Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1276
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: 152423
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:8739 original size:11 final size:11
Alignment explanation
Indices: 8717--8753 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
8707 ACAATATTGT
8717 AAAAAA-TC-A
1 AAAAAATTCAA
8726 AAAAAATTCAA
1 AAAAAATTCAA
8737 AAAAAATTCAA
1 AAAAAATTCAA
8748 AAAAAA
1 AAAAAA
8754 GTTTGTATTC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 6 0.23
10 2 0.08
11 18 0.69
ACGTcount: A:0.78, C:0.08, G:0.00, T:0.14
Consensus pattern (11 bp):
AAAAAATTCAA
Found at i:8845 original size:29 final size:30
Alignment explanation
Indices: 8798--8867 Score: 99
Period size: 29 Copynumber: 2.3 Consensus size: 30
8788 AGTATTGAAG
8798 AAAAAAAAGAAGAAAAAAAATTCAAAATT-A
1 AAAAAAAAGAAGAAAAAAAA-TCAAAATTGA
*
8828 AAAGAAAAAGAAG-AAAAAAATCGAAATTGA
1 AAA-AAAAAGAAGAAAAAAAATCAAAATTGA
8858 AAAAAAAAGA
1 AAAAAAAAGA
8868 GTGATTGAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
29 14 0.38
30 14 0.38
31 9 0.24
ACGTcount: A:0.76, C:0.03, G:0.11, T:0.10
Consensus pattern (30 bp):
AAAAAAAAGAAGAAAAAAAATCAAAATTGA
Found at i:9779 original size:15 final size:16
Alignment explanation
Indices: 9759--9790 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
9749 AGAAAATGAA
9759 AAAGAAAAAGAA-ATG
1 AAAGAAAAAGAAGATG
9774 AAAGAAAAAGAAGATG
1 AAAGAAAAAGAAGATG
9790 A
1 A
9791 GTGTGAGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.72, C:0.00, G:0.22, T:0.06
Consensus pattern (16 bp):
AAAGAAAAAGAAGATG
Found at i:13007 original size:12 final size:12
Alignment explanation
Indices: 12990--13034 Score: 63
Period size: 12 Copynumber: 3.8 Consensus size: 12
12980 TAGTTTCTCG
12990 AAAAAAACTCAA
1 AAAAAAACTCAA
*
13002 AAAAAAATTCAA
1 AAAAAAACTCAA
* *
13014 AAAAAAATTGAA
1 AAAAAAACTCAA
13026 AAAAAAACT
1 AAAAAAACT
13035 AGTTTCCATT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.76, C:0.09, G:0.02, T:0.13
Consensus pattern (12 bp):
AAAAAAACTCAA
Found at i:13088 original size:13 final size:13
Alignment explanation
Indices: 13070--13109 Score: 71
Period size: 13 Copynumber: 3.0 Consensus size: 13
13060 GGATATCAAG
13070 TTGTGAAAAAAAA
1 TTGTGAAAAAAAA
13083 TTGTGAAAAAAAAA
1 TTGTG-AAAAAAAA
13097 TTGTGAAAAAAAA
1 TTGTGAAAAAAAA
13110 AGAGAGCTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
13 13 0.50
14 13 0.50
ACGTcount: A:0.62, C:0.00, G:0.15, T:0.23
Consensus pattern (13 bp):
TTGTGAAAAAAAA
Found at i:13094 original size:14 final size:14
Alignment explanation
Indices: 13070--13110 Score: 75
Period size: 14 Copynumber: 3.0 Consensus size: 14
13060 GGATATCAAG
13070 TTGTG-AAAAAAAA
1 TTGTGAAAAAAAAA
13083 TTGTGAAAAAAAAA
1 TTGTGAAAAAAAAA
13097 TTGTGAAAAAAAAA
1 TTGTGAAAAAAAAA
13111 GAGAGCTAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 5 0.19
14 22 0.81
ACGTcount: A:0.63, C:0.00, G:0.15, T:0.22
Consensus pattern (14 bp):
TTGTGAAAAAAAAA
Found at i:14080 original size:18 final size:18
Alignment explanation
Indices: 14030--14080 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
14020 AAGAGTGACG
**
14030 AGAGAAAAAGAAACGAAAA
1 AGAGAAAAAG-ATTGAAAA
*
14049 AGA-AACAAAAATTGAAAA
1 AGAGAA-AAAGATTGAAAA
14067 AGAGAAAAAGATTG
1 AGAGAAAAAGATTG
14081 GAGAAAGAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
18 18 0.69
19 8 0.31
ACGTcount: A:0.69, C:0.04, G:0.20, T:0.08
Consensus pattern (18 bp):
AGAGAAAAAGATTGAAAA
Found at i:29094 original size:8 final size:8
Alignment explanation
Indices: 29081--29105 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
29071 CGAAAGGAGA
29081 TTTTGAAC
1 TTTTGAAC
29089 TTTTGAAC
1 TTTTGAAC
29097 TTTTGAAC
1 TTTTGAAC
29105 T
1 T
29106 CAGAATTGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.12, G:0.12, T:0.52
Consensus pattern (8 bp):
TTTTGAAC
Found at i:33111 original size:50 final size:50
Alignment explanation
Indices: 33057--33190 Score: 164
Period size: 50 Copynumber: 2.7 Consensus size: 50
33047 CGAGAAGTTT
* * *
33057 GTTCTAAAGATGGAGTTGGAT-GAT-TTTTATAGCGAAAGTTGAGAAAATGG
1 GTTCTAAAGATGG-GTTGGATAGATATTTGATAG-GAAAGGTGAGAAAATGA
* ***
33107 GTTCTAAAGATGGTTTGGATAGATATTTGATAGGCTCGGTGAGAAAATGA
