Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D05
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: 63323194
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1953226 characters in sequence are not A, C, G, or T
File 174 of 199
Found at i:55915949 original size:29 final size:28
Alignment explanation
Indices: 55915854--55915952 Score: 101
Period size: 29 Copynumber: 3.3 Consensus size: 28
55915844 TACATAACTT
* *
55915854 ATTATGTAACAACATAATAAACTACATAATAC
1 ATTATATAATAACATAAT-AACT--A-AATAC
55915886 ATTATATAATAACATAATAACTTAAATA-
1 ATTATATAATAACATAATAAC-TAAATAC
55915914 ACTTATATAATAACATAATAACTAACATAC
1 A-TTATATAATAACATAATAACTAA-ATAC
*
55915944 AATATATAA
1 ATTATATAA
55915953 ACATATATAG
Statistics
Matches: 60, Mismatches: 3, Indels: 11
0.81 0.04 0.15
Matches are distributed among these distances:
28 4 0.07
29 34 0.57
30 2 0.03
31 3 0.05
32 17 0.28
ACGTcount: A:0.56, C:0.12, G:0.01, T:0.31
Consensus pattern (28 bp):
ATTATATAATAACATAATAACTAAATAC
Found at i:55915992 original size:9 final size:9
Alignment explanation
Indices: 55915964--55916237 Score: 250
Period size: 9 Copynumber: 30.2 Consensus size: 9
55915954 CATATATAGA
*
55915964 AACTAACAT
1 AACTTACAT
* *
55915973 AAATTAAAT
1 AACTTACAT
*
55915982 AAGTTACAT
1 AACTTACAT
55915991 AACTTACAT
1 AACTTACAT
* *
55916000 AAATTAAAT
1 AACTTACAT
55916009 AACTTACAT
1 AACTTACAT
55916018 AACTTACAT
1 AACTTACAT
*
55916027 AAAC-AACAT
1 -AACTTACAT
*
55916036 AAATTACAT
1 AACTTACAT
*
55916045 AACTTAAAT
1 AACTTACAT
* *
55916054 AGGA-ATGCAT
1 A--ACTTACAT
55916064 AACTTACAT
1 AACTTACAT
*
55916073 AACCTACAT
1 AACTTACAT
* *
55916082 AAATTAAAT
1 AACTTACAT
55916091 AACTTACAT
1 AACTTACAT
*
55916100 GACTTACAT
1 AACTTACAT
*
55916109 AAATTA-AGT
1 AACTTACA-T
*
55916118 AACCTACAT
1 AACTTACAT
55916127 AACTTACAT
1 AACTTACAT
*
55916136 AAACTTGCAT
1 -AACTTACAT
* *
55916146 AAATTAAAT
1 AACTTACAT
55916155 AACTTACAT
1 AACTTACAT
*
55916164 AACCTACAT
1 AACTTACAT
* *
55916173 AAATTAAAT
1 AACTTACAT
55916182 AACTTACAT
1 AACTTACAT
55916191 AACTTACAT
1 AACTTACAT
*
55916200 AAATTA-AGT
1 AACTTACA-T
55916209 AACTTACAT
1 AACTTACAT
55916218 AACTTACAT
1 AACTTACAT
55916227 AACTTACAT
1 AACTTACAT
55916236 AA
1 AA
55916238 TACATAGAAA
Statistics
Matches: 209, Mismatches: 46, Indels: 20
0.76 0.17 0.07
Matches are distributed among these distances:
8 5 0.02
9 186 0.89
10 17 0.08
11 1 0.00
ACGTcount: A:0.50, C:0.16, G:0.03, T:0.30
Consensus pattern (9 bp):
AACTTACAT
Found at i:55916082 original size:91 final size:90
Alignment explanation
Indices: 55915986--55916237 Score: 312
Period size: 91 Copynumber: 2.8 Consensus size: 90
55915976 TTAAATAAGT
* * * * * * *
55915986 TACATAACTTACATAAATTAAATAACTTACATAACTTACA-TAAACAACATAAATTACATAACTT
1 TACATAAATTAAATAACTTACATAACTTACATAAATTA-AGTAAACTACATAACTTACATAACTT
**
55916050 AAATAGGAA-TGCATAACTTACATAACC
65 AAATA--AATTAAATAACTTACATAACC
* *
55916077 TACATAAATTAAATAACTTACATGACTTACATAAATTAAGTAACCTACATAACTTACATAAACTT
1 TACATAAATTAAATAACTTACATAACTTACATAAATTAAGTAAACTACATAACTTACAT-AACTT
**
55916142 GCATAAATTAAATAACTTACATAACC
65 AAATAAATTAAATAACTTACATAACC
55916168 TACATAAATTAAATAACTTACATAACTTACATAAATTAAGT-AACTTACATAACTTACATAACTT
1 TACATAAATTAAATAACTTACATAACTTACATAAATTAAGTAAAC-TACATAACTTACATAACTT
*
55916232 ACATAA
65 AAATAA
55916238 TACATAGAAA
Statistics
Matches: 141, Mismatches: 16, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
90 15 0.11
91 118 0.84
92 8 0.06
ACGTcount: A:0.50, C:0.17, G:0.03, T:0.31
Consensus pattern (90 bp):
TACATAAATTAAATAACTTACATAACTTACATAAATTAAGTAAACTACATAACTTACATAACTTA
AATAAATTAAATAACTTACATAACC
Found at i:55921751 original size:66 final size:65
Alignment explanation
Indices: 55921654--55921824 Score: 191
Period size: 66 Copynumber: 2.6 Consensus size: 65
55921644 GAGCAAATTA
* * * * *
55921654 CACAACTTAAAGCGGAGGCAACATCGAGAGAAGCTGATGTTCAA-AAAAGATATGAAGAACTCCA
1 CACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAG-TATGAAGAACTCCA
55921718 G
65 G
* *
55921719 CTACAACTTAAAGCAGATGCAGCAGCGGGAGAAGCTGAGGTTCAACGAAAGTATGAAGAACTCCA
1 C-ACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAGTATGAAGAACTCCA
55921784 G
65 G
* * * ** *
55921785 CAGCAGCTTAGAGCAGATGCGGCAGTAAGAGAAGCAGAGG
1 CA-CAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGG
55921825 CGGCAGCGAG
Statistics
Matches: 89, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
65 2 0.02
66 83 0.93
67 4 0.04
ACGTcount: A:0.39, C:0.19, G:0.28, T:0.14
Consensus pattern (65 bp):
CACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAGTATGAAGAACTCCAG
Found at i:55921820 original size:21 final size:21
Alignment explanation
Indices: 55921796--55921907 Score: 89
Period size: 21 Copynumber: 5.3 Consensus size: 21
55921786 AGCAGCTTAG
* *
55921796 AGCAGATGCGGCAGTAAGAGA
1 AGCAGAGGCGGCAGCAAGAGA
*
55921817 AGCAGAGGCGGCAGCGAGAGA
1 AGCAGAGGCGGCAGCAAGAGA
* * * *
55921838 AGAACAGGCTGCAGCAAGGGA
1 AGCAGAGGCGGCAGCAAGAGA
*** *
55921859 AGCAGAGGCTAAAGCGAGAGA
1 AGCAGAGGCGGCAGCAAGAGA
* * * *
55921880 AGCAGAGGCTGTAGCGAGGGA
1 AGCAGAGGCGGCAGCAAGAGA
55921901 AGCAGAG
1 AGCAGAG
55921908 CAGCGTCAAA
Statistics
Matches: 74, Mismatches: 17, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 74 1.00
ACGTcount: A:0.37, C:0.16, G:0.42, T:0.05
Consensus pattern (21 bp):
AGCAGAGGCGGCAGCAAGAGA
Found at i:55921861 original size:42 final size:42
Alignment explanation
Indices: 55921806--55921907 Score: 123
Period size: 42 Copynumber: 2.4 Consensus size: 42
55921796 AGCAGATGCG
* * **
55921806 GCAGTAAGAGAAGCAGAGGCGGCAGCGAGAGAAGAACAGGCT
1 GCAGCAAGGGAAGCAGAGGCGAAAGCGAGAGAAGAACAGGCT
* * *
55921848 GCAGCAAGGGAAGCAGAGGCTAAAGCGAGAGAAGCAGAGGCT
1 GCAGCAAGGGAAGCAGAGGCGAAAGCGAGAGAAGAACAGGCT
* *
55921890 GTAGCGAGGGAAGCAGAG
1 GCAGCAAGGGAAGCAGAG
55921908 CAGCGTCAAA
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 51 1.00
ACGTcount: A:0.37, C:0.16, G:0.42, T:0.05
Consensus pattern (42 bp):
GCAGCAAGGGAAGCAGAGGCGAAAGCGAGAGAAGAACAGGCT
Found at i:55922260 original size:32 final size:32
Alignment explanation
Indices: 55922216--55922276 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
55922206 AATCTGCCAA
*
55922216 ATTTAGCGGCGTTTT-TGGTAAAAGCGCCGGGT
1 ATTTAGCAGCGTTTTCTGG-AAAAGCGCCGGGT
*
55922248 ATTTAGCAGCGTTTTCTGGATAAGCGCCG
1 ATTTAGCAGCGTTTTCTGGAAAAGCGCCG
55922277 CTATAGATCA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
32 23 0.88
33 3 0.12
ACGTcount: A:0.20, C:0.18, G:0.31, T:0.31
Consensus pattern (32 bp):
ATTTAGCAGCGTTTTCTGGAAAAGCGCCGGGT
Found at i:55922320 original size:43 final size:43
Alignment explanation
Indices: 55922251--55922347 Score: 106
Period size: 43 Copynumber: 2.3 Consensus size: 43
55922241 GCCGGGTATT
* * * *
55922251 TAGCAGCGTTTTCTGGATAAGCGCCGCTATAGATCAGGGTCTA
1 TAGCGGCGTTTTCTGGAAAAGCGCCGCTAAAGACCAGGGTCTA
* * * *
55922294 TTGCGGCGTTTT-TGGGAAAAGTGCCGCTAAAGGCCATGGTCTA
1 TAGCGGCGTTTTCT-GGAAAAGCGCCGCTAAAGACCAGGGTCTA
55922337 TAGCGGCGTTT
1 TAGCGGCGTTT
55922348 ATATAAAAAA
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
42 1 0.02
43 43 0.98
ACGTcount: A:0.21, C:0.20, G:0.31, T:0.29
Consensus pattern (43 bp):
TAGCGGCGTTTTCTGGAAAAGCGCCGCTAAAGACCAGGGTCTA
Found at i:55922631 original size:22 final size:22
Alignment explanation
Indices: 55922603--55922645 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
55922593 TTGCGACGCT
* *
55922603 AAAAAGCACCGCTAAAGGCCTA
1 AAAAAGCACCACTAAAAGCCTA
*
55922625 AAAAAGCGCCACTAAAAGCCT
1 AAAAAGCACCACTAAAAGCCT
55922646 GTTTTGGTGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.47, C:0.28, G:0.16, T:0.09
Consensus pattern (22 bp):
AAAAAGCACCACTAAAAGCCTA
Found at i:55927396 original size:11 final size:11
Alignment explanation
Indices: 55927377--55927419 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
55927367 ATATTTTTAT
*
55927377 AAAGTAAAAAG
1 AAAGAAAAAAG
*
55927388 AAAGAAAAAGG
1 AAAGAAAAAAG
55927399 AAAGCAAAAAAG
1 AAAG-AAAAAAG
55927411 -AAGAAAAAA
1 AAAGAAAAAA
55927420 AAGATGGGTC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
10 6 0.21
11 16 0.57
12 6 0.21
ACGTcount: A:0.77, C:0.02, G:0.19, T:0.02
Consensus pattern (11 bp):
AAAGAAAAAAG
Found at i:55930847 original size:17 final size:19
Alignment explanation
Indices: 55930825--55930860 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
55930815 CCCAATCTAC
55930825 CCAAAA-TTTATT-TCCCA
1 CCAAAATTTTATTCTCCCA
55930842 CCAAAATTTTATTCTCCCA
1 CCAAAATTTTATTCTCCCA
55930861 TTTATTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.35
18 6 0.35
19 5 0.29
ACGTcount: A:0.33, C:0.31, G:0.00, T:0.36
Consensus pattern (19 bp):
CCAAAATTTTATTCTCCCA
Found at i:55938521 original size:14 final size:15
Alignment explanation
Indices: 55938504--55938533 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
55938494 ATCATTTTGA
55938504 TTAAT-ATAAATATT
1 TTAATAATAAATATT
55938518 TTAATAATAAATATT
1 TTAATAATAAATATT
55938533 T
1 T
55938534 AGAAGGTCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TTAATAATAAATATT
Found at i:55940298 original size:7 final size:7
Alignment explanation
Indices: 55940286--55940330 Score: 63
Period size: 7 Copynumber: 6.4 Consensus size: 7
55940276 AACTAATCAA
*
55940286 TTTTTAC
1 TTTTCAC
*
55940293 TTTTTAC
1 TTTTCAC
*
55940300 TTTTTAC
1 TTTTCAC
55940307 TTTTCAC
1 TTTTCAC
55940314 TTTTCAC
1 TTTTCAC
55940321 TTTTCAC
1 TTTTCAC
55940328 TTT
1 TTT
55940331 AATAAGTATA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 37 1.00
ACGTcount: A:0.13, C:0.20, G:0.00, T:0.67
Consensus pattern (7 bp):
TTTTCAC
Found at i:55940305 original size:14 final size:14
Alignment explanation
Indices: 55940286--55940330 Score: 72
Period size: 14 Copynumber: 3.2 Consensus size: 14
55940276 AACTAATCAA
*
55940286 TTTTTACTTTTTAC
1 TTTTTACTTTTCAC
55940300 TTTTTACTTTTCAC
1 TTTTTACTTTTCAC
*
55940314 TTTTCACTTTTCAC
1 TTTTTACTTTTCAC
55940328 TTT
1 TTT
55940331 AATAAGTATA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.13, C:0.20, G:0.00, T:0.67
Consensus pattern (14 bp):
TTTTTACTTTTCAC
Found at i:55940393 original size:27 final size:28
Alignment explanation
Indices: 55940357--55940409 Score: 74
Period size: 27 Copynumber: 1.9 Consensus size: 28
55940347 TTCTAAATTT
*
55940357 TTATTTATTT-GTGTACACAAA-AAACTA
1 TTATTGATTTAGTGT-CACAAATAAACTA
55940384 TTATTGATTTAGTGTCACAAATAAAC
1 TTATTGATTTAGTGTCACAAATAAAC
55940410 ACGACATCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 15 0.65
28 8 0.35
ACGTcount: A:0.40, C:0.11, G:0.09, T:0.40
Consensus pattern (28 bp):
TTATTGATTTAGTGTCACAAATAAACTA
Found at i:55942985 original size:14 final size:14
Alignment explanation
Indices: 55942959--55942988 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
55942949 TTTATTAAAA
*
55942959 TTTTATTTTTAATT
1 TTTTAATTTTAATT
55942973 TTTTAATTTTAATT
1 TTTTAATTTTAATT
55942987 TT
1 TT
55942989 ATTCTTCTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTTAATTTTAATT
Found at i:55950619 original size:10 final size:10
Alignment explanation
Indices: 55950604--55950632 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
55950594 ACTTAAGAGT
55950604 TTTATTTAGA
1 TTTATTTAGA
55950614 TTTATTTAGA
1 TTTATTTAGA
55950624 TTTATTTAG
1 TTTATTTAG
