Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1127
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: 17560
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.31
Found at i:2537 original size:13 final size:13
Alignment explanation
Indices: 2519--2544 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2509 TACAAAGATC
2519 ATGTATCGATACA
1 ATGTATCGATACA
2532 ATGTATCGATACA
1 ATGTATCGATACA
2545 TTTAAGTGAT
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3661 original size:49 final size:47
Alignment explanation
Indices: 3495--3729 Score: 247
Period size: 43 Copynumber: 5.1 Consensus size: 47
3485 TGAGAAAAAG
* *
3495 GATGTCAA-GTGCTGATTCAAGGCCAGCTACATTGAACTTAAGATGGAAAA
1 GATGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAA-AT-G--AA
* * *
3545 GGTGCCAATATGCTGATTCAAGGCCAGCTATA-TGGACTTAAA-G--
1 GATGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAATGAA
3588 G-TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAA
1 GATGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT-AA-ATGAA
* * * ** *
3636 GATGCCAATATGCTGATTCAAGGCCAGCAATAGCGGGCTTAAA-G--
1 GATGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAATGAA
3680 G-TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAATGAA
1 GATGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAATGAA
3726 GATG
1 GATG
3730 AGAAAGTGAT
Statistics
Matches: 154, Mismatches: 19, Indels: 27
0.77 0.09 0.14
Matches are distributed among these distances:
42 28 0.18
43 43 0.28
44 4 0.03
45 1 0.01
46 3 0.02
47 4 0.03
48 3 0.02
49 33 0.21
50 14 0.09
51 21 0.14
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.24
Consensus pattern (47 bp):
GATGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAATGAA
Found at i:3704 original size:92 final size:90
Alignment explanation
Indices: 3503--3729 Score: 357
Period size: 92 Copynumber: 2.5 Consensus size: 90
3493 AGGATGTCAA
* *
3503 GTGCTGATTCAAGGCCAGCTACATTGAACTTAAGATGGAAAAGGTGCCAATATGCTGATTCAAGG
1 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAGAT-G--AAGATGCCAATATGCTGATTCAAGG
* *
3568 CCAGCTATATGGACTTAAAGGTGCCAAT
63 CCAGCAATACGGACTTAAAGGTGCCAAT
3596 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCC
1 GTGCTGATTCAAGGCCAGCTACATTGGACTT-AAGATGAAGATGCCAATATGCTGATTCAAGGCC
*
3661 AGCAATAGCGGGCTTAAAGGTGCCAAT
65 AGCAATA-CGGACTTAAAGGTGCCAAT
3688 GTGCTGATTCAAGGCCAGCTACATTGGACTTAA-ATGAAGATG
1 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAGATGAAGATG
3730 AGAAAGTGAT
Statistics
Matches: 127, Mismatches: 5, Indels: 7
0.91 0.04 0.05
Matches are distributed among these distances:
90 9 0.07
91 34 0.27
92 48 0.38
93 31 0.24
94 5 0.04
ACGTcount: A:0.32, C:0.19, G:0.26, T:0.24
Consensus pattern (90 bp):
GTGCTGATTCAAGGCCAGCTACATTGGACTTAAGATGAAGATGCCAATATGCTGATTCAAGGCCA
