Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold920
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: 39492
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.31
Found at i:10972 original size:1 final size:1
Alignment explanation
Indices: 10966--11100 Score: 90
Period size: 1 Copynumber: 135.0 Consensus size: 1
10956 GGCGTCCTCC
* * * * * ** ** **
10966 AAAAAAAACAAACAAAAAAAACAAAACAAAACAAAAAAAACGAAAAAAAACGAAAAAAACGAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * * * * * *
11031 AAACAAAAAAAAACAAAAAAATAAAAAAAACAAACAAAAACAAAAAAAAAAAACAAACAAAAACA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
11096 AAAAA
1 AAAAA
11101 GGGGGTCCGG
Statistics
Matches: 97, Mismatches: 37, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
1 97 1.00
ACGTcount: A:0.85, C:0.12, G:0.02, T:0.01
Consensus pattern (1 bp):
A
Found at i:11097 original size:10 final size:9
Alignment explanation
Indices: 10969--11093 Score: 155
Period size: 9 Copynumber: 13.6 Consensus size: 9
10959 GTCCTCCAAA
10969 AAAAACAAAC
1 AAAAA-AAAC
10979 AAAAAAAAC
1 AAAAAAAAC
10988 AAAACAAAAC
1 AAAA-AAAAC
10998 AAAAAAAAC
1 AAAAAAAAC
11007 GAAAAAAAAC
1 -AAAAAAAAC
*
11017 GAAAAAAAC
1 AAAAAAAAC
*
11026 GAAAAAAAC
1 AAAAAAAAC
11035 AAAAAAAA-
1 AAAAAAAAC
*
11043 ACAAAAAAAT
1 A-AAAAAAAC
11053 AAAAAAAAC
1 AAAAAAAAC
11062 AAACAAAAAC
1 AAA-AAAAAC
11072 AAAAAAAA-
1 AAAAAAAAC
*
11080 AAAACAAAC
1 AAAAAAAAC
11089 AAAAA
1 AAAAA
11094 CAAAAAAGGG
Statistics
Matches: 104, Mismatches: 5, Indels: 13
0.85 0.04 0.11
Matches are distributed among these distances:
8 8 0.08
9 63 0.61
10 33 0.32
ACGTcount: A:0.85, C:0.12, G:0.02, T:0.01
Consensus pattern (9 bp):
AAAAAAAAC
Found at i:11100 original size:19 final size:18
Alignment explanation
Indices: 10969--11093 Score: 155
Period size: 19 Copynumber: 6.8 Consensus size: 18
10959 GTCCTCCAAA
10969 AAAAACAAACAAAAAAAAC
1 AAAAA-AAACAAAAAAAAC
10988 AAAACAAAACAAAAAAAAC
1 AAAA-AAAACAAAAAAAAC
*
11007 GAAAAAAAACGAAAAAAAC
1 -AAAAAAAACAAAAAAAAC
*
11026 GAAAAAAACAAAAAAAA-
1 AAAAAAAACAAAAAAAAC
*
11043 ACAAAAAAATAAAAAAAAC
1 A-AAAAAAACAAAAAAAAC
11062 AAACAAAAACAAAAAAAA-
1 AAA-AAAAACAAAAAAAAC
*
11080 AAAACAAACAAAAA
1 AAAAAAAACAAAAA
11094 CAAAAAAGGG
Statistics
Matches: 94, Mismatches: 7, Indels: 12
0.83 0.06 0.11
Matches are distributed among these distances:
17 10 0.11
18 35 0.37
19 44 0.47
20 5 0.05
ACGTcount: A:0.85, C:0.12, G:0.02, T:0.01
Consensus pattern (18 bp):
AAAAAAAACAAAAAAAAC
Found at i:12582 original size:29 final size:29
Alignment explanation
Indices: 12543--12698 Score: 172
Period size: 29 Copynumber: 5.4 Consensus size: 29
12533 TCACCCTTCA
*
12543 AAAGTCCACAAGTCAGTGGCATATTTTTC
1 AAAGCCCACAAGTCAGTGGCATATTTTTC
*
12572 AAAGCCCACAAGTCAGTGGCATTTTTTTC
1 AAAGCCCACAAGTCAGTGGCATATTTTTC
**
12601 AAAAGCCCACAAGTCAGTGGCA-A-CCTTC
1 -AAAGCCCACAAGTCAGTGGCATATTTTTC
* **
12629 AAAGCCCACAAATCAGTGGCACCCTTTTTC
1 AAAGCCCACAAGTCAGTGGCA-TATTTTTC
* * * *
12659 GAAGCCCACAAGTCGGTGGCATCTTTTCC
1 AAAGCCCACAAGTCAGTGGCATATTTTTC
*
12688 AAAGCTCACAA
1 AAAGCCCACAA
12699 CTCTGTAGCA
Statistics
Matches: 107, Mismatches: 16, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
27 20 0.19
28 3 0.03
29 42 0.39
30 42 0.39
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (29 bp):
AAAGCCCACAAGTCAGTGGCATATTTTTC
Found at i:12608 original size:30 final size:28
Alignment explanation
Indices: 12543--12698 Score: 161