1 GTTCTAAAGATGGGTTGGATAGATATTTGATAGGAAAGGTGAGAAAATGA
*
33157 GTTCTAAAGATGGTTTGGATAGATATTTGATAGG
1 GTTCTAAAGATGGGTTGGATAGATATTTGATAGG
33191 CTCGGTGAAA
Statistics
Matches: 75, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
49 6 0.08
50 62 0.83
51 7 0.09
ACGTcount: A:0.32, C:0.04, G:0.30, T:0.34
Consensus pattern (50 bp):
GTTCTAAAGATGGGTTGGATAGATATTTGATAGGAAAGGTGAGAAAATGA
Found at i:33191 original size:50 final size:50
Alignment explanation
Indices: 33096--33198 Score: 197
Period size: 50 Copynumber: 2.1 Consensus size: 50
33086 TAGCGAAAGT
*
33096 TGAGAAAATGGGTTCTAAAGATGGTTTGGATAGATATTTGATAGGCTCGG
1 TGAGAAAATGAGTTCTAAAGATGGTTTGGATAGATATTTGATAGGCTCGG
33146 TGAGAAAATGAGTTCTAAAGATGGTTTGGATAGATATTTGATAGGCTCGG
1 TGAGAAAATGAGTTCTAAAGATGGTTTGGATAGATATTTGATAGGCTCGG
33196 TGA
1 TGA
33199 AATAAAGAAA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.31, C:0.06, G:0.31, T:0.32
Consensus pattern (50 bp):
TGAGAAAATGAGTTCTAAAGATGGTTTGGATAGATATTTGATAGGCTCGG
Found at i:36092 original size:48 final size:48
Alignment explanation
Indices: 36037--36142 Score: 119
Period size: 48 Copynumber: 2.2 Consensus size: 48
36027 TTGTCTTTTC
* *
36037 TTTCTTTTTCAATTT-TCTCT-TTTTCCTCACA-CTTTTGTTCAATCTTAA
1 TTTCTTTTTCAATTTCTCTCTCTTTT--TCACATCCTTT-TTCAATCTCAA
** *
36085 TTTCTTTTTTGATTTCTTTCTCTTTTTCACATCCTTTTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
36133 TTTCTTTTTC
1 TTTCTTTTTC
36143 CATGACACTC
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
48 37 0.76
49 8 0.16
50 4 0.08
ACGTcount: A:0.14, C:0.23, G:0.02, T:0.61
Consensus pattern (48 bp):
TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
Found at i:39547 original size:15 final size:16
Alignment explanation
Indices: 39522--39553 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
39512 TATCTCACAC
39522 TCATCTTCTTTTTCTT
1 TCATCTTCTTTTTCTT
39538 TCAT-TTCTTTTTCTT
1 TCATCTTCTTTTTCTT
39553 T
1 T
39554 TTCTTTTTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.06, C:0.22, G:0.00, T:0.72
Consensus pattern (16 bp):
TCATCTTCTTTTTCTT
Found at i:40600 original size:11 final size:11
Alignment explanation
Indices: 40586--40634 Score: 52
Period size: 11 Copynumber: 4.8 Consensus size: 11
40576 TTTTTTTAAT
40586 AATTTTTTTTC
1 AATTTTTTTTC
40597 AATTTTTTTTC
1 AATTTTTTTTC
*
40608 ---TTTTTTTG
1 AATTTTTTTTC
*
40616 AA-TTTTTTTG
1 AATTTTTTTTC
40626 AATTTTTTT
1 AATTTTTTT
40635 ACAACACCCG
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
8 7 0.21
10 10 0.29
11 17 0.50
ACGTcount: A:0.16, C:0.04, G:0.04, T:0.76
Consensus pattern (11 bp):
AATTTTTTTTC
Found at i:40621 original size:9 final size:10
Alignment explanation
Indices: 40589--40634 Score: 58
Period size: 10 Copynumber: 4.7 Consensus size: 10
40579 TTTTAATAAT
*
40589 TTTTTTTCAA
1 TTTTTTTGAA
**
40599 TTTTTTT-TC
1 TTTTTTTGAA
40608 TTTTTTTGAA
1 TTTTTTTGAA
40618 TTTTTTTGAA
1 TTTTTTTGAA
40628 TTTTTTT
1 TTTTTTT
40635 ACAACACCCG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
9 7 0.23
10 24 0.77
ACGTcount: A:0.13, C:0.04, G:0.04, T:0.78
Consensus pattern (10 bp):
TTTTTTTGAA
Found at i:40631 original size:19 final size:19
Alignment explanation
Indices: 40590--40633 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
40580 TTTAATAATT
***
40590 TTTTTTCAATTTTTTTTCT
1 TTTTTTCAATTTTTTTGAA
*
40609 TTTTTTGAATTTTTTTGAA
1 TTTTTTCAATTTTTTTGAA
40628 TTTTTT
1 TTTTTT
40634 TACAACACCC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.14, C:0.05, G:0.05, T:0.77
Consensus pattern (19 bp):
TTTTTTCAATTTTTTTGAA
Found at i:49159 original size:22 final size:22
Alignment explanation
Indices: 49129--49172 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
49119 TTTGGTATTT
*
49129 GGGAATTGGTACGAATTGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
49151 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
49173 TGGTTCAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.32, C:0.05, G:0.36, T:0.27
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:54001 original size:152 final size:152
Alignment explanation
Indices: 53725--54026 Score: 550
Period size: 152 Copynumber: 2.0 Consensus size: 152
53715 TGTTCTCTCG
* *
