Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015179.1 Kokia drynarioides strain JFW-HI SEQ_130223, 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: 658618
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Warning! 95 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:12396 original size:24 final size:25
Alignment explanation
Indices: 12333--12397 Score: 62
Period size: 24 Copynumber: 2.6 Consensus size: 25
12323 TAATATTTTA
*
12333 ATATATGAAATATTAATTTTAAATTT
1 ATATATGAAAT-TTAATATTAAATTT
* * * *
12359 TTTTAAGTAA-TTAATATT-AATTT
1 ATATATGAAATTTAATATTAAATTT
12382 ATATATGAAATTTAAT
1 ATATATGAAATTTAAT
12398 TAGAGTATAT
Statistics
Matches: 29, Mismatches: 9, Indels: 4
0.69 0.21 0.10
Matches are distributed among these distances:
23 11 0.38
24 12 0.41
26 6 0.21
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.51
Consensus pattern (25 bp):
ATATATGAAATTTAATATTAAATTT
Found at i:15252 original size:3 final size:3
Alignment explanation
Indices: 15244--15273 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
15234 ATTGTTTGAT
15244 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
15274 CTTTATCCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
TCA
Found at i:18435 original size:59 final size:59
Alignment explanation
Indices: 18371--18482 Score: 199
Period size: 59 Copynumber: 1.9 Consensus size: 59
18361 AAATAAATTG
18371 TTTTTTGTTATAAATATTATTAAATGGATGTTTAACCTTCCATCT-TCCTTGACATTTTA
1 TTTTTTGTTATAAATATTATTAAATGGATGTTTAACCTTCCATCTCT-CTTGACATTTTA
*
18430 TTTTTTGTTATAAATATTATTAAATGGATGTTTAACCTTTCATCTCTCTTGAC
1 TTTTTTGTTATAAATATTATTAAATGGATGTTTAACCTTCCATCTCTCTTGAC
18483 CTTTAACCAT
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
59 50 0.98
60 1 0.02
ACGTcount: A:0.27, C:0.13, G:0.09, T:0.51
Consensus pattern (59 bp):
TTTTTTGTTATAAATATTATTAAATGGATGTTTAACCTTCCATCTCTCTTGACATTTTA
Found at i:18495 original size:24 final size:24
Alignment explanation
Indices: 18460--18510 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
18450 TAAATGGATG
* *
18460 TTTAACCTTTCATC-TCTCTTGACC
1 TTTAACCATTCATCATCT-TTAACC
18484 TTTAACCATTCATCATCTTTAACC
1 TTTAACCATTCATCATCTTTAACC
18508 TTT
1 TTT
18511 CATATTCTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 21 0.88
25 3 0.12
ACGTcount: A:0.22, C:0.29, G:0.02, T:0.47
Consensus pattern (24 bp):
TTTAACCATTCATCATCTTTAACC
Found at i:24598 original size:17 final size:17
Alignment explanation
Indices: 24576--24608 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
24566 ACTAAGATTT
24576 AAATGCAATGACAATGA
1 AAATGCAATGACAATGA
24593 AAATGCAATGACAATG
1 AAATGCAATGACAATG
24609 CTTACTAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.52, C:0.12, G:0.18, T:0.18
Consensus pattern (17 bp):
AAATGCAATGACAATGA
Found at i:25062 original size:21 final size:21
Alignment explanation
Indices: 25016--25056 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
25006 TTTCTCTTTC
*
25016 ACCTCTTCAACACAAACTTCT
1 ACCTCTCCAACACAAACTTCT
25037 ACCTCTCCAACATC-AACTTC
1 ACCTCTCCAACA-CAAACTTC
25057 CTCCTCAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.32, C:0.41, G:0.00, T:0.27
Consensus pattern (21 bp):
ACCTCTCCAACACAAACTTCT
Found at i:27259 original size:54 final size:55
Alignment explanation
Indices: 27192--27301 Score: 141
Period size: 54 Copynumber: 2.0 Consensus size: 55
27182 TTATCCAGAC
* * * * *
27192 AACTGTCAAATGCGGCGACAATTTTGGTCGCAATTTTGGATATGC-CATGCAATG
1 AACTGTCAAATGCGACGACAATTCTGGACACAATTCTGGATATGCTCATGCAATG
* * *
27246 AACTGTTAGATGCGATGACAATTCTGGACACAATTCTGGATATGCTCATGCAATG
1 AACTGTCAAATGCGACGACAATTCTGGACACAATTCTGGATATGCTCATGCAATG
27301 A
1 A
27302 GTTGTCAGAT
Statistics
Matches: 47, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
54 37 0.79
55 10 0.21
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Consensus pattern (55 bp):
AACTGTCAAATGCGACGACAATTCTGGACACAATTCTGGATATGCTCATGCAATG
Found at i:27324 original size:55 final size:55
Alignment explanation
Indices: 27222--27353 Score: 133
Period size: 55 Copynumber: 2.4 Consensus size: 55
27212 ATTTTGGTCG
* * * ** * *
27222 CAATTTTGGATATGC-CATGCAATGAACTGTTAGATGCGATGACAATTCT-GGACA
1 CAATTCTGGATATGCTCATGCAATGAACTGTCAGATGCAACAAAAATTCTAAG-CA
** *
27276 CAATTCTGGATATGCTCATGCAATGAGTTGTCAGATGCAACAAAAATTCTAAGCG
1 CAATTCTGGATATGCTCATGCAATGAACTGTCAGATGCAACAAAAATTCTAAGCA
* *
27331 CAATTCTAGATATGCTTATGCAA
1 CAATTCTGGATATGCTCATGCAA
27354 CGACATTAGT
Statistics
Matches: 64, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
54 14 0.22
55 49 0.77
56 1 0.02
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (55 bp):
CAATTCTGGATATGCTCATGCAATGAACTGTCAGATGCAACAAAAATTCTAAGCA
Found at i:32615 original size:55 final size:54
Alignment explanation
Indices: 32481--32616 Score: 166
Period size: 54 Copynumber: 2.5 Consensus size: 54
32471 ACTACTAATG
* * *
32481 TCGCTGCATGAGCATATCCAGAATTGCGCCCAGAATTGTCGACGATCTAACAGC
1 TCGCTGCATGAGCATATCCAGAATTACACCCAAAATTGTCGACGATCTAACAGC
* * * *
32535 TCACTGCATTAGCATATCCAGAATTACACCCAAAATTGTC-ACCGTATCTGACAGT
1 TCGCTGCATGAGCATATCCAGAATTACACCCAAAATTGTCGA-CG-ATCTAACAGC
* *
32590 TCGCTGCATGAGCATATCGAAAATTAC
1 TCGCTGCATGAGCATATCCAGAATTAC
32617 GTTCAAAATT
Statistics
Matches: 69, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
53 1 0.01
54 37 0.54
55 31 0.45
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.25
Consensus pattern (54 bp):
TCGCTGCATGAGCATATCCAGAATTACACCCAAAATTGTCGACGATCTAACAGC
Found at i:32624 original size:55 final size:54
Alignment explanation
Indices: 32481--32626 Score: 168
Period size: 55 Copynumber: 2.7 Consensus size: 54
32471 ACTACTAATG
* *
32481 TCGCTGCATGAGCATATCCAGAATTGCGCCCAGAATTGTCGACGATCTAACAGC
1 TCGCTGCATGAGCATATCCAGAATTACGCCCAAAATTGTCGACGATCTAACAGC
* * * * *
32535 TCACTGCATTAGCATATCCAGAATTACACCCAAAATTGTC-ACCGTATCTGACAGT
1 TCGCTGCATGAGCATATCCAGAATTACGCCCAAAATTGTCGA-CG-ATCTAACAGC
* * **
32590 TCGCTGCATGAGCATATCGAAAATTACGTTCAAAATT
1 TCGCTGCATGAGCATATCCAGAATTACGCCCAAAATT
32627 ATCGCCACAT
Statistics
Matches: 76, Mismatches: 14, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
53 1 0.01
54 37 0.49
55 38 0.50
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26
Consensus pattern (54 bp):
TCGCTGCATGAGCATATCCAGAATTACGCCCAAAATTGTCGACGATCTAACAGC
Found at i:34537 original size:55 final size:55
Alignment explanation
Indices: 34441--34551 Score: 179
Period size: 55 Copynumber: 2.0 Consensus size: 55
34431 GTATCCATTG
* *
34441 GATGATAAATCATCACTTTGAAATTTGAATAGTGCTTATGAATAATTAATTTGCAA
1 GATGATAAATCATCACTTT-AAATTTGAATAGTGCTCATGAATAACTAATTTGCAA
34497 GATGATAAATCATCAC-TTATAATTTGAATAGTGCTCATGAATAACTAATTTGCAA
1 GATGATAAATCATCACTTTA-AATTTGAATAGTGCTCATGAATAACTAATTTGCAA
34552 TCTATAATTT
Statistics
Matches: 52, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
54 1 0.02
55 35 0.67
56 16 0.31
ACGTcount: A:0.40, C:0.11, G:0.14, T:0.36
Consensus pattern (55 bp):
GATGATAAATCATCACTTTAAATTTGAATAGTGCTCATGAATAACTAATTTGCAA
