Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013950.1 Corchorus capsularis cultivar CVL-1 contig13971, 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: 53800
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.32
Found at i:6257 original size:6 final size:6
Alignment explanation
Indices: 6248--6287 Score: 71
Period size: 6 Copynumber: 6.7 Consensus size: 6
6238 TGAGAATGCA
*
6248 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAGAT AAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAA
6288 GGAAAATGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:11030 original size:48 final size:48
Alignment explanation
Indices: 10975--11241 Score: 324
Period size: 48 Copynumber: 5.5 Consensus size: 48
10965 GACAAATCAA
* *
10975 GCACCTTCCGACCGGGAAGGGCAAAACTAGAAATAGACACT-AAAAAT
1 GCACCTTCCGACCGGGAAGGGCAAAACTAGAAATAAACACTGAAAACT
* * *
11022 AGCACCTTCTGACCGGGAAGGACAAAAC-AGGAAATAAACACTGAAGACT
1 -GCACCTTCCGACCGGGAAGGGCAAAACTA-GAAATAAACACTGAAAACT
* * * * * *
11071 ACACCTTCCGACTGGGAAGGGCAAAAATGGAAAAAAAAACACTAAAAACT
1 GCACCTTCCGACCGGGAAGGGCAAAACT--AGAAATAAACACTGAAAACT
* * * *
11121 GCACCTTCCGACCGGAAAGGGCAAAACTGGTAATATACACTGAAAACT
1 GCACCTTCCGACCGGGAAGGGCAAAACTAGAAATAAACACTGAAAACT
*
11169 GCACCTTCCGACCGGGAAGGGCAAAACTGGAAATAAACACTGAAAACT
1 GCACCTTCCGACCGGGAAGGGCAAAACTAGAAATAAACACTGAAAACT
*
11217 GCACCTT-CGACCGGGAATGGCAAAA
1 GCACCTTCCGACCGGGAAGGGCAAAA
11242 AAGGAATCGA
Statistics
Matches: 186, Mismatches: 28, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
47 18 0.10
48 124 0.67
49 4 0.02
50 39 0.21
51 1 0.01
ACGTcount: A:0.42, C:0.24, G:0.22, T:0.13
Consensus pattern (48 bp):
GCACCTTCCGACCGGGAAGGGCAAAACTAGAAATAAACACTGAAAACT
Found at i:11146 original size:98 final size:97
Alignment explanation
Indices: 10976--11247 Score: 354
Period size: 98 Copynumber: 2.8 Consensus size: 97
10966 ACAAATCAAG
* * *
10976 CACCTTCCGACCGGGAAGGGCAAAACTAG-AAATAGACACTAAAAA-TAGCACCTTCTGACCGGG
1 CACCTTCCGACCGGGAAGGGCAAAACTGGAAAATAAACACTAAAAACT-GCACCTTCCGACCGGG
* *
11039 AAGGACAAAACAGGAAATAAACACTGAAGACTA
65 AAGGGCAAAACAGGAAATAAACACTGAAAACTA
* * * *
11072 CACCTTCCGACTGGGAAGGGCAAAAATGGAAAAAAAAACACTAAAAACTGCACCTTCCGACCGGA
1 CACCTTCCGACCGGGAAGGGCAAAACTGG-AAAATAAACACTAAAAACTGCACCTTCCGACCGGG
* * * *
11137 AAGGGCAAAACTGGTAATATACACTGAAAACTG
65 AAGGGCAAAACAGGAAATAAACACTGAAAACTA
*
11170 CACCTTCCGACCGGGAAGGGCAAAACTGG-AAATAAACACTGAAAACTGCACCTT-CGACCGGGA
1 CACCTTCCGACCGGGAAGGGCAAAACTGGAAAATAAACACTAAAAACTGCACCTTCCGACCGGGA
* *
11233 ATGGCAAAAAAGGAA
66 AGGGCAAAACAGGAA
11248 TCGACATCTA
Statistics
