Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1346
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: 40976
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:12779 original size:10 final size:10
Alignment explanation
Indices: 12764--12812 Score: 55
Period size: 10 Copynumber: 4.9 Consensus size: 10
12754 TTGGGTTAAG
12764 ATTGAGCTGA
1 ATTGAGCTGA
12774 ATTGAGCTCGA
1 ATTGAGCT-GA
12785 A-TGAGCTGA
1 ATTGAGCTGA
* *
12794 CTTGAGCTCA
1 ATTGAGCTGA
*
12804 AGTGAGCTG
1 ATTGAGCTG
12813 GAAACGAGCT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
9 2 0.06
10 27 0.84
11 3 0.09
ACGTcount: A:0.27, C:0.16, G:0.31, T:0.27
Consensus pattern (10 bp):
ATTGAGCTGA
Found at i:12789 original size:20 final size:20
Alignment explanation
Indices: 12766--12812 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
12756 GGGTTAAGAT
12766 TGAGCTGAATTGAGCTCGAA-
1 TGAGCTGAATTGAGCTC-AAG
*
12786 TGAGCTGACTTGAGCTCAAG
1 TGAGCTGAATTGAGCTCAAG
12806 TGAGCTG
1 TGAGCTG
12813 GAAACGAGCT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 2 0.08
20 23 0.92
ACGTcount: A:0.26, C:0.17, G:0.32, T:0.26
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCAAG
Found at i:13316 original size:9 final size:9
Alignment explanation
Indices: 13293--13340 Score: 51
Period size: 9 Copynumber: 5.1 Consensus size: 9
13283 AAGCCTAATC
*
13293 TCAGCTCGT
1 TCAGCTCAT
*
13302 TGAGCTCAT
1 TCAGCTCAT
13311 TCAGCTCATT
1 TCAGCTCA-T
13321 TCCAGCTCAT
1 T-CAGCTCAT
*
13331 TGAGCTCAT
1 TCAGCTCAT
13340 T
1 T
13341 TGCTTGTTTG
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
9 22 0.67
10 4 0.12
11 7 0.21
ACGTcount: A:0.19, C:0.29, G:0.17, T:0.35
Consensus pattern (9 bp):
TCAGCTCAT
Found at i:13329 original size:20 final size:20
Alignment explanation
Indices: 13304--13341 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
13294 CAGCTCGTTG
13304 AGCTCATTCAGCTCATTTCC
1 AGCTCATTCAGCTCATTTCC
*
13324 AGCTCATTGAGCTCATTT
1 AGCTCATTCAGCTCATTT
13342 GCTTGTTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.29, G:0.13, T:0.37
Consensus pattern (20 bp):
AGCTCATTCAGCTCATTTCC
Found at i:13747 original size:13 final size:13
Alignment explanation
Indices: 13729--13754 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
13719 TGTGTCTTAA
13729 TATGAATTAAATT
1 TATGAATTAAATT
13742 TATGAATTAAATT
1 TATGAATTAAATT
13755 GCTTTCAGGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (13 bp):
TATGAATTAAATT
Found at i:15559 original size:30 final size:29
Alignment explanation
Indices: 15458--15561 Score: 91
Period size: 30 Copynumber: 3.4 Consensus size: 29
15448 CGAGTTTAAA
* *
15458 CTAAAATGAGCTAAGCTTTTAGCTCGTGAG
1 CTAAATTGAGCTAAG-GTTTAGCTCGTGAG
* * * * * *
15488 CTAAAGTTGAGCTGAGGCTAAACTCTTAAG
1 CTAAA-TTGAGCTAAGGTTTAGCTCGTGAG
*
15518 CTGAAGTTGAGCTAAGGTTTAGCTCGTGAG
1 CT-AAATTGAGCTAAGGTTTAGCTCGTGAG
15548 CTAAATATGAGCTA
1 CTAAAT-TGAGCTA
15562 GGAGTGAGCT
Statistics
Matches: 55, Mismatches: 16, Indels: 6
0.71 0.21 0.08
Matches are distributed among these distances:
29 3 0.05
30 42 0.76
31 10 0.18
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.29
Consensus pattern (29 bp):
CTAAATTGAGCTAAGGTTTAGCTCGTGAG
Found at i:17754 original size:12 final size:12
Alignment explanation
Indices: 17739--17769 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
17729 TTCTTTTTGC
17739 TTTTCAAAGGCT
1 TTTTCAAAGGCT
17751 TTTTCAAAGGCT
1 TTTTCAAAGGCT
17763 TTTTCAA
1 TTTTCAA
17770 GTTCTCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:17846 original size:6 final size:6
