Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017648.1 Corchorus olitorius cultivar O-4 contig17681, 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: 58439
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:2618 original size:61 final size:61
Alignment explanation
Indices: 2523--2656 Score: 243
Period size: 61 Copynumber: 2.2 Consensus size: 61
2513 ACAACGAAAT
2523 GAAAGAGGGAGGCCGGAGGCAGCAAGTTAGGGGAGATGAGGTTTTCAGAAGAATAGCTCAA
1 GAAAGAGGGAGGCCGGAGGCAGCAAGTTAGGGGAGATGAGGTTTTCAGAAGAATAGCTCAA
* *
2584 GAAAGAGGGAGGTCGGAGGCGGCAAGTTAGGGGAGATGAGGTTTTCAGAAGAATAGCTCAA
1 GAAAGAGGGAGGCCGGAGGCAGCAAGTTAGGGGAGATGAGGTTTTCAGAAGAATAGCTCAA
2645 GAAAG-GGGAGGC
1 GAAAGAGGGAGGC
2657 GAGCTCGACA
Statistics
Matches: 70, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
60 6 0.09
61 64 0.91
ACGTcount: A:0.34, C:0.10, G:0.42, T:0.14
Consensus pattern (61 bp):
GAAAGAGGGAGGCCGGAGGCAGCAAGTTAGGGGAGATGAGGTTTTCAGAAGAATAGCTCAA
Found at i:4832 original size:11 final size:12
Alignment explanation
Indices: 4799--4834 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
4789 GGAAGAAGGA
4799 AGAAGAAAAAAG
1 AGAAGAAAAAAG
*
4811 AGAAAAAAAAAG
1 AGAAGAAAAAAG
4823 A-AAGAAAAAAG
1 AGAAGAAAAAAG
4834 A
1 A
4835 TTTAAACAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 10 0.45
12 12 0.55
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (12 bp):
AGAAGAAAAAAG
Found at i:5482 original size:10 final size:11
Alignment explanation
Indices: 5454--5483 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
5444 CTTAGCAAAG
5454 GGGATTTTTAT
1 GGGATTTTTAT
5465 GGGATTTTTAT
1 GGGATTTTTAT
5476 GGG-TTTTT
1 GGGATTTTT
5484 CAAAATAGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 5 0.26
11 14 0.74
ACGTcount: A:0.13, C:0.00, G:0.30, T:0.57
Consensus pattern (11 bp):
GGGATTTTTAT
Found at i:6933 original size:76 final size:76
Alignment explanation
Indices: 6796--6947 Score: 175
Period size: 76 Copynumber: 2.0 Consensus size: 76
6786 ACAAGGACCC
* * *
6796 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCTTGAGAACCCAGGT
1 CGACTCCACCTGGACGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT
6861 GGGCAGTGTCA
66 GGGCAGTGTCA
* * * **
6872 CGACTCCAGCTGGATGCCCACATGGTTTGTC-TGAAG-ACCCATGT-GTTTCGCCTGATCACCCA
1 CGACTCCACCTGGACGCCCACATGG-TTGCCTTG-AGCACCCATGTGGTTT-GCCTGAGAACCCA
*
6934 GATGGGCTGTGTCA
63 GATGGGCAGTGTCA
6948 TAGCTCATCA
Statistics
Matches: 64, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
75 4 0.06
76 54 0.84
77 6 0.09
ACGTcount: A:0.18, C:0.30, G:0.28, T:0.24
Consensus pattern (76 bp):
CGACTCCACCTGGACGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT
GGGCAGTGTCA
Found at i:9835 original size:12 final size:13
Alignment explanation
Indices: 9811--9838 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
9801 TTGCTATTAC
9811 AAAAATACAAAAA
1 AAAAATACAAAAA
9824 AAAAATACAAAAA
1 AAAAATACAAAAA
9837 AA
1 AA
9839 TGGAAATAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.86, C:0.07, G:0.00, T:0.07
Consensus pattern (13 bp):
AAAAATACAAAAA
Found at i:14670 original size:42 final size:42
Alignment explanation
Indices: 14603--14697 Score: 124
Period size: 42 Copynumber: 2.3 Consensus size: 42
14593 CATCATATCC
*
14603 ATATATG-TCATACATCCTCCATGCATTGTCCATGT-CTTTGT
1 ATATATGTTCATACATCCTCCATGCATTATCCAT-TCCTTTGT
* *
