Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1308
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: 33809
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:3453 original size:38 final size:38
Alignment explanation
Indices: 3399--3474 Score: 109
Period size: 38 Copynumber: 2.0 Consensus size: 38
3389 TGACAATTCT
*
3399 TCTTGCAATGATCCAAGA-AGAAAACAAACTATTAAGAA
1 TCTTGCAATGACCCAAGATA-AAAACAAACTATTAAGAA
* *
3437 TCTTGCAATTACCCAAGATAAAAAGAAACTATTAAGAA
1 TCTTGCAATGACCCAAGATAAAAACAAACTATTAAGAA
3475 GCATATAGAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
38 33 0.97
39 1 0.03
ACGTcount: A:0.50, C:0.16, G:0.12, T:0.22
Consensus pattern (38 bp):
TCTTGCAATGACCCAAGATAAAAACAAACTATTAAGAA
Found at i:5713 original size:56 final size:58
Alignment explanation
Indices: 5627--5741 Score: 198
Period size: 56 Copynumber: 2.0 Consensus size: 58
5617 GATGCCAACA
*
5627 CCAAACACAGATCTGCCACGAAGTAGAT-AAAGAAAAGAAACAAGA-CATTATAAGGG
1 CCAAAAACAGATCTGCCACGAAGTAGATAAAAGAAAAGAAACAAGACCATTATAAGGG
*
5683 CCAAAAACAGATCTGCCACGAAGTAGATAAAAGAAAAGAACCAAGACCATTATAAGGG
1 CCAAAAACAGATCTGCCACGAAGTAGATAAAAGAAAAGAAACAAGACCATTATAAGGG
5741 C
1 C
5742 TATGGCACAC
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
56 27 0.49
57 16 0.29
58 12 0.22
ACGTcount: A:0.50, C:0.19, G:0.19, T:0.12
Consensus pattern (58 bp):
CCAAAAACAGATCTGCCACGAAGTAGATAAAAGAAAAGAAACAAGACCATTATAAGGG
Found at i:6566 original size:14 final size:14
Alignment explanation
Indices: 6546--6579 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
6536 TTCAGATTGC
6546 AAGAAGAAG-AAGA
1 AAGAAGAAGAAAGA
6559 AGAGAAGAAGAAAGA
1 A-AGAAGAAGAAAGA
6574 AAGAAG
1 AAGAAG
6580 CGACTTACAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 1 0.05
14 13 0.68
15 5 0.26
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (14 bp):
AAGAAGAAGAAAGA
Found at i:7150 original size:20 final size:20
Alignment explanation
Indices: 7114--7152 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
7104 TTTTAATAGT
*
7114 AAATATAATATATAATAATA
1 AAATATAATATAAAATAATA
7134 AAATATAAT-TAAAAATAAT
1 AAATATAATAT-AAAATAAT
7153 TTAATTATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 1 0.06
20 16 0.94
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
AAATATAATATAAAATAATA
Found at i:7235 original size:17 final size:19
Alignment explanation
Indices: 7215--7250 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
7205 TTAATTTATT
7215 AAAATTAT-AT-AAATATA
1 AAAATTATAATAAAATATA
7232 AAAATTATAATAAAATATA
1 AAAATTATAATAAAATATA
7251 TTTATATACA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.47
18 2 0.12
19 7 0.41
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
AAAATTATAATAAAATATA
Found at i:7250 original size:27 final size:28
Alignment explanation
Indices: 7214--7266 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
7204 ATTAATTTAT
7214 TAAAATTATATAAATATAAAAATTATAA
1 TAAAATTATATAAATATAAAAATTATAA
** *
7242 TAAAA-TATATTTATATACAAATTAT
1 TAAAATTATATAAATATAAAAATTAT
7267 CGAGTCTTCC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 17 0.77
28 5 0.23
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (28 bp):
TAAAATTATATAAATATAAAAATTATAA
Found at i:7798 original size:10 final size:10
Alignment explanation
Indices: 7775--7842 Score: 54
Period size: 10 Copynumber: 7.1 Consensus size: 10
7765 CTATAAACAA
*
7775 TTATATTATAT
1 TTATA-TATTT
7786 TTATATATTT
1 TTATATATTT
*
7796 TTATATATTA
1 TTATATATTT
