Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015898.1 Corchorus capsularis cultivar CVL-1 contig15919, 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: 60107
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:321 original size:22 final size:22
Alignment explanation
Indices: 291--333 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
281 CATGAGAAAC
* *
291 CAAGCCAAGAAAATGGGTGTCA
1 CAAGACAAGAAAAAGGGTGTCA
313 CAAGACAAGAAAAAGGGTGTC
1 CAAGACAAGAAAAAGGGTGTC
334 CGAGTTTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.44, C:0.16, G:0.28, T:0.12
Consensus pattern (22 bp):
CAAGACAAGAAAAAGGGTGTCA
Found at i:582 original size:13 final size:13
Alignment explanation
Indices: 538--600 Score: 54
Period size: 15 Copynumber: 4.5 Consensus size: 13
528 TTTTATGCAT
**
538 TTAATATATTAAA
1 TTAATATAGAAAA
*
551 TTAATAATGAGAATTA
1 TTAAT-AT-AGAA-AA
567 TTAATATAGAAAA
1 TTAATATAGAAAA
580 TTAATTTATAGAAAA
1 TTAA--TATAGAAAA
595 TTAATA
1 TTAATA
601 ATGAAAATAC
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
13 12 0.29
14 6 0.15
15 17 0.41
16 6 0.15
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.40
Consensus pattern (13 bp):
TTAATATAGAAAA
Found at i:592 original size:29 final size:28
Alignment explanation
Indices: 538--608 Score: 65
Period size: 29 Copynumber: 2.5 Consensus size: 28
528 TTTTATGCAT
** *
538 TTAATATATTAAATTAATAATGAGAATTA
1 TTAATATAGAAAATTAATAATGAGAA-AA
*
567 TTAATATAGAAAATTAATTTAT-AGAAAA
1 TTAATATAGAAAATTAA-TAATGAGAAAA
595 TTAATA-ATGAAAAT
1 TTAATATA-GAAAAT
609 ACCGTTTCTA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
27 1 0.03
28 13 0.36
29 19 0.53
30 3 0.08
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (28 bp):
TTAATATAGAAAATTAATAATGAGAAAA
Found at i:608 original size:13 final size:14
Alignment explanation
Indices: 548--608 Score: 63
Period size: 15 Copynumber: 4.3 Consensus size: 14
538 TTAATATATT
548 AAATTAATAATGAGA
1 AAATTAATAAT-AGA
*
563 ATTATTAAT-ATAGA
1 A-AATTAATAATAGA
*
577 AAATTAATTTATAGA
1 AAATTAA-TAATAGA
592 AAATTAATAAT-GA
1 AAATTAATAATAGA
605 AAAT
1 AAAT
609 ACCGTTTCTA
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
13 11 0.28
14 8 0.20
15 15 0.38
16 6 0.15
ACGTcount: A:0.57, C:0.00, G:0.08, T:0.34
Consensus pattern (14 bp):
AAATTAATAATAGA
Found at i:3693 original size:21 final size:20
Alignment explanation
Indices: 3669--3708 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
3659 AATTCCCATA
3669 AAAAATGATGAAAAATGAAAT
1 AAAAATGATGAAAAA-GAAAT
**
3690 AAAAATTTTGAAAAAGAAA
1 AAAAATGATGAAAAAGAAA
3709 AGGATGAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.68, C:0.00, G:0.12, T:0.20
Consensus pattern (20 bp):
AAAAATGATGAAAAAGAAAT
Found at i:3748 original size:8 final size:7
Alignment explanation
Indices: 3700--3747 Score: 53
Period size: 7 Copynumber: 6.7 Consensus size: 7
3690 AAAAATTTTG
3700 AAAAAGA
1 AAAAAGA
*
3707 AAAGGATGA
1 AAA--AAGA
*
3716 AAAATGA
1 AAAAAGA
3723 AAAAAG-
1 AAAAAGA
3729 AAAAAGA
1 AAAAAGA
3736 AAAAAGA
1 AAAAAGA
3743 AAAAA
1 AAAAA
3748 AAAGCACTTG
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
6 6 0.17
7 24 0.67
9 6 0.17
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.04
Consensus pattern (7 bp):
AAAAAGA
Found at i:3854 original size:12 final size:13