Period size: 30 Copynumber: 5.4 Consensus size: 28
12533 TCACCCTTCA
*
12543 AAAGTCCACAAGTCAGTGGCATATTTTTC
1 AAAGCCCACAAGTCAGTGGCAT-TTTTTC
12572 AAAGCCCACAAGTCAGTGGCATTTTTTTC
1 AAAGCCCACAAGTCAGTGGCA-TTTTTTC
***
12601 AAAAGCCCACAAGTCAGTGGCA-ACCTTC
1 -AAAGCCCACAAGTCAGTGGCATTTTTTC
* *
12629 AAAGCCCACAAATCAGTGGCACCCTTTTTC
1 AAAGCCCACAAGTCAGTGGCA--TTTTTTC
* * *
12659 GAAGCCCACAAGTCGGTGGCATCTTTTCC
1 AAAGCCCACAAGTCAGTGGCAT-TTTTTC
*
12688 AAAGCTCACAA
1 AAAGCCCACAA
12699 CTCTGTAGCA
Statistics
Matches: 106, Mismatches: 15, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
27 20 0.19
28 3 0.03
29 40 0.38
30 43 0.41
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (28 bp):
AAAGCCCACAAGTCAGTGGCATTTTTTC
Found at i:12664 original size:57 final size:59
Alignment explanation
Indices: 12539--12680 Score: 182
Period size: 57 Copynumber: 2.4 Consensus size: 59
12529 TTTATCACCC
* ** * **
12539 TTCAAAAGTCCACAAGTCAGTGGCATATTTTTCAAAGCCCACAAGTCAGTGGCATTTTT
1 TTCAAAAGCCCACAAGTCAGTGGCATATCCTTCAAAGCCCACAAATCAGTGGCACCTTT
12598 TTCAAAAGCCCACAAGTCAGTGGCA-A-CCTTCAAAGCCCACAAATCAGTGGCACCCTTT
1 TTCAAAAGCCCACAAGTCAGTGGCATATCCTTCAAAGCCCACAAATCAGTGGCA-CCTTT
* *
12656 TTC-GAAGCCCACAAGTCGGTGGCAT
1 TTCAAAAGCCCACAAGTCAGTGGCAT
12681 CTTTTCCAAA
Statistics
Matches: 73, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
57 42 0.58
58 7 0.10
59 24 0.33
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.24
Consensus pattern (59 bp):
TTCAAAAGCCCACAAGTCAGTGGCATATCCTTCAAAGCCCACAAATCAGTGGCACCTTT
Found at i:12733 original size:34 final size:34
Alignment explanation
Indices: 12689--13180 Score: 495
Period size: 34 Copynumber: 14.8 Consensus size: 34
12679 ATCTTTTCCA
* * *
12689 AAGCTCACAACTCTGTAGCACTCTTTTTCTTTTT
1 AAGCCCACAACTCCGTGGCACTCTTTTTCTTTTT
*
12723 AAGCCCACAACTCCGTGGCACT-TTTTTCATCTTT
1 AAGCCCACAACTCCGTGGCACTCTTTTTC-TTTTT
12757 AAGCCCACAACTCCGTGGCAC-C-----C-TTTT
1 AAGCCCACAACTCCGTGGCACTCTTTTTCTTTTT
*
12784 AAGCCCACAACTCCGTGGCACT-TTTTTCATCTTT
1 AAGCCCACAACTCCGTGGCACTCTTTTTC-TTTTT
* *
12818 AAGTCCACAACTCCGTGGCAC-CTTTTTCTTTTA
1 AAGCCCACAACTCCGTGGCACTCTTTTTCTTTTT
* **
12851 AAGCCCACAACTCCGTGACACTCTTTTTTCCATTT
1 AAGCCCACAACTCCGTGGCACTC-TTTTTCTTTTT
* *
12886 AAGTCCACAACTCCGTGGCACTCTTTTTCCCTTTTCA
1 AAGCCCACAACTCCGTGGCACTCTTTTT--CTTTT-T
* *
12923 AAACCCACAACTCCGTGGCAC-CTTTTTCTTTTA
1 AAGCCCACAACTCCGTGGCACTCTTTTTCTTTTT
* * *
12956 AAGCCCACAACTCCATGGCACTCTTTTCCCTTTT
1 AAGCCCACAACTCCGTGGCACTCTTTTTCTTTTT
* *
12990 AAGTCCACAACTCCGTGGCACTCTTTTTCCCTTTTCA
1 AAGCCCACAACTCCGTGGCACTCTTTTT--CTTTT-T
* *
13027 AAGCCCACAACTCTGTGGCACT-TTTTTCTTTTA
1 AAGCCCACAACTCCGTGGCACTCTTTTTCTTTTT
*
13060 AAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTT
1 AAGCCCACAACTCCGTGGCACTCTTTTT-CTTTTT
*
13095 -------CAACTCCGTGGCAC-CTTTTTCTTTTA
1 AAGCCCACAACTCCGTGGCACTCTTTTTCTTTTT
* *
13121 AAGCCCACAACTCCGTGGCACTTTTTTTCCCTTTT
1 AAGCCCACAACTCCGTGGCACTCTTTTT-CTTTTT
* *
13156 AAGTCTACAACTCCGTGGCA-TCTTT
1 AAGCCCACAACTCCGTGGCACTCTTT
13181 CTCCCTTCTC
Statistics
Matches: 383, Mismatches: 44, Indels: 62
0.78 0.09 0.13
Matches are distributed among these distances:
26 4 0.01
27 30 0.08
28 14 0.04
29 1 0.00
32 1 0.00
33 84 0.22
34 137 0.36
35 55 0.14
36 18 0.05
37 39 0.10
ACGTcount: A:0.20, C:0.33, G:0.11, T:0.35
Consensus pattern (34 bp):
AAGCCCACAACTCCGTGGCACTCTTTTTCTTTTT
Found at i:12795 original size:61 final size:61
Alignment explanation
