Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011039.1 Corchorus capsularis cultivar CVL-1 contig11060, 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: 91627
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:9119 original size:3 final size:3
Alignment explanation
Indices: 9113--9148 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
9103 AATAATAAGC
*
9113 AGA AGA AGA AGG AGA AGA AGA AGA AGA AGA A-A AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
9149 ATCCCTTGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:12561 original size:13 final size:14
Alignment explanation
Indices: 12540--12595 Score: 53
Period size: 13 Copynumber: 3.9 Consensus size: 14
12530 TTCACCGCAA
12540 TTTCAAAAAGCACT
1 TTTCAAAAAGCACT
12554 TTTC-AAAAGCACT
1 TTTCAAAAAGCACT
*
12567 TATTCCAAACCAAGC-TT
1 T-TT-CAAA--AAGCACT
12584 TTTCAAAAAGCA
1 TTTCAAAAAGCA
12596 ACCTCAATAC
Statistics
Matches: 35, Mismatches: 1, Indels: 12
0.73 0.02 0.25
Matches are distributed among these distances:
13 14 0.40
14 6 0.17
15 5 0.14
16 4 0.11
17 2 0.06
18 4 0.11
ACGTcount: A:0.41, C:0.23, G:0.07, T:0.29
Consensus pattern (14 bp):
TTTCAAAAAGCACT
Found at i:31780 original size:29 final size:29
Alignment explanation
Indices: 31748--31805 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
31738 TATAAATATC
31748 TAGAAGAAGAAAGATTTTGGGATCTAAGT
1 TAGAAGAAGAAAGATTTTGGGATCTAAGT
31777 TAGAAGAAGAAAGATTTTGGGATCTAAGT
1 TAGAAGAAGAAAGATTTTGGGATCTAAGT
31806 AAGATTGCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.41, C:0.03, G:0.28, T:0.28
Consensus pattern (29 bp):
TAGAAGAAGAAAGATTTTGGGATCTAAGT
Found at i:35448 original size:18 final size:19
Alignment explanation
Indices: 35425--35462 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
35415 ATTGATCGGC
*
35425 TGAGTTTAG-TCAGTTTTT
1 TGAGTTCAGTTCAGTTTTT
35443 TGAGTTCAGTTCAGTTTTT
1 TGAGTTCAGTTCAGTTTTT
35462 T
1 T
35463 TTTTATTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.16, C:0.08, G:0.21, T:0.55
Consensus pattern (19 bp):
TGAGTTCAGTTCAGTTTTT
Found at i:42083 original size:34 final size:34
Alignment explanation
Indices: 42045--42112 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
42035 AAATCCTAAT
42045 CTAGTTCTTACCGAGTTTCTAAGTTATAAAATTC
1 CTAGTTCTTACCGAGTTTCTAAGTTATAAAATTC
*
42079 CTAGTTCTTACCGAGTTTTTAAGTTATAAAATTC
1 CTAGTTCTTACCGAGTTTCTAAGTTATAAAATTC
42113 ATAGCAAGAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.29, C:0.16, G:0.12, T:0.43
Consensus pattern (34 bp):
CTAGTTCTTACCGAGTTTCTAAGTTATAAAATTC
Found at i:43706 original size:27 final size:25
Alignment explanation
