Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2603
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: 66178
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35
Found at i:3145 original size:21 final size:21
Alignment explanation
Indices: 3097--3153 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
3087 ATTTTGTCTT
* *
3097 TCTTCTTTGTTTTCCTTTTTTC
1 TCTTC-TTGTTTTGCTTTGTTC
3119 TCTTCTTGTTTTGCTTTCGTTC
1 TCTTCTTGTTTTGCTTT-GTTC
*
3141 T-TTCTTGCTTTGC
1 TCTTCTTGTTTTGC
3154 GGGCTGAAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 22 0.71
22 9 0.29
ACGTcount: A:0.00, C:0.23, G:0.11, T:0.67
Consensus pattern (21 bp):
TCTTCTTGTTTTGCTTTGTTC
Found at i:8455 original size:19 final size:20
Alignment explanation
Indices: 8421--8463 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
8411 TCATGTTTGG
*
8421 TTTAATTTAAAATAAATGTT
1 TTTAATTTAAAATAAATATT
*
8441 TTTAA-TTACAATAAATATT
1 TTTAATTTAAAATAAATATT
8460 TTTA
1 TTTA
8464 TTTTTAAACT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (20 bp):
TTTAATTTAAAATAAATATT
Found at i:15305 original size:51 final size:51
Alignment explanation
Indices: 15250--15369 Score: 172
Period size: 51 Copynumber: 2.4 Consensus size: 51
15240 TGCATGCATA
* * * *
15250 TATCGATATATTGAAGAATGTATCGATAAATTT-GGTCAAAAACTTAGAATG
1 TATCGATACAATGAAAAATGTATCGATAAATTTGGGTCAAAAAC-CAGAATG
*
15301 TATCGATACAATGAAAAATGTATCGATACATTTGGGTCAAAAACCAGAATG
1 TATCGATACAATGAAAAATGTATCGATAAATTTGGGTCAAAAACCAGAATG
15352 TATCGATACAAT-AAAAAT
1 TATCGATACAATGAAAAAT
15370 TTGCTTCGAC
Statistics
Matches: 63, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
50 6 0.10
51 47 0.75
52 10 0.16
ACGTcount: A:0.44, C:0.11, G:0.16, T:0.29
Consensus pattern (51 bp):
TATCGATACAATGAAAAATGTATCGATAAATTTGGGTCAAAAACCAGAATG
Found at i:15411 original size:21 final size:21
Alignment explanation
Indices: 15387--15441 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 21
15377 GACATGGTCC
15387 TGTATCGATACATTTCAAATA
1 TGTATCGATACATTTCAAATA
**
15408 TGTATCGATACA-TTCACTTA
1 TGTATCGATACATTTCAAATA
*
15428 TGTATTGATACATT
1 TGTATCGATACATT
15442 ACTATATTGT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
20 17 0.57
21 13 0.43
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.42
Consensus pattern (21 bp):
TGTATCGATACATTTCAAATA
Found at i:15454 original size:21 final size:20
Alignment explanation
Indices: 15387--15460 Score: 78
Period size: 21 Copynumber: 3.6 Consensus size: 20
15377 GACATGGTCC
* **
15387 TGTATCGATACATTTCAAATA
1 TGTATTGATACA-TTCACTTA
*
15408 TGTATCGATACATTCACTTA
1 TGTATTGATACATTCACTTA
15428 TGTATTGATACATT-ACTATA
1 TGTATTGATACATTCACT-TA
15448 TTGTATTGATACA
1 -TGTATTGATACA
15461 ATTTGTTGAA
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
19 3 0.06
20 21 0.44
21 24 0.50
ACGTcount: A:0.34, C:0.14, G:0.11, T:0.42
Consensus pattern (20 bp):
TGTATTGATACATTCACTTA
Found at i:17068 original size:5 final size:5
Alignment explanation
Indices: 17052--17080 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
17042 ACAAGAATAC
17052 ATAAA A-AAA ATAAA ATAAA ATAAA ATAAA
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA
17081 GAAAGACTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (5 bp):
ATAAA
Found at i:17645 original size:22 final size:22
Alignment explanation
Indices: 17619--17666 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
17609 GATGAGAAAA
17619 CTTTATTTTGGTGACATCTATG
1 CTTTATTTTGGTGACATCTATG
