Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr4
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: 30015117
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1306243 characters in sequence are not A, C, G, or T
File 9 of 85
Found at i:3017964 original size:2 final size:2
Alignment explanation
Indices: 3017951--3017997 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
3017941 TTTGAGCCTT
*
3017951 TA TA TG TA TA TA TA TA 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 TA TA TA TA TA TA TA TA
3017993 TA TA T
1 TA TA T
3017998 TCTCTTTTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3026913 original size:18 final size:18
Alignment explanation
Indices: 3026892--3026975 Score: 86
Period size: 18 Copynumber: 4.8 Consensus size: 18
3026882 ATTTTCTTTT
3026892 ACACGAAAATTTTTGAAA
1 ACACGAAAATTTTTGAAA
*
3026910 ACACGAAAATTTGTGAAA
1 ACACGAAAATTTTTGAAA
**
3026928 ACACGAATTTTTTTTTG-AA
1 ACACGAA--AATTTTTGAAA
*
3026947 ACACG--AATTGTTGAAA
1 ACACGAAAATTTTTGAAA
3026963 ACAC-AAAATTTTT
1 ACACGAAAATTTTT
3026976 TCTTAAGGAC
Statistics
Matches: 53, Mismatches: 8, Indels: 11
0.74 0.11 0.15
Matches are distributed among these distances:
15 5 0.09
16 6 0.11
17 6 0.11
18 24 0.45
19 7 0.13
20 5 0.09
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.32
Consensus pattern (18 bp):
ACACGAAAATTTTTGAAA
Found at i:3026976 original size:37 final size:37
Alignment explanation
Indices: 3026901--3026976 Score: 95
Period size: 35 Copynumber: 2.1 Consensus size: 37
3026891 TACACGAAAA
*
3026901 TTTTTGAAAACACGAAAATTTGTGAAAACACGAATTTT
1 TTTTTGAAAACACG-AAATTTGTGAAAACACAAATTTT
*
3026939 TTTTTG-AAACACG-AA-TTGTTGAAAACACAAAATTT
1 TTTTTGAAAACACGAAATTTG-TGAAAACACAAATTTT
3026974 TTT
1 TTT
3026977 CTTAAGGACG
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
34 3 0.09
35 19 0.54
37 7 0.20
38 6 0.17
ACGTcount: A:0.41, C:0.11, G:0.12, T:0.37
Consensus pattern (37 bp):
TTTTTGAAAACACGAAATTTGTGAAAACACAAATTTT
Found at i:3027493 original size:12 final size:10
Alignment explanation
Indices: 3027468--3027518 Score: 52
Period size: 10 Copynumber: 4.9 Consensus size: 10
3027458 GCTCCTCTTC
3027468 TTCTTTTTTT
1 TTCTTTTTTT
3027478 TTCTTTTTCCTT
1 TTCTTTTT--TT
3027490 TTC-TTTTTT
1 TTCTTTTTTT
3027499 TTCTTTCTTCTT
1 TTCTTT-TT-TT
3027511 TT-TTTTTT
1 TTCTTTTTT
3027519 CTGGTTGGGC
Statistics
Matches: 36, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
9 6 0.17
10 12 0.33
11 9 0.25
12 9 0.25
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (10 bp):
TTCTTTTTTT
Found at i:3027498 original size:21 final size:20
Alignment explanation
Indices: 3027463--3027518 Score: 78
Period size: 21 Copynumber: 2.8 Consensus size: 20
3027453 CTCGAGCTCC
*
3027463 TCTTCTTCTTTTTTTTTCTT
1 TCTTCTTTTTTTTTTTTCTT
3027483 T-TTCCTTTTCTTTTTTTTCTT
1 TCTT-CTTTT-TTTTTTTTCTT
3027504 TCTTCTTTTTTTTTT
1 TCTTCTTTTTTTTTT
3027519 CTGGTTGGGC
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
19 2 0.06
20 11 0.34
21 17 0.53
22 2 0.06
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (20 bp):
TCTTCTTTTTTTTTTTTCTT
Found at i:3027509 original size:16 final size:15
Alignment explanation
Indices: 3027468--3027516 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 15
3027458 GCTCCTCTTC
*
3027468 TTCTTTTTTTTTCTTT
1 TTCTTTTTCTTT-TTT
*
3027484 TTCCTTTTCTTTTTT
1 TTCTTTTTCTTTTTT
3027499 TTCTTTCTTCTTTTTT
1 TTCTTT-TTCTTTTTT
3027515 TT
1 TT
3027517 TTCTGGTTGG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
15 8 0.28
16 21 0.72
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (15 bp):
TTCTTTTTCTTTTTT
Found at i:3027516 original size:25 final size:25
Alignment explanation
Indices: 3027460--3027507 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
3027450 CGACTCGAGC
*
3027460 TCCTCTTCTTCTTTTTTTTTCTTTT
1 TCCTTTTCTTCTTTTTTTTTCTTTT
3027485 TCCTTTTCTT-TTTTTTCTTTCTT
1 TCCTTTTCTTCTTTTTT-TTTCTT
3027508 CTTTTTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 6 0.29
25 15 0.71
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (25 bp):
TCCTTTTCTTCTTTTTTTTTCTTTT
Found at i:3027827 original size:5 final size:6
Alignment explanation
Indices: 3027812--3027905 Score: 68
Period size: 7 Copynumber: 14.8 Consensus size: 6
3027802 AAAAAATTTA
* * *
3027812 TTTTCTT TTTTCT TTTTCT TTTTC- TTTTCT TCTTTCT TCTTCCC CTTTCT
1 TTTTC-T TTTTCT TTTTCT TTTTCT TTTTCT T-TTTCT T-TTTCT TTTTCT
3027862 TCTTTC- -TTTCT TCTTTCT TTTTCT TCTTTCT TTCTTCT TCTTTC
1 T-TTTCT TTTTCT T-TTTCT TTTTCT T-TTTCT TT-TTCT T-TTTC
3027906 CTTCTTTTCT
Statistics
Matches: 72, Mismatches: 6, Indels: 18
0.75 0.06 0.19
Matches are distributed among these distances:
4 4 0.06
5 5 0.07
6 23 0.32
7 39 0.54
8 1 0.01
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (6 bp):
TTTTCT
Found at i:3027849 original size:31 final size:31
Alignment explanation
Indices: 3027813--3027913 Score: 100
Period size: 31 Copynumber: 3.3 Consensus size: 31
3027803 AAAAATTTAT
3027813 TTTCTTTTTTCTTTTTCTTTTTCTTTTCTTC
1 TTTCTTTTTTCTTTTTCTTTTTCTTTTCTTC
* * **
3027844 TTTCTTCTTCCCCTTTCTTCTTTC-TTTCTTC
1 TTTCTTTTTTCTTTTTCTT-TTTCTTTTCTTC
*
3027875 TTTC-TTTTTCTTCTTTCTTTCTTCTTCT-TTC
1 TTTCTTTTTTCTT-TTTCTTT-TTCTTTTCTTC
*
3027906 CTTCTTTT
1 TTTCTTTT
3027914 CTTTCTTTCC
Statistics
Matches: 55, Mismatches: 10, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
30 5 0.09
31 41 0.75
32 9 0.16
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (31 bp):
TTTCTTTTTTCTTTTTCTTTTTCTTTTCTTC
Found at i:3027918 original size:27 final size:25
Alignment explanation
Indices: 3027812--3027922 Score: 117
Period size: 24 Copynumber: 4.5 Consensus size: 25
3027802 AAAAAATTTA
*
3027812 TTTTCTTT-TTTCTTTTTCTTTTTC
1 TTTTCTTTCTTTCTTCTTCTTTTTC
**
3027836 TTTTC-TTCTTTCTTCTTCCCCTTTC
1 TTTTCTTTCTTTCTTCTT-CTTTTTC
3027861 --TTCTTTCTTTCTTCTTTCTTTTTC
1 TTTTCTTTCTTTCTTC-TTCTTTTTC
3027885 --TTCTTTCTTTCTTCTTCTTTCCTTC
1 TTTTCTTTCTTTCTTCTTCTTT--TTC
3027910 TTTTCTTTCTTTC
1 TTTTCTTTCTTTC
3027923 CCGATCAGCC
Statistics
Matches: 74, Mismatches: 5, Indels: 13
0.80 0.05 0.14
Matches are distributed among these distances:
23 11 0.15
24 42 0.57
25 10 0.14
27 11 0.15
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (25 bp):
TTTTCTTTCTTTCTTCTTCTTTTTC
Found at i:3028024 original size:15 final size:16
Alignment explanation
Indices: 3027999--3028038 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
3027989 CTCTCCCCTA
*
3027999 TTTTC-TTCTTT-TTC
1 TTTTCTTTCTTTGCTC
3028013 TTTTCTTTCTTTGCTC
1 TTTTCTTTCTTTGCTC
3028029 TTTT-TTTCTT
1 TTTTCTTTCTT
3028039 CTTTGTTTGC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 5 0.22
15 12 0.52
16 6 0.26
ACGTcount: A:0.00, C:0.20, G:0.03, T:0.78
Consensus pattern (16 bp):
TTTTCTTTCTTTGCTC
Found at i:3028033 original size:22 final size:21
Alignment explanation
Indices: 3028005--3028059 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 21
3027995 CCTATTTTCT
3028005 TCTTTTTCTTTTCTTTCTTTGC
1 TCTTTTT-TTTTCTTTCTTTGC
*
3028027 TCTTTTTTTCTTCTTTGTTTGC
1 TCTTTTTTT-TTCTTTCTTTGC
*
3028049 TGTTTTTTTTT
1 TCTTTTTTTTT
3028060 TTACTTTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
21 4 0.13
22 26 0.87
ACGTcount: A:0.00, C:0.16, G:0.07, T:0.76
Consensus pattern (21 bp):
TCTTTTTTTTTCTTTCTTTGC
Found at i:3028431 original size:29 final size:28
Alignment explanation
Indices: 3028349--3028432 Score: 98
Period size: 29 Copynumber: 3.0 Consensus size: 28
3028339 CAATTTTAAG
3028349 AAAATTTT-GGGGTCAAAATGTAAATTTA
1 AAAATTTTAGGGGTCAAAATGT-AATTTA
* * * * *
3028377 AAAAGTTGAGGGGTTAAAGTGAAATTTCA
1 AAAATTTTAGGGGTCAAAATGTAATTT-A
3028406 AAAATTTTAGGGGTCAAAATGTAATTT
1 AAAATTTTAGGGGTCAAAATGTAATTT
3028433 TTTTTTATTT
Statistics
Matches: 44, Mismatches: 10, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
28 11 0.25
29 33 0.75
ACGTcount: A:0.42, C:0.04, G:0.21, T:0.33
Consensus pattern (28 bp):
AAAATTTTAGGGGTCAAAATGTAATTTA
Found at i:3028902 original size:82 final size:82
Alignment explanation
Indices: 3028767--3029636 Score: 1589
Period size: 82 Copynumber: 10.7 Consensus size: 82
3028757 AAAACAATTT
*
3028767 AAAATACCTCAGCGT--GACTCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAA
1 AAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAA
3028830 AAATAGAAATTTAAAAA
66 AAATAGAAATTTAAAAA
3028847 AAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAA
1 AAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAA
3028912 AAATAGAAATTTAAAAA
66 AAATAGAAATTTAAAAA
3028929 AAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAA
1 AAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAA
3028994 AAATAGAAATTTAAAAA
66 AAATAGAAATTTAAAAA
3029011 AAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAA
1 AAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAA
3029076 AAATAGAAATTTAAAAA
66 AAATAGAAATTTAAAAA
3029093 AAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAA
1 AAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAA
3029158 AAATAGAAATTTAAAAA
66 AAATAGAAATTTAAAAA
3029175 AAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAA
1 AAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAA
3029240 AAATAGAAATTTAAAAA
66 AAATAGAAATTTAAAAA
3029257 AAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAA
1 AAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAA
3029322 AAATAGAAATTTAAAAA
66 AAATAGAAATTTAAAAA
3029339 AAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAA
1 AAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAA
3029404 AAATAGAAATTTAAAAA
66 AAATAGAAATTTAAAAA
3029421 AAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAA
1 AAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAA
3029486 AAATAGAAATTTAAAAA
66 AAATAGAAATTTAAAAA
*
3029503 AAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTTGCAATATGAGTTGATTTTTG--AA
1 AAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAA
* *
3029566 AAACAGAAA-TT---GA
66 AAATAGAAATTTAAAAA
* * * * *
3029579 AAAATACATCAACGT--GACTCGAGGCTCAACTCACTTCTCGCATTATGAGTTGATTTTT
1 AAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
3029637 TTTGAAAAAC
Statistics
Matches: 778, Mismatches: 10, Indels: 10
0.97 0.01 0.01
Matches are distributed among these distances:
74 39 0.05
76 14 0.02
79 2 0.00
80 25 0.03
82 698 0.90
ACGTcount: A:0.38, C:0.21, G:0.16, T:0.25
Consensus pattern (82 bp):
AAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAA
AAATAGAAATTTAAAAA
Found at i:3029199 original size:246 final size:246
Alignment explanation
Indices: 3028631--3029636 Score: 1675
Period size: 246 Copynumber: 4.2 Consensus size: 246
3028621 TAGCTCGGCA
* *
3028631 TGCGACCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTGAAAAACAT--AAATTT-
1 TGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAAAAATAGAAATTTA
* * * * *
3028693 AAAAGAAATACCTCGGCATG-G-TCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGA--TTT-
65 AAAAAAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG
* *
3028753 AAAAAAA-A-CAATTT-----AAAATACCTCAGCGT--GACTCGAGGCTCAACTCACCTCTCGCA
130 AAAAAAATAGAAATTTAAAAAAAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCA
3028809 ATATGAGTTGATTTTTGAAAAAAATAGAAATTTAAAAAAAAATACCTCAGCG
195 ATATGAGTTGATTTTTGAAAAAAATAGAAATTTAAAAAAAAATACCTCAGCG
3028861 TGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAAATAGAAATTTAA
1 TGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAAATAGAAATTTAA
3028926 AAAAAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGA
66 AAAAAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGA
3028991 AAAAAATAGAAATTTAAAAAAAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAA
131 AAAAAATAGAAATTTAAAAAAAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAA
3029056 TATGAGTTGATTTTTGAAAAAAATAGAAATTTAAAAAAAAATACCTCAGCG
196 TATGAGTTGATTTTTGAAAAAAATAGAAATTTAAAAAAAAATACCTCAGCG
3029107 TGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAAATAGAAATTTAA
1 TGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAAATAGAAATTTAA
3029172 AAAAAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGA
66 AAAAAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGA
