Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016674.1 Corchorus olitorius cultivar O-4 contig16707, 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: 63013
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Found at i:1051 original size:24 final size:25
Alignment explanation
Indices: 1005--1055 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 25
995 ATTGGAGTAT
*
1005 TTATTTATCTTGTTGCTTAATTTTA
1 TTATTTATCTTGTTGATTAATTTTA
* *
1030 TTATTT-TCTTGTTTATTTATTTTA
1 TTATTTATCTTGTTGATTAATTTTA
1054 TT
1 TT
1056 GTTCACATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 17 0.74
25 6 0.26
ACGTcount: A:0.18, C:0.06, G:0.06, T:0.71
Consensus pattern (25 bp):
TTATTTATCTTGTTGATTAATTTTA
Found at i:5393 original size:30 final size:31
Alignment explanation
Indices: 5351--5431 Score: 91
Period size: 30 Copynumber: 2.7 Consensus size: 31
5341 TTGAGAAGTT
5351 TGGTAAGG-TTGTGAAAGTTGA-GAAAAAGAA
1 TGGTAAGGTTTGTGAAAGTTGAGGAAAAAG-A
* *
5381 TGGT-AGGTTTGTGAGAA-TTGAGGAAGATGA
1 TGGTAAGGTTTGTGA-AAGTTGAGGAAAAAGA
5411 TGGTAAGGTTTG-GAAAGTTGA
1 TGGTAAGGTTTGTGAAAGTTGA
5432 AAAGAAAAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
29 5 0.11
30 25 0.57
31 14 0.32
ACGTcount: A:0.35, C:0.00, G:0.37, T:0.28
Consensus pattern (31 bp):
TGGTAAGGTTTGTGAAAGTTGAGGAAAAAGA
Found at i:11132 original size:10 final size:10
Alignment explanation
Indices: 11113--11293 Score: 215
Period size: 10 Copynumber: 18.1 Consensus size: 10
11103 TATTTAATAT
11113 ATGATATTAA
1 ATGATATTAA
*
11123 ATGATCTTAA
1 ATGATATTAA
11133 ATGATATTAA
1 ATGATATTAA
11143 ATGATATTAA
1 ATGATATTAA
* *
11153 ACT-AAACTAA
1 A-TGATATTAA
11163 ATGATATTAA
1 ATGATATTAA
11173 ATGATATTAA
1 ATGATATTAA
*
11183 ACT-AAATTAA
1 A-TGATATTAA
* *
11193 ATAATCTTAA
1 ATGATATTAA
11203 ATGATATTAA
1 ATGATATTAA
11213 ATGATATTAA
1 ATGATATTAA
*
11223 TTGATATTAA
1 ATGATATTAA
*
11233 TTGATATTAA
1 ATGATATTAA
*
11243 TATCA-ATTAA
1 -ATGATATTAA
*
11253 ATGATCTTAA
1 ATGATATTAA
*
11263 ATGATCTTAA
1 ATGATATTAA
11273 ATGATATTAA
1 ATGATATTAA
11283 ATGATATTAA
1 ATGATATTAA
11293 A
1 A
11294 CTATTTAATA
Statistics
Matches: 148, Mismatches: 17, Indels: 12
0.84 0.10 0.07
Matches are distributed among these distances:
9 5 0.03
10 139 0.94
11 4 0.03
ACGTcount: A:0.49, C:0.04, G:0.08, T:0.39
Consensus pattern (10 bp):
ATGATATTAA
Found at i:16539 original size:22 final size:22
Alignment explanation
Indices: 16490--16539 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
16480 AAATATTACC
* **
16490 ATAATTATTTTTGGCAGCCATA
1 ATAATTATTTTTGCCAGAAATA
16512 ATAATTATTTTTGCCAAGAAATA
1 ATAATTATTTTTGCC-AGAAATA
16535 A-AATT
1 ATAATT
16540 TGGGAATAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 18 0.75
23 6 0.25
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.40
Consensus pattern (22 bp):
ATAATTATTTTTGCCAGAAATA
Found at i:23323 original size:13 final size:13
Alignment explanation
