Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016607.1 Corchorus olitorius cultivar O-4 contig16640, 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: 85115
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:123 original size:6 final size:7
Alignment explanation
Indices: 111--141 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
101 GTTTTTTTTT
111 CTAAACC
1 CTAAACC
118 CT-AACC
1 CTAAACC
124 CTAAACC
1 CTAAACC
131 CTAAACC
1 CTAAACC
138 CTAA
1 CTAA
142 TTATTAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.26
7 17 0.74
ACGTcount: A:0.42, C:0.42, G:0.00, T:0.16
Consensus pattern (7 bp):
CTAAACC
Found at i:129 original size:13 final size:14
Alignment explanation
Indices: 111--141 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
101 GTTTTTTTTT
111 CTAAACCCT-AACC
1 CTAAACCCTAAACC
124 CTAAACCCTAAACC
1 CTAAACCCTAAACC
138 CTAA
1 CTAA
142 TTATTAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.53
14 8 0.47
ACGTcount: A:0.42, C:0.42, G:0.00, T:0.16
Consensus pattern (14 bp):
CTAAACCCTAAACC
Found at i:366 original size:3 final size:3
Alignment explanation
Indices: 350--405 Score: 94
Period size: 3 Copynumber: 18.3 Consensus size: 3
340 TTAATTAATA
*
350 ATT AGTT ATC ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
396 ATT ATT ATT A
1 ATT ATT ATT A
406 ATTAGTTAAT
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
3 47 0.94
4 3 0.06
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:1168 original size:13 final size:13
Alignment explanation
Indices: 1150--1174 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1140 TTGATTTAGA
1150 AGAAGTGCTTTTG
1 AGAAGTGCTTTTG
1163 AGAAGTGCTTTT
1 AGAAGTGCTTTT
1175 TAAAATTTGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.08, G:0.28, T:0.40
Consensus pattern (13 bp):
AGAAGTGCTTTTG
Found at i:1915 original size:37 final size:37
Alignment explanation
Indices: 1872--1942 Score: 142
Period size: 37 Copynumber: 1.9 Consensus size: 37
1862 AAATGAACTT
1872 GGGCAAATAAAGATAAACAAGTTTTAAAAGTTGTTAG
1 GGGCAAATAAAGATAAACAAGTTTTAAAAGTTGTTAG
1909 GGGCAAATAAAGATAAACAAGTTTTAAAAGTTGT
1 GGGCAAATAAAGATAAACAAGTTTTAAAAGTTGT
1943 AGAGAAATAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.46, C:0.06, G:0.21, T:0.27
Consensus pattern (37 bp):
GGGCAAATAAAGATAAACAAGTTTTAAAAGTTGTTAG
Found at i:2189 original size:32 final size:32
Alignment explanation
Indices: 2146--2213 Score: 100
Period size: 32 Copynumber: 2.1 Consensus size: 32
2136 TCAGCTGGGT
* *
2146 TCGGGTCATACGGGTTTCAAGTCATTCAGGTC
1 TCGGATCATACGAGTTTCAAGTCATTCAGGTC
**
2178 TCGGATCATACGAGTTTCTGGTCATTCAGGTC
1 TCGGATCATACGAGTTTCAAGTCATTCAGGTC
2210 TCGG
1 TCGG
2214 GTTTGGCGGG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.18, C:0.22, G:0.28, T:0.32
Consensus pattern (32 bp):
TCGGATCATACGAGTTTCAAGTCATTCAGGTC
Found at i:6187 original size:29 final size:29
Alignment explanation
Indices: 6145--6232 Score: 97
Period size: 31 Copynumber: 3.0 Consensus size: 29
6135 AATTCGATGG
*
6145 GGTTTAGTAATAAATTGAGCAACTTTAAA
1 GGTTTAGTACTAAATTGAGCAACTTTAAA
* *
6174 GGTTTGGTACTAAATTGAGCATTTCTTTAAA
1 GGTTTAGTACTAAATTGAGCA--ACTTTAAA
** *
6205 CATTTAGTACTAAATTGAGTAA-TTTAAA
1 GGTTTAGTACTAAATTGAGCAACTTTAAA
6233 TCCACGTAGG
Statistics
Matches: 49, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
28 6 0.12
29 19 0.39
31 24 0.49
ACGTcount: A:0.38, C:0.08, G:0.16, T:0.39
Consensus pattern (29 bp):
GGTTTAGTACTAAATTGAGCAACTTTAAA
Found at i:7054 original size:52 final size:52
Alignment explanation
Indices: 6996--7125 Score: 199
Period size: 52 Copynumber: 2.5 Consensus size: 52
6986 AATGCTGTTA
* *
6996 GATGGGAACTTTCCCATTTTGAAAATTGA-CTAAATTGAACACTTTGAAAACT
1 GATGGGAACTTTCCCAATTTGAAAA-AGAGCTAAATTGAACACTTTGAAAACT
* *
7048 TATGGGAACTTTCCCAATTTGAAAAAGAGCTAAATTGAATACTTTGAAAACT
1 GATGGGAACTTTCCCAATTTGAAAAAGAGCTAAATTGAACACTTTGAAAACT
*
7100 GATGGGAACTTTCCCAATATGAAAAA
1 GATGGGAACTTTCCCAATTTGAAAAA
7126 CTTTGAAAGA
Statistics
Matches: 71, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
51 2 0.03
52 69 0.97
