Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold174
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: 2085601
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 25 characters in sequence are not A, C, G, or T
File 10 of 15
Found at i:1146199 original size:2 final size:2
Alignment explanation
Indices: 1146192--1146222 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1146182 AACTATGAAC
1146192 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 T
1146223 GAAACCATTC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1147613 original size:14 final size:15
Alignment explanation
Indices: 1147594--1147623 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
1147584 ATTAAAAAAA
1147594 TAATATTTA-AATTT
1 TAATATTTATAATTT
1147608 TAATATTTATAATTT
1 TAATATTTATAATTT
1147623 T
1 T
1147624 TTATTTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
TAATATTTATAATTT
Found at i:1148376 original size:22 final size:24
Alignment explanation
Indices: 1148348--1148407 Score: 70
Period size: 22 Copynumber: 2.5 Consensus size: 24
1148338 TATAAAATAT
1148348 TAAAAATTTATTTTTAAA-TT-AA
1 TAAAAATTTATTTTTAAATTTAAA
* **
1148370 TATAAATTTATAATTAAATTTAAA
1 TAAAAATTTATTTTTAAATTTAAA
1148394 TAAAAATATTATTT
1 TAAAAAT-TTATTT
1148408 AATTTATAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
22 15 0.52
23 2 0.07
24 8 0.28
25 4 0.14
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
TAAAAATTTATTTTTAAATTTAAA
Found at i:1148625 original size:20 final size:20
Alignment explanation
Indices: 1148600--1148641 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1148590 AATAACAAAT
1148600 ATTTATAAA-ATATATATTTA
1 ATTTATAAATATA-ATATTTA
*
1148620 ATTTATTAATATAATATTTA
1 ATTTATAAATATAATATTTA
1148640 AT
1 AT
1148642 ATAAAATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 17 0.85
21 3 0.15
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
ATTTATAAATATAATATTTA
Found at i:1148882 original size:25 final size:24
Alignment explanation
Indices: 1148845--1148903 Score: 59
Period size: 25 Copynumber: 2.5 Consensus size: 24
1148835 TTTTTTTTTT
** *
1148845 TAAATATTCATATCCAATTTAAATA
1 TAAATATAAATATACAATTTAAA-A
*
1148870 TAAATATAAATATATAATTTAAAA
1 TAAATATAAATATACAATTTAAAA
1148894 -AAAT-TAAATA
1 TAAATATAAATA
1148904 CATAAAAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
22 6 0.20
23 4 0.13
24 1 0.03
25 19 0.63
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (24 bp):
TAAATATAAATATACAATTTAAAA
Found at i:1148908 original size:22 final size:25
Alignment explanation
Indices: 1148860--1148908 Score: 68
Period size: 22 Copynumber: 2.1 Consensus size: 25
1148850 ATTCATATCC
*
1148860 AATTTAAATATAAATATAAATATAT
1 AATTTAAATATAAATATAAATACAT
1148885 AATTTAAA-A-AAAT-TAAATACAT
1 AATTTAAATATAAATATAAATACAT
1148907 AA
1 AA
1148909 AAAAATATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 10 0.43
23 4 0.17
24 1 0.04
25 8 0.35
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (25 bp):
AATTTAAATATAAATATAAATACAT
Found at i:1153447 original size:8 final size:8
Alignment explanation
Indices: 1153436--1153472 Score: 56
Period size: 8 Copynumber: 4.6 Consensus size: 8
1153426 AATTTTATTA
*
1153436 TTTTATAT
1 TTTTAAAT
*
1153444 TTTTAATT
1 TTTTAAAT
1153452 TTTTAAAT
1 TTTTAAAT
1153460 TTTTAAAT
1 TTTTAAAT
1153468 TTTTA
1 TTTTA
1153473 TTATTTTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (8 bp):
TTTTAAAT
Found at i:1153447 original size:16 final size:15
Alignment explanation
Indices: 1153436--1153483 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 15
1153426 AATTTTATTA
*
1153436 TTTTATATTTTTAATT
1 TTTTAT-TTTTTAAAT
*
1153452 TTTTAAATTTTTAAAT
1 TTTT-ATTTTTTAAAT
1153468 TTTTATTATTTTAAAT
1 TTTTATT-TTTTAAAT
1153484 ATATAATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 2 0.07
16 24 0.89
17 1 0.04
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
TTTTATTTTTTAAAT
Found at i:1153472 original size:40 final size:40
Alignment explanation
Indices: 1153389--1153513 Score: 125
Period size: 40 Copynumber: 3.2 Consensus size: 40
1153379 TAAATAATAA
* ** *
1153389 AATTTTTA-TAATTTAAA-A-ATAATTTTTTAAATAAATG
1 AATTTTTATTATTTTAAATATATAATTTTTTAAATATTTT
* * *
1153426 AA-TTTTATTATTTTATATTTTTAATTTTTTAAAT-TTTT
1 AATTTTTATTATTTTAAATATATAATTTTTTAAATATTTT
**
1153464 AAATTTTTATTATTTTAAATATATAATTTTTTTGATATTTT
1 -AATTTTTATTATTTTAAATATATAATTTTTTAAATATTTT
1153505 AATTTTTAT
1 AATTTTTAT
1153514 AATAATATTA
Statistics
Matches: 70, Mismatches: 12, Indels: 9
0.77 0.13 0.10
Matches are distributed among these distances:
36 5 0.07
37 9 0.13
38 1 0.01
39 15 0.21
40 36 0.51
41 4 0.06
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (40 bp):
AATTTTTATTATTTTAAATATATAATTTTTTAAATATTTT
Found at i:1153764 original size:18 final size:18
Alignment explanation
Indices: 1153727--1153838 Score: 66
Period size: 18 Copynumber: 5.7 Consensus size: 18
1153717 TATTATTTAA
1153727 AATATTTTATATTTATAT
1 AATATTTTATATTTATAT
1153745 AA-ATTTTA-ATATTATGAT
1 AATATTTTATAT-TTAT-AT
* *
1153763 AATATTTATCATATAAATTTTAA
1 AATATTT-T-ATAT---TTATAT
1153786 AATATTTATATATTCATATTAT
1 AATATTT-TATATT--TA-TAT
*
1153808 ATATATTTTTTATTTATAT
1 A-ATATTTTATATTTATAT
*
1153827 CATATTTTATAT
1 AATATTTTATAT
1153839 CATATTTTAA
Statistics
Matches: 75, Mismatches: 7, Indels: 24
0.71 0.07 0.23
Matches are distributed among these distances:
16 2 0.03
17 10 0.13
18 16 0.21
19 8 0.11
20 3 0.04
21 2 0.03
22 14 0.19
23 16 0.21
24 4 0.05
ACGTcount: A:0.40, C:0.03, G:0.01, T:0.56
Consensus pattern (18 bp):
AATATTTTATATTTATAT
Found at i:1153812 original size:15 final size:14
Alignment explanation
Indices: 1153787--1153845 Score: 56
Period size: 12 Copynumber: 4.4 Consensus size: 14
1153777 AAATTTTAAA
1153787 ATATTTATATATTC
1 ATATTTATATATTC
1153801 ATATTATATATATT-
1 ATATT-TATATATTC
*
1153815 -T-TTTATTTATATC
1 ATATTTATATAT-TC
1153828 ATATTT-TATA-TC
1 ATATTTATATATTC
1153840 ATATTT
1 ATATTT
1153846 TAATTATTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
11 6 0.16
12 11 0.29
13 1 0.03
14 9 0.24
15 11 0.29
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (14 bp):
ATATTTATATATTC
Found at i:1153837 original size:12 final size:12
Alignment explanation
Indices: 1153820--1153864 Score: 60
Period size: 12 Copynumber: 4.0 Consensus size: 12
1153810 ATATTTTTTA
1153820 TTTATATCATAT
1 TTTATATCATAT
1153832 TTTATATCATAT
1 TTTATATCATAT
1153844 TTTA-AT--TAT
1 TTTATATCATAT
*
1153853 TTTTTATCATAT
1 TTTATATCATAT
1153865 CCAATATTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
9 6 0.21
10 2 0.07
11 2 0.07
12 19 0.66
ACGTcount: A:0.31, C:0.07, G:0.00, T:0.62
Consensus pattern (12 bp):
TTTATATCATAT
Found at i:1153843 original size:17 final size:16
Alignment explanation
Indices: 1153728--1153843 Score: 74
Period size: 17 Copynumber: 7.0 Consensus size: 16
1153718 ATTATTTAAA
1153728 ATATTTTATATTTATAT
1 ATATTTTATA-TTATAT
*
1153745 AAATTTTAATATTATGAT
1 ATATTTT-ATATTAT-AT
* *
1153763 A-ATATT-TATCATAT
1 ATATTTTATATTATAT
* * * *
1153777 AAATTTTAAAATATTT
1 ATATTTTATATTATAT
*
1153793 ATATATTCATATTATAT
1 ATAT-TTTATATTATAT
*
1153810 ATATTTTTTATTTATAT
1 ATATTTTATA-TTATAT
*
1153827 CATATTTTATATCATAT
1 -ATATTTTATATTATAT
1153844 TTTAATTATT
Statistics
Matches: 75, Mismatches: 17, Indels: 14
0.71 0.16 0.13
Matches are distributed among these distances:
14 3 0.04
15 9 0.12
16 11 0.15
17 37 0.49
18 15 0.20
ACGTcount: A:0.40, C:0.03, G:0.01, T:0.56
Consensus pattern (16 bp):
ATATTTTATATTATAT
Found at i:1154384 original size:2 final size:2
Alignment explanation
Indices: 1154377--1154406 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1154367 TCAAAAGGAA
1154377 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
1154407 TAAAAAGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1154515 original size:35 final size:34
Alignment explanation
Indices: 1154464--1154531 Score: 93
Period size: 35 Copynumber: 2.0 Consensus size: 34
1154454 ATAAAATTAA
*
1154464 TAAAATAATAATAATAATATTTATTAAAATATATTT
1 TAAAATAATAAAAATAAT-TTTATTAAAAT-TATTT
*
1154500 TAAAA-AATAAAAATAATTTTTTTAAAATTATT
1 TAAAATAATAAAAATAATTTTATTAAAATTATT
1154532 ATATATATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
33 4 0.13
34 10 0.33
35 11 0.37
36 5 0.17
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (34 bp):
TAAAATAATAAAAATAATTTTATTAAAATTATTT
Found at i:1155345 original size:6 final size:6
Alignment explanation
Indices: 1155336--1155380 Score: 58
Period size: 6 Copynumber: 7.7 Consensus size: 6
1155326 ATATATTTTT
*
1155336 ATTTAA ATTT-A ATTT-A ATTTAA ATTATAA ATTTTA ATTTAA ATTT
