Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006217.1 Hibiscus syriacus cultivar Beakdansim tig00014809_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: 70880
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:556 original size:3 final size:3
Alignment explanation
Indices: 517--594 Score: 81
Period size: 3 Copynumber: 26.0 Consensus size: 3
507 TTTGGGGTTT
* *
517 TTA TTT TTA TTA TT- TTA TTTA TTA CTA TT- TCTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA T-TA TTA TTA TTA TTA
*
562 TTA -TA TTA TTA TTA TTTA TTA TTA ATA TTA TTA
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA
595 CAGGCCCAAA
Statistics
Matches: 63, Mismatches: 6, Indels: 12
0.78 0.07 0.15
Matches are distributed among these distances:
2 5 0.08
3 51 0.81
4 7 0.11
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1705 original size:2 final size:2
Alignment explanation
Indices: 1698--1722 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1688 TAAATTAATA
1698 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1723 AGGTAAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2213 original size:2 final size:2
Alignment explanation
Indices: 2170--2195 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2160 TGTTTATAAA
2170 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
2196 TTGCTTTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4337 original size:43 final size:43
Alignment explanation
Indices: 4276--4361 Score: 118
Period size: 43 Copynumber: 2.0 Consensus size: 43
4266 TAGCTTTAGA
*
4276 GAAGTTAGGAGGGAAAGTTATCCCCTATACGTAAAGTTTTGTT
1 GAAGTTAGGAGGGAAAGTTATCCCATATACGTAAAGTTTTGTT
** * * *
4319 GAAGTTAGGATTGAAAGTTGTCTCATATATGTAAAGTTTTGTT
1 GAAGTTAGGAGGGAAAGTTATCCCATATACGTAAAGTTTTGTT
4362 TGATGCACCG
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.30, C:0.08, G:0.24, T:0.37
Consensus pattern (43 bp):
GAAGTTAGGAGGGAAAGTTATCCCATATACGTAAAGTTTTGTT
Found at i:4601 original size:15 final size:15
Alignment explanation
Indices: 4570--4621 Score: 74
Period size: 15 Copynumber: 3.7 Consensus size: 15
4560 CATTCACATC
4570 TTTGCA-TTTGC--A
1 TTTGCATTTTGCATA
*
4582 TTTGCATTTTGTATA
1 TTTGCATTTTGCATA
4597 TTTGCATTTTGCATA
1 TTTGCATTTTGCATA
4612 TTTGCATTTT
1 TTTGCATTTT
4622 TCGTTTATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
12 6 0.17
13 4 0.11
15 25 0.71
ACGTcount: A:0.17, C:0.12, G:0.13, T:0.58
Consensus pattern (15 bp):
TTTGCATTTTGCATA
Found at i:4607 original size:7 final size:7
Alignment explanation
Indices: 4570--4621 Score: 63
Period size: 7 Copynumber: 7.4 Consensus size: 7
4560 CATTCACATC
4570 TTTGCA-
1 TTTGCAT
4576 TTTGCA-
1 TTTGCAT
4582 TTTGCAT
1 TTTGCAT
*
4589 TTTGTAT
1 TTTGCAT
4596 ATTTGCAT
1 -TTTGCAT
4604 TTTGCAT
1 TTTGCAT
4611 ATTTGCAT
1 -TTTGCAT
4619 TTT
1 TTT
4622 TCGTTTATAT
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
6 12 0.29
7 16 0.39
8 13 0.32
ACGTcount: A:0.17, C:0.12, G:0.13, T:0.58
Consensus pattern (7 bp):
TTTGCAT
Found at i:7805 original size:6 final size:7
Alignment explanation
Indices: 7792--7821 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
7782 AAAAAAAACG
7792 ATGAAAA
1 ATGAAAA
7799 ATGAAAAA
1 ATG-AAAA
7807 ATGAAAA
1 ATGAAAA
7814 ATGAAAA
1 ATGAAAA
7821 A
1 A
7822 AAGAGAAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 15 0.68
