Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024847.1 Corchorus olitorius cultivar O-4 contig24880, 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: 29462
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Found at i:77 original size:47 final size:47
Alignment explanation
Indices: 1--137 Score: 165
Period size: 47 Copynumber: 2.9 Consensus size: 47
* *
1 GTAGTAAAAGAAGGAGAAATTAGTTTAATTCTAGGTAATTAAACTAA
1 GTAGTAAAAGAAGGAGAAATTACTTTAATTCTAAGTAATTAAACTAA
48 GTAGTAAAA-AAGGGAGAAATT-CTTCTAATTCTAAGTAATTAAACTAA
1 GTAGTAAAAGAA-GGAGAAATTACTT-TAATTCTAAGTAATTAAACTAA
* * *
95 GTAGTAGAAGAAGGA-AAGATTAGTTTAA-TCTTAGGTAATTAAA
1 GTAGTAAAAGAAGGAGAA-ATTACTTTAATTC-TAAGTAATTAAA
138 GTAAACAGAG
Statistics
Matches: 79, Mismatches: 5, Indels: 12
0.82 0.05 0.12
Matches are distributed among these distances:
46 8 0.10
47 67 0.85
48 4 0.05
ACGTcount: A:0.46, C:0.05, G:0.19, T:0.30
Consensus pattern (47 bp):
GTAGTAAAAGAAGGAGAAATTACTTTAATTCTAAGTAATTAAACTAA
Found at i:1970 original size:13 final size:13
Alignment explanation
Indices: 1940--1990 Score: 57
Period size: 14 Copynumber: 3.7 Consensus size: 13
1930 CAAGAGACAT
*
1940 TTTTCAAGAAAATTG
1 TTTTCAA-AAAA-AG
*
1955 TTTTCAAAAAAGG
1 TTTTCAAAAAAAG
1968 TTTTCAAAAATAAG
1 TTTTCAAAAA-AAG
1982 TTTTCAAAA
1 TTTTCAAAA
1991 GGTTTTGGGT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
13 11 0.33
14 15 0.45
15 7 0.21
ACGTcount: A:0.45, C:0.08, G:0.10, T:0.37
Consensus pattern (13 bp):
TTTTCAAAAAAAG
Found at i:4230 original size:67 final size:67
Alignment explanation
Indices: 4067--4332 Score: 383
Period size: 67 Copynumber: 4.0 Consensus size: 67
4057 AAGACGATTA
* * * *
4067 CTAGAAAGAATTTTCAAATGTTAATTGGAAGACAATCTCATTAAGGAGTAGACCAGAAGACGG-T
1 CTAGAAAGAATTTTCAAATGTTGATTGGAAGACAATCTCATTAAGGAATACATCAGAAGACGGTT
4131 TG
66 TG
* *
4133 CTAGAAAGAATTTTCAAATGTTGAATGGAAGAAAATCTCATTAAGGAATACATCAGAAGACGGTT
1 CTAGAAAGAATTTTCAAATGTTGATTGGAAGACAATCTCATTAAGGAATACATCAGAAGACGGTT
4198 TG
66 TG
* *
4200 CTAGAAAGAATTTTCAAATGTTGATTGGAAGACAATCTCATTAAGGAAAACATCGGAAGACGGTT
1 CTAGAAAGAATTTTCAAATGTTGATTGGAAGACAATCTCATTAAGGAATACATCAGAAGACGGTT
4265 TG
66 TG
* * * * * *
4267 CTAGAAAGAATTTTCAGATGTTGATTGGAAGACGATCTCGTCAA-GAAGTACACCAGAAGATGGT
1 CTAGAAAGAATTTTCAAATGTTGATTGGAAGACAATCTCATTAAGGAA-TACATCAGAAGACGGT
4331 TT
65 TT
4333 CTCAAGAGTT
Statistics
Matches: 180, Mismatches: 18, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
66 60 0.33
67 120 0.67
ACGTcount: A:0.39, C:0.12, G:0.23, T:0.27
Consensus pattern (67 bp):
CTAGAAAGAATTTTCAAATGTTGATTGGAAGACAATCTCATTAAGGAATACATCAGAAGACGGTT
TG
Found at i:4374 original size:64 final size:64
Alignment explanation
Indices: 4272--4513 Score: 333
Period size: 64 Copynumber: 3.8 Consensus size: 64
4262 GTTTGCTAGA
* * *
4272 AAGAATTTTCAGATGTTGATTGGAAGACGATCTCGTCAAGAAGTACACCAGAAGATGGTTTCTC
1 AAGAATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTC
* * * *
4336 AAGAGTTTTCAGAAGTTGATCGGAAGATGATTTTGTCAAGAAGTACGCCAGAAGATGGTTTCTC
