Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr2
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: 43198478
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2088848 characters in sequence are not A, C, G, or T
File 75 of 131
Found at i:25162655 original size:243 final size:243
Alignment explanation
Indices: 25162225--25162699 Score: 693
Period size: 243 Copynumber: 2.0 Consensus size: 243
25162215 TATTAACTTG
* * * * * *
25162225 ACTGGCATCGGAGTGCATCTTGACGTACAAGATGCATACCTGGCACACAAGGTGCATCTTGGCGC
1 ACTGGCATCGAAGTACATCCTGACGTACAAGACGCATACCTGGCACACAAGGTACAGCTTGGCGC
* * *
25162290 ACAAGCGTATATCTAGTACATGAAATGCATCCTGGCGTATAAGCACATAATCCCGTACTTAATCC
66 ACAAGCGTATATCTAGCACATGAAATGCATCCTGGCGTATAAGCACATAATCCCATACTCAATCC
* *
25162355 AATCCTATGGCATGCCAACTATATCCAACTCAATCCCACTAGTTAATATGATATCAAATTTCAAT
131 AATCCTATGACATGCCAACTATATCCAACTCAATCCCACTAGTTAATAGGATATCAAATTTCAAT
*
25162420 TCCATTTAAAATATAATACACATATCAATTTTTCAATGAACACACCAA
196 TCCATTTAAAATATAATACACATATCAAATTTTCAATGAACACACCAA
*
25162468 ACTGGCATCGAAGTACATCCTGACGTACAAGACGCATACCTGGCACACAAGGTACAGCTTGGTGC
1 ACTGGCATCGAAGTACATCCTGACGTACAAGACGCATACCTGGCACACAAGGTACAGCTTGGCGC
* * * *
25162533 ATAAGTGTATATCTAGCACATGAAATGCATCCTGGGGTATAAG-AGCATAATCTCATACTCAATC
66 ACAAGCGTATATCTAGCACATGAAATGCATCCTGGCGTATAAGCA-CATAATCCCATACTCAATC
* * * *
25162597 CACTCCTATGACATGCCAACTATATCCAACTCAA-CTCGACTAGTTAATAGGGTATCAAATTTTA
130 CAATCCTATGACATGCCAACTATATCCAACTCAATC-CCACTAGTTAATAGGATATCAAATTTCA
** * *
25162661 ATTCTGTTTAGAGTATAATACACATATCAAATTTTCAAT
194 ATTCCATTTAAAATATAATACACATATCAAATTTTCAAT
25162700 CCTATACACT
Statistics
Matches: 205, Mismatches: 25, Indels: 4
0.88 0.11 0.02
Matches are distributed among these distances:
242 2 0.01
243 203 0.99
ACGTcount: A:0.34, C:0.23, G:0.15, T:0.28
Consensus pattern (243 bp):
ACTGGCATCGAAGTACATCCTGACGTACAAGACGCATACCTGGCACACAAGGTACAGCTTGGCGC
ACAAGCGTATATCTAGCACATGAAATGCATCCTGGCGTATAAGCACATAATCCCATACTCAATCC
AATCCTATGACATGCCAACTATATCCAACTCAATCCCACTAGTTAATAGGATATCAAATTTCAAT
TCCATTTAAAATATAATACACATATCAAATTTTCAATGAACACACCAA
Found at i:25163656 original size:20 final size:20
Alignment explanation
Indices: 25163633--25163672 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
25163623 TTAATTAACA
*
25163633 TAATTAACCTTACTTTAATT
1 TAATAAACCTTACTTTAATT
*
25163653 TAATAAACCTTATTTTAATT
1 TAATAAACCTTACTTTAATT
25163673 AAGTTATTAA
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:0.38, C:0.12, G:0.00, T:0.50
Consensus pattern (20 bp):
TAATAAACCTTACTTTAATT
Found at i:25170351 original size:39 final size:40
Alignment explanation
Indices: 25170223--25170459 Score: 274
Period size: 40 Copynumber: 6.0 Consensus size: 40
25170213 AGTTGAAATA
*
25170223 CTATCGAGCCATACCTACTGAATCTACTGAAATGTATG-T
1 CTATCGAGCCATACCTACTGATTCTACTGAAATGTATGCT
* *
25170262 GCTATTGAGCCATACCTAATGAATT-TACTGAAATGTATGCGT
1 -CTATCGAGCCATACCTACTG-ATTCTACTGAAATGTATGC-T
* *
25170304 -TATTGAGCCATACCTACTGATTCTAATGAAA-GTATGCT
1 CTATCGAGCCATACCTACTGATTCTACTGAAATGTATGCT
* * * *
25170342 TTAGCGAGCCATACCTACGGAATT-TACTGAAATGTATGCG
1 CTATCGAGCCATACCTACTG-ATTCTACTGAAATGTATGCT
* *
25170382 CTATCAAGCCATACCTACTAATTCTACTGAAA-GTATGCT
1 CTATCGAGCCATACCTACTGATTCTACTGAAATGTATGCT
*
25170421 CTATCGAGCCATACCTACTGATTCTATTGAAA-GTA-GCT
1 CTATCGAGCCATACCTACTGATTCTACTGAAATGTATGCT
25170459 C
1 C
25170460 AAACGAGCAT
Statistics
Matches: 170, Mismatches: 19, Indels: 18
0.82 0.09 0.09
Matches are distributed among these distances:
38 5 0.03
39 73 0.43
40 89 0.52
41 2 0.01
42 1 0.01
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31
Consensus pattern (40 bp):
CTATCGAGCCATACCTACTGATTCTACTGAAATGTATGCT
Found at i:25170365 original size:79 final size:79
Alignment explanation
Indices: 25170223--25170438 Score: 308
Period size: 79 Copynumber: 2.7 Consensus size: 79
25170213 AGTTGAAATA
* * **
25170223 CTATCGAGCCATACCTACTGAATCTACTGAAATGTATG-TGCTATTGAGCCATACCTAATGAATT
1 CTATCGAGCCATACCTACTGATTCTACTGAAA-GTATGCT-CTATCGAGCCATACCTACGGAATT
25170287 TACTGAAATGTATGCG
64 TACTGAAATGTATGCG
* * * * *
25170303 TTATTGAGCCATACCTACTGATTCTAATGAAAGTATGCTTTAGCGAGCCATACCTACGGAATTTA
1 CTATCGAGCCATACCTACTGATTCTACTGAAAGTATGCTCTATCGAGCCATACCTACGGAATTTA
25170368 CTGAAATGTATGCG
66 CTGAAATGTATGCG
* *
25170382 CTATCAAGCCATACCTACTAATTCTACTGAAAGTATGCTCTATCGAGCCATACCTAC
1 CTATCGAGCCATACCTACTGATTCTACTGAAAGTATGCTCTATCGAGCCATACCTAC
25170439 TGATTCTATT
Statistics
Matches: 119, Mismatches: 16, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
79 90 0.76
80 29 0.24
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31
Consensus pattern (79 bp):
CTATCGAGCCATACCTACTGATTCTACTGAAAGTATGCTCTATCGAGCCATACCTACGGAATTTA
CTGAAATGTATGCG
Found at i:25172410 original size:24 final size:24
Alignment explanation
Indices: 25172378--25172435 Score: 98
Period size: 24 Copynumber: 2.4 Consensus size: 24
25172368 GCAAACAGTT
25172378 ATTAAACACTATTTGTTTGCTTTC
1 ATTAAACACTATTTGTTTGCTTTC
*
25172402 ATTAAACACTATTTGTTTGCTTTT
1 ATTAAACACTATTTGTTTGCTTTC
*
25172426 AGTAAACACT
1 ATTAAACACT
25172436 TAAGAAATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.29, C:0.16, G:0.09, T:0.47
Consensus pattern (24 bp):
ATTAAACACTATTTGTTTGCTTTC
Found at i:25175378 original size:29 final size:28
Alignment explanation
Indices: 25175346--25175410 Score: 69
Period size: 29 Copynumber: 2.2 Consensus size: 28
25175336 TATGAAAAAA
25175346 TATTATGAATATAAAGTTATAATTA-TAAT
1 TATTATGAATA-AAA-TTATAATTATTAAT
*
25175375 TATTTTATTAATAAAATTATAATTATTAAT
1 TA--TTATGAATAAAATTATAATTATTAAT
*
25175405 TCTTAT
1 TATTAT
25175411 AGTTATCATC
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
28 4 0.13
29 11 0.35
30 8 0.26
31 8 0.26
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.51
Consensus pattern (28 bp):
TATTATGAATAAAATTATAATTATTAAT
Found at i:25176923 original size:19 final size:18
Alignment explanation
Indices: 25176899--25176942 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
25176889 TAATGATTAC
25176899 TTAAATTAATTATATAAAA
1 TTAAATTAATTAT-TAAAA
**
25176918 TTAAATTTTTTATTAAAA
1 TTAAATTAATTATTAAAA
25176936 -TAAATTA
1 TTAAATTA
25176943 TATAAATACA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 6 0.27
18 5 0.23
19 11 0.50
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
TTAAATTAATTATTAAAA
Found at i:25177824 original size:26 final size:24
Alignment explanation
Indices: 25177772--25177817 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
25177762 AAGGTCAGTA
25177772 ATTCATATTTCTCTCTCTCTCTTT
1 ATTCATATTTCTCTCTCTCTCTTT
25177796 ATTCATATTTCTCTCTCTCTCT
1 ATTCATATTTCTCTCTCTCTCT
25177818 CTTTATTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.13, C:0.30, G:0.00, T:0.57
Consensus pattern (24 bp):
ATTCATATTTCTCTCTCTCTCTTT
Found at i:25187907 original size:17 final size:18
Alignment explanation
Indices: 25187876--25187909 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
25187866 AATTTAACTT
25187876 TAATTAAATTATTTAAAA
1 TAATTAAATTATTTAAAA
*
25187894 TAATT-AATTTTTTAAA
1 TAATTAAATTATTTAAA
25187910 TTATAAACAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TAATTAAATTATTTAAAA
Found at i:25188173 original size:21 final size:21
Alignment explanation
Indices: 25188114--25188173 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 21
25188104 CCGAACCCCG
*
25188114 AGATTTAAGGTTT-GGGTTTA
1 AGATTTAAGGTTTAGGGTTGA
*
25188134 AGATTTAAGATTTTA-GGTTCGA
1 AGATTTAAG-GTTTAGGGTT-GA
25188156 A-ATTTAAGGTTTAGGGTT
1 AGATTTAAGGTTTAGGGTT
25188174 ATGAATTATG
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
20 13 0.39
21 18 0.55
22 2 0.06
ACGTcount: A:0.28, C:0.02, G:0.27, T:0.43
Consensus pattern (21 bp):
AGATTTAAGGTTTAGGGTTGA
Found at i:25190965 original size:3 final size:3
Alignment explanation
Indices: 25190957--25191000 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
25190947 TTGCTATAAA
25190957 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
25191001 AGTGTAGAGT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:25196878 original size:2 final size:2
Alignment explanation
Indices: 25196862--25196900 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
25196852 NNNCGAATGC
* *
25196862 AT AT AT GT AT TT 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 A
25196901 AGTTTTTGAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
AT
Found at i:25197295 original size:75 final size:75
Alignment explanation
Indices: 25197158--25197297 Score: 167
Period size: 75 Copynumber: 1.9 Consensus size: 75
25197148 CTTACATATA
* * * * * **
25197158 TGTATATGTTCTTTTATTGAATTTAGGTAGGACATTTATATAAGTTTATATGAGGTTTGATTATG
1 TGTATATGTTCTTGTAATGAATTTAAGTAGGAAATTTATATAAGTGTATATGAAATTTGATTATG
25197223 CAAGATTATG
66 CAAGATTATG
* *
25197233 TGTATATGTTCTTGTAATGAATTTAAGTATGAAATTTATAT-A-TGTATGTGAAAATTTCGATTA
1 TGTATATGTTCTTGTAATGAATTTAAGTAGGAAATTTATATAAGTGTATATG-AAATTT-GATTA
25197296 TG
64 TG
25197298 TATGTATATT
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
73 6 0.11
74 5 0.09
75 43 0.80
ACGTcount: A:0.31, C:0.04, G:0.19, T:0.46
Consensus pattern (75 bp):
TGTATATGTTCTTGTAATGAATTTAAGTAGGAAATTTATATAAGTGTATATGAAATTTGATTATG
CAAGATTATG
Found at i:25197454 original size:41 final size:41
Alignment explanation
Indices: 25197384--25197500 Score: 121
Period size: 41 Copynumber: 2.9 Consensus size: 41
25197374 GAATGTAATA
* *
25197384 CAGACTTCACGTCTAGCAGGCT-TGATGCCGGTGA-AAGAATT
1 CAGACTTTACGTCTAGCAGGCTAAG-TGCCGGTGATAAGAA-T
**
25197425 CAGACTTTACGTCTAGCAGGCTAAGTGCCGGTGATCTGAAT
1 CAGACTTTACGTCTAGCAGGCTAAGTGCCGGTGATAAGAAT
* * * * *
25197466 CAGGCTATAAGCCTAGCAGGCTAAGCGCCGGTGAT
1 CAGACTTTACGTCTAGCAGGCTAAGTGCCGGTGAT
25197501 CTGAATATGT
Statistics
Matches: 65, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
41 61 0.94
42 4 0.06
ACGTcount: A:0.26, C:0.23, G:0.28, T:0.23
Consensus pattern (41 bp):
CAGACTTTACGTCTAGCAGGCTAAGTGCCGGTGATAAGAAT
Found at i:25199343 original size:9 final size:9
Alignment explanation
Indices: 25199329--25199355 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
25199319 TATAATATTA
25199329 AATTTAATT
1 AATTTAATT
25199338 AATTTAATT
1 AATTTAATT
25199347 AATTTAATT
1 AATTTAATT
25199356 TTACTTGATC
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
AATTTAATT
Found at i:25201571 original size:21 final size:21
Alignment explanation