GCAATACGGACTTAAAGGTGCCAAT
Found at i:3819 original size:54 final size:50
Alignment explanation
Indices: 3754--4247 Score: 359
Period size: 43 Copynumber: 10.4 Consensus size: 50
3744 ATGCCAATGT
* * * * * *
3754 TGATCACGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGATGTCAATGTGC
1 TGATCAAGGCCAGCTATATTGGACTTAAAGATG-G--AAAGG-TGCCAATATGC
* *
3808 TGATCAAGGCCAGCTACATTGAACTTAAAGATGGAAAGGTGCCAATATGC
1 TGATCAAGGCCAGCTATATTGGACTTAAAGATGGAAAGGTGCCAATATGC
*
3858 TGATTCAAGGCCAGCTATATTGGAC-T-----T--AAAGGTGCCAATGTGC
1 TGA-TCAAGGCCAGCTATATTGGACTTAAAGATGGAAAGGTGCCAATATGC
* * *
3901 TGATTCAAGGCCAGCTACATTGGACTTAAAGA-AGAAAGTTGCCAATATGC
1 TGA-TCAAGGCCAGCTATATTGGACTTAAAGATGGAAAGGTGCCAATATGC
* * *
3951 TGATTC-AGGCCAGCGATATTGGAC-T-----T-G-AACGTGCCAATGTGC
1 TGA-TCAAGGCCAGCTATATTGGACTTAAAGATGGAAAGGTGCCAATATGC
* *
3993 TGATTCAAAGCCAGCTACATTGGAC-TAAAGAT-G-AAGGTGCCAATATGC
1 TGA-TCAAGGCCAGCTATATTGGACTTAAAGATGGAAAGGTGCCAATATGC
*
4041 TGATTCAAGGCCAGCTATATTGGAC-T-----T--AAAGGTGCCAATGTGC
1 TGA-TCAAGGCCAGCTATATTGGACTTAAAGATGGAAAGGTGCCAATATGC
*
4084 TGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G-AAGGTGCCAATATGC
1 TGA-TCAAGGCCAGCTATATTGGACTTAAAGATGGAAAGGTGCCAATATGC
* * * *
4133 TGATTCAAGGCCAGCGAGATTGGGC-T-----T--AAAGGTGCCAATGTGC
1 TGA-TCAAGGCCAGCTATATTGGACTTAAAGATGGAAAGGTGCCAATATGC
*
4176 TGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G-AAGGTGCCAATATGC
1 TGA-TCAAGGCCAGCTATATTGGACTTAAAGATGGAAAGGTGCCAATATGC
*
4225 TGATTCAAGGCCAGCGATATTGG
1 TGA-TCAAGGCCAGCTATATTGG
4248 GCTAGAAGGG
Statistics
Matches: 369, Mismatches: 39, Indels: 69
0.77 0.08 0.14
Matches are distributed among these distances:
42 18 0.05
43 132 0.36
44 3 0.01
45 1 0.00
48 41 0.11
49 89 0.24
50 33 0.09
51 24 0.07
53 1 0.00
54 27 0.07
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.24
Consensus pattern (50 bp):
TGATCAAGGCCAGCTATATTGGACTTAAAGATGGAAAGGTGCCAATATGC
Found at i:3903 original size:43 final size:43
Alignment explanation
Indices: 3842--4239 Score: 438
Period size: 43 Copynumber: 8.7 Consensus size: 43
3832 TTAAAGATGG
*
3842 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
*
3885 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
* *
3928 AAAGAAGAAAGTTGCCAATATGCTGATTC-AGGCCAGCGATATTGGACTT
1 --A-AAG---G-TGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
* * * *
3977 GAACGTGCCAATGTGCTGATTCAAAGCCAGCTACATTGGACTAAAGAT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACT-----T
* *
4025 GAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
*
4068 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
* * *
4111 AAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGAGATTGGGCTT
1 ----A--AAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
*
4160 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