1 AAGAATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTC
* * * *
4400 AAGAATTTTCAGAAGTTGATCAGAAGACGATCTTGTTAAAAAGTACACCAGAAGATAGTTTCTC
1 AAGAATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTC
* * *
4464 AAAAAGCTTTCAGAAGTTGATCGGAAGACGATCTTGTTAAG-AGATACACC
1 AAGAA-TTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAG-TACACC
4514 GAAAGACGGT
Statistics
Matches: 157, Mismatches: 19, Indels: 3
0.88 0.11 0.02
Matches are distributed among these distances:
64 119 0.76
65 38 0.24
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (64 bp):
AAGAATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTC
Found at i:4769 original size:50 final size:49
Alignment explanation
Indices: 4646--4826 Score: 209
Period size: 50 Copynumber: 3.6 Consensus size: 49
4636 TCGAATGAAA
* * *
4646 TTCTTCAAAGTGATCCATTGTGATCAATCAAGTTGACAGTGGTTTAAGTT
1 TTCTTC-AAGTGATCCAGTGCGATCAATCAAGTTTACAGTGGTTTAAGTT
** * *
4696 TTCTAAAAGAGATCCTGTGCGATCAATCAAGTTTACAGTGGTTTAAGTTT
1 TTCTTCAAGTGATCCAGTGCGATCAATCAAGTTTACAGTGGTTTAAG-TT
* *
4746 TTCTTCAAGTGATCCAGTACGATCAATCAAGTTTACAGTGGTTTAAATT
1 TTCTTCAAGTGATCCAGTGCGATCAATCAAGTTTACAGTGGTTTAAGTT
* ** * *
4795 TCCTAAAAATGATCCAAGTGCGGTCAATCAAG
1 TTCTTCAAGTGATCC-AGTGCGATCAATCAAG
4827 GAAGTTTCCT
Statistics
Matches: 110, Mismatches: 19, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
49 49 0.45
50 61 0.55
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Consensus pattern (49 bp):
TTCTTCAAGTGATCCAGTGCGATCAATCAAGTTTACAGTGGTTTAAGTT
Found at i:4911 original size:54 final size:54
Alignment explanation
Indices: 4841--4948 Score: 144
Period size: 54 Copynumber: 2.0 Consensus size: 54
4831 TTTCCTAAAG
* *
4841 GTGATCCAGTGCGGTCAATCAAGAAAATTTACAGTGGTTTAAGTTTATCTTCAA
1 GTGATCCAGTACGGTCAATCAAGAAAATTTACAGTGATTTAAGTTTATCTTCAA
* * * * * *
4895 GTGATCCAGTATGGTCAGTCAAGGAAGTTTTCAGTGATTTAGGTTTATCTTCAA
1 GTGATCCAGTACGGTCAATCAAGAAAATTTACAGTGATTTAAGTTTATCTTCAA
4949 AGTTAGAATC
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
54 46 1.00
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.35
Consensus pattern (54 bp):
GTGATCCAGTACGGTCAATCAAGAAAATTTACAGTGATTTAAGTTTATCTTCAA
Found at i:4987 original size:35 final size:35
Alignment explanation
Indices: 4941--5263 Score: 427
Period size: 35 Copynumber: 9.2 Consensus size: 35
4931 ATTTAGGTTT
* *
4941 ATCTTCAAAGTTAGAATCAGGTGACTCGGTATAGC
1 ATCTTCAAAGTTAGAATCAGATGACTCGGTGTAGC
*
4976 ATCTTCAAAGTT-GAATTCAGATGACTCAGTGTAGC
1 ATCTTCAAAGTTAGAA-TCAGATGACTCGGTGTAGC
* * * *
5011 AACTTCAAA-TTCGAGATCAAATGACTCGGTGTAAC
1 ATCTTCAAAGTTAGA-ATCAGATGACTCGGTGTAGC
*
5046 ATCTTCAAAGTTAGAATCAAATGACTCGGTGTAGC
1 ATCTTCAAAGTTAGAATCAGATGACTCGGTGTAGC
* * *
5081 ATCTTCAAAGTT-GAATTCAAATGACTCAGCGTAGC
1 ATCTTCAAAGTTAGAA-TCAGATGACTCGGTGTAGC
* * * *
5116 ATCTTCAAAGTTGGATTTAGATGACTCAGTGTAGC
1 ATCTTCAAAGTTAGAATCAGATGACTCGGTGTAGC
5151 ATCTTCAAAGTTAGAATCAGATGACTCGGTGTAGC
1 ATCTTCAAAGTTAGAATCAGATGACTCGGTGTAGC
**
5186 ATCTTCAAAGTCGGAATCAGATGACTCGGTGTAGC
1 ATCTTCAAAGTTAGAATCAGATGACTCGGTGTAGC
**
5221 ATCTTCAAAGTCGGAATCAGATGACTCGGTGTAGC