Indices: 23305--23336 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
23295 AGCAGCGCAA
23305 GGCTGCTGAGCAT
1 GGCTGCTGAGCAT
23318 GGCTGCTGAGCAT
1 GGCTGCTGAGCAT
23331 GGCTGC
1 GGCTGC
23337 ACCAGCACTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.12, C:0.25, G:0.41, T:0.22
Consensus pattern (13 bp):
GGCTGCTGAGCAT
Found at i:23857 original size:30 final size:29
Alignment explanation
Indices: 23814--23870 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 29
23804 TTAGGATTAG
23814 TTATTTATGCTTTAATTTTCAA-TTTCCT
1 TTATTTATGCTTTAATTTTCAAGTTTCCT
23842 TTATCTTATGTCTTTAATTTTCAAGTTTC
1 TTAT-TTATG-CTTTAATTTTCAAGTTTC
23871 ATTAATAAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 4 0.15
29 5 0.19
30 13 0.50
31 4 0.15
ACGTcount: A:0.21, C:0.14, G:0.05, T:0.60
Consensus pattern (29 bp):
TTATTTATGCTTTAATTTTCAAGTTTCCT
Found at i:25455 original size:19 final size:18
Alignment explanation
Indices: 25431--25466 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
25421 TGAAGACATA
25431 TTGAAGACAATTTGAAGAT
1 TTGAAGACAA-TTGAAGAT
*
25450 TTGAAGACCATTGAAGA
1 TTGAAGACAATTGAAGA
25467 ATTATTTCCA
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:0.08, G:0.22, T:0.28
Consensus pattern (18 bp):
TTGAAGACAATTGAAGAT
Found at i:45202 original size:13 final size:13
Alignment explanation
Indices: 45184--45248 Score: 78
Period size: 14 Copynumber: 4.8 Consensus size: 13
45174 TAAAGGGCGT
45184 TTTTCAAAAATGA
1 TTTTCAAAAATGA
45197 TTTTCAAGAAACTG-
1 TTTTCAA-AAA-TGA
*
45211 TTTTCAAGAAATAA
1 TTTTCAA-AAATGA
45225 TTTTCAAAAATGA
1 TTTTCAAAAATGA
45238 GTTTTCAAAAA
1 -TTTTCAAAAA
45249 GGTTTTGAGT
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
13 13 0.28
14 31 0.67
15 2 0.04
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.37
Consensus pattern (13 bp):
TTTTCAAAAATGA
Found at i:45502 original size:6 final size:6
Alignment explanation
Indices: 45491--45527 Score: 65
Period size: 6 Copynumber: 6.0 Consensus size: 6
45481 CGATGTGAAT
45491 AAAGAA AAAGAAA AAAGAA AAAGAA AAAGAA AAAGAA
1 AAAGAA AAAG-AA AAAGAA AAAGAA AAAGAA AAAGAA
45528 GAATGTTCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 24 0.80
7 6 0.20
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:45917 original size:18 final size:16
Alignment explanation
Indices: 45894--45948 Score: 65
Period size: 18 Copynumber: 3.2 Consensus size: 16
45884 TTGGTGAAGC
45894 AAAAAAAAAAGCAAAGA
1 AAAAAAAAAAG-AAAGA
*
45911 GAAAAAAAAAGAGAAAGC
1 -AAAAAAAAA-AGAAAGA
*
45929 AAAGAAAAAAGAAAGA
1 AAAAAAAAAAGAAAGA
45945 AAAA
1 AAAA
45949 TCAAAAGGAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
16 9 0.28
17 8 0.25
18 13 0.41
19 2 0.06
ACGTcount: A:0.80, C:0.04, G:0.16, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAAGAAAGA
Found at i:45927 original size:23 final size:22
Alignment explanation
Indices: 45894--45947 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
