Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004923.1 Hibiscus syriacus cultivar Beakdansim tig00011084_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: 49962
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:139 original size:62 final size:62
Alignment explanation
Indices: 64--196 Score: 223
Period size: 62 Copynumber: 2.1 Consensus size: 62
54 TTATTTTCTC
* *
64 TAATAGAAA-CCTATAGTGCTATTATTATTAATAAAAAGGTAGAAGCATTATAATTAAAATAG
1 TAATA-AAAGCCTATAGTGCTATCATTATTAATAAAAAGGTAGAAGCATTATAATTAAAATAA
*
126 TAATAAAAGCCTATAGTGCTATCATTATTAATAAAAAGGTAGAAGTATTATAATTAAAATAA
1 TAATAAAAGCCTATAGTGCTATCATTATTAATAAAAAGGTAGAAGCATTATAATTAAAATAA
188 TAATAAAAG
1 TAATAAAAG
197 AGAAAATAAC
Statistics
Matches: 67, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
61 3 0.04
62 64 0.96
ACGTcount: A:0.50, C:0.06, G:0.12, T:0.32
Consensus pattern (62 bp):
TAATAAAAGCCTATAGTGCTATCATTATTAATAAAAAGGTAGAAGCATTATAATTAAAATAA
Found at i:194 original size:34 final size:33
Alignment explanation
Indices: 92--195 Score: 85
Period size: 29 Copynumber: 3.2 Consensus size: 33
82 CTATTATTAT
*
92 TAATAAAAAGGTAGAAGCATTATAATTAAAATA
1 TAATAAAAAGGTAGAAGTATTATAATTAAAATA
* * ** *
125 GTAAT-AAAAGCCTA-TAGTGCTATCATT---AT-
1 -TAATAAAAAG-GTAGAAGTATTATAATTAAAATA
154 TAATAAAAAGGTAGAAGTATTATAATTAAAATAA
1 TAATAAAAAGGTAGAAGTATTATAATTAAAAT-A
188 TAATAAAA
1 TAATAAAA
196 GAGAAAATAA
Statistics
Matches: 51, Mismatches: 11, Indels: 16
0.65 0.14 0.21
Matches are distributed among these distances:
28 6 0.12
29 14 0.27
30 2 0.04
32 2 0.04
33 13 0.25
34 14 0.27
ACGTcount: A:0.54, C:0.05, G:0.12, T:0.30
Consensus pattern (33 bp):
TAATAAAAAGGTAGAAGTATTATAATTAAAATA
Found at i:325 original size:20 final size:20
Alignment explanation
Indices: 300--434 Score: 91
Period size: 20 Copynumber: 6.8 Consensus size: 20
290 CGATCTCTAA
*
300 ATCGCAACGCGATATCCAGT
1 ATCGCAACGCGATTTCCAGT
**
320 ATCGCAAATC-AGTTTCCAG-
1 ATCGCAACGCGA-TTTCCAGT
** *
339 ATTCGCAACGCGATTTTGACT
1 A-TCGCAACGCGATTTCCAGT
* *
360 ATCGCAACGCGA-TTCTGACT
1 ATCGCAACGCGATTTC-CAGT
*
380 ATCGCAACGCGATCTCCAGT
1 ATCGCAACGCGATTTCCAGT
**
400 ATCGCAAATC-AGTTTCCAG-
1 ATCGCAACGCGA-TTTCCAGT
419 ATTCGCAACGCGATTT
1 A-TCGCAACGCGATTT
435 TGACTATCGC
Statistics
Matches: 89, Mismatches: 17, Indels: 18
0.72 0.14 0.15
Matches are distributed among these distances:
19 6 0.07
20 78 0.88
21 5 0.06
ACGTcount: A:0.27, C:0.28, G:0.19, T:0.26
Consensus pattern (20 bp):
ATCGCAACGCGATTTCCAGT
Found at i:413 original size:80 final size:80
Alignment explanation
Indices: 300--473 Score: 287
Period size: 80 Copynumber: 2.2 Consensus size: 80
290 CGATCTCTAA
300 ATCGCAACGCGATATCCAGTATCGCAAATCAGTTTCCAGATTCGCAACGCGATTTTGACTATCGC
1 ATCGCAACGCGATATCCAGTATCGCAAATCAGTTTCCAGATTCGCAACGCGATTTTGACTATCGC
365 AACGCGATTCTGACT
66 AACGCGATTCTGACT
*
380 ATCGCAACGCGATCTCCAGTATCGCAAATCAGTTTCCAGATTCGCAACGCGATTTTGACTATCGC
1 ATCGCAACGCGATATCCAGTATCGCAAATCAGTTTCCAGATTCGCAACGCGATTTTGACTATCGC
* * * *
445 AATGCGAATATGTA-A
66 AACGCGATTCTG-ACT
460 ATCGCAACGCGATA
1 ATCGCAACGCGATA
474 ATACAGAATC
Statistics
Matches: 87, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
80 86 0.99
81 1 0.01
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.25
Consensus pattern (80 bp):
ATCGCAACGCGATATCCAGTATCGCAAATCAGTTTCCAGATTCGCAACGCGATTTTGACTATCGC
AACGCGATTCTGACT
Found at i:443 original size:40 final size:40
Alignment explanation
Indices: 301--446 Score: 152
Period size: 40 Copynumber: 3.6 Consensus size: 40
291 GATCTCTAAA
* *
301 TCGCAACGCGATATCCAGTATCGCAAATCAGTTTCCAGAT
1 TCGCAACGCGATTTCCACTATCGCAAATCAGTTTCCAGAT
** ** * *
341 TCGCAACGCGATTTTGACTATCGCAACGC-GATT-CTGACT
1 TCGCAACGCGATTTCCACTATCGCAAATCAGTTTCCAGA-T
* *
380 ATCGCAACGCGATCTCCAGTATCGCAAATCAGTTTCCAGAT
1 -TCGCAACGCGATTTCCACTATCGCAAATCAGTTTCCAGAT
**
421 TCGCAACGCGATTTTGACTATCGCAA
1 TCGCAACGCGATTTCCACTATCGCAA
447 TGCGAATATG
Statistics
Matches: 82, Mismatches: 20, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
38 3 0.04
39 4 0.05
40 68 0.83
41 4 0.05
42 3 0.04
ACGTcount: A:0.27, C:0.28, G:0.18, T:0.26
Consensus pattern (40 bp):
TCGCAACGCGATTTCCACTATCGCAAATCAGTTTCCAGAT
Found at i:547 original size:41 final size:41
