Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008974.1 Corchorus capsularis cultivar CVL-1 contig08995, 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: 31772
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.31
Found at i:5928 original size:11 final size:12
Alignment explanation
Indices: 5898--5930 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
5888 TGCTTTATTA
*
5898 ATTTTGCTTTAG
1 ATTTTGATTTAG
5910 ATTTTGATTTAG
1 ATTTTGATTTAG
5922 A-TTTGATTT
1 ATTTTGATTT
5931 GCTTTGCTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 8 0.40
12 12 0.60
ACGTcount: A:0.21, C:0.03, G:0.15, T:0.61
Consensus pattern (12 bp):
ATTTTGATTTAG
Found at i:6421 original size:41 final size:41
Alignment explanation
Indices: 6355--6444 Score: 101
Period size: 42 Copynumber: 2.2 Consensus size: 41
6345 GTTTCCGCTT
* *
6355 TTTTTGAAAAAAAAAAATTAAA-TTTTCTTTTCCGTTTTTCC
1 TTTTT-AAAAAAAAAAATTAAATTTTTATTTTCCGTTTCTCC
* * * *
6396 TTTTTAAAATAAAAAATATATATTTTTATTTTCTGTTTCTGC
1 TTTTTAAAAAAAAAAAT-TAAATTTTTATTTTCCGTTTCTCC
6438 TTTTTAA
1 TTTTTAA
6445 TTTTATTTAA
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
40 11 0.27
41 8 0.20
42 22 0.54
ACGTcount: A:0.33, C:0.09, G:0.04, T:0.53
Consensus pattern (41 bp):
TTTTTAAAAAAAAAAATTAAATTTTTATTTTCCGTTTCTCC
Found at i:9898 original size:21 final size:21
Alignment explanation
Indices: 9874--9920 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 21
9864 CCCTTGCCAA
*
9874 GCCATCCGCGCAGC-ATGCCGC
1 GCCATCCACG-AGCTATGCCGC
9895 GCCA-CCACGAGCTTATGCCGC
1 GCCATCCACGAGC-TATGCCGC
9916 GCCAT
1 GCCAT
9921 GCCGAGTTAC
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
19 3 0.14
20 4 0.18
21 15 0.68
ACGTcount: A:0.17, C:0.45, G:0.26, T:0.13
Consensus pattern (21 bp):
GCCATCCACGAGCTATGCCGC
Found at i:14959 original size:135 final size:134
Alignment explanation
Indices: 14702--14962 Score: 335
Period size: 135 Copynumber: 1.9 Consensus size: 134
14692 AAGACTTGGA
* **
14702 GGGGAAAACCAACAACTGCTTGGTGTCCAGCCCGGTGCTCTGCCTTTTCAACAAGTCAACCATCA
1 GGGGAAAACCAACAACTGCTTGGTGTCCAGCCCGGTCCTCTGCCCCTTCAACAAGTCAACCATCA
* * * *
14767 GGTGAACAACCCACAAGTCATGGCTGAGATTGGTCTCATCGATGAAAGGCATGGGGGGCAAGGAC
66 GGTAAACAACCAACAAGTCATGGCTCAGATTGGTCTCATCGATGAAAGACATGGGGGGCAAGGAC
14832 TCGG
131 TCGG
* * * *
14836 GGGGCAAAACCAAGAACTGCTTGGT-TCCCAGCCTGGTCCTCTTCCCCTTCAACAAGTTAACCAT
1 GGGG-AAAACCAACAACTGCTTGGTGT-CCAGCCCGGTCCTCTGCCCCTTCAACAAGTCAACCAT
