Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006111.1 Hibiscus syriacus cultivar Beakdansim tig00014485_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: 49752
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
Found at i:351 original size:20 final size:20
Alignment explanation
Indices: 320--374 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
310 TTCCCCTTGA
*
320 AGTGCATCGATGCATTCTAC
1 AGTGTATCGATGCATTCTAC
*
340 AGTGTATTGATGCATTCTAC
1 AGTGTATCGATGCATTCTAC
360 AGTGTATCGATGCAT
1 AGTGTATCGATGCAT
375 CCCTAACATG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.35
Consensus pattern (20 bp):
AGTGTATCGATGCATTCTAC
Found at i:1820 original size:57 final size:57
Alignment explanation
Indices: 1719--2170 Score: 718
Period size: 57 Copynumber: 8.0 Consensus size: 57
1709 GATTACCAAT
* *
1719 GGCATTTTGTGTGCAAAAAGTT-AGAAATTCATACTAAGTGTATGAATTTCCATATG
1 GGCACTTTGTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATG
*
1775 GGCACTTTGTGTGCAAAAAGTTAAGAAGTTCATACTAAGTGTATGAATTTCCGTATG
1 GGCACTTTGTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATG
* *
1832 GGCACTTTGTGTGCAAAAAGTTAAGAAGTTCATACTAAG-GTATGAATTTCTGTATG
1 GGCACTTTGTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATG
* *
1888 GGCACTTTGTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGATTTTCTGTATG
1 GGCACTTTGTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATG
* *
1945 GGCACTTTGTGTGTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATG
1 GGCACTTTGTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATG
2002 GGCACTTTGTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATG
1 GGCACTTTGTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATG
* * * *
2059 TGCACTTTGTGTGC-AAAAG-TAAGAAGTTCATACTAAGTGTATGAATTTTCGTATA
1 GGCACTTTGTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATG
** *
2114 GGCACAATGTGTGC-AAAA-TTAAGAAATTCATACTAAGTGTATGAATTTCTGTATG
1 GGCACTTTGTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATG
2169 GG
1 GG
2171 AACTATATGT
Statistics
Matches: 370, Mismatches: 23, Indels: 7
0.93 0.06 0.02
Matches are distributed among these distances:
55 82 0.22
56 80 0.22
57 208 0.56
ACGTcount: A:0.33, C:0.11, G:0.21, T:0.35
Consensus pattern (57 bp):
GGCACTTTGTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATG
Found at i:1899 original size:113 final size:114
Alignment explanation
Indices: 1719--2170 Score: 718
Period size: 113 Copynumber: 4.0 Consensus size: 114
1709 GATTACCAAT
* *
1719 GGCATTTTGTGTGCAAAAAGTT-AGAAATTCATACTAAGTGTATGAATTTCCATATGGGCACTTT
1 GGCACTTTGTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGGCACTTT
*
1783 GTGTGCAAAAAGTTAAGAAGTTCATACTAAGTGTATGAATTTCCGTATG
66 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATG
* *
1832 GGCACTTTGTGTGCAAAAAGTTAAGAAGTTCATACTAAG-GTATGAATTTCTGTATGGGCACTTT
1 GGCACTTTGTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGGCACTTT
* *
1896 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGATTTTCTGTATG
66 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATG
* *
1945 GGCACTTTGTGTGTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGGCACTTT
1 GGCACTTTGTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGGCACTTT
2010 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATG
66 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATG
* * * * **
2059 TGCACTTTGTGTGC-AAAAG-TAAGAAGTTCATACTAAGTGTATGAATTTTCGTATAGGCACAAT
1 GGCACTTTGTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGGCACTTT
*
2122 GTGTGC-AAAA-TTAAGAAATTCATACTAAGTGTATGAATTTCTGTATG
66 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATG
2169 GG
1 GG
2171 AACTATATGT
Statistics
Matches: 314, Mismatches: 23, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
110 37 0.12
111 4 0.01
112 45 0.14
113 130 0.41
114 98 0.31
ACGTcount: A:0.33, C:0.11, G:0.21, T:0.35
Consensus pattern (114 bp):
GGCACTTTGTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGGCACTTT
GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATG
Found at i:2005 original size:170 final size:169
Alignment explanation
Indices: 1719--2170 Score: 707
Period size: 170 Copynumber: 2.7 Consensus size: 169
1709 GATTACCAAT
* * *
1719 GGCATTTTGTGTGCAAAAAGTT-AGAAATTCATACTAAGTGTATGAATTTCCATATGGGCACTTT
1 GGCACTTTGTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATG-ATTTTCGTATGGGCACTTT
*
1783 GTGTGCAAAAAGTTAAGAAGTTCATACTAAGTGTATGAATTTCCGTATGGGCACTTTGTGTGCAA
65 GTGTGC-AAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGGCACTTTGTGTGCAA
* *
1848 AAAGTTAAGAAGTTCATACTAAG-GTATGAATTTCTGTATG
129 AAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATG
1888 GGCACTTTGTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGATTTTCTGTATGGGCACTTT
1 GGCACTTTGTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGATTTTC-GTATGGGCACTTT
*
1953 GTGTGTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGGCACTTTGTGTGCAA
65 GTGTGCAAAA-GTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGGCACTTTGTGTGCAA
2018 AAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATG
129 AAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATG
* * * **
2059 TGCACTTTGTGTGC-AAAAG-TAAGAAGTTCATACTAAGTGTATGAATTTTCGTATAGGCACAAT
1 GGCACTTTGTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATG-ATTTTCGTATGGGCACTTT
*
2122 GTGTGCAAAA-TTAAGAAATTCATACTAAGTGTATGAATTTCTGTATGGG
65 GTGTGCAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGG
2171 AACTATATGT
Statistics
Matches: 264, Mismatches: 14, Indels: 12
0.91 0.05 0.04
Matches are distributed among these distances:
167 38 0.14
169 72 0.27
170 125 0.47
171 29 0.11
ACGTcount: A:0.33, C:0.11, G:0.21, T:0.35
Consensus pattern (169 bp):
GGCACTTTGTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGATTTTCGTATGGGCACTTTG
TGTGCAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGGCACTTTGTGTGCAAAA
AGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATG
Found at i:16445 original size:53 final size:53
Alignment explanation
Indices: 16378--16486 Score: 128
Period size: 53 Copynumber: 2.1 Consensus size: 53
16368 TGTGTAGGTA
* * ** * * *