53725 TGTATGCATCTAAGGCCTTGCTAACAAGCTCTTGAATGGTCCCATTTAGTTTGGACTGCATTTGT
1 TGTATGCATCTAAGGCCTTGCTAACAAGCTCTTGAATAGTCCCATTTAGTTTGGACCGCATTTGT
*
53790 CGGGCCTTTGATCTCGTTATTGGGCCTTGTGGCAATTTGAGCCCATCACGTTCTTGAACTTGGAT
66 CGGGCCTTTGATCTCGTTATTGGGCCTTGTGGCAATGTGAGCCCATCACGTTCTTGAACTTGGAT
*
53855 TGGGCCTTTATGACTTGTATCA
131 TGGGCCTTTATGACTCGTATCA
* *
53877 TGTATGCATCTAAGGCCTTGCTAACAAGCTCTTGAATAGTCCCATTTAGTTTGGGCCGCATTTTT
1 TGTATGCATCTAAGGCCTTGCTAACAAGCTCTTGAATAGTCCCATTTAGTTTGGACCGCATTTGT
53942 CGGGCCTTTGATCTCGTTATTGGGCCTTGTGGCAATGTGAGCCCATCACGTTCTTGAACTTGGAT
66 CGGGCCTTTGATCTCGTTATTGGGCCTTGTGGCAATGTGAGCCCATCACGTTCTTGAACTTGGAT
54007 TGGGCCTTTATGACTCGTAT
131 TGGGCCTTTATGACTCGTAT
54027 GATTCCCCCC
Statistics
Matches: 144, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
152 144 1.00
ACGTcount: A:0.18, C:0.22, G:0.24, T:0.36
Consensus pattern (152 bp):
TGTATGCATCTAAGGCCTTGCTAACAAGCTCTTGAATAGTCCCATTTAGTTTGGACCGCATTTGT
CGGGCCTTTGATCTCGTTATTGGGCCTTGTGGCAATGTGAGCCCATCACGTTCTTGAACTTGGAT
TGGGCCTTTATGACTCGTATCA
Found at i:55095 original size:23 final size:22
Alignment explanation
Indices: 55043--55095 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
55033 TCCACGTCTT
*
55043 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
55065 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
55088 TTTCTTTT
1 TTTCTTTT
55096 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:58888 original size:14 final size:13
Alignment explanation
Indices: 58871--58904 Score: 59
Period size: 14 Copynumber: 2.5 Consensus size: 13
58861 AAAAAAAATC
58871 AAAAAAAATTCGAA
1 AAAAAAAATTC-AA
58885 AAAAAAAATTCAA
1 AAAAAAAATTCAA
58898 AAAAAAA
1 AAAAAAA
58905 GTTTGTATTC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 9 0.45
14 11 0.55
ACGTcount: A:0.79, C:0.06, G:0.03, T:0.12
Consensus pattern (13 bp):
AAAAAAAATTCAA
Found at i:61015 original size:15 final size:14
Alignment explanation
Indices: 60979--61033 Score: 65
Period size: 15 Copynumber: 3.8 Consensus size: 14
60969 TCTATTGAGC
60979 GAGAAAAAGAAAAA
1 GAGAAAAAGAAAAA
*
60993 GAGAAAAACAAAAA
1 GAGAAAAAGAAAAA
*
61007 GAGTGAAAAGAAAAA
1 GAG-AAAAAGAAAAA
*
61022 GAAAGAAAAGAA
1 GAGA-AAAAGAA
61034 TGAGGAGAGT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
14 16 0.47
15 18 0.53
ACGTcount: A:0.75, C:0.02, G:0.22, T:0.02
Consensus pattern (14 bp):
GAGAAAAAGAAAAA
Found at i:63586 original size:56 final size:55
Alignment explanation
Indices: 63470--63587 Score: 159
Period size: 55 Copynumber: 2.1 Consensus size: 55
63460 TGCATGCTTT
* * * *
63470 CATT-AATGCCGTCCATGCATGGTGAATATCTCATTTAATTCATGTTTTGCTTCC
1 CATTAAATGCCGTCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCA
*
63524 CTTTAAATGCCGTTCCATACATGG-GAACATCTCATTTAATTCATGTCTTTGCTGCA
1 CATTAAATGCCG-TCCATACATGGTGAACATCTCATTTAATTCATGT-TTTGCTGCA
63580 CATTAAAT
1 CATTAAAT
63588 CAGCAAGCAG
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
54 3 0.05
55 28 0.51
56 24 0.44
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (55 bp):
CATTAAATGCCGTCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCA
Found at i:64236 original size:20 final size:20
Alignment explanation
Indices: 64211--64262 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
64201 ACGAGTTAAA
* *
64211 TTGAGCTTGAATGAGCTGAC
1 TTGAGCTCGAATGAGCTAAC
*
64231 TTGAGCACGAATGAGCTAAC
1 TTGAGCTCGAATGAGCTAAC
64251 TTGAGCTCGAAT
1 TTGAGCTCGAAT
64263 AGTTGAACCA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.29, C:0.17, G:0.27, T:0.27
Consensus pattern (20 bp):
TTGAGCTCGAATGAGCTAAC
Found at i:66599 original size:17 final size:19
Alignment explanation
Indices: 66577--66621 Score: 58
Period size: 17 Copynumber: 2.4 Consensus size: 19
66567 CTCTTCTCTT
66577 TTTTTTTTAATTCC-AAA-
1 TTTTTTTTAATTCCGAAAC
*
66594 TTTTTTTTACTTCCGAAAC
1 TTTTTTTTAATTCCGAAAC
66613 TTCTTTTTT
1 TT-TTTTTT
66622 TCTTCTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 13 0.54
18 3 0.12
19 2 0.08
20 6 0.25
ACGTcount: A:0.20, C:0.16, G:0.02, T:0.62
Consensus pattern (19 bp):
TTTTTTTTAATTCCGAAAC
Found at i:66743 original size:20 final size:21
Alignment explanation
Indices: 66697--66745 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
