Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold891
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: 37259
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Found at i:1755 original size:18 final size:18
Alignment explanation
Indices: 1732--1766 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1722 TACATCGGCA
*
1732 CTTCAGAGATAGTGAGTG
1 CTTCAGAGATACTGAGTG
1750 CTTCAGAGATACTGAGT
1 CTTCAGAGATACTGAGT
1767 TTCTAACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.29, C:0.14, G:0.29, T:0.29
Consensus pattern (18 bp):
CTTCAGAGATACTGAGTG
Found at i:3645 original size:12 final size:11
Alignment explanation
Indices: 3628--3675 Score: 50
Period size: 12 Copynumber: 4.5 Consensus size: 11
3618 TTAATTAAAT
3628 TTATATTTCATA
1 TTATATTT-ATA
3640 TTATATTT-T-
1 TTATATTTATA
3649 TT-TA-TTATA
1 TTATATTTATA
3658 TTATATTTTATA
1 TTATA-TTTATA
3670 TTATAT
1 TTATAT
3676 AACCACGTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 11
0.74 0.00 0.26
Matches are distributed among these distances:
7 2 0.06
8 3 0.10
9 4 0.13
10 3 0.10
11 1 0.03
12 18 0.58
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (11 bp):
TTATATTTATA
Found at i:3647 original size:18 final size:19
Alignment explanation
Indices: 3621--3673 Score: 56
Period size: 18 Copynumber: 2.8 Consensus size: 19
3611 AAATTTTTTA
*
3621 ATTAAATTTATATT-TCAT
1 ATTATATTTATATTATCAT
* *
3639 ATTATATTT-TTTTATTAT
1 ATTATATTTATATTATCAT
3657 ATTATATTTTATATTAT
1 ATTATA-TTTATATTAT
3674 ATAACCACGT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
17 3 0.11
18 17 0.61
19 3 0.11
20 5 0.18
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (19 bp):
ATTATATTTATATTATCAT
Found at i:3649 original size:30 final size:30
Alignment explanation
Indices: 3613--3675 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
3603 TTTTTTTAAA
3613 ATTTTTTAATTAAATTTATATTTCATATTAT
1 ATTTTTTAATTAAA-TTATATTTCATATTAT
* * *
3644 ATTTTTTTATTATATTATATTTTATATTAT
1 ATTTTTTAATTAAATTATATTTCATATTAT
3674 AT
1 AT
3676 AACCACGTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 17 0.59
31 12 0.41
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (30 bp):
ATTTTTTAATTAAATTATATTTCATATTAT
Found at i:6227 original size:70 final size:70
Alignment explanation
Indices: 6109--6249 Score: 219
Period size: 70 Copynumber: 2.0 Consensus size: 70
6099 CCTAAGATTG
* * * *
6109 TTTATTCTGGGGGCTGTTGGATATGGTATTGGCGACCTCTTTACAAAATTAGATGGTGGCCTCGA
1 TTTACTCTGGGAGCTGTTGGATATGCTATGGGCGACCTCTTTACAAAATTAGATGGTGGCCTCGA
6174 TAAAA
66 TAAAA
* * *
6179 TTTACTCTGGGAGTTGTTGGGTATGCTATGGGCGACCTCTTTACAAAATTAGATGGTGGCCTTGA
1 TTTACTCTGGGAGCTGTTGGATATGCTATGGGCGACCTCTTTACAAAATTAGATGGTGGCCTCGA
6244 TAAAA
66 TAAAA
6249 T
1 T
6250 GAAATCCTGT
Statistics
Matches: 64, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
70 64 1.00
ACGTcount: A:0.24, C:0.14, G:0.27, T:0.35
Consensus pattern (70 bp):
TTTACTCTGGGAGCTGTTGGATATGCTATGGGCGACCTCTTTACAAAATTAGATGGTGGCCTCGA