3029237 AAAAAATAGAAATTTAAAAAAAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAA
131 AAAAAATAGAAATTTAAAAAAAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAA
3029302 TATGAGTTGATTTTTGAAAAAAATAGAAATTTAAAAAAAAATACCTCAGCG
196 TATGAGTTGATTTTTGAAAAAAATAGAAATTTAAAAAAAAATACCTCAGCG
3029353 TGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAAATAGAAATTTAA
1 TGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAAATAGAAATTTAA
3029418 AAAAAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGA
66 AAAAAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGA
*
3029483 AAAAAATAGAAATTTAAAAAAAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTTGCAA
131 AAAAAATAGAAATTTAAAAAAAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAA
* * * *
3029548 TATGAGTTGATTTTTG--AAAAACAGAAA-TT---GAAAAATACATCAACG
196 TATGAGTTGATTTTTGAAAAAAATAGAAATTTAAAAAAAAATACCTCAGCG
* * *
3029593 T--GACTCGAGGCTCAACTCACTTCTCGCATTATGAGTTGATTTTT
1 TGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
3029637 TTTGAAAAAC
Statistics
Matches: 742, Mismatches: 17, Indels: 26
0.95 0.02 0.03
Matches are distributed among these distances:
229 13 0.02
230 40 0.05
231 6 0.01
232 17 0.02
233 1 0.00
234 34 0.05
236 3 0.00
237 7 0.01
238 41 0.06
239 5 0.01
240 14 0.02
243 2 0.00
244 25 0.03
246 534 0.72
ACGTcount: A:0.38, C:0.21, G:0.16, T:0.26
Consensus pattern (246 bp):
TGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAAATAGAAATTTAA
AAAAAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGA
AAAAAATAGAAATTTAAAAAAAAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAA
TATGAGTTGATTTTTGAAAAAAATAGAAATTTAAAAAAAAATACCTCAGCG
Found at i:3030539 original size:18 final size:18
Alignment explanation
Indices: 3030509--3030561 Score: 65
Period size: 18 Copynumber: 2.9 Consensus size: 18
3030499 TTCATCTTGA
3030509 TTTTT-CTTCTTTTTTTGT
1 TTTTTGCTT-TTTTTTTGT
3030527 TTTTTGCTTTTTTTTTGT
1 TTTTTGCTTTTTTTTTGT
3030545 TGTTGTTG-TTTTTTTTT
1 T-TT-TTGCTTTTTTTTT
3030562 TTAGGCATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
18 15 0.47
19 14 0.44
20 3 0.09
ACGTcount: A:0.00, C:0.06, G:0.11, T:0.83
Consensus pattern (18 bp):
TTTTTGCTTTTTTTTTGT
Found at i:3030939 original size:29 final size:29
Alignment explanation
Indices: 3030906--3030982 Score: 91
Period size: 29 Copynumber: 2.7 Consensus size: 29
3030896 AGAAAATTTT
*
3030906 GGGGTCAAAATGTTATTTTAAAAAGTTGA
1 GGGGTCAAAATGTAATTTTAAAAAGTTGA
* * * * * *
3030935 GGGGTTAAAGTGAAATTTCAAAAATTTTA
1 GGGGTCAAAATGTAATTTTAAAAAGTTGA
3030964 GGGGTCAAAATGTAATTTT
1 GGGGTCAAAATGTAATTTT
3030983 TTATTTTGTA
Statistics
Matches: 37, Mismatches: 11, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.38, C:0.04, G:0.23, T:0.35
Consensus pattern (29 bp):
GGGGTCAAAATGTAATTTTAAAAAGTTGA
Found at i:3031228 original size:27 final size:25
Alignment explanation
Indices: 3031188--3031273 Score: 77
Period size: 27 Copynumber: 3.2 Consensus size: 25
3031178 CTAAATGCAC
3031188 ATTTTTATTATTTTATTATTTTTTATA
1 ATTTTTATT-TTTTA-TATTTTTTATA
*
3031215 ATTTTTAATTTTTTGA-ATTTTTT-TCC
1 ATTTTT-ATTTTTT-ATATTTTTTAT-A
*
3031241 ATATTTTATTTTTTATAATATTTTATA
1 AT-TTTTATTTTTTAT-ATTTTTTATA
3031268 ATTTTT
1 ATTTTT
3031274 TTAATAGTTA
Statistics
Matches: 49, Mismatches: 3, Indels: 15
0.73 0.04 0.22
Matches are distributed among these distances:
25 2 0.04
26 20 0.41
27 22 0.45
28 5 0.10
ACGTcount: A:0.26, C:0.02, G:0.01, T:0.71
Consensus pattern (25 bp):
ATTTTTATTTTTTATATTTTTTATA
Found at i:3031264 original size:10 final size:10
Alignment explanation
Indices: 3031251--3031305 Score: 51
Period size: 10 Copynumber: 5.5 Consensus size: 10
3031241 ATATTTTATT
3031251 TTTTATAATA
1 TTTTATAATA
3031261 TTTTATAAT-
1 TTTTATAATA
*
3031270 TTTTTTAATA
1 TTTTATAATA
*
3031280 -GTTATAAATA
1 TTTTAT-AATA
*
3031290 TTTTTATAATT
1 -TTTTATAATA
3031301 TTTTA
1 TTTTA
3031306 AGTTTTTTCT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
9 11 0.31
10 18 0.50
11 3 0.08
12 4 0.11
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.64
Consensus pattern (10 bp):
TTTTATAATA
Found at i:3031278 original size:19 final size:19
Alignment explanation
Indices: 3031190--3031313 Score: 70
Period size: 18 Copynumber: 6.7 Consensus size: 19
3031180 AAATGCACAT
* * *
3031190 TTTTATTATTTTATT-ATT
1 TTTTATAATTTTTTTAATA
3031208 TTTTATAA--TTTTTAAT-
1 TTTTATAATTTTTTTAATA
*
3031224 TTTT-TGAATTTTTTTCCATA
1 TTTTAT-AATTTTTTT-AATA
*
3031244 TTTTAT--TTTTTATAATA
1 TTTTATAATTTTTTTAATA
3031261 TTTTATAATTTTTTTAATA
1 TTTTATAATTTTTTTAATA
*
3031280 -GTTATAAATATTTTTATAAT-
1 TTTTAT-AAT-TTTTT-TAATA
3031300 TTTT-TAAGTTTTTT
1 TTTTATAA-TTTTTT
3031314 CTTTTAATTT
Statistics
Matches: 84, Mismatches: 8, Indels: 27
0.71 0.07 0.23
Matches are distributed among these distances:
15 1 0.01
16 10 0.12
17 11 0.13
18 22 0.26
19 22 0.26
20 11 0.13
21 7 0.08
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (19 bp):
TTTTATAATTTTTTTAATA
Found at i:3031291 original size:46 final size:43
Alignment explanation
Indices: 3031203--3031293 Score: 101
Period size: 46 Copynumber: 2.0 Consensus size: 43
3031193 TATTATTTTA
** * **
3031203 TTATTTTTTATAATTTTTAATTTTTTGAATTTTTTTCCATATT
1 TTATTTTTTATAATTTTTAATTTTTTGAATAGTTATAAATATT
*
3031246 TTATTTTTTATAATATTTTATAATTTTTTTAATAGTTATAAATATT
1 TTATTTTTTAT-A-ATTTT-TAATTTTTTGAATAGTTATAAATATT
3031292 TT
1 TT
3031294 TATAATTTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
43 11 0.28
44 1 0.03
45 5 0.13
46 22 0.56
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (43 bp):
TTATTTTTTATAATTTTTAATTTTTTGAATAGTTATAAATATT
Found at i:3031303 original size:9 final size:9
Alignment explanation
Indices: 3031188--3031312 Score: 57
Period size: 9 Copynumber: 13.7 Consensus size: 9
3031178 CTAAATGCAC
*
3031188 ATTTTTATT
1 ATTTTTATA
3031197 A-TTTTATTA
1 ATTTTTA-TA
*
3031206 TTTTTTATA
1 ATTTTTATA
3031215 A-TTTT-TA
1 ATTTTTATA
3031222 ATTTTT-TGA
1 ATTTTTAT-A
* *
3031231 ATTTTTTTCC
1 ATTTTTAT-A
3031241 ATATTTTAT-
1 AT-TTTTATA
3031250 -TTTTTATA
1 ATTTTTATA
3031258 ATATTTTATA
1 AT-TTTTATA
*
3031268 ATTTTTTTA
1 ATTTTTATA
* *
3031277 ATAGTTATAAA
1 AT--TTTTATA
3031288 TATTTTTATA
1 -ATTTTTATA
3031298 ATTTTT-TA
1 ATTTTTATA
3031306 AGTTTTT
1 A-TTTTT
3031313 TCTTTTAATT
Statistics
Matches: 91, Mismatches: 12, Indels: 26
0.71 0.09 0.20
Matches are distributed among these distances:
7 9 0.10
8 18 0.20
9 31 0.34
10 22 0.24
11 9 0.10
12 2 0.02
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.68
Consensus pattern (9 bp):
ATTTTTATA
Found at i:3032478 original size:46 final size:46
Alignment explanation
Indices: 3032371--3032523 Score: 267
Period size: 46 Copynumber: 3.4 Consensus size: 46
3032361 TACGTATGGT
3032371 CACTTATCAC-TTGTC-CTTGATCAGATAAGTGTAGCT-AGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
3032414 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
* *
3032460 CACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAATGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
3032506 CACTTATCACTTTGTCAC
1 CACTTATCACTTTGTCAC
3032524 CGCTTATCAC
Statistics
Matches: 104, Mismatches: 3, Indels: 3
0.95 0.03 0.03
Matches are distributed among these distances:
43 10 0.10
44 5 0.05
45 21 0.20
46 68 0.65
ACGTcount: A:0.27, C:0.24, G:0.15, T:0.34
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
Found at i:3039865 original size:381 final size:378
Alignment explanation
Indices: 3039155--3039865 Score: 907
Period size: 381 Copynumber: 1.9 Consensus size: 378
3039145 ACTATAACAA
* * *
3039155 CCTAATTTTCAGTGGTGTCAGAAACAGTGGTTCGAGACCACTAAATCCGATGAGTGAGTTCAAAA
1 CCTAATTTTCAGTGGTGTCAGAAACAGTGATCCGAGACCACTAAATCCGATGAATGAGTTCAAAA
* * * * * * * * *
3039220 TTTTTATTATTTAGTATTTATGAGCCAAATGTGATTTTAGGAAGACTTTTGAATTAGTGAATTGT
66 TTTTAATAAATTAATAATTATGAGCCAAATGTGAATTTAGAAAAAATTTTGAATTAGTGAATTGT
* * * ** *
3039285 GTTTTAGAAGAATTTATTAGGATAATTCGTTTCGAAAATAAGGTATCAAGACCTCAGTTTTATAA
131 GTTTAAAAAGAATTTAATAGGATAATTCGGGTCGAAAATAAGGTATCAAGACCTCAGTTTCATAA
* * * * **
3039350 ATCAAGCCGTGAATATTTTATAAATATTTATGGAGTCTCATTAGAGTAGTATTAAAGTTTTGTTA
196 ACCAAGCCATAAATATTTTATAAATATTTATGGAGTCTCATTAGAGTAGTATAAAAGTTTCATTA
* * * *
3039415 GAAAATTTTAACGTTTTGATAGTTAATTAATTAAAAAGGACTAGATTGAAAAAGGTGCAAAACTT
261 GAAAATTTTAACGTTTTGATAGTCAATTAATTAAAAAGAACTAAATTGAAAAAGGTACAAAACTT
3039480 GTTAATTAAAGAAATAATGATTAAATGACTCAAGTGATAAATAAGTGTAGCAG
326 GTTAATTAAAGAAATAATGATTAAATGACTCAAGTGATAAATAAGTGTAGCAG
* * * *
3039533 CCTAATTTTCAGTGGTGTCGGAAACAGTGATCCGAGATCACTAAATCTGACT-AATGAGTCTTAA
1 CCTAATTTTCAGTGGTGTCAGAAACAGTGATCCGAGACCACTAAATCCGA-TGAATGAGT-TCAA
* * *
3039597 AA-TTTAATAAATTAATAATTATGGGTCAAGTGTGAATTTAGAAAAAATTTTGAATTAGTGAATT
64 AATTTTAATAAATTAATAATTATGAGCCAAATGTGAATTTAGAAAAAATTTTGAATTAGTGAA--
* *
3039661 TTGTGATTTAAAAAGAATTTAATAGG-TAAATT-GGGTCTAAAATGAGGTATCAAGACCTCGAG-
127 TTGTG-TTTAAAAAGAATTTAATAGGAT-AATTCGGGTCGAAAATAAGGTATCAAGACCTC-AGT
*
3039723 TTCATAAACCAAGCCATAAATATTTTTATAAATATTTATGGAGTGTCATT-GAGTTAGTATAAAA
189 TTCATAAACCAAGCCATAAATA-TTTTATAAATATTTATGGAGTCTCATTAGAG-TAGTATAAAA
3039787 GTTTCATTAGAAAATTTTAACG-TTTGAATAGTCAATTAATTAAAAAGAACTAAATTGAAAATA-
252 GTTTCATTAGAAAATTTTAACGTTTTG-ATAGTCAATTAATTAAAAAGAACTAAATTGAAAA-AG
* *
3039850 GTATAAAATTTGTTAA
315 GTACAAAACTTGTTAA
3039866 ATTGTGATTA
Statistics
Matches: 282, Mismatches: 40, Indels: 19
0.83 0.12 0.06
Matches are distributed among these distances:
378 99 0.35
379 6 0.02
380 54 0.19
381 122 0.43
382 1 0.00
ACGTcount: A:0.39, C:0.09, G:0.17, T:0.35
Consensus pattern (378 bp):
CCTAATTTTCAGTGGTGTCAGAAACAGTGATCCGAGACCACTAAATCCGATGAATGAGTTCAAAA
TTTTAATAAATTAATAATTATGAGCCAAATGTGAATTTAGAAAAAATTTTGAATTAGTGAATTGT
GTTTAAAAAGAATTTAATAGGATAATTCGGGTCGAAAATAAGGTATCAAGACCTCAGTTTCATAA
ACCAAGCCATAAATATTTTATAAATATTTATGGAGTCTCATTAGAGTAGTATAAAAGTTTCATTA
GAAAATTTTAACGTTTTGATAGTCAATTAATTAAAAAGAACTAAATTGAAAAAGGTACAAAACTT
GTTAATTAAAGAAATAATGATTAAATGACTCAAGTGATAAATAAGTGTAGCAG
Found at i:3040973 original size:46 final size:46
Alignment explanation
Indices: 3040895--3041033 Score: 224
Period size: 46 Copynumber: 3.0 Consensus size: 46
3040885 CATGGAAAAA
* * *
3040895 TGTGAAAAGCAGGTATGGTATTTCGGTAAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
*
3040941 TGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
* *
3040987 TGTGAAAAGTAGGTATGGTATTTCCGTGAATAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
3041033 T
1 T
3041034 ATAGCATTGT
Statistics
Matches: 86, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 86 1.00
ACGTcount: A:0.35, C:0.10, G:0.26, T:0.29
Consensus pattern (46 bp):
TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
Found at i:3043571 original size:21 final size:21
Alignment explanation
Indices: 3043545--3043622 Score: 66
Period size: 21 Copynumber: 3.7 Consensus size: 21
3043535 CAGTTTAATC
* *
3043545 CTTATGGGTTTTTGTTCAGCT
1 CTTATGGGTTTCTGTTCAGCA
* * * * *
3043566 CTTATGAGCTTCCGTTCAACC
1 CTTATGGGTTTCTGTTCAGCA
*
3043587 CTTATGGGTTTCTGTTTAGCA
1 CTTATGGGTTTCTGTTCAGCA
* *
3043608 CTTATGTGCTTCTGT
1 CTTATGGGTTTCTGT
3043623 GCAACCTTCG
Statistics
Matches: 43, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.13, C:0.21, G:0.21, T:0.46
Consensus pattern (21 bp):
CTTATGGGTTTCTGTTCAGCA
Found at i:3043628 original size:42 final size:42
Alignment explanation
Indices: 3043484--3043628 Score: 148
Period size: 42 Copynumber: 3.5 Consensus size: 42
3043474 AGTTAAGTCA
* * * *
3043484 TATGAGTTTTAGTTTAACCC-TATTGGGTTTCCGTTTAGCTCT
1 TATGAGCTTCAGTTCAACCCTTA-TGGGTTTCTGTTTAGCTCT
* * * * *
3043526 TTTGAGCTTCAGTTTAATCCTTATGGGTTTTTGTTCAGCTCT
1 TATGAGCTTCAGTTCAACCCTTATGGGTTTCTGTTTAGCTCT
* *
3043568 TATGAGCTTCCGTTCAACCCTTATGGGTTTCTGTTTAGCACT
1 TATGAGCTTCAGTTCAACCCTTATGGGTTTCTGTTTAGCTCT
* * *
3043610 TATGTGCTTCTGTGCAACC
1 TATGAGCTTCAGTTCAACC
3043629 TTCGGGCTTT
Statistics
Matches: 85, Mismatches: 17, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
42 83 0.98
43 2 0.02
ACGTcount: A:0.16, C:0.20, G:0.19, T:0.45
Consensus pattern (42 bp):
TATGAGCTTCAGTTCAACCCTTATGGGTTTCTGTTTAGCTCT
Found at i:3043997 original size:21 final size:21
Alignment explanation
Indices: 3043971--3044048 Score: 66
