Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold116
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: 1263769
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Warning! 4928 characters in sequence are not A, C, G, or T
File 1 of 5
Found at i:750 original size:15 final size:15
Alignment explanation
Indices: 723--774 Score: 54
Period size: 17 Copynumber: 3.5 Consensus size: 15
713 GCCTGTTTTA
723 TATATTA-AT-AATT
1 TATATTATATAAATT
736 TATATTATATAAATTT
1 TATATTATATAAA-TT
* *
752 TGATATTTTATATATT
1 T-ATATTATATAAATT
768 TATATTA
1 TATATTA
775 ATTTTTTTGT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
13 7 0.22
14 2 0.06
15 7 0.22
16 6 0.19
17 10 0.31
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (15 bp):
TATATTATATAAATT
Found at i:5943 original size:7 final size:7
Alignment explanation
Indices: 5931--5959 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
5921 GAAAAAGAAG
5931 TTTATTT
1 TTTATTT
5938 TTTATTT
1 TTTATTT
5945 TTTATTT
1 TTTATTT
5952 TTTATTT
1 TTTATTT
5959 T
1 T
5960 CACTAAAACC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (7 bp):
TTTATTT
Found at i:6850 original size:18 final size:18
Alignment explanation
Indices: 6827--6872 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
6817 ATATTTTAAA
**
6827 ATTAATATAATATTAATT
1 ATTAATATAATAAAAATT
6845 ATTAATAT-ATAAAAATT
1 ATTAATATAATAAAAATT
6862 ATATAATATAA
1 AT-TAATATAA
6873 AATAACATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 9 0.38
18 14 0.58
19 1 0.04
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
ATTAATATAATAAAAATT
Found at i:7331 original size:16 final size:17
Alignment explanation
Indices: 7294--7341 Score: 53
Period size: 16 Copynumber: 2.7 Consensus size: 17
7284 AAACATACAT
*
7294 TAATCAAATTAATAAATTA
1 TAAT-AAATTAA-AAATCA
7313 TAA-AAATTAAAAATCA
1 TAATAAATTAAAAATCA
7329 TAATATAATTAAA
1 TAATA-AATTAAA
7342 TGATAATTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 8 0.31
17 8 0.31
18 7 0.27
19 3 0.12
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.33
Consensus pattern (17 bp):
TAATAAATTAAAAATCA
Found at i:17284 original size:25 final size:25
Alignment explanation
Indices: 17196--17284 Score: 65
Period size: 25 Copynumber: 3.4 Consensus size: 25
17186 CTATCTAATC
*
17196 TTTTGCTTTT-CCATCATTAACATAT
1 TTTTG-TTTTGCCATCATTAACTTAT
* * *
17221 TTTTGTTTTGGCGTCGCATGATTGA-TTAC
1 TTTTGTTTT---G-C-CATCATTAACTTAT
*
17250 TTTTGCTTTGCCATCATTAACTTAT
1 TTTTGTTTTGCCATCATTAACTTAT
17275 TTTTGTTTTG
1 TTTTGTTTTG
17285 GGGCCAAATA
Statistics
Matches: 48, Mismatches: 9, Indels: 14
0.68 0.13 0.20
Matches are distributed among these distances:
24 11 0.23
25 18 0.38
26 1 0.02
29 11 0.23
30 7 0.15
ACGTcount: A:0.17, C:0.16, G:0.13, T:0.54
Consensus pattern (25 bp):
TTTTGTTTTGCCATCATTAACTTAT
Found at i:17951 original size:2 final size:2
Alignment explanation
Indices: 17944--17968 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
17934 TAAATATTAT
17944 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 T
17969 GCGCGCTTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:28898 original size:28 final size:28
Alignment explanation
Indices: 28858--28919 Score: 83
Period size: 28 Copynumber: 2.2 Consensus size: 28
28848 TAATTTAATT
*
28858 TATTTACATAA-TTATTTTTAAATTTTAA
1 TATTTACATAATTTAATTTT-AATTTTAA
28886 TATTT-CATAAATTTAATTTTAATTTTAA
1 TATTTACAT-AATTTAATTTTAATTTTAA
28914 TATTTA
1 TATTTA
28920 TACTTTTGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
27 3 0.10
28 20 0.67
29 7 0.23
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (28 bp):
TATTTACATAATTTAATTTTAATTTTAA
Found at i:32393 original size:15 final size:15
Alignment explanation
Indices: 32375--32423 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
32365 TTAAATCATC
32375 ATTTTAAAAATTAAT
1 ATTTTAAAAATTAAT
*
32390 ATTTTATAAATTTAA-
1 ATTTTA-AAAATTAAT
* *
32405 AATTTAAATATTAAT
1 ATTTTAAAAATTAAT
32420 ATTT
1 ATTT
32424 ATAATTTTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
14 6 0.22
15 14 0.52
16 7 0.26
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
ATTTTAAAAATTAAT
Found at i:33035 original size:2 final size:2
Alignment explanation
Indices: 33028--33062 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
33018 AAACAAAGCT
33028 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
33063 GGTAATGGAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:34798 original size:9 final size:9
Alignment explanation
Indices: 34765--34836 Score: 56
Period size: 9 Copynumber: 7.7 Consensus size: 9
34755 AATTTATTAA
34765 TTTATATA-
1 TTTATATAT
*
34773 TTAATATTAT
1 TTTATA-TAT
34783 ATTTATATAT
1 -TTTATATAT
34793 TTTATATAT
1 TTTATATAT
*
34802 TATAATAATAT
1 T-TTAT-ATAT
* *
34813 TTAAAATAT
1 TTTATATAT
*
34822 TATATATAT
1 TTTATATAT
34831 TTTATA
1 TTTATA
34837 AATTAATAAT
Statistics
Matches: 51, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
8 5 0.10
9 27 0.53
10 9 0.18
11 10 0.20
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (9 bp):
TTTATATAT
Found at i:34812 original size:20 final size:20
Alignment explanation
Indices: 34789--34850 Score: 69
Period size: 18 Copynumber: 3.3 Consensus size: 20
34779 TTATATTTAT
34789 ATATTTTATATATTATAATA
1 ATATTTTATATATTATAATA
* *
34809 ATATTTAAAATATTAT-AT-
1 ATATTTTATATATTATAATA
*
34827 ATATTTTATA-AAT-TAATA
1 ATATTTTATATATTATAATA
34845 ATATTT
1 ATATTT
34851 ATTATTAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
16 1 0.03
17 4 0.11
18 14 0.40
19 2 0.06
20 14 0.40
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
ATATTTTATATATTATAATA
Found at i:34812 original size:28 final size:28
Alignment explanation
Indices: 34756--34831 Score: 84
Period size: 28 Copynumber: 2.7 Consensus size: 28
34746 ATCGAATTAA
* *
34756 ATTTAT-TAATTTATATATTAATATTAT
1 ATTTATATATTTTATATATTAATATAAT
34783 ATTTATATATTTTATATATT-ATAATAAT
1 ATTTATATATTTTATATATTAAT-ATAAT
* *
34811 ATTTAAAATATTATATATATT
1 ATTT-ATATATTTTATATATT
34832 TTATAAATTA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
27 8 0.19
28 20 0.48
29 14 0.33
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (28 bp):
ATTTATATATTTTATATATTAATATAAT
Found at i:37924 original size:16 final size:16
Alignment explanation
Indices: 37867--37944 Score: 53
Period size: 16 Copynumber: 5.1 Consensus size: 16
37857 ATATATATGT
*
37867 TATTAATATATTTAAAA
1 TATTAATA-ATTTAATA
37884 TATT-ATATATTT--TA
1 TATTAATA-ATTTAATA
*
37898 T-TTAA-ATTTTAATA
1 TATTAATAATTTAATA
37912 TATTAATAATTTAATTA
1 TATTAATAATTTAA-TA
*
37929 TATAAAT-ATTT-ATA
1 TATTAATAATTTAATA
37943 TA
1 TA
37945 ATCAAACATT
Statistics
Matches: 51, Mismatches: 4, Indels: 15
0.73 0.06 0.21
Matches are distributed among these distances:
12 3 0.06
13 3 0.06
14 10 0.20
15 5 0.10
16 18 0.35
17 12 0.24
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TATTAATAATTTAATA
Found at i:39120 original size:2 final size:2
Alignment explanation
Indices: 39113--39146 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
39103 CTTACCGAGA
39113 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
39147 TTAATAAGTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:49715 original size:22 final size:23
Alignment explanation
Indices: 49669--49715 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
49659 AAATTTTATT
* *
49669 AAAATTATATTTTATTAACTAAA
1 AAAATTAGATTTTATTAAATAAA
*
49692 AAAATTAGA-TTTATTAAATTAA
1 AAAATTAGATTTTATTAAATAAA
49714 AA
1 AA
49716 TATTTAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (23 bp):
AAAATTAGATTTTATTAAATAAA
Found at i:50235 original size:15 final size:15
Alignment explanation
Indices: 50215--50245 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
50205 AAAAATCACC
50215 TTTTTTT-TTTTTGT
1 TTTTTTTGTTTTTGT
50229 TTTTTTTGTTTTTGT
1 TTTTTTTGTTTTTGT
50244 TT
1 TT
50246 GCTTAACCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.44
15 9 0.56
