Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016477.1 Corchorus capsularis cultivar CVL-1 contig16498, 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: 133300
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:1744 original size:19 final size:18
Alignment explanation
Indices: 1720--1755 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
1710 TGAAGATTTT
1720 TTGAAGATAATTTGAAGAC
1 TTGAAGATAA-TTGAAGAC
*
1739 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
1756 ATTACTTCAA
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:0.06, G:0.22, T:0.31
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAC
Found at i:6312 original size:13 final size:14
Alignment explanation
Indices: 6294--6331 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
6284 CTCTGCTAGG
*
6294 TTTTTTTTCTG-CC
1 TTTTTTTTCCGCCC
6307 TTTTTTTTCCGCCCC
1 TTTTTTTTCCG-CCC
6322 TTTTTTTTCC
1 TTTTTTTTCC
6332 ATCCCCACTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 10 0.45
15 12 0.55
ACGTcount: A:0.00, C:0.29, G:0.05, T:0.66
Consensus pattern (14 bp):
TTTTTTTTCCGCCC
Found at i:8890 original size:30 final size:30
Alignment explanation
Indices: 8854--8912 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
8844 CAAGGGGGAG
8854 GGAATGATGCGCCCAAGG-CTTACCATGGAA
1 GGAATGATGCG-CCAAGGACTTACCATGGAA
*
8884 GGAATGATGCGCCAAGGACTTATCATGGA
1 GGAATGATGCGCCAAGGACTTACCATGGA
8913 CTTGAAGATG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 6 0.22
30 21 0.78
ACGTcount: A:0.31, C:0.20, G:0.31, T:0.19
Consensus pattern (30 bp):
GGAATGATGCGCCAAGGACTTACCATGGAA
Found at i:13112 original size:72 final size:72
Alignment explanation
Indices: 13021--13154 Score: 164
Period size: 72 Copynumber: 1.9 Consensus size: 72
13011 CCGACAGAAT
*
13021 AAATTTGCAACAATGAAACAT-GAACAGAAAACAAAAACCAA-TCAAAAACTAAAAATGCAAGAG
1 AAATTTCCAACAATGAAACATGGAA-AGAAAA-AAAAACCAAGTCAAAAACTAAAAATGCAAGAG
13084 CAAGGGAGG
64 CAAGGGAGG
* * * * * * *
13093 AAATTTCCAGCAATTAAACATGGAAATAAAATAAAACCAAGTCCAAAAGTAAACATGCAAGA
1 AAATTTCCAACAATGAAACATGGAAAGAAAAAAAAACCAAGTCAAAAACTAAAAATGCAAGA
13155 ATAAAGCCTT
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
71 8 0.15
72 41 0.79
73 3 0.06
ACGTcount: A:0.56, C:0.16, G:0.14, T:0.14
Consensus pattern (72 bp):
AAATTTCCAACAATGAAACATGGAAAGAAAAAAAAACCAAGTCAAAAACTAAAAATGCAAGAGCA
AGGGAGG
Found at i:13661 original size:48 final size:48
Alignment explanation
Indices: 13605--13701 Score: 194
Period size: 48 Copynumber: 2.0 Consensus size: 48
13595 AGAGAACTGC
13605 AATGGAAACAAAAATTCAATTAAAAAAAGCAAAACAAAGAGAAAGAAA
1 AATGGAAACAAAAATTCAATTAAAAAAAGCAAAACAAAGAGAAAGAAA
13653 AATGGAAACAAAAATTCAATTAAAAAAAGCAAAACAAAGAGAAAGAAA
1 AATGGAAACAAAAATTCAATTAAAAAAAGCAAAACAAAGAGAAAGAAA
13701 A
1 A
13702 CAAACATCCA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.69, C:0.08, G:0.12, T:0.10
Consensus pattern (48 bp):
AATGGAAACAAAAATTCAATTAAAAAAAGCAAAACAAAGAGAAAGAAA
Found at i:19746 original size:5 final size:5
Alignment explanation
Indices: 19742--19777 Score: 54
Period size: 5 Copynumber: 7.2 Consensus size: 5
19732 TTTGAGCCCA
* *
19742 ACCCA ACCCA ACCCC ACCCC ACCCC ACCCC ACCCC A
1 ACCCC ACCCC ACCCC ACCCC ACCCC ACCCC ACCCC A
19778 ACAAGCCTCA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.28, C:0.72, G:0.00, T:0.00
Consensus pattern (5 bp):
ACCCC
Found at i:28107 original size:11 final size:11
Alignment explanation
Indices: 28091--28115 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
28081 TTTTACAAGC
