Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002591.1 Hibiscus syriacus cultivar Beakdansim tig00005244_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: 74471
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.34
Found at i:396 original size:2 final size:2
Alignment explanation
Indices: 391--2416 Score: 3103
Period size: 2 Copynumber: 1042.5 Consensus size: 2
381 CTTTAATATT
391 TG TG TG TG TG -G TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
432 TG TG TG TG TG TG TG TG T- TG TG TG TG -G TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
*
472 TG TG TG TG TG TG TG TG GG TG TG -G TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
513 TG TG TG TG TG -G TG TG TG TG TG TG TG TG TG TG TG -G TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
553 TG TG TG TG TG -G TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
594 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
636 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG -G TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
677 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T- TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
718 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG -G
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
759 TG TG TG TG -G TG TG TG TG TG TG TG TG TG TG TG TG TG -G TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
799 TG TG -G TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
840 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
882 TG -G TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG -G TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
922 TG TG TG TG TG T- TG TG TG TG TG TG TG TG TG TG TG TG TG -G TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
*
962 TG TG TG TG TG GG TG TG TG TG TG TG TG TG TG TG -G TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
* *
1003 TG TG TG TG GG TG TG TG TG TG TG TG TG TG TG GG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1045 TG TG TG TG TG TG -G TG TG TG TG TG TG TG -G TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
*
1085 TG TG TG TG TG TG TG GG TG TG TG TG TG TG TG TG TG -G TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
*
1126 TG TG TG TG TG TG TG TG TG TG GG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1168 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
* * *
1210 TG TG -G TG TG TG TG TG CG TG TG CG TG CG T- TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
*
1250 TG -G TG TG TG CG TG TG TG TG TG TG TG -G TG TG TG TG TG -G TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
* *
1289 TG TG TG TG TG TG TG TG TG TG TG TG TG CG TG TG TG TG CG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
* * * * * * *
1331 -G TG TG CG TG TG TG CG TG TG CG TG CG TG CG TG AG T- TG -G CG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
* * * * * * *
1370 TG TG TG CG TG CG TG TG CG TG CG TG TG CG TG CG TG TG CTG CG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG -TG TG TG
*
1413 TG CG TG CTG -G TG TG TG TG TG TG TG TG TG TG TG TG -G TG TG TG
1 TG TG TG -TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
*
