Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018103.1 Corchorus olitorius cultivar O-4 contig18136, 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: 67129
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Found at i:1826 original size:14 final size:14
Alignment explanation
Indices: 1807--1833 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1797 TACAACTTTC
1807 ATTTTAATGTTTTA
1 ATTTTAATGTTTTA
1821 ATTTTAATGTTTT
1 ATTTTAATGTTTT
1834 GATTCTAAAA
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:0.26, C:0.00, G:0.07, T:0.67
Consensus pattern (14 bp):
ATTTTAATGTTTTA
Found at i:3290 original size:19 final size:19
Alignment explanation
Indices: 3268--3315 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
3258 TATGGAAGTT
*
3268 ATTTTCTTTTTTTTTTTTC
1 ATTTTCTTTTTCTTTTTTC
*
3287 ATTTTGTTTTTCTTTTTTC
1 ATTTTCTTTTTCTTTTTTC
*
3306 TTTTTACTTT
1 ATTTT-CTTT
3316 GGGCGGGCTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 21 0.88
20 3 0.12
ACGTcount: A:0.06, C:0.10, G:0.02, T:0.81
Consensus pattern (19 bp):
ATTTTCTTTTTCTTTTTTC
Found at i:4661 original size:19 final size:19
Alignment explanation
Indices: 4622--4657 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
4612 TTTTTAAGTA
4622 AAAAATATAATATATAAAT
1 AAAAATATAATATATAAAT
*
4641 AAAAATTTAATAT-TAAA
1 AAAAATATAATATATAAA
4658 ATAATTAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
AAAAATATAATATATAAAT
Found at i:5872 original size:10 final size:10
Alignment explanation
Indices: 5853--5882 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
5843 GAGAACTCGG
*
5853 ATTTTATTTT
1 ATTTTTTTTT
5863 ATTTTTTTTT
1 ATTTTTTTTT
5873 ATTTTTTTTT
1 ATTTTTTTTT
5883 TAAAAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (10 bp):
ATTTTTTTTT
Found at i:5874 original size:15 final size:14
Alignment explanation
Indices: 5854--5883 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
5844 AGAACTCGGA
5854 TTTTATTTTATTTTT
1 TTTTATTTT-TTTTT
5869 TTTTATTTTTTTTT
1 TTTTATTTTTTTTT
5883 T
1 T
5884 AAAAAAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (14 bp):
TTTTATTTTTTTTT
Found at i:9933 original size:39 final size:39
Alignment explanation
Indices: 9879--9973 Score: 190
Period size: 39 Copynumber: 2.4 Consensus size: 39
9869 TAGGACTATT
9879 GCCATAAAACCTAATTTTGGGATTGAGATTGGAGTATGA
1 GCCATAAAACCTAATTTTGGGATTGAGATTGGAGTATGA
9918 GCCATAAAACCTAATTTTGGGATTGAGATTGGAGTATGA
1 GCCATAAAACCTAATTTTGGGATTGAGATTGGAGTATGA
9957 GCCATAAAACCTAATTT
1 GCCATAAAACCTAATTT
9974 GGTATGAGCC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 56 1.00
ACGTcount: A:0.35, C:0.13, G:0.22, T:0.31
Consensus pattern (39 bp):