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.30
Consensus pattern (52 bp):
GATGGGAACTTTCCCAATTTGAAAAAGAGCTAAATTGAACACTTTGAAAACT
Found at i:11096 original size:8 final size:8
Alignment explanation
Indices: 10908--11731 Score: 247
Period size: 8 Copynumber: 108.9 Consensus size: 8
10898 CATTTTGAAA
10908 TGAA-AAT
1 TGAAGAAT
*
10915 TGAAGTAT
1 TGAAGAAT
*
10923 CGAAGAAT
1 TGAAGAAT
*
10931 TGAATAAT
1 TGAAGAAT
10939 TGAA-ACAT
1 TGAAGA-AT
*
10947 TGAATAAT
1 TGAAGAAT
*
10955 TGAGGAAT
1 TGAAGAAT
10963 TGAA-ACAT
1 TGAAGA-AT
* *
10971 GGAATAAT
1 TGAAGAAT
*
10979 TGAATAAT
1 TGAAGAAT
*
10987 TGAATAAT
1 TGAAGAAT
*
10995 T-AAAAAT
1 TGAAGAAT
*
11002 TGAATAAT
1 TGAAGAAT
11010 TGAAGAA-
1 TGAAGAAT
* ** *
11017 AGACCACCT
1 TGAAGA-AT
* **
11026 TGGATCAT
1 TGAAGAAT
11034 TGAAGTAAAT
1 TGAAG--AAT
*
11044 TGAAGCAT
1 TGAAGAAT
*
11052 TGAATAAT
1 TGAAGAAT
*
11060 TAAAGAAT
1 TGAAGAAT
*
11068 TGAAGCAT
1 TGAAGAAT
*
11076 TGAATAAT
1 TGAAGAAT
11084 TGAAGAAT
1 TGAAGAAT
11092 TGAAGAA-
1 TGAAGAAT
* * **
11099 -AAACCACCC
1 TGAA-GA-AT
* **
11108 TGGATCAT
1 TGAAGAAT
*
11116 TGAAGTGAAC
1 TGAA--GAAT
*
11126 TGAAGCAT
1 TGAAGAAT
11134 TG-A-AAT
1 TGAAGAAT
** * *
11140 CAAAGCAC
1 TGAAGAAT
11148 TGAAGAAT
1 TGAAGAAT
11156 TG-A-AAT
1 TGAAGAAT
*
11162 TGAAGGAT
1 TGAAGAAT
11170 TGAAGAAT
1 TGAAGAAT
*
11178 CG-A-AAT
1 TGAAGAAT
*
11184 TGAAGAGT
1 TGAAGAAT
11192 TG-A-AAT
1 TGAAGAAT
*
11198 TGAAGCAT
1 TGAAGAAT
*
11206 TGGAGAAT
1 TGAAGAAT
11214 TGAAG--T
1 TGAAGAAT
*
11220 TGAAGCAT
1 TGAAGAAT
*
11228 TGACA-TAT
1 TGA-AGAAT
11236 TG-A-AAT
1 TGAAGAAT
11242 TGAA-ACATT
1 TGAAGA-A-T
11251 TGAAGAAT
1 TGAAGAAT
11259 TG-A-AAT
1 TGAAGAAT
* *
11265 TAAAGCAT
1 TGAAGAAT
11273 TGAAGAAT
1 TGAAGAAT
11281 TG-A-AAT
1 TGAAGAAT
11287 TGAA-ACAT
1 TGAAGA-AT
*
11295 TGGAGAAT
1 TGAAGAAT
11303 T-AA-AAT
1 TGAAGAAT
*
11309 TGAAGCAT
1 TGAAGAAT
11317 TGAAGAAT
1 TGAAGAAT
11325 TG-A-AAT
1 TGAAGAAT
* *
11331 TAAAGCAT
1 TGAAGAAT
*
11339 TGAAGTAT
1 TGAAGAAT
*
11347 T-AA-AAC
1 TGAAGAAT
*
11353 TGAAGCAT
1 TGAAGAAT
11361 TGAAGAAT
1 TGAAGAAT
11369 TG-A-AAT
1 TGAAGAAT
**
11375 TGAATCAT
1 TGAAGAAT
11383 TGAAGAAT
1 TGAAGAAT
11391 TG-A-AAT
1 TGAAGAAT
*
11397 TGAAGCAT
1 TGAAGAAT
*
11405 TGAGGAAT
1 TGAAGAAT
11413 TG-A-AAT
1 TGAAGAAT
**
11419 TGAATCAT
1 TGAAGAAT
11427 TGAAGAAT
1 TGAAGAAT
11435 TG-A-AAT
1 TGAAGAAT
*
11441 TGAAGCATT
1 TGAAG-AAT
*
11450 TGAGGAAT
1 TGAAGAAT
*
11458 T-TA-AAT
1 TGAAGAAT
**
11464 TGAATCAT
1 TGAAGAAT
11472 TGAAGAAT
1 TGAAGAAT
11480 TG-A-AAT
1 TGAAGAAT
*
11486 TGAAGCAT
1 TGAAGAAT
11494 TGAAGAA-
1 TGAAGAAT
* *
11501 TCAA-AGT
1 TGAAGAAT
*
11508 TGAAGCAT
1 TGAAGAAT
*
11516 TGACA-TAT
1 TGA-AGAAT
11524 T-AA-AAT
1 TGAAGAAT
11530 TGAA-ACATT
1 TGAAGA-A-T
11539 TGAAGAAT
1 TGAAGAAT
11547 TG-A-AAT
1 TGAAGAAT
* *
11553 TAAAGCAT
1 TGAAGAAT
11561 TGAAGAAT
1 TGAAGAAT
11569 TG-A-AAT
1 TGAAGAAT
11575 TGAA-ACAT
1 TGAAGA-AT
11583 TGAAGAAT
1 TGAAGAAT
11591 T-AA-AAT
1 TGAAGAAT
*
11597 TGAAGCAT
1 TGAAGAAT
*
11605 TGAAGAAC
1 TGAAGAAT
11613 TG-A-AAT
1 TGAAGAAT
* *
11619 TAAAGCAT
1 TGAAGAAT
*
11627 TGACA-TAT
1 TGA-AGAAT
11635 TG-A-AAT
1 TGAAGAAT
11641 TGAA-ACAT
1 TGAAGA-AT
11649 TGAAGAAT
1 TGAAGAAT
*
11657 TGAAAAAT
1 TGAAGAAT
11665 TG-A-AAT
1 TGAAGAAT
*
11671 TGAAGCAT
1 TGAAGAAT
*
11679 TAAAGAAT
1 TGAAGAAT
*
11687 TG-A-ATT
1 TGAAGAAT
*
11693 TGAAGGAT
1 TGAAGAAT
11701 TGAA-ATAT
1 TGAAGA-AT
11709 TG-AGTAAT
1 TGAAG-AAT
11717 TGAAGAAT
1 TGAAGAAT
11725 TGAAGAA
1 TGAAGAA
11732 AGACCACCCT
Statistics
Matches: 595, Mismatches: 139, Indels: 165
0.66 0.15 0.18
Matches are distributed among these distances:
6 111 0.19
7 78 0.13
8 361 0.61
9 30 0.05
10 15 0.03
ACGTcount: A:0.46, C:0.06, G:0.20, T:0.28
Consensus pattern (8 bp):
TGAAGAAT
Found at i:11105 original size:82 final size:78
Alignment explanation
Indices: 10998--11176 Score: 232
Period size: 82 Copynumber: 2.2 Consensus size: 78
10988 GAATAATTAA
* * * * *
10998 AAATTGAATAATTGAAGAAAGACCACCTTGGATCATTGAAGTAAATTGAAGCATTGAATAATTAA
1 AAATTGAAGAATTGAAGAAAAACCACCCTGGATCATTGAAGTAAACTGAAGCATTG-A-AATCAA
* *
11063 AGAATTGAAGCATTG
64 AGAACTGAAGAATTG
*
