Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold1924.1
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: 333483
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.31
Warning! 20016 characters in sequence are not A, C, G, or T
Found at i:9365 original size:28 final size:29
Alignment explanation
Indices: 9306--9367 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 29
9296 ATAAGTTATT
*
9306 TTTTTTTAAAATTTACCGAAATGGGCTGA
1 TTTTTTTAAAATTTACCGAAATGGGCTCA
** * *
9335 TTTTTTTATTATTTACCGGAAT-GGTTCA
1 TTTTTTTAAAATTTACCGAAATGGGCTCA
9363 TTTTT
1 TTTTT
9368 CGTGAAATCG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 9 0.32
29 19 0.68
ACGTcount: A:0.24, C:0.10, G:0.15, T:0.52
Consensus pattern (29 bp):
TTTTTTTAAAATTTACCGAAATGGGCTCA
Found at i:9828 original size:124 final size:124
Alignment explanation
Indices: 9608--9957 Score: 628
Period size: 124 Copynumber: 2.8 Consensus size: 124
9598 TTATTTCGAG
*
9608 TTGACGTTTCTGATCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTG
*
9673 AAATCGCGTCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAATTTTTT
66 AAATCGCGTCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAAATTTTT
9732 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTG
* * *
9797 AAATCGTGCCCTCGTGGACGCGATTTTGCTACAGTTGGTCATGTAAGAAATAAATTTTT
66 AAATCGCGTCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAAATTTTT
* *
9856 TTGACGTTTCTAAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAAAAGAAATTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTG
*
9921 AAATCGCATCCTCGTGGACGCGATTTTGCTACAGTAG
66 AAATCGCGTCCTCGTGGACGCGATTTTGCTACAGTAG
9958 CAAGTTTGGG
Statistics
Matches: 215, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
124 215 1.00
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Consensus pattern (124 bp):
TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTG
AAATCGCGTCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAAATTTTT
Found at i:11228 original size:30 final size:29
Alignment explanation
Indices: 11161--11273 Score: 217
Period size: 29 Copynumber: 3.9 Consensus size: 29
11151 TAAGGAAAAT
11161 GGTTAGGGTTTTTAATTAAATTAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
11190 GGTTAGGGTTTTTAATTAAATTAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
11219 GGTTTAGGGTTTTTAATTAAATTAGGTTAG
1 GG-TTAGGGTTTTTAATTAAATTAGGTTAG
11249 GGTTAGGGTTTTTAATTAAATTAGG
1 GGTTAGGGTTTTTAATTAAATTAGG
11274 ATTTTTATTA
Statistics
Matches: 83, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
29 54 0.65
30 29 0.35
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.45
Consensus pattern (29 bp):
GGTTAGGGTTTTTAATTAAATTAGGTTAG
Found at i:11359 original size:36 final size:36
Alignment explanation
Indices: 11319--11433 Score: 92
Period size: 36 Copynumber: 3.2 Consensus size: 36
11309 ATATCAAATA
*
11319 ATATCAAAATAACTCGAAAAAATTTCTATGCCTATT
1 ATATCAAAATAACTCGAAAAAATTTCTATGCATATT
* **** * * *
11355 ATATC-AAATAAACTTCTATTTTA-TTATAT-CAAATA
1 ATATCAAAAT-AAC-TCGAAAAAATTTCTATGCATATT
*
11390 ATATCAAAATAACTCGAAAAAATTTCTATGCGTATT
1 ATATCAAAATAACTCGAAAAAATTTCTATGCATATT
*
11426 ACATCAAA
1 ATATCAAA
11434 TAATAAATTT
Statistics
Matches: 55, Mismatches: 19, Indels: 10
0.65 0.23 0.12
Matches are distributed among these distances:
34 4 0.07
35 20 0.36
36 27 0.49
37 4 0.07
ACGTcount: A:0.46, C:0.15, G:0.04, T:0.35
Consensus pattern (36 bp):
ATATCAAAATAACTCGAAAAAATTTCTATGCATATT
Found at i:11383 original size:71 final size:71
Alignment explanation
Indices: 11279--11436 Score: 289
Period size: 71 Copynumber: 2.2 Consensus size: 71
11269 TTAGGATTTT
11279 TATTACATCAAATAAAACTTCTATTTTATTATATCAAATAATATCAAAATAACTCGAAAAAATTT
1 TATTACATCAAAT-AAACTTCTATTTTATTATATCAAATAATATCAAAATAACTCGAAAAAATTT
11344 CTATGCC
65 CTATGCC
*
11351 TATTATATCAAATAAACTTCTATTTTATTATATCAAATAATATCAAAATAACTCGAAAAAATTTC
1 TATTACATCAAATAAACTTCTATTTTATTATATCAAATAATATCAAAATAACTCGAAAAAATTTC
*
11416 TATGCG
66 TATGCC
11422 TATTACATCAAATAA
1 TATTACATCAAATAA
11437 TAAATTTAAA
Statistics
Matches: 83, Mismatches: 3, Indels: 1
0.95 0.03 0.01
Matches are distributed among these distances:
71 71 0.86
72 12 0.14
ACGTcount: A:0.46, C:0.14, G:0.03, T:0.37
Consensus pattern (71 bp):
TATTACATCAAATAAACTTCTATTTTATTATATCAAATAATATCAAAATAACTCGAAAAAATTTC
TATGCC
Found at i:14865 original size:7 final size:7
Alignment explanation
Indices: 14855--14879 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
14845 TTATATACAT
14855 AATACTA
1 AATACTA
14862 AATACTA
1 AATACTA
14869 AATACTA
1 AATACTA
14876 AATA
1 AATA
14880 TCAATCGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:15978 original size:10 final size:10
Alignment explanation
Indices: 15959--16010 Score: 50
Period size: 11 Copynumber: 5.0 Consensus size: 10
15949 GCCATTGATG
*
15959 AAAATATAAA
1 AAAATTTAAA
15969 AAAATTTAAA
1 AAAATTTAAA
* *
15979 ATTATTTTAAA
1 A-AAATTTAAA
*
15990 AAAATATAAAA
1 AAAAT-TTAAA
16001 AAAATTTAAA
1 AAAATTTAAA
16011 TTATTTTAAA
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
10 16 0.48
11 17 0.52
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (10 bp):
AAAATTTAAA
Found at i:15994 original size:31 final size:31
Alignment explanation
Indices: 15959--16023 Score: 114
Period size: 31 Copynumber: 2.1 Consensus size: 31
15949 GCCATTGATG
15959 AAAATAT-AAAAAAATTTAAAATTATTTTAAA
1 AAAATATAAAAAAAATTT-AAATTATTTTAAA
15990 AAAATATAAAAAAAATTTAAATTATTTTAAA
1 AAAATATAAAAAAAATTTAAATTATTTTAAA
16021 AAA
1 AAA
16024 TGAAATTGAG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
31 23 0.70
32 10 0.30
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (31 bp):
AAAATATAAAAAAAATTTAAATTATTTTAAA
Found at i:16080 original size:29 final size:29
Alignment explanation
Indices: 16048--16136 Score: 75
Period size: 29 Copynumber: 3.3 Consensus size: 29
16038 AATTTAGATT
16048 AAATATGGATTTGAGAGAATTTTGGAAGG
1 AAATATGGATTTGAGAGAATTTTGGAAGG
* * **
16077 AAAT-T-GA---GAG-GAA-ATTGAAATT
1 AAATATGGATTTGAGAGAATTTTGGAAGG
*
16099 AAATATGGGTTTGAGAGAATTTTGGAAGG
1 AAATATGGATTTGAGAGAATTTTGGAAGG
*
16128 AAATTTGGA
1 AAATATGGA
16137 AGGAAATTGA
Statistics
Matches: 42, Mismatches: 11, Indels: 14
0.63 0.16 0.21
Matches are distributed among these distances:
22 9 0.21
23 4 0.10
24 4 0.10
27 5 0.12
28 4 0.10
29 16 0.38
ACGTcount: A:0.40, C:0.00, G:0.29, T:0.30
Consensus pattern (29 bp):
AAATATGGATTTGAGAGAATTTTGGAAGG
Found at i:16080 original size:51 final size:51
Alignment explanation
Indices: 16025--16146 Score: 176
Period size: 51 Copynumber: 2.4 Consensus size: 51
16015 TTTAAAAAAT
* *
16025 GAAATTGAG-GGAAAATTTAGATTAAATATGGATTTGAGAGAATTTTGGAAG
1 GAAATTGAGAGG-AAATTGAAATTAAATATGGATTTGAGAGAATTTTGGAAG
*
16076 GAAATTGAGAGGAAATTGAAATTAAATATGGGTTTGAGAGAATTTTGGAAG
1 GAAATTGAGAGGAAATTGAAATTAAATATGGATTTGAGAGAATTTTGGAAG
16127 GAAATTTG-GAAGGAAATTGA
1 GAAA-TTGAG-AGGAAATTGA
16147 GAGGATTAGA
Statistics
Matches: 65, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
51 50 0.77
52 15 0.23
ACGTcount: A:0.42, C:0.00, G:0.29, T:0.30
Consensus pattern (51 bp):
GAAATTGAGAGGAAATTGAAATTAAATATGGATTTGAGAGAATTTTGGAAG
Found at i:16136 original size:12 final size:12
Alignment explanation
Indices: 16119--16144 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
16109 TTGAGAGAAT
16119 TTTGGAAGGAAA
1 TTTGGAAGGAAA
16131 TTTGGAAGGAAA
1 TTTGGAAGGAAA
16143 TT
1 TT
16145 GAGAGGATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.00, G:0.31, T:0.31
Consensus pattern (12 bp):
TTTGGAAGGAAA
Found at i:17472 original size:30 final size:30
Alignment explanation
Indices: 17431--17493 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 30
17421 TCAATAATTT
*
17431 AATTGATTGTTTATATT-AGATT-AAAGACTC
1 AATTAATTGTTTATATTCA-ATTAAAAG-CTC
17461 AATTAATTGTTTATATTCAATTAAAAGCTC
1 AATTAATTGTTTATATTCAATTAAAAGCTC
17491 AAT
1 AAT
17494 CAATGATTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
30 25 0.83
31 5 0.17
ACGTcount: A:0.40, C:0.08, G:0.10, T:0.43
Consensus pattern (30 bp):
AATTAATTGTTTATATTCAATTAAAAGCTC
Found at i:18318 original size:11 final size:13
Alignment explanation
Indices: 18294--18325 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
18284 TAGTTTATTA
18294 ATATTTTAATATG
1 ATATTTTAATATG
18307 AT-TTTTAA-ATG
1 ATATTTTAATATG
18318 ATATTTTA
1 ATATTTTA
18326 TTAATTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 5 0.28
12 11 0.61
13 2 0.11
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (13 bp):
ATATTTTAATATG
Found at i:28222 original size:50 final size:50
Alignment explanation
Indices: 28168--28291 Score: 167
Period size: 50 Copynumber: 2.5 Consensus size: 50
28158 CATTTAGGTT
* *
28168 ATGAGAGGTCCCATGTAAGACCATGTCTAGGACATGGCGTTGGCACCAAG
1 ATGAGAGGTCCCATGTAAGACCATGTCTAGGACATGGCATGGGCACCAAG
** * *
28218 ATGAGAGGTCCCCCGTAAGACCATGTCTAGGACATGGCATGGGCACCGAT
1 ATGAGAGGTCCCATGTAAGACCATGTCTAGGACATGGCATGGGCACCAAG
* **
28268 ATGAAAACTCCCATGTAAGACCAT
1 ATGAGAGGTCCCATGTAAGACCAT
28292 ATCTGAGATA
Statistics
