Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011663.1 Corchorus capsularis cultivar CVL-1 contig11684, 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: 66601
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:166 original size:31 final size:32
Alignment explanation
Indices: 101--188 Score: 101
Period size: 31 Copynumber: 2.8 Consensus size: 32
91 CTAATTGTGA
101 TGAAAA-CAATTCTGTTTTGGTTGAACGTAGCAT
1 TGAAAATCAATTCTGTTTTGG-TGAAC-TAGCAT
* *
134 TGCAAATCAATTCTGTTTTGGTGGA-TAGCAT
1 TGAAAATCAATTCTGTTTTGGTGAACTAGCAT
*
165 TGAAAAT-AAATCTGTTTTAGGTGA
1 TGAAAATCAATTCTGTTTT-GGTGA
189 CGAGAAAGAG
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
30 10 0.21
31 16 0.33
33 8 0.17
34 14 0.29
ACGTcount: A:0.31, C:0.10, G:0.22, T:0.38
Consensus pattern (32 bp):
TGAAAATCAATTCTGTTTTGGTGAACTAGCAT
Found at i:3701 original size:15 final size:15
Alignment explanation
Indices: 3667--3710 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
3657 TACCATTATC
*
3667 TTTTTCTTTTTCGTT
1 TTTTTCTTTTTAGTT
* *
3682 ATTTTCTTTTTATTT
1 TTTTTCTTTTTAGTT
*
3697 TTTTTCGTTTTAGT
1 TTTTTCTTTTTAGT
3711 GCTAAATTTT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.07, C:0.09, G:0.07, T:0.77
Consensus pattern (15 bp):
TTTTTCTTTTTAGTT
Found at i:6880 original size:3 final size:3
Alignment explanation
Indices: 6872--6897 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
6862 TTTTGCTTAA
6872 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
6898 ATCCATTGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:8584 original size:29 final size:28
Alignment explanation
Indices: 8552--8614 Score: 76
Period size: 27 Copynumber: 2.2 Consensus size: 28
8542 TTAATTACTT
*
8552 TTACTACTTTTATCATTTTTACTCTTTTC
1 TTACT-CTTTTATCATTATTACTCTTTTC
*
8581 TTACTCTTTTTACCA--ATTACTCTTTTC
1 TTACTC-TTTTATCATTATTACTCTTTTC
8608 TTACTCT
1 TTACTCT
8615 CTTTTATTCA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
26 1 0.03
27 17 0.55
28 1 0.03
29 12 0.39
ACGTcount: A:0.17, C:0.24, G:0.00, T:0.59
Consensus pattern (28 bp):
TTACTCTTTTATCATTATTACTCTTTTC
Found at i:8726 original size:21 final size:21
Alignment explanation
Indices: 8694--9065 Score: 244
Period size: 21 Copynumber: 17.3 Consensus size: 21
8684 CTGATCACCC
8694 TTTACTCTTTACTGATTACTAT
1 TTTACTC-TTACTGATTACTAT
* * *
8716 TTGACTCTTACTAATTA-TCAC
1 TTTACTCTTACTGATTACT-AT
* *
8737 TTTGCTCTTACTGGTTACTAT
1 TTTACTCTTACTGATTACTAT
*
8758 TTTACTCTTACTGATTA-TCT
1 TTTACTCTTACTGATTACTAT
* *
8778 TTTACTGATT-CT--TTACGGAT
1 TTTACT-CTTACTGATTAC-TAT
8798 TTTACTCTTTACTGATTACCT-T
1 TTTACTC-TTACTGATTA-CTAT
* * * *
8820 CTTACTTTTTACTGATTGCCAT
1 TTTAC-TCTTACTGATTACTAT
8842 TTTACTCTTTTACTGATTACTAT
1 TTTACTC--TTACTGATTACTAT
* * *
8865 TTTACTTTTTGCTGATTAGC-CT
1 TTTAC-TCTTACTGATTA-CTAT
*
8887 TTTACTCTTTACTGATCACCT-T