TAAAA
Found at i:8422 original size:99 final size:96
Alignment explanation
Indices: 8232--8424 Score: 350
Period size: 96 Copynumber: 2.0 Consensus size: 96
8222 ATTTTAAGTA
8232 AATTCTATCATTAATTATGATGATGCTGTAGTAGATGAAGTCTTGGCTCAAAGCTTGTATTTTTT
1 AATTCTATCATTAATTATGATGATGCTGTAGTAGATGAAGTCTTGGCTCAAAGCTTGTATTTTTT
8297 TTAAGCAACTAGTGGGGATTTAGAGGGAGTT
66 TTAAGCAACTAGTGGGGATTTAGAGGGAGTT
8328 AATTCTATCATTAATTATGATGATGCTGTAGTAGATGAAGTCTTGGCTCAAAGCTTGTATTTTTT
1 AATTCTATCATTAATTATGATGATGCTGTAGTAGATGAAGTCTTGGCTCAAAGCTTGTA---TTT
*
8393 TTTTTAAGCAACTCGTGGGGATTTAGAGGGAG
63 TTTTTAAGCAACTAGTGGGGATTTAGAGGGAG
8425 CGAGGAGGAT
Statistics
Matches: 93, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
96 59 0.63
99 34 0.37
ACGTcount: A:0.27, C:0.10, G:0.24, T:0.39
Consensus pattern (96 bp):
AATTCTATCATTAATTATGATGATGCTGTAGTAGATGAAGTCTTGGCTCAAAGCTTGTATTTTTT
TTAAGCAACTAGTGGGGATTTAGAGGGAGTT
Found at i:8590 original size:5 final size:6
Alignment explanation
Indices: 8576--8613 Score: 51
Period size: 6 Copynumber: 6.2 Consensus size: 6
8566 TTAAGTGAAC
8576 TTTTAT TTTTAT TTTTA- TTTTAT TTTGATAT TTTTAT T
1 TTTTAT TTTTAT TTTTAT TTTTAT TTT--TAT TTTTAT T
8614 AAATTATAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
5 5 0.17
6 18 0.62
8 6 0.21
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (6 bp):
TTTTAT
Found at i:8596 original size:11 final size:12
Alignment explanation
Indices: 8576--8613 Score: 51
Period size: 11 Copynumber: 3.1 Consensus size: 12
8566 TTAAGTGAAC
8576 TTTTATTTTTAT
1 TTTTATTTTTAT
8588 TTTTA-TTTTAT
1 TTTTATTTTTAT
8599 TTTGATATTTTTAT
1 TTT--TATTTTTAT
8613 T
1 T
8614 AAATTATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 9 0.39
12 5 0.22
13 2 0.09
14 7 0.30
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (12 bp):
TTTTATTTTTAT
Found at i:8598 original size:17 final size:18
Alignment explanation
Indices: 8576--8613 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
8566 TTAAGTGAAC
8576 TTTTATTTT-TATTTTTA
1 TTTTATTTTATATTTTTA
8593 TTTTATTTTGATATTTTTA
1 TTTTATTTT-ATATTTTTA
8612 TT
1 TT
8614 AAATTATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 9 0.47
19 10 0.53
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (18 bp):
TTTTATTTTATATTTTTA
Found at i:14255 original size:15 final size:15
Alignment explanation
Indices: 14235--14274 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
14225 TAATCATGTC
*
14235 CATCCACCACCCGTG
1 CATCCACCACCCATG
*
14250 CATCCACAACCCATG
1 CATCCACCACCCATG
14265 CATCCACCAC
1 CATCCACCAC
14275 TTGTTTACCC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.28, C:0.53, G:0.07, T:0.12
Consensus pattern (15 bp):
CATCCACCACCCATG
Found at i:14836 original size:75 final size:75
Alignment explanation
Indices: 14749--14975 Score: 337
Period size: 75 Copynumber: 3.0 Consensus size: 75
14739 TTATTTCGGA
*
14749 TAGTTGTTGATAGTAGTAATGTGAAATATACAGAAACATTTGTTAATTGTAATTATCGTGCAGAT