8 7 0.32
ACGTcount: A:0.73, C:0.00, G:0.13, T:0.13
Consensus pattern (7 bp):
ATGAAAA
Found at i:7806 original size:8 final size:8
Alignment explanation
Indices: 7795--7845 Score: 52
Period size: 8 Copynumber: 6.6 Consensus size: 8
7785 AAAAACGATG
7795 AAAAATGA
1 AAAAATGA
7803 AAAAATG-
1 AAAAATGA
7810 AAAAATGA
1 AAAAATGA
*
7818 AAAAAAGA
1 AAAAATGA
* *
7826 GAAAAGGA
1 AAAAATGA
*
7834 AAGAAT-A
1 AAAAATGA
7841 AAAAA
1 AAAAA
7846 AATTTGAATC
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
7 12 0.34
8 23 0.66
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (8 bp):
AAAAATGA
Found at i:7810 original size:15 final size:15
Alignment explanation
Indices: 7792--7844 Score: 63
Period size: 15 Copynumber: 3.5 Consensus size: 15
7782 AAAAAAAACG
7792 ATGAAAAATGAAAAA
1 ATGAAAAATGAAAAA
7807 ATGAAAAATGAAAAA
1 ATGAAAAATGAAAAA
* * *
7822 AAGAGAAAAGGAAAGA
1 ATGA-AAAATGAAAAA
7838 AT-AAAAA
1 ATGAAAAA
7845 AAATTTGAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
14 4 0.12
15 19 0.58
16 10 0.30
ACGTcount: A:0.74, C:0.00, G:0.17, T:0.09
Consensus pattern (15 bp):
ATGAAAAATGAAAAA
Found at i:10375 original size:75 final size:75
Alignment explanation
Indices: 10252--10395 Score: 227
Period size: 75 Copynumber: 1.9 Consensus size: 75
10242 ATCAACAAAA
* *
10252 AAGAAAATGCTGGGGCATGCTGAAAGCCCATTTCAATCATAATCAGGAATATTGACGCATTTTGA
1 AAGAAAATGCTGGGGCATGCTGAAAGCCCATTTCAATCAAAATCAGGAATATTGACACATTTTGA
10317 ACGTTTGTAT
66 ACGTTTGTAT
* * *
10327 AAGAAAATGTTGGGGCATGTTGAAAGCCCATTTCAATCAAAAAT-AGGAATGTTGACACATTTTG
1 AAGAAAATGCTGGGGCATGCTGAAAGCCCATTTCAATC-AAAATCAGGAATATTGACACATTTTG
10391 AACGT
65 AACGT
10396 ACACATCAAC
Statistics
Matches: 63, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
75 59 0.94
76 4 0.06
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (75 bp):
AAGAAAATGCTGGGGCATGCTGAAAGCCCATTTCAATCAAAATCAGGAATATTGACACATTTTGA
ACGTTTGTAT
Found at i:10410 original size:75 final size:75
Alignment explanation
Indices: 10252--10424 Score: 224
Period size: 75 Copynumber: 2.3 Consensus size: 75
10242 ATCAACAAAA
* * * *
10252 AAGAAAATGCTGGGGCATGCTGAAAGCCCATTTCAATCATAATCAGGAATATTGACGCATTTTGA
1 AAGAAAATGTTGGGGCATGTTGAAAGCCCATTTCAATCAAAATCAGGAATATTGACACATTTTGA
****
10317 ACGTTTGTAT
66 ACGTACACAT
*
10327 AAGAAAATGTTGGGGCATGTTGAAAGCCCATTTCAATCAAAAAT-AGGAATGTTGACACATTTTG
1 AAGAAAATGTTGGGGCATGTTGAAAGCCCATTTCAATC-AAAATCAGGAATATTGACACATTTTG
10391 AACGTACACAT
65 AACGTACACAT
*
10402 CAA-CAAATGTTGGGGCATGTTGA
1 -AAGAAAATGTTGGGGCATGTTGA
10425 GCGTCCATAT
Statistics
Matches: 86, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
75 80 0.93
76 6 0.07
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (75 bp):
AAGAAAATGTTGGGGCATGTTGAAAGCCCATTTCAATCAAAATCAGGAATATTGACACATTTTGA
ACGTACACAT
Found at i:11763 original size:20 final size:22
Alignment explanation
Indices: 11738--11792 Score: 78
Period size: 20 Copynumber: 2.6 Consensus size: 22
11728 ACATCTACAT
*
11738 TCTTCAAAGATGAT-AGTT-TC
1 TCTTCAAAGATGATAAATTCTC
11758 TCTTCAAAGATGATAAATTCTC
1 TCTTCAAAGATGATAAATTCTC
*
11780 TTTTCAAAGATGA
1 TCTTCAAAGATGA
11793 AAGCTTTATT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 14 0.45
21 3 0.10
22 14 0.45
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.38
Consensus pattern (22 bp):