GCCATAAAACCTAATTTTGGGATTGAGATTGGAGTATGA
Found at i:12555 original size:11 final size:11
Alignment explanation
Indices: 12520--12558 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
12510 AGGTAGGGTG
*
12520 TTTCATTTTCT
1 TTTCCTTTTCT
12531 TTT-CTTTT-T
1 TTTCCTTTTCT
12540 TTTCCTTTTCT
1 TTTCCTTTTCT
12551 TTTCCTTT
1 TTTCCTTT
12559 CTCCTTTCTC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 4 0.16
10 9 0.36
11 12 0.48
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.77
Consensus pattern (11 bp):
TTTCCTTTTCT
Found at i:12743 original size:3 final size:3
Alignment explanation
Indices: 12737--12762 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
12727 TTTCATAGTC
12737 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
12763 TAGACACTGT
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:20400 original size:14 final size:14
Alignment explanation
Indices: 20381--20408 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
20371 CCACCTTAAT
20381 TTAACAGATTTCTA
1 TTAACAGATTTCTA
20395 TTAACAGATTTCTA
1 TTAACAGATTTCTA
20409 CATCTTGAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.14, G:0.07, T:0.43
Consensus pattern (14 bp):
TTAACAGATTTCTA
Found at i:23652 original size:21 final size:21
Alignment explanation
Indices: 23626--23671 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
23616 GAAGAAGCTT
23626 AAGTTCAACCTCAAGTTCATC
1 AAGTTCAACCTCAAGTTCATC
* *
23647 AAGTTCAACCTCCATTTCATC
1 AAGTTCAACCTCAAGTTCATC
23668 AAGT
1 AAGT
23672 CTATTCAAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.33, C:0.28, G:0.09, T:0.30
Consensus pattern (21 bp):
AAGTTCAACCTCAAGTTCATC
Found at i:27845 original size:27 final size:27
Alignment explanation
Indices: 27815--27888 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 27
27805 AGAATCACCT
**
27815 AGGGGCATTTTGGTCATTTGCATATTC
1 AGGGGCATTTTGGTCATTTGCATACCC
**
27842 AGGGGCATTTTGGTCATTTGTGTACCC
1 AGGGGCATTTTGGTCATTTGCATACCC
* *
27869 AAGGGCATTTTGGCCATTTG
1 AGGGGCATTTTGGTCATTTG
27889 GACCCTTTAT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.18, C:0.16, G:0.28, T:0.38
Consensus pattern (27 bp):
AGGGGCATTTTGGTCATTTGCATACCC
Found at i:30634 original size:41 final size:41
Alignment explanation
Indices: 30536--30634 Score: 110
Period size: 41 Copynumber: 2.4 Consensus size: 41
30526 AAATTCGTTT
* * * *
30536 AATTTGATCCCTGATCTAGGATTCTATTTTCTGATTAATGC
1 AATTTGGTCCCTGATTTAGGATTCTATTTACTGATTAATAC
* * *
30577 AATTTGGTCTCTGATTTAGGATTTTATTTACT-ATTTGATAC
1 AATTTGGTCCCTGATTTAGGATTCTATTTACTGA-TTAATAC
*
30618 AATTTGGTCCCGGATTT
1 AATTTGGTCCCTGATTT
30635 TAGAAACTTA
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
