Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016268.1 Corchorus capsularis cultivar CVL-1 contig16289, 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: 82523
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:954 original size:29 final size:29
Alignment explanation
Indices: 897--954 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
887 CGGCCGAAAT
* * *
897 GGCCGAAACAGGCCGGTACGTGGCAGTAC
1 GGCCGAAACAGCCCGGTACATAGCAGTAC
*
926 GGCCGAAACAGCCCGGTACATAGCGGTAC
1 GGCCGAAACAGCCCGGTACATAGCAGTAC
955 AAATTCCGGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.26, C:0.29, G:0.34, T:0.10
Consensus pattern (29 bp):
GGCCGAAACAGCCCGGTACATAGCAGTAC
Found at i:1131 original size:21 final size:20
Alignment explanation
Indices: 1107--1158 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 20
1097 GGGAAAAGGG
*
1107 AAAATGGAAAATTTTAAAAAA
1 AAAAGGGAAAA-TTTAAAAAA
1128 AAAAGGGAAAATTTAAAAAA
1 AAAAGGGAAAATTTAAAAAA
*
1148 GAAAGGGAAAA
1 AAAAGGGAAAA
1159 GGGAAAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 19 0.66
21 10 0.34
ACGTcount: A:0.67, C:0.00, G:0.17, T:0.15
Consensus pattern (20 bp):
AAAAGGGAAAATTTAAAAAA
Found at i:1165 original size:20 final size:20
Alignment explanation
Indices: 1122--1165 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
1112 GGAAAATTTT
***
1122 AAAAAAAAAAGGGAAAATTT
1 AAAAAAAAAAGGGAAAAGGG
*
1142 AAAAAAGAAAGGGAAAAGGG
1 AAAAAAAAAAGGGAAAAGGG
1162 AAAA
1 AAAA
1166 TTTTAAAAAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.70, C:0.00, G:0.23, T:0.07
Consensus pattern (20 bp):
AAAAAAAAAAGGGAAAAGGG
Found at i:1466 original size:2 final size:2
Alignment explanation
Indices: 1454--1486 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1444 TTCTTCTTTC
1454 AT AT A- 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 AT AT AT
1487 TTCAATTATA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1931 original size:59 final size:59
Alignment explanation
Indices: 1839--1956 Score: 236
Period size: 59 Copynumber: 2.0 Consensus size: 59
1829 CAGAAAAATC
1839 TCTTGGGTTTGTTGGGGTCTTTCTTCACCGATTTGACATTCTTTGTGCGTTTTTTTGCT
1 TCTTGGGTTTGTTGGGGTCTTTCTTCACCGATTTGACATTCTTTGTGCGTTTTTTTGCT
1898 TCTTGGGTTTGTTGGGGTCTTTCTTCACCGATTTGACATTCTTTGTGCGTTTTTTTGCT
1 TCTTGGGTTTGTTGGGGTCTTTCTTCACCGATTTGACATTCTTTGTGCGTTTTTTTGCT
1957 ACTGTTGTCC
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.07, C:0.17, G:0.24, T:0.53
Consensus pattern (59 bp):
TCTTGGGTTTGTTGGGGTCTTTCTTCACCGATTTGACATTCTTTGTGCGTTTTTTTGCT
Found at i:2049 original size:20 final size:21
Alignment explanation
Indices: 2024--2066 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
2014 ATGGAATTAA
2024 ATATCCGTC-A-ATATCTCGAT
