Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D12
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: 63843421
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1690000 characters in sequence are not A, C, G, or T
File 12 of 214
Found at i:3360918 original size:42 final size:42
Alignment explanation
Indices: 3360871--3361069 Score: 213
Period size: 42 Copynumber: 4.7 Consensus size: 42
3360861 GCCCAAAGGC
** * *
3360871 TGAACAGAATTTCGTAAGAGCTAAATGAAAACCCATAAGAGT
1 TGAACAGAAGCTCGTAAGAGCTAAATGGAAACTCATAAGAGT
* * *
3360913 TGAACAGAAGCTTGTAAGAGCTGAATGGAAACTCATATGAGT
1 TGAACAGAAGCTCGTAAGAGCTAAATGGAAACTCATAAGAGT
* * * *
3360955 TAAACGGAAGCTCATAAGAGCTGAACAT--AAACTCATAAGAGC
1 TGAACAGAAGCTCGTAAGAGCT-AA-ATGGAAACTCATAAGAGT
** * *
3360997 TGAACAGAAGCTCAAAAGAGCTAAACGGAAACTCATATGAGT
1 TGAACAGAAGCTCGTAAGAGCTAAATGGAAACTCATAAGAGT
* *
3361039 TAAACAGAAGCTCGTAAGAGCTAAACGGAAA
1 TGAACAGAAGCTCGTAAGAGCTAAATGGAAA
3361070 GTAAAACATG
Statistics
Matches: 130, Mismatches: 23, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
40 1 0.01
41 2 0.02
42 124 0.95
43 1 0.01
44 2 0.02
ACGTcount: A:0.44, C:0.16, G:0.22, T:0.19
Consensus pattern (42 bp):
TGAACAGAAGCTCGTAAGAGCTAAATGGAAACTCATAAGAGT
Found at i:3360968 original size:21 final size:21
Alignment explanation
Indices: 3360885--3361069 Score: 136
Period size: 21 Copynumber: 8.8 Consensus size: 21
3360875 CAGAATTTCG
* * *
3360885 TAAGAGCTAAATGAAAACCCA
1 TAAGAGCTAAACGGAAACTCA
* * * * **
3360906 TAAGAGTTGAACAGAAGCTTG
1 TAAGAGCTAAACGGAAACTCA
* *
3360927 TAAGAGCTGAATGGAAACTCA
1 TAAGAGCTAAACGGAAACTCA
* * *
3360948 TATGAGTTAAACGGAAGCTCA
1 TAAGAGCTAAACGGAAACTCA
* **
3360969 TAAGAGCTGAACATAAACTCA
1 TAAGAGCTAAACGGAAACTCA
* * *
3360990 TAAGAGCTGAACAGAAGCTCA
1 TAAGAGCTAAACGGAAACTCA
*
3361011 AAAGAGCTAAACGGAAACTCA
1 TAAGAGCTAAACGGAAACTCA
* * * * *
3361032 TATGAGTTAAACAGAAGCTCG
1 TAAGAGCTAAACGGAAACTCA
3361053 TAAGAGCTAAACGGAAA
1 TAAGAGCTAAACGGAAA
3361070 GTAAAACATG
Statistics
Matches: 122, Mismatches: 42, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 122 1.00
ACGTcount: A:0.45, C:0.16, G:0.22, T:0.18
Consensus pattern (21 bp):
TAAGAGCTAAACGGAAACTCA
Found at i:3361027 original size:84 final size:84
Alignment explanation
Indices: 3360899--3361060 Score: 243
Period size: 84 Copynumber: 1.9 Consensus size: 84
3360889 AGCTAAATGA
* *** * * *
3360899 AAACCCATAAGAGTTGAACAGAAGCTTGTAAGAGCTGAATGGAAACTCATATGAGTTAAACGGAA
1 AAACCCATAAGAGCTGAACAGAAGCTCAAAAGAGCTAAACGGAAACTCATATGAGTTAAACAGAA
3360964 GCTCATAAGAGCTGAACAT
66 GCTCATAAGAGCTGAACAT
*
3360983 AAACTCATAAGAGCTGAACAGAAGCTCAAAAGAGCTAAACGGAAACTCATATGAGTTAAACAGAA
1 AAACCCATAAGAGCTGAACAGAAGCTCAAAAGAGCTAAACGGAAACTCATATGAGTTAAACAGAA
*
3361048 GCTCGTAAGAGCT
66 GCTCATAAGAGCT
3361061 AAACGGAAAG
Statistics
Matches: 69, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
84 69 1.00
ACGTcount: A:0.43, C:0.17, G:0.22, T:0.19
Consensus pattern (84 bp):
AAACCCATAAGAGCTGAACAGAAGCTCAAAAGAGCTAAACGGAAACTCATATGAGTTAAACAGAA
GCTCATAAGAGCTGAACAT
Found at i:3375458 original size:15 final size:15
Alignment explanation
Indices: 3375392--3375461 Score: 52
Period size: 15 Copynumber: 4.6 Consensus size: 15
3375382 ATAGCAAGAA
* *
3375392 TTATATAAAATATTA
1 TTATATAATATATTT
*
3375407 CTACTATAA-ATATTT
1 TTA-TATAATATATTT
* * * *
3375422 ATATTTTATATTTTT
1 TTATATAATATATTT
3375437 GTTATATAATATATTT
1 -TTATATAATATATTT
3375453 TTATATAAT
1 TTATATAAT
3375462 TTGGTATTTA
Statistics
Matches: 42, Mismatches: 10, Indels: 6
0.72 0.17 0.10
Matches are distributed among these distances:
14 3 0.07
15 23 0.55
16 16 0.38
ACGTcount: A:0.40, C:0.03, G:0.01, T:0.56
Consensus pattern (15 bp):
TTATATAATATATTT
Found at i:3376651 original size:9 final size:9
Alignment explanation
Indices: 3376629--3376691 Score: 81
Period size: 9 Copynumber: 6.9 Consensus size: 9
3376619 ATTATGTAGT
*
3376629 GGTTCAATTT
1 GGTT-AATTC
3376639 GGTTAATTC
1 GGTTAATTC
3376648 GGTTAATTC
1 GGTTAATTC
* *
3376657 GGGTAATCC
1 GGTTAATTC
*
3376666 GATTAATTC
1 GGTTAATTC
3376675 GGTTAATTC
1 GGTTAATTC
3376684 GGTTAATT
1 GGTTAATT
3376692 TTTAACCAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
9 42 0.91
10 4 0.09
ACGTcount: A:0.24, C:0.11, G:0.22, T:0.43
Consensus pattern (9 bp):
GGTTAATTC
Found at i:3383952 original size:17 final size:16
Alignment explanation
Indices: 3383930--3383964 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
3383920 AATAGTAGGG
3383930 AAGGAAAAAGAAGAAAA
1 AAGGAAAAA-AAGAAAA
*
3383947 AAGGAAAAAAGGAAAA
1 AAGGAAAAAAAGAAAA
3383963 AA
1 AA
3383965 AAAACCTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (16 bp):
AAGGAAAAAAAGAAAA
Found at i:3383953 original size:8 final size:8
Alignment explanation
Indices: 3383930--3383964 Score: 52
Period size: 8 Copynumber: 4.2 Consensus size: 8
3383920 AATAGTAGGG
3383930 AAGGAAAA
1 AAGGAAAA
*
3383938 AGAAGAAAA
1 A-AGGAAAA
3383947 AAGGAAAA
1 AAGGAAAA
3383955 AAGGAAAA
1 AAGGAAAA
3383963 AA
1 AA
3383965 AAAACCTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
8 17 0.71
9 7 0.29
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (8 bp):
AAGGAAAA
Found at i:3384859 original size:24 final size:24
Alignment explanation
Indices: 3384832--3384877 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
3384822 TAAAATTTTT
3384832 TGTGATT-AAATTATTGCTATTAAA
1 TGTGATTGAAATTATTG-TATTAAA
*
3384856 TGTGCTTGAAATTATTGTATTA
1 TGTGATTGAAATTATTGTATTA
3384878 TATATTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 11 0.55
25 9 0.45
ACGTcount: A:0.33, C:0.04, G:0.15, T:0.48
Consensus pattern (24 bp):
TGTGATTGAAATTATTGTATTAAA
Found at i:3386025 original size:24 final size:23
Alignment explanation
Indices: 3385998--3386042 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
3385988 TATAAGAAAG
3385998 TTAAAATTTTAAAATTAAAAAAAT
1 TTAAAATTTTAAAA-TAAAAAAAT
*
3386022 TTAAATTTTTAAAATAAAAAA
1 TTAAAATTTTAAAATAAAAAA
3386043 TATATTAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (23 bp):
TTAAAATTTTAAAATAAAAAAAT
Found at i:3397731 original size:3 final size:3
Alignment explanation
Indices: 3397725--3397755 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
3397715 AAAGATGATG
3397725 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
3397756 CAAAGCTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:3400509 original size:13 final size:13
Alignment explanation
Indices: 3400491--3400518 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
3400481 CACACCTCAC
3400491 AATTTTTTGAGCT
1 AATTTTTTGAGCT
3400504 AATTTTTTGAGCT
1 AATTTTTTGAGCT
3400517 AA
1 AA
3400519 GAGAAAGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.07, G:0.14, T:0.50
Consensus pattern (13 bp):
AATTTTTTGAGCT
Found at i:3412354 original size:50 final size:50
Alignment explanation
Indices: 3412296--3412401 Score: 212
Period size: 50 Copynumber: 2.1 Consensus size: 50
3412286 TTCCATGAAT
3412296 TTTACATCTTTTTAATTTTGTCCCTAAATCATAATTTCATCAAAATTCTC
1 TTTACATCTTTTTAATTTTGTCCCTAAATCATAATTTCATCAAAATTCTC
3412346 TTTACATCTTTTTAATTTTGTCCCTAAATCATAATTTCATCAAAATTCTC
1 TTTACATCTTTTTAATTTTGTCCCTAAATCATAATTTCATCAAAATTCTC
3412396 TTTACA
1 TTTACA
3412402 AAAGTTGTTT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 56 1.00
ACGTcount: A:0.30, C:0.20, G:0.02, T:0.48
Consensus pattern (50 bp):
TTTACATCTTTTTAATTTTGTCCCTAAATCATAATTTCATCAAAATTCTC
Found at i:3418469 original size:24 final size:24
Alignment explanation
Indices: 3418437--3418483 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
3418427 CTAAATTTAT
*
3418437 AACACTTTCCTTTC-CTTTCTCTTC
1 AACACTTTCC-ATCACTTTCTCTTC
*
3418461 AACATTTTCCATCACTTTCTCTT
1 AACACTTTCCATCACTTTCTCTT
3418484 ATTTCCCTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 2 0.10
24 18 0.90
ACGTcount: A:0.17, C:0.34, G:0.00, T:0.49
Consensus pattern (24 bp):
AACACTTTCCATCACTTTCTCTTC
Found at i:3422776 original size:10 final size:10
Alignment explanation
Indices: 3422715--3422768 Score: 51
Period size: 10 Copynumber: 5.7 Consensus size: 10
3422705 AAATTAGAAA
*
3422715 AAAAAATTAT
1 AAAATATTAT
*
3422725 -AAAT-TTGT
1 AAAATATTAT
*
3422733 AAAATTTTAT
1 AAAATATTAT
*
3422743 AAAA-ATCAT
1 AAAATATTAT
3422752 AAAATATTAT
1 AAAATATTAT
3422762 AAAATAT
1 AAAATAT
3422769 ATAGAAATGT
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
8 3 0.09
9 14 0.40
10 18 0.51
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (10 bp):
AAAATATTAT
Found at i:3423331 original size:16 final size:16
Alignment explanation
Indices: 3423310--3423341 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3423300 TTTTATAATA
3423310 TTTTTTACAATTTTAT
1 TTTTTTACAATTTTAT
*
3423326 TTTTTTACTATTTTAT
1 TTTTTTACAATTTTAT
3423342 AAAAAAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.22, C:0.06, G:0.00, T:0.72
Consensus pattern (16 bp):
TTTTTTACAATTTTAT
Found at i:3423434 original size:22 final size:20
Alignment explanation
Indices: 3423409--3423563 Score: 111
Period size: 20 Copynumber: 7.6 Consensus size: 20
3423399 AAAAAATTCA
3423409 ATTTTTTTATAAATTATTTAT
1 ATTTTTTTATAAATT-TTTAT
*
3423430 GATTTTTTTAT-AATTTTTGT
1 -ATTTTTTTATAAATTTTTAT
*
3423450 GA--TTTTTATAAATTTTTTT
1 -ATTTTTTTATAAATTTTTAT
* * *
3423469 ATTTTATAATAAATTTTAAAT
1 ATTTTTTTATAAATTTT-TAT
*
3423490 ATTTTTTCTACAAATTTTT-T
1 ATTTTTT-TATAAATTTTTAT
* * **
3423510 ATATTTTTAATATATTTCCAT
1 AT-TTTTTTATAAATTTTTAT
*
3423531 AATTTTTTATAAATTTTTAAT
1 ATTTTTTTATAAATTTTT-AT
*
3423552 AATTTTTTATAA
1 ATTTTTTTATAA