Found at i:34770 original size:20 final size:20
Alignment explanation
Indices: 34745--34830 Score: 61
Period size: 20 Copynumber: 4.4 Consensus size: 20
34735 TCTTAGAACC
*
34745 CTTTCATGTTTTAAGTAATT
1 CTTTCATGTTTTAAGAAATT
*
34765 CTTTCATGTATTAA-AAATT
1 CTTTCATGTTTTAAGAAATT
** * *
34784 ACTTAAAT-TCTT-AGAAACT
1 -CTTTCATGTTTTAAGAAATT
* *
34803 CTTTAATGTTTTAAGTAATT
1 CTTTCATGTTTTAAGAAATT
*
34823 CGTTCATG
1 CTTTCATG
34831 CGCTCTAATT
Statistics
Matches: 50, Mismatches: 12, Indels: 8
0.71 0.17 0.11
Matches are distributed among these distances:
18 7 0.14
19 14 0.28
20 29 0.58
ACGTcount: A:0.31, C:0.12, G:0.09, T:0.48
Consensus pattern (20 bp):
CTTTCATGTTTTAAGAAATT
Found at i:34970 original size:57 final size:57
Alignment explanation
Indices: 34899--35036 Score: 170
Period size: 57 Copynumber: 2.4 Consensus size: 57
34889 TAATTTTTTT
* * *
34899 CATGTATTACGAATTACTTACTTTCTTAACACTCTTTCATATTTGAAATAACT-CTTC
1 CATGTATTATGAATTACTTAATTTCTTAAAACTCTTTCATATTTGAAATAA-TACTTC
* * * * *
34956 CATGTATTATGAATTAATTAATTTCTTAAAACTCTTTCATGTTTTAAGTAATACTTT
1 CATGTATTATGAATTACTTAATTTCTTAAAACTCTTTCATATTTGAAATAATACTTC
* *
35013 CATATTTTATGAATTACTTAATTT
1 CATGTATTATGAATTACTTAATTT
35037 ATTAGAATCC
Statistics
Matches: 69, Mismatches: 11, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
56 1 0.01
57 68 0.99
ACGTcount: A:0.32, C:0.14, G:0.06, T:0.48
Consensus pattern (57 bp):
CATGTATTATGAATTACTTAATTTCTTAAAACTCTTTCATATTTGAAATAATACTTC
Found at i:38939 original size:24 final size:24
Alignment explanation
Indices: 38890--38937 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
38880 TGTATGAGAA
38890 TCTTCTTGTTTTTCATTTTCATTT
1 TCTTCTTGTTTTTCATTTTCATTT
38914 TCTTCTTGTTTTTCATTTT-ATTT
1 TCTTCTTGTTTTTCATTTTCATTT
38937 T
1 T
38938 TCCTTTTGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 5 0.21
24 19 0.79
ACGTcount: A:0.08, C:0.15, G:0.04, T:0.73
Consensus pattern (24 bp):
TCTTCTTGTTTTTCATTTTCATTT
Found at i:40640 original size:18 final size:18
Alignment explanation
Indices: 40617--40652 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
40607 AATATTTTTT
40617 TATTTTT-TATTTTTCTCG
1 TATTTTTCT-TTTTTCTCG
40635 TATTTTTCTTTTTTCTCG
1 TATTTTTCTTTTTTCTCG
40653 ACTTTTTGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 16 0.94
19 1 0.06
ACGTcount: A:0.08, C:0.14, G:0.06, T:0.72
Consensus pattern (18 bp):
TATTTTTCTTTTTTCTCG
Found at i:44671 original size:21 final size:20
Alignment explanation
Indices: 44633--44672 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
44623 TACCTGTTGC
* *
44633 CCGTTAACTTTGATCGTTAA
1 CCGTTAACATTGACCGTTAA
44653 CCGTTAACCATTGACCGTTA
1 CCGTTAA-CATTGACCGTTA
44673 TTTATGGAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.25, C:0.25, G:0.15, T:0.35
Consensus pattern (20 bp):
CCGTTAACATTGACCGTTAA
Found at i:60648 original size:19 final size:19
Alignment explanation
Indices: 60626--60663 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
60616 ATCAAAAAGT
60626 CGAGAAAAA-AGAAAAAATA
1 CGAGAAAAATA-AAAAAATA
60645 CGAGAAAAATAAAAAAATA
1 CGAGAAAAATAAAAAAATA
60664 AAAAAAAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 17 0.94
20 1 0.06
ACGTcount: A:0.74, C:0.05, G:0.13, T:0.08
Consensus pattern (19 bp):
CGAGAAAAATAAAAAAATA
Found at i:87387 original size:27 final size:27
Alignment explanation
Indices: 87345--87525 Score: 209
Period size: 27 Copynumber: 6.7 Consensus size: 27
87335 AAACACGTTA
87345 GAAATGGAAGCCTTTGTGGCAATCTAT
1 GAAATGGAAGCCTTTGTGGCAATCTAT
* *
87372 GAAATGGAAGCATTTGTGGCAATTTAT
1 GAAATGGAAGCCTTTGTGGCAATCTAT
* * *
87399 GGAATGAAAGCCTTTGTGGCAATTTAT
1 GAAATGGAAGCCTTTGTGGCAATCTAT
** * *
87426 GAAACAGAAACCTTTGTGGCAATTTAT
1 GAAATGGAAGCCTTTGTGGCAATCTAT
* *
87453 GAAATAGAAACCTTTGTGGCAATCTAT
1 GAAATGGAAGCCTTTGTGGCAATCTAT
* ** * * *
87480 GAAATGGAATCCTTCATCGTAAGCTAT
1 GAAATGGAAGCCTTTGTGGCAATCTAT
87507 GAAATGGAAGCCTTTGTGG
1 GAAATGGAAGCCTTTGTGG
87526 AAAATCCTAT
Statistics
Matches: 131, Mismatches: 23, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 131 1.00
ACGTcount: A:0.33, C:0.13, G:0.24, T:0.30
Consensus pattern (27 bp):
GAAATGGAAGCCTTTGTGGCAATCTAT
Found at i:87687 original size:27 final size:27
Alignment explanation
Indices: 87657--87708 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
87647 GAAGGAATAG
*
87657 TATGTATCGTGAACTCTGAAAGAACAA
1 TATGCATCGTGAACTCTGAAAGAACAA
* *
87684 TATGCATGGTGAACTCTGAAGGAAC
1 TATGCATCGTGAACTCTGAAAGAAC
87709 GATGGGTACA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.37, C:0.15, G:0.23, T:0.25
Consensus pattern (27 bp):
TATGCATCGTGAACTCTGAAAGAACAA
Found at i:90597 original size:6 final size:6
Alignment explanation
Indices: 90581--90613 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
90571 TTATAAATAT
90581 TTTTTC TTTTTTC TTTTTC -TTTTC TTTTTC TTT
1 TTTTTC -TTTTTC TTTTTC TTTTTC TTTTTC TTT
90614 CTTTTTATGT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
5 5 0.20
6 14 0.56
7 6 0.24
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTTC
Found at i:90614 original size:10 final size:11
Alignment explanation
Indices: 90589--90619 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
90579 ATTTTTTCTT
90589 TTTTCTTTTTC
1 TTTTCTTTTTC
90600 TTTTCTTTTTC
1 TTTTCTTTTTC
90611 -TTTCTTTTT
1 TTTTCTTTTT
90620 ATGTGACTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTCTTTTTC
Found at i:95782 original size:16 final size:16
Alignment explanation
Indices: 95761--95792 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
95751 TAATTTCTTG
*
95761 TCTGCTCTGTTCATCC
1 TCTGCTCTATTCATCC
95777 TCTGCTCTATTCATCC
1 TCTGCTCTATTCATCC
95793 CCATTTCACT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.09, C:0.38, G:0.09, T:0.44
Consensus pattern (16 bp):
TCTGCTCTATTCATCC
Found at i:98796 original size:29 final size:29
Alignment explanation
Indices: 98723--98791 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 29
98713 TATTTATAAG
*
98723 GACTAGATTGGTAATTTTGAGAATTTAGGA
1 GACTA-ATTCGTAATTTTGAGAATTTAGGA
*
98753 GTCTAATTCGTAATTTTGGAGAAGTTT-GGA
1 GACTAATTCGTAATTTT-GAGAA-TTTAGGA
98783 GACTTAATT
1 GAC-TAATT
98792 GAATTAGGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
29 11 0.33
30 14 0.42
31 8 0.24
ACGTcount: A:0.30, C:0.06, G:0.25, T:0.39
Consensus pattern (29 bp):
GACTAATTCGTAATTTTGAGAATTTAGGA
Found at i:104271 original size:16 final size:16
Alignment explanation
Indices: 104246--104291 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
104236 GAGGCATGTG
104246 TAAA-AAACAT-AAATA
1 TAAATAAACATGAAA-A
104261 TAAATAAACATGAAAA
1 TAAATAAACATGAAAA
* *
104277 TGAATAAAGATGAAA
1 TAAATAAACATGAAA
104292 TAAGAATAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
15 4 0.15
16 20 0.74
17 3 0.11
ACGTcount: A:0.67, C:0.04, G:0.09, T:0.20
Consensus pattern (16 bp):
TAAATAAACATGAAAA
Found at i:105111 original size:53 final size:50
Alignment explanation
