Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006310.1 Hibiscus syriacus cultivar Beakdansim tig00015074_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: 73174
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31
Found at i:846 original size:17 final size:17
Alignment explanation
Indices: 801--846 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
791 GTTCTAATTG
*
801 TATTTTTA-TATTTTAA
1 TATTTTTATTATTTAAA
*
817 T-TGTTTATATATTTAAA
1 TATTTTTAT-TATTTAAA
834 TATTTTTATTATT
1 TATTTTTATTATT
847 ATTATGTCAT
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
15 5 0.21
16 1 0.04
17 12 0.50
18 6 0.25
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (17 bp):
TATTTTTATTATTTAAA
Found at i:3423 original size:28 final size:28
Alignment explanation
Indices: 3392--3446 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
3382 TGCATTTATG
3392 TGTGGAACCACTAAATCTTGCAATCCTA
1 TGTGGAACCACTAAATCTTGCAATCCTA
3420 TGTGGAACCACTAAATCTTGCAATCCT
1 TGTGGAACCACTAAATCTTGCAATCCT
3447 GTGATGCGTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.29
Consensus pattern (28 bp):
TGTGGAACCACTAAATCTTGCAATCCTA
Found at i:3661 original size:21 final size:21
Alignment explanation
Indices: 3637--3966 Score: 148
Period size: 21 Copynumber: 15.5 Consensus size: 21
3627 TGAAAAAAAA
*
3637 ATAATGTTAACATGAAAATAT
1 ATAATGTTAACATGAAAAGAT
* *
3658 ATAATGTTAATATGAAGAGAT
1 ATAATGTTAACATGAAAAGAT
* *
3679 ATAATATTAACATGAAGAGAT
1 ATAATGTTAACATGAAAAGAT
* * ** *
3700 GTGACATTAACATGAAGAGAT
1 ATAATGTTAACATGAAAAGAT
* * * *
3721 GTGATGTTAAAATGAAGAGAT
1 ATAATGTTAACATGAAAAGAT
** * * *
3742 ACGATATTGACATG--AATAT
1 ATAATGTTAACATGAAAAGAT
** ** *
3761 ATAATGTTAATGTGAAGTGACG
1 ATAATGTTAACATGAAAAGA-T
* *
3783 AGTTATATTAACAT-AAAGAGAT
1 A-TAATGTTAACATGAAA-AGAT
* * *
3805 ATAAAGTTACCATGAAGAGAT
1 ATAATGTTAACATGAAAAGAT
*
3826 ATGGA-GTTAACAT-AAAAGGAGGT
1 AT-AATGTTAACATGAAAA-GA--T
*
3849 TTAATGTTAACATGAAAAGAT
1 ATAATGTTAACATGAAAAGAT
* * * * *
3870 GTGATGTTAATATGGAGAGAT
1 ATAATGTTAACATGAAAAGAT
* *
3891 ATGATGTTAACATGAAGAGAT
1 ATAATGTTAACATGAAAAGAT
* * **
3912 GTGATGTTAACATGAAGTGAT
1 ATAATGTTAACATGAAAAGAT
* *
3933 GAGTGATGTTAACATAAAAAGAT
1 -A-TAATGTTAACATGAAAAGAT
3956 ATAATGTTAAC
1 ATAATGTTAAC
3967 GTAAAGAGAT
Statistics
Matches: 235, Mismatches: 60, Indels: 28
0.73 0.19 0.09
Matches are distributed among these distances:
19 11 0.05
20 3 0.01
21 169 0.72
22 9 0.04
23 39 0.17
24 4 0.02
ACGTcount: A:0.44, C:0.05, G:0.21, T:0.30
Consensus pattern (21 bp):
ATAATGTTAACATGAAAAGAT
Found at i:3715 original size:42 final size:42
Alignment explanation
Indices: 3637--3947 Score: 216
Period size: 42 Copynumber: 7.3 Consensus size: 42
3627 TGAAAAAAAA
* * * * * *
3637 ATAATGTTAACATGAAAATATATAATGTTAATATGAAGAGAT
1 ATAATGTTAACATGAAGAGATGTGATATTAACATGAAGAGAT
* *
3679 ATAATATTAACATGAAGAGATGTGACATTAACATGAAGAGAT
1 ATAATGTTAACATGAAGAGATGTGATATTAACATGAAGAGAT