4203 AAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGC
1 ----A--AAGGTGCCAATATGCTGATTCAAGGCCAGC
4240 GATATTGGGC
Statistics
Matches: 303, Mismatches: 27, Indels: 44
0.81 0.07 0.12
Matches are distributed among these distances:
42 16 0.05
43 137 0.45
45 2 0.01
46 5 0.02
47 2 0.01
48 39 0.13
49 86 0.28
50 16 0.05
ACGTcount: A:0.31, C:0.19, G:0.26, T:0.25
Consensus pattern (43 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
Found at i:3919 original size:301 final size:302
Alignment explanation
Indices: 3375--4028 Score: 1072
Period size: 301 Copynumber: 2.2 Consensus size: 302
3365 ACTTAAGATC
*
3375 AGGTGCCAATGTGCTGATTCAAGGCCAGCAACATTGGACTTAAA-GATGAGATGAGAAAAGTGAT
1 AGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAATGA--AGATGAGAAAAGTGAT
3439 AAAGATGCCAATATGTTGATTCACGGCCAACGATATTGGGCTTAAATGAGAAAAAGGATGTCAAG
64 AAAGATGCCAATATGTTGATTCACGGCCAACGATATTGGGCTTAAATGAGAAAAAGGATGTCAAG
3504 TGCTGATTCAAGGCCAGCTACATTGAACTTAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGC
129 TGCTGATTCAAGGCCAGCTACATTGAACTTAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGC
*
3569 CAGCTATATGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATG
194 CAGCTATATGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAG
*
3634 -AAGATGCCAATATGCTGATTCAAGGCCAGCAATAGCGGGCTTAA
259 AAAGATGCCAATATGCTGATTC-AGGCCAGCAATAGCGGACTTAA
3678 AGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAATGAAGATGAG-AAAGTGATAA
1 AGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAATGAAGATGAGAAAAGTGATAA
3742 AGATGCC-A-ATGTTGA-TCACGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGATGTCAAT
66 AGATGCCAATATGTTGATTCACGGCCAACGATATTGGGCTT-AA-ATGAGAAAAAGGATGTCAA-
3804 GTGCTGA-TCAAGGCCAGCTACATTGAACTTAAAGATGG-AAAGGTGCCAATATGCTGATTCAAG
128 GTGCTGATTCAAGGCCAGCTACATTGAACTT-AAGATGGAAAAGGTGCCAATATGCTGATTCAAG
3867 GCCAGCTATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAG
192 GCCAGCTATA-TGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAG
* * ** *
3932 AAGAAAGTTGCCAATATGCTGATTCAGGCCAGCGATATTGGACTTGA
256 AAGAAAGATGCCAATATGCTGATTCAGGCCAGCAATAGCGGACTTAA
* * *
3979 ACGTGCCAATGTGCTGATTCAAAGCCAGCTACATTGGACTAAAGATGAAG
1 AGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAA-ATGAAG
4029 GTGCCAATAT
Statistics
Matches: 332, Mismatches: 11, Indels: 17
0.92 0.03 0.05
Matches are distributed among these distances:
298 23 0.07
299 9 0.03
300 78 0.23
301 144 0.43
302 33 0.10
303 43 0.13
304 2 0.01
ACGTcount: A:0.34, C:0.17, G:0.25, T:0.24
Consensus pattern (302 bp):
AGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAATGAAGATGAGAAAAGTGATAA
AGATGCCAATATGTTGATTCACGGCCAACGATATTGGGCTTAAATGAGAAAAAGGATGTCAAGTG
CTGATTCAAGGCCAGCTACATTGAACTTAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCA
GCTATATGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAA
AGATGCCAATATGCTGATTCAGGCCAGCAATAGCGGACTTAA
Found at i:4110 original size:183 final size:184
Alignment explanation
Indices: 3800--4247 Score: 767
Period size: 183 Copynumber: 2.4 Consensus size: 184
3790 AAAAGGATGT
*
3800 CAATGTGCTGA-TCAAGGCCAGCTACATTGAACTTAAAGATGGAAAGGTGCCAATATGCTGATTC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G-AAGGTGCCAATATGCTGATTC
3864 AAGGCCAGCTATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTA
64 AAGGCCAGCTATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTA
* * *
3929 AAGAAGAAAGTTGCCAATATGCTGATTC-AGGCCAGCGATATTGGACTTGAACGTGC
129 AAGAAG-AAGGTGCCAATATGCTGATTCAAGGCCAGCGAGATTGGACTTAAACGTGC
*
3985 CAATGTGCTGATTCAAAGCCAGCTACATTGGAC-TAAAGATGAAGGTGCCAATATGCTGATTCAA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAA
4049 GGCCAGCTATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAA
66 GGCCAGCTATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAA
* * *
4114 GATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGAGATTGGGCTTAAAGGTGC
131 GAAGAAGGTGCCAATATGCTGATTCAAGGCCAGCGAGATTGGACTTAAACGTGC
4168 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAA
*
4233 GGCCAGCGATATTGG
66 GGCCAGCTATATTGG
4248 GCTAGAAGGG
Statistics
Matches: 250, Mismatches: 10, Indels: 7
0.94 0.04 0.03
Matches are distributed among these distances:
182 20 0.08
183 147 0.59
184 46 0.18
185 18 0.07
186 19 0.08
ACGTcount: A:0.31, C:0.19, G:0.26, T:0.25
Consensus pattern (184 bp):
CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAA
GGCCAGCTATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAA
GAAGAAGGTGCCAATATGCTGATTCAAGGCCAGCGAGATTGGACTTAAACGTGC
Found at i:4250 original size:92 final size:92
Alignment explanation
Indices: 3791--4247 Score: 758
Period size: 92 Copynumber: 5.0 Consensus size: 92
3781 AAGATGAGAA
* *
3791 AAAGGATGTCAATGTGCTGA-TCAAGGCCAGCTACATTGAACTTAAAGATGGAAAGGTGCCAATA
1 AAAGG-TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G-AAGGTGCCAATA
*
3855 TGCTGATTCAAGGCCAGCTATATTGGACTT
63 TGCTGATTCAAGGCCAGCGATATTGGACTT
* *
3885 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAAGTTGCCAATATG
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATG-AAGGTGCCAATATG
3950 CTGATTC-AGGCCAGCGATATTGGACTT
65 CTGATTCAAGGCCAGCGATATTGGACTT
* * *
3977 GAACGTGCCAATGTGCTGATTCAAAGCCAGCTACATTGGAC-TAAAGATGAAGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
*
4041 TGATTCAAGGCCAGCTATATTGGACTT
66 TGATTCAAGGCCAGCGATATTGGACTT
4068 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
* *
4133 TGATTCAAGGCCAGCGAGATTGGGCTT
66 TGATTCAAGGCCAGCGATATTGGACTT
4160 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
4225 TGATTCAAGGCCAGCGATATTGG
66 TGATTCAAGGCCAGCGATATTGG
