Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1277
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: 28204
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Found at i:960 original size:30 final size:30
Alignment explanation
Indices: 924--980 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
914 AATGTTACTA
*
924 ATTTAAAGTTGAATAAGGTCGTTCAACAAG
1 ATTTAAAGTTGAATAAGGTCATTCAACAAG
954 ATTTAAAGTTGAATAAGGTCATTCAAC
1 ATTTAAAGTTGAATAAGGTCATTCAAC
981 TTCATGATCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.40, C:0.11, G:0.18, T:0.32
Consensus pattern (30 bp):
ATTTAAAGTTGAATAAGGTCATTCAACAAG
Found at i:3186 original size:19 final size:19
Alignment explanation
Indices: 3159--3199 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
3149 TAACTAGCTC
*
3159 AAAATAATAT-TTTTATATT
1 AAAAAAATATATTTTAT-TT
3178 AAAAAAATATATTTTATTT
1 AAAAAAATATATTTTATTT
3197 AAA
1 AAA
3200 TTTAATTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
AAAAAAATATATTTTATTT
Found at i:3262 original size:17 final size:17
Alignment explanation
Indices: 3232--3289 Score: 53
Period size: 17 Copynumber: 3.3 Consensus size: 17
3222 TATTAATATA
**
3232 AAAATAATTTTTTAAAT
1 AAAATAATAATTTAAAT
3249 AAAATAATAATTTAAATT
1 AAAATAATAATTTAAA-T
* * *
3267 TAAATATGTAAATTAAAT
1 AAAATA-ATAATTTAAAT
3285 AAAAT
1 AAAAT
3290 TATATTTATA
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
17 14 0.42
18 11 0.33
19 8 0.24
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.40
Consensus pattern (17 bp):
AAAATAATAATTTAAAT
Found at i:3268 original size:23 final size:23
Alignment explanation
Indices: 3193--3273 Score: 84
Period size: 22 Copynumber: 3.7 Consensus size: 23
3183 AATATATTTT
*
3193 ATTTAAATTTAATTATAAAAAT-
1 ATTTAAATTTAAATATAAAAATA
*
3215 ATATAAATATT-AATATAAAAATA
1 ATTTAAAT-TTAAATATAAAAATA
3238 ATTT---TTTAAATA-AAATAATA
1 ATTTAAATTTAAATATAAA-AATA
3258 ATTTAAATTTAAATAT
1 ATTTAAATTTAAATAT
3274 GTAAATTAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 14
0.74 0.05 0.22
Matches are distributed among these distances:
19 5 0.10
20 13 0.27
22 17 0.35
23 13 0.27
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
ATTTAAATTTAAATATAAAAATA
Found at i:3659 original size:39 final size:41
Alignment explanation
Indices: 3610--3686 Score: 113
Period size: 39 Copynumber: 1.9 Consensus size: 41
3600 TTCTAATTTT
* * *
3610 AATAATTTATATATTTTATTATA-TCATAA-TTATATTTAA
1 AATAATTTATAAATTTTAATATATTAATAATTTATATTTAA
3649 AATAATTTATAAATTTTAATATATTAATAATTTATATT
1 AATAATTTATAAATTTTAATATATTAATAATTTATATT
3687 ATATAAATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
39 21 0.64
40 5 0.15
41 7 0.21
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.53
Consensus pattern (41 bp):
AATAATTTATAAATTTTAATATATTAATAATTTATATTTAA
Found at i:3693 original size:32 final size:33
Alignment explanation
Indices: 3656--3719 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
3646 TAAAATAATT
*
3656 TATAAATTTT-A-ATATATTAATAATTTATATTA
1 TATAAATTTTAAGATATATAAAT-ATTTATATTA
3688 TATAAATTTTAAGATATATAAATATTTATATT
1 TATAAATTTTAAGATATATAAATATTTATATT
3720 TTATTTATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 10 0.34
33 10 0.34
34 9 0.31
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (33 bp):