1 TTTACTC-TTACTGATTA-CTAT
*
8909 TTTACTCTTACTGATTTCCT-T
1 TTTACTCTTACTGA-TTACTAT
* *
8930 TTTACTTCTTACTTATTACTTT
1 TTTAC-TCTTACTGATTACTAT
8952 TTTACTCTTACTGATTACTA-
1 TTTACTCTTACTGATTACTAT
* *
8972 TTTACTTTTTACTGACTACTAT
1 TTTAC-TCTTACTGATTACTAT
**
8994 TTTACTCTTGTTGATTATCT-T
1 TTTACTCTTACTGATTA-CTAT
* *
9015 CTTACCTTTTACTGATTACTAT
1 TTTA-CTCTTACTGATTACTAT
* *
9037 TTTCCTCTTTACTGATTTACCAT
1 TTTACTC-TTACTGA-TTACTAT
9060 TTTACT
1 TTTACT
9066 GATTATTATT
Statistics
Matches: 270, Mismatches: 52, Indels: 55
0.72 0.14 0.15
Matches are distributed among these distances:
18 3 0.01
20 25 0.09
21 107 0.40
22 100 0.37
23 33 0.12
24 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.06, T:0.54
Consensus pattern (21 bp):
TTTACTCTTACTGATTACTAT
Found at i:8824 original size:22 final size:22
Alignment explanation
Indices: 8797--9065 Score: 227
Period size: 22 Copynumber: 12.3 Consensus size: 22
8787 TCTTTACGGA
8797 TTTTACTCTTTACTGATTACCT
1 TTTTACTCTTTACTGATTACCT
* * * *
8819 TCTTACTTTTTACTGATTGCCA
1 TTTTACTCTTTACTGATTACCT
8841 TTTTACTCTTTTACTGATTA-CT
1 TTTTACTC-TTTACTGATTACCT
* *
8863 ATTTTACTTTTTGCTGATTAGCC-
1 -TTTTACTCTTTACTGATTA-CCT
*
8886 TTTTACTCTTTACTGATCACCT
1 TTTTACTCTTTACTGATTACCT
*
8908 TTTTACTC-TTACTGATTTCCT
1 TTTTACTCTTTACTGATTACCT
* *
8929 TTTTACT-TCTTACTTATTACTT
1 TTTTACTCT-TTACTGATTACCT
8951 TTTTACTC-TTACTGATTA-CT
1 TTTTACTCTTTACTGATTACCT
* * *
8971 ATTTACTTTTTACTGACTA-CT
1 TTTTACTCTTTACTGATTACCT
*
8992 ATTTTACTCTTGT--TGATTATCT
1 -TTTTACTCTT-TACTGATTACCT
*
9014 TCTTAC-CTTTTACTGATTA-CT
1 TTTTACTC-TTTACTGATTACCT
* *
9035 ATTTTCCTCTTTACTGATTTACCA
1 -TTTTACTCTTTACTGA-TTACCT
9059 TTTTACT
1 TTTTACT
9066 GATTATTATT
Statistics
Matches: 197, Mismatches: 31, Indels: 37
0.74 0.12 0.14
Matches are distributed among these distances:
20 9 0.05
21 54 0.27
22 104 0.53
23 28 0.14
24 2 0.01
ACGTcount: A:0.19, C:0.21, G:0.06, T:0.55
Consensus pattern (22 bp):
TTTTACTCTTTACTGATTACCT
Found at i:8942 original size:43 final size:43
Alignment explanation
Indices: 8797--9065 Score: 194
Period size: 43 Copynumber: 6.2 Consensus size: 43
8787 TCTTTACGGA
* * * *
8797 TTTTAC-TCTTTACTGATTACCT-TCTTACTTTTTACTGATTGCCA
1 TTTTACTTC-TTACTGATTA-CTATTTTAC-TCTTACTGATTTCCT
* * * *
8841 TTTTACTCTTTTACTGATTACTATTTTACTTTTTGCTGATTAGCC-
1 TTTTACT-TCTTACTGATTACTATTTTAC-TCTTACTGATT-TCCT
*
8886 TTTTAC-TCTTTACTGATCACCT-TTTTACTCTTACTGATTTCCT
1 TTTTACTTC-TTACTGATTA-CTATTTTACTCTTACTGATTTCCT
* * *
8929 TTTTACTTCTTACTTATTACTTTTTTACTCTTACTGA-TTACT
1 TTTTACTTCTTACTGATTACTATTTTACTCTTACTGATTTCCT
* * * **
8971 ATTTACTTTTTACTGACTACTATTTTACTCTTGTTGATTAT-CT
1 TTTTACTTCTTACTGATTACTATTTTACTCTTACTGATT-TCCT
* * *
9014 TCTTACCTT-TTACTGATTACTATTTTCCTCTTTACTGATTTACCA
1 TTTTA-CTTCTTACTGATTACTATTTTACTC-TTACTGATTT-CCT
9059 TTTTACT
1 TTTTACT
9066 GATTATTATT
Statistics