40 1 0.02
41 47 0.98
ACGTcount: A:0.23, C:0.14, G:0.16, T:0.46
Consensus pattern (41 bp):
AATTTGGTCCCTGATTTAGGATTCTATTTACTGATTAATAC
Found at i:31891 original size:35 final size:35
Alignment explanation
Indices: 31852--31994 Score: 112
Period size: 35 Copynumber: 3.9 Consensus size: 35
31842 GAATACTTTG
31852 AAAACTGGATGGGAACTTTCCCAATTTGAAAACTT
1 AAAACTGGATGGGAACTTTCCCAATTTGAAAACTT
* * *
31887 AAAACTGAAAATGACGGGAACCTTCCCTAAATTGAAAAC-T
1 AAAACTG-----GATGGGAACTTTCCC-AATTTGAAAACTT
* **
31927 AAAACCT-GATGGGAACTTTCCCAATTTGGCAATTTT
1 AAAA-CTGGATGGGAACTTTCCCAATTT-GAAAACTT
* *
31963 GAAAACTGG-TGGGAACTTTCCCGACTTGAAAA
1 -AAAACTGGATGGGAACTTTCCCAATTTGAAAA
31995 AAAGCTAAAT
Statistics
Matches: 84, Mismatches: 13, Indels: 22
0.71 0.11 0.18
Matches are distributed among these distances:
34 4 0.05
35 26 0.31
36 19 0.23
37 5 0.06
40 18 0.21
41 12 0.14
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.26
Consensus pattern (35 bp):
AAAACTGGATGGGAACTTTCCCAATTTGAAAACTT
Found at i:32117 original size:53 final size:53
Alignment explanation
Indices: 31959--32295 Score: 463
Period size: 53 Copynumber: 6.4 Consensus size: 53
31949 AATTTGGCAA
* *
31959 TTTTGAAAACTGGTGGGAACTTTCCCGACTTGAAAAAAAGCTAAATTGAATAC
1 TTTTGAAAACTGATGGGAACTTTCCCGACTTGAAAAAGAGCTAAATTGAATAC
* * *
32012 -TTTGAAGACTGATGGGAACTTT-CC--C-T-AAATTAGAAGCTAAATTGAATGC
1 TTTTGAAAACTGATGGGAACTTTCCCGACTTGAAA-AAG-AGCTAAATTGAATAC
* *
32061 TTTTGAAAACTGATGGGAACTTTCCTGACTTGAGAAAGAGCTAAATTGAATAC
1 TTTTGAAAACTGATGGGAACTTTCCCGACTTGAAAAAGAGCTAAATTGAATAC
* * * *
32114 TTTTGAAAACTGATGGGAACTTTCCCAATTTGTAAAAATAGCTAGATTGAATAC
1 TTTTGAAAACTGATGGGAACTTTCCCGACTTG-AAAAAGAGCTAAATTGAATAC
* *
32168 -TTTGAAAACTGGTGGGAACTTTCCCGACTTGAAAAAGAGATAAATTGAATAC
1 TTTTGAAAACTGATGGGAACTTTCCCGACTTGAAAAAGAGCTAAATTGAATAC
32220 TTTTGAAAACTGATGGGAACTTTCCCGACTTGAAAAAGAGCTAAATTGAATAC
1 TTTTGAAAACTGATGGGAACTTTCCCGACTTGAAAAAGAGCTAAATTGAATAC
**
32273 TTTTGAAAACTGATAAGAACTTT
1 TTTTGAAAACTGATGGGAACTTT
32296 TTTTTTAGTT
Statistics
Matches: 248, Mismatches: 26, Indels: 20
0.84 0.09 0.07
Matches are distributed among these distances:
47 3 0.01
48 2 0.01
49 15 0.06
50 21 0.08
51 3 0.01
52 38 0.15
53 143 0.58
54 21 0.08
55 2 0.01
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.30
Consensus pattern (53 bp):
TTTTGAAAACTGATGGGAACTTTCCCGACTTGAAAAAGAGCTAAATTGAATAC
Found at i:36044 original size:41 final size:41
Alignment explanation
Indices: 35997--36899 Score: 727
Period size: 40 Copynumber: 22.7 Consensus size: 41
35987 ACATTCCTAA
* *
35997 TTTGCCCTTCCTCATCGGAAGGTGTTGTCATCATTCCCCAA
1 TTTGCCCTTCCTCATCGGAAGGTGTTGTCATCATTTCCCAG
* * * ** *
36038 ATTGCCCTTCCTCATCGGAA-G-G-TCTCAGCA-TTCGTAA
