Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011419.1 Corchorus capsularis cultivar CVL-1 contig11440, 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: 29285
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:1196 original size:13 final size:13
Alignment explanation
Indices: 1178--1210 Score: 50
Period size: 12 Copynumber: 2.5 Consensus size: 13
1168 TTCACTTCAC
1178 TTTTTTTTCC-AT
1 TTTTTTTTCCAAT
1190 TTTTTTTTCCAAT
1 TTTTTTTTCCAAT
1203 TCTTTTTT
1 T-TTTTTT
1211 AGTTTTTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 10 0.53
13 3 0.16
14 6 0.32
ACGTcount: A:0.09, C:0.15, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTTTTTTCCAAT
Found at i:1325 original size:28 final size:28
Alignment explanation
Indices: 1285--1355 Score: 97
Period size: 28 Copynumber: 2.5 Consensus size: 28
1275 TGATTATTAA
* ** *
1285 TAATGTTTGTTAAGTCTAGCGAAAGAAG
1 TAATGTTTTTTAAGTCTAGAAAAAAAAG
*
1313 TAATGTTTTTTAAGTCTTGAAAAAAAAG
1 TAATGTTTTTTAAGTCTAGAAAAAAAAG
1341 TAATGTTTTTTAAGT
1 TAATGTTTTTTAAGT
1356 AATGTAATGT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.37, C:0.04, G:0.18, T:0.41
Consensus pattern (28 bp):
TAATGTTTTTTAAGTCTAGAAAAAAAAG
Found at i:6561 original size:33 final size:35
Alignment explanation
Indices: 6518--6621 Score: 167
Period size: 33 Copynumber: 2.9 Consensus size: 35
6508 TTCTTGTATA
6518 ATATCATCACATTATAACTGTAAATGTCATAAA-C
1 ATATCATCACATTATAACTGTAAATGTCATAAATC
6552 -TATCATCACATTATAACTGTAAATGTCATAAACTATC
1 ATATCATCACATTATAACTGTAAATGTCAT-AA--ATC
6589 ATATCATCACATTATAACTGTAAATGTCATAAA
1 ATATCATCACATTATAACTGTAAATGTCATAAA
6622 GGTTTCTGAA
Statistics
Matches: 65, Mismatches: 0, Indels: 9
0.88 0.00 0.12
Matches are distributed among these distances:
33 29 0.45
34 2 0.03
35 1 0.02
36 1 0.02
37 3 0.05
38 29 0.45
ACGTcount: A:0.43, C:0.17, G:0.06, T:0.34
Consensus pattern (35 bp):
ATATCATCACATTATAACTGTAAATGTCATAAATC
Found at i:6603 original size:38 final size:35
Alignment explanation
Indices: 6518--6621 Score: 167
Period size: 38 Copynumber: 2.9 Consensus size: 35
6508 TTCTTGTATA
6518 ATATCATCACATTATAACTGTAAATGTCAT-AAAC
1 ATATCATCACATTATAACTGTAAATGTCATAAAAC
6552 -TATCATCACATTATAACTGTAAATGTCATAAACTATC
1 ATATCATCACATTATAACTGTAAATGTCATAAA--A-C
6589 ATATCATCACATTATAACTGTAAATGTCATAAA
1 ATATCATCACATTATAACTGTAAATGTCATAAA
6622 GGTTTCTGAA
Statistics
Matches: 65, Mismatches: 0, Indels: 6
0.92 0.00 0.08
Matches are distributed among these distances:
33 29 0.45
34 2 0.03
36 1 0.02
37 1 0.02
38 32 0.49
ACGTcount: A:0.43, C:0.17, G:0.06, T:0.34
Consensus pattern (35 bp):
ATATCATCACATTATAACTGTAAATGTCATAAAAC
Found at i:6909 original size:24 final size:24
Alignment explanation
Indices: 6877--6931 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
6867 TTATTGCCAC
* *
6877 CATCATCATCTTCACCTTCACCTT
1 CATCATCATCTTCACCTTCAACAT
**
6901 CATCATCATCTTCTTCTTCAACAT