45884 TTGGTGAAGC
45894 AAAAAA-AAAAGCAAAGAGAAA
1 AAAAAAGAAAAGCAAAGAGAAA
45915 AAAAAAGAGAAAGCAAAGA-AAA
1 AAAAAAGA-AAAGCAAAGAGAAA
*
45937 AAGAAAGAAAA
1 AAAAAAGAAAA
45948 ATCAAAAGGA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
21 9 0.30
22 11 0.37
23 10 0.33
ACGTcount: A:0.80, C:0.04, G:0.17, T:0.00
Consensus pattern (22 bp):
AAAAAAGAAAAGCAAAGAGAAA
Found at i:45943 original size:11 final size:12
Alignment explanation
Indices: 45890--45948 Score: 61
Period size: 12 Copynumber: 5.1 Consensus size: 12
45880 GTGCTTGGTG
*
45890 AAGCAAAAAAAA
1 AAGCAAAGAAAA
45902 AAGCAAAGAGAAA
1 AAGCAAAGA-AAA
* *
45915 AA-AAAAG-AGA
1 AAGCAAAGAAAA
45925 AAGCAAAGAAAA
1 AAGCAAAGAAAA
45937 AAG-AAAGAAAA
1 AAGCAAAGAAAA
45948 A
1 A
45949 TCAAAAGGAA
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
10 4 0.10
11 13 0.33
12 17 0.44
13 5 0.13
ACGTcount: A:0.78, C:0.05, G:0.17, T:0.00
Consensus pattern (12 bp):
AAGCAAAGAAAA
Found at i:45955 original size:23 final size:23
Alignment explanation
Indices: 45899--45962 Score: 78
Period size: 23 Copynumber: 2.8 Consensus size: 23
45889 GAAGCAAAAA
45899 AAAAAGCAAAGAGAAAAAA-AAAG
1 AAAAAGCAAA-AGAAAAAAGAAAG
*
45922 AGAAAGC-AAAGAAAAAAGAAAG
1 AAAAAGCAAAAGAAAAAAGAAAG
* *
45944 AAAAATCAAAAGGAAAAAG
1 AAAAAGCAAAAGAAAAAAG
45963 GTTCAACCTG
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
21 8 0.23
22 11 0.31
23 16 0.46
ACGTcount: A:0.75, C:0.05, G:0.19, T:0.02
Consensus pattern (23 bp):
AAAAAGCAAAAGAAAAAAGAAAG
Found at i:46228 original size:87 final size:86
Alignment explanation
Indices: 46082--46250 Score: 293
Period size: 87 Copynumber: 2.0 Consensus size: 86
46072 ATGTTTGAAC
* * *
46082 ATTTCTTAAGGTGAGAAGTTGATCCAGAACCGTCAATTGAGTTGGGAATATCAATGCATGATCAA
1 ATTTCTTAAGGTGAGAAGCTGATCCAGAACCATCAATTGAGTTGGGAATATCAATGCATGACCAA
46147 ATTGGAGGAAGATTTGGGAAAT
66 ATTGGAGG-AGATTTGGGAAAT
*
46169 ATTTCTTAAGGTGGGAAGCTGATCCAGAACCATCAATTGAGTTGGGAATATCAATGCATGACCAA
1 ATTTCTTAAGGTGAGAAGCTGATCCAGAACCATCAATTGAGTTGGGAATATCAATGCATGACCAA
46234 ATTGGAGGAGATTTGGG
66 ATTGGAGGAGATTTGGG
46251 GCATCAATCA
Statistics
Matches: 78, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
86 9 0.12
87 69 0.88
ACGTcount: A:0.33, C:0.12, G:0.27, T:0.28
Consensus pattern (86 bp):
ATTTCTTAAGGTGAGAAGCTGATCCAGAACCATCAATTGAGTTGGGAATATCAATGCATGACCAA
ATTGGAGGAGATTTGGGAAAT
Found at i:47084 original size:37 final size:37
Alignment explanation
Indices: 47043--47542 Score: 401
Period size: 37 Copynumber: 13.6 Consensus size: 37
47033 TTCAAGATTT
* *
47043 CTGTTTAGGTGTCTTATCAAATCCTTATTTAAGGTCC
1 CTGTTTAGGTGTCTTATCAAATCCTTGTTTAAGATCC
* * *
47080 CTGTTTAGGTGT-TTCATTAAAAT-CTTGTTCAAGATTC
1 CTGTTTAGGTGTCTT-A-TCAAATCCTTGTTTAAGATCC
*
47117 TTGTTTAGGTGTCTTATCAAATCCTTGTTTAAGATCC
1 CTGTTTAGGTGTCTTATCAAATCCTTGTTTAAGATCC
* * * *
47154 CTATTTAGGTGTCTTATTAAATCCTTTTTTTAAGGTCC