1454 TG TG TG TG TG TG TG TG TG TG GG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1496 TG -G TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T- TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
* * * *
1536 TG TG -G TG TG TG TG TG CG TG TG CG TG CG TG TG CG -G TG T- TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
*
1575 TG TG TG TG TG TG CG TG TG TG TG TG -G TG TG TG TG TG TG -G TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1615 TG TG -G TG TG T- TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1655 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG -G TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1696 TG TG TG TG TG TG TG TG TG TG TG TG TG T- TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
*
1737 TG TG -G TG TG TG TG TG TG -G TG TG TG GG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1777 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T- TG T-
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
*
1817 TG TG TG TG TG TG TG TG TG TG TG TG TG TG GG TG TG TG -G TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
* * * * * * * *
1858 TG TG CG TG CG TG TG CG TG CG TG TG CG TG CG TG TG CG TG CG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
* * * *
1900 TG CG TG CG TG TG TG CG TG TG TG TG CG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1942 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1984 TG TG TG TG TG TG TG TG TG TG -G TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
* *
2025 TG TG TG TG TG -G TG TG TG TG TG CG TG TG TG TG CG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
* * * *
2066 TG TG TG CG TG TG CG TG TG TG CG TG TG TG TG TG CG TG -G TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
2107 TG -G TG TG TG T- TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
*
2147 TG TG TG TG TG TG TG TG TG TG GG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
*
2189 TT TG TG TG TG TG TG TG TG TG TG TG TG TG TG -G TG -G TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
2229 TG TG TG TG TG TG -G TG TG TG TG TG TG TG -G TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
2269 -G TG TG -G TG TG TG T- TG TG TG TG TG -G TG TG TG TG -G TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
2306 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
2348 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
*
2390 TG TG TG TG TG TG TG TG TG TG CG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
2417 ATGTATGTAT
Statistics
Matches: 1851, Mismatches: 110, Indels: 126
0.89 0.05 0.06
Matches are distributed among these distances:
1 61 0.03
2 1786 0.96
3 4 0.00
ACGTcount: A:0.00, C:0.02, G:0.51, T:0.46
Consensus pattern (2 bp):
TG
Found at i:10946 original size:7 final size:7
Alignment explanation
Indices: 10901--10948 Score: 51
Period size: 7 Copynumber: 6.4 Consensus size: 7
10891 TTATTAGTAT
*
10901 TTATTTT
1 TTATTTA
10908 TTATTTA
1 TTATTTA
10915 TTATTTGA
1 TTATTT-A
10923 CTTATTTAA
1 -TTATTT-A
*
10932 TTAGTTA
1 TTATTTA
10939 TTATTTA
1 TTATTTA
10946 TTA
1 TTA
10949 ATTGCAATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
7 22 0.63
8 6 0.17
9 7 0.20
ACGTcount: A:0.27, C:0.02, G:0.04, T:0.67
Consensus pattern (7 bp):
TTATTTA
Found at i:11071 original size:14 final size:14
Alignment explanation
Indices: 11054--11084 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
