Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010267.1 Kokia drynarioides strain JFW-HI SEQ_125106, whole genome shotgun sequence
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: 375764
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Warning! 335 characters in sequence are not A, C, G, or T
Found at i:506 original size:22 final size:21
Alignment explanation
Indices: 481--527 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
471 CTTCTCTCCA
*
481 TCTTCC-TTATTCTTTCTTTCTT
1 TCTTCCTTTA-TCTTT-TTTATT
*
503 TCTTTCTTTATCTTTTTTATT
1 TCTTCCTTTATCTTTTTTATT
524 TCTT
1 TCTT
528 TTTTCCTTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 9 0.41
22 10 0.45
23 3 0.14
ACGTcount: A:0.06, C:0.21, G:0.00, T:0.72
Consensus pattern (21 bp):
TCTTCCTTTATCTTTTTTATT
Found at i:21558 original size:28 final size:29
Alignment explanation
Indices: 21489--21563 Score: 80
Period size: 32 Copynumber: 2.5 Consensus size: 29
21479 TGTATGTGTG
* *
21489 TGTGTTTGTGTGTATGTGTATGTATGTATA
1 TGTGTTTGTGTGTGTATGTATGTATG-ATA
* *
21519 TCTATCTGTGTGTGTGTATGTATGTATG-TA
1 TGTGT-T-TGTGTGTGTATGTATGTATGATA
21549 TGTGTTTGTGTGTGT
1 TGTGTTTGTGTGTGT
21564 TCATTAGTCA
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
28 9 0.24
29 1 0.03
30 8 0.22
31 1 0.03
32 18 0.49
ACGTcount: A:0.13, C:0.03, G:0.31, T:0.53
Consensus pattern (29 bp):
TGTGTTTGTGTGTGTATGTATGTATGATA
Found at i:22725 original size:44 final size:44
Alignment explanation
Indices: 22657--22748 Score: 148
Period size: 44 Copynumber: 2.1 Consensus size: 44
22647 ATATCCTAAC
*
22657 ATTCATGTAGAATTACAACTTCCACATGTTTAAAAAATACTTGT
1 ATTCATGTAGAATTACAACTTCCACATATTTAAAAAATACTTGT
* * *
22701 ATTCTTGTAGAATTACAACTTCCACGTATTTGAAAAATACTTGT
1 ATTCATGTAGAATTACAACTTCCACATATTTAAAAAATACTTGT
22745 ATTC
1 ATTC
22749 GACACATTCG
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (44 bp):
ATTCATGTAGAATTACAACTTCCACATATTTAAAAAATACTTGT
Found at i:31060 original size:18 final size:18
Alignment explanation
Indices: 31031--31097 Score: 64
Period size: 18 Copynumber: 3.7 Consensus size: 18
31021 TCCTCCTCCT
* *
31031 CCTCCTCCTCTTCTTCTT
1 CCTCCTCTTCTTCTTCTA
*
31049 CTTCCTCTTCTTCTTCTA
1 CCTCCTCTTCTTCTTCTA
* *
31067 CCTCCACTTCTTCATACT-
1 CCTCCTCTTCTTC-TTCTA
*
31085 CCACCTCTTCTTC
1 CCTCCTCTTCTTC
31098 CATAGTCTCC
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
18 37 0.93
19 3 0.08
ACGTcount: A:0.07, C:0.46, G:0.00, T:0.46
Consensus pattern (18 bp):
CCTCCTCTTCTTCTTCTA
Found at i:31076 original size:15 final size:15
Alignment explanation
Indices: 31043--31095 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
31033 TCCTCCTCTT
* **
31043 CTTCTTCTTCCTCTT
1 CTTCTTCTACCTCCA
31058 CTTCTTCTACCTCCA
1 CTTCTTCTACCTCCA
31073 CTTCTTCATA-CTCCA
1 CTTCTTC-TACCTCCA
*
31088 CCTCTTCT
1 CTTCTTCT
31096 TCCATAGTCT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
14 1 0.03
15 30 0.91
16 2 0.06
ACGTcount: A:0.09, C:0.43, G:0.00, T:0.47
Consensus pattern (15 bp):
CTTCTTCTACCTCCA
Found at i:31079 original size:3 final size:3
Alignment explanation
Indices: 30997--31065 Score: 50
Period size: 3 Copynumber: 23.0 Consensus size: 3
30987 GACATCTTGA
* * * * * * *
30997 TCT TCC TCT TCT AT-T TCT TCT TCT TCC TCC TCC TCC TCC TCC TCT
1 TCT TCT TCT TCT -TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
*
31042 TCT TCT TCT TCC TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT
31066 ACCTCCACTT
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
2 1 0.02
3 56 0.97
4 1 0.02
ACGTcount: A:0.01, C:0.43, G:0.00, T:0.55
Consensus pattern (3 bp):
TCT
Found at i:42290 original size:99 final size:100
Alignment explanation
Indices: 42125--42657 Score: 606
Period size: 100 Copynumber: 5.3 Consensus size: 100
42115 CTGTATCACA
* * * * * *
42125 GCCATCACACGATATCTCTCAACGCAAGGGTCGATATCATCAAATTAAAACTACATATTACATAA
1 GCCACCACACGATTTCTCTCAAGGCAAGGATCGA-ATGATCAAATTAAGACTACATATTACATAA
*
42190 CCATGATTCATATACAAGTAATAATCCCTTATCAAC
65 CCATGATTCATATACAAGTAATAATCCCTTATCATC
* * * * *
42226 GCCATCACATGATATCTCTCAAGG-AAGGATCGAATGAGCAAATTAAGACTACATTTTACATAAC
1 GCCACCACACGATTTCTCTCAAGGCAAGGATCGAATGATCAAATTAAGACTACATATTACATAAC
*
42290 CATGATTCATATACAAGTAA-ATATCCCATATCATC
66 CATGATTCATATACAAGTAATA-ATCCCTTATCATC
* * * * * * *
42325 GCCACCACACAATTGCTCTTAAGGCGAGGATCAAATGATCAAATCAAGACTACATATTGCATAAC
1 GCCACCACACGATTTCTCTCAAGGCAAGGATCGAATGATCAAATTAAGACTACATATTACATAAC
*
42390 CATGATTCATATACAAGTAATAATCCCTTATCACC
66 CATGATTCATATACAAGTAATAATCCCTTATCATC
* ** * * * * *
42425 ACCGTCACACGATTTCTCTCGAGGCAAAGATTGAATGAGCAAATTAAGACTACCTATTACATAAC
1 GCCACCACACGATTTCTCTCAAGGCAAGGATCGAATGATCAAATTAAGACTACATATTACATAAC
* * *
42490 CATGATTCATATACAAATAAAAAT-CC-TATTTATC
66 CATGATTCATATACAAGTAATAATCCCTTA-TCATC
* * * * * *
42524 GCCACCACACAATTTCTCTTAAGGCAAGGATCAAATGATCAAATCAAAACTGCATATTACATAAC
1 GCCACCACACGATTTCTCTCAAGGCAAGGATCGAATGATCAAATTAAGACTACATATTACATAAC
* * *
42589 CATGATTCAAATACAAGTAATTATCCCGTATCATC
66 CATGATTCATATACAAGTAATAATCCCTTATCATC
* * * *
42624 ACCACCGCATGATTTCTCTCAAAGCAAGGATCGA
1 GCCACCACACGATTTCTCTCAAGGCAAGGATCGA
42658 TACAGTTTAA
Statistics
Matches: 358, Mismatches: 68, Indels: 13
0.82 0.15 0.03
Matches are distributed among these distances:
98 3 0.01
99 152 0.42
100 178 0.50
101 25 0.07
ACGTcount: A:0.39, C:0.24, G:0.11, T:0.26
Consensus pattern (100 bp):
GCCACCACACGATTTCTCTCAAGGCAAGGATCGAATGATCAAATTAAGACTACATATTACATAAC
CATGATTCATATACAAGTAATAATCCCTTATCATC
Found at i:42527 original size:199 final size:199
Alignment explanation
Indices: 42163--42645 Score: 698
Period size: 199 Copynumber: 2.4 Consensus size: 199
42153 GGTCGATATC
* *
42163 ATCAAATTAAAACTACATATTACATAACCATGATTCATATACAAGTAATAATCCCTTATCAACGC
1 ATCAAATCAAAACTACATATTACATAACCATGATTCATATACAAGTAATAATCCCTTATCAACAC
* * *
42228 CATCACATGATATCTCTCAAGGAAGGATCGAATGAGCAAATTAAGACTACATTTTACATAACCAT
66 CATCACACGATATCTCTCAAGGAAAGATCGAATGAGCAAATTAAGACTACATATTACATAACCAT
* * *
42293 GATTCATATACAAGTAAATATCCCATATCATCGCCACCACACAATTGCTCTTAAGGCGAGGATCA
131 GATTCATATACAAATAAAAATCCCATATCATCGCCACCACACAATTGCTCTTAAGGCAAGGATCA
42358 AATG
196 AATG
* * *
42362 ATCAAATCAAGACTACATATTGCATAACCATGATTCATATACAAGTAATAATCCCTTATCACCAC
1 ATCAAATCAAAACTACATATTACATAACCATGATTCATATACAAGTAATAATCCCTTATCAACAC
* * * * *
42427 CGTCACACGATTTCTCTCGAGGCAAAGATTGAATGAGCAAATTAAGACTACCTATTACATAACCA
66 CATCACACGATATCTCTCAAGG-AAAGATCGAATGAGCAAATTAAGACTACATATTACATAACCA
* * *
42492 TGATTCATATACAAATAAAAATCCTAT-TTATCGCCACCACACAATTTCTCTTAAGGCAAGGATC
130 TGATTCATATACAAATAAAAATCCCATATCATCGCCACCACACAATTGCTCTTAAGGCAAGGATC
42556 AAATG
195 AAATG
* * * * *
42561 ATCAAATCAAAACTGCATATTACATAACCATGATTCAAATACAAGTAATTATCCCGTATCATCAC
1 ATCAAATCAAAACTACATATTACATAACCATGATTCATATACAAGTAATAATCCCTTATCAACAC
* * * *
42626 CACCGCATGATTTCTCTCAA
66 CATCACACGATATCTCTCAA
42646 AGCAAGGATC
Statistics
Matches: 252, Mismatches: 31, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
199 190 0.75
200 62 0.25
ACGTcount: A:0.40, C:0.23, G:0.10, T:0.27
Consensus pattern (199 bp):
ATCAAATCAAAACTACATATTACATAACCATGATTCATATACAAGTAATAATCCCTTATCAACAC
CATCACACGATATCTCTCAAGGAAAGATCGAATGAGCAAATTAAGACTACATATTACATAACCAT
GATTCATATACAAATAAAAATCCCATATCATCGCCACCACACAATTGCTCTTAAGGCAAGGATCA
AATG
Found at i:46542 original size:19 final size:18
Alignment explanation
Indices: 46518--46554 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
46508 AACCAACAAT
*
46518 AATTAAATAATTAATTAAA
1 AATTAAAAAATT-ATTAAA
46537 AATTAAAAAATTATTAAA
1 AATTAAAAAATTATTAAA
46555 CCTATTCAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
AATTAAAAAATTATTAAA
Found at i:47105 original size:17 final size:16
Alignment explanation
Indices: 47079--47112 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
47069 ATATAACTTT
47079 TATAAATATGTTTATTA
1 TATAAATATGTTT-TTA
*
47096 TATAATTATGTTTTTA
1 TATAAATATGTTTTTA
47112 T
1 T
47113 TTTATCCTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (16 bp):
TATAAATATGTTTTTA
Found at i:52367 original size:43 final size:43
Alignment explanation
Indices: 52314--52404 Score: 155
Period size: 43 Copynumber: 2.1 Consensus size: 43
52304 TTAAGCTAAC
* *
52314 TTCTATGATTATCAAAATGGGTAATTAAAAGCCAAAATTCAGA
1 TTCTTTGATTATCAAAATGGATAATTAAAAGCCAAAATTCAGA
*
52357 TTCTTTGATTATTAAAATGGATAATTAAAAGCCAAAATTCAGA
1 TTCTTTGATTATCAAAATGGATAATTAAAAGCCAAAATTCAGA
52400 TTCTT
1 TTCTT
52405 GTAAATTGAT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.42, C:0.11, G:0.12, T:0.35
Consensus pattern (43 bp):
TTCTTTGATTATCAAAATGGATAATTAAAAGCCAAAATTCAGA
Found at i:52597 original size:15 final size:16
Alignment explanation
Indices: 52561--52595 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
52551 TGTTTATAGA
*
52561 AAAAAT-AATTATATC
1 AAAAATAAATAATATC
52576 AAAAATAAATAATATC
1 AAAAATAAATAATATC
52592 AAAA
1 AAAA
52596 TATTCAATAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.26
Consensus pattern (16 bp):
AAAAATAAATAATATC
Found at i:53114 original size:17 final size:19
Alignment explanation
Indices: 53092--53129 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
53082 ATAAATTATT
53092 AAAAAT-TAT-TAAAAATA
1 AAAAATATATATAAAAATA
*
53109 AAAAATATTTATAAAAATA
1 AAAAATATATATAAAAATA
53128 AA
1 AA
53130 TTAACTGATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
18 2 0.11
19 10 0.56
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (19 bp):
AAAAATATATATAAAAATA
Found at i:55788 original size:22 final size:22
Alignment explanation
Indices: 55747--55788 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
55737 TTGTTCAATT
*
55747 AAACTGATCATAATAAGCTTAC
1 AAACTGATCATAAAAAGCTTAC
