Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2530
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: 50084
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:140 original size:15 final size:16
Alignment explanation
Indices: 120--149 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
110 AAACGTTCTT
120 TTTCTTCCT-CTGTCA
1 TTTCTTCCTCCTGTCA
135 TTTCTTCCTCCTGTC
1 TTTCTTCCTCCTGTC
150 CAGTGTAGTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.03, C:0.37, G:0.07, T:0.53
Consensus pattern (16 bp):
TTTCTTCCTCCTGTCA
Found at i:4024 original size:26 final size:26
Alignment explanation
Indices: 3995--4149 Score: 131
Period size: 27 Copynumber: 5.8 Consensus size: 26
3985 AATTGTACAC
3995 GCACTAAGTGTGCGATTTGACTATGT
1 GCACTAAGTGTGCGATTTGACTATGT
* *
4021 GCACTAAGTGTGCGAAATTGA-AATGAT
1 GCACTAAGTGTGCG-ATTTGACTATG-T
* *
4048 GCACTAAGTGTGCGAATTGAACCATG-
1 GCACTAAGTGTGCGATTTG-ACTATGT
4074 GCGGAACTAAGTGT-CGAGTTTGAC-ATGT
1 GC---ACTAAGTGTGCGA-TTTGACTATGT
*
4102 AGCACTAAGTGGTGCGATTTGATTA-GT
1 -GCACTAAGT-GTGCGATTTGACTATGT
*
4129 AGCACTAAGTGTGCGAGTTGA
1 -GCACTAAGTGTGCGATTTGA
4150 ATTATATAGC
Statistics
Matches: 110, Mismatches: 6, Indels: 26
0.77 0.04 0.18
Matches are distributed among these distances:
26 41 0.37
27 43 0.39
28 12 0.11
29 14 0.13
ACGTcount: A:0.28, C:0.14, G:0.29, T:0.28
Consensus pattern (26 bp):
GCACTAAGTGTGCGATTTGACTATGT
Found at i:4050 original size:27 final size:25
Alignment explanation
Indices: 3995--4150 Score: 111
Period size: 26 Copynumber: 5.8 Consensus size: 25
3985 AATTGTACAC
* *
3995 GCACTAAGTGTGCGATTTGACTATGT
1 GCACTAAGTGTGCGAATTGA-AATGT
4021 GCACTAAGTGTGCGAAATTGAAATGAT
1 GCACTAAGTGTGCG-AATTGAAATG-T
4048 GCACTAAGTGTGCGAATTGAACCATG-
1 GCACTAAGTGTGCGAATTGAA--ATGT
* *
4074 GCGGAACTAAGTGT-CGAGTTTGACATGT
1 GC---ACTAAGTGTGCGA-ATTGAAATGT
* *
4102 AGCACTAAGTGGTGCGATTTG-ATTAGT
1 -GCACTAAGT-GTGCGAATTGAAAT-GT
*
4129 AGCACTAAGTGTGCGAGTTGAA
1 -GCACTAAGTGTGCGAATTGAA
4151 TTATATAGCA
Statistics
Matches: 109, Mismatches: 7, Indels: 27
0.76 0.05 0.19
Matches are distributed among these distances:
26 43 0.39
27 42 0.39
28 9 0.08
29 15 0.14
ACGTcount: A:0.29, C:0.14, G:0.29, T:0.28
Consensus pattern (25 bp):
GCACTAAGTGTGCGAATTGAAATGT
Found at i:4153 original size:27 final size:27
Alignment explanation
Indices: 3995--4171 Score: 102
Period size: 27 Copynumber: 6.5 Consensus size: 27
3985 AATTGTACAC
*
3995 GCACTAAGTGTGCGATTTG-ACTATGT-
1 GCACTAAGTGTGCGAATTGAACTA-GTA
*
4021 GCACTAAGTGTGCGAAATTGAAAT-G-A
1 GCACTAAGTGTGCG-AATTGAACTAGTA
* *
4047 TGCACTAAGTGTGCGAATTGAACCA-TG
1 -GCACTAAGTGTGCGAATTGAACTAGTA
*
4074 GCGGAACTAAGTGT-CGAGTTTG-AC-ATGTA
1 GC---ACTAAGTGTGCGA-ATTGAACTA-GTA
* *
4103 GCACTAAGTGGTGCGATTTG-ATTAGTA
1 GCACTAAGT-GTGCGAATTGAACTAGTA
* * *
4130 GCACTAAGTGTGCGAGTTGAATTATATA
1 GCACTAAGTGTGCGAATTGAACTA-GTA
*
4158 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
4172 GACTCAATAT
Statistics
Matches: 123, Mismatches: 11, Indels: 32
0.74 0.07 0.19
Matches are distributed among these distances:
26 40 0.33
27 42 0.34
28 26 0.21
29 15 0.12
ACGTcount: A:0.28, C:0.14, G:0.29, T:0.29
Consensus pattern (27 bp):
GCACTAAGTGTGCGAATTGAACTAGTA
Found at i:5666 original size:45 final size:45
Alignment explanation
Indices: 5531--5999 Score: 354
Period size: 45 Copynumber: 10.1 Consensus size: 45
5521 TACAGTTACC
* * ** *
5531 GTGGAGTAGATTGAAGATAGTGAATCTTATCTCCCTAAAGTTGCA
1 GTGGAGCAGATTAAAGATAGCAAATCTTATCTCCCTGAAGTTGCA
* * *
5576 GTGGAACAGATTAAAGCTATGAGTTACAAATCTTATCTCCATGAAGTTACA
1 GTGGAGCAGATTAAAG--AT-AG---CAAATCTTATCTCCCTGAAGTTGCA
* *
5627 GTGGAGCAAATTAAAGATAGCAAATCTTATTTCCCTGAAGTTGCA
1 GTGGAGCAGATTAAAGATAGCAAATCTTATCTCCCTGAAGTTGCA
* * * * *
5672 GTGGGGCATATTAAAGGTAGCGAATCTTATCTCCCTGAAGTTGTA
1 GTGGAGCAGATTAAAGATAGCAAATCTTATCTCCCTGAAGTTGCA
* * *
5717 GTGGAACAGATTAAAGCTACGAGTTACAAATCTTATCTCCCTGAAGTTACA
1 GTGGAGCAGATTAAAG--A-TAG---CAAATCTTATCTCCCTGAAGTTGCA
* * *
5768 GTGGAGTAGATTGAAGATAGCAAATCTTATTTCCCTGAAGTTGCA
1 GTGGAGCAGATTAAAGATAGCAAATCTTATCTCCCTGAAGTTGCA
* * * * * *
5813 GTGGAACAGATTAAAGCTACAAGTTACAAATTTTATCTCCTTCAATTTGCA
1 GTGGAGCAGATTAAAG--A-TAG---CAAATCTTATCTCCCTGAAGTTGCA
* * * *
5864 ATGGAGCAGATTGAAGAT-GCGAATCTTATTTCCCTGAAGTTGCA
1 GTGGAGCAGATTAAAGATAGCAAATCTTATCTCCCTGAAGTTGCA
* * * * *
5908 GTGAAGGAGATTGAAGCTA-CTAAAT-TTATCTCCCTGAAATTGCA
1 GTGGAGCAGATTAAAGATAGC-AAATCTTATCTCCCTGAAGTTGCA
* * ** *
5952 GTGGAGCAAATTGAAGCGA-CAATTCTTATAC-CCCTGAAGTTGCA
1 GTGGAGCAGATTAAAGATAGCAAATCTTAT-CTCCCTGAAGTTGCA
5996 GTGG
1 GTGG
6000 GTTAGAACGA
Statistics
Matches: 337, Mismatches: 65, Indels: 45
0.75 0.15 0.10
Matches are distributed among these distances:
43 3 0.01
