Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017908.1 Corchorus olitorius cultivar O-4 contig17941, 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: 23850
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.31
Found at i:3120 original size:50 final size:50
Alignment explanation
Indices: 3034--3155 Score: 147
Period size: 50 Copynumber: 2.4 Consensus size: 50
3024 CTCTCCTTCA
* *
3034 AACTGTCTTCTAATTCAATCTTAAAAGGACTATCTTCAGCTTATCCT-TTG
1 AACTGTCTTCCAATTCAATCTTAAAAGGACCATCTTCAGCTTAT-CTATTG
** * * * *
3084 AGTTGTCTTCCAATTCAATCTTAAAGGGGCCGTCTTCTGCTTATCTATTG
1 AACTGTCTTCCAATTCAATCTTAAAAGGACCATCTTCAGCTTATCTATTG
*
3134 AACTGTCTTCCAATTCCATCTT
1 AACTGTCTTCCAATTCAATCTT
3156 TAGAAGACCG
Statistics
Matches: 60, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
49 2 0.03
50 58 0.97
ACGTcount: A:0.24, C:0.24, G:0.12, T:0.40
Consensus pattern (50 bp):
AACTGTCTTCCAATTCAATCTTAAAAGGACCATCTTCAGCTTATCTATTG
Found at i:3167 original size:50 final size:49
Alignment explanation
Indices: 3034--3170 Score: 143
Period size: 50 Copynumber: 2.7 Consensus size: 49
3024 CTCTCCTTCA
* **
3034 AACTGTCTTCTAATTCAATCTTAAAAGGACTATCTTCAGCTTATCCTTTG
1 AACTGTCTTCCAATTCAATCTT-AAAGGACCGTCTTCAGCTTATCCTTTG
** * *
3084 AGTTGTCTTCCAATTCAATCTTAAAGGGGCCGTCTTCTGCTTAT-CTATTG
1 AACTGTCTTCCAATTCAATCTTAAA-GGACCGTCTTCAGCTTATCCT-TTG
*
3134 AACTGTCTTCCAATTCCATCTTTAGAA-GACCGTCTTC
1 AACTGTCTTCCAATTCAATC-TTA-AAGGACCGTCTTC
3171 CGATCAACTT
Statistics
Matches: 72, Mismatches: 11, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
49 5 0.07
50 62 0.86
51 3 0.04
52 2 0.03
ACGTcount: A:0.24, C:0.24, G:0.13, T:0.39
Consensus pattern (49 bp):
AACTGTCTTCCAATTCAATCTTAAAGGACCGTCTTCAGCTTATCCTTTG
Found at i:3507 original size:54 final size:53
Alignment explanation
Indices: 3425--3956 Score: 527
Period size: 54 Copynumber: 10.0 Consensus size: 53
3415 GCACTGGATC
** * * *
3425 ACTTAAAACCACTGGGAACTTTCTGATTGACTACACTGGATCACTTGAAGAAAA
1 ACTT-AAACCACTGTAAACTTTTTGATTGACTGCACTGGATCACTTGAAGATAA
* * * *
3479 ACTTAAACCACT-TGAAACTCTTTTGATTGACCGTACCGGATCACTTTAAAGATAA
1 ACTTAAACCACTGT-AAACT-TTTTGATTGACTGCACTGGATCAC-TTGAAGATAA
* * *
3534 ACTTAAACCACTGTAAATTTTCTTGATTGA-TCGTACTAGATCACTTTGAAGATAA
1 ACTTAAACCACTGTAAACTTT-TTGATTGACT-GCACTGGATCAC-TTGAAGATAA
*