16378 TTAAGATATTGAGAGATGTATGTATTTACACCGATGTAACTATGAGTTAATTG
1 TTAAGATACTGAGAGATATACATACTTACACCAATGTAACTATGAGCTAATTG
* * *
16431 TTAAGTTACTGAGAGATATACATACTTACACCAATGTAAGTATGCGCTAATTG
1 TTAAGATACTGAGAGATATACATACTTACACCAATGTAACTATGAGCTAATTG
16484 TTA
1 TTA
16487 CACTTTTTTT
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
53 46 1.00
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.36
Consensus pattern (53 bp):
TTAAGATACTGAGAGATATACATACTTACACCAATGTAACTATGAGCTAATTG
Found at i:21963 original size:3 final size:3
Alignment explanation
Indices: 21955--21993 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
21945 ACAAGTTAAT
21955 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
21994 ATCATCATCG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:21998 original size:3 final size:3
Alignment explanation
Indices: 21992--22031 Score: 62
Period size: 3 Copynumber: 13.3 Consensus size: 3
21982 TTCTTCTTCT
* *
21992 TCA TCA TCA TCG TCA TCA TCA TCA TCA TCA TCA CCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
22032 TTATATGGAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.30, C:0.35, G:0.03, T:0.33
Consensus pattern (3 bp):
TCA
Found at i:23701 original size:12 final size:12
Alignment explanation
Indices: 23671--23703 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
23661 AAGCCTAATC
23671 ATAAAA-TACAA
1 ATAAAATTACAA
23682 AT-AAATTACAA
1 ATAAAATTACAA
23693 ATAAAATTACA
1 ATAAAATTACA
23704 CTTTTAAGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 3 0.15
11 9 0.45
12 8 0.40
ACGTcount: A:0.67, C:0.09, G:0.00, T:0.24
Consensus pattern (12 bp):
ATAAAATTACAA
Found at i:26266 original size:14 final size:14
Alignment explanation
Indices: 26247--26276 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
26237 TGACCTACAC
26247 TTCAAGAAATTTGG
1 TTCAAGAAATTTGG
26261 TTCAAGAAATTTGG
1 TTCAAGAAATTTGG
26275 TT
1 TT
26277 TTCTTGACAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.33, C:0.07, G:0.20, T:0.40
Consensus pattern (14 bp):
TTCAAGAAATTTGG
Found at i:33755 original size:30 final size:28
Alignment explanation
Indices: 33721--33785 Score: 85
Period size: 28 Copynumber: 2.2 Consensus size: 28
33711 AATAAATTAT
33721 ATATTTTAAAAATGTAATCAATGAAATTTA
1 ATATTTTAAAAATGTAA--AATGAAATTTA
* * *
33751 ATATTTTAAAATTTTAAAATTAAATTTA
1 ATATTTTAAAAATGTAAAATGAAATTTA
33779 ATATTTT
1 ATATTTT
33786 TATATTTTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
28 17 0.53
30 15 0.47
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.48
Consensus pattern (28 bp):
ATATTTTAAAAATGTAAAATGAAATTTA
Found at i:33782 original size:28 final size:29
Alignment explanation
Indices: 33713--33785 Score: 87
Period size: 30 Copynumber: 2.5 Consensus size: 29
33703 TATATCTAAA
33713 TAAA-TTATATATTTTAAAAATGTAATCAAT
1 TAAATTTA-ATATTTTAAAAATGTAA-CAAT
* * *
33743 GAAATTTAATATTTTAAAATTTTAA-AAT
1 TAAATTTAATATTTTAAAAATGTAACAAT
33771 TAAATTTAATATTTT
1 TAAATTTAATATTTT
33786 TATATTTTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
28 17 0.45
30 18 0.47
31 3 0.08
