Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1969
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: 27087
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Found at i:5264 original size:29 final size:29
Alignment explanation
Indices: 5232--5288 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
5222 ATGTTAGAGC
5232 AATTTATCAAAGGGCAATGGTTACTTTGA
1 AATTTATCAAAGGGCAATGGTTACTTTGA
5261 AATTTATCAAAGGGCAATGGTTACTTTG
1 AATTTATCAAAGGGCAATGGTTACTTTG
5289 TTCCATGATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.33, C:0.11, G:0.21, T:0.35
Consensus pattern (29 bp):
AATTTATCAAAGGGCAATGGTTACTTTGA
Found at i:6527 original size:20 final size:19
Alignment explanation
Indices: 6484--6537 Score: 81
Period size: 19 Copynumber: 2.8 Consensus size: 19
6474 TACATTATGC
**
6484 TTGTATCGATACATGTTCA
1 TTGTATCGATACATGGACA
6503 TTGTATCGATACATGGACAA
1 TTGTATCGATACATGGAC-A
6523 TTGTATCGATACATG
1 TTGTATCGATACATG
6538 AAACTGGCAG
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.50
20 16 0.50
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.37
Consensus pattern (19 bp):
TTGTATCGATACATGGACA
Found at i:6584 original size:13 final size:13
Alignment explanation
Indices: 6566--6592 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
6556 CTACCACTGT
6566 TTGTATCGATACA
1 TTGTATCGATACA
6579 TTGTATCGATACA
1 TTGTATCGATACA
6592 T
1 T
6593 GATGAATTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:10407 original size:13 final size:13
Alignment explanation
Indices: 10389--10413 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
10379 CACAAAATGT
10389 TGTATCGATACAA
1 TGTATCGATACAA
10402 TGTATCGATACA
1 TGTATCGATACA
10414 TATTTTTTTG
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:10502 original size:13 final size:13
Alignment explanation
Indices: 10484--10508 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
10474 ATTACTCACA
10484 TGTATCGATACAT
1 TGTATCGATACAT
10497 TGTATCGATACA
1 TGTATCGATACA
10509 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:10645 original size:52 final size:52
Alignment explanation
Indices: 10517--10637 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
10507 CACTGATCTT
*
10517 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
10569 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
10621 TGTATCGATACATGCAG
1 TGTATCGATACATGCAG
10638 ATAAATTTTC
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:17524 original size:1 final size:1
Alignment explanation
Indices: 17520--17591 Score: 72
Period size: 1 Copynumber: 72.0 Consensus size: 1
17510 AAGGTGATGG
* * * * * * * *
17520 AAAAAAAAAACAAACAAACAAACAAAAAAAACACACAAAAAAAAAAAAACAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
17585 AAAAAAA
1 AAAAAAA
17592 GAAAGTGCAA
Statistics