11078 AATAATTGAAGAATTGAAGAAAAACCACCCTGGATCATTGAAGTGAACTGAAGCATTGAAATCAA
1 -A-AATTGAAGAATTGAAGAAAAACCACCCTGGATCATTGAAGTAAACTGAAGCATTGAAATCAA
*
11143 AGCACTGAAGAATTG
64 AGAACTGAAGAATTG
*
11158 AAATTGAAGGATTGAAGAA
1 AAATTGAAGAATTGAAGAA
11177 TCGAAATTGA
Statistics
Matches: 87, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
78 17 0.20
79 1 0.01
80 17 0.20
81 2 0.02
82 50 0.57
ACGTcount: A:0.46, C:0.10, G:0.20, T:0.24
Consensus pattern (78 bp):
AAATTGAAGAATTGAAGAAAAACCACCCTGGATCATTGAAGTAAACTGAAGCATTGAAATCAAAG
AACTGAAGAATTG
Found at i:11172 original size:36 final size:36
Alignment explanation
Indices: 11126--11213 Score: 99
Period size: 36 Copynumber: 2.4 Consensus size: 36
11116 TGAAGTGAAC
11126 TGAAGCATTG-A-AATCAAAGCACTGAAGAATTGAAAT
1 TGAAGCATTGAAGAATCAAA--ACTGAAGAATTGAAAT
* * * *
11162 TGAAGGATTGAAGAATCGAAATTGAAGAGTTGAAAT
1 TGAAGCATTGAAGAATCAAAACTGAAGAATTGAAAT
*
11198 TGAAGCATTGGAGAAT
1 TGAAGCATTGAAGAAT
11214 TGAAGTTGAA
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
36 37 0.84
37 1 0.02
38 6 0.14
ACGTcount: A:0.44, C:0.07, G:0.25, T:0.24
Consensus pattern (36 bp):
TGAAGCATTGAAGAATCAAAACTGAAGAATTGAAAT
Found at i:11207 original size:22 final size:22
Alignment explanation
Indices: 11182--11931 Score: 605
Period size: 22 Copynumber: 33.6 Consensus size: 22
11172 AAGAATCGAA
*
11182 ATTGAAGAGTTGAAATTGAAGC
1 ATTGAAGAATTGAAATTGAAGC
* *
11204 ATTGGAGAATTGAAGTTGAAGC
1 ATTGAAGAATTGAAATTGAAGC
* *
11226 ATTGACA-TATTGAAATTGAAAC
1 ATTGA-AGAATTGAAATTGAAGC
*
11248 ATTTGAAGAATTGAAATTAAAGC
1 A-TTGAAGAATTGAAATTGAAGC
*
11271 ATTGAAGAATTGAAATTGAAAC
1 ATTGAAGAATTGAAATTGAAGC
* *
11293 ATTGGAGAATTAAAATTGAAGC
1 ATTGAAGAATTGAAATTGAAGC
*
11315 ATTGAAGAATTGAAATTAAAGC
1 ATTGAAGAATTGAAATTGAAGC
* * *
11337 ATTGAAGTATTAAAACTGAAGC
1 ATTGAAGAATTGAAATTGAAGC
*
11359 ATTGAAGAATTGAAATTGAATC
1 ATTGAAGAATTGAAATTGAAGC
11381 ATTGAAGAATTGAAATTGAAGC
1 ATTGAAGAATTGAAATTGAAGC
* *
11403 ATTGAGGAATTGAAATTGAATC
1 ATTGAAGAATTGAAATTGAAGC
11425 ATTGAAGAATTGAAATTGAAGC
1 ATTGAAGAATTGAAATTGAAGC
* * *
11447 ATTTGAGGAATTTAAATTGAATC
1 A-TTGAAGAATTGAAATTGAAGC
11470 ATTGAAGAATTGAAATTGAAGC
1 ATTGAAGAATTGAAATTGAAGC
*
11492 ATTGAAGAA-TCAAAGTTGAAGC
1 ATTGAAGAATTGAAA-TTGAAGC
* * *
11514 ATTGACA-TATTAAAATTGAAAC
1 ATTGA-AGAATTGAAATTGAAGC
*
11536 ATTTGAAGAATTGAAATTAAAGC
1 A-TTGAAGAATTGAAATTGAAGC
*
11559 ATTGAAGAATTGAAATTGAAAC
1 ATTGAAGAATTGAAATTGAAGC
*
11581 ATTGAAGAATTAAAATTGAAGC
1 ATTGAAGAATTGAAATTGAAGC
* *
11603 ATTGAAGAACTGAAATTAAAGC
1 ATTGAAGAATTGAAATTGAAGC
* *
11625 ATTGACA-TATTGAAATTGAAAC
1 ATTGA-AGAATTGAAATTGAAGC
11647 ATTGAAGAATTGAAAAATTGAA--
1 ATTGAAGAATTG--AAATTGAAGC
* *
11669 ATTGAAGCATTAAAGAATTGAA--
1 ATTGAAGAATT-GA-AATTGAAGC
* * *
11691 TTTGAAGGATTGAAATATTG-AGTA
1 ATTGAAGAATTG-AA-ATTGAAG-C
** *
11715 ATTGAAGAATTGAAGAAAGACCACC
1 ATTGAAGAATTGAA-ATTGA--AGC
* * * *
11740 CTGGATCATTGAAGT-AAATTGATGC
1 ATTGA--A--GAATTGAAATTGAAGC
* *
11765 TTTGAAAAATTGAAATTGAAG-
1 ATTGAAGAATTGAAATTGAAGC
*** * * **
11786 A---AAGACCACCCAGGATCGTTGC
1 ATTGAAGA--ATTGA-AATTGAAGC
* *
11808 ATTGAATAATTGAAATTGAAAC
1 ATTGAAGAATTGAAATTGAAGC
* *
11830 ATTGATGAATTGAAAGTGAAGC
1 ATTGAAGAATTGAAATTGAAGC
* *
11852 ATTGAAGAATTGAAAGTGAATC
1 ATTGAAGAATTGAAATTGAAGC
* * *
11874 AATGAAGAATTGAATTTGAAGA
1 ATTGAAGAATTGAAATTGAAGC
*
11896 ATTG-A-AATTGAGACATTGAAGG
1 ATTGAAGAATTGA-A-ATTGAAGC
11918 ATTGAAGAATTGAA
1 ATTGAAGAATTGAA
11932 GCTAATTGAA
Statistics
Matches: 576, Mismatches: 113, Indels: 77
0.75 0.15 0.10
Matches are distributed among these distances:
18 3 0.01
20 8 0.01
21 17 0.03
22 435 0.76
23 68 0.12
24 24 0.04
25 10 0.02
26 1 0.00
27 4 0.01
28 2 0.00
29 4 0.01
ACGTcount: A:0.45, C:0.06, G:0.20, T:0.28
Consensus pattern (22 bp):
ATTGAAGAATTGAAATTGAAGC
Found at i:11275 original size:89 final size:87
Alignment explanation
Indices: 11182--11661 Score: 549
Period size: 89 Copynumber: 5.4 Consensus size: 87
11172 AAGAATCGAA
* * * * *
11182 ATTGAAGAGTTGAAATTGAAGCATTGGAGAATTGAAGTTGAAGCATTGACATATTGAAATTGAAA
1 ATTGAAGAATTGAAATTGAAACATTGAAGAATTGAAATTGAAGCATTGA-AAATTGAAATTGAAA
11247 CATTTGAAGAATTGAAATTAAAGC