1 TTTGCCCTTCCTCATCGGAAGGTGTTGTCATCATTTCCCAG
* *
36075 TTTACCCTTCCTCATCGGAAGGTGTTGTCATCA-TTCTCAG
1 TTTGCCCTTCCTCATCGGAAGGTGTTGTCATCATTTCCCAG
* *
36115 TTTGCCCTTCCTCATCGGAAGGTGTTGTCAGCATTTCCCAA
1 TTTGCCCTTCCTCATCGGAAGGTGTTGTCATCATTTCCCAG
* *
36156 TTTGCCCTCCCTCATCGGAAGGTGTTGTCATCA-TTCTCAG
1 TTTGCCCTTCCTCATCGGAAGGTGTTGTCATCATTTCCCAG
* * *
36196 TTTGCCCTTCCTCATTGGAAGGTGTTGTCAGCATTTCCCAA
1 TTTGCCCTTCCTCATCGGAAGGTGTTGTCATCATTTCCCAG
* * *
36237 TTTGCCCTTCCTCATCGGTAGGTATTGTCA--ATAT-CCAG
1 TTTGCCCTTCCTCATCGGAAGGTGTTGTCATCATTTCCCAG
* * * *
36275 TTTGCCCTTCCCCATCGGAAGGTGTTGTCAGCATTTACCAA
1 TTTGCCCTTCCTCATCGGAAGGTGTTGTCATCATTTCCCAG
* * *
36316 TTTGCCCTTCC-CCTCCAGAAGGTGTTGTCAGCA--TCCTCAG
1 TTTGCCCTTCCTCAT-CGGAAGGTGTTGTCATCATTTCC-CAG
* * * *
36356 TTTGCCCTTCCCCATCGGAAGGTGTTGTCAACATTTCGCAA
1 TTTGCCCTTCCTCATCGGAAGGTGTTGTCATCATTTCCCAG
36397 TTTGCCCTTCCTCATCGGAAGGTGTTG--------T--CAG
1 TTTGCCCTTCCTCATCGGAAGGTGTTGTCATCATTTCCCAG
* ** * * *
36428 TTTGCCCTTTCTCATCGGAAAATGTTAT--TGAGTTTACC-G
1 TTTGCCCTTCCTCATCGGAAGGTGTTGTCATCA-TTTCCCAG
* *
36467 ATTTGCCCTTCCTCATCGGAAGGTGTTGT-TTACCTTTCCCAG
1 -TTTGCCCTTCCTCATCGGAAGGTGTTGTCAT-CATTTCCCAG
* * * * *
36509 TTTGCCCTTCCTCACCGAAAGGTGTTGT-TTAAGTTTACCAG
1 TTTGCCCTTCCTCATCGGAAGGTGTTGTCATCA-TTTCCCAG
* * **
36550 TTTGTCCC-TCCTCATCAGAAGGTGTTGT--TAAGTTTAGCAG
1 TTTG-CCCTTCCTCATCGGAAGGTGTTGTCATCA-TTTCCCAG
* * ** *
36590 TTTGTCCTTCCTCATCGGAAGGTGTTGTTAAGA-TTACCAG
1 TTTGCCCTTCCTCATCGGAAGGTGTTGTCATCATTTCCCAG
36630 TTTGCCCTTCCTCATCGGAAGGTGTTGTCAGT-ATTT-CCAG
1 TTTGCCCTTCCTCATCGGAAGGTGTTGTCA-TCATTTCCCAG
* * * **
36670 TTTGCCCCTCCTCATTGGAAGGTGTTGTCAGCATTTGTCAG
1 TTTGCCCTTCCTCATCGGAAGGTGTTGTCATCATTTCCCAG
* * *
36711 TTTGCCTTTTCTCATCGGAAGGTGTTGT-TTACA-TTCCCAG
1 TTTGCCCTTCCTCATCGGAAGGTGTTGTCAT-CATTTCCCAG
* *
36751 TTTGCCCTTCCTCATCGGAAAGTGTTGT-TTACA-TT-CCAG
1 TTTGCCCTTCCTCATCGGAAGGTGTTGTCAT-CATTTCCCAG
* * * * *
36790 TTTGCTCTTCCCCATCAGAAGGTGTTGT--TAAGTTTACCAG
1 TTTGCCCTTCCTCATCGGAAGGTGTTGTCATCA-TTTCCCAG
* * * * *
36830 TTTGCCCTTCCTCATCAGAAGATGTTATTTATCTTTTCCCAG
1 TTTGCCCTTCCTCATCGGAAGGTGTT-GTCATCATTTCCCAG
*
36872 TCTT-CCCTTCCTCACCGGAAGGTGTTGT
1 T-TTGCCCTTCCTCATCGGAAGGTGTTGT
36900 TCCTATTCCT
Statistics
Matches: 713, Mismatches: 106, Indels: 86
0.79 0.12 0.10
Matches are distributed among these distances:
31 25 0.04
33 1 0.00
37 23 0.03
38 39 0.05
39 40 0.06
40 305 0.43
41 243 0.34
42 34 0.05
43 3 0.00
ACGTcount: A:0.17, C:0.27, G:0.20, T:0.36
Consensus pattern (41 bp):
TTTGCCCTTCCTCATCGGAAGGTGTTGTCATCATTTCCCAG
Found at i:36188 original size:81 final size:81
Alignment explanation
Indices: 35990--36899 Score: 777