Alignment explanation
Indices: 17830--17879 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
17820 TTTCTTTTTA
*
17830 TTTCAT TTTCTT TTTCTT CTCTTGCTT TTTCTT TTTC-T TTTC-T TTTCTT
1 TTTCTT TTTCTT TTTCTT -T-TT-CTT TTTCTT TTTCTT TTTCTT TTTCTT
17879 T
1 T
17880 GTTTTCTCTT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
5 10 0.26
6 20 0.51
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (6 bp):
TTTCTT
Found at i:17862 original size:37 final size:37
Alignment explanation
Indices: 17819--17889 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
17809 CTTGCCTCTC
17819 TTTTCTTTTT-ATTTCATTTTCTTT-TTCTTCTCTTGCT
1 TTTTCTTTTTCATTTC-TTTTCTTTGTT-TTCTCTTGCT
*
17856 TTTTCTTTTTCTTTTCTTTTCTTTGTTTTCTCTT
1 TTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTT
17890 TACAAGAATG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 25 0.81
38 6 0.19
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.76
Consensus pattern (37 bp):
TTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTTGCT
Found at i:17890 original size:16 final size:16
Alignment explanation
Indices: 17815--17875 Score: 63
Period size: 16 Copynumber: 3.8 Consensus size: 16
17805 GCCTCTTGCC
*
17815 TCTCTTTTCTTTTTAT
1 TCTCTTTTCTTTTTCT
17831 T-TCATTTTCTTTTTCT
1 TCTC-TTTTCTTTTTCT
*
17847 TCTC-TTGCTTTTTCTT
1 TCTCTTTTCTTTTTC-T
*
17863 TTTCTTTTCTTTT
1 TCTCTTTTCTTTT
17876 CTTTGTTTTC
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
15 11 0.30
16 17 0.46
17 9 0.24
ACGTcount: A:0.03, C:0.20, G:0.02, T:0.75
Consensus pattern (16 bp):
TCTCTTTTCTTTTTCT
Found at i:20608 original size:30 final size:30
Alignment explanation
Indices: 20574--20670 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
20564 TAAACTAAAA
*
20574 TGAGCTAAGTTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
* * * * * * *
20604 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
20634 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
20663 ATGAGCTA
1 -TGAGCTA
20671 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
Found at i:21250 original size:10 final size:10
Alignment explanation
Indices: 21235--21283 Score: 66
Period size: 10 Copynumber: 4.9 Consensus size: 10
21225 TTGGGTTAAG
21235 ATTGAGCTGA
1 ATTGAGCTGA
21245 ATTGAGCTCGA
1 ATTGAGCT-GA
21256 A-TGAGCTGA
1 ATTGAGCTGA
21265 ATTGAGCTCGA
1 ATTGAGCT-GA
21276 A-TGAGCTG
1 ATTGAGCTG
21284 GAAACGAGCT
Statistics
Matches: 36, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
9 4 0.11
10 26 0.72
11 6 0.17
ACGTcount: A:0.29, C:0.14, G:0.31, T:0.27
Consensus pattern (10 bp):
ATTGAGCTGA
Found at i:21260 original size:20 final size:20
Alignment explanation
Indices: 21237--21283 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
21227 GGGTTAAGAT
21237 TGAGCTGAATTGAGCTCGAA
1 TGAGCTGAATTGAGCTCGAA
21257 TGAGCTGAATTGAGCTCGAA
1 TGAGCTGAATTGAGCTCGAA
21277 TGAGCTG
1 TGAGCTG
21284 GAAACGAGCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.28, C:0.15, G:0.32, T:0.26
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAA
Found at i:27070 original size:19 final size:18
Alignment explanation
Indices: 27034--27073 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
27024 TTTCCACTCG
*
27034 TTTCTTTTTCAACTTCTC
1 TTTCTTTTTCAACATCTC
*
27052 TTTCTTTTTCCACAATCTC
1 TTTCTTTTTCAAC-ATCTC
27071 TTT
1 TTT
27074 GTTTGTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTCTTTTTCAACATCTC
Found at i:28139 original size:13 final size:13
Alignment explanation
Indices: 28121--28170 Score: 75