17641 CTTTATTTTGGTGACATCTATG
1 CTTTATTTTGGTGACATCTATG
17663 CTTT
1 CTTT
17667 GGACAAATCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.17, C:0.15, G:0.17, T:0.52
Consensus pattern (22 bp):
CTTTATTTTGGTGACATCTATG
Found at i:20230 original size:23 final size:23
Alignment explanation
Indices: 20178--20247 Score: 72
Period size: 22 Copynumber: 3.0 Consensus size: 23
20168 AAAAATATTT
20178 TATTTAAA-TTTAATTATAAAA-A
1 TATTTAAATTTTAA-TATAAAATA
*
20200 TATATAAATTTTAATATAAAATA
1 TATTTAAATTTTAATATAAAATA
*
20223 TTTTTAAATATTTTAATAATAAAAT
1 TATTT-AA-ATTTTAAT-ATAAAAT
20248 TAATTCTCGA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
22 14 0.35
23 9 0.22
24 2 0.05
25 8 0.20
26 7 0.17
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
TATTTAAATTTTAATATAAAATA
Found at i:20945 original size:15 final size:15
Alignment explanation
Indices: 20925--21008 Score: 60
Period size: 15 Copynumber: 6.1 Consensus size: 15
20915 GCTGCTGTTT
*
20925 TTAAATTTAATAATA
1 TTAAATATAATAATA
*
20940 TTAAATATAATCATA
1 TTAAATATAATAATA
20955 -TAAATATAA-AATA
1 TTAAATATAATAATA
* *
20968 --AAAAATTAT-A-A
1 TTAAATATAATAATA
20979 TTAAA-A-AATAATA
1 TTAAATATAATAATA
20992 -TAAATATAATAAATA
1 TTAAATATAAT-AATA
21007 TT
1 TT
21009 TTAAAATTTA
Statistics
Matches: 54, Mismatches: 6, Indels: 17
0.70 0.08 0.22
Matches are distributed among these distances:
11 3 0.06
12 13 0.24
13 8 0.15
14 12 0.22
15 17 0.31
16 1 0.02
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (15 bp):
TTAAATATAATAATA
Found at i:21013 original size:18 final size:18
Alignment explanation
Indices: 20992--21077 Score: 54
Period size: 18 Copynumber: 4.6 Consensus size: 18
20982 AAAAATAATA
20992 TAAATATAATAAATATTT
1 TAAATATAATAAATATTT
*
21010 TAAAATTTATATAATAAAAATTAT
1 T--AA---ATATAATAAATATT-T
*
21034 TAAA-ATATTAAA-ATTT
1 TAAATATAATAAATATTT
21050 ATATAA-AT-ATAAATATTT
1 -TA-AATATAATAAATATTT
21068 TAAATATAAT
1 TAAATATAAT
21078 TATAATATAA
Statistics
Matches: 54, Mismatches: 3, Indels: 22
0.68 0.04 0.28
Matches are distributed among these distances:
16 3 0.06
17 13 0.24
18 18 0.33
19 1 0.02
20 2 0.04
22 2 0.04
23 13 0.24
24 2 0.04
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
TAAATATAATAAATATTT
Found at i:21025 original size:23 final size:24
Alignment explanation
Indices: 20995--21039 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
20985 AATAATATAA
*
20995 ATATAATAAATATT-TTAAAATTT
1 ATATAATAAAAATTATTAAAATTT
21018 ATATAATAAAAATTATTAAAAT
1 ATATAATAAAAATTATTAAAAT
21040 ATTAAAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (24 bp):
ATATAATAAAAATTATTAAAATTT
Found at i:21045 original size:32 final size:34
Alignment explanation
Indices: 20986--21106 Score: 111
Period size: 34 Copynumber: 3.5 Consensus size: 34
20976 TAATTAAAAA
* *
20986 ATAATATAAATATAATAAATATTTTAAAATTTAT
1 ATAATAAAAATATAATAAATATATTAAAATTTAT
*
21020 ATAATAAAAAT-TATTAAA-ATATTAAAATTTAT
1 ATAATAAAAATATAATAAATATATTAAAATTTAT
* ** * *
21052 ATAAATATAAATATTTTAAATATAATTATAATATAAT
1 AT-AATAAAAATATAATAAATAT-ATTAAAAT-TTAT
*
21089 AAAAATAAAAATATAATA
1 -ATAATAAAAATATAATA
21107 TGAATATAAA
Statistics
Matches: 70, Mismatches: 11, Indels: 9
0.78 0.12 0.10
Matches are distributed among these distances:
32 15 0.21
33 14 0.20
34 16 0.23
35 2 0.03
36 7 0.10
37 15 0.21
38 1 0.01
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (34 bp):
ATAATAAAAATATAATAAATATATTAAAATTTAT
Found at i:21061 original size:6 final size:6
Alignment explanation
