Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2285
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: 107154
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34
Found at i:2743 original size:3 final size:3
Alignment explanation
Indices: 2735--2787 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
2725 TAAAGCATAG
2735 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2783 AAT AA
1 AAT AA
2788 ATTTAAGATG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:3104 original size:17 final size:19
Alignment explanation
Indices: 3072--3110 Score: 64
Period size: 17 Copynumber: 2.2 Consensus size: 19
3062 AAATCATAAA
3072 TAAATATGATATAATATAT
1 TAAATATGATATAATATAT
3091 TAAATAT-A-ATAATATAT
1 TAAATATGATATAATATAT
3108 TAA
1 TAA
3111 TAATCAGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 12 0.60
18 1 0.05
19 7 0.35
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (19 bp):
TAAATATGATATAATATAT
Found at i:3157 original size:5 final size:5
Alignment explanation
Indices: 3133--3183 Score: 50
Period size: 5 Copynumber: 10.0 Consensus size: 5
3123 TATGTTTAAA
* * *
3133 TATAT TATAT CATAT T-TAT TATAT TTTATT TATAT TATTAA TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATA-T TATAT TA-TAT TATAT TATAT
3184 CTTTATTAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
4 4 0.11
5 25 0.68
6 8 0.22
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (5 bp):
TATAT
Found at i:4081 original size:13 final size:13
Alignment explanation
Indices: 4065--4124 Score: 61
Period size: 13 Copynumber: 4.7 Consensus size: 13
4055 TTTATGATTT
*
4065 TATTTTTTATTAA
1 TATTTATTATTAA
*
4078 TATTTATAATTAA
1 TATTTATTATTAA
4091 TATTTATTA-TAA
1 TATTTATTATTAA
* *
4103 TTAATTA-TAATAA
1 -TATTTATTATTAA
4116 TATTTATTA
1 TATTTATTA
4125 CATTTACAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
12 10 0.26
13 29 0.74
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (13 bp):
TATTTATTATTAA
Found at i:4103 original size:25 final size:26
Alignment explanation
Indices: 4065--4124 Score: 79
Period size: 26 Copynumber: 2.3 Consensus size: 26
4055 TTTATGATTT
* *
4065 TATTTTTTATTAA-TATTTATAATTAA
1 TATTTATTATTAATTAATTATAA-TAA
4091 TATTTATTA-TAATTAATTATAATAA
1 TATTTATTATTAATTAATTATAATAA
4116 TATTTATTA
1 TATTTATTA
4125 CATTTACAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
25 15 0.48
26 16 0.52
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (26 bp):
TATTTATTATTAATTAATTATAATAA
Found at i:4897 original size:2 final size:2
Alignment explanation
Indices: 4884--4935 Score: 88
Period size: 2 Copynumber: 26.5 Consensus size: 2
4874 GAAAGTTTAG
*
4884 GA GA GG GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
4926 GA GA GA -A GA G
1 GA GA GA GA GA G
4936 TATGTGTGTA
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 46 0.98
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:5256 original size:19 final size:20
Alignment explanation
Indices: 5213--5248 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
5203 AAATTTAAAT
5213 TATAA-ATTAATAATTATAA
1 TATAATATTAATAATTATAA
5232 TATAATATTAA-AATTAT
1 TATAATATTAATAATTAT
5249 TATTTAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 11 0.69
20 5 0.31
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
TATAATATTAATAATTATAA
Found at i:5256 original size:33 final size:29
Alignment explanation
Indices: 5185--5256 Score: 72
Period size: 33 Copynumber: 2.3 Consensus size: 29
5175 TTATCATGAT
*
5185 TTATATTAATAATATAAAAAATTTAAATTA
1 TTAT-TTAATAATATAAAAAATTAAAATTA
* *
5215 TAAATTAATAATTATAATATAATATTAAAATTA
1 TTATTTAATAA-TATAA-A-AA-ATTAAAATTA
5248 TTATTTAAT
1 TTATTTAAT
5257 TTTTTATCAT
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
29 7 0.21
30 7 0.21
31 1 0.03
32 2 0.06
33 16 0.48
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (29 bp):
TTATTTAATAATATAAAAAATTAAAATTA
Found at i:5857 original size:35 final size:34
Alignment explanation
Indices: 5764--5872 Score: 102
Period size: 35 Copynumber: 3.1 Consensus size: 34
5754 TGTCAAATGA
* *
5764 ATTATAATAAAAAATAT-TATTAAAAT-TATTGA-
1 ATTA-AATAATAAATATATATTAAAATATATTTAT
5796 ATTAAAATATATATAAGTA-AT-TTAAAATGATATTTAT
1 ATT-AAATA-ATA-AA-TATATATTAAAAT-ATATTTAT
5833 ATTAAATAATAAATATATATTAAAATTATATTTAT
1 ATTAAATAATAAATATATATTAAAA-TATATTTAT
5868 ATTAA
1 ATTAA
5873 GAATGAATTA
Statistics
Matches: 64, Mismatches: 2, Indels: 19
0.75 0.02 0.22
Matches are distributed among these distances:
32 7 0.11
33 5 0.08
34 13 0.20
35 25 0.39
36 11 0.17
37 3 0.05
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (34 bp):
ATTAAATAATAAATATATATTAAAATATATTTAT
Found at i:6016 original size:22 final size:21
Alignment explanation
Indices: 5993--6033 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