Alignment explanation
Indices: 3826--3854 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
3816 GATTTTCAAA
3826 AAAATGTTTTTCT
1 AAAATGTTTTTCT
3839 AAAATGTTTTTC-
1 AAAATGTTTTTCT
3851 AAAA
1 AAAA
3855 ACGGTTTTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.25
13 12 0.75
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.45
Consensus pattern (13 bp):
AAAATGTTTTTCT
Found at i:3855 original size:13 final size:14
Alignment explanation
Indices: 3804--3855 Score: 70
Period size: 15 Copynumber: 3.7 Consensus size: 14
3794 AGAGTCATGG
*
3804 TTTTCAAAAAATGA
1 TTTTCAAAAAATGT
3818 TTTTCAAAAAAATGT
1 TTTTC-AAAAAATGT
*
3833 TTTTC-TAAAATGT
1 TTTTCAAAAAATGT
3846 TTTTCAAAAA
1 TTTTCAAAAA
3856 CGGTTTTTGA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
13 12 0.36
14 8 0.24
15 13 0.39
ACGTcount: A:0.44, C:0.08, G:0.06, T:0.42
Consensus pattern (14 bp):
TTTTCAAAAAATGT
Found at i:4223 original size:22 final size:20
Alignment explanation
Indices: 4191--4232 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
4181 AAATAATAAT
4191 AATAAAATACAATCAAAAAAA
1 AATAAAATAC-ATCAAAAAAA
4212 AATACAAATACATCAAAAAAA
1 AATA-AAATACATCAAAAAAA
4233 GTAAAATGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.74, C:0.12, G:0.00, T:0.14
Consensus pattern (20 bp):
AATAAAATACATCAAAAAAA
Found at i:4231 original size:20 final size:19
Alignment explanation
Indices: 4171--4232 Score: 69
Period size: 20 Copynumber: 3.3 Consensus size: 19
4161 CAAAAAAATC
4171 AAAAAAATACAAATA-ATA
1 AAAAAAATACAAATACATA
4189 ATAATAAAATAC-AAT-CA-A
1 A-AA-AAAATACAAATACATA
4207 AAAAAAATACAAATACATCA
1 AAAAAAATACAAATACAT-A
4227 AAAAAA
1 AAAAAA
4233 GTAAAATGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
16 7 0.19
17 5 0.14
18 5 0.14
19 6 0.16
20 14 0.38
ACGTcount: A:0.74, C:0.10, G:0.00, T:0.16
Consensus pattern (19 bp):
AAAAAAATACAAATACATA
Found at i:4519 original size:13 final size:14
Alignment explanation
Indices: 4503--4532 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
4493 TGGTCAAAAC
4503 TTTTGAAAA-GAGT
1 TTTTGAAAACGAGT
4516 TTTTGAAAACGAGT
1 TTTTGAAAACGAGT
4530 TTT
1 TTT
4533 CGGGTTAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.56
14 7 0.44
ACGTcount: A:0.33, C:0.03, G:0.20, T:0.43
Consensus pattern (14 bp):
TTTTGAAAACGAGT
Found at i:5894 original size:22 final size:22
Alignment explanation
Indices: 5869--5942 Score: 76
Period size: 22 Copynumber: 3.2 Consensus size: 22
5859 TCCGAGCACA
*
5869 AATTCAGAAACCTCCGGGTGTT
1 AATTCAGAAACCTCCGGGTATT
* * **
5891 AATTCTGATAAGTCCTCCGGGCACA
1 AATTCAGA-AA--CCTCCGGGTATT
5916 AATTCAGAAACCTCCGGGTATT
1 AATTCAGAAACCTCCGGGTATT
5938 AATTC
1 AATTC
5943 TGATAAGTCC
Statistics
Matches: 40, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
22 21 0.52
23 2 0.05
24 2 0.05
25 15 0.38
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.27
Consensus pattern (22 bp):
AATTCAGAAACCTCCGGGTATT
Found at i:5908 original size:25 final size:25
Alignment explanation
Indices: 5879--5958 Score: 94
Period size: 25 Copynumber: 3.3 Consensus size: 25
5869 AATTCAGAAA
*
5879 CCTCCGGGTGTTAATTCTGATAAGT
1 CCTCCGGGTATTAATTCTGATAAGT
* ** *
5904 CCTCCGGGCACAAATTCAGA-AA--
1 CCTCCGGGTATTAATTCTGATAAGT
5926 CCTCCGGGTATTAATTCTGATAAGT
1 CCTCCGGGTATTAATTCTGATAAGT
5951 CCTCCGGG
1 CCTCCGGG