* * * * * * *
14900 CAGGTAAACAATCAACAGGTCTTGGCTCAGGTTGGTCTCATCGATGGAAGACTTTGGGGGCAA
64 CAGGTAAACAACCAACAAGTCATGGCTCAGATTGGTCTCATCGATGAAAGACATGGGGGGCAA
14963 AACAACAGCC
Statistics
Matches: 107, Mismatches: 18, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
134 5 0.05
135 102 0.95
ACGTcount: A:0.26, C:0.26, G:0.26, T:0.21
Consensus pattern (134 bp):
GGGGAAAACCAACAACTGCTTGGTGTCCAGCCCGGTCCTCTGCCCCTTCAACAAGTCAACCATCA
GGTAAACAACCAACAAGTCATGGCTCAGATTGGTCTCATCGATGAAAGACATGGGGGGCAAGGAC
TCGG
Found at i:17476 original size:7 final size:7
Alignment explanation
Indices: 17466--17648 Score: 61
Period size: 7 Copynumber: 25.7 Consensus size: 7
17456 TCTTTACTGA
17466 TTACTTT
1 TTACTTT
*
17473 TTACTCT
1 TTACTTT
*
17480 TTACTCT
1 TTACTTT
**
17487 TTACTGA
1 TTACTTT
*
17494 TTACTCT
1 TTACTTT
17501 TTACTATT
1 TTACT-TT
17509 TT--TTCT
1 TTACTT-T
**
17515 TTACTGA
1 TTACTTT
*
17522 TTACTCT
1 TTACTTT
17529 TTACTTT
1 TTACTTT
**
17536 TTACTGA
1 TTACTTT
*
17543 TTACCCTT
1 TTA-CTTT
17551 TTACTCTT
1 TTACT-TT
**
17559 TT-CTAA
1 TTACTTT
*
17565 TTACCATT
1 TTA-CTTT
17573 TTACTTT
1 TTACTTT
* **
17580 TCACTGA
1 TTACTTT
*
17587 TTAC-CT
1 TTACTTT
17593 TTACTTT
1 TTACTTT
**
17600 TTACTGA
1 TTACTTT
*
17607 TTACCATT
1 TTA-CTTT
17615 TTACTTT
1 TTACTTT
*
17622 TTA-TTGA
1 TTACTT-T
17629 TTACCTTT
1 TTA-CTTT
17637 TTACTTT
1 TTACTTT
17644 TTACT
1 TTACT
17649 GATTACCATT
Statistics
Matches: 125, Mismatches: 38, Indels: 26
0.66 0.20 0.14
Matches are distributed among these distances:
5 1 0.01
6 12 0.10
7 87 0.70
8 23 0.18
9 2 0.02
ACGTcount: A:0.19, C:0.20, G:0.03, T:0.57
Consensus pattern (7 bp):
TTACTTT
Found at i:17491 original size:42 final size:41
Alignment explanation
Indices: 17440--17752 Score: 189
Period size: 42 Copynumber: 7.6 Consensus size: 41
17430 ATTTCTTCTC
*
17440 ACTCCTTACTATTTTTTCTTTACTGATTACTTTTTACTCTTT
1 ACTCATTACTATTTTTT-TTTACTGATTACTTTTTACTCTTT
* ** *
17482 ACTCTTTACTGATTACTCTTTAC----TA-TTTTT--TCTTT
1 ACTCATTACT-ATTTTTTTTTACTGATTACTTTTTACTCTTT
* * * *
17517 ACTGATTACTCTTTACTTTTTACTGATTACCCTTTTACTCTTT
1 ACTCATTACTATTT-TTTTTTACTGATTA-CTTTTTACTCTTT
* * * * * *
17560 TCTAATTACCATTTTACTTTTCACTGATTAC-CTTTACTTTTT
1 ACTCATTACTATTTT--TTTTTACTGATTACTTTTTACTCTTT
* * * *
17602 ACTGATTACCATTTTACTTTTTATTGATTACCTTTTTACTTTTT
1 ACTCATTACTATTTT--TTTTTACTGATTA-CTTTTTACTCTTT
* * ** * * *
17646 ACTGATTACCATTACTTCTTATTGATTAC-TATTACTCTTT