Matches: 184, Mismatches: 26, Indels: 30
0.77 0.11 0.12
Matches are distributed among these distances:
42 38 0.21
43 65 0.35
44 38 0.21
45 39 0.21
46 4 0.02
ACGTcount: A:0.19, C:0.21, G:0.06, T:0.55
Consensus pattern (43 bp):
TTTTACTTCTTACTGATTACTATTTTACTCTTACTGATTTCCT
Found at i:8983 original size:14 final size:13
Alignment explanation
Indices: 8906--8984 Score: 50
Period size: 14 Copynumber: 5.7 Consensus size: 13
8896 TACTGATCAC
*
8906 CTTTTTACTCTTA
1 CTTTTTACTTTTA
* *
8919 CTGATTTCCTTTTTA
1 CT-TTTTAC-TTTTA
*
8934 CTTCTTACTTATTA
1 CTTTTTACTT-TTA
*
8948 CTTTTTTACTCTTA
1 C-TTTTTACTTTTA
**
8962 CTGATTACTATTTA
1 CTTTTTACT-TTTA
8976 CTTTTTACT
1 CTTTTTACT
8985 GACTACTATT
Statistics
Matches: 48, Mismatches: 13, Indels: 9
0.69 0.19 0.13
Matches are distributed among these distances:
13 10 0.21
14 25 0.52
15 13 0.27
ACGTcount: A:0.18, C:0.20, G:0.03, T:0.59
Consensus pattern (13 bp):
CTTTTTACTTTTA
Found at i:9120 original size:55 final size:55
Alignment explanation
Indices: 9060--9242 Score: 321
Period size: 55 Copynumber: 3.3 Consensus size: 55
9050 GATTTACCAT
* * *
9060 TTTACTGATTATTATTACCTTAACTCTGATTAATCTCTTTTTACTTTATTACTGA
1 TTTACTGATTACTATTACCTTAACTCTGATTAATCTCTTTTCACTTAATTACTGA
* *
9115 TTTACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTCACTTAATTACTGA
1 TTTACTGATTACTATTACCTTAACTCTGATTAATCTCTTTTCACTTAATTACTGA
9170 TTTACTGATTACTATTACCTTAACTCTGATTAATCTCTTTTCACTTAATTACTGA
1 TTTACTGATTACTATTACCTTAACTCTGATTAATCTCTTTTCACTTAATTACTGA
9225 TTTACTGATTACTATTAC
1 TTTACTGATTACTATTAC
9243 TCTTTACTGA
Statistics
Matches: 121, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 121 1.00
ACGTcount: A:0.26, C:0.18, G:0.06, T:0.50
Consensus pattern (55 bp):
TTTACTGATTACTATTACCTTAACTCTGATTAATCTCTTTTCACTTAATTACTGA
Found at i:15242 original size:27 final size:27
Alignment explanation
Indices: 15211--15296 Score: 84
Period size: 27 Copynumber: 3.2 Consensus size: 27
15201 TAGCAACCCT
***
15211 AAAATTGCAAAATTGCCGCAACTAGCC
1 AAAATTGCAAAAACCCCGCAACTAGCC
*
15238 AAAA-TGACAAAAACCCCGTAACTAGCC
1 AAAATTG-CAAAAACCCCGCAACTAGCC
* * * *
15265 AAAATTGCAAGAACCCTGCAACAAGAC
1 AAAATTGCAAAAACCCCGCAACTAGCC
15292 AAAAT
1 AAAAT
15297 CACCAAGGCA
Statistics
Matches: 48, Mismatches: 9, Indels: 4
0.79 0.15 0.07
Matches are distributed among these distances:
26 2 0.04
27 44 0.92
28 2 0.04
ACGTcount: A:0.48, C:0.26, G:0.13, T:0.14
Consensus pattern (27 bp):
AAAATTGCAAAAACCCCGCAACTAGCC
Found at i:18054 original size:14 final size:14
Alignment explanation
Indices: 18035--18061 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
18025 AAAATTCTTT
18035 GGAATTAGGGTTTG
1 GGAATTAGGGTTTG
18049 GGAATTAGGGTTT
1 GGAATTAGGGTTT
18062 TGATTGTGCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.00, G:0.41, T:0.37
Consensus pattern (14 bp):
GGAATTAGGGTTTG
