Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011882.1 Corchorus olitorius cultivar O-4 contig11915, 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: 96665
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:687 original size:11 final size:13
Alignment explanation
Indices: 661--692 Score: 50
Period size: 11 Copynumber: 2.6 Consensus size: 13
651 TTTCTTTTCT
661 TTTTTTTTCAAGA
1 TTTTTTTTCAAGA
674 TTTTTTTTC-A-A
1 TTTTTTTTCAAGA
685 TTTTTTTT
1 TTTTTTTT
693 GACACTTCTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 9 0.47
12 1 0.05
13 9 0.47
ACGTcount: A:0.16, C:0.06, G:0.03, T:0.75
Consensus pattern (13 bp):
TTTTTTTTCAAGA
Found at i:2666 original size:5 final size:6
Alignment explanation
Indices: 2649--2692 Score: 61
Period size: 6 Copynumber: 7.0 Consensus size: 6
2639 TAACAAAACC
*
2649 ACAAAA ACAAAA ACAAAA ACAAAA TACGAAAA ATAAAA ACAAAA
1 ACAAAA ACAAAA ACAAAA ACAAAA -AC-AAAA ACAAAA ACAAAA
2693 CTAAAGGAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
6 27 0.79
7 3 0.09
8 4 0.12
ACGTcount: A:0.80, C:0.14, G:0.02, T:0.05
Consensus pattern (6 bp):
ACAAAA
Found at i:2670 original size:26 final size:26
Alignment explanation
Indices: 2640--2692 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
2630 CTGCAAAATT
2640 AACAAAACCAC-AAAAACAAAAACAAA
1 AACAAAA-CACGAAAAACAAAAACAAA
* *
2666 AACAAAATACGAAAAATAAAAACAAA
1 AACAAAACACGAAAAACAAAAACAAA
2692 A
1 A
2693 CTAAAGGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 2 0.08
26 22 0.92
ACGTcount: A:0.77, C:0.17, G:0.02, T:0.04
Consensus pattern (26 bp):
AACAAAACACGAAAAACAAAAACAAA
Found at i:9995 original size:31 final size:31
Alignment explanation
Indices: 9953--10095 Score: 243
Period size: 31 Copynumber: 4.6 Consensus size: 31
9943 AGCAATTATT
9953 CTTAACATGTTCAATTCATGTTACATATAGC
1 CTTAACATGTTCAATTCATGTTACATATAGC
*
9984 CTTGACATGTTCCAATTCATGTTACATATAGC
1 CTTAACATGTT-CAATTCATGTTACATATAGC
10016 CTTAACATGTTCAATTCATGTTACATATAGC
1 CTTAACATGTTCAATTCATGTTACATATAGC
*
10047 CTTTAA-ATGTTCAATTCTTGTTACATATAGC
1 C-TTAACATGTTCAATTCATGTTACATATAGC
10078 CTTAACATGTTCAATTCA
1 CTTAACATGTTCAATTCA
10096 ATTCATAAAT
Statistics
Matches: 105, Mismatches: 4, Indels: 6
0.91 0.03 0.05
Matches are distributed among these distances:
30 4 0.04
31 67 0.64
32 34 0.32
ACGTcount: A:0.31, C:0.20, G:0.10, T:0.40
Consensus pattern (31 bp):
CTTAACATGTTCAATTCATGTTACATATAGC
Found at i:10031 original size:63 final size:62
Alignment explanation
Indices: 9953--10095 Score: 250
Period size: 63 Copynumber: 2.3 Consensus size: 62
9943 AGCAATTATT
*
9953 CTTAACATGTTCAATTCATGTTACATATAGCCTTGACATGTTCCAATTCATGTTACATATAGC
1 CTTAACATGTTCAATTCATGTTACATATAGCCTTGAAATGTT-CAATTCATGTTACATATAGC
* *
10016 CTTAACATGTTCAATTCATGTTACATATAGCCTTTAAATGTTCAATTCTTGTTACATATAGC
1 CTTAACATGTTCAATTCATGTTACATATAGCCTTGAAATGTTCAATTCATGTTACATATAGC
10078 CTTAACATGTTCAATTCA
1 CTTAACATGTTCAATTCA
10096 ATTCATAAAT
Statistics
Matches: 77, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
62 37 0.48
63 40 0.52