1 ATCTTCAAAGTTAGAATCAGATGACTCGGTGTAGC
5256 ATCTTCAA
1 ATCTTCAA
5264 GTGGGATTCA
Statistics
Matches: 260, Mismatches: 22, Indels: 12
0.88 0.07 0.04
Matches are distributed among these distances:
34 8 0.03
35 245 0.94
36 7 0.03
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (35 bp):
ATCTTCAAAGTTAGAATCAGATGACTCGGTGTAGC
Found at i:5123 original size:105 final size:104
Alignment explanation
Indices: 4941--5263 Score: 470
Period size: 105 Copynumber: 3.1 Consensus size: 104
4931 ATTTAGGTTT
* *
4941 ATCTTCAAAGTTAGAATCAGGTGACTCGGTATAGCATCTTCAAAGTTGAATTCAGATGACTCAGT
1 ATCTTCAAAGTTAGAATCAGATGACTCGGTGTAGCATCTTCAAAGTTGAATTCAGATGACTCAGT
* * *
5006 GTAGCAACTTCAAATTCGAGATCAAATGACTCGGTGTAAC
66 GTAGCATCTTCAAATTCG-GATCAGATGACTCGGTGTAGC
* * *
5046 ATCTTCAAAGTTAGAATCAAATGACTCGGTGTAGCATCTTCAAAGTTGAATTCAAATGACTCAGC
1 ATCTTCAAAGTTAGAATCAGATGACTCGGTGTAGCATCTTCAAAGTTGAATTCAGATGACTCAGT
* *
5111 GTAGCATCTTCAAAGTT-GGATTTAGATGACTCAGTGTAGC
66 GTAGCATCTTCAAA-TTCGGA-TCAGATGACTCGGTGTAGC
* *
5151 ATCTTCAAAGTTAGAATCAGATGACTCGGTGTAGCATCTTCAAAGTCGGAA-TCAGATGACTCGG
1 ATCTTCAAAGTTAGAATCAGATGACTCGGTGTAGCATCTTCAAAGT-TGAATTCAGATGACTCAG
*
5215 TGTAGCATCTTCAAAGTCGGAATCAGATGACTCGGTGTAGC
65 TGTAGCATCTTCAAATTCGG-ATCAGATGACTCGGTGTAGC
5256 ATCTTCAA
1 ATCTTCAA
5264 GTGGGATTCA
Statistics
Matches: 195, Mismatches: 18, Indels: 10
0.87 0.08 0.04
Matches are distributed among these distances:
104 3 0.02
105 186 0.95
106 6 0.03
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (104 bp):
ATCTTCAAAGTTAGAATCAGATGACTCGGTGTAGCATCTTCAAAGTTGAATTCAGATGACTCAGT
GTAGCATCTTCAAATTCGGATCAGATGACTCGGTGTAGC
Found at i:7561 original size:36 final size:35
Alignment explanation
Indices: 7507--8401 Score: 701
Period size: 36 Copynumber: 25.1 Consensus size: 35
7497 ATCCATGTAG
*
7507 TAAGTAAATACAAGCAAAGATTTAATTCAGGGTAAT
1 TAAGTAAA-ACAAGCAAAGACTTAATTCAGGGTAAT
* *
7543 TAAGTAAACACAATCAAAGATTTAATTCAGGGTAAT
1 TAAGTAAA-ACAAGCAAAGACTTAATTCAGGGTAAT
* * *
7579 TAAGTAAAAGCAAGTAAAAACTTAATTCAGTGTAAT
1 TAAGTAAAA-CAAGCAAAGACTTAATTCAGGGTAAT
*
7615 TAAGTAAATACAAGCACAGACTTAATTCAGGGTAAT
1 TAAGTAAA-ACAAGCAAAGACTTAATTCAGGGTAAT
* * *
7651 TAAGTAAATCAAGCAAAGACTTAATTTCAAGGAAAT
1 TAAGTAAAACAAGCAAAGACTTAA-TTCAGGGTAAT
* * *
7687 TAGGTAAAATCAAGCACATACTTAATTCAGGGTAAT
1 TAAGTAAAA-CAAGCAAAGACTTAATTCAGGGTAAT
* *
7723 TAAGTAAATCAAGTAAAGACTTAA-T-----T--T
1 TAAGTAAAACAAGCAAAGACTTAATTCAGGGTAAT
* * * * *
7750 CAAG-AAAATTAGGCAGAGACTTAGTTCAGGGTAAT
1 TAAGTAAAA-CAAGCAAAGACTTAATTCAGGGTAAT
* * * *
7785 TAAGTAAATCAAGCAAAGACATAATTTCAAGGAAAT
1 TAAGTAAAACAAGCAAAGACTTAA-TTCAGGGTAAT
* * *
7821 TAGGTAAGAATAAGCGAAGACTTAATTTCAGGGTAAT
1 TAAGTAA-AACAAGCAAAGACTTAA-TTCAGGGTAAT
* * * *
7858 TAAGCAAACCAAGCAAAGACTTAATTTCAAGGAAAT
1 TAAGTAAAACAAGCAAAGACTTAA-TTCAGGGTAAT
* * * *
7894 TAGGTAAAATCAAGCACAGACTTAATTCAAGGCAAT
1 TAAGTAAAA-CAAGCAAAGACTTAATTCAGGGTAAT
* * *
7930 TAAGTAAATCAAGCAAAGACTTAATTTCAAGGAAAT
1 TAAGTAAAACAAGCAAAGACTTAA-TTCAGGGTAAT
* * * * *
7966 TAGGTAAGAATAAGGAAAGACTTAATTTCAAGGAAAT