Indices: 25201545--25201588 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
25201535 TACAAAAAAC
25201545 AAAATAGTGAAATGTGAAATT
1 AAAATAGTGAAATGTGAAATT
25201566 AAAATAGTGAAATGTGAAATT
1 AAAATAGTGAAATGTGAAATT
25201587 AA
1 AA
25201589 CTTTATTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.55, C:0.00, G:0.18, T:0.27
Consensus pattern (21 bp):
AAAATAGTGAAATGTGAAATT
Found at i:25218921 original size:6 final size:6
Alignment explanation
Indices: 25218840--25218920 Score: 146
Period size: 6 Copynumber: 13.7 Consensus size: 6
25218830 AATTCAAAAA
25218840 AAAATC AAAATC AAAATC AAAATC AAAATC AAAAT- AAAATC AAAATC
1 AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC
*
25218887 AAAATC AAAATC AAAATC AAAATC AAAAAC AAAA
1 AAAATC AAAATC AAAATC AAAATC AAAATC AAAA
25218921 AGAAGAAAGA
Statistics
Matches: 73, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
5 5 0.07
6 68 0.93
ACGTcount: A:0.70, C:0.15, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAATC
Found at i:25218938 original size:41 final size:41
Alignment explanation
Indices: 25218846--25218973 Score: 121
Period size: 41 Copynumber: 3.0 Consensus size: 41
25218836 AAAAAAAATC
* * * *
25218846 AAAATCAAAATCAAAATCAAAATCAAAATAAAATCAAAATCAAAA
1 AAAATCAAAATCAAAATCAAAAACAAAA-AGAA--AAAA-GAGAA
*
25218891 TCAAAATCAAAATCAAAATCAAAAACAAAAAGAAGAAAGAGAA
1 --AAAATCAAAATCAAAATCAAAAACAAAAAGAAAAAAGAGAA
* ** *
25218934 AAAATCAAAATCAAAGTCAAAATGAAAATGAAAAAAGAGA
1 AAAATCAAAATCAAAATCAAAAACAAAAAGAAAAAAGAGA
25218974 GAAGGAAAAA
Statistics
Matches: 71, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
41 35 0.49
43 3 0.04
44 3 0.04
46 3 0.04
47 27 0.38
ACGTcount: A:0.70, C:0.11, G:0.07, T:0.12
Consensus pattern (41 bp):
AAAATCAAAATCAAAATCAAAAACAAAAAGAAAAAAGAGAA
Found at i:25218968 original size:47 final size:46
Alignment explanation
Indices: 25218838--25218984 Score: 163
Period size: 47 Copynumber: 3.1 Consensus size: 46
25218828 CCAATTCAAA
* ** *
25218838 AAAAAATCAAAATCAAAATCAAAATCAAAATCAAAATAA-AATCAA
1 AAAAAATCAAAATCAAAATCAAAATCAAAATCAAAAAAAGAAAGAG
*
25218883 AATCAAAATCAAAATCAAAATCAAAATCAAAAACAAAAAGAAGAAAGAG
1 AA--AAAATCAAAATCAAAATCAAAATCAAAATCAAAAA-AAGAAAGAG
* * *
25218932 AAAAAATCAAAATCAAAGTCAAAATGAAAATGAAAAAAGAGAGAAG-G
1 AAAAAATCAAAATCAAAATCAAAATCAAAATCAAAAAA-AGA-AAGAG
25218979 AAAAAA
1 AAAAAA
25218985 GAAAAAAGAA
Statistics
Matches: 87, Mismatches: 9, Indels: 10
0.82 0.08 0.09
Matches are distributed among these distances:
45 2 0.02
46 1 0.01
47 74 0.85
48 5 0.06
49 5 0.06
ACGTcount: A:0.70, C:0.10, G:0.08, T:0.12
Consensus pattern (46 bp):
AAAAAATCAAAATCAAAATCAAAATCAAAATCAAAAAAAGAAAGAG
Found at i:25220004 original size:42 final size:41
Alignment explanation
Indices: 25219936--25220053 Score: 137
Period size: 42 Copynumber: 2.8 Consensus size: 41
25219926 AAAGGGCGGC
* * *
25219936 TCAAATATTGATCAGAATTGGACATGAGGTGATTAGAGCAAT
1 TCAAAT-TTGATCAGAATGGGGCATGAGGTGATCAGAGCAAT
* *
25219978 TCAAATTCTGATCAGAGTGGGGCATGAAGTGATCAGAGCAAT
1 TCAAATT-TGATCAGAATGGGGCATGAGGTGATCAGAGCAAT
* * *
25220020 TTAAATTTTGATCAGATTGGGGCATGTGGTGATC
1 TCAAA-TTTGATCAGAATGGGGCATGAGGTGATC
25220054 TTGTTATACC
Statistics
Matches: 65, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
41 1 0.02
42 62 0.95
43 2 0.03
ACGTcount: A:0.32, C:0.11, G:0.27, T:0.30
Consensus pattern (41 bp):
TCAAATTTGATCAGAATGGGGCATGAGGTGATCAGAGCAAT
Found at i:25221337 original size:44 final size:44
Alignment explanation
Indices: 25221200--25221337 Score: 113
Period size: 44 Copynumber: 3.2 Consensus size: 44
25221190 AAAGCAAAGC
*
25221200 CTTGCCTCCATCGGTTGTAGTGGAGCTGGTTAAAGATAGCAGAT
1 CTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGAT
* * * * * * * * * * *
25221244 CTTGCCTTC-TTGCATCGACAGCGAAGCAGATCAAA-AGTA-AAG-C
1 CTTGCCTCCATCG-GTTG-CAGTGGAGCTGGTTAAAGA-TAGCAGAT
25221287 CTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGAT
1 CTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGAT
25221331 CTTGCCT
1 CTTGCCT
25221338 TCCTGCATTG
Statistics
Matches: 64, Mismatches: 23, Indels: 14
0.63 0.23 0.14
Matches are distributed among these distances:
42 14 0.22
43 15 0.23
44 22 0.34
45 13 0.20
ACGTcount: A:0.25, C:0.22, G:0.26, T:0.27
Consensus pattern (44 bp):
CTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGAT
Found at i:25221506 original size:88 final size:88
Alignment explanation
Indices: 25221145--25221760 Score: 784
Period size: 88 Copynumber: 7.0 Consensus size: 88
25221135 CAGATCAGTG
* * * *
25221145 AAGATAGCAGATCTTGCCTTCTTGCATCGACAGCGAAGCAGATCGAAAG-CA-AAGCCTTGCCTC
1 AAGATAGCAGATCTTGCCTTCCTGCGTAGACAGCGAAGCAGATC-AAAGACACCAGCCTTGCCTC
* *
25221208 CATCGGTTGTAGTGGAGCTGGTTA
65 CATCGGTTGCAGTGGAGCAGGTTA
* * *
25221232 AAGATAGCAGATCTTGCCTTCTTGCATCGACAGCGAAGCAGATCAAAAGTA-A--AGCCTTGCCT
1 AAGATAGCAGATCTTGCCTTCCTGCGTAGACAGCGAAGCAGATC-AAAG-ACACCAGCCTTGCCT
*
25221294 CCATCGGTTGCAGTGGAGCTGGTTA
64 CCATCGGTTGCAGTGGAGCAGGTTA
* * * *
25221319 AAGATAGCAGATCTTGCCTTCCTGCATTGACAGTGAAGCAGATCGAAA-ACA-AAGCCTTGCC-C
1 AAGATAGCAGATCTTGCCTTCCTGCGTAGACAGCGAAGCAGATC-AAAGACACCAGCCTTGCCTC
*
25221381 CCTCGGTTGCAGTGGAGCAGGTTA
65 CATCGGTTGCAGTGGAGCAGGTTA
* *
25221405 AAAATAGCAGATCTTGCCTTCCTGCGTAGACAGCGAAGCAGATCAAAGACACCAGCCTCGCCTCC
1 AAGATAGCAGATCTTGCCTTCCTGCGTAGACAGCGAAGCAGATCAAAGACACCAGCCTTGCCTCC
* *
25221470 CTCAGTTGCAGTGGAGCAGGTTGA
66 ATCGGTTGCAGTGGAGCAGGTT-A
*
25221494 AA-ATAGCAGATCTTGCCTTCCTGCGTAGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCT
1 AAGATAGCAGATCTTGCCTTCCTGCGTAGACAGCGAAGCAGATCAAAGACACCAGCCTTGCCTC-
* *
25221558 C-TTGGTTGCAGTGGAGCGGGTTA
65 CATCGGTTGCAGTGGAGCAGGTTA
* * * *
25221581 AAGATAGCAGATCTTGCCTTTCTGCGTAGACAACGAAGCAGATCGAAGACTCCAGCCTTGCCTCC
1 AAGATAGCAGATCTTGCCTTCCTGCGTAGACAGCGAAGCAGATCAAAGACACCAGCCTTGCCTCC
* * *
25221646 ATCGATTGCAGTGAAGCGGGTTA
66 ATCGGTTGCAGTGGAGCAGGTTA
* * * *
25221669 AAGATAGCAGATCTTGCCTTTCTGCGTAGAAAGCGAAGCAGATCGAAGACACCAGCCTCGCCTCC
1 AAGATAGCAGATCTTGCCTTCCTGCGTAGACAGCGAAGCAGATCAAAGACACCAGCCTTGCCTCC
* * *
25221734 GTCGGTTACAGTGGAGCAGGTTG
66 ATCGGTTGCAGTGGAGCAGGTTA
25221757 AAGA
1 AAGA
25221761 GTCCTATATC
Statistics
Matches: 482, Mismatches: 36, Indels: 21
0.89 0.07 0.04
Matches are distributed among these distances:
85 4 0.01
86 67 0.14
87 147 0.30
88 260 0.54
89 4 0.01
ACGTcount: A:0.27, C:0.25, G:0.26, T:0.22
Consensus pattern (88 bp):
AAGATAGCAGATCTTGCCTTCCTGCGTAGACAGCGAAGCAGATCAAAGACACCAGCCTTGCCTCC
ATCGGTTGCAGTGGAGCAGGTTA
Found at i:25226658 original size:16 final size:18
Alignment explanation
Indices: 25226623--25226660 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
25226613 ATCCTTATTT
25226623 AAATAAAATACAATAGTA
1 AAATAAAATACAATAGTA
25226641 AAATAAAATA-AA-AGTA
1 AAATAAAATACAATAGTA
25226657 AAAT
1 AAAT
25226661 CCATATAGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 8 0.40
17 2 0.10
18 10 0.50
ACGTcount: A:0.71, C:0.03, G:0.05, T:0.21
Consensus pattern (18 bp):
AAATAAAATACAATAGTA
Found at i:25227705 original size:52 final size:53
Alignment explanation
Indices: 25227603--25227708 Score: 205
Period size: 52 Copynumber: 2.0 Consensus size: 53
25227593 ATATGTATGG
25227603 TAGTTTTTGTGTATATCTCTTTCTTTTTTAATTAGGAGATTAGATGCTAAAGT
1 TAGTTTTTGTGTATATCTCTTTCTTTTTTAATTAGGAGATTAGATGCTAAAGT
25227656 TAGTTTTTGTGTATATCTCTTTC-TTTTTAATTAGGAGATTAGATGCTAAAGT
1 TAGTTTTTGTGTATATCTCTTTCTTTTTTAATTAGGAGATTAGATGCTAAAGT
25227708 T
1 T
25227709 TAGGAGATAA
Statistics
Matches: 53, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 30 0.57
53 23 0.43
ACGTcount: A:0.25, C:0.08, G:0.17, T:0.51
Consensus pattern (53 bp):
TAGTTTTTGTGTATATCTCTTTCTTTTTTAATTAGGAGATTAGATGCTAAAGT
Found at i:25232300 original size:52 final size:52
Alignment explanation
Indices: 25232174--25232302 Score: 242
Period size: 52 Copynumber: 2.5 Consensus size: 52
25232164 ATATGCATGG
25232174 TAGTTTTTGTGTATATCTCTTT-TCTTTTAATTAGGAGATTAGATGCTAAAGT
1 TAGTTTTTGTGTATATCTCTTTCT-TTTTAATTAGGAGATTAGATGCTAAAGT
25232226 TAGTTTTTGTGTATATCTCTTTCTTTTTAATTAGGAGATTAGATGCTAAAGT
1 TAGTTTTTGTGTATATCTCTTTCTTTTTAATTAGGAGATTAGATGCTAAAGT
25232278 TAGTTTTTGTGTATATCTCTTTCTT
1 TAGTTTTTGTGTATATCTCTTTCTT
25232303 AGTTTTTGTG
Statistics
Matches: 76, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
52 75 0.99
53 1 0.01
ACGTcount: A:0.22, C:0.09, G:0.16, T:0.53
Consensus pattern (52 bp):
TAGTTTTTGTGTATATCTCTTTCTTTTTAATTAGGAGATTAGATGCTAAAGT
Found at i:25232309 original size:24 final size:24
Alignment explanation
Indices: 25232277--25232326 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
25232267 GATGCTAAAG
25232277 TTAGTTTTTGTGTATATCTCTTTC
1 TTAGTTTTTGTGTATATCTCTTTC
25232301 TTAGTTTTTGTGTATATCTCTTTC
1 TTAGTTTTTGTGTATATCTCTTTC
25232325 TT
1 TT
25232327 TTTAATTAGG
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:0.12, C:0.12, G:0.12, T:0.64
Consensus pattern (24 bp):
TTAGTTTTTGTGTATATCTCTTTC
Found at i:25233295 original size:40 final size:40
Alignment explanation
Indices: 25233240--25233317 Score: 115
Period size: 40 Copynumber: 1.9 Consensus size: 40
25233230 GAAGTTCGGG
25233240 ACATATATATTTGTTGGTTCTAGC-GACTAGTGTTGGGCAC
1 ACATATATATTTGTTGGTT-TAGCTGACTAGTGTTGGGCAC
*
25233280 ACATATGATA-TTGTTGGTTTATCTGACTAGTGTTGGGC
1 ACATAT-ATATTTGTTGGTTTAGCTGACTAGTGTTGGGC
25233318 GCAAACCATT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
39 3 0.09
40 29 0.83
41 3 0.09
ACGTcount: A:0.22, C:0.13, G:0.26, T:0.40
Consensus pattern (40 bp):
ACATATATATTTGTTGGTTTAGCTGACTAGTGTTGGGCAC
Found at i:25233462 original size:70 final size:70
Alignment explanation
Indices: 25233296--25233467 Score: 184
Period size: 70 Copynumber: 2.5 Consensus size: 70
25233286 GATATTGTTG
* * * *
25233296 GTTTA-TCTGACTAGTGTTGGGCGCAAACCATTGTCGGTTATCCGACTAGTGCAAGATACACCTA
1 GTTTATTC-GACTAGCGTTGGGCGCAAAACATTATCGGTTATCCGACTAGTGCAAGACACACCTA
* *
25233360 TCGTCG
65 TCATCA
* ** * * * * * *
25233366 GTTTATCCGACTAGCACTAGGCGCAAAATATTATCGGTTATCTGACTAGTGCAGGGCACACTTAT
1 GTTTATTCGACTAGCGTTGGGCGCAAAACATTATCGGTTATCCGACTAGTGCAAGACACACCTAT
25233431 CATCA
66 CATCA
*
25233436 GTTTATTCGACTAGCGTTGGGTGCAAAACATT
1 GTTTATTCGACTAGCGTTGGGCGCAAAACATT
25233468 GTCGATTTAA
Statistics
Matches: 80, Mismatches: 21, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
70 79 0.99
71 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.30
Consensus pattern (70 bp):
GTTTATTCGACTAGCGTTGGGCGCAAAACATTATCGGTTATCCGACTAGTGCAAGACACACCTAT
CATCA