Alignment explanation
Indices: 502--616 Score: 137
Period size: 41 Copynumber: 2.8 Consensus size: 41
492 GCGATTTTAG
*
502 AAAATCGCAATGCGAATATATA-AATCGCAACGCGATAATAC
1 AAAATCGCAACGCG-ATATATACAATCGCAACGCGATAATAC
* * *
543 AAAATCGTAACGCGAT-TCTGACTATCGCAACGCGATAATAC
1 AAAATCGCAACGCGATATAT-ACAATCGCAACGCGATAATAC
584 AAAATCGCAACGCGATA-ATACATAATCGCAACG
1 AAAATCGCAACGCGATATATAC--AATCGCAACG
617 TAATTCTGAC
Statistics
Matches: 62, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
39 2 0.03
40 5 0.08
41 46 0.74
42 9 0.15
ACGTcount: A:0.43, C:0.23, G:0.16, T:0.19
Consensus pattern (41 bp):
AAAATCGCAACGCGATATATACAATCGCAACGCGATAATAC
Found at i:549 original size:21 final size:21
Alignment explanation
Indices: 502--661 Score: 127
Period size: 21 Copynumber: 7.8 Consensus size: 21
492 GCGATTTTAG
*
502 AAAATCGCAATGCGA-ATATA-
1 AAAATCGCAACGCGATA-ATAC
*
522 TAAATCGCAACGCGATAATAC
1 AAAATCGCAACGCGATAATAC
* **
543 AAAATCGTAACGCGATTCTGAC
1 AAAATCGCAACGCGATAAT-AC
*
565 --TATCGCAACGCGATAATAC
1 AAAATCGCAACGCGATAATAC
584 AAAATCGCAACGCGATAATAC
1 AAAATCGCAACGCGATAATAC
* *
605 ATAATCGCAA--CG-TAATTC
1 AAAATCGCAACGCGATAATAC
** *
623 TGACTATCGCAATGCGATAATAC
1 --AAAATCGCAACGCGATAATAC
*
646 AAAATCGCAATGCGAT
1 AAAATCGCAACGCGAT
662 TTTCCAAATT
Statistics
Matches: 112, Mismatches: 18, Indels: 19
0.75 0.12 0.13
Matches are distributed among these distances:
18 5 0.04
19 4 0.04
20 37 0.33
21 57 0.51
22 4 0.04
23 5 0.04
ACGTcount: A:0.41, C:0.22, G:0.16, T:0.21
Consensus pattern (21 bp):
AAAATCGCAACGCGATAATAC
Found at i:598 original size:62 final size:62
Alignment explanation
Indices: 523--661 Score: 224
Period size: 62 Copynumber: 2.2 Consensus size: 62
513 GCGAATATAT
* *
523 AAATCGCAACGCGATAATACAAAATCGTAACGCGATTCTGACTATCGCAACGCGATAATACA
1 AAATCGCAACGCGATAATACAAAATCGCAACGCAATTCTGACTATCGCAACGCGATAATACA
* * *
585 AAATCGCAACGCGATAATACATAATCGCAACGTAATTCTGACTATCGCAATGCGATAATACA
1 AAATCGCAACGCGATAATACAAAATCGCAACGCAATTCTGACTATCGCAACGCGATAATACA
*
647 AAATCGCAATGCGAT
1 AAATCGCAACGCGAT
662 TTTCCAAATT
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
62 71 1.00
ACGTcount: A:0.40, C:0.23, G:0.16, T:0.21
Consensus pattern (62 bp):
AAATCGCAACGCGATAATACAAAATCGCAACGCAATTCTGACTATCGCAACGCGATAATACA
Found at i:1105 original size:19 final size:20
Alignment explanation
Indices: 1080--1170 Score: 96
Period size: 19 Copynumber: 4.4 Consensus size: 20
1070 CTTATTTTGG
1080 ATTTTTCACTATCGCAACAC
1 ATTTTTCACTATCGCAACAC
1100 -TTTTTCACTATCGCAACAACAC
1 ATTTTTCACTATCG---CAACAC
*
1122 ATTTTTCAAACTCTCGCAACAC
1 ATTTTTC--ACTATCGCAACAC
* *
1144 A-TTTTAACTATCGTAACAC
1 ATTTTTCACTATCGCAACAC
1163 ATTTTTCA
1 ATTTTTCA
1171 AAATCGCGTT
Statistics
Matches: 59, Mismatches: 5, Indels: 14
0.76 0.06 0.18
Matches are distributed among these distances:
19 25 0.42
20 5 0.08
21 4 0.07
22 13 0.22
23 6 0.10
25 6 0.10
ACGTcount: A:0.32, C:0.27, G:0.04, T:0.36
Consensus pattern (20 bp):
ATTTTTCACTATCGCAACAC
Found at i:1142 original size:44 final size:41
Alignment explanation
Indices: 1091--1172 Score: 110
Period size: 44 Copynumber: 1.9 Consensus size: 41
1081 TTTTTCACTA
* *
1091 TCGCAACACTTTTTCACTATCGCAACAACACATTTTTCAAACTC
1 TCGCAACACATTTTAACTATCG---CAACACATTTTTCAAACTC
*
1135 TCGCAACACATTTTAACTATCGTAACACATTTTTCAAA
1 TCGCAACACATTTTAACTATCGCAACACATTTTTCAAA
1173 ATCGCGTTGC
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
41 15 0.43
44 20 0.57
ACGTcount: A:0.34, C:0.28, G:0.05, T:0.33
Consensus pattern (41 bp):
TCGCAACACATTTTAACTATCGCAACACATTTTTCAAACTC
Found at i:1560 original size:25 final size:25
Alignment explanation
Indices: 1511--1561 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
1501 TTATGTTAAT
* *
1511 TAATTTAATTAATTTTATAATTTTA
1 TAATTTAATTAATATAATAATTTTA
1536 TAATTTAATTAA-ATAATAATATTTA
1 TAATTTAATTAATATAATAAT-TTTA
1561 T
1 T
1562 TTATTTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 6 0.26
25 17 0.74
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (25 bp):
TAATTTAATTAATATAATAATTTTA
Found at i:2114 original size:4 final size:4
Alignment explanation
Indices: 2105--2140 Score: 72
Period size: 4 Copynumber: 9.0 Consensus size: 4
2095 GGTTGATATG