1 CTGTTTAGGTGTCTTATCAAATCC-TTGTTTAAGATCC
* * * * *
47192 CTGTTTAGCTGTCTCATCAAAACCTTGTTCAAGATTC
1 CTGTTTAGGTGTCTTATCAAATCCTTGTTTAAGATCC
* * * * * *
47229 CTATTTAGGTTTCTCATCAAATGCTTATTTAAGGTCC
1 CTGTTTAGGTGTCTTATCAAATCCTTGTTTAAGATCC
* * * *
47266 CTTTTTAAGTGTC--ACCAAAAT-CTTGTTTAAAATCC
1 CTGTTTAGGTGTCTTATC-AAATCCTTGTTTAAGATCC
47301 CTGTTTAGGTGTC--ATCAAAAT-CTTGTTTAAGATCC
1 CTGTTTAGGTGTCTTATC-AAATCCTTGTTTAAGATCC
* * * *
47336 CTGTTTAGGTTTCTTATCAAATTCTTATTTAAGGTCC
1 CTGTTTAGGTGTCTTATCAAATCCTTGTTTAAGATCC
* * * * *
47373 CTATTTAGGTATCTCATCAAAAT-CTTGTTCAAGATTC
1 CTGTTTAGGTGTCTTATC-AAATCCTTGTTTAAGATCC
* * * **
47410 CTGTTTAGGTTTCTTATTAAATCCTTATTTAAGGA-AA
1 CTGTTTAGGTGTCTTATCAAATCCTTGTTTAA-GATCC
* * * *
47447 CTGTTTAGGTGTCTCATAAAAAT-CTTGTTCAAGATTC
1 CTGTTTAGGTGTCTTAT-CAAATCCTTGTTTAAGATCC
* * * *
47484 CTGTTTAGGTTTCTTATCAAATCCTTATTTAAGGTAC
1 CTGTTTAGGTGTCTTATCAAATCCTTGTTTAAGATCC
* *
47521 CAGTTTAGGTTTCTTATTCAAA
1 CTGTTTAGGTGTCTTA-TCAAA
47543 ATTCATGTTT
Statistics
Matches: 371, Mismatches: 76, Indels: 31
0.78 0.16 0.06
Matches are distributed among these distances:
35 56 0.15
36 25 0.07
37 238 0.64
38 52 0.14
ACGTcount: A:0.25, C:0.17, G:0.14, T:0.44
Consensus pattern (37 bp):
CTGTTTAGGTGTCTTATCAAATCCTTGTTTAAGATCC
Found at i:47122 original size:74 final size:74
Alignment explanation
Indices: 47033--47530 Score: 456
Period size: 74 Copynumber: 6.8 Consensus size: 74
47023 CGAAACCTTA
*
47033 TTCAAGATTTCTGTTTAGGTGTCTTATCAAATCCTTATTTAAGGTCCCTGTTTAGGTGTTTCATT
1 TTCAAGATTCCTGTTTAGGTGTCTTATCAAATCCTTATTTAAGGTCCCTGTTTAGGTGTTTCATT
47098 AAAATCTTG
66 AAAATCTTG
* * * *
47107 TTCAAGATTCTTGTTTAGGTGTCTTATCAAATCCTTGTTTAAGATCCCTATTTAGGTGTCTT-AT
1 TTCAAGATTCCTGTTTAGGTGTCTTATCAAATCCTTATTTAAGGTCCCTGTTTAGGTGT-TTCAT
*
47171 T-AAATCCTTTT
65 TAAAAT-C-TTG
* * * * * * * * * * *
47182 TTTAAGGTCCCTGTTTAGCTGTCTCATCAAAACCTTGTTCAAGATTCCTATTTAGGT-TTCTCA-
1 TTCAAGATTCCTGTTTAGGTGTCTTATCAAATCCTTATTTAAGGTCCCTGTTTAGGTGTT-TCAT
* *
47245 TCAAATGCTTA
65 TAAAAT-CTTG
* * * * * * * **
47256 TTTAAGGTCCCTTTTTAAGTGTC--ACCAAAAT-CTTGTTTAAAATCCCTGTTTAGGTG--TCAT
1 TTCAAGATTCCTGTTTAGGTGTCTTATC-AAATCCTTATTTAAGGTCCCTGTTTAGGTGTTTCAT
*
47316 CAAAATCTTG
65 TAAAATCTTG
* * * * * * * *
47326 TTTAAGATCCCTGTTTAGGTTTCTTATCAAATTCTTATTTAAGGTCCCTATTTAGGTATCTCATC
1 TTCAAGATTCCTGTTTAGGTGTCTTATCAAATCCTTATTTAAGGTCCCTGTTTAGGTGTTTCATT
47391 AAAATCTTG
66 AAAATCTTG
* * *** * *
47400 TTCAAGATTCCTGTTTAGGTTTCTTATTAAATCCTTATTTAAGGAAACTGTTTAGGTGTCTCATA
1 TTCAAGATTCCTGTTTAGGTGTCTTATCAAATCCTTATTTAAGGTCCCTGTTTAGGTGTTTCATT
47465 AAAATCTTG
66 AAAATCTTG
* * *
47474 TTCAAGATTCCTGTTTAGGTTTCTTATCAAATCCTTATTTAAGGTACCAGTTTAGGT
1 TTCAAGATTCCTGTTTAGGTGTCTTATCAAATCCTTATTTAAGGTCCCTGTTTAGGT
47531 TTCTTATTCA
Statistics
Matches: 357, Mismatches: 53, Indels: 28
0.82 0.12 0.06
Matches are distributed among these distances:
70 25 0.07
71 8 0.02
72 44 0.12
73 8 0.02
74 214 0.60
75 58 0.16