Matches: 55, Mismatches: 16, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 55 1.00
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:17546 original size:17 final size:15
Alignment explanation
Indices: 17523--17591 Score: 81
Period size: 14 Copynumber: 4.6 Consensus size: 15
17513 GTGATGGAAA
17523 AAAAAAACAAACAAAC
1 AAAAAAA-AAACAAAC
*
17539 AAACAAAAAAAACACAC
1 -AA-AAAAAAAACAAAC
17556 AAAAAAAAAA-AAAC
1 AAAAAAAAAACAAAC
17570 AAAAAAAAAA-AAA-
1 AAAAAAAAAACAAAC
17583 AAAAAAAAA
1 AAAAAAAAA
17592 GAAAGTGCAA
Statistics
Matches: 49, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
13 9 0.18
14 16 0.33
15 8 0.16
16 2 0.04
17 9 0.18
18 5 0.10
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAACAAAC
Found at i:17562 original size:14 final size:12
Alignment explanation
Indices: 17520--17591 Score: 83
Period size: 12 Copynumber: 5.8 Consensus size: 12
17510 AAGGTGATGG
17520 AAAAAAAAAACA
1 AAAAAAAAAACA
* *
17532 AACAAACAAACA
1 AAAAAAAAAACA
*
17544 AAAAAAACACACAAA
1 AAAAAAA-A-A-ACA
17559 AAAAAAAAAACA
1 AAAAAAAAAACA
17571 AAAAAAAAAA-A
1 AAAAAAAAAACA
17582 AAAAAAAAAA
1 AAAAAAAAAA
17592 GAAAGTGCAA
Statistics
Matches: 51, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
11 11 0.22
12 27 0.53
13 2 0.04
14 2 0.04
15 9 0.18
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAACA
Found at i:17863 original size:16 final size:16
Alignment explanation
Indices: 17832--17863 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
17822 TGTTCTTTTC
*
17832 CAAAAAAGAAACAAAA
1 CAAAAAAGAAAAAAAA
17848 CAAAAAAGAAAAAAAA
1 CAAAAAAGAAAAAAAA
17864 GAGAGGAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.84, C:0.09, G:0.06, T:0.00
Consensus pattern (16 bp):
CAAAAAAGAAAAAAAA
Found at i:18977 original size:27 final size:27
Alignment explanation
Indices: 18946--19035 Score: 99
Period size: 27 Copynumber: 3.1 Consensus size: 27
18936 CTTTTCTCTT
*
18946 TTCAAAGCCCACGACTCCGTGGCACTC
1 TTCAAAGCCCACAACTCCGTGGCACTC
18973 TTCAAAGCCCACAACTCCGTGGCACCTTTTTC
1 TTCAAAGCCCACAACTCCGTGGCA-C----TC
*
19005 TGTTTAAAGCCCACAACTCCGTGGCACTC
1 --TTCAAAGCCCACAACTCCGTGGCACTC
19034 TT
1 TT
19036 TTTCTCTTTT
Statistics
Matches: 54, Mismatches: 2, Indels: 14
0.77 0.03 0.20
Matches are distributed among these distances:
27 25 0.46
28 1 0.02
29 2 0.04
32 2 0.04
33 1 0.02
34 23 0.43
ACGTcount: A:0.22, C:0.37, G:0.16, T:0.26
Consensus pattern (27 bp):
TTCAAAGCCCACAACTCCGTGGCACTC
Found at i:19097 original size:66 final size:66
Alignment explanation
Indices: 18973--19691 Score: 900
Period size: 66 Copynumber: 10.9 Consensus size: 66
18963 CGTGGCACTC
* *
18973 TTCAAAGCCCACAACTCCGTGGCACCTTTTTCTGTTTAAAGCCCACAACTCCGTGGCACTCTTTT
1 TTCAAAGCCCACAACTCCGTGGCACCTTCTT-T-TTTAAAGCCCACAACTCCGTGGCAC-C-TTC
19038 TCTCTT
62 T-TCTT
* * *