1 ACTCATTACTATTTTTTTTTACTGATTACTTTTTACTCTTT
* *
17686 ACTGATTACCATTTTTTCTTTACTGATTACTTTTTA--CTTT
1 ACTCATTACTATTTTTT-TTTACTGATTACTTTTTACTCTTT
*
17726 ACTCTTTACTATTTTCTTTTTACTGAT
1 ACTCATTACTATTTT-TTTTTACTGAT
17753 CCCTCTTTAC
Statistics
Matches: 218, Mismatches: 36, Indels: 36
0.75 0.12 0.12
Matches are distributed among these distances:
34 2 0.01
35 20 0.09
37 5 0.02
38 2 0.01
39 2 0.01
40 49 0.22
41 17 0.08
42 65 0.30
43 21 0.10
44 35 0.16
ACGTcount: A:0.20, C:0.20, G:0.04, T:0.57
Consensus pattern (41 bp):
ACTCATTACTATTTTTTTTTACTGATTACTTTTTACTCTTT
Found at i:17531 original size:28 final size:28
Alignment explanation
Indices: 17440--17537 Score: 144
Period size: 28 Copynumber: 3.5 Consensus size: 28
17430 ATTTCTTCTC
*
17440 ACTCCTTACTATTTTTTCTTTACTGATT
1 ACTCTTTACTATTTTTTCTTTACTGATT
* * **
17468 ACTTTTTACTCTTTACTCTTTACTGATT
1 ACTCTTTACTATTTTTTCTTTACTGATT
17496 ACTCTTTACTATTTTTTCTTTACTGATT
1 ACTCTTTACTATTTTTTCTTTACTGATT
17524 ACTCTTTACT-TTTT
1 ACTCTTTACTATTTT
17538 ACTGATTACC
Statistics
Matches: 61, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
27 4 0.07
28 57 0.93
ACGTcount: A:0.17, C:0.20, G:0.03, T:0.59
Consensus pattern (28 bp):
ACTCTTTACTATTTTTTCTTTACTGATT
Found at i:17546 original size:14 final size:14
Alignment explanation
Indices: 17456--17533 Score: 95
Period size: 14 Copynumber: 5.6 Consensus size: 14
17446 TACTATTTTT
17456 TCTTTACTGATTAC
1 TCTTTACTGATTAC
* **
17470 TTTTTACTCTTTAC
1 TCTTTACTGATTAC
17484 TCTTTACTGATTAC
1 TCTTTACTGATTAC
**
17498 TCTTTACT-ATTTTT
1 TCTTTACTGA-TTAC
17512 TCTTTACTGATTAC
1 TCTTTACTGATTAC
17526 TCTTTACT
1 TCTTTACT
17534 TTTTACTGAT
Statistics
Matches: 52, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
13 1 0.02
14 50 0.96
15 1 0.02
ACGTcount: A:0.18, C:0.21, G:0.04, T:0.58
Consensus pattern (14 bp):
TCTTTACTGATTAC
Found at i:17546 original size:28 final size:28
Alignment explanation
Indices: 17391--17546 Score: 99
Period size: 28 Copynumber: 5.6 Consensus size: 28
17381 ATTTTTATTC
* *
17391 ACTTTTTACTGATTACT-CTT-TTCTATT
1 ACTTTTTACTGATTACTGATTACTCT-TT
* ** * *
17418 ACTATTTTACTGATTTCTTCTCACTCCTT
1 ACT-TTTTACTGATTACTGATTACTCTTT
* *
17447 ACTATTTTTTCT--TTACTGATTACTTTTT
1 AC--TTTTTACTGATTACTGATTACTCTTT
* **
17475 ACTCTTTACTCTTTACTGATTACTCTTT
1 ACTTTTTACTGATTACTGATTACTCTTT
*
17503 ACTATTTTTTCT--TTACTGATTACTCTTT
1 AC--TTTTTACTGATTACTGATTACTCTTT
17531 ACTTTTTACTGATTAC
1 ACTTTTTACTGATTAC
