Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold266
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: 45812
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.32
Found at i:6509 original size:69 final size:69
Alignment explanation
Indices: 6371--6541 Score: 190
Period size: 69 Copynumber: 2.5 Consensus size: 69
6361 CTTTCCAAGG
**
6371 AAAATCAACTCATATTGCGAG-AGATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAATTTT
1 AAAATCAACTCATATTGCGAGAAG-TGAGTTGAGCCTCAAGACACGCCGAGGTATTTTTAATTTT
*
6435 TTTTT
65 GTTTT
** * *
6440 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTA-TTTTAGTTTAT
1 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACACGCCGAGGTATTTTTAATTT-T
6504 GTTTT
65 GTTTT
** * *
6509 -AAATTGACTC--ATTGCGAGAGGTGAGTTAAGCCT
1 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCT
6542 TTTAATTTTT
Statistics
Matches: 89, Mismatches: 11, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
66 21 0.24
68 16 0.18
69 50 0.56
70 2 0.02
ACGTcount: A:0.29, C:0.15, G:0.23, T:0.33
Consensus pattern (69 bp):
AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACACGCCGAGGTATTTTTAATTTTG
TTTT
Found at i:6833 original size:148 final size:148
Alignment explanation
Indices: 6545--6895 Score: 451
Period size: 148 Copynumber: 2.4 Consensus size: 148
6535 TAAGCCTTTT
* * *
6545 AATTTTTGTTTTTCAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGACACGCTGAGG
1 AATTTCTGTTTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGG
*
6610 TAATTTTAATTTCTGTTGTTAAAAAAAAATTAACTCATATTGCGAGAAATGAGTTGAGCCTCAGG
66 TAATTTTAATTTCTGTTGTTAAAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGG
6675 ACACGCTGAGGTAATTTC
131 ACACGCTGAGGTAATTTC
* ** *
6693 AATTTCTG-TTTTCAAAATTCAACTTATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAG
1 AATTTCTGTTTTTCAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAG
* * **
6757 GT-ATTTTCAATTTCTGTT-TT-CAAAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTC-
65 GTAATTTT-AATTTCTGTTGTTAAAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCA
* * *
6818 GGTTCACATGTTGAGGTATTTTC
129 GG---ACACGCTGAGGTAATTTC
* *
6841 AATTTCTGTTTTTAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCGTCAA
1 AATTTCTGTTTTT--CAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAA
6896 ATTACACACT
Statistics
Matches: 175, Mismatches: 20, Indels: 14
0.84 0.10 0.07
Matches are distributed among these distances:
145 2 0.01
146 36 0.21
147 16 0.09
148 82 0.47
149 4 0.02
150 31 0.18
151 4 0.02
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.34
Consensus pattern (148 bp):
AATTTCTGTTTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGG
TAATTTTAATTTCTGTTGTTAAAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGG
ACACGCTGAGGTAATTTC
Found at i:6915 original size:76 final size:74
Alignment explanation
Indices: 6559--6890 Score: 429
Period size: 76 Copynumber: 4.5 Consensus size: 74
6549 TTTGTTTTTC
*
6559 AAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTT-AATTTC
