Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold622
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: 179752
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:3943 original size:18 final size:17
Alignment explanation
Indices: 3908--3947 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
3898 AGCGAAATAC
*
3908 AAAGAAAAAAAATGAAA
1 AAAGAAAAAAAATAAAA
*
3925 AAAGAAAGAAAATTAAAA
1 AAAGAAA-AAAAATAAAA
3943 AAAGA
1 AAAGA
3948 GAATGAAAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.80, C:0.00, G:0.12, T:0.07
Consensus pattern (17 bp):
AAAGAAAAAAAATAAAA
Found at i:3950 original size:16 final size:17
Alignment explanation
Indices: 3908--3944 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
3898 AGCGAAATAC
*
3908 AAAGAAAAAAAATGAAA
1 AAAGAAAGAAAATGAAA
*
3925 AAAGAAAGAAAATTAAA
1 AAAGAAAGAAAATGAAA
3942 AAA
1 AAA
3945 AGAGAATGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.81, C:0.00, G:0.11, T:0.08
Consensus pattern (17 bp):
AAAGAAAGAAAATGAAA
Found at i:8031 original size:21 final size:21
Alignment explanation
Indices: 7988--8050 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
7978 TTTGAACCAT
*
7988 TACCAATTT-GTACCAAATACCA
1 TACC-ATTTCGTACC-AATTCCA
8010 TACCATTTCGTACCAATTCCA
1 TACCATTTCGTACCAATTCCA
* *
8031 TACTATTTCGAACCAATTCC
1 TACCATTTCGTACCAATTCC
8051 CAAATACCAA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
21 28 0.76
22 9 0.24
ACGTcount: A:0.33, C:0.30, G:0.05, T:0.32
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:9339 original size:15 final size:15
Alignment explanation
Indices: 9314--9360 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
9304 AGAAAAGAAT
9314 AAAGAAAATGAAAATG
1 AAAG-AAATGAAAATG
*
9330 AAAGAAATGAAAAAG
1 AAAGAAATGAAAATG
9345 AAA-AATATGAAAATG
1 AAAGAA-ATGAAAATG
9360 A
1 A
9361 GATTTCAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 2 0.07
15 22 0.79
16 4 0.14
ACGTcount: A:0.70, C:0.00, G:0.17, T:0.13
Consensus pattern (15 bp):
AAAGAAATGAAAATG
Found at i:9405 original size:11 final size:11
Alignment explanation
Indices: 9389--9449 Score: 54
Period size: 11 Copynumber: 5.5 Consensus size: 11
9379 GTGAAAAGCA
9389 AAAAGAGATTG
1 AAAAGAGATTG
*
9400 AAAAGAAATTG
1 AAAAGAGATTG
*
9411 -AAAGAG-TGG
1 AAAAGAGATTG
*
9420 AAAAAGAAATTG
1 -AAAAGAGATTG
*
9432 AAAGAGAGCTTG
1 AAA-AGAGATTG
9444 AAAAGA
1 AAAAGA
9450 AATCGAGTGG
Statistics
Matches: 39, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
9 2 0.05
10 5 0.13
11 21 0.54
12 11 0.28
ACGTcount: A:0.57, C:0.02, G:0.26, T:0.15
Consensus pattern (11 bp):
AAAAGAGATTG
Found at i:9416 original size:21 final size:21
Alignment explanation
Indices: 9390--9452 Score: 83
Period size: 21 Copynumber: 2.9 Consensus size: 21
9380 TGAAAAGCAA
9390 AAAGAGATTGAAAAGAAATTG
1 AAAGAGATTGAAAAGAAATTG
*
9411 AAAGAG-TGGAAAAAGAAATTG
1 AAAGAGATTG-AAAAGAAATTG
9432 AAAGAGAGCTTGAAAAGAAAT
1 AAAGAGA--TTGAAAAGAAAT
9453 CGAGTGGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
20 2 0.06
21 23 0.64
23 9 0.25
24 2 0.06
ACGTcount: A:0.57, C:0.02, G:0.25, T:0.16
Consensus pattern (21 bp):
AAAGAGATTGAAAAGAAATTG
Found at i:11339 original size:10 final size:10
Alignment explanation
Indices: 11305--11363 Score: 57
Period size: 10 Copynumber: 5.8 Consensus size: 10
11295 AGCTTCGTTT
*
11305 AGCTCATTTCC
1 AGCTCAATT-C
* *
11316 AGCTCACTTG
1 AGCTCAATTC
*
11326 AGCTCAAGTC
1 AGCTCAATTC
11336 AGCTC-ATTC
1 AGCTCAATTC
11345 GAGCTCAATTC
1 -AGCTCAATTC
11356 AGCTCAAT
1 AGCTCAAT
11364 CTTAACCCAA
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
9 3 0.08
10 25 0.62
11 12 0.30
ACGTcount: A:0.25, C:0.31, G:0.15, T:0.29
Consensus pattern (10 bp):
AGCTCAATTC
Found at i:11340 original size:20 final size:20
Alignment explanation
Indices: 11315--11361 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
11305 AGCTCATTTC
11315 CAGCTCACTT-GAGCTCAAGT
1 CAGCTCA-TTCGAGCTCAAGT
*
11335 CAGCTCATTCGAGCTCAATT
1 CAGCTCATTCGAGCTCAAGT
11355 CAGCTCA
1 CAGCTCA
11362 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:11360 original size:30 final size:31
Alignment explanation
Indices: 11305--11362 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 31
11295 AGCTTCGTTT
* *
11305 AGCTCATTTCCAGCTCACTTGAGCTCAAGTC
