Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021544.1 Corchorus olitorius cultivar O-4 contig21577, 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: 75036
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:158 original size:12 final size:12
Alignment explanation
Indices: 141--165 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
131 CTTTGTTTTT
141 TTGGGTTGAATG
1 TTGGGTTGAATG
153 TTGGGTTGAATG
1 TTGGGTTGAATG
165 T
1 T
166 ATTTTTTTGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.00, G:0.40, T:0.44
Consensus pattern (12 bp):
TTGGGTTGAATG
Found at i:562 original size:3 final size:3
Alignment explanation
Indices: 556--587 Score: 55
Period size: 3 Copynumber: 10.3 Consensus size: 3
546 TTTTTTTAAC
556 ATA ATA ATA TATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA A
588 GAGGGGAAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1643 original size:21 final size:21
Alignment explanation
Indices: 1619--1731 Score: 176
Period size: 21 Copynumber: 5.4 Consensus size: 21
1609 CTTCAAATGA
1619 TCTCCAATGAGCTTGGAACCT
1 TCTCCAATGAGCTTGGAACCT
*
1640 TCTCCAATGAGCTTTGAACCT
1 TCTCCAATGAGCTTGGAACCT
1661 TCTCCAATGAGCTTGGAACCT
1 TCTCCAATGAGCTTGGAACCT
*
1682 TCTTCAATGAGCTTGGAA-CT
1 TCTCCAATGAGCTTGGAACCT
1702 TGCTCCAATGAGCTTGGAA-CT
1 T-CTCCAATGAGCTTGGAACCT
1723 TGCTCCAAT
1 T-CTCCAAT
1732 TAACTCCTAG
Statistics
Matches: 87, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
20 3 0.03
21 84 0.97
ACGTcount: A:0.24, C:0.27, G:0.19, T:0.31
Consensus pattern (21 bp):
TCTCCAATGAGCTTGGAACCT
Found at i:3059 original size:15 final size:17
Alignment explanation
Indices: 3032--3064 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
3022 GTCCAAGTGC
3032 AAAATGCCTTAAA-GCA
1 AAAATGCCTTAAATGCA
3048 AAAATGCC-TAAATGCA
1 AAAATGCCTTAAATGCA
3064 A
1 A
3065 GCCCAATGCC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.52, C:0.18, G:0.12, T:0.18
Consensus pattern (17 bp):
AAAATGCCTTAAATGCA
Found at i:3074 original size:19 final size:19
Alignment explanation
Indices: 3050--3105 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
3040 TTAAAGCAAA
3050 AATGCCTAAATGCAAGCCC
1 AATGCCTAAATGCAAGCCC
* *
3069 AATGCCCATATGCAAGCCC
1 AATGCCTAAATGCAAGCCC
3088 AATGTCCT-AATGCAAGCC
1 AATG-CCTAAATGCAAGCC
3106 TAAAGCTAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 30 0.94
20 2 0.06
ACGTcount: A:0.34, C:0.32, G:0.16, T:0.18
Consensus pattern (19 bp):
AATGCCTAAATGCAAGCCC
Found at i:12509 original size:7 final size:7
Alignment explanation
Indices: 12497--12521 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
12487 ACAATTGAGT
12497 TTTTCCC
1 TTTTCCC
12504 TTTTCCC
1 TTTTCCC
12511 TTTTCCC
1 TTTTCCC
12518 TTTT
1 TTTT
12522 AATTTCTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (7 bp):
TTTTCCC
Found at i:13785 original size:6 final size:6
Alignment explanation
Indices: 13774--13805 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
13764 TAGACTGCAC