Indices: 43661--43715 Score: 83
Period size: 27 Copynumber: 2.1 Consensus size: 25
43651 AAATTTTCTA
*
43661 CAATTTTTTTTTAAGAAATTATCCT
1 CAATTTTTTTTGAAGAAATTATCCT
43686 CAATTTTTTTTGACAGAAAATTATCCT
1 CAATTTTTTTTGA-AG-AAATTATCCT
43713 CAA
1 CAA
43716 ATTTAATAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 12 0.44
26 2 0.07
27 13 0.48
ACGTcount: A:0.35, C:0.15, G:0.05, T:0.45
Consensus pattern (25 bp):
CAATTTTTTTTGAAGAAATTATCCT
Found at i:59971 original size:14 final size:14
Alignment explanation
Indices: 59952--59980 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
59942 TGGCGTTTTG
59952 AAATATAGTAAAAA
1 AAATATAGTAAAAA
59966 AAATATAGTAAAAA
1 AAATATAGTAAAAA
59980 A
1 A
59981 TACCCTCCGT
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:0.72, C:0.00, G:0.07, T:0.21
Consensus pattern (14 bp):
AAATATAGTAAAAA
Found at i:68985 original size:14 final size:14
Alignment explanation
Indices: 68966--68998 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
68956 CATGGAGGCG
68966 TTTTTTCTTGTTT-T
1 TTTTTTCTT-TTTAT
68980 TTTTTTCTTTTTAT
1 TTTTTTCTTTTTAT
68994 TTTTT
1 TTTTT
68999 ACCAAATTCC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 3 0.17
14 15 0.83
ACGTcount: A:0.03, C:0.06, G:0.03, T:0.88
Consensus pattern (14 bp):
TTTTTTCTTTTTAT
Found at i:72010 original size:21 final size:19
Alignment explanation
Indices: 71985--72042 Score: 53
Period size: 19 Copynumber: 2.9 Consensus size: 19
71975 GCTGCTCTAA
*
71985 TAATCTTATCTGTACAGTACC
1 TAATCTAATCTGTACAGT--C
* * *
72006 TAATCTAATATGTATAGTG
1 TAATCTAATCTGTACAGTC
*
72025 TAATCTCATCTGTACAGT
1 TAATCTAATCTGTACAGT
72043 TGCTAAACAG
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
19 15 0.50
21 15 0.50
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.40
Consensus pattern (19 bp):
TAATCTAATCTGTACAGTC
Found at i:72164 original size:2 final size:2
Alignment explanation
Indices: 72152--72182 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
72142 AAGTCTCTGA
72152 AT AT A- 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 AT AT
72183 TATCCAATTC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:75254 original size:2 final size:2
Alignment explanation
Indices: 75204--75236 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
75194 TGAAACTAGC
*
75204 AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
75237 ACAGAAATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:77929 original size:20 final size:20
Alignment explanation
Indices: 77892--77929 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
77882 TTCCATGAAG
*
77892 AGAGAGAAGAGAGTGTGAGC
1 AGAGAGAAGAGAGAGTGAGC