ACGTcount: A:0.31, C:0.20, G:0.10, T:0.40
Consensus pattern (62 bp):
CTTAACATGTTCAATTCATGTTACATATAGCCTTGAAATGTTCAATTCATGTTACATATAGC
Found at i:11092 original size:20 final size:20
Alignment explanation
Indices: 11067--11105 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
11057 GAAAATACAA
11067 GGCATTTGATTTACAAATTG
1 GGCATTTGATTTACAAATTG
*
11087 GGCATTTGATTTGCAAATT
1 GGCATTTGATTTACAAATT
11106 CGTGCTCTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.21, T:0.41
Consensus pattern (20 bp):
GGCATTTGATTTACAAATTG
Found at i:20322 original size:21 final size:21
Alignment explanation
Indices: 20296--20336 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
20286 ATCTTCCATA
20296 CCAATGAGCAAGTTATCGAAT
1 CCAATGAGCAAGTTATCGAAT
20317 CCAATGAGCAAGTTATCGAA
1 CCAATGAGCAAGTTATCGAA
20337 GTAATCTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.22
Consensus pattern (21 bp):
CCAATGAGCAAGTTATCGAAT
Found at i:24914 original size:10 final size:10
Alignment explanation
Indices: 24899--24923 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
24889 TTAGCTAATC
24899 ATAACCACTT
1 ATAACCACTT
24909 ATAACCACTT
1 ATAACCACTT
24919 ATAAC
1 ATAAC
24924 AAACATCATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.44, C:0.28, G:0.00, T:0.28
Consensus pattern (10 bp):
ATAACCACTT
Found at i:27183 original size:28 final size:27
Alignment explanation
Indices: 27138--27211 Score: 94
Period size: 28 Copynumber: 2.7 Consensus size: 27
27128 AGGCCTCCTA
* *
27138 ATGTGTAAATGACCAAAATATCCCTGG
1 ATGTGTAAATGACTAAAATACCCCTGG
*
27165 ATGTGTAAAATGACTAAAATACCCCTTG
1 ATGTGT-AAATGACTAAAATACCCCTGG
**
27193 ATGTGCGAATGACTAAAAT
1 ATGTGTAAATGACTAAAAT
27212 GCCCTTGAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
27 18 0.44
28 23 0.56
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.27
Consensus pattern (27 bp):
ATGTGTAAATGACTAAAATACCCCTGG
Found at i:27229 original size:26 final size:26
Alignment explanation
Indices: 27172--27241 Score: 77
Period size: 26 Copynumber: 2.7 Consensus size: 26
27162 TGGATGTGTA
* ** *
27172 AAATGACTAAAATACCCCTTGATGTGC
1 AAATGACTAAAAT-GCCCTTGAAATAC
*
27199 GAATGACTAAAATGCCCTTGAAATAC
1 AAATGACTAAAATGCCCTTGAAATAC
*
27225 AAATGACCAAAATGCCC
1 AAATGACTAAAATGCCC
27242 CTTAAGAAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
26 24 0.67
27 12 0.33
ACGTcount: A:0.41, C:0.23, G:0.14, T:0.21
Consensus pattern (26 bp):
AAATGACTAAAATGCCCTTGAAATAC
Found at i:37698 original size:13 final size:13
Alignment explanation
Indices: 37656--37698 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
37646 TTTGTCAGTC
*
37656 TAAACCAGGATAA
1 TAAACCAAGATAA
* *
37669 TATACCAATATAA
1 TAAACCAAGATAA
37682 -AAACCAAGATAA
1 TAAACCAAGATAA
37694 TAAAC
1 TAAAC
37699 GAAAATACCA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
12 10 0.42
13 14 0.58
ACGTcount: A:0.58, C:0.16, G:0.07, T:0.19
Consensus pattern (13 bp):
TAAACCAAGATAA
Found at i:43173 original size:15 final size:15
Alignment explanation