44 87 0.26
45 127 0.38
47 4 0.01
48 10 0.03
49 4 0.01
51 102 0.30
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.30
Consensus pattern (45 bp):
GTGGAGCAGATTAAAGATAGCAAATCTTATCTCCCTGAAGTTGCA
Found at i:5747 original size:96 final size:96
Alignment explanation
Indices: 5553--5999 Score: 397
Period size: 96 Copynumber: 4.8 Consensus size: 96
5543 GAAGATAGTG
* * * * * *
5553 AATCTTATCTCCCTAAAGTTGCAGTGGAACAGATTAAAGCTATGAGTTACAAATCTTATCTCCAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG--AT-AG---CGAATCTTATTTCCCT
* * * *
5618 GAAGTTACAGTGGAGCAAATTAAAG--A-TAG---CA
60 GAAGTTGCAGTGGAACAGATTAAAGCTACAAGTTACA
* * * * * *
5649 AATCTTATTTCCCTGAAGTTGCAGTGGGGCATATTAAAGGTAGCGAATCTTATCTCCCTGAAGTT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAGCGAATCTTATTTCCCTGAAGTT
* *
5714 GTAGTGGAACAGATTAAAGCTACGAGTTACA
66 GCAGTGGAACAGATTAAAGCTACAAGTTACA
* * *
5745 AATCTTATCTCCCTGAAGTTACAGTGGAGTAGATTGAAGATAGCAAATCTTATTTCCCTGAAGTT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAGCGAATCTTATTTCCCTGAAGTT
5810 GCAGTGGAACAGATTAAAGCTACAAGTTACA
66 GCAGTGGAACAGATTAAAGCTACAAGTTACA
* * * * *
5841 AATTTTATCTCCTTCAATTTGCAATGGAGCAGATTGAAGAT-GCGAATCTTATTTCCCTGAAGTT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAGCGAATCTTATTTCCCTGAAGTT
* *
5905 GCAGT-GAAGGAGATTGAAGCTAC----T--A
66 GCAGTGGAA-CAGATTAAAGCTACAAGTTACA
* * ** **
5930 AAT-TTATCTCCCTGAAATTGCAGTGGAGCAAATTGAAGCGA-C-AATTCTTATACCCCTGAAGT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAGCGAA-TCTTATTTCCCTGAAGT
5992 TGCAGTGG
65 TGCAGTGG
6000 GTTAGAACGA
Statistics
Matches: 298, Mismatches: 43, Indels: 27
0.81 0.12 0.07
Matches are distributed among these distances:
87 2 0.01
88 52 0.17
89 5 0.02
90 35 0.12
91 1 0.00
92 1 0.00
93 4 0.01
94 4 0.01
95 39 0.13
96 155 0.52
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.30
Consensus pattern (96 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAGCGAATCTTATTTCCCTGAAGTT
GCAGTGGAACAGATTAAAGCTACAAGTTACA
Found at i:5806 original size:141 final size:141
Alignment explanation
Indices: 5552--5816 Score: 467
Period size: 141 Copynumber: 1.9 Consensus size: 141
5542 TGAAGATAGT
*
5552 GAATCTTATCTCCCTAAAGTTGCAGTGGAACAGATTAAAGCTATGAGTTACAAATCTTATCTCCA
1 GAATCTTATCTCCCTAAAGTTGCAGTGGAACAGATTAAAGCTACGAGTTACAAATCTTATCTCCA
5617 TGAAGTTACAGTGGAGCAAATTAAAGATAGCAAATCTTATTTCCCTGAAGTTGCAGTGGGGCATA
66 TGAAGTTACAGTGGAGCAAATTAAAGATAGCAAATCTTATTTCCCTGAAGTTGCAGTGGGGCATA
5682 TTAAAGGTAGC
131 TTAAAGGTAGC
* * *
5693 GAATCTTATCTCCCTGAAGTTGTAGTGGAACAGATTAAAGCTACGAGTTACAAATCTTATCTCCC
1 GAATCTTATCTCCCTAAAGTTGCAGTGGAACAGATTAAAGCTACGAGTTACAAATCTTATCTCCA
* * *
5758 TGAAGTTACAGTGGAGTAGATTGAAGATAGCAAATCTTATTTCCCTGAAGTTGCAGTGG
66 TGAAGTTACAGTGGAGCAAATTAAAGATAGCAAATCTTATTTCCCTGAAGTTGCAGTGG
5817 AACAGATTAA
Statistics
Matches: 117, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
141 117 1.00
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Consensus pattern (141 bp):
GAATCTTATCTCCCTAAAGTTGCAGTGGAACAGATTAAAGCTACGAGTTACAAATCTTATCTCCA
TGAAGTTACAGTGGAGCAAATTAAAGATAGCAAATCTTATTTCCCTGAAGTTGCAGTGGGGCATA
TTAAAGGTAGC
Found at i:5922 original size:44 final size:42
Alignment explanation
Indices: 5859--5998 Score: 111
Period size: 44 Copynumber: 3.2 Consensus size: 42
5849 CTCCTTCAAT
* * *
5859 TTGCAATGGAGCAGATTGAAGATGCGAATCTTATTTCCCTGAAG
1 TTGCAGTGAAGCAGATTGAAG-TGC-AATCTTATATCCCTGAAG
* * * *
5903 TTGCAGTGAAGGAGATTGAAGCTACTAAAT-TTATCTCCCTGAAA
1 TTGCAGTGAAGCAGATTGAAG-TGC--AATCTTATATCCCTGAAG
* * * *
5947 TTGCAGTGGAGCAAATTGAAGCGACAATTCTTATACCCCTGAAG
1 TTGCAGTGAAGCAGATTGAAGTG-CAA-TCTTATATCCCTGAAG
5991 TTGCAGTG
1 TTGCAGTG
5999 GGTTAGAACG
Statistics
Matches: 76, Mismatches: 16, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
42 2 0.03
43 1 0.01
44 70 0.92
45 3 0.04
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.29
Consensus pattern (42 bp):
TTGCAGTGAAGCAGATTGAAGTGCAATCTTATATCCCTGAAG
Found at i:6250 original size:14 final size:14
Alignment explanation
Indices: 6231--6264 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
6221 ATCAAATCAT
6231 GCCCAAACTTACAA
1 GCCCAAACTTACAA
6245 GCCCAAACTTACAA
1 GCCCAAACTTACAA
*
6259 ACCCAA
1 GCCCAA
6265 GTGGCCCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.44, C:0.38, G:0.06, T:0.12
Consensus pattern (14 bp):
GCCCAAACTTACAA
Found at i:6928 original size:31 final size:33
Alignment explanation
Indices: 6869--6939 Score: 85
Period size: 31 Copynumber: 2.2 Consensus size: 33
6859 CCGACGGCCC
* *
6869 GCCCGAAATATGAGAGGTTTGGGTAAAAATAT-AG
1 GCCCGAAATAT-AGAGGCTTGGGCAAAAA-ATGAG
6903 GCCCGAAATAT-G-GGCTTGGGCAAAAAATGAG
1 GCCCGAAATATAGAGGCTTGGGCAAAAAATGAG
6934 GCCCGA
