Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001195.1 Hibiscus syriacus cultivar Beakdansim tig00002368_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: 95960
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:3810 original size:21 final size:21
Alignment explanation
Indices: 3785--3842 Score: 89
Period size: 21 Copynumber: 2.8 Consensus size: 21
3775 TTGGGTATTT
3785 TATCGGTTTTGTTATTTTTTC
1 TATCGGTTTTGTTATTTTTTC
3806 TATCGGTTTTGTTATTTTTTC
1 TATCGGTTTTGTTATTTTTTC
* * *
3827 TACCGATTTCGTTATT
1 TATCGGTTTTGTTATT
3843 ATTGGATACT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.12, C:0.12, G:0.14, T:0.62
Consensus pattern (21 bp):
TATCGGTTTTGTTATTTTTTC
Found at i:13537 original size:29 final size:29
Alignment explanation
Indices: 13495--13553 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 29
13485 AAAGATAGTG
13495 ATTGTAGTTAACTTTCA-GGCTGATTCATC
1 ATTGTAGTTAACTTT-ATGGCTGATTCATC
*
13524 ATTGTAGTTAACTTTATGGCTGATTTATC
1 ATTGTAGTTAACTTTATGGCTGATTCATC
13553 A
1 A
13554 GATGAACTAG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
28 1 0.04
29 27 0.96
ACGTcount: A:0.25, C:0.14, G:0.17, T:0.44
Consensus pattern (29 bp):
ATTGTAGTTAACTTTATGGCTGATTCATC
Found at i:24846 original size:42 final size:42
Alignment explanation
Indices: 24724--25054 Score: 378
Period size: 42 Copynumber: 7.8 Consensus size: 42
24714 TGAGAACCAA
* * *
24724 AAACGCCGCCATAGGTCAATATCTATAGCGGCGTTTTTGTAAC
1 AAACGCCGCAAAAGGTC-ATATCTATAGCGGCGTTTTTGGAAC
* * * ** *
24767 AAACGCCGCAAAAGATCGAGATTTATAATGGCGTTTTTGGAAT
1 AAACGCCGCAAAAGGTC-ATATCTATAGCGGCGTTTTTGGAAC
* * * *
24810 AAACGCCGCAAAAGGTCATATTTATAGCGTCATTTTTGGAAT
1 AAACGCCGCAAAAGGTCATATCTATAGCGGCGTTTTTGGAAC
* * * *
24852 AAACGCCGTAAAATGTCGAGATCTATAACGGCGTTTTTGGAAC
1 AAACGCCGCAAAAGGTC-ATATCTATAGCGGCGTTTTTGGAAC
* * * *
24895 AAACGCCACAAAATGTCATATCTATAGCAGCGTTTTTGGAAT
1 AAACGCCGCAAAAGGTCATATCTATAGCGGCGTTTTTGGAAC
*
24937 AAACGCCGCAAAAGGTCATATTTATAGCGGCGTTTTTGGAAC
1 AAACGCCGCAAAAGGTCATATCTATAGCGGCGTTTTTGGAAC
* * *
24979 AAACGCCGC-AAAGATCATGTCTATAGCGGCGTTTATGGAA-
1 AAACGCCGCAAAAGGTCATATCTATAGCGGCGTTTTTGGAAC
*
25019 AAACGCCGCAAAAGGTCGAGATCTATAGCGGCGTTT
1 AAACGCCGCAAAAGGTC-ATATCTATAGCGGCGTTT
25055 GTATCCAAAA
Statistics
Matches: 243, Mismatches: 42, Indels: 7
0.83 0.14 0.02
Matches are distributed among these distances:
40 9 0.04
41 33 0.14
42 118 0.49
43 83 0.34
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.26
Consensus pattern (42 bp):
AAACGCCGCAAAAGGTCATATCTATAGCGGCGTTTTTGGAAC
Found at i:24856 original size:85 final size:85
Alignment explanation
Indices: 24724--25054 Score: 425
Period size: 85 Copynumber: 3.9 Consensus size: 85
24714 TGAGAACCAA
* * * * *
24724 AAACGCCGCCATAGGTCAATATCTATAGCGGCGTTTTTGTAACAAACGCCGCAAAAGATCGAGAT
1 AAACGCCGCAAAAGGTC-ATATCTATAGCGGCGTTTTTGGAATAAACGCCGCAAAAGGTCGAGAT