3423564 CTTTATTGAT
Statistics
Matches: 105, Mismatches: 20, Indels: 17
0.74 0.14 0.12
Matches are distributed among these distances:
18 8 0.08
19 8 0.08
20 39 0.37
21 32 0.30
22 18 0.17
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.63
Consensus pattern (20 bp):
ATTTTTTTATAAATTTTTAT
Found at i:3423455 original size:18 final size:17
Alignment explanation
Indices: 3423434--3423478 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
3423424 ATTTATGATT
3423434 TTTTTATAATTTTTGTGA
1 TTTTTATAATTTTT-TGA
*
3423452 TTTTTATAAATTTTTTTA
1 TTTTTAT-AATTTTTTGA
3423470 -TTTTATAAT
1 TTTTTATAAT
3423479 AAATTTTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
16 3 0.12
17 6 0.24
18 9 0.36
19 7 0.28
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (17 bp):
TTTTTATAATTTTTTGA
Found at i:3423466 original size:11 final size:10
Alignment explanation
Indices: 3423411--3423563 Score: 66
Period size: 11 Copynumber: 15.0 Consensus size: 10
3423401 AAAATTCAAT
3423411 TTTTTTATAAA
1 TTTTTTAT-AA
* *
3423422 TTATTTATGAT
1 TTTTTTAT-AA
3423433 TTTTTTATAA
1 TTTTTTATAA
* *
3423443 -TTTTTGTGA
1 TTTTTTATAA
3423452 -TTTTTATAAA
1 TTTTTTAT-AA
3423462 TTTTTT-T-A
1 TTTTTTATAA
*
3423470 TTTTATAATAAA
1 TTTT-TTAT-AA
** *
3423482 TTTTAAATAT
1 TTTTTTATAA
*
3423492 TTTTTCTACAAA
1 TTTTT-TA-TAA
3423504 TTTTTTAT-A
1 TTTTTTATAA
*
3423513 TTTTTAAT-A
1 TTTTTTATAA
**
3423522 TATTTCCATAA
1 T-TTTTTATAA
3423533 TTTTTTATAAA
1 TTTTTTAT-AA
*
3423544 TTTTTAATAA
1 TTTTTTATAA
3423554 TTTTTTATAA
1 TTTTTTATAA
3423564 CTTTATTGAT
Statistics
Matches: 107, Mismatches: 24, Indels: 23
0.69 0.16 0.15
Matches are distributed among these distances:
8 5 0.05
9 24 0.22
10 30 0.28
11 37 0.35
12 11 0.10
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.63
Consensus pattern (10 bp):
TTTTTTATAA
Found at i:3423522 original size:31 final size:31
Alignment explanation
Indices: 3423480--3423559 Score: 85
Period size: 31 Copynumber: 2.5 Consensus size: 31
3423470 TTTTATAATA
*
3423480 AATTTTAAATATTTTTTCTACA-AATTTTTTAT
1 AATTTTTAATATTTTTTC--CATAATTTTTTAT
*
3423512 -ATTTTTAATA-TATTTCCATAATTTTTTAT
1 AATTTTTAATATTTTTTCCATAATTTTTTAT
3423541 AAATTTTTAATAATTTTTT
1 -AATTTTTAAT-ATTTTTT
3423560 ATAACTTTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
28 2 0.05
29 10 0.25
30 5 0.12
31 18 0.45
32 1 0.03
33 4 0.10
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (31 bp):
AATTTTTAATATTTTTTCCATAATTTTTTAT
Found at i:3423559 original size:42 final size:41
Alignment explanation
Indices: 3423373--3423560 Score: 113
Period size: 42 Copynumber: 4.6 Consensus size: 41
3423363 ATACTATATA
* ** *
3423373 TTTTAT-AATTTTTATGATTTTTATAAAAAAAATTCAAT--TT
1 TTTTATAAATTTTTAT-ATTTTT-TAATAAATTTTAAATAATT
* ** *
3423413 TTTTATAAATTATTTATGATTTTTTTAT-AATTTT-TGTGA-T
1 TTTTATAAATT-TTTAT-ATTTTTTAATAAATTTTAAATAATT
* * *
3423453 TTTTATAAATTTTTTTATTTTATAATAAATTTTAAATATTT
1 TTTTATAAATTTTTATATTTTTTAATAAATTTTAAATAATT
* * **
3423494 TTTCTACAAATTTTT-TATATTTTTAATATA-TTTCCATAATT
1 TTT-TATAAATTTTTATAT-TTTTTAATAAATTTTAAATAATT
3423535 TTTTATAAATTTTTAATAATTTTTTA
1 TTTTATAAATTTTT-AT-ATTTTTTA
3423561 TAACTTTATT
Statistics
Matches: 116, Mismatches: 20, Indels: 22
0.73 0.13 0.14
Matches are distributed among these distances:
38 8 0.07
39 11 0.09
40 33 0.28
41 24 0.21
42 38 0.33
43 2 0.02
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.61
Consensus pattern (41 bp):
TTTTATAAATTTTTATATTTTTTAATAAATTTTAAATAATT
Found at i:3431006 original size:36 final size:36
Alignment explanation
Indices: 3430941--3431043 Score: 98
Period size: 36 Copynumber: 2.9 Consensus size: 36
3430931 GATTCTGGGT
* *
3430941 ATAGTCAGGATTTGCCCCTTGCCCAAAATTCTGCCC
1 ATAGCCAGGATTTGCCCCCTGCCCAAAATTCTGCCC
* * * *
3430977 ATAGCCAGGATTTGCCCCCTGTCCGAAATTTTGTCC
1 ATAGCCAGGATTTGCCCCCTGCCCAAAATTCTGCCC
* * * ** *
3431013 ATAACCAGAACTTGGTCCCTGCCCATAATTC
1 ATAGCCAGGATTTGCCCCCTGCCCAAAATTC
3431044 CCACCTTGTG
Statistics
Matches: 52, Mismatches: 15, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
36 52 1.00
ACGTcount: A:0.23, C:0.32, G:0.17, T:0.28
Consensus pattern (36 bp):
ATAGCCAGGATTTGCCCCCTGCCCAAAATTCTGCCC
Found at i:3432018 original size:2 final size:2
Alignment explanation
Indices: 3432011--3432047 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
3432001 GAAGTTCATA
3432011 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
3432048 TAAGAGGGCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3432899 original size:9 final size:9
Alignment explanation
Indices: 3432852--3433051 Score: 57
Period size: 9 Copynumber: 20.2 Consensus size: 9
3432842 AAATAATAAA
*
3432852 ATAAAAATCA
1 ATAAAAAT-T
3432862 ATAAAAATT
1 ATAAAAATT
* *
3432871 ATTAAATTT
1 ATAAAAATT
3432880 CAATAAAAAATT
1 --AT-AAAAATT
3432892 ATAAAAATCGT
1 ATAAAAAT--T
*
3432903 AAAAAAATTAT
1 ATAAAAA-T-T
3432914 AATAAAAATT
1 -ATAAAAATT
*
3432924 ATAAAATTTT
1 ATAAAA-ATT
*
3432934 ATAAAAATC
1 ATAAAAATT
3432943 ATAAAAA-T
1 ATAAAAATT
*
3432951 ATAGAAA-T
1 ATAAAAATT
3432959 ATAGGGAAAATT
1 ATA---AAAATT
3432971 AT-AAAATT
1 ATAAAAATT
* * *
3432979 TTATAGAGTT
1 ATA-AAAATT
*
3432989 GTAAGAAAATT
1 AT-A-AAAATT
*
3433000 ATAAAGAAAT
1 ATAAA-AATT
*
3433010 ATAAAGAAAT
1 ATAAA-AATT
3433020 AT-AAAATT
1 ATAAAAATT
3433028 CATAAAAAAAATT
1 -AT---AAAAATT
3433041 ATAAAAATT
1 ATAAAAATT
3433050 AT
1 AT
3433052 TTTAACAAAA
Statistics
Matches: 145, Mismatches: 24, Indels: 43
0.68 0.11 0.20
Matches are distributed among these distances:
8 20 0.14
9 42 0.29
10 40 0.28
11 20 0.14
12 17 0.12
13 6 0.04
ACGTcount: A:0.61, C:0.03, G:0.06, T:0.30
Consensus pattern (9 bp):
ATAAAAATT
Found at i:3432929 original size:20 final size:20
Alignment explanation
Indices: 3432906--3432953 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
3432896 AAATCGTAAA
*
3432906 AAAATTATAATAAAAATTAT
1 AAAATTATAATAAAAATCAT
*
3432926 AAAATT-TTATAAAAATCAT
1 AAAATTATAATAAAAATCAT
*
3432945 AAAAATATA
1 AAAATTATA
3432954 GAAATATAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (20 bp):
AAAATTATAATAAAAATCAT
Found at i:3433014 original size:10 final size:10
Alignment explanation
Indices: 3432999--3433024 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
3432989 GTAAGAAAAT
3432999 TATAAAGAAA
1 TATAAAGAAA
3433009 TATAAAGAAA
1 TATAAAGAAA
3433019 TATAAA
1 TATAAA
3433025 ATTCATAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.69, C:0.00, G:0.08, T:0.23
Consensus pattern (10 bp):
TATAAAGAAA
Found at i:3433245 original size:9 final size:9
Alignment explanation
Indices: 3433219--3433312 Score: 57
Period size: 9 Copynumber: 10.2 Consensus size: 9
3433209 TGATTAAATG
3433219 ATATTTTTT
1 ATATTTTTT
***
3433228 ATGCATTTT
1 ATATTTTTT
3433237 ATATTTTTT
1 ATATTTTTT
3433246 ATATTTTTT
1 ATATTTTTT
*
3433255 -TACTATTTT
1 ATA-TTTTTT
3433264 ATAATTTTTT
1 AT-ATTTTTT
* *
3433274 CTAATTTTTA
1 AT-ATTTTTT
**
3433284 ATAAATTTT
1 ATATTTTTT
*
3433293 AAATATTTTT
1 ATAT-TTTTT
3433303 -TATTTTTT
1 ATATTTTTT
3433311 AT
1 AT
3433313 TAAAATTTAA
Statistics
Matches: 62, Mismatches: 18, Indels: 10
0.69 0.20 0.11
Matches are distributed among these distances:
8 7 0.11
9 35 0.56
10 19 0.31
11 1 0.02
ACGTcount: A:0.28, C:0.03, G:0.01, T:0.68
Consensus pattern (9 bp):
ATATTTTTT
Found at i:3433262 original size:27 final size:28
Alignment explanation
Indices: 3433219--3433312 Score: 97
Period size: 27 Copynumber: 3.4 Consensus size: 28
3433209 TGATTAAATG
*
3433219 ATATTTTTTATGCATTTTAT-ATTTTTT
1 ATATTTTTTATACATTTTATAATTTTTT
3433246 ATATTTTTT-TACTATTTTATAATTTTTT
1 ATATTTTTTATAC-ATTTTATAATTTTTT
* * *
3433274 CTAATTTTTAATAAATTTTA-AATATTTTT
1 AT-ATTTTTTATACATTTTATAAT-TTTTT
3433303 -TATTTTTTAT
1 ATATTTTTTAT
3433313 TAAAATTTAA
Statistics
Matches: 57, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
26 2 0.04
27 24 0.42
28 12 0.21
29 17 0.30
30 2 0.04
ACGTcount: A:0.28, C:0.03, G:0.01, T:0.68
Consensus pattern (28 bp):
ATATTTTTTATACATTTTATAATTTTTT
Found at i:3433287 original size:20 final size:18
Alignment explanation
Indices: 3433241--3433283 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
3433231 CATTTTATAT
*
3433241 TTTTTAT-ATTTTTTTAC
1 TTTTTATAATTTTTTTAA
3433258 TATTTTATAATTTTTTCTAA
1 T-TTTTATAATTTTTT-TAA
3433278 TTTTTA
1 TTTTTA
3433284 ATAAATTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 1 0.05
18 6 0.27
19 12 0.55
20 3 0.14
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTTTATAATTTTTTTAA
Found at i:3438409 original size:43 final size:43
Alignment explanation
Indices: 3438359--3438444 Score: 138
Period size: 43 Copynumber: 2.0 Consensus size: 43
3438349 TCATATTTCA
3438359 TTTCTCATCTCATAATCATTTCTCATATTTGT-CATTTCAATAT
1 TTTCTCATCTCATAATCATTTCTCATATTT-TCCATTTCAATAT
* *
3438402 TTTCTCATCTCATATTCATTTCTCATCTTTTCCATTTCAATAT
1 TTTCTCATCTCATAATCATTTCTCATATTTTCCATTTCAATAT
3438445 CAATCACATA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
42 1 0.03
43 39 0.98
ACGTcount: A:0.23, C:0.23, G:0.01, T:0.52
Consensus pattern (43 bp):
TTTCTCATCTCATAATCATTTCTCATATTTTCCATTTCAATAT
Found at i:3448375 original size:20 final size:21
Alignment explanation
Indices: 3448325--3448386 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 21
3448315 TATAAAAAAA
* * *
3448325 TTGTTATTTTTTATTGCTTTC
1 TTGTTATTTTTTACTGTTTTG
*
3448346 TTGTTGTTTTTTACTGTTTTG
1 TTGTTATTTTTTACTGTTTTG
* *
3448367 TTGTT-TTTTTCACTATTTTG
1 TTGTTATTTTTTACTGTTTTG
3448387 CTACCTTTTC
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
20 13 0.37
21 22 0.63
