Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1765
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: 53672
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.35
Found at i:310 original size:13 final size:14
Alignment explanation
Indices: 292--320 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
282 ACCATGAAGC
292 TTCTTTTTT-TTTT
1 TTCTTTTTTCTTTT
305 TTCTTTTTTCTTTT
1 TTCTTTTTTCTTTT
319 TT
1 TT
321 AATCTCTAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (14 bp):
TTCTTTTTTCTTTT
Found at i:311 original size:7 final size:7
Alignment explanation
Indices: 292--320 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
282 ACCATGAAGC
292 TTCTTTT
1 TTCTTTT
299 TT-TTTT
1 TTCTTTT
305 TTCTTTT
1 TTCTTTT
312 TTCTTTT
1 TTCTTTT
319 TT
1 TT
321 AATCTCTAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
6 6 0.29
7 15 0.71
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (7 bp):
TTCTTTT
Found at i:903 original size:28 final size:27
Alignment explanation
Indices: 860--943 Score: 73
Period size: 26 Copynumber: 3.0 Consensus size: 27
850 GAAATGTTTC
* *
860 AATTTAAAAATCTTTTTTAATATTTAA
1 AATTAAAAAATATTTTTTAATATTTAA
**
887 AATATAAAAAATA--TTTTAATATTTTT
1 AAT-TAAAAAATATTTTTTAATATTTAA
*
913 AATTAAATTAAATATTTTGTTATTATTTAA
1 AATTAAA--AAATATTTT-TTAATATTTAA
943 A
1 A
944 GAATAATTTA
Statistics
Matches: 44, Mismatches: 7, Indels: 9
0.73 0.12 0.15
Matches are distributed among these distances:
25 4 0.09
26 14 0.32
27 8 0.18
28 7 0.16
29 2 0.05
30 9 0.20
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (27 bp):
AATTAAAAAATATTTTTTAATATTTAA
Found at i:1866 original size:3 final size:3
Alignment explanation
Indices: 1853--1901 Score: 80
Period size: 3 Copynumber: 16.3 Consensus size: 3
1843 AAAAATATAT
* *
1853 ATA ACA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATG ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1901 A
1 A
1902 AAGAAAGCTC
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:2443 original size:14 final size:14
Alignment explanation
Indices: 2404--2445 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
2394 TGGATTTGAT
2404 TAAATTGAAATTT-
1 TAAATTGAAATTTA
*
2417 TAAA-TAAATATTTA
1 TAAATTGAA-ATTTA
2431 TAAATTGAAATTTA
1 TAAATTGAAATTTA
2445 T
1 T
2446 TTATTATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
12 3 0.12
13 8 0.33
14 10 0.42
15 3 0.12
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (14 bp):
TAAATTGAAATTTA
Found at i:2480 original size:26 final size:27
Alignment explanation
Indices: 2441--2491 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 27
2431 TAAATTGAAA
*
2441 TTTATTTATTATTTAATAATAAAATTT
1 TTTATTTATAATTTAATAATAAAATTT
*
2468 TTTATTTA-AATTTAATTATAAAAT
1 TTTATTTATAATTTAATAATAAAAT
2492 ATATATATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 14 0.64
27 8 0.36
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (27 bp):
TTTATTTATAATTTAATAATAAAATTT
Found at i:2522 original size:24 final size:24
Alignment explanation
Indices: 2487--2543 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 24
2477 ATTTAATTAT
* *
2487 AAAAT-ATATATATTAATATAAAC
1 AAAATAATTTATAATAATATAAAC
* * *