1 GCCCGA
6940 TTAAAAAAAC
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
30 2 0.06
31 20 0.59
32 1 0.03
34 11 0.32
ACGTcount: A:0.35, C:0.15, G:0.31, T:0.18
Consensus pattern (33 bp):
GCCCGAAATATAGAGGCTTGGGCAAAAAATGAG
Found at i:7037 original size:11 final size:11
Alignment explanation
Indices: 7021--7046 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
7011 ATTTTTTTAA
7021 TTTTAAAATAC
1 TTTTAAAATAC
7032 TTTTAAAATAC
1 TTTTAAAATAC
7043 TTTT
1 TTTT
7047 TTTTAAATTT
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:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (11 bp):
TTTTAAAATAC
Found at i:7057 original size:42 final size:42
Alignment explanation
Indices: 7011--7090 Score: 151
Period size: 42 Copynumber: 1.9 Consensus size: 42
7001 AAATATTTTT
7011 ATTTTTTTAATTTTAAAATACTTTTAAAATACTTTTTTTTAA
1 ATTTTTTTAATTTTAAAATACTTTTAAAATACTTTTTTTTAA
*
7053 ATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTT
1 ATTTTTTTAATTTTAAAATACTTTTAAAATACTTTTTT
7091 AATTTTTAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (42 bp):
ATTTTTTTAATTTTAAAATACTTTTAAAATACTTTTTTTTAA
Found at i:7067 original size:31 final size:30
Alignment explanation
Indices: 7045--7103 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 30
7035 TAAAATACTT
*
7045 TTTTTTAAAT-TTTTTTAA-TTTTAAAATA
1 TTTTTAAAATATTTTTTAATTTTTAAAATA
7073 TTTTTAAAATACTTTTTTAATTTTTAAAATA
1 TTTTTAAAATA-TTTTTTAATTTTTAAAATA
7104 AATTTTTGGT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 9 0.33
30 8 0.30
31 10 0.37
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (30 bp):
TTTTTAAAATATTTTTTAATTTTTAAAATA
Found at i:7109 original size:20 final size:20
Alignment explanation
Indices: 7072--7110 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
7062 ATTTTAAAAT
**
7072 ATTTTTAAAATACTTTTTTA
1 ATTTTTAAAATAAATTTTTA
7092 ATTTTTAAAATAAATTTTT
1 ATTTTTAAAATAAATTTTT
7111 GGTATTTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (20 bp):
ATTTTTAAAATAAATTTTTA
Found at i:7945 original size:34 final size:34
Alignment explanation
Indices: 7907--7978 Score: 92
Period size: 34 Copynumber: 2.1 Consensus size: 34
7897 GATTAAGTCC
* *
7907 TTTACTTATTT-TAATTCTTTTATTTATTTACATA
1 TTTACTTATTTATAATTCCTTCATTTATTTA-ATA
* *
7941 TTTACTTATTTATTATTCCTTCATTTTTTTAATA
1 TTTACTTATTTATAATTCCTTCATTTATTTAATA
7975 TTTA
1 TTTA
7979 AAATTATTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
34 18 0.55
35 15 0.45
ACGTcount: A:0.25, C:0.10, G:0.00, T:0.65
Consensus pattern (34 bp):
TTTACTTATTTATAATTCCTTCATTTATTTAATA
Found at i:9415 original size:11 final size:11
Alignment explanation
Indices: 9382--9420 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
9372 TAGCGTAATT
9382 TTTTATTTATTA
1 TTTTATTT-TTA
*
9394 TTGTCATTTTTA
1 TT-TTATTTTTA
9406 TTTTATTTTTA
1 TTTTATTTTTA
9417 TTTT
1 TTTT
9421 TTTGGTATTC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 12 0.50
12 7 0.29
13 5 0.21
ACGTcount: A:0.18, C:0.03, G:0.03, T:0.77
Consensus pattern (11 bp):
TTTTATTTTTA
Found at i:11079 original size:16 final size:16
Alignment explanation
Indices: 11060--11100 Score: 82
Period size: 16 Copynumber: 2.6 Consensus size: 16
11050 AAAGAAAAAG
11060 GGAAGAAAATGACAGA
1 GGAAGAAAATGACAGA
11076 GGAAGAAAATGACAGA
1 GGAAGAAAATGACAGA
11092 GGAAGAAAA
1 GGAAGAAAA
11101 AAGAACGTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.59, C:0.05, G:0.32, T:0.05
Consensus pattern (16 bp):
GGAAGAAAATGACAGA
Found at i:12552 original size:16 final size:16
Alignment explanation
Indices: 12506--12555 Score: 50
Period size: 17 Copynumber: 3.1 Consensus size: 16
12496 TTTAAGTTTC
12506 TTTA-TTTA-TTTACTT
1 TTTACTTTATTTTA-TT
*
12521 TTTACTTTTTTCTTATT
1 TTTACTTTATT-TTATT
*
12538 TTTCCTTTATTTTATT
1 TTTACTTTATTTTATT
12554 TT
1 TT
12556 ATTATTATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
15 4 0.14
16 10 0.34
17 12 0.41
18 3 0.10
ACGTcount: A:0.14, C:0.10, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTACTTTATTTTATT
Found at i:12616 original size:23 final size:24
Alignment explanation
Indices: 12590--12651 Score: 76
Period size: 22 Copynumber: 2.6 Consensus size: 24
12580 GAAATGCATA
12590 TTTTAAATGTTTTATAATAT-TATT
1 TTTTAAAT-TTTTATAATATATATT
*
12614 TTTTAAAATTTTA-AATATATA-T
1 TTTTAAATTTTTATAATATATATT
12636 TTTTAAATTTATTATA
1 TTTTAAATTT-TTATA
12652 TTTTTAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
22 15 0.45
23 10 0.30
24 8 0.24
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.60
Consensus pattern (24 bp):
TTTTAAATTTTTATAATATATATT
Found at i:12636 original size:45 final size:46
Alignment explanation
Indices: 12552--12651 Score: 114