55769 AAACTGA-CATAAAAACGCTT
1 AAACTGATCATAAAAA-GCTT
55789 TCTTTCTCCC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.48, C:0.19, G:0.10, T:0.24
Consensus pattern (22 bp):
AAACTGATCATAAAAAGCTTAC
Found at i:58023 original size:16 final size:16
Alignment explanation
Indices: 57982--58029 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 16
57972 ATTGTAAATT
*
57982 AATTAATTAAATTT-A
1 AATTAATTAATTTTAA
* *
57997 ATTTAAATAATTTTAA
1 AATTAATTAATTTTAA
*
58013 AATTAATTAATTATAA
1 AATTAATTAATTTTAA
58029 A
1 A
58030 TAATTGATTA
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
15 11 0.42
16 15 0.58
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
AATTAATTAATTTTAA
Found at i:63017 original size:8 final size:8
Alignment explanation
Indices: 63004--63029 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
62994 GTTACACTTA
63004 AAATTATT
1 AAATTATT
63012 AAATTATT
1 AAATTATT
63020 AAATTATT
1 AAATTATT
63028 AA
1 AA
63030 TACATTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (8 bp):
AAATTATT
Found at i:68483 original size:21 final size:19
Alignment explanation
Indices: 68451--68492 Score: 57
Period size: 21 Copynumber: 2.1 Consensus size: 19
68441 TGCTAATATA
68451 TTTTAAATATTTATGATTT
1 TTTTAAATATTTATGATTT
*
68470 TTTTATAATTATTTTTGATTT
1 TTTTA-AA-TATTTATGATTT
68491 TT
1 TT
68493 ATACAGGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 5 0.25
20 2 0.10
21 13 0.65
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (19 bp):
TTTTAAATATTTATGATTT
Found at i:68649 original size:2 final size:2
Alignment explanation
Indices: 68644--68668 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
68634 TCACACACAC
68644 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 T
68669 TCTTTTAGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:69633 original size:19 final size:19
Alignment explanation
Indices: 69611--69650 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
69601 TCTAAATTAC
*
69611 ATAATATATAAAAAAATAT
1 ATAAAATATAAAAAAATAT
* *
69630 ATAAAATATAATATAATAT
1 ATAAAATATAAAAAAATAT
69649 AT
1 AT
69651 TATAAACTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
ATAAAATATAAAAAAATAT
Found at i:74393 original size:15 final size:15
Alignment explanation
Indices: 74373--74417 Score: 65
Period size: 15 Copynumber: 3.1 Consensus size: 15
74363 TTTTAATAAA
74373 AATACTTAATCTTTC
1 AATACTTAATCTTTC
*
74388 AATACTTATTCTTTC
1 AATACTTAATCTTTC
*
74403 AA-ACTTAATTTTTC
1 AATACTTAATCTTTC
74417 A
1 A
74418 GTTATGCCAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
14 11 0.41
15 16 0.59
ACGTcount: A:0.33, C:0.18, G:0.00, T:0.49
Consensus pattern (15 bp):
AATACTTAATCTTTC
Found at i:80101 original size:16 final size:16
Alignment explanation
Indices: 80080--80112 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
80070 ATTGGACTGG
80080 ATTTTTAAT-AATTTTT
1 ATTTTT-ATGAATTTTT
80096 ATTTTTATGAATTTTT
1 ATTTTTATGAATTTTT
80112 A
1 A
80113 ATGATTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 2 0.12
16 14 0.88
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (16 bp):
ATTTTTATGAATTTTT
Found at i:86450 original size:31 final size:29
Alignment explanation
Indices: 86386--86456 Score: 88
Period size: 29 Copynumber: 2.4 Consensus size: 29
86376 ATGATAATGT
** *
86386 AAGTGACTAAAACGTAATATTTCAAACAT
1 AAGTGACTAAAACGTAATATGGCAAACAA
*
86415 AAGTGACTAAAATGTAATATGAGGCAAACAA
1 AAGTGACTAAAACGTAATAT--GGCAAACAA
86446 AAGTGACTAAA
1 AAGTGACTAAA
86457 TTTACAGTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
29 19 0.53
31 17 0.47
ACGTcount: A:0.51, C:0.11, G:0.15, T:0.23
Consensus pattern (29 bp):
AAGTGACTAAAACGTAATATGGCAAACAA
Found at i:87474 original size:14 final size:14
Alignment explanation
Indices: 87455--87481 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
87445 AAATGGTGAA
87455 ATTGTATTTTTACG
1 ATTGTATTTTTACG
87469 ATTGTATTTTTAC
1 ATTGTATTTTTAC
87482 TACCGTAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.07, G:0.11, T:0.59
Consensus pattern (14 bp):
ATTGTATTTTTACG
Found at i:89356 original size:15 final size:15
Alignment explanation
Indices: 89336--89365 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
89326 ATTAACTTTA
89336 ACTTTATTTTAACAT
1 ACTTTATTTTAACAT
89351 ACTTTATTTTAACAT
1 ACTTTATTTTAACAT
89366 GTAATGTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.13, G:0.00, T:0.53
Consensus pattern (15 bp):
ACTTTATTTTAACAT
Found at i:89555 original size:31 final size:31
Alignment explanation
Indices: 89518--89600 Score: 85
Period size: 31 Copynumber: 2.7 Consensus size: 31
89508 TATTTGTTTA
*
89518 AATGTATATAACTGAATCAAAATCAAAATTT
1 AATGTATATAACTGAACCAAAATCAAAATTT
* ** * *
89549 CATGTATATATTTGAACCACAATCAAAGTTT
1 AATGTATATAACTGAACCAAAATCAAAATTT
* * *
89580 AATGTGTATAATTGTACCAAA
1 AATGTATATAACTGAACCAAA
89601 TTAAAATATA
Statistics
Matches: 41, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.45, C:0.12, G:0.10, T:0.34
Consensus pattern (31 bp):
AATGTATATAACTGAACCAAAATCAAAATTT
Found at i:95162 original size:21 final size:22
Alignment explanation
Indices: 95138--95191 Score: 56
Period size: 25 Copynumber: 2.4 Consensus size: 22
95128 AAACGAGGTT
*
95138 ATTATTTT-GTTTGTCAGTCTA
1 ATTATTTTAGTTTGTCAGTATA
95159 ATTATAATATTAGTTTGTCAGTATA
1 ATTAT--T-TTAGTTTGTCAGTATA
*
95184 ATTTTTTT
1 ATTATTTT
95192 TTATTTTAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
21 5 0.19
22 2 0.07
23 2 0.07
24 2 0.07
25 16 0.59
ACGTcount: A:0.26, C:0.06, G:0.11, T:0.57
Consensus pattern (22 bp):
ATTATTTTAGTTTGTCAGTATA
Found at i:95984 original size:13 final size:13
Alignment explanation
Indices: 95966--95990 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
95956 AATAAATGTG
95966 ATTTCAATTTTAA
1 ATTTCAATTTTAA
95979 ATTTCAATTTTA
1 ATTTCAATTTTA
95991 TAGGGATTGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (13 bp):
ATTTCAATTTTAA
Found at i:96852 original size:151 final size:148
Alignment explanation
Indices: 96438--96920 Score: 570
Period size: 151 Copynumber: 3.2 Consensus size: 148
96428 GTTTCAAAAA
* * * * * *
96438 TTAACTTAGTTTGCATTTTGTATTTGAAATTGAAGTTTGAGATCGAAGTTGTTAGGACTATGGTT
1 TTAACTTAGTTTGCATTTTGTGTTCGAAATCGAAGTTTGAGAT-GAAGTTGTTAAGAATATCGTT
* * * *
96503 CTGTATATTTGAGCGGAGTGTTGGGATGGGAAGTACTTCCTGATTGGTTTGAATTCGTAATCTTA
65 CTGTTTATTGGAGCGGAGTGTTGGGATGGGAAGTACTTCCTGATTGGTATGAATTCGTAATCATA
* *
96568 AAGCA-TCATGTTTCGAAAG
130 AAG-ATTCGTGTTTCGAATG
* * *
96587 TTAACTTAGTTTGCATTGTGTGTTCGAAGTCGAAGTTT--CA--AAGTTGTTAAGAATA-CAGTT
1 TTAACTTAGTTTGCATTTTGTGTTCGAAATCGAAGTTTGAGATGAAGTTGTTAAGAATATC-GTT
* * *
96647 TTGTTTATTTTGGAGTGGAGTGTAGGGATGGGAAGTACTTCCTGATTGGTATGAATTCGTAATCA
65 CTGTTTA--TTGGAGCGGAGTGTTGGGATGGGAAGTACTTCCTGATTGGTATGAATTCGTAATCA
96712 TAAATG-TTCGTGTTTCGAATG
128 TAAA-GATTCGTGTTTCGAATG
*
96733 TTAAC-TAGGTTTGCATTTTGTGTTCAAAATCGAAGTTTGAGATTGAAGTTGTTAAGAATATCGT
1 TTAACTTA-GTTTGCATTTTGTGTTCGAAATCGAAGTTTGAGA-TGAAGTTGTTAAGAATATCGT
* * *
96797 TCTGTTTGTTCGGGAGCGGAGTGTTGGAATGGGAAGTACTTCCCGATTGGTATGAATTCGTAATC
64 TCTGTTTATT--GGAGCGGAGTGTTGGGATGGGAAGTACTTCCTGATTGGTATGAATTCGTAATC
*
96862 ATAAACGATT-GTGTTTCAAATG
127 ATAAA-GATTCGTGTTTCGAATG
* * *
96884 TTAACTTGGTTTGCATTTTGTGTTTGAAATTGAAGTT
1 TTAACTTAGTTTGCATTTTGTGTTCGAAATCGAAGTT
96921 AAGAATCCGG
Statistics
Matches: 284, Mismatches: 34, Indels: 30
0.82 0.10 0.09
Matches are distributed among these distances:
144 21 0.07
145 2 0.01
146 99 0.35
147 2 0.01
148 1 0.00
149 35 0.12
151 120 0.42
152 4 0.01
ACGTcount: A:0.25, C:0.09, G:0.25, T:0.40
Consensus pattern (148 bp):
TTAACTTAGTTTGCATTTTGTGTTCGAAATCGAAGTTTGAGATGAAGTTGTTAAGAATATCGTTC
TGTTTATTGGAGCGGAGTGTTGGGATGGGAAGTACTTCCTGATTGGTATGAATTCGTAATCATAA
AGATTCGTGTTTCGAATG
Found at i:100686 original size:15 final size:17
Alignment explanation
Indices: 100656--100694 Score: 55
Period size: 15 Copynumber: 2.4 Consensus size: 17
100646 TAGCAAAAAT
100656 ATAATTTCACCATTTTA
1 ATAATTTCACCATTTTA
*
100673 ATAATTT-A-CATTTTT
1 ATAATTTCACCATTTTA
100688 ATAATTT
1 ATAATTT
100695 TTAAATGATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 13 0.62
16 1 0.05
17 7 0.33
ACGTcount: A:0.36, C:0.10, G:0.00, T:0.54
Consensus pattern (17 bp):
ATAATTTCACCATTTTA
Found at i:102154 original size:14 final size:14
Alignment explanation
Indices: 102135--102164 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
102125 CTTGATAATC
*
102135 ATGTGATTAATTGA
1 ATGTGATGAATTGA
102149 ATGTGATGAATTGA
1 ATGTGATGAATTGA
102163 AT
1 AT
102165 ACAAATATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.37, C:0.00, G:0.23, T:0.40
Consensus pattern (14 bp):
ATGTGATGAATTGA
Found at i:105852 original size:69 final size:67
Alignment explanation
Indices: 105686--105895 Score: 348
Period size: 67 Copynumber: 3.1 Consensus size: 67
105676 GTCGGCTAAA
* *
105686 ATGGTTAGGTATAGCAATGAATGAAGAACAGCTTTTATTCACAGTATATCTCTTCTTGTATACAT
1 ATGGTTAGGTATAGCAGTGAATGAAGAACAGCTTATATTCACAGTATATCTCTTCTTGTATACAT
105751 AT
66 AT
* *
105753 ATGGTTAGGTATAGCAGTGAATGAAGAACAGCTAATATTCACAGTGTATCTCTTCTTGTATGTAC
1 ATGGTTAGGTATAGCAGTGAATGAAGAACAGCTTATATTCACAGTATATCTCTTCTTGTA--TAC
105818 ATAT
64 ATAT
* *
105822 ATGGTTAGGTATAGCAGTGAATGAAGAACAGCTTGTATTCACAGTATATCTCTTCTTGTATATAT
1 ATGGTTAGGTATAGCAGTGAATGAAGAACAGCTTATATTCACAGTATATCTCTTCTTGTATACAT
105887 AT
66 AT
105889 ATGGTTA
1 ATGGTTA
105896 AAGTGTGCTA
Statistics
Matches: 133, Mismatches: 8, Indels: 4
0.92 0.06 0.03
Matches are distributed among these distances:
67 69 0.52
69 64 0.48
ACGTcount: A:0.32, C:0.12, G:0.19, T:0.37
Consensus pattern (67 bp):
ATGGTTAGGTATAGCAGTGAATGAAGAACAGCTTATATTCACAGTATATCTCTTCTTGTATACAT