2510 ATAATAATTTATAATATTATAAAT
1 AAAATAATTTATAATAATATAAAC
2534 AAAATAATTT
1 AAAATAATTT
2544 TTTTATTAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
23 4 0.15
24 23 0.85
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (24 bp):
AAAATAATTTATAATAATATAAAC
Found at i:3634 original size:14 final size:14
Alignment explanation
Indices: 3615--3649 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
3605 TATTTTAAAT
3615 ATATATTTAATTTA
1 ATATATTTAATTTA
*
3629 ATATATTTTATTTA
1 ATATATTTAATTTA
3643 AT-TATTT
1 ATATATTT
3650 TGTCAATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 5 0.25
14 15 0.75
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
ATATATTTAATTTA
Found at i:3746 original size:20 final size:18
Alignment explanation
Indices: 3721--3784 Score: 60
Period size: 17 Copynumber: 3.4 Consensus size: 18
3711 AATTAATAAA
*
3721 ATAAAACAATATCTATTATT
1 ATAAAA-AATAT-AATTATT
3741 AT-AAAAATATAATTATT
1 ATAAAAAATATAATTATT
*
3758 AT-AAAAATATAAATATATA
1 ATAAAAAATAT-AAT-TATT
3777 ATAAAAAA
1 ATAAAAAA
3785 ACATAATTTG
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
17 16 0.41
18 8 0.21
19 8 0.21
20 7 0.18
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (18 bp):
ATAAAAAATATAATTATT
Found at i:3757 original size:17 final size:18
Alignment explanation
Indices: 3735--3783 Score: 73
Period size: 17 Copynumber: 2.7 Consensus size: 18
3725 AACAATATCT
3735 ATTATTATAAAAATAT-A
1 ATTATTATAAAAATATAA
3752 ATTATTATAAAAATATAA
1 ATTATTATAAAAATATAA
*
3770 ATATATAATAAAAA
1 AT-TATTATAAAAA
3784 AACATAATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
17 16 0.55
18 3 0.10
19 10 0.34
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
ATTATTATAAAAATATAA
Found at i:3862 original size:22 final size:22
Alignment explanation
Indices: 3836--3879 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
3826 TCTTTGTCTA
3836 AGACTTGATTTTTT-TTCTAAAT
1 AGACTTGATTTTTTGTT-TAAAT
3858 AGACTTGATTTTTTGTTTAAAT
1 AGACTTGATTTTTTGTTTAAAT
3880 TTATTTTTCG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 19 0.90
23 2 0.10
ACGTcount: A:0.27, C:0.07, G:0.11, T:0.55
Consensus pattern (22 bp):
AGACTTGATTTTTTGTTTAAAT
Found at i:7580 original size:2 final size:2
Alignment explanation
Indices: 7575--7618 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
7565 CCATTTGAAC
*
7575 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
7617 AT
1 AT
7619 GCAGCATGAA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:7937 original size:18 final size:17
Alignment explanation
Indices: 7882--7937 Score: 55
Period size: 17 Copynumber: 3.3 Consensus size: 17
7872 CGGTTTAACT
7882 TATTTTT-TA-ATTATA
1 TATTTTTATATATTATA
*
7897 TAATTTTTAT-TATCTTTA
1 T-ATTTTTATATAT-TATA
7915 TATTTTTATATATTATA
1 TATTTTTATATATTATA
7932 TCATTT
1 T-ATTT
7938 AAAAAATAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
15 1 0.03
16 6 0.18
17 15 0.45
18 11 0.33
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (17 bp):
TATTTTTATATATTATA
Found at i:7950 original size:23 final size:24
Alignment explanation
Indices: 7924--7975 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
7914 ATATTTTTAT
*
7924 ATATTATATCAT-TTAAAAAATAA
