Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold687
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: 31953
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Found at i:3757 original size:50 final size:50
Alignment explanation
Indices: 3630--3938 Score: 471
Period size: 50 Copynumber: 6.2 Consensus size: 50
3620 ATACTTAGAA
* *
3630 TCAACAATTATGGCCACCTCCCTCTATTGTCAAATGTTGGTGAAGAATTTG
1 TCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAA-TTG
*
3681 TCAACAATTATGGCCACCTC-CTTCTATTGTCAAAGGTTGGTGAAGAATCG
1 TCAACAATTATGGCCACCTCTC-TCTATTGTCAAAGGTTGGTGAAGAATTG
* *
3731 TCAACAATTATTGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAAAATTG
1 TCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATTG
* *
3781 TCAACAATTATTGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAAAATTG
1 TCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATTG
*
3831 TCAACAATTATGGCCACCTC-CTTCTATTGTCAAAGGTTGGTGAAGAATCG
1 TCAACAATTATGGCCACCTCTC-TCTATTGTCAAAGGTTGGTGAAGAATTG
* *
3881 TCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTAGTGAATG-ATAG
1 TCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAA-GAATTG
3931 TCAACAAT
1 TCAACAAT
3939 GACAATAACT
Statistics
Matches: 243, Mismatches: 10, Indels: 11
0.92 0.04 0.04
Matches are distributed among these distances:
49 1 0.00
50 195 0.80
51 47 0.19
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.32
Consensus pattern (50 bp):
TCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATTG
Found at i:3902 original size:150 final size:151
Alignment explanation
Indices: 3630--3938 Score: 530
Period size: 150 Copynumber: 2.1 Consensus size: 151
3620 ATACTTAGAA
* *
3630 TCAACAATTATGGCCACCTCCCTCTATTGTCAAATGTTGGTGAAGAATTTGTCAACAATTATGGC
1 TCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAAATTGTCAACAATTATGGC
*
3695 CACCTCCTTCTATTGTCAAAGGTTGGTGAAGAATCGTCAACAATTATTGCCACCTCTCTCTATTG
66 CACCTCCTTCTATTGTCAAAGGTTGGTGAAGAATCGTCAACAATTATGGCCACCTCTCTCTATTG
* *
3760 TCAAAGGTTGGTGAAAAATTG
131 TCAAAGGTTAGTGAAAAATAG
* *
3781 TCAACAATTATTGCCACCTCTCTCTATTGTCAAAGGTTGGTGAA-AAATTGTCAACAATTATGGC
1 TCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAAATTGTCAACAATTATGGC
3845 CACCTCCTTCTATTGTCAAAGGTTGGTGAAGAATCGTCAACAATTATGGCCACCTCTCTCTATTG
66 CACCTCCTTCTATTGTCAAAGGTTGGTGAAGAATCGTCAACAATTATGGCCACCTCTCTCTATTG
**
3910 TCAAAGGTTAGTGAATGATAG
131 TCAAAGGTTAGTGAAAAATAG
3931 TCAACAAT
1 TCAACAAT
3939 GACAATAACT
Statistics
Matches: 149, Mismatches: 9, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
150 108 0.72
151 41 0.28
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.32
Consensus pattern (151 bp):
TCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAAATTGTCAACAATTATGGC
CACCTCCTTCTATTGTCAAAGGTTGGTGAAGAATCGTCAACAATTATGGCCACCTCTCTCTATTG
TCAAAGGTTAGTGAAAAATAG
Found at i:8387 original size:50 final size:50
Alignment explanation
Indices: 8328--8586 Score: 448
Period size: 50 Copynumber: 5.2 Consensus size: 50
8318 TATACTTAGA
*
8328 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATT
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
*
8378 GTCAACAATTATGGCCACCTCCTTCTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
*
8428 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATT
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
*
8478 GTCAACAATTATGGCCACCTCCTTCTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
* *
8528 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAATG-ATA
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAA-GAATC
8578 GTCAACAAT
1 GTCAACAAT
8587 GACAATAACT
Statistics