Matches: 151, Mismatches: 22, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
95 19 0.13
96 49 0.32
98 82 0.54
99 1 0.01
ACGTcount: A:0.42, C:0.23, G:0.22, T:0.13
Consensus pattern (97 bp):
CACCTTCCGACCGGGAAGGGCAAAACTGGAAAATAAACACTAAAAACTGCACCTTCCGACCGGGA
AGGGCAAAACAGGAAATAAACACTGAAAACTA
Found at i:11243 original size:146 final size:145
Alignment explanation
Indices: 10975--11247 Score: 397
Period size: 146 Copynumber: 1.9 Consensus size: 145
10965 GACAAATCAA
* *
10975 GCACCTTCCGACCGGGAAGGGCAAAACTAGAAATAGACACTAAAAATAGCACCTTCTGACCGGGA
1 GCACCTTCCGACCGGAAAGGGCAAAACTAGAAATAGACACTAAAAATAGCACCTTCCGACCGGGA
* *
11040 AGGACAAAACAGGAAATAAACACTGAAGACTACACCTTCCGACTGGGAAGGGCAAAAATGGAAAA
66 AGGACAAAACAGGAAATAAACACTGAAAACTACACCTTCCGACCGGGAAGGGCAAAAA-GGAAAA
11105 AAAAACACTAAAAACT
130 AAAAACACTAAAAACT
* * * *
11121 GCACCTTCCGACCGGAAAGGGCAAAACTGGTAATATACACTGAAAACT-GCACCTTCCGACCGGG
1 GCACCTTCCGACCGGAAAGGGCAAAACTAGAAATAGACACT-AAAAATAGCACCTTCCGACCGGG
* * * *
11185 AAGGGCAAAACTGGAAATAAACACTGAAAACTGCACCTT-CGACCGGGAATGGCAAAAAAGGAA
65 AAGGACAAAACAGGAAATAAACACTGAAAACTACACCTTCCGACCGGGAAGGGC-AAAAAGGAA
11248 TCGACATCTA
Statistics
Matches: 113, Mismatches: 12, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
145 16 0.14
146 92 0.81
147 5 0.04
ACGTcount: A:0.42, C:0.23, G:0.22, T:0.13
Consensus pattern (145 bp):
GCACCTTCCGACCGGAAAGGGCAAAACTAGAAATAGACACTAAAAATAGCACCTTCCGACCGGGA
AGGACAAAACAGGAAATAAACACTGAAAACTACACCTTCCGACCGGGAAGGGCAAAAAGGAAAAA
AAAACACTAAAAACT
Found at i:11931 original size:51 final size:51
Alignment explanation
Indices: 11865--12002 Score: 217
Period size: 50 Copynumber: 2.7 Consensus size: 51
11855 TCCAAAGGTT
* * *
11865 TCATTTTTA-TCACAAAATAATCAAAAGGTTCAATCTTTTACTTAATCTTC
1 TCATTTTTATTTACAAACTAACCAAAAGGTTCAATCTTTTACTTAATCTTC
*
11915 TCATTTTTATTTACAAACTAACCAAAAGGTTCAATC-TTTACTTAATCTTT
1 TCATTTTTATTTACAAACTAACCAAAAGGTTCAATCTTTTACTTAATCTTC
*
11965 TCATTTTTATTTACAAACTAACCAAAAGGTTTAATCTT
1 TCATTTTTATTTACAAACTAACCAAAAGGTTCAATCTT
12003 AACCCAAAGA
Statistics
Matches: 81, Mismatches: 5, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
50 57 0.70
51 24 0.30
ACGTcount: A:0.36, C:0.17, G:0.04, T:0.43
Consensus pattern (51 bp):
TCATTTTTATTTACAAACTAACCAAAAGGTTCAATCTTTTACTTAATCTTC
Found at i:16620 original size:427 final size:427
Alignment explanation
Indices: 15825--16681 Score: 1696
Period size: 427 Copynumber: 2.0 Consensus size: 427
15815 AAGGACTTTA
15825 GTATCCACTTTTCGTGATTCTCCACTCCCACTGAACTAGCTATTATTAATGAACCTAATAATTCC
1 GTATCCACTTTTCGTGATTCTCCACTCCCACTGAACTAGCTATTATTAATGAACCTAATAATTCC