Found at i:19544 original size:42 final size:42
Alignment explanation
Indices: 19485--19595 Score: 195
Period size: 42 Copynumber: 2.6 Consensus size: 42
19475 TAACGTGCTA
19485 TATTTTGATGACGATTTAAGAAAAATGAACGATAACATACTG
1 TATTTTGATGACGATTTAAGAAAAATGAACGATAACATACTG
* * *
19527 TATTTTGATAACAATTTAAGACAAATGAACGATAACATACTG
1 TATTTTGATGACGATTTAAGAAAAATGAACGATAACATACTG
19569 TATTTTGATGACGATTTAAGAAAAATG
1 TATTTTGATGACGATTTAAGAAAAATG
19596 CAAATTTTGA
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 63 1.00
ACGTcount: A:0.43, C:0.09, G:0.15, T:0.32
Consensus pattern (42 bp):
TATTTTGATGACGATTTAAGAAAAATGAACGATAACATACTG
Found at i:20359 original size:21 final size:21
Alignment explanation
Indices: 20330--20407 Score: 88
Period size: 21 Copynumber: 3.7 Consensus size: 21
20320 ATCACCCTTT
20330 ACTCTTTACTGATTACTATTTG
1 ACTC-TTACTGATTACTATTTG
*
20352 ACTCTTACTAATTA-TCACTTTG
1 ACTCTTACTGATTACT-A-TTTG
* *
20374 -CTCTTACTGGTTACTATTTT
1 ACTCTTACTGATTACTATTTG
20394 ACTCTTACTGATTA
1 ACTCTTACTGATTA
20408 TCTTTTACTG
Statistics
Matches: 47, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
20 4 0.09
21 34 0.72
22 9 0.19
ACGTcount: A:0.23, C:0.21, G:0.08, T:0.49
Consensus pattern (21 bp):
ACTCTTACTGATTACTATTTG
Found at i:20381 original size:42 final size:43
Alignment explanation
Indices: 20326--20409 Score: 125
Period size: 42 Copynumber: 2.0 Consensus size: 43
20316 ACTGATCACC
20326 CTTTACTCTTTACTGATTACTATTTGACTCTTACTAATTATCA
1 CTTTACTCTTTACTGATTACTATTTGACTCTTACTAATTATCA
* * * *
20369 CTTTGCTC-TTACTGGTTACTATTTTACTCTTACTGATTATC
1 CTTTACTCTTTACTGATTACTATTTGACTCTTACTAATTATC
20410 TTTTACTGAT
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
42 30 0.81
43 7 0.19
ACGTcount: A:0.21, C:0.21, G:0.07, T:0.50
Consensus pattern (43 bp):
CTTTACTCTTTACTGATTACTATTTGACTCTTACTAATTATCA
Found at i:20423 original size:42 final size:42
Alignment explanation
Indices: 20326--20423 Score: 108
Period size: 42 Copynumber: 2.3 Consensus size: 42
20316 ACTGATCACC
*
20326 CTTTACTCTTTACTGATTACTATTTGACTCTTACTAATTATCA
1 CTTTACT-ATTACTGATTACTATTTGACTCTTACTAATTATCA
* * * * *
20369 CTTTGCTCTTACTGGTTACTATTTTACTCTTACTGATTATC-
1 CTTTACTATTACTGATTACTATTTGACTCTTACTAATTATCA
*
20410 TTTTACTGATTACT
1 CTTTACT-ATTACT
20424 ATCTTATTCT
Statistics
Matches: 46, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
41 5 0.11
42 35 0.76
43 6 0.13
ACGTcount: A:0.21, C:0.20, G:0.07, T:0.51
Consensus pattern (42 bp):
CTTTACTATTACTGATTACTATTTGACTCTTACTAATTATCA
Found at i:20833 original size:55 final size:55
Alignment explanation
Indices: 20759--20889 Score: 185
Period size: 55 Copynumber: 2.4 Consensus size: 55
20749 TATCAATTTA
* *
20759 CTGATTAATCTCTTTTTACTTAACTACTGATTTACTGATTACTA-TTACTTCGATT
1 CTGATTAATTTCTTTTTACTTAACTACTGATTTACTGATTACTATTTACTT-GACT
* * *