1 ATTTAA ATTTAA ATTTAA ATTTAA ATT-TAA ATTTAA ATTTAA ATTT
1155381 TATTAAATTC
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
5 10 0.29
6 19 0.54
7 6 0.17
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (6 bp):
ATTTAA
Found at i:1155959 original size:9 final size:9
Alignment explanation
Indices: 1155900--1156007 Score: 54
Period size: 8 Copynumber: 12.7 Consensus size: 9
1155890 ATAAAGATAT
1155900 TATATTATAA
1 TATATTAT-A
* *
1155910 AATATTAAA
1 TATATTATA
1155919 TATATTA-A
1 TATATTATA
* *
1155927 AATTTTA-A
1 TATATTATA
*
1155935 TACA-TATA
1 TATATTATA
1155943 T-TATTTATA
1 TATA-TTATA
1155952 TATATTATA
1 TATATTATA
*
1155961 TTTATTATA
1 TATATTATA
1155970 TTATATT-TA
1 -TATATTATA
1155979 TAT-TTAT-
1 TATATTATA
*
1155986 TATTTTA-A
1 TATATTATA
*
1155994 TATTTTAT-
1 TATATTATA
1156002 TATATT
1 TATATT
1156008 TAAAATTGAT
Statistics
Matches: 77, Mismatches: 12, Indels: 20
0.71 0.11 0.18
Matches are distributed among these distances:
7 8 0.10
8 29 0.38
9 27 0.35
10 13 0.17
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (9 bp):
TATATTATA
Found at i:1155970 original size:29 final size:28
Alignment explanation
Indices: 1155944--1156001 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 28
1155934 ATACATATAT
1155944 TATTTATATATATTATATTTATTATATTA
1 TATTTATATATATTAT-TTTATTATATTA
* * *
1155973 TATTTATATTTATTATTTTAATATTTTA
1 TATTTATATATATTATTTTATTATATTA
1156001 T
1 T
1156002 TATATTTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 11 0.42
29 15 0.58
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (28 bp):
TATTTATATATATTATTTTATTATATTA
Found at i:1155983 original size:20 final size:20
Alignment explanation
Indices: 1155938--1156007 Score: 74
Period size: 20 Copynumber: 3.5 Consensus size: 20
1155928 ATTTTAATAC
1155938 ATATATTATT-TA-TATATATT
1 ATAT-TTATTATATTATAT-TT
1155958 ATATTTATTATATTATATTT
1 ATATTTATTATATTATATTT
*
1155978 ATATTTATTATTTTAATATTT
1 ATATTTATTATATT-ATATTT
1155999 -TATTATATT
1 ATATT-TATT
1156008 TAAAATTGAT
Statistics
Matches: 45, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
19 5 0.11
20 25 0.56
21 15 0.33
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
ATATTTATTATATTATATTT
Found at i:1156006 original size:31 final size:31
Alignment explanation
Indices: 1155930--1156009 Score: 78
Period size: 29 Copynumber: 2.6 Consensus size: 31
1155920 ATATTAAAAT
*
1155930 TTTAATACA-TATATTATTTATATATATTATA
1 TTTAATATATTATA-TATTTATATATATTATA
* *
1155961 TTTATTATA-T-TATATTTATATTTATTAT-
1 TTTAATATATTATATATTTATATATATTATA
*
1155989 TTTAATATTTTATTATATTTA
1 TTTAATATATTA-TATATTTA
1156010 AAATTGATAA
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
28 7 0.17
29 16 0.39
30 2 0.05
31 16 0.39
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.62
Consensus pattern (31 bp):
TTTAATATATTATATATTTATATATATTATA
Found at i:1157741 original size:205 final size:205
Alignment explanation
Indices: 1157382--1157761 Score: 537
Period size: 205 Copynumber: 1.9 Consensus size: 205
1157372 CAGAGTGCTT
* * *
1157382 CAATCTGCAGAAGCAATACATGTGAACATGTCGAAACCTGATTAATACATTGCCACGAAGCACTA
1 CAATCTACAGAAGCAATACACGTGAACATGTCGAAACCTGATTAATACATTGCCACGAAGAACTA
* ** * * * *
1157447 CGAGAAACTATTTTCAAAGCAATCATCTACTCGCTATTTTCTATGCAAACTTCTTGCAGAAATTA
66 CAAGAAACTATTCCCAAAGCAATCATCTACTCGCGAATTTCTATGCAAACATCATGCAGAAATTA
* * *
1157512 AAGTAGAATTAGATGGATTCACATTGACAATTGATGATGCTTTTTATCGGCATGGTATGCCGAGA
131 AAGTAGAATTAGATGGATTCACATTAACAACTGAGGATGCTTTTTATCGGCATGGTATGCCGAGA
1157577 ATACTCTTAC
196 ATACTCTTAC
* * **
1157587 CAATCTACAGAAGCAATACACGTGAACATGTTGAAACCTGATTAGTACATTGCTGCGAAGAACTA
1 CAATCTACAGAAGCAATACACGTGAACATGTCGAAACCTGATTAATACATTGCCACGAAGAACTA
* * **
1157652 CAAGAAACTATTCCCAAAGCATTCATCTACTC-CGAATTTCTTTGCATGCATCATGCAGAAATTA
66 CAAGAAACTATTCCCAAAGCAATCATCTACTCGCGAATTTCTATGCAAACATCATGCAGAAATTA
* *
1157716 ATGTAGAATTAGATGAGATTCACATTAACAACTGGGGATGCTTTTT
131 AAGTAGAATTAGATG-GATTCACATTAACAACTGAGGATGCTTTTT
1157762 GTCAACACGG
Statistics
Matches: 151, Mismatches: 23, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
204 39 0.26
205 112 0.74
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (205 bp):
CAATCTACAGAAGCAATACACGTGAACATGTCGAAACCTGATTAATACATTGCCACGAAGAACTA
CAAGAAACTATTCCCAAAGCAATCATCTACTCGCGAATTTCTATGCAAACATCATGCAGAAATTA
AAGTAGAATTAGATGGATTCACATTAACAACTGAGGATGCTTTTTATCGGCATGGTATGCCGAGA
ATACTCTTAC
Found at i:1160710 original size:2 final size:2
Alignment explanation
Indices: 1160703--1160738 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1160693 TTAAAGGAAA
1160703 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
1160739 GGTTAAGTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1162419 original size:23 final size:25
Alignment explanation
Indices: 1162390--1162452 Score: 78
Period size: 27 Copynumber: 2.6 Consensus size: 25
1162380 TAATAAATTT
1162390 TTATTTTTATAT-T-TAAT-TTAAA
1 TTATTTTTATATATATAATATTAAA
*
1162412 TTATTTTTCATATTATATAATATTTAA
1 TTATTTTT-ATA-TATATAATATTAAA
1162439 TTATTTTTATATAT
1 TTATTTTTATATAT
1162453 CATCTAGTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
22 8 0.23
23 3 0.09
24 1 0.03
25 4 0.11
26 7 0.20
27 12 0.34
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (25 bp):
TTATTTTTATATATATAATATTAAA
Found at i:1162452 original size:28 final size:27
Alignment explanation
Indices: 1162363--1162452 Score: 85
Period size: 28 Copynumber: 3.3 Consensus size: 27
1162353 AAATTAATAA
* *
1162363 TATATATTACATAATTTTAATAAATTTT
1 TATATATTATATAATTTTAAT-TATTTT
* *
1162391 TAT-TTTTATATTTAATTTAAATTATTTT
1 TATATATTATA--TAATTTTAATTATTTT
*
1162419 T-CATATTATATAATATTTAATTATTTT
1 TATATATTATATAAT-TTTAATTATTTT
1162446 TATATAT
1 TATATAT
1162453 CATCTAGTTA
Statistics
Matches: 49, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
26 4 0.08
27 17 0.35
28 19 0.39
29 9 0.18
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (27 bp):
TATATATTATATAATTTTAATTATTTT
Found at i:1164417 original size:18 final size:18
Alignment explanation
Indices: 1164392--1164438 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
1164382 AGAAGAGCAA
*
1164392 CAACAAGAACAGAATCAT
1 CAACAAGAACAGAATCAG
*
1164410 CAAGAAGAAGC-GAATCAG
1 CAACAAGAA-CAGAATCAG
1164428 CAACAAGAACA
1 CAACAAGAACA
1164439 AGAGAAGAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
17 1 0.04
18 22 0.92
19 1 0.04
ACGTcount: A:0.55, C:0.21, G:0.17, T:0.06
Consensus pattern (18 bp):
CAACAAGAACAGAATCAG
Found at i:1165716 original size:26 final size:25
Alignment explanation
Indices: 1165687--1165735 Score: 71
Period size: 26 Copynumber: 1.9 Consensus size: 25
1165677 TTAATATAAA
*
1165687 AATTTTAATTTTATAATTATTTTTTT
1 AATTTTAATATTATAATT-TTTTTTT
*
1165713 AATTTTTATATTATAATTTTTTT
1 AATTTTAATATTATAATTTTTTT
1165736 CTATAAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 5 0.24
26 16 0.76
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (25 bp):
AATTTTAATATTATAATTTTTTTTT
Found at i:1165732 original size:20 final size:20
Alignment explanation
Indices: 1165687--1165732 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
1165677 TTAATATAAA
1165687 AATTTTAATTTTATAATTAT
1 AATTTTAATTTTATAATTAT
**
1165707 TTTTTTAATTTT-TATATTAT
1 AATTTTAATTTTATA-ATTAT
1165727 AATTTT
1 AATTTT
1165733 TTTCTATAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
19 2 0.10
20 19 0.90
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
AATTTTAATTTTATAATTAT
Found at i:1170140 original size:21 final size:23
Alignment explanation
Indices: 1170116--1170161 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
1170106 TATATGACAC
1170116 AAAAATA-ATATAA-AAAATATG
1 AAAAATATATATAAGAAAATATG
*
1170137 AAAAATATATATAAGAATATATG
1 AAAAATATATATAAGAAAATATG
1170160 AA
1 AA
1170162 TTTTTTGGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 7 0.32
22 6 0.27
23 9 0.41
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (23 bp):
AAAAATATATATAAGAAAATATG
Found at i:1171292 original size:21 final size:21
Alignment explanation
Indices: 1171267--1171312 Score: 71
Period size: 18 Copynumber: 2.3 Consensus size: 21
1171257 TTTTAACTTG
1171267 ATAGTAATTAAAAATAATTTT
1 ATAGTAATTAAAAATAATTTT
1171288 ATAG---TTAAAAATAATTTT
1 ATAGTAATTAAAAATAATTTT
1171306 ATAGTAA
1 ATAGTAA
1171313 AAATATTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
18 18 0.82
21 4 0.18
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (21 bp):
ATAGTAATTAAAAATAATTTT
Found at i:1171313 original size:17 final size:18
Alignment explanation
Indices: 1171274--1171317 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
1171264 TTGATAGTAA