13774 CACAAT CACAAT CACAAT CACAAT CACAAT CA
1 CACAAT CACAAT CACAAT CACAAT CACAAT CA
13806 TCCGATAACG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.50, C:0.34, G:0.00, T:0.16
Consensus pattern (6 bp):
CACAAT
Found at i:13961 original size:39 final size:38
Alignment explanation
Indices: 13835--13982 Score: 235
Period size: 38 Copynumber: 3.9 Consensus size: 38
13825 TCGAGTCTAG
13835 CCAACAG-TTAACCCCCTGAGGCACGGGTCCACTCTTA
1 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA
13872 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA
1 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA
* * *
13910 CCAACAGTTTAACCCCCTGTGGTATGGGTCCACTCTTTA
1 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTC-TTA
* *
13949 CCATCAGTTTAACCCCCTGAGGTACGGGTCCACT
1 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACT
13983 ATGCACAGCC
Statistics
Matches: 103, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
37 7 0.07
38 62 0.60
39 34 0.33
ACGTcount: A:0.22, C:0.35, G:0.19, T:0.24
Consensus pattern (38 bp):
CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA
Found at i:13969 original size:77 final size:75
Alignment explanation
Indices: 13835--13982 Score: 233
Period size: 77 Copynumber: 1.9 Consensus size: 75
13825 TCGAGTCTAG
13835 CCAACAGTTAACCCCCTGAGGCACGGGTCCACTCTTACCAACAGTTTAACCCCCTGAGGCACGGG
1 CCAACAGTTAACCCCCTGAGGCACGGGTCCACTCTTACCAACAGTTTAACCCCCTGAGGCACGGG
13900 TCCACTCTTA
66 TCCACTCTTA
* * * * *
13910 CCAACAGTTTAACCCCCTGTGGTATGGGTCCACTCTTTACCATCAGTTTAACCCCCTGAGGTACG
1 CCAACAG-TTAACCCCCTGAGGCACGGGTCCACTC-TTACCAACAGTTTAACCCCCTGAGGCACG
13975 GGTCCACT
64 GGTCCACT
13983 ATGCACAGCC
Statistics
Matches: 66, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
75 7 0.11
76 24 0.36
77 35 0.53
ACGTcount: A:0.22, C:0.35, G:0.19, T:0.24
Consensus pattern (75 bp):
CCAACAGTTAACCCCCTGAGGCACGGGTCCACTCTTACCAACAGTTTAACCCCCTGAGGCACGGG
TCCACTCTTA
Found at i:19844 original size:43 final size:43
Alignment explanation
Indices: 19783--19869 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
19773 GTTTAAAGCT
19783 ATGAAACACCCTATTGAAGAACAATCTATTTTTGCTACTGATG
1 ATGAAACACCCTATTGAAGAACAATCTATTTTTGCTACTGATG
19826 ATGAAACACCCTATTGAAGAACAATCTATTTTTGCTACTGATG
1 ATGAAACACCCTATTGAAGAACAATCTATTTTTGCTACTGATG
19869 A
1 A
19870 AGTTAATCTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (43 bp):
ATGAAACACCCTATTGAAGAACAATCTATTTTTGCTACTGATG
Found at i:24071 original size:31 final size:31
Alignment explanation
Indices: 24027--24117 Score: 87
Period size: 34 Copynumber: 2.8 Consensus size: 31
24017 CCGTTATAAC
*
24027 AAACGCC-CTTATTTTGCGGCGTTTTCATCCT-
1 AAACGCCGC-TATTTTGCGGCGTTTTCAT-ATG
*
24058 AAACGCCGCTATTTATTAGCGGCGTTTTTATATGG
1 AAACGCCGCTA-TT-TT-GCGGCGTTTTCATAT-G
*
24093 AAACGCCGCTATTTAGCGGCGTTTT
1 AAACGCCGCTATTTTGCGGCGTTTT
24118 TAAACCATAA
Statistics
Matches: 51, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
31 9 0.18
32 13 0.25
33 4 0.08
34 14 0.27