5983 ATGAGATAAA
5993 AAAATTTTAAA-TATTAAATT
1 AAAATTTTAAATTATTAAATT
6013 AAAATTTTAAATTTATTAAAT
1 AAAATTTTAAA-TTATTAAAT
6034 ATTATATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 11 0.58
22 8 0.42
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
AAAATTTTAAATTATTAAATT
Found at i:6969 original size:16 final size:16
Alignment explanation
Indices: 6948--6999 Score: 77
Period size: 16 Copynumber: 3.2 Consensus size: 16
6938 ATCTTGTATT
*
6948 AAATAATTTAAATTTA
1 AAATAATTTAATTTTA
6964 AAATAATTTAATTTTA
1 AAATAATTTAATTTTA
* *
6980 AATTAATTTTATTTTA
1 AAATAATTTAATTTTA
6996 AAAT
1 AAAT
7000 TAATAATTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
AAATAATTTAATTTTA
Found at i:7074 original size:2 final size:2
Alignment explanation
Indices: 7067--7106 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
7057 CAAATAATTC
7067 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
7107 GAGATAACTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:8931 original size:22 final size:20
Alignment explanation
Indices: 8885--8936 Score: 59
Period size: 22 Copynumber: 2.5 Consensus size: 20
8875 ATCCACATTC
8885 CTTAAAAAAATTTCTACTTT
1 CTTAAAAAAATTTCTACTTT
* * *
8905 TTTAAAATAATTATCCTTCTTT
1 CTTAAAAAAATT-T-CTACTTT
8927 CTTAAAAAAA
1 CTTAAAAAAA
8937 CTTCCCACTT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
20 10 0.40
21 1 0.04
22 14 0.56
ACGTcount: A:0.42, C:0.13, G:0.00, T:0.44
Consensus pattern (20 bp):
CTTAAAAAAATTTCTACTTT
Found at i:8957 original size:21 final size:21
Alignment explanation
Indices: 8924--8963 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
8914 ATTATCCTTC
8924 TTTCTTAAAAAAACTTCCCACT
1 TTTCTTAAAAAAAC-TCCCACT
*
8946 TTTCTT-ATAAAACTCCCA
1 TTTCTTAAAAAAACTCCCA
8964 TATATATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 6 0.35
22 6 0.35
ACGTcount: A:0.35, C:0.28, G:0.00, T:0.38
Consensus pattern (21 bp):
TTTCTTAAAAAAACTCCCACT
Found at i:9187 original size:30 final size:30
Alignment explanation
Indices: 9153--9229 Score: 86
Period size: 30 Copynumber: 2.6 Consensus size: 30
9143 GTTTAGGTAC
*
9153 AAATTAAAGATT-AAGAACTTACCTGAGTAA
1 AAATTAAAGATTAAAG-ACTTACCTGAATAA
**
9183 AAATTAAA-ATTTAAAGACTTATTTGAATAA
1 AAATTAAAGA-TTAAAGACTTACCTGAATAA
*
9213 AAATTAAAGTTTAAAGA
1 AAATTAAAGATTAAAGA
9230 TTTATAAATA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
29 1 0.03
30 36 0.90
31 3 0.08
ACGTcount: A:0.53, C:0.05, G:0.10, T:0.31
Consensus pattern (30 bp):
AAATTAAAGATTAAAGACTTACCTGAATAA
Found at i:10227 original size:2 final size:2
Alignment explanation
Indices: 10222--10265 Score: 70
Period size: 2 Copynumber: 21.5 Consensus size: 2
10212 AAAAAATGAC
*
10222 TA TA TA TA TA TA TA TG TA TA TCA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA
10265 T
1 T
10266 TGTTAGTTGA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
2 37 0.95
3 2 0.05
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:13862 original size:11 final size:11
Alignment explanation
Indices: 13840--13907 Score: 51
Period size: 10 Copynumber: 6.5 Consensus size: 11
13830 AATTTTAAAA
13840 TATTTATATATT
1 TATTT-TATATT
13852 TATTTTATATT
1 TATTTTATATT
*
13863 TA-TAT-TA-T
1 TATTTTATATT
13871 T-TTTTATATT
1 TATTTTATATT
13881 ATATTTTA-A-T
1 -TATTTTATATT
13891 TATTTTTATATT
1 TA-TTTTATATT
13903 T-TTTT
1 TATTTT
13908 CGTATCATAT
Statistics
Matches: 46, Mismatches: 2, Indels: 18
0.70 0.03 0.27
Matches are distributed among these distances:
8 4 0.09
9 6 0.13
10 13 0.28
11 11 0.24
12 12 0.26
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (11 bp):
TATTTTATATT
Found at i:13866 original size:17 final size:16
Alignment explanation
Indices: 13846--13907 Score: 63
Period size: 17 Copynumber: 3.7 Consensus size: 16
13836 AAAATATTTA
13846 TATATTTATTTTATATT
1 TATATTT-TTTTATATT
13863 TATATTATTTTT-TATAT
1 TATATT-TTTTTATAT-T
* *
13880 TATATTTTAATTATTTT
1 TATATTTT-TTTATATT
13897 TATATTTTTTT
1 TATATTTTTTT
13908 CGTATCATAT
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
16 7 0.18
17 28 0.74
18 3 0.08
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (16 bp):
TATATTTTTTTATATT
Found at i:13878 original size:12 final size:12
Alignment explanation
Indices: 13861--13907 Score: 64
Period size: 12 Copynumber: 4.2 Consensus size: 12
13851 TTATTTTATA
13861 TTTATATTATTT
1 TTTATATTATTT
*
13873 TTTATATTATAT
1 TTTATATTATTT
13885 TTTA-ATTA-TT
1 TTTATATTATTT
13895 TTTATATT-TTT
1 TTTATATTATTT
13906 TT
1 TT
13908 CGTATCATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
10 5 0.16
11 11 0.35
12 15 0.48
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTATATTATTT
Found at i:13882 original size:23 final size:22
Alignment explanation
Indices: 13850--13902 Score: 72
Period size: 23 Copynumber: 2.4 Consensus size: 22
