Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold345
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: 201931
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35
File 1 of 2
Found at i:737 original size:6 final size:6
Alignment explanation
Indices: 726--763 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
716 TGGTACAATT
* *
726 TTATAA TTATAA TTATAA CTCTAA TTATAA TTATAA TT
1 TTATAA TTATAA TTATAA TTATAA TTATAA TTATAA TT
764 TTAGAATAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (6 bp):
TTATAA
Found at i:1169 original size:20 final size:20
Alignment explanation
Indices: 1144--1181 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1134 ATTGTTTTTT
1144 ATATATATTTAAATAAAAAA
1 ATATATATTTAAATAAAAAA
* *
1164 ATATATTTTTATATAAAA
1 ATATATATTTAAATAAAA
1182 TTATAGTATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
ATATATATTTAAATAAAAAA
Found at i:1872 original size:20 final size:22
Alignment explanation
Indices: 1849--1891 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
1839 ATTTATGAGT
1849 AATT-TTGAAA-AATATAAAAA
1 AATTATTGAAATAATATAAAAA
*
1869 AATTAATTTAAATAATATAAAAA
1 AATT-ATTGAAATAATATAAAAA
1892 TTTAGTAAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 4 0.21
22 5 0.26
23 10 0.53
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (22 bp):
AATTATTGAAATAATATAAAAA
Found at i:1923 original size:15 final size:15
Alignment explanation
Indices: 1900--1987 Score: 63
Period size: 15 Copynumber: 5.7 Consensus size: 15
1890 AATTTAGTAA
* *
1900 GATACAAATTACTAT
1 GATATAAATTAATAT
*
1915 GATATAAATATAAAAT
1 GATATAAAT-TAATAT
*
1931 -ATATTAAATTAATAG
1 GATA-TAAATTAATAT
*
1946 GATATAAATATAAAAT
1 GATATAAAT-TAATAT
*
1962 -ATATTAAATTTATAT
1 GATA-TAAATTAATAT
*
1977 AATATAAATTA
1 GATATAAATTA
1988 TTAATTTAAT
Statistics
Matches: 57, Mismatches: 10, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
15 33 0.58
16 24 0.42
ACGTcount: A:0.56, C:0.02, G:0.05, T:0.38
Consensus pattern (15 bp):
GATATAAATTAATAT
Found at i:1950 original size:31 final size:31
Alignment explanation
Indices: 1905--1985 Score: 126
Period size: 31 Copynumber: 2.6 Consensus size: 31
1895 AGTAAGATAC
*
1905 AAATTACTATGATATAAATATAAAATATATT
1 AAATTAATATGATATAAATATAAAATATATT
*
1936 AAATTAATAGGATATAAATATAAAATATATT
1 AAATTAATATGATATAAATATAAAATATATT
* *
1967 AAATTTATATAATATAAAT
1 AAATTAATATGATATAAAT
1986 TATTAATTTA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.57, C:0.01, G:0.04, T:0.38
Consensus pattern (31 bp):
AAATTAATATGATATAAATATAAAATATATT
Found at i:1969 original size:16 final size:16
Alignment explanation
Indices: 1919--1970 Score: 63
Period size: 16 Copynumber: 3.3 Consensus size: 16
1909 TACTATGATA
1919 TAAATATAAAATATAT
1 TAAATATAAAATATAT
**
1935 TAAAT-TAATAGGATA-
1 TAAATATAA-AATATAT
1950 TAAATATAAAATATAT
1 TAAATATAAAATATAT
1966 TAAAT
1 TAAAT
1971 TTATATAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
15 12 0.41
16 17 0.59
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.37
Consensus pattern (16 bp):
TAAATATAAAATATAT
Found at i:1999 original size:23 final size:24
Alignment explanation
Indices: 1947--2036 Score: 87
Period size: 23 Copynumber: 3.7 Consensus size: 24
1937 AATTAATAGG
1947 ATATAAATATAAAATATATTAAATTT-
1 ATAT-AATAT-AAATATATT-AATTTA
1973 ATATAATATAAAT-TATTAATTTA
1 ATATAATATAAATATATTAATTTA
* *
1996 ATATAA-ATAAATATAATATTTTAA
1 ATATAATATAAATATATTAATTT-A
* *
2020 ATATAATTTTAATATAT
1 ATATAATATAAATATAT
2037 AAAATTTCAT
Statistics
Matches: 55, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
22 11 0.20
23 17 0.31
24 11 0.20
25 12 0.22
26 4 0.07
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (24 bp):
ATATAATATAAATATATTAATTTA
Found at i:2229 original size:2 final size:2
Alignment explanation
Indices: 2222--2248 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2212 GATCTTTTAT
2222 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
2249 GAGTAAAATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3098 original size:66 final size:66
Alignment explanation
Indices: 3016--3149 Score: 250
Period size: 66 Copynumber: 2.0 Consensus size: 66
3006 ATAGTACTTT
* *
3016 GATAACTTTTGACCTTTTTTTTATCTTGTGAAATTCTCAATTGAAGGATTACTTTGCATTATTTG
1 GATAACTTTTGACCTTTTTTTTATCTTGTGAAATTCTCAATTGAAAGATTACTTTACATTATTTG
3081 A
66 A
3082 GATAACTTTTGACCTTTTTTTTATCTTGTGAAATTCTCAATTGAAAGATTACTTTACATTATTTG
1 GATAACTTTTGACCTTTTTTTTATCTTGTGAAATTCTCAATTGAAAGATTACTTTACATTATTTG
3147 A
66 A
3148 GA
1 GA
3150 CTACTCAACA
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 66 1.00
ACGTcount: A:0.28, C:0.12, G:0.13, T:0.48
Consensus pattern (66 bp):
GATAACTTTTGACCTTTTTTTTATCTTGTGAAATTCTCAATTGAAAGATTACTTTACATTATTTG
A
Found at i:3379 original size:26 final size:25
Alignment explanation
Indices: 3349--3424 Score: 70
Period size: 26 Copynumber: 3.1 Consensus size: 25
3339 TTCAGTAGAG
*
3349 AAGAGAAAGAAGGAAAAGAAAGTAAA
1 AAGAGAAAGAA-GAAAAGAAAGAAAA
*
3375 AAGAG---GAAAAAAAGAAAGAAAA
1 AAGAGAAAGAAGAAAAGAAAGAAAA
*
3397 AAGA-AAAGAAAAGAAAGGAAAGAAAA
1 AAGAGAAAG--AAGAAAAGAAAGAAAA
3423 AA
1 AA
3425 ATTTCGTATT
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
22 16 0.39
23 3 0.07
24 1 0.02
26 21 0.51
ACGTcount: A:0.75, C:0.00, G:0.24, T:0.01
Consensus pattern (25 bp):
AAGAGAAAGAAGAAAAGAAAGAAAA
Found at i:3396 original size:9 final size:9
Alignment explanation
Indices: 3349--3422 Score: 53
Period size: 9 Copynumber: 7.8 Consensus size: 9
3339 TTCAGTAGAG
3349 AAGAGAAAGA
1 AAGA-AAAGA
*
3359 AGGAAAAGA
1 AAGAAAAGA
3368 AAGTAAAAAGA
1 AAG--AAAAGA
*
3379 GGAAAAAAAGA
1 --AAGAAAAGA
3390 AAG-AAA-A
1 AAGAAAAGA
3397 AAGAAAAGAA
1 AAGAAAAG-A
*
3407 AAGAAAGGA
1 AAGAAAAGA
3416 AAGAAAA
1 AAGAAAA
3423 AAATTTCGTA
Statistics
Matches: 51, Mismatches: 6, Indels: 15
0.71 0.08 0.21
Matches are distributed among these distances:
7 4 0.08
8 6 0.12
9 16 0.31
10 11 0.22
11 12 0.24
13 2 0.04
ACGTcount: A:0.74, C:0.00, G:0.24, T:0.01
Consensus pattern (9 bp):
AAGAAAAGA
Found at i:3396 original size:21 final size:22
Alignment explanation
Indices: 3361--3413 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
3351 GAGAAAGAAG
*
3361 GAAAAGAAAGTAAAAAGAGGAAA
1 GAAAAGAAAGTAAAAA-AGAAAA
3384 -AAAAGAAAG-AAAAAAGAAAA
1 GAAAAGAAAGTAAAAAAGAAAA
3404 GAAAAGAAAG
1 GAAAAGAAAG
3414 GAAAGAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 5 0.18
21 14 0.50
22 9 0.32
ACGTcount: A:0.75, C:0.00, G:0.23, T:0.02
Consensus pattern (22 bp):
GAAAAGAAAGTAAAAAAGAAAA
Found at i:3417 original size:22 final size:22
Alignment explanation
Indices: 3361--3425 Score: 73
Period size: 22 Copynumber: 3.0 Consensus size: 22
3351 GAGAAAGAAG
* *
3361 GAAAAGAAAGTAAAAAGAGGAAA
1 GAAAAGAAAGGAAAAA-AGAAAA
3384 -AAAAGAAA-GAAAAAAGAAAA
1 GAAAAGAAAGGAAAAAAGAAAA
3404 GAAAAGAAAGGAAAGAAA-AAAA
1 GAAAAGAAAGGAAA-AAAGAAAA
3426 TTTCGTATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
20 5 0.14
21 13 0.35
22 16 0.43
23 3 0.08
ACGTcount: A:0.77, C:0.00, G:0.22, T:0.02
Consensus pattern (22 bp):
GAAAAGAAAGGAAAAAAGAAAA
Found at i:3418 original size:19 final size:18
Alignment explanation
Indices: 3349--3422 Score: 59
Period size: 19 Copynumber: 4.1 Consensus size: 18
3339 TTCAGTAGAG
3349 AAGAGAAAG-AAGGAAAAGA
1 AAGA-AAAGAAAGGAAAA-A
*
3368 AAGTAAAA-AGAGGAAAAA
1 AAG-AAAAGAAAGGAAAAA
3386 AAG-AAAGAAA--AAAGAA
1 AAGAAAAGAAAGGAAA-AA
3402 AAGAAAAGAAAGGAAAGAA
1 AAGAAAAGAAAGGAAA-AA
3421 AA
1 AA
3423 AAATTTCGTA
Statistics
Matches: 46, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
15 3 0.07
16 8 0.17
17 9 0.20
18 4 0.09
19 21 0.46
20 1 0.02
ACGTcount: A:0.74, C:0.00, G:0.24, T:0.01
Consensus pattern (18 bp):
AAGAAAAGAAAGGAAAAA