19044 TTCAAAGCCCACGACTCCGTGGCA-C-TC-TTTTTAAAGCCCACAACTCTGTGGCACTCTTTTTC
1 TTCAAAGCCCACAACTCCGTGGCACCTTCTTTTTTAAAGCCCACAACTCCGTGGCAC-CTTCTTC
*
19106 CT
65 TT
** * * *
19108 CCCTAAGCCCACAACTCTGTGGCACTCTT-TTTTCCTTCTAAGCCCACAACTCCGTGGCA---TC
1 TTCAAAGCCCACAACTCCGTGGCAC-CTTCTTTT--TT-AAAGCCCACAACTCCGTGGCACCTTC
19169 --C-T
62 TTCTT
19171 TT--AAGCCCCACAACTCCGTGGCACCTTCTTTTTTAAAGCCCACAACTCCGTGGCACCTTCTTC
1 TTCAAAG-CCCACAACTCCGTGGCACCTTCTTTTTTAAAGCCCACAACTCCGTGGCACCTTCTTC
19234 -T
65 TT
* *
19235 TTCCAAGCCCACAACTCCGTGGCA-CTTCTTCTTTCCAAAGCCCACAAACTCCGTGGCACCTTCT
1 TTCAAAGCCCACAACTCCGTGGCACCTTCTT-TTT-TAAAGCCCAC-AACTCCGTGGCACCTTCT
19299 TCTT
63 TCTT
* **
19303 TCCAAAGCCCACAACTCCGT-GCACCTTC-TTTCCAAAGCCCACAACTCCGTGGCACCTTCTTCT
1 TTCAAAGCCCACAACTCCGTGGCACCTTCTTTTTTAAAGCCCACAACTCCGTGGCACCTTCTTCT
19366 T
66 T
*
19367 TCCAAAG-CCACAACTCCGTGGCACCTTCTTTTTTAAAGCCCACAACTCCGTGGCACCTTCTTCT
1 TTCAAAGCCCACAACTCCGTGGCACCTTCTTTTTTAAAGCCCACAACTCCGTGGCACCTTCTTCT
19431 T
66 T
*
19432 TCCAAAGCCCACAACTCCGTGGCACCTTCCTTTTTTAAAGCCCACAACTCCGTGGCACCTTCTTC
1 TTCAAAGCCCACAACTCCGTGGCACCTT-CTTTTTTAAAGCCCACAACTCCGTGGCACCTTCTTC
19497 -T
65 TT
*
19498 TTCCAAGCCCACAACTCCGTGGCACCTTCTTTTTTAAAGCCCACAACTCCGTGGGCACCTTCTTC
1 TTCAAAGCCCACAACTCCGTGGCACCTTCTTTTTTAAAGCCCACAACTCCGT-GGCACCTTCTTC
19563 TT
65 TT
* * *
19565 TCCAAAGCCCA-AACTCCGTGGCACCTTCTTTTTTAAAGCCCACAACTCCATGGCACTCTTTTTC
1 TTCAAAGCCCACAACTCCGTGGCACCTTCTTTTTTAAAGCCCACAACTCCGTGGCAC-CTTCTT-
19629 CCTT
64 -CTT
* *
19633 TTCAAAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAAGCCCACAACTCCGTTGGCAC
1 TTCAAAGCCCACAACTCCGTGGCACCTTCTT-TTTTAAAGCCCACAACTCCG-TGGCAC
19692 TCTTTTTCCC
Statistics
Matches: 583, Mismatches: 32, Indels: 66
0.86 0.05 0.10
Matches are distributed among these distances:
59 20 0.03
60 2 0.00
61 6 0.01
62 23 0.04
63 13 0.02
64 70 0.12
65 104 0.18
66 145 0.25
67 75 0.13
68 37 0.06
69 20 0.03
70 39 0.07
71 29 0.05
ACGTcount: A:0.21, C:0.37, G:0.12, T:0.29
Consensus pattern (66 bp):
TTCAAAGCCCACAACTCCGTGGCACCTTCTTTTTTAAAGCCCACAACTCCGTGGCACCTTCTTCT
T
Found at i:19211 original size:33 final size:32
Alignment explanation
Indices: 18851--19698 Score: 818
Period size: 33 Copynumber: 26.1 Consensus size: 32
18841 GCATTTTTTC
* * *
18851 TTTAAAG-CCACAATTCCGTGGCACC-TCATC
1 TTTAAAGCCCACAACTCCGTGGCACCTTCTTT
* * *
18881 TTT-AAGCCCACAATTCCGTGGCACC-TCATC
1 TTTAAAGCCCACAACTCCGTGGCACCTTCTTT
18911 TTT-AAGCCCACAACTCCGTGGCACTCTTTTCTCTT
1 TTTAAAGCCCACAACTCCGTGGCAC-C--TTCT-TT
* *
18946 TTCAAAGCCCACGACTCCGTGGCA-C-TC---
1 TTTAAAGCCCACAACTCCGTGGCACCTTCTTT
* *
18973 TTCAAAGCCCACAACTCCGTGGCACCTTTTTCT
1 TTTAAAGCCCACAACTCCGTGGCACCTTCTT-T
19006 GTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCTCTT
1 -TTTAAAGCCCACAACTCCGTGGCAC-C---TTCT-TT
* *
19044 TTCAAAGCCCACGACTCCGTGGCA-C-TC-TT
1 TTTAAAGCCCACAACTCCGTGGCACCTTCTTT
*