ACGTcount: A:0.08, C:0.08, G:0.13, T:0.71
Consensus pattern (21 bp):
TTGTTATTTTTTACTGTTTTG
Found at i:3449764 original size:31 final size:31
Alignment explanation
Indices: 3449729--3449794 Score: 132
Period size: 31 Copynumber: 2.1 Consensus size: 31
3449719 TATTCGAAGG
3449729 CAATTTAATCTTTTTATTTTTCTAAAAAAAC
1 CAATTTAATCTTTTTATTTTTCTAAAAAAAC
3449760 CAATTTAATCTTTTTATTTTTCTAAAAAAAC
1 CAATTTAATCTTTTTATTTTTCTAAAAAAAC
3449791 CAAT
1 CAAT
3449795 AAAAATTTCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.39, C:0.14, G:0.00, T:0.47
Consensus pattern (31 bp):
CAATTTAATCTTTTTATTTTTCTAAAAAAAC
Found at i:3453821 original size:11 final size:11
Alignment explanation
Indices: 3453805--3453830 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
3453795 ATTTTTTTAA
3453805 TTTTAAAATAC
1 TTTTAAAATAC
3453816 TTTTAAAATAC
1 TTTTAAAATAC
3453827 TTTT
1 TTTT
3453831 TTTAATTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (11 bp):
TTTTAAAATAC
Found at i:3453880 original size:8 final size:9
Alignment explanation
Indices: 3453827--3453887 Score: 61
Period size: 9 Copynumber: 6.4 Consensus size: 9
3453817 TTTAAAATAC
3453827 TTTTTTTAA
1 TTTTTTTAA
3453836 TTTTTTTAA
1 TTTTTTTAA
**
3453845 -TTTTAAAA
1 TTTTTTTAA
3453853 TTTTTTTAAA
1 TTTTTTT-AA
3453863 TGCTTTTTTTAA
1 ---TTTTTTTAA
3453875 TTTTTTTAA
1 TTTTTTTAA
3453884 TTTT
1 TTTT
3453888 AAAATACTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
8 6 0.14
9 26 0.60
10 2 0.05
12 2 0.05
13 7 0.16
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.72
Consensus pattern (9 bp):
TTTTTTTAA
Found at i:3453899 original size:40 final size:40
Alignment explanation
Indices: 3453781--3453899 Score: 181
Period size: 39 Copynumber: 3.0 Consensus size: 40
3453771 GCCCGAATAA
3453781 TAAATA-TATTTTTT-ATTTTTTTAATTTTAAAATACTTTT
1 TAAATACT-TTTTTTAATTTTTTTAATTTTAAAATACTTTT
* *
3453820 AAAATACTTTTTTTAATTTTTTTAATTTTAAAAT-TTTTT
1 TAAATACTTTTTTTAATTTTTTTAATTTTAAAATACTTTT
*
3453859 TAAATGCTTTTTTTAATTTTTTTAATTTTAAAATACTTTT
1 TAAATACTTTTTTTAATTTTTTTAATTTTAAAATACTTTT
3453899 T
1 T
3453900 TTAATTTTTA
Statistics
Matches: 72, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
39 47 0.65
40 25 0.35
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.64
Consensus pattern (40 bp):
TAAATACTTTTTTTAATTTTTTTAATTTTAAAATACTTTT
Found at i:3453935 original size:26 final size:27
Alignment explanation
Indices: 3453879--3453938 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 27
3453869 TTTTAATTTT
* * *
3453879 TTTAATTTTAAAATACTTTTTTTAATT
1 TTTATTTTTAAAATACATTTTTTAATA
**
3453906 TTTATTTTTAAAATA-ATTTTTTGGTA
1 TTTATTTTTAAAATACATTTTTTAATA
3453932 TTTATTT
1 TTTATTT
3453939 AAAAAACGGG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 14 0.50
27 14 0.50
ACGTcount: A:0.30, C:0.02, G:0.03, T:0.65
Consensus pattern (27 bp):
TTTATTTTTAAAATACATTTTTTAATA
Found at i:3454130 original size:29 final size:30
Alignment explanation
Indices: 3454091--3454147 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
3454081 GGTGGGAGAG
* *
3454091 GAGGAGAGTAAAAGTTTTGGGGGAAAGTGA
1 GAGGAGAGTAAAAGTATTAGGGGAAAGTGA
3454121 GAGG-GAGTAAAAGTATTAGGGGAAAGT
1 GAGGAGAGTAAAAGTATTAGGGGAAAGT
3454148 AAAAAAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 21 0.84
30 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.42, T:0.19
Consensus pattern (30 bp):
GAGGAGAGTAAAAGTATTAGGGGAAAGTGA
Found at i:3457143 original size:17 final size:16
Alignment explanation
Indices: 3457111--3457152 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 16
3457101 AAAAATGATA
3457111 ATTTAATTTTTAATTT
1 ATTTAATTTTTAATTT
*
3457127 ATTTAACTTTTTTATTT
1 ATTTAA-TTTTTAATTT
*
3457144 AATTAATTT
1 ATTTAATTT
3457153 AATAAATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 9 0.39
17 14 0.61
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (16 bp):
ATTTAATTTTTAATTT
Found at i:3460866 original size:15 final size:15
Alignment explanation
Indices: 3460846--3460898 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
3460836 AGAAGATGGG
3460846 GATGCA-AAGGAAGAA
1 GATGCAGAA-GAAGAA
3460861 GATGCAGAAGAAGAA
1 GATGCAGAAGAAGAA
*
3460876 G-T--AGAAGAAGAC
1 GATGCAGAAGAAGAA
*
3460888 GATGAAGAAGA
1 GATGCAGAAGA
3460899 TGAGTACGAG
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
12 10 0.30
13 1 0.03
14 1 0.03
15 19 0.58
16 2 0.06
ACGTcount: A:0.53, C:0.06, G:0.34, T:0.08
Consensus pattern (15 bp):
GATGCAGAAGAAGAA
Found at i:3460872 original size:12 final size:11
Alignment explanation
Indices: 3460855--3460902 Score: 51
Period size: 12 Copynumber: 4.1 Consensus size: 11
3460845 GGATGCAAAG
3460855 GAAGAAGATGCA
1 GAAGAAGATG-A
*
3460867 GAAGAAGAAGTA
1 GAAGAAGATG-A
*
3460879 GAAGAAGACGA
1 GAAGAAGATGA
3460890 TGAAGAAGATGA
1 -GAAGAAGATGA
3460902 G
1 G
3460903 TACGAGAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
11 2 0.06
12 29 0.94
ACGTcount: A:0.52, C:0.04, G:0.35, T:0.08
Consensus pattern (11 bp):
GAAGAAGATGA
Found at i:3463261 original size:16 final size:17
Alignment explanation
Indices: 3463242--3463276 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
3463232 AATAATAAAT
3463242 TATATTAATAATT-TAA
1 TATATTAATAATTGTAA
*
3463258 TATATTTATAATTGTAA
1 TATATTAATAATTGTAA
3463275 TA
1 TA
3463277 AATATTTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (17 bp):
TATATTAATAATTGTAA
Found at i:3463351 original size:14 final size:13
Alignment explanation
Indices: 3463325--3463363 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 13
3463315 ATAATATATG
3463325 AAAAATATTATTT
1 AAAAATATTATTT
3463338 AAAAATATTAATTT
1 AAAAATATT-ATTT
3463352 ATAAAAT-TTATT
1 A-AAAATATTATT
3463364 ATTAAAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 12 0.50
14 7 0.29
15 5 0.21
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
AAAAATATTATTT
Found at i:3463368 original size:168 final size:169
Alignment explanation
Indices: 3463085--3463422 Score: 624
Period size: 168 Copynumber: 2.0 Consensus size: 169
3463075 AAATTTATTA
* *
3463085 TTAATATTTTTATAATTGTAATAAATATTTATTATTAAATTATTAATATTGAATATTTTTCAATA
1 TTAATATATTTATAATTGTAATAAATATTTATTATTAAATTATTAATATTAAATATTTTTCAATA
* *
3463150 ATATATAAAAAATATTATTTAAAATTATTAATTTTTAAAATTTATTATTAAAATAAAATTGAAAT
66 ATATATAAAAAATATTATTTAAAAATATTAATTTATAAAATTTATTATTAAAATAAAATTGAAAT
3463215 ATTAAATAATTTATTAAAATAATAAATTATATTAATAAT
131 ATTAAATAATTTATTAAAATAATAAATTATATTAATAAT
3463254 TTAATATATTTATAATTGTAATAAATATTTATTATTAAATTATTAATATTAAATA-TTTTCAATA
1 TTAATATATTTATAATTGTAATAAATATTTATTATTAAATTATTAATATTAAATATTTTTCAATA
*
3463318 ATATATGAAAAATATTATTTAAAAATATTAATTTATAAAATTTATTATTAAAATAAAATTGAAAT
66 ATATATAAAAAATATTATTTAAAAATATTAATTTATAAAATTTATTATTAAAATAAAATTGAAAT
3463383 ATTAAATAATTTATTAAAATAATAAATTATATTAATAAT
131 ATTAAATAATTTATTAAAATAATAAATTATATTAATAAT
3463422 T
1 T
3463423 CATTATATGA
Statistics
Matches: 164, Mismatches: 5, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
168 111 0.68
169 53 0.32
ACGTcount: A:0.51, C:0.01, G:0.02, T:0.47
Consensus pattern (169 bp):
TTAATATATTTATAATTGTAATAAATATTTATTATTAAATTATTAATATTAAATATTTTTCAATA
ATATATAAAAAATATTATTTAAAAATATTAATTTATAAAATTTATTATTAAAATAAAATTGAAAT
ATTAAATAATTTATTAAAATAATAAATTATATTAATAAT
Found at i:3463471 original size:168 final size:167
Alignment explanation
Indices: 3463087--3463466 Score: 539
Period size: 168 Copynumber: 2.2 Consensus size: 167
3463077 ATTTATTATT
* * * * *
3463087 AATATTTTTATAATTGTAATAAATATTTATTATTAAATTATTAATATTGAATATTTTTCAATAAT
1 AATATATTTAGAATAGTAATAAATATGTATTATT-AA-TATTAATATTAAATATTTTTCAATAAT
* *
3463152 ATATAAAAAATATTATTTAAAATTATTAATTTTTAAAATTTATTATTAAAATAAAATTGAAATAT
64 ATATAAAAAATATTATTTAAAAATATTAATTTATAAAATTTATTATTAAAATAAAATTGAAATAT
*
3463217 TAAATAATTTATTAAAATAATAAATTATATTAATAATTT
129 TAAATAATTTATTAAAATAATAAATTATATTAATAATTC
* * *
3463256 AATATATTTATAATTGTAATAAATATTTATTATTAAATTATTAATATTAAATA-TTTTCAATAAT
1 AATATATTTAGAATAGTAATAAATATGTATTATT-AA-TATTAATATTAAATATTTTTCAATAAT
*
3463320 ATATGAAAAATATTATTTAAAAATATTAATTTATAAAATTTATTATTAAAATAAAATTGAAATAT
64 ATATAAAAAATATTATTTAAAAATATTAATTTATAAAATTTATTATTAAAATAAAATTGAAATAT
3463385 TAAATAATTTATTAAAATAATAAATTATATTAATAATTC
129 TAAATAATTTATTAAAATAATAAATTATATTAATAATTC
*
3463424 ATTATATGATTAGATATAGATAATTAAATATGTATGT-TTAATA
1 AATATAT--TTAGA-ATAG-TAA-TAAATATGTAT-TATTAATA
3463467 ATATTGAAAA
Statistics
Matches: 195, Mismatches: 10, Indels: 10
0.91 0.05 0.05
Matches are distributed among these distances:
168 117 0.60
169 51 0.26
170 4 0.02
171 5 0.03
172 5 0.03
173 12 0.06
174 1 0.01
ACGTcount: A:0.50, C:0.01, G:0.03, T:0.46
Consensus pattern (167 bp):
AATATATTTAGAATAGTAATAAATATGTATTATTAATATTAATATTAAATATTTTTCAATAATAT
ATAAAAAATATTATTTAAAAATATTAATTTATAAAATTTATTATTAAAATAAAATTGAAATATTA
AATAATTTATTAAAATAATAAATTATATTAATAATTC
Found at i:3463507 original size:15 final size:15
Alignment explanation
Indices: 3463464--3463511 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
3463454 TGTATGTTTA
3463464 ATAATATTGAAAATT
1 ATAATATTGAAAATT
*
3463479 AT--T-TT-AAAA-A
1 ATAATATTGAAAATT
3463489 ATAATATTGAAAATT
1 ATAATATTGAAAATT
3463504 ATAATATT
1 ATAATATT
3463512 TTATTAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 10
0.68 0.05 0.26
Matches are distributed among these distances:
10 2 0.08
11 4 0.15
12 3 0.12
13 3 0.12
14 4 0.15
15 10 0.38
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (15 bp):
ATAATATTGAAAATT
Found at i:3478245 original size:32 final size:32
Alignment explanation