TCTTCAAAGATGATAAATTCTC
Found at i:12577 original size:36 final size:36
Alignment explanation
Indices: 12536--12651 Score: 106
Period size: 36 Copynumber: 3.2 Consensus size: 36
12526 ATGTATCTTA
12536 CTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCG
1 CTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCG
**** * ** * *
12572 CTTGAGGCAATTTTACTCGAAACAACAATTTATCTCA
1 CTTGAGATTGTTTTTCTTAAAACAA-AATTTGTCTCG
* * * *
12609 CTTGAGATTGTTTTTCTTAAAATAAGATTCGTCTTG
1 CTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCG
12645 CTTGAGA
1 CTTGAGA
12652 CAGTTTCACT
Statistics
Matches: 57, Mismatches: 22, Indels: 2
0.70 0.27 0.02
Matches are distributed among these distances:
36 31 0.54
37 26 0.46
ACGTcount: A:0.29, C:0.16, G:0.15, T:0.41
Consensus pattern (36 bp):
CTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCG
Found at i:12683 original size:73 final size:73
Alignment explanation
Indices: 12529--12676 Score: 206
Period size: 73 Copynumber: 2.0 Consensus size: 73
12519 AATAGTAATG
* * * * *
12529 TATCTTACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGGCAATTTTACTCGAAA
1 TATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTCGTCTCGCTTGAGACAATTTCACTAGAAA
*
12594 CAACAATT
66 CAAAAATT
* * * *
12602 TATCTCACTTGAGATTGTTTTTCTTAAAATAAGATTCGTCTTGCTTGAGACAGTTTCACTAGAAA
1 TATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTCGTCTCGCTTGAGACAATTTCACTAGAAA
12667 CAAAAATT
66 CAAAAATT
12675 TA
1 TA
12677 CGTCACTCGA
Statistics
Matches: 65, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
73 65 1.00
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.39
Consensus pattern (73 bp):
TATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTCGTCTCGCTTGAGACAATTTCACTAGAAA
CAAAAATT
Found at i:12895 original size:20 final size:20
Alignment explanation
Indices: 12833--12895 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
12823 CCAGAGAAAG
12833 TTCATAATGAGAAGAACTTA
1 TTCATAATGAGAAGAACTTA
**
12853 -TC-TGAA-GAGGAAGAA-GAA
1 TTCAT-AATGA-GAAGAACTTA
12871 GTTCATAATGAGAAGAACTTA
1 -TTCATAATGAGAAGAACTTA
12892 TTCA
1 TTCA
12896 ACCTTTAGCT
Statistics
Matches: 32, Mismatches: 4, Indels: 14
0.64 0.08 0.28
Matches are distributed among these distances:
18 4 0.12
19 10 0.31
20 14 0.44
21 4 0.12
ACGTcount: A:0.44, C:0.10, G:0.21, T:0.25
Consensus pattern (20 bp):
TTCATAATGAGAAGAACTTA
Found at i:12916 original size:123 final size:123
Alignment explanation
Indices: 12697--13146 Score: 677
Period size: 123 Copynumber: 3.7 Consensus size: 123
12687 TGGATCAACA
* * * *
12697 TTTCCAAAGGAAGTTCATAATGAGAAGAACCCATCTGAAGAAGAAGAAGAAGTTCATAATGAGAA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAA
* * * *
12762 GAACTTGGTCAACCTTTTGTTTGACTCTATCACAGAAGGAGATAGATCATCATACACT
66 GAACTTGTTCAACCTTTTGCTAGACTCTATCACAGAAGGAGATAGATCAGCATACACT
*
12820 TTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAA
* * * *
12885 GAACTTATTCAACCTTTAGCTAGACTCTATCACAGAAAGAGATAGATCAGCATAAACT
66 GAACTTGTTCAACCTTTTGCTAGACTCTATCACAGAAGGAGATAGATCAGCATACACT
*
12943 TTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAA
* * * * **
13008 GAACTTGTTCAACCTTTTGCTCGACGCTATCACAGAAGAAGATAGATTAGCAT-CAAA
66 GAACTTGTTCAACCTTTTGCTAGACTCTATCACAGAAGGAGATAGATCAGCATACACT
* * *