Found at i:25233860 original size:12 final size:12
Alignment explanation
Indices: 25233839--25233876 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
25233829 TTACGAGAAT
*
25233839 ATTGTGTACTAA
1 ATTGTATACTAA
25233851 ATTGTATACTAA
1 ATTGTATACTAA
*
25233863 ATTGTATATTAA
1 ATTGTATACTAA
25233875 AT
1 AT
25233877 AGAATCGACT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.39, C:0.05, G:0.11, T:0.45
Consensus pattern (12 bp):
ATTGTATACTAA
Found at i:25235155 original size:12 final size:12
Alignment explanation
Indices: 25235138--25235164 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
25235128 GTTTGAATAT
25235138 GATGAAGTTGGA
1 GATGAAGTTGGA
25235150 GATGAAGTTGGA
1 GATGAAGTTGGA
25235162 GAT
1 GAT
25235165 TAAAACATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.41, T:0.26
Consensus pattern (12 bp):
GATGAAGTTGGA
Found at i:25250590 original size:34 final size:33
Alignment explanation
Indices: 25250516--25250590 Score: 82
Period size: 34 Copynumber: 2.2 Consensus size: 33
25250506 AATATTGTTT
*
25250516 AATATAAATTAATTTTAATATTTTTCATTAATCA
1 AATATAAATTAATTTAAATATTTTT-ATTAATCA
*
25250550 ATTATAAA-TAATTTAAATAATTATTT-TTAATACA
1 AATATAAATTAATTTAAAT-ATT-TTTATTAAT-CA
25250584 AATATAA
1 AATATAA
25250591 TTTTATTAAC
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
33 14 0.40
34 18 0.51
35 3 0.09
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (33 bp):
AATATAAATTAATTTAAATATTTTTATTAATCA
Found at i:25251599 original size:31 final size:31
Alignment explanation
Indices: 25251533--25251599 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 31
25251523 CCTAGGGAAG
** **
25251533 AGGCGGCACGTAGTGGTGGAGGAGGCAGCTT
1 AGGCGGCACCCAGTGGTGGAGGAGGCAGCGC
* *
25251564 AGGCGGCACCCAGTGGTGGAGGCGGCGGCGC
1 AGGCGGCACCCAGTGGTGGAGGAGGCAGCGC
25251595 AGGCG
1 AGGCG
25251600 ACACAAGTCA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.16, C:0.22, G:0.51, T:0.10
Consensus pattern (31 bp):
AGGCGGCACCCAGTGGTGGAGGAGGCAGCGC
Found at i:25253806 original size:14 final size:14
Alignment explanation
Indices: 25253787--25253814 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
25253777 TTTTTTTAAT
25253787 GATACTATTCTAAC
1 GATACTATTCTAAC
25253801 GATACTATTCTAAC
1 GATACTATTCTAAC
25253815 ATGCAATTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.21, G:0.07, T:0.36
Consensus pattern (14 bp):
GATACTATTCTAAC
Found at i:25255140 original size:62 final size:62
Alignment explanation
Indices: 25254996--25255229 Score: 333
Period size: 62 Copynumber: 3.7 Consensus size: 62
25254986 CAACATTACA
* * * *
25254996 ACATTAGAACACTAAAACTTGTAACAAAATTTGTAATATAAATTTTGTTTGTAATATAAATTAAA
1 ACATTACAACACTAAAAATTGGAACAAACTTTGTAATATAAATTTTG--T-T-ATATAAATTAAA
25255061 T
62 T
*
25255062 ACATTACAACACTAAAAATTGGAACAAACTTTATAATATAAATTTTGTTATATAAATTAAAT
1 ACATTACAACACTAAAAATTGGAACAAACTTTGTAATATAAATTTTGTTATATAAATTAAAT
* *
25255124 ACATTACAACATTAAAAATTGGAACAAACTTTGTAACATAAATTTTGTTATATAAATTAAAT
1 ACATTACAACACTAAAAATTGGAACAAACTTTGTAATATAAATTTTGTTATATAAATTAAAT
* * * *
25255186 ACATTAGAGCATTAAAAATTAGAACAAACTTTGTAATATAAATT
1 ACATTACAACACTAAAAATTGGAACAAACTTTGTAATATAAATT
25255230 AGGTACATTG
Statistics
Matches: 156, Mismatches: 12, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
62 112 0.72
63 1 0.01
64 1 0.01
66 42 0.27
ACGTcount: A:0.49, C:0.09, G:0.07, T:0.35
Consensus pattern (62 bp):
ACATTACAACACTAAAAATTGGAACAAACTTTGTAATATAAATTTTGTTATATAAATTAAAT
Found at i:25270158 original size:21 final size:21
Alignment explanation
Indices: 25270134--25270191 Score: 80
Period size: 21 Copynumber: 2.8 Consensus size: 21
25270124 CATTGTTTCT
* *
25270134 AATCTCACTGCTACAGTATCC
1 AATCTCACCGCTACAGTAACC
*
25270155 AATCTCACCGCTACAGTAACT
1 AATCTCACCGCTACAGTAACC
*
25270176 AATCTCACCGCCACAG
1 AATCTCACCGCTACAG
25270192 CTGTTTTTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.31, C:0.36, G:0.10, T:0.22
Consensus pattern (21 bp):
AATCTCACCGCTACAGTAACC
Found at i:25270351 original size:45 final size:45
Alignment explanation
Indices: 25270287--25270374 Score: 133
Period size: 45 Copynumber: 2.0 Consensus size: 45
25270277 ACAGATACTC
*
25270287 GGTGGATTCAGCACATAGCAACCACCTTATTAATCAATGATGTCT
1 GGTGGATTCAGCACATAGCAACCACCTTACTAATCAATGATGTCT
* *
25270332 GGTGGAATT-AGCACATAGCAGCCACTTTACTAATCAATGATGT
1 GGTGG-ATTCAGCACATAGCAACCACCTTACTAATCAATGATGT
25270375 TCAGTTCACA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
45 36 0.92
46 3 0.08
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.28
Consensus pattern (45 bp):
GGTGGATTCAGCACATAGCAACCACCTTACTAATCAATGATGTCT
Found at i:25270439 original size:51 final size:50
Alignment explanation
Indices: 25270381--25270568 Score: 236
Period size: 51 Copynumber: 3.7 Consensus size: 50
25270371 ATGTTCAGTT
* *
25270381 CACATAGTAGCCTGCACATAGTACTACACATGTGACAATTACCATCCGATA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACAA-TACCATCCGGTA
* *
25270432 CACATAGTAGCTTGCACATAGTACTACACACGTGATCGAA-ACTATCCGGTA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGA-C-AATACCATCCGGTA
* * * * *
25270483 CGCATAGTAGCCTGCACATAGTACTACACATGCGAC-CTATCATTCCGGTA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACAATACCA-TCCGGTA
*
25270533 CACGTAGTAGCCTGCACATAGTACTACACACGTGAC
1 CACATAGTAGCCTGCACATAGTACTACACACGTGAC
25270569 CATCACTTTC
Statistics
Matches: 118, Mismatches: 15, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
49 2 0.02
50 40 0.34
51 73 0.62
52 1 0.01
53 2 0.02
ACGTcount: A:0.32, C:0.28, G:0.17, T:0.23
Consensus pattern (50 bp):
CACATAGTAGCCTGCACATAGTACTACACACGTGACAATACCATCCGGTA
Found at i:25270562 original size:101 final size:101
Alignment explanation
Indices: 25270383--25270567 Score: 291
Period size: 101 Copynumber: 1.8 Consensus size: 101
25270373 GTTCAGTTCA
* * *
25270383 CATAGTAGCCTGCACATAGTACTACACATGTGACAATTACCATCCGATACACATAGTAGCTTGCA
1 CATAGTAGCCTGCACATAGTACTACACATGCGAC-ACTACCATCCGATACACATAGTAGCCTGCA
25270448 CATAGTACTACACACGTGATCGAAACTATCCGGTACG
65 CATAGTACTACACACGTGATCGAAACTATCCGGTACG
* * *
25270485 CATAGTAGCCTGCACATAGTACTACACATGCGAC-CTATCATTCCGGTACACGTAGTAGCCTGCA
1 CATAGTAGCCTGCACATAGTACTACACATGCGACACTACCA-TCCGATACACATAGTAGCCTGCA
25270549 CATAGTACTACACACGTGA
65 CATAGTACTACACACGTGA
25270568 CCATCACTTT
Statistics
Matches: 76, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
100 4 0.05
101 39 0.51
102 33 0.43
ACGTcount: A:0.32, C:0.28, G:0.17, T:0.23
Consensus pattern (101 bp):
CATAGTAGCCTGCACATAGTACTACACATGCGACACTACCATCCGATACACATAGTAGCCTGCAC
ATAGTACTACACACGTGATCGAAACTATCCGGTACG
Found at i:25272219 original size:62 final size:62
Alignment explanation
Indices: 25272153--25272448 Score: 448
Period size: 62 Copynumber: 4.7 Consensus size: 62
25272143 CAATGTACCT
*
25272153 AATTTATATTACAAAGTTTGTTCCAATTTTTAATGTTGTAATGTATTTAATTTATATAACAA
1 AATTTATATTACAAAGTTTGTTCCAATTTTTAGTGTTGTAATGTATTTAATTTATATAACAA
* * *
25272215 AATTTATATTACAAAGTTTGTTCCAATTTTTAATGTTGTAATGTATTTAATCTATATAACGA
1 AATTTATATTACAAAGTTTGTTCCAATTTTTAGTGTTGTAATGTATTTAATTTATATAACAA
25272277 AATTTATATTACAAAGTTTGTTCCAATTTTTAGTGTTGTAATGTATTTAATTTATATAACAA
1 AATTTATATTACAAAGTTTGTTCCAATTTTTAGTGTTGTAATGTATTTAATTTATATAACAA
* * *
25272339 AACTTATATTATAAAGTTTGTTCCAATTTTTAGTGTTGTAATGTATTTAATTTATATTACAAAGA
1 AATTTATATTACAAAGTTTGTTCCAATTTTTAGTGTTGTAATGTATTTAATTTATA-TA-ACA-A
* * * * *
25272404 AATTTTATATTATAAATTTTGTTACAAGTTTTAGTGTTTTAATGT
1 AA-TTTATATTACAAAGTTTGTTCCAATTTTTAGTGTTGTAATGT
25272449 TGTAATGTTG
Statistics
Matches: 217, Mismatches: 13, Indels: 4
0.93 0.06 0.02
Matches are distributed among these distances:
62 173 0.80
63 2 0.01
64 2 0.01
65 3 0.01
66 37 0.17
ACGTcount: A:0.35, C:0.06, G:0.10, T:0.49
Consensus pattern (62 bp):
AATTTATATTACAAAGTTTGTTCCAATTTTTAGTGTTGTAATGTATTTAATTTATATAACAA
Found at i:25273029 original size:18 final size:17
Alignment explanation
Indices: 25273008--25273076 Score: 84
Period size: 18 Copynumber: 3.8 Consensus size: 17
25272998 GCGAGAGGTG
* *
25273008 TGGCTCGAGCTTTGGCTC
1 TGGCTCG-GCTCTGGTTC
25273026 TGGCTCGGGCTCTGGTTC
1 TGGCTC-GGCTCTGGTTC
25273044 TGGCTCTGGCTCTGGTTC
1 TGGCTC-GGCTCTGGTTC
25273062 TGGCTCTGGCTCTGG
1 TGGCTC-GGCTCTGG
25273077 CTCGGCCTCT
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
18 46 0.98
19 1 0.02
ACGTcount: A:0.01, C:0.28, G:0.36, T:0.35
Consensus pattern (17 bp):
TGGCTCGGCTCTGGTTC
Found at i:25273031 original size:6 final size:6
Alignment explanation
Indices: 25273020--25273079 Score: 93
Period size: 6 Copynumber: 10.0 Consensus size: 6
25273010 GCTCGAGCTT
* * *
25273020 TGGCTC TGGCTC GGGCTC TGGTTC TGGCTC TGGCTC TGGTTC TGGCTC
1 TGGCTC TGGCTC TGGCTC TGGCTC TGGCTC TGGCTC TGGCTC TGGCTC
25273068 TGGCTC TGGCTC
1 TGGCTC TGGCTC
25273080 GGCCTCTATA
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 48 1.00
ACGTcount: A:0.00, C:0.30, G:0.35, T:0.35
Consensus pattern (6 bp):
TGGCTC
Found at i:25273739 original size:14 final size:14
Alignment explanation
Indices: 25273720--25273754 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
25273710 CAAATTACAT
25273720 GTTAGAATAGTATC
1 GTTAGAATAGTATC
25273734 GTTAGAATAGTATC
1 GTTAGAATAGTATC
*
25273748 ATTAGAA
1 GTTAGAA
25273755 AAAAATTCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.40, C:0.06, G:0.20, T:0.34
Consensus pattern (14 bp):
GTTAGAATAGTATC
Found at i:25275980 original size:14 final size:14
Alignment explanation
Indices: 25275961--25275996 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
25275951 AAACATTTTT
*
25275961 ACTTTTCCCCCAAA
1 ACTTTTACCCCAAA
25275975 ACTTTTACCCCAAA
1 ACTTTTACCCCAAA
25275989 ACTTTTAC
1 ACTTTTAC
25275997 TCTTCTCCCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.36, G:0.00, T:0.33
Consensus pattern (14 bp):
ACTTTTACCCCAAA
Found at i:25276680 original size:24 final size:24
Alignment explanation
Indices: 25276648--25276700 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
25276638 ACAAAGATTT
* *
25276648 TTATACTAATAAAT-ATCAAATATA
1 TTATACTAACAAATGCT-AAATATA
*
25276672 TTATGCTAACAAATGCTAAATATA
1 TTATACTAACAAATGCTAAATATA
25276696 TTATA
1 TTATA
25276701 TTAAATATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
24 23 0.96
25 1 0.04
ACGTcount: A:0.49, C:0.09, G:0.04, T:0.38
Consensus pattern (24 bp):
TTATACTAACAAATGCTAAATATA
Found at i:25276707 original size:14 final size:14
Alignment explanation