Indices: 21050--21116 Score: 50
Period size: 6 Copynumber: 11.2 Consensus size: 6
21040 ATTAAAATTT
* * *
21050 ATATAA ATATAA ATATTTTAA ATATAA TTAT-A ATAT-A ATAAAA ATAAAA
1 ATATAA ATATAA ATA---TAA ATATAA ATATAA ATATAA ATATAA ATATAA
*
21099 ATAT-A ATATGA ATATAA A
1 ATATAA ATATAA ATATAA A
21117 ATTATAAAGT
Statistics
Matches: 51, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
5 13 0.25
6 32 0.63
9 6 0.12
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (6 bp):
ATATAA
Found at i:21062 original size:17 final size:17
Alignment explanation
Indices: 21010--21067 Score: 61
Period size: 18 Copynumber: 3.5 Consensus size: 17
21000 ATAAATATTT
21010 TAAAATTTATAT-AATA
1 TAAAATTTATATAAATA
21026 -AAAA-TTAT-TAAAATA
1 TAAAATTTATAT-AAATA
21041 TTAAAATTTATATAAATA
1 -TAAAATTTATATAAATA
21059 TAAATATTT
1 TAAA-ATTT
21068 TAAATATAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 12
0.74 0.00 0.26
Matches are distributed among these distances:
13 1 0.03
14 4 0.11
15 8 0.23
17 8 0.23
18 13 0.37
19 1 0.03
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TAAAATTTATATAAATA
Found at i:21112 original size:17 final size:18
Alignment explanation
Indices: 20942--21123 Score: 56
Period size: 17 Copynumber: 9.8 Consensus size: 18
20932 TAATAATATT
*
20942 AAATATAATCATATAAATATA
1 AAATATAA-AATAT-AATA-A
*
20963 AAATAAAAAATTATAATTAAA
1 AAATATAAAA-TATAA-T-AA
20984 AAATAATATAAATATAATAA
1 AAAT-ATA-AAATATAATAA
* * *
21004 ATATTTTAAAAT-TTAT-A
1 A-AATATAAAATATAATAA
* *
21021 TAATA-AAAAT-T-ATTA
1 AAATATAAAATATAATAA
* *
21036 AAATATTAAAAT-TTATAT
1 AAATA-TAAAATATAATAA
**
21054 AAATAT-AAATATTTTAA
1 AAATATAAAATATAATAA
* *
21071 ATATAATTATAATATAATAA
1 AAAT-A-TAAAATATAATAA
*
21091 AAATA-AAAATATAATAT
1 AAATATAAAATATAATAA
*
21108 GAATATAAAATTATAA
1 AAATATAAAA-TATAA
21124 AGTCAGTATT
Statistics
Matches: 123, Mismatches: 22, Indels: 34
0.69 0.12 0.19
Matches are distributed among these distances:
14 2 0.02
15 11 0.09
16 6 0.05
17 29 0.24
18 15 0.12
19 11 0.09
20 19 0.15
21 19 0.15
22 8 0.07
23 3 0.02
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.37
Consensus pattern (18 bp):
AAATATAAAATATAATAA
Found at i:22421 original size:25 final size:26
Alignment explanation
Indices: 22373--22427 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 26
22363 AAGTTTTGAC
22373 TTTTATATATTTATTATATAAAATT-
1 TTTTATATATTTATTATATAAAATTA
* *
22398 TTTTATATTTTTACTTAT-TGAAATTA
1 TTTTATATATTTA-TTATATAAAATTA
22424 TTTT
1 TTTT
22428 GGGTTATTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 18 0.69
26 8 0.31
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.64
Consensus pattern (26 bp):
TTTTATATATTTATTATATAAAATTA
Found at i:27480 original size:9 final size:9
Alignment explanation
Indices: 27466--27507 Score: 50
Period size: 9 Copynumber: 4.8 Consensus size: 9
27456 ATAAGGTTTT
27466 TATTAATAA
1 TATTAATAA
*
27475 TATTAATAT
1 TATTAATAA
*
27484 TATTATTAA
1 TATTAATAA
*
27493 AATTAATAA
1 TATTAATAA
27502 T-TTAAT
1 TATTAAT
27508 TTATCATTTT
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
8 5 0.19
9 22 0.81
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (9 bp):
TATTAATAA
Found at i:28620 original size:21 final size:22
Alignment explanation
Indices: 28596--28640 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
28586 TGATTTTTGC
28596 TTTGTT-TTTGTTTT-ATTGAGT
1 TTTGTTATTT-TTTTAATTGAGT
*
28617 TTTGTTATTTTTTTAATTGGGT
1 TTTGTTATTTTTTTAATTGAGT
28639 TT
1 TT
