Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 ID=Chr10-JGI_221_v2.0
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: 62175169
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 981721 characters in sequence are not A, C, G, or T
File 10 of 202
Found at i:3318487 original size:3 final size:3
Alignment explanation
Indices: 3318481--3318515 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
3318471 AGTGTTGTTT
3318481 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
3318516 CTACTCTAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.31, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:3335296 original size:89 final size:89
Alignment explanation
Indices: 3335108--3335314 Score: 265
Period size: 90 Copynumber: 2.3 Consensus size: 89
3335098 CTCTAGCCCT
* * *
3335108 CAAACTTTTTCAAAAACAGCAATTAAGCCCCTGCTTTTTTTTGCACTCACTTGGGCACTTGAACT
1 CAAACTTTTTCAAAAAAAGCAATTAAGCCCCTACTTTTTTTTGCACTCAATTGGGCACTTGAACT
* *
3335173 TTCAAAATGCATAAAAAAGGCCTT
66 TTCAAAAGGCATAAAAAAGGCCTC
* * * *
3335197 TAAACTTTTTCAAAAAAATCAATTAAGCCCCTACTTTTCTTTTTG-ACTTAATTGGGTACTTGAA
1 CAAACTTTTTCAAAAAAAGCAATTAAGCCCCTAC-TTT-TTTTTGCACTCAATTGGGCACTTGAA
*
3335261 CTTTCAAAAGGCATCAAAAAGGTCC-C
64 CTTTCAAAAGGCATAAAAAAGG-CCTC
* *
3335287 CAAACTTTTCCCAAAAAAGCAATTAAGC
1 CAAACTTTTTCAAAAAAAGCAATTAAGC
3335315 ACCTGTTTTT
Statistics
Matches: 101, Mismatches: 14, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
89 30 0.30
90 63 0.62
91 8 0.08
ACGTcount: A:0.35, C:0.22, G:0.11, T:0.31
Consensus pattern (89 bp):
CAAACTTTTTCAAAAAAAGCAATTAAGCCCCTACTTTTTTTTGCACTCAATTGGGCACTTGAACT
TTCAAAAGGCATAAAAAAGGCCTC
Found at i:3335766 original size:21 final size:18
Alignment explanation
Indices: 3335705--3335768 Score: 65
Period size: 19 Copynumber: 3.3 Consensus size: 18
3335695 TTTTTGATGC
3335705 ATTTTATAATTTTTATAAA
1 ATTTTATAATTTTT-TAAA
* *
3335724 ATTTTACAATTTTTTTACA
1 ATTTTATAA-TTTTTTAAA
3335743 ATTTCTAATAATTTTTTAATA
1 ATTT-T-ATAATTTTTTAA-A
3335764 ATTTT
1 ATTTT
3335769 TATTATATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
19 15 0.41
20 14 0.38
21 8 0.22
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (18 bp):
ATTTTATAATTTTTTAAA
Found at i:3335768 original size:10 final size:10
Alignment explanation
Indices: 3335742--3335789 Score: 53
Period size: 10 Copynumber: 4.8 Consensus size: 10
3335732 ATTTTTTTAC
*
3335742 AATTTCTAAT
1 AATTTTTAAT
3335752 AATTTTTTAAT
1 AA-TTTTTAAT
3335763 AATTTTT-AT
1 AATTTTTAAT
* *
3335772 TATATTTAAT
1 AATTTTTAAT
3335782 AATTTTTA
1 AATTTTTA
3335790 TAACTTTTGT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
9 7 0.23
10 15 0.48
11 9 0.29
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (10 bp):
AATTTTTAAT
Found at i:3336024 original size:22 final size:22
Alignment explanation
Indices: 3335980--3336024 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
3335970 TAATTGTCTC
**
3335980 TTTTTGAAAAAGTTTGAGGGTT
1 TTTTTGAAAAAGTTTGAAAGTT
* *
3336002 TTTTTGATAAATTTTGAAAGTT
1 TTTTTGAAAAAGTTTGAAAGTT
3336024 T
1 T
3336025 AAGTACCCAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.29, C:0.00, G:0.20, T:0.51
Consensus pattern (22 bp):
TTTTTGAAAAAGTTTGAAAGTT
Found at i:3336106 original size:90 final size:90
Alignment explanation
Indices: 3335980--3336185 Score: 261
Period size: 90 Copynumber: 2.3 Consensus size: 90
3335970 TAATTGTCTC
* * *
3335980 TTTTTGAAAAAGTTTGAGGGTTTTTTTGATAAATTTTGAAAGTTTAAGTACCCAATTGAGTGAGA
1 TTTTTGAAAAAGTTTGAGGGCTTTTTTGATAAATTTTGAAAGTTCAAGTACCCAATCGAGTGAGA
* * * * *
3336045 AAAGAAAGTAATGATTTAGTTGCTTT
66 AAAGAAAGCAAAGACTTAATTAC-TT
* * * * *
3336071 TTTTTG-AAAGGTTTGAGGGCTTTTTTGATATATTTTGAAAGTTCAAGTACTCAATCGATTGCGA
1 TTTTTGAAAAAGTTTGAGGGCTTTTTTGATAAATTTTGAAAGTTCAAGTACCCAATCGAGTGAGA
* *
3336135 AAATAAAGCAAAGGCTTAATTACTT
66 AAAGAAAGCAAAGACTTAATTACTT
3336160 TTTTTGAAAAAGTTTGAGGGCTTTTT
1 TTTTTGAAAAAGTTTGAGGGCTTTTT
3336186 ACACCCTTAA
Statistics
Matches: 98, Mismatches: 16, Indels: 3
0.84 0.14 0.03
Matches are distributed among these distances:
89 8 0.08
90 84 0.86
91 6 0.06
ACGTcount: A:0.32, C:0.07, G:0.20, T:0.41
Consensus pattern (90 bp):
TTTTTGAAAAAGTTTGAGGGCTTTTTTGATAAATTTTGAAAGTTCAAGTACCCAATCGAGTGAGA
AAAGAAAGCAAAGACTTAATTACTT
Found at i:3337320 original size:3 final size:3
Alignment explanation
Indices: 3337312--3337341 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
3337302 AATATCCAGC
3337312 AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG
1 AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG
3337342 TTAGTTGACC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.67, T:0.00
Consensus pattern (3 bp):
AGG
Found at i:3338587 original size:20 final size:20
Alignment explanation
Indices: 3338562--3338602 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
3338552 AATGATGAAA
* *
3338562 AATTAAGATAAAATTCTTTT
1 AATTAAGAAAAAATTATTTT
*
3338582 AATTAATAAAAAATTATTTT
1 AATTAAGAAAAAATTATTTT
3338602 A
1 A
3338603 TTTTTATTCG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (20 bp):
AATTAAGAAAAAATTATTTT
Found at i:3341048 original size:2 final size:2
Alignment explanation
Indices: 3341041--3341094 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
3341031 ATGTCCGAGT
3341041 TA TA TA 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
3341083 TA TA TA TA TA TA
1 TA TA TA TA TA TA
3341095 AAAAGGAGTT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3347908 original size:21 final size:22
Alignment explanation
Indices: 3347882--3347922 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
3347872 ATATGGGTCG
*
3347882 GGCTCGAGCTTGAA-CATTTAA
1 GGCTCGAGCTCGAACCATTTAA
3347903 GGCTCGAGCTCGAACCATTT
1 GGCTCGAGCTCGAACCATTT
3347923 TTAACTTTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.27
Consensus pattern (22 bp):
GGCTCGAGCTCGAACCATTTAA
Found at i:3349307 original size:17 final size:18
Alignment explanation
Indices: 3349278--3349326 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 18
3349268 CATTTTTACC
3349278 AATT-TTTTAA-ATAAAAA
1 AATTATTTTAATAT-AAAA
3349295 AATTATTTTAATATAAAA
1 AATTATTTTAATATAAAA
*
3349313 AAGATATTTTAATA
1 AA-TTATTTTAATA
3349327 GTTTTTCGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
17 4 0.14
18 12 0.43
19 12 0.43
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (18 bp):
AATTATTTTAATATAAAA
Found at i:3349310 original size:19 final size:19
Alignment explanation
Indices: 3349278--3349326 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
3349268 CATTTTTACC
3349278 AATT-TTTTAA-ATAAAAA
1 AATTATTTTAATATAAAAA
3349295 AATTATTTTAATATAAAAA
1 AATTATTTTAATATAAAAA
3349314 AGA-TATTTTAATA
1 A-ATTATTTTAATA
3349327 GTTTTTCGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 18 0.62
20 1 0.03
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (19 bp):
AATTATTTTAATATAAAAA
Found at i:3349657 original size:25 final size:27
Alignment explanation
Indices: 3349606--3349668 Score: 94
Period size: 25 Copynumber: 2.4 Consensus size: 27
3349596 TTAAAAAATA
3349606 ACCAAAATATTATAACTTTTTTTTATTT
1 ACCAAAATATTATAAC-TTTTTTTATTT
3349634 ACCAAAATATTAT-A-TTTTTTTATTT
1 ACCAAAATATTATAACTTTTTTTATTT
*
3349659 ACTAAAATAT
1 ACCAAAATAT
3349669 ACAAAAAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
25 20 0.59
27 1 0.03
28 13 0.38
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.51
Consensus pattern (27 bp):
ACCAAAATATTATAACTTTTTTTATTT
Found at i:3350445 original size:18 final size:19
Alignment explanation
Indices: 3350406--3350501 Score: 124
Period size: 19 Copynumber: 5.2 Consensus size: 19
3350396 ATTTTATATT
3350406 TTAAATGAAAATAGAGTTA
1 TTAAATGAAAATAGAGTTA
* *
3350425 TTAAATGAGAATAG-TTTA
1 TTAAATGAAAATAGAGTTA
*
3350443 TTAAATTAAAATAGAGTTA
1 TTAAATGAAAATAGAGTTA
* *
3350462 TTAAATGAGAATA-ATTTA
1 TTAAATGAAAATAGAGTTA
*
3350480 TTAAATTAAAATAGAGTTA
1 TTAAATGAAAATAGAGTTA
3350499 TTA
1 TTA
3350502 CTTAATTAGA
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
18 30 0.47
19 34 0.53
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.38
Consensus pattern (19 bp):
TTAAATGAAAATAGAGTTA
Found at i:3350447 original size:37 final size:37
Alignment explanation
Indices: 3350406--3350501 Score: 174
Period size: 37 Copynumber: 2.6 Consensus size: 37
3350396 ATTTTATATT
* *
3350406 TTAAATGAAAATAGAGTTATTAAATGAGAATAGTTTA
1 TTAAATTAAAATAGAGTTATTAAATGAGAATAATTTA
3350443 TTAAATTAAAATAGAGTTATTAAATGAGAATAATTTA
1 TTAAATTAAAATAGAGTTATTAAATGAGAATAATTTA
3350480 TTAAATTAAAATAGAGTTATTA
1 TTAAATTAAAATAGAGTTATTA
3350502 CTTAATTAGA
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 57 1.00
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.38
Consensus pattern (37 bp):
TTAAATTAAAATAGAGTTATTAAATGAGAATAATTTA
Found at i:3355362 original size:15 final size:16
Alignment explanation
Indices: 3355342--3355379 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
3355332 ACACGAAAAA
3355342 AAAATTT-AAAACACG
1 AAAATTTAAAAACACG
3355357 AAAATTTAAAAACACG
1 AAAATTTAAAAACACG
3355373 AAAATTT
1 AAAATTT
3355380 TTAGAAAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 7 0.32