Period size: 21 Copynumber: 3.7 Consensus size: 21
3043961 CAGTTTAATC
* *
3043971 CTTATGGGTTTTTGTTCAGCT
1 CTTATGGGTTTCTGTTCAGCA
* * * * *
3043992 CTTATGAGCTTCCGTTCAACC
1 CTTATGGGTTTCTGTTCAGCA
*
3044013 CTTATGGGTTTCTGTTTAGCA
1 CTTATGGGTTTCTGTTCAGCA
* *
3044034 CTTATGTGCTTCTGT
1 CTTATGGGTTTCTGT
3044049 GCAACCTTCG
Statistics
Matches: 43, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.13, C:0.21, G:0.21, T:0.46
Consensus pattern (21 bp):
CTTATGGGTTTCTGTTCAGCA
Found at i:3044054 original size:42 final size:42
Alignment explanation
Indices: 3043910--3044054 Score: 148
Period size: 42 Copynumber: 3.5 Consensus size: 42
3043900 AGTTAAGTCA
* * * *
3043910 TATGAGTTTTAGTTTAACCC-TATTGGGTTTCCGTTTAGCTCT
1 TATGAGCTTCAGTTCAACCCTTA-TGGGTTTCTGTTTAGCTCT
* * * * *
3043952 TTTGAGCTTCAGTTTAATCCTTATGGGTTTTTGTTCAGCTCT
1 TATGAGCTTCAGTTCAACCCTTATGGGTTTCTGTTTAGCTCT
* *
3043994 TATGAGCTTCCGTTCAACCCTTATGGGTTTCTGTTTAGCACT
1 TATGAGCTTCAGTTCAACCCTTATGGGTTTCTGTTTAGCTCT
* * *
3044036 TATGTGCTTCTGTGCAACC
1 TATGAGCTTCAGTTCAACC
3044055 TTCGGGCTTT
Statistics
Matches: 85, Mismatches: 17, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
42 83 0.98
43 2 0.02
ACGTcount: A:0.16, C:0.20, G:0.19, T:0.45
Consensus pattern (42 bp):
TATGAGCTTCAGTTCAACCCTTATGGGTTTCTGTTTAGCTCT
Found at i:3044105 original size:426 final size:426
Alignment explanation
Indices: 3043298--3044164 Score: 1707
Period size: 426 Copynumber: 2.0 Consensus size: 426
3043288 TTGTTGAAAA
* * *
3043298 TAAAATTATTGTTAAATTATGAAATTGAATTGATTGTTCAAAACGAGTAGAACGCGAGATTGAGT
1 TAAAGTTATTATTGAATTATGAAATTGAATTGATTGTTCAAAACGAGTAGAACGCGAGATTGAGT
3043363 ACAGTTGTTCTATGCAAATGATGAATTGACGGTAAATTACACAAGTAAATTGAGGTTTAGCATTT
66 ACAGTTGTTCTATGCAAATGATGAATTGACGGTAAATTACACAAGTAAATTGAGGTTTAGCATTT
3043428 GTTGCGAACTTTCGTATTTACTTTCCGTTTAACTCTCATGAGCTTCAGTTAAGTCATATGAGTTT
131 GTTGCGAACTTTCGTATTTACTTTCCGTTTAACTCTCATGAGCTTCAGTTAAGTCATATGAGTTT
3043493 TAGTTTAACCCTATTGGGTTTCCGTTTAGCTCTTTTGAGCTTCAGTTTAATCCTTATGGGTTTTT
196 TAGTTTAACCCTATTGGGTTTCCGTTTAGCTCTTTTGAGCTTCAGTTTAATCCTTATGGGTTTTT
3043558 GTTCAGCTCTTATGAGCTTCCGTTCAACCCTTATGGGTTTCTGTTTAGCACTTATGTGCTTCTGT
261 GTTCAGCTCTTATGAGCTTCCGTTCAACCCTTATGGGTTTCTGTTTAGCACTTATGTGCTTCTGT
3043623 GCAACCTTCGGGCTTTTGTATACGATGTACTCATATCCGTAAGACATTCTTCGATTTGACAAGGG
326 GCAACCTTCGGGCTTTTGTATACGATGTACTCATATCCGTAAGACATTCTTCGATTTGACAAGGG
3043688 TTGGTAAGTGACATATGGAATTAATGTTTGAAGACT
391 TTGGTAAGTGACATATGGAATTAATGTTTGAAGACT
3043724 TAAAGTTATTATTGAATTATGAAATTGAATTGATTGTTCAAAACGAGTAGAACGCGAGATTGAGT
1 TAAAGTTATTATTGAATTATGAAATTGAATTGATTGTTCAAAACGAGTAGAACGCGAGATTGAGT
3043789 ACAGTTGTTCTATGCAAATGATGAATTGACGGTAAATTACACAAGTAAATTGAGGTTTAGCATTT
66 ACAGTTGTTCTATGCAAATGATGAATTGACGGTAAATTACACAAGTAAATTGAGGTTTAGCATTT
3043854 GTTGCGAACTTTCGTATTTACTTTCCGTTTAACTCTCATGAGCTTCAGTTAAGTCATATGAGTTT
131 GTTGCGAACTTTCGTATTTACTTTCCGTTTAACTCTCATGAGCTTCAGTTAAGTCATATGAGTTT
3043919 TAGTTTAACCCTATTGGGTTTCCGTTTAGCTCTTTTGAGCTTCAGTTTAATCCTTATGGGTTTTT
196 TAGTTTAACCCTATTGGGTTTCCGTTTAGCTCTTTTGAGCTTCAGTTTAATCCTTATGGGTTTTT
3043984 GTTCAGCTCTTATGAGCTTCCGTTCAACCCTTATGGGTTTCTGTTTAGCACTTATGTGCTTCTGT
261 GTTCAGCTCTTATGAGCTTCCGTTCAACCCTTATGGGTTTCTGTTTAGCACTTATGTGCTTCTGT
3044049 GCAACCTTCGGGCTTTTGTATACGATGTACTCATATCCGTAAGACATTCTTCGATTTGACAAGGG
326 GCAACCTTCGGGCTTTTGTATACGATGTACTCATATCCGTAAGACATTCTTCGATTTGACAAGGG
3044114 TTGGTAAGTGACATATGGAATTAATGTTTGAAGACT
391 TTGGTAAGTGACATATGGAATTAATGTTTGAAGACT
3044150 TAAAGTTATTATTGA
1 TAAAGTTATTATTGA
3044165 TATTGATCTA
Statistics
Matches: 438, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
426 438 1.00
ACGTcount: A:0.26, C:0.15, G:0.20, T:0.39
Consensus pattern (426 bp):
TAAAGTTATTATTGAATTATGAAATTGAATTGATTGTTCAAAACGAGTAGAACGCGAGATTGAGT
ACAGTTGTTCTATGCAAATGATGAATTGACGGTAAATTACACAAGTAAATTGAGGTTTAGCATTT
GTTGCGAACTTTCGTATTTACTTTCCGTTTAACTCTCATGAGCTTCAGTTAAGTCATATGAGTTT
TAGTTTAACCCTATTGGGTTTCCGTTTAGCTCTTTTGAGCTTCAGTTTAATCCTTATGGGTTTTT
GTTCAGCTCTTATGAGCTTCCGTTCAACCCTTATGGGTTTCTGTTTAGCACTTATGTGCTTCTGT
GCAACCTTCGGGCTTTTGTATACGATGTACTCATATCCGTAAGACATTCTTCGATTTGACAAGGG
TTGGTAAGTGACATATGGAATTAATGTTTGAAGACT
Found at i:3045772 original size:17 final size:17
Alignment explanation
Indices: 3045717--3045778 Score: 54
Period size: 18 Copynumber: 3.5 Consensus size: 17
3045707 GAAACAACAT
* *
3045717 AATTAAAAACAAGAACCA
1 AATTAAAAAGAA-AACGA
* *
3045735 AAATAATAAACAAAACGA
1 AATTAA-AAAGAAAACGA
3045753 AATTGAAAAAGAAAAC-A
1 AATT-AAAAAGAAAACGA
3045770 AATTAAAAA
1 AATTAAAAA
3045779 CCAGCCTAGA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
16 5 0.13
17 5 0.13
18 20 0.53
19 8 0.21
ACGTcount: A:0.71, C:0.10, G:0.06, T:0.13
Consensus pattern (17 bp):
AATTAAAAAGAAAACGA
Found at i:3046718 original size:7 final size:7
Alignment explanation
Indices: 3046708--3046736 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
3046698 AAATTTTTTT
3046708 ATATAAA
1 ATATAAA
3046715 ATATAAA
1 ATATAAA
3046722 ATATAAA
1 ATATAAA
3046729 ATATAAA
1 ATATAAA
3046736 A
1 A
3046737 AAACATTATT
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:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (7 bp):
ATATAAA
Found at i:3046915 original size:114 final size:115
Alignment explanation
Indices: 3046774--3047002 Score: 451
Period size: 114 Copynumber: 2.0 Consensus size: 115
3046764 AATAAGAATG
3046774 ATATTTTAATAAATTTTTTACATCAACTCATTTAAGCATTTTATTATTATTATTTTAGTATAGAT
1 ATATTTTAATAAATTTTTTACATCAACTCATTTAAGCATTTTATTATTATTATTTTAGTATAGAT
3046839 ATTATAGATGTATTTATCCGTTTTACAATGAATCTCATGTTTTTTAGTGT
66 ATTATAGATGTATTTATCCGTTTTACAATGAATCTCATGTTTTTTAGTGT
3046889 ATATTTTAAT-AATTTTTTACATCAACTCATTTAAGCATTTTATTATTATTATTTTAGTATAGAT
1 ATATTTTAATAAATTTTTTACATCAACTCATTTAAGCATTTTATTATTATTATTTTAGTATAGAT
3046953 ATTATAGATGTATTTATCCGTTTTACAATGAATCTCATGTTTTTTAGTGT
66 ATTATAGATGTATTTATCCGTTTTACAATGAATCTCATGTTTTTTAGTGT
3047003 TTAATTGTTC
Statistics
Matches: 114, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
114 104 0.91
115 10 0.09
ACGTcount: A:0.31, C:0.09, G:0.09, T:0.52
Consensus pattern (115 bp):
ATATTTTAATAAATTTTTTACATCAACTCATTTAAGCATTTTATTATTATTATTTTAGTATAGAT
ATTATAGATGTATTTATCCGTTTTACAATGAATCTCATGTTTTTTAGTGT
Found at i:3049165 original size:2 final size:2
Alignment explanation
Indices: 3049158--3049186 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3049148 TTGGTAGCGT
3049158 TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3049187 AATAGAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3049412 original size:26 final size:26
Alignment explanation
Indices: 3049368--3049419 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
3049358 AATTATAAAG
*
3049368 AATATAATTTAAACTTAAATTTCATA
1 AATAAAATTTAAACTTAAATTTCATA
3049394 AATAAAATTATAAAC-TAAATTTCATA
1 AATAAAATT-TAAACTTAAATTTCATA
3049420 CATATATAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 19 0.79
27 5 0.21
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (26 bp):
AATAAAATTTAAACTTAAATTTCATA
Found at i:3060408 original size:17 final size:17
Alignment explanation
Indices: 3060386--3060420 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
3060376 AAGAAAGTGG
*
3060386 AGTGTAAAATCTAAAGC
1 AGTGTAAAATATAAAGC
3060403 AGTGTAAAATATAAAGC
1 AGTGTAAAATATAAAGC
3060420 A
1 A
3060421 CATAATACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.51, C:0.09, G:0.17, T:0.23
Consensus pattern (17 bp):
AGTGTAAAATATAAAGC
Found at i:3068867 original size:19 final size:20
Alignment explanation
Indices: 3068843--3068880 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
3068833 AATTTCCGAC
3068843 TTTTTTGATTAATT-TATTA
1 TTTTTTGATTAATTCTATTA
3068862 TTTTTTGATTAATTCTATT
1 TTTTTTGATTAATTCTATT
3068881 TGAATAATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.24, C:0.03, G:0.05, T:0.68
Consensus pattern (20 bp):
TTTTTTGATTAATTCTATTA
Found at i:3086700 original size:19 final size:20
Alignment explanation
Indices: 3086668--3086711 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
3086658 AATAATTTAT
3086668 TAAAAATTCAT-AAAATAGA
1 TAAAAATTCATAAAAATAGA
3086687 TAAAAATT-ATTAAAAATAGA
1 TAAAAATTCA-TAAAAATAGA
*
3086707 GAAAA
1 TAAAA
3086712 GCGGCTCAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 1 0.05
19 9 0.41
20 12 0.55
ACGTcount: A:0.66, C:0.02, G:0.07, T:0.25
Consensus pattern (20 bp):
TAAAAATTCATAAAAATAGA
Found at i:3095768 original size:21 final size:21
Alignment explanation
Indices: 3095742--3095790 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
3095732 AATAGAAGTT
3095742 GTGAATGAC-GGGAAATTGACA
1 GTGAATGACAGGG-AATTGACA
3095763 GTGAATGACAGGGAATTGACA
1 GTGAATGACAGGGAATTGACA
3095784 -TGAATGA
1 GTGAATGA
3095791 TTTTATTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.26
21 17 0.63
22 3 0.11
ACGTcount: A:0.39, C:0.08, G:0.33, T:0.20
Consensus pattern (21 bp):
GTGAATGACAGGGAATTGACA
Found at i:3101578 original size:41 final size:41
Alignment explanation
Indices: 3101514--3101633 Score: 168
Period size: 41 Copynumber: 2.9 Consensus size: 41
3101504 TCAGATTTAT
* * *
3101514 TGCCAGTGAAATAATTCAAACTTTATGTCTAGCAGGTTTGA
1 TGCCAGTGAAATATTTCAGACTTTATGTCTAGCAGGCTTGA
* *
3101555 TGCCGGTGAAATATTTCAGACTTTATGTCTAGCAAGCTTGA
1 TGCCAGTGAAATATTTCAGACTTTATGTCTAGCAGGCTTGA
* * *
3101596 TGCCAGTGAAATGTTTCGGACTTTACGTCTAGCAGGCT
1 TGCCAGTGAAATATTTCAGACTTTATGTCTAGCAGGCT
3101634 AAGTGCCGGT
Statistics
Matches: 69, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 69 1.00
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.33
Consensus pattern (41 bp):
TGCCAGTGAAATATTTCAGACTTTATGTCTAGCAGGCTTGA
Found at i:3103412 original size:42 final size:42
Alignment explanation
Indices: 3103359--3103551 Score: 201
Period size: 42 Copynumber: 4.6 Consensus size: 42
3103349 AAGGCTGAAT
* * * ** *
3103359 AGAAGCACATAAGTGCTAAACAGAAATTCATAAGGGTTGAAC
1 AGAAGCTCATAAGAGCTGAACAGAAACCCATAAGGGTTAAAC
* * *
3103401 GGAAGCTCATAAGAGCTGAACAAAAACCCATAAGGGTTAAAT
1 AGAAGCTCATAAGAGCTGAACAGAAACCCATAAGGGTTAAAC
* *
3103443 AGAAGCTCAAAAGAGCTGAACAGAAACCCATCAGGGTTAAAC
1 AGAAGCTCATAAGAGCTGAACAGAAACCCATAAGGGTTAAAC
* * * * *
3103485 AGAAGCTCA-ATAGAGCTGAACGGGAACTCATATGAGTTAAAC
1 AGAAGCTCATA-AGAGCTGAACAGAAACCCATAAGGGTTAAAC
* *
3103527 AGAAGCTCGTAAGAGCTAAAC-GAAA
1 AGAAGCTCATAAGAGCTGAACAGAAA
3103552 AGTAAACACG
Statistics
Matches: 126, Mismatches: 23, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
41 4 0.03
42 121 0.96
43 1 0.01
ACGTcount: A:0.45, C:0.17, G:0.22, T:0.16
Consensus pattern (42 bp):
AGAAGCTCATAAGAGCTGAACAGAAACCCATAAGGGTTAAAC
Found at i:3103420 original size:21 final size:21
Alignment explanation
Indices: 3103359--3103547 Score: 103
Period size: 21 Copynumber: 9.0 Consensus size: 21
3103349 AAGGCTGAAT
* *
3103359 AGAAGCACATAAGTGCTAAAC
1 AGAAGCTCATAAGAGCTAAAC
** * * *
3103380 AGAAATTCATAAGGGTTGAAC
1 AGAAGCTCATAAGAGCTAAAC
* *
3103401 GGAAGCTCATAAGAGCTGAAC
1 AGAAGCTCATAAGAGCTAAAC
* * * * * *
3103422 AAAAACCCATAAGGGTTAAAT
1 AGAAGCTCATAAGAGCTAAAC
* *
3103443 AGAAGCTCAAAAGAGCTGAAC
1 AGAAGCTCATAAGAGCTAAAC
* * * * *
3103464 AGAAACCCATCAGGGTTAAAC
1 AGAAGCTCATAAGAGCTAAAC
*
3103485 AGAAGCTCA-ATAGAGCTGAAC
1 AGAAGCTCATA-AGAGCTAAAC
* * *
3103506 GGGAA-CTCATATGAGTTAAAC
1 -AGAAGCTCATAAGAGCTAAAC
*
3103527 AGAAGCTCGTAAGAGCTAAAC
1 AGAAGCTCATAAGAGCTAAAC
3103548 GAAAAGTAAA
Statistics
Matches: 116, Mismatches: 48, Indels: 8
0.67 0.28 0.05
Matches are distributed among these distances:
20 3 0.03
21 109 0.94
22 4 0.03
ACGTcount: A:0.44, C:0.17, G:0.22, T:0.16
Consensus pattern (21 bp):
AGAAGCTCATAAGAGCTAAAC
Found at i:3112692 original size:15 final size:15
Alignment explanation
Indices: 3112657--3112685 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3112647 AACAATCGCC
3112657 ATGTTT-TTTTTTAA
1 ATGTTTATTTTTTAA
3112671 ATGTTTATTTTTTAA
1 ATGTTTATTTTTTAA
3112686 TATTTTACTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.69
Consensus pattern (15 bp):
ATGTTTATTTTTTAA
Found at i:3113653 original size:10 final size:8
Alignment explanation
Indices: 3113615--3113667 Score: 54
Period size: 9 Copynumber: 6.2 Consensus size: 8
3113605 ATAAATTATT
3113615 TAAAAATTA
1 TAAAAA-TA