1 CATCATCATCTTCACCTTCAACAT
6925 CATCATC
1 CATCATC
6932 TCCTTCATTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.38, G:0.00, T:0.38
Consensus pattern (24 bp):
CATCATCATCTTCACCTTCAACAT
Found at i:6913 original size:18 final size:18
Alignment explanation
Indices: 6882--6939 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 18
6872 GCCACCATCA
* * *
6882 TCATCTTCACCTTCACCT
1 TCATCATCATCTTCTCCT
*
6900 TCATCATCATCTTCTTCT
1 TCATCATCATCTTCTCCT
* *
6918 TCAACATCATCATCTCCT
1 TCATCATCATCTTCTCCT
6936 TCAT
1 TCAT
6940 TACCCATATC
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.21, C:0.38, G:0.00, T:0.41
Consensus pattern (18 bp):
TCATCATCATCTTCTCCT
Found at i:6937 original size:24 final size:22
Alignment explanation
Indices: 6901--6964 Score: 76
Period size: 24 Copynumber: 2.9 Consensus size: 22
6891 CCTTCACCTT
*
6901 CATCATCATCTTCTTCTT-CAA
1 CATCATCATCTCCTTCTTCCAA
*
6922 CATCATCATCTCCTTCATTACCCA
1 CATCATCATCTCCTTC-TT-CCAA
*
6946 TATCATCATCTCCTTCTTC
1 CATCATCATCTCCTTCTTC
6965 ATTACCCTCA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
21 15 0.41
22 3 0.08
23 2 0.05
24 17 0.46
ACGTcount: A:0.22, C:0.38, G:0.00, T:0.41
Consensus pattern (22 bp):
CATCATCATCTCCTTCTTCCAA
Found at i:6952 original size:27 final size:27
Alignment explanation
Indices: 6922--6980 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
6912 TCTTCTTCAA
6922 CATCATCAT-CTCCTTCATTACCCAT-AT
1 CATCATC-TCCTCCTTCATTACCC-TCAT
*
6949 CATCATCTCCTTCTTCATTACCCTCAT
1 CATCATCTCCTCCTTCATTACCCTCAT
6976 CATCA
1 CATCA
6981 CCCATATCAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
26 2 0.07
27 27 0.93
ACGTcount: A:0.24, C:0.39, G:0.00, T:0.37
Consensus pattern (27 bp):
CATCATCTCCTCCTTCATTACCCTCAT
Found at i:6975 original size:24 final size:23
Alignment explanation
Indices: 6900--6979 Score: 67
Period size: 24 Copynumber: 3.3 Consensus size: 23
6890 ACCTTCACCT
* *
6900 TCATCATCATCTTCTTC-TTCAACA
1 TCATCATC-TCTTCTTCATT-ACCC
6924 TCATCATCTC--CTTCATTACCC
1 TCATCATCTCTTCTTCATTACCC
6945 ATATCATCATCTCCTTCTTCATTACCC
1 ---TCATCATCT-CTTCTTCATTACCC
6972 TCATCATC
1 TCATCATC
6980 ACCCATATCA
Statistics
Matches: 47, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
21 6 0.13
22 2 0.04
23 2 0.04
24 25 0.53
25 1 0.02
27 11 0.23
ACGTcount: A:0.23, C:0.38, G:0.00, T:0.40
Consensus pattern (23 bp):
TCATCATCTCTTCTTCATTACCC
Found at i:6985 original size:39 final size:39
Alignment explanation
Indices: 6936--7052 Score: 133
Period size: 39 Copynumber: 3.2 Consensus size: 39
6926 ATCATCTCCT
* *
6936 TCATTACCCATATCATCATC-TCCTTCTTCATTACCCTCA
1 TCATCACCCATATCATCATCAT-CATCTTCATTACCCTCA
6975 TCATCACCCATATCATCATCATCATCTTCATTA-CC-C-
1 TCATCACCCATATCATCATCATCATCTTCATTACCCTCA
*
7011 TCATCACCCAT-TC--CATCATGC-TCTTCATTACCTTCA
1 TCATCACCCATATCATCATCAT-CATCTTCATTACCCTCA
7047 TCATCA
1 TCATCA