1 ATATTATATAATATTAAAAAATAA
* *
7947 ATA-TATATAATATTATAATATAA
1 ATATTATATAATATTAAAAAATAA
7970 ATATTA
1 ATATTA
7976 AAAACTATGT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
22 7 0.29
23 15 0.62
24 2 0.08
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (24 bp):
ATATTATATAATATTAAAAAATAA
Found at i:8024 original size:21 final size:20
Alignment explanation
Indices: 7998--8043 Score: 58
Period size: 19 Copynumber: 2.2 Consensus size: 20
7988 AGTTATATAT
7998 ATTTTAAAATTTAGTAAAAA-A
1 ATTTT-AAA-TTAGTAAAAATA
*
8019 ATTTTAAATTATTAAAAATA
1 ATTTTAAATTAGTAAAAATA
8039 ATTTT
1 ATTTT
8044 TTAATATATG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 9 0.39
20 9 0.39
21 5 0.22
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (20 bp):
ATTTTAAATTAGTAAAAATA
Found at i:8080 original size:10 final size:10
Alignment explanation
Indices: 8065--8119 Score: 51
Period size: 10 Copynumber: 5.4 Consensus size: 10
8055 ATATAATATG
8065 AATAAATTTA
1 AATAAATTTA
8075 AATAAATTTA
1 AATAAATTTA
*
8085 AATTATCTATTT-
1 AA-TA--AATTTA
*
8097 -ATAAATATA
1 AATAAATTTA
8106 AATAAATTTA
1 AATAAATTTA
8116 AATA
1 AATA
8120 TAAAATAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
8 3 0.08
10 26 0.72
11 3 0.08
13 4 0.11
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (10 bp):
AATAAATTTA
Found at i:8130 original size:18 final size:16
Alignment explanation
Indices: 8067--8133 Score: 57
Period size: 16 Copynumber: 4.1 Consensus size: 16
8057 ATAATATGAA
*
8067 TAAATTTAAATAAATT
1 TAAATATAAATAAATT
** *
8083 TAAAT-TATCT-ATTT
1 TAAATATAAATAAATT
8097 ATAAATATAAATAAATT
1 -TAAATATAAATAAATT
8114 TAAATATAAAATAAAATT
1 TAAATAT-AAAT-AAATT
8132 TA
1 TA
8134 TATTTTAAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
14 3 0.08
15 8 0.20
16 15 0.38
17 7 0.17
18 7 0.17
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (16 bp):
TAAATATAAATAAATT
Found at i:8143 original size:18 final size:17
Alignment explanation
Indices: 8098--8148 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 17
8088 TATCTATTTA
8098 TAAATA-TAAATAAATT
1 TAAATATTAAATAAATT
*
8114 TAAATATAAAATAAAATT
1 TAAATATTAAAT-AAATT
* *
8132 TATATTTTAAATTAAAT
1 TAAATATTAAA-TAAAT
8149 CAAATTTACT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
16 6 0.21
17 4 0.14
18 17 0.61
19 1 0.04
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TAAATATTAAATAAATT
Found at i:8143 original size:41 final size:42
Alignment explanation
Indices: 8047--8156 Score: 120
Period size: 41 Copynumber: 2.6 Consensus size: 42
8037 TAATTTTTTA
* * * *
8047 ATATATGTATATAATATGAATAAATTT-AAATAAATTTAAATT
1 ATATATTTATA-AATATAAATAAATTTAAAATAAAATAAAATT
*
8089 ATCTATTTATAAATATAAATAAATTTAAATATAAAATAAAATT
1 ATATATTTATAAATATAAATAAATTTAAA-ATAAAATAAAATT
8132 -TATATTT-TAAAT-TAAATCAAATTTA
1 ATATATTTATAAATATAAAT-AAATTTA
8157 CTCATCCCAA
Statistics
Matches: 59, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
40 5 0.08
41 26 0.44
42 17 0.29
43 11 0.19
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (42 bp):
ATATATTTATAAATATAAATAAATTTAAAATAAAATAAAATT
Found at i:9419 original size:16 final size:17
Alignment explanation
Indices: 9398--9430 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