1 ATATCCGTCGATATATC-CGAT
2044 ATATCCGTCGATATATCCGAT
1 ATATCCGTCGATATATCCGAT
2065 AT
1 AT
2067 CTATACCCCT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 9 0.43
21 7 0.33
22 5 0.24
ACGTcount: A:0.30, C:0.23, G:0.12, T:0.35
Consensus pattern (21 bp):
ATATCCGTCGATATATCCGAT
Found at i:2056 original size:12 final size:12
Alignment explanation
Indices: 2024--2062 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
2014 ATGGAATTAA
2024 ATATCCGTC-A-
1 ATATCCGTCGAT
2034 ATAT-C-TCGAT
1 ATATCCGTCGAT
2044 ATATCCGTCGAT
1 ATATCCGTCGAT
2056 ATATCCG
1 ATATCCG
2063 ATATCTATAC
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
8 2 0.08
9 2 0.08
10 8 0.32
11 1 0.04
12 12 0.48
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (12 bp):
ATATCCGTCGAT
Found at i:3307 original size:13 final size:12
Alignment explanation
Indices: 3273--3315 Score: 68
Period size: 12 Copynumber: 3.5 Consensus size: 12
3263 CATCGATACC
3273 TCGATATATCCG
1 TCGATATATCCG
3285 TCGATATATCCG
1 TCGATATATCCG
*
3297 TTCGATGTATCCG
1 -TCGATATATCCG
3310 TCGATA
1 TCGATA
3316 CCTGTATTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
12 17 0.61
13 11 0.39
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.35
Consensus pattern (12 bp):
TCGATATATCCG
Found at i:7860 original size:137 final size:137
Alignment explanation
Indices: 7609--7882 Score: 449
Period size: 137 Copynumber: 2.0 Consensus size: 137
7599 TTGGCTGAAA
* * *
7609 AATTCGCCGATAGGGGAGAGTGGACGCGCTGGGACAAATCATTGGTACGGAGGGTTCTTCAGCGG
1 AATTCGCCGATAGGGGAGAATGGACGCGCTGGGACAAATCATAGGTACAGAGGGTTCTTCAGCGG
* *
7674 AGGACGAGGCTAGGAGATGATCGTCTAAGGAGAATTCGGGGAAGAAGATGCATTGTTGGGGCCAG
66 AGGACGAGGCTAGGAGATGATCGTCTAAGGAGAATTCAGGGAAGAAGATGCATTCTTGGGGCCAG
7739 TTAGGGT
131 TTAGGGT
* * * *
7746 AATTCGCGGATAGGGGAGAATGGACGCGCTGGGACAAATCATAGGTACATAGGGTTTTTTAGCGG
1 AATTCGCCGATAGGGGAGAATGGACGCGCTGGGACAAATCATAGGTACAGAGGGTTCTTCAGCGG
* *
7811 AGGACGAGGCTAGGAGATGATCGTCTAAGGAGAATTTAGGGAAGGAGATGCATTCTTGGGGCCAG
66 AGGACGAGGCTAGGAGATGATCGTCTAAGGAGAATTCAGGGAAGAAGATGCATTCTTGGGGCCAG
7876 TTAGGGT
131 TTAGGGT
7883 TTGAGAGAGG
Statistics
Matches: 126, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
137 126 1.00
ACGTcount: A:0.27, C:0.14, G:0.38, T:0.22
Consensus pattern (137 bp):
AATTCGCCGATAGGGGAGAATGGACGCGCTGGGACAAATCATAGGTACAGAGGGTTCTTCAGCGG
AGGACGAGGCTAGGAGATGATCGTCTAAGGAGAATTCAGGGAAGAAGATGCATTCTTGGGGCCAG
TTAGGGT
Found at i:10349 original size:24 final size:24
Alignment explanation
Indices: 10322--10377 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
10312 AGAACTTAAG
10322 AAGAACTTTAATTAAGAAGAACGT
1 AAGAACTTTAATTAAGAAGAACGT
* *
10346 AAGAACTTTAATTAAGAATAACTT
1 AAGAACTTTAATTAAGAAGAACGT
*
10370 AAAAACTT
1 AAGAACTT