Indices: 105023--105150 Score: 129
Period size: 53 Copynumber: 2.5 Consensus size: 50
105013 ACTACTTTAC
* *
105023 TTAAAAATTCAAA-TTTTTATTTCAAAATAGTTAAAAAA-AAATTTAAATT-TTGT
1 TTAAAAATTTAAACTTTTT-TTT-AAAATAGCTAAAAAATAAATTT---TTATT-T
*
105076 TTAAAAATTTAAACTTTTTCTTTAAAAT-GACTAAAAAATAGATTTTTATTT
1 TTAAAAATTTAAACTTTTT-TTTAAAATAG-CTAAAAAATAAATTTTTATTT
105127 TTAAAAATTTAAACTTTTTTTTAA
1 TTAAAAATTTAAACTTTTTTTTAA
105151 TGAAAAACAC
Statistics
Matches: 67, Mismatches: 4, Indels: 11
0.82 0.05 0.13
Matches are distributed among these distances:
50 5 0.07
51 22 0.33
52 3 0.04
53 24 0.36
54 13 0.19
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (50 bp):
TTAAAAATTTAAACTTTTTTTTAAAATAGCTAAAAAATAAATTTTTATTT
Found at i:105354 original size:148 final size:143
Alignment explanation
Indices: 104854--105361 Score: 432
Period size: 148 Copynumber: 3.5 Consensus size: 143
104844 AAAAAGTTTT
* * * * * ** ** *
104854 CTTTTTTTAAAATAAAATCACTACTTTTCTTAAAAATAAAAAAATTTATTTCGAAATAGTTAAAA
1 CTTTTTTTTAAAGAAAAACACTATTTTTCTTAAAACTCCAAACTTTTATTTCAAAATAGTTAAAA
* * * * *
104919 AAA-TC-AAATTTTGTTTAAAAAATTAAACTTTTCTCTTTTAAATGCCTAAAAAACAGATTTTT-
66 AAATTCAAAATTTTGTTTAAAAATTTAAAATTTT-TCTTTAAAATGAC--AAAAATAGATTTTTA
*
104981 TTTTT--AAATCTAAA
128 TTTTTAAAAATTTAAA
** * * * * * * *
104995 C----TTAAAAAAAAAAAGTTTACTACTTTACTTAAAAATTCAAATTTTTATTTCAAAATAGTTA
1 CTTTTTTTTAAAGAAAAA---CACTATTTTTCTTAAAACTCCAAACTTTTATTTCAAAATAGTT-
* *
105056 AAAAAAAATT-TAAATTTTGTTTAAAAATTTAAACTTTTTCTTTAAAATGACTAAAAAATAGATT
62 -AAAAAAATTCAAAATTTTGTTTAAAAATTTAAAATTTTTCTTTAAAATGAC--AAAAATAGATT
105120 TTTATTTTTAAAAATTTAAA
124 TTTATTTTTAAAAATTTAAA
* * * *
105140 CTTTTTTTTAATGAAAAACACTATTTTTCTTAAAACTCCAAATTTTTAGTTCAAAATAGTTTAAA
1 CTTTTTTTTAAAGAAAAACACTATTTTTCTTAAAACTCCAAACTTTTATTTCAAAATAGTTAAAA
* *
105205 AAATTCAAAATTTTGTTTAAAATTTTAAAATTTTTCTTTAAAATGAC-AAAATA-TTTTTTATTT
66 AAATTCAAAATTTTGTTTAAAAATTTAAAATTTTTCTTTAAAATGACAAAAATAGATTTTTATTT
105268 TTAAAAATTTAAA
131 TTAAAAATTTAAA
* * *
105281 TTTTCTTTTTTTTTTTAAAGAAAATCATTATTTTTCTTAAAACTCTAAACTTTTATTTCAAAATT
1 ----C---TTTTTTTTAAAGAAAAACACTATTTTTCTTAAAACTCCAAACTTTTATTTCAAAA-T
105346 A-TTAAAAAAA-TCAAAA
58 AGTTAAAAAAATTCAAAA
105362 AATTTCCCAA
Statistics
Matches: 307, Mismatches: 37, Indels: 40
0.80 0.10 0.10
Matches are distributed among these distances:
137 10 0.03
140 36 0.12
141 23 0.07
142 39 0.13
143 32 0.10
144 8 0.03
145 48 0.16
146 37 0.12
147 6 0.02
148 57 0.19
149 11 0.04
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.44
Consensus pattern (143 bp):
CTTTTTTTTAAAGAAAAACACTATTTTTCTTAAAACTCCAAACTTTTATTTCAAAATAGTTAAAA
AAATTCAAAATTTTGTTTAAAAATTTAAAATTTTTCTTTAAAATGACAAAAATAGATTTTTATTT
TTAAAAATTTAAA
Found at i:106304 original size:13 final size:14
Alignment explanation
Indices: 106286--106315 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
106276 GCCAATGCAA
106286 TCAGA-GTTAAATG
1 TCAGAGGTTAAATG
106299 TCAGAGGTTAAATG
1 TCAGAGGTTAAATG
106313 TCA
1 TCA
106316 ATGTACTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.37, C:0.10, G:0.23, T:0.30
Consensus pattern (14 bp):
TCAGAGGTTAAATG
Found at i:109511 original size:17 final size:17
Alignment explanation
Indices: 109489--109527 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
109479 AAAGAGTCCA
109489 CCAAACCTTAGAATCTG
1 CCAAACCTTAGAATCTG
* *
109506 CCAAACTTTAGAGTCTG
1 CCAAACCTTAGAATCTG
109523 CCAAA
1 CCAAA
109528 TGAAGAATTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.36, C:0.28, G:0.13, T:0.23
Consensus pattern (17 bp):
CCAAACCTTAGAATCTG
Found at i:111085 original size:61 final size:60
Alignment explanation
Indices: 110961--111074 Score: 142
Period size: 61 Copynumber: 1.9 Consensus size: 60
110951 TAATTTATTT
* * * *
110961 ATTTTTGAAATTTTTAGAATTAGAACTAAATTGATAAATTTTGTACATATTGAGTGCTAA
1 ATTTTTGAATTTTTTAGAATTAGAACTAAAATGATAAATTTTGTAAACATTGAGTGCTAA
*
111021 ATTTATTGAATTTTTTATAATTCA-AACTAAAATGA-AAAGTTTTGTAAACATTGA
1 ATTT-TTGAATTTTTTAGAATT-AGAACTAAAATGATAAA-TTTTGTAAACATTGA
111075 AAGGCAAATT
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
60 7 0.15
61 38 0.83
62 1 0.02
ACGTcount: A:0.40, C:0.05, G:0.11, T:0.43
Consensus pattern (60 bp):
ATTTTTGAATTTTTTAGAATTAGAACTAAAATGATAAATTTTGTAAACATTGAGTGCTAA
Found at i:113971 original size:21 final size:22
Alignment explanation
Indices: 113918--113973 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 22
113908 AAATCAATTT
* *
113918 AATTATAATCGAATGACTATAT
1 AATTATAATTGAATGACTATAA
*
113940 AATGTAT-ATTGAAT-TCTATAA
1 AAT-TATAATTGAATGACTATAA
113961 AATTATAATTGAA
1 AATTATAATTGAA
113974 ACCTTAATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
20 3 0.10
21 14 0.48
22 9 0.31
23 3 0.10
ACGTcount: A:0.46, C:0.05, G:0.09, T:0.39
Consensus pattern (22 bp):
AATTATAATTGAATGACTATAA
Found at i:119601 original size:6 final size:6
Alignment explanation
Indices: 119590--119630 Score: 57
Period size: 6 Copynumber: 7.0 Consensus size: 6
119580 AGAGGCAACC
* *
119590 TATTTT TATTTT TATTTT TAGTTT TAGTTT TATTTT T-TTTT
1 TATTTT TATTTT TATTTT TATTTT TATTTT TATTTT TATTTT
119631 CTTGAATGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
5 4 0.12
6 29 0.88
ACGTcount: A:0.15, C:0.00, G:0.05, T:0.80
Consensus pattern (6 bp):
TATTTT
Found at i:126789 original size:105 final size:107
Alignment explanation
Indices: 126597--126804 Score: 296
Period size: 105 Copynumber: 2.0 Consensus size: 107
126587 AAATAAAAAA
* *
126597 AATAAATTAGGAGTGTGTTGGGCTGAGTAACCGGGATGGAGTGTTTGGGTTGTCATTCCATTTCG
1 AATAAATTAGGAGTGTGTTGGGCTGAGTAACCGGGATGGAGAGCTTGGGTTGTCATTCCATTTCG
* * *
126662 CATTAAAAGGGCCAATGCATTCTTAAGTAAAA-AAAAATGAT
66 CATCAAAAGGACCAATACATTCTTAAGTAAAAGAAAAATGAT
* * *
126703 AATAAATT-GAGAGTGTGTTGGGTTGAGTAATCGGGATGG-GAGCTTGGGTTGTCATTTCATTTC
1 AATAAATTAG-GAGTGTGTTGGGCTGAGTAACCGGGATGGAGAGCTTGGGTTGTCATTCCATTTC
* *
126766 GCGTCAAAAGGACCAATATATTCTTAAGTAAAAGAAAAA
65 GCATCAAAAGGACCAATACATTCTTAAGTAAAAGAAAAA
126805 AAAAAAGAAA
Statistics
Matches: 90, Mismatches: 10, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
105 50 0.56
106 40 0.44
ACGTcount: A:0.33, C:0.11, G:0.26, T:0.30
Consensus pattern (107 bp):
AATAAATTAGGAGTGTGTTGGGCTGAGTAACCGGGATGGAGAGCTTGGGTTGTCATTCCATTTCG
CATCAAAAGGACCAATACATTCTTAAGTAAAAGAAAAATGAT
Found at i:127509 original size:31 final size:31
Alignment explanation
Indices: 127471--127571 Score: 87
Period size: 31 Copynumber: 3.3 Consensus size: 31
127461 GGGAATTATT
127471 GTTTAGATTTAATTCTAATTATCTTTTTAGA
1 GTTTAGATTTAATTCTAATTATCTTTTTAGA
** * ***** **
127502 GTTTAGATTGGATTC-AACTAGGGAATTATT
1 GTTTAGATTTAATTCTAATTATCTTTTTAGA
**
127532 GTTTTTATTTAATTCTAATTATCTTTTTAGA
1 GTTTAGATTTAATTCTAATTATCTTTTTAGA
127563 GTTTAGATT
1 GTTTAGATT
127572 GGATTCAACT
Statistics
Matches: 45, Mismatches: 24, Indels: 2
0.63 0.34 0.03
Matches are distributed among these distances:
30 18 0.40
31 27 0.60
ACGTcount: A:0.28, C:0.06, G:0.14, T:0.52
Consensus pattern (31 bp):