13840 TATTTATATA
*
13850 TTTATTTTATA-TTTATATTATTT
1 TTTATATTATATTTTA-ATTA-TT
13873 TTTATATTATATTTTAATTATT
1 TTTATATTATATTTTAATTATT
13895 TTTATATT
1 TTTATATT
13903 TTTTTCGTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 10 0.36
23 14 0.50
24 4 0.14
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (22 bp):
TTTATATTATATTTTAATTATT
Found at i:16152 original size:50 final size:50
Alignment explanation
Indices: 16085--16184 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
16075 ATTAGGTTAG
16085 GCTTAACTAATGGGTCAATCAATCCATTCTTACCAAACCTAATAGGTGAT
1 GCTTAACTAATGGGTCAATCAATCCATTCTTACCAAACCTAATAGGTGAT
16135 GCTTAACTAATGGGTCAATCAATCCATTCTTACCAAACCTAATAGGTGAT
1 GCTTAACTAATGGGTCAATCAATCCATTCTTACCAAACCTAATAGGTGAT
16185 ATCAGTTTTG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.34, C:0.22, G:0.14, T:0.30
Consensus pattern (50 bp):
GCTTAACTAATGGGTCAATCAATCCATTCTTACCAAACCTAATAGGTGAT
Found at i:20434 original size:34 final size:34
Alignment explanation
Indices: 20374--20438 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 34
20364 CTTCTCAATC
* *
20374 GACCTTTTTCCCTTAATAAAATCTTAAAATAGTT
1 GACCTTTTTCCCTTAACAAAACCTTAAAATAGTT
*
20408 GACCTTTTT-CCTTCAACCAAACCTTAAAATA
1 GACCTTTTTCCCTT-AACAAAACCTTAAAATA
20439 ATCAATCTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
33 4 0.15
34 23 0.85
ACGTcount: A:0.35, C:0.23, G:0.05, T:0.37
Consensus pattern (34 bp):
GACCTTTTTCCCTTAACAAAACCTTAAAATAGTT
Found at i:26614 original size:32 final size:32
Alignment explanation
Indices: 26578--26657 Score: 124
Period size: 32 Copynumber: 2.5 Consensus size: 32
26568 TATTTTTTGT
* * *
26578 TGTATCGATATATTTTGGGTTTTTGACCCAAA
1 TGTATTGATACATTTTAGGTTTTTGACCCAAA
*
26610 TGTATTAATACATTTTAGGTTTTTGACCCAAA
1 TGTATTGATACATTTTAGGTTTTTGACCCAAA
26642 TGTATTGATACATTTT
1 TGTATTGATACATTTT
26658 TTATTGTATC
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 43 1.00
ACGTcount: A:0.28, C:0.11, G:0.15, T:0.46
Consensus pattern (32 bp):
TGTATTGATACATTTTAGGTTTTTGACCCAAA
Found at i:26672 original size:52 final size:52
Alignment explanation
Indices: 26608--26726 Score: 148
Period size: 52 Copynumber: 2.3 Consensus size: 52
26598 TTTTGACCCA
* * * * *
26608 AATGTATTAATACATTTTAGGTTTTTGACCCAAATGTATTGATACATTTTTT
1 AATGTATCAATACATTTTAGGTTTTTGACCCAAACGTATCGATACATTCTTC
* * * *
26660 ATTGTATCAATACATTTTGGGTTTTTGATCCAAACGTATCGATAGATTCTTC
1 AATGTATCAATACATTTTAGGTTTTTGACCCAAACGTATCGATACATTCTTC
*
26712 AATGTATCGATACAT
1 AATGTATCAATACAT
26727 CTAGTTAAAT
Statistics
Matches: 56, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
52 56 1.00
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.44
Consensus pattern (52 bp):
AATGTATCAATACATTTTAGGTTTTTGACCCAAACGTATCGATACATTCTTC
Found at i:27783 original size:39 final size:39
Alignment explanation
Indices: 27729--27811 Score: 139
Period size: 39 Copynumber: 2.1 Consensus size: 39
27719 AGCCCATGTC
27729 ATAAAACATGTCATGAAATTTTCAGCATATTAGTTATTG
1 ATAAAACATGTCATGAAATTTTCAGCATATTAGTTATTG
* *
27768 ATAAAACATGTCATGAAATTTTCAGCCTATTAGTTGTTG
1 ATAAAACATGTCATGAAATTTTCAGCATATTAGTTATTG
*
27807 TTAAA
1 ATAAA
27812 TGTTAGGATC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.39
Consensus pattern (39 bp):
ATAAAACATGTCATGAAATTTTCAGCATATTAGTTATTG
Found at i:28142 original size:13 final size:13
Alignment explanation
Indices: 28124--28148 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28114 ATATTGCACA
28124 GTATCGATACATT
1 GTATCGATACATT
28137 GTATCGATACAT
1 GTATCGATACAT
28149 GACCAAATGT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:28161 original size:20 final size:22
Alignment explanation
Indices: 28136--28189 Score: 67
Period size: 20 Copynumber: 2.5 Consensus size: 22
28126 ATCGATACAT
**
28136 TGTATCGATACATG-ACCA-AA
1 TGTATCGATACATGAAAAAGAA
*
28156 TGTATCGATACTTGAAAAAGAA
1 TGTATCGATACATGAAAAAGAA
28178 TGTATCGATACA
1 TGTATCGATACA
28190 GATCATTGGT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 13 0.46
21 2 0.07
22 13 0.46
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.28
Consensus pattern (22 bp):
TGTATCGATACATGAAAAAGAA
Found at i:28284 original size:33 final size:32
Alignment explanation
Indices: 28222--28289 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 32
28212 GTAGCCAAAT
*
28222 TTGTATCGATACACACAATATGTACCGATACA
1 TTGTATCGATACACACAAAATGTACCGATACA
* *
28254 TTGTATCGATACATCCCAAAATGTATCGATACA
1 TTGTATCGATACA-CACAAAATGTACCGATACA
28287 TTG
1 TTG
28290 GCTTGTAACG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 13 0.41
33 19 0.59
ACGTcount: A:0.35, C:0.21, G:0.13, T:0.31
Consensus pattern (32 bp):
TTGTATCGATACACACAAAATGTACCGATACA
Found at i:31922 original size:13 final size:13
Alignment explanation
