Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024778.1 Corchorus olitorius cultivar O-4 contig24811, 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: 8400
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.34
Found at i:5796 original size:22 final size:22
Alignment explanation
Indices: 5743--6016 Score: 152
Period size: 22 Copynumber: 12.5 Consensus size: 22
5733 ATTATAGTGT
* * *
5743 GGTTATCACAA-TTCATAGTGT
1 GGTTATCAAAATTTCATAGAGA
* * *
5764 GGTAATAAAAATTCCATAGAGA
1 GGTTATCAAAATTTCATAGAGA
*
5786 GGTTATCAAAATTTCATAGGGA
1 GGTTATCAAAATTTCATAGAGA
** *
5808 ATTTATCAAAATTTCGTA-AGA
1 GGTTATCAAAATTTCATAGAGA
* * *
5829 GCGTTATCAGAATTTCATAGTGT
1 G-GTTATCAAAATTTCATAGAGA
* *
5852 GGTTATCAAACTTTCGTA-AGGA
1 GGTTATCAAAATTTCATAGA-GA
* ** * *
5874 GGTTATAAAAAAGGTCATAAAAAA
1 GGTTAT-CAAAATTTCAT-AGAGA
5898 GGTTATCAAAATTTCATAGCA-A
1 GGTTATCAAAATTTCATAG-AGA
* **
5920 GATTATCAAAATTTCATA-ATTT
1 GGTTATCAAAATTTCATAGA-GA
*
5942 GGTTATCGAAATTTCATATG-GA
1 GGTTATCAAAATTTCATA-GAGA
* *
5964 GG-TA-CAAAAATTTCATAGTGT
1 GGTTATC-AAAATTTCATAGAGA
* *
5985 GGCTATCGAAATTTCATTAG-GA
1 GGTTATCAAAATTTCA-TAGAGA
6007 GGTTATCAAA
1 GGTTATCAAA
6017 GTGGTTATCA
Statistics
Matches: 189, Mismatches: 47, Indels: 33
0.70 0.17 0.12
Matches are distributed among these distances:
20 3 0.02
21 25 0.13
22 131 0.69
23 21 0.11
24 8 0.04
25 1 0.01
ACGTcount: A:0.38, C:0.11, G:0.18, T:0.33
Consensus pattern (22 bp):
GGTTATCAAAATTTCATAGAGA
Found at i:5858 original size:44 final size:43
Alignment explanation
Indices: 5743--6196 Score: 184
Period size: 44 Copynumber: 10.5 Consensus size: 43
5733 ATTATAGTGT
* * * * *
5743 GGTTATCACAA-TTCATAGTGTGGTAATAAAAATTCCATAGAGA
1 GGTTATCAAAATTTCATAGTGTGGTTATCAAAATTTCGTA-AGA
* ***
5786 GGTTATCAAAATTTCATAGGGAATTTATCAAAATTTCGTAAGA
1 GGTTATCAAAATTTCATAGTGTGGTTATCAAAATTTCGTAAGA
* *
5829 GCGTTATCAGAATTTCATAGTGTGGTTATCAAACTTTCGTAAGGA
1 G-GTTATCAAAATTTCATAGTGTGGTTATCAAAATTTCGTAA-GA
* ** **** *
5874 GGTTATAAAAAAGGTCATAAAAAAGGTTATCAAAATTTCAT-AGCAA
1 GGTTAT-CAAAATTTCAT-AGTGTGGTTATCAAAATTTCGTAAG--A
* * * * * *
5920 GATTATCAAAATTTCATAATTTGGTTATCGAAATTTCATATGGA
1 GGTTATCAAAATTTCATAGTGTGGTTATCAAAATTTCGTA-AGA
* * * *
5964 GG-TA-CAAAAATTTCATAGTGTGGCTATCGAAATTTCATTAGGA
1 GGTTATC-AAAATTTCATAGTGTGGTTATCAAAATTTC-GTAAGA
* *
6007 GGTTATC---A----A-A--GTGGTTATCAAAAATTTCATAGGGA
1 GGTTATCAAAATTTCATAGTGTGGTTATC-AAAATTTCGTA-AGA
* * * * * * *
6042 TGTTATCAAAA-TTCATACTGAGGCTATCAAAATTTCATAGTGT
1 GGTTATCAAAATTTCATAGTGTGGTTATCAAAATTTCGTA-AGA
* * * *
6085 GGTTATCAACATTTCATTG-GAAGGTTATCAAAATTTCATAGGGCAGA
1 GGTTATCAAAATTTCATAGTG-TGGTTATCAAAATTTCGTA----AGA
* * * * *
6132 GATTATCAAAATTTCATAGTGTGGTTACCAAAACTTCATAGGGA
1 GGTTATCAAAATTTCATAGTGTGGTTATCAAAATTTCGTA-AGA
**
6176 AATTATCAAAATTTCATAGTG
1 GGTTATCAAAATTTCATAGTG