13065 TTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGGAGAAGAAGTCCATAATGAGAA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAA
*
13130 GAATTTGTTCAACCTTT
66 GAACTTGTTCAACCTTT
13147 CCTTAATTCA
Statistics
Matches: 299, Mismatches: 28, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
122 78 0.26
123 221 0.74
ACGTcount: A:0.40, C:0.15, G:0.20, T:0.25
Consensus pattern (123 bp):
TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAA
GAACTTGTTCAACCTTTTGCTAGACTCTATCACAGAAGGAGATAGATCAGCATACACT
Found at i:13017 original size:20 final size:20
Alignment explanation
Indices: 12955--13018 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
12945 TCCAGAGAAA
12955 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
* ***
12975 -ATC-TGAA-GAGGAAGAAGAA
1 GTTCAT-AATGA-GAAGAACTT
12994 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
13014 GTTCA
1 GTTCA
13019 ACCTTTTGCT
Statistics
Matches: 31, Mismatches: 8, Indels: 10
0.63 0.16 0.20
Matches are distributed among these distances:
18 3 0.10
19 10 0.32
20 15 0.48
21 3 0.10
ACGTcount: A:0.42, C:0.09, G:0.23, T:0.25
Consensus pattern (20 bp):
GTTCATAATGAGAAGAACTT
Found at i:13577 original size:3 final size:3
Alignment explanation
Indices: 13540--13626 Score: 103
Period size: 3 Copynumber: 30.3 Consensus size: 3
13530 TTGGGGTTTT
* * *
13540 TTA TTT TTA TTT TTA TTA TT- TTA TTTA TTA CTA TTA TTA TTA TT-
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA
13584 TTA TTA -TA TTA TTA TTA -TA TTA TTA TTA TTA TTA TTA -TA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
13627 ATGCCTAAAC
Statistics
Matches: 72, Mismatches: 6, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
2 10 0.14
3 59 0.82
4 3 0.04
ACGTcount: A:0.30, C:0.01, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:13590 original size:14 final size:14
Alignment explanation
Indices: 13544--13626 Score: 89
Period size: 14 Copynumber: 5.9 Consensus size: 14
13534 GGTTTTTTAT
*
13544 TTTTATTTTTATTA
1 TTTTATTATTATTA
*
13558 TTTTATTTATTACTA
1 TTTTA-TTATTATTA
13573 TTATTATTATT-TTA
1 TT-TTATTATTATTA
*
13587 TTATATTATTATTA
1 TTTTATTATTATTA
*
13601 TATTATTATTATTA
1 TTTTATTATTATTA
13615 TTATTA-TATTAT
1 TT-TTATTATTAT
13627 ATGCCTAAAC
Statistics
Matches: 58, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
13 7 0.12
14 31 0.53
15 17 0.29
16 3 0.05
ACGTcount: A:0.30, C:0.01, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTTATTATTATTA
Found at i:14895 original size:32 final size:32
Alignment explanation
Indices: 14847--14940 Score: 87
Period size: 31 Copynumber: 3.1 Consensus size: 32
14837 TATGTTATAA
14847 TTTAATCACTA-A-TTTTAATACTTTCATTTATT
1 TTTAAT-ACTATAGTTTTAATACTTT-ATTTATT
*
14879 TTTAACTAC-A-AGTTTTATTAC-TT-TTTATAT
1 TTTAA-TACTATAGTTTTAATACTTTATTTAT-T
14909 TTTAATACTATAGTTTTAAT--TTTATTTATT
1 TTTAATACTATAGTTTTAATACTTTATTTATT
14939 TT
1 TT
14941 AGTCACTATT
Statistics
Matches: 53, Mismatches: 2, Indels: 16
0.75 0.03 0.23
Matches are distributed among these distances:
29 8 0.15
30 12 0.23
31 17 0.32
32 15 0.28
33 1 0.02
ACGTcount: A:0.30, C:0.09, G:0.02, T:0.60
Consensus pattern (32 bp):
TTTAATACTATAGTTTTAATACTTTATTTATT
Found at i:15319 original size:15 final size:14
Alignment explanation
Indices: 15317--15351 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
15307 TACTTAATAT
*