55950633 CGGGCCTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.28, C:0.00, G:0.10, T:0.62
Consensus pattern (10 bp):
TTTATTTAGA
Found at i:55952506 original size:54 final size:55
Alignment explanation
Indices: 55952401--55952515 Score: 187
Period size: 54 Copynumber: 2.1 Consensus size: 55
55952391 TTGTGATAGG
*
55952401 AATTAATGGGAAAGTACGTGAAGAAGAAGAAGAAAGAGAAACTAATTAATGATTGAT
1 AATTAATGGGAAAGTACGT--AGAAGAAGAAGAAAGAGAAAATAATTAATGATTGAT
*
55952458 AATTAATGGGAAAGTACGT-TAAGAAGAAGAAAGAGAAAATAATTAATGATTGAT
1 AATTAATGGGAAAGTACGTAGAAGAAGAAGAAAGAGAAAATAATTAATGATTGAT
55952512 AATT
1 AATT
55952516 GAAAATAATT
Statistics
Matches: 56, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
54 37 0.66
57 19 0.34
ACGTcount: A:0.51, C:0.03, G:0.23, T:0.23
Consensus pattern (55 bp):
AATTAATGGGAAAGTACGTAGAAGAAGAAGAAAGAGAAAATAATTAATGATTGAT
Found at i:55952515 original size:14 final size:14
Alignment explanation
Indices: 55952496--55952543 Score: 52
Period size: 14 Copynumber: 3.7 Consensus size: 14
55952486 GAAAGAGAAA
55952496 ATAATTAATGATTG
1 ATAATTAATGATTG
55952510 ATAATTGAA--A---
1 ATAATT-AATGATTG
55952520 ATAATTAATGATTG
1 ATAATTAATGATTG
55952534 ATAATTAATG
1 ATAATTAATG
55952544 GGAGAAAGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 12
0.70 0.00 0.30
Matches are distributed among these distances:
9 2 0.07
10 6 0.21
11 1 0.04
13 1 0.04
14 16 0.57
15 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.12, T:0.40
Consensus pattern (14 bp):
ATAATTAATGATTG
Found at i:55952519 original size:24 final size:24
Alignment explanation
Indices: 55952492--55952539 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
55952482 AGAAGAAAGA
55952492 GAAAATAATTAATGATTGATAATT
1 GAAAATAATTAATGATTGATAATT
55952516 GAAAATAATTAATGATTGATAATT
1 GAAAATAATTAATGATTGATAATT
55952540 AATGGGAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.38
Consensus pattern (24 bp):
GAAAATAATTAATGATTGATAATT
Found at i:55952646 original size:3 final size:3
Alignment explanation
Indices: 55952640--55952674 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
55952630 GATGATGATG
55952640 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
55952675 TAGGTTTAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:55953071 original size:19 final size:19
Alignment explanation
Indices: 55953047--55953093 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
55953037 TAAATCTATG
55953047 AAAAAAAGAAGATTGA-AAC
1 AAAAAAA-AAGATTGATAAC
* *
55953066 AAAAAAAAAGGTTGATAGC
1 AAAAAAAAAGATTGATAAC
55953085 AAAAAAAAA
1 AAAAAAAAA
55953094 AAAACCTCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 7 0.28
19 18 0.72
ACGTcount: A:0.70, C:0.04, G:0.15, T:0.11
Consensus pattern (19 bp):
AAAAAAAAAGATTGATAAC
Found at i:55956972 original size:38 final size:38
Alignment explanation
Indices: 55956925--55956999 Score: 91
Period size: 38 Copynumber: 2.0 Consensus size: 38
55956915 GAAAATAATA
*
55956925 AAATATTAAAAAACAT-TTTTA-TATTTTTAATTGAATTT
1 AAATATT-AAAAACATCTTTTATTA-TTTAAATTGAATTT
* *
55956963 AAATTTTAAAAATATCTTTTATTATTTAAATTGAATT
1 AAATATTAAAAACATCTTTTATTATTTAAATTGAATT
55957000 CAAGTTGTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
37 7 0.22
38 23 0.72
39 2 0.06
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.51
Consensus pattern (38 bp):
AAATATTAAAAACATCTTTTATTATTTAAATTGAATTT
Found at i:55962406 original size:3 final size:3
Alignment explanation
Indices: 55962398--55962444 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
55962388 TCAATTGTAA
55962398 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CA
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CA
55962445 CAATAATAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.34, C:0.34, G:0.00, T:0.32
Consensus pattern (3 bp):
CAT
Found at i:55963055 original size:10 final size:10
Alignment explanation
Indices: 55963027--55963062 Score: 58
Period size: 10 Copynumber: 3.8 Consensus size: 10
55963017 TTAGAACATT
55963027 ATAAAATTAA
1 ATAAAATTAA
55963037 A-AAAA-TAA
1 ATAAAATTAA
55963045 ATAAAATTAA
1 ATAAAATTAA
55963055 ATAAAATT
1 ATAAAATT
55963063 TTAAAAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 4 0.17
9 8 0.33
10 12 0.50
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (10 bp):
ATAAAATTAA
Found at i:55965806 original size:13 final size:13
Alignment explanation
Indices: 55965788--55965812 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
55965778 TTGTCGTGTT
55965788 ATTTAGTTAATTA
1 ATTTAGTTAATTA
55965801 ATTTAGTTAATT
1 ATTTAGTTAATT
55965813 TTAGTTTTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (13 bp):
ATTTAGTTAATTA
Found at i:55966826 original size:39 final size:38
Alignment explanation
Indices: 55966780--55966861 Score: 121
Period size: 39 Copynumber: 2.1 Consensus size: 38
55966770 TTTTAAGGTT
55966780 TTAAAAATATATATAACTTATTTTTTAAAA-TTAAAATTA
1 TTAAAAATATATATAA-TTATTTTTTAAAACTTAAAA-TA
*
55966819 TTAAAAATATATATTATTATTTTTTAAAACTTTAAAATA
1 TTAAAAATATATATAATTATTTTTTAAAAC-TTAAAATA
55966858 TTAA
1 TTAA
55966862 TTAAATGCTT
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
38 13 0.32
39 21 0.52
40 6 0.15
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (38 bp):
TTAAAAATATATATAATTATTTTTTAAAACTTAAAATA
Found at i:55967926 original size:89 final size:88
Alignment explanation
Indices: 55967829--55968005 Score: 300
Period size: 89 Copynumber: 2.0 Consensus size: 88
55967819 AACAGCCCGA
* *
55967829 TTCTGGGCCTAGTTGAAAAAGTGGTTTTGGGACCACAAATCCGACAAGGGAAAATATGATTATTA
1 TTCTGGGCCTAGTCGAAAAAGTGGTTTCGGGACCACAAATCCGACAAGGG-AAATATGATTATTA
55967894 TTATATTTTTATGATCTACAATTT
65 TTATATTTTTATGATCTACAATTT
* *
55967918 TTCTGGGCCTAGTCGGAACAGTGGTTTCGGGACCACAAATCCGACAAGGGAAATATGATTATTAT
1 TTCTGGGCCTAGTCGAAAAAGTGGTTTCGGGACCACAAATCCGACAAGGGAAATATGATTATTAT
*
55967983 TATATTTTTATGATCTCCAATTT
66 TATATTTTTATGATCTACAATTT
55968006 CACGGAAAAA
Statistics
Matches: 83, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
88 37 0.45
89 46 0.55
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.35
Consensus pattern (88 bp):
TTCTGGGCCTAGTCGAAAAAGTGGTTTCGGGACCACAAATCCGACAAGGGAAATATGATTATTAT
TATATTTTTATGATCTACAATTT
Found at i:55969243 original size:102 final size:102
Alignment explanation
Indices: 55969108--55969338 Score: 401
Period size: 102 Copynumber: 2.3 Consensus size: 102
55969098 TTGAATGAAA
*
55969108 AAGGGGGTTGCTAAGTGCTGATTCCCCCGAGGGGTTGCTAAGTGCTGATTCCCCGAAC-CATTGG
1 AAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCG-ACTCATTGG
*
55969172 TGGTTGCTAAGTGCTGATTCAACCGTATCTTAAATGTG
65 TGGTTGCTAAGTGCTAATTCAACCGTATCTTAAATGTG
*
55969210 AAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTGCCCGACTCATTGGT
1 AAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGT
* *
55969275 GGTTGCTAAGTGCTAATTCCACTGTATCTTAAATGTG
66 GGTTGCTAAGTGCTAATTCAACCGTATCTTAAATGTG
55969312 AAGGGGGTTGCTAAGTGCTGATTCCCC
1 AAGGGGGTTGCTAAGTGCTGATTCCCC
55969339 GAACCATTGG
Statistics
Matches: 123, Mismatches: 5, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
101 2 0.02
102 121 0.98
ACGTcount: A:0.20, C:0.20, G:0.29, T:0.30
Consensus pattern (102 bp):
AAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGT
GGTTGCTAAGTGCTAATTCAACCGTATCTTAAATGTG
Found at i:55969363 original size:75 final size:75
Alignment explanation
Indices: 55969238--55969448 Score: 291
Period size: 75 Copynumber: 2.8 Consensus size: 75
55969228 TGATTCCCCC
* * *
55969238 AAGGGGTTGCTAAGTGCTGATTGCCCG-ACTCATTGGTGGTTGCTAAGTGCTAATTCCACTGTAT
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAAC-CATTGGTGGTTGCTAAGTGCTAATCCCACCGTAT
55969302 CTTAAATGTGA
65 CTTAAATGTGA
* *
55969313 AGGGGGTTGCTAAGTGCTGATTCCCCGAACCATTGGTGGTTGCTAAGTGCTGATCCCACCGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAACCATTGGTGGTTGCTAAGTGCTAATCCCACCGTATC
55969378 TTAAATGTGA
66 TTAAATGTGA
* * * * * *
55969388 AAGGGATTGCTAAGTGTTGATTCCCCAAATCACTGGTGGTTGCTAAGTACTGAAT-CCACCG
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAACCATTGGTGGTTGCTAAGTGCT-AATCCCACCG
55969449 ATAACGGATA
Statistics
Matches: 121, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
75 117 0.97
76 4 0.03
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (75 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCGAACCATTGGTGGTTGCTAAGTGCTAATCCCACCGTATC
TTAAATGTGA
Found at i:55973052 original size:14 final size:15
Alignment explanation
Indices: 55973035--55973064 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
55973025 ATTATTTTGA
55973035 TTAAT-ATAAATATT
1 TTAATAATAAATATT
55973049 TTAATAATAAATATT
1 TTAATAATAAATATT
55973064 T
1 T
55973065 AGAAGGTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TTAATAATAAATATT
Found at i:55982725 original size:84 final size:85
Alignment explanation
Indices: 55982579--55982749 Score: 317
Period size: 84 Copynumber: 2.0 Consensus size: 85
55982569 AATTAGATTT
* *
55982579 TTTACTTTGACAAATTCTATTTTTGGAAAAATCTAATTTAGTGGTTGCTTGTTGAGCACGATTCT
1 TTTACTTTGACAAATTCTATTTTTGGAAAAATCTAATTTAGTAGTTGCTTGTTAAGCACGATTCT
55982644 AGGAGTAAAATTATGTGAAA
66 AGGAGTAAAATTATGTGAAA
55982664 TTTA-TTTGACAAATTCTATTTTTGGAAAAATCTAATTTAGTAGTTGCTTGTTAAGCACGATTCT
1 TTTACTTTGACAAATTCTATTTTTGGAAAAATCTAATTTAGTAGTTGCTTGTTAAGCACGATTCT
55982728 AGGAGTAAAATTATGTGAAA
66 AGGAGTAAAATTATGTGAAA
55982748 TT
1 TT
55982750 GATTCTTTGA
Statistics
Matches: 84, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
84 80 0.95
85 4 0.05
ACGTcount: A:0.33, C:0.09, G:0.18, T:0.41
Consensus pattern (85 bp):
TTTACTTTGACAAATTCTATTTTTGGAAAAATCTAATTTAGTAGTTGCTTGTTAAGCACGATTCT
AGGAGTAAAATTATGTGAAA
Found at i:55986041 original size:19 final size:19
Alignment explanation
Indices: 55986017--55986063 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
55986007 TCTCTTTCTT
55986017 TTTGCATT-CATTCCATGCA
1 TTTGCATTACATTCCAT-CA
*
55986036 TTTGCATTACATTGCATCA
1 TTTGCATTACATTCCATCA
*
55986055 TATGCATTA
1 TTTGCATTA
55986064 GATTTTCACA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.26, C:0.21, G:0.11, T:0.43
Consensus pattern (19 bp):
TTTGCATTACATTCCATCA
Found at i:55988527 original size:3 final size:3
Alignment explanation
Indices: 55988519--55988586 Score: 109
Period size: 3 Copynumber: 22.7 Consensus size: 3
55988509 GTGCATCAAA
*
55988519 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAA AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
* *
55988567 AAG AAA AAG AAA AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AA
55988587 AAATGAAAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:55988587 original size:15 final size:15
Alignment explanation
Indices: 55988516--55988596 Score: 92
Period size: 15 Copynumber: 5.3 Consensus size: 15
55988506 ACAGTGCATC
*
55988516 AAAAAGAAGAAGAAG
1 AAAAAGAAGAAAAAG
* *
55988531 AAGAAGAAGAAGAAG
1 AAAAAGAAGAAAAAG
*
55988546 AAGAAGAA-AAAGAAG
1 AAAAAGAAGAAA-AAG
*
55988561 AAGAAGAAGAAAAAG
1 AAAAAGAAGAAAAAG
55988576 AAAAAGAAGAAAAATG
1 AAAAAGAAGAAAAA-G
55988592 AAAAA
1 AAAAA
55988597 ATAAAAGGGA
Statistics
Matches: 60, Mismatches: 3, Indels: 5
0.88 0.04 0.07
Matches are distributed among these distances:
14 2 0.03
15 49 0.82
16 9 0.15
ACGTcount: A:0.74, C:0.00, G:0.25, T:0.01
Consensus pattern (15 bp):
AAAAAGAAGAAAAAG