Indices: 12717--13175 Score: 308
Period size: 61 Copynumber: 7.0 Consensus size: 61
12707 CACTCTTTTT
*
12717 CTTTTTAAGCCCACAACTCCGTGGCACTTTTTTCATCTTTAAGCCCACAACTCCGTGGCACC
1 CTTTTAAAGCCCACAACTCCGTGGCACTTTTTTC-TCTTTAAGCCCACAACTCCGTGGCACC
*
12779 CTTTT-AAGCCCACAACTCCGTGGCACTTTTTTCATCTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAAGCCCACAACTCCGTGGCACTTTTTTC-TCTTTAAGCCCACAACTCCGTGGCACC
* *
12840 TTTTTCTTTTAAAGCCCACAACTCCGTGACACTCTTTTT-TCCATTTAAGTCCACAACTCCGTGG
1 -----CTTTTAAAGCCCACAACTCCGTGGCACT-TTTTTCT-C-TTTAAGCCCACAACTCCGTGG
12904 CACTCTTTTTCC
58 CA--------CC
* * *
12916 CTTTTCAAAACCCACAACTCCGTGGCACCTTTTTCT-TTTAAAGCCCACAACTCCATGGCACTCT
1 CTTTT-AAAGCCCACAACTCCGTGGCACTTTTTTCTCTTT-AAGCCCACAACTCCGTGGCA----
12980 TTTCC
60 ---CC
* * *
12985 CTTTT-AAGTCCACAACTCCGTGGCACTCTTTTTCCCTTTTCAAAGCCCACAACTCTGTGGCACT
1 CTTTTAAAGCCCACAACTCCGTGGCACT-TTTTTCTC-TTT--AAGCCCACAACTCCGTGGCAC-
*
13049 TTTTT
61 ----C
* *
13054 CTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTT------TCAACTCCGTGGCACC
1 CTTTTAAAGCCCACAACTCCGTGGCACT-TTTTTCTCTTTAAGCCCACAACTCCGTGGCACC
* * *
13110 TTTTTCTTTTAAAGCCCACAACTCCGTGGCACTTTTTTTCCCTTTTAAGTCTACAACTCCGTGGC
1 -----CTTTTAAAGCCCACAACTCCGTGGCAC-TTTTTTCTC-TTTAAGCCCACAACTCCGTGGC
13175 A
59 A
13176 TCTTTCTCCC
Statistics
Matches: 332, Mismatches: 22, Indels: 80
0.76 0.05 0.18
Matches are distributed among these distances:
61 103 0.31
62 9 0.03
64 1 0.00
66 6 0.02
67 41 0.12
68 47 0.14
69 22 0.07
70 51 0.15
71 29 0.09
72 21 0.06
76 2 0.01
ACGTcount: A:0.20, C:0.34, G:0.11, T:0.35
Consensus pattern (61 bp):
CTTTTAAAGCCCACAACTCCGTGGCACTTTTTTCTCTTTAAGCCCACAACTCCGTGGCACC
Found at i:12894 original size:35 final size:36
Alignment explanation
Indices: 12778--13212 Score: 426
Period size: 35 Copynumber: 12.8 Consensus size: 36
12768 TCCGTGGCAC
12778 CCTTTT-AAGCCCACAACTCCGTGGCA--CTTTTTT
1 CCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTT
* *
12811 CATCTTT-AAGTCCACAACTCCGTGGCAC-C-TTTTT
1 CCT-TTTAAAGCCCACAACTCCGTGGCACTCTTTTTT
*
12845 -CTTTTAAAGCCCACAACTCCGTGACACTCTTTTTT
1 CCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTT
* * *
12880 CCATTT-AAGTCCACAACTCCGTGGCACTCTTTTTC
1 CCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTT
*
12915 CCTTTTCAAAACCCACAACTCCGTGGCAC-C-TTTTT
1 CCTTTT-AAAGCCCACAACTCCGTGGCACTCTTTTTT
* *
12950 -CTTTTAAAGCCCACAACTCCATGGCACTC-TTTTC
1 CCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTT
* *
12984 CCTTTT-AAGTCCACAACTCCGTGGCACTCTTTTTC
1 CCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTT
*
13019 CCTTTTCAAAGCCCACAACTCTGTGGCA--CTTTTTT
1 CCTTTT-AAAGCCCACAACTCCGTGGCACTCTTTTTT
*
13054 -CTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTC
1 CCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTT
13089 CCTTTT--------CAACTCCGTGGCAC-C-TTTTT
1 CCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTT
13115 -CTTTTAAAGCCCACAACTCCGTGGCACT-TTTTTT
1 CCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTT
* * * *
13149 CCCTTTT-AAGTCTACAACTCCGTGGCA-TCTTTCTC
1 -CCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTT
* * *
13184 CCTTCTCAAAGCCACACAAGTCGGTGGCA
1 CCTT-TTAAAGCC-CACAACTCCGTGGCA
13213 ACCTTCTTTT
Statistics
Matches: 337, Mismatches: 33, Indels: 60
0.78 0.08 0.14
Matches are distributed among these distances:
25 5 0.01
26 4 0.01
27 1 0.00
28 14 0.04
32 3 0.01
33 76 0.23
34 74 0.22
35 92 0.27
36 19 0.06
37 49 0.15
