Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011423.1 Corchorus capsularis cultivar CVL-1 contig11444, 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: 91654
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--60 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
43 TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC
61 ACAGATATAA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:3071 original size:45 final size:45
Alignment explanation
Indices: 3007--3096 Score: 128
Period size: 45 Copynumber: 2.0 Consensus size: 45
2997 ATGATCGATG
* *
3007 TCCAAAATGGAAGTTCAAGGGCAA-AAGGAAACCAACTGTCCCAAA
1 TCCAAAATGGAAGGTCAAGGGCAACAA-AAAACCAACTGTCCCAAA
* *
3052 TCCAAAATGGAAGGTCAAGGGTAACAAAAAAGCAACTGTCCCAAA
1 TCCAAAATGGAAGGTCAAGGGCAACAAAAAACCAACTGTCCCAAA
3097 CAAGAAAAGA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
45 38 0.95
46 2 0.05
ACGTcount: A:0.46, C:0.21, G:0.20, T:0.13
Consensus pattern (45 bp):
TCCAAAATGGAAGGTCAAGGGCAACAAAAAACCAACTGTCCCAAA
Found at i:4397 original size:13 final size:13
Alignment explanation
Indices: 4379--4403 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4369 CTGATGATTA
4379 ACCTAGAAGTTTC
1 ACCTAGAAGTTTC
4392 ACCTAGAAGTTT
1 ACCTAGAAGTTT
4404 TTCCTTTCTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
ACCTAGAAGTTTC
Found at i:5634 original size:63 final size:63
Alignment explanation
Indices: 5561--5872 Score: 554
Period size: 63 Copynumber: 5.0 Consensus size: 63
5551 TGGATCTGAC
5561 TCAGAGCATGGGGGAACTGGAACTGAAGCAATTGGCTCGGAAGAAGTGAGAGCCACTTGTAAT
1 TCAGAGCATGGGGGAACTGGAACTGAAGCAATTGGCTCGGAAGAAGTGAGAGCCACTTGTAAT
**
5624 TCAGAGCATGGGGGAACTATAACTGAAGCAATTGGCTCGGAAGAAGTGAGAGCCACTTGTAACT
1 TCAGAGCATGGGGGAACTGGAACTGAAGCAATTGGCTCGGAAGAAGTGAGAGCCACTTGTAA-T
5688 T-AGAGCATGGGGGAACTGGAACTGAAGCAATTGGCTCGGAAGAAGTGAGAGCCACTTGTAAT
1 TCAGAGCATGGGGGAACTGGAACTGAAGCAATTGGCTCGGAAGAAGTGAGAGCCACTTGTAAT
*
5750 TCAGAGCATGGGGGAACTGGAACTGAAGCAATTGGCTCAGAAGAAGTGAGAGCCACTTGTAAT
1 TCAGAGCATGGGGGAACTGGAACTGAAGCAATTGGCTCGGAAGAAGTGAGAGCCACTTGTAAT
** *
5813 TCAGAGCATGGGATAACTGGAACTGAAGCAATTGTCTCGGAAGAAGTGAGAGCCACTTGT
1 TCAGAGCATGGGGGAACTGGAACTGAAGCAATTGGCTCGGAAGAAGTGAGAGCCACTTGT
5873 GACAATCAGC
Statistics
Matches: 238, Mismatches: 9, Indels: 4
0.95 0.04 0.02
Matches are distributed among these distances:
62 2 0.01
63 234 0.98
64 2 0.01
ACGTcount: A:0.32, C:0.16, G:0.32, T:0.20
Consensus pattern (63 bp):
TCAGAGCATGGGGGAACTGGAACTGAAGCAATTGGCTCGGAAGAAGTGAGAGCCACTTGTAAT
Found at i:7404 original size:291 final size:291
Alignment explanation
Indices: 6880--7464 Score: 1125