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (15 bp):
TTTTTTTGTTTTTGT
Found at i:57148 original size:21 final size:21
Alignment explanation
Indices: 57122--57163 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
57112 AAAATTAATT
*
57122 TTTAT-ATTAATATTTATATAA
1 TTTATAATTAA-ATTTAAATAA
57143 TTTATAATTAAATTTAAATAA
1 TTTATAATTAAATTTAAATAA
57164 AAATATAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
TTTATAATTAAATTTAAATAA
Found at i:61238 original size:2 final size:2
Alignment explanation
Indices: 61231--61256 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
61221 GTGAATCATT
61231 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
61257 ACATTTGATT
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):
TA
Found at i:62429 original size:6 final size:6
Alignment explanation
Indices: 62415--62455 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
62405 AATTGAATGG
* * *
62415 ATATGT ATACAT ATATAT ATATAT ATATAT ATATAT GTATA
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATA
62456 AAGAGAAGTG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.46
Consensus pattern (6 bp):
ATATAT
Found at i:62434 original size:4 final size:4
Alignment explanation
Indices: 62415--62455 Score: 55
Period size: 4 Copynumber: 10.2 Consensus size: 4
62405 AATTGAATGG
* * *
62415 ATAT GTAT ACAT ATAT ATAT ATAT ATAT ATAT ATAT GTAT A
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT A
62456 AAGAGAAGTG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.46
Consensus pattern (4 bp):
ATAT
Found at i:62455 original size:10 final size:10
Alignment explanation
Indices: 62415--62455 Score: 55
Period size: 10 Copynumber: 4.1 Consensus size: 10
62405 AATTGAATGG
* *
62415 ATATGTATAC
1 ATATATATAT
62425 ATATATATAT
1 ATATATATAT
62435 ATATATATAT
1 ATATATATAT
*
62445 ATATATGTAT
1 ATATATATAT
62455 A
1 A
62456 AAGAGAAGTG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 28 1.00
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.46
Consensus pattern (10 bp):
ATATATATAT
Found at i:66483 original size:2 final size:2
Alignment explanation
Indices: 66476--66504 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
66466 GTCTATATGC
66476 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
66505 GTTATGAATT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:71109 original size:15 final size:15
Alignment explanation
Indices: 71065--71112 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
71055 GAATTAAATT
71065 AAATTAAAATTTTT-A
1 AAATT-AAATTTTTAA
* * *
71080 AATTTCAATTATTAA
1 AAATTAAATTTTTAA
71095 AAATTAAATTTTTAA
1 AAATTAAATTTTTAA
71110 AAA
1 AAA
71113 ATTTATTTAA
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
14 6 0.23
15 20 0.77
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AAATTAAATTTTTAA
Found at i:73685 original size:2 final size:2
Alignment explanation
Indices: 73678--73728 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
73668 TATGAGTAAA
73678 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
73720 TC TC TC TC T
1 TC TC TC TC T
73729 TCACATCGTG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:74326 original size:16 final size:16
Alignment explanation
Indices: 74305--74336 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
74295 AATAAATTTA
*
74305 ATTTTTAAATTTGATT
1 ATTTTTAAATTCGATT
74321 ATTTTTAAATTCGATT
1 ATTTTTAAATTCGATT
74337 TAAGATTTTT
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:0.31, C:0.03, G:0.06, T:0.59
Consensus pattern (16 bp):
ATTTTTAAATTCGATT
Found at i:78265 original size:3 final size:3
Alignment explanation
Indices: 78257--78289 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
78247 TAAGTAAGTG
78257 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
78290 TTAAAAAACA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:78943 original size:2 final size:2
Alignment explanation
Indices: 78936--78963 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
78926 AAAAATTGTC
78936 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
78964 TGAAATTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:83933 original size:59 final size:59
Alignment explanation
Indices: 83861--83980 Score: 186
Period size: 59 Copynumber: 2.0 Consensus size: 59
83851 AGGTTGACAG
** * * **
83861 TATATCTACTAATAAACCTGGAATATTAGATTTGATATCTAATTTTTTGAATTCATTCT
1 TATATCTACTAATAAACCTGGAATAGCAGATTTGATATCTAACTCTTAAAATTCATTCT
83920 TATATCTACTAATAAACCTGGAATAGCAGATTTGATATCTAACTCTTAAAATTCATTCT
1 TATATCTACTAATAAACCTGGAATAGCAGATTTGATATCTAACTCTTAAAATTCATTCT
83979 TA
1 TA
83981 CTTCCAACAC
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
59 55 1.00
ACGTcount: A:0.36, C:0.14, G:0.08, T:0.42
Consensus pattern (59 bp):
TATATCTACTAATAAACCTGGAATAGCAGATTTGATATCTAACTCTTAAAATTCATTCT
Found at i:97552 original size:2 final size:2
Alignment explanation
Indices: 97545--97593 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
97535 GAGAAGAAAA
97545 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
97587 AG AG AG A
1 AG AG AG A
97594 TTACATTAAG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:100224 original size:75 final size:75
Alignment explanation
Indices: 100099--100249 Score: 212
Period size: 75 Copynumber: 2.0 Consensus size: 75
100089 GATGAAACGA
* ** *
100099 TAATCCGAGATAATCTGCATGATATTTACAATCAACAAATATTTCAGCATATTTCACAGTATTAC
1 TAATCCGAGATAATCTGCACGATAACTACAATCAACAAATATTTCAGCATATTTCACAGTACTAC
100164 TATCAACAAC
66 TATCAACAAC
* * * * * *
100174 TAATCCGAGATAATCTGCACGATAACTACAATTAACAAATGTTTCTGCATATTTCGCATTGCTAC
1 TAATCCGAGATAATCTGCACGATAACTACAATCAACAAATATTTCAGCATATTTCACAGTACTAC
100239 TATCAACAAC
66 TATCAACAAC
100249 T
1 T
100250 TCATACGTCA
Statistics
Matches: 66, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
75 66 1.00
ACGTcount: A:0.38, C:0.21, G:0.09, T:0.32
Consensus pattern (75 bp):
TAATCCGAGATAATCTGCACGATAACTACAATCAACAAATATTTCAGCATATTTCACAGTACTAC
TATCAACAAC
Found at i:100684 original size:15 final size:15
Alignment explanation
Indices: 100666--100707 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
100656 GTGGGTAAAT
*
100666 GGGTGGTGGATGTAC
1 GGGTGGTGGATGCAC
* *
100681 GGGTTGTAGATGCAC
1 GGGTGGTGGATGCAC
100696 GGGTGGTGGATG
1 GGGTGGTGGATG
100708 GACAGGATCA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.14, C:0.07, G:0.52, T:0.26
Consensus pattern (15 bp):
GGGTGGTGGATGCAC
Found at i:103552 original size:14 final size:15
Alignment explanation
Indices: 103519--103558 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
103509 TTATAGGCTT
103519 TAAACTAATTACCCC
1 TAAACTAATTACCCC
*
103534 TAAACTAATTA-CGC
1 TAAACTAATTACCCC
103548 TAAACTTAATT
1 TAAAC-TAATT
103559 CCACATAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 7 0.30
15 16 0.70
ACGTcount: A:0.42, C:0.23, G:0.03, T:0.33
Consensus pattern (15 bp):
TAAACTAATTACCCC
Found at i:104623 original size:20 final size:20
Alignment explanation
Indices: 104597--104642 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
104587 TATATTAAAT
*
104597 AATAAATATATTAA-ATTTTA
1 AATAAATA-AATAATATTTTA
*
104617 TATAAATAAATAATATTTTA
1 AATAAATAAATAATATTTTA
104637 AATAAA
1 AATAAA
104643 ATTATAATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
AATAAATAAATAATATTTTA
Found at i:104628 original size:28 final size:27
Alignment explanation
Indices: 104585--104639 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
104575 AAAATTTTAA
104585 TTTATATTAAATAATAAATATATTAAAT
1 TTTATATTAAATAAT-AATATATTAAAT
*
104613 TTTATA-TAAATAAATAATATTTTAAAT
1 TTTATATTAAAT-AATAATATATTAAAT
104640 AAAATTATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 16 0.64
28 9 0.36
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (27 bp):
TTTATATTAAATAATAATATATTAAAT
Found at i:105957 original size:47 final size:47
Alignment explanation
Indices: 105888--105979 Score: 139
Period size: 47 Copynumber: 2.0 Consensus size: 47
105878 ATTTTATGAG
* *