3589 ACTTAAACCACTGTAAAC---TTGATTGATTGCACTGGATCACTTTGAAGATAA
1 ACTTAAACCACTGTAAACTTTTTGATTGACTGCACTGGATCAC-TTGAAGATAA
* * * *
3640 ACTT-AACCACTGTAAACTTTCTTGATTGACCGCACTGGGTCACCTGAAGGTAA
1 ACTTAAACCACTGTAAACTTT-TTGATTGACTGCACTGGATCACTTGAAGATAA
3693 ACTTAAACCACTGTAAAC---TTGATTGA-TCGCACTGGATCACTTTGAAGATAA
1 ACTTAAACCACTGTAAACTTTTTGATTGACT-GCACTGGATCAC-TTGAAGATAA
* *
3744 ACTTAAACCACTGTAAAC---TTGATTGA-TCGCACTAGATCATTTTGAAGATAA
1 ACTTAAACCACTGTAAACTTTTTGATTGACT-GCACTGGATCA-CTTGAAGATAA
* * * *
3795 ACCTAAACCACCGTAAACTTTCTTGATTGACCGCACTGGATCGCTTGAAGATAA
1 ACTTAAACCACTGTAAACTTT-TTGATTGACTGCACTGGATCACTTGAAGATAA
* * * *
3849 ACTTAAACCACTGTAAACTTTCTTGATTGACCGCATTGGATCGCTTAAAGATAA
1 ACTTAAACCACTGTAAACTTT-TTGATTGACTGCACTGGATCACTTGAAGATAA
* * * * *
3903 AGTTAAACCACTATAAACTTGATTGATTGACCGCATTGGATCACTTGAAG-TAA
1 ACTTAAACCACTGTAAACTT-TTTGATTGACTGCACTGGATCACTTGAAGATAA
3956 A
1 A
3957 TTGAAGCATT
Statistics
Matches: 414, Mismatches: 43, Indels: 43
0.83 0.09 0.09
Matches are distributed among these distances:
50 32 0.08
51 105 0.25
52 1 0.00
53 28 0.07
54 161 0.39
55 86 0.21
56 1 0.00
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.30
Consensus pattern (53 bp):
ACTTAAACCACTGTAAACTTTTTGATTGACTGCACTGGATCACTTGAAGATAA
Found at i:3833 original size:210 final size:206
Alignment explanation
Indices: 3425--3929 Score: 638
Period size: 210 Copynumber: 2.4 Consensus size: 206
3415 GCACTGGATC
** ** *
3425 ACTTAAAACCACTGGGAACTTTC-TGATTGACTACACTGGATCACTTGAAGAAAAACTTAAACCA
1 ACTT-AAACCACTGTAAACTTTCTTGATTGACCGCACTGGATCACTTGAAGATAAACTTAAACCA
* *
3489 CTTGAAACTCTTTTGATTGACCGTACCGGATCACTTTAAAGATAAACTTAAACCACTGTAAATTT
65 CTT-AAA--C--TTGATTGATCGCACCGGATCACTTTAAAGATAAACTTAAACCACTGTAAA---
* * * **
3554 TCTTGATTGATCGTACTAGATCACTTTGAAGATAAACTTAAACCACTGTAAACTTGATTGATTGC
122 TCTTGATTGATCGCACTAGATCACTTTGAAGATAAACCTAAACCACCGTAAACTTGATTGACCGC
3619 ACTGGATCACTTTGAAGATAA
187 ACTGGATCAC-TTGAAGATAA
* * *
3640 ACTT-AACCACTGTAAACTTTCTTGATTGACCGCACTGGGTCACCTGAAGGTAAACTTAAACCAC
1 ACTTAAACCACTGTAAACTTTCTTGATTGACCGCACTGGATCACTTGAAGATAAACTTAAACCAC
* *
3704 TGTAAACTTGATTGATCGCACTGGATCACTTTGAAGATAAACTTAAACCACTGTAAA-CTTGATT
66 T-TAAACTTGATTGATCGCACCGGATCACTTTAAAGATAAACTTAAACCACTGTAAATCTTGATT
*
3768 GATCGCACTAGATCATTTTGAAGATAAACCTAAACCACCGTAAACTTTCTTGATTGACCGCACTG
