Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A12
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: 103038859
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4950000 characters in sequence are not A, C, G, or T
File 88 of 320
Found at i:28013309 original size:79 final size:79
Alignment explanation
Indices: 28013080--28013345 Score: 211
Period size: 79 Copynumber: 3.3 Consensus size: 79
28013070 ATATAACACC
* * * * * * *
28013080 AGCACGAATGCTCTTCGGGGTTTAGCACGGATATA-TCATTAGCACGAATGCTCTTCGGAACTTA
1 AGCAC-AATGC-CTTC-GGGCTTAGCCCGGATATAGTAACTCGCACAAATGC-CTTCGGGACTTA
* * *
28013144 GCCCGGATACA-TCAC-T
62 ACCCGGATATAGTAACTT
* * *
28013160 AGCATGAATGCTCTTCGAGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAA
1 AGCA-CAATGC-CTTCG-GGCTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAA
*
28013225 CCCGGATTTAGTAAC-T
63 CCCGGATATAGTAACTT
* *
28013241 CGCACCAATGCCTTCGGGCTTAGCCCGGA-ATTAGTAACTCGCACAAATGCCTTC-GGATCTTAG
1 AGCA-CAATGCCTTCGGGCTTAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAA
* * *
28013304 TCCGGATATGGTCACTT
63 CCCGGATATAGTAACTT
*
28013321 AGCACAAAGCCTTCGGGACTTAGCC
1 AGCACAATGCCTTCGGG-CTTAGCC
28013346 TGGACATCAT
Statistics
Matches: 152, Mismatches: 26, Indels: 16
0.78 0.13 0.08
Matches are distributed among these distances:
78 4 0.03
79 62 0.41
80 62 0.41
81 24 0.16
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.26
Consensus pattern (79 bp):
AGCACAATGCCTTCGGGCTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCC
GGATATAGTAACTT
Found at i:28013696 original size:29 final size:29
Alignment explanation
Indices: 28013657--28013735 Score: 106
Period size: 29 Copynumber: 2.7 Consensus size: 29
28013647 CTTAATAATC
*
28013657 AACCACGCACACTTAGTGCCATGTACTTT-A
1 AACC-CGCACACTTAGTGCCATGCA-TTTCA
*
28013687 AACTCGCACACTTAGTGCCATGCATTTCA
1 AACCCGCACACTTAGTGCCATGCATTTCA
*
28013716 AGCCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
28013736 ATCCACAACC
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
28 3 0.07
29 38 0.86
30 3 0.07
ACGTcount: A:0.28, C:0.33, G:0.15, T:0.24
Consensus pattern (29 bp):
AACCCGCACACTTAGTGCCATGCATTTCA
Found at i:28015680 original size:37 final size:37
Alignment explanation
Indices: 28015630--28015708 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
28015620 TTATTACGAA
* *
28015630 GTCTTACCCGGACATAA-TCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATTC-CCACACGAAGTCATCGG
*
28015667 GTCTTACCCGGACAAAATTCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
28015704 GTCTT
1 GTCTT
28015709 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 36 0.95
38 2 0.05
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.25
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
Found at i:28015905 original size:47 final size:47
Alignment explanation
Indices: 28015878--28016455 Score: 740
Period size: 47 Copynumber: 12.0 Consensus size: 47
28015868 CTCGGCCCCG
*
28015878 TCACAAATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
1 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
28015925 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
1 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
*
28015972 TTACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
1 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
* *
28016019 TCAGATATATACACTTTCACATTCATCACATC-G-CATTCA-TCAC--A
1 TCACATATATACACTTTCACATTCATCACATCGGCCATT-AGGC-CTTA
* ** **
28016063 TCGGC-TAT-TAGGC-CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCT
1 TC-ACATATATA--CACTT-TCAC--AT-T-CA---TCACA-TCGGC-CAT---TA----GGCCT
28016125 TA
46 TA
*
28016127 TTACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
1 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
28016174 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
1 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
* *
28016221 TTACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTA
1 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
*
28016268 TCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTA
1 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
* *
28016315 TCACACATATACACTTTCACATACATCACATCGGCCATTAGGCCTTA
1 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
*
28016362 TCACATATATACACTTTTACATTCATCACATCGGCCATTAGGCCTTA
1 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
* *
28016409 TCACATATATACACTTTCACATGCTTCACATCGGCCATTAGGCCTTA
1 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
28016456 CTATCATTTC
Statistics
Matches: 471, Mismatches: 30, Indels: 60
0.84 0.05 0.11
Matches are distributed among these distances:
43 2 0.00
44 9 0.02
45 10 0.02
46 3 0.01
47 400 0.85
48 1 0.00
49 2 0.00
52 5 0.01
53 2 0.00
54 3 0.01
55 3 0.01
56 8 0.02
59 2 0.00
60 1 0.00
61 2 0.00
62 1 0.00
63 7 0.01
64 8 0.02
65 2 0.00
ACGTcount: A:0.30, C:0.29, G:0.09, T:0.33
Consensus pattern (47 bp):
TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
Found at i:28016057 original size:14 final size:14
Alignment explanation
Indices: 28016038--28016065 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
28016028 TACACTTTCA
28016038 CATTCATCACATCG
1 CATTCATCACATCG
28016052 CATTCATCACATCG
1 CATTCATCACATCG
28016066 GCTATTAGGC
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:0.29, C:0.36, G:0.07, T:0.29
Consensus pattern (14 bp):
CATTCATCACATCG
Found at i:28016073 original size:108 final size:108
Alignment explanation
Indices: 28015944--28016159 Score: 396
Period size: 108 Copynumber: 2.0 Consensus size: 108
28015934 TACACTTTCA
*
28015944 CATTCATCACATCGGCCATTAGGCCTTATTACATATATACACTTTCACATTCATCACATCGGCCA
1 CATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCA
*
28016009 TTAGGCCTTATCAGATATATACACTTTCACATTCATCACATCG
66 TTAGGCCTTATCACATATATACACTTTCACATTCATCACATCG
*
28016052 CATTCATCACATCGGCTATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCA
1 CATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCA
*
28016117 TTAGGCCTTATTACATATATACACTTTCACATTCATCACATCG
66 TTAGGCCTTATCACATATATACACTTTCACATTCATCACATCG
28016160 GCCATTAGGC
Statistics
Matches: 104, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
108 104 1.00
ACGTcount: A:0.30, C:0.29, G:0.09, T:0.33
Consensus pattern (108 bp):
CATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCA
TTAGGCCTTATCACATATATACACTTTCACATTCATCACATCG
Found at i:28016088 original size:61 final size:61
Alignment explanation
Indices: 28015991--28016112 Score: 226
Period size: 61 Copynumber: 2.0 Consensus size: 61
28015981 TACACTTTCA
*
28015991 CATTCATCACATCGGCCATTAGGCCTTATCAGATATATACACTTTCACATTCATCACATCG
1 CATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCG
*
28016052 CATTCATCACATCGGCTATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCG
1 CATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCG
28016113 GCCATTAGGC
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
61 59 1.00
ACGTcount: A:0.30, C:0.30, G:0.09, T:0.32
Consensus pattern (61 bp):
CATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCG
Found at i:28018651 original size:24 final size:24
Alignment explanation
Indices: 28018623--28018670 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
28018613 GAACATATAT
*
28018623 ATATATG-AGGTTATAATATGGTTA
1 ATATATGTAGGCT-TAATATGGTTA
*
28018647 ATATATGTATGCTTAATATGGTTA
1 ATATATGTAGGCTTAATATGGTTA
28018671 GATTGAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 18 0.86
25 3 0.14
ACGTcount: A:0.35, C:0.02, G:0.19, T:0.44
Consensus pattern (24 bp):
ATATATGTAGGCTTAATATGGTTA
Found at i:28029325 original size:21 final size:21
Alignment explanation
Indices: 28029299--28029367 Score: 102
Period size: 21 Copynumber: 3.3 Consensus size: 21
28029289 NNNNNNNNNN
28029299 GTGCATGTCATAACATATCAT
1 GTGCATGTCATAACATATCAT
* ***
28029320 GTGCATATCAGGTCATATCAT
1 GTGCATGTCATAACATATCAT
28029341 GTGCATGTCATAACATATCAT
1 GTGCATGTCATAACATATCAT
28029362 GTGCAT
1 GTGCAT
28029368 ATCAGGTCAT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.33
Consensus pattern (21 bp):
GTGCATGTCATAACATATCAT
Found at i:28029350 original size:16 final size:15
Alignment explanation
Indices: 28029323--28029371 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 15
28029313 ATATCATGTG
*
28029323 CATATCAGGTCATAT
1 CATATCATGTCATAT
* *
28029338 CATGTGCATGTCATAA
1 CATAT-CATGTCATAT
28029354 CATATCATGTGCATAT
1 CATATCATGT-CATAT
28029370 CA
1 CA
28029372 GGTCATATCA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
15 9 0.33
16 18 0.67
ACGTcount: A:0.33, C:0.20, G:0.14, T:0.33
Consensus pattern (15 bp):
CATATCATGTCATAT
Found at i:28029358 original size:42 final size:42
Alignment explanation
Indices: 28029299--28029384 Score: 172
Period size: 42 Copynumber: 2.0 Consensus size: 42
28029289 NNNNNNNNNN
28029299 GTGCATGTCATAACATATCATGTGCATATCAGGTCATATCAT
1 GTGCATGTCATAACATATCATGTGCATATCAGGTCATATCAT
28029341 GTGCATGTCATAACATATCATGTGCATATCAGGTCATATCAT
1 GTGCATGTCATAACATATCATGTGCATATCAGGTCATATCAT
28029383 GT
1 GT
28029385 ATATCAATAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Consensus pattern (42 bp):
GTGCATGTCATAACATATCATGTGCATATCAGGTCATATCAT
Found at i:28029378 original size:21 final size:21
Alignment explanation
Indices: 28029312--28029384 Score: 110
Period size: 21 Copynumber: 3.5 Consensus size: 21
28029302 CATGTCATAA
28029312 CATATCATGTGCATATCAGGT
1 CATATCATGTGCATATCAGGT
* ***
28029333 CATATCATGTGCATGTCATAA
1 CATATCATGTGCATATCAGGT
28029354 CATATCATGTGCATATCAGGT
1 CATATCATGTGCATATCAGGT
28029375 CATATCATGT
1 CATATCATGT
28029385 ATATCAATAT
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.34
Consensus pattern (21 bp):
CATATCATGTGCATATCAGGT
Found at i:28033341 original size:16 final size:18
Alignment explanation
Indices: 28033308--28033348 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
28033298 AAATAAATCG
* *
28033308 AAAGGGAAATAGGAG-AA
1 AAAGGAAAAGAGGAGAAA
28033325 AAAGGAAAAGAGG-GAAA
1 AAAGGAAAAGAGGAGAAA
28033342 AAAGGAA
1 AAAGGAA
28033349 TTTGATAGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 1 0.05
17 20 0.95
ACGTcount: A:0.63, C:0.00, G:0.34, T:0.02
Consensus pattern (18 bp):
AAAGGAAAAGAGGAGAAA
Found at i:28038930 original size:26 final size:25
Alignment explanation
Indices: 28038876--28038943 Score: 66
Period size: 26 Copynumber: 2.6 Consensus size: 25
28038866 ACACACCTTA
* *
28038876 GCTCTTATGAGCTTGCCGATTATATG
1 GCTCTTATGAGCTT-CAGATTATAAG
28038902 GCTCTTCATGAGCTTCTAGATT-TAAG
1 GCTCTT-ATGAGCTTC-AGATTATAAG
*
28038928 GCTCTTTGTGAGCTTC
1 GCTC-TTATGAGCTTC
28038944 CCGATAGTGC
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
26 22 0.61
27 14 0.39
ACGTcount: A:0.18, C:0.21, G:0.22, T:0.40
Consensus pattern (25 bp):
GCTCTTATGAGCTTCAGATTATAAG
Found at i:28039054 original size:25 final size:25
Alignment explanation
Indices: 28038995--28039054 Score: 95
Period size: 24 Copynumber: 2.4 Consensus size: 25
28038985 GAGTCCTGTT
28038995 TTATGGCTCTTTGTGAGCTTCCCAA
1 TTATGGCTCTTTGTGAGCTTCCCAA
* *
28039020 -TATGGTTCTTTGTGAGCTTCCTAA
1 TTATGGCTCTTTGTGAGCTTCCCAA
28039044 TTATGGCTCTT
1 TTATGGCTCTT
28039055 ATAAGCGTCC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
24 22 0.71
25 9 0.29
ACGTcount: A:0.15, C:0.20, G:0.20, T:0.45
Consensus pattern (25 bp):
TTATGGCTCTTTGTGAGCTTCCCAA
Found at i:28044845 original size:42 final size:42
Alignment explanation
Indices: 28044784--28044950 Score: 219
Period size: 42 Copynumber: 4.0 Consensus size: 42
28044774 GAAAATATTT
**
28044784 GAGATAGCTTTAGCTATGCATTGGCACTTAGTGTGCGAGATA
1 GAGATAGCTTCGGCTATGCATTGGCACTTAGTGTGCGAGATA
* *
28044826 GGGATAGCTTCGGCTATGCATTGGCACTTAGTGTACGAGATCA
1 GAGATAGCTTCGGCTATGCATTGGCACTTAGTGTGCGAGAT-A
* * *