17547 CCTTTTACTC
Statistics
Matches: 101, Mismatches: 17, Indels: 21
0.73 0.12 0.15
Matches are distributed among these distances:
26 13 0.13
27 3 0.03
28 64 0.63
29 6 0.06
30 14 0.14
31 1 0.01
ACGTcount: A:0.19, C:0.21, G:0.04, T:0.57
Consensus pattern (28 bp):
ACTTTTTACTGATTACTGATTACTCTTT
Found at i:17567 original size:22 final size:22
Alignment explanation
Indices: 17514--17752 Score: 229
Period size: 22 Copynumber: 11.4 Consensus size: 22
17504 CTATTTTTTC
17514 TTTACTGATTA-C-TCTTTACTT
1 TTTACTGATTACCAT-TTTACTT
*
17535 TTTACTGATTACCCTTTTACTCT
1 TTTACTGATTACCATTTTACT-T
*
17558 TTT-CTAATTACCATTTTACTT
1 TTTACTGATTACCATTTTACTT
*
17579 TTCACTGATTACC--TTTACTT
1 TTTACTGATTACCATTTTACTT
17599 TTTACTGATTACCATTTTACTT
1 TTTACTGATTACCATTTTACTT
* *
17621 TTTATTGATTACCTTTTTACTT
1 TTTACTGATTACCATTTTACTT
17643 TTTACTGATTACCA--TTACTT
1 TTTACTGATTACCATTTTACTT
* * * *
17663 CTTATTGATTA-C-TATTACTC
1 TTTACTGATTACCATTTTACTT
17683 TTTACTGATTACCATTTT--TT
1 TTTACTGATTACCATTTTACTT
*
17703 CTTTACTGATTA-CTTTTTAC--
1 -TTTACTGATTACCATTTTACTT
** *
17723 TTTACTCTTTACTATTTT-CTT
1 TTTACTGATTACCATTTTACTT
17744 TTTACTGAT
1 TTTACTGAT
17753 CCCTCTTTAC
Statistics
Matches: 179, Mismatches: 23, Indels: 32
0.76 0.10 0.14
Matches are distributed among these distances:
19 11 0.06
20 58 0.32
21 33 0.18
22 72 0.40
23 5 0.03
ACGTcount: A:0.21, C:0.19, G:0.04, T:0.56
Consensus pattern (22 bp):
TTTACTGATTACCATTTTACTT
Found at i:17595 original size:64 final size:65
Alignment explanation
Indices: 17514--17725 Score: 258
Period size: 64 Copynumber: 3.3 Consensus size: 65
17504 CTATTTTTTC
*
17514 TTTACTGATTACTCTTTACTTTTTACTGATTACCCTTTTACTCTTTTCTAATTACCATTTTACTT
1 TTTACTGATTACTCTTTACTTTTTACTGATTACCCTTTTACTCTTTTCTGATTACCATTTTACTT
* * * *
17579 TTCACTGATTAC-CTTTACTTTTTACTGATTACCATTTTACT-TTTTATTGATTACCTTTTTACT
1 TTTACTGATTACTCTTTACTTTTTACTGATTACCCTTTTACTCTTTT-CTGATTACCATTTTACT
17642 T
65 T
* * * * *
17643 TTTACTGATTAC-CATTACTTCTTATTGATTA--CTATTACTCTTTACTGATTACCATTTT--TT
1 TTTACTGATTACTCTTTACTTTTTACTGATTACCCTTTTACTCTTTTCTGATTACCATTTTACTT
*
17703 CTTTACTGATTACTTTTTACTTT
1 -TTTACTGATTACTCTTTACTTT
17726 ACTCTTTACT
Statistics
Matches: 126, Mismatches: 17, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
60 2 0.02
61 12 0.10
62 24 0.19
63 7 0.06
64 70 0.56
65 11 0.09
ACGTcount: A:0.21, C:0.19, G:0.04, T:0.56
Consensus pattern (65 bp):
TTTACTGATTACTCTTTACTTTTTACTGATTACCCTTTTACTCTTTTCTGATTACCATTTTACTT