130 GATCGCACTAGATCACTTTGAAGATAAACCTAAACCACCGTAAA----CTTGATTGACCGCACTG
*
3833 GATCGCTTGAAGATAA
191 GATCACTTGAAGATAA
* * * *
3849 ACTTAAACCACTGTAAACTTTCTTGATTGACCGCATTGGATCGCTTAAAGATAAAGTTAAACCAC
1 ACTTAAACCACTGTAAACTTTCTTGATTGACCGCACTGGATCACTTGAAGATAAACTTAAACCAC
3914 TATAAACTTGATTGAT
66 T-TAAACTTGATTGAT
3930 TGACCGCATT
Statistics
Matches: 256, Mismatches: 27, Indels: 19
0.85 0.09 0.06
Matches are distributed among these distances:
206 47 0.18
209 14 0.05
210 134 0.52
212 1 0.00
213 15 0.06
214 40 0.16
215 5 0.02
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.30
Consensus pattern (206 bp):
ACTTAAACCACTGTAAACTTTCTTGATTGACCGCACTGGATCACTTGAAGATAAACTTAAACCAC
TTAAACTTGATTGATCGCACCGGATCACTTTAAAGATAAACTTAAACCACTGTAAATCTTGATTG
ATCGCACTAGATCACTTTGAAGATAAACCTAAACCACCGTAAACTTGATTGACCGCACTGGATCA
CTTGAAGATAA
Found at i:3975 original size:8 final size:8
Alignment explanation
Indices: 3955--4097 Score: 86
Period size: 8 Copynumber: 18.6 Consensus size: 8
3945 ACTTGAAGTA
3955 AATTGAAG
1 AATTGAAG
* *
3963 CATTGGAG
1 AATTGAAG
3971 AATTGAAG
1 AATTGAAG
*
3979 AATTTAA-
1 AATTGAAG
3986 ACATTGAAG
1 A-ATTGAAG
*
3995 AATTGGAG
1 AATTGAAG
* *
4003 CATTGAAT
1 AATTGAAG
*
4011 ACTTGAAG
1 AATTGAAG
*
4019 AATTGGAG
1 AATTGAAG
*
4027 CATTGAAG
1 AATTGAAG
*
4035 TATTG-A-
1 AATTGAAG
4041 AATTGAAG
1 AATTGAAG
*
4049 CATTGAA-
1 AATTGAAG
4056 ATATTG-A-
1 A-ATTGAAG
4063 AATTGAAG
1 AATTGAAG
**
4071 CTTTGAAG
1 AATTGAAG
4079 AATTG-A-
1 AATTGAAG
4085 AATTGAAG
1 AATTGAAG
*
4093 CATTG
1 AATTG
4098 GAATATTGAA
Statistics
Matches: 100, Mismatches: 26, Indels: 18
0.69 0.18 0.12
Matches are distributed among these distances:
6 13 0.13
7 8 0.08
8 78 0.78
9 1 0.01
ACGTcount: A:0.41, C:0.06, G:0.23, T:0.30
Consensus pattern (8 bp):
AATTGAAG
Found at i:4050 original size:22 final size:21
Alignment explanation
Indices: 3995--4114 Score: 141
Period size: 22 Copynumber: 5.4 Consensus size: 21
3985 AACATTGAAG
*
3995 AATTGGAGCATTGAATACTTGAA
1 AATTGAAGCATTGAATA-TTG-A
*
4018 GAATTGGAGCATTGAAGTATTGA
1 -AATTGAAGCATTGAA-TATTGA
4041 AATTGAAGCATTGAAATATTGA
1 AATTGAAGCATTG-AATATTGA
* *
4063 AATTGAAGCTTTGAAGAATTGA
1 AATTGAAGCATTGAA-TATTGA
4085 AATTGAAGCATTGGAATATTGA
1 AATTGAAGCATT-GAATATTGA
4107 AATTGAAG
1 AATTGAAG
4115 AAAGGCCACC
Statistics
Matches: 87, Mismatches: 5, Indels: 10