28044869 -AGATAGCTTCGGCTATGCATTGGCACTTTGTGTGCGTGATT
1 GAGATAGCTTCGGCTATGCATTGGCACTTAGTGTGCGAGATA
* * * *
28044910 GAGTTAGCTTCGGCTACGTATTGACACTTAGTGTGCGAGAT
1 GAGATAGCTTCGGCTATGCATTGGCACTTAGTGTGCGAGAT
28044951 TCTGAGTAAC
Statistics
Matches: 108, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
42 107 0.99
43 1 0.01
ACGTcount: A:0.22, C:0.17, G:0.29, T:0.32
Consensus pattern (42 bp):
GAGATAGCTTCGGCTATGCATTGGCACTTAGTGTGCGAGATA
Found at i:28045051 original size:32 final size:32
Alignment explanation
Indices: 28045015--28045081 Score: 116
Period size: 32 Copynumber: 2.1 Consensus size: 32
28045005 TGAGTATGAG
*
28045015 ATTGGTACGAGATGGTATAGGTATGTACGGAA
1 ATTGGTACAAGATGGTATAGGTATGTACGGAA
*
28045047 ATTGGTACAAGATGGTATAGGTATGTATGGAA
1 ATTGGTACAAGATGGTATAGGTATGTACGGAA
28045079 ATT
1 ATT
28045082 CAATTGAGTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.33, C:0.04, G:0.31, T:0.31
Consensus pattern (32 bp):
ATTGGTACAAGATGGTATAGGTATGTACGGAA
Found at i:28047852 original size:46 final size:46
Alignment explanation
Indices: 28047800--28047918 Score: 186
Period size: 46 Copynumber: 2.6 Consensus size: 46
28047790 ACATCTCTCA
* *
28047800 CATTAGCCATTTGGCTTTACCATATATCCATCTCATACACGTTTCG
1 CATTAGCCATTCGGCTTTACCATATATCCATCTCATACACATTTCG
*
28047846 CATTAGCCATTCGGCTTTACC-TCATACCCATCTCATACACATTTCG
1 CATTAGCCATTCGGCTTTACCAT-ATATCCATCTCATACACATTTCG
*
28047892 CATTAGCCATTCGGCTTTACCACATAT
1 CATTAGCCATTCGGCTTTACCATATAT
28047919 ATGCACTTCC
Statistics
Matches: 66, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
45 1 0.02
46 65 0.98
ACGTcount: A:0.24, C:0.31, G:0.10, T:0.34
Consensus pattern (46 bp):
CATTAGCCATTCGGCTTTACCATATATCCATCTCATACACATTTCG
Found at i:28047966 original size:47 final size:47
Alignment explanation
Indices: 28047892--28048270 Score: 598
Period size: 47 Copynumber: 8.1 Consensus size: 47
28047882 ACACATTTCG
* * * * * **
28047892 CATTAGCCATTCGGCTTTACCACATATATGCACT-TCCACGTTTGTCA
1 CATTGGCCATTCGGCCTTATCACATATATGCA-TGTTCACATTCATCA
** **
28047939 CATTGGCCATTTTGCCTTATCACATATATGCATGTTCTTATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
28047986 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
28048033 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
28048080 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
* *
28048127 CATTGGCCATTCGGCCTTATGACACATATGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
28048174 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
* **
28048221 CATTGGCTATTCGGCCTTATCACATATATGCACATTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
28048268 CAT
1 CAT
28048271 AAAATCCTAA
Statistics
Matches: 309, Mismatches: 22, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
46 1 0.00
47 308 1.00
ACGTcount: A:0.25, C:0.27, G:0.12, T:0.35
Consensus pattern (47 bp):
CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
Found at i:28051650 original size:28 final size:28
Alignment explanation
Indices: 28051618--28051774 Score: 120
Period size: 28 Copynumber: 5.5 Consensus size: 28
28051608 CTGACTGATT
*
28051618 TCGCACACATAGCGCTCGATTAAAGAAC
1 TCGCACACATAGTGCTCGATTAAAGAAC
* * *
28051646 TCGCACACATAGTGCCTCAATTACCA-ATC
1 TCGCACACATAGTG-CTCGATTA-AAGAAC
* * *
28051675 TCGTACACATAGTGATCGATTGAAGAAC
1 TCGCACACATAGTGCTCGATTAAAGAAC
* * ** *
28051703 TCGCACACATAGTGCCTCAACTACTGATC
1 TCGCACACATAGTG-CTCGATTAAAGAAC
* * *
28051732 TGGCACACATAGTGCTCGGTTGAAGAAC
1 TCGCACACATAGTGCTCGATTAAAGAAC
*
28051760 TTC-CACACACAGTGC
1 -TCGCACACATAGTGC
28051775 CTCATAATTC
Statistics
Matches: 96, Mismatches: 28, Indels: 10
0.72 0.21 0.07
Matches are distributed among these distances:
27 1 0.01
28 51 0.53
29 43 0.45
30 1 0.01
ACGTcount: A:0.31, C:0.29, G:0.18, T:0.22
Consensus pattern (28 bp):
TCGCACACATAGTGCTCGATTAAAGAAC
Found at i:28051682 original size:29 final size:29
Alignment explanation
Indices: 28051645--28051746 Score: 100
Period size: 29 Copynumber: 3.6 Consensus size: 29
28051635 GATTAAAGAA
28051645 CTCGCACACATAGTGCCTCAATTACCAAT
1 CTCGCACACATAGTGCCTCAATTACCAAT
* * * **
28051674 CTCGTACACATAGTG-ATCGATTGAAGAA-
1 CTCGCACACATAGTGCCTCAATT-ACCAAT
* **
28051702 CTCGCACACATAGTGCCTCAACTACTGAT
1 CTCGCACACATAGTGCCTCAATTACCAAT
*
28051731 CTGGCACACATAGTGC
1 CTCGCACACATAGTGC
28051747 TCGGTTGAAG
Statistics
Matches: 57, Mismatches: 13, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
28 21 0.37
29 36 0.63
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.24
Consensus pattern (29 bp):
CTCGCACACATAGTGCCTCAATTACCAAT
Found at i:28051694 original size:57 final size:57
Alignment explanation
Indices: 28051618--28051778 Score: 216
Period size: 57 Copynumber: 2.8 Consensus size: 57
28051608 CTGACTGATT
* * *
28051618 TCGCACACATAGCGCTCGATTAAAGAACTCGCACACATAGTGCCTCAATTACCAATC
1 TCGCACACATAGTGCTCGATTGAAGAACTCGCACACATAGTGCCTCAACTACCAATC
* * **
28051675 TCGTACACATAGTGATCGATTGAAGAACTCGCACACATAGTGCCTCAACTACTGATC
1 TCGCACACATAGTGCTCGATTGAAGAACTCGCACACATAGTGCCTCAACTACCAATC
* * *
28051732 TGGCACACATAGTGCTCGGTTGAAGAACTTC-CACACACAGTGCCTCA
1 TCGCACACATAGTGCTCGATTGAAGAAC-TCGCACACATAGTGCCTCA
28051779 TAATTCCAGC
Statistics
Matches: 91, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
57 89 0.98
58 2 0.02
ACGTcount: A:0.31, C:0.29, G:0.17, T:0.22
Consensus pattern (57 bp):
TCGCACACATAGTGCTCGATTGAAGAACTCGCACACATAGTGCCTCAACTACCAATC
Found at i:28051856 original size:40 final size:40
Alignment explanation
Indices: 28051806--28052304 Score: 809
Period size: 40 Copynumber: 12.5 Consensus size: 40
28051796 CCTTCGAGGT
* * * *
28051806 TTAGCTCGGATATACCACTAGCACGAATGCTCTTCAGAAC
1 TTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAAC
*
28051846 TTAGCCCGGATATATCACTAGCACGAATGCTCTTCGGAAC
1 TTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAAC
* *
28051886 TTAGCCCGGATACATCACTAGCACGAATGCTCTTCAGAAA
1 TTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAAC
* *
28051926 TTAGACCGGATACATCACTAGCACGAATGCTCTTCGAAAC
1 TTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAAC
**
28051966 TTAGCCCGGATACATCACTAGCGGGAATGCTCTTCGGAAC
1 TTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAAC
* *
28052006 TTAGCCCGGATATATCACTAGCACGAATGCTCTTCGAAAC
1 TTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAAC
28052046 TTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAAC
1 TTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAAC
*
28052086 TTAGCCCGGATATATCACTAGCACGAATGCTCTTCGGAAC
1 TTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAAC
28052126 TTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAAC
1 TTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAAC
* *
28052166 TTAGCCTGGATACATCACTAGCACAAATGCTCTTCGGAAC
1 TTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAAC
** *
28052206 TTAGCTTGGATACATCACTAGTACGAATGCTCTTCGGAAC
1 TTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAAC
* *
28052246 GTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGGAC
1 TTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAAC
28052286 TTAGCCCGGATACATCACT
1 TTAGCCCGGATACATCACT
28052305 CTCAATTCTC
Statistics
Matches: 426, Mismatches: 33, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 426 1.00
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (40 bp):
TTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAAC
Found at i:28053973 original size:28 final size:27
Alignment explanation
Indices: 28053887--28053976 Score: 83
Period size: 27 Copynumber: 3.2 Consensus size: 27
28053877 GTGACAGAGT
* *
28053887 CACCAGATACAGATATTTTATGGCAGTGC
1 CACCAGA-ACAGATAATTTGTGGCA-TGC
* ** *
28053916 CACCAGAATAGAT-ATACGTGGCAGGGC
1 CACCAGAACAGATAATTTGTGGCA-TGC
28053943 CACCAGAACAGATAATTTGTGGCATAGC
1 CACCAGAACAGATAATTTGTGGCAT-GC
28053971 CACCAG
1 CACCAG
28053977 GACGCTTCCT
Statistics
Matches: 49, Mismatches: 10, Indels: 5
0.77 0.16 0.08
Matches are distributed among these distances:
27 21 0.43
28 21 0.43
29 7 0.14
ACGTcount: A:0.33, C:0.23, G:0.23, T:0.20
Consensus pattern (27 bp):
CACCAGAACAGATAATTTGTGGCATGC
Found at i:28054129 original size:28 final size:28
Alignment explanation
Indices: 28054082--28054146 Score: 103
Period size: 28 Copynumber: 2.3 Consensus size: 28
28054072 AAATTAACCC
*
28054082 TAGGGGTATAAAGGTCATTTAGCATACA
1 TAGGGGTATAAAGGTAATTTAGCATACA
* *
28054110 TAGGGGTATAATGGTAATTTTGCATACA
1 TAGGGGTATAAAGGTAATTTAGCATACA
28054138 TAGGGGTAT
1 TAGGGGTAT
28054147 TCTAGTAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.32, C:0.08, G:0.28, T:0.32
Consensus pattern (28 bp):
TAGGGGTATAAAGGTAATTTAGCATACA
Found at i:28058894 original size:27 final size:27
Alignment explanation
Indices: 28058864--28059040 Score: 158
Period size: 27 Copynumber: 6.5 Consensus size: 27
28058854 AAATTGTACA
* * *
28058864 GCACTAAGGGTGCGATTTGACTATGTT
1 GCACTAAGTGTGCGAATTGACTATGTG
* * *
28058891 GCACTCAGTGTGCGAAATGAATATGAT-
1 GCACTAAGTGTGCGAATTGACTATG-TG
* *
28058918 GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCGAATTGACTATGTG
** *
28058945 GCACTAAGTGTGCGAGCCTGACTATGTA
1 GCACTAAGTGTGCGA-ATTGACTATGTG
* * *
28058973 GCACTAAGTGTGCGATTTGATTACGTG
1 GCACTAAGTGTGCGAATTGACTATGTG
* * * *
28059000 GCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGAATTGACTATGTG
*
28059027 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
28059041 GGCTCAATGT
Statistics
Matches: 122, Mismatches: 25, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
27 99 0.81
28 23 0.19
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.28
Consensus pattern (27 bp):
GCACTAAGTGTGCGAATTGACTATGTG
Found at i:28058977 original size:82 final size:81
Alignment explanation
Indices: 28058864--28059019 Score: 197
Period size: 82 Copynumber: 1.9 Consensus size: 81
28058854 AAATTGTACA
** * * *
28058864 GCACTAAGGGTGCGATTTGACTATGTTGCACTCAGTGTGCGAAATGAATATGAT-GCACTAAGTG
1 GCACTAAGGGTGCGACCTGACTATGTAGCACTAAGTGTGCGAAATGAATACG-TGGCACTAAGTG
28058928 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
* ** *
28058945 GCACTAAGTGTGCGAGCCTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTGGCACTAAGTG
1 GCACTAAGGGTGCGA-CCTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTG
*
28059010 TGCGAGTTGA
65 TGCGAATTGA
28059020 TTATATAGCA
Statistics
Matches: 63, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
81 15 0.24
82 48 0.76
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.28
Consensus pattern (81 bp):
GCACTAAGGGTGCGACCTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:28059031 original size:82 final size:81
Alignment explanation
Indices: 28058860--28059040 Score: 193
Period size: 82 Copynumber: 2.2 Consensus size: 81
28058850 GATTAAATTG
* ** * * *
28058860 TACAGCACTAAGGGTGCGATTTGACTATGTTGCACTCAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGACCTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
28058925 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
28058941 TGCGGCACTAAGTGTGCGAGCCTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TGGCACT
1 TACAGCACTAAGTGTGCGA-CCTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
28059005 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
28059023 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
28059041 GGCTCAATGT
Statistics
Matches: 80, Mismatches: 18, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
81 17 0.21
82 63 0.79
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.28
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGACCTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:28066118 original size:27 final size:27
Alignment explanation
Indices: 28066055--28066230 Score: 169
Period size: 27 Copynumber: 6.6 Consensus size: 27
28066045 TAAATTGTAC
* *
28066055 AGCACTAAGGGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGAATTGACTATGT
* * *
28066082 -GCACTCAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGAATTGACTATGT
* *
28066107 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGAATTGACTATGT
* **
28066135 GGCACTAAGTGTGCGAGCCTGACTATGT
1 AGCACTAAGTGTGCGA-ATTGACTATGT
* *
28066163 AGCACTAAGTGTGCG-ATTGATTACGT
1 AGCACTAAGTGTGCGAATTGACTATGT
* * * *
28066189 GGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAATTGACTATGT
28066216 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
28066231 GGCTCAATGT
Statistics
Matches: 120, Mismatches: 24, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
26 41 0.34
27 58 0.48
28 21 0.17
ACGTcount: A:0.27, C:0.17, G:0.29, T:0.27
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAATTGACTATGT
Found at i:28066221 original size:81 final size:80
Alignment explanation
Indices: 28066052--28066230 Score: 200
Period size: 81 Copynumber: 2.2 Consensus size: 80
28066042 GATTAAATTG
* ** * *
28066052 TACAGCACTAAGGGTGCGATTTGACTATGTGCACTCAGTGTGCGAAATGAATATGATGCACTAAG
1 TACAGCACTAAGTGTGCGACCTGACTATGTGCACTAAGTGTGCGAAATGAATACGATGCACTAAG
28066117 TGTGCGAATTGACCA
66 TGTGCGAATTGACCA
* * * *
28066132 TGCGGCACTAAGTGTGCGAGCCTGACTATGTAGCACTAAGTGTGCG-ATTGATTACG-TGGCACT
1 TACAGCACTAAGTGTGCGA-CCTGACTATGT-GCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
28066195 AAGTGTGCGAGTTGATTA
63 AAGTGTGCGAATTGACCA
*
28066213 TATAGCACTAAGTGTGCG
1 TACAGCACTAAGTGTGCG
28066231 GGCTCAATGT
Statistics
Matches: 81, Mismatches: 15, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
80 17 0.21
81 51 0.63
82 13 0.16
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.27
Consensus pattern (80 bp):
TACAGCACTAAGTGTGCGACCTGACTATGTGCACTAAGTGTGCGAAATGAATACGATGCACTAAG
TGTGCGAATTGACCA
Found at i:28083314 original size:40 final size:40
Alignment explanation
Indices: 28083257--28083470 Score: 263
Period size: 40 Copynumber: 5.3 Consensus size: 40
28083247 CTAACGGGGT
* * * *
28083257 TAAGTCCTGAAGACATTTGTGCTAGTGATTAATTCCGGGC
1 TAAGTCCCGAAGGCATTTGTGCTAGTTACTAATTCCGGGC
28083297 TAAGTCCCGAAGGCATTTGTG-TGAGTTACTAATTCCGGGC
1 TAAGTCCCGAAGGCATTTGTGCT-AGTTACTAATTCCGGGC
* *
28083337 TAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCTGGGC
1 TAAGTCCCGAAGGCATTTGTGCTAGTTACTAATTCCGGGC
* *
28083377 TAAGCCCCGAAGGCATTTGTGCGAGTTACT-ATATCCGGGC
1 TAAGTCCCGAAGGCATTTGTGCTAGTTACTAAT-TCCGGGC
* * * *
28083417 TAGGTCCCGAAGGCATTTGTGCTAGTGAC-CATATCCGGAC
1 TAAGTCCCGAAGGCATTTGTGCTAGTTACTAAT-TCCGGGC
*
28083457 TAAGACCCGAAGGC
1 TAAGTCCCGAAGGC
28083471 CTTGTGCGAG
Statistics
Matches: 155, Mismatches: 15, Indels: 8
0.87 0.08 0.04
Matches are distributed among these distances:
39 3 0.02
40 152 0.98
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (40 bp):
TAAGTCCCGAAGGCATTTGTGCTAGTTACTAATTCCGGGC
Found at i:28085889 original size:44 final size:44
Alignment explanation
Indices: 28085736--28085901 Score: 136
Period size: 47 Copynumber: 3.6 Consensus size: 44
28085726 ATGATAGCCC
* * ** *
28085736 GTGTAAGACCACGTCTGGGACATGGCATCGGCGTAGAGGTGAGTGCCA
1 GTGTAAGA-CATGTCTGGGACAT-GCATCGGC-TA-AGTTTTGTGCTA
* * * * *
28085784 GTGTAAGACATGTTTGGGACATGCATCGGCCTCGATGATGTTAT-CTG
1 GTGTAAGACATGTCTGGGACATGCATCGG-CT--AAG-TTTTGTGCTA
* *
28085831 GTGTAAGACGTGTCTGCGACATGCATCGGCTAAGTTTTGTGCTA
1 GTGTAAGACATGTCTGGGACATGCATCGGCTAAGTTTTGTGCTA
*
28085875 GTGTAAGACATGTCTGGTACATGCATC
1 GTGTAAGACATGTCTGGGACATGCATC
28085902 AGCACGTATA
Statistics
Matches: 93, Mismatches: 20, Indels: 14
0.73 0.16 0.11
Matches are distributed among these distances:
43 4 0.04
44 28 0.30
46 10 0.11
47 41 0.44
48 10 0.11
ACGTcount: A:0.22, C:0.19, G:0.31, T:0.28
Consensus pattern (44 bp):
GTGTAAGACATGTCTGGGACATGCATCGGCTAAGTTTTGTGCTA
Found at i:28086880 original size:55 final size:54
Alignment explanation
Indices: 28086765--28086896 Score: 142
Period size: 55 Copynumber: 2.4 Consensus size: 54
28086755 TTTAAACTTT
* * * *
28086765 TAAA-TCAATATTGTCCACGATTAGGCCACACGGGCGTGTGCCATAGCCGTGTC
1 TAAAGTCAGTATTGCCCACGAGTAGGCCACACGGGCGTGTGCCATAGCCGTGCC
* * *
28086818 AATAAGTCAGTATTGCCCACGAGTAGGCCACACGGGCGTGTGTCAT-GATCGTGCCC
1 TA-AAGTCAGTATTGCCCACGAGTAGGCCACACGGGCGTGTGCCATAG-CCGTG-CC
* *
28086874 TAAAGTCAGTGTTGCACACGAGT
1 TAAAGTCAGTATTGCCCACGAGT
28086897 TGAGGATGTG
Statistics
Matches: 65, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
53 1 0.02
54 3 0.05
55 59 0.91
56 2 0.03
ACGTcount: A:0.25, C:0.25, G:0.27, T:0.23
Consensus pattern (54 bp):
TAAAGTCAGTATTGCCCACGAGTAGGCCACACGGGCGTGTGCCATAGCCGTGCC
Found at i:28088269 original size:349 final size:349
Alignment explanation
Indices: 28087630--28088668 Score: 1979
Period size: 349 Copynumber: 3.0 Consensus size: 349
28087620 CTCCTGATCA
* * *
28087630 AAAGCCAATTGTAATGAGAAGTATTTATCAAAACTTATTAGCATGATGCGTACAATTTTAGATTG
1 AAAGCCAATTGTAATGAGAAGTATTTATCAAAACTTATTGGCATGATGCGTACAAGTGTAGATTG
*
28087695 ATATAAAATATCATATCCTTATATACAAAAAAATTCTCAACAATAATGGTTTAGCTACTAACTTA
66 ATATAAAATATCATATCCTTATATACAAAAAAATTCTCAACAATAATGGTTTAGCTACTAACTTG
* *
28087760 AGGGATTTAATCATTAATTTTGATAAACCATTTCATACATATAAACAATAGGCTTTTGCAAGTTA
131 AGGCATTTAATCATTAATTTTGATAAACCATTTCATACATATAAACAATAGGCTTTTGCTAGTTA
*
28087825 CTCGCACTAATAATCTAGCATATAATAATCATTGAAAGTATGAGTAATAAAGTCACCGACATTAG
196 CTCGCACTAATAATCTAGCATATAATAATCATTGAAAGTATGAGTAATAAAGTCACCAACATTAG
*
28087890 CCAGACTTGTACCAATTGCATTACCTAAAAGTTTTGTTCATAAACAAATCATTAAATAAATAATC
261 CCAGACTTGTACCAATTGCATTATCTAAAAGTTTTGTTCATAAACAAATCATTAAATAAATAATC
28087955 TCGCAAACTACAAGTTTTGTTCAT
326 TCGCAAACTACAAGTTTTGTTCAT
28087979 AAAGCCAATTGTAATGAGAAGTATTTATCAAAACTTATTGGCATGATGCGTACAAGTGTAGATTG
1 AAAGCCAATTGTAATGAGAAGTATTTATCAAAACTTATTGGCATGATGCGTACAAGTGTAGATTG
28088044 ATATAAAATATCATATCCTTATATACAAAAAAATTCTCAACAATAATGGTTTAGCTACTAACTTG
66 ATATAAAATATCATATCCTTATATACAAAAAAATTCTCAACAATAATGGTTTAGCTACTAACTTG
*
28088109 AGGCATTTAATCATTAATTTTGATAAACCATTTCATACATATAAACAATAGGCTTTTTCTAGTTA
131 AGGCATTTAATCATTAATTTTGATAAACCATTTCATACATATAAACAATAGGCTTTTGCTAGTTA
28088174 CTCGCACTAATAATCTAGCATATAATAATCATTGAAAGTATGAGTAATAAAGTCACCAACATTAG
196 CTCGCACTAATAATCTAGCATATAATAATCATTGAAAGTATGAGTAATAAAGTCACCAACATTAG
28088239 CCAGACTTGTACCAATTGCATTATCTAAAAGTTTTGTTCATAAACAAATCATTAAATAAATAATC
261 CCAGACTTGTACCAATTGCATTATCTAAAAGTTTTGTTCATAAACAAATCATTAAATAAATAATC
28088304 TCGCAAACTACAAGTTTTGTTCAT
326 TCGCAAACTACAAGTTTTGTTCAT
28088328 AAAGCCAATTGTAATGAGAAGTATTTATCAAAACTTATTGGCATGATGCGTACAAGTGTAGATTG
1 AAAGCCAATTGTAATGAGAAGTATTTATCAAAACTTATTGGCATGATGCGTACAAGTGTAGATTG
*
28088393 ATATAAAATATCATATCCTTATATACAAAAAAATTCTTAACAATAATGGTTTAGCTACTAACTTG
66 ATATAAAATATCATATCCTTATATACAAAAAAATTCTCAACAATAATGGTTTAGCTACTAACTTG
28088458 AGGCATTTAATCATTAATTTTGATAAACCATTTCATACATATAAACAATAGGCTTTTGCTAGTTA
131 AGGCATTTAATCATTAATTTTGATAAACCATTTCATACATATAAACAATAGGCTTTTGCTAGTTA
*
28088523 CACGCACTAATAATCTAGCATATAATAATCATTGAAAGTATGAGTAATAAAGTCACCAACATTAG
196 CTCGCACTAATAATCTAGCATATAATAATCATTGAAAGTATGAGTAATAAAGTCACCAACATTAG
28088588 CCAGACTTGTACCAATTGCATTATCTAAAAGTTTTGTTCATAAACAAATCATTAAATAAATAATC
261 CCAGACTTGTACCAATTGCATTATCTAAAAGTTTTGTTCATAAACAAATCATTAAATAAATAATC
28088653 TCGCAAACTACAAGTT
326 TCGCAAACTACAAGTT
28088669 GCGAGTGATA
Statistics
Matches: 678, Mismatches: 12, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
349 678 1.00
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.33
Consensus pattern (349 bp):
AAAGCCAATTGTAATGAGAAGTATTTATCAAAACTTATTGGCATGATGCGTACAAGTGTAGATTG
ATATAAAATATCATATCCTTATATACAAAAAAATTCTCAACAATAATGGTTTAGCTACTAACTTG
AGGCATTTAATCATTAATTTTGATAAACCATTTCATACATATAAACAATAGGCTTTTGCTAGTTA
CTCGCACTAATAATCTAGCATATAATAATCATTGAAAGTATGAGTAATAAAGTCACCAACATTAG
CCAGACTTGTACCAATTGCATTATCTAAAAGTTTTGTTCATAAACAAATCATTAAATAAATAATC
TCGCAAACTACAAGTTTTGTTCAT
Found at i:28091499 original size:40 final size:40
Alignment explanation
Indices: 28091445--28092068 Score: 1081
Period size: 40 Copynumber: 15.6 Consensus size: 40
28091435 CATTTGAATG
28091445 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
*
28091485 ATATCCGGGTTAAGACCCGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
*
28091525 ATATCCGGGTTAAGACCCGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
28091565 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
28091605 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
28091645 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
*
28091685 ATATCCGGG-TAAGACCCGAAGGCATTTGTGCGAACTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
*
28091724 ATATCCGGGCTAAGACCTGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
28091764 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
*
28091804 ATATCCGGGATAAGACCCGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
28091844 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
* *
28091884 ATATCCGGGATAAGACCCGAAGGCATTTGTGCGAACTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
* *
28091924 ATATCCGGGCTAAGACCCGACGGCGTTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
*
28091964 ATATCCGGGCTAAGACCCGAAGGCAATTGTGC-AAGTTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAA-TTGAT
* * * *
28092004 ATATCCGGGCTATGACCCGAAGGCATTCGTGCGAGTTGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
* *
28092044 ATACCCGGGTTAAGACCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCA
28092069 ATTGAGCTTG
Statistics
Matches: 556, Mismatches: 25, Indels: 6
0.95 0.04 0.01
Matches are distributed among these distances:
39 40 0.07
40 515 0.93
41 1 0.00
ACGTcount: A:0.27, C:0.20, G:0.28, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
Found at i:28099215 original size:40 final size:40
Alignment explanation
Indices: 28099145--28099766 Score: 1027
Period size: 40 Copynumber: 15.6 Consensus size: 40
28099135 CATTTGAATG
28099145 ATATCCGGGCTAAGA-CCGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
*
28099184 ATATCCGGGTTAAGACCCGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
*
28099224 ATATCCGGGTTAAGACCCGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
*
28099264 ATATCCGGGCTAAGACCTGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
28099304 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
*
28099344 ATATCCGGGATAAGACCCGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
28099384 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAA-TGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
* *
28099423 ATATCCGGGATAAGACCCGAAGGCATTTGTGCGAACTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
* **
28099463 ATATCCGAGCTAAGACCTAAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
28099503 ATATCCGGGCTAAGACCC-AAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
*
28099542 ATATCCGGGATAAGACCCGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
* *
28099582 ATATCCGGGATAAGACCCGAAGGCATTTGTGCGAACTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
* *
28099622 ATATCCGGGCTAAGACCCGACGGCGTTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
*
28099662 ATATCCGGGCTAAGACCCGAAGGCAATTGTGC-AAGTTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAA-TTGAT
* * *
28099702 ATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
* *
28099742 ATACCCGGGTTAAGACCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCA
28099767 ATTGAGCTTG
Statistics
Matches: 549, Mismatches: 29, Indels: 9
0.94 0.05 0.02
Matches are distributed among these distances:
39 92 0.17
40 456 0.83
41 1 0.00
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.24
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
Found at i:28102892 original size:40 final size:42
Alignment explanation
Indices: 28102789--28102935 Score: 127
Period size: 43 Copynumber: 3.5 Consensus size: 42
28102779 GAAATCCGAG
**
28102789 CTCGTTGAGCAGTCCGAGTTCGTGATATATGTGAGAATCCGAA
