Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018818.1 Corchorus olitorius cultivar O-4 contig18851, 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: 54792
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:13 original size:2 final size:2
Alignment explanation
Indices: 1--41 Score: 73
Period size: 2 Copynumber: 20.0 Consensus size: 2
1 AT AT AGT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
42 TATTTTAGTG
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 36 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5360 original size:45 final size:45
Alignment explanation
Indices: 5309--5395 Score: 149
Period size: 45 Copynumber: 1.9 Consensus size: 45
5299 AATATGCAAA
*
5309 GTTGACAAGAAATTTTAGGGAATCTAACTTTACCT-CCATCAAAAC
1 GTTGACAAGAAATTTCAGGGAATCTAA-TTTACCTCCCATCAAAAC
5354 GTTGACAAGAAATTTCAGGGAATCTAATTTACCTCCCATCAA
1 GTTGACAAGAAATTTCAGGGAATCTAATTTACCTCCCATCAA
5396 CGTTCGTATC
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
44 7 0.17
45 33 0.82
ACGTcount: A:0.37, C:0.21, G:0.14, T:0.29
Consensus pattern (45 bp):
GTTGACAAGAAATTTCAGGGAATCTAATTTACCTCCCATCAAAAC
Found at i:5548 original size:45 final size:45
Alignment explanation
Indices: 5484--5578 Score: 156
Period size: 45 Copynumber: 2.1 Consensus size: 45
5474 AATATGCAAA
5484 GTTGACAAGAAATTTCAGGGAATCTAACTTTAC-CTCCATCAAAAC
1 GTTGACAAGAAATTTCAGGGAATCTAACTTTACTC-CCATCAAAAC
* *
5529 GTTGACAAGAAATTTCAGGGAATCTACCTTTACTCCCATCAAACC
1 GTTGACAAGAAATTTCAGGGAATCTAACTTTACTCCCATCAAAAC
5574 GTTGA
1 GTTGA
5579 TCAAAAGTTA
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
45 46 0.98
46 1 0.02
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.27
Consensus pattern (45 bp):
GTTGACAAGAAATTTCAGGGAATCTAACTTTACTCCCATCAAAAC
Found at i:5724 original size:45 final size:45
Alignment explanation
Indices: 5660--5753 Score: 179
Period size: 45 Copynumber: 2.1 Consensus size: 45
5650 AATATGCAAA
5660 GTTGACAAGAAATTTCAGGGAATCTAACTTTACCTCCATCAAAAC
1 GTTGACAAGAAATTTCAGGGAATCTAACTTTACCTCCATCAAAAC
*
5705 GTTGACAAGAAATTTCAGGGAATCTAACTTTACCTCCATCAAACC
1 GTTGACAAGAAATTTCAGGGAATCTAACTTTACCTCCATCAAAAC
5750 GTTG
1 GTTG
5754 GATCAAAAAG
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 48 1.00
ACGTcount: A:0.35, C:0.22, G:0.15, T:0.28
Consensus pattern (45 bp):
GTTGACAAGAAATTTCAGGGAATCTAACTTTACCTCCATCAAAAC
Found at i:5872 original size:178 final size:178
Alignment explanation
Indices: 5140--6064 Score: 1659
Period size: 178 Copynumber: 5.2 Consensus size: 178
5130 TCTAATATTT
* * * *
5140 AAATTTCAGGGAATCAAACTTGACCTCAATCAAACCGTTGACAAGAAATTTCAGGGAATCTAACT
1 AAATTTCAGGGAATCTAACTTTACCTCCATCAAAACGTTGACAAGAAATTTCAGGGAATCTAACT
*
5205 TTACCTCCATCAAACCGTAGGATCAAAAAGTAAAACTCATCTTAACCGTCCATTTGAACTCTGAA