0.85 0.05 0.10
Matches are distributed among these distances:
21 2 0.02
22 59 0.68
23 6 0.07
24 18 0.21
25 2 0.02
ACGTcount: A:0.41, C:0.05, G:0.23, T:0.31
Consensus pattern (21 bp):
AATTGAAGCATTGAATATTGA
Found at i:4084 original size:44 final size:43
Alignment explanation
Indices: 3995--4114 Score: 159
Period size: 44 Copynumber: 2.7 Consensus size: 43
3985 AACATTGAAG
* * *
3995 AATTGGAGCATTGAATACTTGAAGAATTGGAGCATTGAAGTATTGA
1 AATTGAAGCATTGAATA-TTG-A-AATTGAAGCATTGAAGAATTGA
*
4041 AATTGAAGCATTGAAATATTGAAATTGAAGCTTTGAAGAATTGA
1 AATTGAAGCATTG-AATATTGAAATTGAAGCATTGAAGAATTGA
4085 AATTGAAGCATTGGAATATTGAAATTGAAG
1 AATTGAAGCATT-GAATATTGAAATTGAAG
4115 AAAGGCCACC
Statistics
Matches: 68, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
44 47 0.69
45 2 0.03
46 15 0.22
47 4 0.06
ACGTcount: A:0.41, C:0.05, G:0.23, T:0.31
Consensus pattern (43 bp):
AATTGAAGCATTGAATATTGAAATTGAAGCATTGAAGAATTGA
Found at i:4190 original size:26 final size:25
Alignment explanation
Indices: 4144--4201 Score: 71
Period size: 26 Copynumber: 2.3 Consensus size: 25
4134 TCTGAAAAAT
*
4144 ATTGAAGAAAGACCACCCTGGGTCA
1 ATTGAAGAAAGACCACCCTGGATCA
* * *
4169 ACTTGAAGAAAGATCGCTCTGGATCA
1 A-TTGAAGAAAGACCACCCTGGATCA
4195 ATTGAAG
1 ATTGAAG
4202 TAAACTGAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 7 0.25
26 21 0.75
ACGTcount: A:0.36, C:0.19, G:0.24, T:0.21
Consensus pattern (25 bp):
ATTGAAGAAAGACCACCCTGGATCA
Found at i:5435 original size:19 final size:19
Alignment explanation
Indices: 5413--5449 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
5403 CCTTTTTGAG
* *
5413 AAAACATTTTTTTTTTTAA
1 AAAACAATTTTTATTTTAA
5432 AAAACAATTTTTATTTTA
1 AAAACAATTTTTATTTTA
5450 GGGACTATCC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (19 bp):
AAAACAATTTTTATTTTAA
Found at i:6187 original size:19 final size:21
Alignment explanation
Indices: 6163--6206 Score: 65
Period size: 19 Copynumber: 2.2 Consensus size: 21
6153 CTCTAAAGCC
*
6163 TTTTTGAGAAAAC-ATTTTT-
1 TTTTTGAAAAAACAATTTTTA
6182 TTTTTGAAAAAACAATTTTTA
1 TTTTTGAAAAAACAATTTTTA
6203 TTTT
1 TTTT
6207 AGGGACTATC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 12 0.55
20 6 0.27
21 4 0.18
ACGTcount: A:0.34, C:0.05, G:0.07, T:0.55
Consensus pattern (21 bp):
TTTTTGAAAAAACAATTTTTA
