Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014350.1 Corchorus olitorius cultivar O-4 contig14383, 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: 77254
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:10762 original size:23 final size:23
Alignment explanation
Indices: 10727--10770 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
10717 CCGCTATGCC
*
10727 CCTTTCTTGCTTTTTTTTTTTTA
1 CCTTTCTTGCTTTTTCTTTTTTA
10750 CCTTT-TTGTCTTTTTCTTTTT
1 CCTTTCTTG-CTTTTTCTTTTT
10771 CTTGTCTTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 3 0.16
23 16 0.84
ACGTcount: A:0.02, C:0.18, G:0.05, T:0.75
Consensus pattern (23 bp):
CCTTTCTTGCTTTTTCTTTTTTA
Found at i:15559 original size:32 final size:32
Alignment explanation
Indices: 15480--15569 Score: 112
Period size: 32 Copynumber: 2.8 Consensus size: 32
15470 TGGCGTTTAC
* * *
15480 TGAAGAAAACGCCACCAATTAGTGACTTCTCA
1 TGAAGAAAACGCCACTATTTAGTGGCTTCTCA
15512 TGAAGAAAACGCCACTATTTAGTGGCTTCT-A
1 TGAAGAAAACGCCACTATTTAGTGGCTTCTCA
*
15543 TTGAA-ACAAACGCCACTATTAAGTGGC
1 -TGAAGA-AAACGCCACTATTTAGTGGC
15570 AAATCCTAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
31 2 0.04
32 50 0.96
ACGTcount: A:0.36, C:0.22, G:0.18, T:0.24
Consensus pattern (32 bp):
TGAAGAAAACGCCACTATTTAGTGGCTTCTCA
Found at i:24193 original size:23 final size:24
Alignment explanation
Indices: 24145--24194 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 24
24135 ATCATTATAT
24145 AAACACAAATAATTATGTTTTAAAAA
1 AAACACAAATAATTA--TTTTAAAAA
24171 AAACACAAATAATTA-TTTAAAAA
1 AAACACAAATAATTATTTTAAAAA
24194 A
1 A
24195 TCATATATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
23 9 0.38
26 15 0.62
ACGTcount: A:0.62, C:0.08, G:0.02, T:0.28
Consensus pattern (24 bp):
AAACACAAATAATTATTTTAAAAA
Found at i:24365 original size:28 final size:28
Alignment explanation
Indices: 24325--24378 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
24315 AACCACCACC
*
24325 TTGATCAGCTTTTGAATTTGAAGACATT
1 TTGATCAGCTTTTGAATATGAAGACATT
*
24353 TTGATCATCTTTTGAATATGAAGACA
1 TTGATCAGCTTTTGAATATGAAGACA
24379 CTCAACTTAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.31, C:0.11, G:0.17, T:0.41
Consensus pattern (28 bp):
TTGATCAGCTTTTGAATATGAAGACATT
Found at i:25444 original size:26 final size:26
Alignment explanation
Indices: 25415--25468 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
25405 AAAAGTCACC
* * *
25415 CAGGGGCATTTTGGTCATTTTTACTT
1 CAGGGGCACTTTAGTCATTTTTAATT
25441 CAGGGGCACTTTAGTCATTTTTAATT
1 CAGGGGCACTTTAGTCATTTTTAATT
25467 CA
1 CA
25469 TTGCTAGCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.20, C:0.17, G:0.20, T:0.43
Consensus pattern (26 bp):
CAGGGGCACTTTAGTCATTTTTAATT
Found at i:29740 original size:40 final size:40
Alignment explanation
Indices: 29675--30301 Score: 516
Period size: 40 Copynumber: 14.9 Consensus size: 40
