Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005427.1 Hibiscus syriacus cultivar Beakdansim tig00012443_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: 61615
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:7919 original size:23 final size:23
Alignment explanation
Indices: 7893--7940 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
7883 CGTGCGCGTG
7893 CAATCGAAACTCAGTGCTACGTA
1 CAATCGAAACTCAGTGCTACGTA
7916 CAATCGAAACTCAGTGCTACGTA
1 CAATCGAAACTCAGTGCTACGTA
7939 CA
1 CA
7941 GAATCCATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.35, C:0.27, G:0.17, T:0.21
Consensus pattern (23 bp):
CAATCGAAACTCAGTGCTACGTA
Found at i:16182 original size:32 final size:32
Alignment explanation
Indices: 16097--16232 Score: 123
Period size: 32 Copynumber: 4.2 Consensus size: 32
16087 TGCTCTTGTG
* * *
16097 CATTATCTGAATGCAACACTAACTTTGATGTA
1 CATTATCTGAATGCAACACTGACTCTGCTGTA
* * *
16129 CATTATCTAAATACAACACTGACTCTGCTATA
1 CATTATCTGAATGCAACACTGACTCTGCTGTA
* * *
16161 CATTATCTGAATGTAATACTGAC-CATGTTG-A
1 CATTATCTGAATGCAACACTGACTC-TGCTGTA
* * * *
16192 GCATTATCTGAATGTAATACTGACTCTACTGTG
1 -CATTATCTGAATGCAACACTGACTCTGCTGTA
16225 CATTATCT
1 CATTATCT
16233 AAATATTATA
Statistics
Matches: 85, Mismatches: 15, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
31 2 0.02
32 82 0.96
33 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.35
Consensus pattern (32 bp):
CATTATCTGAATGCAACACTGACTCTGCTGTA
Found at i:17833 original size:53 final size:52
Alignment explanation
Indices: 17765--17868 Score: 181
Period size: 53 Copynumber: 2.0 Consensus size: 52
17755 AAACCATCAC
* *
17765 TTTTTCTTGCAAACATAGAACCTAAAGCCTTGATTCATTAAAAATATGTTTT
1 TTTTTCTTACAAACATAGAACCTAAAGCCTTGATTCATTAAAAAGATGTTTT
17817 TTTTCTCTTACAAACATAGAACCTAAAGCCTTGATTCATTAAAAAGATGTTT
1 TTTT-TCTTACAAACATAGAACCTAAAGCCTTGATTCATTAAAAAGATGTTT
17869 CTAGAGGAAT
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
52 4 0.08
53 45 0.92
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (52 bp):
TTTTTCTTACAAACATAGAACCTAAAGCCTTGATTCATTAAAAAGATGTTTT
Found at i:18314 original size:243 final size:244
Alignment explanation
Indices: 17847--18315 Score: 708
Period size: 243 Copynumber: 1.9 Consensus size: 244
17837 ACCTAAAGCC
** *
17847 TTGATTCATTAAAAAGATGTTTCTAGAGGAATTATGAACAAATTTGAAGCATAAAAATAGGCTCA
1 TTGATTCATTAAAAAGATGTTGATAGAGGAATTATAAACAAATTTGAAGCATAAAAATAGGCTCA
* * * * * *
17912 AGATATTACCTTTGCTATGGAACTTTGAGAGGAAAAACAGGGGAAAAGAGAAGGAAGAAGAAGTG
66 AGATATTACCTTTGCTATGGAACTTAGAGAGGAAAAACAGGGAAAAAAAGAAAGAAGAAAAAGTA
* * * *
17977 AAGAGGATAAGAAGATGAAAAGATAATAGAGTCTTCATCTTTGGAAAAATGGGAAATTACTCAAT
131 AAGAGAATAAGAAGATGAAAAGATAATAAAGTCTTCATCTTAGAAAAAATGGGAAATTACTCAAT
*
18042 TGGCCATTCCTCATCTTTCAACTAAACAAAACTCTCATTTTATGGCTAA
196 TGGCCAATCCTCATCTTTCAACTAAACAAAACTCTCATTTTATGGCTAA
* * * *
18091 TTGATTCATTAAAAATATGTTGATGGAGGAATTATAAACGAATTTGAAGCCTAAAAATAGGCTCA
1 TTGATTCATTAAAAAGATGTTGATAGAGGAATTATAAACAAATTTGAAGCATAAAAATAGGCTCA
* * *
18156 ATATATTACCTTTTCTATGGAACTTAGAGAGGAACAAA-A-GGAAAAAAAGAAAGAAGAAAAATT