ACGTcount: A:0.20, C:0.34, G:0.11, T:0.35
Consensus pattern (36 bp):
CCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTT
Found at i:13039 original size:104 final size:102
Alignment explanation
Indices: 12694--13187 Score: 573
Period size: 104 Copynumber: 4.9 Consensus size: 102
12684 TTCCAAAGCT
* * *
12694 CACAACTCTGTAGCACTCTTTTT-CTTTTTAAGCCCACAACTCCGTGGCACTTTTTTCATCTTT-
1 CACAACTCCGTGGCACTCTTTTTCCTTTTAAAGCCCACAACTCCGTGGCACTTTTTTC-T-TTTA
*
12757 AAGCCCACAACTCCGTGGCA-------CCCTTTTAAGCC
64 AAGCCCACAACTCCGTGGCACTCTTTTCCCTTTTAAGTC
* * *
12789 CACAACTCCGTGGCACT-TTTTTCATCTTT-AAGTCCACAACTCCGTGGCACCTTTTTCTTTTAA
1 CACAACTCCGTGGCACTCTTTTTCCT-TTTAAAGCCCACAACTCCGTGGCACTTTTTTCTTTTAA
* * *
12852 AGCCCACAACTCCGTGACACTCTTTTTTCCATTTAAGTC
65 AGCCCACAACTCCGTGGCACTC-TTTTCCCTTTTAAGTC
* *
12891 CACAACTCCGTGGCACTCTTTTTCCCTTTTCAAAACCCACAACTCCGTGGCACCTTTTTCTTTTA
1 CACAACTCCGTGGCACTCTTTTT-CCTTTT-AAAGCCCACAACTCCGTGGCACTTTTTTCTTTTA
*
12956 AAGCCCACAACTCCATGGCACTCTTTTCCCTTTTAAGTC
64 AAGCCCACAACTCCGTGGCACTCTTTTCCCTTTTAAGTC
*
12995 CACAACTCCGTGGCACTCTTTTTCCCTTTTCAAAGCCCACAACTCTGTGGCACTTTTTTCTTTTA
1 CACAACTCCGTGGCACTCTTTTT-CCTTTT-AAAGCCCACAACTCCGTGGCACTTTTTTCTTTTA
13060 AAGCCCACAACTCCGTGGCACTCTTTTTCCC-TTT---T-
64 AAGCCCACAACTCCGTGGCACTC-TTTTCCCTTTTAAGTC
13095 --CAACTCCGTGGCAC-CTTTTT-CTTTTAAAGCCCACAACTCCGTGGCACTTTTTTTCCCTTTT
1 CACAACTCCGTGGCACTCTTTTTCCTTTTAAAGCCCACAACTCCGTGGCAC-TTTTTT--CTTTT
* *
13156 -AAGTCTACAACTCCGTGGCA-TCTTTCTCCCTT
63 AAAGCCCACAACTCCGTGGCACTCTTT-TCCCTT
13188 CTCAAAGCCA
Statistics
Matches: 355, Mismatches: 23, Indels: 41
0.85 0.05 0.10
Matches are distributed among these distances:
93 3 0.01
94 49 0.14
95 59 0.17
96 22 0.06
97 11 0.03
98 14 0.04
101 1 0.00
102 26 0.07
103 8 0.02
104 103 0.29
105 59 0.17
ACGTcount: A:0.20, C:0.34, G:0.11, T:0.36
Consensus pattern (102 bp):
CACAACTCCGTGGCACTCTTTTTCCTTTTAAAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAA
GCCCACAACTCCGTGGCACTCTTTTCCCTTTTAAGTC
Found at i:13233 original size:33 final size:34
Alignment explanation
Indices: 13185--13319 Score: 215
Period size: 33 Copynumber: 4.1 Consensus size: 34
13175 ATCTTTCTCC
13185 CTTCTCAAAG-CCACACAAGTCGGTGGCAA-CCTT
1 CTTCT-AAAGCCCACACAAGTCGGTGGCAACCCTT
*
13218 CTTTTAAAGCCCACACAAGTCGGTGGCAACCCTT
1 CTTCTAAAGCCCACACAAGTCGGTGGCAACCCTT
13252 -TTCTAAAGCCCACACAAGTCGGTGGCAACCCTT
1 CTTCTAAAGCCCACACAAGTCGGTGGCAACCCTT
*
13285 C-TCTAAAGCCCACACAAGTCGGTGGCAACCATT
1 CTTCTAAAGCCCACACAAGTCGGTGGCAACCCTT
13318 CT
1 CT
13320 AAGCCTAATA
Statistics
Matches: 95, Mismatches: 3, Indels: 7
0.90 0.03 0.07
Matches are distributed among these distances:
32 4 0.04
33 87 0.92
34 4 0.04
ACGTcount: A:0.27, C:0.33, G:0.18, T:0.21
Consensus pattern (34 bp):
CTTCTAAAGCCCACACAAGTCGGTGGCAACCCTT
Found at i:13433 original size:49 final size:47
Alignment explanation
Indices: 13330--13638 Score: 373
Period size: 49 Copynumber: 6.5 Consensus size: 47
13320 AAGCCTAATA
* *
13330 TAGCTGGCCTTGACTCAGCACATTGGCACC-A---TTAAGTCCAATA
1 TAGCTGGCCTTGAATCAGCACATTGGCACCTATCTTTAAGTCCAATG
*
13373 TAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATG
1 TAGCTGGCCTTGAATCAGCACATTGGCACC--TATCTTTAAGTCCAATG
* *
13422 TAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTTTAAGTCCAGTG
1 TAGCTGGCCTTGAATCAGCACATTGGCACC-T-ATCTTTAAGTCCAATG
*
13471 TAGCTGGCCTTGAATCAGCACATTGGCACCTCACCTTTAAGTCCAATG
1 TAGCTGGCCTTGAATCAGCACATTGGCACCT-ATCTTTAAGTCCAATG