* *
7806 TAAT-TATAT
1 TTATATATTT
*
7815 TTA-ATA-TA
1 TTATATATTT
7823 TTATATATTT
1 TTATATATTT
7833 TTATA-ATTT
1 TTATATATTT
7842 T
1 T
7843 AATTTATTTA
Statistics
Matches: 45, Mismatches: 9, Indels: 8
0.73 0.15 0.13
Matches are distributed among these distances:
8 3 0.07
9 15 0.33
10 22 0.49
11 5 0.11
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (10 bp):
TTATATATTT
Found at i:7813 original size:29 final size:26
Alignment explanation
Indices: 7774--7831 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 26
7764 ACTATAAACA
*
7774 ATTATATTATATTTATATATTTTTATAT
1 ATTATATTATATTTA-ATA-TATTATAT
7802 ATTATAATTATATTTAATATATTATAT
1 ATTAT-ATTATATTTAATATATTATAT
7829 ATT
1 ATT
7832 TTTATAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
27 10 0.36
28 8 0.29
29 10 0.36
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (26 bp):
ATTATATTATATTTAATATATTATAT
Found at i:7821 original size:7 final size:8
Alignment explanation
Indices: 7781--7849 Score: 51
Period size: 8 Copynumber: 9.1 Consensus size: 8
7771 ACAATTATAT
7781 TATATTTA
1 TATATTTA
*
7789 TATATTTT
1 TATATTTA
7797 TATATATTA
1 TATAT-TTA
7806 TA-A-TTA
1 TATATTTA
*
7812 TAT-TTAA
1 TATATTTA
7819 TATA-TTA
1 TATATTTA
*
7826 TATATTTT
1 TATATTTA
7834 TATAATTT-
1 TAT-ATTTA
7842 TA-ATTTA
1 TATATTTA
7849 T
1 T
7850 TTATCACTGA
Statistics
Matches: 49, Mismatches: 5, Indels: 15
0.71 0.07 0.22
Matches are distributed among these distances:
6 9 0.18
7 12 0.24
8 20 0.41
9 8 0.16
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
TATATTTA
Found at i:7833 original size:37 final size:35
Alignment explanation
Indices: 7773--7852 Score: 112
Period size: 37 Copynumber: 2.3 Consensus size: 35
7763 AACTATAAAC
7773 AATTATA-TT-ATATTTATATATTTTTATATATTAT
1 AATTATATTTAATATTTATATATTTTTATA-ATTAT
*
7807 AATTATATTTAATATATTATATATTTTTATAATTTT
1 AATTATATTTAATAT-TTATATATTTTTATAATTAT
7843 AATT-TATTTA
1 AATTATATTTA
7853 TCACTGAATA
Statistics
Matches: 42, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
34 7 0.17
35 8 0.19
36 12 0.29
37 15 0.36
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (35 bp):
AATTATATTTAATATTTATATATTTTTATAATTAT
Found at i:7853 original size:27 final size:28
Alignment explanation
Indices: 7774--7853 Score: 76
Period size: 27 Copynumber: 2.9 Consensus size: 28
7764 ACTATAAACA
* *
7774 ATTAT-ATTATATTTATATATTTTTATAT
1 ATTATAATAATATTTA-ATATATTTATAT
*
7802 ATTATAATTATATTTAATATA-TTATAT
1 ATTATAATAATATTTAATATATTTATAT
* * *
7829 ATTTTTATAAT-TTTAATTTATTTAT
1 ATTATAATAATATTTAATATATTTAT
7854 CACTGAATAT
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
26 8 0.18
27 18 0.40
28 9 0.20
29 10 0.22
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (28 bp):
ATTATAATAATATTTAATATATTTATAT
Found at i:8398 original size:4 final size:4
Alignment explanation
Indices: 8389--8413 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
8379 TATGGCGGTT
8389 GATA GATA GATA GATA GATA GATA G
1 GATA GATA GATA GATA GATA GATA G
8414 CAATCGAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.28, T:0.24
Consensus pattern (4 bp):
GATA
Found at i:13090 original size:2 final size:2
Alignment explanation
Indices: 13083--13119 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
13073 GCTTATTAAG
*
13083 TC TC TC TC TC TT TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
13120 TTAATTTTCG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.46, G:0.00, T:0.54
Consensus pattern (2 bp):