Period size: 291 Copynumber: 2.0 Consensus size: 291
6870 GGGTACAACA
6880 TGATCTCAGCAGCAATTGGCATGTTTTATGTCAAGAGGCTCCAGTTCCAAGACAAGAATCCTTAG
1 TGATCTCAGCAGCAATTGGCATGTTTTATGTCAAGAGGCTCCAGTTCCAAGACAAGAATCCTTAG
*
6945 AGGTCCTACTGGATGAACCATCTAATGCTCCTGTTAGGAATTCAGTTACACTTTTGCCACAACAG
66 AGGTCCTACTGGATGAACAATCTAATGCTCCTGTTAGGAATTCAGTTACACTTTTGCCACAACAG
*
7010 CCATCTTCAAGTACACCTATGGCTGAAAGTGAAACATGCACTGAGAACCAAAGGACCACATCTAC
131 CCATCTTCAAGTACACCTATGGCTGAAAGTGAAACATGCACTGACAACCAAAGGACCACATCTAC
*
7075 TCCGTTAAGACCACCGAATGATCTTCCTTGTCAAGTCGACACTTTCAGACCCGTGAGTGTGACAC
196 TCCGTCAAGACCACCGAATGATCTTCCTTGTCAAGTCGACACTTTCAGACCCGTGAGTGTGACAC
7140 CTCAGCCTGCTGAGTCAAACCCACTTCGAAT
261 CTCAGCCTGCTGAGTCAAACCCACTTCGAAT
*
7171 TGATCTCAGCAGCAATTGGCATGTTTTATGTCAAGAGGCTCCAGTTCCAAGACAAGCATCCTTAG
1 TGATCTCAGCAGCAATTGGCATGTTTTATGTCAAGAGGCTCCAGTTCCAAGACAAGAATCCTTAG
7236 AGGTCCTACTGGATGAACAATCTAATGCTCCTGTTAGGAATTCAGTTACACTTTTGCCACAACAG
66 AGGTCCTACTGGATGAACAATCTAATGCTCCTGTTAGGAATTCAGTTACACTTTTGCCACAACAG
7301 CCATCTTCAAGTACACCTATGGCTGAAAGTGAAACATGCACTGACAACCAAAGGACCACATCTAC
131 CCATCTTCAAGTACACCTATGGCTGAAAGTGAAACATGCACTGACAACCAAAGGACCACATCTAC
7366 TCCGTCAAGACCACCGAATGATCTTCCTTGTCAAGTCGACACTTTCAGACCCGTGAGTGTGACAC
196 TCCGTCAAGACCACCGAATGATCTTCCTTGTCAAGTCGACACTTTCAGACCCGTGAGTGTGACAC
*
7431 CTCAGCCTGCTGTGTCAAACCCACTTCGAAT
261 CTCAGCCTGCTGAGTCAAACCCACTTCGAAT
7462 TGA
1 TGA
7465 GCTGGCGCGA
Statistics
Matches: 289, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
291 289 1.00
ACGTcount: A:0.29, C:0.27, G:0.19, T:0.25
Consensus pattern (291 bp):
TGATCTCAGCAGCAATTGGCATGTTTTATGTCAAGAGGCTCCAGTTCCAAGACAAGAATCCTTAG
AGGTCCTACTGGATGAACAATCTAATGCTCCTGTTAGGAATTCAGTTACACTTTTGCCACAACAG
CCATCTTCAAGTACACCTATGGCTGAAAGTGAAACATGCACTGACAACCAAAGGACCACATCTAC
TCCGTCAAGACCACCGAATGATCTTCCTTGTCAAGTCGACACTTTCAGACCCGTGAGTGTGACAC
CTCAGCCTGCTGAGTCAAACCCACTTCGAAT
Found at i:8674 original size:78 final size:77
Alignment explanation
Indices: 8339--8676 Score: 402
Period size: 78 Copynumber: 4.4 Consensus size: 77
8329 ACCTCCTACA
* * * * * *
8339 TCAGCCCTGCATGGAAGGATGCGTAATCAGCA--AA-TAGCAAATAACCCTCCGGCAATCTCACC
1 TCAGCCTTGCAAGGAAGGATGCCTAATCAGCAGCAACTAGCAAATAATCTTCCGGCAATTTCACC
* * *
8401 AAATC-TACATGTG
66 AGACCGCAC-T-TG
** **
8414 TCAGCCTTGCTTGGAAGGACACCTAAT---CAGCAACTAGCAAATAATCTTCCGGCAATTTCACC
1 TCAGCCTTGCAAGGAAGGATGCCTAATCAGCAGCAACTAGCAAATAATCTTCCGGCAATTTCACC
8476 AGACCTGCACTTG
66 AGACC-GCACTTG
* * * *
8489 TCAGCCTTGCAAGGGAGTATGCCTAATCAACAGCAGCTAGCAAATAATCTTCCGGCAATTTCACC
1 TCAGCCTTGCAAGGAAGGATGCCTAATCAGCAGCAACTAGCAAATAATCTTCCGGCAATTTCACC
*
8554 AGACCCGTACTTG
66 AGA-CCGCACTTG
