Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1635
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: 51690
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:3142 original size:28 final size:30
Alignment explanation
Indices: 3092--3153 Score: 110
Period size: 29 Copynumber: 2.1 Consensus size: 30
3082 ATAAGGTAAA
3092 TTCACACAAAATGGGAGAAATAG-AAATCT
1 TTCACACAAAATGGGAGAAATAGAAAATCT
3121 TTCACACAAAA-GGGAGAAATAGAAAATCT
1 TTCACACAAAATGGGAGAAATAGAAAATCT
3150 TTCA
1 TTCA
3154 TTAAGGGGGA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
28 11 0.34
29 21 0.66
ACGTcount: A:0.48, C:0.15, G:0.16, T:0.21
Consensus pattern (30 bp):
TTCACACAAAATGGGAGAAATAGAAAATCT
Found at i:3829 original size:32 final size:33
Alignment explanation
Indices: 3766--3830 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
3756 ACACACCCAG
*
3766 ATGTATCGATACATATTGCTTAGTATCGATACA
1 ATGTATCAATACATATTGCTTAGTATCGATACA
* *
3799 ATGTATCAATACATGTT-CTTTGTATCGATACA
1 ATGTATCAATACATATTGCTTAGTATCGATACA
3831 CCATGAAATG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 14 0.48
33 15 0.52
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.38
Consensus pattern (33 bp):
ATGTATCAATACATATTGCTTAGTATCGATACA
Found at i:3957 original size:20 final size:20
Alignment explanation
Indices: 3932--3991 Score: 111
Period size: 20 Copynumber: 3.0 Consensus size: 20
3922 ATGGCTATAT
3932 TGAATTGTATCGATACATTA
1 TGAATTGTATCGATACATTA
3952 TGAATTGTATCGATACATTA
1 TGAATTGTATCGATACATTA
*
3972 TGAATTGTATTGATACATTA
1 TGAATTGTATCGATACATTA
3992 AGTCCAATGG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.35, C:0.08, G:0.15, T:0.42
Consensus pattern (20 bp):
TGAATTGTATCGATACATTA
Found at i:4422 original size:31 final size:31
Alignment explanation
Indices: 4344--4470 Score: 130
Period size: 31 Copynumber: 4.0 Consensus size: 31
4334 AAGTGATTGA
* *
4344 GAGGTTCTATCTTAGCTTTTGAAAAAGATAGGG
1 GAGGTTCTATCTTAGCCTGTG-AAAAGATA-GG
* *
4377 AGAAAGGTTTTATCTTAACCTGTGAAAAGATAGG
1 -G--AGGTTCTATCTTAGCCTGTGAAAAGATAGG
* *
4411 GAGGTTCTATCTTAGCCTGTGAAAAAATAGA
1 GAGGTTCTATCTTAGCCTGTGAAAAGATAGG
* *
4442 GAGGCTCTATCTTAGCCT-TCAAAAGATAG
1 GAGGTTCTATCTTAGCCTGTGAAAAGATAG
4471 TGTTGTAAGG
Statistics
Matches: 80, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
30 9 0.11
31 43 0.54
33 1 0.01
34 3 0.04
35 8 0.10
36 16 0.20
ACGTcount: A:0.34, C:0.13, G:0.24, T:0.30
Consensus pattern (31 bp):
GAGGTTCTATCTTAGCCTGTGAAAAGATAGG
Found at i:4759 original size:15 final size:16
Alignment explanation
Indices: 4730--4762 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
4720 TTGAGCTTAC
4730 ATAATATTTCCATGCAT
1 ATAATATTT-CATGCAT
4747 ATAATATTT-ATGCAT
1 ATAATATTTCATGCAT
4762 A
1 A
4763 AGAATCATGC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
17 9 0.56
ACGTcount: A:0.39, C:0.12, G:0.06, T:0.42
Consensus pattern (16 bp):
ATAATATTTCATGCAT
Found at i:4983 original size:59 final size:59
Alignment explanation
Indices: 4866--4998 Score: 139
Period size: 59 Copynumber: 2.3 Consensus size: 59
4856 TGTAATTGTT
* ** * * *
4866 ATGCATTTTACGGCCATTTAGGTTGTTTTACATAATCTAAGGTTACTTTCGCACTTTCC
1 ATGCATTTTAAGGCCATTTAGAATGTTTTACATAATCTAAGGTCACTTTAGCAATTTCC
* *
4925 ATGCATTTTAAGGTCATTTAGAATGTTTTACATAATCT-AGTGTCATTTTAG-AGATTTCC
1 ATGCATTTTAAGGCCATTTAGAATGTTTTACATAATCTAAG-GTCACTTTAGCA-ATTTCC
*
4984 AT-CACTTT-AGGCCAT
1 ATGCATTTTAAGGCCAT
4999 ATGGGCATTT
Statistics
Matches: 62, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
57 6 0.10
58 8 0.13
59 48 0.77
ACGTcount: A:0.26, C:0.17, G:0.15, T:0.42
Consensus pattern (59 bp):
ATGCATTTTAAGGCCATTTAGAATGTTTTACATAATCTAAGGTCACTTTAGCAATTTCC
Found at i:7747 original size:62 final size:62
Alignment explanation
Indices: 7677--7796 Score: 177
Period size: 62 Copynumber: 1.9 Consensus size: 62
7667 CTAATGGCAC
* **
7677 TAGTTTTATAACATTTTGAGGTCATCAAGGTCTCCAAGGAACCAAGTTTTCAAAACTAGCAG
1 TAGTTTTATAACATTTTGAAGTCATCAAGGTCTAAAAGGAACCAAGTTTTCAAAACTAGCAG
* * * *
7739 TAGTTTTATTACATTTTGAAGTTATCAAGGTCTAAAATGAACCAAGTTTTCGAAACTA
1 TAGTTTTATAACATTTTGAAGTCATCAAGGTCTAAAAGGAACCAAGTTTTCAAAACTA
7797 CGTTGGGCTA