Found at i:17769 original size:40 final size:40
Alignment explanation
Indices: 17682--17775 Score: 118
Period size: 40 Copynumber: 2.4 Consensus size: 40
17672 TACTATTACT
** * * *
17682 CTTTACTGATTACCATTTTTTCTTTACTGATTACTTTTTA
1 CTTTACTCTTTACTATTTTTTCTTTACTGATCACTCTTTA
*
17722 CTTTACTCTTTACTATTTTCTT-TTTACTGATCCCTCTTTA
1 CTTTACTCTTTACTATTTT-TTCTTTACTGATCACTCTTTA
17762 CTTTACTCTTTACT
1 CTTTACTCTTTACT
17776 CTTTACCATT
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
40 45 0.96
41 2 0.04
ACGTcount: A:0.17, C:0.22, G:0.03, T:0.57
Consensus pattern (40 bp):
CTTTACTCTTTACTATTTTTTCTTTACTGATCACTCTTTA
Found at i:17777 original size:19 final size:19
Alignment explanation
Indices: 17712--17781 Score: 59
Period size: 19 Copynumber: 3.6 Consensus size: 19
17702 TCTTTACTGA
*
17712 TTACTTTTTACTTTACTCT
1 TTACTCTTTACTTTACTCT
* * **
17731 TTACTATTTTCTTTTTACTGA
1 TTACTCTTTAC--TTTACTCT
**
17752 TCCCTCTTTACTTTACTCT
1 TTACTCTTTACTTTACTCT
17771 TTACTCTTTAC
1 TTACTCTTTAC
17782 CATTTTACTA
Statistics
Matches: 37, Mismatches: 12, Indels: 4
0.70 0.23 0.08
Matches are distributed among these distances:
19 24 0.65
21 13 0.35
ACGTcount: A:0.16, C:0.24, G:0.01, T:0.59
Consensus pattern (19 bp):
TTACTCTTTACTTTACTCT
Found at i:17865 original size:34 final size:33
Alignment explanation
Indices: 17764--17872 Score: 109
Period size: 34 Copynumber: 3.4 Consensus size: 33
17754 CCTCTTTACT
*
17764 TTACTCTTTACTCTTTACCA---TTTT-ACTAA
1 TTACTCTTTACTCTTTACCATTTTTTTCACTGA
* * * * * *
17793 TCACTCTTCATTCTTTACCATTTTTATCTATTGG
1 TTACTCTTTACTCTTTACCATTTTTTTC-ACTGA
17827 TTACTCTTTACTCTTTACCATTTTTCTTCACTGA
1 TTACTCTTTACTCTTTACCATTTTT-TTCACTGA
17861 TTACTCTTTACT
1 TTACTCTTTACT
17873 GATTGCCTTT
Statistics
Matches: 61, Mismatches: 13, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
29 17 0.28
32 3 0.05
34 39 0.64
35 2 0.03
ACGTcount: A:0.19, C:0.25, G:0.03, T:0.53
Consensus pattern (33 bp):
TTACTCTTTACTCTTTACCATTTTTTTCACTGA
Found at i:17969 original size:26 final size:27
Alignment explanation
Indices: 17940--18159 Score: 126
Period size: 26 Copynumber: 8.3 Consensus size: 27
17930 CTTTGTTGAC
17940 TACT-ATTGCGCTTTTCTTACTCTTTT
1 TACTGATTGCGCTTTTCTTACTCTTTT
* *
17966 TACTGAATAT-TG--TTTCCTACTCTTTT
1 TACTG-AT-TGCGCTTTTCTTACTCTTTT
* *
17992 TACTGA-TGACTCTTTTCTTACTCTTCT
1 TACTGATTG-CGCTTTTCTTACTCTTTT
*
18019 TACTGAATAT-TG--TTTCTTACTCTTTT