Matches: 199, Mismatches: 9, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
50 198 0.99
51 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.30
Consensus pattern (50 bp):
GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
Found at i:10104 original size:38 final size:38
Alignment explanation
Indices: 10062--10136 Score: 100
Period size: 38 Copynumber: 2.0 Consensus size: 38
10052 AATTATTGTG
* *
10062 AAAAATATATTTTTATATTTTAT-AATTA-AATTTAAATA
1 AAAAAT-TATTTTT-TATTATATAAATAATAATTTAAATA
10100 AAAAATTATTTTTTATTATATAAATAATAATTTAAAT
1 AAAAATTATTTTTTATTATATAAATAATAATTTAAAT
10137 TATGTAGAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
36 7 0.21
37 11 0.33
38 15 0.45
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (38 bp):
AAAAATTATTTTTTATTATATAAATAATAATTTAAATA
Found at i:10562 original size:19 final size:17
Alignment explanation
Indices: 10528--10562 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 17
10518 CCCAAAAATT
10528 AAAAAAAGAAAAAAGAA
1 AAAAAAAGAAAAAAGAA
10545 AAAAAAATGAAAATAAGA
1 AAAAAAA-GAAAA-AAGA
10563 TTGGTGTGCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 5 0.31
19 4 0.25
ACGTcount: A:0.83, C:0.00, G:0.11, T:0.06
Consensus pattern (17 bp):
AAAAAAAGAAAAAAGAA
Found at i:11456 original size:1 final size:1
Alignment explanation
Indices: 11450--11474 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
11440 CGCTGATATT
11450 CCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCC
11475 GCTCTTCCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:13259 original size:15 final size:14
Alignment explanation
Indices: 13239--13286 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
13229 GGTCCATATT
13239 AATATTTATTGATAA
1 AATATTTATT-ATAA
*
13254 AATATTT-TTATTTA
1 AATATTTATTA-TAA
13268 AAT-TTTATTATAA
1 AATATTTATTATAA
13281 AATATT
1 AATATT
13287 AATATAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
13 9 0.32
14 12 0.43
15 7 0.25
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (14 bp):
AATATTTATTATAA
Found at i:13850 original size:22 final size:22
Alignment explanation
Indices: 13822--13877 Score: 60
Period size: 26 Copynumber: 2.4 Consensus size: 22
13812 AAATTAAATA
13822 TAAATAATTT-TATTTTTTTATT
1 TAAATAATTTATATTTTTTTA-T
13844 TAAATAAATTTAACTATTTTTTTAT
1 TAAAT-AATTT-A-TATTTTTTTAT
13869 TAATATAAT
1 TAA-ATAAT
13878 ATTTTTACTA
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
22 5 0.17
23 5 0.17
25 7 0.24
26 12 0.41
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (22 bp):
TAAATAATTTATATTTTTTTAT
Found at i:14189 original size:20 final size:21
Alignment explanation
Indices: 14162--14203 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
14152 AAAATATATT
14162 AAAAATA-TA-AAAAATTAAA
1 AAAAATATTACAAAAATTAAA
*
14181 AAAATATATTACAAATATTAAA
1 AAAA-ATATTACAAAAATTAAA
14203 A
1 A
14204 TATTTATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
19 4 0.21
20 3 0.16
21 2 0.11
22 10 0.53
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.26
Consensus pattern (21 bp):
AAAAATATTACAAAAATTAAA
Found at i:17818 original size:12 final size:12
Alignment explanation
Indices: 17801--17825 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
17791 GTAATCGAAA
17801 TTTATATAACTT
1 TTTATATAACTT
17813 TTTATATAACTT
1 TTTATATAACTT
17825 T
1 T
17826 ATAATATCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.08, G:0.00, T:0.60
Consensus pattern (12 bp):
TTTATATAACTT
Found at i:18961 original size:31 final size:33
Alignment explanation
Indices: 18906--18967 Score: 92
Period size: 31 Copynumber: 1.9 Consensus size: 33
18896 ATATTTGAAT
* *
18906 AATATAAATTATTAATATATTAAAATTTATATA