1 AGCTCATTTCCAGCTCAATTCAGCTCAAGTC
*
11336 AGCTCA-TTCGAGCTCAATTCAGCTCAA
1 AGCTCATTTCCAGCTCAATTCAGCTCAA
11363 TCTTAACCCA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 18 0.75
31 6 0.25
ACGTcount: A:0.26, C:0.31, G:0.16, T:0.28
Consensus pattern (31 bp):
AGCTCATTTCCAGCTCAATTCAGCTCAAGTC
Found at i:12975 original size:22 final size:21
Alignment explanation
Indices: 12941--12983 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
12931 GGCTGTTAAA
*
12941 AAAAGGAGCTTAAAGATCATT
1 AAAAGGAGCTTAAAGAGCATT
*
12962 AAAAGGAGTTTTAAAGAGCATT
1 AAAAGGAG-CTTAAAGAGCATT
12984 TTATGCCCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.47, C:0.07, G:0.21, T:0.26
Consensus pattern (21 bp):
AAAAGGAGCTTAAAGAGCATT
Found at i:13860 original size:13 final size:11
Alignment explanation
Indices: 13824--13856 Score: 66
Period size: 11 Copynumber: 3.0 Consensus size: 11
13814 TAGTAGTTTC
13824 TTCAAAAAAAA
1 TTCAAAAAAAA
13835 TTCAAAAAAAA
1 TTCAAAAAAAA
13846 TTCAAAAAAAA
1 TTCAAAAAAAA
13857 AATTTGGTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.73, C:0.09, G:0.00, T:0.18
Consensus pattern (11 bp):
TTCAAAAAAAA
Found at i:13921 original size:16 final size:17
Alignment explanation
Indices: 13900--13938 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
13890 TATCAAGTTG
13900 AAAAAAAAA-TTCGTGA
1 AAAAAAAAATTTCGTGA
13916 AAAAAAAAATTTCGTGA
1 AAAAAAAAATTTCGTGA
13933 AAAAAA
1 AAAAAA
13939 GAAGAAGCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 9 0.41
17 13 0.59
ACGTcount: A:0.67, C:0.05, G:0.10, T:0.18
Consensus pattern (17 bp):
AAAAAAAAATTTCGTGA
Found at i:19453 original size:22 final size:21
Alignment explanation
Indices: 19419--19461 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
19409 GGCTGTTAAA
*
19419 AAAAGGAGCTTAAAGATCATT
1 AAAAGGAGCTTAAAGAGCATT
*
19440 AAAAGGAGTTTTAAAGAGCATT
1 AAAAGGAG-CTTAAAGAGCATT
19462 TTATGCCCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.47, C:0.07, G:0.21, T:0.26
Consensus pattern (21 bp):
AAAAGGAGCTTAAAGAGCATT
Found at i:21097 original size:82 final size:82
Alignment explanation
Indices: 20938--21100 Score: 213
Period size: 82 Copynumber: 2.0 Consensus size: 82
20928 TTGTGTCTGC
* * * *
20938 AGGTCATTGAATTCAGCTACTTAATGGCTAAGGAGACATGCATTTAAGGTGCTGTTAACATGCAA
1 AGGTCATTGAATTCAGCTACTTAATGGCAAAGGAAACATGCATTTAAGGAGATGTTAACATGCAA
21003 GGAACGACATTTAAAGA
66 GGAACGACATTTAAAGA
**
21020 AGGTCATTGAAATTC-GACTACTTAATGGCAAAGGAAACATGCA-TTAAGGAGATGTTCCCATGC
1 AGGTCATTG-AATTCAG-CTACTTAATGGCAAAGGAAACATGCATTTAAGGAGATGTTAACATGC
* **
21083 ATGGAACGGTATTTAAAG
64 AAGGAACGACATTTAAAG
21101 GGAAGTAAAA
Statistics
Matches: 70, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
82 41 0.59
83 29 0.41
ACGTcount: A:0.36, C:0.15, G:0.23, T:0.26
Consensus pattern (82 bp):
AGGTCATTGAATTCAGCTACTTAATGGCAAAGGAAACATGCATTTAAGGAGATGTTAACATGCAA
GGAACGACATTTAAAGA
Found at i:21392 original size:20 final size:20
Alignment explanation
Indices: 21346--21392 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
21336 AGCTCGTTTC
*
21346 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
21366 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
21386 CAGCTCA
1 CAGCTCA
21393 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:25102 original size:20 final size:22
Alignment explanation
Indices: 25072--25116 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
25062 AATCTTGAAT
25072 GAAATTGAGA-GAAGAA-AAAAA
1 GAAATTGAGAGGAA-AAGAAAAA
25093 GAAA-TGAGAGGAAAAGAAAAA
1 GAAATTGAGAGGAAAAGAAAAA
25114 GAA
1 GAA
25117 TAAAAGAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.67, C:0.00, G:0.27, T:0.07
Consensus pattern (22 bp):
GAAATTGAGAGGAAAAGAAAAA
Found at i:25135 original size:14 final size:14
Alignment explanation
Indices: 25089--25135 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
25079 AGAGAAGAAA
* *
25089 AAAAGAAATGAGAGG
1 AAAAGAAA-AAGATG
25104 AAAAGAAAAAGAAT-
1 AAAAGAAAAAG-ATG
25118 AAAAGAAAAAGATG
1 AAAAGAAAAAGATG
25132 AAAA
1 AAAA
25136 TGAGATTCCA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
13 2 0.07
14 17 0.61
15 9 0.32
ACGTcount: A:0.72, C:0.00, G:0.21, T:0.06
Consensus pattern (14 bp):
AAAAGAAAAAGATG
Found at i:25185 original size:12 final size:12
Alignment explanation