TATAAATTTTAAGATATATAAATATTTATATTA
Found at i:3696 original size:40 final size:41
Alignment explanation
Indices: 3611--3729 Score: 99
Period size: 39 Copynumber: 3.0 Consensus size: 41
3601 TCTAATTTTA
* * * *
3611 ATAATTTATATATTTTATTATA-TCATAA-TTATATT-TAAA
1 ATAATTTATAAATTTTAATATATTAATAATTTATATTAT-AT
3650 ATAATTTATAAATTTTAATATATTAATAATTTATATTATAT
1 ATAATTTATAAATTTTAATATATTAATAATTTATATTATAT
* * *
3691 A-AATTT-TAAGATATATAA-ATATTTATATTTTAT-TTATAT
1 ATAATTTATAA-AT-TTTAATATATTAATAATTTATATTATAT
3730 TATATTTTTA
Statistics
Matches: 68, Mismatches: 7, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
39 29 0.43
40 25 0.37
41 13 0.19
42 1 0.01
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.54
Consensus pattern (41 bp):
ATAATTTATAAATTTTAATATATTAATAATTTATATTATAT
Found at i:3698 original size:16 final size:15
Alignment explanation
Indices: 3651--3715 Score: 53
Period size: 16 Copynumber: 4.1 Consensus size: 15
3641 ATATTTAAAA
3651 TAATT-TATAAATTT
1 TAATTATATAAATTT
*
3665 TAA-TATATTAATAATT
1 TAATTATA-TAA-ATTT
3681 TATATTATATAAATTT
1 TA-ATTATATAAATTT
*
3697 TAAGATATATAAATATT
1 TAA-TTATATAAAT-TT
3714 TA
1 TA
3716 TATTTTATTT
Statistics
Matches: 41, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
13 1 0.02
14 5 0.12
15 4 0.10
16 19 0.46
17 8 0.20
18 4 0.10
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (15 bp):
TAATTATATAAATTT
Found at i:5174 original size:20 final size:22
Alignment explanation
Indices: 5149--5189 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
5139 TTTATAAAAA
5149 TAAATAAA-TT-ATTTAATTTT
1 TAAATAAATTTAATTTAATTTT
5169 TAAATAAATTTAATTTAATTT
1 TAAATAAATTTAATTTAATTT
5190 AAAATAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.42
21 2 0.11
22 9 0.47
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
TAAATAAATTTAATTTAATTTT
Found at i:5196 original size:21 final size:20
Alignment explanation
Indices: 5150--5196 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
5140 TTATAAAAAT
*
5150 AAATAAATTATTTAATTTTT
1 AAATAAATTATTTAATTTTA
5170 AAATAAATTTAATTTAA-TTTA
1 AAATAAA-TT-ATTTAATTTTA
5191 AAATAA
1 AAATAA
5197 TTAAAATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 7 0.29
21 11 0.46
22 6 0.25
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
AAATAAATTATTTAATTTTA
Found at i:5753 original size:12 final size:11
Alignment explanation
Indices: 5736--5782 Score: 62
Period size: 12 Copynumber: 4.3 Consensus size: 11
5726 ATTATTAAAG
5736 AAAAAATGAATA
1 AAAAAAT-AATA
5748 AAAAAATATATA
1 AAAAAATA-ATA
5760 AAAAAAT-ATA
1 AAAAAATAATA
5770 AAAAAATAA-A
1 AAAAAATAATA
5780 AAA
1 AAA
5783 TATATTTATT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
10 14 0.42
11 2 0.06
12 17 0.52
ACGTcount: A:0.81, C:0.00, G:0.02, T:0.17
Consensus pattern (11 bp):
AAAAAATAATA
Found at i:5762 original size:10 final size:10
Alignment explanation
Indices: 5744--5787 Score: 56
Period size: 10 Copynumber: 4.5 Consensus size: 10
5734 AGAAAAAATG
5744 AATA-AAAAA
1 AATATAAAAA
5753 ATATATAAAAA
1 A-ATATAAAAA
5764 AATATAAAAA
1 AATATAAAAA
5774 AATA-AAAAA
1 AATATAAAAA
*
5783 TATAT
1 AATAT
5788 TTATTTTTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
9 9 0.29
10 16 0.52
11 6 0.19