Found at i:55989924 original size:43 final size:44
Alignment explanation
Indices: 55989859--55989952 Score: 109
Period size: 43 Copynumber: 2.2 Consensus size: 44
55989849 AAGCACCAAC
* * * * *
55989859 CTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTAC-AAT
1 CTTATCTCCCTAAGCAGCAGTGGAATAGATCGAAGATGACGAAT
* * *
55989902 CTTATCTCCCTAAGTAGTAGTGGAATAGATCGAAGATGGCGAAT
1 CTTATCTCCCTAAGCAGCAGTGGAATAGATCGAAGATGACGAAT
55989946 CTTATCT
1 CTTATCT
55989953 TCCCAAGGTA
Statistics
Matches: 42, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
43 32 0.76
44 10 0.24
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.30
Consensus pattern (44 bp):
CTTATCTCCCTAAGCAGCAGTGGAATAGATCGAAGATGACGAAT
Found at i:55990109 original size:45 final size:45
Alignment explanation
Indices: 55990065--55990565 Score: 657
Period size: 45 Copynumber: 11.2 Consensus size: 45
55990055 GGAGCAGACT
* * * *
55990065 GAAGATAGCAGATATTGTCTTTCTGTACTGGCAGCGGAGTAGA-C
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
*
55990109 TGAAGATAGCAGATCTTATCTTCCTGTATTGGCAGCGAAGTAGATC
1 -GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
55990155 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* *
55990200 GAAGATAGTAGATCTTGTCTTCCTATATTGGCAGCGAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* *
55990245 GAAGATAACAGATGTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
*
55990290 GAAGATAGCAGATCTTGTCTTCCTGTATTGGTAGCGAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* *
55990335 GAAGATAGCAGATCTTGTCTTCCTGTATTGGTAGTGAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
55990380 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* * * * *
55990425 AAAGATAGCAGATCTTGCCTTCTTGTACTGGCAGCGAAGCAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* * * ** * * ** * *
55990470 GAAGACACCAG-CCTTACCTTCCTGTACTGACATTGGAGCAGA-C
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* * * * * *
55990513 TTAAGATAGCAGATCTTGCCTTCTTGTACTGACAGCGAAGCAGATC
1 -GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
55990559 GAAGATA
1 GAAGATA
55990566 CCATAGTTTG
Statistics
Matches: 409, Mismatches: 43, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
43 1 0.00
44 32 0.08
45 374 0.91
46 2 0.00
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.28
Consensus pattern (45 bp):
GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
Found at i:55991744 original size:3 final size:3
Alignment explanation
Indices: 55991736--55991777 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
55991726 AAGTTAGTAC
* * *
55991736 TAT TAT TAT TAT TAT TAT TAT TTT TAA TAT TAT TTT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
55991778 CATCATATTT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:55991753 original size:12 final size:12
Alignment explanation
Indices: 55991736--55991777 Score: 66
Period size: 12 Copynumber: 3.5 Consensus size: 12
55991726 AAGTTAGTAC
*
55991736 TATTATTATTAT
1 TATTATTATTTT
55991748 TATTATTATTTT
1 TATTATTATTTT
*
55991760 TAATATTATTTT
1 TATTATTATTTT
55991772 TATTAT
1 TATTAT
55991778 CATCATATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
TATTATTATTTT
Found at i:55992068 original size:16 final size:16
Alignment explanation
Indices: 55992047--55992105 Score: 64
Period size: 16 Copynumber: 3.6 Consensus size: 16
55992037 AAAGTATACA
*
55992047 TATATATACATACTTT
1 TATATATACATAATTT
**
55992063 TATATATACATGTTTT
1 TATATATACATAATTT
* *
55992079 TACATATTTCATAATTT
1 TATATA-TACATAATTT
55992096 TATATATACA
1 TATATATACA
55992106 CATATATGTA
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
16 22 0.65
17 12 0.35
ACGTcount: A:0.37, C:0.10, G:0.02, T:0.51
Consensus pattern (16 bp):
TATATATACATAATTT
Found at i:55992224 original size:35 final size:35
Alignment explanation
Indices: 55992184--55992254 Score: 99
Period size: 35 Copynumber: 2.0 Consensus size: 35
55992174 TTAAAATATG
*
55992184 TGTACATACATATGT-TCTTCATATTTTCATAATTT
1 TGTACATACATATATCT-TTCATATTTTCATAATTT
* *
55992219 TGTACATATATATATCTTTTATATTTTCATAATTT
1 TGTACATACATATATCTTTCATATTTTCATAATTT
55992254 T
1 T
55992255 TTGGATCATT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
35 31 0.97
36 1 0.03
ACGTcount: A:0.30, C:0.11, G:0.04, T:0.55
Consensus pattern (35 bp):
TGTACATACATATATCTTTCATATTTTCATAATTT
Found at i:55994046 original size:35 final size:35
Alignment explanation
Indices: 55993979--55994049 Score: 99
Period size: 35 Copynumber: 2.0 Consensus size: 35
55993969 AATGATCCAA
*
55993979 AAAATTATGAAAATATAAAAGATATATATATGTAC
1 AAAATTATGAAAATATAAAAGACATATATATGTAC
* *
55994014 AAAATTATGAAAATAT-GAAGAACATATGTATGTAC
1 AAAATTATGAAAATATAAAAG-ACATATATATGTAC
55994049 A
1 A
55994050 CATATTTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
34 3 0.09
35 29 0.91
ACGTcount: A:0.55, C:0.04, G:0.11, T:0.30
Consensus pattern (35 bp):
AAAATTATGAAAATATAAAAGACATATATATGTAC
Found at i:55994144 original size:16 final size:16
Alignment explanation
Indices: 55994124--55994185 Score: 79
Period size: 16 Copynumber: 3.8 Consensus size: 16
55994114 TTATACATAT
55994124 ATATGTATATATAAAA
1 ATATGTATATATAAAA
* *
55994140 TTATGAAATATATAAAA
1 ATATG-TATATATAAAA
*
55994157 ACATGTATATATAAAA
1 ATATGTATATATAAAA
*
55994173 GTATGTATATATA
1 ATATGTATATATA
55994186 TGTATACTTT
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
16 25 0.66
17 13 0.34
ACGTcount: A:0.53, C:0.02, G:0.08, T:0.37
Consensus pattern (16 bp):
ATATGTATATATAAAA
Found at i:55994482 original size:3 final size:3
Alignment explanation
Indices: 55994476--55994524 Score: 89
Period size: 3 Copynumber: 16.3 Consensus size: 3
55994466 TGATAGTAAC
*
55994476 AAT AAT AAT AAT AAC AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
55994524 A
1 A
55994525 GTACTAACTT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:55996652 original size:14 final size:14
Alignment explanation
Indices: 55996615--55996644 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
55996605 TTTATTAAAA
55996615 TTTTATTTTTAATT
1 TTTTATTTTTAATT
*
55996629 TTTTAATTTTAATT
1 TTTTATTTTTAATT
55996643 TT
1 TT
55996645 CTTTTTTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTTATTTTTAATT
Found at i:55996689 original size:5 final size:5
Alignment explanation
Indices: 55996679--55996707 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
55996669 CCTCTCTTTC
55996679 TATTT TATTT TATTT TATTT TATTT TATT
1 TATTT TATTT TATTT TATTT TATTT TATT
55996708 CAAAATAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
TATTT
Found at i:55999383 original size:31 final size:31
Alignment explanation
Indices: 55999365--55999422 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
55999355 ATTTTATTAT
55999365 AATATTTTTA-TATTTAAAATTTAAATTTAAA
1 AATATTTTTATTATTTAAAA-TTAAATTTAAA
*
55999396 AATATTTTTATTATTT-AAATTGAATTT
1 AATATTTTTATTATTTAAAATTAAATTT
55999423 GAATTGTACC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
30 7 0.28
31 13 0.52
32 5 0.20
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (31 bp):
AATATTTTTATTATTTAAAATTAAATTTAAA
Found at i:55999456 original size:14 final size:14
Alignment explanation
Indices: 55999437--55999464 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
55999427 TGTACCCTCT
55999437 CAATACATGGAAGG
1 CAATACATGGAAGG
55999451 CAATACATGGAAGG
1 CAATACATGGAAGG
55999465 GTCTATAGTC
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:0.43, C:0.14, G:0.29, T:0.14
Consensus pattern (14 bp):
CAATACATGGAAGG
Found at i:56008607 original size:32 final size:32
Alignment explanation
Indices: 56008555--56008626 Score: 96
Period size: 32 Copynumber: 2.3 Consensus size: 32
56008545 ATTATGGATA
56008555 AAAT-AATAAGAAATAATATAGT-ATAAAATT
1 AAATAAATAAGAAATAATATAGTAATAAAATT
*
56008585 AAATAAATAATAATATAATATAGTAATAAAATT
1 AAATAAATAAGAA-ATAATATAGTAATAAAATT
*
56008618 -TATAAATAA
1 AAATAAATAA
56008627 ATTTTTTAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
30 4 0.11
31 7 0.19
32 18 0.49
33 8 0.22
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (32 bp):
AAATAAATAAGAAATAATATAGTAATAAAATT
Found at i:56020302 original size:21 final size:22
Alignment explanation
Indices: 56020276--56020322 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
56020266 CTCTGCTCAA
*
56020276 ACTCCACCTGCTGCGGAGTAC-
1 ACTCCACCTGCTGCGAAGTACT
56020297 ACTCCACCTGCTGCGAAGTACT
1 ACTCCACCTGCTGCGAAGTACT
56020319 ACTC
1 ACTC
56020323 ACTCCTTCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.21
Consensus pattern (22 bp):
ACTCCACCTGCTGCGAAGTACT
Found at i:56030949 original size:33 final size:33
Alignment explanation
Indices: 56030912--56030978 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
56030902 AGGAGGCATA
* *
56030912 AAAGATGGGCCCAGCTGTAAAGAGGACCTGATG
1 AAAGATGAGCCCACCTGTAAAGAGGACCTGATG
* *
56030945 AAAGATGAGCCCACCTGTAAAGAGTACTTGATG
1 AAAGATGAGCCCACCTGTAAAGAGGACCTGATG
56030978 A
1 A
56030979 GATTTTTCTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.36, C:0.18, G:0.28, T:0.18
Consensus pattern (33 bp):
AAAGATGAGCCCACCTGTAAAGAGGACCTGATG
Found at i:56038314 original size:27 final size:28
Alignment explanation
Indices: 56038284--56038341 Score: 66
Period size: 27 Copynumber: 2.1 Consensus size: 28
56038274 ATTATAAATT
56038284 TAAATCTTAACATTTATT-TATTTTTT-G
1 TAAAT-TTAACATTTATTCTATTTTTTAG
* * *
56038311 TAAATTTGACCTTTATTCTTTTTTTTAG
1 TAAATTTAACATTTATTCTATTTTTTAG
56038339 TAA
1 TAA
56038342 GCTTTCAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
26 10 0.38
27 12 0.46
28 4 0.15
ACGTcount: A:0.28, C:0.09, G:0.05, T:0.59
Consensus pattern (28 bp):
TAAATTTAACATTTATTCTATTTTTTAG
Found at i:56039248 original size:21 final size:21
Alignment explanation
Indices: 56039223--56039265 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
56039213 ATGATTTCAA
56039223 ACTACTAATCAATCAAATAAT
1 ACTACTAATCAATCAAATAAT
56039244 ACTACTAATCAATCAAATAAT
1 ACTACTAATCAATCAAATAAT
56039265 A
1 A
56039266 TAAGAAATAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.53, C:0.19, G:0.00, T:0.28
Consensus pattern (21 bp):
ACTACTAATCAATCAAATAAT
Found at i:56039571 original size:16 final size:16
Alignment explanation
Indices: 56039550--56039581 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
56039540 TAAATTTAGC
56039550 GAATTTTTTTCTATAT
1 GAATTTTTTTCTATAT
56039566 GAATTTTTTTCTATAT
1 GAATTTTTTTCTATAT
56039582 TATAGATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.06, G:0.06, T:0.62
Consensus pattern (16 bp):
GAATTTTTTTCTATAT
Found at i:56042326 original size:67 final size:65
Alignment explanation
Indices: 56042174--56042328 Score: 152
Period size: 66 Copynumber: 2.3 Consensus size: 65
56042164 CTACTGTCGT
* * * * * *
56042174 TTTTTGGAGATATGCTTCATCTCTATGGAGAGTGATTAAACGGTTTATGGGGGGCTTGATTGTCA
1 TTTTTGGAGATATGC-TCACCTCTATGGAGAGTGATTAAACAGTTCATGAGGGCCTTGACTGTCA
56042239 A
65 A
* * **
56042240 TTTTTGGTGTTATGCCTCACCTCTATGGAGAGCTG-TTGGACAGTTCATGAAGGGCCTTGACTG-
1 TTTTTGGAGATATG-CTCACCTCTATGGAGAG-TGATTAAACAGTTCATG-AGGGCCTTGACTGT
56042303 CTAA
63 C-AA
56042307 TTTTTGGAGATATGTCTCACCT
1 TTTTTGGAGATATG-CTCACCT
56042329 TCGTGGAAAG
Statistics
Matches: 72, Mismatches: 13, Indels: 7
0.78 0.14 0.08
Matches are distributed among these distances:
66 38 0.53