* * * ** * *
3721 GTGATGTTAAAATGAAGAGATACGATATTGACATG-A-ATAT
1 ATAATGTTAACATGAAGAGATGTGATATTAACATGAAGAGAT
** * *
3761 ATAATGTTAATGTGAAGTGACGA-GTTATATTAACATAAAGAGAT
1 ATAATGTTAACATGAA--GA-GATGTGATATTAACATGAAGAGAT
* * * * * *
3805 ATAAAGTTACCATGAAGAGATATGGA-GTTAACATAAAAGGAGGT
1 ATAATGTTAACATGAAGAGATGT-GATATTAACAT-GAA-GAGAT
* * * * *
3849 TTAATGTTAACATGAAAAGATGTGATGTTAATATGGAGAGAT
1 ATAATGTTAACATGAAGAGATGTGATATTAACATGAAGAGAT
* * *
3891 ATGATGTTAACATGAAGAGATGTGATGTTAACATGAAGTGAT
1 ATAATGTTAACATGAAGAGATGTGATATTAACATGAAGAGAT
*
3933 GAGTGATGTTAACAT
1 -A-TAATGTTAACAT
3948 AAAAAGATAT
Statistics
Matches: 207, Mismatches: 50, Indels: 22
0.74 0.18 0.08
Matches are distributed among these distances:
40 15 0.07
41 3 0.01
42 122 0.59
43 11 0.05
44 56 0.27
ACGTcount: A:0.43, C:0.05, G:0.22, T:0.30
Consensus pattern (42 bp):
ATAATGTTAACATGAAGAGATGTGATATTAACATGAAGAGAT
Found at i:3939 original size:65 final size:64
Alignment explanation
Indices: 3852--3992 Score: 167
Period size: 65 Copynumber: 2.2 Consensus size: 64
3842 AGGAGGTTTA
* ** * * *
3852 ATGTTAACATGAAAAGATGTGATGTTAATATGGAGAGATATGATGTTAACATGAAGAGA-TGTG
1 ATGTTAACATGAAAAGATGTGATGTTAACATAAAAAGATATAATGTTAACATAAAGAGAGTGTG
** *
3915 ATGTTAACATGAAGTGATGAGTGATGTTAACATAAAAAGATATAATGTTAACGTAAAGAGATGTG
1 ATGTTAACATGAAAAGAT--GTGATGTTAACATAAAAAGATATAATGTTAACATAAAGAGA-GTG
3980 TG
63 TG
3982 ATGTTAACATG
1 ATGTTAACATG
3993 GTGATGTTAA
Statistics
Matches: 65, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
63 16 0.25
65 34 0.52
67 15 0.23
ACGTcount: A:0.40, C:0.04, G:0.25, T:0.30
Consensus pattern (64 bp):
ATGTTAACATGAAAAGATGTGATGTTAACATAAAAAGATATAATGTTAACATAAAGAGAGTGTG
Found at i:3963 original size:44 final size:44
Alignment explanation
Indices: 3852--3992 Score: 178
Period size: 44 Copynumber: 3.2 Consensus size: 44
3842 AGGAGGTTTA
* *
3852 ATGTTAACATGAAAAGATGTGATGTTAATATGGAGAGAT-A-TG
1 ATGTTAACATGAAAAGATGTGATGTTAACATGAAGAGATGAGTG
* *
3894 ATGTTAACATGAAGAGATGTGATGTTAACATGAAGTGATGAGTG
1 ATGTTAACATGAAAAGATGTGATGTTAACATGAAGAGATGAGTG
* * * * * *
3938 ATGTTAACATAAAAAGATATAATGTTAACGTAAAGAGATGTGTG
1 ATGTTAACATGAAAAGATGTGATGTTAACATGAAGAGATGAGTG
3982 ATGTTAACATG
1 ATGTTAACATG
3993 GTGATGTTAA
Statistics
Matches: 84, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
42 35 0.42
43 1 0.01
44 48 0.57
ACGTcount: A:0.40, C:0.04, G:0.25, T:0.30
Consensus pattern (44 bp):
ATGTTAACATGAAAAGATGTGATGTTAACATGAAGAGATGAGTG
Found at i:3975 original size:86 final size:86
Alignment explanation
Indices: 3790--3992 Score: 203
Period size: 86 Copynumber: 2.3 Consensus size: 86
3780 ACGAGTTATA
* * * **
3790 TTAACATAAAGAGATATAAAGTTACCATGAAGAGATATGGAGTTAACATAAAAGGAGGTTTAATG
1 TTAACATAAAGAGATATGATGTTAACATGAAGAGATATGGAGTTAACATAAAAGGAGGAGTAATG
* * *
3855 TTAACATGAAAAGATGTGATG
66 TTAACATAAAAAGATATAATG
* ** * * * *
3876 TTAATATGGAGAGATATGATGTTAACATGAAGAGATGT-GATGTTAACAT-GAAGTGATGAGTGA