9388 ATAAGGTTGG
9398 AACAAA-AAAAAACAAA
1 AACAAACAAAAAACAAA
9414 AACAAACAAAAAACAAA
1 AACAAACAAAAAACAAA
9431 GAACTAGAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (17 bp):
AACAAACAAAAAACAAA
Found at i:13785 original size:13 final size:14
Alignment explanation
Indices: 13754--13791 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
13744 CTTCTTACTC
13754 ATATCAAA-AT-AT
1 ATATCAAATATAAT
13766 ATATCAAATATAAT
1 ATATCAAATATAAT
13780 -TATCAAATATAA
1 ATATCAAATATAA
13792 ATTCTTTAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 8 0.33
13 14 0.58
14 2 0.08
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.34
Consensus pattern (14 bp):
ATATCAAATATAAT
Found at i:14018 original size:31 final size:32
Alignment explanation
Indices: 13983--14071 Score: 94
Period size: 31 Copynumber: 2.7 Consensus size: 32
13973 ATATTATAAT
13983 TATATTTAAAATATTTTTTATATAAAATTT-A
1 TATATTTAAAATATTTTTTATATAAAATTTAA
*
14014 TATA-TTAATAAT-TTATATTATATAAAATTTAA
1 TATATTTAA-AATATT-TTTTATATAAAATTTAA
*
14046 AATATTTAAATATATTTATATTATAT
1 TATATTTAAA-ATATTT-T-TTATAT
14072 TTTAATTTTT
Statistics
Matches: 47, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
30 6 0.13
31 21 0.45
32 5 0.11
33 7 0.15
34 2 0.04
35 6 0.13
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (32 bp):
TATATTTAAAATATTTTTTATATAAAATTTAA
Found at i:14928 original size:13 final size:13
Alignment explanation
Indices: 14878--14930 Score: 52
Period size: 13 Copynumber: 3.8 Consensus size: 13
14868 AATTTTTAAT
*
14878 AAAAATTTTAATA
1 AAAAATTTAAATA
* *
14891 AAAAAATCAAATTA
1 AAAAATTTAAA-TA
14905 AATTAAATTTAAATA
1 AA--AAATTTAAATA
14920 AAAAATTTAAA
1 AAAAATTTAAA
14931 AATTCGGATC
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
13 17 0.53
14 4 0.12
15 4 0.12
16 7 0.22
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (13 bp):
AAAAATTTAAATA
Found at i:16235 original size:16 final size:15
Alignment explanation
Indices: 16185--16227 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
16175 TTATTATATA
* *
16185 TAATAATATTATAATT
1 TAATAATA-TAAAAAT
16201 TAATAATATAAAAAT
1 TAATAATATAAAAAT
16216 TAATAA-ATAAAA
1 TAATAATATAAAA
16228 TTATTAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 6 0.24
15 11 0.44
16 8 0.32
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
TAATAATATAAAAAT
Found at i:16458 original size:21 final size:20
Alignment explanation
Indices: 16434--16481 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
16424 ATTTTAAAAA
16434 TTATAA-TAATATTTATATATT
1 TTATAATTAA-ATTTA-ATATT
16455 TTATAATTAAATTTAAT-TT
1 TTATAATTAAATTTAATATT
16474 TT-TAATTA
1 TTATAATTA
16482 TTAAATATCA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
18 6 0.23
19 4 0.15
20 2 0.08
21 11 0.42
22 3 0.12
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
TTATAATTAAATTTAATATT
Found at i:16722 original size:17 final size:15
Alignment explanation
Indices: 16687--16716 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
16677 ATTTAAATTT
*
16687 ATATTCATAAACTTA
1 ATATTAATAAACTTA
16702 ATATTAATAAACTTA
1 ATATTAATAAACTTA
16717 TAATATACAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (15 bp):