8567 TCAGCCTTGCAAGGAAGGATGCCTAATCAGCAGCAACTAGCAAATAATCTTCCGGCAATTTCACC
1 TCAGCCTTGCAAGGAAGGATGCCTAATCAGCAGCAACTAGCAAATAATCTTCCGGCAATTTCACC
8632 AGATCCGCACTTG
66 AGA-CCGCACTTG
* *
8645 TCAGTCTTGCAAGGAAGGATGCCCAATCAGCA
1 TCAGCCTTGCAAGGAAGGATGCCTAATCAGCA
8677 ATTAGCACAT
Statistics
Matches: 227, Mismatches: 27, Indels: 15
0.84 0.10 0.06
Matches are distributed among these distances:
72 2 0.01
74 2 0.01
75 73 0.32
76 1 0.00
77 2 0.01
78 145 0.64
79 2 0.01
ACGTcount: A:0.31, C:0.28, G:0.19, T:0.22
Consensus pattern (77 bp):
TCAGCCTTGCAAGGAAGGATGCCTAATCAGCAGCAACTAGCAAATAATCTTCCGGCAATTTCACC
AGACCGCACTTG
Found at i:14223 original size:76 final size:74
Alignment explanation
Indices: 14073--14224 Score: 180
Period size: 76 Copynumber: 2.0 Consensus size: 74
14063 ATATATATAT
* * * *
14073 ATATTTCTTGCCCATGCAAACAATATATAAATGGGCCAAAGGCTCAGCTTCAATGAGTATTGGGC
1 ATATTTCTTACCCATCCAAACAATATATAAATGGGCCAAAGGCTCAGCTTCAATGAATAATGGGC
* *
14138 CCTTTGGCC
66 CATTAGGCC
* * *
14147 ATATTTCTTACCCATCCAAACAATATATATATATGGGCCAATGGCTGATCTTCAATGAATCAATG
1 ATATTTCTTACCCATCCAAACAATATATA-A-ATGGGCCAAAGGCTCAGCTTCAATGAAT-AATG
*
14212 GG-TATTAGGCC
63 GGCCATTAGGCC
14223 AT
1 AT
14225 TTGCATCAAG
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
74 27 0.42
75 1 0.02
76 32 0.49
77 5 0.08
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.30
Consensus pattern (74 bp):
ATATTTCTTACCCATCCAAACAATATATAAATGGGCCAAAGGCTCAGCTTCAATGAATAATGGGC
CATTAGGCC
Found at i:29604 original size:48 final size:48
Alignment explanation
Indices: 29533--29682 Score: 228
Period size: 48 Copynumber: 3.1 Consensus size: 48
29523 GTAATCCCAT
*
29533 GAATCAGTTGATGGTGCAGCACGCAAACTAGAGTACCTCCTCTCACCA
1 GAATCAGTAGATGGTGCAGCACGCAAACTAGAGTACCTCCTCTCACCA
* *
29581 GAATCAGTAGACGGTGCAGCACGCAAGCTAGAGTACCTCCTCTCACCA
1 GAATCAGTAGATGGTGCAGCACGCAAACTAGAGTACCTCCTCTCACCA
* ** *
29629 GCATCAGTAGATGGTGTTGCACGCAAACTATAGTACCTCCTCTCACCA
1 GAATCAGTAGATGGTGCAGCACGCAAACTAGAGTACCTCCTCTCACCA
*
29677 GCATCA
1 GAATCA
29683 ACATTGTGGT
Statistics
Matches: 93, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 93 1.00
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.21
Consensus pattern (48 bp):
GAATCAGTAGATGGTGCAGCACGCAAACTAGAGTACCTCCTCTCACCA
Found at i:35515 original size:13 final size:15
Alignment explanation
Indices: 35485--35517 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
35475 TTTTATTGTT
35485 TTTTTTTTCTTTCTC
1 TTTTTTTTCTTTCTC
35500 TTTTTTTT-TTTC-C
1 TTTTTTTTCTTTCTC
35513 TTTTT
1 TTTTT
35518 GGCACAAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 6 0.33
14 4 0.22