20814 CTGATT-ATTTTTTTCTTACTTGACTACTGATTTACTGATTACTATTTCCTTGACT
1 CTGATTAATTTCTTT-TTACTTAACTACTGATTTACTGATTACTATTTACTTGACT
20869 CTGATTAATTTCTTTTTACTT
1 CTGATTAATTTCTTTTTACTT
20890 TTTAGATTTC
Statistics
Matches: 67, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
54 6 0.09
55 49 0.73
56 12 0.18
ACGTcount: A:0.22, C:0.18, G:0.08, T:0.53
Consensus pattern (55 bp):
CTGATTAATTTCTTTTTACTTAACTACTGATTTACTGATTACTATTTACTTGACT
Found at i:21599 original size:51 final size:51
Alignment explanation
Indices: 21495--21856 Score: 455
Period size: 51 Copynumber: 7.1 Consensus size: 51
21485 ACTTCTAATT
*
21495 CCAAA-ATGACA-TTTTATTTACTAATTACT-TAAAAATTCAATCTTTTAT
1 CCAAAGATGACATTTTTATTTACTAATTACTCTAAAAATTCAATCTTTTAC
* * * * *
21543 TCAAAGATTAGATCTTTATTTACTAATTACTCTAAAGATTCAATCTTTTAC
1 CCAAAGATGACATTTTTATTTACTAATTACTCTAAAAATTCAATCTTTTAC
* * *
21594 CCAAAG-TCGACATTTTTATTTACCAATTACTC-AAAAATCCAAATCTTTTAT
1 CCAAAGAT-GACATTTTTATTTACTAATTACTCTAAAAATTC-AATCTTTTAC
* * * * * * * *
21645 TCAAAGGTTAAATCTTTACTTACTAATTACTTTAAAGATTCAATCTTTTAC
1 CCAAAGATGACATTTTTATTTACTAATTACTCTAAAAATTCAATCTTTTAC
*
21696 CCAAAGATGACATTTTCATTTACTAATTACTCTAAAAATTCAATCTTTTAC
1 CCAAAGATGACATTTTTATTTACTAATTACTCTAAAAATTCAATCTTTTAC
* *
21747 CCAAGGATGACATTTTTATTTACTAATTACTCTTAAAAATTCCATCTTTTAC
1 CCAAAGATGACATTTTTATTTACTAATTACTC-TAAAAATTCAATCTTTTAC
* *
21799 CCAAAGATGACATTTTTATTTACTAATTACTCTTAAAAATTCCATCCTTTAC
1 CCAAAGATGACATTTTTATTTACTAATTACTC-TAAAAATTCAATCTTTTAC
21851 CCAAAG
1 CCAAAG
21857 GTTATACCTT
Statistics
Matches: 268, Mismatches: 38, Indels: 12
0.84 0.12 0.04
Matches are distributed among these distances:
48 4 0.01
49 4 0.01
50 24 0.09
51 155 0.58
52 81 0.30
ACGTcount: A:0.36, C:0.19, G:0.05, T:0.41
Consensus pattern (51 bp):
CCAAAGATGACATTTTTATTTACTAATTACTCTAAAAATTCAATCTTTTAC
Found at i:24432 original size:27 final size:27
Alignment explanation
Indices: 24355--24434 Score: 115
Period size: 27 Copynumber: 3.0 Consensus size: 27
24345 AGGTGAACCT
* * *
24355 AAAAATGACTAAAATGCCCCTGAGTAC
1 AAAAATGACCAAAATGCCCCTGGGTGC
24382 AAAAATGACCAAAATGCCCCTGGGTGC
1 AAAAATGACCAAAATGCCCCTGGGTGC
* *
24409 AAAAATGACCAAAATACCCTTGGGTG
1 AAAAATGACCAAAATGCCCCTGGGTG
24435 ACCCTAATGC
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 48 1.00
ACGTcount: A:0.41, C:0.23, G:0.19, T:0.17
Consensus pattern (27 bp):
AAAAATGACCAAAATGCCCCTGGGTGC
Found at i:28857 original size:21 final size:21
Alignment explanation
Indices: 28804--28863 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 21
28794 TTTGGAGCAA
*
28804 GAATATTCCAATTGATTCTAT
1 GAATATTCCAATTGATTCTAG
** * *
28825 GTCTACTACAATTGATTCTAG
1 GAATATTCCAATTGATTCTAG
*
28846 GAATATTCCAATCGATTC
1 GAATATTCCAATTGATTC
28864 CAAGTTATGC
Statistics
Matches: 29, Mismatches: 10, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.32, C:0.18, G:0.12, T:0.38
