Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 ID=Chr11-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 62681010
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1052928 characters in sequence are not A, C, G, or T
File 127 of 210
Found at i:38646634 original size:21 final size:21
Alignment explanation
Indices: 38646596--38646635 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
38646586 AATTTAAAAT
**
38646596 ATTTTTAAAATACTTTTTTTA
1 ATTTTTAAAATAAATTTTTTA
38646617 ATTTTTAAAATAAATTTTT
1 ATTTTTAAAATAAATTTTT
38646636 GGTATTTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (21 bp):
ATTTTTAAAATAAATTTTTTA
Found at i:38646642 original size:22 final size:21
Alignment explanation
Indices: 38646595--38646653 Score: 59
Period size: 22 Copynumber: 2.8 Consensus size: 21
38646585 TAATTTAAAA
* *
38646595 TATTTTTAAAAT-ACTTTTTT
1 TATTTTTAAAATAAATTTTTG
38646615 TAATTTTTAAAATAAATTTTTGG
1 T-ATTTTTAAAATAAATTTTT-G
38646638 TATTTATTAAAA-AAAT
1 TATTT-TTAAAATAAAT
38646654 GAGCCGGGCG
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
20 1 0.03
21 11 0.33
22 14 0.42
23 7 0.21
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.54
Consensus pattern (21 bp):
TATTTTTAAAATAAATTTTTG
Found at i:38647032 original size:58 final size:58
Alignment explanation
Indices: 38646900--38647036 Score: 186
Period size: 58 Copynumber: 2.4 Consensus size: 58
38646890 TATTGTTATT
* *
38646900 AAATTTTAATAAGATTATTATTAAAAATAATTTAATAAAAATAATAAATAATTTAACC
1 AAATTTTAATAAAATTATTATTAAAAATAATTTAATAAAAATAATAAATAATTTAACA
* * * * * *
38646958 ATATTTTAACATAATTATTATTAAATATAATTTAAT-AAAATAATATATAATTTAATA
1 AAATTTTAATAAAATTATTATTAAAAATAATTTAATAAAAATAATAAATAATTTAACA
38647015 AAATTCTTAATAAAATTATTAT
1 AAATT-TTAATAAAATTATTAT
38647037 ATGAATTAAA
Statistics
Matches: 67, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
57 22 0.33
58 45 0.67
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (58 bp):
AAATTTTAATAAAATTATTATTAAAAATAATTTAATAAAAATAATAAATAATTTAACA
Found at i:38647950 original size:43 final size:43
Alignment explanation
Indices: 38647899--38648125 Score: 282
Period size: 43 Copynumber: 5.3 Consensus size: 43
38647889 TTATGTGAAA
* * *
38647899 AAACGCCGCTAAAGATCATGACCTTTAGCGGTGCTTTTGCCAC
1 AAACGCCGCTAAAGATCGTGACCTTTAGCGGCGCTTTAGCCAC
* * *
38647942 AAACGCCGCTAAAGATCTTGACCTTTAGCGGTGCTTTTA-TCAC
1 AAACGCCGCTAAAGATCGTGACCTTTAGCGGCGC-TTTAGCCAC
38647985 AAACGCCGCTAAAGATCGTGACCTTTAGCGGCGCTTTAGCCAC
1 AAACGCCGCTAAAGATCGTGACCTTTAGCGGCGCTTTAGCCAC
* **
38648028 AAACGCCGCTAAAGATCGTGAGCTTTAGCAACGCTTTAGCCAC
1 AAACGCCGCTAAAGATCGTGACCTTTAGCGGCGCTTTAGCCAC
** * *
38648071 AAACGCCGCTAAAGAAT--AAACCTTTAGCGACGCTTCTAG-CAA
1 AAACGCCGCTAAAG-ATCGTGACCTTTAGCGGCGCTT-TAGCCAC
38648113 AAACGCCGCTAAA
1 AAACGCCGCTAAA
38648126 AACATAACTT
Statistics
Matches: 166, Mismatches: 14, Indels: 9
0.88 0.07 0.05
Matches are distributed among these distances:
42 33 0.20
43 128 0.77
44 5 0.03
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (43 bp):
AAACGCCGCTAAAGATCGTGACCTTTAGCGGCGCTTTAGCCAC
Found at i:38649999 original size:18 final size:18
Alignment explanation
Indices: 38649978--38650017 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
38649968 AAAATAAAAT
38649978 AAAAGAATAAAAGCAATA
1 AAAAGAATAAAAGCAATA
** *
38649996 AAAAGCGTGAAAGCAATA
1 AAAAGAATAAAAGCAATA
38650014 AAAA
1 AAAA
38650018 AGACAGACAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.68, C:0.07, G:0.15, T:0.10
Consensus pattern (18 bp):
AAAAGAATAAAAGCAATA
Found at i:38652844 original size:12 final size:12
Alignment explanation
Indices: 38652827--38652852 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
38652817 TACCACTTCA
38652827 CAATAGAGTTTT
1 CAATAGAGTTTT
38652839 CAATAGAGTTTT
1 CAATAGAGTTTT
38652851 CA
1 CA
38652853 TCACTGTTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (12 bp):
CAATAGAGTTTT
Found at i:38654452 original size:19 final size:19
Alignment explanation
Indices: 38654412--38654454 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
38654402 AATTTTAATT
*
38654412 AATATAAATAAACAAATTA
1 AATATAAATAAACAAATAA
*
38654431 AATAGTAAAT-AACAGATAA
1 AATA-TAAATAAACAAATAA
38654450 AATAT
1 AATAT
38654455 TTTTGCGGCG
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 1 0.05
19 15 0.71
20 5 0.24
ACGTcount: A:0.65, C:0.05, G:0.05, T:0.26
Consensus pattern (19 bp):
AATATAAATAAACAAATAA
Found at i:38654634 original size:41 final size:41
Alignment explanation
Indices: 38654459--38654634 Score: 298
Period size: 41 Copynumber: 4.3 Consensus size: 41
38654449 AAATATTTTT
* *
38654459 GCGGCGCTTTCTCAAAAACGCCGCTAAAGCTCTGAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGATCTGAGCATTA
*
38654500 GCGGCGCTTTTCCAAAAACGCCGCTAAAGATCTGAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGATCTGAGCATTA
* *
38654541 GCGTCGCTTTTTCAAAAACGCCACTAAAGATCTGAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGATCTGAGCATTA
*
38654582 GCGGCGCTTTTTCAAAAACGCCGCTAAAGATCTGAGTATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGATCTGAGCATTA
38654623 GCGGCGCTTTTT
1 GCGGCGCTTTTT
38654635 TAAAGACCTG
Statistics
Matches: 126, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 126 1.00
ACGTcount: A:0.27, C:0.26, G:0.22, T:0.26
Consensus pattern (41 bp):
GCGGCGCTTTTTCAAAAACGCCGCTAAAGATCTGAGCATTA
Found at i:38654735 original size:39 final size:40
Alignment explanation
Indices: 38654678--38654813 Score: 157
Period size: 40 Copynumber: 3.4 Consensus size: 40
38654668 GGGCTTAGGT
*
38654678 TTTTTTGCGGCGTTTTTCCAAAAAACGCCGCTAATGCTT-A
1 TTTTTAGCGGCG-TTTTCCAAAAAACGCCGCTAATGCTTGA
* * *
38654718 TTTTTAGCGGCGCTTTCCTAAAAGCGCCGCTAATGCTTGA
1 TTTTTAGCGGCGTTTTCCAAAAAACGCCGCTAATGCTTGA
* * ****
38654758 TCTTTAGCTGCGTTTTGTGTAAAACGCCGCTAATGCTTGA
1 TTTTTAGCGGCGTTTTCCAAAAAACGCCGCTAATGCTTGA
*
38654798 TTTTTAGCGGTGTTTT
1 TTTTTAGCGGCGTTTT
38654814 TTGTCCAAAC
Statistics
Matches: 80, Mismatches: 15, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
39 23 0.29
40 57 0.71
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.39
Consensus pattern (40 bp):
TTTTTAGCGGCGTTTTCCAAAAAACGCCGCTAATGCTTGA
Found at i:38656343 original size:7 final size:8
Alignment explanation
Indices: 38656326--38656354 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
38656316 AATTTATTTT
38656326 AAAAATAA
1 AAAAATAA
38656334 AAAAATAA
1 AAAAATAA
38656342 AAAAATAA
1 AAAAATAA
38656350 AAAAA
1 AAAAA
38656355 AGTATTTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (8 bp):
AAAAATAA
Found at i:38658087 original size:20 final size:20
Alignment explanation
Indices: 38658064--38658127 Score: 83
Period size: 20 Copynumber: 3.2 Consensus size: 20
38658054 ACACTTTGGC
*
38658064 GCCTTTATTTGCACTTCGGT
1 GCCTATATTTGCACTTCGGT
* * *
38658084 GCCTCTGTTTGCACTTCGAT
1 GCCTATATTTGCACTTCGGT
*
38658104 GCCTATATTTGCACTACGGT
1 GCCTATATTTGCACTTCGGT
38658124 GCCT
1 GCCT
38658128 CTGGTTAGCA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.12, C:0.28, G:0.20, T:0.39
Consensus pattern (20 bp):
GCCTATATTTGCACTTCGGT
Found at i:38658113 original size:40 final size:41
Alignment explanation
Indices: 38658064--38658144 Score: 119
Period size: 40 Copynumber: 2.0 Consensus size: 41
38658054 ACACTTTGGC
* * *
38658064 GCCTTTATTTGCACTTCGGTGCCTCT-GTTTGCACTTCGAT
1 GCCTATATTTGCACTACGGTGCCTCTGGTTAGCACTTCGAT
*
38658104 GCCTATATTTGCACTACGGTGCCTCTGGTTAGCATTTCGAT
1 GCCTATATTTGCACTACGGTGCCTCTGGTTAGCACTTCGAT
38658145 ACCCTCTGGT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
40 24 0.67
41 12 0.33
ACGTcount: A:0.14, C:0.26, G:0.21, T:0.40
Consensus pattern (41 bp):
GCCTATATTTGCACTACGGTGCCTCTGGTTAGCACTTCGAT
Found at i:38660131 original size:15 final size:15
Alignment explanation
Indices: 38660111--38660141 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
38660101 ACTCTTCCCC
38660111 CTAAAAGTCCTCTTA
1 CTAAAAGTCCTCTTA
38660126 CTAAAAGTCCTCTTA
1 CTAAAAGTCCTCTTA
38660141 C
1 C
38660142 CCCTAACTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.29, G:0.06, T:0.32
Consensus pattern (15 bp):
CTAAAAGTCCTCTTA
Found at i:38674043 original size:27 final size:27
Alignment explanation
Indices: 38674013--38674076 Score: 67
Period size: 30 Copynumber: 2.3 Consensus size: 27
38674003 TCGTTCCTTC
*
38674013 TTATTTTAATAATTAAATCGTGAATTA
1 TTATTTTAAAAATTAAATCGTGAATTA
* *
38674040 TTATTTATTAAAAAATTAAATTGTGATTTA
1 TTA-TT-TT-AAAAATTAAATCGTGAATTA
38674070 TT-TTTTA
1 TTATTTTA
38674077 TTAACTAGCA
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
26 1 0.03
27 5 0.16
28 4 0.13
29 2 0.06
30 19 0.61
ACGTcount: A:0.39, C:0.02, G:0.06, T:0.53
Consensus pattern (27 bp):
TTATTTTAAAAATTAAATCGTGAATTA
Found at i:38674059 original size:30 final size:30
Alignment explanation
Indices: 38674023--38674080 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
38674013 TTATTTTAAT
38674023 AATTAAATCGTGAATTATTATTTATTAAAA
1 AATTAAATCGTGAATTATTATTTATTAAAA
* * *
38674053 AATTAAATTGTGATTTATTTTTTATTAA
1 AATTAAATCGTGAATTATTATTTATTAA
38674081 CTAGCATTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.50
Consensus pattern (30 bp):
AATTAAATCGTGAATTATTATTTATTAAAA
Found at i:38674622 original size:22 final size:24
Alignment explanation
Indices: 38674586--38674637 Score: 63
Period size: 22 Copynumber: 2.2 Consensus size: 24
38674576 CATAAGGGTA
*
38674586 AAAAAAATTCTAATTAAAATTTTT
1 AAAAAAATTCTAATTAAAACTTTT
* *
38674610 AAAAAAA-TC-AATTTAACCTTTT
1 AAAAAAATTCTAATTAAAACTTTT
38674632 AAAAAA
1 AAAAAA
38674638 TGCGTCTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 16 0.64
23 2 0.08
24 7 0.28
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.35
Consensus pattern (24 bp):
AAAAAAATTCTAATTAAAACTTTT
Found at i:38675348 original size:18 final size:17
Alignment explanation
Indices: 38675327--38675370 Score: 70
Period size: 17 Copynumber: 2.5 Consensus size: 17
38675317 AGTTAAAATT
38675327 TATTTTATAATAAGATAA
1 TATTTTATAATAA-ATAA
*
38675345 TATTTTACAATAAATAA
1 TATTTTATAATAAATAA
38675362 TATTTTATA
1 TATTTTATA
38675371 TAGACTTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 12 0.50
18 12 0.50
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (17 bp):
TATTTTATAATAAATAA
Found at i:38675363 original size:17 final size:18
Alignment explanation
Indices: 38675327--38675368 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
38675317 AGTTAAAATT
*
38675327 TATTTTATAATAAGATAA
1 TATTTTACAATAAGATAA
38675345 TATTTTACAATAA-ATAA
1 TATTTTACAATAAGATAA
38675362 TATTTTA
1 TATTTTA
38675369 TATAGACTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 11 0.48
18 12 0.52
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (18 bp):
TATTTTACAATAAGATAA
Found at i:38675588 original size:19 final size:20
Alignment explanation
Indices: 38675538--38675593 Score: 64
Period size: 19 Copynumber: 2.9 Consensus size: 20
38675528 TTCAATAAAA
*
38675538 TAATATTAAAA-TTATTACT
1 TAATTTTAAAATTTATTACT
*
38675557 TCAATTTT-TAATTTATTAC-
1 T-AATTTTAAAATTTATTACT
38675576 TAATTTTAAAATTTATTA
1 TAATTTTAAAATTTATTA
38675594 TTACAATGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
18 6 0.19
19 13 0.42
20 12 0.39