*
3113624 TAAAAATGG
1 TAAAAAT-A
3113633 TAAAAA-A
1 TAAAAATA
3113640 TAAAAATCA
1 TAAAAAT-A
3113649 TTAAAAATA
1 -TAAAAATA
3113658 TAAAAATA
1 TAAAAATA
3113666 TA
1 TA
3113668 TAATTTTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
7 6 0.16
8 11 0.29
9 14 0.37
10 7 0.18
ACGTcount: A:0.68, C:0.02, G:0.04, T:0.26
Consensus pattern (8 bp):
TAAAAATA
Found at i:3113661 original size:25 final size:25
Alignment explanation
Indices: 3113615--3113663 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
3113605 ATAAATTATT
* *
3113615 TAAAAATTATAAAAATGGTAAAAAA
1 TAAAAATCATAAAAATGATAAAAAA
3113640 TAAAAATCATTAAAAAT-ATAAAAA
1 TAAAAATCA-TAAAAATGATAAAAA
3113664 TATATAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 14 0.67
26 7 0.33
ACGTcount: A:0.69, C:0.02, G:0.04, T:0.24
Consensus pattern (25 bp):
TAAAAATCATAAAAATGATAAAAAA
Found at i:3113785 original size:91 final size:92
Alignment explanation
Indices: 3113679--3113863 Score: 363
Period size: 91 Copynumber: 2.0 Consensus size: 92
3113669 AATTTTTTTT
3113679 TTAAAAAATTAGTGTGAAGAACATGTAAATTGACATACAGGCTGCAATGTATAAAAATTTAGCAT
1 TTAAAAAATTAGTGTGAAGAACATGTAAATTGACATACAGGCTGCAATGTATAAAAATTTAGCAT
3113744 TTTAGTCGGTATTTTTATTAAAAACAA
66 TTTAGTCGGTATTTTTATTAAAAACAA
3113771 TTAAAAAATT-GTGTGAAGAACATGTAAATTGACATACAGGCTGCAATGTATAAAAATTTAGCAT
1 TTAAAAAATTAGTGTGAAGAACATGTAAATTGACATACAGGCTGCAATGTATAAAAATTTAGCAT
3113835 TTTAGTCGGTATTTTTATTAAAAACAA
66 TTTAGTCGGTATTTTTATTAAAAACAA
3113862 TT
1 TT
3113864 TAACTTATTT
Statistics
Matches: 93, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
91 83 0.89
92 10 0.11
ACGTcount: A:0.42, C:0.09, G:0.15, T:0.35
Consensus pattern (92 bp):
TTAAAAAATTAGTGTGAAGAACATGTAAATTGACATACAGGCTGCAATGTATAAAAATTTAGCAT
TTTAGTCGGTATTTTTATTAAAAACAA
Found at i:3113944 original size:27 final size:24
Alignment explanation
Indices: 3113905--3113974 Score: 72
Period size: 23 Copynumber: 2.8 Consensus size: 24
3113895 TAACTATTTT
3113905 TAAAAAAAATAAA-GACTAAATTTAA
1 TAAAAAAAATAAATGA-TAAA-TTAA
3113930 CTAAAATAAAATAAATGATAAATTAA
1 -TAAAA-AAAATAAATGATAAATTAA
* *
3113956 T-AAAAATATAAATGTTAAA
1 TAAAAAAAATAAATGATAAA
3113975 AATTAAATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
23 13 0.32
24 3 0.08
25 1 0.03
26 9 0.22
27 12 0.30
28 2 0.05
ACGTcount: A:0.66, C:0.03, G:0.04, T:0.27
Consensus pattern (24 bp):
TAAAAAAAATAAATGATAAATTAA
Found at i:3113955 original size:26 final size:25
Alignment explanation
Indices: 3113905--3113961 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 25
3113895 TAACTATTTT
3113905 TAAAAAAAATAAAGACTAAATTTAA
1 TAAAAAAAATAAAGACTAAATTTAA
3113930 CTAAAATAAAATAAATGA-TAAA-TTAA
1 -TAAAA-AAAATAAA-GACTAAATTTAA
3113956 TAAAAA
1 TAAAAA
3113962 TATAAATGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
24 1 0.03
25 5 0.17
26 9 0.31
27 12 0.41
28 2 0.07
ACGTcount: A:0.68, C:0.04, G:0.04, T:0.25
Consensus pattern (25 bp):
TAAAAAAAATAAAGACTAAATTTAA
Found at i:3114749 original size:3 final size:3
Alignment explanation
Indices: 3114741--3114775 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
3114731 GTAACTTCAA
3114741 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
3114776 AAGATTCTCT
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:3119264 original size:12 final size:12
Alignment explanation
Indices: 3119247--3119300 Score: 62
Period size: 11 Copynumber: 4.8 Consensus size: 12
3119237 AACTAATCCT
3119247 CTCTCAAATTTC
1 CTCTCAAATTTC
*
3119259 CTCTC-AATTTG
1 CTCTCAAATTTC
3119270 CTCTCAAA-TTC
1 CTCTCAAATTTC
3119281 CT-TCAAAATTT-
1 CTCTC-AAATTTC
3119292 CTCTCAAAT
1 CTCTCAAAT
3119301 CCATATTTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
10 2 0.06
11 23 0.64
12 11 0.31
ACGTcount: A:0.28, C:0.30, G:0.02, T:0.41
Consensus pattern (12 bp):
CTCTCAAATTTC
Found at i:3119273 original size:23 final size:22
Alignment explanation
Indices: 3119246--3119300 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
3119236 AAACTAATCC
3119246 TCTCTCAAATTTCCTCTC-AATT
1 TCTCTCAAATTTCCT-TCAAATT
3119268 TGCTCTCAAA-TTCCTTCAAAATT
1 T-CTCTCAAATTTCCTTC-AAATT
3119291 TCTCTCAAAT
1 TCTCTCAAAT
3119301 CCATATTTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
21 2 0.07
22 14 0.48
23 13 0.45
ACGTcount: A:0.27, C:0.29, G:0.02, T:0.42
Consensus pattern (22 bp):
TCTCTCAAATTTCCTTCAAATT
Found at i:3119322 original size:51 final size:51
Alignment explanation
Indices: 3119262--3119359 Score: 126
Period size: 51 Copynumber: 1.9 Consensus size: 51
3119252 AAATTTCCTC
*
3119262 TCAATTTGCTCTCAAATTCCT-TCAAAATTTCTCTCAAATCCATATTTATTT
1 TCAATTTGCTCCCAAATTCCTCT-AAAATTTCTCTCAAATCCATATTTATTT
* * * * *
3119313 TCAATTTGCTCCCAAGTTCCTCTTAAATTTCTTTTAAATCCCTATTT
1 TCAATTTGCTCCCAAATTCCTCTAAAATTTCTCTCAAATCCATATTT
3119360 TTAAATAATT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
51 39 0.98
52 1 0.03
ACGTcount: A:0.27, C:0.24, G:0.03, T:0.46
Consensus pattern (51 bp):
TCAATTTGCTCCCAAATTCCTCTAAAATTTCTCTCAAATCCATATTTATTT
Found at i:3121167 original size:124 final size:124
Alignment explanation
Indices: 3120946--3121464 Score: 768
Period size: 124 Copynumber: 4.2 Consensus size: 124
3120936 CCTAAACATG
* * *
3120946 CTACTGTAGTAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATTCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
* * * * * *
3121011 TAGAAGCGATTTTATACTGTTTGCTCAAAAACGTCAAGTCGAAATTATTTTTCCAGGAC
66 TTGAAGCGTTTTTAAACTATTTGCTCAAAAACGTCAACTCAAAATTATTTTTCCAGGAC
* *
3121070 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGTGATTTCACAAATTCTTCTCATAAAGCATCTTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
* *
3121135 TTGAAGCGTTTTTAAACTATTTGCTCAGAAACGTCAACTCAAAATTATTTTTTCAGGAC
66 TTGAAGCGTTTTTAAACTATTTGCTCAAAAACGTCAACTCAAAATTATTTTTCCAGGAC
* * * * * * *
3121194 CTATTGTAGCAAAAGCGCGTTCACGTGGGCGCAACTTCACAAATTCTTCTTATAAAGCATCCTAC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
3121259 TTGAAGCGTTTTTTTAAACTATTTGCTCAAAAACGTCAACTCAAAATTATTTCTTCCAGGAC
66 TTGAAGCG--TTTTTAAACTATTTGCTCAAAAACGTCAACTCAAAATTATTT-TTCCAGGAC
* *
3121321 CAACTGTAGCAAAAGCGCGTTCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
* * * * *
3121386 TTGAAGCGTTTTTAAACTATTTTCTCAGAAACGTCAAGTCGAAATTATTTTTCCAAGAC
66 TTGAAGCGTTTTTAAACTATTTGCTCAAAAACGTCAACTCAAAATTATTTTTCCAGGAC
3121445 CTACTGTAGCAAAAGCGCGT
1 CTACTGTAGCAAAAGCGCGT
3121465 NNNNNNNNNN
Statistics
Matches: 355, Mismatches: 37, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
124 202 0.57
125 38 0.11
126 41 0.12
127 74 0.21
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.31
Consensus pattern (124 bp):
CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
TTGAAGCGTTTTTAAACTATTTGCTCAAAAACGTCAACTCAAAATTATTTTTCCAGGAC
Found at i:3121396 original size:251 final size:248
Alignment explanation
Indices: 3120946--3121464 Score: 804
Period size: 251 Copynumber: 2.1 Consensus size: 248
3120936 CCTAAACATG
* * * * *
3120946 CTACTGTAGTAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATTCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCAACTTCACAAATTCTTCTCATAAAGCATCCTAC
* * * * *
3121011 TAGAAGCGATTTTATACTGTTTGCTCAAAAACGTCAAGTCGAAATTATTTTTCCAGGACCTACTG
66 TAGAAGCGATTTTAAACTATTTGCTCAAAAACGTCAACTCAAAATTATTTTTCCAGGACCAACTG
* *
3121076 TAGCAAAAGCGCGTCCACGAGGGCGTGATTTCACAAATTCTTCTCATAAAGCATCTTGCTTGAAG
131 TAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGCTTGAAG
* *
3121141 CGTTTTTAAACTATTTGCTCAGAAACGTCAACTCAAAATTATTTTTTCAGGAC
196 CGTTTTTAAACTATTTGCTCAGAAACGTCAACTCAAAATTATTTTTCCAAGAC
* * *
3121194 CTATTGTAGCAAAAGCGCGTTCACGTGGGCGCAACTTCACAAATTCTTCTTATAAAGCATCCTAC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCAACTTCACAAATTCTTCTCATAAAGCATCCTAC
* *
3121259 TTGAAGCGTTTTTTTAAACTATTTGCTCAAAAACGTCAACTCAAAATTATTTCTTCCAGGACCAA
66 TAGAAGCG--ATTTTAAACTATTTGCTCAAAAACGTCAACTCAAAATTATTT-TTCCAGGACCAA
*
3121324 CTGTAGCAAAAGCGCGTTCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGCTTG
128 CTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGCTTG
* * *
3121389 AAGCGTTTTTAAACTATTTTCTCAGAAACGTCAAGTCGAAATTATTTTTCCAAGAC
193 AAGCGTTTTTAAACTATTTGCTCAGAAACGTCAACTCAAAATTATTTTTCCAAGAC
3121445 CTACTGTAGCAAAAGCGCGT
1 CTACTGTAGCAAAAGCGCGT
3121465 NNNNNNNNNN
Statistics
Matches: 244, Mismatches: 24, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
248 64 0.26
250 37 0.15
251 143 0.59
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.31
Consensus pattern (248 bp):
CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCAACTTCACAAATTCTTCTCATAAAGCATCCTAC
TAGAAGCGATTTTAAACTATTTGCTCAAAAACGTCAACTCAAAATTATTTTTCCAGGACCAACTG
TAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGCTTGAAG
CGTTTTTAAACTATTTGCTCAGAAACGTCAACTCAAAATTATTTTTCCAAGAC
Found at i:3128529 original size:42 final size:42
Alignment explanation
Indices: 3128448--3128559 Score: 134
Period size: 42 Copynumber: 2.7 Consensus size: 42
3128438 TTACAAACAA
* * **
3128448 AAACGCCGCTAAAGACCATGTTCTTTAAAATAATATTTTTTT
1 AAACGCCGCTAAAGACCATGTTCTTTAGAAGAATATTTTTAC
** * *
3128490 AAACGCCGCTAAAGACCATGTTCTTTAGCGGCATTTTTTTAC
1 AAACGCCGCTAAAGACCATGTTCTTTAGAAGAATATTTTTAC
* *
3128532 AAACGCCGCAAAAGAACATGTTCTTTAG
1 AAACGCCGCTAAAGACCATGTTCTTTAG
3128560 TGGCGCTTTT
Statistics
Matches: 60, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 60 1.00
ACGTcount: A:0.33, C:0.21, G:0.14, T:0.32
Consensus pattern (42 bp):
AAACGCCGCTAAAGACCATGTTCTTTAGAAGAATATTTTTAC
Found at i:3128575 original size:42 final size:42
Alignment explanation
Indices: 3128490--3128576 Score: 120
Period size: 42 Copynumber: 2.1 Consensus size: 42
3128480 ATATTTTTTT
* * * *
3128490 AAACGCCGCTAAAGACCATGTTCTTTAGCGGCATTTTTTTAC
1 AAACGCCGCAAAAGAACATGTTCTTTAGCGGCACTTTTATAC
* *
3128532 AAACGCCGCAAAAGAACATGTTCTTTAGTGGCGCTTTTATAC
1 AAACGCCGCAAAAGAACATGTTCTTTAGCGGCACTTTTATAC
3128574 AAA
1 AAA
3128577 AACGCCACTA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.30
Consensus pattern (42 bp):
AAACGCCGCAAAAGAACATGTTCTTTAGCGGCACTTTTATAC
Found at i:3128961 original size:21 final size:21
Alignment explanation
Indices: 3128893--3128963 Score: 88
Period size: 21 Copynumber: 3.4 Consensus size: 21
3128883 TTTTGCTCTG
* *
3128893 CTCTGCTTCTCTCGCTGCAAC
1 CTCTGCTTCCCTCGCTGCAGC
*
3128914 CTCCGCTTCCCTCGCTGCAGC
1 CTCTGCTTCCCTCGCTGCAGC
* * *
3128935 CGCTGCTTCCCTCGCTTCCGC
1 CTCTGCTTCCCTCGCTGCAGC
3128956 CTCTGCTT
1 CTCTGCTT
3128964 TAAGTTGTAG
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.04, C:0.48, G:0.17, T:0.31
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTGCAGC
Found at i:3129339 original size:112 final size:112
Alignment explanation
Indices: 3129196--3130227 Score: 1897
Period size: 112 Copynumber: 9.2 Consensus size: 112
3129186 GGTTATCAAT
3129196 CGCTTTACAATAAACGCCACTAATTCCCCCCCAAAGGCCACAAAACGGCACCGTCTGGGTGTATT
1 CGCTTTACAATAAACGCCACTAATTCCCCCCCAAAGGCCACAAAACGGCACCGTCTGGGTGTATT
3129261 ATTTTTGGCGTTTTTAATAAACGCTACTAATGTTCACTCTTTAGCAG
66 ATTTTTGGCGTTTTTAATAAACGCTACTAATGTTCACTCTTTAGCAG
3129308 CGCTTTACAATAAACGCCACTAATTCCCCCCCAAAGGCCACAAAACGGCACCGTCTGGGTGTATT
1 CGCTTTACAATAAACGCCACTAATTCCCCCCCAAAGGCCACAAAACGGCACCGTCTGGGTGTATT
* * *
3129373 ATTTCTGGCGTTTTTTATAAACGCTGCTAATGTTCACTCTTTAGC-G
66 ATTTTTGGCGTTTTTAATAAACGCTACTAATGTTCACTCTTTAGCAG
3129419 ACGCTTTACAATAAACGCCACTAATTCCCCCCCAAAGGCCACAAAACGGCACCGTCTGGGTGTAT
1 -CGCTTTACAATAAACGCCACTAATTCCCCCCCAAAGGCCACAAAACGGCACCGTCTGGGTGTAT
* * *
3129484 TATTTCTGGCGTTTTTTATAAACGCTGCTAATGTTCACTCTTTAGC-G
65 TATTTTTGGCGTTTTTAATAAACGCTACTAATGTTCACTCTTTAGCAG
3129531 ACGCTTTACAATAAACGCCACTAATTCCCCCCCAAAGGCCACAAAACGGCACCGTCTGGGTGTAT
1 -CGCTTTACAATAAACGCCACTAATTCCCCCCCAAAGGCCACAAAACGGCACCGTCTGGGTGTAT
3129596 TATTTTTGGCGTTTTTAATAAACGCTACTAATGTTCACTCTTTAGCAG
65 TATTTTTGGCGTTTTTAATAAACGCTACTAATGTTCACTCTTTAGCAG
3129644 CGCTTTACAATAAACGCCACTAATTCCCCCCCAAAGGCCACAAAACGGCACCGTCTGGGTGTATT
1 CGCTTTACAATAAACGCCACTAATTCCCCCCCAAAGGCCACAAAACGGCACCGTCTGGGTGTATT
3129709 ATTTTTGGCGTTTTTAATAAACGCTACTAATGTTCACTCTTTAGCAG
66 ATTTTTGGCGTTTTTAATAAACGCTACTAATGTTCACTCTTTAGCAG
3129756 CGCTTTACAATAAACGCCACTAATTCCCCCCCAAAGGCCACAAAACGGCACCGTCTGGGTGTATT
1 CGCTTTACAATAAACGCCACTAATTCCCCCCCAAAGGCCACAAAACGGCACCGTCTGGGTGTATT