AT
Found at i:109354 original size:30 final size:30
Alignment explanation
Indices: 109285--109401 Score: 105
Period size: 30 Copynumber: 4.0 Consensus size: 30
109275 ATTTAACTCC
* * * *
109285 TAAAATTTCTAAAAATTGTATTCTGGCCCA
1 TAAAATTTCTAAAAATTGCATTTTGACCCT
* * * *
109315 TGAACTTTCTAAAAATTTCATTTTTACCCT
1 TAAAATTTCTAAAAATTGCATTTTGACCCT
*
109345 TAAAATTTCT-AAAATTGCATTTT-AACC-
1 TAAAATTTCTAAAAATTGCATTTTGACCCT
* * *
109372 TAAACTTTTTGAAAATTGCATTTTGACCCT
1 TAAAATTTCTAAAAATTGCATTTTGACCCT
109402 AAACTTCCAA
Statistics
Matches: 69, Mismatches: 15, Indels: 6
0.77 0.17 0.07
Matches are distributed among these distances:
27 8 0.12
28 16 0.23
29 15 0.22
30 30 0.43
ACGTcount: A:0.34, C:0.17, G:0.07, T:0.42
Consensus pattern (30 bp):
TAAAATTTCTAAAAATTGCATTTTGACCCT
Found at i:113716 original size:21 final size:21
Alignment explanation
Indices: 113666--113716 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
113656 AAATCGAAAT
*
113666 AAAAAATATTAACTTCTATTA
1 AAAAAATATTAACTCCTATTA
* * *
113687 AAAACATATTAGCTCCTGTTA
1 AAAAAATATTAACTCCTATTA
113708 AAAAAATAT
1 AAAAAATAT
113717 AGAAACAACA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.51, C:0.12, G:0.04, T:0.33
Consensus pattern (21 bp):
AAAAAATATTAACTCCTATTA
Found at i:124250 original size:12 final size:12
Alignment explanation
Indices: 124233--124258 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
124223 AACTGTAATT
124233 AAGTATAACAAC
1 AAGTATAACAAC
124245 AAGTATAACAAC
1 AAGTATAACAAC
124257 AA
1 AA
124259 ATAATGGCAT
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:0.62, C:0.15, G:0.08, T:0.15
Consensus pattern (12 bp):
AAGTATAACAAC
Found at i:129669 original size:31 final size:31
Alignment explanation
Indices: 129603--129670 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 31
129593 ATAAAATAAT
* *
129603 CATTAAATTATTTAAAAATTATCATTTAAGT
1 CATTAAATTATTAAAAAATTATCATTTAAGC
129634 CATTAAATTATTAAAAAAAATT-T-ATTTAAGC
1 CATTAAATTATT--AAAAAATTATCATTTAAGC
129665 CATTAA
1 CATTAA
129671 GATGTTAAGT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
31 25 0.76
32 1 0.03
33 7 0.21
ACGTcount: A:0.49, C:0.07, G:0.03, T:0.41
Consensus pattern (31 bp):
CATTAAATTATTAAAAAATTATCATTTAAGC
Found at i:130861 original size:8 final size:9
Alignment explanation
Indices: 130839--130870 Score: 55
Period size: 9 Copynumber: 3.4 Consensus size: 9
130829 ATATTAACCC
130839 ATTTTTTAT
1 ATTTTTTAT
130848 ATTTTTTAT
1 ATTTTTTAT
130857 ATTTTTTAAT
1 ATTTTTT-AT
130867 ATTT
1 ATTT
130871 GCTAATGTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 16 0.73
10 6 0.27
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (9 bp):
ATTTTTTAT
Found at i:131571 original size:22 final size:22
Alignment explanation
Indices: 131540--131581 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
131530 TATTATACAT
*
131540 CAACCTGCTGATTGAGTTTTGA
1 CAACCAGCTGATTGAGTTTTGA
131562 CAACCAGCTGATTGAGTTTT
1 CAACCAGCTGATTGAGTTTT
131582 AATTCAATTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.36
Consensus pattern (22 bp):
CAACCAGCTGATTGAGTTTTGA
Found at i:141346 original size:78 final size:78
Alignment explanation
Indices: 141253--141400 Score: 206
Period size: 78 Copynumber: 1.9 Consensus size: 78
141243 GCTTGGAGAG
* *
141253 GTAAAGTAAACTCTGGATATTTCTTTGATTTAATTTTCTGCGTTTCTTTTTGGTGTTTGTTCGGT
1 GTAAAGTAAACTCTGGATATTTCTTTGATTTAATTTTCTGCGATTCTTTTTGGTGTTTGTTCGAT
141318 GAGAAAAATGGAA
66 GAGAAAAATGGAA
* * * * ** * *
141331 GTAAAGTTAATTCTGGGTGTTTCTTTGATTTTTTTTTCTGGGATTCTTTTTGGTGTTTGTTTGAT
1 GTAAAGTAAACTCTGGATATTTCTTTGATTTAATTTTCTGCGATTCTTTTTGGTGTTTGTTCGAT
141396 GAGAA
66 GAGAA
141401 TATGAAGGTA
Statistics
Matches: 60, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
78 60 1.00
ACGTcount: A:0.20, C:0.07, G:0.23, T:0.49
Consensus pattern (78 bp):
GTAAAGTAAACTCTGGATATTTCTTTGATTTAATTTTCTGCGATTCTTTTTGGTGTTTGTTCGAT
GAGAAAAATGGAA
Found at i:149393 original size:16 final size:16
Alignment explanation
Indices: 149372--149418 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
149362 TTATTTGTTC
149372 AATCATTTTAATTTTG
1 AATCATTTTAATTTTG
* *
149388 AATCATTTCAGA-TTCG
1 AATCATTTTA-ATTTTG
*
149404 AATCATTTTGATTTT
1 AATCATTTTAATTTT
149419 TGTTGAATGT
Statistics
Matches: 24, Mismatches: 5, Indels: 4
0.73 0.15 0.12
Matches are distributed among these distances:
15 1 0.04
16 22 0.92
17 1 0.04
ACGTcount: A:0.30, C:0.11, G:0.09, T:0.51
Consensus pattern (16 bp):
AATCATTTTAATTTTG
Found at i:149503 original size:24 final size:23
Alignment explanation
Indices: 149453--149504 Score: 56
Period size: 21 Copynumber: 2.3 Consensus size: 23
149443 TTTCTTTAGA
*
149453 TAATAATGTTATGTATTTATATG
1 TAATATTGTTATGTATTTATATG
149476 --ATATTGTTAT-TATTTATCAGTG
1 TAATATTGTTATGTATTTAT-A-TG
149498 TAATATT
1 TAATATT
149505 CTAAATAAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 7
0.75 0.03 0.22
Matches are distributed among these distances:
20 7 0.29
21 10 0.42
22 2 0.08
24 5 0.21
ACGTcount: A:0.33, C:0.02, G:0.12, T:0.54
Consensus pattern (23 bp):
TAATATTGTTATGTATTTATATG
Found at i:154884 original size:31 final size:31
Alignment explanation
Indices: 154860--154944 Score: 102
Period size: 31 Copynumber: 2.8 Consensus size: 31
154850 TTTTATATTA
154860 TTTAAAAGTT-GAAGAAAAAAATTTTAAGTCT
1 TTTAAAAGTTGGAA-AAAAAAATTTTAAGTCT
* *
154891 TTTAAAAGTTGGTAAAAAAAATTTTGAGTC-
1 TTTAAAAGTTGGAAAAAAAAATTTTAAGTCT
* **
154921 CTTAAAAGTTAAAAAAAAAAATTT
1 TTTAAAAGTTGGAAAAAAAAATTT
154945 GGGACCTCTT
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
30 20 0.43
31 25 0.53
32 2 0.04
ACGTcount: A:0.51, C:0.04, G:0.12, T:0.34
Consensus pattern (31 bp):
TTTAAAAGTTGGAAAAAAAAATTTTAAGTCT
Found at i:154990 original size:31 final size:31
Alignment explanation
Indices: 154860--154992 Score: 100
Period size: 31 Copynumber: 4.3 Consensus size: 31
154850 TTTTATATTA
* * *
154860 TTTAAAAGTT-G-AAGAAAAAAATTTTAAGTC
1 TTTAAAAGTTGGTAAAAAAAAAATTTT-GGAC
*
154890 TTTTAAAAGTTGGT--AAAAAAAATTTTGAGTC
1 -TTTAAAAGTTGGTAAAAAAAAAATTTTG-GAC
* * *
154921 CTTAAAAGTT--AAAAAAAAAAATTTGGGACC
1 TTTAAAAGTTGGTAAAAAAAAAATTTTGGA-C
154951 TCTTAAAAGTTGGTAAAAAAAAAATTTTGG-C
1 T-TTAAAAGTTGGTAAAAAAAAAATTTTGGAC
154982 TTTCAAAAGTT
1 TTT-AAAAGTT
154993 AAAATTTTTT
Statistics
Matches: 83, Mismatches: 9, Indels: 20
0.74 0.08 0.18
Matches are distributed among these distances:
29 1 0.01
30 24 0.29
31 42 0.51
32 1 0.01
33 15 0.18
ACGTcount: A:0.47, C:0.06, G:0.14, T:0.33
Consensus pattern (31 bp):
TTTAAAAGTTGGTAAAAAAAAAATTTTGGAC
Found at i:160871 original size:13 final size:13
Alignment explanation
Indices: 160853--160877 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
160843 TTAAAGTAAT
160853 TTCAAATTATTTA
1 TTCAAATTATTTA
160866 TTCAAATTATTT
1 TTCAAATTATTT
160878 TAAATTGAAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (13 bp):
TTCAAATTATTTA
Found at i:166086 original size:224 final size:219
Alignment explanation
Indices: 165697--166106 Score: 660
Period size: 224 Copynumber: 1.8 Consensus size: 219
165687 CTTTTTTTGT
* * *
165697 TCGAATTAGTAAAGTTCTATACATTTGGATGCATAATTTAGATTATTTTTTATAATTAAGTTGAT
1 TCGAATTAGTAAAGTTCAATACATTTGGATACAGAATTTAGATTATTTTTTATAATTAAGTTGAT
165762 CTCAATGCTTATATTATTGTTTTGCAACGAATTAAATGGTTTGAAAAGAGTAAGGTTAATCGGTT
66 CTCAATGCTTATATTATTGTTTTGCAACGAATTAAATGGTTTGAAAAGAGTAAGGTTAATCGGTT
*
165827 AGGAGGATTTAATGTTTTATGTTTGATTATAGATTTTGATTTTCATGGAAAATTTGAATTTTTTG
131 AGGAGGATTTAATGTTTTATGTTTGATTATAGATTTTGATTTTCAGGGAAAATTTGAATTTTTTG
165892 TTTTGTTTTGTTCGAATAAGATGC
196 TTTTGTTTTGTTCGAATAAGATGC
*
165916 TCGAATTAGTAAAGTTCAATACATTTGGATACAGAATTTAGAATTTTTTTTTTTTTATAAATTAA
1 TCGAATTAGTAAAGTTCAATACATTTGGATACAGAATTTAG-A----TTATTTTTTAT-AATTAA
* * * *
165981 GTTGATCTCAATGCTTATATTATTGTTTTGTAATGAGTTAAATGGTTTG-AAGGAGTAAGGTTAA
60 GTTGATCTCAATGCTTATATTATTGTTTTGCAACGAATTAAATGGTTTGAAAAGAGTAAGGTTAA
* *
166045 TCGGTTAGGAGGATTTAGTGTTTTATGTTTGATTCTAGATTTTGATTTTCAGGGAAAATTTG
125 TCGGTTAGGAGGATTTAATGTTTTATGTTTGATTATAGATTTTGATTTTCAGGGAAAATTTG
166107 TTTATATTTT
Statistics
Matches: 174, Mismatches: 11, Indels: 7
0.91 0.06 0.04
Matches are distributed among these distances:
219 38 0.22
220 1 0.01
224 83 0.48
225 52 0.30
ACGTcount: A:0.30, C:0.06, G:0.19, T:0.45
Consensus pattern (219 bp):
TCGAATTAGTAAAGTTCAATACATTTGGATACAGAATTTAGATTATTTTTTATAATTAAGTTGAT
CTCAATGCTTATATTATTGTTTTGCAACGAATTAAATGGTTTGAAAAGAGTAAGGTTAATCGGTT
AGGAGGATTTAATGTTTTATGTTTGATTATAGATTTTGATTTTCAGGGAAAATTTGAATTTTTTG
TTTTGTTTTGTTCGAATAAGATGC
Found at i:166287 original size:232 final size:232
Alignment explanation
Indices: 165992--166770 Score: 685
Period size: 232 Copynumber: 3.2 Consensus size: 232
165982 TTGATCTCAA
** * * * *
165992 TGCTTATATTATTGTTTTGTAATGAGTTAAATGGTTTGAAGGAGTAAGGTTAATCGGTTAGGAGG
1 TGCTTATATTATTGTTTCATAATGAATTAAATGGTTTGAAAGAGTAAGGTTAATTGATTAGGAGG
*
166057 ATTTAGTGTTTTATGTTTGATTCTAGATTTTGATTTTCAGGGAAAATTTG-TTTATAT-TTTTGG
66 ATTTAGTCTTTTATGTTTGATTCTAGATTTTGATTTTCAGGGAAAATTTGATTTATATATTTTGG
* * * *
166120 TTGAAATAAATGTTTGAATTAGT-AAGCTCTATGCATTTGGATTACAGAATGCGGAAAATTTTTG
131 TTGAAATAGATGTTTGAATTAGTAAAG-TTTATACATTTGGATTACAGAATACGGAAAATTTTTG
* **
166184 A-GTTTTAAATTTTTTTTAAGAAAA-AA-ATCAGTTAACTAAG
195 ACATTTTAAA----TTGCAA-AAAATAATATCAGTTAACTAAG
* * *
166224 TGCTTATGTTATTGTTTCATAGTGAATTAAATGTTTTGAAAGAGTAAGGTTAATTGATTAGGAGG
1 TGCTTATATTATTGTTTCATAATGAATTAAATGGTTTGAAAGAGTAAGGTTAATTGATTAGGAGG
* *
166289 ATTTAGTCTTTTATGTTCGATTCTATATTTTGATTTTCAGGGAAAATTTGATATATATATATACA
66 ATTTAGTCTTTTATGTTTGATTCTAGATTTTGATTTTCAGGGAAAATTTG--AT-T-TATAT---
*
