Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007070.1 Corchorus capsularis cultivar CVL-1 contig07091, 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: 20145
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Found at i:960 original size:1 final size:1
Alignment explanation
Indices: 954--979 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
944 CAATCTATTT
954 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
980 CACATCCTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:4122 original size:25 final size:25
Alignment explanation
Indices: 4078--4127 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
4068 CAGAAAAAGA
4078 AGTCTATAAATATGCCATATTTGAC
1 AGTCTATAAATATGCCATATTTGAC
* * *
4103 AGTCTATAACTGTGCTATATTTGAC
1 AGTCTATAAATATGCCATATTTGAC
4128 TCATGATAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (25 bp):
AGTCTATAAATATGCCATATTTGAC
Found at i:7015 original size:25 final size:25
Alignment explanation
Indices: 6987--7059 Score: 63
Period size: 25 Copynumber: 3.2 Consensus size: 25
6977 TTTACTTTCA
6987 TTTTCATTAAGCATATCCACATTTG
1 TTTTCATTAAGCATATCCACATTTG
* *
7012 TTTTC----A-CAT-T-TAC-TTTCA
1 TTTTCATTAAGCATATCCACATTT-G
7030 TTTTCATTAAGCATATCCACATTTG
1 TTTTCATTAAGCATATCCACATTTG
7055 TTTTC
1 TTTTC
7060 GCAGCATATG
Statistics
Matches: 35, Mismatches: 4, Indels: 18
0.61 0.07 0.32
Matches are distributed among these distances:
17 3 0.09
18 7 0.20
19 1 0.03
20 3 0.09
21 1 0.03
22 1 0.03
23 3 0.09
24 1 0.03
25 12 0.34
26 3 0.09
ACGTcount: A:0.25, C:0.21, G:0.05, T:0.49
Consensus pattern (25 bp):
TTTTCATTAAGCATATCCACATTTG
Found at i:7037 original size:43 final size:43
Alignment explanation
Indices: 6976--7059 Score: 168
Period size: 43 Copynumber: 2.0 Consensus size: 43
6966 TGACCATTAT
6976 ATTTACTTTCATTTTCATTAAGCATATCCACATTTGTTTTCAC
1 ATTTACTTTCATTTTCATTAAGCATATCCACATTTGTTTTCAC
7019 ATTTACTTTCATTTTCATTAAGCATATCCACATTTGTTTTC
1 ATTTACTTTCATTTTCATTAAGCATATCCACATTTGTTTTC
7060 GCAGCATATG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.25, C:0.20, G:0.05, T:0.50
Consensus pattern (43 bp):
ATTTACTTTCATTTTCATTAAGCATATCCACATTTGTTTTCAC
Found at i:7083 original size:43 final size:43
Alignment explanation
Indices: 6979--7085 Score: 128
Period size: 43 Copynumber: 2.5 Consensus size: 43
6969 CCATTATATT
* **
6979 TACTTTCATTTTCATTAAGCATATCCACATTTGTTTTCACATT
1 TACTGTCATTTTCATTAAGCATATCCACATTTGTTTTCACACA
* *
7022 TACTTTCATTTTCATTAAGCATATCCACATTTGTTTTCGCAGCA
1 TACTGTCATTTTCATTAAGCATATCCACATTTGTTTTCACA-CA
*
7066 TA-TGGTCATTTT-TTTAAGCA
1 TACT-GTCATTTTCATTAAGCA
7086 GGTTCATTAG
Statistics