Indices: 43147--43184 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
43137 TTTGCTTTGT
43147 TTTCTAGTTTAATTGC
1 TTTCT-GTTTAATTGC
43163 TTTCTGTTTAATTGC
1 TTTCTGTTTAATTGC
43178 TTTCTGT
1 TTTCTGT
43185 CAACCTCTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 17 0.77
16 5 0.23
ACGTcount: A:0.13, C:0.13, G:0.13, T:0.61
Consensus pattern (15 bp):
TTTCTGTTTAATTGC
Found at i:65509 original size:76 final size:76
Alignment explanation
Indices: 65366--65517 Score: 175
Period size: 76 Copynumber: 2.0 Consensus size: 76
65356 TAAGGATGCC
* * *
65366 GACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCTTGAGGACCCAGGTG
1 GACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGCACCCAGATG
65431 GGCGGTGTCAT
66 GGCGGTGTCAT
* * * * *
65442 GACTCCAGCTGGGTGCCCACATGGTTTGTC-TGAAG-ACCCATGT-GTTTCGCCTGATCACCTAG
1 GACTCCACCTGGGCGCCCACATGG-TTGCCTTG-AGCACCCATGTGGTTT-GCCTGAGCACCCAG
*
65504 ATGGGCTGTGTCAT
63 ATGGGCGGTGTCAT
65518 AGCTCATCAC
Statistics
Matches: 64, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
75 4 0.06
76 54 0.84
77 6 0.09
ACGTcount: A:0.16, C:0.28, G:0.30, T:0.26
Consensus pattern (76 bp):
GACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGCACCCAGATG
GGCGGTGTCAT
Found at i:68077 original size:78 final size:78
Alignment explanation
Indices: 67982--68138 Score: 314
Period size: 78 Copynumber: 2.0 Consensus size: 78
67972 TCTTCAATGC
67982 GAAGCTTATGCTTGTTCCATCATCTCCGGTACCTCTGATTGAAAGTTTCCAACCAAATTATCCCC
1 GAAGCTTATGCTTGTTCCATCATCTCCGGTACCTCTGATTGAAAGTTTCCAACCAAATTATCCCC
68047 ATTCAACTTCTGT
66 ATTCAACTTCTGT
68060 GAAGCTTATGCTTGTTCCATCATCTCCGGTACCTCTGATTGAAAGTTTCCAACCAAATTATCCCC
1 GAAGCTTATGCTTGTTCCATCATCTCCGGTACCTCTGATTGAAAGTTTCCAACCAAATTATCCCC
68125 ATTCAACTTCTGT
66 ATTCAACTTCTGT
68138 G
1 G
68139 CTACCTGATG
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
78 79 1.00
ACGTcount: A:0.24, C:0.28, G:0.13, T:0.34
Consensus pattern (78 bp):
GAAGCTTATGCTTGTTCCATCATCTCCGGTACCTCTGATTGAAAGTTTCCAACCAAATTATCCCC
ATTCAACTTCTGT
Found at i:69624 original size:27 final size:27
Alignment explanation
Indices: 69573--69624 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
69563 AGTTTAATTG
**
69573 CTAATTACTGTTTACTTCTTTTTTTTA
1 CTAATTACTGTTTACTTCTCCTTTTTA
69600 CTAATTACTGTTTACTTCTCCTTTT
1 CTAATTACTGTTTACTTCTCCTTTT
69625 ACTCTTTAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.17, C:0.19, G:0.04, T:0.60
Consensus pattern (27 bp):
CTAATTACTGTTTACTTCTCCTTTTTA
Found at i:69747 original size:47 final size:47
Alignment explanation
Indices: 69614--70018 Score: 571
Period size: 47 Copynumber: 8.5 Consensus size: 47
69604 TTACTGTTTA
* * *
69614 CTTCTCCTTTTACTCTTTAGTTTAATTACTCAGAATTAAACTAGACTCT
1 CTTCTTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTA-AC-CT
* * * *
69663 GCTTACTTCCTTTACTGTTTAGTTTAATTACCTAGAATTAAGCTAACCT
1 -CTT-CTTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAACCT
* **
69712 TTTC-TCGTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAATAT
1 CTTCTTC-TTTTACTATTTAGTTTAATTACCCAGAATTAAACTAACCT