Matches: 63, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
50 63 1.00
ACGTcount: A:0.30, C:0.24, G:0.27, T:0.19
Consensus pattern (50 bp):
ATGAGAGGTCCCATGTAAGACCATGTCTAGGACATGGCATGGGCACCAAG
Found at i:42064 original size:33 final size:33
Alignment explanation
Indices: 42003--42070 Score: 84
Period size: 33 Copynumber: 2.1 Consensus size: 33
41993 TAATCAATTT
* *
42003 AATATTAAATTTAATCTAATATTTATCTTGATA
1 AATATTAAATTTAATCTAATATTAATCTTAATA
* *
42036 AATATTATA-TTAATTTAATATTAAATCTTAATA
1 AATATTAAATTTAATCTAATATT-AATCTTAATA
42069 AA
1 AA
42071 ATAATAGAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
32 12 0.40
33 18 0.60
ACGTcount: A:0.47, C:0.04, G:0.01, T:0.47
Consensus pattern (33 bp):
AATATTAAATTTAATCTAATATTAATCTTAATA
Found at i:42205 original size:19 final size:19
Alignment explanation
Indices: 42155--42207 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
42145 AATAAAATAC
*
42155 TATTAAGATAGATATTAAAT
1 TATTAAAATA-ATATTAAAT
**
42175 T-TT-ATTTAATATTAAAT
1 TATTAAAATAATATTAAAT
42192 TATTAAAATAATATTA
1 TATTAAAATAATATTA
42208 TTTTTGGACT
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
17 10 0.37
18 5 0.19
19 11 0.41
20 1 0.04
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (19 bp):
TATTAAAATAATATTAAAT
Found at i:44805 original size:35 final size:35
Alignment explanation
Indices: 44766--44833 Score: 82
Period size: 35 Copynumber: 1.9 Consensus size: 35
44756 TCTGAGGAGT
* *
44766 TAGTAAACCATTTCCATGGTGTCGCTCCGTAGAGC
1 TAGTAAACCATTTCCATGATGTCGCTCCATAGAGC
* * * *
44801 TAGTAGATCATTTTCATGATGTCTCTCCATAGA
1 TAGTAAACCATTTCCATGATGTCGCTCCATAGA
44834 ACCAATATAT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
35 27 1.00
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.34
Consensus pattern (35 bp):
TAGTAAACCATTTCCATGATGTCGCTCCATAGAGC
Found at i:50442 original size:14 final size:14
Alignment explanation
Indices: 50423--50450 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
50413 GAGCATTAAT
50423 TTAAAGAGATTTTA
1 TTAAAGAGATTTTA
50437 TTAAAGAGATTTTA
1 TTAAAGAGATTTTA
50451 ATTTTCGAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.14, T:0.43
Consensus pattern (14 bp):
TTAAAGAGATTTTA
Found at i:53468 original size:6 final size:6
Alignment explanation
Indices: 53457--53485 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
53447 GTTAAACTCA
53457 CCACCG CCACCG CCACCG CCACCG CCACC
1 CCACCG CCACCG CCACCG CCACCG CCACC
53486 ACCCCAACCG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.69, G:0.14, T:0.00
Consensus pattern (6 bp):
CCACCG
Found at i:53487 original size:15 final size:15
Alignment explanation
Indices: 53455--53502 Score: 59
Period size: 15 Copynumber: 3.4 Consensus size: 15
53445 GAGTTAAACT
53455 CACCACCGCCACCG-
1 CACCACCGCCACCGC
53469 --CCACCGCCACCGC
1 CACCACCGCCACCGC
53482 CACCACC-CCAACCGC
1 CACCACCGCC-ACCGC
53497 CACCAC
1 CACCAC
53503 TGCCGCCACT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
12 12 0.40
14 2 0.07
15 16 0.53
ACGTcount: A:0.23, C:0.67, G:0.10, T:0.00
Consensus pattern (15 bp):
CACCACCGCCACCGC
Found at i:53508 original size:27 final size:27
Alignment explanation
Indices: 53455--53511 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
53445 GAGTTAAACT
*
53455 CACCACCGCCACCGCCACCGCCACCGC
1 CACCACCGCCACCGCCACCACCACCGC
**
53482 CACCACC-CCAACCGCCACCACTGCCGC
1 CACCACCGCC-ACCGCCACCACCACCGC
53509 CAC
1 CAC
53512 TGATACCGCC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 2 0.08
27 24 0.92
ACGTcount: A:0.21, C:0.65, G:0.12, T:0.02
Consensus pattern (27 bp):
CACCACCGCCACCGCCACCACCACCGC
Found at i:61524 original size:20 final size:20
Alignment explanation
Indices: 61501--61551 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
61491 TGCAAGTTAT
* *
61501 AAAAAAT-TAAATTTTATAA
1 AAAAAATATAAATGTTAGAA
61520 AAAAAATATAAATGTTAGAA
1 AAAAAATATAAATGTTAGAA
*
61540 AAAAATTATAAA
1 AAAAAATATAAA
61552 AAACGTAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 7 0.25
20 21 0.75
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (20 bp):
AAAAAATATAAATGTTAGAA
Found at i:61598 original size:12 final size:12
Alignment explanation
Indices: 61578--61613 Score: 56
Period size: 11 Copynumber: 3.1 Consensus size: 12
61568 AAAAAATTGC
*
61578 AAAATTTATAAA
1 AAAAATTATAAA
61590 AAAAATTAT-AA
1 AAAAATTATAAA
61601 AAAAATTATAAA
1 AAAAATTATAAA
61613 A
1 A
61614 TGCATCAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.50
12 11 0.50
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (12 bp):
AAAAATTATAAA
Found at i:61830 original size:10 final size:10
Alignment explanation
Indices: 61796--61880 Score: 52
Period size: 10 Copynumber: 8.4 Consensus size: 10
61786 GGTATGATAC
61796 TTTTTATAAT
1 TTTTTATAAT
*
61806 TTTTTTTACGA-
1 TTTTTATA--AT
61817 TTTTTATAATT
1 TTTTTATAA-T
*
61828 TTTTTCTAA-
1 TTTTTATAAT
61837 TTTTTA-AAT
1 TTTTTATAAT
61846 ATTTTTAT-AT
1 -TTTTTATAAT
*
61856 TTTTTACTAAA
1 TTTTTA-TAAT
* *
61867 ATTTAATAAT
1 TTTTTATAAT
61877 TTTT
1 TTTT
61881 AGATTGTAAC
Statistics
Matches: 57, Mismatches: 9, Indels: 18
0.68 0.11 0.21
Matches are distributed among these distances:
8 2 0.04
9 12 0.21
10 22 0.39
11 20 0.35
12 1 0.02
ACGTcount: A:0.29, C:0.04, G:0.01, T:0.66
Consensus pattern (10 bp):
TTTTTATAAT
Found at i:61841 original size:21 final size:19
Alignment explanation
Indices: 61796--61861 Score: 71
Period size: 21 Copynumber: 3.3 Consensus size: 19
61786 GGTATGATAC
61796 TTTTTATAATTTTTTTTACGA
1 TTTTTATAATTTTTTTTA--A
61817 TTTTTATAATTTTTTTCTAA
1 TTTTTATAATTTTTTT-TAA
* *
61837 TTTTTA-AATATTTTTATAT
1 TTTTTATAAT-TTTTTTTAA
61856 TTTTTA
1 TTTTTA
61862 CTAAAATTTA
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
19 11 0.27
20 12 0.29
21 16 0.39
22 2 0.05
ACGTcount: A:0.26, C:0.03, G:0.02, T:0.70
Consensus pattern (19 bp):
TTTTTATAATTTTTTTTAA
Found at i:61850 original size:19 final size:20
Alignment explanation
Indices: 61796--61881 Score: 70
Period size: 20 Copynumber: 4.3 Consensus size: 20
61786 GGTATGATAC
*
61796 TTTTTATAAT-TTTTTTTACGA
1 TTTTTATAATATTTTTATA--A
* *
61817 TTTTTATAATTTTTTTCTAA
1 TTTTTATAATATTTTTATAA
*
61837 TTTTTA-AATATTTTTATAT
1 TTTTTATAATATTTTTATAA
* *
61856 TTTTTACTAA-AATTTAATAA
1 TTTTTA-TAATATTTTTATAA
61876 TTTTTA
1 TTTTTA
61882 GATTGTAACA
Statistics
Matches: 55, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
19 16 0.29
20 20 0.36
21 12 0.22
22 7 0.13
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.65
Consensus pattern (20 bp):
TTTTTATAATATTTTTATAA
Found at i:61871 original size:29 final size:30
Alignment explanation
Indices: 61816--61881 Score: 82
Period size: 29 Copynumber: 2.2 Consensus size: 30
61806 TTTTTTTACG
* **
61816 ATTTTTATAATTTTTTTCTAATTTTTAA-A
1 ATTTTTATAATTTTTTACTAAAATTTAATA
61845 TATTTTTAT-ATTTTTTACTAAAATTTAATA
1 -ATTTTTATAATTTTTTACTAAAATTTAATA
61875 ATTTTTA
1 ATTTTTA
61882 GATTGTAACA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 23 0.72
30 9 0.28
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (30 bp):
ATTTTTATAATTTTTTACTAAAATTTAATA
Found at i:63903 original size:92 final size:93
Alignment explanation
Indices: 63761--63929 Score: 252
Period size: 92 Copynumber: 1.8 Consensus size: 93
63751 TTTTGTTGCG
* * * * **
63761 TAGTATGCTTTTCACCTAAAATCGTGATTGTGTTATAAATTGAAATACTAAATGTATTTACAAGT
1 TAGTATGCTTTTCACCCAAAATCATGATTGTGTTATAAATTGAAATACTAAATGCAATTACAAAC
63826 AATTACACTCAATTTTTTTTTTCTTTCA
66 AATTACACTCAATTTTTTTTTTCTTTCA
*
63854 TAGTATG-TTTTCACCCAAAATCATGATTGT-TCTATAAATTGAAATACTAAGTGCAATTACAAA
1 TAGTATGCTTTTCACCCAAAATCATGATTGTGT-TATAAATTGAAATACTAAATGCAATTACAAA
63917 CAATTACACTCAA
65 CAATTACACTCAA
63930 ATTTAATTAC
Statistics
Matches: 68, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
91 1 0.01
92 60 0.88
93 7 0.10
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.40
Consensus pattern (93 bp):
TAGTATGCTTTTCACCCAAAATCATGATTGTGTTATAAATTGAAATACTAAATGCAATTACAAAC
AATTACACTCAATTTTTTTTTTCTTTCA
Found at i:72306 original size:26 final size:27
Alignment explanation
Indices: 72253--72307 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 27
72243 AAATAAAATA
* * *
72253 AAAAACTTAAAAATATGTTTGGTAATT
1 AAAAACTTAAAAATATATATGCTAATT
*
72280 AAAAACTTAAAAATA-ATATGCTTATT
1 AAAAACTTAAAAATATATATGCTAATT
72306 AA
1 AA
72308 TTAAAAATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 9 0.38
27 15 0.62
ACGTcount: A:0.53, C:0.05, G:0.07, T:0.35
Consensus pattern (27 bp):
AAAAACTTAAAAATATATATGCTAATT
Found at i:72330 original size:15 final size:13
Alignment explanation
Indices: 72302--72327 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
72292 ATAATATGCT
72302 TATTAATTAAAAA
1 TATTAATTAAAAA
72315 TATTAATTAAAAA
1 TATTAATTAAAAA
72328 AATTTTAAAC
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:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
TATTAATTAAAAA
Found at i:72331 original size:22 final size:22
Alignment explanation
Indices: 72306--72350 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