* * *
24789 TTATAATGGCGTTTTTGGAAT
65 CTATAACGGCGTTTTTGGAAC
* * * * *
24810 AAACGCCGCAAAAGGTCATATTTATAGCGTCATTTTTGGAATAAACGCCGTAAAATGTCGAGATC
1 AAACGCCGCAAAAGGTCATATCTATAGCGGCGTTTTTGGAATAAACGCCGCAAAAGGTCGAGATC
24875 TATAACGGCGTTTTTGGAAC
66 TATAACGGCGTTTTTGGAAC
* * * * *
24895 AAACGCCACAAAATGTCATATCTATAGCAGCGTTTTTGGAATAAACGCCGCAAAAGGTC-ATATT
1 AAACGCCGCAAAAGGTCATATCTATAGCGGCGTTTTTGGAATAAACGCCGCAAAAGGTCGAGATC
*
24959 TATAGCGGCGTTTTTGGAAC
66 TATAACGGCGTTTTTGGAAC
* * *
24979 AAACGCCGC-AAAGATCATGTCTATAGCGGCGTTTATGGAA-AAACGCCGCAAAAGGTCGAGATC
1 AAACGCCGCAAAAGGTCATATCTATAGCGGCGTTTTTGGAATAAACGCCGCAAAAGGTCGAGATC
*
25042 TATAGCGGCGTTT
66 TATAACGGCGTTT
25055 GTATCCAAAA
Statistics
Matches: 212, Mismatches: 32, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
82 17 0.08
83 42 0.20
84 30 0.14
85 108 0.51
86 15 0.07
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.26
Consensus pattern (85 bp):
AAACGCCGCAAAAGGTCATATCTATAGCGGCGTTTTTGGAATAAACGCCGCAAAAGGTCGAGATC
TATAACGGCGTTTTTGGAAC
Found at i:24964 original size:127 final size:126
Alignment explanation
Indices: 24744--25054 Score: 416
Period size: 127 Copynumber: 2.5 Consensus size: 126
24734 ATAGGTCAAT
* * **
24744 ATCTATAGCGGCGTTTTTGTAACAAACGCCGCAAAAGATCGAGATTTATAATGGCGTTTTTGGAA
1 ATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAG-TCGAGATCTATAGCGGCGTTTTTGGAA
* *
24809 TAAACGCCGCAAAAGGTCATATTTATAGCGTCATTTTTGGAATAAACGCCGTAAAATG-TCGA-G
65 TAAACGCCGCAAAAGGTCATATTTATAGCGGCATTTTTGGAACAAACGCCG-AAAA-GATC-ATG
* * * *
24872 ATCTATAACGGCGTTTTTGGAACAAACGCCACAAAATGTC-ATATCTATAGCAGCGTTTTTGGAA
1 ATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAA-GTCGAGATCTATAGCGGCGTTTTTGGAA
* *
24936 TAAACGCCGCAAAAGGTCATATTTATAGCGGCGTTTTTGGAACAAACGCCGCAAAGATCATG
65 TAAACGCCGCAAAAGGTCATATTTATAGCGGCATTTTTGGAACAAACGCCGAAAAGATCATG
*
24998 -TCTATAGCGGCGTTTATGGAA-AAACGCCGCAAAAGGTCGAGATCTATAGCGGCGTTT
1 ATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAA-GTCGAGATCTATAGCGGCGTTT
25055 GTATCCAAAA
Statistics
Matches: 161, Mismatches: 18, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
124 15 0.09
125 37 0.23
126 6 0.04
127 67 0.42
128 35 0.22
129 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (126 bp):
ATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGTCGAGATCTATAGCGGCGTTTTTGGAAT
AAACGCCGCAAAAGGTCATATTTATAGCGGCATTTTTGGAACAAACGCCGAAAAGATCATG
Found at i:29160 original size:41 final size:41
Alignment explanation
Indices: 29055--29573 Score: 389
Period size: 41 Copynumber: 12.6 Consensus size: 41
29045 GTAAACTTGT
** * * *
29055 GGCGTTTGCATAAAAACGCCACTGAAACACGAGTCTTTAGC
1 GGCGTTTATATAAAAACGCCACTAAAATACGAGTCTATAGC
* * * *
29096 GGCGTTTTTATAAGAAAATGCCACTAAAACAAGAGTCTATAGC
1 GGCGTTTATAT-A-AAAACGCCACTAAAATACGAGTCTATAGC
* * **
29139 GGCGTTTATATAAAAACGCCACTAAAGTACGAGTCTTTAAT