Found at i:3508 original size:32 final size:32
Alignment explanation
Indices: 3472--3537 Score: 80
Period size: 32 Copynumber: 2.1 Consensus size: 32
3462 ATATTATAAA
*
3472 TTTATATAATAT-TTATAAATATTTTTTATATT
1 TTTATAT-ATATGTCATAAATATTTTTTATATT
* **
3504 TTTATATTTATGTCATATTTATTTTTTATATT
1 TTTATATATATGTCATAAATATTTTTTATATT
3536 TT
1 TT
3538 ATTTTAATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 3 0.10
32 26 0.90
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.67
Consensus pattern (32 bp):
TTTATATATATGTCATAAATATTTTTTATATT
Found at i:3534 original size:24 final size:23
Alignment explanation
Indices: 3496--3584 Score: 83
Period size: 24 Copynumber: 3.7 Consensus size: 23
3486 ATAAATATTT
3496 TTTATATTTTTATATTTATGTCATA
1 TTTAT-TTTTTATATTTAT-TCATA
*
3521 TTTATTTTTTATATTTTATT-TTAA
1 TTTATTTTTTATA-TTTATTCAT-A
* *
3545 TTAATTTTTAATATTGTATTCATA
1 TTTATTTTTTATATT-TATTCATA
3569 -TTATTTTTATATATTT
1 TTTATTTTT-TATATTT
3585 TAAGTATTAA
Statistics
Matches: 53, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
23 11 0.21
24 31 0.58
25 11 0.21
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.67
Consensus pattern (23 bp):
TTTATTTTTTATATTTATTCATA
Found at i:4001 original size:22 final size:22
Alignment explanation
Indices: 3954--4011 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
3944 ATTCTGACAT
*
3954 TTATTATTTATATCATATTCATA
1 TTATT-TTTATATAATATTCATA
*
3977 TTATTTTTATATAATATT-TTAA
1 TTATTTTTATATAATATTCAT-A
*
3999 TTATTTTTTTATA
1 TTATTTTTATATA
4012 TTTCATCCTC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 1 0.03
22 25 0.81
23 5 0.16
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (22 bp):
TTATTTTTATATAATATTCATA
Found at i:5367 original size:11 final size:11
Alignment explanation
Indices: 5353--5389 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
5343 GTATTTTTTG
5353 ATATTATATTT
1 ATATTATATTT
5364 ATATTATATTT
1 ATATTATATTT
5375 -TAATT-TATTT
1 AT-ATTATATTT
5385 ATATT
1 ATATT
5390 TTTATAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
10 9 0.38
11 15 0.62
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
ATATTATATTT
Found at i:5368 original size:21 final size:19
Alignment explanation
Indices: 5344--5402 Score: 57
Period size: 21 Copynumber: 2.9 Consensus size: 19
5334 AGGTTTTAAG
5344 TATTTTTTGATATTATATTTA
1 TATTTTTTGA-ATT-TATTTA
*
5365 TATTATATTTTAATTTATTTA
1 TATT-T-TTTGAATTTATTTA
5386 TATTTTTAT-AATTTATT
1 TATTTTT-TGAATTTATT
5403 ATAATAATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
19 10 0.29
20 2 0.06
21 14 0.41
22 4 0.12
23 4 0.12
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.68
Consensus pattern (19 bp):
TATTTTTTGAATTTATTTA
Found at i:5386 original size:16 final size:17
Alignment explanation
Indices: 5360--5438 Score: 62
Period size: 17 Copynumber: 4.8 Consensus size: 17
5350 TTGATATTAT
5360 ATTTATATTATATTTTA
1 ATTTATATTATATTTTA
5377 ATTTAT-TTATATTTTTA
1 ATTTATATTATA-TTTTA
* *
5394 TAATT-TATTATA--ATA
1 -ATTTATATTATATTTTA
5409 ATTTAATATTA-ATTTTAA
1 ATTT-ATATTATATTTT-A
5427 ATTTA-ATTATAT
1 ATTTATATTATAT
5439 AAAATTTAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 18
0.69 0.06 0.25
Matches are distributed among these distances:
14 3 0.06
15 3 0.06
16 14 0.29
17 16 0.33
18 13 0.27
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
ATTTATATTATATTTTA
Found at i:5399 original size:19 final size:21
Alignment explanation
Indices: 5359--5402 Score: 65
Period size: 19 Copynumber: 2.2 Consensus size: 21
5349 TTTGATATTA
*
5359 TATTTATATTATATTTTAATT
1 TATTTATATTATATTATAATT
5380 TATTTATATT-T-TTATAATT
1 TATTTATATTATATTATAATT
5399 TATT
1 TATT
5403 ATAATAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 11 0.50
20 1 0.05
21 10 0.45
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (21 bp):
TATTTATATTATATTATAATT
Found at i:5411 original size:32 final size:32
Alignment explanation
Indices: 5360--5451 Score: 82
Period size: 32 Copynumber: 2.8 Consensus size: 32
5350 TTGATATTAT
*
5360 ATTTATATTATATTTTAATTTAT-TTATATTTTTATA
1 ATTTA-ATTATA-TATAATTTATATTA-A-TTTTA-A
5396 ATTT-ATTATA-ATAATTTAATATTAATTTTAA
1 ATTTAATTATATATAATTT-ATATTAATTTTAA
* *
5427 ATTTAATTATATAAAATTTAAATTA
1 ATTTAATTATATATAATTTATATTA
5452 TAAAAAATAT
Statistics
Matches: 49, Mismatches: 3, Indels: 12
0.77 0.05 0.19
Matches are distributed among these distances:
31 5 0.10
32 22 0.45
33 9 0.18
34 9 0.18
36 4 0.08
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (32 bp):
ATTTAATTATATATAATTTATATTAATTTTAA
Found at i:5450 original size:16 final size:16
Alignment explanation
Indices: 5402--5459 Score: 55
Period size: 16 Copynumber: 3.5 Consensus size: 16
5392 TATAATTTAT
5402 TATAATAATTTAATATTAA
1 TATAA-AATTTAA-ATT-A
* *
5421 TTTTAAATTT-AATTA
1 TATAAAATTTAAATTA
5436 TATAAAATTTAAATTA
1 TATAAAATTTAAATTA
*
5452 TAAAAAAT
1 TATAAAAT
5460 ATTTAAATAA
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
15 9 0.27
16 15 0.45
17 1 0.03
18 5 0.15
19 3 0.09
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TATAAAATTTAAATTA
Found at i:5486 original size:18 final size:19
Alignment explanation
Indices: 5442--5496 Score: 55
Period size: 18 Copynumber: 3.0 Consensus size: 19
5432 ATTATATAAA
*
5442 ATTTAAATTATAA-A-AAAT
1 ATTTAAA-TATAATATAATT
5460 ATTTAAATA-AATAATAATT
1 ATTTAAATATAAT-ATAATT
5479 ATTT-AATATAATATAATT
1 ATTTAAATATAATATAATT
5497 TAAATTTATG
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
16 2 0.06
17 2 0.06
18 18 0.56
19 10 0.31
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
ATTTAAATATAATATAATT
Found at i:5735 original size:23 final size:24
Alignment explanation
Indices: 5693--5767 Score: 73
Period size: 24 Copynumber: 3.0 Consensus size: 24
5683 AAATATAATA
5693 TGAATATATAATTAATTTAAAAAT
1 TGAATATATAATTAATTTAAAAAT
*
5717 TGAA-ATATAATATAATTAAAAAAT
1 TGAATATATAAT-TAATTTAAAAAT
* *
5741 ATAAATAT-TATATTAATATAAATAAT
1 -TGAATATATA-ATTAATTTAAA-AAT
5767 T
1 T
5768 TAAAATTTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
23 7 0.17
24 15 0.36
25 13 0.31
26 7 0.17
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (24 bp):
TGAATATATAATTAATTTAAAAAT
Found at i:5787 original size:16 final size:17
Alignment explanation
Indices: 5762--5836 Score: 57
Period size: 16 Copynumber: 4.5 Consensus size: 17
5752 ATTAATATAA
*
5762 ATAATTTAAAAT-TTAT
1 ATAATATAAAATATTAT
*
5778 ATAATATAAATTATTAT
1 ATAATATAAAATATTAT
* * * *
5795 TTTAT-TAATATTTTAT
1 ATAATATAAAATATTAT
*
5811 ATAAATATAAAATATTTT
1 AT-AATATAAAATATTAT
5829 A-AATATAA
1 ATAATATAA
5837 TTATAAAATA
Statistics
Matches: 44, Mismatches: 12, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
16 26 0.59
17 9 0.20
18 9 0.20
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
ATAATATAAAATATTAT
Found at i:5788 original size:25 final size:25
Alignment explanation
Indices: 5719--5788 Score: 81
Period size: 26 Copynumber: 2.8 Consensus size: 25
5709 TTAAAAATTG
* *
5719 AAATATAATATAAT-TAAAAAATAT
1 AAATATTATATAATATAAATAATAT
*
5743 AAATATTATATTAATATAAATAATTT
1 AAATATTATA-TAATATAAATAATAT
5769 AAA-ATTTATATAATATAAAT
1 AAATA-TTATATAATATAAAT
5789 TATTATTTTA
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
24 9 0.22
25 15 0.38
26 16 0.40
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (25 bp):
AAATATTATATAATATAAATAATAT
Found at i:5796 original size:21 final size:21
Alignment explanation
Indices: 5738--5805 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 21
5728 ATAATTAAAA
5738 AATATAAA-TATTATATTAATAT
1 AATATAAATTATTAT-TT-ATAT
* **
5760 AA-ATAATTTAAAATTTATAT
1 AATATAAATTATTATTTATAT
5780 AATATAAATTATTATTT-TATT
1 AATATAAATTATTATTTATA-T
5801 AATAT
1 AATAT