GTTTAGATTTAATTCTAATTATCTTTTTAGA
Found at i:127513 original size:61 final size:61
Alignment explanation
Indices: 127435--127586 Score: 261
Period size: 61 Copynumber: 2.5 Consensus size: 61
127425 GGATTTATAA
*
127435 TTTAGAGTTTA-ATTTGGATCCAACTAGGGAATTATTGTTTAGATTTAATTCTAATTATCTT
1 TTTAGAGTTTAGA-TTGGATTCAACTAGGGAATTATTGTTTAGATTTAATTCTAATTATCTT
**
127496 TTTAGAGTTTAGATTGGATTCAACTAGGGAATTATTGTTTTTATTTAATTCTAATTATCTT
1 TTTAGAGTTTAGATTGGATTCAACTAGGGAATTATTGTTTAGATTTAATTCTAATTATCTT
127557 TTTAGAGTTTAGATTGGATTCAACTAGGGA
1 TTTAGAGTTTAGATTGGATTCAACTAGGGA
127587 TTTCCATGTA
Statistics
Matches: 87, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
61 86 0.99
62 1 0.01
ACGTcount: A:0.29, C:0.07, G:0.17, T:0.47
Consensus pattern (61 bp):
TTTAGAGTTTAGATTGGATTCAACTAGGGAATTATTGTTTAGATTTAATTCTAATTATCTT
Found at i:137471 original size:23 final size:23
Alignment explanation
Indices: 137434--137477 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
137424 TCATCATCTT
*
137434 TTTGCATGCATTTTAT-CATTCA
1 TTTGCATGCACTTTATGCATTCA
137456 TTTGCATTGCACTTTATGCATT
1 TTTGCA-TGCACTTTATGCATT
137478 AAATTTTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 6 0.32
23 9 0.47
24 4 0.21
ACGTcount: A:0.20, C:0.18, G:0.11, T:0.50
Consensus pattern (23 bp):
TTTGCATGCACTTTATGCATTCA
Found at i:138623 original size:22 final size:22
Alignment explanation
Indices: 138598--138640 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
138588 AAAATATTTC
*
138598 ATTA-ATAATTTGGGTTTAATTA
1 ATTATATAAATTGGG-TTAATTA
*
138620 ATTATTTAAATTGGGTTAATT
1 ATTATATAAATTGGGTTAATT
138641 TTATTCTTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
ATTATATAAATTGGGTTAATTA
Found at i:141155 original size:25 final size:25
Alignment explanation
Indices: 141127--141185 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 25
141117 AAATTTCACC
* *
141127 CAAAAAATAAAAAAAGGAAAAGAAA
1 CAAAAAAAAAAAAAAAGAAAAGAAA
*
141152 CAAAAAAAAAAAAAAAGAGAAGAAA
1 CAAAAAAAAAAAAAAAGAAAAGAAA
*
141177 -AAAGAAAAA
1 CAAAAAAAAA
141186 TGAGAGGTCA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
24 8 0.27
25 22 0.73
ACGTcount: A:0.83, C:0.03, G:0.12, T:0.02
Consensus pattern (25 bp):
CAAAAAAAAAAAAAAAGAAAAGAAA
Found at i:141163 original size:22 final size:21
Alignment explanation
Indices: 141130--141185 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
141120 TTTCACCCAA
141130 AAAATAAAAAAAGGAAAAGA-AAC
1 AAAA-AAAAAAA--AAAAGAGAAC
*
141153 AAAAAAAAAAAAAAAGAGAAG
1 AAAAAAAAAAAAAAAGAGAAC
*
141174 AAAAAAGAAAAA
1 AAAAAAAAAAAA
141186 TGAGAGGTCA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 6 0.20
21 13 0.43
22 7 0.23
23 4 0.13
ACGTcount: A:0.84, C:0.02, G:0.12, T:0.02
Consensus pattern (21 bp):
AAAAAAAAAAAAAAAGAGAAC
Found at i:141167 original size:20 final size:22
Alignment explanation
Indices: 141130--141185 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 22
141120 TTTCACCCAA
141130 AAAATAAAAAAAGGAAAAGA-AAC
1 AAAA-AAAAAAA-GAAAAGAGAAC
*
141153 AAAAAAAAAAA-AAAAGAGAAG
1 AAAAAAAAAAAGAAAAGAGAAC
141174 AAAAAAGAAAAA
1 AAAAAA-AAAAA
141186 TGAGAGGTCA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
20 6 0.20
21 8 0.27
22 12 0.40
23 4 0.13
ACGTcount: A:0.84, C:0.02, G:0.12, T:0.02
Consensus pattern (22 bp):
AAAAAAAAAAAGAAAAGAGAAC
Found at i:141620 original size:112 final size:112
Alignment explanation
Indices: 141504--141712 Score: 303
Period size: 112 Copynumber: 1.9 Consensus size: 112
141494 CCATTTTAAA
* * * * *
141504 TCTTTTCATTCATACGAGCTTTGCC-TCAAATAAAATTCTATTTTATCCACCTTACTACCTTGTT
1 TCTTTTCATTCACACGAGCTTTGCCTTC-AATAAAATTCAATTTTATCCACCTTACAACCCTATT
*
141568 CAAGCATTTTTGCATCGAAATAACAGTTAGTGGACCAATTATTTTTAT
65 AAAGCATTTTTGCATCGAAATAACAGTTAGTGGACCAATTATTTTTAT
* *
141616 TCTTTTCATTCACGCGAGCTTTGCCTTCAATAAAATTCAATTTTGTCCACCTTACAACCCTATTA
1 TCTTTTCATTCACACGAGCTTTGCCTTCAATAAAATTCAATTTTATCCACCTTACAACCCTATTA
* * *
141681 AAGCATTTTTGCATTGAAATGATAGTTAGTGG
66 AAGCATTTTTGCATCGAAATAACAGTTAGTGG
141713 TCTAACGATA
Statistics
Matches: 85, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
112 83 0.98
113 2 0.02
ACGTcount: A:0.28, C:0.21, G:0.11, T:0.40
Consensus pattern (112 bp):
TCTTTTCATTCACACGAGCTTTGCCTTCAATAAAATTCAATTTTATCCACCTTACAACCCTATTA
AAGCATTTTTGCATCGAAATAACAGTTAGTGGACCAATTATTTTTAT
Found at i:142284 original size:49 final size:49
Alignment explanation
Indices: 142135--142350 Score: 154
Period size: 49 Copynumber: 4.4 Consensus size: 49
142125 GGAAACATAG
* * * *
142135 AGATATGAAGGGAAAGGTTGAGGCCACAACGGCGAACCCGGTACCTTAAA
1 AGATATGAAGGGAAAGGTTGAGGTCACAACGGCAAACCTGATACCTT-AA
* * * ** ** * *
142185 AAATGTGATGGG-AAGGATTGAGG-CTGTAACGAAAAATCC-GGTACCATAA
1 AGATATGAAGGGAAAGG-TTGAGGTC-ACAACGGCAAA-CCTGATACCTTAA
* *
142234 AGATATGAAGGGAAAGGTTTAGGTCGCAACGGCAAACCTGATACCTTAA
1 AGATATGAAGGGAAAGGTTGAGGTCACAACGGCAAACCTGATACCTTAA
* * ** * *
142283 AGATGTGATA-GG-AAGGATTGAGGTCATAACGGTGAATCTGATACCTTGA
1 AGATATGA-AGGGAAAGG-TTGAGGTCACAACGGCAAACCTGATACCTTAA
142332 AGATATGAAGGGAAAGGTT
1 AGATATGAAGGGAAAGGTT
142351 AAGGCTGCAA
Statistics
Matches: 129, Mismatches: 27, Indels: 21
0.73 0.15 0.12
Matches are distributed among these distances:
48 7 0.05
49 82 0.64
50 38 0.29
51 2 0.02
ACGTcount: A:0.37, C:0.13, G:0.30, T:0.20
Consensus pattern (49 bp):
AGATATGAAGGGAAAGGTTGAGGTCACAACGGCAAACCTGATACCTTAA
Found at i:142340 original size:98 final size:95
Alignment explanation
Indices: 142135--142502 Score: 313
Period size: 98 Copynumber: 3.7 Consensus size: 95
142125 GGAAACATAG
* * * * *
142135 AGATATGAAGGGAAAGGTTGAGGCCACAACGGCGAACCCGGTACCTTAAAAAATGTGATGGGAAG
1 AGATATGAAGGGAAAGGTTAAGG-CGCAACGGCGAACCTGATACCTT-AAAGATGTGATGGGAAG
* * * * *
142200 GATTGAGGCTGTAACGAAAAATCCGGTACCATAA
64 GATTGAGGC-ATAACGGAGAAT-CTGTACCATGA
* * *
142234 AGATATGAAGGGAAAGGTTTAGGTCGCAACGGCAAACCTGATACCTTAAAGATGTGATAGGAAGG
1 AGATATGAAGGGAAAGGTTAAGG-CGCAACGGCGAACCTGATACCTTAAAGATGTGATGGGAAGG
* *
142299 ATTGAGGTCATAACGGTGAATCTGATACCTTGA
65 ATTGAGG-CATAACGGAGAATCTG-TACCATGA
** * * *
142332 AGATATGAAGGGAAAGGTTAAGGCTGCAAAAGCGTACCTAATATCTTTAGAAGATGTGATGGGAA
1 AGATATGAAGGGAAAGGTTAAGGC-GCAACGGCGAACCTGATA-CCTTA-AAGATGTGATGGGAA
* * ** * *
142397 TGATTGAGGCCACAAAAGCGAATCTTGTACCACGA
63 GGATTGAGG-CATAACGGAGAATC-TGTACCATGA
* * * * * * * *
142432 AGATATGAAGGGAAAGGTTGAAGCCGCAATGGTGAACCTTATACCTTAGAGATATGAAGGGAAAG
1 AGATATGAAGGGAAAGGTT-AAGGCGCAACGGCGAACCTGATACCTTAAAGATGTGATGGGAAGG
142497 ATTGAG
65 ATTGAG
142503 TCCGCAATGG
Statistics
Matches: 220, Mismatches: 42, Indels: 15
0.79 0.15 0.05
Matches are distributed among these distances:
97 3 0.01
98 91 0.41
99 50 0.23
100 70 0.32
101 6 0.03
ACGTcount: A:0.37, C:0.14, G:0.29, T:0.21
Consensus pattern (95 bp):
AGATATGAAGGGAAAGGTTAAGGCGCAACGGCGAACCTGATACCTTAAAGATGTGATGGGAAGGA
TTGAGGCATAACGGAGAATCTGTACCATGA
Found at i:142420 original size:100 final size:98
Alignment explanation
Indices: 142233--142450 Score: 242
Period size: 100 Copynumber: 2.2 Consensus size: 98