Period size: 45 Copynumber: 2.2 Consensus size: 46
12542 CTTTATTTTA
* *
12552 TTTTATTATTATTAGTTTTATAAAATTTGAAATGCATA-TTTTAAAT
1 TTTTA-TAATATTAGTTTTATAAAATTTGAAATACATATTTTTAAAT
* * *
12598 GTTTTATAATATTA-TTTTTTAAAATTTTAAATATATATTTTTAAAT
1 -TTTTATAATATTAGTTTTATAAAATTTGAAATACATATTTTTAAAT
12644 TTATTATA
1 TT-TTATA
12652 TTTTTAAATT
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
45 21 0.46
46 20 0.43
47 5 0.11
ACGTcount: A:0.38, C:0.01, G:0.04, T:0.57
Consensus pattern (46 bp):
TTTTATAATATTAGTTTTATAAAATTTGAAATACATATTTTTAAAT
Found at i:12643 original size:21 final size:19
Alignment explanation
Indices: 12600--12675 Score: 84
Period size: 17 Copynumber: 3.8 Consensus size: 19
12590 TTTTAAATGT
12600 TTTATAATATTATTTTTTAAAA
1 TTTA-AATATTA-TTTTT-AAA
12622 TTTTAAATATATATTTTTAAA
1 -TTTAAATAT-TATTTTTAAA
*
12643 TTT-ATTA-TATTTTTAAA
1 TTTAAATATTATTTTTAAA
12660 TTTAAATATTATTTTT
1 TTTAAATATTATTTTT
12676 TAATATTATA
Statistics
Matches: 48, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
17 13 0.27
18 3 0.06
19 10 0.21
20 3 0.06
21 3 0.06
22 10 0.21
23 6 0.12
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTAAATATTATTTTTAAA
Found at i:12649 original size:38 final size:37
Alignment explanation
Indices: 12607--12684 Score: 106
Period size: 37 Copynumber: 2.1 Consensus size: 37
12597 TGTTTTATAA
12607 TATTAT-TTTTTAAAATTTTAAATATATATTTTTAAAT-T
1 TATTATATTTTT-AAA-TTTAAATAT-TATTTTTAAATAT
*
12645 TATTATATTTTTAAATTTAAATATTATTTTTTAATAT
1 TATTATATTTTTAAATTTAAATATTATTTTTAAATAT
12682 TAT
1 TAT
12685 AAAATATTTA
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
36 10 0.27
37 13 0.35
38 9 0.24
39 5 0.14
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (37 bp):
TATTATATTTTTAAATTTAAATATTATTTTTAAATAT
Found at i:12676 original size:21 final size:21
Alignment explanation
Indices: 12600--12692 Score: 83
Period size: 21 Copynumber: 4.5 Consensus size: 21
12590 TTTTAAATGT
12600 TTTATAATATTAT-TTTTTAAAA
1 TTTA-AATATTATATTTTT-AAA
12622 TTTTAAATA-TATATTTTTAAA
1 -TTTAAATATTATATTTTTAAA
12643 -TT---TATTATATTTTTAAA
1 TTTAAATATTATATTTTTAAA
12660 TTTAAATATTAT-TTTTTAATA
1 TTTAAATATTATATTTTTAA-A
12681 TTATAAAATATT
1 TT-T-AAATATT
12693 TAAAATATAT
Statistics
Matches: 61, Mismatches: 0, Indels: 18
0.77 0.00 0.23
Matches are distributed among these distances:
16 2 0.03
17 12 0.20
18 2 0.03
19 2 0.03
20 7 0.11
21 15 0.25
22 10 0.16
23 11 0.18
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TTTAAATATTATATTTTTAAA
Found at i:12695 original size:37 final size:37
Alignment explanation
Indices: 12623--12696 Score: 96
Period size: 37 Copynumber: 2.0 Consensus size: 37
12613 TTTTTAAAAT
* * *
12623 TTTAAATATATATTTTTAAATTTATTATATTTTTAAA
1 TTTAAATATATATTTTTAAATTTATAAAATATTTAAA
*
12660 TTTAAATAT-TATTTTTTAATATTATAAAATATTTAAA
1 TTTAAATATATATTTTTAAAT-TTATAAAATATTTAAA
12697 ATATATTATG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
36 10 0.31
37 22 0.69
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (37 bp):
TTTAAATATATATTTTTAAATTTATAAAATATTTAAA
Found at i:12843 original size:28 final size:28
Alignment explanation
Indices: 12811--12864 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
12801 TACATTTTTT
* *
12811 AAATTGTATATATTTTTTAATTTTAAAA
1 AAATTATATATATATTTTAATTTTAAAA
12839 AAATTATATATATATTTTAATTTTAA
1 AAATTATATATATATTTTAATTTTAA
12865 TTTTAAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (28 bp):
AAATTATATATATATTTTAATTTTAAAA
Found at i:12893 original size:39 final size:38
Alignment explanation
Indices: 12750--12895 Score: 117
Period size: 39 Copynumber: 3.8 Consensus size: 38
12740 TTTTTATCAT
*
12750 ATTTTAAATGTATATTTGTTAAAAATTATA-TTTATATTTTA
1 ATTTTAAATATA-ATTT-TT-AAAATTATATTTTA-ATTTTA
* *
12791 ATTTTAAATATACATTTTTTAAATTGTATATATT--TTTTA
1 ATTTTAAATATA-A-TTTTTAAAAT-TATATTTTAATTTTA
* * *
12830 ATTTTAAA-A-AAATTAT-ATA-TATATTTTAATTTTA
1 ATTTTAAATATAATTTTTAAAATTATATTTTAATTTTA
12864 ATTTTAAATATAACTTTTTAAAATTATATTTT
1 ATTTTAAATATAA-TTTTTAAAATTATATTTT
12896 TTAAAATTAT
Statistics
Matches: 83, Mismatches: 12, Indels: 22
0.71 0.10 0.19
Matches are distributed among these distances:
32 7 0.08
34 14 0.17
35 4 0.05
36 3 0.04
37 4 0.05
38 3 0.04
39 21 0.25
40 4 0.05
41 18 0.22
42 5 0.06
ACGTcount: A:0.40, C:0.01, G:0.02, T:0.56
Consensus pattern (38 bp):
ATTTTAAATATAATTTTTAAAATTATATTTTAATTTTA
Found at i:12896 original size:15 final size:15
Alignment explanation
Indices: 12878--12909 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
12868 TAAATATAAC
12878 TTTTTAAAATTATAT
1 TTTTTAAAATTATAT
12893 TTTTTAAAATTATAT
1 TTTTTAAAATTATAT
12908 TT
1 TT
12910 AAAGATATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTTTAAAATTATAT
Found at i:13040 original size:13 final size:14
Alignment explanation
Indices: 13024--13054 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
13014 TTTGTTAAAA
13024 ATATTA-AAAATTT
1 ATATTAGAAAATTT
13037 ATATTAGAAAATTT
1 ATATTAGAAAATTT
13051 ATAT
1 ATAT
13055 ATATTAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.35
14 11 0.65
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (14 bp):
ATATTAGAAAATTT
Found at i:18115 original size:70 final size:70
Alignment explanation
Indices: 18002--18132 Score: 235
Period size: 70 Copynumber: 1.9 Consensus size: 70
17992 CGAGCCAAAC
* *
18002 ATTAATCATTTACTGCCAAATGATAGAGACGTTCGCTAGAGAGAAAATAATATAGATTAATGTAT
1 ATTAATCATTTACTGCCAAATGATAAAGACATTCGCTAGAGAGAAAATAATATAGATTAATGTAT
18067 ATTAT
66 ATTAT
*
18072 ATTAATCATTTACTGCCAAATGATAAAGACATTCGCTAGAGAGAAAATAATATATATTAAT
1 ATTAATCATTTACTGCCAAATGATAAAGACATTCGCTAGAGAGAAAATAATATAGATTAAT
18133 ATGGTTTAAG
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
70 58 1.00
ACGTcount: A:0.44, C:0.11, G:0.14, T:0.32
Consensus pattern (70 bp):
ATTAATCATTTACTGCCAAATGATAAAGACATTCGCTAGAGAGAAAATAATATAGATTAATGTAT
ATTAT
Found at i:18767 original size:30 final size:30
Alignment explanation
Indices: 18731--18835 Score: 174
Period size: 30 Copynumber: 3.5 Consensus size: 30
18721 GTAGCAGAGC
* *
18731 AGTTCATATCACTCAGACATGGGCGGTTCG
1 AGTTCATATCACCCAGACATAGGCGGTTCG
*
18761 AGTTCATATCACCCAGACGTAGGCGGTTCG
1 AGTTCATATCACCCAGACATAGGCGGTTCG
*
18791 AGTTCATATCACCCAGACATAGGCGGTTAG
1 AGTTCATATCACCCAGACATAGGCGGTTCG
18821 AGTTCATATCACCCA
1 AGTTCATATCACCCA
18836 AAGCAACCAC
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 70 1.00
ACGTcount: A:0.27, C:0.26, G:0.23, T:0.25
Consensus pattern (30 bp):
AGTTCATATCACCCAGACATAGGCGGTTCG
Found at i:21096 original size:40 final size:40
Alignment explanation
Indices: 21039--21132 Score: 170
Period size: 40 Copynumber: 2.4 Consensus size: 40
21029 TGATACTGTG
* *
21039 ATGGGCTAAGGCGCTACTGCATGATTTTTTTTGTATTGAA
1 ATGGGCTAAGGCCCTACTGCATGATTGTTTTTGTATTGAA
21079 ATGGGCTAAGGCCCTACTGCATGATTGTTTTTGTATTGAA
1 ATGGGCTAAGGCCCTACTGCATGATTGTTTTTGTATTGAA
21119 ATGGGCTAAGGCCC
1 ATGGGCTAAGGCCC
21133 AAACTGGACT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 52 1.00
ACGTcount: A:0.22, C:0.16, G:0.27, T:0.35
Consensus pattern (40 bp):
ATGGGCTAAGGCCCTACTGCATGATTGTTTTTGTATTGAA
Found at i:21587 original size:18 final size:18
Alignment explanation
Indices: 21547--21590 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
21537 TAAAAAAACG
21547 TTTTGAAATTGAATAACA
1 TTTTGAAATTGAATAACA
* *
21565 ATTTGTAAA-TGAATAATA
1 TTTTG-AAATTGAATAACA
21583 TTTTGAAA
1 TTTTGAAA
21591 ACGAACGACA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
17 3 0.14
18 16 0.73
19 3 0.14
ACGTcount: A:0.45, C:0.02, G:0.11, T:0.41
Consensus pattern (18 bp):
TTTTGAAATTGAATAACA
Found at i:23614 original size:29 final size:29
Alignment explanation
Indices: 23577--23645 Score: 93
Period size: 29 Copynumber: 2.4 Consensus size: 29
23567 TTACTGCGTC
* *
23577 TGTGTGTGTTTGCTTATTACTATCGTTTG
1 TGTGTGTGTTTGCGTATTACTATCGTATG
*
23606 TGTGTGTGTTTGCGTATTTCTATCGTATG
1 TGTGTGTGTTTGCGTATTACTATCGTATG
* *
23635 TCTCTGTGTTT
1 TGTGTGTGTTT
23646 TAAGGCCTTC
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.09, C:0.12, G:0.25, T:0.55
Consensus pattern (29 bp):
TGTGTGTGTTTGCGTATTACTATCGTATG
Found at i:23865 original size:13 final size:13
Alignment explanation
Indices: 23847--23871 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
23837 TAAAAAGAGT
23847 TTAAAATTAAAAA
1 TTAAAATTAAAAA
23860 TTAAAATTAAAA
1 TTAAAATTAAAA
23872 CAAAGTAAAA
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
TTAAAATTAAAAA
Found at i:23880 original size:23 final size:23
Alignment explanation
Indices: 23854--23898 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
23844 AGTTTAAAAT
23854 TAAAAATTAAAAT-TAAAACAAAG
1 TAAAAA-TAAAATATAAAACAAAG
*
23877 TAAAAATAAATTATAAAACAAA
1 TAAAAATAAAATATAAAACAAA
23899 AGAAAAGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.71, C:0.04, G:0.02, T:0.22
Consensus pattern (23 bp):
TAAAAATAAAATATAAAACAAAG
Found at i:23904 original size:23 final size:23
Alignment explanation
Indices: 23867--23912 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
23857 AAATTAAAAT
23867 TAAAACAAAGTAAAA-ATAAATTA
1 TAAAACAAAGTAAAAGA-AAATTA
23890 TAAAACAAAAG-AAAAGAAAATTA
1 TAAAAC-AAAGTAAAAGAAAATTA
23913 ATGAGGAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 16 0.76
24 5 0.24
ACGTcount: A:0.72, C:0.04, G:0.07, T:0.17
Consensus pattern (23 bp):
TAAAACAAAGTAAAAGAAAATTA
Found at i:24939 original size:21 final size:20