66687 TTTGAATACA
*
66697 ATTTTTTTTTCGAATTTTTTT
1 ATTTTTTTTTCGAATTTTTTC
*
66718 AATTTTTTTT-GAATTTTTTC
1 ATTTTTTTTTCGAATTTTTTC
*
66738 CTTTTTTT
1 ATTTTTTT
66746 ACAATATCGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 15 0.62
21 9 0.38
ACGTcount: A:0.14, C:0.06, G:0.04, T:0.76
Consensus pattern (21 bp):
ATTTTTTTTTCGAATTTTTTC
Found at i:67906 original size:56 final size:55
Alignment explanation
Indices: 67790--67907 Score: 159
Period size: 55 Copynumber: 2.1 Consensus size: 55
67780 TGCATGCTTT
* * * *
67790 CATT-AATGCCGTCCATGCATGGTGAATATCTCATTTAATTCATGTTTTGCTTCC
1 CATTAAATGCCGTCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCA
*
67844 CTTTAAATGCCGTTCCATACATGG-GAACATCTCATTTAATTCATGTCTTTGCTGCA
1 CATTAAATGCCG-TCCATACATGGTGAACATCTCATTTAATTCATGT-TTTGCTGCA
67900 CATTAAAT
1 CATTAAAT
67908 CAGCAAGCAG
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
54 3 0.05
55 28 0.51
56 24 0.44
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (55 bp):
CATTAAATGCCGTCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCA
Found at i:68556 original size:20 final size:20
Alignment explanation
Indices: 68531--68585 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
68521 ACGAGTTAAA
* *
68531 TTGAGCTTGAATGAGCTGAC
1 TTGAGCTCGAATGAGCTAAC
*
68551 TTGAGCACGAATGAGCTAAC
1 TTGAGCTCGAATGAGCTAAC
68571 TTGAGCTCGAATGAG
1 TTGAGCTCGAATGAG
68586 TTGAACCACA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.25
Consensus pattern (20 bp):
TTGAGCTCGAATGAGCTAAC
Found at i:73014 original size:20 final size:20
Alignment explanation
Indices: 72968--73014 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
72958 AGCTCGTTTC
*
72968 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
72988 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
73008 CAGCTCA
1 CAGCTCA
73015 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:75661 original size:22 final size:22
Alignment explanation
Indices: 75610--75675 Score: 80
Period size: 21 Copynumber: 3.0 Consensus size: 22
75600 GGTATTTGGG
* *
75610 AATTGGTTCGAAATAGTATGG-
1 AATTGGTACGAAATGGTATGGT
75631 AATTGGTACGAAATGGTATGGT
1 AATTGGTACGAAATGGTATGGT
* *
75653 ATTTGGTACGAATTGGTAATGGT
1 AATTGGTACGAAATGGT-ATGGT
75676 TCAAAGAGGT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
21 19 0.49
22 15 0.38
23 5 0.13
ACGTcount: A:0.30, C:0.05, G:0.30, T:0.35
Consensus pattern (22 bp):
AATTGGTACGAAATGGTATGGT
Found at i:79838 original size:15 final size:15
Alignment explanation
Indices: 79818--79927 Score: 53
Period size: 17 Copynumber: 6.9 Consensus size: 15
79808 TTTTCACTCA
79818 CTTTTTCTTTTTCTT
1 CTTTTTCTTTTTCTT
*
79833 CTTTTTCTTTTATCGCT
1 CTTTTTCTTTT-TC-TT
* *
79850 CTCTTTTCATTCTCTT
1 CT-TTTTCTTTTTCTT
**
79866 -TTTTTGAATTTTCTTT
1 CTTTTT-CTTTTTC-TT
*
79882 TTTTTTCATTTTTCTT
1 CTTTTTC-TTTTTCTT
* * *
79898 TTCTTTTGTATTTTCGT
1 CT-TTTTCT-TTTTCTT
79915 C-TTTTCTTTTTCT
1 CTTTTTCTTTTTCT
79928 CTCATTTGAT
Statistics
Matches: 73, Mismatches: 13, Indels: 19
0.70 0.12 0.18
Matches are distributed among these distances:
14 9 0.12
15 22 0.30
16 10 0.14
17 25 0.34
18 7 0.10
ACGTcount: A:0.05, C:0.18, G:0.04, T:0.73
Consensus pattern (15 bp):
CTTTTTCTTTTTCTT
Found at i:79884 original size:17 final size:17
Alignment explanation
Indices: 79859--79912 Score: 63
Period size: 17 Copynumber: 3.2 Consensus size: 17
79849 TCTCTTTTCA
*
79859 TTCTCTTTTTTTGAATT
1 TTCTTTTTTTTTGAATT
* *
79876 TTCTTTTTTTTTCATTT
1 TTCTTTTTTTTTGAATT
* *
79893 TTCTTTTCTTTTGTATT
1 TTCTTTTTTTTTGAATT
79910 TTC
1 TTC
79913 GTCTTTTCTT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.07, C:0.13, G:0.04, T:0.76
Consensus pattern (17 bp):
TTCTTTTTTTTTGAATT
Found at i:79894 original size:12 final size:11
Alignment explanation
Indices: 79874--79924 Score: 50
Period size: 12 Copynumber: 4.4 Consensus size: 11
79864 TTTTTTTGAA
79874 TTTTCTTTTT-
1 TTTTCTTTTTC
79884 TTTTCATTTTTC
1 TTTTC-TTTTTC
*
79896 TTTTCTTTTGTA
1 TTTTCTTTT-TC
79908 TTTTCGTCTTTTC
1 TTTTC-T-TTTTC
79921 TTTT
1 TTTT
79925 TCTCTCATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
10 5 0.15
11 9 0.26
12 11 0.32
13 6 0.18
14 3 0.09
ACGTcount: A:0.04, C:0.14, G:0.04, T:0.78
Consensus pattern (11 bp):