Consensus pattern (21 bp):
GAATATTCCAATTGATTCTAG
Found at i:29631 original size:23 final size:23
Alignment explanation
Indices: 29578--29631 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 23
29568 CTTGTGAAGG
*
29578 TTTCTTTGTTGCCCAGTTCAGGT
1 TTTCTTTGTTGCCCAGTTCAGAT
*
29601 TTTCTTTGTTGTCCAGTTCA-AT
1 TTTCTTTGTTGCCCAGTTCAGAT
29623 TTTCATTTG
1 TTTC-TTTG
29632 GTGAGTGGGT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 5 0.18
23 23 0.82
ACGTcount: A:0.11, C:0.19, G:0.17, T:0.54
Consensus pattern (23 bp):
TTTCTTTGTTGCCCAGTTCAGAT
Found at i:29781 original size:2 final size:2
Alignment explanation
Indices: 29774--29800 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
29764 TTGTTTAGAA
29774 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
29801 ACTACATAGG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:30846 original size:2 final size:2
Alignment explanation
Indices: 30829--30867 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
30819 CATTATCATC
* *
30829 AT AT AC AT AC AT AT AT AT AT AT A- AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
30868 GTATGTATGT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:36622 original size:24 final size:24
Alignment explanation
Indices: 36590--36650 Score: 104
Period size: 24 Copynumber: 2.5 Consensus size: 24
36580 AAATCATCCC
*
36590 ATTAATCAAAGCATCGTTCCAGAA
1 ATTAATCAAAGCATCGTTCCAAAA
*
36614 ATTAATCAAAGCATTGTTCCAAAA
1 ATTAATCAAAGCATCGTTCCAAAA
36638 ATTAATCAAAGCA
1 ATTAATCAAAGCA
36651 CCATTACCCA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.46, C:0.18, G:0.10, T:0.26
Consensus pattern (24 bp):
ATTAATCAAAGCATCGTTCCAAAA
Found at i:46779 original size:20 final size:20
Alignment explanation
Indices: 46750--46794 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
46740 TGAACATTCA
* *
46750 TACTTGTAATTATTTTCAAT
1 TACTTCTAATTATTCTCAAT
46770 TACTTCTAATTATTCTCAAT
1 TACTTCTAATTATTCTCAAT
46790 TACTT
1 TACTT
46795 GTATAAATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.29, C:0.16, G:0.02, T:0.53
Consensus pattern (20 bp):
TACTTCTAATTATTCTCAAT
Found at i:49028 original size:12 final size:12
Alignment explanation
Indices: 48994--49047 Score: 72
Period size: 12 Copynumber: 4.4 Consensus size: 12
48984 TAATACAGGC
*
48994 ATCGACAGATAT
1 ATCGACGGATAT
*
49006 ATCGAATGGATAT
1 ATCG-ACGGATAT
49019 ATCGACGGATAT
1 ATCGACGGATAT
*
49031 ATCGATGGATAT
1 ATCGACGGATAT
49043 ATCGA
1 ATCGA
49048 GGTATCGATG
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
12 27 0.73
13 10 0.27
ACGTcount: A:0.37, C:0.13, G:0.22, T:0.28
Consensus pattern (12 bp):
ATCGACGGATAT
Found at i:49029 original size:25 final size:24
Alignment explanation
Indices: 48994--49047 Score: 90
Period size: 25 Copynumber: 2.2 Consensus size: 24
48984 TAATACAGGC