1 TAGTTGTTGATAGTAGTAATGTGAAATATGCAGAAACATTTGTTAATTGTAATTATCGTGCAGAT
14814 TATCTCAGAT
66 TATCTCAGAT
* * * *
14824 TAGTTATTGATAGTAGCAATGTGAAATATGCAGAAACATTTCTTAATTGTAGTTATCGTGCAGAT
1 TAGTTGTTGATAGTAGTAATGTGAAATATGCAGAAACATTTGTTAATTGTAATTATCGTGCAGAT
*
14889 TATCTCGGAT
66 TATCTCAGAT
* * * * * *
14899 TAGTTGTTGATAGTAGTATTGTGAAATATGCTGAAACATTTGTTGATTGTAATTATCATACATAT
1 TAGTTGTTGATAGTAGTAATGTGAAATATGCAGAAACATTTGTTAATTGTAATTATCGTGCAGAT
*
14964 TATCTAAGAT
66 TATCTCAGAT
14974 TA
1 TA
14976 TCGTTTCATC
Statistics
Matches: 134, Mismatches: 18, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
75 134 1.00
ACGTcount: A:0.33, C:0.08, G:0.19, T:0.40
Consensus pattern (75 bp):
TAGTTGTTGATAGTAGTAATGTGAAATATGCAGAAACATTTGTTAATTGTAATTATCGTGCAGAT
TATCTCAGAT
Found at i:16041 original size:105 final size:105
Alignment explanation
Indices: 15859--16175 Score: 580
Period size: 105 Copynumber: 3.0 Consensus size: 105
15849 TGATAGCAGG
15859 TTATACCCGAGGTTGGTCAGTCTGATGGAGCTATCAGATTACTCCAAAAAATGGAGAGCGAAGGT
1 TTATACCCGAGGTTGGTCAGTCTGATGGAGCTATCAGATTACTCCAAAAAATGGAGAGCGAAGGT
*
15924 GTTAGGCTAGATGTAGTCGCTATCACAATTCACAGCTATA
66 GTTAGGCTAGATGTAGTTGCTATCACAATTCACAGCTATA
* * *
15964 TTATACCCAAGGTTGATCAGTCTGATGGAGCTATCAGATTACTCCAAAAAATGGAGAGCAAAGGT
1 TTATACCCGAGGTTGGTCAGTCTGATGGAGCTATCAGATTACTCCAAAAAATGGAGAGCGAAGGT
16029 GTTAGGCTAGATGTAGTTGCTATCACAATTCACAGCTATA
66 GTTAGGCTAGATGTAGTTGCTATCACAATTCACAGCTATA
* *
16069 TTATACCCGAGGTTGGTCAGTCTGATGGCGCTATCAGATTACTCCAAAAAATGGAGAGTGAAGGT
1 TTATACCCGAGGTTGGTCAGTCTGATGGAGCTATCAGATTACTCCAAAAAATGGAGAGCGAAGGT
16134 GTTAGGCTAGATGTAGTTGCTATCACAATTCACAGCTATA
66 GTTAGGCTAGATGTAGTTGCTATCACAATTCACAGCTATA
16174 TT
1 TT
16176 GCTCAGACTC
Statistics
Matches: 203, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
105 203 1.00
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.28
Consensus pattern (105 bp):
TTATACCCGAGGTTGGTCAGTCTGATGGAGCTATCAGATTACTCCAAAAAATGGAGAGCGAAGGT
GTTAGGCTAGATGTAGTTGCTATCACAATTCACAGCTATA
Found at i:21147 original size:13 final size:13
Alignment explanation
Indices: 21129--21165 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
21119 ATTAATATTA
21129 AAATTTTAATTTT
1 AAATTTTAATTTT
21142 AAATTTTAATTTT
1 AAATTTTAATTTT
21155 -AATTTTAATTT
1 AAATTTTAATTT
21166 AATTTAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 11 0.46
13 13 0.54
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
AAATTTTAATTTT
Found at i:21160 original size:12 final size:12
Alignment explanation
Indices: 21130--21170 Score: 66
Period size: 13 Copynumber: 3.4 Consensus size: 12
21120 TTAATATTAA
21130 AATTTTAATTTT
1 AATTTTAATTTT
21142 AAATTTTAATTTT
1 -AATTTTAATTTT
21155 AATTTTAA-TTT
1 AATTTTAATTTT
21166 AATTT
1 AATTT
21171 AAAATTAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 8 0.29
12 8 0.29
13 12 0.43
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (12 bp):
AATTTTAATTTT
