Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016275.1 Corchorus capsularis cultivar CVL-1 contig16296, 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: 50242
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.31
Found at i:1319 original size:145 final size:145
Alignment explanation
Indices: 1056--1346 Score: 564
Period size: 145 Copynumber: 2.0 Consensus size: 145
1046 ATATTGTGAC
1056 AACCAAGCAGCAATCTACAACACTAAAAATGAAAGGTTGTCAAATAGCAGCAAGCATATTGCTAT
1 AACCAAGCAGCAATCTACAACACTAAAAATGAAAGGTTGTCAAATAGCAGCAAGCATATTGCTAT
*
1121 GAGATATAATCATGTGAGAAGTGTTGTGAATAAAGGTAAGGTGAATCTTGAGTACTTGCCTACAA
66 GAGATATAATCATGTGAGAAGTGTTGTGAAGAAAGGTAAGGTGAATCTTGAGTACTTGCCTACAA
1186 GTCAAATGTTGGCAG
131 GTCAAATGTTGGCAG
1201 AACCAAGCAGCAATCTACAACACTAAAAATGAAAGGTTGTCAAATAGCAGCAAGCATATTGCTAT
1 AACCAAGCAGCAATCTACAACACTAAAAATGAAAGGTTGTCAAATAGCAGCAAGCATATTGCTAT
*
1266 GAGATATAATCATGTGAGAAGTTTTGTGAAGAAAGGTAAGGTGAATCTTGAGTACTTGCCTACAA
66 GAGATATAATCATGTGAGAAGTGTTGTGAAGAAAGGTAAGGTGAATCTTGAGTACTTGCCTACAA
1331 GTCAAATGTTGGCAG
131 GTCAAATGTTGGCAG
1346 A
1 A
1347 CCCTCTTACA
Statistics
Matches: 144, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
145 144 1.00
ACGTcount: A:0.39, C:0.14, G:0.22, T:0.25
Consensus pattern (145 bp):
AACCAAGCAGCAATCTACAACACTAAAAATGAAAGGTTGTCAAATAGCAGCAAGCATATTGCTAT
GAGATATAATCATGTGAGAAGTGTTGTGAAGAAAGGTAAGGTGAATCTTGAGTACTTGCCTACAA
GTCAAATGTTGGCAG
Found at i:8281 original size:63 final size:62
Alignment explanation
Indices: 8206--8356 Score: 169
Period size: 63 Copynumber: 2.4 Consensus size: 62
8196 TGACATCCAT
* * * *
8206 AATTAAATACATAGTCTAGACACAT-CATACATTGCTGAATAATACCATAAATTCCGAGTACAC
1 AATTAAACACATAGTCT-GA-AAATACATACACTGCTGAATAATACCATAAACTCCGAGTACAC
* * * *
8269 AATTAAACACATAGTCTGAAAATAGCATCCACTGCTGAATAATACCATGAACTCCTAGTACAT
1 AATTAAACACATAGTCTGAAAATA-CATACACTGCTGAATAATACCATAAACTCCGAGTACAC
* * *
8332 AATTAAATATATAGTTTGAAAATAC
1 AATTAAACACATAGTCTGAAAATAC
8357 CACCAACTAC
Statistics
Matches: 75, Mismatches: 11, Indels: 5
0.82 0.12 0.05
Matches are distributed among these distances:
61 3 0.04
62 3 0.04
63 69 0.92
ACGTcount: A:0.44, C:0.19, G:0.10, T:0.28
Consensus pattern (62 bp):
AATTAAACACATAGTCTGAAAATACATACACTGCTGAATAATACCATAAACTCCGAGTACAC
Found at i:11897 original size:26 final size:25
Alignment explanation
Indices: 11855--12104 Score: 142
Period size: 27 Copynumber: 9.6 Consensus size: 25
11845 TTACCATTCT
11855 TTTTTACT-TTTTGTACTGATTACCA
1 TTTTTACTCTTTT-TACTGATTACCA
*
11880 TATTTTACTCTTTTTACTGATTACCCC
1 T-TTTTACTCTTTTTACTGATTA-CCA
*
11907 TTTTCT-TTCTGTTTTGACTGAATT-CCA
1 TTTT-TACTCT-TTTT-ACTG-ATTACCA
*
11934 CTTTTTACTCTTTTTACTTAATTACCA
1 -TTTTTACTCTTTTTAC-TGATTACCA
* *
11961 TTTTTTACTCTCCTTTTTTACTTAGTACCA
1 -TTTTTA--CT-C-TTTTTACTGATTACCA