3129821 ATTTTTGGCGTTTTTAATAAACGCTACTAATGTTCACTCTTTAGCAG
66 ATTTTTGGCGTTTTTAATAAACGCTACTAATGTTCACTCTTTAGCAG
3129868 CGCTTTACAATAAACGCCACTAATTCCCCCCCAAAGGCCACAAAACGGCACCGTCTGGGTGTATT
1 CGCTTTACAATAAACGCCACTAATTCCCCCCCAAAGGCCACAAAACGGCACCGTCTGGGTGTATT
3129933 ATTTTTGGCGTTTTTAATAAACGCTACTAATGTTCACTCTTTAGCAG
66 ATTTTTGGCGTTTTTAATAAACGCTACTAATGTTCACTCTTTAGCAG
3129980 CGCTTTACAATAAACGCCACTAATTCCCCCCCAAAGGCCACAAAACGGCACCGTCTGGGTGTATT
1 CGCTTTACAATAAACGCCACTAATTCCCCCCCAAAGGCCACAAAACGGCACCGTCTGGGTGTATT
3130045 ATTTTTGGCGTTTTTAATAAACGCTACTAATGTTCACTCTTTAGCAG
66 ATTTTTGGCGTTTTTAATAAACGCTACTAATGTTCACTCTTTAGCAG
3130092 CGCTTTACAATAAACGCCACTAATTCCCCCCCAAAGGCCACAAAACGGCACCGTCTGGGTGTATT
1 CGCTTTACAATAAACGCCACTAATTCCCCCCCAAAGGCCACAAAACGGCACCGTCTGGGTGTATT
** * * * *
3130157 ATTTCCGGCGTTTTTTATAAACGCTGCTAATGCTCACTCTTTAGCGG
66 ATTTTTGGCGTTTTTAATAAACGCTACTAATGTTCACTCTTTAGCAG
* **
3130204 CGCTTTTCCTTAAACGCCACTAAT
1 CGCTTTACAATAAACGCCACTAAT
3130228 GCTCACTCTT
Statistics
Matches: 903, Mismatches: 15, Indels: 4
0.98 0.02 0.00
Matches are distributed among these distances:
111 1 0.00
112 901 1.00
113 1 0.00
ACGTcount: A:0.27, C:0.27, G:0.16, T:0.29
Consensus pattern (112 bp):
CGCTTTACAATAAACGCCACTAATTCCCCCCCAAAGGCCACAAAACGGCACCGTCTGGGTGTATT
ATTTTTGGCGTTTTTAATAAACGCTACTAATGTTCACTCTTTAGCAG
Found at i:3130218 original size:40 final size:40
Alignment explanation
Indices: 3130174--3130347 Score: 285
Period size: 40 Copynumber: 4.3 Consensus size: 40
3130164 GCGTTTTTTA
*
3130174 TAAACGCTGCTAATGCTCACTCTTTAGCGGCGCTTTTCCT
1 TAAACGCCGCTAATGCTCACTCTTTAGCGGCGCTTTTCCT
*
3130214 TAAACGCCACTAATGCTCACTCTTTAGCGGCGCTTTTCCT
1 TAAACGCCGCTAATGCTCACTCTTTAGCGGCGCTTTTCCT
*
3130254 TAAACGCCACTAATGCTCACTCTTTAGCGGCGCTTTTCCT
1 TAAACGCCGCTAATGCTCACTCTTTAGCGGCGCTTTTCCT
* * *
3130294 TAAACGCCGCTAATGCTCACTCTTTAGCAGCGTTTTTGCT
1 TAAACGCCGCTAATGCTCACTCTTTAGCGGCGCTTTTCCT
3130334 CTAAACGCCGCTAA
1 -TAAACGCCGCTAA
3130348 AAGTGCCGCT
Statistics
Matches: 127, Mismatches: 6, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
40 114 0.90
41 13 0.10
ACGTcount: A:0.21, C:0.31, G:0.16, T:0.32
Consensus pattern (40 bp):
TAAACGCCGCTAATGCTCACTCTTTAGCGGCGCTTTTCCT
Found at i:3131626 original size:11 final size:11
Alignment explanation
Indices: 3131606--3131642 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
3131596 GGCCCGGCCC
3131606 ATATTAAATAT
1 ATATTAAATAT
*
3131617 ATATTTAATAT
1 ATATTAAATAT
*
3131628 ATATAAAATAT
1 ATATTAAATAT
3131639 ATAT
1 ATAT
3131643 ATTTGATTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
ATATTAAATAT
Found at i:3131645 original size:24 final size:23
Alignment explanation
Indices: 3131611--3131678 Score: 91
Period size: 24 Copynumber: 2.9 Consensus size: 23
3131601 GGCCCATATT
3131611 AAATATATATTTAATATATATAA
1 AAATATATATTTAATATATATAA
* * *
3131634 AATATATATATTTGATTAAAAATAA
1 AA-ATATATATTT-AATATATATAA
3131659 AAATATATATTTAATATATA
1 AAATATATATTTAATATATA
3131679 ATTCAGGCCG
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
23 7 0.19
24 20 0.54
25 10 0.27
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (23 bp):
AAATATATATTTAATATATATAA
Found at i:3133554 original size:22 final size:24
Alignment explanation
Indices: 3133515--3133565 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
3133505 TAGTAGAACT
* *
3133515 GAAATTAAATTATAATTTT-TTGA
1 GAAATAAAAATATAATTTTATTGA
3133538 GAAATAAAAATAT-ATTTTATTGA
1 GAAATAAAAATATAATTTTATTGA
*
3133561 TAAAT
1 GAAAT
3133566 TCATAAATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 5 0.21
23 19 0.79
ACGTcount: A:0.49, C:0.00, G:0.08, T:0.43
Consensus pattern (24 bp):
GAAATAAAAATATAATTTTATTGA
Found at i:3134914 original size:24 final size:25
Alignment explanation
Indices: 3134882--3134935 Score: 92
Period size: 25 Copynumber: 2.2 Consensus size: 25
3134872 ATTTAATACA
*
3134882 TTAAAAAAA-TATAGTAAATATATT
1 TTAAAAAAACTATAGTAAATAAATT
3134906 TTAAAAAAACTATAGTAAATAAATT
1 TTAAAAAAACTATAGTAAATAAATT
3134931 TTAAA
1 TTAAA
3134936 TATATTCATG
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
24 9 0.32
25 19 0.68
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.35
Consensus pattern (25 bp):
TTAAAAAAACTATAGTAAATAAATT
Found at i:3144552 original size:10 final size:10
Alignment explanation
Indices: 3144537--3144565 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
3144527 TATTATATTC
3144537 GGGCCGGGCA
1 GGGCCGGGCA
3144547 GGGCCGGGCA
1 GGGCCGGGCA
3144557 GGGCCGGGC
1 GGGCCGGGC
3144566 CCGGGCCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.07, C:0.31, G:0.62, T:0.00
Consensus pattern (10 bp):
GGGCCGGGCA
Found at i:3144708 original size:18 final size:16
Alignment explanation
Indices: 3144676--3144709 Score: 50
Period size: 18 Copynumber: 2.0 Consensus size: 16
3144666 CTCCCATATT
3144676 TCGGGCGGGCGGGCCG
1 TCGGGCGGGCGGGCCG
3144692 TCGGGCAGGGCCGGGCCG
1 TCGGGC-GGG-CGGGCCG
3144710 CCCGGCCTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 3 0.19
18 7 0.44
ACGTcount: A:0.03, C:0.32, G:0.59, T:0.06
Consensus pattern (16 bp):
TCGGGCGGGCGGGCCG
Found at i:3148612 original size:26 final size:26
Alignment explanation
Indices: 3148534--3148619 Score: 82
Period size: 26 Copynumber: 3.1 Consensus size: 26
3148524 ATTGAACCTA
* *
3148534 AAAAAAAGCTTAGGTACCAAATTAGGAA
1 AAAAAAAGTTTAGGTACCAAATT--GAG
**
3148562 AAAAAGTCAAGTTTAGGTATTAAATTGAG
1 AAAAA---AAGTTTAGGTACCAAATTGAG
*
3148591 AAAAAAAGTTTAGGTACCAAATTCAG
1 AAAAAAAGTTTAGGTACCAAATTGAG
3148617 AAA
1 AAA
3148620 CTAAATGTTA
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
26 21 0.44
28 5 0.10
29 7 0.15
31 15 0.31
ACGTcount: A:0.51, C:0.08, G:0.17, T:0.23
Consensus pattern (26 bp):
AAAAAAAGTTTAGGTACCAAATTGAG
Found at i:3153952 original size:5 final size:5
Alignment explanation
Indices: 3153944--3153990 Score: 76
Period size: 5 Copynumber: 9.2 Consensus size: 5
3153934 TATTTTATTA
*
3153944 AATCT AATCT AATCT AATCT AATGT AATCT AATCT AATCTT AATCT A
1 AATCT AATCT AATCT AATCT AATCT AATCT AATCT AATC-T AATCT A
3153991 TTCCATATAT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
5 34 0.87
6 5 0.13
ACGTcount: A:0.40, C:0.17, G:0.02, T:0.40
Consensus pattern (5 bp):
AATCT
Found at i:3156211 original size:106 final size:107
Alignment explanation
Indices: 3156080--3156293 Score: 421
Period size: 106 Copynumber: 2.0 Consensus size: 107
3156070 AATATTTTAA
3156080 TTTTTAAAAATAAATATTTATTATTTAATTCAAATTAATTTACTATTAATTAATAAAAATATTAA
1 TTTTTAAAAATAAATATTTATTATTTAATTCAAATTAATTTACTATTAATTAATAAAAATATTAA
3156145 AAATATAGATTCCTTGTACGTAATTGAGCGTTATATCCAAGC
66 AAATATAGATTCCTTGTACGTAATTGAGCGTTATATCCAAGC
3156187 TTTTTAAAAAT-AATATTTATTATTTAATTCAAATTAATTTACTATTAATTAATAAAAATATTAA
1 TTTTTAAAAATAAATATTTATTATTTAATTCAAATTAATTTACTATTAATTAATAAAAATATTAA
3156251 AAATATAGATTCCTTGTACGTAATTGAGCGTTATATCCAAGC
66 AAATATAGATTCCTTGTACGTAATTGAGCGTTATATCCAAGC
3156293 T
1 T
3156294 AGCATGCTTA
Statistics
Matches: 107, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
106 96 0.90
107 11 0.10
ACGTcount: A:0.43, C:0.08, G:0.07, T:0.43
Consensus pattern (107 bp):
TTTTTAAAAATAAATATTTATTATTTAATTCAAATTAATTTACTATTAATTAATAAAAATATTAA
AAATATAGATTCCTTGTACGTAATTGAGCGTTATATCCAAGC
Found at i:3157571 original size:19 final size:20
Alignment explanation
Indices: 3157542--3157582 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
3157532 ACAAGTTAAC
3157542 AAATAATTTAAAAAATTATA
1 AAATAATTTAAAAAATTATA
*
3157562 AAAT-ATTTAAAAAATTTTA
1 AAATAATTTAAAAAATTATA
3157581 AA
1 AA
3157583 TTTTTTTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
AAATAATTTAAAAAATTATA
Found at i:3158655 original size:2 final size:2
Alignment explanation
Indices: 3158648--3158672 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3158638 GCATGTAGCT
3158648 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
3158673 GAAATTGATG
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:3158736 original size:2 final size:2
Alignment explanation
Indices: 3158729--3158753 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3158719 TGCATGAGCT
3158729 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
3158754 GAAATTGATG
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:3158769 original size:81 final size:82
Alignment explanation
Indices: 3158633--3158795 Score: 319
Period size: 81 Copynumber: 2.0 Consensus size: 82
3158623 AAGCATCTCT
3158633 TGTTTGCATGTAGCTTATATATATATATATATATATATATGAAATTGATGTTTGATAATGTTGGA
1 TGTTTGCATGTAGCTTATATATATATATATATATATATATGAAATTGATGTTTGATAATGTTGGA
3158698 ATAGTAACTTGGTTATA
66 ATAGTAACTTGGTTATA
3158715 TGTTTGCATG-AGCTTATATATATATATATATATATATATGAAATTGATGTTTGATAATGTTGGA
1 TGTTTGCATGTAGCTTATATATATATATATATATATATATGAAATTGATGTTTGATAATGTTGGA
3158779 ATAGTAACTTGGTTATA
66 ATAGTAACTTGGTTATA
3158796 GTATGCCGTT
Statistics
Matches: 81, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
81 71 0.88
82 10 0.12
ACGTcount: A:0.34, C:0.04, G:0.17, T:0.45
Consensus pattern (82 bp):
TGTTTGCATGTAGCTTATATATATATATATATATATATATGAAATTGATGTTTGATAATGTTGGA
ATAGTAACTTGGTTATA
Found at i:3160834 original size:2 final size:2
Alignment explanation
Indices: 3160827--3160859 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3160817 AATATACACA
3160827 TC TC TC TC TC 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
3160860 ATATATATAT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:3164341 original size:45 final size:45
Alignment explanation
Indices: 3164277--3164456 Score: 360
Period size: 45 Copynumber: 4.0 Consensus size: 45
3164267 TCTTTGTAAA
3164277 AACAAGTAACCTTGTGAACTTAAATTGTTATCTAAAAACCAAGTG
1 AACAAGTAACCTTGTGAACTTAAATTGTTATCTAAAAACCAAGTG
3164322 AACAAGTAACCTTGTGAACTTAAATTGTTATCTAAAAACCAAGTG
1 AACAAGTAACCTTGTGAACTTAAATTGTTATCTAAAAACCAAGTG
3164367 AACAAGTAACCTTGTGAACTTAAATTGTTATCTAAAAACCAAGTG
1 AACAAGTAACCTTGTGAACTTAAATTGTTATCTAAAAACCAAGTG
3164412 AACAAGTAACCTTGTGAACTTAAATTGTTATCTAAAAACCAAGTG
1 AACAAGTAACCTTGTGAACTTAAATTGTTATCTAAAAACCAAGTG
3164457 TGTCTGGATT
Statistics
Matches: 135, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 135 1.00
ACGTcount: A:0.42, C:0.16, G:0.13, T:0.29
Consensus pattern (45 bp):
AACAAGTAACCTTGTGAACTTAAATTGTTATCTAAAAACCAAGTG
Found at i:3165978 original size:13 final size:13
Alignment explanation
Indices: 3165956--3166007 Score: 54
Period size: 13 Copynumber: 4.0 Consensus size: 13
3165946 ATTGTAAAAG
3165956 TTAT-TAAAAATT
1 TTATATAAAAATT
3165968 TTATATAAAAATT
1 TTATATAAAAATT
* *
3165981 GTATTTTAAAATATT
1 TTA-TATAAAA-ATT
3165996 TTA-ATAAAAATT
1 TTATATAAAAATT
3166008 GAATAAATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
12 7 0.21
13 15 0.45
14 6 0.18
15 5 0.15
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (13 bp):
TTATATAAAAATT
Found at i:3167256 original size:21 final size:20
Alignment explanation
Indices: 3167217--3167257 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
3167207 CATTTTTTTC
3167217 TTCTTTTTTACTGTCTTGTT
1 TTCTTTTTTACTGTCTTGTT
* *
3167237 TTCTTTATTTTCTTTCTTGTT
1 TTCTTT-TTTACTGTCTTGTT
3167258 CTTTAAAACA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.05, C:0.15, G:0.07, T:0.73
Consensus pattern (20 bp):
TTCTTTTTTACTGTCTTGTT
Found at i:3168080 original size:275 final size:275
Alignment explanation
Indices: 3167589--3168140 Score: 1104
Period size: 275 Copynumber: 2.0 Consensus size: 275
3167579 GAAGGGTGGG
3167589 ATTAATTTCCCTTTTTGCCGTCCATGTTGCACGCATTTTGCAAATTCATCCTCTGCTTTAATTTG
1 ATTAATTTCCCTTTTTGCCGTCCATGTTGCACGCATTTTGCAAATTCATCCTCTGCTTTAATTTG
3167654 ATTTTGTGTTTTTAATTTTGTTTTGATTCAAATTTAATCCATTGTATTTGCTTTTGCAAATTAGA
66 ATTTTGTGTTTTTAATTTTGTTTTGATTCAAATTTAATCCATTGTATTTGCTTTTGCAAATTAGA
3167719 TTGTATATTAGTCTGTTAATATTGTTATTGTTATTGTTATTAAGCTGCTGTTATTTTTGTTATTA
131 TTGTATATTAGTCTGTTAATATTGTTATTGTTATTGTTATTAAGCTGCTGTTATTTTTGTTATTA
3167784 TATATTATTATTATACACATACACGCGCATATGTATTTTATTATATATATATATGTATACATTTT
196 TATATTATTATTATACACATACACGCGCATATGTATTTTATTATATATATATATGTATACATTTT
3167849 AAATGTTTTAAATTC
261 AAATGTTTTAAATTC
3167864 ATTAATTTCCCTTTTTGCCGTCCATGTTGCACGCATTTTGCAAATTCATCCTCTGCTTTAATTTG
