Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011351.1 Corchorus capsularis cultivar CVL-1 contig11372, 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: 65924
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Found at i:7986 original size:18 final size:18
Alignment explanation
Indices: 7963--7999 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
7953 TAGGTTTCCC
7963 TTTGGGCC-TTAGTATAGT
1 TTTGGGCCTTTAGT-TAGT
7981 TTTGGGCCTTTAGTTAGT
1 TTTGGGCCTTTAGTTAGT
7999 T
1 T
8000 GTTAGTTGGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.14, C:0.11, G:0.27, T:0.49
Consensus pattern (18 bp):
TTTGGGCCTTTAGTTAGT
Found at i:10081 original size:10 final size:11
Alignment explanation
Indices: 10066--10120 Score: 51
Period size: 10 Copynumber: 5.1 Consensus size: 11
10056 TCGCATGGAG
10066 CAACCGGCCA-
1 CAACCGGCCAT
10076 CAACCGGCCAT
1 CAACCGGCCAT
* ** *
10087 CGCATGGGGCAT
1 C-AACCGGCCAT
10099 CAACCGGCCA-
1 CAACCGGCCAT
10109 CAACCGGCCAT
1 CAACCGGCCAT
10120 C
1 C
10121 GCATGGGGCA
Statistics
Matches: 34, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
10 20 0.59
11 7 0.21
12 7 0.21
ACGTcount: A:0.25, C:0.44, G:0.24, T:0.07
Consensus pattern (11 bp):
CAACCGGCCAT
Found at i:10091 original size:30 final size:30
Alignment explanation
Indices: 10055--10148 Score: 118
Period size: 33 Copynumber: 3.0 Consensus size: 30
10045 CGCATGCGCT
10055 ATCGCATGGAGCAACCGGCCACAACCGGCC
1 ATCGCATGGAGCAACCGGCCACAACCGGCC
*
10085 ATCGCATGGGGCATCAACCGGCCACAACCGGCC
1 ATCGCAT--GG-AGCAACCGGCCACAACCGGCC
* *
10118 ATCGCATGGGGCATCC-GCGCACAACCGGCC
1 ATCGCATGGAGCAACCGGC-CACAACCGGCC
10148 A
1 A
10149 ATGGATCCTT
Statistics
Matches: 56, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
29 2 0.04
30 23 0.41
31 2 0.04
32 2 0.04
33 27 0.48
ACGTcount: A:0.24, C:0.39, G:0.28, T:0.09
Consensus pattern (30 bp):
ATCGCATGGAGCAACCGGCCACAACCGGCC
Found at i:10107 original size:33 final size:33
Alignment explanation
Indices: 10066--10132 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
10056 TCGCATGGAG
10066 CAACCGGCCACAACCGGCCATCGCATGGGGCAT
1 CAACCGGCCACAACCGGCCATCGCATGGGGCAT
10099 CAACCGGCCACAACCGGCCATCGCATGGGGCAT
1 CAACCGGCCACAACCGGCCATCGCATGGGGCAT
10132 C
1 C
10133 CGCGCACAAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.24, C:0.40, G:0.27, T:0.09
Consensus pattern (33 bp):
CAACCGGCCACAACCGGCCATCGCATGGGGCAT
Found at i:10815 original size:14 final size:14
Alignment explanation
Indices: 10798--10827 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
10788 GTCTAAGGCC
10798 GACGAACGAAGGAT
1 GACGAACGAAGGAT
10812 GACGAACGAAGGAT
1 GACGAACGAAGGAT
10826 GA
1 GA
10828 TTTATCTAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.43, C:0.13, G:0.37, T:0.07
Consensus pattern (14 bp):
GACGAACGAAGGAT
Found at i:10994 original size:37 final size:36
Alignment explanation
Indices: 10942--11530 Score: 726
Period size: 37 Copynumber: 16.1 Consensus size: 36
10932 GTATCAACTG
* * * *
10942 CTGTGTTTAATTAATTACCATGAATTAAGTCCTTTTA
1 CTGT-TTTACTTAATTTCCCTGAATTAAGTCCTTTAA
*