ATATTAATAAACTTA
Found at i:17463 original size:40 final size:39
Alignment explanation
Indices: 17386--17464 Score: 140
Period size: 39 Copynumber: 2.0 Consensus size: 39
17376 TTAAAAAAAA
*
17386 TCTTAAAATAATTAAAAAGTAAATAAGTTTTTATTTTTT
1 TCTTAAAATAATTAAAAAATAAATAAGTTTTTATTTTTT
*
17425 TCTTAAAATAATTAAAAAATAAATGAGTTTTTATTTTTT
1 TCTTAAAATAATTAAAAAATAAATAAGTTTTTATTTTTT
17464 T
1 T
17465 GATCTATTAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.49
Consensus pattern (39 bp):
TCTTAAAATAATTAAAAAATAAATAAGTTTTTATTTTTT
Found at i:18225 original size:18 final size:17
Alignment explanation
Indices: 18202--18245 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
18192 ATGTAATATT
18202 ATATAATATAAATAAAAA
1 ATATAATATAAAT-AAAA
* *
18220 ATATAAAAT-AATTAAA
1 ATATAATATAAATAAAA
18236 ATATAATATA
1 ATATAATATA
18246 TATTTATTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
16 11 0.50
17 3 0.14
18 8 0.36
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
ATATAATATAAATAAAA
Found at i:18283 original size:29 final size:28
Alignment explanation
Indices: 18226--18290 Score: 69
Period size: 29 Copynumber: 2.3 Consensus size: 28
18216 AAAAATATAA
***
18226 AATAATTAAAATATAATATATATTTATT
1 AATAATTAAAATATAATATATACAAATT
18254 AATATATTAAAATAT-ATATGATACAAATT
1 AATA-ATTAAAATATAATAT-ATACAAATT
*
18283 AAGAATTA
1 AATAATTA
18291 TTCAAAAATG
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
28 12 0.39
29 19 0.61
ACGTcount: A:0.55, C:0.02, G:0.03, T:0.40
Consensus pattern (28 bp):
AATAATTAAAATATAATATATACAAATT
Found at i:18737 original size:24 final size:24
Alignment explanation
Indices: 18692--18737 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
18682 TTATTTAATT
*
18692 AATATTTCAAAATTTTGAATATTA
1 AATATTTCAAAATTTTAAATATTA
*
18716 AATATTT-ATAATTTTAACATAT
1 AATATTTCAAAATTTTAA-ATAT
18738 ACATTTGAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (24 bp):
AATATTTCAAAATTTTAAATATTA
Found at i:19823 original size:27 final size:27
Alignment explanation
Indices: 19768--19850 Score: 91
Period size: 27 Copynumber: 3.1 Consensus size: 27
19758 ATTACATTCG
* *
19768 ATAATTTATA-TATTTATATTTTTATA
1 ATAATTTATATTATATATATTTTTAAA
19794 ATAATTTATATTATA-ATTATTTTTAAA
1 ATAATTTATATTATATA-TATTTTTAAA
*
19821 AT-ATTATATATTTTTATATATTTTTAAA
1 ATAATT-TATA-TTATATATATTTTTAAA
19849 AT
1 AT
19851 TTTTATTTAT
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
26 14 0.29
27 18 0.37
28 16 0.33
29 1 0.02
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (27 bp):
ATAATTTATATTATATATATTTTTAAA
Found at i:19839 original size:10 final size:10
Alignment explanation
Indices: 19824--19911 Score: 69
Period size: 9 Copynumber: 9.2 Consensus size: 10
19814 TTTTAAAATA
19824 TTATATATTT
1 TTATATATTT
19834 TTATATATTT
1 TTATATATTT
*
19844 TTA-AAATTT
1 TTATATATTT
*
19853 TTATTTA-TT
1 TTATATATTT
*
19862 TTATA-ATAT
1 TTATATATTT
19871 TTATATTATTT
1 TTATA-TATTT
**
19882 TT-TATATAA
1 TTATATATTT
*
19891 TAATATATTT
1 TTATATATTT
*
19901 TAAT-TATTT
1 TTATATATTT
19910 TT
1 TT
19912 TTATGTTATG
Statistics
Matches: 61, Mismatches: 12, Indels: 11
0.73 0.14 0.13
Matches are distributed among these distances:
8 1 0.02
9 30 0.49
10 25 0.41
11 5 0.08
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (10 bp):
TTATATATTT
Found at i:19861 original size:29 final size:28
Alignment explanation
Indices: 19783--19872 Score: 89
Period size: 29 Copynumber: 3.2 Consensus size: 28
19773 TTATATATTT
*
19783 ATATTTTTATAATAATT-TATA--TTATA
1 ATATTTTTAAAAT-ATTATATATTTTATA
19809 ATTATTTTTAAAATATTATATATTTT-TA
1 A-TATTTTTAAAATATTATATATTTTATA
* *
19837 TATATTTTTAAAATTTTTATTTATTTTATA
1 -ATATTTTTAAAA-TATTATATATTTTATA
19867 ATATTT
1 ATATTT
19873 ATATTATTTT
Statistics
Matches: 54, Mismatches: 3, Indels: 11
0.79 0.04 0.16
Matches are distributed among these distances:
26 4 0.07
27 15 0.28
28 13 0.24
29 20 0.37
30 2 0.04
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (28 bp):
ATATTTTTAAAATATTATATATTTTATA
Found at i:19882 original size:28 final size:29
Alignment explanation
Indices: 19851--19920 Score: 74
Period size: 26 Copynumber: 2.5 Consensus size: 29
19841 TTTTTAAAAT
*
19851 TTTTATTTATTTTATAATAT-TTAT-ATTA
1 TTTT-TTTATATTATAATATATTATAATTA
* *
19879 -TTTTTTATATAATAATATATTTTAATTA
1 TTTTTTTATATTATAATATATTATAATTA
*
19907 TTTTTTTATGTTAT
1 TTTTTTTATATTAT
19921 GCCTAAAATA
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
26 13 0.38
27 6 0.18
28 4 0.12
29 11 0.32
ACGTcount: A:0.31, C:0.00, G:0.01, T:0.67
Consensus pattern (29 bp):
TTTTTTTATATTATAATATATTATAATTA
Found at i:19902 original size:47 final size:47
Alignment explanation
Indices: 19768--19910 Score: 125
Period size: 47 Copynumber: 3.0 Consensus size: 47
19758 ATTACATTCG
* *
19768 ATAAT-TTATATATTTATATTTTTATAATAAT-TTATATTATAATTATTTT
1 ATAATATT-TATA-TTAT-TTTTTAT-ATAATAATATATTTTAATTATTTT
* ** * *
19817 -TAAAATATTATA-TATTTTTATATATTTTTAAAAT-TTTTATTTATTTT
1 ATAATAT-TTATATTATTTTT-TATA-TAATAATATATTTTAATTATTTT
19864 ATAATATTTATATTATTTTTTATATAATAATATATTTTAATTATTTT
1 ATAATATTTATATTATTTTTTATATAATAATATATTTTAATTATTTT
19911 TTTATGTTAT
Statistics
Matches: 74, Mismatches: 12, Indels: 18
0.71 0.12 0.17
Matches are distributed among these distances:
46 11 0.15
47 40 0.54
48 17 0.23
49 5 0.07
50 1 0.01
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (47 bp):
ATAATATTTATATTATTTTTTATATAATAATATATTTTAATTATTTT
Found at i:20513 original size:5 final size:5
Alignment explanation
Indices: 20503--20533 Score: 53
Period size: 5 Copynumber: 6.0 Consensus size: 5
20493 TTTACAGTAT
20503 AATTA AATTA AATTA AATTA AATTTA AATTA
1 AATTA AATTA AATTA AATTA AA-TTA AATTA
20534 TAAAAAATTG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 20 0.80
6 5 0.20
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
AATTA
Found at i:20523 original size:15 final size:16
Alignment explanation
Indices: 20503--20533 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
20493 TTTACAGTAT
20503 AATTAAA-TTAAATTA
1 AATTAAATTTAAATTA
20518 AATTAAATTTAAATTA
1 AATTAAATTTAAATTA
20534 TAAAAAATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
AATTAAATTTAAATTA
Found at i:21174 original size:22 final size:23
Alignment explanation
Indices: 21147--21208 Score: 65
Period size: 22 Copynumber: 2.7 Consensus size: 23
21137 TATTTATTTA
21147 ATATAAATTATAA-AAAATAAAT