1171274 TTAAAAATAATTTTATAG
1 TTAAAAATAATTTTATAG
1171292 TTAAAAATAATTTTATAG
1 TTAAAAATAATTTTATAG
1171310 -TAAAAATA
1 TTAAAAATA
1171318 TTTAAAAACT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 8 0.31
18 18 0.69
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.41
Consensus pattern (18 bp):
TTAAAAATAATTTTATAG
Found at i:1172701 original size:29 final size:29
Alignment explanation
Indices: 1172647--1172703 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
1172637 ATTTTTATTT
*
1172647 AAATAATAAAATATTTAAATTTAATTATA
1 AAATAATAAAATATTTAAATTAAATTATA
1172676 AAATAATAAAA-ATATT-AATATAAATTAT
1 AAATAATAAAATAT-TTAAAT-TAAATTAT
1172704 TTTAATATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
28 5 0.20
29 20 0.80
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (29 bp):
AAATAATAAAATATTTAAATTAAATTATA
Found at i:1174315 original size:26 final size:26
Alignment explanation
Indices: 1174294--1174350 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
1174284 AAATTTTTCA
*
1174294 TTAATT-TAAAAATAAAATATTTATT
1 TTAATTATAAAAATAAAAAATTTATT
* *
1174319 TTTATTATAAAAATAAAAAATTTAAT
1 TTAATTATAAAAATAAAAAATTTATT
1174345 TTAATT
1 TTAATT
1174351 TAATTTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
25 5 0.19
26 22 0.81
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (26 bp):
TTAATTATAAAAATAAAAAATTTATT
Found at i:1174369 original size:25 final size:24
Alignment explanation
Indices: 1174331--1174387 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 24
1174321 TATTATAAAA
*
1174331 ATAAAAAATTTAATTTAATTT-AATT
1 ATAAATAATTTAATTT--TTTAAATT
1174356 -TAAATAATTATAATTTTTTAAATT
1 ATAAATAATT-TAATTTTTTAAATT
1174380 ATAAATAA
1 ATAAATAA
1174388 AATAAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
23 3 0.11
24 12 0.43
25 13 0.46
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (24 bp):
ATAAATAATTTAATTTTTTAAATT
Found at i:1174728 original size:6 final size:6
Alignment explanation
Indices: 1174717--1174746 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
1174707 GGTTTGAAGA
*
1174717 AGAATT AGAATT AGAATT AAAATT AGAATT
1 AGAATT AGAATT AGAATT AGAATT AGAATT
1174747 TTTCTCTTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.53, C:0.00, G:0.13, T:0.33
Consensus pattern (6 bp):
AGAATT
Found at i:1175782 original size:3 final size:3
Alignment explanation
Indices: 1175774--1175826 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
1175764 TTTCGGTCCC
1175774 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1175822 ATA AT
1 ATA AT
1175827 GTTGTATGAG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1176014 original size:21 final size:22
Alignment explanation
Indices: 1175988--1176035 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
1175978 GATATTTAAA
1175988 AAATTTTATAATTAAAT-ACTT
1 AAATTTTATAATTAAATAACTT
** *
1176009 AAATTTTATTTTTAAATAAGTT
1 AAATTTTATAATTAAATAACTT
1176031 AAATT
1 AAATT
1176036 GATGGATTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 15 0.65
22 8 0.35
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (22 bp):
AAATTTTATAATTAAATAACTT
Found at i:1178144 original size:17 final size:17
Alignment explanation
Indices: 1178122--1178154 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
1178112 AATTTCTCTA
1178122 AATCATATTAATTAATT
1 AATCATATTAATTAATT
1178139 AATCATATTAATTAAT
1 AATCATATTAATTAAT
1178155 AAAATCATCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.45
Consensus pattern (17 bp):
AATCATATTAATTAATT
Found at i:1179424 original size:2 final size:2
Alignment explanation
Indices: 1179417--1179442 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1179407 ATACAAACAC
1179417 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
1179443 GCTGACCAGA
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:1179739 original size:11 final size:11
Alignment explanation
Indices: 1179710--1179775 Score: 51
Period size: 11 Copynumber: 5.6 Consensus size: 11
1179700 AAATTAAAAG
1179710 AAAAATTATAAT
1 AAAAA-TATAAT
* *
1179722 TAAAATATGAT
1 AAAAATATAAT
1179733 AAAAATATAAT
1 AAAAATATAAT
1179744 ATAAATATATCAAT
1 A-AAA-ATAT-AAT
***
1179758 ATTTATATAAT
1 AAAAATATAAT
1179769 AAAAATA
1 AAAAATA
1179776 ATTAACATAT
Statistics
Matches: 41, Mismatches: 10, Indels: 7
0.71 0.17 0.12
Matches are distributed among these distances:
11 22 0.54
12 11 0.27
13 4 0.10
14 4 0.10
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (11 bp):
AAAAATATAAT
Found at i:1180023 original size:23 final size:23
Alignment explanation
Indices: 1179968--1180012 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1179958 ATGAATATAT
* *
1179968 AAATAATAGTAAAAATAATTAAA
1 AAATAAAAATAAAAATAATTAAA
*
1179991 AAATAAAAATAAAAATTATTAA
1 AAATAAAAATAAAAATAATTAA
1180013 TATATTAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (23 bp):
AAATAAAAATAAAAATAATTAAA
Found at i:1180042 original size:91 final size:90
Alignment explanation
Indices: 1179930--1180096 Score: 228
Period size: 91 Copynumber: 1.8 Consensus size: 90
1179920 TTAATGTGAT
* * **
1179930 AATTTACAAAAAATAAAATAAATATAATATGAATATAT-AAATAATAGTAAAAATAATTAAAAAA
1 AATTTACAAAAAATAAAATAAATACAAGAAAAATATATAAAATAATAGTAAAAATAATT--AAAA
1179994 TAAAAATAAAAATTATTAATATATTAA
64 TAAAAATAAAAATTATTAATATATTAA
* * * *
1180021 AATTTATAAAAAATAATATAAATACAAGAAAAATATATAAAATCATAGTAAAACTAATTAAAATA
1 AATTTACAAAAAATAAAATAAATACAAGAAAAATATATAAAATAATAGTAAAAATAATTAAAATA
*
1180086 ATAATAAAAAT
66 AAAATAAAAAT
1180097 GGTGGGAGAA
Statistics
Matches: 66, Mismatches: 9, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
90 16 0.24
91 32 0.48
92 18 0.27
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.29
Consensus pattern (90 bp):
AATTTACAAAAAATAAAATAAATACAAGAAAAATATATAAAATAATAGTAAAAATAATTAAAATA
AAAATAAAAATTATTAATATATTAA
Found at i:1180073 original size:21 final size:20
Alignment explanation
Indices: 1180029--1180096 Score: 59
Period size: 21 Copynumber: 3.3 Consensus size: 20
1180019 AAAATTTATA
1180029 AAAAATAATATAAATACA-AG-
1 AAAAATAATA-AAAT-CATAGT
1180049 AAAAATATATAAAATCATAGT
1 AAAAATA-ATAAAATCATAGT
* * *
1180070 AAAACTAATTAAAATAATAAT
1 AAAAATAA-TAAAATCATAGT
1180091 AAAAAT
1 AAAAAT
1180097 GGTGGGAGAA
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
19 2 0.05
20 14 0.35
21 24 0.60
ACGTcount: A:0.68, C:0.04, G:0.03, T:0.25
Consensus pattern (20 bp):
AAAAATAATAAAATCATAGT
Found at i:1180167 original size:4 final size:4
Alignment explanation
Indices: 1180158--1180191 Score: 61
Period size: 4 Copynumber: 8.8 Consensus size: 4
1180148 ACATCACGCC
1180158 AATA AATA AATA AATA AAT- AATA AATA AATA AAT
1 AATA AATA AATA AATA AATA AATA AATA AATA AAT
1180192 TATTTGCAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 3 0.10
4 26 0.90
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
AATA
Found at i:1180182 original size:15 final size:15
Alignment explanation
Indices: 1180162--1180191 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1180152 CACGCCAATA
1180162 AATAAATAAATAAAT
1 AATAAATAAATAAAT
1180177 AATAAATAAATAAAT
1 AATAAATAAATAAAT
1180192 TATTTGCAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (15 bp):
AATAAATAAATAAAT
Found at i:1183483 original size:2 final size:2
Alignment explanation
Indices: 1183476--1183502 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1183466 ACTCATTTTC
1183476 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 A
1183503 GAACATAAAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1184772 original size:12 final size:12
Alignment explanation
Indices: 1184755--1184779 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1184745 CAACTACGTC
1184755 TAACTCTTAAAG
1 TAACTCTTAAAG
1184767 TAACTCTTAAAG
1 TAACTCTTAAAG
1184779 T
1 T
1184780 TCTTCATTTT
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:0.40, C:0.16, G:0.08, T:0.36
Consensus pattern (12 bp):
TAACTCTTAAAG
Found at i:1184825 original size:12 final size:13
Alignment explanation
Indices: 1184800--1184828 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1184790 TTTTTAAAAA
1184800 AATATTTATATTT
1 AATATTTATATTT
1184813 AATATTTAT-TTT
1 AATATTTATATTT
1184825 AATA
1 AATA
1184829 CATATTCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.44
13 9 0.56
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
AATATTTATATTT
Found at i:1185820 original size:10 final size:10
Alignment explanation
Indices: 1185784--1185889 Score: 53
Period size: 10 Copynumber: 10.7 Consensus size: 10
1185774 TCTGACAATT
*
1185784 TATATATATA
1 TATATTTATA
*
1185794 TATATATATA
1 TATATTTATA
*
1185804 TAGTATTTATG
1 TA-TATTTATA