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (10 bp):
AATATAAAAA
Found at i:5948 original size:26 final size:25
Alignment explanation
Indices: 5901--5953 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
5891 TTTTTAAATT
* * *
5901 TTTTTAAATAATAATAATTAATTTA
1 TTTTTAAATAAAAATAAATAATATA
5926 TTTTTAAATAAAAATAACATAATATA
1 TTTTTAAATAAAAATAA-ATAATATA
5952 TT
1 TT
5954 AATATTAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
25 16 0.67
26 8 0.33
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (25 bp):
TTTTTAAATAAAAATAAATAATATA
Found at i:12189 original size:8 final size:8
Alignment explanation
Indices: 12176--12205 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
12166 ACTCTCCTTC
12176 ATTTTTTT
1 ATTTTTTT
12184 A-TTTTTT
1 ATTTTTTT
12191 ATTTTTTT
1 ATTTTTTT
12199 ATTTTTT
1 ATTTTTT
12206 AACTTTTGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.33
8 14 0.67
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (8 bp):
ATTTTTTT
Found at i:12196 original size:15 final size:15
Alignment explanation
Indices: 12176--12206 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
12166 ACTCTCCTTC
12176 ATTTTTTTATTTTTT
1 ATTTTTTTATTTTTT
12191 ATTTTTTTATTTTTT
1 ATTTTTTTATTTTTT
12206 A
1 A
12207 ACTTTTGGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (15 bp):
ATTTTTTTATTTTTT
Found at i:12212 original size:15 final size:15
Alignment explanation
Indices: 12179--12212 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
12169 CTCCTTCATT
**
12179 TTTTTATTTTTTATT
1 TTTTTATTTTTTAAC
12194 TTTTTATTTTTTAAC
1 TTTTTATTTTTTAAC
12209 TTTT
1 TTTT
12213 GGAGGAAATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.15, C:0.03, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTTTATTTTTTAAC
Found at i:12514 original size:2 final size:2
Alignment explanation
Indices: 12507--12536 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
12497 TGAGAGTGGG
12507 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
12537 ACATACACAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:13824 original size:42 final size:42
Alignment explanation
Indices: 13752--13836 Score: 118
Period size: 42 Copynumber: 2.0 Consensus size: 42
13742 ATCAAAATAT
13752 GACTTTCAAATTAAGTTTCGAGTTCGTGAATGCTGCCAAAGA
1 GACTTTCAAATTAAGTTTCGAGTTCGTGAATGCTGCCAAAGA
* * **
13794 GACTTTCAAATT-AGTTTTGAATTTTTTGAATGCTGCCAAAGA
1 GACTTTCAAATTAAGTTTCG-AGTTCGTGAATGCTGCCAAAGA
13836 G
1 G
13837 GGTGGCGATG
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
41 6 0.16
42 32 0.84
ACGTcount: A:0.31, C:0.14, G:0.20, T:0.35
Consensus pattern (42 bp):
GACTTTCAAATTAAGTTTCGAGTTCGTGAATGCTGCCAAAGA
Found at i:14099 original size:18 final size:18
Alignment explanation
Indices: 14076--14114 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
14066 AATCGATTGA
*
14076 AAATTTTTAAAATTAAAT
1 AAATTTGTAAAATTAAAT
*
14094 AAATTTGTAAAATTTAAT
1 AAATTTGTAAAATTAAAT
14112 AAA
1 AAA
14115 AAAATTTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (18 bp):
AAATTTGTAAAATTAAAT
Found at i:15138 original size:20 final size:20
Alignment explanation
Indices: 15113--15156 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
15103 TATTAATTCT
* *
15113 ATTTTTAATATATTTAATATA