5806 TTTATATAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
20 8 0.22
21 23 0.62
22 6 0.16
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
AATATAAATTATTATTTATAT
Found at i:5826 original size:20 final size:21
Alignment explanation
Indices: 5801--5846 Score: 67
Period size: 22 Copynumber: 2.2 Consensus size: 21
5791 TTATTTTATT
5801 AATATTTT-ATATAAATATAA
1 AATATTTTAATATAAATATAA
*
5821 AATATTTTAAATATAATTATAA
1 AATATTTT-AATATAAATATAA
5843 AATA
1 AATA
5847 ATAAAATAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 8 0.35
22 15 0.65
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
AATATTTTAATATAAATATAA
Found at i:5830 original size:28 final size:28
Alignment explanation
Indices: 5748--5854 Score: 69
Period size: 29 Copynumber: 3.6 Consensus size: 28
5738 AATATAAATA
* * *
5748 TTATATTAATAT-AAATAATTTAA-AAT
1 TTATATAAATATAAAATATTTTAATATT
5774 TTATAT-AATATAAATTATTATTTTATTAATATT
1 TTATATAAATATAAA--A-TA--TT-TTAATATT
*
5807 TTATATAAATATAAAATATTTTAAATATAA
1 TTATATAAATATAAAATATTTT-AATAT-T
5837 TTATA-AAATAATAAAATA
1 TTATATAAAT-ATAAAATA
5855 ATAAAATATG
Statistics
Matches: 66, Mismatches: 3, Indels: 20
0.74 0.03 0.22
Matches are distributed among these distances:
25 5 0.08
26 8 0.12
28 3 0.05
29 13 0.20
30 13 0.20
31 3 0.05
32 5 0.08
33 8 0.12
34 8 0.12
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (28 bp):
TTATATAAATATAAAATATTTTAATATT
Found at i:5858 original size:22 final size:22
Alignment explanation
Indices: 5809--5859 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
5799 TTAATATTTT
* *
5809 ATATAAATATAAAATATTTTAA
1 ATATAAATATAAAATATATAAA
*
5831 ATATAATTATAAAATA-ATAAA
1 ATATAAATATAAAATATATAAA
5852 ATAATAAA
1 AT-ATAAA
5860 ATATGATATT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 5 0.21
22 19 0.79
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (22 bp):
ATATAAATATAAAATATATAAA
Found at i:6361 original size:33 final size:34
Alignment explanation
Indices: 6309--6381 Score: 87
Period size: 33 Copynumber: 2.2 Consensus size: 34
6299 TCTGTGCATA
* * *
6309 TAATATTTTAGATATTTTATAT-TTATCTAAATAT
1 TAATACTTTAGATAATTTATATCATAT-TAAATAT
6343 TAATACTTTA-ATAATTTATATCATATTAAATAT
1 TAATACTTTAGATAATTTATATCATATTAAATAT
*
6376 AAATAC
1 TAATAC
6382 AAGATAAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
33 22 0.65
34 12 0.35
ACGTcount: A:0.44, C:0.05, G:0.01, T:0.49
Consensus pattern (34 bp):
TAATACTTTAGATAATTTATATCATATTAAATAT
Found at i:7289 original size:16 final size:17
Alignment explanation
Indices: 7268--7301 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
7258 GATCAAATAA
*
7268 AAATATT-ATAATAATT
1 AAATATTAAAAATAATT
7284 AAATATTAAAAATAATT
1 AAATATTAAAAATAATT
7301 A
1 A
7302 TGTTAAATGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
AAATATTAAAAATAATT
Found at i:7415 original size:14 final size:14
Alignment explanation
Indices: 7398--7443 Score: 58
Period size: 14 Copynumber: 3.2 Consensus size: 14
7388 TGTTTTTAAA
7398 TTATTATATAAAAT
1 TTATTATATAAAAT
*
7412 TTATTATATTAATAAA
1 TTATTATA-TAA-AAT
7428 TTATTA-ATAAAAT
1 TTATTATATAAAAT
7441 TTA
1 TTA
7444 AAATATTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
13 5 0.18
14 11 0.39
15 4 0.14
16 8 0.29
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TTATTATATAAAAT
Found at i:7456 original size:30 final size:30
Alignment explanation
Indices: 7394--7452 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
7384 TTTTTGTTTT
**
7394 TAAATTATTATATAAAATTTATTATATTAA
1 TAAATTATTATATAAAATTTAAAATATTAA
7424 TAAATTATTA-ATAAAATTTAAAATATTAA
1 TAAATTATTATATAAAATTTAAAATATTAA
7453 ATAATAATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 17 0.63
30 10 0.37
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (30 bp):
TAAATTATTATATAAAATTTAAAATATTAA
Found at i:8054 original size:13 final size:13
Alignment explanation
Indices: 8038--8068 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
8028 TTAAAAAAAC
8038 TATTTTTAATTAA
1 TATTTTTAATTAA
*
8051 TATTTTTATTTAA
1 TATTTTTAATTAA
8064 TATTT
1 TATTT
8069 AAATAATACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
TATTTTTAATTAA
Found at i:8287 original size:19 final size:18
Alignment explanation
Indices: 8260--8296 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
8250 AAAAATATAT
*
8260 TTTTTAATAATTATTTTTA
1 TTTTAAATAATT-TTTTTA
8279 TTTTAAATAATTTTTTTA
1 TTTTAAATAATTTTTTTA
8297 AAAAAAATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTTAAATAATTTTTTTA
Found at i:9197 original size:2 final size:2
Alignment explanation
Indices: 9190--9220 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
9180 TCAATAATTC
9190 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 A
9221 ATAAATCTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:21065 original size:9 final size:10
Alignment explanation
Indices: 21039--21124 Score: 51
Period size: 9 Copynumber: 9.2 Consensus size: 10
21029 CTAATAACTC
21039 ATATATTTAT
1 ATATATTTAT
21049 ATAATATTTAT
1 AT-ATATTTAT
*
21060 AT-TATTTTT
1 ATATATTTAT
*
21069 TTAT-TTTA-
1 ATATATTTAT
*
21077 ATATGTTTA-
1 ATATATTTAT
21086 A-A-ATTT-T
1 ATATATTTAT
21093 ATATATTTAT
1 ATATATTTAT
* *
21103 ATAAATTTTT
1 ATATATTTAT
* *
21113 AAATAATTAT
1 ATATATTTAT
21123 AT
1 AT
21125 TTTATATAAA
Statistics
Matches: 57, Mismatches: 12, Indels: 14
0.69 0.14 0.17
Matches are distributed among these distances:
7 4 0.07
8 5 0.09
9 19 0.33
10 19 0.33
11 10 0.18
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (10 bp):
ATATATTTAT
Found at i:21112 original size:20 final size:20
Alignment explanation
Indices: 21084--21124 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
21074 TTAATATGTT
* *
21084 TAAAATTTTATATATTTATA
1 TAAAATTTTAAATAATTATA
*
21104 TAAATTTTTAAATAATTATA
1 TAAAATTTTAAATAATTATA
21124 T
1 T
21125 TTTATATAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TAAAATTTTAAATAATTATA
Found at i:29767 original size:25 final size:24
Alignment explanation
Indices: 29711--29767 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 24
29701 TATTAATTAT
*
29711 ATTATTTTATTATATTTTATTTAT
1 ATTATTTTATTATATTTTATTTAA
29735 ATCATATTTT-TTATATTTTTATTTAAA
1 AT--TATTTTATTATA-TTTTATTT-AA
29762 ATTATT
1 ATTATT
29768 AAATTTATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
24 2 0.07
25 9 0.32
26 14 0.50
27 3 0.11
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.67
Consensus pattern (24 bp):
ATTATTTTATTATATTTTATTTAA
Found at i:31044 original size:12 final size:12
Alignment explanation
Indices: 31027--31051 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
31017 AAGTTGTAAC
31027 TCTTAATTTGTA
1 TCTTAATTTGTA
31039 TCTTAATTTGTA
1 TCTTAATTTGTA
31051 T
1 T
31052 TGTAAAATCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.08, G:0.08, T:0.60
Consensus pattern (12 bp):
TCTTAATTTGTA
Found at i:31627 original size:20 final size:20
Alignment explanation
Indices: 31580--31649 Score: 65
Period size: 20 Copynumber: 3.5 Consensus size: 20
31570 ATATTTAAAA
*
31580 TATTATATATTAATATAAATTT
1 TATTATATATT-A-ATAATTTT
31602 TA--ATATATTAATAATTTT
1 TATTATATATTAATAATTTT
** *
31620 TATTATATATTTTTAATTTA
1 TATTATATATTAATAATTTT
31640 T-TTATATATT
1 TATTATATATT
31650 TATTTAATGT
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
18 9 0.21
19 10 0.24
20 21 0.50
22 2 0.05
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TATTATATATTAATAATTTT
Found at i:32958 original size:17 final size:16
Alignment explanation
Indices: 32929--32995 Score: 61
Period size: 15 Copynumber: 4.1 Consensus size: 16
32919 ATAATTGTAA
32929 TATATTTAA-AAATTT
1 TATATTTAATAAATTT
32944 TATATTTATATAAATTT
1 TATATTTA-ATAAATTT
32961 TAATATAATTAAT-AA-TT
1 T-ATAT--TTAATAAATTT