28091 TTTTGCCTATT
1 TTTTGCCTATT
28102 TTTTGCCTATT
1 TTTTGCCTATT
28113 TTT
1 TTT
28116 CTGTACAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.16, G:0.08, T:0.68
Consensus pattern (11 bp):
TTTTGCCTATT
Found at i:37112 original size:87 final size:87
Alignment explanation
Indices: 36976--37149 Score: 348
Period size: 87 Copynumber: 2.0 Consensus size: 87
36966 CTTAAAACAA
36976 TTTCAACTAGAGGAGATCATACAGCTTCACAACAACTACAGAGATCAAGCCATCATACTTGCCCC
1 TTTCAACTAGAGGAGATCATACAGCTTCACAACAACTACAGAGATCAAGCCATCATACTTGCCCC
37041 ACAACTATTTCCCTTAAAAGTC
66 ACAACTATTTCCCTTAAAAGTC
37063 TTTCAACTAGAGGAGATCATACAGCTTCACAACAACTACAGAGATCAAGCCATCATACTTGCCCC
1 TTTCAACTAGAGGAGATCATACAGCTTCACAACAACTACAGAGATCAAGCCATCATACTTGCCCC
37128 ACAACTATTTCCCTTAAAAGTC
66 ACAACTATTTCCCTTAAAAGTC
37150 ATAATTCCTG
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
87 87 1.00
ACGTcount: A:0.36, C:0.29, G:0.11, T:0.24
Consensus pattern (87 bp):
TTTCAACTAGAGGAGATCATACAGCTTCACAACAACTACAGAGATCAAGCCATCATACTTGCCCC
ACAACTATTTCCCTTAAAAGTC
Found at i:43274 original size:24 final size:24
Alignment explanation
Indices: 43247--43324 Score: 75
Period size: 24 Copynumber: 3.2 Consensus size: 24
43237 ACCACATTTA
* * *
43247 ATGGTGGGCGCGCTGCCACTTCGG
1 ATGGTGGGTGCGCTCCCACTTCCG
* * * *
43271 ATGGGGGGTGTGCTCCCGCTTCCA
1 ATGGTGGGTGCGCTCCCACTTCCG
* *
43295 ATGGTGGGTGCACTCCCACTTCTG
1 ATGGTGGGTGCGCTCCCACTTCCG
43319 ATGGTG
1 ATGGTG
43325 AGCATTCTAC
Statistics
Matches: 41, Mismatches: 13, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.10, C:0.27, G:0.37, T:0.26
Consensus pattern (24 bp):
ATGGTGGGTGCGCTCCCACTTCCG
Found at i:43604 original size:28 final size:28
Alignment explanation
Indices: 43572--43671 Score: 105
Period size: 28 Copynumber: 3.6 Consensus size: 28
43562 TTGTCTTTGA
*
43572 GAGCGTACTACCTCTTCAC-GATC-TATGG
1 GAGCGTACTACCGCTTCACAG-TCAT-TGG
*
43600 GAGCGTACTACCGCTTCGCAGTCATTGG
1 GAGCGTACTACCGCTTCACAGTCATTGG
* * *
43628 GAGCGTACTACCGCTCCGCGGTCATTGG
1 GAGCGTACTACCGCTTCACAGTCATTGG
* *
43656 AAGCGTACTACGGCTT
1 GAGCGTACTACCGCTT
43672 TGCAGTCTTT
Statistics
Matches: 63, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
28 61 0.97
29 2 0.03
ACGTcount: A:0.19, C:0.29, G:0.27, T:0.25
Consensus pattern (28 bp):
GAGCGTACTACCGCTTCACAGTCATTGG
Found at i:43683 original size:28 final size:28
Alignment explanation
Indices: 43601--43683 Score: 112
Period size: 28 Copynumber: 3.0 Consensus size: 28
43591 GATCTATGGG
*
43601 AGCGTACTACCGCTTCGCAGTCATTGGG
1 AGCGTACTACCGCTTCGCAGTCATTGGA
* *
43629 AGCGTACTACCGCTCCGCGGTCATTGGA
1 AGCGTACTACCGCTTCGCAGTCATTGGA
* * *
43657 AGCGTACTACGGCTTTGCAGTCTTTGG
1 AGCGTACTACCGCTTCGCAGTCATTGG
43684 GCGCACTCCC
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 47 1.00
ACGTcount: A:0.17, C:0.28, G:0.29, T:0.27
Consensus pattern (28 bp):
AGCGTACTACCGCTTCGCAGTCATTGGA
Found at i:43784 original size:27 final size:27
Alignment explanation
Indices: 43754--43914 Score: 85
Period size: 27 Copynumber: 5.9 Consensus size: 27
43744 GGCATCTCCA
43754 GATGGTGGGTGTACGGCGCCCTCTTGC
1 GATGGTGGGTGTACGGCGCCCTCTTGC
* * * ** *
43781 GATGGTGGGCGTGCAGCGCTTTCTTGT
1 GATGGTGGGTGTACGGCGCCCTCTTGC
* *
43808 TATGGTGGGCATGT--GGCGCCCTCTTTC
1 GATGGTGGG--TGTACGGCGCCCTCTTGC
* *
43835 AAGATGGTTGGCGTACGGCGCCCTCTT-C
1 --GATGGTGGGTGTACGGCGCCCTCTTGC
* * * * * *
43863 CAAGATGGATGTACGGCGCTCTCTTCC
1 GATGGTGGGTGTACGGCGCCCTCTTGC
* *
43890 AAGATGGTGGGTGTATGGCGTCCTC
1 --GATGGTGGGTGTACGGCGCCCTC
43915 GTCCAAGATG
Statistics
Matches: 95, Mismatches: 30, Indels: 16