10378 GGGAAGATTG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.52, C:0.09, G:0.11, T:0.29
Consensus pattern (24 bp):
AAGAACTTTAATTAAGAAGAACGT
Found at i:14052 original size:2 final size:2
Alignment explanation
Indices: 14045--14075 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
14035 AATGGTAAAT
14045 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
14076 AACTATTTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:18376 original size:400 final size:400
Alignment explanation
Indices: 17636--18428 Score: 1487
Period size: 400 Copynumber: 2.0 Consensus size: 400
17626 AAATTAGCTC
17636 CTGAGTACTTCATGAAAGTTGTAGATCATTAAATTACCTTTAAATAGACACTTGAATCACCTTGA
1 CTGAGTACTTCATGAAAGTTGTAGATCATTAAATTACCTTTAAATAGACACTTGAATCACCTTGA
*
17701 TCGGACAAACAGAATAAAAAATAAAAGAATTAAAGATGAAACGTTAAATCGTCCAACCTAGAATT
66 TCGGACAAACAGAACAAAAAATAAAAGAATTAAAGATGAAACGTTAAATCGTCCAACCTAGAATT
17766 TGTGAGGGATTAAATAGCATAAAACATAAAAGTATATGGATCATTTGCTAAATATTCCAGCAAAA
131 TGTGAGGGATTAAATAGCATAAAACATAAAAGTATATGGATCATTTGCTAAATATTCCAGCAAAA
*
17831 GAAGATTAGTTTATTGAGAGTGGGACCCATCAATAGTAACTTTTAATCAAAGTTCCCAAAACACC
196 GAAGATTAGTTTATTGAGAGCGGGACCCATCAATAGTAACTTTTAATCAAAGTTCCCAAAACACC
*
17896 CTTGGTTCATCAACCTAAACCACGAAAAAACCGAGCATGAAAGTACCGAAATGTCCCTGACAATT
261 CTTGGTTCATCAACCTAAACCACGAAAAAACCGAGCATGAAAGTACCGAAATGTCCATGACAATT
*
17961 TGTTCTTGGGTGAATGTGGTGCATTTTATAGCTGGATGAAAACGTAACTTCCATTCCAACTTTAA
326 TGTTCTTGGGTGAATGTGGTGCATTTTATAGCTGGACGAAAACGTAACTTCCATTCCAACTTTAA
18026 TGTGGTGCTT
391 TGTGGTGCTT
*
18036 CTGAGTACTTCATGAAAGTTGTAGATCATTAAATTACCTTTAAATAGATACTTGAATCACCTTGA
1 CTGAGTACTTCATGAAAGTTGTAGATCATTAAATTACCTTTAAATAGACACTTGAATCACCTTGA
*
18101 TCGGACAAACAGAACAAAAAATAAAAGAATTAAAGATTAAACGTTAAATCGTCCAACCTAGAATT
66 TCGGACAAACAGAACAAAAAATAAAAGAATTAAAGATGAAACGTTAAATCGTCCAACCTAGAATT
* *
18166 TGTGAGGGATTAAATAGCATAAAGCATAAAAGTATATGGATCATTTGCTAAATATTCTAGCAAAA
131 TGTGAGGGATTAAATAGCATAAAACATAAAAGTATATGGATCATTTGCTAAATATTCCAGCAAAA
18231 GAAGATTAGTTTATTGAGAGCGGGACCCATCAATAGTAACTTTTAATCAAAGTTCCCAAAACACC
196 GAAGATTAGTTTATTGAGAGCGGGACCCATCAATAGTAACTTTTAATCAAAGTTCCCAAAACACC
*
18296 CTTGGTTCATCAACCTAAACCACGAAAAAACCGAGCATGAAAGTACCGAAATGTCTATGACAATT
261 CTTGGTTCATCAACCTAAACCACGAAAAAACCGAGCATGAAAGTACCGAAATGTCCATGACAATT
* *
18361 TGTTCTTGGGTGAATGTGGTGCATTTTATAGCTGGACGAAAACGTAATTTCCTTTCCAACTTTAA
326 TGTTCTTGGGTGAATGTGGTGCATTTTATAGCTGGACGAAAACGTAACTTCCATTCCAACTTTAA
18426 TGT
391 TGT
18429 ACAGTATAGA
Statistics
Matches: 382, Mismatches: 11, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
400 382 1.00
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (400 bp):
CTGAGTACTTCATGAAAGTTGTAGATCATTAAATTACCTTTAAATAGACACTTGAATCACCTTGA