14644 GTATATGTTCATACATCCAT-CGTGCATTATCCATTCCTTTGT
1 ATATATGTTCATACATCC-TCCATGCATTATCCATTCCTTTGT
14686 ATATATGTTCAT
1 ATATATGTTCAT
14698 GCAAAGGTCA
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
41 7 0.15
42 39 0.83
43 1 0.02
ACGTcount: A:0.23, C:0.22, G:0.12, T:0.43
Consensus pattern (42 bp):
ATATATGTTCATACATCCTCCATGCATTATCCATTCCTTTGT
Found at i:14712 original size:42 final size:42
Alignment explanation
Indices: 14622--14721 Score: 112
Period size: 42 Copynumber: 2.4 Consensus size: 42
14612 ATACATCCTC
* * **
14622 CATGCATTGTCCATGT-CTTTGTGTATATGTTCATACATCCAT
1 CATGCATTATCCAT-TCCTTTGTATATATGTTCATACAAACAT
* * **
14664 CGTGCATTATCCATTCCTTTGTATATATGTTCATGCAAAGGT
1 CATGCATTATCCATTCCTTTGTATATATGTTCATACAAACAT
14706 CATGCATTATCCATTC
1 CATGCATTATCCATTC
14722 ATTACTACAT
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
41 1 0.02
42 47 0.98
ACGTcount: A:0.23, C:0.22, G:0.14, T:0.41
Consensus pattern (42 bp):
CATGCATTATCCATTCCTTTGTATATATGTTCATACAAACAT
Found at i:15860 original size:16 final size:15
Alignment explanation
Indices: 15842--15877 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
15832 CAAGACATGT
15842 TTTTCAAGAAAATTG
1 TTTTCAAGAAAATTG
*
15857 TTTTCAAGAAAA-GG
1 TTTTCAAGAAAATTG
15871 TTTTCAA
1 TTTTCAA
15878 AAATAGCTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 8 0.40
15 12 0.60
ACGTcount: A:0.39, C:0.08, G:0.14, T:0.39
Consensus pattern (15 bp):
TTTTCAAGAAAATTG
Found at i:15862 original size:15 final size:14
Alignment explanation
Indices: 15842--15901 Score: 70
Period size: 14 Copynumber: 4.3 Consensus size: 14
15832 CAAGACATGT
*
15842 TTTTCAAGAAAATTG
1 TTTTCAAGAAAA-GG
15857 TTTTCAAGAAAAGG
1 TTTTCAAGAAAAGG
*
15871 TTTTCAA-AAATAGC
1 TTTTCAAGAAA-AGG
15885 TTTTCAA-AAAAGG
1 TTTTCAAGAAAAGG
15898 TTTT
1 TTTT
15902 GAGTCTTTTA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
13 9 0.22
14 20 0.49
15 12 0.29
ACGTcount: A:0.40, C:0.08, G:0.13, T:0.38
Consensus pattern (14 bp):
TTTTCAAGAAAAGG
Found at i:17612 original size:50 final size:50
Alignment explanation
Indices: 17508--17656 Score: 155
Period size: 49 Copynumber: 3.0 Consensus size: 50
17498 GCTTTGACTT
* * *
17508 TTCCACAAGCCAAACTCGTTTCCATACGAGTCAATT-AGCAACATAGGCTT--
1 TTCCACAAGACAAACTCGTTTCCATACGAGTCAGTTCA--AACATTGG-TTCC
* * *
17558 TTCCACAAGGCAAACTCGTTTCCATACGGGTCAGTTCAAACTTTGGTTCC
1 TTCCACAAGACAAACTCGTTTCCATACGAGTCAGTTCAAACATTGGTTCC
* *
17608 TT-C-CAAGACTAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCC
1 TTCCACAAGAC-AAACTCGTTTCCATACGAGTCAGTTCAAACATTGGTTCC
17657 ACCCAAGCAA
Statistics
Matches: 86, Mismatches: 9, Indels: 9
0.83 0.09 0.09
Matches are distributed among these distances:
48 7 0.08
49 43 0.50
50 35 0.41
51 1 0.01
ACGTcount: A:0.27, C:0.28, G:0.16, T:0.29
Consensus pattern (50 bp):
TTCCACAAGACAAACTCGTTTCCATACGAGTCAGTTCAAACATTGGTTCC
Found at i:17802 original size:69 final size:69
Alignment explanation
Indices: 17723--17876 Score: 211
Period size: 69 Copynumber: 2.2 Consensus size: 69
17713 TTCCAAGACT
* * * *
17723 AAACTTGTTTCCATGCGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCAT-GTGCTTTTCCAT
1 AAACTCGTTTCCATACGAGTCAGTTCAAACCTTGGTTCCATCCAAGCAGCATAG-GCTTTTCCAC
17787 AAGCC
65 AAGCC
* *
17792 AAACTCGTTTCCATACGAGTCAGTTCAAACCTTGGTTCCGTCCAGGCAGCATAGGCTTTTCCACA
1 AAACTCGTTTCCATACGAGTCAGTTCAAACCTTGGTTCCATCCAAGCAGCATAGGCTTTTCCACA