ACGTcount: A:0.25, C:0.17, G:0.14, T:0.44
Consensus pattern (74 bp):
TTCAAGATTCCTGTTTAGGTGTCTTATCAAATCCTTATTTAAGGTCCCTGTTTAGGTGTTTCATT
AAAATCTTG
Found at i:47236 original size:112 final size:110
Alignment explanation
Indices: 47046--47396 Score: 404
Period size: 112 Copynumber: 3.2 Consensus size: 110
47036 AAGATTTCTG
* * *
47046 TTTAGGTGTCTTATCAAATCCTTATTTAAGGTCCCTGTTTAGGTGTTTCATTAAAATCTTGTTCA
1 TTTAGGTGTCTTATAAAATCCTTATTTAAGGTCCCTGTTTA-GTGTCTCATCAAAATCTTGTTCA
* * * *
47111 AGATTCTTGTTTAGGTGTCTTATCAAATCCTTGTTTAAGATCCCTA
65 AGATTCCTGTTTAGGTTTCTTATCAAATCCTTATTTAAGGTCCCTA
* * *
47157 TTTAGGTGTCTTATTAAATCCTTTTTTTAAGGTCCCTGTTTAGCTGTCTCATCAAAACCTTGTTC
1 TTTAGGTGTCTTATAAAATCC-TTATTTAAGGTCCCTGTTTAG-TGTCTCATCAAAATCTTGTTC
* * * *
47222 AAGATTCCTATTTAGGTTTCTCATCAAATGCTTATTTAAGGTCCCTT
64 AAGATTCCTGTTTAGGTTTCTTATCAAATCCTTATTTAAGGTCCCTA
* * * ** * *
47269 TTTAAGTGTC--ACCAAAAT-CTTGTTTAAAATCCCTGTTTAG-GTGTCATCAAAATCTTGTTTA
1 TTTAGGTGTCTTA-TAAAATCCTTATTTAAGGTCCCTGTTTAGTGTCTCATCAAAATCTTGTTCA
* *
47330 AGATCCCTGTTTAGGTTTCTTATCAAATTCTTATTTAAGGTCCCTA
65 AGATTCCTGTTTAGGTTTCTTATCAAATCCTTATTTAAGGTCCCTA
* *
47376 TTTAGGTATCTCATCAAAATC
1 TTTAGGTGTCTTAT-AAAATC
47397 TTGTTCAAGA
Statistics
Matches: 203, Mismatches: 30, Indels: 15
0.82 0.12 0.06
Matches are distributed among these distances:
107 67 0.33
109 24 0.12
110 2 0.01
111 25 0.12
112 85 0.42
ACGTcount: A:0.25, C:0.18, G:0.14, T:0.44
Consensus pattern (110 bp):
TTTAGGTGTCTTATAAAATCCTTATTTAAGGTCCCTGTTTAGTGTCTCATCAAAATCTTGTTCAA
GATTCCTGTTTAGGTTTCTTATCAAATCCTTATTTAAGGTCCCTA
Found at i:47302 original size:35 final size:35
Alignment explanation
Indices: 47263--47342 Score: 124
Period size: 35 Copynumber: 2.3 Consensus size: 35
47253 TTATTTAAGG
*
47263 TCCCTTTTTAAGTGTCACCAAAATCTTGTTTAAAA
1 TCCCTGTTTAAGTGTCACCAAAATCTTGTTTAAAA
* * *
47298 TCCCTGTTTAGGTGTCATCAAAATCTTGTTTAAGA
1 TCCCTGTTTAAGTGTCACCAAAATCTTGTTTAAAA
47333 TCCCTGTTTA
1 TCCCTGTTTA
47343 GGTTTCTTAT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 41 1.00
ACGTcount: A:0.26, C:0.20, G:0.12, T:0.41
Consensus pattern (35 bp):
TCCCTGTTTAAGTGTCACCAAAATCTTGTTTAAAA
Found at i:47644 original size:54 final size:54
Alignment explanation
Indices: 47562--47917 Score: 380
Period size: 54 Copynumber: 6.6 Consensus size: 54
47552 TAGGTGTTTC
* **
47562 AGATGACCCGGTGTAGTCTTCCATAGAAGTTTTCAGAGATCTAAGTTGATCTTA
1 AGATGACCCAGTGCGGTCTTCCATAGAAGTTTTCAGAGATCTAAGTTGATCTTA
*
47616 AGATGACCCAGTGCGGTCTTCCATAGAAGTTTTCAGAGATCTAAATTGATCTTA
1 AGATGACCCAGTGCGGTCTTCCATAGAAGTTTTCAGAGATCTAAGTTGATCTTA
* * * * * * *
47670 AGATGGCCTAGTGTGGTCTTTCATGGAAGTTTTTAGAGATCTAAGTTGATCTTC
1 AGATGACCCAGTGCGGTCTTCCATAGAAGTTTTCAGAGATCTAAGTTGATCTTA
* * *
47724 AGATAACCCAGTGCGGTCTTTCATAGAAGTTTTCAGAGATCTAAGTTGATCTTC
1 AGATGACCCAGTGCGGTCTTCCATAGAAGTTTTCAGAGATCTAAGTTGATCTTA
* * * * *** *
47778 AGATGACCCAATGTGGTCTTCCATAGAGGTTTTCAGAGATTTTTTTTTATCTTA