TCGGACAAACAGAACAAAAAATAAAAGAATTAAAGATGAAACGTTAAATCGTCCAACCTAGAATT
TGTGAGGGATTAAATAGCATAAAACATAAAAGTATATGGATCATTTGCTAAATATTCCAGCAAAA
GAAGATTAGTTTATTGAGAGCGGGACCCATCAATAGTAACTTTTAATCAAAGTTCCCAAAACACC
CTTGGTTCATCAACCTAAACCACGAAAAAACCGAGCATGAAAGTACCGAAATGTCCATGACAATT
TGTTCTTGGGTGAATGTGGTGCATTTTATAGCTGGACGAAAACGTAACTTCCATTCCAACTTTAA
TGTGGTGCTT
Found at i:18961 original size:16 final size:16
Alignment explanation
Indices: 18928--18987 Score: 57
Period size: 16 Copynumber: 3.8 Consensus size: 16
18918 CGAACTCGAT
* * *
18928 TGACCCGAAATCCGAA
1 TGACCCGAGACCCAAA
*
18944 TGACTCGAGACCCAAA
1 TGACCCGAGACCCAAA
*
18960 TGACCCGAGACCCGAA
1 TGACCCGAGACCCAAA
* *
18976 TTACCTGAGACC
1 TGACCCGAGACC
18988 TGTTTGAGAT
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.33, C:0.33, G:0.20, T:0.13
Consensus pattern (16 bp):
TGACCCGAGACCCAAA
Found at i:27352 original size:30 final size:30
Alignment explanation
Indices: 27316--27378 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
27306 TGTATTCAAG
27316 TCCATGATAAGTCCTT-GACGCATCATTCCC
1 TCCATGATAAG-CCTTGGACGCATCATTCCC
*
27346 TCCATGATAAGCCTTGGGCGCATCATTCCC
1 TCCATGATAAGCCTTGGACGCATCATTCCC
27376 TCC
1 TCC
27379 CCCTTGAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 4 0.13
30 27 0.87
ACGTcount: A:0.21, C:0.35, G:0.16, T:0.29
Consensus pattern (30 bp):
TCCATGATAAGCCTTGGACGCATCATTCCC
Found at i:27787 original size:33 final size:33
Alignment explanation
Indices: 27750--27855 Score: 151
Period size: 33 Copynumber: 3.2 Consensus size: 33
27740 AAAACAGTGC
* *
27750 TATTTTCAAAGCTATAATCAACCAAAACAGATT
1 TATTTTCAATGCTATGATCAACCAAAACAGATT
* * *
27783 TATTTTCAATGCTATGATCAA-CGAAACAAAAT
1 TATTTTCAATGCTATGATCAACCAAAACAGATT
27815 TATTTTCAATGCTATGATCAACCAAAACAGATT
1 TATTTTCAATGCTATGATCAACCAAAACAGATT
*
27848 TGTTTTCA
1 TATTTTCA
27856 TCACAATTAG
Statistics
Matches: 63, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
32 29 0.46
33 34 0.54
ACGTcount: A:0.41, C:0.17, G:0.08, T:0.34
Consensus pattern (33 bp):
TATTTTCAATGCTATGATCAACCAAAACAGATT
Found at i:27818 original size:32 final size:32
Alignment explanation
Indices: 27750--27843 Score: 125
Period size: 32 Copynumber: 2.9 Consensus size: 32
27740 AAAACAGTGC
* * * *
27750 TATTTTCAAAGCTATAATCAACCAAAACAGATT
1 TATTTTCAATGCTATGATCAA-CAAAACAAAAT
*
27783 TATTTTCAATGCTATGATCAACGAAACAAAAT
1 TATTTTCAATGCTATGATCAACAAAACAAAAT
27815 TATTTTCAATGCTATGATCAACCAAAACA
1 TATTTTCAATGCTATGATCAA-CAAAACA
27844 GATTTGTTTT
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
32 29 0.54
33 25 0.46
ACGTcount: A:0.44, C:0.18, G:0.07, T:0.31
Consensus pattern (32 bp):
TATTTTCAATGCTATGATCAACAAAACAAAAT
Found at i:27908 original size:33 final size:33
Alignment explanation