1 ATATAAATTATAATAAAATAAAT
* *
21169 ATATAATAATATAATAATATAAAT
1 ATATAA-ATTATAATAAAATAAAT
* *
21193 ATA-AAAATATATTAAA
1 ATATAAATTATAATAAA
21209 TTATTTATAT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
22 15 0.44
23 8 0.24
24 11 0.32
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (23 bp):
ATATAAATTATAATAAAATAAAT
Found at i:21179 original size:30 final size:32
Alignment explanation
Indices: 21145--21204 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
21135 TTTATTTATT
*
21145 TAATATAA-ATTATAAA-A-AATAAATATATAA
1 TAATATAATAATATAAATATAA-AAATATATAA
21175 TAATATAATAATATAAATATAAAAATATAT
1 TAATATAATAATATAAATATAAAAATATAT
21205 TAAATTATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
30 8 0.31
31 7 0.27
32 9 0.35
33 2 0.08
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (32 bp):
TAATATAATAATATAAATATAAAAATATATAA
Found at i:21474 original size:38 final size:38
Alignment explanation
Indices: 21432--21507 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
21422 TGACTTGACC
21432 GATAGTGCTTTAAATAAATAAAGAATTAAAGGAAAACA
1 GATAGTGCTTTAAATAAATAAAGAATTAAAGGAAAACA
21470 GATAGTGCTTTAAATAAATAAAGAATTAAAGGAAAACA
1 GATAGTGCTTTAAATAAATAAAGAATTAAAGGAAAACA
21508 AAAATGAAGC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.55, C:0.05, G:0.16, T:0.24
Consensus pattern (38 bp):
GATAGTGCTTTAAATAAATAAAGAATTAAAGGAAAACA
Found at i:41245 original size:10 final size:10
Alignment explanation
Indices: 41217--41277 Score: 50
Period size: 10 Copynumber: 5.6 Consensus size: 10
41207 AAAAAAAACT
41217 TAAATATAATA
1 TAAA-ATAATA
*
41228 AAAAATAATA
1 TAAAATAATA
* *
41238 TAACATAACA
1 TAAAATAATA
41248 TAATTAATAATA
1 TAA--AATAATA
41260 TAAATATAATA
1 TAAA-ATAATA
41271 TGAAAAT
1 T-AAAAT
41278 TTTTCAATAT
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
10 17 0.43
11 12 0.30
12 11 0.28
ACGTcount: A:0.64, C:0.03, G:0.02, T:0.31
Consensus pattern (10 bp):
TAAAATAATA
Found at i:44561 original size:29 final size:29
Alignment explanation
Indices: 44529--44584 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
44519 AAGATGAAAA
44529 TAAATATTA-TAAATATTAAAATTTAAATT
1 TAAAT-TTACTAAATATTAAAATTTAAATT
* * *
44558 TAAATTTACTGAATATTACATTTTAAA
1 TAAATTTACTAAATATTAAAATTTAAA
44585 AATAATTATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 3 0.13
29 20 0.87
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.45
Consensus pattern (29 bp):
TAAATTTACTAAATATTAAAATTTAAATT
Found at i:44824 original size:2 final size:2
Alignment explanation
Indices: 44817--44845 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
44807 ATTTCAAGTT
44817 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
44846 TTGGATCAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:48486 original size:2 final size:2
Alignment explanation
Indices: 48481--48532 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
48471 TATTTAATGT
48481 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
48523 TA TA TA TA TA
1 TA TA TA TA TA
48533 GAAGATCATA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:50724 original size:18 final size:17
Alignment explanation
Indices: 50683--50737 Score: 64
Period size: 17 Copynumber: 3.4 Consensus size: 17
