Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014265.1 Corchorus olitorius cultivar O-4 contig14298, 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: 79141
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:10 original size:2 final size:2
Alignment explanation
Indices: 4--50 Score: 58
Period size: 2 Copynumber: 23.5 Consensus size: 2
1 CAA
* * * *
4 AT AT AT AT AT AT AT AT AT AT AT AT AT GT TT GT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
46 AT AT A
1 AT AT A
51 AGGTATACTA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (2 bp):
AT
Found at i:763 original size:31 final size:31
Alignment explanation
Indices: 667--749 Score: 157
Period size: 31 Copynumber: 2.7 Consensus size: 31
657 TTTGTGCACG
*
667 TGGCATGCCACGTGTCACTTTTTGAAACACA
1 TGGCATGCCACATGTCACTTTTTGAAACACA
698 TGGCATGCCACATGTCACTTTTTGAAACACA
1 TGGCATGCCACATGTCACTTTTTGAAACACA
729 TGGCATGCCACATGTCACTTT
1 TGGCATGCCACATGTCACTTT
750 GGGGTACACA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 51 1.00
ACGTcount: A:0.25, C:0.27, G:0.18, T:0.30
Consensus pattern (31 bp):
TGGCATGCCACATGTCACTTTTTGAAACACA
Found at i:1890 original size:12 final size:13
Alignment explanation
Indices: 1857--1897 Score: 57
Period size: 12 Copynumber: 3.2 Consensus size: 13
1847 CAGGTAACGT
*
1857 TATTTGATTTGGA
1 TATTTGATTTTGA
1870 TGATTTGATTTTGA
1 T-ATTTGATTTTGA
1884 T-TTTGATTTTGA
1 TATTTGATTTTGA
1896 TA
1 TA
1898 GGTGACGAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
12 12 0.48
13 1 0.04
14 12 0.48
ACGTcount: A:0.22, C:0.00, G:0.20, T:0.59
Consensus pattern (13 bp):
TATTTGATTTTGA
Found at i:3307 original size:17 final size:17
Alignment explanation
Indices: 3285--3322 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 17
3275 TCATTGAGAC
3285 AGAAAAACAGAAAAAA-A
1 AGAAAAA-AGAAAAAAGA
3302 AGAAAAAAGAAAAAAGA
1 AGAAAAAAGAAAAAAGA
3319 AGAA
1 AGAA
3323 GCTATTTTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 8 0.40
17 12 0.60
ACGTcount: A:0.82, C:0.03, G:0.16, T:0.00
Consensus pattern (17 bp):
AGAAAAAAGAAAAAAGA
Found at i:8245 original size:17 final size:16
Alignment explanation
Indices: 8213--8244 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
8203 TCAACATACA
8213 CTTTTGATTTTTTTTT
1 CTTTTGATTTTTTTTT
8229 CTTTTGATTTTTTTTT
1 CTTTTGATTTTTTTTT
8245 TTTAAACTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.06, C:0.06, G:0.06, T:0.81
Consensus pattern (16 bp):
CTTTTGATTTTTTTTT
Found at i:8608 original size:15 final size:15
Alignment explanation
Indices: 8588--8616 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
8578 TCAGAGGAAG
8588 AACAGGCGACCGCAA
1 AACAGGCGACCGCAA
8603 AACAGGCGACCGCA
1 AACAGGCGACCGCA
8617 GGATTGCTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.38, C:0.34, G:0.28, T:0.00
Consensus pattern (15 bp):
AACAGGCGACCGCAA
Found at i:11769 original size:33 final size:33
Alignment explanation
Indices: 11732--11837 Score: 142