142223 CGGTACCATA
* ** *
142233 AAGATATGAAGGGAAAGGTTTAGGTCGCAACGGCAAACCTGATACCTTAAAGATGTGATAGGAAG
1 AAGATATGAAGGGAAAGGTTAAGGTCGCAAAAGCAAACCTAATACCTTAAAGATGTGATAGGAAG
* * ** * **
142298 GATTGAGGTCATAACGGTGAATC-TGATACCTTG
66 GATTGAGGCCACAAAAGCGAATCTTG-TACCACG
** * *
142331 AAGATATGAAGGGAAAGGTTAAGG-CTGCAAAAGCGTACCTAATATCTTTAGAAGATGTGATGGG
1 AAGATATGAAGGGAAAGGTTAAGGTC-GCAAAAGCAAACCTAATA-CCTTA-AAGATGTGATAGG
*
142395 AATGATTGAGGCCACAAAAGCGAATCTTGTACCACG
63 AAGGATTGAGGCCACAAAAGCGAATCTTGTACCACG
142431 AAGATATGAAGGGAAAGGTT
1 AAGATATGAAGGGAAAGGTT
142451 GAAGCCGCAA
Statistics
Matches: 100, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
97 1 0.01
98 36 0.36
99 4 0.04
100 57 0.57
101 2 0.02
ACGTcount: A:0.37, C:0.12, G:0.28, T:0.22
Consensus pattern (98 bp):
AAGATATGAAGGGAAAGGTTAAGGTCGCAAAAGCAAACCTAATACCTTAAAGATGTGATAGGAAG
GATTGAGGCCACAAAAGCGAATCTTGTACCACG
Found at i:142525 original size:49 final size:49
Alignment explanation
Indices: 142432--142525 Score: 136
Period size: 49 Copynumber: 1.9 Consensus size: 49
142422 TGTACCACGA
* * *
142432 AGATATGAAGGGAAAGGTTGAAGCCGCAATGGTGAACCTTATACCTTAG
1 AGATATGAAGGGAAAGATTGAAGCCGCAATGGTAAACCTCATACCTTAG
*
142481 AGATATGAAGGGAAAGATTG-AGTCCGCAATGGTAAATCTCATACC
1 AGATATGAAGGGAAAGATTGAAG-CCGCAATGGTAAACCTCATACC
142526 CTGAAGATGA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
48 2 0.05
49 38 0.95
ACGTcount: A:0.36, C:0.15, G:0.27, T:0.22
Consensus pattern (49 bp):
AGATATGAAGGGAAAGATTGAAGCCGCAATGGTAAACCTCATACCTTAG
Found at i:142729 original size:70 final size:70
Alignment explanation
Indices: 142616--142757 Score: 284
Period size: 70 Copynumber: 2.0 Consensus size: 70
142606 AATCTTACAT
142616 CTCTAGAGCTGAAGAGGAGTAAATTGAAGCCGCAACGACGAATCTTCTACCTCGAAGATGTAGAT
1 CTCTAGAGCTGAAGAGGAGTAAATTGAAGCCGCAACGACGAATCTTCTACCTCGAAGATGTAGAT
142681 CAAAG
66 CAAAG
142686 CTCTAGAGCTGAAGAGGAGTAAATTGAAGCCGCAACGACGAATCTTCTACCTCGAAGATGTAGAT
1 CTCTAGAGCTGAAGAGGAGTAAATTGAAGCCGCAACGACGAATCTTCTACCTCGAAGATGTAGAT
142751 CAAAG
66 CAAAG
142756 CT
1 CT
142758 AAGTAGCAAG
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 72 1.00
ACGTcount: A:0.35, C:0.20, G:0.24, T:0.20
Consensus pattern (70 bp):
CTCTAGAGCTGAAGAGGAGTAAATTGAAGCCGCAACGACGAATCTTCTACCTCGAAGATGTAGAT
CAAAG
Found at i:142853 original size:39 final size:39
Alignment explanation
Indices: 142810--143507 Score: 620
Period size: 39 Copynumber: 17.5 Consensus size: 39
142800 AAAGCAAAAC
**
142810 GAAGTCATCCAATCTCTTACCCCGATCATAAGGCAGATT
1 GAAGTCATCCAATCTCTTACCCCGATCATGGGGCAGATT
* * *
142849 GAAGTCATTCAATCTCTTACCCCGATCATGAGGTAGATT
1 GAAGTCATCCAATCTCTTACCCCGATCATGGGGCAGATT
* * *
142888 GAAGACATCATCCAAACTCTTACCTCAATCATGGGGCAGATT
1 GAAG---TCATCCAATCTCTTACCCCGATCATGGGGCAGATT
* * * * * *
142930 GAAGCCATCTAATCTCTTACCCCAACCATGAGGTAGATT
1 GAAGTCATCCAATCTCTTACCCCGATCATGGGGCAGATT
*
142969 GAAGTCATCTAATCTCTTACCCCGATCATGGGGCAGATT
1 GAAGTCATCCAATCTCTTACCCCGATCATGGGGCAGATT
143008 GAAGACATCATCCAATCTCTTACCCCGATCATGGGG-AGGATT
1 GAAG---TCATCCAATCTCTTACCCCGATCATGGGGCA-GATT
* * * *
143050 GAAGACACACCAATCCCTTACCCCGATCATGAGGCAGATT
1 GAAGTCA-TCCAATCTCTTACCCCGATCATGGGGCAGATT
* * *
143090 GAAGATACA-CCAATCTCTTACCCTGATCATGAGGAAGATT
1 GAAG-T-CATCCAATCTCTTACCCCGATCATGGGGCAGATT
* * * * * *
143130 AAAG-AATTCAATCCCTTACCCCAATCATGGGGCGGATT
1 GAAGTCATCCAATCTCTTACCCCGATCATGGGGCAGATT
* * * *
143168 GAAGACA-CAAAAAACTCTTACCCCAATCATGGGGCAGATT
1 GAAGTCATC--CAATCTCTTACCCCGATCATGGGGCAGATT
* * * * **
143208 GAAGCCATTCAATCTCTTAACCCGATCATAGGATAGATT
1 GAAGTCATCCAATCTCTTACCCCGATCATGGGGCAGATT
*
143247 GAAGACATCATCAAATCTCTTACCCCCGATCATGGGGCAGATT
1 GAAG---TCATCCAATCTCTTA-CCCCGATCATGGGGCAGATT
* *
143290 GAAGACCATCCAATCTCTTACCTCGATCATGGGGGCAGATT
1 GAAG-TCATCCAATCTCTTACCCCGATCAT-GGGGCAGATT
* *
143331 GAAGACATCATCCAATCTCTTACCTCGATCATGAGGCAGATT
1 GAAG---TCATCCAATCTCTTACCCCGATCATGGGGCAGATT
** *
143373 GAAGTCATCCAATCTCTTACCTTGATTATGGGGCAGATT
1 GAAGTCATCCAATCTCTTACCCCGATCATGGGGCAGATT
* ** * *
143412 GAAGACAT-C--TCTCTTACCCTAATCATGGGGCAAACT
1 GAAGTCATCCAATCTCTTACCCCGATCATGGGGCAGATT
* **
143448 -AAGGTCCATCCAATCTCTTATCCCGATCATGGGATAGATT
1 GAA-GT-CATCCAATCTCTTACCCCGATCATGGGGCAGATT
* * *
143488 GAAGCCATCTAATCTTTTAC
1 GAAGTCATCCAATCTCTTAC
143508 TCTAAGTCAA
Statistics
Matches: 542, Mismatches: 88, Indels: 58
0.79 0.13 0.08
Matches are distributed among these distances:
35 2 0.00
36 23 0.04
37 4 0.01
38 29 0.05
39 187 0.35
40 124 0.23
41 32 0.06
42 96 0.18
43 45 0.08
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.26
Consensus pattern (39 bp):
GAAGTCATCCAATCTCTTACCCCGATCATGGGGCAGATT
Found at i:142949 original size:81 final size:82
Alignment explanation
Indices: 142814--143507 Score: 650
Period size: 81 Copynumber: 8.7 Consensus size: 82
142804 CAAAACGAAG
** * *
142814 TCATCCAATCTCTTACCCCGATCATAAGGCAGATTGAAG--TCATTCAATCTCTTACCCCGATCA
1 TCATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGACACATCCAATCTCTTACCCCGATCA
*
142877 TGAGGTAGATTGAAGAC
66 TGAGGCAGATTGAAGAC
* * * * * *
142894 ATCATCCAAACTCTTACCTCAATCATGGGGCAGATTGAAG-C-CATCTAATCTCTTACCCCAACC
1 -TCATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGACACATCCAATCTCTTACCCCGATC
*
142957 ATGAGGTAGATTGAAG--
65 ATGAGGCAGATTGAAGAC
*
142973 TCATCTAATCTCTTACCCCGATCATGGGGCAGATTGAAGACATCATCCAATCTCTTACCCCGATC
1 TCATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGACA-CATCCAATCTCTTACCCCGATC
*
143038 ATG-GGGAGGATTGAAGAC
65 ATGAGGCA-GATTGAAGAC
* * * * *
143056 ACA-CCAATCCCTTACCCCGATCATGAGGCAGATTGAAGATACA-CCAATCTCTTACCCTGATCA
1 TCATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGACACATCCAATCTCTTACCCCGATCA
* *
143119 TGAGGAAGATTAAAGA-
66 TGAGGCAGATTGAAGAC
* * * * ** * *
143135 --ATTCAATCCCTTACCCCAATCATGGGGCGGATTGAAGACACA-AAAAACTCTTACCCCAATCA
1 TCATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGACACATCCAATCTCTTACCCCGATCA
*
143197 TGGGGCAGATTGAAG-C
66 TGAGGCAGATTGAAGAC
* * * ** *
143213 -CATTCAATCTCTTAACCCGATCATAGGATAGATTGAAGACATCATCAAATCTCTTACCCCCGAT
1 TCATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGACA-CATCCAATCTCTTA-CCCCGAT
*
143277 CATGGGGCAGATTGAAGAC
64 CATGAGGCAGATTGAAGAC
* *
143296 -CATCCAATCTCTTACCTCGATCATGGGGGCAGATTGAAGACATCATCCAATCTCTTACCTCGAT
1 TCATCCAATCTCTTACCCCGATCAT-GGGGCAGATTGAAGACA-CATCCAATCTCTTACCCCGAT
143360 CATGAGGCAGATTGAAG--
64 CATGAGGCAGATTGAAGAC
** * **
143377 TCATCCAATCTCTTACCTTGATTATGGGGCAGATTGAAG--ACAT-C--TCTCTTACCCTAATCA
1 TCATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGACACATCCAATCTCTTACCCCGATCA
* * * *
143437 TGGGGCAAACT-AAG-G
66 TGAGGCAGATTGAAGAC
* ** * *
143452 TCCATCCAATCTCTTATCCCGATCATGGGATAGATTGAAG-C-CATCTAATCTTTTAC
1 T-CATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGACACATCCAATCTCTTAC
143508 TCTAAGTCAA
Statistics
Matches: 517, Mismatches: 73, Indels: 48
0.81 0.11 0.08
Matches are distributed among these distances:
74 3 0.01
75 22 0.04
76 35 0.07
77 2 0.00
78 100 0.19
79 42 0.08