2105 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
2141 ACTTTGGCAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:7857 original size:1 final size:1
Alignment explanation
Indices: 7846--7911 Score: 51
Period size: 1 Copynumber: 66.0 Consensus size: 1
7836 ACATCAGAGG
* * * * * * * * *
7846 AAAAGAAAAAAAATAAAAAAAAAGAAATAAAAAAGAAAAAAGAAAACAAAAAGAAAAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
7911 A
1 A
7912 GAGATTGAAT
Statistics
Matches: 47, Mismatches: 18, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
1 47 1.00
ACGTcount: A:0.86, C:0.02, G:0.09, T:0.03
Consensus pattern (1 bp):
A
Found at i:7863 original size:7 final size:7
Alignment explanation
Indices: 7846--7913 Score: 61
Period size: 7 Copynumber: 9.9 Consensus size: 7
7836 ACATCAGAGG
7846 AAAAGAA
1 AAAAGAA
*
7853 AAAAAATA
1 AAAAGA-A
*
7861 AAAAAAA
1 AAAAGAA
*
7868 AGAAATAA
1 A-AAAGAA
7876 AAAAGAA
1 AAAAGAA
7883 AAAAG--
1 AAAAGAA
*
7888 AAAA-CA
1 AAAAGAA
7894 AAAAGAA
1 AAAAGAA
7901 AAAAGAA
1 AAAAGAA
7908 AAAAGA
1 AAAAGA
7914 GATTGAATCA
Statistics
Matches: 52, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
5 4 0.08
6 4 0.08
7 31 0.60
8 13 0.25
ACGTcount: A:0.85, C:0.01, G:0.10, T:0.03
Consensus pattern (7 bp):
AAAAGAA
Found at i:7867 original size:11 final size:11
Alignment explanation
Indices: 7845--7911 Score: 62
Period size: 11 Copynumber: 5.6 Consensus size: 11
7835 TACATCAGAG
7845 GAAAAGAAAAAA
1 GAAAA-AAAAAA
*
7857 AATAAAAAAAAA
1 GA-AAAAAAAAA
*
7869 GAAATAAAAAA
1 GAAAAAAAAAA
7880 GAAAAAAGAAAA
1 GAAAAAA-AAAA
*
7892 CAAAAAGAAAAAA
1 -GAAAA-AAAAAA
7905 GAAAAAA
1 GAAAAAA
7912 GAGATTGAAT
Statistics
Matches: 45, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
11 16 0.36
12 16 0.36
13 11 0.24
14 2 0.04
ACGTcount: A:0.85, C:0.01, G:0.10, T:0.03
Consensus pattern (11 bp):
GAAAAAAAAAA
Found at i:7884 original size:18 final size:17
Alignment explanation
Indices: 7846--7911 Score: 87
Period size: 18 Copynumber: 3.6 Consensus size: 17
7836 ACATCAGAGG
*
7846 AAAAGAAAAAAAATAAAAA
1 AAAAG-AAAAAAA-AAGAA
7865 AAAAGAAATAAAAAAGAA
1 AAAAGAAA-AAAAAAGAA
7883 AAAAGAAAACAAAAAGAA
1 AAAAGAAAA-AAAAAGAA
7901 AAAAGAAAAAA
1 AAAAGAAAAAA
7912 GAGATTGAAT
Statistics
Matches: 44, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
17 3 0.07
18 32 0.73
19 9 0.20
ACGTcount: A:0.86, C:0.02, G:0.09, T:0.03
Consensus pattern (17 bp):
AAAAGAAAAAAAAAGAA
Found at i:7891 original size:25 final size:25
Alignment explanation
Indices: 7846--7913 Score: 88
Period size: 25 Copynumber: 2.8 Consensus size: 25
7836 ACATCAGAGG
7846 AAAAGAAAAAA-AATAAAA-AAAA-A
1 AAAAGAAAAAAGAA-AAAAGAAAACA
* *
7869 GAAATAAAAAAGAAAAAAGAAAACA
1 AAAAGAAAAAAGAAAAAAGAAAACA
7894 AAAAGAAAAAAGAAAAAAGA
1 AAAAGAAAAAAGAAAAAAGA
7914 GATTGAATCA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
23 13 0.34
24 6 0.16
25 19 0.50
ACGTcount: A:0.85, C:0.01, G:0.10, T:0.03
Consensus pattern (25 bp):
AAAAGAAAAAAGAAAAAAGAAAACA
Found at i:7912 original size:14 final size:14
Alignment explanation
Indices: 7846--7913 Score: 61
Period size: 15 Copynumber: 4.9 Consensus size: 14
7836 ACATCAGAGG
*
7846 AAAAGAAAAAAAATA
1 AAAAGAAAAAAGA-A
* *
7861 AAAAAAAAGAAATAA
1 AAAAGAAA-AAAGAA
7876 AAAAGAAAAAAG--
1 AAAAGAAAAAAGAA
*
7888 AAAA-CAAAAAGAA
1 AAAAGAAAAAAGAA
7901 AAAAGAAAAAAGA
1 AAAAGAAAAAAGA
7914 GATTGAATCA
Statistics
Matches: 43, Mismatches: 6, Indels: 9
0.74 0.10 0.16
Matches are distributed among these distances:
11 6 0.14
12 4 0.09
13 4 0.09
14 10 0.23
15 15 0.35
16 4 0.09
ACGTcount: A:0.85, C:0.01, G:0.10, T:0.03
Consensus pattern (14 bp):
AAAAGAAAAAAGAA
Found at i:9304 original size:502 final size:502
Alignment explanation
Indices: 8362--9371 Score: 1984
Period size: 502 Copynumber: 2.0 Consensus size: 502
8352 GAAAAATGAT
*
8362 AAAAGGGGGTTCAAGATGTAAATTTTGAATAACATTTTGAAGCCAAAAGAGGATTCGAGTTGAAA
1 AAAAGGGGGTTCAAGATATAAATTTTGAATAACATTTTGAAGCCAAAAGAGGATTCGAGTTGAAA
8427 ACCTGAAAAGGCAGCTCGAGTATTGAATAGTGCAACAATGATATAAGAGACAATCTTATGCTCTT
66 ACCTGAAAAGGCAGCTCGAGTATTGAATAGTGCAACAATGATATAAGAGACAATCTTATGCTCTT
8492 GATGAAGCACTGCACATCCCAAAGATGTTCATGAGATTCTGGAATCAAGAAGTATCTCTATGAGA
131 GATGAAGCACTGCACATCCCAAAGATGTTCATGAGATTCTGGAATCAAGAAGTATCTCTATGAGA