11991 TTTTTACT-TTTTT--T--TTACCA
1 TTTTTACTCTTTTTACTGATTACCA
* * *
12011 TTTATATCCCTTTTTACTGAATACCA
1 TTTTTA-CTCTTTTTACTGATTACCA
**
12037 CTTTTTACTCTTTTTTACTGACCACCA
1 -TTTTTACTC-TTTTTACTGATTACCA
*
12064 TTTCTTACTCTTATTTACTAATTACTC-
1 TTT-TTACTCTT-TTTACTGATTAC-CA
12091 TTTTTCAC-CTTTTT
1 TTTTT-ACTCTTTTT
12105 TTTATCTTAC
Statistics
Matches: 179, Mismatches: 19, Indels: 54
0.71 0.08 0.21
Matches are distributed among these distances:
20 10 0.06
21 1 0.01
22 6 0.03
24 6 0.03
25 4 0.02
26 44 0.25
27 70 0.39
28 12 0.07
29 11 0.06
30 8 0.04
31 7 0.04
ACGTcount: A:0.19, C:0.22, G:0.04, T:0.56
Consensus pattern (25 bp):
TTTTTACTCTTTTTACTGATTACCA
Found at i:11903 original size:55 final size:56
Alignment explanation
Indices: 11838--11966 Score: 146
Period size: 55 Copynumber: 2.4 Consensus size: 56
11828 TTATTTTTGA
11838 TTACTAATTACCATTCTTTT-TTACT-TTTTGTACTG-ATTACCA-TATTTTACTCTTT
1 TTACTAATTACCATTCTTTTCTTACTGTTTTG-ACTGAATT-CCACT-TTTTACTCTTT
* * *
11893 TTACTGATTACC--CCTTTTCTTTCTGTTTTGACTGAATTCCACTTTTTACTCTTT
1 TTACTAATTACCATTCTTTTCTTACTGTTTTGACTGAATTCCACTTTTTACTCTTT
11947 TTACTTAATTACCATT-TTTT
1 TTAC-TAATTACCATTCTTTT
11967 ACTCTCCTTT
Statistics
Matches: 62, Mismatches: 5, Indels: 13
0.77 0.06 0.16
Matches are distributed among these distances:
53 5 0.08
54 26 0.42
55 27 0.44
56 4 0.06
ACGTcount: A:0.19, C:0.20, G:0.05, T:0.56
Consensus pattern (56 bp):
TTACTAATTACCATTCTTTTCTTACTGTTTTGACTGAATTCCACTTTTTACTCTTT
Found at i:12531 original size:72 final size:70
Alignment explanation
Indices: 12436--12650 Score: 229
Period size: 71 Copynumber: 3.0 Consensus size: 70
12426 CACTTTAACC
* * * * *
12436 CTTAATTATCGATTCACTAATTACTAT-TTTTACCTTGACT-CTTTAATCATTGATTAATCT-CT
1 CTTAATTATCAATTTACTGATTACTATCTTTTA-CTTGACTAC-TGAATCACTGATT-A-CTAC-
12498 TACCTTGACT
61 TACCTTGACT
* * *
12508 CTTAATTATCAATTTACTGATTACTATCTTTTACTTGATTACTGATTTACTGATTACTACTACCT
1 CTTAATTATCAATTTACTGATTACTATCTTTTACTTGACTACTGAATCACTGATTACTACTACCT
12573 TGACT
66 TGACT
* * * * * *
12578 CTTAATTATCAATTTACTGATTAATCTCTTTTTACTTAACTACTGATTTACTGATTACTATTACC
1 CTTAATTATCAATTTACTGATTACTATC-TTTTACTTGACTACTGAATCACTGATTACTACTACC
12643 TTGACT
65 TTGACT
12649 CT
1 CT
12651 GATTAATCTC
Statistics
Matches: 126, Mismatches: 13, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
70 38 0.30
71 43 0.34
72 39 0.31
73 6 0.05
ACGTcount: A:0.27, C:0.20, G:0.06, T:0.47
Consensus pattern (70 bp):
CTTAATTATCAATTTACTGATTACTATCTTTTACTTGACTACTGAATCACTGATTACTACTACCT
TGACT
Found at i:12568 original size:18 final size:17
Alignment explanation
Indices: 12519--12569 Score: 54
Period size: 15 Copynumber: 3.1 Consensus size: 17
12509 TTAATTATCA
12519 ATTTACTGATTACTATCT
1 ATTTACTGATTACTA-CT
*
12537 -TTTACTTGATTACT--G
1 ATTTAC-TGATTACTACT
12552 ATTTACTGATTACTACT