TTTTCTTTTTC
Found at i:82135 original size:13 final size:14
Alignment explanation
Indices: 82118--82170 Score: 65
Period size: 12 Copynumber: 3.8 Consensus size: 14
82108 AACCGTATGC
82118 AATTTTTTTTTTC-
1 AATTTTTTTTTTCA
82131 AA-TTTTTTTTTCA
1 AATTTTTTTTTTCA
82144 AATTTTTTTTTTCGA
1 AATTTTTTTTTTC-A
*
82159 ACTCTTTTTTTT
1 AAT-TTTTTTTT
82171 ACGTACCTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
12 10 0.29
13 4 0.11
14 10 0.29
15 3 0.09
16 8 0.23
ACGTcount: A:0.17, C:0.09, G:0.02, T:0.72
Consensus pattern (14 bp):
AATTTTTTTTTTCA
Found at i:82138 original size:12 final size:13
Alignment explanation
Indices: 82121--82154 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
82111 CGTATGCAAT
82121 TTTTTTTTTC-AA
1 TTTTTTTTTCAAA
82133 TTTTTTTTTCAAA
1 TTTTTTTTTCAAA
82146 TTTTTTTTT
1 TTTTTTTTT
82155 TCGAACTCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.15, C:0.06, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTTTTTTTCAAA
Found at i:82139 original size:14 final size:13
Alignment explanation
Indices: 82117--82170 Score: 65
Period size: 14 Copynumber: 3.9 Consensus size: 13
82107 AAACCGTATG
82117 CAATTTTTTTTTT
1 CAATTTTTTTTTT
82130 CAA-TTTTTTTTT
1 CAATTTTTTTTTT
82142 CAAATTTTTTTTTT
1 C-AATTTTTTTTTT
82156 CGAACTCTTTTTTTT
1 C-AA-T-TTTTTTTT
82171 ACGTACCTAT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
12 10 0.28
13 5 0.14
14 12 0.33
15 1 0.03
16 8 0.22
ACGTcount: A:0.17, C:0.11, G:0.02, T:0.70
Consensus pattern (13 bp):
CAATTTTTTTTTT
Found at i:82522 original size:22 final size:22
Alignment explanation
Indices: 82471--82536 Score: 80
Period size: 21 Copynumber: 3.0 Consensus size: 22
82461 GGTATTTGGG
* *
82471 AATTGGTTCGAAATAGTATGG-
1 AATTGGTACGAAATGGTATGGT
82492 AATTGGTACGAAATGGTATGGT
1 AATTGGTACGAAATGGTATGGT
* *
82514 ATTTGGTACGAATTGGTAATGGT
1 AATTGGTACGAAATGGT-ATGGT
82537 TCAAAGAGGT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
21 19 0.49
22 15 0.38
23 5 0.13
ACGTcount: A:0.30, C:0.05, G:0.30, T:0.35
Consensus pattern (22 bp):
AATTGGTACGAAATGGTATGGT
Found at i:94874 original size:21 final size:21
Alignment explanation
Indices: 94817--94874 Score: 61
Period size: 19 Copynumber: 2.9 Consensus size: 21
94807 AAGGCAAAGG
94817 AACAAAAAG-AAAAGATG-GAA
1 AACAAAAAGAAAAAG-TGAGAA
* *
94837 AA-AGAAA-AAAGAGTGAGAA
1 AACAAAAAGAAAAAGTGAGAA
94856 AACAAAAAGAAAAAGTGAG
1 AACAAAAAGAAAAAGTGAG
94875 TTGAAATTGA
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
18 2 0.07
19 13 0.43
20 6 0.20
21 9 0.30
ACGTcount: A:0.69, C:0.03, G:0.22, T:0.05
Consensus pattern (21 bp):
AACAAAAAGAAAAAGTGAGAA
Found at i:98385 original size:27 final size:27
Alignment explanation
Indices: 98355--98532 Score: 187
Period size: 27 Copynumber: 6.6 Consensus size: 27
98345 ATATTGAGCC
* * * *
98355 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
98382 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
98409 CGCACACTTAGTGCTACATAGTTAGACT
1 CGCACACTTAGTGCTACATAGTCA-AAT
** * *
98437 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
98464 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
98491 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
98518 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
98533 GTACAATTTA
Statistics
Matches: 127, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
27 104 0.82
28 23 0.18
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.28
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:98494 original size:82 final size:81
Alignment explanation
Indices: 98376--98531 Score: 215
Period size: 82 Copynumber: 1.9 Consensus size: 81
98366 TGCTATATAA
* * * *
98376 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTTAGACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCA-AATCGCA
98441 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
98458 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
98522 CACTTAGTGC
65 CACTTAGTGC
98532 TGTACAATTT
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
81 17 0.26
82 48 0.74
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.28
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:101087 original size:22 final size:22