15890 AGACTCAACTTTTCCTCGTACTATGGCTAGGGCAATTAATCTGTAATGCTTTGACTAATCCAGAT
66 AGACTCAACTTTTCCTCGTACTATGGCTAGGGCAATTAATCTGTAATGCTTTGACTAATCCAGAT
15955 AGCTAATGAAATAACCATTAATGGTTATTGCATCAAGCTTCTTTTCATGTGGATTTAATAATATT
131 AGCTAATGAAATAACCATTAATGGTTATTGCATCAAGCTTCTTTTCATGTGGATTTAATAATATT
16020 CTTAATTCTGCCAGGTAGCCCTAAACATGCAGGTGCCTTAAACTAGGTTTCCTTCCGTCCGCAAT
196 CTTAATTCTGCCAGGTAGCCCTAAACATGCAGGTGCCTTAAACTAGGTTTCCTTCCGTCCGCAAT
16085 TCATAAGGAGTCTTAGGAATTGTCTTACTAGGAACCCTATTAAACAGATATGCACAATATTGCAT
261 TCATAAGGAGTCTTAGGAATTGTCTTACTAGGAACCCTATTAAACAGATATGCACAATATTGCAT
*
16150 GCATCCATAATGTCAAAGGCACAAAACTGTAACTTAATATACTCCTAACCATGTCCATATGAGTT
326 GCATCCACAATGTCAAAGGCACAAAACTGTAACTTAATATACTCCTAACCATGTCCATATGAGTT
16215 ATAAATCCGCCTTTCAATCACATCGATTAATTATGGT
391 ATAAATCCGCCTTTCAATCACATCGATTAATTATGGT
16252 GTATCCACTTTTCGTGATTCTCCACTCCCACTGAACTAGCTATTATTAATGAACCTAATAATTCC
1 GTATCCACTTTTCGTGATTCTCCACTCCCACTGAACTAGCTATTATTAATGAACCTAATAATTCC
*
16317 ATACTCAACTTTTCCTCGTACTATGGCTAGGGCAATTAATCTGTAATGCTTTGACTAATCCAGAT
66 AGACTCAACTTTTCCTCGTACTATGGCTAGGGCAATTAATCTGTAATGCTTTGACTAATCCAGAT
16382 AGCTAATGAAATAACCATTAATGGTTATTGCATCAAGCTTCTTTTCATGTGGATTTAATAATATT
131 AGCTAATGAAATAACCATTAATGGTTATTGCATCAAGCTTCTTTTCATGTGGATTTAATAATATT
16447 CTTAATTCTGCCAGGTAGCCCTAAACATGCAGGTGCCTTAAACTAGGTTTCCTTCCGTCCGCAAT
196 CTTAATTCTGCCAGGTAGCCCTAAACATGCAGGTGCCTTAAACTAGGTTTCCTTCCGTCCGCAAT
16512 TCATAAGGAGTCTTAGGAATTGTCTTACTAGGAACCCTATTAAACAGATATGCACAATATTGCAT
261 TCATAAGGAGTCTTAGGAATTGTCTTACTAGGAACCCTATTAAACAGATATGCACAATATTGCAT
16577 GCATCCACAATGTCAAAGGCACAAAACTGTAACTTAATATACTCCTAACCATGTCCATATGAGTT
326 GCATCCACAATGTCAAAGGCACAAAACTGTAACTTAATATACTCCTAACCATGTCCATATGAGTT
16642 ATAAATCCGCCTTTCAATCACATCGATTAATTATGGT
391 ATAAATCCGCCTTTCAATCACATCGATTAATTATGGT
16679 GTA
1 GTA
16682 CTGGGCATAG
Statistics
Matches: 428, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
427 428 1.00
ACGTcount: A:0.31, C:0.22, G:0.14, T:0.33
Consensus pattern (427 bp):
GTATCCACTTTTCGTGATTCTCCACTCCCACTGAACTAGCTATTATTAATGAACCTAATAATTCC
AGACTCAACTTTTCCTCGTACTATGGCTAGGGCAATTAATCTGTAATGCTTTGACTAATCCAGAT
AGCTAATGAAATAACCATTAATGGTTATTGCATCAAGCTTCTTTTCATGTGGATTTAATAATATT
CTTAATTCTGCCAGGTAGCCCTAAACATGCAGGTGCCTTAAACTAGGTTTCCTTCCGTCCGCAAT
TCATAAGGAGTCTTAGGAATTGTCTTACTAGGAACCCTATTAAACAGATATGCACAATATTGCAT
GCATCCACAATGTCAAAGGCACAAAACTGTAACTTAATATACTCCTAACCATGTCCATATGAGTT
ATAAATCCGCCTTTCAATCACATCGATTAATTATGGT
Found at i:18830 original size:41 final size:43
Alignment explanation
Indices: 18773--18865 Score: 163
Period size: 41 Copynumber: 2.2 Consensus size: 43