Indices: 27871--27975 Score: 95
Period size: 33 Copynumber: 3.2 Consensus size: 33
27861 ATTAGTATCC
* *
27871 AAAACAGATTTTGTTTCATCACAAACAACACCT
1 AAAACAGATTTAGTGTCATCACAAACAACACCT
**
27904 AAAACAGATTTAGTGTCATTGCAAACAACA-CT
1 AAAACAGATTTAGTGTCATCACAAACAACACCT
** * * * * *
27936 CAAATTAGGTTTAGTATCATCGCAAATAACATCT
1 -AAAACAGATTTAGTGTCATCACAAACAACACCT
27970 AAAACA
1 AAAACA
27976 CTCTTTTCAA
Statistics
Matches: 58, Mismatches: 12, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
32 2 0.03
33 54 0.93
34 2 0.03
ACGTcount: A:0.44, C:0.20, G:0.10, T:0.27
Consensus pattern (33 bp):
AAAACAGATTTAGTGTCATCACAAACAACACCT
Found at i:37180 original size:30 final size:30
Alignment explanation
Indices: 37144--37206 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
37134 TGTCTTTAAG
*
37144 TCCATGATAAGTCCTT-GGCGTATCATTCCC
1 TCCATGATAAG-CCTTGGGCGCATCATTCCC
37174 TCCATGATAAGCCTTGGGCGCATCATTCCC
1 TCCATGATAAGCCTTGGGCGCATCATTCCC
37204 TCC
1 TCC
37207 CTTTTGAAGA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 4 0.13
30 27 0.87
ACGTcount: A:0.19, C:0.33, G:0.17, T:0.30
Consensus pattern (30 bp):
TCCATGATAAGCCTTGGGCGCATCATTCCC
Found at i:37627 original size:33 final size:33
Alignment explanation
Indices: 37590--37696 Score: 187
Period size: 33 Copynumber: 3.2 Consensus size: 33
37580 AAAACAGTCC
37590 TATTTTCAATGCTATGATCAACCAAAACAGATT
1 TATTTTCAATGCTATGATCAACCAAAACAGATT
* *
37623 TATTTTCAATGCTATGATCAACCAAAACAAAAT
1 TATTTTCAATGCTATGATCAACCAAAACAGATT
37656 TATTTTCAATGCTATGATCAACCAAAACAGATT
1 TATTTTCAATGCTATGATCAACCAAAACAGATT
*
37689 TGTTTTCA
1 TATTTTCA
37697 TCACAATTAG
Statistics
Matches: 69, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 69 1.00
ACGTcount: A:0.39, C:0.18, G:0.08, T:0.35
Consensus pattern (33 bp):
TATTTTCAATGCTATGATCAACCAAAACAGATT
Found at i:37729 original size:66 final size:66
Alignment explanation
Indices: 37590--37713 Score: 178
Period size: 66 Copynumber: 1.9 Consensus size: 66
37580 AAAACAGTCC
* * *
37590 TATTTTCAATGCTATGATCAACCAAAACAGATTTATTTTCAATGCTATGATCAACCAAAACAAAA
1 TATTTTCAATGCTATGATCAACCAAAACAGATTTATTTTCAATACAATGAGCAACCAAAACAAAA
37655 T
66 T
* * *
37656 TATTTTCAATGCTATGATCAACCAAAACAGATTTGTTTTC-ATCACAATTAGCATCCAA
1 TATTTTCAATGCTATGATCAACCAAAACAGATTTATTTTCAAT-ACAATGAGCAACCAA
37714 GACAGATTTT
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
65 2 0.04
66 49 0.96
ACGTcount: A:0.40, C:0.19, G:0.08, T:0.33
Consensus pattern (66 bp):
TATTTTCAATGCTATGATCAACCAAAACAGATTTATTTTCAATACAATGAGCAACCAAAACAAAA
T
Found at i:37752 original size:33 final size:33
Alignment explanation
Indices: 37677--37755 Score: 97
Period size: 33 Copynumber: 2.4 Consensus size: 33
37667 CTATGATCAA
** *
37677 CCAAAACAGATTTGTTTTCATCACAATTAGCAT