1 CTCGTTGAGTGGTCCGAGTTCGTGATATATGTGAGAATCC-AA
** * *
28102832 CTTATTGAGTGGTCCAAGTTCGTGATATATGTG-GCATCC-A
1 CTCGTTGAGTGGTCCGAGTTCGTGATATATGTGAGAATCCAA
* * * ** * * * *
28102872 CTCGTTGAGTGGTCTGAGTTCATTATGGATGCGAGCATCTGAG
1 CTCGTTGAGTGGTCCGAGTTCGTGATATATGTGAGAATC-CAA
28102915 CTCGTTGAGTGGTCCGAGTTC
1 CTCGTTGAGTGGTCCGAGTTC
28102936 ATAATGGATG
Statistics
Matches: 83, Mismatches: 18, Indels: 6
0.78 0.17 0.06
Matches are distributed among these distances:
40 25 0.30
41 5 0.06
42 5 0.06
43 48 0.58
ACGTcount: A:0.20, C:0.18, G:0.29, T:0.32
Consensus pattern (42 bp):
CTCGTTGAGTGGTCCGAGTTCGTGATATATGTGAGAATCCAA
Found at i:28108032 original size:47 final size:47
Alignment explanation
Indices: 28107974--28108399 Score: 611
Period size: 47 Copynumber: 9.1 Consensus size: 47
28107964 TTAGGATTTT
** *
28107974 ATGTGATGAATGTGAATGTGCATATATGTGATAAGGCCGAATAGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* **
28108021 ATGTGAGGAATGTGAACATGCATATATGTGATAAGGCTAAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
*
28108068 ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
*
28108115 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCTGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
** * **
28108162 ATGTGATGAATAAGAACATGCATATATGTGATAACGCAAAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* *
28108209 ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGACCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
28108256 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* **
28108303 ATGTGATGAATGAGAACATGCATATATGTGATAAGGCAAAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * * * * * *
28108350 ATGTGACGAACGTGGAA-GTGTATATATGTGGTAAAGCCGAATGGCTA
1 ATGTGATGAATGT-GAACATGCATATATGTGATAAGGCCGAATGGCCA
28108397 ATG
1 ATG
28108400 CGAAATGTGT
Statistics
Matches: 339, Mismatches: 39, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
47 336 0.99
48 3 0.01
ACGTcount: A:0.35, C:0.12, G:0.27, T:0.26
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
Found at i:28108073 original size:22 final size:22
Alignment explanation
Indices: 28108046--28108168 Score: 58
Period size: 22 Copynumber: 5.3 Consensus size: 22
28108036 ACATGCATAT
28108046 ATGTGATAAGGCTAAATGGCCA
1 ATGTGATAAGGCTAAATGGCCA
*
28108068 ATGTGATGAATG-TGAACAT-G-CA
1 ATGTGAT-AAGGCT-AA-ATGGCCA
**
28108090 TATGTGTGATAAGGCCGAATGGCCA
1 -A--TGTGATAAGGCTAAATGGCCA
* *
28108115 ATGTGATGAATG-TGAACAT-GCATA
1 ATGTGAT-AAGGCT-AA-ATGGC-CA
*
28108139 TATGTGATAAGGCTGAATGGCCA
1 -ATGTGATAAGGCTAAATGGCCA
28108162 ATGTGAT
1 ATGTGAT
28108169 GAATAAGAAC
Statistics
Matches: 74, Mismatches: 11, Indels: 32
0.63 0.09 0.27
Matches are distributed among these distances:
22 23 0.31
23 18 0.24
24 17 0.23
25 16 0.22
ACGTcount: A:0.33, C:0.11, G:0.28, T:0.27
Consensus pattern (22 bp):
ATGTGATAAGGCTAAATGGCCA
Found at i:28108204 original size:141 final size:141
Alignment explanation
Indices: 28107974--28108399 Score: 674
Period size: 141 Copynumber: 3.0 Consensus size: 141
28107964 TTAGGATTTT
** * * *
28107974 ATGTGATGAATGTGAATGTGCATATATGTGATAAGGCCGAATAGCCAATGTGAGGAATGTGAACA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGAGAACA
*
28108039 TGCATATATGTGATAAGGCTAAATGGCCAATGTGATGAATGTGAACATGCATATGTGTGATAAGG
66 TGCATATATGTGATAAGGCAAAATGGCCAATGTGATGAATGTGAACATGCATATGTGTGATAAGG
28108104 CCGAATGGCCA
131 CCGAATGGCCA
* *
28108115 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCTGAATGGCCAATGTGATGAATAAGAACA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGAGAACA
*
28108180 TGCATATATGTGATAACGCAAAATGGCCAATGTGATGAATGTGAACATGCATATGTGTGATAAGG
66 TGCATATATGTGATAAGGCAAAATGGCCAATGTGATGAATGTGAACATGCATATGTGTGATAAGG
*
28108245 CCGAATGACCA
131 CCGAATGGCCA
28108256 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGAGAACA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGAGAACA
* * * * * * *
28108321 TGCATATATGTGATAAGGCAAAATGGCCAATGTGACGAACGTGGAA-GTGTATATATGTGGTAAA
66 TGCATATATGTGATAAGGCAAAATGGCCAATGTGATGAATGT-GAACATGCATATGTGTGATAAG
*
28108385 GCCGAATGGCTA
130 GCCGAATGGCCA
28108397 ATG
1 ATG
28108400 CGAAATGTGT
Statistics
Matches: 262, Mismatches: 22, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
141 259 0.99
142 3 0.01
ACGTcount: A:0.35, C:0.12, G:0.27, T:0.26
Consensus pattern (141 bp):
ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGAGAACA
TGCATATATGTGATAAGGCAAAATGGCCAATGTGATGAATGTGAACATGCATATGTGTGATAAGG
CCGAATGGCCA
Found at i:28108429 original size:46 final size:46
Alignment explanation
Indices: 28108373--28108491 Score: 202
Period size: 46 Copynumber: 2.6 Consensus size: 46
28108363 GGAAGTGTAT
*
28108373 ATATGTGGTAAAGCCGAATGGCTAATGCGAAATGTGTATGAGATGG
1 ATATGTGGTAAAGCCGAATGGCTAATGCGAAACGTGTATGAGATGG
* *
28108419 ATATGAGGTAAAGTCGAATGGCTAATGCGAAACGTGTATGAGATGG
1 ATATGTGGTAAAGCCGAATGGCTAATGCGAAACGTGTATGAGATGG
*
28108465 ATATGTGGTAAAGCCAAATGGCTAATG
1 ATATGTGGTAAAGCCGAATGGCTAATG
28108492 TGAGAGATGT
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 67 1.00
ACGTcount: A:0.34, C:0.09, G:0.31, T:0.25
Consensus pattern (46 bp):
ATATGTGGTAAAGCCGAATGGCTAATGCGAAACGTGTATGAGATGG
Found at i:28111033 original size:28 final size:28
Alignment explanation
Indices: 28111001--28111065 Score: 103
Period size: 28 Copynumber: 2.3 Consensus size: 28
28110991 ATTTACTAGA
*
28111001 ATACCCCTATGTATGCAAAATTACCATT
1 ATACCCCTATGTATGCAAAATGACCATT
* *
28111029 ATACCCCTATGTATGCTAAATGACCTTT
1 ATACCCCTATGTATGCAAAATGACCATT
28111057 ATACCCCTA
1 ATACCCCTA
28111066 GGGTTAATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.32, C:0.28, G:0.08, T:0.32
Consensus pattern (28 bp):
ATACCCCTATGTATGCAAAATGACCATT
Found at i:28111229 original size:27 final size:28
Alignment explanation
Indices: 28111171--28111260 Score: 112
Period size: 27 Copynumber: 3.2 Consensus size: 28
28111161 AGGAAGCGTC
*
28111171 CTGGTGGCTA-TGCCACAAATTATCTGTT
1 CTGGTGGC-ACTGCCACAAAATATCTGTT
* **
28111199 CTGGTGGCCCTGCCAC-GTATATCTGTT
1 CTGGTGGCACTGCCACAAAATATCTGTT
28111226 CTGGTGGCACTGCCACAAAATATCTGTAT
1 CTGGTGGCACTGCCACAAAATATCTGT-T
28111255 CTGGTG
1 CTGGTG
28111261 ACTCTGTCAC
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
27 23 0.44
28 22 0.42
29 7 0.13
ACGTcount: A:0.19, C:0.24, G:0.24, T:0.32
Consensus pattern (28 bp):
CTGGTGGCACTGCCACAAAATATCTGTT
Found at i:28111271 original size:29 final size:28
Alignment explanation
Indices: 28111181--28111271 Score: 94
Period size: 27 Copynumber: 3.2 Consensus size: 28
28111171 CTGGTGGCTA
* * *
28111181 TGCCACAAATTATCTGTTCTGGTGGCCC
1 TGCCACAAAATATCTGTTCTGGTGACAC
** *
28111209 TGCCAC-GTATATCTGTTCTGGTGGCAC
1 TGCCACAAAATATCTGTTCTGGTGACAC
*
28111236 TGCCACAAAATATCTGTATCTGGTGACTC
1 TGCCACAAAATATCTGT-TCTGGTGACAC
*
28111265 TGTCACA
1 TGCCACA
28111272 TTTTCTGTAT
Statistics
Matches: 52, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
27 23 0.44
28 14 0.27
29 15 0.29
ACGTcount: A:0.21, C:0.26, G:0.21, T:0.32
Consensus pattern (28 bp):
TGCCACAAAATATCTGTTCTGGTGACAC
Found at i:28111279 original size:55 final size:56
Alignment explanation
Indices: 28111171--28111285 Score: 137
Period size: 55 Copynumber: 2.1 Consensus size: 56
28111161 AGGAAGCGTC
* * *
28111171 CTGGTGGCTATGCCACAAATTATCTGTTCTGGTGGCCCTGCCACGTATATCTGT-T
1 CTGGTGGCTATGCCACAAAATATCTGTTCTGGTGACCCTGCCACATATATCTGTAT
* * *
28111226 CTGGTGGC-ACTGCCACAAAATATCTGTATCTGGTGACTCTGTCACAT-TTTCTGTAT
1 CTGGTGGCTA-TGCCACAAAATATCTGT-TCTGGTGACCCTGCCACATATATCTGTAT
28111282 CTGG
1 CTGG
28111286 CAGCCATGCT
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
54 1 0.02
55 30 0.59
56 20 0.39
ACGTcount: A:0.18, C:0.24, G:0.23, T:0.35
Consensus pattern (56 bp):
CTGGTGGCTATGCCACAAAATATCTGTTCTGGTGACCCTGCCACATATATCTGTAT
Found at i:28116492 original size:27 final size:27
Alignment explanation
Indices: 28116454--28116631 Score: 169
Period size: 27 Copynumber: 6.6 Consensus size: 27
28116444 ACATTGAGCC
* * *
28116454 CGCACACTTAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* * *
28116481 CGCACACTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
**
28116508 CGCACACTTAGTGCTACATAGTCAGGCT
1 CGCACACTTAGTGCTACATAGTCA-AAT
** * *
28116536 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
28116563 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
* *
28116590 CGCACACTGAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
*
28116617 CGCACCCTTAGTGCT
1 CGCACACTTAGTGCT
28116632 GTACAATTTA
Statistics
Matches: 123, Mismatches: 25, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
27 100 0.81
28 23 0.19
ACGTcount: A:0.28, C:0.29, G:0.17, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:28116593 original size:82 final size:81
Alignment explanation
Indices: 28116475--28116630 Score: 197
Period size: 82 Copynumber: 1.9 Consensus size: 81
28116465 TGCTATATAA
* * * **
28116475 TCAACTCGCACACTTAGTGCCACGTAATCAAATCGCACACTTAGTGCTACATAGTCAGGCTCGCA
1 TCAACTCGCACACTTAGTGCCACATAATCAAATCGCACACTGAGTGCAACATAGTCA-AATCGCA
28116540 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
28116557 TCAATTCGCACACTTAGTG-CATCATATTCATTTCGCACACTGAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCCA-CATAATCAAATCGCACACTGAGTGCAACATAGTCAAATCGCA
*
28116621 CCCTTAGTGC
65 CACTTAGTGC
28116631 TGTACAATTT
Statistics
Matches: 63, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
81 16 0.25
82 47 0.75
ACGTcount: A:0.28, C:0.29, G:0.17, T:0.26
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCCACATAATCAAATCGCACACTGAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:28123659 original size:27 final size:27
Alignment explanation
Indices: 28123629--28123806 Score: 162
Period size: 27 Copynumber: 6.6 Consensus size: 27
28123619 ATATTGAGCC
* *
28123629 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* * *
28123656 CGCACACTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
28123683 CGCACACTTAGTGCTACATAGTCAGACT
1 CGCACACTTAGTGCTACATAATCA-ACT
* ** *
28123711 CGCACACTTAGTGCCGA-ATGGTCAATT
1 CGCACACTTAGTG-CTACATAATCAACT
* **
28123738 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* * *
28123765 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
28123792 CGCACCCTTAGTGCT
1 CGCACACTTAGTGCT
28123807 GTACAATTTA
Statistics
Matches: 126, Mismatches: 20, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
25 1 0.01
26 1 0.01
27 100 0.79
28 22 0.17
29 2 0.02
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:28123768 original size:82 final size:81
Alignment explanation
Indices: 28123650--28123805 Score: 215
Period size: 82 Copynumber: 1.9 Consensus size: 81
28123640 TGCTATATAA
* * *
28123650 TCAACTCGCACACTTAGTGCCACGTAATCAAATCGCACACTTAGTGCTACATAGTCAGACTCGCA
1 TCAACTCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCAACATAGTCA-AATCGCA
28123715 CACTTAGTGCCGAATGG
65 CACTTAGTGCCGAATGG
* * **
28123732 TCAATTCGCACACTTAGTG-CATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCCA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
*
28123796 CCCTTAGTGC
65 CACTTAGTGC
28123806 TGTACAATTT
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
81 17 0.26
82 48 0.74
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGAATGG
Found at i:28143552 original size:40 final size:40
Alignment explanation
Indices: 28143466--28143660 Score: 270
Period size: 40 Copynumber: 4.9 Consensus size: 40
28143456 GGATATAACC
* * * * *
28143466 ACTCGCAC-AAGGCCTTCGGG-TTTAGTCCGG-ATATGGTC
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTA
* * *
28143504 ACTAGCACAAATACCTTCGGGACTTAGCCCGGATTTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTA
*
28143544 ACACGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTA
28143584 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTA
*