1 ATTTTTAAGATA-TTAATAAA
15134 ATTTTTAAGATATTAATAAA
1 ATTTTTAAGATATTAATAAA
15154 ATT
1 ATT
15157 ATTTTATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (20 bp):
ATTTTTAAGATATTAATAAA
Found at i:15617 original size:17 final size:19
Alignment explanation
Indices: 15594--15641 Score: 64
Period size: 17 Copynumber: 2.6 Consensus size: 19
15584 ATTACTCTTT
15594 TAATAAATATTAAAAAT-A
1 TAATAAATATTAAAAATGA
*
15612 -AATAAAAATTAAAAATGA
1 TAATAAATATTAAAAATGA
15630 TAATAATATATT
1 TAATAA-ATATT
15642 TTTATTATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
17 15 0.60
18 1 0.04
19 5 0.20
20 4 0.16
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (19 bp):
TAATAAATATTAAAAATGA
Found at i:15714 original size:26 final size:25
Alignment explanation
Indices: 15678--15726 Score: 71
Period size: 26 Copynumber: 1.9 Consensus size: 25
15668 TTAATTAATT
*
15678 TATATTAATTATTATATAATAAAAAA
1 TATATTAATTAATATATAA-AAAAAA
*
15704 TATATTTATTAATATATAAAAAA
1 TATATTAATTAATATATAAAAAA
15727 TGTTATATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 4 0.19
26 17 0.81
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (25 bp):
TATATTAATTAATATATAAAAAAAA
Found at i:15733 original size:26 final size:26
Alignment explanation
Indices: 15677--15737 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
15667 TTTAATTAAT
*
15677 TTATATTAATTATTATATAATAAAAA
1 TTATATTAATTAATATATAATAAAAA
* * *
15703 ATATATTTATTAATATATAA-AAAATG
1 TTATATTAATTAATATATAATAAAA-A
15729 TTATATTAA
1 TTATATTAA
15738 AATAGAAGTG
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
25 4 0.14
26 24 0.86
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (26 bp):
TTATATTAATTAATATATAATAAAAA
Found at i:16206 original size:35 final size:35
Alignment explanation
Indices: 16137--16211 Score: 93
Period size: 35 Copynumber: 2.2 Consensus size: 35
16127 ATATAATACG
*
16137 AATA-ATTAATATATTAAAATTTATATAAATATAT
1 AATATATTAATATATTAAAATATATATAAATATAT
*
16171 AATATATTAAATATAATTATAATATA-ATAAA-ATAT
1 AATATATT-AATAT-ATTAAAATATATATAAATATAT
16206 AATATA
1 AATATA
16212 AATAGATAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
34 4 0.11
35 13 0.36
36 10 0.28
37 9 0.25
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (35 bp):
AATATATTAATATATTAAAATATATATAAATATAT
Found at i:16228 original size:21 final size:21
Alignment explanation
Indices: 16159--16221 Score: 69
Period size: 20 Copynumber: 3.0 Consensus size: 21
16149 ATTAAAATTT
*
16159 ATATAAATATATAATAT-ATTAA
1 ATAT-AAT-TATAATATAATAAA
16181 ATATAATTATAATATAATAAA
1 ATATAATTATAATATAATAAA
16202 ATATAA-TATAA-ATAGATAAA
1 ATATAATTATAATATA-ATAAA
16222 TTTATAAAAC
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
19 3 0.08
20 18 0.47
21 13 0.34
22 4 0.11
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (21 bp):
ATATAATTATAATATAATAAA
Found at i:16503 original size:2 final size:2
Alignment explanation
Indices: 16496--16534 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
16486 ATTTAAAATA
16496 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
16535 GAGAGAGAGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:16806 original size:18 final size:19
Alignment explanation
Indices: 16765--16808 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