TC
Found at i:18327 original size:25 final size:23
Alignment explanation
Indices: 18290--18338 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 23
18280 TATTATTAAA
18290 TAATATTGATATAATATTTAATATT
1 TAATATTGATATAATA--TAATATT
18315 TAATATT-ATTATAATATAATATT
1 TAATATTGA-TATAATATAATATT
18338 T
1 T
18339 TTTATAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 8 0.35
24 1 0.04
25 14 0.61
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (23 bp):
TAATATTGATATAATATAATATT
Found at i:18337 original size:41 final size:36
Alignment explanation
Indices: 18253--18330 Score: 97
Period size: 38 Copynumber: 2.1 Consensus size: 36
18243 AAAATAACCA
*
18253 AAATAA-A-TGATAAATATTTCACATTAATATTATT
1 AAATAATATTGATAAATATTTAACATTAATATTATT
*
18287 AAATAATATTGATATAATATTTAATATTTAATATTATT
1 AAATAATATTGATA-AATATTTAACA-TTAATATTATT
18325 ATAATA
1 A-AATA
18331 TAATATTTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
34 6 0.16
35 1 0.03
36 5 0.14
37 9 0.24
38 12 0.32
39 4 0.11
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (36 bp):
AAATAATATTGATAAATATTTAACATTAATATTATT
Found at i:18417 original size:47 final size:46
Alignment explanation
Indices: 18315--18432 Score: 109
Period size: 47 Copynumber: 2.5 Consensus size: 46
18305 ATTTAATATT
*
18315 TAATA-TTATTATAATATAATATTTTTTATAATAATAATAATAATA
1 TAATATTTATTATAATATAATATTTATTATAATAATAATAATAATA
* *
18360 TAATATTTTATTATATATCATAA-ATTTATTA-AATATTAA-ATATTATA
1 TAATA-TTTATTATA-AT-ATAATATTTATTATAATAATAATA-ATAATA
18407 TCAATATTTATTTGATAATATTAATA
1 T-AATATTTA-TT-ATAATA-TAATA
18433 AAAATATTTA
Statistics
Matches: 60, Mismatches: 3, Indels: 16
0.76 0.04 0.20
Matches are distributed among these distances:
45 5 0.08
46 1 0.02
47 26 0.43
48 20 0.33
49 8 0.13
ACGTcount: A:0.47, C:0.02, G:0.01, T:0.50
Consensus pattern (46 bp):
TAATATTTATTATAATATAATATTTATTATAATAATAATAATAATA
Found at i:18928 original size:12 final size:12
Alignment explanation
Indices: 18911--18938 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
18901 TTAATTAAAG
18911 TTTATTTTATTA
1 TTTATTTTATTA
18923 TTTATTTTATTA
1 TTTATTTTATTA
18935 TTTA
1 TTTA
18939 AATATTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (12 bp):
TTTATTTTATTA
Found at i:18950 original size:24 final size:24
Alignment explanation
Indices: 18923--19019 Score: 76
Period size: 24 Copynumber: 4.1 Consensus size: 24
18913 TATTTTATTA
* *
18923 TTTATTTTATTATTTAAATATTAT
1 TTTATATTATTATTTAAATATAAT
*
18947 TTTATATTAATATTT--ATATAAT
1 TTTATATTATTATTTAAATATAAT
* *
18969 TTTATAATTA-AATTTAAATAAAAAT
1 TTTAT-ATTATTATTTAAAT-ATAAT
* *
18994 ATTATTTTATTA-TTAAATAATAAT
1 TTTATATTATTATTTAAAT-ATAAT
19018 TT
1 TT
19020 AAATAAATTA
Statistics
Matches: 58, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
22 15 0.26
23 4 0.07
24 30 0.52
25 9 0.16
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (24 bp):
TTTATATTATTATTTAAATATAAT
Found at i:18962 original size:12 final size:12
Alignment explanation
Indices: 18899--18984 Score: 51
Period size: 12 Copynumber: 7.4 Consensus size: 12
18889 TCAAGTTCAA
18899 ATTTA-ATTAA-
1 ATTTATATTAAT
* *
18909 AGTTTATTTTATT
1 A-TTTATATTAAT
* *
18922 ATTTATTTTATT
1 ATTTATATTAAT
18934 ATTTAAATATT-AT
1 ATTT--ATATTAAT
18947 -TTTATATTAAT
1 ATTTATATTAAT
18958 ATTTATA-TAAT
1 ATTTATATTAAT
18969 -TTTATAATTAA-
1 ATTTAT-ATTAAT
18980 ATTTA
1 ATTTA
18985 AATAAAAATA
Statistics
Matches: 62, Mismatches: 4, Indels: 18
0.74 0.05 0.21