4248 GCTAGAAGGG
Statistics
Matches: 342, Mismatches: 18, Indels: 8
0.93 0.05 0.02
Matches are distributed among these distances:
90 20 0.06
91 64 0.19
92 191 0.56
93 35 0.10
94 32 0.09
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (92 bp):
AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
TGATTCAAGGCCAGCGATATTGGACTT
Found at i:4309 original size:32 final size:32
Alignment explanation
Indices: 4250--4385 Score: 125
Period size: 32 Copynumber: 4.1 Consensus size: 32
4240 GATATTGGGC
*
4250 TAGA-AGGGTTGCCACTGAGACTTGTGTGGGCTT
1 TAGAGAGGGTTGCCAC--CGACTTGTGTGGGCTT
4283 TAGAGAGGGTTGCCACCGACTTGTGTGGGCTT
1 TAGAGAGGGTTGCCACCGACTTGTGTGGGCTT
** *
4315 T-GAGAAGGCCTGCCACCACCGCCTTGTGTGGGCTT
1 TAGAG-AGGGTTG---CCACCGACTTGTGTGGGCTT
*
4350 TAGAG-GGGATTGCCACCAACTTGTGTGTGGGCTT
1 TAGAGAGGG-TTGCCACCGAC-T-TGTGTGGGCTT
4384 TA
1 TA
4386 AGAAAAAGAG
Statistics
Matches: 86, Mismatches: 8, Indels: 17
0.77 0.07 0.15
Matches are distributed among these distances:
31 3 0.03
32 27 0.31
33 5 0.06
34 26 0.30
35 22 0.26
36 3 0.03
ACGTcount: A:0.17, C:0.21, G:0.35, T:0.28
Consensus pattern (32 bp):
TAGAGAGGGTTGCCACCGACTTGTGTGGGCTT
Found at i:4364 original size:35 final size:35
Alignment explanation
Indices: 4268--4367 Score: 120
Period size: 35 Copynumber: 2.9 Consensus size: 35
4258 TTGCCACTGA
4268 GACTTGTGTGGGCTTTAGAGAGGGTTG---CCACC
1 GACTTGTGTGGGCTTTAGAGAGGGTTGCCACCACC
**
4300 GACTTGTGTGGGCTTT-GAGAAGGCCTGCCACCACC
1 GACTTGTGTGGGCTTTAGAG-AGGGTTGCCACCACC
*
4335 GCCTTGTGTGGGCTTTAGAG-GGGATTGCCACCA
1 GACTTGTGTGGGCTTTAGAGAGGG-TTGCCACCA
4368 ACTTGTGTGT
Statistics
Matches: 57, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
31 3 0.05
32 21 0.37
34 2 0.04
35 28 0.49
36 3 0.05
ACGTcount: A:0.16, C:0.23, G:0.35, T:0.26
Consensus pattern (35 bp):
GACTTGTGTGGGCTTTAGAGAGGGTTGCCACCACC
Found at i:4473 original size:29 final size:29
Alignment explanation
Indices: 4422--4653 Score: 247
Period size: 29 Copynumber: 8.0 Consensus size: 29
4412 GCTTACAAAA
* * * *
4422 GAAAAAGAGTGCCACGGAGTTGTCGACTTT
1 GAAAAAGA-TGCCACTGACTTGTGGGCTTT
* * *
4452 GGAAAAGATGCCACCGACTTGTGGGCTTC
1 GAAAAAGATGCCACTGACTTGTGGGCTTT
* *
4481 GAAAAAGGGTGCCACTGATTTGTGGGCTTT
1 GAAAAA-GATGCCACTGACTTGTGGGCTTT
* *
4511 G--AAGGTTGCCACTGACTTGTGGGCTTTT
1 GAAAAAGATGCCACTGACTTGTGGGC-TTT
*
4539 GAAAAAAATGCCAC-GAACTTGTGGGCTTT
1 GAAAAAGATGCCACTG-ACTTGTGGGCTTT
4568 GAAAAAGATGCCACTGACTTGTGGGCTTT
1 GAAAAAGATGCCACTGACTTGTGGGCTTT
* * *
4597 -TAAAGGTTGCCACTGACTTGTGGGCTTT
1 GAAAAAGATGCCACTGACTTGTGGGCTTT
* *
4625 GAAAAATATGCCACTGACTTGTGGACTTT
1 GAAAAAGATGCCACTGACTTGTGGGCTTT
4654 TGAAGGGTGA
Statistics
Matches: 169, Mismatches: 26, Indels: 15
0.80 0.12 0.07
Matches are distributed among these distances:
27 18 0.11
28 31 0.18
29 74 0.44
30 46 0.27