16 15 0.68
ACGTcount: A:0.61, C:0.11, G:0.05, T:0.24
Consensus pattern (16 bp):
AAAATTTAAAAACACG
Found at i:3355397 original size:16 final size:17
Alignment explanation
Indices: 3355349--3355405 Score: 64
Period size: 16 Copynumber: 3.4 Consensus size: 17
3355339 AAAAAAATTT
*
3355349 AAAACACGAAAATTTA-
1 AAAACACGAAATTTTAG
3355365 AAAACACGAAAATTTTTAG
1 AAAACACG-AAA-TTTTAG
*
3355384 AAAACAC-AAATTTTTG
1 AAAACACGAAATTTTAG
3355400 AAAACA
1 AAAACA
3355406 TAAAAAATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
16 19 0.53
17 6 0.17
18 4 0.11
19 7 0.19
ACGTcount: A:0.58, C:0.12, G:0.07, T:0.23
Consensus pattern (17 bp):
AAAACACGAAATTTTAG
Found at i:3355467 original size:18 final size:17
Alignment explanation
Indices: 3355429--3355501 Score: 67
Period size: 18 Copynumber: 4.2 Consensus size: 17
3355419 AGAATTTGTG
* *
3355429 AAACACGAGAATTGTTGA
1 AAACACGAAAATT-TTAA
*
3355447 AAACACAAAAATTTTGAA
1 AAACACGAAAATTTT-AA
*
3355465 AAAAACGAAAA-TTTAA
1 AAACACGAAAATTTTAA
*
3355481 AGACACGAAAATTTTTAA
1 AAACACGAAAA-TTTTAA
3355499 AAA
1 AAA
3355502 AACACGACAC
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
16 11 0.25
17 5 0.11
18 28 0.64
ACGTcount: A:0.58, C:0.10, G:0.11, T:0.22
Consensus pattern (17 bp):
AAACACGAAAATTTTAA
Found at i:3355476 original size:63 final size:62
Alignment explanation
Indices: 3355366--3355483 Score: 152
Period size: 63 Copynumber: 1.9 Consensus size: 62
3355356 GAAAATTTAA
* *
3355366 AAACACGAAAATTTTTAGAAAACACAAATTTTTGAAAACATAAAAAATTTTAAAGAATTTGTG
1 AAACACGAAAATTGTTAGAAAACACAAAATTTTGAAAACATAAAAAA-TTTAAAGAATTTGTG
*
3355429 AAACACGAGAATTGTT-GAAAACACAAAAATTTTGAAAA-A-AACGAAAATTTAAAGA
1 AAACACGAAAATTGTTAGAAAACAC-AAAATTTTGAAAACATAA--AAAATTTAAAGA
3355484 CACGAAAATT
Statistics
Matches: 49, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
61 2 0.04
62 17 0.35
63 30 0.61
ACGTcount: A:0.55, C:0.08, G:0.11, T:0.25
Consensus pattern (62 bp):
AAACACGAAAATTGTTAGAAAACACAAAATTTTGAAAACATAAAAAATTTAAAGAATTTGTG
Found at i:3355609 original size:18 final size:17
Alignment explanation
Indices: 3355527--3355610 Score: 64
Period size: 18 Copynumber: 4.8 Consensus size: 17
3355517 TTTAAACATA
*
3355527 AAAAATTTT-AAAACAC
1 AAAAATTTTGAAAATAC
* *
3355543 AGAAATTTTGGAAATAC
1 AAAAATTTTGAAAATAC
*
3355560 AAAAATTTTAGAAACAT-G
1 AAAAATTTT-GAAA-ATAC
* *
3355578 GAAATTTTTAGAAAATAC
1 AAAAATTTT-GAAAATAC
3355596 AAAAAATTTTGAAAA
1 -AAAAATTTTGAAAA
3355611 ATGAATTTTT
Statistics
Matches: 52, Mismatches: 11, Indels: 8
0.73 0.15 0.11
Matches are distributed among these distances:
16 8 0.15
17 15 0.29
18 20 0.38
19 9 0.17
ACGTcount: A:0.56, C:0.06, G:0.10, T:0.29
Consensus pattern (17 bp):
AAAAATTTTGAAAATAC
Found at i:3355622 original size:36 final size:36
Alignment explanation
Indices: 3355554--3355621 Score: 95
Period size: 36 Copynumber: 1.9 Consensus size: 36
3355544 GAAATTTTGG
*
3355554 AAATACAAAAATTTTAGAAACATGGAAATTTTTAGA
1 AAATACAAAAATTTTAGAAAAATGGAAATTTTTAGA
*
3355590 AAATACAAAAAATTTT-GAAAAAT-GAATTTTTT
1 AAATAC-AAAAATTTTAGAAAAATGGAAATTTTT
3355622 TCTTGTGAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
35 8 0.28
36 12 0.41
37 9 0.31
ACGTcount: A:0.53, C:0.04, G:0.09, T:0.34
Consensus pattern (36 bp):
AAATACAAAAATTTTAGAAAAATGGAAATTTTTAGA
Found at i:3355982 original size:23 final size:22
Alignment explanation
Indices: 3355954--3356004 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 22
3355944 CGCTACTCGA
3355954 TTTTTCTCTTCTTCTTCTTT-CTT
1 TTTTTCT-TTCTTCTT-TTTCCTT
*
3355977 TTTTTCTTTTTTCTTTTTCCCTT
1 TTTTTCTTTCTTCTTTTT-CCTT
3356000 TTTTT
1 TTTTT
3356005 TTTTTGCCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
21 3 0.12
22 7 0.28
23 15 0.60
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (22 bp):
TTTTTCTTTCTTCTTTTTCCTT
Found at i:3355983 original size:15 final size:15
Alignment explanation
Indices: 3355965--3355994 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3355955 TTTTCTCTTC
3355965 TTCTTCTTTCTTTTT
1 TTCTTCTTTCTTTTT
*
3355980 TTCTTTTTTCTTTTT
1 TTCTTCTTTCTTTTT
3355995 CCCTTTTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (15 bp):
TTCTTCTTTCTTTTT
Found at i:3355995 original size:21 final size:23
Alignment explanation
Indices: 3355954--3356009 Score: 64
Period size: 22 Copynumber: 2.5 Consensus size: 23
3355944 CGCTACTCGA
* *
3355954 TTTTTCTCTTCTTCTTCTTT-CTT
1 TTTTTCT-TTTTTCTTCTTTCCCT
3355977 TTTTTCTTTTTTCTT-TTTCCCT
1 TTTTTCTTTTTTCTTCTTTCCCT
3355999 TTTTT-TTTTTT
1 TTTTTCTTTTTT
3356010 GCCAATTGGG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 9 0.30
22 14 0.47
23 7 0.23
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (23 bp):
TTTTTCTTTTTTCTTCTTTCCCT
Found at i:3356000 original size:15 final size:15
Alignment explanation
Indices: 3355971--3356008 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
3355961 CTTCTTCTTC
**
3355971 TTTCTTTTTTTCTTT
1 TTTCTTTTTCCCTTT
3355986 TTTCTTTTTCCCTTT
1 TTTCTTTTTCCCTTT
3356001 TTT-TTTTT
1 TTTCTTTTT
3356009 TGCCAATTGG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 5 0.24
15 16 0.76
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (15 bp):
TTTCTTTTTCCCTTT
Found at i:3356190 original size:15 final size:15
Alignment explanation
Indices: 3356170--3356207 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
3356160 GGTTTGCTTC
3356170 TTTTTTTGGGCTGTT
1 TTTTTTTGGGCTGTT
3356185 TTTTTTTGGGCTGTT
1 TTTTTTTGGGCTGTT
3356200 TTTTTTTG
1 TTTTTTTG
3356208 CTTGGGTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.00, C:0.05, G:0.24, T:0.71
Consensus pattern (15 bp):
TTTTTTTGGGCTGTT
Found at i:3356226 original size:14 final size:14
Alignment explanation
Indices: 3356170--3356227 Score: 53
Period size: 16 Copynumber: 3.7 Consensus size: 14
3356160 GGTTTGCTTC
3356170 TTTTTTTGGGCTGTTT
1 TTTTTTTGGG-T-TTT
*
3356186 TTTTTTGGGCTGTTTT
1 TTTTTTTGG--GTTTT
3356202 TTTTTGCTTGGGTTTT
1 TTTTT--TTGGGTTTT
3356218 TTTTTTTGGG
1 TTTTTTTGGG
3356228 GGCTACTTGA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 5 0.14
16 26 0.72
17 1 0.03
18 4 0.11
ACGTcount: A:0.00, C:0.05, G:0.26, T:0.69
Consensus pattern (14 bp):
TTTTTTTGGGTTTT
Found at i:3356325 original size:6 final size:6
Alignment explanation
Indices: 3356312--3356387 Score: 55
Period size: 6 Copynumber: 12.2 Consensus size: 6
3356302 TTTTATTTTA
* **
3356312 TTTT-T TTTTCT TTTTCCTT TTTTCTT TTTTCTT TTTTCT TCTTCT CCTTCT
1 TTTTCT TTTTCT TTTT-C-T TTTTC-T TTTTC-T TTTTCT TTTTCT TTTTCT
* * *
3356363 TCTTCT TCTTCT TCTTCT TTTTCT T
1 TTTTCT TTTTCT TTTTCT TTTTCT T
3356388 CTTCACGAAC
Statistics
Matches: 64, Mismatches: 4, Indels: 5
0.88 0.05 0.07
Matches are distributed among these distances:
5 4 0.06
6 39 0.61
7 16 0.25
8 5 0.08
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (6 bp):
TTTTCT
Found at i:3356325 original size:7 final size:7
Alignment explanation
Indices: 3356315--3356351 Score: 65
Period size: 7 Copynumber: 5.3 Consensus size: 7
3356305 TATTTTATTT
3356315 TTTTTTC
1 TTTTTTC
*
3356322 TTTTTCC
1 TTTTTTC
3356329 TTTTTTC
1 TTTTTTC
3356336 TTTTTTC
1 TTTTTTC
3356343 TTTTTTC
1 TTTTTTC
3356350 TT
1 TT
3356352 CTTCTCCTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (7 bp):
TTTTTTC
Found at i:3356355 original size:3 final size:3
Alignment explanation
Indices: 3356347--3356391 Score: 72
Period size: 3 Copynumber: 15.0 Consensus size: 3
3356337 TTTTTCTTTT
* *
3356347 TTC TTC TTC TCC TTC TTC TTC TTC TTC TTC TTC TTT TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
3356392 ACGAACCCTA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:3356507 original size:12 final size:12
Alignment explanation
Indices: 3356490--3356517 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
3356480 TCTTTCTTTC
3356490 TTTTTTTTCTCT
1 TTTTTTTTCTCT
3356502 TTTTTTTTCTCT
1 TTTTTTTTCTCT
3356514 TTTT
1 TTTT
3356518 CGCAAGGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (12 bp):
TTTTTTTTCTCT
Found at i:3356510 original size:21 final size:21
Alignment explanation
Indices: 3356477--3356517 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
3356467 TCCTCTTCTC
*
3356477 CTCTCTTTCTTTCTTTTTTTT
1 CTCTCTTTCTTTCTCTTTTTT
* *
3356498 CTCTTTTTTTTTCTCTTTTT
1 CTCTCTTTCTTTCTCTTTTT
3356518 CGCAAGGTTT
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:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (21 bp):
CTCTCTTTCTTTCTCTTTTTT
Found at i:3356761 original size:30 final size:29
Alignment explanation
Indices: 3356727--3356850 Score: 146
Period size: 29 Copynumber: 4.2 Consensus size: 29
3356717 GGCCGAAACA
*
3356727 TAATTTTGAGAAAGTTTAGAGGTCAAAATG
1 TAATTTTCAGAAAGTTTAG-GGTCAAAATG
* *
3356757 TAATTTTTAGAAAGTTTAGGGGTTAAAATG
1 TAATTTTCAGAAAGTTTA-GGGTCAAAATG
*
3356787 TAA-TTTCAAAAAGTTTATGGGTCAAAATG
1 TAATTTTCAGAAAGTTTA-GGGTCAAAATG
3356816 TAA-TTTCA-AAAGTTTAGGAGTCAAAATG
1 TAATTTTCAGAAAGTTTAGG-GTCAAAATG
*
3356844 CAATTTT
1 TAATTTT
3356851 TTTATTTTTT
Statistics
Matches: 84, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
27 2 0.02
28 19 0.23
29 33 0.39
30 29 0.35
31 1 0.01