66 AGATATTACCTTTGCTATGGAACTTAGAGAGGAA-AAACAGGGAAAAAAAGAAAGAAGAAAAAGT
18219 AAAGAGAATAAGAAGATGAAAAGATAATAAAGTCTTCATCTTAGAAAAAATGGGAAATTACTCAA
130 AAAGAGAATAAGAAGATGAAAAGATAATAAAGTCTTCATCTTAGAAAAAATGGGAAATTACTCAA
* *
18284 TTGGTCAATCCTCATCTTTCTACTAAACAAAA
195 TTGGCCAATCCTCATCTTTCAACTAAACAAAA
18316 ATGGGAATTA
Statistics
Matches: 201, Mismatches: 23, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
243 108 0.54
244 90 0.45
245 3 0.01
ACGTcount: A:0.44, C:0.11, G:0.18, T:0.26
Consensus pattern (244 bp):
TTGATTCATTAAAAAGATGTTGATAGAGGAATTATAAACAAATTTGAAGCATAAAAATAGGCTCA
AGATATTACCTTTGCTATGGAACTTAGAGAGGAAAAACAGGGAAAAAAAGAAAGAAGAAAAAGTA
AAGAGAATAAGAAGATGAAAAGATAATAAAGTCTTCATCTTAGAAAAAATGGGAAATTACTCAAT
TGGCCAATCCTCATCTTTCAACTAAACAAAACTCTCATTTTATGGCTAA
Found at i:22316 original size:31 final size:31
Alignment explanation
Indices: 22261--22343 Score: 105
Period size: 31 Copynumber: 2.7 Consensus size: 31
22251 ATTAAAAGTT
* * *
22261 TATAAAAA-AATTATAAGTTTTAGAAAACAC
1 TATAAAAATCATTAAAAGTTATAGAAAACAC
* *
22291 TCTAAAAATCATTAAAAGTTATAGAAAACGC
1 TATAAAAATCATTAAAAGTTATAGAAAACAC
*
22322 TATAAAAATCATTAAAAATTAT
1 TATAAAAATCATTAAAAGTTAT
22344 TTTTATAATT
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
30 7 0.16
31 38 0.84
ACGTcount: A:0.55, C:0.08, G:0.06, T:0.30
Consensus pattern (31 bp):
TATAAAAATCATTAAAAGTTATAGAAAACAC
Found at i:23455 original size:2 final size:2
Alignment explanation
Indices: 23450--23480 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
23440 TTTTTTCCAA
23450 AT AT AT 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 AT AT AT A
23481 AAGTAACATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:28998 original size:3 final size:3
Alignment explanation
Indices: 28990--29042 Score: 56
Period size: 3 Copynumber: 17.7 Consensus size: 3
28980 TTGTTTTTAA
* *
28990 TAT TAT TAT TAA TA- TAT TAT TAT AAT T-T TATT TAT TAT TAT ATAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT -TAT
29035 TAT TAT TA
1 TAT TAT TA
29043 AATAATTACA
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
2 4 0.09
3 33 0.77
4 6 0.14
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:29021 original size:25 final size:27
Alignment explanation
Indices: 28987--29040 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 27
28977 CATTTGTTTT
28987 TAATATTA-TTATTA-ATATATTATTA
1 TAATATTATTTATTATATATATTATTA
*
29012 TAATTTTATTTATTATTATATATTATTA
1 TAATATTATTTATTA-TATATATTATTA
29040 T
1 T
29041 TAAATAATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
25 7 0.28
26 6 0.24
28 12 0.48
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (27 bp):
TAATATTATTTATTATATATATTATTA
Found at i:29035 original size:10 final size:10
Alignment explanation
Indices: 28993--29040 Score: 64
Period size: 10 Copynumber: 4.9 Consensus size: 10
28983 TTTTTAATAT
28993 TATTATTAATA
1 TATTATT-ATA
29004 TATTATTATA
1 TATTATTATA
*
29014 -ATT-TTATT
1 TATTATTATA
29022 TATTATTATA
1 TATTATTATA
29032 TATTATTAT
1 TATTATTAT
29041 TAAATAATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
8 4 0.12
9 6 0.18
10 16 0.48
11 7 0.21