Found at i:21189 original size:6 final size:6
Alignment explanation
Indices: 21133--21260 Score: 68
Period size: 6 Copynumber: 21.0 Consensus size: 6
21123 ATATTAAAAT
* * * * *
21133 TTTAAT TTTAAA TTTTAA TTTTAA TTTTAA TTT-AA TTTAAA ATTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* **
21180 --TAAA TTTAAA TAATTTAA TTTTTA TCTTAAA -TTAAA TTTAAAA TTTAAA
1 TTTAAA TTTAAA T--TTAAA TTTAAA T-TTAAA TTTAAA TTT-AAA TTTAAA
* *
21229 ATT-AA TTAATAAA TATTAAA TTAAAA TTTAAA
1 TTTAAA TT--TAAA T-TTAAA TTTAAA TTTAAA
21261 CCGTAAATTT
Statistics
Matches: 99, Mismatches: 11, Indels: 24
0.74 0.08 0.18
Matches are distributed among these distances:
4 4 0.04
5 13 0.13
6 58 0.59
7 15 0.15
8 8 0.08
9 1 0.01
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (6 bp):
TTTAAA
Found at i:21194 original size:42 final size:43
Alignment explanation
Indices: 21107--21221 Score: 107
Period size: 42 Copynumber: 2.7 Consensus size: 43
21097 TTATGTATAA
* *
21107 AATTTT-ATTTTAA-TTAATATTAAAATT--TTAATTTTAAATTTT
1 AATTTTAATTTTAATTTAAT-TTAAAATTAAATAAATTTAAA--TT
21149 AATTTTAATTTTAATTTAATTTAAAATTAAATAAATTTAAA-T
1 AATTTTAATTTTAATTTAATTTAAAATTAAATAAATTTAAATT
* * *
21191 AA-TTTAATTTTTATCTTAAATTAAATTTAAA
1 AATTTTAATTTTAAT-TTAATTTAAAATTAAA
21222 ATTTAAAATT
Statistics
Matches: 63, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
41 11 0.17
42 23 0.37
43 15 0.24
44 5 0.08
45 9 0.14
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (43 bp):
AATTTTAATTTTAATTTAATTTAAAATTAAATAAATTTAAATT
Found at i:21232 original size:19 final size:19
Alignment explanation
Indices: 21206--21260 Score: 60
Period size: 19 Copynumber: 2.8 Consensus size: 19
21196 AATTTTTATC
21206 TTAAATTAAATTTAAAAT-
1 TTAAATTAAATTTAAAATA
*
21224 TTAAAATT-AATTAATAAATA
1 TT-AAATTAAATTTA-AAATA
21244 TTAAATTAAAATTTAAA
1 TTAAATT-AAATTTAAA
21261 CCGTAAATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
18 7 0.23
19 14 0.47
20 4 0.13
21 5 0.17
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
TTAAATTAAATTTAAAATA
Found at i:21240 original size:48 final size:47
Alignment explanation
Indices: 21107--21224 Score: 122
Period size: 43 Copynumber: 2.6 Consensus size: 47
21097 TTATGTATAA
* * *
21107 AATTTT-ATTTTAATT-AATATTAAAATT--TTAATTTTAAAT--TTT
1 AATTTTAATTTAAATTAAAT-TTAAAATTAAATAAATTTAAATAATTT
* *
21149 AATTTTAATTTTAATTTAATTTAAAATTAAATAAATTTAAATAATTT
1 AATTTTAATTTAAATTAAATTTAAAATTAAATAAATTTAAATAATTT
*
21196 AATTTTTATCTTAAATTAAATTTAAAATT
1 AATTTTAAT-TTAAATTAAATTTAAAATT
21225 TAAAATTAAT
Statistics
Matches: 64, Mismatches: 5, Indels: 8
0.83 0.06 0.10
Matches are distributed among these distances:
42 6 0.09
43 17 0.27
44 3 0.05
45 10 0.16
47 11 0.17
48 17 0.27
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (47 bp):
AATTTTAATTTAAATTAAATTTAAAATTAAATAAATTTAAATAATTT
Found at i:23404 original size:34 final size:34
Alignment explanation
Indices: 23360--23542 Score: 217