ACGTcount: A:0.40, C:0.05, G:0.19, T:0.36
Consensus pattern (29 bp):
TAATTTTCAGAAAGTTTAGGGTCAAAATG
Found at i:3368213 original size:21 final size:23
Alignment explanation
Indices: 3368189--3368235 Score: 62
Period size: 21 Copynumber: 2.1 Consensus size: 23
3368179 ACCAAACAAT
3368189 AAATAAACATA-TAA-TCTAGAA
1 AAATAAACATACTAAGTCTAGAA
* *
3368210 AAATAAATATACTAAGTTTAGAA
1 AAATAAACATACTAAGTCTAGAA
3368233 AAA
1 AAA
3368236 ACCACATCTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 10 0.45
22 3 0.14
23 9 0.41
ACGTcount: A:0.62, C:0.06, G:0.06, T:0.26
Consensus pattern (23 bp):
AAATAAACATACTAAGTCTAGAA
Found at i:3368476 original size:2 final size:2
Alignment explanation
Indices: 3368469--3368499 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
3368459 AACCAGAACA
3368469 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3368500 GAAAAAACAG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3370269 original size:18 final size:17
Alignment explanation
Indices: 3370243--3370302 Score: 56
Period size: 18 Copynumber: 3.6 Consensus size: 17
3370233 GAAATAAATA
*
3370243 ATATACAATATATTTTTT
1 ATATTCAAT-TATTTTTT
3370261 ATATTCAATGTATTTTTT
1 ATATTCAAT-TATTTTTT
3370279 GA-ATT--ATTATTTTTT
1 -ATATTCAATTATTTTTT
3370294 ATATT-AATT
1 ATATTCAATT
3370303 GAAATAAATA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 1 0.03
15 11 0.30
16 5 0.14
18 19 0.51
19 1 0.03
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.60
Consensus pattern (17 bp):
ATATTCAATTATTTTTT
Found at i:3370299 original size:15 final size:16
Alignment explanation
Indices: 3370253--3370299 Score: 53
Period size: 15 Copynumber: 2.9 Consensus size: 16
3370243 ATATACAATA
3370253 TATTTTTTATATTCAATG
1 TATTTTTTATATT--ATG
3370271 TATTTTTTGA-ATTAT-
1 TATTTTTT-ATATTATG
3370286 TATTTTTTATATTA
1 TATTTTTTATATTA
3370300 ATTGAAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
14 1 0.04
15 12 0.44
16 2 0.07
18 11 0.41
19 1 0.04
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.66
Consensus pattern (16 bp):
TATTTTTTATATTATG
Found at i:3371454 original size:3 final size:3
Alignment explanation
Indices: 3371446--3371488 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
3371436 TGGCTATTGT
3371446 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
3371489 AACCAAAAGG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:3373255 original size:25 final size:24
Alignment explanation
Indices: 3373212--3373260 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
3373202 AAATAAATGT
*
3373212 TTATGTTTCTTTTATTGTTTATTTA
1 TTATGTTTATTTTATTGTTT-TTTA
3373237 TTAT-TTTATTTTATCTGTTTTTTA
1 TTATGTTTATTTTAT-TGTTTTTTA
3373261 ATTCTTAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 13 0.59
25 9 0.41
ACGTcount: A:0.16, C:0.04, G:0.06, T:0.73
Consensus pattern (24 bp):
TTATGTTTATTTTATTGTTTTTTA
Found at i:3373417 original size:2 final size:2
Alignment explanation
Indices: 3373410--3373450 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
3373400 TTTAATAGTG
3373410 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3373451 ACATTCACAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3373740 original size:31 final size:31
Alignment explanation
Indices: 3373705--3373772 Score: 111
Period size: 31 Copynumber: 2.2 Consensus size: 31
3373695 TTACAATTTG
3373705 GTCATTAAACTATTCAA-AAGTTTTCATTTAA
1 GTCATTAAACTATTCAATAA-TTTTCATTTAA
*
3373736 GTCATTAAACTATTCAATAATTTTTATTTAA
1 GTCATTAAACTATTCAATAATTTTCATTTAA
3373767 GTCATT
1 GTCATT
3373773 GGATTGTTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
31 33 0.94
32 2 0.06
ACGTcount: A:0.37, C:0.12, G:0.06, T:0.46
Consensus pattern (31 bp):
GTCATTAAACTATTCAATAATTTTCATTTAA
Found at i:3381344 original size:24 final size:24
Alignment explanation
Indices: 3381317--3381365 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
3381307 CCAAACAAAG
3381317 ATTGTGCCTCCTCCCAATCATTCA
1 ATTGTGCCTCCTCCCAATCATTCA
3381341 ATTGTGCCTCCTCCCAATCATTCA
1 ATTGTGCCTCCTCCCAATCATTCA
3381365 A
1 A
3381366 GTACGCTTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.22, C:0.37, G:0.08, T:0.33
Consensus pattern (24 bp):
ATTGTGCCTCCTCCCAATCATTCA
Found at i:3386780 original size:14 final size:14
Alignment explanation
Indices: 3386761--3386789 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
3386751 TAGATGTGGC
3386761 TTATTATGCGTATT
1 TTATTATGCGTATT
3386775 TTATTATGCGTATT
1 TTATTATGCGTATT
3386789 T
1 T
3386790 GGATAAGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.07, G:0.14, T:0.59
Consensus pattern (14 bp):
TTATTATGCGTATT
Found at i:3388830 original size:51 final size:51
Alignment explanation
Indices: 3388701--3388811 Score: 152
Period size: 51 Copynumber: 2.2 Consensus size: 51
3388691 TTAGCCTTTG
** * * *
3388701 ATGTGTAAATGTTGCAAACTGAATTTGTTAAACTAAAACTAAATTGACAGA
1 ATGTGTAAATGTTATAGACTAAATTTGTTAAACTAAAACTAAATTGAAAGA
*
3388752 ATGTGTAAATGTTATAGACTAAATTTGTTAAA-TCAAGACTAAATTGAAAGA
1 ATGTGTAAATGTTATAGACTAAATTTGTTAAACT-AAAACTAAATTGAAAGA
3388803 ATGTGTAAA
1 ATGTGTAAA
3388812 CTTTAAGGGT
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
50 1 0.02
51 52 0.98
ACGTcount: A:0.44, C:0.07, G:0.16, T:0.32
Consensus pattern (51 bp):
ATGTGTAAATGTTATAGACTAAATTTGTTAAACTAAAACTAAATTGAAAGA
Found at i:3404052 original size:13 final size:13
Alignment explanation
Indices: 3404034--3404059 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3404024 AATTGAGTTG
3404034 GTGTTATCAGTCA
1 GTGTTATCAGTCA
3404047 GTGTTATCAGTCA
1 GTGTTATCAGTCA
3404060 ACCATACACC
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:0.23, C:0.15, G:0.23, T:0.38
Consensus pattern (13 bp):
GTGTTATCAGTCA
Found at i:3414349 original size:208 final size:210
Alignment explanation
Indices: 3413983--3414401 Score: 653
Period size: 208 Copynumber: 2.0 Consensus size: 210
3413973 TTTGGTCTCT
* * * *
3413983 ACCTCTTCCTTCGTGCATGTGTGCAATGGATTTGAAGACAACCTCAAAGTTATGATGTTTCCATA
1 ACCTCTTCCTTCGTGCACGTGTGCAATGGATTCGAAGACAACATC-AAGTTATGATGTTCCCATA
*
3414048 TTTGATAAACAGTGGGACCATATAAACTTAACTCTAGGTCTCCAAATATTTGGATAGTGAGTTGC
65 TTTGATAAACAGTGGGACCATATAAACTTAACTCTAGGTCTCCAAATATTTGGATAGTGAGTTAC
* * *
3414113 AAGATAATAAACAAAGCAACAATTTAAAAGATTCGATAGAAAGGGAAGGTAATATTCTTCAAAGT
130 AAGATAATAAACAAAGCAACAATTTAAAAGATTCGATAAAAAGGAAAGGCAATATTCTTCAAAGT
*
3414178 AGGTTGAATATATTCA
195 AGGTTGAAGATATTCA
*
3414194 ACCTC-TCCTTCGTGCACGTGTGCAATGGATTCGAAGACAATATC-AGTTATGATGTTCCCATAT
1 ACCTCTTCCTTCGTGCACGTGTGCAATGGATTCGAAGACAACATCAAGTTATGATGTTCCCATAT
*
3414257 TTGATAAACAGTGGGACCATATAAACTTAACTCTAGGTCTCCAAGTATTTGGATAGTGAGTTACA
66 TTGATAAACAGTGGGACCATATAAACTTAACTCTAGGTCTCCAAATATTTGGATAGTGAGTTACA
* * * * * * *
3414322 AGATAATAACCAATGCGACAATTTAAAAGGTTTGATAAAAAGGAAAGGCAATATTTTTCGAAGTA
131 AGATAATAAACAAAGCAACAATTTAAAAGATTCGATAAAAAGGAAAGGCAATATTCTTCAAAGTA
3414387 GGTTGAAGATATTCA
196 GGTTGAAGATATTCA
3414402 CCATTGGAGA
Statistics
Matches: 190, Mismatches: 18, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
208 150 0.79
210 35 0.18
211 5 0.03
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.30
Consensus pattern (210 bp):
ACCTCTTCCTTCGTGCACGTGTGCAATGGATTCGAAGACAACATCAAGTTATGATGTTCCCATAT
TTGATAAACAGTGGGACCATATAAACTTAACTCTAGGTCTCCAAATATTTGGATAGTGAGTTACA
AGATAATAAACAAAGCAACAATTTAAAAGATTCGATAAAAAGGAAAGGCAATATTCTTCAAAGTA
GGTTGAAGATATTCA
Found at i:3432492 original size:16 final size:17
Alignment explanation
Indices: 3432471--3432509 Score: 57
Period size: 15 Copynumber: 2.5 Consensus size: 17
3432461 ACTTGAAAGA
3432471 CTTGAACCCAAAAC-AG
1 CTTGAACCCAAAACAAG
3432487 CTTGAA-CCAAAACAAG
1 CTTGAACCCAAAACAAG
3432503 -TTGAACC
1 CTTGAACC
3432510 TGGAATTGAC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 12 0.57
16 9 0.43
ACGTcount: A:0.44, C:0.28, G:0.13, T:0.15
Consensus pattern (17 bp):
CTTGAACCCAAAACAAG
Found at i:3434597 original size:123 final size:120
Alignment explanation
Indices: 3434404--3434709 Score: 418
Period size: 123 Copynumber: 2.5 Consensus size: 120
3434394 AGAGGCAAGC
* * * *
3434404 TACCAGGTGAT-AGTTTTGGTGGTGGTGAGTATGAAGGTGATGAAGATTTTGGTGGTTTTGCTGC
1 TACCTGGTGATGA-TTTTGGTGGTGGCGAGTATGAAGGTGACGAAGATTTTGGTGGTTTTGCTCC
*
3434468 TCCTGGTGGTGTTTTACTAATGTATGGTCCTGGTGCAGCAGCTGGCGGTGGTACTT
65 CCCTGGTGGTGTTTTACTAATGTATGGTCCTGGTGCAGCAGCTGGCGGTGGTACTT
*
3434524 TACCTGGTGGTGATTTTGGTGGTGGCGAGTATGAAGGTGACGACGAAGATTTTGGTGGTTTTGC-
1 TACCTGGTGATGATTTTGGTGGTGGCGAGTATGAAGGT---GACGAAGATTTTGGTGGTTTTGCT
* *
3434588 CCCCGCTGGTGGTGTTTTGCTACTGTATGGTCCTGGTGCAGCAGCTGGCGGTGGTACTT
63 CCCC-CTGGTGGTGTTTTACTAATGTATGGTCCTGGTGCAGCAGCTGGCGGTGGTACTT
* * * *
3434647 TACCTGGTGATGATTTTGGTGGTGGAGGAAAGTGTGGAGGTGATGAAGATTTTGGTGGTTTTG
1 TACCTGGTGATGATTTTGGTGGTGG-CG--AGTATGAAGGTGACGAAGATTTTGGTGGTTTTG
3434710 TTGGTGGTGA
Statistics
Matches: 165, Mismatches: 13, Indels: 13
0.86 0.07 0.07
Matches are distributed among these distances:
120 33 0.20
121 1 0.01
122 2 0.01
123 119 0.72
124 1 0.01
126 9 0.05
ACGTcount: A:0.15, C:0.12, G:0.38, T:0.35
Consensus pattern (120 bp):
TACCTGGTGATGATTTTGGTGGTGGCGAGTATGAAGGTGACGAAGATTTTGGTGGTTTTGCTCCC