1 ATTTACTGATTACTACT
12569 A
1 A
12570 CCTTGACTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 9
0.71 0.05 0.24
Matches are distributed among these distances:
15 8 0.30
16 5 0.19
17 6 0.22
18 8 0.30
ACGTcount: A:0.27, C:0.16, G:0.08, T:0.49
Consensus pattern (17 bp):
ATTTACTGATTACTACT
Found at i:12589 original size:70 final size:71
Alignment explanation
Indices: 12498--12650 Score: 254
Period size: 71 Copynumber: 2.2 Consensus size: 71
12488 ATTAATCTCT
* * *
12498 TACCTTGACTCTTAATTATCAATTTACTGATTACTATC-TTTTACTTGATTACTGATTTACTGAT
1 TACCTTGACTCTTAATTATCAATTTACTGATTAATATCTTTTTACTTAACTACTGATTTACTGAT
12562 TACTAC
66 TACTAC
*
12568 TACCTTGACTCTTAATTATCAATTTACTGATTAATCTCTTTTTACTTAACTACTGATTTACTGAT
1 TACCTTGACTCTTAATTATCAATTTACTGATTAATATCTTTTTACTTAACTACTGATTTACTGAT
*
12633 TACTAT
66 TACTAC
12639 TACCTTGACTCT
1 TACCTTGACTCT
12651 GATTAATCTC
Statistics
Matches: 77, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
70 36 0.47
71 41 0.53
ACGTcount: A:0.27, C:0.20, G:0.07, T:0.47
Consensus pattern (71 bp):
TACCTTGACTCTTAATTATCAATTTACTGATTAATATCTTTTTACTTAACTACTGATTTACTGAT
TACTAC
Found at i:12653 original size:55 final size:55
Alignment explanation
Indices: 12594--13021 Score: 768
Period size: 55 Copynumber: 7.8 Consensus size: 55
12584 TATCAATTTA
* * *
12594 CTGATTAATCTCTTTTTACTTAACTACTGATTTACTGATTACTATTACCTTGACT
1 CTGATTAATCTCTTTTCACTTAATTACTGATTTACTGATTACTATTACTTTGACT
*
12649 CTGATTAATCTCTTCTT-ACTTAACTACTGATTTACTGATTACTATTACTTTGACT
1 CTGATTAATCTCTT-TTCACTTAATTACTGATTTACTGATTACTATTACTTTGACT
12704 CTGATTAATCTCTTTTCACTTAATTACTGATTTACTGATTACTATTACTTTGACT
1 CTGATTAATCTCTTTTCACTTAATTACTGATTTACTGATTACTATTACTTTGACT
*
12759 CTGATTAATCTCTTTTCACTTAATTACTGATTTACTGATTACTATTACCTTGACT
1 CTGATTAATCTCTTTTCACTTAATTACTGATTTACTGATTACTATTACTTTGACT
12814 CTGATTAATCTCTTTTCACTTAATTACTGATTTACTGATTACTATTACTTTGACT
1 CTGATTAATCTCTTTTCACTTAATTACTGATTTACTGATTACTATTACTTTGACT
*
12869 CTGATTAATCTCTTTTCACTTAATTACTGATTTACTGATTACTATTACCTTGACT
1 CTGATTAATCTCTTTTCACTTAATTACTGATTTACTGATTACTATTACTTTGACT
12924 CTGATTAATCTCTTTTCACTTAATTACTGATTTACTGATTACTATTACTTTGACT
1 CTGATTAATCTCTTTTCACTTAATTACTGATTTACTGATTACTATTACTTTGACT
* *
12979 CTGATTAATCTCTTTTCACTTAATTACTGATTGACTGGTTACT
1 CTGATTAATCTCTTTTCACTTAATTACTGATTTACTGATTACT
13022 GTTCGGACTG
Statistics
Matches: 363, Mismatches: 8, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
54 2 0.01
55 359 0.99
56 2 0.01
ACGTcount: A:0.25, C:0.19, G:0.08, T:0.48
Consensus pattern (55 bp):
CTGATTAATCTCTTTTCACTTAATTACTGATTTACTGATTACTATTACTTTGACT
Found at i:13917 original size:50 final size:49
Alignment explanation
Indices: 13863--13996 Score: 160
Period size: 49 Copynumber: 2.7 Consensus size: 49
13853 TGCTCAAGGG
* * * * *
13863 TGACATCTCTACTTACTAATCATTAAAAGTTTCCATATCTTACCCAAAGA