Period size: 33 Copynumber: 3.2 Consensus size: 33
11722 CAGAACCATT
*
11732 TCCTCCTCACCCGCCGCAGCCATTCCCTCCTCA
1 TCCTCCTCACCCGCCGCAACCATTCCCTCCTCA
* *
11765 TCCTCCTCACCCACCAG-AACCATTTCCTCCTCA
1 TCCTCCTCACCCGCC-GCAACCATTCCCTCCTCA
* *
11798 TCCTCCACACCCGCCGCATCCATTCCCTCCTCA
1 TCCTCCTCACCCGCCGCAACCATTCCCTCCTCA
*
11831 CCCTCCT
1 TCCTCCT
11838 AGACCACCTG
Statistics
Matches: 62, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
32 1 0.02
33 60 0.97
34 1 0.02
ACGTcount: A:0.15, C:0.57, G:0.06, T:0.23
Consensus pattern (33 bp):
TCCTCCTCACCCGCCGCAACCATTCCCTCCTCA
Found at i:14845 original size:226 final size:227
Alignment explanation
Indices: 14450--14905 Score: 842
Period size: 226 Copynumber: 2.0 Consensus size: 227
14440 ACCCAATTAC
*
14450 AAATCAACTATATAATAGATTGGGTCCGTTTGGCCCAACTTATTTAACAGCTTATCTATTGAAAA
1 AAATCAACTATATAATAGATTGGGTCCGTTTGGCCCAACTTATTTAACAGCTTATCTACTGAAAA
14515 AAAAAACCTTAAACTGGGCCAAACGGAAGATCCAGAAGTGTTTTTCGGTTGTTTTTGAAGTAAAA
66 AAAAAACCTTAAACTGGGCCAAACGGAAGATCCAGAAGTGTTTTTCGGTTGTTTTTGAAGTAAAA
* * * *
14580 GGCAGAAGCTCTGAATTAAAACTTTTTTCAGAAACATTTTTTTAGAAAAGCTTTAAGTTAGGCCA
131 AGCAGAAGCTCTGAATTAAAACTTTTTCCAGAAACATTTTTTTAGAAAAACTTTAAGTTAGACCA
14645 AACGGGCACAAATAGGTATAATTCTATGATTT
196 AACGGGCACAAATAGGTATAATTCTATGATTT
14677 AAATCAACTATATAATAGATTGGGTCCGTTTGGCCCAACTTATTTAACAGCTTATCTACTG-AAA
1 AAATCAACTATATAATAGATTGGGTCCGTTTGGCCCAACTTATTTAACAGCTTATCTACTGAAAA
*
14741 AAAAAACCTTAAACTGGGTCAAACGGAAGATCCAGAAGTGTTTTTCGGTTGTTTTTGAAGTAAAA
66 AAAAAACCTTAAACTGGGCCAAACGGAAGATCCAGAAGTGTTTTTCGGTTGTTTTTGAAGTAAAA
*
14806 AGCAGAAGCTCTGAATTGAAACTTTTTCCAGAAACATTTTTTTAGAAAAACTTTAAGTTAGACCA
131 AGCAGAAGCTCTGAATTAAAACTTTTTCCAGAAACATTTTTTTAGAAAAACTTTAAGTTAGACCA
14871 AACGGGCACAAATAGGTATAATTCTATGATTT
196 AACGGGCACAAATAGGTATAATTCTATGATTT
14903 AAA
1 AAA
14906 GAATTATTAA
Statistics
Matches: 222, Mismatches: 7, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
226 162 0.73
227 60 0.27
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Consensus pattern (227 bp):
AAATCAACTATATAATAGATTGGGTCCGTTTGGCCCAACTTATTTAACAGCTTATCTACTGAAAA
AAAAAACCTTAAACTGGGCCAAACGGAAGATCCAGAAGTGTTTTTCGGTTGTTTTTGAAGTAAAA
AGCAGAAGCTCTGAATTAAAACTTTTTCCAGAAACATTTTTTTAGAAAAACTTTAAGTTAGACCA
AACGGGCACAAATAGGTATAATTCTATGATTT
Found at i:15439 original size:30 final size:30
Alignment explanation
Indices: 15404--15466 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
15394 CGATGACTCA
*
15404 ATTCTGAACTAATCGTAATTTAATATGACT
1 ATTCTGAACTAATCGTAATTCAATATGACT
15434 ATTCTGAACTAATCGTAATTCAATATGACT
1 ATTCTGAACTAATCGTAATTCAATATGACT
15464 ATT
1 ATT
15467 GATTATCGAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.40
Consensus pattern (30 bp):
ATTCTGAACTAATCGTAATTCAATATGACT
Found at i:15511 original size:15 final size:15
Alignment explanation
Indices: 15491--15521 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
15481 TTTTTATATA
15491 ATAATAAAAAATACT