Period size: 81 Copynumber: 11.4 Consensus size: 81
35980 TCCCTCAACA
* * **
35990 TTCCTAATTTGCCCTTCCTCATCGGAAGGTGTTGTCATCATTCCCCAAATTGCCCTTCCTCATCG
1 TTCCCAATTTGCCCTTCCTCATCGGAAGGTGTTGTCATCATT-CTCAGTTTGCCCTTCCTCATCG
*
36055 GAA-G-G-TCTCAGCA-
65 GAAGGTGTTGTCAGCAT
** *
36068 TTCGTAATTTACCCTTCCTCATCGGAAGGTGTTGTCATCATTCTCAGTTTGCCCTTCCTCATCGG
1 TTCCCAATTTGCCCTTCCTCATCGGAAGGTGTTGTCATCATTCTCAGTTTGCCCTTCCTCATCGG
36133 AAGGTGTTGTCAGCAT
66 AAGGTGTTGTCAGCAT
* *
36149 TTCCCAATTTGCCCTCCCTCATCGGAAGGTGTTGTCATCATTCTCAGTTTGCCCTTCCTCATTGG
1 TTCCCAATTTGCCCTTCCTCATCGGAAGGTGTTGTCATCATTCTCAGTTTGCCCTTCCTCATCGG
36214 AAGGTGTTGTCAGCAT
66 AAGGTGTTGTCAGCAT
* * *
36230 TTCCCAATTTGCCCTTCCTCATCGGTAGGTATTGTCA--ATATC-CAGTTTGCCCTTCCCCATCG
1 TTCCCAATTTGCCCTTCCTCATCGGAAGGTGTTGTCATCAT-TCTCAGTTTGCCCTTCCTCATCG
36292 GAAGGTGTTGTCAGCAT
65 GAAGGTGTTGTCAGCAT
* * * * * *
36309 TTACCAATTTGCCCTTCC-CCTCCAGAAGGTGTTGTCAGCATCCTCAGTTTGCCCTTCCCCATCG
1 TTCCCAATTTGCCCTTCCTCAT-CGGAAGGTGTTGTCATCATTCTCAGTTTGCCCTTCCTCATCG
*
36373 GAAGGTGTTGTCAACAT
65 GAAGGTGTTGTCAGCAT
* *
36390 TTCGCAATTTGCCCTTCCTCATCGGAAGGTGTTG---------TCAGTTTGCCCTTTCTCATCGG
1 TTCCCAATTTGCCCTTCCTCATCGGAAGGTGTTGTCATCATTCTCAGTTTGCCCTTCCTCATCGG
** * *
36446 AAAATGTTAT-TG-AGT
66 AAGGTGTTGTCAGCA-T
* * * * * * *
36461 TTACCGATTTGCCCTTCCTCATCGGAAGGTGTTGTTTACCTTTCCCAGTTTGCCCTTCCTCACCG
1 TTCCCAATTTGCCCTTCCTCATCGGAAGGTGTTG-TCATCATTCTCAGTTTGCCCTTCCTCATCG
* *
36526 AAAGGTGTTGTTTA--AGT
65 GAAGGTGTTG-TCAGCA-T
* * * * *** ** *
36543 TTACCAGTTTGTCCC-TCCTCATCAGAAGGTGTTGTTAAGTTTAGCAGTTTGTCCTTCCTCATCG
1 TTCCCAATTTG-CCCTTCCTCATCGGAAGGTGTTGTCATCATTCTCAGTTTGCCCTTCCTCATCG
*
36607 GAAGGTGTTGTTAAG-A-
65 GAAGGTGTTG-TCAGCAT
* * * *
36623 TTACCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTCAGT-ATT-TCCAGTTTGCCCCTCCTCATT
1 TTCCCAATTTGCCCTTCCTCATCGGAAGGTGTTGTCA-TCATTCT-CAGTTTGCCCTTCCTCATC
36686 GGAAGGTGTTGTCAGCAT
64 GGAAGGTGTTGTCAGCAT
** * * * * *
36704 TTGTCAGTTTGCCTTTTCTCATCGGAAGGTGTTGT-TTACATTCCCAGTTTGCCCTTCCTCATCG
1 TTCCCAATTTGCCCTTCCTCATCGGAAGGTGTTGTCAT-CATTCTCAGTTTGCCCTTCCTCATCG
* *
36768 GAAAGTGTTGTTTA-CA-
65 GAAGGTGTTG-TCAGCAT
* * * * * *** *
36784 TT-CCAGTTTGCTCTTCCCCATCAGAAGGTGTTGTTAAGTTTAC-CAGTTTGCCCTTCCTCATCA
1 TTCCCAATTTGCCCTTCCTCATCGGAAGGTGTTGTCATCATT-CTCAGTTTGCCCTTCCTCATCG
* * * * *
36847 GAAGATGTTATTTATCTT
65 GAAGGTGTT-GTCAGCAT
* *
36865 TTCCCAGTCTT-CCCTTCCTCACCGGAAGGTGTTGT
1 TTCCCAAT-TTGCCCTTCCTCATCGGAAGGTGTTGT
36900 TCCTATTCCT
Statistics
Matches: 697, Mismatches: 94, Indels: 78
0.80 0.11 0.09
Matches are distributed among these distances:
70 1 0.00
71 32 0.05
72 27 0.04
77 22 0.03
78 43 0.06
79 131 0.19
80 75 0.11
81 300 0.43
82 61 0.09
83 5 0.01