1 TTAACATAAAGAGATATGATGTTAACATGAAGAGATATGGA-GTTAACATAAAAG-GAGGAGTAA
3939 TGTTAACATAAAAAGATATAATG
64 TGTTAACATAAAAAGATATAATG
* *
3962 TTAACGTAAAGAGATGTGTGATGTTAACATG
1 TTAACATAAAGAGA--TATGATGTTAACATG
3993 GTGATGTTAA
Statistics
Matches: 93, Mismatches: 20, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
85 5 0.05
86 74 0.80
88 14 0.15
ACGTcount: A:0.42, C:0.05, G:0.24, T:0.29
Consensus pattern (86 bp):
TTAACATAAAGAGATATGATGTTAACATGAAGAGATATGGAGTTAACATAAAAGGAGGAGTAATG
TTAACATAAAAAGATATAATG
Found at i:3998 original size:14 final size:14
Alignment explanation
Indices: 3979--4010 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
3969 AAAGAGATGT
3979 GTGATGTTAACATG
1 GTGATGTTAACATG
*
3993 GTGATGTTAATATG
1 GTGATGTTAACATG
4007 GTGA
1 GTGA
4011 GATTTGTTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.28, C:0.03, G:0.31, T:0.38
Consensus pattern (14 bp):
GTGATGTTAACATG
Found at i:4469 original size:24 final size:27
Alignment explanation
Indices: 4424--4477 Score: 78
Period size: 24 Copynumber: 2.1 Consensus size: 27
4414 CGCTACTACT
4424 ACCACCACCACCATTACTGTCGTCGCC
1 ACCACCACCACCATTACTGTCGTCGCC
*
4451 ACCACCACCA-CATT-C-GTCGTCGTC
1 ACCACCACCACCATTACTGTCGTCGCC
4475 ACC
1 ACC
4478 GCCGCCGATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 11 0.42
25 1 0.04
26 4 0.15
27 10 0.38
ACGTcount: A:0.22, C:0.48, G:0.11, T:0.19
Consensus pattern (27 bp):
ACCACCACCACCATTACTGTCGTCGCC
Found at i:10853 original size:2 final size:2
Alignment explanation
Indices: 10846--10873 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
10836 CGTTTGCAAT
10846 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
10874 CATACATACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:13440 original size:12 final size:12
Alignment explanation
Indices: 13423--13459 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
13413 ATAAGAACCC
13423 TCTTCTCCTGAT
1 TCTTCTCCTGAT
13435 TCTTCTCCTGAT
1 TCTTCTCCTGAT
*
13447 TCTTCTCTTGAT
1 TCTTCTCCTGAT
13459 T
1 T
13460 TAACCTTTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.08, C:0.30, G:0.08, T:0.54
Consensus pattern (12 bp):
TCTTCTCCTGAT
Found at i:19542 original size:251 final size:245
Alignment explanation
Indices: 19094--19544 Score: 672
Period size: 251 Copynumber: 1.8 Consensus size: 245
19084 TTGTGTAACA
* * * * *
19094 TTACTTTATTTTGTATATTTTTTTATATTAATACATGTTTTATTTTATTTTATTTTCGTCTCATA
1 TTACTTTAATTTG-ATATTTTTTTATATTAATAAAAGTTTTATTTTATTTTATTTTCATCTCAGA
* * *
19159 TTGTTATTTTATAACAATTAGTAAAATTAACATACATACACTTTTTTAAATAGAAGTACATACAT
65 TTGTTATTTTATAACAATTAGTAAAATCAACATACATACACTTTTTCAAATAGAAGTACATACAG
*
19224 TTAGATGCATATTCAAACATAGGTATGGGAACACGACTCTGAATAAATCCTCTAAACACAAAAAG
130 TTAGATGCATATTCAAACAAAGGTATGGGAACACGACTCTGAATAAATCCTCTAAACACAAAAAG
19289 AAATGTTAACAACTTGTTATTGTGCATTGATCATATTGTTGCTGCGTAGCT
195 AAATGTTAACAACTTGTTATTGTGCATTGATCATATTGTTGCTGCGTAGCT
*