35 11 0.22
ACGTcount: A:0.20, C:0.23, G:0.21, T:0.36
Consensus pattern (31 bp):
AAACGCCGCTATTTTGCGGCGTTTTCATATG
Found at i:24085 original size:34 final size:34
Alignment explanation
Indices: 24042--24107 Score: 89
Period size: 35 Copynumber: 1.9 Consensus size: 34
24032 CCCTTATTTT
*
24042 GCGGCGTTTTCATCCT-AAACGCCGCTATTTATTA
1 GCGGCGTTTTCAT-ATGAAACGCCGCTATTTATTA
*
24076 GCGGCGTTTTTATATGGAAACGCCGCTATTTA
1 GCGGCGTTTTCATAT-GAAACGCCGCTATTTA
24108 GCGGCGTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
33 1 0.04
34 12 0.43
35 15 0.54
ACGTcount: A:0.21, C:0.23, G:0.21, T:0.35
Consensus pattern (34 bp):
GCGGCGTTTTCATATGAAACGCCGCTATTTATTA
Found at i:26503 original size:160 final size:161
Alignment explanation
Indices: 26141--26610 Score: 703
Period size: 160 Copynumber: 2.9 Consensus size: 161
26131 GTTTAGGATC
* *
26141 CCACTAATTAGCGGCGTCTTATGTGAAAACGCTGCTATATATTATAGGCATAGAGTT-AGAAACT
1 CCACTAATTAGCGGCGTCTGATGTCAAAACGCTGCTATATATTATAGGCATAGAGTTGA-AAACT
* *
26205 TTCTTTGTTTTAGGAGAGAGGGAATTTTTCCCTAAAAAAAAGGAAAAAAAAAATCTCTCCCTCCA
65 TTCTTTGTTTTAGGGGAGAGGGAATTTTTCCCTCAAAAAAA--AAAAAAAAAATCTCTCCCTCCA
*
26270 TATATTAAAATAGCGGCGTTTCCTTTTCTAGACG
128 TATATTAAAATAGCGGCGTTTCCTTCTCTAGACG
* * *
26304 ACACTAATTAGCGGCGTCTGATGTCTAAACGCCGCTATATATTATAGGCATAGAGTTGAAAACTT
1 CCACTAATTAGCGGCGTCTGATGTCAAAACGCTGCTATATATTATAGGCATAGAGTTGAAAACTT
* *
26369 TCTTTGTTTTAGGGGAGAGGGAATTTTTCCAT-AAAAAAAAAGAAAAAAATCTCTCCCTCCATAT
66 TCTTTGTTTTAGGGGAGAGGGAATTTTTCCCTCAAAAAAAAAAAAAAAAATCTCTCCCTCCATAT
** *
26433 ATTAAAATATTGGGGTTTCCTTCTCTAGACG
131 ATTAAAATAGCGGCGTTTCCTTCTCTAGACG
* * * *
26464 CCACTAATTAGCGGCGTCTGATGTCAAAACGCTGCTATATATTATAGGCGTTGAGTTGGAAATTT
1 CCACTAATTAGCGGCGTCTGATGTCAAAACGCTGCTATATATTATAGGCATAGAGTTGAAAACTT
26529 TCTTTGTTTTAGGGG-GAGGGAATTTTTCCCTCCAAAAAAAAGAAAAAAAAATCTCTCCCTCCAT
66 TCTTTGTTTTAGGGGAGAGGGAATTTTTCCCT-CAAAAAAAA-AAAAAAAAATCTCTCCCTCCAT
* *
26593 ATATTAATATGGCGGCGT
129 ATATTAAAATAGCGGCGT
26611 CTGTCTATCG
Statistics
Matches: 277, Mismatches: 26, Indels: 9
0.89 0.08 0.03
Matches are distributed among these distances:
159 15 0.05
160 124 0.45
161 8 0.03
162 41 0.15
163 88 0.32
164 1 0.00
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (161 bp):
CCACTAATTAGCGGCGTCTGATGTCAAAACGCTGCTATATATTATAGGCATAGAGTTGAAAACTT
TCTTTGTTTTAGGGGAGAGGGAATTTTTCCCTCAAAAAAAAAAAAAAAAATCTCTCCCTCCATAT
ATTAAAATAGCGGCGTTTCCTTCTCTAGACG
Found at i:26665 original size:162 final size:160
Alignment explanation
Indices: 26141--26665 Score: 698
Period size: 160 Copynumber: 3.2 Consensus size: 160
26131 GTTTAGGATC
* * * *
26141 CCACTAATTAGCGGCGTCTTATGTGAAAACGCTGCTATATATTATAGGCATAGAGTTAGAAACTT
1 CCACTAATTAGCGGCGTCTGATGTCAAAACGCCGCTATATATTATAGGCATAGAGTTGGAAACTT
*
26206 TCTTTGTTTTAGGAGAGAGGGAATTTTTCCCTAAAAAAAAGGAAAAAAAAAATCTCTCCCTCCAT
66 TCTTTGTTTTAGG-GGGAGGGAATTTTTCCCTAAAAAAAA-G-AAAAAAAAATCTCTCCCTCCAT
* *
26271 ATATTAAAATAGCGGCGTTTCCTTTTCTAGACG
128 ATATTAATATAGCGGCGTTTCCTTATCTAGACG