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGT-ATTTTCAATTTC
*
6623 TGTTGTTAAAAA
65 TGTT-TT-TAAA
* ** *
6635 AAAATTAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCT
*
6700 G-TTTT-CA
66 GTTTTTAAA
* * ** * *
6707 AAATTCAACTTATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCT
*
6772 GTTTTCAAA
66 GTTTTTAAA
* * *
6781 AAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTC-GGTTCACATGTTGAGGTATTTTCAATT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG---ACACGCTGAGGTATTTTCAATT
6845 TCTGTTTTTAAA
63 TCTGTTTTTAAA
6857 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
6891 GTCAAATTAC
Statistics
Matches: 228, Mismatches: 22, Indels: 12
0.87 0.08 0.05
Matches are distributed among these distances:
72 61 0.27
73 4 0.02
74 37 0.16
75 5 0.02
76 121 0.53
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.33
Consensus pattern (74 bp):
AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCT
GTTTTTAAA
Found at i:7306 original size:27 final size:25
Alignment explanation
Indices: 7276--7331 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
7266 CTGTTTTCAT
*
7276 TATTATGTTTTTGAAAGAATCAACTCA
1 TATTATG-TTTTCAAA-AATCAACTCA
* *
7303 TATTCTGTTTTCAAAATTCAACTCA
1 TATTATGTTTTCAAAAATCAACTCA
7328 TATT
1 TATT
7332 GCGAGAAATG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 13 0.50
26 7 0.27
27 6 0.23
ACGTcount: A:0.34, C:0.14, G:0.07, T:0.45
Consensus pattern (25 bp):
TATTATGTTTTCAAAAATCAACTCA
Found at i:7432 original size:73 final size:72
Alignment explanation
Indices: 7305--7501 Score: 306
Period size: 73 Copynumber: 2.7 Consensus size: 72
7295 TCAACTCATA
* * *
7305 TTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAT
1 TTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAA
7370 TTTCAAT
66 TTTCAAT
7377 TTCTGCTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTA
1 TTCTG-TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTA
7442 ATTTCAAT
65 ATTTCAAT
* *
7450 TTCTGTTGTCAAAAAAATCAACTCATATTGCGA-AAAGTGAGTTGAGCCTCAG
1 TTCTGTTTTC--AAAATTCAACTCATATTGCGAGAAA-TGAGTTGAGCCTCAG
7502 TTCACATGTT
Statistics
Matches: 116, Mismatches: 5, Indels: 6
0.91 0.04 0.05
Matches are distributed among these distances:
72 9 0.08
73 72 0.62
74 35 0.30
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Consensus pattern (72 bp):
TTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAA
TTTCAAT
Found at i:8774 original size:5 final size:5
Alignment explanation
Indices: 8764--8815 Score: 56
Period size: 5 Copynumber: 11.0 Consensus size: 5
8754 AAGTCAAAGG
* *
8764 GAGAA GAGAA GAGAA GA-AA GAGAA -A-AA GGGAA GAGAA AAGAA GAGAA
1 GAGAA GAGAA GAGAA GAGAA GAGAA GAGAA GAGAA GAGAA GAGAA GAGAA
*
8811 AAGAA
1 GAGAA
8816 CGCCGAGACT
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
3 2 0.05
4 5 0.13
5 32 0.82
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (5 bp):
GAGAA
Found at i:9715 original size:18 final size:17
Alignment explanation
Indices: 9646--9843 Score: 102
Period size: 17 Copynumber: 11.3 Consensus size: 17