1185815 TATATTT-TA
1 TATATTTATA
*
1185824 TTATATTTTTA
1 -TATATTTATA
*
1185835 -AAATATTATA
1 TATAT-TTATA
*
1185845 TATA-TAATA
1 TATATTTATA
1185854 -AT-TTTA-A
1 TATATTTATA
1185861 TATATTTATAA
1 TATATTTAT-A
*
1185872 TTTATATTATA
1 TATAT-TTATA
*
1185883 TAAATTT
1 TATATTT
1185890 TAAAATATAT
Statistics
Matches: 74, Mismatches: 11, Indels: 22
0.69 0.10 0.21
Matches are distributed among these distances:
7 1 0.01
8 6 0.08
9 12 0.16
10 30 0.41
11 21 0.28
12 4 0.05
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (10 bp):
TATATTTATA
Found at i:1185861 original size:9 final size:11
Alignment explanation
Indices: 1185781--1185926 Score: 52
Period size: 10 Copynumber: 12.5 Consensus size: 11
1185771 GAGTCTGACA
1185781 ATTTATATATAT
1 ATTTATA-ATAT
1185793 ATATATATATATAGT
1 AT-T-TATA-ATA-T
*
1185808 ATTTAT-GTAT
1 ATTTATAATAT
*
1185818 ATTT-TATTAT
1 ATTTATAATAT
* *
1185828 ATTTTTAAAAT
1 ATTTATAATAT
1185839 ATTATATATATAAT
1 ATT-TATA-AT-AT
1185853 AATTT-TAATAT
1 -ATTTATAATAT
1185864 ATTTATAATTTAT
1 ATTTATAA--TAT
1185877 ATTATATAA-AT
1 ATT-TATAATAT
*
1185888 -TTTAAAATAT
1 ATTTATAATAT
*
1185898 ATATTCATATTAT
1 AT-TT-ATAATAT
*
1185911 A-TTATATTAT
1 ATTTATAATAT
*
1185921 AATTAT
1 ATTTAT
1185927 TTTATAATTA
Statistics
Matches: 107, Mismatches: 9, Indels: 37
0.70 0.06 0.24
Matches are distributed among these distances:
9 5 0.05
10 28 0.26
11 23 0.21
12 9 0.08
13 19 0.18
14 17 0.16
15 6 0.06
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (11 bp):
ATTTATAATAT
Found at i:1185863 original size:16 final size:16
Alignment explanation
Indices: 1185844--1185898 Score: 51
Period size: 17 Copynumber: 3.4 Consensus size: 16
1185834 AAAATATTAT
1185844 ATATATAATAATTTTA
1 ATATATAATAATTTTA
*
1185860 ATATATTTATAATTTATA
1 ATATA-TAATAATTT-TA
*
1185878 TTATAT-A-AATTTTA
1 ATATATAATAATTTTA
*
1185892 AAATATA
1 ATATATA
1185899 TATTCATATT
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
14 6 0.19
15 5 0.16
16 6 0.19
17 9 0.28
18 6 0.19
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
ATATATAATAATTTTA
Found at i:1185897 original size:34 final size:34
Alignment explanation
Indices: 1185826--1185924 Score: 96
Period size: 34 Copynumber: 2.9 Consensus size: 34
1185816 ATATTTTATT
* *
1185826 ATATTTTTAAAATATTATA-TATATAATAATTTTA
1 ATATATTTATAAT-TTATATTATATAATAATTTTA
1185860 ATATATTTATAATTTATATTATAT-A-AATTTTA
1 ATATATTTATAATTTATATTATATAATAATTTTA
* * * *
1185892 AAATATATATTCATATTATATTATATTATAATT
1 ATATATTTA-TAAT-TTATATTATATAATAATT
1185925 ATTTTATAAT
Statistics
Matches: 55, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
32 14 0.25
33 9 0.16
34 27 0.49
35 1 0.02
36 4 0.07
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (34 bp):
ATATATTTATAATTTATATTATATAATAATTTTA
Found at i:1185916 original size:16 final size:16
Alignment explanation
Indices: 1185839--1185939 Score: 61
Period size: 16 Copynumber: 6.4 Consensus size: 16
1185829 TTTTTAAAAT
*
1185839 ATTATA-TATATAATA
1 ATTATATTATATTATA
* *
1185854 ATTTTAATATATTTATA
1 ATTATATTATA-TTATA
1185871 ATTTATATTATA-TA-A
1 A-TTATATTATATTATA
* **
1185886 ATTTTAAAATA-TAT-
1 ATTATATTATATTATA
1185900 ATTCATATTATATTAT-
1 ATT-ATATTATATTATA
*
1185916 ATTATAATTATTTTATA
1 ATTAT-ATTATATTATA
1185933 ATTATAT
1 ATTATAT
1185940 AATAGTGGTT
Statistics
Matches: 67, Mismatches: 11, Indels: 15
0.72 0.12 0.16
Matches are distributed among these distances:
14 12 0.18
15 14 0.21
16 23 0.34
17 10 0.15
18 8 0.12
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (16 bp):
ATTATATTATATTATA
Found at i:1188000 original size:19 final size:19
Alignment explanation
Indices: 1187976--1188013 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
1187966 ACATAGATAT
1187976 AAAGATATAATCTTTTAAA
1 AAAGATATAATCTTTTAAA
1187995 AAAGATATAATCTTTTAAA
1 AAAGATATAATCTTTTAAA
1188014 GATTTTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.37
Consensus pattern (19 bp):
AAAGATATAATCTTTTAAA
Found at i:1189476 original size:13 final size:15
Alignment explanation
Indices: 1189460--1189496 Score: 53
Period size: 13 Copynumber: 2.7 Consensus size: 15
1189450 TTTTATATCG
1189460 AATATAAATA-TT-A
1 AATATAAATACTTCA
1189473 AATATAAATACTTCA
1 AATATAAATACTTCA
1189488 AA-ATAAATA
1 AATATAAATA
1189497 AAATCTAAGC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 10 0.45
14 9 0.41
15 3 0.14
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.32
Consensus pattern (15 bp):
AATATAAATACTTCA
Found at i:1190080 original size:24 final size:23
Alignment explanation
Indices: 1190052--1190099 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 23
1190042 AAAATATATA
*
1190052 TTAAATGTATTATATTAATTATTT
1 TTAAATATATTATATTAATT-TTT
*
1190076 TTAAATATATTATATTTATTTTT
1 TTAAATATATTATATTAATTTTT
1190099 T
1 T
1190100 ATTTTTATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 4 0.18
24 18 0.82
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.62
Consensus pattern (23 bp):
TTAAATATATTATATTAATTTTT
Found at i:1191246 original size:3 final size:3
Alignment explanation
Indices: 1191238--1191281 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
1191228 TCAAGTTCGT
1191238 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1191282 TCCTGTTTTC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1193586 original size:2 final size:2
Alignment explanation
Indices: 1193581--1193613 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1193571 CCTATAACCT
*
1193581 TC TC TC TC AC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1193614 ATATATATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.03, C:0.48, G:0.00, T:0.48
Consensus pattern (2 bp):
TC
Found at i:1193618 original size:2 final size:2
Alignment explanation
Indices: 1193613--1193641 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1193603 TCTCTCTCTC
1193613 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 T
1193642 TTCTTTAGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1195569 original size:3 final size:3
Alignment explanation
Indices: 1195561--1195590 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
1195551 TTAAAAACCT
1195561 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1195591 AACATGCACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1197761 original size:12 final size:11
Alignment explanation
Indices: 1197720--1197760 Score: 50
Period size: 12 Copynumber: 3.8 Consensus size: 11
1197710 CGAAAATTTG
1197720 ATATTATTTAA
1 ATATTATTTAA
1197731 ATTATTATTTAA
1 A-TATTATTTAA
*
1197743 A-AAT-TTTAA
1 ATATTATTTAA
1197752 ATATTATTT
1 ATATTATTT
1197761 TTATATTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
9 6 0.24
10 4 0.16
11 4 0.16
12 11 0.44
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
ATATTATTTAA
Found at i:1198655 original size:25 final size:25
Alignment explanation
Indices: 1198622--1198673 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
1198612 TTATGTTACG
*
1198622 TTTGGTTTATTAAAGTGAAATAAAA
1 TTTGATTTATTAAAGTGAAATAAAA
*
1198647 TTTGATTTATTGAAGTGAAATAAAA
1 TTTGATTTATTAAAGTGAAATAAAA
1198672 TT
1 TT
1198674 ATAATGGAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.42, C:0.00, G:0.15, T:0.42
Consensus pattern (25 bp):
TTTGATTTATTAAAGTGAAATAAAA
Found at i:1199571 original size:28 final size:29
Alignment explanation
Indices: 1199532--1199594 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 29
1199522 TTACTTTTTC
* *
1199532 AAATAAATTTTTATATTTTTA-TTATATTT
1 AAATAGATTTTTA-CTTTTTATTTATATTT
*
1199561 AAATAGATTTTTACTTTTTATTTGTATTT
1 AAATAGATTTTTACTTTTTATTTATATTT
1199590 AAATA
1 AAATA
1199595 TTGATTTACG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
28 6 0.20
29 24 0.80
ACGTcount: A:0.37, C:0.02, G:0.03, T:0.59
Consensus pattern (29 bp):
AAATAGATTTTTACTTTTTATTTATATTT
Found at i:1200740 original size:150 final size:152
Alignment explanation
Indices: 1200477--1200759 Score: 410
Period size: 150 Copynumber: 1.9 Consensus size: 152
1200467 CCCAAATACA
1200477 AAATCTCTTTTGATTTGCTATTAGCATTCAATCGATTCTCCGAAAAAAAAAATATAAACAGTAAA
1 AAATCTCTTTTGATTTGCTATTAGCATTCAATCGATTCT-C--AAAAAAAAATATAAACAGTAAA
* ** *
1200542 TTTCAAACTTAATTTTATTAATTCATACGGTCATTATTAAAAAAATAATATTTAACAACTTTTAA
63 TTTCAAACTTAATTCTATTAATTCATACAATCATTATTAAAAAAATAATATTTAACAACTTTAAA
1200607 ATTGTCACATCAAAGTTCACATATG
128 ATTGTCACATCAAAGTTCACATATG
* * *
1200632 AAATCTCTTTTGATTTGTTATTAGCATTTAATCGATTCAT-AAAAAAAAATAT-AATA-TAAATT
1 AAATCTCTTTTGATTTGCTATTAGCATTCAATCGATTC-TCAAAAAAAAATATAAACAGTAAATT
* * * *
1200694 TCGAACTTAATTCTATTAATTTATACAATCATTATTAAAGAGATAATATTTAACAACTTTAAAAT