1 AATATAAATTATTAATATAATAAAATATATATA
18939 AATAT-AATTA-TAATATAATAAAATATATA
1 AATATAAATTATTAATATAATAAAATATATA
18968 ACTTCAACTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 17 0.63
32 5 0.19
33 5 0.19
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (33 bp):
AATATAAATTATTAATATAATAAAATATATATA
Found at i:19724 original size:6 final size:6
Alignment explanation
Indices: 19713--19745 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
19703 GGCTTTGAAG
19713 GAAAAA GAAAAA -AAAAA GAAAAA GAAAAA GAAA
1 GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAA
19746 GAAAGATCGG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (6 bp):
GAAAAA
Found at i:19730 original size:11 final size:12
Alignment explanation
Indices: 19713--19745 Score: 59
Period size: 11 Copynumber: 2.8 Consensus size: 12
19703 GGCTTTGAAG
19713 GAAAAAGAAAAA
1 GAAAAAGAAAAA
19725 -AAAAAGAAAAA
1 GAAAAAGAAAAA
19736 GAAAAAGAAA
1 GAAAAAGAAA
19746 GAAAGATCGG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 11 0.55
12 9 0.45
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (12 bp):
GAAAAAGAAAAA
Found at i:20694 original size:145 final size:145
Alignment explanation
Indices: 20448--20708 Score: 407
Period size: 145 Copynumber: 1.8 Consensus size: 145
20438 ACTATAGGTG
* * * * * *
20448 CTAGAGGCCTTCTATTGCCTCAGATGCAAGGCGCCATAAAGGCACTCGCCTAAGTGAAGTAAGGT
1 CTAGAGGCCTTATATTCCCTCAGATGCAAGGCGCAATAAAAGCACTCACCTAAGTGAAGTAAGGC
* * **
20513 GCAATATGGATATGTGTGTGTTTTTGTATGTGTCTATATATATATATATATTGTCAAGGATGCAA
66 ACAATATGGATATGTGTGTGATTTTGTATGCATCTATATATATATATATATTGTCAAGGATGCAA
20578 GGCACACTCTATGCA
131 GGCACACTCTATGCA
20593 CTAGAGGCCTTATATTCCCTCAGGA-GCAAGGCGCAATAAAAGCACTCACCTAAGTGAAGTAAGG
1 CTAGAGGCCTTATATTCCCTCA-GATGCAAGGCGCAATAAAAGCACTCACCTAAGTGAAGTAAGG
*
20657 CACAATATGTATATGTGTGTGATTTTGTATGCATCTATATATATATATATAT
65 CACAATATGGATATGTGTGTGATTTTGTATGCATCTATATATATATATATAT
20709 ATAATTATAA
Statistics
Matches: 104, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
145 102 0.98
146 2 0.02
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (145 bp):
CTAGAGGCCTTATATTCCCTCAGATGCAAGGCGCAATAAAAGCACTCACCTAAGTGAAGTAAGGC
ACAATATGGATATGTGTGTGATTTTGTATGCATCTATATATATATATATATTGTCAAGGATGCAA
GGCACACTCTATGCA
Found at i:20742 original size:13 final size:13
Alignment explanation
Indices: 20700--20742 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
20690 TCTATATATA
20700 TATATATATATAAT
1 TATA-ATATATAAT
***
20714 TATAATATAGGCT
1 TATAATATATAAT
20727 TATAATATATAAT
1 TATAATATATAAT
20740 TAT
1 TAT
20743 CATAATAAAC
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
13 19 0.83
14 4 0.17
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.47
Consensus pattern (13 bp):
TATAATATATAAT
Found at i:21123 original size:91 final size:91
Alignment explanation
Indices: 20993--21163 Score: 306
Period size: 91 Copynumber: 1.9 Consensus size: 91
20983 AAAAGCATGC
*
20993 CTAGGCGCACTAGACATGTGCCTGATCAAATGCGCCTTGCCTGAAAGGGTTTGAGGCGCTTTTGT
1 CTAGGCGCACTAGACACGTGCCTGATCAAATGCGCCTTGCCTGAAAGGGTTTGAGGCGCTTTTGT
21058 TGTCTAACACTAAGGTGCAGGCACTT
66 TGTCTAACACTAAGGTGCAGGCACTT
* * *
21084 CTAGGCGCACTGGACACGTGCTTGATCAAATGCGCCTTGCCTGAAAGGGTTTGAGGTGCTTTTGT
1 CTAGGCGCACTAGACACGTGCCTGATCAAATGCGCCTTGCCTGAAAGGGTTTGAGGCGCTTTTGT
21149 TGTCTAACACTAAGG
66 TGTCTAACACTAAGG
21164 CGCAAGGCGC
Statistics
Matches: 76, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
91 76 1.00
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (91 bp):
CTAGGCGCACTAGACACGTGCCTGATCAAATGCGCCTTGCCTGAAAGGGTTTGAGGCGCTTTTGT
TGTCTAACACTAAGGTGCAGGCACTT
Found at i:25599 original size:2 final size:2