28143624 ACTCTCACAAATGCCTTCGGGACTTAGCCCGGAATTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTA
28143661 ATCATTCAGG
Statistics
Matches: 140, Mismatches: 14, Indels: 4
0.89 0.09 0.03
Matches are distributed among these distances:
38 7 0.05
39 10 0.07
40 122 0.87
41 1 0.01
ACGTcount: A:0.27, C:0.27, G:0.23, T:0.24
Consensus pattern (40 bp):
ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTA
Found at i:28151911 original size:34 final size:33
Alignment explanation
Indices: 28151819--28151912 Score: 102
Period size: 34 Copynumber: 2.8 Consensus size: 33
28151809 TTGTATATTG
* *
28151819 TACTAATTCTGTAATGGGCTTAGGCCCCACTGA
1 TACTGATTCTGAAATGGGCTTAGGCCCCACTGA
*
28151852 TACTG-TTACTGAAATGAGCTTAGGCCCACACT-A
1 TACTGATT-CTGAAATGGGCTTAGGCCC-CACTGA
* *
28151885 TTTCTGATTCTGAAATGGGCTAAGGCCC
1 -TACTGATTCTGAAATGGGCTTAGGCCC
28151913 TAACTGAAAC
Statistics
Matches: 51, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
32 2 0.04
33 22 0.43
34 25 0.49
35 2 0.04
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (33 bp):
TACTGATTCTGAAATGGGCTTAGGCCCCACTGA
Found at i:28153434 original size:71 final size:71
Alignment explanation
Indices: 28153326--28153472 Score: 258
Period size: 71 Copynumber: 2.1 Consensus size: 71
28153316 TTAAAATTTC
28153326 AAAATAATTTTTCAGTTCAGGGAGACTATCCCATGTCTTAAAGTATAAATCACACAATGCACAAA
1 AAAATAATTTTTCAGTTCAGGGAGACTATCCCATGTCTTAAAGTATAAATCACACAATGCACAAA
28153391 AATCCA
66 AATCCA
* * *
28153397 AAAATAATTTTTCAGTTCAGGGGGACTATCTCATGTCTTAAAGTATGAATCACACAATGCACAAA
1 AAAATAATTTTTCAGTTCAGGGAGACTATCCCATGTCTTAAAGTATAAATCACACAATGCACAAA
28153462 AATCCA
66 AATCCA
*
28153468 CAAAT
1 AAAAT
28153473 TATTCCAAAA
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
71 72 1.00
ACGTcount: A:0.41, C:0.19, G:0.12, T:0.27
Consensus pattern (71 bp):
AAAATAATTTTTCAGTTCAGGGAGACTATCCCATGTCTTAAAGTATAAATCACACAATGCACAAA
AATCCA
Found at i:28153933 original size:32 final size:31
Alignment explanation
Indices: 28153877--28153937 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 31
28153867 AATAAAATAA
** *
28153877 ACAAAAACAAAAGTATAGACAAAAAATAAAAG
1 ACAAAAACAAAAACATAAAC-AAAAATAAAAG
*
28153909 ACAAAAACAAAAACATAAATAAAAATAAA
1 ACAAAAACAAAAACATAAACAAAAATAAA
28153938 TAAAATATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
31 9 0.36
32 16 0.64
ACGTcount: A:0.75, C:0.10, G:0.05, T:0.10
Consensus pattern (31 bp):
ACAAAAACAAAAACATAAACAAAAATAAAAG
Found at i:28153947 original size:17 final size:17
Alignment explanation
Indices: 28153927--28153960 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
28153917 AAAAACATAA
28153927 ATAAAAATAAATAAAAT
1 ATAAAAATAAATAAAAT
* *
28153944 ATAAAAGTAAATGAAAT
1 ATAAAAATAAATAAAAT
28153961 CACTTTGGTT
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:0.71, C:0.00, G:0.06, T:0.24
Consensus pattern (17 bp):
ATAAAAATAAATAAAAT
Found at i:28154072 original size:30 final size:29
Alignment explanation
Indices: 28154014--28154084 Score: 97
Period size: 30 Copynumber: 2.4 Consensus size: 29
28154004 AGAGAAAAAT
*
28154014 ATGGCCATGTGCTAGGCCATGTGAGCCAC
1 ATGGCCATGTGGTAGGCCATGTGAGCCAC
* * *
28154043 ATGGCCGTGTGGTCAGGTCATGTGCGCCAC
1 ATGGCCATGTGGT-AGGCCATGTGAGCCAC
28154073 ATGGCCATGTGG
1 ATGGCCATGTGG
28154085 AATCACCCAG
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
29 11 0.31
30 25 0.69
ACGTcount: A:0.17, C:0.25, G:0.35, T:0.23
Consensus pattern (29 bp):
ATGGCCATGTGGTAGGCCATGTGAGCCAC
Found at i:28154429 original size:13 final size:12
Alignment explanation
Indices: 28154408--28154486 Score: 52
Period size: 12 Copynumber: 6.3 Consensus size: 12
28154398 GTTTTTTCAA
28154408 AAATTCTTTTTC
1 AAATTCTTTTTC
*
28154420 AAATTCCTTTTTG
1 AAATT-CTTTTTC
* *
28154433 ACATTTTTTTTC
1 AAATTCTTTTTC
*
28154445 AAAAGTTTTTTTTTC
1 -AAA--TTCTTTTTC
*
28154460 AATTTCTTTTTC
1 AAATTCTTTTTC
* *
28154472 -ATTTCTTTTTT
1 AAATTCTTTTTC
28154483 AAAT
1 AAAT
28154487 CAAATATTTT
Statistics
Matches: 53, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
11 10 0.19
12 20 0.38
13 12 0.23
14 2 0.04
15 9 0.17
ACGTcount: A:0.23, C:0.13, G:0.03, T:0.62
Consensus pattern (12 bp):
AAATTCTTTTTC
Found at i:28154482 original size:39 final size:38
Alignment explanation
Indices: 28154399--28154481 Score: 98
Period size: 39 Copynumber: 2.2 Consensus size: 38
28154389 GACCACTTTG
28154399 TTTTTTCAAAAATTCTTTTTCAAATTCCTTTTTGACATT
1 TTTTTTCAAAAATTCTTTTTCAAATTCCTTTTT-ACATT
* * *
28154438 TTTTTTCAAAAGTTTTTTTTTC-AATTTCTTTTT-CATT
1 TTTTTTCAAAA-ATTCTTTTTCAAATTCCTTTTTACATT
28154475 TCTTTTT
1 T-TTTTT
28154482 TAAATCAAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
37 5 0.13
38 5 0.13
39 21 0.54
40 8 0.21
ACGTcount: A:0.20, C:0.13, G:0.02, T:0.64
Consensus pattern (38 bp):
TTTTTTCAAAAATTCTTTTTCAAATTCCTTTTTACATT
Found at i:28159094 original size:46 final size:43
Alignment explanation
Indices: 28158951--28159086 Score: 123
Period size: 46 Copynumber: 3.0 Consensus size: 43
28158941 CCTGCCCCTA
*
28158951 AGTGAACTCGGACTCAACTCAACGAGTTCAGATGCCTAGTTA-CATTT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCC-A---ACCA-TT
* * * *
28158998 CA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATA
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGG--ATGC-CAACCATT
28159044 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCAT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGC-CAACCAT
28159087 CCTAGTGACA
Statistics
Matches: 74, Mismatches: 9, Indels: 14
0.76 0.09 0.14
Matches are distributed among these distances:
44 9 0.12
45 1 0.01
46 29 0.39
47 29 0.39
48 1 0.01
49 4 0.05
50 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.23
Consensus pattern (43 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCAACCATT
Found at i:28166552 original size:46 final size:46
Alignment explanation
Indices: 28166485--28166657 Score: 197
Period size: 46 Copynumber: 3.7 Consensus size: 46
28166475 AACCCGCCCC
* *
28166485 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCATCCA
* * * * * *
28166531 TAAGTGAACTCGGACTCAACTCAACGAGTTCAGATGCCTAG-TTACA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACG-TTCGCATCCA
* * *
28166577 TTTCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 --TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCATCCA
*
28166624 TAAGTGAACTCGGACTCAACTCAATGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
28166658 TGCTCAACCA
Statistics
Matches: 102, Mismatches: 20, Indels: 10
0.77 0.15 0.08
Matches are distributed among these distances:
45 2 0.02
46 65 0.64
47 33 0.32
48 2 0.02
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.23
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCATCCA
Found at i:28166597 original size:93 final size:93
Alignment explanation
Indices: 28166490--28166660 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
28166480 GCCCCTAAGT
* *
28166490 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
28166555 CGAGTTCAGATGCCTAGTTACATTTCAC
66 CGAGTTCAGATGCCTAGTTACATTTCAC
*
28166583 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
* *
28166648 TGAGTTCGGATGC
66 CGAGTTCAGATGC
28166661 TCAACCATCC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCAGATGCCTAGTTACATTTCAC
Found at i:28167112 original size:30 final size:30
Alignment explanation
Indices: 28167078--28167137 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
28167068 ATTTAATAAG
*
28167078 AACTTTGGAAAAATTACACTTTTGCGCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
28167108 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
28167138 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.30, C:0.23, G:0.10, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:28188310 original size:29 final size:29
Alignment explanation
Indices: 28188271--28188349 Score: 106
Period size: 29 Copynumber: 2.7 Consensus size: 29
28188261 CTTAATAATC
*
28188271 AACCACGCACACTTAGTGCCATGTACTTT-A
1 AACC-CGCACACTTAGTGCCATGCA-TTTCA
*
28188301 AACTCGCACACTTAGTGCCATGCATTTCA
1 AACCCGCACACTTAGTGCCATGCATTTCA
*
28188330 AGCCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
28188350 ATCTCACAAC
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
28 3 0.07
29 38 0.86
30 3 0.07
ACGTcount: A:0.28, C:0.33, G:0.15, T:0.24
Consensus pattern (29 bp):
AACCCGCACACTTAGTGCCATGCATTTCA
Found at i:28194433 original size:23 final size:23
Alignment explanation
Indices: 28194385--28194493 Score: 134
Period size: 23 Copynumber: 4.7 Consensus size: 23
28194375 GAGCCATAAT
28194385 CAGTAAGCTC-TATCGAGC-TGAA
1 CAGTAAGCTCATA-CGAGCTTGAA
28194407 CAGTAAGCTCATACGAGCTTGAA
1 CAGTAAGCTCATACGAGCTTGAA
28194430 CAGTAAGCTCATACGAGCTTGAA
1 CAGTAAGCTCATACGAGCTTGAA
* **
28194453 CAGTAAGCTCCA-ATGAGCTAAAAA
1 CAGTAAGCT-CATACGAGCT-TGAA
*
28194477 CAGTAAGCTCTTACGAG
1 CAGTAAGCTCATACGAG
28194494 ATGATATATC
Statistics
Matches: 77, Mismatches: 5, Indels: 8
0.86 0.06 0.09
Matches are distributed among these distances:
22 15 0.19
23 45 0.58
24 17 0.22
ACGTcount: A:0.36, C:0.22, G:0.21, T:0.21
Consensus pattern (23 bp):
CAGTAAGCTCATACGAGCTTGAA
Found at i:28197634 original size:43 final size:44
Alignment explanation
Indices: 28197541--28197699 Score: 146
Period size: 43 Copynumber: 3.7 Consensus size: 44
28197531 GATTATCGAG
* * *** * *
28197541 ATGTGATTACATGTAAGACCATGTCTACAACATTGACATTG-TA
1 ATGTGATTATATGTAAGACCATATCTGGGACATTGGCATCGATA
* * *
28197584 TTGTGATTATGTGTAAGACCATGTCTGGGACATTGGCATCGATA
1 ATGTGATTATATGTAAGACCATATCTGGGACATTGGCATCGATA
* * *
28197628 AT-TGATT-TCATGTAAGACCCTATCTGGGACAATGGCATCAAT-
1 ATGTGATTAT-ATGTAAGACCATATCTGGGACATTGGCATCGATA
* *
28197670 ATGTGATAACATGTAAGACCATATCTGGGA
1 ATGTGATTATATGTAAGACCATATCTGGGA
28197700 TACGACATTG
Statistics
Matches: 95, Mismatches: 17, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
42 3 0.03
43 89 0.94
44 3 0.03
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.31
Consensus pattern (44 bp):
ATGTGATTATATGTAAGACCATATCTGGGACATTGGCATCGATA
Found at i:28206442 original size:40 final size:41
Alignment explanation
Indices: 28206391--28206495 Score: 106
Period size: 41 Copynumber: 2.5 Consensus size: 41
28206381 AACTATGTTT
* * *
28206391 AGCACTTAGTGTGCGAATTGGAATAACTTCGGTTTTATGTG
1 AGCACTAAGTGTGCGAATTGAAATAACTTCGGTTTAATGTG
**
28206432 -GCACTAAGTGTGC-AATACTGAAATAGTTTCGGTTTAATGTG
1 AGCACTAAGTGTGCGAAT--TGAAATAACTTCGGTTTAATGTG
28206473 ATAGCACTAAGTGTGCGATATTG
1 --AGCACTAAGTGTGCGA-ATTG
28206496 TTATAGCTTT
Statistics
Matches: 52, Mismatches: 5, Indels: 11
0.76 0.07 0.16
Matches are distributed among these distances:
39 3 0.06
40 12 0.23
41 19 0.37
44 15 0.29
45 1 0.02
46 2 0.04
ACGTcount: A:0.28, C:0.12, G:0.26, T:0.34
Consensus pattern (41 bp):
AGCACTAAGTGTGCGAATTGAAATAACTTCGGTTTAATGTG
Found at i:28207519 original size:117 final size:117
Alignment explanation
Indices: 28207387--28207638 Score: 468
Period size: 117 Copynumber: 2.2 Consensus size: 117
28207377 GCGTGTCTCA
* *
28207387 ACCGTGTGTGACACACGGTTATGTTATATGGCCGTGTGTCCCTTGGAGTACCCTTTCGAATTAAG
1 ACCGTGTGGGGCACACGGTTATGTTATATGGCCGTGTGTCCCTTGGAGTACCCTTTCGAATTAAG
*
28207452 GCAGTATACCCTACAGTTTTGACATGGCCTAAACATACAGGCGTGTCTATTG
66 GCAATATACCCTACAGTTTTGACATGGCCTAAACATACAGGCGTGTCTATTG
28207504 ACCGTGTGGGGCACACGGTTATGTTATATGGCCGTGTGTCCCTTGGAGTACCCTTTCGAATTAAG
1 ACCGTGTGGGGCACACGGTTATGTTATATGGCCGTGTGTCCCTTGGAGTACCCTTTCGAATTAAG
28207569 GCAATATACCCTACAGTTTTGACATGGCCTAAACATACAGGCGTGTCTATTG
66 GCAATATACCCTACAGTTTTGACATGGCCTAAACATACAGGCGTGTCTATTG
*
28207621 ACCGTGTGGAGCACACGG
1 ACCGTGTGGGGCACACGG
28207639 GCTGGCACAT
Statistics
Matches: 131, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
117 131 1.00
ACGTcount: A:0.23, C:0.23, G:0.25, T:0.29
Consensus pattern (117 bp):
ACCGTGTGGGGCACACGGTTATGTTATATGGCCGTGTGTCCCTTGGAGTACCCTTTCGAATTAAG