17857 AGCC
66 AGCC
**
17861 ACAGTTCGTTTCCATA
1 A-AACTCGTTTCCATA
17877 TGATGCATTA
Statistics
Matches: 75, Mismatches: 8, Indels: 3
0.87 0.09 0.03
Matches are distributed among these distances:
69 62 0.83
70 13 0.17
ACGTcount: A:0.24, C:0.29, G:0.18, T:0.29
Consensus pattern (69 bp):
AAACTCGTTTCCATACGAGTCAGTTCAAACCTTGGTTCCATCCAAGCAGCATAGGCTTTTCCACA
AGCC
Found at i:17803 original size:105 final size:105
Alignment explanation
Indices: 17608--17806 Score: 317
Period size: 105 Copynumber: 1.9 Consensus size: 105
17598 CTTTGGTTCC
17608 TTCCAAGACTAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCACCCAAGCAACATGGG
1 TTCCAAGACTAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCACCCAAGCAACATGGG
* **
17673 CTTTTCCATAAGCCTAGTTCATTTCCATATGAATTCAGTT
66 CTTTTCCATAAGCCAAACTCATTTCCATATGAATTCAGTT
* * * * *
17713 TTCCAAGACTAAACTTGTTTCCATGCGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCATGTG
1 TTCCAAGACTAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCACCCAAGCAACATGGG
*
17778 CTTTTCCATAAGCCAAACTCGTTTCCATA
66 CTTTTCCATAAGCCAAACTCATTTCCATA
17807 CGAGTCAGTT
Statistics
Matches: 85, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
105 85 1.00
ACGTcount: A:0.26, C:0.27, G:0.16, T:0.31
Consensus pattern (105 bp):
TTCCAAGACTAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCACCCAAGCAACATGGG
CTTTTCCATAAGCCAAACTCATTTCCATATGAATTCAGTT
Found at i:17941 original size:35 final size:34
Alignment explanation
Indices: 17895--18305 Score: 434
Period size: 35 Copynumber: 11.8 Consensus size: 34
17885 TACCATCTTC
*
17895 TCAGATGACTCGGTGTAGCATCTTTAAAGTTATAT
1 TCAGATGACTCGGTGTAGCATCTTCAAAGTTA-AT
* *
17930 TCAGATGACTCGATGTAGCATCTTCAAAGATGAAT
1 TCAGATGACTCGGTGTAGCATCTTCAAAG-TTAAT
* *
17965 TCAAATGACTCGGTCTAGCATCTTCAAAGTTGAAT
1 TCAGATGACTCGGTGTAGCATCTTCAAAGTT-AAT
* * * * *
18000 CCAGATAACTCAGTGTAGCATCTTCAAAGATGAAC
1 TCAGATGACTCGGTGTAGCATCTTCAAAG-TTAAT
* *
18035 TCAGATAACTCAGTGTAGCATCCTT-AAAGTTGAAT
1 TCAGATGACTCGGTGTAGCAT-CTTCAAAGTT-AAT
* * *
18070 CCAGATGACTCGGTGTAGCATCTTCAAAGATGACT
1 TCAGATGACTCGGTGTAGCATCTTCAAAG-TTAAT
* *
18105 TCAGATGACTCGGTGTAGCATCTTCAAAGATGACT
1 TCAGATGACTCGGTGTAGCATCTTCAAAG-TTAAT
*
18140 TCAGATGACTCGGTGTAGCATTTTCAAAGTTGAACT
1 TCAGATGACTCGGTGTAGCATCTTCAAAGTT-AA-T
*
18176 T-AGATGACTCGGTGTAGCATTTTCAAAGTTATAT
1 TCAGATGACTCGGTGTAGCATCTTCAAAGTTA-AT
* *
18210 TCAGATGACTCGGTGTAGCATCTTCAATA-TGAAC
1 TCAGATGACTCGGTGTAGCATCTTCAA-AGTTAAT
* * * * *
18244 TC-GGTGGGCTCGGTGCATCATCTTCAAAGATGAAT
1 TCAGAT-GACTCGGTGTAGCATCTTCAAAG-TTAAT
18279 TCAGATGACTCGGTGTAGCATCTTCAA
1 TCAGATGACTCGGTGTAGCATCTTCAA
18306 TATGAACTCA
Statistics
Matches: 322, Mismatches: 38, Indels: 32
0.82 0.10 0.08
Matches are distributed among these distances:
33 3 0.01
34 30 0.09
35 277 0.86
36 12 0.04
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (34 bp):
TCAGATGACTCGGTGTAGCATCTTCAAAGTTAAT
Found at i:18017 original size:70 final size:70
Alignment explanation
Indices: 17895--18305 Score: 519
Period size: 70 Copynumber: 5.9 Consensus size: 70
17885 TACCATCTTC
* *
17895 TCAGATGACTCGGTGTAGCATCTTTAAAGTT-ATATTCAGATGACTCGATGTAGCATCTTCAAAG
1 TCAGATGACTCGGTGTAGCATCTTCAAAGTTGA-ATTCAGATGACTCGGTGTAGCATCTTCAAAG
17959 ATGAAT
65 ATGAAT
* * * * *
17965 TCAAATGACTCGGTCTAGCATCTTCAAAGTTGAATCCAGATAACTCAGTGTAGCATCTTCAAAGA