65 TCAAACTTAATTCTATTAATTCATACAATCATTATTAAAAAAATAATATTTAACAACTTTAAAAT
1200759 T
130 T
1200760 CGAATTTTAA
Statistics
Matches: 116, Mismatches: 11, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
150 64 0.55
151 3 0.03
152 12 0.10
155 36 0.31
156 1 0.01
ACGTcount: A:0.43, C:0.12, G:0.06, T:0.39
Consensus pattern (152 bp):
AAATCTCTTTTGATTTGCTATTAGCATTCAATCGATTCTCAAAAAAAAATATAAACAGTAAATTT
CAAACTTAATTCTATTAATTCATACAATCATTATTAAAAAAATAATATTTAACAACTTTAAAATT
GTCACATCAAAGTTCACATATG
Found at i:1204077 original size:29 final size:31
Alignment explanation
Indices: 1204043--1204108 Score: 77
Period size: 29 Copynumber: 2.2 Consensus size: 31
1204033 ACTTTTTTTA
*
1204043 AAATAAAATT-TTGTACTTTT-ATTT-TACTT
1 AAATAAAATTCTTAT-CTTTTAATTTATACTT
*
1204072 AAAT-AAATTCTTATCTTTTAATTTATATTT
1 AAATAAAATTCTTATCTTTTAATTTATACTT
1204102 AAATAAA
1 AAATAAA
1204109 CCATTGTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
28 10 0.32
29 11 0.35
30 8 0.26
31 2 0.06
ACGTcount: A:0.41, C:0.06, G:0.02, T:0.52
Consensus pattern (31 bp):
AAATAAAATTCTTATCTTTTAATTTATACTT
Found at i:1204198 original size:30 final size:30
Alignment explanation
Indices: 1204164--1204242 Score: 97
Period size: 30 Copynumber: 2.6 Consensus size: 30
1204154 AAAGTATAAA
**
1204164 TTAAAAATTTATTTGAA-TGCAAATTAAAAG
1 TTAAAAATTTATTT-AAGTAAAAATTAAAAG
1204194 TTAAAAATTTATTTAAGTAAAAATTAAAAG
1 TTAAAAATTTATTTAAGTAAAAATTAAAAG
* * *
1204224 TTAGAAGTTTATTTTAGTA
1 TTAAAAATTTATTTAAGTA
1204243 TAATAAAAGT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
29 2 0.05
30 41 0.95
ACGTcount: A:0.48, C:0.01, G:0.10, T:0.41
Consensus pattern (30 bp):
TTAAAAATTTATTTAAGTAAAAATTAAAAG
Found at i:1207081 original size:21 final size:22
Alignment explanation
Indices: 1207057--1207102 Score: 60
Period size: 24 Copynumber: 2.1 Consensus size: 22
1207047 GATTTAATTT
1207057 AAATTA-TT-ATTTAATAATAAA
1 AAATTATTTAATTTAATAA-AAA
1207078 AAATTATTTAAATTTAATAAAAA
1 AAATTATTT-AATTTAATAAAAA
1207101 AA
1 AA
1207103 TATAAATATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 6 0.27
22 2 0.09
23 5 0.23
24 9 0.41
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (22 bp):
AAATTATTTAATTTAATAAAAA
Found at i:1207114 original size:20 final size:20
Alignment explanation
Indices: 1207071--1207122 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
1207061 TATTATTTAA
*
1207071 TAATAAAAAATTATTTAAATT
1 TAATAAAAAA-TATATAAATT
1207092 TAATAAAAAA-ATATAAATAT
1 TAATAAAAAATATATAAAT-T
*
1207112 TAATATAAAAT
1 TAATAAAAAAT
1207123 TAATATTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 7 0.26
20 10 0.37
21 10 0.37
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
TAATAAAAAATATATAAATT
Found at i:1207121 original size:21 final size:22
Alignment explanation
Indices: 1207057--1207121 Score: 68
Period size: 21 Copynumber: 3.0 Consensus size: 22
1207047 GATTTAATTT
1207057 AAATTATT--ATTTAATAATAAA
1 AAATTATTAAATTTAAT-ATAAA
1207078 AAATTATTTAAATTTAATA-AAA
1 AAATTA-TTAAATTTAATATAAA
1207100 AAA-TA-TAAATATTAATATAAA
1 AAATTATTAAAT-TTAATATAAA
1207121 A
1 A
1207122 TTAATATTTA
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
19 5 0.13
20 6 0.15
21 12 0.31
22 8 0.21
23 1 0.03
24 7 0.18
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
AAATTATTAAATTTAATATAAA
Found at i:1207298 original size:16 final size:16
Alignment explanation
Indices: 1207253--1207298 Score: 58
Period size: 15 Copynumber: 2.8 Consensus size: 16
1207243 TATTTGATAT
1207253 AAATATATTTAATTTAAA
1 AAATATATTT-A-TTAAA
*
1207271 AAAT-TATATATTAAA
1 AAATATATTTATTAAA
1207286 AAATATATTTATT
1 AAATATATTTATT
1207299 TTTATATTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
15 9 0.36
16 8 0.32
17 4 0.16
18 4 0.16
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
AAATATATTTATTAAA
Found at i:1207936 original size:23 final size:23
Alignment explanation
Indices: 1207910--1207964 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
1207900 AAGTTAAAGA
1207910 TATATTTTTTATTAATTATAA-AT
1 TATATTTTTTATTAATT-TAATAT
** *
1207933 TATATTTAATATTTATTTAATAT
1 TATATTTTTTATTAATTTAATAT
1207956 TA-ATTTTTT
1 TATATTTTTT
1207965 TAAATATTAA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
22 8 0.31
23 18 0.69
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (23 bp):
TATATTTTTTATTAATTTAATAT
Found at i:1207972 original size:16 final size:17
Alignment explanation
Indices: 1207938--1207974 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
1207928 TAAATTATAT
1207938 TTAATATTTATTTAATA
1 TTAATATTTATTTAATA
1207955 TTAAT-TTT-TTTAAATA
1 TTAATATTTATTT-AATA
1207971 TTAA
1 TTAA
1207975 AAAAATTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 3 0.16
16 11 0.58
17 5 0.26
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TTAATATTTATTTAATA
Found at i:1210798 original size:3 final size:3
Alignment explanation
Indices: 1210790--1210827 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
1210780 AAAAGAAGCC
1210790 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1210828 GATTCAGATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1215702 original size:6 final size:6
Alignment explanation
Indices: 1215687--1215719 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
1215677 AAATTCACAC
*
1215687 AAAAAA AAAAAG AAAAAG AAAAAG AAAAAG AAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAA
1215720 TCAACCCAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:1216357 original size:16 final size:16
Alignment explanation
Indices: 1216336--1216376 Score: 82
Period size: 16 Copynumber: 2.6 Consensus size: 16
1216326 TCTTTAAGCT
1216336 TCAAATTTTGAAGTTC
1 TCAAATTTTGAAGTTC
1216352 TCAAATTTTGAAGTTC
1 TCAAATTTTGAAGTTC
1216368 TCAAATTTT
1 TCAAATTTT
1216377 TTTATTATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.32, C:0.12, G:0.10, T:0.46
Consensus pattern (16 bp):
TCAAATTTTGAAGTTC
Found at i:1217035 original size:5 final size:5
Alignment explanation
Indices: 1217018--1217088 Score: 67
Period size: 5 Copynumber: 14.0 Consensus size: 5
1217008 ATAAATGTAA
* *
1217018 TAATT TAAAT TAATT TAATT TAAATT ATAA-- AAATT TAATT TAAATT
1 TAATT TAATT TAATT TAATT T-AATT -TAATT TAATT TAATT T-AATT
1217064 TAATT TAATT TAAATT TAA-T TAATT
1 TAATT TAATT T-AATT TAATT TAATT
1217089 AAATAATTCA
Statistics
Matches: 55, Mismatches: 4, Indels: 14
0.75 0.05 0.19
Matches are distributed among these distances:
3 2 0.04
4 4 0.07
5 32 0.58
6 16 0.29
7 1 0.02
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (5 bp):
TAATT
Found at i:1217038 original size:15 final size:16
Alignment explanation
Indices: 1217018--1217092 Score: 93
Period size: 16 Copynumber: 4.6 Consensus size: 16
1217008 ATAAATGTAA
1217018 TAATTTAAA-TTAATT
1 TAATTTAAATTTAATT
1217033 TAATTTAAATTATAAAAATT
1 TAATTTAAATT-T---AATT
1217053 TAATTTAAATTTAATT
1 TAATTTAAATTTAATT
1217069 TAATTTAAATTTAA-T
1 TAATTTAAATTTAATT
1217084 TAA-TTAAAT
1 TAATTTAAAT
1217093 AATTCAAAGT
Statistics
Matches: 55, Mismatches: 0, Indels: 11
0.83 0.00 0.17
Matches are distributed among these distances:
14 6 0.11
15 13 0.24
16 19 0.35
17 1 0.02
19 1 0.02
20 15 0.27
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
TAATTTAAATTTAATT
Found at i:1217084 original size:11 final size:11
Alignment explanation
Indices: 1217019--1217082 Score: 66
Period size: 11 Copynumber: 6.1 Consensus size: 11
1217009 TAAATGTAAT
*
1217019 AATTTAAATT-
1 AATTTAATTTA
1217029 AATTTAATTTA
1 AATTTAATTTA
1217040 AATTATAA---A
1 AATT-TAATTTA
1217049 AATTTAATTTA
1 AATTTAATTTA
1217060 AATTTAATTT-
1 AATTTAATTTA
1217070 AATTTAAATTTA
1 AATTT-AATTTA
1217082 A
1 A
1217083 TTAATTAAAT
Statistics
Matches: 46, Mismatches: 1, Indels: 12
0.78 0.02 0.20
Matches are distributed among these distances:
8 3 0.07
9 5 0.11
10 14 0.30
11 20 0.43
12 4 0.09
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (11 bp):
AATTTAATTTA
Found at i:1217346 original size:21 final size:23
Alignment explanation
Indices: 1217316--1217367 Score: 63
Period size: 21 Copynumber: 2.3 Consensus size: 23
1217306 CTCTGAATTT
* *
1217316 TATTAATTAATATT-TTAAA-AA
1 TATTATTTAAAATTATTAAATAA
1217337 TATTATTTAAAATTATTAAATAA
1 TATTATTTAAAATTATTAAATAA
*
1217360 TAATATTT
1 TATTATTT
1217368 TATTTAATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 12 0.46
22 5 0.19
23 9 0.35
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
TATTATTTAAAATTATTAAATAA
Found at i:1217367 original size:23 final size:21
Alignment explanation
Indices: 1217322--1217367 Score: 56
Period size: 23 Copynumber: 2.1 Consensus size: 21
1217312 ATTTTATTAA
* *
1217322 TTAATATTTTAAAAATATTAT
1 TTAAAATTTTAAAAATAATAT