Period size: 34 Copynumber: 5.4 Consensus size: 34
23350 AAAAATTACT
**
23360 ATTTAATCAACAATGACAACCTACCAAATCTCCC
1 ATTTAATCAACAATGGTAACCTACCAAATCTCCC
* ** * *
23394 ATTTAGTCAACAATGGTAAGTTACCAAATTTTCC
1 ATTTAATCAACAATGGTAACCTACCAAATCTCCC
* *
23428 ATTTAATCAACAATGGTAAGCTACCAAATCTTCC
1 ATTTAATCAACAATGGTAACCTACCAAATCTCCC
* * *
23462 ATTTAGTCAACAATGGCAAACC-ACCAAATCACCC
1 ATTTAATCAACAATGG-TAACCTACCAAATCTCCC
* *
23496 ATTTAATCAACAATGGTAAACTACCAAATC-ACC
1 ATTTAATCAACAATGGTAACCTACCAAATCTCCC
23529 ATTTAATCAACAAT
1 ATTTAATCAACAAT
23543 TCTCCCACTT
Statistics
Matches: 128, Mismatches: 19, Indels: 5
0.84 0.12 0.03
Matches are distributed among these distances:
33 19 0.15
34 106 0.83
35 3 0.02
ACGTcount: A:0.41, C:0.25, G:0.07, T:0.27
Consensus pattern (34 bp):
ATTTAATCAACAATGGTAACCTACCAAATCTCCC
Found at i:23497 original size:102 final size:101
Alignment explanation
Indices: 23360--23542 Score: 269
Period size: 102 Copynumber: 1.8 Consensus size: 101
23350 AAAAATTACT
* * ** *
23360 ATTTAATCAACAATGACAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAGTTACCAAATTT
1 ATTTAATCAACAATGACAACCTACCAAATCACCCATTTAATCAACAATGGTAAACTACCAAA-TC
*
23425 TCCATTTAATCAACAATGGTAAGCTACCAAATCTTCC
65 ACCATTTAATCAACAATGGTAAGCTACCAAATCTTCC
* *
23462 ATTTAGTCAACAATGGCAAACC-ACCAAATCACCCATTTAATCAACAATGGTAAACTACCAAATC
1 ATTTAATCAACAATGAC-AACCTACCAAATCACCCATTTAATCAACAATGGTAAACTACCAAATC
23526 ACCATTTAATCAACAAT
65 ACCATTTAATCAACAAT
23543 TCTCCCACTT
Statistics
Matches: 72, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
101 17 0.24
102 51 0.71
103 4 0.06
ACGTcount: A:0.41, C:0.25, G:0.07, T:0.27
Consensus pattern (101 bp):
ATTTAATCAACAATGACAACCTACCAAATCACCCATTTAATCAACAATGGTAAACTACCAAATCA
CCATTTAATCAACAATGGTAAGCTACCAAATCTTCC
Found at i:27737 original size:34 final size:34
Alignment explanation
Indices: 27691--27875 Score: 169
Period size: 34 Copynumber: 5.5 Consensus size: 34
27681 GTAAAAACTA
**
27691 TCATTTAATCAACAATGACAACCTACCAAATCTC
1 TCATTTAATCAACAATGGTAACCTACCAAATCTC
* * * *
27725 TCATTTAGTCAACAATGGTAAGCTATCAAAAT-TT
1 TCATTTAATCAACAATGGTAACCTA-CCAAATCTC
** *
27759 TCATTTAATCAACAATGGTAAGTTACTAAATCTC
1 TCATTTAATCAACAATGGTAACCTACCAAATCTC
* ** *
27793 TCATTTAATTAACAATGACAAACC-ACCAAATCAC
1 TCATTTAATCAACAATG-GTAACCTACCAAATCTC
* * * * *
27827 CCATTTAATCAATAATGGTAAACTACTAAATCAC
1 TCATTTAATCAACAATGGTAACCTACCAAATCTC
27861 T-ATTTAATCAACAAT
1 TCATTTAATCAACAAT
27876 TAAGACAAAA
Statistics
Matches: 121, Mismatches: 26, Indels: 9
0.78 0.17 0.06
Matches are distributed among these distances:
33 21 0.17
34 93 0.77
35 7 0.06
ACGTcount: A:0.42, C:0.21, G:0.06, T:0.31
Consensus pattern (34 bp):
TCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:28500 original size:23 final size:23
Alignment explanation
Indices: 28445--28516 Score: 67
Period size: 23 Copynumber: 3.2 Consensus size: 23
28435 TATTTCTAGA
* *
28445 TTATTAATTTTTAA-ATTTATAT
1 TTATTAATTTTTAATATATAAAT