1 ATAATAAAAAATACT
15506 ATAATAAAAAATACT
1 ATAATAAAAAATACT
15521 A
1 A
15522 CAAGCTACTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (15 bp):
ATAATAAAAAATACT
Found at i:18046 original size:74 final size:75
Alignment explanation
Indices: 17930--18080 Score: 286
Period size: 75 Copynumber: 2.0 Consensus size: 75
17920 ATTTACATGT
17930 AGCGGTGTACGGGTCTTCCTTTGCGATTCTTATCTT-AAAAAAAATGCCTCAAGGGTTATTTGAT
1 AGCGGTGTACGGGTCTTCCTTTGCGATTCTTATCTTAAAAAAAAATGCCTCAAGGGTTATTTGAT
17994 ATATAAATGG
66 ATATAAATGG
18004 AGCGGTGTACGGGTCTTCCTTTGCGATTCTTATCTTAAAAAAAAATGCCTCAAGGGTTATTTGAT
1 AGCGGTGTACGGGTCTTCCTTTGCGATTCTTATCTTAAAAAAAAATGCCTCAAGGGTTATTTGAT
*
18069 ATATAAGTGG
66 ATATAAATGG
18079 AG
1 AG
18081 AATTAATCAT
Statistics
Matches: 75, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
74 36 0.48
75 39 0.52
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.34
Consensus pattern (75 bp):
AGCGGTGTACGGGTCTTCCTTTGCGATTCTTATCTTAAAAAAAAATGCCTCAAGGGTTATTTGAT
ATATAAATGG
Found at i:24717 original size:35 final size:35
Alignment explanation
Indices: 24677--24751 Score: 141
Period size: 35 Copynumber: 2.1 Consensus size: 35
24667 AGTTCGTTTA
*
24677 TGTTCACGAACAGCCTCGTTTATTGTTCATTTAAG
1 TGTTCACGAACAGACTCGTTTATTGTTCATTTAAG
24712 TGTTCACGAACAGACTCGTTTATTGTTCATTTAAG
1 TGTTCACGAACAGACTCGTTTATTGTTCATTTAAG
24747 TGTTC
1 TGTTC
24752 GTTTATATAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.23, C:0.19, G:0.17, T:0.41
Consensus pattern (35 bp):
TGTTCACGAACAGACTCGTTTATTGTTCATTTAAG
Found at i:24819 original size:19 final size:19
Alignment explanation
Indices: 24777--24829 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 19
24767 GAACGTTCGT
* *
24777 TTATTATATAATTATTTATA
1 TTATTA-ATAATAATATATA
24797 -TATTAATAATAATATATA
1 TTATTAATAATAATATATA
* *
24815 TTATTTATAAAAATA
1 TTATTAATAATAATA
24830 ATAATATTCT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
18 11 0.39
19 17 0.61
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TTATTAATAATAATATATA
Found at i:24829 original size:25 final size:28
Alignment explanation
Indices: 24781--24836 Score: 82
Period size: 25 Copynumber: 2.1 Consensus size: 28
24771 GTTCGTTTAT
*
24781 TATATAATTATTTATATATTAATAATAA
1 TATATAATTATTTATATATAAATAATAA
24809 TATAT-ATTATTTATA-A-AAATAATAA
1 TATATAATTATTTATATATAAATAATAA
24834 TAT
1 TAT
24837 TCTATTATCT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
25 11 0.41
26 1 0.04
27 10 0.37
28 5 0.19
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (28 bp):
TATATAATTATTTATATATAAATAATAA
Found at i:24973 original size:18 final size:18
Alignment explanation
Indices: 24946--24980 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
24936 AATTATTATA
24946 TTGTTCATGAACAATTTT
1 TTGTTCATGAACAATTTT
*
24964 TTGTTTATGAACAATTT
1 TTGTTCATGAACAATTT
24981 CAATTTTTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.29, C:0.09, G:0.11, T:0.51
Consensus pattern (18 bp):