19073 TTTAAAGCCCACAACTCTGTGGCA-C-TCTTT
1 TTTAAAGCCCACAACTCCGTGGCACCTTCTTT
* *
19103 TTCCTCCCTAAGCCCACAACTCTGTGGCACTCTT-TTT
1 TT--T---AAAGCCCACAACTCCGTGGCAC-CTTCTTT
* *
19140 TCCTTCTAAGCCCACAACTCCGTGGCA---TC--C
1 T--TT-AAAGCCCACAACTCCGTGGCACCTTCTTT
19170 TTT-AAGCCCCACAACTCCGTGGCACCTTCTTT
1 TTTAAAG-CCCACAACTCCGTGGCACCTTCTTT
19202 TTTAAAGCCCACAACTCCGTGGCACCTTCTTCT
1 TTTAAAGCCCACAACTCCGTGGCACCTTCTT-T
**
19235 TTCCAAGCCCACAACTCCGTGGCA-CTTCTTCT
1 TTTAAAGCCCACAACTCCGTGGCACCTTCTT-T
*
19267 TTCCAAAGCCCACAAACTCCGTGGCACCTTCTTCT
1 TT-TAAAGCCCAC-AACTCCGTGGCACCTTCTT-T
*
19302 TTCCAAAGCCCACAACTCCGT-GCACCTTC-TT
1 TT-TAAAGCCCACAACTCCGTGGCACCTTCTTT
**
19333 TCCAAAGCCCACAACTCCGTGGCACCTTCTTCT
1 TTTAAAGCCCACAACTCCGTGGCACCTTCTT-T
*
19366 TTCCAAAG-CCACAACTCCGTGGCACCTTCTTT
1 TT-TAAAGCCCACAACTCCGTGGCACCTTCTTT
19398 TTTAAAGCCCACAACTCCGTGGCACCTTCTTCT
1 TTTAAAGCCCACAACTCCGTGGCACCTTCTT-T
*
19431 TTCCAAAGCCCACAACTCCGTGGCACCTTCCTTT
1 TT-TAAAGCCCACAACTCCGTGGCACCTT-CTTT
19465 TTTAAAGCCCACAACTCCGTGGCACCTTCTTCT
1 TTTAAAGCCCACAACTCCGTGGCACCTTCTT-T
**
19498 TTCCAAGCCCACAACTCCGTGGCACCTTCTTT
1 TTTAAAGCCCACAACTCCGTGGCACCTTCTTT
19530 TTTAAAGCCCACAACTCCGTGGGCACCTTCTTCT
1 TTTAAAGCCCACAACTCCGT-GGCACCTTCTT-T
*
19564 TTCCAAAGCCCA-AACTCCGTGGCACCTTCTTT
1 TT-TAAAGCCCACAACTCCGTGGCACCTTCTTT
* *
19596 TTTAAAGCCCACAACTCCATGGCACTCTTTTTCCCT
1 TTTAAAGCCCACAACTCCGTGGCAC-CTTCTT---T
* *
19632 TTTCAAAGCCCACAACTCCGTGGCACTTTTTTCT
1 TTT-AAAGCCCACAACTCCGTGGCACCTTCTT-T
19666 TTTAAAGCCCACAACTCCGTTGGCA-C-TCTTT
1 TTTAAAGCCCACAACTCCG-TGGCACCTTCTTT
19697 TT
1 TT
19699 CCCTTGTTAA
Statistics
Matches: 719, Mismatches: 38, Indels: 121
0.82 0.04 0.14
Matches are distributed among these distances:
26 3 0.00
27 40 0.06
28 3 0.00
29 30 0.04
30 74 0.10
31 31 0.04
32 106 0.15
33 169 0.24
34 101 0.14
35 78 0.11
36 28 0.04
37 49 0.07
38 5 0.01
39 2 0.00
ACGTcount: A:0.21, C:0.37, G:0.12, T:0.30
Consensus pattern (32 bp):
TTTAAAGCCCACAACTCCGTGGCACCTTCTTT
Found at i:19778 original size:32 final size:31
Alignment explanation
Indices: 19740--19845 Score: 151
Period size: 32 Copynumber: 3.3 Consensus size: 31
19730 TTTTTCCTTC
19740 CCAAAGCCCACACAAGTCGGTGGCAACTCTT
1 CCAAAGCCCACACAAGTCGGTGGCAACTCTT
19771 CCTAAAGCCCACACAAGTCGGTGGCAAACCTTCTT
1 CC-AAAGCCCACACAAGTCGGTGGC-AA-C-TCTT
*
19806 CCAAAGCCCACACAAGTCGGTGGCAACCCTT
1 CCAAAGCCCACACAAGTCGGTGGCAACTCTT
*
19837 -CGAAGCCCA
1 CCAAAGCCCA
19846 ATATAGCTGG
Statistics
Matches: 69, Mismatches: 2, Indels: 9
0.86 0.03 0.11
Matches are distributed among these distances:
30 8 0.12
31 5 0.07
32 23 0.33
33 4 0.06
34 23 0.33
35 6 0.09
ACGTcount: A:0.29, C:0.37, G:0.19, T:0.15
Consensus pattern (31 bp):
CCAAAGCCCACACAAGTCGGTGGCAACTCTT
Found at i:19817 original size:34 final size:34
Alignment explanation
Indices: 19740--19837 Score: 157
