Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013522.1 Corchorus capsularis cultivar CVL-1 contig13543, 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: 24222
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.34
Found at i:7511 original size:7 final size:7
Alignment explanation
Indices: 7491--7585 Score: 63
Period size: 7 Copynumber: 14.0 Consensus size: 7
7481 TACCATTTTT
7491 TCTTTAC
1 TCTTTAC
**
7498 TGATTAC
1 TCTTTAC
*
7505 TTTTTAC
1 TCTTTAC
7512 TCTTTAC
1 TCTTTAC
*
7519 -CATT-C
1 TCTTTAC
7524 TTCTTTAC
1 -TCTTTAC
**
7532 TGATTAC
1 TCTTTAC
7539 TCTTTAC
1 TCTTTAC
7546 TCTTTAC
1 TCTTTAC
*
7553 -CTTT-T
1 TCTTTAC
7558 TCTTTAC
1 TCTTTAC
**
7565 TAATTAC
1 TCTTTAC
*
7572 TCTTCAC
1 TCTTTAC
7579 TCTTTAC
1 TCTTTAC
7586 CATCTTTCTT
Statistics
Matches: 64, Mismatches: 19, Indels: 10
0.69 0.20 0.11
Matches are distributed among these distances:
5 1 0.02
6 11 0.17
7 51 0.80
8 1 0.02
ACGTcount: A:0.18, C:0.25, G:0.02, T:0.55
Consensus pattern (7 bp):
TCTTTAC
Found at i:7533 original size:34 final size:34
Alignment explanation
Indices: 7448--7598 Score: 173
Period size: 34 Copynumber: 4.4 Consensus size: 34
7438 TTACTGATTG
* * *
7448 CCATTACTT-TTTACTGATTAATATTTTACTCCTTA
1 CCATT-CTTCTTTACTGATTACT-CTTTACTCTTTA
* *
7483 CCATTTTTTCTTTACTGATTACTTTTTACTCTTTA
1 CCA-TTCTTCTTTACTGATTACTCTTTACTCTTTA
7518 CCATTCTTCTTTACTGATTACTCTTTACTCTTTA
1 CCATTCTTCTTTACTGATTACTCTTTACTCTTTA
* * *
7552 CC-TTTTTCTTTACTAATTACTCTTCACTCTTTA
1 CCATTCTTCTTTACTGATTACTCTTTACTCTTTA
7585 CCA-TCTTTCTTTAC
1 CCATTC-TTCTTTAC
7599 CATTTTTACT
Statistics
Matches: 103, Mismatches: 9, Indels: 9
0.85 0.07 0.07
Matches are distributed among these distances:
33 31 0.30
34 39 0.38
35 19 0.18
36 14 0.14
ACGTcount: A:0.19, C:0.25, G:0.02, T:0.54
Consensus pattern (34 bp):
CCATTCTTCTTTACTGATTACTCTTTACTCTTTA
Found at i:7647 original size:21 final size:22
Alignment explanation
Indices: 7623--7689 Score: 66
Period size: 21 Copynumber: 3.1 Consensus size: 22
7613 TTTTACTGAA
7623 TTACTGATTACT-ATTACTATT
1 TTACTGATTACTAATTACTATT
* ** *
7644 TTACTGGTTACTCTTTACT-CT
1 TTACTGATTACTAATTACTATT
* *
7665 TTACTAATTACTAATTACCATT
1 TTACTGATTACTAATTACTATT
7687 TTA
1 TTA
7690 TTCTTTACTG
Statistics
Matches: 35, Mismatches: 9, Indels: 3
0.74 0.19 0.06
Matches are distributed among these distances:
21 26 0.74
22 9 0.26
ACGTcount: A:0.27, C:0.18, G:0.04, T:0.51
Consensus pattern (22 bp):
TTACTGATTACTAATTACTATT
Found at i:7776 original size:34 final size:34
Alignment explanation
