Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D10
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: 67973905
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1760000 characters in sequence are not A, C, G, or T
File 12 of 228
Found at i:4312961 original size:29 final size:28
Alignment explanation
Indices: 4312925--4313039 Score: 108
Period size: 29 Copynumber: 3.9 Consensus size: 28
4312915 TAAGAAAAAA
*
4312925 TTATAAAAATCACAAAAAATTGTAAAATT
1 TTATAAAAATCA-AAAAAATTATAAAATT
*
4312954 TTATAAAAATCATAAAAATTATAAAA-T
1 TTATAAAAATCAAAAAAATTATAAAATT
* *
4312981 ATATAGAAATATAGAAAAAAAATTATAAAATT
1 TTATA-AAA-AT--CAAAAAAATTATAAAATT
*
4313013 TTAT-AAAGTCATAAGAAAATTATAAAA
1 TTATAAAAATCA-AA-AAAATTATAAAA
4313040 AATGTAAAGA
Statistics
Matches: 71, Mismatches: 8, Indels: 14
0.76 0.09 0.15
Matches are distributed among these distances:
27 6 0.08
28 17 0.24
29 27 0.38
30 3 0.04
31 14 0.20
32 4 0.06
ACGTcount: A:0.62, C:0.03, G:0.04, T:0.30
Consensus pattern (28 bp):
TTATAAAAATCAAAAAAATTATAAAATT
Found at i:4313055 original size:19 final size:20
Alignment explanation
Indices: 4313028--4313079 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
4313018 AAGTCATAAG
4313028 AAAATTATAAAAAATGTAAA
1 AAAATTATAAAAAATGTAAA
* **
4313048 GAAA-TATAAAATTTGTAAA
1 AAAATTATAAAAAATGTAAA
4313067 AAAATTATAAAAA
1 AAAATTATAAAAA
4313080 TTATCGTACT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
19 16 0.62
20 10 0.38
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.27
Consensus pattern (20 bp):
AAAATTATAAAAAATGTAAA
Found at i:4313346 original size:30 final size:29
Alignment explanation
Indices: 4313311--4313377 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 29
4313301 TTATAATTTT
*
4313311 TTTCTTCTA-ATTTTTAATAAAATTTTAATA
1 TTTCTT-TACATTTCTAATAAAA-TTTAATA
*
4313341 TTTCTTTATCATTTCTATTAAAATTTAATA
1 TTTCTTTA-CATTTCTAATAAAATTTAATA
4313371 TTT-TTTA
1 TTTCTTTA
4313378 TTGATTTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
29 6 0.18
30 16 0.48
31 11 0.33
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (29 bp):
TTTCTTTACATTTCTAATAAAATTTAATA
Found at i:4313403 original size:17 final size:17
Alignment explanation
Indices: 4313369--4313402 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
4313359 TAAAATTTAA
*
4313369 TATTTTTTATTGATTTT
1 TATTTTTTATTAATTTT
4313386 TATTTTTTA-TAATTTT
1 TATTTTTTATTAATTTT
4313402 T
1 T
4313403 TGCCACATGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (17 bp):
TATTTTTTATTAATTTT
Found at i:4313728 original size:91 final size:91
Alignment explanation
Indices: 4313508--4313769 Score: 242
Period size: 91 Copynumber: 2.9 Consensus size: 91
4313498 GTCAAATAGT
* * * ** *
4313508 ATTTTTGATACATTTT-ACAGTTCAAATACCTAATTGAGTGCAATAAAAAATTAAGGATTTAATT
1 ATTTTTAATACATTTTGAAAGTTCAAATACCTAATTGAGTGCAAAAAAAAAGCAAGGACTTAATT
***
4313572 GCTTTTTTTGAAAAAAAATTTGAGGGC
66 GCTTTTTTTG-AAAAAAATTTGACAAC
* * * * * *
4313599 ATTTTTAATACATTTTGAAAGTTCGAGTACCCAGTTGAGTGCAAAAAAAAAGGCATGGCCTTAAT
1 ATTTTTAATACATTTTGAAAGTTCAAATACCTAATTGAGTGCAAAAAAAAA-GCAAGGACTTAAT
* *
4313664 TGCTTTTTTTG-AATAAGTTTGACAAC
65 TGCTTTTTTTGAAAAAAATTTGACAAC
* ** * * *
4313690 TTTTTTAATGTATTTTGAAAGTTTAAATACCTAATTGAGTG-AAAAAAAGAGAGTAAGAACTTAA
1 ATTTTTAATACATTTTGAAAGTTCAAATACCTAATTGAGTGCAAAAAAA-A-AGCAAGGACTTAA
*
4313754 TTACTTTTTTTTGAAA
64 TTGC-TTTTTTTGAAA
4313770 TGTTTAAAGG
Statistics
Matches: 135, Mismatches: 30, Indels: 10
0.77 0.17 0.06
Matches are distributed among these distances:
90 7 0.05
91 70 0.52
92 37 0.27
93 21 0.16
ACGTcount: A:0.37, C:0.09, G:0.15, T:0.38
Consensus pattern (91 bp):
ATTTTTAATACATTTTGAAAGTTCAAATACCTAATTGAGTGCAAAAAAAAAGCAAGGACTTAATT
GCTTTTTTTGAAAAAAATTTGACAAC
Found at i:4327557 original size:75 final size:75
Alignment explanation
Indices: 4327434--4327584 Score: 302
Period size: 75 Copynumber: 2.0 Consensus size: 75
4327424 TGGCAATGTT
4327434 ATTAAAAAAATTCAAGCTTTTTGCATTTGCTGTCCTGCAGATGCATTGCTTTTAAGTTTTAGCAT
1 ATTAAAAAAATTCAAGCTTTTTGCATTTGCTGTCCTGCAGATGCATTGCTTTTAAGTTTTAGCAT
4327499 CTGAAAACAA
66 CTGAAAACAA
4327509 ATTAAAAAAATTCAAGCTTTTTGCATTTGCTGTCCTGCAGATGCATTGCTTTTAAGTTTTAGCAT
1 ATTAAAAAAATTCAAGCTTTTTGCATTTGCTGTCCTGCAGATGCATTGCTTTTAAGTTTTAGCAT
4327574 CTGAAAACAA
66 CTGAAAACAA
4327584 A
1 A
4327585 CTAACTTATC
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
75 76 1.00
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.37
Consensus pattern (75 bp):
ATTAAAAAAATTCAAGCTTTTTGCATTTGCTGTCCTGCAGATGCATTGCTTTTAAGTTTTAGCAT
CTGAAAACAA
Found at i:4334307 original size:16 final size:16
Alignment explanation
Indices: 4334279--4334320 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
4334269 TGTTTTTTTT
4334279 TTTTTACTT-TATAATA
1 TTTTTA-TTATATAATA
*
4334295 TTTTTATTATATAGTA
1 TTTTTATTATATAATA
4334311 TATTTTATTA
1 T-TTTTATTA
4334321 ACTTTTTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 2 0.09
16 13 0.57
17 8 0.35
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.64
Consensus pattern (16 bp):
TTTTTATTATATAATA
Found at i:4334467 original size:31 final size:32
Alignment explanation
Indices: 4334403--4334478 Score: 145
Period size: 32 Copynumber: 2.4 Consensus size: 32
4334393 CTTTTCAACT
4334403 ACATCTATAGTTGTGAAAAATAAATAAAAAAA
1 ACATCTATAGTTGTGAAAAATAAATAAAAAAA
4334435 ACATCTATAGTTGTGAAAAATAAAT-AAAAAA
1 ACATCTATAGTTGTGAAAAATAAATAAAAAAA
4334466 ACATCTATAGTTG
1 ACATCTATAGTTG
4334479 CTTCCTACTA
Statistics
Matches: 44, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
31 19 0.43
32 25 0.57
ACGTcount: A:0.54, C:0.08, G:0.11, T:0.28
Consensus pattern (32 bp):
ACATCTATAGTTGTGAAAAATAAATAAAAAAA
Found at i:4335956 original size:27 final size:28
Alignment explanation
Indices: 4335907--4335961 Score: 78
Period size: 27 Copynumber: 2.0 Consensus size: 28
4335897 AATTTTAAAA
*
4335907 AAAATCTTTAAAATAAATATAAAATATT
1 AAAATCTTTAAAAAAAATATAAAATATT
4335935 AAAAT-TTTACAAAAAAAT-TAAAATATT
1 AAAATCTTTA-AAAAAAATATAAAATATT
4335962 TTGATTTGTC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 13 0.52
28 12 0.48
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.35
Consensus pattern (28 bp):
AAAATCTTTAAAAAAAATATAAAATATT
Found at i:4340837 original size:14 final size:14
Alignment explanation
Indices: 4340820--4340849 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
4340810 TCCACAAGGT
*
4340820 TTTAAACATAAACA
1 TTTAAACACAAACA
4340834 TTTAAACACAAACA
1 TTTAAACACAAACA
4340848 TT
1 TT
4340850 CCTCCCATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.53, C:0.17, G:0.00, T:0.30
Consensus pattern (14 bp):
TTTAAACACAAACA
Found at i:4343506 original size:138 final size:138
Alignment explanation
Indices: 4343247--4343520 Score: 422
Period size: 138 Copynumber: 2.0 Consensus size: 138
4343237 GACGCTACCG
* * *
4343247 ATGCTGATATCTCGTTAGAATTGTATCTTTCAATGAACAAACCCCAAAGGGTTGAAGTCGGTGAA
1 ATGCCGATAGCTCGTTAGAATGGTATCTTTCAATGAACAAACCCCAAAGGGTTGAAGTCGGTGAA
* * * * *
4343312 CGTAACAATCATTATAAACTGAATATCAATGAAGCCCTTACTTTGGCAACTACGAGTGATAATTT
66 CGTAACAATCATCATAAACTGAAGATCAATGAAGCCATTACTTTAGCAACTACGAGTGATAAGTT
4343377 TACATCCA
131 TACATCCA
* * * * *
4343385 ATGCCGATAGCTCGTTAGAATGGTCTCTTTCAATGAATAAACCCCCAGGGGTTGAAGTTGGTGAA
1 ATGCCGATAGCTCGTTAGAATGGTATCTTTCAATGAACAAACCCCAAAGGGTTGAAGTCGGTGAA
*
4343450 CGTAACAATCATCATAAACTGAAGATCAATGAAGCCATTACTTTAGCAACTGCGAGTGATAAGTT
66 CGTAACAATCATCATAAACTGAAGATCAATGAAGCCATTACTTTAGCAACTACGAGTGATAAGTT
4343515 TACATC
131 TACATC
4343521 GAAGAAAAGA
Statistics
Matches: 122, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
138 122 1.00
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (138 bp):
ATGCCGATAGCTCGTTAGAATGGTATCTTTCAATGAACAAACCCCAAAGGGTTGAAGTCGGTGAA
CGTAACAATCATCATAAACTGAAGATCAATGAAGCCATTACTTTAGCAACTACGAGTGATAAGTT
TACATCCA
Found at i:4343563 original size:138 final size:137
Alignment explanation
Indices: 4343277--4343550 Score: 304
Period size: 138 Copynumber: 2.0 Consensus size: 137
4343267 TTGTATCTTT
* * *
4343277 CAATGAACAAACCCCAAAGGGTTGAAGTCGGTGAACGTAACAATCATTATAAACTGAATATCAAT
1 CAATGAATAAACCCCAAAGGGTTGAAGTCGGTGAACGTAACAATCATCATAAACTGAAGATCAAT
* * * * * * * *
4343342 GAAGCCCTTACTTTGGCAACTACGAGTGATAATTTTACATCCAATGCCGATAGCTCGTTAGAATG
66 GAAGCCATTACTTTAGCAACTACGAGTGATAAGTTTACATCCAATG-CAAAAGCACGTAACAATG
*** **
4343407 GTCTCTTT
130 GAAACTGA
* * *
4343415 CAATGAATAAACCCCCAGGGGTTGAAGTTGGTGAACGTAACAATCATCATAAACTGAAGATCAAT
1 CAATGAATAAACCCCAAAGGGTTGAAGTCGGTGAACGTAACAATCATCATAAACTGAAGATCAAT
* *
4343480 GAAGCCATTACTTTAGCAACTGCGAGTGATAAGTTTACATCGAA-G-AAAAG-ACG-AACAATGG
66 GAAGCCATTACTTTAGCAACTACGAGTGATAAGTTTACATCCAATGCAAAAGCACGTAACAAT--
4343541 GGAAACTGA
129 GGAAACTGA
4343550 C
1 C
4343551 GAATAGAAAT
Statistics
Matches: 113, Mismatches: 21, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
133 4 0.04
134 2 0.02
135 8 0.07
137 1 0.01
138 98 0.87
ACGTcount: A:0.37, C:0.19, G:0.20, T:0.24