TTGTTCATGAACAATTTT
Found at i:26206 original size:25 final size:25
Alignment explanation
Indices: 26172--26221 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
26162 CTTGTGTTAC
26172 AATTAATAGCCTCGATAAATAATAT
1 AATTAATAGCCTCGATAAATAATAT
26197 AATTAATAGCCTCGATAAATAATAT
1 AATTAATAGCCTCGATAAATAATAT
26222 GGGAACAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.48, C:0.12, G:0.08, T:0.32
Consensus pattern (25 bp):
AATTAATAGCCTCGATAAATAATAT
Found at i:30088 original size:33 final size:33
Alignment explanation
Indices: 30050--30116 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
30040 ATCAGTATAC
*
30050 TTATCACTTAATCATTAATTTCGTAAAATCTTA
1 TTATCACTTAATCATCAATTTCGTAAAATCTTA
30083 TTATCACTTAATCATCAATTTCGTAAAATCTTA
1 TTATCACTTAATCATCAATTTCGTAAAATCTTA
30116 T
1 T
30117 CCCATTAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.36, C:0.16, G:0.03, T:0.45
Consensus pattern (33 bp):
TTATCACTTAATCATCAATTTCGTAAAATCTTA
Found at i:31909 original size:15 final size:15
Alignment explanation
Indices: 31889--31919 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
31879 ATATATATAT
*
31889 AGTTAAGTAATTCTA
1 AGTTAACTAATTCTA
31904 AGTTAACTAATTCTA
1 AGTTAACTAATTCTA
31919 A
1 A
31920 TACACTCGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.10, G:0.10, T:0.39
Consensus pattern (15 bp):
AGTTAACTAATTCTA
Found at i:38423 original size:1 final size:1
Alignment explanation
Indices: 38412--38455 Score: 79
Period size: 1 Copynumber: 44.0 Consensus size: 1
38402 GTTCATGCAC
*
38412 TTTTGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
38456 GTGGCAACCA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
1 41 1.00
ACGTcount: A:0.00, C:0.00, G:0.02, T:0.98
Consensus pattern (1 bp):
T
Found at i:54655 original size:84 final size:81
Alignment explanation
Indices: 54509--54692 Score: 287
Period size: 84 Copynumber: 2.2 Consensus size: 81
54499 TTATCCCTGT
* *
54509 ATGACGAAACTTCGTCAAATAATCAAGACCAAAAATTGCTTGAGGCGCCCCCAAAGAGCTTATCC
1 ATGAAGAAACTTCGTCAAATAATCAAGACCAAAAATTGCTTGAGGCGCCCCCAAAAAGCTTATCC
*
54574 CAATATGTTATTGCCC
66 CAAGATGTTATTGCCC
*
54590 ATGACGATGAAACTTCGTCAAATAATCAAGGCCAAAAATTGCTTGAGGCGCCCCCAAAAAGCTTA
1 ATGA--A-GAAACTTCGTCAAATAATCAAGACCAAAAATTGCTTGAGGCGCCCCCAAAAAGCTTA
**
54655 TCCCAAGATGTTATTGCTT
63 TCCCAAGATGTTATTGCCC
54674 ATGAAGAAACTTCGTCAAA
1 ATGAAGAAACTTCGTCAAA
54693 AGAAGTGTCC
Statistics
Matches: 94, Mismatches: 6, Indels: 6
0.89 0.06 0.06
Matches are distributed among these distances:
81 18 0.19
82 1 0.01
84 75 0.80
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.24
Consensus pattern (81 bp):
ATGAAGAAACTTCGTCAAATAATCAAGACCAAAAATTGCTTGAGGCGCCCCCAAAAAGCTTATCC
CAAGATGTTATTGCCC
Found at i:56287 original size:3 final size:3
Alignment explanation
Indices: 56273--56322 Score: 73
Period size: 3 Copynumber: 16.7 Consensus size: 3
56263 ATCTAATTCA
* * *