ACGTcount: A:0.25, C:0.18, G:0.28, T:0.28
Consensus pattern (29 bp):
GAAAAAGATGCCACTGACTTGTGGGCTTT
Found at i:4536 original size:57 final size:57
Alignment explanation
Indices: 4422--4648 Score: 212
Period size: 57 Copynumber: 3.9 Consensus size: 57
4412 GCTTACAAAA
* * * * * *
4422 GAAAAA-GAGTGCCACGGAGTTGTCGACTTTGGAAAAGATGCCACCGACTTGTGGGCTT
1 GAAAAAGGA-TGCCACTGACTTGTGGGCTTT-GAAAAGTTGCCACTGACTTGTGGGCTT
* * *
4480 CGAAAAAGGGTGCCACTGATTTGTGGGCTTTG-AAGGTTGCCACTGACTTGTGGGCTTTT
1 -GAAAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGTTGCCACTGACTTGTGGGC--TT
* *
4539 GAAAAA-AATGCCAC-GAACTTGTGGGCTTTGAAAAAGATGCCACTGACTTGTGGGCTT
1 GAAAAAGGATGCCACTG-ACTTGTGGGCTTTG-AAAAGTTGCCACTGACTTGTGGGCTT
** * *
4596 -TTAAAGGTTGCCACTGACTTGTGGGCTTTGAAAAATATGCCACTGACTTGTGG
1 GAAAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGT-TGCCACTGACTTGTGG
4649 ACTTTTGAAG
Statistics
Matches: 140, Mismatches: 19, Indels: 20
0.78 0.11 0.11
Matches are distributed among these distances:
56 8 0.06
57 77 0.55
58 8 0.06
59 46 0.33
60 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.29, T:0.28
Consensus pattern (57 bp):
GAAAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGTTGCCACTGACTTGTGGGCTT
Found at i:4654 original size:57 final size:57
Alignment explanation
Indices: 4448--4659 Score: 232
Period size: 57 Copynumber: 3.7 Consensus size: 57
4438 GAGTTGTCGA
* * ** * *
4448 CTTTGGAAAAGATGCCACCGACTTGTGGGCTTCGAAAAAGGGTGCCACTGATTTGTGGG
1 CTTTGAAAAAGATGCCACTGACTTGTGGGCTT--TTAAAGGATGCCACTGACTTGTGGG
* * **
4507 CTTTG--AAGGTTGCCACTGACTTGTGGGCTTTTGAAAAAAATGCCAC-GAACTTGTGGG
1 CTTTGAAAAAGATGCCACTGACTTGTGGGCTTTT--AAAGGATGCCACTG-ACTTGTGGG
*
4564 CTTTGAAAAAGATGCCACTGACTTGTGGGCTTTTAAAGGTTGCCACTGACTTGTGGG
1 CTTTGAAAAAGATGCCACTGACTTGTGGGCTTTTAAAGGATGCCACTGACTTGTGGG
* * *
4621 CTTTGAAAAATATGCCACTGACTTGTGGACTTTTGAAGG
1 CTTTGAAAAAGATGCCACTGACTTGTGGGCTTTTAAAGG
4660 GTGAGGAATG
Statistics
Matches: 130, Mismatches: 17, Indels: 14
0.81 0.11 0.09
Matches are distributed among these distances:
56 1 0.01
57 98 0.75
58 1 0.01
59 30 0.23
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.30
Consensus pattern (57 bp):
CTTTGAAAAAGATGCCACTGACTTGTGGGCTTTTAAAGGATGCCACTGACTTGTGGG
Found at i:4657 original size:87 final size:85
Alignment explanation
Indices: 4448--4653 Score: 288
Period size: 87 Copynumber: 2.4 Consensus size: 85
4438 GAGTTGTCGA
* * * * * *
4448 CTTTGGAAAAGATGCCACCGACTTGTGGGCTTCGAAAAAGGGTGCCACTGATTTGTGGGCTTTGA
1 CTTTGAAAAAAATGCCA-CGACTTGTGGGCTTTGAAAAAGGATGCCACTGACTTGTGGGCTTTAA
4513 AGGTTGCCACTGACTTGTGGG
65 AGGTTGCCACTGACTTGTGGG
4534 CTTTTGAAAAAAATGCCACGAACTTGTGGGCTTTGAAAAA-GATGCCACTGACTTGTGGGCTTTT
1 C-TTTGAAAAAAATGCCACG-ACTTGTGGGCTTTGAAAAAGGATGCCACTGACTTGTGGGC-TTT
4598 AAAGGTTGCCACTGACTTGTGGG
63 AAAGGTTGCCACTGACTTGTGGG