1 GGCGTTTATATAAAAACGCCACTAAAATACGAGTCTATAGC
* * * **
29180 GGCGTTTATATAAAAATGCTACTAAAACATTAGTCT-TCAGC
1 GGCGTTTATATAAAAACGCCACTAAAATACGAGTCTAT-AGC
* * * * * *
29221 GGCGTTTGTATAAAAATGCCAGTAAAACACGAGTTTTTAGC
1 GGCGTTTATATAAAAACGCCACTAAAATACGAGTCTATAGC
* * * * * *
29262 GACGTTTGTATAAGAACGCCGCTAAAGTACGAGTCTTTTA-C
1 GGCGTTTATATAAAAACGCCACTAAAATACGAGTC-TATAGC
* * **
29303 GGCGTTTATATAGAAACGCCACTAAAACAATAGTCTATAGC
1 GGCGTTTATATAAAAACGCCACTAAAATACGAGTCTATAGC
* * *
29344 GGCGTTTATATAAAAACGTCACTAAAGTACGAGTCTTTAGC
1 GGCGTTTATATAAAAACGCCACTAAAATACGAGTCTATAGC
* * * * ** *
29385 GACATTTGTATAAAAATGCCACTAACGTATGAGTCTATAGC
1 GGCGTTTATATAAAAACGCCACTAAAATACGAGTCTATAGC
** *
29426 GGCGTTTA-A-AAAAACGCCACTAACGTATGAGTCTATAGC
1 GGCGTTTATATAAAAACGCCACTAAAATACGAGTCTATAGC
* * * ** * *
29465 GACATTTGTACCAAAGCGTCACTAAAATACGAGTCTATAGC
1 GGCGTTTATATAAAAACGCCACTAAAATACGAGTCTATAGC
* * * * * * * * *
29506 GGCGTTTTTATAAAAACACCGCTAAAGTACTACTTTGTCGC
1 GGCGTTTATATAAAAACGCCACTAAAATACGAGTCTATAGC
*
29547 GGCGTTTTATATAAAAACGCCGCTAAA
1 GGCG-TTTATATAAAAACGCCACTAAA
29574 GTTACTATTT
Statistics
Matches: 378, Mismatches: 91, Indels: 17
0.78 0.19 0.03
Matches are distributed among these distances:
39 34 0.09
40 6 0.02
41 276 0.73
42 27 0.07
43 35 0.09
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (41 bp):
GGCGTTTATATAAAAACGCCACTAAAATACGAGTCTATAGC
Found at i:29287 original size:123 final size:122
Alignment explanation
Indices: 29054--29448 Score: 443
Period size: 123 Copynumber: 3.2 Consensus size: 122
29044 TGTAAACTTG
** * ** *
29054 TGGCGTTTGCATAAAAACGCCACTGAAACACGAGTCTTTAGCGGCGTTTTTATAAGAAAATGCCA
1 TGGCGTTTATATAAAAACGCCACTAAAACAATAGTC-TTAGCGGCGTTTATAT-A-AAAATGCCA
* * * *
29119 CTAAAACAAGAGTCTATAGCGGCGTTTATATAAAAACGCCACTAAAGTACGAGTCTTTAA
63 CTAAAACACGAGTCTTTAGCGACGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTAA
* * * * *
29179 TGGCGTTTATATAAAAATGCTACTAAAACATTAGTCTTCAGCGGCGTTTGTATAAAAATGCCAGT
1 TGGCGTTTATATAAAAACGCCACTAAAACAATAGTCTT-AGCGGCGTTTATATAAAAATGCCACT
* * * *
29244 AAAACACGAGTTTTTAGCGACGTTTGTATAAGAACGCCGCTAAAGTACGAGTCTTTTA
65 AAAACACGAGTCTTTAGCGACGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTAA
* * * *
29302 CGGCGTTTATATAGAAACGCCACTAAAACAATAGTCTATAGCGGCGTTTATATAAAAACGTCACT
1 TGGCGTTTATATAAAAACGCCACTAAAACAATAGTCT-TAGCGGCGTTTATATAAAAATGCCACT
** * * * * * *
29367 AAAGTACGAGTCTTTAGCGACATTTGTATAAAAATGCCACTAACGTATGAGTCTATAG
65 AAAACACGAGTCTTTAGCGACGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTAA
*
29425 CGGCGTTTA-A-AAAAACGCCACTAA
1 TGGCGTTTATATAAAAACGCCACTAA
29449 CGTATGAGTC
Statistics
Matches: 229, Mismatches: 39, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
121 13 0.06
122 1 0.00
123 169 0.74
124 4 0.02
125 42 0.18
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.27
Consensus pattern (122 bp):