Indices: 3478209--3478270 Score: 108
Period size: 32 Copynumber: 1.9 Consensus size: 32
3478199 TCAACACAAA
3478209 AATT-AATGATGTTAATGTTGTTAATAAAAAGG
1 AATTAAATGATG-TAATGTTGTTAATAAAAAGG
3478241 AATTAAATGATGTAATGTTGTTAATAAAAA
1 AATTAAATGATGTAATGTTGTTAATAAAAA
3478271 AGAGTATGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 22 0.76
33 7 0.24
ACGTcount: A:0.47, C:0.00, G:0.16, T:0.37
Consensus pattern (32 bp):
AATTAAATGATGTAATGTTGTTAATAAAAAGG
Found at i:3479818 original size:32 final size:32
Alignment explanation
Indices: 3479775--3479846 Score: 128
Period size: 32 Copynumber: 2.3 Consensus size: 32
3479765 AGTTGTACTG
*
3479775 TGATAG-CAAAACTGCTATTAACATTTGAGTT
1 TGATAGACAAAACTGCCATTAACATTTGAGTT
3479806 TGATAGACAAAACTGCCATTAACATTTGAGTT
1 TGATAGACAAAACTGCCATTAACATTTGAGTT
3479838 TGATAGACA
1 TGATAGACA
3479847 CTTTATCAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
31 6 0.15
32 33 0.85
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.32
Consensus pattern (32 bp):
TGATAGACAAAACTGCCATTAACATTTGAGTT
Found at i:3483424 original size:14 final size:13
Alignment explanation
Indices: 3483405--3483438 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
3483395 TTTTTAAAAA
3483405 TTAAAACAAAAATT
1 TTAAAA-AAAAATT
*
3483419 TTAAAAAAATATT
1 TTAAAAAAAAATT
3483432 TTAAAAA
1 TTAAAAA
3483439 TATTTTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 13 0.68
14 6 0.32
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (13 bp):
TTAAAAAAAAATT
Found at i:3483432 original size:13 final size:13
Alignment explanation
Indices: 3483405--3483448 Score: 56
Period size: 11 Copynumber: 3.5 Consensus size: 13
3483395 TTTTTAAAAA
*
3483405 TTAAAACAAAAATT
1 TTAAAA-AAATATT
3483419 TTAAAAAAATATT
1 TTAAAAAAATATT
3483432 TT--AAAAATATT
1 TTAAAAAAATATT
3483443 TTAAAA
1 TTAAAA
3483449 TTAAAAAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
11 11 0.41
13 10 0.37
14 6 0.22
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (13 bp):
TTAAAAAAATATT
Found at i:3483481 original size:11 final size:10
Alignment explanation
Indices: 3483424--3483486 Score: 55
Period size: 11 Copynumber: 6.5 Consensus size: 10
3483414 AAATTTTAAA
3483424 AAAATATTTT
1 AAAATATTTT
3483434 AAAAATATTTT
1 -AAAATATTTT
3483445 -AAA-A--TT
1 AAAATATTTT
*
3483451 AAAA-AATTT
1 AAAATATTTT
3483460 AAAAGTATTTTT
1 AAAA-TA-TTTT
3483472 AAAATATTTT
1 AAAATATTTT
3483482 AAAAT
1 AAAAT
3483487 TAAAAAAATT
Statistics
Matches: 45, Mismatches: 1, Indels: 13
0.76 0.02 0.22
Matches are distributed among these distances:
6 2 0.04
7 4 0.09
8 1 0.02
9 9 0.20
10 9 0.20
11 13 0.29
12 7 0.16
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (10 bp):
AAAATATTTT
Found at i:3483515 original size:11 final size:11
Alignment explanation
Indices: 3483501--3483526 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
3483491 AAAATTTAAA
3483501 AAAAGTATTTT
1 AAAAGTATTTT
3483512 AAAAGTATTTT
1 AAAAGTATTTT
3483523 AAAA
1 AAAA
3483527 TTAAAAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (11 bp):
AAAAGTATTTT
Found at i:3488326 original size:174 final size:175
Alignment explanation
Indices: 3488025--3488372 Score: 495
Period size: 174 Copynumber: 2.0 Consensus size: 175
3488015 CTTCAAGCAA
* * * *
3488025 GGAACAAAATAAAAGCATAAAGTGACCATACAGAATGTTTCCATTTAAAACGACCATCACAGCAA
1 GGAACAAAACAAAAGCATAAAGTGACCATACAGAATGTTTCCATCTAAAACAACCATCACAGAAA
* *
3488090 ACCGCAGTAACATCATCAGAAAGACTGAATATTTCAAGGCCAATAACCCCAAACAATGTGATGCT
66 AACGCAGTAACATCATAAGAAAGACTGAATATTTCAAGGCCAATAACCCCAAACAATGTGATGCT
* * *
3488155 TACTATATTTTCAACATTGTGGGAGCCCTAAATCCTCACCACAAT
131 TACTACAATTTCAACATTGTGGGAACCCTAAATCCTCACCACAAT
*
3488200 GGAACAAAACAAAAGCATGAATGTGACCATACAGAATGTTTCCA-CTAAAA-AACCATCACAGAA
1 GGAACAAAACAAAAGCAT-AAAGTGACCATACAGAATGTTTCCATCTAAAACAACCATCACAGAA
* * ** **
3488263 AAATGCAGTGACATCATAAGAAAGACTGAATATTTCAAGGCCAA-AATTTCCAAACCGTGTGATG
65 AAACGCAGTAACATCATAAGAAAGACTGAATATTTCAAGGCCAATAA-CCCCAAACAATGTGATG
* *
3488327 CTTACTACAATTTCAACATTGTGGGAACCTTAGATCCTCACCACAA
129 CTTACTACAATTTCAACATTGTGGGAACCCTAAATCCTCACCACAA
3488373 CGGACATGCA
Statistics
Matches: 153, Mismatches: 18, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
173 2 0.01
174 105 0.69
175 22 0.14
176 24 0.16
ACGTcount: A:0.41, C:0.22, G:0.14, T:0.22
Consensus pattern (175 bp):
GGAACAAAACAAAAGCATAAAGTGACCATACAGAATGTTTCCATCTAAAACAACCATCACAGAAA
AACGCAGTAACATCATAAGAAAGACTGAATATTTCAAGGCCAATAACCCCAAACAATGTGATGCT
TACTACAATTTCAACATTGTGGGAACCCTAAATCCTCACCACAAT
Found at i:3503918 original size:45 final size:46
Alignment explanation
Indices: 3503843--3503997 Score: 174
Period size: 45 Copynumber: 3.5 Consensus size: 46
3503833 TACACGGTGG
* *
3503843 ATCAGCACATAGC-ACCACCCTTATAGTCAATAGTACTC-GGTGAA
1 ATCAGCACATAGCAACCACCTTTATACTCAATAGTACTCAGGTGAA
*
3503887 ATCAGCACATAGCAACCACCTTTATACTCAATGGTAC-CAGGTGAA
1 ATCAGCACATAGCAACCACCTTTATACTCAATAGTACTCAGGTGAA
* ** * * * *
3503932 ATCAGCACATAGCCACCACCTTTATTTTCATTAATA-TCGGGTGGA
1 ATCAGCACATAGCAACCACCTTTATACTCAATAGTACTCAGGTGAA
* *
3503977 ATCAGCACATAGGATCCACCT
1 ATCAGCACATAGCAACCACCT
3503998 ATATTTCCAA
Statistics
Matches: 94, Mismatches: 14, Indels: 5
0.83 0.12 0.04
Matches are distributed among these distances:
44 14 0.15
45 80 0.85
ACGTcount: A:0.33, C:0.27, G:0.15, T:0.25
Consensus pattern (46 bp):
ATCAGCACATAGCAACCACCTTTATACTCAATAGTACTCAGGTGAA
Found at i:3509822 original size:22 final size:23
Alignment explanation
Indices: 3509795--3509945 Score: 137
Period size: 25 Copynumber: 6.3 Consensus size: 23
3509785 CACTAATGAA
* *
3509795 CAGAGAGCACTAAAGTGCTATA-
1 CAGAGAGCACCAACGTGCTATAT
** *
3509817 CAGAGAGCA-CAGGTGTGCTA-AA
1 CAGAGAGCACCA-ACGTGCTATAT
** *
3509839 CAGAGAGCACTGACGTGCTAAAAT
1 CAGAGAGCACCAACGTGCT-ATAT
3509863 CAGAGAGCACCAACGTGCTAGTAGT
1 CAGAGAGCACCAACGTGCTA-TA-T
3509888 CAGAGAGCACCAACGTGCTAATAAT
1 CAGAGAGCACCAACGTGCT-AT-AT
3509913 CAGAGAGCACCAACGTGCTAATAAT
1 CAGAGAGCACCAACGTGCT-AT-AT
3509938 CAGAGAGC
1 CAGAGAGC
3509946 GCGCTAAAGT
Statistics
Matches: 109, Mismatches: 11, Indels: 15
0.81 0.08 0.11
Matches are distributed among these distances:
21 2 0.02
22 29 0.27
23 2 0.02
24 19 0.17
25 55 0.50
26 2 0.02
ACGTcount: A:0.38, C:0.22, G:0.25, T:0.15
Consensus pattern (23 bp):
CAGAGAGCACCAACGTGCTATAT
Found at i:3509896 original size:25 final size:25
Alignment explanation
Indices: 3509839--3509945 Score: 171
Period size: 25 Copynumber: 4.3 Consensus size: 25
3509829 GTGTGCTAAA
**
3509839 CAGAGAGCACTGACGTGCTAA-AAT
1 CAGAGAGCACCAACGTGCTAATAAT
* *
3509863 CAGAGAGCACCAACGTGCTAGTAGT
1 CAGAGAGCACCAACGTGCTAATAAT
3509888 CAGAGAGCACCAACGTGCTAATAAT
1 CAGAGAGCACCAACGTGCTAATAAT
3509913 CAGAGAGCACCAACGTGCTAATAAT
1 CAGAGAGCACCAACGTGCTAATAAT
3509938 CAGAGAGC
1 CAGAGAGC
3509946 GCGCTAAAGT
Statistics
Matches: 76, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
24 18 0.24
25 58 0.76
ACGTcount: A:0.37, C:0.23, G:0.24, T:0.15
Consensus pattern (25 bp):
CAGAGAGCACCAACGTGCTAATAAT
Found at i:3510952 original size:16 final size:16
Alignment explanation
Indices: 3510931--3510967 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
3510921 GTTTTATCTA
3510931 TATAATAATATAATAT
1 TATAATAATATAATAT
3510947 TATAATAATATAATAT
1 TATAATAATATAATAT
*
3510963 AATAA
1 TATAA
3510968 CTTACTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TATAATAATATAATAT
Found at i:3510967 original size:8 final size:8
Alignment explanation
Indices: 3510930--3510961 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
3510920 TGTTTTATCT
3510930 ATATAATA
1 ATATAATA
3510938 ATATAATA
1 ATATAATA
*
3510946 TTATAATA
1 ATATAATA
3510954 ATATAATA
1 ATATAATA
3510962 TAATAACTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (8 bp):
ATATAATA
Found at i:3513023 original size:25 final size:25
Alignment explanation
Indices: 3512960--3513023 Score: 60
Period size: 25 Copynumber: 2.6 Consensus size: 25
3512950 TTTTAATTTA
* *
3512960 ATTAGATTCATTTTATGATAGAATT
1 ATTAAATTCATTTTATGATAAAATT
* *
3512985 ATTTACTATC-TTTT-TGATAAAAATT
1 ATTAAAT-TCATTTTATGAT-AAAATT
3513010 ATTAAATTCATTTT
1 ATTAAATTCATTTT
3513024 CATAATTATT
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
24 6 0.20
25 22 0.73
26 2 0.07
ACGTcount: A:0.36, C:0.06, G:0.06, T:0.52
Consensus pattern (25 bp):
ATTAAATTCATTTTATGATAAAATT
Found at i:3515061 original size:19 final size:19
Alignment explanation
Indices: 3515027--3515063 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
3515017 TTTAAAATAC
**
3515027 TTTTAAAATATTTTTTTAT
1 TTTTAAAATAAATTTTTAT
3515046 TTTTAAAATAAATTTTTA
1 TTTTAAAATAAATTTTTA
3515064 GTGTTTATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTTAAAATAAATTTTTAT
Found at i:3515070 original size:20 final size:19
Alignment explanation
Indices: 3515028--3515070 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
3515018 TTAAAATACT
** *
3515028 TTTAAAATATTTTTTTATT
1 TTTAAAATAAATTTTTATG
3515047 TTTAAAATAAATTTTTAGTG
1 TTTAAAATAAATTTTTA-TG
3515067 TTTA
1 TTTA
3515071 TTAAAAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (19 bp):
TTTAAAATAAATTTTTATG
Found at i:3515345 original size:13 final size:13
Alignment explanation
Indices: 3515327--3515352 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3515317 TAACCAGTTT
3515327 GATGAGCATATTC
1 GATGAGCATATTC
3515340 GATGAGCATATTC
1 GATGAGCATATTC
3515353 ACTTCTATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (13 bp):
GATGAGCATATTC
Found at i:3515375 original size:5 final size:6
Alignment explanation