48994 ATCGACAGATATATCGAATGGATAT
1 ATCGACAGATATATCG-ATGGATAT
*
49019 ATCGACGGATATATCGATGGATAT
1 ATCGACAGATATATCGATGGATAT
49043 ATCGA
1 ATCGA
49048 GGTATCGATG
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
24 13 0.46
25 15 0.54
ACGTcount: A:0.37, C:0.13, G:0.22, T:0.28
Consensus pattern (24 bp):
ATCGACAGATATATCGATGGATAT
Found at i:49055 original size:20 final size:22
Alignment explanation
Indices: 49004--49057 Score: 67
Period size: 24 Copynumber: 2.4 Consensus size: 22
48994 ATCGACAGAT
49004 ATATCGAATGGATATATCGACGG
1 ATATCG-ATGGATATATCGACGG
49027 ATATATCGATGGATATATCGA-GG
1 --ATATCGATGGATATATCGACGG
49050 -TATCGATG
1 ATATCGATG
49058 AAATTCAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
20 8 0.28
23 2 0.07
24 13 0.45
25 6 0.21
ACGTcount: A:0.33, C:0.11, G:0.26, T:0.30
Consensus pattern (22 bp):
ATATCGATGGATATATCGACGG
Found at i:49229 original size:12 final size:13
Alignment explanation
Indices: 49212--49240 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
49202 TAGACATTAC
49212 TTTTTTTTA-ATT
1 TTTTTTTTATATT
49224 TTTTTTTTATATT
1 TTTTTTTTATATT
49237 TTTT
1 TTTT
49241 ACTGCGAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (13 bp):
TTTTTTTTATATT
Found at i:49789 original size:111 final size:111
Alignment explanation
Indices: 49595--49815 Score: 397
Period size: 111 Copynumber: 2.0 Consensus size: 111
49585 GGTAATCCAG
*
49595 TTAAAATATTCAAGTCATGACATATAAGGTTTATAAACCTCCATATAATTGTGCACAGATTCCAA
1 TTAAAATATTCAAGTCATGACATATAAGGTTTATAAACCTCCATATAATTGTGCACAGACTCCAA
* *
49660 ACATGCCTCTCAACTAATACTTGTTAGCCATCTAATAGGGGGGCAA
66 ACATGCCTCTCAACTAATACTTGTTAACCATCAAATAGGGGGGCAA
*
49706 TTAAAATATTCAAGTCATGACATATAAGGTTTATAAACCTCCATATAATTGTGCACATACTCCAA
1 TTAAAATATTCAAGTCATGACATATAAGGTTTATAAACCTCCATATAATTGTGCACAGACTCCAA
*
49771 ATATGCCTCTCAACTAATACTTGTTAACCATCAAATAGGGGGGCA
66 ACATGCCTCTCAACTAATACTTGTTAACCATCAAATAGGGGGGCA
49816 CTCACCCGAA
Statistics
Matches: 105, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
111 105 1.00
ACGTcount: A:0.37, C:0.20, G:0.14, T:0.30
Consensus pattern (111 bp):
TTAAAATATTCAAGTCATGACATATAAGGTTTATAAACCTCCATATAATTGTGCACAGACTCCAA
ACATGCCTCTCAACTAATACTTGTTAACCATCAAATAGGGGGGCAA
Found at i:53626 original size:17 final size:16
Alignment explanation
Indices: 53584--53631 Score: 62
Period size: 15 Copynumber: 3.0 Consensus size: 16
53574 GAGTCTTAAG
53584 TAAGTAGACAAGAGTC
1 TAAGTAGACAAGAGTC
* *
53600 T-TGGAGACAAGAGTC
1 TAAGTAGACAAGAGTC
53615 TCAAGTAGACAAGAGTC
1 T-AAGTAGACAAGAGTC
53632 CAAAAGAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
15 13 0.50
16 1 0.04
17 12 0.46
ACGTcount: A:0.40, C:0.15, G:0.27, T:0.19
Consensus pattern (16 bp):
TAAGTAGACAAGAGTC
Found at i:54250 original size:22 final size:22
Alignment explanation
Indices: 54222--54286 Score: 112
Period size: 22 Copynumber: 3.0 Consensus size: 22