Period size: 13 Copynumber: 3.8 Consensus size: 13
28111 TAGCTCTCTC
28121 TTTTTTTTTCAAA
1 TTTTTTTTTCAAA
28134 TTTTTTTTTCACAA
1 TTTTTTTTTCA-AA
28148 -TTTTTTTTCAAA
1 TTTTTTTTTCAAA
*
28160 ATTTTTTTTCA
1 TTTTTTTTTCA
28171 CAACTTGATA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
12 2 0.06
13 31 0.89
14 2 0.06
ACGTcount: A:0.22, C:0.10, G:0.00, T:0.68
Consensus pattern (13 bp):
TTTTTTTTTCAAA
Found at i:28158 original size:26 final size:26
Alignment explanation
Indices: 28122--28173 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
28112 AGCTCTCTCT
*
28122 TTTTTTTTCAAATTTTTTTTTCACAA
1 TTTTTTTTCAAAATTTTTTTTCACAA
28148 TTTTTTTTCAAAATTTTTTTTCACAA
1 TTTTTTTTCAAAATTTTTTTTCACAA
28174 CTTGATATCC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.25, C:0.12, G:0.00, T:0.63
Consensus pattern (26 bp):
TTTTTTTTCAAAATTTTTTTTCACAA
Found at i:28229 original size:12 final size:12
Alignment explanation
Indices: 28212--28254 Score: 59
Period size: 12 Copynumber: 3.5 Consensus size: 12
28202 GGAAACTAGT
28212 TTTTTTTTTGAA
1 TTTTTTTTTGAA
*
28224 TTTTTTTTTCAAA
1 TTTTTTTTT-GAA
*
28237 TTTTTTTTTGAG
1 TTTTTTTTTGAA
28249 TTTTTT
1 TTTTTT
28255 CGAGAAACTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
12 16 0.59
13 11 0.41
ACGTcount: A:0.14, C:0.02, G:0.07, T:0.77
Consensus pattern (12 bp):
TTTTTTTTTGAA
Found at i:28229 original size:13 final size:13
Alignment explanation
Indices: 28211--28254 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
28201 TGGAAACTAG
28211 TTTTTTTTTTGAA
1 TTTTTTTTTTGAA
*
28224 -TTTTTTTTTCAA
1 TTTTTTTTTTGAA
* *
28236 ATTTTTTTTTGAG
1 TTTTTTTTTTGAA
28249 TTTTTT
1 TTTTTT
28255 CGAGAAACTA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
12 11 0.42
13 15 0.58
ACGTcount: A:0.14, C:0.02, G:0.07, T:0.77
Consensus pattern (13 bp):
TTTTTTTTTTGAA
Found at i:30779 original size:20 final size:19
Alignment explanation
Indices: 30756--30820 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
30746 AAGCTCAAAC
30756 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
30776 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
30796 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
30816 GAGCT
1 GAGCT
30821 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:32628 original size:33 final size:33
Alignment explanation
Indices: 32590--32652 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
32580 GATTACTCAC
32590 TTCACTCG-TTTCTTTT-ACAGACTCTCTTTCTTT
1 TTCACTCGATTTCTTTTCA-AG-CTCTCTTTCTTT
*
32623 TTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTCACTCGATTTCTTTTCAAGCTCTCTTTC
32653 AATTTCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.13, C:0.27, G:0.06, T:0.54
Consensus pattern (33 bp):
TTCACTCGATTTCTTTTCAAGCTCTCTTTCTTT
Found at i:32679 original size:21 final size:21
Alignment explanation
Indices: 32650--32705 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 21
32640 CAAGCTCTCT
*
32650 TTCAATTTCTTTTTTCGCTTT-
1 TTCATTTTCTTTTTTC-CTTTC
* ** *
32671 TTCTTTTTCAATTTTCTTTTC
1 TTCATTTTCTTTTTTCCTTTC
32692 TTCATTTTCTTTTT
1 TTCATTTTCTTTTT
32706 CTCTCACTTT
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
20 3 0.12
21 23 0.88
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.71
Consensus pattern (21 bp):
TTCATTTTCTTTTTTCCTTTC
Found at i:32679 original size:27 final size:26
Alignment explanation
Indices: 32649--32774 Score: 78
Period size: 28 Copynumber: 4.6 Consensus size: 26
32639 TCAAGCTCTC
32649 TTTCAATTTCTTTTTTCGCTTTTTCTT
1 TTTCAATTTCTTTTTTC-CTTTTTCTT
* *