* * *
26304 ACACTAATTAGCGGCGTCTGATGTCTAAACGCCGCTATATATTATAGGCATAGAGTTGAAAACTT
1 CCACTAATTAGCGGCGTCTGATGTCAAAACGCCGCTATATATTATAGGCATAGAGTTGGAAACTT
* *
26369 TCTTTGTTTTAGGGGAGAGGGAATTTTTCCATAAAAAAAA-AGAAAAAAATCTCTCCCTCCATAT
66 TCTTTGTTTTAGGGG-GAGGGAATTTTTCCCTAAAAAAAAGAAAAAAAAATCTCTCCCTCCATAT
* ** * *
26433 ATTAAAATATTGGGGTTTCCTTCTCTAGACG
130 ATTAATATAGCGGCGTTTCCTTATCTAGACG
* * * *
26464 CCACTAATTAGCGGCGTCTGATGTCAAAACGCTGCTATATATTATAGGCGTTGAGTTGGAAATTT
1 CCACTAATTAGCGGCGTCTGATGTCAAAACGCCGCTATATATTATAGGCATAGAGTTGGAAACTT
26529 TCTTTGTTTTAGGGGGAGGGAATTTTTCCCTCCAAAAAAAAGAAAAAAAAATCTCTCCCTCCATA
66 TCTTTGTTTTAGGGGGAGGGAATTTTTCCCT--AAAAAAAAGAAAAAAAAATCTCTCCCTCCATA
* * *
26594 TATTAATATGGCGGCGTCTGT-C-TATCGAAACG
129 TATTAATATAGCGGCGT-T-TCCTTATCTAGACG
* * *
26626 CCACTAAATGGCGGCGTCTTGATGTC-AGACGCCGCTATAT
1 CCACTAATTAGCGGCGTC-TGATGTCAAAACGCCGCTATAT
26666 TCAATTTCAG
Statistics
Matches: 320, Mismatches: 35, Indels: 15
0.86 0.09 0.04
Matches are distributed among these distances:
159 15 0.05
160 123 0.38
161 8 0.03
162 70 0.22
163 103 0.32
164 1 0.00
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Consensus pattern (160 bp):
CCACTAATTAGCGGCGTCTGATGTCAAAACGCCGCTATATATTATAGGCATAGAGTTGGAAACTT
TCTTTGTTTTAGGGGGAGGGAATTTTTCCCTAAAAAAAAGAAAAAAAAATCTCTCCCTCCATATA
TTAATATAGCGGCGTTTCCTTATCTAGACG
Found at i:27697 original size:120 final size:113
Alignment explanation
Indices: 27472--27703 Score: 392
Period size: 120 Copynumber: 2.0 Consensus size: 113
27462 TTAGAAACTT
27472 TTTTTATTAGTTACTAATATACCTGACAAACTTATACTATATATTATTATATTATATATATAATG
1 TTTTTATTAGTTACTAATATACCTGACAAACTTATACTATATATTATTATATTATATATATAATG
27537 CATGCACCTAATCTGCTTTCCTTGATATTTCCATGTCAAATAGAGTAC
66 CATGCACCTAATCTGCTTTCCTTGATATTTCCATGTCAAATAGAGTAC
27585 TTTTTATTAGTTACTAATATACCTGACAAACTTATACTATATATTATTACATTATATATTATATA
1 TTTTTATTAGTTACTAATATACCTGACAAACTTATAC--TATA-TATT--A-T-TATATTATATA
*
27650 TATAATGCATGCACCTAATCTGCTTTCCTTGATATTTCCCTGTCAAATAGAGTA
59 TATAATGCATGCACCTAATCTGCTTTCCTTGATATTTCCATGTCAAATAGAGTA
27704 GTATATTGCA
Statistics
Matches: 111, Mismatches: 1, Indels: 7
0.93 0.01 0.06
Matches are distributed among these distances:
113 37 0.33
115 4 0.04
116 4 0.04
118 1 0.01
119 1 0.01
120 64 0.58
ACGTcount: A:0.34, C:0.16, G:0.08, T:0.43
Consensus pattern (113 bp):
TTTTTATTAGTTACTAATATACCTGACAAACTTATACTATATATTATTATATTATATATATAATG
CATGCACCTAATCTGCTTTCCTTGATATTTCCATGTCAAATAGAGTAC
Found at i:29743 original size:39 final size:39
Alignment explanation
Indices: 29700--29778 Score: 140
Period size: 39 Copynumber: 2.0 Consensus size: 39
29690 TCTGTTTGCC
*
29700 TACTTATTAAAGTAGGCAACATAAACTCTTTTTGTGTAT
1 TACTTATTAAAGTAGGCAACATAAACTATTTTTGTGTAT
*
29739 TACTTATTAAAGTAGGCAACTTAAACTATTTTTGTGTAT
1 TACTTATTAAAGTAGGCAACATAAACTATTTTTGTGTAT
29778 T
1 T
29779 TGTAGTTGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.33, C:0.11, G:0.13, T:0.43
Consensus pattern (39 bp):
TACTTATTAAAGTAGGCAACATAAACTATTTTTGTGTAT