54212 CTTTTGAAGG
54222 ATGGCCGAATCTCACGGCCACC
1 ATGGCCGAATCTCACGGCCACC
* *
54244 ATGGCCGAATCCCACGGCCACT
1 ATGGCCGAATCTCACGGCCACC
54266 ATGGCCGAATCTCACGGCCAC
1 ATGGCCGAATCTCACGGCCAC
54287 ATACTAACCC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.23, C:0.40, G:0.23, T:0.14
Consensus pattern (22 bp):
ATGGCCGAATCTCACGGCCACC
Found at i:58259 original size:17 final size:16
Alignment explanation
Indices: 58217--58264 Score: 62
Period size: 15 Copynumber: 3.0 Consensus size: 16
58207 GAGTTTCAAG
58217 TAAGTAGACAAGAGTC
1 TAAGTAGACAAGAGTC
* *
58233 T-TGGAGACAAGAGTC
1 TAAGTAGACAAGAGTC
58248 TCAAGTAGACAAGAGTC
1 T-AAGTAGACAAGAGTC
58265 CAAAAGAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
15 13 0.50
16 1 0.04
17 12 0.46
ACGTcount: A:0.40, C:0.15, G:0.27, T:0.19
Consensus pattern (16 bp):
TAAGTAGACAAGAGTC
Found at i:58649 original size:44 final size:44
Alignment explanation
Indices: 58595--58690 Score: 131
Period size: 44 Copynumber: 2.2 Consensus size: 44
58585 CACCGTCTTT
* *
58595 GTCAAATTGAAAAGC-CAACATGGCTTTTTATCACAGGCACCTTG
1 GTCAAATTGAAAA-CAAAACATGGCTTTTTATCACAGCCACCTTG
* * *
58639 GTCAAGTTGAAAACAAAATATGGCTTTTTATCATAGCCACCTTG
1 GTCAAATTGAAAACAAAACATGGCTTTTTATCACAGCCACCTTG
58683 GTCAAATT
1 GTCAAATT
58691 TAATAATTAG
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
43 1 0.02
44 44 0.98
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (44 bp):
GTCAAATTGAAAACAAAACATGGCTTTTTATCACAGCCACCTTG
Found at i:58841 original size:22 final size:22
Alignment explanation
Indices: 58816--58876 Score: 86
Period size: 22 Copynumber: 2.8 Consensus size: 22
58806 TGAAGGATGC
* *
58816 CCGAATGTCACGGCCACCATGG
1 CCGAATCTCACGGCCACCATGA
* *
58838 CCGAATCCCACGGCCACTATGA
1 CCGAATCTCACGGCCACCATGA
58860 CCGAATCTCACGGCCAC
1 CCGAATCTCACGGCCAC
58877 ATACTAACCC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.25, C:0.41, G:0.21, T:0.13
Consensus pattern (22 bp):
CCGAATCTCACGGCCACCATGA
Found at i:59056 original size:22 final size:22
Alignment explanation
Indices: 59026--59067 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
59016 TACCATTATG
*
59026 TGGCTGAATCTCACGGCCACCA
1 TGGCCGAATCTCACGGCCACCA
59048 TGGCCGAATCTCACGGCCAC
1 TGGCCGAATCTCACGGCCAC
59068 AGTCTTTAGT
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:0.21, C:0.38, G:0.24, T:0.17
Consensus pattern (22 bp):
TGGCCGAATCTCACGGCCACCA
Found at i:63543 original size:20 final size:21
Alignment explanation
Indices: 63506--63544 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
63496 GAGTCGCGAG
63506 GCAAACCACATGGGGCGCCAA
1 GCAAACCACATGGGGCGCCAA
63527 GCAAACCACAT-GGGCGCC
1 GCAAACCACATGGGGCGCC
63545 CAGTGCTAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.31, C:0.36, G:0.28, T:0.05
Consensus pattern (21 bp):
GCAAACCACATGGGGCGCCAA
Done.