6197 GAGAAACCAA
Statistics
Matches: 317, Mismatches: 64, Indels: 59
0.72 0.15 0.13
Matches are distributed among these distances:
34 10 0.03
35 16 0.05
36 1 0.00
37 1 0.00
38 1 0.00
41 2 0.01
42 2 0.01
43 71 0.22
44 136 0.43
45 20 0.06
46 23 0.07
47 33 0.10
48 1 0.00
ACGTcount: A:0.37, C:0.11, G:0.18, T:0.33
Consensus pattern (43 bp):
GGTTATCAAAATTTCATAGTGTGGTTATCAAAATTTCGTAAGA
Found at i:5908 original size:12 final size:12
Alignment explanation
Indices: 5873--5908 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
5863 TTTCGTAAGG
5873 AGGTTATAAAAA
1 AGGTTATAAAAA
*
5885 AGGTCATAAAAA
1 AGGTTATAAAAA
5897 AGGTTATCAAAA
1 AGGTTAT-AAAA
5909 TTTCATAGCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 17 0.81
13 4 0.19
ACGTcount: A:0.56, C:0.06, G:0.17, T:0.22
Consensus pattern (12 bp):
AGGTTATAAAAA
Found at i:5975 original size:43 final size:43
Alignment explanation
Indices: 5927--6009 Score: 123
Period size: 43 Copynumber: 1.9 Consensus size: 43
5917 CAAGATTATC
* *
5927 AAAATTTCATAATTTGGTTATCGAAATTTCA-TATGGAGGTACA
1 AAAATTTCATAATGTGGCTATCGAAATTTCATTA-GGAGGTACA
*
5970 AAAATTTCATAGTGTGGCTATCGAAATTTCATTAGGAGGT
1 AAAATTTCATAATGTGGCTATCGAAATTTCATTAGGAGGT
6010 TATCAAAGTG
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
43 34 0.94
44 2 0.06
ACGTcount: A:0.35, C:0.10, G:0.19, T:0.36
Consensus pattern (43 bp):
AAAATTTCATAATGTGGCTATCGAAATTTCATTAGGAGGTACA
Found at i:6069 original size:78 final size:77
Alignment explanation
Indices: 5941--6093 Score: 186
Period size: 78 Copynumber: 2.0 Consensus size: 77
5931 TTTCATAATT
* * * * *
5941 TGGTTATCGAAATTTCATATGGAGGTACAAAAATTTCATAGTGTGGCTATCGAAATTTCATTAG-
1 TGGTTATCAAAATTTCATAGGGAGGTACAAAAATTTCATACTGAGGCTATCAAAATTTCA-TAGT
6005 GAGGTTATCAAAG
65 GAGGTTATCAAAG
*
6018 TGGTTATCAAAAATTTCATAGGGATGTTATC-AAAA-TTCATACTGAGGCTATCAAAATTTCATA
1 TGGTTATC-AAAATTTCATAGGGA-GGTA-CAAAAATTTCATACTGAGGCTATCAAAATTTCATA
*
6081 GTGTGGTTATCAA
63 GTGAGGTTATCAA
6094 CATTTCATTG
Statistics
Matches: 65, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
77 11 0.17
78 46 0.71
79 7 0.11
80 1 0.02
ACGTcount: A:0.35, C:0.11, G:0.20, T:0.35
Consensus pattern (77 bp):
TGGTTATCAAAATTTCATAGGGAGGTACAAAAATTTCATACTGAGGCTATCAAAATTTCATAGTG
AGGTTATCAAAG
Found at i:6091 original size:22 final size:22
Alignment explanation
Indices: 6019--6238 Score: 176
Period size: 22 Copynumber: 9.9 Consensus size: 22
6009 TTATCAAAGT
*
6019 GGTTATCAAAAATTTCATAGGGA
1 GGTTATC-AAAATTTCATAGTGA
* *
6042 TGTTATCAAAA-TTCATACTGA
1 GGTTATCAAAATTTCATAGTGA
* *
6063 GGCTATCAAAATTTCATAGTGT
1 GGTTATCAAAATTTCATAGTGA
* *
6085 GGTTATCAACATTTCATTG-GAA
1 GGTTATCAAAATTTCATAGTG-A
*
6107 GGTTATCAAAATTTCATAGGGCA
1 GGTTATCAAAATTTCATAGTG-A
*
6130 GAGATTATCAAAATTTCATAGTGT
1 G-G-TTATCAAAATTTCATAGTGA
* * *
6154 GGTTACCAAAACTTCATAGGGA