Indices: 25168--25241 Score: 55
Period size: 12 Copynumber: 6.2 Consensus size: 12
25158 AGTGAAAAGC
25168 AAAAAGAGATTG
1 AAAAAGAGATTG
*
25180 AAAAAGAAATTG
1 AAAAAGAGATTG
25192 AAAAAGA-A--G
1 AAAAAGAGATTG
*
25201 AAAAAGAAAGAGTGG
1 AAAAAG--AGA-TTG
*
25216 AAAAAGAAATTG
1 AAAAAGAGATTG
* *
25228 AAAGAGAGCTTG
1 AAAAAGAGATTG
25240 AA
1 AA
25242 CAGAAATTGA
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
9 7 0.14
11 2 0.04
12 32 0.64
13 2 0.04
15 7 0.14
ACGTcount: A:0.62, C:0.01, G:0.24, T:0.12
Consensus pattern (12 bp):
AAAAAGAGATTG
Found at i:26913 original size:82 final size:82
Alignment explanation
Indices: 26760--26922 Score: 229
Period size: 82 Copynumber: 2.0 Consensus size: 82
26750 TTGTGTCTGC
* * * *
26760 AGGTCATTGAATTCGGCTACTTAATGGCTAAGGAGACATGCATTTAAGGTGCTGTTAACATGCAA
1 AGGTCATTGAATTCGGCTACTTAATGGCAAAGGAAACATGCATTTAAGGAGATGTTAACATGCAA
26825 GGAACGGCATTTAAAGA
66 GGAACGGCATTTAAAGA
* **
26842 AGGTCATTGAAATTCGGCTATTTAATGGCAAAGGAAACATGCA-TTAAGGAGATGTTCCCATGCA
1 AGGTCATTG-AATTCGGCTACTTAATGGCAAAGGAAACATGCATTTAAGGAGATGTTAACATGCA
* *
26906 TGGAACGGTATTTAAAG
65 AGGAACGGCATTTAAAG
26923 GGAAGTAAAA
Statistics
Matches: 71, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
82 41 0.58
83 30 0.42
ACGTcount: A:0.34, C:0.14, G:0.25, T:0.27
Consensus pattern (82 bp):
AGGTCATTGAATTCGGCTACTTAATGGCAAAGGAAACATGCATTTAAGGAGATGTTAACATGCAA
GGAACGGCATTTAAAGA
Found at i:31566 original size:21 final size:21
Alignment explanation
Indices: 31540--31602 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
31530 TTGGTATTTG
31540 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
*
31561 GGAATTGGTATGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
31582 GGTATTTGGTACGAATTGGTA
1 GG-AATTGGTACGAAATGGTA
31603 ATGGTTCAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 22 0.59
22 15 0.41
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.33
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:37115 original size:17 final size:18
Alignment explanation
Indices: 37093--37139 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
37083 TTTCATTCTC
37093 TTTTTTGAATTTTT-TTT
1 TTTTTTGAATTTTTCTTT
*
37110 TTTTTT-CATTTTTCTTT
1 TTTTTTGAATTTTTCTTT
* *
37127 TCTTTTGTATTTT
1 TTTTTTGAATTTT
37140 CGCTCTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
16 6 0.24
17 14 0.56
18 5 0.20
ACGTcount: A:0.09, C:0.06, G:0.04, T:0.81
Consensus pattern (18 bp):
TTTTTTGAATTTTTCTTT
Found at i:39341 original size:14 final size:14
Alignment explanation
Indices: 39322--39357 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
39312 TATGCAATTT
39322 TTTTTTTTTTTCAA
1 TTTTTTTTTTTCAA
39336 TTTTTTTTTTTCAA
1 TTTTTTTTTTTCAA
39350 TTTTTTTT
1 TTTTTTTT
39358 ACGTACCTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.11, C:0.06, G:0.00, T:0.83
Consensus pattern (14 bp):
TTTTTTTTTTTCAA
Found at i:39679 original size:21 final size:21
Alignment explanation
Indices: 39653--39715 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
39643 TTGGTATTTG
39653 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
*
39674 GGAATTGGTATGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
39695 GGTATTTGGTACGAATTGGTA
1 GG-AATTGGTACGAAATGGTA
39716 ATGGTTCAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 22 0.59
22 15 0.41
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.33
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:45750 original size:12 final size:11
Alignment explanation
Indices: 45719--45761 Score: 59
Period size: 11 Copynumber: 3.9 Consensus size: 11
45709 ATCGTATACA
*
45719 ATTTTTTTTTA
1 ATTTTTTTTTG
**
45730 ATTAATTTTTG
1 ATTTTTTTTTG
45741 ATTTTTTTTTG
1 ATTTTTTTTTG
45752 ATTTTTTTTT
1 ATTTTTTTTT
45762 CAAATTTTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.16, C:0.00, G:0.05, T:0.79
Consensus pattern (11 bp):
ATTTTTTTTTG
Found at i:48724 original size:17 final size:18
Alignment explanation
Indices: 48676--48726 Score: 59
Period size: 17 Copynumber: 2.8 Consensus size: 18
48666 GTTCTCGCAC
48676 CTTTTCTTTTCTTTCTCAAT
1 CTTTTC-TTTCTTT-TCAAT
*
48696 CTTTTCTCTCTTTTCAAT
1 CTTTTCTTTCTTTTCAAT
*
48714 -TTTTGTTTCTTTT
1 CTTTTCTTTCTTTT
48727 TCGGTTTCTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