28641 GAGTTTAAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 10 0.48
22 11 0.52
ACGTcount: A:0.11, C:0.00, G:0.18, T:0.71
Consensus pattern (22 bp):
TTTGTTATTTTTTTAATTGAGT
Found at i:28641 original size:21 final size:21
Alignment explanation
Indices: 28596--28641 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
28586 TGATTTTTGC
*
28596 TTTGTTTTTGTTTTATTGAGT
1 TTTGTTTTTGTTTTATTGAGG
28617 TTTGTTATTT-TTTTAATTG-GG
1 TTTGTT-TTTGTTTT-ATTGAGG
28638 TTTG
1 TTTG
28642 AGTTTAAGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
21 15 0.68
22 7 0.32
ACGTcount: A:0.11, C:0.00, G:0.20, T:0.70
Consensus pattern (21 bp):
TTTGTTTTTGTTTTATTGAGG
Found at i:28678 original size:45 final size:45
Alignment explanation
Indices: 28627--28743 Score: 216
Period size: 45 Copynumber: 2.6 Consensus size: 45
28617 TTTGTTATTT
28627 TTTTAATTGGGTTTGAGTTTAAGTTTATATAGATTTTTAGTTGGG
1 TTTTAATTGGGTTTGAGTTTAAGTTTATATAGATTTTTAGTTGGG
* *
28672 TTTTAATTGGGTTTGGGTTTAAGGTTATATAGATTTTTAGTTGGG
1 TTTTAATTGGGTTTGAGTTTAAGTTTATATAGATTTTTAGTTGGG
28717 TTTTAATTGGGTTTGAGTTTAAGTTTA
1 TTTTAATTGGGTTTGAGTTTAAGTTTA
28744 AATTTATATT
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 68 1.00
ACGTcount: A:0.21, C:0.00, G:0.26, T:0.53
Consensus pattern (45 bp):
TTTTAATTGGGTTTGAGTTTAAGTTTATATAGATTTTTAGTTGGG
Found at i:30041 original size:13 final size:13
Alignment explanation
Indices: 30023--30048 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
30013 TACAGCAAGT
30023 ATGTATCGATACA
1 ATGTATCGATACA
30036 ATGTATCGATACA
1 ATGTATCGATACA
30049 CAAAAAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:32299 original size:21 final size:21
Alignment explanation
Indices: 32266--32310 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
32256 TTGCAAGTTG
*
32266 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
32288 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
32308 AAA
1 AAA
32311 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:34134 original size:15 final size:15
Alignment explanation
Indices: 34114--34144 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
34104 TAAAAATGTC
*
34114 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
34129 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
34144 C
1 C
34145 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:36237 original size:20 final size:20
Alignment explanation
Indices: 36158--36237 Score: 79
Period size: 20 Copynumber: 3.8 Consensus size: 20
36148 AATGTCCAAA
*
36158 ATGTATCGATACATGTTTCT
1 ATGTATCGATACATTTTTCT
* *
36178 GTGTATCGATACATCTGGAAATTCT
1 ATGTATCGATACAT-T----TTTCT
36203 ATGTATCGATACATTTTTCT
1 ATGTATCGATACATTTTTCT
*
36223 TTGTATCGATACATT
1 ATGTATCGATACATT
36238 GTATCGATAC
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
20 31 0.63
24 1 0.02
25 17 0.35
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCT
Found at i:36241 original size:13 final size:13
Alignment explanation
Indices: 36223--36261 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
36213 ACATTTTTCT
36223 TTGTATCGATACA
1 TTGTATCGATACA
36236 TTGTATCGATACA
1 TTGTATCGATACA
*
36249 CTGTATCGATACA
1 TTGTATCGATACA
36262 GGGTGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:36406 original size:21 final size:21
Alignment explanation
Indices: 36382--36428 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
36372 AAATCTTTTG
36382 CAAAAT-ACTT-GTTTTTCACTT
1 CAAAATAACTTCGTTTTTCA--T
36403 C-AAATAACTTCGTTTTTCAT