*
13519 TAGCTGGCCTTGAATCAGCACATTGGCA-C---CTTTAAGTCCAATA
1 TAGCTGGCCTTGAATCAGCACATTGGCACCTATCTTTAAGTCCAATG
* * *
13562 TAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTTTAAGTTCAACG
1 TAGCTGGCCTTGAATCAGCACATTGGCACC---T--ATCTTTAAGTCCAATG
*
13614 TAGCTGGCCTTGAATCAGCATATTG
1 TAGCTGGCCTTGAATCAGCACATTG
13639 ACATCTTTTT
Statistics
Matches: 236, Mismatches: 14, Indels: 23
0.86 0.05 0.08
Matches are distributed among these distances:
43 68 0.29
44 1 0.00
46 1 0.00
47 1 0.00
48 46 0.19
49 83 0.35
52 36 0.15
ACGTcount: A:0.25, C:0.26, G:0.19, T:0.30
Consensus pattern (47 bp):
TAGCTGGCCTTGAATCAGCACATTGGCACCTATCTTTAAGTCCAATG
Found at i:13592 original size:43 final size:43
Alignment explanation
Indices: 13457--13594 Score: 195
Period size: 43 Copynumber: 3.1 Consensus size: 43
13447 GCACCTTCAT
* *
13457 CTTTAAGTCCAGTGTAGCTGGCCTTGAATCAGCACATTGGCACCTCAC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGG-----CAC
*
13505 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
*
13548 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
13591 CTTT
1 CTTT
13595 TCCATCTTTA
Statistics
Matches: 87, Mismatches: 3, Indels: 5
0.92 0.03 0.05
Matches are distributed among these distances:
43 48 0.55
48 39 0.45
ACGTcount: A:0.25, C:0.26, G:0.20, T:0.30
Consensus pattern (43 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
Found at i:13626 original size:52 final size:55
Alignment explanation
Indices: 13548--13666 Score: 163
Period size: 52 Copynumber: 2.2 Consensus size: 55
13538 ACATTGGCAC
* * *
13548 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-C-CTTTTC-CAT
1 CTTTAAGTTCAACATAGCTGGCCTTGAATCAGCATATTGACATCTCTTTTCTCAT
* *
13600 CTTTAAGTTCAACGTAGCTGGCCTTGAATCAGCATATTGACATCTTTTTTCTCAT
1 CTTTAAGTTCAACATAGCTGGCCTTGAATCAGCATATTGACATCTCTTTTCTCAT
*
13655 CTTTAAGCTCAA
1 CTTTAAGTTCAA
13667 TATCGTTGGC
Statistics
Matches: 58, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
52 38 0.66
53 1 0.02
54 5 0.09
55 14 0.24
ACGTcount: A:0.25, C:0.24, G:0.14, T:0.37
Consensus pattern (55 bp):
CTTTAAGTTCAACATAGCTGGCCTTGAATCAGCATATTGACATCTCTTTTCTCAT
Found at i:13685 original size:55 final size:54
Alignment explanation
Indices: 13548--13701 Score: 163
Period size: 55 Copynumber: 2.9 Consensus size: 54
13538 ACATTGGCAC
* *
13548 CTTTAAG-TCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-C-CTTTTCCAT
1 CTTTAAGCT-CAACATAGCTGGCCTTGAATCAGCATATTGGCATCTTTTTTCCAT
* * *
13600 CTTTAAGTTCAACGTAGCTGGCCTTGAATCAGCATATTGACATCTTTTTTCTCAT
1 CTTTAAGCTCAACATAGCTGGCCTTGAATCAGCATATTGGCATCTTTTTTC-CAT
* * * * *
13655 CTTTAAGCTCAATATCGTTGG-CTGTGAATCAACAGATTGGCATCTTT
1 CTTTAAGCTCAACATAGCTGGCCT-TGAATCAGCATATTGGCATCTTT
13702 ATCACTCTTC
Statistics
Matches: 85, Mismatches: 12, Indels: 7
0.82 0.12 0.07
Matches are distributed among these distances:
52 37 0.44
53 2 0.02
54 7 0.08
55 39 0.46
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.37
Consensus pattern (54 bp):
CTTTAAGCTCAACATAGCTGGCCTTGAATCAGCATATTGGCATCTTTTTTCCAT
Found at i:14604 original size:13 final size:13
Alignment explanation
Indices: 14586--14610 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
14576 CATAAAGTGT
14586 TGTATCGATACAA
1 TGTATCGATACAA
14599 TGTATCGATACA
1 TGTATCGATACA
14611 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:14608 original size:33 final size:33
Alignment explanation
Indices: 14566--14632 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