67 34 0.47
ACGTcount: A:0.21, C:0.15, G:0.26, T:0.37
Consensus pattern (65 bp):
TTTTTGGAGATATGCTCACCTCTATGGAGAGTGATTAAACAGTTCATGAGGGCCTTGACTGTCAA
Found at i:56046566 original size:18 final size:19
Alignment explanation
Indices: 56046543--56046580 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
56046533 GGAAGCAAGC
*
56046543 AATGATTGAAGA-AATCAG
1 AATGATTGAAAAGAATCAG
56046561 AATGATTGAAAAGAATCAG
1 AATGATTGAAAAGAATCAG
56046580 A
1 A
56046581 CCTGGAGTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.53, C:0.05, G:0.21, T:0.21
Consensus pattern (19 bp):
AATGATTGAAAAGAATCAG
Found at i:56054625 original size:14 final size:14
Alignment explanation
Indices: 56054599--56054628 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
56054589 TTTATTAAAA
*
56054599 TTTTATTTTTAATT
1 TTTTAATTTTAATT
56054613 TTTTAATTTTAATT
1 TTTTAATTTTAATT
56054627 TT
1 TT
56054629 ATTCTTCTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTTAATTTTAATT
Found at i:56056891 original size:27 final size:25
Alignment explanation
Indices: 56056854--56056909 Score: 67
Period size: 27 Copynumber: 2.2 Consensus size: 25
56056844 TAAATTATGG
*
56056854 ATAAAATAATAAGAAATAATATAGT
1 ATAAAATAATAAGAAATAATATAAT
**
56056879 ATAAAATTAAATAATTAATAATATAAT
1 ATAAAA-T-AATAAGAAATAATATAAT
56056906 ATAA
1 ATAA
56056910 TATAGTAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 6 0.23
26 1 0.04
27 19 0.73
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (25 bp):
ATAAAATAATAAGAAATAATATAAT
Found at i:56063121 original size:32 final size:32
Alignment explanation
Indices: 56063070--56063133 Score: 94
Period size: 31 Copynumber: 2.0 Consensus size: 32
56063060 CTTATGGATA
56063070 AAATAATAAAGAAATAATATAGT-ATAAAATT
1 AAATAATAAAGAAATAATATAGTAATAAAATT
* *
56063101 AAATAATTAATAATATAATATAGTAATAAAATT
1 AAATAATAAAGAA-ATAATATAGTAATAAAATT
56063134 TATAAATATC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 11 0.38
32 10 0.34
33 8 0.28
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (32 bp):
AAATAATAAAGAAATAATATAGTAATAAAATT
Found at i:56064221 original size:2 final size:2
Alignment explanation
Indices: 56064214--56064239 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
56064204 TGGAAACTAC
56064214 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
56064240 TAGAGAAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:56067051 original size:14 final size:14
Alignment explanation
Indices: 56067034--56067061 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
56067024 CTGAAGATAA
56067034 GTGGGGGCGAATAT
1 GTGGGGGCGAATAT
56067048 GTGGGGGCGAATAT
1 GTGGGGGCGAATAT
56067062 AACCTTAAAG
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:0.21, C:0.07, G:0.50, T:0.21
Consensus pattern (14 bp):
GTGGGGGCGAATAT
Found at i:56068974 original size:34 final size:34
Alignment explanation
Indices: 56068936--56069004 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
56068926 CACCGGGCTC
56068936 TACGTATTCCATTTGCTCTGGCCCTGCAACGCAA
1 TACGTATTCCATTTGCTCTGGCCCTGCAACGCAA
56068970 TACGTATTCCATTTGCTCTGGCCCTGCAACGCAA
1 TACGTATTCCATTTGCTCTGGCCCTGCAACGCAA
56069004 T
1 T
56069005 CATATATGTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.20, C:0.32, G:0.17, T:0.30
Consensus pattern (34 bp):
TACGTATTCCATTTGCTCTGGCCCTGCAACGCAA
Found at i:56069753 original size:340 final size:340
Alignment explanation
Indices: 56069133--56070127 Score: 1936
Period size: 340 Copynumber: 2.9 Consensus size: 340
56069123 AACAGGATGA
56069133 AAATCATTGCCTTATTACCTGACTTAGTGGCTGAAATGTGTTGAGAGATTAGAACTGAAAATGAA
1 AAATCATTGCCTTATTACCTGACTTAGTGGCTGAAATGTGTTGAGAGATTAGAACTGAAAATGAA
56069198 GCAGTGAAGTTGACTTCCTTGACTATCTTACAAAGCTAGCAGATAATAAAAAACAATCATTGCAT
66 GCAGTGAAGTTGACTTCCTTGACTATCTTACAAAGCTAGCAGATAATAAAAAACAATCATTGCAT
56069263 AGTCATGGATGAAGCAAATGAAAGAAAATTACCTTTGACGGGATGCTTGAAATTTGGTGATAGAC
131 AGTCATGGATGAAGCAAATGAAAGAAAATTACCTTTGACGGGATGCTTGAAATTTGGTGATAGAC
56069328 CTTGGAGATGAAAACAAATTAAAAACAGTGAAGAAGAAAGAATGTTGTGGGCAGAAAGGCAGAAC
196 CTTGGAGATGAAAACAAATTAAAAACAGTGAAGAAGAAAGAATGTTGTGGGCAGAAAGGCAGAAC
56069393 TATTAAGCAAAGAAAAGCATGTAATGAAATAAGCAAATGAAAGAAAAGTAGGTAGAGTGGATGGT
261 TATTAAGCAAAGAAAAGCATGTAATGAAATAAGCAAATGAAAGAAAAGTAGGTAGAGTGGATGGT
56069458 TGAAATCAGTAGAGG
326 TGAAATCAGTAGAGG
56069473 AAATCATTGCCTTATTACCTGACTTAGTGGCTGAAATGTGTTGAGAGATTAGAACTGAAAATGAA
1 AAATCATTGCCTTATTACCTGACTTAGTGGCTGAAATGTGTTGAGAGATTAGAACTGAAAATGAA
56069538 GCAGTGAAGTTGACTTCCTTGACTATCTTACAAAGCTAGCAGATAATAAAAAACAATCATTGCAT
66 GCAGTGAAGTTGACTTCCTTGACTATCTTACAAAGCTAGCAGATAATAAAAAACAATCATTGCAT
56069603 AGTCATGGATGAAGCAAATGAAAGAAAATTACCTTTGACGGGATGCTTGAAATTTGGTGATAGAC
131 AGTCATGGATGAAGCAAATGAAAGAAAATTACCTTTGACGGGATGCTTGAAATTTGGTGATAGAC
56069668 CTTGGAGATGAAAACAAATTAAAAACAGTGAAGAAGAAAGAATGTTGTGGGCAGAAAGGCAGAAC
196 CTTGGAGATGAAAACAAATTAAAAACAGTGAAGAAGAAAGAATGTTGTGGGCAGAAAGGCAGAAC
56069733 TATTAAGCAAAGAAAAGCATGTAATGAAATAAGCAAATGAAAGAAAAGTAGGTAGAGTGGATGGT
261 TATTAAGCAAAGAAAAGCATGTAATGAAATAAGCAAATGAAAGAAAAGTAGGTAGAGTGGATGGT
56069798 TGAAATCAGTAGAGG
326 TGAAATCAGTAGAGG
56069813 AAATCATTGCCTTATTACCTGACTTAGTGGCTGAAATGTGTTGAGAGATTAGAACTGAAAATGAA
1 AAATCATTGCCTTATTACCTGACTTAGTGGCTGAAATGTGTTGAGAGATTAGAACTGAAAATGAA
56069878 GCAGTGAAGTTGACTTCCTTGACTATCTTACAAAGCTAGCAGATAATAAAAAACAATCATTGCAT
66 GCAGTGAAGTTGACTTCCTTGACTATCTTACAAAGCTAGCAGATAATAAAAAACAATCATTGCAT
56069943 AGTCATGGATGAAGCAAATGAAAGAAAATTACCTTTGACGGGATGCTTGAAATTTGGTGATAGAC
131 AGTCATGGATGAAGCAAATGAAAGAAAATTACCTTTGACGGGATGCTTGAAATTTGGTGATAGAC
* *
56070008 CTTGGAGATGAAAACAAATTAAAAACAGTGAAGAAGAAAGACTGTTGTGGGCTGAAAGGCAGAAC
196 CTTGGAGATGAAAACAAATTAAAAACAGTGAAGAAGAAAGAATGTTGTGGGCAGAAAGGCAGAAC
* *
56070073 CATTAAGCAAAGAAAAGCATATGTAATGAAATAAGCAAATGAAAGCAAAGTAGGT
261 TATTAAGCAAAGAAAAGC--ATGTAATGAAATAAGCAAATGAAAGAAAAGTAGGT
56070128 TGAAATTTTG
Statistics
Matches: 649, Mismatches: 4, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
340 615 0.95
342 34 0.05
ACGTcount: A:0.41, C:0.11, G:0.23, T:0.24
Consensus pattern (340 bp):
AAATCATTGCCTTATTACCTGACTTAGTGGCTGAAATGTGTTGAGAGATTAGAACTGAAAATGAA
GCAGTGAAGTTGACTTCCTTGACTATCTTACAAAGCTAGCAGATAATAAAAAACAATCATTGCAT
AGTCATGGATGAAGCAAATGAAAGAAAATTACCTTTGACGGGATGCTTGAAATTTGGTGATAGAC
CTTGGAGATGAAAACAAATTAAAAACAGTGAAGAAGAAAGAATGTTGTGGGCAGAAAGGCAGAAC
TATTAAGCAAAGAAAAGCATGTAATGAAATAAGCAAATGAAAGAAAAGTAGGTAGAGTGGATGGT
TGAAATCAGTAGAGG
Found at i:56093267 original size:25 final size:26
Alignment explanation
Indices: 56093211--56093267 Score: 98
Period size: 27 Copynumber: 2.2 Consensus size: 26
56093201 CTAAATTATT
56093211 TAACTAAATTTCAATACATCTATATAC
1 TAACTAAATTTCAATACATC-ATATAC
56093238 TAACTAAATTTCAATACATC-TATAC
1 TAACTAAATTTCAATACATCATATAC
56093263 TAACT
1 TAACT
56093268 CTGTAAATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
25 10 0.33
27 20 0.67
ACGTcount: A:0.44, C:0.19, G:0.00, T:0.37
Consensus pattern (26 bp):
TAACTAAATTTCAATACATCATATAC
Found at i:56095622 original size:21 final size:21
Alignment explanation
Indices: 56095590--56095630 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
56095580 AGGCTCGAGG
56095590 GGCCTGTTTTAGGCC-ATACAA
1 GGCCTGTTTTA-GCCTATACAA
56095611 GGCCT-TTCTTAGCCTATACA
1 GGCCTGTT-TTAGCCTATACA
56095631 CCAAATGTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.22, C:0.27, G:0.20, T:0.32
Consensus pattern (21 bp):
GGCCTGTTTTAGCCTATACAA
Found at i:56101100 original size:28 final size:28
Alignment explanation
Indices: 56101064--56101120 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
56101054 CAATAAACTC
56101064 AGCGACCAATTGTTGATGAAAAAGAGTA
1 AGCGACCAATTGTTGATGAAAAAGAGTA
*
56101092 AGCGGCCAATTGTTGATGAAAAAGAGTA
1 AGCGACCAATTGTTGATGAAAAAGAGTA
56101120 A
1 A
56101121 TAGAGTATAT
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:0.42, C:0.11, G:0.26, T:0.21
Consensus pattern (28 bp):
AGCGACCAATTGTTGATGAAAAAGAGTA
Found at i:56104432 original size:43 final size:43
Alignment explanation
Indices: 56104322--56104768 Score: 250
Period size: 44 Copynumber: 10.3 Consensus size: 43
56104312 AGATTTACTA
** * * * *
56104322 TCTTCGATCTGCTCCACTATTGTTTAGGGAGATAAGATCTGTAA
1 TCTTCGATCTGCTCCACTGCTGCTTAGGGAGATAAG-GCTGGAG
* ** * * * * *
56104366 TTTTTAACCTACTCCACTGCTGCTCAGGGAGACAAGGCTGGGG
1 TCTTCGATCTGCTCCACTGCTGCTTAGGGAGATAAGGCTGGAG
* * * ** *
56104409 TCTTCGATTTGCTCCACTACTGCTTAGGGAGATAAGATCTATAA
1 TCTTCGATCTGCTCCACTGCTGCTTAGGGAGATAAG-GCTGGAG
* ** * * * *
56104453 TTTTTAACCTACTCCACTGCTGCTTAGTGAGATAAGGCTGGGG
1 TCTTCGATCTGCTCCACTGCTGCTTAGGGAGATAAGGCTGGAG
* * * * * *
56104496 ACTTCGATATGCTCCACTCCTGCTTAGGGAGATAAGATCTGTAA
1 TCTTCGATCTGCTCCACTGCTGCTTAGGGAGATAAG-GCTGGAG
* * * * * * *
56104540 TTTTCAACCTACTCCACTGCTGCTCAGGGAGATAAGGTTGGGG
1 TCTTCGATCTGCTCCACTGCTGCTTAGGGAGATAAGGCTGGAG
* * ** * *
56104583 ACTTCGATCTGCTCCACTACTGCTTAGGGAGATAATATCTGTAA
1 TCTTCGATCTGCTCCACTGCTGCTTAGGGAGATAA-GGCTGGAG
* * * * * *
56104627 TTTTCAACCTACTCCACTGCTGCTCAAGGAGATAAGGCTGGAG
1 TCTTCGATCTGCTCCACTGCTGCTTAGGGAGATAAGGCTGGAG
* * * * *
56104670 ACTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAA
1 TCTTCGATCTGCTCCACTGCTGCTTAGGGAGATAAG-GCTGGAG
* * * * **
56104714 T-TTCCAACCTACTCCACTGCTGCTCAGGGAGAT-AGGCTGGTC
1 TCTT-CGATCTGCTCCACTGCTGCTTAGGGAGATAAGGCTGGAG
*
56104756 TCTTTGATCTGCT
1 TCTTCGATCTGCT
56104769 TCGCTGTTAG
Statistics
Matches: 280, Mismatches: 117, Indels: 14
0.68 0.28 0.03
Matches are distributed among these distances:
42 9 0.03
43 127 0.45
44 144 0.51
ACGTcount: A:0.24, C:0.23, G:0.22, T:0.31
Consensus pattern (43 bp):
TCTTCGATCTGCTCCACTGCTGCTTAGGGAGATAAGGCTGGAG
Found at i:56104468 original size:87 final size:87
Alignment explanation
Indices: 56104323--56104753 Score: 702
Period size: 87 Copynumber: 5.0 Consensus size: 87
56104313 GATTTACTAT
* * *
56104323 CTTCGATCTGCTCCACTATTGTTTAGGGAGATAAGATCTGTAATTTTTAACCTACTCCACTGCTG
1 CTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAACCTACTCCACTGCTG
* *
56104388 CTCAGGGAGACAAGGCTGGGGT
66 CTCAGGGAGATAAGGCTGGGGA
* * *
56104410 CTTCGATTTGCTCCACTACTGCTTAGGGAGATAAGATCTATAATTTTTAACCTACTCCACTGCTG
1 CTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAACCTACTCCACTGCTG
* *
56104475 CTTAGTGAGATAAGGCTGGGGA
66 CTCAGGGAGATAAGGCTGGGGA
* *
56104497 CTTCGATATGCTCCACTCCTGCTTAGGGAGATAAGATCTGTAATTTTCAACCTACTCCACTGCTG
1 CTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAACCTACTCCACTGCTG
*
56104562 CTCAGGGAGATAAGGTTGGGGA
66 CTCAGGGAGATAAGGCTGGGGA
*
56104584 CTTCGATCTGCTCCACTACTGCTTAGGGAGATAATATCTGTAATTTTCAACCTACTCCACTGCTG
1 CTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAACCTACTCCACTGCTG
* *
56104649 CTCAAGGAGATAAGGCTGGAGA
66 CTCAGGGAGATAAGGCTGGGGA
*
56104671 CTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTCCAACCTACTCCACTGCTG
1 CTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAACCTACTCCACTGCTG
56104736 CTCAGGGAGAT-AGGCTGG
66 CTCAGGGAGATAAGGCTGG
56104754 TCTCTTTGAT
Statistics
Matches: 320, Mismatches: 24, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
86 7 0.02
87 313 0.98
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.30
Consensus pattern (87 bp):
CTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAACCTACTCCACTGCTG
CTCAGGGAGATAAGGCTGGGGA
Found at i:56104900 original size:88 final size:88