1 GGTTATCAAAATTTCATAGTGA
**
6176 AATTATCAAAATTTCATAGTG-
1 GGTTATCAAAATTTCATAGTGA
** * *
6197 GAGAAACCAAAATTTCATAGCGA
1 G-GTTATCAAAATTTCATAGTGA
** *
6220 TTTTATCAAATTTTCATAG
1 GGTTATCAAAATTTCATAG
6239 GAACCAGGGG
Statistics
Matches: 153, Mismatches: 37, Indels: 15
0.75 0.18 0.07
Matches are distributed among these distances:
21 18 0.12
22 105 0.69
23 10 0.07
24 2 0.01
25 18 0.12
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.34
Consensus pattern (22 bp):
GGTTATCAAAATTTCATAGTGA
Found at i:6153 original size:69 final size:69
Alignment explanation
Indices: 6066--6194 Score: 197
Period size: 69 Copynumber: 1.9 Consensus size: 69
6056 ATACTGAGGC
* * * * *
6066 TATCAAAATTTCATAGTGTGGTTATCAACATTTCAT-TGGAAGGTTATCAAAATTTCATAGGGCA
1 TATCAAAATTTCATAGTGTGGTTACCAAAACTTCATAGGGAA-ATTATCAAAATTTCATAGGGCA
6130 GAGAT
65 GAGAT
6135 TATCAAAATTTCATAGTGTGGTTACCAAAACTTCATAGGGAAATTATCAAAATTTCATAG
1 TATCAAAATTTCATAGTGTGGTTACCAAAACTTCATAGGGAAATTATCAAAATTTCATAG
6195 TGGAGAAACC
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
69 50 0.93
70 4 0.07
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.34
Consensus pattern (69 bp):
TATCAAAATTTCATAGTGTGGTTACCAAAACTTCATAGGGAAATTATCAAAATTTCATAGGGCAG
AGAT
Found at i:6239 original size:66 final size:68
Alignment explanation
Indices: 6017--6218 Score: 175
Period size: 69 Copynumber: 3.0 Consensus size: 68
6007 GGTTATCAAA
* * ** ** * *
6017 GTGGTTATCAAAAATTTCATAGGGATGTTATCAAAA-TTCATACTG-AG-GCTATCAAAATTTCA
1 GTGGTTA-CCAAAACTTCATAGGGAAATTATCAAAATTTCATAGGGCAGAGATACCAAAATTTCA
*
6079 TAGT
65 TAGC
* * * * * *
6083 GTGGTTATCAACATTTCAT-TGGAAGGTTATCAAAATTTCATAGGGCAGAGATTATCAAAATTTC
1 GTGGTTACCAAAACTTCATAGGGAA-ATTATCAAAATTTCATAGGGCAGAGA-TACCAAAATTTC
*
6147 ATAGT
64 ATAGC
6152 GTGGTTACCAAAACTTCATAGGGAAATTATCAAAATTTCATAGTGG-AGA-A-ACCAAAATTTCA
1 GTGGTTACCAAAACTTCATAGGGAAATTATCAAAATTTCATAG-GGCAGAGATACCAAAATTTCA
6214 TAGC
65 TAGC
6218 G
1 G
6219 ATTTTATCAA
Statistics
Matches: 114, Mismatches: 15, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
64 3 0.03
65 19 0.17
66 29 0.25
67 2 0.02
68 2 0.02
69 53 0.46
70 6 0.05
ACGTcount: A:0.37, C:0.13, G:0.18, T:0.32
Consensus pattern (68 bp):
GTGGTTACCAAAACTTCATAGGGAAATTATCAAAATTTCATAGGGCAGAGATACCAAAATTTCAT
AGC
Found at i:6929 original size:22 final size:22
Alignment explanation
Indices: 6904--7095 Score: 147
Period size: 22 Copynumber: 8.8 Consensus size: 22
6894 TGATAGGAAC
* *
6904 GTTATTAAAATTTCATAGTGTG
1 GTTATCAAAATTTCATAGTGAG
* * * *
6926 GTTATTAAATTTTAATAGGGAG
1 GTTATCAAAATTTCATAGTGAG
* **
6948 GTTATCAAAATTTCACAGCAAG
1 GTTATCAAAATTTCATAGTGAG
6970 GTTATCAAAATTTCATAGTGTA-
1 GTTATCAAAATTTCATAGTG-AG
* * * * *
6992 ATAATTAAAATTTCATAATGTG
1 GTTATCAAAATTTCATAGTGAG
*
7014 GTTATCAAAATTTCTTAG-GAAG