Matches: 57, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
43 48 0.84
44 9 0.16
ACGTcount: A:0.25, C:0.20, G:0.08, T:0.47
Consensus pattern (43 bp):
TACTGTCATTTTCATTAAGCATATCCACATTTGTTTTCACACA
Found at i:8607 original size:15 final size:14
Alignment explanation
Indices: 8577--8622 Score: 60
Period size: 15 Copynumber: 3.3 Consensus size: 14
8567 ATCGTAGAGT
8577 AAAA-AGAAAC-AA
1 AAAATAGAAACGAA
8589 AAAATACGAAACGAA
1 AAAATA-GAAACGAA
8604 AAAATAGAAAACGAA
1 AAAATAG-AAACGAA
8619 AAAA
1 AAAA
8623 CAGAGGGAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
12 4 0.13
13 1 0.03
14 6 0.20
15 19 0.63
ACGTcount: A:0.76, C:0.09, G:0.11, T:0.04
Consensus pattern (14 bp):
AAAATAGAAACGAA
Found at i:9710 original size:11 final size:11
Alignment explanation
Indices: 9694--9727 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
9684 AATGAAGCAT
9694 AAAATAAAAAA
1 AAAATAAAAAA
9705 AAAAT--AAAA
1 AAAATAAAAAA
9714 AAAATAAAAAA
1 AAAATAAAAAA
9725 AAA
1 AAA
9728 CTAGAAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
9 9 0.43
11 12 0.57
ACGTcount: A:0.91, C:0.00, G:0.00, T:0.09
Consensus pattern (11 bp):
AAAATAAAAAA
Found at i:9713 original size:9 final size:9
Alignment explanation
Indices: 9701--9726 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
9691 CATAAAATAA
9701 AAAAAAAAT
1 AAAAAAAAT
9710 AAAAAAAAT
1 AAAAAAAAT
9719 AAAAAAAA
1 AAAAAAAA
9727 ACTAGAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (9 bp):
AAAAAAAAT
Found at i:9713 original size:16 final size:16
Alignment explanation
Indices: 9692--9724 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
9682 GCAATGAAGC
9692 ATAAAATAAAA-AAAAA
1 ATAAAA-AAAATAAAAA
9708 ATAAAAAAAATAAAAA
1 ATAAAAAAAATAAAAA
9724 A
1 A
9725 AAACTAGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (16 bp):
ATAAAAAAAATAAAAA
Found at i:9973 original size:50 final size:49
Alignment explanation
Indices: 9827--10117 Score: 320
Period size: 49 Copynumber: 5.9 Consensus size: 49
9817 CAATTTTCGG
*
9827 TTTTCACCTGCTATTTTCCAAAATGCCCTTCCCGGACGGAAGGCATTTAC
1 TTTT-ACCTGCTATTTTCCAAAATGCCCTTCCCGGACGGAAGGCATTTGC
9877 TTTTACCTGCTATTTTCCAAAATGCCCTTCCCGGACGGAAGGCATTTGC
1 TTTTACCTGCTATTTTCCAAAATGCCCTTCCCGGACGGAAGGCATTTGC
* * * * *
9926 TTTTACCTGCTAGTTTCCAAGAATGCCCTTCCCAGATGGAAGACATTTGA
1 TTTTACCTGCTATTTTCCAA-AATGCCCTTCCCGGACGGAAGGCATTTGC
* * * * * * *
9976 TTTCATCTGTTTTTTTCCCAAAATGCCCTTTCCGGACGGAAGGCACTT-A
1 TTTTACCTGCTATTTT-CCAAAATGCCCTTCCCGGACGGAAGGCATTTGC
* ** * *
10025 TTTTACTTGCTATTTTTTCCAAAAATGCCCTTCCCGGACGGAAGGCGCTGGT
1 TTTTACCTGCTA--TTTTCC-AAAATGCCCTTCCCGGACGGAAGGCATTTGC