18763 ATTTGCATCC
*
18773 TAACAATTTAATATCCCAAATATAATCCTTAATGGG-AAA-AA
1 TAACAATTTAATATCCCAAATATAATCCTCAATGGGAAAACAA
18814 TAACAATTTAATATCCCAAATATAATCCTCAATGGGAAAACAA
1 TAACAATTTAATATCCCAAATATAATCCTCAATGGGAAAACAA
18857 TAACAATTT
1 TAACAATTT
18866 TGCATGCTAT
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
41 35 0.71
42 3 0.06
43 11 0.22
ACGTcount: A:0.48, C:0.16, G:0.06, T:0.29
Consensus pattern (43 bp):
TAACAATTTAATATCCCAAATATAATCCTCAATGGGAAAACAA
Found at i:21705 original size:52 final size:52
Alignment explanation
Indices: 21637--21740 Score: 181
Period size: 52 Copynumber: 2.0 Consensus size: 52
21627 GAATGCAATC
*
21637 TACTATTTGCTAAATGTAAAAATTGAATTTACTAAATACCAAAAGTAGATTA
1 TACTATATGCTAAATGTAAAAATTGAATTTACTAAATACCAAAAGTAGATTA
* *
21689 TACTATATGCTGAATGTCAAAATTGAATTTACTAAATACCAAAAGTAGATTA
1 TACTATATGCTAAATGTAAAAATTGAATTTACTAAATACCAAAAGTAGATTA
21741 GAAAATGATA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.45, C:0.11, G:0.11, T:0.34
Consensus pattern (52 bp):
TACTATATGCTAAATGTAAAAATTGAATTTACTAAATACCAAAAGTAGATTA
Found at i:28719 original size:38 final size:38
Alignment explanation
Indices: 28669--28766 Score: 110
Period size: 38 Copynumber: 2.6 Consensus size: 38
28659 CTAAAACCTG
*
28669 AAACTGACGGGAACTTTCCCTAAATCGAA-A-AAAACTA
1 AAACTGATGGGAACTTTCCCTAAAT-GAAGACAAAACTA
* * *
28706 AAACCTGATGGGAACTTTCCCAAAATGAAGACGAAAGCTG
1 AAA-CTGATGGGAACTTTCCCTAAATGAAGAC-AAAACTA
*
28746 AGACTGATGGGAACTTTCCCT
1 AAACTGATGGGAACTTTCCCT
28767 CTTTTGAAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
37 6 0.12
38 21 0.41
39 17 0.33
40 7 0.14
ACGTcount: A:0.39, C:0.21, G:0.19, T:0.20
Consensus pattern (38 bp):
AAACTGATGGGAACTTTCCCTAAATGAAGACAAAACTA
Found at i:29078 original size:16 final size:16
Alignment explanation
Indices: 29057--29149 Score: 62
Period size: 16 Copynumber: 5.4 Consensus size: 16
29047 CGAATTAAGC
29057 TAATTACTGATTTACT
1 TAATTACTGATTTACT
* *
29073 TAATTACACCGAATTAAGC-
1 TAATT--ACTG-ATTTA-CT
29092 TAATTACTGATTTACT
1 TAATTACTGATTTACT
* * *
29108 TAATTACACCGAATTAAGT
1 TAATT--ACTG-ATTTACT
*
29127 TGATTACTGATTTACT
1 TAATTACTGATTTACT
29143 TAATTAC
1 TAATTAC
29150 ACCGAATTGA
Statistics
Matches: 57, Mismatches: 12, Indels: 16
0.67 0.14 0.19
Matches are distributed among these distances:
15 1 0.02
16 25 0.44
17 6 0.11
18 6 0.11
19 18 0.32
20 1 0.02
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (16 bp):
TAATTACTGATTTACT
Found at i:29202 original size:19 final size:19
Alignment explanation
Indices: 29037--29293 Score: 111
Period size: 19 Copynumber: 14.4 Consensus size: 19