7053 TCACCCTGAT
Statistics
Matches: 70, Mismatches: 3, Indels: 13
0.81 0.03 0.15
Matches are distributed among these distances:
33 15 0.21
34 2 0.03
35 3 0.04
36 17 0.24
37 1 0.01
38 2 0.03
39 29 0.41
40 1 0.01
ACGTcount: A:0.25, C:0.38, G:0.01, T:0.36
Consensus pattern (39 bp):
TCATCACCCATATCATCATCATCATCTTCATTACCCTCA
Found at i:7091 original size:21 final size:22
Alignment explanation
Indices: 7067--7114 Score: 71
Period size: 24 Copynumber: 2.1 Consensus size: 22
7057 CCTGATCACC
7067 TTCATCACCA-TCTTCTTGATT
1 TTCATCACCACTCTTCTTGATT
7088 TTCATCACCACCTTCTTCTTGATT
1 TTCATCACCA-C-TCTTCTTGATT
7112 TTC
1 TTC
7115 TTGAACCCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
21 10 0.42
24 14 0.58
ACGTcount: A:0.17, C:0.31, G:0.04, T:0.48
Consensus pattern (22 bp):
TTCATCACCACTCTTCTTGATT
Found at i:7611 original size:34 final size:34
Alignment explanation
Indices: 7571--7640 Score: 131
Period size: 34 Copynumber: 2.1 Consensus size: 34
7561 AGAAATTGGG
*
7571 AAACAATGAAGAAAATCGCCAAGAAAGCAGAGGA
1 AAACAATGAAGAAAATCACCAAGAAAGCAGAGGA
7605 AAACAATGAAGAAAATCACCAAGAAAGCAGAGGA
1 AAACAATGAAGAAAATCACCAAGAAAGCAGAGGA
7639 AA
1 AA
7641 GAAACTGGGT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.59, C:0.14, G:0.21, T:0.06
Consensus pattern (34 bp):
AAACAATGAAGAAAATCACCAAGAAAGCAGAGGA
Found at i:9781 original size:31 final size:31
Alignment explanation
Indices: 9745--9888 Score: 152
Period size: 31 Copynumber: 4.8 Consensus size: 31
9735 GGCATGTCAT
*
9745 ATGTCACTTTTTGGTACACGTGGAGTGACAT
1 ATGTCACTTTTTGGTACACGTGGAGTGACAC
* * * *
9776 GTGTCACTTTTTGGTACATGTGGCGTGTCAC
1 ATGTCACTTTTTGGTACACGTGGAGTGACAC
* * *
9807 ATGTCACTTTTTTGTACACGT-GACTGACAT
1 ATGTCACTTTTTGGTACACGTGGAGTGACAC
* * * *
9837 GTGTCAC-TTTTAG--CACGTGGCGTGCCAC
1 ATGTCACTTTTTGGTACACGTGGAGTGACAC
9865 ATGTCACTTTTTGGTACACGTGGA
1 ATGTCACTTTTTGGTACACGTGGA
9889 ATACCACGTC
Statistics
Matches: 88, Mismatches: 21, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
27 5 0.06
28 11 0.12
29 10 0.11
30 11 0.12
31 51 0.58
ACGTcount: A:0.19, C:0.20, G:0.25, T:0.36
Consensus pattern (31 bp):
ATGTCACTTTTTGGTACACGTGGAGTGACAC
Found at i:9795 original size:62 final size:60
Alignment explanation
Indices: 9719--9888 Score: 227
Period size: 62 Copynumber: 2.8 Consensus size: 60
9709 GTGCACGTGG
* * * *
9719 CACTTTTGAAACATGTGGCATGTCATATGTCACTTTTTGGTACACGTGGAGTGACATGTGT
1 CACTTTT-AGACATGTGGCGTGTCACATGTCACTTTTTGGTACACGTGGACTGACATGTGT
* *
9780 CACTTTTTGGTACATGTGGCGTGTCACATGTCACTTTTTTGTACACGT-GACTGACATGTGT
1 CAC-TTTTAG-ACATGTGGCGTGTCACATGTCACTTTTTGGTACACGTGGACTGACATGTGT
* *
9841 CACTTTTAG-CACGTGGCGTGCCACATGTCACTTTTTGGTACACGTGGA
1 CACTTTTAGACATGTGGCGTGTCACATGTCACTTTTTGGTACACGTGGA
9889 ATACCACGTC
Statistics
Matches: 96, Mismatches: 10, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
58 33 0.34
59 2 0.02
60 5 0.05
61 18 0.19
62 38 0.40