1 TGACATTTTTACTTACTAATCACTAAAA-ATTCAATATCTTACCCAAAGA
* * * *
13913 TGACATTTTTACTTACTAATTACTAAAAATTCAATCTTTTACCTAAAGA
1 TGACATTTTTACTTACTAATCACTAAAAATTCAATATCTTACCCAAAGA
**
13962 TGACATTTTTACTTACTAATTGCTAAAAATTCAAT
1 TGACATTTTTACTTACTAATCACTAAAAATTCAAT
13997 CTTTTATTTA
Statistics
Matches: 74, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
49 50 0.68
50 24 0.32
ACGTcount: A:0.37, C:0.19, G:0.05, T:0.39
Consensus pattern (49 bp):
TGACATTTTTACTTACTAATCACTAAAAATTCAATATCTTACCCAAAGA
Found at i:13968 original size:49 final size:49
Alignment explanation
Indices: 13787--14002 Score: 195
Period size: 50 Copynumber: 4.4 Consensus size: 49
13777 AATTACTTTT
* * * *
13787 TAAAACTTCAATCTTTTATTCAAAAGGT-ACATCTCTACTTACTAATTACTC
1 TAAAAATTCAATCTTTTA-CCTAAAGATGACATCTCTACTTACTAATTA--C
* * * * *
13838 TAAAAA-TCAATCTTTT-GCTCAAGGGTGACATCTCTACTTACTAATCAT
1 TAAAAATTCAATCTTTTACCT-AAAGATGACATCTCTACTTACTAATTAC
* * * * * * *
13886 TAAAAGTTTCCATATCTTACCCAAAGATGACATTTTTACTTACTAATTAC
1 TAAAA-ATTCAATCTTTTACCTAAAGATGACATCTCTACTTACTAATTAC
* * *
13936 TAAAAATTCAATCTTTTACCTAAAGATGACATTTTTACTTACTAATTGC
1 TAAAAATTCAATCTTTTACCTAAAGATGACATCTCTACTTACTAATTAC
13985 TAAAAATTCAATCTTTTA
1 TAAAAATTCAATCTTTTA
14003 TTTACAAGTT
Statistics
Matches: 136, Mismatches: 24, Indels: 12
0.79 0.14 0.07
Matches are distributed among these distances:
48 6 0.04
49 61 0.45
50 63 0.46
51 6 0.04
ACGTcount: A:0.36, C:0.19, G:0.06, T:0.39
Consensus pattern (49 bp):
TAAAAATTCAATCTTTTACCTAAAGATGACATCTCTACTTACTAATTAC
Found at i:15956 original size:18 final size:18
Alignment explanation
Indices: 15933--15968 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
15923 ACTTGTGCAT
15933 GTCTAACTAATTGCTAAA
1 GTCTAACTAATTGCTAAA
15951 GTCTAACTAATTGCTAAA
1 GTCTAACTAATTGCTAAA
15969 TTGAATGCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.17, G:0.11, T:0.33
Consensus pattern (18 bp):
GTCTAACTAATTGCTAAA
Found at i:16221 original size:19 final size:20
Alignment explanation
Indices: 16197--16234 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
16187 CTGAGTGCAA
16197 AAATGACCAAAATG-CCCTC
1 AAATGACCAAAATGTCCCTC
16216 AAATGACCAAAATGTCCCT
1 AAATGACCAAAATGTCCCT
16235 GGGCGACCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.42, C:0.29, G:0.11, T:0.18
Consensus pattern (20 bp):
AAATGACCAAAATGTCCCTC
Found at i:17794 original size:13 final size:13
Alignment explanation
Indices: 17776--17800 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17766 GAAAGTTGTT
17776 GAGAGAAGCAAAA
1 GAGAGAAGCAAAA
17789 GAGAGAAGCAAA
1 GAGAGAAGCAAA
17801 TAATATTTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.60, C:0.08, G:0.32, T:0.00
Consensus pattern (13 bp):
GAGAGAAGCAAAA
Found at i:17882 original size:65 final size:65