1 TCAGATGACTCGGTGTAGCATCTTCAAAGTTGAATTCAGATGACTCGGTGTAGCATCTTCAAAGA
*
18030 TGAAC
66 TGAAT
* * *
18035 TCAGATAACTCAGTGTAGCATCCTT-AAAGTTGAATCCAGATGACTCGGTGTAGCATCTTCAAAG
1 TCAGATGACTCGGTGTAGCAT-CTTCAAAGTTGAATTCAGATGACTCGGTGTAGCATCTTCAAAG
*
18099 ATGACT
65 ATGAAT
* * * *
18105 TCAGATGACTCGGTGTAGCATCTTCAAAGATGACTTCAGATGACTCGGTGTAGCATTTTCAAAGT
1 TCAGATGACTCGGTGTAGCATCTTCAAAGTTGAATTCAGATGACTCGGTGTAGCATCTTCAAAGA
18170 TGAACT
66 TGAA-T
* *
18176 T-AGATGACTCGGTGTAGCATTTTCAAAGTT-ATATTCAGATGACTCGGTGTAGCATCTTC-AAT
1 TCAGATGACTCGGTGTAGCATCTTCAAAGTTGA-ATTCAGATGACTCGGTGTAGCATCTTCAAAG
*
18238 ATGAAC
65 ATGAAT
* * * * *
18244 TC-GGTGGGCTCGGTGCATCATCTTCAAAGATGAATTCAGATGACTCGGTGTAGCATCTTCAA
1 TCAGAT-GACTCGGTGTAGCATCTTCAAAGTTGAATTCAGATGACTCGGTGTAGCATCTTCAA
18306 TATGAACTCA
Statistics
Matches: 295, Mismatches: 37, Indels: 18
0.84 0.11 0.05
Matches are distributed among these distances:
68 3 0.01
69 57 0.19
70 229 0.78
71 6 0.02
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (70 bp):
TCAGATGACTCGGTGTAGCATCTTCAAAGTTGAATTCAGATGACTCGGTGTAGCATCTTCAAAGA
TGAAT
Found at i:18078 original size:105 final size:105
Alignment explanation
Indices: 17895--18305 Score: 494
Period size: 105 Copynumber: 3.9 Consensus size: 105
17885 TACCATCTTC
* * * *
17895 TCAGATGACTCGGTGTAGCATCTTTAAAG-TTATATTCAGATGACTCGATGTAGCATCTTCAAAG
1 TCAGATGACTCGGTGTAGCATCTTCAAAGATGA-ACTCAGATGACTCGGTGTAGCATCTTCAAAG
* * *
17959 ATGAATTCAAATGACTCGGTCTAGCATCTTCAAAGTTGAAT
65 ATGAATCCAGATGACTCGGTGTAGCATCTTCAAAGTTGAAT
* * * * *
18000 CCAGATAACTCAGTGTAGCATCTTCAAAGATGAACTCAGATAACTCAGTGTAGCATCCTT-AAAG
1 TCAGATGACTCGGTGTAGCATCTTCAAAGATGAACTCAGATGACTCGGTGTAGCAT-CTTCAAAG
* * *
18064 TTGAATCCAGATGACTCGGTGTAGCATCTTCAAAGATGACT
65 ATGAATCCAGATGACTCGGTGTAGCATCTTCAAAGTTGAAT
*
18105 TCAGATGACTCGGTGTAGCATCTTCAAAGATG-ACTTCAGATGACTCGGTGTAGCATTTTCAAAG
1 TCAGATGACTCGGTGTAGCATCTTCAAAGATGAAC-TCAGATGACTCGGTGTAGCATCTTCAAAG
* * *
18169 TTGAA-CTTAGATGACTCGGTGTAGCATTTTCAAAGTT-ATAT
65 ATGAATC-CAGATGACTCGGTGTAGCATCTTCAAAGTTGA-AT
* * * * *
18210 TCAGATGACTCGGTGTAGCATCTTC-AATATGAACTC-GGTGGGCTCGGTGCATCATCTTCAAAG
1 TCAGATGACTCGGTGTAGCATCTTCAAAGATGAACTCAGAT-GACTCGGTGTAGCATCTTCAAAG
*
18273 ATGAATTCAGATGACTCGGTGTAGCATCTTCAA
65 ATGAATCCAGATGACTCGGTGTAGCATCTTCAA
18306 TATGAACTCA
Statistics
Matches: 262, Mismatches: 35, Indels: 19
0.83 0.11 0.06
Matches are distributed among these distances:
103 2 0.01
104 60 0.23
105 195 0.74
106 5 0.02
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (105 bp):
TCAGATGACTCGGTGTAGCATCTTCAAAGATGAACTCAGATGACTCGGTGTAGCATCTTCAAAGA
TGAATCCAGATGACTCGGTGTAGCATCTTCAAAGTTGAAT
Found at i:18266 original size:34 final size:34
Alignment explanation
Indices: 18218--18341 Score: 133
Period size: 34 Copynumber: 3.6 Consensus size: 34
18208 ATTCAGATGA
*
18218 CTCGGTGTAGCATCTTCAATATGAACTCGGTGGG
1 CTCGGTGCAGCATCTTCAATATGAACTCGGTGGG
* * * * *
18252 CTCGGTGCATCATCTTCAAAGATGAATTCAGAT-GA
1 CTCGGTGCAGCATCTTC-AATATGAACTC-GGTGGG
* *
18287 CTCGGTGTAGCATCTTCAATATGAACTCAGTGGG
1 CTCGGTGCAGCATCTTCAATATGAACTCGGTGGG
18321 CTCGGTGCAGCAAATCTTCAA
1 CTCGGTGCAGC--ATCTTCAA
18342 ACAGATTAGG
Statistics
Matches: 71, Mismatches: 14, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
33 1 0.01
34 35 0.49
35 25 0.35
36 10 0.14
ACGTcount: A:0.26, C:0.22, G:0.24, T:0.28
Consensus pattern (34 bp):