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
62 51 1.00
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (62 bp):
TAGTTTTATAACATTTTGAAGTCATCAAGGTCTAAAAGGAACCAAGTTTTCAAAACTAGCAG
Found at i:16820 original size:23 final size:22
Alignment explanation
Indices: 16788--16830 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
16778 TAATTCTTCA
*
16788 TTTAAGTCATTTCCTTCATTCCT
1 TTTAAGTCATTT-ATTCATTCCT
*
16811 TTTAATTCATTTATTCATTC
1 TTTAAGTCATTTATTCATTC
16831 TAATGCAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.21, C:0.21, G:0.02, T:0.56
Consensus pattern (22 bp):
TTTAAGTCATTTATTCATTCCT
Found at i:22711 original size:52 final size:52
Alignment explanation
Indices: 22630--22750 Score: 215
Period size: 52 Copynumber: 2.3 Consensus size: 52
22620 GAAAATTTAT
* *
22630 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAACTTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
*
22682 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
22734 CTGCATGTATCGATACA
1 CTGCATGTATCGATACA
22751 AAGATCAGTG
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 66 1.00
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
Found at i:22763 original size:52 final size:51
Alignment explanation
Indices: 22630--22771 Score: 205
Period size: 52 Copynumber: 2.7 Consensus size: 51
22620 GAAAATTTAT
*
22630 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAACTTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
* *
22682 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
*
22734 CTGCATGTATCGATACA-AAGATCAGTGTATCGATACAT
1 CTGCATGTATCGATACATTA-AT-AGTGTATCGATACAT
22772 GTGAGTAATG
Statistics
Matches: 82, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
51 2 0.02
52 80 0.98
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (51 bp):
CTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAATTTGC
Found at i:22852 original size:13 final size:13
Alignment explanation
Indices: 22834--22858 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
22824 CAAAAAAATA
22834 TGTATCGATACAT
1 TGTATCGATACAT
22847 TGTATCGATACA
1 TGTATCGATACA
22859 ACATTTTATG
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:22854 original size:33 final size:33
Alignment explanation
Indices: 22812--22878 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
22802 AGTAGCTTAA
22812 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
22845 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
22878 A
1 A
22879 AATCGTTGAA
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:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:23903 original size:174 final size:174
Alignment explanation
Indices: 23604--24093 Score: 803
Period size: 174 Copynumber: 2.9 Consensus size: 174
23594 GTTTTAGAGA
* * *
23604 TGATGAAGGTGCCAATATGTTGATTCACGGCCAACGATATTAGGCTTAAAGATGAGAAAAAGGAT
1 TGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTAGGCTTAAAGATGAGAAAAAGGAT
23669 GTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGCCAATATGCTGA
66 GTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGCCAATATGCTGA
23734 TTCAAGGCCAGCGATATTGGACTTAAAAATGATGATGAGAAAAG
131 TTCAAGGCCAGCGATATTGGACTTAAAAATGATGATGAGAAAAG
23778 TGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTAGGCTTAAAGATGAGAAAAAGGAT
1 TGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTAGGCTTAAAGATGAGAAAAAGGAT
23843 GTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGCCAATATGCTGA
66 GTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGCCAATATGCTGA
23908 TTCAAGGCCAGCGATATTGGACTTAAAAATGATGATGAGAAAAG
131 TTCAAGGCCAGCGATATTGGACTTAAAAATGATGATGAGAAAAG
*
23952 TGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGC-T-----T-----AAAGG-T
1 TGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTAGGCTTAAAGATGAGAAAAAGGAT
* * * *
24005 GCCAATGTGCTAATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGATGCCAATATGCTGA
66 GTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGCCAATATGCTGA
24067 TTCAAGGCCAGCGATATTGGACTTAAA
131 TTCAAGGCCAGCGATATTGGACTTAAA
24094 GGTGCCAATG
Statistics
Matches: 308, Mismatches: 8, Indels: 15
0.93 0.02 0.05
Matches are distributed among these distances:
159 44 0.14
161 1 0.00
162 41 0.13
163 5 0.02
168 1 0.00
173 1 0.00
174 215 0.70
ACGTcount: A:0.36, C:0.14, G:0.24, T:0.25
Consensus pattern (174 bp):
TGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTAGGCTTAAAGATGAGAAAAAGGAT
GTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGCCAATATGCTGA
TTCAAGGCCAGCGATATTGGACTTAAAAATGATGATGAGAAAAG
Found at i:24076 original size:49 final size:49
Alignment explanation
Indices: 24004--24563 Score: 709
Period size: 49 Copynumber: 11.9 Consensus size: 49
23994 GGCTTAAAGG
* *
24004 TGCCAATGTGCTAATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGA
1 TGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGA
* *
24053 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT-AA-A-G--G-
1 TGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGA
*
24096 TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGA
1 TGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGA
* *
24145 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT-AA-A-G--G-
1 TGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGA
*
24188 TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGA
1 TGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGA
* *
24237 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT-AA-A-G--G-
1 TGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGA
*
24280 TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGA
1 TGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGA
* *
24329 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT-AA-A-G--G-
1 TGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGA
* *
24372 TGCCAATGTGCTGAATCAAGGCCAGCTACATTGGACTTAAAGATGAAGA
1 TGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGA
* * *
24421 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGA
* * *
24470 TGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGA
* * *
24522 CGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCTTAAAG
1 TGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAG
24564 GGGTTGCCAC
Statistics
Matches: 444, Mismatches: 40, Indels: 51
0.83 0.07 0.10
Matches are distributed among these distances:
43 139 0.31
44 12 0.03
45 4 0.01
46 8 0.02
47 4 0.01
48 12 0.03
49 223 0.50
50 1 0.00
52 41 0.09
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.24
Consensus pattern (49 bp):
TGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGA
Found at i:24114 original size:92 final size:92
Alignment explanation
Indices: 23957--24564 Score: 1036
Period size: 92 Copynumber: 6.5 Consensus size: 92
23947 AAAAGTGATA
* * * * *
23957 AAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCTTAAAGGTGCCAATGTGCTAATTCA
1 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCA
24022 AGGCCAGCTACATTGGACTTAAAGATG
66 AGGCCAGCTACATTGGACTTAAAGATG
24049 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCA
1 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCA
24114 AGGCCAGCTACATTGGACTTAAAGATG
66 AGGCCAGCTACATTGGACTTAAAGATG
24141 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCA
1 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCA
24206 AGGCCAGCTACATTGGACTTAAAGATG
66 AGGCCAGCTACATTGGACTTAAAGATG
24233 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCA
1 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCA
24298 AGGCCAGCTACATTGGACTTAAAGATG
66 AGGCCAGCTACATTGGACTTAAAGATG
*
24325 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGAATCA
1 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCA
24390 AGGCCAGCTACATTGGACTTAAAGATG
66 AGGCCAGCTACATTGGACTTAAAGATG
24417 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCT
1 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT----A--AAGGTGCCAATGTGCT
*
24482 GAGTCAAGGCCAGCTACATTGGACTTAAAGATGG
60 GATTCAAGGCCAGCTACATTGGACTTAAAGAT-G
** * *
24516 AAAAGGCGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCTTAAAGG
1 --AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGG
24565 GGTTGCCACC
Statistics
Matches: 496, Mismatches: 11, Indels: 15
0.95 0.02 0.03
Matches are distributed among these distances:
92 404 0.81
95 4 0.01
96 1 0.00