1 CAAAATAACTTCGTTTTTCAT
36423 CAAAAT
1 CAAAAT
36429 CAGCATCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
20 6 0.26
21 9 0.39
22 8 0.35
ACGTcount: A:0.34, C:0.19, G:0.04, T:0.43
Consensus pattern (21 bp):
CAAAATAACTTCGTTTTTCAT
Found at i:36425 original size:20 final size:19
Alignment explanation
Indices: 36384--36426 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
36374 ATCTTTTGCA
36384 AAATACTTGTTTTTCACTTC
1 AAATACTTGTTTTTCAC-TC
36404 AAATAACTTCGTTTTTCA-TC
1 AAAT-ACTT-GTTTTTCACTC
36424 AAA
1 AAA
36427 ATCAGCATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 9 0.43
21 4 0.19
22 8 0.38
ACGTcount: A:0.33, C:0.19, G:0.05, T:0.44
Consensus pattern (19 bp):
AAATACTTGTTTTTCACTC
Found at i:43353 original size:19 final size:20
Alignment explanation
Indices: 43331--43377 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
43321 TAAAAGTTTT
43331 AATTTAAAAATATA-AAAAA
1 AATTTAAAAATATATAAAAA
* **
43350 AATTTATAAATATATAATTA
1 AATTTAAAAATATATAAAAA
43370 AATTTAAA
1 AATTTAAA
43378 TTTTAAATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
19 13 0.57
20 10 0.43
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
AATTTAAAAATATATAAAAA
Found at i:43653 original size:25 final size:27
Alignment explanation
Indices: 43620--43731 Score: 88
Period size: 29 Copynumber: 4.1 Consensus size: 27
43610 ATAAAATTGG
*
43620 ATATAATTTA-ATTATTATTATAT-TT
1 ATATTATTTATATTATTATTATATATT
* *
43645 ATATTATTTATATTATAATTTTAAAATATT
1 ATATTATTTATATTAT--TATT-ATATATT
* *
43675 ATA-TATTTATATGATTTTTA-ATATT
1 ATATTATTTATATTATTATTATATATT
*
43700 ATATTATATTATAATTATTTATTCTATATT
1 ATATTAT-TTAT-ATTA-TTATTATATATT
43730 AT
1 AT
43732 TTTGTGATTT
Statistics
Matches: 70, Mismatches: 7, Indels: 15
0.76 0.08 0.16
Matches are distributed among these distances:
25 17 0.24
26 9 0.13
27 8 0.11
28 6 0.09
29 18 0.26
30 12 0.17
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.59
Consensus pattern (27 bp):
ATATTATTTATATTATTATTATATATT
Found at i:43658 original size:23 final size:24
Alignment explanation
Indices: 43632--43732 Score: 77
Period size: 23 Copynumber: 4.3 Consensus size: 24
43622 ATAATTTAAT
43632 TATTATTATATTTATATTATT-TA
1 TATTATTATATTTATATTATTATA
* * *
43655 TATTATAAT-TTTAAAATATTATA
1 TATTATTATATTTATATTATTATA
* *
43678 TATT-TATATGATTTTTAATATTATA
1 TATTAT-TAT-ATTTATATTATTATA
* *
43703 T-TATATTATAATTAT-TTATTCTA
1 TAT-TATTATATTTATATTATTATA
43726 TATTATT
1 TATTATT
43733 TTGTGATTTT
Statistics
Matches: 61, Mismatches: 10, Indels: 14
0.72 0.12 0.16
Matches are distributed among these distances:
22 10 0.16
23 27 0.44
24 6 0.10
25 17 0.28
26 1 0.02
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.60
Consensus pattern (24 bp):
TATTATTATATTTATATTATTATA
Found at i:44165 original size:15 final size:16
Alignment explanation
Indices: 44145--44207 Score: 51
Period size: 15 Copynumber: 3.9 Consensus size: 16
44135 GTTTAATTTT
44145 TAAAATTCATATA-TA
1 TAAAATTCATATATTA
44160 TAAAATAT-ATATATTA
1 TAAAAT-TCATATATTA
*
44176 TGAAATTCAT-TCATTTA
1 TAAAATTCATAT-A-TTA
* *
44193 TATAATTTATATATT
1 TAAAATTCATATATT
44208 TTTAAAATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 11
0.72 0.08 0.21
Matches are distributed among these distances:
15 13 0.34
16 13 0.34
17 11 0.29
18 1 0.03
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.48
Consensus pattern (16 bp):
TAAAATTCATATATTA
Found at i:44236 original size:11 final size:11
Alignment explanation