15317 ATATATATATATTA
1 ATATATAAATATTA
15331 ATGATATAAATATTA
1 AT-ATATAAATATTA
15346 ATATAT
1 ATATAT
15352 TTTCTTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (14 bp):
ATATATAAATATTA
Found at i:24035 original size:40 final size:40
Alignment explanation
Indices: 23991--24072 Score: 146
Period size: 40 Copynumber: 2.0 Consensus size: 40
23981 ACCGTAGTGC
*
23991 TACACATAAGGTCGTTCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
*
24031 TACACATAAGGTTGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
24071 TA
1 TA
24073 TAAACCTGCA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.26
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:31518 original size:21 final size:21
Alignment explanation
Indices: 31492--31536 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
31482 GATTTCTGGG
* *
31492 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
31513 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
31534 CAA
1 CAA
31537 ACGAACAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:32608 original size:31 final size:31
Alignment explanation
Indices: 32422--32595 Score: 303
Period size: 31 Copynumber: 5.6 Consensus size: 31
32412 AGGGTCGAGG
32422 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
32453 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
32484 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
32515 GTTTACCTATGTCCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
32546 GTTTACCTATGTCCTTTGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
32577 GATTACCTAGGTTCTTCGG
1 GTTTACCTATGTTCTTCGG
32596 AATCTATAGA
Statistics
Matches: 137, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 137 1.00
ACGTcount: A:0.19, C:0.20, G:0.23, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:35793 original size:21 final size:21
Alignment explanation
Indices: 35767--35811 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
35757 GATTTCTGGG
* *
35767 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
35788 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
35809 CAA
1 CAA
35812 ACGAACAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:36764 original size:31 final size:31
Alignment explanation
Indices: 36694--36848 Score: 251
Period size: 31 Copynumber: 5.0 Consensus size: 31
36684 AGGGTCGAGG
36694 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
36725 G-TTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
36755 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
36786 GTTTACCTATGTCCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
36817 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
36848 G
1 G
36849 GTCCTTCGGG
Statistics
Matches: 117, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
30 30 0.26
31 86 0.74
32 1 0.01
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.37
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:38127 original size:23 final size:19
Alignment explanation
Indices: 38097--38151 Score: 65
Period size: 19 Copynumber: 2.7 Consensus size: 19
38087 TTGTGCATAA
38097 GGTATCGATACCTCCCTTGAATT
1 GGTATCGATACC-CCC-TG-A-T
38120 GGTATCGATACCCCCTGAT
1 GGTATCGATACCCCCTGAT
*
38139 GGTACCGATACCC
1 GGTATCGATACCC
38152 TCTTCGGGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 13 0.42
20 1 0.03