10979 CTGCTTTTACTTAATTTCCCTGAATTAAGTCTTTTAA
1 CTG-TTTTACTTAATTTCCCTGAATTAAGTCCTTTAA
* *
11016 CTGCTTTTACTTAATTACCCTGAATTAAGTCCTTTTA
1 CTG-TTTTACTTAATTTCCCTGAATTAAGTCCTTTAA
* *
11053 CTACTTTTACTTAATTTCCCTGAATTAAGCCCTTTAA
1 CT-GTTTTACTTAATTTCCCTGAATTAAGTCCTTTAA
11090 CTGGTTTTACTTAATTTCCCTGAATTAAGTCCTTTAA
1 CT-GTTTTACTTAATTTCCCTGAATTAAGTCCTTTAA
11127 CTGCTTTTACTTAA-TTCCCTGAATTAAG-CCATTTAA
1 CTG-TTTTACTTAATTTCCCTGAATTAAGTCC-TTTAA
*
11163 CTGGTTTTACTTAATTTCCATGAATTAAGTCCTTTAA
1 CT-GTTTTACTTAATTTCCCTGAATTAAGTCCTTTAA
* *
11200 CTGCTTTTACTTAATTTCCATGAATTAAGCCCTTTAA
1 CTG-TTTTACTTAATTTCCCTGAATTAAGTCCTTTAA
*
11237 CTGGTTTTACTTAATTTCCATGAATTAAGTCCTTTAA
1 CT-GTTTTACTTAATTTCCCTGAATTAAGTCCTTTAA
11274 CTGCTTTTACTTAATTTCCCTGAATTAAGTCCTTTAA
1 CTG-TTTTACTTAATTTCCCTGAATTAAGTCCTTTAA
*
11311 CTGTGTTTACTTAATTT-CCTGAATTAAGTACTTTAA
1 CTGT-TTTACTTAATTTCCCTGAATTAAGTCCTTTAA
* * * *
11347 TTGTGTTTACTTAATTGCCCTAAATTAAGTTC-TTAA
1 CTGT-TTTACTTAATTTCCCTGAATTAAGTCCTTTAA
* * *
11383 ATGTGTGTACTTAATTT-CCTGAATTAAGTACTTTAA
1 CTGT-TTTACTTAATTTCCCTGAATTAAGTCCTTTAA
* * *
11419 CTGTGTTTACTTAATTGCCCTGAATTAAGTTC-TTAT
1 CTGT-TTTACTTAATTTCCCTGAATTAAGTCCTTTAA
*
11455 CTGTGTTTACTTAATTT-CCTGAATTAAGTACTTTAA
1 CTGT-TTTACTTAATTTCCCTGAATTAAGTCCTTTAA
* *
11491 CTGTGTTTACTTAATTGCCCTGAATTAAGTTC-TTAA
1 CTGT-TTTACTTAATTTCCCTGAATTAAGTCCTTTAA
11527 CTGT
1 CTGT
11531 ACTTTCTTTT
Statistics
Matches: 497, Mismatches: 39, Indels: 33
0.87 0.07 0.06
Matches are distributed among these distances:
35 27 0.05
36 150 0.30
37 316 0.64
38 4 0.01
ACGTcount: A:0.26, C:0.18, G:0.10, T:0.46
Consensus pattern (36 bp):
CTGTTTTACTTAATTTCCCTGAATTAAGTCCTTTAA
Found at i:11273 original size:184 final size:183
Alignment explanation
Indices: 10942--11519 Score: 737
Period size: 184 Copynumber: 3.2 Consensus size: 183
10932 GTATCAACTG
* * * *
10942 CTGTGTTTAATTAATTACCATGAATTAAGTCC-TTTTACTGCTTTTACTTAATTTCCCTGAATTA
1 CTGTGTTTACTTAATTACCCTGAATTAAG-CCATTTAACTGGTTTTACTTAATTTCCCTGAATTA
* * * *
11006 AGTCTTTTAACTGCTTTTACTTAATTACCCTGAATTAAGTCCTTTTACTACTTTTACTTAATTTC
65 AGTCCTTTAACTGCTTTTACTTAATT-TCCTGAATTAAGTCCTTTAACT-GTTTTACTTAATTTC
*
11071 CCTGAATTAAGCCCTTTAACTGGTTTTACTTAATTTCCCTGAATTAAGTCCTTTAA
128 CCTGAATTAAGTCCTTTAACTGGTTTTACTTAATTTCCCTGAATTAAGTCCTTTAA
*
11127 CTGCT-TTTACTTAATT-CCCTGAATTAAGCCATTTAACTGGTTTTACTTAATTTCCATGAATTA
1 CTG-TGTTTACTTAATTACCCTGAATTAAGCCATTTAACTGGTTTTACTTAATTTCCCTGAATTA
*
11190 AGTCCTTTAACTGCTTTTACTTAATTTCCATGAATTAAGCCCTTTAACTGGTTTTACTTAATTTC
65 AGTCCTTTAACTGCTTTTACTTAATTTCC-TGAATTAAGTCCTTTAACT-GTTTTACTTAATTTC
* *
11255 CATGAATTAAGTCCTTTAACTGCTTTTACTTAATTTCCCTGAATTAAGTCCTTTAA
128 CCTGAATTAAGTCCTTTAACTGGTTTTACTTAATTTCCCTGAATTAAGTCCTTTAA
* * * * *
11311 CTGTGTTTACTTAATT-TCCTGAATTAAG-TACTTTAA-TTGTGTTTACTTAATTGCCCTAAATT
1 CTGTGTTTACTTAATTACCCTGAATTAAGCCA-TTTAACTGGT-TTTACTTAATTTCCCTGAATT
* * * * *
11373 AAGTTC-TTAAATG-TGTGTACTTAATTTCCTGAATTAAGTACTTTAACTGTGTTTACTTAATTG
64 AAGTCCTTTAACTGCT-TTTACTTAATTTCCTGAATTAAGTCCTTTAACTGT-TTTACTTAATTT
* * *
11436 CCCTGAATTAAGTTC-TTATCT-GTGTTTACTTAATTT-CCTGAATTAAGTACTTTAA