Indices: 25276687--25276720 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
25276677 CTAACAAATG
25276687 CTAAATATATTATA
1 CTAAATATATTATA
*
25276701 TTAAATATATTATA
1 CTAAATATATTATA
25276715 CTAAAT
1 CTAAAT
25276721 CTTCTATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (14 bp):
CTAAATATATTATA
Found at i:25277368 original size:12 final size:12
Alignment explanation
Indices: 25277353--25277382 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
25277343 CAAAACCTTC
*
25277353 ATCTTCATCTTT
1 ATCTTCAACTTT
25277365 ATCTTCAACTTT
1 ATCTTCAACTTT
25277377 ATCTTC
1 ATCTTC
25277383 TCAATTGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.20, C:0.27, G:0.00, T:0.53
Consensus pattern (12 bp):
ATCTTCAACTTT
Found at i:25279975 original size:95 final size:96
Alignment explanation
Indices: 25279816--25279999 Score: 345
Period size: 95 Copynumber: 1.9 Consensus size: 96
25279806 AGGTTGTTAC
25279816 AAAATATAAAAAAAAAATAATTCTAAATAAGATTTTTATATGTAGTTTTTAAATAGAATTTCATT
1 AAAATATAAAAAAAAAATAATTCTAAATAAGATTTTTATATGTAGTTTTTAAATAGAATTTCATT
25279881 TATATATATTTAAATATATTAAATGGTACAA
66 TATATATATTTAAATATATTAAATGGTACAA
25279912 AAAATA-AAAAAAAAAATAGATTCTAAAT-AGATTTTTATATGTAGTTTTTAAATAGAATTTCAT
1 AAAATATAAAAAAAAAATA-ATTCTAAATAAGATTTTTATATGTAGTTTTTAAATAGAATTTCAT
25279975 TTATATATATTTAAATATATTAAAT
65 TTATATATATTTAAATATATTAAAT
25280000 AGAATTTAAA
Statistics
Matches: 87, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
95 72 0.83
96 15 0.17
ACGTcount: A:0.50, C:0.03, G:0.06, T:0.41
Consensus pattern (96 bp):
AAAATATAAAAAAAAAATAATTCTAAATAAGATTTTTATATGTAGTTTTTAAATAGAATTTCATT
TATATATATTTAAATATATTAAATGGTACAA
Found at i:25283746 original size:24 final size:24
Alignment explanation
Indices: 25283719--25283770 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
25283709 TTTTTGGTTA
25283719 TTGGGCTAATTATGT-TTTTGTAAT
1 TTGGGCTAA-TATGTATTTTGTAAT
*
25283743 TTGGGCTAATATTTATTTTGTAAT
1 TTGGGCTAATATGTATTTTGTAAT
25283767 TTGG
1 TTGG
25283771 ACTATTTTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 4 0.15
24 22 0.85
ACGTcount: A:0.21, C:0.04, G:0.21, T:0.54
Consensus pattern (24 bp):
TTGGGCTAATATGTATTTTGTAAT
Found at i:25287414 original size:28 final size:29
Alignment explanation
Indices: 25287383--25287442 Score: 86
Period size: 28 Copynumber: 2.1 Consensus size: 29
25287373 CCTAAACCTT
25287383 AAAATCCTAAACCCAAATTTA-ATTTTCA
1 AAAATCCTAAACCCAAATTTATATTTTCA
** *
25287411 AAAATCCTAAACCTTAATTTATTTTTTCA
1 AAAATCCTAAACCCAAATTTATATTTTCA
25287440 AAA
1 AAA
25287443 GCCTTACCCA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 19 0.68
29 9 0.32
ACGTcount: A:0.45, C:0.18, G:0.00, T:0.37
Consensus pattern (29 bp):
AAAATCCTAAACCCAAATTTATATTTTCA
Found at i:25287828 original size:14 final size:14
Alignment explanation
Indices: 25287809--25287838 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
25287799 GTTTGACTAA
25287809 AAGAATTCATTTTC
1 AAGAATTCATTTTC
25287823 AAGAATTCATTTTC
1 AAGAATTCATTTTC
25287837 AA
1 AA
25287839 AAACACGGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.40, C:0.13, G:0.07, T:0.40
Consensus pattern (14 bp):
AAGAATTCATTTTC
Found at i:25287952 original size:16 final size:16
Alignment explanation
Indices: 25287931--25287964 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
25287921 GGTCAGCCTC
*
25287931 TCATTTCCTTCTCATT
1 TCATTTCCTCCTCATT
25287947 TCATTTCCTCCTCATT
1 TCATTTCCTCCTCATT
25287963 TC
1 TC
25287965 CTCTCCGTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.12, C:0.35, G:0.00, T:0.53
Consensus pattern (16 bp):
TCATTTCCTCCTCATT
Found at i:25303227 original size:17 final size:17
Alignment explanation
Indices: 25303205--25303268 Score: 83
Period size: 17 Copynumber: 3.8 Consensus size: 17
25303195 TTAATGAGAT
25303205 AAAAATAAATAAATAAC
1 AAAAATAAATAAATAAC
*
25303222 AAAAATAAATAAATACC
1 AAAAATAAATAAATAAC
* *
25303239 AAAAATAAACAAATGAC
1 AAAAATAAATAAATAAC
* *
25303256 TAAAATCAATAAA
1 AAAAATAAATAAA
25303269 CCAATCAGGA
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 40 1.00
ACGTcount: A:0.72, C:0.09, G:0.02, T:0.17
Consensus pattern (17 bp):
AAAAATAAATAAATAAC
Found at i:25307404 original size:35 final size:35
Alignment explanation
Indices: 25307364--25307437 Score: 121
Period size: 35 Copynumber: 2.1 Consensus size: 35
25307354 CCATAAAACA
* *
25307364 CCAATGCTTATAAGAGCTAATCTAACCGAAACACG
1 CCAATGCTCATAAGAGCTAATCCAACCGAAACACG
*
25307399 CCAATGCTCATAAGAGCTAATCCAACCGAAATACG
1 CCAATGCTCATAAGAGCTAATCCAACCGAAACACG
25307434 CCAA
1 CCAA
25307438 ATAGAGAGTA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.41, C:0.28, G:0.14, T:0.18
Consensus pattern (35 bp):
CCAATGCTCATAAGAGCTAATCCAACCGAAACACG
Found at i:25329884 original size:4 final size:4
Alignment explanation
Indices: 25329875--25330010 Score: 92
Period size: 4 Copynumber: 34.0 Consensus size: 4
25329865 GAAGGAGAGG
* *
25329875 GAAA GAAA GAAA GAAA GAAA GAAA GGAGAG GAAA GAAA G-AA -AAA GAAG
1 GAAA GAAA GAAA GAAA GAAA GAAA -GA-AA GAAA GAAA GAAA GAAA GAAA
*
25329923 GAAA GAAAA GGAAA G-GA GAAGA GAAA -AAA -AAA GAAA GAAA G-AA G-AA
1 GAAA G-AAA -GAAA GAAA GAA-A GAAA GAAA GAAA GAAA GAAA GAAA GAAA
*
25329969 GAAAA GGAAAA GAGAA G-AA -AAA GAAA GAAA GAAG GAAA GAAA
1 G-AAA -G-AAA GA-AA GAAA GAAA GAAA GAAA GAAA GAAA GAAA
25330011 AGGGAAAAAA
Statistics
Matches: 109, Mismatches: 8, Indels: 30
0.74 0.05 0.20
Matches are distributed among these distances:
3 22 0.20
4 60 0.55
5 20 0.18
6 7 0.06
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:25329910 original size:18 final size:17
Alignment explanation
Indices: 25329875--25330010 Score: 80
Period size: 18 Copynumber: 8.2 Consensus size: 17
25329865 GAAGGAGAGG
*
25329875 GAAAGAAAGA-AAGAAA
1 GAAAGAAAGAGAGGAAA
25329891 GAAAGAAAGGAGAGGAAA
1 GAAAGAAA-GAGAGGAAA
*
25329909 GAAAGAAAAAGAAGGAAA
1 GAAAGAAAGAG-AGGAAA
25329927 GAAAAGGAAAG-GA-GAAGA
1 G-AAA-GAAAGAGAGGAA-A
*
25329945 GAAA-AAA-A-AAGAAA
1 GAAAGAAAGAGAGGAAA
*
25329959 GAAAG-AAGA-AGAAAA
1 GAAAGAAAGAGAGGAAA
25329974 GGAAAAGAGAAGA-A--AAA
1 -G-AAAGA-AAGAGAGGAAA
25329991 GAAAGAAAGA-AGGAAA
1 GAAAGAAAGAGAGGAAA
25330007 GAAA
1 GAAA
25330011 AGGGAAAAAA
Statistics
Matches: 99, Mismatches: 5, Indels: 32
0.73 0.04 0.24
Matches are distributed among these distances:
14 13 0.13
15 16 0.16
16 17 0.17
17 17 0.17
18 23 0.23
19 9 0.09
20 4 0.04
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (17 bp):
GAAAGAAAGAGAGGAAA
Found at i:25329927 original size:36 final size:36
Alignment explanation
Indices: 25329880--25330007 Score: 138
Period size: 36 Copynumber: 3.6 Consensus size: 36
25329870 AGAGGGAAAG
25329880 AAAGAAAGAAAGAAAGAAAGGAGAGGAAAGAAAGAA
1 AAAGAAAGAAAGAAAGAAAGGAGAGGAAAGAAAGAA
* * *
25329916 AAAGAAGGAAAGAAAAGGAAAGGAGA--AGAGAAAAAA
1 AAAGAAAGAAAG-AAA-GAAAGGAGAGGAAAGAAAGAA
* *
25329952 AAAGAAAGAAAG-AAG-AAGAAAAGGAAAAGAGAAGAA
1 AAAGAAAGAAAGAAAGAAAGGAGAGG-AAAGA-AAGAA
*
25329988 AAAGAAAGAAAGAAGGAAAG
1 AAAGAAAGAAAGAAAGAAAG
25330008 AAAAGGGAAA
Statistics
Matches: 75, Mismatches: 9, Indels: 14
0.77 0.09 0.14
Matches are distributed among these distances:
32 5 0.07
33 1 0.01
34 2 0.03
35 4 0.05
36 46 0.61
37 5 0.07
38 12 0.16
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (36 bp):
AAAGAAAGAAAGAAAGAAAGGAGAGGAAAGAAAGAA
Found at i:25329992 original size:64 final size:64
Alignment explanation
Indices: 25329866--25330010 Score: 149
Period size: 64 Copynumber: 2.3 Consensus size: 64
25329856 GGGGGGGCAG
* * * *
25329866 AAGGAGAGGGAAAGAAAGAAAGAAAGAAAGAAAGGAGAGGAAAGAAAGAAAAAGAAGGAAAGAA
1 AAGGAAAGGGAAAGAAAGAAAGAAAGAAAGAAAGAAGAAGAAAGAAAGAAAAAGAAGAAAAGAA
*
25329930 AAGGAAAGGAGAAGAGAAA-AAA-AAAGAAAGAAAGAAGAAG-AA-AAGGAAAAGAGAAGAAAA-
1 AAGGAAAGG-GAA-AGAAAGAAAGAAAGAAAGAAAGAAGAAGAAAGAAAGAAAA-AGAAGAAAAG
25329990 AGA
63 A-A
25329993 AA-GAAAGAAGGAAAGAAA
1 AAGGAAAG--GGAAAGAAA
25330011 AGGGAAAAAA
Statistics
Matches: 70, Mismatches: 5, Indels: 14
0.79 0.06 0.16
Matches are distributed among these distances:
62 18 0.26
63 16 0.23
64 25 0.36
65 6 0.09
66 5 0.07
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (64 bp):
AAGGAAAGGGAAAGAAAGAAAGAAAGAAAGAAAGAAGAAGAAAGAAAGAAAAAGAAGAAAAGAA
Found at i:25330011 original size:32 final size:32
Alignment explanation
Indices: 25329884--25330055 Score: 131
Period size: 36 Copynumber: 5.2 Consensus size: 32
25329874 GGAAAGAAAG
* *
25329884 AAAGAAAGAAAGAAAGGAGAGGAAAGA-AAGAA
1 AAAGAAAGAAAG-AAGGAAAGAAAAGAGAAGAA
* * *
25329916 AAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAAAAA
1 AAAGAAAGAAAG--AAGGAAA-GAAAAGAG-AAGAA
25329952 AAAGAAAGAAAGAAGAAGAAAAGGAAAAGAGAAGAA
1 AAAGAAAGAAAGAAG--G-AAA-GAAAAGAGAAGAA
*
25329988 AAAGAAAGAAAGAAGGAAAGAAAAGGGAA-AA
1 AAAGAAAGAAAGAAGGAAAGAAAAGAGAAGAA
* * *
25330019 AAA-AAGGGAAGGAAGGAAA-AAAA-AAAAGAA
1 AAAGAA-AGAAAGAAGGAAAGAAAAGAGAAGAA
25330049 AAA-AAAG
1 AAAGAAAG
25330056 GTAATTTTAT
Statistics
Matches: 117, Mismatches: 14, Indels: 21
0.77 0.09 0.14
Matches are distributed among these distances:
29 3 0.03
30 13 0.11
31 16 0.14
32 20 0.17
33 10 0.09
34 9 0.08
36 35 0.30
37 11 0.09
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (32 bp):
AAAGAAAGAAAGAAGGAAAGAAAAGAGAAGAA
Found at i:25330024 original size:44 final size:42
Alignment explanation
Indices: 25329906--25330049 Score: 114
Period size: 44 Copynumber: 3.3 Consensus size: 42
25329896 AAAGGAGAGG
* * *
25329906 AAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAAAAA
1 AAAGAAAG--AAAGAA-G-AAGAAAAGAAAAAGAGAAGAAAAAAAA
*
25329952 AAAGAAAGAAAGAAGAAGAAAAGGAAAAGAGAAGAAAAAGAAA
1 AAAGAAAGAAAGAAGAAGAAAAGAAAAAGAGAAGAAAAA-AAA
* * *
25329995 GAAAGAAGGAAAGAA-AAGGGAAAA-AAAAAGGGAAGGAAGGAAAAA
1 -AAAGAAAGAAAGAAGAA--GAAAAGAAAAAGAGAA-GAA-AAAAAA
25330040 AAA-AAAGAAA
1 AAAGAAAGAAA
25330050 AAAAAGGTAA
Statistics
Matches: 85, Mismatches: 7, Indels: 15
0.79 0.07 0.14
Matches are distributed among these distances:
42 22 0.26
43 12 0.14
44 30 0.35
45 11 0.13
46 10 0.12
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (42 bp):
AAAGAAAGAAAGAAGAAGAAAAGAAAAAGAGAAGAAAAAAAA
Found at i:25330056 original size:22 final size:22
Alignment explanation
Indices: 25329946--25330056 Score: 57
Period size: 22 Copynumber: 4.9 Consensus size: 22
25329936 AGGAGAAGAG
25329946 AAAAAAAAAGAAAGAAAGAA-GAA
1 AAAAAAAAAGAAA-AAA-AAGGAA
*
25329969 GAAAAGGAAAAGAGAAGAAAAA-GAA
1 -AAAA--AAAA-AGAAAAAAAAGGAA