5959 CAATTGGTAA
Statistics
Matches: 43, Mismatches: 9, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
22 16 0.37
23 2 0.05
24 2 0.05
25 23 0.53
ACGTcount: A:0.24, C:0.26, G:0.23, T:0.28
Consensus pattern (25 bp):
CCTCCGGGTATTAATTCTGATAAGT
Found at i:5921 original size:47 final size:47
Alignment explanation
Indices: 5852--5960 Score: 200
Period size: 47 Copynumber: 2.3 Consensus size: 47
5842 TTTGCATTGG
* *
5852 TAAGTCCTCCGAGCACAAATTCAGAAACCTCCGGGTGTTAATTCTGA
1 TAAGTCCTCCGGGCACAAATTCAGAAACCTCCGGGTATTAATTCTGA
5899 TAAGTCCTCCGGGCACAAATTCAGAAACCTCCGGGTATTAATTCTGA
1 TAAGTCCTCCGGGCACAAATTCAGAAACCTCCGGGTATTAATTCTGA
5946 TAAGTCCTCCGGGCA
1 TAAGTCCTCCGGGCA
5961 ATTGGTAAAA
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
47 60 1.00
ACGTcount: A:0.28, C:0.27, G:0.20, T:0.25
Consensus pattern (47 bp):
TAAGTCCTCCGGGCACAAATTCAGAAACCTCCGGGTATTAATTCTGA
Found at i:5963 original size:22 final size:23
Alignment explanation
Indices: 5891--5963 Score: 64
Period size: 22 Copynumber: 3.2 Consensus size: 23
5881 TCCGGGTGTT
5891 AATTCTGATAAGTCCTCCGGGCAC
1 AATTCTGATAAGTCCTCCGGG-AC
* *
5915 AAATTCAGA-AA--CCTCCGGGTATT
1 -AATTCTGATAAGTCCTCCGGG-A-C
5938 AATTCTGATAAGTCCTCCGGG-C
1 AATTCTGATAAGTCCTCCGGGAC
5960 AATT
1 AATT
5964 GGTAAAACCT
Statistics
Matches: 39, Mismatches: 5, Indels: 11
0.71 0.09 0.20
Matches are distributed among these distances:
22 20 0.51
23 2 0.05
24 2 0.05
25 15 0.38
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.27
Consensus pattern (23 bp):
AATTCTGATAAGTCCTCCGGGAC
Found at i:6111 original size:25 final size:25
Alignment explanation
Indices: 6082--6162 Score: 78
Period size: 25 Copynumber: 3.3 Consensus size: 25
6072 AATTCAGAAA
*
6082 CCTCCGGGTGTTAATTCTGATAAGT
1 CCTCCGGGTATTAATTCTGATAAGT
* ** *
6107 CCTCCGGGCACAAATTCAGA-AA--
1 CCTCCGGGTATTAATTCTGATAAGT
*
6129 CCTTCCGAGTATTAATTCTGATAAGT
1 CC-TCCGGGTATTAATTCTGATAAGT
6155 CCTCCGGG
1 CCTCCGGG
6163 CAATTGGTAA
Statistics
Matches: 41, Mismatches: 11, Indels: 8
0.68 0.18 0.13
Matches are distributed among these distances:
22 2 0.05
23 13 0.32
24 4 0.10
25 20 0.49
26 2 0.05
ACGTcount: A:0.25, C:0.26, G:0.21, T:0.28
Consensus pattern (25 bp):
CCTCCGGGTATTAATTCTGATAAGT
Found at i:6124 original size:47 final size:48
Alignment explanation
Indices: 6055--6164 Score: 186
Period size: 48 Copynumber: 2.3 Consensus size: 48
6045 TTTGCATTAG
* * *
6055 TAAGTCCTCCGAGCACAAATTCAGAAACC-TCCGGGTGTTAATTCTGA
1 TAAGTCCTCCGGGCACAAATTCAGAAACCTTCCGAGTATTAATTCTGA
6102 TAAGTCCTCCGGGCACAAATTCAGAAACCTTCCGAGTATTAATTCTGA
1 TAAGTCCTCCGGGCACAAATTCAGAAACCTTCCGAGTATTAATTCTGA
6150 TAAGTCCTCCGGGCA
1 TAAGTCCTCCGGGCA
6165 ATTGGTAAAA
Statistics
Matches: 59, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
47 28 0.47
48 31 0.53
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.25
Consensus pattern (48 bp):
TAAGTCCTCCGGGCACAAATTCAGAAACCTTCCGAGTATTAATTCTGA
Found at i:6251 original size:204 final size:203
Alignment explanation
Indices: 5791--6415 Score: 1106
Period size: 203 Copynumber: 3.1 Consensus size: 203
5781 ACGAGTTAGT
* *
5791 TCAAGTTTTTATTATATTTTAAAATCCTTGATCGAAGGTGTCAATTCAAAGTTTGCATTGGTAAG
1 TCAAGTTTTTATCATATTTTAAAATCCTTGATCGAAGGTGTCAATTCAGAGTTTGCATTGGTAAG
5856 TCCTCCGAGCACAAATTCAGAAACCTCCGGGTGTTAATTCTGATAAGTCCTCCGGGCACAAATTC