32676 TTTCAATTTTCTTTTCTTCATTTTCTTTT
1 TTTCAA-TTTCTTTT-TTCCTTTT-TCTT
* *
32705 TCTCTCACTTT-TTCGATTT-CTTTTTCTT
1 T-T-TCAATTTCTT--TTTTCCTTTTTCTT
* * *
32733 TTGCAATTTC-TTTTTCTTTTTGTTTT
1 TTTCAATTTCTTTTTTCCTTTT-TCTT
32759 CTTTCAATTTCTTTTT
1 -TTTCAATTTCTTTTT
32775 CAATCTCTTT
Statistics
Matches: 75, Mismatches: 12, Indels: 23
0.68 0.11 0.21
Matches are distributed among these distances:
24 3 0.04
25 4 0.05
26 9 0.12
27 16 0.21
28 20 0.27
29 13 0.17
30 6 0.08
31 4 0.05
ACGTcount: A:0.09, C:0.18, G:0.03, T:0.70
Consensus pattern (26 bp):
TTTCAATTTCTTTTTTCCTTTTTCTT
Found at i:32698 original size:14 final size:14
Alignment explanation
Indices: 32649--32705 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
32639 TCAAGCTCTC
32649 TTTCAA-TTTCTTT
1 TTTCAATTTTCTTT
**
32662 TTTCGCTTTT-TCTT
1 TTTCAATTTTCT-TT
32676 TTTCAATTTTCTTT
1 TTTCAATTTTCTTT
32690 TCTTC-ATTTTCTTT
1 T-TTCAATTTTCTTT
32704 TT
1 TT
32706 CTCTCACTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
13 6 0.17
14 26 0.72
15 4 0.11
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.72
Consensus pattern (14 bp):
TTTCAATTTTCTTT
Found at i:32733 original size:18 final size:18
Alignment explanation
Indices: 32712--32762 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 18
32702 TTTTCTCTCA
32712 CTTTTTCGATTTCTTTTT
1 CTTTTTCGATTTCTTTTT
* *
32730 CTTTTGCAATTTCTTTTT
1 CTTTTTCGATTTCTTTTT
*
32748 CTTTTT-GTTTTCTTT
1 CTTTTTCGATTTCTTT
32763 CAATTTCTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
17 7 0.25
18 21 0.75
ACGTcount: A:0.06, C:0.16, G:0.06, T:0.73
Consensus pattern (18 bp):
CTTTTTCGATTTCTTTTT
Found at i:32775 original size:6 final size:6
Alignment explanation
Indices: 32667--32762 Score: 59
Period size: 6 Copynumber: 15.7 Consensus size: 6
32657 TCTTTTTTCG
* * * **
32667 CTTTTT CTTTTT CAATTTT CTTTTCTT CATTTT CTTTTT CTCTCA CTTTTT
1 CTTTTT CTTTTT C-TTTTT C-TTT-TT CTTTTT CTTTTT CTTTTT CTTTTT
** * ** *
32718 CGATTT CTTTTT CTTTTG CAATTT CTTTTT CTTTTT -GTTTT CTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTT
32763 CAATTTCTTT
Statistics
Matches: 64, Mismatches: 23, Indels: 6
0.69 0.25 0.06
Matches are distributed among these distances:
5 4 0.06
6 48 0.75
7 9 0.14
8 3 0.05
ACGTcount: A:0.07, C:0.19, G:0.03, T:0.71
Consensus pattern (6 bp):
CTTTTT
Found at i:34379 original size:10 final size:10
Alignment explanation
Indices: 34364--34425 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
34354 TTTGAACCAT
*
34364 TACCAATTCG
1 TACCAATTCA
*
34374 TACCAAATACCA
1 TACC-AAT-TCA
*
34386 TACCATTTCA
1 TACCAATTCA
34396 TACCAATTCCA
1 TACCAATT-CA
* *
34407 TACCATTTCG
1 TACCAATTCA
34417 TACCAATTC
1 TACCAATTC
34426 CCAAATACCA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
10 22 0.54
11 14 0.34
12 5 0.12
ACGTcount: A:0.34, C:0.32, G:0.03, T:0.31
Consensus pattern (10 bp):
TACCAATTCA
Found at i:34409 original size:21 final size:21
Alignment explanation
Indices: 34364--34426 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
34354 TTTGAACCAT
* *
34364 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
*
34386 TACCATTTCATACCAATTCCA
1 TACCATTTCGTACCAATTCCA
34407 TACCATTTCGTACCAATTCC
1 TACCATTTCGTACCAATTCC
34427 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 25 0.68
22 12 0.32
ACGTcount: A:0.33, C:0.33, G:0.03, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:35469 original size:20 final size:20
Alignment explanation
Indices: 35444--35501 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
35434 TTGTCACTTC