72296 TATGCTTATT
*
72306 AATTAAAAATATTAATTAAAAA
1 AATTAAAAACATTAATTAAAAA
** *
72328 AATTTTAAACATTCATTAAAAA
1 AATTAAAAACATTAATTAAAAA
72350 A
1 A
72351 TAGTTAAATA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.33
Consensus pattern (22 bp):
AATTAAAAACATTAATTAAAAA
Found at i:101307 original size:28 final size:30
Alignment explanation
Indices: 101253--101308 Score: 89
Period size: 28 Copynumber: 1.9 Consensus size: 30
101243 TTAAATTACT
*
101253 TATTATTTAAGTAAATAGATCTTTATTATC
1 TATTATTTAAGTAAATAGATATTTATTATC
101283 TATT-TTTAAGTAAA-AGATATTTATTA
1 TATTATTTAAGTAAATAGATATTTATTA
101309 ATTAAATAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 11 0.44
29 10 0.40
30 4 0.16
ACGTcount: A:0.39, C:0.04, G:0.07, T:0.50
Consensus pattern (30 bp):
TATTATTTAAGTAAATAGATATTTATTATC
Found at i:102502 original size:47 final size:46
Alignment explanation
Indices: 102413--102503 Score: 110
Period size: 47 Copynumber: 2.0 Consensus size: 46
102403 AATAAAATGA
* * * * * * *
102413 ATAAAATTATGGAAATGTAAAAAGATATATATATGTGTGTATATAC
1 ATAAAATCATAGAAATGTAAAAAGAAAAATACATATATGTATATAC
102459 ATAAAATCATAGAAATGTAAAAAAGAAAAATACATATATGTATAT
1 ATAAAATCATAGAAATGT-AAAAAGAAAAATACATATATGTATAT
102504 CTTTTAAAAT
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
46 16 0.43
47 21 0.57
ACGTcount: A:0.54, C:0.03, G:0.12, T:0.31
Consensus pattern (46 bp):
ATAAAATCATAGAAATGTAAAAAGAAAAATACATATATGTATATAC
Found at i:104094 original size:3 final size:3
Alignment explanation
Indices: 104086--104119 Score: 59
Period size: 3 Copynumber: 11.0 Consensus size: 3
104076 ATAAAAATTG
104086 ATA ATA ATA ATA ATA ATA ATA ATA ATA GATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA
104120 CATTTAATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:111005 original size:17 final size:17
Alignment explanation
Indices: 110983--111046 Score: 67
Period size: 17 Copynumber: 3.6 Consensus size: 17
110973 AATCTTAGAG
110983 TTCTAATTGTATACAGC
1 TTCTAATTGTATACAGC
* *
111000 TTCTAATTATGTCATA-GGG
1 TTCTAA-T-TGT-ATACAGC
111019 TTCTAATTGTATACAGC
1 TTCTAATTGTATACAGC
*
111036 TTTTAATTGTA
1 TTCTAATTGTA
111047 GCCTTTGATT
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
16 3 0.08
17 20 0.53
18 2 0.05
19 10 0.26
20 3 0.08
ACGTcount: A:0.28, C:0.12, G:0.14, T:0.45
Consensus pattern (17 bp):
TTCTAATTGTATACAGC
Found at i:113089 original size:131 final size:131
Alignment explanation
Indices: 112934--113267 Score: 472
Period size: 131 Copynumber: 2.5 Consensus size: 131
112924 CATGGTTTTA
* * *
112934 ATCTGCTCCGCTACTGCTTAGGGAGATAAGATTTACAATCTTCAACCTACTCCACTGCTGCTCAA
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAATCTTCAACCTACTCCACTGCTGCTCAA
* * * *
112999 GGAGATAGGACTAGTGACTTAAATCTGCTTCCTACTATTTGGGGAAGATAAGATTCGCCGTATTC
66 GGAGATAGGACTAGTGACTTAAATCTACTTCCTACTATCTCGGGAAGATAAAATTCGCCGTATTC
113064 G
131 G
* *
113065 ATCTGCTCCACTACTACTTAGGGAGATAAGATCTGCAATCTTCAACCTACTCCACTGCTACTCAA
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAATCTTCAACCTACTCCACTGCTGCTCAA
** * * * *
113130 TAAGATAGGACTAGTGGCTTAAATCTACTTCCTACTATCTCGGGAAGATAAAATTCTCCGTCTTT
66 GGAGATAGGACTAGTGACTTAAATCTACTTCCTACTATCTCGGGAAGATAAAATTCGCCGTATTC
113195 G
131 G
* ** * *
113196 ATCTGCTTCACT-CATGCTTAAAGAGATAAGATCTGCAATCTTCAACCTATTCCACTGCTGCTTA
1 ATCTGCTCCACTAC-TGCTTAGGGAGATAAGATCTGCAATCTTCAACCTACTCCACTGCTGCTCA
113260 AGGAGATA
65 AGGAGATA
113268 AGGTTTGATA
Statistics
Matches: 178, Mismatches: 24, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
130 1 0.01
131 177 0.99
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.30
Consensus pattern (131 bp):
ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAATCTTCAACCTACTCCACTGCTGCTCAA
GGAGATAGGACTAGTGACTTAAATCTACTTCCTACTATCTCGGGAAGATAAAATTCGCCGTATTC
G
Found at i:113118 original size:44 final size:45
Alignment explanation
Indices: 112939--113126 Score: 109
Period size: 44 Copynumber: 4.3 Consensus size: 45
112929 TTTTAATCTG
* * *
112939 CTCCGCTACTGCTTAGGGAGATAAGATTTA-CAATCTTCAACCTA
1 CTCCACTACTACTTAGGGAGATAAGATCTAGCAATCTTCAACCTA
* * * * * ** * * *
112983 CTCCACTGCTGCTCAAGGAGATAGGA-CTAGTGA-CTTAAATCTG
1 CTCCACTACTACTTAGGGAGATAAGATCTAGCAATCTTCAACCTA
* * * * ** * * * *
113026 CTTC-CTACTATTTGGGGAAGATAAGAT-TCGCCGTATTCGATCTG
1 CTCCACTACTACTTAGGG-AGATAAGATCTAGCAATCTTCAACCTA
113070 CTCCACTACTACTTAGGGAGATAAGATCT-GCAATCTTCAACCTA
1 CTCCACTACTACTTAGGGAGATAAGATCTAGCAATCTTCAACCTA
*
113114 CTCCACTGCTACT
1 CTCCACTACTACT
113127 CAATAAGATA
Statistics
Matches: 102, Mismatches: 36, Indels: 12
0.68 0.24 0.08
Matches are distributed among these distances:
42 7 0.07
43 21 0.21
44 62 0.61
45 12 0.12
ACGTcount: A:0.27, C:0.26, G:0.18, T:0.29
Consensus pattern (45 bp):
CTCCACTACTACTTAGGGAGATAAGATCTAGCAATCTTCAACCTA
Found at i:122217 original size:28 final size:30
Alignment explanation
Indices: 122163--122218 Score: 89
Period size: 28 Copynumber: 1.9 Consensus size: 30
122153 TTAAATTACT
*
122163 TATTATTTAAGTAAATAGATCTTTATTATC
1 TATTATTTAAGTAAATAGATATTTATTATC
122193 TATT-TTTAAGTAAA-AGATATTTATTA
1 TATTATTTAAGTAAATAGATATTTATTA
122219 ATTAAATAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 11 0.44
29 10 0.40
30 4 0.16
ACGTcount: A:0.39, C:0.04, G:0.07, T:0.50
Consensus pattern (30 bp):
TATTATTTAAGTAAATAGATATTTATTATC
Found at i:123412 original size:47 final size:46
Alignment explanation
Indices: 123323--123413 Score: 110
Period size: 47 Copynumber: 2.0 Consensus size: 46
123313 AATAAAATGA
* * * * * * *
123323 ATAAAATTATGGAAATGTAAAAAGATATATATATGTGTGTATATAC
1 ATAAAATCATAGAAATGTAAAAAGAAAAATACATATATGTATATAC
123369 ATAAAATCATAGAAATGTAAAAAAGAAAAATACATATATGTATAT
1 ATAAAATCATAGAAATGT-AAAAAGAAAAATACATATATGTATAT
123414 CTTTTAAAAT
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
46 16 0.43
47 21 0.57
ACGTcount: A:0.54, C:0.03, G:0.12, T:0.31
Consensus pattern (46 bp):
ATAAAATCATAGAAATGTAAAAAGAAAAATACATATATGTATATAC
Found at i:125004 original size:3 final size:3
Alignment explanation
Indices: 124996--125029 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
124986 ATAAAAATTG
124996 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
125030 ATGATAATAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:127257 original size:44 final size:45
Alignment explanation
Indices: 127174--127264 Score: 116
Period size: 44 Copynumber: 2.0 Consensus size: 45
127164 ATAACATTAT
* *
127174 TAATTTATATGTTTTTTTGTAAATTTTAATTTTATAATTTTT-TA
1 TAATTTATATGTTTTTTTCTAAATTATAATTTTATAATTTTTCTA
*
127218 TAATTTATATG-TTTTTTCTATATTAT-ATATTTATGAATTTTTCTA
1 TAATTTATATGTTTTTTTCTAAATTATAAT-TTTAT-AATTTTTCTA
127263 TA
1 TA
127265 CTTATTTCCA
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
42 2 0.05
43 17 0.41
44 18 0.44
45 4 0.10
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.64
Consensus pattern (45 bp):
TAATTTATATGTTTTTTTCTAAATTATAATTTTATAATTTTTCTA
Found at i:127978 original size:16 final size:17
Alignment explanation
Indices: 127957--127989 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
127947 TATCTTTTCG
127957 AATTTT-TATAGGTTTA
1 AATTTTATATAGGTTTA
*
127973 AATTTTATATAGTTTTA
1 AATTTTATATAGGTTTA
127990 TACAATTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.33, C:0.00, G:0.09, T:0.58
Consensus pattern (17 bp):
AATTTTATATAGGTTTA
Found at i:129276 original size:3 final size:3
Alignment explanation
Indices: 129268--129299 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
129258 AAATTAGTTA
129268 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
129300 AACGATAGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:129640 original size:31 final size:32
Alignment explanation
Indices: 129602--129664 Score: 119
Period size: 31 Copynumber: 2.0 Consensus size: 32
129592 AGACAAATTA
129602 CAAGAGTAATTGAATCCTAAT-AAAACTCTTT
1 CAAGAGTAATTGAATCCTAATAAAAACTCTTT
129633 CAAGAGTAATTGAATCCTAATAAAAACTCTTT
1 CAAGAGTAATTGAATCCTAATAAAAACTCTTT
129665 AAAATTATCT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 21 0.68
32 10 0.32
ACGTcount: A:0.43, C:0.16, G:0.10, T:0.32
Consensus pattern (32 bp):
CAAGAGTAATTGAATCCTAATAAAAACTCTTT
Found at i:140116 original size:58 final size:59
Alignment explanation
Indices: 140015--140130 Score: 180
Period size: 58 Copynumber: 2.0 Consensus size: 59
140005 GTTAAGTTCA
* * **
140015 GGTACCAAATTGGACCAAAAAAATATTAAGTATCAACTTAAGAAAATGTGTCAAGTTTG
1 GGTACCAAATTAGACCAAAAAAAGATTAAGTATCAACTTAAGAAAAAATGTCAAGTTTG
*
140074 GGTACCAAATTAGACC-AAAAAGGATTAAGTATCAACTTAAGAAAAAATGTCAAGTTT
1 GGTACCAAATTAGACCAAAAAAAGATTAAGTATCAACTTAAGAAAAAATGTCAAGTTT
140131 AGAGGCCAAG
Statistics
Matches: 52, Mismatches: 5, Indels: 1
0.90 0.09 0.02
Matches are distributed among these distances:
58 37 0.71
59 15 0.29
ACGTcount: A:0.46, C:0.12, G:0.16, T:0.26
Consensus pattern (59 bp):
GGTACCAAATTAGACCAAAAAAAGATTAAGTATCAACTTAAGAAAAAATGTCAAGTTTG
Found at i:140152 original size:58 final size:55
Alignment explanation
Indices: 140031--140152 Score: 138