66 TCCTCCGAGCACAAATTCAGAAACCTCCGGGTGTTAATTCTGATAAGTCCTCCGGGCACAAATTC
5921 AGAAACCTCCGGGTATTAATTCTGATAAGTCCTCCGGGCAATTGGTAAAACCTCCGGGTACCATT
131 AGAAACCTCCGGGTATTAATTCTGATAAGTCCTCCGGGCAATTGGTAAAACCTCCGGGTACCATT
5986 TCATTCCA
196 TCATTCCA
* *
5994 TCAAGTTTTTGTCATATTTTAAAATCCTTGATCGAAGGTGTCAATTCAGAGTTTGCATTAGTAAG
1 TCAAGTTTTTATCATATTTTAAAATCCTTGATCGAAGGTGTCAATTCAGAGTTTGCATTGGTAAG
6059 TCCTCCGAGCACAAATTCAGAAACCTCCGGGTGTTAATTCTGATAAGTCCTCCGGGCACAAATTC
66 TCCTCCGAGCACAAATTCAGAAACCTCCGGGTGTTAATTCTGATAAGTCCTCCGGGCACAAATTC
*
6124 AGAAACCTTCCGAGTATTAATTCTGATAAGTCCTCCGGGCAATTGGTAAAACCTCCGGGTACCAT
131 AGAAACC-TCCGGGTATTAATTCTGATAAGTCCTCCGGGCAATTGGTAAAACCTCCGGGTACCAT
6189 TTCATTCCA
195 TTCATTCCA
*
6198 TCAAGTTTTTATCATATTTTAAAATCCTTGATCGAAGGTGTCAATTTAGAGTTTGCATTGGTAAG
1 TCAAGTTTTTATCATATTTTAAAATCCTTGATCGAAGGTGTCAATTCAGAGTTTGCATTGGTAAG
* * * *
6263 TCCTCCGGGCACAAATTCAGAAAACTCTGGGTGTTAATTCTGATAAGTCCTCCGGGCACAATTTC
66 TCCTCCGAGCACAAATTCAGAAACCTCCGGGTGTTAATTCTGATAAGTCCTCCGGGCACAAATTC
**
6328 AGAAACCTCCGGGTATTAATTCTGATAAGTCCTCCGGGCAACGGGTAAAACCTCCGGGTACCATT
131 AGAAACCTCCGGGTATTAATTCTGATAAGTCCTCCGGGCAATTGGTAAAACCTCCGGGTACCATT
* *
6393 TCATTTCG
196 TCATTCCA
6401 TCAAGTTTTTCATCA
1 TCAAGTTTTT-ATCA
6416 AAGATTCATG
Statistics
Matches: 403, Mismatches: 17, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
203 204 0.51
204 199 0.49
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.32
Consensus pattern (203 bp):
TCAAGTTTTTATCATATTTTAAAATCCTTGATCGAAGGTGTCAATTCAGAGTTTGCATTGGTAAG
TCCTCCGAGCACAAATTCAGAAACCTCCGGGTGTTAATTCTGATAAGTCCTCCGGGCACAAATTC
AGAAACCTCCGGGTATTAATTCTGATAAGTCCTCCGGGCAATTGGTAAAACCTCCGGGTACCATT
TCATTCCA
Found at i:6329 original size:47 final size:47
Alignment explanation
Indices: 6259--6367 Score: 182
Period size: 47 Copynumber: 2.3 Consensus size: 47
6249 TTTGCATTGG
* *
6259 TAAGTCCTCCGGGCACAAATTCAGAAAACTCTGGGTGTTAATTCTGA
1 TAAGTCCTCCGGGCACAAATTCAGAAAACTCCGGGTATTAATTCTGA
* *
6306 TAAGTCCTCCGGGCACAATTTCAGAAACCTCCGGGTATTAATTCTGA
1 TAAGTCCTCCGGGCACAAATTCAGAAAACTCCGGGTATTAATTCTGA
6353 TAAGTCCTCCGGGCA
1 TAAGTCCTCCGGGCA
6368 ACGGGTAAAA
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 58 1.00
ACGTcount: A:0.28, C:0.25, G:0.21, T:0.27
Consensus pattern (47 bp):
TAAGTCCTCCGGGCACAAATTCAGAAAACTCCGGGTATTAATTCTGA
Found at i:6362 original size:25 final size:25
Alignment explanation
Indices: 6291--6365 Score: 77
Period size: 25 Copynumber: 3.1 Consensus size: 25
6281 AGAAAACTCT
*
6291 GGGTGTTAATTCTGATAAGTCCTCC
1 GGGTATTAATTCTGATAAGTCCTCC
* * *
6316 GGGCA-CAATTTCAGA-AA--CCTCC
1 GGGTATTAA-TTCTGATAAGTCCTCC
6338 GGGTATTAATTCTGATAAGTCCTCC
1 GGGTATTAATTCTGATAAGTCCTCC
6363 GGG
1 GGG
6366 CAACGGGTAA
Statistics
Matches: 38, Mismatches: 7, Indels: 10
0.69 0.13 0.18
Matches are distributed among these distances:
22 14 0.37
23 4 0.11
24 4 0.11
25 16 0.42
ACGTcount: A:0.24, C:0.23, G:0.24, T:0.29
Consensus pattern (25 bp):
GGGTATTAATTCTGATAAGTCCTCC
Found at i:7346 original size:12 final size:13
Alignment explanation
Indices: 7329--7357 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
7319 GAGGGGCAGG
7329 AAAATAGAAAAA-
1 AAAATAGAAAAAT
7341 AAAATAGAAAAAT
1 AAAATAGAAAAAT
7354 AAAA
1 AAAA
7358 GGAAAAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.83, C:0.00, G:0.07, T:0.10