17 11 0.39
18 5 0.18
19 6 0.21
20 6 0.21
ACGTcount: A:0.08, C:0.22, G:0.02, T:0.69
Consensus pattern (18 bp):
CTTTTCTTTCTTTTCAAT
Found at i:49718 original size:12 final size:11
Alignment explanation
Indices: 49701--49730 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
49691 TGGAAACTAG
49701 TTTTTTTTGAAA
1 TTTTTTTTG-AA
49713 TTTTTTTTGAA
1 TTTTTTTTGAA
49724 TTTTTTT
1 TTTTTTT
49731 CGAGAAACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 9 0.50
12 9 0.50
ACGTcount: A:0.17, C:0.00, G:0.07, T:0.77
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:57319 original size:11 final size:11
Alignment explanation
Indices: 57305--57332 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
57295 TTTTAATTAA
57305 TTTTTTTGATT
1 TTTTTTTGATT
57316 TTTTTTTGATT
1 TTTTTTTGATT
57327 TTTTTT
1 TTTTTT
57333 CAAATTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.07, C:0.00, G:0.07, T:0.86
Consensus pattern (11 bp):
TTTTTTTGATT
Found at i:61350 original size:14 final size:14
Alignment explanation
Indices: 61331--61363 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
61321 ACTAGCTCTC
*
61331 TTTTTTTT-ACAAT
1 TTTTTTTTCAAAAT
61344 TTTTTTTTCAAAAT
1 TTTTTTTTCAAAAT
61358 TTTTTT
1 TTTTTT
61364 CACAACTTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.44
14 10 0.56
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.73
Consensus pattern (14 bp):
TTTTTTTTCAAAAT
Found at i:61417 original size:16 final size:13
Alignment explanation
Indices: 61406--61437 Score: 57
Period size: 12 Copynumber: 2.5 Consensus size: 13
61396 TGGAAACTAG
61406 TTTTTTTTGAAAT
1 TTTTTTTTGAAAT
61419 TTTTTTTTG-AAT
1 TTTTTTTTGAAAT
61431 TTTTTTT
1 TTTTTTT
61438 CGAGAAACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 10 0.53
13 9 0.47
ACGTcount: A:0.16, C:0.00, G:0.06, T:0.78
Consensus pattern (13 bp):
TTTTTTTTGAAAT
Found at i:67272 original size:20 final size:20
Alignment explanation
Indices: 67226--67272 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
67216 AGCTCGTTTC
*
67226 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* * *
67246 CAACTCATTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
67266 CAGCTCA
1 CAGCTCA
67273 ATCTTAACCC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.34, G:0.13, T:0.23
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:79634 original size:11 final size:12
Alignment explanation
Indices: 79611--79639 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
79601 AAAAAAAAAA
79611 TTTTTGAATTTT
1 TTTTTGAATTTT
79623 TTTTTGAATTTT
1 TTTTTGAATTTT
79635 TTTTT
1 TTTTT
79640 CAAATTTCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.14, C:0.00, G:0.07, T:0.79
Consensus pattern (12 bp):
TTTTTGAATTTT
Found at i:85946 original size:20 final size:20
Alignment explanation
Indices: 85923--85969 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
85913 GGGTTAAGAT
*
85923 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
85943 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
85963 TGAGCTG
1 TGAGCTG
85970 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
Found at i:86931 original size:22 final size:22
Alignment explanation
Indices: 86903--86946 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
86893 TTTTGAACCA
86903 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
86925 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
86947 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:89442 original size:23 final size:22
Alignment explanation
Indices: 89390--89442 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
89380 TCCACGTCTT
*
89390 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
89412 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
89435 TTTCTTTT
1 TTTCTTTT
89443 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:94246 original size:16 final size:17
Alignment explanation
Indices: 94215--94263 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
94205 GAAAAGAGCG
*
94215 AAAATACAAAAGAAAAGA
1 AAAAT-CAAAAAAAAAGA
*
94233 AAAATGAAAAAAAAAGA
1 AAAATCAAAAAAAAAGA
*
94250 AAATTCAAAAAAAA
1 AAAATCAAAAAAAA
94264 GAATGAAAAG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
17 22 0.81
18 5 0.19