* * * * *
25329994 AGAAAGAAGGAAAGAAAAGG-G
1 AAAAAAAAAGAAAAAAAAGGAA
** **
25330015 AAAAAAAAAGGGAAGGAAGGAA
1 AAAAAAAAAGAAAAAAAAGGAA
25330037 AAAAAAAAAGAAAAAAAAGG
1 AAAAAAAAAGAAAAAAAAGG
25330057 TAATTTTATT
Statistics
Matches: 62, Mismatches: 20, Indels: 12
0.66 0.21 0.13
Matches are distributed among these distances:
21 19 0.31
22 20 0.32
24 7 0.11
25 5 0.08
26 7 0.11
27 4 0.06
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (22 bp):
AAAAAAAAAGAAAAAAAAGGAA
Found at i:25336959 original size:3 final size:3
Alignment explanation
Indices: 25336951--25336976 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
25336941 TCTTAATACT
25336951 AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AA
25336977 TAATAATACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:25337064 original size:19 final size:21
Alignment explanation
Indices: 25337040--25337078 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
25337030 ACTAAAACAA
*
25337040 AAAATATTA-CAA-AATATAC
1 AAAATAATAGCAACAATATAC
25337059 AAAATAATAGCAACAATATA
1 AAAATAATAGCAACAATATA
25337079 ATAAAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 3 0.18
21 6 0.35
ACGTcount: A:0.64, C:0.10, G:0.03, T:0.23
Consensus pattern (21 bp):
AAAATAATAGCAACAATATAC
Found at i:25337257 original size:27 final size:27
Alignment explanation
Indices: 25337227--25337311 Score: 125
Period size: 27 Copynumber: 3.1 Consensus size: 27
25337217 CCAATCAATA
25337227 TGGCACCATTGGTGCCGCCAATGGCAT
1 TGGCACCATTGGTGCCGCCAATGGCAT
* **
25337254 TGGCACCATTGGTGCCGCTAATGGTTT
1 TGGCACCATTGGTGCCGCCAATGGCAT
* *
25337281 TGGCACCTTTGGTGCCGCCAATGACAT
1 TGGCACCATTGGTGCCGCCAATGGCAT
25337308 TGGC
1 TGGC
25337312 GTGACCAAGG
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 50 1.00
ACGTcount: A:0.16, C:0.27, G:0.29, T:0.27
Consensus pattern (27 bp):
TGGCACCATTGGTGCCGCCAATGGCAT
Found at i:25337392 original size:26 final size:27
Alignment explanation
Indices: 25337363--25337430 Score: 104
Period size: 26 Copynumber: 2.6 Consensus size: 27
25337353 GTTTTTTTTT
*
25337363 TATATATTTTGGTAAAT-AAAAATTTA
1 TATATATTTTGGTAAATAAAAAAGTTA
25337389 TATATATTTTGGTAAATAAAAAAAGTTA
1 TATATATTTTGGTAAAT-AAAAAAGTTA
25337417 TA-ATATTTTGGTAA
1 TATATATTTTGGTAA
25337431 TTTTTTATTT
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
26 17 0.44
27 12 0.31
28 10 0.26
ACGTcount: A:0.46, C:0.00, G:0.10, T:0.44
Consensus pattern (27 bp):
TATATATTTTGGTAAATAAAAAAGTTA
Found at i:25338161 original size:15 final size:15
Alignment explanation
Indices: 25338141--25338187 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
25338131 CCCCTCCTCT
25338141 TTTTTTTTCTTCTTC
1 TTTTTTTTCTTCTTC
*
25338156 TTTTTTTTCTTTTTC
1 TTTTTTTTCTTCTTC
* *
25338171 TTCTTCTTCTTCTTC
1 TTTTTTTTCTTCTTC
25338186 TT
1 TT
25338188 CTCCTTCTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTTTTTTCTTCTTC
Found at i:25338174 original size:3 final size:3
Alignment explanation
Indices: 25338147--25338210 Score: 67
Period size: 3 Copynumber: 21.7 Consensus size: 3
25338137 CTCTTTTTTT
* * * *
25338147 TTC TTC TTC TTT TTT TTC TTT TTC TTC TTC TTC TTC TTC TTC TCC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
* *
25338195 TT- TGC TTC TTT TTC TT
1 TTC TTC TTC TTC TTC TT
25338211 TTGCTGCCCA
Statistics
Matches: 50, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
2 1 0.02
3 49 0.98
ACGTcount: A:0.00, C:0.27, G:0.02, T:0.72
Consensus pattern (3 bp):
TTC
Found at i:25338211 original size:6 final size:6
Alignment explanation
Indices: 25338138--25338212 Score: 53
Period size: 6 Copynumber: 12.0 Consensus size: 6
25338128 CTCCCCCTCC
* * * *
25338138 TCTTTT TTTTTCT TCTTCTT T-TTTT TCTTTT TCTTCT TCTTCT TCTTCT
1 TCTTTT TCTTT-T TCTT-TT TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT
**
25338187 TCTCCT TCTTTGCT TCTTTT TCTTTT
1 TCTTTT TCTTT--T TCTTTT TCTTTT
25338213 GCTGCCCAAC
Statistics
Matches: 58, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
5 3 0.05
6 42 0.72
7 6 0.10
8 7 0.12
ACGTcount: A:0.00, C:0.24, G:0.01, T:0.75
Consensus pattern (6 bp):
TCTTTT
Found at i:25338603 original size:21 final size:21
Alignment explanation
Indices: 25338569--25338662 Score: 65
Period size: 20 Copynumber: 4.6 Consensus size: 21
25338559 TTTGGTACTA
25338569 TCTCAT-ATTCTTTTAATATTC
1 TCTCATAATT-TTTTAATATTC
25338590 TCTCATAATTTTTTCAAT-TTC
1 TCTCATAATTTTTT-AATATTC
* *
25338611 T-TCAT-TTTTTTTTATACTTC
1 TCTCATAATTTTTTAATA-TTC
* *
25338631 -ATCATAATTTTTT-ATATTT
1 TCTCATAATTTTTTAATATTC
* *
25338650 TGTCAGAATTTTT
1 TCTCATAATTTTT
25338663 ATATTCCTTT
Statistics
Matches: 60, Mismatches: 6, Indels: 15
0.74 0.07 0.19
Matches are distributed among these distances:
18 2 0.03
19 8 0.13
20 24 0.40
21 20 0.33
22 6 0.10
ACGTcount: A:0.23, C:0.14, G:0.02, T:0.61
Consensus pattern (21 bp):
TCTCATAATTTTTTAATATTC
Found at i:25338615 original size:20 final size:21
Alignment explanation
Indices: 25338571--25338643 Score: 55
Period size: 21 Copynumber: 3.6 Consensus size: 21
25338561 TGGTACTATC
*
25338571 TCAT-ATTCTTTTAATA-TTCT
1 TCATAATT-TTTTCATACTTCT
*
25338591 CTCATAATTTTTTCA-ATTTCT
1 -TCATAATTTTTTCATACTTCT
* * *
25338612 TCAT-TTTTTTTTATACTTCA
1 TCATAATTTTTTCATACTTCT
25338632 TCATAATTTTTT
1 TCATAATTTTTT
25338644 ATATTTTGTC
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
19 7 0.17
20 13 0.31
21 19 0.45
22 3 0.07
ACGTcount: A:0.23, C:0.15, G:0.00, T:0.62
Consensus pattern (21 bp):
TCATAATTTTTTCATACTTCT
Found at i:25339188 original size:18 final size:18
Alignment explanation
Indices: 25339135--25339188 Score: 69
Period size: 18 Copynumber: 3.1 Consensus size: 18
25339125 GGTTTTTTTA
25339135 TTTTGTTA-GGTTTAGGGG
1 TTTTGTTAGGGTTTA-GGG
25339153 TTTTGTTAGGG-TTAGGG
1 TTTTGTTAGGGTTTAGGG
25339170 TTTT-TTAAGGGTTTAGGG
1 TTTTGTT-AGGGTTTAGGG
25339188 T
1 T
25339189 CAAAACTTAG
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
16 2 0.06
17 11 0.33
18 18 0.55
19 2 0.06
ACGTcount: A:0.13, C:0.00, G:0.37, T:0.50
Consensus pattern (18 bp):
TTTTGTTAGGGTTTAGGG
Found at i:25346911 original size:21 final size:20
Alignment explanation
Indices: 25346868--25346912 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
25346858 TCCCTTGTAA
*
25346868 TTTTGGTACTTCCTTATATT
1 TTTTGGTACTTCCTCATATT
25346888 TTTTGGTA-TTCTCTCATAATT
1 TTTTGGTACTTC-CTCAT-ATT
25346909 TTTT
1 TTTT
25346913 ATACATACTC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 3 0.14
20 12 0.55
21 7 0.32
ACGTcount: A:0.16, C:0.13, G:0.09, T:0.62
Consensus pattern (20 bp):
TTTTGGTACTTCCTCATATT
Found at i:25347002 original size:20 final size:20
Alignment explanation
Indices: 25346934--25347002 Score: 84
Period size: 20 Copynumber: 3.5 Consensus size: 20
25346924 ATACTTCCTT
* *
25346934 AGATTTCTTCGTATTCCCTC
1 AGATTTTTTGGTATTCCCTC
* *
25346954 AGAATTTTTGGTATTTCCTC
1 AGATTTTTTGGTATTCCCTC
* *
25346974 ATATTTTTTGGTACTCCCTC
1 AGATTTTTTGGTATTCCCTC
25346994 AGATTTTTT
1 AGATTTTTT
25347003 TTTGTACTTC
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.17, C:0.20, G:0.12, T:0.51
Consensus pattern (20 bp):
AGATTTTTTGGTATTCCCTC
Found at i:25347009 original size:22 final size:22
Alignment explanation
Indices: 25346948--25347025 Score: 65
Period size: 22 Copynumber: 3.7 Consensus size: 22
25346938 TTCTTCGTAT
*
25346948 TCCCTCAGAA--TTTTTGGTAT
1 TCCCTCAGAATTTTTTTGGTAC
* *
25346968 TTCCTCA-TA-TTTTTTGGTAC
1 TCCCTCAGAATTTTTTTGGTAC
* *
25346988 TCCCTCAGATTTTTTTTTGTAC
1 TCCCTCAGAATTTTTTTGGTAC
* *
25347010 TTCCTCATAATTTTTT
1 TCCCTCAGAATTTTTT
25347026 GTATTGTTTC
Statistics
Matches: 45, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
19 1 0.02
20 21 0.47
22 23 0.51
ACGTcount: A:0.17, C:0.21, G:0.09, T:0.54
Consensus pattern (22 bp):
TCCCTCAGAATTTTTTTGGTAC
Found at i:25347025 original size:20 final size:20
Alignment explanation
Indices: 25346950--25347028 Score: 70
Period size: 20 Copynumber: 3.9 Consensus size: 20
25346940 CTTCGTATTC
* * *
25346950 CCTCAGAATTTTTGGTATTT
1 CCTCATAATTTTTTGTACTT
*
25346970 CCTCAT-ATTTTTTGGTACTC
1 CCTCATAATTTTTT-GTACTT
**
25346990 CCTCAGATTTTTTTTTGTACTT
1 CCTC--ATAATTTTTTGTACTT
25347012 CCTCATAATTTTTTGTA
1 CCTCATAATTTTTTGTA
25347029 TTGTTTCAAA
Statistics
Matches: 47, Mismatches: 8, Indels: 8
0.75 0.13 0.13
Matches are distributed among these distances:
19 6 0.13
20 24 0.51
22 11 0.23
23 6 0.13
ACGTcount: A:0.18, C:0.19, G:0.10, T:0.53
Consensus pattern (20 bp):
CCTCATAATTTTTTGTACTT
Found at i:25347593 original size:20 final size:20
Alignment explanation
Indices: 25347546--25347631 Score: 83
Period size: 20 Copynumber: 4.5 Consensus size: 20
25347536 GTATTCCTTT
*
25347546 ATAATTTTTGGTACTTGCTC
1 ATAATTTTTGGTACTTCCTC
*
25347566 ATATTTTTTGGTA-TTCCCTC
1 ATAATTTTTGGTACTT-CCTC
* *
25347586 GTAATTTTT--TACATT-TTC
1 ATAATTTTTGGTAC-TTCCTC
25347604 ATAATTTTTGGTACTTCCTC
1 ATAATTTTTGGTACTTCCTC
25347624 A-AATTTTT
1 ATAATTTTT
25347632 TATATTTTTT
Statistics
Matches: 53, Mismatches: 7, Indels: 13
0.73 0.10 0.18
Matches are distributed among these distances:
18 12 0.23
19 11 0.21
20 30 0.57
ACGTcount: A:0.21, C:0.15, G:0.09, T:0.55
Consensus pattern (20 bp):
ATAATTTTTGGTACTTCCTC
Found at i:25347606 original size:38 final size:37
Alignment explanation
Indices: 25347564--25347639 Score: 100
Period size: 38 Copynumber: 2.0 Consensus size: 37
25347554 TGGTACTTGC
* *
25347564 TCATATTTTTTGGTA-TTCCCTCGTAATTTTTTACATTT
1 TCATAATTTTTGGTACTT-CCTC-AAATTTTTTACATTT
*
25347602 TCATAATTTTTGGTACTTCCTCAAATTTTTTATATTT
1 TCATAATTTTTGGTACTTCCTCAAATTTTTTACATTT
25347639 T
1 T
25347640 TTTCATATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
37 14 0.41
38 18 0.53
39 2 0.06
ACGTcount: A:0.21, C:0.14, G:0.07, T:0.58
Consensus pattern (37 bp):
TCATAATTTTTGGTACTTCCTCAAATTTTTTACATTT
Found at i:25347647 original size:11 final size:10
Alignment explanation
Indices: 25347627--25347656 Score: 51
Period size: 11 Copynumber: 2.9 Consensus size: 10
25347617 CTTCCTCAAA
25347627 TTTTTTATAT
1 TTTTTTATAT
25347637 TTTTTTCATAT
1 TTTTTT-ATAT
25347648 TTTTTTATA
1 TTTTTTATA
25347657 CATTCTCATG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (10 bp):
TTTTTTATAT
Found at i:25347695 original size:20 final size:20
Alignment explanation
Indices: 25347497--25347708 Score: 77
Period size: 20 Copynumber: 10.6 Consensus size: 20
25347487 ATTCCTTCGT
25347497 GTATATCCTCA-ATTTTTTT-