80 34 0.07
81 126 0.24
82 79 0.15
83 46 0.09
84 28 0.05
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.26
Consensus pattern (82 bp):
TCATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGACACATCCAATCTCTTACCCCGATCA
TGAGGCAGATTGAAGAC
Found at i:143039 original size:120 final size:121
Alignment explanation
Indices: 142815--143496 Score: 727
Period size: 120 Copynumber: 5.7 Consensus size: 121
142805 AAAACGAAGT
* * *
142815 CATCCAATCTCTTACCCCGATCATAAGGCAGATTGAAGTCATTCAATCTCTTACCCCGATCATGA
1 CATCCAATCTCTTACCCCAATCATGAGGCAGATTGAAGTCATCCAATCTCTTACCCCGATCATGA
* * *
142880 GGTAGATTGAAGACATCATCCAAACTCTTACCTCAATCATGGGGCAGATTGAAG-C
66 GGTAGATTGAAGACATCATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGAC
* * * * *
142935 CATCTAATCTCTTACCCCAACCATGAGGTAGATTGAAGTCATCTAATCTCTTACCCCGATCATGG
1 CATCCAATCTCTTACCCCAATCATGAGGCAGATTGAAGTCATCCAATCTCTTACCCCGATCATGA
*
143000 GGCAGATTGAAGACATCATCCAATCTCTTACCCCGATCATGGGG-AGGATTGAAGAC
66 GGTAGATTGAAGACATCATCCAATCTCTTACCCCGATCATGGGGCA-GATTGAAGAC
* * *
143056 ACA-CCAATCCCTTACCCCGATCATGAGGCAGATTGAAGATACA-CCAATCTCTTACCCTGATCA
1 -CATCCAATCTCTTACCCCAATCATGAGGCAGATTGAAG-T-CATCCAATCTCTTACCCCGATCA
* * * * *
143119 TGAGGAAGATTAAAGA-AT--T-CAATCCCTTACCCCAATCATGGGGCGGATTGAAGAC
63 TGAGGTAGATTGAAGACATCATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGAC
** * * * * *
143174 ACA-AAAAACTCTTACCCCAATCATGGGGCAGATTGAAGCCATTCAATCTCTTAACCCGATCAT-
1 -CATCCAATCTCTTACCCCAATCATGAGGCAGATTGAAGTCATCCAATCTCTTACCCCGATCATG
*
143237 AGGATAGATTGAAGACATCATCAAATCTCTTACCCCCGATCATGGGGCAGATTGAAGAC
65 AGG-TAGATTGAAGACATCATCCAATCTCTTA-CCCCGATCATGGGGCAGATTGAAGAC
* * * *
143296 CATCCAATCTCTTACCTCGATCATGGGGGCAGATTGAAGACATCATCCAATCTCTTACCTCGATC
1 CATCCAATCTCTTACCCCAATCAT-GAGGCAGATTGAAG---TCATCCAATCTCTTACCCCGATC
* ** *
143361 ATGAGGCAGATTGAAG---TCATCCAATCTCTTACCTTGATTATGGGGCAGATTGAAGA-
62 ATGAGGTAGATTGAAGACATCATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGAC
* * * * *
143417 CAT-C--TCTCTTACCCTAATCATGGGGCAAACT-AAGGTCCATCCAATCTCTTATCCCGATCAT
1 CATCCAATCTCTTACCCCAATCATGAGGCAGATTGAA-GT-CATCCAATCTCTTACCCCGATCAT
*
143478 G-GGATAGATTGAAGCCATC
64 GAGG-TAGATTGAAGACATC
143497 TAATCTTTTA
Statistics
Matches: 474, Mismatches: 63, Indels: 52
0.80 0.11 0.09
Matches are distributed among these distances:
114 3 0.01
115 32 0.07
116 7 0.01
117 36 0.08
118 82 0.17
119 2 0.00
120 107 0.23
121 46 0.10
122 96 0.20
123 30 0.06
126 30 0.06
127 3 0.01
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.25
Consensus pattern (121 bp):
CATCCAATCTCTTACCCCAATCATGAGGCAGATTGAAGTCATCCAATCTCTTACCCCGATCATGA
GGTAGATTGAAGACATCATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGAC
Found at i:152272 original size:15 final size:16
Alignment explanation
Indices: 152246--152286 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
152236 AAAGATTCTT
*
152246 TCTTTCCCTTACTTTC
1 TCTTTCCTTTACTTTC
*
152262 -CTTTGCTTTACTTTC
1 TCTTTCCTTTACTTTC
152277 TCTTTCCTTT
1 TCTTTCCTTT
152287 CCCTCTCCTT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
15 13 0.62
16 8 0.38
ACGTcount: A:0.05, C:0.32, G:0.02, T:0.61
Consensus pattern (16 bp):
TCTTTCCTTTACTTTC
Found at i:156350 original size:3 final size:3
Alignment explanation
Indices: 156331--156396 Score: 77
Period size: 3 Copynumber: 23.3 Consensus size: 3
156321 GTATCTCCAT
* * *
156331 TTC TTC -TC TTC TGC TTC TTC TTC -GC CTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
156377 TTC TTC -TC TTC TTC TT- TTC T
1 TTC TTC TTC TTC TTC TTC TTC T
156397 ATTGCCTAGC
Statistics
Matches: 54, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
2 7 0.13
3 47 0.87
ACGTcount: A:0.00, C:0.35, G:0.03, T:0.62
Consensus pattern (3 bp):
TTC
Found at i:165249 original size:4 final size:4
Alignment explanation
Indices: 165232--165262 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
165222 TAGCTTGATG
*
165232 TTTC TTTA TTTC TTTC TTTC TTTC TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT
165263 TACATTGGAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTC
Found at i:168629 original size:3 final size:3
Alignment explanation
Indices: 168616--168648 Score: 57
Period size: 3 Copynumber: 10.7 Consensus size: 3
168606 CATTAATTTC
168616 ATT ATTT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT AT
168649 ACAAAATTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:171429 original size:4 final size:4
Alignment explanation
Indices: 171422--171448 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
171412 ATATCATACA
171422 TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TAT
171449 AATATTTAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.22, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:172437 original size:24 final size:24
Alignment explanation
Indices: 172391--172825 Score: 273
Period size: 24 Copynumber: 18.2 Consensus size: 24
172381 AACAAATTAT
* *
172391 GTTTACGCTTGCCAGACTT-TATAC
1 GTTTACGCTCGTCAG-CTTATATAC
* *
172415 GTTTATGCTCGTTAGCTTATATAC
1 GTTTACGCTCGTCAGCTTATATAC
* * * * *
172439 ATTTATGCTCGTCATCTTACACAC
1 GTTTACGCTCGTCAGCTTATATAC
* *
172463 GTTTATGCTCGTCAGCTTATATAT
1 GTTTACGCTCGTCAGCTTATATAC
172487 GTTTACGCTCGTCAGCTTATATAC
1 GTTTACGCTCGTCAGCTTATATAC
* * * * * * *
172511 TTTTATGCTCATAAGCTTACACAT
1 GTTTACGCTCGTCAGCTTATATAC
* *
172535 GTTTACACTCGTTAGCTTATATAC
1 GTTTACGCTCGTCAGCTTATATAC
* *
172559 GTTTACGCTCGCCATCTTATATAC
1 GTTTACGCTCGTCAGCTTATATAC
* * ** *
172583 ATTTACGCTCGTCATCTTGCACAC
1 GTTTACGCTCGTCAGCTTATATAC
*
172607 GTTTACGCTCATCAGCTTATATAC
1 GTTTACGCTCGTCAGCTTATATAC
* * ** * *
172631 GTTTACACTTGTCAGCTTGCACAT
1 GTTTACGCTCGTCAGCTTATATAC
* *
172655 GTTTACGCTCGTCATCTTATTTAC
1 GTTTACGCTCGTCAGCTTATATAC
* * ** *
172679 GTTTACACTCGTCAACTTGCACAC
1 GTTTACGCTCGTCAGCTTATATAC
* ** * *
172703 GTTTACGCTTGTCAGCTTGCACAT
1 GTTTACGCTCGTCAGCTTATATAC
* ** *
172727 GTTATA--CTCGTTAGCTTGCACAC
1 GTT-TACGCTCGTCAGCTTATATAC
* * * ** * *
172750 ATTTAAGCTTGTCAGCTTGCACAT
1 GTTTACGCTCGTCAGCTTATATAC
* ** * *
172774 GTTTATGCTCGTCAGCTTGCACAT
1 GTTTACGCTCGTCAGCTTATATAC
172798 GTTTACGCTCGTCAGCTTATATAC
1 GTTTACGCTCGTCAGCTTATATAC
172822 GTTT
1 GTTT
172826 CTAACGCATA
Statistics
Matches: 321, Mismatches: 86, Indels: 8
0.77 0.21 0.02
Matches are distributed among these distances:
22 2 0.01
23 19 0.06
24 298 0.93
25 2 0.01
ACGTcount: A:0.22, C:0.25, G:0.15, T:0.39
Consensus pattern (24 bp):
GTTTACGCTCGTCAGCTTATATAC
Found at i:172484 original size:48 final size:48
Alignment explanation
Indices: 172413--172825 Score: 351
Period size: 48 Copynumber: 8.6 Consensus size: 48
172403 CAGACTTTAT
* * * ** * *
172413 ACGTTTATGCTCGTTAGCTTATATACATTTATGCTCGTCATCTTACAC
1 ACGTTTACGCTCGTCAGCTTATATACGTTTACACTCGTCAGCTTGCAC
* * * ** *
172461 ACGTTTATGCTCGTCAGCTTATATATGTTTACGCTCGTCAGCTTATAT
1 ACGTTTACGCTCGTCAGCTTATATACGTTTACACTCGTCAGCTTGCAC
* * * * * * * * ** *
172509 ACTTTTATGCTCATAAGCTTACACATGTTTACACTCGTTAGCTTATAT