Found at i:30113 original size:27 final size:26
Alignment explanation
Indices: 30050--30102 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
30040 CTTCCTTGCC
30050 CAGCTACATAATTCCAGATTTTTTTG
1 CAGCTACATAATTCCAGATTTTTTTG
30076 CAGCTACATAATTCCAGATTTTTTTG
1 CAGCTACATAATTCCAGATTTTTTTG
30102 C
1 C
30103 TCTTGTTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.26, C:0.21, G:0.11, T:0.42
Consensus pattern (26 bp):
CAGCTACATAATTCCAGATTTTTTTG
Found at i:34535 original size:21 final size:21
Alignment explanation
Indices: 34509--34621 Score: 183
Period size: 21 Copynumber: 5.4 Consensus size: 21
34499 TGCTAGGAGA
34509 TCATTGGAGCAA-GTTCCAAGC
1 TCATTGGAG-AAGGTTCCAAGC
34530 TCATTGGAGAAGGTTCCAAGC
1 TCATTGGAGAAGGTTCCAAGC
34551 TCATTGGAGAAGGTTCCAAGC
1 TCATTGGAGAAGGTTCCAAGC
*
34572 TCATTGGAAAAGGTTCCAAGC
1 TCATTGGAGAAGGTTCCAAGC
* *
34593 TCATTGGAGAATGTTTCAAGC
1 TCATTGGAGAAGGTTCCAAGC
34614 TCATTGGA
1 TCATTGGA
34622 ATTGCCTAAG
Statistics
Matches: 87, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
20 2 0.02
21 85 0.98
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.27
Consensus pattern (21 bp):
TCATTGGAGAAGGTTCCAAGC
Found at i:35525 original size:25 final size:24
Alignment explanation
Indices: 35489--35535 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
35479 TCCTTCTATT
35489 CATCTATCATC-AAGTTTTTCATC
1 CATCTATCATCAAAGTTTTTCATC
35512 CATCTCATCCATCAAAGTTTTTCA
1 CATCT-AT-CATCAAAGTTTTTCA
35536 AATTTTCTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 5 0.24
24 2 0.10
25 4 0.19
26 10 0.48
ACGTcount: A:0.28, C:0.28, G:0.04, T:0.40
Consensus pattern (24 bp):
CATCTATCATCAAAGTTTTTCATC
Found at i:38021 original size:21 final size:21
Alignment explanation
Indices: 37991--38030 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
37981 CTAAAAATAG
*
37991 GACAAGTCCTGCCCAGGACTT
1 GACAACTCCTGCCCAGGACTT
38012 GACAACTCCTGCCCAGGAC
1 GACAACTCCTGCCCAGGAC
38031 CTGGTCTGTT
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:0.25, C:0.38, G:0.23, T:0.15
Consensus pattern (21 bp):
GACAACTCCTGCCCAGGACTT
Found at i:38088 original size:50 final size:50
Alignment explanation
Indices: 38013--38134 Score: 181
Period size: 50 Copynumber: 2.4 Consensus size: 50
38003 CCAGGACTTG
* **
38013 ACAACTCCTGCCCAGGACCTGGTCTGTTGAAAGACGGAAGAAAAATCGGA
1 ACAACTCCTGCCCAGGACTTGGTCTGTTGAAAGACGGAAGAAAAATCAAA
*
38063 ACAACTCCTGCCCAGGACTTGGTCTGTTGAAAGACGGAAGAAAATTCAAA
1 ACAACTCCTGCCCAGGACTTGGTCTGTTGAAAGACGGAAGAAAAATCAAA
* * *
38113 ATAAGTCCTGTCCAGGACTTGG
1 ACAACTCCTGCCCAGGACTTGG
38135 ACAACTCCTG
Statistics
Matches: 65, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 65 1.00
ACGTcount: A:0.33, C:0.23, G:0.25, T:0.20
Consensus pattern (50 bp):
ACAACTCCTGCCCAGGACTTGGTCTGTTGAAAGACGGAAGAAAAATCAAA
Found at i:38722 original size:25 final size:24
Alignment explanation
Indices: 38686--38732 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
38676 TCCTTCTATT