Consensus pattern (137 bp):
CAATGAATAAACCCCAAAGGGTTGAAGTCGGTGAACGTAACAATCATCATAAACTGAAGATCAAT
GAAGCCATTACTTTAGCAACTACGAGTGATAAGTTTACATCCAATGCAAAAGCACGTAACAATGG
AAACTGA
Found at i:4344828 original size:18 final size:18
Alignment explanation
Indices: 4344805--4344852 Score: 73
Period size: 18 Copynumber: 2.7 Consensus size: 18
4344795 TTTTTTTAAT
4344805 TTTAAAATGTTATACTA-A
1 TTTAAAATGTTA-ACTAGA
4344823 TTTAAAATGTTAACTAGA
1 TTTAAAATGTTAACTAGA
4344841 TTTAAAAT-TTAA
1 TTTAAAATGTTAA
4344853 AATTAGACAA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
17 8 0.28
18 21 0.72
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (18 bp):
TTTAAAATGTTAACTAGA
Found at i:4374547 original size:16 final size:16
Alignment explanation
Indices: 4374526--4374557 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
4374516 CCGTTTACCG
4374526 ATTCCTTGCCTATTCC
1 ATTCCTTGCCTATTCC
*
4374542 ATTCCTTGCTTATTCC
1 ATTCCTTGCCTATTCC
4374558 CTCAGCAGCT
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:0.12, C:0.34, G:0.06, T:0.47
Consensus pattern (16 bp):
ATTCCTTGCCTATTCC
Found at i:4375529 original size:25 final size:23
Alignment explanation
Indices: 4375495--4375552 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 23
4375485 GTTAACATGG
*
4375495 AGTTCATGTTTTGGTTTCTATATTA
1 AGTTGATGTTTT--TTTCTATATTA
*
4375520 AGTTGATG--TTTTTCTGTATTA
1 AGTTGATGTTTTTTTCTATATTA
4375541 AGTTGATGTTTT
1 AGTTGATGTTTT
4375553 CCGTTTGTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
21 18 0.62
23 4 0.14
25 7 0.24
ACGTcount: A:0.19, C:0.05, G:0.19, T:0.57
Consensus pattern (23 bp):
AGTTGATGTTTTTTTCTATATTA
Found at i:4375533 original size:21 final size:21
Alignment explanation
Indices: 4375509--4375552 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
4375499 CATGTTTTGG
4375509 TTTCTATATTAAGTTGATGTT
1 TTTCTATATTAAGTTGATGTT
*
4375530 TTTCTGTATTAAGTTGATGTT
1 TTTCTATATTAAGTTGATGTT
4375551 TT
1 TT
4375553 CCGTTTGTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.20, C:0.05, G:0.16, T:0.59
Consensus pattern (21 bp):
TTTCTATATTAAGTTGATGTT
Found at i:4375610 original size:21 final size:21
Alignment explanation
Indices: 4375569--4375611 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
4375559 GTGTTTATGG
*
4375569 ATTATATATAATTTTTATAGT
1 ATTATATATAATATTTATAGT
*
4375590 ATTATATATTATGATTT-TAGT
1 ATTATATATAAT-ATTTATAGT
4375611 A
1 A
4375612 AATTCATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (21 bp):
ATTATATATAATATTTATAGT
Found at i:4375669 original size:55 final size:54
Alignment explanation
Indices: 4375604--4375709 Score: 124
Period size: 55 Copynumber: 1.9 Consensus size: 54
4375594 TATATTATGA
* * *
4375604 TTTTAGTAAATTCATA-TAAGAATGATTATATTAAGAATTTTATTAAATTATATCT
1 TTTTAGTAAATT-ATATTAAGAATAATTATATTAA-AATATGATTAAATTATATCT
* * *
4375659 TTTTATTAAATTATATTTAATAATAATTATGTTAAAATATGATTAAATTAT
1 TTTTAGTAAATTATA-TTAAGAATAATTATATTAAAATATGATTAAATTAT
4375710 TTATTATTTA
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
54 3 0.07
55 25 0.58
56 15 0.35
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (54 bp):
TTTTAGTAAATTATATTAAGAATAATTATATTAAAATATGATTAAATTATATCT
Found at i:4375928 original size:15 final size:16
Alignment explanation
Indices: 4375908--4375946 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
4375898 TTGAATTATT
4375908 ATTACAGCTC-ATTCC
1 ATTACAGCTCTATTCC
4375923 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCC
4375939 ATTACAGC
1 ATTACAGC
4375947 GAACCAAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 10 0.43
16 13 0.57
ACGTcount: A:0.28, C:0.31, G:0.08, T:0.33
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:4376139 original size:23 final size:23
Alignment explanation
Indices: 4376085--4376152 Score: 82
Period size: 23 Copynumber: 2.9 Consensus size: 23
4376075 ATTAATATTT
**
4376085 TTCGTGAACATGTTCAATTATATG
1 TTCGTGAACATGTTTGATTA-ATG
** *
4376109 TTTATGAACATGTTTGTTTAATG
1 TTCGTGAACATGTTTGATTAATG
4376132 TTCGTGAACATGTTTGATTAA
1 TTCGTGAACATGTTTGATTAA
4376153 GTTAAATGAA
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
23 21 0.58
24 15 0.42
ACGTcount: A:0.28, C:0.09, G:0.18, T:0.46
Consensus pattern (23 bp):
TTCGTGAACATGTTTGATTAATG
Found at i:4376162 original size:23 final size:23
Alignment explanation
Indices: 4376089--4376168 Score: 81
Period size: 23 Copynumber: 3.4 Consensus size: 23
4376079 ATATTTTTCG
** *
4376089 TGAACATGTTCAATTATATGTTTA
1 TGAACATGTTTGATTA-ATGTTAA
* **
4376113 TGAACATGTTTGTTTAATGTTCG
1 TGAACATGTTTGATTAATGTTAA
4376136 TGAACATGTTTGATTAA-GTTAAA
1 TGAACATGTTTGATTAATGTT-AA
4376159 TGAACATGTT
1 TGAACATGTT
4376169 CGTGAATATT
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
22 3 0.06
23 31 0.66
24 13 0.28
ACGTcount: A:0.31, C:0.07, G:0.17, T:0.44
Consensus pattern (23 bp):
TGAACATGTTTGATTAATGTTAA
Found at i:4376356 original size:16 final size:15
Alignment explanation
Indices: 4376322--4376353 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
4376312 CAGCACCCAA
4376322 TTAAACTATACAATT
1 TTAAACTATACAATT
4376337 TTAAACTATACAATT
1 TTAAACTATACAATT
4376352 TT
1 TT
4376354 TAATGAAGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.44, C:0.12, G:0.00, T:0.44
Consensus pattern (15 bp):
TTAAACTATACAATT
Found at i:4383933 original size:4 final size:4
Alignment explanation
Indices: 4383924--4383965 Score: 84
Period size: 4 Copynumber: 10.5 Consensus size: 4
4383914 TTTCATGTAT
4383924 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT
4383966 TCATTCAAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 38 1.00
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:4395750 original size:75 final size:76
Alignment explanation
Indices: 4395661--4395811 Score: 286
Period size: 75 Copynumber: 2.0 Consensus size: 76
4395651 CAGATTGGCA
*
4395661 TATGTGAATTCAAGATATGAAAAGAGAATAAATTTCTATAAAATGGGGAAATA-GGTGGCTGCAA
1 TATGTGAATTCAAGATATGAAAAGAGAATAAATTTCTATAAAAGGGGGAAATAGGGTGGCTGCAA
4395725 ATATCAAATAG
66 ATATCAAATAG
4395736 TATGTGAATTCAAGATATGAAAAGAGAATAAATTTCTATAAAAGGGGGAAATAGGGTGGCTGCAA
1 TATGTGAATTCAAGATATGAAAAGAGAATAAATTTCTATAAAAGGGGGAAATAGGGTGGCTGCAA
4395801 ATATCAAATAG
66 ATATCAAATAG
4395812 AGGAGTTTCA
Statistics
Matches: 74, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
75 52 0.70
76 22 0.30
ACGTcount: A:0.45, C:0.07, G:0.23, T:0.26
Consensus pattern (76 bp):
TATGTGAATTCAAGATATGAAAAGAGAATAAATTTCTATAAAAGGGGGAAATAGGGTGGCTGCAA
ATATCAAATAG
Found at i:4404028 original size:28 final size:28
Alignment explanation
Indices: 4403997--4404057 Score: 106
Period size: 28 Copynumber: 2.2 Consensus size: 28
4403987 ATATGGTCCA
4403997 GTTGAAACATTCTTAGATAATTG-TGGTT
1 GTTGAAACATTCTTAGATAATTGCT-GTT
4404025 GTTGAAACATTCTTAGATAATTGCTGTT
1 GTTGAAACATTCTTAGATAATTGCTGTT
4404053 GTTGA
1 GTTGA
4404058 TGAACTAAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
28 31 0.97
29 1 0.03
ACGTcount: A:0.28, C:0.08, G:0.21, T:0.43
Consensus pattern (28 bp):
GTTGAAACATTCTTAGATAATTGCTGTT
Found at i:4414333 original size:54 final size:55
Alignment explanation
Indices: 4414256--4414375 Score: 179
Period size: 54 Copynumber: 2.2 Consensus size: 55
4414246 AGAATCCACC
*
4414256 TTTTTTCAACTTGAGAGCAAGTTTTACAATTATTTGTGCAAAAATTCCACT-TTT
1 TTTTTTCAACTTGAGAGCAAGTTTTACAATTATTTGTGCAAAAAATCCACTATTT
* * *
4414310 TTTTTTCAATTTGAGAGCAAGTTTTCCATTTATTTGTGCAAAAAATCCACTAGTTT
1 TTTTTTCAACTTGAGAGCAAGTTTTACAATTATTTGTGCAAAAAATCCACTA-TTT
*
4414366 TTGTTTCAAC
1 TTTTTTCAAC
4414376 AAGGAAAATT
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
54 47 0.81
56 11 0.19
ACGTcount: A:0.28, C:0.15, G:0.12, T:0.45
Consensus pattern (55 bp):
TTTTTTCAACTTGAGAGCAAGTTTTACAATTATTTGTGCAAAAAATCCACTATTT
Found at i:4417915 original size:13 final size:13
Alignment explanation
Indices: 4417899--4417923 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4417889 AAACAATTAT
4417899 TTTATTTTTATAC
1 TTTATTTTTATAC
4417912 TTTATTTTTATA
1 TTTATTTTTATA
4417924 AAATTTAGGA
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:0.24, C:0.04, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTATTTTTATAC
Found at i:4430424 original size:6 final size:6
Alignment explanation
Indices: 4430413--4430455 Score: 50
Period size: 6 Copynumber: 7.0 Consensus size: 6
4430403 TTCAAACCCA
* * *
4430413 TTTATT TTTATTT TTTATT TCTATT TTTATT TCTATT TCTATT
1 TTTATT TTTA-TT TTTATT TTTATT TTTATT TTTATT TTTATT
4430456 CCAGTCTAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
6 27 0.82
7 6 0.18
ACGTcount: A:0.16, C:0.07, G:0.00, T:0.77
Consensus pattern (6 bp):
TTTATT
Found at i:4430441 original size:12 final size:12
Alignment explanation
Indices: 4430413--4430455 Score: 59
Period size: 12 Copynumber: 3.5 Consensus size: 12
4430403 TTCAAACCCA
*
4430413 TTTATTTTTATTT
1 TTTATTTCTA-TT
4430426 TTTATTTCTATT
1 TTTATTTCTATT