Indices: 44203--44245 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
44193 TATAATTTAT
44203 ATATTTTTAAA
1 ATATTTTTAAA
**
44214 AT-TTTAAAAAA
1 ATATTT-TTAAA
44225 ATATTTTTAAA
1 ATATTTTTAAA
44236 ATATTTTTAA
1 ATATTTTTAA
44246 CTTCTTTTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
10 3 0.12
11 20 0.77
12 3 0.12
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (11 bp):
ATATTTTTAAA
Found at i:47801 original size:14 final size:13
Alignment explanation
Indices: 47777--47805 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
47767 GACAAAATAC
47777 TTTGGTTTTTTTT
1 TTTGGTTTTTTTT
47790 TTTGGTTTTTTTT
1 TTTGGTTTTTTTT
47803 TTT
1 TTT
47806 AATGCATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (13 bp):
TTTGGTTTTTTTT
Found at i:49241 original size:30 final size:31
Alignment explanation
Indices: 49196--49271 Score: 91
Period size: 30 Copynumber: 2.5 Consensus size: 31
49186 GGAGAATTTT
* * *
49196 AAAATTTTACTATTTTGAAATTCATTAATTC
1 AAAATATTAATATTTTAAAATTCATTAATTC
* * *
49227 AAATTATTAA-ATTTTAAAATTTATTAATTT
1 AAAATATTAATATTTTAAAATTCATTAATTC
49257 AAAATATTAATATTT
1 AAAATATTAATATTT
49272 GTAATTGCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
30 26 0.70
31 11 0.30
ACGTcount: A:0.45, C:0.04, G:0.01, T:0.50
Consensus pattern (31 bp):
AAAATATTAATATTTTAAAATTCATTAATTC
Found at i:49252 original size:17 final size:15
Alignment explanation
Indices: 49193--49261 Score: 52
Period size: 15 Copynumber: 4.5 Consensus size: 15
49183 TTTGGAGAAT
* *
49193 TTTAAAATTTTACTAT
1 TTTAAAA-TTTATTAA
* *
49209 TTTGAAATTCATTAA
1 TTTAAAATTTATTAA
*
49224 -TTCAAA-TTATTAAA
1 TTTAAAATTTATT-AA
49238 TTTTAAAATTTATTAA
1 -TTTAAAATTTATTAA
49254 TTTAAAAT
1 TTTAAAAT
49262 ATTAATATTT
Statistics
Matches: 42, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
13 4 0.10
14 7 0.17
15 13 0.31
16 13 0.31
17 5 0.12
ACGTcount: A:0.43, C:0.04, G:0.01, T:0.51
Consensus pattern (15 bp):
TTTAAAATTTATTAA
Found at i:54381 original size:19 final size:19
Alignment explanation
Indices: 54344--54381 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
54334 TTGATTAAGT
*
54344 TGTTTCTGGAGGAAGTTCA
1 TGTTTCTGGAGGAACTTCA
54363 TGTTTCT-GAGGAACCTTCA
1 TGTTTCTGGAGGAA-CTTCA
54382 GATCAGAGTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.21, C:0.16, G:0.26, T:0.37
Consensus pattern (19 bp):
TGTTTCTGGAGGAACTTCA
Found at i:58143 original size:21 final size:21
Alignment explanation
Indices: 58113--58165 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
58103 TTATTAAAAT
*
58113 TATATCTTTTCCATTTAATAAA
1 TATAT-TTTTCCATTCAATAAA
* *
58135 TATATTTTTTCATTCAATAAG
1 TATATTTTTCCATTCAATAAA
58156 TATATTTTTC
1 TATATTTTTC
58166 ACTTAAATAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
21 22 0.81
22 5 0.19
ACGTcount: A:0.32, C:0.11, G:0.02, T:0.55
Consensus pattern (21 bp):
TATATTTTTCCATTCAATAAA
Found at i:58174 original size:21 final size:21
Alignment explanation
Indices: 58113--58175 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
58103 TTATTAAAAT
* *
58113 TATATCTTTTCCATTTAATAAA
1 TATAT-TTTTTCATTAAATAAA
* *
58135 TATATTTTTTCATTCAATAAG
1 TATATTTTTTCATTAAATAAA
58156 TATA-TTTTTCACTTAAATAA
1 TATATTTTTTCA-TTAAATAA
58176 TGATTATATA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
20 7 0.19
21 24 0.67
22 5 0.14
ACGTcount: A:0.37, C:0.11, G:0.02, T:0.51
Consensus pattern (21 bp):
TATATTTTTTCATTAAATAAA
Found at i:58796 original size:17 final size:18
Alignment explanation