1 TACTG-AT-TGCGCTTTTCTTACTCTTTT
* *
18045 TACTGATGGCTCTTTTCTTACTCTTTT
1 TACTGATTGCGCTTTTCTTACTCTTTT
* *
18072 TACTGAATAT-TG--TTTCTTACTCCTTT
1 TACTG-AT-TGCGCTTTTCTTACTCTTTT
* **
18098 TATTGA-TGATTCTTTTCTTACTCTTTT
1 TACTGATTG-CGCTTTTCTTACTCTTTT
* *
18125 TACTGAAT--ACTGTTTCTTACTCTTTTT
1 TACTGATTGCGCT-TTTCTTACTC-TTTT
18152 TACTGATT
1 TACTGATT
18160 ACTAATTGAC
Statistics
Matches: 150, Mismatches: 22, Indels: 43
0.70 0.10 0.20
Matches are distributed among these distances:
23 2 0.01
25 7 0.05
26 67 0.45
27 65 0.43
28 7 0.05
29 1 0.01
30 1 0.01
ACGTcount: A:0.16, C:0.20, G:0.08, T:0.56
Consensus pattern (27 bp):
TACTGATTGCGCTTTTCTTACTCTTTT
Found at i:18007 original size:53 final size:53
Alignment explanation
Indices: 17950--18158 Score: 346
Period size: 53 Copynumber: 3.9 Consensus size: 53
17940 TACTATTGCG
*
17950 CTTTTCTTACTCTTTTTACTGAATATTGTTTCCTACTCTTTTTACTGATGACT
1 CTTTTCTTACTCTTTTTACTGAATATTGTTTCTTACTCTTTTTACTGATGACT
* *
18003 CTTTTCTTACTCTTCTTACTGAATATTGTTTCTTACTCTTTTTACTGATGGCT
1 CTTTTCTTACTCTTTTTACTGAATATTGTTTCTTACTCTTTTTACTGATGACT
* * *
18056 CTTTTCTTACTCTTTTTACTGAATATTGTTTCTTACTCCTTTTATTGATGATT
1 CTTTTCTTACTCTTTTTACTGAATATTGTTTCTTACTCTTTTTACTGATGACT
*
18109 CTTTTCTTACTCTTTTTACTGAATACTGTTTCTTACTCTTTTTTACTGAT
1 CTTTTCTTACTCTTTTTACTGAATATTGTTTCTTACTC-TTTTTACTGAT
18159 TACTAATTGA
Statistics
Matches: 144, Mismatches: 11, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
53 135 0.94
54 9 0.06
ACGTcount: A:0.16, C:0.20, G:0.08, T:0.56
Consensus pattern (53 bp):
CTTTTCTTACTCTTTTTACTGAATATTGTTTCTTACTCTTTTTACTGATGACT
Found at i:26195 original size:2 final size:2
Alignment explanation
Indices: 26188--26219 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
26178 CTATGGCCAT
*
26188 TA TA TA TA TA TA TA TA GA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
26220 AAGGTGATGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:26706 original size:13 final size:14
Alignment explanation
Indices: 26684--26713 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
26674 AAAGGCCGAA
26684 ATTAATTAATAAAT
1 ATTAATTAATAAAT
26698 ATTAA-TAATAAAT
1 ATTAATTAATAAAT
26711 ATT
1 ATT
26714 TTGTAGAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
ATTAATTAATAAAT
Found at i:27475 original size:6 final size:6
Alignment explanation
Indices: 27464--27488 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
27454 CAGGCTGCAC