4430438 TTTATTTCTATT
1 TTTATTTCTATT
*
4430450 TCTATT
1 TTTATT
4430456 CCAGTCTAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
12 19 0.68
13 9 0.32
ACGTcount: A:0.16, C:0.07, G:0.00, T:0.77
Consensus pattern (12 bp):
TTTATTTCTATT
Found at i:4430449 original size:18 final size:19
Alignment explanation
Indices: 4430415--4430455 Score: 66
Period size: 18 Copynumber: 2.2 Consensus size: 19
4430405 CAAACCCATT
*
4430415 TATTTTTATTTTTTATTTC
1 TATTTTTATTTTCTATTTC
4430434 TATTTTTA-TTTCTATTTC
1 TATTTTTATTTTCTATTTC
4430452 TATT
1 TATT
4430456 CCAGTCTAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 13 0.62
19 8 0.38
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.76
Consensus pattern (19 bp):
TATTTTTATTTTCTATTTC
Found at i:4431431 original size:21 final size:22
Alignment explanation
Indices: 4431386--4431430 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
4431376 CTAAATAGAG
4431386 ATTTAATTTTTCTATAATTTAT
1 ATTTAATTTTTCTATAATTTAT
4431408 ATTT-ATTTTATCATATAATTTAT
1 ATTTAATTTT-TC-TATAATTTAT
4431431 TAAAATTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 5 0.24
22 6 0.29
23 10 0.48
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.62
Consensus pattern (22 bp):
ATTTAATTTTTCTATAATTTAT
Found at i:4432305 original size:21 final size:21
Alignment explanation
Indices: 4432279--4432334 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
4432269 AACAGCGGTG
*
4432279 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGATACTGTA
*
4432300 GCGGTGAGATTGGATACTGTA
1 GCGGTGAGATTAGATACTGTA
* *
4432321 GCGGTAAAATTAGA
1 GCGGTGAGATTAGA
4432335 AACAGCGGTG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.29, C:0.09, G:0.34, T:0.29
Consensus pattern (21 bp):
GCGGTGAGATTAGATACTGTA
Found at i:4433054 original size:113 final size:113
Alignment explanation
Indices: 4432915--4433142 Score: 447
Period size: 113 Copynumber: 2.0 Consensus size: 113
4432905 AGACTATATC
*
4432915 CCCATACCTATTCCAAATATATGCCGAAAGATGTAATTTACGGTAAAACAAGAGTCCAGGTAGCA
1 CCCATACCTATTCCAAATATATGCCGAAACATGTAATTTACGGTAAAACAAGAGTCCAGGTAGCA
4432980 TATATTACAGTTCTTAATACAATATATGATTACTATCAGTATGTTGTG
66 TATATTACAGTTCTTAATACAATATATGATTACTATCAGTATGTTGTG
4433028 CCCATACCTATTCCAAATATATGCCGAAACATGTAATTTACGGTAAAACAAGAGTCCAGGTAGCA
1 CCCATACCTATTCCAAATATATGCCGAAACATGTAATTTACGGTAAAACAAGAGTCCAGGTAGCA
4433093 TATATTACAGTTCTTAATACAATATATGATTACTATCAGTATGTTGTG
66 TATATTACAGTTCTTAATACAATATATGATTACTATCAGTATGTTGTG
4433141 CC
1 CC
4433143 ATGATTGAAG
Statistics
Matches: 114, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
113 114 1.00
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (113 bp):
CCCATACCTATTCCAAATATATGCCGAAACATGTAATTTACGGTAAAACAAGAGTCCAGGTAGCA
TATATTACAGTTCTTAATACAATATATGATTACTATCAGTATGTTGTG
Found at i:4437688 original size:17 final size:17
Alignment explanation
Indices: 4437666--4437698 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
4437656 ATAGAAAGTC
*
4437666 AAAGATATTGGTATCAG
1 AAAGATATGGGTATCAG
4437683 AAAGATATGGGTATCA
1 AAAGATATGGGTATCA
4437699 AAATCTGGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.42, C:0.06, G:0.24, T:0.27
Consensus pattern (17 bp):
AAAGATATGGGTATCAG
Found at i:4441195 original size:17 final size:17
Alignment explanation
Indices: 4441173--4441205 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
4441163 ATAGAAAGTC
*
4441173 AAAGATATGGGTATCAG
1 AAAGATATAGGTATCAG
4441190 AAAGATATAGGTATCA
1 AAAGATATAGGTATCA
4441206 AAATCTGGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.06, G:0.24, T:0.24
Consensus pattern (17 bp):
AAAGATATAGGTATCAG
Found at i:4442411 original size:28 final size:28
Alignment explanation
Indices: 4442379--4442451 Score: 128
Period size: 28 Copynumber: 2.6 Consensus size: 28
4442369 CGCCTCCTAG
4442379 GCCCGGGCCCAGCCCGGCCTGAAATTTT
1 GCCCGGGCCCAGCCCGGCCTGAAATTTT
4442407 GCCCGGGCCCAGCCCGGCCTGAAATTTT
1 GCCCGGGCCCAGCCCGGCCTGAAATTTT
* *
4442435 GCCCAGGCCCGGCCCGG
1 GCCCGGGCCCAGCCCGG
4442452 GAAAAATATC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.12, C:0.42, G:0.32, T:0.14
Consensus pattern (28 bp):
GCCCGGGCCCAGCCCGGCCTGAAATTTT
Found at i:4442510 original size:26 final size:26
Alignment explanation
Indices: 4442475--4442526 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
4442465 AGCCCGACCC
* * *
4442475 ATTTTTAAAATAAACATTAAAAAATT
1 ATTTTAAAAATAAAAAATAAAAAATT
4442501 ATTTTAAAAATAAAAAATAAAAAATT
1 ATTTTAAAAATAAAAAATAAAAAATT
4442527 TTAAAAGTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (26 bp):
ATTTTAAAAATAAAAAATAAAAAATT
Found at i:4442520 original size:33 final size:32
Alignment explanation
Indices: 4442481--4442574 Score: 89
Period size: 34 Copynumber: 2.8 Consensus size: 32
4442471 ACCCATTTTT
4442481 AAAATAAACATTAAAAAATTATTTTAAAAATAA
1 AAAATAAA-ATTAAAAAATTATTTTAAAAATAA
** * * *
4442514 AAAATAAAAAATTTTAAAAGTATTTTAAAATTTA
1 AAAAT--AAAATTAAAAAATTATTTTAAAAATAA
*
4442548 AAAATAAAAATAAAAAATATATATTTA
1 AAAATAAAATTAAAAAAT-TAT-TTTA
4442575 TTATATTCGG
Statistics
Matches: 48, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
32 9 0.19
33 8 0.17
34 28 0.58
35 3 0.06
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.33
Consensus pattern (32 bp):
AAAATAAAATTAAAAAATTATTTTAAAAATAA
Found at i:4443116 original size:21 final size:22
Alignment explanation
Indices: 4443086--4443127 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
4443076 TTTTAATATT
*
4443086 TTTTATTTTTTAAAA-TAATTC
1 TTTTAATTTTTAAAATTAATTC
4443107 TTTTAATTTTTAAAATTAATT
1 TTTTAATTTTTAAAATTAATT
4443128 AATTGATGAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (22 bp):
TTTTAATTTTTAAAATTAATTC
Found at i:4443482 original size:35 final size:35
Alignment explanation
Indices: 4443432--4443503 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
4443422 AAATACTCAC
4443432 AATCTTATATAGATCAAGAATAATGTATAAAAATG
1 AATCTTATATAGATCAAGAATAATGTATAAAAATG
*
4443467 AATCTTATATTGATCAAGAATAATGTATAAAAATG
1 AATCTTATATAGATCAAGAATAATGTATAAAAATG
4443502 AA
1 AA
4443504 GGTTTATCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.51, C:0.06, G:0.11, T:0.32
Consensus pattern (35 bp):
AATCTTATATAGATCAAGAATAATGTATAAAAATG
Found at i:4447118 original size:24 final size:24
Alignment explanation
Indices: 4447091--4447141 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 24
4447081 TTTGGAGAAT
4447091 TTTGTGTTT-ACGTTTTGAGGG-TTA
1 TTTGT-TTTGACGTTTTG-GGGTTTA
*
4447115 TTTGTTTTGAGGTTTTGGGGTTTA
1 TTTGTTTTGACGTTTTGGGGTTTA
4447139 TTT
1 TTT
4447142 TTTATTTTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
23 6 0.25
24 18 0.75
ACGTcount: A:0.10, C:0.02, G:0.29, T:0.59
Consensus pattern (24 bp):
TTTGTTTTGACGTTTTGGGGTTTA
Found at i:4448077 original size:42 final size:43
Alignment explanation
Indices: 4448021--4448141 Score: 145
Period size: 42 Copynumber: 2.8 Consensus size: 43
4448011 TTCCAATATG
*
4448021 TGATTTCGTGTAAGACCATGTCTGGGACATTGGCATC-GTATA
1 TGATTACGTGTAAGACCATGTCTGGGACATTGGCATCAGTATA
* * * *
4448063 TGATTACGTGTAAGACCCTGTCTGGGACAGTGGCATCATTATT
1 TGATTACGTGTAAGACCATGTCTGGGACATTGGCATCAGTATA
* * * **
4448106 TGATTGCATGTAAGACCACGTCTGGGATGTTGGCAT
1 TGATTACGTGTAAGACCATGTCTGGGACATTGGCAT
4448142 TATTCGAGCT
Statistics
Matches: 66, Mismatches: 12, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
42 34 0.52
43 32 0.48
ACGTcount: A:0.23, C:0.17, G:0.27, T:0.32
Consensus pattern (43 bp):
TGATTACGTGTAAGACCATGTCTGGGACATTGGCATCAGTATA
Found at i:4448140 original size:43 final size:42
Alignment explanation
Indices: 4448029--4448141 Score: 115
Period size: 43 Copynumber: 2.7 Consensus size: 42
4448019 TGTGATTTCG
* *
4448029 TGTAAGACCATGTCTGGGACA-TTGGCATCGTATATGATTACG
1 TGTAAGACCACGTCTGGGA-AGTTGGCATCGTATATGATTACA
* * *
4448071 TGTAAGACC-CTGTCTGGGACAG-TGGCATCATTATTTGATTGCA
1 TGTAAGACCAC-GTCTGGGA-AGTTGGCATC-GTATATGATTACA
*
4448114 TGTAAGACCACGTCTGGGATGTTGGCAT
1 TGTAAGACCACGTCTGGGAAGTTGGCAT
4448142 TATTCGAGCT
Statistics
Matches: 60, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
42 27 0.45
43 32 0.53
44 1 0.02
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.31
Consensus pattern (42 bp):
TGTAAGACCACGTCTGGGAAGTTGGCATCGTATATGATTACA
Found at i:4455206 original size:22 final size:22
Alignment explanation
Indices: 4455154--4455195 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
4455144 TATGATTTTT
4455154 AAAAAA-AATATATTGATTAAC
1 AAAAAATAATATATTGATTAAC
4455175 AAAAAATAATATATTGATTAA
1 AAAAAATAATATATTGATTAA
4455196 TGGAAAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.31
Consensus pattern (22 bp):
AAAAAATAATATATTGATTAAC
Found at i:4455252 original size:22 final size:19
Alignment explanation
Indices: 4455203--4455253 Score: 50
Period size: 22 Copynumber: 2.5 Consensus size: 19
4455193 TAATGGAAAA
4455203 TAATTTTTTTAAAAATAAC
1 TAATTTTTTTAAAAATAAC
*
4455222 T-TTTCTTTTTAAAAAGCATAAC
1 TAATT-TTTTT-AAAA--ATAAC