Indices: 7713--7962 Score: 202
Period size: 34 Copynumber: 7.6 Consensus size: 34
7703 GCCATTACTT
* *
7713 TTTACTGATTAATATTTTACTCTTTACCATTTTTC
1 TTTACTGATTACT-CTTTACTCTTTACCATTTTTC
* *
7748 TTTACTGATTACTCTTTACTCTTCACCATTCTTC
1 TTTACTGATTACTCTTTACTCTTTACCATTTTTC
* *
7782 TTTACTGA-CATCTCTTTACTCTTTACCATTTTCC
1 TTTACTGATTA-CTCTTTACTCTTTACCATTTTTC
*
7816 TTTGCTGATTACTCTTTACTC--TA-C-----TC
1 TTTACTGATTACTCTTTACTCTTTACCATTTTTC
** * * **
7842 TTTACTCTTTA-TCATTT-TTCTTTACTGATTACTC
1 TTTACTGATTACTC-TTTACTCTTTAC-CATTTTTC
*
7876 TTTTCT--TTACTCTTTACTCTTTACCATTTTTC
1 TTTACTGATTACTCTTTACTCTTTACCATTTTTC
* * *
7908 TTTACTGATTACTCTTTTACTTTTTACTATTTTAC
1 TTTACTGATTACTC-TTTACTCTTTACCATTTTTC
*
7943 TTTGCTGATTACTCTTTACT
1 TTTACTGATTACTCTTTACT
7963 TTACTCTTTA
Statistics
Matches: 172, Mismatches: 26, Indels: 35
0.74 0.11 0.15
Matches are distributed among these distances:
25 4 0.02
26 12 0.07
27 2 0.01
31 1 0.01
32 18 0.10
33 10 0.06
34 82 0.48
35 43 0.25
ACGTcount: A:0.18, C:0.23, G:0.04, T:0.56
Consensus pattern (34 bp):
TTTACTGATTACTCTTTACTCTTTACCATTTTTC
Found at i:7805 original size:7 final size:7
Alignment explanation
Indices: 7793--7980 Score: 98
Period size: 7 Copynumber: 28.1 Consensus size: 7
7783 TTACTGACAT
7793 CTCTTTA
1 CTCTTTA
7800 CTCTTTA
1 CTCTTTA
*
7807 C-CATTTT
1 CTC-TTTA
*
7814 C-CTTTG
1 CTCTTTA
**
7820 CTGATTA
1 CTCTTTA
7827 CTCTTTA
1 CTCTTTA
7834 CTC--TA
1 CTCTTTA
7839 CTCTTTA
1 CTCTTTA
7846 CTCTTTA
1 CTCTTTA
7853 -TCATTT-
1 CTC-TTTA
*
7859 TTCTTTA
1 CTCTTTA
**
7866 CTGATTA
1 CTCTTTA
7873 CTCTTT-
1 CTCTTTA
7879 -TCTTTA
1 CTCTTTA
7885 CTCTTTA
1 CTCTTTA
7892 CTCTTTA
1 CTCTTTA
7899 C-CATTT-
1 CTC-TTTA
*
7905 TTCTTTA
1 CTCTTTA
**
7912 CTGATTA
1 CTCTTTA
7919 CTCTTTTA
1 CTC-TTTA
*
7927 CTTTTTA
1 CTCTTTA
*
7934 CTATTT-
1 CTCTTTA
*
7940 -TACTTTG
1 CT-CTTTA
**
7947 CTGATTA
1 CTCTTTA
7954 CTCTTTA
1 CTCTTTA
7961 --CTTTA
1 CTCTTTA
7966 CTCTTTA
1 CTCTTTA
7973 CTCTTTA
1 CTCTTTA
7980 C
1 C
7981 CATTTTTCTT
Statistics
Matches: 137, Mismatches: 26, Indels: 36
0.69 0.13 0.18
Matches are distributed among these distances:
5 16 0.12
6 17 0.12
7 98 0.72
8 6 0.04
ACGTcount: A:0.16, C:0.24, G:0.03, T:0.57
Consensus pattern (7 bp):
CTCTTTA
Found at i:7829 original size:256 final size:256
Alignment explanation
Indices: 7343--7837 Score: 850
Period size: 256 Copynumber: 1.9 Consensus size: 256
7333 TACTAAATAT
* *
7343 CATTTTTACTCACTTTTTACTGAATTACTGATTATTATTACTATTTTACTGGTTACTGGTTACTC
1 CATTTTTACTCACTTTTTACTGAATTACTGATTACTATTACTATTTTACTGGTTACTCGTTACTC