ACGTcount: A:0.80, C:0.04, G:0.08, T:0.08
Consensus pattern (17 bp):
AAAATCAAAAAAAAAGA
Found at i:94264 original size:16 final size:16
Alignment explanation
Indices: 94214--94266 Score: 63
Period size: 16 Copynumber: 3.2 Consensus size: 16
94204 AGAAAAGAGC
94214 GAAAATACAAAAGAAAA
1 GAAAATACAAAA-AAAA
94231 GAAAAATGA-AAAAAAAA
1 G-AAAAT-ACAAAAAAAA
*
94248 GAAAATTCAAAAAAAA
1 GAAAATACAAAAAAAA
94264 GAA
1 GAA
94267 TGAAAAGAGA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
16 16 0.50
17 6 0.19
18 9 0.28
19 1 0.03
ACGTcount: A:0.77, C:0.04, G:0.11, T:0.08
Consensus pattern (16 bp):
GAAAATACAAAAAAAA
Found at i:98555 original size:22 final size:22
Alignment explanation
Indices: 98527--98570 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
98517 TTTTGAACCA
98527 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
98549 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
98571 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:108194 original size:18 final size:19
Alignment explanation
Indices: 108173--108231 Score: 52
Period size: 18 Copynumber: 3.1 Consensus size: 19
108163 TGAAGGCAAA
108173 GGAACAAAAAGAAAAGA-T
1 GGAACAAAAAGAAAAGAGT
*
108191 GGAA-AAAGAAAAAAAGAGT
1 GGAACAAA-AAGAAAAGAGT
108210 GAGAAAACAAAAAGAAAA-AGT
1 G-G--AACAAAAAGAAAAGAGT
108231 G
1 G
108232 AGTTGAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
17 3 0.09
18 12 0.36
19 2 0.06
20 1 0.03
21 4 0.12
22 8 0.24
23 3 0.09
ACGTcount: A:0.68, C:0.03, G:0.24, T:0.05
Consensus pattern (19 bp):
GGAACAAAAAGAAAAGAGT
Found at i:108233 original size:21 final size:21
Alignment explanation
Indices: 108175--108233 Score: 63
Period size: 20 Copynumber: 2.9 Consensus size: 21
108165 AAGGCAAAGG
108175 AACAAAAAG-AAAAGATG-GAA
1 AACAAAAAGAAAAAG-TGAGAA
*
108195 AA-AGAAAA-AAAGAGTGAGAA
1 AACA-AAAAGAAAAAGTGAGAA
108215 AACAAAAAGAAAAAGTGAG
1 AACAAAAAGAAAAAGTGAG
108234 TTGAAATTGA
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
19 3 0.09
20 19 0.59
21 10 0.31
ACGTcount: A:0.69, C:0.03, G:0.22, T:0.05
Consensus pattern (21 bp):
AACAAAAAGAAAAAGTGAGAA
Found at i:113477 original size:24 final size:25
Alignment explanation
Indices: 113424--113477 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 25
113414 AACAAATTCT
* *
113424 TTTTTTCATTTTCATCACTCGTTTC
1 TTTTTTCATTTTAATCACTCGTCTC
113449 -TTTTTC-TTTTGAATCACTC-TCTC
1 TTTTTTCATTTT-AATCACTCGTCTC
113472 TTTTTT
1 TTTTTT
113478 TATCACTCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 7 0.28
24 18 0.72
ACGTcount: A:0.11, C:0.22, G:0.04, T:0.63
Consensus pattern (25 bp):
TTTTTTCATTTTAATCACTCGTCTC
Found at i:119505 original size:21 final size:23
Alignment explanation
Indices: 119460--119506 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
119450 TCACCTGCAA
* *
119460 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
119483 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
119504 TAA
1 TAA
119507 TCATAACACA
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:120880 original size:20 final size:20
Alignment explanation
Indices: 120834--120871 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
120824 AGCTCGTTTC
120834 CAGCTCACTTGAGCTCAAGT
1 CAGCTCACTTGAGCTCAAGT
120854 CAGCTCA-TTCGAGCTCAA
1 CAGCTCACTT-GAGCTCAA
120872 TTTAGCTCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.26, C:0.32, G:0.18, T:0.24
Consensus pattern (20 bp):
CAGCTCACTTGAGCTCAAGT
Found at i:122451 original size:10 final size:11
Alignment explanation
Indices: 122430--122455 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
122420 CAAAAAAATC
122430 AAAATTCAAAA
1 AAAATTCAAAA
122441 AAAATTCAAAA
1 AAAATTCAAAA
122452 AAAA
1 AAAA
122456 GAAAAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.77, C:0.08, G:0.00, T:0.15
Consensus pattern (11 bp):
AAAATTCAAAA
Found at i:122461 original size:10 final size:10
Alignment explanation
Indices: 122448--122475 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
122438 AAAAAAATTC
122448 AAAAAAAAGA
1 AAAAAAAAGA
122458 AAAAAAAAGA
1 AAAAAAAAGA
122468 AAAAAAAA
1 AAAAAAAA
122476 AGAAGTGTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (10 bp):
AAAAAAAAGA
Found at i:122462 original size:11 final size:11
Alignment explanation