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (10 bp):
TATTATTATA
Found at i:30347 original size:29 final size:28
Alignment explanation
Indices: 30314--30376 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 28
30304 TTTTTACAAG
* *
30314 TTTTATTTA-TTTTAAATATATAGTTTTAA
1 TTTTATTCATTTTTAAAT-TATA-TGTTAA
*
30343 TTTTATTCATTTTTTAATTATATGTTAA
1 TTTTATTCATTTTTAAATTATATGTTAA
30371 TTTTAT
1 TTTTAT
30377 ATGTTTACTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
28 11 0.37
29 12 0.40
30 7 0.23
ACGTcount: A:0.30, C:0.02, G:0.03, T:0.65
Consensus pattern (28 bp):
TTTTATTCATTTTTAAATTATATGTTAA
Found at i:30730 original size:29 final size:29
Alignment explanation
Indices: 30697--30753 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
30687 ATATTTCTAA
30697 ATAAATAAATATTTTATTT-ATAAATATAT
1 ATAAATAAATATTTT-TTTCATAAATATAT
* *
30726 ATAAATTAATATTTTTTTCATAATTATA
1 ATAAATAAATATTTTTTTCATAAATATA
30754 ATTTTGAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 3 0.12
29 22 0.88
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (29 bp):
ATAAATAAATATTTTTTTCATAAATATAT
Found at i:34593 original size:15 final size:15
Alignment explanation
Indices: 34573--34604 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
34563 GATTAATACC
34573 TTTTGCATACATGCA
1 TTTTGCATACATGCA
*
34588 TTTTGCATACATTCA
1 TTTTGCATACATGCA
34603 TT
1 TT
34605 ATTCATTGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATGCA
Found at i:38407 original size:8 final size:9
Alignment explanation
Indices: 38380--38410 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
38370 AAATGGCAAT
38380 CATTCTTTA
1 CATTCTTTA
38389 CATTCTTTA
1 CATTCTTTA
38398 CATT-TTTA
1 CATTCTTTA
38406 CATTC
1 CATTC
38411 ATTATTTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.38
9 13 0.62
ACGTcount: A:0.23, C:0.23, G:0.00, T:0.55
Consensus pattern (9 bp):
CATTCTTTA
Found at i:41949 original size:21 final size:19
Alignment explanation
Indices: 41925--41975 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 19
41915 ATTATGCTTG
41925 AAGAAAAAATGAAATGAAAAA
1 AAGAAAAAA-GAAA-GAAAAA
41946 AAGAGAAAAAGAAAGAAAAA
1 AAGA-AAAAAGAAAGAAAAA
41966 AAGAAGAAAA
1 AAGAA-AAAA
41976 AAGGAGGGTC
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
19 1 0.04
20 14 0.50
21 8 0.29
22 5 0.18
ACGTcount: A:0.78, C:0.00, G:0.18, T:0.04
Consensus pattern (19 bp):
AAGAAAAAAGAAAGAAAAA
Found at i:41960 original size:12 final size:11
Alignment explanation
Indices: 41925--41978 Score: 51
Period size: 11 Copynumber: 4.9 Consensus size: 11
41915 ATTATGCTTG
41925 AAGAAAAAATGA
1 AAGAAAAAA-GA
41937 AATGAAAAAA-A
1 AA-GAAAAAAGA
*
41948 GAG-AAAAAGA
1 AAGAAAAAAGA
41958 AAGAAAAAA-A
1 AAGAAAAAAGA
41968 GAAGAAAAAAG
1 -AAGAAAAAAG
41979 GAGGGTCAGG
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
9 5 0.14
10 5 0.14
11 16 0.46
12 2 0.06
13 7 0.20
ACGTcount: A:0.78, C:0.00, G:0.19, T:0.04
Consensus pattern (11 bp):
AAGAAAAAAGA
Found at i:41976 original size:21 final size:22
Alignment explanation
Indices: 41925--41976 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
41915 ATTATGCTTG
*