1 TAAGTAA-AACAAGCAAAGACTTAA-TTCAGGGTAAT
* * * *
8003 TAGGTAAGAATAAGCAAAGACTTAATTTCAAGGAAAT
1 TAAGTAA-AACAAGCAAAGACTTAA-TTCAGGGTAAT
** * *
8040 TGGGTAAGAACAAGCAAAGACTTAATTTCAAGGAAAT
1 TAAGTAA-AACAAGCAAAGACTTAA-TTCAGGGTAAT
* * * *
8077 TAGGTAAAATCAAGCACAGACTTAATTTAGGGTGAT
1 TAAGTAAAA-CAAGCAAAGACTTAATTCAGGGTAAT
*
8113 TAAGTAAATCAAGCAAAGACTTAATTCAGGGTAAT
1 TAAGTAAAACAAGCAAAGACTTAATTCAGGGTAAT
* ** *
8148 TAAGTAAACCAAGCAAAGACTTAATTTCAACGAAAT
1 TAAGTAAAACAAGCAAAGACTTAA-TTCAGGGTAAT
* * *
8184 TAGGTAAGAACAAGCAAAGACTTAATTTCAAGGAAAT
1 TAAGTAA-AACAAGCAAAGACTTAA-TTCAGGGTAAT
* *
8221 TAGGTAAAATCAAGCACAA-ACTTAATTCAGGGTAAA
1 TAAGTAAAA-CAAGCA-AAGACTTAATTCAGGGTAAT
*
8257 TAAGTAAAAGC-AGTCAAGGACTTAATTCAGGGTAAT
1 TAAGTAAAA-CAAG-CAAAGACTTAATTCAGGGTAAT
* * *
8293 TAAGT-AAA-GAGTCAATAAACTTAATTCTGGGTAAT
1 TAAGTAAAACAAG-CAA-AGACTTAATTCAGGGTAAT
** *
8328 TAAGTAGAGTCAA--TAA-ACTTAATTC-GAGGTAAT
1 TAAGTA-AAACAAGCAAAGACTTAATTCAG-GGTAAT
* *
8361 TAAGTAAAGTCAA-TAAAGAACTTAATTCAGGGTAAT
1 TAAGTAAA-ACAAGCAAAG-ACTTAATTCAGGGTAAT
8397 TAAGT
1 TAAGT
8402 GGGGGATATT
Statistics
Matches: 716, Mismatches: 106, Indels: 74
0.80 0.12 0.08
Matches are distributed among these distances:
26 3 0.00
27 14 0.02
28 1 0.00
29 1 0.00
32 2 0.00
33 26 0.04
34 10 0.01
35 129 0.18
36 306 0.43
37 221 0.31
38 3 0.00
ACGTcount: A:0.46, C:0.11, G:0.17, T:0.25
Consensus pattern (35 bp):
TAAGTAAAACAAGCAAAGACTTAATTCAGGGTAAT
Found at i:7789 original size:62 final size:64
Alignment explanation
Indices: 7706--8187 Score: 315
Period size: 73 Copynumber: 6.9 Consensus size: 64
7696 TCAAGCACAT
* *
7706 ACTTAATTCAGGGTAATTAAGTAAATCAAGTAAAGACTTAATTTCAAGAAAATTAGG-CAG-AG
1 ACTTAATTCAGGGTAATTAAGTAAATCAAGCAAAGACTTAATTTCAAGGAAATTAGGACAGAAG
* * *
7768 ACTTAGTTCAGGGTAATTAAGTAAATCAAGCAAAGACATAATTTCAAGGAAATTAGGTAAGAATA
1 ACTTAATTCAGGGTAATTAAGTAAATCAAGCAAAGACTTAATTTCAAGGAAATTA-G---G-A-C
7833 AGCGAAG
60 A--GAAG
* *
7840 ACTTAATTTCAGGGTAATTAAGCAAACCAAGCAAAGACTTAATTTCAAGGAAATTAGGTAAAATC
1 ACTTAA-TTCAGGGTAATTAAGTAAATCAAGCAAAGACTTAATTTCAAGGAAATTAGG----A-C
7905 AAGCACAG
60 -AG-A-AG
* * *
7913 ACTTAATTCAAGGCAATTAAGTAAATCAAGCAAAGACTTAATTTCAAGGAAATTAGGTAAGAATA
1 ACTTAATTCAGGGTAATTAAGTAAATCAAGCAAAGACTTAATTTCAAGGAAATTA-G---G-A-C
7978 AGGAAAG
60 A-G-AAG
* * * *
7985 ACTTAATTTCAAGGAAATTAGGTAAGAAT-AAGCAAAGACTTAATTTCAAGGAAATTGGGTAAGA
1 ACTTAA-TTCAGGGTAATTAAGT-A-AATCAAGCAAAGACTTAATTTCAAGGAAA-T---T-AGG
8049 ACAAGCAAAG
58 AC-AG--AAG
* * * * * ** *
8059 ACTTAATTTCAAGGAAATTAGGTAAAATCAAGCACAGACTTAATTT-AGGGTGATTAAGTAAATC
1 ACTTAA-TTCAGGGTAATTAAGT-AAATCAAGCAAAGACTTAATTTCAAGGAAATT-AG--GA-C
8123 AAGCAAAG
60 -AG--AAG
* *
8131 ACTTAATTCAGGGTAATTAAGTAAACCAAGCAAAGACTTAATTTCAACGAAATTAGG
1 ACTTAATTCAGGGTAATTAAGTAAATCAAGCAAAGACTTAATTTCAAGGAAATTAGG
8188 TAAGAACAAG
Statistics
Matches: 349, Mismatches: 34, Indels: 68
0.77 0.08 0.15
Matches are distributed among these distances:
62 51 0.15
63 1 0.00
66 1 0.00
69 6 0.02
70 22 0.06
71 22 0.06
72 82 0.23
73 83 0.24
74 73 0.21
75 4 0.01
76 1 0.00
78 2 0.01
79 1 0.00