97 1 0.00
98 47 0.09
99 1 0.00
101 38 0.08
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (92 bp):
AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCA
AGGCCAGCTACATTGGACTTAAAGATG
Found at i:24672 original size:34 final size:34
Alignment explanation
Indices: 24634--25329 Score: 616
Period size: 34 Copynumber: 20.8 Consensus size: 34
24624 GGGAAGGGAG
*
24634 AAAGATGCCACGGAGTTGTGGAC-TTAAAAGGGAA
1 AAAGATGCCACGGAGTTGTGGGCTTTAAAA-GGAA
*
24668 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAAA
1 AAAGA-TGCCACGGAGTTGTGGGCTTTAAAAGGAA
*
24703 AAAG-TGCCACAGAGTTGTGGGCTTTGAAAAGGGAA
1 AAAGATGCCACGGAGTTGTGGGCTTT-AAAA-GGAA
24738 AAAGAGTGCCACGGAGTTGTGGGCTTTAAACA-GAA
1 AAAGA-TGCCACGGAGTTGTGGGCTTTAAA-AGGAA
* *
24773 AAAGGTGCCACGGAATTGTGGGCTTTGAAAAGGGAA
1 AAAGATGCCACGGAGTTGTGGGCTTT-AAAA-GGAA
24809 AAAGAGTGCCACGGAGTTGTGGGCTTTAAACA-GAA
1 AAAGA-TGCCACGGAGTTGTGGGCTTTAAA-AGGAA
*
24844 AAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAA
1 AAAGATGCCACGGAGTTGTGGGCTTT-AAAAGG-AA
**
24880 AAAGAGTGCCACAAAGTTGTGGGCTTTAAAA-GAA
1 AAAGA-TGCCACGGAGTTGTGGGCTTTAAAAGGAA
* *
24914 GAAGGTGCCACGGAGTTGTGGGCTTTGAAAA-GAA
1 AAAGATGCCACGGAGTTGTGGGCTTT-AAAAGGAA
* * * * * *
24948 GAAGGTTGCCACCGACTTGTGTGGGCTTTAGGAAGGGAG
1 -AAAGATGCCACGGA-GT-TGTGGGCTTTA--AAAGGAA
*
24987 AAAGATGCCACGGAGTTGTGGAC-TTAAAAGGGAA
1 AAAGATGCCACGGAGTTGTGGGCTTTAAAA-GGAA
*
25021 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAAA
1 AAAGA-TGCCACGGAGTTGTGGGCTTTAAAAGGAA
*
25056 AAAG-TGCCACGGAGTTGTGGGCTTTAAAAAGAA
1 AAAGATGCCACGGAGTTGTGGGCTTTAAAAGGAA
* *
25089 AAAGGTGCCACGGAGTTGTGGGC-TTAAACGG--
1 AAAGATGCCACGGAGTTGTGGGCTTTAAAAGGAA
* *
25120 ---G-TGCCACGGAGTTGTGGAC-TTAAAGATGAA
1 AAAGATGCCACGGAGTTGTGGGCTTTAAA-AGGAA
* *
25150 AAA-AGTGCCACAGAATTGTGGGCTTTAAAAGG--
1 AAAGA-TGCCACGGAGTTGTGGGCTTTAAAAGGAA
* *
25182 ---G-TGCCACGGAGTTGTGGAC-TTAAAGATGAA
1 AAAGATGCCACGGAGTTGTGGGCTTTAAA-AGGAA
*
25212 AAA-AGTGCCACGGAATTGTGGGCTTTAAAAGG--
1 AAAGA-TGCCACGGAGTTGTGGGCTTTAAAAGGAA
*
25244 ---G-TGCCACGGAGTTGTGGAC-TTAAAAGGAA
1 AAAGATGCCACGGAGTTGTGGGCTTTAAAAGGAA
* *
25273 CAAGGTGCCACGGAGTTGTGGGCTTT-AAA-GAA
1 AAAGATGCCACGGAGTTGTGGGCTTTAAAAGGAA
* * *
25305 AAA-ATGCCACTGAGTCGTGGACTTT
1 AAAGATGCCACGGAGTTGTGGGCTTT
25330 GAGACAAAAT
Statistics
Matches: 549, Mismatches: 59, Indels: 111
0.76 0.08 0.15
Matches are distributed among these distances:
27 35 0.06
28 35 0.06
31 18 0.03
32 6 0.01
33 98 0.18
34 127 0.23
35 100 0.18
36 43 0.08
37 72 0.13
38 13 0.02
39 2 0.00
ACGTcount: A:0.33, C:0.13, G:0.33, T:0.21
Consensus pattern (34 bp):
AAAGATGCCACGGAGTTGTGGGCTTTAAAAGGAA
Found at i:24689 original size:71 final size:70
Alignment explanation
Indices: 24634--25329 Score: 695
Period size: 71 Copynumber: 10.4 Consensus size: 70
24624 GGGAAGGGAG
*
24634 AAAGATGCCACGGAGTTGTGGAC-TTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAA
1 AAAGGTGCCACGGAGTTGTGGACTTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAA
24698 A-GAA
66 AGGAA
* * *
24702 AAAAGTGCCACAGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
1 AAAGGTGCCACGGAGTTGTGGACTTT-AAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
24767 ACA-GAA
65 A-AGGAA
* *
24773 AAAGGTGCCACGGAATTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
1 AAAGGTGCCACGGAGTTGTGGACTTT-AAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
24838 ACA-GAA
65 A-AGGAA
* * **
24844 AAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAAAAAGAGTGCCACAAAGTTGTGGGCTTTAA
1 AAAGGTGCCACGGAGTTGTGGACTTT-AAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
24909 AA-GAA
65 AAGGAA
* * * * *
24914 GAAGGTGCCACGGAGTTGTGGGCTTTGAAAA--GAAGAAG-GTTGCCACCGACTTGTGTGGGCTT
1 AAAGGTGCCACGGAGTTGTGGACTTT-AAAAGGGAAAAAGAG-TGCCACGGA-GT-TGTGGGCTT
* *
24976 TAGGAAGGGAG
62 TA--AAAGGAA
*
24987 AAAGATGCCACGGAGTTGTGGAC-TTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAA
1 AAAGGTGCCACGGAGTTGTGGACTTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAA
25051 A-GAA
66 AGGAA
* * *
25055 AAAAGTGCCACGGAGTTGTGGGCTTTAAAA-AGAAAAAG-GTGCCACGGAGTTGTGGGC-TT-AA
1 AAAGGTGCCACGGAGTTGTGGACTTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAA
*
25116 ACG--