19340 TTACTTTAATTTG-TA-TTTTTTATATTAATAAAAGTTTTATTTTATTTTATTTTCATCTCGGAT
1 TTACTTTAATTTGATATTTTTTTATATTAATAAAAGTTTTATTTTATTTTATTTTCATCTCAGAT
* *
19403 TGTTATTTTGTAACAATTAGTAATATTGACTACAACATACATACACTGTTTCTCATATAGAAGTA
66 TGTTATTTTATAACAATTAGTAA-A---A-T-CAACATACATACACT-TTT-TCAAATAGAAGTA
* *
19468 CATACAGTTAGATGCATGTTCAAACAAAGGTATGGGAACACGACTCTGAATAAATCCTCTGAACA
123 CATACAGTTAGATGCATATTCAAACAAAGGTATGGGAACACGACTCTGAATAAATCCTCTAAACA
*
19533 CAGAAAGAAATG
188 CAAAAAGAAATG
19545 GAACACATCC
Statistics
Matches: 182, Mismatches: 15, Indels: 11
0.88 0.07 0.05
Matches are distributed among these distances:
243 65 0.36
244 3 0.02
246 12 0.07
247 1 0.01
248 1 0.01
249 14 0.08
250 3 0.02
251 83 0.46
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.41
Consensus pattern (245 bp):
TTACTTTAATTTGATATTTTTTTATATTAATAAAAGTTTTATTTTATTTTATTTTCATCTCAGAT
TGTTATTTTATAACAATTAGTAAAATCAACATACATACACTTTTTCAAATAGAAGTACATACAGT
TAGATGCATATTCAAACAAAGGTATGGGAACACGACTCTGAATAAATCCTCTAAACACAAAAAGA
AATGTTAACAACTTGTTATTGTGCATTGATCATATTGTTGCTGCGTAGCT
Found at i:20001 original size:2 final size:2
Alignment explanation
Indices: 19977--20136 Score: 84
Period size: 2 Copynumber: 84.5 Consensus size: 2
19967 GATTCTGTAG
*
19977 TA TA T- TA TA TA T- TG TA TA GTA TA TA TCA TA TA TA TA GTA TA
1 TA TA TA TA TA TA TA TA TA TA -TA TA TA T-A TA TA TA TA -TA TA
* *
20018 TA CTA TA T- TA TT TA GTA TA T- TG T- TA T- TA TA GTA T- TA TA
1 TA -TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA -TA TA TA TA
*
20056 T- TA TA TA TA T- TA TA GTA TA TA TA TT TA T- TA TA T- TA T- TA
1 TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA
*
20094 TA TA TA T- TA TA GTA TT TA TA T- TA T- TA T- TA TA TA T- TA TA
1 TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
20132 TA TA T
1 TA TA T
20137 CGTAGTATTT
Statistics
Matches: 126, Mismatches: 7, Indels: 50
0.69 0.04 0.27
Matches are distributed among these distances:
1 17 0.13
2 93 0.74
3 16 0.13
ACGTcount: A:0.39, C:0.01, G:0.05, T:0.55
Consensus pattern (2 bp):
TA
Found at i:20017 original size:9 final size:9
Alignment explanation
Indices: 19977--20157 Score: 123
Period size: 9 Copynumber: 20.0 Consensus size: 9
19967 GATTCTGTAG
19977 TATATTATA
1 TATATTATA
19986 TAT-TGTATA
1 TATAT-TATA
19995 GTATA-TATCA
1 -TATATTAT-A
20005 TATATATAGTA
1 TATAT-TA-TA
*
20016 TATACTATA
1 TATATTATA
20025 T-TATT-TA
1 TATATTATA
*
20032 GTATATTGTTA
1 -TATATT-ATA
*
20043 TTATAGTAT-
1 -TATATTATA
20052 TATATTATA
1 TATATTATA
20061 TATATTATA
1 TATATTATA
20070 GTATA-TATA
1 -TATATTATA
*
20079 TTTATTATA
1 TATATTATA
20088 T-TATTATA
1 TATATTATA
20096 TATATTATA
1 TATATTATA
20105 GTAT-TTATA
1 -TATATTATA
20114 T-TATTATTA
1 TATATTA-TA
20123 TATATTATA
1 TATATTATA
**
20132 TATATCGTA
1 TATATTATA
20141 GTAT-TTATA
1 -TATATTATA
20150 T-TATTATA
1 TATATTATA
20158 GAGTATACCA
Statistics
Matches: 140, Mismatches: 11, Indels: 43
0.72 0.06 0.22