16755 AAAATATGTT
16765 ATATTTATTTTTTTATAAA
1 ATATTTATTTTTTTATAAA
*
16784 TTATTT-TTTATTTT-TAAA
1 ATATTTATTT-TTTTATAAA
16802 ATATTTA
1 ATATTTA
16809 AAAAATAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
18 12 0.57
19 9 0.43
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (19 bp):
ATATTTATTTTTTTATAAA
Found at i:16884 original size:21 final size:22
Alignment explanation
Indices: 16833--16884 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 22
16823 TACATATATA
*
16833 TTAATTT-ATTAATAAATTTAT
1 TTAATTTGTTTAATAAATTTAT
**
16854 TT-ATGAGTTTAAT-AATTTAT
1 TTAATTTGTTTAATAAATTTAT
16874 TTAATTTGTTT
1 TTAATTTGTTT
16885 TAAGTTAAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 4
0.73 0.15 0.12
Matches are distributed among these distances:
20 11 0.46
21 13 0.54
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.60
Consensus pattern (22 bp):
TTAATTTGTTTAATAAATTTAT
Found at i:16965 original size:20 final size:20
Alignment explanation
Indices: 16942--16982 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
16932 TATAAATATT
16942 ATTATAAAAATATTTTAAAA
1 ATTATAAAAATATTTTAAAA
*
16962 ATTATAAAATTATTTTAAAA
1 ATTATAAAAATATTTTAAAA
16982 A
1 A
16983 ATAAATAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
ATTATAAAAATATTTTAAAA
Found at i:16992 original size:21 final size:20
Alignment explanation
Indices: 16947--16996 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
16937 ATATTATTAT
*
16947 AAAAA-TATTTTAAAAATTA
1 AAAAATTATTTTAAAAAATA
*
16966 TAAAATTATTTTAAAAAATA
1 AAAAATTATTTTAAAAAATA
16986 AATAAATTATT
1 AA-AAATTATT
16997 AAATTAATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 4 0.15
20 14 0.54
21 8 0.31
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
AAAAATTATTTTAAAAAATA
Found at i:17983 original size:24 final size:26
Alignment explanation
Indices: 17953--18013 Score: 81
Period size: 28 Copynumber: 2.3 Consensus size: 26
17943 AAGTGTCATG
17953 TATATATTT-AAATTAT-TATTTTTA
1 TATATATTTAAAATTATATATTTTTA
17977 TATATATTTAAAAAATTATATATTTTTA
1 TATATATTT--AAAATTATATATTTTTA
*
18005 TATTTATTT
1 TATATATTT
18014 TTAAATATAT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
24 9 0.28
27 7 0.22
28 16 0.50
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (26 bp):
TATATATTTAAAATTATATATTTTTA
Found at i:18026 original size:22 final size:22
Alignment explanation
Indices: 17996--18037 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
17986 AAAAAATTAT
*
17996 ATATTTTTATATT-TATTTTTAA
1 ATATATTTA-ATTATATTTTTAA
18018 ATATATTTAATTATATTTTT
1 ATATATTTAATTATATTTTT
18038 GAGTTTAATC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (22 bp):
ATATATTTAATTATATTTTTAA
Found at i:19052 original size:24 final size:24
Alignment explanation
Indices: 18985--19052 Score: 70
Period size: 24 Copynumber: 2.8 Consensus size: 24
18975 ATAATATAAT
18985 TAAATATAAT-ATTAATA-TTATA
1 TAAATATAATAATTAATATTTATA
*
19007 TAAATATGTAATAAATTAATATTTTTA
1 TAAATA--TAAT-AATTAATATTTATA
19034 -AAATATAAATAATTAATAT
1 TAAATAT-AATAATTAATAT
19053 ATTAAACTTT
Statistics
Matches: 39, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
22 6 0.15
24 14 0.36
25 3 0.08
26 12 0.31
27 4 0.10