Period size: 34 Copynumber: 2.9 Consensus size: 34
19730 TTTTTCCTTC
19740 CCAAAGCCCACACAAGTCGGTGGC-AA-C-TCTT
1 CCAAAGCCCACACAAGTCGGTGGCAAACCTTCTT
19771 CCTAAAGCCCACACAAGTCGGTGGCAAACCTTCTT
1 CC-AAAGCCCACACAAGTCGGTGGCAAACCTTCTT
*
19806 CCAAAGCCCACACAAGTCGGTGGCAACCCTTC
1 CCAAAGCCCACACAAGTCGGTGGCAAACCTTC
19838 GAAGCCCAAT
Statistics
Matches: 62, Mismatches: 1, Indels: 5
0.91 0.01 0.07
Matches are distributed among these distances:
31 2 0.03
32 22 0.35
33 2 0.03
34 30 0.48
35 6 0.10
ACGTcount: A:0.29, C:0.37, G:0.18, T:0.16
Consensus pattern (34 bp):
CCAAAGCCCACACAAGTCGGTGGCAAACCTTCTT
Found at i:20028 original size:49 final size:49
Alignment explanation
Indices: 19843--20363 Score: 624
Period size: 49 Copynumber: 10.5 Consensus size: 49
19833 CCTTCGAAGC
19843 CCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTTTAAGT
1 CCAATATAGCTGGCCTTGAATCAGCATATTGGCACC--TT-CATCTTTAAGT
* *
19895 CCAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTTTAAGT
1 CCAATATAGCTGGCCTTGAATCAGCATATTGGCACC--TT-CATCTTTAAGT
* * *
19947 CCAATGTAGCTTGGCCTTGACTCAGCACATTGGCACCTTCATCTTTAAGT
1 CCAATATAGC-TGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGT
* *
19997 CCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGT
1 CCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGT
* * * *
20046 CCAATGTAGCTGGCCTTGACTCAGCACATTGGCA-CATCATCATTTTAAGT
1 CCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATC--TTTAAGT
* * * *
20096 CCAATATCGCTGACCTTGAATCAGCATATTGGCATCTTCATCTTGAAGT
1 CCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGT
* * * *
20145 CCAATGTAGCTAGCCTTGACTCAGCACATTTGGCA----C--CTTTAAGT
1 CCAATATAGCTGGCCTTGAATCAGCATA-TTGGCACCTTCATCTTTAAGT
* *
20189 CCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGT
1 CCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGT
* * * *
20238 CCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCATCATCATTTTAAGT
1 CCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATC--TTTAAGT
* *
20289 CCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGT
1 CCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGT
* *
20338 TCAATGTAGCTGGCCTTGAATCAGCA
1 CCAATATAGCTGGCCTTGAATCAGCA
20364 CGTTGACAAT
Statistics
Matches: 407, Mismatches: 49, Indels: 29
0.84 0.10 0.06
Matches are distributed among these distances:
43 6 0.01
44 30 0.07
46 1 0.00
47 1 0.00
48 6 0.01
49 168 0.41
50 61 0.15
51 51 0.13
52 59 0.14
53 24 0.06
ACGTcount: A:0.25, C:0.26, G:0.17, T:0.32
Consensus pattern (49 bp):
CCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGT
Found at i:20103 original size:99 final size:100
Alignment explanation
Indices: 19843--20431 Score: 781
Period size: 99 Copynumber: 5.9 Consensus size: 100
19833 CCTTCGAAGC
* * * * ** *
19843 CCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTTTAAGTCCAATGTCGCTGG
1 CCAATGTAGCTGGCCTTGACTCAGCACATTGGCACATCAT-CATCTTTAAGTCCAATATCGCTGG
*
19908 CCTTGAATCAGCATATTGGCACCTTTTCCATCTTTAAGT
65 CCTTGAATCAGCATATTGGCA--TCTT-CATCTTTAAGT
*
19947 CCAATGTAGCTTGGCCTTGACTCAGCACATTGGCAC--CTTCATCTTTAAGTCCAATATCGCTGG
1 CCAATGTAGC-TGGCCTTGACTCAGCACATTGGCACATCATCATCTTTAAGTCCAATATCGCTGG
20010 CCTTGAATCAGCATATTGGCATCTTCATCTTTAAGT
65 CCTTGAATCAGCATATTGGCATCTTCATCTTTAAGT
*
20046 CCAATGTAGCTGGCCTTGACTCAGCACATTGGCACATCATCAT-TTTAAGTCCAATATCGCTGAC
1 CCAATGTAGCTGGCCTTGACTCAGCACATTGGCACATCATCATCTTTAAGTCCAATATCGCTGGC
*
20110 CTTGAATCAGCATATTGGCATCTTCATCTTGAAGT
66 CTTGAATCAGCATATTGGCATCTTCATCTTTAAGT
*
20145 CCAATGTAGCTAGCCTTGACTCAGCACATTTGG-----CA-C--CTTTAAGTCCAATATCGCTGG
1 CCAATGTAGCTGGCCTTGACTCAGCACA-TTGGCACATCATCATCTTTAAGTCCAATATCGCTGG
20202 CCTTGAATCAGCATATTGGCATCTTCATCTTTAAGT
65 CCTTGAATCAGCATATTGGCATCTTCATCTTTAAGT
20238 CCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCATCATCAT-TTTAAGTCCAATATCGCTGG
1 CCAATGTAGCTGGCCTTGACTCAGCACATTGGCA-CATCATCATCTTTAAGTCCAATATCGCTGG
20302 CCTTGAATCAGCATATTGGCATCTTCATCTTTAAGT
65 CCTTGAATCAGCATATTGGCATCTTCATCTTTAAGT
* * * * * *
20338 TCAATGTAGCTGGCCTTGAATCAGCACGTTGACA-ATCCTTTTTCTCATCTTTAAGCCCAATATC
1 CCAATGTAGCTGGCCTTGACTCAGCACATTGGCACAT-C-----ATCATCTTTAAGTCCAATATC
* * *
20402 GTTGGCCATGAATCAACATATTGGCATCTT
60 GCTGGCCTTGAATCAGCATATTGGCATCTT
20432 TATCACTTTT
Statistics
Matches: 442, Mismatches: 22, Indels: 41
0.88 0.04 0.08
Matches are distributed among these distances:
92 4 0.01
93 81 0.18
94 1 0.00
95 2 0.00
98 29 0.07
99 104 0.24
100 98 0.22
102 44 0.10
103 2 0.00
104 13 0.03
105 64 0.14
ACGTcount: A:0.25, C:0.26, G:0.17, T:0.33
Consensus pattern (100 bp):
CCAATGTAGCTGGCCTTGACTCAGCACATTGGCACATCATCATCTTTAAGTCCAATATCGCTGGC
CTTGAATCAGCATATTGGCATCTTCATCTTTAAGT
Found at i:20224 original size:192 final size:193
Alignment explanation
Indices: 19843--20364 Score: 805
Period size: 192 Copynumber: 2.7 Consensus size: 193
19833 CCTTCGAAGC
* * * * ** *
19843 CCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTTTAAGTCCAATGTCGCTGG
1 CCAATGTAGCTGGCCTTGACTCAGCACATTGGCACATCAT-CAT-TTTAAGTCCAATATCGCTGG
*
19908 CCTTGAATCAGCATATTGGCACCTTTTCCATCTTTAAGTCCAATGTAGCTTGGCCTTGACTCAGC
64 CCTTGAATCAGCATATTGGCA--TCTT-CATCTTTAAGTCCAATGTAGC-TGGCCTTGACTCAGC
19973 ACATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCAT
125 ACATTGGCA-C--CA-CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCAT
20038 CTTTAAGT
186 CTTTAAGT
*
20046 CCAATGTAGCTGGCCTTGACTCAGCACATTGGCACATCATCATTTTAAGTCCAATATCGCTGACC
1 CCAATGTAGCTGGCCTTGACTCAGCACATTGGCACATCATCATTTTAAGTCCAATATCGCTGGCC
* *
20111 TTGAATCAGCATATTGGCATCTTCATCTTGAAGTCCAATGTAGCTAGCCTTGACTCAGCACATTT
66 TTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACA-TT
20176 GGCA-C-CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGT
130 GGCACCACTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGT
20238 CCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCATCATCATTTTAAGTCCAATATCGCTGGC
1 CCAATGTAGCTGGCCTTGACTCAGCACATTGGCA-CATCATCATTTTAAGTCCAATATCGCTGGC
* *
20303 CTTGAATCAGCATATTGGCATCTTCATCTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCAC
65 CTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCAC
20365 GTTGACAATC
Statistics
Matches: 301, Mismatches: 16, Indels: 14
0.91 0.05 0.04
Matches are distributed among these distances:
192 91 0.30
193 87 0.29
194 1 0.00
197 17 0.06
198 26 0.09
199 3 0.01
201 39 0.13
202 3 0.01
203 34 0.11
ACGTcount: A:0.25, C:0.26, G:0.17, T:0.32
Consensus pattern (193 bp):
CCAATGTAGCTGGCCTTGACTCAGCACATTGGCACATCATCATTTTAAGTCCAATATCGCTGGCC
TTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTG
GCACCACTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGT
Found at i:20539 original size:122 final size:124
Alignment explanation
Indices: 20321--20608 Score: 501
Period size: 122 Copynumber: 2.3 Consensus size: 124
20311 AGCATATTGG
* *
20321 CATCTTCATCTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACGTTGACAATCCTTTTTCTCAT
1 CATCTTCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACGTTGACAATCCTTTTTCTCAT
*
20386 CTTTAAGCCCAATATCGTTGGCCATGAATCAACATATTGGCATCTTTATC-ACTTTTCT
66 CTTTAAGCCCAATATCGTTGGCCATGAATCAACATAGTGGCATCTTTATCAACTTTTCT
*
20444 CATCTTCATCTTTAAGTCCAATATTGCTGGCCTTGAATCAGCACGTTGAC-ATCCTTTTTCTCAT
1 CATCTTCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACGTTGACAATCCTTTTTCTCAT
20508 CTTTAAGCCCAATATCGTTGGCCATGAATCAACATAGTGGCATCTTTATCAACTTTTCT
66 CTTTAAGCCCAATATCGTTGGCCATGAATCAACATAGTGGCATCTTTATCAACTTTTCT
* *
20567 CATCATCAT-TTTAAGTCCAATATCGCTGGCCTTGAATCAGCA
1 CATCTTCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCA
20609 TATTGGCATC
Statistics
Matches: 158, Mismatches: 6, Indels: 3
0.95 0.04 0.02
Matches are distributed among these distances:
122 95 0.60
123 63 0.40
ACGTcount: A:0.25, C:0.25, G:0.13, T:0.37
Consensus pattern (124 bp):
CATCTTCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACGTTGACAATCCTTTTTCTCAT
CTTTAAGCCCAATATCGTTGGCCATGAATCAACATAGTGGCATCTTTATCAACTTTTCT
Found at i:20820 original size:169 final size:170
Alignment explanation
Indices: 20444--20963 Score: 936
Period size: 169 Copynumber: 3.1 Consensus size: 170
20434 TCACTTTTCT
* * *
20444 CATCTTCATCTTTAAGTCCAATATTGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATC
1 CATCTTCATCTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATC
*
20509 TTTAAGCCCAATATCGTTGGCCATGAATCAACATAGTGGCATCTTTATCAACTTTTCTCATCATC
66 TTTAAGCCCAATATCGTTGGCCATGAATCAACATATTGGCATCTTTATC-ACTTTTCTCATCATC
20574 ATTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGG
130 ATTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGG
*
20615 CATCTTCATCTTTAAGTTCAATGTAGCTGACCTTGAATCAGCACGTTGACATCCTTTTTCTCATC
1 CATCTTCATCTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATC
20680 TTTAAGCCCAATATCGTTGGCCATGAATCAACATATTGGCATCTTTATCAC-TTTCTCATCATCA
66 TTTAAGCCCAATATCGTTGGCCATGAATCAACATATTGGCATCTTTATCACTTTTCTCATCATCA
20744 TTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGG
131 TTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGG
20784 CATCTTCATCTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATC
1 CATCTTCATCTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATC
* *
20849 TTTAGGCCCAATATCGTTGGCCATGAATCAACATATTGGCATCTTTATCACTTTTCTCATCTTCA
66 TTTAAGCCCAATATCGTTGGCCATGAATCAACATATTGGCATCTTTATCACTTTTCTCATCATCA
20914 TCTTTAAGTCCAATAT-GCTGGCCTTGAATCAGCATATTGG
131 T-TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGG
*
20954 CACCTTCATC
1 CATCTTCATC
20964 ATCTTAAAAC
Statistics
Matches: 338, Mismatches: 9, Indels: 5
0.96 0.03 0.01
Matches are distributed among these distances:
169 167 0.49
170 48 0.14
171 123 0.36
ACGTcount: A:0.25, C:0.25, G:0.14, T:0.37
Consensus pattern (170 bp):
CATCTTCATCTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATC
TTTAAGCCCAATATCGTTGGCCATGAATCAACATATTGGCATCTTTATCACTTTTCTCATCATCA
TTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGG
Found at i:21795 original size:13 final size:13
Alignment explanation
Indices: 21777--21801 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
21767 CATAAAATGT
21777 TGTATCGATACAA
1 TGTATCGATACAA
21790 TGTATCGATACA
1 TGTATCGATACA
21802 TATTTTTTTT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:21885 original size:13 final size:13
Alignment explanation
Indices: 21867--21891 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
21857 ATTACTCACA
21867 TGTATCGATACAT
1 TGTATCGATACAT
21880 TGTATCGATACA
1 TGTATCGATACA
21892 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:22028 original size:52 final size:52
Alignment explanation
Indices: 21900--22020 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
21890 CACTGATCTT
*
21900 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
21952 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
22004 TGTATCGATACATGCAG
1 TGTATCGATACATGCAG
22021 ATAAATTTTC
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:25708 original size:15 final size:17
Alignment explanation
Indices: 25677--25708 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
25667 AGCAAGATGA
25677 AAGTGTCCAAAATGAAG
1 AAGTGTCCAAAATGAAG
25694 AAGT-TCCAAAA-GAAG
1 AAGTGTCCAAAATGAAG
25709 TTGATGAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 4 0.27
16 7 0.47
17 4 0.27
ACGTcount: A:0.50, C:0.12, G:0.22, T:0.16
Consensus pattern (17 bp):
AAGTGTCCAAAATGAAG
Done.