1 GTTATCAAAATTTCATAGTG-AG
* *
7036 G-TACCAAAATTTCATAGTGTG
1 GTTATCAAAATTTCATAGTGAG
* * * **
7057 GTAATCGAATTTTCATAAAGAG
1 GTTATCAAAATTTCATAGTGAG
7079 GTTATCAAAATTTCATA
1 GTTATCAAAATTTCATA
7096 CTGGTTGAAA
Statistics
Matches: 128, Mismatches: 37, Indels: 10
0.73 0.21 0.06
Matches are distributed among these distances:
21 17 0.13
22 110 0.86
23 1 0.01
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.38
Consensus pattern (22 bp):
GTTATCAAAATTTCATAGTGAG
Found at i:6959 original size:44 final size:44
Alignment explanation
Indices: 6904--7095 Score: 172
Period size: 44 Copynumber: 4.4 Consensus size: 44
6894 TGATAGGAAC
* * * *
6904 GTTATTAAAATTTCATAGTGTGGTTATTAAATTTTAATAGGGAG
1 GTTATCAAAATTTCATAGTGTGGTTATCAAAATTTCATAGGGAG
* *** *
6948 GTTATCAAAATTTCACAGCAAGGTTATCAAAATTTCATAGTGTA-
1 GTTATCAAAATTTCATAGTGTGGTTATCAAAATTTCATAG-GGAG
* * * * * *
6992 ATAATTAAAATTTCATAATGTGGTTATCAAAATTTCTTAGGAAG
1 GTTATCAAAATTTCATAGTGTGGTTATCAAAATTTCATAGGGAG
* * * * **
7036 G-TACCAAAATTTCATAGTGTGGTAATCGAATTTTCATAAAGAG
1 GTTATCAAAATTTCATAGTGTGGTTATCAAAATTTCATAGGGAG
7079 GTTATCAAAATTTCATA
1 GTTATCAAAATTTCATA
7096 CTGGTTGAAA
Statistics
Matches: 113, Mismatches: 32, Indels: 6
0.75 0.21 0.04
Matches are distributed among these distances:
43 34 0.30
44 77 0.68
45 2 0.02
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.38
Consensus pattern (44 bp):
GTTATCAAAATTTCATAGTGTGGTTATCAAAATTTCATAGGGAG
Found at i:7017 original size:66 final size:66
Alignment explanation
Indices: 6904--7093 Score: 229
Period size: 66 Copynumber: 2.9 Consensus size: 66
6894 TGATAGGAAC
* * * **
6904 GTTATTAAAATTTCATAGTGTGGTTATTAAATTTTAATAGGGAGGTTATCAAAATTTCACAGCAA
1 GTTATCAAAATTTCATAGTGTGGTAATTAAATTTTCATAAAGAGGTTATCAAAATTTCACAGCAA
6969 G
66 G
** * * * ** *
6970 GTTATCAAAATTTCATAGTGTAATAATTAAAATTTCATAATGTGGTTATCAAAATTTCTTAGGAA
1 GTTATCAAAATTTCATAGTGTGGTAATTAAATTTTCATAAAGAGGTTATCAAAATTTCACAGCAA
7035 G
66 G
* **
7036 G-TACCAAAATTTCATAGTGTGGTAATCGAATTTTCATAAAGAGGTTATCAAAATTTCA
1 GTTATCAAAATTTCATAGTGTGGTAATTAAATTTTCATAAAGAGGTTATCAAAATTTCA
7094 TACTGGTTGA
Statistics
Matches: 103, Mismatches: 21, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
65 48 0.47
66 55 0.53
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.37
Consensus pattern (66 bp):
GTTATCAAAATTTCATAGTGTGGTAATTAAATTTTCATAAAGAGGTTATCAAAATTTCACAGCAA
G
Found at i:7521 original size:22 final size:22
Alignment explanation
Indices: 7490--7591 Score: 102
Period size: 22 Copynumber: 4.6 Consensus size: 22
7480 TAAAACTAAT
*
7490 TCAAATTTTCATAGCGTGGTTA
1 TCAAAATTTCATAGCGTGGTTA
* *
7512 TCAAAATTTCATATCGAGGTTA
1 TCAAAATTTCATAGCGTGGTTA
*
7534 -CTAAAATTTTATAG-G-GGTATTA
1 TC-AAAATTTCATAGCGTGG--TTA
*
7556 TCAAAATTTCATAGTGTGGTTA
1 TCAAAATTTCATAGCGTGGTTA
*
7578 GCAAAATTTCATAG
1 TCAAAATTTCATAG