35444 TTTTTTTTCCTTTTTTTTGA
1 TTTTTTTTCCTTTTTTTTGA
***
35464 TTTTTTTGAATTTTTTTTGA
1 TTTTTTTTCCTTTTTTTTGA
* *
35484 -ATTTCTTCTCTTTTTTTT
1 TTTTTTTTC-CTTTTTTTT
35502 AAATCCAATA
Statistics
Matches: 29, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
19 4 0.14
20 25 0.86
ACGTcount: A:0.09, C:0.09, G:0.05, T:0.78
Consensus pattern (20 bp):
TTTTTTTTCCTTTTTTTTGA
Found at i:35484 original size:11 final size:11
Alignment explanation
Indices: 35454--35487 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
35444 TTTTTTTTCC
35454 TTTTTTTTG-A
1 TTTTTTTTGAA
35464 -TTTTTTTGAA
1 TTTTTTTTGAA
35474 TTTTTTTTGAA
1 TTTTTTTTGAA
35485 TTT
1 TTT
35488 CTTCTCTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 8 0.36
10 1 0.05
11 13 0.59
ACGTcount: A:0.15, C:0.00, G:0.09, T:0.76
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:37124 original size:20 final size:19
Alignment explanation
Indices: 37101--37165 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
37091 AAGCTCAAAC
37101 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
37121 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
37141 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
37161 GAGCT
1 GAGCT
37166 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:39164 original size:33 final size:30
Alignment explanation
Indices: 39112--39200 Score: 101
Period size: 28 Copynumber: 2.9 Consensus size: 30
39102 ATAAGGCCAG
* *
39112 AAAACACTATAAAAGAAAAATAAAAACAAAAAA
1 AAAACAC-A-AAAA-AAAAAAAAAAAAAAAAAA
*
39145 AAAACACAAAAAAATAAAAAAAAAAAAAAA
1 AAAACACAAAAAAAAAAAAAAAAAAAAAAA
*
39175 AAAA-A-AAAAAAAAAAAAACAAAAAAA
1 AAAACACAAAAAAAAAAAAAAAAAAAAA
39201 TATAGGTTAG
Statistics
Matches: 51, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
28 19 0.37
29 1 0.02
30 19 0.37
31 4 0.08
32 1 0.02
33 7 0.14
ACGTcount: A:0.88, C:0.07, G:0.01, T:0.04
Consensus pattern (30 bp):
AAAACACAAAAAAAAAAAAAAAAAAAAAAA
Found at i:39220 original size:1 final size:1
Alignment explanation
Indices: 39122--39200 Score: 95
Period size: 1 Copynumber: 79.0 Consensus size: 1
39112 AAAACACTAT
* * * * * *
39122 AAAAGAAAAATAAAAACAAAAAAAAAACACAAAAAAATAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
*
39187 AAAAAACAAAAAAA
1 AAAAAAAAAAAAAA
39201 TATAGGTTAG
Statistics
Matches: 64, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
1 64 1.00
ACGTcount: A:0.91, C:0.05, G:0.01, T:0.03
Consensus pattern (1 bp):
A
Found at i:39220 original size:44 final size:43
Alignment explanation
Indices: 39122--39202 Score: 128
Period size: 42 Copynumber: 1.9 Consensus size: 43
39112 AAAACACTAT
* * *
39122 AAAAGAAAAATAAAAACAAAAAAAAAACACAAAAAAATAAAAA
1 AAAAAAAAAAAAAAAACAAAAAAAAAAAACAAAAAAATAAAAA
39165 AAAAAAAAAAAAAAAA-AAAAAAAAAAAACAAAAAAATA
1 AAAAAAAAAAAAAAAACAAAAAAAAAAAACAAAAAAATA
39203 TAGGTTAGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
42 21 0.60
43 14 0.40
ACGTcount: A:0.90, C:0.05, G:0.01, T:0.04
Consensus pattern (43 bp):
AAAAAAAAAAAAAAAACAAAAAAAAAAAACAAAAAAATAAAAA
Found at i:39286 original size:21 final size:23
Alignment explanation
Indices: 39239--39288 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
39229 AGTAAATAAT
39239 GAAAAACAAAATAATAAAACAAC
1 GAAAAACAAAATAATAAAACAAC
*
39262 GAAAAA-AAAA-AATGAAAAGAA-
1 GAAAAACAAAATAAT-AAAACAAC
39283 GAAAAA
1 GAAAAA
39289 GGATAAATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
21 9 0.36
22 10 0.40
23 6 0.24
ACGTcount: A:0.78, C:0.06, G:0.10, T:0.06
Consensus pattern (23 bp):
GAAAAACAAAATAATAAAACAAC
Done.