CTCGGTGCAGCATCTTCAATATGAACTCGGTGGG
Found at i:23711 original size:18 final size:18
Alignment explanation
Indices: 23688--23723 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
23678 CTCTTACCCT
23688 CTTATTCTTATTGGGTTG
1 CTTATTCTTATTGGGTTG
23706 CTTATTCTTATTGGGTTG
1 CTTATTCTTATTGGGTTG
23724 GTTTCATTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.11, C:0.11, G:0.22, T:0.56
Consensus pattern (18 bp):
CTTATTCTTATTGGGTTG
Found at i:28002 original size:134 final size:133
Alignment explanation
Indices: 27730--28516 Score: 721
Period size: 135 Copynumber: 5.9 Consensus size: 133
27720 TAGTTCTTTT
* *
27730 TTTCCAAAAATATCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTGCATTTAAGTTTAGTATTTTC
1 TTTCC-AAAATACCCTTTCGGTCGAAGGGTCATTTCCGTCTTTTGCATTTAAGTTTAGTATTTTC
*
27795 AAATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTGCATTTAAGTTTAGTATT
65 --ATTTCCAAAAATACCCTTTCGGTCGAAGGGTCAGTTTCGTCTTTTGCATTTAAGTTTAGTATT
27860 TTCAAA
128 TTCAAA
* *
27866 TTTCCAAGATACCCTTTCGGTCGAATGGTCATTTCCGTCTTTTGCATTTAAGTTTAGTATTTTCA
1 TTTCCAAAATACCCTTTCGGTCGAAGGGTCATTTCCGTCTTTTGCATTTAAGTTTAGTATTTTC-
*
27931 AATTTCC-AAAATACCCTTTCGGTCGAAGGGTCA-TTTCCATCTTTTGCATTTAAGTTTAGTATT
65 -ATTTCCAAAAATACCCTTTCGGTCGAAGGGTCAGTTT-CGTCTTTTGCATTTAAGTTTAGTATT
27994 TTCAAA
128 TTCAAA
* *
28000 TTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTCCGTCTTTTGCACTTAAGTGTAGTATTTTC
1 TTTCC-AAAATACCCTTTCGGTCGAAGGGTCATTTCCGTCTTTTGCATTTAAGTTTAGTATTTTC
* *
28065 ATTTCCAAAAATACCCTTTCGGTCAAAGGGTCAGTCTT-GTCTATTTGCATTTAGGTTTAGTATT
65 ATTTCCAAAAATACCCTTTCGGTCGAAGGGTCAGT-TTCGTCT-TTTGCATTTAAGTTTAGTATT
*
28129 TT--GA
128 TTCAAA
* * * * *
28133 TTTCCAGAAATTCCCTTTCGGTCAAAGGGTCGGTTT-TGTCTTTTTGCATTCAAGTTTAGTATTT
1 TTTCCA-AAATACCCTTTCGGTCGAAGGGTC-ATTTCCGTC-TTTTGCATTTAAGTTTAGTATTT
* * * *
28197 TCATTTCCAGAGATACCCTTTCGGTTGAAGGGTCAGTTTCGTCTTTTTGCA-TTCAGTTT--TAG
63 TCATTTCCAAAAATACCCTTTCGGTCGAAGGGTCAGTTTCGTC-TTTTGCATTTAAGTTTAGTA-
*
28259 TTTT--AT
126 TTTTCAAA
* * * *
28265 TTTCCAAAAATA-CATTTCCGGTCGATGGGTCAGTTTCATCAGGT-TGTTGCATTTAAGTCTAGT
1 TTTCC-AAAATACCCTTT-CGGTCGAAGGGTCA-TTTC--C--GTCTTTTGCATTTAAGTTTAGT
* * * * *
28328 -CTTTC-TTTCCAAAGAATAACCTTTCGGTCAAAAGGTCA-ATTCTGTCATTCTTG-AGTTTAAG
59 ATTTTCATTTCCAAA-AATACCCTTTCGGTCGAAGGGTCAGTTTC-GTC-TT-TTGCA-TTTAAG
* *
28389 TTTA--CTTTT--GA
119 TTTAGTATTTTCAAA
* * *
28400 TTTCCAAAAATACCCTTTCGGT-GAAAGGTTCAGTTT-CATCATTTTTGCATTTCA-TTT--TAT
1 TTTCC-AAAATACCCTTTCGGTCG-AAGGGTCA-TTTCCGTC--TTTTGCATTTAAGTTTAGTAT
* * *
28460 TCT-ACTTTCCAAAAATACCCTTTCGGT-GAAAGTGTCAGTTTCATCATTTTCGCATTT
61 TTTCA-TTTCCAAAAATACCCTTTCGGTCG-AAGGGTCAGTTTCGTC-TTTT-GCATTT
28517 CAATTTATTC
Statistics
Matches: 548, Mismatches: 65, Indels: 81
0.79 0.09 0.12
Matches are distributed among these distances:
130 4 0.01
131 36 0.07
132 43 0.08
133 69 0.13
134 185 0.34
135 191 0.35
136 18 0.03
137 2 0.00
ACGTcount: A:0.23, C:0.18, G:0.16, T:0.42
Consensus pattern (133 bp):
TTTCCAAAATACCCTTTCGGTCGAAGGGTCATTTCCGTCTTTTGCATTTAAGTTTAGTATTTTCA
TTTCCAAAAATACCCTTTCGGTCGAAGGGTCAGTTTCGTCTTTTGCATTTAAGTTTAGTATTTTC
AAA
Found at i:28114 original size:202 final size:196
Alignment explanation
Indices: 27730--28243 Score: 694
Period size: 202 Copynumber: 2.6 Consensus size: 196
27720 TAGTTCTTTT
*
27730 TTTCCAAAAATATCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTGCATTTAAGTTTAGTATTTTC
1 TTTCC-AAAATACCCTTTCGGTCGAAGGGTCA-TTTCGTCTTTTGCATTTAAGTTTAGTATTTTC
* *
27795 AAATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTGCATTTAAGTTTAGTATT
64 AAATTTCCAAAAATACCCTTTCGGTCGAAGGGTCA-TTTCGTCTTTTGCACTTAAGTGTAGTATT
* * *
27860 TTCAAATTTCCAAGATACCCTTTCGGTCGAATGGTCATTTCCGTCTTTTGCATTTAAGTTTAGTA
128 TTC-AATTTCCAAAATACCCTTTCGGTCAAAGGGTCATTT-CGTCTTTTGCATTTAAGTTTAGTA
27925 TTTTCAAA
191 TTTT--AA
*
27933 TTTCCAAAATACCCTTTCGGTCGAAGGGTCATTTCCATCTTTTGCATTTAAGTTTAGTATTTTCA
1 TTTCCAAAATACCCTTTCGGTCGAAGGGTCATTT-CGTCTTTTGCATTTAAGTTTAGTATTTTCA
27998 AATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTCCGTCTTTTGCACTTAAGTGTAGTATTT
65 AATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTT-CGTCTTTTGCACTTAAGTGTAGTATTT
*
28063 TC-ATTTCCAAAAATACCCTTTCGGTCAAAGGGTCAGTCTT-GTCTATTTGCATTTAGGTTTAGT
129 TCAATTTCC-AAAATACCCTTTCGGTCAAAGGGTCA-T-TTCGTCT-TTTGCATTTAAGTTTAGT
*
28126 ATTTTGA
190 ATTTTAA
* * * * *
28133 TTTCCAGAAATTCCCTTTCGGTCAAAGGGTCGGTTTTGTCTTTTTGCATTCAAGTTTAGTATTTT
1 TTTCCA-AAATACCCTTTCGGTCGAAGGGTC-ATTTCGTC-TTTTGCATTTAAGTTTAGTATTTT
* * *
28198 C--ATTTCCAGAGATACCCTTTCGGTTGAAGGGTCAGTTTCGTCTTTT
63 CAAATTTCCAAAAATACCCTTTCGGTCGAAGGGTCA-TTTCGTCTTTT
28244 TGCATTCAGT
Statistics
Matches: 283, Mismatches: 18, Indels: 23
0.87 0.06 0.07
Matches are distributed among these distances:
200 51 0.18
201 60 0.21
202 165 0.58
203 7 0.02
ACGTcount: A:0.23, C:0.18, G:0.16, T:0.42
Consensus pattern (196 bp):
TTTCCAAAATACCCTTTCGGTCGAAGGGTCATTTCGTCTTTTGCATTTAAGTTTAGTATTTTCAA
ATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTCGTCTTTTGCACTTAAGTGTAGTATTTTC
AATTTCCAAAATACCCTTTCGGTCAAAGGGTCATTTCGTCTTTTGCATTTAAGTTTAGTATTTTA
A
Found at i:28250 original size:67 final size:66
Alignment explanation
Indices: 27730--28486 Score: 741
Period size: 67 Copynumber: 11.3 Consensus size: 66
27720 TAGTTCTTTT
*
27730 TTTCCAAAAATATCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTGCATTTAAGTTTAGTATTTTC
1 TTTCCAAAAATACCCTTTCGGTCGAAGGGTCA-TTTCGTCTTTTGCATTTAAGTTTAGTATTTTC
27795 AAA
65 -AA
27798 TTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTGCATTTAAGTTTAGTATTTTC
1 TTTCCAAAAATACCCTTTCGGTCGAAGGGTCA-TTTCGTCTTTTGCATTTAAGTTTAGTATTTTC
27863 AAA
65 -AA
* *
27866 TTTCC-AAGATACCCTTTCGGTCGAATGGTCATTTCCGTCTTTTGCATTTAAGTTTAGTATTTTC
1 TTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTT-CGTCTTTTGCATTTAAGTTTAGTATTTTC
27930 AAA
65 -AA
*
27933 TTTCC-AAAATACCCTTTCGGTCGAAGGGTCATTTCCATCTTTTGCATTTAAGTTTAGTATTTTC
1 TTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTT-CGTCTTTTGCATTTAAGTTTAGTATTTTC
27997 AAA
65 -AA
* *
28000 TTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTCCGTCTTTTGCACTTAAGTGTAGTATTTTC
1 TTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTT-CGTCTTTTGCATTTAAGTTTAGTATTTTC
28065 -A
65 AA
* *
28066 TTTCCAAAAATACCCTTTCGGTCAAAGGGTCAGTCTT-GTCTATTTGCATTTAGGTTTAGTATTT
1 TTTCCAAAAATACCCTTTCGGTCGAAGGGTCA-T-TTCGTCT-TTTGCATTTAAGTTTAGTATTT
*
28130 T-GA
63 TCAA
* * * * * *
28133 TTTCCAGAAATTCCCTTTCGGTCAAAGGGTCGGTTTTGTCTTTTTGCATTCAAGTTTAGTATTTT
1 TTTCCAAAAATACCCTTTCGGTCGAAGGGTC-ATTTCGTC-TTTTGCATTTAAGTTTAGTATTTT
28198 C-A
64 CAA
* * * *
28200 TTTCCAGAGATACCCTTTCGGTTGAAGGGTCAGTTTCGTCTTTTTGCA-TTCAGTTT--TAGTTT
1 TTTCCAAAAATACCCTTTCGGTCGAAGGGTCA-TTTCGTC-TTTTGCATTTAAGTTTAGTA-TTT
*
28262 T-AT
63 TCAA