29665 TGTCCGTTTC
* * *
29675 CCAGTTTGCCCTTCCCCACCTGAAGGTGTTGTTTAGTTTA
1 CCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTTAGATTA
* *
29715 CCAATTTGCCCTTCCTCATCGGAAGGTGTTGTTTAAGTCTACTTTA
1 CCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTT-AG---A--TTA
* * * * *
29761 CCCAATTTGCCCTTCCTCACCGGGAGGTGTTGCTTAGATTA
1 -CCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTTAGATTA
* * *
29802 CCAATTTTCCCTTCCCCACCGGAAGGTGTTGTTTAGATTA
1 CCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTTAGATTA
* * * *
29842 CCAATTTGCCCTTCCCCATCGGAAGGTGTTGTCTAAATTC
1 CCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTTAGATTA
* *
29882 CCAGTTTACCCTTCCTCATCGGAAGGTGTTGTTTAAGTCTACTTTA
1 CCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTT-AG---A--TTA
* * * * * *
29928 CCCAATTTGCCCTTCCCTACCGGAAGGTGTTGTCTAAATTC
1 -CCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTTAGATTA
* * * * * *
29969 CCAATTTACCCTTCCCCATCGGAAGGTGTTGTCTAAACTC
1 CCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTTAGATTA
*
30009 CCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTAAGTTTAATTTA
1 CCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTT-AG----A-TTA
* * * *
30055 CCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTCTAAATTC
1 CCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTTAGATTA
*
30095 CCAGTTTGCCCTTCCCTATCGGAAGGTGTTGTTTAAGTTTAGTTTA
1 CCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTT-AG---A--TTA
* * * * *
30141 CCAGTTTGCCCTTCCCCACCGGAAGGTGTGGTCTAAATTC
1 CCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTTAGATTA
*
30181 CCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTAAGTTTAGTTTA
1 CCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTT-AG---A--TTA
** * * *
30227 CCAGTTTGCCCTTCCCCGCCGGAAGGTGTTGTCTAAATTC
1 CCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTTAGATTA
* *
30267 CCAGTTTGCCCTTCCTCATTGGAAGGTGTTGTTTA
1 CCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTTA
30302 AGTCTGCTTT
Statistics
Matches: 480, Mismatches: 75, Indels: 64
0.78 0.12 0.10
Matches are distributed among these distances:
40 294 0.61
41 12 0.03
42 2 0.00
43 2 0.00
44 3 0.01
45 4 0.01
46 104 0.22
47 59 0.12
ACGTcount: A:0.18, C:0.27, G:0.20, T:0.35
Consensus pattern (40 bp):
CCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTTAGATTA
Found at i:29933 original size:127 final size:127
Alignment explanation
Indices: 29674--30328 Score: 683
Period size: 127 Copynumber: 5.1 Consensus size: 127
29664 TTGTCCGTTT
* * *
29674 CCCAGTTTGCCCTTCCCCACCTGAAGGTGTTGTTTAGTTTACCAATTTGCCCTTCCTCATCGGAA
1 CCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAGATTACCAATTTGCCCTTCCCCATCGGAA
* * * * *
29739 GGTGTTGTTTAAGTCTACTTTACCCAATTTGCCCTTCCTCACCGGGAGGTGTTGCTT-AG----A
66 GGTGTTGTCTAA----A--TT-CCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTAAGTCTAA
29799 -TTA
124 TTTA
* *
29802 -CCAATTTTCCCTTCCCCACCGGAAGGTGTTGTTTAGATTACCAATTTGCCCTTCCCCATCGGAA
1 CCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAGATTACCAATTTGCCCTTCCCCATCGGAA
* *
29866 GGTGTTGTCTAAATTCCCAGTTTACCCTTCCTCATCGGAAGGTGTTGTTTAAGTCTACTTTA
66 GGTGTTGTCTAAATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTAAGTCTAATTTA
* * * * * *
29928 CCCAATTTGCCCTTCCCTACCGGAAGGTGTTGTCTAAATTCCCAATTTACCCTTCCCCATCGGAA
1 CCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAGATTACCAATTTGCCCTTCCCCATCGGAA
* *
29993 GGTGTTGTCTAAACTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTAAGTTTAATTTA
66 GGTGTTGTCTAAATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTAAGTCTAATTTA
* * * * *
30055 -CCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTCTAAATTCCCAGTTTGCCCTTCCCTATCGGAA
1 CCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAGATTACCAATTTGCCCTTCCCCATCGGAA
* * * * *
30119 GGTGTTGTTTAAGTTTAGTTTACCAGTTTGCCCTTCCCCACCGGAAGGTG-TG-----GTCTAAA
66 GGTGTTGTCTAA----A--TTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTAAGTCTAAT
30178 TT-
125 TTA
* * * *
30180 CCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTAAGTTTAGTTTACCAGTTTGCCCTTCCCCG
1 CCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTT-AG---A--TTACCAATTTGCCCTTCCCCA
* * **
30245 CCGGAAGGTGTTGTCTAAATTCCCAGTTTGCCCTTCCTCATTGGAAGGTGTTGTTTAAGTCTGCT
60 TCGGAAGGTGTTGTCTAAATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTAAGTCTAAT
30310 TTA
125 TTA
*
30313 CCCAGTTTACCCTTCC
1 CCCAGTTTGCCCTTCC
30329 TCATCGGGAG
Statistics
Matches: 449, Mismatches: 51, Indels: 49
0.82 0.09 0.09
Matches are distributed among these distances:
120 30 0.07
121 4 0.01
123 1 0.00
126 138 0.31
127 189 0.42
128 1 0.00
130 2 0.00
131 2 0.00
132 67 0.15
133 15 0.03
ACGTcount: A:0.18, C:0.27, G:0.19, T:0.35
Consensus pattern (127 bp):
CCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAGATTACCAATTTGCCCTTCCCCATCGGAA
GGTGTTGTCTAAATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTAAGTCTAATTTA
Found at i:29958 original size:167 final size:166
Alignment explanation
Indices: 29672--30258 Score: 641
Period size: 167 Copynumber: 3.5 Consensus size: 166
29662 CCTTGTCCGT
* * ** *
29672 TTCCCAGTTTGCCCTTCCCCACCTGAAGGTGTTGTTTAGTTTACCAATTTGCCCTTCCTCATCGG
1 TTCCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTTAAATTACCAGTTTGCCCTTCCTCATCGG
*
29737 AAGGTGTTGTTTAAGTCTACTTTACCCAATTTGCCCTT-CCTCACCGGGAGGTGTTGCTTAGATT
66 AAGGTGTTGTTTAAGTCTACTTTACCCAATTTGCCCTTCCCT-ACCGGAAGGTGTTG-TTAGATT
* * *
29801 ACCAATTTTCCCTTCCCCACCGGAAGGTGTTGTTTAGA
129 ACCAATTTACCCTTCCCCACCGGAAGGTGTTGTCTAAA
* * * * *
29839 TTACCAATTTGCCCTTCCCCATCGGAAGGTGTTGTCTAAATTCCCAGTTTACCCTTCCTCATCGG
1 TTCCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTTAAATTACCAGTTTGCCCTTCCTCATCGG
* *