1 ATTAATTTCCCTTTTTGCCGTCCATGTTGCACGCATTTTGCAAATTCATCCTCTGCTTTAATTTG
3167929 ATTTTGTGTTTTTAATTTTGTTTTGATTCAAATTTAATCCATTGTATTTGCTTTTGCAAATTAGA
66 ATTTTGTGTTTTTAATTTTGTTTTGATTCAAATTTAATCCATTGTATTTGCTTTTGCAAATTAGA
3167994 TTGTATATTAGTCTGTTAATATTGTTATTGTTATTGTTATTAAGCTGCTGTTATTTTTGTTATTA
131 TTGTATATTAGTCTGTTAATATTGTTATTGTTATTGTTATTAAGCTGCTGTTATTTTTGTTATTA
3168059 TATATTATTATTATACACATACACGCGCATATGTATTTTATTATATATATATATGTATACATTTT
196 TATATTATTATTATACACATACACGCGCATATGTATTTTATTATATATATATATGTATACATTTT
3168124 AAATGTTTTAAATTC
261 AAATGTTTTAAATTC
3168139 AT
1 AT
3168141 ATCCATATCT
Statistics
Matches: 277, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
275 277 1.00
ACGTcount: A:0.26, C:0.12, G:0.11, T:0.51
Consensus pattern (275 bp):
ATTAATTTCCCTTTTTGCCGTCCATGTTGCACGCATTTTGCAAATTCATCCTCTGCTTTAATTTG
ATTTTGTGTTTTTAATTTTGTTTTGATTCAAATTTAATCCATTGTATTTGCTTTTGCAAATTAGA
TTGTATATTAGTCTGTTAATATTGTTATTGTTATTGTTATTAAGCTGCTGTTATTTTTGTTATTA
TATATTATTATTATACACATACACGCGCATATGTATTTTATTATATATATATATGTATACATTTT
AAATGTTTTAAATTC
Found at i:3170065 original size:1 final size:1
Alignment explanation
Indices: 3170059--3170097 Score: 78
Period size: 1 Copynumber: 39.0 Consensus size: 1
3170049 TCCTTTTCGA
3170059 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
3170098 ATTATTTGAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 38 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:3178988 original size:2 final size:2
Alignment explanation
Indices: 3178981--3179011 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3178971 ATTCCTAGAC
3178981 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
3179012 AGCTTCAAAA
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:3183665 original size:30 final size:30
Alignment explanation
Indices: 3183625--3183690 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 30
3183615 TTTAAATTCG
* *
3183625 CCTTAATTTTCGTTTGAGAATATTCAACTT
1 CCTTATTTTTCGTTTCAGAATATTCAACTT
* *
3183655 CTTTATTTTTCGTTTCAGAATATTCAATTT
1 CCTTATTTTTCGTTTCAGAATATTCAACTT
3183685 CCTTAT
1 CCTTAT
3183691 CAAAAACAGT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.24, C:0.17, G:0.08, T:0.52
Consensus pattern (30 bp):
CCTTATTTTTCGTTTCAGAATATTCAACTT
Found at i:3186275 original size:84 final size:83
Alignment explanation
Indices: 3186108--3186601 Score: 487
Period size: 84 Copynumber: 5.9 Consensus size: 83
3186098 ATGCAGTACT
* * * ** * * * *
3186108 TGCAGACCAAACGAAACGTTCCCTGTATGATATGAAAA-CTGCATCAAA--GACTCCTCACCCAT
1 TGCAGACCAAACAAAAAGTTCTCAATATGATA-CAAAACCTGCACCAAAGCGACTCCTCGCCCGT
* **
3186170 CGAATACCGCCAGTACCAA
65 CGAATACCACCAGCGCCAA
* * * *
3186189 TGCAGGCCTATCGAAAAGTTCTCAATATGATACAAAACCTGCACCAAAGCAGACTCCTCGCCCGT
1 TGCAGACCAAACAAAAAGTTCTCAATATGATACAAAACCTGCACCAAAGC-GACTCCTCGCCCGT
**
3186254 TTAATACCACCAGCGCCAA
65 CGAATACCACCAGCGCCAA
* * *
3186273 TGCTGACCGAACAAAAAGTTCTCAGTATGATACAAAACCTGCACCAAAGCCGACTCCTCGCCCGT
1 TGCAGACCAAACAAAAAGTTCTCAATATGATACAAAACCTGCACCAAAG-CGACTCCTCGCCCGT
3186338 CGAATACCACCAGCGCCAA
65 CGAATACCACCAGCGCCAA
* *
3186357 TGCAGACCAAACAAAAAGTTCTCAATATGGTACAAAACCTGCAGCAAAGTCGACTCCTC-CCCTG
1 TGCAGACCAAACAAAAAGTTCTCAATATGATACAAAACCTGCACCAAAG-CGACTCCTCGCCC-G
*
3186421 TCGAATACCGCCAGCGCCAA
64 TCGAATACCACCAGCGCCAA
* * * * * * *
3186441 TGCAGACCAAACAAAAAGTTCTCAATCTGAAACGGAAA-CTGCACTAAAGTCGACTTCTCACCCA
1 TGCAGACCAAACAAAAAGTTCTCAATATGATAC-AAAACCTGCACCAAAG-CGACTCCTCGCCCG
* ** * **
3186505 TCGAACACCACTTGTGCCTG
64 TCGAATACCACCAGCGCCAA
* * *
3186525 TGCAGACCAAACAAAAAGTTCTCAATATGATACTAAAA-CTGCACCAAACCCGACTCCTCACCCA
1 TGCAGACCAAACAAAAAGTTCTCAATATGATAC-AAAACCTGCACCAAA-GCGACTCCTCGCCCG
* *
3186589 TTGAATAGCACCA
64 TCGAATACCACCA
3186602 ATACCATTGT
Statistics
Matches: 346, Mismatches: 58, Indels: 15
0.83 0.14 0.04
Matches are distributed among these distances:
80 4 0.01
81 34 0.10
83 3 0.01
84 298 0.86
85 7 0.02
ACGTcount: A:0.35, C:0.32, G:0.15, T:0.18
Consensus pattern (83 bp):
TGCAGACCAAACAAAAAGTTCTCAATATGATACAAAACCTGCACCAAAGCGACTCCTCGCCCGTC
GAATACCACCAGCGCCAA
Found at i:3188432 original size:28 final size:30
Alignment explanation
Indices: 3188398--3188462 Score: 89
Period size: 28 Copynumber: 2.2 Consensus size: 30
3188388 TGGTTTAATG
*
3188398 TGCAATTGTATACATG-AATTTTGATTT-A
1 TGCAATTGTATACATGAAATTTTAATTTGA
*
3188426 TGCAATTTTATACATGAAATTTTAATTTGA
1 TGCAATTGTATACATGAAATTTTAATTTGA
*
3188456 TCCAATT
1 TGCAATT
3188463 CTTGTAAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
28 15 0.47
29 10 0.31
30 7 0.22
ACGTcount: A:0.34, C:0.09, G:0.11, T:0.46
Consensus pattern (30 bp):
TGCAATTGTATACATGAAATTTTAATTTGA
Found at i:3188528 original size:75 final size:76
Alignment explanation
Indices: 3188429--3188579 Score: 295
Period size: 75 Copynumber: 2.0 Consensus size: 76
3188419 TGATTTATGC
3188429 AATTTTATACATGAAATTTTAATTTGATCCAATTCTTGTAAATTATTAACACAATTATTAATGTA
1 AATTTTATACATGAAATTTTAATTTGATCCAATTCTTGTAAATTATTAACACAATTATTAATGTA
3188494 ACATCATTTTT
66 ACATCATTTTT
3188505 AATTTTATAC-TGAAATTTTAATTTGATCCAATTCTTGTAAATTATTAACACAATTATTAATGTA
1 AATTTTATACATGAAATTTTAATTTGATCCAATTCTTGTAAATTATTAACACAATTATTAATGTA
3188569 ACATCATTTTT
66 ACATCATTTTT
3188580 TTATTATATA
Statistics
Matches: 75, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
75 65 0.87
76 10 0.13
ACGTcount: A:0.38, C:0.11, G:0.05, T:0.46
Consensus pattern (76 bp):
AATTTTATACATGAAATTTTAATTTGATCCAATTCTTGTAAATTATTAACACAATTATTAATGTA
ACATCATTTTT
Found at i:3195327 original size:11 final size:11
Alignment explanation
Indices: 3195305--3195340 Score: 63
Period size: 11 Copynumber: 3.2 Consensus size: 11
3195295 AACTAATCCT
3195305 CTCTCAAATTTC
1 CTCTC-AATTTC
3195317 CTCTCAATTTC
1 CTCTCAATTTC
3195328 CTCTCAATTTC
1 CTCTCAATTTC
3195339 CT
1 CT
3195341 TCCAAAATTC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 19 0.79
12 5 0.21
ACGTcount: A:0.19, C:0.36, G:0.00, T:0.44
Consensus pattern (11 bp):
CTCTCAATTTC
Found at i:3198745 original size:11 final size:11
Alignment explanation
Indices: 3198723--3198768 Score: 74
Period size: 11 Copynumber: 4.1 Consensus size: 11
3198713 ACAAATCCTA
3198723 TCTCATATTTCC
1 TCTCA-ATTTCC
3198735 TCTCAATTTCC
1 TCTCAATTTCC
*
3198746 TCTCAATTTTC
1 TCTCAATTTCC
3198757 TCTCAATTTCC
1 TCTCAATTTCC
3198768 T
1 T
3198769 TCCAAAATTC
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
11 27 0.84
12 5 0.16
ACGTcount: A:0.17, C:0.33, G:0.00, T:0.50
Consensus pattern (11 bp):
TCTCAATTTCC
Found at i:3198779 original size:22 final size:22
Alignment explanation
Indices: 3198734--3198780 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
3198724 CTCATATTTC
**
3198734 CTCTCAATTTCCTCTCAATTTT
1 CTCTCAATTTCCTCTCAAAATT
3198756 CTCTCAATTTCCT-TCCAAAATT
1 CTCTCAATTTCCTCT-CAAAATT
3198778 CTC
1 CTC
3198781 ATAAATCCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 1 0.05
22 21 0.95
ACGTcount: A:0.21, C:0.34, G:0.00, T:0.45
Consensus pattern (22 bp):
CTCTCAATTTCCTCTCAAAATT
Found at i:3198811 original size:51 final size:51
Alignment explanation
Indices: 3198756--3198868 Score: 165
Period size: 51 Copynumber: 2.2 Consensus size: 51
3198746 TCTCAATTTT
* * *
3198756 CTCTCAATTTCCTTCCAAAATTCTCAT-AAATCCATATTTAATTTCAATCTC
1 CTCTCAATTTCATTCCAAAAATCTC-TCAAACCCATATTTAATTTCAATCTC
* *
3198807 CTCTCAATTTCATTCCAAAAATCTCTCAAACCCATATTTAATTTCAATTTG
1 CTCTCAATTTCATTCCAAAAATCTCTCAAACCCATATTTAATTTCAATCTC
3198858 CTCTCAATTTC
1 CTCTCAATTTC
3198869 TTTTTTTAAA
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
50 1 0.02
51 55 0.98
ACGTcount: A:0.31, C:0.27, G:0.01, T:0.41
Consensus pattern (51 bp):
CTCTCAATTTCATTCCAAAAATCTCTCAAACCCATATTTAATTTCAATCTC
Found at i:3205189 original size:48 final size:48
Alignment explanation
Indices: 3205070--3205196 Score: 157
Period size: 48 Copynumber: 2.7 Consensus size: 48
3205060 NNNNNNNNNN
* * **
3205070 TGTAAGACCATGTCTGGGACATGGCATCAGC-TCGAGATGAGTGCCAA
1 TGTAAGACCATGTCTGGGACATGGCATCGGCACCGAGATGAGACCCAA
* * *
3205117 TGTAAGACCATGTCTGGGACATGGCATCGGCACCGATATGTGACCCCA
1 TGTAAGACCATGTCTGGGACATGGCATCGGCACCGAGATGAGACCCAA
* * *
3205165 TGTAAGACCATATCTGGGATATGGCATTGGCA
1 TGTAAGACCATGTCTGGGACATGGCATCGGCA
3205197 TCCTACTAGG
Statistics
Matches: 69, Mismatches: 10, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
47 30 0.43
48 39 0.57
ACGTcount: A:0.27, C:0.22, G:0.28, T:0.23
Consensus pattern (48 bp):
TGTAAGACCATGTCTGGGACATGGCATCGGCACCGAGATGAGACCCAA
Found at i:3207953 original size:9 final size:9
Alignment explanation
Indices: 3207935--3208000 Score: 89
Period size: 9 Copynumber: 7.4 Consensus size: 9
3207925 TTTGGTTAAA
3207935 AATTAACCG
1 AATTAACCG
*
3207944 AATTACCCG
1 AATTAACCG
3207953 AATTAACCG
1 AATTAACCG
* *
3207962 GATTACCCG
1 AATTAACCG
3207971 AATTAACCG
1 AATTAACCG
*
3207980 AATT-CCCG
1 AATTAACCG
3207988 AATTAACCG
1 AATTAACCG
3207997 AATT
1 AATT
3208001 GAATCACTAC
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
8 7 0.15
9 41 0.85
ACGTcount: A:0.38, C:0.26, G:0.12, T:0.24
Consensus pattern (9 bp):
AATTAACCG
Found at i:3207958 original size:18 final size:18
Alignment explanation
Indices: 3207935--3208000 Score: 116
Period size: 18 Copynumber: 3.7 Consensus size: 18
3207925 TTTGGTTAAA
3207935 AATTAACCGAATTACCCG
1 AATTAACCGAATTACCCG
*
3207953 AATTAACCGGATTACCCG
1 AATTAACCGAATTACCCG
3207971 AATTAACCGAATT-CCCG
1 AATTAACCGAATTACCCG
3207988 AATTAACCGAATT
1 AATTAACCGAATT
3208001 GAATCACTAC
Statistics
Matches: 46, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
17 17 0.37
18 29 0.63
ACGTcount: A:0.38, C:0.26, G:0.12, T:0.24
Consensus pattern (18 bp):
AATTAACCGAATTACCCG
Found at i:3208373 original size:85 final size:86
Alignment explanation
Indices: 3208261--3208433 Score: 330
Period size: 85 Copynumber: 2.0 Consensus size: 86
3208251 TAACCGAAAA
3208261 ATTAAAAAATAATTAACCGACTCCCGACCGAAAAAATTCGGTTAACCGACCGATTAACCGAATTT
1 ATTAAAAAAT-ATTAACCGACTCCCGACCGAAAAAATTCGGTTAACCGACCGATTAACCGAATTT
3208326 GGTCGGTTAACCGAATTTTTTC
65 GGTCGGTTAACCGAATTTTTTC
3208348 ATTAAAAAAT-TTAACCGACTCCCGACCGAAAAAATTCGGTTAACCGACCGATTAACCGAATTTG
1 ATTAAAAAATATTAACCGACTCCCGACCGAAAAAATTCGGTTAACCGACCGATTAACCGAATTTG
3208412 GTCGGTTAACCGAATTTTTTC
66 GTCGGTTAACCGAATTTTTTC
3208433 A
1 A
3208434 ATTTTACCCG
Statistics
Matches: 86, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
85 76 0.88
87 10 0.12
ACGTcount: A:0.35, C:0.22, G:0.15, T:0.28
Consensus pattern (86 bp):
ATTAAAAAATATTAACCGACTCCCGACCGAAAAAATTCGGTTAACCGACCGATTAACCGAATTTG
GTCGGTTAACCGAATTTTTTC
Found at i:3211012 original size:31 final size:31
Alignment explanation
Indices: 3210946--3211012 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 31
3210936 CGTAAAAATT
* *
3210946 TAAAAATTTTAATTAAACCTCTCAAACTTTT
1 TAAAAATTTTAATTAAACCTCTAAAACTTTG
*
3210977 TAAAAATTTTAATTAGA-CT-TAAAACTTAATG
1 TAAAAATTTTAATTAAACCTCTAAAACTT--TG
3211008 TAAAA
1 TAAAA
3211013 TTCTGCCACT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
29 7 0.23
30 2 0.06
31 22 0.71
ACGTcount: A:0.48, C:0.10, G:0.03, T:0.39
Consensus pattern (31 bp):
TAAAAATTTTAATTAAACCTCTAAAACTTTG
Found at i:3212975 original size:30 final size:31
Alignment explanation
Indices: 3212935--3212997 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 31
3212925 ACTAAATTTT
*
3212935 AAAATGTTTCAAA-ATAATCACTGAATTATTA
1 AAAATGTTTCAAATA-AATCACTGAACTATTA
**
3212966 AAAAT-TTTCATTTAAATCACTGAACTATTA
1 AAAATGTTTCAAATAAATCACTGAACTATTA
3212996 AA
1 AA
3212998 GTCACGCTCT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
30 22 0.79
31 6 0.21
ACGTcount: A:0.48, C:0.11, G:0.05, T:0.37
Consensus pattern (31 bp):
AAAATGTTTCAAATAAATCACTGAACTATTA
Found at i:3213346 original size:31 final size:31
Alignment explanation
Indices: 3213278--3213346 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
3213268 AACTAAACAA
** * *
3213278 TCAATAACTTAAATAAAAACTTTTGAATAGT
1 TCAATAACTTAAATAAAAACTTGAGAACACT
* *
3213309 TTAATAACTTAAATGAAAACTTGAGAACACT
1 TCAATAACTTAAATAAAAACTTGAGAACACT
3213340 TCAATAA
1 TCAATAA
3213347 TTATTTTATA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.49, C:0.12, G:0.07, T:0.32
Consensus pattern (31 bp):
TCAATAACTTAAATAAAAACTTGAGAACACT