9636 CGGTATTTAA
*
9646 AAAAAATTCGTG-TTTC
1 AAAAATTTCGTGTTTTC
*
9662 AAAAATCTTCGTATTTTC
1 AAAAAT-TTCGTGTTTTC
*
9680 -AAAATTCCAGTG-TTTC
1 AAAAATTTC-GTGTTTTC
9696 AAAAATTATCGTGTTTTC
1 AAAAATT-TCGTGTTTTC
*
9714 AAAAAAATTTCCTTGTTTTC
1 --AAAAATTT-CGTGTTTTC
* ** * *
9734 AAAAGTCCCGT-ATTCC
1 AAAAATTTCGTGTTTTC
* *
9750 GAAAATTTTCTTGTTTTC
1 -AAAAATTTCGTGTTTTC
*
9768 AAAAAAATTC-TGTGTTTC
1 -AAAAATTTCGTGT-TTTC
* *
9786 ATAAATTTCCATGTTTTC
1 AAAAATTT-CGTGTTTTC
* *
9804 AAAAAATCTCGT-CTTTC
1 -AAAAATTTCGTGTTTTC
9821 AAAAATTTTCGTGTTTTC
1 AAAAA-TTTCGTGTTTTC
9839 AAAAA
1 AAAAA
9844 AAATTGACCG
Statistics
Matches: 136, Mismatches: 29, Indels: 32
0.69 0.15 0.16
Matches are distributed among these distances:
16 19 0.14
17 48 0.35
18 44 0.32
19 10 0.07
20 15 0.11
ACGTcount: A:0.34, C:0.16, G:0.09, T:0.41
Consensus pattern (17 bp):
AAAAATTTCGTGTTTTC
Found at i:9721 original size:20 final size:20
Alignment explanation
Indices: 9696--9737 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
9686 CCAGTGTTTC
9696 AAAAATTAT-CGTGTTTTCAA
1 AAAAATT-TCCGTGTTTTCAA
*
9716 AAAAATTTCCTTGTTTTCAA
1 AAAAATTTCCGTGTTTTCAA
9736 AA
1 AA
9738 GTCCCGTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 1 0.05
20 19 0.95
ACGTcount: A:0.40, C:0.12, G:0.07, T:0.40
Consensus pattern (20 bp):
AAAAATTTCCGTGTTTTCAA
Found at i:9736 original size:54 final size:52
Alignment explanation
Indices: 9675--9842 Score: 146
Period size: 54 Copynumber: 3.2 Consensus size: 52
9665 AATCTTCGTA
9675 TTTTCAAAATTCCAGTGTTTCAAAAATTATCGTGTTTTCAAAAAAATTTCCTTG
1 TTTTCAAAATTCCAGTGTTTCAAAAATTATCGTGTTTTCAAAAAAATTT-C-TG
* * * * * * *
9729 TTTTCAAAAGTCCCGTATTCCGAAAATTTTCTTGTTTTCAAAAAAA-TTCTG
1 TTTTCAAAATTCCAGTGTTTCAAAAATTATCGTGTTTTCAAAAAAATTTCTG
* * * *
9780 TGTTTCATAAATTTCCA-TGTTTTCAAAAAATCTCGT-CTTTC-AAAAATTTTCGTG
1 T-TTTCA-AAA-TTCCAGTG-TTTCAAAAATTATCGTGTTTTCAAAAAAATTTC-TG
9834 TTTTCAAAA
1 TTTTCAAAA
9843 AAAATTGACC
Statistics
Matches: 91, Mismatches: 17, Indels: 14
0.75 0.14 0.11
Matches are distributed among these distances:
51 3 0.03
52 14 0.15
53 18 0.20
54 56 0.62
ACGTcount: A:0.32, C:0.16, G:0.09, T:0.43
Consensus pattern (52 bp):
TTTTCAAAATTCCAGTGTTTCAAAAATTATCGTGTTTTCAAAAAAATTTCTG
Found at i:9821 original size:35 final size:34
Alignment explanation
Indices: 9717--9844 Score: 116
Period size: 35 Copynumber: 3.7 Consensus size: 34
9707 TGTTTTCAAA
* * *
9717 AAAATTTCCTTGTTTTC-AAAAGTCCCGTATTCC
1 AAAATTTCCTTGTTTTCAAAAAATCTCGTATTTC
* *
9750 GAAAATTTTCTTGTTTTCAAAAAAAT-TCTGTGTTTC
1 -AAAATTTCCTTGTTTTC-AAAAAATCTC-GTATTTC
* *
9786 ATAAATTTCCATGTTTTCAAAAAATCTCGTCTTTC
1 A-AAATTTCCTTGTTTTCAAAAAATCTCGTATTTC
* *
9821 AAAAATTTTCGTGTTTTCAAAAAA
1 -AAAATTTCCTTGTTTTCAAAAAA
9845 AATTGACCGT
Statistics
Matches: 78, Mismatches: 10, Indels: 11
0.79 0.10 0.11
Matches are distributed among these distances:
34 16 0.21
35 35 0.45
36 27 0.35
ACGTcount: A:0.33, C:0.16, G:0.09, T:0.42
Consensus pattern (34 bp):
AAAATTTCCTTGTTTTCAAAAAATCTCGTATTTC
Found at i:9891 original size:35 final size:37
Alignment explanation