38686 CATCTATCATC-AAGTTTTTCATC
1 CATCTATCATCAAAGTTTTTCATC
38709 CATCTCATCCATCAAAGTTTTTCA
1 CATCT-AT-CATCAAAGTTTTTCA
38733 AATTTTCTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 5 0.24
24 2 0.10
25 4 0.19
26 10 0.48
ACGTcount: A:0.28, C:0.28, G:0.04, T:0.40
Consensus pattern (24 bp):
CATCTATCATCAAAGTTTTTCATC
Found at i:40745 original size:33 final size:34
Alignment explanation
Indices: 40719--40785 Score: 93
Period size: 33 Copynumber: 2.0 Consensus size: 34
40709 TTTCAATGCT
*
40719 ATGATCAACCAAAACAGATTTGTTTTC-ATCACA
1 ATGAGCAACCAAAACAGATTTGTTTTCAATCACA
* *
40752 ATTAGCATCCAAAACAGATTTGTTTTC-ATCACA
1 ATGAGCAACCAAAACAGATTTGTTTTCAATCACA
40785 A
1 A
40786 ACAACACCTA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.39, C:0.21, G:0.09, T:0.31
Consensus pattern (34 bp):
ATGAGCAACCAAAACAGATTTGTTTTCAATCACA
Found at i:40799 original size:33 final size:32
Alignment explanation
Indices: 40726--40830 Score: 131
Period size: 33 Copynumber: 3.2 Consensus size: 32
40716 GCTATGATCA
** *
40726 ACCAAAACAGATTTGTTTTCATCACAATTAGC
1 ACCAAAACAGATTTGTTTTCATCACAAACAAC
40758 ATCCAAAACAGATTTGTTTTCATCACAAACAAC
1 A-CCAAAACAGATTTGTTTTCATCACAAACAAC
*
40791 ACCTAAAACAGATTTAG-TGTCATCACAAACAAC
1 ACC-AAAACAGATTT-GTTTTCATCACAAACAAC
40824 ACTCAAA
1 AC-CAAA
40831 TTAGTTTTAG
Statistics
Matches: 65, Mismatches: 4, Indels: 7
0.86 0.05 0.09
Matches are distributed among these distances:
32 3 0.05
33 60 0.92
34 2 0.03
ACGTcount: A:0.43, C:0.24, G:0.08, T:0.26
Consensus pattern (32 bp):
ACCAAAACAGATTTGTTTTCATCACAAACAAC
Found at i:40840 original size:33 final size:33
Alignment explanation
Indices: 40762--40866 Score: 115
Period size: 33 Copynumber: 3.2 Consensus size: 33
40752 ATTAGCATCC
*
40762 AAAACAGATTT-GTTTTCATCACAAACAACACCT
1 AAAACAGATTTAG-TATCATCACAAACAACACCT
*
40795 AAAACAGATTTAGTGTCATCACAAACAACA-CT
1 AAAACAGATTTAGTATCATCACAAACAACACCT
** * * *
40827 CAAATTAGTTTTAGTATCATCACTAACAACATCT
1 -AAAACAGATTTAGTATCATCACAAACAACACCT
40861 AAAACA
1 AAAACA
40867 CTCTTTGCAA
Statistics
Matches: 61, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
32 2 0.03
33 56 0.92
34 3 0.05
ACGTcount: A:0.45, C:0.22, G:0.07, T:0.27
Consensus pattern (33 bp):
AAAACAGATTTAGTATCATCACAAACAACACCT
Found at i:43039 original size:22 final size:22
Alignment explanation
Indices: 43011--43053 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
43001 TTTTCCACAA
* *
43011 CAAGTCCAGGGCAGGAGTTGTC
1 CAAGTCCAGGACAGGACTTGTC
*
43033 CAAGTCCTGGACAGGACTTGT
1 CAAGTCCAGGACAGGACTTGT
43054 TCTGAATTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.23, C:0.23, G:0.33, T:0.21
Consensus pattern (22 bp):
CAAGTCCAGGACAGGACTTGTC
Found at i:43108 original size:50 final size:50
Alignment explanation
Indices: 43033--43153 Score: 174
Period size: 50 Copynumber: 2.4 Consensus size: 50
43023 AGGAGTTGTC
* * *
43033 CAAGTCCTGGACAGGACTTGTTCTGAATTTTCTTCCGTTTTTCAACAGAT
1 CAAGTCCTGGGCAGGAGTTGTTCTGAATTTTCTTCCGTCTTTCAACAGAT
*