Indices: 122448--122479 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
122438 AAAAAAATTC
122448 AAAAAAAAG-A
1 AAAAAAAAGAA
122458 AAAAAAAAGAA
1 AAAAAAAAGAA
122469 AAAAAAAAGAA
1 AAAAAAAAGAA
122480 GTGTGATACA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 9 0.43
11 12 0.57
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (11 bp):
AAAAAAAAGAA
Found at i:124127 original size:21 final size:21
Alignment explanation
Indices: 124100--124142 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
124090 TAGGTACGTA
124100 AAAAAAAGAGTTCGAAAAAAAAG
1 AAAAAAA-A-TTCGAAAAAAAAG
*
124123 AAAAAAAATTTGAAAAAAAA
1 AAAAAAAATTCGAAAAAAAA
124143 ATTGAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 11 0.58
22 1 0.05
23 7 0.37
ACGTcount: A:0.74, C:0.02, G:0.12, T:0.12
Consensus pattern (21 bp):
AAAAAAAATTCGAAAAAAAAG
Found at i:124129 original size:12 final size:12
Alignment explanation
Indices: 124114--124158 Score: 67
Period size: 12 Copynumber: 3.9 Consensus size: 12
124104 AAAGAGTTCG
124114 AAAAAAAA--GA
1 AAAAAAAATTGA
*
124124 AAAAAAATTTGA
1 AAAAAAAATTGA
124136 AAAAAAAATTGA
1 AAAAAAAATTGA
124148 AAAAAAAATTG
1 AAAAAAAATTG
124159 CATACGGTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
10 7 0.23
12 24 0.77
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.16
Consensus pattern (12 bp):
AAAAAAAATTGA
Found at i:126397 original size:19 final size:19
Alignment explanation
Indices: 126370--126412 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
126360 GCGAAAATAC
* *
126370 AAAAGAAAAGAAAAATGAA
1 AAAAAAAAAGAAAAATCAA
*
126389 AAAAAAAAAGAAAATTCAA
1 AAAAAAAAAGAAAAATCAA
126408 AAAAA
1 AAAAA
126413 GAGAATGAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.81, C:0.02, G:0.09, T:0.07
Consensus pattern (19 bp):
AAAAAAAAAGAAAAATCAA
Found at i:130577 original size:21 final size:21
Alignment explanation
Indices: 130532--130594 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
130522 TTTGAACCAT
* *
130532 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
130554 TACCATTTCGTACCAATTCCA
1 TACCATTTCGTACCAATTCCA
* *
130575 TACTATTTCGAACCAATTCC
1 TACCATTTCGTACCAATTCC
130595 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 24 0.65
22 13 0.35
ACGTcount: A:0.33, C:0.32, G:0.05, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:130747 original size:21 final size:23
Alignment explanation
Indices: 130722--130768 Score: 80
Period size: 21 Copynumber: 2.1 Consensus size: 23
130712 TTATCTTACT
130722 TCTTTGAACAC-AA-ATATTCTA
1 TCTTTGAACACAAATATATTCTA
130743 TCTTTGAACACAAATATATTCTA
1 TCTTTGAACACAAATATATTCTA
130766 TCT
1 TCT
130769 CCTTCTCGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 11 0.46
22 2 0.08
23 11 0.46
ACGTcount: A:0.36, C:0.19, G:0.04, T:0.40
Consensus pattern (23 bp):
TCTTTGAACACAAATATATTCTA
Found at i:131599 original size:14 final size:14
Alignment explanation
Indices: 131580--131630 Score: 93
Period size: 14 Copynumber: 3.6 Consensus size: 14
131570 ACTAGCTTCT
131580 TTTTTTTTCACGAA
1 TTTTTTTTCACGAA
131594 TTTTTTTTTCACGAA
1 -TTTTTTTTCACGAA
131609 TTTTTTTTCACGAA
1 TTTTTTTTCACGAA
131623 TTTTTTTT
1 TTTTTTTT
131631 TTCAACTTGA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
14 22 0.61
15 14 0.39
ACGTcount: A:0.18, C:0.12, G:0.06, T:0.65
Consensus pattern (14 bp):
TTTTTTTTCACGAA
Found at i:131599 original size:15 final size:15
Alignment explanation
Indices: 131579--131631 Score: 99
Period size: 15 Copynumber: 3.6 Consensus size: 15
131569 AACTAGCTTC
131579 TTTTTTTTTCACGAA
1 TTTTTTTTTCACGAA
131594 TTTTTTTTTCACGAA
1 TTTTTTTTTCACGAA
131609 -TTTTTTTTCACGAA
1 TTTTTTTTTCACGAA
131623 TTTTTTTTT
1 TTTTTTTTT
131632 TCAACTTGAT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
14 14 0.38
15 23 0.62
ACGTcount: A:0.17, C:0.11, G:0.06, T:0.66
Consensus pattern (15 bp):
TTTTTTTTTCACGAA
Found at i:131692 original size:13 final size:13
Alignment explanation
Indices: 131674--131729 Score: 98
Period size: 13 Copynumber: 4.5 Consensus size: 13
131664 GGAAACCAAA
131674 TTTTTTTTTGAAT
1 TTTTTTTTTGAAT
131687 TTTTTTTTTGAAT
1 TTTTTTTTTGAAT
131700 TTTTTTTTTGAA-
1 TTTTTTTTTGAAT
131712 -TTTTTTTTGAAT
1 TTTTTTTTTGAAT
131724 TTTTTT
1 TTTTTT
131730 GAAGAAACTA
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