7408 TTTACTAATTACTAATTACCATTTTATTATTTACTGATTGCCATTACTTTTTACTGATTAATATT
66 TTTACTAATTACTAATTACCATTTTATTATTTACTGATTGCCATTACTTTTTACTGATTAATATT
* * *
7473 TTACTCCTTACCATTTTTTCTTTACTGATTACTTTTTACTCTTTACCATTCTTCTTTACTGATTA
131 TTACTCCTTACCATTTTTTCTTTACTGATTACTCTTTACTCTTCACCATTCTTCTTTACTGAATA
*
7538 CTCTTTACTCTTTACCTTTTTCTTTACTAATTACTCTTCACTCTTTACCATCTTTCTTTAC
196 CTCTTTACTCTTTACCTTTTCCTTTACTAATTACTCTTCACTCTTTACCATCTTTCTTTAC
*
7599 CATTTTTACTCACTTTTTACTGAATTACTGATTACTATTACTATTTTACTGGTTACTCTTTACTC
1 CATTTTTACTCACTTTTTACTGAATTACTGATTACTATTACTATTTTACTGGTTACTCGTTACTC
*
7664 TTTACTAATTACTAATTACCATTTTATTCTTTACTGATTGCCATTACTTTTTACTGATTAATATT
66 TTTACTAATTACTAATTACCATTTTATTATTTACTGATTGCCATTACTTTTTACTGATTAATATT
*
7729 TTACTCTTTACCA-TTTTTCTTTACTGATTACTCTTTACTCTTCACCATTCTTCTTTACTGACAT
131 TTACTCCTTACCATTTTTTCTTTACTGATTACTCTTTACTCTTCACCATTCTTCTTTACTGA-AT
* * *
7793 -CTCTTTACTCTTTACCATTTTCCTTTGCTGATTACTCTTTACTCT
195 ACTCTTTACTCTTTACC-TTTTCCTTTACTAATTACTCTTCACTCT
7838 ACTCTTTACT
Statistics
Matches: 225, Mismatches: 12, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
255 62 0.28
256 163 0.72
ACGTcount: A:0.22, C:0.21, G:0.04, T:0.53
Consensus pattern (256 bp):
CATTTTTACTCACTTTTTACTGAATTACTGATTACTATTACTATTTTACTGGTTACTCGTTACTC
TTTACTAATTACTAATTACCATTTTATTATTTACTGATTGCCATTACTTTTTACTGATTAATATT
TTACTCCTTACCATTTTTTCTTTACTGATTACTCTTTACTCTTCACCATTCTTCTTTACTGAATA
CTCTTTACTCTTTACCTTTTCCTTTACTAATTACTCTTCACTCTTTACCATCTTTCTTTAC
Found at i:7842 original size:12 final size:12
Alignment explanation
Indices: 7825--7849 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
7815 CTTTGCTGAT
7825 TACTCTTTACTC
1 TACTCTTTACTC
7837 TACTCTTTACTC
1 TACTCTTTACTC
7849 T
1 T
7850 TTATCATTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.32, G:0.00, T:0.52
Consensus pattern (12 bp):
TACTCTTTACTC
Found at i:7865 original size:20 final size:19
Alignment explanation
Indices: 7824--7978 Score: 98
Period size: 19 Copynumber: 7.8 Consensus size: 19
7814 CCTTTGCTGA
**
7824 TTACTCTTTACTCTACTCT
1 TTACTCTTTACTCTTTTCT
7843 TTACTCTTTA-TCATTTTTCT
1 TTACTCTTTACTC--TTTTCT
**
7863 TTACTGATTACTCTTTTCT
1 TTACTCTTTACTCTTTTCT
*
7882 TTACTCTTTACTCTTTACCAT
1 TTACTCTTTACTCTTT-TC-T
* * *
7903 TT-TTCTTTACTGATTACTCTT
1 TTACTCTTTACT-CTT-TTC-T
* *
7924 TTACTTTTTACTATTTTACT
1 TTACTCTTTACTCTTTT-CT
* ** *
7944 TTGCTGATTACTCTTTACT
1 TTACTCTTTACTCTTTTCT
7963 TTACTCTTTACTCTTT
1 TTACTCTTTACTCTTT
7979 ACCATTTTTC
Statistics
Matches: 104, Mismatches: 23, Indels: 18