CCTGGTGGTGTTTTACTAATGTATGGTCCTGGTGCAGCAGCTGGCGGTGGTACTT
Found at i:3436827 original size:11 final size:11
Alignment explanation
Indices: 3436813--3436851 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
3436803 CAAAACAGTG
3436813 GGAAAATAGTA
1 GGAAAATAGTA
*
3436824 GGAAAATAGCA
1 GGAAAATAGTA
* *
3436835 GCAAAATAGTG
1 GGAAAATAGTA
3436846 GGAAAA
1 GGAAAA
3436852 CAACAAATTT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.54, C:0.05, G:0.28, T:0.13
Consensus pattern (11 bp):
GGAAAATAGTA
Found at i:3439643 original size:30 final size:30
Alignment explanation
Indices: 3439587--3439643 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
3439577 CATTATGTCA
* *
3439587 TTTTTTTAGTTACATTGTTACCAAATGAGT
1 TTTTTTTAGTTACATTATTACAAAATGAGT
*
3439617 TTTTTTTA-TTACTATTATTTCAAAATG
1 TTTTTTTAGTTAC-ATTATTACAAAATG
3439644 TAAACCAACA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 4 0.17
30 19 0.83
ACGTcount: A:0.28, C:0.09, G:0.09, T:0.54
Consensus pattern (30 bp):
TTTTTTTAGTTACATTATTACAAAATGAGT
Found at i:3440071 original size:2 final size:2
Alignment explanation
Indices: 3440023--3440052 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3440013 ACCATTTTTA
3440023 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3440053 TCATCTCTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3440204 original size:8 final size:8
Alignment explanation
Indices: 3440182--3440211 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
3440172 TGTAGAAAAT
3440182 AATTTATA
1 AATTTATA
3440190 TAATTTATA
1 -AATTTATA
3440199 AATTTATA
1 AATTTATA
3440207 AATTT
1 AATTT
3440212 TTTATACAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 13 0.62
9 8 0.38
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (8 bp):
AATTTATA
Found at i:3440217 original size:19 final size:20
Alignment explanation
Indices: 3440193--3440240 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
3440183 ATTTATATAA
* *
3440193 TTTATAAATTTATAAATT-T
1 TTTATAAATATAAAAATTAT
3440212 TTTATACAATATAAAAATTAT
1 TTTATA-AATATAAAAATTAT
*
3440233 TTTTTAAA
1 TTTATAAA
3440241 AAATATTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 6 0.25
20 12 0.50
21 6 0.25
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (20 bp):
TTTATAAATATAAAAATTAT
Found at i:3440691 original size:13 final size:14
Alignment explanation
Indices: 3440659--3440691 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
3440649 TTGTTATAAC
3440659 TAAA-TTAATTTAA
1 TAAATTTAATTTAA
3440672 TAAATTTAATTT-A
1 TAAATTTAATTTAA
3440685 TAAATTT
1 TAAATTT
3440692 TGTAATGAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
TAAATTTAATTTAA
Found at i:3445060 original size:17 final size:18
Alignment explanation
Indices: 3445040--3445080 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
3445030 ATAAACATAA
3445040 ATCATTCATTTCAT-TAT-
1 ATCATT-ATTTCATGTATC
*
3445057 ATCAATATTTCATGTATC
1 ATCATTATTTCATGTATC
3445075 ATCATT
1 ATCATT
3445081 TTCATGAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
16 7 0.35
17 8 0.40
18 5 0.25
ACGTcount: A:0.32, C:0.17, G:0.02, T:0.49
Consensus pattern (18 bp):
ATCATTATTTCATGTATC
Found at i:3445574 original size:26 final size:25
Alignment explanation
Indices: 3445541--3445589 Score: 80
Period size: 26 Copynumber: 1.9 Consensus size: 25
3445531 TCAAGCGAGC
3445541 TATATTGGGAAGCTCATGAAGAGCCA
1 TATATTGGGAAGCTCAT-AAGAGCCA
*
3445567 TATATTGGGACGCTCATAAGAGC
1 TATATTGGGAAGCTCATAAGAGC
3445590 TGCGGTATGT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 6 0.27
26 16 0.73
ACGTcount: A:0.33, C:0.16, G:0.27, T:0.24
Consensus pattern (25 bp):
TATATTGGGAAGCTCATAAGAGCCA
Found at i:3446985 original size:36 final size:36
Alignment explanation
Indices: 3446941--3447010 Score: 131
Period size: 36 Copynumber: 1.9 Consensus size: 36
3446931 CCATGTCTGG
*
3446941 GACATGGCATTGGCACCGAGATGAGAGGTCCCATGT
1 GACATGGCATAGGCACCGAGATGAGAGGTCCCATGT
3446977 GACATGGCATAGGCACCGAGATGAGAGGTCCCAT
1 GACATGGCATAGGCACCGAGATGAGAGGTCCCAT
3447011 ATAAGACCAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.27, C:0.23, G:0.33, T:0.17
Consensus pattern (36 bp):
GACATGGCATAGGCACCGAGATGAGAGGTCCCATGT
Found at i:3447042 original size:50 final size:50
Alignment explanation
Indices: 3446977--3447142 Score: 233
Period size: 50 Copynumber: 3.3 Consensus size: 50
3446967 GGTCCCATGT
* *
3446977 GACATGGCATAGGCACCGAGATGAGAGGTCCCATATAAGACCATGTCTGG
1 GACATGGCATTGGCACCGAGATGAGAGGTCCCATGTAAGACCATGTCTGG
* **
3447027 GACATGGCGTTGGCACCGAGATGAGAGGTCCCCCGTAAGACCATGTCTGG
1 GACATGGCATTGGCACCGAGATGAGAGGTCCCATGTAAGACCATGTCTGG
* * **
3447077 GACATGGCATGGGCACCGACATGAGTACATCCCATGTAAGACCATGTCTGG
1 GACATGGCATTGGCACCGAGATGAG-AGGTCCCATGTAAGACCATGTCTGG
*
3447128 GACATGGCTTTGGCA
1 GACATGGCATTGGCA
3447143 TGTTATGATC
Statistics
Matches: 101, Mismatches: 14, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
50 67 0.66
51 34 0.34
ACGTcount: A:0.26, C:0.24, G:0.31, T:0.19
Consensus pattern (50 bp):
GACATGGCATTGGCACCGAGATGAGAGGTCCCATGTAAGACCATGTCTGG
Found at i:3450109 original size:14 final size:13
Alignment explanation
Indices: 3450089--3450120 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 13
3450079 CTTGTATATT
3450089 AAATAAAATAATA
1 AAATAAAATAATA
3450102 ATAATAAAATAATA
1 A-AATAAAATAATA
3450116 AAATA
1 AAATA
3450121 TCTCATTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (13 bp):
AAATAAAATAATA
Found at i:3450112 original size:11 final size:11
Alignment explanation
Indices: 3450090--3450147 Score: 55
Period size: 11 Copynumber: 5.1 Consensus size: 11
3450080 TTGTATATTA
3450090 AATAAAATAAT
1 AATAAAATAAT
3450101 AATAATAA-AAT
1 AATAA-AATAAT
*
3450112 AATAAAATATCT
1 AATAAAATA-AT
* *
3450124 CATTAAAATATT
1 -AATAAAATAAT
3450136 AATAAAATAAT
1 AATAAAATAAT
3450147 A
1 A
3450148 TTTATCTAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
10 2 0.05
11 24 0.63
12 4 0.11
13 8 0.21
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (11 bp):
AATAAAATAAT
Found at i:3453557 original size:25 final size:23
Alignment explanation
Indices: 3453528--3453588 Score: 61
Period size: 25 Copynumber: 2.5 Consensus size: 23
3453518 TATAAAATTG
3453528 TTATTTAATTATAC-TGAAAAAAAT
1 TTATTTAATT-TACAT-AAAAAAAT
*
3453552 TATATTTTAATTTTCATAAAAAAAT
1 T-TA-TTTAATTTACATAAAAAAAT
3453577 TTAATTTAATTT
1 TT-ATTTAATTT
3453589 CAATCCCTCC
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
24 10 0.31
25 14 0.44
26 8 0.25
ACGTcount: A:0.46, C:0.03, G:0.02, T:0.49
Consensus pattern (23 bp):
TTATTTAATTTACATAAAAAAAT
Found at i:3453560 original size:26 final size:24
Alignment explanation
Indices: 3453521--3453588 Score: 66
Period size: 26 Copynumber: 2.7 Consensus size: 24
3453511 TTAAAATTAT
*
3453521 AAAATTGTTATTTAATTATAC-TGAAA
1 AAAATT-TAATTTAATT-TACAT-AAA
* *
3453547 AAAATTATATTTTAATTTTCATAAA
1 AAAATT-TAATTTAATTTACATAAA
3453572 AAAATTTAATTTAATTT
1 AAAATTTAATTTAATTT
3453589 CAATCCCTCC
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
24 10 0.28
25 11 0.31
26 15 0.42
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (24 bp):
AAAATTTAATTTAATTTACATAAA
Found at i:3455203 original size:16 final size:14
Alignment explanation
Indices: 3455166--3455204 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 14
3455156 TTCTGCATTT
3455166 TTACAAAAATAATA
1 TTACAAAAATAATA
*
3455180 TTAAAAAAATAATTAA
1 TTACAAAAATAA-T-A
3455196 TTACAAAAA
1 TTACAAAAA
3455205 AAGAGTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 11 0.52
15 1 0.05
16 9 0.43
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (14 bp):
TTACAAAAATAATA
Found at i:3455214 original size:30 final size:31
Alignment explanation
Indices: 3455166--3455229 Score: 78
Period size: 30 Copynumber: 2.1 Consensus size: 31
3455156 TTCTGCATTT
*
3455166 TTACAAAAATAATATTAAAA-AAATAATTAA
1 TTACAAAAATAAGATTAAAACAAATAATTAA
* *
3455196 TTACAAAAA-AAGAGTTAAAACAAATTATTTA
1 TTACAAAAATAAGA-TTAAAACAAATAATTAA
3455227 TTA
1 TTA
3455230 AAATGCAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
29 3 0.10
30 15 0.52
31 11 0.38
ACGTcount: A:0.61, C:0.05, G:0.03, T:0.31
Consensus pattern (31 bp):
TTACAAAAATAAGATTAAAACAAATAATTAA
Found at i:3458199 original size:27 final size:27
Alignment explanation
Indices: 3458169--3458224 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
3458159 TATATTGTAT
3458169 TATTTTAATTT-TTAATAAATTTTTATA
1 TATTTTAATTTATTAA-AAATTTTTATA
* * *
3458196 TATTTTTATTTATTGAAAGTTTTTATA
1 TATTTTAATTTATTAAAAATTTTTATA
3458223 TA
1 TA
3458225 GTCATCTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 22 0.88
28 3 0.12
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (27 bp):
TATTTTAATTTATTAAAAATTTTTATA
Found at i:3458206 original size:33 final size:33
Alignment explanation
Indices: 3458134--3458196 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 33
3458124 CTGCTCATGT
3458134 TATT-TTTTAATTTTTTAAAAATATTTATATTG
1 TATTATTTTAATTTTTTAAAAATATTTATATTG
*
3458166 TATTATTTTAA-TTTTTAATAAATTTTTATAT
1 TATTATTTTAATTTTTTAA-AAATATTTATAT
3458197 ATTTTTATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 11 0.39