TGGCGTTTATATAAAAACGCCACTAAAACAATAGTCTTAGCGGCGTTTATATAAAAATGCCACTA
AAACACGAGTCTTTAGCGACGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTAA
Found at i:29571 original size:42 final size:42
Alignment explanation
Indices: 29504--29586 Score: 132
Period size: 42 Copynumber: 2.0 Consensus size: 42
29494 CGAGTCTATA
29504 GCGGCGTTTTTATAAAAACACCGCTAAAG-TACTACTTTGTC
1 GCGGCGTTTTTATAAAAACACCGCTAAAGTTACTACTTTGTC
* *
29545 GCGGCGTTTTATATAAAAACGCCGCTAAAGTTACTATTTTGT
1 GCGGCGTTTT-TATAAAAACACCGCTAAAGTTACTACTTTGT
29587 GGCGTTTGGA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
41 10 0.26
42 18 0.47
43 10 0.26
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (42 bp):
GCGGCGTTTTTATAAAAACACCGCTAAAGTTACTACTTTGTC
Found at i:30755 original size:18 final size:18
Alignment explanation
Indices: 30732--30770 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
30722 GACAAACGAG
30732 AAAGTAAATCTTGAATTT
1 AAAGTAAATCTTGAATTT
30750 AAAGTAAATCTTGAATTT
1 AAAGTAAATCTTGAATTT
30768 AAA
1 AAA
30771 TTTTGTTTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.49, C:0.05, G:0.10, T:0.36
Consensus pattern (18 bp):
AAAGTAAATCTTGAATTT
Found at i:51752 original size:13 final size:13
Alignment explanation
Indices: 51734--51764 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
51724 ACAAAACCCT
51734 AACAACTAAACCA
1 AACAACTAAACCA
51747 AACAACTAAACCA
1 AACAACTAAACCA
51760 AACAA
1 AACAA
51765 ATTCCCTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.65, C:0.29, G:0.00, T:0.06
Consensus pattern (13 bp):
AACAACTAAACCA
Found at i:63344 original size:23 final size:23
Alignment explanation
Indices: 63313--63420 Score: 153
Period size: 23 Copynumber: 4.7 Consensus size: 23
63303 ACAGGTAAAA
*
63313 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
63336 ATATAATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
63359 ATATAATGTAATAAGTAGCACTT
1 ATATAATGTAATAGGTAGCGCTT
*
63382 ATATAATGTAATAGGTAGCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* **
63405 ACATAATAAAATAGGT
1 ATATAATGTAATAGGT
63421 TAATTACTGA
Statistics
Matches: 76, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 76 1.00
ACGTcount: A:0.39, C:0.07, G:0.19, T:0.34
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:63478 original size:87 final size:87
Alignment explanation
Indices: 63377--63600 Score: 360
Period size: 87 Copynumber: 2.6 Consensus size: 87
63367 TAATAAGTAG
* * *
63377 CACTTATATAATGTAATAGGTAGCGTTTACATAATAAAATAGGTTAATTACTGA-AAATATTATC
1 CACTTATATAATGTAATAGGTAGCGCTTATATAATAAAATAGGTTAATTACT-ATAAACATTATC
*
63441 AAGCACAATAACATATTATGTAC
65 AAGCACAATAACATATTAGGTAC
63464 CACTTATATAATGTAATAGGTAGCGCTTATATAATAAAATAGGTTAATTACTATAAACATTATCA
1 CACTTATATAATGTAATAGGTAGCGCTTATATAATAAAATAGGTTAATTACTATAAACATTATCA
*
63529 AGCACAATAACATATTAGGTAG
66 AGCACAATAACATATTAGGTAC
* * *