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (20 bp):
TAATTTTAAAATTTATTACT
Found at i:38681379 original size:4 final size:4
Alignment explanation
Indices: 38681370--38681427 Score: 89
Period size: 4 Copynumber: 13.8 Consensus size: 4
38681360 TTGCTTGTAC
38681370 ATAA ATAA ATAA ATAAA ATGAAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA
1 ATAA ATAA ATAA AT-AA AT--AA ATAA ATAA ATAA ATAA ATAA ATAA ATAA
38681421 ATAA ATA
1 ATAA ATA
38681428 CTCAAGTTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
4 43 0.83
5 4 0.08
6 5 0.10
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:38686532 original size:18 final size:18
Alignment explanation
Indices: 38686506--38686545 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
38686496 ACATGGGCAA
* *
38686506 GGCCAATATGGGCTTGTG
1 GGCCAATATGAGCATGTG
*
38686524 GGCCCATATGAGCATGTG
1 GGCCAATATGAGCATGTG
38686542 GGCC
1 GGCC
38686546 TACAATTCTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.17, C:0.23, G:0.38, T:0.23
Consensus pattern (18 bp):
GGCCAATATGAGCATGTG
Found at i:38691272 original size:19 final size:19
Alignment explanation
Indices: 38691248--38691360 Score: 172
Period size: 19 Copynumber: 5.8 Consensus size: 19
38691238 AATTTTTGAG
38691248 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
**
38691267 GATATGCAATCCAAGATAT
1 GATATGCAATCTTAGATAT
38691286 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
38691307 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
**
38691326 GATATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
38691345 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
38691361 ATATATGATT
Statistics
Matches: 84, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
19 67 0.80
21 17 0.20
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.35
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:38691293 original size:40 final size:40
Alignment explanation
Indices: 38691249--38691355 Score: 182
Period size: 40 Copynumber: 2.7 Consensus size: 40
38691239 ATTTTTGAGG
38691249 ATATGCAATCTTAGATATGATATGCAATCCAAGATATGAT
1 ATATGCAATCTTAGATATGATATGCAATCCAAGATATGAT
**
38691289 ATATGCAATCTTAGATATGATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGATATGCAATCCAAGATATGAT
38691329 ATAT--AATCTTAGATATGATATGCAATC
1 ATATGCAATCTTAGATATGATATGCAATC
38691356 TTAGAATATA
Statistics
Matches: 65, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
38 23 0.35
40 42 0.65
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.36
Consensus pattern (40 bp):
ATATGCAATCTTAGATATGATATGCAATCCAAGATATGAT
Found at i:38691315 original size:59 final size:56
Alignment explanation
Indices: 38691248--38691367 Score: 170
Period size: 59 Copynumber: 2.1 Consensus size: 56
38691238 AATTTTTGAG
*
38691248 GATATGCAATCTTAGATATGATATGCAATCCAAGATATGATATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATATGATATACAATCCAAGATATG--ATATGCAATCTTAGA-AT
* **
38691307 GATATGCAATCTTAGATATGATATATAATCTTAGATATGATATGCAATCTTAGAAT
1 GATATGCAATCTTAGATATGATATACAATCCAAGATATGATATGCAATCTTAGAAT
38691363 -ATATG
1 GATATG
38691368 ATTTTGTAAT
Statistics
Matches: 57, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
55 5 0.09
56 2 0.04
57 15 0.26
59 35 0.61
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36
Consensus pattern (56 bp):
GATATGCAATCTTAGATATGATATACAATCCAAGATATGATATGCAATCTTAGAAT
Found at i:38692181 original size:23 final size:25
Alignment explanation
Indices: 38692127--38692175 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
38692117 TATGTACATG
* *
38692127 TATATTTTTTTAACGGATATTTTCC
1 TATATTTTTTTAAAGAATATTTTCC
38692152 TATATTTTTTTAAAGAATATTTTC
1 TATATTTTTTTAAAGAATATTTTC
38692176 ATATTTATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.29, C:0.08, G:0.06, T:0.57
Consensus pattern (25 bp):
TATATTTTTTTAAAGAATATTTTCC
Found at i:38695027 original size:41 final size:39
Alignment explanation
Indices: 38694939--38695029 Score: 96
Period size: 39 Copynumber: 2.3 Consensus size: 39
38694929 NNNNNNGTAT
*
38694939 TGTAT-TTATATATAAATTCTATAACTCAAAATTTTATT
1 TGTATATTATATATAAATTCTATAACTCAAAATTTTATG
* * * *
38694977 TGTAAATTATATATATATT-TTTAATCTTCATAATTTTCATG
1 TGTATATTATATATAAATTCTATAA-C-TCAAAATTTT-ATG
38695018 TGTATATTATAT
1 TGTATATTATAT
38695030 GTCTTCTGAT
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
38 8 0.19
39 13 0.30
40 9 0.21
41 13 0.30
ACGTcount: A:0.36, C:0.07, G:0.04, T:0.53
Consensus pattern (39 bp):
TGTATATTATATATAAATTCTATAACTCAAAATTTTATG
Found at i:38695604 original size:98 final size:98
Alignment explanation
Indices: 38695471--38695667 Score: 333
Period size: 98 Copynumber: 2.0 Consensus size: 98
38695461 TAAAAAATAA
* *
38695471 TAAAGGAAATATTCCGAGTTTGGGATTTTAAAGGAAAT-GTGCCCTAACGTATTGGGTGTGATTT
1 TAAAGGAAATATTCCGAGTTTGAGATTCTAAAGG-AATCGTGCCCTAACGTATTGGGTGTGATTT
38695535 CTTAAATCTTGGATAAGTAGATGTTCTTTTAAAG
65 CTTAAATCTTGGATAAGTAGATGTTCTTTTAAAG
* *
38695569 TAAATGAAATATTCCGAGTTTGAGATTCTAGAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGAGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
*
38695634 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTAGATGTTCTTTTAAAG
38695667 T
1 T
38695668 TTTATTGTAC
Statistics
Matches: 93, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
97 3 0.03
98 90 0.97
ACGTcount: A:0.29, C:0.10, G:0.23, T:0.37
Consensus pattern (98 bp):
TAAAGGAAATATTCCGAGTTTGAGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
TTAAATCTTGGATAAGTAGATGTTCTTTTAAAG
Found at i:38700974 original size:132 final size:132
Alignment explanation
Indices: 38700802--38701096 Score: 398
Period size: 132 Copynumber: 2.2 Consensus size: 132
38700792 CGGATTTTAC
* * * * *
38700802 CTCCCTGAGTAGTAGTGGAGCAGATTGAAAATTGCAGATTTTACCTCCCTGTGGTTACAGTGGAG
1 CTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAG
* * * *
38700867 TACATTGAAG-CTAGTAATTCTA-CTTTCCTGGGCAATAGTGGAATAGATTGAAGATT-TCAGAT
66 TACATTGAAGTC-AGTAATCCTATC-TCCCTGGGCAACAGTGGAATAGATTGAAGATTGTAAG-T
38700929 CTTAT
128 CTTAT
* **
38700934 CTCCCTAAGCAGTAGTGGAGTAGATCGAAGATGGTGGATTTTACCTCCCTGTGGTTACAGTGGAG
1 CTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAG
* * *
38700999 TACATTGAAGTCAGTAATCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTAAGTCTT
66 TACATTGAAGTCAGTAATCCTATCTCCCTGGGCAACAGTGGAATAGATTGAAGATTGTAAGTCTT
38701064 AT
131 AT
*
38701066 CTCCCTAAGCAGTAGTGGAGCAGATCAAAGA
1 CTCCCTAAGCAGTAGTGGAGCAGATCGAAGA
38701097 CGGCGAATCT
Statistics
Matches: 143, Mismatches: 17, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
132 138 0.97
133 5 0.03
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (132 bp):
CTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAG
TACATTGAAGTCAGTAATCCTATCTCCCTGGGCAACAGTGGAATAGATTGAAGATTGTAAGTCTT
AT
Found at i:38701108 original size:44 final size:44
Alignment explanation
Indices: 38701060--38701373 Score: 126
Period size: 44 Copynumber: 7.1 Consensus size: 44
38701050 AGATTGTAAG
*
38701060 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGCGAA
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAA
* ** ** *
38701104 TCTTATCTTTCC-AAG-A-TAGTGGGAAGCAGATTTAAG-CCACCAA
1 TCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATCGAAGACGGCGAA
* * * * * * * * ** *
38701147 GCCTTGTCTCCCTCAGCAGCAGCGGAGAAGGTTGAAGATTG-TAGA
1 -TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGA-A
*
38701192 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGTGAA
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAA
* ** ** *
38701236 TCTTATCTTTCC-AAG-A-TAGTGGAAAGCAGATTTAAG-CCACCAA
1 TCTTATC-TCCCTAAGCAGTAGTGG--AGCAGATCGAAGACGGCGAA
* * * * * * * * ** *
38701279 GCCTTGTCTCCCTCAGCAGTAGCGGAGAAGGTTGAATATTG-TAGA
1 -TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGA-A
* *
38701324 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGACGAA
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAA
38701368 TCTTAT
1 TCTTAT
38701374 TTTTCCAAGA
Statistics
Matches: 189, Mismatches: 61, Indels: 40
0.65 0.21 0.14
Matches are distributed among these distances:
42 10 0.05
43 17 0.09
44 141 0.75
45 14 0.07
46 7 0.04
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.25
Consensus pattern (44 bp):
TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAA
Found at i:38701157 original size:132 final size:132
Alignment explanation
Indices: 38701043--38701467 Score: 735
Period size: 132 Copynumber: 3.2 Consensus size: 132
38701033 GCAGTGGAAT
*
38701043 AGGTTGAAGATTGTA-AGTCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGCGAATCT
1 AGGTTGAAGATTGTAGA-TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCT
38701107 TATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTCAGCAGCAGCGG
65 TATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTCAGCAGCAGCGG
38701172 AGA
130 AGA
*
38701175 AGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGTGAATCTT
1 AGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTT
* *
38701240 ATCTTTCCAAGATAGTGGAAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTCAGCAGTAGCGGA
66 ATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTCAGCAGCAGCGGA
38701305 GA
131 GA
* * *
38701307 AGGTTGAATATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGACGAATCTT
1 AGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTT
* *
38701372 ATTTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGGA
66 ATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTCAGCAGCAGCGGA
38701437 GA
131 GA
* *
38701439 AGGTTGAAGATTGTAAATCCTATCTCCCT
1 AGGTTGAAGATTGTAGATCTTATCTCCCT
38701468 GAAGTTGCAG
Statistics
Matches: 277, Mismatches: 15, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
132 276 1.00
133 1 0.00
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.25
Consensus pattern (132 bp):
AGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTT
ATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTCAGCAGCAGCGGA
GA
Found at i:38701507 original size:44 final size:41
Alignment explanation
Indices: 38701459--38701648 Score: 125
Period size: 44 Copynumber: 4.4 Consensus size: 41
38701449 TTGTAAATCC
*
38701459 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCTCAGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGA-TAAAACCT-AG-TCT
* ** *** *
38701503 TATCTCTCC-AAAGTTGCAG-AAAGCAGATCGCATCTAGTCT
1 TATCTC-CCTGAAGTTGCAGTGGAGCAGATAAAACCTAGTCT
* *
38701543 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGA-TAA--AACCTAGTCT
* ** *
38701587 TATC-CTCCTGAAGTTGCAGTGGGGCAGACTGAAGATGGCAAGTCT
1 TATCTC-CCTGAAGTTGCAGTGGAGCAGA-T-AA-A-ACCTAGTCT
38701632 TATCTCCCTGAAGTTGC
1 TATCTCCCTGAAGTTGC
38701649 NNNNNNNNNN
Statistics
Matches: 117, Mismatches: 19, Indels: 19
0.75 0.12 0.12
Matches are distributed among these distances:
39 2 0.02
40 18 0.15
41 8 0.07
42 5 0.04
43 6 0.05
44 50 0.43
45 27 0.23
46 1 0.01
ACGTcount: A:0.27, C:0.23, G:0.24, T:0.27
Consensus pattern (41 bp):
TATCTCCCTGAAGTTGCAGTGGAGCAGATAAAACCTAGTCT
Found at i:38701527 original size:264 final size:264
Alignment explanation
Indices: 38701043--38701530 Score: 732
Period size: 264 Copynumber: 1.8 Consensus size: 264
38701033 GCAGTGGAAT
*
38701043 AGGTTGAAGATTGTAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGCGAATCTT
1 AGGTTGAAGATTGTAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACGAATCTT
38701108 ATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTCAGCAGCAGCGGA
66 ATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTCAGCAGCAGCGGA
* * * * * *
38701173 GAAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGTGAATC
131 GAAGGTTGAAGATTGTAAATCCTATCTCCCTAAGCAGCAGTGGAGCAGATCGAAAACGCTCAATC
* **
38701238 TTATCTTTCCAAGATAGTGGAAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTCAGCAGTAGCG
196 TTATCTCTCCAAGATAGCAGAAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTCAGCAGTAGCG
38701303 GAGA
261 GAGA
* * *
38701307 AGGTTGAATATTGT-AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGACGAATCT
1 AGGTTGAAGATTGTAAG-TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACGAATCT
* *
38701371 TATTTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGCGG
65 TATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTCAGCAGCAGCGG
** * *
38701436 AGAAGGTTGAAGATTGTAAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGAT-TAAAAC-CTCAG
130 AGAAGGTTGAAGATTGTAAATCCTATCTCCCT-AAGCAGCAGTGGAGCAGATCGAAAACGCTCA-
*
38701499 ATCTTATCTCTCCAA-AGTTGCAGAAAGCAGAT
193 ATCTTATCTCTCCAAGA-TAGCAGAAAGCAGAT
38701531 CGCATCTAGT
Statistics
Matches: 200, Mismatches: 20, Indels: 8
0.88 0.09 0.04
Matches are distributed among these distances:
263 5 0.03
264 180 0.90
265 15 0.08
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.25
Consensus pattern (264 bp):
AGGTTGAAGATTGTAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACGAATCTT
ATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTCAGCAGCAGCGGA
GAAGGTTGAAGATTGTAAATCCTATCTCCCTAAGCAGCAGTGGAGCAGATCGAAAACGCTCAATC
TTATCTCTCCAAGATAGCAGAAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTCAGCAGTAGCG
GAGA
Found at i:38701643 original size:45 final size:44
Alignment explanation
Indices: 38701538--38701648 Score: 163
Period size: 44 Copynumber: 2.5 Consensus size: 44
38701528 GATCGCATCT
38701538 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCA
* *
38701582 AGTCTTATC-CTCCTGAAGTTGCAGTGGGGCAGACTGAAG-ATGGCA
1 AGTCTTATCTC-CCTGAAGTTGCAGTGGAGCAGACT-AAGTA-AGCA
38701627 AGTCTTATCTCCCTGAAGTTGC
1 AGTCTTATCTCCCTGAAGTTGC
38701649 NNNNNNNNNN
Statistics
Matches: 61, Mismatches: 2, Indels: 7
0.87 0.03 0.10
Matches are distributed among these distances:
43 1 0.02
44 33 0.54
45 26 0.43
46 1 0.02
ACGTcount: A:0.25, C:0.22, G:0.26, T:0.27
Consensus pattern (44 bp):
AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCA
Found at i:38710048 original size:3 final size:3
Alignment explanation
Indices: 38710021--38710073 Score: 70
Period size: 3 Copynumber: 16.7 Consensus size: 3
38710011 AAATAAAAAA
*
38710021 AAT ACAT AAT TAT ACAT ATAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT A-AT AAT AAT A-AT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT
38710069 AAT AA
1 AAT AA
38710074 GGTAAATATT
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
3 36 0.80
4 9 0.20
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:38711714 original size:44 final size:43
Alignment explanation
Indices: 38711664--38712467 Score: 417
Period size: 44 Copynumber: 18.4 Consensus size: 43
38711654 CTGCTCTCTA
* *
38711664 CAACTTCAGAGAGATAAGATCCAAGGTTTTAATCCGCTCCACTG
1 CAACTTCAGGGAGATAAGAT-CAAGGTTTTAATCTGCTCCACTG
* * * * *
38711708 CAACTTCAGTGAGATAGGATTATCGGCTTTAATCTGCTCCACTG
1 CAACTTCAGGGAGATAAGATCA-AGGTTTTAATCTGCTCCACTG
* * *
38711752 CAACTTCAGGGAGATAAGATTTGCCA--TCTTCAGTCTGCTCCACTG
1 CAACTTCAGGGAGATAAGA--T-CAAGGT-TTTAATCTGCTCCACTG
** * * *
38711797 CAACTTCAGGGAGATAAGA-CTTGCTTACTTAGTCTACTCCACTG
1 CAACTTCAGGGAGATAAGATCAAGGTT--TTAATCTGCTCCACTG
* * * *** *
38711841 CAACTTCAGGAAGATAAGA-CTA-GATGCGATCTGCT-CTCTG
1 CAACTTCAGGGAGATAAGATCAAGGTTTTAATCTGCTCCACTG
* *
38711881 CAACTTCAGAGAGATAAGATCCAAGGTTTTAATCCGCTCCACTG
1 CAACTTCAGGGAGATAAGAT-CAAGGTTTTAATCTGCTCCACTG
* * * *
38711925 CAACTTCAGGGAGATAGGATTATCGGCTTTAATCTGCTCCACTG
1 CAACTTCAGGGAGATAAGATCA-AGGTTTTAATCTGCTCCACTG
** *
38711969 CAACTTCAGGGAGATAAGAT--TTGTCATCTTCAGTCTGCTCCACTG
1 CAACTTCAGGGAGATAAGATCAAGGT--T-TT-AATCTGCTCCACTG
** * *** *
38712014 CAACTTCAGGGAGATAAGA-C-TTGATGCGATCTGCT-CTCTG
1 CAACTTCAGGGAGATAAGATCAAGGTTTTAATCTGCTCCACTG
** **
38712054 CAACTTCAAAGAGATAAGATCCAAGGTTTTAATCCACTCCACTG
1 CAACTTCAGGGAGATAAGAT-CAAGGTTTTAATCTGCTCCACTG
* * * * * *
38712098 CAACTTCAGGAAGATAGGATTATTGGCTTTAACCTGCTCCACTG
1 CAACTTCAGGGAGATAAGATCA-AGGTTTTAATCTGCTCCACTG
* * *
38712142 CAACTTCAGGGAGATAAGATTTTCCA--TCTTCAGTCTGC-CTCACTG
1 CAACTTCAGGGAGATAAGA---TCAAGGT-TTTAATCTGCTC-CACTG
* ** * * *
38712187 TAACTTCA-GGAGGATAAGA-CTTGCTTTCTTAGTCTGCTCCACTA
1 CAACTTCAGGGA-GATAAGATCAAG-GTT-TTAATCTGCTCCACTG
* * **
38712231 CAACTTCAGGGAGACAAGATCCAAGATTTTAATCCACTCCACTG
1 CAACTTCAGGGAGATAAGAT-CAAGGTTTTAATCTGCTCCACTG
* * * * * * *
38712275 CAACTTCAGGAAGATAGGATTATCGGCTTTAACCTGATCCACTG
1 CAACTTCAGGGAGATAAGATCA-AGGTTTTAATCTGCTCCACTG
* * *
38712319 CAACTTCAGGGAGATAAGATTTTCCA--TCTTCAGTCTGC-CTCACTG
1 CAACTTCAGGGAGATAAGA---TCAAGGT-TTTAATCTGCTC-CACTG
** * * *
38712364 CAACTTCA-GGAGGATAAGA-CTTGCTTTCTTAGTCTGCTCCACTA
1 CAACTTCAGGGA-GATAAGATCAAG-GTT-TTAATCTGCTCCACTG
* * **
38712408 CAACTTCAGGGAGACAAGATCCAAGATTTTAATCCACTCCACTG
1 CAACTTCAGGGAGATAAGAT-CAAGGTTTTAATCTGCTCCACTG
*
38712452 CAACTTCAGGAAGATA
1 CAACTTCAGGGAGATA
38712468 GGATTATCGG
Statistics
Matches: 574, Mismatches: 133, Indels: 106
0.71 0.16 0.13
Matches are distributed among these distances:
40 42 0.07
41 15 0.03
42 4 0.01
43 25 0.04
44 348 0.61
45 133 0.23
46 5 0.01
47 2 0.00
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (43 bp):
CAACTTCAGGGAGATAAGATCAAGGTTTTAATCTGCTCCACTG
Found at i:38711921 original size:84 final size:84
Alignment explanation
Indices: 38711833--38712113 Score: 319
Period size: 84 Copynumber: 3.3 Consensus size: 84
38711823 ACTTAGTCTA
38711833 CTCCACTGCAACTTCAGGAAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAA
1 CTCCACTGCAACTTCAGGAAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAA
38711898 GATCCAAGGTTTTAATCCG
66 GATCCAAGGTTTTAATCCG
* * * * *** * *
38711917 CTCCACTGCAACTTCAGGGAGATAGGATTATCGGCTTTAATCTGCTCCACTGCAACTTCAGGGAG
1 CTCCACTGCAACTTCAGGAAGATAAGACTA---GATGCGATCTGCT-CTCTGCAACTTCAGAGAG
****** * * *
38711982 ATAAGATTTGTCATCTTCAGTCTG
62 ATAAGATCCAAGGT-TTTAATCCG
* * *
38712006 CTCCACTGCAACTTCAGGGAGATAAGACTTGATGCGATCTGCTCTCTGCAACTTCAAAGAGATAA
1 CTCCACTGCAACTTCAGGAAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAA
*
38712071 GATCCAAGGTTTTAATCCA
66 GATCCAAGGTTTTAATCCG
38712090 CTCCACTGCAACTTCAGGAAGATA
1 CTCCACTGCAACTTCAGGAAGATA
38712114 GGATTATTGG
Statistics
Matches: 153, Mismatches: 39, Indels: 10
0.76 0.19 0.05
Matches are distributed among these distances:
84 55 0.36
85 23 0.15
86 9 0.06
87 9 0.06
88 24 0.16
89 33 0.22
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.27
Consensus pattern (84 bp):
CTCCACTGCAACTTCAGGAAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAA
GATCCAAGGTTTTAATCCG
Found at i:38711922 original size:173 final size:177
Alignment explanation
Indices: 38711786--38712479 Score: 980
Period size: 177 Copynumber: 4.0 Consensus size: 177
38711776 CATCTTCAGT
* * *
38711786 CTGCTCCACTGCAACTTCAGGGAGATAAGACTTG-CTTACTT-AGTCT-ACTCCACTGCAACTTC
1 CTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCAT-CTTCAGTCTGCCT-CACTGCAACTTC
* * * * *
38711848 AGGAAGATAAGACTAG-ATGC-GA-TCTGCT-CTCTGCAACTTCAGAGAGATAAGATCCAAGGTT
64 AGGAAGATAAGACTTGCATGCTGAGTCTGCTCCACTACAACTTCAGAGAGACAAGATCCAAGATT
* * *
38711909 TTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATCGGCTTTAAT
129 TTAATCCACTCCACTGCAACTTCAGGAAGATAGGATTATCGGCTTTAAC
*
38711958 CTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTCATCTTCAGTCTG-CTCCACTGCAACTTCA
1 CTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCT-CACTGCAACTTCA
* * * * * *
38712022 GGGAGATAAGACTTG-ATGC-GA-TCTGCT-CTCTGCAACTTCAAAGAGATAAGATCCAAGGTTT
65 GGAAGATAAGACTTGCATGCTGAGTCTGCTCCACTACAACTTCAGAGAGACAAGATCCAAGATTT
*
38712083 TAATCCACTCCACTGCAACTTCAGGAAGATAGGATTATTGGCTTTAAC
130 TAATCCACTCCACTGCAACTTCAGGAAGATAGGATTATCGGCTTTAAC
* *
38712131 CTGCTCCACTGCAACTTCAGGGAGATAAGATTTTCCATCTTCAGTCTGCCTCACTGTAACTTCAG
1 CTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTCAG
* * * * *
38712196 GAGGATAAGACTTGCTTTCTTAGTCTGCTCCACTACAACTTCAGGGAGACAAGATCCAAGATTTT
66 GAAGATAAGACTTGCATGCTGAGTCTGCTCCACTACAACTTCAGAGAGACAAGATCCAAGATTTT
38712261 AATCCACTCCACTGCAACTTCAGGAAGATAGGATTATCGGCTTTAAC
131 AATCCACTCCACTGCAACTTCAGGAAGATAGGATTATCGGCTTTAAC
* *
38712308 CTGATCCACTGCAACTTCAGGGAGATAAGATTTTCCATCTTCAGTCTGCCTCACTGCAACTTCAG
1 CTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTCAG
* * * * *
38712373 GAGGATAAGACTTGCTTTCTTAGTCTGCTCCACTACAACTTCAGGGAGACAAGATCCAAGATTTT
66 GAAGATAAGACTTGCATGCTGAGTCTGCTCCACTACAACTTCAGAGAGACAAGATCCAAGATTTT
38712438 AATCCACTCCACTGCAACTTCAGGAAGATAGGATTATCGGCT
131 AATCCACTCCACTGCAACTTCAGGAAGATAGGATTATCGGCT
38712480 ACTGATCTGT
Statistics
Matches: 488, Mismatches: 26, Indels: 11
0.93 0.05 0.02
Matches are distributed among these distances:
172 36 0.07
173 196 0.40
174 4 0.01
175 1 0.00
176 6 0.01
177 245 0.50
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (177 bp):
CTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTCAG
GAAGATAAGACTTGCATGCTGAGTCTGCTCCACTACAACTTCAGAGAGACAAGATCCAAGATTTT
AATCCACTCCACTGCAACTTCAGGAAGATAGGATTATCGGCTTTAAC
Found at i:38711987 original size:217 final size:217
Alignment explanation
Indices: 38711612--38712036 Score: 778
Period size: 217 Copynumber: 2.0 Consensus size: 217
38711602 AGTGCTTCAA
* * * * *
38711612 TCTACTCCTCTGTAACTTTAGGGAGATGAGACTAGATGCGATCTGCTCTCTACAACTTCAGAGAG
1 TCTACTCCACTGCAACTTCAGGAAGATAAGACTAGATGCGATCTGCTCTCTACAACTTCAGAGAG
*
38711677 ATAAGATCCAAGGTTTTAATCCGCTCCACTGCAACTTCAGTGAGATAGGATTATCGGCTTTAATC
66 ATAAGATCCAAGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATCGGCTTTAATC
38711742 TGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCTCCACTGCAACTTCAGG
131 TGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCTCCACTGCAACTTCAGG
38711807 GAGATAAGACTTGCTTACTTAG
196 GAGATAAGACTTGCTTACTTAG
*
38711829 TCTACTCCACTGCAACTTCAGGAAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAG
1 TCTACTCCACTGCAACTTCAGGAAGATAAGACTAGATGCGATCTGCTCTCTACAACTTCAGAGAG
38711894 ATAAGATCCAAGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATCGGCTTTAATC
66 ATAAGATCCAAGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATCGGCTTTAATC
*
38711959 TGCTCCACTGCAACTTCAGGGAGATAAGATTTGTCATCTTCAGTCTGCTCCACTGCAACTTCAGG
131 TGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCTCCACTGCAACTTCAGG
38712024 GAGATAAGACTTG
196 GAGATAAGACTTG
38712037 ATGCGATCTG
Statistics
Matches: 200, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
217 200 1.00
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.28
Consensus pattern (217 bp):
TCTACTCCACTGCAACTTCAGGAAGATAAGACTAGATGCGATCTGCTCTCTACAACTTCAGAGAG
ATAAGATCCAAGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATCGGCTTTAATC
TGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCTCCACTGCAACTTCAGG
GAGATAAGACTTGCTTACTTAG
Found at i:38712101 original size:217 final size:216
Alignment explanation
Indices: 38711664--38712249 Score: 699
Period size: 217 Copynumber: 2.7 Consensus size: 216
38711654 CTGCTCTCTA
*
38711664 CAACTTCAGAGAGATAAGATCCAAGGTTTTAATCCGCTCCACTGCAACTTCAGTGAGATAGGATT
1 CAACTTCAGAGAGATAAGATCCAAGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATT
38711729 ATCGGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCTCCA
66 ATCGGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTG-CATCTTCAGTCTGCTCCA
* * *
38711794 CTGCAACTTCAGGGAGATAAGACTTGCTTACTTAGTCTACTCCACTGCAACTTCAGGAAGATAAG
130 CTGCAACTTCAGGGAGATAAGACTTGCATACTGAGTCTACTCCACTGCAACTTCAAGAAGATAAG
* * ** *
38711859 ACTAGATGCGATCTGCTCTCTG
195 ACAAGATGCAATCCACTCACTG
38711881 CAACTTCAGAGAGATAAGATCCAAGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATT
1 CAACTTCAGAGAGATAAGATCCAAGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATT
38711946 ATCGGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTCATCTTCAGTCTGCTCCA
66 ATCGGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTG-CATCTTCAGTCTGCTCCA
* * *
38712011 CTGCAACTTCAGGGAGATAAGACTTG-ATGC-GA-TCTGCT-CTCTGCAACTTCAA-AGAGATAA
130 CTGCAACTTCAGGGAGATAAGACTTGCATACTGAGTCTACTCCACTGCAACTTCAAGA-AGATAA
* **
38712071 GATCCAAGGTTTTAATCCACTCCACTG
194 GA--CAA-GATGCAATCCACT-CACTG
* * * * *
38712098 CAACTTCAG-GAAGATAGGAT-TATTGGCTTTAA-CCTGCTCCACTGCAACTTCAGGGAGATAAG
1 CAACTTCAGAG-AGATAAGATCCA-AGGTTTTAATCC-GCTCCACTGCAACTTCAGGGAGATAGG
* ** * * * * *
38712160 ATTTTCCATCTTCAGTCTGC-CTCACTGTAACTTCA-GGAGGATAAGACTTGCTTTCTT-AGTCT
63 ATTAT-CGGCTTTAATCTGCTC-CACTGCAACTTCAGGGA-GATAAGATTTGC-ATCTTCAGTCT
* *
38712222 GCTCCACTACAACTTCAGGGAGACAAGA
124 GCTCCACTGCAACTTCAGGGAGATAAGA
38712250 TCCAAGATTT
Statistics
Matches: 326, Mismatches: 31, Indels: 24
0.86 0.08 0.06
Matches are distributed among these distances:
212 1 0.00
213 20 0.06
214 5 0.02
215 3 0.01
216 13 0.04
217 248 0.76
218 36 0.11
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.28
Consensus pattern (216 bp):
CAACTTCAGAGAGATAAGATCCAAGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATT
ATCGGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCATCTTCAGTCTGCTCCAC
TGCAACTTCAGGGAGATAAGACTTGCATACTGAGTCTACTCCACTGCAACTTCAAGAAGATAAGA
CAAGATGCAATCCACTCACTG
Found at i:38735262 original size:13 final size:13
Alignment explanation
Indices: 38735233--38735266 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
38735223 AATCCTTTCA
*
38735233 AAAAAATCAAAAT
1 AAAAAATAAAAAT
38735246 -AAAAATAAAAAT
1 AAAAAATAAAAAT
38735258 AAAAAATAA
1 AAAAAATAA
38735267 GAGAAAAAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.82, C:0.03, G:0.00, T:0.15
Consensus pattern (13 bp):
AAAAAATAAAAAT
Found at i:38736161 original size:21 final size:24
Alignment explanation
Indices: 38736127--38736186 Score: 72
Period size: 23 Copynumber: 2.6 Consensus size: 24
38736117 TTCGAGTAAA
38736127 AAAAAGTAAAAAATGAAAAA-G-TG
1 AAAAAGT-AAAAATGAAAAATGATG
*
38736150 AAAAAG-AAAAATAAAAAATGATG
1 AAAAAGTAAAAATGAAAAATGATG
*
38736173 AAAGAGTAAAAATG
1 AAAAAGTAAAAATG
38736187 GAGAGGCTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
21 11 0.35
22 1 0.03
23 13 0.42
24 6 0.19
ACGTcount: A:0.70, C:0.00, G:0.17, T:0.13
Consensus pattern (24 bp):
AAAAAGTAAAAATGAAAAATGATG
Found at i:38737838 original size:129 final size:128
Alignment explanation
Indices: 38737392--38738519 Score: 1558
Period size: 129 Copynumber: 8.8 Consensus size: 128
38737382 ATCAGTGAAT
* * *
38737392 ATTATAGATCTTGTCTCCCTAAGCAGTAGCGGAACAGATCGAAGACGGCAAAT-TCTATCTTCAA
1 ATTACAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGAC-AATCT-TATCTTCAA
* * *
38737456 GAGTAAGGAAGCAGATTTAAGCCACAAGTCCTATTTCCCTGGTCAGCAATGGAATAGGTT-GGAA
64 GTGTAAGGAAGCAGATTTAAGCCACAAGTCCTATATCCCTGGTCAGCAGTGGAATAGGTTGGGAA
* * ** * *
38737520 ATTACAGATCTTGTGT-CCT-AGTAGTAGCGGAGCAGATCGAAGACGGTGAATCTTAACTTCAAA
1 ATTACAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGAC-GACAATCTTATCTTCAAG
* * * * * * *
38737583 AGTAGGGAAGTAGATTTAAGCCACAAGTCCTATCTCCCTGGCCAGTAGTGGAGTAGGTT-GGAA
65 TGTAAGGAAGCAGATTTAAGCCACAAGTCCTATATCCCTGGTCAGCAGTGGAATAGGTTGGGAA
* * * *
38737646 ATTATAGATCTTGTCTCCCTAAGCAATAGCGGAGCAAATCGAAGTC-AGCGAATCTTATCTTCAA
1 ATTACAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGA-C-AATCTTATCTTCAA
* * *
38737710 GTGTAAGGAAGCAGATTTAAGACACAAGTCATATATCCCTGGTCAGTAGTGGAATAGGTTGGGAA
64 GTGTAAGGAAGCAGATTTAAGCCACAAGTCCTATATCCCTGGTCAGCAGTGGAATAGGTTGGGAA
* * *
38737775 ATTACAGATCTTGTCTTCCTAAGCAGTAGTGGAGAAGATCGAAGACGACATATCTTATCTTCAAG
1 ATTACAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGACA-ATCTTATCTTCAAG
* * *
38737840 TGTAAGGAAGCAAATTTAAGCCACAGGTCCTATATCCCTGGTCAGTAGTGGAATAGGTTGGGAA
65 TGTAAGGAAGCAGATTTAAGCCACAAGTCCTATATCCCTGGTCAGCAGTGGAATAGGTTGGGAA
* **
38737904 ATTACAGATCTTGTCTCCCTAAGCAGTTGCGGAGCAGATCGAAGACGGTGAATCTTATCTTCAAG
1 ATTACAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGAC-GACAATCTTATCTTCAAG
* *
38737969 TGTAAGGAAGCAGATTTAAGCCACAGGTCCTATATCCCTGGTCAGCAGTGAAATAGGTTGGGAA
65 TGTAAGGAAGCAGATTTAAGCCACAAGTCCTATATCCCTGGTCAGCAGTGGAATAGGTTGGGAA
*
38738033 ATTACAGATCTTGTCTCCCTAAGCAATAGCGGAGCAGATCGAAGACGACAAATCTTATCTTCAAG
1 ATTACAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGAC-AATCTTATCTTCAAG
* * * *
38738098 AGTAAGGAAGCAGATTTAAGCCACAAGTCCTAAATCCTTGGTTAGCAGTGGAATAGGTTGGGAA
65 TGTAAGGAAGCAGATTTAAGCCACAAGTCCTATATCCCTGGTCAGCAGTGGAATAGGTTGGGAA
* *
38738162 ATTACAGATCTTGTATCCCTAAGCAGTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCAAG
1 ATTACAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGAC-AATCTTATCTTCAAG
* * *
38738227 TGTAAGGAAGAAGATTTAAGCCACAGGTCCTATATCCCTGGTCAGCAGTGGAATATGTTGGGAA
65 TGTAAGGAAGCAGATTTAAGCCACAAGTCCTATATCCCTGGTCAGCAGTGGAATAGGTTGGGAA
* * * * * *
38738291 ATTACAGATCTTGTCTCCCTAAGCAATAGCAGAGCAGATTGAGGACGGCGAATGTTATCTTCAAG
1 ATTACAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGAC-AATCTTATCTTCAAG
*
38738356 TGTAAGGAAGCAGATTTAAGCCACAAGTCCTATATCCCTGGTCAGCAGTGGAATAGGTTTGGAA
65 TGTAAGGAAGCAGATTTAAGCCACAAGTCCTATATCCCTGGTCAGCAGTGGAATAGGTTGGGAA
*
38738420 ATTACAGATCTTGTCTTCCTAAGCAGTAGCGGAGCAGATCG-A-A-GAC-AT-TTAATCTTCAAG
1 ATTACAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGACAATCTT-ATCTTCAAG
* * *
38738480 AGTAAGGAAGCAGATTTAAGCCACAAGTTCTATCTCCCTG
65 TGTAAGGAAGCAGATTTAAGCCACAAGTCCTATATCCCTG
38738520 AAGTTACAGT
Statistics
Matches: 895, Mismatches: 93, Indels: 28
0.88 0.09 0.03
Matches are distributed among these distances:
123 2 0.00
124 48 0.05
126 106 0.12
127 9 0.01
128 101 0.11
129 626 0.70
130 3 0.00
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.26
Consensus pattern (128 bp):
ATTACAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGACAATCTTATCTTCAAGT
GTAAGGAAGCAGATTTAAGCCACAAGTCCTATATCCCTGGTCAGCAGTGGAATAGGTTGGGAA
Found at i:38745648 original size:35 final size:35
Alignment explanation
Indices: 38745609--38745675 Score: 82
Period size: 35 Copynumber: 1.9 Consensus size: 35
38745599 ATGCTACCCC
* *
38745609 ATAGAGCCTACAAACCATCATCACA-GTGTTGCTCT
1 ATAGAACCTACAAACCACCATCA-AGGTGTTGCTCT
* *
38745644 ATAGAACCTATAAACTACCATCAAGGTGTTGC
1 ATAGAACCTACAAACCACCATCAAGGTGTTGC
38745676 CCTGAAGGAC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
34 1 0.04
35 26 0.96
ACGTcount: A:0.34, C:0.25, G:0.15, T:0.25
Consensus pattern (35 bp):
ATAGAACCTACAAACCACCATCAAGGTGTTGCTCT
Found at i:38750401 original size:31 final size:30
Alignment explanation
Indices: 38750308--38750432 Score: 126
Period size: 30 Copynumber: 4.1 Consensus size: 30
38750298 TTTAATTTTA
* * *
38750308 GCAAGGTACAACCATATACGAATCAATTGG
1 GCAAGGTATAACCATATACAAATCAATTCG
** *
38750338 GCAACTTATACCCATATACCAAA-CAATTCG
1 GCAAGGTATAACCATATA-CAAATCAATTCG
* *
38750368 GCAAGGTATAACCATAAACTAATCAAGTTCG
1 GCAAGGTATAACCATATACAAATCAA-TTCG
* *
38750399 GCAATGTATAATCATATACAAATCCAATTCG
1 GCAAGGTATAACCATATACAAAT-CAATTCG
38750430 GCA
1 GCA
38750433 TCCTATATTC
Statistics
Matches: 76, Mismatches: 15, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
29 3 0.04
30 37 0.49
31 33 0.43
32 3 0.04
ACGTcount: A:0.41, C:0.22, G:0.14, T:0.23
Consensus pattern (30 bp):
GCAAGGTATAACCATATACAAATCAATTCG
Found at i:38753108 original size:29 final size:29
Alignment explanation
Indices: 38753073--38753183 Score: 172
Period size: 29 Copynumber: 3.8 Consensus size: 29
38753063 AACGCAACCT
38753073 AAAGAAGTGCCTTTGTGGCTATCTCTGTA
1 AAAGAAGTGCCTTTGTGGCTATCTCTGTA
38753102 AAAGAAGTGCCTTTGTGGCTATCTCTGTA
1 AAAGAAGTGCCTTTGTGGCTATCTCTGTA
*
38753131 AAAGAAGTGCCTTTGTGGCTATCTCTATTA
1 AAAGAAGTGCCTTTGTGGCTATCTCT-GTA
*
38753161 AAAGGAA--GCCTTTGTGGCGATCT
1 AAA-GAAGTGCCTTTGTGGCTATCT
38753184 TTGTTAAATG
Statistics
Matches: 78, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
29 70 0.90
30 5 0.06
31 3 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.33
Consensus pattern (29 bp):
AAAGAAGTGCCTTTGTGGCTATCTCTGTA
Found at i:38753196 original size:29 final size:28
Alignment explanation
Indices: 38753139--38753261 Score: 106
Period size: 29 Copynumber: 4.3 Consensus size: 28
38753129 TAAAAGAAGT
*
38753139 GCCTTTGTGGCTATCTCTATTAAAAGGAA
1 GCCTTTGTGGC-ATCTCTATTAAATGGAA
* *
38753168 GCCTTTGTGGCGATCTTTGTTAAATGGAA
1 GCCTTTGTGGC-ATCTCTATTAAATGGAA
* *
38753197 GCCTTCT-AGGCAATTTCTATTAAATGGAA
1 GCCTT-TGTGGC-ATCTCTATTAAATGGAA
* * * *
38753226 GTCTTTGTGGCATTCTCTGTCAAA-GGAT
1 GCCTTTGTGGCA-TCTCTATTAAATGGAA
38753254 GCCTTTGT
1 GCCTTTGT
38753262 AACGTCCCAA
Statistics
Matches: 75, Mismatches: 16, Indels: 7
0.77 0.16 0.07
Matches are distributed among these distances:
28 12 0.16
29 62 0.83
30 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.37
Consensus pattern (28 bp):
GCCTTTGTGGCATCTCTATTAAATGGAA
Found at i:38753201 original size:58 final size:56
Alignment explanation
Indices: 38753081--38753261 Score: 163
Period size: 58 Copynumber: 3.1 Consensus size: 56
38753071 CTAAAGAAGT
* *
38753081 GCCTTTGTGGCTATCTCT-GTAAAA-GAAGTGCCTTTGTGGCTATCTCTG-TAAAAGAA
1 GCCTTTGTGGCTATCTCTATTAAAAGGAA--GCCTTTGTGGC-ATCTCTGTTAAAGGAA
*
38753137 GTGCCTTTGTGGCTATCTCTATTAAAAGGAAGCCTTTGTGGCGATCTTTGTTAAATGGAA
1 --GCCTTTGTGGCTATCTCTATTAAAAGGAAGCCTTTGTGGC-ATCTCTGTTAAA-GGAA
* * * * * * *
38753197 GCCTTCT-AGGCAATTTCTATTAAATGGAAGTCTTTGTGGCATTCTCTGTCAAAGGAT
1 GCCTT-TGTGGCTATCTCTATTAAAAGGAAGCCTTTGTGGCA-TCTCTGTTAAAGGAA
38753254 GCCTTTGT
1 GCCTTTGT
38753262 AACGTCCCAA
Statistics
Matches: 103, Mismatches: 13, Indels: 15
0.79 0.10 0.11
Matches are distributed among these distances:
56 1 0.01
57 9 0.09
58 77 0.75
59 10 0.10
60 6 0.06
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.36
Consensus pattern (56 bp):
GCCTTTGTGGCTATCTCTATTAAAAGGAAGCCTTTGTGGCATCTCTGTTAAAGGAA
Found at i:38756928 original size:34 final size:34
Alignment explanation
Indices: 38756890--38756958 Score: 120
Period size: 34 Copynumber: 2.0 Consensus size: 34
38756880 ATACAACGTA
*
38756890 AGAAGGTGGTGGAGAGGTCTCGAGAGGATCCAAC
1 AGAAGGTGGTGGAGAGGTCTAGAGAGGATCCAAC
*
38756924 AGAAGGTGGTGGAGAGGTCTAGAGAGGATCTAAC
1 AGAAGGTGGTGGAGAGGTCTAGAGAGGATCCAAC
38756958 A