GCAATATACCCTACAGTTTTGACATGGCCTAAACATACAGGCGTGTCTATTG
Found at i:28211986 original size:42 final size:42
Alignment explanation
Indices: 28211927--28212017 Score: 164
Period size: 42 Copynumber: 2.2 Consensus size: 42
28211917 ACCCTGTTTT
* *
28211927 CACACGGCCTATGACATGGGCGTGTCTAGTTACCATGTGAGG
1 CACACGGCCTACGACATGGGCGTGTATAGTTACCATGTGAGG
28211969 CACACGGCCTACGACATGGGCGTGTATAGTTACCATGTGAGG
1 CACACGGCCTACGACATGGGCGTGTATAGTTACCATGTGAGG
28212011 CACACGG
1 CACACGG
28212018 AATGTTCACA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.23, C:0.25, G:0.31, T:0.21
Consensus pattern (42 bp):
CACACGGCCTACGACATGGGCGTGTATAGTTACCATGTGAGG
Found at i:28217148 original size:19 final size:19
Alignment explanation
Indices: 28217124--28217163 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
28217114 AAATCCCAAT
28217124 ACCAAAAAATGTTAATCTA
1 ACCAAAAAATGTTAATCTA
28217143 ACCAAAAAATGTTAATCTA
1 ACCAAAAAATGTTAATCTA
28217162 AC
1 AC
28217164 ACATTTATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.53, C:0.17, G:0.05, T:0.25
Consensus pattern (19 bp):
ACCAAAAAATGTTAATCTA
Found at i:28220750 original size:86 final size:85
Alignment explanation
Indices: 28220613--28220771 Score: 221
Period size: 86 Copynumber: 1.9 Consensus size: 85
28220603 TGTGATTACA
* * * * *
28220613 TGTAAGACCATGGTTGGGACATTGGCATTGTAGTTTGATTACATGTAAGACCATGTCTGGGACAT
1 TGTAAGACCATGGTTGGGACAGTGGCATCGTAGTGTGATAACATGTAAGACCATATCTGGGACA-
28220678 TGGCATTGTTATATGATTTCG
65 TGGCATTGTTATATGATTTCG
* * *
28220699 TGTAAGACCCTGTTTGGGACAGTGGCATCGATA-TGTGATAACATGTAAGACCATATCTGGGATA
1 TGTAAGACCATGGTTGGGACAGTGGCATCG-TAGTGTGATAACATGTAAGACCATATCTGGGACA
28220763 TGGCATTGT
65 TGGCATTGT
28220772 ATGAGCTTTA
Statistics
Matches: 64, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
85 9 0.14
86 53 0.83
87 2 0.03
ACGTcount: A:0.26, C:0.14, G:0.27, T:0.33
Consensus pattern (85 bp):
TGTAAGACCATGGTTGGGACAGTGGCATCGTAGTGTGATAACATGTAAGACCATATCTGGGACAT
GGCATTGTTATATGATTTCG
Found at i:28220760 original size:43 final size:43
Alignment explanation
Indices: 28220596--28220768 Score: 181
Period size: 43 Copynumber: 4.0 Consensus size: 43
28220586 CATTAGGATT
*
28220596 ATCGAGATGTGATTACATGTAAGACCATGGT-TGGGACATTGGC
1 ATCGATATGTGATTACATGTAAGACCAT-GTCTGGGACATTGGC
* *
28220639 ATTG-TAGTTTGATTACATGTAAGACCATGTCTGGGACATTGGC
1 ATCGATA-TGTGATTACATGTAAGACCATGTCTGGGACATTGGC
* * * * * * * *
28220682 ATTGTTATATGATTTCGTGTAAGACCCTGTTTGGGACAGTGGC
1 ATCGATATGTGATTACATGTAAGACCATGTCTGGGACATTGGC
* * *
28220725 ATCGATATGTGATAACATGTAAGACCATATCTGGGATA-TGGC
1 ATCGATATGTGATTACATGTAAGACCATGTCTGGGACATTGGC
28220767 AT
1 AT
28220769 TGTATGAGCT
Statistics
Matches: 108, Mismatches: 19, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
42 9 0.08
43 97 0.90
44 2 0.02
ACGTcount: A:0.27, C:0.14, G:0.27, T:0.32
Consensus pattern (43 bp):
ATCGATATGTGATTACATGTAAGACCATGTCTGGGACATTGGC
Found at i:28222635 original size:27 final size:27
Alignment explanation
Indices: 28222597--28222697 Score: 139
Period size: 27 Copynumber: 3.6 Consensus size: 27
28222587 TTAAACAGCT
*
28222597 TATGAAAAGAATGCCTTTGTGGCAATA
1 TATGAAAGGAATGCCTTTGTGGCAATA
* * *
28222624 TATGAAACGAATGTCTTTGTGACAATA
1 TATGAAAGGAATGCCTTTGTGGCAATA
28222651 TATGAAAGGAATGCCTTTGTGGCAATA
1 TATGAAAGGAATGCCTTTGTGGCAATA
28222678 TACAATGAAAGGAATGCCTT
1 T---ATGAAAGGAATGCCTT
28222698 GACGGCGTAC
Statistics
Matches: 65, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
27 49 0.75
30 16 0.25
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.30
Consensus pattern (27 bp):
TATGAAAGGAATGCCTTTGTGGCAATA
Found at i:28230299 original size:43 final size:43
Alignment explanation
Indices: 28230221--28230302 Score: 103
Period size: 43 Copynumber: 1.9 Consensus size: 43
28230211 TTAAGTATGA
* *
28230221 AATTATCACAACTTCTATTACATTATAATTATTTTAAATGGAT
1 AATTATCACAAATTCTATTACATTAAAATTATTTTAAATGGAT
* **
28230264 AATTATCATAAATTCTATTTTATTTAAAATT-TTTTAAAT
1 AATTATCACAAATTCTATTACA-TTAAAATTATTTTAAAT
28230303 AATGATTCTA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
43 26 0.79
44 7 0.21
ACGTcount: A:0.40, C:0.09, G:0.02, T:0.49
Consensus pattern (43 bp):
AATTATCACAAATTCTATTACATTAAAATTATTTTAAATGGAT
Found at i:28231992 original size:19 final size:19
Alignment explanation
Indices: 28231936--28231981 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 19
28231926 AATATCCACC
28231936 TCGTGTGTC-AGATTTGCACT
1 TCGTGTGTCAAGA--TGCACT
28231956 TCGTGTGTCAAGATGCACT
1 TCGTGTGTCAAGATGCACT
28231975 TCGTGTG
1 TCGTGTG
28231982 CTTGTATGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 13 0.52
20 9 0.36
21 3 0.12
ACGTcount: A:0.15, C:0.20, G:0.28, T:0.37
Consensus pattern (19 bp):
TCGTGTGTCAAGATGCACT
Found at i:28233859 original size:16 final size:16
Alignment explanation
Indices: 28233840--28233897 Score: 64
Period size: 16 Copynumber: 3.6 Consensus size: 16
28233830 TAATAAGATT
28233840 TAATATTAAATTAATA
1 TAATATTAAATTAATA
**
28233856 TAATATTTATCTTAATA
1 TAATA-TTAAATTAATA
* *
28233873 -AATATTATATTAATT
1 TAATATTAAATTAATA
28233888 TAATATTAAA
1 TAATATTAAA
28233898 GTGATTAACT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
15 9 0.26
16 17 0.49
17 9 0.26
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (16 bp):
TAATATTAAATTAATA
Found at i:28233882 original size:21 final size:20
Alignment explanation
Indices: 28233852--28233892 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
28233842 ATATTAAATT
*
28233852 AATATAATATTTATCTTAATA
1 AATATAATATTAAT-TTAATA
*
28233873 AATATTATATTAATTTAATA
1 AATATAATATTAATTTAATA
28233893 TTAAAGTGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (20 bp):
AATATAATATTAATTTAATA
Found at i:28233890 original size:5 final size:6
Alignment explanation
Indices: 28233839--28233896 Score: 56
Period size: 5 Copynumber: 10.7 Consensus size: 6
28233829 TTAATAAGAT
* *
28233839 TTAATA TTAA-A TTAATA -TAATA TTTATC TTAATA --AATA TT-ATA
1 TTAATA TTAATA TTAATA TTAATA TTAATA TTAATA TTAATA TTAATA
28233882 TTAAT- TTAATA TTAA
1 TTAATA TTAATA TTAA
28233897 AGTGATTAAC
Statistics
Matches: 42, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
4 4 0.10
5 20 0.48
6 18 0.43
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (6 bp):
TTAATA
Found at i:28235556 original size:43 final size:42
Alignment explanation
Indices: 28235401--28235557 Score: 181
Period size: 43 Copynumber: 3.7 Consensus size: 42
28235391 TGTGATTTCG
* *
28235401 TGTAAGACCACATCTGGGACGTTGGCATCA-ATTTGAGATTTACA
1 TGTAAGACCACGTCTGGGACATTGGCATCATATTT--GA-TTACA
* ** *
28235445 TGTAAGACCATGTCTGCAACATTGGCATCATATTTGATTTCA
1 TGTAAGACCACGTCTGGGACATTGGCATCATATTTGATTACA
** *
28235487 TGTAAGACCTTGTCTGGGACAGTGGCATCGATATTTGATTACA
1 TGTAAGACCACGTCTGGGACATTGGCATC-ATATTTGATTACA
*
28235530 TGTAAGACCACGTCTGGGACTTTGGCAT
1 TGTAAGACCACGTCTGGGACATTGGCAT
28235558 TGTACGAGCT
Statistics
Matches: 96, Mismatches: 15, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
42 29 0.30
43 38 0.40
44 25 0.26
45 4 0.04
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.32
Consensus pattern (42 bp):
TGTAAGACCACGTCTGGGACATTGGCATCATATTTGATTACA
Found at i:28239491 original size:19 final size:18
Alignment explanation
Indices: 28239469--28239505 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
28239459 AGAATTGGCC
28239469 AAATGGGCCGGAATGGGCT
1 AAATGGGCCGG-ATGGGCT
*
28239488 AAATGGGCCTGATGGGCT
1 AAATGGGCCGGATGGGCT
28239506 GTTGGGCCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.24, C:0.16, G:0.41, T:0.19
Consensus pattern (18 bp):
AAATGGGCCGGATGGGCT
Found at i:28239643 original size:29 final size:29
Alignment explanation
Indices: 28239574--28239643 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 29
28239564 GTGAGCATGA
*
28239574 ATAT-AATATGATTTGGGCCTAATGGGCC
1 ATATAAATATGAATTGGGCCTAATGGGCC
* *
28239602 ATATAAATGTGAATTGGGCCTAGTGGGCC
1 ATATAAATATGAATTGGGCCTAATGGGCC
28239631 ATA-AGAATATGAA
1 ATATA-AATATGAA
28239644 CTAGGCCCCA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
28 5 0.14
29 31 0.86
ACGTcount: A:0.34, C:0.11, G:0.26, T:0.29
Consensus pattern (29 bp):
ATATAAATATGAATTGGGCCTAATGGGCC
Found at i:28239650 original size:29 final size:29
Alignment explanation
Indices: 28239589--28239650 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
28239579 ATATGATTTG
* * *
28239589 GGCCTAATGGGCCATATAAATGTGAATTG
1 GGCCTAATGGGCCATATAAATATGAACTA
*
28239618 GGCCTAGTGGGCCATA-AGAATATGAACTA
1 GGCCTAATGGGCCATATA-AATATGAACTA
28239647 GGCC
1 GGCC
28239651 CCATTTGAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 1 0.04
29 27 0.96
ACGTcount: A:0.31, C:0.18, G:0.29, T:0.23
Consensus pattern (29 bp):
GGCCTAATGGGCCATATAAATATGAACTA
Found at i:28241385 original size:21 final size:19
Alignment explanation
Indices: 28241359--28241398 Score: 62
Period size: 21 Copynumber: 2.0 Consensus size: 19
28241349 ACAATCAAAT
28241359 ATAAAATACCATATCAATTCA
1 ATAAAATACCAT-TC-ATTCA
28241380 ATAAAATACCATTCATTCA
1 ATAAAATACCATTCATTCA
28241399 TGTTCATCAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.26
20 2 0.11
21 12 0.63
ACGTcount: A:0.50, C:0.20, G:0.00, T:0.30
Consensus pattern (19 bp):
ATAAAATACCATTCATTCA
Found at i:28252887 original size:27 final size:27
Alignment explanation
Indices: 28252857--28253033 Score: 180
Period size: 27 Copynumber: 6.6 Consensus size: 27
28252847 ATATCGAGTC
* *
28252857 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
*
28252884 CGCACACTTAGTGCTACATAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
28252911 CGCACACTTAGTGC-ACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
** ** *
28252938 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
28252965 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* *
28252992 CGCACACTTAGTGCAACATAGTCGAA-T
1 CGCACACTTAGTGCTACATAATC-AACT
28253019 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
28253034 GTACAATTTA
Statistics
Matches: 130, Mismatches: 15, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
26 7 0.05
27 115 0.88
28 8 0.06
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:28252939 original size:54 final size:53
Alignment explanation
Indices: 28252857--28253032 Score: 208
Period size: 54 Copynumber: 3.3 Consensus size: 53
28252847 ATATCGAGTC
* * * *
28252857 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACATAATCAAAT
1 CGCACACTTAGTGC-ACATAATCAACTCGCACACTTAGTGCAACATAGTCAAAT
* ** * *
28252911 CGCACACTTAGTGCACATAGTCAAACTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCACATAATC-AACTCGCACACTTAGTGCAACATAGTCAAAT
* ** *
28252965 CGCACACTTAGTGCATCATATTCATTTCGCACACTTAGTGCAACATAGTCGAAT
1 CGCACACTTAGTGCA-CATAATCAACTCGCACACTTAGTGCAACATAGTCAAAT
28253019 CGCACACTTAGTGC
1 CGCACACTTAGTGC
28253033 TGTACAATTT
Statistics
Matches: 104, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
53 6 0.06
54 92 0.88
55 6 0.06
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.26
Consensus pattern (53 bp):
CGCACACTTAGTGCACATAATCAACTCGCACACTTAGTGCAACATAGTCAAAT
Found at i:28252969 original size:81 final size:81
Alignment explanation
Indices: 28252878--28253032 Score: 233
Period size: 81 Copynumber: 1.9 Consensus size: 81
28252868 TGCTATATAA
28252878 TCAACTCGCACACTTAGTGC-TACATAATCAAATCGCACACTTAGTGC-ACATAGTCAAACTCGC
1 TCAACTCGCACACTTAGTGCAT-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGC
28252941 ACACTTAGTGCCGCATGG
64 ACACTTAGTGCCGCATGG
* * ** *
28252959 TCAATTCGCACACTTAGTGCATCATATTCATTTCGCACACTTAGTGCAACATAGTCGAATCGCAC
1 TCAACTCGCACACTTAGTGCATCATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
28253024 ACTTAGTGC
66 ACTTAGTGC
28253033 TGTACAATTT
Statistics
Matches: 67, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
81 56 0.84
82 11 0.16