* *
69759 TTTCTCCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAACCT
1 CTTCTTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAACCT
69806 CTTCTTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAACCT
1 CTTCTTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAACCT
* * *
69853 CTTCTTCTTTTACTTTTTAGTTTAATTACCCAAAACTAAACTAACCT
1 CTTCTTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAACCT
*
69900 CTTCTTCTTTTACTTTTTAGTTTAATTACCCAGAATTAAACTAACCT
1 CTTCTTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAACCT
* *
69947 CTTTTTCTTTTAC-ATTTTAGTTTAATTACCAAGAATTAAACTAACCT
1 CTTCTTCTTTTACTA-TTTAGTTTAATTACCCAGAATTAAACTAACCT
*
69994 CTTCTTCTTTTACTTTTTAGTTTAA
1 CTTCTTCTTTTACTATTTAGTTTAA
70019 CTAACCTCTT
Statistics
Matches: 322, Mismatches: 28, Indels: 13
0.89 0.08 0.04
Matches are distributed among these distances:
46 2 0.01
47 276 0.86
48 3 0.01
49 2 0.01
50 5 0.02
51 34 0.11
ACGTcount: A:0.28, C:0.20, G:0.05, T:0.46
Consensus pattern (47 bp):
CTTCTTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAACCT
Found at i:70025 original size:32 final size:32
Alignment explanation
Indices: 69985--70050 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
69975 CCAAGAATTA
*
69985 AACTAACCTCTTCTTCTTTTACTTTTTAGTTT
1 AACTAACCTCTTCTTCTTTTACTATTTAGTTT
70017 AACTAACCTCTTCTTCTTTTACTATTTAGTTT
1 AACTAACCTCTTCTTCTTTTACTATTTAGTTT
70049 AA
1 AA
70051 TTACCCAGAA
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:0.23, C:0.21, G:0.03, T:0.53
Consensus pattern (32 bp):
AACTAACCTCTTCTTCTTTTACTATTTAGTTT
Found at i:70038 original size:126 final size:126
Alignment explanation
Indices: 69891--70410 Score: 729
Period size: 126 Copynumber: 4.0 Consensus size: 126
69881 CCCAAAACTA
* *
69891 AACTAACCTCTTCTTCTTTTACTTTTTAGTTTAATTACCCAGAATTAAACTAACCTCTTTTTCTT
1 AACTAACCTCTTCTTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAACCTCTTCTTCTT
*
69956 TTACAT-TTTAGTTTAATTACCAAGAATTAAACTAACCTCTTCTTCTTTTACTTTTTAGTTT
66 TTAC-TGTTTAGTTTAATTACCCAGAATTAAACTAACCTCTTCTTCTTTTACTTTTTAGTTT
70017 AACTAACCTCTTCTTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAACCTCTTCTTCTT
1 AACTAACCTCTTCTTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAACCTCTTCTTCTT
* * *
70082 TTACTGTTTAGTTTAATTATCCAGAATTAAACTAACCTATTATTCTTTTACTTTTTAGTTT
66 TTACTGTTTAGTTTAATTACCCAGAATTAAACTAACCTCTTCTTCTTTTACTTTTTAGTTT
* * * * *
70143 AACTAACCTCTTTTTCTTTTACTAATTAGTTAAATTACCCATAATTGAACTAACCTCTTCTTCTT
1 AACTAACCTCTTCTTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAACCTCTTCTTCTT
*
70208 TTACTGTTTAGTTTAATTACCCAGAATTAAACTAGCCTCTTCTTCTTTTACTATTTAGTTTAATT
66 TTACTGTTTAGTTTAATTACCCAGAATTAAACTAACCTCTTCTTCTTTTAC-------TTT--TT
*
70273 ACCCAGAATTA
122 ----AG--TTT
*
70284 AACTAACCTCTT-TTCTTTTACTGTTTAGTTTAATTACCCAGAATTAAACTAACCTCTTCTTCTT
1 AACTAACCTCTTCTTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAACCTCTTCTTCTT
* * *
70348 TTAATGTTTAGTTTAATTACCCAGAATTAAACTAGCCTCTTCTTCTTTTACTTTTTACTTT
66 TTACTGTTTAGTTTAATTACCCAGAATTAAACTAACCTCTTCTTCTTTTACTTTTTAGTTT