Alignment explanation
Indices: 17778--17926 Score: 280
Period size: 65 Copynumber: 2.3 Consensus size: 65
17768 AAGTTGTTGA
17778 GAGAAGCAAAAGAGAGAAGCAAATAATATTTTAATAATGTTTGTTAAAGTATTCAAACAAATATG
1 GAGAAGCAAAAGAGAGAAGCAAATAATATTTTAATAATGTTTGTTAAAGTATTCAAACAAATATG
* *
17843 GAGAAGTAAAAGAGAGAAGCAAATAATATTTTAATAATGTTTGTTAAAGTATTCAAACAAATTTG
1 GAGAAGCAAAAGAGAGAAGCAAATAATATTTTAATAATGTTTGTTAAAGTATTCAAACAAATATG
17908 GAGAAGCAAAAGAGAGAAG
1 GAGAAGCAAAAGAGAGAAG
17927 TCCGAAGAGA
Statistics
Matches: 81, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
65 81 1.00
ACGTcount: A:0.50, C:0.05, G:0.19, T:0.26
Consensus pattern (65 bp):
GAGAAGCAAAAGAGAGAAGCAAATAATATTTTAATAATGTTTGTTAAAGTATTCAAACAAATATG
Found at i:18169 original size:65 final size:65
Alignment explanation
Indices: 18050--18528 Score: 658
Period size: 65 Copynumber: 7.4 Consensus size: 65
18040 TTAGAAAATT
* * * *
18050 TCAAGGAGTACACCAGAAGATGATTTATC-AAGAGTTTTCAGAAGTTGATCGGAAGACGATTTTG
1 TCAAGAAGTACACCAGAAGATGGTTTCTCAAAGAGTTTTCAGAAGTTGATCGGAAGACGATCTTG
* *
18114 TCAAGAAGTACACCAGAAGATGATTTCTCAAAGAGTTTTCAGAAGTTTATCGGAAGACGATCTTG
1 TCAAGAAGTACACCAGAAGATGGTTTCTCAAAGAGTTTTCAGAAGTTGATCGGAAGACGATCTTG
* * * **
18179 TTAAGAAGTACACCAGAAGATGGTCTCTAAAAGAGTTTTCAGAAGTTGATCGGAATTCGATCTTG
1 TCAAGAAGTACACCAGAAGATGGTTTCTCAAAGAGTTTTCAGAAGTTGATCGGAAGACGATCTTG
* * * *
18244 TTAAGAAGTACACCAGAAGATGGTCTCTCAAAGAGTTTCCAGAAGTTGATCGGAGGACGATCTTG
1 TCAAGAAGTACACCAGAAGATGGTTTCTCAAAGAGTTTTCAGAAGTTGATCGGAAGACGATCTTG
* * * * **
18309 TCAAGAAATACACCAGAAGATGGTTTCTCTAAGAGTTTCCAGAAGTGGATCGGGTGACGATCTTG
1 TCAAGAAGTACACCAGAAGATGGTTTCTCAAAGAGTTTTCAGAAGTTGATCGGAAGACGATCTTG
* * * * *
18374 TCAAGGAGTACACCAGAAGATGGTTTATC-AAGAGTTTTTAGAAGTTGATTGGGAGACGATCTTG
1 TCAAGAAGTACACCAGAAGATGGTTTCTCAAAGAGTTTTCAGAAGTTGATCGGAAGACGATCTTG
* * * **
18438 TCAAGGAGTACACCAGAAGATGGTTTCTCAAAGAGTTTTCAGAAGTGGGTCGGGTGACGATCTTG
1 TCAAGAAGTACACCAGAAGATGGTTTCTCAAAGAGTTTTCAGAAGTTGATCGGAAGACGATCTTG
18503 TCAAGAAGTACACCAGAAGAT-GTTTC
1 TCAAGAAGTACACCAGAAGATGGTTTC
18529 CTCAGAAAGA
Statistics
Matches: 375, Mismatches: 38, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
64 90 0.24
65 285 0.76
ACGTcount: A:0.33, C:0.15, G:0.25, T:0.27
Consensus pattern (65 bp):
TCAAGAAGTACACCAGAAGATGGTTTCTCAAAGAGTTTTCAGAAGTTGATCGGAAGACGATCTTG
Found at i:18935 original size:50 final size:50
Alignment explanation
Indices: 18871--19274 Score: 488
Period size: 50 Copynumber: 8.1 Consensus size: 50
18861 AAAATGATTA
*
18871 TTTTAAGA-GTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
1 TTTTAAGATG-GAATTGGAAGACAGTTCGAAGGATAAGCGGAAGACGGTCC
* * * * * * *
18921 TTTTAAGATGGAATTGTAAGAC-GATTCGAATGTTGATCGGAACACGATCC
1 TTTTAAGATGGAATTGGAAGACAG-TTCGAAGGATAAGCGGAAGACGGTCC
* *
18971 TCTAAAGATGGAATTGGAAGACAGTTCGAAGGATAAGCGGAAGACGGTCC