Indices: 31904--31928 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31894 CATAAAGTGT
31904 TGTATCGATACAA
1 TGTATCGATACAA
31917 TGTATCGATACA
1 TGTATCGATACA
31929 TATTTTTTTG
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:32009 original size:13 final size:13
Alignment explanation
Indices: 31991--32015 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31981 ATCACTTAAA
31991 TGTATCGATACAT
1 TGTATCGATACAT
32004 TGTATCGATACA
1 TGTATCGATACA
32016 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:32068 original size:52 final size:51
Alignment explanation
Indices: 32004--32152 Score: 244
Period size: 52 Copynumber: 2.9 Consensus size: 51
31994 ATCGATACAT
**
32004 TGTATCGATACACTGATCTTTGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACT-ATCAATGTATCGATACATGCAGGCAAATTTGCCCAGA
*
32056 TGTATCGATACACTATAAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACTAT-CAATGTATCGATACATGCAGGCAAATTTGCCCAGA
32108 TGTATCGATACACTATTCAATGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACACTA-TCAATGTATCGATACATGCAGGCAAATTT
32153 TCATATTTCG
Statistics
Matches: 91, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
51 2 0.02
52 88 0.97
53 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.30
Consensus pattern (51 bp):
TGTATCGATACACTATCAATGTATCGATACATGCAGGCAAATTTGCCCAGA
Found at i:45950 original size:1 final size:1
Alignment explanation
Indices: 45944--46058 Score: 104
Period size: 1 Copynumber: 115.0 Consensus size: 1
45934 GGCGTTTTCC
* ** ** * *
45944 AAAAAAACAAAAAAAAAAAAAAAAAAAAAACGAAAAAATGAAAAAACAAAAAAAAAAAAACAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * * * *
46009 AAAAACAAAAAAAAACAAAAACAATAAAAAAACAAACAAAAACAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
46059 GGGGGTCCGG
Statistics
Matches: 88, Mismatches: 26, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 88 1.00
ACGTcount: A:0.88, C:0.09, G:0.02, T:0.02
Consensus pattern (1 bp):
A
Found at i:45988 original size:40 final size:38
Alignment explanation
Indices: 45944--46056 Score: 145
Period size: 39 Copynumber: 2.8 Consensus size: 38
45934 GGCGTTTTCC
*
45944 AAAAAAACAAAAAAAAAAAAAAAAAAAAAACGAAAAAAT
1 AAAAAAACAAAAAAAAAAAAAAAAAAAAAAC-AAAAAAA
*
45983 GAAAAAACAAAAAAAAAAAAACAAAAAAAAACAAAAAAA
1 AAAAAAACAAAAAAAAAAAAA-AAAAAAAAACAAAAAAA
46022 AACAAAAACAATAAAAAAACAAACAAAAACAAAAA
1 AA-AAAAACAA-AAAAAAA-AAA-AAAAA-AAAAA
46057 AAGGGGGTCC
Statistics
Matches: 65, Mismatches: 3, Indels: 8
0.86 0.04 0.11
Matches are distributed among these distances:
39 27 0.42
40 18 0.28
41 7 0.11
42 7 0.11
43 6 0.09
ACGTcount: A:0.88, C:0.09, G:0.02, T:0.02
Consensus pattern (38 bp):
AAAAAAACAAAAAAAAAAAAAAAAAAAAAACAAAAAAA
Found at i:47533 original size:30 final size:30
Alignment explanation
Indices: 47497--47793 Score: 166
Period size: 30 Copynumber: 10.1 Consensus size: 30
47487 CATCAACCTT
*
47497 CAAAGCCCACAAATCAGTGGCACCCTTTTC
1 CAAAGCCCACAAGTCAGTGGCACCCTTTTC
* * *
47527 CGAAGCCCACAAGTCGGTGGCA-TCTTTTC
1 CAAAGCCCACAAGTCAGTGGCACCCTTTTC
* * * *
47556 CAAAGTCCACAACTCCGTGGCACTCTTTTTC
1 CAAAGCCCACAAGTCAGTGGCAC-CCTTTTC
** * * ** **
47587 TTGTGTAAGCTCACAACTCTA-TAACACTATTTT-
1 ----CAAAGCCCACAAGTC-AGTGGCACCCTTTTC
* *
47620 --TAGCCCACAAGTTAGTGGCACCCTTTTC
1 CAAAGCCCACAAGTCAGTGGCACCCTTTTC
* ***
47648 AAAAGCCCACAAGTCAGTGGCATATTTTTC
1 CAAAGCCCACAAGTCAGTGGCACCCTTTTC
* *
47678 AAAAGCCCACAAGTCAGTGGCAACC-TTT-
1 CAAAGCCCACAAGTCAGTGGCACCCTTTTC
* * *
47706 AAAAGCCCACAAGTCAATGGCAACC--TT-
1 CAAAGCCCACAAGTCAGTGGCACCCTTTTC
* *
47733 CAAAGCCCATAAATCAGTGGCACCCTTTTC
1 CAAAGCCCACAAGTCAGTGGCACCCTTTTC
* * * *
47763 CGAAGACCACAAATCGGTGGCA-CCTTTTC
1 CAAAGCCCACAAGTCAGTGGCACCCTTTTC
47792 CA
1 CA
47794 TCTTTAAGTC
Statistics
Matches: 207, Mismatches: 46, Indels: 29
0.73 0.16 0.10
Matches are distributed among these distances:
26 1 0.00
27 39 0.19
28 24 0.12
29 37 0.18
30 82 0.40
31 5 0.02
34 4 0.02
35 15 0.07
ACGTcount: A:0.29, C:0.30, G:0.16, T:0.25
Consensus pattern (30 bp):
CAAAGCCCACAAGTCAGTGGCACCCTTTTC
Found at i:47718 original size:28 final size:29
Alignment explanation
Indices: 47621--47760 Score: 169
Period size: 30 Copynumber: 4.9 Consensus size: 29
47611 CACTATTTTT
* *
47621 AGCCCACAAGTTAGTGGCACCCTTTTCAAA
1 AGCCCACAAGTCAGTGGCAACC-TTTCAAA
**
47651 AGCCCACAAGTCAGTGGCATATTTTTCAAA
1 AGCCCACAAGTCAGTGGCA-ACCTTTCAAA
47681 AGCCCACAAGTCAGTGGCAACCTTT-AAA
1 AGCCCACAAGTCAGTGGCAACCTTTCAAA
*
47709 AGCCCACAAGTCAATGGCAACC-TTC-AA
1 AGCCCACAAGTCAGTGGCAACCTTTCAAA
* * *
47736 AGCCCATAAATCAGTGGCACCCTTT
1 AGCCCACAAGTCAGTGGCAACCTTT
47761 TCCGAAGACC
Statistics
Matches: 96, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
27 22 0.23
28 26 0.27
29 4 0.04
30 44 0.46
ACGTcount: A:0.33, C:0.29, G:0.16, T:0.21
Consensus pattern (29 bp):
AGCCCACAAGTCAGTGGCAACCTTTCAAA
Found at i:47773 original size:85 final size:86