29904 AAGGTGTTGTTTAAGTCTACTTTACCCAATTTGCCCTTCCCTACCGGAAGGTGTTGTCTAAATTC
66 AAGGTGTTGTTTAAGTCTACTTTACCCAATTTGCCCTTCCCTACCGGAAGGTGTTGT-TAGATTA
*
29969 CCAATTTACCCTTCCCCATCGGAAGGTGTTGTCTAAA
130 CCAATTTACCCTTCCCCACCGGAAGGTGTTGTCTAAA
* * *
30006 CTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTAAGTTTAATTTACCAGTTTGCCCTTCCC
1 TTCCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTT-A----AA-TTACCAGTTTGCCCTTCCT
* * * *
30071 CACCGGAAGGTGTTGTCTAA----A--TT-CCCAGTTTGCCCTTCCCTATCGGAAGGTGTTGTTT
60 CATCGGAAGGTGTTGTTTAAGTCTACTTTACCCAATTTGCCCTTCCCTACCGGAAGGTGTTG-TT
* * *
30129 AAGTTTAGTTTACCAGTTTGCCCTTCCCCACCGGAAGGTGTGGTCTAAA
124 -AG---A--TTACCAATTTACCCTTCCCCACCGGAAGGTGTTGTCTAAA
* *
30178 TTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTAAGTTTAGTTTACCAGTTTGCCCTTCCC
1 TTCCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTTAA----A--TTACCAGTTTGCCCTTCCT
**
30243 CGCCGGAAGGTGTTGT
60 CATCGGAAGGTGTTGT
30259 CTAAATTCCC
Statistics
Matches: 363, Mismatches: 37, Indels: 35
0.83 0.09 0.08
Matches are distributed among these distances:
166 32 0.09
167 181 0.50
168 4 0.01
169 1 0.00
170 1 0.00
171 2 0.01
172 108 0.30
173 34 0.09
ACGTcount: A:0.18, C:0.27, G:0.20, T:0.35
Consensus pattern (166 bp):
TTCCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTTAAATTACCAGTTTGCCCTTCCTCATCGG
AAGGTGTTGTTTAAGTCTACTTTACCCAATTTGCCCTTCCCTACCGGAAGGTGTTGTTAGATTAC
CAATTTACCCTTCCCCACCGGAAGGTGTTGTCTAAA
Found at i:30079 original size:86 final size:86
Alignment explanation
Indices: 29705--30387 Score: 645
Period size: 86 Copynumber: 8.0 Consensus size: 86
29695 TGAAGGTGTT
* * * * *
29705 GTTTAGTTTACCAATTTGCCCTTCCTCATCGGAAGGTGTTGTTTAAGTCTACTTTACCCAATTTG
1 GTTTAGTTTACCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTCTAA----A--TT-CCCAGTTTG
* * *
29770 CCCTTCCTCACCGGGAGGTGTTGCTT-A
59 CCCTTCCTCATCGGAAGGTGTTGTTTAA
* * * * * *
29797 G---A--TTACCAATTTTCCCTTCCCCACCGGAAGGTGTTGTTTAGATTACCAATTTGCCCTTCC
1 GTTTAGTTTACCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTCTAAATTCCCAGTTTGCCCTTCC
* *
29857 CCATCGGAAGGTGTTGTCTAA
66 TCATCGGAAGGTGTTGTTTAA
* * * * * *
29878 ----A--TTCCCAGTTTACCCTTCCTCATCGGAAGGTGTTGTTTAAGTCTACTTTACCCAATTTG
1 GTTTAGTTTACCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTCTAA----A--TT-CCCAGTTTG
* *
29937 CCCTTCC-CTACCGGAAGGTGTTGTCTAA
59 CCCTTCCTC-ATCGGAAGGTGTTGTTTAA
* * * * *
29965 ----A--TTCCCAATTTACCCTTCCCCATCGGAAGGTGTTGTCTAAACTCCCAGTTTGCCCTTCC
1 GTTTAGTTTACCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTCTAAATTCCCAGTTTGCCCTTCC
30024 TCATCGGAAGGTGTTGTTTAA
66 TCATCGGAAGGTGTTGTTTAA
*
30045 GTTTAATTTACCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTCTAAATTCCCAGTTTGCCCTTCC
1 GTTTAGTTTACCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTCTAAATTCCCAGTTTGCCCTTCC
30110 -CTATCGGAAGGTGTTGTTTAA
66 TC-ATCGGAAGGTGTTGTTTAA
*