1217343 TTAAAATTATTAAATAATAATAT
1 TTAAAATT-TTAAA-AATAATAT
1217366 TT
1 TT
1217368 TATTTAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 7 0.33
22 5 0.24
23 9 0.43
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TTAAAATTTTAAAAATAATAT
Found at i:1218549 original size:21 final size:21
Alignment explanation
Indices: 1218525--1218616 Score: 70
Period size: 22 Copynumber: 4.5 Consensus size: 21
1218515 TATTTGAGGT
1218525 TTATATTTAATTTAATATAAA
1 TTATATTTAATTTAATATAAA
1218546 TTATTATTTAA-TTAATA-AAA
1 TTA-TATTTAATTTAATATAAA
* *
1218566 --AAATTAAATTTAATTATAAA
1 TTATATTTAATTTAA-TATAAA
* *
1218586 ATATA-TAAATATTAATATAAAA
1 TTATATTTAAT-TTAATAT-AAA
1218608 TTA-ATTTAA
1 TTATATTTAA
1218617 ATATTATAAT
Statistics
Matches: 57, Mismatches: 5, Indels: 17
0.72 0.06 0.22
Matches are distributed among these distances:
17 5 0.09
18 5 0.09
19 2 0.04
20 6 0.11
21 18 0.32
22 21 0.37
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
TTATATTTAATTTAATATAAA
Found at i:1218621 original size:23 final size:22
Alignment explanation
Indices: 1218553--1218622 Score: 72
Period size: 21 Copynumber: 3.1 Consensus size: 22
1218543 AAATTATTAT
* *
1218553 TTAATTAATAAAAAAATTAAAT-
1 TTAATT-ATAAAATATTTAAATA
*
1218575 TTAATTATAAAATATATAAATA
1 TTAATTATAAAATATTTAAATA
1218597 TTAA-TATAAAATTAATTTAAATA
1 TTAATTATAAAA-T-ATTTAAATA
1218620 TTA
1 TTA
1218623 TAATATATTT
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
21 19 0.46
22 11 0.27
23 11 0.27
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
TTAATTATAAAATATTTAAATA
Found at i:1218646 original size:19 final size:18
Alignment explanation
Indices: 1218532--1218652 Score: 59
Period size: 19 Copynumber: 6.3 Consensus size: 18
1218522 GGTTTATATT
*
1218532 TAATTT-AATATAAATTA
1 TAATTTAAATATAAAATA
* * *
1218549 TTATTTAATTAATAAAAAAA
1 TAATTTAAAT-AT-AAAATA
*
1218569 TTAAATTTAATTATAAAATATA
1 -T-AATTTAAATAT-AAA-ATA
1218591 TAAATATT-AATATAAAAT-
1 T-AAT-TTAAATATAAAATA
*
1218609 TAATTTAAATATTATAATA
1 TAATTTAAATA-TAAAATA
*
1218628 TATTTTAAATAGTAAAATA
1 TAATTTAAATA-TAAAATA
*
1218647 AAATTT
1 TAATTT
1218653 TCAAACTTAA
Statistics
Matches: 81, Mismatches: 13, Indels: 18
0.72 0.12 0.16
Matches are distributed among these distances:
16 2 0.02
17 12 0.15
18 8 0.10
19 24 0.30
20 7 0.09
21 16 0.20
22 12 0.15
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (18 bp):
TAATTTAAATATAAAATA
Found at i:1220620 original size:22 final size:22
Alignment explanation
Indices: 1220594--1220639 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
1220584 TCATAATTTC
*
1220594 AAAATAAAACCTAAATCGACAT
1 AAAATAAAACCTAAACCGACAT
1220616 AAAATAAAACCTAAACCGACAT
1 AAAATAAAACCTAAACCGACAT
1220638 AA
1 AA
1220640 CTTACTGAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.61, C:0.20, G:0.04, T:0.15
Consensus pattern (22 bp):
AAAATAAAACCTAAACCGACAT
Found at i:1224163 original size:21 final size:20
Alignment explanation
Indices: 1224121--1224167 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
1224111 GGTTAAAATA
1224121 TTATATATTTATATAATTTT
1 TTATATATTTATATAATTTT
*
1224141 TTGATATATTTATA-ATTTATT
1 TT-ATATATTTATATAATT-TT
1224162 TTATAT
1 TTATAT
1224168 GAATTTTAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
20 9 0.38
21 15 0.62
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (20 bp):
TTATATATTTATATAATTTT
Found at i:1224499 original size:33 final size:34
Alignment explanation
Indices: 1224457--1224529 Score: 87
Period size: 32 Copynumber: 2.2 Consensus size: 34
1224447 TATTTTCAAG
1224457 TTATATTTATACAAATTTTTAAGATATTAATA-AT
1 TTATATTTATACAAA-TTTTAAGATATTAATATAT
** * *
1224491 TTAT-TTTATATTAATTTTAATATATTTATATAT
1 TTATATTTATACAAATTTTAAGATATTAATATAT
1224524 TTATAT
1 TTATAT
1224530 ATTTATATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
32 14 0.42
33 14 0.42
34 5 0.15
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.58
Consensus pattern (34 bp):
TTATATTTATACAAATTTTAAGATATTAATATAT
Found at i:1224523 original size:8 final size:8
Alignment explanation
Indices: 1224510--1224550 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
1224500 ATTAATTTTA
1224510 ATATATTT
1 ATATATTT
1224518 ATATATTT
1 ATATATTT
1224526 ATATATTT
1 ATATATTT
*
1224534 ATATTTTT
1 ATATATTT
*
1224542 TTAT-TTT
1 ATATATTT
1224549 AT
1 AT
1224551 GTCATATTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
7 4 0.13
8 26 0.87
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (8 bp):
ATATATTT
Found at i:1224528 original size:14 final size:15
Alignment explanation
Indices: 1224497--1224539 Score: 52
Period size: 16 Copynumber: 2.9 Consensus size: 15
1224487 TAATTTATTT
*
1224497 TATATTAAT-TTTAA
1 TATATTTATATTTAA
*
1224511 TATATTTATATATTTA
1 TATATTTATAT-TTAA
1224527 TATATTTATATTT
1 TATATTTATATTT
1224540 TTTTATTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 8 0.32
15 3 0.12
16 14 0.56
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TATATTTATATTTAA
Found at i:1224980 original size:28 final size:26
Alignment explanation
Indices: 1224918--1224980 Score: 65
Period size: 28 Copynumber: 2.3 Consensus size: 26
1224908 TTATATACAT
1224918 TTTAA-TATTTTTTATTCATATTATA
1 TTTAATTATTTTTTATTCATATTATA
* * *
1224943 TTTATGTTATTTTTTATTTTATTTTATAA
1 TTTA-ATTATTTTTTA-TTCATATTAT-A
1224972 TTTAATTAT
1 TTTAATTAT
1224981 ATTTCGTATC
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
25 4 0.13
27 9 0.30
28 12 0.40
29 5 0.17
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.68
Consensus pattern (26 bp):
TTTAATTATTTTTTATTCATATTATA
Found at i:1225548 original size:29 final size:32
Alignment explanation
Indices: 1225506--1225578 Score: 91
Period size: 29 Copynumber: 2.4 Consensus size: 32
1225496 TTTAGATATA
* *
1225506 ATTATTTATGTATTTAT-ATCATATTTAAA-T
1 ATTATTTATTTATTTATAATAATATTTAAAGT
1225536 ATT-TTTATTTA-TTATAATAATATTTAAAGT
1 ATTATTTATTTATTTATAATAATATTTAAAGT
*
1225566 ATTATATATTTAT
1 ATTATTTATTTAT
1225579 ATAAATTTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
28 4 0.11
29 18 0.50
30 7 0.19
31 7 0.19
ACGTcount: A:0.38, C:0.01, G:0.03, T:0.58
Consensus pattern (32 bp):
ATTATTTATTTATTTATAATAATATTTAAAGT
Found at i:1226307 original size:21 final size:23
Alignment explanation
Indices: 1226269--1226319 Score: 61
Period size: 21 Copynumber: 2.3 Consensus size: 23
1226259 TAAAATATTA
*
1226269 TATATAAAATTATATTTTAATTT
1 TATATAAAATTATATTTTAAATT
*
1226292 TATATTAAA-TAT-TTTTAAATT
1 TATATAAAATTATATTTTAAATT
*
1226313 TAAATAA
1 TATATAA
1226320 TTTTTTATTA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 13 0.54
22 3 0.12
23 8 0.33
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (23 bp):
TATATAAAATTATATTTTAAATT
Found at i:1226332 original size:15 final size:15
Alignment explanation
Indices: 1226286--1226335 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
1226276 AATTATATTT
*
1226286 TAATTTTATATTAAA
1 TAATTTTTTATTAAA
*
1226301 T-ATTTTTAAATTTAAA
1 TAATTTTT-TA-TTAAA
1226317 TAATTTTTTATTAAA
1 TAATTTTTTATTAAA
1226332 TAAT
1 TAAT
1226336 AATTTAAATC
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
14 5 0.17
15 11 0.38
16 7 0.24
17 6 0.21
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TAATTTTTTATTAAA
Found at i:1226576 original size:13 final size:13
Alignment explanation
Indices: 1226558--1226583 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1226548 ATATCTACTT
1226558 AATAATAAATATA
1 AATAATAAATATA
1226571 AATAATAAATATA
1 AATAATAAATATA
1226584 GTCATTATTA
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AATAATAAATATA
Found at i:1226859 original size:16 final size:16
Alignment explanation
Indices: 1226840--1226921 Score: 64
Period size: 16 Copynumber: 5.1 Consensus size: 16
1226830 ATTTTAAAAA
1226840 ATAATTAAAATATAAT
1 ATAATTAAAATATAAT
1226856 ATAATATAAAA-ATAAT
1 ATAAT-TAAAATATAAT
* *
1226872 ATAAAT-ATATATAA-
1 ATAATTAAAATATAAT
*
1226886 ATATATTAAAAT-TTAT
1 ATA-ATTAAAATATAAT
*
1226902 ATAATATAAAGTATTAAT
1 ATAAT-TAAAATA-TAAT
1226920 AT
1 AT
1226922 TTTAAAAATT
Statistics
Matches: 51, Mismatches: 7, Indels: 14
0.71 0.10 0.19
Matches are distributed among these distances:
14 5 0.10
15 11 0.22
16 25 0.49
17 5 0.10
18 5 0.10
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (16 bp):
ATAATTAAAATATAAT
Found at i:1226870 original size:27 final size:27
Alignment explanation
Indices: 1226836--1226890 Score: 78
Period size: 27 Copynumber: 2.0 Consensus size: 27
1226826 ATTAATTTTA
1226836 AAAAATAAT-TAAA-ATATAATATAATAT
1 AAAAATAATATAAATATAT-ATA-AATAT
1226863 AAAAATAATATAAATATATATAAATAT
1 AAAAATAATATAAATATATATAAATAT
1226890 A