Alignment explanation
Indices: 47621--47789 Score: 189
Period size: 85 Copynumber: 2.0 Consensus size: 86
47611 CACTATTTTT
* * * * * * *
47621 AGCCCACAAGTTAGTGGCACCCTTTTCAAAAGCCCACAAGTCAGTGGCATATTTTTCAAAAGCCC
1 AGCCCACAAGTCAATGGCAACC-TTTCAAAAGCCCACAAATCAGTGGCACACTTTTCAAAAGACC
*
47686 ACAAGTCAGTGGCAACCTTTAAA
65 ACAAATCAGTGGC-ACCTTTAAA
* * **
47709 AGCCCACAAGTCAATGGCAACC-TTC-AAAGCCCATAAATCAGTGGCACCCTTTTCCGAAGACCA
1 AGCCCACAAGTCAATGGCAACCTTTCAAAAGCCCACAAATCAGTGGCACACTTTTCAAAAGACCA
*
47772 CAAATCGGTGGCACCTTT
66 CAAATCAGTGGCACCTTT
47790 TCCATCTTTA
Statistics
Matches: 68, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
84 6 0.09
85 40 0.59
86 3 0.04
88 19 0.28
ACGTcount: A:0.32, C:0.30, G:0.17, T:0.21
Consensus pattern (86 bp):
AGCCCACAAGTCAATGGCAACCTTTCAAAAGCCCACAAATCAGTGGCACACTTTTCAAAAGACCA
CAAATCAGTGGCACCTTTAAA
Found at i:47837 original size:52 final size:52
Alignment explanation
Indices: 47780--47991 Score: 199
Period size: 52 Copynumber: 4.2 Consensus size: 52
47770 CACAAATCGG
* *
47780 TGGCACCTTTTCCATCTTTAAGTCCAATGTAGCCGACCTTGAATCAGCACAT
1 TGGCACCTTTTCCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACAT
* *
47832 TGGCA-------C--CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATAT
1 TGGCACCTTTTCCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACAT
*
47875 TGGCACCTTTTCCATCTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACAT
1 TGGCACCTTTTCCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACAT
* * * * * * * * *
47927 TGACATCCTTTTTCTCAGCTTTAAGCCCAATATCGTTGGCCGTGAATCAACATAT
1 TGGCA-CC-TTTTC-CATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACAT
*
47982 TGGCATCTTT
1 TGGCACCTTT
47992 ATCACTTTTC
Statistics
Matches: 129, Mismatches: 19, Indels: 23
0.75 0.11 0.13
Matches are distributed among these distances:
43 38 0.29
45 1 0.01
50 1 0.01
52 43 0.33
53 5 0.04
54 6 0.05
55 35 0.27
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.33
Consensus pattern (52 bp):
TGGCACCTTTTCCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACAT
Found at i:47863 original size:43 final size:43
Alignment explanation
Indices: 47795--47884 Score: 144
Period size: 43 Copynumber: 2.1 Consensus size: 43
47785 CCTTTTCCAT
*
47795 CTTTAAGTCCAATGTAGCCGACCTTGAATCAGCACATTGGCAC
1 CTTTAAGTCCAATATAGCCGACCTTGAATCAGCACATTGGCAC
* * *
47838 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC
1 CTTTAAGTCCAATATAGCCGACCTTGAATCAGCACATTGGCAC
47881 CTTT
1 CTTT
47885 TCCATCTTTA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.27, C:0.26, G:0.18, T:0.30
Consensus pattern (43 bp):
CTTTAAGTCCAATATAGCCGACCTTGAATCAGCACATTGGCAC
Found at i:48770 original size:13 final size:13
Alignment explanation
Indices: 48752--48776 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
48742 CATAAAGTGT
48752 TGTATCGATACAA
1 TGTATCGATACAA
48765 TGTATCGATACA
1 TGTATCGATACA
48777 TATTTTTTTG
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:48917 original size:52 final size:51
Alignment explanation
Indices: 48852--49000 Score: 226
Period size: 52 Copynumber: 2.9 Consensus size: 51
48842 ATCGATACAT
* **
48852 TGTATTGATACACTGATCTTTGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACT-ATCAATGTATCGATACATGCAGGCAAATTTGCCCAGA
* *
48904 TGTATCGATACACTATAAAATGTATCGATACATGCAGGAAAATTTGCCCAGA
1 TGTATCGATACACTAT-CAATGTATCGATACATGCAGGCAAATTTGCCCAGA
48956 TGTATCGATACACTATTCAATGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACACTA-TCAATGTATCGATACATGCAGGCAAATTT
49001 TCATATTTCG
Statistics
Matches: 88, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
51 2 0.02
52 85 0.97
53 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (51 bp):
TGTATCGATACACTATCAATGTATCGATACATGCAGGCAAATTTGCCCAGA
Found at i:53911 original size:21 final size:21
Alignment explanation
Indices: 53866--53912 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
53856 CTAATTTCAA
*
53866 CAGGAAACAAGAGCAAACATT
1 CAGGAAACAAGAGCAAACATC
*
53887 CAGGAAACAAG-GACAAGCATC
1 CAGGAAACAAGAG-CAAACATC
53908 CAGGA
1 CAGGA
53913 TTTAGGCAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 1 0.04
21 22 0.96
ACGTcount: A:0.49, C:0.21, G:0.23, T:0.06
Consensus pattern (21 bp):
CAGGAAACAAGAGCAAACATC
Found at i:59118 original size:1 final size:1
Alignment explanation
Indices: 59112--59173 Score: 52
Period size: 1 Copynumber: 62.0 Consensus size: 1
59102 TGGCAATTGT
*** * * * * *
59112 AAAAAAAAAAAGGTAAAAAAAACAAAAAAAAAACAAAAAAAAAGAAGAAAAAAATAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
59174 GTGAAGATCT
Statistics
Matches: 48, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 48 1.00
ACGTcount: A:0.87, C:0.03, G:0.06, T:0.03
Consensus pattern (1 bp):
A
Found at i:59140 original size:11 final size:11