11 11 0.27
13 30 0.73
ACGTcount: A:0.14, C:0.00, G:0.07, T:0.79
Consensus pattern (13 bp):
TTTTTTTTTGAAT
Found at i:131715 original size:24 final size:25
Alignment explanation
Indices: 131674--131729 Score: 96
Period size: 24 Copynumber: 2.2 Consensus size: 25
131664 GGAAACCAAA
131674 TTTTTTTTTGAATTTTTTTTTTGAAT
1 TTTTTTTTTGAA-TTTTTTTTTGAAT
131700 TTTTTTTTTGAA-TTTTTTTTGAAT
1 TTTTTTTTTGAATTTTTTTTTGAAT
131724 TTTTTT
1 TTTTTT
131730 GAAGAAACTA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
24 18 0.60
26 12 0.40
ACGTcount: A:0.14, C:0.00, G:0.07, T:0.79
Consensus pattern (25 bp):
TTTTTTTTTGAATTTTTTTTTGAAT
Found at i:134209 original size:21 final size:23
Alignment explanation
Indices: 134164--134210 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
134154 TCACCTGCAA
* *
134164 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
134187 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
134208 TAA
1 TAA
134211 TCATAACACA
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:140905 original size:20 final size:20
Alignment explanation
Indices: 140882--140935 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
140872 AGTTTTTCCC
*
140882 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
140902 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
140922 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
140936 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:140917 original size:30 final size:30
Alignment explanation
Indices: 140882--140955 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
140872 AGTTTTTCCC
140882 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
140912 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
140942 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
140956 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:140945 original size:20 final size:20
Alignment explanation
Indices: 140882--140946 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
140872 AGTTTTTCCC
* * * *
140882 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
140902 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
140921 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
140942 AGCTC
1 AGCTC
140947 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:148866 original size:30 final size:29
Alignment explanation
Indices: 148832--148927 Score: 77
Period size: 30 Copynumber: 3.2 Consensus size: 29
148822 TAAACTAAAA
*
148832 TGAGCTAAGTTTTATCTCGTGAGCTAAAGT
1 TGAGCTAAG-TTTAACTCGTGAGCTAAAGT
* *** * * *
148862 TGAGCTGAGGCAAACTCCTAAGCTGAAGT
1 TGAGCTAAGTTTAACTCGTGAGCTAAAGT
*
148891 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAA-GTTTAACTCGTGAGCTAAAGT
148920 ATGAGCTA
1 -TGAGCTA
148928 GGAGTGAGCT
Statistics
Matches: 48, Mismatches: 16, Indels: 4
0.71 0.24 0.06
Matches are distributed among these distances:
29 21 0.44
30 27 0.56
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.29
Consensus pattern (29 bp):
TGAGCTAAGTTTAACTCGTGAGCTAAAGT
Found at i:167486 original size:20 final size:20
Alignment explanation
Indices: 167463--167522 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
167453 CAACTCCGAC
167463 CAGCTCAATTGAGCTCATTT
1 CAGCTCAATTGAGCTCATTT
*
167483 CAGCTCAATCGAGCTCAATTT
1 CAGCTCAATTGAGCTC-ATTT
* *
167504 -AGCTCAACTCAGCTCATTT
1 CAGCTCAATTGAGCTCATTT
167523 ATTTTATTGG
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
19 4 0.11
20 27 0.77
21 4 0.11
ACGTcount: A:0.27, C:0.28, G:0.13, T:0.32
Consensus pattern (20 bp):
CAGCTCAATTGAGCTCATTT
Found at i:167517 original size:10 final size:10
Alignment explanation
Indices: 167463--167519 Score: 62
Period size: 10 Copynumber: 5.7 Consensus size: 10
167453 CAACTCCGAC
167463 CAGCTCAATT
1 CAGCTCAATT
* *
167473 GAGCTCATTT
1 CAGCTCAATT
167483 CAGCTCAA-T
1 CAGCTCAATT
167492 CGAGCTCAATT
1 C-AGCTCAATT
* *
167503 TAGCTCAACT
1 CAGCTCAATT
167513 CAGCTCA
1 CAGCTCA
167520 TTTATTTTAT
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
9 2 0.05
10 35 0.92
11 1 0.03
ACGTcount: A:0.28, C:0.30, G:0.14, T:0.28
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:168164 original size:73 final size:74
Alignment explanation
Indices: 168035--168182 Score: 257