Alignment explanation
Indices: 24910--24955 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
24900 CTAAATCAAT
24910 AATAAATAAA-ATAAAATATA
1 AATAAATAAATA-AAAATATA
*
24930 AATAATATAATTAAAAATATA
1 AATAA-ATAAATAAAAATATA
24951 AATAA
1 AATAA
24956 CATCATTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 5 0.22
21 17 0.74
22 1 0.04
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (20 bp):
AATAAATAAATAAAAATATA
Found at i:27352 original size:24 final size:24
Alignment explanation
Indices: 27226--27525 Score: 119
Period size: 24 Copynumber: 12.8 Consensus size: 24
27216 TGAATTGGAT
* *
27226 AATTTACAATAAATAATATATAATA
1 AATTTAAAAT-AATAATATATGATA
* *
27251 AATTTGAAATAATAATACATG-TAA
1 AATTTAAAATAATAATATATGAT-A
*
27275 AATTT-AAA-AAT--TTTGATGAT-
1 AATTTAAAATAATAATAT-ATGATA
** * **
27295 AATTCTAGGATAATCATACGTGATA
1 AATT-TAAAATAATAATATATGATA
** * *
27320 AATCCAAAATAATAGTATATAATA
1 AATTTAAAATAATAATATATGATA
*
27344 AATTT-AAA-AATATTA-ATGATA
1 AATTTAAAATAATAATATATGATA
* *
27365 AATTTGAAATAGAT-ATACATGATA
1 AATTTAAAATA-ATAATATATGATA
* * * *
27389 AATTTAAAGTAAT-GT-TATCAATG
1 AATTTAAAATAATAATATAT-GATA
27412 AATTTAAAATAATAATAT-TGATA
1 AATTTAAAATAATAATATATGATA
* * *
27435 AA-TTACAAATAACAAAACATGATA
1 AATTTA-AAATAATAATATATGATA
* **
27459 AATCTAAAATAATAATATACAATA
1 AATTTAAAATAATAATATATGATA
* * * * *
27483 CACTT-AGATAATATTA-ATGATT
1 AATTTAAAATAATAATATATGATA
27505 AATTTAATAATAATAAGTATA
1 AATTTAA-AATAATAA-TATA
27526 AACATTCAAA
Statistics
Matches: 196, Mismatches: 56, Indels: 45
0.66 0.19 0.15
Matches are distributed among these distances:
20 5 0.03
21 14 0.07
22 25 0.13
23 53 0.27
24 81 0.41
25 17 0.09
26 1 0.01
ACGTcount: A:0.53, C:0.05, G:0.07, T:0.35
Consensus pattern (24 bp):
AATTTAAAATAATAATATATGATA
Found at i:28680 original size:45 final size:44
Alignment explanation
Indices: 28616--28729 Score: 122
Period size: 44 Copynumber: 2.6 Consensus size: 44
28606 TCTTCCTGAC
* * * *
28616 CCACTGTAGCTTCGGGGAGATAAGGCTCACT-TCGTTTAACCTACT
1 CCACTGTAACTTCAGGGAGATAAGGCTCA-TATC-TTCAACCGACT
* ** * *
28661 CCACTGCAACTTCAGGGAGATAAGATTGATATCTTCAACCGGCT
1 CCACTGTAACTTCAGGGAGATAAGGCTCATATCTTCAACCGACT
28705 CCACTGTAACTTCAGGGAGATAAGG
1 CCACTGTAACTTCAGGGAGATAAGG
28730 TTGGTTATCT
Statistics
Matches: 57, Mismatches: 11, Indels: 3
0.80 0.15 0.04
Matches are distributed among these distances:
44 32 0.56
45 25 0.44
ACGTcount: A:0.27, C:0.25, G:0.23, T:0.25
Consensus pattern (44 bp):
CCACTGTAACTTCAGGGAGATAAGGCTCATATCTTCAACCGACT
Found at i:29010 original size:132 final size:132
Alignment explanation
Indices: 28824--29159 Score: 446
Period size: 132 Copynumber: 2.5 Consensus size: 132
28814 AACGCCAAGG
* * * * * * *
28824 AGATAAGATTCGCTGCCTTCGATCTGCTCTACTATTGCTTAAGGATACATGATCTACAATCTTCG
1 AGATAAGATTTGCTGCCTTCGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTACAATCTTCA
* *
28889 ACCTACTCCACTGCTACTC-AGAGAGA-AGGGATTGGTGACTTAAATCTGCTTCCCTACTACCTT
66 ACCTACTCCACCGCTACTCAAG-GAGATA-GGACTGGTGACTTAAATCTGCTTCCCTACTACCTT
28952 GGGA
129 GGGA
* * *
28956 AGATAGGATTTGCTGCCTTCGATCTGCTCCACTACTGCTTAGGGAGACAGGATCTACGATCTTCA
1 AGATAAGATTTGCTGCCTTCGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTACAATCTTCA
* *
29021 ACCTACTCCACCGCTACTCAAGGAGATAGGACTGGTGGCTTAAATCTGGTTCCCTACTACCTTGG
66 ACCTACTCCACCGCTACTCAAGGAGATAGGACTGGTGACTTAAATCTGCTTCCCTACTACCTTGG
29086 GA
131 GA
* * *
29088 AGATAATATTT-AT-CATCTTCGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTATAATCTT
1 AGATAAGATTTGCTGC--CTTCGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTACAATCTT
*
29151 CAATCTACT
64 CAACCTACT
29160 TTGCTGCCAA
Statistics
Matches: 180, Mismatches: 20, Indels: 8
0.87 0.10 0.04
Matches are distributed among these distances:
130 1 0.01
131 1 0.01
132 175 0.97
133 3 0.02
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.30
Consensus pattern (132 bp):
AGATAAGATTTGCTGCCTTCGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTACAATCTTCA
ACCTACTCCACCGCTACTCAAGGAGATAGGACTGGTGACTTAAATCTGCTTCCCTACTACCTTGG
GA
Found at i:29182 original size:45 final size:45
Alignment explanation
Indices: 29132--29466 Score: 501
Period size: 45 Copynumber: 7.4 Consensus size: 45
29122 CTGCTTAGGG
* * **
29132 AGACAAGATCT-ATAATCTTCAATCTACTTTGCTGCCAATACAGGA
1 AGACAAGATCTGCT-ATCTTCGATCTACTTCCCTGCCAATACAGGA
* * *
29177 AGACAAGATCTGCTATCTTCAATCTACTTCGCTGCTAATACAGGA
1 AGACAAGATCTGCTATCTTCGATCTACTTCCCTGCCAATACAGGA
* *
29222 AGACAAGATCTGCTATCTTCGGTCTACTTCCCTACCAATACAGGA
1 AGACAAGATCTGCTATCTTCGATCTACTTCCCTGCCAATACAGGA
*
29267 AGACAAGATCTGCTATCTTCGATCTACTTCCCTGCCAATATAGGA
1 AGACAAGATCTGCTATCTTCGATCTACTTCCCTGCCAATACAGGA