56273 TCT TCG TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT CCT TCT CCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
56321 TC
1 TC
56323 GTGACTACTA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.00, C:0.38, G:0.02, T:0.60
Consensus pattern (3 bp):
TCT
Found at i:69892 original size:19 final size:19
Alignment explanation
Indices: 69868--69904 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
69858 TGTATCTGTA
69868 ATCGTTTCACCACCGTTTG
1 ATCGTTTCACCACCGTTTG
*
69887 ATCGTTTCATCACCGTTT
1 ATCGTTTCACCACCGTTT
69905 TGGATCCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.16, C:0.30, G:0.14, T:0.41
Consensus pattern (19 bp):
ATCGTTTCACCACCGTTTG
Found at i:72119 original size:81 final size:81
Alignment explanation
Indices: 71984--72145 Score: 315
Period size: 81 Copynumber: 2.0 Consensus size: 81
71974 TCCACAATTC
*
71984 AACAGGGCCAAGTTCAACACTTTCAAGTATTGGTTTTAAGCCAGAATTCCCAAGTCAAGCAGGAA
1 AACAGGGCCAAGTTCAACACTTTCAAGTATTGGTTTTAAGCCAGAATTCCCAAGTCAAGCAAGAA
72049 TAATGTAAACATGCAT
66 TAATGTAAACATGCAT
72065 AACAGGGCCAAGTTCAACACTTTCAAGTATTGGTTTTAAGCCAGAATTCCCAAGTCAAGCAAGAA
1 AACAGGGCCAAGTTCAACACTTTCAAGTATTGGTTTTAAGCCAGAATTCCCAAGTCAAGCAAGAA
72130 TAATGTAAACATGCAT
66 TAATGTAAACATGCAT
72146 GTATTAATAT
Statistics
Matches: 80, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
81 80 1.00
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.25
Consensus pattern (81 bp):
AACAGGGCCAAGTTCAACACTTTCAAGTATTGGTTTTAAGCCAGAATTCCCAAGTCAAGCAAGAA
TAATGTAAACATGCAT
Found at i:73857 original size:14 final size:14
Alignment explanation
Indices: 73840--73868 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
73830 ATCCCACTTA
73840 AATAATCGTGAACG
1 AATAATCGTGAACG
73854 AATAATCGTGAACG
1 AATAATCGTGAACG
73868 A
1 A
73869 CATGTAAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.14, G:0.21, T:0.21
Consensus pattern (14 bp):
AATAATCGTGAACG
Found at i:75868 original size:48 final size:48
Alignment explanation
Indices: 75792--75888 Score: 167
Period size: 48 Copynumber: 2.0 Consensus size: 48
75782 GTGACAGTGA
* *
75792 CCTTCTTCTTCTCCTTCTCAATCTTGACCCCTTTGATCACACTTACAT
1 CCTTCTTCTTCTCCCTCTCAATCATGACCCCTTTGATCACACTTACAT
*
75840 CCTTCTTCTTCTCCCTCTCAATCATGACCTCTTTGATCACACTTACAT
1 CCTTCTTCTTCTCCCTCTCAATCATGACCCCTTTGATCACACTTACAT
75888 C
1 C
75889 ATCAGCAATC
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.18, C:0.38, G:0.04, T:0.40
Consensus pattern (48 bp):
CCTTCTTCTTCTCCCTCTCAATCATGACCCCTTTGATCACACTTACAT
Found at i:76188 original size:25 final size:21
Alignment explanation
Indices: 76151--76211 Score: 104
Period size: 21 Copynumber: 2.9 Consensus size: 21
76141 CCTCTCCAGT
*
76151 TTGAGAAAGCCTTCCTTCTCA
1 TTGAGCAAGCCTTCCTTCTCA
76172 TTGAGCAAGCCTTCCTTCTCA
1 TTGAGCAAGCCTTCCTTCTCA
*
76193 TTGAGCAAGCTTTCCTTCT
1 TTGAGCAAGCCTTCCTTCT
76212 TCAACTTCTC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.20, C:0.30, G:0.15, T:0.36
Consensus pattern (21 bp):
TTGAGCAAGCCTTCCTTCTCA