0.67 0.21 0.11
Matches are distributed among these distances:
26 18 0.19
27 40 0.42
28 1 0.01
29 36 0.38
ACGTcount: A:0.12, C:0.24, G:0.35, T:0.29
Consensus pattern (27 bp):
GATGGTGGGTGTACGGCGCCCTCTTGC
Found at i:43854 original size:29 final size:28
Alignment explanation
Indices: 43822--43926 Score: 115
Period size: 29 Copynumber: 3.8 Consensus size: 28
43812 GTGGGCATGT
*
43822 GGCGCCCTCTTTCAAGATGGTTGGCGTAC
1 GGCGCCCTCTTCCAAGATGGTTGG-GTAC
*
43851 GGCGCCCTCTTCCAAGATGGAT--GTAC
1 GGCGCCCTCTTCCAAGATGGTTGGGTAC
* * *
43877 GGCGCTCTCTTCCAAGATGGTGGGTGTAT
1 GGCGCCCTCTTCCAAGATGGTTGG-GTAC
* *
43906 GGCGTCCTCGTCCAAGATGGT
1 GGCGCCCTCTTCCAAGATGGT
43927 GGATGCACGA
Statistics
Matches: 64, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
26 23 0.36
29 41 0.64
ACGTcount: A:0.15, C:0.27, G:0.31, T:0.27
Consensus pattern (28 bp):
GGCGCCCTCTTCCAAGATGGTTGGGTAC
Found at i:43886 original size:26 final size:27
Alignment explanation
Indices: 43847--44000 Score: 141
Period size: 29 Copynumber: 5.5 Consensus size: 27
43837 GATGGTTGGC
*
43847 GTACGGCGCCCTCTTCCAAGA-TGGAT
1 GTACGGCGCTCTCTTCCAAGAGTGGAT
*
43873 GTACGGCGCTCTCTTCCAAGATGGTGGGT
1 GTACGGCGCTCTCTTCCAAGA--GTGGAT
* *
43902 GTATGGCG-TCCTCGTCCAAGATGGTGGAT
1 GTACGGCGCT-CTCTTCCAAGA--GTGGAT
* * * *
43931 GCACGACGCTCTCGTCCAAGATGGCGGAT
1 GTACGGCGCTCTCTTCCAAGA--GTGGAT
*
43960 GTACAGCGCTCTCTTCCAAGATGTGGAT
1 GTACGGCGCTCTCTTCCAAGA-GTGGAT
43988 GTACGGCGCTCTC
1 GTACGGCGCTCTC
44001 GGGAGTTCTA
Statistics
Matches: 107, Mismatches: 16, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
26 20 0.19
28 18 0.17
29 68 0.64
30 1 0.01
ACGTcount: A:0.18, C:0.27, G:0.31, T:0.25
Consensus pattern (27 bp):
GTACGGCGCTCTCTTCCAAGAGTGGAT
Found at i:43950 original size:58 final size:56
Alignment explanation
Indices: 43834--44001 Score: 196
Period size: 58 Copynumber: 3.0 Consensus size: 56
43824 CGCCCTCTTT
* * *
43834 CAAGATGGTTGGCGTACGGCGCCCTCTTCCAAGA--TGGATGTACGGCGCTCTCTTC
1 CAAGATGGTGGGTGTACGGCG-CCTCTTCCAAGATGTGGATGTACGGCGCTCTCGTC
* * * *
43889 CAAGATGGTGGGTGTATGGCGTCCTCGTCCAAGATGGTGGATGCACGACGCTCTCGTC
1 CAAGATGGTGGGTGTACGGCG-CCTCTTCCAAGAT-GTGGATGTACGGCGCTCTCGTC
* * *
43947 CAAGATGGCGGATGTACAGCGCTCTCTTCCAAGATGTGGATGTACGGCGCTCTCG
1 CAAGATGGTGGGTGTACGGCGC-CTCTTCCAAGATGTGGATGTACGGCGCTCTCG
44002 GGAGTTCTAT
Statistics
Matches: 94, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
55 29 0.31
57 19 0.20
58 46 0.49
ACGTcount: A:0.18, C:0.26, G:0.32, T:0.24
Consensus pattern (56 bp):
CAAGATGGTGGGTGTACGGCGCCTCTTCCAAGATGTGGATGTACGGCGCTCTCGTC
Found at i:44144 original size:29 final size:28
Alignment explanation
Indices: 44032--44143 Score: 136
Period size: 28 Copynumber: 3.9 Consensus size: 28
44022 CTTGTGGGGT
*
44032 GTACTACCTCTTCGTGAGCTTGGAGGAC
1 GTACTACCACTTCGTGAGCTTGGAGGAC
* * ** *
44060 ATAATACCACTTCACGAGCTTGGAAGAC
1 GTACTACCACTTCGTGAGCTTGGAGGAC
44088 GTACTACCACTTCGTGAGCTTTGGAGGGA-
1 GTACTACCACTTCGTGAGC-TTGGA-GGAC
44117 GTACTACCACTTCGTGAGCTTTGGAGG
1 GTACTACCACTTCGTGAGC-TTGGAGG
44144 GCATATTACA
Statistics
Matches: 71, Mismatches: 11, Indels: 4
0.83 0.13 0.05
Matches are distributed among these distances:
28 39 0.55
29 30 0.42
30 2 0.03
ACGTcount: A:0.23, C:0.23, G:0.27, T:0.27
Consensus pattern (28 bp):
GTACTACCACTTCGTGAGCTTGGAGGAC
Found at i:44892 original size:59 final size:59
Alignment explanation
Indices: 44730--45222 Score: 593
Period size: 59 Copynumber: 8.4 Consensus size: 59
44720 GTTTTAGGTT
* * * * * *