Found at i:3225328 original size:21 final size:21
Alignment explanation
Indices: 3225303--3225345 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
3225293 AAATAAAAAA
*
3225303 ATATATTTT-TTATTAATATTT
1 ATATATTTTATAATTAAT-TTT
3225324 ATATATTTTATAATTAATTTT
1 ATATATTTTATAATTAATTTT
3225345 A
1 A
3225346 AATAAATAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (21 bp):
ATATATTTTATAATTAATTTT
Found at i:3225882 original size:20 final size:20
Alignment explanation
Indices: 3225857--3225897 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
3225847 CAAACCCTCT
3225857 CCCTCGCTCCCAAGTAAATG
1 CCCTCGCTCCCAAGTAAATG
3225877 CCCTCGCTCCCAAGTAAATG
1 CCCTCGCTCCCAAGTAAATG
3225897 C
1 C
3225898 AGAGCCAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.24, C:0.41, G:0.15, T:0.20
Consensus pattern (20 bp):
CCCTCGCTCCCAAGTAAATG
Found at i:3230556 original size:30 final size:30
Alignment explanation
Indices: 3230521--3230629 Score: 83
Period size: 30 Copynumber: 3.3 Consensus size: 30
3230511 AGAAGAAAAA
3230521 GGATAAAGAGAAAAAGAAGGAAAAGAAGTC
1 GGATAAAGAGAAAAAGAAGGAAAAGAAGTC
* **
3230551 AGATAATGAGGATGAACAAAAGAAGGACAAGAAGAAGAG
1 GGATAA--A-GA-G-A-AAAAGAAGG--AA-AAGAAGTC
* * *
3230590 GGATAAGGAGAAAAAGAAAGAAGAGAAGTC
1 GGATAAAGAGAAAAAGAAGGAAAAGAAGTC
3230620 GGATAAAGAG
1 GGATAAAGAG
3230630 GATGATGTAG
Statistics
Matches: 60, Mismatches: 10, Indels: 18
0.68 0.11 0.20
Matches are distributed among these distances:
30 19 0.32
31 2 0.03
32 1 0.02
33 10 0.17
34 2 0.03
35 2 0.03
36 11 0.18
38 2 0.03
39 11 0.18
ACGTcount: A:0.57, C:0.04, G:0.32, T:0.07
Consensus pattern (30 bp):
GGATAAAGAGAAAAAGAAGGAAAAGAAGTC
Found at i:3230666 original size:3 final size:3
Alignment explanation
Indices: 3230652--3230682 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
3230642 GATGCCAAAG
*
3230652 AGA AGG AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
3230683 AGATAATAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:3230775 original size:81 final size:81
Alignment explanation
Indices: 3230667--3230817 Score: 268
Period size: 81 Copynumber: 1.9 Consensus size: 81
3230657 GAGAAGAAGA
* *
3230667 AGAAGAAGAAGAAGAAAGATAATAAGGATAAGGAGAAAAAGAAAGACAAGAAGT-GTGATAAAGA
1 AGAAGAAGAAGAAGAAAGATAAGAAGGATAAGGAGAAAAAGAAAGAAAAGAAGTCG-GATAAAGA
3230731 GGATGAGGAAGAGGAGG
65 GGATGAGGAAGAGGAGG
3230748 AGAAGAAGAAGAAGAAAGATAAGAAGGATAAGGAGAAAAAGAAAGAAAAGAAGTCGGATAAAGAG
1 AGAAGAAGAAGAAGAAAGATAAGAAGGATAAGGAGAAAAAGAAAGAAAAGAAGTCGGATAAAGAG
3230813 GATGA
66 GATGA
3230818 TGTAGAAGAT
Statistics
Matches: 67, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
81 66 0.99
82 1 0.01
ACGTcount: A:0.58, C:0.01, G:0.33, T:0.08
Consensus pattern (81 bp):
AGAAGAAGAAGAAGAAAGATAAGAAGGATAAGGAGAAAAAGAAAGAAAAGAAGTCGGATAAAGAG
GATGAGGAAGAGGAGG
Found at i:3230787 original size:183 final size:187
Alignment explanation
Indices: 3230585--3231097 Score: 667
Period size: 183 Copynumber: 2.7 Consensus size: 187
3230575 GGACAAGAAG
* *
3230585 AAGAGGGATAAGGAGAAAAAGAAAGAAGAGAAGTCGGATAAAGAGGATGATGTAGAAGATGCCAA
1 AAGAAGGATAAGGAGAAAAAGAAAGAAAAGAAGTCGGATAAAGAGGATGATGTAGAAGATGCCAA
*
3230650 AGAGAAGGAGAAGAAGAAGAAGAAGAAGAAGAAAGATAATAAGGATAAGGAGAAAAAGAAAGACA
66 AGAGAAGGAGAAGAAGAAGAAGAAGAAGAAGAAAGATAACAAGGATAAGGAGAAAAAGAAAGACA
*
3230715 AGAAGTGTGATAAAGAGGATGA-G-GAAGA-G-GAGGAGAAGAAGAAGAAGAAAGAT
131 AGAAGTGCGATAAAGAGGATGATGAGAAGACGAGAGGAGAAGAAGAAGAAGAAAGAT
3230768 AAGAAGGATAAGGAGAAAAAGAAAGAAAAGAAGTCGGATAAAGAGGATGATGTAGAAGATGCCAA
1 AAGAAGGATAAGGAGAAAAAGAAAGAAAAGAAGTCGGATAAAGAGGATGATGTAGAAGATGCC-A
3230833 AGAGGAGAAGGAGAAGGAGAAGGAGAAGGAGAAGAAGAAGAAGAAAGATAACAAGGATAAGGAGA
65 A-A-GAGAAGGAG-A--AG-A--AG-A--AGAAGAAGAAGAAGAAAGATAACAAGGATAAGGAGA
* *
3230898 AAAAGAAAGATAAGAAGTGCGATAAAGAGGATGATGTAGAAGATGCCGAAGAGGAGGAGAAGAAG
119 AAAAGAAAGACAAGAAGTGCGATAAAGAGGATGATG-AGAAGA---CG-AGAGGAGAAGAAGAAG
3230963 AAGAAAGAT
179 AAGAAAGAT
* *
3230972 AAGAAGGATAAGGAGAAAAAGAAAGAAAAGAAGTCGGATAAAGAGCATGGA-GTAGAAGATGAC-
1 AAGAAGGATAAGGAGAAAAAGAAAGAAAAGAAGTCGGATAAAGAGGAT-GATGTAGAAGATGCCA
* * *
3231035 AA-AG-AGGAG-A-AA-AAGAAG-A-AA-AAGAAAGAGAAGAAGGATAAGGAGAAAAAGAAAGAG
65 AAGAGAAGGAGAAGAAGAAGAAGAAGAAGAAGAAAGATAACAAGGATAAGGAGAAAAAGAAAGAC
3231092 AAGAAG
130 AAGAAG
3231098 CACGAGGATG
Statistics
Matches: 297, Mismatches: 11, Indels: 44
0.84 0.03 0.12
Matches are distributed among these distances:
183 100 0.34
184 4 0.01
185 2 0.01
186 14 0.05
187 1 0.00
188 1 0.00
189 2 0.01
190 2 0.01
192 3 0.01
193 1 0.00
194 1 0.00
195 67 0.23
196 1 0.00
198 10 0.03
199 2 0.01
201 1 0.00
202 2 0.01
204 81 0.27
205 2 0.01
ACGTcount: A:0.56, C:0.03, G:0.34, T:0.08
Consensus pattern (187 bp):
AAGAAGGATAAGGAGAAAAAGAAAGAAAAGAAGTCGGATAAAGAGGATGATGTAGAAGATGCCAA
AGAGAAGGAGAAGAAGAAGAAGAAGAAGAAGAAAGATAACAAGGATAAGGAGAAAAAGAAAGACA
AGAAGTGCGATAAAGAGGATGATGAGAAGACGAGAGGAGAAGAAGAAGAAGAAAGAT
Found at i:3230842 original size:81 final size:81
Alignment explanation
Indices: 3230659--3230826 Score: 252
Period size: 81 Copynumber: 2.1 Consensus size: 81
3230649 AAGAGAAGGA
* *
3230659 GAAGAAGA--AGAAGAAGAAGAAGAAAGATAATAAGGATAAGGAGAAAAAGAAAGACAAGAAGTG
1 GAAGAAGAGCAGAAGAAGAAGAAGAAAGATAAGAAGGATAAGGAGAAAAAGAAAGAAAAGAAGTG
3230722 TGATAAAGAGGATGAG
66 TGATAAAGAGGATGAG
* *
3230738 GAAGAGGAGGAGAAGAAGAAGAAGAAAGATAAGAAGGATAAGGAGAAAAAGAAAGAAAAGAAGTC
1 GAAGAAGAGCAGAAGAAGAAGAAGAAAGATAAGAAGGATAAGGAGAAAAAGAAAGAAAAGAAGT-
*
3230803 G-GATAAAGAGGATGAT
65 GTGATAAAGAGGATGAG
*
3230819 GTAGAAGA
1 GAAGAAGA
3230827 TGCCAAAGAG
Statistics
Matches: 80, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
79 7 0.09
81 72 0.90
82 1 0.01
ACGTcount: A:0.57, C:0.01, G:0.33, T:0.08
Consensus pattern (81 bp):
GAAGAAGAGCAGAAGAAGAAGAAGAAAGATAAGAAGGATAAGGAGAAAAAGAAAGAAAAGAAGTG
TGATAAAGAGGATGAG
Found at i:3230846 original size:6 final size:6
Alignment explanation
Indices: 3230835--3230877 Score: 68
Period size: 6 Copynumber: 7.2 Consensus size: 6
3230825 GATGCCAAAG
* *
3230835 AGGAGA AGGAGA AGGAGA AGGAGA AGGAGA AGAAGA AGAAGA A
1 AGGAGA AGGAGA AGGAGA AGGAGA AGGAGA AGGAGA AGGAGA A
3230878 AGATAACAAG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.56, C:0.00, G:0.44, T:0.00
Consensus pattern (6 bp):
AGGAGA
Found at i:3230889 original size:114 final size:114
Alignment explanation
Indices: 3230745--3230967 Score: 376
Period size: 114 Copynumber: 2.0 Consensus size: 114
3230735 GAGGAAGAGG
*
3230745 AGGAGAAGAAGAAGAAGAAAGATAAGAAGGATAAGGAGAAAAAGAAAGAAAAGAAGT-CGGATAA
1 AGGAGAAGAAGAAGAAGAAAGATAACAAGGATAAGGAGAAAAAGAAAGAAAAGAAGTGC-GATAA
* *
3230809 AGAGGATGATGTAGAAGATGCCAAAGAGGAGAAGGAGAAGGAGAAGGAGA
65 AGAGGATGATGTAGAAGATGCCAAAGAGGAGAAGAAGAAGAAGAAGGAGA
*
3230859 AGGAGAAGAAGAAGAAGAAAGATAACAAGGATAAGGAGAAAAAGAAAGATAAGAAGTGCGATAAA
1 AGGAGAAGAAGAAGAAGAAAGATAACAAGGATAAGGAGAAAAAGAAAGAAAAGAAGTGCGATAAA
* *
3230924 GAGGATGATGTAGAAGATGCCGAAGAGGAGGAGAAGAAGAAGAA
66 GAGGATGATGTAGAAGATGCCAAAGAGGAGAAGAAGAAGAAGAA
3230968 AGATAAGAAG
Statistics
Matches: 102, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
114 101 0.99
115 1 0.01
ACGTcount: A:0.54, C:0.03, G:0.35, T:0.08
Consensus pattern (114 bp):
AGGAGAAGAAGAAGAAGAAAGATAACAAGGATAAGGAGAAAAAGAAAGAAAAGAAGTGCGATAAA
GAGGATGATGTAGAAGATGCCAAAGAGGAGAAGAAGAAGAAGAAGGAGA
Found at i:3230953 original size:90 final size:90
Alignment explanation
Indices: 3230859--3231097 Score: 338
Period size: 90 Copynumber: 2.6 Consensus size: 90
3230849 GAGAAGGAGA
* *
3230859 AGGAGAAGAAGAAGAAGAAAGATAACAAGGATAAGGAGAAAAAGAAAGATAAGAAGT-GCGATAA
1 AGGAGAAGAAGAAGAAGAAAGATAAGAAGGATAAGGAGAAAAAGAAAGAAAAGAAGTCG-GATAA
* * *
3230923 AGAGGAT-GATGTAGAAGATGCCGAAG
65 AGAGCATGGA-GTAGAAGATGACAAAG
*
3230949 AGGAGGAGAAGAAGAAGAAAGATAAGAAGGATAAGGAGAAAAAGAAAGAAAAGAAGTCGGATAAA
1 AGGAGAAGAAGAAGAAGAAAGATAAGAAGGATAAGGAGAAAAAGAAAGAAAAGAAGTCGGATAAA
3231014 GAGCATGGAGTAGAAGATGACAAAG
66 GAGCATGGAGTAGAAGATGACAAAG
* * *
3231039 AGGAGAAAAAGAAGAAAAAGAAAGAGAAGAAGGATAAGGAGAAAAAGAAAGAGAAGAAG
1 AGGAG---AAGAAGAAGAAGAAAGATAAGAAGGATAAGGAGAAAAAGAAAGAAAAGAAG
3231098 CACGAGGATG
Statistics
Matches: 134, Mismatches: 10, Indels: 7
0.89 0.07 0.05
Matches are distributed among these distances:
90 84 0.63
91 3 0.02
93 47 0.35
ACGTcount: A:0.57, C:0.03, G:0.33, T:0.07
Consensus pattern (90 bp):
AGGAGAAGAAGAAGAAGAAAGATAAGAAGGATAAGGAGAAAAAGAAAGAAAAGAAGTCGGATAAA
GAGCATGGAGTAGAAGATGACAAAG
Found at i:3231105 original size:27 final size:27
Alignment explanation
Indices: 3231051--3231105 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
3231041 GAGAAAAAGA
* *
3231051 AGAAAAAGAAAGAGAAGAAGGATAAGG
1 AGAAAAAGAAAGAGAAGAAGCACAAGG
*
3231078 AGAAAAAGAAAGAGAAGAAGCACGAGG
1 AGAAAAAGAAAGAGAAGAAGCACAAGG
3231105 A
1 A
3231106 TGAAGAGGAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.62, C:0.04, G:0.33, T:0.02
Consensus pattern (27 bp):
AGAAAAAGAAAGAGAAGAAGCACAAGG
Found at i:3231144 original size:204 final size:202
Alignment explanation
Indices: 3230661--3231105 Score: 505
Period size: 204 Copynumber: 2.2 Consensus size: 202
3230651 GAGAAGGAGA
* * * * * * *
3230661 AGAAGAAGAAGAAGAAGAAGAAAGATAATAAGGATAAGGAGAAAAAGAAAGACAAGAAGTGTGAT
1 AGAAGGAGAAGAAGAAAAAGAAAGAGAACAAGCACAAGGAGAAAAAGAAAGAGAAGAA--GTGAT
*
3230726 AAAGAGGATGA-G--GAAGA----G--GAGGAGAAGAAGAAGAAGAAAGATAAGAAGGATAAGGA
64 AAAGAAGATGATGTAGAAGATGCCGAAGAGGAGAAGAAGAAGAAGAAAGATAAGAAGGATAAGGA
* * *
3230782 GAAAAAGAAAGAAAAGAAGTCGGATAAAGAGGATGATGTAGAAGATGCCAAAGAGGAGAAGGAGA
129 GAAAAAGAAAGAAAAGAAGTCGGATAAAGAGCATGATGTAGAAGATGACAAAGAGGAGAAGAAGA
**
3230847 AGGAGAAGG
194 AAAAGAAGG
* * * * *
3230856 AGAAGGAGAAGAAGAAGAAGAAAGATAACAAGGATAAGGAGAAAAAGAAAGATAAGAAGTGCGAT
1 AGAAGGAGAAGAAGAAAAAGAAAGAGAACAAGCACAAGGAGAAAAAGAAAGAGAAGAAGT--GAT
* *
3230921 AAAGAGGATGATGTAGAAGATGCCGAAGAGGAGGAGAAGAAGAAGAAAGATAAGAAGGATAAGGA
64 AAAGAAGATGATGTAGAAGATGCCGAAGAGGAGAAGAAGAAGAAGAAAGATAAGAAGGATAAGGA
3230986 GAAAAAGAAAGAAAAGAAGTCGGATAAAGAGCATGGA-GTAGAAGATGACAAAGAGGAGAAAAAG
129 GAAAAAGAAAGAAAAGAAGTCGGATAAAGAGCAT-GATGTAGAAGATGACAAAGAGGAG---AAG
3231050 AAGAAAAAGAAAGAG
190 AAGAAAAAG-AAG-G
* * * *
3231065 AAGAAGGATAAGGAGAAAAAGAAAGAGAAGAAGCACGAGGA
1 -AGAAGGAGAAGAAGAAAAAGAAAGAGAACAAGCACAAGGA
3231106 TGAAGAGGAC
Statistics
Matches: 215, Mismatches: 17, Indels: 21
0.85 0.07 0.08
Matches are distributed among these distances:
193 2 0.01
195 69 0.32
196 1 0.00
198 5 0.02
202 1 0.00
204 90 0.42
205 2 0.01
207 9 0.04
208 3 0.01
209 1 0.00
210 32 0.15
ACGTcount: A:0.56, C:0.03, G:0.34, T:0.07
Consensus pattern (202 bp):
AGAAGGAGAAGAAGAAAAAGAAAGAGAACAAGCACAAGGAGAAAAAGAAAGAGAAGAAGTGATAA
AGAAGATGATGTAGAAGATGCCGAAGAGGAGAAGAAGAAGAAGAAAGATAAGAAGGATAAGGAGA
AAAAGAAAGAAAAGAAGTCGGATAAAGAGCATGATGTAGAAGATGACAAAGAGGAGAAGAAGAAA
AAGAAGG
Found at i:3231590 original size:2 final size:2
Alignment explanation
Indices: 3231583--3231607 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3231573 GATGAATAAT
3231583 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
3231608 TATATATATA
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:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:3232856 original size:2 final size:2
Alignment explanation
Indices: 3232849--3232889 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
3232839 TTAGTGTAGC
* *
3232849 AT AT AT AT AT AT AT AT AT AT GT AT AT AT GT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3232890 CACGCAGATT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3234586 original size:37 final size:38
Alignment explanation
Indices: 3234536--3234610 Score: 109
Period size: 39 Copynumber: 2.0 Consensus size: 38
3234526 TAGTATTTTA
3234536 TAATAACTATCAATTT-TAAAAAAA-AATATGTCCAAAT
1 TAATAACTATCAATTTATAAAAAAATAA-ATGTCCAAAT
*
3234573 TAATAATTATCAATTTACTAAAAAAATAAATGTCCAAA
1 TAATAACTATCAATTTA-TAAAAAAATAAATGTCCAAA
3234611 ATTTAAAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
37 15 0.44
39 17 0.50
40 2 0.06
ACGTcount: A:0.55, C:0.11, G:0.03, T:0.32
Consensus pattern (38 bp):
TAATAACTATCAATTTATAAAAAAATAAATGTCCAAAT
Found at i:3235440 original size:2 final size:2
Alignment explanation
Indices: 3235435--3235460 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3235425 TCACACACCC