Period size: 58 Copynumber: 2.1 Consensus size: 55
140021 AAATTGGACC
* **
140031 AAAAAAATATTAAGTATCAACTTAAGAAAATGTGTCAAGTTTGGGTACCAAATTAG
1 AAAAAAAGATTAAGTATCAACTTAAGAAAAAATGTCAAGTTTGGG-ACCAAATTAG
* *
140087 ACCAAAAAGGATTAAGTATCAACTTAAGAAAAAATGTCAAGTTTAGAGG-CCAAGTTAGG
1 A--AAAAAAGATTAAGTATCAACTTAAGAAAAAATGTCAAGTTT-G-GGACCAAATTA-G
140146 AAAAAAA
1 AAAAAAA
140153 ATTTAAATTT
Statistics
Matches: 55, Mismatches: 6, Indels: 9
0.79 0.09 0.13
Matches are distributed among these distances:
56 1 0.02
57 5 0.09
58 44 0.80
59 3 0.05
60 2 0.04
ACGTcount: A:0.49, C:0.10, G:0.17, T:0.24
Consensus pattern (55 bp):
AAAAAAAGATTAAGTATCAACTTAAGAAAAAATGTCAAGTTTGGGACCAAATTAG
Found at i:145620 original size:20 final size:19
Alignment explanation
Indices: 145589--145629 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 19
145579 AAATGAAAAA
145589 TTAGAATTTTTATAAA-TAT
1 TTAGAATTTTTA-AAATTAT
145608 TTAGAATTTTTTAAAATTAT
1 TTAGAA-TTTTTAAAATTAT
145628 TT
1 TT
145630 TTGTATTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (19 bp):
TTAGAATTTTTAAAATTAT
Found at i:145624 original size:19 final size:20
Alignment explanation
Indices: 145589--145629 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
145579 AAATGAAAAA
145589 TTAGAATTTTTATAAA-TAT
1 TTAGAATTTTTATAAATTAT
145608 TTAGAATTTTT-TAAAATTAT
1 TTAGAATTTTTAT-AAATTAT
145628 TT
1 TT
145630 TTGTATTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 1 0.05
19 14 0.70
20 5 0.25
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (20 bp):
TTAGAATTTTTATAAATTAT
Found at i:153428 original size:18 final size:19
Alignment explanation
Indices: 153405--153453 Score: 68
Period size: 18 Copynumber: 2.7 Consensus size: 19
153395 TTTCAATTAA
153405 ATAAATTATTAAAAA-ATT
1 ATAAATTATTAAAAATATT
153423 ATAAA-TATTAAAAATATT
1 ATAAATTATTAAAAATATT
*
153441 AAAAATTA-TAAAA
1 ATAAATTATTAAAA
153454 TTTAATTTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
17 9 0.32
18 17 0.61
19 2 0.07
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
ATAAATTATTAAAAATATT
Found at i:153437 original size:9 final size:9
Alignment explanation
Indices: 153411--153446 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
153401 TTAAATAAAT
153411 TATTAAAAA
1 TATTAAAAA
*
153420 -ATTATAAA
1 TATTAAAAA
153428 TATTAAAAA
1 TATTAAAAA
153437 TATTAAAAA
1 TATTAAAAA
153446 T
1 T
153447 TATAAAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
8 7 0.29
9 17 0.71
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (9 bp):
TATTAAAAA
Found at i:153458 original size:16 final size:15
Alignment explanation
Indices: 153416--153458 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
153406 TAAATTATTA
*
153416 AAAAATTATAAATATT
1 AAAAATT-TAAAAATT
153432 AAAAATATTAAAAATT
1 AAAAAT-TTAAAAATT
153448 ATAAAATTTAA
1 A-AAAATTTAA
153459 TTTTCTATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 18 0.75
17 6 0.25
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
AAAAATTTAAAAATT
Found at i:161761 original size:24 final size:23
Alignment explanation
Indices: 161717--161761 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
161707 GTTTTATGGC
*
161717 TTTTAGGGTTTAGGGTGCAGGCT
1 TTTTAGGGTTTAGGGTCCAGGCT
161740 TTTTAGGAG-TTAGGGGTCCAGG
1 TTTTAGG-GTTTA-GGGTCCAGG
161762 AAAATTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.16, C:0.09, G:0.40, T:0.36
Consensus pattern (23 bp):
TTTTAGGGTTTAGGGTCCAGGCT
Found at i:161923 original size:125 final size:125
Alignment explanation
Indices: 161793--162058 Score: 324
Period size: 125 Copynumber: 2.1 Consensus size: 125
161783 GTTTCTAGTT
** * * * * * *
161793 AAATAGTGGGAAATCGCTT-CTACTAGGATGCTATTTAAGAATAAATTGTGAAATAGTGGCCTCA
1 AAATAGTGTAAAATCGCTTGATACCAGGATGCTATATAAGAAGAAATTGTGAAATAGCGCCCTCA
* *
161857 TGGACGCGATTTCGCTACAG-TGGTCATGT-GAGAAATAAATTTTTTTTGACGTTTTCTGAGG
66 TGGACGCGATTTCGCTACAGTTGGTCATGTAG-GAAAT-AATTTTTTTTAACG-TTTCTGAGC
* * * * **
161918 AAATAGTATAAAATCG-TTGATACCAGGCTGCTATATGAGAAGAAATTGTGAAATCGCGCCCTTG
1 AAATAGTGTAAAATCGCTTGATACCAGGATGCTATATAAGAAGAAATTGTGAAATAGCGCCCTCA
161982 TGGACGCGATTTCGCTACAGTTGGTCATGTAGGAAATAATTTTTTTTAACGTTTCTGAGC
66 TGGACGCGATTTCGCTACAGTTGGTCATGTAGGAAATAATTTTTTTTAACGTTTCTGAGC
*
162042 AAATAGTGTCAAATCGC
1 AAATAGTGTAAAATCGC
162059 GCCCTCGTGG
Statistics
Matches: 119, Mismatches: 18, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
124 24 0.20
125 80 0.67
126 14 0.12
127 1 0.01
ACGTcount: A:0.30, C:0.14, G:0.23, T:0.32
Consensus pattern (125 bp):
AAATAGTGTAAAATCGCTTGATACCAGGATGCTATATAAGAAGAAATTGTGAAATAGCGCCCTCA
TGGACGCGATTTCGCTACAGTTGGTCATGTAGGAAATAATTTTTTTTAACGTTTCTGAGC
Found at i:162110 original size:84 final size:85
Alignment explanation
Indices: 161968--162171 Score: 365
Period size: 85 Copynumber: 2.4 Consensus size: 85
161958 AGAAATTGTG
*
161968 AAATCGCGCCCTTGTGGACGCGATTTCGCTACAGTTGGTCATGTAGGAAAT-AATTTTTTTTAAC
1 AAATCGCGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAGGAAATAAATTTTTTTTAAC
*
162032 GTTTCTGAGCAAATAGTGTC
66 GGTTCTGAGCAAATAGTGTC
* *
162052 AAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTTGGTCATGTAGGAAATAAATTTTTTTTGAC
1 AAATCGCGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAGGAAATAAATTTTTTTTAAC
162117 GGTTCTGAGCAAATAGTGTC
66 GGTTCTGAGCAAATAGTGTC
162137 AAATCGCGCCCTCGTGGACGCGATTTCGCTACAGT
1 AAATCGCGCCCTCGTGGACGCGATTTCGCTACAGT
162172 AGCAAGTTTG
Statistics
Matches: 114, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
84 49 0.43
85 65 0.57
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (85 bp):
AAATCGCGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAGGAAATAAATTTTTTTTAAC
GGTTCTGAGCAAATAGTGTC
Found at i:168140 original size:82 final size:85
Alignment explanation
Indices: 168035--168191 Score: 212
Period size: 82 Copynumber: 1.9 Consensus size: 85
168025 AGACTTGATG
* * *
168035 CGATCTACTCTGCTGTAACCTCAGAGAGATAAGATC-CT-TT-AATCCGCTCCACTGTAACTTCG
1 CGATCTACTCCGCTGTAACCTCAGAGAGATAAGATCTCTGTTCAATCCGCTCCACTGTAACCTCA
168097 GGGAGATAGGATAGTGTCTT
66 GGGAGATAGGATAGTGTCTT
* * * *
168117 CGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCT
1 CGATCTACTCCGCTGTAACCTCAGAGAGATAAGATCTCT-G-TTCAATCCGCTCCACTGTAACCT
168182 CAGGGAGATA
64 CAGGGAGATA
168192 AGATCTGAAA
Statistics
Matches: 63, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
82 32 0.51
83 2 0.03
86 2 0.03
87 27 0.43
ACGTcount: A:0.25, C:0.25, G:0.22, T:0.28
Consensus pattern (85 bp):
CGATCTACTCCGCTGTAACCTCAGAGAGATAAGATCTCTGTTCAATCCGCTCCACTGTAACCTCA
GGGAGATAGGATAGTGTCTT
Found at i:168177 original size:44 final size:43
Alignment explanation
Indices: 168047--168415 Score: 202
Period size: 44 Copynumber: 8.5 Consensus size: 43
168037 ATCTACTCTG
* * *
168047 CTGTAACCTCAGAGAGATAAGATC-CT--TT-AATCCGCTCCA
1 CTGTAATCTCAGGGAGATAAGATCTCTGCTTCAATCTGCTCCA
* * ** * *
168086 CTGTAA-CTTCGGGGAGATAGGAT-AGTGTCTTCGATCTGCTCCG
1 CTGTAATC-TCAGGGAGATAAGATCTCTG-CTTCAATCTGCTCCA
168129 CTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCA
1 CTGTAATCTCAGGGAGATAAGATCTCT-GCTTCAATCTGCTCCA
* * * *** *
168173 CTGTAACCTCAGGGAGATAAGATCTGAAATTCTTTGGTCTGTTCCA
1 CTGTAATCTCAGGGAGATAAGATCT---CTGCTTCAATCTGCTCCA
* * * **
168219 CTGTAATCTCAGGGAGATAAGA-C-CTGATGT-GATCTACTCTG
1 CTGTAATCTCAGGGAGATAAGATCTCTGCT-TCAATCTGCTCCA
* * ** * *
168260 CTGTAA-CTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCA
1 CTGTAATC-TCAGGGAGATAAGAT-CTCTGCTTCAATCTGCTCCA
* * *
168304 CTGTAATCTCAGGGAGATAGGAT-TACTAGCTTCAATCTACTCCG
1 CTGTAATCTCAGGGAGATAAGATCT-CT-GCTTCAATCTGCTCCA
* * * *** *
168348 TTGTAATCTCAGGGAGATAAGATCTGAAATTCTTTGGTCTGTTCCA
1 CTGTAATCTCAGGGAGATAAGATCT---CTGCTTCAATCTGCTCCA
168394 CTGTAATCTCAGGGAGATAAGA
1 CTGTAATCTCAGGGAGATAAGA
168416 CCTGTATAAT
Statistics
Matches: 248, Mismatches: 58, Indels: 41
0.71 0.17 0.12
Matches are distributed among these distances:
38 1 0.00
39 19 0.08
40 1 0.00
41 27 0.11
42 4 0.02
43 30 0.12
44 97 0.39
45 4 0.02
46 62 0.25
47 3 0.01
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (43 bp):
CTGTAATCTCAGGGAGATAAGATCTCTGCTTCAATCTGCTCCA
Found at i:168233 original size:46 final size:45
Alignment explanation
Indices: 168113--168415 Score: 214
Period size: 44 Copynumber: 6.8 Consensus size: 45
168103 TAGGATAGTG
* * *
168113 TCTTCGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCT--CT
1 TCTTTGATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTGAAT
* ** *
168156 GGCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAAT
1 -TCTTTGATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTG-AAT
* * *
168203 TCTTTGGTCTGTTCCACTGTAATCTCAGGGAGATAAGACCTG-A-
1 TCTTTGATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTGAAT
* * ** * **
168246 --TGTGATCTACTCTGCTGTAA-CTTCAGAGAGATAAGATCCTTTA-
1 TCTTTGATCTGCTCCACTGTAATC-TCAGGGAGATAAGAT-CTGAAT
* * * *
168289 T-TTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGAT-T-ACT
1 TCTTTGATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTGAAT
* ** * **
168331 AGCTTCAATCTACTCCGTTGTAATCTCAGGGAGATAAGATCTGAAAT