Indices: 58776--58813 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
58766 TAATTAAATT
58776 ATTGAAT-TAAAAAATAA
1 ATTGAATGTAAAAAATAA
* *
58793 ATTGATTGTAAAAAATTA
1 ATTGAATGTAAAAAATAA
58811 ATT
1 ATT
58814 TTAATATTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.55, C:0.00, G:0.08, T:0.37
Consensus pattern (18 bp):
ATTGAATGTAAAAAATAA
Found at i:63023 original size:22 final size:23
Alignment explanation
Indices: 62984--63026 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
62974 TATGATTATT
*
62984 TAATATAATTAATTTTTAAAAAA
1 TAATATAATTAATATTTAAAAAA
*
63007 TAATATTA-TAATATTTAAAA
1 TAATATAATTAATATTTAAAA
63027 TTTATAATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (23 bp):
TAATATAATTAATATTTAAAAAA
Found at i:63029 original size:31 final size:31
Alignment explanation
Indices: 62994--63057 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
62984 TAATATAATT
* * *
62994 AATTTTTAA-AAAATAATATTATAATATTTAA
1 AATTTATAATAAAATAATAATAAAAT-TTTAA
*
63025 AATTTATAATAAAATATTAATAAAATTTTAA
1 AATTTATAATAAAATAATAATAAAATTTTAA
63056 AA
1 AA
63058 AAATTATATT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
31 15 0.54
32 13 0.46
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (31 bp):
AATTTATAATAAAATAATAATAAAATTTTAA
Found at i:63062 original size:11 final size:11
Alignment explanation
Indices: 63022--63062 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
63012 TTATAATATT
63022 TAAAATTTATAA
1 TAAAATTT-TAA
*
63034 TAAAATATTAA
1 TAAAATTTTAA
63045 TAAAATTTTAA
1 TAAAATTTTAA
*
63056 AAAAATT
1 TAAAATT
63063 ATATTAATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
11 19 0.73
12 7 0.27
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (11 bp):
TAAAATTTTAA
Found at i:63105 original size:18 final size:20
Alignment explanation
Indices: 63084--63140 Score: 55
Period size: 20 Copynumber: 2.8 Consensus size: 20
63074 CTTTAATTTT
63084 TAAT-ATTTTTTTAAAAT-A
1 TAATAATTTTTTTAAAATAA
* *
63102 TAATGATAATTTTTAAAATAA
1 TAATAAT-TTTTTTAAAATAA
63123 TAATTAATTTATTTTAAA
1 TAA-TAATTT-TTTTAAA
63141 TAAAAGTAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
18 4 0.13
19 2 0.06
20 10 0.32
21 5 0.16
22 10 0.32
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (20 bp):
TAATAATTTTTTTAAAATAA
Found at i:63130 original size:19 final size:19
Alignment explanation
Indices: 63091--63132 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
63081 TTTTAATATT
63091 TTTTTAAAATATAATGATAA
1 TTTTTAAAATATAAT-ATAA
63111 TTTTTAAAATAATAAT-TAA
1 TTTTTAAAAT-ATAATATAA
63130 TTT
1 TTT
63133 ATTTTAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 6 0.29
20 10 0.48
21 5 0.24
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (19 bp):
TTTTTAAAATATAATATAA
Found at i:64573 original size:39 final size:41
Alignment explanation
Indices: 64526--64605 Score: 112
Period size: 41 Copynumber: 2.0 Consensus size: 41
64516 TAAAGTACTA
* *
64526 TTTATAAAAA-AATATAATT-AATA-AATTATTTTTTAAATT
1 TTTATAAAAATAATAT-ATTAAATATAAATATATTTTAAATT
64565 TTTATAAAAATAATATATTAAATATAAATATATTTTAAATT
1 TTTATAAAAATAATATATTAAATATAAATATATTTTAAATT
64606 AAAATTTAAG
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
39 13 0.36
40 9 0.25
41 14 0.39
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (41 bp):
TTTATAAAAATAATATATTAAATATAAATATATTTTAAATT
Found at i:64949 original size:17 final size:17
Alignment explanation
Indices: 64866--64951 Score: 60