105888 ATGTCAAAATCCCAGTTCTAATTTTTTGTCGAGGGCCACATAAAACT
1 ATGTCAAAATCCCAATTCTAATTTTTTGTCGAGGGCCAAATAAAACT
* * *
105935 ATGTCAATATCCCAATTTTAATTTTTTGTCGAGGGTCAAATAAAA
1 ATGTCAAAATCCCAATTCTAATTTTTTGTCGAGGGCCAAATAAAA
105980 TCAGGTTAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
47 40 1.00
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.35
Consensus pattern (47 bp):
ATGTCAAAATCCCAATTCTAATTTTTTGTCGAGGGCCAAATAAAACT
Found at i:106058 original size:26 final size:25
Alignment explanation
Indices: 105998--106059 Score: 63
Period size: 26 Copynumber: 2.4 Consensus size: 25
105988 AAATTTTGAA
105998 TAATTATTTAAATATTAATAAAAATT
1 TAATTA-TTAAATATTAATAAAAATT
** *
106024 TAAAAATTAAAT-TTTATAAAAATTTT
1 TAATTATTAAATATTAATAAAAA--TT
106050 TAATTATTAA
1 TAATTATTAA
106060 CTAATAAATT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
24 9 0.31
25 6 0.21
26 14 0.48
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (25 bp):
TAATTATTAAATATTAATAAAAATT
Found at i:108077 original size:12 final size:12
Alignment explanation
Indices: 108062--108104 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 12
108052 GCTTTTTTAG
108062 TATTTTTTCATT
1 TATTTTTTCATT
108074 TATTTATTT-ATT
1 TATTT-TTTCATT
*
108086 TATTATTTTCAGT
1 TATT-TTTTCATT
108099 TATTTT
1 TATTTT
108105 CTTAATTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
12 17 0.63
13 10 0.37
ACGTcount: A:0.21, C:0.05, G:0.02, T:0.72
Consensus pattern (12 bp):
TATTTTTTCATT
Found at i:108211 original size:14 final size:15
Alignment explanation
Indices: 108182--108214 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
108172 TAATAAAAAA
*
108182 TAAATAAAATATTTT
1 TAAATAAAATAATTT
108197 TAAAT-AAATAATTT
1 TAAATAAAATAATTT
108211 TAAA
1 TAAA
108215 ATTCGAGCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
TAAATAAAATAATTT
Found at i:110653 original size:30 final size:30
Alignment explanation
Indices: 110617--110676 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
110607 TCTTTCAGTC
*
110617 AGTAATCCTTTGTTATCTTTTGATTCCAAA
1 AGTAATCCTTTGTTATCTGTTGATTCCAAA
110647 AGTAATCCTTTGTTATCTGTTGATTCCAAA
1 AGTAATCCTTTGTTATCTGTTGATTCCAAA
110677 TCCTATGGAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.27, C:0.17, G:0.12, T:0.45
Consensus pattern (30 bp):
AGTAATCCTTTGTTATCTGTTGATTCCAAA
Found at i:111375 original size:75 final size:75
Alignment explanation
Indices: 111252--111416 Score: 312
Period size: 75 Copynumber: 2.2 Consensus size: 75
111242 GCTTAAGTTC
111252 TTGGGATGACTGGGACACCAAGGACAATGGGAAGGAAGTTACTACAAAAGTGACTCCTTCTCATA
1 TTGGGATGACTGGGACACCAAGGACAATGGGAAGGAAGTTACTACAAAAGTGACTCCTTCTCATA
111317 GCAATGATGG
66 GCAATGATGG
111327 TTGGGATGACTGGGACACCAAGGACAATGGGAAGGAAGTTACTACAAAAGTGACTCCTTCTCATA
1 TTGGGATGACTGGGACACCAAGGACAATGGGAAGGAAGTTACTACAAAAGTGACTCCTTCTCATA
111392 GCAATGATGG
66 GCAATGATGG
* *
111402 TTGGGCTGGCTGGGA
1 TTGGGATGACTGGGA
111417 TGATGCCAAG
Statistics
Matches: 88, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
75 88 1.00
ACGTcount: A:0.31, C:0.17, G:0.30, T:0.22
Consensus pattern (75 bp):
TTGGGATGACTGGGACACCAAGGACAATGGGAAGGAAGTTACTACAAAAGTGACTCCTTCTCATA
GCAATGATGG
Found at i:112376 original size:16 final size:16
Alignment explanation
Indices: 112357--112391 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
112347 TATATATATA
112357 TATATATATATGCGTG
1 TATATATATATGCGTG
*
112373 TATATATGTATGCGTG
1 TATATATATATGCGTG
112389 TAT
1 TAT
112392 CATGCCCCAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.29, C:0.06, G:0.20, T:0.46
Consensus pattern (16 bp):
TATATATATATGCGTG
Found at i:112379 original size:2 final size:2
Alignment explanation
Indices: 112328--112367 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
112318 GTAAAAACAA
112328 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
112368 GCGTGTATAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:116531 original size:28 final size:28
Alignment explanation
Indices: 116472--116528 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 28
116462 TTAAATAATA
116472 TTATATAATTTATTAAAAATATATAAAT
1 TTATATAATTTATTAAAAATATATAAAT
* **
116500 TTATATAATTTTTTATCAA-ATATAAAT
1 TTATATAATTTATTAAAAATATATAAAT
116527 TT
1 TT
116529 TATGTATAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 10 0.38
28 16 0.62
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (28 bp):
TTATATAATTTATTAAAAATATATAAAT
Found at i:116611 original size:27 final size:29
Alignment explanation
Indices: 116558--116623 Score: 79
Period size: 27 Copynumber: 2.4 Consensus size: 29
116548 AATTTTTAAT
116558 TTTTAAAAT-TA-ATAAAATAATACATAA
1 TTTTAAAATATATATAAAATAATACATAA
*
116585 TTTTAAAATATATTTAAAA-AATA-ATAA
1 TTTTAAAATATATATAAAATAATACATAA
*
116612 -ATTAAAATATAT
1 TTTTAAAATATAT
116624 GTCTTTAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
26 11 0.31
27 13 0.37
28 6 0.17
29 5 0.14
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (29 bp):
TTTTAAAATATATATAAAATAATACATAA
Found at i:121902 original size:17 final size:17
Alignment explanation
Indices: 121880--121914 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
121870 AAAAAAAATT
*
121880 ATAAATAATCAATCATA
1 ATAAATAAACAATCATA
*
121897 ATAAATAAACAATTATA
1 ATAAATAAACAATCATA
121914 A
1 A
121915 ATAATCGTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.63, C:0.09, G:0.00, T:0.29
Consensus pattern (17 bp):
ATAAATAAACAATCATA
Found at i:121914 original size:14 final size:14
Alignment explanation
Indices: 121876--121918 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 14
121866 TGGTAAAAAA
*
121876 AATTATAAATAATC
1 AATTATAAATAAAC
121890 AATCATAATAAATAAAC
1 AAT--T-ATAAATAAAC
121907 AATTATAAATAA
1 AATTATAAATAA
121919 TCGTAAGTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
14 11 0.44
15 1 0.04
16 1 0.04
17 12 0.48
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (14 bp):
AATTATAAATAAAC
Found at i:124024 original size:2 final size:2
Alignment explanation
Indices: 124017--124050 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
124007 ATTATTGTGA
*
124017 AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
124051 GACTTAGAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:124765 original size:13 final size:13
Alignment explanation
Indices: 124747--124784 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
124737 TTATAATTTT
*
124747 AAATATAATATGA
1 AAATATAATATAA
124760 AAATATAATATAA
1 AAATATAATATAA
124773 AAATA-AATATAA
1 AAATATAATATAA
124785 TATATTTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 7 0.29
13 17 0.71
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (13 bp):
AAATATAATATAA
Found at i:124780 original size:30 final size:29
Alignment explanation
Indices: 124746--124808 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 29
124736 TTTATAATTT
124746 TAAATATAATATGA-AAATATAATATAAAAA
1 TAAATATAATAT-ATAAATA-AATATAAAAA
*
124776 TAAATATAATATATTTAATAAATATAAAAA
1 TAAATATAATATA-TAAATAAATATAAAAA
124806 TAA
1 TAA
124809 TAAACATAAC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
29 1 0.03
30 25 0.83
31 4 0.13
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (29 bp):
TAAATATAATATATAAATAAATATAAAAA
Found at i:124782 original size:17 final size:18
Alignment explanation
Indices: 124760--124802 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
124750 TATAATATGA
124760 AAATATAATATA-AAAAT
1 AAATATAATATATAAAAT
**
124777 AAATATAATATATTTAAT
1 AAATATAATATATAAAAT
124795 AAATATAA
1 AAATATAA
124803 AAATAATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 12 0.52
18 11 0.48
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
AAATATAATATATAAAAT
Found at i:131519 original size:20 final size:18
Alignment explanation
Indices: 131450--131513 Score: 62
Period size: 20 Copynumber: 3.5 Consensus size: 18
131440 TATGATATAG
131450 AATATAATTTAAATTTATA
1 AATATAATTTAAATTT-TA
131469 AATAT-A-TTAAATTTTA
1 AATATAATTTAAATTTTA
*