0.72 0.16 0.12
Matches are distributed among these distances:
18 2 0.02
19 45 0.43
20 35 0.34
21 15 0.14
22 7 0.07
ACGTcount: A:0.16, C:0.23, G:0.03, T:0.59
Consensus pattern (19 bp):
TTACTCTTTACTCTTTTCT
Found at i:7925 original size:46 final size:46
Alignment explanation
Indices: 7793--7930 Score: 222
Period size: 46 Copynumber: 3.0 Consensus size: 46
7783 TTACTGACAT
* * * *
7793 CTCTTTACTCTTTACCATTTTCCTTTGCTGATTACTCTTTACTCTA
1 CTCTTTACTCTTTACCATTTTTCTTTACTGATTACTCTTTTCTTTA
*
7839 CTCTTTACTCTTTATCATTTTTCTTTACTGATTACTCTTTTCTTTA
1 CTCTTTACTCTTTACCATTTTTCTTTACTGATTACTCTTTTCTTTA
7885 CTCTTTACTCTTTACCATTTTTCTTTACTGATTACTCTTTTACTTT
1 CTCTTTACTCTTTACCATTTTTCTTTACTGATTACTCTTTT-CTTT
7931 TTACTATTTT
Statistics
Matches: 85, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
46 81 0.95
47 4 0.05
ACGTcount: A:0.15, C:0.25, G:0.03, T:0.57
Consensus pattern (46 bp):
CTCTTTACTCTTTACCATTTTTCTTTACTGATTACTCTTTTCTTTA
Found at i:7934 original size:35 final size:34
Alignment explanation
Indices: 7882--7964 Score: 121
Period size: 35 Copynumber: 2.4 Consensus size: 34
7872 ACTCTTTTCT
* *
7882 TTACTCTTTACTCTTTACCATTTTTCTTTACTGA
1 TTACTCTTTACTTTTTACCATTTTACTTTACTGA
* *
7916 TTACTCTTTTACTTTTTACTATTTTACTTTGCTGA
1 TTACTC-TTTACTTTTTACCATTTTACTTTACTGA
7951 TTACTCTTTACTTT
1 TTACTCTTTACTTT
7965 ACTCTTTACT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
34 14 0.32
35 30 0.68
ACGTcount: A:0.17, C:0.20, G:0.04, T:0.59
Consensus pattern (34 bp):
TTACTCTTTACTTTTTACCATTTTACTTTACTGA
Found at i:7944 original size:15 final size:15
Alignment explanation
Indices: 7916--7945 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
7906 TCTTTACTGA
*
7916 TTACTCTTTTACTTT
1 TTACTATTTTACTTT
7931 TTACTATTTTACTTT
1 TTACTATTTTACTTT
7946 GCTGATTACT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.17, G:0.00, T:0.67
Consensus pattern (15 bp):
TTACTATTTTACTTT
Found at i:7956 original size:127 final size:126
Alignment explanation
Indices: 7756--8006 Score: 387
Period size: 127 Copynumber: 2.0 Consensus size: 126
7746 TCTTTACTGA
*
7756 TTACTCTTTACTCTTCACCATTCTTCTTTACTGACATCTCTTTACTCTTTACCATTTTCCTTTGC
1 TTACTCTTTACTCTTCACCATTCTTCTTTACTGACATCTCTTTACTCTTTACCATTTTACTTTGC
* *
7821 TGATTACTCTTTACTCTACTCTTTACTCTTTATCATTTTTCTTTACTGATTACTCTTTTCT
66 TGATTACTCTTTACTCTACTCTTTACTCTTTACCATTTTTCTTTACTAATTACTCTTTTCT
* * * * *
7882 TTACTCTTTACTCTTTACCATTTTTCTTTACTGA-TTACTCTTTTACTTTTTACTATTTTACTTT
1 TTACTCTTTACTCTTCACCATTCTTCTTTACTGACAT-CTC-TTTACTCTTTACCATTTTACTTT
* *