21 2 0.06
22 3 0.10
23 12 0.39
ACGTcount: A:0.22, C:0.31, G:0.20, T:0.27
Consensus pattern (19 bp):
GGTATCGATACCCCCTGAT
Found at i:40161 original size:20 final size:20
Alignment explanation
Indices: 40112--40159 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
40102 TGATGTTTTG
40112 TGGATGTTT-AAGTTTGCTT
1 TGGATGTTTGAAGTTTGCTT
* *
40131 TGAATGGTTTGAA-TTTGTTT
1 TGGAT-GTTTGAAGTTTGCTT
40151 TGGATGTTT
1 TGGATGTTT
40160 TGGATAGTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 8 0.33
20 14 0.58
21 2 0.08
ACGTcount: A:0.17, C:0.02, G:0.27, T:0.54
Consensus pattern (20 bp):
TGGATGTTTGAAGTTTGCTT
Found at i:45625 original size:132 final size:132
Alignment explanation
Indices: 45466--45729 Score: 492
Period size: 132 Copynumber: 2.0 Consensus size: 132
45456 ACTAAACAAT
*
45466 GCCATTAATGTCCAGTGTTTCATTTCAGACTGATTTTGCTTCTTGATTATAGAAAGTGGATTCAT
1 GCCATTAATGTCCAGTGTTTCATTTCAGACTGAATTTGCTTCTTGATTATAGAAAGTGGATTCAT
* *
45531 TGGTTGTTACACATAGCAACCAAGTTAACACAAGCTGCAAAATTTTATTAAAGCTAAGATCTAAA
66 TGGTTGTTACACATACCAACCAAGTTAACACAAGCTGCAAAATTTTATTAAAACTAAGATCTAAA
45596 AC
131 AC
45598 GCCATTAATGTCCAGTGTTTCATTTCAGACTGAATTTGCTTCTTGATTATAGAAAGTGGATTCAT
1 GCCATTAATGTCCAGTGTTTCATTTCAGACTGAATTTGCTTCTTGATTATAGAAAGTGGATTCAT
*
45663 TGGTTGTTACACATACCATCCAAGTTAACACAAGCTGCAAAATTTTATTAAAACTAAGATCTAAA
66 TGGTTGTTACACATACCAACCAAGTTAACACAAGCTGCAAAATTTTATTAAAACTAAGATCTAAA
45728 AC
131 AC
45730 TTTTAGTTTT
Statistics
Matches: 128, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
132 128 1.00
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (132 bp):
GCCATTAATGTCCAGTGTTTCATTTCAGACTGAATTTGCTTCTTGATTATAGAAAGTGGATTCAT
TGGTTGTTACACATACCAACCAAGTTAACACAAGCTGCAAAATTTTATTAAAACTAAGATCTAAA
AC
Found at i:47152 original size:16 final size:16
Alignment explanation
Indices: 47128--47158 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
47118 ACCGACTATA
47128 ATATAATGAATTATTT
1 ATATAATGAATTATTT
*
47144 ATATTATGAATTATT
1 ATATAATGAATTATT
47159 AGATTTTGTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (16 bp):
ATATAATGAATTATTT
Found at i:47176 original size:22 final size:22
Alignment explanation
Indices: 47151--47192 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
47141 TTTATATTAT
* *
47151 GAATTATTAGATTTTGTGTTTC
1 GAATTATTAAATTTTATGTTTC
*
47173 GAATTTTTAAATTTTATGTT
1 GAATTATTAAATTTTATGTT
47193 CGGATATTAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.26, C:0.02, G:0.14, T:0.57
Consensus pattern (22 bp):
GAATTATTAAATTTTATGTTTC
Found at i:48612 original size:29 final size:29
Alignment explanation
Indices: 48580--48651 Score: 92
Period size: 29 Copynumber: 2.5 Consensus size: 29
48570 TTTCATTTAA
*
48580 GTACTTAAAGTATTTTTCGGTCAAAATAG
1 GTACTTAAAGTATTTTTCGATCAAAATAG
* * *
48609 GTACCTAAAGTATTTTTTGATCAAAGTAG
1 GTACTTAAAGTATTTTTCGATCAAAATAG
48638 GTA-TATAAAGTATT
1 GTACT-TAAAGTATT
48652 AATTTTTTTC
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.36, C:0.08, G:0.17, T:0.39
Consensus pattern (29 bp):
GTACTTAAAGTATTTTTCGATCAAAATAG
Found at i:48779 original size:32 final size:30
Alignment explanation
Indices: 48733--48807 Score: 96
Period size: 32 Copynumber: 2.4 Consensus size: 30
48723 TAGAAAATTG
* *
48733 AATACTTTAAATACTTATTTTGACCAAAAAA
1 AATAATTTAGATACTTATTTTGA-CAAAAAA
*