Indices: 3515358--3515382 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
3515348 TATTCACTTC
3515358 TATTTT TATTTT TATTTT TATTTT T
1 TATTTT TATTTT TATTTT TATTTT T
3515383 CCACTACAAA
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:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TATTTT
Found at i:3526420 original size:21 final size:22
Alignment explanation
Indices: 3526383--3526423 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
3526373 TTTGTTTTGA
3526383 TTTTTAAGTTCTCTTTATTTAC
1 TTTTTAAGTTCTCTTTATTTAC
*
3526405 TTTTTAAGTT-TTTTTATTT
1 TTTTTAAGTTCTCTTTATTT
3526424 GTCCTTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.17, C:0.07, G:0.05, T:0.71
Consensus pattern (22 bp):
TTTTTAAGTTCTCTTTATTTAC
Found at i:3526547 original size:35 final size:34
Alignment explanation
Indices: 3526497--3526562 Score: 105
Period size: 35 Copynumber: 1.9 Consensus size: 34
3526487 AAATGTTTTA
*
3526497 TTTTTTAATTATAAATATATTTTTTTAAAATTATT
1 TTTTTTAATTATAAATAT-TATTTTTAAAATTATT
*
3526532 TTTTTTAATTTTAAATATTATTTTTAAAATT
1 TTTTTTAATTATAAATATTATTTTTAAAATT
3526563 TTAAATATGC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 12 0.41
35 17 0.59
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (34 bp):
TTTTTTAATTATAAATATTATTTTTAAAATTATT
Found at i:3526562 original size:21 final size:21
Alignment explanation
Indices: 3526519--3526593 Score: 71
Period size: 21 Copynumber: 3.5 Consensus size: 21
3526509 AAATATATTT
**
3526519 TTTTAAA-ATTATTTTTTTTAA
1 TTTTAAATATTA-TTTTTAAAA
3526540 TTTTAAATATTATTTTTAAAA
1 TTTTAAATATTATTTTTAAAA
**
3526561 TTTTAAATATGCTTTTTAATAA
1 TTTTAAATATTATTTTTAA-AA
* *
3526583 TATAAAATATT
1 TTTTAAATATT
3526594 TAAAATATAT
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
21 31 0.69
22 14 0.31
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.57
Consensus pattern (21 bp):
TTTTAAATATTATTTTTAAAA
Found at i:3526590 original size:22 final size:21
Alignment explanation
Indices: 3526552--3526592 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
3526542 TTAAATATTA
* *
3526552 TTTTTAAAATTTTAAATATGC
1 TTTTTAAAATATAAAATATGC
3526573 TTTTTAATAATATAAAATAT
1 TTTTTAA-AATATAAAATAT
3526593 TTAAAATATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (21 bp):
TTTTTAAAATATAAAATATGC
Found at i:3526675 original size:9 final size:9
Alignment explanation
Indices: 3526661--3526685 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
3526651 TTTTAAATGT
3526661 ATATTTTAA
1 ATATTTTAA
3526670 ATATTTTAA
1 ATATTTTAA
3526679 ATATTTT
1 ATATTTT
3526686 TTATTTAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (9 bp):
ATATTTTAA
Found at i:3526805 original size:22 final size:20
Alignment explanation
Indices: 3526779--3526833 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 20
3526769 AACTTTTTTT
3526779 AAAATATATATTAAAAAAGGTA
1 AAAATATATATTAAAAAA--TA
* * *
3526801 AAAATTTATATTAGAAAATT
1 AAAATATATATTAAAAAATA
3526821 AAAATATATATTA
1 AAAATATATATTA
3526834 TAATTAGTCA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 13 0.45
22 16 0.55
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (20 bp):
AAAATATATATTAAAAAATA
Found at i:3530412 original size:16 final size:15
Alignment explanation
Indices: 3530391--3530432 Score: 59
Period size: 16 Copynumber: 2.8 Consensus size: 15
3530381 TATCTTTAAA
3530391 AATAATTTAAAAAAGT
1 AATAATTTAAAAAA-T
3530407 AATAATTTAAAAAAT
1 AATAATTTAAAAAAT
*
3530422 TAT-ATTTAAAA
1 AATAATTTAAAA
3530433 TTAAAAACTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 8 0.32
15 3 0.12
16 14 0.56
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (15 bp):
AATAATTTAAAAAAT
Found at i:3530548 original size:24 final size:22
Alignment explanation
Indices: 3530520--3530648 Score: 92
Period size: 21 Copynumber: 6.0 Consensus size: 22
3530510 ATATATTTTA
*
3530520 AATATTTTATAATATTAAAATAAT
1 AATATTTTAAAAT-TTAAAA-AAT
*
3530544 TATA-TTTAAAATTTAAAAAAT
1 AATATTTTAAAATTTAAAAAAT
3530565 AATA-TTT-AAA-TT-AAAAAT
1 AATATTTTAAAATTTAAAAAAT
*
3530583 -ATATATTTAAAATTTAAAATAT
1 AATAT-TTTAAAATTTAAAAAAT
* *
3530605 AATATTATAAACCATTTAAAATAT
1 AATATTTTAAA--ATTTAAAAAAT
* * *
3530629 AA-ATTTCAAATTTTATAAAA
1 AATATTTTAAAATTTAAAAAA
3530649 CCAATAATAA
Statistics
Matches: 87, Mismatches: 10, Indels: 19
0.75 0.09 0.16
Matches are distributed among these distances:
17 3 0.03
18 6 0.07
19 5 0.06
20 6 0.07
21 18 0.21
22 16 0.18
23 17 0.20
24 16 0.18
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (22 bp):
AATATTTTAAAATTTAAAAAAT
Found at i:3530559 original size:7 final size:7
Alignment explanation
Indices: 3530547--3530641 Score: 52
Period size: 7 Copynumber: 13.6 Consensus size: 7
3530537 AAATAATTAT
3530547 ATTTAAA
1 ATTTAAA
3530554 ATTTAAA
1 ATTTAAA
** *
3530561 AAATAAT
1 ATTTAAA
3530568 ATTT-AA
1 ATTTAAA
*
3530574 ATTAAAA
1 ATTTAAA
* *
3530581 ATAT-AT
1 ATTTAAA
3530587 ATTTAAA
1 ATTTAAA
3530594 ATTTAAA
1 ATTTAAA
* *
3530601 ATATAAT
1 ATTTAAA
3530608 ATTATAAA
1 ATT-TAAA
3530616 CCATTTAAA
1 --ATTTAAA
*
3530625 ATAT-AA
1 ATTTAAA
*
3530631 ATTTCAA
1 ATTTAAA
3530638 ATTT
1 ATTT
3530642 TATAAAACCA
Statistics
Matches: 64, Mismatches: 18, Indels: 12
0.68 0.19 0.13
Matches are distributed among these distances:
6 13 0.20
7 41 0.64
8 3 0.05
9 4 0.06
10 3 0.05
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (7 bp):
ATTTAAA
Found at i:3530571 original size:21 final size:21
Alignment explanation
Indices: 3530520--3530641 Score: 108
Period size: 22 Copynumber: 5.7 Consensus size: 21
3530510 ATATATTTTA
*
3530520 AATATTTTATAATATTAAAATAAT
1 AATA-TTTAAAAT-TTAAAA-AAT
*
3530544 TATATTTAAAATTTAAAAAAT
1 AATATTTAAAATTTAAAAAAT
3530565 AATATTT-AAA-TT-AAAAAT
1 AATATTTAAAATTTAAAAAAT
*
3530583 ATATATTTAAAATTTAAAATAT
1 A-ATATTTAAAATTTAAAAAAT
*
3530605 AATATTATAAACCATTTAAAATAT
1 AATATT-TAAA--ATTTAAAAAAT
*
3530629 AA-ATTTCAAATTT
1 AATATTTAAAATTT
3530642 TATAAAACCA
Statistics
Matches: 86, Mismatches: 5, Indels: 18
0.79 0.05 0.17
Matches are distributed among these distances:
18 7 0.08
19 8 0.09
20 10 0.12
21 16 0.19
22 19 0.22
23 10 0.12
24 16 0.19
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (21 bp):
AATATTTAAAATTTAAAAAAT
Found at i:3530581 original size:20 final size:21
Alignment explanation
Indices: 3530533--3530615 Score: 89
Period size: 20 Copynumber: 4.0 Consensus size: 21
3530523 ATTTTATAAT
* *
3530533 ATTAAAATAATTATATTTAAA
1 ATTAAAAAAATAATATTTAAA
*
3530554 ATTTAAAAAATAATATTT-AA
1 ATTAAAAAAATAATATTTAAA
*
3530574 ATTAAAAATAT-ATATTTAAA
1 ATTAAAAAAATAATATTTAAA
* *
3530594 ATTTAAAATATAATATTATAAA
1 ATTAAAAAAATAATATT-TAAA
3530616 CCATTTAAAA
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
19 6 0.11
20 23 0.43
21 20 0.38
22 4 0.08
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
ATTAAAAAAATAATATTTAAA
Found at i:3530622 original size:64 final size:62
Alignment explanation
Indices: 3530521--3530640 Score: 147
Period size: 64 Copynumber: 1.9 Consensus size: 62
3530511 TATATTTTAA
* *
3530521 ATATTTTATAATATTAAAATAATTATATTTAAAATTTAAAAAATAATATTT-AAATTAAAAAT
1 ATATTTTAAAATATTAAAATAATAATATTTAAAATTTAAAAAATAA-ATTTCAAATTAAAAAT
*
3530583 ATATATTTAAAAT-TTAAAAT-ATAATATTATAAACCATTTAAAATATAAATTTCAAATT
1 ATAT-TTTAAAATATTAAAATAATAATATT-TAAA--ATTTAAAAAATAAATTTCAAATT
3530641 TTATAAAACC
Statistics
Matches: 50, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
61 7 0.14
62 15 0.30
63 11 0.22
64 17 0.34
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (62 bp):
ATATTTTAAAATATTAAAATAATAATATTTAAAATTTAAAAAATAAATTTCAAATTAAAAAT
Found at i:3531054 original size:16 final size:17
Alignment explanation
Indices: 3531023--3531056 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
3531013 TCATATTCTA
3531023 TAAAAAAATAAATTATT
1 TAAAAAAATAAATTATT
*
3531040 TAAATAAAT-AATTATT
1 TAAAAAAATAAATTATT
3531056 T
1 T
3531057 TTTTGGGTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TAAAAAAATAAATTATT
Found at i:3537402 original size:29 final size:29
Alignment explanation
Indices: 3537369--3537576 Score: 204
Period size: 29 Copynumber: 7.2 Consensus size: 29
3537359 TGTATACAAC
*
3537369 CCCTA-GAATCATGCGAGCCTATGTGTGAA
1 CCCTAGGAA-CATGCGAGCCTATGTGCGAA
* ** *
3537398 CCCTAGGAACATACGAGCCTACATGTGAA
1 CCCTAGGAACATGCGAGCCTATGTGCGAA
* *
3537427 CCCTAGGTACATGCAAGCCTATGTGCGAA
1 CCCTAGGAACATGCGAGCCTATGTGCGAA
* * * *
3537456 CCCTAGGTACATGCGAACTTATATGCGAA
1 CCCTAGGAACATGCGAGCCTATGTGCGAA
* * * * *
3537485 TCCTAGGAACATGTGAACTTATGTGTGAA
1 CCCTAGGAACATGCGAGCCTATGTGCGAA
**
3537514 CCCTAGGAACATGCGAATCTATGTGCGAA
1 CCCTAGGAACATGCGAGCCTATGTGCGAA
* * *
3537543 CTCTAGGAACATGCGAGCCTA-ATGCGAT
1 CCCTAGGAACATGCGAGCCTATGTGCGAA
3537571 CCCTAG
1 CCCTAG
3537577 TTGCATGTAA
Statistics
Matches: 149, Mismatches: 29, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
28 10 0.07
29 136 0.91
30 3 0.02
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.23
Consensus pattern (29 bp):
CCCTAGGAACATGCGAGCCTATGTGCGAA
Found at i:3537440 original size:58 final size:58
Alignment explanation
Indices: 3537369--3537563 Score: 230
Period size: 58 Copynumber: 3.4 Consensus size: 58
3537359 TGTATACAAC
* * * *
3537369 CCCTA-GAATCATGCGAGCCTATGTGTGAACCCTAGGAACATACGAGCCTACATGTGAA
1 CCCTAGGAA-CATGCGAGCCTATGTGTGAACCCTAGGAACATGCGAACCTATATGCGAA
* * * * *
3537427 CCCTAGGTACATGCAAGCCTATGTGCGAACCCTAGGTACATGCGAACTTATATGCGAA
1 CCCTAGGAACATGCGAGCCTATGTGTGAACCCTAGGAACATGCGAACCTATATGCGAA
* * * * * *
3537485 TCCTAGGAACATGTGAACTTATGTGTGAACCCTAGGAACATGCGAATCTATGTGCGAA