127 CCCTGAATTAAGTCCTTTAACTGGT-TTTACTTAATTTCCCTGAATTAAGTCCTTTAA
*
11491 CTGTGTTTACTTAATTGCCCTGAATTAAG
1 CTGTGTTTACTTAATTACCCTGAATTAAG
11520 TTCTTAACTG
Statistics
Matches: 351, Mismatches: 32, Indels: 24
0.86 0.08 0.06
Matches are distributed among these distances:
180 35 0.10
181 30 0.09
182 42 0.12
183 28 0.08
184 202 0.58
185 13 0.04
186 1 0.00
ACGTcount: A:0.26, C:0.18, G:0.10, T:0.46
Consensus pattern (183 bp):
CTGTGTTTACTTAATTACCCTGAATTAAGCCATTTAACTGGTTTTACTTAATTTCCCTGAATTAA
GTCCTTTAACTGCTTTTACTTAATTTCCTGAATTAAGTCCTTTAACTGTTTTACTTAATTTCCCT
GAATTAAGTCCTTTAACTGGTTTTACTTAATTTCCCTGAATTAAGTCCTTTAA
Found at i:11626 original size:40 final size:41
Alignment explanation
Indices: 11537--11644 Score: 121
Period size: 40 Copynumber: 2.6 Consensus size: 41
11527 CTGTACTTTC
* * *
11537 TTTTCTTAATTACCCTGAATTGAGACTTTACTCTTCTTAAT
1 TTTTCTTAATTACACTGAATTAAGACGTTACTCTTCTTAAT
*
11578 TTCCTTCTTAATTACACTGAATTAAG-GGTTACT-TCTCTTAAT
1 TT--TTCTTAATTACACTGAATTAAGACGTTACTCT-TCTTAAT
**
11620 TTTTCTTAATTATGCTGAATTAAGA
1 TTTTCTTAATTACACTGAATTAAGA
11645 TTTTAATAAT
Statistics
Matches: 57, Mismatches: 6, Indels: 8
0.80 0.08 0.11
Matches are distributed among these distances:
40 20 0.35
41 3 0.05
42 14 0.25
43 20 0.35
ACGTcount: A:0.27, C:0.17, G:0.09, T:0.47
Consensus pattern (41 bp):
TTTTCTTAATTACACTGAATTAAGACGTTACTCTTCTTAAT
Found at i:15125 original size:481 final size:480
Alignment explanation
Indices: 14224--15184 Score: 1715
Period size: 481 Copynumber: 2.0 Consensus size: 480
14214 TGAGACTTGG
* * * *
14224 TGATCGGTCGTCAGCAATCATAAAAATAATCCCCACAAAAACTAACTAAACTAGCTAGGGCAAGT
1 TGATCGGTCATCAACAATCACAAAAATAATCCCCACAAAAACTAACTAAACTAACTAGGGCAAGT
*
14289 AGGGGTCGAATCCCACAGAGAAGGGTTATAATTATCAAAGGAAAGAAAGATCTTTTTCAAAAATC
66 AGGGGTCGAATCCCACAGAGAAGGGTTATAATTATCAAAGGAAAGAAAGATCTTTTCCAAAAATC
*
14354 AATTAGAAAACAGGGATTGTGAATATCAATTATAAAGAAAACAATTAAACTAAAAACAAAGCAAA
131 AACTAGAAAACAGGGATTGTGAATATCAATTATAAAGAAAACAATTAAACTAAAAACAAAGCAAA
* *
14419 GAAAATTAAATCTAGATCTGAAGCAAATTAATAGAGCAAACAATAATTATAAAGCATACTTCTTC
196 GAAAATTAAATCTAGATCTAAAGCAAATTAATAAAGCAAACAATAATTATAAAGCATACTTCTTC
* *
14484 TCCGATGGTATGATTCAATCAGATTAACTATGGATCATTGACTTAAAAGGTGAATTAAGCATCTT
261 TCCAATGGTATGATTCAATCAGATTAACTATGGATCACTGACTTAAAAGGTGAATTAAGCATCTT
* *
14549 ATTCTTGACTAACAACTGCTATAGGTTTCCCAACATGTATATTAGATAAGAGGCCGGTTAAAGCT
326 ATTATTGACTAACAACTGCTATAGGTTTCCCAACATGTATATTACATAAGAGGCCGGTTAAAGCT
*
14614 GCAGTTATCCCTTTTATTCCTTCAGCAATCGATTACTTTTTTAGGGCTTAAAGATTACTTGAGAA
391 GCAGTTATCCCTTTTATTCCTTCAGCAATCGATTACTTTTTTAGGGCTTAAAGATCACTTGAGAA
14679 CAAAGCATTAAGAATAATTAATTTT
456 CAAAGCATTAAGAATAATTAATTTT
* * *
14704 TGATCGGTCATCAACAATTACAAAAATAATCCCCACATAAACTAACTAAACTAATTAGGGCAAGT
1 TGATCGGTCATCAACAATCACAAAAATAATCCCCACAAAAACTAACTAAACTAACTAGGGCAAGT
14769 AGGGGTCGAATCCCACAGAGAAGGGTTATAATTATCAAAGGAAAGAAAGATCTTTTCCAAAAATC
66 AGGGGTCGAATCCCACAGAGAAGGGTTATAATTATCAAAGGAAAGAAAGATCTTTTCCAAAAATC
14834 AACTAGAAAACAGGGGATTGTGAATATCAATTATAAAGAAAACAATTAAACTAAAAACAAAGCAA
131 AACTAGAAAACA-GGGATTGTGAATATCAATTATAAAGAAAACAATTAAACTAAAAACAAAGCAA