32978 TATA-TTATATAAATTT
1 TATATTTA-ATAAATTT
32994 TA
1 TA
32996 AAATATTCAT
Statistics
Matches: 44, Mismatches: 0, Indels: 15
0.75 0.00 0.25
Matches are distributed among these distances:
13 3 0.07
14 2 0.05
15 10 0.23
16 8 0.18
17 10 0.23
18 6 0.14
19 2 0.05
20 3 0.07
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TATATTTAATAAATTT
Found at i:32977 original size:18 final size:17
Alignment explanation
Indices: 32919--32978 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 17
32909 CTTCGGCTAG
*
32919 ATAATTGTAATATATTTA
1 ATAATTTTAATATA-TTA
*
32937 AAAATTTT-ATAT-TTA
1 ATAATTTTAATATATTA
32952 TATAAATTTTAATATAATTA
1 -AT-AATTTTAATAT-ATTA
32972 ATAATTT
1 ATAATTT
32979 ATATTATATA
Statistics
Matches: 34, Mismatches: 3, Indels: 10
0.72 0.06 0.21
Matches are distributed among these distances:
15 3 0.09
16 1 0.03
17 10 0.29
18 15 0.44
19 2 0.06
20 3 0.09
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (17 bp):
ATAATTTTAATATATTA
Found at i:33001 original size:35 final size:35
Alignment explanation
Indices: 32921--32996 Score: 111
Period size: 35 Copynumber: 2.2 Consensus size: 35
32911 TCGGCTAGAT
* *
32921 AATTGTAATATATTTAAAAATTTTATATTTATATA
1 AATTTTAATATAATTAAAAATTTTATATTTATATA
*
32956 AATTTTAATATAATTAATAA-TTTATA-TTATATA
1 AATTTTAATATAATTAAAAATTTTATATTTATATA
32989 AATTTTAA
1 AATTTTAA
32997 AATATTCATA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
33 15 0.39
34 6 0.16
35 17 0.45
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.51
Consensus pattern (35 bp):
AATTTTAATATAATTAAAAATTTTATATTTATATA
Found at i:33041 original size:10 final size:11
Alignment explanation
Indices: 33017--33050 Score: 52
Period size: 10 Copynumber: 3.1 Consensus size: 11
33007 TATATAATTT
33017 TTTTATATTATA
1 TTTTATA-TATA
33029 TTTTATA-ATA
1 TTTTATATATA
33039 TTTTATATATA
1 TTTTATATATA
33050 T
1 T
33051 CTTAATTATC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 10 0.48
11 4 0.19
12 7 0.33
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
TTTTATATATA
Found at i:33047 original size:24 final size:24
Alignment explanation
Indices: 32977--33048 Score: 78
Period size: 24 Copynumber: 3.0 Consensus size: 24
32967 AATTAATAAT
*
32977 TTATATTATATAA-ATTTTAAAATA
1 TTATATTATATAATATTTT-ATATA
*
33001 TTCATA-TATATAAT-TTTTTTATA
1 TT-ATATTATATAATATTTTATATA
*
33024 TTATATTTTATAATATTTTATATA
1 TTATATTATATAATATTTTATATA
33048 T
1 T
33049 ATCTTAATTA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
22 3 0.08
23 12 0.30
24 22 0.55
25 3 0.08
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.58
Consensus pattern (24 bp):
TTATATTATATAATATTTTATATA
Found at i:36329 original size:26 final size:25
Alignment explanation
Indices: 36280--36347 Score: 83
Period size: 22 Copynumber: 2.9 Consensus size: 25
36270 TATGTACAAT
36280 ATTAATTAATTTA-AAA-AAAATAA
1 ATTAATTAATTTATAAATAAAATAA
*
36303 ATTTAATTAATTTATAAATAAATTAA
1 A-TTAATTAATTTATAAATAAAATAA
36329 A--AA-TAATTTATAAATAAAA
1 ATTAATTAATTTATAAATAAAA
36348 AGTAATAATT
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
22 15 0.38
23 3 0.08
24 12 0.30
25 3 0.08
26 7 0.17
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (25 bp):
ATTAATTAATTTATAAATAAAATAA
Found at i:36334 original size:11 final size:11
Alignment explanation
Indices: 36297--36346 Score: 57
Period size: 11 Copynumber: 4.6 Consensus size: 11
36287 AATTTAAAAA
36297 AAATAAATT-T
1 AAATAAATTAT
* *
36307 AATTAATTTAT
1 AAATAAATTAT
*
36318 AAATAAATTAA
1 AAATAAATTAT
*
36329 AAATAATTTAT
1 AAATAAATTAT
36340 AAATAAA
1 AAATAAA
36347 AAGTAATAAT
Statistics
Matches: 31, Mismatches: 8, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
10 7 0.23
11 24 0.77
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
AAATAAATTAT
Found at i:36655 original size:17 final size:17
Alignment explanation
Indices: 36616--36657 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
36606 ATAATTTATA
36616 AATAAATTAAAAATAATT
1 AATAAA-TAAAAATAATT
*
36634 TATAAATAAAAAGTAA-T
1 AATAAATAAAAA-TAATT
36651 AATAAAT
1 AATAAAT
36658 GTATAATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 13 0.62
18 8 0.38
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (17 bp):
AATAAATAAAAATAATT
Found at i:36822 original size:25 final size:28
Alignment explanation
Indices: 36760--36822 Score: 80
Period size: 25 Copynumber: 2.4 Consensus size: 28
36750 CATTATCAAA
36760 AAATAATAAATGTAAAAATAAATTTAGT
1 AAATAATAAATGTAAAAATAAATTTAGT
*
36788 AAA-AATAAAT-T-AAAATAATTTTA-T
1 AAATAATAAATGTAAAAATAAATTTAGT
*
36812 AAATAAAAAAT
1 AAATAATAAAT
36823 CATACTTTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
24 4 0.12
25 17 0.53
26 1 0.03
27 7 0.22
28 3 0.09
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (28 bp):
AAATAATAAATGTAAAAATAAATTTAGT
Found at i:37133 original size:28 final size:31
Alignment explanation
Indices: 37102--37163 Score: 85
Period size: 28 Copynumber: 2.1 Consensus size: 31
37092 AATGTAAATT
*
37102 TTTTAAAAT-TAATTTA-ATATTATT-TTTA
1 TTTTAAAATATAATTAATATATTATTATTTA
37130 TTTTAAAATAATAATTAATATATTATTATTTA
1 TTTTAAAAT-ATAATTAATATATTATTATTTA
37162 TT
1 TT
37164 AAATTTTTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
28 9 0.31
30 6 0.21
31 8 0.28
32 6 0.21
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (31 bp):
TTTTAAAATATAATTAATATATTATTATTTA
Found at i:37146 original size:34 final size:36
Alignment explanation
Indices: 37108--37188 Score: 96
Period size: 34 Copynumber: 2.3 Consensus size: 36
37098 AATTTTTTAA
37108 AATTAATTTAATATTATTT-TT-A-TTTTAAAATAAT
1 AATTAATTTAATATTATTTATTAATTTTTAAAAT-AT
* * *
37142 AATTAATATATTATTATTTATTAAATTTTTAAAATTT
1 AATTAATTTAATATTATTTATT-AATTTTTAAAATAT
37179 AATTAATTTA
1 AATTAATTTA
37189 TAAAAAAATT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
34 17 0.44
35 2 0.05
37 11 0.28
38 9 0.23
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (36 bp):
AATTAATTTAATATTATTTATTAATTTTTAAAATAT
Found at i:37182 original size:67 final size:68
Alignment explanation
Indices: 37054--37189 Score: 190
Period size: 70 Copynumber: 2.0 Consensus size: 68
37044 TCAATTTAAT
*
37054 TTTTTATTTTAAAAAAATAATTAATATTTTAATTTATTAATGTAAATTTTTTAAAATTAATTTAA
1 TTTTTATTTTAAAAAAATAATTAATATATTAATTTATTAATGTAAATTTTTTAAAATTAA-TTAA
37119 TATTA
65 T-TTA
* *
37124 TTTTTATTTTAAAATAATAATTAATATATT-A-TTATTTAT-TAAA-TTTTTAAAATTTAATTAA
1 TTTTTATTTTAAAAAAATAATTAATATATTAATTTATTAATGTAAATTTTTTAAAA-TTAATTAA
37185 TTTA
65 TTTA
37189 T
1 T
37190 AAAAAAATTA
Statistics
Matches: 62, Mismatches: 3, Indels: 7
0.86 0.04 0.10
Matches are distributed among these distances:
65 4 0.06
66 14 0.23
67 8 0.13
68 7 0.11
69 1 0.02
70 28 0.45
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (68 bp):
TTTTTATTTTAAAAAAATAATTAATATATTAATTTATTAATGTAAATTTTTTAAAATTAATTAAT
TTA
Found at i:38703 original size:27 final size:27
Alignment explanation
Indices: 38650--38703 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 27
38640 TAAGGTAAAT
* * *
38650 ATTTGTTTAAAGTTTTTTTTCTTTTTA
1 ATTTGTATAAAGTTTGTTTTATTTTTA
38677 ATTTGTAT-AAGTTTGTTTTATTGTTTA
1 ATTTGTATAAAGTTTGTTTTATT-TTTA
38704 TATATATTGG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 12 0.52
27 11 0.48
ACGTcount: A:0.20, C:0.02, G:0.11, T:0.67
Consensus pattern (27 bp):
ATTTGTATAAAGTTTGTTTTATTTTTA
Found at i:40020 original size:3 final size:3
Alignment explanation
Indices: 40012--40037 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
40002 TGATGTCCAT
40012 TCA TCA TCA TCA TCA TCA TCA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TC
40038 TTCCCTGCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.35, G:0.00, T:0.35
Consensus pattern (3 bp):