15 8 0.44
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (15 bp):
TTTTTTTTCTTTCTC
Found at i:38640 original size:29 final size:30
Alignment explanation
Indices: 38607--38667 Score: 70
Period size: 30 Copynumber: 2.1 Consensus size: 30
38597 TGCAACTCTG
* **
38607 TTTTTGTTTCTTCTTAC-AACGTAAATAAT
1 TTTTTGTTTCGTCGAACAAACGTAAATAAT
* *
38636 TTTTTTTTTGGTCGAACAAACGTAAATAAT
1 TTTTTGTTTCGTCGAACAAACGTAAATAAT
38666 TT
1 TT
38668 ATTAATTTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
29 12 0.46
30 14 0.54
ACGTcount: A:0.30, C:0.11, G:0.10, T:0.49
Consensus pattern (30 bp):
TTTTTGTTTCGTCGAACAAACGTAAATAAT
Found at i:39704 original size:2 final size:2
Alignment explanation
Indices: 39665--39692 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
39655 TAACTTGTAA
39665 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39693 GGGTTTATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40191 original size:21 final size:21
Alignment explanation
Indices: 40165--40207 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
40155 TGAAACTGGA
40165 TTGCTAAACACCGTCCCATTT
1 TTGCTAAACACCGTCCCATTT
40186 TTGCTAAACACCGTCCCATTT
1 TTGCTAAACACCGTCCCATTT
40207 T
1 T
40208 GATGCTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.23, C:0.33, G:0.09, T:0.35
Consensus pattern (21 bp):
TTGCTAAACACCGTCCCATTT
Found at i:40612 original size:33 final size:31
Alignment explanation
Indices: 40569--40678 Score: 102
Period size: 33 Copynumber: 3.4 Consensus size: 31
40559 GGTGCCGTTC
40569 CCCTGGGGCGGCTGAGCCATGGCCAAGCCGCC-
1 CCCTGGGGCGGCT-A-CCATGGCCAAGCCGCCT
*
40601 CTCCTGGGGCGGCACTACCATGGCCAGGCCGCCT
1 C-CCTGGGGCGG--CTACCATGGCCAAGCCGCCT
40635 CCCTGGGGCGGCCCTACCATGG--ATAGACCGCC-
1 CCCTGGGGCGG--CTACCATGGCCA-AG-CCGCCT
40667 CCCTGGGGCGGC
1 CCCTGGGGCGGC
40679 ACCGGTACTA
Statistics
Matches: 69, Mismatches: 3, Indels: 14
0.80 0.03 0.16
Matches are distributed among these distances:
30 1 0.01
31 1 0.01
32 13 0.19
33 50 0.72
34 2 0.03
35 2 0.03
ACGTcount: A:0.12, C:0.41, G:0.35, T:0.12
Consensus pattern (31 bp):
CCCTGGGGCGGCTACCATGGCCAAGCCGCCT
Found at i:40676 original size:32 final size:32
Alignment explanation
Indices: 40596--40680 Score: 116
Period size: 33 Copynumber: 2.6 Consensus size: 32
40586 CATGGCCAAG
* *
40596 CCGCCCTCCTGGGGCGGCACTACCATGGCCAGG
1 CCGCCC-CCTGGGGCGGCACTACCATGGACAGA
* *
40629 CCGCCTCCCTGGGGCGGCCCTACCATGGATAGA
1 CCGCC-CCCTGGGGCGGCACTACCATGGACAGA
40662 CCGCCCCCTGGGGCGGCAC
1 CCGCCCCCTGGGGCGGCAC
40681 CGGTACTAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
32 13 0.28
33 32 0.70
34 1 0.02
ACGTcount: A:0.12, C:0.44, G:0.33, T:0.12