1 AGATGACCCAGTGCGGTCTTCCATAGAAGTTTTCAGAGATCTAAGTTGATCTTA
* * * * *
47832 AGATGATCTAGTGCGGTCATTTCA-AAAAGTTTTC-GAGGATC-AGAGTTGATCCT-
1 AGATGACCCAGTGCGGTC-TTCCATAGAAGTTTTCAGA-GATCTA-AGTTGATCTTA
* *
47885 AGATGATCCAGTGCGGTTATTCCA-AGAAGTTTT
1 AGATGACCCAGTGCGG-TCTTCCATAGAAGTTTT
47918 TAATGATCCA
Statistics
Matches: 252, Mismatches: 46, Indels: 9
0.82 0.15 0.03
Matches are distributed among these distances:
53 29 0.12
54 219 0.87
55 4 0.02
ACGTcount: A:0.27, C:0.16, G:0.22, T:0.35
Consensus pattern (54 bp):
AGATGACCCAGTGCGGTCTTCCATAGAAGTTTTCAGAGATCTAAGTTGATCTTA
Found at i:47832 original size:162 final size:163
Alignment explanation
Indices: 47559--47855 Score: 434
Period size: 162 Copynumber: 1.8 Consensus size: 163
47549 GTTTAGGTGT
* * *
47559 TTCAGATGACCCGGTGTAGTCTTCCATAGAAGTTTTCAGAGATCTAAGTTGATCTTAAGATGACC
1 TTCAGATAACCCAGTGCAGTCTTCCATAGAAGTTTTCAGAGATCTAAGTTGATCTTAAGATGACC
* * *
47624 CAGTGCGGTCTTCCATAGAAGTTTTCAGAGATCTAAATTGATCTTAAGATGGCCTAGTGTGGTC-
66 CAATGCGGTCTTCCATAGAAGTTTTCAGAGATCTAAATTGATCTTAAGATGACCTAGTGCGGTCA
47688 TTTCATGGAAGTTTTTAGAGATCTAAGTTGATC
131 TTTCATGGAAGTTTTTAGAGATCTAAGTTGATC
* * *
47721 TTCAGATAACCCAGTGCGGTCTTTCATAGAAGTTTTCAGAGATCTAAGTTGATCTTCAGATGACC
1 TTCAGATAACCCAGTGCAGTCTTCCATAGAAGTTTTCAGAGATCTAAGTTGATCTTAAGATGACC
* * * *** * *
47786 CAATGTGGTCTTCCATAGAGGTTTTCAGAGATTTTTTTTTATCTTAAGATGATCTAGTGCGGTCA
66 CAATGCGGTCTTCCATAGAAGTTTTCAGAGATCTAAATTGATCTTAAGATGACCTAGTGCGGTCA
47851 TTTCA
131 TTTCA
47856 AAAAGTTTTC
Statistics
Matches: 117, Mismatches: 17, Indels: 1
0.87 0.13 0.01
Matches are distributed among these distances:
162 112 0.96
163 5 0.04
ACGTcount: A:0.26, C:0.16, G:0.22, T:0.36
Consensus pattern (163 bp):
TTCAGATAACCCAGTGCAGTCTTCCATAGAAGTTTTCAGAGATCTAAGTTGATCTTAAGATGACC
CAATGCGGTCTTCCATAGAAGTTTTCAGAGATCTAAATTGATCTTAAGATGACCTAGTGCGGTCA
TTTCATGGAAGTTTTTAGAGATCTAAGTTGATC
Found at i:47881 original size:162 final size:162
Alignment explanation
Indices: 47559--47917 Score: 433
Period size: 162 Copynumber: 2.2 Consensus size: 162
47549 GTTTAGGTGT
* ** *
47559 TTCAGATGACCCGGTGTAGTCTTCCATAGAAGTTTTCAGAGATCTAAGTTGATCTTAAGATGACC
1 TTCAGATGACCCAGTGCGGTCTTTCATAGAAGTTTTCAGAGATCTAAGTTGATCTTAAGATGACC
* * *
47624 CAGTGCGGTCTTCCATAGAAGTTTTCAGAGATCTAAATTGATCTTAAGATGGCCTAGTGTGGTCT
66 CAATGCGGTCTTCCATAGAAGTTTTCAGAGATCTAAATTGATCTTAAGATGACCTAGTGCGGTCT
** *
47689 TTCATGGAAGTTTTTAGAGATCTAAGTTGATC
131 TTCATAAAAGTTTTGAGAGATCTAAGTTGATC
* *
47721 TTCAGATAACCCAGTGCGGTCTTTCATAGAAGTTTTCAGAGATCTAAGTTGATCTTCAGATGACC
1 TTCAGATGACCCAGTGCGGTCTTTCATAGAAGTTTTCAGAGATCTAAGTTGATCTTAAGATGACC
* * * *** * *
47786 CAATGTGGTCTTCCATAGAGGTTTTCAGAGATTTTTTTTTATCTTAAGATGATCTAGTGCGGTCA
66 CAATGCGGTCTTCCATAGAAGTTTTCAGAGATCTAAATTGATCTTAAGATGACCTAGTGCGGTC-
47851 TTTCA-AAAAGTTTTCGAG-GATC-AGAGTTGATC
130 TTTCATAAAAGTTTT-GAGAGATCTA-AGTTGATC
* *
47883 CT-AGATGATCCAGTGCGGT-TATTCCA-AGAAGTTTT