* *
14899 ATAAAATTAAATTTAGATCTAAAGCAAATTAATAAAGCAAACAATAATTATAAAGCATACTTCTT
195 AGAAAATTAAATCTAGATCTAAAGCAAATTAATAAAGCAAACAATAATTATAAAGCATACTTCTT
14964 CTCCAATGGTATGATTCAATCAGATTAACTATGGATCACTGACTTAAAAGGTGAATTAAGCATCT
260 CTCCAATGGTATGATTCAATCAGATTAACTATGGATCACTGACTTAAAAGGTGAATTAAGCATCT
* *
15029 TATTATTGACTGACAACTGGTATAGGTTTCCCAACATGTATATTACATAAGAGGCCGGTTAAAGC
325 TATTATTGACTAACAACTGCTATAGGTTTCCCAACATGTATATTACATAAGAGGCCGGTTAAAGC
* *
15094 TGCAGTTATCCCTTTTATTCCTTCAGCAATCGATTACTTTTTTGGGGCTTAAAGATCGCTTGAGA
390 TGCAGTTATCCCTTTTATTCCTTCAGCAATCGATTACTTTTTTAGGGCTTAAAGATCACTTGAGA
15159 ACAAAGCATTAAGAATAATTAATTTT
455 ACAAAGCATTAAGAATAATTAATTTT
15185 ACAGACATGC
Statistics
Matches: 458, Mismatches: 22, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
480 133 0.29
481 325 0.71
ACGTcount: A:0.41, C:0.16, G:0.15, T:0.28
Consensus pattern (480 bp):
TGATCGGTCATCAACAATCACAAAAATAATCCCCACAAAAACTAACTAAACTAACTAGGGCAAGT
AGGGGTCGAATCCCACAGAGAAGGGTTATAATTATCAAAGGAAAGAAAGATCTTTTCCAAAAATC
AACTAGAAAACAGGGATTGTGAATATCAATTATAAAGAAAACAATTAAACTAAAAACAAAGCAAA
GAAAATTAAATCTAGATCTAAAGCAAATTAATAAAGCAAACAATAATTATAAAGCATACTTCTTC
TCCAATGGTATGATTCAATCAGATTAACTATGGATCACTGACTTAAAAGGTGAATTAAGCATCTT
ATTATTGACTAACAACTGCTATAGGTTTCCCAACATGTATATTACATAAGAGGCCGGTTAAAGCT
GCAGTTATCCCTTTTATTCCTTCAGCAATCGATTACTTTTTTAGGGCTTAAAGATCACTTGAGAA
CAAAGCATTAAGAATAATTAATTTT
Found at i:17084 original size:53 final size:53
Alignment explanation
Indices: 17026--17129 Score: 154
Period size: 53 Copynumber: 2.0 Consensus size: 53
17016 GCCACGTGTC
* ** *
17026 ACTTTTTGGTACACGTGACGTGGCATGTGTCACTTTTTGGTACATGTGGCACG
1 ACTTTTTGGTACACGTGACGTGCCACATGTCACTTTTTGGTACACGTGGCACG
* *
17079 ACTTTTTGGTACATGTGGCGTGCCACATGTCACTTTTTGGTACACGTGGCA
1 ACTTTTTGGTACACGTGACGTGCCACATGTCACTTTTTGGTACACGTGGCA
17130 TGCCACGTCG
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
53 45 1.00
ACGTcount: A:0.17, C:0.20, G:0.27, T:0.36
Consensus pattern (53 bp):
ACTTTTTGGTACACGTGACGTGCCACATGTCACTTTTTGGTACACGTGGCACG
Found at i:21935 original size:39 final size:40
Alignment explanation
Indices: 21877--21954 Score: 95
Period size: 39 Copynumber: 2.0 Consensus size: 40
21867 AAATAAAAAA
* * *
21877 TTAAAAAGCAAAACAGAAAATAAAA-ATATTTTTTTTATT
1 TTAAAAAGAAAAACAGAAAAGAAAAGATATTATTTTTATT
* * *
21916 TTAAAAGGAAAAACGGAAAAGAAAAGTTATTATTTTTAT
1 TTAAAAAGAAAAACAGAAAAGAAAAGATATTATTTTTAT
21955 CGACGCAAAC
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
39 21 0.66
40 11 0.34
ACGTcount: A:0.53, C:0.04, G:0.10, T:0.33
Consensus pattern (40 bp):
TTAAAAAGAAAAACAGAAAAGAAAAGATATTATTTTTATT
Found at i:25016 original size:11 final size:10
Alignment explanation
Indices: 24998--25031 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
24988 AATTGTCTTC
24998 AAATCTTCAA
1 AAATCTTCAA
25008 AATATCTTCAA
1 AA-ATCTTCAA
25019 GAAATCTTCAA
1 -AAATCTTCAA
25030 AA
1 AA
25032 CACGAACTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 4 0.18
11 16 0.73
12 2 0.09
ACGTcount: A:0.50, C:0.18, G:0.03, T:0.29
Consensus pattern (10 bp):