Period size: 73 Copynumber: 2.0 Consensus size: 74
168025 CAAGTTCATT
168035 TCCTTAGCCATGAAGCTGCCCATTGAAGTACCATCAGCTGAATTTGGACATACCTTTAAAGATAC
1 TCCTTAGCCATGAAGCTGCCCATTGAAGTACCATCAGCTGAATTTGGACATACCTTTAAAGATAC
168100 -TTTCTAGA
66 ATTTCTAGA
168108 TCCTTAGCCATGAAGCTGCCCATTG-AGTA-CATTCAGCTGAATTTGGACATAGCCTTTAAAGAT
1 TCCTTAGCCATGAAGCTGCCCATTGAAGTACCA-TCAGCTGAATTTGGACATA-CCTTTAAAGAT
168171 ACATTTCTAGA
64 ACATTTCTAGA
168182 T
1 T
168183 TAGTTTAATT
Statistics
Matches: 72, Mismatches: 0, Indels: 5
0.94 0.00 0.06
Matches are distributed among these distances:
71 2 0.03
72 23 0.32
73 38 0.53
74 9 0.12
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.31
Consensus pattern (74 bp):
TCCTTAGCCATGAAGCTGCCCATTGAAGTACCATCAGCTGAATTTGGACATACCTTTAAAGATAC
ATTTCTAGA
Found at i:168941 original size:12 final size:12
Alignment explanation
Indices: 168920--168949 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
168910 TTGGAGTATC
*
168920 AAAAATAATTCA
1 AAAAAAAATTCA
168932 AAAAAAAATTCA
1 AAAAAAAATTCA
168944 AAAAAA
1 AAAAAA
168950 GTGAAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.77, C:0.07, G:0.00, T:0.17
Consensus pattern (12 bp):
AAAAAAAATTCA
Found at i:168995 original size:14 final size:14
Alignment explanation
Indices: 168953--168999 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
168943 AAAAAAAGTG
168953 AAAAAA-AGAGCAA
1 AAAAAAGAGAGCAA
* *
168966 AAAAAAGAAAGAAA
1 AAAAAAGAGAGCAA
*
168980 AAAAAAGTGAGCAA
1 AAAAAAGAGAGCAA
168994 AAAAAA
1 AAAAAA
169000 TCAAGTTAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
13 6 0.21
14 22 0.79
ACGTcount: A:0.79, C:0.04, G:0.15, T:0.02
Consensus pattern (14 bp):
AAAAAAGAGAGCAA
Found at i:169010 original size:28 final size:26
Alignment explanation
Indices: 168943--169014 Score: 74
Period size: 28 Copynumber: 2.7 Consensus size: 26
168933 AAAAAAATTC
*
168943 AAAA-AAAGTGAAAAAAAGAGCAAAA
1 AAAAGAAAGTAAAAAAAAGAGCAAAA
*
168968 AAAAGAAAGAAAAAAAAAGTGAGCAAAA
1 AAAAGAAAGTAAAAAAAA--GAGCAAAA
**
168996 AAAATCAAGTTAAAAAAAA
1 AAAAGAAAG-TAAAAAAAA
169015 AGTGAAAAGT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
25 4 0.11
26 11 0.29
28 15 0.39
29 8 0.21
ACGTcount: A:0.75, C:0.04, G:0.14, T:0.07
Consensus pattern (26 bp):
AAAAGAAAGTAAAAAAAAGAGCAAAA
Found at i:169808 original size:10 final size:10
Alignment explanation
Indices: 169793--169817 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
169783 CCAATGATTA
169793 TCTTTTTGAT
1 TCTTTTTGAT
169803 TCTTTTTGAT
1 TCTTTTTGAT
169813 TCTTT
1 TCTTT
169818 CGTGTCATCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.08, C:0.12, G:0.08, T:0.72
Consensus pattern (10 bp):
TCTTTTTGAT
Found at i:169924 original size:17 final size:18
Alignment explanation
Indices: 169891--169924 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
169881 AAGAAAAAGA
169891 ATTGAAAAAAGAATTGAG
1 ATTGAAAAAAGAATTGAG
*
169909 ATTGAGAAAA-AATTGA
1 ATTGAAAAAAGAATTGA
169925 AAAAAGAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.56, C:0.00, G:0.21, T:0.24
Consensus pattern (18 bp):
ATTGAAAAAAGAATTGAG
Found at i:175915 original size:1 final size:1
Alignment explanation
Indices: 175909--175944 Score: 63
Period size: 1 Copynumber: 36.0 Consensus size: 1
175899 CTATGGGAGG
*
175909 AAAAAAAAAAAAAAAAAATAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
175945 TGGAAGAAAC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:0.97, C:0.00, G:0.00, T:0.03
Consensus pattern (1 bp):
A
Found at i:175933 original size:18 final size:18
Alignment explanation
Indices: 175910--175945 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
175900 TATGGGAGGA
175910 AAAAAAAAAAAAAAAAAT
1 AAAAAAAAAAAAAAAAAT
175928 AAAAAAAAAAAAAAAAAT
1 AAAAAAAAAAAAAAAAAT
175946 GGAAGAAACG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.94, C:0.00, G:0.00, T:0.06
Consensus pattern (18 bp):
AAAAAAAAAAAAAAAAAT
Found at i:179099 original size:1 final size:1
Alignment explanation
Indices: 179093--179137 Score: 90
Period size: 1 Copynumber: 45.0 Consensus size: 1
179083 GGCCCTCCAG
179093 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
179138 GACTGCATAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 44 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Done.