44730 GTGCGACCGAGGGATGCTCG-TT-TTTTTTTTCGCACGAGTGGGGGATGCCCATTAGGTC
1 GTGCGACCGAGGGATGCTCGATTGTTCTTATT-GCTCGTGTGGGGGATGCCCACTGGGTC
* * *
44788 GTGTGACCGAGGGATGCTCGATT-TTCTTATTGCAT-GAGTGGGGGATGCCAACTGGGTC
1 GTGCGACCGAGGGATGCTCGATTGTTCTTATTGC-TCGTGTGGGGGATGCCCACTGGGTC
* * ** * * * * * *
44846 ATGTGATTGAGAGATGTTTGATTGTTCTTATTGCTCGTGTGGGGGATACCCATTTGGTC
1 GTGCGACCGAGGGATGCTCGATTGTTCTTATTGCTCGTGTGGGGGATGCCCACTGGGTC
* * *
44905 GTGCGACCGAGGGATGCTCGATTGTTCTTATTGCTTGTGTGGGGGATACCCACTAGGTC
1 GTGCGACCGAGGGATGCTCGATTGTTCTTATTGCTCGTGTGGGGGATGCCCACTGGGTC
* * *
44964 GTGCGACCGAGGGATGCTCGATCGTTTTTATTGC-CTGTGTGGGGGATGCCCGACTGTGTC
1 GTGCGACCGAGGGATGCTCGATTGTTCTTATTGCTC-GTGTGGGGGATGCCC-ACTGGGTC
*
45024 GTGCGACCGAGGGATGCTCGATTGTTCTTATTACTCGTGTGGGGGATGCCCACTGGGTC
1 GTGCGACCGAGGGATGCTCGATTGTTCTTATTGCTCGTGTGGGGGATGCCCACTGGGTC
* * ** * *
45083 GTGCCACCGAGGGATGCTCTATCATTCTTATTGCTCGTGTGGGCGATACCCACTGGGTC
1 GTGCGACCGAGGGATGCTCGATTGTTCTTATTGCTCGTGTGGGGGATGCCCACTGGGTC
* *
45142 GTGCGACCGAGGGATGCTCGATCGTTCTTATTGCTCGTGTGGGGGATGCCCACTGGGTT
1 GTGCGACCGAGGGATGCTCGATTGTTCTTATTGCTCGTGTGGGGGATGCCCACTGGGTC
45201 GTGCGACCG-GGAGATGCTCGAT
1 GTGCGACCGAGG-GATGCTCGAT
45223 CGTTATTGTT
Statistics
Matches: 376, Mismatches: 51, Indels: 15
0.85 0.12 0.03
Matches are distributed among these distances:
58 61 0.16
59 262 0.70
60 52 0.14
61 1 0.00
ACGTcount: A:0.15, C:0.20, G:0.34, T:0.30
Consensus pattern (59 bp):
GTGCGACCGAGGGATGCTCGATTGTTCTTATTGCTCGTGTGGGGGATGCCCACTGGGTC
Found at i:45094 original size:178 final size:177
Alignment explanation
Indices: 44767--45222 Score: 605
Period size: 178 Copynumber: 2.6 Consensus size: 177
44757 TTTCGCACGA
* * * * *
44767 GTGGGGGATGCCCATTAGGTCGTGTGACCGAGGGATGCTCGAT--TTTCTTATTGCATGAGTGGG
1 GTGGGGGATACCCACTAGGTCGTGCGACCGAGGGATGCTCGATCGTTT-TTATTGCCTGTGTGGG
* * * ** * * * *
44830 GGATGCCAACTGGGTCATGTGATTGAGAGATGTTTGATTGTTCTTATTGCTCGTGTGGGGGATAC
65 GGATGCCCACTGGGTCGTGCGACCGAGGGATGCTCGATTGTTCTTATTACTCGTGTGGGGGATAC
* * * ** *
44895 CCATTTGGTCGTGCGACCGAGGGATGCTCGATTGTTCTTATTGCTTGT
130 CCACTGGGTCGTGCCACCGAGGGATGCTCGATCATTCTTATTGCTCGT
44943 GTGGGGGATACCCACTAGGTCGTGCGACCGAGGGATGCTCGATCGTTTTTATTGCCTGTGTGGGG
1 GTGGGGGATACCCACTAGGTCGTGCGACCGAGGGATGCTCGATCGTTTTTATTGCCTGTGTGGGG
* *
45008 GATGCCCGACTGTGTCGTGCGACCGAGGGATGCTCGATTGTTCTTATTACTCGTGTGGGGGATGC
66 GATGCCC-ACTGGGTCGTGCGACCGAGGGATGCTCGATTGTTCTTATTACTCGTGTGGGGGATAC
*
45073 CCACTGGGTCGTGCCACCGAGGGATGCTCTATCATTCTTATTGCTCGT
130 CCACTGGGTCGTGCCACCGAGGGATGCTCGATCATTCTTATTGCTCGT
* * *
45121 GTGGGCGATACCCACTGGGTCGTGCGACCGAGGGATGCTCGATCGTTCTTATTG-CTCGTGTGGG
1 GTGGGGGATACCCACTAGGTCGTGCGACCGAGGGATGCTCGATCGTTTTTATTGCCT-GTGTGGG
*
45185 GGATGCCCACTGGGTTGTGCGACCG-GGAGATGCTCGAT
65 GGATGCCCACTGGGTCGTGCGACCGAGG-GATGCTCGAT
45223 CGTTATTGTT
Statistics
Matches: 247, Mismatches: 28, Indels: 9
0.87 0.10 0.03
Matches are distributed among these distances:
176 42 0.17
177 48 0.19
178 157 0.64
ACGTcount: A:0.15, C:0.20, G:0.35, T:0.30
Consensus pattern (177 bp):
GTGGGGGATACCCACTAGGTCGTGCGACCGAGGGATGCTCGATCGTTTTTATTGCCTGTGTGGGG
GATGCCCACTGGGTCGTGCGACCGAGGGATGCTCGATTGTTCTTATTACTCGTGTGGGGGATACC
CACTGGGTCGTGCCACCGAGGGATGCTCGATCATTCTTATTGCTCGT
Found at i:52107 original size:31 final size:31
Alignment explanation
Indices: 52069--52144 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 31
52059 CTAAATACTT
* *
52069 AATTCAGGATATAATGTTTG-CACCAAAATTC
1 AATTCAGGATATAAGGTTTGCCA-CAAAATGC
52100 AATTCAGGATATAAGGTTTGCCACAAAATGC
1 AATTCAGGATATAAGGTTTGCCACAAAATGC
**
52131 AATTTGGGATATAA