29027 GATTATTTAC
29037 TTAATTACACCGAATTAAG
1 TTAATTACACCGAATTAAG
* * * *
29056 CTAATT--ACTG-ATTTAC
1 TTAATTACACCGAATTAAG
29072 TTAATTACACCGAATTAAG
1 TTAATTACACCGAATTAAG
* * * *
29091 CTAATT--ACTG-ATTTAC
1 TTAATTACACCGAATTAAG
29107 TTAATTACACCGAATTAAG
1 TTAATTACACCGAATTAAG
* * * *
29126 TTGATT--ACTG-ATTTAC
1 TTAATTACACCGAATTAAG
*
29142 TTAATTACACCGAATTGAG
1 TTAATTACACCGAATTAAG
* *
29161 TTAATT--ACC-AATTTAC
1 TTAATTACACCGAATTAAG
29177 TTAATTACACCGAATTAAG
1 TTAATTACACCGAATTAAG
* * *
29196 TTGATT--ACCAAATT-AC
1 TTAATTACACCGAATTAAG
* * *
29212 TTAATTTAATTACC-AATTTAC
1 TTAA-TT-A-CACCGAATTAAG
* *
29233 TTAATTGCATCGAATTAAG
1 TTAATTACACCGAATTAAG
* * *
29252 TTGATT--ACCAAATT-AC
1 TTAATTACACCGAATTAAG
29268 TTAATTACACCGAATTAAG
1 TTAATTACACCGAATTAAG
*
29287 TTGATTA
1 TTAATTA
29294 TCAATTTGCT
Statistics
Matches: 171, Mismatches: 45, Indels: 44
0.66 0.17 0.17
Matches are distributed among these distances:
16 48 0.28
17 27 0.16
18 21 0.12
19 60 0.35
20 6 0.04
21 9 0.05
ACGTcount: A:0.37, C:0.16, G:0.09, T:0.38
Consensus pattern (19 bp):
TTAATTACACCGAATTAAG
Found at i:29203 original size:35 final size:35
Alignment explanation
Indices: 29031--29217 Score: 284
Period size: 35 Copynumber: 5.3 Consensus size: 35
29021 CTATTTGATT
*
29031 ATTTACTTAATTACACCGAATTAAGCTAATTACTG
1 ATTTACTTAATTACACCGAATTAAGTTAATTACTG
*
29066 ATTTACTTAATTACACCGAATTAAGCTAATTACTG
1 ATTTACTTAATTACACCGAATTAAGTTAATTACTG
*
29101 ATTTACTTAATTACACCGAATTAAGTTGATTACTG
1 ATTTACTTAATTACACCGAATTAAGTTAATTACTG
* **
29136 ATTTACTTAATTACACCGAATTGAGTTAATTACCA
1 ATTTACTTAATTACACCGAATTAAGTTAATTACTG
* **
29171 ATTTACTTAATTACACCGAATTAAGTTGATTACCA
1 ATTTACTTAATTACACCGAATTAAGTTAATTACTG
*
29206 AATTACTTAATT
1 ATTTACTTAATT
29218 TAATTACCAA
Statistics
Matches: 143, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 143 1.00
ACGTcount: A:0.37, C:0.16, G:0.09, T:0.39
Consensus pattern (35 bp):
ATTTACTTAATTACACCGAATTAAGTTAATTACTG
Found at i:29223 original size:21 final size:21
Alignment explanation
Indices: 29199--29238 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
29189 AATTAAGTTG
29199 ATTACCAAATTACTTAATTTA
1 ATTACCAAATTACTTAATTTA
*
29220 ATTACCAATTTACTTAATT
1 ATTACCAAATTACTTAATT
29239 GCATCGAATT
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:0.40, C:0.15, G:0.00, T:0.45
Consensus pattern (21 bp):
ATTACCAAATTACTTAATTTA
Found at i:29227 original size:56 final size:56
Alignment explanation
Indices: 29161--29273 Score: 208
Period size: 56 Copynumber: 2.0 Consensus size: 56
29151 CCGAATTGAG