Period size: 17 Copynumber: 5.2 Consensus size: 17
64856 GAAGAATAAG
64866 ATATAAATATAAA-ATTA
1 ATATAAA-ATAAATATTA
64883 AT-T--AATAAATAATTA
1 ATATAAAATAAAT-ATTA
64898 A-ATAAAAT--ATCATTAA
1 ATATAAAATAAAT-ATT-A
** *
64914 ATATATGATAAATTTTA
1 ATATAAAATAAATATTA
64931 ATATAAAATAAATATTA
1 ATATAAAATAAATATTA
64948 ATAT
1 ATAT
64952 TTTTGAGTAA
Statistics
Matches: 53, Mismatches: 7, Indels: 18
0.68 0.09 0.23
Matches are distributed among these distances:
13 5 0.09
14 1 0.02
15 11 0.21
16 3 0.06
17 29 0.55
18 2 0.04
19 2 0.04
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.38
Consensus pattern (17 bp):
ATATAAAATAAATATTA
Found at i:65047 original size:10 final size:10
Alignment explanation
Indices: 65034--65064 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
65024 TTTTAATTTT
65034 TATAAATATA
1 TATAAATATA
*
65044 TATAATTATA
1 TATAAATATA
65054 TATAAATATA
1 TATAAATATA
65064 T
1 T
65065 TTTAATTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (10 bp):
TATAAATATA
Found at i:65777 original size:15 final size:15
Alignment explanation
Indices: 65730--65779 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
65720 AAATATTTTA
65730 TATTTAAATTTATTT
1 TATTTAAATTTATTT
* * *
65745 AATTAAAAATTTA--A
1 TATT-TAAATTTATTT
65759 TATTTAAATTTATTT
1 TATTTAAATTTATTT
65774 TATTTA
1 TATTTA
65780 TATAAATATT
Statistics
Matches: 26, Mismatches: 6, Indels: 6
0.68 0.16 0.16
Matches are distributed among these distances:
13 7 0.27
14 3 0.12
15 9 0.35
16 7 0.27
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TATTTAAATTTATTT
Found at i:65897 original size:8 final size:8
Alignment explanation
Indices: 65884--65916 Score: 57
Period size: 8 Copynumber: 4.1 Consensus size: 8
65874 TTTATTACAA
65884 AAAAATTT
1 AAAAATTT
65892 AAAAATTT
1 AAAAATTT
65900 AAAAATTT
1 AAAAATTT
*
65908 AAATATTT
1 AAAAATTT
65916 A
1 A
65917 TTAAATATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (8 bp):
AAAAATTT
Found at i:65960 original size:29 final size:30
Alignment explanation
Indices: 65903--65963 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 30
65893 AAAATTTAAA
* * *
65903 AATTTAAATATTTATTAAATATTATTATTT
1 AATTTAAATATTTATAAAATAATAATATTT
*
65933 AATTTAAATTTTTA-AAAATAATAATATTT
1 AATTTAAATATTTATAAAATAATAATATTT
65962 AA
1 AA
65964 ATTATAAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
29 14 0.52
30 13 0.48
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (30 bp):
AATTTAAATATTTATAAAATAATAATATTT
Found at i:65983 original size:24 final size:24
Alignment explanation
Indices: 65934--65979 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 24
65924 TTATTATTTA
*
65934 ATTTAAATTTTTAAAAATAATAAT
1 ATTTAAATTTATAAAAATAATAAT
65958 ATTTAAA-TTATAAAAATAATAA
1 ATTTAAATTTATAAAAATAATAA
65980 ATATATTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 14 0.67
24 7 0.33
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (24 bp):
ATTTAAATTTATAAAAATAATAAT
Found at i:66002 original size:37 final size:37
Alignment explanation
Indices: 65961--66031 Score: 99
Period size: 37 Copynumber: 1.9 Consensus size: 37
65951 TAATAATATT
*
65961 TAAATT-ATAAAAATAATAAATATATTTTAAAATTATA
1 TAAATTAATAAAAATAATAAATAT-TTTAAAAATTATA
* *
65998 TAAATTAATTAAATTAATAAATATTTTAAAAATT
1 TAAATTAATAAAAATAATAAATATTTTAAAAATT
66032 TGGCAATGTA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
37 15 0.50
38 15 0.50
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (37 bp):
TAAATTAATAAAAATAATAAATATTTTAAAAATTATA
Done.