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.36
Consensus pattern (60 bp):
CACTTTTAGACATGTGGCGTGTCACATGTCACTTTTTGGTACACGTGGACTGACATGTGT
Found at i:9874 original size:58 final size:60
Alignment explanation
Indices: 9745--9886 Score: 207
Period size: 58 Copynumber: 2.4 Consensus size: 60
9735 GGCATGTCAT
* * * *
9745 ATGTCACTTTTTGGTACACGTGGAGTGACATGTGTCACTTTTTGGTACATGTGGCGTGTCAC
1 ATGTCACTTTTTGGTACACGT-GACTGACATGTGTCACTTTTTAG-ACACGTGGCGTGCCAC
*
9807 ATGTCACTTTTTTGTACACGTGACTGACATGTGTCAC-TTTTAG-CACGTGGCGTGCCAC
1 ATGTCACTTTTTGGTACACGTGACTGACATGTGTCACTTTTTAGACACGTGGCGTGCCAC
9865 ATGTCACTTTTTGGTACACGTG
1 ATGTCACTTTTTGGTACACGTG
9887 GAATACCACG
Statistics
Matches: 74, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
58 34 0.46
60 5 0.07
61 15 0.20
62 20 0.27
ACGTcount: A:0.18, C:0.20, G:0.25, T:0.37
Consensus pattern (60 bp):
ATGTCACTTTTTGGTACACGTGACTGACATGTGTCACTTTTTAGACACGTGGCGTGCCAC
Found at i:11248 original size:48 final size:47
Alignment explanation
Indices: 11120--11249 Score: 118
Period size: 48 Copynumber: 2.7 Consensus size: 47
11110 CCAAAATAAT
* * * * * *
11120 AAGCTAACCATTAGGATCCTTAGTGACCATAATTGGGCAAAATGCCA
1 AAGCTAAACATTACGACCCTCAATGACCAAAATTGGGCAAAATGCCA
* * * *
11167 AATGCTAACCATTACGACCCTCAATCACAAAAATTGGTCAAAATGGCC-
1 AA-GCTAAACATTACGACCCTCAATGACCAAAATTGGGCAAAAT-GCCA
* *
11215 AAGACTAAACATTATGACCCTCGATGACCAAAATT
1 AAG-CTAAACATTACGACCCTCAATGACCAAAATT
11250 CCAAAGGCTA
Statistics
Matches: 67, Mismatches: 13, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
47 3 0.04
48 61 0.91
49 3 0.04
ACGTcount: A:0.39, C:0.24, G:0.15, T:0.22
Consensus pattern (47 bp):
AAGCTAAACATTACGACCCTCAATGACCAAAATTGGGCAAAATGCCA
Found at i:12037 original size:49 final size:49
Alignment explanation
Indices: 11932--12043 Score: 145
Period size: 49 Copynumber: 2.3 Consensus size: 49
11922 GCAAAAATTG
* *** * *
11932 GCCAAAACTTAACCATTGTTACCCTAGGTGGCCAAAATTGGCCATTATG
1 GCCAAAGCTTAACCACCATTACCCTAGGTGGCCAAAATTGGCCATAATA
**
11981 GATAAAGCTTAACCACCATTACCCTAGGTGGCCAAAATTGGCCATAATA
1 GCCAAAGCTTAACCACCATTACCCTAGGTGGCCAAAATTGGCCATAATA
12030 GCCAAAGC-TAACCA
1 GCCAAAGCTTAACCA
12044 TCACAACGAT
Statistics
Matches: 53, Mismatches: 10, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
48 6 0.11
49 47 0.89
ACGTcount: A:0.35, C:0.26, G:0.17, T:0.22
Consensus pattern (49 bp):
GCCAAAGCTTAACCACCATTACCCTAGGTGGCCAAAATTGGCCATAATA
Found at i:13988 original size:2 final size:2
Alignment explanation
Indices: 13981--14006 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
13971 TTCAAAGCGA
13981 GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT
14007 TTTTTTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:14349 original size:22 final size:23
Alignment explanation
Indices: 14301--14343 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
14291 TTTTATACAA
*