63551 CGCTTATATAACGTAATAGGTAGTGCTTATATAATAAAATAGGTTAATTA
1 CACTTATATAATGTAATAGGTAGCGCTTATATAATAAAATAGGTTAATTA
63601 TTTAATTTGT
Statistics
Matches: 128, Mismatches: 8, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
86 1 0.01
87 127 0.99
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.33
Consensus pattern (87 bp):
CACTTATATAATGTAATAGGTAGCGCTTATATAATAAAATAGGTTAATTACTATAAACATTATCA
AGCACAATAACATATTAGGTAC
Found at i:63561 original size:23 final size:23
Alignment explanation
Indices: 63535--63594 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
63525 ATCAAGCACA
*
63535 ATAACATATTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
* *
63558 ATAACGTAATAGGTAGTGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
* *
63581 ATAATAAAATAGGT
1 ATAACATAATAGGT
63595 TAATTATTTA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.40, C:0.08, G:0.18, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:63875 original size:18 final size:19
Alignment explanation
Indices: 63843--63889 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
63833 TTAAATACAA
* *
63843 TAAAACAATATTATT-TAT
1 TAAAAAAATAATATTATAT
* *
63861 TAATAAAATAATATTATTT
1 TAAAAAAATAATATTATAT
63880 TAAAAAAATA
1 TAAAAAAATA
63890 TTAGAATAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
18 12 0.52
19 11 0.48
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (19 bp):
TAAAAAAATAATATTATAT
Found at i:63917 original size:14 final size:14
Alignment explanation
Indices: 63898--63942 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 14
63888 TATTAGAATA
*
63898 ATTTATTTAATATT
1 ATTTATTAAATATT
63912 ATTTATGTAAATATT
1 ATTTAT-TAAATATT
63927 A-TTATTAAAATATT
1 ATTTATT-AAATATT
63941 AT
1 AT
63943 ATCTATAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
13 1 0.04
14 18 0.67
15 8 0.30
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (14 bp):
ATTTATTAAATATT
Found at i:63956 original size:28 final size:28
Alignment explanation
Indices: 63921--63993 Score: 78
Period size: 28 Copynumber: 2.6 Consensus size: 28
63911 TATTTATGTA
63921 AATATTATTATTAAAATATTAT-ATCTAT
1 AATATTATTATTAAAATATTATGAT-TAT
* * * *
63949 AATTTTATAAATAAAAAATTATGATTAT
1 AATATTATTATTAAAATATTATGATTAT
*
63977 TATATT-TTATTAAAATA
1 AATATTATTATTAAAATA
63994 AAAATATTAT
Statistics
Matches: 35, Mismatches: 9, Indels: 3
0.74 0.19 0.06
Matches are distributed among these distances:
27 8 0.23
28 25 0.71
29 2 0.06
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (28 bp):
AATATTATTATTAAAATATTATGATTAT
Found at i:63984 original size:30 final size:31
Alignment explanation
Indices: 63933--64015 Score: 86
Period size: 31 Copynumber: 2.7 Consensus size: 31
63923 TATTATTATT
63933 AAAATATTAT--ATCTATAATTTTA-T-AAATA
1 AAAATATTATAAAT-TAT-ATTTTATTAAAATA
*
63962 AAAA-ATTATGATTATTATATTTTATTAAAATA
1 AAAATATTAT-A-AATTATATTTTATTAAAATA