TCA
Found at i:40326 original size:13 final size:13
Alignment explanation
Indices: 40304--40350 Score: 53
Period size: 12 Copynumber: 3.8 Consensus size: 13
40294 TGAAAAACGT
*
40304 TATATGAATAAAA
1 TATATAAATAAAA
*
40317 TATATTAAT-AAA
1 TATATAAATAAAA
*
40329 TATAAAAATAAAA
1 TATATAAATAAAA
40342 TA-ATAAATA
1 TATATAAATA
40351 TGACATAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
12 16 0.55
13 13 0.45
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (13 bp):
TATATAAATAAAA
Found at i:41578 original size:14 final size:15
Alignment explanation
Indices: 41559--41591 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
41549 TAGAAATTTT
*
41559 ATTTTTATTGAA-AA
1 ATTTTTATTAAATAA
41573 ATTTTTATTAAATAA
1 ATTTTTATTAAATAA
41588 ATTT
1 ATTT
41592 ATTTGATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (15 bp):
ATTTTTATTAAATAA
Found at i:42762 original size:26 final size:25
Alignment explanation
Indices: 42733--42797 Score: 67
Period size: 26 Copynumber: 2.5 Consensus size: 25
42723 ATAAAAATAA
*
42733 ATAAATAAATAATAATTTTATTTTAG
1 ATAAATAAAT-ATAATTTTATTTAAG
* * *
42759 ATAAATTTAATTTAATTTTATTTAAT
1 ATAAA-TAAATATAATTTTATTTAAG
*
42785 ATAAATATATATA
1 ATAAATAAATATA
42798 TATATATATA
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
25 5 0.16
26 22 0.71
27 4 0.13
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (25 bp):
ATAAATAAATATAATTTTATTTAAG
Found at i:42796 original size:2 final size:2
Alignment explanation
Indices: 42783--42816 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
42773 ATTTTATTTA
*
42783 AT AT AA 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
42817 TTCAAAATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:44685 original size:3 final size:3
Alignment explanation
Indices: 44677--44709 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
44667 CAGCGAAATG
*
44677 TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
44710 ACTTTCCATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:44923 original size:2 final size:2
Alignment explanation
Indices: 44916--44952 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
44906 TCACCAAATT
44916 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
44953 CGTGGGATGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:45090 original size:19 final size:21
Alignment explanation
Indices: 45053--45102 Score: 68
Period size: 19 Copynumber: 2.4 Consensus size: 21
45043 TTTTATATTT
45053 ATATTGTTATATTATTTTTATA
1 ATATT-TTATATTATTTTTATA
45075 ATATTTTA-ATTATTTTT-TA
1 ATATTTTATATTATTTTTATA
*
45094 ATAATTTAT
1 ATATTTTAT
45103 TTGTATCACC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
19 9 0.35
20 9 0.35
21 3 0.12
22 5 0.19
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (21 bp):
ATATTTTATATTATTTTTATA
Found at i:45501 original size:22 final size:21
Alignment explanation
Indices: 45442--45501 Score: 59
Period size: 22 Copynumber: 2.9 Consensus size: 21
45432 ATTATTATTT
*
45442 TTAAAATTAAA-AATTTTAAA
1 TTAAAATAAAATAATTTTAAA
* * **
45462 TTTAAATATAATTTTTTTAAA
1 TTAAAATAAAATAATTTTAAA
45483 TTAATAATAAAATAATTTT
1 TTAA-AATAAAATAATTTT
45502 TAGCTATATC
Statistics
Matches: 29, Mismatches: 9, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
20 8 0.28
21 10 0.34
22 11 0.38
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
TTAAAATAAAATAATTTTAAA
Found at i:47216 original size:16 final size:16
Alignment explanation
Indices: 47185--47219 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
47175 GTTTTCTTAT
**
47185 TAATAATTATTTATTA
1 TAATAATTATAAATTA
47201 TAATAATTATAAATTA
1 TAATAATTATAAATTA
47217 TAA
1 TAA
47220 ATATTTTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
TAATAATTATAAATTA
Found at i:48544 original size:15 final size:15
Alignment explanation
Indices: 48519--48558 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
48509 AAACTTAATA
48519 AAAAAATATTAAATT
1 AAAAAATATTAAATT
48534 ACAAAAA-ATTAAATT
1 A-AAAAATATTAAATT
48549 AAAAAATATT
1 AAAAAATATT
48559 TTTAAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 5 0.22
15 13 0.57
16 5 0.22
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (15 bp):
AAAAAATATTAAATT
Found at i:48583 original size:16 final size:16
Alignment explanation
Indices: 48562--48592 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
48552 AAATATTTTT
*
48562 AAAAAATAAATTAGAG
1 AAAAAATAAAATAGAG
48578 AAAAAATAAAATAGA
1 AAAAAATAAAATAGA
48593 TTAACTTAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.74, C:0.00, G:0.10, T:0.16
Consensus pattern (16 bp):
AAAAAATAAAATAGAG
Found at i:51973 original size:2 final size:2
Alignment explanation
Indices: 51966--51991 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
51956 TTCATATTAA
51966 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
51992 TTCTTATAGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:58154 original size:22 final size:24
Alignment explanation
Indices: 58127--58174 Score: 64
Period size: 22 Copynumber: 2.0 Consensus size: 24
58117 TTTTGATTCG
58127 AATTCGAA-AAATTTAA-TTAATT
1 AATTCGAATAAATTTAATTTAATT
58149 AATTCGAATCTAAATTTAATTTAATT
1 AATTCGAA--TAAATTTAATTTAATT
58175 CGAGTTGATA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 8 0.36
25 8 0.36
26 6 0.27
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (24 bp):
AATTCGAATAAATTTAATTTAATT
Found at i:58242 original size:16 final size:16
Alignment explanation
Indices: 58221--58277 Score: 71
Period size: 16 Copynumber: 3.6 Consensus size: 16
58211 AATTCGAAAT
*
58221 TCGAAATGATTCAAAC
1 TCGAAATGATTCGAAC
*
58237 TCGAAATGA-TCTGAAT
1 TCGAAATGATTC-GAAC
*
58253 TCGAAATGATCCGAAC
1 TCGAAATGATTCGAAC
58269 TCGAAATGA
1 TCGAAATGA
58278 CCTGGACAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
15 2 0.06
16 32 0.91
17 1 0.03
ACGTcount: A:0.40, C:0.18, G:0.18, T:0.25
Consensus pattern (16 bp):
TCGAAATGATTCGAAC
Found at i:59159 original size:16 final size:16
Alignment explanation
Indices: 59140--59185 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
59130 AACTCGAACT
*
59140 CAAAATGATCTAAATC
1 CAAAATAATCTAAATC
*
59156 CAAAATAATTTAAATC
1 CAAAATAATCTAAATC
* *
59172 CGAAATAATTTAAA
1 CAAAATAATCTAAA
59186 AATTTTAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.54, C:0.13, G:0.04, T:0.28
Consensus pattern (16 bp):
CAAAATAATCTAAATC
Found at i:64069 original size:16 final size:16
Alignment explanation
Indices: 64048--64079 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
64038 GATAATAAAT
64048 AGAAGGAGAAGAAGAA
1 AGAAGGAGAAGAAGAA
64064 AGAAGGAGAAGAAGAA
1 AGAAGGAGAAGAAGAA
64080 GAGGAAAGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (16 bp):
AGAAGGAGAAGAAGAA
Found at i:66054 original size:20 final size:19
Alignment explanation
Indices: 66029--66066 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
66019 ATAATATGAA
*
66029 TATATAAATATTTTAATATT
1 TATATAAAT-TATTAATATT
66049 TATATAAATTATTAATAT
1 TATATAAATTATTAATAT
66067 ATGTAAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TATATAAATTATTAATATT
Found at i:66327 original size:20 final size:21
Alignment explanation
Indices: 66302--66350 Score: 57
Period size: 20 Copynumber: 2.3 Consensus size: 21
66292 CGAATAAATT
66302 TTTTTA-GTATAAAATT-TATA
1 TTTTTATG-ATAAAATTATATA
*
66322 TTTTTATGATATAATTATATA
1 TTTTTATGATAAAATTATATA
66343 TATTTTAT
1 T-TTTTAT
66351 AAAAATAGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
20 13 0.52
21 6 0.24
22 6 0.24
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (21 bp):
TTTTTATGATAAAATTATATA
Found at i:66615 original size:28 final size:28
Alignment explanation
Indices: 66538--66626 Score: 69