1 TTCAGATGACCCAGTGCGGTCT-TT-CATAGAAGTTTT
47918 TAATGATCCA
Statistics
Matches: 169, Mismatches: 23, Indels: 11
0.83 0.11 0.05
Matches are distributed among these distances:
160 1 0.01
161 27 0.16
162 134 0.79
163 7 0.04
ACGTcount: A:0.26, C:0.16, G:0.22, T:0.35
Consensus pattern (162 bp):
TTCAGATGACCCAGTGCGGTCTTTCATAGAAGTTTTCAGAGATCTAAGTTGATCTTAAGATGACC
CAATGCGGTCTTCCATAGAAGTTTTCAGAGATCTAAATTGATCTTAAGATGACCTAGTGCGGTCT
TTCATAAAAGTTTTGAGAGATCTAAGTTGATC
Found at i:47957 original size:33 final size:33
Alignment explanation
Indices: 47886--47958 Score: 83
Period size: 33 Copynumber: 2.2 Consensus size: 33
47876 GTTGATCCTA
* * *
47886 GATGATCCAGTGCGGTTATTCCAAGAAGTTTTT
1 GATGATCCAGTGCGGTCATTACAAGAAGTTTTC
* * * *
47919 AATGATCCAGTGTGGTCGTTACAAGCAGTTTTC
1 GATGATCCAGTGCGGTCATTACAAGAAGTTTTC
47952 GATGATC
1 GATGATC
47959 AGAGTTGATC
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.34
Consensus pattern (33 bp):
GATGATCCAGTGCGGTCATTACAAGAAGTTTTC
Found at i:48009 original size:54 final size:55
Alignment explanation
Indices: 47921--48069 Score: 210
Period size: 54 Copynumber: 2.7 Consensus size: 55
47911 AAGTTTTTAA
* * *
47921 TGATCCAGTGTGGTCGTTACAAGCAGTTTTCGATGATCAGAGTTGATCT-TCAAT
1 TGATCCAGTGCGGTCGTTACAAGAAGTTTTCGATGATCAGAGTTGATCTCTAAAT
* * *
47975 TGATCCAGTGCGGTCATTTCAAGAAGTTTACGATGATCAGAGTTGATCTCTAAAT
1 TGATCCAGTGCGGTCGTTACAAGAAGTTTTCGATGATCAGAGTTGATCTCTAAAT
* *
48030 TGATCCAGTGCGGTCGTTCCAAGAAAGTTTTCCATGATCA
1 TGATCCAGTGCGGTCGTTACAAG-AAGTTTTCGATGATCA
48070 AGGTTGAATT
Statistics
Matches: 83, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
54 44 0.53
55 25 0.30
56 14 0.17
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.33
Consensus pattern (55 bp):
TGATCCAGTGCGGTCGTTACAAGAAGTTTTCGATGATCAGAGTTGATCTCTAAAT
Found at i:48096 original size:55 final size:54
Alignment explanation
Indices: 47917--48085 Score: 200
Period size: 54 Copynumber: 3.1 Consensus size: 54
47907 CAAGAAGTTT
* *
47917 TTAA-TGATCCAGTGTGGTCGTTACAAGCAGTTTTCGATGATCAGAGTTGA-TC
1 TTAATTGATCCAGTGCGGTCGTTACAAGAAGTTTTCGATGATCAGAGTTGATTC
* * *
47969 TTCAATTGATCCAGTGCGGTCATTTCAAGAAGTTTACGATGATCAGAGTTGATCTC
1 TT-AATTGATCCAGTGCGGTCGTTACAAGAAGTTTTCGATGATCAGAGTTGAT-TC
* * *
48025 TAAATTGATCCAGTGCGGTCGTTCCAAGAAAGTTTTCCATGATCA-AGGTTGAATTC
1 TTAATTGATCCAGTGCGGTCGTTACAAG-AAGTTTTCGATGATCAGA-GTTG-ATTC
48081 TTAAT
1 TTAAT
48086 AATCTAGTGC
Statistics
Matches: 99, Mismatches: 11, Indels: 10
0.82 0.09 0.08
Matches are distributed among these distances:
52 2 0.02
53 2 0.02
54 41 0.41
55 25 0.25
56 27 0.27
57 2 0.02
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.34
Consensus pattern (54 bp):
TTAATTGATCCAGTGCGGTCGTTACAAGAAGTTTTCGATGATCAGAGTTGATTC
Found at i:48134 original size:7 final size:7
Alignment explanation
Indices: 48125--48390 Score: 424
Period size: 7 Copynumber: 38.0 Consensus size: 7
48115 ATTTTGCATT
*
48125 TCAAAAT
1 TCAAAAC
*