11044 TCTTTTTAAA
11054 TTATTAGAATTTAT
1 TTATTAGAATTTAT
*
11068 TTATTTGAATTTAT
1 TTATTAGAATTTAT
11082 TTA
1 TTA
11085 AATAATTTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.61
Consensus pattern (14 bp):
TTATTAGAATTTAT
Found at i:13958 original size:32 final size:32
Alignment explanation
Indices: 13917--13978 Score: 124
Period size: 32 Copynumber: 1.9 Consensus size: 32
13907 TAAGAAAAGT
13917 CTATTTTAGGTGTATGTGTATGCTTTTATTTA
1 CTATTTTAGGTGTATGTGTATGCTTTTATTTA
13949 CTATTTTAGGTGTATGTGTATGCTTTTATT
1 CTATTTTAGGTGTATGTGTATGCTTTTATT
13979 GTTTAAGGAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.18, C:0.06, G:0.19, T:0.56
Consensus pattern (32 bp):
CTATTTTAGGTGTATGTGTATGCTTTTATTTA
Found at i:15195 original size:81 final size:81
Alignment explanation
Indices: 14935--15350 Score: 487
Period size: 81 Copynumber: 5.1 Consensus size: 81
14925 CCCCATTTTT
* *
14935 AGAGAATCTCTGTCATGTCATAGTGTTTCATCCCATCCGAAATGAAAGATGCATTCTAGGGAAGC
1 AGAGAATCTCTGTCATGTCATAGTG-TTCATCCCATCCGAAATGAAAGGTGCATTCCAGGGAAGC
15000 ATTTTCCATTATTATTC
65 ATTTTCCATTATTATTC
* * *
15017 AGAGAATCTCTGTCATATCATAGTGTTCCATCCCATTCGAAATGAAAGGCGCATTCCACGGGAAG
1 AGAGAATCTCTGTCATGTCATAGTGTT-CATCCCATCCGAAATGAAAGGTGCATTCCA-GGGAAG
*
15082 CATTTTCTATTATTATTC
64 CATTTTCCATTATTATTC
** * * * *
15100 AGAGAATCTCTACCATGTCATAGTGTTCAATCCCATCCAAAATAAAAGATGCTTTCCAGTGG-AG
1 AGAGAATCTCTGTCATGTCATAGTGTTC-ATCCCATCCGAAATGAAAGGTGCATTCCAG-GGAAG
15164 CATTTTCCA-TATTATTC
64 CATTTTCCATTATTATTC
** * * * ** *
15181 AGAGAATCTCTACCATGTCATAATGTTCATCTCATCCAAAATGAAAGGTGTGTTCCATGGGAAGT
1 AGAGAATCTCTGTCATGTCATAGTGTTCATCCCATCCGAAATGAAAGGTGCATTCCA-GGGAAGC
* * *
15246 GTTTTCCATGATTATTA
65 ATTTTCCATTATTATTC
* ** *
15263 AGAGAATCTCTGTTATGTCATAGT-TTCATCATATCCGAAATGAAAGGTGCGTTCCAGGGGAAGC
1 AGAGAATCTCTGTCATGTCATAGTGTTCATCCCATCCGAAATGAAAGGTGCATTCCA-GGGAAGC
*
15327 GTTTTCCATTATTATTC
65 ATTTTCCATTATTATTC
*
15344 AAAGAAT
1 AGAGAAT
15351 TTTCCATTTG
Statistics
Matches: 288, Mismatches: 39, Indels: 15
0.84 0.11 0.04
Matches are distributed among these distances:
80 26 0.09
81 102 0.35
82 88 0.31
83 72 0.25
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.33
Consensus pattern (81 bp):
AGAGAATCTCTGTCATGTCATAGTGTTCATCCCATCCGAAATGAAAGGTGCATTCCAGGGAAGCA
TTTTCCATTATTATTC
Found at i:15342 original size:163 final size:164
Alignment explanation
Indices: 14892--15350 Score: 500
Period size: 163 Copynumber: 2.8 Consensus size: 164
14882 AAATCTAAAG
* * * * *
14892 AAAAAGAAATGTGTGTTTCAAT-GGAAGTGTTTTCC-CCATT-TTTAGAGAATCTCTGTCATGTC
1 AAAATGAAAGGTGTG-TTCCATGGGAAGTGTTTTCCATCATTATTAAGAGAATCTCTGTCATGTC
*
14954 ATAGTGTTTCATCCCATCCGAAATGAAAGATGCATTCTA-GGGAAGCATTTTCCATTATTATTCA
65 ATA--GTTTCATCCCATCCGAAATGAAAGATGCATTCCAGGGGAAGCATTTTCCATTATTATTCA
** * *
15018 GAGAATCTCTGTCATATCATAGTGTTCCATCCCATTC
128 GAGAATCTCTACCATATCATAATGTTCCATCCCATCC
* * ** * ** * * * **
15055 GAAATGAAAGGCGCATTCCACGGGAAGCATTTTCTATTATTATTCAGAGAATCTCTACCATGTCA
1 AAAATGAAAGGTGTGTTCCATGGGAAGTGTTTTCCATCATTATTAAGAGAATCTCTGTCATGTCA
* * * *
15120 TAGTGTTCAATCCCATCCAAAATAAAAGATGCTTTCCAGTGG-AGCATTTTCCA-TATTATTCAG
66 TAGT-TTC-ATCCCATCCGAAATGAAAGATGCATTCCAGGGGAAGCATTTTCCATTATTATTCAG
* *
15183 AGAATCTCTACCATGTCATAATGTT-CATCTCATCC
129 AGAATCTCTACCATATCATAATGTTCCATCCCATCC
* *