29312 AGACAAGATCTGCTATCTTCGATCTACTTCCCTGCCAATACAGGA
1 AGACAAGATCTGCTATCTTCGATCTACTTCCCTGCCAATACAGGA
* * ** *
29357 AGACAAGATTTGCTATATTCGATCTACTTTGCTACCAATACAGGA
1 AGACAAGATCTGCTATCTTCGATCTACTTCCCTGCCAATACAGGA
*
29402 AGACAAGATCTGCTATCTTCGATCTACTTCACTGCCAATACAGGA
1 AGACAAGATCTGCTATCTTCGATCTACTTCCCTGCCAATACAGGA
*
29447 AGACAAGATCTGATATCTTC
1 AGACAAGATCTGCTATCTTC
29467 TATCCAACAA
Statistics
Matches: 266, Mismatches: 23, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
45 265 1.00
46 1 0.00
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.28
Consensus pattern (45 bp):
AGACAAGATCTGCTATCTTCGATCTACTTCCCTGCCAATACAGGA
Found at i:30394 original size:18 final size:18
Alignment explanation
Indices: 30373--30414 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
30363 TAATTAAATT
30373 AATTATAAATT-TTAAAAA
1 AATTATAAATTATT-AAAA
* *
30391 AATTAAAAATTATTTAAA
1 AATTATAAATTATTAAAA
30409 AATTAT
1 AATTAT
30415 TTATTAAGTC
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 18 0.90
19 2 0.10
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
AATTATAAATTATTAAAA
Found at i:30409 original size:10 final size:11
Alignment explanation
Indices: 30393--30417 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
30383 TTTAAAAAAA
30393 TTAAAAATTAT
1 TTAAAAATTAT
30404 TTAAAAATTAT
1 TTAAAAATTAT
30415 TTA
1 TTA
30418 TTAAGTCTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (11 bp):
TTAAAAATTAT
Found at i:31239 original size:97 final size:96
Alignment explanation
Indices: 31051--31367 Score: 489
Period size: 96 Copynumber: 3.3 Consensus size: 96
31041 AACAACTAGT
* *
31051 TTTATTTGA-TTTTTCCTTAAAAACCCTAAATACTAAACCCCAATCTAA-TTTTTTAAATTTATA
1 TTTATTTGATTTTTTCCTTAAAAACCCTAAACACTAAACCCTAATCTAATTTTTTTAAATTTATA
*
31114 ATTAATTTACTCAAGTAATCCTAAACCCTAA
66 ATTAATTTACTCAAGTAACCCTAAACCCTAA
*
31145 TTTATTTGATTTTTTCCTTAAAAACCCTAAACACTAAACCATAATCTAATTTTTTTAAAATTTAT
1 TTTATTTGATTTTTTCCTTAAAAACCCTAAACACTAAACCCTAATCTAATTTTTTT-AAATTTAT
31210 AATTAATTTACTCAAGTAACCCTAAACCCTAA
65 AATTAATTTACTCAAGTAACCCTAAACCCTAA
* *
31242 TTTATTT-AATTTTTCCTTAAAAACCATAAACACTAAACCCTAATCTAATTTTTTTTAAATTTAT
1 TTTATTTGATTTTTTCCTTAAAAACCCTAAACACTAAACCCTAATCTAA-TTTTTTTAAATTTAT
* * * *
31306 AATTAATTTAATTAAGAAACCCTAAACCCTTA
65 AATTAATTTACTCAAGTAACCCTAAACCCTAA
*
31338 TTTATTTAATTTTTTCCTT-AAAACCCTAAA
1 TTTATTTGATTTTTTCCTTAAAAACCCTAAA
31368 ATCTAAAAAC
Statistics
Matches: 205, Mismatches: 13, Indels: 8
0.91 0.06 0.04
Matches are distributed among these distances:
94 9 0.04
95 36 0.18
96 97 0.47
97 63 0.31
ACGTcount: A:0.39, C:0.18, G:0.02, T:0.42
Consensus pattern (96 bp):
TTTATTTGATTTTTTCCTTAAAAACCCTAAACACTAAACCCTAATCTAATTTTTTTAAATTTATA
ATTAATTTACTCAAGTAACCCTAAACCCTAA
Found at i:32120 original size:9 final size:9
Alignment explanation
Indices: 32106--32199 Score: 116
Period size: 9 Copynumber: 10.4 Consensus size: 9
32096 GTAGTGATTC
32106 AATTCGGTT
1 AATTCGGTT
*
32115 AATTCGATT
1 AATTCGGTT
*
32124 AATTCGGAT
1 AATTCGGTT
*
32133 AATTCGGAT
1 AATTCGGTT
*
32142 AATTCGGAT
1 AATTCGGTT
*
32151 AATTTGGTT
1 AATTCGGTT
* *
32160 AATTTGGGT
1 AATTCGGTT
32169 AATTCGGTT
1 AATTCGGTT
32178 AATTCGGTT
1 AATTCGGTT
*
32187 AATTCGATT
1 AATTCGGTT
32196 AATT
1 AATT
32200 TTTAACCAAA
Statistics
Matches: 76, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 76 1.00
ACGTcount: A:0.29, C:0.09, G:0.20, T:0.43
Consensus pattern (9 bp):
AATTCGGTT
Found at i:32424 original size:44 final size:44
Alignment explanation
Indices: 32373--32459 Score: 165
Period size: 44 Copynumber: 2.0 Consensus size: 44
32363 CAAAATTTTA
32373 AAATCAATCTTGACTTTGGGTCACAACTTGAAAACCAAACAACC
1 AAATCAATCTTGACTTTGGGTCACAACTTGAAAACCAAACAACC
*
32417 AAATCAATCTTGACTTTGGGTCACAACTTGGAAACCAAACAAC
1 AAATCAATCTTGACTTTGGGTCACAACTTGAAAACCAAACAAC
32460 GAGGATGGGG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.40, C:0.24, G:0.13, T:0.23
Consensus pattern (44 bp):
AAATCAATCTTGACTTTGGGTCACAACTTGAAAACCAAACAACC
Found at i:33043 original size:53 final size:53
Alignment explanation
Indices: 32981--33086 Score: 212
Period size: 53 Copynumber: 2.0 Consensus size: 53
32971 GTGTCTCCTT
32981 TTTAATTAATGGTTACGAATTACTATATATGTTTTTTTTAATTTTACAAAAAA
1 TTTAATTAATGGTTACGAATTACTATATATGTTTTTTTTAATTTTACAAAAAA
33034 TTTAATTAATGGTTACGAATTACTATATATGTTTTTTTTAATTTTACAAAAAA
1 TTTAATTAATGGTTACGAATTACTATATATGTTTTTTTTAATTTTACAAAAAA
33087 ATTCAACATC
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.38, C:0.06, G:0.08, T:0.49
Consensus pattern (53 bp):
TTTAATTAATGGTTACGAATTACTATATATGTTTTTTTTAATTTTACAAAAAA
Found at i:41014 original size:11 final size:11
Alignment explanation
Indices: 40998--41040 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