1 GTAT-TCCTCATATTTTTTTG
* *
25347516 GTAATTCTTCATCTTTTTTT-
1 GT-ATTCCTCATATTTTTTTG
* *
25347536 GTATTCCT-TTATAATTTTTG
1 GTATTCCTCATAT-TTTTTTG
*
25347556 GTACTTGCTCATA-TTTTTTG
1 GTA-TTCCTCATATTTTTTTG
* *
25347576 GTATTCCCTCGTAATTTTTT-
1 GTATT-CCTCATATTTTTTTG
** * *
25347596 ACATT-TTCATA-ATTTTTG
1 GTATTCCTCATATTTTTTTG
*
25347614 GTACTTCCTCAAATTTTTTAT-
1 GTA-TTCCTCATATTTTTT-TG
* * **
25347635 ATTTTTTTCATATTTTTTT-
1 GTATTCCTCATATTTTTTTG
* *
25347654 ATACATT-CTCATGTTTTTTTTG
1 GT--ATTCCTCAT-ATTTTTTTG
*
25347676 TTATTCCTCATATTTTTTTG
1 GTATTCCTCATATTTTTTTG
25347696 GTACTTCCTCATA
1 GTA-TTCCTCATA
25347709 ATTATTGGTA
Statistics
Matches: 142, Mismatches: 32, Indels: 36
0.68 0.15 0.17
Matches are distributed among these distances:
17 5 0.04
18 7 0.05
19 24 0.17
20 64 0.45
21 38 0.27
22 4 0.03
ACGTcount: A:0.19, C:0.15, G:0.07, T:0.59
Consensus pattern (20 bp):
GTATTCCTCATATTTTTTTG
Found at i:25347718 original size:20 final size:21
Alignment explanation
Indices: 25347679--25347718 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
25347669 TTTTTTGTTA
* *
25347679 TTCCTCATATTTTTTTGGTAC
1 TTCCTCATATATTATTGGTAC
25347700 TTCCTCATA-ATTATTGGTA
1 TTCCTCATATATTATTGGTA
25347719 TTATTATGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.20, C:0.17, G:0.10, T:0.53
Consensus pattern (21 bp):
TTCCTCATATATTATTGGTAC
Found at i:25347926 original size:18 final size:18
Alignment explanation
Indices: 25347885--25347926 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
25347875 TATATTTCAC
*
25347885 AATAATTTTAAAAAATAT
1 AATAAATTTAAAAAATAT
25347903 AA-AAATTTAAATAAATA-
1 AATAAATTTAAA-AAATAT
25347920 AATAAAT
1 AATAAAT
25347927 AAAAATTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 10 0.48
18 11 0.52
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
AATAAATTTAAAAAATAT
Found at i:25348026 original size:2 final size:2
Alignment explanation
Indices: 25348021--25348054 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
25348011 TTGTACTTTC
25348021 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
25348055 TTGTATTCCC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25348137 original size:20 final size:20
Alignment explanation
Indices: 25348063--25348263 Score: 131
Period size: 20 Copynumber: 10.0 Consensus size: 20
25348053 ATTTGTATTC
* * *
25348063 CCTCATGATTTTCGGTGCTT
1 CCTCATAATTTTTGGTACTT
* * *
25348083 TCTAATAATTTTTTTGTA-TT
1 CCTCATAA-TTTTTGGTACTT
*
25348103 CCTTCATAATGTTTGGTACTT
1 CC-TCATAATTTTTGGTACTT
** *
25348124 CCTCATTTTTTTTGGCA-TT
1 CCTCATAATTTTTGGTACTT
* *
25348143 CCTTTATAATTTTTGGTACAT
1 CC-TCATAATTTTTGGTACTT
*
25348164 CCTCATAATTTTTAGTACTT
1 CCTCATAATTTTTGGTACTT
* * *
25348184 CCACAAAATTTTT-CTACTT
1 CCTCATAATTTTTGGTACTT
* *
25348203 CCTCATATTTTTTAGTA-TAT
1 CCTCATAATTTTTGGTACT-T
* *
25348223 CCTCATAATTTTTGGTAATC
1 CCTCATAATTTTTGGTACTT
**
25348243 CCTCATGGTTTTTTGGTACTT
1 CCTCAT-AATTTTTGGTACTT
25348264 TCTTATATTT
Statistics
Matches: 136, Mismatches: 36, Indels: 17
0.72 0.19 0.09
Matches are distributed among these distances:
19 20 0.15
20 87 0.64
21 29 0.21
ACGTcount: A:0.20, C:0.18, G:0.10, T:0.51
Consensus pattern (20 bp):
CCTCATAATTTTTGGTACTT
Found at i:25348214 original size:19 final size:19
Alignment explanation
Indices: 25348163--25348215 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 19
25348153 TTTTGGTACA
**
25348163 TCCTCATAATTTTTAGTACT
1 TCCTCAT-ATTTTTTCTACT
* * *
25348183 TCCACAAAATTTTTCTACT
1 TCCTCATATTTTTTCTACT
25348202 TCCTCATATTTTTT
1 TCCTCATATTTTTT
25348216 AGTATATCCT
Statistics
Matches: 25, Mismatches: 8, Indels: 1
0.74 0.24 0.03
Matches are distributed among these distances:
19 20 0.80
20 5 0.20
ACGTcount: A:0.25, C:0.23, G:0.02, T:0.51
Consensus pattern (19 bp):
TCCTCATATTTTTTCTACT
Found at i:25348233 original size:39 final size:39
Alignment explanation
Indices: 25348090--25348236 Score: 145
Period size: 40 Copynumber: 3.7 Consensus size: 39
25348080 CTTTCTAATA
* *
25348090 ATTTTTTTGTATTCCTTCATAATGTTTGGTACTTCCTCAT
1 ATTTTTTAGTATTCCTTCATAAT-TTTTGTACTTCCTCAT
* * * * *
25348130 TTTTTTTGGCATTCCTTTATAATTTTTGGTACATCCTCAT
1 ATTTTTTAGTATTCCTTCATAATTTTT-GTACTTCCTCAT
* * * *
25348170 AATTTTTAGTACTTCC-ACAAAATTTTTCTACTTCCTCAT
1 ATTTTTTAGTA-TTCCTTCATAATTTTTGTACTTCCTCAT
25348209 ATTTTTTAGTATATCC-TCATAATTTTTG
1 ATTTTTTAGTAT-TCCTTCATAATTTTTG
25348237 GTAATCCCTC
Statistics
Matches: 85, Mismatches: 19, Indels: 7
0.77 0.17 0.06
Matches are distributed among these distances:
38 1 0.01
39 35 0.41
40 45 0.53
41 4 0.05
ACGTcount: A:0.22, C:0.18, G:0.07, T:0.53
Consensus pattern (39 bp):
ATTTTTTAGTATTCCTTCATAATTTTTGTACTTCCTCAT
Found at i:25348344 original size:20 final size:20
Alignment explanation
Indices: 25348316--25348378 Score: 65
Period size: 20 Copynumber: 3.1 Consensus size: 20
25348306 ATTTTTTGGC
* *
25348316 ATTCTCTCATAATTTATGGT
1 ATTCCCTCATAATTTATAGT
* *
25348336 ATTCCCTCAAAATTTTTAGT
1 ATTCCCTCATAATTTATAGT
*
25348356 ACTT-CCTCATAATTTTTAGT
1 A-TTCCCTCATAATTTATAGT
25348376 ATT
1 ATT
25348379 ACCTTAAATT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
19 2 0.05
20 33 0.89
21 2 0.05
ACGTcount: A:0.27, C:0.17, G:0.06, T:0.49
Consensus pattern (20 bp):
ATTCCCTCATAATTTATAGT
Found at i:25348388 original size:19 final size:19
Alignment explanation
Indices: 25348340--25348391 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 19
25348330 TATGGTATTC
25348340 CCTCAAAATTTTTAGTACTT
1 CCTC-AAATTTTTAGTACTT
25348360 CCTCATAATTTTTAGTA-TT
1 CCTCA-AATTTTTAGTACTT
*
25348379 ACCTTAAATTTTT
1 -CCTCAAATTTTT
25348392 TGGTATGGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
19 10 0.34
20 19 0.66
ACGTcount: A:0.29, C:0.17, G:0.04, T:0.50
Consensus pattern (19 bp):
CCTCAAATTTTTAGTACTT
Found at i:25348629 original size:20 final size:21
Alignment explanation
Indices: 25348604--25348657 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 21
25348594 GTACACCCTC
**
25348604 ATAATTTTTGGTATTTCC-TT
1 ATAATTTTTGGTATCACCTTT
25348624 ATAATTTTTGGTA-CACCTTT
1 ATAATTTTTGGTATCACCTTT
25348644 ATAATTTTTGGTAT
1 ATAATTTTTGGTAT
25348658 AGTCCTAGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
19 2 0.07
20 28 0.93
ACGTcount: A:0.24, C:0.09, G:0.11, T:0.56
Consensus pattern (21 bp):
ATAATTTTTGGTATCACCTTT
Found at i:25348670 original size:40 final size:40
Alignment explanation
Indices: 25348594--25348672 Score: 106
Period size: 40 Copynumber: 2.0 Consensus size: 40
25348584 ATAAATGATA
* *
25348594 GTACACCCTCATAATTTTTGGTATTTCCTTATAATTTTTG
1 GTACACCCTCATAATTTTTGGTATGTCCTTAGAATTTTTG
* *
25348634 GTACACCTTTATAATTTTTGGTATAGTCC-TAGAATTTTT
1 GTACACCCTCATAATTTTTGGTAT-GTCCTTAGAATTTTT
25348673 TGTATGGTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
40 31 0.91
41 3 0.09
ACGTcount: A:0.24, C:0.15, G:0.11, T:0.49
Consensus pattern (40 bp):
GTACACCCTCATAATTTTTGGTATGTCCTTAGAATTTTTG
Found at i:25349023 original size:21 final size:21
Alignment explanation
Indices: 25348997--25349041 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
25348987 AAAATTTTAC
*
25348997 AAAGGTAACTTTACCATATTG
1 AAAGGTAACTTTACCATACTG
25349018 AAAGGTAACTTTACCATACTG
1 AAAGGTAACTTTACCATACTG
25349039 AAA
1 AAA
25349042 TATTTACTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.42, C:0.16, G:0.13, T:0.29
Consensus pattern (21 bp):
AAAGGTAACTTTACCATACTG
Found at i:25349370 original size:37 final size:37
Alignment explanation
Indices: 25349329--25349399 Score: 133
Period size: 37 Copynumber: 1.9 Consensus size: 37
25349319 GAATTCTTGT
25349329 TTGGCTTTGTTTGTACTAGAACGGTTCACCACTCTTA
1 TTGGCTTTGTTTGTACTAGAACGGTTCACCACTCTTA
*
25349366 TTGGCTTTGTTTGTACTAGGACGGTTCACCACTC
1 TTGGCTTTGTTTGTACTAGAACGGTTCACCACTC
25349400 AACTTGTACT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.17, C:0.23, G:0.21, T:0.39
Consensus pattern (37 bp):
TTGGCTTTGTTTGTACTAGAACGGTTCACCACTCTTA
Found at i:25356163 original size:69 final size:67
Alignment explanation
Indices: 25355961--25356217 Score: 246
Period size: 69 Copynumber: 3.8 Consensus size: 67
25355951 TTTATCTGAC
* * * * * *
25355961 GTCATAGCCCAACTATGGTCTTACATAGTATAAACCCATGTTTAATGTCTTGGCAACTCCATATA
1 GTCATAGCCTAACTATGGTCTTACACATTATAAACCCATGTTTAATGTCCTGACAACTCCATATG
25356026 TT
66 TT
* * * * * * *
25356028 GTCATACCCTAATTATGGTCTTAAACAATATAAACCCTTGTTTAATGTCTTGGAGAACTCCATAT
1 GTCATAGCCTAACTATGGTCTTACACATTATAAACCCATGTTTAATGTCCT-GACAACTCCATAT
25356093 GTT
65 GTT
* * * * *
25356096 -TCCATAGCCTAACTATGGTCTTACATATTGTGAATCCCATGTTTAATATCCTGACAAACTTCAT
1 GT-CATAGCCTAACTATGGTCTTACACATTAT-AAACCCATGTTTAATGTCCTGAC-AACTCCAT
25356160 ATGTT
63 ATGTT
* * * * * *
25356165 GTAATAGTCTAATTATGGTCTTACACATTGTGAATCTCATGTTTAATGTCCTG
1 GTCATAGCCTAACTATGGTCTTACACATTAT-AAACCCATGTTTAATGTCCTG
25356218 GCAGACTGTA
Statistics
Matches: 157, Mismatches: 28, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
67 45 0.29
68 38 0.24
69 73 0.46
70 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (67 bp):
GTCATAGCCTAACTATGGTCTTACACATTATAAACCCATGTTTAATGTCCTGACAACTCCATATG
TT
Found at i:25359369 original size:41 final size:41
Alignment explanation
Indices: 25359306--25359401 Score: 106
Period size: 41 Copynumber: 2.3 Consensus size: 41
25359296 TGATTCCAGT
* *
25359306 TGGAAGCGTTTTCAGCTGATTTG-AAGAAAATCGCGTCTAGC
1 TGGAAGCGTTTTCAGATGATTTGCAAGAAAAT-GCGTCTAGA
* * *
25359347 TGGATGCGTTTTCA-ATGTATTTGCAGGAAAATGCTTCTAGA
1 TGGAAGCGTTTTCAGATG-ATTTGCAAGAAAATGCGTCTAGA
*
25359388 TGAAAGCGTTTTCA
1 TGGAAGCGTTTTCA
25359402 TTGTGCATTT
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
40 2 0.04
41 37 0.80
42 7 0.15
ACGTcount: A:0.27, C:0.15, G:0.25, T:0.33
Consensus pattern (41 bp):
TGGAAGCGTTTTCAGATGATTTGCAAGAAAATGCGTCTAGA
Found at i:25361943 original size:41 final size:41
Alignment explanation
Indices: 25361862--25361970 Score: 145
Period size: 41 Copynumber: 2.8 Consensus size: 41
25361852 CTTCGAGTCA
* * *
25361862 ATGAGGCACTAGGTGCCAATTTA--A-TTCAG-TTTAATCG
1 ATGAGACACTAGGTGTCAATTTACTACTTCGGATTTAATCG
* *
25361899 ATGAGACACTTGGTGTCAATTTACTACTTCGGATTTATTCG
1 ATGAGACACTAGGTGTCAATTTACTACTTCGGATTTAATCG
25361940 ATGAGACACTAGGTGTCAATTTACTACTTCG
1 ATGAGACACTAGGTGTCAATTTACTACTTCG
25361971 AATTATCCGA
Statistics
Matches: 62, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
37 20 0.32
39 1 0.02
40 4 0.06
41 37 0.60