Alignment explanation
Indices: 101059--101102 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
101049 TTTTGAACCA
101059 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
101081 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
101103 AAATACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.36, G:0.05, T:0.34
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:102393 original size:19 final size:20
Alignment explanation
Indices: 102369--102413 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
102359 CTTTTCATTC
*
102369 TCTTTTTTTGAATTTTC-TT
1 TCTTTTTTTCAATTTTCTTT
*
102388 TCTTTTTTTCATTTTTCTTT
1 TCTTTTTTTCAATTTTCTTT
102408 TCTTTT
1 TCTTTT
102414 GTATTTTCGC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 15 0.65
20 8 0.35
ACGTcount: A:0.07, C:0.13, G:0.02, T:0.78
Consensus pattern (20 bp):
TCTTTTTTTCAATTTTCTTT
Found at i:102441 original size:15 final size:15
Alignment explanation
Indices: 102393--102444 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
102383 TTCTTTCTTT
*
102393 TTTTCATTTTTCTTTTC
1 TTTTC-TTTTTC-TCTC
* *
102410 TTTTGTATTTTCGCTC
1 TTTTCT-TTTTCTCTC
102426 TTTTCTTTTTCTCTC
1 TTTTCTTTTTCTCTC
102441 TTTT
1 TTTT
102445 GATCTACAGA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
15 12 0.41
16 8 0.28
17 9 0.31
ACGTcount: A:0.04, C:0.19, G:0.04, T:0.73
Consensus pattern (15 bp):
TTTTCTTTTTCTCTC
Found at i:103076 original size:22 final size:22
Alignment explanation
Indices: 103046--103089 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
103036 TTTGGTATTT
103046 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
103068 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
103090 TGGTTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:105073 original size:21 final size:23
Alignment explanation
Indices: 105028--105074 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
105018 TCACCTGCAA
* *
105028 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
105051 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
105072 TAA
1 TAA
105075 TCATAAACAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:105891 original size:102 final size:102
Alignment explanation
Indices: 105710--105932 Score: 419
Period size: 102 Copynumber: 2.2 Consensus size: 102
105700 TGTCACCTTT
*
105710 AACTCTCCTCCATCGTTGAGCCATTGAAGTTTGTACGGAGTTGGATGCTTGGTGGTTGGTAGATT
1 AACT-TCCTCCATCGATGAGCCATTGAAGTTTGTACGGAGTTGGATGCTTGGTGGTTGGTAGATT
105775 TAATTTTTCCACCATGAGAGTGCTCGCTACGTTCGTAC
65 TAATTTTTCCACCATGAGAGTGCTCGCTACGTTCGTAC
105813 AACTTCCTCCATCGATGAGCCATTGAAGTTTGTACGGAGTTGGATGCTTGGTGGTTGGTAGATTT
1 AACTTCCTCCATCGATGAGCCATTGAAGTTTGTACGGAGTTGGATGCTTGGTGGTTGGTAGATTT
105878 AATTTTTCCACCATGAGAGTGCTCGCTACGTTCGTAC
66 AATTTTTCCACCATGAGAGTGCTCGCTACGTTCGTAC
*
105915 AGCTTCCTCCATCGATGA
1 AACTTCCTCCATCGATGA
105933 TGACACTACA
Statistics
Matches: 118, Mismatches: 2, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
102 114 0.97
103 4 0.03
ACGTcount: A:0.20, C:0.21, G:0.25, T:0.34
Consensus pattern (102 bp):
AACTTCCTCCATCGATGAGCCATTGAAGTTTGTACGGAGTTGGATGCTTGGTGGTTGGTAGATTT
AATTTTTCCACCATGAGAGTGCTCGCTACGTTCGTAC
Found at i:110713 original size:10 final size:10
Alignment explanation
Indices: 110698--110746 Score: 55
Period size: 10 Copynumber: 4.9 Consensus size: 10
110688 TTGGGTTAAG
110698 ATTGAGCTGA
1 ATTGAGCTGA
110708 ATTGAGCTCGA
1 ATTGAGCT-GA
110719 A-TGAGCTGA
1 ATTGAGCTGA
* *
110728 CTTGAGCTCA
1 ATTGAGCTGA
*
110738 AGTGAGCTG
1 ATTGAGCTG
110747 GAAACGAGCT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
9 2 0.06
10 27 0.84
11 3 0.09
ACGTcount: A:0.27, C:0.16, G:0.31, T:0.27
Consensus pattern (10 bp):
ATTGAGCTGA
Found at i:110723 original size:20 final size:20
Alignment explanation
Indices: 110700--110746 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
110690 GGGTTAAGAT
110700 TGAGCTGAATTGAGCTCGAA-
1 TGAGCTGAATTGAGCTC-AAG
*
110720 TGAGCTGACTTGAGCTCAAG
1 TGAGCTGAATTGAGCTCAAG
110740 TGAGCTG
1 TGAGCTG
110747 GAAACGAGCT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 2 0.08
20 23 0.92
ACGTcount: A:0.26, C:0.17, G:0.32, T:0.26
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCAAG
Found at i:112044 original size:24 final size:23