1 AATTCAGGATATAA
52145 CGTTACAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
31 38 0.95
32 2 0.05
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.30
Consensus pattern (31 bp):
AATTCAGGATATAAGGTTTGCCACAAAATGC
Found at i:52169 original size:29 final size:31
Alignment explanation
Indices: 52137--52203 Score: 111
Period size: 31 Copynumber: 2.2 Consensus size: 31
52127 ATGCAATTTG
52137 GGATATAACGTTAC-AAAA-CAAGCAATTAA
1 GGATATAACGTTACGAAAAGCAAGCAATTAA
*
52166 GGATATAACGTTACGAAAAGCGAGCAATTAA
1 GGATATAACGTTACGAAAAGCAAGCAATTAA
52197 GGATATA
1 GGATATA
52204 GTCTGTTAGT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
29 14 0.40
30 4 0.11
31 17 0.49
ACGTcount: A:0.48, C:0.12, G:0.19, T:0.21
Consensus pattern (31 bp):
GGATATAACGTTACGAAAAGCAAGCAATTAA
Found at i:52382 original size:31 final size:31
Alignment explanation
Indices: 52321--52389 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
52311 CCCTAACTGA
*
52321 TTATATCCTTAATTGCTTAAAACCGAAAACG
1 TTATATCCTTAATTGCTTAAAACAGAAAACG
** * *
52352 TTATATCCTTAATTGCTTGCAGCAGCAAACG
1 TTATATCCTTAATTGCTTAAAACAGAAAACG
52383 TTATATC
1 TTATATC
52390 ATAAATTGAT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.35
Consensus pattern (31 bp):
TTATATCCTTAATTGCTTAAAACAGAAAACG
Found at i:53335 original size:16 final size:15
Alignment explanation
Indices: 53314--53357 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 15
53304 CCTTATATGC
53314 AATAAAAAGTTATTTA
1 AATAAAAA-TTATTTA
53330 AATAAAATATT-TTTA
1 AATAAAA-ATTATTTA
53345 AA-AAAAATTATTT
1 AATAAAAATTATTT
53358 TCTTCTGAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
13 3 0.12
14 7 0.27
15 6 0.23
16 9 0.35
17 1 0.04
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (15 bp):
AATAAAAATTATTTA
Found at i:53344 original size:15 final size:16
Alignment explanation
Indices: 53326--53358 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
53316 TAAAAAGTTA
*
53326 TTTAAATAAAA-TATT
1 TTTAAAAAAAATTATT
53341 TTTAAAAAAAATTATT
1 TTTAAAAAAAATTATT
53357 TT
1 TT
53359 CTTCTGAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TTTAAAAAAAATTATT
Found at i:53512 original size:31 final size:30
Alignment explanation
Indices: 53422--53512 Score: 112
Period size: 31 Copynumber: 3.0 Consensus size: 30
53412 TTTTCTACCG
* * *
53422 CAAGCAATTAAGGATATAACGTTAT-AATA
1 CAAGCAATTAAGGATATAACGTTTTGATTT
*
53451 CAAGCAATTAAGGATATAATGTTTTTGATTT
1 CAAGCAATTAAGGATATAACG-TTTTGATTT
*
53482 CAAGCAATTAAGGATATAACATTTTCGATTT
1 CAAGCAATTAAGGATATAACGTTTT-GATTT
53513 TAGGGTTGCT
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
29 20 0.38
30 7 0.13
31 26 0.49
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.35
Consensus pattern (30 bp):
CAAGCAATTAAGGATATAACGTTTTGATTT
Found at i:53700 original size:2 final size:2
Alignment explanation
Indices: 53693--53759 Score: 62
Period size: 2 Copynumber: 38.0 Consensus size: 2
53683 AAAAACCGAC
53693 AT AT AT AT -T AT AT A- AT AT AT AT A- AT -T AT -T AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
53730 -T AT AT TT A- AT AT -T AT AT AT AT AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
53760 TAGAAATTTA
Statistics
Matches: 54, Mismatches: 2, Indels: 18
0.73 0.03 0.24
Matches are distributed among these distances:
1 9 0.17
2 45 0.83
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:53713 original size:9 final size:8
Alignment explanation
Indices: 53693--53759 Score: 62
Period size: 7 Copynumber: 9.5 Consensus size: 8
53683 AAAAACCGAC
53693 ATATATAT