43083 CAAGTCCTGGGCAGGAGTTGTTCTGATTTTTCTTCCGTCTTTCAACAGAT
1 CAAGTCCTGGGCAGGAGTTGTTCTGAATTTTCTTCCGTCTTTCAACAGAT
43133 CGGAA--CCTGGGCAGGAGTTGT
1 C--AAGTCCTGGGCAGGAGTTGT
43154 CAAGTCCTGG
Statistics
Matches: 65, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
50 63 0.97
52 2 0.03
ACGTcount: A:0.20, C:0.21, G:0.24, T:0.35
Consensus pattern (50 bp):
CAAGTCCTGGGCAGGAGTTGTTCTGAATTTTCTTCCGTCTTTCAACAGAT
Found at i:45322 original size:37 final size:37
Alignment explanation
Indices: 45272--45346 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
45262 GGTTTCGTTG
45272 CATCTAAGGAAGGAAAGGTTCCTTGAAAAGAGGAAGT
1 CATCTAAGGAAGGAAAGGTTCCTTGAAAAGAGGAAGT
45309 CATCTAAGGAAGGAAAGGTTCCTTGAAAAGAGGAAGT
1 CATCTAAGGAAGGAAAGGTTCCTTGAAAAGAGGAAGT
45346 C
1 C
45347 TAAGCTCTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.40, C:0.12, G:0.29, T:0.19
Consensus pattern (37 bp):
CATCTAAGGAAGGAAAGGTTCCTTGAAAAGAGGAAGT
Found at i:45991 original size:50 final size:50
Alignment explanation
Indices: 45873--45992 Score: 179
Period size: 50 Copynumber: 2.4 Consensus size: 50
45863 TAAAAACAGG
*
45873 ACAAGTCCTGCCCAGGACGTGGTCTGTTGAAAGACGACAGAAAAATCAAA
1 ACAAGTCCTGCCCAGGACTTGGTCTGTTGAAAGACGACAGAAAAATCAAA
* * *
45923 ACAACTCCTGCCCAGGACTTGGTCTGTTGAAAGACGGA-AGAAAATTCAGA
1 ACAAGTCCTGCCCAGGACTTGGTCTGTTGAAAGAC-GACAGAAAAATCAAA
*
45973 ACAAGTCCTGTCCAGGACTT
1 ACAAGTCCTGCCCAGGACTT
45993 AGACAACTCC
Statistics
Matches: 63, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
50 61 0.97
51 2 0.03
ACGTcount: A:0.34, C:0.23, G:0.23, T:0.19
Consensus pattern (50 bp):
ACAAGTCCTGCCCAGGACTTGGTCTGTTGAAAGACGACAGAAAAATCAAA
Found at i:46003 original size:22 final size:22
Alignment explanation
Indices: 45973--46014 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
45963 AAAATTCAGA
* *
45973 ACAAGTCCTGTCCAGGACTTAG
1 ACAACTCCTGCCCAGGACTTAG
*
45995 ACAACTCCTGCCCGGGACTT
1 ACAACTCCTGCCCAGGACTT
46015 GTTGCGGGAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.24, C:0.33, G:0.21, T:0.21
Consensus pattern (22 bp):
ACAACTCCTGCCCAGGACTTAG
Found at i:50175 original size:15 final size:15
Alignment explanation
Indices: 50155--50185 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
50145 CTTTATGCCT
50155 TAACCGGGTAATTGA
1 TAACCGGGTAATTGA
50170 TAACCGGGTAATTGA
1 TAACCGGGTAATTGA
50185 T
1 T
50186 TTGTTAAGTA
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:0.32, C:0.13, G:0.26, T:0.29
Consensus pattern (15 bp):
TAACCGGGTAATTGA
Found at i:50548 original size:23 final size:24
Alignment explanation
Indices: 50518--50562 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
50508 TTTTTTTTTG
*
50518 GTTTGCGTTTT-TGAAAAAAAAGA
1 GTTTGCGTTTTCTAAAAAAAAAGA
50541 GTTTGCGTTTTCTAAAAAAAAA
1 GTTTGCGTTTTCTAAAAAAAAA
50563 TATTTTGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.40, C:0.07, G:0.18, T:0.36
Consensus pattern (24 bp):
GTTTGCGTTTTCTAAAAAAAAAGA
Found at i:60216 original size:7 final size:7