* *
4621 CTTTGAAAAATATGCCACTGACTTGTGGACTTT
1 CTTTGAAAAAAATGCCAC-GACTTGTGGGCTTT
4654 TGAAGGGTGA
Statistics
Matches: 108, Mismatches: 8, Indels: 8
0.87 0.06 0.06
Matches are distributed among these distances:
86 49 0.45
87 59 0.55
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.30
Consensus pattern (85 bp):
CTTTGAAAAAAATGCCACGACTTGTGGGCTTTGAAAAAGGATGCCACTGACTTGTGGGCTTTAAA
GGTTGCCACTGACTTGTGGG
Found at i:6095 original size:1 final size:1
Alignment explanation
Indices: 6089--6181 Score: 96
Period size: 1 Copynumber: 93.0 Consensus size: 1
6079 ATCCGAACCC
* * * * * * * *
6089 TTTTTTTTTTGTTTTTTTTTGTTTGTTTTTTTTTGTTTTTTTTGTTTTTTGTTTTTTTTGTTTTG
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* *
6154 TTTTTTTTTGTTTTGTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
6182 GTGGTTATGG
Statistics
Matches: 72, Mismatches: 20, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 72 1.00
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (1 bp):
T
Found at i:6105 original size:10 final size:10
Alignment explanation
Indices: 6090--6183 Score: 111
Period size: 10 Copynumber: 9.1 Consensus size: 10
6080 TCCGAACCCT
6090 TTTTTTTTTG
1 TTTTTTTTTG
6100 TTTTTTTTTG
1 TTTTTTTTTG
*
6110 TTTGTTTTTTTT
1 -TT-TTTTTTTG
6122 TGTTTTTTTTG
1 T-TTTTTTTTG
6133 TTTTTTGTTT-
1 TTTTTT-TTTG
6143 TTTTTGTTTTG
1 TTTTT-TTTTG
6154 TTTTTTTTTG
1 TTTTTTTTTG
*
6164 TTTTGTTTT-
1 TTTTTTTTTG
6173 TTTTTTTTTG
1 TTTTTTTTTG
6183 T
1 T
6184 GGTTATGGAG
Statistics
Matches: 73, Mismatches: 4, Indels: 14
0.80 0.04 0.15
Matches are distributed among these distances:
9 8 0.11
10 37 0.51
11 20 0.27
12 8 0.11
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (10 bp):
TTTTTTTTTG
Found at i:6108 original size:14 final size:14
Alignment explanation
Indices: 6089--6183 Score: 131
Period size: 14 Copynumber: 6.9 Consensus size: 14
6079 ATCCGAACCC
6089 TTTTTTTTTTGTTT
1 TTTTTTTTTTGTTT
*
6103 TTTTTTGTTTG-TT
1 TTTTTTTTTTGTTT
*
6116 TTTTTTTGTT-TTT
1 TTTTTTTTTTGTTT
*
6129 TTTGTTTTTTGTTT
1 TTTTTTTTTTGTTT
*
6143 TTTTTGTTTTGTTT
1 TTTTTTTTTTGTTT
6157 TTTTTTGTTTTGTTT
1 TTTTTT-TTTTGTTT
6172 TTTTTTTTTTGT
1 TTTTTTTTTTGT
6184 GGTTATGGAG
Statistics
Matches: 70, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
13 20 0.29
14 36 0.51
15 14 0.20
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (14 bp):
TTTTTTTTTTGTTT
Found at i:6137 original size:40 final size:40
Alignment explanation
Indices: 6089--6178 Score: 148
Period size: 40 Copynumber: 2.2 Consensus size: 40
6079 ATCCGAACCC
6089 TTTTTTTTTTGTTTTTTTT-TGTTTGTTTTTTTTTGTTTT-
1 TTTTTTTTTTGTTTTTTTTGT-TTTGTTTTTTTTTGTTTTG
6128 TTTTGTTTTTTGTTTTTTTTGTTTTGTTTTTTTTTGTTTTG
1 TTTT-TTTTTTGTTTTTTTTGTTTTGTTTTTTTTTGTTTTG
6169 TTTTTTTTTT
1 TTTTTTTTTT
6179 TTTGTGGTTA
Statistics