1 ACGTTTACGCTCGTCAGCTTATATACGTTTACACTCGTCAGCTTGCAC
* * * * *
172557 ACGTTTACGCTCGCCATCTTATATACATTTACGCTCGTCATCTTGCAC
1 ACGTTTACGCTCGTCAGCTTATATACGTTTACACTCGTCAGCTTGCAC
* *
172605 ACGTTTACGCTCATCAGCTTATATACGTTTACACTTGTCAGCTTGCAC
1 ACGTTTACGCTCGTCAGCTTATATACGTTTACACTCGTCAGCTTGCAC
* * * *
172653 ATGTTTACGCTCGTCATCTTATTTACGTTTACACTCGTCAACTTGCAC
1 ACGTTTACGCTCGTCAGCTTATATACGTTTACACTCGTCAGCTTGCAC
* ** * * * *
172701 ACGTTTACGCTTGTCAGCTTGCACATG-TTATACTCGTTAGCTTGCAC
1 ACGTTTACGCTCGTCAGCTTATATACGTTTACACTCGTCAGCTTGCAC
* * * ** * * **
172748 ACATTTAAGCTTGTCAGCTTGCACATGTTTATGCTCGTCAGCTTGCAC
1 ACGTTTACGCTCGTCAGCTTATATACGTTTACACTCGTCAGCTTGCAC
*
172796 ATGTTTACGCTCGTCAGCTTATATACGTTT
1 ACGTTTACGCTCGTCAGCTTATATACGTTT
172826 CTAACGCATA
Statistics
Matches: 298, Mismatches: 66, Indels: 2
0.81 0.18 0.01
Matches are distributed among these distances:
47 42 0.14
48 256 0.86
ACGTcount: A:0.22, C:0.25, G:0.15, T:0.39
Consensus pattern (48 bp):
ACGTTTACGCTCGTCAGCTTATATACGTTTACACTCGTCAGCTTGCAC
Found at i:172497 original size:72 final size:72
Alignment explanation
Indices: 172391--172720 Score: 329
Period size: 72 Copynumber: 4.6 Consensus size: 72
172381 AACAAATTAT
* * * *
172391 GTTTACGCTTGCCAGACTT-TATACGTTTATGCTCGTTAGCTTATATACATTTATGCTCGTCATC
1 GTTTACGCTCGTCAG-CTTATATACGTTTACGCTCGTCAGCTTATATACATTTATGCTCGTCATC
172455 TTACACAC
65 TTACACAC
* * * * * *
172463 GTTTATGCTCGTCAGCTTATATATGTTTACGCTCGTCAGCTTATATACTTTTATGCTCATAAGCT
1 GTTTACGCTCGTCAGCTTATATACGTTTACGCTCGTCAGCTTATATACATTTATGCTCGTCATCT
*
172528 TACACAT
66 TACACAC
* * * * *
172535 GTTTACACTCGTTAGCTTATATACGTTTACGCTCGCCATCTTATATACATTTACGCTCGTCATCT
1 GTTTACGCTCGTCAGCTTATATACGTTTACGCTCGTCAGCTTATATACATTTATGCTCGTCATCT
*
172600 TGCACAC
66 TACACAC
* * * ** * ** *
172607 GTTTACGCTCATCAGCTTATATACGTTTACACTTGTCAGCTTGCACATGTTTACGCTCGTCATCT
1 GTTTACGCTCGTCAGCTTATATACGTTTACGCTCGTCAGCTTATATACATTTATGCTCGTCATCT
***
172672 TATTTAC
66 TACACAC
* * ** * *
172679 GTTTACACTCGTCAACTTGCACACGTTTACGCTTGTCAGCTT
1 GTTTACGCTCGTCAGCTTATATACGTTTACGCTCGTCAGCTT
172721 GCACATGTTA
Statistics
Matches: 210, Mismatches: 47, Indels: 2
0.81 0.18 0.01
Matches are distributed among these distances:
71 3 0.01
72 207 0.99
ACGTcount: A:0.22, C:0.25, G:0.14, T:0.39
Consensus pattern (72 bp):
GTTTACGCTCGTCAGCTTATATACGTTTACGCTCGTCAGCTTATATACATTTATGCTCGTCATCT
TACACAC
Found at i:174324 original size:23 final size:22
Alignment explanation
Indices: 174293--174336 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
174283 AAAGAAATAC
*
174293 AATTAACCCAATTTAATTAATT
1 AATTAACCCAAATTAATTAATT
*
174315 AATTCAACCCAAATTATTTAAT
1 AATT-AACCCAAATTAATTAAT
174337 GAAATATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.45, C:0.16, G:0.00, T:0.39
Consensus pattern (22 bp):
AATTAACCCAAATTAATTAATT
Found at i:177586 original size:59 final size:60
Alignment explanation
Indices: 177408--177636 Score: 275
Period size: 59 Copynumber: 3.8 Consensus size: 60
177398 TTGGTTCTCA
* * * *
177408 ATTAAATGAAACAATATGCCAAAAATAATGTGTT-GAAAAATATTTAAAAGAACTTGTATTTC
1 ATTAAATGAAACAATAT--CAAAAATAATGT-TTACAAAAATATTCAAAAGAACTTCTATTTT
** * * * *
177470 ATTAAATGTTACAATATGCCAAAACTAATGTGTACAAAATTATTCAACAGAACTTCTATTTT
1 ATTAAATGAAACAATAT--CAAAAATAATGTTTACAAAAATATTCAAAAGAACTTCTATTTT
* *
177532 ATTAAATGAAAAAATAT-AAAAATATTGTTTACAAAAATATTCAAAAGAACTTCTATTTT
1 ATTAAATGAAACAATATCAAAAATAATGTTTACAAAAATATTCAAAAGAACTTCTATTTT
*
177591 ATTAAATGAAACAATAT-AAAAATAATGTTTACAAAAATGTTCAAAA
1 ATTAAATGAAACAATATCAAAAATAATGTTTACAAAAATATTCAAAA
177637 TAAATCAATC
Statistics
Matches: 145, Mismatches: 21, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
59 80 0.55
61 1 0.01
62 64 0.44
ACGTcount: A:0.50, C:0.09, G:0.08, T:0.33
Consensus pattern (60 bp):
ATTAAATGAAACAATATCAAAAATAATGTTTACAAAAATATTCAAAAGAACTTCTATTTT
Found at i:177918 original size:18 final size:18
Alignment explanation
Indices: 177895--177941 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
177885 TCCCATAAGG
*
177895 CGATGGGAATTGAGGTTA
1 CGATGGGAATTAAGGTTA
* *
177913 CGATGGGAACTAAGGTTG
1 CGATGGGAATTAAGGTTA
*
177931 CAATGGGAATT
1 CGATGGGAATT
177942 TTGCTGGGTA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.30, C:0.09, G:0.36, T:0.26
Consensus pattern (18 bp):
CGATGGGAATTAAGGTTA
Found at i:178121 original size:18 final size:18
Alignment explanation
Indices: 178094--178134 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
178084 ACTGGAAAAT
*
178094 GGATAGATATAAAGG-TTA
1 GGATACATAT-AAGGATTA
178112 GGATACATATAAGGATTA
1 GGATACATATAAGGATTA
178130 GGATA
1 GGATA
178135 TGCACCCAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 4 0.19
18 17 0.81
ACGTcount: A:0.44, C:0.02, G:0.27, T:0.27
Consensus pattern (18 bp):
GGATACATATAAGGATTA
Found at i:180245 original size:14 final size:15
Alignment explanation
Indices: 180218--180251 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
180208 TTTTCTCTTA
180218 TTTACTTTACTTTATT
1 TTTACTTTA-TTTATT
180234 TTTACTTT-TTTATT
1 TTTACTTTATTTATT
180248 TTTA
1 TTTA
180252 TGCTTTCACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 10 0.56
16 8 0.44
ACGTcount: A:0.18, C:0.09, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTACTTTATTTATT
Found at i:187671 original size:12 final size:12
Alignment explanation
Indices: 187646--187680 Score: 61
Period size: 12 Copynumber: 2.8 Consensus size: 12
187636 AAAAAATATC
187646 AATTAAATTAAAA
1 AATTAAA-TAAAA
187659 AATTAAATAAAA
1 AATTAAATAAAA
187671 AATTAAATAA
1 AATTAAATAA
187681 TATTAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 15 0.68
13 7 0.32
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (12 bp):
AATTAAATAAAA
Found at i:187671 original size:31 final size:31
Alignment explanation
Indices: 187624--187700 Score: 88
Period size: 30 Copynumber: 2.5 Consensus size: 31
187614 ATCTATTCAC
* *
187624 AAAAAAATTATAA-AAAAATATCAATTAA-ATT
1 AAAAAAATTA-AATAAAAA-ATTAAATAATATT
187655 -AAAAAATTAAATAAAAAATTAAATAATATT
1 AAAAAAATTAAATAAAAAATTAAATAATATT
*
187685 AAAAAAATGAAATAAA
1 AAAAAAATTAAATAAA
187701 CTCTTACCAT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
29 9 0.22
30 17 0.43
31 14 0.35
ACGTcount: A:0.71, C:0.01, G:0.01, T:0.26
Consensus pattern (31 bp):
AAAAAAATTAAATAAAAAATTAAATAATATT
Found at i:187673 original size:20 final size:21
Alignment explanation
Indices: 187650--187691 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 21
187640 AATATCAATT
187650 AAATTAAA-AA-ATTAAATAAA
1 AAATTAAATAATATTAAA-AAA
187670 AAATTAAATAATATTAAAAAA
1 AAATTAAATAATATTAAAAAA
187691 A
1 A
187692 TGAAATAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 8 0.40
21 6 0.30
22 6 0.30
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (21 bp):
AAATTAAATAATATTAAAAAA
Found at i:199110 original size:4 final size:4
Alignment explanation
Indices: 199101--199127 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
199091 TTATAATTGT
199101 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