77912 AGAGAGACAGAGA-AGTGA
1 AGAGAGA-AGAGAGAGTGA
77930 CGAATAGTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.45, C:0.05, G:0.42, T:0.08
Consensus pattern (20 bp):
AGAGAGAAGAGAGAGTGAGC
Found at i:78675 original size:74 final size:74
Alignment explanation
Indices: 78573--78745 Score: 231
Period size: 74 Copynumber: 2.3 Consensus size: 74
78563 AGAGATTAAG
* * * * *
78573 TTTTGTCGATTTGTTATGTATC-TCCTTTTGTCGTCATATATATCATTATTCATTAATCTTGAGG
1 TTTTGTCGATTT-ATGTGTATCTTTCTTTTGTCGTCACACATATCATTATTCATTAATCTTGAGG
78637 TAAAATTCAT
65 TAAAATTCAT
* * *
78647 TTTTGTCGATTTATGTGTATCTTTCTTTTGTCGTCACACATATTATTCTTCATTAATTTTGAGGT
1 TTTTGTCGATTTATGTGTATCTTTCTTTTGTCGTCACACATATCATTATTCATTAATCTTGAGGT
*
78712 AAAGTTCAT
66 AAAATTCAT
* *
78721 TTTTGTGGATTTATGTATATCTTTC
1 TTTTGTCGATTTATGTGTATCTTTC
78746 AAAAAAAATT
Statistics
Matches: 87, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
73 7 0.08
74 80 0.92
ACGTcount: A:0.22, C:0.13, G:0.13, T:0.52
Consensus pattern (74 bp):
TTTTGTCGATTTATGTGTATCTTTCTTTTGTCGTCACACATATCATTATTCATTAATCTTGAGGT
AAAATTCAT
Found at i:78835 original size:112 final size:112
Alignment explanation
Indices: 78638--78857 Score: 413
Period size: 112 Copynumber: 2.0 Consensus size: 112
78628 ATCTTGAGGT
*
78638 AAAATTCATTTTTGTCGATTTATGTGTATCTTTCTTTTGTCGTCACACATATTATTCTTCATTAA
1 AAAATTCATTTTTGTCGATTTATGTGTATCTTTCTTTTGTCGTCACACATATCATTCTTCATTAA
*
78703 TTTTGAGGTAAAGTTCATTTTTGTGGATTTATGTATATCTTTCAAAA
66 TTTTGAGGTAAAGTTCATTTTTGTCGATTTATGTATATCTTTCAAAA
*
78750 AAAATTCATTTTTGTCGATTTATGTGTATCTTTCTTTTGTCGTCACACATATCATTTTTCATTAA
1 AAAATTCATTTTTGTCGATTTATGTGTATCTTTCTTTTGTCGTCACACATATCATTCTTCATTAA
78815 TTTTGAGGTAAAGTTCATTTTTGTCGATTTATGTATATCTTTC
66 TTTTGAGGTAAAGTTCATTTTTGTCGATTTATGTATATCTTTC
78858 TTTTGTTATC
Statistics
Matches: 105, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
112 105 1.00
ACGTcount: A:0.25, C:0.12, G:0.12, T:0.51
Consensus pattern (112 bp):
AAAATTCATTTTTGTCGATTTATGTGTATCTTTCTTTTGTCGTCACACATATCATTCTTCATTAA
TTTTGAGGTAAAGTTCATTTTTGTCGATTTATGTATATCTTTCAAAA
Found at i:78933 original size:106 final size:104
Alignment explanation
Indices: 78771--79258 Score: 544
Period size: 106 Copynumber: 4.7 Consensus size: 104
78761 TTGTCGATTT
*
78771 ATGTGTATCTTTCTTTTGTCGTCACACATATCATTTTTCATTAATTTTGAGGTAAAGTTCATTTT
1 ATGTGTATCTTTCTTTTGTCGTCACACATATCATTCTTCATTAATTTTGAGGTAAAGTTCATTTT
78836 TGTCGATTTATGTATATCTTTC-TT-TTGTTATCCAAAAAAAA
66 TGTCGATTTATGTATATCTTTCATTATTGTTAT-C---AAAAA
* *
78877 ATGTATATCTTTCTTTTGTCGTTACACATATCATTCTTCATTAATTTTGAGGTAAAGTTCATTTT
1 ATGTGTATCTTTCTTTTGTCGTCACACATATCATTCTTCATTAATTTTGAGGTAAAGTTCATTTT