Indices: 9752--9894 Score: 172
Period size: 35 Copynumber: 3.9 Consensus size: 37
9742 CGTATTCCGA
*
9752 AAATTTTCTTGTTTTCAAAAAAATTCT-GTGTTTCAT
1 AAATTTTCGTGTTTTCAAAAAAATTCTCGTGTTTCAT
* * * *
9788 AAATTTCCATGTTTTC-AAAAAA-TCTCGTCTTTCAA
1 AAATTTTCGTGTTTTCAAAAAAATTCTCGTGTTTCAT
9823 AAATTTTCGTGTTTTCAAAAAAAATTGAC-CGTGTTTCAT
1 AAATTTTCGTGTTTTC-AAAAAAATT--CTCGTGTTTCAT
9862 AAATTTTCGTG-TTTC-AAAAAATTCTCGTGTTTC
1 AAATTTTCGTGTTTTCAAAAAAATTCTCGTGTTTC
9895 GTATTTTATC
Statistics
Matches: 92, Mismatches: 8, Indels: 15
0.80 0.07 0.13
Matches are distributed among these distances:
34 4 0.04
35 35 0.38
36 22 0.24
37 6 0.07
38 5 0.05
39 19 0.21
40 1 0.01
ACGTcount: A:0.31, C:0.15, G:0.10, T:0.44
Consensus pattern (37 bp):
AAATTTTCGTGTTTTCAAAAAAATTCTCGTGTTTCAT
Found at i:9927 original size:19 final size:18
Alignment explanation
Indices: 9905--9944 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
9895 GTATTTTATC
9905 AAAAATTTTATGTTTTCAA
1 AAAAATTTTATGTTTT-AA
*
9924 AAAAATTTTGTGTTTTAA
1 AAAAATTTTATGTTTTAA
9942 AAA
1 AAA
9945 TTTTCGTGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.45
Consensus pattern (18 bp):
AAAAATTTTATGTTTTAA
Found at i:9972 original size:20 final size:19
Alignment explanation
Indices: 9947--9999 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
9937 TTTAAAAATT
9947 TTCGTGTTTCAAAAAGAAAA
1 TTCGTGTTTCAAAAA-AAAA
** *
9967 TTCGTGTTTCCTAAAAAAT
1 TTCGTGTTTCAAAAAAAAA
9986 TTCGTGTTTCAAAA
1 TTCGTGTTTCAAAA
10000 TTTTCGTTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.38
Consensus pattern (19 bp):
TTCGTGTTTCAAAAAAAAA
Found at i:9984 original size:56 final size:55
Alignment explanation
Indices: 9918--10038 Score: 147
Period size: 56 Copynumber: 2.2 Consensus size: 55
9908 AATTTTATGT
* * *
9918 TTTCAAAAAAATTTTGTGTTTTAAAAATTTTCGTGTTTCAAAAAGAAA-A-TTCGTG
1 TTTCTAAAAAATTTCGTG-TTTAAAAATTTTCGT-TTTCAAAAAAAAAGAGTTCGTG
* *
9973 TTTCCTAAAAAATTTCGTGTTTCAAAATTTTCGTTTTTAAAAAAAAAGAGTTTCGTG
1 TTT-CTAAAAAATTTCGTGTTTAAAAATTTTCGTTTTCAAAAAAAAAGAG-TTCGTG
10030 TTTCTAAAA
1 TTTCTAAAA
10039 TGCTTGTATT
Statistics
Matches: 57, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
54 11 0.19
55 18 0.32
56 19 0.33
57 9 0.16
ACGTcount: A:0.37, C:0.09, G:0.12, T:0.42
Consensus pattern (55 bp):
TTTCTAAAAAATTTCGTGTTTAAAAATTTTCGTTTTCAAAAAAAAAGAGTTCGTG
Found at i:9999 original size:16 final size:16
Alignment explanation
Indices: 9924--10015 Score: 60
Period size: 16 Copynumber: 5.3 Consensus size: 16
9914 ATGTTTTCAA
* *
9924 AAAAATTTTGTGTTTT
1 AAAAATTTCGTGTTTC
9940 AAAAATTTTCGTGTTTC
1 AAAAA-TTTCGTGTTTC
*
9957 AAAAAGAAAATTCGTGTTTCC
1 ---AA-AAATTTCGTGTTT-C
9978 TAAAAAATTTCGTGTTTC
1 --AAAAATTTCGTGTTTC
* *
9996 AAAATTTTCGT-TTTT
1 AAAAATTTCGTGTTTC
10011 AAAAA
1 AAAAA
10016 AAAAGAGTTT
Statistics
Matches: 62, Mismatches: 8, Indels: 13
0.75 0.10 0.16
Matches are distributed among these distances:
15 7 0.11
16 15 0.24
17 9 0.15
18 1 0.02
19 12 0.19
20 14 0.23
21 4 0.06
ACGTcount: A:0.37, C:0.09, G:0.11, T:0.43