1 -TCTTTGATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTG-AAT
* *
168378 TCTTTGGTCTGTTCCACTGTAATCTCAGGGAGATAAGA
1 TCTTTGATCTGCTCCACTGTAATCTCAGGGAGATAAGA
168416 CCTGTATAAT
Statistics
Matches: 198, Mismatches: 47, Indels: 26
0.73 0.17 0.10
Matches are distributed among these distances:
40 1 0.01
41 27 0.14
42 3 0.02
43 1 0.01
44 96 0.48
45 2 0.01
46 65 0.33
47 3 0.02
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (45 bp):
TCTTTGATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTGAAT
Found at i:180835 original size:20 final size:20
Alignment explanation
Indices: 180810--180856 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
180800 AATAAGAAAG
180810 ATATAAATAATA-TCAATAT-A
1 ATATAAAT-ATAGT-AATATCA
180830 ATATAAATATAGTAATATCA
1 ATATAAATATAGTAATATCA
180850 ATATAAA
1 ATATAAA
180857 AACAAATATC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 8 0.32
20 17 0.68
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.34
Consensus pattern (20 bp):
ATATAAATATAGTAATATCA
Found at i:186118 original size:10 final size:10
Alignment explanation
Indices: 186088--186129 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
186078 ATCACAAGTC
186088 TTGTGATATA
1 TTGTGATATA
*
186098 GTGTGATATA
1 TTGTGATATA
186108 TTGTGATATA
1 TTGTGATATA
*
186118 TATATGATATA
1 T-TGTGATATA
186129 T
1 T
186130 GTAGAAATCT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
10 19 0.68
11 9 0.32
ACGTcount: A:0.33, C:0.00, G:0.19, T:0.48
Consensus pattern (10 bp):
TTGTGATATA
Found at i:193834 original size:17 final size:17
Alignment explanation
Indices: 193794--193842 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 17
193784 TTTAGATAGT
*
193794 AAAAGAAAAAGAAGAGG
1 AAAAGAAAAAGAAGAAG
** *
193811 AGGAGAAGAAGAAGAAG
1 AAAAGAAAAAGAAGAAG
*
193828 AAAAGAAAAATAAGA
1 AAAAGAAAAAGAAGA
193843 GAAGAAATAG
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.69, C:0.00, G:0.29, T:0.02
Consensus pattern (17 bp):
AAAAGAAAAAGAAGAAG
Found at i:194928 original size:21 final size:21
Alignment explanation
Indices: 194904--194974 Score: 97
Period size: 21 Copynumber: 3.4 Consensus size: 21
194894 TGTTGATGAG
*
194904 TTGGGGCAGCTTTTTGCTGAA
1 TTGGGGCAGCTTATTGCTGAA
* * *
194925 TTGGAGTAGCTTATTGCTGAG
1 TTGGGGCAGCTTATTGCTGAA
*
194946 TTGGGGCAGCTTCTTGCTGAA
1 TTGGGGCAGCTTATTGCTGAA
194967 TTGGGGCA
1 TTGGGGCA
194975 ACCTTGATTA
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.15, C:0.14, G:0.35, T:0.35
Consensus pattern (21 bp):
TTGGGGCAGCTTATTGCTGAA
Found at i:197475 original size:26 final size:27
Alignment explanation
Indices: 197440--197554 Score: 90
Period size: 27 Copynumber: 4.3 Consensus size: 27
197430 CAAAAGGGCA
* **
197440 TTCTCTTCATAAATCGCC-CAAAGGCT
1 TTCTTTTCATAAATAACCACAAAGGCT
* * * *
197466 TTCTTTTCATAGATAGCTATAAAGGCT
1 TTCTTTTCATAAATAACCACAAAGGCT
* *
197493 GTCTTTTCA-AAGATAACCATAAAGGCT
1 TTCTTTTCATAA-ATAACCACAAAGGCT
* * *
197520 TCCTTTTCATAGATCACCACAAAGGCT
1 TTCTTTTCATAAATAACCACAAAGGCT
*
197547 TCCTTTTC
1 TTCTTTTC
197555 TAGTGTGTTT
Statistics
Matches: 72, Mismatches: 14, Indels: 5
0.79 0.15 0.05
Matches are distributed among these distances:
26 15 0.21
27 56 0.78
28 1 0.01
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.35
Consensus pattern (27 bp):
TTCTTTTCATAAATAACCACAAAGGCT
Found at i:197489 original size:27 final size:27
Alignment explanation
Indices: 197459--197554 Score: 120
Period size: 27 Copynumber: 3.6 Consensus size: 27
197449 TAAATCGCCC
* *
197459 AAAGGCTTTCTTTTCATAGATAGCTAT
1 AAAGGCTTTCTTTTCATAGATAACCAT
* *
197486 AAAGGCTGTCTTTTCAAAGATAACCAT
1 AAAGGCTTTCTTTTCATAGATAACCAT
* * *
197513 AAAGGCTTCCTTTTCATAGATCACCAC
1 AAAGGCTTTCTTTTCATAGATAACCAT
*
197540 AAAGGCTTCCTTTTC
1 AAAGGCTTTCTTTTC
197555 TAGTGTGTTT
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 60 1.00
ACGTcount: A:0.30, C:0.22, G:0.14, T:0.34
Consensus pattern (27 bp):
AAAGGCTTTCTTTTCATAGATAACCAT
Found at i:200976 original size:11 final size:11
Alignment explanation
Indices: 200937--200974 Score: 67
Period size: 11 Copynumber: 3.5 Consensus size: 11
200927 ATAATACGTG
200937 AAACACATGTT
1 AAACACATGTT
200948 AAACACATGTT
1 AAACACATGTT
*
200959 AAACATATGTT
1 AAACACATGTT
200970 AAACA
1 AAACA
200975 TACCTTACAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.50, C:0.16, G:0.08, T:0.26
Consensus pattern (11 bp):
AAACACATGTT
Found at i:201194 original size:45 final size:45
Alignment explanation
Indices: 201126--201255 Score: 151
Period size: 45 Copynumber: 2.9 Consensus size: 45
201116 GGAAGGAAGA
* *
201126 ATTAGTGGCTTCGTCCACGACCTACATGATAGCTTGTCTATGAAT
1 ATTAGTGGCTTCATCCACAACCTACATGATAGCTTGTCTATGAAT
* *
201171 ATTAGTGGCTTCATCCACAACCTACATAGCA-A-CTTGTTTGTGAAT
1 ATTAGTGGCTTCATCCACAACCTACAT-G-ATAGCTTGTCTATGAAT
* *
201216 ATTAGTGG-TTTATCCACAACCTACAT-AGTAGCTTATCTAT
1 ATTAGTGGCTTCATCCACAACCTACATGA-TAGCTTGTCTAT
201256 AAATTTGGAG
Statistics
Matches: 72, Mismatches: 8, Indels: 11
0.79 0.09 0.12
Matches are distributed among these distances:
41 1 0.01
43 1 0.01
44 23 0.32
45 44 0.61
46 2 0.03
47 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.35
Consensus pattern (45 bp):
ATTAGTGGCTTCATCCACAACCTACATGATAGCTTGTCTATGAAT
Found at i:202186 original size:92 final size:92
Alignment explanation
Indices: 202029--202216 Score: 331
Period size: 92 Copynumber: 2.0 Consensus size: 92
202019 CAAAATTACT
* * *
202029 AATATTTACAAATGAGATTTCTTAATACATTTAATTTTGAAGTTAATGTGTTTTTCCTGAATAAC
1 AATATTTACAAATGAAATTTCTTAATACATTTAATTCTAAAGTTAATGTGTTTTTCCTGAATAAC
*
202094 GACGAATAACCAAGGTATTTAGTTTTG
66 GACGAATAACCAAGGTATTTAATTTTG
202121 AATATTTACAAATGAAATTTCTTAATACATTTAATTCTAAAGTTAATGTGTTTTTCCTGAATAAC
1 AATATTTACAAATGAAATTTCTTAATACATTTAATTCTAAAGTTAATGTGTTTTTCCTGAATAAC
*
202186 GATGAATAACCAAGGTATTTAATTTTG
66 GACGAATAACCAAGGTATTTAATTTTG
202213 AATA
1 AATA
202217 AATAAACGAA
Statistics
Matches: 91, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
92 91 1.00
ACGTcount: A:0.37, C:0.10, G:0.12, T:0.41
Consensus pattern (92 bp):
AATATTTACAAATGAAATTTCTTAATACATTTAATTCTAAAGTTAATGTGTTTTTCCTGAATAAC
GACGAATAACCAAGGTATTTAATTTTG
Found at i:211878 original size:39 final size:41
Alignment explanation
Indices: 211818--211905 Score: 101
Period size: 41 Copynumber: 2.2 Consensus size: 41
211808 ATAGGAGCGA
*
211818 AAATGGG-GAGAAAGAATGAGGAAAG-AGAAAAAAAAAAAG
1 AAATGGGAGAGAAAGAAGGAGGAAAGAAGAAAAAAAAAAAG
* ***
211857 AAATGGGAGAGAAA-AGGGAGGAAAGATAGAGGGAAAAAAAG
1 AAATGGGAGAGAAAGAAGGAGGAAAGA-AGAAAAAAAAAAAG
211898 AAATGGGA
1 AAATGGGA
211906 AGGAAAAAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
39 16 0.39
40 6 0.15
41 19 0.46
ACGTcount: A:0.59, C:0.00, G:0.35, T:0.06
Consensus pattern (41 bp):
AAATGGGAGAGAAAGAAGGAGGAAAGAAGAAAAAAAAAAAG
Found at i:212511 original size:30 final size:30
Alignment explanation
Indices: 212465--212525 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 30
212455 TCAGAATTAT
*
212465 TATATAAAATTTTAAATTATGTATAT-ATAA
1 TATATAAAATTTTAAA-TATGTAAATAATAA
212495 TATA-AAAATATTTAAATATGTAAATAATAA
1 TATATAAAAT-TTTAAATATGTAAATAATAA
212525 T
1 T
212526 TATTTAATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
29 13 0.46
30 15 0.54
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (30 bp):
TATATAAAATTTTAAATATGTAAATAATAA
Found at i:212513 original size:23 final size:22
Alignment explanation
Indices: 212487--212536 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 22
212477 TAAATTATGT
212487 ATATATAATATAA-AAATATTTAA
1 ATATATAA-ATAATAAATATTT-A
* *
212510 ATATGTAAATAATAATTATTTA
1 ATATATAAATAATAAATATTTA
212532 ATATA
1 ATATA
212537 ATTAAAATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
22 9 0.39
23 14 0.61
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (22 bp):
ATATATAAATAATAAATATTTA
Found at i:215993 original size:27 final size:32
Alignment explanation
Indices: 215963--216047 Score: 99
Period size: 33 Copynumber: 2.8 Consensus size: 32
215953 CTTAAAGATA
*
215963 TTTAATTTT-TTTTGAATTT-TA-AC-TA-TT
1 TTTAATTTTATTTTCAATTTATATACATATTT
*
215990 TTTATTTTTATTTTCAATTTATATACATTATTT
1 TTTAATTTTATTTTCAATTTATATACA-TATTT
*
216023 TTTAATTTTATTTTCAATTCATATA
1 TTTAATTTTATTTTCAATTTATATA
216048 TATTTAAGTT
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
27 8 0.17
28 9 0.19
29 2 0.04
30 2 0.04
32 2 0.04
33 25 0.52
ACGTcount: A:0.28, C:0.06, G:0.01, T:0.65
Consensus pattern (32 bp):
TTTAATTTTATTTTCAATTTATATACATATTT
Found at i:216568 original size:23 final size:23
Alignment explanation
Indices: 216542--216621 Score: 99
Period size: 23 Copynumber: 3.4 Consensus size: 23
216532 AATGTTCACT
*
216542 AACATGTTCATTTAAC-TTAATCG
1 AACATGTTCA-TGAACATTAATCG
* *
216565 AACATGTTCACGAACATTAAACG
1 AACATGTTCATGAACATTAATCG
*
216588 AACATGTTCATGAACATATAATTG
1 AACATGTTCATGAACAT-TAATCG
216612 AACATGTTCA
1 AACATGTTCA
216622 CAAACAATGA
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
22 3 0.06
23 32 0.65
24 14 0.29
ACGTcount: A:0.40, C:0.17, G:0.11, T:0.31