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.26
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCATCATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:28260093 original size:27 final size:27
Alignment explanation
Indices: 28260063--28260240 Score: 180
Period size: 27 Copynumber: 6.6 Consensus size: 27
28260053 ATATCGAGTC
* *
28260063 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
*
28260090 CGCACACTTAGTGCTACATAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
* *
28260117 CGCACACTTAGTGCCACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
** ** *
28260145 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
28260172 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* *
28260199 CGCACACTTAGTGCAACATAGTCGAA-T
1 CGCACACTTAGTGCTACATAATC-AACT
28260226 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
28260241 GTACAATTTA
Statistics
Matches: 131, Mismatches: 16, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
27 105 0.80
28 26 0.20
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:28260202 original size:82 final size:81
Alignment explanation
Indices: 28260084--28260239 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
28260074 TGCTATATAA
*
28260084 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCCACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
28260149 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * ** *
28260166 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCGAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
28260230 CACTTAGTGC
65 CACTTAGTGC
28260240 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.26
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:28270583 original size:38 final size:37
Alignment explanation
Indices: 28270498--28270601 Score: 100
Period size: 38 Copynumber: 2.7 Consensus size: 37
28270488 GAAGATTGTG
* * * *
28270498 GAATATTATTGGATGGAATAGCTCTTATGAGCTTACTG
1 GAATATTATCGGAT-GAATAGCTCTTATAAGCATACTA
** *
28270536 GCGTTTTATCGGATAGAATAGCTCTTATAAGCATACTA
1 GAATATTATCGGAT-GAATAGCTCTTATAAGCATACTA
* *
28270574 GAATGTTATCGAATGTAATAGCTCTTAT
1 GAATATTATCGGATG-AATAGCTCTTAT
28270602 GAGGATATGG
Statistics
Matches: 53, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
37 1 0.02
38 52 0.98
ACGTcount: A:0.31, C:0.12, G:0.20, T:0.37
Consensus pattern (37 bp):
GAATATTATCGGATGAATAGCTCTTATAAGCATACTA
Found at i:28270619 original size:38 final size:38
Alignment explanation
Indices: 28270510--28270656 Score: 102
Period size: 38 Copynumber: 3.9 Consensus size: 38
28270500 ATATTATTGG
* * *
28270510 ATGGAATAGCTCTTATGAGCTTACTGGCGT-T-TTATCGG
1 ATGGAATAGCTCTTATGAGC-AAATGG-GTGTGTTATCGA
* * * * **
28270548 ATAGAATAGCTCTTATAAGCATACT-AGAATGTTATCGA
1 ATGGAATAGCTCTTATGAGCA-AATGGGTGTGTTATCGA
* * * *
28270586 ATGTAATAGCTCTTATGAGGATATGGGTGTGTTATCGG
1 ATGGAATAGCTCTTATGAGCAAATGGGTGTGTTATCGA
* * *
28270624 ATGGAATAGTTCTTCTGAGCAAATTGGTGTGTT
1 ATGGAATAGCTCTTATGAGCAAATGGGTGTGTT
28270657 CCAGTTGGTT
Statistics
Matches: 83, Mismatches: 22, Indels: 8
0.73 0.19 0.07
Matches are distributed among these distances:
36 1 0.01
37 2 0.02
38 80 0.96
ACGTcount: A:0.27, C:0.12, G:0.25, T:0.36
Consensus pattern (38 bp):
ATGGAATAGCTCTTATGAGCAAATGGGTGTGTTATCGA
Found at i:28279965 original size:22 final size:23
Alignment explanation
Indices: 28279937--28279991 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
28279927 TATAAATCCG
28279937 AATAAAAATAAG-ATGAAAGA-AA
1 AATAAAAATAAGTATGAAA-ATAA
* *
28279959 AATAAAAATTAGTATTAAAATAA
1 AATAAAAATAAGTATGAAAATAA
28279982 AATAAAAATA
1 AATAAAAATA
28279992 TAAACATAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 12 0.43
23 16 0.57
ACGTcount: A:0.71, C:0.00, G:0.07, T:0.22
Consensus pattern (23 bp):
AATAAAAATAAGTATGAAAATAA
Found at i:28282077 original size:55 final size:55
Alignment explanation
Indices: 28281990--28282115 Score: 155
Period size: 55 Copynumber: 2.3 Consensus size: 55
28281980 TGTTAGTTTA
* * * * *
28281990 ACAGGTTTGACCACGGTTTCTTGGCACAGGCGTGTCGCACACCCGTGTTGATTTG
1 ACAGGTTCGACCACGGGTTCTAGACACAGGCGTGTCGAACACCCGTGTTGATTTG
* * * *
28282045 ACAGGTTCGGCCACGGGTTCTAGACACGGGCGTGTCGAACGCCCGTGTTGTTTTG
1 ACAGGTTCGACCACGGGTTCTAGACACAGGCGTGTCGAACACCCGTGTTGATTTG
28282100 ACAGGTTC-ACCCACGG
1 ACAGGTTCGA-CCACGG
28282116 CCATATCGCA
Statistics
Matches: 60, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
55 60 1.00
ACGTcount: A:0.17, C:0.27, G:0.31, T:0.25
Consensus pattern (55 bp):
ACAGGTTCGACCACGGGTTCTAGACACAGGCGTGTCGAACACCCGTGTTGATTTG
Found at i:28283274 original size:46 final size:46
Alignment explanation
Indices: 28283207--28283298 Score: 166
Period size: 46 Copynumber: 2.0 Consensus size: 46
28283197 ATTAAGCAAG
28283207 GAATCATAAAACTCCCTAGATCTTTTAGCTTGTTGGGTAGTTTATT
1 GAATCATAAAACTCCCTAGATCTTTTAGCTTGTTGGGTAGTTTATT
* *
28283253 GAATCGTAAAACTCCCTAGATCTTTTAGTTTGTTGGGTAGTTTATT
1 GAATCATAAAACTCCCTAGATCTTTTAGCTTGTTGGGTAGTTTATT
28283299 CTGTAGAATA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.25, C:0.14, G:0.18, T:0.42
Consensus pattern (46 bp):
GAATCATAAAACTCCCTAGATCTTTTAGCTTGTTGGGTAGTTTATT
Found at i:28287728 original size:25 final size:25
Alignment explanation
Indices: 28287700--28287780 Score: 72
Period size: 25 Copynumber: 3.2 Consensus size: 25
28287690 ACATAAATGC
** *
28287700 GAAGCTGATGTGAGCCATGTAACGA
1 GAAGCTGATCCGAGCCATATAACGA
* *
28287725 GAAGCTTATCCGAGCTATATAACGA
1 GAAGCTGATCCGAGCCATATAACGA
* * ***
28287750 GAAGCTTATCCGGGTTGTATAACGA
1 GAAGCTGATCCGAGCCATATAACGA
28287775 GAAGCT
1 GAAGCT
28287781 CATAAGAGCC
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 48 1.00
ACGTcount: A:0.32, C:0.17, G:0.27, T:0.23
Consensus pattern (25 bp):
GAAGCTGATCCGAGCCATATAACGA
Found at i:28287805 original size:24 final size:24
Alignment explanation
Indices: 28287775--28287988 Score: 75
Period size: 25 Copynumber: 8.6 Consensus size: 24
28287765 TGTATAACGA
28287775 GAAGCTCATAAGAGCCATAATCAG
1 GAAGCTCATAAGAGCCATAATCAG
**
28287799 GAAGCTCATGCGAGCCAATAA-CAG
1 GAAGCTCATAAGAGCC-ATAATCAG
* *
28287823 GTAA-CTTC-GAAGAGCCATTAATTAG
1 G-AAGC-TCATAAGAGCCA-TAATCAG
*** *
28287848 GAAGCTCCGGATAGCCATATATC-G
1 GAAGCTCATAAGAGCCATA-ATCAG
* *
28287872 AGAAGTTC--AAGCAAGCCA-ATATCGG
1 -GAAGCTCATAAG--AGCCATA-ATCAG
*
28287897 GAAGCTC-TAGAGAGCCATTAATCAA
1 GAAGCTCATA-AGAGCCA-TAATCAG
* * *
28287922 GAAGCTCACAAAGAGCCTTTAATCGG
1 GAAGCTCA-TAAGAGCC-ATAATCAG
* * *
28287948 GAATCTCACGAAGAGCCATATATCGG
1 GAAGCTCA-TAAGAGCCATA-ATCAG
*
28287974 GATGCTCATAAGAGC
1 GAAGCTCATAAGAGC
28287989 TGTGGTGTGT
Statistics
Matches: 145, Mismatches: 25, Indels: 39
0.69 0.12 0.19
Matches are distributed among these distances:
23 2 0.01
24 50 0.34
25 52 0.36
26 40 0.28
27 1 0.01
ACGTcount: A:0.36, C:0.21, G:0.23, T:0.19
Consensus pattern (24 bp):
GAAGCTCATAAGAGCCATAATCAG
Found at i:28287972 original size:26 final size:26
Alignment explanation
Indices: 28287830--28287981 Score: 86
Period size: 26 Copynumber: 6.0 Consensus size: 26
28287820 CAGGTAACTT
**
28287830 CGAAGAGCCAT-TAATTAGGAAGCTC-
1 CGAAGAGCCATAT-ATCGGGAAGCTCA
* * * *
28287855 CGGATAGCCATATATCGAGAAGTTCA
1 CGAAGAGCCATATATCGGGAAGCTCA
* *
28287881 AGCA-AGCCA-ATATCGGGAAGCTCTA
1 CGAAGAGCCATATATCGGGAAGCTC-A
**
28287906 -G-AGAGCCAT-TAATCAAGAAGCTCA
1 CGAAGAGCCATAT-ATCGGGAAGCTCA
* * *
28287930 CAAAGAGCC-TTTAATCGGGAATCTCA
1 CGAAGAGCCATAT-ATCGGGAAGCTCA
*
28287956 CGAAGAGCCATATATCGGGATGCTCA
1 CGAAGAGCCATATATCGGGAAGCTCA
28287982 TAAGAGCTGT
Statistics
Matches: 97, Mismatches: 20, Indels: 19
0.71 0.15 0.14
Matches are distributed among these distances:
23 1 0.01
24 20 0.21
25 34 0.35
26 40 0.41
27 2 0.02
ACGTcount: A:0.36, C:0.22, G:0.23, T:0.20
Consensus pattern (26 bp):
CGAAGAGCCATATATCGGGAAGCTCA
Found at i:28291531 original size:25 final size:26
Alignment explanation
Indices: 28291503--28291554 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
28291493 AACATAATTA
* *
28291503 AATAATAAGGATCAAAATAAAA-TAG
1 AATAAGAAAGATCAAAATAAAAGTAG
*
28291528 AATAAGAAAGTTCAAAATAAAAGTAG
1 AATAAGAAAGATCAAAATAAAAGTAG
28291554 A
1 A
28291555 TTTAACCAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 19 0.83
26 4 0.17
ACGTcount: A:0.63, C:0.04, G:0.13, T:0.19
Consensus pattern (26 bp):
AATAAGAAAGATCAAAATAAAAGTAG
Found at i:28294380 original size:107 final size:107
Alignment explanation
Indices: 28294180--28294382 Score: 325
Period size: 107 Copynumber: 1.9 Consensus size: 107
28294170 AACGCCATAA
28294180 TTTTATGTTGAGCTTTAGTGGCATTAGCGGCGCTTTTTGAAAAACGCCGCTATAGATCGAGCATT
1 TTTTATGTTGAGCTTTAGTGGCATTAGCGGCGCTTTTTGAAAAACGCCGCTATAGATCGAGCATT
* **
28294245 AGCGGCGCTTTCTGAAAAACGCCGCAAAAAAATTAAGCACCG
66 AGCGGCCCTTTCTGAAAAACGCAACAAAAAAATTAAGCACCG
* * *
28294287 TTTTATGTTGATCTTTAGTGGCATTAGCGGCGCTTTTTTAAAAACGTCGCTATAGATCGAGCATT
1 TTTTATGTTGAGCTTTAGTGGCATTAGCGGCGCTTTTTGAAAAACGCCGCTATAGATCGAGCATT
* * *
28294352 AGCGGCCCTTTTTTAAAATCGCAACAAAAAA
66 AGCGGCCCTTTCTGAAAAACGCAACAAAAAA
28294383 CATTTTATGT
Statistics
Matches: 87, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
107 87 1.00
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.31
Consensus pattern (107 bp):
TTTTATGTTGAGCTTTAGTGGCATTAGCGGCGCTTTTTGAAAAACGCCGCTATAGATCGAGCATT
AGCGGCCCTTTCTGAAAAACGCAACAAAAAAATTAAGCACCG
Found at i:28295294 original size:15 final size:15
Alignment explanation
Indices: 28295276--28295316 Score: 57
Period size: 14 Copynumber: 2.7 Consensus size: 15
28295266 AAAAAAATTT
28295276 AAAATTAAAAAATAA
1 AAAATTAAAAAATAA
*
28295291 AAAAAT-AAAAATAA
1 AAAATTAAAAAATAA
28295305 AAAACTTAAAAA
1 AAAA-TTAAAAA
28295317 TTTAATATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
14 12 0.55
15 6 0.27
16 4 0.18
ACGTcount: A:0.80, C:0.02, G:0.00, T:0.17
Consensus pattern (15 bp):
AAAATTAAAAAATAA
Found at i:28297269 original size:15 final size:15
Alignment explanation
Indices: 28297249--28297280 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
28297239 TTTTTTATGT
28297249 ACTTACAACAATTTA
1 ACTTACAACAATTTA
28297264 ACTTACAACAATTTA
1 ACTTACAACAATTTA
28297279 AC
1 AC
28297281 CCATTATCTT
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:0.47, C:0.22, G:0.00, T:0.31
Consensus pattern (15 bp):
ACTTACAACAATTTA
Found at i:28297773 original size:28 final size:28
Alignment explanation
Indices: 28297748--28297811 Score: 92
Period size: 28 Copynumber: 2.2 Consensus size: 28
28297738 TAAAATATAG
*
28297748 TTGGTATCCCAAGTATTCCGTCATATAAA
1 TTGGTAT-CCAAGTACTCCGTCATATAAA
**
28297777 TTGGTATTTAAGTACTCCGTCATATAAA
1 TTGGTATCCAAGTACTCCGTCATATAAA
28297805 TTGGTAT
1 TTGGTAT
28297812 TTATGCACTA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
28 25 0.78
29 7 0.22
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.39
Consensus pattern (28 bp):
TTGGTATCCAAGTACTCCGTCATATAAA
Found at i:28297812 original size:28 final size:28
Alignment explanation
Indices: 28297758--28297814 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
28297748 TTGGTATCCC
*
28297758 AAGTATTCCGTCATATAAATTGGTATTT
1 AAGTACTCCGTCATATAAATTGGTATTT
28297786 AAGTACTCCGTCATATAAATTGGTATTT
1 AAGTACTCCGTCATATAAATTGGTATTT
28297814 A
1 A
28297815 TGCACTAACA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.40
Consensus pattern (28 bp):
AAGTACTCCGTCATATAAATTGGTATTT
Found at i:28298898 original size:41 final size:41
Alignment explanation
Indices: 28298850--28298928 Score: 140
Period size: 41 Copynumber: 1.9 Consensus size: 41
28298840 TAATTTTAAT
28298850 ATGTTTAGATTAAGACAGATTTATTAGCTGCTGTTAATAAA
1 ATGTTTAGATTAAGACAGATTTATTAGCTGCTGTTAATAAA
**
28298891 ATGTTTAGATTAAGACAGATTTATTAGCTTTTGTTAAT
1 ATGTTTAGATTAAGACAGATTTATTAGCTGCTGTTAAT
28298929 CAATGTGTCC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.34, C:0.06, G:0.16, T:0.43
Consensus pattern (41 bp):