131485 TAT-TAATATATAATATTTTA
1 AATATAAT-T-TAA-ATTTTA
131505 AATATAATT
1 AATATAATT
131514 ATAATAAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 11
0.74 0.04 0.22
Matches are distributed among these distances:
15 1 0.03
16 5 0.14
17 8 0.22
18 2 0.05
19 8 0.22
20 9 0.24
21 4 0.11
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
AATATAATTTAAATTTTA
Found at i:131528 original size:21 final size:21
Alignment explanation
Indices: 131504--131556 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
131494 ATAATATTTT
131504 AAATATAATTATAATAAAAAA
1 AAATATAATTATAATAAAAAA
* * *
131525 AAATATAAATATGATATAAAA
1 AAATATAATTATAATAAAAAA
*
131546 ATATA-AATTAT
1 AAATATAATTAT
131557 TAAACTTAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 5 0.19
21 22 0.81
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (21 bp):
AAATATAATTATAATAAAAAA
Found at i:131560 original size:27 final size:27
Alignment explanation
Indices: 131450--131576 Score: 77
Period size: 27 Copynumber: 4.7 Consensus size: 27
131440 TATGATATAG
* **
131450 AATATAATTTAAATTTATAAATATATTA
1 AATATAATATAAAAATATAAAT-TATTA
* * * *
131478 AATTTTATATTAATATATAATATT-TTA
1 AATATAATATAAAAATATAA-ATTATTA
* *
131505 AATATAATTATAATAAA-AAAAAATA-TA
1 AATATAA-TATAA-AAATATAAATTATTA
*
131532 AATATGATATAAAAATATAAATTATTA
1 AATATAATATAAAAATATAAATTATTA
131559 AACT-TAA-AT-AAAATATAA
1 AA-TATAATATAAAAATATAA
131577 TCTATCTATA
Statistics
Matches: 77, Mismatches: 15, Indels: 17
0.71 0.14 0.16
Matches are distributed among these distances:
25 12 0.16
26 13 0.17
27 24 0.31
28 24 0.31
29 4 0.05
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.40
Consensus pattern (27 bp):
AATATAATATAAAAATATAAATTATTA
Found at i:135149 original size:3 final size:3
Alignment explanation
Indices: 135141--135165 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
135131 TTTAAGATTT
135141 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
135166 CATCTCTTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:139407 original size:24 final size:22
Alignment explanation
Indices: 139361--139408 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
139351 TAAAGATAAT
*
139361 AAAAATAATTATAAAATTTTTA
1 AAAAATAATTATAAAATTATTA
139383 AAAAATAATTATATAAATTAATTA
1 AAAAATAATTATA-AAATT-ATTA
139407 AA
1 AA
139409 TTAAATTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 13 0.57
23 5 0.22
24 5 0.22
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
AAAAATAATTATAAAATTATTA
Found at i:140156 original size:9 final size:9
Alignment explanation
Indices: 140142--140174 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
140132 AATATAATAG
140142 TTAAAAAAT
1 TTAAAAAAT
*
140151 TTAAAAATT
1 TTAAAAAAT
140160 TTAAAAAA-
1 TTAAAAAAT
140168 TTAAAAA
1 TTAAAAA
140175 TGATTAAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (9 bp):
TTAAAAAAT
Found at i:140181 original size:18 final size:18
Alignment explanation
Indices: 140109--140183 Score: 68
Period size: 18 Copynumber: 4.2 Consensus size: 18
140099 GATGATGAAA
140109 AAAATAATTTAAAAATA-T
1 AAAA-AATTTAAAAATATT
* *
140127 AAAAAA-AT-ATAATAGTT
1 AAAAAATTTAAAAATA-TT
*
140144 AAAAAATTTAAAAATTTT
1 AAAAAATTTAAAAATATT
140162 AAAAAA-TTAAAAATGATT
1 AAAAAATTTAAAAAT-ATT
140180 AAAA
1 AAAA
140184 CCCAAAATCA
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
15 5 0.11
16 1 0.02
17 17 0.37
18 19 0.41
19 4 0.09
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (18 bp):
AAAAAATTTAAAAATATT
Found at i:141083 original size:2 final size:2
Alignment explanation
Indices: 141076--141107 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
141066 TAAACCTGTC
141076 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
141108 TGTGCAACAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:150455 original size:16 final size:17
Alignment explanation
Indices: 150436--150468 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
150426 ATATATTATG
150436 TATAAAATAAT-TAAAA
1 TATAAAATAATATAAAA
*
150452 TATAATATAATATAAAA
1 TATAAAATAATATAAAA
150469 ATATTTTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
TATAAAATAATATAAAA
Found at i:150490 original size:33 final size:32
Alignment explanation
Indices: 150451--150528 Score: 95
Period size: 33 Copynumber: 2.4 Consensus size: 32
150441 AATAATTAAA
*
150451 ATATAATAT-AATATAAAAATATTTTTAAAATTT
1 ATATAATATAAAT-TAAAAATA-TATTAAAATTT
**
150484 ATATAATATAAATTATTAATATATTAAAATTT
1 ATATAATATAAATTAAAAATATATTAAAATTT
150516 ATATAAATATAAA
1 ATAT-AATATAAA
150529 ATATTATGAT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
32 14 0.35
33 23 0.57
34 3 0.08
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (32 bp):
ATATAATATAAATTAAAAATATATTAAAATTT
Found at i:150517 original size:18 final size:18
Alignment explanation
Indices: 150476--150535 Score: 67
Period size: 16 Copynumber: 3.6 Consensus size: 18
150466 AAAATATTTT
150476 TAAAAT-TTATAT-AATA
1 TAAAATATTATATAAATA
* *
150492 TAAATTATTA-ATATAT-
1 TAAAATATTATATAAATA
150508 TAAAAT-TTATATAAATA
1 TAAAATATTATATAAATA
150525 TAAAATATTAT
1 TAAAATATTAT
150536 GATTTGAGTA
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
15 3 0.09
16 17 0.49
17 11 0.31
18 4 0.11
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
TAAAATATTATATAAATA
Found at i:151389 original size:22 final size:23
Alignment explanation
Indices: 151353--151395 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
151343 CGATTACATT
*
151353 TTTAATCAATTATAATTATAAAA
1 TTTAATCAATAATAATTATAAAA
151376 TTTAAT-AATAATAATTATAA
1 TTTAATCAATAATAATTATAA
151396 TTATAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (23 bp):
TTTAATCAATAATAATTATAAAA
Found at i:151391 original size:28 final size:29
Alignment explanation
Indices: 151355--151409 Score: 94
Period size: 28 Copynumber: 1.9 Consensus size: 29
151345 ATTACATTTT
*
151355 TAATCAATTATAATTATAAAATTTAATAA
1 TAATCAATTATAATTATAAAAATTAATAA
151384 TAAT-AATTATAATTATAAAAATTAAT
1 TAATCAATTATAATTATAAAAATTAAT
151410 TTTAAATAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 21 0.84
29 4 0.16
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (29 bp):
TAATCAATTATAATTATAAAAATTAATAA
Found at i:157404 original size:4 final size:4
Alignment explanation
Indices: 157395--157419 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
157385 ATTCAAAGCT
157395 TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA T
157420 AATATGGATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:157928 original size:44 final size:44
Alignment explanation
Indices: 157878--157962 Score: 170
Period size: 44 Copynumber: 1.9 Consensus size: 44
157868 AAAATCTGCT
157878 TTGGTAATGATAATATGTGAAAGATTCAAAGGCTCTCTCACTGA
1 TTGGTAATGATAATATGTGAAAGATTCAAAGGCTCTCTCACTGA
157922 TTGGTAATGATAATATGTGAAAGATTCAAAGGCTCTCTCAC
1 TTGGTAATGATAATATGTGAAAGATTCAAAGGCTCTCTCAC
157963 CGATAATTAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.32
Consensus pattern (44 bp):
TTGGTAATGATAATATGTGAAAGATTCAAAGGCTCTCTCACTGA
Found at i:158278 original size:18 final size:19
Alignment explanation
Indices: 158260--158304 Score: 65
Period size: 18 Copynumber: 2.3 Consensus size: 19
158250 AATAAAATTT
158260 TTTAAATATTAATATTTTTAA
1 TTTAAAT-TTAATATTTTT-A
158281 TTTAAATTTAATA-TTTTA
1 TTTAAATTTAATATTTTTA
158299 TTTAAA
1 TTTAAA
158305 AAATAAATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.29
19 4 0.17
20 6 0.25
21 7 0.29
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TTTAAATTTAATATTTTTA
Found at i:161049 original size:17 final size:18
Alignment explanation
Indices: 161023--161077 Score: 51
Period size: 19 Copynumber: 3.0 Consensus size: 18
161013 TAAAATAATT
161023 TAAA-ATAATATAATATA
1 TAAACATAATATAATATA
*
161040 T-AACATAATAAAAAATATA
1 TAAACATAAT--ATAATATA
*
161059 TAAATATAATATTAATATA
1 TAAACATAATA-TAATATA
161078 AATTATTATA
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
16 2 0.07
17 6 0.20
18 1 0.03
19 14 0.47
20 7 0.23