4455244 TAATTTTTTT
1 TAATTTTTTT
4455254 TGAAAAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 7
0.74 0.06 0.21
Matches are distributed among these distances:
18 2 0.08
19 6 0.24
20 4 0.16
22 11 0.44
23 2 0.08
ACGTcount: A:0.37, C:0.08, G:0.02, T:0.53
Consensus pattern (19 bp):
TAATTTTTTTAAAAATAAC
Found at i:4461245 original size:54 final size:54
Alignment explanation
Indices: 4461143--4461250 Score: 173
Period size: 54 Copynumber: 2.0 Consensus size: 54
4461133 CTAAGTTGTC
* *
4461143 GGGCTTGGTGTGTGGAGGAGATGGGAAAGAGGTGGTTGCTGCCACGGGCGGCGG
1 GGGCTTGGTATGTGGAGGAGATGGGAAAGAGGTGGTTGCTACCACGGGCGGCGG
*
4461197 GGGCTTGGTATGTGGAGGAGATGGGAAAGAGGTGGTTGGTA-CACCGGGCGGCGG
1 GGGCTTGGTATGTGGAGGAGATGGGAAAGAGGTGGTTGCTACCA-CGGGCGGCGG
4461251 AGCTGGGACA
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
53 2 0.04
54 48 0.96
ACGTcount: A:0.17, C:0.12, G:0.53, T:0.19
Consensus pattern (54 bp):
GGGCTTGGTATGTGGAGGAGATGGGAAAGAGGTGGTTGCTACCACGGGCGGCGG
Found at i:4462026 original size:43 final size:43
Alignment explanation
Indices: 4461978--4462064 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
4461968 AATGGTGTCT
4461978 TCGTAGCATATTTTGACCTAATTTTCTCATCCGTCCAAATAAC
1 TCGTAGCATATTTTGACCTAATTTTCTCATCCGTCCAAATAAC
4462021 TCGTAGCATATTTTGACCTAATTTTCTCATCCGTCCAAATAAC
1 TCGTAGCATATTTTGACCTAATTTTCTCATCCGTCCAAATAAC
4462064 T
1 T
4462065 TACTTAAAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.28, C:0.25, G:0.09, T:0.38
Consensus pattern (43 bp):
TCGTAGCATATTTTGACCTAATTTTCTCATCCGTCCAAATAAC
Found at i:4462786 original size:7 final size:7
Alignment explanation
Indices: 4462774--4462803 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
4462764 AAAGTATTTT
4462774 AAAATTA
1 AAAATTA
4462781 AAAATTA
1 AAAATTA
4462788 AAAATTA
1 AAAATTA
4462795 AAAA-TA
1 AAAATTA
4462801 AAA
1 AAA
4462804 TATATATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 5 0.22
7 18 0.78
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (7 bp):
AAAATTA
Found at i:4477892 original size:20 final size:20
Alignment explanation
Indices: 4477867--4477916 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
4477857 TGGCTTAAAA
4477867 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
4477887 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
4477904 GTGGTAGTGGATT
1 TTGGTAGTGGATT
4477917 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:4482531 original size:20 final size:20
Alignment explanation
Indices: 4482506--4482555 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
4482496 TGGCTTAAAA
4482506 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
4482526 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
4482543 GTGGTAGTGGATT
1 TTGGTAGTGGATT
4482556 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:4484945 original size:23 final size:23
Alignment explanation
Indices: 4484919--4484970 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
4484909 AATTAAAAAG
4484919 ATGAAAGCAT-TATAGCTATCATT
1 ATGAAAGCATAT-TAGCTATCATT
*
4484942 ATGAAAGCATATTAGCTATTATT
1 ATGAAAGCATATTAGCTATCATT
4484965 ATGAAA
1 ATGAAA
4484971 CCAAGTTGCA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.35
Consensus pattern (23 bp):
ATGAAAGCATATTAGCTATCATT
Found at i:4493003 original size:8 final size:8
Alignment explanation
Indices: 4492990--4493017 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
4492980 CGTTTATTTT
4492990 AAATATTA
1 AAATATTA
4492998 AAATATTA
1 AAATATTA
4493006 AAATATTA
1 AAATATTA
4493014 AAAT
1 AAAT
4493018 CTAATATTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (8 bp):
AAATATTA
Found at i:4493436 original size:18 final size:17
Alignment explanation
Indices: 4493396--4493443 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
4493386 TATTATTAAG
*
4493396 TTTA-TATAAGATATTA
1 TTTATTATAAAATATTA
4493412 TTTATTATAAAATATTA
1 TTTATTATAAAATATTA
*
4493429 TCTTATTAAAAAATA
1 T-TTATTATAAAATA
4493444 AATTTTGATT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
16 4 0.14
17 12 0.43
18 12 0.43
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (17 bp):
TTTATTATAAAATATTA
Found at i:4506063 original size:29 final size:27
Alignment explanation
Indices: 4505998--4506073 Score: 73
Period size: 29 Copynumber: 2.7 Consensus size: 27
4505988 ATTTAAAATT
4505998 TTATAAAAAGTA-TAAAATCATAAAAA
1 TTATAAAAAGTATTAAAATCATAAAAA
*
4506024 TAATATAAAAAAGTATTAAAATTGATATAAAA
1 T--TAT-AAAAAGTATTAAAA-TCATA-AAAA
* *
4506056 TTATAAAAATTATAAAAA
1 TTATAAAAAGTATTAAAA
4506074 AATCGCAATA
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
26 1 0.02
28 3 0.07
29 20 0.49
30 8 0.20
31 4 0.10
32 5 0.12
ACGTcount: A:0.64, C:0.01, G:0.04, T:0.30
Consensus pattern (27 bp):
TTATAAAAAGTATTAAAATCATAAAAA
Found at i:4506073 original size:9 final size:9
Alignment explanation
Indices: 4505908--4506073 Score: 88
Period size: 9 Copynumber: 17.4 Consensus size: 9
4505898 AAAATATAAG
4505908 AAAATTGATA
1 AAAATT-ATA
4505918 TAAAATTATA
1 -AAAATTATA
* *
4505928 AATATTTTA
1 AAAATTATA
*
4505937 AATATTATA
1 AAAATTATA
4505946 AAAATCTA-A
1 AAAAT-TATA
*
4505955 GAAATTAT-
1 AAAATTATA
4505963 AAAA-TATA
1 AAAATTATA
*
4505971 TAATATTAATA
1 -AAAATT-ATA
*
4505982 AAATATATTTA
1 AAA-AT-TATA
*
4505993 AAATTTTATA
1 AAA-ATTATA
*
4506003 AAAAGTAT-
1 AAAATTATA
*
4506011 AAAATCATA
1 AAAATTATA
4506020 AAAATAATATAA
1 AAAAT--TAT-A
* *
4506032 AAAAGTATT
1 AAAATTATA
4506041 AAAATTGATA
1 AAAATT-ATA
4506051 TAAAATTATA
1 -AAAATTATA
4506061 AAAATTATA
1 AAAATTATA
4506070 AAAA
1 AAAA
4506074 AATCGCAATA
Statistics
Matches: 121, Mismatches: 20, Indels: 30
0.71 0.12 0.18
Matches are distributed among these distances:
7 3 0.02
8 11 0.09
9 53 0.44
10 22 0.18
11 26 0.21
12 6 0.05
ACGTcount: A:0.61, C:0.01, G:0.03, T:0.35
Consensus pattern (9 bp):
AAAATTATA
Found at i:4506553 original size:27 final size:28
Alignment explanation
Indices: 4506505--4506578 Score: 82
Period size: 27 Copynumber: 2.7 Consensus size: 28
4506495 GTTTATATCA
* * *
4506505 ATTTTTATTTTTTTTTATTTTTAAA-A-
1 ATTTTAATATTTTTTTAATTTTAAATAG
4506531 ATTTTAATACTTTTTTTAATTTTAAATAG
1 ATTTTAATA-TTTTTTTAATTTTAAATAG
*
4506560 GTTTTAATA-TTTTTTAATT
1 ATTTTAATATTTTTTTAATT
4506579 ATTATATTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
26 7 0.17
27 25 0.61
28 1 0.02
29 8 0.20
ACGTcount: A:0.30, C:0.01, G:0.03, T:0.66
Consensus pattern (28 bp):
ATTTTAATATTTTTTTAATTTTAAATAG
Found at i:4506613 original size:26 final size:25
Alignment explanation
Indices: 4506571--4506632 Score: 65
Period size: 26 Copynumber: 2.5 Consensus size: 25
4506561 TTTTAATATT
* *
4506571 TTTTAATTA-TTATATTTTTTAT-A
1 TTTTAAATATTTATATTTTATATCA
4506594 TTTTAAAATATTTATAATTTTATATCA
1 TTTT-AAATATTTAT-ATTTTATATCA
*
4506621 TTTTTAATATTT
1 TTTTAAATATTT
4506633 TACCATTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
23 4 0.12
24 4 0.12
25 4 0.12
26 15 0.47
27 5 0.16
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.65
Consensus pattern (25 bp):
TTTTAAATATTTATATTTTATATCA
Found at i:4506644 original size:36 final size:33
Alignment explanation
Indices: 4506561--4506649 Score: 90
Period size: 36 Copynumber: 2.6 Consensus size: 33
4506551 TTTAAATAGG
*
4506561 TTTTAATATTTTT-TAATTATTATATTTTTTATA
1 TTTTAAAATTTTTATAATT-TTATATTTTTTATA
*
4506594 TTTTAAAATATTTATAATTTTATATCATTTTTAATA
1 TTTTAAAATTTTTATAATTTTATAT--TTTTT-ATA
** *
4506630 TTTTACCATTTTTATGATTT
1 TTTTAAAATTTTTATAATTT
4506650 GTTAATAATT
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
33 17 0.37
34 5 0.11
35 5 0.11
36 19 0.41
ACGTcount: A:0.31, C:0.03, G:0.01, T:0.64
Consensus pattern (33 bp):
TTTTAAAATTTTTATAATTTTATATTTTTTATA
Found at i:4510018 original size:11 final size:11
Alignment explanation
Indices: 4510004--4510028 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
4509994 AAATTGATAT
4510004 AAAATTATAAA
1 AAAATTATAAA
4510015 AAAATTATAAA
1 AAAATTATAAA
4510026 AAA
1 AAA
4510029 TCGTAAGAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (11 bp):
AAAATTATAAA
Found at i:4510026 original size:9 final size:9
Alignment explanation
Indices: 4509853--4510027 Score: 77
Period size: 9 Copynumber: 18.1 Consensus size: 9
4509843 TAGTTTTTCC
*
4509853 ATTAAAAAA
1 ATTATAAAA
*
4509862 ATTTTAAAA
1 ATTATAAAA
*
4509871 ATTATAAAT
1 ATTATAAAA
4509880 ATT-TCAAAA
1 ATTAT-AAAA
*
4509889 AATATAAAA
1 ATTATAAAA
*
4509898 AATATAAGAA
1 ATTATAA-AA
4509908 ATTAT-AAA
1 ATTATAAAA
*
4509916 ATATATATAAT
1 AT-TATA-AAA
4509927 ATTAATAAAA
1 ATT-ATAAAA
*
4509937 CATATTTAAAA
1 -AT-TATAAAA
*
4509948 TTTTATAAAA
1 -ATTATAAAA
**
4509958 CGTAT-AAA
1 ATTATAAAA
*
4509966 ATCATAAAA
1 ATTATAAAA
4509975 ATAATATAAAA
1 AT--TATAAAA
* *
4509986 AGGTATTAAA
1 A-TTATAAAA
4509996 ATTGATATAAA
1 ATT-ATA-AAA
4510007 ATTATAAAAAA
1 ATTAT--AAAA
4510018 ATTATAAAA
1 ATTATAAAA
4510027 A
1 A
4510028 ATCGTAAGAA
Statistics
Matches: 126, Mismatches: 23, Indels: 34