33 17 0.61
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (33 bp):
TATTATTTTAATTTTTTAAAAATATTTATATTG
Found at i:3462466 original size:7 final size:8
Alignment explanation
Indices: 3462451--3462501 Score: 57
Period size: 8 Copynumber: 5.9 Consensus size: 8
3462441 ATATAATAAA
3462451 TATTTTTT
1 TATTTTTT
3462459 TATTTTTT
1 TATTTTTT
*
3462467 TATTTTTAAAA
1 TATTTTT---T
3462478 TACTTTTTT
1 TA-TTTTTT
3462487 TATTTTTT
1 TATTTTTT
3462495 TATTTTT
1 TATTTTT
3462502 AAAATAAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
8 28 0.76
9 2 0.05
11 2 0.05
12 5 0.14
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (8 bp):
TATTTTTT
Found at i:3462484 original size:27 final size:28
Alignment explanation
Indices: 3462448--3462507 Score: 113
Period size: 28 Copynumber: 2.2 Consensus size: 28
3462438 CGAATATAAT
3462448 AAATA-TTTTTTTATTTTTTTATTTTTA
1 AAATACTTTTTTTATTTTTTTATTTTTA
3462475 AAATACTTTTTTTATTTTTTTATTTTTA
1 AAATACTTTTTTTATTTTTTTATTTTTA
3462503 AAATA
1 AAATA
3462508 AATTTTTTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 5 0.16
28 27 0.84
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (28 bp):
AAATACTTTTTTTATTTTTTTATTTTTA
Found at i:3462513 original size:29 final size:28
Alignment explanation
Indices: 3462448--3462515 Score: 111
Period size: 28 Copynumber: 2.5 Consensus size: 28
3462438 CGAATATAAT
3462448 AAAT-ATTTTTTTATTTTTTTATTTTTA
1 AAATAATTTTTTTATTTTTTTATTTTTA
*
3462475 AAATACTTTTTTTATTTTTTTATTTTTA
1 AAATAATTTTTTTATTTTTTTATTTTTA
*
3462503 AAATAAATTTTTT
1 AAATAATTTTTTT
3462516 GTGTTTATTA
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
27 4 0.11
28 33 0.89
ACGTcount: A:0.29, C:0.01, G:0.00, T:0.69
Consensus pattern (28 bp):
AAATAATTTTTTTATTTTTTTATTTTTA
Found at i:3462514 original size:22 final size:22
Alignment explanation
Indices: 3462488--3462532 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
3462478 TACTTTTTTT
3462488 ATTTTTT-TATTT-TTAAAATAA
1 ATTTTTTGTATTTATTAAAA-AA
*
3462509 ATTTTTTGTGTTTATTAAAAAA
1 ATTTTTTGTATTTATTAAAAAA
3462531 AT
1 AT
3462533 GGGACGGGCC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 7 0.33
22 8 0.38
23 6 0.29
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (22 bp):
ATTTTTTGTATTTATTAAAAAA
Found at i:3481707 original size:24 final size:24
Alignment explanation
Indices: 3481675--3481724 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
3481665 AGGGATCCAC
3481675 TTATTATGATATAAACTAATATGG
1 TTATTATGATATAAACTAATATGG
3481699 TTATTATGATATAAACTAATATGG
1 TTATTATGATATAAACTAATATGG
3481723 TT
1 TT
3481725 TTACTTTTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.40, C:0.04, G:0.12, T:0.44
Consensus pattern (24 bp):
TTATTATGATATAAACTAATATGG
Found at i:3486532 original size:13 final size:13
Alignment explanation
Indices: 3486514--3486538 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3486504 AAATTACTAA
3486514 AAAATAAATACAT
1 AAAATAAATACAT
3486527 AAAATAAATACA
1 AAAATAAATACA
3486539 ATAATAGATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.08, G:0.00, T:0.20
Consensus pattern (13 bp):
AAAATAAATACAT
Found at i:3486995 original size:17 final size:17
Alignment explanation
Indices: 3486973--3487011 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
3486963 AATTTAGATG
*
3486973 TAAAATATACTA-AAATA
1 TAAAATAAACTAGAAA-A
3486990 TAAAATAAACTAGAAAA
1 TAAAATAAACTAGAAAA
3487007 TAAAA
1 TAAAA
3487012 ATGGAGTCAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 17 0.85
18 3 0.15
ACGTcount: A:0.69, C:0.05, G:0.03, T:0.23
Consensus pattern (17 bp):
TAAAATAAACTAGAAAA
Found at i:3487116 original size:19 final size:20
Alignment explanation
Indices: 3487074--3487117 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
3487064 TATAACTAAG
*
3487074 ATATAAAAAAGATATTAAAT
1 ATATAAAAAAGATAATAAAT
*
3487094 ATATAAATAA-ATAATAAAT
1 ATATAAAAAAGATAATAAAT
3487113 ATATA
1 ATATA
3487118 TATATAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 13 0.59
20 9 0.41
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (20 bp):
ATATAAAAAAGATAATAAAT
Found at i:3487220 original size:14 final size:14
Alignment explanation
Indices: 3487201--3487242 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
3487191 TCTATCATTA
3487201 TTATATTAAATATG
1 TTATATTAAATATG
*
3487215 TTATATTTATATAT-
1 TTATA-TTAAATATG
*
3487229 TTATATTAAGTATG
1 TTATATTAAATATG
3487243 GCATTAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
13 6 0.26
14 10 0.43
15 7 0.30
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (14 bp):
TTATATTAAATATG
Found at i:3492167 original size:26 final size:25
Alignment explanation
Indices: 3492138--3492308 Score: 124
Period size: 26 Copynumber: 6.8 Consensus size: 25
3492128 GAGTCATGAT
3492138 CGGTAAGCTCATTCCGAGCTGAAGAA
1 CGGTAAGCTCATTCCGAGCTGAA-AA
3492164 CGGTAAGCTCTATT--GAGCTG-AAA
1 CGGTAAGCTC-ATTCCGAGCTGAAAA
* ** *
3492187 CGGTAAACTCA-TAAGAGCTGATATAT
1 CGGTAAGCTCATTCCGAGCTGA-A-AA
* *
3492213 TGGTAAGCTCATTCCAAGCTGAAGAA
1 CGGTAAGCTCATTCCGAGCTGAA-AA
3492239 CGGTAAGCTCGA-T-CGAGCTG-AAA
1 CGGTAAGCTC-ATTCCGAGCTGAAAA
*** *
3492262 CGGTAAGCTCA-TAAAAGCTGATATAT
1 CGGTAAGCTCATTCCGAGCTGA-A-AA
3492288 CGGTAAGCTCATTCCGAGCTG
1 CGGTAAGCTCATTCCGAGCTG
3492309 TGGTGAGTTC
Statistics
Matches: 115, Mismatches: 17, Indels: 25
0.73 0.11 0.16
Matches are distributed among these distances:
21 1 0.01
22 3 0.03
23 34 0.30
24 2 0.02
25 14 0.12
26 44 0.38
27 17 0.15
ACGTcount: A:0.32, C:0.20, G:0.25, T:0.23
Consensus pattern (25 bp):
CGGTAAGCTCATTCCGAGCTGAAAA
Found at i:3492262 original size:75 final size:75
Alignment explanation
Indices: 3492136--3492308 Score: 292
Period size: 75 Copynumber: 2.3 Consensus size: 75
3492126 TCGAGTCATG
* *
3492136 ATCGGTAAGCTCATTCCGAGCTGAAGAACGGTAAGCTCTATTGAGCTGAAACGGTAAACTCATAA
1 ATCGGTAAGCTCATTCCGAGCTGAAGAACGGTAAGCTCGATCGAGCTGAAACGGTAAACTCATAA
*
3492201 GAGCTGATAT
66 AAGCTGATAT
* * *
3492211 ATTGGTAAGCTCATTCCAAGCTGAAGAACGGTAAGCTCGATCGAGCTGAAACGGTAAGCTCATAA
1 ATCGGTAAGCTCATTCCGAGCTGAAGAACGGTAAGCTCGATCGAGCTGAAACGGTAAACTCATAA
3492276 AAGCTGATAT
66 AAGCTGATAT
3492286 ATCGGTAAGCTCATTCCGAGCTG
1 ATCGGTAAGCTCATTCCGAGCTG
3492309 TGGTGAGTTC
Statistics
Matches: 90, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
75 90 1.00
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.24
Consensus pattern (75 bp):
ATCGGTAAGCTCATTCCGAGCTGAAGAACGGTAAGCTCGATCGAGCTGAAACGGTAAACTCATAA
AAGCTGATAT
Found at i:3495258 original size:23 final size:22
Alignment explanation
Indices: 3495228--3495270 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
3495218 TTTTTGAGAT
3495228 ATTAAAAATATATCATTTAATCA
1 ATTAAAAATA-ATCATTTAATCA
*
3495251 ATTAAAAATAATGATTTAAT
1 ATTAAAAATAATCATTTAAT
3495271 AATACCAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (22 bp):
ATTAAAAATAATCATTTAATCA
Found at i:3502448 original size:243 final size:243
Alignment explanation
Indices: 3502020--3502460 Score: 740
Period size: 243 Copynumber: 1.8 Consensus size: 243
3502010 GCTTCACCGG
* *
3502020 ACATGAACGAAATAATGGAAGTTCGTCAAACATATCTATACCAGCTGACTCGAGGGGGAATTGTT
1 ACATGAACGAAATAATGAAAGTTCATCAAACATATCTATACCAGCTGACTCGAGGGGGAATTGTT
*
3502085 AGAGCTTAGTCAGCTTCTAAAACAACCCTACCCAGTACTAGATCAGACAGGAAGTCTATTGCTTA
66 AGAGCTTAGTCAGCTTCTAAAACAACCCTACCCAGTACTAGATCAGACAGAAAGTCTATTGCTTA
*
3502150 AACTAATGTTATTATTGTCAAGTATTGCTCTACAAACATCAAGGCAATTAGACAATGCTGCCCAA
131 AACTAATGTTATTAATGTCAAGTATTGCTCTACAAACATCAAGGCAATTAGACAATGCTGCCCAA
3502215 ATAAATACACAGATATTGCAAATCTGTCTATTAGAAGGGATTCACAAT
196 ATAAATACACAGATATTGCAAATCTGTCTATTAGAAGGGATTCACAAT
* *
3502263 ACATGAACTAAATAATGAAAGTTCATCAAACATATCTATACCAGCTGACTCGAGGGGTAATTGTT
1 ACATGAACGAAATAATGAAAGTTCATCAAACATATCTATACCAGCTGACTCGAGGGGGAATTGTT
* * * * * * *
3502328 AGAGCTTAGGT-GGTTTGTAAAACAACCCTACCCTGTAGTAGATCAGGCAGAAAGTCTGTTGCTT
66 AGAGCTTA-GTCAGCTTCTAAAACAACCCTACCCAGTACTAGATCAGACAGAAAGTCTATTGCTT
*
3502392 AAACTAATGTTATTAATGTCAAGTATTGCTCTACAAATATCAAGGCAATTAGACAATGCTGCCCA
130 AAACTAATGTTATTAATGTCAAGTATTGCTCTACAAACATCAAGGCAATTAGACAATGCTGCCCA
3502457 AATA
195 AATA
3502461 TATATATATT
Statistics
Matches: 183, Mismatches: 14, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
243 181 0.99
244 2 0.01
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.27
Consensus pattern (243 bp):
ACATGAACGAAATAATGAAAGTTCATCAAACATATCTATACCAGCTGACTCGAGGGGGAATTGTT
AGAGCTTAGTCAGCTTCTAAAACAACCCTACCCAGTACTAGATCAGACAGAAAGTCTATTGCTTA
AACTAATGTTATTAATGTCAAGTATTGCTCTACAAACATCAAGGCAATTAGACAATGCTGCCCAA
ATAAATACACAGATATTGCAAATCTGTCTATTAGAAGGGATTCACAAT
Found at i:3521739 original size:19 final size:20
Alignment explanation
Indices: 3521717--3521768 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 20
3521707 AAATATATAC
3521717 ATTTTGGAATTTTAT-AAA-T
1 ATTTT-GAATTTTATAAAATT
3521736 ATTTT-AATTTT-TAAAATT
1 ATTTTGAATTTTATAAAATT
3521754 ATTTTTGAATTTTAT
1 A-TTTTGAATTTTAT
3521769 TTTTGTAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
16 1 0.04
17 9 0.32
18 2 0.07
19 9 0.32
20 6 0.21
21 1 0.04
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.60