AAATCTTCAA
Found at i:44821 original size:124 final size:124
Alignment explanation
Indices: 44597--44825 Score: 422
Period size: 124 Copynumber: 1.8 Consensus size: 124
44587 TGAGTAGGCG
*
44597 TTGGAAAGCTAGCTTTGAGATCTACAACTTTCCTTTGAAGACCGAAGCCCAGTTCTGCCATCTTC
1 TTGGAAAGCTAGCTTTGAGATCTACAACTTTCCTTCGAAGACCGAAGCCCAGTTCTGCCATCTTC
*
44662 AAGCCTGAAATTACTGTCAAAGTTGTTGTGTGATTCCAGACGTCCTTTGAAGACTAGCT
66 AAGCCTGAAATTACTGTCAAAGTTGTTGTGCGATTCCAGACGTCCTTTGAAGACTAGCT
*
44721 TTGGAAAGCTAGCTTTGAGATCTACAACTTTCCTTCGAAGACCGAAGCCTAGTTCTGCCATCTTC
1 TTGGAAAGCTAGCTTTGAGATCTACAACTTTCCTTCGAAGACCGAAGCCCAGTTCTGCCATCTTC
*
44786 AAGCCTGAAATTGCTGTCAAAGTTGTTGTGCGATTCCAGA
66 AAGCCTGAAATTACTGTCAAAGTTGTTGTGCGATTCCAGA
44826 ATTTTTTAGA
Statistics
Matches: 101, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
124 101 1.00
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.31
Consensus pattern (124 bp):
TTGGAAAGCTAGCTTTGAGATCTACAACTTTCCTTCGAAGACCGAAGCCCAGTTCTGCCATCTTC
AAGCCTGAAATTACTGTCAAAGTTGTTGTGCGATTCCAGACGTCCTTTGAAGACTAGCT
Found at i:50893 original size:20 final size:20
Alignment explanation
Indices: 50857--50896 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
50847 TAAAATTAAA
50857 CCTATTTTTATGATCATTTT
1 CCTATTTTTATGATCATTTT
*
50877 CCTATGTTTT-TGGTCATTTT
1 CCTAT-TTTTATGATCATTTT
50897 TATGTGTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.15, C:0.15, G:0.10, T:0.60
Consensus pattern (20 bp):
CCTATTTTTATGATCATTTT
Found at i:57978 original size:28 final size:27
Alignment explanation
Indices: 57886--57989 Score: 172
Period size: 27 Copynumber: 3.8 Consensus size: 27
57876 GTAGGGGATC
*
57886 AAAATGCCCCTGAATGTAAAAATGACT
1 AAAATGCCCCTGAATGCAAAAATGACT
* *
57913 AAAATGCCCCTGAATGTAAAAATGAGT
1 AAAATGCCCCTGAATGCAAAAATGACT
57940 AAAATGCCCCTGAATGCAAAAATGACT
1 AAAATGCCCCTGAATGCAAAAATGACT
57967 AAAATGCCCCCTGAATGCAAAAA
1 AAAATG-CCCCTGAATGCAAAAA
57990 AAATAACCAA
Statistics
Matches: 73, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
27 57 0.78
28 16 0.22
ACGTcount: A:0.45, C:0.20, G:0.15, T:0.19
Consensus pattern (27 bp):
AAAATGCCCCTGAATGCAAAAATGACT
Found at i:58002 original size:31 final size:28
Alignment explanation
Indices: 57885--58009 Score: 121
Period size: 27 Copynumber: 4.5 Consensus size: 28
57875 AGTAGGGGAT
* *
57885 CAAAATG-CCCCTGAATGTAAAAATGAC
1 CAAAATGCCCCCTGAATGCAAAAATAAC
* * * *
57912 TAAAATG-CCCCTGAATGTAAAAATGAG
1 CAAAATGCCCCCTGAATGCAAAAATAAC
* *
57939 TAAAATG-CCCCTGAATGCAAAAATGAC
1 CAAAATGCCCCCTGAATGCAAAAATAAC
*
57966 TAAAATGCCCCCTGAATGCAAAAAAAATAAC
1 CAAAATGCCCCCTGAATGC---AAAAATAAC
57997 CAAAATGCCCCCT
1 CAAAATGCCCCCT
58010 AGAAGACCCC
Statistics
Matches: 88, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
27 57 0.65
28 11 0.12
31 20 0.23
ACGTcount: A:0.45, C:0.23, G:0.14, T:0.18
Consensus pattern (28 bp):
CAAAATGCCCCCTGAATGCAAAAATAAC
Found at i:58309 original size:52 final size:51
Alignment explanation
Indices: 58223--58789 Score: 251
Period size: 50 Copynumber: 11.3 Consensus size: 51
58213 ATTTTTGAGT
* **