8557 CGAGCATAACAACCATTTCTTCAAGTTAGTGGACGCTCAAAGACACATATATACTAGACCAACCT
196 CGAGCATAACAACCATTTCTTCAAGTTAGTGGACGCTCAAAGACACATATATACTAGACCAACCT
*
8622 GAAAGAACTTACCTTTCCAGAATTAACCTACACCTTAAATCAGTCAATAATTTTGACACTTGCCA
261 GAAAGAACTTACCTTTCCAGAATTAACCTACAACTTAAATCAGTCAATAATTTTGACACTTGCCA
8687 TTGGACTATGATTTTTGAATGATTTAAAAGAGTAGTTGATTTATTTAATATTCTTTGAAATCATG
326 TTGGACTATGATTTTTGAATGATTTAAAAGAGTAGTTGATTTATTTAATATTCTTTGAAATCATG
8752 CTTATGATTTGATTCAATTGTGAACCTGTAAGGGGATATATTTTACAAAATTATTTCATTCTTTG
391 CTTATGATTTGATTCAATTGTGAACCTGTAAGGGGATATATTTTACAAAATTATTTCATTCTTTG
8817 ATAAAGAAATGAGGAAAAACATTTTCAAACATGGCAGTCTCAAAGTA
456 ATAAAGAAATGAGGAAAAACATTTTCAAACATGGCAGTCTCAAAGTA
8864 AAAAGGGGGTTCAAGATATAAATTTTGAATAACATTTTGAAGCCAAAAGAGGATTCGAGTTGAAA
1 AAAAGGGGGTTCAAGATATAAATTTTGAATAACATTTTGAAGCCAAAAGAGGATTCGAGTTGAAA
8929 ACCTGAAAAGGCAGCTCGAGTATTGAATAGTGCAACAATGATATAAGAGACAATCTTATGCTCTT
66 ACCTGAAAAGGCAGCTCGAGTATTGAATAGTGCAACAATGATATAAGAGACAATCTTATGCTCTT
8994 GATGAAGCACTGCACATCCCAAAGATGTTCATGAGATTCTGGAATCAAGAAGTATCTCTATGAGA
131 GATGAAGCACTGCACATCCCAAAGATGTTCATGAGATTCTGGAATCAAGAAGTATCTCTATGAGA
9059 CGAGCATAACAACCATTTCTTCAAGTTAGTGGACGCTCAAAGACACATATATACTAGACCAACCT
196 CGAGCATAACAACCATTTCTTCAAGTTAGTGGACGCTCAAAGACACATATATACTAGACCAACCT
9124 GAAAGAACTTACCTTTCCAGAATTAACCTACAACTTAAATCAGTCAATAATTTTGACACTTGCCA
261 GAAAGAACTTACCTTTCCAGAATTAACCTACAACTTAAATCAGTCAATAATTTTGACACTTGCCA
*
9189 TTGGACTATGATTTTTGAATGATTTAAAAGAGTAGTTGATTTATTTAATATTCTTTGAACTCATG
326 TTGGACTATGATTTTTGAATGATTTAAAAGAGTAGTTGATTTATTTAATATTCTTTGAAATCATG
*
9254 CTTATGATTTGATTCAATTGTGAACCTGTAATGGGATATATTTTACAAAATTATTTCATTCTTTG
391 CTTATGATTTGATTCAATTGTGAACCTGTAAGGGGATATATTTTACAAAATTATTTCATTCTTTG
9319 ATAAAGAAATGAGGAAAAACATTTTCAAACATGGCAGTCTCAAAGTA
456 ATAAAGAAATGAGGAAAAACATTTTCAAACATGGCAGTCTCAAAGTA
9366 AAAAGG
1 AAAAGG
9372 TCTTTGAAGC
Statistics
Matches: 504, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
502 504 1.00
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.30
Consensus pattern (502 bp):
AAAAGGGGGTTCAAGATATAAATTTTGAATAACATTTTGAAGCCAAAAGAGGATTCGAGTTGAAA
ACCTGAAAAGGCAGCTCGAGTATTGAATAGTGCAACAATGATATAAGAGACAATCTTATGCTCTT
GATGAAGCACTGCACATCCCAAAGATGTTCATGAGATTCTGGAATCAAGAAGTATCTCTATGAGA
CGAGCATAACAACCATTTCTTCAAGTTAGTGGACGCTCAAAGACACATATATACTAGACCAACCT
GAAAGAACTTACCTTTCCAGAATTAACCTACAACTTAAATCAGTCAATAATTTTGACACTTGCCA
TTGGACTATGATTTTTGAATGATTTAAAAGAGTAGTTGATTTATTTAATATTCTTTGAAATCATG
CTTATGATTTGATTCAATTGTGAACCTGTAAGGGGATATATTTTACAAAATTATTTCATTCTTTG
ATAAAGAAATGAGGAAAAACATTTTCAAACATGGCAGTCTCAAAGTA
Found at i:9987 original size:49 final size:50
Alignment explanation
Indices: 9925--10042 Score: 123
Period size: 49 Copynumber: 2.3 Consensus size: 50
9915 CCATATTATC
* ** * *
9925 CATGTGGGTATCTTGAAAGTTCACATCAGCAT-AAAAAGATAGAAGT-TT
1 CATGTGGGCATCTTGAAAGCCCACATCAACATGAAAAAGACAGAAGTATT
* *
9973 CATGTGGGGCATCTTGAAGGCCCACATCAACGTGAAAAAGACAGAAGTAATT
1 CATGT-GGGCATCTTGAAAGCCCACATCAACATGAAAAAGACAGAAGT-ATT
*
10025 CATGTAGGGCATTTTGAA
1 CATGT-GGGCATCTTGAA
10043 GGCTCACCTT
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
48 5 0.09
49 21 0.37
50 13 0.23
52 18 0.32
ACGTcount: A:0.36, C:0.15, G:0.24, T:0.25
Consensus pattern (50 bp):
CATGTGGGCATCTTGAAAGCCCACATCAACATGAAAAAGACAGAAGTATT
Found at i:10062 original size:52 final size:50
Alignment explanation
Indices: 9946--10045 Score: 130
Period size: 52 Copynumber: 2.0 Consensus size: 50
9936 CTTGAAAGTT
* * *
9946 CACATCAGCAT-AAAAAGATAGAAGTTTCATGTGGGGCATCTTGAAGGCC
1 CACATCAACATGAAAAAGACAGAAGTTTCATGTAGGGCATCTTGAAGGCC
* *
9995 CACATCAACGTGAAAAAGACAGAAGTAATTCATGTAGGGCATTTTGAAGGC
1 CACATCAACATGAAAAAGACAGAAGT--TTCATGTAGGGCATCTTGAAGGC
10046 TCACCTTAGT
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
49 9 0.21
50 13 0.30
52 21 0.49
ACGTcount: A:0.37, C:0.17, G:0.24, T:0.22
Consensus pattern (50 bp):
CACATCAACATGAAAAAGACAGAAGTTTCATGTAGGGCATCTTGAAGGCC
Found at i:11409 original size:100 final size:99
Alignment explanation
Indices: 11237--11430 Score: 316
Period size: 100 Copynumber: 1.9 Consensus size: 99
11227 CCCAATGATC
* *
11237 TGTAAAACCTCTGGGTTATATGTAAACCTCAGGGTAGGATGTTTTCGCATGAAAATGAGAAAGCG