Alignment explanation
Indices: 59126--59173 Score: 62
Period size: 11 Copynumber: 4.5 Consensus size: 11
59116 AAAAAAAGGT
59126 AAAAAAAACAA
1 AAAAAAAACAA
59137 AAAAAAAAC-A
1 AAAAAAAACAA
*
59147 AAAAAAAAGAA
1 AAAAAAAACAA
* *
59158 GAAAAAAATAA
1 AAAAAAAACAA
59169 AAAAA
1 AAAAA
59174 GTGAAGATCT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
10 9 0.28
11 23 0.72
ACGTcount: A:0.90, C:0.04, G:0.04, T:0.02
Consensus pattern (11 bp):
AAAAAAAACAA
Found at i:59180 original size:21 final size:21
Alignment explanation
Indices: 59126--59173 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
59116 AAAAAAAGGT
* *
59126 AAAAAAAACAAAAAAAAAACA
1 AAAAAAAAGAAGAAAAAAACA
*
59147 AAAAAAAAGAAGAAAAAAATA
1 AAAAAAAAGAAGAAAAAAACA
59168 AAAAAA
1 AAAAAA
59174 GTGAAGATCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.90, C:0.04, G:0.04, T:0.02
Consensus pattern (21 bp):
AAAAAAAAGAAGAAAAAAACA
Found at i:61153 original size:18 final size:20
Alignment explanation
Indices: 61116--61154 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
61106 CTTGATAATT
*
61116 TAATTTTTATTTTATATTAA
1 TAATTTTTACTTTATATTAA
61136 TAATTTTT-CTTT-TATTAA
1 TAATTTTTACTTTATATTAA
61154 T
1 T
61155 CGCTTGTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 7 0.39
19 3 0.17
20 8 0.44
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (20 bp):
TAATTTTTACTTTATATTAA
Found at i:65121 original size:13 final size:13
Alignment explanation
Indices: 65103--65166 Score: 83
Period size: 13 Copynumber: 4.9 Consensus size: 13
65093 CAGCATTCTC
*
65103 TGTATCGATACAT
1 TGTATCGATACAG
*
65116 TGTATCGATATAG
1 TGTATCGATACAG
*
65129 TGTATCGATACAT
1 TGTATCGATACAG
* *
65142 TATATCGATATAG
1 TGTATCGATACAG
65155 TGTATCGATACA
1 TGTATCGATACA
65167 AAGGGTTTAT
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
13 42 1.00
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:65139 original size:26 final size:26
Alignment explanation
Indices: 65103--65166 Score: 119
Period size: 26 Copynumber: 2.5 Consensus size: 26
65093 CAGCATTCTC
*
65103 TGTATCGATACATTGTATCGATATAG
1 TGTATCGATACATTATATCGATATAG
65129 TGTATCGATACATTATATCGATATAG
1 TGTATCGATACATTATATCGATATAG
65155 TGTATCGATACA
1 TGTATCGATACA
65167 AAGGGTTTAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (26 bp):
TGTATCGATACATTATATCGATATAG
Found at i:66996 original size:22 final size:22
Alignment explanation
Indices: 66970--67014 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
66960 CGAAAGTGTT
66970 AAATTATTTT-ACTAAGGGGGAG
1 AAATT-TTTTGACTAAGGGGGAG
*
66992 AAATTTTTTGATTAAGGGGGAG
1 AAATTTTTTGACTAAGGGGGAG
67014 A
1 A
67015 GAAAAGAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.36, C:0.02, G:0.29, T:0.33
Consensus pattern (22 bp):
AAATTTTTTGACTAAGGGGGAG
Found at i:67672 original size:32 final size:33
Alignment explanation
Indices: 67631--67698 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
67621 GTAGCCAAAT
*
67631 TTGTATCGATACA-CACAATATGTA-CTGATACA
1 TTGTATCGATACATCACAAAATGTATC-GATACA
*
67663 TTGTATCGATACATCCCAAAATGTATCGATACA
1 TTGTATCGATACATCACAAAATGTATCGATACA
67696 TTG
1 TTG
67699 GCTTGTAACG
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
32 13 0.41
33 18 0.56
34 1 0.03
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.32
Consensus pattern (33 bp):
TTGTATCGATACATCACAAAATGTATCGATACA
Found at i:73988 original size:22 final size:21
Alignment explanation
Indices: 73960--74013 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
73950 AAAATCTAAT
73960 TTATTTTTTAAAATTAATTTAA
1 TTATTTTTTAAAATTAATTT-A
* * *
73982 TTATTTTTATGAAATTTATTTT
1 TTATTTTT-TAAAATTAATTTA
74004 TTATTTTTTA
1 TTATTTTTTA
74014 TAATAAAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
21 1 0.04
22 16 0.59
23 10 0.37
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (21 bp):
TTATTTTTTAAAATTAATTTA
Found at i:74013 original size:23 final size:23
Alignment explanation
Indices: 73958--74016 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 23
73948 TTAAAATCTA
73958 ATTTATTTTTTA-AAATTAATTT
1 ATTTATTTTTTATAAATTAATTT
* *
73980 AATTA-TTTTTATGAAATTTATTT
1 ATTTATTTTTTAT-AAATTAATTT
74003 -TTTATTTTTTATAA
1 ATTTATTTTTTATAA
74017 TAAAATTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
21 6 0.19
22 9 0.29
23 16 0.52
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (23 bp):
ATTTATTTTTTATAAATTAATTT
Found at i:78244 original size:26 final size:26
Alignment explanation
Indices: 78202--78251 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
78192 ATTAATATTT
*
78202 TAAATTTATATATAATAAAATAAAAA
1 TAAATTTATATAAAATAAAATAAAAA
*
78228 TAAATTTCATA-AAAATAAATTAAA
1 TAAATTT-ATATAAAATAAAATAAA
78252 TTAATTTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 18 0.86
27 3 0.14