Consensus pattern (16 bp):
AAAAATTTCGTGTTTC
Found at i:10014 original size:15 final size:16
Alignment explanation
Indices: 9646--10015 Score: 99
Period size: 17 Copynumber: 21.3 Consensus size: 16
9636 CGGTATTTAA
*
9646 AAAAAATTCGTGTTTC
1 AAAAATTTCGTGTTTC
*
9662 AAAAATCTTCGTATTTTC
1 AAAAAT-TTCGT-GTTTC
*
9680 -AAAATTCCAGTGTTTC
1 AAAAATTTC-GTGTTTC
9696 AAAAATTATCGTGTTTTC
1 AAAAATT-TCGTG-TTTC
*
9714 AAAAAAATTTCCTTGTTTTC
1 --AAAAATTT-CGTG-TTTC
* ** * *
9734 AAAAGTCCCGTATTCC
1 AAAAATTTCGTGTTTC
* *
9750 GAAAATTTTCTTGTTTTC
1 -AAAAATTTCGTG-TTTC
*
9768 AAAAAAATTCTGTGTTTC
1 -AAAAATTTC-GTGTTTC
* *
9786 ATAAATTTCCATGTTTTC
1 AAAAATTT-CGTG-TTTC
* *
9804 AAAAAATCTCGTCTTTC
1 -AAAAATTTCGTGTTTC
9821 AAAAATTTTCGTGTTTTC
1 AAAAA-TTTCGTG-TTTC
*
9839 AAAAAAAATTGACCGTGTTTC
1 ---AAAAATT--TCGTGTTTC
*
9860 ATAAATTTTCGTGTTTC
1 A-AAAATTTCGTGTTTC
9877 AAAAAATTCTCGTGTTTC
1 -AAAAATT-TCGTGTTTC
** *
9895 --GTA-TT--T-TATC
1 AAAAATTTCGTGTTTC
**
9905 AAAAATTTTATGTTTTC
1 AAAAATTTCGTG-TTTC
* *
9922 AAAAAAATTTTGTGTTTT
1 --AAAAATTTCGTGTTTC
9940 AAAAATTTTCGTGTTTC
1 AAAAA-TTTCGTGTTTC
*
9957 AAAAAGAAAATTCGTGTTTCC
1 ---AA-AAATTTCGTGTTT-C
9978 TAAAAAATTTCGTGTTTC
1 --AAAAATTTCGTGTTTC
* *
9996 AAAATTTTCGT-TTTT
1 AAAAATTTCGTGTTTC
10011 AAAAA
1 AAAAA
10016 AAAAGAGTTT
Statistics
Matches: 263, Mismatches: 51, Indels: 81
0.67 0.13 0.21
Matches are distributed among these distances:
10 3 0.01
11 1 0.00
12 1 0.00
13 3 0.01
14 1 0.00
15 9 0.03
16 34 0.13
17 72 0.27
18 54 0.21
19 37 0.14
20 31 0.12
21 13 0.05
22 4 0.02
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.43
Consensus pattern (16 bp):
AAAAATTTCGTGTTTC
Found at i:10063 original size:18 final size:19
Alignment explanation
Indices: 10042--10077 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
10032 TCTAAAATGC
10042 TTGTATTTT-AAAAAAAAT
1 TTGTATTTTCAAAAAAAAT
*
10060 TTGTGTTTTCAAAAAAAA
1 TTGTATTTTCAAAAAAAA
10078 AAGGAAAAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.47, C:0.03, G:0.08, T:0.42
Consensus pattern (19 bp):
TTGTATTTTCAAAAAAAAT
Found at i:15729 original size:38 final size:35
Alignment explanation
Indices: 15648--15733 Score: 91
Period size: 36 Copynumber: 2.3 Consensus size: 35
15638 AAAAATAAAA
* * *
15648 AATATATAAATAATATAGTATTAAAGATGTATACAT
1 AATATATAAA-AATACAATATTAAAGATATATACAT
* *
15684 AACATATAAAAATACAATATTAAATGATATATATAT
1 AATATATAAAAATACAATATTAAA-GATATATACAT
15720 GCAATATATAAAAA
1 --AATATATAAAAA
15734 AATGTATACA
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
35 12 0.29
36 18 0.44
38 11 0.27
ACGTcount: A:0.57, C:0.05, G:0.06, T:0.33
Consensus pattern (35 bp):
AATATATAAAAATACAATATTAAAGATATATACAT
Found at i:15759 original size:25 final size:27
Alignment explanation
Indices: 15731--15784 Score: 67
Period size: 25 Copynumber: 2.0 Consensus size: 27
15721 CAATATATAA
*
15731 AAAAATGTATACATA-ATATA-ATATT
1 AAAAATATATACATAGATATACATATT
*
15756 AAAAATATTTACATAGTATATACATATT
1 AAAAATATATACATAG-ATATACATATT
15784 A
1 A
15785 GAGATAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 13 0.54