1 A
1226891 TTAAAATTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
27 15 0.58
28 7 0.27
29 4 0.15
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (27 bp):
AAAAATAATATAAATATATATAAATAT
Found at i:1226921 original size:32 final size:35
Alignment explanation
Indices: 1226867--1226943 Score: 90
Period size: 32 Copynumber: 2.3 Consensus size: 35
1226857 TAATATAAAA
*
1226867 ATAATATAAATATATATAAATATATTAAAATTTAT
1 ATAATATAAATATATATAAATATATTAAAAATTAT
* *
1226902 ATAATATAAA-GTAT-T-AATATTTTAAAAATTAT
1 ATAATATAAATATATATAAATATATTAAAAATTAT
1226934 ATGAA-ATAAA
1 AT-AATATAAA
1226944 ATCAAAAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
32 22 0.58
33 3 0.08
34 3 0.08
35 10 0.26
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (35 bp):
ATAATATAAATATATATAAATATATTAAAAATTAT
Found at i:1226923 original size:24 final size:23
Alignment explanation
Indices: 1226854--1226923 Score: 63
Period size: 24 Copynumber: 3.0 Consensus size: 23
1226844 TTAAAATATA
* **
1226854 ATATAATATAAA-AATAATATAA
1 ATATAATATAAATATTAATATTT
*
1226876 ATAT-ATATAAATATATTAAAATTT
1 ATATAATAT-AA-ATATTAATATTT
1226900 ATATAATATAAAGTATTAATATTT
1 ATATAATATAAA-TATTAATATTT
1226924 TAAAAATTAT
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
21 4 0.11
22 6 0.16
23 2 0.05
24 22 0.58
25 4 0.11
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.41
Consensus pattern (23 bp):
ATATAATATAAATATTAATATTT
Found at i:1227008 original size:23 final size:21
Alignment explanation
Indices: 1226981--1227033 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
1226971 GTAATTACTC
1226981 TTAAAAATTAATATTTAATATAT
1 TTAAAAATTAA-ATTTAA-ATAT
* *
1227004 TTAAAATTTAAATTTCAATAT
1 TTAAAAATTAAATTTAAATAT
*
1227025 TTATAAATT
1 TTAAAAATT
1227034 TTTTTTCGTC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 11 0.42
22 5 0.19
23 10 0.38
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (21 bp):
TTAAAAATTAAATTTAAATAT
Found at i:1227009 original size:22 final size:20
Alignment explanation
Indices: 1226984--1227033 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 20
1226974 ATTACTCTTA
1226984 AAAATTAATATTTAATATATTT
1 AAAATTAA-ATTTAA-ATATTT
*
1227006 AAAATTTAAATTTCAATATTT
1 AAAA-TTAAATTTAAATATTT
1227027 ATAAATT
1 A-AAATT
1227034 TTTTTTCGTC
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 9 0.36
22 12 0.48
23 4 0.16
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (20 bp):
AAAATTAAATTTAAATATTT
Found at i:1228451 original size:11 final size:11
Alignment explanation
Indices: 1228435--1228462 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
1228425 TTATAATTTA
1228435 AATTTTAAAAT
1 AATTTTAAAAT
1228446 AATTTTAAAAT
1 AATTTTAAAAT
1228457 AATTTT
1 AATTTT
1228463 TTTTATTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (11 bp):
AATTTTAAAAT
Found at i:1228518 original size:36 final size:36
Alignment explanation
Indices: 1228469--1228557 Score: 101
Period size: 36 Copynumber: 2.4 Consensus size: 36
1228459 TTTTTTTTAT
*
1228469 TATTTTTAATATTATTTAACATAAAT-TAAATTTTAATA
1 TATTTTT--TATTATTTAACATAAGTAT-AATTTTAATA
* *
1228507 TATTTTTTATTATTTAATATAAGTATGATTTTAATA
1 TATTTTTTATTATTTAACATAAGTATAATTTTAATA
*
1228543 -ATTTTTAATTATTTA
1 TATTTTTTATTATTTA
1228558 TTATATATTT
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
35 14 0.30
36 24 0.52
37 1 0.02
38 7 0.15
ACGTcount: A:0.39, C:0.01, G:0.02, T:0.57
Consensus pattern (36 bp):
TATTTTTTATTATTTAACATAAGTATAATTTTAATA
Found at i:1229084 original size:173 final size:173
Alignment explanation
Indices: 1228795--1230527 Score: 3439
Period size: 173 Copynumber: 10.0 Consensus size: 173
1228785 TTTTTCTTTT
1228795 TTTTTTTTTTAAATCTTCATAAATCTCTACACATTTTCCATTTATGTTATGTTCAGTCATAATCT
1 TTTTTTTTTTAAATCTTCATAAATCTCTACACATTTTCCATTTATGTTATGTTCAGTCATAATCT
1228860 CTTTGAGGTTCTGTGTTTACGTGTAAATTCCTGCACTCCTTTGCATACTGAAACAAAAGCATGGT
66 CTTTGAGGTTCTGTGTTTACGTGTAAATTCCTGCACTCCTTTGCATACTGAAACAAAAGCATGGT
1228925 GTTCTAACATTTCTTTATAACTAGATCAGATTTGAGTTGGGTG
131 GTTCTAACATTTCTTTATAACTAGATCAGATTTGAGTTGGGTG
1228968 TTTTTTTTTTAAATCTTCATAAATCTCTACACATTTTCCATTTATGTTATGTTCAGTCATAATCT
1 TTTTTTTTTTAAATCTTCATAAATCTCTACACATTTTCCATTTATGTTATGTTCAGTCATAATCT
1229033 CTTTGAGGTTCTGTGTTTACGTGTAAATTCCTGCACTCCTTTGCATACTGAAACAAAAGCATGGT
66 CTTTGAGGTTCTGTGTTTACGTGTAAATTCCTGCACTCCTTTGCATACTGAAACAAAAGCATGGT
1229098 GTTCTAACATTTCTTTATAACTAGATCAGATTTGAGTTGGGTG
131 GTTCTAACATTTCTTTATAACTAGATCAGATTTGAGTTGGGTG
1229141 TTTTTTTTTTAAATCTTCATAAATCTCTACACATTTTCCATTTATGTTATGTTCAGTCATAATCT
1 TTTTTTTTTTAAATCTTCATAAATCTCTACACATTTTCCATTTATGTTATGTTCAGTCATAATCT
1229206 CTTTGAGGTTCTGTGTTTACGTGTAAATTCCTGCACTCCTTTGCATACTGAAACAAAAGCATGGT
66 CTTTGAGGTTCTGTGTTTACGTGTAAATTCCTGCACTCCTTTGCATACTGAAACAAAAGCATGGT
1229271 GTTCTAACATTTCTTTATAACTAGATCAGATTTGAGTTGGGTG
131 GTTCTAACATTTCTTTATAACTAGATCAGATTTGAGTTGGGTG
1229314 TTTTTTTTTTAAATCTTCATAAATCTCTACACATTTTCCATTTATGTTATGTTCAGTCATAATCT
1 TTTTTTTTTTAAATCTTCATAAATCTCTACACATTTTCCATTTATGTTATGTTCAGTCATAATCT
1229379 CTTTGAGGTTCTGTGTTTACGTGTAAATTCCTGCACTCCTTTGCATACTGAAACAAAAGCATGGT
66 CTTTGAGGTTCTGTGTTTACGTGTAAATTCCTGCACTCCTTTGCATACTGAAACAAAAGCATGGT
1229444 GTTCTAACATTTCTTTATAACTAGATCAGATTTGAGTTGGGTG
131 GTTCTAACATTTCTTTATAACTAGATCAGATTTGAGTTGGGTG
*
1229487 TTTTTTTTTTAAATCTTCATAAATCTCTACACATTTTCCTTTTATGTTATGTTCAGTCATAATCT
1 TTTTTTTTTTAAATCTTCATAAATCTCTACACATTTTCCATTTATGTTATGTTCAGTCATAATCT
1229552 CTTTGAGGTTCTGTGTTTACGTGTAAATTCCTGCACTCCTTTGCATACTGAAACAAAAGCATGGT
66 CTTTGAGGTTCTGTGTTTACGTGTAAATTCCTGCACTCCTTTGCATACTGAAACAAAAGCATGGT
1229617 GTTCTAACATTTCTTTATAACTAGATCAGATTTGAGTTGGGTG
131 GTTCTAACATTTCTTTATAACTAGATCAGATTTGAGTTGGGTG
1229660 TTTTTTTTTTAAATCTTCATAAATCTCTACACATTTTCCATTTATGTTATGTTCAGTCATAATCT
1 TTTTTTTTTTAAATCTTCATAAATCTCTACACATTTTCCATTTATGTTATGTTCAGTCATAATCT
1229725 CTTTGAGGTTCTGTGTTTACGTGTAAATTCCTGCACTCCTTTGCATACTGAAACAAAAGCATGGT
66 CTTTGAGGTTCTGTGTTTACGTGTAAATTCCTGCACTCCTTTGCATACTGAAACAAAAGCATGGT
1229790 GTTCTAACATTTCTTTATAACTAGATCAGATTTGAGTTGGGTG
131 GTTCTAACATTTCTTTATAACTAGATCAGATTTGAGTTGGGTG
1229833 TTTTTTTTTTAAATCTTCATAAATCTCTACACATTTTCCATTTATGTTATGTTCAGTCATAATCT
1 TTTTTTTTTTAAATCTTCATAAATCTCTACACATTTTCCATTTATGTTATGTTCAGTCATAATCT
1229898 CTTTGAGGTTCTGTGTTTACGTGTAAATTCCTGCACTCCTTTGCATACTGAAACAAAAGCATGGT
66 CTTTGAGGTTCTGTGTTTACGTGTAAATTCCTGCACTCCTTTGCATACTGAAACAAAAGCATGGT
1229963 GTTCTAACATTTCTTTATAACTAGATCAGATTTGAGTTGGGTG
131 GTTCTAACATTTCTTTATAACTAGATCAGATTTGAGTTGGGTG
*
1230006 TTTTTTTTTTAAATCTTCATAAATCTCTACACATTTTCCTTTTATGTTATGTTCAGTCATAATCT
1 TTTTTTTTTTAAATCTTCATAAATCTCTACACATTTTCCATTTATGTTATGTTCAGTCATAATCT
1230071 CTTTGAGGTTCTGTGTTTACGTGTAAATTCCTGCACTCCTTTGCATACTGAAACAAAAGCATGGT
66 CTTTGAGGTTCTGTGTTTACGTGTAAATTCCTGCACTCCTTTGCATACTGAAACAAAAGCATGGT
1230136 GTTCTAACATTTCTTTATAACTAGATCAGATTTGAGTTGGGTG
131 GTTCTAACATTTCTTTATAACTAGATCAGATTTGAGTTGGGTG
1230179 TTTTTTTTTTAAATCTTCATAAATCTCTACACATTTTCCATTTATGTTATGTTCAGTCATAATCT
1 TTTTTTTTTTAAATCTTCATAAATCTCTACACATTTTCCATTTATGTTATGTTCAGTCATAATCT
1230244 CTTTGAGGTTCTGTGTTTACGTGTAAATTCCTGCACTCCTTTGCATACTGAAACAAAAGCATGGT
66 CTTTGAGGTTCTGTGTTTACGTGTAAATTCCTGCACTCCTTTGCATACTGAAACAAAAGCATGGT
1230309 GTTCTAACATTTCTTTATAACTAGATCAGATTTGAGTTGGGTG
131 GTTCTAACATTTCTTTATAACTAGATCAGATTTGAGTTGGGTG
1230352 TTTTTTTTTTAAATCTTCATAAATCTCTACACATTTTCCATTTATGTTATGTTCAGTCATAATCT
1 TTTTTTTTTTAAATCTTCATAAATCTCTACACATTTTCCATTTATGTTATGTTCAGTCATAATCT
*
1230417 CTTTGAGGTTCTGTGTTTACGTGTAAATTCCTGCACTCCTTTGCATACTGAAACAAAAGCACGGT
66 CTTTGAGGTTCTGTGTTTACGTGTAAATTCCTGCACTCCTTTGCATACTGAAACAAAAGCATGGT
1230482 GTTCTAACATTTCTTTATAACTAGATCAGATTTGAGTTGGGTG
131 GTTCTAACATTTCTTTATAACTAGATCAGATTTGAGTTGGGTG
1230525 TTT
1 TTT
1230528 AAAAAAATTT
Statistics
Matches: 1555, Mismatches: 5, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
173 1555 1.00
ACGTcount: A:0.25, C:0.17, G:0.14, T:0.44
Consensus pattern (173 bp):
TTTTTTTTTTAAATCTTCATAAATCTCTACACATTTTCCATTTATGTTATGTTCAGTCATAATCT
CTTTGAGGTTCTGTGTTTACGTGTAAATTCCTGCACTCCTTTGCATACTGAAACAAAAGCATGGT
GTTCTAACATTTCTTTATAACTAGATCAGATTTGAGTTGGGTG
Found at i:1230767 original size:27 final size:30
Alignment explanation
Indices: 1230719--1230784 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 30
1230709 CATTTTAGTG
1230719 ATTTAAATAAAATCAATTTAAATATTATTTT
1 ATTTAAATAAAATCAA-TTAAATATTATTTT
* *
1230750 ATTT-AATAAAAT-AA-TAAATTTTATTTA
1 ATTTAAATAAAATCAATTAAATATTATTTT
*
1230777 AATTAAAT
1 ATTTAAAT
1230785 TATAAAATAT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
27 14 0.45
28 3 0.10
29 2 0.06
30 8 0.26
31 4 0.13
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (30 bp):