Alignment explanation
Indices: 56104808--56105722 Score: 1262
Period size: 88 Copynumber: 10.4 Consensus size: 88
56104798 CTATCTTCAG
* * * * * * * *
56104808 TCTGCTCCACTGTCAGTACAGGAAGGCAAGA-CTGGC-GTTTTCAACCTGCTCCGCTGTAACCCA
1 TCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCT-GCTATTTTTAACCTGCTCCGCCGCAACCCA
*
56104871 GGGAGGCAAGGCTTTGTGAT-TTCGA
65 GGGAGGCAAGGC-TGGTG-TCTTCGA
* * * * * * * * **
56104896 TCTGCTTCGTTGTCAGTACAGGAAGGTAATATCTGCTATTGTCAACCTGTTCCGCTACAACCCAG
1 TCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCCGCAACCCAG
56104961 GGAGGCAAGGCTGGTGTCTTCGA
66 GGAGGCAAGGCTGGTGTCTTCGA
* *
56104984 TCTGCTACGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCTGCCGCAACCCAG
1 TCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCCGCAACCCAG
* *
56105049 GGAGGCAATGCTGGTGTCTTCAA
66 GGAGGCAAGGCTGGTGTCTTCGA
* * * *
56105072 TCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATTTACTATTTTTAACCTGCTCCGCTGTAACCCAG
1 TCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCCGCAACCCAG
*
56105137 GGAGGCAAGGCTAGTGTCTTCGA
66 GGAGGCAAGGCTGGTGTCTTCGA
* *
56105160 TCTTCTTCGCTGTCGGTGTAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCCGCAACCCAG
1 TCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCCGCAACCCAG
56105225 GGAGGCAAGGCTGGTGTCTTCGA
66 GGAGGCAAGGCTGGTGTCTTCGA
* * * *
56105248 TCTGCTTCGCTGTCGGTACAAGAAGGCAATATCTGCTATTTTTAACCTGCTCTGCCGCAACCCAG
1 TCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCCGCAACCCAG
*
56105313 AGAGGCAAGGCTGGTGTCTTCGA
66 GGAGGCAAGGCTGGTGTCTTCGA
* *
56105336 TCTGCTTCGCTGTCGGTGCAGGAAGGCAATATCTGCTATTTTTAACCTGCTCTGCCGCAACCCAG
1 TCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCCGCAACCCAG
*
56105401 AGAGGCAAGGCTGGTGTCTTCGA
66 GGAGGCAAGGCTGGTGTCTTCGA
* * *
56105424 TCTGCTTCGCTGTCGGTGCAAGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCCGCAGCCTAG
1 TCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCCGCAACCCAG
*
56105489 GGAGGCAAGGCTGATGTCTTCGA
66 GGAGGCAAGGCTGGTGTCTTCGA
* * * * **
56105512 TCTGCTTCACTGTCGGTGCAAGAAGGCAAGATCTGCTATTTTTAACCTGCTTCTCTACAACCCAG
1 TCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCCGCAACCCAG
56105577 GGAGGCAAGGCTGGTGTCTTCGA
66 GGAGGCAAGGCTGGTGTCTTCGA
* * * * *
56105600 TCTGCTTCGCTGTCGGTGCAAGAAGGCAAGATCTGCTATTTTTAAACTGCTCCACTGTAACCCAG
1 TCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCCGCAACCCAG
* *
56105665 GGAGGCAAAGC-GAGTGACTTCGA
66 GGAGGCAAGGCTG-GTGTCTTCGA
*
56105688 TCTGCTTCGCTGTCGGTGCAGGAAGGTAAGATCTG
1 TCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTG
56105723 TTATCTTCAC
Statistics
Matches: 748, Mismatches: 75, Indels: 8
0.90 0.09 0.01
Matches are distributed among these distances:
87 2 0.00
88 710 0.95
89 36 0.05
ACGTcount: A:0.21, C:0.25, G:0.27, T:0.27
Consensus pattern (88 bp):
TCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCCGCAACCCAG
GGAGGCAAGGCTGGTGTCTTCGA
Found at i:56105099 original size:44 final size:43
Alignment explanation
Indices: 56104958--56105629 Score: 110
Period size: 44 Copynumber: 15.3 Consensus size: 43
56104948 CGCTACAACC
* * *
56104958 CAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTACGCTGTCGGTG
1 CAGGAAGGCAA-GCTGGTGTCTTCAATCTGCTTCGCTGTCGGTG
* * * * * * ****
56105002 CAGGAAGGCAAGATCTGCTATTTTTAACCTGC-TCTGCCG-CAACC
1 CAGGAAGGCAAG--CTGGTGTCTTCAATCTGCTTC-GCTGTCGGTG
*
56105046 CAGGGAGGCAATGCTGGTGTCTTCAATCTGCTTCGCTGTCGGTG
1 CAGGAAGGCAA-GCTGGTGTCTTCAATCTGCTTCGCTGTCGGTG
* ** * * * * * ****
56105090 CAGGAAGGCAAGATTTACTATTTTTAACCTGCTCCGCTGT-AACC
1 CAGGAAGGCAAG--CTGGTGTCTTCAATCTGCTTCGCTGTCGGTG
* * * *
56105134 CAGGGAGGCAAGGCTAGTGTCTTCGATCTTCTTCGCTGTCGGTG
1 CAGGAAGGCAA-GCTGGTGTCTTCAATCTGCTTCGCTGTCGGTG
* * * * * * * * ****
56105178 TAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCCG-CAACC
1 CAGGAAGGCAAG--CTGGTGTCTTCAATCTGCTTCGCTGTCGGTG
* * *
56105222 CAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTA
1 CAGGAAGGCAA-GCTGGTGTCTTCAATCTGCTTCGCTGTCGGTG
* * * * * * * * ****
56105266 CAAGAAGGCAATATCTGCTATTTTTAACCTGC-TCTGCCG-CAACC
1 CAGGAAGGC-A-AGCTGGTGTCTTCAATCTGCTTC-GCTGTCGGTG
*
56105310 CA-GAGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTG
1 CAGGA-AGGCAA-GCTGGTGTCTTCAATCTGCTTCGCTGTCGGTG
* * * * * * * ****
56105354 CAGGAAGGCAATATCTGCTATTTTTAACCTGC-TCTGCCG-CAACC
1 CAGGAAGGC-A-AGCTGGTGTCTTCAATCTGCTTC-GCTGTCGGTG
*
56105398 CA-GAGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTG
1 CAGGA-AGGCAA-GCTGGTGTCTTCAATCTGCTTCGCTGTCGGTG
* * * * * * * * * *
56105442 CAAGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCCG-CAG-C
1 CAGGAAGGCAAG--CTGGTGTCTTCAATCTGCTTCGCTGTCGGTG
* * * *
56105485 CTAGGGAGGCAAGGCTGATGTCTTCGATCTGCTTCACTGTCGGTG
1 C-AGGAAGGCAA-GCTGGTGTCTTCAATCTGCTTCGCTGTCGGTG
* * * * * * * * ****
56105530 CAAGAAGGCAAGATCTGCTATTTTTAACCTGCTTCTCT-ACAACC
1 CAGGAAGGCAAG--CTGGTGTCTTCAATCTGCTTCGCTGTCGGTG
* *
56105574 CAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTG
1 CAGGAAGGCAA-GCTGGTGTCTTCAATCTGCTTCGCTGTCGGTG
*
56105618 CAAGAAGGCAAG
1 CAGGAAGGCAAG
56105630 ATCTGCTATT
Statistics
Matches: 404, Mismatches: 184, Indels: 81
0.60 0.28 0.12
Matches are distributed among these distances:
42 2 0.00
43 126 0.31
44 150 0.37
45 124 0.31
46 2 0.00
ACGTcount: A:0.20, C:0.25, G:0.28, T:0.27
Consensus pattern (43 bp):
CAGGAAGGCAAGCTGGTGTCTTCAATCTGCTTCGCTGTCGGTG
Found at i:56105564 original size:45 final size:45
Alignment explanation
Indices: 56105425--56105657 Score: 127
Period size: 44 Copynumber: 5.3 Consensus size: 45
56105415 TGTCTTCGAT
*
56105425 CTGCTTCGCTGTCGGTGCAAGAAGGCAAGATCTGCTATTTTTAAC
1 CTGCTTCACTGTCGGTGCAAGAAGGCAAGATCTGCTATTTTTAAC
* ** * * * * * * ** *
56105470 CTGC-TC-C-GCCGCAGCCTAGGGAGGCAAG-GCTGATGTCTTCGAT
1 CTGCTTCACTGTCGGTG-C-AAGAAGGCAAGATCTGCTATTTTTAAC
56105513 CTGCTTCACTGTCGGTGCAAGAAGGCAAGATCTGCTATTTTTAAC
1 CTGCTTCACTGTCGGTGCAAGAAGGCAAGATCTGCTATTTTTAAC
* * **** * * * * * * ** *
56105558 CTGCTTCTCT-ACAACCCAGGGAGGCAAG-GCTGGTGTCTTCGAT
1 CTGCTTCACTGTCGGTGCAAGAAGGCAAGATCTGCTATTTTTAAC
* *
56105601 CTGCTTCGCTGTCGGTGCAAGAAGGCAAGATCTGCTATTTTTAAA
1 CTGCTTCACTGTCGGTGCAAGAAGGCAAGATCTGCTATTTTTAAC
*
56105646 CTGCTCCACTGT
1 CTGCTTCACTGT
56105658 AACCCAGGGA
Statistics
Matches: 124, Mismatches: 56, Indels: 16
0.63 0.29 0.08
Matches are distributed among these distances:
42 4 0.03
43 31 0.25
44 44 0.35
45 41 0.33
46 4 0.03
ACGTcount: A:0.21, C:0.25, G:0.26, T:0.28
Consensus pattern (45 bp):
CTGCTTCACTGTCGGTGCAAGAAGGCAAGATCTGCTATTTTTAAC
Found at i:56106950 original size:6 final size:6
Alignment explanation
Indices: 56106939--56106980 Score: 50
Period size: 6 Copynumber: 6.8 Consensus size: 6
56106929 TCTCACTTTG
*
56106939 CTTTTT CTTTTT CTTTTTT CCTTTT CTTTTTT CTTTTT -TTTT
1 CTTTTT CTTTTT C-TTTTT CTTTTT C-TTTTT CTTTTT CTTTT
56106981 GAAATATTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
5 4 0.12
6 17 0.53
7 11 0.34
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (6 bp):
CTTTTT
Found at i:56106958 original size:13 final size:13
Alignment explanation
Indices: 56106940--56106980 Score: 66
Period size: 13 Copynumber: 3.2 Consensus size: 13
56106930 CTCACTTTGC
56106940 TTTTTCTTTTTCT
1 TTTTTCTTTTTCT
*
56106953 TTTTTCCTTTTCT
1 TTTTTCTTTTTCT
56106966 TTTTTCTTTTT-T
1 TTTTTCTTTTTCT
56106978 TTT
1 TTT
56106981 GAAATATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
12 4 0.15
13 22 0.85
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (13 bp):
TTTTTCTTTTTCT
Found at i:56106962 original size:8 final size:7
Alignment explanation
Indices: 56106940--56106977 Score: 53
Period size: 7 Copynumber: 5.7 Consensus size: 7
56106930 CTCACTTTGC
56106940 TTTTTC-
1 TTTTTCT
56106946 TTTTTCT
1 TTTTTCT
56106953 TTTTTC-
1 TTTTTCT
*
56106959 CTTTTCT
1 TTTTTCT
56106966 TTTTTCT
1 TTTTTCT
56106973 TTTTT
1 TTTTT
56106978 TTTGAAATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
6 11 0.39
7 17 0.61
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (7 bp):
TTTTTCT
Found at i:56112175 original size:27 final size:27
Alignment explanation
Indices: 56112110--56112170 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
56112100 ACATTACTTG
56112110 AAAAA-AAATATA-A-ATATATACATA
1 AAAAATAAATATACATATATATACATA
*
56112134 AAAAATAAATATACATATATATAGATTA
1 AAAAATAAATATACATATATATACA-TA
56112162 AAAAGATAA
1 AAAA-ATAA
56112171 TTACAAATGA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
24 5 0.16
25 7 0.23
26 1 0.03
27 8 0.26
28 6 0.19
29 4 0.13
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.26
Consensus pattern (27 bp):
AAAAATAAATATACATATATATACATA
Found at i:56114322 original size:61 final size:59
Alignment explanation
Indices: 56114205--56114384 Score: 164
Period size: 61 Copynumber: 2.9 Consensus size: 59
56114195 TTGGTCTAGT
* * * *
56114205 AACAAAATTAGCCCTCTAATGTTTACACATTTGATCAATTT-GATCCTAAATATAAAAAATTC
1 AACAAATTTA-CCCTC-AATGTTTACAAATTTG-TCAATTTAG-TTCTAAATCTAAAAAATTC
* * *
56114267 AACAAATTTATCCCTCAATGTTTACAAATTTTGTCATTTTAGTTCTAATTCTAAAAATTTC
1 AACAAATTTA-CCCTCAATGTTTACAAA-TTTGTCAATTTAGTTCTAAATCTAAAAAATTC
* ** * * *
56114328 AAAAAATTTGACCCTCAAAATTTACAAAATTTGTGAATTTAATTCTAACTCTAAAAA
1 AACAAATTT-ACCCTCAATGTTTAC-AAATTTGTCAATTTAGTTCTAAATCTAAAAA
56114385 TTAAACATAT
Statistics
Matches: 99, Mismatches: 15, Indels: 9
0.80 0.12 0.07
Matches are distributed among these distances:
61 76 0.77
62 23 0.23
ACGTcount: A:0.41, C:0.16, G:0.06, T:0.37
Consensus pattern (59 bp):
AACAAATTTACCCTCAATGTTTACAAATTTGTCAATTTAGTTCTAAATCTAAAAAATTC
Found at i:56114385 original size:61 final size:61
Alignment explanation
Indices: 56114233--56114386 Score: 166
Period size: 61 Copynumber: 2.5 Consensus size: 61
56114223 ATGTTTACAC
* * * * * * **
56114233 ATTTGATCAATTTGATCCTAAATATAAAAAATTCAACAAATTTATCCCTCAATGTTTACAAA
1 ATTTG-TCAATTTAATTCTAACTCTAAAAATTTCAAAAAATTTATCCCTCAAAATTTACAAA
* * * *
56114295 TTTTGTCATTTTAGTTCTAATTCTAAAAATTTCAAAAAATTTGA-CCCTCAAAATTTACAAA
1 ATTTGTCAATTTAATTCTAACTCTAAAAATTTCAAAAAATTT-ATCCCTCAAAATTTACAAA
*
56114356 ATTTGTGAATTTAATTCTAACTCTAAAAATT
1 ATTTGTCAATTTAATTCTAACTCTAAAAATT
56114387 AAACATATAA
Statistics
Matches: 75, Mismatches: 16, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
61 70 0.93
62 5 0.07
ACGTcount: A:0.41, C:0.14, G:0.05, T:0.40
Consensus pattern (61 bp):
ATTTGTCAATTTAATTCTAACTCTAAAAATTTCAAAAAATTTATCCCTCAAAATTTACAAA
Found at i:56124620 original size:19 final size:19
Alignment explanation
Indices: 56124598--56124641 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
56124588 GCATACTGAA
56124598 ACATAAAATGCATCCTGGC
1 ACATAAAATGCATCCTGGC
* **
56124617 ACATGAGGTGCATCCTGGC
1 ACATAAAATGCATCCTGGC
*
56124636 GCATAA
1 ACATAA
56124642 GTGCACAAAC
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.32, C:0.25, G:0.23, T:0.20
Consensus pattern (19 bp):
ACATAAAATGCATCCTGGC
Found at i:56132875 original size:21 final size:21
Alignment explanation
Indices: 56132843--56132883 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
56132833 GAACAATTGG
56132843 TGTATAGGCTAAGAA-AGGCCT
1 TGTATAGGCTAA-AACAGGCCT
56132864 TGTAT-GGCCTAAAACAGGCC
1 TGTATAGG-CTAAAACAGGCC
56132884 CCTCGAGCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.32, C:0.20, G:0.27, T:0.22