1 ATATATAT
53701 -TATATA-
1 ATATATAT
53707 ATATATAT
1 ATATATAT
53715 A-AT-TAT
1 ATATATAT
53721 -TATATAT
1 ATATATAT
53728 AT-TATAT
1 ATATATAT
*
53735 TTA-ATAT
1 ATATATAT
53742 -TATATAT
1 ATATATAT
53749 ATATA-AT
1 ATATATAT
53756 ATAT
1 ATAT
53760 TAGAAATTTA
Statistics
Matches: 50, Mismatches: 1, Indels: 17
0.74 0.01 0.25
Matches are distributed among these distances:
6 7 0.14
7 37 0.74
8 6 0.12
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (8 bp):
ATATATAT
Found at i:54751 original size:64 final size:64
Alignment explanation
Indices: 54674--54796 Score: 192
Period size: 64 Copynumber: 1.9 Consensus size: 64
54664 GTGAATTGTA
* * * *
54674 AAGTCTTTAATTCAGTGTCAATTAAATCTGATGTGATTATGTGAATTGTTAAGTGTTAACTGTG
1 AAGTCTTTAATTCAATGTCAATTAAATCTAATGTGATTATGTGAATTGTGAAGTCTTAACTGTG
* *
54738 AAGTCTTTAATTCAATGTCAATTCAATCTAATGTGATTATTTGAATTGTGAAGTCTTAA
1 AAGTCTTTAATTCAATGTCAATTAAATCTAATGTGATTATGTGAATTGTGAAGTCTTAA
54797 ATTCAGTCTT
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
64 53 1.00
ACGTcount: A:0.32, C:0.09, G:0.17, T:0.42
Consensus pattern (64 bp):
AAGTCTTTAATTCAATGTCAATTAAATCTAATGTGATTATGTGAATTGTGAAGTCTTAACTGTG
Found at i:58446 original size:29 final size:31
Alignment explanation
Indices: 58380--58446 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
58370 TTTAACGGAC
58380 TATATCCTTAATTGCTCACTTTTCGTAACGT
1 TATATCCTTAATTGCTCACTTTTCGTAACGT
**
58411 TATATCCTTAATTGCT-TGTTTT-GTAACGT
1 TATATCCTTAATTGCTCACTTTTCGTAACGT
58440 TATATCC
1 TATATCC
58447 CAAATTGAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
29 14 0.41
30 4 0.12
31 16 0.47
ACGTcount: A:0.22, C:0.19, G:0.10, T:0.48
Consensus pattern (31 bp):
TATATCCTTAATTGCTCACTTTTCGTAACGT
Found at i:61663 original size:46 final size:45
Alignment explanation
Indices: 61581--61672 Score: 103
Period size: 46 Copynumber: 2.0 Consensus size: 45
61571 TGTTATTTTC
* * * * * * *
61581 CAAGTAGAGTGATTCCTAGGAGAGTGCTCTCTATGGAGAGTCATTT
1 CAAGAAGAGTGATTCCCAAGAAAGTACTCTCCATGGAAAGTC-TTT
*
61627 CAAGAAGAGTGATTCCCAAGAAAGTACTTTCCATGGAAAGTCTTT
1 CAAGAAGAGTGATTCCCAAGAAAGTACTCTCCATGGAAAGTCTTT
61672 C
1 C
61673 CCTACTCTCC
Statistics
Matches: 38, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
45 4 0.11
46 34 0.89
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.28
Consensus pattern (45 bp):
CAAGAAGAGTGATTCCCAAGAAAGTACTCTCCATGGAAAGTCTTT
Found at i:61949 original size:23 final size:23
Alignment explanation
Indices: 61918--61973 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
61908 TGAATAAAAT
* * *
61918 ACCGGACCGAAGTGGTCGGTTCA
1 ACCGTACCGAACTGGCCGGTTCA
* *
61941 ACTGTACCGGACTGGCCGGTTCA
1 ACCGTACCGAACTGGCCGGTTCA
61964 ACCGTACCGA
1 ACCGTACCGA
61974 TATGTTTATA
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.21, C:0.30, G:0.30, T:0.18
Consensus pattern (23 bp):
ACCGTACCGAACTGGCCGGTTCA
Found at i:80966 original size:6 final size:7
Alignment explanation
Indices: 80951--80978 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
80941 AAATACTGAG
80951 AAAATAA
1 AAAATAA
80958 AAAATAA
1 AAAATAA
80965 AAAATAA
1 AAAATAA
80972 AAAATAA
1 AAAATAA
80979 GAGATTAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (7 bp):
AAAATAA
Found at i:81872 original size:4 final size:4
Alignment explanation
Indices: 81858--81898 Score: 68
Period size: 4 Copynumber: 10.8 Consensus size: 4
81848 GCAATTAGAG
81858 TATT T-TT TATT TATT TATT TA-T TATT TATT TATT TATT TAT
1 TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT TAT