66 TTACCTCCATCAAACCGTTGGATCAAAAAGTAAAACTCATCTTAACCGTCCATTTGAACTCTGAA
5270 CACTTTTACACCATACCCAAGGAAGTCAGAATATGCAAAGTTGACAAG
131 CACTTTTACACCATACCCAAGGAAGTCAGAATATGCAAAGTTGACAAG
*
5318 AAATTTTAGGGAATCTAACTTTACCTCCATCAAAACGTTGACAAGAAATTTCAGGGAATCTAA-T
1 AAATTTCAGGGAATCTAACTTTACCTCCATCAAAACGTTGACAAGAAATTTCAGGGAATCTAACT
*
5382 TTACCTCCCATC-AA-CGTTCGTATC-AAAAGT-AAACTCATCTTAACCGTCCATTTGAACTCTG
66 TTACCT-CCATCAAACCGTT-GGATCAAAAAGTAAAACTCATCTTAACCGTCCATTTGAACTCTG
5443 AACACTTTTACACCATACCCAAGGAAGTCAGAATATGCAAAGTTGACAAG
129 AACACTTTTACACCATACCCAAGGAAGTCAGAATATGCAAAGTTGACAAG
*
5493 AAATTTCAGGGAATCTAACTTTACCTCCATCAAAACGTTGACAAGAAATTTCAGGGAATCTACCT
1 AAATTTCAGGGAATCTAACTTTACCTCCATCAAAACGTTGACAAGAAATTTCAGGGAATCTAACT
*
5558 TTA-CTCCCATCAAACCGTT-GATC-AAAAGTTAAACTCATCTTAACCGTCCATTTGAACTCTGA
66 TTACCT-CCATCAAACCGTTGGATCAAAAAGTAAAACTCATCTTAACCGTCCATTTGAACTCTGA
*
5620 ACACTTTTACACCATACCTAAGGAAGTCAGAATATGCAAAGTTGACAAG
130 ACACTTTTACACCATACCCAAGGAAGTCAGAATATGCAAAGTTGACAAG
5669 AAATTTCAGGGAATCTAACTTTACCTCCATCAAAACGTTGACAAGAAATTTCAGGGAATCTAACT
1 AAATTTCAGGGAATCTAACTTTACCTCCATCAAAACGTTGACAAGAAATTTCAGGGAATCTAACT
5734 TTACCTCCATCAAACCGTTGGATCAAAAAGTAAAACTCATCTTAACCGTCCATTTGAACTCTGAA
66 TTACCTCCATCAAACCGTTGGATCAAAAAGTAAAACTCATCTTAACCGTCCATTTGAACTCTGAA
5799 CACTTTTACACCATACCCAAGGAAGTCAGAATATGCAAAGTTGACAAG
131 CACTTTTACACCATACCCAAGGAAGTCAGAATATGCAAAGTTGACAAG
*
5847 AAATTTCAGGGAATCTAACTTTACCTCCATCAAAACGTTGACAAGAAATTTCAGGGAATCTACCT
1 AAATTTCAGGGAATCTAACTTTACCTCCATCAAAACGTTGACAAGAAATTTCAGGGAATCTAACT
5912 TTACCTCCATCAAACCGTTGGATCAAAAAGTAAAACTCATCTTAACCGTCCATTTGAACTCTGAA
66 TTACCTCCATCAAACCGTTGGATCAAAAAGTAAAACTCATCTTAACCGTCCATTTGAACTCTGAA
*
5977 CACTTTTACACCATACCTAAGGAAGTCAGAATATGCAAAGTTGACAAG
131 CACTTTTACACCATACCCAAGGAAGTCAGAATATGCAAAGTTGACAAG
6025 AAATTTCAGGGAATCTAACTTTACCTCCATCAAAACGTTG
1 AAATTTCAGGGAATCTAACTTTACCTCCATCAAAACGTTG
6065 GATCAAAAAG
Statistics
Matches: 722, Mismatches: 16, Indels: 18
0.96 0.02 0.02
Matches are distributed among these distances:
175 159 0.22
176 175 0.24
177 23 0.03
178 365 0.51
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.26
Consensus pattern (178 bp):
AAATTTCAGGGAATCTAACTTTACCTCCATCAAAACGTTGACAAGAAATTTCAGGGAATCTAACT
TTACCTCCATCAAACCGTTGGATCAAAAAGTAAAACTCATCTTAACCGTCCATTTGAACTCTGAA
CACTTTTACACCATACCCAAGGAAGTCAGAATATGCAAAGTTGACAAG
Found at i:5902 original size:45 final size:45
Alignment explanation
Indices: 5838--5931 Score: 170
Period size: 45 Copynumber: 2.1 Consensus size: 45
5828 AATATGCAAA
5838 GTTGACAAGAAATTTCAGGGAATCTAACTTTACCTCCATCAAAAC
1 GTTGACAAGAAATTTCAGGGAATCTAACTTTACCTCCATCAAAAC
* *
5883 GTTGACAAGAAATTTCAGGGAATCTACCTTTACCTCCATCAAACC
1 GTTGACAAGAAATTTCAGGGAATCTAACTTTACCTCCATCAAAAC
5928 GTTG
1 GTTG