1 TTTTAAGATGGAATTGGAAGACAGTTCGAAGGATAAGCGGAAGACGGTCC
* * * * * * * *
19021 TTTTAAGATGGAATTGGAAGAAAATTCGGATGTTGATCGGAAGACGATCC
1 TTTTAAGATGGAATTGGAAGACAGTTCGAAGGATAAGCGGAAGACGGTCC
* *
19071 TCTAAAGATGGAATTGGAAGACAGTTCGAAGGATAAGCGGAAGACGGTCC
1 TTTTAAGATGGAATTGGAAGACAGTTCGAAGGATAAGCGGAAGACGGTCC
*
19121 TTTTAAGATGGAATTGGAAGACAATTCGAAGGATAAGCGGAAGACGGTCC
1 TTTTAAGATGGAATTGGAAGACAGTTCGAAGGATAAGCGGAAGACGGTCC
** * *
19171 TTTTAAGATTTAATTGGAAGACAGTTTGAAGGATAAGCGGAAGATGGTCC
1 TTTTAAGATGGAATTGGAAGACAGTTCGAAGGATAAGCGGAAGACGGTCC
** * * * **
19221 TTTCGAGATGGAATTGGAAGACAATTCTAAGGATAAACGGAAGACAATCC
1 TTTTAAGATGGAATTGGAAGACAGTTCGAAGGATAAGCGGAAGACGGTCC
19271 TTTT
1 TTTT
19275 GGAAGATAAT
Statistics
Matches: 294, Mismatches: 57, Indels: 6
0.82 0.16 0.02
Matches are distributed among these distances:
49 1 0.00
50 291 0.99
51 2 0.01
ACGTcount: A:0.35, C:0.12, G:0.28, T:0.25
Consensus pattern (50 bp):
TTTTAAGATGGAATTGGAAGACAGTTCGAAGGATAAGCGGAAGACGGTCC
Found at i:19054 original size:100 final size:100
Alignment explanation
Indices: 18881--19247 Score: 563
Period size: 100 Copynumber: 3.7 Consensus size: 100
18871 TTTTAAGAGT
* * *
18881 GAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTAAGATGGAATTGTAAGACGAT
1 GAATTGGAAGACAGTTCGAAGGATAAGCGGAAGACGGTCCTTTTAAGATGGAATTGGAAGACAAT
*
18946 TCGAATGTTGATCGGAACACGATCCTCTAAAGATG
66 TCGAATGTTGATCGGAAGACGATCCTCTAAAGATG
*
18981 GAATTGGAAGACAGTTCGAAGGATAAGCGGAAGACGGTCCTTTTAAGATGGAATTGGAAGAAAAT
1 GAATTGGAAGACAGTTCGAAGGATAAGCGGAAGACGGTCCTTTTAAGATGGAATTGGAAGACAAT
*
19046 TCGGATGTTGATCGGAAGACGATCCTCTAAAGATG
66 TCGAATGTTGATCGGAAGACGATCCTCTAAAGATG
19081 GAATTGGAAGACAGTTCGAAGGATAAGCGGAAGACGGTCCTTTTAAGATGGAATTGGAAGACAAT
1 GAATTGGAAGACAGTTCGAAGGATAAGCGGAAGACGGTCCTTTTAAGATGGAATTGGAAGACAAT
* * * * * * * *
19146 TCGAAGGATAAGCGGAAGACGGTCCTTTTAAGATT
66 TCGAATGTTGATCGGAAGACGATCCTCTAAAGATG
* * * **
19181 TAATTGGAAGACAGTTTGAAGGATAAGCGGAAGATGGTCCTTTCGAGATGGAATTGGAAGACAAT
1 GAATTGGAAGACAGTTCGAAGGATAAGCGGAAGACGGTCCTTTTAAGATGGAATTGGAAGACAAT
19246 TC
66 TC
19248 TAAGGATAAA
Statistics
Matches: 246, Mismatches: 21, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
100 246 1.00
ACGTcount: A:0.35, C:0.12, G:0.29, T:0.24
Consensus pattern (100 bp):
GAATTGGAAGACAGTTCGAAGGATAAGCGGAAGACGGTCCTTTTAAGATGGAATTGGAAGACAAT
TCGAATGTTGATCGGAAGACGATCCTCTAAAGATG
Found at i:23999 original size:9 final size:9
Alignment explanation
Indices: 23985--24018 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
23975 AGAAGAAAAG
23985 AAAAATGGA
1 AAAAATGGA
23994 AAAAATGGA
1 AAAAATGGA
*
24003 AAGAATGAGA
1 AAAAATG-GA
24013 AAAAAT
1 AAAAAT
24019 AAAAGATGCA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 15 0.68
10 7 0.32
ACGTcount: A:0.68, C:0.00, G:0.21, T:0.12