7592 GAAGATTATA
Statistics
Matches: 67, Mismatches: 7, Indels: 12
0.78 0.08 0.14
Matches are distributed among these distances:
20 2 0.03
21 2 0.03
22 59 0.88
23 2 0.03
24 2 0.03
ACGTcount: A:0.34, C:0.11, G:0.17, T:0.38
Consensus pattern (22 bp):
TCAAAATTTCATAGCGTGGTTA
Found at i:7577 original size:44 final size:44
Alignment explanation
Indices: 7509--7592 Score: 118
Period size: 44 Copynumber: 1.9 Consensus size: 44
7499 CATAGCGTGG
*
7509 TTATCAAAATTTCATATCGAGGTTA-CTAAAATTTTATAGGGGTA
1 TTATCAAAATTTCATATCGAGGTTAGC-AAAATTTCATAGGGGTA
*
7553 TTATCAAAATTTCATAGT-GTGGTTAGCAAAATTTCATAGG
1 TTATCAAAATTTCATA-TCGAGGTTAGCAAAATTTCATAGG
7593 AAGATTATAA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
44 34 0.94
45 2 0.06
ACGTcount: A:0.36, C:0.10, G:0.17, T:0.38
Consensus pattern (44 bp):
TTATCAAAATTTCATATCGAGGTTAGCAAAATTTCATAGGGGTA
Found at i:7600 original size:44 final size:44
Alignment explanation
Indices: 7509--7606 Score: 112
Period size: 44 Copynumber: 2.2 Consensus size: 44
7499 CATAGCGTGG
* *
7509 TTATCAAAATTTCATATCGAGGTTACTAAAATTTTATAGGGGTA
1 TTATCAAAATTTCATATCGAGGTTACTAAAATTTCATAGGAGTA
*
7553 TTATCAAAATTTCATAGT-GTGGTTAGC-AAAATTTCATAGGAAG-A
1 TTATCAAAATTTCATA-TCGAGGTTA-CTAAAATTTCATAGG-AGTA
*
7597 TTATAAAAAT
1 TTATCAAAAT
7607 CTCAATTTCA
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
44 44 0.94
45 3 0.06
ACGTcount: A:0.40, C:0.08, G:0.15, T:0.37
Consensus pattern (44 bp):
TTATCAAAATTTCATATCGAGGTTACTAAAATTTCATAGGAGTA
Found at i:7635 original size:22 final size:24
Alignment explanation
Indices: 7610--8043 Score: 142
Period size: 22 Copynumber: 19.0 Consensus size: 24
7600 TAAAAATCTC
7610 AATTTCATAAGGA-GGTTATC-AA
1 AATTTCATAAGGATGGTTATCAAA
*
7632 AA-TT-ATATAGTATGGTTATCAAA
1 AATTTCATA-AGGATGGTTATCAAA
*
7655 AATTTCATAAGGAT-G-TAT-AAG
1 AATTTCATAAGGATGGTTATCAAA
* * * *
7676 AATCTCATAAAG-TTGTTATTAAA
1 AATTTCATAAGGATGGTTATCAAA
* **
7699 AATTTCATAAAGATCAAATTAT-AAA
1 AATTTCATAAGGAT--GGTTATCAAA
7724 AATTTCATAGGAAGGTTATGAGGTTATC-AA
1 AATTTCAT---AAGG--AT--GGTTATCAAA
7754 AATTTCAT-AGTG-TGGTTATC-AA
1 AATTTCATAAG-GATGGTTATCAAA
*
7776 AATTTCATAAGG-GGGTTATC-AA
1 AATTTCATAAGGATGGTTATCAAA
** * *
7798 AACCTCA-CA-GAGTGATTATC-AA
1 AATTTCATAAGGA-TGGTTATCAAA
***
7820 AATTTCAT-AGAGAT-CAAATCATCAA
1 AATTTCATAAG-GATGGTTATCA--AA
* *
7845 AATTTCAT-AGTATAGTTATC-AA
1 AATTTCATAAGGATGGTTATCAAA
7867 AATTTCATAAGGA-GGTTATC-AA
1 AATTTCATAAGGATGGTTATCAAA
* *
7889 AATTTCA-AAGCAAGGTTATC-AA
1 AATTTCATAAGGATGGTTATCAAA
7911 AATTTCAT-AGTGA-GGTTATC-AA
1 AATTTCATAAG-GATGGTTATCAAA
* * *
7933 CATTTCA-CAGTG-TGATTATC-AA
1 AATTTCATAAG-GATGGTTATCAAA
* *
7955 AATTTCATATGGA-GGATA-C-AA
1 AATTTCATAAGGATGGTTATCAAA
*
7976 AATTTCAT-AGTG-TGGTTAAC-AA
1 AATTTCATAAG-GATGGTTATCAAA
7998 AATTTCAT-AGAGA-GGTTATC-AA
1 AATTTCATAAG-GATGGTTATCAAA