ACGTcount: A:0.46, C:0.11, G:0.18, T:0.25
Consensus pattern (64 bp):
ACTTAATTCAGGGTAATTAAGTAAATCAAGCAAAGACTTAATTTCAAGGAAATTAGGACAGAAG
Found at i:7972 original size:145 final size:145
Alignment explanation
Indices: 7782--8300 Score: 646
Period size: 145 Copynumber: 3.6 Consensus size: 145
7772 AGTTCAGGGT
* *
7782 AATTAAGT-AAATCAAGCAAAGACATAATTTCAAGGAAATTAGGTAAGAATAAGCGAAGACTTAA
1 AATTAAGTAAAATCAAGCAAAGACTTAATTTCAAGGAAATTAAGTAA-AATAAGCGAAGACTTAA
*
7846 TTTCAGGGTAATTAAGCAAACCAAGCAAAGACTTAATTTCAAGGAAATTAGGTAA-AATCAAGCA
65 -TTCAGGGTAATTAAGTAAACCAAGCAAAGACTTAATTTCAAGGAAATTAGGTAAGAA-CAAGCA
* *
7910 CAGACTTAA-TTCAAGGC
128 AAGACTTAATTTCAAGGA
*
7927 AATTAAGT-AAATCAAGCAAAGACTTAATTTCAAGGAAATTAGGTAAGAATAAG-GAAAGACTTA
1 AATTAAGTAAAATCAAGCAAAGACTTAATTTCAAGGAAATTAAGTAA-AATAAGCG-AAGACTTA
* * * ** *
7990 ATTTCAAGGAAATTAGGTAAGAATAAGCAAAGACTTAATTTCAAGGAAATTGGGTAAGAACAAGC
64 A-TTCAGGGTAATTAAGTAA-ACCAAGCAAAGACTTAATTTCAAGGAAATTAGGTAAGAACAAGC
8055 AAAGACTTAATTTCAAGGA
127 AAAGACTTAATTTCAAGGA
* * * ** *
8074 AATTAGGTAAAATCAAGCACAGACTTAATTT-AGGGTGATTAAGT-AAATCAAGCAAAGACTTAA
1 AATTAAGTAAAATCAAGCAAAGACTTAATTTCAAGGAAATTAAGTAAAAT-AAGCGAAGACTTAA
*
8137 TTCAGGGTAATTAAGTAAACCAAGCAAAGACTTAATTTCAACGAAATTAGGTAAGAACAAGCAAA
65 TTCAGGGTAATTAAGTAAACCAAGCAAAGACTTAATTTCAAGGAAATTAGGTAAGAACAAGCAAA
8202 GACTTAATTTCAAGGA
130 GACTTAATTTCAAGGA
* * **
8218 AATTAGGTAAAATCAAGCACAA-ACTTAA-TTCAGGGTAAA-TAAGTAAAAGCAGTC-AAGGACT
1 AATTAAGTAAAATCAAGCA-AAGACTTAATTTCAAGG-AAATTAAGTAAAATAAG-CGAA-GACT
8279 TAATTCAGGGTAATTAAGTAAA
62 TAATTCAGGGTAATTAAGTAAA
8301 GAGTCAATAA
Statistics
Matches: 332, Mismatches: 29, Indels: 26
0.86 0.07 0.07
Matches are distributed among these distances:
143 2 0.01
144 98 0.30
145 126 0.38
146 60 0.18
147 25 0.08
148 21 0.06
ACGTcount: A:0.47, C:0.11, G:0.18, T:0.24
Consensus pattern (145 bp):
AATTAAGTAAAATCAAGCAAAGACTTAATTTCAAGGAAATTAAGTAAAATAAGCGAAGACTTAAT
TCAGGGTAATTAAGTAAACCAAGCAAAGACTTAATTTCAAGGAAATTAGGTAAGAACAAGCAAAG
ACTTAATTTCAAGGA
Found at i:7985 original size:109 final size:108
Alignment explanation
Indices: 7782--8264 Score: 584
Period size: 109 Copynumber: 4.4 Consensus size: 108
7772 AGTTCAGGGT
* * * *
7782 AATTAAGT-AAATCAAGCAAAGACATAATTTCAAGGAAATTAGGTAAGAAT-AAGCGAAGACTTA
1 AATTAGGTAAAATCAAGCAAAGACTTAA-TTCAAGGAAATTAAGT-A-AATCAAGCAAAGACTTA
* * * * *
7845 ATTTCAGGGTAATTAAGCAAACCAAGCAAAGACTTAATTTCAAGGA
63 ATTTCAAGGAAATTAGGTAAAACAAGCAAAGACTTAATTTCAAGGA
* *
7891 AATTAGGTAAAATCAAGCACAGACTTAATTCAAGGCAATTAAGTAAATCAAGCAAAGACTTAATT
1 AATTAGGTAAAATCAAGCAAAGACTTAATTCAAGGAAATTAAGTAAATCAAGCAAAGACTTAATT
* *
7956 TCAAGGAAATTAGGTAAGAATAAGGAAAGACTTAATTTCAAGGA
66 TCAAGGAAATTAGGTAA-AACAAGCAAAGACTTAATTTCAAGGA
** *
8000 AATTAGGTAAGAAT-AAGCAAAGACTTAATTTCAAGGAAATTGGGTAAGAACAAGCAAAGACTTA
1 AATTAGGTAA-AATCAAGCAAAGACTTAA-TTCAAGGAAATTAAGTAA-ATCAAGCAAAGACTTA
* * *
8064 ATTTCAAGGAAATTAGGTAAAATCAAGCACAGACTTAATTT-AGGGT
63 ATTTCAAGGAAATTAGGTAAAA-CAAGCAAAGACTTAATTTCAAGGA
* * * * *
8110 GATTAAGT-AAATCAAGCAAAGACTTAATTCAGGGTAATTAAGTAAACCAAGCAAAGACTTAATT