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.35
Consensus pattern (18 bp):
TAAACATAATATAATATA
Found at i:161060 original size:26 final size:27
Alignment explanation
Indices: 161024--161094 Score: 74
Period size: 26 Copynumber: 2.6 Consensus size: 27
161014 AAAATAATTT
161024 AAAATAATATAATATATAACA-TAATAA
1 AAAAT-ATATAATATATAACATTAATAA
* *
161051 AAAATATATAA-ATATAATATTAATAT
1 AAAATATATAATATATAACATTAATAA
* *
161077 AAATTATTATAATTTATA
1 AAAATA-TATAATATATA
161095 TAATATAAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
25 7 0.19
26 16 0.43
27 10 0.27
28 4 0.11
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (27 bp):
AAAATATATAATATATAACATTAATAA
Found at i:161078 original size:17 final size:17
Alignment explanation
Indices: 161056--161172 Score: 57
Period size: 17 Copynumber: 6.9 Consensus size: 17
161046 AATAAAAAAT
161056 ATATAAATATAATATTA
1 ATATAAATATAATATTA
* *
161073 ATATAAATTATTATAATTT
1 ATATAAA-TATAAT-ATTA
161092 ATAT-AATATAA-A-TA
1 ATATAAATATAATATTA
* * *
161106 AT-TAACTAATCAAAATTT
1 ATATAAAT-AT-AATATTA
*
161124 ATATAAATATAA-AATA
1 ATATAAATATAATATTA
* * *
161140 TTTTAAATATTAT-TATA
1 ATATAAATATAATAT-TA
161157 ATATAATATATAATAT
1 ATATAA-ATATAATAT
161173 ATACTTATGT
Statistics
Matches: 72, Mismatches: 16, Indels: 22
0.65 0.15 0.20
Matches are distributed among these distances:
13 1 0.01
14 5 0.07
15 3 0.04
16 13 0.18
17 20 0.28
18 18 0.25
19 12 0.17
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (17 bp):
ATATAAATATAATATTA
Found at i:161777 original size:2 final size:2
Alignment explanation
Indices: 161770--161794 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
161760 AATAACGTTG
161770 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 T
161795 CAAATTCTGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:161921 original size:2 final size:2
Alignment explanation
Indices: 161914--161940 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
161904 GGATTATCAA
161914 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
161941 AGTAGAAAAT
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:163111 original size:2 final size:2
Alignment explanation
Indices: 163106--163130 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
163096 TCTTTTTTTA
163106 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 A
163131 ACACTCAGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:165456 original size:3 final size:3
Alignment explanation
Indices: 165448--165482 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
165438 ACAGACAGAG
165448 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
165483 GAGAGGAAGT
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:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:172308 original size:21 final size:23
Alignment explanation
Indices: 172274--172331 Score: 66
Period size: 21 Copynumber: 2.6 Consensus size: 23
172264 AAATTTAAAA
*
172274 TATATATATATTTAAATTTTATT
1 TATATATATATTTAAATTATATT
*
172297 TATAT-TAT-TTTATATTATATT
1 TATATATATATTTAAATTATATT
*
172318 TTTATATCATATTT
1 TATATAT-ATATTT
172332 TATTTTTTCG
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
21 15 0.52
22 4 0.14
23 7 0.24
24 3 0.10
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (23 bp):
TATATATATATTTAAATTATATT
Found at i:172316 original size:15 final size:15
Alignment explanation
Indices: 172289--172330 Score: 54
Period size: 13 Copynumber: 3.0 Consensus size: 15
172279 ATATATTTAA
172289 ATTTTAT-TTATATT
1 ATTTTATATTATATT
172303 ATTTTATATTATA-T
1 ATTTTATATTATATT
*
172317 -TTTTATATCATATT
1 ATTTTATATTATATT
172331 TTATTTTTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
13 11 0.44
14 9 0.36
15 5 0.20
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (15 bp):
ATTTTATATTATATT
Found at i:174482 original size:18 final size:17
Alignment explanation
Indices: 174459--174501 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
174449 TGGTTTCTTC
174459 AAAAAAATTGAAAAACAA
1 AAAAAAATTGAAAAA-AA
* **
174477 AAAAAATTTGACGAAAA
1 AAAAAAATTGAAAAAAA
174494 AAAAAAAT
1 AAAAAAAT
174502 CAGCTGAATG
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.74, C:0.05, G:0.07, T:0.14
Consensus pattern (17 bp):
AAAAAAATTGAAAAAAA
Found at i:175944 original size:2 final size:2
Alignment explanation
Indices: 175937--175969 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
175927 TGAATACATC
175937 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
175970 CCAAATATCC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:180975 original size:25 final size:22
Alignment explanation
Indices: 180928--180968 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
180918 TAACATAAAT
*
180928 TATTAAATATAAATATATTATA
1 TATTAAACATAAATATATTATA
180950 TATTAAACAT-AATATATTA
1 TATTAAACATAAATATATTA
180969 ATTATATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (22 bp):
TATTAAACATAAATATATTATA
Found at i:180982 original size:19 final size:20
Alignment explanation
Indices: 180960--180998 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
180950 TATTAAACAT
180960 AATATATTA-ATTATATTTA
1 AATATATTATATTATATTTA
*
180979 AATATATTATCTTATATTTA
1 AATATATTATATTATATTTA
180999 TTATAATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.54
Consensus pattern (20 bp):
AATATATTATATTATATTTA
Found at i:182627 original size:2 final size:2
Alignment explanation
Indices: 182620--182658 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
182610 TGAGTCAGTT
* *
182620 TA TA TA TA TG TA TA TA TA TA TA TA TA TA TA CA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
182659 TTTATTTTGC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:186550 original size:21 final size:21
Alignment explanation
Indices: 186526--186568 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
186516 TGCATGGATA
186526 TAGAACTACAGTATATGTTTG
1 TAGAACTACAGTATATGTTTG
186547 TAGAACTACAGTATATGTTTG
1 TAGAACTACAGTATATGTTTG
186568 T
1 T
186569 TTCTATGTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.33, C:0.09, G:0.19, T:0.40
Consensus pattern (21 bp):
TAGAACTACAGTATATGTTTG
Found at i:196077 original size:19 final size:19
Alignment explanation
Indices: 196051--196094 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
196041 ATATTTACGT
196051 TATT-TAAAA-TTATTAAA
1 TATTATAAAACTTATTAAA
*
196068 TAATTATAAAACTTTTTAAA
1 T-ATTATAAAACTTATTAAA
196088 TATTATA
1 TATTATA
196095 TTTAGTCATT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 1 0.04
18 3 0.13
19 11 0.48
20 8 0.35
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (19 bp):
TATTATAAAACTTATTAAA
Found at i:203915 original size:18 final size:16
Alignment explanation
Indices: 203881--203916 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
203871 TATCAACTCG
203881 AAATGATTCAAATAAA
1 AAATGATTCAAATAAA
*
203897 AAATGATTCAAATATA
1 AAATGATTCAAATAAA
203913 AAAT
1 AAAT
203917 AATTTAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.61, C:0.06, G:0.06, T:0.28
Consensus pattern (16 bp):
AAATGATTCAAATAAA
Found at i:203925 original size:16 final size:16
Alignment explanation
Indices: 203881--203932 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
203871 TATCAACTCG
* *
203881 AAATGATTCAAATAAA
1 AAATAATTCAAATATA
*
203897 AAATGATTCAAATATA
1 AAATAATTCAAATATA
* *
203913 AAATAATTTAAATTTA
1 AAATAATTCAAATATA
203929 AAAT
1 AAAT
203933 TATCAAAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.33
Consensus pattern (16 bp):
AAATAATTCAAATATA
Found at i:204047 original size:37 final size:37
Alignment explanation
Indices: 204006--204078 Score: 110
Period size: 37 Copynumber: 2.0 Consensus size: 37
203996 CCGATAAACT
*
204006 TGAATATTAAATTTAATTAACTCAAAGTTGATTAACA
1 TGAATATTAAATTTAATTAACTCAAAGTTAATTAACA
* * *
204043 TGAATATTAAATTTTATTAACTTAAATTTAATTAAC
1 TGAATATTAAATTTAATTAACTCAAAGTTAATTAAC
204079 TCAAACAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.42