66 AGGAA
* * *
25119 ---GGTGCCACGGAGTTGTGGAC-TT-AAAGATGAAAAA-AGTGCCACAGAATTGTGGGCTTTAA
1 AAAGGTGCCACGGAGTTGTGGACTTTAAAAG-GGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
25178 AA-G--
65 AAGGAA
* *
25181 ---GGTGCCACGGAGTTGTGGAC-TT-AAAGATGAAAAA-AGTGCCACGGAATTGTGGGCTTTAA
1 AAAGGTGCCACGGAGTTGTGGACTTTAAAAG-GGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
25240 AA-G--
65 AAGGAA
*
25243 ---GGTGCCACGGAGTTGTGGAC-TTAAAA-GGAACAAG-GTGCCACGGAGTTGTGGGCTTT-AA
1 AAAGGTGCCACGGAGTTGTGGACTTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAA
25301 A-GAA
66 AGGAA
* * *
25305 AAA-ATGCCACTGAGTCGTGGACTTT
1 AAAGGTGCCACGGAGTTGTGGACTTT
25330 GAGACAAAAT
Statistics
Matches: 558, Mismatches: 43, Indels: 57
0.85 0.07 0.09
Matches are distributed among these distances:
59 3 0.01
60 6 0.01
61 67 0.12
62 86 0.15
63 6 0.01
64 16 0.03
65 5 0.01
66 3 0.01
67 20 0.04
68 60 0.11
69 11 0.02
70 84 0.15
71 149 0.27
72 5 0.01
73 36 0.06
74 1 0.00
ACGTcount: A:0.33, C:0.13, G:0.33, T:0.21
Consensus pattern (70 bp):
AAAGGTGCCACGGAGTTGTGGACTTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAA
AGGAA
Found at i:24815 original size:141 final size:135
Alignment explanation
Indices: 24634--25329 Score: 744
Period size: 141 Copynumber: 5.2 Consensus size: 135
24624 GGGAAGGGAG
* *
24634 AAAGATGCCACGGAGTTGTGGAC-TTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAA
1 AAAGGTGCCACGGAGTTGTGGGCTTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAA
* * *
24698 AGAAAAAAGTGCCACAGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCT
66 AG--AAAGGTGCCACGGAGTTGTGGAC-TT-AAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCT
24763 TTAAACAGAA
127 TTAAA-AGAA
*
24773 AAAGGTGCCACGGAATTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
1 AAAGGTGCCACGGAGTTGTGGGCTTT-AAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
* * **
24838 ACAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAAAAAGAGTGCCACAAAGTTGTGGG
65 A-AG--AAAGGTGCCACGGAGTTGTGGAC-TT-AAAAGGGAAAAAGAGTGCCACGGAGTTGTGGG
24903 CTTTAAAAGAA
125 CTTTAAAAGAA
* * * *
24914 GAAGGTGCCACGGAGTTGTGGGCTTTGAAAA--GAAGAAG-GTTGCCACCGACTTGTGTGGGCTT
1 AAAGGTGCCACGGAGTTGTGGGCTTT-AAAAGGGAAAAAGAG-TGCCACGGA-GT-TGTGGGCTT
*
24976 TAGGAAGGGAGAAAGATGCCACGGAGTTGTGGACTTAAAAGGGAAAAAGAGTGCCACGGAGTTGT
62 TA--AA---AGAAAGGTGCCACGGAGTTGTGGACTTAAAAGGGAAAAAGAGTGCCACGGAGTTGT
25041 GGGCTTTAAAAGAA
122 GGGCTTTAAAAGAA
* *
25055 AAAAGTGCCACGGAGTTGTGGGCTTTAAAA-AGAAAAAG-GTGCCACGGAGTTGTGGGC-TTAAA
1 AAAGGTGCCACGGAGTTGTGGGCTTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAA
* * * *
25117 CG---GGTGCCACGGAGTTGTGGACTT-AAAGATGAAAAA-AGTGCCACAGAATTGTGGGCTTTA
66 AGAAAGGTGCCACGGAGTTGTGGACTTAAAAG-GGAAAAAGAGTGCCACGGAGTTGTGGGCTTTA
25177 AAAG--
130 AAAGAA
* * *
25181 ---GGTGCCACGGAGTTGTGGAC-TT-AAAGATGAAAAA-AGTGCCACGGAATTGTGGGCTTTAA
1 AAAGGTGCCACGGAGTTGTGGGCTTTAAAAG-GGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
*
25240 AAG---GGTGCCACGGAGTTGTGGACTTAAAA-GGAACAAG-GTGCCACGGAGTTGTGGGCTTT-
65 AAGAAAGGTGCCACGGAGTTGTGGACTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTA
25299 AAAGAA
130 AAAGAA
* * * *
25305 AAA-ATGCCACTGAGTCGTGGACTTT
1 AAAGGTGCCACGGAGTTGTGGGCTTT
25330 GAGACAAAAT
Statistics
Matches: 492, Mismatches: 41, Indels: 60
0.83 0.07 0.10
Matches are distributed among these distances:
121 3 0.01
122 6 0.01
123 67 0.14
124 28 0.06
125 3 0.01
126 16 0.03
127 2 0.00
128 30 0.06
129 27 0.05
132 1 0.00
135 2 0.00
137 3 0.01
138 8 0.02
139 35 0.07
140 15 0.03
141 154 0.31
142 67 0.14
143 23 0.05
145 2 0.00
ACGTcount: A:0.33, C:0.13, G:0.33, T:0.21
Consensus pattern (135 bp):
AAAGGTGCCACGGAGTTGTGGGCTTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAA
AGAAAGGTGCCACGGAGTTGTGGACTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
AAGAA
Found at i:25188 original size:28 final size:28
Alignment explanation
Indices: 25087--25270 Score: 120
Period size: 28 Copynumber: 6.2 Consensus size: 28
25077 CTTTAAAAAG
* * *
25087 AAAAAGGTGCCACGGAGTTGTGGGC-TT
1 AAAAGGGTGCCACGGAATTGTGGACTTT
* *
25114 AAACGGGTGCCACGGAGTTGTGGACTTAAAGAT
1 AAAAGGGTGCCACGGAATTGTGGACTT-----T