81899 ATAATACATG
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
3 6 0.17
4 29 0.83
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:81882 original size:15 final size:15
Alignment explanation
Indices: 81858--81895 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
81848 GCAATTAGAG
*
81858 TATTTTTTATTTATT
1 TATTTATTATTTATT
81873 TATTTATTATTTATT
1 TATTTATTATTTATT
81888 TATTTATT
1 TATTTATT
81896 TATATAATAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (15 bp):
TATTTATTATTTATT
Found at i:81885 original size:19 final size:19
Alignment explanation
Indices: 81858--81898 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
81848 GCAATTAGAG
*
81858 TATTTTTTATTTATTTATT
1 TATTATTTATTTATTTATT
81877 TATTATTTATTTATTTATT
1 TATTATTTATTTATTTATT
81896 TAT
1 TAT
81899 ATAATACATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (19 bp):
TATTATTTATTTATTTATT
Found at i:82420 original size:22 final size:22
Alignment explanation
Indices: 82373--82427 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
82363 ATGATCCCAT
* * *
82373 TATGAAATTTTGATAAGCTTCG
1 TATGAAATTTTAATAAGATACG
82395 TATGAAATTTTAATAACGATAC-
1 TATGAAATTTTAATAA-GATACG
*
82417 TATGGAATTTT
1 TATGAAATTTT
82428 GAGAATCTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 25 0.89
23 3 0.11
ACGTcount: A:0.36, C:0.07, G:0.15, T:0.42
Consensus pattern (22 bp):
TATGAAATTTTAATAAGATACG
Found at i:82729 original size:13 final size:13
Alignment explanation
Indices: 82711--82740 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
82701 TTAAACTATC
82711 AAATGGAAAAATA
1 AAATGGAAAAATA
*
82724 AAATGGTAAAATA
1 AAATGGAAAAATA
82737 AAAT
1 AAAT
82741 AATTATAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.13, T:0.20
Consensus pattern (13 bp):
AAATGGAAAAATA
Found at i:90428 original size:4 final size:4
Alignment explanation
Indices: 90419--90453 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
90409 TACCTTTATT
90419 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATA
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATA
90454 AAGAACTGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.51, C:0.00, G:0.23, T:0.26
Consensus pattern (4 bp):
ATAG
Found at i:91599 original size:33 final size:33
Alignment explanation
Indices: 91518--91636 Score: 134
Period size: 33 Copynumber: 3.5 Consensus size: 33
91508 CCGCGCAACA
*
91518 CCGGCCACAAGACCGGCCACGCGACATGGACATGT
1 CCGGCCAC-A-ACCGGCCACGCGACATGGACATGC
*
91553 CCGGCCATC-ACCGGCCACGCGACATGGACATGG
1 CCGGCCA-CAACCGGCCACGCGACATGGACATGC
* ** *
91586 CCGGCTACAACCGGCCAAACGAC-TCGGCCATGC
1 CCGGCCACAACCGGCCACGCGACAT-GGACATGC
91619 CCGGCCACAACCGGCCAC
1 CCGGCCACAACCGGCCAC
91637 TCGATCCTTT
Statistics
Matches: 73, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
32 2 0.03
33 63 0.86
35 7 0.10
36 1 0.01
ACGTcount: A:0.24, C:0.42, G:0.27, T:0.08
Consensus pattern (33 bp):
CCGGCCACAACCGGCCACGCGACATGGACATGC
Found at i:99471 original size:20 final size:19
Alignment explanation
Indices: 99446--99493 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
99436 TATAAAGTTT
*
99446 TTTTTAATAACCTTATTAAG
1 TTTTTAATAACCATATT-AG
99466 TTTTT-ATGAACCATATTAG
1 TTTTTAAT-AACCATATTAG
99485 TTTTTAATA
1 TTTTTAATA
99494 TATAACCTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 10 0.40
20 15 0.60
ACGTcount: A:0.33, C:0.08, G:0.06, T:0.52
Consensus pattern (19 bp):
TTTTTAATAACCATATTAG
Found at i:101658 original size:55 final size:58
Alignment explanation
Indices: 101572--101685 Score: 198