3235435 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
3235461 CCCCTAATTA
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:3241258 original size:503 final size:503
Alignment explanation
Indices: 3240296--3241284 Score: 1879
Period size: 503 Copynumber: 2.0 Consensus size: 503
3240286 GGATGACAGA
3240296 TGTCCCACGCCTGTCAAAGGAGTGACCTCTGTAGTGTGTGCTTGCTTCGTTGTTGGCTTAGTAGG
1 TGTCCCACGCCTGTCAAAGGAGTGACCTCTGTAGTGTGTGCTTGCTTCGTTGTTGGCTTAGTAGG
3240361 GTAAGGAGTTTTTAGAGGGTCATGTTCTTGTGGGTCTTTAGTTTGCAGTGGTCTCATGAAGTGAA
66 GTAAGGAGTTTTTAGAGGGTCATGTTCTTGTGGGTCTTTAGTTTGCAGTGGTCTCATGAAGTGAA
3240426 CTTGTGAGGTGAAGGTATAACAAAGAAGAACACATGTGATGAGAAAAGGAAAGACTTAATTACCA
131 CTTGTGAGGTGAAGGTATAACAAAGAAGAACACATGTGATGAGAAAAGGAAAGACTTAATTACCA
3240491 GCATTCGAGGATGTATTTTTCGAGATAAATACGTAGCAAAGGAGCAAAGGAGACTCCATCTTCAT
196 GCATTCGAGGATGTATTTTTCGAGATAAATACGTAGCAAAGGAGCAAAGGAGACTCCATCTTCAT
3240556 TTTGAACGAAGTATTTACCGATTGATGCAAGACCATATGATCTTTGGGTCAGGCCATCTTGGCCA
261 TTTGAACGAAGTATTTACCGATTGATGCAAGACCATATGATCTTTGGGTCAGGCCATCTTGGCCA
3240621 GTGATTTGATCACAGGTCAAGATGGAGTGAGCGGCCAAAAGCCTGAGCATTCGATCAACAATGGA
326 GTGATTTGATCACAGGTCAAGATGGAGTGAGCGGCCAAAAGCCTGAGCATTCGATCAACAATGGA
* **
3240686 AGGGGCGTTTGGATTATTGGTGGGAAGCTTAGAGACGATCTCAGCAACCGACACCATACCAGGAG
391 AGGGGCGTTTGGATTATTGGTGGGAAGCTTAGAGACGATCTCAGAAACCGACACCATACCAAAAG
*
3240751 GAGTGTCGGCGGCTTCGGCTATAATATCTAAAAAACCCAGATCGCCGG
456 GAGTGCCGGCGGCTTCGGCTATAATATCTAAAAAACCCAGATCGCCGG
3240799 TGTCCCACGCCTGTCAAAGGAGTGACCTCTGTAGTGTGTGCTTGCTTCGTTGTTGGCTTAGTAGG
1 TGTCCCACGCCTGTCAAAGGAGTGACCTCTGTAGTGTGTGCTTGCTTCGTTGTTGGCTTAGTAGG
3240864 GTAAGGAGTTTTTAGAGGGTCATGTTCTTGTGGGTCTTTAGTTTGCAGTGGTCTCATGAAGTGAA
66 GTAAGGAGTTTTTAGAGGGTCATGTTCTTGTGGGTCTTTAGTTTGCAGTGGTCTCATGAAGTGAA
3240929 CTTGTGAGGTGAAGGTATAACAAAGAAGAACACATGTGATGAGAAAAGGAAAGACTTAATTACCA
131 CTTGTGAGGTGAAGGTATAACAAAGAAGAACACATGTGATGAGAAAAGGAAAGACTTAATTACCA
3240994 GCATTCGAGGATGTATTTTTCGAGATAAATACGTAGCAAAGGAGCAAAGGAGACTCCATCTTCAT
196 GCATTCGAGGATGTATTTTTCGAGATAAATACGTAGCAAAGGAGCAAAGGAGACTCCATCTTCAT
3241059 TTTGAACGAAGTATTTACCGATTGATGCAAGACCATATGATCTTTGGGTCAGGCCATCTTGGCCA
261 TTTGAACGAAGTATTTACCGATTGATGCAAGACCATATGATCTTTGGGTCAGGCCATCTTGGCCA
3241124 GTGATTTGATCACAGGTCAAGATGGAGTGAGCGGCCAAAAGCCTGAGCATTCGATCAACAATGGA
326 GTGATTTGATCACAGGTCAAGATGGAGTGAGCGGCCAAAAGCCTGAGCATTCGATCAACAATGGA
* * * *
3241189 AGGGGCGTTTGGATTATTGGTGGGGAGCTTAGAGACGATCTCGGAAACCGACAGCGTACCAAAAG
391 AGGGGCGTTTGGATTATTGGTGGGAAGCTTAGAGACGATCTCAGAAACCGACACCATACCAAAAG
* * *
3241254 GAGTGCCGGCGGCTTTGGCTATGATCTCTAA
456 GAGTGCCGGCGGCTTCGGCTATAATATCTAA
3241285 CAAGCCGAGA
Statistics
Matches: 475, Mismatches: 11, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
503 475 1.00
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.27
Consensus pattern (503 bp):
TGTCCCACGCCTGTCAAAGGAGTGACCTCTGTAGTGTGTGCTTGCTTCGTTGTTGGCTTAGTAGG
GTAAGGAGTTTTTAGAGGGTCATGTTCTTGTGGGTCTTTAGTTTGCAGTGGTCTCATGAAGTGAA
CTTGTGAGGTGAAGGTATAACAAAGAAGAACACATGTGATGAGAAAAGGAAAGACTTAATTACCA
GCATTCGAGGATGTATTTTTCGAGATAAATACGTAGCAAAGGAGCAAAGGAGACTCCATCTTCAT
TTTGAACGAAGTATTTACCGATTGATGCAAGACCATATGATCTTTGGGTCAGGCCATCTTGGCCA
GTGATTTGATCACAGGTCAAGATGGAGTGAGCGGCCAAAAGCCTGAGCATTCGATCAACAATGGA
AGGGGCGTTTGGATTATTGGTGGGAAGCTTAGAGACGATCTCAGAAACCGACACCATACCAAAAG
GAGTGCCGGCGGCTTCGGCTATAATATCTAAAAAACCCAGATCGCCGG
Found at i:3242408 original size:11 final size:11
Alignment explanation
Indices: 3242392--3242421 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
3242382 AAGTACTCAA
3242392 TTTTTTTAAAT
1 TTTTTTTAAAT
3242403 TTTTTTTAAAT
1 TTTTTTTAAAT
3242414 TTCTTTTT
1 TT-TTTTT
3242422 TTTTTTACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.72
12 5 0.28
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (11 bp):
TTTTTTTAAAT
Found at i:3243193 original size:45 final size:45
Alignment explanation
Indices: 3243137--3243224 Score: 122
Period size: 45 Copynumber: 2.0 Consensus size: 45
3243127 ACGGTAGCAG
* * ** *
3243137 TAACGGTAACAGTGACAGTATTCAACATGCAAAGTGCTGAATCTA
1 TAACAGTAACAGTAACAGTATTCAACACACAAAGTGCCGAATCTA
*
3243182 TAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAATC
1 TAACAGTAACAGTAACAGTATTCAACACACAAAGTGCCGAATC
3243225 GGTAATTGTA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.40, C:0.20, G:0.18, T:0.22
Consensus pattern (45 bp):
TAACAGTAACAGTAACAGTATTCAACACACAAAGTGCCGAATCTA
Found at i:3247982 original size:17 final size:17
Alignment explanation
Indices: 3247960--3247999 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
3247950 TCTAGCCCGG
*
3247960 CGCCGCCACCATTCTGT
1 CGCCGCCACCATTCTGA
*
3247977 CGCCGCCACCGTTCTGA
1 CGCCGCCACCATTCTGA
3247994 CGCCGC
1 CGCCGC
3248000 GCCGCACGTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.10, C:0.50, G:0.23, T:0.17
Consensus pattern (17 bp):
CGCCGCCACCATTCTGA
Found at i:3248579 original size:87 final size:87
Alignment explanation
Indices: 3248385--3248642 Score: 358
Period size: 87 Copynumber: 3.0 Consensus size: 87
3248375 ATATTTGCGA
* * ** * * *
3248385 TGGATCTGGTTGAAGATAATAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACA
1 TGGAGCTGATTGAAGATAGCAGATCTTGCCTTCCTGCATTAACAACGAAGCAGATCGAA-A-ACA
3248450 AA-CCTTGCCTCTC-TCGGTTATGG
64 AAGCCTTGCCTC-CATCGGTTATGG
* * *
3248473 TGGAGCTGATTGAAAATAGCAGATCTTGCCTTCCTGCGTTAACAACGAAGCAGATTGAAAACAAA
1 TGGAGCTGATTGAAGATAGCAGATCTTGCCTTCCTGCATTAACAACGAAGCAGATCGAAAACAAA
* *
3248538 GCCTTGTCTCCATCGGTTATTG
66 GCCTTGCCTCCATCGGTTATGG
*
3248560 TGGAGCTGATTGAAGATAGCAGATCTTGCCTTCCTGCATTAACAACGGAGCAGATCGAAAACAAA
1 TGGAGCTGATTGAAGATAGCAGATCTTGCCTTCCTGCATTAACAACGAAGCAGATCGAAAACAAA
3248625 GCCTTGCCTCCATCGGTT
66 GCCTTGCCTCCATCGGTT
3248643 GCAGTGAAGC
Statistics
Matches: 151, Mismatches: 17, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
86 6 0.04
87 96 0.64
88 49 0.32
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.26
Consensus pattern (87 bp):
TGGAGCTGATTGAAGATAGCAGATCTTGCCTTCCTGCATTAACAACGAAGCAGATCGAAAACAAA
GCCTTGCCTCCATCGGTTATGG
Found at i:3248873 original size:175 final size:175
Alignment explanation
Indices: 3248644--3249431 Score: 1387
Period size: 175 Copynumber: 4.5 Consensus size: 175
3248634 CCATCGGTTG
* * ** * * * **
3248644 CAGTGAAGCTGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCGTCAG
1 CAGTGGAGCGGATTAAAACCAATGATCTTATCTCTCTAAAGTTACAGTAGAGTAGATCGCACCAG
*
3248709 GTCTTATTTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGATCTTATCTCCCTGAGATT
66 GTCTTATTTCCCTGAGATTACAGTGGAACAGACCGAAGAATTTCAGATCTTATCTCCCTGAGATT
3248774 ACAGCGGAGCAGATTGAAGATAGTAATCCTATCTCCCTGAGATTA
131 ACAGCGGAGCAGATTGAAGATAGTAATCCTATCTCCCTGAGATTA
3248819 CAGTGGAGCGGATTAAAACCAATGATCTTATCTCTCTAAAGTTACAGTAGAGTAGATCGCACCAG
1 CAGTGGAGCGGATTAAAACCAATGATCTTATCTCTCTAAAGTTACAGTAGAGTAGATCGCACCAG
3248884 GTCTTATTTCCCTGAGATTACAGTGGAACAGACCGAAGAATTTCAGATCTTATCTCCCTGAGATT
66 GTCTTATTTCCCTGAGATTACAGTGGAACAGACCGAAGAATTTCAGATCTTATCTCCCTGAGATT
3248949 ACAGCGGAGCAGATTGAAGATAGTAATCCTATCTCCCTGAGATTA
131 ACAGCGGAGCAGATTGAAGATAGTAATCCTATCTCCCTGAGATTA
3248994 CAGTGGAGCGGATTAAAACCAATGATCTTATCTCTCTAAAGTTACAGTAGAGTAGATCGCACCAG
1 CAGTGGAGCGGATTAAAACCAATGATCTTATCTCTCTAAAGTTACAGTAGAGTAGATCGCACCAG
3249059 GTCTTATTTCCCTGAGATTACAGTGGAACAGACCGAAGAATTTCAGATCTTATCTCCCTGAGATT
66 GTCTTATTTCCCTGAGATTACAGTGGAACAGACCGAAGAATTTCAGATCTTATCTCCCTGAGATT
3249124 ACAGCGGAGCAGATTGAAGATAGTAATCCTATCTCCCTGAGATTA
131 ACAGCGGAGCAGATTGAAGATAGTAATCCTATCTCCCTGAGATTA
3249169 CAGTGGAGCGGATTAAAACCAATGATCTTATCTCTCTAAAGTTACAGTAGAGTAGATCGCACCAG
1 CAGTGGAGCGGATTAAAACCAATGATCTTATCTCTCTAAAGTTACAGTAGAGTAGATCGCACCAG
3249234 GTCTTATTTCCCTGAGATTACAGTGGAACAGACCGAAGAATTTCAGATCTTATCTCCCTGAGATT
66 GTCTTATTTCCCTGAGATTACAGTGGAACAGACCGAAGAATTTCAGATCTTATCTCCCTGAGATT
* *
3249299 ACAGCGGAGCAGATTGAAGTTAGTAATCCTATCTCCCTTAGATTA
131 ACAGCGGAGCAGATTGAAGATAGTAATCCTATCTCCCTGAGATTA
* ** * * * * *
3249344 CAGTGGAGTGGATTAAAATAAAGGATCTTATCTCTCTAAAGTTACAGTGGAGAAGATCGTATCAG
1 CAGTGGAGCGGATTAAAACCAATGATCTTATCTCTCTAAAGTTACAGTAGAGTAGATCGCACCAG
*
3249409 GTCTTATCTCCCTGAGATTACAG
66 GTCTTATTTCCCTGAGATTACAG
3249432 CGAAGCAGAT
Statistics
Matches: 592, Mismatches: 21, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
175 592 1.00
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (175 bp):
CAGTGGAGCGGATTAAAACCAATGATCTTATCTCTCTAAAGTTACAGTAGAGTAGATCGCACCAG
GTCTTATTTCCCTGAGATTACAGTGGAACAGACCGAAGAATTTCAGATCTTATCTCCCTGAGATT
ACAGCGGAGCAGATTGAAGATAGTAATCCTATCTCCCTGAGATTA
Found at i:3249433 original size:129 final size:129
Alignment explanation
Indices: 3249276--3249854 Score: 906
Period size: 129 Copynumber: 4.5 Consensus size: 129
3249266 CCGAAGAATT
* * *
3249276 TCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGTTAGTAATCCTATCTCCCTTAGA
1 TCAGGTCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGA
* * *
3249341 TTACAGTGGAGTGGATTAAAATAAAGGATCTTATCTCTCTAAAGTTACAGTGGAGAAGATCGTA
66 TTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCGTA
*
3249405 TCAGGTCTTATCTCCCTGAGATTACAGCGAAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGA
1 TCAGGTCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGA
*
3249470 TTACTGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCGTA
66 TTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCGTA
* *
3249534 TCAGGTCTTATCACCCTAAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGA
1 TCAGGTCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGA
* *
3249599 TTACAGTAGAGCGGATTAAAAAAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCGTA
66 TTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCGTA
* *
3249663 TCAGGTCTTATCACCCTAAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGA
1 TCAGGTCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGA
** * *
3249728 TTACAGTGGAATGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCA
66 TTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCGTA
* * * * * * * * **
3249792 TCAGGTTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTTTATCTCCCTGA
1 TCAGGTCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGA
3249855 CGTTGCGGAG
Statistics
Matches: 418, Mismatches: 32, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
129 418 1.00
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (129 bp):
TCAGGTCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGA
TTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCGTA
Found at i:3250410 original size:17 final size:17
Alignment explanation
Indices: 3250388--3250425 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
3250378 TCTAGCCCGG
*
3250388 CGCCGCCACCATTCTGT
1 CGCCGCCACCATTCTGA
*
3250405 CGCCGCCACCGTTCTGA
1 CGCCGCCACCATTCTGA
3250422 CGCC
1 CGCC
3250426 ACGCCGCATG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.11, C:0.50, G:0.21, T:0.18
Consensus pattern (17 bp):
CGCCGCCACCATTCTGA
Found at i:3256763 original size:5 final size:6
Alignment explanation
Indices: 3256718--3256742 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
3256708 GGTGCATTTC
3256718 TTCTTT TTCTTT TTCTTT TTCTTT T
1 TTCTTT TTCTTT TTCTTT TTCTTT T
3256743 CTACGGTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (6 bp):
TTCTTT
Found at i:3257329 original size:39 final size:39
Alignment explanation
Indices: 3257275--3257471 Score: 303
Period size: 39 Copynumber: 5.2 Consensus size: 39
3257265 TTTTGCCCCA
*
3257275 GCCCGCGCCAGCCCCAGCCCCTTCACCCGGTACACAGTC
1 GCCCGCGCCACCCCCAGCCCCTTCACCCGGTACACAGTC
* *
3257314 GCCCGCGCCAGCCCCAGCCCCTTCACCCGGAACACAGTC
1 GCCCGCGCCACCCCCAGCCCCTTCACCCGGTACACAGTC
*
3257353 GCCCGCGCCACCCCCAGCCCCTTCACCTGGTACAC---C
1 GCCCGCGCCACCCCCAGCCCCTTCACCCGGTACACAGTC
* * *
3257389 -CCCGCCCCCCCCCCAGCCCCTTCACCGGGTACACAGTC
1 GCCCGCGCCACCCCCAGCCCCTTCACCCGGTACACAGTC
3257427 GCCCGCGCCACCCCCAGCCCCTTCACCCGGTACACAGTC
1 GCCCGCGCCACCCCCAGCCCCTTCACCCGGTACACAGTC
3257466 GCCCGC
1 GCCCGC
3257472 TCCGGCGTCG
Statistics
Matches: 144, Mismatches: 10, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
35 31 0.22
36 1 0.01
38 1 0.01
39 111 0.77
ACGTcount: A:0.15, C:0.57, G:0.19, T:0.10
Consensus pattern (39 bp):
GCCCGCGCCACCCCCAGCCCCTTCACCCGGTACACAGTC
Done.