5932 GATCAAAAAG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.34, C:0.23, G:0.15, T:0.28
Consensus pattern (45 bp):
GTTGACAAGAAATTTCAGGGAATCTAACTTTACCTCCATCAAAAC
Found at i:6121 original size:133 final size:133
Alignment explanation
Indices: 5883--6191 Score: 546
Period size: 133 Copynumber: 2.3 Consensus size: 133
5873 CCATCAAAAC
* *
5883 GTTGACAAGAAATTTCAGGGAATCTACCTTTACCTCCATCAAACCGTTGGATCAAAAAGTAAAAC
1 GTTGACAAGAAATTTCAGGGAATCTAACTTTACCTCCATCAAAACGTTGGATCAAAAAGTAAAAC
*
5948 TCATCTTAACCGTCCATTTGAACTCTGAACACTTTTACACCATACCTAAGGAAGTCAGAATATGC
66 TCATCTTAACCGTCCATTTGAACTCTGAACACTTTTACACCATACCCAAGGAAGTCAGAATATGC
6013 AAA
131 AAA
6016 GTTGACAAGAAATTTCAGGGAATCTAACTTTACCTCCATCAAAACGTTGGATCAAAAAGTAAAAC
1 GTTGACAAGAAATTTCAGGGAATCTAACTTTACCTCCATCAAAACGTTGGATCAAAAAGTAAAAC
*
6081 TCATCTTAACCGTCCATTTGAACTCTGAACACTTTTACACCATACCCAAGGAAGTCTGAATATGC
66 TCATCTTAACCGTCCATTTGAACTCTGAACACTTTTACACCATACCCAAGGAAGTCAGAATATGC
6146 AAA
131 AAA
** * *
6149 GTTGACAAGAAATTTCAACGAATCTAACTTCACCTCAATCAAA
1 GTTGACAAGAAATTTCAGGGAATCTAACTTTACCTCCATCAAA
6192 CCGTCGACAA
Statistics
Matches: 168, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
133 168 1.00
ACGTcount: A:0.38, C:0.23, G:0.13, T:0.26
Consensus pattern (133 bp):
GTTGACAAGAAATTTCAGGGAATCTAACTTTACCTCCATCAAAACGTTGGATCAAAAAGTAAAAC
TCATCTTAACCGTCCATTTGAACTCTGAACACTTTTACACCATACCCAAGGAAGTCAGAATATGC
AAA
Found at i:6217 original size:45 final size:45
Alignment explanation
Indices: 6152--6283 Score: 210
Period size: 45 Copynumber: 2.9 Consensus size: 45
6142 ATGCAAAGTT
* **
6152 GACAAGAAATTTCAACGAATCTAACTTCACCTCAATCAAACCGTC
1 GACAAGAAATTTTAGGGAATCTAACTTCACCTCAATCAAACCGTC
6197 GACAAGAAATTTTAGGGAATCTAACTTCACCTCAATCAAACCGTC
1 GACAAGAAATTTTAGGGAATCTAACTTCACCTCAATCAAACCGTC
* * *
6242 GACAAGAAATTTTAGGGAATTTAACTTTACCTCCATCAAACC
1 GACAAGAAATTTTAGGGAATCTAACTTCACCTCAATCAAACC
6284 ATTGAATCAA
Statistics
Matches: 81, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 81 1.00
ACGTcount: A:0.39, C:0.25, G:0.11, T:0.25
Consensus pattern (45 bp):
GACAAGAAATTTTAGGGAATCTAACTTCACCTCAATCAAACCGTC
Found at i:7799 original size:11 final size:12
Alignment explanation
Indices: 7766--7800 Score: 54
Period size: 13 Copynumber: 2.9 Consensus size: 12
7756 ATTTAAGTAC
7766 ATTATTTTTATA
1 ATTATTTTTATA
7778 ATTACTTTTTATA
1 ATTA-TTTTTATA
7791 A-TATTTTTAT
1 ATTATTTTTAT
7801 TTATTTAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 7 0.32
12 6 0.27
13 9 0.41
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (12 bp):
ATTATTTTTATA
Found at i:8150 original size:26 final size:26
Alignment explanation
Indices: 8121--8195 Score: 72
Period size: 26 Copynumber: 3.1 Consensus size: 26
8111 GGGATTACAA
8121 TTTTGGTGCCTTCCTTGGAGATGACC
1 TTTTGGTGCCTTCCTTGGAGATGACC
* * *
8147 TTTT--T---TTTCTTGG-GATTACAA