Consensus pattern (37 bp):
TGAATATTAAATTTAATTAACTCAAAGTTAATTAACA
Found at i:204069 original size:15 final size:15
Alignment explanation
Indices: 204049--204079 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
204039 AACATGAATA
*
204049 TTAAATTTTATTAAC
1 TTAAATTTAATTAAC
204064 TTAAATTTAATTAAC
1 TTAAATTTAATTAAC
204079 T
1 T
204080 CAAACAATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (15 bp):
TTAAATTTAATTAAC
Found at i:206538 original size:539 final size:534
Alignment explanation
Indices: 205526--206597 Score: 2009
Period size: 539 Copynumber: 2.0 Consensus size: 534
205516 TAATTTATAC
*
205526 GAATTACTATCTAGATAAGATGCTTCTTTTTGTTTATATCCTATCATTTGGTTATTTAATCATTG
1 GAATTACTATCTAGATAAGATGCTTCTTTTTGTTTATATCCTATCATTTGGTTATATAATCATTG
205591 TGAAGTCCAGATGGGTTGTTTAGTTATCTAGCGTCGGTTCTAGAACAATTGAAGTTTCATTCAAT
66 TGAAGTCCAGATGGGTTGTTTAGTTATCTAGCGTCGGTTCTAGAACAATTGAAGTTTCATTCAAT
205656 GTTTACTCATGTTCACTCTTTGCAGCTGCTACCTGTTTTTTAACATTGTTTTCTGTTTTTGTCCA
131 GTTTACTCATGTTCACTCTTTGCAGCTGCTACCTGTTTTTTAACATTGTTTTCTGTTTTTGTCCA
*
205721 TTGCACGATGATACATTAAGAAATGCTGTTGCTGCTTTTAATGGGAAGAGTTGAAAAAAAAAATA
196 TTGCACGATGATACATTAAGAAATGCTGTTGCTGCTTTTAATGGGAAGAGTTGAAAAAAAAAAAA
*
205786 GGTTTCATATATTCCTCTGACTTTGCTTATTTGAAGTCCTGTAACTGGTCTTAACATTTGCATAT
261 GGTTTCATATATTCCTCTGACTTTGCTTATTTGAAGTCCTGCAACTGGTCTTAACATTTGCATAT
205851 GCTTGCGCTGCTAAATTTTTTCCATATAGGTCAGAAGTGCAATGTCTACATTGATGGCAGAAGGT
326 GCTTGCGCTGCTAAATTTTTTCCATATAGGTCAGAAGTGCAATGTCTACATTGATGGCAGAAGGT
205916 CCTAAACCGGATCTTGTTAAAGGACCTGAGACTCAAGAGGTAGGCATTTTAAGCTCTTTCTTTAT
391 CCTAAACCGGATCTTGTTAAAGGACCTGAGACTCAAGAGGTAGGCATTTTAAGCTCTTTCTTTAT
* *
205981 GCTATCTGTGGTTTGCAGTTTATAAGCGAGCATTAAACTTGTGTTGCCTATTTTGTTTTTTTTCC
456 GCTATCTGTGGTTTGCAGTTCATAAGCAAGCATTAAACTTGTGTTGCCTATTTTGTTTTTTTTCC
206046 CAGGAGGATGATAT
521 CAGGAGGATGATAT
206060 GAATTACTATCTAGATAAGATGCTTCTTTTTGTTTATATCCTATCATTTGGTTATATAATCATTG
1 GAATTACTATCTAGATAAGATGCTTCTTTTTGTTTATATCCTATCATTTGGTTATATAATCATTG
206125 TGAAGTCCAGATGGGTTGTTTAGTTATCTAGCGTCGGTTCTAGAACAATTGAAGTTTCATTCAAT
66 TGAAGTCCAGATGGGTTGTTTAGTTATCTAGCGTCGGTTCTAGAACAATTGAAGTTTCATTCAAT
* *
206190 GTTTGCTCATGTTCACTCTTTGCAGCTGCTACCTTTTTTTTTTAACATTGTTTTCTGTTTTTGTC
131 GTTTACTCATGTTCACTCTTTGCAGCTGCTACC--TGTTTTTTAACATTGTTTTCTGTTTTTGTC
* *
206255 CATTGGAGGATGATACATTAAGAAATGCTGTTGCTGCTTTTAATGGGAAGAGTTGAAAAAAAAAA
194 CATTGCACGATGATACATTAAGAAATGCTGTTGCTGCTTTTAATGGGAAGAGTTG---AAAAAAA
206320 AAAAAGGTTTCATATATTCCTCTGACTTTGCTTATTTGAAGTCCTGCAACTGGTCTTAACATTTG
256 AAAAAGGTTTCATATATTCCTCTGACTTTGCTTATTTGAAGTCCTGCAACTGGTCTTAACATTTG
206385 CATATGCTTGCGCTGCTAAATTTTTTCCATATAGGTCAGAAGTGCAATGTCTACATTGATGGCAG
321 CATATGCTTGCGCTGCTAAATTTTTTCCATATAGGTCAGAAGTGCAATGTCTACATTGATGGCAG
*
206450 AAGGTCCTAAACCGGATCTTGTTAAAGGACCTGGGACTCAAGAGGTAGGCATTTTAAGCTCTTTC
386 AAGGTCCTAAACCGGATCTTGTTAAAGGACCTGAGACTCAAGAGGTAGGCATTTTAAGCTCTTTC
206515 TTTATGCTATCTGTGGTTTGCAGTTCATAAGCAAGCATTAAACTTGTGTTGCCTATTTTGTTTTT
451 TTTATGCTATCTGTGGTTTGCAGTTCATAAGCAAGCATTAAACTTGTGTTGCCTATTTTGTTTTT
206580 TTTCCCAGGAGGATGATA
516 TTTCCCAGGAGGATGATA
206598 AAATTATTGA
Statistics
Matches: 523, Mismatches: 10, Indels: 5
0.97 0.02 0.01
Matches are distributed among these distances:
534 161 0.31
536 82 0.16
539 280 0.54
ACGTcount: A:0.25, C:0.16, G:0.19, T:0.40
Consensus pattern (534 bp):
GAATTACTATCTAGATAAGATGCTTCTTTTTGTTTATATCCTATCATTTGGTTATATAATCATTG
TGAAGTCCAGATGGGTTGTTTAGTTATCTAGCGTCGGTTCTAGAACAATTGAAGTTTCATTCAAT
GTTTACTCATGTTCACTCTTTGCAGCTGCTACCTGTTTTTTAACATTGTTTTCTGTTTTTGTCCA
TTGCACGATGATACATTAAGAAATGCTGTTGCTGCTTTTAATGGGAAGAGTTGAAAAAAAAAAAA
GGTTTCATATATTCCTCTGACTTTGCTTATTTGAAGTCCTGCAACTGGTCTTAACATTTGCATAT
GCTTGCGCTGCTAAATTTTTTCCATATAGGTCAGAAGTGCAATGTCTACATTGATGGCAGAAGGT
CCTAAACCGGATCTTGTTAAAGGACCTGAGACTCAAGAGGTAGGCATTTTAAGCTCTTTCTTTAT
GCTATCTGTGGTTTGCAGTTCATAAGCAAGCATTAAACTTGTGTTGCCTATTTTGTTTTTTTTCC
CAGGAGGATGATAT
Found at i:209388 original size:19 final size:20
Alignment explanation
Indices: 209356--209394 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
209346 TATTTATATA
209356 TTAATATAAAAATA-TATTT
1 TTAATATAAAAATATTATTT
* *
209375 TTAATATTATAATATTATTT
1 TTAATATAAAAATATTATTT
209395 AAATAATTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TTAATATAAAAATATTATTT
Found at i:210878 original size:2 final size:2
Alignment explanation
Indices: 210871--210910 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
210861 TGTTCTTACT
210871 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
210911 GACTAGCTAG
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.06
2 34 0.94
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:211540 original size:137 final size:139
Alignment explanation
Indices: 211374--211663 Score: 440
Period size: 139 Copynumber: 2.1 Consensus size: 139
211364 ATGATATCTT
* * *
211374 TATCTTCTTCAAGTATGTTTATTATCTGTCTTGAATCTAC-TT-TTATTAATATATTCGTTATAT
1 TATCTTCTTCAAGCATGTTTATTATCTGTCTTGAATCTACTTTGTTATTAATATATTCATTACAT
* *
211437 AATCGTTAATATATTAATATACTTGTGCATTCACGCGCACGTGGATATACATGTTTATCATTATT
66 AATCGTTAATATATTAATATACTCGTGCATTCACGCGCACGTGAATATACATGTTTATCATTATT
* *
211502 TTGTTATGA
131 TTATCATGA
* * *
211511 TATCTTCTTCAAGCATGTTTATTATCTGTCTTTAATCTACTTTGTTGTTAATATATTTATTACAT
1 TATCTTCTTCAAGCATGTTTATTATCTGTCTTGAATCTACTTTGTTATTAATATATTCATTACAT
* * *
211576 AATTGTTAATATATTAATATACTCGTGCATTCACGCGCATGTGAATATACATGTTTGTCATTATT
66 AATCGTTAATATATTAATATACTCGTGCATTCACGCGCACGTGAATATACATGTTTATCATTATT
211641 TTATCATGA
131 TTATCATGA
*
211650 TATCTTCTTTAAGC
1 TATCTTCTTCAAGC
211664 GTATTTTATT
Statistics
Matches: 137, Mismatches: 14, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
137 38 0.28
138 2 0.01
139 97 0.71
ACGTcount: A:0.28, C:0.14, G:0.11, T:0.48
Consensus pattern (139 bp):
TATCTTCTTCAAGCATGTTTATTATCTGTCTTGAATCTACTTTGTTATTAATATATTCATTACAT
AATCGTTAATATATTAATATACTCGTGCATTCACGCGCACGTGAATATACATGTTTATCATTATT
TTATCATGA
Found at i:212694 original size:18 final size:19
Alignment explanation
Indices: 212656--212694 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
212646 CCCAAAAATA
* *
212656 AAATGATCATGAGATTAGT
1 AAATGATAATGAGAGTAGT
212675 AAATGATAATGA-AGTAGT
1 AAATGATAATGAGAGTAGT
212693 AA
1 AA
212695 CGCTTGATGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.49, C:0.03, G:0.21, T:0.28
Consensus pattern (19 bp):
AAATGATAATGAGAGTAGT
Found at i:213191 original size:148 final size:146
Alignment explanation
Indices: 212846--213427 Score: 710
Period size: 148 Copynumber: 3.9 Consensus size: 146
212836 CAAGAAAATG
* *
212846 ATGATCAAACACCAGTGGTAAA-ACAACATGGAAATCAATCTGAGGTAAGTATCGGATAATATAT
1 ATGACCAAACACCAGTGG-AAACACAACATGGAAATCAATCTAAGGTAAGTATCGGATAATATAT
* * * * *
212910 ATA-A-ATATTACTGTTACTTATCTTTGGCGTCTTGGATGCTGTATGATATATTTTTATATATGA
65 ATATATATAATACTGTTACTTAGCTTTGGTGTCTTGGATGCTGTATAATATATGTTTATATATG-
*
212973 ATATATGTAGGGTCTAAAAGATA
129 ---TATGTA--GTCTAAATGATA
* *
212996 ATGACCAAACACCAGTGGTAACACAACATGGAAATCAATCTAAGGTAAGTAGCGGATAATATATA
1 ATGACCAAACACCAGTGGAAACACAACATGGAAATCAATCTAAGGTAAGTATCGGATAATATATA
*
213061 TTATATATAAAATACTGTTACTTAGCTTTGGTGTCTTGGATGCTGTATAATATATGTTCAGT-TA
66 -TATATAT--AATACTGTTACTTAGCTTTGGTGTCTTGGATGCTGTATAATATATGTTTA-TATA
*
213125 TGTATGTA-TGTAAATGATA
127 TGTATGTAGTCTAAATGATA
* *
213144 ATGACCAAACACCGGTGGAAACACCACATGGAAATCAATCTAAGGTAAGTATCGGAT--TATATA
1 ATGACCAAACACCAGTGGAAACACAACATGGAAATCAATCTAAGGTAAGTATCGGATAATATATA
*
213207 TAGTATATAATACTGTTACTTAGCTTTGGTGTCTTGGACGCTGTATAATATATGTTTATATACGT
66 TA-TATATAATACTGTTACTTAGCTTTGGTGTCTTGGATGCTGTATAATATATG-TT-TATA--T
* *
213272 ATATATGTAGGGTTTAAATGATA
126 ATGTATGTA--GTCTAAATGATA
* ** * *
213295 ATGACCAAACACCAGTGGTAACACAACATGGAAAGAAATCTAAGGTACGCATCGGATAATATATA
1 ATGACCAAACACCAGTGGAAACACAACATGGAAATCAATCTAAGGTAAGTATCGGAT-A-ATATA
* * *
213360 TATATATATAATACTGTTACTTAGCTTTGGGGTCTTGGATGCTGTTTAATATACGTTTATATATG
64 TATATATATAATACTGTTACTTAGCTTTGGTGTCTTGGATGCTGTATAATATATGTTTATATATG
213425 TAT
129 TAT