41925 AAGAA-AAAATGAAATGAAAAA
1 AAGAAGAAAAAGAAATGAAAAA
41946 AAG-AGAAAAAGAAA-GAAAAA
1 AAGAAGAAAAAGAAATGAAAAA
41966 AAGAAGAAAAA
1 AAGAAGAAAAA
41977 AGGAGGGTCA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 10 0.36
21 18 0.64
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.04
Consensus pattern (22 bp):
AAGAAGAAAAAGAAATGAAAAA
Found at i:43682 original size:113 final size:113
Alignment explanation
Indices: 43484--44496 Score: 1767
Period size: 113 Copynumber: 9.0 Consensus size: 113
43474 TTGCAAAGAT
43484 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
43549 AGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
*
43597 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
43662 AGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
* *
43710 TCAAATCCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGATCTCATCTGA
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
* * *
43775 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGT
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
** * * * *
43823 TTGAATTCATCATTTGATGGATCAGCTTTTCCAGAGAGAGTTCATAATAAGAAGAACTCATCTGA
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
43888 AGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
*
43936 TCAAATCCATCACTTGATGGATCAGTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
* * * *
44001 ACAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGT
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
** * * * *
44049 TTGAATTCATCATTTGATGGATCAGCTTTTCCAGAGAGAGTTCATAATAAGAAGAACTCATCTGA
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
44114 AGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
44162 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
44227 AGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
* * * *
44275 TTAAATTCATCACTTGATGGATCAGCTTTTCCAAAGAAAATTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
44340 AGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
44388 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
*
44453 AG-AGGAATAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTT
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTT
44497 GCATGACTCT
Statistics
Matches: 845, Mismatches: 55, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
112 41 0.05
113 804 0.95
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.28
Consensus pattern (113 bp):
TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
AGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
Found at i:44625 original size:104 final size:104
Alignment explanation
Indices: 44476--44731 Score: 299
Period size: 103 Copynumber: 2.4 Consensus size: 104
44466 GTTCATAATG
* * *
44476 AGAAGAGCTTGTTCAACCTTTGCATGACTCTATCATAAAAAGAGATAGA-TCAGCATAAAC-TTT
1 AGAAGAGCTTGTTCAACCTTTGCATGACTCTATCACAGAAGGAGATAGACT-AGCATAAACATTT
44539 TCCAAAGAAAGT-TT-ATAATGAGAAGAACTAATCTGAAG-A-A
65 T-C--AG-AAGTGTTCATAATGAGAAGAACTAATCTGAAGAATA
* *
44579 AGAAGAGCTTGTTCGACCTTTTGCATGACTCTATCACAGAAGGAGATAGACTAGCATCAACATTT
1 AGAAGAGCTTGTTCAACC-TTTGCATGACTCTATCACAGAAGGAGATAGACTAGCATAAACATTT
*