1 TTTTGGTGCCTTCCTTGGAGATGAC-C
8168 TTTTGGTGCCTTCCTTGGAGATGACC
1 TTTTGGTGCCTTCCTTGGAGATGACC
8194 TT
1 TT
8196 AGTACCAAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 14
0.64 0.11 0.25
Matches are distributed among these distances:
20 5 0.14
21 11 0.31
23 1 0.03
24 1 0.03
26 13 0.36
27 5 0.14
ACGTcount: A:0.13, C:0.19, G:0.23, T:0.45
Consensus pattern (26 bp):
TTTTGGTGCCTTCCTTGGAGATGACC
Found at i:8153 original size:47 final size:47
Alignment explanation
Indices: 8100--8195 Score: 192
Period size: 47 Copynumber: 2.0 Consensus size: 47
8090 CAGCACCAAT
8100 TTTTTTTTCTTGGGATTACAATTTTGGTGCCTTCCTTGGAGATGACC
1 TTTTTTTTCTTGGGATTACAATTTTGGTGCCTTCCTTGGAGATGACC
8147 TTTTTTTTCTTGGGATTACAATTTTGGTGCCTTCCTTGGAGATGACC
1 TTTTTTTTCTTGGGATTACAATTTTGGTGCCTTCCTTGGAGATGACC
8194 TT
1 TT
8196 AGTACCAAAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 49 1.00
ACGTcount: A:0.15, C:0.17, G:0.21, T:0.48
Consensus pattern (47 bp):
TTTTTTTTCTTGGGATTACAATTTTGGTGCCTTCCTTGGAGATGACC
Found at i:8171 original size:21 final size:21
Alignment explanation
Indices: 8100--8171 Score: 56
Period size: 21 Copynumber: 3.2 Consensus size: 21
8090 CAGCACCAAT
8100 TTTTTTTTCTTGGGATTACAA
1 TTTTTTTTCTTGGGATTACAA
* * *
8121 TTTTGGTGCCTTCCTTGGAGATGAC-C
1 TTTT--T---TTTCTTGG-GATTACAA
8147 TTTTTTTTCTTGGGATTACAA
1 TTTTTTTTCTTGGGATTACAA
8168 TTTT
1 TTTT
8172 GGTGCCTTCC
Statistics
Matches: 38, Mismatches: 6, Indels: 14
0.66 0.10 0.24
Matches are distributed among these distances:
20 5 0.13
21 15 0.39
23 1 0.03
24 1 0.03
26 11 0.29
27 5 0.13
ACGTcount: A:0.15, C:0.14, G:0.18, T:0.53
Consensus pattern (21 bp):
TTTTTTTTCTTGGGATTACAA
Found at i:11343 original size:6 final size:6
Alignment explanation
Indices: 11332--11364 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
11322 TGTTTCAGGG
11332 TTTTGT TTTTGT TTTTGT TTTTGT TTTTGT TTT
1 TTTTGT TTTTGT TTTTGT TTTTGT TTTTGT TTT
11365 CCACCTTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (6 bp):
TTTTGT
Found at i:11845 original size:16 final size:17
Alignment explanation
Indices: 11817--11848 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
11807 CTAACAAGGT
11817 AATTTTCCTTTTGTCAC
1 AATTTTCCTTTTGTCAC
11834 AATTTT-CTTTTGTCA
1 AATTTTCCTTTTGTCA
11849 ATTATAATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.19, C:0.19, G:0.06, T:0.56
Consensus pattern (17 bp):
AATTTTCCTTTTGTCAC
Found at i:30073 original size:22 final size:21
Alignment explanation
Indices: 30021--30074 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 21
30011 GCTTCTTGGA
30021 AATAATTCTTC-AATGATCTTC
1 AATAA-TCTTCAAATGATCTTC
*
30042 -A-AATCTTCAAATTATCTTC
1 AATAATCTTCAAATGATCTTC
30061 AATAAGTCTTCAAA
1 AATAA-TCTTCAAA
30075 CACGAACTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 5 0.18