*
10077 TTTTACCTG---TTTTCCTAAAACGCCCTTCCCGGACGGAAGGC
1 TTTTACCTGCTATTTTCC-AAAATGCCCTTCCCGGACGGAAGGC
10118 GCTAGTTTTG
Statistics
Matches: 207, Mismatches: 28, Indels: 15
0.83 0.11 0.06
Matches are distributed among these distances:
47 30 0.14
49 71 0.34
50 64 0.31
51 34 0.16
52 8 0.04
ACGTcount: A:0.21, C:0.27, G:0.18, T:0.33
Consensus pattern (49 bp):
TTTTACCTGCTATTTTCCAAAATGCCCTTCCCGGACGGAAGGCATTTGC
Found at i:10029 original size:99 final size:98
Alignment explanation
Indices: 9827--10068 Score: 299
Period size: 99 Copynumber: 2.4 Consensus size: 98
9817 CAATTTTCGG
* *
9827 TTTTCACCTGCTATTTTCCAAAATGCCCTTCCCGGACGGAAGGCATTTACTTTTACCTGCTATTT
1 TTTT-ACCTGCTATTTTCCAAAATGCCCTTCCCGGACGGAAGACATTTACTTTCACCTGCTATTT
* *
9892 TCCAAAATGCCCTTCCCGGACGGAAGGCATTTGC
65 TCCAAAATGCCCTTCCCGGACGGAAGGCACTTGA
* * * * * *
9926 TTTTACCTGCTAGTTTCCAAGAATGCCCTTCCCAGATGGAAGACATTTGA-TTTCATCTGTTTTT
1 TTTTACCTGCTATTTTCCAA-AATGCCCTTCCCGGACGGAAGACATTT-ACTTTCACCTGCTATT
*
9990 TTCCCAAAATGCCCTTTCCGGACGGAAGGCACTT-A
64 TT-CCAAAATGCCCTTCCCGGACGGAAGGCACTTGA
*
10025 TTTTACTTGCTATTTTTTCCAAAAATGCCCTTCCCGGACGGAAG
1 TTTTACCTGCTA--TTTTCC-AAAATGCCCTTCCCGGACGGAAG
10069 GCGCTGGTTT
Statistics
Matches: 122, Mismatches: 15, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
98 15 0.12
99 51 0.42
100 30 0.25
101 24 0.20
102 2 0.02
ACGTcount: A:0.22, C:0.27, G:0.17, T:0.34
Consensus pattern (98 bp):
TTTTACCTGCTATTTTCCAAAATGCCCTTCCCGGACGGAAGACATTTACTTTCACCTGCTATTTT
CCAAAATGCCCTTCCCGGACGGAAGGCACTTGA
Found at i:10107 original size:47 final size:47
Alignment explanation
Indices: 9840--10165 Score: 191
Period size: 49 Copynumber: 6.7 Consensus size: 47
9830 TCACCTGCTA
** *
9840 TTTTCC-AAAATGCCCTTCCCGGACGGAAGGCATTTACTTTTAC-CTGCT
1 TTTTCCTAAAATGCCCTTCCCGGACGGAAGGC-GCTAGTTTT-CTC-GCT
** *
9888 ATTTTCC-AAAATGCCCTTCCCGGACGGAAGGCATTTGCTTTTAC-CTGCT
1 -TTTTCCTAAAATGCCCTTCCCGGACGGAAGGCGCTAG-TTTT-CTC-GCT
* * * * ** * * *
9937 AGTTTCC-AAGAATGCCCTTCCCAGATGGAAGACATTTGATTTCATCTGTTT
1 -TTTTCCTAA-AATGCCCTTCCCGGACGGAAGGCGCTAGTTTTC-TC-G-CT
* * * *
9988 TTTTCCCAAAATGCCCTTTCCGGACGGAAGGCACTTA-TTTTACTTGCTATT
1 TTTTCCTAAAATGCCCTTCCCGGACGGAAGGCGC-TAGTTTT-CTCGC---T
* *
10039 TTTTCCAAAAATGCCCTTCCCGGACGGAAGGCGCTGGTTTT-TAC-CT
1 TTTTCCTAAAATGCCCTTCCCGGACGGAAGGCGCTAGTTTTCT-CGCT
*
10085 GTTTTCCTAAAACGCCCTTCCCGGACGGAAGGCGCTAGTTTTGCTCGCT
1 -TTTTCCTAAAATGCCCTTCCCGGACGGAAGGCGCTAGTTTT-CTCGCT
* * *
10134 TTTTCTTAAAATGCCCTTTCCGGACGAAAGGC
1 TTTTCCTAAAATGCCCTTCCCGGACGGAAGGC
10166 AAGTTCACTT
Statistics
Matches: 229, Mismatches: 31, Indels: 35
0.78 0.11 0.12
Matches are distributed among these distances:
46 1 0.00
47 38 0.17
48 32 0.14
49 59 0.26
50 58 0.25
51 41 0.18
ACGTcount: A:0.21, C:0.27, G:0.19, T:0.33
Consensus pattern (47 bp):
TTTTCCTAAAATGCCCTTCCCGGACGGAAGGCGCTAGTTTTCTCGCT
Found at i:13047 original size:167 final size:164
Alignment explanation
Indices: 12664--13107 Score: 597
Period size: 167 Copynumber: 2.7 Consensus size: 164
12654 TGAGTCATTT
*
12664 GTCAATTGAGAAATGACCAAAAAGTTTAATTATTTAATCCCCTCAAGAATGAAAAGTTAGGACAT
1 GTCAATTGAGAAATGACCAAAAAG-TTAATTATTTAAT-CCCTCAAGAATCAAAAGTTAGGACAT
* * * * ** *
12729 TTAAGTAATCTGCCAAGTAAGTAAAGATGAAAAAAATTAGTTCTCTATCTCATCATCAATCCTTG
64 TTAAGTAATCTGCCAAGTAGGAAAAGACGAAAAAAATTAGTTCTCTAACTCAAAATCAAGCCTTG
* * * *
12794 ATGGGGATCTTTTATTAATTCCACTACTCTATTCAA
129 ATAGGGATCTTTTAGTAATTCCAATACTCTATTAAA
* *
12830 GTCCATTGAGAAATGACCAAAAAGATTACTTATTTAATCCTCTCAAGAATCAAAAGTTAGGACAT
1 GTCAATTGAGAAATGACCAAAAAG-TTAATTATTTAATCC-CTCAAGAATCAAAAGTTAGGACAT
*
12895 TTAAGTAATCTGCCAAGTAGGAAAAGACGAAAAAAATAAGTTCTCTAACTCCAAAAGT-AAGCCT
64 TTAAGTAATCTGCCAAGTAGGAAAAGACGAAAAAAATTAGTTCTCTAACT-CAAAA-TCAAGCC-
12959 TTG-TAGGGATCTTTTAGTAATTCCAATACTCTATTAAA
126 TTGATAGGGATCTTTTAGTAATTCCAATACTCTATTAAA
* * *
12997 GTCAATTGAGAAATGACCAAAAAGTCTAGTTATTTAATCACCTAAAGAATCAAAAGTTAGGGCAT
1 GTCAATTGAGAAATGACCAAAAAGT-TAATTATTTAATC-CCTCAAGAATCAAAAGTTAGGACAT
* *
13062 TTAAGTAATCGGTCAAGT-GTGAAAAGACGAAAAAAATTAGTTCTCT
64 TTAAGTAATCTGCCAAGTAG-GAAAAGACGAAAAAAATTAGTTCTCT
13108 CGCTCCTCAT
Statistics
Matches: 248, Mismatches: 23, Indels: 13
0.87 0.08 0.05
Matches are distributed among these distances:
165 2 0.01
166 105 0.42
167 136 0.55
168 5 0.02
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.30
Consensus pattern (164 bp):
GTCAATTGAGAAATGACCAAAAAGTTAATTATTTAATCCCTCAAGAATCAAAAGTTAGGACATTT
AAGTAATCTGCCAAGTAGGAAAAGACGAAAAAAATTAGTTCTCTAACTCAAAATCAAGCCTTGAT
AGGGATCTTTTAGTAATTCCAATACTCTATTAAA
Found at i:13269 original size:31 final size:31
Alignment explanation
Indices: 13234--13299 Score: 91
Period size: 31 Copynumber: 2.1 Consensus size: 31
13224 AACTTTATGT
*
13234 TTTCCGATTGTACCCTTATTTTTAA-AAA-ATA
1 TTTCCAATTGTACCC-T-TTTTTAAGAAACATA
13265 TTTCCAATTGTACCCTTTTTTAAGAAACATA
1 TTTCCAATTGTACCCTTTTTTAAGAAACATA
13296 TTTC
1 TTTC
13300 TAAATTGCCA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
29 7 0.22
30 4 0.12
31 21 0.66
ACGTcount: A:0.30, C:0.18, G:0.06, T:0.45
Consensus pattern (31 bp):
TTTCCAATTGTACCCTTTTTTAAGAAACATA
Found at i:13497 original size:37 final size:38
Alignment explanation
Indices: 13415--13497 Score: 105
Period size: 38 Copynumber: 2.2 Consensus size: 38
13405 AGACAGTCAA
* **