1 CCCTAGGAACATGCGAGCCTATGTGTGAACCCTAGGAACATGCGAACCTATATGCGAA
*
3537543 CTCTAGGAACATGCGAGCCTA
1 CCCTAGGAACATGCGAGCCTA
3537564 ATGCGATCCC
Statistics
Matches: 111, Mismatches: 25, Indels: 2
0.80 0.18 0.01
Matches are distributed among these distances:
58 109 0.98
59 2 0.02
ACGTcount: A:0.30, C:0.24, G:0.23, T:0.23
Consensus pattern (58 bp):
CCCTAGGAACATGCGAGCCTATGTGTGAACCCTAGGAACATGCGAACCTATATGCGAA
Found at i:3537472 original size:17 final size:17
Alignment explanation
Indices: 3537417--3537473 Score: 52
Period size: 17 Copynumber: 3.6 Consensus size: 17
3537407 CATACGAGCC
*
3537417 TACATGTGAACCCTAGG
1 TACATGCGAACCCTAGG
*
3537434 TACATGC-AAGCCTA--
1 TACATGCGAACCCTAGG
*
3537448 T--GTGCGAACCCTAGG
1 TACATGCGAACCCTAGG
3537463 TACATGCGAAC
1 TACATGCGAAC
3537474 TTATATGCGA
Statistics
Matches: 30, Mismatches: 5, Indels: 10
0.67 0.11 0.22
Matches are distributed among these distances:
12 3 0.10
13 6 0.20
14 1 0.03
15 1 0.03
16 6 0.20
17 13 0.43
ACGTcount: A:0.30, C:0.26, G:0.23, T:0.21
Consensus pattern (17 bp):
TACATGCGAACCCTAGG
Found at i:3537609 original size:34 final size:34
Alignment explanation
Indices: 3537564--3537629 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 34
3537554 TGCGAGCCTA
* * * *
3537564 ATGCGATCCCTAGTTGCATGTAAGCATATATGCC
1 ATGCGAACCCTAGGTACATGCAAGCATATATGCC
*
3537598 ATGCGAACCCTAGGTACATGCAAGCCTATATG
1 ATGCGAACCCTAGGTACATGCAAGCATATATG
3537630 ATCATGTGAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 27 1.00
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (34 bp):
ATGCGAACCCTAGGTACATGCAAGCATATATGCC
Found at i:3544630 original size:24 final size:24
Alignment explanation
Indices: 3544603--3544648 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
3544593 TCTTCTTCGA
* *
3544603 TTCCTATTCACTCCTTTATTTTTT
1 TTCCCATTCACTCATTTATTTTTT
*
3544627 TTCCCATTCATTCATTTATTTT
1 TTCCCATTCACTCATTTATTTT
3544649 CTCTCTCTGC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.15, C:0.24, G:0.00, T:0.61
Consensus pattern (24 bp):
TTCCCATTCACTCATTTATTTTTT
Found at i:3556008 original size:2 final size:2
Alignment explanation
Indices: 3556003--3556036 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3555993 GGAAAAAAAC
3556003 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
3556037 GAGTTTTCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3558627 original size:68 final size:68
Alignment explanation
Indices: 3558555--3558698 Score: 288
Period size: 68 Copynumber: 2.1 Consensus size: 68
3558545 GCTCTAATTC
3558555 TAAAAAATTCAATAAATTCAACCCTCAATATTTACAAAATATGTCAATTTAGTCCTAACTCTAAA
1 TAAAAAATTCAATAAATTCAACCCTCAATATTTACAAAATATGTCAATTTAGTCCTAACTCTAAA
3558620 AAT
66 AAT
3558623 TAAAAAATTCAATAAATTCAACCCTCAATATTTACAAAATATGTCAATTTAGTCCTAACTCTAAA
1 TAAAAAATTCAATAAATTCAACCCTCAATATTTACAAAATATGTCAATTTAGTCCTAACTCTAAA
3558688 AAT
66 AAT
3558691 TAAAAAAT
1 TAAAAAAT
3558699 ATATGTATTT
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 76 1.00
ACGTcount: A:0.49, C:0.17, G:0.03, T:0.32
Consensus pattern (68 bp):
TAAAAAATTCAATAAATTCAACCCTCAATATTTACAAAATATGTCAATTTAGTCCTAACTCTAAA
AAT
Found at i:3561280 original size:36 final size:35
Alignment explanation
Indices: 3561234--3561337 Score: 93
Period size: 36 Copynumber: 2.9 Consensus size: 35
3561224 CAACGGTGCA
* *
3561234 CATTTTTTACGCTTTATATTGCCAACGGAT-GGTGTG
1 CATTTCTTACG-TTTATATTGCCAACGAATGGGT-TG
* *
3561270 CATTTCTTACGTTTCATATTACCAATGAATGGGTTG
1 CATTTCTTACGTTT-ATATTGCCAACGAATGGGTTG
* * * *
3561306 CATCTCTCACATTTTATATTGCCAATGAATGG
1 CATTTCTTAC-GTTTATATTGCCAACGAATGG
3561338 CTTGAACTTC
Statistics
Matches: 57, Mismatches: 8, Indels: 6
0.80 0.11 0.08
Matches are distributed among these distances:
35 3 0.05
36 48 0.84
37 6 0.11
ACGTcount: A:0.24, C:0.18, G:0.17, T:0.40
Consensus pattern (35 bp):
CATTTCTTACGTTTATATTGCCAACGAATGGGTTG
Found at i:3564114 original size:44 final size:44
Alignment explanation
Indices: 3564036--3564126 Score: 128
Period size: 44 Copynumber: 2.1 Consensus size: 44
3564026 GTAGGTCAAA
* *
3564036 TAATATCAAAATAACCTACACTAATCAGAATTTAAGTGGGTAAC
1 TAATATCAAAATAACCTACACTAATCAGAATTTAAGTGAGAAAC
* ** *
3564080 TAATATTAAAATAACCTACACTAATTTGAGTTTAAGTGAGAAAC
1 TAATATCAAAATAACCTACACTAATCAGAATTTAAGTGAGAAAC
3564124 TAA
1 TAA
3564127 AAATAGAATT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.46, C:0.13, G:0.11, T:0.30
Consensus pattern (44 bp):
TAATATCAAAATAACCTACACTAATCAGAATTTAAGTGAGAAAC
Found at i:3568183 original size:19 final size:19
Alignment explanation
Indices: 3568155--3568205 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 19
3568145 AAGATAGCAT
3568155 ATTAAATTTAATTAATTTG
1 ATTAAATTTAATTAATTTG
* * *
3568174 ATTAATTTTATTTTATTTG
1 ATTAAATTTAATTAATTTG
* *
3568193 ATCAAAATTAATT
1 ATTAAATTTAATT
3568206 TCCCAAAAAT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (19 bp):
ATTAAATTTAATTAATTTG
Found at i:3575745 original size:42 final size:41
Alignment explanation
Indices: 3575687--3575844 Score: 169
Period size: 42 Copynumber: 3.8 Consensus size: 41
3575677 ACCAAAAATT
*
3575687 TATTTTAAAAATTAAAACAAAAATAAAAAAATTATTTTAAAAA
1 TATTTT-AAAATTAAAA-AAAAATAAAAAAAGTATTTTAAAAA
**
3575730 TATTTTAAAATTAAAAAAAAA-AATTTAAAGTATTTTAAAAA
1 TATTTTAAAATTAAAAAAAAATAA-AAAAAGTATTTTAAAAA
* ** * *
3575771 TATTTTTAAAATTTAAAAAATTTTAAAAAAGTATTTTAAAAG
1 TA-TTTTAAAATTAAAAAAAAATAAAAAAAGTATTTTAAAAA
* *
3575813 TATTTTAAAATT--TAAAAAATAAAAAAATTATT
1 TATTTTAAAATTAAAAAAAAATAAAAAAAGTATT
3575845 GTATTCGGGT
Statistics
Matches: 97, Mismatches: 15, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
39 15 0.15
40 2 0.02
41 31 0.32
42 42 0.43
43 7 0.07
ACGTcount: A:0.59, C:0.01, G:0.02, T:0.38
Consensus pattern (41 bp):
TATTTTAAAATTAAAAAAAAATAAAAAAAGTATTTTAAAAA
Found at i:3575748 original size:20 final size:20
Alignment explanation
Indices: 3575725--3575790 Score: 53
Period size: 20 Copynumber: 3.1 Consensus size: 20
3575715 AAATTATTTT
3575725 AAAAATATTTTAAAATTAAA
1 AAAAATATTTTAAAATTAAA
* * **
3575745 AAAAAAAATTTAAAGTATT-TT
1 AAAAATATTTTAAA--ATTAAA
3575766 AAAAATATTTTTAAAATTTAAA
1 AAAAATA-TTTTAAAA-TTAAA
3575788 AAA
1 AAA
3575791 TTTTAAAAAA
Statistics
Matches: 33, Mismatches: 8, Indels: 8
0.67 0.16 0.16
Matches are distributed among these distances:
20 13 0.39
21 8 0.24
22 12 0.36
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (20 bp):
AAAAATATTTTAAAATTAAA
Found at i:3575776 original size:11 final size:11
Alignment explanation
Indices: 3575713--3575822 Score: 72
Period size: 11 Copynumber: 10.4 Consensus size: 11
3575703 ACAAAAATAA
3575713 AAAAATTATTTT
1 AAAAA-TATTTT
3575725 AAAAATATTTT
1 AAAAATATTTT
***
3575736 -AAAAT-TAAA
1 AAAAATATTTT
* *
3575745 AAAAAAAATTT
1 AAAAATATTTT
*
3575756 -AAAGTATTTT
1 AAAAATATTTT
3575766 AAAAATATTTT
1 AAAAATATTTT
*
3575777 -TAAA-A-TTT
1 AAAAATATTTT
3575785 AAAAA-ATTTT
1 AAAAATATTTT
3575795 AAAAAAGTATTTT
1 -AAAAA-TATTTT
*
3575808 AAAAGTATTTT
1 AAAAATATTTT
3575819 AAAA
1 AAAA
3575823 TTTAAAAAAT
Statistics
Matches: 75, Mismatches: 15, Indels: 17
0.70 0.14 0.16
Matches are distributed among these distances:
8 3 0.04
9 6 0.08
10 22 0.29
11 30 0.40
12 9 0.12
13 5 0.07
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:3578916 original size:24 final size:24
Alignment explanation
Indices: 3578888--3578939 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
3578878 TTTCTAGACG
* *
3578888 ATTTAATATTTATGAGTATAATAT
1 ATTTAACATTTATGAGCATAATAT
* *
3578912 ATTTAGCATTTATTAGCATAATAT
1 ATTTAACATTTATGAGCATAATAT
3578936 ATTT
1 ATTT
3578940 GACTTTGATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.04, G:0.08, T:0.50
Consensus pattern (24 bp):
ATTTAACATTTATGAGCATAATAT
Found at i:3583423 original size:21 final size:21
Alignment explanation
Indices: 3583398--3583438 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
3583388 GATTTATACA
3583398 ATAATAATAAAATAATAGCAT
1 ATAATAATAAAATAATAGCAT
* * *
3583419 ATAATAGTGAAATGATAGCA
1 ATAATAATAAAATAATAGCA
3583439 AAATAGTAGG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.56, C:0.05, G:0.12, T:0.27
Consensus pattern (21 bp):
ATAATAATAAAATAATAGCAT
Found at i:3591139 original size:16 final size:17
Alignment explanation
Indices: 3591120--3591153 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
3591110 TGACACCGAA
3591120 TTTTC-TTTTTCTTTTT
1 TTTTCTTTTTTCTTTTT
3591136 TTTTCTTTTTTCTTTTT
1 TTTTCTTTTTTCTTTTT
3591153 T
1 T
3591154 CCCTTAAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (17 bp):
TTTTCTTTTTTCTTTTT
Found at i:3597157 original size:5 final size:5
Alignment explanation
Indices: 3597149--3597175 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
3597139 TTTGCCATCT
3597149 TAAAA TAAAA TAAAA TAAAA TAAAA TA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TA
3597176 TTTAATTGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (5 bp):
TAAAA
Found at i:3613141 original size:40 final size:40
Alignment explanation
Indices: 3613086--3613180 Score: 172
Period size: 40 Copynumber: 2.4 Consensus size: 40
3613076 ACGTTAGCGT
3613086 GATTTGCTGACGTGGACACAAATAGCGCCCTCTAGGACGC
1 GATTTGCTGACGTGGACACAAATAGCGCCCTCTAGGACGC
* *
3613126 GATTTGCTGATGTGGACACAAATAGCGCCCTTTAGGACGC
1 GATTTGCTGACGTGGACACAAATAGCGCCCTCTAGGACGC
3613166 GATTTGCTGACGTGG
1 GATTTGCTGACGTGG
3613181 CATGAACAGT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 52 1.00
ACGTcount: A:0.23, C:0.23, G:0.29, T:0.24
Consensus pattern (40 bp):