* *
8020 AATTCCATGAGGA-GGTTATCAAA
1 AATTTCATAAGGATGGTTATCAAA
8043 A
1 A
8044 TTTTATAGTG
Statistics
Matches: 326, Mismatches: 44, Indels: 83
0.72 0.10 0.18
Matches are distributed among these distances:
20 6 0.02
21 39 0.12
22 182 0.56
23 31 0.10
24 12 0.04
25 29 0.09
26 6 0.02
27 1 0.00
28 3 0.01
30 17 0.05
ACGTcount: A:0.41, C:0.10, G:0.16, T:0.33
Consensus pattern (24 bp):
AATTTCATAAGGATGGTTATCAAA
Found at i:7710 original size:23 final size:23
Alignment explanation
Indices: 7646--7712 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 23
7636 ATATAGTATG
* *
7646 GTTATCAAAAATTTCATAAGGAT
1 GTTATTAAAAATTTCATAAAGAT
* * *
7669 G-TA-TAAGAATCTCATAAAGTT
1 GTTATTAAAAATTTCATAAAGAT
7690 GTTATTAAAAATTTCATAAAGAT
1 GTTATTAAAAATTTCATAAAGAT
7713 CAAATTATAA
Statistics
Matches: 34, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
21 14 0.41
22 4 0.12
23 16 0.47
ACGTcount: A:0.45, C:0.07, G:0.12, T:0.36
Consensus pattern (23 bp):
GTTATTAAAAATTTCATAAAGAT
Found at i:7764 original size:122 final size:121
Alignment explanation
Indices: 7621--7854 Score: 305
Period size: 121 Copynumber: 1.9 Consensus size: 121
7611 ATTTCATAAG
* * *
7621 GAGGTTATCAAAATTATATAGTATGGTTATCAAAAATTTCATAAGGATG-TAT-AAGAATCTCAT
1 GAGGTTATCAAAATTATATAGTATGGTTATC-AAAATTTCATAAGGAGGTTATCAA-AACCTCAC
*
7684 AAAGTTG-TTATTAAAAATTTCATAAAGATCAAATTATAAAAATTTCATAGGAAGGTTAT
64 AAAG-TGATTA-TAAAAATTTCATAAAGATCAAATCATAAAAATTTCATAGGAAGGTTAT
* *
7743 GAGGTTATCAAAATT-TCATAGTGTGGTTATCAAAATTTCATAAGGGGGTTATCAAAACCTCACA
1 GAGGTTATCAAAATTAT-ATAGTATGGTTATCAAAATTTCATAAGGAGGTTATCAAAACCTCACA
* * * *
7807 GAGTGATTATCAAAATTTCATAGAGATCAAATCATCAAAATTTCATAG
65 AAGTGATTATAAAAATTTCATAAAGATCAAATCATAAAAATTTCATAG
7855 TATAGTTATC
Statistics
Matches: 98, Mismatches: 10, Indels: 9
0.84 0.09 0.08
Matches are distributed among these distances:
121 53 0.54
122 43 0.44
123 2 0.02
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.33
Consensus pattern (121 bp):
GAGGTTATCAAAATTATATAGTATGGTTATCAAAATTTCATAAGGAGGTTATCAAAACCTCACAA
AGTGATTATAAAAATTTCATAAAGATCAAATCATAAAAATTTCATAGGAAGGTTAT
Found at i:7876 original size:91 final size:90
Alignment explanation
Indices: 7749--7920 Score: 256
Period size: 91 Copynumber: 1.9 Consensus size: 90
7739 TTATGAGGTT
* * * *
7749 ATCAAAATTTCATAGTGTGGTTATCAAAATTTCATAAGGGGGTTATCAAAACCTCACAG-AGTGA
1 ATCAAAATTTCATAGTATAGTTATCAAAATTTCATAAGGAGGTTATCAAAACCTCAAAGAAG-G-
7813 TTATCAAAATTTCATAGAGATCAAATC
64 TTATCAAAATTTCATAGAGATCAAATC
**
7840 ATCAAAATTTCATAGTATAGTTATCAAAATTTCATAAGGAGGTTATCAAAATTTCAAAGCAAGGT
1 ATCAAAATTTCATAGTATAGTTATCAAAATTTCATAAGGAGGTTATCAAAACCTCAAAG-AAGGT
7905 TATCAAAATTTCATAG
65 TATCAAAATTTCATAG
7921 TGAGGTTATC
Statistics
Matches: 73, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
91 70 0.96