Consensus pattern (32 bp):
CCGCCCCCTGGGGCGGCACTACCATGGACAGA
Found at i:41741 original size:25 final size:26
Alignment explanation
Indices: 41701--41753 Score: 74
Period size: 25 Copynumber: 2.1 Consensus size: 26
41691 GTCCATATTT
41701 ATTTTTTAAAATAAAATAATAATT-AA
1 ATTTTTTAAAATAAAATAA-AATTCAA
*
41727 ATTTTTTATAA-AAAATAAAATTCAA
1 ATTTTTTAAAATAAAATAAAATTCAA
41752 AT
1 AT
41754 ATTAAAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 4 0.16
25 11 0.44
26 10 0.40
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (26 bp):
ATTTTTTAAAATAAAATAAAATTCAA
Found at i:41906 original size:29 final size:30
Alignment explanation
Indices: 41848--41908 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 30
41838 GTTCTAATTA
* *
41848 ATGTATACATATAAATTATTCAATTTTATT
1 ATGTATAAATATAAATTATTCAATTATATT
*
41878 ATGTATAAATAT-AATTATTTAATTATATT
1 ATGTATAAATATAAATTATTCAATTATATT
41907 AT
1 AT
41909 ATTATTTATA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 17 0.61
30 11 0.39
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (30 bp):
ATGTATAAATATAAATTATTCAATTATATT
Found at i:52867 original size:14 final size:14
Alignment explanation
Indices: 52848--52876 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
52838 GATGCCGAAC
52848 ACATTGAGATGAAG
1 ACATTGAGATGAAG
52862 ACATTGAGATGAAG
1 ACATTGAGATGAAG
52876 A
1 A
52877 GAGAGGCAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.07, G:0.28, T:0.21
Consensus pattern (14 bp):
ACATTGAGATGAAG
Found at i:54606 original size:3 final size:3
Alignment explanation
Indices: 54598--54624 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
54588 AGCCAAAAAG
54598 TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT
54625 AAGTTTGTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:55663 original size:17 final size:17
Alignment explanation
Indices: 55641--55675 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
55631 CCAACATCTG
*
55641 AAGCAAACAGTTTTATT
1 AAGCAAACAATTTTATT
55658 AAGCAAACAATTTTATT
1 AAGCAAACAATTTTATT
55675 A
1 A
55676 TTTCTGATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.46, C:0.11, G:0.09, T:0.34
Consensus pattern (17 bp):
AAGCAAACAATTTTATT
Found at i:67784 original size:2 final size:2
Alignment explanation
Indices: 67777--67803 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
67767 ACTGCACACC
67777 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 T
67804 CATGTAGAGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:81708 original size:18 final size:18
Alignment explanation
Indices: 81664--81710 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