40988 TATTTTTTAA
40998 TTTTAAAATAT
1 TTTTAAAATAT
41009 TTTTAAAATACT
1 TTTTAAAATA-T
* *
41021 TTTT-TATTAT
1 TTTTAAAATAT
41031 TTTTAAAATA
1 TTTTAAAATA
41041 AATTTATGGT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
10 5 0.19
11 16 0.62
12 5 0.19
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:41023 original size:22 final size:22
Alignment explanation
Indices: 40998--41040 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
40988 TATTTTTTAA
40998 TTTTAAAATATTTTTAAAATAC
1 TTTTAAAATATTTTTAAAATAC
** *
41020 TTTTTTATTATTTTTAAAATA
1 TTTTAAAATATTTTTAAAATA
41041 AATTTATGGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (22 bp):
TTTTAAAATATTTTTAAAATAC
Found at i:41150 original size:37 final size:38
Alignment explanation
Indices: 41087--41161 Score: 100
Period size: 37 Copynumber: 2.0 Consensus size: 38
41077 GGTGTAAAGG
* *
41087 CCCAATTTTGGCCCAACTTAAACCAACCCTAAC-CAAA
1 CCCAATTTTGGCCCAACCTAAACCAACCCAAACACAAA
*
41124 CCCAA-TTTGGCCCAACCTAATCCCAACCCAAACACAAA
1 CCCAATTTTGGCCCAACCTAA-ACCAACCCAAACACAAA
41162 AAATAAATAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
36 14 0.42
37 15 0.45
38 4 0.12
ACGTcount: A:0.39, C:0.40, G:0.05, T:0.16
Consensus pattern (38 bp):
CCCAATTTTGGCCCAACCTAAACCAACCCAAACACAAA
Found at i:41366 original size:23 final size:22
Alignment explanation
Indices: 41340--41388 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
41330 GTTTTTGGTT
41340 TTTTGGAGAAGGATTATTCTTTG
1 TTTTGGAGAAGG-TTATTCTTTG
* * *
41363 TTTTGGAGGAGGTTTTTTTTTG
1 TTTTGGAGAAGGTTATTCTTTG
41385 TTTT
1 TTTT
41389 TTGGAGGTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 12 0.52
23 11 0.48
ACGTcount: A:0.14, C:0.02, G:0.27, T:0.57
Consensus pattern (22 bp):
TTTTGGAGAAGGTTATTCTTTG
Found at i:41389 original size:23 final size:24
Alignment explanation
Indices: 41331--41404 Score: 73
Period size: 23 Copynumber: 3.2 Consensus size: 24
41321 TAGGGGTGGG
* * *
41331 TTTTTGGTTTTTTGGAGAAGGATTA
1 TTTTTTGTTTTTTGGAGGAGG-TTT
*
41356 TTCTTTG--TTTTGGAGGAGGTTT
1 TTTTTTGTTTTTTGGAGGAGGTTT
*
41378 TTTTTTGTTTTTTGGAGG-TGTTT
1 TTTTTTGTTTTTTGGAGGAGGTTT
41401 TTTT
1 TTTT
41405 GTAAAAAAGG
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
22 8 0.20
23 19 0.46
24 9 0.22
25 5 0.12
ACGTcount: A:0.11, C:0.01, G:0.27, T:0.61
Consensus pattern (24 bp):
TTTTTTGTTTTTTGGAGGAGGTTT
Found at i:41758 original size:9 final size:9
Alignment explanation
Indices: 41732--41777 Score: 51
Period size: 9 Copynumber: 5.2 Consensus size: 9
41722 GAGAGCTTTG
41732 TTTTATTA-
1 TTTTATTAT
41740 TTTTATTAT
1 TTTTATTAT
*
41749 TTTTACTAT
1 TTTTATTAT
41758 TATTTA-TAT
1 T-TTTATTAT
*
41767 TATTATTAT
1 TTTTATTAT
41776 TT
1 TT
41778 CTCATGTATA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
8 11 0.34
9 17 0.53
10 4 0.12
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (9 bp):
TTTTATTAT
Found at i:41769 original size:24 final size:23
Alignment explanation
Indices: 41734--41813 Score: 80
Period size: 24 Copynumber: 3.5 Consensus size: 23
41724 GAGCTTTGTT
*
41734 TTATTATTTTATTATTTTTACTA
1 TTATTATATTATTATTTTTACTA
41757 TTATTTATATTATTATTATTT-CTCA
1 TTA-TTATATTATTATT-TTTACT-A
41782 TGTA-TATATTA-T-TTTTTA-TA
1 T-TATTATATTATTATTTTTACTA
41802 TTATTATATTAT
1 TTATTATATTAT
41814 ATATGCCCTC
Statistics
Matches: 49, Mismatches: 1, Indels: 16
0.74 0.02 0.24
Matches are distributed among these distances:
19 2 0.04
20 9 0.18
21 4 0.08
22 2 0.04
23 4 0.08
24 21 0.43
25 5 0.10
26 2 0.04
ACGTcount: A:0.29, C:0.04, G:0.01, T:0.66
Consensus pattern (23 bp):
TTATTATATTATTATTTTTACTA
Found at i:41816 original size:15 final size:15
Alignment explanation
Indices: 41742--41817 Score: 54
Period size: 15 Copynumber: 5.1 Consensus size: 15
41732 TTTTATTATT
*
41742 TTATTAT-TTTTACTA
1 TTATTATATTATA-TA
41757 TTATTTATATTAT-TA
1 TTA-TTATATTATATA
*
41772 TTATTTCTCATGTATATA
1 TTA-TTAT-AT-TATATA
41790 TTATT-T-TT-TATA
1 TTATTATATTATATA
41802 TTATTATATTATATA
1 TTATTATATTATATA
41817 T
1 T
41818 GCCCTCTCCA
Statistics
Matches: 51, Mismatches: 2, Indels: 16
0.74 0.03 0.23
Matches are distributed among these distances:
12 9 0.18
13 2 0.04
14 3 0.06
15 17 0.33
16 7 0.14
17 8 0.16
18 5 0.10
ACGTcount: A:0.30, C:0.04, G:0.01, T:0.64
Consensus pattern (15 bp):
TTATTATATTATATA
Found at i:42177 original size:14 final size:14
Alignment explanation
Indices: 42158--42189 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
42148 GTATTTCTAT
42158 TATATACATATATA
1 TATATACATATATA
*
42172 TATATACATTTATA
1 TATATACATATATA
42186 TATA
1 TATA
42190 GTATTATTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (14 bp):
TATATACATATATA
Done.