* * *
78942 TGTCGATTTA--T-CA--TTT--TTGTCGATT-T------
66 TGTCGATTTATGTATATCTTTCATTATTG-TTATCAAAAA
78968 ATGTGTATCTTTCTTTTGTCGTCACACATATCATTCTTCATTAATTTTGAGGTAAAGTTCATTTT
1 ATGTGTATCTTTCTTTTGTCGTCACACATATCATTCTTCATTAATTTTGAGGTAAAGTTCATTTT
* * * * ***
79033 TGTCGATTTATGTATATCTTTAAAAAAATTCATTTTTGTCGATTT
66 TGTCGATTTATGTATATCTTT-----CATT-ATTGTTATCAAAAA
*
79078 ATGTGTATCTTTCTTTTGTCGTCACACATATCATTTTTCATTAATTTTGAGGTAAAGTTCATTTT
1 ATGTGTATCTTTCTTTTGTCGTCACACATATCATTCTTCATTAATTTTGAGGTAAAGTTCATTTT
79143 TGTCGATTTATGTATATCTTTC-TT-TTGTTATCCAAAAAAAA
66 TGTCGATTTATGTATATCTTTCATTATTGTTAT-C---AAAAA
* * * *
79184 ATGTATATCTTTCTTTTGTCGTTACACATATCATTTTTCATTAATTTTGAGGTAAAATTCATTTT
1 ATGTGTATCTTTCTTTTGTCGTCACACATATCATTCTTCATTAATTTTGAGGTAAAGTTCA-TTT
79249 TTGTCGATTT
65 TTGTCGATTT
79259 CGTGTGCATG
Statistics
Matches: 333, Mismatches: 22, Indels: 53
0.82 0.05 0.13
Matches are distributed among these distances:
91 73 0.22
93 1 0.00
94 1 0.00
96 3 0.01
100 2 0.01
101 6 0.02
102 7 0.02
103 6 0.02
104 5 0.02
106 131 0.39
107 13 0.04
110 85 0.26
ACGTcount: A:0.25, C:0.13, G:0.11, T:0.51
Consensus pattern (104 bp):
ATGTGTATCTTTCTTTTGTCGTCACACATATCATTCTTCATTAATTTTGAGGTAAAGTTCATTTT
TGTCGATTTATGTATATCTTTCATTATTGTTATCAAAAA
Found at i:78955 original size:17 final size:17
Alignment explanation
Indices: 78935--78969 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
78925 GAGGTAAAGT
78935 TCATTTTTGTCGATTTA
1 TCATTTTTGTCGATTTA
78952 TCATTTTTGTCGATTTA
1 TCATTTTTGTCGATTTA
78969 T
1 T
78970 GTGTATCTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.17, C:0.11, G:0.11, T:0.60
Consensus pattern (17 bp):
TCATTTTTGTCGATTTA
Found at i:78980 original size:91 final size:91
Alignment explanation
Indices: 78877--79043 Score: 316
Period size: 91 Copynumber: 1.8 Consensus size: 91
78867 CCAAAAAAAA
*
78877 ATGTATATCTTTCTTTTGTCGTTACACATATCATTCTTCATTAATTTTGAGGTAAAGTTCATTTT
1 ATGTATATCTTTCTTTTGTCGTCACACATATCATTCTTCATTAATTTTGAGGTAAAGTTCATTTT
78942 TGTCGATTTATCATTTTTGTCGATTT
66 TGTCGATTTATCATTTTTGTCGATTT
*
78968 ATGTGTATCTTTCTTTTGTCGTCACACATATCATTCTTCATTAATTTTGAGGTAAAGTTCATTTT
1 ATGTATATCTTTCTTTTGTCGTCACACATATCATTCTTCATTAATTTTGAGGTAAAGTTCATTTT
79033 TGTCGATTTAT
66 TGTCGATTTAT
79044 GTATATCTTT
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
91 74 1.00
ACGTcount: A:0.22, C:0.14, G:0.13, T:0.51
Consensus pattern (91 bp):
ATGTATATCTTTCTTTTGTCGTCACACATATCATTCTTCATTAATTTTGAGGTAAAGTTCATTTT
TGTCGATTTATCATTTTTGTCGATTT
Found at i:79079 original size:110 final size:110
Alignment explanation
Indices: 78952--79163 Score: 415
Period size: 110 Copynumber: 1.9 Consensus size: 110