213428 ACATATAGGG
Statistics
Matches: 380, Mismatches: 32, Indels: 40
0.84 0.07 0.09
Matches are distributed among these distances:
144 45 0.12
145 5 0.01
146 12 0.03
148 71 0.19
149 2 0.01
150 64 0.17
151 68 0.18
152 5 0.01
153 4 0.01
154 47 0.12
155 56 0.15
156 1 0.00
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.34
Consensus pattern (146 bp):
ATGACCAAACACCAGTGGAAACACAACATGGAAATCAATCTAAGGTAAGTATCGGATAATATATA
TATATATAATACTGTTACTTAGCTTTGGTGTCTTGGATGCTGTATAATATATGTTTATATATGTA
TGTAGTCTAAATGATA
Found at i:213412 original size:298 final size:298
Alignment explanation
Indices: 212846--213412 Score: 886
Period size: 299 Copynumber: 1.9 Consensus size: 298
212836 CAAGAAAATG
* *
212846 ATGATCAAACACCAGTGGTAAAACAACATGGAAATCAATCTGAGGTAAGTATCGGATAATATATA
1 ATGACCAAACACCAGTGGTAAAACAACATGGAAATCAATCTAAGGTAAGTATCGGATAATATATA
* * * * * *
212911 TAAATATTACTGTTACTTATCTTTGGCGTCTTGGATGCTGTATGATATATTTTTATATATGAATA
66 TAAATAATACTGTTACTTAGCTTTGGCGTCTTGGACGCTGTATAATATATGTTTATATACGAATA
**
212976 TATGTAGGGTCTAAAAGATAATGACCAAACACCAGTGGTAACACAACATGGAAATCAATCTAAGG
131 TATGTAGGGTCTAAAAGATAATGACCAAACACCAGTGGTAACACAACATGGAAAGAAATCTAAGG
* *
213041 TAAGTAGCGGATAATATATATTATATATAAAATACTGTTACTTAGCTTTGGTGTCTTGGATGCTG
196 TAAGCAGCGGATAATATATATTATATATAAAATACTGTTACTTAGCTTTGGGGTCTTGGATGCTG
213106 TATAATATATGTTCAGTTATGTATGTATGTAAATGATA
261 TATAATATATGTTCAGTTATGTATGTATGTAAATGATA
* * *
213144 ATGACCAAACACCGGTGG-AAACACCACATGGAAATCAATCTAAGGTAAGTATCGGATTATATAT
1 ATGACCAAACACCAGTGGTAAA-ACAACATGGAAATCAATCTAAGGTAAGTATCGGATAATATAT
* * *
213208 AGTATATAATACTGTTACTTAGCTTTGGTGTCTTGGACGCTGTATAATATATGTTTATATACGTA
65 A-TAAATAATACTGTTACTTAGCTTTGGCGTCTTGGACGCTGTATAATATATGTTTATATACGAA
* *
213273 TATATGTAGGGTTTAAATGATAATGACCAAACACCAGTGGTAACACAACATGGAAAGAAATCTAA
129 TATATGTAGGGTCTAAAAGATAATGACCAAACACCAGTGGTAACACAACATGGAAAGAAATCTAA
* * *
213338 GGTACGCATCGGATAATATATA-TATATATATAATACTGTTACTTAGCTTTGGGGTCTTGGATGC
194 GGTAAGCAGCGGATAATATATATTATATATAAAATACTGTTACTTAGCTTTGGGGTCTTGGATGC
*
213402 TGTTTAATATA
259 TGTATAATATA
213413 CGTTTATATA
Statistics
Matches: 243, Mismatches: 24, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
297 3 0.01
298 106 0.44
299 134 0.55
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.33
Consensus pattern (298 bp):
ATGACCAAACACCAGTGGTAAAACAACATGGAAATCAATCTAAGGTAAGTATCGGATAATATATA
TAAATAATACTGTTACTTAGCTTTGGCGTCTTGGACGCTGTATAATATATGTTTATATACGAATA
TATGTAGGGTCTAAAAGATAATGACCAAACACCAGTGGTAACACAACATGGAAAGAAATCTAAGG
TAAGCAGCGGATAATATATATTATATATAAAATACTGTTACTTAGCTTTGGGGTCTTGGATGCTG
TATAATATATGTTCAGTTATGTATGTATGTAAATGATA
Found at i:218722 original size:6 final size:6
Alignment explanation
Indices: 218674--218736 Score: 55
Period size: 6 Copynumber: 11.2 Consensus size: 6
218664 ATTAATATAT
* * *
218674 TAAATA TAAATTT TAAAT- T-AAT- TAAATA -AGATA T-AATA AAAATA
1 TAAATA TAAA-TA TAAATA TAAATA TAAATA TAAATA TAAATA TAAATA
218718 TAAATA TAAATA TAAATA T
1 TAAATA TAAATA TAAATA T
218737 TAAAATTTAT
Statistics
Matches: 47, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
4 4 0.09
5 11 0.23
6 27 0.57
7 5 0.11
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (6 bp):
TAAATA
Found at i:218763 original size:18 final size:19
Alignment explanation
Indices: 218742--218780 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
218732 AATATTAAAA
218742 TTTATATAT-AATAAATTT
1 TTTATATATAAATAAATTT
*
218760 TTTATATATAAATATATTT
1 TTTATATATAAATAAATTT
218779 TT
1 TT
218781 AATGTATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
TTTATATATAAATAAATTT
Found at i:219202 original size:22 final size:23
Alignment explanation
Indices: 219157--219205 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
219147 TAATTTTTTA
*
219157 TATTTACATTTTAAAATATAATT
1 TATTTACATTTTAAAAAATAATT
219180 TATTTA-ATTTTTAAAAAAT-ATT
1 TATTTACA-TTTTAAAAAATAATT
219202 TATT
1 TATT
219206 CACCTTACAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 8 0.33
23 16 0.67
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (23 bp):
TATTTACATTTTAAAAAATAATT
Found at i:220829 original size:14 final size:15
Alignment explanation
Indices: 220803--220832 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
220793 CCTCTATGAA
220803 ATATATATAAGTGAG
1 ATATATATAAGTGAG
220818 ATATAT-TAAGTGAG
1 ATATATATAAGTGAG
220832 A
1 A
220833 AAAAAACTCA
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:0.47, C:0.00, G:0.20, T:0.33
Consensus pattern (15 bp):
ATATATATAAGTGAG
Found at i:220934 original size:21 final size:22
Alignment explanation
Indices: 220874--220949 Score: 66
Period size: 22 Copynumber: 3.5 Consensus size: 22
220864 ATATAATTTT
* *
220874 TTAAATTAAATTATTATAATAAA
1 TTAAAATAAAATA-TATAATAAA
*
220897 TT-ATATAAAATATATAATAAA
1 TTAAAATAAAATATATAATAAA
* *
220918 TTAAAATATAAAAATA-AAAAAA
1 TTAAAATA-AAATATATAATAAA
*
220940 TTAAATTAAA
1 TTAAAATAAA
220950 TCCACAAATG
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
21 13 0.30
22 23 0.52
23 8 0.18
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (22 bp):
TTAAAATAAAATATATAATAAA
Found at i:221034 original size:26 final size:26
Alignment explanation
Indices: 221002--221054 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
220992 AAAAATCATA
*
221002 AATATAATAAAATATATTAATAAATAAC
1 AATAAAAT-AAAT-TATTAATAAATAAC
*
221030 AATAAAATAAATTATTAATATATAA
1 AATAAAATAAATTATTAATAAATAA
221055 AATTTTATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 12 0.52
27 4 0.17
28 7 0.30
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (26 bp):
AATAAAATAAATTATTAATAAATAAC
Found at i:221037 original size:23 final size:22
Alignment explanation
Indices: 220999--221043 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
220989 CTTAAAAATC
* *
220999 ATAAATATAATAAAATATATTA
1 ATAAATACAATAAAATAAATTA
221021 ATAAATAACAATAAAATAAATTA
1 ATAAAT-ACAATAAAATAAATTA
221044 TTAATATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (22 bp):
ATAAATACAATAAAATAAATTA
Found at i:222844 original size:13 final size:13
Alignment explanation
Indices: 222826--222884 Score: 59
Period size: 13 Copynumber: 4.6 Consensus size: 13
222816 TTTATTAAAT
222826 ATTAATTATATAA
1 ATTAATTATATAA
*
222839 ATTAATTAAAT-A
1 ATTAATTATATAA
*
222851 TTTAA-TATATTAA
1 ATTAATTATA-TAA
**
222864 AACAATTATATAA
1 ATTAATTATATAA
222877 ATTAATTA
1 ATTAATTA
222885 AAAAATTTAT
Statistics
Matches: 35, Mismatches: 8, Indels: 6
0.71 0.16 0.12
Matches are distributed among these distances:
11 3 0.09
12 6 0.17
13 22 0.63
14 4 0.11
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (13 bp):
ATTAATTATATAA
Found at i:223497 original size:15 final size:15
Alignment explanation
Indices: 223477--223511 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
223467 ATGCACATTA
223477 CATATGTAATGTTCC
1 CATATGTAATGTTCC
* *
223492 CATATGTAGTGTTTC
1 CATATGTAATGTTCC
223507 CATAT
1 CATAT
223512 TTTATCCATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.43
Consensus pattern (15 bp):
CATATGTAATGTTCC
Found at i:224666 original size:2 final size:2
Alignment explanation
Indices: 224659--224689 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
224649 TCATCTTTTA
224659 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
224690 CATAATTTAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:229001 original size:2 final size:2
Alignment explanation
Indices: 228994--229032 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
228984 GAGCTGCATT
228994 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
229033 TAATTTGATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:229584 original size:5 final size:5
Alignment explanation
Indices: 229576--229600 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
229566 AGTCCAAATG
229576 CAAAA CAAAA CAAAA CAAAA CAAAA
1 CAAAA CAAAA CAAAA CAAAA CAAAA
229601 GAAGGAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.20, G:0.00, T:0.00
Consensus pattern (5 bp):
CAAAA