Consensus pattern (21 bp):
TGTATAGGCTAAAACAGGCCT
Found at i:56141342 original size:40 final size:40
Alignment explanation
Indices: 56141282--56141357 Score: 125
Period size: 40 Copynumber: 1.9 Consensus size: 40
56141272 TCTTCGGGGC
**
56141282 TTTAGCGGCGTTTTTGAAAAAGCGCCGCGAATGCTCTATT
1 TTTAGCGGCGTTTTCCAAAAAGCGCCGCGAATGCTCTATT
*
56141322 TTTAGCGGCGTTTTCCAAAAAGCGCCGCTAATGCTC
1 TTTAGCGGCGTTTTCCAAAAAGCGCCGCGAATGCTC
56141358 CGACTGCAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.22, C:0.24, G:0.24, T:0.30
Consensus pattern (40 bp):
TTTAGCGGCGTTTTCCAAAAAGCGCCGCGAATGCTCTATT
Found at i:56152574 original size:91 final size:89
Alignment explanation
Indices: 56152430--56152672 Score: 287
Period size: 91 Copynumber: 2.7 Consensus size: 89
56152420 CCTCAAATGC
* * * * * * *
56152430 AATTAAACCCTTGCTTTTATTTTGCATTCATTTGGTTACTTAAACTTTT-AAAATGCATCAAAAA
1 AATTAAGCCCCTGATTTTATTTTACACTCAATTGG-TACTTAAA-TTTTCAAAATACATCAAAAA
*
56152494 AGCCCTCAAA-TATTTTCAAAAAAAATT
64 AGCCCTCAAACT-TTTT-AAAAAAAAGT
* *
56152521 AATTAAGCCCCTGATTTTATTTTTCACTCAATTGAGTACTTAAATTTTCAAAATACATCAAAAAG
1 AATTAAGCCCCTGATTTTATTTTACACTCAATTG-GTACTTAAATTTTCAAAATACATCAAAAAA
56152586 GCCCTCAAACTTTTTAAAAAAAAGT
65 GCCCTCAAACTTTTTAAAAAAAAGT
* * *
56152611 AATTAAGCCCCTGATTTT-TTTTACACTCAATTGGGTACTTGAACTGTC-AAATACATCAAAAA
1 AATTAAGCCCCTGATTTTATTTTACACTCAATT-GGTACTTAAATTTTCAAAATACATCAAAAA
56152673 GACCCTTTGA
Statistics
Matches: 135, Mismatches: 13, Indels: 11
0.85 0.08 0.07
Matches are distributed among these distances:
88 14 0.10
89 24 0.18
90 32 0.24
91 63 0.47
92 2 0.01
ACGTcount: A:0.38, C:0.18, G:0.08, T:0.36
Consensus pattern (89 bp):
AATTAAGCCCCTGATTTTATTTTACACTCAATTGGTACTTAAATTTTCAAAATACATCAAAAAAG
CCCTCAAACTTTTTAAAAAAAAGT
Found at i:56152937 original size:89 final size:91
Alignment explanation
Indices: 56152727--56152949 Score: 299
Period size: 89 Copynumber: 2.5 Consensus size: 91
56152717 TAGTTGACCA
* * *
56152727 TTCAAGTACCCAATTGAGTGCAAAA-AAAATCGAGGGCTTAATTGCTTTTTTTGAAAAAGTTTGA
1 TTCAAGTACCCAATTGAGTGCAAAATAAAAGCAAGGGCTTAATTGCTATTTTTGAAAAAGTTTGA
* * *
56152791 GGGCCTTTTTTTATACAATTTGAAAG
66 GGACCTCTTTTGATACAATTTGAAAG
* * * *
56152817 TTCAAGTACCCAATTGAGTGCAAAGTGAAAGCTAGGGCTTAATTG-TATTTTTGAAAAATTTTGA
1 TTCAAGTACCCAATTGAGTGCAAAATAAAAGCAAGGGCTTAATTGCTATTTTTGAAAAAGTTTGA
* *
56152881 GGACC-CTTTTGATGCATTTTGAAAG
66 GGACCTCTTTTGATACAATTTGAAAG
* *
56152906 TTCAAGTACCAAAGTGAGTGCAAAATAAAAGCAAGGGCTTAATT
1 TTCAAGTACCCAATTGAGTGCAAAATAAAAGCAAGGGCTTAATT
56152950 ATTTTTTTTT
Statistics
Matches: 116, Mismatches: 16, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
89 55 0.47
90 45 0.39
91 16 0.14
ACGTcount: A:0.35, C:0.13, G:0.20, T:0.33
Consensus pattern (91 bp):
TTCAAGTACCCAATTGAGTGCAAAATAAAAGCAAGGGCTTAATTGCTATTTTTGAAAAAGTTTGA
GGACCTCTTTTGATACAATTTGAAAG
Found at i:56162212 original size:17 final size:17
Alignment explanation
Indices: 56162190--56162223 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
56162180 AAAATTTAAG
56162190 GGAAAAGATTTGAACAC
1 GGAAAAGATTTGAACAC
56162207 GGAAAAGATTTGAACAC
1 GGAAAAGATTTGAACAC
56162224 AAGACCTTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.12, G:0.24, T:0.18
Consensus pattern (17 bp):
GGAAAAGATTTGAACAC
Found at i:56167201 original size:8 final size:8
Alignment explanation
Indices: 56167185--56167214 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
56167175 AACAAAAATA
56167185 ACAATTTT
1 ACAATTTT
*
56167193 ACCATTTT
1 ACAATTTT
56167201 ACAATTTT
1 ACAATTTT
56167209 ACAATT
1 ACAATT
56167215 ATCTTTGGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.37, C:0.17, G:0.00, T:0.47
Consensus pattern (8 bp):
ACAATTTT
Found at i:56172428 original size:61 final size:61
Alignment explanation
Indices: 56172333--56172457 Score: 250
Period size: 61 Copynumber: 2.0 Consensus size: 61
56172323 AATAATTTTT
56172333 AAAGCCATATTTGTTAATTTTACCAAAATGTATTTAATTTACTTACTTTGTTTGTGAGATA
1 AAAGCCATATTTGTTAATTTTACCAAAATGTATTTAATTTACTTACTTTGTTTGTGAGATA
56172394 AAAGCCATATTTGTTAATTTTACCAAAATGTATTTAATTTACTTACTTTGTTTGTGAGATA
1 AAAGCCATATTTGTTAATTTTACCAAAATGTATTTAATTTACTTACTTTGTTTGTGAGATA
56172455 AAA
1 AAA
56172458 CATCTTAGCA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 64 1.00
ACGTcount: A:0.34, C:0.10, G:0.11, T:0.45
Consensus pattern (61 bp):
AAAGCCATATTTGTTAATTTTACCAAAATGTATTTAATTTACTTACTTTGTTTGTGAGATA
Found at i:56172497 original size:37 final size:36
Alignment explanation
Indices: 56172455--56172547 Score: 107
Period size: 38 Copynumber: 2.5 Consensus size: 36
56172445 TTGTGAGATA
*
56172455 AAACATCT-TAGCAAATTTCAATAAAACTTGCAGCGG
1 AAACAT-TATAGCAAATTTCAATAAAACTTGCAGCAG
* **
56172491 ACAACATTATAGCAAATTGACCTTAAAACTTGCAGCAG
1 A-AACATTATAGCAAATT-TCAATAAAACTTGCAGCAG
56172529 AAAGCATTATAGCAAATTT
1 AAA-CATTATAGCAAATTT
56172548 ACCTTATCTT
Statistics
Matches: 48, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
36 2 0.04
37 16 0.33
38 30 0.62
ACGTcount: A:0.43, C:0.18, G:0.13, T:0.26
Consensus pattern (36 bp):
AAACATTATAGCAAATTTCAATAAAACTTGCAGCAG
Found at i:56172537 original size:38 final size:38
Alignment explanation
Indices: 56172476--56172553 Score: 122
Period size: 38 Copynumber: 2.1 Consensus size: 38
56172466 CAAATTTCAA
*
56172476 TAAAACTTGCAGCGGACAACATTATAGCAAATTGACCT
1 TAAAACTTGCAGCAGACAACATTATAGCAAATTGACCT
*
56172514 TAAAACTTGCAGCAGA-AAGCATTATAGCAAATTTACCT
1 TAAAACTTGCAGCAGACAA-CATTATAGCAAATTGACCT
56172552 TA
1 TA
56172554 TCTTGATTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
37 2 0.05
38 35 0.95
ACGTcount: A:0.41, C:0.19, G:0.14, T:0.26
Consensus pattern (38 bp):
TAAAACTTGCAGCAGACAACATTATAGCAAATTGACCT
Found at i:56174103 original size:2 final size:2
Alignment explanation
Indices: 56174096--56174123 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
56174086 TGGGAAGTAA
56174096 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
56174124 TAGAGAAGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:56176461 original size:12 final size:12
Alignment explanation
Indices: 56176440--56176470 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
56176430 GTCTGTAATA
*
56176440 ATTCACTAACCT
1 ATTCATTAACCT
56176452 ATTCATTAACCT
1 ATTCATTAACCT
56176464 ATTCATT
1 ATTCATT
56176471 CTGGACATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.32, C:0.26, G:0.00, T:0.42
Consensus pattern (12 bp):
ATTCATTAACCT
Found at i:56186303 original size:125 final size:124
Alignment explanation
Indices: 56186081--56186335 Score: 447
Period size: 125 Copynumber: 2.0 Consensus size: 124
56186071 TGCTTCTGGG
*
56186081 TAGCTCTTTTCGTATTAATTTGTATCTATAGTAGACTATGTCTGCTGATCATCCTGTCTTAAAAT
1 TAGCTGTTTTCGTATTAATTTGTATCTATAGTAGACTATGTCTGCTGATCATCCTGTCTTAAAAT
* *
56186146 CTATAACTGTAGAGGAAATCATTGCTTCAGATCTTATTACCTTGACTATCATACAAAGC
66 CTAAAACTGTAGAGGAAACCATTGCTTCAGATCTTATTACCTTGACTATCATACAAAGC
*
56186205 ATAGCTGTTTTCGTATTAATTTGTATCTATAGTAGATTATGTCTGCTGATCATCCTGTCTTAAAA
1 -TAGCTGTTTTCGTATTAATTTGTATCTATAGTAGACTATGTCTGCTGATCATCCTGTCTTAAAA
* *
56186270 TCTAAAACTGTTGAGGAAACCATTGCTTCAGATCTTATTACCTTGACTATCTTACAAAGC
65 TCTAAAACTGTAGAGGAAACCATTGCTTCAGATCTTATTACCTTGACTATCATACAAAGC
56186330 TAGCTG
1 TAGCTG
56186336 CTATAACAGT
Statistics
Matches: 124, Mismatches: 6, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
124 6 0.05
125 118 0.95
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.39
Consensus pattern (124 bp):
TAGCTGTTTTCGTATTAATTTGTATCTATAGTAGACTATGTCTGCTGATCATCCTGTCTTAAAAT
CTAAAACTGTAGAGGAAACCATTGCTTCAGATCTTATTACCTTGACTATCATACAAAGC
Found at i:56189827 original size:14 final size:14
Alignment explanation
Indices: 56189808--56189839 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
56189798 TATAAAAAAC
*
56189808 TATAAAATTCTGAA
1 TATAAAATTCCGAA
56189822 TATAAAATTCCGAA
1 TATAAAATTCCGAA
56189836 TATA
1 TATA
56189840 GTTTACGTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.50, C:0.09, G:0.06, T:0.34
Consensus pattern (14 bp):
TATAAAATTCCGAA
Found at i:56191703 original size:58 final size:58
Alignment explanation
Indices: 56191583--56191712 Score: 149
Period size: 58 Copynumber: 2.2 Consensus size: 58
56191573 TCATTATAGG
* * * * *
56191583 GTTCATGGAAGGGGCCG-AATGTAGAAGATATGCCTCACCTCCGTCGAGAGCCCAAGGA
1 GTTCATAGAA-GGGCTGAAATGTAGAAGATATACCTCACCTCCATCGAGAGCCCAAAGA
* *
56191641 GTTCACTA-AAGGGCTGAAATGTAGAAGATATATCTTACCTCCATCGAGAGCCCAAA-A
1 GTTCA-TAGAAGGGCTGAAATGTAGAAGATATACCTCACCTCCATCGAGAGCCCAAAGA
56191698 GGTTCATAGAAGGGC
1 -GTTCATAGAAGGGC
56191713 CCTAATGTCC
Statistics
Matches: 61, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
57 8 0.13
58 52 0.85
59 1 0.02
ACGTcount: A:0.32, C:0.22, G:0.27, T:0.20
Consensus pattern (58 bp):
GTTCATAGAAGGGCTGAAATGTAGAAGATATACCTCACCTCCATCGAGAGCCCAAAGA
Found at i:56194842 original size:61 final size:60
Alignment explanation
Indices: 56194725--56194904 Score: 166
Period size: 61 Copynumber: 2.9 Consensus size: 60
56194715 TTGGTCTAGT
* * * *
56194725 AACAAAATTAGCCCTCTAATGTTTAC-ACATTTGATCAATTT-GATCCTAAATATAAAAAAATC
1 AACAAATTTA-CCCTC-AATGTTTACAAAATTTG-TCAATTTAG-TTCTAAATCTAAAAAAATC
* * **
56194787 AACAAATTTATCCCTCAATGTTTACAAAATTTGTCATTTTAGTTCTAATTCTAAAAATTTC
1 AACAAATTTA-CCCTCAATGTTTACAAAATTTGTCAATTTAGTTCTAAATCTAAAAAAATC
* ** * * *
56194848 AAAAAATTTGACCCTCAAAATTTACAAAATTTGTGAATTTAATTCTAACTCTAAAAA
1 AACAAATTT-ACCCTCAATGTTTACAAAATTTGTCAATTTAGTTCTAAATCTAAAAA
56194905 TTAAACATAT
Statistics
Matches: 99, Mismatches: 16, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
61 77 0.78
62 22 0.22
ACGTcount: A:0.42, C:0.16, G:0.06, T:0.36
Consensus pattern (60 bp):
AACAAATTTACCCTCAATGTTTACAAAATTTGTCAATTTAGTTCTAAATCTAAAAAAATC
Found at i:56206345 original size:6 final size:6
Alignment explanation
Indices: 56206334--56206361 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
56206324 AAACTAAGTT
56206334 TTTTTA TTTTTA TTTTTA TTTTTA TTTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTT
56206362 AAAAGGGATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTTA
Found at i:56213024 original size:13 final size:13
Alignment explanation
Indices: 56213008--56213032 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
56212998 AAACAAACAT
56213008 AGAAAAAATATTA
1 AGAAAAAATATTA
56213021 AGAAAAAATATT
1 AGAAAAAATATT
56213033 TGTTTTTTAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (13 bp):
AGAAAAAATATTA
Found at i:56220448 original size:44 final size:43
Alignment explanation
Indices: 56220345--56220718 Score: 226
Period size: 44 Copynumber: 8.6 Consensus size: 43
56220335 TTTTAATCCA
* * ** *
56220345 CTCCACTGTAACTTCAGGGAGATAGGAT-AGTGTCTTCGATCTA
1 CTCCACTGTAACCTCAGGGAGATAAGATCTCTG-CTTCGATCTG
* * *
56220388 CTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTG
1 CTCCACTGTAACCTCAGGGAGATAAGATCTCT-GCTTCGATCTG
* * * * *
56220432 CTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCTCCGGTCTA
1 CTCCACTGTAACCTCAGGGAGATAAGATCT---CTGCTTCGATCTG
* * * *
56220478 CTCCACTGTAACCTCAAGGAAATAAGA-C-CTGATGT-GATCTT
1 CTCCACTGTAACCTCAGGGAGATAAGATCTCTGCT-TCGATCTG
* * * * *
56220519 CTCTACTGTAACTTCAGAGAGATAAGATC-CT--TT-AATCCG
1 CTCCACTGTAACCTCAGGGAGATAAGATCTCTGCTTCGATCTG
* ** * * * *
56220558 CTCCATTGTAATTTCAAGGAGATAGGAT-TACTATCTTTGATCTG