14556 TTCAACGATT
14566 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
*** *
14599 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
14632 T
1 T
14633 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:14691 original size:13 final size:13
Alignment explanation
Indices: 14673--14697 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
14663 ATCACTTAAA
14673 TGTATCGATACAT
1 TGTATCGATACAT
14686 TGTATCGATACA
1 TGTATCGATACA
14698 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:18640 original size:20 final size:20
Alignment explanation
Indices: 18615--18685 Score: 105
Period size: 20 Copynumber: 3.7 Consensus size: 20
18605 ATTTAGGACA
18615 ATGTATCGATACAATATGTC
1 ATGTATCGATACAATATGTC
18635 ATGTATCGATACAA-A---C
1 ATGTATCGATACAATATGTC
18651 AGTGTATCGATACAATATGTC
1 A-TGTATCGATACAATATGTC
18672 ATGTATCGATACAA
1 ATGTATCGATACAA
18686 ACAGTGGTAG
Statistics
Matches: 46, Mismatches: 0, Indels: 10
0.82 0.00 0.18
Matches are distributed among these distances:
16 2 0.04
17 13 0.28
18 1 0.02
19 1 0.02
20 27 0.59
21 2 0.04
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (20 bp):
ATGTATCGATACAATATGTC
Found at i:18658 original size:17 final size:17
Alignment explanation
Indices: 18636--18691 Score: 69
Period size: 17 Copynumber: 3.1 Consensus size: 17
18626 CAATATGTCA
18636 TGTATCGATACAAACAG
1 TGTATCGATACAAACAG
18653 TGTATCGATACAATATGTCA-
1 TGTATCGATACAA-A---CAG
18673 TGTATCGATACAAACAG
1 TGTATCGATACAAACAG
18690 TG
1 TG
18692 GTAGGGTAGC
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
16 2 0.06
17 15 0.44
18 1 0.03
19 1 0.03
20 13 0.38
21 2 0.06
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.29
Consensus pattern (17 bp):
TGTATCGATACAAACAG
Found at i:18666 original size:37 final size:37
Alignment explanation
Indices: 18616--18691 Score: 152
Period size: 37 Copynumber: 2.1 Consensus size: 37
18606 TTTAGGACAA
18616 TGTATCGATACAATATGTCATGTATCGATACAAACAG
1 TGTATCGATACAATATGTCATGTATCGATACAAACAG
18653 TGTATCGATACAATATGTCATGTATCGATACAAACAG
1 TGTATCGATACAATATGTCATGTATCGATACAAACAG
18690 TG
1 TG
18692 GTAGGGTAGC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.30
Consensus pattern (37 bp):
TGTATCGATACAATATGTCATGTATCGATACAAACAG
Found at i:18758 original size:19 final size:19
Alignment explanation
Indices: 18714--18769 Score: 85
Period size: 19 Copynumber: 2.9 Consensus size: 19
18704 CTGTTAGTTT
**
18714 CATGTATCGATACAATTGTG
1 CATGTATCGATACAA-TGAA
18734 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
18753 CATGTATCGATACAATG
1 CATGTATCGATACAATG
18770 TATTGGTACA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
19 19 0.56
20 15 0.44
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.30
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:19550 original size:15 final size:16
Alignment explanation
Indices: 19521--19568 Score: 57
Period size: 15 Copynumber: 3.2 Consensus size: 16
19511 AGTCATAATC
*
19521 TTTT-TCAATGAAAAT
1 TTTTGTCAATAAAAAT
*
19536 TTTTGTC-ATAGAAA-
1 TTTTGTCAATAAAAAT
19550 TTTTGTCAATAAAAAT
1 TTTTGTCAATAAAAAT
19566 TTT
1 TTT
19569 CAGTGACAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
14 7 0.26
15 15 0.56
16 5 0.19
ACGTcount: A:0.38, C:0.06, G:0.08, T:0.48
Consensus pattern (16 bp):
TTTTGTCAATAAAAAT
Found at i:19794 original size:17 final size:19
Alignment explanation