14301 TTTAGTCTTTTAATTTTTATTTC
1 TTTAGTCTTTTAACTTTTATTTC
14324 TTTAG-CTTTTAACTTTTATT
1 TTTAGTCTTTTAACTTTTATT
14344 ATTTTAACTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.19, C:0.09, G:0.05, T:0.67
Consensus pattern (23 bp):
TTTAGTCTTTTAACTTTTATTTC
Found at i:16297 original size:165 final size:163
Alignment explanation
Indices: 15826--16307 Score: 563
Period size: 165 Copynumber: 2.9 Consensus size: 163
15816 TGAGTCATTT
15826 GTCAATTGAGAAATGACCAAAAAGTTTAATTATTTAATCCCCTTCTCAAGAATCAAAAGTTAGGA
1 GTCAATTGAGAAATGACCAAAAAG-TTAATTATTTAAT-CCC--CTCAAGAATCAAAAGTTAGGA
* * *
15891 CATTTAAGTAATCTGCCAAGTAGGTAAAGACGAAAAAGATTAGTTCTCTAGCTCATCATCAATTC
62 CATTTAAGTAATCTGGCAAGTAGGAAAAGACGAAAAA-ATTAGTTCTCTAGCTCCTCAT-AATTC
* * * * *
15956 TTGATGGGGATTTTTTATTAATTCCACTACTCTATTCAA
125 CTGGTGGGGATCTTTTAGTAATTCCACTACTCTATTAAA
* * *
15995 GTCTATTGAGAAATGACCAAAAAATTACTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACATT
1 GTCAATTGAGAAATGACCAAAAAGTTAATTATTTAATCCCCTCAAGAATCAAAAGTTAGGACATT
* ** * * * * * **
16060 TAAGTAATCTTGCAAGTAGGAAAAGAC-AAAAAAAAAGTTATTTAACTCC-AAAAGCAAGCCTTG
66 TAAGTAATCTGGCAAGTAGGAAAAGACGAAAAAATTAGTTCTCTAGCTCCTCATA--ATTCC-TG
* *
16123 GTAGGGATCTTTTAGTAATTCCACTACTCTGTTAAA
128 GTGGGGATCTTTTAGTAATTCCACTACTCTATTAAA
* * * * *
16159 GTCAATTGAGAAATGACTAAAAAGTCTAGTTATTTAATCACCTCAAGAATCAAAAGTTGGGATAT
1 GTCAATTGAGAAATGACCAAAAAGT-TAATTATTTAATCCCCTCAAGAATCAAAAGTTAGGACAT
* * * *
16224 TTAAGTAATCTGGCAAGTGGGAAAAGACGAAAAAATTAGTTCTCTCGCTCCTCATTATTCCGGGT
65 TTAAGTAATCTGGCAAGTAGGAAAAGACGAAAAAATTAGTTCTCTAGCTCCTCATAATTCCTGG-
16289 TGGGGATCTTTTAGTAATT
129 TGGGGATCTTTTAGTAATT
16308 TCCATATGTT
Statistics
Matches: 261, Mismatches: 45, Indels: 18
0.81 0.14 0.06
Matches are distributed among these distances:
161 1 0.00
162 1 0.00
163 13 0.05
164 61 0.23
165 131 0.50
166 16 0.06
167 4 0.02
168 12 0.05
169 22 0.08
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (163 bp):
GTCAATTGAGAAATGACCAAAAAGTTAATTATTTAATCCCCTCAAGAATCAAAAGTTAGGACATT
TAAGTAATCTGGCAAGTAGGAAAAGACGAAAAAATTAGTTCTCTAGCTCCTCATAATTCCTGGTG
GGGATCTTTTAGTAATTCCACTACTCTATTAAA
Found at i:16510 original size:23 final size:23
Alignment explanation
Indices: 16475--16519 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
16465 GAGCCCAATT
* *
16475 AACTTTGGTCTAGTTGGGTAATG
1 AACTTAGGCCTAGTTGGGTAATG
*
16498 AACTTAGGCCTAGTTGTGTAAT
1 AACTTAGGCCTAGTTGGGTAAT
16520 TAATAGATAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.24, C:0.11, G:0.27, T:0.38
Consensus pattern (23 bp):
AACTTAGGCCTAGTTGGGTAATG
Found at i:18161 original size:21 final size:21
Alignment explanation
Indices: 18135--18178 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
18125 GCTTTATATA
18135 TAATACATCATTAGTGGAATT
1 TAATACATCATTAGTGGAATT
18156 TAATACATCATTAGTGGAATT
1 TAATACATCATTAGTGGAATT
18177 TA
1 TA