* * * *
28265 TTTCCAAAAATA-CATTTCCGGTCGATGGGTCAGTTTCATCAGGTTGTTGCATTTAAGTCTAGT-
1 TTTCCAAAAATACCCTTT-CGGTCGAAGGGTCA-TTTCGTC---TT-TTGCATTTAAGTTTAGTA
*
28328 CTTTC--
60 TTTTCAA
* * * * *
28333 TTTCCAAAGAATAACCTTTCGGTCAAAAGGTCAATTCTGTCATTCTTG-AGTTTAAGTTTA--CT
1 TTTCCAAA-AATACCCTTTCGGTCGAAGGGTCATTTC-GTC-TT-TTGCA-TTTAAGTTTAGTAT
*
28395 TTT-GA
61 TTTCAA
* * *
28400 TTTCCAAAAATACCCTTTCGGT-GAAAGGTTCAGTTTCATCATTTTTGCATTTCA-TTT--TATT
1 TTTCCAAAAATACCCTTTCGGTCG-AAGGGTCA-TTTCGTC--TTTTGCATTTAAGTTTAGTATT
* *
28461 CT-AC
62 TTCAA
28465 TTTCCAAAAATACCCTTTCGGT
1 TTTCCAAAAATACCCTTTCGGT
28487 GAAAGTGTCA
Statistics
Matches: 597, Mismatches: 59, Indels: 69
0.82 0.08 0.10
Matches are distributed among these distances:
64 6 0.01
65 61 0.10
66 79 0.13
67 273 0.46
68 147 0.25
69 26 0.04
70 4 0.01
71 1 0.00
ACGTcount: A:0.23, C:0.18, G:0.16, T:0.42
Consensus pattern (66 bp):
TTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTCGTCTTTTGCATTTAAGTTTAGTATTTTCA
A
Found at i:30783 original size:10 final size:10
Alignment explanation
Indices: 30768--30796 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
30758 TGTTTGAAAC
30768 GTCTGTCGCT
1 GTCTGTCGCT
30778 GTCTGTCGCT
1 GTCTGTCGCT
30788 GTCTGTCGC
1 GTCTGTCGC
30797 AGAACTGGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.00, C:0.31, G:0.31, T:0.38
Consensus pattern (10 bp):
GTCTGTCGCT
Found at i:33162 original size:16 final size:17
Alignment explanation
Indices: 33129--33163 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
33119 GTTATGTGTT
*
33129 AAAAATAAAAACATATA
1 AAAAATAAAAACACATA
33146 AAAAATAAAAAC-CATA
1 AAAAATAAAAACACATA
33162 AA
1 AA
33164 TAGAACTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.77, C:0.09, G:0.00, T:0.14
Consensus pattern (17 bp):
AAAAATAAAAACACATA
Found at i:40096 original size:14 final size:15
Alignment explanation
Indices: 40070--40099 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
40060 CTAAGTCCAA
40070 TCCTTGTTTATTTAT
1 TCCTTGTTTATTTAT
40085 TCCTTG-TTATTTAT
1 TCCTTGTTTATTTAT
40099 T
1 T
40100 TTTCCTAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.13, C:0.13, G:0.07, T:0.67
Consensus pattern (15 bp):
TCCTTGTTTATTTAT
Found at i:40257 original size:12 final size:12
Alignment explanation
Indices: 40240--40264 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
40230 CGATCCCCCC
40240 CCCTCTTGTAAT
1 CCCTCTTGTAAT
40252 CCCTCTTGTAAT
1 CCCTCTTGTAAT
40264 C
1 C
40265 AAGTTAAGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.36, G:0.08, T:0.40
Consensus pattern (12 bp):
CCCTCTTGTAAT
Found at i:44838 original size:154 final size:154
Alignment explanation
Indices: 44583--44884 Score: 559
Period size: 154 Copynumber: 2.0 Consensus size: 154
44573 TTCAGTTAAG
*
44583 GACATTATGGGGAGTGAAACAAAATTCACCATGATAGTGAGCTTGAATTCAATTGGAATTTTTTC
1 GACATTATGGGGAGTGAAACAAAATTCACCATGATAGAGAGCTTGAATTCAATTGGAATTTTTTC
44648 CATAGTCTTATGGAGATAATCTAAGACTATTGGTGAAATTTTGGTTTATTCTGAGTTCGTTTGCA
66 CATAGTCTTATGGAGATAATCTAAGACTATTGGTGAAATTTTGGTTTATTCTGAGTTCGTTTGCA
44713 ACTTTTGCATTCTTTTCAATAAAT
131 ACTTTTGCATTCTTTTCAATAAAT
* *
44737 GACATTCTGGGGAGTGAAACTAAATTCACCATGATAGAGAGCTTGAATTCAATTGGAATTTTTTC
1 GACATTATGGGGAGTGAAACAAAATTCACCATGATAGAGAGCTTGAATTCAATTGGAATTTTTTC
* *
44802 CATAGTCTTATGGAGATAATGTAAGCCTATTGGTGAAATTTTGGTTTATTCTGAGTTCGTTTGCA