GATTTGCTGACGTGGACACAAATAGCGCCCTCTAGGACGC
Found at i:3616841 original size:75 final size:75
Alignment explanation
Indices: 3616715--3616870 Score: 285
Period size: 75 Copynumber: 2.1 Consensus size: 75
3616705 CCTTTAAGGG
*
3616715 CATGAATCCGAATCCCACTAAGGCAAAAATGATAAAACATTTCCCTGGAGGACCTTAGGCGCTCC
1 CATGAATCCGAATCCCACTAAGGCAAAAATGATAAAACATTTCCCTAGAGGACCTTAGGCGCTCC
* *
3616780 CGATAAACTC
66 CAAGAAACTC
3616790 CATGAATCCGAATCCCACTAAGGCAAAAATGATAAAACATTTCCCTAGAGGACCTTAGGCGCTCC
1 CATGAATCCGAATCCCACTAAGGCAAAAATGATAAAACATTTCCCTAGAGGACCTTAGGCGCTCC
3616855 CAAGAAACTC
66 CAAGAAACTC
3616865 CATGAA
1 CATGAA
3616871 CCCCTTTGGG
Statistics
Matches: 78, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
75 78 1.00
ACGTcount: A:0.37, C:0.28, G:0.17, T:0.19
Consensus pattern (75 bp):
CATGAATCCGAATCCCACTAAGGCAAAAATGATAAAACATTTCCCTAGAGGACCTTAGGCGCTCC
CAAGAAACTC
Found at i:3620422 original size:40 final size:40
Alignment explanation
Indices: 3620332--3620423 Score: 143
Period size: 40 Copynumber: 2.3 Consensus size: 40
3620322 AATTTATTTT
3620332 AAAA-ATTAAAAAAGTATTTTTAAAAAAATTTAAAATTAA
1 AAAATATTAAAAAAGTATTTTTAAAAAAATTTAAAATTAA
*
3620371 AAAATAATAAAAAAGTATTTTTAAAAAAA-TTAAAATTAA
1 AAAATATTAAAAAAGTATTTTTAAAAAAATTTAAAATTAA
*
3620410 AACAATTTTAAAAA
1 AA-AATATTAAAAA
3620424 TAAATATATT
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
39 16 0.33
40 32 0.67
ACGTcount: A:0.65, C:0.01, G:0.02, T:0.32
Consensus pattern (40 bp):
AAAATATTAAAAAAGTATTTTTAAAAAAATTTAAAATTAA
Found at i:3621657 original size:15 final size:16
Alignment explanation
Indices: 3621637--3621673 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
3621627 ACAAAATCAA
3621637 ATAAAA-TTACATAAT
1 ATAAAAGTTACATAAT
*
3621652 ATAAAAGTTACATTAT
1 ATAAAAGTTACATAAT
3621668 ATAAAA
1 ATAAAA
3621674 ATTAAATGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.59, C:0.05, G:0.03, T:0.32
Consensus pattern (16 bp):
ATAAAAGTTACATAAT
Found at i:3621865 original size:60 final size:60
Alignment explanation
Indices: 3621791--3621912 Score: 174
Period size: 60 Copynumber: 2.0 Consensus size: 60
3621781 ATACTAAACT
* * * * * *
3621791 AAACACAACAATTTATAGCTTAATCCTAAATTGCTAATAAATTAAATT-TTAAATAATTAC
1 AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAATT-AATTATAAAATAATTAC
3621851 AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTATAAAATAATTAC
1 AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTATAAAATAATTAC
3621911 AA
1 AA
3621913 TATTCATACA
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
59 4 0.07
60 51 0.93
ACGTcount: A:0.53, C:0.13, G:0.02, T:0.32
Consensus pattern (60 bp):
AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTATAAAATAATTAC
Found at i:3621934 original size:23 final size:21
Alignment explanation
Indices: 3621900--3621967 Score: 86
Period size: 23 Copynumber: 3.2 Consensus size: 21
3621890 AATTAATTAT
3621900 AAAATAATTACAATATTCATAC
1 AAAA-AATTACAATATTCATAC
*
3621922 AAACAATATTACAATATCCATAC
1 AAA-AA-ATTACAATATTCATAC
3621945 --AAAATTACAATATTCATAC
1 AAAAAATTACAATATTCATAC
3621964 AAAA
1 AAAA
3621968 TACTAATCCA
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
19 15 0.38
20 2 0.05
21 3 0.08
22 4 0.10
23 16 0.40
ACGTcount: A:0.56, C:0.16, G:0.00, T:0.28
Consensus pattern (21 bp):
AAAAAATTACAATATTCATAC
Found at i:3621951 original size:19 final size:19
Alignment explanation
Indices: 3621905--3622368 Score: 123
Period size: 19 Copynumber: 23.3 Consensus size: 19
3621895 ATTATAAAAT
3621905 AATTACAATATTCATACAAACA
1 AATTACAATATTCATAC--A-A
*
3621927 ATATTACAATATCCATACAA
1 A-ATTACAATATTCATACAA
3621947 AATTACAATATTCATACAA
1 AATTACAATATTCATACAA
* * *
3621966 AA-TACTA-ATCCAAAACTATA
1 AATTACAATATTC-ATAC-A-A
*
3621986 AA-TACAAAATTAATT-ATAAAA
1 AATTAC--AA-T-ATTCATACAA
3622007 TAATTACAATATTCATACAA
1 -AATTACAATATTCATACAA
* *
3622027 CATTATAATATTCATACAA
1 AATTACAATATTCATACAA
* *
3622046 AA-TACTAATCA--AAAACTATA
1 AATTAC-AAT-ATTCATAC-A-A
*
3622066 AA-TACAAAATTAATT-ATAAAA
1 AATTAC--AA-T-ATTCATACAA
3622087 TAATTACAATATTCATACAA
1 -AATTACAATATTCATACAA
*
3622107 AATTACAA-AAT--TACAA
1 AATTACAATATTCATACAA
* *
3622123 TATTCATACAA-AAT--TACAA
1 -AAT--TACAATATTCATACAA
3622142 AATTACAATATTCATACAA
1 AATTACAATATTCATACAA
* *
3622161 AA-TACTAATCA--AAAACTATA
1 AATTAC-AAT-ATTCATAC-A-A
*
3622181 AA-TACAAAATTAATT-ATAAAA
1 AATTAC--AA-T-ATTCATACAA
*
3622202 TAATTACAATATTCATAAAA
1 -AATTACAATATTCATACAA
*
3622222 AATTACAATATTTATACAAAA
1 AATTACAATATTCATAC--AA
*
3622243 AATTACACTATTCATACAA
1 AATTACAATATTCATACAA
* *
3622262 AA-TACTAATCA--AAAACTATA
1 AATTAC-AAT-ATTCATAC-A-A
*
3622282 AA-TACAAAATTAATT-ATAAAA
1 AATTAC--AA-T-ATTCATACAA
3622303 TAATTACAATATTCATACAA
1 -AATTACAATATTCATACAA
*
3622323 AATTATAATATTCATACAAA
1 AATTACAATATTCATAC-AA
*
3622343 AAGTTACAATATACATACAA
1 AA-TTACAATATTCATACAA
3622363 AATTAC
1 AATTAC
3622369 CCATTGGCGC
Statistics
Matches: 341, Mismatches: 46, Indels: 113
0.68 0.09 0.23
Matches are distributed among these distances:
16 10 0.03
17 7 0.02
18 28 0.08
19 128 0.38
20 62 0.18
21 49 0.14
22 20 0.06
23 35 0.10
25 2 0.01
ACGTcount: A:0.56, C:0.13, G:0.00, T:0.30
Consensus pattern (19 bp):
AATTACAATATTCATACAA
Found at i:3622013 original size:80 final size:80
Alignment explanation
Indices: 3621929--3622114 Score: 336
Period size: 80 Copynumber: 2.3 Consensus size: 80
3621919 TACAAACAAT
* *
3621929 ATTACAATATCCATACAAAATTACAATATTCATACAAAATACTAATCCAAAACTATAAATACAAA
1 ATTACAATATTCATACAAAATTACAATATTCATACAAAATACTAATCAAAAACTATAAATACAAA
3621994 ATTAATTATAAAATA
66 ATTAATTATAAAATA
* *
3622009 ATTACAATATTCATACAACATTATAATATTCATACAAAATACTAATCAAAAACTATAAATACAAA
1 ATTACAATATTCATACAAAATTACAATATTCATACAAAATACTAATCAAAAACTATAAATACAAA
3622074 ATTAATTATAAAATA
66 ATTAATTATAAAATA
3622089 ATTACAATATTCATACAAAATTACAA
1 ATTACAATATTCATACAAAATTACAA
3622115 AATTACAATA
Statistics
Matches: 100, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
80 100 1.00
ACGTcount: A:0.56, C:0.14, G:0.00, T:0.30
Consensus pattern (80 bp):
ATTACAATATTCATACAAAATTACAATATTCATACAAAATACTAATCAAAAACTATAAATACAAA
ATTAATTATAAAATA
Found at i:3622115 original size:8 final size:8
Alignment explanation
Indices: 3622102--3622149 Score: 60
Period size: 8 Copynumber: 5.6 Consensus size: 8
3622092 ACAATATTCA
3622102 TACAAAAT
1 TACAAAAT
3622110 TACAAAAT
1 TACAAAAT
*
3622118 TACAATATT
1 TACAA-AAT
3622127 CATACAAAAT
1 --TACAAAAT
3622137 TACAAAAT
1 TACAAAAT
3622145 TACAA
1 TACAA
3622150 TATTCATACA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
8 26 0.74
9 2 0.06
10 2 0.06
11 5 0.14
ACGTcount: A:0.58, C:0.15, G:0.00, T:0.27
Consensus pattern (8 bp):
TACAAAAT
Found at i:3622124 original size:27 final size:27
Alignment explanation
Indices: 3622088--3622163 Score: 152
Period size: 27 Copynumber: 2.8 Consensus size: 27
3622078 ATTATAAAAT
3622088 AATTACAATATTCATACAAAATTACAA
1 AATTACAATATTCATACAAAATTACAA
3622115 AATTACAATATTCATACAAAATTACAA
1 AATTACAATATTCATACAAAATTACAA
3622142 AATTACAATATTCATACAAAAT
1 AATTACAATATTCATACAAAAT
3622164 ACTAATCAAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 49 1.00
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.30
Consensus pattern (27 bp):
AATTACAATATTCATACAAAATTACAA
Found at i:3622186 original size:54 final size:54
Alignment explanation
Indices: 3622088--3622192 Score: 133
Period size: 54 Copynumber: 1.9 Consensus size: 54
3622078 ATTATAAAAT
* * **
3622088 AATTACAATATTCATACAAAATTACAAAATTACAATATTCATACAAAATTACAA
1 AATTACAATATTCATACAAAATTACAAAATAAAAATATAAATACAAAATTACAA
*
3622142 AATTACAATATTCATACAAAA-TAC-TAATCAAAAACTATAAATACAAAATTA
1 AATTACAATATTCATACAAAATTACAAAAT-AAAAA-TATAAATACAAAATTA
3622193 ATTATAAAAT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
52 3 0.07
53 6 0.14
54 35 0.80
ACGTcount: A:0.57, C:0.14, G:0.00, T:0.29
Consensus pattern (54 bp):
AATTACAATATTCATACAAAATTACAAAATAAAAATATAAATACAAAATTACAA
Found at i:3622360 original size:101 final size:100
Alignment explanation
Indices: 3621889--3622365 Score: 527
Period size: 101 Copynumber: 4.8 Consensus size: 100
3621879 AATTACTAAC
*
3621889 AAATTAATTATAAAATAATTACAATATTCATACAAACAATATTACAATATCCATAC-AAAATTAC
1 AAATTAATTATAAAATAATTACAATATTCAT--AAA-AA-ATTACAATATTCATACAAAAATTAC
*
3621953 AATATTCATACAAAATACTAATCCAAAACTATAAATACA
62 AATATTCATACAAAATACTAATCAAAAACTATAAATACA
* * *
3621992 AAATTAATTATAAAATAATTACAATATTCATACAACATTATAATATTCATAC-AAAA-TAC--TA
1 AAATTAATTATAAAATAATTACAATATTCATAAAAAATTACAATATTCATACAAAAATTACAATA
* * * *
3622053 ATCA-A-AAACTA-TAAAT-ACAAAA-T-TAATTATA
66 TTCATACAAAATACT-AATCA-AAAACTATAAATACA
* * * * *
3622084 AAA-TAATTACAATATTCA-TACAA-AAT--TACAAAATTACAATATTCATACAAAATTACAAAA
1 AAATTAATTATAA-AATAATTACAATATTCATAAAAAATTACAATATTCATAC------A-AAAA
3622144 TTACAATATTCATACAAAATACTAATCAAAAACTATAAATACA
58 TTACAATATTCATACAAAATACTAATCAAAAACTATAAATACA
* *
3622187 AAATTAATTATAAAATAATTACAATATTCATAAAAAATTACAATATTTATACAAAAAATTACACT
1 AAATTAATTATAAAATAATTACAATATTCATAAAAAATTACAATATTCATAC-AAAAATTACAAT
3622252 ATTCATACAAAATACTAATCAAAAACTATAAATACA
65 ATTCATACAAAATACTAATCAAAAACTATAAATACA
* *
3622288 AAATTAATTATAAAATAATTACAATATTCATACAAAATTATAATATTCATACAAAAAGTTACAAT
1 AAATTAATTATAAAATAATTACAATATTCATAAAAAATTACAATATTCATACAAAAA-TTACAAT
*
3622353 ATACATACAAAAT
65 ATTCATACAAAAT
3622366 TACCCATTGG
Statistics
Matches: 316, Mismatches: 32, Indels: 54
0.79 0.08 0.13
Matches are distributed among these distances:
88 20 0.06
90 2 0.01
91 13 0.04
92 12 0.04
93 2 0.01
94 12 0.04
95 1 0.00
96 9 0.03
97 3 0.01