Period size: 28 Copynumber: 3.2 Consensus size: 28
66528 CAAATTATTT
* *
66538 ATTTATAA-ATATAAATA-TTTAAAAAA
1 ATTTATAATATATTAATATTTTAAATAA
*
66564 ATATT-T-ATATTTTAAATTATTTTTAAATAA
1 AT-TTATAATATATT-AA-TA-TTTTAAATAA
**
66594 ATTTATAATATATTAATATTTTACTTAA
1 ATTTATAATATATTAATATTTTAAATAA
66622 ATTTA
1 ATTTA
66627 ACTGAAACAG
Statistics
Matches: 49, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
25 1 0.02
26 6 0.12
27 4 0.08
28 15 0.31
29 4 0.08
30 13 0.27
31 6 0.12
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (28 bp):
ATTTATAATATATTAATATTTTAAATAA
Found at i:67239 original size:19 final size:20
Alignment explanation
Indices: 67204--67245 Score: 52
Period size: 19 Copynumber: 2.1 Consensus size: 20
67194 ATGTTTCATA
*
67204 TTTTAGAAATATTAT-AATT
1 TTTTAGAAAAATTATAAATT
67223 TTTTA-AAAAATTAATAAATT
1 TTTTAGAAAAATT-ATAAATT
67243 TTT
1 TTT
67246 CAATTTGATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 6 0.30
19 7 0.35
20 7 0.35
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (20 bp):
TTTTAGAAAAATTATAAATT
Found at i:69292 original size:3 final size:3
Alignment explanation
Indices: 69284--69308 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
69274 GGTCAAAGAT
69284 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
69309 GTGGAACATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:69602 original size:11 final size:12
Alignment explanation
Indices: 69572--69614 Score: 54
Period size: 11 Copynumber: 3.6 Consensus size: 12
69562 ATATTTATGA
69572 TAAAAATATATATT
1 TAAAAATATA-A-T
69586 TAAAAATATAA-
1 TAAAAATATAAT
69597 TAAAAATA-AAT
1 TAAAAATATAAT
69608 TAAAAAT
1 TAAAAAT
69615 TTATCCATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
10 2 0.07
11 15 0.54
13 1 0.04
14 10 0.36
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
TAAAAATATAAT
Found at i:70949 original size:20 final size:20
Alignment explanation
Indices: 70911--70949 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
70901 AATATTTAAA
**
70911 TTTTTAGTATTTTGTAATTT
1 TTTTTAGTATTTTCAAATTT
*
70931 TTTTTATTATTTTCAAATT
1 TTTTTAGTATTTTCAAATT
70950 GATTTTTTTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.23, C:0.03, G:0.05, T:0.69
Consensus pattern (20 bp):
TTTTTAGTATTTTCAAATTT
Found at i:85813 original size:58 final size:58
Alignment explanation
Indices: 85704--85905 Score: 171
Period size: 58 Copynumber: 3.5 Consensus size: 58
85694 ATAAATTTAC
* * * * * * *
85704 ATAAAAG-TCCTAGATTATG-AAAATGGCCTAAATGGCTTTAACATGCTTAAAATTGT
1 ATAAAAGTTCCTAGATCATGAAAAATGACCTAAATGACCTCAACATTCATAAAATTGT
*
85760 ATAAAAGTTCCTAGATCATGAAAAATGACCTAAATGACCTCAACATTCATAAAATTGC
1 ATAAAAGTTCCTAGATCATGAAAAATGACCTAAATGACCTCAACATTCATAAAATTGT
* * * * * * *
85818 ATGAAAA-TTTCTAGATCACGCAAAATGACATAAATAAACC-CAACATTAATTAAATT-T
1 AT-AAAAGTTCCTAGATCATGAAAAATGACCTAAAT-GACCTCAACATTCATAAAATTGT
* * *
85875 ACATAAAAGTCCCTAGATTATAAAAAATGAC
1 --ATAAAAGTTCCTAGATCATGAAAAATGAC
85906 GTAATAGACC
Statistics
Matches: 117, Mismatches: 22, Indels: 11
0.78 0.15 0.07
Matches are distributed among these distances:
56 7 0.06
57 11 0.09
58 74 0.63
59 25 0.21
ACGTcount: A:0.46, C:0.16, G:0.11, T:0.28
Consensus pattern (58 bp):
ATAAAAGTTCCTAGATCATGAAAAATGACCTAAATGACCTCAACATTCATAAAATTGT
Found at i:89046 original size:21 final size:20
Alignment explanation
Indices: 89022--89060 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
89012 AAAAATAATT
*
89022 ATTTTAATATATATTTTTTAA
1 ATTTGAATATA-ATTTTTTAA
*
89043 ATTTGAATTTAATTTTTT
1 ATTTGAATATAATTTTTT
89061 TATGATCATT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (20 bp):
ATTTGAATATAATTTTTTAA
Found at i:89769 original size:2 final size:2
Alignment explanation
Indices: 89762--89803 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
89752 TTCATGAACA
89762 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
89804 CATTTTCACT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:89918 original size:16 final size:17
Alignment explanation
Indices: 89897--89932 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
89887 AATTACACAC
89897 AATTAATTCAAA-TATG
1 AATTAATTCAAACTATG
89913 AATTAATTCAAACTATG
1 AATTAATTCAAACTATG
89930 AAT
1 AAT
89933 ATGATTCAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 12 0.63
17 7 0.37
ACGTcount: A:0.50, C:0.08, G:0.06, T:0.36
Consensus pattern (17 bp):
AATTAATTCAAACTATG
Found at i:89943 original size:17 final size:16
Alignment explanation
Indices: 89897--89943 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 16
89887 AATTACACAC
*
89897 AATTAATTCAAATATG
1 AATTAATTCAACTATG
89913 AATTAATTCAAACTATG
1 AATTAATTC-AACTATG
*
89930 AATATGATTCAACT
1 AAT-TAATTCAACT
89944 TAATTTAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
16 9 0.33
17 13 0.48
18 5 0.19
ACGTcount: A:0.47, C:0.11, G:0.06, T:0.36
Consensus pattern (16 bp):
AATTAATTCAACTATG
Found at i:90649 original size:16 final size:17
Alignment explanation
Indices: 90616--90651 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
90606 ATTTATTAAT
90616 TTTAAATAAAATAAATA
1 TTTAAATAAAATAAATA
*
90633 TTTAAATAATA-AAATA
1 TTTAAATAAAATAAATA
90649 TTT
1 TTT
90652 TTATAAACCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
TTTAAATAAAATAAATA
Found at i:93513 original size:14 final size:16
Alignment explanation
Indices: 93487--93520 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
93477 TTTAAATTTA
93487 ATAAAATTATGT-AAT
1 ATAAAATTATGTAAAT
93502 ATAAAA-TATGTAAAT
1 ATAAAATTATGTAAAT
93517 ATAA
1 ATAA
93521 TTTTTTATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (16 bp):
ATAAAATTATGTAAAT
Found at i:93990 original size:5 final size:5
Alignment explanation
Indices: 93976--94039 Score: 51
Period size: 5 Copynumber: 12.8 Consensus size: 5
93966 AAAAATTAAA
* * * *
93976 TAATT T-ATT TAATT TAATT AAATT TAAAT TAAGTTT TAATT TTA-T TATTT
1 TAATT TAATT TAATT TAATT TAATT TAATT TAA--TT TAATT TAATT TAATT
*
94026 TAAAT TAATT TAAT
1 TAATT TAATT TAAT
94040 ATATAAATAT
Statistics
Matches: 45, Mismatches: 10, Indels: 8
0.71 0.16 0.13
Matches are distributed among these distances:
4 6 0.13
5 35 0.78
7 4 0.09
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.58
Consensus pattern (5 bp):
TAATT
Found at i:94013 original size:27 final size:26
Alignment explanation
Indices: 93983--94033 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
93973 AAATAATTTA
93983 TTTAATTTAATTAAATTTAAATTAAGT
1 TTTAATTTAATT-AATTTAAATTAAGT
* *
94010 TTTAATTTTATTATTTTAAATTAA
1 TTTAATTTAATTAATTTAAATTAA
94034 TTTAATATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 11 0.50
27 11 0.50
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (26 bp):
TTTAATTTAATTAATTTAAATTAAGT
Found at i:94037 original size:10 final size:9
Alignment explanation
Indices: 93971--94039 Score: 52
Period size: 9 Copynumber: 7.6 Consensus size: 9
93961 TGTTTAAAAA
*
93971 TTAAATAAT
1 TTAATTAAT
*
93980 TTATTTAAT
1 TTAATTAAT
93989 TTAATTAAAT
1 TTAATT-AAT
*
93999 TTAAATTAAG
1 TT-AATTAAT
94009 TT--TTAAT
1 TTAATTAAT
* *
94016 TTTATTATT
1 TTAATTAAT
94025 TTAAATTAAT
1 TT-AATTAAT
94035 TTAAT
1 TTAAT
94040 ATATAAATAT
Statistics
Matches: 47, Mismatches: 8, Indels: 10
0.72 0.12 0.15
Matches are distributed among these distances:
7 6 0.13
9 21 0.45
10 16 0.34
11 4 0.09
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (9 bp):
TTAATTAAT
Found at i:94160 original size:15 final size:17
Alignment explanation
Indices: 94140--94174 Score: 56
Period size: 15 Copynumber: 2.2 Consensus size: 17
94130 ATTTAAATTT
94140 TAATTT-TTTTAA-TCA
1 TAATTTATTTTAACTCA
94155 TAATTTATTTTAACTCA
1 TAATTTATTTTAACTCA
94172 TAA
1 TAA
94175 ATACTTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 6 0.33