Found at i:7003 original size:22 final size:21
Alignment explanation
Indices: 6978--7019 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
6968 ATTTCTCTTT
6978 CTTTTTCTTTTTATCCTTTTCA
1 CTTTTTCTTTTT-TCCTTTTCA
*
7000 CTTTTTCTTTTTTTCTTTTC
1 CTTTTTCTTTTTTCCTTTTC
7020 TGATGGGAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.05, C:0.21, G:0.00, T:0.74
Consensus pattern (21 bp):
CTTTTTCTTTTTTCCTTTTCA
Found at i:10032 original size:67 final size:67
Alignment explanation
Indices: 9692--10248 Score: 454
Period size: 67 Copynumber: 8.4 Consensus size: 67
9682 TCAAAGTTCG
* * * * * * ***
9692 CCCTTTGACCGAAAGGGCATTTTTGGAAA-GTAGA-A-TAAACTTAAATGCAGAAATGATGGAAC
1 CCCTTCGACCGAAAGGGTATTTTTGGAAACGAAAATACTAAACTTGAATGCA-AAAAGACAAAAC
9754 TGA
65 TGA
* ** * *
9757 CCCTTTC-ACCGAAAGGGTATTTTTGGAAATC--AAA-A-GAAACTAAAATGCAAGAATGACAGA
1 CCC-TTCGACCGAAAGGGTATTTTTGGAAA-CGAAAATACTAAACTTGAATGCAA-AAAGACAAA
*
9817 ATTGA
63 ACTGA
* * * * * **
9822 CCCTTTGATCGAAA-GGTATTTTTTGGAAA-GAAAA-ACTAGACTTAAATGCAACAACCTGATGA
1 CCCTTCGACCGAAAGGGTA-TTTTTGGAAACGAAAATACTAAACTTGAATGCAA-AA--AGACAA
9884 AACTGA
62 AACTGA
* * * *
9890 CCCTTCGACCGGAAGGGTATTTTTGGAAA-GTAAA-ACTAAACCTGAATGCAAAAAGACGAAACT
1 CCCTTCGACCGAAAGGGTATTTTTGGAAACGAAAATACTAAACTTGAATGCAAAAAGACAAAACT
9953 GA
66 GA
* * * *
9955 CCCTTCGACCGAAAGGGTATCTCTGGAAACGAAAACACTAAACTTGAATGCAAAAAGACAAAACC
1 CCCTTCGACCGAAAGGGTATTTTTGGAAACGAAAATACTAAACTTGAATGCAAAAAGACAAAACT
10020 GA
66 GA
* * * *
10022 CCCTTTGACCGAAAGGGTATTTCTGGAAATC-AAAATACTAAACTTGAATGCAAAAAGACAAGAT
1 CCCTTCGACCGAAAGGGTATTTTTGGAAA-CGAAAATACTAAACTTGAATGCAAAAAGACAAAAC
10086 TGA
65 TGA
* * * * * * * *
10089 CCCTT-AACTGAAAAGGTATTTTTGGAAATGAAAATACTACACTTAAATGC-AAACGACGGAAA-
1 CCCTTCGACCGAAAGGGTATTTTTGGAAACGAAAATACTAAACTTGAATGCAAAAAGAC-AAAAC
10151 TGA
65 TGA
* *
10154 CCCTTCGACCGAAAGGGTA-TTTTGGAAATTTGAAAATACTAAACTTAAATGC-AAAAGACGAAA
1 CCCTTCGACCGAAAGGGTATTTTTGGAAA--CGAAAATACTAAACTTGAATGCAAAAAGAC-AAA
10217 A-TGA
63 ACTGA
10221 CCCTTCGACCGAAAGGGTA-TTTTGGAAA
1 CCCTTCGACCGAAAGGGTATTTTTGGAAA
10249 AAAGAACTGA
Statistics
Matches: 416, Mismatches: 56, Indels: 38
0.82 0.11 0.07
Matches are distributed among these distances:
64 7 0.02
65 132 0.32
66 69 0.17
67 156 0.38
68 48 0.12
69 4 0.01
ACGTcount: A:0.41, C:0.17, G:0.19, T:0.23