Found at i:76508 original size:24 final size:24
Alignment explanation
Indices: 76476--76522 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
76466 ATCCTGTCTC
* *
76476 CCTCACTTATCGTCGTTTTATCCG
1 CCTCACTTATCGCCATTTTATCCG
76500 CCTCACTTATCGCCATTTTATCC
1 CCTCACTTATCGCCATTTTATCC
76523 TCCGCCGCCG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.15, C:0.36, G:0.09, T:0.40
Consensus pattern (24 bp):
CCTCACTTATCGCCATTTTATCCG
Found at i:76764 original size:15 final size:16
Alignment explanation
Indices: 76739--76768 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
76729 TTCTTTCTCT
76739 CTCCTCTCTTCACTTG
1 CTCCTCTCTTCACTTG
76755 CTCCTC-CTTCACTT
1 CTCCTCTCTTCACTT
76769 ACTAAACTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.07, C:0.47, G:0.03, T:0.43
Consensus pattern (16 bp):
CTCCTCTCTTCACTTG
Found at i:76838 original size:2 final size:2
Alignment explanation
Indices: 76831--76858 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
76821 CCCTCTAACA
76831 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
76859 GGGCCGGGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:77124 original size:33 final size:33
Alignment explanation
Indices: 77081--77175 Score: 121
Period size: 33 Copynumber: 3.1 Consensus size: 33
77071 ATCAATGAAA
* *
77081 ATTCAGTTTGACATGAGCAATCGAAGAAAACAT
1 ATTCAATTTGACATGAGCAATGGAAGAAAACAT
*
77114 ATTCAATTTGACATGAGAAATGGAAGAAAACA-
1 ATTCAATTTGACATGAGCAATGGAAGAAAACAT
77146 A-T--A--TGACATGAGCAATGGAAGAAAACAT
1 ATTCAATTTGACATGAGCAATGGAAGAAAACAT
77174 AT
1 AT
77176 ATTAACAAAC
Statistics
Matches: 56, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
27 23 0.41
28 1 0.02
29 1 0.02
31 1 0.02
32 1 0.02
33 29 0.52
ACGTcount: A:0.47, C:0.12, G:0.19, T:0.22
Consensus pattern (33 bp):
ATTCAATTTGACATGAGCAATGGAAGAAAACAT
Found at i:77152 original size:27 final size:27
Alignment explanation
Indices: 77117--77177 Score: 95
Period size: 27 Copynumber: 2.2 Consensus size: 27
77107 AAAACATATT
*
77117 CAATTTGACATGAGAAATGGAAGAAAA
1 CAATATGACATGAGAAATGGAAGAAAA
*
77144 CAATATGACATGAGCAATGGAAGAAAA
1 CAATATGACATGAGAAATGGAAGAAAA
77171 CATATAT
1 CA-ATAT
77178 TAACAAACAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 27 0.87
28 4 0.13
ACGTcount: A:0.51, C:0.10, G:0.20, T:0.20
Consensus pattern (27 bp):
CAATATGACATGAGAAATGGAAGAAAA
Found at i:78479 original size:31 final size:32
Alignment explanation
Indices: 78444--78520 Score: 88
Period size: 31 Copynumber: 2.5 Consensus size: 32
78434 ATTTGATAAA
* *
78444 AAAAAAGTTGGAGGGCTT-TTTGGTCATTCTG
1 AAAAAAGATAGAGGGCTTATTTGGTCATTCTG
** *
78475 AAAAAAGATAGTTGGCTTATTTGGTCATTTTG
1 AAAAAAGATAGAGGGCTTATTTGGTCATTCTG
78507 -AAAAAG-TAGAGGGC
1 AAAAAAGATAGAGGGC
78521 CAAAATAGTT
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
30 6 0.16
31 20 0.53
32 12 0.32
ACGTcount: A:0.32, C:0.08, G:0.27, T:0.32
Consensus pattern (32 bp):
AAAAAAGATAGAGGGCTTATTTGGTCATTCTG
Done.