1 CCAAAACAGATTTGTTTTCATCACAAACAACAT
* *
37710 CCAAGACAGATTTTTTTTCATCACAAACAACA-
1 CCAAAACAGATTTGTTTTCATCACAAACAACAT
37742 CCTAAAACAGATTT
1 CC-AAAACAGATTT
37756 AGTGTCATTG
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
32 2 0.05
33 37 0.95
ACGTcount: A:0.39, C:0.23, G:0.08, T:0.30
Consensus pattern (33 bp):
CCAAAACAGATTTGTTTTCATCACAAACAACAT
Found at i:37770 original size:33 final size:32
Alignment explanation
Indices: 37727--37816 Score: 90
Period size: 33 Copynumber: 2.7 Consensus size: 32
37717 AGATTTTTTT
* *
37727 TCATCACAAACAACACCTAAAACAGATTTAGTG
1 TCATCGCAAACAACA-CTAAAACAGATTTAGTA
* ** *
37760 TCATTGCAAACAACACTCAAATTAGGTTTAGTA
1 TCATCGCAAACAACACT-AAAACAGATTTAGTA
*
37793 TCATCGCAAATAACATCTAAAACA
1 TCATCGCAAACAACA-CTAAAACA
37817 CTCTTTTCAG
Statistics
Matches: 45, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
32 2 0.04
33 41 0.91
34 2 0.04
ACGTcount: A:0.44, C:0.22, G:0.09, T:0.24
Consensus pattern (32 bp):
TCATCGCAAACAACACTAAAACAGATTTAGTA
Found at i:40478 original size:30 final size:30
Alignment explanation
Indices: 40442--40500 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
40432 CTTTAAGTCC
40442 ATGATAAGTCCTT-GGCGCATCATTCCCTCT
1 ATGATAAG-CCTTGGGCGCATCATTCCCTCT
40472 ATGATAAGCCTTGGGCGCATCATTCCCTC
1 ATGATAAGCCTTGGGCGCATCATTCCCTC
40501 CCCCTTGAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 4 0.14
30 24 0.86
ACGTcount: A:0.20, C:0.31, G:0.19, T:0.31
Consensus pattern (30 bp):
ATGATAAGCCTTGGGCGCATCATTCCCTCT
Found at i:48116 original size:30 final size:30
Alignment explanation
Indices: 48080--48141 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
48070 TGTCTTCAAG
48080 TCCATAATAAGTCCTT-GGCGCATCATTCCC
1 TCCATAATAAG-CCTTGGGCGCATCATTCCC
*
48110 TCCATAATAAGCCTTGGGTGCATCATTCCC
1 TCCATAATAAGCCTTGGGCGCATCATTCCC
48140 TC
1 TC
48142 TCCCTTGAAG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 4 0.13
30 26 0.87
ACGTcount: A:0.23, C:0.32, G:0.15, T:0.31
Consensus pattern (30 bp):
TCCATAATAAGCCTTGGGCGCATCATTCCC
Found at i:48564 original size:32 final size:33
Alignment explanation
Indices: 48499--48617 Score: 213
Period size: 33 Copynumber: 3.6 Consensus size: 33
48489 GTCCTCTTTT
* *
48499 CAATGCTATGATGAACCAAAACAGAATTATTTG
1 CAATGCTATGATCAACCAAAACAAAATTATTTG
48532 CAATGCTATGATCAACCAAAA-AAAATTATTTG
1 CAATGCTATGATCAACCAAAACAAAATTATTTG
48564 CAATGCTATGATCAACCAAAACAAAATTATTTG
1 CAATGCTATGATCAACCAAAACAAAATTATTTG
48597 CAATGCTATGATCAACCAAAA
1 CAATGCTATGATCAACCAAAA
48618 TAGAATTGTT
Statistics
Matches: 83, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
32 31 0.37
33 52 0.63
ACGTcount: A:0.45, C:0.18, G:0.11, T:0.26
Consensus pattern (33 bp):
CAATGCTATGATCAACCAAAACAAAATTATTTG