Consensus pattern (23 bp):
AACATGTTCATGAACATTAATCG
Found at i:216580 original size:12 final size:12
Alignment explanation
Indices: 216563--216604 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
216553 TTAACTTAAT
216563 CGAACATGTTCA
1 CGAACATGTTCA
**
216575 CGAACAT-TAAA
1 CGAACATGTTCA
216586 CGAACATGTTCA
1 CGAACATGTTCA
*
216598 TGAACAT
1 CGAACAT
216605 ATAATTGAAC
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
11 9 0.38
12 15 0.62
ACGTcount: A:0.40, C:0.21, G:0.14, T:0.24
Consensus pattern (12 bp):
CGAACATGTTCA
Found at i:220859 original size:21 final size:22
Alignment explanation
Indices: 220825--220880 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 22
220815 TTAAAAATAA
* *
220825 TACAACTATATTAATATTTA-AT
1 TACAAATAT-TTAATAATTATAT
220847 TACAAATATTTAATAATTATAT
1 TACAAATATTTAATAATTATAT
*
220869 T-TAAATATTTAA
1 TACAAATATTTAA
220881 AACATAATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
21 19 0.63
22 11 0.37
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.46
Consensus pattern (22 bp):
TACAAATATTTAATAATTATAT
Found at i:222367 original size:13 final size:13
Alignment explanation
Indices: 222351--222402 Score: 54
Period size: 12 Copynumber: 4.1 Consensus size: 13
222341 TTTTATAAAG
222351 TGTTTTTGAAAAA
1 TGTTTTTGAAAAA
*
222364 TG-TTATGAAAAA
1 TGTTTTTGAAAAA
*
222376 GTGTTTTTGAGAAA
1 -TGTTTTTGAAAAA
*
222390 TATTTTT-AAAAA
1 TGTTTTTGAAAAA
222402 T
1 T
222403 TTTGATTTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
12 14 0.44
13 10 0.31
14 8 0.25
ACGTcount: A:0.40, C:0.00, G:0.15, T:0.44
Consensus pattern (13 bp):
TGTTTTTGAAAAA
Found at i:222400 original size:26 final size:26
Alignment explanation
Indices: 222341--222401 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
222331 TTAACCATGC
* *
222341 TTTTATAAAGTGTTTTTGAAAAATGT
1 TTTTAAAAAGTGTTTTTGAAAAATAT
* * *
222367 TATGAAAAAGTGTTTTTGAGAAATAT
1 TTTTAAAAAGTGTTTTTGAAAAATAT
222393 TTTTAAAAA
1 TTTTAAAAA
222402 TTTTGATTTA
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.41, C:0.00, G:0.15, T:0.44
Consensus pattern (26 bp):
TTTTAAAAAGTGTTTTTGAAAAATAT
Found at i:230838 original size:3 final size:3
Alignment explanation
Indices: 230830--230864 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
230820 TATTTATTAA
230830 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
230865 CAAATAAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:231200 original size:17 final size:15
Alignment explanation
Indices: 231180--231213 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 15
231170 TGGGGAGAAA
231180 GAAAGAAAGGAAAAAGG
1 GAAAGAAA-G-AAAAGG
231197 GAAAGAAAGAAAAGG
1 GAAAGAAAGAAAAGG
231212 GA
1 GA
231214 GAAATAGTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.47
16 1 0.06
17 8 0.47
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (15 bp):
GAAAGAAAGAAAAGG
Found at i:231217 original size:17 final size:18
Alignment explanation
Indices: 231179--231217 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
231169 CTGGGGAGAA
231179 AGAAAGAAAGGAAAAAGG
1 AGAAAGAAAGGAAAAAGG
*
231197 -GAAAGAAA-GAAAAGGG
1 AGAAAGAAAGGAAAAAGG
231213 AGAAA
1 AGAAA
231218 TAGTGATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (18 bp):
AGAAAGAAAGGAAAAAGG
Found at i:231629 original size:11 final size:11
Alignment explanation
Indices: 231607--231649 Score: 50
Period size: 11 Copynumber: 3.6 Consensus size: 11
231597 AAAATTGAAG
231607 TTAAAGTAGAAA
1 TTAAA-TAGAAA
*
231619 TTGAATAGAAA
1 TTAAATAGAAA
231630 TTAAATAAGAAA
1 TTAAAT-AGAAA
231642 TTTAAATA
1 -TTAAATA
231650 TTAAATGTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 11 0.41
12 10 0.37
13 6 0.22
ACGTcount: A:0.58, C:0.00, G:0.12, T:0.30
Consensus pattern (11 bp):
TTAAATAGAAA
Found at i:232587 original size:18 final size:18
Alignment explanation
Indices: 232566--232630 Score: 69
Period size: 18 Copynumber: 3.6 Consensus size: 18
232556 AACGACTAAC
* *
232566 TGTTATTGAATAATTGAT
1 TGTTACTGAATAACTGAT
232584 TGTTACTGAATAACTGAT
1 TGTTACTGAATAACTGAT
* *
232602 TGCTACTGAGA-AAATGAT
1 TGTTACTGA-ATAACTGAT
*
232620 TATTACTGAAT
1 TGTTACTGAAT
232631 GATATTGATA
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
17 1 0.03
18 37 0.95
19 1 0.03
ACGTcount: A:0.35, C:0.08, G:0.17, T:0.40
Consensus pattern (18 bp):
TGTTACTGAATAACTGAT
Found at i:233138 original size:17 final size:17
Alignment explanation
Indices: 233116--233153 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
233106 TGGTAATGGC
233116 ATGTACCTAAAATGTCT
1 ATGTACCTAAAATGTCT
233133 ATGTACCTAAAATGTCT
1 ATGTACCTAAAATGTCT
233150 ATGT
1 ATGT
233154 GTGTCATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.37
Consensus pattern (17 bp):
ATGTACCTAAAATGTCT
Found at i:233905 original size:13 final size:14
Alignment explanation
Indices: 233876--233908 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
233866 TTTTTTACGC
*
233876 AAATAATATATAAA
1 AAATAATATACAAA
233890 AAATAAT-TACAAA
1 AAATAATATACAAA
233903 AAATAA
1 AAATAA
233909 GTAAACTGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.24
Consensus pattern (14 bp):
AAATAATATACAAA
Found at i:235783 original size:16 final size:15
Alignment explanation
Indices: 235729--235795 Score: 50
Period size: 16 Copynumber: 4.4 Consensus size: 15
235719 ACTGTTTATT
235729 TTATTTATTTTTGTAA
1 TTATTTATTTTT-TAA
*
235745 TTA---ATTTTTTAC
1 TTATTTATTTTTTAA
* *
235757 TTGTCTCATTTTTGTAA
1 TTAT-TTATTTTT-TAA
235774 TTATTTATTTTTTATA
1 TTATTTATTTTTTA-A
235790 TTATTT
1 TTATTT
235796 GTGTAAAAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
12 4 0.10
13 6 0.15
15 2 0.05
16 23 0.57
17 5 0.12
ACGTcount: A:0.22, C:0.04, G:0.04, T:0.69
Consensus pattern (15 bp):
TTATTTATTTTTTAA
Found at i:243092 original size:6 final size:6
Alignment explanation
Indices: 243081--243126 Score: 56
Period size: 6 Copynumber: 7.2 Consensus size: 6
243071 CTTTTATAGA
*
243081 TCATTT TCATTT TCATTCT CTCTTTT TCATTTT TCATTT TCATTT T
1 TCATTT TCATTT TCATT-T -TCATTT TCA-TTT TCATTT TCATTT T
243127 TCCACCCTAG
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
6 23 0.66
7 8 0.23
8 4 0.11
ACGTcount: A:0.13, C:0.20, G:0.00, T:0.67
Consensus pattern (6 bp):
TCATTT
Found at i:244769 original size:5 final size:5
Alignment explanation
Indices: 244761--244790 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
244751 ATATATATAT
244761 AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA
1 AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA
244791 TGAACATATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
AAAGA
Found at i:245274 original size:34 final size:34
Alignment explanation
Indices: 245236--245306 Score: 97
Period size: 34 Copynumber: 2.1 Consensus size: 34
245226 TGTTTGTATG
* *
245236 TTTAAATCGATTGTCATGCTGTAATACTGTTTCT
1 TTTAAATCGATTGTCATGCTGGAATACTGCTTCT
* * *
245270 TTTAAATCGATTGTTATGGTGGAATATTGCTTCT
1 TTTAAATCGATTGTCATGCTGGAATACTGCTTCT
245304 TTT
1 TTT
245307 TCTTTTGAGT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.23, C:0.11, G:0.17, T:0.49
Consensus pattern (34 bp):
TTTAAATCGATTGTCATGCTGGAATACTGCTTCT
Found at i:261777 original size:15 final size:14
Alignment explanation
Indices: 261753--261783 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
261743 ATTATATGAT
261753 ATAAAAATTAAATA
1 ATAAAAATTAAATA
261767 ATAAGAAATTAAATA
1 ATAA-AAATTAAATA
261782 AT
1 AT
261784 GGAGGCAGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (14 bp):
ATAAAAATTAAATA
Found at i:262883 original size:65 final size:64
Alignment explanation
Indices: 262800--262928 Score: 249
Period size: 65 Copynumber: 2.0 Consensus size: 64
262790 GTGTTTTTTT
262800 TTTTTTTTTTGCTTATCTTTTACTATTCTGGAAGTTTTTATGCTAGTACGTTGGCATGATTTAG
1 TTTTTTTTTTGCTTATCTTTTACTATTCTGGAAGTTTTTATGCTAGTACGTTGGCATGATTTAG
262864 TTTTTTTTTTGCTTAATCTTTTACTATTCTGGAAGTTTTTATGCTAGTACGTTGGCATGATTTAG
1 TTTTTTTTTTGCTT-ATCTTTTACTATTCTGGAAGTTTTTATGCTAGTACGTTGGCATGATTTAG
262929 GAGCAACATG
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
64 14 0.22
65 50 0.78
ACGTcount: A:0.18, C:0.11, G:0.17, T:0.54
Consensus pattern (64 bp):
TTTTTTTTTTGCTTATCTTTTACTATTCTGGAAGTTTTTATGCTAGTACGTTGGCATGATTTAG
Found at i:273946 original size:3 final size:3
Alignment explanation
Indices: 273938--273972 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
273928 AGGATAATAT
273938 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
273973 TCTGTTTTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:275208 original size:26 final size:27
Alignment explanation
Indices: 275172--275222 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 27
275162 GTGTCAGTAT
*
275172 ATTAATATTAATATT-AAATAAAAATA
1 ATTAATATTAATATTGAAACAAAAATA
*
275198 ATTATTATTAATATTGAAACAAAAA
1 ATTAATATTAATATTGAAACAAAAA
275223 AAACTTCTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 14 0.64
27 8 0.36
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (27 bp):
ATTAATATTAATATTGAAACAAAAATA