13415 TCCTATTTAATTTTGCCTTTTGTCTTTGTTTTGAATCG
1 TCCTATTTAATTTTGCCTTTTGTCTTTGTCTCCAATCG
** *
13453 TTTTATTTAATTTTGCTTTTTGTCTTTGTCTCCAA-CG
1 TCCTATTTAATTTTGCCTTTTGTCTTTGTCTCCAATCG
13490 TCCTATTT
1 TCCTATTT
13498 GGGCTTAGAT
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
37 8 0.22
38 29 0.78
ACGTcount: A:0.13, C:0.17, G:0.11, T:0.59
Consensus pattern (38 bp):
TCCTATTTAATTTTGCCTTTTGTCTTTGTCTCCAATCG
Found at i:14643 original size:19 final size:20
Alignment explanation
Indices: 14616--14653 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
14606 CTTTATTATT
14616 TTTTGAATTT-AATATTTTAC
1 TTTTGAATTTCAAT-TTTTAC
14636 TTTT-AATTTCAATTTTTA
1 TTTTGAATTTCAATTTTTA
14654 AATGTAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTGAATTTCAATTTTTAC
Found at i:14934 original size:66 final size:66
Alignment explanation
Indices: 14819--14949 Score: 165
Period size: 66 Copynumber: 2.0 Consensus size: 66
14809 TGTCTCTATG
* ** * * *
14819 TGGTTATCAAAATTTCATAAGACGGTTATTATAATTTCATGAGGAGGTTATCAAAATTCCATAGT
1 TGGTTACCAAAATTTCATAAGAAAGTTATCAAAATTTCATGAGGAGGTTACCAAAATTCCATAGT
14884 T
66 T
* * *
14885 TGGTTACCAAAATTTCATATGAAAGTTATCAAAATTTCAT-AGTGTGGTTACCAAAATTTCATAG
1 TGGTTACCAAAATTTCATAAGAAAGTTATCAAAATTTCATGAG-GAGGTTACCAAAATTCCATAG
14949 T
65 T
14950 GTCAGGTTAT
Statistics
Matches: 55, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
65 2 0.04
66 53 0.96
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.37
Consensus pattern (66 bp):
TGGTTACCAAAATTTCATAAGAAAGTTATCAAAATTTCATGAGGAGGTTACCAAAATTCCATAGT
T
Found at i:14948 original size:22 final size:22
Alignment explanation
Indices: 14817--15002 Score: 139
Period size: 22 Copynumber: 8.4 Consensus size: 22
14807 CTTGTCTCTA
14817 TGTGGTTATCAAAATTTCATAAG
1 TGTGGTTATCAAAATTTCAT-AG
** * *
14840 -ACGGTTATTATAATTTCATGAG
1 TGTGGTTATCAAAATTTCAT-AG
* *
14862 -GAGGTTATCAAAATTCCATAG
1 TGTGGTTATCAAAATTTCATAG
* *
14883 TTTGGTTACCAAAATTTCATA-
1 TGTGGTTATCAAAATTTCATAG
**
14904 TGAAAGTTATCAAAATTTCATAG
1 TG-TGGTTATCAAAATTTCATAG
*
14927 TGTGGTTACCAAAATTTCATAG
1 TGTGGTTATCAAAATTTCATAG
* *
14949 TGTCAGGTTATTAAAATTTCTTAG
1 TGT--GGTTATCAAAATTTCATAG
*
14973 -GTTGGTTAAT-GAAATTTCATAG
1 TG-TGGTT-ATCAAAATTTCATAG
*
14995 GGTGGTTA
1 TGTGGTTA
15003 ATTATCACAA
Statistics
Matches: 129, Mismatches: 26, Indels: 18
0.75 0.15 0.10
Matches are distributed among these distances:
21 4 0.03
22 102 0.79
23 6 0.05
24 17 0.13
ACGTcount: A:0.33, C:0.10, G:0.18, T:0.39
Consensus pattern (22 bp):
TGTGGTTATCAAAATTTCATAG
Found at i:15083 original size:22 final size:21
Alignment explanation
Indices: 15056--15177 Score: 95