1 AATTAGGTAAAATCAAGCAAAGACTTAATTCAAGGAAATTAAGTAAATCAAGCAAAGACTTAATT
*
8174 TCAACGAAATTAGGTAAGAACAAGCAAAGACTTAATTTCAAGGA
66 TCAAGGAAATTAGGTAA-AACAAGCAAAGACTTAATTTCAAGGA
*
8218 AATTAGGTAAAATCAAGCACAA-ACTTAATTCAGGGTAAA-TAAGTAAA
1 AATTAGGTAAAATCAAGCA-AAGACTTAATTCAAGG-AAATTAAGTAAA
8265 AGCAGTCAAG
Statistics
Matches: 324, Mismatches: 37, Indels: 26
0.84 0.10 0.07
Matches are distributed among these distances:
107 54 0.17
108 57 0.18
109 113 0.35
110 50 0.15
111 50 0.15
ACGTcount: A:0.47, C:0.11, G:0.18, T:0.24
Consensus pattern (108 bp):
AATTAGGTAAAATCAAGCAAAGACTTAATTCAAGGAAATTAAGTAAATCAAGCAAAGACTTAATT
TCAAGGAAATTAGGTAAAACAAGCAAAGACTTAATTTCAAGGA
Found at i:8174 original size:218 final size:218
Alignment explanation
Indices: 7507--8300 Score: 859
Period size: 218 Copynumber: 3.7 Consensus size: 218
7497 ATCCATGTAG
* * * * ** *
7507 TAAGTAAATACAAGCAAAGATTTAA-TTCAGGGTAATTAAGTAA-ACACAATCAAAGATTTAA-T
1 TAAGTAAAT-CAAGCAAAGACTTAATTTCAAGGAAATTAGGTAAGA-A-AAGGAAAGACTTAATT
* * * * * * * *
7569 TCAGGGTAATTAAGTAAAAGCAAGTAAAAACTTAA-TTC-AGTGTAATTAAGTAA-ATACAAGCA
63 TCAAGGAAATTAGGTAAAATCAAGCAAAGACTTAATTTCAAG-GAAATTAGGTAAGA-ACAAGCA
*
7631 CAGACTTAA-TTCAGGGTAATTAAGTAAATCAAGCAAAGACTTAATTTCAAGGAAATTAGGTAAA
126 AAGACTTAATTTCAGGGTAATTAAGTAAATCAAGCAAAGACTTAATTTCAAGGAAATTAGGTAAA
*
7695 ATCAAGCACATACTTAATTCAGGGTAAT
191 ATCAAGCACAGACTTAATTCAGGGTAAT
* * * *
7723 TAAGTAAATCAAGTAAAGACTTAATTTCAAGAAAATTA-G---G--CA-G--AGACTT-AGTTCA
1 TAAGTAAATCAAGCAAAGACTTAATTTCAAGGAAATTAGGTAAGAAAAGGAAAGACTTAATTTCA
* * * * * *
7778 GGGTAATTAAGT-AAATCAAGCAAAGACATAATTTCAAGGAAATTAGGTAAGAATAAGCGAAGAC
66 AGGAAATTAGGTAAAATCAAGCAAAGACTTAATTTCAAGGAAATTAGGTAAGAACAAGCAAAGAC
* *
7842 TTAATTTCAGGGTAATTAAGCAAACCAAGCAAAGACTTAATTTCAAGGAAATTAGGTAAAATCAA
131 TTAATTTCAGGGTAATTAAGTAAATCAAGCAAAGACTTAATTTCAAGGAAATTAGGTAAAATCAA
* *
7907 GCACAGACTTAATTCAAGGCAAT
196 GCACAGACTTAATTCAGGGTAAT
7930 TAAGTAAATCAAGCAAAGACTTAATTTCAAGGAAATTAGGTAAGAATAAGGAAAGACTTAATTTC
1 TAAGTAAATCAAGCAAAGACTTAATTTCAAGGAAATTAGGTAAGAA-AAGGAAAGACTTAATTTC
*
7995 AAGGAAATTAGGTAAGAAT-AAGCAAAGACTTAATTTCAAGGAAATTGGGTAAGAACAAGCAAAG
65 AAGGAAATTAGGTAA-AATCAAGCAAAGACTTAATTTCAAGGAAATTAGGTAAGAACAAGCAAAG
* * * * * ** *
8059 ACTTAATTTCAAGGAAATTAGGTAAAATCAAGCACAGACTTAATTT-AGGGTGATTAAGT-AAAT
129 ACTTAATTTCAGGGTAATTAAGT-AAATCAAGCAAAGACTTAATTTCAAGGAAATTAGGTAAAAT
*
8122 CAAGCAAAGACTTAATTCAGGGTAAT
193 CAAGCACAGACTTAATTCAGGGTAAT
* * *
8148 TAAGTAAACCAAGCAAAGACTTAATTTCAACGAAATTAGGTAAGAACAAGCAAAGACTTAATTTC
1 TAAGTAAATCAAGCAAAGACTTAATTTCAAGGAAATTAGGTAAGAA-AAGGAAAGACTTAATTTC
* *
8213 AAGGAAATTAGGTAAAATCAAGCACAA-ACTTAA-TTCAGGGTAAA-TAAGTAA-AAGC-AGTCA
65 AAGGAAATTAGGTAAAATCAAGCA-AAGACTTAATTTCAAGG-AAATTAGGTAAGAA-CAAG-CA
*
8273 AGGACTTAA-TTCAGGGTAATTAAGTAAA
126 AAGACTTAATTTCAGGGTAATTAAGTAAA
8301 GAGTCAATAA
Statistics
Matches: 495, Mismatches: 57, Indels: 53
0.82 0.09 0.09
Matches are distributed among these distances:
205 16 0.03
206 47 0.09
207 117 0.24
208 1 0.00
209 1 0.00
211 1 0.00
214 1 0.00
215 18 0.04