ATGTTTAGATTAAGACAGATTTATTAGCTGCTGTTAATAAA
Found at i:28309299 original size:26 final size:28
Alignment explanation
Indices: 28309252--28309308 Score: 68
Period size: 26 Copynumber: 2.1 Consensus size: 28
28309242 ATTAAATCAT
28309252 AAAATCGTATAAAATCCAAATT-TA-CA
1 AAAATCGTATAAAATCCAAATTATAGCA
28309278 AAAATC-TAT-AAATGCCATAATTATAGCA
1 AAAATCGTATAAAAT-CCA-AATTATAGCA
28309306 AAA
1 AAA
28309309 TACTCCCCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
24 4 0.15
25 6 0.22
26 10 0.37
27 2 0.07
28 5 0.19
ACGTcount: A:0.54, C:0.14, G:0.05, T:0.26
Consensus pattern (28 bp):
AAAATCGTATAAAATCCAAATTATAGCA
Found at i:28323902 original size:50 final size:50
Alignment explanation
Indices: 28323823--28323917 Score: 127
Period size: 50 Copynumber: 1.9 Consensus size: 50
28323813 AACGAAGGCT
*
28323823 TTCCAAAGAATTCGCCACAAAGACATTTCAGAAAATTCGCCACAAAGACA
1 TTCCAAAGAATTCGCCACAAAGACATTTCAGAAAATTCACCACAAAGACA
* ** * * *
28323873 TTCCAAAGTATTTTCCACAAAGGCTTTTCAGAGAATTCACCACAA
1 TTCCAAAGAATTCGCCACAAAGACATTTCAGAAAATTCACCACAA
28323918 CTATGTTTCA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
50 38 1.00
ACGTcount: A:0.40, C:0.25, G:0.12, T:0.23
Consensus pattern (50 bp):
TTCCAAAGAATTCGCCACAAAGACATTTCAGAAAATTCACCACAAAGACA
Found at i:28323915 original size:25 final size:25
Alignment explanation
Indices: 28323817--28323985 Score: 105
Period size: 25 Copynumber: 6.8 Consensus size: 25
28323807 GTTCATAACG
* *
28323817 AAGGCTTTCCAAAGAATTCGCCACA
1 AAGGCTTTTCAGAGAATTCGCCACA
* * *
28323842 AAGACATTTCAGAAAATTCGCCACA
1 AAGGCTTTTCAGAGAATTCGCCACA
* * * * * **
28323867 AAGACATTCCAAAGTATTTTCCACA
1 AAGGCTTTTCAGAGAATTCGCCACA
*
28323892 AAGGCTTTTCAGAGAATTCACCACA
1 AAGGCTTTTCAGAGAATTCGCCACA
* * *
28323917 ACTATG--TTTCAAAAAAATT-GCCACA
1 A--AGGCTTTTC-AGAGAATTCGCCACA
*
28323942 AAGG-TGTTCCAGAGTAATT-GCCACA
1 AAGGCT-TTTCAGAG-AATTCGCCACA
28323967 AAGGCTTTTCAGAGAATTC
1 AAGGCTTTTCAGAGAATTC
28323986 CGTGTTTACC
Statistics
Matches: 109, Mismatches: 27, Indels: 16
0.72 0.18 0.11
Matches are distributed among these distances:
23 2 0.02
24 6 0.06
25 92 0.84
26 7 0.06
27 2 0.02
ACGTcount: A:0.38, C:0.22, G:0.15, T:0.25
Consensus pattern (25 bp):
AAGGCTTTTCAGAGAATTCGCCACA
Found at i:28326992 original size:18 final size:17
Alignment explanation
Indices: 28326971--28327009 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
28326961 TTTTCTATAA
28326971 TTTTA-TATATTTAGAATT
1 TTTTATTAT-TTTA-AATT
28326989 TTTTATTATTTTAAATT
1 TTTTATTATTTTAAATT
28327006 TTTT
1 TTTT
28327010 TATTTTTCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 8 0.40
18 9 0.45
19 3 0.15
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (17 bp):
TTTTATTATTTTAAATT
Found at i:28326998 original size:17 final size:18
Alignment explanation
Indices: 28326971--28327009 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 18
28326961 TTTTCTATAA
28326971 TTTTATATA-TTTAGAATT
1 TTTTATATATTTTA-AATT
28326989 TTTTAT-TATTTTAAATT
1 TTTTATATATTTTAAATT
28327006 TTTT
1 TTTT
28327010 TATTTTTCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (18 bp):
TTTTATATATTTTAAATT
Found at i:28327063 original size:21 final size:22
Alignment explanation
Indices: 28327039--28327087 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 22
28327029 AATATTCTAT
* *
28327039 AATTT-ATATATTATAAAAATA
1 AATTTCATAAATTAAAAAAATA
28327060 AATTTTCATAAATTAAAAAAATA
1 AA-TTTCATAAATTAAAAAAATA
28327083 AATTT
1 AATTT
28327088 TTTATTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 2 0.08
22 6 0.25
23 16 0.67
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (22 bp):
AATTTCATAAATTAAAAAAATA
Found at i:28331711 original size:28 final size:28
Alignment explanation
Indices: 28331679--28331734 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
28331669 CAAACTGTGA
*
28331679 CAGCAATTGAGAAGCACGCTATCTTTTG
1 CAGCAATTGACAAGCACGCTATCTTTTG
28331707 CAGCAATTGACAAGCACGCTATCTTTTG
1 CAGCAATTGACAAGCACGCTATCTTTTG
28331735 TGTATTCCTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.29
Consensus pattern (28 bp):
CAGCAATTGACAAGCACGCTATCTTTTG
Found at i:28333641 original size:27 final size:27
Alignment explanation
Indices: 28333611--28333788 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
28333601 ATATTGAGTC
* * * *
28333611 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
28333638 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
28333665 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
28333693 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
28333720 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
28333747 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
28333774 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
28333789 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:28333750 original size:82 final size:81
Alignment explanation
Indices: 28333632--28333787 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
28333622 TGCTATATAA
* *
28333632 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
28333697 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
28333714 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
28333778 CACTTAGTGC
65 CACTTAGTGC
28333788 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:28339899 original size:46 final size:46
Alignment explanation
Indices: 28339849--28339977 Score: 222
Period size: 46 Copynumber: 2.8 Consensus size: 46
28339839 TGGTTGAGCA
* *
28339849 TCCGAACTCGTGGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
28339895 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
* *
28339941 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
28339978 GCGGGTTACA
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 79 1.00
ACGTcount: A:0.20, C:0.22, G:0.29, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
Found at i:28347454 original size:47 final size:47
Alignment explanation
Indices: 28347336--28347508 Score: 189
Period size: 45 Copynumber: 3.7 Consensus size: 47
28347326 GGATGGTTGA
* *
28347336 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAAT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGA-GGATGCAAAG
* *
28347384 G--TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA-GATGTAACTAG
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGAGGATGCAA--AG
* * *
28347429 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGC-AAC
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGA-GGATGCAAAG
*
28347476 GC--CCGAGCTCGTTGAGTTGAGTCCGAGTTCACT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACT
28347509 TAGGGGCGGG
Statistics
Matches: 108, Mismatches: 10, Indels: 17
0.80 0.07 0.13
Matches are distributed among these distances:
43 6 0.06
45 33 0.31
46 29 0.27
47 32 0.30
48 3 0.03
49 1 0.01
50 4 0.04
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (47 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGAGGATGCAAAG
Found at i:28347770 original size:19 final size:20
Alignment explanation
Indices: 28347733--28347770 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
28347723 ATAAGGTGGT
28347733 AAGATGATGAATGATGTTTA
1 AAGATGATGAATGATGTTTA
28347753 AAGATG-TGATAT-ATGTTT
1 AAGATGATGA-ATGATGTTT
28347771 TGGTGGTACC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.37, C:0.00, G:0.24, T:0.39
Consensus pattern (20 bp):
AAGATGATGAATGATGTTTA
Found at i:28368354 original size:48 final size:48
Alignment explanation
Indices: 28368283--28368497 Score: 213
Period size: 48 Copynumber: 4.5 Consensus size: 48
28368273 AGGGGATATA
* *
28368283 TTGATTTGGCTTCGGGCCATGATATTGGAACTTCGGGTGCGAGTTACT
1 TTGATTTGGCTTTGGGCCATGATATTGGAACTTCAGGTGCGAGTTACT
* *
28368331 TTGATTTGGCTTTGGGCCATGATATTGGCACTTCAGGTGCGAGTTATT
1 TTGATTTGGCTTTGGGCCATGATATTGGAACTTCAGGTGCGAGTTACT
* * * *
28368379 TTAATTTGGCTTTGAGCCATGATA-TCGACACTTCAGGTGCGAGCTT-CA
1 TTGATTTGGCTTTGGGCCATGATATTGGA-ACTTCAGGTGCGAG-TTACT
* ** * * ** *
28368427 TTGATTTGGCTATGACCCATGATATTAGCACTTTGGGTGCGAGATA-T
1 TTGATTTGGCTTTGGGCCATGATATTGGAACTTCAGGTGCGAGTTACT
*
28368474 ATTG-TGTTGGCTTCGGGCCATGAT
1 -TTGAT-TTGGCTTTGGGCCATGAT
28368498 GTGAGCACTT
Statistics
Matches: 138, Mismatches: 23, Indels: 12
0.80 0.13 0.07
Matches are distributed among these distances:
47 4 0.03
48 130 0.94
49 4 0.03
ACGTcount: A:0.19, C:0.17, G:0.28, T:0.36
Consensus pattern (48 bp):
TTGATTTGGCTTTGGGCCATGATATTGGAACTTCAGGTGCGAGTTACT
Found at i:28368507 original size:96 final size:95
Alignment explanation
Indices: 28368277--28368507 Score: 252
Period size: 96 Copynumber: 2.4 Consensus size: 95
28368267 GTCATTAGGG
* * *
28368277 GATATATTGATTTGGCTTCGGGCCATGATATTG-GAACTTCGGGTGCGAGTTACTTTGATTTGGC
1 GATATATTG-TTTGGCTTCGGGCCATGATA-TGAGCACTTCAGGTGCGAGTTACATTGATTTGGC
* ** *
28368341 TTTGGGCCATGATATTGGCACTTCAGGTGCGA
64 TATGACCCATGATATTAGCACTTCAGGTGCGA
* * * * *
28368373 GTTATTTTAATTTGGCTTTGAGCCATGATATCGA-CACTTCAGGTGCGAGCTT-CATTGATTTGG
1 GATATATT-GTTTGGCTTCGGGCCATGATAT-GAGCACTTCAGGTGCGAG-TTACATTGATTTGG
**
28368436 CTATGACCCATGATATTAGCACTTTGGGTGCGA
63 CTATGACCCATGATATTAGCACTTCAGGTGCGA
*
28368469 GATATATTGTGTTGGCTTCGGGCCATGATGTGAGCACTT
1 GATATATTGT-TTGGCTTCGGGCCATGATATGAGCACTT
28368508 AGTGTGCAAG
Statistics
Matches: 109, Mismatches: 20, Indels: 12
0.77 0.14 0.09
Matches are distributed among these distances:
95 4 0.04
96 103 0.94
97 2 0.02
ACGTcount: A:0.20, C:0.16, G:0.28, T:0.36
Consensus pattern (95 bp):
GATATATTGTTTGGCTTCGGGCCATGATATGAGCACTTCAGGTGCGAGTTACATTGATTTGGCTA
TGACCCATGATATTAGCACTTCAGGTGCGA
Found at i:28370098 original size:14 final size:14
Alignment explanation
Indices: 28370081--28370109 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
28370071 AATAACTAAA
28370081 ATAAGTATTTTTGG
1 ATAAGTATTTTTGG
28370095 ATAAGTATTTTTGG
1 ATAAGTATTTTTGG
28370109 A
1 A
28370110 CTTAAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.31, C:0.00, G:0.21, T:0.48
Consensus pattern (14 bp):
ATAAGTATTTTTGG
Found at i:28373071 original size:19 final size:19
Alignment explanation
Indices: 28373037--28373073 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
28373027 GGAAAAAATA
**
28373037 AAAAAAATAATTAGAAAAC
1 AAAAAAATAAAGAGAAAAC
28373056 AAAAAAATAAAGAGAAAA
1 AAAAAAATAAAGAGAAAA
28373074 TGAAGAATGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.78, C:0.03, G:0.08, T:0.11
Consensus pattern (19 bp):
AAAAAAATAAAGAGAAAAC
Found at i:28374574 original size:4 final size:4
Alignment explanation
Indices: 28374565--28374615 Score: 59
Period size: 4 Copynumber: 12.5 Consensus size: 4
28374555 ATTTAATTGA
* *
28374565 TTAT TTAT TTAT TTAGT TAAT TTAAT TGA- TTAT TTAT TTAT TTAT TTAT
1 TTAT TTAT TTAT TTA-T TTAT TT-AT TTAT TTAT TTAT TTAT TTAT TTAT
28374614 TT
1 TT
28374616 TTGAAAATAG
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
3 2 0.05
4 32 0.80
5 6 0.15
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (4 bp):
TTAT
Found at i:28374584 original size:29 final size:29
Alignment explanation
Indices: 28374551--28374608 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
28374541 TCTACAAATG
28374551 GTTAATTTAATTGATTATTTATTTATTTA
1 GTTAATTTAATTGATTATTTATTTATTTA
28374580 GTTAATTTAATTGATTATTTATTTATTTA
1 GTTAATTTAATTGATTATTTATTTATTTA
28374609 TTTATTTTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.62
Consensus pattern (29 bp):
GTTAATTTAATTGATTATTTATTTATTTA
Found at i:28380231 original size:3 final size:3
Alignment explanation
Indices: 28380223--28380247 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
28380213 CGATTGCTCC
28380223 GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA G
28380248 TTCAAGAAAG
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:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
GAA
Done.