Period size: 22 Copynumber: 5.6 Consensus size: 21
15046 ATGGCATAAC
15056 GAGGTTATAAGAATTTCATAGT
1 GAGGTTATAA-AATTTCATAGT
* *
15078 GTGGTTGACAAAATTTCATTAG-
1 GAGGTT-ATAAAATTTCA-TAGT
* * *
15100 GAGGTTACTAATATTTCATGGG
1 GAGGTTA-TAAAATTTCATAGT
*
15122 GAGGTTATCAAAATTTTATAGT
1 GAGGTTAT-AAAATTTCATAGT
* *
15144 GTGGTAATCAAAATTTCATA-T
1 GAGGTTAT-AAAATTTCATAGT
15165 GAAGGTTATAAAA
1 G-AGGTTATAAAA
15178 GTCTCAATTT
Statistics
Matches: 79, Mismatches: 15, Indels: 13
0.74 0.14 0.12
Matches are distributed among these distances:
21 10 0.13
22 63 0.80
23 6 0.08
ACGTcount: A:0.36, C:0.07, G:0.21, T:0.36
Consensus pattern (21 bp):
GAGGTTATAAAATTTCATAGT
Found at i:15252 original size:22 final size:21
Alignment explanation
Indices: 15217--15368 Score: 80
Period size: 22 Copynumber: 6.9 Consensus size: 21
15207 TGATAGAAGG
*
15217 TTATCAAATCTCATAGAGTGA
1 TTATCAAATTTCATAGAGTGA
15238 TTATCGAAATTTCATAGAGATCAGA
1 TTATC-AAATTTCATAGAG-T--GA
*
15263 TTATCAGAATTT-ATAG-GAAGA
1 TTATCA-AATTTCATAGAG-TGA
**
15284 TTATCAAAATTTCATAGTCTTG-
1 TTATC-AAATTTCATAG-AGTGA
* *
15306 TTATCAAAATTTCAAAGCGT-A
1 TTATC-AAATTTCATAGAGTGA
*
15327 GTTATCAAAATTACATA-ATGTGA
1 -TTATC-AAATTTCATAGA-GTGA
*
15350 TTATCAGAATTACATAGAG
1 TTATCA-AATTTCATAGAG
15369 GGGTCAACAA
Statistics
Matches: 107, Mismatches: 9, Indels: 29
0.74 0.06 0.20
Matches are distributed among these distances:
21 20 0.19
22 64 0.60
23 6 0.06
24 5 0.05
25 12 0.11
ACGTcount: A:0.40, C:0.11, G:0.14, T:0.35
Consensus pattern (21 bp):
TTATCAAATTTCATAGAGTGA
Found at i:15284 original size:21 final size:22
Alignment explanation
Indices: 15200--15343 Score: 84
Period size: 22 Copynumber: 6.5 Consensus size: 22
15190 TAAGGAGTAC
* *
15200 CAAAATTTGATA-GAAGGTTAT
1 CAAAATTTCATAGGAAGATTAT
* *
15221 C-AAATCTCATA-GAGTGATTAT
1 CAAAATTTCATAGGA-AGATTAT
*
15242 CGAAATTTCATAGAGATCAGATTAT
1 CAAAATTTCATAG-GA--AGATTAT
*
15267 CAGAATTT-ATAGGAAGATTAT
1 CAAAATTTCATAGGAAGATTAT
***
15288 CAAAATTTCATAGTCTTG-TTAT
1 CAAAATTTCATAG-GAAGATTAT
* *
15310 CAAAATTTCAAAGCGTAG-TTAT
1 CAAAATTTCATAG-GAAGATTAT
*
15332 CAAAATTACATA
1 CAAAATTTCATA
15344 ATGTGATTAT
Statistics
Matches: 97, Mismatches: 19, Indels: 13
0.75 0.15 0.10
Matches are distributed among these distances:
20 10 0.10
21 21 0.22
22 45 0.46
23 3 0.03
24 6 0.06
25 12 0.12
ACGTcount: A:0.41, C:0.11, G:0.14, T:0.34
Consensus pattern (22 bp):
CAAAATTTCATAGGAAGATTAT
Found at i:15392 original size:24 final size:23
Alignment explanation
Indices: 15365--15415 Score: 59
Period size: 22 Copynumber: 2.2 Consensus size: 23
15355 AGAATTACAT
* *