Matches are distributed among these distances:
10 11 0.18
11 11 0.18
12 34 0.55
13 2 0.03
14 4 0.06
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.60
Consensus pattern (12 bp):
ATTTATATTAAT
Found at i:18970 original size:22 final size:22
Alignment explanation
Indices: 18940--18989 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
18930 TATTATTTAA
*
18940 ATATTATTTTAT-ATTAATATTT
1 ATATAATTTTATAATTAA-ATTT
18962 ATATAATTTTATAATTAAATTT
1 ATATAATTTTATAATTAAATTT
*
18984 AAATAA
1 ATATAA
18990 AAATATTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 20 0.80
23 5 0.20
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
ATATAATTTTATAATTAAATTT
Found at i:18995 original size:36 final size:36
Alignment explanation
Indices: 18955--19026 Score: 85
Period size: 36 Copynumber: 2.0 Consensus size: 36
18945 ATTTTATATT
*
18955 AATATTTATATAATT-TTATAATTA-AATTTAAATAAA
1 AATA-TTATATAATTATTA-AATAATAATTTAAATAAA
* *
18991 AATATTATTTTATTATTAAATAATAATTTAAATAAA
1 AATATTATATAATTATTAAATAATAATTTAAATAAA
19027 TTAAAATATT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
35 12 0.39
36 19 0.61
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (36 bp):
AATATTATATAATTATTAAATAATAATTTAAATAAA
Found at i:19027 original size:46 final size:51
Alignment explanation
Indices: 18938--19034 Score: 125
Period size: 52 Copynumber: 2.0 Consensus size: 51
18928 TTTATTATTT
*
18938 AAATATTATTTTATATTAATATTTATATAATTTTATAATTAAATTTAAATAA
1 AAATATTATTTTATATTAATA-TTATATAATTTTATAATTAAATTAAAATAA
18990 AAATATTATTTTATTATTAA-A-TA-ATAA-TTTA-AA-TAAATTAAAATA
1 AAATATTATTTTA-TATTAATATTATATAATTTTATAATTAAATTAAAATA
19035 TTTAAAGATC
Statistics
Matches: 43, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
46 11 0.26
47 2 0.05
48 4 0.09
49 4 0.09
50 2 0.05
52 14 0.33
53 6 0.14
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (51 bp):
AAATATTATTTTATATTAATATTATATAATTTTATAATTAAATTAAAATAA
Found at i:22566 original size:12 final size:11
Alignment explanation
Indices: 22541--22576 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
22531 AACAAATATG
22541 ATATATTTAAT
1 ATATATTTAAT
22552 ATATATTTAA-
1 ATATATTTAAT
*
22562 ATATAATTAAT
1 ATATATTTAAT
22573 ATAT
1 ATAT
22577 TATAATTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 9 0.39
11 14 0.61
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (11 bp):
ATATATTTAAT
Found at i:22841 original size:13 final size:13
Alignment explanation
Indices: 22823--22847 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
22813 TCCAAAAGAA
22823 TTTCGAATTTTTT
1 TTTCGAATTTTTT
22836 TTTCGAATTTTT
1 TTTCGAATTTTT
22848 AAGTTTCTCT
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:0.16, C:0.08, G:0.08, T:0.68
Consensus pattern (13 bp):
TTTCGAATTTTTT
Found at i:25340 original size:41 final size:42
Alignment explanation
Indices: 25295--25391 Score: 126
Period size: 46 Copynumber: 2.2 Consensus size: 42
25285 TGGATATATT
25295 TTAAA-CTTAGCTAATATATCA-TTTATAGTAATAACATTATA
1 TTAAATCTTAGCTAATATATCATTTTATAGTAATAA-ATTATA
*
25336 TTAAATGTAAAATAGCTAATATATCATTTTATAGTAATAAATTATA
1 TTAAATCT----TAGCTAATATATCATTTTATAGTAATAAATTATA
25382 TTAAATCTTA
1 TTAAATCTTA
25392 AATTAATAGT
Statistics
Matches: 48, Mismatches: 2, Indels: 11
0.79 0.03 0.18
Matches are distributed among these distances:
41 5 0.10
42 3 0.06
46 27 0.56
47 13 0.27
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.42
Consensus pattern (42 bp):
TTAAATCTTAGCTAATATATCATTTTATAGTAATAAATTATA