19 11 0.39
20 2 0.07
21 2 0.07
22 8 0.29
ACGTcount: A:0.39, C:0.19, G:0.04, T:0.39
Consensus pattern (21 bp):
AATAATCTTCAAATGATCTTC
Found at i:34174 original size:32 final size:32
Alignment explanation
Indices: 34138--34198 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
34128 AACAAATTAT
34138 TAATAATC-AAATCAGATCAATGA-AGAAAAGTG
1 TAAT-ATCAAAATCAGATCAA-GATAGAAAAGTG
*
34170 TAATATCAAAATCTGATCAAGATAGAAAA
1 TAATATCAAAATCAGATCAAGATAGAAAA
34199 CAAATAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
31 5 0.19
32 21 0.81
ACGTcount: A:0.54, C:0.10, G:0.13, T:0.23
Consensus pattern (32 bp):
TAATATCAAAATCAGATCAAGATAGAAAAGTG
Found at i:34811 original size:2 final size:2
Alignment explanation
Indices: 34804--34835 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
34794 AACACAATAG
34804 AT AT 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
34836 TGGAGAGCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39935 original size:31 final size:31
Alignment explanation
Indices: 39897--39964 Score: 136
Period size: 31 Copynumber: 2.2 Consensus size: 31
39887 GAGAATAGGT
39897 AATGGACAAAATATAGATATATGGGGTGATA
1 AATGGACAAAATATAGATATATGGGGTGATA
39928 AATGGACAAAATATAGATATATGGGGTGATA
1 AATGGACAAAATATAGATATATGGGGTGATA
39959 AATGGA
1 AATGGA
39965 TAAGGTCTCC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.46, C:0.03, G:0.26, T:0.25
Consensus pattern (31 bp):
AATGGACAAAATATAGATATATGGGGTGATA
Found at i:43344 original size:20 final size:20
Alignment explanation
Indices: 43319--43358 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
43309 AATTTCATTA
43319 TCCAAGAAAGCAGGAACAAG
1 TCCAAGAAAGCAGGAACAAG
43339 TCCAAGAAAGCAGGAACAAG
1 TCCAAGAAAGCAGGAACAAG
43359 AAAGCAAGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.20, G:0.25, T:0.05
Consensus pattern (20 bp):
TCCAAGAAAGCAGGAACAAG
Found at i:43369 original size:18 final size:19
Alignment explanation
Indices: 43322--43380 Score: 77
Period size: 20 Copynumber: 3.2 Consensus size: 19
43312 TTCATTATCC
*
43322 AAGAAAGCAGGAACAAGTCC
1 AAGAAAGCAGGAACAAGT-A
43342 AAGAAAGCAGGAACAAG-A
1 AAGAAAGCAGGAACAAGTA
*
43360 AAGCAAGCA-GAACAAGTA
1 AAGAAAGCAGGAACAAGTA
43378 AAG
1 AAG
43381 GTACCCCTTC
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
17 7 0.19
18 12 0.33
20 17 0.47
ACGTcount: A:0.56, C:0.15, G:0.25, T:0.03
Consensus pattern (19 bp):
AAGAAAGCAGGAACAAGTA
Found at i:49760 original size:446 final size:446
Alignment explanation
Indices: 48896--49803 Score: 1136
Period size: 446 Copynumber: 2.0 Consensus size: 446
48886 TTAAATAGAG
* * * * * ***
48896 TAAGATAGAATTTGTAAATGATTAAGTAGTATAAAATAGAAAAGTATGAGGGTCATTTGATAAAT
1 TAAGATACAATTAGTAAAGGACTAAGTAGTATAAAATAGAAAAATATGAGAACCATTTGATAAAT