** * *
25147 GAAAAAAGTGCCACAGAATTGTGGGCTTT
1 -AAAAGGGTGCCACGGAATTGTGGACTTT
*
25176 AAAAGGGTGCCACGGAGTTGTGGACTTAAAGAT
1 AAAAGGGTGCCACGGAATTGTGGACTT-----T
** *
25209 GAAAAAAGTGCCACGGAATTGTGGGCTTT
1 -AAAAGGGTGCCACGGAATTGTGGACTTT
*
25238 AAAAGGGTGCCACGGAGTTGTGGAC-TT
1 AAAAGGGTGCCACGGAATTGTGGACTTT
25265 AAAAGG
1 AAAAGG
25271 AACAAGGTGC
Statistics
Matches: 122, Mismatches: 22, Indels: 26
0.72 0.13 0.15
Matches are distributed among these distances:
27 30 0.25
28 44 0.36
29 2 0.02
33 2 0.02
34 44 0.36
ACGTcount: A:0.32, C:0.14, G:0.33, T:0.22
Consensus pattern (28 bp):
AAAAGGGTGCCACGGAATTGTGGACTTT
Found at i:25188 original size:62 final size:61
Alignment explanation
Indices: 24992--25301 Score: 415
Period size: 62 Copynumber: 4.9 Consensus size: 61
24982 GGGAGAAAGA
24992 TGCCACGGAGTTGTGGACTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAAAA
1 TGCCACGGAGTTGTGGACTTAAAA-GGAAAAA-AGTGCCACGGAGTTGTGGGCTTTAAAAG----
*
25057 AAG
60 -GG
* * * *
25060 TGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGC-TTAAACGGG
1 TGCCACGGAGTTGTGGAC-TTAAAAGGAAAAAAGTGCCACGGAGTTGTGGGCTTTAAAAGGG
* * *
25121 TGCCACGGAGTTGTGGACTTAAAGATGAAAAAAGTGCCACAGAATTGTGGGCTTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAA-AGGAAAAAAGTGCCACGGAGTTGTGGGCTTTAAAAGGG
* *
25183 TGCCACGGAGTTGTGGACTTAAAGATGAAAAAAGTGCCACGGAATTGTGGGCTTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAA-AGGAAAAAAGTGCCACGGAGTTGTGGGCTTTAAAAGGG
* *
25245 TGCCACGGAGTTGTGGACTTAAAAGGAACAAGGTGCCACGGAGTTGTGGGCTTTAAA
1 TGCCACGGAGTTGTGGACTTAAAAGGAAAAAAGTGCCACGGAGTTGTGGGCTTTAAA
25302 GAAAAAATGC
Statistics
Matches: 223, Mismatches: 16, Indels: 13
0.88 0.06 0.05
Matches are distributed among these distances:
60 5 0.02
61 72 0.32
62 92 0.41
66 6 0.03
67 19 0.09
68 23 0.10
69 6 0.03
ACGTcount: A:0.32, C:0.14, G:0.33, T:0.22
Consensus pattern (61 bp):
TGCCACGGAGTTGTGGACTTAAAAGGAAAAAAGTGCCACGGAGTTGTGGGCTTTAAAAGGG
Found at i:25382 original size:59 final size:60
Alignment explanation
Indices: 25309--25422 Score: 196
Period size: 59 Copynumber: 1.9 Consensus size: 60
25299 AAAGAAAAAA
25309 TGCCACTGAGTCGTGGACTTTGAGACA-A-AATGCCACTGAGTCGTGGACTTTAAAGAGAT
1 TGCCACTGAGTCGTGGACTTTGAGA-AGAGAATGCCACTGAGTCGTGGACTTTAAAGAGAT
*
25368 TGCCACTGAGTCGTGGACTTTGAGAAGAGATTGCCACTGAGTCGTGGACTTTAAA
1 TGCCACTGAGTCGTGGACTTTGAGAAGAGAATGCCACTGAGTCGTGGACTTTAAA
25423 AAGGTATTTG
Statistics
Matches: 52, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
58 1 0.02
59 26 0.50
60 25 0.48
ACGTcount: A:0.27, C:0.18, G:0.28, T:0.26
Consensus pattern (60 bp):
TGCCACTGAGTCGTGGACTTTGAGAAGAGAATGCCACTGAGTCGTGGACTTTAAAGAGAT
Found at i:25399 original size:31 final size:31
Alignment explanation
Indices: 25309--25419 Score: 176
Period size: 31 Copynumber: 3.7 Consensus size: 31
25299 AAAGAAAAAA
*
25309 TGCCACTGAGTCGTGGACTTTGAGACA-A-AA
1 TGCCACTGAGTCGTGGACTTTGAGA-AGAGAT
25339 TGCCACTGAGTCGTGGACTTT-A-AAGAGAT
1 TGCCACTGAGTCGTGGACTTTGAGAAGAGAT
25368 TGCCACTGAGTCGTGGACTTTGAGAAGAGAT
1 TGCCACTGAGTCGTGGACTTTGAGAAGAGAT
25399 TGCCACTGAGTCGTGGACTTT
1 TGCCACTGAGTCGTGGACTTT
25420 AAAAAGGTAT
Statistics
Matches: 76, Mismatches: 1, Indels: 7
0.90 0.01 0.08
Matches are distributed among these distances:
27 1 0.01
28 2 0.03
29 23 0.30
30 22 0.29
31 28 0.37
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.27
Consensus pattern (31 bp):
TGCCACTGAGTCGTGGACTTTGAGAAGAGAT
Found at i:26439 original size:15 final size:14
Alignment explanation
Indices: 26419--26466 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 14
26409 CTTATCGAGA
26419 TTTTCTGTTTTGTTT
1 TTTTCT-TTTTGTTT
26434 TTTTCTTCTTT-TTT
1 TTTTCTT-TTTGTTT
*
26448 TTTTTTTTTTGCTTT
1 TTTTCTTTTTG-TTT
26463 TTTT
1 TTTT
26467 TGTGTTTGGA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
13 3 0.10
14 10 0.34
15 16 0.55
ACGTcount: A:0.00, C:0.08, G:0.06, T:0.85
Consensus pattern (14 bp):
TTTTCTTTTTGTTT
Found at i:26447 original size:18 final size:17
Alignment explanation
Indices: 26421--26467 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 17
26411 TATCGAGATT
*
26421 TTCTGTTTTGTTTTTTTC
1 TTCT-TTTTTTTTTTTTC
*
26439 TTCTTTTTTTTTTTTTT
1 TTCTTTTTTTTTTTTTC