0.69 0.13 0.19
Matches are distributed among these distances:
8 10 0.08
9 51 0.40
10 27 0.21
11 36 0.29
12 2 0.02
ACGTcount: A:0.62, C:0.02, G:0.03, T:0.33
Consensus pattern (9 bp):
ATTATAAAA
Found at i:4510388 original size:28 final size:26
Alignment explanation
Indices: 4510357--4510527 Score: 90
Period size: 28 Copynumber: 6.4 Consensus size: 26
4510347 TATTTTTGTA
4510357 ATTTTTATAAGTTTATATCAATTTTAAT
1 ATTTTTATAA-TTTATAT-AATTTTAAT
* * *
4510385 ATTTTTTATTATTTTTAAAAATTTTAAT
1 A-TTTTTATAATTTAT-ATAATTTTAAT
* * *
4510413 ATGTTTTTTAATTTTAAATAGGTTTTAAT
1 AT-TTTTATAA-TTTATATA-ATTTTAAT
4510442 ATTTTT-TAA-TTAT-TATATTTT-AT
1 ATTTTTATAATTTATATA-ATTTTAAT
*
4510465 A-TTTTACAATTT-TAATAATTTTATAT
1 ATTTTTATAATTTAT-ATAATTTTA-AT
*
4510491 CATTTTTA-ATATTT-TATAATTTTTAT
1 -ATTTTTATA-ATTTATATAATTTTAAT
4510517 GATTTTT-TAAT
1 -ATTTTTATAAT
4510528 AATTTTTATG
Statistics
Matches: 113, Mismatches: 15, Indels: 33
0.70 0.09 0.20
Matches are distributed among these distances:
22 4 0.04
23 6 0.05
24 13 0.12
25 7 0.06
26 11 0.10
27 14 0.12
28 37 0.33
29 21 0.19
ACGTcount: A:0.33, C:0.02, G:0.03, T:0.62
Consensus pattern (26 bp):
ATTTTTATAATTTATATAATTTTAAT
Found at i:4510446 original size:27 final size:25
Alignment explanation
Indices: 4510376--4510527 Score: 96
Period size: 27 Copynumber: 5.8 Consensus size: 25
4510366 AGTTTATATC
4510376 AATTTTAATATTTTTTATTATTTTTAAA
1 AATTTTAATATTTTTTA--A-TTTTAAA
4510404 AATTTTAATATGTTTTTTAATTTTAAA
1 AATTTTAATA--TTTTTTAATTTTAAA
*
4510431 TAGGTTTTAATATTTTTTAATTATT--A
1 -A-ATTTTAATATTTTTTAATT-TTAAA
* ** *
4510457 TATTTT-ATATTTTACAATTTTAAT
1 AATTTTAATATTTTTTAATTTTAAA
* *
4510481 AATTTT-ATATCATTTTTAATATTTTAT
1 AATTTTAATAT--TTTTTAAT-TTTAAA
*
4510508 AATTTTTATGATTTTTTAAT
1 AATTTTAAT-ATTTTTTAAT
4510528 AATTTTTATG
Statistics
Matches: 102, Mismatches: 10, Indels: 25
0.74 0.07 0.18
Matches are distributed among these distances:
22 2 0.02
23 11 0.11
24 13 0.13
26 7 0.07
27 36 0.35
28 16 0.16
29 10 0.10
30 7 0.07
ACGTcount: A:0.34, C:0.01, G:0.03, T:0.62
Consensus pattern (25 bp):
AATTTTAATATTTTTTAATTTTAAA
Found at i:4510500 original size:17 final size:17
Alignment explanation
Indices: 4510377--4510535 Score: 76
Period size: 19 Copynumber: 8.9 Consensus size: 17
4510367 GTTTATATCA
* *
4510377 ATTTTAATATTTTTTATT
1 ATTTT-ATAATTTTTAAT
* *
4510395 ATTTTTAAAAATTTTAAT
1 A-TTTTATAATTTTTAAT
* *
4510413 ATGTTTTTTAATTTTAAAT
1 A--TTTTATAATTTTTAAT
*
4510432 AGGTTTTAATATTTTTTAAT
1 A--TTTT-ATAATTTTTAAT
*
4510452 -TATTAT-A-TTTT-AT
1 ATTTTATAATTTTTAAT
*
4510465 ATTTTACAA-TTTTAAT
1 ATTTTATAATTTTTAAT
4510481 AATTTTATATCATTTTTAAT
1 -ATTTTATA--ATTTTTAAT
4510501 ATTTTATAATTTTTATGAT
1 ATTTTATAATTTTTA--AT
*
4510520 TTTTTAATAATTTTTA
1 ATTTT-ATAATTTTTA
4510536 TGGGAAACAT
Statistics
Matches: 109, Mismatches: 19, Indels: 24
0.72 0.12 0.16
Matches are distributed among these distances:
13 2 0.02
14 8 0.07
15 5 0.05
16 4 0.04
17 17 0.16
18 10 0.09
19 37 0.34
20 26 0.24
ACGTcount: A:0.33, C:0.01, G:0.03, T:0.63
Consensus pattern (17 bp):
ATTTTATAATTTTTAAT
Found at i:4521420 original size:10 final size:9
Alignment explanation
Indices: 4521390--4521475 Score: 59
Period size: 10 Copynumber: 8.9 Consensus size: 9
4521380 ATATTTATAC
*
4521390 TTTTATACT
1 TTTTATAAT
4521399 TTTCTATAAAT
1 TTT-TAT-AAT
*
4521410 TTTGTCTAAT
1 TTT-TATAAT
4521420 TTTTATAATT
1 TTTTATAA-T
4521430 TTTTGATAA-
1 TTTT-ATAAT
4521439 TTTT-TAAT
1 TTTTATAAT
*
4521447 TCTTTAAAAAT
1 T-TTT-ATAAT
4521458 TTTATATAAT
1 TTT-TATAAT
4521468 TTTTATAA
1 TTTTATAA
4521476 AAAAATAATA
Statistics
Matches: 62, Mismatches: 6, Indels: 18
0.72 0.07 0.21
Matches are distributed among these distances:
7 3 0.05
8 1 0.02
9 19 0.31
10 23 0.37
11 16 0.26
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (9 bp):
TTTTATAAT
Found at i:4521560 original size:20 final size:20
Alignment explanation
Indices: 4521537--4521578 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
4521527 GCATGTCACG
4521537 TGTCATTATCATATGTTGTT
1 TGTCATTATCATATGTTGTT
4521557 TGTCATTATCATATGTTGTT
1 TGTCATTATCATATGTTGTT
4521577 TG
1 TG
4521579 ACACATTGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.19, C:0.10, G:0.17, T:0.55
Consensus pattern (20 bp):
TGTCATTATCATATGTTGTT
Found at i:4524545 original size:12 final size:12
Alignment explanation
Indices: 4524528--4524577 Score: 52
Period size: 12 Copynumber: 4.4 Consensus size: 12
4524518 ACTTGATAGA
4524528 TAAAATAAAATT
1 TAAAATAAAATT
*
4524540 TAAAATATAATT
1 TAAAATAAAATT
**
4524552 TTTAA-AAAA--
1 TAAAATAAAATT
4524561 TAAAATAAAATT
1 TAAAATAAAATT
4524573 TAAAA
1 TAAAA
4524578 GATAATTCTA
Statistics
Matches: 29, Mismatches: 6, Indels: 6
0.71 0.15 0.15
Matches are distributed among these distances:
9 3 0.10
10 4 0.14
11 3 0.10
12 19 0.66
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (12 bp):
TAAAATAAAATT
Found at i:4524564 original size:33 final size:33
Alignment explanation
Indices: 4524527--4524598 Score: 117
Period size: 33 Copynumber: 2.2 Consensus size: 33
4524517 AACTTGATAG
* * *
4524527 ATAAAATAAAATTTAAAATATAATTTTTAAAAA
1 ATAAAATAAAATTTAAAAGATAATTCTAAAAAA
4524560 ATAAAATAAAATTTAAAAGATAATTCTAAAAAA
1 ATAAAATAAAATTTAAAAGATAATTCTAAAAAA
4524593 ATAAAA
1 ATAAAA
4524599 GAATATTATA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.67, C:0.01, G:0.01, T:0.31
Consensus pattern (33 bp):
ATAAAATAAAATTTAAAAGATAATTCTAAAAAA
Found at i:4527087 original size:17 final size:17
Alignment explanation
Indices: 4527065--4527098 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
4527055 ATATATTTTA
*
4527065 TAATTATTTAACTTAAT
1 TAATTATATAACTTAAT
*
4527082 TAATTATATAATTTAAT
1 TAATTATATAACTTAAT
4527099 AGCTAACAAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (17 bp):
TAATTATATAACTTAAT
Found at i:4527342 original size:18 final size:19
Alignment explanation
Indices: 4527308--4527343 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
4527298 CCTACATGAA
4527308 TTTAATTCAATTATATAAC
1 TTTAATTCAATTATATAAC
*
4527327 TTTAATTTAA-TATATAA
1 TTTAATTCAATTATATAA
4527344 ATTATTTCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (19 bp):
TTTAATTCAATTATATAAC
Found at i:4528140 original size:36 final size:36
Alignment explanation
Indices: 4528099--4528167 Score: 138
Period size: 36 Copynumber: 1.9 Consensus size: 36
4528089 AATATTAAGA
4528099 TAAACTCATCATAATATTTTAATTCAATATTGAATT
1 TAAACTCATCATAATATTTTAATTCAATATTGAATT
4528135 TAAACTCATCATAATATTTTAATTCAATATTGA
1 TAAACTCATCATAATATTTTAATTCAATATTGA
4528168 TTTTGCGTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.42, C:0.12, G:0.03, T:0.43
Consensus pattern (36 bp):
TAAACTCATCATAATATTTTAATTCAATATTGAATT
Found at i:4528153 original size:18 final size:18
Alignment explanation
Indices: 4528099--4528153 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
4528089 AATATTAAGA
4528099 TAAACTCATCATAATATT
1 TAAACTCATCATAATATT
* * *
4528117 TTAATTCA--ATATTGAATT
1 TAAACTCATCATAAT--ATT
4528135 TAAACTCATCATAATATT
1 TAAACTCATCATAATATT
4528153 T
1 T
4528154 TAATTCAATA
Statistics
Matches: 27, Mismatches: 6, Indels: 8
0.66 0.15 0.20
Matches are distributed among these distances:
16 4 0.15
18 19 0.70
20 4 0.15
ACGTcount: A:0.42, C:0.13, G:0.02, T:0.44
Consensus pattern (18 bp):
TAAACTCATCATAATATT
Found at i:4535367 original size:13 final size:13
Alignment explanation
Indices: 4535331--4535359 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
4535321 AAAAAATCAG
4535331 AAAATTTATAAAC
1 AAAATTTATAAAC
4535344 AAAATTTAT-AAC
1 AAAATTTATAAAC
4535356 AAAA
1 AAAA
4535360 AGTTATAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.44
13 9 0.56
ACGTcount: A:0.66, C:0.07, G:0.00, T:0.28
Consensus pattern (13 bp):
AAAATTTATAAAC
Found at i:4538835 original size:37 final size:37
Alignment explanation
Indices: 4538774--4538956 Score: 307
Period size: 37 Copynumber: 5.0 Consensus size: 37
4538764 TACGTATGAT
* *
4538774 CACTTATCAC-TTG-TCCCTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
4538809 CACCTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
4538846 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
4538883 CACTTATCACTTTGTTTCTTCATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
4538920 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
4538957 TAAAGCTATC
Statistics
Matches: 139, Mismatches: 7, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
35 9 0.06
36 3 0.02
37 127 0.91
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.38
Consensus pattern (37 bp):
CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
Found at i:4538973 original size:46 final size:46
Alignment explanation
Indices: 4538920--4539286 Score: 437
Period size: 46 Copynumber: 7.6 Consensus size: 46
4538910 TAAGTGTAGC
* * **
4538920 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
*
4538966 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