30131 GTTTAGTTTACCAGTTTGCCCTTCCCCACCGGAAGGTGTGGTCTAAATTCCCAGTTTGCCCTTCC
1 GTTTAGTTTACCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTCTAAATTCCCAGTTTGCCCTTCC
30196 TCATCGGAAGGTGTTGTTTAA
66 TCATCGGAAGGTGTTGTTTAA
*
30217 GTTTAGTTTACCAGTTTGCCCTTCCCCGCCGGAAGGTGTTGTCTAAATTCCCAGTTTGCCCTTCC
1 GTTTAGTTTACCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTCTAAATTCCCAGTTTGCCCTTCC
*
30282 TCATTGGAAGGTGTTGTTTAA
66 TCATCGGAAGGTGTTGTTTAA
* * * * * * ** *
30303 GTCT-GCTTTACCCAGTTTACCCTTCCTCATCGGGAGATGTTGTCTACAATTCTTAGTGTGCCCT
1 GTTTAG-TTTA-CCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTCTA-AATTCCCAGTTTGCCCT
*
30367 CCCTCATC-GAGAGGTGTTGTT
63 TCCTCATCGGA-AGGTGTTGTT
30388 CCTATTCCTG
Statistics
Matches: 522, Mismatches: 47, Indels: 48
0.85 0.08 0.08
Matches are distributed among these distances:
80 95 0.18
81 5 0.01
83 2 0.00
84 2 0.00
85 2 0.00
86 247 0.47
87 137 0.26
88 30 0.06
89 1 0.00
92 1 0.00
ACGTcount: A:0.18, C:0.26, G:0.20, T:0.36
Consensus pattern (86 bp):
GTTTAGTTTACCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTCTAAATTCCCAGTTTGCCCTTCC
TCATCGGAAGGTGTTGTTTAA
Found at i:36266 original size:28 final size:28
Alignment explanation
Indices: 36235--36312 Score: 129
Period size: 28 Copynumber: 2.8 Consensus size: 28
36225 AAACGATAGA
*
36235 ACCACCGGCATCGACCCCAAACGGCAAC
1 ACCACCGGCATCGACCCCAAACGACAAC
* *
36263 ACCACCGGCGTCGTCCCCAAACGACAAC
1 ACCACCGGCATCGACCCCAAACGACAAC
36291 ACCACCGGCATCGACCCCAAAC
1 ACCACCGGCATCGACCCCAAAC
36313 CAATTGCAGA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 45 1.00
ACGTcount: A:0.31, C:0.47, G:0.17, T:0.05
Consensus pattern (28 bp):
ACCACCGGCATCGACCCCAAACGACAAC
Found at i:44816 original size:21 final size:21
Alignment explanation
Indices: 44792--44836 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
44782 ATGACACTGC
* *
44792 CCACCTGGGTGATCAGACAAA
1 CCACATGGGTCATCAGACAAA
*
44813 CCACATGGGTCTTCAGACAAA
1 CCACATGGGTCATCAGACAAA
44834 CCA
1 CCA
44837 TGTGGGCGCC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.31, G:0.20, T:0.16
Consensus pattern (21 bp):
CCACATGGGTCATCAGACAAA
Found at i:50982 original size:19 final size:18
Alignment explanation
Indices: 50958--50993 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
50948 TGAAGACTTA
50958 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
50977 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
50994 ATTATCTCGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:53036 original size:34 final size:34
Alignment explanation
Indices: 52993--53057 Score: 112
Period size: 34 Copynumber: 1.9 Consensus size: 34
52983 TATATCATAT
52993 TAAAATCCATAAATAACATACATTTCAAATGTAA
1 TAAAATCCATAAATAACATACATTTCAAATGTAA
**
53027 TAAAATCCATAAATAACATTTATTTCAAATG
1 TAAAATCCATAAATAACATACATTTCAAATG
53058 CACCATATGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.51, C:0.14, G:0.03, T:0.32