1 TGTAAAACCTCTGGGTCATATGTAAACCTCAGGGTAGGATGTTTTCGCATGAAAATGAGAAAGCA
11302 ATTTTCAAAGTTTCTCATTTAATGTTCAAAGATT
66 ATTTTCAAAGTTTCTCATTTAATGTTCAAAGATT
* * *
11336 TGTAAAGCCTCTGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTTCGCATGAAAATGAGAAAGT
1 TGTAAAACCTCTGGGTCATATGT-AAACCTCAGGGTAGGATGTTTTCGCATGAAAATGAGAAAGC
* *
11401 AATTTTCAAAGTTTTTCGTTTAATGTTCAA
65 AATTTTCAAAGTTTCTCATTTAATGTTCAA
11431 GAAAATTAAA
Statistics
Matches: 87, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
99 20 0.23
100 67 0.77
ACGTcount: A:0.31, C:0.13, G:0.21, T:0.35
Consensus pattern (99 bp):
TGTAAAACCTCTGGGTCATATGTAAACCTCAGGGTAGGATGTTTTCGCATGAAAATGAGAAAGCA
ATTTTCAAAGTTTCTCATTTAATGTTCAAAGATT
Found at i:11465 original size:20 final size:20
Alignment explanation
Indices: 11437--11511 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
11427 TCAAGAAAAT
* *
11437 TAAATCCTCCGGGTAATTTG
1 TAAAACCTCTGGGTAATTTG
*
11457 TAAAACCTCTGGGTAATTTA
1 TAAAACCTCTGGGTAATTTG
* * *
11477 TAAATCCTCTGGGTCATCTG
1 TAAAACCTCTGGGTAATTTG
*
11497 TAAAACCTCAGGGTA
1 TAAAACCTCTGGGTA
11512 GGAAGTTTTC
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (20 bp):
TAAAACCTCTGGGTAATTTG
Found at i:11593 original size:139 final size:139
Alignment explanation
Indices: 11333--11609 Score: 428
Period size: 139 Copynumber: 2.0 Consensus size: 139
11323 ATGTTCAAAG
* *
11333 ATTTGTAAAGCCTCTGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTTCGCATGAAAATGAGAA
1 ATTTATAAAGCCTCTGGGTCATCTGTAAAACCTCAGGGTAGGAAGTTTTCGCATGAAAATGAGAA
* * * * * **
11398 AGTAATTTTCAAAGTTTTTCGTTTAATGTTCAAGAAAATTAAATCCTCCGGGTAATTTGTAAAAC
66 AATAATTTCCAAAGTTTCTCATTTAATGTTCAAGAAAATTAAAACCTCAAGGTAATTTGTAAAAC
*
11463 CTCTGGGTA
131 CTCCGGGTA
*
11472 ATTTATAAATCCTCTGGGTCATCTGTAAAACCTCAGGGTAGGAAGTTTTCGCATGAAAATGAGAA
1 ATTTATAAAGCCTCTGGGTCATCTGTAAAACCTCAGGGTAGGAAGTTTTCGCATGAAAATGAGAA
* * *
11537 AATGATTTCCAAAGTTTCTCATTTAATGTTCTAGAAAATTAAAACCTCAAGGTAATTTGTAAATC
66 AATAATTTCCAAAGTTTCTCATTTAATGTTCAAGAAAATTAAAACCTCAAGGTAATTTGTAAAAC
11602 CTCCGGGT
131 CTCCGGGT
11610 CATCTGTAAA
Statistics
Matches: 124, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
139 124 1.00
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Consensus pattern (139 bp):
ATTTATAAAGCCTCTGGGTCATCTGTAAAACCTCAGGGTAGGAAGTTTTCGCATGAAAATGAGAA
AATAATTTCCAAAGTTTCTCATTTAATGTTCAAGAAAATTAAAACCTCAAGGTAATTTGTAAAAC
CTCCGGGTA
Found at i:11668 original size:119 final size:119
Alignment explanation
Indices: 11457--12346 Score: 1483
Period size: 119 Copynumber: 7.5 Consensus size: 119
11447 GGGTAATTTG
* * * *
11457 TAAAACCTCTGGGTAATTTATAAATCCTCTGGGTCATCTGTAAAACCTCAGGGTAGGAAGTTTTC
1 TAAAACCTCAGGGTAATTTGTAAATCCTCCGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTTC
** *
11522 GCATGAAAATGAGAAAATGATTTCCAAAGTTTCTCATTTAATGTTCTAGAAAAT
66 GCATGAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAATGTTCAAGAAAAT
*
11576 TAAAACCTCAAGGTAATTTGTAAATCCTCCGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTTC
1 TAAAACCTCAGGGTAATTTGTAAATCCTCCGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTTC
*
11641 GCATGAAAATGAGAAAGAGATTTCCAAAGTTTCTCATTTAATGTTCAAGAAAAT
66 GCATGAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAATGTTCAAGAAAAT
* *
11695 TAAATCCTTC-GGGTAATTTGTAAATCCTCCGGGTCATCTGTAAAACCTCAGGGTATGATGTTTT
1 TAAAACC-TCAGGGTAATTTGTAAATCCTCCGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTT
* **
11759 CGCATGAAAAT--G--A--GATTTCCAAAGTTTCTCATTTAATGTTCTAGATTAT
65 CGCATGAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAATGTTCAAGAAAAT
11808 TAAAACCTCAGGGTAATTTGTAAATCCTCCGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTTC
1 TAAAACCTCAGGGTAATTTGTAAATCCTCCGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTTC
11873 GCATGAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAATGTTCAAGAAAAT
66 GCATGAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAATGTTCAAGAAAAT
11927 TAAAACCTCAGGGTAATTTGTAAATCCTCCGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTTC
1 TAAAACCTCAGGGTAATTTGTAAATCCTCCGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTTC
11992 GCATGAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAATGTTCAAGAAAAT
66 GCATGAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAATGTTCAAGAAAAT
* * *
12046 TAAAACCTCGGGGTAATTTGTAAATCCTCCGGGTCATCTGTAAAATCTCAGGGTATGATGTTTTC
1 TAAAACCTCAGGGTAATTTGTAAATCCTCCGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTTC
*
12111 GCATGAAAATGAGAAAGCGATTTCTAAAGTTTCTCATTTAATGTTCAAGAAAAT
66 GCATGAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAATGTTCAAGAAAAT
*
12165 TAAAACCTCAGGGTAATTTGTAAATCCTCCGGGTCATCTGTAAAACCTCAGGGTATGATGTTTTC
1 TAAAACCTCAGGGTAATTTGTAAATCCTCCGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTTC
* * * *
12230 GGATGAAAATGAGAAAGCGATTACCAAATTTTCTCATTTAATGTTCTAGAAAAT
66 GCATGAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAATGTTCAAGAAAAT
*
12284 TAAAACCTCCA-GGTAATTTGTAAATCCTCC-GGTCATCTGTAAAACCTCAGGGTATGATGTTTT
1 TAAAACCT-CAGGGTAATTTGTAAATCCTCCGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTT
12347 TACTTTAATT
Statistics
Matches: 732, Mismatches: 30, Indels: 19
0.94 0.04 0.02
Matches are distributed among these distances:
112 2 0.00
113 103 0.14
115 2 0.00
117 2 0.00
118 33 0.05
119 586 0.80
120 4 0.01
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Consensus pattern (119 bp):
TAAAACCTCAGGGTAATTTGTAAATCCTCCGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTTC
GCATGAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAATGTTCAAGAAAAT
Found at i:11720 original size:20 final size:20
Alignment explanation
Indices: 11695--11749 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
11685 TCAAGAAAAT
* *
11695 TAAATCCTTCGGGTAATTTG
1 TAAATCCTCCGGGTAATCTG
*
11715 TAAATCCTCCGGGTCATCTG
1 TAAATCCTCCGGGTAATCTG
* *
11735 TAAAACCTCAGGGTA
1 TAAATCCTCCGGGTA
11750 TGATGTTTTC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (20 bp):
TAAATCCTCCGGGTAATCTG
Found at i:11836 original size:20 final size:20
Alignment explanation
Indices: 11808--11862 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
11798 TCTAGATTAT
*
11808 TAAAACCTCAGGGTAATTTG
1 TAAAACCTCAGGGTAATCTG
* * *
11828 TAAATCCTCCGGGTCATCTG
1 TAAAACCTCAGGGTAATCTG
11848 TAAAACCTCAGGGTA
1 TAAAACCTCAGGGTA
11863 GGATGTTTTC
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (20 bp):
TAAAACCTCAGGGTAATCTG
Found at i:11910 original size:351 final size:354
Alignment explanation
Indices: 11457--12346 Score: 1520
Period size: 351 Copynumber: 2.5 Consensus size: 354
11447 GGGTAATTTG
* * * *
11457 TAAAACCTCTGGGTAATTTATAAATCCTCTGGGTCATCTGTAAAACCTCAGGGTAGGAAGTTTTC
1 TAAAACCTCAGGGTAATTTGTAAATCCTCCGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTTC
**
11522 GCATGAAAATGAGAAAATGATTTCCAAAGTTTCTCATTTAATGTTCTAGAAAATTAAAACCTCAA
66 GCATGAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAATGTTCTAGAAAATTAAAACCTCAA
11587 GGTAATTTGTAAATCCTCCGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTTCGCATGAAAATG
131 GGTAATTTGTAAATCCTCCGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTTCGCATGAAAATG
*
11652 AGAAAGAGATTTCCAAAGTTTCTCATTTAATGTTCAAGAAAATTAAATCCTTC-GGGTAATTTGT
196 AGAAAGAGATTTCCAAAGTTTCTCATTTAATGTTCAAGAAAATTAAAACC-TCGGGGTAATTTGT
11716 AAATCCTCCGGGTCATCTGTAAAACCTCAGGGTATGATGTTTTCGCATGAAAAT-G-A-GATTTC
260 AAATCCTCCGGGTCATCTGTAAAACCTCAGGGTATGATGTTTTCGCATGAAAATAGAACGATTTC
* **
11778 CAAAGTTTCTCATTTAATGTTCTAGATTAT
325 CAAAGTTTCTCATTTAATGTTCAAGAAAAT
11808 TAAAACCTCAGGGTAATTTGTAAATCCTCCGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTTC
1 TAAAACCTCAGGGTAATTTGTAAATCCTCCGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTTC
* *
11873 GCATGAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAATGTTCAAGAAAATTAAAACCTCAG
66 GCATGAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAATGTTCTAGAAAATTAAAACCTCAA
11938 GGTAATTTGTAAATCCTCCGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTTCGCATGAAAATG
131 GGTAATTTGTAAATCCTCCGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTTCGCATGAAAATG
*
12003 AGAAAGCGATTTCCAAAGTTTCTCATTTAATGTTCAAGAAAATTAAAACCTCGGGGTAATTTGTA
196 AGAAAGAGATTTCCAAAGTTTCTCATTTAATGTTCAAGAAAATTAAAACCTCGGGGTAATTTGTA
*
12068 AATCCTCCGGGTCATCTGTAAAATCTCAGGGTATGATGTTTTCGCATGAAAATGAGAAAGCGATT
261 AATCCTCCGGGTCATCTGTAAAACCTCAGGGTATGATGTTTTCGCATGAAAAT-AG-AA-CGATT
*
12133 TCTAAAGTTTCTCATTTAATGTTCAAGAAAAT
323 TCCAAAGTTTCTCATTTAATGTTCAAGAAAAT