*
4539012 CACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
1 CACTTATCAC---T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
* *
4539064 CACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTAT
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
*
4539116 CACTTATCACTTTCTCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
*
4539162 CACTTATCACTTTATCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
* ** *
4539208 TACTTATCACTTTCCATTTGTCACTTGATCAGATAAGTATAGCTAAAGCTAC
1 CACTTATCA-----C-TTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
*
4539260 CACTTATCACTTTATCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
4539287 AGTACTCAAA
Statistics
Matches: 291, Mismatches: 17, Indels: 26
0.87 0.05 0.08
Matches are distributed among these distances:
46 154 0.53
47 1 0.00
49 1 0.00
50 1 0.00
51 4 0.01
52 130 0.45
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
Found at i:4539039 original size:52 final size:52
Alignment explanation
Indices: 4538963--4539280 Score: 426
Period size: 52 Copynumber: 6.3 Consensus size: 52
4538953 TAGCTAAAGC
* *
4538963 TATCACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACT
1 TATCACTTTTCAC-TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
4539016 TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
* * *
4539068 TATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
4539120 TATCAC-TTT--C---TCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
4539166 TATCAC-TTT-A----TCACTTGATCAGATAAGTATAGCCGAAGCTATTACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
* * ** *
4539212 TATCACTTTCCATTTGTCACTTGATCAGATAAGTATAGCTAAAGCTACCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
4539264 TATCACTTTATCACTTG
1 TATCACTTT-TCACTTG
4539281 ATCAGAAGTA
Statistics
Matches: 241, Mismatches: 16, Indels: 16
0.88 0.06 0.06
Matches are distributed among these distances:
46 84 0.35
47 2 0.01
48 1 0.00
49 1 0.00
51 2 0.01
52 134 0.56
53 17 0.07
ACGTcount: A:0.29, C:0.23, G:0.13, T:0.35
Consensus pattern (52 bp):
TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
Found at i:4539134 original size:98 final size:97
Alignment explanation
Indices: 4538920--4539286 Score: 427
Period size: 98 Copynumber: 3.8 Consensus size: 97
4538910 TAAGTGTAGC
* * * *
4538920 CACTTATCACTTT--GTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCAC--T-TTG
1 CACTTATCACTTTCCTTCACTTGATCAGATAAGTATAGCCAAAGCTATCACTTATCACTTTATTG
*
4538980 TCTCTTGATCAGATAAGTATAGCCGAAGCTAT
66 TCACTTGATCAGATAAGTATAGCCGAAGCTAT
* *
4539012 CACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTT
1 CACTTATCAC-TTTC-C-T-TCACTTGATCAGATAAGTATAGCCAAAGCTATCACTTATCACTTT
* *
4539077 CCACTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTAT
62 --A-TTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
*
4539116 CACTTATCACTTT-C-TCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTA---
1 CACTTATCACTTTCCTTCACTTGATCAGATAAGTATAGCCAAAGCTATCACTTATCACTTTATTG
4539176 TCACTTGATCAGATAAGTATAGCCGAAGCTAT
66 TCACTTGATCAGATAAGTATAGCCGAAGCTAT
* * *
4539208 TACTTATCACTTTCCATTTGTCACTTGATCAGATAAGTATAGCTAAAGCTACCACTTATCACTTT
1 CACTTATCACTTTCC---T-TCACTTGATCAGATAAGTATAGCCAAAGCTATCACTTATCACTTT
4539273 A---TCACTTGATCAGA
62 ATTGTCACTTGATCAGA
4539287 AGTACTCAAA
Statistics
Matches: 243, Mismatches: 14, Indels: 30
0.85 0.05 0.10
Matches are distributed among these distances:
92 52 0.21
93 4 0.02
96 1 0.00
98 139 0.57
100 1 0.00
101 1 0.00
103 3 0.01
104 42 0.17
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (97 bp):
CACTTATCACTTTCCTTCACTTGATCAGATAAGTATAGCCAAAGCTATCACTTATCACTTTATTG
TCACTTGATCAGATAAGTATAGCCGAAGCTAT
Found at i:4545420 original size:13 final size:13
Alignment explanation
Indices: 4545402--4545435 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
4545392 AAAATAAAAT
4545402 AAAAAGAAAAAGA
1 AAAAAGAAAAAGA
4545415 AAAAAGAAAAAGA
1 AAAAAGAAAAAGA
*
4545428 AGAAAGAA
1 AAAAAGAA
4545436 TGTTGTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (13 bp):
AAAAAGAAAAAGA
Found at i:4545424 original size:6 final size:6
Alignment explanation
Indices: 4545397--4545435 Score: 51
Period size: 6 Copynumber: 6.2 Consensus size: 6
4545387 AGATAAAAAT
*
4545397 AAAATA AAAAGA AAAAGAA AAAAGA AAAAGA AGAAAGA A
1 AAAAGA AAAAGA AAAAG-A AAAAGA AAAAGA A-AAAGA A
4545436 TGTTGTTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
6 18 0.60
7 12 0.40
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (6 bp):
AAAAGA
Found at i:4545687 original size:19 final size:18
Alignment explanation
Indices: 4545660--4545695 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
4545650 AAGAAGCGAG
*
4545660 TTTTTTTTTTATCTTTTTA
1 TTTTATTTTTAT-TTTTTA
4545679 TTTTATTTTTATTTTTT
1 TTTTATTTTTATTTTTT
4545696 GATAATTTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.11, C:0.03, G:0.00, T:0.86
Consensus pattern (18 bp):
TTTTATTTTTATTTTTTA
Found at i:4551100 original size:42 final size:42
Alignment explanation
Indices: 4551062--4551166 Score: 147
Period size: 42 Copynumber: 2.5 Consensus size: 42
4551052 GTAAGAGCAG
*
4551062 AACGGAAACCCATAAAGGTTCAACTGAAGCTCAAAAGAGTTA
1 AACGGAAACCCATAAAGGTTAAACTGAAGCTCAAAAGAGTTA
* *** *
4551104 AACGAAAACCCATTGGGGTTAAAGTGAAGCTCAAAAGAGTTA
1 AACGGAAACCCATAAAGGTTAAACTGAAGCTCAAAAGAGTTA
*
4551146 AACGGAAACCCATTAAGGTTA
1 AACGGAAACCCATAAAGGTTA
4551167 TAGTTAACTG
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 54 1.00
ACGTcount: A:0.44, C:0.17, G:0.21, T:0.18
Consensus pattern (42 bp):
AACGGAAACCCATAAAGGTTAAACTGAAGCTCAAAAGAGTTA
Found at i:4551166 original size:21 final size:21
Alignment explanation
Indices: 4551062--4551166 Score: 63
Period size: 21 Copynumber: 5.0 Consensus size: 21
4551052 GTAAGAGCAG
*
4551062 AACGGAAACCCATAAAGGTTC
1 AACGGAAACCCATAAAGGTTA
* * *
4551083 AACTGAAGCTCA-AAAGAGTTA
1 AACGGAAACCCATAAAG-GTTA
* ***
4551104 AACGAAAACCCATTGGGGTTA
1 AACGGAAACCCATAAAGGTTA
* *
4551125 AA-GTGAAGCTCA-AAAGAGTTA
1 AACG-GAAACCCATAAAG-GTTA
*
4551146 AACGGAAACCCATTAAGGTTA
1 AACGGAAACCCATAAAGGTTA
4551167 TAGTTAACTG
Statistics
Matches: 58, Mismatches: 20, Indels: 12
0.64 0.22 0.13
Matches are distributed among these distances:
20 6 0.10
21 47 0.81
22 5 0.09
ACGTcount: A:0.44, C:0.17, G:0.21, T:0.18
Consensus pattern (21 bp):
AACGGAAACCCATAAAGGTTA
Found at i:4551213 original size:32 final size:32
Alignment explanation
Indices: 4551172--4551243 Score: 135
Period size: 32 Copynumber: 2.2 Consensus size: 32
4551162 GGTTATAGTT
4551172 AACTGAAGCTCATGAGAACTAAACGAAAAGTA
1 AACTGAAGCTCATGAGAACTAAACGAAAAGTA
4551204 AACTGAAGCTCATGAGAACTAAACGAAAAGTA
1 AACTGAAGCTCATGAGAACTAAACGAAAAGTA
4551236 AACATGAA
1 AAC-TGAA
4551244 TGTTTGCAAC
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
32 35 0.90
33 4 0.10
ACGTcount: A:0.51, C:0.15, G:0.18, T:0.15
Consensus pattern (32 bp):
AACTGAAGCTCATGAGAACTAAACGAAAAGTA
Found at i:4554877 original size:12 final size:11
Alignment explanation
Indices: 4554832--4554857 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
4554822 ATTTTTTTAA
4554832 TTTTAAAATAT
1 TTTTAAAATAT
4554843 TTTTAAAATAT
1 TTTTAAAATAT
4554854 TTTT
1 TTTT
4554858 TTAATTTTAA
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:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:4557891 original size:24 final size:24
Alignment explanation
Indices: 4557857--4557908 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
4557847 TTTCTAGAAA
* *
4557857 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGCATTTATGAGCATAATAT
*
4557881 ATTTAGCATTTATTAGCATAATAT
1 ATTTAGCATTTATGAGCATAATAT
4557905 ATTT
1 ATTT
4557909 GAATTTGATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.37, C:0.04, G:0.10, T:0.50
Consensus pattern (24 bp):
ATTTAGCATTTATGAGCATAATAT
Found at i:4557919 original size:24 final size:24
Alignment explanation
Indices: 4557857--4557920 Score: 76
Period size: 24 Copynumber: 2.7 Consensus size: 24
4557847 TTTCTAGAAA
* * *
4557857 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGAATTTATTAGCATAATAT
*
4557881 ATTTAGCATTTATTAGCATAATAT
1 ATTTAGAATTTATTAGCATAATAT
4557905 ATTT-GAATTTGATTAG
1 ATTTAGAATTT-ATTAG
4557921 AATTAGATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
23 5 0.14
24 30 0.86
ACGTcount: A:0.36, C:0.03, G:0.12, T:0.48
Consensus pattern (24 bp):
ATTTAGAATTTATTAGCATAATAT
Found at i:4559393 original size:24 final size:24
Alignment explanation
Indices: 4559359--4559410 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
4559349 TTTCTAGAAG
* **
4559359 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGCATTTATGACCATAATAT
*
4559383 ATTTAGCATTTATTACCATAATAT
1 ATTTAGCATTTATGACCATAATAT
4559407 ATTT
1 ATTT
4559411 GGTTTTGATT
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:0.37, C:0.06, G:0.08, T:0.50
Consensus pattern (24 bp):
ATTTAGCATTTATGACCATAATAT