1 A
38756959 CCCCAAGTGA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.32, C:0.12, G:0.41, T:0.16
Consensus pattern (34 bp):
AGAAGGTGGTGGAGAGGTCTAGAGAGGATCCAAC
Found at i:38758475 original size:23 final size:21
Alignment explanation
Indices: 38758398--38758482 Score: 71
Period size: 23 Copynumber: 3.8 Consensus size: 21
38758388 AGATAAAAGA
*
38758398 GAAACAAAGCCCTAAATTTGTG
1 GAAACAAATCCCTAAATTT-TG
*
38758420 GAATACAAATGCCTAAATTTTAG
1 GAA-ACAAATCCCTAAATTTT-G
* *
38758443 CCAAAGAAATCCCTAAAATTTTG
1 -GAAACAAATCCCT-AAATTTTG
*
38758466 GAAGACAAATGCCTAAA
1 GAA-ACAAATCCCTAAA
38758483 ACTTAGCCTA
Statistics
Matches: 50, Mismatches: 8, Indels: 10
0.74 0.12 0.15
Matches are distributed among these distances:
22 9 0.18
23 32 0.64
24 9 0.18
ACGTcount: A:0.45, C:0.18, G:0.14, T:0.24
Consensus pattern (21 bp):
GAAACAAATCCCTAAATTTTG
Found at i:38760835 original size:45 final size:45
Alignment explanation
Indices: 38760726--38760835 Score: 157
Period size: 45 Copynumber: 2.4 Consensus size: 45
38760716 ATGCTGAAAA
* * * * *
38760726 TAAGACCATAACTGAAAGACACTATGGCATCATTGTATATAGGGC
1 TAAGACCATAGCTGAAAGATACTATGACATCATTGTATACAGGAC
*
38760771 TAAGACCATGGCTGAAAGATACTATGACATCATTGTATACAGGAC
1 TAAGACCATAGCTGAAAGATACTATGACATCATTGTATACAGGAC
*
38760816 TAAGCCCATAGCTGAAAGAT
1 TAAGACCATAGCTGAAAGAT
38760836 GCTACGATAT
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 57 1.00
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.24
Consensus pattern (45 bp):
TAAGACCATAGCTGAAAGATACTATGACATCATTGTATACAGGAC
Found at i:38762654 original size:21 final size:20
Alignment explanation
Indices: 38762625--38762670 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
38762615 CAAAATGCAA
38762625 TCAACCTAACA-TGAATTAAAT
1 TCAACCTAA-ATTG-ATTAAAT
*
38762646 TCAAGCTAAATTGATTAAAT
1 TCAACCTAAATTGATTAAAT
38762666 T-AACC
1 TCAACC
38762671 ATTCCAACAA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 3 0.14
20 9 0.41
21 10 0.45
ACGTcount: A:0.46, C:0.17, G:0.07, T:0.30
Consensus pattern (20 bp):
TCAACCTAAATTGATTAAAT
Found at i:38776327 original size:50 final size:50
Alignment explanation
Indices: 38776264--38776387 Score: 151
Period size: 50 Copynumber: 2.5 Consensus size: 50
38776254 CAATGTCATA
* ** * *
38776264 TCCCAGATATGGTCTTACATGGGAGTTCTCATAT-AGGTGCCCATACCATG
1 TCCCAGACATGGTCTTACATGGGACCTCTCATATCA-GTGCCAACACCATG
** * *
38776314 TCCCAGACATGGTCTTACGGGGGACCTCTCATCTCAGTGCCAACGCCATG
1 TCCCAGACATGGTCTTACATGGGACCTCTCATATCAGTGCCAACACCATG
38776364 TCCCAGACATGGTCTTACATGGGA
1 TCCCAGACATGGTCTTACATGGGA
38776388 TCTCATCCTC
Statistics
Matches: 62, Mismatches: 11, Indels: 2
0.83 0.15 0.03
Matches are distributed among these distances:
50 61 0.98
51 1 0.02
ACGTcount: A:0.23, C:0.28, G:0.23, T:0.26
Consensus pattern (50 bp):
TCCCAGACATGGTCTTACATGGGACCTCTCATATCAGTGCCAACACCATG
Found at i:38778852 original size:22 final size:22
Alignment explanation
Indices: 38778810--38778853 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
38778800 CCTAGAATTA
*
38778810 ATTAAACTGTAGCTCTGATACC
1 ATTAAACTGTAACTCTGATACC
*
38778832 ATTAAA-TGTAACATCTTATACC
1 ATTAAACTGTAAC-TCTGATACC
38778854 CAGACCGACC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.36, C:0.20, G:0.09, T:0.34
Consensus pattern (22 bp):
ATTAAACTGTAACTCTGATACC
Found at i:38782359 original size:65 final size:65
Alignment explanation
Indices: 38782255--38782386 Score: 255
Period size: 65 Copynumber: 2.0 Consensus size: 65
38782245 ATTGTTTCGT
38782255 AAACAATTCAGAGCAAAAAAGCTGACCCTAATTCAAAATCCCTAGTACCTTAATTTTTTAGCCTA
1 AAACAATTCAGAGCAAAAAAGCTGACCCTAATTCAAAATCCCTAGTACCTTAATTTTTTAGCCTA
*
38782320 AAACAATTCAGAGCAAAAAAGCTGACCCTAATTTAAAATCCCTAGTACCTTAATTTTTTAGCCTA
1 AAACAATTCAGAGCAAAAAAGCTGACCCTAATTCAAAATCCCTAGTACCTTAATTTTTTAGCCTA
38782385 AA
1 AA
38782387 TCCCTAATTC
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
65 66 1.00
ACGTcount: A:0.41, C:0.22, G:0.09, T:0.28
Consensus pattern (65 bp):
AAACAATTCAGAGCAAAAAAGCTGACCCTAATTCAAAATCCCTAGTACCTTAATTTTTTAGCCTA
Found at i:38789714 original size:14 final size:15
Alignment explanation
Indices: 38789695--38789726 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
38789685 CAAGCATTAA
38789695 AAAAGAAAGAAA-AG
1 AAAAGAAAGAAATAG
38789709 AAAAGAAAGAAATAG
1 AAAAGAAAGAAATAG
38789724 AAA
1 AAA
38789727 GGGAGACACA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.78, C:0.00, G:0.19, T:0.03
Consensus pattern (15 bp):
AAAAGAAAGAAATAG
Found at i:38796867 original size:22 final size:21
Alignment explanation
Indices: 38796833--38796875 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 21
38796823 TAATTTTTTT
38796833 AATTTAAAAAATATCAAAAAATA
1 AATTTAAAAAATA--AAAAAATA
38796856 AATTT-AAAAATAAAAAAATA
1 AATTTAAAAAATAAAAAAATA
38796876 TCTAAAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 8 0.40
22 7 0.35
23 5 0.25
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (21 bp):
AATTTAAAAAATAAAAAAATA
Found at i:38796874 original size:30 final size:31
Alignment explanation
Indices: 38796833--38796914 Score: 91
Period size: 30 Copynumber: 2.7 Consensus size: 31
38796823 TAATTTTTTT
*
38796833 AATTTAAAAAATATCAAAAAATAAATTTAAA
1 AATTAAAAAAATATCAAAAAATAAATTTAAA
* *
38796864 AA-TAAAAAAATATC-TAAAAT-TATTTAAA
1 AATTAAAAAAATATCAAAAAATAAATTTAAA
*
38796892 AATTACAAAAATGAT-AAAAAATA
1 AATTAAAAAAAT-ATCAAAAAATA
38796915 TTTTTAATAT
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
28 9 0.21
29 13 0.31
30 18 0.43
31 2 0.05
ACGTcount: A:0.67, C:0.04, G:0.01, T:0.28
Consensus pattern (31 bp):
AATTAAAAAAATATCAAAAAATAAATTTAAA
Found at i:38796916 original size:29 final size:28
Alignment explanation
Indices: 38796838--38796917 Score: 90
Period size: 29 Copynumber: 2.8 Consensus size: 28
38796828 TTTTTAATTT
38796838 AAAAAATATCAAAAAATAAATTTAAAAATA
1 AAAAAATATCAAAAAAT--ATTTAAAAATA
* *
38796868 AAAAAATATCTAAAATTATTTAAAAATTA
1 AAAAAATATCAAAAAATATTTAAAAA-TA
*
38796897 CAAAAATGAT-AAAAAATATTT
1 AAAAAAT-ATCAAAAAATATTT
38796918 TTAATATTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
28 9 0.21
29 17 0.40
30 17 0.40
ACGTcount: A:0.66, C:0.04, G:0.01, T:0.29
Consensus pattern (28 bp):
AAAAAATATCAAAAAATATTTAAAAATA
Found at i:38805319 original size:6 final size:6
Alignment explanation
Indices: 38805310--38805337 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
38805300 TAGCCTATTA
38805310 CAGTAT CAGTAT CAGTAT CAGTAT CAGT
1 CAGTAT CAGTAT CAGTAT CAGTAT CAGT
38805338 GTGGGCCTTA
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:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (6 bp):
CAGTAT
Found at i:38808514 original size:27 final size:27
Alignment explanation
Indices: 38808462--38808521 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
38808452 CTAGAAAAAA
* **
38808462 GAAGCCTTTGTGGTGATCTATGAAATG
1 GAAGCCTGTGTGGTGATCTACAAAATG
38808489 GAAGCCTGTGTGGTGGATC-ACAAAATG
1 GAAGCCTGTGTGGT-GATCTACAAAATG
*
38808516 AAAGCC
1 GAAGCC
38808522 CTTGTGGCAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 24 0.86
28 4 0.14
ACGTcount: A:0.30, C:0.15, G:0.30, T:0.25
Consensus pattern (27 bp):
GAAGCCTGTGTGGTGATCTACAAAATG
Found at i:38810263 original size:19 final size:19
Alignment explanation
Indices: 38810241--38810288 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
38810231 AATTTTCTAT
38810241 ATTTTAAAAAAAATTTGGA
1 ATTTTAAAAAAAATTTGGA
* * * *
38810260 ATTTTTACAAATATTTTGA
1 ATTTTAAAAAAAATTTGGA
38810279 ATTTTAAAAA
1 ATTTTAAAAA
38810289 TTATTTTGAA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.48, C:0.02, G:0.06, T:0.44
Consensus pattern (19 bp):
ATTTTAAAAAAAATTTGGA
Found at i:38810310 original size:20 final size:19
Alignment explanation
Indices: 38810241--38810313 Score: 76
Period size: 20 Copynumber: 3.8 Consensus size: 19
38810231 AATTTTCTAT
** *
38810241 ATTTTAAAAAAAATTTGGA
1 ATTTTAAAAATTATTTTGA
*
38810260 ATTTTTACAAA-TATTTTGA
1 A-TTTTAAAAATTATTTTGA
38810279 ATTTTAAAAATTATTTTGA
1 ATTTTAAAAATTATTTTGA
*
38810298 ATATTTGAAAATTATT
1 AT-TTTAAAAATTATT
38810314 GTAAATTATT
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
18 8 0.17
19 18 0.39
20 20 0.43
ACGTcount: A:0.44, C:0.01, G:0.07, T:0.48
Consensus pattern (19 bp):
ATTTTAAAAATTATTTTGA
Found at i:38819433 original size:2 final size:2
Alignment explanation
Indices: 38819416--38819452 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
38819406 AAATTCTTAA
*
38819416 AT AT AA AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
38819453 TTCTATATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:38820049 original size:19 final size:19
Alignment explanation
Indices: 38820006--38820051 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
38819996 CATTTAAATT
*
38820006 AAAATTAAATTAAAATATT
1 AAAATTAAATTAAAATATA
* **
38820025 AGAATTAAATTAACTTATA
1 AAAATTAAATTAAAATATA
38820044 AAAATTAA
1 AAAATTAA
38820052 TTTTAATTTA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (19 bp):
AAAATTAAATTAAAATATA
Found at i:38820050 original size:25 final size:25
Alignment explanation
Indices: 38820002--38820050 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
38819992 GACACATTTA
*
38820002 AATTAAAATTAAATTAAAATATTAG
1 AATTAAAATTAAATTAAAAAATTAG
*
38820027 AATT-AAATTAACTTATAAAAATTA
1 AATTAAAATTAAATTA-AAAAATTA
38820051 ATTTTAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 10 0.48
25 11 0.52
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (25 bp):
AATTAAAATTAAATTAAAAAATTAG
Found at i:38829399 original size:17 final size:17
Alignment explanation
Indices: 38829377--38829419 Score: 70
Period size: 17 Copynumber: 2.5 Consensus size: 17
38829367 AATTTATAGC
38829377 TAAATATATATTA-ATAA
1 TAAATATA-ATTATATAA
38829394 TAAATATAATTATATAA
1 TAAATATAATTATATAA
38829411 TAAATATAA
1 TAAATATAA
38829420 ATTTAATTCC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
16 4 0.16
17 21 0.84
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
TAAATATAATTATATAA
Found at i:38838883 original size:50 final size:50
Alignment explanation
Indices: 38838641--38838883 Score: 267
Period size: 50 Copynumber: 4.9 Consensus size: 50
38838631 TGATAATAAC
* * * **
38838641 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA--TGTTTTCTAT
1 ATGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTTATCTCG
* * * * ** * *
38838689 ACTGTCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCG
1 A-TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTTATCTCG
* * * *
38838740 GTGCCCATGCCATGTCCCAGACATGGTCTTACGA-GGGACCTCTCATCTCG
1 ATGCCAACGCCATGTCCCAGACATGGTCTTAC-ATGGGACCTCTTATCTCG
* *
38838790 GTGCCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTTATCTCG
1 ATGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTTATCTCG
*
38838840 ATGCCAACGCCATGTCCTAGACATGGTCTTACATGGGACCTCTT
1 ATGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTT
38838884 TACCCAAATG
Statistics
Matches: 165, Mismatches: 25, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
48 1 0.01
49 34 0.21
50 125 0.76
51 5 0.03
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.28
Consensus pattern (50 bp):
ATGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTTATCTCG
Found at i:38844322 original size:27 final size:27
Alignment explanation
Indices: 38844292--38844478 Score: 243
Period size: 27 Copynumber: 7.0 Consensus size: 27
38844282 CTACATTAAC
**
38844292 CGAAATACCCTTATAGGGTAAAATGAT
1 CGAAATACCCCCATAGGGTAAAATGAT
*
38844319 CGAAATACCCTCATAGGGTAAAATGAT
1 CGAAATACCCCCATAGGGTAAAATGAT
** *
38844346 CGAAATACCCTTATA-GGTAAAATGAC
1 CGAAATACCCCCATAGGGTAAAATGAT
* *
38844372 CGAAATACCCCCATAAGGTAGAATGA-
1 CGAAATACCCCCATAGGGTAAAATGAT
*
38844398 CTGAAATACCCCCATAGGGTACAATGAT
1 C-GAAATACCCCCATAGGGTAAAATGAT
* *
38844426 TGAAATACCCCCATAGGGTAAAATGAA
1 CGAAATACCCCCATAGGGTAAAATGAT
*
38844453 CGAAATACCACCATAGGGTAAAATGA
1 CGAAATACCCCCATAGGGTAAAATGA
38844479 CTGTTATACC
Statistics
Matches: 144, Mismatches: 13, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
26 24 0.17
27 120 0.83
ACGTcount: A:0.42, C:0.20, G:0.18, T:0.20
Consensus pattern (27 bp):
CGAAATACCCCCATAGGGTAAAATGAT
Found at i:38844424 original size:80 final size:81
Alignment explanation
Indices: 38844290--38844481 Score: 262
Period size: 80 Copynumber: 2.4 Consensus size: 81
38844280 CTCTACATTA
** *
38844290 ACCGAAATACCCTTATAGGGTAAAATGA-TCGAAATACCCTCATAGGGTAAAATGATCGAAATAC
1 ACCGAAATACCCCCATAGGGTAAAATGACT-GAAATACCCCCATAGGGTAAAATGATCGAAATAC
**
38844354 CCTTATA-GGTAAAATG
65 CCCCATAGGGTAAAATG
* * * *
38844370 ACCGAAATACCCCCATAAGGTAGAATGACTGAAATACCCCCATAGGGTACAATGATTGAAATACC
1 ACCGAAATACCCCCATAGGGTAAAATGACTGAAATACCCCCATAGGGTAAAATGATCGAAATACC
38844435 CCCATAGGGTAAAATG
66 CCCATAGGGTAAAATG
* *
38844451 AACGAAATACCACCATAGGGTAAAATGACTG
1 ACCGAAATACCCCCATAGGGTAAAATGACTG
38844482 TTATACCCTT
Statistics
Matches: 97, Mismatches: 13, Indels: 3
0.86 0.12 0.03
Matches are distributed among these distances:
80 60 0.62
81 37 0.38
ACGTcount: A:0.41, C:0.20, G:0.18, T:0.20
Consensus pattern (81 bp):
ACCGAAATACCCCCATAGGGTAAAATGACTGAAATACCCCCATAGGGTAAAATGATCGAAATACC
CCCATAGGGTAAAATG
Found at i:38845888 original size:27 final size:27
Alignment explanation
Indices: 38845846--38846032 Score: 216
Period size: 27 Copynumber: 7.0 Consensus size: 27
38845836 CTACATTAAC
** *
38845846 CGAAATACCCTTATAGGGTAAAACGAT
1 CGAAATACCCCCATAGGGTAAAATGAT
*
38845873 CGAAATACCCTCATAGGGTAAAATGAT
1 CGAAATACCCCCATAGGGTAAAATGAT
** *
38845900 CGAAATACCCTTATA-GGTAAAATGAC
1 CGAAATACCCCCATAGGGTAAAATGAT
*** *
38845926 CGAAATACCCCCATAAAATAGAATGA-
1 CGAAATACCCCCATAGGGTAAAATGAT
38845952 CTGAAATACCCCCATAGGGTAAAATGAT
1 C-GAAATACCCCCATAGGGTAAAATGAT
* * *
38845980 TGAAATACCCCCATAGGGTAAAAGGAA
1 CGAAATACCCCCATAGGGTAAAATGAT
*
38846007 CGAAATACCACCATAGGGTAAAATGA
1 CGAAATACCCCCATAGGGTAAAATGA
38846033 CTGTTATACC
Statistics
Matches: 138, Mismatches: 19, Indels: 6
0.85 0.12 0.04
Matches are distributed among these distances:
26 24 0.17
27 114 0.83
ACGTcount: A:0.43, C:0.20, G:0.18, T:0.19
Consensus pattern (27 bp):
CGAAATACCCCCATAGGGTAAAATGAT
Found at i:38846043 original size:81 final size:80
Alignment explanation
Indices: 38845874--38846035 Score: 216
Period size: 80 Copynumber: 2.0 Consensus size: 80
38845864 TAAAACGATC
* ** * * *
38845874 GAAATACCCTCATAGGGTAAAATGATCGAAATACCCTTATAGGTAAAATGACCGAAATACCCCCA
1 GAAATACCCCCATAGGGTAAAATGATCGAAATACCCCCATAGGTAAAAGGAACGAAATACCACCA
*
38845939 TAAAATAGAATGACT
66 TAAAATAAAATGACT
*
38845954 GAAATACCCCCATAGGGTAAAATGATTGAAATACCCCCATAGGGTAAAAGGAACGAAATACCACC
1 GAAATACCCCCATAGGGTAAAATGATCGAAATACCCCCATA-GGTAAAAGGAACGAAATACCACC
***
38846019 ATAGGGTAAAATGACT
65 ATAAAATAAAATGACT
38846035 G
1 G
38846036 TTATACCCTT
Statistics
Matches: 70, Mismatches: 11, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
80 37 0.53
81 33 0.47
ACGTcount: A:0.43, C:0.20, G:0.18, T:0.19
Consensus pattern (80 bp):
GAAATACCCCCATAGGGTAAAATGATCGAAATACCCCCATAGGTAAAAGGAACGAAATACCACCA
TAAAATAAAATGACT
Found at i:38847351 original size:27 final size:27
Alignment explanation
Indices: 38847321--38847505 Score: 241
Period size: 27 Copynumber: 6.9 Consensus size: 27
38847311 ACATTAACCA
**
38847321 AAATACCCTTATAGGGTAAAATGATCG
1 AAATACCCCCATAGGGTAAAATGATCG
*
38847348 AAATACCCTCATAGGGTAAAATGATCG
1 AAATACCCCCATAGGGTAAAATGATCG
**
38847375 AAATACCCTTATA-GGTAAAATGA-CTG
1 AAATACCCCCATAGGGTAAAATGATC-G
* *
38847401 AAATACCCCCATAAGGTAGAATGA-CTG
1 AAATACCCCCATAGGGTAAAATGATC-G
*
38847428 AAATACCCCCATAGGGTAAAATGATTG
1 AAATACCCCCATAGGGTAAAATGATCG
*
38847455 AAATACCCCCATAGGGTAAAATGAACG
1 AAATACCCCCATAGGGTAAAATGATCG
*
38847482 AAATACCACCATAGGGTAAAATGA
1 AAATACCCCCATAGGGTAAAATGA
38847506 CTGTTATACC
Statistics
Matches: 144, Mismatches: 11, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
25 1 0.01
26 22 0.15
27 121 0.84
ACGTcount: A:0.43, C:0.18, G:0.18, T:0.21
Consensus pattern (27 bp):
AAATACCCCCATAGGGTAAAATGATCG
Found at i:38847532 original size:81 final size:79
Alignment explanation
Indices: 38847335--38847508 Score: 235
Period size: 80 Copynumber: 2.2 Consensus size: 79
38847325 ACCCTTATAG
**
38847335 GGTAAAATGA-TCGAAATACCCTCATAGGGTAAAATGATCGAAATACCCTTATAGGTAAAATGAC
1 GGTAAAATGACT-GAAATACCC-CATAGGGTAAAATGATCGAAATACCCCCATAGGTAAAATGAC
*
38847399 TGAAATACCCCCATAA
64 TGAAATACCACCATAA
* *
38847415 GGTAGAATGACTGAAATACCCCCATAGGGTAAAATGATTGAAATACCCCCATAGGGTAAAATGAA
1 GGTAAAATGACTGAAATA-CCCCATAGGGTAAAATGATCGAAATACCCCCATA-GGTAAAATG-A
*
38847480 C-GAAATACCACCATAG
63 CTGAAATACCACCATAA
38847496 GGTAAAATGACTG
1 GGTAAAATGACTG
38847509 TTATACCCTT
Statistics
Matches: 83, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
80 43 0.52
81 38 0.46
82 2 0.02
ACGTcount: A:0.42, C:0.18, G:0.19, T:0.21
Consensus pattern (79 bp):
GGTAAAATGACTGAAATACCCCATAGGGTAAAATGATCGAAATACCCCCATAGGTAAAATGACTG
AAATACCACCATAA
Found at i:38852434 original size:69 final size:69
Alignment explanation
Indices: 38852353--38852490 Score: 267
Period size: 69 Copynumber: 2.0 Consensus size: 69
38852343 TATTCCAACT
38852353 TACATAGAAGTCTAACATTGAACCACCTACAACTCACACATGTACTGGAATGCGCCTATCATGAG
1 TACATAGAAGTCTAACATTGAACCACCTACAACTCACACATGTACTGGAATGCGCCTATCATGAG
38852418 TGCC
66 TGCC
*
38852422 TACATAGAAGTCTGACATTGAACCACCTACAACTCACACATGTACTGGAATGCGCCTATCATGAG
1 TACATAGAAGTCTAACATTGAACCACCTACAACTCACACATGTACTGGAATGCGCCTATCATGAG
38852487 TGCC
66 TGCC
38852491 AAAAGAAATA
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
69 68 1.00
ACGTcount: A:0.33, C:0.28, G:0.17, T:0.23
Consensus pattern (69 bp):
TACATAGAAGTCTAACATTGAACCACCTACAACTCACACATGTACTGGAATGCGCCTATCATGAG
TGCC
Found at i:38866356 original size:13 final size:12
Alignment explanation
Indices: 38866324--38866357 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
38866314 GTTTCATATG
38866324 CATAAT-ATAAA
1 CATAATCATAAA
38866335 CATAATCATAAA
1 CATAATCATAAA
38866347 CATCAATCATA
1 CAT-AATCATA
38866358 TCCAAAAGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 6 0.29
12 8 0.38
13 7 0.33
ACGTcount: A:0.56, C:0.18, G:0.00, T:0.26
Consensus pattern (12 bp):
CATAATCATAAA
Found at i:38866673 original size:41 final size:41
Alignment explanation
Indices: 38866627--38866709 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
38866617 CAAGTTAGTG
38866627 ATTAAACACATAACCTAGCAAAAATCACCACATGATAAACT
1 ATTAAACACATAACCTAGCAAAAATCACCACATGATAAACT
38866668 ATTAAACACATAACCTAGCAAAAATCACCACATGATAAACT
1 ATTAAACACATAACCTAGCAAAAATCACCACATGATAAACT
38866709 A
1 A
38866710 ACTTTCATGA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.52, C:0.24, G:0.05, T:0.19
Consensus pattern (41 bp):
ATTAAACACATAACCTAGCAAAAATCACCACATGATAAACT
Found at i:38870250 original size:21 final size:21
Alignment explanation
Indices: 38870224--38870286 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
38870214 TTGGTATTTG
38870224 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
*
38870245 GGAATTGGTATGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
38870266 GGTATTTGGTACGAATTGGTA
1 GG-AATTGGTACGAAATGGTA
38870287 ATGGTTCAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 22 0.59
22 15 0.41
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.33
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:38871399 original size:9 final size:10
Alignment explanation
Indices: 38871366--38871401 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
38871356 TTTGCAAGTT
38871366 TTGAGCTAAA
1 TTGAGCTAAA
38871376 TTGAGCTAAA
1 TTGAGCTAAA
*
38871386 TTGAGCT-CA
1 TTGAGCTAAA
38871395 TTGAGCT
1 TTGAGCT
38871402 TGAAAGGAGC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
9 8 0.32
10 17 0.68
ACGTcount: A:0.31, C:0.14, G:0.22, T:0.33
Consensus pattern (10 bp):
TTGAGCTAAA
Found at i:38874382 original size:17 final size:16
Alignment explanation
Indices: 38874360--38874393 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
38874350 GAGGATGACA
38874360 TTTGTTTGATGTTTATT
1 TTTGTTTG-TGTTTATT
*
38874377 TTTGTTTGTTTTTATT
1 TTTGTTTGTGTTTATT
38874393 T
1 T
38874394 CATAATATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.09, C:0.00, G:0.15, T:0.76
Consensus pattern (16 bp):
TTTGTTTGTGTTTATT
Found at i:38880354 original size:18 final size:20
Alignment explanation
Indices: 38880331--38880370 Score: 66
Period size: 18 Copynumber: 2.1 Consensus size: 20
38880321 ACTTGTTATG
38880331 TTAATATGT-TT-AATTTAA
1 TTAATATGTCTTAAATTTAA
38880349 TTAATATGTCTTAAATTTAA
1 TTAATATGTCTTAAATTTAA
38880369 TT
1 TT
38880371 CGTGTTAGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 9 0.45
19 2 0.10
20 9 0.45
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.55
Consensus pattern (20 bp):
TTAATATGTCTTAAATTTAA
Found at i:38892298 original size:19 final size:20
Alignment explanation
Indices: 38892261--38892298 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
38892251 AAGAGAAAGG
38892261 GAAAATGTGAATAAATATAT
1 GAAAATGTGAATAAATATAT
38892281 GAAAATGTGAAT-AATATA
1 GAAAATGTGAATAAATATA
38892299 CTTTATGGGC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.55, C:0.00, G:0.16, T:0.29
Consensus pattern (20 bp):
GAAAATGTGAATAAATATAT
Found at i:38892704 original size:21 final size:23
Alignment explanation
Indices: 38892680--38892730 Score: 63
Period size: 21 Copynumber: 2.3 Consensus size: 23
38892670 ATTGTTTGTA
38892680 TTTAAGTACATTTT-GTTA-CAT
1 TTTAAGTACATTTTAGTTAGCAT
*
38892701 TTTATG-ACATTTTAGTTAGCAT
1 TTTAAGTACATTTTAGTTAGCAT
*
38892723 TTTTAGTA
1 TTTAAGTA
38892731 TTGCATTAGG
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
20 7 0.29
21 9 0.38
22 7 0.29
23 1 0.04
ACGTcount: A:0.27, C:0.08, G:0.12, T:0.53
Consensus pattern (23 bp):
TTTAAGTACATTTTAGTTAGCAT
Found at i:38900199 original size:30 final size:30
Alignment explanation
Indices: 38900165--38900259 Score: 163
Period size: 30 Copynumber: 3.2 Consensus size: 30
38900155 GTCTCAGCCC
*
38900165 TGTGAGGCACATGGCCTGACCACACTGTCG
1 TGTGAGGCACATGGCCTGACCACACTGCCG
38900195 TGTGAGGCACATGGCCTGACCACACTGCCG
1 TGTGAGGCACATGGCCTGACCACACTGCCG
**
38900225 TGTGAGGCACACAGCCTGACCACACTGCCG
1 TGTGAGGCACATGGCCTGACCACACTGCCG
38900255 TGTGA
1 TGTGA
38900260 CCCCTGATAG
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 62 1.00
ACGTcount: A:0.21, C:0.32, G:0.29, T:0.18
Consensus pattern (30 bp):
TGTGAGGCACATGGCCTGACCACACTGCCG