Period size: 55 Copynumber: 2.0 Consensus size: 58
101562 GACCAAACAT
*
101572 TAAACAATGATAATTACTATATAACTATCATAATAATAAACAACTAAACCACATAAAG
1 TAAACAATGATAATTACTATATAACTATCATAATAACAAACAACTAAACCACATAAAG
101630 TAAACAATGATAA-T-C-ATATAACTATCATAATAACAAACAACTAAACCACATAAAG
1 TAAACAATGATAATTACTATATAACTATCATAATAACAAACAACTAAACCACATAAAG
101685 T
1 T
101686 TGGACAAAAC
Statistics
Matches: 55, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
55 40 0.73
56 1 0.02
57 1 0.02
58 13 0.24
ACGTcount: A:0.55, C:0.17, G:0.04, T:0.25
Consensus pattern (58 bp):
TAAACAATGATAATTACTATATAACTATCATAATAACAAACAACTAAACCACATAAAG
Found at i:101712 original size:21 final size:21
Alignment explanation
Indices: 101671--101718 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
101661 AACAAACAAC
101671 TAAACCACATAAAGTTGGACA
1 TAAACCACATAAAGTTGGACA
*
101692 -AAACCTACATATAG-TGAGACA
1 TAAACC-ACATAAAGTTG-GACA
101713 TAAACC
1 TAAACC
101719 CAAGATCTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
20 7 0.30
21 11 0.48
22 5 0.22
ACGTcount: A:0.48, C:0.21, G:0.12, T:0.19
Consensus pattern (21 bp):
TAAACCACATAAAGTTGGACA
Found at i:107522 original size:135 final size:134
Alignment explanation
Indices: 107268--107549 Score: 341
Period size: 135 Copynumber: 2.1 Consensus size: 134
107258 CAAGTGGCTA
* * *
107268 TTGGTTTTGCTCCCCGAGTCCTTGCCCCCCAAGTCTTTTATCGATGAGACCAACCTGAGCCACGA
1 TTGGTTTTGC-CCCCGAGTCCTTGCCCCCCAAGTCTTTCATAGATGAGACCAACCTCAGCCACGA
* * * ** *
107333 CCTGTTGATTGTTCACTTGATGGTTAACTTATCGAAGGGGAAGAGGACCAGGCTGGGCACCAAAC
65 CCTGTGGATTGTTCACCTGATGGTTAACCTATCGAAAAGGAAGAGCACCAGGCTGGGCACCAAAC
*
107398 ATTTG
130 AGTTG
* * *
107403 TTGGTTTTGCCCCCTGGGTCCTTGCCCCCCAAGTCTTTCATAGATGAGACCAATCTCAGCCATGA
1 TTGGTTTTGCCCCC-GAGTCCTTGCCCCCCAAGTCTTTCATAGATGAGACCAACCTCAGCCACGA
* * * * * * * * *
107468 CTTGTGGGTTGTTCACCTGATGGTTGACCTGTTGAAAAGGCAGAGCATCGGGCTGGGCACCAAGC
65 CCTGTGGATTGTTCACCTGATGGTTAACCTATCGAAAAGGAAGAGCACCAGGCTGGGCACCAAAC
107533 AGTTG
130 AGTTG
107538 TTGGTTTT-CCCC
1 TTGGTTTTGCCCC
107550 TCCAAGTCTT
Statistics
Matches: 124, Mismatches: 22, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
134 8 0.06
135 116 0.94
ACGTcount: A:0.20, C:0.26, G:0.26, T:0.28
Consensus pattern (134 bp):
TTGGTTTTGCCCCCGAGTCCTTGCCCCCCAAGTCTTTCATAGATGAGACCAACCTCAGCCACGAC
CTGTGGATTGTTCACCTGATGGTTAACCTATCGAAAAGGAAGAGCACCAGGCTGGGCACCAAACA
GTTG
Found at i:108028 original size:2 final size:2
Alignment explanation
Indices: 108021--108050 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
108011 ACCTTCGACT
*
108021 AG AG AG AG AG AG AG AG AG AG AG AG AA AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
108051 TCGGGGATCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:118890 original size:10 final size:10
Alignment explanation
Indices: 118877--118902 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
118867 ATATCTCGAT
118877 ATATCCGTAA
1 ATATCCGTAA
118887 ATATCCGTAA
1 ATATCCGTAA
118897 ATATCC
1 ATATCC
118903 ATATTAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.38, C:0.23, G:0.08, T:0.31
Consensus pattern (10 bp):
ATATCCGTAA
Found at i:121169 original size:3 final size:3
Alignment explanation
Indices: 121157--121202 Score: 85
Period size: 3 Copynumber: 15.7 Consensus size: 3
121147 GCTCACGGAA
121157 GAT G-T GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
121203 GGGAAATGAA
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 40 0.95
ACGTcount: A:0.33, C:0.00, G:0.35, T:0.33
Consensus pattern (3 bp):
GAT
Done.