15365 AGAGGGGTCAACAAAATTTTATAA
1 AGAGGGCT-AACAAAATTTCATAA
*
15389 AGA-GGCTATCAAAATTTCATAA
1 AGAGGGCTAACAAAATTTCATAA
15411 AGAGG
1 AGAGG
15416 TTATCAAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
22 16 0.70
23 4 0.17
24 3 0.13
ACGTcount: A:0.45, C:0.10, G:0.22, T:0.24
Consensus pattern (23 bp):
AGAGGGCTAACAAAATTTCATAA
Found at i:15426 original size:21 final size:22
Alignment explanation
Indices: 15376--15429 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 22
15366 GAGGGGTCAA
*
15376 CAAAATTTTATAAAGAGGCTAT
1 CAAAATTTCATAAAGAGGCTAT
*
15398 CAAAATTTCATAAAGAGGTTAT
1 CAAAATTTCATAAAGAGGCTAT
*
15420 CAAATTTTCA
1 CAAAATTTCA
15430 AAATGTGATT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.33
Consensus pattern (22 bp):
CAAAATTTCATAAAGAGGCTAT
Found at i:15583 original size:20 final size:20
Alignment explanation
Indices: 15536--15604 Score: 86
Period size: 19 Copynumber: 3.4 Consensus size: 20
15526 TATGGAGTAT
15536 TCAAAATTTCAGAGAGGATA
1 TCAAAATTTCAGAGAGGATA
*
15556 TC-AAATTTCAGGGAGGATA
1 TCAAAATTTCAGAGAGGATA
* *
15575 TCAAAATTTCATATGAAGGTTA
1 TCAAAATTTCAGA-G-AGGATA
15597 TCAAAATT
1 TCAAAATT
15605 ACATAGTTTA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
19 18 0.43
20 10 0.24
21 1 0.02
22 13 0.31
ACGTcount: A:0.42, C:0.10, G:0.17, T:0.30
Consensus pattern (20 bp):
TCAAAATTTCAGAGAGGATA
Found at i:15601 original size:22 final size:22
Alignment explanation
Indices: 15573--15653 Score: 92
Period size: 22 Copynumber: 3.7 Consensus size: 22
15563 TCAGGGAGGA
15573 TATCAAAATTTCATATGAAGGT
1 TATCAAAATTTCATATGAAGGT
* **
15595 TATCAAAATTACATAGTTTA-GT
1 TATCAAAATTTCATA-TGAAGGT
* * *
15617 TTTCAAAATTTCATAAGAGGGT
1 TATCAAAATTTCATATGAAGGT
15639 TATCAAAATTTCATA
1 TATCAAAATTTCATA
15654 GTATGTAGAT
Statistics
Matches: 47, Mismatches: 10, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
22 45 0.96
23 2 0.04
ACGTcount: A:0.41, C:0.10, G:0.11, T:0.38
Consensus pattern (22 bp):
TATCAAAATTTCATATGAAGGT
Found at i:15667 original size:44 final size:43
Alignment explanation
Indices: 15573--15672 Score: 130
Period size: 44 Copynumber: 2.3 Consensus size: 43
15563 TCAGGGAGGA
*
15573 TATCAAAATTTCATATGAAGGTTATCAAAATTACATAGTTTAG
1 TATCAAAATTTCATAAGAAGGTTATCAAAATTACATAGTTTAG
* * *
15616 TTTTCAAAATTTCATAAGAGGGTTATCAAAATTTCATAGTATGTAG
1 -TATCAAAATTTCATAAGAAGGTTATCAAAATTACATAGT-T-TAG
15662 -ATCAAAATTTC
1 TATCAAAATTTC
15673 CTTGTCTGGG
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
44 45 0.92
45 1 0.02
46 3 0.06
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (43 bp):
TATCAAAATTTCATAAGAAGGTTATCAAAATTACATAGTTTAG
Done.