29161 TTAATTACCAATTTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAAT
1 TTAATTACCAATTTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAAT
* *
29217 TTAATTACCAATTTACTTAATTGCATCGAATTAAGTTGATTACCAAATTACTTAAT
1 TTAATTACCAATTTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAAT
29273 T
1 T
29274 ACACCGAATT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 55 1.00
ACGTcount: A:0.38, C:0.15, G:0.06, T:0.41
Consensus pattern (56 bp):
TTAATTACCAATTTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAAT
Found at i:29259 original size:35 final size:35
Alignment explanation
Indices: 29220--29300 Score: 126
Period size: 35 Copynumber: 2.3 Consensus size: 35
29210 ACTTAATTTA
* *
29220 ATTACCAATTTACTTAATTGCATCGAATTAAGTTG
1 ATTACCAATTTACTTAATTACACCGAATTAAGTTG
*
29255 ATTACCAAATTACTTAATTACACCGAATTAAGTTG
1 ATTACCAATTTACTTAATTACACCGAATTAAGTTG
*
29290 ATTATCAATTT
1 ATTACCAATTT
29301 GCTTTTTCTT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 41 1.00
ACGTcount: A:0.37, C:0.15, G:0.09, T:0.40
Consensus pattern (35 bp):
ATTACCAATTTACTTAATTACACCGAATTAAGTTG
Found at i:31698 original size:32 final size:32
Alignment explanation
Indices: 31660--31725 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
31650 CTCTTGGACC
31660 AGAACAGGGAAGCGGTGATAATCCAAAAGAGA
1 AGAACAGGGAAGCGGTGATAATCCAAAAGAGA
*
31692 AGAACAGGGAAGGGGTGATAATCCAAAAGAGA
1 AGAACAGGGAAGCGGTGATAATCCAAAAGAGA
31724 AG
1 AG
31726 CTGGTCATCT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.47, C:0.11, G:0.33, T:0.09
Consensus pattern (32 bp):
AGAACAGGGAAGCGGTGATAATCCAAAAGAGA
Found at i:32100 original size:44 final size:44
Alignment explanation
Indices: 32037--32121 Score: 170
Period size: 44 Copynumber: 1.9 Consensus size: 44
32027 CTATGCAATA
32037 AGACATGACATGTAAATGCAACAATGTTGATTAAATTACTAAAT
1 AGACATGACATGTAAATGCAACAATGTTGATTAAATTACTAAAT
32081 AGACATGACATGTAAATGCAACAATGTTGATTAAATTACTA
1 AGACATGACATGTAAATGCAACAATGTTGATTAAATTACTA
32122 CATGAAGCTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.45, C:0.12, G:0.14, T:0.29
Consensus pattern (44 bp):
AGACATGACATGTAAATGCAACAATGTTGATTAAATTACTAAAT
Found at i:37886 original size:14 final size:14
Alignment explanation
Indices: 37867--37897 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
37857 CACAATTTAT
37867 ATTCTGAAATATGG
1 ATTCTGAAATATGG
37881 ATTCTGAAATATGG
1 ATTCTGAAATATGG
37895 ATT
1 ATT
37898 ACACAATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.35, C:0.06, G:0.19, T:0.39
Consensus pattern (14 bp):
ATTCTGAAATATGG
Found at i:39918 original size:62 final size:62