15218 AAAATGAAAGGTGTGTTCCATGGGAAGTGTTTTCCATGATTATTAAGAGAATCTCTGTTATGTCA
1 AAAATGAAAGGTGTGTTCCATGGGAAGTGTTTTCCATCATTATTAAGAGAATCTCTGTCATGTCA
** * * * *
15283 TAGTTTCATCATATCCGAAATGAAAGGTGCGTTCCAGGGGAAGCGTTTTCCATTATTATTCAAAG
66 TAGTTTCATCCCATCCGAAATGAAAGATGCATTCCAGGGGAAGCATTTTCCATTATTATTCAGAG
15348 AAT
131 AAT
15351 TTTCCATTTG
Statistics
Matches: 239, Mismatches: 49, Indels: 16
0.79 0.16 0.05
Matches are distributed among these distances:
161 26 0.11
162 17 0.07
163 99 0.41
164 37 0.15
165 58 0.24
166 2 0.01
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Consensus pattern (164 bp):
AAAATGAAAGGTGTGTTCCATGGGAAGTGTTTTCCATCATTATTAAGAGAATCTCTGTCATGTCA
TAGTTTCATCCCATCCGAAATGAAAGATGCATTCCAGGGGAAGCATTTTCCATTATTATTCAGAG
AATCTCTACCATATCATAATGTTCCATCCCATCC
Found at i:18732 original size:71 final size:71
Alignment explanation
Indices: 18616--18766 Score: 257
Period size: 71 Copynumber: 2.1 Consensus size: 71
18606 AATCAACTTT
* *
18616 AACCCTAAACCCTACTTTAAAAACACAAATATTCTAACATACAATCAATTTTAGCCTTAAACTTC
1 AACCCTAAACCCTACTTTAAAAACACAAACATTCTAACATACAATCAATTTTAACCTTAAACTTC
18681 TTTAAA
66 TTTAAA
* *
18687 AACCCTATACCCTACTTTAAAAACACAAACATTCTAACATACAATCTATTTTAACCTTAAACTTC
1 AACCCTAAACCCTACTTTAAAAACACAAACATTCTAACATACAATCAATTTTAACCTTAAACTTC
18752 TTTAAA
66 TTTAAA
*
18758 AACCTTAAA
1 AACCCTAAA
18767 TCATACAAAT
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
71 74 1.00
ACGTcount: A:0.44, C:0.25, G:0.01, T:0.31
Consensus pattern (71 bp):
AACCCTAAACCCTACTTTAAAAACACAAACATTCTAACATACAATCAATTTTAACCTTAAACTTC
TTTAAA
Found at i:22120 original size:10 final size:10
Alignment explanation
Indices: 22107--22136 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
22097 TAACAATAAA
*
22107 AAATAAAAAT
1 AAATTAAAAT
22117 AAATTAAAAT
1 AAATTAAAAT
22127 AAATTAAAAT
1 AAATTAAAAT
22137 TTAAAGGTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (10 bp):
AAATTAAAAT
Found at i:22705 original size:25 final size:24
Alignment explanation
Indices: 22661--22710 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 24
22651 TATGTATTGA
22661 ATATCTTAATAATTATTTATATTTT
1 ATATCTTAATAATTATTTAT-TTTT
*
22686 ATATTTTAATAATT-TCTTATTTTT
1 ATATCTTAATAATTAT-TTATTTTT
22710 A
1 A
22711 AAAAAATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 6 0.26
25 17 0.74
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (24 bp):
ATATCTTAATAATTATTTATTTTT
Found at i:25513 original size:23 final size:24
Alignment explanation
Indices: 25472--25521 Score: 77
Period size: 23 Copynumber: 2.1 Consensus size: 24
25462 ATAAAAATAA
25472 TTTTTAAAAGATTAAATTAACATC
1 TTTTTAAAAGATTAAATTAACATC
25496 TTTTTAAAA-A-TAATATTAACATC
1 TTTTTAAAAGATTAA-ATTAACATC
25519 TTT
1 TTT
25522 AGACAAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
22 3 0.12
23 13 0.52
24 9 0.36
ACGTcount: A:0.44, C:0.08, G:0.02, T:0.46
Consensus pattern (24 bp):
TTTTTAAAAGATTAAATTAACATC
Found at i:25843 original size:15 final size:15
Alignment explanation
Indices: 25797--25844 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
25787 AATTCAATAG
25797 AATTTATT-AATTAT
1 AATTTATTAAATTAT
* **
25811 AATATAATTAAAAAAT
1 AAT-TTATTAAATTAT
25827 AATTTATTAAATTAT
1 AATTTATTAAATTAT
25842 AAT
1 AAT
25845 ATACAACAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
14 3 0.12