1 CTCCACTGTAACCTCAGGGAGATAAGATCT-CT-GCTTCGATCTG
* * *
56220602 CTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTG
1 CTCCACTGTAACCTCAGGGAGATAAGATCTCT-GCTTCGATCTG
* * * * *
56220646 CTCCGCTGTAACCTCAGGGAGATAAGATCTGAAATTCTTTGGTCTG
1 CTCCACTGTAACCTCAGGGAGATAAGATCT---CTGCTTCGATCTG
* *
56220692 TTCCACTGTAATCTCAGGGAGATAAGA
1 CTCCACTGTAACCTCAGGGAGATAAGA
56220719 CCTGTATAAT
Statistics
Matches: 256, Mismatches: 58, Indels: 31
0.74 0.17 0.09
Matches are distributed among these distances:
39 26 0.10
40 3 0.01
41 28 0.11
42 3 0.01
43 26 0.10
44 103 0.40
45 3 0.01
46 62 0.24
47 2 0.01
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.30
Consensus pattern (43 bp):
CTCCACTGTAACCTCAGGGAGATAAGATCTCTGCTTCGATCTG
Found at i:56220647 original size:214 final size:214
Alignment explanation
Indices: 56220277--56220722 Score: 642
Period size: 214 Copynumber: 2.1 Consensus size: 214
56220267 GCATCTTCAG
* *
56220277 GGAAATAAGACTTGATGCGACCTACTCTGCTGTAACCTCAGAGAGATAAGATCCTTTATTTTAAT
1 GGAAATAAGACCTGATGCGACCTACTCTACTGTAACCTCAGAGAGATAAGATCC----TTTTAAT
* * *
56220342 CCACTCCACTGTAACTTCAGGGAGATAGGATAGTGTCTTCGATCTACTCCGCTGTAATCTCAGGG
62 CCACTCCACTGTAACTTCAAGGAGATAGGATACTATCTTCGATCTACTCCGCTGTAATCTCAGGG
56220407 AGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCTCC
127 AGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCTCC
56220472 GGTCTACTCCACTGTAACCTCAA
192 GGTCTACTCCACTGTAACCTCAA
* * * * *
56220495 GGAAATAAGACCTGATGTGATCTTCTCTACTGTAACTTCAGAGAGATAAGATCC-TTTAATCCGC
1 GGAAATAAGACCTGATGCGACCTACTCTACTGTAACCTCAGAGAGATAAGATCCTTTTAATCCAC
* * * *
56220559 TCCATTGTAATTTCAAGGAGATAGGATTACTATCTTTGATCTGCTCCGCTGTAATCTCAGGGAGA
66 TCCACTGTAACTTCAAGGAGATAGGA-TACTATCTTCGATCTACTCCGCTGTAATCTCAGGGAGA
* **
56220624 TAAGATCTCTGGCTTCAATCTGCTCCGCTGTAACCTCAGGGAGATAAGATCTGAAATTCTTTGGT
130 TAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCTCCGGT
** * *
56220689 CTGTTCCACTGTAATCTCAG
195 CTACTCCACTGTAACCTCAA
*
56220709 GGAGATAAGACCTG
1 GGAAATAAGACCTG
56220723 TATAATAAAC
Statistics
Matches: 205, Mismatches: 22, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
213 32 0.16
214 125 0.61
218 48 0.23
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (214 bp):
GGAAATAAGACCTGATGCGACCTACTCTACTGTAACCTCAGAGAGATAAGATCCTTTTAATCCAC
TCCACTGTAACTTCAAGGAGATAGGATACTATCTTCGATCTACTCCGCTGTAATCTCAGGGAGAT
AAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCTCCGGTC
TACTCCACTGTAACCTCAA
Found at i:56224502 original size:43 final size:43
Alignment explanation
Indices: 56224388--56224716 Score: 201
Period size: 43 Copynumber: 7.7 Consensus size: 43
56224378 ATTTTATCCA
* * ** * *
56224388 CTCCACTGTAACTTCAGGGAGATAGGATAGTGTCTTCGATCTA
1 CTCCACTGTAACCTCAGGGAGATAAGATCTTGGCTTCGATCTG
* * *
56224431 CTCCGCTGTAATCTCAGGGAGATAAGATCTTGGCTTCAATCTG
1 CTCCACTGTAACCTCAGGGAGATAAGATCTTGGCTTCGATCTG
* * * *
56224474 CTCCACTGTAACCTCAGGGAGATAAGATC-TGAAATCTCCGGTCTA
1 CTCCACTGTAACCTCAGGGAGATAAGATCTTG---GCTTCGATCTG
* * * * *
56224519 CTCCACTGTAACCTCAAGGAAATAAGA-CCT-GATGT-GATCTT
1 CTCCACTGTAACCTCAGGGAGATAAGATCTTGGCT-TCGATCTG
* * * ** *
56224560 CTCTACTGTAACTTCAGAGAGATAAGATC----CTTTAATCCG
1 CTCCACTGTAACCTCAGGGAGATAAGATCTTGGCTTCGATCTG
* ** * * * *
56224599 CTTCCATTGTAATTTCAAGGAGATAGGAT-TACT-ACTTTGATCTG
1 C-TCCACTGTAACCTCAGGGAGATAAGATCT--TGGCTTCGATCTG
* * *
56224643 CTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTG
1 CTCCACTGTAACCTCAGGGAGATAAGATCT-TGGCTTCGATCTG
*
56224687 CTCCGCTGTAACCTCAGGGAGATAAGATCT
1 CTCCACTGTAACCTCAGGGAGATAAGATCT
56224717 GAATTCTCTT
Statistics
Matches: 222, Mismatches: 49, Indels: 29
0.74 0.16 0.10
Matches are distributed among these distances:
38 1 0.00
39 5 0.02
40 21 0.09
41 27 0.12
42 3 0.01
43 85 0.38
44 48 0.22
45 32 0.14
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.29
Consensus pattern (43 bp):
CTCCACTGTAACCTCAGGGAGATAAGATCTTGGCTTCGATCTG
Found at i:56224582 original size:215 final size:214
Alignment explanation
Indices: 56224321--56224764 Score: 601
Period size: 215 Copynumber: 2.1 Consensus size: 214
56224311 GCATCTTCAG
* *
56224321 GGAAATAAGACTTGATGCGACCCTACTCTGCTGTAACTCAGAGAGATAAGATCCTTTATTTTATC
1 GGAAATAAGACCTGATGCGACCCTACTCTACTGTAACTCAGAGAGATAAGATCCTTTA----ATC
* * *
56224386 CAC-TCCACTGTAACTTCAGGGAGATAGGA-TAGTGTCTTCGATCTACTCCGCTGTAATCTCAGG
62 CACTTCCACTGTAACTTCAAGGAGATAGGATTACT-ACTTCGATCTACTCCGCTGTAATCTCAGG
56224449 GAGATAAGATCT-TGGCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAATCTC-
126 GAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAATCTCT
56224512 CGGTCTACTCCACTGTAACCTCAA
191 CGGTCTACTCCACTGTAACCTCAA
* * * *
56224536 GGAAATAAGACCTGATGTGA-TCTTCTCTACTGTAACTTCAGAGAGATAAGATCCTTTAATCCGC
1 GGAAATAAGACCTGATGCGACCCTACTCTACTGTAAC-TCAGAGAGATAAGATCCTTTAATCCAC
* * * *
56224600 TTCCATTGTAATTTCAAGGAGATAGGATTACTACTTTGATCTGCTCCGCTGTAATCTCAGGGAGA
65 TTCCACTGTAACTTCAAGGAGATAGGATTACTACTTCGATCTACTCCGCTGTAATCTCAGGGAGA
* * *
56224665 TAAGATCTCTGGCTTCAATCTGCTCCGCTGTAACCTCAGGGAGATAAGATCTGAATTCTCTTTGG
130 TAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAATCTC-TCGG
** * *
56224730 TCTGTTCCACTGTAATCTCAG
194 TCTACTCCACTGTAACCTCAA
*
56224751 GGAGATAAGACCTG
1 GGAAATAAGACCTG
56224765 TATAATAAAC
Statistics
Matches: 202, Mismatches: 21, Indels: 12
0.86 0.09 0.05
Matches are distributed among these distances:
211 5 0.02
212 61 0.30
213 52 0.26
214 13 0.06
215 71 0.35
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (214 bp):
GGAAATAAGACCTGATGCGACCCTACTCTACTGTAACTCAGAGAGATAAGATCCTTTAATCCACT
TCCACTGTAACTTCAAGGAGATAGGATTACTACTTCGATCTACTCCGCTGTAATCTCAGGGAGAT
AAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAATCTCTCGGTC
TACTCCACTGTAACCTCAA
Found at i:56233829 original size:12 final size:12
Alignment explanation
Indices: 56233812--56233836 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
56233802 AGACTAAAAC
56233812 TATTACTGTAAG
1 TATTACTGTAAG
56233824 TATTACTGTAAG
1 TATTACTGTAAG
56233836 T
1 T
56233837 GTTCTAAAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.08, G:0.16, T:0.44
Consensus pattern (12 bp):
TATTACTGTAAG
Found at i:56239368 original size:26 final size:28
Alignment explanation
Indices: 56239334--56239386 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 28
56239324 AACAATCATT
56239334 GCATAGTCATGAACTAAGC-AATGAAAA
1 GCATAGTCATGAACTAAGCAAATGAAAA
* *
56239361 GCAT-GTCATGGATTAAGCAAATGAAA
1 GCATAGTCATGAACTAAGCAAATGAAA
56239387 GAAAATTACC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 12 0.52
27 11 0.48
ACGTcount: A:0.45, C:0.13, G:0.21, T:0.21
Consensus pattern (28 bp):
GCATAGTCATGAACTAAGCAAATGAAAA
Found at i:56241565 original size:40 final size:40
Alignment explanation
Indices: 56241506--56241581 Score: 107
Period size: 40 Copynumber: 1.9 Consensus size: 40
56241496 TCTTCGGGGC
* * *
56241506 TTTAGCGGCGTTTTTCAAAAACCTCCGCGAATGCTCTATT
1 TTTAGCGACGTTTTCCAAAAACCGCCGCGAATGCTCTATT
* *
56241546 TTTAGCGACGTTTTCCAAAAAGCGCCGCTAATGCTC
1 TTTAGCGACGTTTTCCAAAAACCGCCGCGAATGCTC
56241582 CGACTGCAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 31 1.00
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.32
Consensus pattern (40 bp):
TTTAGCGACGTTTTCCAAAAACCGCCGCGAATGCTCTATT
Found at i:56250000 original size:23 final size:22
Alignment explanation
Indices: 56249948--56250000 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
56249938 TCCACGTCTT
*
56249948 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
56249970 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
56249993 TTTCTTTT
1 TTTCTTTT
56250001 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:56255028 original size:27 final size:27
Alignment explanation
Indices: 56254998--56255050 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
56254988 AACAATCATT
56254998 GCATAATCATGAATTAAGC-AATGAAAA
1 GCAT-ATCATGAATTAAGCAAATGAAAA
* *
56255025 GCATGTCATGGATTAAGCAAATGAAA
1 GCATATCATGAATTAAGCAAATGAAA
56255051 GAAAATTAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 12 0.52
27 11 0.48
ACGTcount: A:0.47, C:0.11, G:0.19, T:0.23
Consensus pattern (27 bp):
GCATATCATGAATTAAGCAAATGAAAA
Found at i:56257328 original size:11 final size:11
Alignment explanation
Indices: 56257312--56257359 Score: 51
Period size: 11 Copynumber: 4.1 Consensus size: 11
56257302 TTTACTGTGC
56257312 AAAAATATTTT
1 AAAAATATTTT
56257323 AAAAATACTTATT
1 AAAAATA-TT-TT
**
56257336 AAATTTAATTTT
1 AAAAAT-ATTTT
56257348 AAAAATATTTT
1 AAAAATATTTT
56257359 A
1 A
56257360 TATTATTTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
11 13 0.43
12 8 0.27
13 8 0.27
14 1 0.03
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:56262826 original size:22 final size:21
Alignment explanation
Indices: 56262796--56262840 Score: 72
Period size: 22 Copynumber: 2.1 Consensus size: 21
56262786 ACACCAAAAC
*
56262796 AGGCTTTTAGCGGCGCTTTTTT
1 AGGCCTTTAGCGGCG-TTTTTT
56262818 AGGCCTTTAGCGGCGTTTTTT
1 AGGCCTTTAGCGGCGTTTTTT
56262839 AG
1 AG
56262841 CGCCGCAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.11, C:0.18, G:0.29, T:0.42
Consensus pattern (21 bp):
AGGCCTTTAGCGGCGTTTTTT
Found at i:56263064 original size:43 final size:43
Alignment explanation
Indices: 56262996--56263311 Score: 363
Period size: 43 Copynumber: 7.4 Consensus size: 43
56262986 AGAGTAAGAG
* * * ****
56262996 CTTTAGTGGCG-CTTTAGTAGAAGCGCCGCTAAAGACTAATAC
1 CTTTAGTGGCGTTTTTAGTAAAAGCGCCGCTATAGACTAGGGT
*
56263038 CTTTAGCGGCGTTTTTAGTAAAAGCGCCGCTATAGA-TCAGGGT
1 CTTTAGTGGCGTTTTTAGTAAAAGCGCCGCTATAGACT-AGGGT
** *
56263081 CTTTAGTGGCGTTTTTAGTATTAGCGCCGCTATAGACTGGGGT
1 CTTTAGTGGCGTTTTTAGTAAAAGCGCCGCTATAGACTAGGGT
* * *
56263124 CTTTAGCGTCGTTTTTAGTTAAAGCGCCGCTATAGA-TCAGGGT
1 CTTTAGTGGCGTTTTTAGTAAAAGCGCCGCTATAGACT-AGGGT
** *
56263167 CTTTAGTGGCGTTTTTAGTATTAGCGCCGCTATAGACTGGGGT
1 CTTTAGTGGCGTTTTTAGTAAAAGCGCCGCTATAGACTAGGGT
* *
56263210 CTTTAGCGGCGTTTTTAGTTAAAGCGCCGCTATAGACTAGGGT
1 CTTTAGTGGCGTTTTTAGTAAAAGCGCCGCTATAGACTAGGGT
*
56263253 CTTTAGTGGCGTTTTT-GCTCAAAGCGCCGCTATAGA-TCAGGGT
1 CTTTAGTGGCGTTTTTAG-TAAAAGCGCCGCTATAGACT-AGGGT
* *
56263296 CTTTAGCGGCGCTTTT
1 CTTTAGTGGCGTTTTT
56263312 CCCAAAAACG
Statistics
Matches: 234, Mismatches: 33, Indels: 13
0.84 0.12 0.05
Matches are distributed among these distances:
42 14 0.06
43 218 0.93
44 2 0.01
ACGTcount: A:0.20, C:0.19, G:0.28, T:0.34
Consensus pattern (43 bp):
CTTTAGTGGCGTTTTTAGTAAAAGCGCCGCTATAGACTAGGGT
Found at i:56263128 original size:86 final size:86
Alignment explanation
Indices: 56263038--56263311 Score: 439
Period size: 86 Copynumber: 3.2 Consensus size: 86
56263028 AGACTAATAC
*
56263038 CTTTAGCGGCGTTTTTAGTAAAAGCGCCGCTATAGATCAGGGTCTTTAGTGGCGTTTTTAGTATT
1 CTTTAGCGGCGTTTTTAGTTAAAGCGCCGCTATAGATCAGGGTCTTTAGTGGCGTTTTTAGTATT
56263103 AGCGCCGCTATAGACTGGGGT
66 AGCGCCGCTATAGACTGGGGT
*
56263124 CTTTAGCGTCGTTTTTAGTTAAAGCGCCGCTATAGATCAGGGTCTTTAGTGGCGTTTTTAGTATT
1 CTTTAGCGGCGTTTTTAGTTAAAGCGCCGCTATAGATCAGGGTCTTTAGTGGCGTTTTTAGTATT
56263189 AGCGCCGCTATAGACTGGGGT
66 AGCGCCGCTATAGACTGGGGT
56263210 CTTTAGCGGCGTTTTTAGTTAAAGCGCCGCTATAGA-CTAGGGTCTTTAGTGGCGTTTTT-GCTC
1 CTTTAGCGGCGTTTTTAGTTAAAGCGCCGCTATAGATC-AGGGTCTTTAGTGGCGTTTTTAG-T-
* *
56263273 A-AAGCGCCGCTATAGA-TCAGGGT
63 ATTAGCGCCGCTATAGACT-GGGGT
*
56263296 CTTTAGCGGCGCTTTT