65 CA-TTGAAGAATTGAAATTAAAGC
* *
11271 ATTGAAGAATTGAAATTGAAACATTGGAGAATTAAAATTGAAGCATTGAAGAATTGAAATT-AAA
1 ATTGAAGAATTGAAATTGAAACATTGAAGAATTGAAATTGAAGCATTGAA-AATTGAAATTGAAA
* * * *
11335 GCATTGAAGTATTAAAACTGAAGC
65 -CATTGAAGAATTGAAATTAAAGC
* * *
11359 ATTGAAGAATTGAAATTGAATCATTGAAGAATTGAAATTGAAGCATTGAGGAATTGAAATTGAAT
1 ATTGAAGAATTGAAATTGAAACATTGAAGAATTGAAATTGAAGCATTGA-AAATTGAAATTGAAA
*
11424 CATTGAAGAATTGAAATTGAAGC
65 CATTGAAGAATTGAAATTAAAGC
* * * *
11447 ATTTGAGGAATTTAAATTGAATCATTGAAGAATTGAAATTGAAGCATTGAAGAA-TCAAAGTTGA
1 A-TTGAAGAATTGAAATTGAAACATTGAAGAATTGAAATTGAAGCATTGAA-AATTGAAA-TTGA
* * *
11511 AGCATTGACA-TATTAAAATTGAAA-C
63 AACATTGA-AGAATTGAAATT-AAAGC
* *
11536 ATTTGAAGAATTGAAATT-AAAGCATTGAAGAATTGAAATTGAAACATTGAAGAATTAAAATTGA
1 A-TTGAAGAATTGAAATTGAAA-CATTGAAGAATTGAAATTGAAGCATTGAA-AATTGAAATTGA
* *
11600 AGCATTGAAGAACTGAAATTAAAGC
63 AACATTGAAGAATTGAAATTAAAGC
*
11625 ATTGACA-TATTGAAATTGAAACATTGAAGAATTGAAA
1 ATTGA-AGAATTGAAATTGAAACATTGAAGAATTGAAA
11662 AATTGAAATT
Statistics
Matches: 342, Mismatches: 34, Indels: 31
0.84 0.08 0.08
Matches are distributed among these distances:
88 137 0.40
89 198 0.58
90 7 0.02
ACGTcount: A:0.46, C:0.06, G:0.20, T:0.29
Consensus pattern (87 bp):
ATTGAAGAATTGAAATTGAAACATTGAAGAATTGAAATTGAAGCATTGAAAATTGAAATTGAAAC
ATTGAAGAATTGAAATTAAAGC
Found at i:11309 original size:111 final size:110
Alignment explanation
Indices: 11194--11661 Score: 595
Period size: 111 Copynumber: 4.2 Consensus size: 110
11184 TGAAGAGTTG
* * * *
11194 AAATTGAAGCATTGGAGAATTGAAGTTGAAGCATTGACA-TATTGAAATTGAAACATTTGAAGAA
1 AAATTGAAACATTGAAGAATTGAAATTAAAGCATTGA-AGTATTGAAATTGAAACA-TTGAAGAA
* *
11258 TTGAAATTAAAGCATTGAAGAATTGAAATTGAAACATTGGAGA-ATTA
64 TTGAAATTGAAGCATTGAAGAATTGAAATTGAAACATT-GACATATTA
* * * *
11305 AAATTGAAGCATTGAAGAATTGAAATTAAAGCATTGAAGTATTAAAACTGAAGCATTGAAGAATT
1 AAATTGAAACATTGAAGAATTGAAATTAAAGCATTGAAGTATTGAAATTGAAACATTGAAGAATT
* * * *
11370 GAAATTGAATCATTGAAGAATTGAAATTGAAGCATTGAGGA-ATTG
66 GAAATTGAAGCATTGAAGAATTGAAATTGAAACATTGA-CATATTA
* * * * * *
11415 AAATTGAATCATTGAAGAATTGAAATTGAAGCATTTGAGGAATTTAAATTGAATCATTGAAGAAT
1 AAATTGAAACATTGAAGAATTGAAATTAAAGCA-TTGAAGTATTGAAATTGAAACATTGAAGAAT
* *
11480 TGAAATTGAAGCATTGAAGAA-TCAAAGTTGAAGCATTGACATATTA
65 TGAAATTGAAGCATTGAAGAATTGAAA-TTGAAACATTGACATATTA
*
11526 AAATTGAAACATTTGAAGAATTGAAATTAAAGCATTGAAGAATTGAAATTGAAACATTGAAGAAT
1 AAATTGAAACA-TTGAAGAATTGAAATTAAAGCATTGAAGTATTGAAATTGAAACATTGAAGAAT
* * *
11591 TAAAATTGAAGCATTGAAGAACTGAAATT-AAAGCATTGACATATTG
65 TGAAATTGAAGCATTGAAGAATTGAAATTGAAA-CATTGACATATTA
11637 AAATTGAAACATTGAAGAATTGAAA
1 AAATTGAAACATTGAAGAATTGAAA
11662 AATTGAAATT
Statistics
Matches: 319, Mismatches: 30, Indels: 17
0.87 0.08 0.05
Matches are distributed among these distances:
109 2 0.01
110 101 0.32
111 191 0.60
112 25 0.08
ACGTcount: A:0.46, C:0.06, G:0.19, T:0.29
Consensus pattern (110 bp):
AAATTGAAACATTGAAGAATTGAAATTAAAGCATTGAAGTATTGAAATTGAAACATTGAAGAATT
GAAATTGAAGCATTGAAGAATTGAAATTGAAACATTGACATATTA
Found at i:11706 original size:288 final size:288
Alignment explanation
Indices: 11182--11728 Score: 845
Period size: 288 Copynumber: 1.9 Consensus size: 288
11172 AAGAATCGAA
* * ** *
11182 ATTGAAGAGTTGAAATTGAAGCATTGGAGAATTGAAGTTGAAGCATTGACATATTGAAATTGAAA
1 ATTGAAGAATTGAAATTGAAGCATTGAAGAATCAAAGTTGAAGCATTGACATATTAAAATTGAAA
*
11247 CATTTGAAGAATTGAAATTAAAGCATTGAAGAATTGAAATTGAAACATTGGAGAATTAAAATTGA
66 CATTTGAAGAATTGAAATTAAAGCATTGAAGAATTGAAATTGAAACATTGAAGAATTAAAATTGA
* *
11312 AGCATTGAAGAATTGAAATTAAAGCATTGAAGTATTAAAACTGAAGCATTGAAGAATTGAAATTG
131 AGCATTGAAGAACTGAAATTAAAGCATTGAAGTATTAAAACTGAAACATTGAAGAATTGAAATTG
* *
11377 AATCATTGAAGAATTGAAATTGAAGCATTGAGGAATTG-AA-ATTGAATCATTGAAGAATTGAAA
196 AA-CATTGAAGAATTAAAATTGAA-CATTGAGGAATTGAAATATTGAATAATTGAAGAATTGAAA
11440 TTGAAGCATTTGAGGAATTTAAATTGAATC
259 TTGAAGCATTTGAGGAATTTAAATTGAATC
11470 ATTGAAGAATTGAAATTGAAGCATTGAAGAATCAAAGTTGAAGCATTGACATATTAAAATTGAAA
1 ATTGAAGAATTGAAATTGAAGCATTGAAGAATCAAAGTTGAAGCATTGACATATTAAAATTGAAA
11535 CATTTGAAGAATTGAAATTAAAGCATTGAAGAATTGAAATTGAAACATTGAAGAATTAAAATTGA