92 1 0.01
93 2 0.03
ACGTcount: A:0.41, C:0.13, G:0.14, T:0.32
Consensus pattern (90 bp):
ATCAAAATTTCATAGTATAGTTATCAAAATTTCATAAGGAGGTTATCAAAACCTCAAAGAAGGTT
ATCAAAATTTCATAGAGATCAAATC
Found at i:8044 original size:22 final size:22
Alignment explanation
Indices: 7742--8155 Score: 291
Period size: 22 Copynumber: 19.0 Consensus size: 22
7732 AGGAAGGTTA
7742 TGAGGTTATCAAAATTTCATAG
1 TGAGGTTATCAAAATTTCATAG
*
7764 TGTGGTTATCAAAATTTCATAAG
1 TGAGGTTATCAAAATTTCAT-AG
* ** *
7787 -GGGGTTATCAAAACCTCACAG
1 TGAGGTTATCAAAATTTCATAG
* * *
7808 AGTGATTATCAAAATTTCATAGAG
1 TGAGGTTATCAAAATTTCAT--AG
* ** *
7832 ATCAAATCATCAAAATTTCATAG
1 -TGAGGTTATCAAAATTTCATAG
*
7855 T-ATAGTTATCAAAATTTCATAAG
1 TGA-GGTTATCAAAATTTCAT-AG
*
7878 -GAGGTTATCAAAATTTCAAAG
1 TGAGGTTATCAAAATTTCATAG
**
7899 CAAGGTTATCAAAATTTCATAG
1 TGAGGTTATCAAAATTTCATAG
* *
7921 TGAGGTTATCAACATTTCACAG
1 TGAGGTTATCAAAATTTCATAG
* *
7943 TGTGATTATCAAAATTTCATA-
1 TGAGGTTATCAAAATTTCATAG
*
7964 TGGAGGATA-CAAAATTTCATAG
1 T-GAGGTTATCAAAATTTCATAG
* *
7986 TGTGGTTAACAAAATTTCATAG
1 TGAGGTTATCAAAATTTCATAG
* *
8008 AGAGGTTATCAAAATTCCATGAG
1 TGAGGTTATCAAAATTTCAT-AG
*
8031 -GAGGTTATCAAAATTTTATAG
1 TGAGGTTATCAAAATTTCATAG
**
8052 TGTA-AATATCAAAATTT--TA-
1 TG-AGGTTATCAAAATTTCATAG
* * * * *
8071 --AAG-TGT-AATATTTTAGAG
1 TGAGGTTATCAAAATTTCATAG
* *
8089 GGAGTTTATCAAAATTTCATAG
1 TGAGGTTATCAAAATTTCATAG
* *
8111 TGTGGTTATAAAAATTTCATAG
1 TGAGGTTATCAAAATTTCATAG
*
8133 -GAAGGTTATTAAAATTTCATAG
1 TG-AGGTTATCAAAATTTCATAG
8155 T
1 T
8156 ATGGTTGTTT
Statistics
Matches: 309, Mismatches: 58, Indels: 49
0.74 0.14 0.12
Matches are distributed among these distances:
15 6 0.02
16 3 0.01
17 1 0.00
20 3 0.01
21 28 0.09
22 241 0.78
23 10 0.03
24 2 0.01
25 15 0.05
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (22 bp):
TGAGGTTATCAAAATTTCATAG
Found at i:8062 original size:131 final size:134
Alignment explanation
Indices: 7743--8068 Score: 335
Period size: 131 Copynumber: 2.4 Consensus size: 134
7733 GGAAGGTTAT
* * *** * ** **
7743 GAGGTTATCAAAATTTCATAGTGTGGTTATCAAAATTTCATAAG-GGGGTTATCAAAACCTCACA
1 GAGGTTATCAAAATTCCAAAGCAAGGTTATCAAAATTTCAT-AGTGAGAATATCAAAATTTCACA
*
7807 GAGTGATTATCAAAATTTCATAGAGATCAAATCATCAAAATTTCATAGTATAGTTATCAAAATTT
65 GAGTGATTATCAAAATTTCATAGAGA-CAAATCATCAAAATTTCATAGTATAGTTAACAAAATTT
7872 CATAAG
129 CATAAG
* ** *
7878 GAGGTTATCAAAATTTCAAAGCAAGGTTATCAAAATTTCATAGTGAGGTTATCAACATTTCACAG
1 GAGGTTATCAAAATTCCAAAGCAAGGTTATCAAAATTTCATAGTGAGAATATCAAAATTTCACAG
* ** * *
7943 TGTGATTATCAAAATTTCATATG-GA-GGAT-A-CAAAATTTCATAGTGTGGTTAACAAAATTTC
66 AGTGATTATCAAAATTTCATA-GAGACAAATCATCAAAATTTCATAGTATAGTTAACAAAATTTC
8004 AT-AG
130 ATAAG
* * *
8008 AGAGGTTATCAAAATTCCATGAG-GAGGTTATCAAAATTTTATAGTGTA-AATATCAAAATTT
1 -GAGGTTATCAAAATTCCA-AAGCAAGGTTATCAAAATTTCATAGTG-AGAATATCAAAATTT