Consensus pattern (20 bp):
ATTTTGAATTTTATAAAATT
Found at i:3521768 original size:13 final size:14
Alignment explanation
Indices: 3521752--3521780 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
3521742 ATTTTTAAAA
3521752 TTATTTTTG-AATT
1 TTATTTTTGTAATT
3521765 TTATTTTTGTAATT
1 TTATTTTTGTAATT
3521779 TT
1 TT
3521781 TGTTGAGAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.21, C:0.00, G:0.07, T:0.72
Consensus pattern (14 bp):
TTATTTTTGTAATT
Found at i:3521778 original size:25 final size:26
Alignment explanation
Indices: 3521736--3521786 Score: 61
Period size: 25 Copynumber: 2.0 Consensus size: 26
3521726 TTTTATAAAT
3521736 ATTTTAATTTTTAAAATTATTT-TTGA
1 ATTTTAATTTTTAAAATT-TTTGTTGA
**
3521762 ATTTT-ATTTTTGTAATTTTTGTTGA
1 ATTTTAATTTTTAAAATTTTTGTTGA
3521787 GAGAGTGACC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
24 3 0.14
25 14 0.64
26 5 0.23
ACGTcount: A:0.27, C:0.00, G:0.08, T:0.65
Consensus pattern (26 bp):
ATTTTAATTTTTAAAATTTTTGTTGA
Found at i:3521870 original size:9 final size:9
Alignment explanation
Indices: 3521851--3521890 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
3521841 CACAAATATG
*
3521851 TTATTCAAA
1 TTATTCGAA
*
3521860 TTATTTGAA
1 TTATTCGAA
*
3521869 TTATTCGAG
1 TTATTCGAA
3521878 TTATTCGAA
1 TTATTCGAA
3521887 TTAT
1 TTAT
3521891 AAAATTCAAC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.33, C:0.07, G:0.10, T:0.50
Consensus pattern (9 bp):
TTATTCGAA
Found at i:3528288 original size:363 final size:361
Alignment explanation
Indices: 3527630--3529055 Score: 1726
Period size: 363 Copynumber: 4.0 Consensus size: 361
3527620 CTAAATCTGT
* * * * * * *
3527630 AAATGTTATTCCGAAATCTTACATTACCTTTAACAGTGTGAGATTATTGAACTAGATTTTTATAA
1 AAATGTTATTCAGAAATCTTACATTACCTTTGACAATGTGAGATTATTGAACCATATCTTTCTAA
* * ** * *
3527695 ACCTAACAAATTTGAACGGCAAGAAAACATGGACATAG---------TTCTTTCTTTTCCATGTT
66 ACCTAACAAATTTGAATGGCAAGAGAACATCAACAGAGTTCTTTCTTTTCTTTCTTTTCCATGTG
* * * *
3527751 TGCCATTCCTTAAAACAACAAGCACTTGTCTAGGGCATACAAACTAAATAGACTCACACCACCGT
131 TGCCATTCCTTAAAACAACAAGCACTTGCCTAGGGCATATAGACCAAATAGACTCACACCACC-T
* *
3527816 ATTTTCATTAAAAAGAAAACAACAAATCTCTCAAAGTTACTAGATCTTAAATTTAGGGTATGATT
195 ATTTCCATTAAAAAGAAAACGACAAATCTCTCAAAGTTACTAGATCTTAAATTTAGGGTATGATT
** * *
3527881 TGGTTAAGGGAAAATAAAATTAGATCTGGTAACAGAAGTATCGAAATGTAAAATTACTTATTACA
260 TGGTTAAGGGAAAATAAAATTATCTCTGATAACAGAATTATCGAAATGTAAAATTACTTATTACA
* * *
3527946 TCATGGGCTCAAAGTAATCTTTGAAATCTAAATGTAA
325 TTATGGGCTCAAAATAATCTTTGAAATCTAAACGTAA
* *
3527983 AAATATTATTAAGAAATCTTACATTACCTTTGACAATGT-ATGATTATTGAACCATATCTTTCTA
1 AAATGTTATTCAGAAATCTTACATTACCTTTGACAATGTGA-GATTATTGAACCATATCTTTCTA
* *
3528047 AACCTAACAAATTTGAATGGCAAGAGAACATCACCGGAGTTCTTTCTTTTCTTTTCTTTTCCATG
65 AACCTAACAAATTTGAATGGCAAGAGAACATCAACAGAGTTCTTTCTTTTC-TTTCTTTTCCATG
* * **
3528112 TATGCCATTCCTTAAAACAACAAGTACTTGCCTAGGGTGTATAGACCAAATAGACTCACACCATC
129 TGTGCCATTCCTTAAAACAACAAGCACTTGCCTAGGGCATATAGACCAAATAGACTCACACCA-C
* * * * * * *
3528177 CTATTTCCATTAAGAAGAAAATGACAAATCCCTTAAAGTTACTAAATATTAAATTTAGGGTGTGA
193 CTATTTCCATTAAAAAGAAAACGACAAATCTCTCAAAGTTACTAGATCTTAAATTTAGGGTATGA
* * * *
3528242 TTTGGTTAAGGGAAAATAAGATTATCTCTGATAACATAATTATCGAAATATGAAATTACTTATTA
258 TTTGGTTAAGGGAAAATAAAATTATCTCTGATAACAGAATTATCGAAATGTAAAATTACTTATTA
* * *
3528307 CATTATGGGCTCAAAATAATATTTGAAATCCAAACATAA
323 CATTATGGGCTCAAAATAATCTTTGAAATCTAAACGTAA
* * * *
3528346 AAATGTTATTCCGAAATCTTACGTTACCTTTGACAATATGAGATTATTGAACCATATCTTTTTAA
1 AAATGTTATTCAGAAATCTTACATTACCTTTGACAATGTGAGATTATTGAACCATATCTTTCTAA
* * * *
3528411 ACCTAACAAATTTGAATGGCAAGAGAACATTAAAAGAGTTATTTC--TTCTTT-TTTT-AATGTG
66 ACCTAACAAATTTGAATGGCAAGAGAACATCAACAGAGTTCTTTCTTTTCTTTCTTTTCCATGTG
* * *
3528472 TGTCAGTCCTTAAAACAATAAGCACTTGCCTAGGGCATATAGACCAAATAGACTCACACCACTCT
131 TGCCATTCCTTAAAACAACAAGCACTTGCCTAGGGCATATAGACCAAATAGACTCACACCAC-CT
* * * * *
3528537 ATTTCTATTAAAAAGAAAACGTCAAATCTCTTAAAGTTATTAGATCTTAAATTTAGGGTGTGATT
195 ATTTCCATTAAAAAGAAAACGACAAATCTCTCAAAGTTACTAGATCTTAAATTTAGGGTATGATT
* * *
3528602 TGGTTAAGGTAAAATAAAATTATCTCTGATAACACAATTATTGAAATGTAAAATTACTTATTACA
260 TGGTTAAGGGAAAATAAAATTATCTCTGATAACAGAATTATCGAAATGTAAAATTACTTATTACA
* * *
3528667 TTATAGGCTCAAAGTAATCTTTAAAATCTAAACGTAA
325 TTATGGGCTCAAAATAATCTTTGAAATCTAAACGTAA
* * * * *
3528704 AAATGTTATTCTGAAATCTTACACTACCTTTGACAATGCGAGATTATTAAAACATATCTTTCTAA
1 AAATGTTATTCAGAAATCTTACATTACCTTTGACAATGTGAGATTATTGAACCATATCTTTCTAA
* * *
3528769 ACTTTACAAATTTGAATGGCAAGAGAACATCAACAAAGTTCTTTCTTTTCTTTTCTTTTCTTTTC
66 ACCTAACAAATTTGAATGGCAAGAGAACATCAACAGAG----TTC-TTTCTTTTC-TTTCTTTTC
* *
3528834 CATGTGTGTCATTCCTTAAAACAACAAGCACTTGTCTAGGGC-T-TAGACCAAATAGACTCATCA
125 CATGTGTGCCATTCCTTAAAACAACAAGCACTTGCCTAGGGCATATAGACCAAATAGACTCA-CA
* * *** * *
3528897 -C-CCAATTTTCATT--AAA-AATTTGACAAATCTCTCAAAGTTATTTGATCTTAAATTTAGAGG
189 CCACCTATTTCCATTAAAAAGAAAACGACAAATCTCTCAAAGTTACTAGATCTTAAATTTAG-GG
* * * * *
3528957 -ATAATTTGGTTAAGGGAAAAATAAAATGATCTGTGATTACAGAATTATCAAAATGTAAAATTAC
253 TATGATTTGGTTAAGGG-AAAATAAAATTATCTCTGATAACAGAATTATCGAAATGTAAAATTAC
* *
3529021 TTATTATATTATGGGCTCAAAATAATTTTTGAAAT
317 TTATTACATTATGGGCTCAAAATAATCTTTGAAAT
3529056 TCTTATATGT
Statistics
Matches: 919, Mismatches: 127, Indels: 45
0.84 0.12 0.04
Matches are distributed among these distances:
352 1 0.00
353 85 0.09
357 1 0.00
358 298 0.32
359 4 0.00
360 3 0.00
361 51 0.06
362 81 0.09
363 314 0.34
364 11 0.01
365 4 0.00
366 21 0.02
367 7 0.01
368 38 0.04
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.34
Consensus pattern (361 bp):
AAATGTTATTCAGAAATCTTACATTACCTTTGACAATGTGAGATTATTGAACCATATCTTTCTAA
ACCTAACAAATTTGAATGGCAAGAGAACATCAACAGAGTTCTTTCTTTTCTTTCTTTTCCATGTG
TGCCATTCCTTAAAACAACAAGCACTTGCCTAGGGCATATAGACCAAATAGACTCACACCACCTA
TTTCCATTAAAAAGAAAACGACAAATCTCTCAAAGTTACTAGATCTTAAATTTAGGGTATGATTT
GGTTAAGGGAAAATAAAATTATCTCTGATAACAGAATTATCGAAATGTAAAATTACTTATTACAT
TATGGGCTCAAAATAATCTTTGAAATCTAAACGTAA
Found at i:3530547 original size:14 final size:15
Alignment explanation
Indices: 3530525--3530564 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
3530515 CAATCAAACA
3530525 CCAGAAAA-TATTTT
1 CCAGAAAATTATTTT
*
3530539 CCAGTAAATTATTTT
1 CCAGAAAATTATTTT
*
3530554 ACAGAAAATTA
1 CCAGAAAATTA
3530565 AAACATTTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
14 7 0.32
15 15 0.68
ACGTcount: A:0.45, C:0.12, G:0.07, T:0.35
Consensus pattern (15 bp):
CCAGAAAATTATTTT
Found at i:3530595 original size:34 final size:35
Alignment explanation
Indices: 3530529--3530596 Score: 102
Period size: 34 Copynumber: 2.0 Consensus size: 35
3530519 CAAACACCAG
* *
3530529 AAAATATTTTCCAGTAAATTATTTTACAGAAAATT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAATT
*
3530564 AAAACATTTTCCAG-AAATCATTTTACGGAAAAT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAT
3530597 ATTTTACTGG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.12, G:0.07, T:0.35
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAATT
Found at i:3531740 original size:6 final size:6
Alignment explanation
Indices: 3531724--3531775 Score: 52
Period size: 6 Copynumber: 8.0 Consensus size: 6
3531714 TCTCTTCATT
3531724 TTTTCTC TTTTTC -TTTTC TTTTTC TTTTTCC TTTTCATC TTTTTC TTCTTTC
1 TTTT-TC TTTTTC TTTTTC TTTTTC TTTTT-C TTTT--TC TTTTTC TT-TTTC
3531776 ACATTTTTTG
Statistics
Matches: 40, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
5 5 0.12
6 16 0.40
7 13 0.32
8 5 0.12
9 1 0.03
ACGTcount: A:0.02, C:0.23, G:0.00, T:0.75
Consensus pattern (6 bp):
TTTTTC
Found at i:3531740 original size:13 final size:12
Alignment explanation
Indices: 3531724--3531775 Score: 52
Period size: 15 Copynumber: 4.0 Consensus size: 12
3531714 TCTCTTCATT
3531724 TTTTCTCTTTTTC
1 TTTT-TCTTTTTC
3531737 -TTTTCTTTTTC
1 TTTTTCTTTTTC
3531748 TTTTTCCTTTTCATC
1 TTTTT-CTTTT--TC
3531763 TTTTTCTTCTTTC
1 TTTTTCTT-TTTC
3531776 ACATTTTTTG
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
11 8 0.24
12 7 0.21
13 7 0.21
14 3 0.09
15 9 0.26
ACGTcount: A:0.02, C:0.23, G:0.00, T:0.75
Consensus pattern (12 bp):
TTTTTCTTTTTC
Found at i:3537842 original size:21 final size:22
Alignment explanation
Indices: 3537816--3537864 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
3537806 GATATATGTG
3537816 ATATTTAATATAA-CA-TTTTAA
1 ATATTTAAT-TAATCATTTTTAA
*
3537837 ATATTTTATTAATCATTTTTAA
1 ATATTTAATTAATCATTTTTAA
3537859 A-ATTTA
1 ATATTTA
3537865 TAGTTATTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 3 0.12
21 14 0.58
22 7 0.29
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (22 bp):
ATATTTAATTAATCATTTTTAA
Found at i:3556460 original size:20 final size:20
Alignment explanation
Indices: 3556418--3556460 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
3556408 ATTTACCCAA
* *
3556418 ATTATTAGTATTATTATTAT
1 ATTAGTAGTATTATAATTAT
3556438 ATTAGTAGTATTTATAATT-T
1 ATTAGTAGTA-TTATAATTAT
3556458 ATT
1 ATT
3556461 TAAATTATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.58
Consensus pattern (20 bp):
ATTAGTAGTATTATAATTAT
Found at i:3567911 original size:31 final size:31
Alignment explanation
Indices: 3567841--3567922 Score: 114