Found at i:25451 original size:2 final size:2
Alignment explanation
Indices: 25444--25474 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
25434 TATTATTGTG
25444 TA 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 TA T
25475 TTCTGTACAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:25985 original size:17 final size:16
Alignment explanation
Indices: 25947--25994 Score: 66
Period size: 17 Copynumber: 3.1 Consensus size: 16
25937 AATTATTAAA
25947 TTAAATTTAAAT-A-T
1 TTAAATTTAAATAATT
25961 TT-AATTTAAATAATT
1 TTAAATTTAAATAATT
25976 CTTAAATTTAAATAATT
1 -TTAAATTTAAATAATT
25993 TT
1 TT
25995 TATTTATTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
13 9 0.30
14 3 0.10
15 1 0.03
16 4 0.13
17 13 0.43
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (16 bp):
TTAAATTTAAATAATT
Found at i:29602 original size:23 final size:23
Alignment explanation
Indices: 29576--29698 Score: 54
Period size: 23 Copynumber: 5.6 Consensus size: 23
29566 TTCATCTTCT
29576 ATTTATATTATATTATATTTATA
1 ATTTATATTATATTATATTTATA
*
29599 ATTT-TAATA-ATTTATATTATATAA
1 ATTTATATTATA-TTATATT-TAT-A
29623 ATTT-TA--A-A--ATATTTATA
1 ATTTATATTATATTATATTTATA
* * *
29640 ATTTAT-GTAT-TATATGTTTAGA
1 ATTTATATTATAT-TATATTTATA
29662 GA-TTATATTATATTATAATTT-TA
1 -ATTTATATTATATTAT-ATTTATA
* *
29685 TTTTATGTTATATT
1 ATTTATATTATATT
29699 TTAATATTAT
Statistics
Matches: 77, Mismatches: 8, Indels: 30
0.67 0.07 0.26
Matches are distributed among these distances:
17 5 0.06
18 4 0.05
19 6 0.08
21 1 0.01
22 24 0.31
23 26 0.34
24 11 0.14
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (23 bp):
ATTTATATTATATTATATTTATA
Found at i:29612 original size:32 final size:33
Alignment explanation
Indices: 29576--29654 Score: 92
Period size: 32 Copynumber: 2.4 Consensus size: 33
29566 TTCATCTTCT
* *
29576 ATTTATATTATATTATA-TTTATAAT-TTTAATA
1 ATTTATATTATATTAAATTTTAAAATATTT-ATA
29608 ATTTATATTATA-TAAATTTTAAAATATTTATA
1 ATTTATATTATATTAAATTTTAAAATATTTATA
29640 ATTTATGTATTATAT
1 ATTTA--TATTATAT
29655 GTTTAGAGAT
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
31 3 0.08
32 27 0.68
33 3 0.08
34 7 0.17
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (33 bp):
ATTTATATTATATTAAATTTTAAAATATTTATA
Found at i:29690 original size:18 final size:17
Alignment explanation
Indices: 29664--29709 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
29654 TGTTTAGAGA
29664 TTATATTATATTATAATT
1 TTATATTATATTAT-ATT
* *
29682 TTATTTTATGTTATATT
1 TTATATTATATTATATT
29699 TTAATATTATA
1 TT-ATATTATA
29710 AAGTTTTAGA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (17 bp):
TTATATTATATTATATT
Found at i:29703 original size:23 final size:23
Alignment explanation
Indices: 29664--29708 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
29654 TGTTTAGAGA
*
29664 TTATATTATATTATAATTTTATT
1 TTATATTATATTATAATATTATT
* *
29687 TTATGTTATATTTTAATATTAT
1 TTATATTATATTATAATATTAT
29709 AAAGTTTTAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (23 bp):
TTATATTATATTATAATATTATT
Found at i:30365 original size:16 final size:16
Alignment explanation
Indices: 30344--30377 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
30334 TATCTCTCAA
30344 TACTCTCTCTGTGGAG
1 TACTCTCTCTGTGGAG
30360 TACTCTCTCTGTGGAG
1 TACTCTCTCTGTGGAG
30376 TA
1 TA
30378 TTATATTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.15, C:0.24, G:0.24, T:0.38
Consensus pattern (16 bp):
TACTCTCTCTGTGGAG
Done.