8069 TAAAGTGTAA
Statistics
Matches: 165, Mismatches: 21, Indels: 14
0.82 0.10 0.07
Matches are distributed among these distances:
130 2 0.01
131 78 0.47
132 4 0.02
133 2 0.01
134 2 0.01
135 76 0.46
136 1 0.01
ACGTcount: A:0.40, C:0.11, G:0.16, T:0.33
Consensus pattern (134 bp):
GAGGTTATCAAAATTCCAAAGCAAGGTTATCAAAATTTCATAGTGAGAATATCAAAATTTCACAG
AGTGATTATCAAAATTTCATAGAGACAAATCATCAAAATTTCATAGTATAGTTAACAAAATTTCA
TAAG
Found at i:8076 original size:131 final size:125
Alignment explanation
Indices: 7840--8148 Score: 306
Period size: 131 Copynumber: 2.4 Consensus size: 125
7830 AGATCAAATC
* * * *
7840 ATCAAAATTTCATAGTATAGTTATCAAAATTTCATA-AGGAGGTTATCAAAATTTCAAAGCAAGG
1 ATCAAAATTTCATAGTGTGGTTAACAAAATTTCATAGA-GAGGTTATCAAAATTCCAAAGCAAGG
** * * * *
7904 TTATCAAAATTTCATAGTGAGGTTATCAACATTTCACAGTGTGATTATCAAAATTTCATATGGAG
65 TTATCAAAATTTCATAGTGAGAATATCAAAATTTCAAAGTGT-A--AT----ATTTCAGAGGGAG
7969 GAT
123 GAT
* *
7972 A-CAAAATTTCATAGTGTGGTTAACAAAATTTCATAGAGAGGTTATCAAAATTCCATGAG-GAGG
1 ATCAAAATTTCATAGTGTGGTTAACAAAATTTCATAGAGAGGTTATCAAAATTCCA-AAGCAAGG
* * * **
8035 TTATCAAAATTTTATAGTGTA-AATATCAAAATTTTAAAGTGTAATATTTTAGAGGGAGTTT
65 TTATCAAAATTTCATAGTG-AGAATATCAAAATTTCAAAGTGTAATATTTCAGAGGGAGGAT
*
8096 ATCAAAATTTCATAGTGTGGTTATA-AAAATTTCATAG-GAAGGTTATTAAAATT
1 ATCAAAATTTCATAGTGTGGTTA-ACAAAATTTCATAGAG-AGGTTATCAAAATT
8149 TCATAGTATG
Statistics
Matches: 153, Mismatches: 18, Indels: 19
0.81 0.09 0.10
Matches are distributed among these distances:
124 13 0.08
125 46 0.30
126 1 0.01
128 2 0.01
130 1 0.01
131 85 0.56
132 5 0.03
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.35
Consensus pattern (125 bp):
ATCAAAATTTCATAGTGTGGTTAACAAAATTTCATAGAGAGGTTATCAAAATTCCAAAGCAAGGT
TATCAAAATTTCATAGTGAGAATATCAAAATTTCAAAGTGTAATATTTCAGAGGGAGGAT
Found at i:8200 original size:20 final size:20
Alignment explanation
Indices: 8175--8216 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
8165 TATAAACTAA
8175 GATTTTTATAACTTCCCTAT
1 GATTTTTATAACTTCCCTAT
*
8195 GATTTTTATAACTTTCCTAT
1 GATTTTTATAACTTCCCTAT
8215 GA
1 GA
8217 AATTTCGATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.26, C:0.17, G:0.07, T:0.50
Consensus pattern (20 bp):
GATTTTTATAACTTCCCTAT
Found at i:8227 original size:22 final size:22
Alignment explanation
Indices: 8208--8286 Score: 81
Period size: 22 Copynumber: 3.6 Consensus size: 22
8198 TTTTATAACT
8208 TTCCTATGAAATTTCGATAATC
1 TTCCTATGAAATTTCGATAATC
*
8230 TTCCTATGAAATTTTGATAATC
1 TTCCTATGAAATTTCGATAATC
* * * *
8252 -ACACAATAAAATTTTGATAATC
1 TTC-CTATGAAATTTCGATAATC
8274 -TCCATATGAAATT
1 TTCC-TATGAAATT
8287 ATTTATAAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
21 2 0.04
22 46 0.96
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.39
Consensus pattern (22 bp):
TTCCTATGAAATTTCGATAATC
Done.