63994 AAAATATTATAAATTATATTTT
1 AAAATATTATAAATTATATTTT
64016 TTTATTTTTT
Statistics
Matches: 46, Mismatches: 1, Indels: 12
0.78 0.02 0.20
Matches are distributed among these distances:
28 5 0.11
29 4 0.09
30 6 0.13
31 14 0.30
32 12 0.26
33 5 0.11
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (31 bp):
AAAATATTATAAATTATATTTTATTAAAATA
Found at i:64746 original size:28 final size:31
Alignment explanation
Indices: 64715--64801 Score: 80
Period size: 30 Copynumber: 2.9 Consensus size: 31
64705 ATATTATTAT
64715 TAAAATATTATATCTA-TA-ATTTTA-T-AAA
1 TAAAATATTATAT-TATTATATTTTATTAAAA
64743 TAAACA-ATTATAATTATTATATTTTATTAAAA
1 TAAA-ATATTAT-ATTATTATATTTTATTAAAA
*
64775 TAAAATTATTATA-AATTATA-TTTATTA
1 TAAAA-TATTATATTATTATATTTTATTA
64802 TTTATTATAA
Statistics
Matches: 50, Mismatches: 1, Indels: 14
0.77 0.02 0.22
Matches are distributed among these distances:
28 11 0.22
29 5 0.10
30 13 0.26
31 8 0.16
32 8 0.16
33 5 0.10
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.48
Consensus pattern (31 bp):
TAAAATATTATATTATTATATTTTATTAAAA
Found at i:65426 original size:197 final size:196
Alignment explanation
Indices: 64902--65532 Score: 840
Period size: 197 Copynumber: 3.2 Consensus size: 196
64892 CACATATGTT
* * * * *
64902 ACATCGAAACCGATAATTATAATGTAATAGATAAATTTATAATGTTATCAGTATAAATATACCGG
1 ACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATG-TATCGGTAGAAATATACTGG
* * *** *
64967 TTTTATGAGAGAATATGTCTACATAATGTATCGACACAAATTTAAAAAGTGTCGATACATTTTGT
65 TTTTATGAGAAAATATGTCTACATAATGTATCGACAC--ATTTTAAGTTTGTCGATAC-TTTTTT
* *
65032 CCAGAATGAATGTCAAACGAGGTGCACGCATAAAGAGTCGATACATTTATTAAAAGTATCGATCC
127 CCAGAATGAATGTCCAACGAGGTGCACGCATAAAGTGTCGATACATTTATTAAAAGTATCGATCC
65097 CAAAA
192 CAAAA
* * *
65102 ACATCGAAACTGATAATTACAATGTAATAGGTAAATTTACAATGTATTCGATAGAAATATA-TCG
1 ACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATGTA-TCGGTAGAAATATACT-G
* * * *
65166 GTTTTATGAGAAAATAGGTCTACGTAATGTATCGACACATTTTAAGTTTGTCTATAATTTTTTCC
64 GTTTTATGAGAAAATATGTCTACATAATGTATCGACACATTTTAAGTTTGTCGATACTTTTTTCC
* * *
65231 AAAATGAATGTCCAACGAGGTGTACACATAAAGTGTCGATACATTTATTAAAAGTATCGATCCCA
129 AGAATGAATGTCCAACGAGGTGCACGCATAAAGTGTCGATACATTTATTAAAAGTATCGATCCCA
65296 AAA
194 AAA
* * *
65299 A-ATCCAAACCAATAATTATAATGTAATAGGT-AATTTACAATGTACCCGGTAGAAATATACTGG
1 ACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATGTA-TCGGTAGAAATATACTGG
*
65362 TTTTATGAGAAAATATGTCTACATAATGTATCGACACGTTTTAAGTTTTTGTCGATACTTTTTTC
65 TTTTATGAGAAAATATGTCTACATAATGTATCGACACATTTTAAG--TTTGTCGATACTTTTTTC
* * * *
65427 CAGAATGAATGCCCAACGAGGTGCACGCATAAAGTGCCGATACATTTA--AAATTGTATCTATCC
128 CAGAATGAATGTCCAACGAGGTGCACGCATAAAGTGTCGATACATTTATTAAA-AGTATCGATCC
65490 CAAAA
192 CAAAA
* *
65495 ATATCGAAACCGATAATTATAATTTAATAGGTAAATTT
1 ACATCGAAACCGATAATTATAATGTAATAGGTAAATTT
65533 GTAATGTTAC
Statistics