ACGTcount: A:0.48, C:0.01, G:0.03, T:0.48
Consensus pattern (29 bp):
TAAATTTAATATTTTAAAAATGTAACAAT
Found at i:33987 original size:33 final size:29
Alignment explanation
Indices: 33909--33966 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
33899 TTTTTATTTT
*
33909 TAAAAATTAAATATATAAAAATATTAAATC
1 TAAAATTTAAA-ATATAAAAATATTAAATC
*
33939 TAAGATTTAAAATATAAAAATATTAAAT
1 TAAAATTTAAAATATAAAAATATTAAAT
33967 TTGATTACAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 17 0.65
30 9 0.35
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (29 bp):
TAAAATTTAAAATATAAAAATATTAAATC
Found at i:36908 original size:16 final size:16
Alignment explanation
Indices: 36883--36918 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
36873 GGATGATTAA
* *
36883 TTTTATTTTAATTTAT
1 TTTTAATTTAATATAT
36899 TTTTAATTTAATATAT
1 TTTTAATTTAATATAT
36915 TTTT
1 TTTT
36919 TCACCAACCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (16 bp):
TTTTAATTTAATATAT
Found at i:37140 original size:24 final size:25
Alignment explanation
Indices: 37113--37168 Score: 69
Period size: 24 Copynumber: 2.2 Consensus size: 25
37103 TATTAAATTA
37113 ATTTTACATCTTAAC-ATTAAAAAT
1 ATTTTACATCTTAACTATTAAAAAT
** *
37137 ATTTTTTATCTTAACTTATTAAATAT
1 ATTTTACATCTTAAC-TATTAAAAAT
37163 ATTTTA
1 ATTTTA
37169 TTCTTTGCAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 13 0.50
26 13 0.50
ACGTcount: A:0.39, C:0.09, G:0.00, T:0.52
Consensus pattern (25 bp):
ATTTTACATCTTAACTATTAAAAAT
Found at i:37143 original size:26 final size:25
Alignment explanation
Indices: 37120--37167 Score: 71
Period size: 26 Copynumber: 1.9 Consensus size: 25
37110 TTAATTTTAC
37120 ATCTTAAC-ATTAAAAATATTTTTT
1 ATCTTAACTATTAAAAATATTTTTT
*
37144 ATCTTAACTTATTAAATATATTTT
1 ATCTTAAC-TATTAAAAATATTTT
37168 ATTCTTTGCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 8 0.38
26 13 0.62
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (25 bp):
ATCTTAACTATTAAAAATATTTTTT
Found at i:37169 original size:24 final size:25
Alignment explanation
Indices: 37103--37169 Score: 68
Period size: 24 Copynumber: 2.7 Consensus size: 25
37093 TAAATTCACA
37103 TATTAAAT-TAATTTTACATCTTAACAT
1 TATTAAATAT-ATTTT--ATCTTAACAT
* *
37130 TA-AAAATATTTTTTATCTTAAC-T
1 TATTAAATATATTTTATCTTAACAT
37153 TATTAAATATATTTTAT
1 TATTAAATATATTTTAT
37170 TCTTTGCATA
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
23 3 0.09
24 20 0.59
26 8 0.24
27 3 0.09
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.52
Consensus pattern (25 bp):
TATTAAATATATTTTATCTTAACAT
Found at i:37196 original size:29 final size:29
Alignment explanation
Indices: 37142--37274 Score: 142
Period size: 29 Copynumber: 4.5 Consensus size: 29
37132 AAAATATTTT
* *
37142 TTATCTTAACTTATTAAATATATTTTATTC
1 TTATCTTAACTTA-AAAAAATATTTTATTC
* *
37172 TT-TGCATAACTTAAAAAAATATTTTATTT
1 TTAT-CTTAACTTAAAAAAATATTTTATTC
* * *
37201 TTATTTTAATTTAAAAAATATATTTTAATC
1 TTATCTTAACTTAAAAAA-ATATTTTATTC
* * *
37231 TTATCTTAAATTAAAAATATAATTTATTC
1 TTATCTTAACTTAAAAAAATATTTTATTC
37260 TTATCTTAACTTAAA
1 TTATCTTAACTTAAA