44644 TCAGAAGTGTTCATAATGAGAAGAACTCATCTGAAGAATA
65 TCAGAAGTGTTCATAATGAGAAGAACTAATCTGAAGAATA
* * * *
44684 AGAAGCAGAACTTATTCAACCTTTACATGATTATATCACAGAAGGAGA
1 AGAAG-AG--CTTGTTCAACCTTTGCATGACTCTATCACAGAAGGAGA
44732 CAATTGTCAT
Statistics
Matches: 132, Mismatches: 11, Indels: 16
0.83 0.07 0.10
Matches are distributed among these distances:
101 4 0.03
102 4 0.03
103 40 0.30
104 38 0.29
105 11 0.08
106 2 0.02
107 24 0.18
108 9 0.07
ACGTcount: A:0.40, C:0.16, G:0.18, T:0.26
Consensus pattern (104 bp):
AGAAGAGCTTGTTCAACCTTTGCATGACTCTATCACAGAAGGAGATAGACTAGCATAAACATTTT
CAGAAGTGTTCATAATGAGAAGAACTAATCTGAAGAATA
Found at i:44941 original size:3 final size:3
Alignment explanation
Indices: 44933--44985 Score: 56
Period size: 3 Copynumber: 17.7 Consensus size: 3
44923 TTGTTTTTAA
* *
44933 TAT TAT TAT TAA TA- TAT TAT TAT AAT T-T TATT TAT TAT TAT ATAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT -TAT
44978 TAT TAT TA
1 TAT TAT TA
44986 AATAATTACA
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
2 4 0.09
3 33 0.77
4 6 0.14
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:44964 original size:25 final size:27
Alignment explanation
Indices: 44930--44983 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 27
44920 CATTTGTTTT
44930 TAATATTA-TTATTA-ATATATTATTA
1 TAATATTATTTATTATATATATTATTA
*
44955 TAATTTTATTTATTATTATATATTATTA
1 TAATATTATTTATTA-TATATATTATTA
44983 T
1 T
44984 TAAATAATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
25 7 0.28
26 6 0.24
28 12 0.48
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (27 bp):
TAATATTATTTATTATATATATTATTA
Found at i:44978 original size:10 final size:10
Alignment explanation
Indices: 44936--44983 Score: 64
Period size: 10 Copynumber: 4.9 Consensus size: 10
44926 TTTTTAATAT
44936 TATTATTAATA
1 TATTATT-ATA
44947 TATTATTATA
1 TATTATTATA
*
44957 -ATT-TTATT
1 TATTATTATA
44965 TATTATTATA
1 TATTATTATA
44975 TATTATTAT
1 TATTATTAT
44984 TAAATAATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
8 4 0.12
9 6 0.18
10 16 0.48
11 7 0.21
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (10 bp):
TATTATTATA
Found at i:46244 original size:29 final size:28
Alignment explanation
Indices: 46212--46274 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 28
46202 TTTTTACAGG
* *
46212 TTTTATTTATT-TTAAATATATAGTTTTAA
1 TTTTATTCATTGTTAAAT-TATA-TGTTAA
*
46241 TTTTATTCATTGTTTAATTATATGTTAA
1 TTTTATTCATTGTTAAATTATATGTTAA
46269 TTTTAT
1 TTTTAT
46275 ATGTTTTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
28 11 0.37
29 14 0.47
30 5 0.17
ACGTcount: A:0.30, C:0.02, G:0.05, T:0.63
Consensus pattern (28 bp):
TTTTATTCATTGTTAAATTATATGTTAA
Found at i:46629 original size:29 final size:30
Alignment explanation
Indices: 46596--46653 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
46586 ATATTTCTAA
46596 ATAAATAAATATTTTGTTT-ATAAATATAT
1 ATAAATAAATATTTTGTTTCATAAATATAT
* * *
46625 ATAAATTAATATTTTTTTTCATAATTATA
1 ATAAATAAATATTTTGTTTCATAAATATA
46654 ATTTTGAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 17 0.68
30 8 0.32
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (30 bp):