Found at i:38904449 original size:8 final size:8
Alignment explanation
Indices: 38904438--38904462 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
38904428 TAAACTAAGT
38904438 AAATAAAA
1 AAATAAAA
38904446 AAATAAAA
1 AAATAAAA
38904454 AAATAAAA
1 AAATAAAA
38904462 A
1 A
38904463 TAAAAATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (8 bp):
AAATAAAA
Found at i:38905987 original size:6 final size:6
Alignment explanation
Indices: 38905969--38905999 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
38905959 AAGCATGTTA
*
38905969 TATCTG TACCTG TATCTG TATCTG TATCTG T
1 TATCTG TATCTG TATCTG TATCTG TATCTG T
38906000 TTTTGGGGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.16, C:0.19, G:0.16, T:0.48
Consensus pattern (6 bp):
TATCTG
Found at i:38926132 original size:20 final size:19
Alignment explanation
Indices: 38926107--38926146 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
38926097 TAAGAGCCAA
38926107 AATTATATGATATTTAGAAT
1 AATTATATGAT-TTTAGAAT
*
38926127 AATTATATGATTTTATAAT
1 AATTATATGATTTTAGAAT
38926146 A
1 A
38926147 TTAAATTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.47
Consensus pattern (19 bp):
AATTATATGATTTTAGAAT
Found at i:38929965 original size:27 final size:25
Alignment explanation
Indices: 38929935--38930000 Score: 78
Period size: 25 Copynumber: 2.6 Consensus size: 25
38929925 TCCGACCCAT
38929935 AGCTCGTGTGAGCAGGCCCATTTTCAC
1 AGCTCGTGTGAGCAGGCCCA-TTT-AC
** **
38929962 AGCTCGTGTGAGCATTCTGATTTAC
1 AGCTCGTGTGAGCAGGCCCATTTAC
38929987 AGCTCGTGTGAGCA
1 AGCTCGTGTGAGCA
38930001 TACATGTACA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
25 16 0.46
26 3 0.09
27 16 0.46
ACGTcount: A:0.20, C:0.24, G:0.27, T:0.29
Consensus pattern (25 bp):
AGCTCGTGTGAGCAGGCCCATTTAC
Found at i:38932391 original size:20 final size:20
Alignment explanation
Indices: 38932355--38932392 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
38932345 GTATTCCAAC
*
38932355 CGAGACTGCTATCTGTAAAT
1 CGAGACTGCCATCTGTAAAT
*
38932375 CGAGACTGCCATGTGTAA
1 CGAGACTGCCATCTGTAA
38932393 GAGGTTCGAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (20 bp):
CGAGACTGCCATCTGTAAAT
Found at i:38942686 original size:34 final size:34
Alignment explanation
Indices: 38942627--38942691 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 34
38942617 AGTTCAGTTC
* *
38942627 GGCCTTAGCCCATTACGGTATCAGTATCAGTGTG
1 GGCCTTAGCCCATTACAGTATCAGTAACAGTGTG
38942661 GGCCTTAGCCCATTACAGTGA-CAGTAACAGT
1 GGCCTTAGCCCATTACAGT-ATCAGTAACAGT
38942692 TCGGACATGC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 27 0.96
35 1 0.04
ACGTcount: A:0.25, C:0.25, G:0.25, T:0.26
Consensus pattern (34 bp):
GGCCTTAGCCCATTACAGTATCAGTAACAGTGTG
Found at i:38942982 original size:25 final size:27
Alignment explanation
Indices: 38942949--38943001 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
38942939 TACAGTCATA
38942949 ATAACATAA-AGCAT-ACAATCATTTT
1 ATAACATAAGAGCATAACAATCATTTT
* *
38942974 ATAACATAAGGGCATAACAGTCATTTT
1 ATAACATAAGAGCATAACAATCATTTT
38943001 A
1 A
38943002 CCACGTGAGG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 9 0.38
26 4 0.17
27 11 0.46
ACGTcount: A:0.45, C:0.15, G:0.09, T:0.30
Consensus pattern (27 bp):
ATAACATAAGAGCATAACAATCATTTT
Found at i:38949252 original size:58 final size:57
Alignment explanation
Indices: 38949134--38949482 Score: 213
Period size: 58 Copynumber: 6.0 Consensus size: 57
38949124 TTCTGTCACG
* * * * * * * *
38949134 AAGGCATCATTTTAACATAGTTTGCAA-TAAGGCATTCCTTTAATAGAGATGGCCAAA
1 AAGGCATCTTTTTAACAGAGATAGCAACAAAGG-ATTCTTTTAATAGAGATAGCCACA
*
38949191 AAGGCATCTTTTTAACAGAGATAGCAACAAAGGAATTCTTTTAATAGAGATAGCCATA
1 AAGGCATCTTTTTAACAGAGATAGCAACAAAGG-ATTCTTTTAATAGAGATAGCCACA
* * * * * * ** * *
38949249 AAGGCCTCCTTTGAATAGAGGTGGCCTCAAAGGCATTCTTTTAACAGAGATAGCCATA
1 AAGGCATCTTTTTAACAGAGATAGCAACAAAGG-ATTCTTTTAATAGAGATAGCCACA
* * * ** * * * *
38949307 AAGACAT-TCTTTTAACAAAGATAGCCACAAAGGATTCCTAATAACAAAGTTCGCCACA
1 AAGGCATCT-TTTTAACAGAGATAGCAACAAAGGATT-CTTTTAATAGAGATAGCCACA
* * * * * * * *
38949365 AAGGCTTCTTTATAACAGAGTTCGCCACAGAGGCTTTTTTATAATAGAGATCA-CCACA
1 AAGGCATCTTTTTAACAGAGATAGCAACAAAGGATTCTTT-TAATAGAGAT-AGCCACA
* * * *
38949423 AAGGC-TCTTTTATAACAGAGATCA-CAAAAAAGGATTTCTTATAGTAGAGATTGCCACA
1 AAGGCATCTTTT-TAACAGAGAT-AGCAACAAAGGA-TTCTTTTAATAGAGATAGCCACA
38949481 AA
1 AA
38949483 CGCTTCCTTT
Statistics
Matches: 222, Mismatches: 60, Indels: 19
0.74 0.20 0.06
Matches are distributed among these distances:
57 32 0.14
58 185 0.83
59 5 0.02
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.27
Consensus pattern (57 bp):
AAGGCATCTTTTTAACAGAGATAGCAACAAAGGATTCTTTTAATAGAGATAGCCACA
Found at i:38949274 original size:87 final size:86
Alignment explanation
Indices: 38949169--38949339 Score: 229
Period size: 87 Copynumber: 2.0 Consensus size: 86
38949159 AATAAGGCAT
38949169 TCCTTTAATAGAGATGGCCAAAAAGGCA-TCTTTTTAACAGAGATAGCAACAAAGGA-ATTCTTT
1 TCCTTTAATAGAGATGGCCAAAAAGGCATTC-TTTTAACAGAGATAGCAACAAA-GACATTCTTT
* * *
38949232 TAATAGAGATAGCCATAAAGGCC
64 TAACAAAGATAGCCACAAAGGCC
* ** * *
38949255 TCCTTTGAATAGAGGTGGCCTCAAAGGCATTCTTTTAACAGAGATAGCCATAAAGACATTCTTTT
1 TCCTTT-AATAGAGATGGCCAAAAAGGCATTCTTTTAACAGAGATAGCAACAAAGACATTCTTTT
38949320 AACAAAGATAGCCACAAAGG
65 AACAAAGATAGCCACAAAGG
38949340 ATTCCTAATA
Statistics
Matches: 74, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
86 8 0.11
87 64 0.86
88 2 0.03
ACGTcount: A:0.38, C:0.18, G:0.19, T:0.26
Consensus pattern (86 bp):
TCCTTTAATAGAGATGGCCAAAAAGGCATTCTTTTAACAGAGATAGCAACAAAGACATTCTTTTA
ACAAAGATAGCCACAAAGGCC
Found at i:38949367 original size:87 final size:87
Alignment explanation
Indices: 38949185--38949384 Score: 210
Period size: 87 Copynumber: 2.3 Consensus size: 87
38949175 AATAGAGATG
* * * *
38949185 GCCAAAAAGGCA-TCTTTTTAACAGAGATAGCAACAAAGGAATTCTTTTAATAGAGATAGCCATA
1 GCCACAAAGGCATTC-TTTTAACAGAGATAGCAACAAAGGAATTCTTTTAACAAAGATAGCCACA
* * * * *
38949249 AAGGCCTCCTTTGAATAGAGGTG
65 AAGGACTCCTATGAACAAAGGTC
* * *
38949272 GCCTCAAAGGCATTCTTTTAACAGAGATAGCCATAAA-GACATTCTTTTAACAAAGATAGCCACA
1 GCCACAAAGGCATTCTTTTAACAGAGATAGCAACAAAGGA-ATTCTTTTAACAAAGATAGCCACA
* *
38949336 AAGGATTCCTAAT-AACAAAGTTC
65 AAGGACTCCT-ATGAACAAAGGTC
38949359 GCCACAAAGGC-TTCTTTATAACAGAG
1 GCCACAAAGGCATTCTTT-TAACAGAG
38949385 TTCGCCACAG
Statistics
Matches: 94, Mismatches: 15, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
86 8 0.09
87 83 0.88
88 3 0.03
ACGTcount: A:0.39, C:0.19, G:0.17, T:0.25
Consensus pattern (87 bp):
GCCACAAAGGCATTCTTTTAACAGAGATAGCAACAAAGGAATTCTTTTAACAAAGATAGCCACAA
AGGACTCCTATGAACAAAGGTC
Found at i:38949386 original size:29 final size:29
Alignment explanation
Indices: 38949178--38949445 Score: 177
Period size: 29 Copynumber: 9.2 Consensus size: 29
38949168 TTCCTTTAAT
* * * *
38949178 AGAGATGGCCAAAAAGGCATCTTTTTAAC
1 AGAGATCGCCACAAAGGCTTCTTTATAAC
* * * *
38949207 AGAGATAGCAACAAAGGAATTCTTT-TAAT
1 AGAGATCGCCACAAAGG-CTTCTTTATAAC
* * * * *
38949236 AGAGATAGCCATAAAGGCCTCCTTT-GAAT
1 AGAGATCGCCACAAAGG-CTTCTTTATAAC
* * *
38949265 AGAGGTGGCCTCAAAGGCATTCTTT-TAAC
1 AGAGATCGCCACAAAGGC-TTCTTTATAAC
* * *
38949294 AGAGATAGCCATAAAGACATTCTTT-TAAC
1 AGAGATCGCCACAAAGGC-TTCTTTATAAC
* * * * *
38949323 AAAGATAGCCACAAAGGATTCCTAATAAC
1 AGAGATCGCCACAAAGGCTTCTTTATAAC
* *
38949352 AAAGTTCGCCACAAAGGCTTCTTTATAAC
1 AGAGATCGCCACAAAGGCTTCTTTATAAC
* * * *
38949381 AGAGTTCGCCACAGAGGCTTTTTTATAAT
1 AGAGATCGCCACAAAGGCTTCTTTATAAC
*
38949410 AGAGATCACCACAAAGGC-TCTTTTATAAC
1 AGAGATCGCCACAAAGGCTTC-TTTATAAC
38949439 AGAGATC
1 AGAGATC
38949446 ACAAAAAAGG
Statistics
Matches: 191, Mismatches: 44, Indels: 8
0.79 0.18 0.03
Matches are distributed among these distances:
28 6 0.03
29 180 0.94
30 5 0.03
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.26
Consensus pattern (29 bp):
AGAGATCGCCACAAAGGCTTCTTTATAAC
Found at i:38949446 original size:29 final size:28
Alignment explanation
Indices: 38949360--38949465 Score: 113
Period size: 29 Copynumber: 3.6 Consensus size: 28
38949350 ACAAAGTTCG
* *
38949360 CCACAAAGGCTTCTTTATAACAGAGTTCG
1 CCACAAAGGCTT-TTTATAACAGAGATCA
* *
38949389 CCACAGAGGCTTTTTTATAATAGAGATCA
1 CCACAAAGGC-TTTTTATAACAGAGATCA
38949418 CCACAAAGGCTCTTTTATAACAGAGATCA
1 CCACAAAGGCT-TTTTATAACAGAGATCA
* * *
38949447 CAAAAAAGGATTTCTTATA
1 CCACAAAGGCTTT-TTATA
38949466 GTAGAGATTG
Statistics
Matches: 65, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
28 3 0.05
29 60 0.92
30 2 0.03
ACGTcount: A:0.37, C:0.20, G:0.15, T:0.28
Consensus pattern (28 bp):
CCACAAAGGCTTTTTATAACAGAGATCA
Found at i:38949471 original size:29 final size:29
Alignment explanation
Indices: 38949401--38949473 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 29
38949391 ACAGAGGCTT
* * *
38949401 TTTTATAATAGAGATCACCACAAAGGCTC
1 TTTTATAATAGAGATCACAAAAAAGGATC
*
38949430 TTTTATAACAGAGATCACAAAAAAGGAT-
1 TTTTATAATAGAGATCACAAAAAAGGATC
*
38949458 TTCTTATAGTAGAGAT
1 TT-TTATAATAGAGAT
38949474 TGCCACAAAC
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
28 2 0.05
29 35 0.95
ACGTcount: A:0.41, C:0.14, G:0.15, T:0.30
Consensus pattern (29 bp):
TTTTATAATAGAGATCACAAAAAAGGATC
Found at i:38964176 original size:60 final size:60
Alignment explanation
Indices: 38964083--38964202 Score: 213
Period size: 60 Copynumber: 2.0 Consensus size: 60
38964073 AAAGCTTTTG
*
38964083 AATTTGTTTTCCTCTAGGTTTGATCTTAGTGAAATTAGGTTTCATTAATTCTCAAAATTT
1 AATTTGTTCTCCTCTAGGTTTGATCTTAGTGAAATTAGGTTTCATTAATTCTCAAAATTT
* *
38964143 AATTTGTTCTCCTCTAGGTTTGGTCTTAGTGAAATTAGGTTTCATTAATTCTCAGAATTT
1 AATTTGTTCTCCTCTAGGTTTGATCTTAGTGAAATTAGGTTTCATTAATTCTCAAAATTT
38964203 GAGTTTGTAT
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
60 57 1.00
ACGTcount: A:0.25, C:0.12, G:0.15, T:0.47
Consensus pattern (60 bp):
AATTTGTTCTCCTCTAGGTTTGATCTTAGTGAAATTAGGTTTCATTAATTCTCAAAATTT
Found at i:38971201 original size:38 final size:38
Alignment explanation
Indices: 38971101--38971220 Score: 111
Period size: 38 Copynumber: 3.2 Consensus size: 38
38971091 ATGCAGTTCT
*
38971101 CACATACAATTGTT-GGATTCACCGACCAGTGCTGGG-A
1 CACATACAATT-TTCGGATACACCGACCAGTGCTGGGCA
* * ** * *
38971138 -AAATATATATTTGTCAAATATACCGACCAATGCTGGGCA
1 CACATACA-ATTT-TCGGATACACCGACCAGTGCTGGGCA
* *
38971177 CACATACAATTTTCGGATACACCGACTAGTGCTAGGCA
1 CACATACAATTTTCGGATACACCGACCAGTGCTGGGCA
38971215 CACATA
1 CACATA
38971221 TAGCAATCAA
Statistics
Matches: 63, Mismatches: 15, Indels: 9
0.72 0.17 0.10
Matches are distributed among these distances:
36 6 0.10
37 4 0.06
38 43 0.68
39 5 0.08
40 5 0.08
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.25
Consensus pattern (38 bp):
CACATACAATTTTCGGATACACCGACCAGTGCTGGGCA
Found at i:38979109 original size:26 final size:26
Alignment explanation
Indices: 38979080--38979141 Score: 97
Period size: 26 Copynumber: 2.4 Consensus size: 26
38979070 CCTATAAGTG
38979080 TTCTGAAACTGATACATGCTATGATA
1 TTCTGAAACTGATACATGCTATGATA
* *
38979106 TTCTGAAACTGATATATGTTATGATA
1 TTCTGAAACTGATACATGCTATGATA
*
38979132 TTCTAAAACT
1 TTCTGAAACT
38979142 ACTGCAGGTA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.39
Consensus pattern (26 bp):
TTCTGAAACTGATACATGCTATGATA