50673 ACGAATATCT
50683 TAAAATTTATAT-AATA
1 TAAAATTTATATAAATA
50699 T-AAA-TTAT-TAATATA
1 TAAAATTTATATAA-ATA
50714 TCAAAATTTATATAAATA
1 T-AAAATTTATATAAATA
50732 TAAAAT
1 TAAAAT
50738 ATTTTAAACA
Statistics
Matches: 33, Mismatches: 0, Indels: 11
0.75 0.00 0.25
Matches are distributed among these distances:
13 1 0.03
14 5 0.15
15 7 0.21
16 1 0.03
17 8 0.24
18 8 0.24
19 3 0.09
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (17 bp):
TAAAATTTATATAAATA
Found at i:50770 original size:20 final size:19
Alignment explanation
Indices: 50745--50794 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
50735 AATATTTTAA
50745 ACATGATTACGATATAATAT
1 ACATGATTACGATATAA-AT
* * *
50765 ATATGAATAAGATATAAAT
1 ACATGATTACGATATAAAT
50784 ACATGAATTAC
1 ACATG-ATTAC
50795 TAAGTACTTG
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.50, C:0.08, G:0.10, T:0.32
Consensus pattern (19 bp):
ACATGATTACGATATAAAT
Found at i:51555 original size:3 final size:3
Alignment explanation
Indices: 51549--51579 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
51539 AACCAAACAA
51549 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
51580 TTGTGATGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:52619 original size:22 final size:22
Alignment explanation
Indices: 52594--52635 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
52584 GTGAAATGAC
*
52594 ATTTTTTTTAAAATTTTTAATA
1 ATTTTATTTAAAATTTTTAATA
*
52616 ATTTTATTTAAATTTTTTAA
1 ATTTTATTTAAAATTTTTAA
52636 AAAAATTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (22 bp):
ATTTTATTTAAAATTTTTAATA
Found at i:52790 original size:20 final size:21
Alignment explanation
Indices: 52764--52824 Score: 63
Period size: 20 Copynumber: 2.9 Consensus size: 21
52754 TAAAATGATG
52764 AATAAAATTATTAATTTT-TA
1 AATAAAATTATTAATTTTATA
*
52784 CATAAAA-TATATAATTATTATA
1 AATAAAATTAT-TAATT-TTATA
*
52806 AATAATATTAATTAATTTT
1 AATAAAATT-ATTAATTTT
52825 GAAAGATGTA
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
19 3 0.09
20 11 0.33
21 2 0.06
22 9 0.27
23 6 0.18
24 2 0.06
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (21 bp):
AATAAAATTATTAATTTTATA
Found at i:53019 original size:35 final size:35
Alignment explanation
Indices: 52937--53024 Score: 87
Period size: 35 Copynumber: 2.6 Consensus size: 35
52927 TAGACATCAA
* * *
52937 TTAAAATT-TTTTTATT-ATTTTAAAAAATTATAT
1 TTAATATTATTTTTATTAAATTTAAAAAAATATAT
*
52970 TTAATATTAATTTTATTAAATTTAAAAATAATATA-
1 TTAATATTATTTTTATTAAATTTAAAAA-AATATAT
53005 TTAAT-TATATTTTTA-TAAAT
1 TTAATAT-TATTTTTATTAAAT
53025 ATATTAATTT
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
33 7 0.15
34 13 0.28
35 21 0.46
36 5 0.11
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (35 bp):
TTAATATTATTTTTATTAAATTTAAAAAAATATAT
Found at i:53046 original size:23 final size:23
Alignment explanation
Indices: 52999--53042 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
52989 ATTTAAAAAT
* *
52999 AATATATTAATTATATTTTTATA
1 AATATATTAATTATAATATTATA
53022 AATATATTAATT-TAATATTAT
1 AATATATTAATTATAATATTAT
53043 TAAACACTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
AATATATTAATTATAATATTATA
Done.