ATAAATAAATATTTTGTTTCATAAATATAT
Found at i:53359 original size:155 final size:152
Alignment explanation
Indices: 53046--53326 Score: 449
Period size: 155 Copynumber: 1.8 Consensus size: 152
53036 TTTTGTAAGA
* * *
53046 AAAATAATTTAACTTATATATATATATTTTATAAATAAGATATTTATTTATTTAGAAATATCAGA
1 AAAATAAATTAAATTATATATATATATTTTATAAATAAGATATTTATTTATTTAAAAATATCAGA
53111 AAAAGACTTCTAGTTGCTTTAAGACAGTCATTTTCTTAATATTAAAAAATAAATAAATATTAATA
66 AAAAGACTTCTAGTTGCTTTAAGACAGTCATTTTCTTAATATTAAAAAATAAATAAATATTAATA
**
53176 AAATATTTTTCTAAAAATAACT
131 AAATATAATTCTAAAAATAACT
*
53198 AAAATAAATTAAATTATATATATATATATTTATGAAAGTAGGATATTTAGTTTA-TTAAAAATAT
1 AAAATAAATTAAATTATATATATATAT-TTTAT-AAA-TAAGATATTTA-TTTATTTAAAAATAT
*
53262 CAGAAAATGACTTCTAGTTGCTTTAAGACAGTCATTTTCTTAATATT-AAAAATAAATAAATATT
62 CAGAAAAAGACTTCTAGTTGCTTTAAGACAGTCATTTTCTTAATATTAAAAAATAAATAAATATT
53326 A
127 A
53327 TTATTTAATC
Statistics
Matches: 120, Mismatches: 5, Indels: 6
0.92 0.04 0.05
Matches are distributed among these distances:
152 25 0.21
153 5 0.04
154 21 0.17
155 65 0.54
156 4 0.03
ACGTcount: A:0.47, C:0.06, G:0.07, T:0.40
Consensus pattern (152 bp):
AAAATAAATTAAATTATATATATATATTTTATAAATAAGATATTTATTTATTTAAAAATATCAGA
AAAAGACTTCTAGTTGCTTTAAGACAGTCATTTTCTTAATATTAAAAAATAAATAAATATTAATA
AAATATAATTCTAAAAATAACT
Found at i:55453 original size:3 final size:3
Alignment explanation
Indices: 55440--55532 Score: 81
Period size: 3 Copynumber: 32.7 Consensus size: 3
55430 CTGTAATGTA
* * *
55440 AAT ATT AAT AAT AAT AAT AAT AAT -AT AA- ATAT AAA AAT AAT AGT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT
* * *
55484 AA- AAT AA- AAT AA- AAT AAT ATT AAT AAT AAT -AG AAT AAT AAA AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
55528 AAT AA
1 AAT AA
55533 AAAACAAATG
Statistics
Matches: 71, Mismatches: 12, Indels: 14
0.73 0.12 0.14
Matches are distributed among these distances:
2 10 0.14
3 60 0.85
4 1 0.01
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:55473 original size:17 final size:17
Alignment explanation
Indices: 55453--55514 Score: 67
Period size: 17 Copynumber: 3.7 Consensus size: 17
55443 ATTAATAATA
55453 ATAATAATAATATAAAT
1 ATAATAATAATATAAAT
*
55470 ATAAAAATAATAGTAAA-
1 ATAATAATAATA-TAAAT
*
55487 ATAA-AATAAAAT-AAT
1 ATAATAATAATATAAAT
55502 ATTAATAATAATA
1 A-TAATAATAATA
55515 GAATAATAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
14 2 0.05
15 2 0.05
16 9 0.24
17 21 0.55
18 4 0.11
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.31
Consensus pattern (17 bp):
ATAATAATAATATAAAT
Found at i:55512 original size:33 final size:33
Alignment explanation
Indices: 55449--55533 Score: 95
Period size: 33 Copynumber: 2.6 Consensus size: 33
55439 AAATATTAAT
*
55449 AATAATAATAATAATATAAATATAAAAATAATAG
1 AATAATAA-AATAAAATAAATATAAAAATAATAG
*
55483 TAA-AATAAAATAAAAT-AATATTAATAATAATAG
1 -AATAATAAAATAAAATAAATA-TAAAAATAATAG
*
55516 AATAATAAAA-ATAATAAA
1 AATAATAAAATAAAATAAA
55534 AAACAAATGG
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
32 10 0.23
33 27 0.61
34 5 0.11
35 2 0.05
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.28