7946 GCTGATTACTCTTTACTTTACTCTTTACTCTTTACCATTTTTCTTTACTAATTTCTCTTTT
64 GCTGATTACTCTTTACTCTACTCTTTACTCTTTACCATTTTTCTTTACTAATTACTCTTTT
8007 TTGAATACTG
Statistics
Matches: 113, Mismatches: 10, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
125 1 0.01
126 35 0.31
127 77 0.68
ACGTcount: A:0.16, C:0.24, G:0.03, T:0.57
Consensus pattern (126 bp):
TTACTCTTTACTCTTCACCATTCTTCTTTACTGACATCTCTTTACTCTTTACCATTTTACTTTGC
TGATTACTCTTTACTCTACTCTTTACTCTTTACCATTTTTCTTTACTAATTACTCTTTTCT
Found at i:7986 original size:46 final size:48
Alignment explanation
Indices: 7906--8005 Score: 123
Period size: 46 Copynumber: 2.1 Consensus size: 48
7896 TTACCATTTT
* * * *
7906 TCTTTACTGATTACTCTTTTACTTTTTACTATTTTACTTTGCTGATTAC
1 TCTTTACT-ATTACTCTTTTACTCTTTACCATTTTACTTTACTAATTAC
* *
7955 TCTTTACT-TTACTC-TTTACTCTTTACCATTTTTCTTTACTAATTTC
1 TCTTTACTATTACTCTTTTACTCTTTACCATTTTACTTTACTAATTAC
8001 TCTTT
1 TCTTT
8006 TTTGAATACT
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
46 31 0.69
47 6 0.13
49 8 0.18
ACGTcount: A:0.17, C:0.21, G:0.03, T:0.59
Consensus pattern (48 bp):
TCTTTACTATTACTCTTTTACTCTTTACCATTTTACTTTACTAATTAC
Found at i:8005 original size:27 final size:25
Alignment explanation
Indices: 7828--7994 Score: 99
Period size: 27 Copynumber: 6.3 Consensus size: 25
7818 TGCTGATTAC
7828 TCTTTACTC--TACTCTTTACTCTTT
1 TCTTTACTCTTTACTCTTTACT-TTT
* **
7852 ATCATTT-TTCTTTACTGATTACTCTTT
1 -TC-TTTACTCTTTACTCTTTACT-TTT
7879 TCTTTACTCTTTACTCTTTACCATTTT
1 TCTTTACTCTTTACTCTTTA-C-TTTT
**
7906 TCTTTACTGATTACTCTTTTACTTTT
1 TCTTTACTCTTTACTC-TTTACTTTT
* * **
7932 TACTATT-TTACTTTGCTGATTACTCTTT
1 T-CT-TTACT-CTTTACTCTTTACT-TTT
*
7960 ACTTTACTCTTTACTCTTTACCATTTT
1 TCTTTACTCTTTACTCTTTA-C-TTTT
7987 TCTTTACT
1 TCTTTACT
7995 AATTTCTCTT
Statistics
Matches: 108, Mismatches: 20, Indels: 26
0.70 0.13 0.17
Matches are distributed among these distances:
25 7 0.06
26 32 0.30
27 54 0.50
28 15 0.14
ACGTcount: A:0.16, C:0.23, G:0.02, T:0.59
Consensus pattern (25 bp):
TCTTTACTCTTTACTCTTTACTTTT
Found at i:8039 original size:22 final size:21
Alignment explanation
Indices: 8012--8217 Score: 139
Period size: 20 Copynumber: 10.0 Consensus size: 21
8002 CTTTTTTGAA
* *
8012 TACTGATTGCCTTTTTGCTTTT
1 TACTGATTACCTTTTTAC-TTT
* *
8034 TACTGATTACTTTTTTACTTC
1 TACTGATTACCTTTTTACTTT
* *
8055 TCCTGATTTCC-TTTTACTTT
1 TACTGATTACCTTTTTACTTT
*
8075 TACTGATTACC-TTTTACTCT
1 TACTGATTACCTTTTTACTTT
*
8095 TACTGATCACC-TTTTACTTTT
1 TACTGATTACCTTTTTAC-TTT
*
8116 TACT-A--A-CTATTTTACTCT
1 TACTGATTACCT-TTTTACTTT