66 CATTTGAAGAATTGAAATTAAAGCATTGAAGAATTGAAATTGAAACATTGAAGAATTAAAATTGA
* *
11600 AGCATTGAAGAACTGAAATTAAAGCATTGACA-TATTGAAATTGAAACATTGAAGAATTGAAAAA
131 AGCATTGAAGAACTGAAATTAAAGCATTGA-AGTATTAAAACTGAAACATTGAAGAATTG--AAA
* * *
11664 TTGAA-ATTGAAGCATTAAAGAATTGAA-TTTGAAGG-ATTGAAATATTGAGTAATTGAAGAATT
193 TTGAACATTGAAGAATT-AA-AATTGAACATTG-AGGAATTGAAATATTGAATAATTGAAGAATT
11726 GAA
255 GAA
11729 GAAAGACCAC
Statistics
Matches: 236, Mismatches: 15, Indels: 14
0.89 0.06 0.05
Matches are distributed among these distances:
288 194 0.82
289 7 0.03
290 35 0.15
ACGTcount: A:0.46, C:0.05, G:0.20, T:0.29
Consensus pattern (288 bp):
ATTGAAGAATTGAAATTGAAGCATTGAAGAATCAAAGTTGAAGCATTGACATATTAAAATTGAAA
CATTTGAAGAATTGAAATTAAAGCATTGAAGAATTGAAATTGAAACATTGAAGAATTAAAATTGA
AGCATTGAAGAACTGAAATTAAAGCATTGAAGTATTAAAACTGAAACATTGAAGAATTGAAATTG
AACATTGAAGAATTAAAATTGAACATTGAGGAATTGAAATATTGAATAATTGAAGAATTGAAATT
GAAGCATTTGAGGAATTTAAATTGAATC
Found at i:11857 original size:8 final size:8
Alignment explanation
Indices: 11808--11932 Score: 60
Period size: 8 Copynumber: 16.9 Consensus size: 8
11798 GGATCGTTGC
*
11808 ATTGAATA
1 ATTGAAGA
11816 ATTG-A-A
1 ATTGAAGA
11822 ATTGAA-A
1 ATTGAAGA
*
11829 CATTGATGA
1 -ATTGAAGA
11838 ATTG-A-A
1 ATTGAAGA
* *
11844 AGTGAAGC
1 ATTGAAGA
11852 ATTGAAGA
1 ATTGAAGA
11860 ATTG-A-A
1 ATTGAAGA
* *
11866 AGTGAATCA
1 ATTGAA-GA
11875 A-TGAAGA
1 ATTGAAGA
11882 ATTG-A-A
1 ATTGAAGA
*
11888 TTTGAAGA
1 ATTGAAGA
11896 ATTG-A-A
1 ATTGAAGA
11902 ATTG-AGA
1 ATTGAAGA
*
11909 CATTGAAGG
1 -ATTGAAGA
11918 ATTGAAGA
1 ATTGAAGA
11926 ATTGAAG
1 ATTGAAG
11933 CTAATTGAAC
Statistics
Matches: 91, Mismatches: 12, Indels: 28
0.69 0.09 0.21
Matches are distributed among these distances:
6 23 0.25
7 12 0.13
8 51 0.56
9 5 0.05
ACGTcount: A:0.46, C:0.03, G:0.23, T:0.28
Consensus pattern (8 bp):
ATTGAAGA
Found at i:11893 original size:14 final size:14
Alignment explanation
Indices: 11876--11931 Score: 69
Period size: 14 Copynumber: 3.9 Consensus size: 14
11866 AGTGAATCAA
*
11876 TGAAGAATTGAATT
1 TGAAGAATTGAAAT
11890 TGAAGAATTGAAAT
1 TGAAGAATTGAAAT
11904 TG-AGACATTGAAGGAT
1 TGAAGA-ATTGAA--AT
11920 TGAAGAATTGAA
1 TGAAGAATTGAA
11932 GCTAATTGAA
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
13 3 0.08
14 21 0.57
16 10 0.27
17 3 0.08
ACGTcount: A:0.45, C:0.02, G:0.25, T:0.29
Consensus pattern (14 bp):
TGAAGAATTGAAAT
Found at i:13585 original size:19 final size:19
Alignment explanation
Indices: 13561--13598 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
13551 TTTGAAACCA
*
13561 TTTTTTTT-AGAAATCTTT
1 TTTTTTTTGAAAAATCTTT
13579 TTTTTTTTGAAAAATCTTT
1 TTTTTTTTGAAAAATCTTT
13598 T
1 T
13599 AAAAGAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.24, C:0.05, G:0.05, T:0.66
Consensus pattern (19 bp):
TTTTTTTTGAAAAATCTTT
Found at i:18321 original size:52 final size:52
Alignment explanation
Indices: 18260--18389 Score: 217
Period size: 52 Copynumber: 2.5 Consensus size: 52
18250 AATTTTGTTA
* *
18260 GATGGGAACTTTCCCATTTTGAAAACTG-GCTAAATTGAACACTTTGAAAACT
1 GATGGGAACTTTCCCAATTTGAAAA-AGAGCTAAATTGAACACTTTGAAAACT
*
18312 GATGGGAACTTTCCCAATTTGAAAAAGAGCTAAATTGAAGACTTTGAAAACT
1 GATGGGAACTTTCCCAATTTGAAAAAGAGCTAAATTGAACACTTTGAAAACT
18364 GATGGGAACTTTCCCAATTTGAAAAA
1 GATGGGAACTTTCCCAATTTGAAAAA
18390 CATTGAAAGA
Statistics
Matches: 74, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
51 1 0.01
52 73 0.99
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.28
Consensus pattern (52 bp):
GATGGGAACTTTCCCAATTTGAAAAAGAGCTAAATTGAACACTTTGAAAACT
Found at i:20947 original size:130 final size:130
Alignment explanation
Indices: 20714--20975 Score: 497
Period size: 130 Copynumber: 2.0 Consensus size: 130
20704 TACCTAAACT
20714 ACCATAATGCAATTTTGATTCCTAAATACTTAGAGTACTAATTTCTAAGCTTGTTTATCCTTGAT
1 ACCATAATGCAATTTTGATTCCTAAATACTTAGAGTACTAATTTCTAAGCTTGTTTATCCTTGAT
*
20779 TCCAAATTAATTTATTCAATATAAACTATCAAACAAAAGTCATTTCTTTTTAATTACTAGACTAA
66 TCCAAATTAATTTATTCAATACAAACTATCAAACAAAAGTCATTTCTTTTTAATTACTAGACTAA
* *
20844 ACCATAATGCAATTTTGATTCCTAAATACTTAGAGTACTAATTTTTAGGCTTGTTTATCCTTGAT