Consensus pattern (34 bp):
TAAAATCCATAAATAACATACATTTCAAATGTAA
Found at i:54763 original size:63 final size:62
Alignment explanation
Indices: 54687--54886 Score: 285
Period size: 63 Copynumber: 3.2 Consensus size: 62
54677 ATTCCACTAA
*
54687 AAAAAACAGCATCTTTTACCTCAACTTATAAAAAAACAGAACTTTTGTATATATGGAAACCTC
1 AAAAAACAGCATCTTTTACCTCAACTTAT-AAAAAACAGAAATTTTGTATATATGGAAACCTC
* * * *
54750 AAAAAACAGCATCTTTTACCTGAAGCTTATAAAAGACAGAAAATTTGTATCTATGGAAACCTC
1 AAAAAACAGCATCTTTTACCTCAA-CTTATAAAAAACAGAAATTTTGTATATATGGAAACCTC
* * * *
54813 AAATAACAACAT-TTTTACCTCAAACATATAACAAACAGAAATTTTGTATATATGGAAACCTC
1 AAAAAACAGCATCTTTTACCTC-AACTTATAAAAAACAGAAATTTTGTATATATGGAAACCTC
54875 AAAAAACAGCAT
1 AAAAAACAGCAT
54887 TTTGGTTCTC
Statistics
Matches: 120, Mismatches: 15, Indels: 5
0.86 0.11 0.04
Matches are distributed among these distances:
62 51 0.43
63 64 0.53
64 5 0.04
ACGTcount: A:0.46, C:0.18, G:0.09, T:0.27
Consensus pattern (62 bp):
AAAAAACAGCATCTTTTACCTCAACTTATAAAAAACAGAAATTTTGTATATATGGAAACCTC
Found at i:55361 original size:18 final size:18
Alignment explanation
Indices: 55338--55388 Score: 93
Period size: 18 Copynumber: 2.8 Consensus size: 18
55328 GGAAGGATTG
55338 ACAATAGGGACCTCATTC
1 ACAATAGGGACCTCATTC
*
55356 ACAATAGGGACCTCATTG
1 ACAATAGGGACCTCATTC
55374 ACAATAGGGACCTCA
1 ACAATAGGGACCTCA
55389 GAAGGAGGTG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.20
Consensus pattern (18 bp):
ACAATAGGGACCTCATTC
Found at i:62568 original size:20 final size:20
Alignment explanation
Indices: 62543--62589 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
62533 GTCGCATAGC
* *
62543 TTCCCGCGCGACCAAAAAAG
1 TTCCCGCACAACCAAAAAAG
62563 TTCCCGCACAACCAAAAAAG
1 TTCCCGCACAACCAAAAAAG
62583 TTCCCGC
1 TTCCCGC
62590 CAAGTCAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.34, C:0.38, G:0.15, T:0.13
Consensus pattern (20 bp):
TTCCCGCACAACCAAAAAAG
Found at i:63045 original size:17 final size:18
Alignment explanation
Indices: 63023--63058 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
63013 TGTATTTTAA
*
63023 TTTATTTTTG-TCTTATG
1 TTTATTTTGGATCTTATG
63040 TTTATTTTGGATCTTATG
1 TTTATTTTGGATCTTATG
63058 T
1 T
63059 AAGACTTATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.14, C:0.06, G:0.14, T:0.67
Consensus pattern (18 bp):
TTTATTTTGGATCTTATG
Found at i:75152 original size:20 final size:21
Alignment explanation
Indices: 75108--75157 Score: 68
Period size: 20 Copynumber: 2.4 Consensus size: 21
75098 ATTGTTTTGC
*
75108 TTTGATTGCCTATTGCTTTGA
1 TTTGATTGCCTATTGCCTTGA
75129 -TTGATTGCCTATT-CCTTGA
1 TTTGATTGCCTATTGCCTTGA
75148 TTTGAATTGC
1 TTTG-ATTGC
75158 TGCATTGCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
19 5 0.19
20 16 0.62
21 5 0.19
ACGTcount: A:0.16, C:0.16, G:0.18, T:0.50
Consensus pattern (21 bp):
TTTGATTGCCTATTGCCTTGA
Done.