166354 CACACACACACATATTTGGTTGAAATAGATGTTTGAATTAGTGAAGTTTCATACATTTGGA-TAC
124 -----------AT-TTTGGTTGAAATAGATGTTTGAATTAGTAAAGTTT-ATACATTTGGATTAC
* * * * * *
166418 AGAATACAGAAAAATTGTGAACATTTTACATTGCAAAAAATAATTTCAGTTATCTAAG
176 AGAATACGGAAAATTTTTG-ACATTTTAAATTGCAAAAAATAATATCAGTTAACTAAG
* * * *
166476 TGCTTATTTTATTGTTTCATAATGAACTAAACGGTTTGAAAGAGTAAGGTTAATTGATGAGGAGG
1 TGCTTATATTATTGTTTCATAATGAATTAAATGGTTTGAAAGAGTAAGGTTAATTGATTAGGAGG
* * * * *
166541 ATTTAGTCTTTTATG-CTGATTCTAGATTTTGATTTTCAGTGAAAATTTGAAATTTTTTTTGTTT
66 ATTTAGTCTTTTATGTTTGATTCTAGATTTTGATTTTCAGGGAAAATTTG--A-TTTATATATTT
* *
166605 TGATTTGGTAAATAGATGTTTGAATTCGTAAAGTTTTATACATTTGGATTACAGAATACGGAAAA
128 TG-GTT-G-AAATAGATGTTTGAATTAGTAAAG-TTTATACATTTGGATTACAGAATACGGAAAA
* ***** * * *
166670 TTTTTGAACA-TTTACATTTTTTTGTTTTTAATAATTTCGGTTTATCTAAG
189 TTTTTG-ACATTTTA-A----ATTGCAAAAAATAATATCAG-TTAACTAAG
* * *
166720 TGCTTATATTATTGTTCCATAATGAATTAAAAGGTTGGAAAGAGTAAGGTT
1 TGCTTATATTATTGTTTCATAATGAATTAAATGGTTTGAAAGAGTAAGGTT
166771 TGATTCTAGA
Statistics
Matches: 450, Mismatches: 58, Indels: 66
0.78 0.10 0.11
Matches are distributed among these distances:
232 103 0.23
235 5 0.01
236 4 0.01
237 6 0.01
238 37 0.08
239 26 0.06
243 13 0.03
244 55 0.12
250 7 0.02
251 39 0.09
252 88 0.20
253 47 0.10
254 14 0.03
255 6 0.01
ACGTcount: A:0.32, C:0.07, G:0.18, T:0.43
Consensus pattern (232 bp):
TGCTTATATTATTGTTTCATAATGAATTAAATGGTTTGAAAGAGTAAGGTTAATTGATTAGGAGG
ATTTAGTCTTTTATGTTTGATTCTAGATTTTGATTTTCAGGGAAAATTTGATTTATATATTTTGG
TTGAAATAGATGTTTGAATTAGTAAAGTTTATACATTTGGATTACAGAATACGGAAAATTTTTGA
CATTTTAAATTGCAAAAAATAATATCAGTTAACTAAG
Found at i:166768 original size:244 final size:249
Alignment explanation
Indices: 166115--166770 Score: 689
Period size: 252 Copynumber: 2.7 Consensus size: 249
166105 TGTTTATATT
* * * * *
166115 TTTGGTTGAAATAAATGTTTGAATTAGTAAGCTCTATGCATTTGGATTACAGAATGCGGAAAATT
1 TTTGGTTGAAATAGATGTTTGAATTAGTAAGTTTTATACATTTGGATTACAGAATACGGAAAATT
** * ** * *
166180 TTTG-AGTTTTAAATTTTTT-TTAAGAAA-AAAATCAGTTAACTAAGTGCTTATGTTATTGTTTC
66 TTTGAACATTTACATTTTTTGTTAA-AAATAATTTCAGTTATCTAAGTGCTTATATTATTGTTTC
* * * * *
166242 ATAGTGAATTAAATGTTTTGAAAGAGTAAGGTTAATTGATTAGGAGGATTTAGTCTTTTATGTTC
130 ATAATGAATTAAAAGGTTTGAAAGAGTAAGGTTAATTGATGAGGAGGATTTAGTCTTTTATGCTC
*
166307 GATTCTATATTTTGATTTTCAGGGAAAATTTGATATATATATATACACACACACACACATA
195 GATTCTAGATTTTGATTTTCAGGGAAAATTTGATATATATATAT------ACACACACATA
* * *
166368 TTTGGTTGAAATAGATGTTTGAATTAGTGAAGTTTCATACATTTGGA-TACAGAATACAGAAAAA
1 TTTGGTTGAAATAGATGTTTGAATTAGT-AAGTTTTATACATTTGGATTACAGAATACGGAAAAT
* ** *
166432 TTGTGAACATTTTACA----TTGCAAAAAATAATTTCAGTTATCTAAGTGCTTATTTTATTGTTT
65 TTTTGAACA-TTTACATTTTTTGTTAAAAATAATTTCAGTTATCTAAGTGCTTATATTATTGTTT
* *
166493 CATAATGAACTAAACGGTTTGAAAGAGTAAGGTTAATTGATGAGGAGGATTTAGTCTTTTATGCT
129 CATAATGAATTAAAAGGTTTGAAAGAGTAAGGTTAATTGATGAGGAGGATTTAGTCTTTTATGCT
* ********
166558 -GATTCTAGATTTTGATTTTCAGTGAAAATTTGA-A-AT-T-T-T-TTTTGTTTTGA
194 CGATTCTAGATTTTGATTTTCAGGGAAAATTTGATATATATATATACACACACAT-A
*
166608 TTTGG-T-AAATAGATGTTTGAATTCGTAAAGTTTTATACATTTGGATTACAGAATACGGAAAAT
1 TTTGGTTGAAATAGATGTTTGAATTAGT-AAGTTTTATACATTTGGATTACAGAATACGGAAAAT
*** *
166671 TTTTGAACATTTACATTTTTTTGTTTTTAATAATTTCGGTTTATCTAAGTGCTTATATTATTGTT
65 TTTTGAACATTTACA-TTTTTTGTTAAAAATAATTTCAG-TTATCTAAGTGCTTATATTATTGTT
* *
166736 CCATAATGAATTAAAAGGTTGGAAAGAGTAAGGTT
128 TCATAATGAATTAAAAGGTTTGAAAGAGTAAGGTT
166771 TGATTCTAGA
Statistics
Matches: 339, Mismatches: 51, Indels: 35
0.80 0.12 0.08
Matches are distributed among these distances:
238 42 0.12
239 25 0.07
240 6 0.02
243 13 0.04
244 55 0.16
246 1 0.00
247 1 0.00
248 1 0.00
249 2 0.01
250 1 0.00
251 36 0.11
252 91 0.27
253 45 0.13
254 15 0.04
255 5 0.01
ACGTcount: A:0.33, C:0.07, G:0.18, T:0.42
Consensus pattern (249 bp):
TTTGGTTGAAATAGATGTTTGAATTAGTAAGTTTTATACATTTGGATTACAGAATACGGAAAATT
TTTGAACATTTACATTTTTTGTTAAAAATAATTTCAGTTATCTAAGTGCTTATATTATTGTTTCA
TAATGAATTAAAAGGTTTGAAAGAGTAAGGTTAATTGATGAGGAGGATTTAGTCTTTTATGCTCG
ATTCTAGATTTTGATTTTCAGGGAAAATTTGATATATATATATACACACACATA
Found at i:172397 original size:18 final size:18
Alignment explanation
Indices: 172348--172412 Score: 60
Period size: 18 Copynumber: 3.5 Consensus size: 18
172338 TCAACAAAAG
* *
172348 ATTTAAAAATTTAAAATA
1 ATTTTAAAATTCAAAATA
**
172366 AGTTTTTATCATTCAAAATA
1 A--TTTTAAAATTCAAAATA
172386 ATTTTAAAATTCAAAAT-
1 ATTTTAAAATTCAAAATA
172403 ATTTATAAAA
1 ATTT-TAAAA
172413 ATTTTAAAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
17 4 0.11
18 20 0.53
20 14 0.37
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.42
Consensus pattern (18 bp):
ATTTTAAAATTCAAAATA
Found at i:176786 original size:155 final size:154
Alignment explanation
Indices: 176500--176968 Score: 403
Period size: 164 Copynumber: 3.0 Consensus size: 154
176490 TTTTATTAGT
* * *
176500 CACTTATTCGAGTTCT-GCTAATGTAAGAAGTGTGTTATGAATTCT-CGAAATT--ATACTTTAC
1 CACTTACTCGAGTT-TGGCTAATGTAAGAAGTGTGTCATGAATTCTCCGAACTTGCATACTTTAC
* * * * *** * *
176561 TCAAACTCTTCTTTTACTCTAAAATACCCATGTTTGAAACTTGTTTTTGACACATATTCATTTAC
65 TCAAACTTTTCTTTT-CTCTAAAATACCCATGCTTGATATTTGTTTTTGACATGCATGCA--AAC
176626 A--GGTTTTGATTGTTTTTAGACATA-A
127 ATGGGTTTTGATTGTTTTTAGACATACA
* *
176651 CACTTACTCGAGTTTGGCTAATGCAAGAAGTGTGTCATGAATTCTCCGAACTGTGCATACTTTGC
1 CACTTACTCGAGTTTGGCTAATGTAAGAAGTGTGTCATGAATTCTCCGAACT-TGCATACTTTAC
* * * *
176716 TCAATCTTTTCGTTTTCTCTAAAACATCCATGCTTGATATTTGTTTTTGACATGCATGCAAGCAT
65 TCAAACTTTTC-TTTTCTCTAAAATACCCATGCTTGATATTTGTTTTTGACATGCATGCAAACAT
* * **
176781 GGGTTTTTGGTTGGTCATGTATACTCGTATTACA
129 GGG-TTTTGATT-GT--T-TTTAGAC--A-TACA
* * * ** * ** * * *
176815 CACTTACTCAAGTTCGGTTAATGTTCGACGTGCATCATGAATTCTCTGAACTATGCTTACCTTAC
1 CACTTACTCGAGTTTGGCTAATGTAAGAAGTGTGTCATGAATTCTCCGAACT-TGCATACTTTAC
**
176880 TCAAACTTTTCATTTTCTCTAAAATACCCATGCTCAATATTTGTTTTTGACATGCATGCAAACAT
65 TCAAACTTTTC-TTTTCTCTAAAATACCCATGCTTGATATTTGTTTTTGACATGCATGCAAACAT
* *
176945 GCGTTTTTTATTGTTTTTAGACAT
129 G-GGTTTTGATTGTTTTTAGACAT
176969 GTACATTCAT
Statistics
Matches: 251, Mismatches: 49, Indels: 30
0.76 0.15 0.09
Matches are distributed among these distances:
150 1 0.00
151 40 0.16
152 5 0.02
153 3 0.01
155 54 0.22
156 11 0.04
157 3 0.01
158 1 0.00
159 1 0.00
160 8 0.03
161 1 0.00
162 1 0.00
163 4 0.02
164 117 0.47
165 1 0.00
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.41
Consensus pattern (154 bp):
CACTTACTCGAGTTTGGCTAATGTAAGAAGTGTGTCATGAATTCTCCGAACTTGCATACTTTACT
CAAACTTTTCTTTTCTCTAAAATACCCATGCTTGATATTTGTTTTTGACATGCATGCAAACATGG
GTTTTGATTGTTTTTAGACATACA
Found at i:181112 original size:29 final size:30
Alignment explanation
Indices: 181054--181114 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 30
181044 AAGTTGGGAC
* * **
181054 AAAAATATTATGTCTGAATTTTTTTTTTTG
1 AAAAAGATTATGTCTGAATATTTTAATTTG
181084 AAAAAGATTATGTCTGAA-ATTTTAATTTG
1 AAAAAGATTATGTCTGAATATTTTAATTTG
181113 AA
1 AA
181115 CAAAAAAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
29 10 0.37
30 17 0.63
ACGTcount: A:0.38, C:0.03, G:0.11, T:0.48
Consensus pattern (30 bp):
AAAAAGATTATGTCTGAATATTTTAATTTG
Found at i:181956 original size:148 final size:148
Alignment explanation
Indices: 181688--181981 Score: 579
Period size: 148 Copynumber: 2.0 Consensus size: 148
181678 GGTCAATGAT
181688 AGTGTTCATATTAACCTCAGCAGCTATTAACCTCACATTGATTGATCGGTTCCTTTTTCCGCTAT
1 AGTGTTCATATTAACCTCAGCAGCTATTAACCTCACATTGATTGATCGGTTCCTTTTTCCGCTAT
181753 GGCAGAAGATAAGCCAATGCCCCTTCACCGGATTCGACTTGGTCACTTATTTAACATGACAGGTA
66 GGCAGAAGATAAGCCAATGCCCCTTCACCGGATTCGACTTGGTCACTTATTTAACATGACAGGTA
181818 TGGCTGTTGCTTCCTTAA
131 TGGCTGTTGCTTCCTTAA
181836 AGTGTTCATATTAACCTCAGCAGCTATTAACCTCACATTGATTGATCGGTTCCTTTTTCCGCTAT
1 AGTGTTCATATTAACCTCAGCAGCTATTAACCTCACATTGATTGATCGGTTCCTTTTTCCGCTAT
*
181901 GGCAGAAGATAAGCCAATGCCCCTTCACCGGATTGGACTTGGTCACTTATTTAACATGACAGGTA
66 GGCAGAAGATAAGCCAATGCCCCTTCACCGGATTCGACTTGGTCACTTATTTAACATGACAGGTA
181966 TGGCTGTTGCTTCCTT
131 TGGCTGTTGCTTCCTT
181982 GGTGGAATCA
Statistics
Matches: 145, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
148 145 1.00
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.33
Consensus pattern (148 bp):
AGTGTTCATATTAACCTCAGCAGCTATTAACCTCACATTGATTGATCGGTTCCTTTTTCCGCTAT
GGCAGAAGATAAGCCAATGCCCCTTCACCGGATTCGACTTGGTCACTTATTTAACATGACAGGTA
TGGCTGTTGCTTCCTTAA
Found at i:185791 original size:5 final size:5
Alignment explanation
Indices: 185783--185808 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
185773 CTCCCTCCCT
185783 CACCC CACCC CACCC CACCC CACCC C
1 CACCC CACCC CACCC CACCC CACCC C
185809 CAAATGGTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.81, G:0.00, T:0.00
Consensus pattern (5 bp):
CACCC
Found at i:198233 original size:16 final size:17
Alignment explanation
Indices: 198193--198252 Score: 54
Period size: 16 Copynumber: 3.5 Consensus size: 17
198183 AATTTAACAT
198193 TTATAAAATATTCATAAA
1 TTATAAAA-ATTCATAAA
*
198211 ATA-AAAAATTCA-AAA
1 TTATAAAAATTCATAAA
*
198226 TTATAAAAAAAGTCATAAA
1 TTAT--AAAAATTCATAAA
198245 TTA-AAAAA
1 TTATAAAAA
198253 ACACGAAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
15 5 0.14
16 10 0.29
17 4 0.11
18 10 0.29
19 6 0.17
ACGTcount: A:0.65, C:0.05, G:0.02, T:0.28
Consensus pattern (17 bp):
TTATAAAAATTCATAAA
Found at i:198234 original size:18 final size:18
Alignment explanation
Indices: 198213--198253 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
198203 TTCATAAAAT
*
198213 AAAAAATTCA-AAATTATA
1 AAAAAAGTCATAAATTA-A
198231 AAAAAAGTCATAAATTAA
1 AAAAAAGTCATAAATTAA
198249 AAAAA
1 AAAAA
198254 CACGAAATAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 15 0.71