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.44
Consensus pattern (24 bp):
TAAATATAATAATTAATATTTATA
Found at i:19065 original size:23 final size:24
Alignment explanation
Indices: 18976--19068 Score: 79
Period size: 26 Copynumber: 4.0 Consensus size: 24
18966 AAATATGATA
*
18976 TAATATAATT-AAATAT-AAT-AT
1 TAATATTATTAAAATATAAATAAT
*
18997 TAATATTA-TATAAATATGTAATAAAT
1 TAATATTATTA-AAATAT-AAAT-AAT
*
19023 TAATATTTTTAAAATATAAATAAT
1 TAATATTATTAAAATATAAATAAT
* *
19047 TAATA-TATTAAACTTTAAATAA
1 TAATATTATTAAAATATAAATAA
19069 ATTTTTTATA
Statistics
Matches: 59, Mismatches: 6, Indels: 12
0.77 0.08 0.16
Matches are distributed among these distances:
20 1 0.02
21 7 0.12
22 6 0.10
23 14 0.24
24 11 0.19
25 3 0.05
26 15 0.25
27 2 0.03
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (24 bp):
TAATATTATTAAAATATAAATAAT
Found at i:19071 original size:24 final size:25
Alignment explanation
Indices: 18990--19071 Score: 80
Period size: 26 Copynumber: 3.3 Consensus size: 25
18980 ATAATTAAAT
*
18990 ATAATATTAATATTA-TATAAATATGTA
1 ATAA-ATTAATATTATTA-AAATAT-AA
*
19017 ATAAATTAATATTTTTAAAATATAA
1 ATAAATTAATATTATTAAAATATAA
* *
19042 AT-AATTAATA-TATTAAACTTTAA
1 ATAAATTAATATTATTAAAATATAA
19065 ATAAATT
1 ATAAATT
19072 TTTTATAAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
23 12 0.25
24 12 0.25
25 3 0.06
26 15 0.31
27 6 0.12
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (25 bp):
ATAAATTAATATTATTAAAATATAA
Found at i:20139 original size:6 final size:6
Alignment explanation
Indices: 20122--20151 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
20112 TGCACGTCCC
*
20122 TGGCTA TAGCTA TGGCTA TGGCTA TGGCTA
1 TGGCTA TGGCTA TGGCTA TGGCTA TGGCTA
20152 GCTGTTGCTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.20, C:0.17, G:0.30, T:0.33
Consensus pattern (6 bp):
TGGCTA
Found at i:20424 original size:18 final size:17
Alignment explanation
Indices: 20401--20434 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
20391 AATTTATTAA
20401 ATTCATATAATATAAATT
1 ATTCATATAA-ATAAATT
20419 ATTCATATAAATAAAT
1 ATTCATATAAATAAAT
20435 AATACTTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (17 bp):
ATTCATATAAATAAATT
Found at i:20489 original size:21 final size:21
Alignment explanation
Indices: 20465--20505 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
20455 AGACATAATA
*
20465 ATATGACATATGTGTGTTTAT
1 ATATGACATATGTGTATTTAT
20486 ATATGACATATGTGTATTTA
1 ATATGACATATGTGTATTTA
20506 AAAATAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.32, C:0.05, G:0.17, T:0.46
Consensus pattern (21 bp):
ATATGACATATGTGTATTTAT
Found at i:23856 original size:6 final size:7
Alignment explanation
Indices: 23839--23864 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
23829 TCAAAACAGA
23839 AAAAAAT
1 AAAAAAT
23846 AAAAAAT
1 AAAAAAT
23853 AAAAAAT
1 AAAAAAT
23860 AAAAA
1 AAAAA
23865 GAAGGCACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAAAT
Found at i:25494 original size:3 final size:3
Alignment explanation
Indices: 25486--25534 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
25476 GTAAACAAAA
25486 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
25534 A
1 A
25535 TCAGAAAGGG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Done.