Matches: 48, Mismatches: 0, Indels: 5
0.91 0.00 0.09
Matches are distributed among these distances:
39 4 0.08
40 39 0.81
41 5 0.10
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (40 bp):
TTTTTTTTTTGTTTTTTTTGTTTTGTTTTTTTTTGTTTTG
Found at i:9448 original size:19 final size:20
Alignment explanation
Indices: 9411--9450 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
9401 TCCCGTGTAA
9411 ATGTATCGATACAATATTTG
1 ATGTATCGATACAATATTTG
9431 ATGTATCGATAC-ATATTTG
1 ATGTATCGATACAATATTTG
9450 A
1 A
9451 AAATATAGCC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.35, C:0.10, G:0.15, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACAATATTTG
Found at i:9521 original size:13 final size:13
Alignment explanation
Indices: 9503--9528 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
9493 CAATTTTTTG
9503 TGTATCGATACAT
1 TGTATCGATACAT
9516 TGTATCGATACAT
1 TGTATCGATACAT
9529 ACTTGCTTGT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:10329 original size:110 final size:114
Alignment explanation
Indices: 10159--10380 Score: 391
Period size: 110 Copynumber: 2.0 Consensus size: 114
10149 CAAGTTCGTA
*
10159 CATTCTCCCCCTTAATAAAGTAATTGTAGCAATTACGCATTCTCCCCTTTATCTTCCCCGTT-TA
1 CATTATCCCCCTTAATAAAGTAATTGTAGCAATTACGCATTCTCCCCTTTATCTTCCCCGTTGTA
10223 TTAA-TAATTCT-CCCCTTAATCAAGTAAT-TCATATCAAAAATTTACG
66 TTAAGTAATTCTCCCCCTTAATCAAGTAATGTCATATCAAAAATTTACG
10269 CATTATCCCCCTTAATAAAGTAATTGTAGCAAGTTACGCATTCTCCCCTTTATCTT-CCCGTTGT
1 CATTATCCCCCTTAATAAAGTAATTGTAGCAA-TTACGCATTCTCCCCTTTATCTTCCCCGTTGT
10333 ATTAAGTAATTCTCCCCCTTAATCAAGTAATGTCATATCAAAAATTTA
65 ATTAAGTAATTCTCCCCCTTAATCAAGTAATGTCATATCAAAAATTTA
10381 TTGCACACAT
Statistics
Matches: 106, Mismatches: 1, Indels: 6
0.94 0.01 0.05
Matches are distributed among these distances:
110 37 0.35
111 29 0.27
112 7 0.07
113 17 0.16
114 16 0.15
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (114 bp):
CATTATCCCCCTTAATAAAGTAATTGTAGCAATTACGCATTCTCCCCTTTATCTTCCCCGTTGTA
TTAAGTAATTCTCCCCCTTAATCAAGTAATGTCATATCAAAAATTTACG
Found at i:13504 original size:19 final size:20
Alignment explanation
Indices: 13467--13506 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
13457 TCCCGTGTAA
13467 ATGTATCGATACAATATTTG
1 ATGTATCGATACAATATTTG
13487 ATGTATCGATAC-ATATTTG
1 ATGTATCGATACAATATTTG
13506 A
1 A
13507 AAATATAGCC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.35, C:0.10, G:0.15, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACAATATTTG
Found at i:13577 original size:13 final size:13
Alignment explanation
Indices: 13559--13584 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
13549 CAATTTTTTG
13559 TGTATCGATACAT
1 TGTATCGATACAT
13572 TGTATCGATACAT
1 TGTATCGATACAT
13585 ACTTGCTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Done.