15 16 0.62
16 7 0.27
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
AATTTATTAAATTAT
Found at i:31721 original size:4 final size:4
Alignment explanation
Indices: 31712--31967 Score: 191
Period size: 4 Copynumber: 65.2 Consensus size: 4
31702 GCAAAAAGAT
*
31712 GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAG- GAGG
1 GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA
* * * * * * * *
31759 GAGG GAGG GAGG GAGG GAGG GAG- GGGG GAGG GAGA GAGA GAGA GAGA
1 GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA
* * * * * *
31806 GAGA GAGA AAGA GA-A G-GA GGGA GGGA GGGA GAGG GAGG GAGA GAGA
1 GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA
* * * * * *
31852 GGGA CG-GA GGGA GGGA GAGA GAGG GAGA GAGA GGGA GAGA GAGG GAGA
1 GAGA -GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA
* * * * * * *
31900 GAGA GGGA GAGG GAAA GAGA GGGA GAGA GAGA G-GG GAAA GAGA GGGA
1 GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA
* *
31947 GGGA GGGA GAGA GAGA GAGA G
1 GAGA GAGA GAGA GAGA GAGA G
31968 TGAAATTATA
Statistics
Matches: 215, Mismatches: 30, Indels: 14
0.83 0.12 0.05
Matches are distributed among these distances:
3 12 0.06
4 202 0.94
5 1 0.00
ACGTcount: A:0.39, C:0.00, G:0.60, T:0.00
Consensus pattern (4 bp):
GAGA
Found at i:31727 original size:10 final size:10
Alignment explanation
Indices: 31712--31967 Score: 191
Period size: 10 Copynumber: 26.1 Consensus size: 10
31702 GCAAAAAGAT
31712 GAGAGAGAGA
1 GAGAGAGAGA
31722 GAGAGAGAGA
1 GAGAGAGAGA
31732 GAGAGAGAGA
1 GAGAGAGAGA
31742 GAGAGAGAGA
1 GAGAGAGAGA
*
31752 GAG-GAGGGA
1 GAGAGAGAGA
* * *
31761 GGGAGGGAGG
1 GAGAGAGAGA
* *
31771 GAGGGAGGGA
1 GAGAGAGAGA
* * *
31781 G-GGGGGAGG
1 GAGAGAGAGA
31790 GAGAGAGAGA
1 GAGAGAGAGA
31800 GAGAGAGAGA
1 GAGAGAGAGA
*
31810 GAGAAAGAGA
1 GAGAGAGAGA
*
31820 -AG-GAGGGA
1 GAGAGAGAGA
* *
31828 GGGAGGGAGA
1 GAGAGAGAGA
* *
31838 GGGAGGGAGA
1 GAGAGAGAGA
*
31848 GAGAGGGACG-
1 GAGAGAGA-GA
* *
31858 GAGGGAGGGA
1 GAGAGAGAGA
*
31868 GAGAGAGGGA
1 GAGAGAGAGA
*
31878 GAGAGAGGGA
1 GAGAGAGAGA
*
31888 GAGAGAGGGA
1 GAGAGAGAGA
*
31898 GAGAGAGGGA
1 GAGAGAGAGA
* *
31908 GAGGGAAAGA
1 GAGAGAGAGA
*
31918 GAGGGAGAGA
1 GAGAGAGAGA
*
31928 GAGAG-GGGA
1 GAGAGAGAGA
* *
31937 AAGAGAGGGA
1 GAGAGAGAGA
* *
31947 GGGAGGGAGA
1 GAGAGAGAGA
31957 GAGAGAGAGA
1 GAGAGAGAGA
31967 G
1 G
31968 TGAAATTATA
Statistics
Matches: 199, Mismatches: 40, Indels: 14
0.79 0.16 0.06
Matches are distributed among these distances:
8 4 0.02
9 24 0.12
10 170 0.85
11 1 0.01
ACGTcount: A:0.39, C:0.00, G:0.60, T:0.00
Consensus pattern (10 bp):
GAGAGAGAGA
Found at i:32944 original size:14 final size:14
Alignment explanation
Indices: 32913--32983 Score: 65
Period size: 14 Copynumber: 5.1 Consensus size: 14
32903 AATAACGATT
* * *
32913 TAATGATTTACTAC
1 TAATAATTTAATAA
*
32927 TAATTATTTAATAA
1 TAATAATTTAATAA
32941 TAATAATGATT--TAA
1 TAATAAT--TTAATAA
*
32955 TAATGATTTAATAA
1 TAATAATTTAATAA
32969 TAATAATTTAATAA
1 TAATAATTTAATAA
32983 T
1 T
32984 GATTACTAAT
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
12 2 0.04
14 43 0.91
16 2 0.04
ACGTcount: A:0.48, C:0.03, G:0.04, T:0.45
Consensus pattern (14 bp):
TAATAATTTAATAA
Found at i:32955 original size:11 final size:11
Alignment explanation
Indices: 32941--33017 Score: 79