Found at i:232135 original size:21 final size:21
Alignment explanation
Indices: 232111--232150 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
232101 TTAAATATAA
232111 GATAT-AATATAATATAAAAAT
1 GATATAAATAT-ATATAAAAAT
232132 GATATAAATATATATAAAA
1 GATATAAATATATATAAAA
232151 TTTTTAGATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (21 bp):
GATATAAATATATATAAAAAT
Found at i:232146 original size:10 final size:11
Alignment explanation
Indices: 232096--232149 Score: 56
Period size: 11 Copynumber: 4.9 Consensus size: 11
232086 TACGAGAAAA
*
232096 ATAATTTAAAT
1 ATAATATAAAT
*
232107 ATAAGATATAAT
1 ATAATATA-AAT
*
232119 ATAATATAAAA
1 ATAATATAAAT
*
232130 ATGATATAAAT
1 ATAATATAAAT
232141 AT-ATATAAA
1 ATAATATAAA
232150 ATTTTTAGAT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
10 7 0.19
11 19 0.53
12 10 0.28
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (11 bp):
ATAATATAAAT
Found at i:237462 original size:2 final size:2
Alignment explanation
Indices: 237455--237481 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
237445 ATATCTACTA
237455 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
237482 CCATATAAAA
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:239506 original size:16 final size:16
Alignment explanation
Indices: 239481--239551 Score: 51
Period size: 16 Copynumber: 4.6 Consensus size: 16
239471 TTATTTTATG
239481 ATTT-TAATTATTAAT
1 ATTTATAATTATTAAT
* *
239496 ATTTATAATTAATACT
1 ATTTATAATTATTAAT
239512 -TATTATAATTAATTAA-
1 AT-TTATAATT-ATTAAT
* * *
239528 AATAATATTTATT-AT
1 ATTTATAATTATTAAT
239543 ATTTATAAT
1 ATTTATAAT
239552 CATAATAAAC
Statistics
Matches: 41, Mismatches: 10, Indels: 10
0.67 0.16 0.16
Matches are distributed among these distances:
14 1 0.02
15 14 0.34
16 23 0.56
17 3 0.07
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (16 bp):
ATTTATAATTATTAAT
Found at i:244466 original size:68 final size:68
Alignment explanation
Indices: 244357--244497 Score: 275
Period size: 68 Copynumber: 2.1 Consensus size: 68
244347 TGACGGAACC
244357 GATGTTAGGTCGATTGAATTCAACCCATGGCAGTACGAAGATTTGGCTGCTAACTAAAGCATATG
1 GATGTTAGGTCGATTGAATTCAACCCATGGCAGTACGAAGATTTGGCTGCTAACTAAAGCATATG
244422 CTT
66 CTT
244425 GATGTTAGGTCGATTGAATTCAACCCATGGCAGTACGAAGATTTGGCTGCTAACTAAAGCATATG
1 GATGTTAGGTCGATTGAATTCAACCCATGGCAGTACGAAGATTTGGCTGCTAACTAAAGCATATG
244490 CTT
66 CTT
244493 G-TGTT
1 GATGTT
244498 GCATTTGCGT
Statistics
Matches: 73, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
67 4 0.05
68 69 0.95
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.30
Consensus pattern (68 bp):
GATGTTAGGTCGATTGAATTCAACCCATGGCAGTACGAAGATTTGGCTGCTAACTAAAGCATATG
CTT
Found at i:244694 original size:87 final size:87
Alignment explanation
Indices: 244594--244773 Score: 278
Period size: 87 Copynumber: 2.1 Consensus size: 87
244584 TTGGTTTTGT
* *
244594 ATTGGTTAGTGTCAGT-TGTAGAACAA-TTAAATATGGTTAATTTTTGCACG-TTTCCTAGAATT
1 ATTGGTTACTGTCAGTCT-TAGAA-AACTTAAATATGGTTAATTTTTGCA-GATTTCCCAGAATT
244656 CTATTGTTTTATTAGTTTTTGATCC
63 CTATTGTTTTATTAGTTTTTGATCC
*
244681 ATTGGTTACTGTCAGTCTTAGAAAACTTAAATATGGTTAGTTTTTGCAGATTTCCCAGAATTCTA
1 ATTGGTTACTGTCAGTCTTAGAAAACTTAAATATGGTTAATTTTTGCAGATTTCCCAGAATTCTA
244746 TTGTTTTATTAGTTTTTGATCC
66 TTGTTTTATTAGTTTTTGATCC
244768 A-TGGTT
1 ATTGGTT
244774 CGCAACAAAT
Statistics
Matches: 87, Mismatches: 3, Indels: 7
0.90 0.03 0.07
Matches are distributed among these distances:
86 8 0.09
87 78 0.90
88 1 0.01
ACGTcount: A:0.25, C:0.11, G:0.17, T:0.47
Consensus pattern (87 bp):
ATTGGTTACTGTCAGTCTTAGAAAACTTAAATATGGTTAATTTTTGCAGATTTCCCAGAATTCTA
TTGTTTTATTAGTTTTTGATCC
Found at i:252661 original size:57 final size:54
Alignment explanation
Indices: 252557--252664 Score: 128
Period size: 54 Copynumber: 1.9 Consensus size: 54
252547 GCTGGAATTG
* * * *
252557 AAAAGTGATGATAATTAGACAAAAAAAATGCCACTATTTTGATGGATGGCACTA
1 AAAAGTGATGATAATTAAACAAAAAAAAAGCCACAAATTTGATGGATGGCACTA
*
252611 AAAAGTGGTGATAATTAAACAAAGAAAAAAAGACCCACAAATTTG-TGGATGGCA
1 AAAAGTGATGATAATTAAAC-AA-AAAAAAAG--CCACAAATTTGATGGATGGCA
252665 ACCAATGTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
54 18 0.40
55 2 0.04
56 7 0.16
57 9 0.20
58 9 0.20
ACGTcount: A:0.47, C:0.11, G:0.19, T:0.22
Consensus pattern (54 bp):
AAAAGTGATGATAATTAAACAAAAAAAAAGCCACAAATTTGATGGATGGCACTA
Found at i:254021 original size:23 final size:23
Alignment explanation
Indices: 253989--254034 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
253979 TAAAGTTAAG
*
253989 TTTAAGTTTAAAT-TTTAAATTTT
1 TTTAAATTTAAATCTTT-AATTTT
254012 TTTAAATTTAAATCTTTAATTTT
1 TTTAAATTTAAATCTTTAATTTT
254035 AGTAATTAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 18 0.86
24 3 0.14
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (23 bp):
TTTAAATTTAAATCTTTAATTTT
Found at i:256181 original size:14 final size:14
Alignment explanation
Indices: 256159--256200 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
256149 ACATTCGTAT
* *
256159 TATATATATTTAAA
1 TATAAATATTAAAA
256173 TATAAATATTAAAA
1 TATAAATATTAAAA
*
256187 TATAATTATTAAAA
1 TATAAATATTAAAA
256201 AAAATAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
TATAAATATTAAAA
Found at i:261231 original size:20 final size:21
Alignment explanation
Indices: 261206--261250 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
261196 ATAACATGAA
* *
261206 ATATCATATAT-TTCAAATTT
1 ATATCATACATATTAAAATTT
261226 ATATCATACATATTAAAATTT
1 ATATCATACATATTAAAATTT
261247 ATAT
1 ATAT
261251 AAATATAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (21 bp):
ATATCATACATATTAAAATTT
Found at i:261271 original size:16 final size:16
Alignment explanation
Indices: 261250--261300 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
261240 AAAATTTATA
261250 TAAATATAAAATAATT
1 TAAATATAAAATAATT
*
261266 TAAATATAATTATAA--
1 TAAATATAA-AATAATT
261281 TAAA-ATAAAAT-ATT
1 TAAATATAAAATAATT
261295 TAAATA
1 TAAATA
261301 CATACTCGGT
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
12 1 0.03
13 2 0.07
14 8 0.28
15 5 0.17
16 9 0.31
17 4 0.14
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
TAAATATAAAATAATT
Found at i:274338 original size:46 final size:46
Alignment explanation
Indices: 274271--274365 Score: 181
Period size: 46 Copynumber: 2.1 Consensus size: 46
274261 GTAACACCTT
274271 TGAGCATATCCATTGATTCCCTGCATGTATATATTCAACAGAGGCA
1 TGAGCATATCCATTGATTCCCTGCATGTATATATTCAACAGAGGCA
*
274317 TGAGCATATCCATTGATTCCCTGCATGTATATATTCAACGGAGGCA
1 TGAGCATATCCATTGATTCCCTGCATGTATATATTCAACAGAGGCA
274363 TGA
1 TGA
274366 TTCTGGTTGA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (46 bp):
TGAGCATATCCATTGATTCCCTGCATGTATATATTCAACAGAGGCA
Found at i:280613 original size:2 final size:2
Alignment explanation
Indices: 280601--280635 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
280591 CTAGAATTTT
*
280601 AG AG GG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
280636 ATTTAAAGGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
AG
Found at i:281029 original size:16 final size:17
Alignment explanation
Indices: 281005--281070 Score: 59
Period size: 17 Copynumber: 3.9 Consensus size: 17
280995 TATTTTAAAA
281005 ATTATATAATATAAATT
1 ATTATATAATATAAATT
281022 ATTA-ATAA-ATTAAATT
1 ATTATATAATA-TAAATT
*
281038 -TTATATAAATATAAAAT
1 ATTATAT-AATATAAATT
*
281055 ATT-TTTAATGATAAAT
1 ATTATATAAT-ATAAAT
281071 ATTTTACCAT
Statistics
Matches: 40, Mismatches: 3, Indels: 12
0.73 0.05 0.22
Matches are distributed among these distances:
15 4 0.10
16 15 0.38
17 18 0.45
18 3 0.08
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (17 bp):
ATTATATAATATAAATT
Found at i:295694 original size:2 final size:2
Alignment explanation
Indices: 295687--295720 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
295677 AAACAATAAC
295687 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
295721 TTCAAGATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.