19 6 0.29
ACGTcount: A:0.71, C:0.05, G:0.02, T:0.22
Consensus pattern (18 bp):
AAAAAAGTCATAAATTAA
Found at i:202259 original size:5 final size:5
Alignment explanation
Indices: 202249--202277 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
202239 CTAATTAGAT
202249 TTAGC TTAGC TTAGC TTAGC TTAGC TTAG
1 TTAGC TTAGC TTAGC TTAGC TTAGC TTAG
202278 TATGTAGCTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.21, C:0.17, G:0.21, T:0.41
Consensus pattern (5 bp):
TTAGC
Found at i:206430 original size:17 final size:16
Alignment explanation
Indices: 206387--206439 Score: 52
Period size: 17 Copynumber: 3.2 Consensus size: 16
206377 GCAAACTATG
*
206387 AACTGCAAGCTCACCA
1 AACTGCGAGCTCACCA
* *
206403 AATGTGTGAGCTCACCA
1 AA-CTGCGAGCTCACCA
*
206420 AGACTGCGAGCTCTCCA
1 A-ACTGCGAGCTCACCA
206437 AAC
1 AAC
206440 ATTAAAGCTC
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
16 4 0.14
17 24 0.83
18 1 0.03
ACGTcount: A:0.32, C:0.32, G:0.19, T:0.17
Consensus pattern (16 bp):
AACTGCGAGCTCACCA
Found at i:207048 original size:28 final size:28
Alignment explanation
Indices: 207016--207073 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
207006 AACGCAAACT
207016 CACGCTCTCCTGCATTGACAACAATACC
1 CACGCTCTCCTGCATTGACAACAATACC
207044 CACGCTCTCCTGCATTGACAACAATACC
1 CACGCTCTCCTGCATTGACAACAATACC
207072 CA
1 CA
207074 TGTCAATTGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.29, C:0.40, G:0.10, T:0.21
Consensus pattern (28 bp):
CACGCTCTCCTGCATTGACAACAATACC
Found at i:207411 original size:185 final size:185
Alignment explanation
Indices: 207057--207392 Score: 498
Period size: 185 Copynumber: 1.8 Consensus size: 185
207047 GCTCTCCTGC
** * *
207057 ATTGACAACAATACCCATGTCAATTGAGTTAAGACTCAATCAACAATATTTTTGAACAATCTCAT
1 ATTGACAACAATACCCATACCAATTGAGATAAAACTCAATCAACAATATTTTTGAACAATCTCAT
* *
207122 TATAGGTTCTAATCATATTTGCTCTTTTTAACATAATACCTAAAACTACCTATAGCTTCTCCCCA
66 TATAGGTTCTAATCATATCTGCTCTTTTTAACACAATACCTAAAACTACCTATAGCTTCTCCCCA
*
207187 ACTCATAAATAGGAGGATAATGCACTTCAGCACACTCGAATCCATGTCCTTTTGT
131 ACCCATAAATAGGAGGATAATGCACTTCAGCACACTCGAATCCATGTCCTTTTGT
* *
207242 ATTGGCAACAATACCCATACCAATTGAGATAAAACTCAATCAACAATATTTTTGAACAATCTTAT
1 ATTGACAACAATACCCATACCAATTGAGATAAAACTCAATCAACAATATTTTTGAACAATCTCAT
* * * *
207307 TATAGGTTCTAATCATATCTG-TTTTGTTTAACACAATATCTAGAACTATCC-ATAGCCTT-TCT
66 TATAGGTTCTAATCATATCTGCTCTT-TTTAACACAATACCTAAAACTA-CCTATAG-CTTCTCC
*
207369 TCAACCCATAAATAGGAGGATAAT
128 CCAACCCATAAATAGGAGGATAAT
207393 AGGTTTCAGC
Statistics
Matches: 134, Mismatches: 14, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
184 3 0.02
185 126 0.94
186 5 0.04
ACGTcount: A:0.36, C:0.21, G:0.10, T:0.33
Consensus pattern (185 bp):
ATTGACAACAATACCCATACCAATTGAGATAAAACTCAATCAACAATATTTTTGAACAATCTCAT
TATAGGTTCTAATCATATCTGCTCTTTTTAACACAATACCTAAAACTACCTATAGCTTCTCCCCA
ACCCATAAATAGGAGGATAATGCACTTCAGCACACTCGAATCCATGTCCTTTTGT
Found at i:207449 original size:185 final size:185
Alignment explanation
Indices: 207061--207467 Score: 482
Period size: 185 Copynumber: 2.2 Consensus size: 185
207051 TCCTGCATTG
** * *
207061 ACAACAATACCCATGTCAATTGAGTTAAGACTCAATCAACAATATTTTTGAACAATCTCATTATA
1 ACAACAATACCCATACCAATTGAGATAAAACTCAATCAACAATATTTTTGAACAATCTCATTATA
* * *
207126 GGTTCTAATCATATTTGCTCTTTTTAACATAATACCTAAAACTACCTATAGCTTCTCCCCAACTC
66 GGTTCTAATCATATCTGCTCTTTTTAACACAATACCTAAAACTACCTATAGCTTCTCCCCAACCC
* ** * *
207191 ATAAATAGGAGGATAATGCACTTCAGCACACTCGAATCCATGTCCTTTTGTATTG
131 ATAAATAGGAGGATAATGCACTTCAGCACACTCGAATCCATATCCTCCTATATTA
* *
207246 GCAACAATACCCATACCAATTGAGATAAAACTCAATCAACAATATTTTTGAACAATCTTATTATA
1 ACAACAATACCCATACCAATTGAGATAAAACTCAATCAACAATATTTTTGAACAATCTCATTATA
* * * **
207311 GGTTCTAATCATATCTG-TTTTGTTTAACACAATATCTAGAACTATCC-ATAGCCTT-TCTTCAA
66 GGTTCTAATCATATCTGCTCTT-TTTAACACAATACCTAAAACTA-CCTATAG-CTTCTCCCCAA
** * *
207373 CCCATAAATAGGAGGATAATAG-GTTTCAGCGCACTCGAA-CTTATATCCTCCTATATTA
128 CCCATAAATAGGAGGATAAT-GCACTTCAGCACACTCGAATC-CATATCCTCCTATATTA
* ** * *
207431 ACAATAATACTTATACCAATCGAAATAAAACTCAATC
1 ACAACAATACCCATACCAATTGAGATAAAACTCAATC
207468 GTTGTTTGAA
Statistics
Matches: 188, Mismatches: 29, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
184 4 0.02
185 178 0.95
186 6 0.03
ACGTcount: A:0.36, C:0.22, G:0.10, T:0.32
Consensus pattern (185 bp):
ACAACAATACCCATACCAATTGAGATAAAACTCAATCAACAATATTTTTGAACAATCTCATTATA
GGTTCTAATCATATCTGCTCTTTTTAACACAATACCTAAAACTACCTATAGCTTCTCCCCAACCC
ATAAATAGGAGGATAATGCACTTCAGCACACTCGAATCCATATCCTCCTATATTA
Found at i:208248 original size:20 final size:20
Alignment explanation
Indices: 208223--208260 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
208213 ATAAAATTTA
208223 AATTTTTTATAAA-TATTTTG
1 AATTTTTTA-AAATTATTTTG
208243 AATTTTTTAAAATTATTT
1 AATTTTTTAAAATTATTT
208261 ATTTTTTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.61
Consensus pattern (20 bp):
AATTTTTTAAAATTATTTTG
Found at i:213870 original size:29 final size:28
Alignment explanation
Indices: 213852--213907 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
213842 TTTTGGATGT
213852 TCGGAGGCATAAATGGTAATTTTGGGAAC
1 TCGGAGGCA-AAATGGTAATTTTGGGAAC
* *
213881 TCGGAGGTAAAATGGTAATTTTTGGAA
1 TCGGAGGCAAAATGGTAATTTTGGGAA
213908 AGTTTAGAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 17 0.68
29 8 0.32
ACGTcount: A:0.32, C:0.07, G:0.30, T:0.30
Consensus pattern (28 bp):
TCGGAGGCAAAATGGTAATTTTGGGAAC
Found at i:214059 original size:30 final size:29
Alignment explanation
Indices: 213786--214179 Score: 212
Period size: 30 Copynumber: 13.5 Consensus size: 29
213776 AAGTGTATAT
* *
213786 TTTTTGGAAATTCGAGGG-CAAAATGATAA
1 TTTTTGGAAGTTCGAGGGTAAAAATG-TAA
* * *
213815 -TTTTAGACA-TCCGAGGG-AAAATTGTAA
1 TTTTTGGA-AGTTCGAGGGTAAAAATGTAA
* * *
213842 -TTTTGGATGTTCG-GAGGCATAAATGGTAA
1 TTTTTGGAAGTTCGAG-GGTAAAAAT-GTAA
* *
213871 TTTTGGGAA-CTCG-GAGGT-AAAATGGTAA
1 TTTTTGGAAGTTCGAG-GGTAAAAAT-GTAA
* **
213899 TTTTTGGAAAGTT-TAGAATCAAAAAATGTAA
1 TTTTTGG-AAGTTCGAGGGT--AAAAATGTAA
* *
213930 TTTTTGGAAGTTTGGGGGT-AAAATGGTAA
1 TTTTTGGAAGTTCGAGGGTAAAAAT-GTAA
* *
213959 GTTTTGGAAGTTC-AGGGGTAAAAATGAAA
1 TTTTTGGAAGTTCGA-GGGTAAAAATGTAA
* * *
213988 TTTTTGTAAAGTGCGA-GATCAAAAATG-ATA
1 TTTTTG-GAAGTTCGAGGGT-AAAAATGTA-A
*
214018 TTTTTGTGAAGTTCGAGGTTAAAAATGGTAA
1 TTTTTG-GAAGTTCGAGGGTAAAAAT-GTAA
* * *
214049 TTTTAGGAAGTTTG-GAGGCAAAAATGTAA
1 TTTTTGGAAGTTCGAG-GGTAAAAATGTAA
* *
214078 TTTTTTTGAAGTTCGGGGGTAAAAATGTAA
1 -TTTTTGGAAGTTCGAGGGTAAAAATGTAA
214108 TTTTTGTGAAGTTCGAGGGTAAAAATGTAA
1 TTTTTG-GAAGTTCGAGGGTAAAAATGTAA
* *
214138 TTTTTGGAAAGTTTG-TGG--AAAATGTAA
1 TTTTTGG-AAGTTCGAGGGTAAAAATGTAA
*
214165 TTTTTGTGATGTTCG
1 TTTTTG-GAAGTTCG
214180 GGGAACAAAA
Statistics
Matches: 288, Mismatches: 48, Indels: 60
0.73 0.12 0.15
Matches are distributed among these distances:
26 1 0.00
27 34 0.12
28 43 0.15
29 58 0.20
30 122 0.42
31 24 0.08
32 6 0.02
ACGTcount: A:0.34, C:0.05, G:0.26, T:0.35
Consensus pattern (29 bp):
TTTTTGGAAGTTCGAGGGTAAAAATGTAA
Found at i:214082 original size:90 final size:87
Alignment explanation
Indices: 213862--214171 Score: 278
Period size: 90 Copynumber: 3.5 Consensus size: 87
213852 TCGGAGGCAT
* * * * **
213862 AAATGGTAATTTTGGGAA-CTCGGAGGTAAAATGGTAATTTTTGGAAAGTTTAGAATCAAAAAAT
1 AAATGGTAATTTT-GGAAGTTTGGAGGAAAAAT-GTAATTTTTGTAAAGTCGAG-ATC-AAAAAT
* *
213926 GTAATTTTTG-GAAGTTTGGGGGT-A
62 GTAATTTTTGTGAAGTTCGAGGGTAA
* *
213950 AAATGGTAAGTTTTGGAAGTTCAGG-GGTAAAAATGAAATTTTTGTAAAGTGCGAGATCAAAAAT
1 AAATGGTAA-TTTTGGAAGTT-TGGAGG-AAAAATGTAATTTTTGTAAAGT-CGAGATCAAAAAT
*
214014 G-ATATTTTTGTGAAGTTCGAGGTTAA
62 GTA-ATTTTTGTGAAGTTCGAGGGTAA
* * * *
214040 AAATGGTAATTTTAGGAAGTTTGGAGGCAAAAATGTAATTTTTTTGAAGTTCGGGGGT-AAAAAT
1 AAATGGTAATTTT-GGAAGTTTGGAGG-AAAAATGTAATTTTTGTAAAG-TC-GAGATCAAAAAT
214104 GTAATTTTTGTGAAGTTCGAGGGTAA
62 GTAATTTTTGTGAAGTTCGAGGGTAA
*
214130 AAAT-GTAATTTTTGGAAAGTTT-GTGG-AAAATGTAATTTTTGT
1 AAATGGTAA-TTTTGG-AAGTTTGGAGGAAAAATGTAATTTTTGT
214172 GATGTTCGGG
Statistics
Matches: 187, Mismatches: 20, Indels: 31
0.79 0.08 0.13
Matches are distributed among these distances:
87 16 0.09
88 27 0.14
89 49 0.26
90 90 0.48
91 5 0.03
ACGTcount: A:0.35, C:0.03, G:0.26, T:0.36
Consensus pattern (87 bp):
AAATGGTAATTTTGGAAGTTTGGAGGAAAAATGTAATTTTTGTAAAGTCGAGATCAAAAATGTAA
TTTTTGTGAAGTTCGAGGGTAA
Found at i:214239 original size:88 final size:87
Alignment explanation
Indices: 214019--214239 Score: 223
Period size: 88 Copynumber: 2.5 Consensus size: 87
214009 AAAATGATAT
* * * *
214019 TTTTGTGAAGTTCGAGGTTAAAAATGGTAATTTTAGG-AAGTTTGGAGGCAAAAATGTAATTTTT
1 TTTTGTGAAGTTCGAGGGTAAAAAT-ATAATTTTTGGAAAGTTT-GTGG--AAAATGTAATTTTT
* * *
214083 TTGAAGTTCGGGGGTAAAAATGTAAT
62 GTGAAGTTCGGGGGAAAAAATGTAAC
*
214109 TTTTGTGAAGTTCGAGGGTAAAAATGTAATTTTTGGAAAGTTTGTGGAAAATGTAATTTTTGTGA
1 TTTTGTGAAGTTCGAGGGTAAAAATATAATTTTTGGAAAGTTTGTGGAAAATGTAATTTTTGTGA
* *
214174 TGTTC-GGGGAACAAAAGTTTAAC
66 AGTTCGGGGGAA-AAAA-TGTAAC
* * * * *
214197 TTTTGTGAAGTTTGGGGGATCAAAATATGA-TTTTGGAGAGTTT
1 TTTTGTGAAGTTCGAGGG-TAAAAATATAATTTTTGGAAAGTTT
214240 AATGACCTAT
Statistics
Matches: 113, Mismatches: 14, Indels: 10
0.82 0.10 0.07
Matches are distributed among these distances:
86 5 0.04
87 25 0.22
88 32 0.28
89 21 0.19
90 30 0.27
ACGTcount: A:0.31, C:0.04, G:0.27, T:0.38
Consensus pattern (87 bp):
TTTTGTGAAGTTCGAGGGTAAAAATATAATTTTTGGAAAGTTTGTGGAAAATGTAATTTTTGTGA
AGTTCGGGGGAAAAAATGTAAC
Found at i:215491 original size:21 final size:20
Alignment explanation
Indices: 215467--215506 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
215457 TTGGTATTCT
215467 TGTTTACTGTTTGATATTGAA
1 TGTTTACTGTTTG-TATTGAA