48132 TCAAAAT
1 TCAAAAC
*
48139 TCAAAAT
1 TCAAAAC
*
48146 TCAAAAT
1 TCAAAAC
48153 TCAAAAC
1 TCAAAAC
48160 TCAAAAC
1 TCAAAAC
48167 TCAAAAC
1 TCAAAAC
48174 TCAAAAC
1 TCAAAAC
*
48181 TCAAAGC
1 TCAAAAC
*
48188 TCAAACC
1 TCAAAAC
48195 TCAAAAC
1 TCAAAAC
48202 TCAAAAC
1 TCAAAAC
48209 TCAAAAC
1 TCAAAAC
48216 TCAAAAC
1 TCAAAAC
48223 TCAAAAC
1 TCAAAAC
48230 TCAAAAC
1 TCAAAAC
48237 TCAAAAC
1 TCAAAAC
48244 TCAAAAC
1 TCAAAAC
48251 TCAAAAC
1 TCAAAAC
48258 TCAAAAC
1 TCAAAAC
48265 TCAAAAC
1 TCAAAAC
48272 TCAAAAC
1 TCAAAAC
48279 TCAAAAC
1 TCAAAAC
48286 TCAAAAC
1 TCAAAAC
48293 TCAAAAC
1 TCAAAAC
48300 TCAAAAC
1 TCAAAAC
48307 TCAAAAC
1 TCAAAAC
48314 TCAAAAC
1 TCAAAAC
48321 TCAAAAC
1 TCAAAAC
48328 TCAAAAC
1 TCAAAAC
*
48335 TCAAAAT
1 TCAAAAC
*
48342 TCAAAAT
1 TCAAAAC
48349 TCAAAAC
1 TCAAAAC
*
48356 TCAAAAT
1 TCAAAAC
*
48363 TCAAAAT
1 TCAAAAC
*
48370 TCAAAAT
1 TCAAAAC
*
48377 TCAAAAT
1 TCAAAAC
48384 TCAAAAC
1 TCAAAAC
48391 CTGCATTTCA
Statistics
Matches: 251, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 251 1.00
ACGTcount: A:0.56, C:0.25, G:0.00, T:0.18
Consensus pattern (7 bp):
TCAAAAC
Found at i:51562 original size:19 final size:19
Alignment explanation
Indices: 51538--51597 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 19
51528 ATCACATCAC
51538 ACACATGGGTACTCTCTCA
1 ACACATGGGTACTCTCTCA
*** *
51557 ACACAT-AAAAGTC-C-CAA
1 ACACATGGGTACTCTCTC-A
51574 ACACATGGGTACTCTCTCA
1 ACACATGGGTACTCTCTCA
51593 ACACA
1 ACACA
51598 CAAAATGGTC
Statistics
Matches: 29, Mismatches: 8, Indels: 8
0.64 0.18 0.18
Matches are distributed among these distances:
16 1 0.03
17 8 0.28
18 6 0.21
19 13 0.45
20 1 0.03
ACGTcount: A:0.37, C:0.32, G:0.12, T:0.20
Consensus pattern (19 bp):
ACACATGGGTACTCTCTCA
Found at i:51629 original size:38 final size:38
Alignment explanation
Indices: 51538--51619 Score: 141
Period size: 36 Copynumber: 2.2 Consensus size: 38
51528 ATCACATCAC
*
51538 ACACATGGGTACTCTCTCAACACATAAAA--GTCCCAA
1 ACACATGGGTACTCTCTCAACACACAAAATGGTCCCAA
51574 ACACATGGGTACTCTCTCAACACACAAAATGGTCCCAA
1 ACACATGGGTACTCTCTCAACACACAAAATGGTCCCAA
51612 ACACATGG
1 ACACATGG
51620 ACCATCTCTC
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
36 28 0.65
38 15 0.35
ACGTcount: A:0.38, C:0.30, G:0.13, T:0.18
Consensus pattern (38 bp):
ACACATGGGTACTCTCTCAACACACAAAATGGTCCCAA
Found at i:53572 original size:25 final size:23
Alignment explanation
Indices: 53504--53572 Score: 68
Period size: 25 Copynumber: 2.8 Consensus size: 23
53494 CCTAAAAGAA
53504 AAAAAGCAAAAAAAAAAAATCTGC
1 AAAAAGCAAAAAAAAAAAATCT-C
* *
53528 ATAAAAGCAAAACAACAAAATCAT-
1 A-AAAAGCAAAAAAAAAAAATC-TC
53552 AAAAAGACAAAAAAGAAAAAA
1 AAAAAG-CAAAAAA-AAAAAA
53573 AGATATGCCA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
23 5 0.14
24 8 0.22
25 23 0.62
26 1 0.03
ACGTcount: A:0.74, C:0.12, G:0.07, T:0.07
Consensus pattern (23 bp):
AAAAAGCAAAAAAAAAAAATCTC
Done.