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (26 bp):
TAAATTTATATAAAATAAAATAAAAA
Found at i:78286 original size:21 final size:22
Alignment explanation
Indices: 78219--78285 Score: 73
Period size: 22 Copynumber: 2.9 Consensus size: 22
78209 ATATATAATA
*
78219 AAATAAAAATAAATTTCATAAAAAT
1 AAAT-AAAATTAATTT--TAAAAAT
*
78244 AAATTAAATTAATTTTAAAAAT
1 AAATAAAATTAATTTTAAAAAT
78266 AAA-AAAATTAGATTTTAAAA
1 AAATAAAATTA-ATTTTAAAA
78286 TTTTTTAAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
21 6 0.16
22 19 0.50
24 9 0.24
25 4 0.11
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.33
Consensus pattern (22 bp):
AAATAAAATTAATTTTAAAAAT
Found at i:78764 original size:29 final size:29
Alignment explanation
Indices: 78699--78764 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
78689 ATTTCTCAAC
**
78699 ATATTTATAAAAAAAAACTTATTTTGGGAA
1 ATATTT-TAAAAAAAAACTTATTTACGGAA
* *
78729 ATGTTTTACAAAAAAACTTATTTACGGAA
1 ATATTTTAAAAAAAAACTTATTTACGGAA
*
78758 TTATTTT
1 ATATTTT
78765 TTTCATATTC
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
29 25 0.83
30 5 0.17
ACGTcount: A:0.44, C:0.06, G:0.09, T:0.41
Consensus pattern (29 bp):
ATATTTTAAAAAAAAACTTATTTACGGAA
Found at i:84018 original size:21 final size:21
Alignment explanation
Indices: 83993--84033 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
83983 AAAAAATAAA
*
83993 AATAAAAATTAATATTTTATC
1 AATAAAAATTAATATATTATC
*
84014 AATAATAATTAATATATTAT
1 AATAAAAATTAATATATTAT
84034 TTTGAATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (21 bp):
AATAAAAATTAATATATTATC
Found at i:85013 original size:26 final size:28
Alignment explanation
Indices: 84983--85039 Score: 75
Period size: 26 Copynumber: 2.1 Consensus size: 28
84973 TCAATAAACT
84983 AATA-TTAATTCAAATAAAT-AAT-TTAA
1 AATATTTAATT-AAATAAATAAATCTTAA
*
85009 AATATTTAATTAAATAATTAAATCTTAA
1 AATATTTAATTAAATAAATAAATCTTAA
85037 AAT
1 AAT
85040 TCAAAATAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
26 11 0.41
27 9 0.33
28 7 0.26
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (28 bp):
AATATTTAATTAAATAAATAAATCTTAA
Found at i:85354 original size:2 final size:2
Alignment explanation
Indices: 85347--85400 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
85337 TACCTATCAA
85347 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
85389 AT AT AT AT AT AT
1 AT AT AT AT AT AT
85401 TGAATGTTAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:88146 original size:15 final size:16
Alignment explanation
Indices: 88126--88158 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
88116 GTAATTATAT
88126 ATTTAAAA-AATAAAA
1 ATTTAAAATAATAAAA
*
88141 ATTTAAAATAATATAA
1 ATTTAAAATAATAAAA
88157 AT
1 AT
88159 AATTTTATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
ATTTAAAATAATAAAA
Found at i:89467 original size:21 final size:20
Alignment explanation
Indices: 89437--89475 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
89427 TAAGTAAACA
89437 ATATCTCATAAGTTCAATATGT
1 ATATCTCATAA-TT-AATATGT
89459 ATAT-TCATAATTAATAT
1 ATATCTCATAATTAATAT
89476 CAAAATAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 5 0.29
20 2 0.12
21 6 0.35
22 4 0.24
ACGTcount: A:0.41, C:0.10, G:0.05, T:0.44
Consensus pattern (20 bp):
ATATCTCATAATTAATATGT
Found at i:93049 original size:24 final size:24
Alignment explanation
Indices: 93013--93067 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 24
93003 ACATTTACAA
*
93013 ATAAATAA--AATAATAAATCAAGT
1 ATAAATAATGAATAAAAAATCAA-T
*
93036 AT-AATAATGAATAAAAAATTAAT
1 ATAAATAATGAATAAAAAATCAAT
93059 ATAAATAAT
1 ATAAATAAT
93068 TTATGTATGA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
22 5 0.19
23 5 0.19
24 17 0.63
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (24 bp):
ATAAATAATGAATAAAAAATCAAT
Found at i:96467 original size:73 final size:74
Alignment explanation
Indices: 96390--96530 Score: 187
Period size: 74 Copynumber: 1.9 Consensus size: 74
96380 AAAATTAAGA
* ** ** **
96390 TTTAATTAAA-TTAAAAAATT-TGTGTTGAAATTAATGTATTAATTATTAATTTTTAATAAAATA
1 TTTAATTAAATTTAAAAAATTATAT-TAAAAATTAAAATATTAACAATTAATTTTTAATAAAATA
96453 AAAATAAAAT
65 AAAATAAAAT
*
96463 TTTAATTAAATTTAAAAAATTATATTAAAAATTAAAATATTAACAATTGATTTTTAATAAAATAA
1 TTTAATTAAATTTAAAAAATTATATTAAAAATTAAAATATTAACAATTAATTTTTAATAAAATAA
96528 AAA
66 AAA
96531 ATTTTAGATA
Statistics
Matches: 58, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
73 10 0.17
74 46 0.79
75 2 0.03
ACGTcount: A:0.54, C:0.01, G:0.04, T:0.42
Consensus pattern (74 bp):
TTTAATTAAATTTAAAAAATTATATTAAAAATTAAAATATTAACAATTAATTTTTAATAAAATAA
AAATAAAAT
Found at i:98080 original size:4 final size:4
Alignment explanation
Indices: 98064--98116 Score: 60
Period size: 4 Copynumber: 14.2 Consensus size: 4
98054 CCACTTGCCT
* *