58223 GGATCGTCGTT-CGATCAGCTTCTTCAAACCGTCTTCTGATTCAATC-ACAAA
1 GGATCGTC-TTCCGATCAACTTCTTCAAACCGTCTTCCAATTCAATCTA-AAA
*
58274 GGATCGTCTTCCGAATCAACTTCTTCGAAA-TGTCTTCCAATTCAATCTTAAAA
1 GGATCGTCTTCCG-ATCAACTTCTTC-AAACCGTCTTCCAATTCAATC-TAAAA
* * * * * * *
58327 GGACCGTCTTCCGCT-TA-TCCTTCGAACTGTCTTCCAATTCCATCTTAAAA
1 GGATCGTCTTCCGATCAACTTCTTCAAACCGTCTTCCAATTCAATC-TAAAA
* * * * * * *
58377 GGACCGTCTTCC-ACTTATCCTC-T-GAACTGTCTTCCAATTCACTCTTAAAA
1 GGATCGTCTTCCGA-TCAACTTCTTCAAACCGTCTTCCAATTCAATC-TAAAA
* * * * * *
58427 GGATCGTCTTCCGCT-TA-TCCTTCGAACTGTCTTCCAATTCCATCTTAAAA
1 GGATCGTCTTCCGATCAACTTCTTCAAACCGTCTTCCAATTCAATC-TAAAA
* * * * * * * *
58477 GGACCGTCTTCCGCT-TA-TCCTTCGAACTGTCTTCCAATTCACTTTTAAAA
1 GGATCGTCTTCCGATCAACTTCTTCAAACCGTCTTCCAATTCA-ATCTAAAA
* * * ** * *
58527 GGATCGTCTTCCGCT-TA-TCCTTTGAACTGTCTTCCAATTCACTCTTAAAA
1 GGATCGTCTTCCGATCAACTTCTTCAAACCGTCTTCCAATTCAATC-TAAAA
* * * * * * *
58577 GGACCGTCTTCCGCT-TA-TCCTTCGAACTGTCTTCCAATTCCATCTTAAAA
1 GGATCGTCTTCCGATCAACTTCTTCAAACCGTCTTCCAATTCAATC-TAAAA
* * * ** *
58627 GGATCGTCTTCCGCT-TA-TCCTTTGAACTGTCTTCCAATTCAATCTTAAAA
1 GGATCGTCTTCCGATCAACTTCTTCAAACCGTCTTCCAATTCAATC-TAAAA
* * * * ** *
58677 GGACCGTCTTCCGCT-TA-TCCTTTGAACTGTCTTCCAATTCAATCTTAAAA
1 GGATCGTCTTCCGATCAACTTCTTCAAACCGTCTTCCAATTCAATC-TAAAA
* * * * **
58727 GGGTCGTCTTCGGATTAAC-T-TTCGAATTGTCTTCCAATTCAATCTTAAAA
1 GGATCGTCTTCCGATCAACTTCTTCAAACCGTCTTCCAATTCAATC-TAAAA
*
58777 GGACCGTCTTCCG
1 GGATCGTCTTCCG
58790 CTTATCCTTC
Statistics
Matches: 448, Mismatches: 52, Indels: 33
0.84 0.10 0.06
Matches are distributed among these distances:
48 1 0.00
49 4 0.01
50 383 0.85
51 14 0.03
52 27 0.06
53 18 0.04
54 1 0.00
ACGTcount: A:0.24, C:0.28, G:0.13, T:0.35
Consensus pattern (51 bp):
GGATCGTCTTCCGATCAACTTCTTCAAACCGTCTTCCAATTCAATCTAAAA
Found at i:58361 original size:50 final size:50
Alignment explanation
Indices: 58296--58816 Score: 819
Period size: 50 Copynumber: 10.4 Consensus size: 50
58286 GAATCAACTT
*
58296 CTTCGAAATGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
1 CTTCGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
* *
58346 CTTCGAACTGTCTTCCAATTCCATCTTAAAAGGACCGTCTTCCACTTATC
1 CTTCGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
* *
58396 C-TCTGAACTGTCTTCCAATTCACTCTTAAAAGGATCGTCTTCCGCTTATC
1 CTTC-GAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
*
58446 CTTCGAACTGTCTTCCAATTCCATCTTAAAAGGACCGTCTTCCGCTTATC
1 CTTCGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
* * *
58496 CTTCGAACTGTCTTCCAATTCACTTTTAAAAGGATCGTCTTCCGCTTATC
1 CTTCGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
* *
58546 CTTTGAACTGTCTTCCAATTCACTCTTAAAAGGACCGTCTTCCGCTTATC
1 CTTCGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
* *
58596 CTTCGAACTGTCTTCCAATTCCATCTTAAAAGGATCGTCTTCCGCTTATC
1 CTTCGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
*
58646 CTTTGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
1 CTTCGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
* ** * * *
58696 CTTTGAACTGTCTTCCAATTCAATCTTAAAAGGGTCGTCTTCGGATTAAC