Consensus pattern (9 bp):
AAAAATGGA
Found at i:24016 original size:19 final size:17
Alignment explanation
Indices: 23984--24018 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
23974 AAGAAGAAAA
23984 GAAAAATGGAAAAAATG
1 GAAAAATGGAAAAAATG
24001 GAAAGAATGAGAAAAAAT
1 GAAA-AATG-GAAAAAAT
24019 AAAAGATGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 4 0.25
19 8 0.50
ACGTcount: A:0.66, C:0.00, G:0.23, T:0.11
Consensus pattern (17 bp):
GAAAAATGGAAAAAATG
Found at i:24050 original size:14 final size:13
Alignment explanation
Indices: 24031--24062 Score: 55
Period size: 13 Copynumber: 2.4 Consensus size: 13
24021 AAGATGCAAT
24031 AAAAAGTGTTTTTC
1 AAAAAGTG-TTTTC
24045 AAAAAGTGTTTTC
1 AAAAAGTGTTTTC
24058 AAAAA
1 AAAAA
24063 TCATGTTCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.47, C:0.06, G:0.12, T:0.34
Consensus pattern (13 bp):
AAAAAGTGTTTTC
Found at i:26628 original size:18 final size:19
Alignment explanation
Indices: 26605--26644 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
26595 TTCTTGAAAT
26605 AATTCTTC-AATTATCTTC
1 AATTCTTCAAATTATCTTC
26623 AATTCTTCAAATTATCTTC
1 AATTCTTCAAATTATCTTC
26642 AAT
1 AAT
26645 AAATCTTCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.33, C:0.20, G:0.00, T:0.47
Consensus pattern (19 bp):
AATTCTTCAAATTATCTTC
Found at i:30476 original size:21 final size:20
Alignment explanation
Indices: 30437--30478 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
30427 TCCTTTGCTT
*
30437 ATTGTCTTCAATGCTCTTCA
1 ATTGTCTTCAATGCACTTCA
*
30457 ATTGATCTTCAATGGACTTCA
1 ATTG-TCTTCAATGCACTTCA
30478 A
1 A
30479 ACCTTCAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.26, C:0.21, G:0.12, T:0.40
Consensus pattern (20 bp):
ATTGTCTTCAATGCACTTCA
Found at i:33613 original size:21 final size:20
Alignment explanation
Indices: 33568--33605 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
33558 TAAATATTAG
33568 AAGA-TTTTTCGGAAAGAGA
1 AAGAGTTTTTCGGAAAGAGA
*
33587 AAGAGTTTTTCGGGAAGAG
1 AAGAGTTTTTCGGAAAGAG
33606 GAAGGAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.37, C:0.05, G:0.32, T:0.26
Consensus pattern (20 bp):
AAGAGTTTTTCGGAAAGAGA
Found at i:47010 original size:458 final size:458
Alignment explanation
Indices: 46153--47070 Score: 1800
Period size: 458 Copynumber: 2.0 Consensus size: 458
46143 CGCCCAAGGC
46153 TTATCATGGAAGGAATTATGCGCCAAGGACTTATTATAGACTTGAAGACAAGCATGGAGAGCATG
1 TTATCATGGAAGGAATTATGCGCCAAGGACTTATTATAGACTTGAAGACAAGCATGGAGAGCATG
46218 GAAAGGATGATCAAGGGCTGCAAGGAAGCATGGACAAGCTTAAAGGAGAGGATGGAATCGTAATT
66 GAAAGGATGATCAAGGGCTGCAAGGAAGCATGGACAAGCTTAAAGGAGAGGATGGAATCGTAATT
46283 CACCAAGAAGATGCCATTAAGATGCCATTTGATCCTTTGAAGATGCCATTAGGTCCGATGACAAG
131 CACCAAGAAGATGCCATTAAGATGCCATTTGATCCTTTGAAGATGCCATTAGGTCCGATGACAAG