**
28467 TTAATGCATTTTTAATATATAAAT
1 TT-ATTAATTTTTAATATATAAAT
* *
28491 TTATTAATTTATAATTTAT-AAT
1 TTATTAATTTTTAATATATAAAT
28513 TTAT
1 TTAT
28517 ATATTATTAT
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
22 9 0.22
23 23 0.57
24 8 0.20
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.58
Consensus pattern (23 bp):
TTATTAATTTTTAATATATAAAT
Found at i:28503 original size:18 final size:16
Alignment explanation
Indices: 28474--28539 Score: 59
Period size: 15 Copynumber: 4.1 Consensus size: 16
28464 TATTTAATGC
28474 ATTT-TTAA-TATATAA
1 ATTTATTAATTATAT-A
28489 ATTTATTAATT-TATA
1 ATTTATTAATTATATA
28504 ATTTA-TAATTTATATA
1 ATTTATTAA-TTATATA
*
28520 TTATTATTAAATTATATA
1 AT-TTATT-AATTATATA
28538 AT
1 AT
28540 ATTACTTATT
Statistics
Matches: 42, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
14 3 0.07
15 12 0.29
16 12 0.29
17 4 0.10
18 9 0.21
19 2 0.05
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
ATTTATTAATTATATA
Found at i:28507 original size:7 final size:7
Alignment explanation
Indices: 28474--28517 Score: 52
Period size: 7 Copynumber: 6.0 Consensus size: 7
28464 TATTTAATGC
*
28474 ATTTTTA
1 ATTTATA
*
28481 ATATATAA
1 ATTTAT-A
28489 ATTTATTA
1 ATTTA-TA
28497 ATTTATA
1 ATTTATA
28504 ATTTATA
1 ATTTATA
28511 ATTTATA
1 ATTTATA
28518 TATTATTATT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
7 20 0.62
8 11 0.34
9 1 0.03
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (7 bp):
ATTTATA
Found at i:28542 original size:18 final size:18
Alignment explanation
Indices: 28482--28543 Score: 62
Period size: 18 Copynumber: 3.7 Consensus size: 18
28472 GCATTTTTAA
28482 TATATAA-ATTTATT-AAT
1 TATATAATA-TTATTAAAT
*
28499 T-TATAAT-TTA-TAATT
1 TATATAATATTATTAAAT
*
28514 TATATATTATTATTAAAT
1 TATATAATATTATTAAAT
28532 TATATAATATTA
1 TATATAATATTA
28544 CTTATTAATA
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
14 1 0.03
15 6 0.17
16 10 0.28
17 4 0.11
18 15 0.42
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TATATAATATTATTAAAT
Found at i:28551 original size:22 final size:19
Alignment explanation
Indices: 28510--28551 Score: 57
Period size: 22 Copynumber: 2.1 Consensus size: 19
28500 TATAATTTAT
28510 AATTTATATATTATTATTA
1 AATTTATATATTATTATTA
28529 AATTATATAATATTACTTATTA
1 AATT-TAT-ATATTA-TTATTA
28551 A
1 A
28552 TAAATAGAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 4 0.20
20 3 0.15
21 6 0.30
22 7 0.35
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (19 bp):
AATTTATATATTATTATTA
Found at i:28847 original size:2 final size:2
Alignment explanation
Indices: 28842--28867 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
28832 AGTTTTTTAA
28842 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
28868 TTCCTTCATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29937 original size:24 final size:24
Alignment explanation
Indices: 29910--29979 Score: 76
Period size: 24 Copynumber: 3.0 Consensus size: 24