70409 AA
1 AA
70411 TTACCCAGAA
Statistics
Matches: 354, Mismatches: 24, Indels: 33
0.86 0.06 0.08
Matches are distributed among these distances:
125 5 0.01
126 225 0.64
127 1 0.00
131 2 0.01
133 6 0.02
135 2 0.01
139 2 0.01
140 97 0.27
141 14 0.04
ACGTcount: A:0.28, C:0.20, G:0.05, T:0.47
Consensus pattern (126 bp):
AACTAACCTCTTCTTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAACCTCTTCTTCTT
TTACTGTTTAGTTTAATTACCCAGAATTAAACTAACCTCTTCTTCTTTTACTTTTTAGTTT
Found at i:70069 original size:79 final size:79
Alignment explanation
Indices: 69938--70097 Score: 277
Period size: 79 Copynumber: 2.0 Consensus size: 79
69928 CCCAGAATTA
*
69938 AACTAACCTCTTTTTCTTTTACATTTTAGTTTAATTACCAAGAATTAAACTAACCTCTTCTTCTT
1 AACTAACCTCTTCTTCTTTTACATTTTAGTTTAATTACCAAGAATTAAACTAACCTCTTCTTCTT
*
70003 TTACTTTTTAGTTT
66 TTACTGTTTAGTTT
*
70017 AACTAACCTCTTCTTCTTTTAC-TATTTAGTTTAATTACCCAGAATTAAACTAACCTCTTCTTCT
1 AACTAACCTCTTCTTCTTTTACAT-TTTAGTTTAATTACCAAGAATTAAACTAACCTCTTCTTCT
70081 TTTACTGTTTAGTTT
65 TTTACTGTTTAGTTT
70096 AA
1 AA
70098 TTATCCAGAA
Statistics
Matches: 77, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
78 1 0.01
79 76 0.99
ACGTcount: A:0.27, C:0.20, G:0.04, T:0.49
Consensus pattern (79 bp):
AACTAACCTCTTCTTCTTTTACATTTTAGTTTAATTACCAAGAATTAAACTAACCTCTTCTTCTT
TTACTGTTTAGTTT
Found at i:70086 original size:47 final size:47
Alignment explanation
Indices: 70017--70144 Score: 211
Period size: 47 Copynumber: 2.7 Consensus size: 47
70007 TTTTTAGTTT
70017 AACTAACCTCTTCTTCTTTTACTATTTAGTTTAATTACCCAGAATTA
1 AACTAACCTCTTCTTCTTTTACTATTTAGTTTAATTACCCAGAATTA
* *
70064 AACTAACCTCTTCTTCTTTTACTGTTTAGTTTAATTATCCAGAATTA
1 AACTAACCTCTTCTTCTTTTACTATTTAGTTTAATTACCCAGAATTA
* * *
70111 AACTAACCTATTATTCTTTTACTTTTTAGTTTAA
1 AACTAACCTCTTCTTCTTTTACTATTTAGTTTAA
70145 CTAACCTCTT
Statistics
Matches: 76, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 76 1.00
ACGTcount: A:0.29, C:0.19, G:0.05, T:0.48
Consensus pattern (47 bp):
AACTAACCTCTTCTTCTTTTACTATTTAGTTTAATTACCCAGAATTA
Found at i:70147 original size:79 final size:79
Alignment explanation
Indices: 70064--70223 Score: 230
Period size: 79 Copynumber: 2.0 Consensus size: 79
70054 CCCAGAATTA
** * *
70064 AACTAACCTCTTCTTCTTTTACTGTTTAGTTTAATTATCCAGAATTAAACTAACCTATTATTCTT
1 AACTAACCTCTTCTTCTTTTACTAATTAGTTAAATTACCCAGAATTAAACTAACCTATTATTCTT
*
70129 TTACTTTTTAGTTT
66 TTACTGTTTAGTTT
* * * * *
70143 AACTAACCTCTTTTTCTTTTACTAATTAGTTAAATTACCCATAATTGAACTAACCTCTTCTTCTT
1 AACTAACCTCTTCTTCTTTTACTAATTAGTTAAATTACCCAGAATTAAACTAACCTATTATTCTT
70208 TTACTGTTTAGTTT
66 TTACTGTTTAGTTT
70222 AA
1 AA
70224 TTACCCAGAA
Statistics
Matches: 71, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
79 71 1.00
ACGTcount: A:0.28, C:0.19, G:0.05, T:0.49
Consensus pattern (79 bp):
AACTAACCTCTTCTTCTTTTACTAATTAGTTAAATTACCCAGAATTAAACTAACCTATTATTCTT
TTACTGTTTAGTTT
Found at i:70172 original size:32 final size:32
Alignment explanation
Indices: 70111--70173 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