Matches are distributed among these distances:
7 4 0.03
8 33 0.24
9 66 0.47
10 22 0.16
11 14 0.10
12 1 0.01
ACGTcount: A:0.38, C:0.02, G:0.06, T:0.55
Consensus pattern (9 bp):
TATATTATA
Found at i:20061 original size:75 final size:76
Alignment explanation
Indices: 19977--20212 Score: 205
Period size: 75 Copynumber: 3.2 Consensus size: 76
19967 GATTCTGTAG
*
19977 TATATTATATAT-TGTATAGTATATATCATATA-TATAGTA-TATACTATATTAT-TTA-GTATA
1 TATATTATATATAT-TATAGTATATAT-ATATATTATAGTATTATA-TATATTATAGTATGTATA
*
20037 TTGTTATTATAGTAT
63 TTATTATTATA-TAT
* *
20052 TATATTATATATATTATAGTATATATATTTATTATATTATTATATATATTATAGTAT-T-TA-TA
1 TATATTATATATATTATAGTATATATATATATTATAGTATTATATATATTATAGTATGTATATTA
20114 TTATTAT-TA-
66 TTATTATATAT
** * * **
20123 TATATTATATATATCGTAGTATTTATAT-TATTATAG-AGTATA-CCATTATAGT-TGT-TATAT
1 TATATTATATATATTATAGTATATATATATATTATAGTATTATATATATTATAGTATGTATAT-T
**
20183 ATTAGAATTATAT
65 ATTATTA-TATAT
20196 TATATTATATATATTAT
1 TATATTATATATATTAT
20213 TTATTTCGTT
Statistics
Matches: 135, Mismatches: 15, Indels: 24
0.78 0.09 0.14
Matches are distributed among these distances:
67 1 0.01
68 11 0.08
69 5 0.04
70 13 0.10
71 26 0.19
72 4 0.03
73 15 0.11
74 12 0.09
75 40 0.30
76 8 0.06
ACGTcount: A:0.38, C:0.02, G:0.06, T:0.53
Consensus pattern (76 bp):
TATATTATATATATTATAGTATATATATATATTATAGTATTATATATATTATAGTATGTATATTA
TTATTATATAT
Found at i:20110 original size:29 final size:29
Alignment explanation
Indices: 20041--20127 Score: 110
Period size: 29 Copynumber: 3.0 Consensus size: 29
20031 AGTATATTGT
*
20041 TATTATAGTATTATATTATATATATTATA-G
1 TATTATAGTATT-TATTATAT-TATTATATA
20071 TA-TATA-TATTTATTATATTATTATATA
1 TATTATAGTATTTATTATATTATTATATA
20098 TATTATAGTATTTA-TATTATTATTATATA
1 TATTATAGTATTTATTA-TATTATTATATA
20127 T
1 T
20128 TATATATATC
Statistics
Matches: 52, Mismatches: 1, Indels: 9
0.84 0.02 0.15
Matches are distributed among these distances:
26 7 0.13
27 10 0.19
28 10 0.19
29 23 0.44
30 2 0.04
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.57
Consensus pattern (29 bp):
TATTATAGTATTTATTATATTATTATATA
Found at i:24659 original size:30 final size:30
Alignment explanation
Indices: 24625--24697 Score: 110
Period size: 30 Copynumber: 2.4 Consensus size: 30
24615 TAGAAGACAG
24625 AAGACGCATTGTGGTCATCGCGTCTTTCTA
1 AAGACGCATTGTGGTCATCGCGTCTTTCTA
* * *
24655 AAGACGTATTGTGGTCGTCGCGTCTTTCTG
1 AAGACGCATTGTGGTCATCGCGTCTTTCTA
*
24685 AAGACACATTGTG
1 AAGACGCATTGTG
24698 TTCACTGCTA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.33
Consensus pattern (30 bp):
AAGACGCATTGTGGTCATCGCGTCTTTCTA
Found at i:31410 original size:33 final size:33
Alignment explanation
Indices: 31368--31430 Score: 126
Period size: 33 Copynumber: 1.9 Consensus size: 33
31358 CCCAAGAACA
31368 CGAGGTATTCGAGATTGTTTTCTCCTTCGGTCG
1 CGAGGTATTCGAGATTGTTTTCTCCTTCGGTCG
31401 CGAGGTATTCGAGATTGTTTTCTCCTTCGG
1 CGAGGTATTCGAGATTGTTTTCTCCTTCGG