1 CTTCGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
* *
58746 TTTCGAATTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
1 CTTCGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
*
58796 CTTCGAATTGTCTTCCAATTC
1 CTTCGAACTGTCTTCCAATTC
58817 CATTCTTTAG
Statistics
Matches: 431, Mismatches: 38, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
49 2 0.00
50 427 0.99
51 2 0.00
ACGTcount: A:0.23, C:0.29, G:0.12, T:0.36
Consensus pattern (50 bp):
CTTCGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
Found at i:58458 original size:23 final size:23
Alignment explanation
Indices: 58432--58511 Score: 63
Period size: 23 Copynumber: 3.3 Consensus size: 23
58422 TAAAAGGATC
58432 GTCTTCCGCTTATCCTTCGAACT
1 GTCTTCCGCTTATCCTTCGAACT
** * * *
58455 GTCTTCCAATTCCAT-CTTAAAAGGACC
1 GTCTTCCGCTT--ATCCTT---CGAACT
58482 GTCTTCCGCTTATCCTTCGAACT
1 GTCTTCCGCTTATCCTTCGAACT
58505 GTCTTCC
1 GTCTTCC
58512 AATTCACTTT
Statistics
Matches: 41, Mismatches: 10, Indels: 12
0.65 0.16 0.19
Matches are distributed among these distances:
23 19 0.46
24 3 0.07
25 4 0.10
26 3 0.07
27 12 0.29
ACGTcount: A:0.17, C:0.34, G:0.12, T:0.36
Consensus pattern (23 bp):
GTCTTCCGCTTATCCTTCGAACT
Found at i:58658 original size:23 final size:23
Alignment explanation
Indices: 58632--58711 Score: 63
Period size: 23 Copynumber: 3.3 Consensus size: 23
58622 TAAAAGGATC
58632 GTCTTCCGCTTATCCTTTGAACT
1 GTCTTCCGCTTATCCTTTGAACT
** * * *
58655 GTCTTCCAATTCAAT-CTTAAAAGGACC
1 GTCTTCCGCTT--ATCCTT---TGAACT
58682 GTCTTCCGCTTATCCTTTGAACT
1 GTCTTCCGCTTATCCTTTGAACT
58705 GTCTTCC
1 GTCTTCC
58712 AATTCAATCT
Statistics
Matches: 41, Mismatches: 10, Indels: 12
0.65 0.16 0.19
Matches are distributed among these distances:
23 19 0.46
24 3 0.07
25 4 0.10
26 3 0.07
27 12 0.29
ACGTcount: A:0.19, C:0.30, G:0.12, T:0.39
Consensus pattern (23 bp):
GTCTTCCGCTTATCCTTTGAACT
Found at i:59132 original size:64 final size:64
Alignment explanation
Indices: 58993--59436 Score: 488
Period size: 64 Copynumber: 7.0 Consensus size: 64
58983 CAAACTCTAA
* * * * * * *
58993 ACAAGATCGTCTTCCGATCAACCTCCGAAAATTCTTTGAGAGACCATCTTCTGGTGAACTTCTTA
1 ACAAGATCGTCTTCCGATCAACTTCTGAAAACTC-TTGATAAACCATCTTCTGGTGTACTTCTTG
* * * * *
59058 ACAAGATCGTCTTCCGATCGACTTCCGAAGACTCTTGATAAGCAATCTTCTGGTGTACTTCTTG
1 ACAAGATCGTCTTCCGATCAACTTCTGAAAACTCTTGATAAACCATCTTCTGGTGTACTTCTTG
* * * * * *
59122 ACTAGATCGTCTTCCGACCAACTTCTGAAAACTCTTGATAAACCATCTTCTGGTATTCTTTTTA
1 ACAAGATCGTCTTCCGATCAACTTCTGAAAACTCTTGATAAACCATCTTCTGGTGTACTTCTTG
** * *
59186 ACAAGATCAACTTCCGATCAACTTCTGAAAACTCTTGATAAGCCATCTTCTGGTGTACTCCTTG
1 ACAAGATCGTCTTCCGATCAACTTCTGAAAACTCTTGATAAACCATCTTCTGGTGTACTTCTTG
* * *
59250 ACAAGATCATCTTCCGATCCAA-TTCTGAAAACTCTTGATAAACCATTTTCTGGTGTACTCCTTG
1 ACAAGATCGTCTTCCGAT-CAACTTCTGAAAACTCTTGATAAACCATCTTCTGGTGTACTTCTTG
* * **
59314 A-AA-A--G--ATCCGATCAACTTCTGAAAACTCTTGATAAACCATCTTCTGGTGTATTTCTAA
1 ACAAGATCGTCTTCCGATCAACTTCTGAAAACTCTTGATAAACCATCTTCTGGTGTACTTCTTG
* * * ** * * *
59372 ACAACATCGTCTCCCGACCCGCTTTTGAAAACTCTTGATAACCCATCTTCTGGTGTACTCCTTG