48764 AATAAATTTAGATACTTATTTTGATAAAAAA
1 AAT-AATTTAGATACTTATTTTGACAAAAAA
*
48795 AATACTTTAGATA
1 AATAATTTAGATA
48808 TTTAGATTAA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
30 9 0.23
31 12 0.31
32 18 0.46
ACGTcount: A:0.49, C:0.08, G:0.05, T:0.37
Consensus pattern (30 bp):
AATAATTTAGATACTTATTTTGACAAAAAA
Found at i:55607 original size:24 final size:24
Alignment explanation
Indices: 55580--55646 Score: 62
Period size: 24 Copynumber: 2.8 Consensus size: 24
55570 GGTAAATGAC
* * **
55580 AAAATAAAATATTGAATGCTAAAA
1 AAAATAAAAAAATGAATAATAAAA
*
55604 AAAAGAAAAAAATGAATAATAAAA
1 AAAATAAAAAAATGAATAATAAAA
* * *
55628 CAAATAAATAAATAAATAA
1 AAAATAAAAAAATGAATAA
55647 ATAATAATGT
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.72, C:0.03, G:0.06, T:0.19
Consensus pattern (24 bp):
AAAATAAAAAAATGAATAATAAAA
Found at i:55637 original size:16 final size:16
Alignment explanation
Indices: 55609--55650 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
55599 TAAAAAAAAG
*
55609 AAAAAAATGAAT-AAT
1 AAAAAAATAAATAAAT
55624 AAAACAAATAAATAAAT
1 AAAA-AAATAAATAAAT
*
55641 AAATAAATAA
1 AAAAAAATAA
55651 TAATGTATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 4 0.17
16 13 0.57
17 6 0.26
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.19
Consensus pattern (16 bp):
AAAAAAATAAATAAAT
Found at i:56429 original size:21 final size:22
Alignment explanation
Indices: 56403--56461 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
56393 GGGCCTAAAA
56403 AATAATTATATATAAAT-TAAT
1 AATAATTATATATAAATATAAT
* *
56424 AATAATAATACTAAAAATATAAT
1 AATAATTATA-TATAAATATAAT
56447 AAGTAATTAT-TATAA
1 AA-TAATTATATATAA
56462 TAATAGTAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
21 9 0.29
22 10 0.32
23 6 0.19
24 6 0.19
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (22 bp):
AATAATTATATATAAATATAAT
Found at i:68279 original size:23 final size:23
Alignment explanation
Indices: 68253--68313 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
68243 CTCATATAAA
*
68253 TGCACCGAAGTGCCACATAGAAT
1 TGCACCGTAGTGCCACATAGAAT
* *
68276 TGCACCGTAGTGCCGCGTAGAAT
1 TGCACCGTAGTGCCACATAGAAT
68299 TGCACCGTAGTGCCA
1 TGCACCGTAGTGCCA
68314 TATAAAAATG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.26, C:0.28, G:0.26, T:0.20
Consensus pattern (23 bp):
TGCACCGTAGTGCCACATAGAAT
Found at i:68500 original size:103 final size:103
Alignment explanation
Indices: 68329--68647 Score: 572
Period size: 103 Copynumber: 3.1 Consensus size: 103
68319 AAATGTCCAT
* *
68329 AAGGACCACATATCATTCCTTAAGAATCATATACATAT-ACTAGAGATCAAGTATGTGTCTCACC
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAG-GATCAAGTATGTGTCTCACC
68393 AGACTTCACACATGTTCCAAAGAATACATATATGTCCCG
65 AGACTTCACACATGTTCCAAAGAATACATATATGTCCCG
68432 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
*
68497 GACTTCACACATATTCCAAAGAATAC--ATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
68533 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
68598 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
68636 AATGACCACATA
1 AAGGACCACATA
68648 GACCCTCGAC
Statistics
Matches: 208, Mismatches: 5, Indels: 6
0.95 0.02 0.03
Matches are distributed among these distances:
101 100 0.48
103 105 0.50
104 3 0.01
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Done.