Found at i:278844 original size:59 final size:60
Alignment explanation
Indices: 278778--278896 Score: 222
Period size: 60 Copynumber: 2.0 Consensus size: 60
278768 AATTAAAAAA
*
278778 ATTCTTTTAAGTTCGCGCTTTGCC-ATAATTATTATTTTTTAAAATTTCTAAACTTACTC
1 ATTCTTTTAAGTTCGCGCTTGGCCTATAATTATTATTTTTTAAAATTTCTAAACTTACTC
278837 ATTCTTTTAAGTTCGCGCTTGGCCTATAATTATTATTTTTTAAAATTTCTAAACTTACTC
1 ATTCTTTTAAGTTCGCGCTTGGCCTATAATTATTATTTTTTAAAATTTCTAAACTTACTC
278897 GTCGGATTTA
Statistics
Matches: 58, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
59 23 0.40
60 35 0.60
ACGTcount: A:0.27, C:0.17, G:0.08, T:0.49
Consensus pattern (60 bp):
ATTCTTTTAAGTTCGCGCTTGGCCTATAATTATTATTTTTTAAAATTTCTAAACTTACTC
Found at i:282343 original size:39 final size:39
Alignment explanation
Indices: 282283--282362 Score: 142
Period size: 39 Copynumber: 2.1 Consensus size: 39
282273 AGCAGACGTG
* *
282283 ACTGTGAAAGTGGGCACTTCTACAATAATTGTGACAACC
1 ACTGTGAAAGTAGGCAATTCTACAATAATTGTGACAACC
282322 ACTGTGAAAGTAGGCAATTCTACAATAATTGTGACAACC
1 ACTGTGAAAGTAGGCAATTCTACAATAATTGTGACAACC
282361 AC
1 AC
282363 AACGAAAACA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.36, C:0.20, G:0.19, T:0.25
Consensus pattern (39 bp):
ACTGTGAAAGTAGGCAATTCTACAATAATTGTGACAACC
Found at i:284117 original size:21 final size:21
Alignment explanation
Indices: 284093--284138 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
284083 TTTTAAATGG
*
284093 TTTTTATTAAT-TTTATTAATA
1 TTTTTA-TAATATTTAATAATA
284114 TTTTTATAATATTTAATAATA
1 TTTTTATAATATTTAATAATA
284135 TTTT
1 TTTT
284139 AGAAATTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 4 0.17
21 19 0.83
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (21 bp):
TTTTTATAATATTTAATAATA
Found at i:289375 original size:25 final size:26
Alignment explanation
Indices: 289347--289399 Score: 81
Period size: 25 Copynumber: 2.1 Consensus size: 26
289337 CATTAGTTAC
289347 AAAGCTTGTAATAAAAAAGT-AACAA
1 AAAGCTTGTAATAAAAAAGTAAACAA
* *
289372 AAAGTTTGTAATAACAAAGTAAACAA
1 AAAGCTTGTAATAAAAAAGTAAACAA
289398 AA
1 AA
289400 CAAAATAACT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 18 0.72
26 7 0.28
ACGTcount: A:0.60, C:0.08, G:0.11, T:0.21
Consensus pattern (26 bp):
AAAGCTTGTAATAAAAAAGTAAACAA
Found at i:290754 original size:16 final size:16
Alignment explanation
Indices: 290735--290766 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
290725 CTTGCAATTC
290735 GATAGGCTCACACTTT
1 GATAGGCTCACACTTT
*
290751 GATAGGCTCGCACTTT
1 GATAGGCTCACACTTT
290767 TCTTATTATC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.22, C:0.25, G:0.22, T:0.31
Consensus pattern (16 bp):
GATAGGCTCACACTTT
Found at i:290861 original size:65 final size:64
Alignment explanation
Indices: 290744--290864 Score: 172
Period size: 65 Copynumber: 1.9 Consensus size: 64
290734 CGATAGGCTC
* * * *
290744 ACACTTTGATAGGCTCGCACTTTTCTTATTATCTTTAACATGCTCGCAACTTTACAAGGCTCGT
1 ACACTTTGATAGGCTCGCACTTTGCTCATTATCTTCAACAGGCTCGCAACTTTACAAGGCTCGT
*
290808 ACACTTTGATA-GCTCGCACATTTGGCTCATTGTCTTCAACAGGCTCGCAACTTTACA
1 ACACTTTGATAGGCTCGCAC-TTT-GCTCATTATCTTCAACAGGCTCGCAACTTTACA
290865 GCTCACACTG
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
63 8 0.16
64 14 0.28
65 28 0.56
ACGTcount: A:0.24, C:0.26, G:0.15, T:0.35
Consensus pattern (64 bp):
ACACTTTGATAGGCTCGCACTTTGCTCATTATCTTCAACAGGCTCGCAACTTTACAAGGCTCGT
Found at i:290959 original size:104 final size:103
Alignment explanation
Indices: 290838--291030 Score: 287
Period size: 104 Copynumber: 1.9 Consensus size: 103
290828 TTTGGCTCAT
* *
290838 TGTCTTCAACAGGCTCGCAACTTTACAGCTCACACTGAGCTTCCACATGTTGCTAAGCTCGCACC
1 TGTCTTCAACAGGCTCGCAACTTTACAGCTCACACTAAGCTTCCACATGTTGCTAAGCTCGCACA
* *
290903 TTTGACAGGCTCACACATTTGCATACTGTCTTCAACATG
66 TTTGACAGACTCACAC-TTCGCATACTGTCTTCAACATG
* * * * * *
290942 TGTCTTCAATAGGCTCGCACCTTTATAGCTCACACTAAGCTTCCACATGTTGTTGAGCTCTCACA
1 TGTCTTCAACAGGCTCGCAACTTTACAGCTCACACTAAGCTTCCACATGTTGCTAAGCTCGCACA
291007 TTTGACAGACTCACACTTCGCATA
66 TTTGACAGACTCACACTTCGCATA
291031 TTATTTTCAA
Statistics
Matches: 79, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
103 7 0.09
104 72 0.91
ACGTcount: A:0.24, C:0.30, G:0.16, T:0.30
Consensus pattern (103 bp):
TGTCTTCAACAGGCTCGCAACTTTACAGCTCACACTAAGCTTCCACATGTTGCTAAGCTCGCACA
TTTGACAGACTCACACTTCGCATACTGTCTTCAACATG
Found at i:293834 original size:51 final size:51
Alignment explanation
Indices: 293764--293895 Score: 133
Period size: 51 Copynumber: 2.6 Consensus size: 51
293754 TGGTTTTAGG
* * * ***
293764 TCACGTGTGTAGTACTAAGTGCAAGCTACTATGCGTACCTGATAGCT-TCGA
1 TCACATGTGTGGTACTAAGTGCAAGCCACTATGCGTAAAAGATAGCTCT-GA
* * *
293815 TCACATGTGTGGTACTAAGTGCAGGCCACTATGTGTAAAAGATAGCTCTGG
1 TCACATGTGTGGTACTAAGTGCAAGCCACTATGCGTAAAAGATAGCTCTGA
* *
293866 TCACAAGTGTGGTACTATGTG-AAGGCCACT
1 TCACATGTGTGGTACTAAGTGCAA-GCCACT
293896 TTGTGAAGAA
Statistics
Matches: 67, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
50 1 0.01
51 65 0.97
52 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.28
Consensus pattern (51 bp):
TCACATGTGTGGTACTAAGTGCAAGCCACTATGCGTAAAAGATAGCTCTGA
Found at i:293912 original size:51 final size:50
Alignment explanation
Indices: 293804--293937 Score: 144
Period size: 51 Copynumber: 2.6 Consensus size: 50
293794 ATGCGTACCT
* * * *
293804 GATAGCTTCGATCACATGTGTGGTACTAAGTGCAGGCCACTATGTGTAAAA
1 GATAGCTT-GGTCACAAGTGTGGTACTATGTGAAGGCCACTATGTGTAAAA
*
293855 GATAGCTCTGGTCACAAGTGTGGTACTATGTGAAGGCCACTTTGTG-AAGAA
1 GATAGCT-TGGTCACAAGTGTGGTACTATGTGAAGGCCACTATGTGTAA-AA
* * * *
293906 GGTAGCTTTGACTACAAGGGTGGTACTATGTG
1 GATAGCTTGGTC-ACAAGTGTGGTACTATGTG
293938 CAGGTCACCG
Statistics
Matches: 71, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
50 5 0.07
51 65 0.92
52 1 0.01
ACGTcount: A:0.27, C:0.16, G:0.29, T:0.28
Consensus pattern (50 bp):
GATAGCTTGGTCACAAGTGTGGTACTATGTGAAGGCCACTATGTGTAAAA
Found at i:297889 original size:40 final size:39
Alignment explanation
Indices: 297845--298140 Score: 247
Period size: 40 Copynumber: 7.8 Consensus size: 39
297835 GAAGTTTGCA
* *
297845 CCCAGCGCTAGTCAGATTAACCAACGATATTGAATGTGAG
1 CCCAGCGCTAGTCGGATAAACCAACGATATT-AATGTGAG
* * *
297885 CCCAGCTCTAGTTGGATAAACCAACGATATT--TG-CA-
1 CCCAGCGCTAGTCGGATAAACCAACGATATTAATGTGAG
* * * *
297920 CCAAGTGCTAGTCGGATATACCAACGATAATAATAGTGAG
1 CCCAGCGCTAGTCGGATAAACCAACGATATTAAT-GTGAG
* * *
297960 CCCAGCTCTAGTTGGATAAACCAACGATATT--TG-CA-
1 CCCAGCGCTAGTCGGATAAACCAACGATATTAATGTGAG
* * * *
297995 CCAAGTGCTAGTCGGATATACCAACGATAATAATAGTGAG
1 CCCAGCGCTAGTCGGATAAACCAACGATATTAAT-GTGAG
* * *
298035 CCCAGCTCTAGTTGGATAAACCAACGATATT--TG-CA-
1 CCCAGCGCTAGTCGGATAAACCAACGATATTAATGTGAG
* * * *
298070 CCAAGTGCTAGTCGGATATACCAACGATAATAATAGTGAG
1 CCCAGCGCTAGTCGGATAAACCAACGATATTAAT-GTGAG
* *
298110 CCCAGCTCTAGTTGGATAAACCAACGATATT
1 CCCAGCGCTAGTCGGATAAACCAACGATATT
298141 TGCACCTAGT
Statistics
Matches: 195, Mismatches: 46, Indels: 30
0.72 0.17 0.11
Matches are distributed among these distances:
35 75 0.38
36 3 0.02
37 7 0.04
38 5 0.03
39 3 0.02
40 102 0.52
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.24
Consensus pattern (39 bp):
CCCAGCGCTAGTCGGATAAACCAACGATATTAATGTGAG
Found at i:297943 original size:35 final size:35
Alignment explanation
Indices: 297892--298173 Score: 216
Period size: 35 Copynumber: 7.6 Consensus size: 35
297882 GAGCCCAGCT
*
297892 CTAGTTGGATAAACCAACGATATTTGCACCAAGTG
1 CTAGTCGGATAAACCAACGATATTTGCACCAAGTG
* *
297927 CTAGTCGGATATACCAACGATAATAATAGTG-AGCCCAGCT-
1 CTAGTCGGATAAACCAACGAT-AT--T--TGCA-CCAAG-TG
*
297967 CTAGTTGGATAAACCAACGATATTTGCACCAAGTG
1 CTAGTCGGATAAACCAACGATATTTGCACCAAGTG
* *
298002 CTAGTCGGATATACCAACGATAATAATAGTG-AGCCCAGCT-
1 CTAGTCGGATAAACCAACGAT-AT--T--TGCA-CCAAG-TG
*
298042 CTAGTTGGATAAACCAACGATATTTGCACCAAGTG
1 CTAGTCGGATAAACCAACGATATTTGCACCAAGTG
* *
298077 CTAGTCGGATATACCAACGATAATAATAGTG-AGCCCAGCT-
1 CTAGTCGGATAAACCAACGAT-AT--T--TGCA-CCAAG-TG
* *
298117 CTAGTTGGATAAACCAACGATATTTGCACCTAGTG
1 CTAGTCGGATAAACCAACGATATTTGCACCAAGTG
* *
298152 CTAGTCGGATATACCGACGATA
1 CTAGTCGGATAAACCAACGATA
298174 ATAATTTTGA
Statistics
Matches: 199, Mismatches: 21, Indels: 54
0.73 0.08 0.20
Matches are distributed among these distances:
34 3 0.02
35 94 0.47
36 9 0.05
37 3 0.02
38 3 0.02
39 9 0.05
40 75 0.38
41 3 0.02
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.24
Consensus pattern (35 bp):
CTAGTCGGATAAACCAACGATATTTGCACCAAGTG
Found at i:298232 original size:75 final size:75
Alignment explanation
Indices: 297839--298218 Score: 620
Period size: 75 Copynumber: 5.1 Consensus size: 75
297829 CATAGAGAAG
* * * *
297839 TTTGCACCCAGCGCTAGTCAGAT-TAACCAACGATATTGAAT-GTGAGCCCAGCTCTAGTTGGAT
1 TTTGCACCAAGTGCTAGTCGGATAT-ACCAACGATAAT-AATAGTGAGCCCAGCTCTAGTTGGAT
297902 AAACCAACGATA
64 AAACCAACGATA
297914 TTTGCACCAAGTGCTAGTCGGATATACCAACGATAATAATAGTGAGCCCAGCTCTAGTTGGATAA
1 TTTGCACCAAGTGCTAGTCGGATATACCAACGATAATAATAGTGAGCCCAGCTCTAGTTGGATAA
297979 ACCAACGATA
66 ACCAACGATA
297989 TTTGCACCAAGTGCTAGTCGGATATACCAACGATAATAATAGTGAGCCCAGCTCTAGTTGGATAA