Alignment explanation
Indices: 25592--25634 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
25582 TATGCTTTTC
25592 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
25634 A
1 A
25635 GCTTTTTTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:25705 original size:37 final size:35
Alignment explanation
Indices: 25664--25743 Score: 99
Period size: 37 Copynumber: 2.2 Consensus size: 35
25654 ATCATCATTT
* * *
25664 TTTTAAATATTAA-TATTTAAATTTATTAAATATTATA
1 TTTTAAATA-TAATTATATAAATTAATT-AA-ATTAAA
25701 TTTTAAATATAATTATATAAATTAATTAAATTAAA
1 TTTTAAATATAATTATATAAATTAATTAAATTAAA
25736 TTTTAAAT
1 TTTTAAAT
25744 TTTTGATCCA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
35 13 0.33
36 5 0.13
37 21 0.54
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (35 bp):
TTTTAAATATAATTATATAAATTAATTAAATTAAA
Found at i:25737 original size:23 final size:21
Alignment explanation
Indices: 25703--25744 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
25693 ATATTATATT
25703 TTAAATATAATTATATAAATTAA
1 TTAAATATAATT-T-TAAATTAA
25726 TTAAAT-TAAATTTTAAATT
1 TTAAATAT-AATTTTAAATT
25745 TTTGATCCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
21 6 0.33
22 2 0.11
23 10 0.56
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
TTAAATATAATTTTAAATTAA
Found at i:25928 original size:20 final size:21
Alignment explanation
Indices: 25903--25950 Score: 62
Period size: 22 Copynumber: 2.3 Consensus size: 21
25893 ATTTTTATAT
25903 TTATAAAAGT-TATTTATAAA
1 TTATAAAAGTATATTTATAAA
*
25923 TTATAAAAATTATATTTATAAA
1 TTAT-AAAAGTATATTTATAAA
*
25945 TAATAA
1 TTATAA
25951 TTAAATTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 4 0.17
21 7 0.29
22 13 0.54
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (21 bp):
TTATAAAAGTATATTTATAAA
Found at i:25952 original size:19 final size:19
Alignment explanation
Indices: 25925--25966 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
25915 TTTATAAATT
*
25925 ATAAAAATTATATTTATAA
1 ATAAAAATTAAATTTATAA
*
25944 ATAATAATTAAATTTAT-A
1 ATAAAAATTAAATTTATAA
25962 ATAAA
1 ATAAA
25967 TACTAATAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
ATAAAAATTAAATTTATAA
Found at i:27295 original size:10 final size:10
Alignment explanation
Indices: 27247--27307 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
27237 AATAATTTAT
27247 TTAATTT-AA
1 TTAATTTGAA
* *
27256 TTTATATTGAG
1 TTAAT-TTGAA
*
27267 TTAATTTAAA
1 TTAATTTGAA
27277 TAATAATTTGAA
1 T--TAATTTGAA
*
27289 TTAATTTAAA
1 TTAATTTGAA
27299 TTAATTTGA
1 TTAATTTGA
27308 TTTTTATTTA
Statistics
Matches: 40, Mismatches: 8, Indels: 7
0.73 0.15 0.13
Matches are distributed among these distances:
9 4 0.10
10 22 0.55
11 5 0.12
12 9 0.22
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.51
Consensus pattern (10 bp):
TTAATTTGAA
Found at i:29576 original size:19 final size:20
Alignment explanation
Indices: 29552--29590 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
29542 ATTTTATATA
29552 TAATTAATATATT-AATAAT
1 TAATTAATATATTAAATAAT
*
29571 TAATTATTATATTAAATAAT
1 TAATTAATATATTAAATAAT
29591 ATTGTAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TAATTAATATATTAAATAAT
Found at i:30462 original size:22 final size:22
Alignment explanation
Indices: 30435--30486 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 22
30425 TATATAAAAA
30435 AATATATATAATATAATTTAT-T
1 AATATATATAATA-AATTTATAT
30457 AATATAT-T-A-AAATTTATAT
1 AATATATATAATAAATTTATAT
30476 AA-ATATATAAT
1 AATATATATAAT
30487 TTATTATAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 9
0.74 0.00 0.26
Matches are distributed among these distances:
18 11 0.42
19 5 0.19
20 2 0.08
21 1 0.04
22 7 0.27
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
AATATATATAATAAATTTATAT
Found at i:30470 original size:18 final size:16
Alignment explanation
Indices: 30449--30500 Score: 59
Period size: 17 Copynumber: 3.0 Consensus size: 16
30439 TATATAATAT
30449 AATTTATTAATATATTAA
1 AATTTATTAA-ATA-TAA
*
30467 AATTTATATAAATATAT
1 AATTTAT-TAAATATAA
30484 AATTTATTATAATATAA
1 AATTTATTA-AATATAA
30501 TTATAATAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
16 2 0.07
17 15 0.50
18 10 0.33
19 3 0.10
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
AATTTATTAAATATAA
Found at i:30516 original size:21 final size:20
Alignment explanation
Indices: 30492--30530 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
30482 ATAATTTATT
* *
30492 ATAATATAATTATAATAAAAA
1 ATAACATAAATAT-ATAAAAA
30513 ATAACATAAATATATAAA
1 ATAACATAAATATATAAA
30531 TTTAAATATG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (20 bp):
ATAACATAAATATATAAAAA
Found at i:30537 original size:23 final size:23
Alignment explanation
Indices: 30474--30538 Score: 57
Period size: 23 Copynumber: 2.9 Consensus size: 23
30464 TAAAATTTAT
* *
30474 ATAAATATAT-AATTTATTATAAT
1 ATAAATATATAAATTTA-AATAAC
*
30497 ATAATTATAATAAA---AAATAAC
1 ATAAATAT-ATAAATTTAAATAAC
30518 ATAAATATATAAATTTAAATA
1 ATAAATATATAAATTTAAATA
30539 TGCAAAATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 10
0.70 0.09 0.21
Matches are distributed among these distances:
20 5 0.15
21 11 0.33
22 1 0.03
23 12 0.36
24 2 0.06
25 2 0.06
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (23 bp):
ATAAATATATAAATTTAAATAAC
Found at i:30782 original size:11 final size:11
Alignment explanation
Indices: 30759--30792 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
30749 TTATTTTATT
30759 TTAAATT-AAA
1 TTAAATTAAAA
30769 TTAAATTAAAA
1 TTAAATTAAAA
*
30780 TTAATTTAAAA
1 TTAAATTAAAA
30791 TT
1 TT
30793 TTATTTAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 7 0.32
11 15 0.68
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
TTAAATTAAAA
Found at i:30858 original size:40 final size:39
Alignment explanation
Indices: 30750--30860 Score: 109
Period size: 40 Copynumber: 2.8 Consensus size: 39
30740 GAAAATTATT
* *
30750 TATTTTATTT-TAAATTAAATTAAATTAAAATTAATTTAA
1 TATTTTATTTATAAA-TAAATTAAAATAAAAATAATTTAA
* * * *
30789 AATTTTATTTAATTATTACAA-TAATATAAAAATAATTTTAA
1 TATTTTATTT-ATAAATA-AATTAAAATAAAAATAA-TTTAA
*
30830 TATTATATTTATAAATAAATTAAAATAAAAA
1 TATTTTATTTATAAATAAATTAAAATAAAAA
30861 AGTTATATTT
Statistics
Matches: 56, Mismatches: 11, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
39 11 0.20
40 28 0.50
41 17 0.30
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (39 bp):
TATTTTATTTATAAATAAATTAAAATAAAAATAATTTAA
Found at i:30896 original size:42 final size:40
Alignment explanation
Indices: 30762--30904 Score: 105
Period size: 40 Copynumber: 3.5 Consensus size: 40
30752 TTTTATTTTA
* * * *
30762 AATTA-AATTAAATTAAAATTAA-TTTAAAATTTTATTTAAT
1 AATTACAA-TAAAATAAAAATAATTTTAATATTATA-TTAAT
* * *
30802 TATTACAATAATATAAAAATAATTTTAATATTATATTTAT
1 AATTACAATAAAATAAAAATAATTTTAATATTATATTAAT
* * *
30842 AAATA-AATTAAAATAAAAAAGTTATATTTATTA-TATATTAAT
1 AATTACAA-TAAAAT-AAAAA-TAAT-TTTAATATTATATTAAT
30884 AATTACAATAAAATTAAAAAT
1 AATTACAATAAAA-TAAAAAT
30905 GTTCAAATTA
Statistics
Matches: 81, Mismatches: 14, Indels: 15
0.74 0.13 0.14
Matches are distributed among these distances:
39 2 0.02
40 27 0.33
41 18 0.22
42 25 0.31
43 9 0.11
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (40 bp):
AATTACAATAAAATAAAAATAATTTTAATATTATATTAAT
Done.