1 ACCATAATGCAATTTTGATTCCTAAATACTTAGAGTACTAATTTCTAAGCTTGTTTATCCTTGAT
20909 TCCAAATTAATTTATTCAATACAAACTATCAAACAAAAGTCATTTCTTTTTAATTACTAGACTAA
66 TCCAAATTAATTTATTCAATACAAACTATCAAACAAAAGTCATTTCTTTTTAATTACTAGACTAA
20974 AC
1 AC
20976 AATATTAATT
Statistics
Matches: 129, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
130 129 1.00
ACGTcount: A:0.37, C:0.16, G:0.07, T:0.40
Consensus pattern (130 bp):
ACCATAATGCAATTTTGATTCCTAAATACTTAGAGTACTAATTTCTAAGCTTGTTTATCCTTGAT
TCCAAATTAATTTATTCAATACAAACTATCAAACAAAAGTCATTTCTTTTTAATTACTAGACTAA
Found at i:25436 original size:29 final size:28
Alignment explanation
Indices: 25348--25436 Score: 65
Period size: 29 Copynumber: 3.1 Consensus size: 28
25338 AAGTGAACCT
* ***
25348 AAAATGACCAAAATACCCCTAAAT-ATGT
1 AAAATGACCAAAATGCCCCT-AATGACCA
* * *
25376 AAAATGACAAAAATGCCCCT-CTGAACATA
1 AAAATGACCAAAATGCCCCTAATG-AC-CA
25405 AAAATGACCAAAATGCCCCTAGATGACCA
1 AAAATGACCAAAATGCCCCTA-ATGACCA
25434 AAA
1 AAA
25437 TCCCCCTGAA
Statistics
Matches: 47, Mismatches: 9, Indels: 9
0.72 0.14 0.14
Matches are distributed among these distances:
26 1 0.02
28 19 0.40
29 23 0.49
30 2 0.04
31 2 0.04
ACGTcount: A:0.49, C:0.24, G:0.10, T:0.17
Consensus pattern (28 bp):
AAAATGACCAAAATGCCCCTAATGACCA
Found at i:34706 original size:29 final size:31
Alignment explanation
Indices: 34648--34707 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
34638 ATACCCGGGA
34648 GGTCCCTCTACTTACACAAAAAGATCAATTT
1 GGTCCCTCTACTTACACAAAAAGATCAATTT
34679 GGTCCCTCTAC-TA-A-AAAAACGATCAATTT
1 GGTCCCTCTACTTACACAAAAA-GATCAATTT
34708 AGTTCATCTA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
28 5 0.18
29 10 0.36
30 2 0.07
31 11 0.39
ACGTcount: A:0.37, C:0.25, G:0.10, T:0.28
Consensus pattern (31 bp):
GGTCCCTCTACTTACACAAAAAGATCAATTT
Found at i:34717 original size:29 final size:28
Alignment explanation
Indices: 34665--34719 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
34655 CTACTTACAC
* *
34665 AAAAAGATCAATTTGGTCCCTCTACTAA
1 AAAAAGATCAATTTAGTCCATCTACTAA
*
34693 AAAAACGATCAATTTAGTTCATCTACT
1 AAAAA-GATCAATTTAGTCCATCTACT
34720 TGTGAGATTG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 5 0.22
29 18 0.78
ACGTcount: A:0.40, C:0.20, G:0.09, T:0.31
Consensus pattern (28 bp):
AAAAAGATCAATTTAGTCCATCTACTAA
Found at i:41600 original size:31 final size:31
Alignment explanation
Indices: 41559--41634 Score: 107
Period size: 31 Copynumber: 2.5 Consensus size: 31
41549 TTTATTAATT
* *
41559 GGACTTAATTGATCCAATCTGATAAGAAGAG
1 GGACTAAATTGATCCAATCTGACAAGAAGAG
* * *
41590 GGACTGAATTGATCCAATCTTACAAGTAGAG
1 GGACTAAATTGATCCAATCTGACAAGAAGAG
41621 GGACTAAATTGATC
1 GGACTAAATTGATC
41635 GTTTTGTTAG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.37, C:0.14, G:0.22, T:0.26
Consensus pattern (31 bp):
GGACTAAATTGATCCAATCTGACAAGAAGAG
Found at i:41658 original size:29 final size:31
Alignment explanation
Indices: 41613--41685 Score: 105
Period size: 29 Copynumber: 2.4 Consensus size: 31
41603 CCAATCTTAC
*
41613 AAGTAGAGGGACTAAATTGATCGTTTTGT-T
1 AAGTAGAGGGACCAAATTGATCGTTTTGTGT
**
41643 -AGTAGAGGGACCAAATTGATTTTTTTGTGT
1 AAGTAGAGGGACCAAATTGATCGTTTTGTGT
41673 AAGTAGAGGGACC
1 AAGTAGAGGGACC
41686 TACTGCGTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
29 25 0.66
30 1 0.03
31 12 0.32
ACGTcount: A:0.30, C:0.08, G:0.29, T:0.33
Consensus pattern (31 bp):
AAGTAGAGGGACCAAATTGATCGTTTTGTGT
Found at i:43105 original size:15 final size:15
Alignment explanation
Indices: 43087--43115 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
43077 TCTTCTTCTT
43087 CTTTTTATTTTTTAA
1 CTTTTTATTTTTTAA
43102 CTTTTTATTTTTTA
1 CTTTTTATTTTTTA
43116 CACAAGGATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.76
Consensus pattern (15 bp):
CTTTTTATTTTTTAA
Found at i:44821 original size:91 final size:92
Alignment explanation
Indices: 44654--44840 Score: 261
Period size: 91 Copynumber: 2.0 Consensus size: 92
44644 GTTAAGAAAT
* * *
44654 TGTAAACACTAATGGTTGGATTTAGCTTCTGCATGTGCATATGCAATCCTTATTGACCTTTGAGA
1 TGTAAACACTAATGGTTGGATATAGCTTCTGCA---GAATATGCAATCCTTATTGACCTTTGAAA
*