Consensus pattern (13 bp):
AAAATAGAAAAAT
Found at i:9947 original size:22 final size:22
Alignment explanation
Indices: 9898--9940 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
9888 AGCTCATTCG
*
9898 AATTTCTGAAATTGAATTACAC
1 AATTTATGAAATTGAATTACAC
9920 AATTTATGAAATTGAATTACA
1 AATTTATGAAATTGAATTACA
9941 TTATTTAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.37
Consensus pattern (22 bp):
AATTTATGAAATTGAATTACAC
Found at i:18841 original size:13 final size:13
Alignment explanation
Indices: 18820--18859 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
18810 AAGGGCTTTA
18820 AATTAATTAATAAT
1 AATT-ATTAATAAT
*
18834 AATTATTAAAAAT
1 AATTATTAATAAT
*
18847 AATTATTATTAAT
1 AATTATTAATAAT
18860 TTCTCCTAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
13 19 0.83
14 4 0.17
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
AATTATTAATAAT
Found at i:18849 original size:16 final size:16
Alignment explanation
Indices: 18828--18858 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
18818 TAAATTAATT
18828 AATAATAATTATTAAA
1 AATAATAATTATTAAA
*
18844 AATAATTATTATTAA
1 AATAATAATTATTAA
18859 TTTCTCCTAG
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:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
AATAATAATTATTAAA
Found at i:22477 original size:21 final size:22
Alignment explanation
Indices: 22430--22479 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
22420 AAATAATGTC
22430 CGTAGCAAATGTAAATAAAGCT
1 CGTAGCAAATGTAAATAAAGCT
22452 CGTAGCAAATGTAAAT-AAGCT
1 CGTAGCAAATGTAAATAAAGCT
*
22473 TGTAGCA
1 CGTAGCA
22480 TATAGGAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
21 11 0.41
22 16 0.59
ACGTcount: A:0.42, C:0.14, G:0.20, T:0.24
Consensus pattern (22 bp):
CGTAGCAAATGTAAATAAAGCT
Found at i:23106 original size:25 final size:25
Alignment explanation
Indices: 23021--23106 Score: 75
Period size: 25 Copynumber: 3.3 Consensus size: 25
23011 TGAAAAACAA
23021 TAAGAAAAGCTTAAGCAATTAGCAT
1 TAAGAAAAGCTTAAGCAATTAGCAT
** ** *
23046 TAAGAAAA-CAGAAGTGACAAAAATGAAT
1 TAAGAAAAGCTTAA--G-CAATTA-GCAT
*
23074 GAAGAAAAGCTTAAGCAATTAGCAT
1 TAAGAAAAGCTTAAGCAATTAGCAT
23099 TAAGAAAA
1 TAAGAAAA
23107 CAATTCTAGA
Statistics
Matches: 44, Mismatches: 12, Indels: 10
0.67 0.18 0.15
Matches are distributed among these distances:
24 3 0.07
25 18 0.41
26 5 0.11
27 5 0.11
28 10 0.23
29 3 0.07
ACGTcount: A:0.55, C:0.09, G:0.17, T:0.19
Consensus pattern (25 bp):
TAAGAAAAGCTTAAGCAATTAGCAT
Found at i:25162 original size:13 final size:13
Alignment explanation
Indices: 25144--25193 Score: 59
Period size: 13 Copynumber: 4.0 Consensus size: 13
25134 AATTTCTAAA
25144 AAACTGATTTCAG
1 AAACTGATTTCAG
**
25157 AAACTGAAATCAG
1 AAACTGATTTCAG
25170 --ACTGATTTCAG
1 AAACTGATTTCAG
*
25181 AATCTGATTTCAG
1 AAACTGATTTCAG
25194 TGTGATTTCA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
11 9 0.30
13 21 0.70
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (13 bp):
AAACTGATTTCAG
Found at i:25178 original size:24 final size:24
Alignment explanation
Indices: 25146--25210 Score: 76
Period size: 24 Copynumber: 2.7 Consensus size: 24
25136 TTTCTAAAAA
25146 ACTGATTTCAGAAACTGAAATCAG
1 ACTGATTTCAGAAACTGAAATCAG
* **
25170 ACTGATTTCAGAATCTGATTTCAG
1 ACTGATTTCAGAAACTGAAATCAG