1 ACAAGATCGTCTTCCGATCAACTTCTGAAAACTCTTGATAAACCATCTTCTGGTGTACTTCTTG
59436 A
1 A
59437 AATTTTCAAA
Statistics
Matches: 319, Mismatches: 52, Indels: 17
0.82 0.13 0.04
Matches are distributed among these distances:
57 3 0.01
58 44 0.14
59 2 0.01
60 1 0.00
62 2 0.01
63 2 0.01
64 232 0.73
65 33 0.10
ACGTcount: A:0.27, C:0.26, G:0.14, T:0.33
Consensus pattern (64 bp):
ACAAGATCGTCTTCCGATCAACTTCTGAAAACTCTTGATAAACCATCTTCTGGTGTACTTCTTG
Found at i:59420 original size:186 final size:190
Alignment explanation
Indices: 59036--59436 Score: 497
Period size: 186 Copynumber: 2.1 Consensus size: 190
59026 CTTTGAGAGA
* * * * * * * *
59036 CCATCTTCTGGTGAACTTCTTAACAAGATCGTCTTCCGATCGACTTCCGAAGACTCTTGATAAGC
1 CCATCTTCTGGTGTACTCCTTGACAAGATCATCTTCCGATCCAATTCCGAAAACTCTTGATAAAC
* * *
59101 AATCTTCTGGTGTACTTCTTGACTAGATCGTCTTCCGACCAACTTCTGAAAACTCTTGATAAACC
66 AATCTTCTGGTGTACTCCTTGAC-AGATAG-CATCCGACCAACTTCTGAAAACTCTTGATAAACC
* * * * * *
59166 ATCTTCTGGTATTCTTTTTAACAAGATCAACTTCCGATCAACTTCTGAAAACTCTTGATAAG
129 ATCTTCTGGTATTCTTCTAAACAACATCAACTCCCGACCAACTTCTGAAAACTCTTGATAAC
*
59228 CCATCTTCTGGTGTACTCCTTGACAAGATCATCTTCCGATCCAATTCTGAAAACTCTTGATAAAC
1 CCATCTTCTGGTGTACTCCTTGACAAGATCATCTTCCGATCCAATTCCGAAAACTCTTGATAAAC
* * *
59293 CATTTTCTGGTGTACTCCTTGA-A-A-AG-ATCCGATCAACTTCTGAAAACTCTTGATAAACCAT
66 AATCTTCTGGTGTACTCCTTGACAGATAGCATCCGACCAACTTCTGAAAACTCTTGATAAACCAT
* ** ** *
59354 CTTCTGGTGTAT-TTCTAAACAACATCGTCTCCCGACCCGCTTTTGAAAACTCTTGATAAC
131 CTTCTGGTAT-TCTTCTAAACAACATCAACTCCCGACCAACTTCTGAAAACTCTTGATAAC
59414 CCATCTTCTGGTGTACTCCTTGA
1 CCATCTTCTGGTGTACTCCTTGA
59437 AATTTTCAAA
Statistics
Matches: 181, Mismatches: 27, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
186 102 0.56
187 1 0.01
188 1 0.01
189 1 0.01
190 1 0.01
192 75 0.41
ACGTcount: A:0.27, C:0.26, G:0.14, T:0.34
Consensus pattern (190 bp):
CCATCTTCTGGTGTACTCCTTGACAAGATCATCTTCCGATCCAATTCCGAAAACTCTTGATAAAC
AATCTTCTGGTGTACTCCTTGACAGATAGCATCCGACCAACTTCTGAAAACTCTTGATAAACCAT
CTTCTGGTATTCTTCTAAACAACATCAACTCCCGACCAACTTCTGAAAACTCTTGATAAC
Found at i:64124 original size:28 final size:27
Alignment explanation
Indices: 64059--64136 Score: 129
Period size: 27 Copynumber: 2.8 Consensus size: 27
64049 GTAGGGGATC
*
64059 AAAATGCCCCTGAATGTAAAAATGACT
1 AAAATGCCCCTGAATGAAAAAATGACT
64086 AAAATGCCCCTGAATGAAAAAATGACT
1 AAAATGCCCCTGAATGAAAAAATGACT
64113 AAAATGCCCCCTGAATGCAAAAAA
1 AAAATG-CCCCTGAATG-AAAAAA
64137 AATTACCAAA
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
27 32 0.67
28 10 0.21
29 6 0.12
ACGTcount: A:0.47, C:0.21, G:0.14, T:0.18
Consensus pattern (27 bp):
AAAATGCCCCTGAATGAAAAAATGACT
Found at i:65522 original size:26 final size:26
Alignment explanation
Indices: 65471--65522 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
65461 AAGTCACTCG
* **
65471 GGGGCATTTTGGTCATTTTTGCTTCA
1 GGGGCATTTTGGTCATCTTTAATTCA
65497 GGGGCATTTTGGTCATCTTTAATTCA
1 GGGGCATTTTGGTCATCTTTAATTCA
65523 ATTCTAACTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.15, C:0.15, G:0.25, T:0.44
Consensus pattern (26 bp):
GGGGCATTTTGGTCATCTTTAATTCA
Done.