Period size: 31 Copynumber: 2.7 Consensus size: 31
3567831 TGTTGATGTA
3567841 GAGGACTTAATTGATTTTTT-ATTAATTTAC
1 GAGGACTTAATTGATTTTTTAATTAATTTAC
* *
3567871 GAGGACTTAATTTATTTTTTAATTATTTTA-
1 GAGGACTTAATTGATTTTTTAATTAATTTAC
*
3567901 GAAGGGCTTAATTGATTTTTTA
1 G-AGGACTTAATTGATTTTTTA
3567923 CGTATTATAT
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
30 20 0.43
31 26 0.57
ACGTcount: A:0.29, C:0.05, G:0.15, T:0.51
Consensus pattern (31 bp):
GAGGACTTAATTGATTTTTTAATTAATTTAC
Found at i:3568442 original size:8 final size:9
Alignment explanation
Indices: 3568400--3568483 Score: 53
Period size: 10 Copynumber: 8.9 Consensus size: 9
3568390 TAACATATTA
3568400 ATAATATTTT
1 ATAAT-TTTT
**
3568410 ATAAAATTT
1 ATAATTTTT
*
3568419 AGTAGTTTTT
1 A-TAATTTTT
3568429 ATAATTTTT
1 ATAATTTTT
3568438 A-AATTTTT
1 ATAATTTTT
* *
3568446 ATGATATTTG
1 ATAAT-TTTT
*
3568456 ATAATTTTG
1 ATAATTTTT
*
3568465 GTAGATTTTCT
1 ATA-ATTTT-T
3568476 ATAATTTT
1 ATAATTTT
3568484 CAAAAGTTTT
Statistics
Matches: 57, Mismatches: 12, Indels: 10
0.72 0.15 0.13
Matches are distributed among these distances:
8 8 0.14
9 20 0.35
10 27 0.47
11 2 0.04
ACGTcount: A:0.33, C:0.01, G:0.08, T:0.57
Consensus pattern (9 bp):
ATAATTTTT
Found at i:3571448 original size:36 final size:34
Alignment explanation
Indices: 3571351--3571449 Score: 84
Period size: 31 Copynumber: 2.9 Consensus size: 34
3571341 TAAATTTTAA
*
3571351 AAAAATAAACATATTATCAA-ATAAATTTAAA-TATT
1 AAAAATAAAAATA-TAT-AATA-AAATTTAAATTATT
*
3571386 AAAAATTAAAAA-ATA-AATAAAA--TAAATTCTT
1 AAAAA-TAAAAATATATAATAAAATTTAAATTATT
3571417 AAAAATAAAAATATATTAACTAAAATTTAAATT
1 AAAAATAAAAATATA-TAA-TAAAATTTAAATT
3571450 TTGAGGAAAC
Statistics
Matches: 53, Mismatches: 2, Indels: 17
0.74 0.03 0.24
Matches are distributed among these distances:
30 10 0.19
31 11 0.21
32 5 0.09
33 3 0.06
34 7 0.13
35 6 0.11
36 11 0.21
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (34 bp):
AAAAATAAAAATATATAATAAAATTTAAATTATT
Found at i:3586146 original size:17 final size:16
Alignment explanation
Indices: 3586123--3586163 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
3586113 ATAGTAAAAA
3586123 TATAATTTTAT-TATT
1 TATAATTTTATATATT
3586138 TCAATAA-TTTATATATT
1 T--ATAATTTTATATATT
3586155 TATAATTTT
1 TATAATTTT
3586164 TAAAAGGTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 7
0.76 0.00 0.24
Matches are distributed among these distances:
15 5 0.23
16 8 0.36
17 9 0.41
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (16 bp):
TATAATTTTATATATT
Found at i:3591598 original size:22 final size:22
Alignment explanation
Indices: 3591573--3591619 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
3591563 ATTAATTAAT
*
3591573 TTATTACTTATTA-TTATGATTG
1 TTATTA-TTACTATTTATGATTG
*
3591595 TTATTATTACTATTTATTATTG
1 TTATTATTACTATTTATGATTG
3591617 TTA
1 TTA
3591620 CTGATATTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 5 0.23
22 17 0.77
ACGTcount: A:0.28, C:0.04, G:0.06, T:0.62
Consensus pattern (22 bp):
TTATTATTACTATTTATGATTG
Found at i:3592131 original size:2 final size:2
Alignment explanation
Indices: 3592124--3592154 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
3592114 ATTTAGACTA
*
3592124 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3592155 CCTTAATTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3594034 original size:36 final size:33
Alignment explanation
Indices: 3593983--3594063 Score: 99
Period size: 36 Copynumber: 2.3 Consensus size: 33
3593973 ATAATTTTTC
3593983 AAACACATATGCCAAAAGCATATATTTATACTTAT
1 AAACACATATGCCAAAAGCATATA-TT-TACTTAT
* *
3594018 AAACTACATGTGCCAAATGCATATATTTACTTAT
1 AAAC-ACATATGCCAAAAGCATATATTTACTTAT
*
3594052 AATCCACATATG
1 AA-ACACATATG
3594064 TCGAATGCAT
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
34 15 0.38
35 7 0.17
36 18 0.45
ACGTcount: A:0.42, C:0.19, G:0.07, T:0.32
Consensus pattern (33 bp):
AAACACATATGCCAAAAGCATATATTTACTTAT
Found at i:3594071 original size:34 final size:36
Alignment explanation
Indices: 3593986--3594074 Score: 110
Period size: 34 Copynumber: 2.5 Consensus size: 36
3593976 ATTTTTCAAA
*
3593986 CACATATGCCAAAAGCATATATTTATACTTATAAAC
1 CACATATGCCAAATGCATATATTTATACTTATAAAC
* * *
3594022 TACATGTGCCAAATGCATATA-TT-TACTTATAATC
1 CACATATGCCAAATGCATATATTTATACTTATAAAC
* *
3594056 CACATATGTCGAATGCATA
1 CACATATGCCAAATGCATA
3594075 CATATATATA
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
34 25 0.56
35 2 0.04
36 18 0.40
ACGTcount: A:0.39, C:0.19, G:0.09, T:0.33
Consensus pattern (36 bp):
CACATATGCCAAATGCATATATTTATACTTATAAAC
Found at i:3594303 original size:41 final size:41
Alignment explanation
Indices: 3594248--3594543 Score: 412
Period size: 41 Copynumber: 7.2 Consensus size: 41
3594238 CTTAATTTAA
*
3594248 CAGATTCATCGGCACTTAGCCTGCTAGGCTTATAACCTGATT
1 CAGA-TCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATT
* * * * *
3594290 TAGATCACCGGCACTTAGTCTGCTAAGCTTATAGCTTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATT
* * *
3594331 CAGTTCATCGACACTTAGCCTGCTAGGCTTATAACCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATT
* * * *
3594372 TAGATCACCGGCACTTAGCCTGCTAAGCTTATAGCTTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATT
* *
3594413 CAGTTCACCGGTACTTAGCCTGCTAGGCTTATAACCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATT
3594454 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATT
* * *
3594495 CAGTTCACCGGCACTTAGCCTGCTAGACTTATAGCCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATT
*
3594536 CAGTTCAC
1 CAGATCAC
3594544 ATAAGATATA
Statistics
Matches: 222, Mismatches: 32, Indels: 1
0.87 0.13 0.00
Matches are distributed among these distances:
41 219 0.99
42 3 0.01
ACGTcount: A:0.24, C:0.27, G:0.19, T:0.31
Consensus pattern (41 bp):
CAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATT
Found at i:3594351 original size:82 final size:82
Alignment explanation
Indices: 3594252--3594535 Score: 469
Period size: 82 Copynumber: 3.5 Consensus size: 82
3594242 ATTTAACAGA
* *
3594252 TTCATCGGCACTTAGCCTGCTAGGCTTATAACCTGATTTAGATCACCGGCACTTAGTCTGCTAAG
1 TTCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTTAGATCACCGGCACTTAGCCTGCTAAG
3594317 CTTATAGCTTGATTCAG
66 CTTATAGCTTGATTCAG
* *
3594334 TTCATCGACACTTAGCCTGCTAGGCTTATAACCTGATTTAGATCACCGGCACTTAGCCTGCTAAG
1 TTCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTTAGATCACCGGCACTTAGCCTGCTAAG
3594399 CTTATAGCTTGATTCAG
66 CTTATAGCTTGATTCAG
* * *
3594416 TTCACCGGTACTTAGCCTGCTAGGCTTATAACCTGATTCAGATCACCGGCACTTAGCCTGCTAGG
1 TTCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTTAGATCACCGGCACTTAGCCTGCTAAG
* *
3594481 CTTATAACCTGATTCAG
66 CTTATAGCTTGATTCAG
* *
3594498 TTCACCGGCACTTAGCCTGCTAGACTTATAGCCTGATT
1 TTCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATT
3594536 CAGTTCACAT
Statistics
Matches: 190, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
82 190 1.00
ACGTcount: A:0.23, C:0.26, G:0.19, T:0.31
Consensus pattern (82 bp):
TTCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTTAGATCACCGGCACTTAGCCTGCTAAG
CTTATAGCTTGATTCAG
Found at i:3596672 original size:21 final size:21
Alignment explanation
Indices: 3596610--3596755 Score: 107
Period size: 21 Copynumber: 7.0 Consensus size: 21
3596600 GTTGTTACAC
* *
3596610 TTTCCGTTTAGCT-TTCTCGAG
1 TTTCTGTTTAGCTCTTAT-GAG
** *
3596631 TTTCTGTTTAATTCATATGAG
1 TTTCTGTTTAGCTCTTATGAG
*
3596652 TTTCTGTTTAGCTCTTTTGAG
1 TTTCTGTTTAGCTCTTATGAG
* *
3596673 CTTT-TGTTTAACCCTTATGAG
1 -TTTCTGTTTAGCTCTTATGAG
** * *
3596694 TTTCCATTTAGCTTTTACGAG
1 TTTCTGTTTAGCTCTTATGAG
* * * * *
3596715 CTTCTGTTCAACCCTTATGGG
1 TTTCTGTTTAGCTCTTATGAG
3596736 TTTCTGTTTAGCTCTTATGA
1 TTTCTGTTTAGCTCTTATGA
3596756 ACTTTTGTTC
Statistics
Matches: 90, Mismatches: 32, Indels: 6
0.70 0.25 0.05
Matches are distributed among these distances:
20 3 0.03
21 82 0.91
22 5 0.06
ACGTcount: A:0.16, C:0.18, G:0.16, T:0.49
Consensus pattern (21 bp):
TTTCTGTTTAGCTCTTATGAG
Found at i:3596681 original size:42 final size:41
Alignment explanation
Indices: 3596610--3596748 Score: 145
Period size: 42 Copynumber: 3.3 Consensus size: 41
3596600 GTTGTTACAC
** *
3596610 TTTCCGTTTAGCTTTCTCGAG-TTTCTGTTTAATTCATATGAG
1 TTTCCGTTTAGCTTT-TCGAGCTTT-TGTTTAACCCTTATGAG
* *
3596652 TTTCTGTTTAGCTCTTTTGAGCTTTTGTTTAACCCTTATGAG
1 TTTCCGTTTAGCT-TTTCGAGCTTTTGTTTAACCCTTATGAG
* * * *
3596694 TTTCCATTTAGCTTTTACGAGCTTCTGTTCAACCCTTATGGG
1 TTTCCGTTTAGCTTTT-CGAGCTTTTGTTTAACCCTTATGAG
*
3596736 TTTCTGTTTAGCT
1 TTTCCGTTTAGCT
3596749 CTTATGAACT
Statistics
Matches: 81, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
41 3 0.04
42 73 0.90
43 5 0.06
ACGTcount: A:0.15, C:0.19, G:0.17, T:0.50
Consensus pattern (41 bp):
TTTCCGTTTAGCTTTTCGAGCTTTTGTTTAACCCTTATGAG
Found at i:3596751 original size:84 final size:84
Alignment explanation
Indices: 3596610--3596764 Score: 213
Period size: 84 Copynumber: 1.8 Consensus size: 84
3596600 GTTGTTACAC
* * * ** * *
3596610 TTTCCGTTTAGCTTTCTCGAGTTTCTGTTTAATTCATATGAGTTTCTGTTTAGCTCTTTTGAGCT
1 TTTCCATTTAGCTTTCTCGAGCTTCTGTTCAACCCATATGAGTTTCTGTTTAGCTCTTATGAACT