ATTTAAATAAAATCAATTAAATATTATTTT
Found at i:1232116 original size:12 final size:12
Alignment explanation
Indices: 1232101--1232137 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
1232091 ATAATATGTA
*
1232101 ATATATATATAT
1 ATATGTATATAT
*
1232113 ATATGTATATGT
1 ATATGTATATAT
1232125 ATATGTATATAT
1 ATATGTATATAT
1232137 A
1 A
1232138 AGATGTTGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.43, C:0.00, G:0.08, T:0.49
Consensus pattern (12 bp):
ATATGTATATAT
Found at i:1234761 original size:20 final size:21
Alignment explanation
Indices: 1234726--1234765 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
1234716 TATTTTTATT
*
1234726 TAAATTTAATTATAAAATATA
1 TAAATATAATTATAAAATATA
1234747 TAAATATAA-TATAAAATAT
1 TAAATATAATTATAAAATAT
1234766 TTTTTAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAATATAATTATAAAATATA
Found at i:1235606 original size:17 final size:19
Alignment explanation
Indices: 1235586--1235626 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
1235576 TAAAATAATA
*
1235586 ATTTTAAATA-TT-TTTAT
1 ATTTTAAAAATTTATTTAT
*
1235603 ATTTAAAAAATTTATTTAT
1 ATTTTAAAAATTTATTTAT
1235622 ATTTT
1 ATTTT
1235627 TTACATATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 2
0.79 0.12 0.08
Matches are distributed among these distances:
17 8 0.42
18 2 0.11
19 9 0.47
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
ATTTTAAAAATTTATTTAT
Found at i:1235618 original size:21 final size:21
Alignment explanation
Indices: 1235594--1235642 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
1235584 TAATTTTAAA
1235594 TATTTTTATATTTAAAAAATT
1 TATTTTTATATTTAAAAAATT
* * * * *
1235615 TATTTATATTTTTTACATATT
1 TATTTTTATATTTAAAAAATT
1235636 TATTTTT
1 TATTTTT
1235643 CAAATTTATA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (21 bp):
TATTTTTATATTTAAAAAATT
Found at i:1235654 original size:15 final size:15
Alignment explanation
Indices: 1235616--1235657 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
1235606 TAAAAAATTT
* *
1235616 ATTTATATTTTTTAC
1 ATTTATATTTTTCAA
1235631 ATATT-TATTTTTCAA
1 AT-TTATATTTTTCAA
1235646 ATTTATATTTTT
1 ATTTATATTTTT
1235658 ATTCATGTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
14 2 0.09
15 19 0.83
16 2 0.09
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.67
Consensus pattern (15 bp):
ATTTATATTTTTCAA
Found at i:1236013 original size:10 final size:10
Alignment explanation
Indices: 1236000--1236053 Score: 53
Period size: 10 Copynumber: 5.7 Consensus size: 10
1235990 TTTATATTAA
1236000 TTTAAAATAT
1 TTTAAAATAT
1236010 TTTAAAAT-T
1 TTTAAAATAT
1236019 ATTT-AAA-A-
1 -TTTAAAATAT
* *
1236027 TTTAAATTAA
1 TTTAAAATAT
1236037 TTTAAAATAT
1 TTTAAAATAT
1236047 TTTAAAA
1 TTTAAAA
1236054 AAATTAAGGA
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
7 3 0.08
8 2 0.06
9 5 0.14
10 26 0.72
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (10 bp):
TTTAAAATAT
Found at i:1236016 original size:27 final size:27
Alignment explanation
Indices: 1235986--1236052 Score: 68
Period size: 27 Copynumber: 2.5 Consensus size: 27
1235976 TTGATATGAA
*
1235986 AAAATTTATATT-AATTTAAAATATTTT
1 AAAATTTAT-TTAAATTTAAAATAATTT
*
1236013 AAAA-TTATTTAAAATTTAAATTAATTT
1 AAAATTTATTT-AAATTTAAAATAATTT
*
1236040 AAAATAT-TTTAAA
1 AAAATTTATTTAAA
1236053 AAAATTAAGG
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
25 2 0.06
26 7 0.21
27 24 0.71
28 1 0.03
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (27 bp):
AAAATTTATTTAAATTTAAAATAATTT
Found at i:1236053 original size:27 final size:27
Alignment explanation
Indices: 1235998--1236053 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
1235988 AATTTATATT
*
1235998 AATTTAAAATATTTTAAAATTATTTAA
1 AATTTAAAATAATTTAAAATTATTTAA
*
1236025 AATTTAAATTAATTTAAAA-TATTTTAA
1 AATTTAAAATAATTTAAAATTA-TTTAA
1236052 AA
1 AA
1236054 AAATTAAGGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 2 0.08
27 24 0.92
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (27 bp):
AATTTAAAATAATTTAAAATTATTTAA
Found at i:1236216 original size:16 final size:17
Alignment explanation
Indices: 1236182--1236224 Score: 70
Period size: 16 Copynumber: 2.5 Consensus size: 17
1236172 AGTTTTAAAT
1236182 ATTAAATTTTATTTTTAA
1 ATTAAATTTTA-TTTTAA
1236200 ATTAAATTTTA-TTTAA
1 ATTAAATTTTATTTTAA
1236216 ATTAAATTT
1 ATTAAATTT
1236225 AAATAAATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
16 14 0.56
18 11 0.44
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
ATTAAATTTTATTTTAA
Found at i:1238187 original size:11 final size:11
Alignment explanation
Indices: 1238155--1238180 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1238145 AACTATAAGT
1238155 AAAAAATAAAA
1 AAAAAATAAAA
1238166 AAAAAATAAAA
1 AAAAAATAAAA
1238177 AAAA
1 AAAA
1238181 CCTAAAACAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (11 bp):
AAAAAATAAAA
Found at i:1239714 original size:11 final size:11
Alignment explanation
Indices: 1239677--1239713 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
1239667 ATATATAATT
1239677 ATATAAATAAA
1 ATATAAATAAA
1239688 ATATAAAT-AA
1 ATATAAATAAA
*
1239698 A-ATAATTAAA
1 ATATAAATAAA
1239708 ATATAA
1 ATATAA
1239714 TATGAATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
9 5 0.22
10 6 0.26
11 12 0.52
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (11 bp):
ATATAAATAAA
Found at i:1239715 original size:25 final size:25
Alignment explanation
Indices: 1239681--1239793 Score: 69
Period size: 25 Copynumber: 4.6 Consensus size: 25
1239671 ATAATTATAT
*
1239681 AAATAAAATATAAATAAAATAATTA
1 AAATATAATATAAATAAAATAATTA
* * *
1239706 AAATATAATATGAAT-ATATATTTTA
1 AAATATAATATAAATAAAATA-ATTA
* * *
1239731 AAAT-TTATATAAATAAAAAATATTTT
1 AAATATAATATAAAT--AAAATAATTA
1239757 AAATATTAATAT--ATAAATATAA-TA
1 AAATA-TAATATAAATAAA-ATAATTA
1239781 AAA-ATAA-ATAAAT
1 AAATATAATATAAAT
1239794 TACTAGGTTT
Statistics
Matches: 68, Mismatches: 11, Indels: 20
0.69 0.11 0.20
Matches are distributed among these distances:
21 2 0.03
22 3 0.04
23 3 0.04
24 19 0.28
25 23 0.34
26 9 0.13
27 4 0.06
28 5 0.07
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (25 bp):
AAATATAATATAAATAAAATAATTA
Found at i:1240149 original size:12 final size:12
Alignment explanation
Indices: 1240124--1240166 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
1240114 ATTTATCTAT
* *
1240124 TATATATATATA
1 TATATATTTTTA
1240136 TATATATTTTTA
1 TATATATTTTTA
*
1240148 TATTTATTTTTA
1 TATATATTTTTA
*
1240160 TAAATAT
1 TATATAT
1240167 ATTAAATATA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TATATATTTTTA
Found at i:1240178 original size:15 final size:15
Alignment explanation
Indices: 1240158--1240187 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1240148 TATTTATTTT
1240158 TATAAATATATTAAA
1 TATAAATATATTAAA
*
1240173 TATAAATATTTTAAA
1 TATAAATATATTAAA
1240188 AAATAAAAGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
TATAAATATATTAAA
Found at i:1241274 original size:23 final size:22
Alignment explanation
Indices: 1241233--1241278 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
1241223 CACCTATTTT
*
1241233 ATAAAATATAATTAAAAAATAA
1 ATAAAATACAATTAAAAAATAA
*
1241255 ATAAAATACATATTATAAAATAA
1 ATAAAATACA-ATTAAAAAATAA
1241278 A
1 A
1241279 CTCTATTTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 9 0.43
23 12 0.57
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (22 bp):
ATAAAATACAATTAAAAAATAA
Found at i:1242301 original size:2 final size:2
Alignment explanation
Indices: 1242294--1242331 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
1242284 GAAGATGGTT
*
1242294 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TG TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1242332 CTTTTCTACT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.47, G:0.03, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1244426 original size:16 final size:17
Alignment explanation
Indices: 1244402--1244434 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1244392 TTTGATTCAT
*
1244402 TTATAATTTTTTAAAAA
1 TTATAATTTCTTAAAAA
1244419 TTAT-ATTTCTTAAAAA
1 TTATAATTTCTTAAAAA
1244435 AATTTATTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (17 bp):
TTATAATTTCTTAAAAA
Found at i:1248666 original size:3 final size:3
Alignment explanation
Indices: 1248658--1248683 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1248648 ACAAGTGAAC
1248658 CAT CAT CAT CAT CAT CAT CAT CAT CA
1 CAT CAT CAT CAT CAT CAT CAT CAT CA
1248684 CCGTTTGGCA
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:0.35, C:0.35, G:0.00, T:0.31
Consensus pattern (3 bp):
CAT
Done.