Alignment explanation
Indices: 39688--40066 Score: 225
Period size: 62 Copynumber: 6.0 Consensus size: 62
39678 GAAACATGAT
* * ** *
39688 AAAACTGACCCTTTGTCCGAAAGGGTATTTTGGGAAATA-AAATCTAAATGTAAAAAGA-GTGAC
1 AAAACTGACCCTTTATCCGAAAGGGTATTCTGGGAAATAGAAA-CTAAATG--CGAGGATGTGAC
** * * * ** *
39751 AAAGTTGACCCTTTATCCGAAAGGATATTCTAGGAAACCAAGATTAAACTTGTATGC-AGAGTTG
1 AAAACTGACCCTTTATCCGAAAGGGTATTCTGGGAAA--TAG---AAAC-TAAATGCGAG-GATG
*
39815 TGAG
59 TGAC
* * * * * *
39819 AAAATTGACCCTTTGTCTGAAAGGGAATT-TAGCGAAATCAGAAATTAAATGCG-GGAGTGTGAC
1 AAAACTGACCCTTTATCCGAAAGGGTATTCT-GGGAAAT-AGAAACTAAATGCGAGGA-TGTGAC
** * * *
39882 TGAACTGA-CCTTTATCCGAAAGGGTATTCTGGGAAATTGAAACTATATGCGAGGATGTGGC
1 AAAACTGACCCTTTATCCGAAAGGGTATTCTGGGAAATAGAAACTAAATGCGAGGATGTGAC
* * * ** * *
39943 AAAACTGACCCTTTGTCCGAAAGGGTATTTTGGGAAATAGAAACTATACACTAGGATGTAAC
1 AAAACTGACCCTTTATCCGAAAGGGTATTCTGGGAAATAGAAACTAAATGCGAGGATGTGAC
* * * * *
40005 AAAACTGGCCCTTTGTCTGAAAGGGTATTTTGGG-AATACTAAACTTAAATGC-AGGAATGTGA
1 AAAACTGACCCTTTATCCGAAAGGGTATTCTGGGAAATA-GAAAC-TAAATGCGAGG-ATGTGA
40067 TGAAACTAGC
Statistics
Matches: 243, Mismatches: 54, Indels: 38
0.73 0.16 0.11
Matches are distributed among these distances:
61 26 0.11
62 111 0.46
63 57 0.23
64 3 0.01
65 1 0.00
66 1 0.00
67 4 0.02
68 33 0.14
69 7 0.03
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.27
Consensus pattern (62 bp):
AAAACTGACCCTTTATCCGAAAGGGTATTCTGGGAAATAGAAACTAAATGCGAGGATGTGAC
Found at i:40211 original size:26 final size:26
Alignment explanation
Indices: 40158--40212 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
40148 TAGGGTCACC
* * **
40158 CAGGGGCATTTTGGTCATTTTTGCTT
1 CAGGGGCACTTTAGTCATTTTTAATT
40184 CAGGGGCACTTTAGTCATTTTTAATT
1 CAGGGGCACTTTAGTCATTTTTAATT
40210 CAG
1 CAG
40213 CGCTAGCTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.18, C:0.16, G:0.24, T:0.42
Consensus pattern (26 bp):
CAGGGGCACTTTAGTCATTTTTAATT
Found at i:41332 original size:19 final size:18
Alignment explanation
Indices: 41308--41343 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
41298 TGAAGATTTC
41308 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
41327 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
41344 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:42606 original size:301 final size:302
Alignment explanation
Indices: 42150--42751 Score: 1161
Period size: 301 Copynumber: 2.0 Consensus size: 302
42140 TTCTATGTTG
42150 CTTGTTTTGATTGACTGGGTCGACACTTTCATGATAAATTGAGTTAGCATTAGCTAAATTAAGTT
1 CTTGTTTTGATTGACTGGGTCGACACTTTCATGATAAATTGAGTTAGCATTAGCTAAATTAAGTT