26456 TTGCTTTTTTTT
1 TT-CTTTTTTTT
26468 GTGTTTGGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
17 13 0.50
18 13 0.50
ACGTcount: A:0.00, C:0.09, G:0.06, T:0.85
Consensus pattern (17 bp):
TTCTTTTTTTTTTTTTC
Found at i:33730 original size:52 final size:52
Alignment explanation
Indices: 33649--33769 Score: 215
Period size: 52 Copynumber: 2.3 Consensus size: 52
33639 GAAAATTTAT
* *
33649 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAACTTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
*
33701 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
33753 CTGCATGTATCGATACA
1 CTGCATGTATCGATACA
33770 AAGATCAGTG
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 66 1.00
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
Found at i:33782 original size:52 final size:51
Alignment explanation
Indices: 33649--33790 Score: 205
Period size: 52 Copynumber: 2.7 Consensus size: 51
33639 GAAAATTTAT
*
33649 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAACTTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
* *
33701 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
*
33753 CTGCATGTATCGATACA-AAGATCAGTGTATCGATACAT
1 CTGCATGTATCGATACATTA-AT-AGTGTATCGATACAT
33791 GTGAGTAATG
Statistics
Matches: 82, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
51 2 0.02
52 80 0.98
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (51 bp):
CTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAATTTGC
Found at i:33871 original size:13 final size:13
Alignment explanation
Indices: 33853--33877 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
33843 CAAAAAAATA
33853 TGTATCGATACAT
1 TGTATCGATACAT
33866 TGTATCGATACA
1 TGTATCGATACA
33878 ACATTTTATG
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:33873 original size:33 final size:33
Alignment explanation
Indices: 33831--33897 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
33821 AGTAGCTTAA
33831 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
33864 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
33897 A
1 A
33898 AATCGTTGAA
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:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:40312 original size:21 final size:21
Alignment explanation
Indices: 40286--40327 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
40276 ATAGCATGAC
40286 AAAGAATTCCTTTCTTTTCCT
1 AAAGAATTCCTTTCTTTTCCT
40307 AAAGAATTCCTTTCTTTTCCT
1 AAAGAATTCCTTTCTTTTCCT
40328 TTATGGATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.24, G:0.05, T:0.48
Consensus pattern (21 bp):
AAAGAATTCCTTTCTTTTCCT
Found at i:40920 original size:20 final size:20
Alignment explanation
Indices: 40891--40944 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
40881 TTTACCCAGA
*
40891 TGTATCGATACATT-TTGCAT
1 TGTATCGATACATTACT-CAT
*
40911 TGTATTGATACATTACTCAT
1 TGTATCGATACATTACTCAT
40931 TGTATCGATACATT
1 TGTATCGATACATT
40945 GTATCAATAC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
20 29 0.97
21 1 0.03
ACGTcount: A:0.28, C:0.15, G:0.13, T:0.44
Consensus pattern (20 bp):
TGTATCGATACATTACTCAT
Found at i:40955 original size:33 final size:33
Alignment explanation
Indices: 40908--41010 Score: 170
Period size: 33 Copynumber: 3.1 Consensus size: 33
40898 ATACATTTTG
** *
40908 CATTGTATTGATACATTACTCATTGTATCGATA
1 CATTGTATCAATACATTGCTCATTGTATCGATA
40941 CATTGTATCAATACATTGCTCATTGTATCGATA
1 CATTGTATCAATACATTGCTCATTGTATCGATA
*
40974 CATTGTATCAATATATTGCTCATTGTATCGATA
1 CATTGTATCAATACATTGCTCATTGTATCGATA
41007 CATT
1 CATT
41011 TTACAATGTA
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 66 1.00
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.42
Consensus pattern (33 bp):
CATTGTATCAATACATTGCTCATTGTATCGATA
Found at i:40966 original size:20 final size:20
Alignment explanation
Indices: 40941--40978 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
40931 TGTATCGATA
40941 CATTGTATCAATACATTGCT
1 CATTGTATCAATACATTGCT
*
40961 CATTGTATCGATACATTG
1 CATTGTATCAATACATTG
40979 TATCAATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.39
Consensus pattern (20 bp):
CATTGTATCAATACATTGCT