Alignment explanation
Indices: 111990--112045 Score: 58
Period size: 24 Copynumber: 2.4 Consensus size: 23
111980 GATTAATTAA
**
111990 GAAATGGTATTTGGTTTTGGTAC
1 GAAATGGTATTTGGAATTGGTAC
***
112013 GTTTTGGTATTTGGGAATTGGTAC
1 GAAATGGTATTT-GGAATTGGTAC
112037 GAAATGGTA
1 GAAATGGTA
112046 ATGGTTCAAA
Statistics
Matches: 24, Mismatches: 8, Indels: 1
0.73 0.24 0.03
Matches are distributed among these distances:
23 9 0.38
24 15 0.62
ACGTcount: A:0.23, C:0.04, G:0.32, T:0.41
Consensus pattern (23 bp):
GAAATGGTATTTGGAATTGGTAC
Found at i:115525 original size:21 final size:21
Alignment explanation
Indices: 115496--115550 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 21
115486 GTATTACGGT
115496 ATTGTAAAAAGAAAAT-AAAAAA
1 ATTG-AAAAA-AAAATCAAAAAA
115518 ATTG-AAAAAAAATCGAAAAAA
1 ATTGAAAAAAAAATC-AAAAAA
*
115539 ATTCAAAAAAAA
1 ATTGAAAAAAAA
115551 GTTTGTATTC
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
19 5 0.17
20 4 0.14
21 9 0.31
22 11 0.38
ACGTcount: A:0.73, C:0.04, G:0.07, T:0.16
Consensus pattern (21 bp):
ATTGAAAAAAAAATCAAAAAA
Found at i:115526 original size:11 final size:11
Alignment explanation
Indices: 115512--115550 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
115502 AAAAGAAAAT
115512 AAAAAAATTGA
1 AAAAAAATTGA
*
115523 AAAAAAATCG-
1 AAAAAAATTGA
*
115533 AAAAAAATTCA
1 AAAAAAATTGA
115544 AAAAAAA
1 AAAAAAA
115551 GTTTGTATTC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
10 8 0.33
11 16 0.67
ACGTcount: A:0.77, C:0.05, G:0.05, T:0.13
Consensus pattern (11 bp):
AAAAAAATTGA
Found at i:117434 original size:22 final size:22
Alignment explanation
Indices: 117406--117449 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
117396 TTTTGAACCA
117406 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
117428 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
117450 AAATACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.36, G:0.05, T:0.34
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:118014 original size:21 final size:21
Alignment explanation
Indices: 117999--118044 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
117989 TGAGAGAATA
117999 AAAAAGAAATGAGAGAAAAAG
1 AAAAAGAAATGAGAGAAAAAG
* *
118020 AAAAAGAAATAAAAGAAAAAG
1 AAAAAGAAATGAGAGAAAAAG
118041 AAAA
1 AAAA
118045 TGAGAGTGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.17, T:0.04
Consensus pattern (21 bp):
AAAAAGAAATGAGAGAAAAAG
Found at i:118033 original size:15 final size:15
Alignment explanation
Indices: 118015--118043 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
118005 AAATGAGAGA
118015 AAAAGAAAAAGAAAT
1 AAAAGAAAAAGAAAT
118030 AAAAGAAAAAGAAA
1 AAAAGAAAAAGAAA
118044 ATGAGAGTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (15 bp):
AAAAGAAAAAGAAAT
Found at i:118120 original size:27 final size:30
Alignment explanation
Indices: 118090--118146 Score: 75
Period size: 28 Copynumber: 2.0 Consensus size: 30
118080 AATTTGAGAT
* *
118090 TGAGA-TTGAAAAAGAAAA-AGA-TGAAAA
1 TGAGATTTCAAAAACAAAAGAGAGTGAAAA
118117 TGAGATTTCAAAAACAAAAGAGAGTGAAAA
1 TGAGATTTCAAAAACAAAAGAGAGTGAAAA
118147 GCAAAAAGAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 5 0.20
28 11 0.44
29 3 0.12
30 6 0.24
ACGTcount: A:0.60, C:0.04, G:0.21, T:0.16
Consensus pattern (30 bp):
TGAGATTTCAAAAACAAAAGAGAGTGAAAA
Found at i:118166 original size:12 final size:12
Alignment explanation
Indices: 118149--118188 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
118139 AGTGAAAAGC
118149 AAAAAGAGATTG
1 AAAAAGAGATTG
*
118161 AAAAAGAAATTG
1 AAAAAGAGATTG
* *
118173 AAAGAGAGCTTG
1 AAAAAGAGATTG
118185 AAAA
1 AAAA
118189 GAAATCGAGT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.60, C:0.03, G:0.23, T:0.15
Consensus pattern (12 bp):
AAAAAGAGATTG
Found at i:123929 original size:24 final size:25
Alignment explanation
Indices: 123902--123948 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
123892 GTTTAAGTGC
123902 AGAATTCTC-CTTGAGTTTTCTTCA
1 AGAATTCTCTCTTGAGTTTTCTTCA
123926 AGAATTCTCTCTTGAGTTTTCTT
1 AGAATTCTCTCTTGAGTTTTCTT
123949 TAGAAGTTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 9 0.41
25 13 0.59
ACGTcount: A:0.19, C:0.19, G:0.13, T:0.49