29900 ACACTATATT
29910 TATTATAATTATAAATATAATAAA
1 TATTATAATTATAAATATAATAAA
*
29934 TATTAT--TTAATTAATTATAATAAA
1 TATTATAATT-A-TAAATATAATAAA
29958 TA-T-TAATTATAAATATTAATAA
1 TATTATAATTATAAATA-TAATAA
29980 TAAAAAAATT
Statistics
Matches: 39, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
22 8 0.21
23 9 0.23
24 22 0.56
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (24 bp):
TATTATAATTATAAATATAATAAA
Found at i:31229 original size:3 final size:3
Alignment explanation
Indices: 31221--31247 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
31211 GTTTTGATGG
31221 TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC
31248 CTGGACCGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:32445 original size:15 final size:15
Alignment explanation
Indices: 32427--32459 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
32417 TAGAAAAATT
*
32427 TATATATTTTTATTA
1 TATATATTTATATTA
32442 TATATATTTATATTA
1 TATATATTTATATTA
32457 TAT
1 TAT
32460 CTCAATTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
TATATATTTATATTA
Found at i:33052 original size:14 final size:14
Alignment explanation
Indices: 33033--33064 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
33023 TTAAAATAAT
33033 TATTTTTATATTAA
1 TATTTTTATATTAA
33047 TATTTTTATATTAA
1 TATTTTTATATTAA
33061 -ATTT
1 TATTT
33065 AAATAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
TATTTTTATATTAA
Found at i:34010 original size:66 final size:64
Alignment explanation
Indices: 33887--34015 Score: 172
Period size: 66 Copynumber: 2.0 Consensus size: 64
33877 AGACGGGGTT
* *
33887 AACAATGATTTTCCCTTCATTTTCAGACAAGGATGTCAGACAATTTGAGAAATTTTTTTAGTCGG
1 AACAATGATTTTCCCTTCATTTTCAGACAAAGACGTCAGACAATTTGAGAAA-TTTTTTAGTCGG
* *
33952 AACAATGGGTTTTCCCTTCATTTTCAGACAAAGACGTGAGACAATTTG-GCATAA-TTTTTAGTC
1 AACAAT-GATTTTCCCTTCATTTTCAGACAAAGACGTCAGACAATTTGAG-A-AATTTTTTAGTC
34015 G
63 G
34016 AAACTTCCCG
Statistics
Matches: 57, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
65 17 0.30
66 38 0.67
67 2 0.04
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Consensus pattern (64 bp):
AACAATGATTTTCCCTTCATTTTCAGACAAAGACGTCAGACAATTTGAGAAATTTTTTAGTCGG
Found at i:34205 original size:14 final size:15
Alignment explanation
Indices: 34186--34214 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
34176 ATTTTTTATT
34186 TTTATTTT-ATTTAA
1 TTTATTTTAATTTAA
34200 TTTATTTTAATTTAA
1 TTTATTTTAATTTAA
34215 ATAATAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
TTTATTTTAATTTAA
Found at i:36020 original size:18 final size:18
Alignment explanation
Indices: 35988--36027 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
35978 ATATAATATA
*
35988 TATTTAATAAACATATTT
1 TATTTAATAAACATACTT
**
36006 TATTTAATATGCATACTT
1 TATTTAATAAACATACTT
36024 TATT
1 TATT
36028 AAATCTTATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.07, G:0.03, T:0.53
Consensus pattern (18 bp):
TATTTAATAAACATACTT
Done.