**
215488 TGTTTTTTGTTTGTATTGA
1 TGTTTACTGTTTGTATTGA
215507 TTTTTAAATG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.17, C:0.03, G:0.20, T:0.60
Consensus pattern (20 bp):
TGTTTACTGTTTGTATTGAA
Found at i:215889 original size:6 final size:6
Alignment explanation
Indices: 215880--215927 Score: 53
Period size: 6 Copynumber: 7.8 Consensus size: 6
215870 CAAATTTAGG
* *
215880 TTAAAT TTAAAT TTAGGAAT TTAAAC TTAAA- ATAAAT TTAAAT TTAAA
1 TTAAAT TTAAAT TTA--AAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAA
215928 AACAAAATTA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
5 4 0.11
6 26 0.72
8 6 0.17
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.42
Consensus pattern (6 bp):
TTAAAT
Found at i:215891 original size:17 final size:16
Alignment explanation
Indices: 215866--215925 Score: 52
Period size: 17 Copynumber: 3.8 Consensus size: 16
215856 GAACATTATT
*
215866 AATTCAAATTTAGGTTA
1 AATTTAAATTTAGG-TA
215883 AATTTAAATTTAGG--
1 AATTTAAATTTAGGTA
* **
215897 AATTTAAACTTAAAATA
1 AATTTAAA-TTTAGGTA
215914 AATTTAAATTTA
1 AATTTAAATTTA
215926 AAAACAAAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
14 8 0.23
15 3 0.09
16 3 0.09
17 21 0.60
ACGTcount: A:0.48, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
AATTTAAATTTAGGTA
Found at i:215926 original size:17 final size:17
Alignment explanation
Indices: 215897--215951 Score: 74
Period size: 17 Copynumber: 3.2 Consensus size: 17
215887 TAAATTTAGG
215897 AATTTAAACTTAAAATA
1 AATTTAAACTTAAAATA
* *
215914 AATTTAAATTTAAAAACA
1 AATTTAAACTT-AAAATA
*
215932 AAATTAAACTTAAAATA
1 AATTTAAACTTAAAATA
215949 AAT
1 AAT
215952 CTGAAACAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
17 17 0.55
18 14 0.45
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (17 bp):
AATTTAAACTTAAAATA
Found at i:221616 original size:3 final size:3
Alignment explanation
Indices: 221608--221634 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
221598 ACCCCATATC
221608 TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT
221635 GGTTTCATTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:222496 original size:22 final size:21
Alignment explanation
Indices: 222454--222496 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
222444 TAAGTGAGTA
* * *
222454 TTTTTTATTAAATTTCAAATT
1 TTTTTTAATAAAGTTAAAATT
222475 TTTTTTAATAAAGTTAATAATT
1 TTTTTTAATAAAGTTAA-AATT
222497 GAATTTACAT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.58
Consensus pattern (21 bp):
TTTTTTAATAAAGTTAAAATT
Found at i:228752 original size:74 final size:72
Alignment explanation
Indices: 228659--228809 Score: 187
Period size: 74 Copynumber: 2.1 Consensus size: 72
228649 ATACCTACAC
* ** ** ** *
228659 CATACATACATACATACATTA-TCTTAACCGTTTCATAATAGCTCTTCGTTACGTAGTGTATATC
1 CATACATACATACATACATTATTC-TAACCGTTTCACAATAAATAATCGTTACAAAGTGTACATC
228723 CATCCATA
65 CATCCATA
228731 CATACATACACGTACATACATTATTCTAACCGTTTCACAATAAATAATCGTTACAAAGTGTACAT
1 CATACATACA--TACATACATTATTCTAACCGTTTCACAATAAATAATCGTTACAAAGTGTACAT
*
228796 CCATCCATC
64 CCATCCATA
228805 CATAC
1 CATAC
228810 GTATATTATT
Statistics
Matches: 67, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
72 10 0.15
74 55 0.82
75 2 0.03
ACGTcount: A:0.35, C:0.25, G:0.07, T:0.32
Consensus pattern (72 bp):
CATACATACATACATACATTATTCTAACCGTTTCACAATAAATAATCGTTACAAAGTGTACATCC
ATCCATA
Found at i:237272 original size:14 final size:14
Alignment explanation
Indices: 237250--237291 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
237240 TCGAATCTTG
* *
237250 ACCTTGAACCTCGA
1 ACCTCGAACCTCAA
237264 ACCTCGAACCTCAA
1 ACCTCGAACCTCAA
*
237278 ACTTCGAACC-CAA
1 ACCTCGAACCTCAA
237291 A
1 A
237292 ATCAAACTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
13 4 0.16
14 21 0.84
ACGTcount: A:0.36, C:0.38, G:0.10, T:0.17
Consensus pattern (14 bp):
ACCTCGAACCTCAA
Found at i:237307 original size:18 final size:19
Alignment explanation
Indices: 237274--237309 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
237264 ACCTCGAACC
*
237274 TCAAACTTCGAACCCAAAA
1 TCAAACTTCAAACCCAAAA
237293 TCAAACTT-AAACCCAAA
1 TCAAACTTCAAACCCAAA
237310 CTTTGAACCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.50, C:0.31, G:0.03, T:0.17
Consensus pattern (19 bp):
TCAAACTTCAAACCCAAAA
Found at i:244613 original size:24 final size:24
Alignment explanation
Indices: 244586--244650 Score: 57
Period size: 24 Copynumber: 2.8 Consensus size: 24
244576 TGGTAGAATT
244586 AATTTGTATATTTTTATAATAAAA
1 AATTTGTATATTTTTATAATAAAA
* * *
244610 AA-TTG-A-AATTTTATCATTATAA
1 AATTTGTATATTTTTAT-AATAAAA
*
244632 TATTT-TATATTTTTATAAT
1 AATTTGTATATTTTTATAAT
244651 TTTTAAAAGT
Statistics
Matches: 31, Mismatches: 6, Indels: 9
0.67 0.13 0.20
Matches are distributed among these distances:
21 7 0.23
22 7 0.23
23 8 0.26
24 9 0.29
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.54
Consensus pattern (24 bp):
AATTTGTATATTTTTATAATAAAA
Found at i:247987 original size:19 final size:16
Alignment explanation
Indices: 247948--247988 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 16
247938 AATTTTAACA
247948 TTTTTTATTTTTAGTAT
1 TTTTTTATTTTTA-TAT
247965 TTTTTATATTTTTATAT
1 TTTTT-TATTTTTATAT
247982 TGTTTTT
1 T-TTTTT
247989 TTAGTTTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 10 0.45
18 12 0.55
ACGTcount: A:0.17, C:0.00, G:0.05, T:0.78
Consensus pattern (16 bp):
TTTTTTATTTTTATAT
Found at i:247996 original size:19 final size:17
Alignment explanation
Indices: 247948--247999 Score: 59
Period size: 19 Copynumber: 2.9 Consensus size: 17
247938 AATTTTAACA
247948 TTTTTTATTTTTAGTATT
1 TTTTTTATTTTTA-TATT
*
247966 TTTTATATTTTTATATTGT
1 TTTTTTATTTTTATA-T-T
*
247985 TTTTTTAGTTTTATA
1 TTTTTTATTTTTATA
248000 ATCTTATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
17 2 0.07
18 13 0.45
19 14 0.48
ACGTcount: A:0.19, C:0.00, G:0.06, T:0.75
Consensus pattern (17 bp):
TTTTTTATTTTTATATT
Found at i:251978 original size:62 final size:60
Alignment explanation
Indices: 251880--252034 Score: 170
Period size: 62 Copynumber: 2.5 Consensus size: 60
251870 TTGGTTTAAT
* *
251880 AACAAATTTAACCCTCCAATGTTTAT-ATATTCTATCAATTTAATAT-AAACTCTAAAAAATTC
1 AACAAATTTAACCCT-CAATATTTATAAAATT-TATCAATTTAAT-TCAAA-TCTAAAAAATTC
* * *
251942 AACAAATTTAACCCATCAATATTTATAAAATTTATCATTTTAATTCAAATTTTAAAAATTC
1 AACAAATTTAACCC-TCAATATTTATAAAATTTATCAATTTAATTCAAATCTAAAAAATTC
* * * *
252003 AATAAATTTAACCTTCAACATTTACAAAATTT
1 AACAAATTTAACCCTCAATATTTATAAAATTT
252035 CTTAATATAA
Statistics
Matches: 81, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
60 16 0.20
61 23 0.28
62 37 0.46
63 5 0.06
ACGTcount: A:0.45, C:0.15, G:0.01, T:0.39
Consensus pattern (60 bp):
AACAAATTTAACCCTCAATATTTATAAAATTTATCAATTTAATTCAAATCTAAAAAATTC
Found at i:252060 original size:61 final size:62
Alignment explanation
Indices: 251912--252060 Score: 151
Period size: 60 Copynumber: 2.4 Consensus size: 62
251902 TTATATATTC
* * * *
251912 TATCAATTTAATAT-AAACTCTAAAAAATTCAACAAATTTAACCCATCAATATTTATAAAATT
1 TATCAATATAAT-TCAAATTCTAAAAAATTCAACAAATTTAACCCATCAACATTTACAAAATT
* * * * *
251974 TATCATTTTAATTCAAATT-TTAAAAATTCAATAAATTTAA-CCTTCAACATTTACAAAATT
1 TATCAATATAATTCAAATTCTAAAAAATTCAACAAATTTAACCCATCAACATTTACAAAATT
* * **
252034 TCTTAATATAATTGTAATTCTAAAAAA
1 TATCAATATAATTCAAATTCTAAAAAA
252061 AATTAAAAGG
Statistics
Matches: 71, Mismatches: 14, Indels: 5
0.79 0.16 0.06
Matches are distributed among these distances:
60 30 0.42
61 26 0.37
62 15 0.21
ACGTcount: A:0.48, C:0.13, G:0.01, T:0.39
Consensus pattern (62 bp):
TATCAATATAATTCAAATTCTAAAAAATTCAACAAATTTAACCCATCAACATTTACAAAATT
Found at i:259181 original size:10 final size:10
Alignment explanation
Indices: 259168--259207 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
259158 ATTCATATTT
*
259168 TTTTAAAATA
1 TTTTAAATTA
259178 TTTTAAATTA
1 TTTTAAATTA
*
259188 TATTTATATTA
1 T-TTTAAATTA
259199 TTTTAAATT
1 TTTTAAATT
259208 TAATATTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
10 17 0.65
11 9 0.35
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (10 bp):
TTTTAAATTA
Found at i:259193 original size:21 final size:23
Alignment explanation
Indices: 259169--259225 Score: 66
Period size: 21 Copynumber: 2.6 Consensus size: 23
259159 TTCATATTTT
259169 TTTAAAATATTTTAAA-TT-ATA
1 TTTAAAATATTTTAAATTTAATA
* *
259190 TTTATATTATTTTAAATTTAATA
1 TTTAAAATATTTTAAATTTAATA
*
259213 TTTAATA-ATTTTA
1 TTTAAAATATTTTA
259226 TAAAGAGAGT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
21 14 0.48
22 8 0.28
23 7 0.24
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (23 bp):
TTTAAAATATTTTAAATTTAATA
Found at i:260838 original size:2 final size:2
Alignment explanation
Indices: 260831--260861 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
260821 ATTTTGGATT
260831 TA TA TA TA TA TA TA -A TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
260862 AAAGAGAGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:260851 original size:15 final size:15
Alignment explanation
Indices: 260831--260859 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
260821 ATTTTGGATT
260831 TATATATATATATAA
1 TATATATATATATAA
260846 TATATATATATATA
1 TATATATATATATA
260860 TAAAAGAGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TATATATATATATAA
Found at i:261830 original size:48 final size:47
Alignment explanation
Indices: 261754--261884 Score: 131
Period size: 48 Copynumber: 2.7 Consensus size: 47
261744 AATGGTCTGT
* * **
261754 TGGTT-AGAGATGTTCACTCCAAAAAACTTATTCTCGCTCATG-TCATGG
1 TGGTTAAG-GATGTTCACTTC-AAGAACTTATTCTCGCAAATGAT-ATGG
*