Period size: 11 Copynumber: 7.0 Consensus size: 11
32931 TATTTAATAA
32941 TAATAATGATT
1 TAATAATGATT
32952 TAATAATGATTT
1 TAATAATGA-TT
*
32964 AATAATAATAATT
1 --TAATAATGATT
32977 TAATAATGA-T
1 TAATAATGATT
* *
32987 TACTAATAATT
1 TAATAATGATT
32998 T--TAATGATT
1 TAATAATGATT
33007 TAATAATGATT
1 TAATAATGATT
33018 AGTAGTAATT
Statistics
Matches: 55, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
9 8 0.15
10 8 0.15
11 27 0.49
12 2 0.04
13 2 0.04
14 8 0.15
ACGTcount: A:0.47, C:0.01, G:0.06, T:0.45
Consensus pattern (11 bp):
TAATAATGATT
Found at i:33815 original size:7 final size:7
Alignment explanation
Indices: 33803--33830 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
33793 TAATATTGTT
33803 GTTTAGG
1 GTTTAGG
33810 GTTTAGG
1 GTTTAGG
33817 GTTTAGG
1 GTTTAGG
33824 GTTTAGG
1 GTTTAGG
33831 TTAATATCCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.14, C:0.00, G:0.43, T:0.43
Consensus pattern (7 bp):
GTTTAGG
Found at i:34713 original size:24 final size:24
Alignment explanation
Indices: 34686--34744 Score: 73
Period size: 27 Copynumber: 2.3 Consensus size: 24
34676 AGTTTTTTAC
34686 TATTAAATCATTATTAGTAATAAT
1 TATTAAATCATTATTAGTAATAAT
*
34710 TATTATAATTTCATTATTAGTAATCAT
1 TATTA-AA--TCATTATTAGTAATAAT
*
34737 TACTAAAT
1 TATTAAAT
34745 TATTTGTATC
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
24 6 0.20
25 2 0.07
26 2 0.07
27 20 0.67
ACGTcount: A:0.42, C:0.07, G:0.03, T:0.47
Consensus pattern (24 bp):
TATTAAATCATTATTAGTAATAAT
Found at i:34797 original size:13 final size:11
Alignment explanation
Indices: 34781--34857 Score: 61
Period size: 11 Copynumber: 6.7 Consensus size: 11
34771 ATAATAAAAA
34781 CATTATTACTAAT
1 CATTATTA--AAT
34794 CATTATTAAAT
1 CATTATTAAAT
34805 CATTAAAGTTCAAAT
1 CATT--A-TT-AAAT
34820 CATTA--AAAT
1 CATTATTAAAT
* *
34829 TATTAGT-AAT
1 CATTATTAAAT
34839 CATTATTAAAT
1 CATTATTAAAT
34850 CATTATTA
1 CATTATTA
34858 TCAAATCATT
Statistics
Matches: 54, Mismatches: 3, Indels: 16
0.74 0.04 0.22
Matches are distributed among these distances:
9 8 0.15
10 8 0.15
11 18 0.33
13 10 0.19
14 2 0.04
15 8 0.15
ACGTcount: A:0.44, C:0.10, G:0.03, T:0.43
Consensus pattern (11 bp):
CATTATTAAAT
Found at i:34809 original size:21 final size:20
Alignment explanation
Indices: 34785--34860 Score: 55
Period size: 21 Copynumber: 3.5 Consensus size: 20
34775 TAAAAACATT
34785 ATTACTAATCATTATTAAATC
1 ATTA-TAATCATTATTAAATC
* *
34806 ATTA-AAGTTCAAATCATTAAAATT
1 ATTATAA--TC--ATTATT-AAATC
34830 ATTAGTAATCATTATTAAATC
1 ATTA-TAATCATTATTAAATC
*
34851 ATTATTATCA
1 ATTATAATCA
34861 AATCATTAGC
Statistics
Matches: 43, Mismatches: 5, Indels: 15
0.68 0.08 0.24
Matches are distributed among these distances:
19 2 0.05
20 5 0.12
21 14 0.33
22 5 0.12
23 5 0.12
24 10 0.23
26 2 0.05
ACGTcount: A:0.45, C:0.11, G:0.03, T:0.42
Consensus pattern (20 bp):
ATTATAATCATTATTAAATC
Found at i:34854 original size:24 final size:24
Alignment explanation
Indices: 34781--34857 Score: 74
Period size: 24 Copynumber: 3.3 Consensus size: 24
34771 ATAATAAAAA
*
34781 CATTATTACTAATCATTATTAAAT
1 CATTATTAGTAATCATTATTAAAT
* *
34805 CATTA-AAGT--TCAAATCATTAAA-
1 CATTATTAGTAATC--ATTATTAAAT
34827 -ATTATTAGTAATCATTATTAAAT
1 CATTATTAGTAATCATTATTAAAT
34850 CATTATTA
1 CATTATTA
34858 TCAAATCATT
Statistics
Matches: 41, Mismatches: 5, Indels: 14
