explanation
Indices: 67735--67766 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
67725 CATTATATAA
67735 GTTAAATACAAAATAT
1 GTTAAATACAAAATAT
67751 GTTAAATAC-AAATAT
1 GTTAAATACAAAATAT
67766 G
1 G
67767 GTGAAATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.53, C:0.06, G:0.09, T:0.31
Consensus pattern (16 bp):
GTTAAATACAAAATAT
Done.