261802 TGGTTAAGGATGTTCACTTCATAGAACTTATTCTCGCAAATGATTTGG
1 TGGTTAAGGATGTTCACTTCA-AGAACTTATTCTCGCAAATGATATGG
* * *
261850 TGGCTAAGAATGTTCATTTCGAAGAACTTATTCTC
1 TGGTTAAGGATGTTCACTTC-AAGAACTTATTCTC
261885 ACTAATGACC
Statistics
Matches: 71, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
47 1 0.01
48 66 0.93
49 4 0.06
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.36
Consensus pattern (47 bp):
TGGTTAAGGATGTTCACTTCAAGAACTTATTCTCGCAAATGATATGG
Found at i:262154 original size:23 final size:23
Alignment explanation
Indices: 262128--262171 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
262118 ATTTTATGTT
262128 TATATATTGT-ATATAAAAATAAC
1 TATAT-TTGTAATATAAAAATAAC
*
262151 TATATTTTTAATATAAAAATA
1 TATATTTGTAATATAAAAATA
262172 TGTATAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 3 0.16
23 16 0.84
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (23 bp):
TATATTTGTAATATAAAAATAAC
Found at i:264632 original size:126 final size:126
Alignment explanation
Indices: 264407--264771 Score: 509
Period size: 126 Copynumber: 2.9 Consensus size: 126
264397 CTAACCTGAG
* *
264407 AAGAATCATCACTAGTAAACATCGAAAGTGCAACTACTATGCTAGTTCAATGAAGAACATATTGA
1 AAGAATCATCACTAGTAAACATCGAAAGTGCAACTACTATGCTAGTGCAATGAAGAACATATCGA
* * *
264472 CATTGAACTCGAGATATGCAAAAGAATAACAACATATGCAGCAAA-TGGCATAAGATCCGGA
66 CATTAAACTCGAGATATGCAAAAGAATAACAACATATGCAGCAAACT-GCATAAGAACCAGA
* * * * *
264533 AAGAACCATCACTAGTAAACATCGAAAGCGCAACCACTGTGCTAGTGCAATGAAGAACATATCAA
1 AAGAATCATCACTAGTAAACATCGAAAGTGCAACTACTATGCTAGTGCAATGAAGAACATATCGA
* *
264598 CATTAAACTTGAGATATGCAAACA-AATAACAACATATGCAGCAAACTGCGTAAGAACCAGA
66 CATTAAACTCGAGATATGCAAA-AGAATAACAACATATGCAGCAAACTGCATAAGAACCAGA
* * * * *
264659 AAGAATCATCACTAGTATACATTGAGAGTGCAACTGCAATGCTAGTGCAATGAAGAACATATCGA
1 AAGAATCATCACTAGTAAACATCGAAAGTGCAACTACTATGCTAGTGCAATGAAGAACATATCGA
*
264724 CATTAAACTCGAGATATGCAAATGAATAATAACAACATATGCAGCAAA
66 CATTAAACTCGAGATATGC-AA--AAGAATAACAACATATGCAGCAAA
264772 ATCGTATGAG
Statistics
Matches: 210, Mismatches: 23, Indels: 9
0.87 0.10 0.04
Matches are distributed among these distances:
126 183 0.87
127 4 0.02
128 1 0.00
129 22 0.10
ACGTcount: A:0.44, C:0.19, G:0.17, T:0.20
Consensus pattern (126 bp):
AAGAATCATCACTAGTAAACATCGAAAGTGCAACTACTATGCTAGTGCAATGAAGAACATATCGA
CATTAAACTCGAGATATGCAAAAGAATAACAACATATGCAGCAAACTGCATAAGAACCAGA
Found at i:266866 original size:30 final size:29
Alignment explanation
Indices: 266810--266875 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 29
266800 TGGTTTAATG
*
266810 TGTAATTATATACATGAATTTTGATTTTA
1 TGTAATTATATACATGAATTTCGATTTTA
*
266839 TGTAACTT-TATACATGAAATTTCGATTTGA
1 TGTAA-TTATATACATG-AATTTCGATTTTA
*
266869 TCTAATT
1 TGTAATT
266876 CTTGTAAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 15 0.47
30 17 0.53
ACGTcount: A:0.33, C:0.08, G:0.11, T:0.48
Consensus pattern (29 bp):
TGTAATTATATACATGAATTTCGATTTTA
Found at i:274363 original size:58 final size:56
Alignment explanation
Indices: 274243--274365 Score: 151
Period size: 56 Copynumber: 2.2 Consensus size: 56
274233 AAAGAAAAAC
* * *
274243 ACTCAAGTATCAAATTGAAAAGAAAAAACTCAAGCACTATTGAATATCGAAGCCAA
1 ACTCAGGTACCAAATTGAAAAGAAAAAACTCAAGCACAATTGAATATCGAAGCCAA
*
274299 ACTCAGGTACCAAATTGGAAAA-AAAAAACTCAAGTACCAAATTGAATAAT-GAAGCCAA
1 ACTCAGGTACCAAATT-GAAAAGAAAAAACTCAAGCA-C-AATTGAAT-ATCGAAGCCAA
*
274357 AGTCAGGTA
1 ACTCAGGTA
274366 TAAAATATTA
Statistics
Matches: 58, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
56 27 0.47
57 6 0.10
58 23 0.40
59 2 0.03
ACGTcount: A:0.50, C:0.17, G:0.15, T:0.19
Consensus pattern (56 bp):
ACTCAGGTACCAAATTGAAAAGAAAAAACTCAAGCACAATTGAATATCGAAGCCAA
Found at i:274529 original size:18 final size:18
Alignment explanation
Indices: 274491--274531 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
274481 AAAAACCCAC
* *
274491 CATATATATACACACATA
1 CATATACATACACACACA
*
274509 CATATACATACACATACA
1 CATATACATACACACACA
274527 CATAT
1 CATAT
274532 TGTTCTCTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.49, C:0.24, G:0.00, T:0.27
Consensus pattern (18 bp):
CATATACATACACACACA
Found at i:280400 original size:29 final size:29
Alignment explanation
Indices: 280360--280429 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 29
280350 AATAATAACG
*
280360 TAAGTGACTAAAACGTAACATTT-CAAACA
1 TAAGTGATTAAAACGTAAC-TTTACAAACA
*
280389 TAAGTGATTAAAATGTAACTTTAGACAAACA
1 TAAGTGATTAAAACGTAACTTT--ACAAACA
*
280420 AAAGTGATTA
1 TAAGTGATTA
280430 TTTTTGTAGT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
28 3 0.09
29 17 0.49
31 15 0.43
ACGTcount: A:0.49, C:0.11, G:0.13, T:0.27
Consensus pattern (29 bp):
TAAGTGATTAAAACGTAACTTTACAAACA
Found at i:284033 original size:1 final size:1
Alignment explanation
Indices: 284027--284056 Score: 51
Period size: 1 Copynumber: 30.0 Consensus size: 1
284017 TGTAATATCC
*
284027 TTTTTTTTTTTTCTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
284057 GCGTCGCGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.03, G:0.00, T:0.97
Consensus pattern (1 bp):
T
Found at i:286033 original size:2 final size:2
Alignment explanation
Indices: 286026--286058 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
286016 GTCATATCAA
286026 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
286059 GCATTTTATC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:287599 original size:17 final size:17
Alignment explanation
Indices: 287567--287661 Score: 65
Period size: 17 Copynumber: 5.6 Consensus size: 17
287557 ATATTCGTAC
287567 AATAAT-AAAT-AAATA
1 AATAATAAAATAAAATA
287582 AATAATAAAATAAAATA
1 AATAATAAAATAAAATA
* *** *
287599 AATATTATTTTATAAT-
1 AATAATAAAATAAAATA
287615 AATAATAATAAT-AAATA
1 AATAATAA-AATAAAATA
*
287632 AATAAATATAAATAATAAGA
1 AAT-AATA-AAATAA-AATA
287652 AA-AATAAAAT
1 AATAATAAAAT
287662 GAGATTTCGA
Statistics
Matches: 61, Mismatches: 11, Indels: 14
0.71 0.13 0.16
Matches are distributed among these distances:
15 6 0.10
16 13 0.21
17 24 0.39
18 11 0.18
19 2 0.03
20 5 0.08
ACGTcount: A:0.68, C:0.00, G:0.01, T:0.31
Consensus pattern (17 bp):
AATAATAAAATAAAATA
Found at i:287647 original size:33 final size:33
Alignment explanation
Indices: 287571--287658 Score: 81
Period size: 33 Copynumber: 2.6 Consensus size: 33
287561 TCGTACAATA
*
287571 ATAAATAAATAAATAATAA-AATAAAATAAATATT
1 ATAAAT-AAT-AATAATAATAATAAAATAAATAAT
**
287605 ATTTTATAATAATAATAATAAT-AAATAAATAAAT
1 A-TAAATAATAATAATAATAATAAAATAAAT-AAT
* *
287639 ATAAATAATAAGAAAAATAA
1 ATAAATAATAATAATAATAA
287659 AATGAGATTT
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
33 31 0.70
34 10 0.23
35 3 0.07
ACGTcount: A:0.68, C:0.00, G:0.01, T:0.31
Consensus pattern (33 bp):
ATAAATAATAATAATAATAATAAAATAAATAAT
Found at i:290227 original size:26 final size:25
Alignment explanation
Indices: 290181--290234 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 25
290171 AAAATACCAA
*
290181 AAAAATTTATTTGCATAAAATGATT
1 AAAAATTTATTTGCATAAAATAATT
*
290206 AAAAATTTATTTTG-ATTTAAATAATT
1 AAAAATTTA-TTTGCA-TAAAATAATT
290232 AAA
1 AAA
290235 TGAAATTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 10 0.40
26 15 0.60
ACGTcount: A:0.50, C:0.02, G:0.06, T:0.43
Consensus pattern (25 bp):
AAAAATTTATTTGCATAAAATAATT
Found at i:296356 original size:150 final size:149
Alignment explanation
Indices: 296077--296375 Score: 535
Period size: 150 Copynumber: 2.0 Consensus size: 149
296067 TACCATTTAA
* **
296077 CTTTGGTTTTCTTTATTCATAATTAAAAACCATAAATATTTGAATTGAATCAAATTTTATTTTTA
1 CTTTGGTTTCCTTTATTCATAATTAAAAACCATAAATATTTGAATTGAATCAAAAATTATTTTTA
*
296142 TAAGATCAAAATAAAATATTTTATTTCTAAATGAGCGAAAAAACTTAAAAGTAACTTTAACAAAA
66 TAAAATCAAAATAAAATATTTTATTTCTAAATGAGCGAAAAAACTTAAAAGTAACTTTAACAAAA
296207 GGGATGAACCAAAGCAATG
131 GGGATGAACCAAAGCAATG
296226 CTTTGGTTTCCTTTATTCATAATTAAAAACCATAAATATTTGAATTGAATCAAAAATTATTTTTT
1 CTTTGGTTTCCTTTATTCATAATTAAAAACCATAAATATTTGAATTGAATCAAAAATTA-TTTTT
* *
296291 ATAAAATCAAAATAAAATATTTTATTTCTAAATTAGTGAAAAAACTTAAAAGTAACTTTAACAAA
65 ATAAAATCAAAATAAAATATTTTATTTCTAAATGAGCGAAAAAACTTAAAAGTAACTTTAACAAA
296356 AGGGATGAACCAAAGCAATG
130 AGGGATGAACCAAAGCAATG
296376 AAATTCAATT
Statistics
Matches: 143, Mismatches: 6, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
149 56 0.39
150 87 0.61
ACGTcount: A:0.45, C:0.10, G:0.09, T:0.35
Consensus pattern (149 bp):
CTTTGGTTTCCTTTATTCATAATTAAAAACCATAAATATTTGAATTGAATCAAAAATTATTTTTA
TAAAATCAAAATAAAATATTTTATTTCTAAATGAGCGAAAAAACTTAAAAGTAACTTTAACAAAA
GGGATGAACCAAAGCAATG
Found at i:297591 original size:22 final size:21
Alignment explanation
Indices: 297549--297595 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
297539 TTACTGCTGT
**
297549 TTTTCCATTGTTTTATTATTA
1 TTTTCCATTGTTTTACCATTA
*
297570 TTTTCCTATTGTTTTCCCATTA
1 TTTTCC-ATTGTTTTACCATTA
297592 TTTT
1 TTTT
297596 ATTATCATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 6 0.27
22 16 0.73
ACGTcount: A:0.15, C:0.15, G:0.04, T:0.66
Consensus pattern (21 bp):
TTTTCCATTGTTTTACCATTA
Found at i:297612 original size:33 final size:33
Alignment explanation
Indices: 297532--297612 Score: 92
Period size: 33 Copynumber: 2.5 Consensus size: 33
297522 CAGAAAAAAC
* ** * *
297532 TATCATTTTACTGCTGTTTTTCCATTGTTTTAT
1 TATCATTTCACTATTGTTTTCCCATTATTTTAT
*
297565 TATTATTTTC-CTATTGTTTTCCCATTATTTTAT
1 TATCA-TTTCACTATTGTTTTCCCATTATTTTAT
297598 TATCATTTCACTATT
1 TATCATTTCACTATT
297613 ATATTGTTAC
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
32 4 0.10
33 32 0.82
34 3 0.08
ACGTcount: A:0.19, C:0.16, G:0.05, T:0.60
Consensus pattern (33 bp):
TATCATTTCACTATTGTTTTCCCATTATTTTAT