0.68 0.08 0.23
Matches are distributed among these distances:
21 6 0.15
22 11 0.27
23 10 0.24
24 14 0.34
ACGTcount: A:0.44, C:0.10, G:0.03, T:0.43
Consensus pattern (24 bp):
CATTATTAGTAATCATTATTAAAT
Found at i:37965 original size:18 final size:18
Alignment explanation
Indices: 37924--37976 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
37914 TTTTATGTTG
* *
37924 TTTAATTGAATGTTATATT
1 TTTAATTGAATATTAT-GT
37943 TTTAACTT-AATATTATGT
1 TTTAA-TTGAATATTATGT
37961 TTTAATTGAATATTAT
1 TTTAATTGAATATTAT
37977 ATATATTTAG
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
17 2 0.07
18 14 0.47
19 12 0.40
20 2 0.07
ACGTcount: A:0.34, C:0.02, G:0.08, T:0.57
Consensus pattern (18 bp):
TTTAATTGAATATTATGT
Found at i:43033 original size:23 final size:23
Alignment explanation
Indices: 43002--43056 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 23
42992 TAAGCTACCA
* * *
43002 AAAGACAGAGAAAAAATTGTTAT
1 AAAGGCAGAGAAAAAAGTGTCAT
* *
43025 AAAGGCAGAGATAAACGTGTCAT
1 AAAGGCAGAGAAAAAAGTGTCAT
43048 AAAGGCAGA
1 AAAGGCAGA
43057 AAACATGTCA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.51, C:0.09, G:0.24, T:0.16
Consensus pattern (23 bp):
AAAGGCAGAGAAAAAAGTGTCAT
Found at i:43065 original size:20 final size:22
Alignment explanation
Indices: 43023--43066 Score: 56
Period size: 20 Copynumber: 2.0 Consensus size: 22
43013 AAAAATTGTT
*
43023 ATAAAGGCAGAGATAAACGTGTC
1 ATAAAGGCA-AGATAAACATGTC
43046 ATAAAGGC-AGA-AAACATGTC
1 ATAAAGGCAAGATAAACATGTC
43066 A
1 A
43067 CAAATACATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 9 0.45
21 3 0.15
23 8 0.40
ACGTcount: A:0.48, C:0.14, G:0.23, T:0.16
Consensus pattern (22 bp):
ATAAAGGCAAGATAAACATGTC
Found at i:43691 original size:18 final size:18
Alignment explanation
Indices: 43668--43714 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
43658 ATTTATGAGA
43668 GAATTGAAAT-ATGTGAAG
1 GAATTGAAATCA-GTGAAG
*
43686 GAATTGGAATCAGTGAAG
1 GAATTGAAATCAGTGAAG
*
43704 GAATTGGAATC
1 GAATTGAAATC
43715 TGTCAGGAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 26 0.96
19 1 0.04
ACGTcount: A:0.40, C:0.04, G:0.30, T:0.26
Consensus pattern (18 bp):
GAATTGAAATCAGTGAAG
Found at i:43724 original size:17 final size:17
Alignment explanation
Indices: 43684--43748 Score: 103
Period size: 17 Copynumber: 3.8 Consensus size: 17
43674 AAATATGTGA
* *
43684 AGGAATTGGAATCAGTGA
1 AGGAATTGGAATCTGT-C
43702 AGGAATTGGAATCTGTC
1 AGGAATTGGAATCTGTC
43719 AGGAATTGGAATCTGTC
1 AGGAATTGGAATCTGTC
43736 AGGAATTGGAATC
1 AGGAATTGGAATC
43749 CAATTCTATA
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
17 30 0.67
18 15 0.33
ACGTcount: A:0.34, C:0.09, G:0.31, T:0.26
Consensus pattern (17 bp):
AGGAATTGGAATCTGTC
Found at i:44600 original size:36 final size:36
Alignment explanation
Indices: 44560--44639 Score: 92
Period size: 36 Copynumber: 2.2 Consensus size: 36
44550 AACCCGAACT
*
44560 CGACCCTACCC-AA-ATATCACACTTAAAAAACCGACC
1 CGACCCGACCCGAATATATCA-A-TTAAAAAACCGACC
* * *
44596 CGACCCGACCCGAATATATGAATTAGAAACCCGACC
1 CGACCCGACCCGAATATATCAATTAAAAAACCGACC
44632 CGACCCGA
1 CGACCCGA
44640 AATAAAAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
36 30 0.79
37 3 0.08
38 5 0.13
ACGTcount: A:0.38, C:0.38, G:0.12, T:0.12
Consensus pattern (36 bp):