Found at i:40991 original size:13 final size:13
Alignment explanation
Indices: 40928--40991 Score: 59
Period size: 13 Copynumber: 5.4 Consensus size: 13
40918 ATACATTACT
*
40928 CATTGTATCGATA
1 CATTGTATCAATA
40941 CATTGTATCAATA
1 CATTGTATCAATA
40954 CATTG---C--T-
1 CATTGTATCAATA
*
40961 CATTGTATCGATA
1 CATTGTATCAATA
40974 CATTGTATCAATA
1 CATTGTATCAATA
*
40987 TATTG
1 CATTG
40992 CTCATTGTAT
Statistics
Matches: 42, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
7 5 0.12
8 1 0.02
10 2 0.05
12 1 0.02
13 33 0.79
ACGTcount: A:0.31, C:0.16, G:0.12, T:0.41
Consensus pattern (13 bp):
CATTGTATCAATA
Found at i:43392 original size:28 final size:28
Alignment explanation
Indices: 43360--43461 Score: 141
Period size: 28 Copynumber: 3.6 Consensus size: 28
43350 TTTCATAATC
* *
43360 GGGGATACTCCAATCCCGTTATTTCCGA
1 GGGGATACTCCAACCCCGTTATTTCAGA
* **
43388 GGGGATACTCCAACCCCATTATTTCATC
1 GGGGATACTCCAACCCCGTTATTTCAGA
**
43416 GGGGATACTCCAACCCCGTTATTTTGGA
1 GGGGATACTCCAACCCCGTTATTTCAGA
43444 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
43462 GCTTTATTTC
Statistics
Matches: 64, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 64 1.00
ACGTcount: A:0.23, C:0.30, G:0.22, T:0.25
Consensus pattern (28 bp):
GGGGATACTCCAACCCCGTTATTTCAGA
Found at i:43514 original size:51 final size:50
Alignment explanation
Indices: 43444--43560 Score: 155
Period size: 51 Copynumber: 2.3 Consensus size: 50
43434 TTATTTTGGA
* *
43444 GGGGATACTCCAACCCCGGCTTTATTTCCAAAAT-ATTGATTTCTCACAATT
1 GGGGATACTCCAACCCCGGCCTTATTT-CAAAATCATCGATTTCTCACAA-T
* * *
43495 GGGGATACTTCAACCCCGGCCTTATTTCTAAATCATCGATTTTTCACAAT
1 GGGGATACTCCAACCCCGGCCTTATTTCAAAATCATCGATTTCTCACAAT
*
43545 CGGGATACTCCAACCC
1 GGGGATACTCCAACCC
43561 TGTTATTTTC
Statistics
Matches: 58, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
50 20 0.34
51 38 0.66
ACGTcount: A:0.26, C:0.28, G:0.15, T:0.31
Consensus pattern (50 bp):
GGGGATACTCCAACCCCGGCCTTATTTCAAAATCATCGATTTCTCACAAT
Found at i:43711 original size:78 final size:78
Alignment explanation
Indices: 43531--43714 Score: 235
Period size: 78 Copynumber: 2.3 Consensus size: 78
43521 TCTAAATCAT
* * * *
43531 CGATTTTTCACAATCGGGATACTCCAACCCTGTTATTTTCGAGGGAATGCTCCAATCCCGATTTT
1 CGATTTTCCATAATCGGGATACTCCAACCCTGTTATTTTCGAGGGAATACTCCAATCCCCATTTT
*
43596 ATTTTCAAAATAC
66 ATTTTCAAAACAC
* * * * *
43609 TGATTTTCTATAATCAAGGATACTCCAACCCTGTTATTTTCGAGGGAATATTTCAA-CCCCATTT
1 CGATTTTCCATAATC-GGGATACTCCAACCCTGTTATTTTCGAGGGAATACTCCAATCCCCATTT
**
43673 TATTTTCGGAACAC
65 TATTTTCAAAACAC
43687 CGATTTTCCATAATCGGGGATACTCCAA
1 CGATTTTCCATAATC-GGGATACTCCAA
43715 TCCCGTTGTT
Statistics
Matches: 89, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
78 53 0.60
79 36 0.40
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (78 bp):
CGATTTTCCATAATCGGGATACTCCAACCCTGTTATTTTCGAGGGAATACTCCAATCCCCATTTT
ATTTTCAAAACAC
Found at i:47489 original size:35 final size:35
Alignment explanation
Indices: 47450--47520 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
47440 TTTCATTGTA
47450 AGGCCATTCATGTATGGATTTAAGTGTGAAATAAT
1 AGGCCATTCATGTATGGATTTAAGTGTGAAATAAT
*
47485 AGGCCATTCATGTGTGGATTTAAGTGTGAAATAAT
1 AGGCCATTCATGTATGGATTTAAGTGTGAAATAAT
47520 A
1 A
47521 TTTCTCAATT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.34, C:0.08, G:0.24, T:0.34
Consensus pattern (35 bp):
AGGCCATTCATGTATGGATTTAAGTGTGAAATAAT
Found at i:48723 original size:14 final size:14
Alignment explanation
Indices: 48704--48730 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
48694 AAATTAAATA
48704 AAAATATATTTTAT
1 AAAATATATTTTAT
48718 AAAATATATTTTA
1 AAAATATATTTTA
48731 ATTAACTTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
AAAATATATTTTAT
Found at i:48994 original size:17 final size:18
Alignment explanation
Indices: 48969--49002 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
48959 ATAATTTTAA
*
48969 AACTTAAAA-TAAAAATT
1 AACTCAAAAGTAAAAATT
48986 AACTCAAAAGTAAAAAT
1 AACTCAAAAGTAAAAAT
49003 ATTTTTTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.65, C:0.09, G:0.03, T:0.24
Consensus pattern (18 bp):
AACTCAAAAGTAAAAATT
Done.