* *
8134 TACTTATTATC-TTTTACTTTT
1 TACTGATTACCTTTTTAC-TTT
* *
8155 TACTAATTA-CTATTTTACTCT
1 TACTGATTACCT-TTTTACTTT
*
8176 TACTGACTACCCTTTTT--TTT
1 TACTGATTA-CCTTTTTACTTT
8196 TACTGATTA-CTGTTTTACTTT
1 TACTGATTACCT-TTTTACTTT
8217 T
1 T
8218 TACTATTTTA
Statistics
Matches: 148, Mismatches: 21, Indels: 31
0.74 0.10 0.16
Matches are distributed among these distances:
17 1 0.01
18 9 0.06
19 11 0.07
20 59 0.40
21 40 0.27
22 26 0.18
23 2 0.01
ACGTcount: A:0.18, C:0.20, G:0.05, T:0.56
Consensus pattern (21 bp):
TACTGATTACCTTTTTACTTT
Found at i:8076 original size:41 final size:42
Alignment explanation
Indices: 8012--8214 Score: 199
Period size: 41 Copynumber: 5.0 Consensus size: 42
8002 CTTTTTTGAA
* * *
8012 TACTGATTGCCTTTTTGCTTTTTACTGATTACTTTTTTACT-T
1 TACTGATTTCC-TTTTACTTTTTACTGATTACTATTTTACTCT
* *
8054 CTCCTGATTTCCTTTTAC-TTTTACTGATTAC-CTTTTACTCT
1 -TACTGATTTCCTTTTACTTTTTACTGATTACTATTTTACTCT
**
8095 TACTGATCACCTTTTACTTTTTACT-A--ACTATTTTACTCT
1 TACTGATTTCCTTTTACTTTTTACTGATTACTATTTTACTCT
* *
8134 TACTTATTAT-CTTTTACTTTTTACTAATTACTATTTTACTCT
1 TACTGATT-TCCTTTTACTTTTTACTGATTACTATTTTACTCT
** *
8176 TACTGACTACCCTTTT--TTTTTACTGATTACTGTTTTACT
1 TACTGA-TTTCCTTTTACTTTTTACTGATTACTATTTTACT
8215 TTTTACTATT
Statistics
Matches: 135, Mismatches: 16, Indels: 20
0.79 0.09 0.12
Matches are distributed among these distances:
38 2 0.01
39 30 0.22
40 23 0.17
41 42 0.31
42 23 0.17
43 15 0.11
ACGTcount: A:0.19, C:0.21, G:0.05, T:0.56
Consensus pattern (42 bp):
TACTGATTTCCTTTTACTTTTTACTGATTACTATTTTACTCT
Found at i:8164 original size:14 final size:13
Alignment explanation
Indices: 8068--8179 Score: 59
Period size: 14 Copynumber: 8.4 Consensus size: 13
8058 TGATTTCCTT
8068 TTAC-TTTTACTGA
1 TTACTTTTTACT-A
* *
8081 TTACCTTTTACTC
1 TTACTTTTTACTA
** * *
8094 TTACTGATCACCTT
1 TTACTTTTTA-CTA
8108 TTACTTTTTACTA
1 TTACTTTTTACTA
*
8121 --ACTATTTTACTC
1 TTACT-TTTTACTA
* *
8133 TTACTTATTATCTT
1 TTACTTTTTA-CTA
8147 TTACTTTTTACTAA
1 TTACTTTTTACT-A
*
8161 TTACTATTTTACTC
1 TTACT-TTTTACTA
8175 TTACT
1 TTACT
8180 GACTACCCTT
Statistics
Matches: 75, Mismatches: 16, Indels: 15
0.71 0.15 0.14
Matches are distributed among these distances:
11 3 0.04
12 7 0.09
13 18 0.24
14 40 0.53
15 7 0.09
ACGTcount: A:0.22, C:0.21, G:0.02, T:0.55
Consensus pattern (13 bp):
TTACTTTTTACTA
Found at i:8213 original size:15 final size:15
Alignment explanation
Indices: 8193--8237 Score: 63
Period size: 15 Copynumber: 3.0 Consensus size: 15
8183 TACCCTTTTT
*
8193 TTTTACTGATTACTG