98064 TTTC TTT- TTTC TTTC TTTC TTTC TTTC TTT- TCTC TTT- TTTC TTCC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
98109 TTT- TTTC T
1 TTTC TTTC T
98117 CCAAAGTTTA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
3 11 0.27
4 30 0.73
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTC
Found at i:98080 original size:11 final size:11
Alignment explanation
Indices: 98064--98116 Score: 60
Period size: 11 Copynumber: 5.1 Consensus size: 11
98054 CCACTTGCCT
98064 TTTCTTTTTTC
1 TTTCTTTTTTC
98075 TTTCTTTCTTTC
1 TTTCTTT-TTTC
98087 TTTC--TTTTC
1 TTTCTTTTTTC
98096 --TCTTTTTTC
1 TTTCTTTTTTC
*
98105 TTCCTTTTTTC
1 TTTCTTTTTTC
98116 T
1 T
98117 CCAAAGTTTA
Statistics
Matches: 36, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
7 2 0.06
9 9 0.25
10 1 0.03
11 16 0.44
12 8 0.22
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (11 bp):
TTTCTTTTTTC
Found at i:98084 original size:8 final size:8
Alignment explanation
Indices: 98064--98116 Score: 60
Period size: 7 Copynumber: 7.1 Consensus size: 8
98054 CCACTTGCCT
98064 TTTCTTT-
1 TTTCTTTC
98071 TTTCTTTC
1 TTTCTTTC
98079 TTTCTTTC
1 TTTCTTTC
98087 TTTCTTT-
1 TTTCTTTC
*
98094 TCTCTTT-
1 TTTCTTTC
*
98101 TTTCTTCC
1 TTTCTTTC
98109 TTT-TTTC
1 TTTCTTTC
98116 T
1 T
98117 CCAAAGTTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
7 22 0.55
8 18 0.45
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (8 bp):
TTTCTTTC
Found at i:103755 original size:52 final size:52
Alignment explanation
Indices: 103677--103805 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
103667 CGAAATATGA
* *
103677 AAATTTGCCAGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTCCATAGTGTATCGATACATCTGGGC
* *
103729 AAATTTGCCTGTATGTATTGATACATTCCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTCCATAGTGTATCGATACATCTGGGC
103781 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
103806 AAGATCAGTG
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 71 1.00
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.34
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTCCATAGTGTATCGATACATCTGGGC
Found at i:103816 original size:52 final size:52
Alignment explanation
Indices: 103677--103825 Score: 219
Period size: 52 Copynumber: 2.9 Consensus size: 52
103667 CGAAATATGA
* *
103677 AAATTTGCCAGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTACATAGTGTATCGATACATCTGGGC
* * *
103729 AAATTTGCCTGTATGTATTGATACATTCCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTACATAGTGTATCGATACATCTGGGC
* *
103781 AAATTTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTACAT-AGTGTATCGATACA
103826 ATATATCGAT
Statistics
Matches: 87, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
51 2 0.02
52 85 0.98
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTACATAGTGTATCGATACATCTGGGC
Found at i:103915 original size:19 final size:17
Alignment explanation
Indices: 103891--103988 Score: 86
Period size: 19 Copynumber: 5.9 Consensus size: 17
103881 ACTAGTACAT
103891 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAA-TTA
103910 TGTATCGATAC--A-T-
1 TGTATCGATACAAATTA
103923 TGTATCGATACAACACTTA
1 TGTATCGATACAA-A-TTA
103942 TGTATCGATAC--A-T-
1 TGTATCGATACAAATTA
103955 TGTATCGATACAACATTAA
1 TGTATCGATACAA-ATT-A
103974 TGTATCGATACAAAT
1 TGTATCGATACAAAT
103989 CGTTGAAATT
Statistics
Matches: 67, Mismatches: 0, Indels: 25
0.73 0.00 0.27
Matches are distributed among these distances:
13 22 0.33
14 2 0.03
16 4 0.06
17 1 0.01
18 3 0.04
19 35 0.52
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.34
Consensus pattern (17 bp):
TGTATCGATACAAATTA
Found at i:103927 original size:32 final size:32
Alignment explanation
Indices: 103886--103985 Score: 175
Period size: 32 Copynumber: 3.1 Consensus size: 32
103876 TTCGTACTAG
*
103886 TACATTGTATCGATACAAAACTTATGTATCGA
1 TACATTGTATCGATACAACACTTATGTATCGA
103918 TACATTGTATCGATACAACACTTATGTATCGA
1 TACATTGTATCGATACAACACTTATGTATCGA
103950 TACATTGTATCGATACAACA-TTAATGTATCGA
1 TACATTGTATCGATACAACACTT-ATGTATCGA
103982 TACA
1 TACA
103986 AATCGTTGAA
Statistics
Matches: 66, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
31 2 0.03
32 64 0.97
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.34
Consensus pattern (32 bp):
TACATTGTATCGATACAACACTTATGTATCGA
Found at i:103928 original size:13 final size:13
Alignment explanation
Indices: 103910--103966 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
103900 ACAAAACTTA
103910 TGTATCGATACAT
1 TGTATCGATACAT
103923 TGTATCGATACAACACTT
1 TGTATCGAT---ACA--T
103941 ATGTATCGATACAT
1 -TGTATCGATACAT
103955 TGTATCGATACA
1 TGTATCGATACA
103967 ACATTAATGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 21 0.55
14 1 0.03
16 6 0.16
18 1 0.03
19 9 0.24
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAT
Done.