CGACCCGACCCGAATATATCAATTAAAAAACCGACC
Found at i:51611 original size:31 final size:32
Alignment explanation
Indices: 51566--51641 Score: 84
Period size: 31 Copynumber: 2.4 Consensus size: 32
51556 ATTTACGCAG
*
51566 GATGGT-GAAGAGATTATAAGGAGAAAGAGAA
1 GATGGTGGAAGAGATTAGAAGGAGAAAGAGAA
* * *
51597 GATGGTGGAA-AGATTAGAATGAGGAAGATAA
1 GATGGTGGAAGAGATTAGAAGGAGAAAGAGAA
*
51628 GATGATGGAGAGAG
1 GATGGTGGA-AGAG
51642 TTTTTGAAGG
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
31 31 0.84
32 4 0.11
33 2 0.05
ACGTcount: A:0.45, C:0.00, G:0.38, T:0.17
Consensus pattern (32 bp):
GATGGTGGAAGAGATTAGAAGGAGAAAGAGAA
Found at i:53025 original size:29 final size:30
Alignment explanation
Indices: 52930--53022 Score: 152
Period size: 30 Copynumber: 3.1 Consensus size: 30
52920 GTGGTCCTTA
52930 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
52960 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
* * *
52990 TGGATAGTTACCG-GGGTCTTTGTGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
53019 TGGA
1 TGGA
53023 TAGGTCCTTC
Statistics
Matches: 60, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
29 18 0.30
30 42 0.70
ACGTcount: A:0.20, C:0.22, G:0.27, T:0.31
Consensus pattern (30 bp):
TGGACAGTTACCGAGGATCTTTATGACCTC
Found at i:53624 original size:21 final size:21
Alignment explanation
Indices: 53600--53642 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
53590 AAAGAAGATA
53600 TTGTATAAT-CTCTGAATAATT
1 TTGTA-AATGCTCTGAATAATT
* *
53621 TTGTAAATGTTTTGAATAATT
1 TTGTAAATGCTCTGAATAATT
53642 T
1 T
53643 AAATGTTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 3 0.16
21 16 0.84
ACGTcount: A:0.33, C:0.05, G:0.12, T:0.51
Consensus pattern (21 bp):
TTGTAAATGCTCTGAATAATT
Found at i:56971 original size:46 final size:46
Alignment explanation
Indices: 56884--56971 Score: 106
Period size: 46 Copynumber: 1.9 Consensus size: 46
56874 TTATATATAT
* * **
56884 ATAATTTCAAGCAGATATAAATAGTACATAAGTTTTTAAATGGTAC
1 ATAAGTTCAAGCAGATATAAATAGTACAAAAGTTTGAAAATGGTAC
**
56930 ATAAGTTCAAGCAGATATAAATAGTTTTAAAAG-TTGAAAATG
1 ATAAGTTCAAGCAGATATAAATAG-TACAAAAGTTTGAAAATG
56972 TGAATGTTTT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
46 30 0.86
47 5 0.14
ACGTcount: A:0.45, C:0.07, G:0.15, T:0.33
Consensus pattern (46 bp):
ATAAGTTCAAGCAGATATAAATAGTACAAAAGTTTGAAAATGGTAC
Found at i:66602 original size:30 final size:31
Alignment explanation
Indices: 66539--66607 Score: 95
Period size: 32 Copynumber: 2.2 Consensus size: 31
66529 TCTAAAACAG
* *
66539 AAAAACATACAACACCCAAAACTCCTATCAAA
1 AAAAAAATACAACACCCAAAAC-CCAATCAAA
*
66571 AAAAAAATACAACACCCAAAA-CCAATTAAA
1 AAAAAAATACAACACCCAAAACCCAATCAAA
66601 AAAAAAA
1 AAAAAAA
66608 AACACTAACT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
30 14 0.41
32 20 0.59
ACGTcount: A:0.65, C:0.25, G:0.00, T:0.10
Consensus pattern (31 bp):
AAAAAAATACAACACCCAAAACCCAATCAAA
Found at i:70569 original size:21 final size:21
Alignment explanation
Indices: 70544--70583 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
70534 AATGCTAGAG
*
70544 GGGTATCGATACCCTGTTACA
1 GGGTACCGATACCCTGTTACA
70565 GGGTACCGATACCCTGTTA
1 GGGTACCGATACCCTGTTA
70584 TAGTATTGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.23, C:0.25, G:0.25, T:0.28
Consensus pattern (21 bp):
GGGTACCGATACCCTGTTACA
Done.