216 36 0.07
217 31 0.06
218 131 0.26
219 72 0.15
220 23 0.05
ACGTcount: A:0.47, C:0.11, G:0.17, T:0.25
Consensus pattern (218 bp):
TAAGTAAATCAAGCAAAGACTTAATTTCAAGGAAATTAGGTAAGAAAAGGAAAGACTTAATTTCA
AGGAAATTAGGTAAAATCAAGCAAAGACTTAATTTCAAGGAAATTAGGTAAGAACAAGCAAAGAC
TTAATTTCAGGGTAATTAAGTAAATCAAGCAAAGACTTAATTTCAAGGAAATTAGGTAAAATCAA
GCACAGACTTAATTCAGGGTAAT
Found at i:11597 original size:18 final size:18
Alignment explanation
Indices: 11574--11610 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
11564 CTCCTCTTGC
*
11574 ATGAAAACACTTCTTTTT
1 ATGAAAACAATTCTTTTT
*
11592 ATGAAAACAATTTTTTTT
1 ATGAAAACAATTCTTTTT
11610 A
1 A
11611 ACTACCCTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.38, C:0.11, G:0.05, T:0.46
Consensus pattern (18 bp):
ATGAAAACAATTCTTTTT
Found at i:12282 original size:20 final size:19
Alignment explanation
Indices: 12251--12291 Score: 64
Period size: 20 Copynumber: 2.1 Consensus size: 19
12241 AACTAATTCA
12251 AATCAAAGAATAAGCAATC
1 AATCAAAGAATAAGCAATC
*
12270 AATCAAAGCAATAATCAATC
1 AATCAAAG-AATAAGCAATC
12290 AA
1 AA
12292 AGCAAAACAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.59, C:0.17, G:0.07, T:0.17
Consensus pattern (19 bp):
AATCAAAGAATAAGCAATC
Found at i:12287 original size:16 final size:15
Alignment explanation
Indices: 12266--12312 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 15
12256 AAGAATAAGC
12266 AATCAATCAAAGCAA
1 AATCAATCAAAGCAA
12281 TAATCAATCAAAGCAA
1 -AATCAATCAAAGCAA
12297 AA-CAATGCAAAG-AA
1 AATCAAT-CAAAGCAA
12311 AA
1 AA
12313 AGTAAATGGA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
14 8 0.27
15 7 0.23
16 15 0.50
ACGTcount: A:0.62, C:0.17, G:0.09, T:0.13
Consensus pattern (15 bp):
AATCAATCAAAGCAA
Found at i:17393 original size:21 final size:22
Alignment explanation
Indices: 17351--17394 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
17341 TTTTCCGTTA
*
17351 TTTTCCTTTAATTAGTTGTAAT
1 TTTTCCTTTAATTAGATGTAAT
* *
17373 TTTTCTTTTAATTGGAT-TAAT
1 TTTTCCTTTAATTAGATGTAAT
17394 T
1 T
17395 GCTTATTTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.23, C:0.07, G:0.09, T:0.61
Consensus pattern (22 bp):
TTTTCCTTTAATTAGATGTAAT
Found at i:19664 original size:26 final size:26
Alignment explanation
Indices: 19613--19663 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 26
19603 AATTTTTTTT
19613 TCTTTTTTTTTAGAAAACGCAAAAAC
1 TCTTTTTTTTTAGAAAACGCAAAAAC
19639 TCTTTTTTTTTCCA-AAAACGCAAAA
1 TCTTTTTTTTT--AGAAAACGCAAAA
19664 CACAAAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
26 11 0.48
27 11 0.48
28 1 0.04
ACGTcount: A:0.37, C:0.18, G:0.06, T:0.39
Consensus pattern (26 bp):
TCTTTTTTTTTAGAAAACGCAAAAAC
Found at i:21477 original size:21 final size:21
Alignment explanation
Indices: 21415--21488 Score: 69
Period size: 21 Copynumber: 3.5 Consensus size: 21
21405 TTTTAGCTCA
* * * *
21415 ATCACTGGCCATAACCATGTC
1 ATCACCGGCCACAGCCATGCC
*
21436 ATCACCGGCCACAGCCGTGCC
1 ATCACCGGCCACAGCCATGCC
21457 ATCACCGGCCA-AGCCCATGCC
1 ATCACCGGCCACAG-CCATGCC