**
25194 TGTGATTTCAGCAAACT
1 ACTGATTTCAG-AAACT
25211 ATAAGAAAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
24 30 0.88
25 4 0.12
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (24 bp):
ACTGATTTCAGAAACTGAAATCAG
Found at i:31748 original size:2 final size:2
Alignment explanation
Indices: 31741--31772 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
31731 AAACAGAATT
31741 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
31773 AGAAACCCTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:33523 original size:43 final size:43
Alignment explanation
Indices: 33475--33563 Score: 169
Period size: 43 Copynumber: 2.1 Consensus size: 43
33465 CATACTCTCC
33475 TTTAATCTTTTCTTTTCTAAGCCTTTATTATTGATGTCTCAAT
1 TTTAATCTTTTCTTTTCTAAGCCTTTATTATTGATGTCTCAAT
*
33518 TTTAATCTTTTCTTTTCTAAGCCTTTATTATTGATGTTTCAAT
1 TTTAATCTTTTCTTTTCTAAGCCTTTATTATTGATGTCTCAAT
33561 TTT
1 TTT
33564 CTTTTACTCA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.20, C:0.15, G:0.07, T:0.58
Consensus pattern (43 bp):
TTTAATCTTTTCTTTTCTAAGCCTTTATTATTGATGTCTCAAT
Found at i:39048 original size:151 final size:153
Alignment explanation
Indices: 38717--39037 Score: 380
Period size: 151 Copynumber: 2.1 Consensus size: 153
38707 TCAAAGTTCT
* **
38717 ACCATATCGTGGTGTTTTATCCAAAAAAATGCCACCATAAGTGTTTTATAATATTCTATAAGAAA
1 ACCATATCGAGGCATTTTATCCAAAAAAATGCCACCATAAGTGTTTTATAATATTCTATAAGAAA
* * * * * **
38782 AATATATAAATGGGAAAAATGAATTATTTGGGTAGAATATTTTCCCACCAAATTTTTTCATGTGT
66 AAAATATAAACGGAAAAAATGAATTATTTGGGCAGAATATTTTCCCACCAAATTTTTTCATATCC
*
38847 CGCCATTTTCAAACCAAAACGCC
131 CGCCATTTTCAAACCAAAACACC
* ** * * *
38870 ACCATATTGAGGGGTTTTATCCAAAAAAA-GCCATCATAAGTGTTTTATACTATTTTATAA-AAA
1 ACCATATCGAGGCATTTTATCCAAAAAAATGCCACCATAAGTGTTTTATAATATTCTATAAGAAA
*
38933 AAAATATAAACGGAAAAAATGAATTATTTGGGC-GGATAATTTTCCCACCAAATTTTTTCATATC
66 AAAATATAAACGGAAAAAATGAATTATTTGGGCAGAAT-ATTTTCCCACCAAATTTTTTCATATC
*** * *
38997 CCGGTGTTTTCAAGCTAAAACACC
130 CCGCCATTTTCAAACCAAAACACC
*
39021 A-TAGTATCGAGGCATTT
1 ACCA-TATCGAGGCATTT
39038 CTGTCGAAAA
Statistics
Matches: 142, Mismatches: 24, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
150 4 0.03
151 84 0.59
152 28 0.20
153 26 0.18
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (153 bp):
ACCATATCGAGGCATTTTATCCAAAAAAATGCCACCATAAGTGTTTTATAATATTCTATAAGAAA
AAAATATAAACGGAAAAAATGAATTATTTGGGCAGAATATTTTCCCACCAAATTTTTTCATATCC
CGCCATTTTCAAACCAAAACACC
Found at i:41683 original size:19 final size:19
Alignment explanation
Indices: 41659--41698 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
41649 GCAGTGATCA
41659 AACAAACCTGATTTGCTAC
1 AACAAACCTGATTTGCTAC
41678 AACAAACCTGATTTGCTAC
1 AACAAACCTGATTTGCTAC
41697 AA
1 AA
41699 ACAATCAAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.40, C:0.25, G:0.10, T:0.25
Consensus pattern (19 bp):
AACAAACCTGATTTGCTAC
Found at i:41761 original size:11 final size:11
Alignment explanation
Indices: 41745--41769 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
41735 TAGCCATAGA
41745 CAAGAAATCTT
1 CAAGAAATCTT
41756 CAAGAAATCTT
1 CAAGAAATCTT
41767 CAA
1 CAA
41770 AACACGAACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.48, C:0.20, G:0.08, T:0.24
Consensus pattern (11 bp):
CAAGAAATCTT
Found at i:42773 original size:21 final size:21