Found at i:38991455 original size:15 final size:16
Alignment explanation
Indices: 38991423--38991455 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
38991413 CACTATCAAT
38991423 AAAATTAATATGTTATA
1 AAAATTAATA-GTTATA
38991440 AAAATTAATA-TTATA
1 AAAATTAATAGTTATA
38991455 A
1 A
38991456 TATTTATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
17 10 0.62
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (16 bp):
AAAATTAATAGTTATA
Found at i:38991654 original size:26 final size:25
Alignment explanation
Indices: 38991610--38991665 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 25
38991600 CTATAATTAT
* *
38991610 ATATATTATATAATAAGACCCATGC
1 ATATATTACATAATAAGACCCACGC
*
38991635 ATATATGTACATAGTAAGACCCACGC
1 ATATAT-TACATAATAAGACCCACGC
38991661 ATATA
1 ATATA
38991666 ATATAATTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
25 6 0.22
26 21 0.78
ACGTcount: A:0.43, C:0.18, G:0.11, T:0.29
Consensus pattern (25 bp):
ATATATTACATAATAAGACCCACGC
Found at i:38992987 original size:3 final size:3
Alignment explanation
Indices: 38992930--38992974 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
38992920 AATTAGTCTC
38992930 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
38992975 GCCCCAATTA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:39009120 original size:30 final size:30
Alignment explanation
Indices: 39009083--39009185 Score: 138
Period size: 30 Copynumber: 3.4 Consensus size: 30
39009073 GGCTATCGAT
39009083 TATGAAAAGGGATGGGTGACGACCATCAAC
1 TATGAAAAGGGATGGGTGACGACCATCAAC
*
39009113 AATGAAAAGGGAT-GGTGACGACCATCGAAC
1 TATGAAAAGGGATGGGTGACGACCATC-AAC
* * *
39009143 TATGAAAAGGGATGGCT-TCGACTATCAATC
1 TATGAAAAGGGATGGGTGACGACCATCAA-C
39009173 TATGAAAAGGGAT
1 TATGAAAAGGGAT
39009186 AACTTTGGCT
Statistics
Matches: 65, Mismatches: 5, Indels: 6
0.86 0.07 0.08
Matches are distributed among these distances:
29 15 0.23
30 48 0.74
31 2 0.03
ACGTcount: A:0.38, C:0.15, G:0.28, T:0.19
Consensus pattern (30 bp):
TATGAAAAGGGATGGGTGACGACCATCAAC
Found at i:39009198 original size:30 final size:30
Alignment explanation
Indices: 39009142--39009200 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
39009132 GACCATCGAA
**
39009142 CTATGAAAAGGGATGGCTTCGACTATCAAT
1 CTATGAAAAGGGATAACTTCGACTATCAAT
* *
39009172 CTATGAAAAGGGATAACTTTGGCTATCAA
1 CTATGAAAAGGGATAACTTCGACTATCAA
39009201 ATTATAAATG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.22, T:0.27
Consensus pattern (30 bp):
CTATGAAAAGGGATAACTTCGACTATCAAT
Found at i:39012612 original size:25 final size:25
Alignment explanation
Indices: 39012584--39012631 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
39012574 CAAGCAAGTC
39012584 ATATCAAGAA-GCTCACAAAGAGCCT
1 ATATC-AGAACGCTCACAAAGAGCCT
*
39012609 ATATCAGAACGCTCATAAAGAGC
1 ATATCAGAACGCTCACAAAGAGC
39012632 TGCGATATGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 4 0.19
25 17 0.81
ACGTcount: A:0.44, C:0.23, G:0.17, T:0.17
Consensus pattern (25 bp):
ATATCAGAACGCTCACAAAGAGCCT
Found at i:39017479 original size:23 final size:23
Alignment explanation
Indices: 39017452--39017497 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
39017442 TTAGAGTACA
*
39017452 AAATTATGAGGTATTCACAATAT
1 AAATTATGAGATATTCACAATAT
39017475 AAATTATGAGATATTCACAATAT
1 AAATTATGAGATATTCACAATAT
39017498 CCAAAGAGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.46, C:0.09, G:0.11, T:0.35
Consensus pattern (23 bp):
AAATTATGAGATATTCACAATAT
Found at i:39019049 original size:22 final size:22
Alignment explanation
Indices: 39019014--39019065 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
39019004 TAAGTAAGTC
*
39019014 AAAAAAAT-TGGT-AAATATTTT
1 AAAAAAATATAGTAAAATA-TTT
*
39019035 ATAAAAATATAGTAAAATATTT
1 AAAAAAATATAGTAAAATATTT
39019057 AAAAAAATA
1 AAAAAAATA
39019066 CGTAATAACT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
21 7 0.27
22 14 0.54
23 5 0.19
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.33
Consensus pattern (22 bp):
AAAAAAATATAGTAAAATATTT
Found at i:39023141 original size:2 final size:2
Alignment explanation
Indices: 39023129--39023165 Score: 65
Period size: 2 Copynumber: 18.0 Consensus size: 2
39023119 GGACTTTGTA
39023129 AT AT GAT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39023166 GAAATTGAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 32 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:39024448 original size:2 final size:2
Alignment explanation
Indices: 39024441--39024469 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
39024431 TGAGATGAAC
39024441 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
39024470 CATACATACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:39029904 original size:22 final size:22
Alignment explanation
Indices: 39029873--39029927 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
39029863 AAAAAAGTAG
*
39029873 GCACCAAAGTGCAAATCAATAA
1 GCACCGAAGTGCAAATCAATAA
* **
39029895 GCACTGAAGTGCAAATCGCTAA
1 GCACCGAAGTGCAAATCAATAA
39029917 GCACCGAAGTG
1 GCACCGAAGTG
39029928 TGAAAAAGTA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.40, C:0.24, G:0.22, T:0.15
Consensus pattern (22 bp):
GCACCGAAGTGCAAATCAATAA
Found at i:39030491 original size:19 final size:20
Alignment explanation
Indices: 39030444--39030492 Score: 73
Period size: 19 Copynumber: 2.5 Consensus size: 20
39030434 TACAATATTC
39030444 ATATATTCTTATATTTTTCA
1 ATATATTCTTATATTTTTCA
*
39030464 CTATATTCTT-TATTTTTCA
1 ATATATTCTTATATTTTTCA
*
39030483 ATATTTTCTT
1 ATATATTCTT
39030493 GTAAACTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 17 0.65
20 9 0.35
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.63
Consensus pattern (20 bp):
ATATATTCTTATATTTTTCA
Found at i:39035365 original size:2 final size:2
Alignment explanation
Indices: 39035358--39035390 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
39035348 AAATAGAAAG
39035358 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
39035391 TAGATTTTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:39041659 original size:25 final size:26
Alignment explanation
Indices: 39041613--39041665 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 26
39041603 ATAAAATTGA
39041613 AACAAATCAATATAAATAAAAT-ATT
1 AACAAATCAATATAAATAAAATAATT
* * * *
39041638 AACAAATCGATATTATTTAAATAATT
1 AACAAATCAATATAAATAAAATAATT
39041664 AA
1 AA
39041666 TATTGATCTA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
25 18 0.78
26 5 0.22
ACGTcount: A:0.58, C:0.08, G:0.02, T:0.32
Consensus pattern (26 bp):
AACAAATCAATATAAATAAAATAATT
Found at i:39044277 original size:48 final size:48
Alignment explanation
Indices: 39044205--39044399 Score: 221
Period size: 48 Copynumber: 4.0 Consensus size: 48
39044195 TCGAAAGAAA
* * * *
39044205 AATAGATTTCTCGGTGGCCTGCACACAGTCCGTACCACCTTTGTGTAAT
1 AATAGA-TTCTCGGTGGCCTGCACACAGTCCGTGCCACCCTTGTATCAT
* * *
39044254 AATAGATTCTCGGTGGCCTGCACATAGTCCATGCCACCCTTGTATCTT
1 AATAGATTCTCGGTGGCCTGCACACAGTCCGTGCCACCCTTGTATCAT
* * *
39044302 AACATG-TTATTGGTGGCCTGCACACAGTCCGTGCCACCCTTGTATCAT
1 AATA-GATTCTCGGTGGCCTGCACACAGTCCGTGCCACCCTTGTATCAT
* * ** * *
39044350 AATAGAATGTTAGTGGCCTGCACACAGTTCGTGCCACCCTTGTGTCAT
1 AATAGATTCTCGGTGGCCTGCACACAGTCCGTGCCACCCTTGTATCAT
39044398 AA
1 AA
39044400 CAGAATATCG
Statistics
Matches: 125, Mismatches: 19, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
47 1 0.01
48 117 0.94
49 7 0.06
ACGTcount: A:0.23, C:0.27, G:0.21, T:0.30
Consensus pattern (48 bp):
AATAGATTCTCGGTGGCCTGCACACAGTCCGTGCCACCCTTGTATCAT
Found at i:39044385 original size:96 final size:96
Alignment explanation
Indices: 39044217--39044401 Score: 253
Period size: 96 Copynumber: 1.9 Consensus size: 96
39044207 TAGATTTCTC
* * * * *
39044217 GGTGGCCTGCACACAGTCCGTACCACCTTTGTGTAATAATAGATTCTCGGTGGCCTGCACATAGT
1 GGTGGCCTGCACACAGTCCGTACCACCCTTGTATAATAATAGAATCTCAGTGGCCTGCACACAGT
*
39044282 CCATGCCACCCTTGTATCTTAACATGTTATT
66 CCATGCCACCCTTGTATCATAACATGTTATT
* * * *
39044313 GGTGGCCTGCACACAGTCCGTGCCACCCTTGTATCATAATAGAATGTTAGTGGCCTGCACACAGT
1 GGTGGCCTGCACACAGTCCGTACCACCCTTGTATAATAATAGAATCTCAGTGGCCTGCACACAGT
* * *
39044378 TCGTGCCACCCTTGTGTCATAACA
66 CCATGCCACCCTTGTATCATAACA
39044402 GAATATCGGT
Statistics
Matches: 76, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
96 76 1.00
ACGTcount: A:0.22, C:0.28, G:0.21, T:0.29
Consensus pattern (96 bp):
GGTGGCCTGCACACAGTCCGTACCACCCTTGTATAATAATAGAATCTCAGTGGCCTGCACACAGT
CCATGCCACCCTTGTATCATAACATGTTATT
Found at i:39045921 original size:25 final size:25
Alignment explanation
Indices: 39045892--39045941 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
39045882 AATTGTTTGA
*
39045892 ATATGATTATGCAGTGAATTGGATT
1 ATATGAATATGCAGTGAATTGGATT
39045917 ATATGAATATGCAGTGAATTGGATT
1 ATATGAATATGCAGTGAATTGGATT
39045942 TCTATGGTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.34, C:0.04, G:0.24, T:0.38
Consensus pattern (25 bp):
ATATGAATATGCAGTGAATTGGATT
Found at i:39054500 original size:24 final size:24
Alignment explanation
Indices: 39054451--39054501 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
39054441 CCACTATTAA
* **
39054451 ATGGATTCCTTCTATTCAAGTGTC
1 ATGGATGCCTTCTATTCAAGAATC
39054475 ATGGATGCCTTCTACTT-AAGAATC
1 ATGGATGCCTTCTA-TTCAAGAATC
39054499 ATG
1 ATG
39054502 TCTCAAACCC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 21 0.91
25 2 0.09
ACGTcount: A:0.25, C:0.20, G:0.18, T:0.37
Consensus pattern (24 bp):
ATGGATGCCTTCTATTCAAGAATC
Found at i:39055092 original size:38 final size:38
Alignment explanation
Indices: 39055037--39055114 Score: 102
Period size: 38 Copynumber: 2.1 Consensus size: 38
39055027 GAACAATAAT
* *
39055037 AATACCAACAATCACATAAACTGGTTTTCTATTTCAAC
1 AATACCAACAATCACATAAACTGATTTTCTATTTAAAC
* * * *
39055075 AATACCAACATTTACATAAGCTGATTTTTTATTTAAAC
1 AATACCAACAATCACATAAACTGATTTTCTATTTAAAC
39055113 AA
1 AA
39055115 CAAAAAAATT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.41, C:0.19, G:0.05, T:0.35
Consensus pattern (38 bp):
AATACCAACAATCACATAAACTGATTTTCTATTTAAAC
Found at i:39058148 original size:14 final size:14
Alignment explanation
Indices: 39058129--39058191 Score: 62
Period size: 14 Copynumber: 4.7 Consensus size: 14
39058119 TGTTTAACTA
39058129 ATTATT-TTAGTGTT
1 ATTATTATTA-TGTT
*
39058143 ATTATTATTATTTT
1 ATTATTATTATGTT
39058157 ATTATTATTA--TT
1 ATTATTATTATGTT
* *
39058169 ATTATTACTAT-TA
1 ATTATTATTATGTT
39058182 ATTATTATTA
1 ATTATTATTA
39058192 GTTTCATCTT
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
12 11 0.26
13 10 0.23
14 19 0.44
15 3 0.07
ACGTcount: A:0.32, C:0.02, G:0.03, T:0.63
Consensus pattern (14 bp):
ATTATTATTATGTT
Found at i:39058149 original size:3 final size:3
Alignment explanation
Indices: 39058141--39058191 Score: 77
Period size: 3 Copynumber: 17.0 Consensus size: 3
39058131 TATTTTAGTG
*
39058141 TTA TTA TTA TTA TT- TTA TTA TTA TTA TTA TTA TTA CTA TTAA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA
39058186 TTA TTA
1 TTA TTA
39058192 GTTTCATCTT
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
2 2 0.05
3 39 0.89
4 3 0.07
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Done.