Indices: 19762--19796 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
19752 TTTAAAAATT
19762 ATATATTATATAAATTTTG
1 ATATATTATATAAATTTTG
19781 ATATATTA-AT-AATTTT
1 ATATATTATATAAATTTT
19797 TAATTTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 2 0.12
19 8 0.50
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (19 bp):
ATATATTATATAAATTTTG
Found at i:19888 original size:22 final size:24
Alignment explanation
Indices: 19863--19914 Score: 83
Period size: 22 Copynumber: 2.3 Consensus size: 24
19853 TTTTATCTAG
19863 TAATATATTTTT-TATTATATTT-
1 TAATATATTTTTATATTATATTTA
19885 TAAT-TATTTTTATATTATATTTA
1 TAATATATTTTTATATTATATTTA
19908 TAATATA
1 TAATATA
19915 ATTATGTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
21 7 0.26
22 14 0.52
23 4 0.15
24 2 0.07
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (24 bp):
TAATATATTTTTATATTATATTTA
Found at i:19891 original size:14 final size:12
Alignment explanation
Indices: 19866--19906 Score: 50
Period size: 11 Copynumber: 3.6 Consensus size: 12
19856 TATCTAGTAA
19866 TATATTTTTTAT
1 TATATTTTTTAT
*
19878 TATA-TTTTAAT
1 TATATTTTTTAT
*
19889 TAT-TTTTATAT
1 TATATTTTTTAT
19900 TATATTT
1 TATATTT
19907 ATAATATAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
11 17 0.71
12 7 0.29
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (12 bp):
TATATTTTTTAT
Found at i:19908 original size:17 final size:18
Alignment explanation
Indices: 19866--19908 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
19856 TATCTAGTAA
19866 TATATTT-TTTATTATAT
1 TATATTTATTTATTATAT
* *
19883 TTTAATTATTT-TTATAT
1 TATATTTATTTATTATAT
19900 TATATTTAT
1 TATATTTAT
19909 AATATAATTA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
17 18 0.86
18 3 0.14
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (18 bp):
TATATTTATTTATTATAT
Found at i:19919 original size:22 final size:22
Alignment explanation
Indices: 19867--19946 Score: 80
Period size: 22 Copynumber: 3.8 Consensus size: 22
19857 ATCTAGTAAT
*
19867 ATATT-TTTTATTATATTT-TA
1 ATATTATTATATTATATTTATA
*
19887 ATTATTTTTATATTATATTTATA
1 A-TATTATTATATTATATTTATA
* *
19910 ATATAATTATGTTATATTTA-A
1 ATATTATTATATTATATTTATA
19931 A-ATTATTATATT-TATT
1 ATATTATTATATTATATT
19947 AAAAAATACC
Statistics
Matches: 51, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
19 4 0.08
20 10 0.20
21 6 0.12
22 28 0.55
23 3 0.06
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.62
Consensus pattern (22 bp):
ATATTATTATATTATATTTATA
Found at i:24201 original size:28 final size:28
Alignment explanation
Indices: 24160--24216 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
24150 TTTGGCAACC
*
24160 TTTAAGTTATAACCATTATTATTATTAT
1 TTTAAGTTACAACCATTATTATTATTAT
*
24188 TTTAAGTTACAACCATTATTCTTATTAT
1 TTTAAGTTACAACCATTATTATTATTAT
24216 T
1 T
24217 ATTATTATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.33, C:0.11, G:0.04, T:0.53
Consensus pattern (28 bp):
TTTAAGTTACAACCATTATTATTATTAT
Found at i:24662 original size:28 final size:29
Alignment explanation
Indices: 24608--24663 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 29
24598 GTAGGCCCTC
*
24608 AAGTTAGTAATAGTATTTACTGTTAAAATA
1 AAGTTAGTAATAATATTTAC-GTTAAAATA
24638 AAGTTAGTAATAAT-TTTAAC-TTAAAA
1 AAGTTAGTAATAATATTT-ACGTTAAAA
24664 AAATAGCATA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
28 6 0.25
29 3 0.12
30 15 0.62
ACGTcount: A:0.46, C:0.04, G:0.11, T:0.39
Consensus pattern (29 bp):