Consensus pattern (25 bp):
AGAATTCTCTCTTGAGTTTTCTTCA
Found at i:126365 original size:299 final size:300
Alignment explanation
Indices: 125825--126425 Score: 1179
Period size: 299 Copynumber: 2.0 Consensus size: 300
125815 CACTTATATT
125825 GTGTTAGATCAACTTGAATACTTGGTTTACGTTCACCTAACAATCTCCATTCATTCTATAACCTC
1 GTGTTAGATCAACTTGAATACTTGGTTTACGTTCACCTAACAATCTCCATTCATTCTATAACCTC
125890 TTTGAACCAATTTGAGCCTTTATTCTTTCTTTCTTAACCTATCTTCGACAAACCTTAATATTACT
66 TTTGAACCAATTTGAGCCTTTATTCTTTCTTTCTTAACCTATCTTCGACAAACCTTAATATTACT
125955 CCAATTCACGATCGGGCACATCAACGACTCGACTCTCATCACCGAGGCCGGGGCGTATCAACTTG
131 CCAATTCACGATCGGGCACATCAACGACTCGACTCTCATCACCGAGGCCGGGGCGTATCAACTTG
126020 TTCTTTAGAGATGTTGTACGATTACATGGTATCCCTAGGTCGATTGTTTCTGACAGGGATGTGAA
196 TTCTTTAGAGATGTTGTACGATTACATGGTATCCCTAGGTCGATTGTTTCTGACAGGGATGTGAA
126085 GGTTTTGAGTCATTTCTGGAGGACTTTGTGGAGCAAATTAG
261 GGTTTTGAGTCATTT-TGGAGGACTTTGTGGAGCAAATTAG
126126 GTGTTAGATCAACTTGAATACTTGGTTTACGTTCACCTAACAATCTCCATTCATTCTATAACCTC
1 GTGTTAGATCAACTTGAATACTTGGTTTACGTTCACCTAACAATCTCCATTCATTCTATAACCTC
126191 TTTGAACCAATTTGAGCC-TTATTCTTTCTTTCTTAACCTATCTTC-ACAAACCTTAATATTACT
66 TTTGAACCAATTTGAGCCTTTATTCTTTCTTTCTTAACCTATCTTCGACAAACCTTAATATTACT
126254 CCAATTCACGATCGGGCACATCAACGACTCGACTCTCATCACCGAGGCCGGGGCGTATCAACTTG
131 CCAATTCACGATCGGGCACATCAACGACTCGACTCTCATCACCGAGGCCGGGGCGTATCAACTTG
126319 TTCTTTAGAGATGTTGTACGATTACATGGTATCCCTAGGTCGATTGTTTCTGACAGGGATGTGAA
196 TTCTTTAGAGATGTTGTACGATTACATGGTATCCCTAGGTCGATTGTTTCTGACAGGGATGTGAA
126384 GGTTTTGAGTCATTTTGGAGGACTTTGTGGAGCAAATTAG
261 GGTTTTGAGTCATTTTGGAGGACTTTGTGGAGCAAATTAG
126424 GT
1 GT
126426 ACAAAACTTA
Statistics
Matches: 300, Mismatches: 0, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
298 27 0.09
299 163 0.54
300 27 0.09
301 83 0.28
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.35
Consensus pattern (300 bp):
GTGTTAGATCAACTTGAATACTTGGTTTACGTTCACCTAACAATCTCCATTCATTCTATAACCTC
TTTGAACCAATTTGAGCCTTTATTCTTTCTTTCTTAACCTATCTTCGACAAACCTTAATATTACT
CCAATTCACGATCGGGCACATCAACGACTCGACTCTCATCACCGAGGCCGGGGCGTATCAACTTG
TTCTTTAGAGATGTTGTACGATTACATGGTATCCCTAGGTCGATTGTTTCTGACAGGGATGTGAA
GGTTTTGAGTCATTTTGGAGGACTTTGTGGAGCAAATTAG
Found at i:135237 original size:30 final size:30
Alignment explanation
Indices: 135175--135249 Score: 91
Period size: 30 Copynumber: 2.5 Consensus size: 30
135165 ACTTAAGCCA
135175 AGCTCAAACGAGCTAAAGTAAGCTAAATTG
1 AGCTCAAACGAGCTAAAGTAAGCTAAATTG
* * *
135205 AGCTCCAACGAGCTAAATTAAGCT-CATGTG
1 AGCTCAAACGAGCTAAAGTAAGCTAAAT-TG
135235 AGCT-AAATCGAGCTA
1 AGCTCAAA-CGAGCTA
135250 GGAAAAACTA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
29 4 0.10
30 35 0.90
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.21
Consensus pattern (30 bp):
AGCTCAAACGAGCTAAAGTAAGCTAAATTG
Found at i:139989 original size:10 final size:10
Alignment explanation
Indices: 139965--140013 Score: 55
Period size: 10 Copynumber: 4.9 Consensus size: 10
139955 AGCTCGTTTC
*
139965 CAGCTCACTT
1 CAGCTCAATT
* *
139975 GAGCTCAAGT
1 CAGCTCAATT
139985 CAGCTC-ATT
1 CAGCTCAATT
139994 CGAGCTCAATT
1 C-AGCTCAATT
140005 CAGCTCAAT
1 CAGCTCAAT
140014 CTTAACCCAA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
9 3 0.09
10 25 0.78
11 4 0.12
ACGTcount: A:0.27, C:0.31, G:0.16, T:0.27
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:139990 original size:20 final size:20
Alignment explanation
Indices: 139965--140011 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
139955 AGCTCGTTTC
139965 CAGCTCACTT-GAGCTCAAGT
1 CAGCTCA-TTCGAGCTCAAGT
*
139985 CAGCTCATTCGAGCTCAATT
1 CAGCTCATTCGAGCTCAAGT
140005 CAGCTCA
1 CAGCTCA
140012 ATCTTAACCC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 2 0.08
20 23 0.92
ACGTcount: A:0.26, C:0.32, G:0.17, T:0.26
Consensus pattern (20 bp):
CAGCTCATTCGAGCTCAAGT
Found at i:149196 original size:20 final size:20
Alignment explanation
Indices: 149173--149219 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
149163 TGGTTAAGAT
*
149173 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
149193 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
149213 TGAGCTG
1 TGAGCTG
149220 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Done.