66 CATAGTCTTATGGAGATAATCTAAGACTATTGGTGAAATTTTGGTTTATTCTGAGTTCGTTTGCA
44867 ACTTTTGCATTCTTTTCA
131 ACTTTTGCATTCTTTTCA
44885 GTTAAGGACA
Statistics
Matches: 143, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
154 143 1.00
ACGTcount: A:0.28, C:0.13, G:0.20, T:0.39
Consensus pattern (154 bp):
GACATTATGGGGAGTGAAACAAAATTCACCATGATAGAGAGCTTGAATTCAATTGGAATTTTTTC
CATAGTCTTATGGAGATAATCTAAGACTATTGGTGAAATTTTGGTTTATTCTGAGTTCGTTTGCA
ACTTTTGCATTCTTTTCAATAAAT
Found at i:46482 original size:211 final size:211
Alignment explanation
Indices: 46118--46540 Score: 801
Period size: 211 Copynumber: 2.0 Consensus size: 211
46108 CTCCAATGCC
* *
46118 TCAGGGTATATTTTCTTTACTTTTTCTTTTCTGCTCTCTTCTGTCTAAGTTCTACCAAGTGGCAA
1 TCAGGGTAAATTTTCTTTACTTTTTATTTTCTGCTCTCTTCTGTCTAAGTTCTACCAAGTGGCAA
46183 ACATGCCACCTAAGGTTGATGAAGGCAGATCTAGCCATGGTATGCAAACTAGAAGCAAAAACATG
66 ACATGCCACCTAAGGTTGATGAAGGCAGATCTAGCCATGGTATGCAAACTAGAAGCAAAAACATG
46248 GTTGATCCTTCACAATTACCTTTGGAGTCTGATTCAAAGATCTTGTTGCAATATCTCACTGAAGA
131 GTTGATCCTTCACAATTACCTTTGGAGTCTGATTCAAAGATCTTGTTGCAATATCTCACTGAAGA
46313 TAAGAATTAAATTTCT
196 TAAGAATTAAATTTCT
46329 TCAGGGTAAATTTTCTTTACTTTTTATTTTCTGCTCTCTTCTGTCTAAGTTCTACCAAGTGGCAA
1 TCAGGGTAAATTTTCTTTACTTTTTATTTTCTGCTCTCTTCTGTCTAAGTTCTACCAAGTGGCAA
* *
46394 ACATGCCACCTAAGGTTGATGAAGGTATATCTAGCCATGGTATGCAAACTAGAAGCAAAAACATG
66 ACATGCCACCTAAGGTTGATGAAGGCAGATCTAGCCATGGTATGCAAACTAGAAGCAAAAACATG
46459 GTTGATCCTTCACAATTACCTTTGGAGTCTGATTCAAAGATCTTGTTGCAATATCTCACTGAAGA
131 GTTGATCCTTCACAATTACCTTTGGAGTCTGATTCAAAGATCTTGTTGCAATATCTCACTGAAGA
*
46524 TATGAATTAAATTTCT
196 TAAGAATTAAATTTCT
46540 T
1 T
46541 TGGCACATGA
Statistics
Matches: 207, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
211 207 1.00
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (211 bp):
TCAGGGTAAATTTTCTTTACTTTTTATTTTCTGCTCTCTTCTGTCTAAGTTCTACCAAGTGGCAA
ACATGCCACCTAAGGTTGATGAAGGCAGATCTAGCCATGGTATGCAAACTAGAAGCAAAAACATG
GTTGATCCTTCACAATTACCTTTGGAGTCTGATTCAAAGATCTTGTTGCAATATCTCACTGAAGA
TAAGAATTAAATTTCT
Found at i:53652 original size:153 final size:154
Alignment explanation
Indices: 53386--53704 Score: 532
Period size: 153 Copynumber: 2.1 Consensus size: 154
53376 TTATGACCGG
* * *
53386 TTTTCAATTAAGGACATTATGGGGAGTGAAACCAAATTCACCATGATAGAGAGTTTGAATTCAAT
1 TTTTCAGTTAAGGACATTATGGGGAGTGAAACCAAATTCACCAGGATAGAGAGCTTGAATTCAAT
53451 TGGAATTTTTTCCATAGTCTTATGGAGATAATCTAAGACTATTGGTGAAATTTTGGTTTATTCTA
66 TGGAATTTTTTCCATAGTCTTATGGAGATAATCTAAGACTATTGGTGAAATTTTGGTTTATTCTA
*
53516 AGTTCGTTTGCAACTTTTGTATTA
131 AGTTCGTTTGCAACTTTTGCATTA
* *
53540 TTTTCAGTTAAGGACATTCT-GGGAGTGAAACCAAATTCACCAGGATAGAGAGCTTGAATTCACT
1 TTTTCAGTTAAGGACATTATGGGGAGTGAAACCAAATTCACCAGGATAGAGAGCTTGAATTCAAT
* * * *
53604 TGGAATTTTTTCCATAGTCTTATGGGGATAATGTAAGCCTATTGGTGAAATTTTGGTTTATTCTG
66 TGGAATTTTTTCCATAGTCTTATGGAGATAATCTAAGACTATTGGTGAAATTTTGGTTTATTCTA
*
53669 AGTTCGTTTGCAACTTTTGCATTC
131 AGTTCGTTTGCAACTTTTGCATTA
53693 TTTTCAGTTAAG
1 TTTTCAGTTAAG
53705 TACACATGGC
Statistics
Matches: 154, Mismatches: 11, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
153 136 0.88
154 18 0.12
ACGTcount: A:0.28, C:0.13, G:0.20, T:0.39
Consensus pattern (154 bp):
TTTTCAGTTAAGGACATTATGGGGAGTGAAACCAAATTCACCAGGATAGAGAGCTTGAATTCAAT
TGGAATTTTTTCCATAGTCTTATGGAGATAATCTAAGACTATTGGTGAAATTTTGGTTTATTCTA
AGTTCGTTTGCAACTTTTGCATTA
Done.