Found at i:48684 original size:33 final size:33
Alignment explanation
Indices: 48646--48751 Score: 124
Period size: 33 Copynumber: 3.2 Consensus size: 33
48636 AATTAGCATC
* *
48646 CAAAACAGATTTAGTATCATCACAAACAATACT
1 CAAAACAGATTTAGTATCATCGCAAACAACACT
* * * *
48679 TAAAACAGATTTAGTGTCATTGCAAATAACACT
1 CAAAACAGATTTAGTATCATCGCAAACAACACT
**
48712 CAAATTAGATTTAGTATCATCGCAAACAACA-T
1 CAAAACAGATTTAGTATCATCGCAAACAACACT
48744 CTAAAACA
1 C-AAAACA
48752 CTCTTTGCAA
Statistics
Matches: 58, Mismatches: 14, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
32 2 0.03
33 56 0.97
ACGTcount: A:0.46, C:0.19, G:0.08, T:0.26
Consensus pattern (33 bp):
CAAAACAGATTTAGTATCATCGCAAACAACACT
Found at i:54305 original size:13 final size:13
Alignment explanation
Indices: 54287--54327 Score: 64
Period size: 13 Copynumber: 3.2 Consensus size: 13
54277 GGTGGCATCG
54287 GCATGGCATGGGT
1 GCATGGCATGGGT
54300 GCATGGCATGGGT
1 GCATGGCATGGGT
* *
54313 GCTTGTCATGGGT
1 GCATGGCATGGGT
54326 GC
1 GC
54328 TGTCCGCGCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.12, C:0.17, G:0.44, T:0.27
Consensus pattern (13 bp):
GCATGGCATGGGT
Found at i:54385 original size:21 final size:21
Alignment explanation
Indices: 54352--54404 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 21
54342 CCAGGGCACA
** * *
54352 TGGGTGCTTAGGCCAACCGGC
1 TGGGTGCACAGGCAAACCGCC
*
54373 TGGGTGCACAGGCAAAGCGCC
1 TGGGTGCACAGGCAAACCGCC
*
54394 TGGGCGCACAG
1 TGGGTGCACAG
54405 CCAGCGTCGG
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.19, C:0.28, G:0.40, T:0.13
Consensus pattern (21 bp):
TGGGTGCACAGGCAAACCGCC
Found at i:54937 original size:110 final size:110
Alignment explanation
Indices: 54813--55033 Score: 442
Period size: 110 Copynumber: 2.0 Consensus size: 110
54803 AAGTGCAATA
54813 AAAATAAATAAATTACAAATATGTAAATCAAGAAGATAGATTTTAATTAATGGAAATTCCCAACT
1 AAAATAAATAAATTACAAATATGTAAATCAAGAAGATAGATTTTAATTAATGGAAATTCCCAACT
54878 CTAAAGCATTGATTCTTAGGTTATTAATTTAATCATTGGTACCAG
66 CTAAAGCATTGATTCTTAGGTTATTAATTTAATCATTGGTACCAG
54923 AAAATAAATAAATTACAAATATGTAAATCAAGAAGATAGATTTTAATTAATGGAAATTCCCAACT
1 AAAATAAATAAATTACAAATATGTAAATCAAGAAGATAGATTTTAATTAATGGAAATTCCCAACT
54988 CTAAAGCATTGATTCTTAGGTTATTAATTTAATCATTGGTACCAG
66 CTAAAGCATTGATTCTTAGGTTATTAATTTAATCATTGGTACCAG
55033 A
1 A
55034 TATGAATTCT
Statistics
Matches: 111, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
110 111 1.00
ACGTcount: A:0.44, C:0.11, G:0.12, T:0.33
Consensus pattern (110 bp):
AAAATAAATAAATTACAAATATGTAAATCAAGAAGATAGATTTTAATTAATGGAAATTCCCAACT
CTAAAGCATTGATTCTTAGGTTATTAATTTAATCATTGGTACCAG
Found at i:69501 original size:22 final size:22
Alignment explanation
Indices: 69473--69533 Score: 86