31431 CATCAGAGAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.13, C:0.21, G:0.27, T:0.40
Consensus pattern (33 bp):
CGAGGTATTCGAGATTGTTTTCTCCTTCGGTCG
Found at i:45834 original size:29 final size:31
Alignment explanation
Indices: 45766--45835 Score: 72
Period size: 29 Copynumber: 2.3 Consensus size: 31
45756 TTAACGGATG
*
45766 AGTAACATAATTGAATGAAAAATAAAAGTAT
1 AGTAATATAATTGAATGAAAAATAAAAGTAT
* ** * *
45797 AATGTTATAATTG-AT-AAAATTAAAAGTTT
1 AGTAATATAATTGAATGAAAAATAAAAGTAT
45826 AGTAATATAA
1 AGTAATATAA
45836 ACAAATCAAC
Statistics
Matches: 30, Mismatches: 9, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
29 19 0.63
30 2 0.07
31 9 0.30
ACGTcount: A:0.54, C:0.01, G:0.11, T:0.33
Consensus pattern (31 bp):
AGTAATATAATTGAATGAAAAATAAAAGTAT
Found at i:58801 original size:31 final size:33
Alignment explanation
Indices: 58765--58836 Score: 87
Period size: 31 Copynumber: 2.2 Consensus size: 33
58755 TTGTACTCAT
58765 TAATAAAAT-ATGACATATCAT-AT-AAAAATAA
1 TAATAAAATAAT-ACATATCATGATAAAAAATAA
* *
58796 TAATAAAATAATTCATGTCATGATAAAAAATAA
1 TAATAAAATAATACATATCATGATAAAAAATAA
58829 TATATAAA
1 TA-ATAAA
58837 GTTCAGTAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
31 16 0.46
32 4 0.11
33 10 0.29
34 5 0.14
ACGTcount: A:0.60, C:0.06, G:0.04, T:0.31
Consensus pattern (33 bp):
TAATAAAATAATACATATCATGATAAAAAATAA
Found at i:60138 original size:23 final size:23
Alignment explanation
Indices: 60112--60190 Score: 88
Period size: 23 Copynumber: 3.4 Consensus size: 23
60102 TTTGGTTCTC
*
60112 GAACATTAAATAAATATGTTCAT
1 GAACATTAAATGAATATGTTCAT
* *
60135 GAACATTATATGAATATGGTT-GT
1 GAACATTAAATGAATAT-GTTCAT
* *
60158 GACCATTAAATGAATATATTCAT
1 GAACATTAAATGAATATGTTCAT
*
60181 AAACATTAAA
1 GAACATTAAA
60191 CAAACATTCA
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
22 2 0.04
23 40 0.89
24 3 0.07
ACGTcount: A:0.46, C:0.09, G:0.11, T:0.34
Consensus pattern (23 bp):
GAACATTAAATGAATATGTTCAT
Found at i:60901 original size:20 final size:20
Alignment explanation
Indices: 60876--60945 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 20
60866 GCGAAGTTCG
60876 CGTTGCGATTCATTCCAAAT
1 CGTTGCGATTCATTCCAAAT
* * *
60896 CGTTGCGA-T-AGTCGAAGTT
1 CGTTGCGATTCATTCCAA-AT
60915 CGCGTTGCGATTCATTCCAAAT
1 --CGTTGCGATTCATTCCAAAT
60937 CGTTGCGAT
1 CGTTGCGAT
60946 AGGCGAAGTT
Statistics
Matches: 39, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
18 5 0.13
19 2 0.05
20 17 0.44
21 8 0.21
22 2 0.05
23 5 0.13
ACGTcount: A:0.21, C:0.23, G:0.23, T:0.33
Consensus pattern (20 bp):
CGTTGCGATTCATTCCAAAT
Found at i:60912 original size:41 final size:42
Alignment explanation
Indices: 60817--61174 Score: 625
Period size: 41 Copynumber: 8.6 Consensus size: 42
60807 GATTCGCAAC
* * * *
60817 GCGATAGTCGAAGTTTGCATTGCGATTTATTCCAAATTCGTT
1 GCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAATTCGTT
60859 GCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAA-TCGTT