37275 TATTTATATA
Statistics
Matches: 85, Mismatches: 15, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
29 50 0.59
30 35 0.41
ACGTcount: A:0.41, C:0.08, G:0.01, T:0.51
Consensus pattern (29 bp):
TTATCTTAACTTAAAAAAATATTTTATTC
Found at i:37203 original size:59 final size:59
Alignment explanation
Indices: 37139--37274 Score: 166
Period size: 59 Copynumber: 2.3 Consensus size: 59
37129 TTAAAAATAT
** * * *
37139 TTTTTATCTTAACTTATTAAATATATTTTATTCTT-TGCATAACTTAAAAAAATATTTTA
1 TTTTTATCTTAACTTAAAAAATATATTTTAATCTTAT-CATAAATTAAAAAAATAATTTA
* * * *
37198 TTTTTATTTTAATTTAAAAAATATATTTTAATCTTATCTTAAATTAAAAATATAATTTA
1 TTTTTATCTTAACTTAAAAAATATATTTTAATCTTATCATAAATTAAAAAAATAATTTA
*
37257 TTCTTATCTTAACTTAAA
1 TTTTTATCTTAACTTAAA
37275 TATTTATATA
Statistics
Matches: 64, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
59 63 0.98
60 1 0.02
ACGTcount: A:0.40, C:0.07, G:0.01, T:0.52
Consensus pattern (59 bp):
TTTTTATCTTAACTTAAAAAATATATTTTAATCTTATCATAAATTAAAAAAATAATTTA
Found at i:37352 original size:27 final size:26
Alignment explanation
Indices: 37321--37383 Score: 74
Period size: 26 Copynumber: 2.4 Consensus size: 26
37311 ATAAAAATAT
* * *
37321 AATATATTTTTTGTAGTTAAGATAAA
1 AATATATTTTGTGTAGCTAAAATAAA
37347 AA-ATATATTTGTGTAGCTAAAATAAA
1 AATATAT-TTTGTGTAGCTAAAATAAA
37373 AATATGATTTT
1 AATAT-ATTTT
37384 AAGTTAAGAT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
25 4 0.13
26 20 0.65
27 5 0.16
28 2 0.06
ACGTcount: A:0.44, C:0.02, G:0.11, T:0.43
Consensus pattern (26 bp):
AATATATTTTGTGTAGCTAAAATAAA
Found at i:37413 original size:28 final size:28
Alignment explanation
Indices: 37297--37588 Score: 128
Period size: 30 Copynumber: 10.6 Consensus size: 28
37287 TTTTTATAAC
* * *
37297 ATTTTAAATTTAAGATAAAAATATAATAT
1 ATTTTTAAGTTAAGATAAGAATA-AATAT
*
37326 ATTTTTTGTAGTTAAGAT-A-AA-AAATAT
1 A-TTTTT-AAGTTAAGATAAGAATAAATAT
* * *
37353 ATTTGT--G-T-AGCTAA-AATAAAAAT
1 ATTTTTAAGTTAAGATAAGAATAAATAT
*
37376 ATGATTTTAAGTTAAGATAAGAATAAAGAT
1 AT--TTTTAAGTTAAGATAAGAATAAATAT
* *
37406 ATTTTTAAGTTAAAATAAGAATTAATTAT
1 ATTTTTAAGTTAAGATAAGAA-TAAATAT
**
37435 ATTAATAA-TTAAAGGATAA-AAT--ATAT
1 ATTTTTAAGTT-AA-GATAAGAATAAATAT
** * * * * *
37461 -TTAATAATTTAAGTTAAAAATATATTTT
1 ATTTTTAAGTTAAGATAAGAATA-AATAT
** *
37489 ATGTAATAAATTAAGATAAGAATAAAATAT
1 AT-TTTTAAGTTAAGATAAGAAT-AAATAT
* * *
37519 ATTTTTAAGTAAATATAA-ATTAAATAT
1 ATTTTTAAGTTAAGATAAGAATAAATAT
* *
37546 -TTTTAAAGTTAAAATAAGAATAAATAT
1 ATTTTTAAGTTAAGATAAGAATAAATAT
*
37573 ATTTTTAAGTAAAGAT
1 ATTTTTAAGTTAAGAT
37589 GTAAATCAAT
Statistics
Matches: 202, Mismatches: 37, Indels: 49
0.70 0.13 0.17
Matches are distributed among these distances:
21 3 0.01
22 4 0.02
23 8 0.04
24 4 0.02
25 15 0.07
26 23 0.11
27 21 0.10
28 39 0.19
29 35 0.17
30 41 0.20
31 9 0.04
ACGTcount: A:0.51, C:0.00, G:0.09, T:0.40
Consensus pattern (28 bp):
ATTTTTAAGTTAAGATAAGAATAAATAT
Found at i:37468 original size:25 final size:25
Alignment explanation
Indices: 37432--37487 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
37422 AAGAATTAAT