78942 TGTCGATTTA
78952 TCATTTTTGTCGATTTATGTGTATCTTTCTTTTGTCGTCACACATATCATTCTTCATTAATTTTG
1 TCATTTTTGTCGATTTATGTGTATCTTTCTTTTGTCGTCACACATATCATTCTTCATTAATTTTG
79017 AGGTAAAGTTCATTTTTGTCGATTTATGTATATCTTTAAAAAAAT
66 AGGTAAAGTTCATTTTTGTCGATTTATGTATATCTTTAAAAAAAT
*
79062 TCATTTTTGTCGATTTATGTGTATCTTTCTTTTGTCGTCACACATATCATTTTTCATTAATTTTG
1 TCATTTTTGTCGATTTATGTGTATCTTTCTTTTGTCGTCACACATATCATTCTTCATTAATTTTG
79127 AGGTAAAGTTCATTTTTGTCGATTTATGTATATCTTT
66 AGGTAAAGTTCATTTTTGTCGATTTATGTATATCTTT
79164 CTTTTGTTAT
Statistics
Matches: 101, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
110 101 1.00
ACGTcount: A:0.23, C:0.13, G:0.12, T:0.52
Consensus pattern (110 bp):
TCATTTTTGTCGATTTATGTGTATCTTTCTTTTGTCGTCACACATATCATTCTTCATTAATTTTG
AGGTAAAGTTCATTTTTGTCGATTTATGTATATCTTTAAAAAAAT
Found at i:79199 original size:110 final size:106
Alignment explanation
Indices: 78968--79258 Score: 343
Period size: 110 Copynumber: 2.7 Consensus size: 106
78958 TTGTCGATTT
* *
78968 ATGTGTATCTTTCTTTTGTCGTCACACATATCATTCTTCATTAATTTTGAGGTAAAGTTCATTTT
1 ATGTATATCTTTCTTTTGTCGTCACACATATCATTTTTCATTAATTTTGAGGTAAAGTTCATTTT
**** ***
79033 TGTCGATTTATGTATATCTTTAAAAAAATTCATTTTTGTCGATTT
66 TGTCGATTTATGTATATCTTTAAAAAAATTCA----TAAAAAAAA
*
79078 ATGTGTATCTTTCTTTTGTCGTCACACATATCATTTTTCATTAATTTTGAGGTAAAGTTCATTTT
1 ATGTATATCTTTCTTTTGTCGTCACACATATCATTTTTCATTAATTTTGAGGTAAAGTTCATTTT
******
79143 TGTCGATTTATGTATATCTTT-CTTTTGTT-ATCCAAAAAAAA
66 TGTCGATTTATGTATATCTTTAAAAAAATTCAT--AAAAAAAA
* *
79184 ATGTATATCTTTCTTTTGTCGTTACACATATCATTTTTCATTAATTTTGAGGTAAAATTCATTTT
1 ATGTATATCTTTCTTTTGTCGTCACACATATCATTTTTCATTAATTTTGAGGTAAAGTTCA-TTT
79249 TTGTCGATTT
65 TTGTCGATTT
79259 CGTGTGCATG
Statistics
Matches: 161, Mismatches: 17, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
104 1 0.01
106 59 0.37
107 13 0.08
108 1 0.01
109 2 0.01
110 85 0.53
ACGTcount: A:0.25, C:0.13, G:0.11, T:0.51
Consensus pattern (106 bp):
ATGTATATCTTTCTTTTGTCGTCACACATATCATTTTTCATTAATTTTGAGGTAAAGTTCATTTT
TGTCGATTTATGTATATCTTTAAAAAAATTCATAAAAAAAA
Found at i:79199 original size:307 final size:309
Alignment explanation
Indices: 78643--79258 Score: 1173
Period size: 307 Copynumber: 2.0 Consensus size: 309
78633 GAGGTAAAAT
*
78643 TCATTTTTGTCGATTTATGTGTATCTTTCTTTTGTCGTCACACATATTATTCTTCATTAATTTTG
1 TCATTTTTGTCGATTTATGTGTATCTTTCTTTTGTCGTCACACATATCATTCTTCATTAATTTTG
*
78708 AGGTAAAGTTCATTTTTGTGGATTTATGTATATCTTTCAAAAAAAATTCATTTTTGTCGATTTAT
66 AGGTAAAGTTCATTTTTGTCGATTTATGTATATCTTT-AAAAAAAATTCATTTTTGTCGATTTAT
78773 GTGTATCTTTCTTTTGTCGTCACACATATCATTTTTCATTAATTTTGAGGTAAAGTTCATTTTTG