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (41 bp):
ATGAGACACTAGGTGTCAATTTACTACTTCGGATTTAATCG
Found at i:25366247 original size:14 final size:14
Alignment explanation
Indices: 25366228--25366257 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
25366218 TGATTGTTTT
25366228 TAATCTAATTTAAC
1 TAATCTAATTTAAC
25366242 TAATCTAATTTAAC
1 TAATCTAATTTAAC
25366256 TA
1 TA
25366258 CGAACGCAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.43, C:0.13, G:0.00, T:0.43
Consensus pattern (14 bp):
TAATCTAATTTAAC
Found at i:25368470 original size:24 final size:24
Alignment explanation
Indices: 25368443--25368492 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
25368433 CCAAAGTCAA
25368443 CTTAAGATTTCAGAAACTGAAACC
1 CTTAAGATTTCAGAAACTGAAACC
*
25368467 CTTAGGATTTCAGAAACTGAAACC
1 CTTAAGATTTCAGAAACTGAAACC
25368491 CT
1 CT
25368493 AAGCGCCACA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.38, C:0.22, G:0.14, T:0.26
Consensus pattern (24 bp):
CTTAAGATTTCAGAAACTGAAACC
Found at i:25369683 original size:2 final size:2
Alignment explanation
Indices: 25369676--25369715 Score: 55
Period size: 2 Copynumber: 20.0 Consensus size: 2
25369666 TGTTATAAAC
*
25369676 AT AT AT AT AT AT AT AT AT AC AT -T CAT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT
25369716 TATTTCATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 1 0.03
2 32 0.94
3 1 0.03
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:25369845 original size:17 final size:20
Alignment explanation
Indices: 25369801--25369846 Score: 55
Period size: 18 Copynumber: 2.5 Consensus size: 20
25369791 GCATACTTAC
25369801 ATATATTTTTATATTACATA
1 ATATATTTTTATATTACATA
*
25369821 AT-T-TTTTT-TAATACA-A
1 ATATATTTTTATATTACATA
25369837 ATATATTTTT
1 ATATATTTTT
25369847 TCTTTTCATG
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
16 3 0.13
17 7 0.30
18 10 0.43
19 1 0.04
20 2 0.09
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (20 bp):
ATATATTTTTATATTACATA
Found at i:25373376 original size:247 final size:247
Alignment explanation
Indices: 25372914--25373405 Score: 849
Period size: 247 Copynumber: 2.0 Consensus size: 247
25372904 CCCGATGTCG
* * *
25372914 AATCCAGAAACTACTCGATCTTTAGAGGAGTACCTACAAGTATTGCCCTCTGAGATAGAAGTAAT
1 AATCCAGAAACTACTCGACCTTTAGAGGAGCACCTACAAGTATTGCCCTCTGAGATAGAAATAAT
* * *
25372979 CAAACAAGATTTTGAAAAGAGGAGTTTGGAGTTAGGGAAGAAAATAGAGCAACTAGAATAAGAAA
66 CAAACAAGATTTTGAAAAGAGGAGTTTGGAGTTAAGGAAGAAAATAGAACAACTAGAAGAAGAAA
25373044 AAATGCAATTAGGACTAGATGTTGATGTTCAAAAATTAGAGGCCGACAAACTGAGAAAAGGGAAG
131 AAATGCAATTAGGACTAGATGTTGATGTTCAAAAATTAGAGGCCGACAAACTGAGAAAAGGGAAG
*
25373109 AACAAGGTAGAGGAAGATTTAGACAGCCTGAAGACAGATTACAAGAAGTTAC
196 AACAAGGCAGAGGAAGATTTAGACAGCCTGAAGACAGATTACAAGAAGTTAC
* *
25373161 AATCCATAAACTGCTCGACCTTTAGAGGAGCACCTACAAGTATTGCCCTCTGAGATAGAAATAAT
1 AATCCAGAAACTACTCGACCTTTAGAGGAGCACCTACAAGTATTGCCCTCTGAGATAGAAATAAT
25373226 CAAACAAGATTTTGAAAAGAGGAGTTTGGAGTTAAGGAAGAAAATAGAACAACTAGAAGAAGAAA
66 CAAACAAGATTTTGAAAAGAGGAGTTTGGAGTTAAGGAAGAAAATAGAACAACTAGAAGAAGAAA
* * *
25373291 AAATGCAATTAGGACTTGATGTTGATGTTCAAAAATTAGAGGCTGATAAACTGAGAAAAGGGAAG
131 AAATGCAATTAGGACTAGATGTTGATGTTCAAAAATTAGAGGCCGACAAACTGAGAAAAGGGAAG
* * *
25373356 AACAAGGCAGAGGGAGATTTAGACAGTCTGAAGACGGATTACAAGAAGTT
196 AACAAGGCAGAGGAAGATTTAGACAGCCTGAAGACAGATTACAAGAAGTT
25373406 GCATAGGTCA
Statistics
Matches: 230, Mismatches: 15, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
247 230 1.00
ACGTcount: A:0.43, C:0.12, G:0.24, T:0.21
Consensus pattern (247 bp):
AATCCAGAAACTACTCGACCTTTAGAGGAGCACCTACAAGTATTGCCCTCTGAGATAGAAATAAT
CAAACAAGATTTTGAAAAGAGGAGTTTGGAGTTAAGGAAGAAAATAGAACAACTAGAAGAAGAAA
AAATGCAATTAGGACTAGATGTTGATGTTCAAAAATTAGAGGCCGACAAACTGAGAAAAGGGAAG
AACAAGGCAGAGGAAGATTTAGACAGCCTGAAGACAGATTACAAGAAGTTAC
Found at i:25379265 original size:68 final size:68
Alignment explanation
Indices: 25379156--25379291 Score: 272
Period size: 68 Copynumber: 2.0 Consensus size: 68
25379146 CAAATTGAGA
25379156 AGCTATGTTGTGCCCTGATTTGGACAACTTGGAGATTGAGACAATACATGTTGTACCATACAACC
1 AGCTATGTTGTGCCCTGATTTGGACAACTTGGAGATTGAGACAATACATGTTGTACCATACAACC
25379221 TGG
66 TGG
25379224 AGCTATGTTGTGCCCTGATTTGGACAACTTGGAGATTGAGACAATACATGTTGTACCATACAACC
1 AGCTATGTTGTGCCCTGATTTGGACAACTTGGAGATTGAGACAATACATGTTGTACCATACAACC
25379289 TGG
66 TGG
25379292 TTAATCTCTA
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 68 1.00
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.29
Consensus pattern (68 bp):
AGCTATGTTGTGCCCTGATTTGGACAACTTGGAGATTGAGACAATACATGTTGTACCATACAACC
TGG
Found at i:25382524 original size:44 final size:44
Alignment explanation
Indices: 25382437--25382540 Score: 138
Period size: 44 Copynumber: 2.4 Consensus size: 44
25382427 AAACCTTATC
* ** * *
25382437 CCCTAAAGTTGCAGTGGAGCAGGTTGAATATACAAGTCTTACTT
1 CCCTGAAGTTGCAGTGGAGCAGACTGAAGATACAAGTCCTACTT
*
25382481 CCCTGAAGTTGCAGTGGAGCAGACTGAAGCTACTAA-TCCTACTT
1 CCCTGAAGTTGCAGTGGAGCAGACTGAAGATAC-AAGTCCTACTT
25382525 CCCTGAAGTTGCAGTG
1 CCCTGAAGTTGCAGTG
25382541 AAGCGGATTA
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
44 51 0.96
45 2 0.04
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.27
Consensus pattern (44 bp):
CCCTGAAGTTGCAGTGGAGCAGACTGAAGATACAAGTCCTACTT
Found at i:25384289 original size:2 final size:2
Alignment explanation
Indices: 25384282--25384321 Score: 55
Period size: 2 Copynumber: 20.0 Consensus size: 2
25384272 TGTTATAAAC
*
25384282 AT AT AT AT AT AT AT AT AT AC AT -T CAT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT
25384322 TATTTCATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 1 0.03
2 32 0.94
3 1 0.03
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:25384451 original size:17 final size:20
Alignment explanation
Indices: 25384407--25384452 Score: 55
Period size: 18 Copynumber: 2.5 Consensus size: 20
25384397 GCATACTTAC
25384407 ATATATTTTTATATTACATA
1 ATATATTTTTATATTACATA
*
25384427 AT-T-TTTTT-TAATACA-A
1 ATATATTTTTATATTACATA
25384443 ATATATTTTT
1 ATATATTTTT
25384453 TCTTTTCATG
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
16 3 0.13
17 7 0.30
18 10 0.43
19 1 0.04
20 2 0.09
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (20 bp):
ATATATTTTTATATTACATA
Found at i:25387918 original size:96 final size:96
Alignment explanation
Indices: 25387681--25387923 Score: 405
Period size: 96 Copynumber: 2.5 Consensus size: 96
25387671 AGCCCCTTAA
* ** **
25387681 GCCAAAACCACCGAAAGAAGAGGAATCACCTGTAACAAGGGAACGACCTCCACCACTTAAATTGC
1 GCCAAAACCACCGAAACAAGAGGAATCACCTGTAACAAGGGAACGGTCTCCACCACCAAAATTGC
*
25387746 CACCGCCAGTTGTTAAGCCCCCGACACCAGT
66 CACCGCCAGTTATTAAGCCCCCGACACCAGT
*
25387777 GTCAAAACCACCGAAACAAGAGGAATCACCTGTAACAAGGGAACGGTCTCCACCACCAAAATTGC
1 GCCAAAACCACCGAAACAAGAGGAATCACCTGTAACAAGGGAACGGTCTCCACCACCAAAATTGC
25387842 CACCGCCAGTTATTAAGCCCCCGACACCAGT
66 CACCGCCAGTTATTAAGCCCCCGACACCAGT
* *
25387873 GCCAAAACCACCGACACAAGAGGAATCACCTATAACAAGGGAACGGTCTCC
1 GCCAAAACCACCGAAACAAGAGGAATCACCTGTAACAAGGGAACGGTCTCC
25387924 GCCAGTTATT
Statistics
Matches: 137, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
96 137 1.00
ACGTcount: A:0.36, C:0.33, G:0.19, T:0.13
Consensus pattern (96 bp):
GCCAAAACCACCGAAACAAGAGGAATCACCTGTAACAAGGGAACGGTCTCCACCACCAAAATTGC
CACCGCCAGTTATTAAGCCCCCGACACCAGT
Found at i:25387973 original size:78 final size:78
Alignment explanation
Indices: 25387844--25388001 Score: 271
Period size: 78 Copynumber: 2.0 Consensus size: 78
25387834 AAAATTGCCA
* *
25387844 CCGCCAGTTATTAAGCCCCCGACACCAGTGCCAAAACCACCGACACAAGAGGAATCACCTATAAC
1 CCGCCAGTTATTAAGCCCCCGACACCAGTGCAAAAACCACCGAAACAAGAGGAATCACCTATAAC
25387909 AAGGGAACGGTCT
66 AAGGGAACGGTCT
* * *
25387922 CCGCCAGTTATTAAGCCCCCGCCACCAGTGGAAAAACCACCGAAACAAGAGGAATCACCTGTAAC
1 CCGCCAGTTATTAAGCCCCCGACACCAGTGCAAAAACCACCGAAACAAGAGGAATCACCTATAAC
25387987 AAGGGAACGGTCT
66 AAGGGAACGGTCT
25388000 CC
1 CC
25388002 ACCACCAAAA
Statistics
Matches: 75, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
78 75 1.00
ACGTcount: A:0.34, C:0.33, G:0.20, T:0.13
Consensus pattern (78 bp):
CCGCCAGTTATTAAGCCCCCGACACCAGTGCAAAAACCACCGAAACAAGAGGAATCACCTATAAC
AAGGGAACGGTCT
Found at i:25388067 original size:24 final size:24
Alignment explanation
Indices: 25388040--25388113 Score: 82
Period size: 24 Copynumber: 3.2 Consensus size: 24
25388030 AAGCCCCTGA
*
25388040 CACCACCAGTCCACTCTCCACCAC
1 CACCACCAGTTCACTCTCCACCAC
*
25388064 CACCACCAATTCA-T-T-CACCAC
1 CACCACCAGTTCACTCTCCACCAC
* * *
25388085 CTCCACCTGTTCACTCTCCTCCAC
1 CACCACCAGTTCACTCTCCACCAC
25388109 CACCA
1 CACCA
25388114 GTGCATTCTC
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
21 16 0.40
22 2 0.05
23 2 0.05
24 20 0.50
ACGTcount: A:0.24, C:0.54, G:0.03, T:0.19
Consensus pattern (24 bp):
CACCACCAGTTCACTCTCCACCAC
Found at i:25388111 original size:21 final size:21
Alignment explanation
Indices: 25388087--25388130 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
25388077 TTCACCACCT
* * *
25388087 CCACCTGTTCACTCTCCTCCA
1 CCACCAGTGCACTCTCCGCCA
*
25388108 CCACCAGTGCATTCTCCGCCA
1 CCACCAGTGCACTCTCCGCCA
25388129 CC
1 CC
25388131 TCTTTCTCCT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.52, G:0.09, T:0.23
Consensus pattern (21 bp):
CCACCAGTGCACTCTCCGCCA
Found at i:25390531 original size:3 final size:3
Alignment explanation
Indices: 25390519--25390584 Score: 50
Period size: 3 Copynumber: 21.7 Consensus size: 3
25390509 CCAAAATACT
*
25390519 TAA T-A TAA TAA T-A TAA TAA TAA TGAA TAGA TAGA TAA -AA GGAA -AA
1 TAA TAA TAA TAA TAA TAA TAA TAA T-AA TA-A TA-A TAA TAA -TAA TAA
25390564 TAA TAAA TAA TAA TAA TAA TA
1 TAA T-AA TAA TAA TAA TAA TA
25390585 TCAAATTTAT
Statistics
Matches: 55, Mismatches: 0, Indels: 16
0.77 0.00 0.23
Matches are distributed among these distances:
2 8 0.15
3 32 0.58
4 15 0.27
ACGTcount: A:0.64, C:0.00, G:0.08, T:0.29
Consensus pattern (3 bp):
TAA
Found at i:25392129 original size:45 final size:44
Alignment explanation
Indices: 25392060--25392630 Score: 282
Period size: 44 Copynumber: 12.6 Consensus size: 44
25392050 TTTAATATGT
* * * *
25392060 TCCACTACAACTTCAAGGAAATAAGATTCGCTATCTTCAGTCTGC
1 TCCACTGCAACTTCAGGGAGATAAGATTCG-TATCTTCAATCTGC
* *
25392105 TCCACTGCAACTTCAGGGAGATAAGACTT-GTATCTTCAACCTAC
1 TCCACTGCAACTTCAGGGAGATAAGA-TTCGTATCTTCAATCTGC
* * ** * *
25392149 CCCACTGCAACTTCAGGGAGATAATG-TTTGTGGCTTTAATCTAC