37432 TATA-TTAATAATTAAAGGAT-AAAA
1 TATATTTAATAATTAAA-GATAAAAA
* *
37456 TATATTTAATAATTTAAGTTAAAAA
1 TATATTTAATAATTAAAGATAAAAA
37481 TATATTT
1 TATATTT
37488 TATGTAATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 6 0.21
25 22 0.79
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (25 bp):
TATATTTAATAATTAAAGATAAAAA
Found at i:37528 original size:54 final size:54
Alignment explanation
Indices: 37384--37582 Score: 142
Period size: 54 Copynumber: 3.6 Consensus size: 54
37374 ATATGATTTT
* *
37384 AAGTTAAGATAAGAATAAAGATATTTTTAAGTT-AAAATAAGAATTAATTATATTAAT-
1 AAGTTAAAATAAGAATAAATATATTTTTAAGTTAAAAAT-A-AATT-A--ATATTAATA
* * * * *
37441 AA-TTAAAGGATAA-AATATATTTAATAATTTAAGTTAAAAATATATT-TTATGTAATA
1 AAGTTAAA--ATAAGAATAAATAT-AT-TTTTAAGTTAAAAATAAATTAATAT-TAATA
* * **
37497 AA-TTAAGATAAGAATAAAATATATTTTTAAG-TAAATATAAATTAAATATTTTTA
1 AAGTTAAAATAAGAAT-AAATATATTTTTAAGTTAAAAATAAATT-AATATTAATA
37551 AAGTTAAAATAAGAATAAATATATTTTTAAGT
1 AAGTTAAAATAAGAATAAATATATTTTTAAGT
37583 AAAGATGTAA
Statistics
Matches: 112, Mismatches: 17, Indels: 28
0.71 0.11 0.18
Matches are distributed among these distances:
53 10 0.09
54 33 0.29
55 24 0.21
56 14 0.12
57 8 0.07
58 9 0.08
59 9 0.08
60 5 0.04
ACGTcount: A:0.53, C:0.00, G:0.08, T:0.39
Consensus pattern (54 bp):
AAGTTAAAATAAGAATAAATATATTTTTAAGTTAAAAATAAATTAATATTAATA
Found at i:37544 original size:27 final size:27
Alignment explanation
Indices: 37504--37585 Score: 105
Period size: 27 Copynumber: 3.0 Consensus size: 27
37494 ATAAATTAAG
37504 ATAAGAATAAAATATATTTTTAAGTAAA
1 ATAAGAAT-AAATATATTTTTAAGTAAA
* *
37532 TATAA-ATTAAATAT-TTTTAAAGTTAAA
1 -ATAAGAATAAATATATTTTTAAG-TAAA
37559 ATAAGAATAAATATATTTTTAAGTAAA
1 ATAAGAATAAATATATTTTTAAGTAAA
37586 GATGTAAATC
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
26 11 0.24
27 22 0.48
28 9 0.20
29 4 0.09
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (27 bp):
ATAAGAATAAATATATTTTTAAGTAAA
Found at i:37587 original size:23 final size:23
Alignment explanation
Indices: 37506--37587 Score: 58
Period size: 25 Copynumber: 3.2 Consensus size: 23
37496 AAATTAAGAT
37506 AAGAATAAAATATATTTTTAAGTA
1 AAGAAT-AAATATATTTTTAAGTA
*
37530 AA-TATAAATTAAATATTTTTAAAGTTAAAA
1 AAGAATAAA-T--ATATTTTT-AAG-T---A
37560 TAAGAATAAATATATTTTTAAGTA
1 -AAGAATAAATATATTTTTAAGTA
37584 AAGA
1 AAGA
37588 TGTAAATCAA
Statistics
Matches: 46, Mismatches: 2, Indels: 21
0.67 0.03 0.30
Matches are distributed among these distances:
22 3 0.07
23 7 0.15
24 3 0.07
25 8 0.17
26 3 0.07
27 2 0.04
28 3 0.07
29 8 0.17
30 1 0.02
31 3 0.07
32 5 0.11
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (23 bp):
AAGAATAAATATATTTTTAAGTA
Found at i:37906 original size:16 final size:16
Alignment explanation
Indices: 37885--37915 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
37875 ACATGTTATC
37885 ACACTTGGTATCATTG
1 ACACTTGGTATCATTG
37901 ACACTTGGTATCATT
1 ACACTTGGTATCATT
37916 TGATTTGAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.26, C:0.19, G:0.16, T:0.39
Consensus pattern (16 bp):
ACACTTGGTATCATTG
Done.