1 TTTGCACCAAGTGCTAGTCGGATATACCAACGATAATAATAGTGAGCCCAGCTCTAGTTGGATAA
298054 ACCAACGATA
66 ACCAACGATA
298064 TTTGCACCAAGTGCTAGTCGGATATACCAACGATAATAATAGTGAGCCCAGCTCTAGTTGGATAA
1 TTTGCACCAAGTGCTAGTCGGATATACCAACGATAATAATAGTGAGCCCAGCTCTAGTTGGATAA
298129 ACCAACGATA
66 ACCAACGATA
* * ** * *
298139 TTTGCACCTAGTGCTAGTCGGATATACCGACGATAATAATTTTGAGCCCAGATTTAGTTGGATAA
1 TTTGCACCAAGTGCTAGTCGGATATACCAACGATAATAATAGTGAGCCCAGCTCTAGTTGGATAA
* *
298204 ACCTATGATA
66 ACCAACGATA
298214 TTTGC
1 TTTGC
298219 GCGCAGCACT
Statistics
Matches: 291, Mismatches: 12, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
74 3 0.01
75 287 0.99
76 1 0.00
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.26
Consensus pattern (75 bp):
TTTGCACCAAGTGCTAGTCGGATATACCAACGATAATAATAGTGAGCCCAGCTCTAGTTGGATAA
ACCAACGATA
Found at i:307178 original size:41 final size:41
Alignment explanation
Indices: 307107--307261 Score: 222
Period size: 41 Copynumber: 3.8 Consensus size: 41
307097 GTTTGAATGA
*
307107 AAAACGCCACTAAAAACTGAGTAATAGTGGCTTTTTCGTGC
1 AAAACGCCACTAAAAACTGAGTAATAGTGGCGTTTTCGTGC
* * *
307148 AAAACGCCACTAAAAATTGAGCAATTGTGGCGTTTTCGTGC
1 AAAACGCCACTAAAAACTGAGTAATAGTGGCGTTTTCGTGC
* *
307189 AAAACGCCGCTAAAAACTGAGTAATAGTGGCGTTTTCATGC
1 AAAACGCCACTAAAAACTGAGTAATAGTGGCGTTTTCGTGC
* *
307230 AAAACGCCGCAAAAAACTGAG-ATATAGTGGCG
1 AAAACGCCACTAAAAACTGAGTA-ATAGTGGCG
307262 CTTTAGGTCC
Statistics
Matches: 103, Mismatches: 10, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
40 1 0.01
41 102 0.99
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.23
Consensus pattern (41 bp):
AAAACGCCACTAAAAACTGAGTAATAGTGGCGTTTTCGTGC
Found at i:307276 original size:41 final size:41
Alignment explanation
Indices: 307107--307284 Score: 157
Period size: 41 Copynumber: 4.3 Consensus size: 41
307097 GTTTGAATGA
* * **
307107 AAAACGCCACTAAAAACTGAGTAATAGTGGCTTTTTC-GTGC
1 AAAACGCCGCAAAAAACTGAGTAATAGTGGCGCTTTCAG-GC
* * * * * *
307148 AAAACGCCACTAAAAATTGAGCAATTGTGGCGTTTTC-GTGC
1 AAAACGCCGCAAAAAACTGAGTAATAGTGGCGCTTTCAG-GC
* * *
307189 AAAACGCCGCTAAAAACTGAGTAATAGTGGCGTTTTCATGC
1 AAAACGCCGCAAAAAACTGAGTAATAGTGGCGCTTTCAGGC
307230 AAAACGCCGCAAAAAACTGAG-ATATAGTGGCGCTTT-AGGTC
1 AAAACGCCGCAAAAAACTGAGTA-ATAGTGGCGCTTTCAGG-C
* *
307271 CAAACGCCACAAAA
1 AAAACGCCGCAAAA
307285 GGTTGAACTA
Statistics
Matches: 120, Mismatches: 14, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
40 3 0.03
41 117 0.98
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.22
Consensus pattern (41 bp):
AAAACGCCGCAAAAAACTGAGTAATAGTGGCGCTTTCAGGC
Found at i:307276 original size:82 final size:82
Alignment explanation
Indices: 307107--307284 Score: 227
Period size: 82 Copynumber: 2.2 Consensus size: 82
307097 GTTTGAATGA
* * * *
307107 AAAACGCCACTAAAAACTGAGTAATAGTGGCTTTTTCGTGCAAAACGCCACTAAAAATTGAGCAA
1 AAAACGCCACTAAAAACTGAGTAATAGTGGCGTTTTCATGCAAAACGCCACAAAAAACTGAGCAA
* *
307172 TTGTGGCGTTTTCGTGC
66 TAGTGGCGTTTACGTGC
* *
307189 AAAACGCCGCTAAAAACTGAGTAATAGTGGCGTTTTCATGCAAAACGCCGCAAAAAACTGAG-AT
1 AAAACGCCACTAAAAACTGAGTAATAGTGGCGTTTTCATGCAAAACGCCACAAAAAACTGAGCA-
*
307253 ATAGTGGCGCTTTAGGT-C
65 ATAGTGGCG-TTTACGTGC
*
307271 CAAACGCCAC-AAAA
1 AAAACGCCACTAAAA
307285 GGTTGAACTA
Statistics
Matches: 83, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
81 5 0.06
82 73 0.88
83 5 0.06
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.22
Consensus pattern (82 bp):
AAAACGCCACTAAAAACTGAGTAATAGTGGCGTTTTCATGCAAAACGCCACAAAAAACTGAGCAA
TAGTGGCGTTTACGTGC
Found at i:307876 original size:29 final size:29
Alignment explanation
Indices: 307839--307894 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
307829 AAAATATGAA
*
307839 GCCTAACCCTTAAATCATAACCCATGACC
1 GCCTAACCCCTAAATCATAACCCATGACC
307868 GCCTAACCCCTAAATCATAACCCATGA
1 GCCTAACCCCTAAATCATAACCCATGA
307895 TCTAAACTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.36, C:0.38, G:0.07, T:0.20
Consensus pattern (29 bp):
GCCTAACCCCTAAATCATAACCCATGACC
Found at i:307906 original size:26 final size:27
Alignment explanation
Indices: 307843--307907 Score: 69
Period size: 29 Copynumber: 2.3 Consensus size: 27
307833 TATGAAGCCT
307843 AACCCTTAAATCATAACCCATGACCGCCTA
1 AACCC-TAAATCATAACCCATGA-C-CCTA
* *
307873 ACCCCTAAATCATAACCCATGA-TCTA
1 AACCCTAAATCATAACCCATGACCCTA
*
307899 AACTCTAAA
1 AACCCTAAA
307908 CCATTTAAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
26 10 0.32
29 17 0.55
30 4 0.13
ACGTcount: A:0.40, C:0.34, G:0.05, T:0.22
Consensus pattern (27 bp):
AACCCTAAATCATAACCCATGACCCTA
Found at i:308086 original size:14 final size:15
Alignment explanation
Indices: 308067--308103 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
308057 AAACACTTAT
308067 ACCCTAAA-TTATAA
1 ACCCTAAATTTATAA
*
308081 ACCCTAAATTTGTAA
1 ACCCTAAATTTATAA
308096 ACCCTAAA
1 ACCCTAAA
308104 AATAAATTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.46, C:0.24, G:0.03, T:0.27
Consensus pattern (15 bp):
ACCCTAAATTTATAA
Found at i:308935 original size:75 final size:75
Alignment explanation
Indices: 308721--308938 Score: 203
Period size: 75 Copynumber: 2.9 Consensus size: 75
308711 CGTTCTATGT
* * * ** * * *
308721 TTTGTTTTTAGTGGCGCTTTGTACAAACGCCACAAAAATGTATTACGAGTTTAAG-AAACGACAC
1 TTTGTTTTTAGTGGCGCTTTATAAAAACGCCGCAAATTTGTATTAAGAGTTTTAGTAAACGACGC
308785 CG-TTTATAC
66 CGTTTTATAC
* * * * * * * *
308794 -TTGTTATTGGTGGCGCTTTGACAAAAATGCCGCAAATTTGTGTTATGTGTTTT-CTAAACGACG
1 TTTGTTTTTAGTGGCGCTTT-ATAAAAACGCCGCAAATTTGTATTAAGAGTTTTAGTAAACGACG
*
308857 CCGTTTTATTC
65 CCGTTTTATAC
** *
308868 TTTGTTTTTAGTGGCGCTTTATATAAAACGCCGCAAATTTGTATTAAG-GTTTTAGTGGACGATG
1 TTTGTTTTTAGTGGCGCTTTATA-AAAACGCCGCAAATTTGTATTAAGAGTTTTAGTAAACGACG
308932 CCGTTTT
65 CCGTTTT
308939 GGCAATGTTA
Statistics
Matches: 113, Mismatches: 26, Indels: 10
0.76 0.17 0.07
Matches are distributed among these distances:
72 17 0.15
73 32 0.28
74 13 0.12
75 51 0.45
ACGTcount: A:0.25, C:0.16, G:0.21, T:0.39
Consensus pattern (75 bp):
TTTGTTTTTAGTGGCGCTTTATAAAAACGCCGCAAATTTGTATTAAGAGTTTTAGTAAACGACGC
CGTTTTATAC
Found at i:309233 original size:20 final size:20
Alignment explanation
Indices: 309188--309239 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
309178 CCCCACCCAA
*
309188 ATTTCCCCAAATCCCTAACT
1 ATTTCCCCAAATCCCTAAAT
*
309208 -TTTCCCCTAATCCCTAAAT
1 ATTTCCCCAAATCCCTAAAT
*
309227 ATTTCCCCGAATC
1 ATTTCCCCAAATC
309240 AAAATCGAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 17 0.61
20 11 0.39
ACGTcount: A:0.27, C:0.38, G:0.02, T:0.33
Consensus pattern (20 bp):
ATTTCCCCAAATCCCTAAAT
Found at i:309281 original size:19 final size:19
Alignment explanation
Indices: 309257--309294 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
309247 AAATATCCTT
*
309257 CTGCCGTTGAAGGCTCCGA
1 CTGCCGTTGAAGACTCCGA
309276 CTGCCGTTGAAGACTCCGA
1 CTGCCGTTGAAGACTCCGA
309295 GTGGACGACC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.18, C:0.32, G:0.29, T:0.21
Consensus pattern (19 bp):
CTGCCGTTGAAGACTCCGA
Found at i:317807 original size:13 final size:14
Alignment explanation
Indices: 317789--317817 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
317779 TTATAAATAT
317789 TTATAATA-TTTAA
1 TTATAATATTTTAA
317802 TTATAATATTTTAA
1 TTATAATATTTTAA
317816 TT
1 TT
317818 CGTTGTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TTATAATATTTTAA
Found at i:319998 original size:24 final size:25
Alignment explanation
Indices: 319960--320016 Score: 91
Period size: 24 Copynumber: 2.4 Consensus size: 25
319950 TAGTTTGTTC
*
319960 AATCGA-TTTTCTTACAATTGGCTT
1 AATCGACTTTTCTTACAATCGGCTT
319984 AATCGACTTTT-TTACAATCGGCTT
1 AATCGACTTTTCTTACAATCGGCTT
320008 AATCGACTT
1 AATCGACTT
320017 GAACACATCA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
24 27 0.87
25 4 0.13
ACGTcount: A:0.26, C:0.19, G:0.12, T:0.42
Consensus pattern (25 bp):
AATCGACTTTTCTTACAATCGGCTT
Found at i:328283 original size:67 final size:67
Alignment explanation
Indices: 328209--328342 Score: 259
Period size: 67 Copynumber: 2.0 Consensus size: 67
328199 ATAATCATAA
328209 TTAACTCAAACAACCTACCCATCATGTATATATTAAGTAAAAGTATCATAAACACATCTGTATTA
1 TTAACTCAAACAACCTACCCATCATGTATATATTAAGTAAAAGTATCATAAACACATCTGTATTA
328274 AG
66 AG
*
328276 TTAACTCAAACACCCTACCCATCATGTATATATTAAGTAAAAGTATCATAAACACATCTGTATTA
1 TTAACTCAAACAACCTACCCATCATGTATATATTAAGTAAAAGTATCATAAACACATCTGTATTA
328341 AG
66 AG
328343 AATTGAATCA
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
67 66 1.00
ACGTcount: A:0.43, C:0.20, G:0.07, T:0.30
Consensus pattern (67 bp):
TTAACTCAAACAACCTACCCATCATGTATATATTAAGTAAAAGTATCATAAACACATCTGTATTA
AG
Found at i:332204 original size:9 final size:9
Alignment explanation
Indices: 332187--332220 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
332177 TTAAGTTATT
*
332187 TTAAGTTAA
1 TTAATTTAA
332196 TTAATTTAA
1 TTAATTTAA
*
332205 TTAGTTTAA
1 TTAATTTAA
332214 TTAATTT
1 TTAATTT
332221 TTTTTCCGCG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (9 bp):
TTAATTTAA
Done.