44719 GCGAAACTTTGAATTGTTGCATCTGAGCTG
63 GCGAAACTTTGAATTATTGCATCTGAGCTG
* *
44749 TGTAAA-AGCTAATGGTTGGATATAGCTTCTGCA-AATATGCATTCCTTATTGACCTTTGAAAGG
1 TGTAAACA-CTAATGGTTGGATATAGCTTCTGCAGAATATGCAATCCTTATTGACCTTTGAAAGC
*
44812 GCAACTTTGAATTATTGCATCTGAGCTG
65 GAAACTTTGAATTATTGCATCTGAGCTG
44840 T
1 T
44841 TTGGCCTGTA
Statistics
Matches: 84, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
91 53 0.63
94 1 0.01
95 30 0.36
ACGTcount: A:0.27, C:0.16, G:0.21, T:0.36
Consensus pattern (92 bp):
TGTAAACACTAATGGTTGGATATAGCTTCTGCAGAATATGCAATCCTTATTGACCTTTGAAAGCG
AAACTTTGAATTATTGCATCTGAGCTG
Found at i:51400 original size:32 final size:32
Alignment explanation
Indices: 51335--51400 Score: 96
Period size: 32 Copynumber: 2.1 Consensus size: 32
51325 CCACCATAAG
* **
51335 CATGATAAGCTCAATACTAATGAGCTTTGTTA
1 CATGATAAGCTCAATACAAATGAGCTTCCTTA
*
51367 CATGATAAGCTCGATACAAATGAGCTTCCTTA
1 CATGATAAGCTCAATACAAATGAGCTTCCTTA
51399 CA
1 CA
51401 AGGAAGGCAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.30
Consensus pattern (32 bp):
CATGATAAGCTCAATACAAATGAGCTTCCTTA
Found at i:52694 original size:6 final size:6
Alignment explanation
Indices: 52683--52728 Score: 92
Period size: 6 Copynumber: 7.7 Consensus size: 6
52673 GCAAGAAGAA
52683 ATTGAG ATTGAG ATTGAG ATTGAG ATTGAG ATTGAG ATTGAG ATTG
1 ATTGAG ATTGAG ATTGAG ATTGAG ATTGAG ATTGAG ATTGAG ATTG
52729 CAGAGGTTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.35
Consensus pattern (6 bp):
ATTGAG
Found at i:53455 original size:32 final size:32
Alignment explanation
Indices: 53419--53483 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
53409 TTGATAATTC
53419 CACGTCATTTGTACTTTATATGCCACGTGTCA
1 CACGTCATTTGTACTTTATATGCCACGTGTCA
53451 CACGTCATTTGTACTTTATATGCCACGTGTCA
1 CACGTCATTTGTACTTTATATGCCACGTGTCA
53483 C
1 C
53484 TCTCACTCTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.22, C:0.26, G:0.15, T:0.37
Consensus pattern (32 bp):
CACGTCATTTGTACTTTATATGCCACGTGTCA
Found at i:58460 original size:70 final size:69
Alignment explanation
Indices: 58335--58550 Score: 298
Period size: 70 Copynumber: 3.2 Consensus size: 69
58325 ATTGCAGAAA
*
58335 AGTAA-AA-CCATAAGCAATGTGACCAGACCCAAAACTAACAATTCAGAAATA-GAATCACTATG
1 AGTAAGAATCCATAAGCAATGTGACCA-ACCCAAAACTAACAATTCAGAAA-AGGAATCACTAGG
58397 AAAAAC
64 AAAAAC
*
58403 AGTAAGAATCCATAAGCAATGTGAACCAACCCAAAACTAACAATTCAGAAAAGGAATCTCTAGGA
1 AGTAAGAATCCATAAGCAATGTG-ACCAACCCAAAACTAACAATTCAGAAAAGGAATCACTAGGA
58468 AAAAC
65 AAAAC
** ** * *
58473 AGTAAGAATTTATAAGCAATGTGACCAACCCAAAACTAATGATTCAG--AAGAAATCACAAGGAA
1 AGTAAGAATCCATAAGCAATGTGACCAACCCAAAACTAACAATTCAGAAAAGGAATCACTAGGAA
58536 AAAC
66 AAAC
58540 AGTAAGAATCC
1 AGTAAGAATCC
58551 TCACCTTCTC
Statistics
Matches: 133, Mismatches: 11, Indels: 9
0.87 0.07 0.06
Matches are distributed among these distances:
67 26 0.20
68 5 0.04
69 25 0.19
70 73 0.55
71 4 0.03
ACGTcount: A:0.50, C:0.19, G:0.14, T:0.17
Consensus pattern (69 bp):
AGTAAGAATCCATAAGCAATGTGACCAACCCAAAACTAACAATTCAGAAAAGGAATCACTAGGAA
AAAC
Found at i:62115 original size:49 final size:49
Alignment explanation
Indices: 62049--62183 Score: 136
Period size: 49 Copynumber: 2.8 Consensus size: 49
62039 ATCATTTACA
** *
62049 TTTCC-TGCACTTTTTCTCAATTTTTACTACAAAATTGAAT-TTTTA-TT
1 TTTCCTTGCACTTTTTCTCAATTTTTAAGAAAAAATTG-ATCTTTTACTT
*
62096 TTTCCTTGCACCTTTTTCTCAAGTTTTAAGAAAAAATTGATCTTTTACTT
1 TTTCCTTGCA-CTTTTTCTCAATTTTTAAGAAAAAATTGATCTTTTACTT
* * * * *
62146 TTT-ATTGCTCTTTTTATCAATTTTT-GGACAAAATTGAT
1 TTTCCTTGCACTTTTTCTCAATTTTTAAGAAAAAATTGAT
62184 TGGCACGCTC
Statistics
Matches: 74, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
47 16 0.22
48 20 0.27
49 33 0.45
50 5 0.07
ACGTcount: A:0.26, C:0.16, G:0.07, T:0.51
Consensus pattern (49 bp):
TTTCCTTGCACTTTTTCTCAATTTTTAAGAAAAAATTGATCTTTTACTT
Found at i:63715 original size:2 final size:2
Alignment explanation
Indices: 63705--63738 Score: 50
Period size: 2 Copynumber: 16.5 Consensus size: 2
63695 TTATATAACT
*
63705 TA TA AA TA TA TA TA TA TA TA TA TA TA CTA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA T