42215 GTGAATTAATCACTCCATGCTTAATTTTATGTAGCAATTGGATGTGAATTAATCCTCCGTCCAAG
66 GTGAATTAATCACTCCATGCTTAATTTTATGTAGCAATTGGATGTGAATTAATCCTCCGTCCAAG
42280 AGAGAAAAGAATCAATGGGCGAGAAATTTCTCATTGTGCTTGTTATTAAATTAATTGTTCTTCAT
131 AGAGAAAAGAATCAATGGGCGAGAAATTTCTCATTGTGCTTGTTATTAAATTAATTGTTCTTCAT
*
42345 GCTTTATTCCTAAGTGATCTCTAAGCCCTAAGAAAGTAATTGATTGCTGAAAGAGTAAAACGGAT
196 GCTTTATTCCTAAGTGATCTCTAAGCCCTAAGAAAGTAATTGATTGCTAAAAGAGTAAAACGGAT
42410 AGATTGACTTTAATCGGTAATCTAATCTAATTAAGGTAATTA
261 AGATTGACTTTAATCGGTAATCTAATCTAATTAAGGTAATTA
*
42452 CTTGTTTTGATTGACTGGGTCGACACTTTCATGATAAATTGAGTTAGCATTAGCTAGATTAAGTT
1 CTTGTTTTGATTGACTGGGTCGACACTTTCATGATAAATTGAGTTAGCATTAGCTAAATTAAGTT
42517 GTGAATTAATCACTCCA-GCTTAATTTTATGTAGCAATTGGATGTGAATTAATCCTCCGTCCAAG
66 GTGAATTAATCACTCCATGCTTAATTTTATGTAGCAATTGGATGTGAATTAATCCTCCGTCCAAG
*
42581 AGAGAAAAGAATCAATGGGCGAGAAATTTCTCATTGTGCTTGTTATTAAATTACTTGTTCTTCAT
131 AGAGAAAAGAATCAATGGGCGAGAAATTTCTCATTGTGCTTGTTATTAAATTAATTGTTCTTCAT
*
42646 GCTTTATTCCTAAGTGATCTCTAAGCCCTAAGAAAGTAATTGATTGCTAAAAGAGTAAAAGGGAT
196 GCTTTATTCCTAAGTGATCTCTAAGCCCTAAGAAAGTAATTGATTGCTAAAAGAGTAAAACGGAT
42711 AGATTGACTTTAATCGGTAATCTAATCTAATTAAGGTAATT
261 AGATTGACTTTAATCGGTAATCTAATCTAATTAAGGTAATT
42752 TAGGTTAAGT
Statistics
Matches: 296, Mismatches: 4, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
301 215 0.73
302 81 0.27
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (302 bp):
CTTGTTTTGATTGACTGGGTCGACACTTTCATGATAAATTGAGTTAGCATTAGCTAAATTAAGTT
GTGAATTAATCACTCCATGCTTAATTTTATGTAGCAATTGGATGTGAATTAATCCTCCGTCCAAG
AGAGAAAAGAATCAATGGGCGAGAAATTTCTCATTGTGCTTGTTATTAAATTAATTGTTCTTCAT
GCTTTATTCCTAAGTGATCTCTAAGCCCTAAGAAAGTAATTGATTGCTAAAAGAGTAAAACGGAT
AGATTGACTTTAATCGGTAATCTAATCTAATTAAGGTAATTA
Found at i:42947 original size:15 final size:16
Alignment explanation
Indices: 42927--42960 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
42917 GATTGATCTC
*
42927 TTAGTTA-ATTTACTT
1 TTAGTTAGATTTAATT
42942 TTAGTTAGATTTAATT
1 TTAGTTAGATTTAATT
42958 TTA
1 TTA
42961 ATTCTTCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.29, C:0.03, G:0.09, T:0.59
Consensus pattern (16 bp):
TTAGTTAGATTTAATT
Found at i:52803 original size:15 final size:16
Alignment explanation
Indices: 52783--52816 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
52773 GATTGCTCTC
*
52783 TTAGTTA-ATTTACTT
1 TTAGTTAGATTTAATT
52798 TTAGTTAGATTTAATT
1 TTAGTTAGATTTAATT
52814 TTA
1 TTA
52817 ATTCTTCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.29, C:0.03, G:0.09, T:0.59
Consensus pattern (16 bp):
TTAGTTAGATTTAATT
Done.