98 3 0.01
99 23 0.07
100 7 0.02
101 127 0.40
102 4 0.01
103 43 0.14
104 13 0.04
105 2 0.01
107 20 0.06
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (100 bp):
AAATTAATTATAAAATAATTACAATATTCATAAAAAATTACAATATTCATACAAAAATTACAATA
TTCATACAAAATACTAATCAAAAACTATAAATACA
Found at i:3622416 original size:27 final size:27
Alignment explanation
Indices: 3622373--3622445 Score: 119
Period size: 27 Copynumber: 2.7 Consensus size: 27
3622363 AATTACCCAT
*
3622373 TGGCGCCTCCCTGTGAGGCACTTTTAA
1 TGGCGCCTCCCTATGAGGCACTTTTAA
*
3622400 TGGCGCCTCCTTATGAGGCACTTTTAA
1 TGGCGCCTCCCTATGAGGCACTTTTAA
*
3622427 TGGTGCCTCCCTATGAGGC
1 TGGCGCCTCCCTATGAGGC
3622446 GCCACCCGAC
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.15, C:0.29, G:0.26, T:0.30
Consensus pattern (27 bp):
TGGCGCCTCCCTATGAGGCACTTTTAA
Found at i:3624121 original size:20 final size:20
Alignment explanation
Indices: 3624098--3624145 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
3624088 AAAAAAATTT
*
3624098 TAAAAATATATATAAAAACA
1 TAAAAATATATAAAAAAACA
* * *
3624118 TAAATATTTATAAAAAAATA
1 TAAAAATATATAAAAAAACA
*
3624138 TAATAATA
1 TAAAAATA
3624146 AATTTAAATT
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (20 bp):
TAAAAATATATAAAAAAACA
Found at i:3624138 original size:32 final size:31
Alignment explanation
Indices: 3624099--3624177 Score: 81
Period size: 31 Copynumber: 2.5 Consensus size: 31
3624089 AAAAAATTTT
3624099 AAAAATATATATAAAAACATAAATATTTATAA
1 AAAAATATATATAAAAACATAAAT-TTTATAA
** *
3624131 AAAAATATA-ATAATAAATTTAAATTTTATAT
1 AAAAATATATATAA-AAACATAAATTTTATAA
* *
3624162 TAATAT-TATATAAAAA
1 AAAAATATATATAAAAA
3624178 AAATCCCCAC
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
30 5 0.12
31 18 0.45
32 17 0.43
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (31 bp):
AAAAATATATATAAAAACATAAATTTTATAA
Found at i:3625514 original size:9 final size:9
Alignment explanation
Indices: 3625487--3625523 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
3625477 TGAGTTTTCA
3625487 AATTCGAAT
1 AATTCGAAT
* *
3625496 AACTCAAAT
1 AATTCGAAT
3625505 AATTCGAAT
1 AATTCGAAT
3625514 AATTCGAAT
1 AATTCGAAT
3625523 A
1 A
3625524 TCAAACTATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.49, C:0.14, G:0.08, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:3625644 original size:30 final size:30
Alignment explanation
Indices: 3625582--3625644 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
3625572 ACTTTTCCCT
* *
3625582 CAAAACTTTTACTCCTTCCCACTTTCCCCC
1 CAAAACTTTTACTCCCTCCCACTTCCCCCC
3625612 CAAAACTTTTACTCTCCTCCC-C-TCCCCTCC
1 CAAAACTTTTACTC-CCTCCCACTTCCCC-CC
3625642 CAA
1 CAA
3625645 CCCCCCAATC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 4 0.14
30 20 0.69
31 5 0.17
ACGTcount: A:0.21, C:0.49, G:0.00, T:0.30
Consensus pattern (30 bp):
CAAAACTTTTACTCCCTCCCACTTCCCCCC
Found at i:3631234 original size:18 final size:18
Alignment explanation
Indices: 3631211--3631247 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
3631201 TTTTTTTTAG
3631211 CTTTGTTGATGTTATATA
1 CTTTGTTGATGTTATATA
3631229 CTTTGTTGATGTTATATA
1 CTTTGTTGATGTTATATA
3631247 C
1 C
3631248 ATGTGGATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.22, C:0.08, G:0.16, T:0.54
Consensus pattern (18 bp):
CTTTGTTGATGTTATATA
Found at i:3632350 original size:12 final size:12
Alignment explanation
Indices: 3632316--3632350 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
3632306 CGGATAGTAT
3632316 TAATTTTTTATA
1 TAATTTTTTATA
*
3632328 TTATTTGTTTATA
1 TAATTT-TTTATA
3632341 TAATTTTTTA
1 TAATTTTTTA
3632351 AAATATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.69
Consensus pattern (12 bp):
TAATTTTTTATA
Found at i:3632385 original size:18 final size:20
Alignment explanation
Indices: 3632350--3632390 Score: 59
Period size: 18 Copynumber: 2.1 Consensus size: 20
3632340 ATAATTTTTT
*
3632350 AAAATATATATAATACATTA
1 AAAATATATATAAAACATTA
3632370 AAAATAT-TA-AAAACATTA
1 AAAATATATATAAAACATTA
3632388 AAA
1 AAA
3632391 TAAATATTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 11 0.55
19 2 0.10
20 7 0.35
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (20 bp):
AAAATATATATAAAACATTA
Found at i:3632612 original size:11 final size:11
Alignment explanation
Indices: 3632596--3632626 Score: 55
Period size: 10 Copynumber: 2.9 Consensus size: 11
3632586 ACAGAACAAT
3632596 AAAAAATAGTA
1 AAAAAATAGTA
3632607 AAAAAA-AGTA
1 AAAAAATAGTA
3632617 AAAAAATAGT
1 AAAAAATAGT
3632627 TTTTTTTGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.53
11 9 0.47
ACGTcount: A:0.74, C:0.00, G:0.10, T:0.16
Consensus pattern (11 bp):
AAAAAATAGTA
Found at i:3635783 original size:16 final size:18
Alignment explanation
Indices: 3635748--3635786 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 18
3635738 TCTGTTACTG
3635748 CTTGTTACTTGATACTCT
1 CTTGTTACTTGATACTCT
*
3635766 CTTGTTAC-TG-TTCTCT
1 CTTGTTACTTGATACTCT
3635782 CTTGT
1 CTTGT
3635787 ATAATCTCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 10 0.50
17 2 0.10
18 8 0.40
ACGTcount: A:0.10, C:0.23, G:0.13, T:0.54
Consensus pattern (18 bp):
CTTGTTACTTGATACTCT
Found at i:3636238 original size:24 final size:24
Alignment explanation
Indices: 3636211--3636256 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
3636201 ATTTGGGAAT
3636211 GGTGGAGGATATGGCGACGGTGAC
1 GGTGGAGGATATGGCGACGGTGAC
* *
3636235 GGTGGTGGATATGGCGGCGGTG
1 GGTGGAGGATATGGCGACGGTG
3636257 GAGGATATGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.15, C:0.11, G:0.54, T:0.20
Consensus pattern (24 bp):
GGTGGAGGATATGGCGACGGTGAC
Found at i:3636257 original size:18 final size:18
Alignment explanation
Indices: 3636234--3636293 Score: 111
Period size: 18 Copynumber: 3.3 Consensus size: 18
3636224 GCGACGGTGA
3636234 CGGTGGTGGATATGGCGG
1 CGGTGGTGGATATGGCGG
*
3636252 CGGTGGAGGATATGGCGG
1 CGGTGGTGGATATGGCGG
3636270 CGGTGGTGGATATGGCGG
1 CGGTGGTGGATATGGCGG
3636288 CGGTGG
1 CGGTGG
3636294 CGGTGGTGGA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 40 1.00
ACGTcount: A:0.12, C:0.12, G:0.57, T:0.20
Consensus pattern (18 bp):
CGGTGGTGGATATGGCGG
Found at i:3644588 original size:20 final size:20
Alignment explanation
Indices: 3644563--3644616 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
3644553 AATATGTACG
3644563 TATATATATTATAAAATATA
1 TATATATATTATAAAATATA
* *
3644583 TATATAAATTATAAAGTATA
1 TATATATATTATAAAATATA
3644603 -ATATATATATATAA
1 TATATATAT-TATAA
3644617 GTAGGCATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
19 7 0.23
20 23 0.77
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (20 bp):
TATATATATTATAAAATATA
Found at i:3644627 original size:45 final size:45
Alignment explanation
Indices: 3644487--3644629 Score: 114
Period size: 45 Copynumber: 3.1 Consensus size: 45
3644477 ATACATGTAG
* * * *
3644487 ATATATATAAGTTATAAAATATAA-AAATATGTATAAGTATGTGTAT
1 ATATATATAAATTATAAAATATAATATATATATATAAGTA-G-GAAT
* * *
3644533 ATATATAAGTAAATTATGAAAATAT-GTACGTATATATATTA-TA-AAAT
1 ATATAT-A-TAAATTAT-AAAATATAATA--TATATATATAAGTAGGAAT
* *
3644580 ATATATATAAATTATAAAGTATAATATATATATATAAGTAGGCAT
1 ATATATATAAATTATAAAATATAATATATATATATAAGTAGGAAT
3644625 ATATA
1 ATATA
3644630 ACAAAATCTA
Statistics
Matches: 76, Mismatches: 12, Indels: 19
0.71 0.11 0.18
Matches are distributed among these distances:
43 10 0.13
44 8 0.11
45 17 0.22
46 7 0.09
47 9 0.12
48 7 0.09
49 8 0.11
50 2 0.03
51 8 0.11
ACGTcount: A:0.51, C:0.01, G:0.09, T:0.38
Consensus pattern (45 bp):
ATATATATAAATTATAAAATATAATATATATATATAAGTAGGAAT
Found at i:3644673 original size:3 final size:3
Alignment explanation
Indices: 3644659--3644736 Score: 68
Period size: 3 Copynumber: 24.7 Consensus size: 3
3644649 TAAATGGGTA
* *
3644659 AAT AAA AAT AAT AAT AAGGT AAGT AAT AAT AAT AA- ATAC AAT AAT AAT
1 AAT AAT AAT AAT AAT AA--T AA-T AAT AAT AAT AAT A-AT AAT AAT AAT
* *
3644707 GAT AAT AAT AAT AGT AAT AAT AAAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT -AAT AAT AA
3644737 AAGATGATAA
Statistics
Matches: 63, Mismatches: 7, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
2 1 0.02
3 51 0.81
4 8 0.13
5 3 0.05
ACGTcount: A:0.64, C:0.01, G:0.06, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:3644713 original size:39 final size:34
Alignment explanation
Indices: 3644659--3644779 Score: 109
Period size: 36 Copynumber: 3.3 Consensus size: 34
3644649 TAAATGGGTA
*
3644659 AATAAAAATAATAATAAGGTAAGTAATAATAATAAAT
1 AATAAAAATGATAATAA--TAA-TAATAATAATAAAT
* *
3644696 ACAATAATAATGATAATAATAATAGTAATAATAAAT
1 --AATAAAAATGATAATAATAATAATAATAATAAAT
*
3644732 AATAAAAGATGATAATACATTAA-AATAATGAAGAAAAT
1 AATAAAA-ATGATAATA-A-TAATAATAAT-AA-TAAAT
3644770 AATAAAAATG
1 AATAAAAATG
3644780 CTAAAAAGGG
Statistics
Matches: 71, Mismatches: 6, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
34 6 0.08
35 9 0.13
36 19 0.27
37 11 0.15
38 11 0.15
39 15 0.21
ACGTcount: A:0.64, C:0.02, G:0.08, T:0.26
Consensus pattern (34 bp):
AATAAAAATGATAATAATAATAATAATAATAAAT
Found at i:3646075 original size:21 final size:19
Alignment explanation
Indices: 3646050--3646089 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 19
3646040 CCGGCCCGAT
3646050 TTTTAATAAACACAAAAAATA
1 TTTTAA-AAACA-AAAAAATA
*
3646071 TTTTAAAAATAAAAAAATA
1 TTTTAAAAACAAAAAAATA
3646090 AAAAAAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 8 0.44
20 4 0.22
21 6 0.33
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (19 bp):
TTTTAAAAACAAAAAAATA
Done.