70101 TCCAGAATTA
**
70111 AACTAACCTATTATTCTTTTACTTTTTAGTTT
1 AACTAACCTATTATTCTTTTACTAATTAGTTT
* *
70143 AACTAACCTCTTTTTCTTTTACTAATTAGTT
1 AACTAACCTATTATTCTTTTACTAATTAGTT
70174 AAATTACCCA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.25, C:0.17, G:0.03, T:0.54
Consensus pattern (32 bp):
AACTAACCTATTATTCTTTTACTAATTAGTTT
Found at i:70197 original size:47 final size:47
Alignment explanation
Indices: 70143--70457 Score: 506
Period size: 47 Copynumber: 6.7 Consensus size: 47
70133 TTTTTAGTTT
* * * * *
70143 AACTAACCTCTTTTTCTTTTACTAATTAGTTAAATTACCCATAATTG
1 AACTAACCTCTTCTTCTTTTACTATTTAGTTTAATTACCCAGAATTA
*
70190 AACTAACCTCTTCTTCTTTTACTGTTTAGTTTAATTACCCAGAATTA
1 AACTAACCTCTTCTTCTTTTACTATTTAGTTTAATTACCCAGAATTA
*
70237 AACTAGCCTCTTCTTCTTTTACTATTTAGTTTAATTACCCAGAATTA
1 AACTAACCTCTTCTTCTTTTACTATTTAGTTTAATTACCCAGAATTA
*
70284 AACTAACCTCTT-TTCTTTTACTGTTTAGTTTAATTACCCAGAATTA
1 AACTAACCTCTTCTTCTTTTACTATTTAGTTTAATTACCCAGAATTA
* *
70330 AACTAACCTCTTCTTCTTTTAATGTTTAGTTTAATTACCCAGAATTA
1 AACTAACCTCTTCTTCTTTTACTATTTAGTTTAATTACCCAGAATTA
* * *
70377 AACTAGCCTCTTCTTCTTTTACTTTTTACTTTAATTACCCAGAATTA
1 AACTAACCTCTTCTTCTTTTACTATTTAGTTTAATTACCCAGAATTA
70424 AACTAACCTCTTCTTCTTTTACTATTTAGTTTAA
1 AACTAACCTCTTCTTCTTTTACTATTTAGTTTAA
70458 AACTATCTTC
Statistics
Matches: 249, Mismatches: 18, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
46 45 0.18
47 204 0.82
ACGTcount: A:0.28, C:0.21, G:0.05, T:0.46
Consensus pattern (47 bp):
AACTAACCTCTTCTTCTTTTACTATTTAGTTTAATTACCCAGAATTA
Found at i:70370 original size:140 final size:140
Alignment explanation
Indices: 70143--70457 Score: 540
Period size: 140 Copynumber: 2.2 Consensus size: 140
70133 TTTTTAGTTT
* * * *
70143 AACTAACCTCTTTTTCTTTTACTAATTAGTTAAATTACCCATAATTGAACTAACCTCTTCTTCTT
1 AACTAACCTC-TTTTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAACCTCTTCTTCTT
* *
70208 TTACTGTTTAGTTTAATTACCCAGAATTAAACTAGCCTCTTCTTCTTTTACTATTTAGTTTAATT
65 TTAATGTTTAGTTTAATTACCCAGAATTAAACTAGCCTCTTCTTCTTTTACTATTTACTTTAATT
70273 ACCCAGAATTA
130 ACCCAGAATTA
*
70284 AACTAACCTCTTTTCTTTTACTGTTTAGTTTAATTACCCAGAATTAAACTAACCTCTTCTTCTTT
1 AACTAACCTCTTTTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAACCTCTTCTTCTTT
*
70349 TAATGTTTAGTTTAATTACCCAGAATTAAACTAGCCTCTTCTTCTTTTACTTTTTACTTTAATTA
66 TAATGTTTAGTTTAATTACCCAGAATTAAACTAGCCTCTTCTTCTTTTACTATTTACTTTAATTA
70414 CCCAGAATTA
131 CCCAGAATTA
70424 AACTAACCTCTTCTTCTTTTACTATTTAGTTTAA
1 AACTAACCTCTT-TTCTTTTACTATTTAGTTTAA
70458 AACTATCTTC
Statistics
Matches: 164, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
140 134 0.82
141 30 0.18
ACGTcount: A:0.28, C:0.21, G:0.05, T:0.46
Consensus pattern (140 bp):
AACTAACCTCTTTTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAACCTCTTCTTCTTT
TAATGTTTAGTTTAATTACCCAGAATTAAACTAGCCTCTTCTTCTTTTACTATTTACTTTAATTA
CCCAGAATTA
Found at i:81027 original size:19 final size:18
Alignment explanation
Indices: 80994--81029 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