Consensus pattern (67 bp):
CCCTTCGACCGAAAGGGTATTTTTGGAAACGAAAATACTAAACTTGAATGCAAAAAGACAAAACT
GA
Found at i:10171 original size:132 final size:132
Alignment explanation
Indices: 9692--10256 Score: 511
Period size: 133 Copynumber: 4.3 Consensus size: 132
9682 TCAAAGTTCG
* * * * * * *
9692 CCCTTTGACCGAAAGGGCATTTTTGGAAAGTAGAA-TAAACTTAAATGCAGAAATGATGG-AACT
1 CCCTTCGACCGAAAAGGTATTTTTGGAAAGAAAAACTAAACTTAAATGCA-AAACGACGGAAACT
* * *
9755 GACCCTTTC-ACCGAAAGGGTATTTTTGGAAA-TCAAAA-GAAACTAAAATGCAAGAATGAC-AG
65 GACCC-TTCGACCGAAAGGGTATTTTTGGAAATTCAAAACTAAACTTAAATGCAA-AAAGACGA-
9816 AATTGA
127 AATTGA
* * * *
9822 CCCTTTGATCG-AAAGGTATTTTTTGGAAAGAAAAACTAGACTTAAATGCAACAACCTGA-TGAA
1 CCCTTCGACCGAAAAGGTA-TTTTTGGAAAGAAAAACTAAACTTAAATGCAA-AA-C-GACGGAA
* * * *
9885 ACTGACCCTTCGACCGGAAGGGTATTTTTGGAAAGT-AAAACTAAACCTGAATGCAAAAAGACGA
62 ACTGACCCTTCGACCGAAAGGGTATTTTTGGAAATTCAAAACTAAACTTAAATGCAAAAAGACGA
*
9949 AACTGA
127 AATTGA
* * * * * *
9955 CCCTTCGACCGAAAGGGTATCTCTGGAAACGAAAACACTAAACTTGAATGCAAAAAGAC-AAAAC
1 CCCTTCGACCGAAAAGGTATTTTTGGAAA-GAAAA-ACTAAACTTAAATGCAAAACGACGGAAAC
* * * *
10019 CGACCCTTTGACCGAAAGGGTATTTCTGGAAA-TCAAAATACTAAACTTGAATGCAAAAAGAC-A
64 TGACCCTTCGACCGAAAGGGTATTTTTGGAAATTC-AAA-ACTAAACTTAAATGCAAAAAGACGA
10082 AGATTGA
127 A-ATTGA
* * *
10089 CCCTT-AACTGAAAAGGTATTTTTGGAAATGAAAATACTACACTTAAATGC-AAACGACGGAAA-
1 CCCTTCGACCGAAAAGGTATTTTTGGAAA-GAAAA-ACTAAACTTAAATGCAAAACGACGGAAAC
*
10151 TGACCCTTCGACCGAAAGGGTA-TTTTGGAAATTTGAAAATACTAAACTTAAATGC-AAAAGACG
64 TGACCCTTCGACCGAAAGGGTATTTTTGGAAA-TT-CAAA-ACTAAACTTAAATGCAAAAAGACG
*
10214 AAAATGA
126 AAATTGA
*
10221 CCCTTCGACCGAAAGGGTA-TTTTGGAAA-AAAGAACT
1 CCCTTCGACCGAAAAGGTATTTTTGGAAAGAAA-AACT
10257 GATGACCTTT
Statistics
Matches: 360, Mismatches: 50, Indels: 50
0.78 0.11 0.11
Matches are distributed among these distances:
129 5 0.01
130 31 0.09
131 25 0.07
132 89 0.25
133 138 0.38
134 57 0.16
135 15 0.04
ACGTcount: A:0.41, C:0.17, G:0.19, T:0.23
Consensus pattern (132 bp):
CCCTTCGACCGAAAAGGTATTTTTGGAAAGAAAAACTAAACTTAAATGCAAAACGACGGAAACTG
ACCCTTCGACCGAAAGGGTATTTTTGGAAATTCAAAACTAAACTTAAATGCAAAAAGACGAAATT
GA
Found at i:12570 original size:33 final size:33
Alignment explanation
Indices: 12512--12597 Score: 91
Period size: 33 Copynumber: 2.6 Consensus size: 33
12502 AATTGGTCGG
* * * * *