* * * *
48961 AATTCAAATAAGAAAATGTTTGTCGACAGAGATCTTGAAACATAAAAATTCCCTTTTAGACCTTT
66 AATCCAAACAAGAAAATGTTTGTCGACAGAGATCTTGAAACATAAAAATTCCCTTTGAGACCCTT
* * *
49026 CATGAAACTCGTAGATCAAATTCAGCTTTCGGGTCCTTCATGCAAGTCGTACATCATGCAATAAC
131 AACGAAACTCATAGATCAAATTCAGCTTTCGGGTCCTTCATGCAAGTCGTACATCATGCAATAAC
* * * * * *
49091 TTTTTAATCGACTCTTGAATAACTTTAATCGGACATGTAGATCGAAAATTATATGATATTAAATA
196 TTTTTAACCGACACATAAATAACTTTAATCAGACATGTAGATCGAAAATTATATGACATTAAATA
*
49156 GACCGGCAATCAAAACCACCAAAATTCGGAAAACATTTTCTCTGAATTGAAACATAAAAATTGGC
261 GACCGGCAATCAAAACCACCAAAATTCGGAAAACATTTTCTCTGAATTGAAAAATAAAAATTGGC
* * *
49221 TTTTGAGTATTTCATGAAAGTTGTAGATCATGAAATTACCATTTTATAGACACCTGAATCACCTT
326 TTTTGAGTATTTAATGAAAGCTCTAGATCATGAAATTACCATTTTATAGACACCTGAATCACCTT
* *
49286 AATCAGATAAATATAACAAAAAAATAAATAAATAAAACTTAGGTGTTAAAATCGAT
391 AATCAGACAAATAGAACAAAAAAATAAATAAATAAAACTTAGGTGTTAAAATCGAT
*
49342 TAAGATACAATTAGTAAAGGACTAAGTAGTATAAAGTAGAAAAATATGAGAACCATTTGATAAAT
1 TAAGATACAATTAGTAAAGGACTAAGTAGTATAAAATAGAAAAATATGAGAACCATTTGATAAAT
** *
49407 AATCCAAACAAGAAAATGTTTGTCGATGGAGATCTTGAATCATAAAAATTCCCTTCTGA-ACCCT
66 AATCCAAACAAGAAAATGTTTGTCGACAGAGATCTTGAAACATAAAAATTCCCTT-TGAGACCCT
* * * * *
49471 TAACGAAATTCATAGATCAAATTTAGCTTTTGGGTCCTTTATG-ATAGTCGTAGATCATGCAATA
130 TAACGAAACTCATAGATCAAATTCAGCTTTCGGGTCCTTCATGCA-AGTCGTACATCATGCAATA
* * * * * *
49535 A-TCTTTTCACCGACACATAAATAATTTTAATTAGACATGTGGATCTAAAATTATATGACATTTA
194 ACT-TTTTAACCGACACATAAATAACTTTAATCAGACATGTAGATCGAAAATTATATGACATTAA
* * ** * ** * *
49599 ATATACCGGCAATCGAAACCA-CAAAATTTTGCAAGTATTTT-TTTTAATTGAAAAAT-AAAATT
258 ATAGACCGGCAATCAAAACCACCAAAATTCGGAAAACATTTTCTCTGAATTGAAAAATAAAAATT
*
49661 GGCTTTTGAGTATTTAATGAAAGCTCTAGATCATGAAATTACC-TTTTAATAGACATCTGAATC-
323 GGCTTTTGAGTATTTAATGAAAGCTCTAGATCATGAAATTACCATTTT-ATAGACACCTGAATCA
* * * * * * *
49724 TCTTCAATCGGACAAATAGAAC-AAAGAATTAATAAATAAAACTAAAGAGTT-AAATCGAT
387 CCTT-AATCAGACAAATAGAACAAAAAAATAAATAAATAAAACTTAGGTGTTAAAATCGAT
* *
49783 TAAAATAGAATTTA-TAAAGGA
1 TAAGATACAA-TTAGTAAAGGA
49804 TTAAATAACA
Statistics
Matches: 395, Mismatches: 61, Indels: 17
0.84 0.13 0.04
Matches are distributed among these distances:
441 23 0.06
442 34 0.09
443 74 0.19
444 12 0.03
445 17 0.04
446 233 0.59
447 2 0.01
ACGTcount: A:0.42, C:0.13, G:0.14, T:0.31
Consensus pattern (446 bp):
TAAGATACAATTAGTAAAGGACTAAGTAGTATAAAATAGAAAAATATGAGAACCATTTGATAAAT
AATCCAAACAAGAAAATGTTTGTCGACAGAGATCTTGAAACATAAAAATTCCCTTTGAGACCCTT
AACGAAACTCATAGATCAAATTCAGCTTTCGGGTCCTTCATGCAAGTCGTACATCATGCAATAAC
TTTTTAACCGACACATAAATAACTTTAATCAGACATGTAGATCGAAAATTATATGACATTAAATA
GACCGGCAATCAAAACCACCAAAATTCGGAAAACATTTTCTCTGAATTGAAAAATAAAAATTGGC
TTTTGAGTATTTAATGAAAGCTCTAGATCATGAAATTACCATTTTATAGACACCTGAATCACCTT
AATCAGACAAATAGAACAAAAAAATAAATAAATAAAACTTAGGTGTTAAAATCGAT