1 TCCACTGCAACTTCAGGGAGATAA-GATTCGTATCTTCAATCTGC
* *
25392193 TCCACTACAACTTCAGGGAGATAAGATTTGTAGCCTATCTTCAATCTGC
1 TCCACTGCAACTTCAGGGAGATAAGA--T-T--CGTATCTTCAATCTGC
* * * * *
25392242 TCAACTGTAACTTCAGGGAGATAAGATT-GTTTATTTTTAACCTGC
1 TCCACTGCAACTTCAGGGAGATAAGATTCG--TATCTTCAATCTGC
* ** * * * *
25392287 TCCACTGTAACTTCAATGAGATAAGGTTTG-AT-AT-GATCTGC
1 TCCACTGCAACTTCAGGGAGATAAGATTCGTATCTTCAATCTGC
* * * * *
25392328 TCTACTGCAACTTTAGAGAGATAAGA-TCGATAATTTATAGCTTTAATCTGT
1 TCCACTGCAACTTCAGGGAGATAAGATTCG------TAT--CTTCAATCTGC
* * * * *
25392379 TCCACGGCAACTTCATGGAAATAAGATTCGCTTTCTTCAGTCTGC
1 TCCACTGCAACTTCAGGGAGATAAGATTCG-TATCTTCAATCTGC
* * * *
25392424 TCCACTGCAACTTTAGGGAGATAAGACTCGTTATGGTAGATTTAATCTGAC
1 TCCACTGCAACTTCAGGGAGATAAGATTCG-TA---T--CTTCAATCTG-C
* * * * *
25392475 -CTACTGCAACTTCAGAGG-TATAGGATT--TATCGTTTTAATCCGC
1 TCCACTGCAACTTCAG-GGAGATAAGATTCGTATC--TTCAATCTGC
* * * ** *
25392518 TCCAATGCAACTTCAAGGAGATAGGATTAATAGCTTCAATCTGC
1 TCCACTGCAACTTCAGGGAGATAAGATTCGTATCTTCAATCTGC
* * * *
25392562 TCTACTGCAACTTCAGGGAGATAAGATTGGTATTTTCAACCTGC
1 TCCACTGCAACTTCAGGGAGATAAGATTCGTATCTTCAATCTGC
** *
25392606 TCCGTTTCAACTTCAGGGAGATAAG
1 TCCACTGCAACTTCAGGGAGATAAG
25392631 GTTGGTTATC
Statistics
Matches: 398, Mismatches: 91, Indels: 75
0.71 0.16 0.13
Matches are distributed among these distances:
40 2 0.01
41 25 0.06
42 1 0.00
43 8 0.02
44 160 0.40
45 94 0.24
46 8 0.02
47 8 0.02
48 1 0.00
49 33 0.08
50 27 0.07
51 28 0.07
52 3 0.01
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (44 bp):
TCCACTGCAACTTCAGGGAGATAAGATTCGTATCTTCAATCTGC
Found at i:25392605 original size:319 final size:317
Alignment explanation
Indices: 25391999--25392608 Score: 775
Period size: 319 Copynumber: 1.9 Consensus size: 317
25391989 TTAGACTTGT
* * *
25391999 TATGATCTGCTCTACTGTAACTTCAGAGAAATAAGATCGGTAATTTATAGTTTTAATATGTTCCA
1 TATGATCTGCTCTACTGCAACTTCAGAGAAATAAGATCGATAATTTATAGCTTTAATATGTTCCA
*
25392064 CTACAACTTCAAGGAAATAAGATTCGCTATCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAA
66 CGACAACTTCAAGGAAATAAGATTCGCTATCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAA
** * * * *
25392129 GACTTGTATCTTCAACCTACCCCACTGCAACTTCAGGGAGATAATGTTTGTGGCTTTAATCTACT
131 GACTTGTAGATTCAACCTACCCCACTGCAACTTCAGGGAGATAAGGTTTATCGCTTTAATCCACT
* * * * *
25392194 CCACTACAACTTCAGGGAGATAAGATTTGTAGCCTATCTTCAATCTGCTCAACTGTAACTTCAGG
196 CCAATACAACTTCAAGGAGATAAGA-TTGTA-CATAGCTTCAATCTGCTCAACTGCAACTTCAGG
* *
25392259 GAGATAAGATTGTTTATTTTTAACCTGCTCCACTGTAACTTCAATGAGATAAGGTTTGA
259 GAGATAAGATTGTGTATTTTCAACCTGCTCCACTGTAACTTCAATGAGATAAGGTTTGA
* * *
25392318 TATGATCTGCTCTACTGCAACTTTAGAGAGATAAGATCGATAATTTATAGCTTTAATCTGTTCCA
1 TATGATCTGCTCTACTGCAACTTCAGAGAAATAAGATCGATAATTTATAGCTTTAATATGTTCCA
* * * *
25392383 CGGCAACTTCATGGAAATAAGATTCGCTTTCTTCAGTCTGCTCCACTGCAACTTTAGGGAGATAA
66 CGACAACTTCAAGGAAATAAGATTCGCTATCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAA
* * * * *
25392448 GACTCGTTATGGTAGATTTAATCTGA-CCTACTGCAACTTCA--GAGGTATAGGATTTATCGTTT
131 GA--C--T-T-GTAGATTCAACCT-ACCCCACTGCAACTTCAGGGAGATA-AGG-TTTATCGCTT
* * * *
25392510 TAATCCGCTCCAATGCAACTTCAAGGAGATAGGA-T-TA-ATAGCTTCAATCTGCTCTACTGCAA
187 TAATCCACTCCAATACAACTTCAAGGAGATAAGATTGTACATAGCTTCAATCTGCTCAACTGCAA
25392572 CTTCAGGGAGATAAGATTG-GTATTTTCAACCTGCTCC
252 CTTCAGGGAGATAAGATTGTGTATTTTCAACCTGCTCC
25392609 GTTTCAACTT
Statistics
Matches: 249, Mismatches: 33, Indels: 18
0.83 0.11 0.06
Matches are distributed among these distances:
319 137 0.55
320 40 0.16
321 1 0.00
322 2 0.01
323 7 0.03
324 3 0.01
325 58 0.23
326 1 0.00
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (317 bp):
TATGATCTGCTCTACTGCAACTTCAGAGAAATAAGATCGATAATTTATAGCTTTAATATGTTCCA
CGACAACTTCAAGGAAATAAGATTCGCTATCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAA
GACTTGTAGATTCAACCTACCCCACTGCAACTTCAGGGAGATAAGGTTTATCGCTTTAATCCACT
CCAATACAACTTCAAGGAGATAAGATTGTACATAGCTTCAATCTGCTCAACTGCAACTTCAGGGA
GATAAGATTGTGTATTTTCAACCTGCTCCACTGTAACTTCAATGAGATAAGGTTTGA
Found at i:25392900 original size:44 final size:43
Alignment explanation
Indices: 25392798--25392925 Score: 114
Period size: 44 Copynumber: 2.9 Consensus size: 43
25392788 AATATGCTCC
* * *
25392798 GCTTTAGTCTGTTCCACTGCAACTTCAGAGAGATAAT-ACTTGTA
1 GCTTTAATCTGCTCCACTGCAACTTCAGGGAGAT-ATGA-TTGTA
* * * * *
25392842 ACTTCAATCCGCTCCACTGCAACTTTAGGGAGATATGATTATTA
1 GCTTTAATCTGCTCCACTGCAACTTCAGGGAGATATGATT-GTA
* * * *
25392886 GCTTTAATCTGCTCCATTGTAACTTCAGGGAAATAAGATT
1 GCTTTAATCTGCTCCACTGCAACTTCAGGGAGATATGATT
25392926 CGCCATTTTC
Statistics
Matches: 66, Mismatches: 16, Indels: 4
0.77 0.19 0.05
Matches are distributed among these distances:
43 4 0.06
44 62 0.94
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (43 bp):
GCTTTAATCTGCTCCACTGCAACTTCAGGGAGATATGATTGTA
Found at i:25394232 original size:15 final size:15
Alignment explanation
Indices: 25394212--25394254 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
25394202 TGGCCTCTCA
25394212 TTTTTCTTTTTCCTT
1 TTTTTCTTTTTCCTT
* *
25394227 TTTTTCTCTTCTCTTT
1 TTTTTCT-TTTTCCTT
25394243 TCTTTTCTTTTT
1 T-TTTTCTTTTT
25394255 TCATCATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
15 7 0.30
16 10 0.43
17 6 0.26
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTTTCTTTTTCCTT
Found at i:25395696 original size:13 final size:13
Alignment explanation
Indices: 25395678--25395702 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
25395668 TATTTTAATA
25395678 TTATTTTGTGTGT
1 TTATTTTGTGTGT
25395691 TTATTTTGTGTG
1 TTATTTTGTGTG
25395703 CATTTGATTG
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:0.08, C:0.00, G:0.24, T:0.68
Consensus pattern (13 bp):
TTATTTTGTGTGT
Found at i:25415600 original size:20 final size:21
Alignment explanation
Indices: 25415577--25415617 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
25415567 GTATAAAAGC
25415577 TAAAAGTGA-ATAATAA-ATAA
1 TAAAA-TGATATAATAAGATAA
25415597 TAAAATGATATAATAAGATAA
1 TAAAATGATATAATAAGATAA
25415618 ATATATATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 3 0.16
20 12 0.63
21 4 0.21
ACGTcount: A:0.63, C:0.00, G:0.10, T:0.27
Consensus pattern (21 bp):
TAAAATGATATAATAAGATAA
Found at i:25415656 original size:14 final size:13
Alignment explanation
Indices: 25415624--25415672 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 13
25415614 ATAAATATAT
25415624 ATAAAAATTAAAAA
1 ATAAAAA-TAAAAA
*
25415638 TTAAAAATAAACAA
1 ATAAAAATAAA-AA
*
25415652 ATAAAATATAAAAT
1 ATAAAA-ATAAAAA
25415666 ATAAAAA
1 ATAAAAA
25415673 ATAATGCAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
13 5 0.17
14 20 0.67
15 5 0.17
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (13 bp):
ATAAAAATAAAAA
Found at i:25415663 original size:21 final size:20
Alignment explanation
Indices: 25415622--25415676 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 20
25415612 AGATAAATAT
*
25415622 ATATAAAAATTAAAAATTAAA
1 ATATAAAAAAT-AAAATTAAA
25415643 A-ATAAACAAATAAAATATAAA
1 ATATAAA-AAATAAAAT-TAAA
25415664 ATATAAAAAATAA
1 ATATAAAAAATAA
25415677 TGCAAAACTA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
20 10 0.33
21 15 0.50
22 5 0.17
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.24
Consensus pattern (20 bp):
ATATAAAAAATAAAATTAAA
Found at i:25419136 original size:11 final size:13
Alignment explanation
Indices: 25419112--25419143 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
25419102 TAGTTTATTA
25419112 ATATTTTAATATG
1 ATATTTTAATATG
25419125 AT-TTTTAA-ATG
1 ATATTTTAATATG
25419136 ATATTTTA
1 ATATTTTA
25419144 TTAATTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 5 0.28
12 11 0.61
13 2 0.11
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (13 bp):
ATATTTTAATATG
Found at i:25421066 original size:54 final size:54
Alignment explanation
Indices: 25420962--25421066 Score: 138
Period size: 54 Copynumber: 1.9 Consensus size: 54
25420952 TGTATAATAT
* * * * *
25420962 AAGGTCACACGGCTGTGTGGCCAGGCCGTGTAACTCTCTATGATCGTGTGGCTC
1 AAGGTCACACGACTATGTCGCCAGGCCGTGTAACTCTCTATGACCATGTGGCTC
* * *
25421016 AAGGTCACACGACTATGTCTCCAGGCCGTGTAATTCTCTATGCCCATGTGG
1 AAGGTCACACGACTATGTCGCCAGGCCGTGTAACTCTCTATGACCATGTGG
25421067 ATTGACCTGC
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
54 43 1.00
ACGTcount: A:0.19, C:0.27, G:0.28, T:0.27
Consensus pattern (54 bp):
AAGGTCACACGACTATGTCGCCAGGCCGTGTAACTCTCTATGACCATGTGGCTC
Found at i:25430812 original size:43 final size:43
Alignment explanation
Indices: 25430743--25430824 Score: 128
Period size: 43 Copynumber: 1.9 Consensus size: 43
25430733 ATTGTATCTA
** *
25430743 CATTTTAAAGCTGATTTCTTATTACCTATAGGAAAGACCCAGT
1 CATTTTAAAGCTGACATCTTACTACCTATAGGAAAGACCCAGT
*
25430786 CATTTTAAAGCTGACATCTTGCTACCTATAGGAAAGACC
1 CATTTTAAAGCTGACATCTTACTACCTATAGGAAAGACC
25430825 AAGAACATGT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 35 1.00
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.32
Consensus pattern (43 bp):
CATTTTAAAGCTGACATCTTACTACCTATAGGAAAGACCCAGT
Found at i:25437069 original size:81 final size:82
Alignment explanation
Indices: 25436947--25437112 Score: 325
Period size: 81 Copynumber: 2.0 Consensus size: 82
25436937 ATTTGTTTAC
25436947 TTTGTTGACGTGACAATCTAATTTTTTAAAACCAATTAACTTTTTAATCCATACGTATGATACAT
1 TTTGTTGACGTGACAATCTAATTTTTTAAAACCAATTAACTTTTTAATCCATACGTATGATACAT
25437012 TAGTAA-TAATTAATTT
66 TAGTAATTAATTAATTT
25437028 TTTGTTGACGTGACAATCTAATTTTTTAAAACCAATTAACTTTTTAATCCATACGTATGATACAT
1 TTTGTTGACGTGACAATCTAATTTTTTAAAACCAATTAACTTTTTAATCCATACGTATGATACAT
25437093 TAGTAATTAATTAATTT
66 TAGTAATTAATTAATTT
25437110 TTT
1 TTT
25437113 AAAATTAAAA
Statistics
Matches: 84, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
81 71 0.85
82 13 0.15
ACGTcount: A:0.35, C:0.12, G:0.08, T:0.45
Consensus pattern (82 bp):
TTTGTTGACGTGACAATCTAATTTTTTAAAACCAATTAACTTTTTAATCCATACGTATGATACAT
TAGTAATTAATTAATTT
Found at i:25451333 original size:18 final size:19
Alignment explanation
Indices: 25451297--25451337 Score: 66
Period size: 18 Copynumber: 2.2 Consensus size: 19
25451287 TCTCATTGCA
*
25451297 TCATTTTATATTTCATTTC
1 TCATTTTATATTCCATTTC
25451316 TCATTTTATA-TCCATTTC
1 TCATTTTATATTCCATTTC
25451334 TCAT
1 TCAT
25451338 CTTTTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 11 0.52
19 10 0.48
ACGTcount: A:0.22, C:0.20, G:0.00, T:0.59
Consensus pattern (19 bp):
TCATTTTATATTCCATTTC
Done.