130 GTGTATCTTTCTTTTGTCGTCACACATATCATTTTTCATTAATTTTGAGGTAAAGTTCATTTTTG
78838 TCGATTTATGTATATCTTTCTTTTGTTATCCAAAAAAAAATGTATATCTTTCTTTTGTCGTTACA
195 TCGATTTATGTATATCTTTCTTTTGTTATCCAAAAAAAAATGTATATCTTTCTTTTGTCGTTACA
*
78903 CATATCATTCTTCATTAATTTTGAGGTAAAGTTCA-TTTTTGTCGATTTA
260 CATATCATTCTTCATTAATTTTGAGGTAAAATTCATTTTTTGTCGATTTA
78952 TCATTTTTGTCGATTTATGTGTATCTTTCTTTTGTCGTCACACATATCATTCTTCATTAATTTTG
1 TCATTTTTGTCGATTTATGTGTATCTTTCTTTTGTCGTCACACATATCATTCTTCATTAATTTTG
79017 AGGTAAAGTTCATTTTTGTCGATTTATGTATATCTTT-AAAAAAATTCATTTTTGTCGATTTATG
66 AGGTAAAGTTCATTTTTGTCGATTTATGTATATCTTTAAAAAAAATTCATTTTTGTCGATTTATG
79081 TGTATCTTTCTTTTGTCGTCACACATATCATTTTTCATTAATTTTGAGGTAAAGTTCATTTTTGT
131 TGTATCTTTCTTTTGTCGTCACACATATCATTTTTCATTAATTTTGAGGTAAAGTTCATTTTTGT
79146 CGATTTATGTATATCTTTCTTTTGTTATCCAAAAAAAAATGTATATCTTTCTTTTGTCGTTACAC
196 CGATTTATGTATATCTTTCTTTTGTTATCCAAAAAAAAATGTATATCTTTCTTTTGTCGTTACAC
*
79211 ATATCATTTTTCATTAATTTTGAGGTAAAATTCATTTTTTGTCGATTT
261 ATATCATTCTTCATTAATTTTGAGGTAAAATTCATTTTTTGTCGATTT
79259 CGTGTGCATG
Statistics
Matches: 302, Mismatches: 4, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
307 189 0.63
308 13 0.04
309 100 0.33
ACGTcount: A:0.25, C:0.13, G:0.12, T:0.51
Consensus pattern (309 bp):
TCATTTTTGTCGATTTATGTGTATCTTTCTTTTGTCGTCACACATATCATTCTTCATTAATTTTG
AGGTAAAGTTCATTTTTGTCGATTTATGTATATCTTTAAAAAAAATTCATTTTTGTCGATTTATG
TGTATCTTTCTTTTGTCGTCACACATATCATTTTTCATTAATTTTGAGGTAAAGTTCATTTTTGT
CGATTTATGTATATCTTTCTTTTGTTATCCAAAAAAAAATGTATATCTTTCTTTTGTCGTTACAC
ATATCATTCTTCATTAATTTTGAGGTAAAATTCATTTTTTGTCGATTTA
Found at i:79392 original size:54 final size:54
Alignment explanation
Indices: 79327--79434 Score: 189
Period size: 54 Copynumber: 2.0 Consensus size: 54
79317 TCGATTTCAT
* *
79327 ATGTGTATCTTCCTTTTGTCGTCACACATATCATTATATTAATCATTAATTTTC
1 ATGTATATCTTCCTTTTGTCGTCACACATAACATTATATTAATCATTAATTTTC
*
79381 ATGTATATCTTCCTTTTGTCGTCACATATAACATTATATTAATCATTAATTTTC
1 ATGTATATCTTCCTTTTGTCGTCACACATAACATTATATTAATCATTAATTTTC
79435 TTGTCGATTT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 51 1.00
ACGTcount: A:0.28, C:0.18, G:0.06, T:0.48
Consensus pattern (54 bp):
ATGTATATCTTCCTTTTGTCGTCACACATAACATTATATTAATCATTAATTTTC
Found at i:84076 original size:22 final size:22
Alignment explanation
Indices: 84036--84078 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
84026 TGAAAATGAA
* *
84036 ACTGAAACAGAAACTGAGACTC
1 ACTGAAACACAAACAGAGACTC
*
84058 ACTGAAACACAAAGAGAGACT
1 ACTGAAACACAAACAGAGACT
84079 GAAACTGAGA
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:0.49, C:0.21, G:0.19, T:0.12
Consensus pattern (22 bp):
ACTGAAACACAAACAGAGACTC
Done.