Matches: 378, Mismatches: 45, Indels: 18
0.86 0.10 0.04
Matches are distributed among these distances:
195 72 0.19
196 42 0.11
197 157 0.42
198 18 0.05
199 2 0.01
200 87 0.23
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.32
Consensus pattern (196 bp):
ACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATGTATCGGTAGAAATATACTGGT
TTTATGAGAAAATATGTCTACATAATGTATCGACACATTTTAAGTTTGTCGATACTTTTTTCCAG
AATGAATGTCCAACGAGGTGCACGCATAAAGTGTCGATACATTTATTAAAAGTATCGATCCCAAA
A
Found at i:65627 original size:23 final size:23
Alignment explanation
Indices: 65571--65627 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
65561 TTTATGATAG
65571 AATATGTTAATATAAACGCTACCT
1 AATATGTT-ATATAAACGCTACCT
* ** *
65595 ATTACATTATATAAGCGCTACCT
1 AATATGTTATATAAACGCTACCT
65618 AATATGTTAT
1 AATATGTTAT
65628 TATATGATAA
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
23 21 0.81
24 5 0.19
ACGTcount: A:0.39, C:0.16, G:0.09, T:0.37
Consensus pattern (23 bp):
AATATGTTATATAAACGCTACCT
Found at i:65755 original size:87 final size:86
Alignment explanation
Indices: 65580--65821 Score: 317
Period size: 87 Copynumber: 2.8 Consensus size: 86
65570 GAATATGTTA
* * * * *
65580 ATATAAACGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTAT-ATGATAAGATTTC
1 ATATAAACACTACCTATTACATTATATAAACGTTACCTAATATGTTATTATCTTGATAATATTTC
*
65644 CAGTAATTAACTTATTTTATT
66 CAGTAATTAACATATTTTATT
* * *
65665 ATATAAGCGA-TATCTATTACATTATATAAACGTTACCTAATATGTTATTGTGCTTGATAATATT
1 ATATAAAC-ACTACCTATTACATTATATAAACGTTACCTAATATGTTATTAT-CTTGATAATATT
*
65729 TCTAGTAATTAACATATTTTATT
64 TCCAGTAATTAACATATTTTATT
* * *
65752 ATATAAACACTACCTATTACATTATATAAACGTTACCTAATTTGTTATTTTACTTAATAATATTT
1 ATATAAACACTACCTATTACATTATATAAACGTTACCTAATATGTTATTAT-CTTGATAATATTT
*
65817 TCAGT
65 CCAGT
65822 TAAATGATAT
Statistics
Matches: 135, Mismatches: 18, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
85 44 0.33
86 1 0.01
87 90 0.67
ACGTcount: A:0.36, C:0.13, G:0.07, T:0.43
Consensus pattern (86 bp):
ATATAAACACTACCTATTACATTATATAAACGTTACCTAATATGTTATTATCTTGATAATATTTC
CAGTAATTAACATATTTTATT
Found at i:71290 original size:21 final size:21
Alignment explanation
Indices: 71264--71335 Score: 74
Period size: 21 Copynumber: 3.3 Consensus size: 21
71254 ACTAGATATC
71264 AAAACAATTAAGATTGTAATG
1 AAAACAATTAAGATTGTAATG
* * * *
71285 AAAACAAACATAACAATTG-CATC
1 AAAAC-AA-TTAA-GATTGTAATG
71308 AAAACAATTAAGATTGTAATG
1 AAAACAATTAAGATTGTAATG
71329 AAAACAA
1 AAAACAA
71336 ACATAACAAT
Statistics
Matches: 39, Mismatches: 8, Indels: 8
0.71 0.15 0.15
Matches are distributed among these distances:
20 4 0.10
21 17 0.44
22 4 0.10
23 10 0.26
24 4 0.10
ACGTcount: A:0.57, C:0.11, G:0.10, T:0.22
Consensus pattern (21 bp):
AAAACAATTAAGATTGTAATG
Found at i:71324 original size:44 final size:44
Alignment explanation