3596675 TTTGTTTAACCCTTATGAG
66 TTTGTTTAACCCTTATGAG
* *
3596694 TTTCCATTTAGCTTT-TACGAGCTTCTGTTCAACCCTTATGGGTTTCTGTTTAGCTCTTATGAAC
1 TTTCCATTTAGCTTTCT-CGAGCTTCTGTTCAACCCATATGAGTTTCTGTTTAGCTCTTATGAAC
3596758 TTTTGTT
65 TTTTGTT
3596765 CAATCTTCAG
Statistics
Matches: 61, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
83 1 0.02
84 60 0.98
ACGTcount: A:0.15, C:0.18, G:0.16, T:0.50
Consensus pattern (84 bp):
TTTCCATTTAGCTTTCTCGAGCTTCTGTTCAACCCATATGAGTTTCTGTTTAGCTCTTATGAACT
TTTGTTTAACCCTTATGAG
Found at i:3596765 original size:42 final size:42
Alignment explanation
Indices: 3596646--3596767 Score: 163
Period size: 42 Copynumber: 2.9 Consensus size: 42
3596636 GTTTAATTCA
* *
3596646 TATGAGTTTCTGTTTAGCTCTTTTGAGCTTTTGTTTAACCCT
1 TATGAGTTTCTGTTTAGCTCTTATGAGCTTTTGTTCAACCCT
** * * *
3596688 TATGAGTTTCCATTTAGCTTTTACGAGCTTCTGTTCAACCCT
1 TATGAGTTTCTGTTTAGCTCTTATGAGCTTTTGTTCAACCCT
* *
3596730 TATGGGTTTCTGTTTAGCTCTTATGAACTTTTGTTCAA
1 TATGAGTTTCTGTTTAGCTCTTATGAGCTTTTGTTCAA
3596768 TCTTCAGGCT
Statistics
Matches: 66, Mismatches: 14, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
42 66 1.00
ACGTcount: A:0.17, C:0.18, G:0.16, T:0.48
Consensus pattern (42 bp):
TATGAGTTTCTGTTTAGCTCTTATGAGCTTTTGTTCAACCCT
Found at i:3612290 original size:26 final size:23
Alignment explanation
Indices: 3612247--3612297 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 23
3612237 AATTTATTGG
3612247 TACTAGTCTCATTCCACCGCCTCTA
1 TACTAGTCTCATTCCA-C-CCTCTA
* *
3612272 TACTAGTTCTCCTTTCACCCTCTA
1 TACTAG-TCTCATTCCACCCTCTA
3612296 TA
1 TA
3612298 AGGTTATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 8 0.35
25 7 0.30
26 8 0.35
ACGTcount: A:0.20, C:0.37, G:0.06, T:0.37
Consensus pattern (23 bp):
TACTAGTCTCATTCCACCCTCTA
Found at i:3615724 original size:23 final size:23
Alignment explanation
Indices: 3615670--3615724 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
3615660 TTTTTCACAA
* *
3615670 TTCCAATATAAATTAACAGTTTT
1 TTCCAATATAAATGAACAGTTAT
* *
3615693 TTTCTATATAAATGAA-AGTCTAT
1 TTCCAATATAAATGAACAGT-TAT
3615716 TTCCAATAT
1 TTCCAATAT
3615725 CTCAGATGAT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
22 3 0.12
23 22 0.88
ACGTcount: A:0.38, C:0.13, G:0.05, T:0.44
Consensus pattern (23 bp):
TTCCAATATAAATGAACAGTTAT
Found at i:3621307 original size:26 final size:28
Alignment explanation
Indices: 3621248--3621305 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
3621238 ACTAAAATGT
*
3621248 TATAATTTTTTTTATTTACCAAAATATA
1 TATAAATTTTTTTATTTACCAAAATATA
3621276 TATAAATTTTTTTATTTACCAAAATATA
1 TATAAATTTTTTTATTTACCAAAATATA
3621304 TA
1 TA
3621306 AAAAAACAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (28 bp):
TATAAATTTTTTTATTTACCAAAATATA
Found at i:3621400 original size:27 final size:27
Alignment explanation
Indices: 3621359--3621465 Score: 187
Period size: 27 Copynumber: 4.0 Consensus size: 27
3621349 ACTCCCTGGG
*
3621359 ACAAGGGAACACTGTTGGCGGCACCAA
1 ACAAGGGAACCCTGTTGGCGGCACCAA
3621386 ACAAGGGAACCCTGTTGGCGGCACCAA
1 ACAAGGGAACCCTGTTGGCGGCACCAA
3621413 ACAAGGGAACCCTGTTGGCGGCACCAA
1 ACAAGGGAACCCTGTTGGCGGCACCAA
**
3621440 ACAAGGGTTCCCTGTTGGCGGCACCA
1 ACAAGGGAACCCTGTTGGCGGCACCA
3621466 CTCGTGTTAT
Statistics
Matches: 77, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 77 1.00
ACGTcount: A:0.28, C:0.29, G:0.30, T:0.13
Consensus pattern (27 bp):
ACAAGGGAACCCTGTTGGCGGCACCAA
Found at i:3621577 original size:11 final size:13
Alignment explanation
Indices: 3621551--3621575 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3621541 TGCGGAAAAA
3621551 AAGAGAGAAAGAG
1 AAGAGAGAAAGAG
3621564 AAGAGAGAAAGA
1 AAGAGAGAAAGA
3621576 AGTTATTTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (13 bp):
AAGAGAGAAAGAG
Found at i:3624260 original size:18 final size:18
Alignment explanation
Indices: 3624216--3624260 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
3624206 ATCCCAACGA
*
3624216 TCACCACCACCTTCTTCT
1 TCACCACCACATTCTTCT
* *
3624234 TCGCAACCACATTCTTCT
1 TCACCACCACATTCTTCT
3624252 TCACCACCA
1 TCACCACCA
3624261 ACCATATCAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.22, C:0.47, G:0.02, T:0.29
Consensus pattern (18 bp):
TCACCACCACATTCTTCT
Found at i:3625252 original size:10 final size:10
Alignment explanation
Indices: 3625230--3625266 Score: 56
Period size: 10 Copynumber: 3.6 Consensus size: 10
3625220 AAATACCTGA
3625230 TTTTTCTCTTC
1 TTTTTCTC-TC
3625241 TTTTTCTCTC
1 TTTTTCTCTC
*
3625251 TTTTTCTCTT
1 TTTTTCTCTC
3625261 TTTTTC
1 TTTTTC
3625267 CGAACCACCT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
10 17 0.68
11 8 0.32
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (10 bp):
TTTTTCTCTC
Found at i:3625454 original size:18 final size:19
Alignment explanation
Indices: 3625426--3625461 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
3625416 TCAGTCCATT
3625426 TTTTTTCTGTTTTTTTTGG
1 TTTTTTCTGTTTTTTTTGG
3625445 TTTTTT-TGTTTTTTTTG
1 TTTTTTCTGTTTTTTTTG
3625462 ATATATTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.00, C:0.03, G:0.14, T:0.83
Consensus pattern (19 bp):
TTTTTTCTGTTTTTTTTGG
Found at i:3625460 original size:9 final size:9
Alignment explanation
Indices: 3625425--3625461 Score: 56
Period size: 9 Copynumber: 4.0 Consensus size: 9
3625415 ATCAGTCCAT
3625425 TTTTTTTCTG
1 TTTTTTT-TG
3625435 TTTTTTTTG
1 TTTTTTTTG
*
3625444 GTTTTTTTG
1 TTTTTTTTG
3625453 TTTTTTTTG
1 TTTTTTTTG
3625462 ATATATTTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
9 18 0.72
10 7 0.28
ACGTcount: A:0.00, C:0.03, G:0.14, T:0.84
Consensus pattern (9 bp):
TTTTTTTTG
Found at i:3625496 original size:27 final size:27
Alignment explanation
Indices: 3625462--3625527 Score: 116
Period size: 27 Copynumber: 2.5 Consensus size: 27
3625452 GTTTTTTTTG
3625462 ATATATTTTGGTAAATAAAAAAATTAT
1 ATATATTTTGGTAAATAAAAAAATTAT
3625489 ATATATTTTGGTAAATAAAAAAATTAT
1 ATATATTTTGGTAAATAAAAAAATTAT
*
3625516 A-ACATTTTGGTA
1 ATATATTTTGGTA
3625528 TTTTTTAAAT
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
26 10 0.26
27 28 0.74
ACGTcount: A:0.48, C:0.02, G:0.09, T:0.41
Consensus pattern (27 bp):
ATATATTTTGGTAAATAAAAAAATTAT
Found at i:3629844 original size:35 final size:35
Alignment explanation
Indices: 3629799--3629866 Score: 127
Period size: 35 Copynumber: 1.9 Consensus size: 35
3629789 AAGAATATTA
*
3629799 AAAAAATAAAATTTCTTATTATTTGTTAAAATATC
1 AAAAAATAAAATTTCTTATTATTTGTCAAAATATC
3629834 AAAAAATAAAATTTCTTATTATTTGTCAAAATA
1 AAAAAATAAAATTTCTTATTATTTGTCAAAATA
3629867 ATTGCATTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.41
Consensus pattern (35 bp):
AAAAAATAAAATTTCTTATTATTTGTCAAAATATC
Found at i:3642455 original size:11 final size:12
Alignment explanation
Indices: 3642429--3642457 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
3642419 AAAACAACGC
3642429 TATTTTTTATTA
1 TATTTTTTATTA
3642441 TATTTTTTATT-
1 TATTTTTTATTA
3642452 TATTTT
1 TATTTT
3642458 CTTTTTTTGC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 6 0.35
12 11 0.65
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (12 bp):
TATTTTTTATTA
Found at i:3646887 original size:15 final size:16
Alignment explanation
Indices: 3646867--3646897 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3646857 TAGAAAATTC
3646867 AGTAC-TTAATTTTTT
1 AGTACTTTAATTTTTT
3646882 AGTACTTTAATTTTTT
1 AGTACTTTAATTTTTT
3646898 TAATTTATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.26, C:0.06, G:0.06, T:0.61
Consensus pattern (16 bp):
AGTACTTTAATTTTTT
Found at i:3646988 original size:75 final size:75
Alignment explanation
Indices: 3646897--3647050 Score: 299
Period size: 75 Copynumber: 2.1 Consensus size: 75
3646887 TTTAATTTTT
*
3646897 TTAATTTATCAAACATACCCTAAATGTTAATTTACCCTCTCTTTTTTCAATATAAGCATCATATT
1 TTAATTTATCAAACATACCCTAAATGTTAATTTACCCTCTCTCTTTTCAATATAAGCATCATATT
3646962 GCACATTCTA
66 GCACATTCTA
3646972 TTAATTTATCAAACATACCCTAAATGTTAATTTACCCTCTCTCTTTTCAATATAAGCATCATATT
1 TTAATTTATCAAACATACCCTAAATGTTAATTTACCCTCTCTCTTTTCAATATAAGCATCATATT
3647037 GCACATTCTA
66 GCACATTCTA
3647047 TTAA
1 TTAA
3647051 ATTTCAAGGG
Statistics
Matches: 78, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
75 78 1.00
ACGTcount: A:0.34, C:0.21, G:0.04, T:0.41
Consensus pattern (75 bp):
TTAATTTATCAAACATACCCTAAATGTTAATTTACCCTCTCTCTTTTCAATATAAGCATCATATT
GCACATTCTA
Found at i:3653650 original size:20 final size:20
Alignment explanation
Indices: 3653625--3653664 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
3653615 AATATTTTCC
*
3653625 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
3653645 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
3653665 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:3653670 original size:34 final size:35
Alignment explanation
Indices: 3653613--3653679 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
3653603 CAAACACCAA
*
3653613 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
3653648 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
3653680 TATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Done.