Consensus pattern (33 bp):
AATAATAAAATAAAATAAATATAAAAATAATAG
Found at i:56190 original size:118 final size:118
Alignment explanation
Indices: 55880--56396 Score: 599
Period size: 118 Copynumber: 4.4 Consensus size: 118
55870 CAAGTTTTTC
* * ** * *
55880 TCCTTCTTCAGATGAGTTCTTCTCATTATGAACACTTCTGGAAATGTTGATGTTGATCTATCTCC
1 TCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACTGGAAATACTAATGTTGATCCA--T-C
** *
55945 TTCTGTGAT-AGAGTC-ATGC-AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCT
63 --GAGTGATGA-ATTCGA-GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCT
* * * *
56002 TCC-TCTTCAGATAAGTTCTTATCATTATGAATTTCT-CTGG--A-A--AA-GTTGATGCATCGA
1 TCCTTCTTCAGATGAGTTCTTCTCATTATGAA-CTCTACTGGAAATACTAATGTTGATCCATCGA
* * * *
56059 GTGATGAATTCGAGTAAAAGATTGAACAAGTTTTTTTCATTATGAACTTCTTCT
65 GTGATGAATTCGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCT
*
56113 TCCTTCTTCAGACGAGTTCTTCTCATTATGAACTCTACTGGAAATACTAATGTTGATCCATCGAG
1 TCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACTGGAAATACTAATGTTGATCCATCGAG
*
56178 TGATGAATTCGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTC-CCAT
66 TGATGAATTCGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTC-T
** *
56231 TCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACTGGAAATGTTGATGTTGATCCATCGAG
1 TCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACTGGAAATACTAATGTTGATCCATCGAG
* * **
56296 TCATGGATTTTAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCT
66 TGATGAATTCGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCT
* * * *
56349 TTCTTCTTCAGATGAGTTCTTCTCATTGTGAACTCTAATGAAAATACT
1 TCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACTGGAAATACT
56397 GATCCATTGA
Statistics
Matches: 341, Mismatches: 40, Indels: 32
0.83 0.10 0.08
Matches are distributed among these distances:
110 9 0.03
111 43 0.13
112 30 0.09
113 1 0.00
114 1 0.00
115 8 0.02
116 1 0.00
117 3 0.01
118 208 0.61
119 2 0.01
121 30 0.09
122 5 0.01
ACGTcount: A:0.27, C:0.19, G:0.16, T:0.38
Consensus pattern (118 bp):
TCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACTGGAAATACTAATGTTGATCCATCGAG
TGATGAATTCGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCT
Found at i:56652 original size:22 final size:22
Alignment explanation
Indices: 56600--56653 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
56590 AAATATTTCT
* *
56600 TCTTTGAAAAGAGAATTTATCA
1 TCTTTGAAGAGAGAATCTATCA
56622 TCTTTGAAGAGAGAATCTATCA
1 TCTTTGAAGAGAGAATCTATCA
56644 TCTTTGAAGA
1 TCTTTGAAGA
56654 ATGTAGATGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.37, C:0.11, G:0.17, T:0.35
Consensus pattern (22 bp):
TCTTTGAAGAGAGAATCTATCA
Found at i:57299 original size:18 final size:18
Alignment explanation
Indices: 57276--57313 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
57266 TATATGAAAG
57276 AATAAATTGAATTTCAAA
1 AATAAATTGAATTTCAAA
*
57294 AATAAATTGAATTTTAAA
1 AATAAATTGAATTTCAAA
57312 AA
1 AA
57314 GATAAACTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.58, C:0.03, G:0.05, T:0.34
Consensus pattern (18 bp):
AATAAATTGAATTTCAAA
Done.