Indices: 71261--71349 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
71251 GTAACTAGAT
71261 ATCAAAACAATTAAGATTGTAATGAAAACAAACATAACAATTGC
1 ATCAAAACAATTAAGATTGTAATGAAAACAAACATAACAATTGC
71305 ATCAAAACAATTAAGATTGTAATGAAAACAAACATAACAATTGC
1 ATCAAAACAATTAAGATTGTAATGAAAACAAACATAACAATTGC
71349 A
1 A
71350 GGGCTCTTTG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.55, C:0.13, G:0.09, T:0.22
Consensus pattern (44 bp):
ATCAAAACAATTAAGATTGTAATGAAAACAAACATAACAATTGC
Found at i:80800 original size:49 final size:49
Alignment explanation
Indices: 80700--80793 Score: 125
Period size: 49 Copynumber: 1.9 Consensus size: 49
80690 CACAGATCAG
* * * * *
80700 GGGGCGCGCTATACCCACGTGGCGTCAGATCACCGTATATCGCGGGACA
1 GGGGCGCACTATACCCACGTGACGCCAAATCACCGTATAACGCGGGACA
* *
80749 GGGGCGCACTATACTCACGTGACGCCAAATCAGCGTATAACGCGG
1 GGGGCGCACTATACCCACGTGACGCCAAATCACCGTATAACGCGG
80794 TTCAGGGAAC
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
49 38 1.00
ACGTcount: A:0.23, C:0.30, G:0.31, T:0.16
Consensus pattern (49 bp):
GGGGCGCACTATACCCACGTGACGCCAAATCACCGTATAACGCGGGACA
Found at i:91784 original size:2 final size:2
Alignment explanation
Indices: 91777--91810 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
91767 ATGCTAGATG
* *
91777 TA TA TA TA TA TA TA TT TA TT TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
91811 GTAATTTGAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (2 bp):
TA
Found at i:91817 original size:20 final size:20
Alignment explanation
Indices: 91777--91817 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
91767 ATGCTAGATG
* *
91777 TATATATATATATATTTATT
1 TATATATATATATAGTAATT
91797 TATATATATATATAGTAATT
1 TATATATATATATAGTAATT
91817 T
1 T
91818 GATGAAGGTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (20 bp):
TATATATATATATAGTAATT
Found at i:95385 original size:2 final size:2
Alignment explanation
Indices: 95378--95416 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
95368 TTTTGTAAAC
95378 TA TA TA TA TA TA TA TA TA TA -A TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
95417 ATGAATTTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:95403 original size:17 final size:17
Alignment explanation
Indices: 95381--95414 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
95371 TGTAAACTAT
95381 ATATATATATATATATA
1 ATATATATATATATATA
95398 ATATATATATATATATA
1 ATATATATATATATATA
95415 TAATGAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATATATATATATATATA
Found at i:95403 original size:19 final size:19
Alignment explanation
Indices: 95379--95418 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
95369 TTTGTAAACT
95379 ATATATATATATATATATA
1 ATATATATATATATATATA
95398 ATATATATATATATATATA
1 ATATATATATATATATATA
95417 AT
1 AT
95419 GAATTTAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
ATATATATATATATATATA
Done.