Found at i:4560193 original size:9 final size:9
Alignment explanation
Indices: 4560179--4560221 Score: 77
Period size: 9 Copynumber: 4.8 Consensus size: 9
4560169 TTTGGTTAAA
4560179 AATTACCCG
1 AATTACCCG
4560188 AATTACCCG
1 AATTACCCG
4560197 AATTACCCG
1 AATTACCCG
*
4560206 AATTAACCG
1 AATTACCCG
4560215 AATTACC
1 AATTACC
4560222 GAAAAATACC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
9 32 1.00
ACGTcount: A:0.37, C:0.30, G:0.09, T:0.23
Consensus pattern (9 bp):
AATTACCCG
Found at i:4561124 original size:26 final size:26
Alignment explanation
Indices: 4561095--4561144 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
4561085 ACCCTCTAAA
*
4561095 TTTAGTTTCT-TCAAGAATATTTTTTT
1 TTTA-TTTCTATCAAAAATATTTTTTT
*
4561121 TTTATTTTTATCAAAAATATTTTT
1 TTTATTTCTATCAAAAATATTTTT
4561145 AATATTATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 4 0.19
26 17 0.81
ACGTcount: A:0.28, C:0.06, G:0.04, T:0.62
Consensus pattern (26 bp):
TTTATTTCTATCAAAAATATTTTTTT
Found at i:4564650 original size:16 final size:16
Alignment explanation
Indices: 4564629--4564659 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
4564619 ATTTCCTAAT
*
4564629 AATAATTAATTAATGC
1 AATAATTAAATAATGC
4564645 AATAATTAAATAATG
1 AATAATTAAATAATG
4564660 AATTTTACTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.03, G:0.06, T:0.35
Consensus pattern (16 bp):
AATAATTAAATAATGC
Found at i:4567803 original size:24 final size:24
Alignment explanation
Indices: 4567776--4567827 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
4567766 TTAGTAAGTC
*
4567776 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
4567800 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
4567824 AAAT
1 AAAT
4567828 TTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:4568057 original size:30 final size:30
Alignment explanation
Indices: 4568023--4568085 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 30
4568013 ACTTAACAAG
*
4568023 CAAATACCTCTAAAATAATAACAAAACTAA
1 CAAATACATCTAAAATAATAACAAAACTAA
** * * *
4568053 CAAATGTATTTAAAATAATAATAAAATTAA
1 CAAATACATCTAAAATAATAACAAAACTAA
4568083 CAA
1 CAA
4568086 TAAAATAAGT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.60, C:0.13, G:0.02, T:0.25
Consensus pattern (30 bp):
CAAATACATCTAAAATAATAACAAAACTAA
Found at i:4571509 original size:31 final size:30
Alignment explanation
Indices: 4571468--4571557 Score: 85
Period size: 36 Copynumber: 2.9 Consensus size: 30
4571458 TTTACTATTA
*
4571468 AATATT-TATAAATTTTAAAATATATTTAT
1 AATATTATATAAATTTTAAAATATATTAAT
*
4571497 TATATTAATATAAATATTTTTCAATAATATATTAAT
1 AATATT-ATAT-AA-A-TTTT-AA-AATATATTAAT
*
4571533 AATATTATATAAAATTTAAAA-ATAT
1 AATATTATATAAATTTTAAAATATAT
4571558 CATTGTTAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 14
0.74 0.06 0.21
Matches are distributed among these distances:
29 9 0.18
30 2 0.04
31 5 0.10
32 5 0.10
33 2 0.04
34 6 0.12
35 6 0.12
36 15 0.30
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (30 bp):
AATATTATATAAATTTTAAAATATATTAAT
Found at i:4571579 original size:55 final size:55
Alignment explanation
Indices: 4571520--4571630 Score: 213
Period size: 55 Copynumber: 2.0 Consensus size: 55
4571510 ATATTTTTCA
4571520 ATAATATATTAATAATATTATATAAAATTTAAAAATATCATTGTTAAAATGTATT
1 ATAATATATTAATAATATTATATAAAATTTAAAAATATCATTGTTAAAATGTATT
*
4571575 ATAATATATTAATAATATTATATAAAATTTAAAAATATTATTGTTAAAATGTATT
1 ATAATATATTAATAATATTATATAAAATTTAAAAATATCATTGTTAAAATGTATT
4571630 A
1 A
4571631 GTAAAAGAAA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 55 1.00
ACGTcount: A:0.51, C:0.01, G:0.04, T:0.44
Consensus pattern (55 bp):
ATAATATATTAATAATATTATATAAAATTTAAAAATATCATTGTTAAAATGTATT
Found at i:4572113 original size:18 final size:17
Alignment explanation
Indices: 4572081--4572114 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
4572071 GTTGAAGATA
4572081 ATGATAATCTATATTAG
1 ATGATAATCTATATTAG
*
4572098 ATGATGAATGTATATTA
1 ATGAT-AATCTATATTA
4572115 TTTTTTATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.41, C:0.03, G:0.15, T:0.41
Consensus pattern (17 bp):
ATGATAATCTATATTAG
Found at i:4579039 original size:27 final size:27
Alignment explanation
Indices: 4578978--4579040 Score: 69
Period size: 27 Copynumber: 2.3 Consensus size: 27
4578968 ATTCTTCTCA
4578978 TATTTAA-AATTTAATCCATAACTTTT
1 TATTTAATAATTTAATCCATAACTTTT
*
4579004 TATTCTAATAATTTAGTCC-T-ACTCTTT
1 TATT-TAATAATTTAATCCATAACT-TTT
4579031 TGATTTAATA
1 T-ATTTAATA
4579041 TCATTTTAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
26 7 0.22
27 13 0.41
28 12 0.38
ACGTcount: A:0.33, C:0.13, G:0.03, T:0.51
Consensus pattern (27 bp):
TATTTAATAATTTAATCCATAACTTTT
Found at i:4579184 original size:29 final size:29
Alignment explanation
Indices: 4579152--4579217 Score: 78
Period size: 29 Copynumber: 2.3 Consensus size: 29
4579142 ACCAAAAAAA
*
4579152 GCCATTTTTTTCAAAATTTACCGAAATTG
1 GCCATTTTTTTCAAAATTTACCGAAATGG
* * ** *
4579181 GCCAATTTTTTGATTATTTACCGGAATGG
1 GCCATTTTTTTCAAAATTTACCGAAATGG
4579210 GCCATTTT
1 GCCATTTT
4579218 CTGCGAAATC
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.26, C:0.17, G:0.15, T:0.42
Consensus pattern (29 bp):
GCCATTTTTTTCAAAATTTACCGAAATGG
Found at i:4580910 original size:24 final size:24
Alignment explanation
Indices: 4580839--4580917 Score: 77
Period size: 24 Copynumber: 3.1 Consensus size: 24
4580829 TTCCTAATTG
*
4580839 TTATAATTTTTATATATTTTTTAAT
1 TTATAATTTTTAT-TATTTTTTAAA
* *
4580864 TTGAAAATTTAACCTATTATTTTTTAAA
1 TT-ATAATTT---TTATTATTTTTTAAA
*
4580892 TTATAATTTTTATTATTTTTAAAA
1 TTATAATTTTTATTATTTTTTAAA
4580916 TT
1 TT
4580918 TTAAAAAATA
Statistics
Matches: 44, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
24 15 0.34
25 2 0.05
26 6 0.14
27 6 0.14
28 12 0.27
29 3 0.07
ACGTcount: A:0.35, C:0.03, G:0.01, T:0.61
Consensus pattern (24 bp):
TTATAATTTTTATTATTTTTTAAA
Found at i:4581183 original size:34 final size:34
Alignment explanation
Indices: 4581140--4581212 Score: 119
Period size: 34 Copynumber: 2.1 Consensus size: 34
4581130 TAAAATAAAA
*
4581140 AAATTTGCTTATATACTTAATATTACAAGCATGG
1 AAATTTGCTTATATAATTAATATTACAAGCATGG
* *
4581174 AAATTTGCTTATATAATTAATATTACATGCATGT
1 AAATTTGCTTATATAATTAATATTACAAGCATGG
4581208 AAATT
1 AAATT
4581213 CAGAGAAGGA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.41
Consensus pattern (34 bp):
AAATTTGCTTATATAATTAATATTACAAGCATGG
Found at i:4583022 original size:20 final size:20
Alignment explanation
Indices: 4582992--4583029 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
4582982 TTTGTTTATT
4582992 TTTTCCAATTATATCATGTGA
1 TTTTCCAATTA-ATCATGTGA
4583013 TTTT-CAATTAATCATGT
1 TTTTCCAATTAATCATGT
4583030 TTAGTTAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 7 0.41
20 6 0.35
21 4 0.24
ACGTcount: A:0.29, C:0.13, G:0.08, T:0.50
Consensus pattern (20 bp):
TTTTCCAATTAATCATGTGA
Found at i:4589317 original size:21 final size:21
Alignment explanation
Indices: 4589293--4589366 Score: 62
Period size: 19 Copynumber: 3.3 Consensus size: 21
4589283 GTTTGATAAA
4589293 AAAATAAATTTTTTTATTTAT
1 AAAATAAATTTTTTTATTTAT
*
4589314 AAAAATAATTATTTTACTTGTTTTTAT
1 -AAAATAA--ATTTT--TT-TATTTAT
4589341 AAAATAAA--TTTTTATTTAT
1 AAAATAAATTTTTTTATTTAT
*
4589360 ATAATAA
1 AAAATAA
4589367 TATAGATAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 13
0.73 0.05 0.22
Matches are distributed among these distances:
19 12 0.27
20 2 0.05
22 9 0.20
24 6 0.14
26 9 0.20
27 6 0.14
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (21 bp):
AAAATAAATTTTTTTATTTAT
Found at i:4589505 original size:25 final size:26
Alignment explanation
Indices: 4589471--4589528 Score: 109
Period size: 25 Copynumber: 2.3 Consensus size: 26
4589461 CTTTGCACTA
4589471 TATCATAAAAACCCGTAGAATAC-TT
1 TATCATAAAAACCCGTAGAATACTTT
4589496 TATCATAAAAACCCGTAGAATACTTT
1 TATCATAAAAACCCGTAGAATACTTT
4589522 TATCATA
1 TATCATA
4589529 TAGAGTGTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
25 23 0.72
26 9 0.28
ACGTcount: A:0.43, C:0.19, G:0.07, T:0.31
Consensus pattern (26 bp):
TATCATAAAAACCCGTAGAATACTTT
Found at i:4590284 original size:14 final size:15
Alignment explanation
Indices: 4590265--4590294 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
4590255 TTTTATAATA
4590265 AAATCTATTT-TTAT
1 AAATCTATTTGTTAT
4590279 AAATCTATTTGTTAT
1 AAATCTATTTGTTAT
4590294 A
1 A
4590295 TTTCAGGTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.37, C:0.07, G:0.03, T:0.53
Consensus pattern (15 bp):
AAATCTATTTGTTAT
Found at i:4592830 original size:17 final size:17
Alignment explanation
Indices: 4592808--4592841 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
4592798 ATCCACTAAT
*
4592808 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
4592825 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
4592842 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:4597470 original size:17 final size:17