**
21478 AAGACCGGCCA
1 ATCACCGGCCA
21489 TCGTCGTGTC
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 2 0.05
21 42 0.95
ACGTcount: A:0.26, C:0.42, G:0.20, T:0.12
Consensus pattern (21 bp):
ATCACCGGCCACAGCCATGCC
Found at i:29293 original size:65 final size:65
Alignment explanation
Indices: 29103--29462 Score: 465
Period size: 66 Copynumber: 5.5 Consensus size: 65
29093 TCACCGAAAA
*** * * *
29103 GGTATTTTTGGAAAGAGAAAACCAAACCTAGATGTGAAAAATATGAAACTGACCCTTCGACCGAA
1 GGTATTTTTGGAAA-AGAAAATTGAACTTAGATGCG-AAAATATGAAACTGACCCTTCGACCGGA
29168 AG
64 AG
* * * *
29170 GGTAGTTTTGGGAAACAAAATTGAACTTAGATATG-GCAAATATGAAACTGACCCTTCGACCGGA
1 GGTATTTTTGGAAAAGAAAATTGAACTTAG--ATGCGAAAATATGAAACTGACCCTTCGACCGGA
29234 AG
64 AG
* * * *
29236 GGTATTTTTGGAAAACAAAATTGAACTTAGATGCGAAAAGATGAAGCTGACCCTTCGACCGAAAG
1 GGTATTTTTGGAAAAGAAAATTGAACTTAGATGCGAAAATATGAAACTGACCCTTCGACCGGAAG
* *
29301 GATATTTTTGGAAATAGAAAA-TGAACTTAGATGCG-AAATATGAAACTGACCTTTCGACCGGAA
1 GGTATTTTTGGAAA-AGAAAATTGAACTTAGATGCGAAAATATGAAACTGACCCTTCGACCGGAA
29364 G
65 G
* *
29365 GGTATTTTTGGACTATAGAAAATTGAACTTAGGTGCGAAAATATGAAACTGACCCTTCGACCGGA
1 GGTATTTTTGGA--AAAGAAAATTGAACTTAGATGCGAAAATATGAAACTGACCCTTCGACCGGA
29430 AG
64 AG
*
29432 GGTATTTTTGGAAAATAAAATTGAACTTAGA
1 GGTATTTTTGGAAAAGAAAATTGAACTTAGA
Statistics
Matches: 257, Mismatches: 28, Indels: 18
0.85 0.09 0.06
Matches are distributed among these distances:
64 39 0.15
65 76 0.30
66 86 0.33
67 53 0.21
68 3 0.01
ACGTcount: A:0.38, C:0.14, G:0.23, T:0.25
Consensus pattern (65 bp):
GGTATTTTTGGAAAAGAAAATTGAACTTAGATGCGAAAATATGAAACTGACCCTTCGACCGGAAG
Found at i:29296 original size:131 final size:129
Alignment explanation
Indices: 29103--29462 Score: 472
Period size: 131 Copynumber: 2.7 Consensus size: 129
29093 TCACCGAAAA
*** * *
29103 GGTATTTTTGGAAAGAGAAAACCAAACCTAGATGTGAAAAATATGAAACTGACCCTTCGACCGAA
1 GGTATTTTTGGAAA-AGAAAATTGAACTTAGATGCG-AAAATATGAAACTGACCCTTCGACCGAA
*
29168 AGGGTAGTTTTGGGAAACAAAATTGAACTTAGATATG-GCAAATATGAAACTGACCCTTCGACCG
64 AGGGTA-TTTTGGGAAATAAAATTGAACTTAGA-ATGCG-AAATATGAAACTGACCCTTCGACCG
29232 GAAG
126 GAAG
* * *
29236 GGTATTTTTGGAAAACAAAATTGAACTTAGATGCGAAAAGATGAAGCTGACCCTTCGACCGAAAG
1 GGTATTTTTGGAAAAGAAAATTGAACTTAGATGCGAAAATATGAAACTGACCCTTCGACCGAAAG
* * * *
29301 GATATTTTTGGAAATAGAAAATGAACTTAG-ATGCGAAATATGAAACTGACCTTTCGACCGGAAG
66 GGTATTTTGGGAAATA-AAATTGAACTTAGAATGCGAAATATGAAACTGACCCTTCGACCGGAAG
* * *
29365 GGTATTTTTGGACTATAGAAAATTGAACTTAGGTGCGAAAATATGAAACTGACCCTTCGACCGGA
1 GGTATTTTTGGA--AAAGAAAATTGAACTTAGATGCGAAAATATGAAACTGACCCTTCGACCGAA
*
29430 AGGGTATTTTTGGAAAATAAAATTGAACTTAGA
64 AGGGTA-TTTTGGGAAATAAAATTGAACTTAGA
Statistics
Matches: 198, Mismatches: 23, Indels: 13
0.85 0.10 0.06
Matches are distributed among these distances:
129 43 0.22
130 11 0.06
131 105 0.53
132 25 0.13
133 14 0.07
ACGTcount: A:0.38, C:0.14, G:0.23, T:0.25
Consensus pattern (129 bp):
GGTATTTTTGGAAAAGAAAATTGAACTTAGATGCGAAAATATGAAACTGACCCTTCGACCGAAAG
GGTATTTTGGGAAATAAAATTGAACTTAGAATGCGAAATATGAAACTGACCCTTCGACCGGAAG
Done.