Alignment explanation
Indices: 60204--60228 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
60194 ACAATTGAGT
60204 TTTTCCC
1 TTTTCCC
60211 TTTTCCC
1 TTTTCCC
60218 TTTTCCC
1 TTTTCCC
60225 TTTT
1 TTTT
60229 AATTTCTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (7 bp):
TTTTCCC
Found at i:68454 original size:47 final size:47
Alignment explanation
Indices: 68333--68913 Score: 905
Period size: 47 Copynumber: 12.4 Consensus size: 47
68323 TTGACTACTC
* * *
68333 TTTACTACTTAGTTTAATTACCTAGAATTAAAATAAGTTCTACTTCT
1 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAATTTCTTCTTCT
* * *
68380 TTT--TATTTAGATTAATTACCTAGAATTAAACTAAATTCTTCTTCT
1 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAATTTCTTCTTCT
* * * *
68425 TTTTCTACTTAGTTTAATTACCTAGAATTAAACTAAATTCTCCCTCT
1 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAATTTCTTCTTCT
* *
68472 TTTACTACTTAGTTTAATTACCTAGAATTAAACTGATTTCTCCTTCT
1 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAATTTCTTCTTCT
* * *
68519 TTTACTACTTAGTTTGATTACCTAGAATTAAACCAAATTCTTCTTCT
1 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAATTTCTTCTTCT
*
68566 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAATTTCTCCTTCT
1 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAATTTCTTCTTCT
* *
68613 TTTACTACTTAGTTTAATTACCTAGAATTAAACCACTTTCTTCTTCT
1 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAATTTCTTCTTCT
*
68660 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAATTTCTCCTTCT
1 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAATTTCTTCTTCT
* *
68707 TTTACTACTTAGTTTAATTACCTAGAATTAAACCACTTTCTTCTTCT
1 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAATTTCTTCTTCT
* * * *
68754 TTTTCTACTTAGTTTAATTACCTAGAATTAAACTAAATTCTCCCTCT
1 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAATTTCTTCTTCT
*
68801 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAATTTCTTCCTCT
1 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAATTTCTTCTTCT
68848 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAATTTCTTCTTCT
1 TTTACTACTTAGTTTAATTACCTAGAATTAAACTAATTTCTTCTTCT
*
68895 TTTACTATTTAGTTTAATT
1 TTTACTACTTAGTTTAATT
68914 CTATCTTCTT
Statistics
Matches: 490, Mismatches: 42, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
45 40 0.08
47 450 0.92
ACGTcount: A:0.30, C:0.18, G:0.05, T:0.47
Consensus pattern (47 bp):
TTTACTACTTAGTTTAATTACCTAGAATTAAACTAATTTCTTCTTCT
Found at i:73968 original size:27 final size:27
Alignment explanation
Indices: 73930--74000 Score: 108
Period size: 27 Copynumber: 2.7 Consensus size: 27
73920 ACAGTAATTT
*
73930 TGACCAAAATGCCCCTGGGGTGAAAAA
1 TGACCAAAATGCCCCTGGGGCGAAAAA
* *
73957 TGACCAAAATGCCCTTGAGGCGAAAAA
1 TGACCAAAATGCCCCTGGGGCGAAAAA
73984 -GACCAAAATGCCCCTGG
1 TGACCAAAATGCCCCTGG
74001 TGAATTTTTA
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
26 15 0.38
27 24 0.62
ACGTcount: A:0.37, C:0.25, G:0.24, T:0.14
Consensus pattern (27 bp):
TGACCAAAATGCCCCTGGGGCGAAAAA
Done.