*
12165 TAAAACCTCAGGGTAATTTGTAAATCCTCCGGGTCATCTGTAAAACCTCAGGGTATGATGTTTTC
1 TAAAACCTCAGGGTAATTTGTAAATCCTCCGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTTC
* * * *
12230 GGATGAAAATGAGAAAGCGATTACCAAATTTTCTCATTTAATGTTCTAGAAAATTAAAACCTCCA
66 GCATGAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAATGTTCTAGAAAATTAAAACCTCAA
*
12295 GGTAATTTGTAAATCCTCC-GGTCATCTGTAAAACCTCAGGGTATGATGTTTT
131 GGTAATTTGTAAATCCTCCGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTT
12347 TACTTTAATT
Statistics
Matches: 509, Mismatches: 23, Indels: 9
0.94 0.04 0.02
Matches are distributed among these distances:
350 2 0.00
351 299 0.59
353 1 0.00
355 1 0.00
356 32 0.06
357 174 0.34
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Consensus pattern (354 bp):
TAAAACCTCAGGGTAATTTGTAAATCCTCCGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTTC
GCATGAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAATGTTCTAGAAAATTAAAACCTCAA
GGTAATTTGTAAATCCTCCGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTTCGCATGAAAATG
AGAAAGAGATTTCCAAAGTTTCTCATTTAATGTTCAAGAAAATTAAAACCTCGGGGTAATTTGTA
AATCCTCCGGGTCATCTGTAAAACCTCAGGGTATGATGTTTTCGCATGAAAATAGAACGATTTCC
AAAGTTTCTCATTTAATGTTCAAGAAAAT
Found at i:11955 original size:20 final size:20
Alignment explanation
Indices: 11927--11981 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
11917 TCAAGAAAAT
*
11927 TAAAACCTCAGGGTAATTTG
1 TAAAACCTCAGGGTAATCTG
* * *
11947 TAAATCCTCCGGGTCATCTG
1 TAAAACCTCAGGGTAATCTG
11967 TAAAACCTCAGGGTA
1 TAAAACCTCAGGGTA
11982 GGATGTTTTC
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (20 bp):
TAAAACCTCAGGGTAATCTG
Found at i:12074 original size:20 final size:20
Alignment explanation
Indices: 12046--12100 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 20
12036 TCAAGAAAAT
* *
12046 TAAAACCTCGGGGTAATTTG
1 TAAAACCTCCGGGTAATCTG
* *
12066 TAAATCCTCCGGGTCATCTG
1 TAAAACCTCCGGGTAATCTG
* *
12086 TAAAATCTCAGGGTA
1 TAAAACCTCCGGGTA
12101 TGATGTTTTC
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (20 bp):
TAAAACCTCCGGGTAATCTG
Found at i:12193 original size:20 final size:20
Alignment explanation
Indices: 12165--12219 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
12155 TCAAGAAAAT
*
12165 TAAAACCTCAGGGTAATTTG
1 TAAAACCTCAGGGTAATCTG
* * *
12185 TAAATCCTCCGGGTCATCTG
1 TAAAACCTCAGGGTAATCTG
12205 TAAAACCTCAGGGTA
1 TAAAACCTCAGGGTA
12220 TGATGTTTTC
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (20 bp):
TAAAACCTCAGGGTAATCTG
Found at i:12312 original size:20 final size:19
Alignment explanation
Indices: 12284--12331 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
12274 TCTAGAAAAT
*
12284 TAAAACCTCCAGGTAATTTG
1 TAAAACCTCC-GGTAATCTG
* *
12304 TAAATCCTCCGGTCATCTG
1 TAAAACCTCCGGTAATCTG
12323 TAAAACCTC
1 TAAAACCTC
12332 AGGGTATGAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 15 0.62
20 9 0.38
ACGTcount: A:0.31, C:0.27, G:0.12, T:0.29
Consensus pattern (19 bp):
TAAAACCTCCGGTAATCTG
Found at i:12488 original size:3 final size:3
Alignment explanation
Indices: 12480--12552 Score: 96
Period size: 3 Copynumber: 24.7 Consensus size: 3
12470 CGAGACTATA
* * *
12480 TAT TAT TAT TAT TA- TAT TAC AAC TAT TAT TCA- TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT
12524 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
12553 GTACAAATAT
Statistics
Matches: 63, Mismatches: 4, Indels: 6
0.86 0.05 0.08
Matches are distributed among these distances:
2 3 0.05
3 59 0.94
4 1 0.02
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:14112 original size:62 final size:62
Alignment explanation
Indices: 14011--14170 Score: 293
Period size: 62 Copynumber: 2.6 Consensus size: 62
14001 AAATAATAAC
* *
14011 TAATTAAAATAATAATAAAAACCCATAGTGTTATTATTATTAATAAAAAGGTAGAAGCATTA
1 TAATTAAAATAATAATAAAAACCCATAGTGCTATCATTATTAATAAAAAGGTAGAAGCATTA
*
14073 TAATTAAAATAATAATAAAAACCCATAGTGCTATCATTATTAATAAAAAGGTAGAAGTATTA
1 TAATTAAAATAATAATAAAAACCCATAGTGCTATCATTATTAATAAAAAGGTAGAAGCATTA
14135 TAATTAAAATAATAATAAAAACCCATAGTGCTATCA
1 TAATTAAAATAATAATAAAAACCCATAGTGCTATCA
14171 CATATGTATA
Statistics
Matches: 95, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
62 95 1.00