Found at i:300325 original size:23 final size:23
Alignment explanation
Indices: 300297--300347 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
300287 TAATATTTTA
300297 AAAATATAATA-CTTAAAAAAATT
1 AAAATA-AATATCTTAAAAAAATT
* **
300320 AAAATAAATATTTTTTAAAAATT
1 AAAATAAATATCTTAAAAAAATT
300343 AAAAT
1 AAAAT
300348 TTTTATACTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 4 0.17
23 20 0.83
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (23 bp):
AAAATAAATATCTTAAAAAAATT
Found at i:304397 original size:29 final size:29
Alignment explanation
Indices: 304365--304423 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
304355 ATTGATTAAT
304365 CATTTTATAACTTTTCATAATTCACTGTC
1 CATTTTATAACTTTTCATAATTCACTGTC
304394 CATTTTATAACTTTTCATAATTCACTGTC
1 CATTTTATAACTTTTCATAATTCACTGTC
304423 C
1 C
304424 GGAAAAAAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.27, C:0.22, G:0.03, T:0.47
Consensus pattern (29 bp):
CATTTTATAACTTTTCATAATTCACTGTC
Found at i:305229 original size:20 final size:20
Alignment explanation
Indices: 305204--305245 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
305194 TAAGTAGTTA
*
305204 TATTTATAAGATTATTATTT
1 TATTTATAAAATTATTATTT
305224 TATTTATAAAATTATTATTT
1 TATTTATAAAATTATTATTT
305244 TA
1 TA
305246 ATAAATAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (20 bp):
TATTTATAAAATTATTATTT
Found at i:305255 original size:21 final size:20
Alignment explanation
Indices: 305209--305257 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
305199 AGTTATATTT
* **
305209 ATAAGATTATTATTTTATTT
1 ATAAAATTATTATTTTATAA
305229 ATAAAATTATTATTTTAATAA
1 ATAAAATTATTATTTT-ATAA
305250 ATAAAATT
1 ATAAAATT
305258 TATGTTAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 15 0.60
21 10 0.40
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (20 bp):
ATAAAATTATTATTTTATAA
Found at i:306493 original size:2 final size:2
Alignment explanation
Indices: 306488--306521 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
306478 AGTTTTTTTC
306488 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
306522 CGATAAATTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:308158 original size:9 final size:9
Alignment explanation
Indices: 308144--308168 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
308134 ACAAAACAAC
308144 AAACAAAAA
1 AAACAAAAA
308153 AAACAAAAA
1 AAACAAAAA
308162 AAACAAA
1 AAACAAA
308169 GATTTGGGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (9 bp):
AAACAAAAA
Found at i:310343 original size:18 final size:18
Alignment explanation
Indices: 310320--310354 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
310310 TTAAATATAT
310320 TATATA-AATTTATAAAAA
1 TATATACAA-TTATAAAAA
310338 TATATACAATTATAAAA
1 TATATACAATTATAAAA
310355 TACAAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (18 bp):
TATATACAATTATAAAAA
Found at i:310625 original size:24 final size:26
Alignment explanation
Indices: 310598--310652 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
310588 CTTTTTTATA
*
310598 TTTTATT-AATTTATATATT-TTAAT
1 TTTTATTAAAATTATATATTGTTAAT
*
310622 TTTTTTTAAAAATTATATATTGTTAAT
1 TTTTATT-AAAATTATATATTGTTAAT
310649 TTTT
1 TTTT
310653 TAATAATAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
24 6 0.23
26 11 0.42
27 9 0.35
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (26 bp):
TTTTATTAAAATTATATATTGTTAAT
Found at i:319622 original size:24 final size:22
Alignment explanation
Indices: 319576--319619 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
319566 ATCCTTCATG
* *
319576 TATATACCAATTTGAAGAAAAA
1 TATATACCAATATGAAAAAAAA
319598 TATATACCAATATGAAAAAAAA
1 TATATACCAATATGAAAAAAAA
319620 AATGTCTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.59, C:0.09, G:0.07, T:0.25
Consensus pattern (22 bp):
TATATACCAATATGAAAAAAAA
Found at i:333085 original size:10 final size:10
Alignment explanation
Indices: 333059--333088 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
333049 TTTGACACAA
*
333059 TACCTAGAGC
1 TACCTATAGC
333069 TACCTATAGC
1 TACCTATAGC
333079 TACCTATAGC
1 TACCTATAGC
333089 CCCTCTCAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.30, C:0.30, G:0.13, T:0.27
Consensus pattern (10 bp):
TACCTATAGC
Found at i:340215 original size:23 final size:22
Alignment explanation
Indices: 340189--340322 Score: 94
Period size: 23 Copynumber: 5.8 Consensus size: 22
340179 TTACTGTTCA
*
340189 GCACTGTGTGTGCATACT-ATTT
1 GCACT-TGTGTGCCTACTGATTT
* *
340211 CGCACTTCGTGTACTTACTG-TTT
1 -GCACTT-GTGTGCCTACTGATTT
*
340234 CGCACTTCGTGTGCTTACTGATTT
1 -GCACTT-GTGTGCCTACTGATTT
*
340258 GCGCTATGTGTGCCTACTGATTT
1 GCACT-TGTGTGCCTACTGATTT
*
340281 GCGCTATGTGTGCCTACTGGA-TT
1 GCACT-TGTGTGCCTACT-GATTT
* *
340304 GCGCTGTGTGTGCTTACTG
1 GCACT-TGTGTGCCTACTG
340323 TTTCCCCAGC
Statistics
Matches: 99, Mismatches: 7, Indels: 11
0.85 0.06 0.09
Matches are distributed among these distances:
22 2 0.02
23 91 0.92
24 6 0.06
ACGTcount: A:0.13, C:0.22, G:0.25, T:0.40
Consensus pattern (22 bp):
GCACTTGTGTGCCTACTGATTT
Found at i:340276 original size:46 final size:46
Alignment explanation
Indices: 340226--340326 Score: 118
Period size: 46 Copynumber: 2.2 Consensus size: 46
340216 TTCGTGTACT
*
340226 TACTGTTTCGCACT-TCGTGTGCTTACT-GATTTGCGCTATGTGTGCC
1 TACTGTTTCGCACTAT-GTGTGCCTACTGGA-TTGCGCTATGTGTGCC
* * *
340272 TACTGATTT-GCGCTATGTGTGCCTACTGGATTGCGCTGTGTGTGCT
1 TACTG-TTTCGCACTATGTGTGCCTACTGGATTGCGCTATGTGTGCC
340318 TACTGTTTC
1 TACTGTTTC
340327 CCCAGCACTT
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
45 3 0.06
46 38 0.81
47 6 0.13
ACGTcount: A:0.11, C:0.22, G:0.26, T:0.42
Consensus pattern (46 bp):
TACTGTTTCGCACTATGTGTGCCTACTGGATTGCGCTATGTGTGCC
Found at i:346760 original size:9 final size:9
Alignment explanation
Indices: 346746--346776 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
346736 TAAGGCCCAA
346746 ATTTGTGTC
1 ATTTGTGTC
346755 ATTTGTGTC
1 ATTTGTGTC
*
346764 ATTTGTGTT
1 ATTTGTGTC
346773 ATTT
1 ATTT
346777 TACTTTTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.13, C:0.06, G:0.19, T:0.61
Consensus pattern (9 bp):
ATTTGTGTC
Found at i:347805 original size:16 final size:18
Alignment explanation
Indices: 347784--347816 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
347774 ATATTTTCTA
347784 TTAATT-GTACA-TAATT
1 TTAATTGGTACAGTAATT
347800 TTAATTGGTACAGTAAT
1 TTAATTGGTACAGTAAT
347817 AAATATAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 5 0.33
18 4 0.27
ACGTcount: A:0.36, C:0.06, G:0.12, T:0.45
Consensus pattern (18 bp):
TTAATTGGTACAGTAATT
Found at i:351315 original size:26 final size:25
Alignment explanation
Indices: 351275--351343 Score: 79
Period size: 26 Copynumber: 2.7 Consensus size: 25
351265 AAATGATGAA
351275 ATTTTTAA-TAGAAATGAA-TTAGTTT
1 ATTTTTAATTA-AAATGAATTTA-TTT
* *
351300 ATTTTTTATCTAAAATTAATTTATTT
1 ATTTTTAAT-TAAAATGAATTTATTT
351326 ATTTTTAATTAAAATGAA
1 ATTTTTAATTAAAATGAA
351344 CAAAATGAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
25 15 0.41
26 17 0.46
27 5 0.14
ACGTcount: A:0.41, C:0.01, G:0.06, T:0.52
Consensus pattern (25 bp):
ATTTTTAATTAAAATGAATTTATTT
Found at i:354651 original size:4 final size:4
Alignment explanation
Indices: 354642--354674 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
354632 CACACTTTGA
354642 GAGG GAGG GAGG GAGG GAGG GAGG GAGG GAGG G
1 GAGG GAGG GAGG GAGG GAGG GAGG GAGG GAGG G
354675 CGTGCTTCCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.24, C:0.00, G:0.76, T:0.00
Consensus pattern (4 bp):
GAGG
Found at i:357806 original size:2 final size:2
Alignment explanation
Indices: 357799--357829 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
357789 GTGATTATTG
357799 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
357830 TAAAGAATCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:357978 original size:3 final size:3
Alignment explanation
Indices: 357972--358012 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
357962 AAAAAGGAAT
* *
357972 AGA AGA AGA AG- AGA AGA AGA AGA AGA TGA TGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
358013 GAGATAACAG
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.06
3 33 0.94
ACGTcount: A:0.61, C:0.00, G:0.34, T:0.05
Consensus pattern (3 bp):
AGA
Found at i:358884 original size:15 final size:15
Alignment explanation
Indices: 358864--358892 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
358854 GCTGCTTTTA
358864 ACCATCATCATCATC
1 ACCATCATCATCATC
358879 ACCATCATCATCAT
1 ACCATCATCATCAT
358893 ATTCAAGATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.38, G:0.00, T:0.28
Consensus pattern (15 bp):
ACCATCATCATCATC
Found at i:360031 original size:2 final size:2
Alignment explanation
Indices: 360024--360051 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
360014 CTTGAATCTC
360024 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
360052 TGGTCTCAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:361901 original size:15 final size:15
Alignment explanation
Indices: 361855--361927 Score: 53
Period size: 15 Copynumber: 4.9 Consensus size: 15
361845 GCAAAACGAT
*
361855 AATATAAATGATTAA
1 AATATAAATAATTAA
* * *
361870 AACAT-AATATTTTA
1 AATATAAATAATTAA
361884 AATATAAATAATTAA
1 AATATAAATAATTAA
*
361899 AAT-TAATATGA-TATA
1 AATATAA-ATAATTA-A
*
361914 AATAAAAATAATTA
1 AATATAAATAATTA
361928 TTTTTATAAT
Statistics
Matches: 43, Mismatches: 10, Indels: 9
0.69 0.16 0.15
Matches are distributed among these distances:
14 15 0.35
15 24 0.56
16 4 0.09
ACGTcount: A:0.60, C:0.01, G:0.03, T:0.36
Consensus pattern (15 bp):
AATATAAATAATTAA
Done.