63739 TATTTTTAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:64808 original size:45 final size:45
Alignment explanation
Indices: 64744--64869 Score: 200
Period size: 45 Copynumber: 2.8 Consensus size: 45
64734 AGCAACAATT
*
64744 AATATTAGGTTTATTTTGATGAATTACCTAGAGATGGAGGAGTAG
1 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGGAGTAG
* * *
64789 AATATTAGCTTTATTTTGATGAATTATCTAGTGATGGAGGAGTAT
1 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGGAGTAG
64834 AATATTAGCTTTAATTTT-ATGAATTACCTAGAGATG
1 AATATTAGCTTT-ATTTTGATGAATTACCTAGAGATG
64870 AATTAGAATT
Statistics
Matches: 74, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
45 69 0.93
46 5 0.07
ACGTcount: A:0.33, C:0.06, G:0.21, T:0.40
Consensus pattern (45 bp):
AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGGAGTAG
Found at i:74845 original size:20 final size:21
Alignment explanation
Indices: 74820--74858 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
74810 AATAACAATT
*
74820 TTCCAACC-ACATTCCCATAA
1 TTCCAACCTACATTACCATAA
74840 TTCCAACCTACATTACCAT
1 TTCCAACCTACATTACCAT
74859 CTCTCACCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.33, C:0.38, G:0.00, T:0.28
Consensus pattern (21 bp):
TTCCAACCTACATTACCATAA
Found at i:75358 original size:18 final size:17
Alignment explanation
Indices: 75325--75360 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
75315 TCAAAAGCAG
75325 AAGAGAAGACAGAAGAA
1 AAGAGAAGACAGAAGAA
*
75342 AAGAGAGAGAGAGAAGAA
1 AAGAGA-AGACAGAAGAA
75360 A
1 A
75361 GCTTTTGTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.64, C:0.03, G:0.33, T:0.00
Consensus pattern (17 bp):
AAGAGAAGACAGAAGAA
Found at i:75422 original size:1 final size:1
Alignment explanation
Indices: 75416--75444 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
75406 ACAACTTGAA
75416 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
75445 GTGAATAATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:76089 original size:13 final size:13
Alignment explanation
Indices: 76071--76096 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
76061 ATGGGCATGT
76071 GTATATATATATA
1 GTATATATATATA
76084 GTATATATATATA
1 GTATATATATATA
76097 CACTATTACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (13 bp):
GTATATATATATA
Found at i:77581 original size:29 final size:30
Alignment explanation
Indices: 77518--77584 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 30
77508 AGCAAAAGGG
* * * *
77518 CTTATCTGGCCAAAATTGGTAGTTAAGGAG
1 CTTATTTGGCCAAAATTGGAAGTTAAGAAA
*
77548 CTTATTTGGCCAAAATT-GAAGTTCAGAAA
1 CTTATTTGGCCAAAATTGGAAGTTAAGAAA
77577 CTTATTTG
1 CTTATTTG
77585 ACAGTTGGCG
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 16 0.50
30 16 0.50
ACGTcount: A:0.31, C:0.13, G:0.21, T:0.34
Consensus pattern (30 bp):
CTTATTTGGCCAAAATTGGAAGTTAAGAAA
Found at i:79507 original size:21 final size:21
Alignment explanation
Indices: 79457--79501 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
79447 GTGACACTGC
* *
79457 CCACCTGGGTTCTCAAGCAAA
1 CCACATGGGTGCTCAAGCAAA
*
79478 CCACATGGGTGCTCAAGGAAA
1 CCACATGGGTGCTCAAGCAAA
79499 CCA
1 CCA
79502 TGTGGGCGCC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.31, G:0.22, T:0.16
Consensus pattern (21 bp):
CCACATGGGTGCTCAAGCAAA
Found at i:83677 original size:4 final size:4
Alignment explanation
Indices: 83670--83769 Score: 191
Period size: 4 Copynumber: 25.0 Consensus size: 4
83660 TATAATGTAC
*
83670 CATA CATA CATA CGTA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
83718 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
83766 CATA
1 CATA
83770 TATATATATA
Statistics
Matches: 94, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
4 94 1.00
ACGTcount: A:0.49, C:0.25, G:0.01, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:83774 original size:2 final size:2
Alignment explanation
Indices: 83767--83796 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
83757 ACATACATAC
83767 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
83797 TTGCACTAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.