AAGTTAGTAATAATATTTACGTTAAAATA
Found at i:25616 original size:20 final size:19
Alignment explanation
Indices: 25572--25620 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
25562 CAAATATAAT
25572 ATTTAATAAATATATTAAA
1 ATTTAATAAATATATTAAA
* *
25591 AATTAATAGATATAATTAAA
1 ATTTAATAAATAT-ATTAAA
*
25611 TTTTAA-AAAT
1 ATTTAATAAAT
25621 TAATTAACGA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (19 bp):
ATTTAATAAATATATTAAA
Found at i:25616 original size:27 final size:29
Alignment explanation
Indices: 25586--25642 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 29
25576 AATAAATATA
25586 TTAAAAATTAA-T-A-GATATAATTAAATT
1 TTAAAAATTAATTAACGA-ATAATTAAATT
25613 TTAAAAATTAATTAACGAATAATTAAATT
1 TTAAAAATTAATTAACGAATAATTAAATT
25642 T
1 T
25643 AATAATTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
27 11 0.41
28 1 0.04
29 13 0.48
30 2 0.07
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.40
Consensus pattern (29 bp):
TTAAAAATTAATTAACGAATAATTAAATT
Found at i:25904 original size:2 final size:2
Alignment explanation
Indices: 25897--25926 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
25887 TAGAGGATGG
25897 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
25927 GAATGCATAC
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
Found at i:26602 original size:24 final size:23
Alignment explanation
Indices: 26541--26602 Score: 61
Period size: 24 Copynumber: 2.6 Consensus size: 23
26531 TTATGGGTAA
*
26541 TTTTTTTATTAAAAAATATTTAT
1 TTTTTTTTTTAAAAAATATTTAT
*** *
26564 TATTAAATTTAAAAAAATATTTAAT
1 T-TTTTTTTTTAAAAAATATTT-AT
26589 TTTTTTTTTTAAAA
1 TTTTTTTTTTAAAA
26603 TGTATATATA
Statistics
Matches: 28, Mismatches: 9, Indels: 3
0.70 0.22 0.08
Matches are distributed among these distances:
23 1 0.04
24 24 0.86
25 3 0.11
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
TTTTTTTTTTAAAAAATATTTAT
Found at i:26641 original size:21 final size:21
Alignment explanation
Indices: 26600--26642 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
26590 TTTTTTTTTA
* *
26600 AAATGTATATATATTTTTATT
1 AAATGTATATATAATTATATT
*
26621 AAATGTATATGTAATTATATT
1 AAATGTATATATAATTATATT
26642 A
1 A
26643 TAGAAGCTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (21 bp):
AAATGTATATATAATTATATT
Found at i:27676 original size:21 final size:21
Alignment explanation
Indices: 27652--27727 Score: 64
Period size: 21 Copynumber: 3.6 Consensus size: 21
27642 TACTTGGAAT
27652 TATGTACAT-TAGACATGGCTA
1 TATGTACATATAGACAT-GCTA
*
27673 TATGTACATATAGGCATGCTA
1 TATGTACATATAGACATGCTA
* * * ***
27694 TACGTTCATATTGTTGTGCTA
1 TATGTACATATAGACATGCTA
*
27715 TATGTATATATAG
1 TATGTACATATAG
27728 CTAAGCTTAT
Statistics
Matches: 43, Mismatches: 11, Indels: 2
0.77 0.20 0.04
Matches are distributed among these distances:
21 37 0.86
22 6 0.14
ACGTcount: A:0.30, C:0.12, G:0.18, T:0.39
Consensus pattern (21 bp):
TATGTACATATAGACATGCTA
Found at i:39427 original size:25 final size:22
Alignment explanation
Indices: 39380--39427 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 22
39370 TGAGATTAAA
*
39380 ATTTTTATCAAAACATGGATTT
1 ATTTTTATCAAAACATGCATTT
39402 ATTTTTATACAAAATTCATGCATTT
1 ATTTTTAT-CAAAA--CATGCATTT
39427 A
1 A
39428 AAGGGGATCA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 8 0.36
23 5 0.23
25 9 0.41
ACGTcount: A:0.38, C:0.10, G:0.06, T:0.46
Consensus pattern (22 bp):
ATTTTTATCAAAACATGCATTT
Done.