Found at i:49771 original size:21 final size:20
Alignment explanation
Indices: 49737--49776 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
49727 TCAATCGGAC
*
49737 AAATAGAACAAAGAATTAAT
1 AAATAAAACAAAGAATTAAT
*
49757 AAATAAAACTAAAGAGTTAA
1 AAATAAAAC-AAAGAATTAA
49777 ATCGATTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.65, C:0.05, G:0.10, T:0.20
Consensus pattern (20 bp):
AAATAAAACAAAGAATTAAT
Found at i:53885 original size:17 final size:17
Alignment explanation
Indices: 53863--53895 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
53853 CAAACCAAAC
53863 CAAAAAAAAAAAGAAAA
1 CAAAAAAAAAAAGAAAA
*
53880 CAAAAAACAAAAGAAA
1 CAAAAAAAAAAAGAAA
53896 GAAGAGAAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.85, C:0.09, G:0.06, T:0.00
Consensus pattern (17 bp):
CAAAAAAAAAAAGAAAA
Found at i:53993 original size:20 final size:20
Alignment explanation
Indices: 53965--54003 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
53955 GAAAGGAAAA
*
53965 GAAAGAAAAGAAAAAGGAAG
1 GAAAAAAAAGAAAAAGGAAG
*
53985 GAAAAAAAAGAAGAAGGAA
1 GAAAAAAAAGAAAAAGGAA
54004 ATTAAGGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (20 bp):
GAAAAAAAAGAAAAAGGAAG
Found at i:53994 original size:25 final size:27
Alignment explanation
Indices: 53939--53996 Score: 77
Period size: 25 Copynumber: 2.3 Consensus size: 27
53929 CCAAAAAGGG
53939 AAAAG-AAAGAAAAATAGAAAGGAAAA
1 AAAAGAAAAGAAAAATAGAAAGGAAAA
* *
53965 GAAAGAAAAG-AAAA-AGGAAGGAAAA
1 AAAAGAAAAGAAAAATAGAAAGGAAAA
53990 AAAAGAA
1 AAAAGAA
53997 GAAGGAAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 16 0.57
26 8 0.29
27 4 0.14
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (27 bp):
AAAAGAAAAGAAAAATAGAAAGGAAAA
Found at i:54000 original size:16 final size:16
Alignment explanation
Indices: 53961--54004 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
53951 AATAGAAAGG
*
53961 AAAAGAAAGAAAAGAA
1 AAAAGAAGGAAAAGAA
*
53977 AAAGGAAGGAAAA-AA
1 AAAAGAAGGAAAAGAA
53992 AAGAAGAAGGAAA
1 AA-AAGAAGGAAA
54005 TTAAGGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 4 0.17
16 20 0.83
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (16 bp):
AAAAGAAGGAAAAGAA
Found at i:54145 original size:27 final size:27
Alignment explanation
Indices: 54077--54146 Score: 65
Period size: 27 Copynumber: 2.6 Consensus size: 27
54067 TTACTATTTT
54077 ACCCTTTGATGGA-TAAAGTACTAAATC
1 ACCCTTTGAT-GATTAAAGTACTAAATC
* * *
54104 ACCC-TTAAGTTATTAAATTA-TGAAATC
1 ACCCTTTGA-TGATTAAAGTACT-AAATC
54131 ACCCTTTGATGATTAA
1 ACCCTTTGATGATTAA
54147 TTTTAAGAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
26 5 0.15
27 26 0.76
28 3 0.09
ACGTcount: A:0.37, C:0.17, G:0.11, T:0.34
Consensus pattern (27 bp):
ACCCTTTGATGATTAAAGTACTAAATC
Done.