18179 GCGGTACAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.09, G:0.14, T:0.39
Consensus pattern (21 bp):
TAATACATCATTAGTGGAATT
Found at i:19229 original size:48 final size:47
Alignment explanation
Indices: 19173--19268 Score: 183
Period size: 48 Copynumber: 2.0 Consensus size: 47
19163 ATAGACAATC
19173 TTTATCACCTTGTTCAATTTTAAAACAGAAATGCACTAGTTTGAATAT
1 TTTATCACCTTGTTCAATTTTAAAACAGAAATGCACTAG-TTGAATAT
19221 TTTATCACCTTGTTCAATTTTAAAACAGAAATGCACTAGTTGAATAT
1 TTTATCACCTTGTTCAATTTTAAAACAGAAATGCACTAGTTGAATAT
19268 T
1 T
19269 CTAACAAAAT
Statistics
Matches: 48, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
47 9 0.19
48 39 0.81
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.40
Consensus pattern (47 bp):
TTTATCACCTTGTTCAATTTTAAAACAGAAATGCACTAGTTGAATAT
Found at i:19982 original size:15 final size:15
Alignment explanation
Indices: 19958--19989 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
19948 GGACTCGTTT
*
19958 CTGTAGTCTGCTAAA
1 CTGTAATCTGCTAAA
19973 CTGTAATCTGCTAAA
1 CTGTAATCTGCTAAA
19988 CT
1 CT
19990 CCACTGGTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.34
Consensus pattern (15 bp):
CTGTAATCTGCTAAA
Found at i:22555 original size:2 final size:2
Alignment explanation
Indices: 22548--22575 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
22538 CAAACAATTA
22548 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
22576 TTTCATAGAC
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:23079 original size:49 final size:49
Alignment explanation
Indices: 23000--23153 Score: 152
Period size: 49 Copynumber: 3.2 Consensus size: 49
22990 GGGTAAAAAT
* * *
23000 TGGCCAAAGCTTAACCATCATTACCCTAGGTGGCCAAAATTGGCCATTA
1 TGGCCAAAGCTTAACCACCACTACCCTAGGTGGCCAAAATTGGCCATAA
* * *
23049 TGGACCAAA-CTTAACCACCACTACCTTAGGTGGCTAAAATTGGTCATAA
1 TGG-CCAAAGCTTAACCACCACTACCCTAGGTGGCCAAAATTGGCCATAA
* * * * * * * *
23098 TGGCCAAAGC-TAACCATCACAACTCTCGATGGCCACAATTGGACAAAA
1 TGGCCAAAGCTTAACCACCACTACCCTAGGTGGCCAAAATTGGCCATAA
23146 T-GCCAAAG
1 TGGCCAAAG
23154 GTAACCATCA
Statistics
Matches: 87, Mismatches: 16, Indels: 6
0.80 0.15 0.06
Matches are distributed among these distances:
47 7 0.08
48 34 0.39
49 41 0.47
50 5 0.06
ACGTcount: A:0.34, C:0.27, G:0.18, T:0.21
Consensus pattern (49 bp):
TGGCCAAAGCTTAACCACCACTACCCTAGGTGGCCAAAATTGGCCATAA
Found at i:24907 original size:38 final size:37
Alignment explanation
Indices: 24865--24936 Score: 99
Period size: 37 Copynumber: 1.9 Consensus size: 37
24855 AAATTAGTCC
* * *
24865 AAATGGTCATGGCAAAGCATCACGACCTAAGGTGACCA
1 AAATGGTCAAGAC-AAGCATCACGACCCAAGGTGACCA
*
24903 AAATGGTCAAGACTAGCATCACGACCCAAGGTGA
1 AAATGGTCAAGACAAGCATCACGACCCAAGGTGA
24937 AAATAAGTGG
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
37 19 0.63
38 11 0.37
ACGTcount: A:0.38, C:0.24, G:0.24, T:0.15
Consensus pattern (37 bp):
AAATGGTCAAGACAAGCATCACGACCCAAGGTGACCA
Done.