27 5 0.21
28 6 0.25
ACGTcount: A:0.54, C:0.06, G:0.04, T:0.37
Consensus pattern (27 bp):
AAAAATATATACATAGATATACATATT
Found at i:16109 original size:21 final size:22
Alignment explanation
Indices: 16063--16110 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 22
16053 TATATTAAAG
*
16063 ATATATACATATGTAACAAAAC
1 ATATATACATATGTAACAAAAA
*
16085 ATATACTA-ATAT-TAATAAAAA
1 ATATA-TACATATGTAACAAAAA
16106 ATATA
1 ATATA
16111 ATAAGGGTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 12 0.52
22 9 0.39
23 2 0.09
ACGTcount: A:0.58, C:0.08, G:0.02, T:0.31
Consensus pattern (22 bp):
ATATATACATATGTAACAAAAA
Found at i:16324 original size:20 final size:21
Alignment explanation
Indices: 16287--16328 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
16277 GAAACTAAAA
*
16287 AAAAATAATTCTAATAATAGT
1 AAAAATAATACTAATAATAGT
16308 AAAAATATACTACTAATAATA
1 AAAAATA-A-TACTAATAATA
16329 ATAACGATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 1 0.06
23 10 0.56
ACGTcount: A:0.60, C:0.07, G:0.02, T:0.31
Consensus pattern (21 bp):
AAAAATAATACTAATAATAGT
Found at i:17009 original size:24 final size:25
Alignment explanation
Indices: 16971--17023 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 25
16961 TTCAAAAAGG
*
16971 TATAATTTTTTTTGTATTTTTAATA
1 TATAATTTTTTTTGTATTTATAATA
16996 TATAA-TTTTTTTGTATTTATAATA
1 TATAATTTTTTTTGTATTTATAATA
17020 TATA
1 TATA
17024 TAAGTTTATG
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
24 22 0.81
25 5 0.19
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (25 bp):
TATAATTTTTTTTGTATTTATAATA
Found at i:31317 original size:9 final size:9
Alignment explanation
Indices: 31303--31331 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
31293 AATATCAAAA
31303 TTAATTATC
1 TTAATTATC
31312 TTAATTATC
1 TTAATTATC
31321 TTAATTA-C
1 TTAATTATC
31329 TTA
1 TTA
31332 CTGTTTTGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 4 0.20
9 16 0.80
ACGTcount: A:0.34, C:0.10, G:0.00, T:0.55
Consensus pattern (9 bp):
TTAATTATC
Found at i:39037 original size:26 final size:27
Alignment explanation
Indices: 39008--39062 Score: 67
Period size: 26 Copynumber: 2.0 Consensus size: 27
38998 TGAATACTTA
*
39008 ATTTTAATATACATATTT-AAATTTTT
1 ATTTTAATATAAATATTTAAAATTTTT
* *
39034 ATTTTATTATAAATTTTTAGAAATTTTT
1 ATTTTAATATAAATATTTA-AAATTTTT
39062 A
1 A
39063 GAAATCTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 15 0.62
28 9 0.38
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (27 bp):
ATTTTAATATAAATATTTAAAATTTTT
Found at i:41252 original size:20 final size:20
Alignment explanation
Indices: 41227--41273 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
41217 GATATTTGTT
41227 TTTATATTGATATT-ACTA-TA
1 TTTATATT-ATATTGA-TATTA
41247 TTTATATTATATTGATATTA
1 TTTATATTATATTGATATTA
41267 TTTATAT
1 TTTATAT
41274 CTTTCTTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.28
20 18 0.72
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.60
Consensus pattern (20 bp):
TTTATATTATATTGATATTA
Done.