Period size: 22 Copynumber: 2.6 Consensus size: 22
69463 GTTTTTTCTA
*
69473 AAAAAAAAAAGATTTTTGCGTCGAT
1 AAAAAAAAAAG---TTTGAGTCGAT
69498 AAAAAAAAAAGTTTGAGTCGAT
1 AAAAAAAAAAGTTTGAGTCGAT
69520 AAAAAAAAAAGTTT
1 AAAAAAAAAAGTTT
69534 TTTTCGTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
22 24 0.69
25 11 0.31
ACGTcount: A:0.56, C:0.05, G:0.15, T:0.25
Consensus pattern (22 bp):
AAAAAAAAAAGTTTGAGTCGAT
Found at i:69580 original size:38 final size:33
Alignment explanation
Indices: 69520--69603 Score: 96
Period size: 35 Copynumber: 2.4 Consensus size: 33
69510 TTGAGTCGAT
* *
69520 AAAAAAAAAAGTTTTTTTCGTTTTTCCGATTTTTCTA
1 AAAAAAAAAAATTTTTTCCGTTTTTCC---TTTT-TA
69557 AAAAAAAAAAATTATTTTCCGTTTTTCCTTTTTA
1 AAAAAAAAAAATT-TTTTCCGTTTTTCCTTTTTA
69591 AAATAAAAAAAAT
1 AAA-AAAAAAAAT
69604 AAATTTATTT
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
34 5 0.12
35 13 0.30
37 12 0.28
38 13 0.30
ACGTcount: A:0.43, C:0.10, G:0.05, T:0.43
Consensus pattern (33 bp):
AAAAAAAAAAATTTTTTCCGTTTTTCCTTTTTA
Found at i:79224 original size:33 final size:32
Alignment explanation
Indices: 79184--79291 Score: 126
Period size: 33 Copynumber: 3.3 Consensus size: 32
79174 AGCACTTGTG
*
79184 ACCGGCCACGCGACTTGGAGATGCCCGCGCAAC
1 ACCGGCCACGCGACATGGAGATGCCCG-GCAAC
* *
79217 ACCGGCCATGCGACATGGAGATGCCCGGCCATC
1 ACCGGCCACGCGACATGGAGATGCCCGG-CAAC
* ** *
79250 ACCGGCCGCGCGACATGGCCATGCCCGGCCAC
1 ACCGGCCACGCGACATGGAGATGCCCGGCAAC
79282 AACCGGCCAC
1 -ACCGGCCAC
79292 ATGACTCGGC
Statistics
Matches: 63, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
32 3 0.05
33 60 0.95
ACGTcount: A:0.20, C:0.42, G:0.30, T:0.08
Consensus pattern (32 bp):
ACCGGCCACGCGACATGGAGATGCCCGGCAAC
Found at i:79287 original size:10 final size:10
Alignment explanation
Indices: 79274--79325 Score: 50
Period size: 10 Copynumber: 4.9 Consensus size: 10
79264 ATGGCCATGC
79274 CCGGCCACAA
1 CCGGCCACAA
79284 CCGGCCACATGA
1 CCGGCCACA--A
***
79296 CTCGGCCATGC
1 C-CGGCCACAA
79307 CCGGCCACAA
1 CCGGCCACAA
79317 CCGGCCACA
1 CCGGCCACA
79326 TGATTCTTTA
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
10 24 0.73
11 1 0.03
12 2 0.06
13 6 0.18
ACGTcount: A:0.23, C:0.48, G:0.23, T:0.06
Consensus pattern (10 bp):
CCGGCCACAA
Found at i:79303 original size:33 final size:33
Alignment explanation
Indices: 79266--79328 Score: 126
Period size: 33 Copynumber: 1.9 Consensus size: 33
79256 CGCGCGACAT
79266 GGCCATGCCCGGCCACAACCGGCCACATGACTC
1 GGCCATGCCCGGCCACAACCGGCCACATGACTC
79299 GGCCATGCCCGGCCACAACCGGCCACATGA
1 GGCCATGCCCGGCCACAACCGGCCACATGA
79329 TTCTTTAGCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.22, C:0.44, G:0.25, T:0.08
Consensus pattern (33 bp):
GGCCATGCCCGGCCACAACCGGCCACATGACTC
Done.