Alignment explanation
Indices: 4597448--4597481 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
4597438 ATCCACTAAT
*
4597448 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
4597465 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
4597482 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:4605754 original size:6 final size:6
Alignment explanation
Indices: 4605743--4605769 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
4605733 ACTAGTGTCT
4605743 ATTTTA ATTTTA ATTTTA ATTTTA ATT
1 ATTTTA ATTTTA ATTTTA ATTTTA ATT
4605770 AGATAAAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
ATTTTA
Found at i:4609747 original size:18 final size:18
Alignment explanation
Indices: 4609724--4609759 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
4609714 TTACTGCAGC
4609724 GGACAACTCGACCCGCGT
1 GGACAACTCGACCCGCGT
*
4609742 GGACAACTCGACCTGCGT
1 GGACAACTCGACCCGCGT
4609760 AGGGTAACCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.22, C:0.36, G:0.28, T:0.14
Consensus pattern (18 bp):
GGACAACTCGACCCGCGT
Found at i:4610998 original size:21 final size:21
Alignment explanation
Indices: 4610970--4611019 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
4610960 TAATTGTTAC
4610970 AATA-TTAAT-TGTATAAAAA
1 AATATTTAATATGTATAAAAA
*
4610989 AATACTTTAATATTTATAAAAA
1 AATA-TTTAATATGTATAAAAA
*
4611011 TATATTTAA
1 AATATTTAA
4611020 CATTTTAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
19 4 0.15
21 10 0.38
22 12 0.46
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (21 bp):
AATATTTAATATGTATAAAAA
Found at i:4611026 original size:22 final size:22
Alignment explanation
Indices: 4610981--4611024 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
4610971 ATATTAATTG
*
4610981 TATAAAAAAATACTTTAATATT
1 TATAAAAAAATACTTTAACATT
*
4611003 TATAAAAATATA-TTTAACATT
1 TATAAAAAAATACTTTAACATT
4611024 T
1 T
4611025 TAATTTAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (22 bp):
TATAAAAAAATACTTTAACATT
Found at i:4614574 original size:22 final size:22
Alignment explanation
Indices: 4614549--4614590 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
4614539 TCTCACATTA
*
4614549 GGTTTTTGATTTTTAGGGTTAG
1 GGTTTATGATTTTTAGGGTTAG
4614571 GGTTTATGATTTTTAGGGTT
1 GGTTTATGATTTTTAGGGTT
4614591 TTAGAGAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.14, C:0.00, G:0.31, T:0.55
Consensus pattern (22 bp):
GGTTTATGATTTTTAGGGTTAG
Found at i:4620169 original size:3 final size:3
Alignment explanation
Indices: 4620161--4620185 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
4620151 ATAAAGAAGG
4620161 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
4620186 GGATTAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:4620229 original size:5 final size:6
Alignment explanation
Indices: 4620210--4620267 Score: 62
Period size: 6 Copynumber: 9.2 Consensus size: 6
4620200 TTTGGAATTC
* *
4620210 AAATAA AAATAA AAATAA AACATTAC AAATAA AAATAA AAAGAAA AAATAA
1 AAATAA AAATAA AAATAA AA-A-TAA AAATAA AAATAA AAA-TAA AAATAA
*
4620261 ATATAA A
1 AAATAA A
4620268 CTAAATTGGT
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
6 33 0.75
7 7 0.16
8 4 0.09
ACGTcount: A:0.78, C:0.03, G:0.02, T:0.17
Consensus pattern (6 bp):
AAATAA
Found at i:4621521 original size:32 final size:32
Alignment explanation
Indices: 4621475--4621566 Score: 116
Period size: 32 Copynumber: 2.8 Consensus size: 32
4621465 CCGAATATAA
*
4621475 TAAATATATATTTTTTATTTTTAAAAATA-TTT
1 TAAA-ATATTTTTTTTATTTTTAAAAATATTTT
*
4621507 TAAAATACTTTTTTTTATTTTT-AAATTATTTT
1 TAAAATA-TTTTTTTTATTTTTAAAAATATTTT
4621539 TAAAATATTTTTTTTAATTTTCTAAAAA
1 TAAAATATTTTTTTT-ATTTT-TAAAAA
4621567 AAATTTTGGT
Statistics
Matches: 52, Mismatches: 3, Indels: 8
0.83 0.05 0.13
Matches are distributed among these distances:
31 16 0.31
32 32 0.62
33 1 0.02
34 3 0.06
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (32 bp):
TAAAATATTTTTTTTATTTTTAAAAATATTTT
Found at i:4621535 original size:11 final size:11
Alignment explanation
Indices: 4621521--4621550 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
4621511 ATACTTTTTT
4621521 TTATTTTTAAA
1 TTATTTTTAAA
4621532 TTATTTTTAAA
1 TTATTTTTAAA
*
4621543 ATATTTTT
1 TTATTTTT
4621551 TTTAATTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
TTATTTTTAAA
Found at i:4624573 original size:9 final size:9
Alignment explanation
Indices: 4624559--4624585 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
4624549 GGAACATTTA
4624559 TTTTAATAT
1 TTTTAATAT
4624568 TTTTAATAT
1 TTTTAATAT
4624577 TTTTAATAT
1 TTTTAATAT
4624586 ATTATAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (9 bp):
TTTTAATAT
Found at i:4624918 original size:40 final size:39
Alignment explanation
Indices: 4624861--4624937 Score: 111
Period size: 39 Copynumber: 1.9 Consensus size: 39
4624851 CATTAGGTAT
4624861 TTTATTAGTTTTCTTTTGTCCAAAAAAATTGAATAGGTTC
1 TTTATTAGTTTTCTTTTGT-CAAAAAAATTGAATAGGTTC
* *
4624901 TTTATTAGGTTTT-TTTTGTCTAAAAAATTGATTAGGT
1 TTTATTA-GTTTTCTTTTGTCAAAAAAATTGAATAGGT
4624938 GGTTGACTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
39 16 0.47
40 13 0.38
41 5 0.15
ACGTcount: A:0.29, C:0.06, G:0.14, T:0.51
Consensus pattern (39 bp):
TTTATTAGTTTTCTTTTGTCAAAAAAATTGAATAGGTTC
Found at i:4624937 original size:39 final size:40
Alignment explanation
Indices: 4624847--4624937 Score: 116
Period size: 40 Copynumber: 2.3 Consensus size: 40
4624837 TTGGAAGTAC
*
4624847 AATTCATTAGGTATTTTATTAGTTTTCTTTTGTCCAAAAA
1 AATTGATTAGGTATTTTATTAGTTTTCTTTTGTCCAAAAA
* *
4624887 AATTGAATAGGT-TCTTTATTAGGTTTT-TTTTGT-CTAAAA
1 AATTGATTAGGTAT-TTTATTA-GTTTTCTTTTGTCCAAAAA
4624926 AATTGATTAGGT
1 AATTGATTAGGT
4624938 GGTTGACTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
39 17 0.38
40 23 0.51
41 5 0.11
ACGTcount: A:0.30, C:0.07, G:0.14, T:0.49
Consensus pattern (40 bp):
AATTGATTAGGTATTTTATTAGTTTTCTTTTGTCCAAAAA
Found at i:4626847 original size:84 final size:84
Alignment explanation
Indices: 4626745--4626898 Score: 215
Period size: 84 Copynumber: 1.8 Consensus size: 84
4626735 TACAGTACAG
* * * * *
4626745 TTTTACTATATATTAATTTATAGTTTGTGTATTTAT-AAGAGGATTGAATTGAAATTTTTT-TTT
1 TTTTACTATACATTAATTTATAATTTCTCTATTTATGAA-AGGACTGAATTG--ATTTTTTATTT
4626808 -TTTTTTGAGGTTAAAGTGAAA
63 ATTTTTTGAGGTTAAAGTGAAA
4626829 TTTTACTATACATTAATTTATAATTTCTCTATTTATGAAAGGACTGAATTGATTTTTTATTTATT
1 TTTTACTATACATTAATTTATAATTTCTCTATTTATGAAAGGACTGAATTGATTTTTTATTTATT
4626894 TTTTG
66 TTTTG
4626899 GGACCAAAAC
Statistics
Matches: 62, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
82 7 0.11
83 3 0.05
84 50 0.81
85 2 0.03
ACGTcount: A:0.30, C:0.04, G:0.12, T:0.54
Consensus pattern (84 bp):
TTTTACTATACATTAATTTATAATTTCTCTATTTATGAAAGGACTGAATTGATTTTTTATTTATT
TTTTGAGGTTAAAGTGAAA
Found at i:4631606 original size:11 final size:10
Alignment explanation
Indices: 4631589--4631614 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
4631579 TAAGTGAAGG
4631589 GAAAAAAAAA
1 GAAAAAAAAA
4631599 GAAAAAAAAA
1 GAAAAAAAAA
4631609 GAAAAA
1 GAAAAA
4631615 CCCAAATACA
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:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (10 bp):
GAAAAAAAAA
Found at i:4638478 original size:10 final size:9
Alignment explanation
Indices: 4638463--4638557 Score: 55
Period size: 10 Copynumber: 9.7 Consensus size: 9
4638453 ATTAAAGTAC
4638463 ATAAAAAGTT
1 ATAAAAA-TT
*
4638473 ATAAAATTT
1 ATAAAAATT
*
4638482 AAAAAAATT
1 ATAAAAATT
*
4638491 ATTAAAAATA
1 A-TAAAAATT
*
4638501 ATAAAAAAGT
1 AT-AAAAATT
*
4638511 ATAAATATT
1 ATAAAAATT
4638520 AGTAAGAAATT
1 A-TAA-AAATT
* *
4638531 CTAAAAATC
1 ATAAAAATT
4638540 ATTAAAACTATT
1 A-TAAAA--ATT
4638552 ATAAAA
1 ATAAAA
4638558 TATTTTAGGA
Statistics
Matches: 64, Mismatches: 14, Indels: 13
0.70 0.15 0.14
Matches are distributed among these distances:
9 21 0.33
10 31 0.48
11 9 0.14
12 3 0.05
ACGTcount: A:0.62, C:0.03, G:0.04, T:0.31
Consensus pattern (9 bp):
ATAAAAATT
Found at i:4644593 original size:50 final size:50
Alignment explanation
Indices: 4644469--4644717 Score: 284
Period size: 50 Copynumber: 4.8 Consensus size: 50
4644459 GATAATAACA
* * ** * *
4644469 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGAT-GG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCAT-CTCGG
* *
4644520 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
4644570 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* *
4644620 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T-CGG
* *
4644675 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
4644718 TTACCCAAAT
Statistics
Matches: 170, Mismatches: 21, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
49 1 0.01
50 92 0.54
51 33 0.19
53 2 0.01
54 1 0.01
55 2 0.01
56 39 0.23
ACGTcount: A:0.20, C:0.29, G:0.24, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Done.