1 TTTTACTGTTTACTG
* *
8208 TTTTACTTTTTACTA
1 TTTTACTGTTTACTG
8223 TTTTACTGTTTACTG
1 TTTTACTGTTTACTG
8238 ATTACCATCA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.18, C:0.13, G:0.09, T:0.60
Consensus pattern (15 bp):
TTTTACTGTTTACTG
Found at i:8412 original size:53 final size:53
Alignment explanation
Indices: 8355--8563 Score: 382
Period size: 53 Copynumber: 3.9 Consensus size: 53
8345 TACTATTGCG
*
8355 CTTTTCTTACTCTTTTTACTGAATATTGTTTCCTACTCTTTTTACTGATGACT
1 CTTTTCTTACTCTTTTTACTGAATATTGTTTCTTACTCTTTTTACTGATGACT
*
8408 CTTTTCTTACTCTTTTTACTGAATATTGTTTCTTACTCTTTTTACTGATGGCT
1 CTTTTCTTACTCTTTTTACTGAATATTGTTTCTTACTCTTTTTACTGATGACT
8461 CTTTTCTTACTCTTTTTACTGAATATTGTTTCTTACTCTTTTTACTGATGACT
1 CTTTTCTTACTCTTTTTACTGAATATTGTTTCTTACTCTTTTTACTGATGACT
*
8514 CTTTTCTTACTCTTTTTACTGAATACTGTTTCTTACTCTTTTCTACTGAT
1 CTTTTCTTACTCTTTTTACTGAATATTGTTTCTTACTCTTTT-TACTGAT
8564 TACTGATTAC
Statistics
Matches: 151, Mismatches: 4, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
53 144 0.95
54 7 0.05
ACGTcount: A:0.16, C:0.20, G:0.08, T:0.56
Consensus pattern (53 bp):
CTTTTCTTACTCTTTTTACTGAATATTGTTTCTTACTCTTTTTACTGATGACT
Found at i:8568 original size:27 final size:26
Alignment explanation
Indices: 8357--8568 Score: 259
Period size: 26 Copynumber: 8.0 Consensus size: 26
8347 CTATTGCGCT
*
8357 TTTCTTACTCTTTTTACTGAATATTG
1 TTTCTTACTCTTTTTACTGAATACTG
* *
8383 TTTCCTACTCTTTTTACTG-ATGACTCT
1 TTTCTTACTCTTTTTACTGAAT-ACT-G
*
8410 TTTCTTACTCTTTTTACTGAATATTG
1 TTTCTTACTCTTTTTACTGAATACTG
* *
8436 TTTCTTACTCTTTTTACTG-ATGGCTCT
1 TTTCTTACTCTTTTTACTGAAT-ACT-G
*
8463 TTTCTTACTCTTTTTACTGAATATTG
1 TTTCTTACTCTTTTTACTGAATACTG
*
8489 TTTCTTACTCTTTTTACTG-ATGACTCT
1 TTTCTTACTCTTTTTACTGAAT-ACT-G
8516 TTTCTTACTCTTTTTACTGAATACTG
1 TTTCTTACTCTTTTTACTGAATACTG
*
8542 TTTCTTACTCTTTTCTACTGATTACTG
1 TTTCTTACTCTTTT-TACTGAATACTG
8569 ATTACTAATT
Statistics
Matches: 160, Mismatches: 16, Indels: 19
0.82 0.08 0.10
Matches are distributed among these distances:
25 6 0.04
26 75 0.47
27 73 0.46
28 6 0.04
ACGTcount: A:0.17, C:0.20, G:0.08, T:0.56
Consensus pattern (26 bp):
TTTCTTACTCTTTTTACTGAATACTG
Found at i:14210 original size:15 final size:15
Alignment explanation
Indices: 14190--14218 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
14180 GAGAAATTTT
14190 ACCAAATTTAAGGAG
1 ACCAAATTTAAGGAG
14205 ACCAAATTTAAGGA
1 ACCAAATTTAAGGA
14219 AACTTCCCGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.14, G:0.17, T:0.21
Consensus pattern (15 bp):
ACCAAATTTAAGGAG
Done.