46348 AGCAAGAGCTAAGAGATTCAAGGATGCACTCATGGGCCTTGTTCGAACTCATCTTGAAGACTTGA
196 AGCAAGAGCTAAGAGATTCAAGGATGCACTCATGGGCCTTGTTCGAACTCATCTTGAAGACTTGA
46413 AGACCATTGAAGTTCAATTCAAGAGCTTTGGTGATGATTTGGGCAAGAAATTACAAATCAATTAC
261 AGACCATTGAAGTTCAATTCAAGAGCTTTGGTGATGATTTGGGCAAGAAATTACAAATCAATTAC
46478 AAGTTCATCACATTGCTTGCTATTGATTCTAGATGGCCGGATTGACATCATGGCATGAGCCCATT
326 AAGTTCATCACATTGCTTGCTATTGATTCTAGATGGCCGGATTGACATCATGGCATGAGCCCATT
*
46543 ATCATTAGTTATCTTTGTTTAGGCTTAATTCTATCTTAGATTGGCTTATTCTTAAGTTTGGACCT
391 ATCATTAGTTATCTTTGTTTAGGCTTAATTCTATCTTAGATTAGCTTATTCTTAAGTTTGGACCT
46608 TAT
456 TAT
46611 TTATCATGGAAGGAATTATGCGCCAAGGACTTATTATAGACTTGAAGACAAGCATGGAGAGCATG
1 TTATCATGGAAGGAATTATGCGCCAAGGACTTATTATAGACTTGAAGACAAGCATGGAGAGCATG
46676 GAAAGGATGATCAAGGGCTGCAAGGAAGCATGGACAAGCTTAAAGGAGAGGATGGAATCGTAATT
66 GAAAGGATGATCAAGGGCTGCAAGGAAGCATGGACAAGCTTAAAGGAGAGGATGGAATCGTAATT
46741 CACCAAGAAGATGCCATTAAGATGCCATTTGATCCTTTGAAGATGCCATTAGGTCCGATGACAAG
131 CACCAAGAAGATGCCATTAAGATGCCATTTGATCCTTTGAAGATGCCATTAGGTCCGATGACAAG
46806 AGCAAGAGCTAAGAGATTCAAGGATGCACTCATGGGCCTTGTTCGAACTCATCTTGAAGACTTGA
196 AGCAAGAGCTAAGAGATTCAAGGATGCACTCATGGGCCTTGTTCGAACTCATCTTGAAGACTTGA
46871 AGACCATTGAAGTTCAATTCAAGAGCTTTGGTGATGATTTGGGCAAGAAATTACAAATCAATTAC
261 AGACCATTGAAGTTCAATTCAAGAGCTTTGGTGATGATTTGGGCAAGAAATTACAAATCAATTAC
46936 AAGTTCATCACATTGCTTGCTATTGATTCTAGATGGCCGGATTGACATCATGGCATGAGCCCATT
326 AAGTTCATCACATTGCTTGCTATTGATTCTAGATGGCCGGATTGACATCATGGCATGAGCCCATT
* * *
47001 TTCATTAGTTATCTTTGTTTAGGCTTAATTCTATCTTAGATTAGCTTATTTTTATGTTTGGACCT
391 ATCATTAGTTATCTTTGTTTAGGCTTAATTCTATCTTAGATTAGCTTATTCTTAAGTTTGGACCT
47066 TAT
456 TAT
47069 TT
1 TT
47071 GGATTGGGCC
Statistics
Matches: 456, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
458 456 1.00
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (458 bp):
TTATCATGGAAGGAATTATGCGCCAAGGACTTATTATAGACTTGAAGACAAGCATGGAGAGCATG
GAAAGGATGATCAAGGGCTGCAAGGAAGCATGGACAAGCTTAAAGGAGAGGATGGAATCGTAATT
CACCAAGAAGATGCCATTAAGATGCCATTTGATCCTTTGAAGATGCCATTAGGTCCGATGACAAG
AGCAAGAGCTAAGAGATTCAAGGATGCACTCATGGGCCTTGTTCGAACTCATCTTGAAGACTTGA
AGACCATTGAAGTTCAATTCAAGAGCTTTGGTGATGATTTGGGCAAGAAATTACAAATCAATTAC
AAGTTCATCACATTGCTTGCTATTGATTCTAGATGGCCGGATTGACATCATGGCATGAGCCCATT
ATCATTAGTTATCTTTGTTTAGGCTTAATTCTATCTTAGATTAGCTTATTCTTAAGTTTGGACCT
TAT
Found at i:47802 original size:10 final size:9
Alignment explanation
Indices: 47789--47823 Score: 52
Period size: 10 Copynumber: 3.7 Consensus size: 9
47779 ACTTATATCG
47789 AAAAATATAA
1 AAAAATA-AA
47799 AAAAATAAA
1 AAAAATAAA
47808 ATAAAATAAA
1 A-AAAATAAA
47818 AAAAAT
1 AAAAAT
47824 TTTCGACCAG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 8 0.33
10 16 0.67
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (9 bp):
AAAAATAAA
Done.