Alignment explanation
Indices: 42747--42789 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
42737 TGCATTTAGA
42747 AAGTTTCAGTCGATTAAATGC
1 AAGTTTCAGTCGATTAAATGC
* *
42768 AAGTTTTAGTCGATTGAATGC
1 AAGTTTCAGTCGATTAAATGC
42789 A
1 A
42790 GTGGCCATCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.35
Consensus pattern (21 bp):
AAGTTTCAGTCGATTAAATGC
Found at i:43327 original size:43 final size:43
Alignment explanation
Indices: 43227--43315 Score: 151
Period size: 43 Copynumber: 2.1 Consensus size: 43
43217 CATACTCTCC
* *
43227 TTTAATCTTTTCTTTTCTAAGGCTTTATTTTTTATGTCTCAAT
1 TTTAATCTTTTCTTTTCTAAGGCTTTATTATTGATGTCTCAAT
*
43270 TTTAATCTTTTCTTTTCTAAGTCTTTATTATTGATGTCTCAAT
1 TTTAATCTTTTCTTTTCTAAGGCTTTATTATTGATGTCTCAAT
43313 TTT
1 TTT
43316 CTTTTACTCT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.19, C:0.13, G:0.07, T:0.61
Consensus pattern (43 bp):
TTTAATCTTTTCTTTTCTAAGGCTTTATTATTGATGTCTCAAT
Found at i:44518 original size:22 final size:20
Alignment explanation
Indices: 44492--44539 Score: 64
Period size: 22 Copynumber: 2.4 Consensus size: 20
44482 ATCGGGCTAG
44492 AGGAGAGAGAAAAACAAGAAGT
1 AGGAGAGAGAAAAA-AAGAA-T
44514 AGGAGAG-GAAAAAAAGAAT
1 AGGAGAGAGAAAAAAAGAAT
44533 A-GAGAGA
1 AGGAGAGA
44540 TCTAATCAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 5 0.20
19 2 0.08
20 5 0.20
21 6 0.24
22 7 0.28
ACGTcount: A:0.60, C:0.02, G:0.33, T:0.04
Consensus pattern (20 bp):
AGGAGAGAGAAAAAAAGAAT
Found at i:44539 original size:20 final size:21
Alignment explanation
Indices: 44494--44539 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
44484 CGGGCTAGAG
44494 GAGAGAGAAAAACAAGAAGTA
1 GAGAGAGAAAAACAAGAAGTA
44515 G-GAGAGGAAAAA-AAGAA-TA
1 GAGAGA-GAAAAACAAGAAGTA
44534 GAGAGA
1 GAGAGA
44540 TCTAATCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
19 3 0.13
20 13 0.57
21 7 0.30
ACGTcount: A:0.61, C:0.02, G:0.33, T:0.04
Consensus pattern (21 bp):
GAGAGAGAAAAACAAGAAGTA
Found at i:44802 original size:30 final size:29
Alignment explanation
Indices: 44760--44816 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 29
44750 GATCAGGGCC
*
44760 AAACGTTTAGAAA-GCTACAAATGAAGGCT
1 AAACCTTTAGAAACGCTACAAAT-AAGGCT
*
44789 AAACCTTTCAGAAACGCTCCAAATAAGG
1 AAACCTTT-AGAAACGCTACAAATAAGG
44817 ACATATTCTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 7 0.29
30 9 0.38
31 8 0.33
ACGTcount: A:0.44, C:0.19, G:0.18, T:0.19
Consensus pattern (29 bp):
AAACCTTTAGAAACGCTACAAATAAGGCT
Found at i:48964 original size:31 final size:33
Alignment explanation
Indices: 48929--49000 Score: 80
Period size: 31 Copynumber: 2.3 Consensus size: 33
48919 TAAATTATTG
*
48929 CAAATTAAAAT-AAAT-TAAGCATTAAATTAAA
1 CAAATTAAAATAAAATGAAAGCATTAAATTAAA
* * *
48960 CAAA-T-AATTAAAATGAAAGCCTTCAATTAAA
1 CAAATTAAAATAAAATGAAAGCATTAAATTAAA
48991 CAAATTAAAA
1 CAAATTAAAA
49001 GTTGATAGAT
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
29 3 0.09
30 5 0.16
31 21 0.66
32 1 0.03
33 2 0.06
ACGTcount: A:0.60, C:0.10, G:0.04, T:0.26
Consensus pattern (33 bp):
CAAATTAAAATAAAATGAAAGCATTAAATTAAA
Found at i:49233 original size:2 final size:2
Alignment explanation
Indices: 49226--49256 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
49216 TTGCTTTAGG
49226 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