12512 TGCCGCCCTCAGAGGGCAGCATGGCCATGGGGA
1 TGCCGCCCTCCGTGGGCGGCGTGGCCATGGGCA
* * *
12545 TGCTGCCCTCGGTGGGCGGCGTGGCCATGGTCA
1 TGCCGCCCTCCGTGGGCGGCGTGGCCATGGGCA
*
12578 TGCCGCCCTCCTTGGGCGGC
1 TGCCGCCCTCCGTGGGCGGC
12598 ACAGCCATGA
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.09, C:0.34, G:0.40, T:0.17
Consensus pattern (33 bp):
TGCCGCCCTCCGTGGGCGGCGTGGCCATGGGCA
Found at i:12913 original size:33 final size:33
Alignment explanation
Indices: 12843--12958 Score: 108
Period size: 33 Copynumber: 3.5 Consensus size: 33
12833 CAGGTGGTGG
* * ** *
12843 GGGCGCCACCCCAATGCCGACGCCGCCCCCAG-G
1 GGGCGCCACCGCTATGGTGACGCCG-CCCCAGCA
12876 GGGCGCCACCGCTATGGTGACGCCGCCCCAGCA
1 GGGCGCCACCGCTATGGTGACGCCGCCCCAGCA
* * * * * *
12909 GGGCGACACCGCCAAGGTGGCGCCGGCCCAACA
1 GGGCGCCACCGCTATGGTGACGCCGCCCCAGCA
*
12942 GGGCGCCATCGCTATGG
1 GGGCGCCACCGCTATGG
12959 CGACCCCTGG
Statistics
Matches: 67, Mismatches: 15, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
32 6 0.09
33 61 0.91
ACGTcount: A:0.16, C:0.42, G:0.34, T:0.07
Consensus pattern (33 bp):
GGGCGCCACCGCTATGGTGACGCCGCCCCAGCA
Found at i:18973 original size:17 final size:18
Alignment explanation
Indices: 18934--18967 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
18924 AAGGGTAGTT
18934 AAAA-AATTGTTTTCATA
1 AAAAGAATTGTTTTCATA
18951 AAAAGAATTGTTTTCAT
1 AAAAGAATTGTTTTCAT
18968 GCAAGAGGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.44, C:0.06, G:0.09, T:0.41
Consensus pattern (18 bp):
AAAAGAATTGTTTTCATA
Found at i:19634 original size:19 final size:18
Alignment explanation
Indices: 19610--19645 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
19600 AAAATTTATT
19610 GAAGATAATTTGAAGAATA
1 GAAGATAA-TTGAAGAATA
*
19629 GAAGATCATTGAAGAAT
1 GAAGATAATTGAAGAAT
19646 TATCTCAAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.50, C:0.03, G:0.22, T:0.25
Consensus pattern (18 bp):
GAAGATAATTGAAGAATA
Found at i:21880 original size:14 final size:14
Alignment explanation
Indices: 21861--22170 Score: 286
Period size: 14 Copynumber: 22.8 Consensus size: 14
21851 AAACAATTTG
21861 CTCAAAAACAGGAA
1 CTCAAAAACAGGAA
*
21875 CTCAAAAACATGAA
1 CTCAAAAACAGGAA
*
21889 CTCAAAAACAGAAA
1 CTCAAAAACAGGAA
21903 CTCAAAAACA-GAA
1 CTCAAAAACAGGAA
* *
21916 ATCAAAAACAGCAA
1 CTCAAAAACAGGAA
* *