ACGTcount: A:0.52, C:0.09, G:0.09, T:0.31
Consensus pattern (62 bp):
TAATTAAAATAATAATAAAAACCCATAGTGCTATCATTATTAATAAAAAGGTAGAAGCATTA
Found at i:15759 original size:29 final size:29
Alignment explanation
Indices: 15703--15760 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
15693 GGATTTTATG
**
15703 ATATTTTAGAAATTTTATGAGTTGTTTTT
1 ATATTTTAGAAATTTTATGAGTAATTTTT
15732 ATATTTTAGAAATTTT-TAGAGTAATTTTT
1 ATATTTTAGAAATTTTAT-GAGTAATTTTT
15761 TAAAAAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 1 0.04
29 25 0.96
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.57
Consensus pattern (29 bp):
ATATTTTAGAAATTTTATGAGTAATTTTT
Found at i:22003 original size:149 final size:149
Alignment explanation
Indices: 21733--22036 Score: 599
Period size: 149 Copynumber: 2.0 Consensus size: 149
21723 AAATATTTGG
21733 AGTAATGCTTTTATATTCGAATAAATTTATCGAACATACTTTAGAAAATCATTTTGGAAAATCTT
1 AGTAATGCTTTTATATTCGAATAAATTTATCGAACATACTTTAGAAAATCATTTTGGAAAATCTT
21798 AAAATTCATTTAACTTAATTTGTTATATCGAAATATCAAAATGTTTTCAACAATCTCCCCCTTTT
66 AAAATTCATTTAACTTAATTTGTTATATCGAAATATCAAAATGTTTTCAACAATCTCCCCCTTTT
21863 TGATATAACAAAACATTTT
131 TGATATAACAAAACATTTT
*
21882 AGTAATGTTTTTATATTCGAATAAATTTATCGAACATACTTTAGAAAATCATTTTGGAAAATCTT
1 AGTAATGCTTTTATATTCGAATAAATTTATCGAACATACTTTAGAAAATCATTTTGGAAAATCTT
21947 AAAATTCATTTAACTTAATTTGTTATATCGAAATATCAAAATGTTTTCAACAATCTCCCCCTTTT
66 AAAATTCATTTAACTTAATTTGTTATATCGAAATATCAAAATGTTTTCAACAATCTCCCCCTTTT
22012 TGATATAACAAAACATTTT
131 TGATATAACAAAACATTTT
22031 AGTAAT
1 AGTAAT
22037 TTTAAGATTT
Statistics
Matches: 154, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 154 1.00
ACGTcount: A:0.38, C:0.13, G:0.08, T:0.40
Consensus pattern (149 bp):
AGTAATGCTTTTATATTCGAATAAATTTATCGAACATACTTTAGAAAATCATTTTGGAAAATCTT
AAAATTCATTTAACTTAATTTGTTATATCGAAATATCAAAATGTTTTCAACAATCTCCCCCTTTT
TGATATAACAAAACATTTT
Found at i:24369 original size:21 final size:21
Alignment explanation
Indices: 24343--24382 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
24333 CAGAACCCCA
*
24343 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
24364 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
24383 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:24417 original size:20 final size:21
Alignment explanation
Indices: 24363--24425 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 21
24353 GATTCCCCTG
24363 TGGGGGGAATCGGTTCCCCTTCAA
1 TGGGGGG-ATCGGTT-CCC-TCAA
* *
24387 AGGGGGAATCGGTTCCCTC-A
1 TGGGGGGATCGGTTCCCTCAA
*
24407 TGGGGGGATCGATTCCCTC
1 TGGGGGGATCGGTTCCCTC
24426 TGCACAAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 17 0.50
21 2 0.06
22 3 0.09
23 7 0.21
24 5 0.15
ACGTcount: A:0.16, C:0.25, G:0.35, T:0.24
Consensus pattern (21 bp):
TGGGGGGATCGGTTCCCTCAA
Found at i:28273 original size:22 final size:21
Alignment explanation
Indices: 28231--28270 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
28221 GAGTTTGTTT
*
28231 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
28252 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
28271 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:35740 original size:23 final size:23
Alignment explanation
Indices: 35709--35777 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 23
35699 CACCATAACT
* * *
35709 CGTATAAATGCACCGAAGTGTCG
1 CGTAGAAATGCACCGAAGTGCCA
*
35732 CGTAGAAATGCACCGTAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * *
35755 CGTAGAATTGTACTGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
35778 TATAAAATGT
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.30, C:0.22, G:0.26, T:0.22
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:48656 original size:15 final size:15
Alignment explanation
Indices: 48636--48700 Score: 114
Period size: 15 Copynumber: 4.3 Consensus size: 15
48626 GAAAGCGTAT
48636 GAAGTGGACAAGAAG
1 GAAGTGGACAAGAAG
48651 GAAGTGGACAAGAAG
1 GAAGTGGACAAGAAG
48666 GAAGTGGACAAGAAG
1 GAAGTGGACAAGAAG
48681 GAAGT-GAGCAAGAAG
1 GAAGTGGA-CAAGAAG
48696 GAAGT
1 GAAGT
48701 TGCCATCCAT
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
14 2 0.04
15 47 0.96
ACGTcount: A:0.46, C:0.06, G:0.40, T:0.08
Consensus pattern (15 bp):
GAAGTGGACAAGAAG
Done.