1 GCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAATTCGTT
*
60900 GCGATAGTCGAAGTTCGCGTTGCGATTCATTCCAAA-TCGTT
1 GCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAATTCGTT
60941 GCGATAGGCGAAGTTCGCGTTGCGATTCATTCC-AATTCGTT
1 GCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAATTCGTT
60982 GCGATAGGCGAAGTTCGCGTTGCGATTCATTCC-AATTCGTT
1 GCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAATTCGTT
61023 GCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAATTCGTT
1 GCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAATTCGTT
*
61065 GCGATAGGTGAAGTTCGCGTTGCGATTCATTCCAAATTCGTT
1 GCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAATTCGTT
61107 GCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAATTCGTT
1 GCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAATTCGTT
*
61149 GCGATAGGCGAAGTTCGCATTGCGAT
1 GCGATAGGCGAAGTTCGCGTTGCGAT
61175 AGTCCAAATA
Statistics
Matches: 305, Mismatches: 9, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
40 2 0.01
41 156 0.51
42 147 0.48
ACGTcount: A:0.22, C:0.21, G:0.26, T:0.32
Consensus pattern (42 bp):
GCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAATTCGTT
Found at i:61265 original size:6 final size:6
Alignment explanation
Indices: 61254--61286 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
61244 AACACGTATT
61254 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
61287 CGAGACGGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.33, C:0.52, G:0.15, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:66191 original size:18 final size:19
Alignment explanation
Indices: 66156--66192 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
66146 CACGAAATGT
66156 AAGATTACCAGTGAGAATAA
1 AAGATTACCAG-GAGAATAA
66176 AAGATTACCA-GAGAATA
1 AAGATTACCAGGAGAATA
66193 GGATTACTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.51, C:0.11, G:0.19, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGAGAATAA
Found at i:72190 original size:15 final size:16
Alignment explanation
Indices: 72170--72199 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
72160 ATAAATTTGT
72170 ATAAAAA-TAAAAAAA
1 ATAAAAACTAAAAAAA
72185 ATAAAAACTAAAAAA
1 ATAAAAACTAAAAAA
72200 TGTTACATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.83, C:0.03, G:0.00, T:0.13
Consensus pattern (16 bp):
ATAAAAACTAAAAAAA
Found at i:72957 original size:30 final size:29
Alignment explanation
Indices: 72898--72957 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 29
72888 AACAGGGAAA
* *
72898 TATTAAAATTTTGTAAAAAATATAGAAAT
1 TATTAAAATTTTATAAAAAATATAAAAAT
72927 TATTAAAATTTTCCATAAAAAA-ATAAAAAT
1 TATTAAAATTTT--ATAAAAAATATAAAAAT
72957 T
1 T
72958 CAAGATTCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
29 12 0.44
30 8 0.30
31 7 0.26
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.37
Consensus pattern (29 bp):
TATTAAAATTTTATAAAAAATATAAAAAT
Done.