80984 TTGAGATAAT
80994 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
81012 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
81030 TGAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:82071 original size:22 final size:20
Alignment explanation
Indices: 82042--82091 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
82032 GTAAGTGATG
*
82042 AAGTAGTGAAATTGATGATTA
1 AAGTAGTGAAATTG-TGAATA
*
82063 AAGTGAGTGAATTTGTGAATA
1 AAGT-AGTGAAATTGTGAATA
82084 AAGGTAGT
1 AA-GTAGT
82092 AGAAGAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
21 14 0.56
22 11 0.44
ACGTcount: A:0.40, C:0.00, G:0.28, T:0.32
Consensus pattern (20 bp):
AAGTAGTGAAATTGTGAATA
Found at i:92060 original size:5 final size:5
Alignment explanation
Indices: 92045--92081 Score: 58
Period size: 5 Copynumber: 7.6 Consensus size: 5
92035 GTAAAACATT
*
92045 AAAAC -AAAC AAAAC AAAAC AAACC AAAAC AAAAC AAA
1 AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAA
92082 GCAACCATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
4 4 0.14
5 25 0.86
ACGTcount: A:0.78, C:0.22, G:0.00, T:0.00
Consensus pattern (5 bp):
AAAAC
Found at i:92073 original size:15 final size:14
Alignment explanation
Indices: 92045--92081 Score: 65
Period size: 15 Copynumber: 2.6 Consensus size: 14
92035 GTAAAACATT
92045 AAAACAAACAAAAC
1 AAAACAAACAAAAC
92059 AAAACAAACCAAAAC
1 AAAACAAA-CAAAAC
92074 AAAACAAA
1 AAAACAAA
92082 GCAACCATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 8 0.36
15 14 0.64
ACGTcount: A:0.78, C:0.22, G:0.00, T:0.00
Consensus pattern (14 bp):
AAAACAAACAAAAC
Found at i:96260 original size:60 final size:60
Alignment explanation
Indices: 96150--96327 Score: 295
Period size: 60 Copynumber: 3.0 Consensus size: 60
96140 ACTTATATTT
* * * *
96150 TAAATGCAACTAATAAAAACTTTTTTAGCAAACGAC-AACTAATGTTAAATTGATGGAGTTC
1 TAAATGCAACAAATGAAAAC-ATTTT-GCAAATGACAAACTAATGTTAAATTGATGGAGTTC
96211 TAAATGCAACAAATGAAAACATTTTGCAAATGACAAACTAATGTTAAATTGATGGAGTTC
1 TAAATGCAACAAATGAAAACATTTTGCAAATGACAAACTAATGTTAAATTGATGGAGTTC
96271 TAAATGCAACAAATGAAAACATTTTGCAAATGACAAACTAATGTTAAATTGATGGAG
1 TAAATGCAACAAATGAAAACATTTTGCAAATGACAAACTAATGTTAAATTGATGGAG
96328 AATTGCTAAA
Statistics
Matches: 112, Mismatches: 4, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
59 8 0.07
60 86 0.77
61 18 0.16
ACGTcount: A:0.45, C:0.12, G:0.15, T:0.29
Consensus pattern (60 bp):
TAAATGCAACAAATGAAAACATTTTGCAAATGACAAACTAATGTTAAATTGATGGAGTTC
Found at i:96601 original size:29 final size:29
Alignment explanation
Indices: 96523--96598 Score: 109
Period size: 29 Copynumber: 2.7 Consensus size: 29
96513 AAATGAACTT
*
96523 AAAATGATCAAAATGCCCCTGAATATGCA
1 AAAATGACCAAAATGCCCCTGAATATGCA
* *
96552 AAAATGACCATAATGCCCCTGAATGTG-A
1 AAAATGACCAAAATGCCCCTGAATATGCA
*
96580 AAAATGACCAAAAAGCCCC
1 AAAATGACCAAAATGCCCC
96599 CTGGGTTTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
28 18 0.43
29 24 0.57
ACGTcount: A:0.45, C:0.24, G:0.14, T:0.17
Consensus pattern (29 bp):
AAAATGACCAAAATGCCCCTGAATATGCA
Done.