27464 CACAAT CACAAT CACAAT CACAAT C
1 CACAAT CACAAT CACAAT CACAAT C
27489 TAGCCAACAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.36, G:0.00, T:0.16
Consensus pattern (6 bp):
CACAAT
Found at i:27576 original size:39 final size:39
Alignment explanation
Indices: 27499--27718 Score: 363
Period size: 39 Copynumber: 5.7 Consensus size: 39
27489 TAGCCAACAG
* *
27499 TTAACCCCTTGAGGCACGGGTCCACTC-TTACCAACAGT
1 TTAACCCCCTGAGGCACGGGTCCACTCTTTACCATCAGT
27537 TTAACCCCCTGAGGCACGGGTCCACTC-TTACCAATCAGT
1 TTAACCCCCTGAGGCACGGGTCCACTCTTTACC-ATCAGT
*
27576 TTAACCCCCTGAGGCACAGGTCCACTCTTTACCATCAGT
1 TTAACCCCCTGAGGCACGGGTCCACTCTTTACCATCAGT
*
27615 TTAACCCCCTGAGGCGCGGGTCCACTCTTTACCATCAGT
1 TTAACCCCCTGAGGCACGGGTCCACTCTTTACCATCAGT
*
27654 TTAACCCCCTGAGGCGCGGGTCCACTCTTTACCATCAGT
1 TTAACCCCCTGAGGCACGGGTCCACTCTTTACCATCAGT
*
27693 TTAACCCCCTGAGGCGCGGGTCCACT
1 TTAACCCCCTGAGGCACGGGTCCACT
27719 ATGCACAGCC
Statistics
Matches: 175, Mismatches: 5, Indels: 3
0.96 0.03 0.02
Matches are distributed among these distances:
38 31 0.18
39 139 0.79
40 5 0.03
ACGTcount: A:0.20, C:0.36, G:0.20, T:0.24
Consensus pattern (39 bp):
TTAACCCCCTGAGGCACGGGTCCACTCTTTACCATCAGT
Found at i:29743 original size:156 final size:156
Alignment explanation
Indices: 29457--29813 Score: 384
Period size: 156 Copynumber: 2.3 Consensus size: 156
29447 TCATCTCAAA
* ** ** * *
29457 CAGACTTAGTATGAAAAACTTATGCTAGTTTTTCAGTTAAGGACAGTTTGAGGTGTCAAACCAAC
1 CAGACTTAGTATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAACTCAAGGAGACAAACCAAC
* * * * * * *
29522 TTCTCTATGCTAGAGAGTTCGGTTTTACTTAGAATTTTTCCCATAGCCTTATGGGGATAATCTAA
66 TTCACCATGCAACAGAGCTCAGTTTTACTTAGAATTTTTCCCATAGCCTTATGGAGATAATCTAA
*
29587 GT-CTACTGGTGG-AAA-ATT-AGC-CTTGT
131 GTAC--CT--TGGCAAAGATTCAGCTCAT-T
** * * *
29613 TGGACTTAGTATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAACTCAAGGAGAGAAACCTAG
1 CAGACTTAGTATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAACTCAAGGAGACAAACCAAC
* * * *
29678 TTCACCAT-CAAACAGAGCTCAGTTTTACTTATAATTTTTTCCATAGTCTTATGGAGATATTCTA
66 TTCACCATGC-AACAGAGCTCAGTTTTACTTAGAATTTTTCCCATAGCCTTATGGAGATAATCTA
*
29742 AGTACCTTGGCAAAGTTTCAGCTCATT
130 AGTACCTTGGCAAAGATTCAGCTCATT
*
29769 CAGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACA
1 CAGACTTAGTATGAAAAACTTATGCTAGTTTTTCATTTAAGGACA
29814 GTTTGAGATA
Statistics
Matches: 167, Mismatches: 28, Indels: 12
0.81 0.14 0.06
Matches are distributed among these distances:
153 3 0.02
154 3 0.02
155 5 0.03
156 153 0.92
157 3 0.02
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Consensus pattern (156 bp):
CAGACTTAGTATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAACTCAAGGAGACAAACCAAC
TTCACCATGCAACAGAGCTCAGTTTTACTTAGAATTTTTCCCATAGCCTTATGGAGATAATCTAA
GTACCTTGGCAAAGATTCAGCTCATT
Found at i:30330 original size:21 final size:21
Alignment explanation
Indices: 30306--30345 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
30296 AGAAGTGTTC
*
30306 GCCTTCCTCAGCAAGTAAAAT
1 GCCTTCCTCAACAAGTAAAAT
30327 GCCTTCCTCAACAAGTAAA
1 GCCTTCCTCAACAAGTAAA
30346 TCCCACCAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.35, C:0.30, G:0.12, T:0.23
Consensus pattern (21 bp):
GCCTTCCTCAACAAGTAAAAT
Found at i:31347 original size:166 final size:165
Alignment explanation
Indices: 30928--31380 Score: 622
Period size: 167 Copynumber: 2.7 Consensus size: 165
30918 TCCTCACCCT
* * * * *
30928 GGATTAATGAGGAGCGAGAGAACTAATTTTTTTCGTCTTTTCAC-ACTTGACTGATTACTTAAAT
1 GGATTGATGATGAGCTAGAGAACTAATTTTTTTCGTCTTTTC-CTACTTGGCAGATTACTTAAAT
* ** *
30992 GCCCTAACTTTTGATTCTTGAGTTGATTAAATAACTAGACTTTTTGGTCATTTCTCAATTGACTT
65 GTCCTAACTTTTGATTCTTGAGGGGATTAAATAACTA-ACTTTTTGGTCATTTCTCAATGGACTT
* * *
31057 TAATAGAGTAGTGAAATTACTAAAAGATCCCTATCAA
129 GAATAGAGTAGTGAAATTAATAAAAGATCCCCATCAA
* * ** * * *
31094 GGCTTGTTTTTGGAGTTAGAGAACTTATTTTTTTCGTCTTTTCCTACTTGGCAGATTACTTAGAT
1 GGATTGATGAT-GAGCTAGAGAACTAATTTTTTTCGTCTTTTCCTACTTGGCAGATTACTTAAAT
* *
31159 GT-CTAAACTTTTGATTCTTGAGGGGATTAAATAAGTAATCTTTTTGGCCATTTCTCAATGGACT
65 GTCCT-AACTTTTGATTCTTGAGGGGATTAAATAACTAA-CTTTTTGGTCATTTCTCAATGGACT
*
31223 TGAATAGAGTAGTGGAATTAATAAAAGATCCCCATCAA
128 TGAATAGAGTAGTGAAATTAATAAAAGATCCCCATCAA
* *
31261 GGATTGATGATGAGCTAGAGAACTAATCTTTTTCGTCTTTACCTACTTGGCAGATTACTTAAATG
1 GGATTGATGATGAGCTAGAGAACTAATTTTTTTCGTCTTTTCCTACTTGGCAGATTACTTAAATG
31326 TCCTAACTTTTGATTCTTGAGGGGATTAAATAACTAAACTTTTTGGTCATTTCTC
66 TCCTAACTTTTGATTCTTGAGGGGATTAAATAACT-AACTTTTTGGTCATTTCTC
31381 CATTGACAAA
Statistics
Matches: 248, Mismatches: 33, Indels: 12
0.85 0.11 0.04
Matches are distributed among these distances:
166 105 0.42
167 143 0.58
ACGTcount: A:0.29, C:0.15, G:0.17, T:0.39
Consensus pattern (165 bp):
GGATTGATGATGAGCTAGAGAACTAATTTTTTTCGTCTTTTCCTACTTGGCAGATTACTTAAATG
TCCTAACTTTTGATTCTTGAGGGGATTAAATAACTAACTTTTTGGTCATTTCTCAATGGACTTGA
ATAGAGTAGTGAAATTAATAAAAGATCCCCATCAA
Done.