16 6 0.33
17 6 0.33
ACGTcount: A:0.37, C:0.09, G:0.00, T:0.54
Consensus pattern (17 bp):
TAATTTATTTTAACTCA
Found at i:94958 original size:13 final size:13
Alignment explanation
Indices: 94940--94964 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
94930 AAACTATATT
94940 TTTTTTATTTTTA
1 TTTTTTATTTTTA
94953 TTTTTTATTTTT
1 TTTTTTATTTTT
94965 TCTTAACCAA
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:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTTATTTTTA
Found at i:95023 original size:23 final size:24
Alignment explanation
Indices: 94993--95041 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 24
94983 TTACTAAATT
*
94993 TTTAAATAATAATA-ATTAATTAA
1 TTTAAATAAAAATATATTAATTAA
*
95016 TTTAAATAAAAATATTTTAATTAA
1 TTTAAATAAAAATATATTAATTAA
95040 TT
1 TT
95042 CATTTCAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 13 0.57
24 10 0.43
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (24 bp):
TTTAAATAAAAATATATTAATTAA
Found at i:95061 original size:32 final size:28
Alignment explanation
Indices: 94996--95071 Score: 71
Period size: 28 Copynumber: 2.5 Consensus size: 28
94986 CTAAATTTTT
*
94996 AAATAATAATAATTAATTAATTTAAATAA
1 AAATAAT-TTAATTAATTAATTTAAATAA
* *
95025 AAATATTTTAATTAATTCATTTCAAAAGTAA
1 AAATAATTTAATTAATTAATTT--AAA-TAA
*
95056 TAAATAATTCAATTAA
1 -AAATAATTTAATTAA
95072 AATAAGTTTA
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
28 13 0.34
29 6 0.16
30 3 0.08
31 3 0.08
32 13 0.34
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.39
Consensus pattern (28 bp):
AAATAATTTAATTAATTAATTTAAATAA
Found at i:95341 original size:29 final size:28
Alignment explanation
Indices: 95263--95346 Score: 98
Period size: 29 Copynumber: 2.9 Consensus size: 28
95253 AAATAATAAC
* * *
95263 TTAAAAATAAATATATTTTTGACCAAATC
1 TTAAAAATAAATATATTTTTTA-TAAATA
*
95292 TTAAAAATAAATAAATATTTTT-TAAATA
1 TTAAAAATAAATATAT-TTTTTATAAATA
95320 TTAAAAAGTAAATATATTTTTTATAAA
1 TTAAAAA-TAAATATATTTTTTATAAA
95347 AATTTTAAGA
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
28 16 0.34
29 27 0.57
30 4 0.09
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.42
Consensus pattern (28 bp):
TTAAAAATAAATATATTTTTTATAAATA
Found at i:99482 original size:2 final size:2
Alignment explanation
Indices: 99475--99506 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
99465 TTCATGAACA
99475 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
99507 CATTTTCACT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:101581 original size:22 final size:21
Alignment explanation
Indices: 101534--101581 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 21
101524 CTAGTAAAAT
101534 AAAAATATATAATTATATTTA
1 AAAAATATATAATTATATTTA
* *
101555 TAAAATATA-AATTTTATGGTTA
1 AAAAATATATAATTATAT--TTA
101577 AAAAA
1 AAAAA
101582 AATTTATTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 7 0.32
21 8 0.36
22 7 0.32
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (21 bp):
AAAAATATATAATTATATTTA
Found at i:102888 original size:24 final size:22
Alignment explanation
Indices: 102837--102889 Score: 54
Period size: 24 Copynumber: 2.4 Consensus size: 22
102827 GTAATATAAA
*
102837 ATATT-TAAATATAATTTTTAT
1 ATATTATAAATATAATTATTAT
* *
102858 ATTTTATAATATATTAATTATTCT
1 ATATTATAA-ATA-TAATTATTAT
102882 ATATTATA
1 ATATTATA
102890 TTTTTATTGT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
21 4 0.16
22 3 0.12
23 3 0.12
24 15 0.60
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.57
Consensus pattern (22 bp):
ATATTATAAATATAATTATTAT
Found at i:103370 original size:15 final size:16
Alignment explanation
Indices: 103344--103410 Score: 68
Period size: 16 Copynumber: 4.4 Consensus size: 16
103334 TTAAATTTAG
* **
103344 ATTAAGTTTTAATTTT
1 ATTAATTTTTAATTAA
103360 ATT-ATTTTTAATTAA
1 ATTAATTTTTAATTAA
103375 ATTAATTTTTAA--AA
1 ATTAATTTTTAATTAA
*
103389 ATAAATTTTTAATTAA
1 ATTAATTTTTAATTAA
*
103405 AATAAT
1 ATTAAT
103411 ATATTTTTAT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
14 13 0.31
15 12 0.29
16 17 0.40
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (16 bp):
ATTAATTTTTAATTAA
Found at i:103395 original size:14 final size:15
Alignment explanation
Indices: 103363--103401 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
103353 TAATTTTATT
*
103363 ATTTTTAATTAAATTA
1 ATTTTTAA-TAAATAA
103379 ATTTTTAA-AAATAA
1 ATTTTTAATAAATAA
103393 ATTTTTAAT
1 ATTTTTAAT
103402 TAAAATAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 13 0.62
16 8 0.38
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
ATTTTTAATAAATAA
Found at i:104553 original size:16 final size:16
Alignment explanation
Indices: 104519--104556 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
104509 ATTGTTTTTT
* *
104519 AATTTT-TTCTTAATC
1 AATTTTATTATTAATA
104534 AATTTTATTATTAATA
1 AATTTTATTATTAATA
104550 AATTTTA
1 AATTTTA
104557 AATAATAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (16 bp):
AATTTTATTATTAATA
Found at i:104569 original size:21 final size:20
Alignment explanation
Indices: 104543--104581 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
104533 CAATTTTATT
104543 ATTAATAAATTTTAAATAATA
1 ATTAATAAA-TTTAAATAATA
*
104564 ATTAATTAATTTAAATAA
1 ATTAATAAATTTAAATAA
104582 AAATATTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
ATTAATAAATTTAAATAATA
Found at i:104901 original size:29 final size:30
Alignment explanation
Indices: 104865--104931 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 30
104855 ATCAAGCCTT
*
104865 AAAA-AAATAAATATTTTT-TAAATA-TTAA
1 AAAATAAATAAAT-TTTTTATAAAAATTTAA
* *
104893 AAAATAAATATATTTTTTATAAAAATTTTA
1 AAAATAAATAAATTTTTTATAAAAATTTAA
104923 AAAATAAAT
1 AAAATAAAT
104932 TTTTTTCTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
28 9 0.27
29 12 0.36
30 12 0.36
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (30 bp):
AAAATAAATAAATTTTTTATAAAAATTTAA
Found at i:105007 original size:4 final size:4
Alignment explanation
Indices: 104998--105022 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
104988 ATAAAAGTTC
104998 AATA AATA AATA AATA AATA AATA A
1 AATA AATA AATA AATA AATA AATA A
105023 GTAACTTACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:105227 original size:3 final size:3
Alignment explanation
Indices: 105219--105254 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
105209 TTGTTGCAGT
*
105219 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC ATC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
105255 ATCTCTTTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.03, C:0.33, G:0.00, T:0.64
Consensus pattern (3 bp):
TTC
Found at i:105601 original size:13 final size:14
Alignment explanation
Indices: 105583--105613 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
105573 AAGTTTATTC
105583 TTTTCTCTT-TTTT
1 TTTTCTCTTCTTTT
105596 TTTTCTCTTCTTTT
1 TTTTCTCTTCTTTT
105610 TTTT
1 TTTT
105614 TTCTCGTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.53
14 8 0.47
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (14 bp):
TTTTCTCTTCTTTT
Found at i:105606 original size:18 final size:17
Alignment explanation
Indices: 105580--105615 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
105570 TTCAAGTTTA
*
105580 TTCTTTTCTCTTTTTTTT
1 TTCTCTTCT-TTTTTTTT
105598 TTCTCTTCTTTTTTTTT
1 TTCTCTTCTTTTTTTTT
105615 T
1 T
105616 CTCGTTTTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (17 bp):
TTCTCTTCTTTTTTTTT
Found at i:105609 original size:16 final size:16
Alignment explanation
Indices: 105588--105618 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
105578 TATTCTTTTC
105588 TCTTTTTTTTTTCTCT