81654 GTGGGTAATG
81664 CCCA-GAATTTTGCAAAT
1 CCCATGAATTTTGCAAAT
*
81681 CCCCTGAATTTTGCAAAT
1 CCCATGAATTTTGCAAAT
81699 CTCCAT-AATTTT
1 C-CCATGAATTTT
81711 CATCAAAACC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
17 3 0.12
18 20 0.77
19 3 0.12
ACGTcount: A:0.30, C:0.26, G:0.09, T:0.36
Consensus pattern (18 bp):
CCCATGAATTTTGCAAAT
Found at i:81709 original size:102 final size:101
Alignment explanation
Indices: 81523--81727 Score: 306
Period size: 102 Copynumber: 2.0 Consensus size: 101
81513 CATTGTCTGG
81523 ACCAGAACTTACCGGAGAACCATGCTGATGTGGGTAATGCCCAGAATTTTCCAAACCCCGATGAT
1 ACCAGAACTTACCGGAGAACCATGCTGATGTGGGTAATGCCCAGAATTTTCCAAACCCCGA-GAT
*
81588 TTTGCACACCACCAGAA-TTTCTATCAAAACCTCCAGA
65 TTTGCAAACCACCAGAATTTTC-ATCAAAACCTCCAGA
*
81625 ACCAGAACTTACCGGAGAACCATGCTGATGTGGGTAATGCCCAGAATTTTGCAAATCCCCTGA-A
1 ACCAGAACTTACCGGAGAACCATGCTGATGTGGGTAATGCCCAGAATTTTCCAAA-CCCC-GAGA
* * * *
81689 TTTTGCAAATCTCCATAATTTTCATCAAAACCTTCAGA
64 TTTTGCAAACCACCAGAATTTTCATCAAAACCTCCAGA
81727 A
1 A
81728 TTTTCATCAT
Statistics
Matches: 94, Mismatches: 6, Indels: 6
0.89 0.06 0.06
Matches are distributed among these distances:
102 84 0.89
103 8 0.09
104 2 0.02
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.25
Consensus pattern (101 bp):
ACCAGAACTTACCGGAGAACCATGCTGATGTGGGTAATGCCCAGAATTTTCCAAACCCCGAGATT
TTGCAAACCACCAGAATTTTCATCAAAACCTCCAGA
Found at i:81840 original size:15 final size:15
Alignment explanation
Indices: 81820--81859 Score: 80
Period size: 15 Copynumber: 2.7 Consensus size: 15
81810 GAGTTGGGCA
81820 ACAACAATGGGATTG
1 ACAACAATGGGATTG
81835 ACAACAATGGGATTG
1 ACAACAATGGGATTG
81850 ACAACAATGG
1 ACAACAATGG
81860 TGATGAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.42, C:0.15, G:0.25, T:0.17
Consensus pattern (15 bp):
ACAACAATGGGATTG
Found at i:88667 original size:22 final size:22
Alignment explanation
Indices: 88642--88683 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
88632 CACCCAAAAC
*
88642 GTAATTTCTAGATCCACTACTG
1 GTAATTCCTAGATCCACTACTG
88664 GTAATTCCTAGATCCACTAC
1 GTAATTCCTAGATCCACTAC
88684 CGCGATATCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (22 bp):
GTAATTCCTAGATCCACTACTG
Found at i:89798 original size:13 final size:14
Alignment explanation
Indices: 89772--89800 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
89762 TGGAGATATC
89772 TAGCCTATTTTCAA
1 TAGCCTATTTTCAA
89786 TAGCCTA-TTTCAA
1 TAGCCTATTTTCAA
89799 TA
1 TA
89801 TTCATGTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.31, C:0.21, G:0.07, T:0.41
Consensus pattern (14 bp):
TAGCCTATTTTCAA
Done.