ACGTcount: A:0.17, C:0.27, G:0.20, T:0.36
Consensus pattern (81 bp):
TTCCCAATTTGCCCTTCCTCATCGGAAGGTGTTGTCATCATTCTCAGTTTGCCCTTCCTCATCGG
AAGGTGTTGTCAGCAT
Found at i:36994 original size:50 final size:49
Alignment explanation
Indices: 36913--37060 Score: 178
Period size: 49 Copynumber: 3.0 Consensus size: 49
36903 TATTCCTGTT
*
36913 ATGCCCCTTCCTGGT-TGGAAGGTCTCC-GTTTT-CTTTATTTTAATT-CAAAA
1 ATGCCCCTTCCTGGTCT-GAAGGTC-CCAGTTTTCCTTTA--GT-ATTCCAAAA
36963 ATGCCCCTTCCTGGTCTGAAGGTCCCAGTTTTCCTTTAGTATTCCAAAA
1 ATGCCCCTTCCTGGTCTGAAGGTCCCAGTTTTCCTTTAGTATTCCAAAA
* * * *
37012 ATGCCCCTTCCCGATCGGAAGGTCCCAATTTTCCTTTAGTATTCCAAAA
1 ATGCCCCTTCCTGGTCTGAAGGTCCCAGTTTTCCTTTAGTATTCCAAAA
37061 TGCTCTTCCC
Statistics
Matches: 89, Mismatches: 5, Indels: 9
0.86 0.05 0.09
Matches are distributed among these distances:
48 3 0.03
49 53 0.60
50 27 0.30
51 6 0.07
ACGTcount: A:0.22, C:0.27, G:0.16, T:0.36
Consensus pattern (49 bp):
ATGCCCCTTCCTGGTCTGAAGGTCCCAGTTTTCCTTTAGTATTCCAAAA
Found at i:43879 original size:21 final size:24
Alignment explanation
Indices: 43830--43884 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
43820 CCTCTTGACA
* *
43830 AATAATTATATTTTTTGTTAATAG
1 AATAATTATAATTTATGTTAATAG
43854 AATAATTATAATTTAT-TT-AT-G
1 AATAATTATAATTTATGTTAATAG
43875 AATAATTATA
1 AATAATTATA
43885 GTTATTGGCT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 11 0.38
22 2 0.07
23 2 0.07
24 14 0.48
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (24 bp):
AATAATTATAATTTATGTTAATAG
Found at i:58396 original size:3 final size:3
Alignment explanation
Indices: 58388--58416 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
58378 GAAAGTATAT
58388 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
58417 TTGAAAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:60102 original size:17 final size:17
Alignment explanation
Indices: 60076--60114 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
60066 GAATCCAAAC
*
60076 GACCCGAACCCGAAAAT
1 GACCCAAACCCGAAAAT
60093 GACCCAAACCCGAAAAT
1 GACCCAAACCCGAAAAT
60110 GACCC
1 GACCC
60115 GAACTCGATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.41, C:0.38, G:0.15, T:0.05
Consensus pattern (17 bp):
GACCCAAACCCGAAAAT
Found at i:66018 original size:15 final size:16
Alignment explanation
Indices: 65982--66019 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
65972 AACCGACAAC
65982 GACCC-AACCCAAAATT
1 GACCCGAACCCAAAA-T
65998 GACCCGAACCCAAAA-
1 GACCCGAACCCAAAAT
66013 GACCCGA
1 GACCCGA
66020 CATTTGAGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.33
16 5 0.24
17 9 0.43
ACGTcount: A:0.42, C:0.39, G:0.13, T:0.05
Consensus pattern (16 bp):
GACCCGAACCCAAAAT
Done.