1 TCTTTTTTTTTTCTCT
105604 TCTTTTTTTTTTCTC
1 TCTTTTTTTTTTCTC
105619 GTTTTGGAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (16 bp):
TCTTTTTTTTTTCTCT
Found at i:110645 original size:2 final size:2
Alignment explanation
Indices: 110638--110674 Score: 51
Period size: 2 Copynumber: 19.0 Consensus size: 2
110628 ATAATTTTAA
110638 AT AT AT AT AT AT AT AT AT AT AT AT GAT -T AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT
110675 GAAATAAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
1 2 0.06
2 28 0.88
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:110767 original size:27 final size:26
Alignment explanation
Indices: 110727--110815 Score: 83
Period size: 28 Copynumber: 3.3 Consensus size: 26
110717 ATGTTTATGT
110727 TATAAATATATAAATATATAAAAAATAA
1 TATAAA-ATATAAATAT-TAAAAAATAA
* **
110755 TATAAAATTTAAATATTTTAAAATTTAA
1 TATAAAATATAAATA--TTAAAAAATAA
110783 -AT-AAATATATAATATTAAAAAATAA
1 TATAAAATATA-AATATTAAAAAATAA
110808 TTATAAAA
1 -TATAAAA
110816 CAGATCCGTA
Statistics
Matches: 49, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
25 9 0.18
26 6 0.12
27 16 0.33
28 17 0.35
29 1 0.02
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (26 bp):
TATAAAATATAAATATTAAAAAATAA
Found at i:111162 original size:13 final size:13
Alignment explanation
Indices: 111144--111190 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
111134 ATTTTAATTT
111144 TTTATTATTAATA
1 TTTATTATTAATA
111157 TTTATTA-TAATTA
1 TTTATTATTAA-TA
* *
111170 ATTA-TAATAATA
1 TTTATTATTAATA
111182 TTTATTATT
1 TTTATTATT
111191 TTAATAATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
12 10 0.36
13 18 0.64
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TTTATTATTAATA
Found at i:139271 original size:18 final size:17
Alignment explanation
Indices: 139246--139287 Score: 66
Period size: 18 Copynumber: 2.4 Consensus size: 17
139236 TCCTTCGTAC
139246 CAAAAAAAAAAAACAAA
1 CAAAAAAAAAAAACAAA
*
139263 CACAAAAAAACAAACAAA
1 CA-AAAAAAAAAAACAAA
139281 CAAAAAA
1 CAAAAAA
139288 GAAGGGTCTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.30
18 16 0.70
ACGTcount: A:0.83, C:0.17, G:0.00, T:0.00
Consensus pattern (17 bp):
CAAAAAAAAAAAACAAA
Found at i:139286 original size:14 final size:14
Alignment explanation
Indices: 139252--139278 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
139242 GTACCAAAAA
139252 AAAAAAACAAACAC
1 AAAAAAACAAACAC
139266 AAAAAAACAAACA
1 AAAAAAACAAACA
139279 AACAAAAAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.81, C:0.19, G:0.00, T:0.00
Consensus pattern (14 bp):
AAAAAAACAAACAC
Found at i:140542 original size:28 final size:28
Alignment explanation
Indices: 140508--140971 Score: 542
Period size: 28 Copynumber: 16.8 Consensus size: 28
140498 TGTTCATCTC
* * *
140508 TTCAAAGCCCACAAGTTAGTTGCATCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
140536 TTCAAAGCCCACAAGTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* *
140564 TTCAAAGTCCACAAGTTAGTGGCA-CCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCC-T
*
140592 TTCAAAGCCCATAAGTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
140620 TTCAAAGCCCACAAGTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
*
140648 TTCATAGCCCACAAGTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* *
140676 TTCAAAGCCCACAAGTTAGTGG--T-AT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* *
140701 TTCGAAGCCCACAAGTCAGTAGCATCCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCC-T
*
140730 TTCAAAGCCCACAAGTCAGTGGCATCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* *
140758 TTCAAAGCCCATAAGTAAGTGGCATCCGT
1 TTCAAAGCCCACAAGTCAGTGGCATCC-T
*
140787 TT-AAAGCCCACAAATCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* *
140814 TTCAAAGCCCACAAGTCAATGACA-CC-
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* *
140840 --C-CAG-CCATAAGTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
*
140864 TTCAAAAG-CCACAAGTCAGTGGCA-CAT
1 TTC-AAAGCCCACAAGTCAGTGGCATCCT
* *
140891 ATTCAAAGCCAACAAGTTAGTGGCA-CCAT
1 -TTCAAAGCCCACAAGTCAGTGGCATCC-T
*
140920 TTTAAAGCCCACAAGTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
*
140948 TTCAAAGGCCACACAAGTCGGTGG
1 TTCAAA-GCC-CACAAGTCAGTGG
140972 TAACTTTCTC
Statistics
Matches: 372, Mismatches: 44, Indels: 38
0.82 0.10 0.08
Matches are distributed among these distances:
22 13 0.03
23 4 0.01
24 1 0.00
25 20 0.05
26 2 0.01
27 14 0.04
28 270 0.73
29 36 0.10
30 12 0.03
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.23
Consensus pattern (28 bp):
TTCAAAGCCCACAAGTCAGTGGCATCCT
Found at i:141822 original size:24 final size:24
Alignment explanation
Indices: 141764--141852 Score: 97
Period size: 20 Copynumber: 4.0 Consensus size: 24
141754 AAAGTCACAT
141764 TTTTTACCCAGATGTATCGATACA
1 TTTTTACCCAGATGTATCGATACA
*
141788 TTCTT---CA-ATGTATCGATATC-
1 TTTTTACCCAGATGTATCGATA-CA
141808 TTTTTACCCAGATGTATCGATACA
1 TTTTTACCCAGATGTATCGATACA
141832 TTTTT---CA-ATGTATCGATACA
1 TTTTTACCCAGATGTATCGATACA
141852 T
1 T
141853 CTAGTTAAAA
Statistics
Matches: 57, Mismatches: 2, Indels: 16
0.76 0.03 0.21
Matches are distributed among these distances:
20 29 0.51
21 5 0.09
23 3 0.05
24 20 0.35
ACGTcount: A:0.28, C:0.19, G:0.11, T:0.42
Consensus pattern (24 bp):
TTTTTACCCAGATGTATCGATACA
Found at i:141827 original size:44 final size:44
Alignment explanation
Indices: 141764--141849 Score: 163
Period size: 44 Copynumber: 2.0 Consensus size: 44
141754 AAAGTCACAT
141764 TTTTTACCCAGATGTATCGATACATTCTTCAATGTATCGATATC
1 TTTTTACCCAGATGTATCGATACATTCTTCAATGTATCGATATC
*
141808 TTTTTACCCAGATGTATCGATACATTTTTCAATGTATCGATA
1 TTTTTACCCAGATGTATCGATACATTCTTCAATGTATCGATA
141850 CATCTAGTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.28, C:0.19, G:0.12, T:0.42
Consensus pattern (44 bp):
TTTTTACCCAGATGTATCGATACATTCTTCAATGTATCGATATC
Found at i:150275 original size:13 final size:13
Alignment explanation
Indices: 150257--150282 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
150247 ACATTTCACC
150257 ATGTATCAATACA
1 ATGTATCAATACA
150270 ATGTATCAATACA
1 ATGTATCAATACA
150283 CTATATTGAT
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:0.46, C:0.15, G:0.08, T:0.31
Consensus pattern (13 bp):
ATGTATCAATACA
Found at i:158851 original size:40 final size:40
Alignment explanation
Indices: 158773--158851 Score: 99
Period size: 40 Copynumber: 2.0 Consensus size: 40
158763 AAATCAAAAA
* *
158773 TATAATATAAATAAATCTAAATAAATTTTAATTATTTATT
1 TATAATATAAATAAATCTAAATAAATTTAAAATATTTATT
*
158813 TATAATATAAAT-AATTTAAAATTAAATTTAAAAT-TTTAT
1 TATAATATAAATAAATCT-AAA-TAAATTTAAAATATTTAT
158852 ATTACGCCAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
39 4 0.12
40 20 0.59
41 10 0.29
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (40 bp):
TATAATATAAATAAATCTAAATAAATTTAAAATATTTATT
Found at i:165746 original size:15 final size:15
Alignment explanation
Indices: 165716--165745 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
165706 TCCTACTCTC
165716 TCTTTTTTTTCTTTT
1 TCTTTTTTTTCTTTT
165731 TCTTTTTTTT-TTTT
1 TCTTTTTTTTCTTTT
165745 T
1 T
165746 TTGTAATTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (15 bp):
TCTTTTTTTTCTTTT
Found at i:165969 original size:23 final size:21
Alignment explanation
Indices: 165925--165971 Score: 67
Period size: 23 Copynumber: 2.1 Consensus size: 21
165915 TTATTTGGAT
165925 TATTATTTAATTAATAAAAAA
1 TATTATTTAATTAATAAAAAA
*
165946 TATTATTTGAATTTAATAATAAA
1 TATTATTT-AA-TTAATAAAAAA
165969 TAT
1 TAT
165972 ATATAAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 8 0.35
22 2 0.09
23 13 0.57
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (21 bp):
TATTATTTAATTAATAAAAAA
Done.