21930 ATCAAAAACAGAAA
1 CTCAAAAACAGGAA
21944 CTCAAAAACAGGAA
1 CTCAAAAACAGGAA
21958 CT-AAATAA-AGGAA
1 CTCAAA-AACAGGAA
*
21971 CTCAAAAACA-AAA
1 CTCAAAAACAGGAA
* *
21984 ATCAAAAACAGAAA
1 CTCAAAAACAGGAA
*
21998 CTCAAACACAGGAA
1 CTCAAAAACAGGAA
*
22012 CTAAAAAACAGGAA
1 CTCAAAAACAGGAA
22026 CTCAAAAACA-GAA
1 CTCAAAAACAGGAA
* *
22039 ATCAGAAAC-GGCAA
1 CTCAAAAACAGG-AA
* *
22053 AT-AAAAAC-GAAAA
1 CTCAAAAACAG-GAA
*
22066 CTCAAAATCAGGAA
1 CTCAAAAACAGGAA
22080 CT-AAATAA-AGGAA
1 CTCAAA-AACAGGAA
22093 CTCAAAAACA-GAA
1 CTCAAAAACAGGAA
* **
22106 ATCAAAAACAACAA
1 CTCAAAAACAGGAA
* *
22120 ATCAAAAACAGAAA
1 CTCAAAAACAGGAA
22134 CTC-AAAACAGGAA
1 CTCAAAAACAGGAA
*
22147 CTCAAAAAC-TGAA
1 CTCAAAAACAGGAA
*
22160 ATCAAAAACAG
1 CTCAAAAACAG
22171 CAAATCAATT
Statistics
Matches: 246, Mismatches: 34, Indels: 32
0.79 0.11 0.10
Matches are distributed among these distances:
13 101 0.41
14 144 0.59
15 1 0.00
ACGTcount: A:0.62, C:0.19, G:0.10, T:0.09
Consensus pattern (14 bp):
CTCAAAAACAGGAA
Found at i:21909 original size:27 final size:27
Alignment explanation
Indices: 21861--22178 Score: 273
Period size: 27 Copynumber: 11.7 Consensus size: 27
21851 AAACAATTTG
*
21861 CTCAAAAACAGGAACTCAAAAACATGAA
1 CTCAAAAACAGAAACTCAAAAACA-GAA
21889 CTCAAAAACAGAAACTCAAAAACAGAA
1 CTCAAAAACAGAAACTCAAAAACAGAA
*
21916 ATCAAAAACAGCAAA-TCAAAAACAGAAA
1 CTCAAAAACAG-AAACTCAAAAACAG-AA
*
21944 CTCAAAAACAGGAACT-AAATAA-AGGAA
1 CTCAAAAACAGAAACTCAAA-AACA-GAA
*
21971 CTCAAAAACA-AAAATCAAAAACAGAAA
1 CTCAAAAACAGAAACTCAAAAACAG-AA
* * *
21998 CTCAAACACAGGAACTAAAAAACAGGAA
1 CTCAAAAACAGAAACTCAAAAACA-GAA
* *
22026 CTCAAAAACAGAAA-TCAGAAACGGCAA
1 CTCAAAAACAGAAACTCAAAAACAG-AA
* *
22053 AT-AAAAAC-GAAAACTCAAAATCAGGAA
1 CTCAAAAACAG-AAACTCAAAAACA-GAA
*
22080 CT-AAATAA-AGGAACTCAAAAACAGAA
1 CTCAAA-AACAGAAACTCAAAAACAGAA
* *
22106 ATCAAAAACA-ACAAATCAAAAACAGAAA
1 CTCAAAAACAGA-AACTCAAAAACAG-AA
* *
22134 CTC-AAAACAGGAACTCAAAAACTGAA
1 CTCAAAAACAGAAACTCAAAAACAGAA
*
22160 ATCAAAAACAGCAAA-TCAA
1 CTCAAAAACAG-AAACTCAA
22179 TTAAGACTCA
Statistics
Matches: 236, Mismatches: 31, Indels: 47
0.75 0.10 0.15
Matches are distributed among these distances:
25 1 0.00
26 26 0.11
27 132 0.56
28 76 0.32
29 1 0.00
ACGTcount: A:0.62, C:0.19, G:0.10, T:0.09
Consensus pattern (27 bp):
CTCAAAAACAGAAACTCAAAAACAGAA
Done.