49257 TTAGTAGTTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:55304 original size:6 final size:6
Alignment explanation
Indices: 55293--55324 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
55283 CTAACATAGT
55293 AAATAA AAATAA AAATAA AAATAA AAATAA AA
1 AAATAA AAATAA AAATAA AAATAA AAATAA AA
55325 TAATCTATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAATAA
Found at i:55570 original size:62 final size:61
Alignment explanation
Indices: 55454--55584 Score: 147
Period size: 62 Copynumber: 2.1 Consensus size: 61
55444 AAACCAGTCT
* * ** **
55454 TAAATTGAAGCAAATTAACATGAACATGCCTCAAATCGCAGAGATCTACCATAATCAAGCAA
1 TAAATTGAAACAAATCAACATGAACATGCCTCAAATCGCAGAGAAATAAAATAAT-AAGCAA
* * * *
55516 TAAATTGAAACAAATCAGCATGAACATGCCTCAAATCGTAGTA-AAATAAAATAATAAGGAG
1 TAAATTGAAACAAATCAACATGAACATGCCTCAAATCGCAG-AGAAATAAAATAATAAGCAA
55577 TAAATTGA
1 TAAATTGA
55585 GAAGGGAAGG
Statistics
Matches: 58, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
61 12 0.21
62 45 0.78
63 1 0.02
ACGTcount: A:0.48, C:0.16, G:0.14, T:0.22
Consensus pattern (61 bp):
TAAATTGAAACAAATCAACATGAACATGCCTCAAATCGCAGAGAAATAAAATAATAAGCAA
Found at i:58003 original size:18 final size:18
Alignment explanation
Indices: 57980--58017 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
57970 TTAACGATGA
57980 ACTAAACCGGATTAAACT
1 ACTAAACCGGATTAAACT
57998 ACTAAACCGGATTAAACT
1 ACTAAACCGGATTAAACT
58016 AC
1 AC
58018 CACAAAGCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.45, C:0.24, G:0.11, T:0.21
Consensus pattern (18 bp):
ACTAAACCGGATTAAACT
Found at i:59496 original size:15 final size:16
Alignment explanation
Indices: 59476--59515 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
59466 GGCAATTGGG
59476 CGGGTTCGGG-TACTT
1 CGGGTTCGGGCTACTT
**
59491 CGGGTTCGGGCTTTTT
1 CGGGTTCGGGCTACTT
59507 CGGGTTCGG
1 CGGGTTCGG
59516 TCTCGAGTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 10 0.45
16 12 0.55
ACGTcount: A:0.03, C:0.20, G:0.42, T:0.35
Consensus pattern (16 bp):
CGGGTTCGGGCTACTT
Found at i:59724 original size:10 final size:9
Alignment explanation
Indices: 59665--59728 Score: 57
Period size: 8 Copynumber: 7.4 Consensus size: 9
59655 AAGTTTATTG
59665 ATAATATAT
1 ATAATATAT
59674 AT-ATATAAT
1 ATAATAT-AT
59683 ATAATA-AT
1 ATAATATAT
*
59691 ATAATATAAC
1 ATAATAT-AT
59701 ATAAT-TAT
1 ATAATATAT
*
59709 -CAATATAT
1 ATAATATAT
59717 AT-ATATAT
1 ATAATATAT
59725 ATAA
1 ATAA
59729 AGATTGAATA
Statistics
Matches: 44, Mismatches: 4, Indels: 14
0.71 0.06 0.23
Matches are distributed among these distances:
7 3 0.07
8 24 0.55
9 8 0.18
10 9 0.20
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (9 bp):
ATAATATAT
Found at i:60015 original size:31 final size:33
Alignment explanation
Indices: 59980--60051 Score: 89
Period size: 31 Copynumber: 2.3 Consensus size: 33
59970 TAAATTATTG
*
59980 CAAATTAAAAT-AAAT-TAAGCATTAAATTAAA
1 CAAATTAAAATAAAATGAAAGCATTAAATTAAA
* *
60011 CAAA-T-AATTAAAATGAAAGCCTTAAATTAAA
1 CAAATTAAAATAAAATGAAAGCATTAAATTAAA
60042 CAAATTAAAA
1 CAAATTAAAA
60052 GTTGATAGAT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
29 3 0.09
30 5 0.15
31 22 0.67
32 1 0.03
33 2 0.06
ACGTcount: A:0.61, C:0.08, G:0.04, T:0.26
Consensus pattern (33 bp):
CAAATTAAAATAAAATGAAAGCATTAAATTAAA
Done.