1 CTTTAGCGGCGTTTTT
56263312 CCCAAAAACG
Statistics
Matches: 178, Mismatches: 6, Indels: 8
0.93 0.03 0.04
Matches are distributed among these distances:
85 3 0.02
86 174 0.98
87 1 0.01
ACGTcount: A:0.19, C:0.19, G:0.28, T:0.35
Consensus pattern (86 bp):
CTTTAGCGGCGTTTTTAGTTAAAGCGCCGCTATAGATCAGGGTCTTTAGTGGCGTTTTTAGTATT
AGCGCCGCTATAGACTGGGGT
Found at i:56263180 original size:129 final size:129
Alignment explanation
Indices: 56263038--56263311 Score: 401
Period size: 129 Copynumber: 2.1 Consensus size: 129
56263028 AGACTAATAC
*
56263038 CTTTAGCGGCGTTTTTAGTAAAAGCGCCGCTATAGA-TCAGGGTCTTTAGTGGCGTTTTTAG-TA
1 CTTTAGCGGCGTTTTTAGTAAAAGCGCCGCTATAGACT-AGGGTCTTTAGCGGCGTTTTTAGTTA
* * * *
56263101 TTAGCGCCGCTATAGACTGGGGTCTTTAGCGTCGTTTTTAG-TTAAAGCGCCGCTATAGATCAGG
65 -AAGCGCCGCTATAGACTAGGGTCTTTAGCGGCGTTTTT-GCTCAAAGCGCCGCTATAGATCAGG
56263165 GT
128 GT
* ** *
56263167 CTTTAGTGGCGTTTTTAGTATTAGCGCCGCTATAGACTGGGGTCTTTAGCGGCGTTTTTAGTTAA
1 CTTTAGCGGCGTTTTTAGTAAAAGCGCCGCTATAGACTAGGGTCTTTAGCGGCGTTTTTAGTTAA
*
56263232 AGCGCCGCTATAGACTAGGGTCTTTAGTGGCGTTTTTGCTCAAAGCGCCGCTATAGATCAGGGT
66 AGCGCCGCTATAGACTAGGGTCTTTAGCGGCGTTTTTGCTCAAAGCGCCGCTATAGATCAGGGT
*
56263296 CTTTAGCGGCGCTTTT
1 CTTTAGCGGCGTTTTT
56263312 CCCAAAAACG
Statistics
Matches: 130, Mismatches: 12, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
128 1 0.01
129 126 0.97
130 3 0.02
ACGTcount: A:0.19, C:0.19, G:0.28, T:0.35
Consensus pattern (129 bp):
CTTTAGCGGCGTTTTTAGTAAAAGCGCCGCTATAGACTAGGGTCTTTAGCGGCGTTTTTAGTTAA
AGCGCCGCTATAGACTAGGGTCTTTAGCGGCGTTTTTGCTCAAAGCGCCGCTATAGATCAGGGT
Found at i:56263331 original size:43 final size:43
Alignment explanation
Indices: 56263241--56263366 Score: 119
Period size: 43 Copynumber: 2.9 Consensus size: 43
56263231 AAGCGCCGCT
* * * * * * *
56263241 ATAGACTAGGGTCTTTAGTGGCGTTTTTGCTC-AAAGCGCCGCT
1 ATAGACCAGGGTCTTTAGCGGCGCTTTT-CCCAAAAACGCCACA
*
56263284 ATAGATCAGGGTCTTTAGCGGCGCTTTTCCCAAAAACGCCACA
1 ATAGACCAGGGTCTTTAGCGGCGCTTTTCCCAAAAACGCCACA
** * * *
56263327 ATAGACCCTGATCTATAGCGGCGCTTTTACCAAAAACGCC
1 ATAGACCAGGGTCTTTAGCGGCGCTTTTCCCAAAAACGCC
56263367 GCTAAAGACC
Statistics
Matches: 68, Mismatches: 14, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
42 2 0.03
43 66 0.97
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.26
Consensus pattern (43 bp):
ATAGACCAGGGTCTTTAGCGGCGCTTTTCCCAAAAACGCCACA
Found at i:56263346 original size:129 final size:129
Alignment explanation
Indices: 56263038--56263355 Score: 316
Period size: 129 Copynumber: 2.5 Consensus size: 129
56263028 AGACTAATAC
* ** * * * * * * * * *
56263038 CTTTAGCGGCGTTTTTAGTAAAAGCGCCGCTATAGATCAGGGTCTTTAGTGGCGTTTTTAGTATT
1 CTTTAGCGGCGCTTTTACCAAAAACGCCACAATAGACCCGGATCTATAGCGGCGTTTTTAGTATA
* * *
56263103 AGCGCCGCTATAGACTGGGGTCTTTAGCGTCGTTTTTAGTTAAAGCGCCGCTATAGATCAGGGT
66 AGCGCCGCTATAGACTAGGGTCTTTAGCGGCGTTTTTAGTCAAAGCGCCGCTATAGATCAGGGT
* * ** ** * * * ** * *
56263167 CTTTAGTGGCGTTTTTAGTATTAGCGCCGCTATAGACTGGGGTCTTTAGCGGCGTTTTTAGT-TA
1 CTTTAGCGGCGCTTTTACCAAAAACGCCACAATAGACCCGGATCTATAGCGGCGTTTTTAGTAT-
*
56263231 AAGCGCCGCTATAGACTAGGGTCTTTAGTGGCGTTTTT-GCTCAAAGCGCCGCTATAGATCAGGG
65 AAGCGCCGCTATAGACTAGGGTCTTTAGCGGCGTTTTTAG-TCAAAGCGCCGCTATAGATCAGGG
56263295 T
129 T
* * *
56263296 CTTTAGCGGCGCTTTTCCCAAAAACGCCACAATAGACCCTGATCTATAGCGGCGCTTTTA
1 CTTTAGCGGCGCTTTTACCAAAAACGCCACAATAGACCCGGATCTATAGCGGCGTTTTTA
56263356 CCAAAAACGC
Statistics
Matches: 159, Mismatches: 28, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
128 2 0.01
129 157 0.99
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.33
Consensus pattern (129 bp):
CTTTAGCGGCGCTTTTACCAAAAACGCCACAATAGACCCGGATCTATAGCGGCGTTTTTAGTATA
AGCGCCGCTATAGACTAGGGTCTTTAGCGGCGTTTTTAGTCAAAGCGCCGCTATAGATCAGGGT
Found at i:56263563 original size:10 final size:9
Alignment explanation
Indices: 56263532--56263561 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
56263522 TTAAACAAAT
56263532 AATATAATA
1 AATATAATA
56263541 AATATCAATA
1 AATAT-AATA
56263551 AATATAATA
1 AATATAATA
56263560 AA
1 AA
56263562 ATTCGTATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (9 bp):
AATATAATA
Found at i:56263754 original size:21 final size:21
Alignment explanation
Indices: 56263725--56263836 Score: 116
Period size: 21 Copynumber: 5.3 Consensus size: 21
56263715 TTTGACGCTG
56263725 CTCTGCTTCCCTCGCTGCAGC
1 CTCTGCTTCCCTCGCTGCAGC
* **
56263746 CTCTACTTCCCTCGCTTTAGC
1 CTCTGCTTCCCTCGCTGCAGC
*
56263767 CTCTGCTTCCCTCGCTGTAGC
1 CTCTGCTTCCCTCGCTGCAGC
* * * *
56263788 CTGTACTTCTCTCGCTGCCGC
1 CTCTGCTTCCCTCGCTGCAGC
* * *
56263809 CTCTGCTTCTCTTGCTGCCGC
1 CTCTGCTTCCCTCGCTGCAGC
*
56263830 ATCTGCT
1 CTCTGCT
56263837 CTAAGCTGCT
Statistics
Matches: 77, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 77 1.00
ACGTcount: A:0.05, C:0.43, G:0.17, T:0.35
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTGCAGC
Found at i:56263772 original size:42 final size:42
Alignment explanation
Indices: 56263725--56263826 Score: 132
Period size: 42 Copynumber: 2.4 Consensus size: 42
56263715 TTTGACGCTG
**
56263725 CTCTGCTTCCCTCGCTGCAGCCTCTACTTCCCTCGCTTTAGC
1 CTCTGCTTCCCTCGCTGCAGCCTCTACTTCCCTCGCTGCAGC
* * * *
56263767 CTCTGCTTCCCTCGCTGTAGCCTGTACTTCTCTCGCTGCCGC
1 CTCTGCTTCCCTCGCTGCAGCCTCTACTTCCCTCGCTGCAGC
* *
56263809 CTCTGCTTCTCTTGCTGC
1 CTCTGCTTCCCTCGCTGC
56263827 CGCATCTGCT
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 51 1.00
ACGTcount: A:0.05, C:0.43, G:0.17, T:0.35
Consensus pattern (42 bp):
CTCTGCTTCCCTCGCTGCAGCCTCTACTTCCCTCGCTGCAGC
Found at i:56263898 original size:66 final size:66
Alignment explanation
Indices: 56263808--56263952 Score: 177
Period size: 66 Copynumber: 2.2 Consensus size: 66
56263798 CTCGCTGCCG
* * *
56263808 CCTCTGCTTCTCTTGCTGCCGCATCTGCTCTAAGCTGCT-CCTGGAGTTCTTCATA-CTTTCGTT
1 CCTCAGCTTCTCTCGCTGCCGCATCCGCTCTAAGCTG-TACCTGGAGTTCTTCATATC-TTCGTT
56263871 GAA
64 GAA
* * * * *
56263874 CCTCAGCTTCTCTCGCTGCTGCATCCGCTTTAAGTTGTAGCTGGAGTTCTTCATATCTTCTTTGA
1 CCTCAGCTTCTCTCGCTGCCGCATCCGCTCTAAGCTGTACCTGGAGTTCTTCATATCTTCGTTGA
56263939 A
66 A
*
56263940 CATCAGCTTCTCT
1 CCTCAGCTTCTCT
56263953 GGATGTTGCC
Statistics
Matches: 68, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
65 1 0.01
66 66 0.97
67 1 0.01
ACGTcount: A:0.14, C:0.30, G:0.17, T:0.39
Consensus pattern (66 bp):
CCTCAGCTTCTCTCGCTGCCGCATCCGCTCTAAGCTGTACCTGGAGTTCTTCATATCTTCGTTGA
A
Found at i:56263967 original size:66 final size:66
Alignment explanation
Indices: 56263848--56263977 Score: 190
Period size: 66 Copynumber: 2.0 Consensus size: 66
56263838 TAAGCTGCTC
* *
56263848 CTGGAGTTCTTCATACTTTCGTTGAACCTCAGCTTCTCTCGCTGCTGCATCCGCTTTAAGTTGTA
1 CTGGAGTTCTTCATACTTTCGTTGAACATCAGCTTCTCTCGATGCTGCATCCGCTTTAAGTTGTA
56263913 G
66 G
* * * *
56263914 CTGGAGTTCTTCATA-TCTTCTTTGAACATCAGCTTCTCTGGATGTTGCCTCCGCTTTAAGTTGT
1 CTGGAGTTCTTCATACT-TTCGTTGAACATCAGCTTCTCTCGATGCTGCATCCGCTTTAAGTTGT
56263978 GTAATTTGCT
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
65 1 0.02
66 56 0.98
ACGTcount: A:0.15, C:0.25, G:0.19, T:0.40
Consensus pattern (66 bp):
CTGGAGTTCTTCATACTTTCGTTGAACATCAGCTTCTCTCGATGCTGCATCCGCTTTAAGTTGTA
G
Found at i:56269384 original size:16 final size:16
Alignment explanation
Indices: 56269363--56269395 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
56269353 ACTAAGCTAC
56269363 GTAAGTTATGTATTAT
1 GTAAGTTATGTATTAT
*
56269379 GTAAGTTATTTATTAT
1 GTAAGTTATGTATTAT
56269395 G
1 G
56269396 GCAATTATGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.30, C:0.00, G:0.18, T:0.52
Consensus pattern (16 bp):
GTAAGTTATGTATTAT
Found at i:56269443 original size:9 final size:9
Alignment explanation
Indices: 56269431--56269850 Score: 111
Period size: 9 Copynumber: 48.8 Consensus size: 9
56269421 CAAATTATGC
56269431 TATGTAAGT
1 TATGTAAGT
*
56269440 TATGTATGT
1 TATGTAAGT
** *
56269449 CGTATAAGT
1 TATGTAAGT
56269458 TATGTAAG-
1 TATGTAAGT
56269466 T-TGTAAGT
1 TATGTAAGT
56269474 TATGTAAGT
1 TATGTAAGT
*
56269483 TAT-TTA-T
1 TATGTAAGT
* *
56269490 TATGAAAAT
1 TATGTAAGT
*
56269499 TAAGTAAGT
1 TATGTAAGT
*
56269508 TATGTAATT
1 TATGTAAGT
*
56269517 TACG-AA-T
1 TATGTAAGT
**
56269524 TAT-TAAAA
1 TATGTAAGT
*
56269532 AATTGTAAGT
1 TA-TGTAAGT
56269542 TATGTAAG-
1 TATGTAAGT
56269550 T-TGTAAGT
1 TATGTAAGT
*
56269558 TATGTATA-A
1 TATGTA-AGT
*
56269567 CAT-TAA-T
1 TATGTAAGT
**
56269574 TAACTAAGT
1 TATGTAAGT
*
56269583 TATGTAATT
1 TATGTAAGT
*
56269592 TATGTATA-A
1 TATGTA-AGT
56269601 TACTGATTAA-T
1 TA-TG--TAAGT
**
56269612 TAACTAAGT
1 TATGTAAGT
*
56269621 TATGTAATT
1 TATGTAAGT
56269630 TATGT-A--
1 TATGTAAGT
*
56269636 TAT-TAACT
1 TATGTAAGT
*
56269644 AAT-TAAGT
1 TATGTAAGT
56269652 TATGT--GT
1 TATGTAAGT
56269659 GT-TGTAAG-
1 -TATGTAAGT
56269667 T-TGTAAGT
1 TATGTAAGT
56269675 TATGTAAGT
1 TATGTAAGT
56269684 TA--TAAGT
1 TATGTAAGT
56269691 TATGTAAGT
1 TATGTAAGT
56269700 TA--TAAGT
1 TATGTAAGT
56269707 TATGTAAG-
1 TATGTAAGT
56269715 T-TGTAAGT
1 TATGTAAGT
*
56269723 TATGTATA-A
1 TATGTA-AGT
56269732 TAT-TAA-T
1 TATGTAAGT
**
56269739 TAACTAAGT
1 TATGTAAGT
*
56269748 TATGTAATT
1 TATGTAAGT
*
56269757 TATGTATCACAT
1 TATGTA--A-GT
56269769 TAATGTAAGT
1 T-ATGTAAGT
**
56269779 TATGTAACA
1 TATGTAAGT
*
56269788 TATGTATA-A
1 TATGTA-AGT
56269797 TAT-TAA-T
1 TATGTAAGT
**
56269804 TAACTAAGT
1 TATGTAAGT
*
56269813 TATGTAATT
1 TATGTAAGT
*
56269822 TATGTATCATAT
1 TATGTA--A-GT
56269834 TAATGTAAGT
1 T-ATGTAAGT
56269844 TATGTAA
1 TATGTAA
56269851 CTTACGCATC
Statistics
Matches: 306, Mismatches: 58, Indels: 94
0.67 0.13 0.21
Matches are distributed among these distances:
5 1 0.00
6 4 0.01
7 61 0.20
8 41 0.13
9 162 0.53
10 14 0.05
11 7 0.02
12 6 0.02
13 10 0.03
ACGTcount: A:0.38, C:0.03, G:0.15, T:0.44
Consensus pattern (9 bp):
TATGTAAGT
Found at i:56269474 original size:16 final size:16
Alignment explanation
Indices: 56269433--56269563 Score: 72
Period size: 16 Copynumber: 7.8 Consensus size: 16
56269423 AATTATGCTA
*
56269433 TGTAAGTTATGTATGT
1 TGTAAGTTATGTAAGT
*
56269449 CGTATAAGTTATGTAAGT
1 --TGTAAGTTATGTAAGT
56269467 TGTAAGTTATGTAAGT
1 TGTAAGTTATGTAAGT
* * * *
56269483 TATTTA-TTATGAAAAT
1 T-GTAAGTTATGTAAGT
56269499 TAAGTAAGTTATGTAA-T
1 T--GTAAGTTATGTAAGT
* *
56269516 T-TACGAATTAT-TAAAAAAT
1 TGTA--AGTTATGT---AAGT
56269535 TGTAAGTTATGTAAGT
1 TGTAAGTTATGTAAGT
56269551 TGTAAGTTATGTA
1 TGTAAGTTATGTA
56269564 TAACATTAAT
Statistics
Matches: 89, Mismatches: 13, Indels: 24
0.71 0.10 0.19
Matches are distributed among these distances:
14 2 0.02
15 1 0.01
16 46 0.52
17 7 0.08
18 28 0.31
19 3 0.03
20 2 0.02
ACGTcount: A:0.37, C:0.02, G:0.18, T:0.44
Consensus pattern (16 bp):
TGTAAGTTATGTAAGT
Found at i:56269526 original size:34 final size:33
Alignment explanation
Indices: 56269467--56269551 Score: 91
Period size: 34 Copynumber: 2.5 Consensus size: 33
56269457 TTATGTAAGT
***
56269467 TGTAAGTTATGTAAGTTATTTATTATGAAAATTAA
1 TGTAAGTTATGTAAGTTACGAATTATGAAAA--AA
* *
56269502 -GTAAGTTATGTAATTTACGAATTATTAAAAAA
1 TGTAAGTTATGTAAGTTACGAATTATGAAAAAA
56269534 TTGTAAGTTATGTAAGTT
1 -TGTAAGTTATGTAAGTT
56269552 GTAAGTTATG
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
32 2 0.05
34 40 0.95
ACGTcount: A:0.40, C:0.01, G:0.15, T:0.44
Consensus pattern (33 bp):
TGTAAGTTATGTAAGTTACGAATTATGAAAAAA
Done.