199128 TTACTACACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:199280 original size:16 final size:16
Alignment explanation
Indices: 199254--199306 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
199244 CCAAAGCAAC
*
199254 AACTTTTGTTTAGAAT
1 AACTGTTGTTTAGAAT
** *
199270 ATTTGTTGTTTAGAAC
1 AACTGTTGTTTAGAAT
199286 AACTGTTGTTTAAGAAT
1 AACTGTTGTTT-AGAAT
199303 AACT
1 AACT
199307 ATGTTCAAAG
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
16 21 0.72
17 8 0.28
ACGTcount: A:0.32, C:0.08, G:0.15, T:0.45
Consensus pattern (16 bp):
AACTGTTGTTTAGAAT
Found at i:202290 original size:199 final size:198
Alignment explanation
Indices: 201915--202297 Score: 523
Period size: 199 Copynumber: 1.9 Consensus size: 198
201905 AATTATTAGG
** * * *
201915 TTTTAGGTTTTGAAAATGGAAGGAAAAGAAAGAAACGAATAAAGTTAAAAAGGAAAGGTAAACGG
1 TTTTAGGTTTAAAAAATGAAAAGAAAAGAAAGAAACGAATAAAGTTAAAAAGGAAAGGTAAACGA
* * * * *
201980 ATATTAATTAAAAAATGTTTTTTAAGTTGATTAAGTCTTAGCTCAATTGGCATGAATATTATTGC
66 ATATTAATAAAAAAATGTTTTTTAAGTCGATTAAGTCTTAACTCAATTGACATGAACATTATTGC
* * ** * * *
202045 CAATGTAAGAGGACATGAGTTTGAATGTACTCAAGCGTATTATCCTCCTATTTATAAAAACTATC
131 CAATGCAAGAGGACATGAATTCAAATGCAATCAAACGTATTATCCTCCTATTTATAAAAACTATC
202110 GGC
196 GGC
* *
202113 TTTTAGGTTTAAAAAATGAAAAGAAAAGAAAGAAATGAATAAAGTTAAAAAGGAAAGGTAAATGA
1 TTTTAGGTTTAAAAAATGAAAAGAAAAGAAAGAAACGAATAAAGTTAAAAAGGAAAGGTAAACGA
* * *
202178 ATATTAATAAAAAAAATGTTTTTTAAGTCGATTAAGTCTTAACTCGATTGACATGGACATTGTTG
66 ATATTAAT-AAAAAAATGTTTTTTAAGTCGATTAAGTCTTAACTCAATTGACATGAACATTATTG
** * *
202243 CCAATGCAAGAGGATGTGAATTCAAATGCAATGAAATGTATTATCCTCCTATTTA
130 CCAATGCAAGAGGACATGAATTCAAATGCAATCAAACGTATTATCCTCCTATTTA
202298 CGGGTTGGGG
Statistics
Matches: 158, Mismatches: 26, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
198 66 0.42
199 92 0.58
ACGTcount: A:0.42, C:0.09, G:0.18, T:0.31
Consensus pattern (198 bp):
TTTTAGGTTTAAAAAATGAAAAGAAAAGAAAGAAACGAATAAAGTTAAAAAGGAAAGGTAAACGA
ATATTAATAAAAAAATGTTTTTTAAGTCGATTAAGTCTTAACTCAATTGACATGAACATTATTGC
CAATGCAAGAGGACATGAATTCAAATGCAATCAAACGTATTATCCTCCTATTTATAAAAACTATC
GGC
Found at i:202459 original size:24 final size:25
Alignment explanation
Indices: 202404--202458 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
202394 AAAATTTTTA
*
202404 TAAAAATATAATTATTTTTAATTTT
1 TAAAAATATAATTATTTTTAATTTC
202429 TAAAAATATAA-TATTTTCGTAA-TTC
1 TAAAAATATAATTATTTT--TAATTTC
202454 TAAAA
1 TAAAA
202459 TTTTTCTAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
24 6 0.22
25 18 0.67
26 3 0.11
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (25 bp):
TAAAAATATAATTATTTTTAATTTC
Found at i:202566 original size:29 final size:28
Alignment explanation
Indices: 202534--202599 Score: 80
Period size: 30 Copynumber: 2.3 Consensus size: 28
202524 ATATTTTTTG
*
202534 AAATTTTTT-ATAGTTTTATAAAAATATTT
1 AAATTTTTTCATA-TTTTATAAAAA-ATTA
*
202563 AAATTATTTTCATATTTTTTAAAAAATTA
1 AAATT-TTTTCATATTTTATAAAAAATTA
202592 AAATTTTT
1 AAATTTTT
202600 AAATAATTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
28 3 0.09
29 13 0.39
30 14 0.42
31 3 0.09
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (28 bp):
AAATTTTTTCATATTTTATAAAAAATTA
Found at i:203192 original size:18 final size:18
Alignment explanation
Indices: 203171--203207 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
203161 TGCTATTTAG
*
203171 TTAATTCGGTTAATTTGA
1 TTAATTCAGTTAATTTGA
*
203189 TTAATTCAGTTTATTTGA
1 TTAATTCAGTTAATTTGA
203207 T
1 T
203208 CAAATGAACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.27, C:0.05, G:0.14, T:0.54
Consensus pattern (18 bp):
TTAATTCAGTTAATTTGA
Found at i:207382 original size:23 final size:22
Alignment explanation
Indices: 207356--207408 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
207346 ATGACGTGTC
* *
207356 AATGACATGAAAAAATATATTGA
1 AATGACAT-AAAAAAGATATCGA
* *
207379 AATGACATTAAATAGATATCGA
1 AATGACATAAAAAAGATATCGA
207401 AATGACAT
1 AATGACAT
207409 TAAATAATTA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
22 18 0.69
23 8 0.31
ACGTcount: A:0.53, C:0.08, G:0.13, T:0.26
Consensus pattern (22 bp):
AATGACATAAAAAAGATATCGA
Found at i:207402 original size:22 final size:22
Alignment explanation
Indices: 207372--207414 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
207362 ATGAAAAAAT
*
207372 ATATTGAAATGACATTAAATAG
1 ATATCGAAATGACATTAAATAG
207394 ATATCGAAATGACATTAAATA
1 ATATCGAAATGACATTAAATA
207415 ATTAATAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.07, G:0.12, T:0.30
Consensus pattern (22 bp):
ATATCGAAATGACATTAAATAG
Found at i:211582 original size:20 final size:20
Alignment explanation
Indices: 211559--211613 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
211549 TGGGTACACC
211559 TTTATAATTATTT-GTAATCT
1 TTTATAATT-TTTAGTAATCT
*
211579 TTTATGATTTTTAGTAATCT
1 TTTATAATTTTTAGTAATCT
* *
211599 CTCATAA-TTTTAGTA
1 TTTATAATTTTTAGTA
211614 TACCATAAGA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 11 0.37
20 19 0.63
ACGTcount: A:0.29, C:0.07, G:0.07, T:0.56
Consensus pattern (20 bp):
TTTATAATTTTTAGTAATCT
Found at i:211892 original size:18 final size:20
Alignment explanation
Indices: 211856--211968 Score: 76
Period size: 20 Copynumber: 5.7 Consensus size: 20
211846 GCATTTCGCC
211856 ATAATTTTTTATATCCTCTT
1 ATAATTTTTTATATCCTCTT
211876 ATAATTTTTT-T-TGCTCTCTT
1 ATAATTTTTTATAT-C-CTCTT
*
211896 ATAATTATTTGTA-AT-CTATT
1 ATAATT-TTT-TATATCCTCTT
* * *
211916 A-ATTTTTTTGTATTCTCTT
1 ATAATTTTTTATATCCTCTT
* *
211935 GTAATTTTTTATATGCCTTTT
1 ATAATTTTTTATAT-CCTCTT
*
211956 A-AATTTTTCATAT
1 ATAATTTTTTATAT
211969 GTTTTTAAAA
Statistics
Matches: 72, Mismatches: 11, Indels: 20
0.70 0.11 0.19
Matches are distributed among these distances:
17 1 0.01
18 6 0.08
19 9 0.12
20 47 0.65
21 7 0.10
22 1 0.01
23 1 0.01
ACGTcount: A:0.24, C:0.11, G:0.04, T:0.61
Consensus pattern (20 bp):
ATAATTTTTTATATCCTCTT
Found at i:212351 original size:21 final size:22
Alignment explanation
Indices: 212326--212366 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
212316 TTTTTAATGA
212326 AATAT-TTTATTA-TTCAAAAAT
1 AATATATTT-TTACTTCAAAAAT
212347 AATATATTTTTACTTCAAAA
1 AATATATTTTTACTTCAAAA
212367 TTATATCTCG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.46
Consensus pattern (22 bp):
AATATATTTTTACTTCAAAAAT
Found at i:212963 original size:21 final size:20
Alignment explanation
Indices: 212925--212975 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
212915 GAGTGCAAAC
212925 CAAAAAAATTAAGAGGAAATA
1 CAAAAAAA-TAAGAGGAAATA
* * *
212946 TCAAAAAAATATGCGGAAGTA
1 -CAAAAAAATAAGAGGAAATA
212967 CAAAAAAAT
1 CAAAAAAAT
212976 TATAAGAGGA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 9 0.35
21 9 0.35
22 8 0.31
ACGTcount: A:0.63, C:0.08, G:0.14, T:0.16
Consensus pattern (20 bp):
CAAAAAAATAAGAGGAAATA
Found at i:213244 original size:19 final size:20
Alignment explanation
Indices: 213198--213246 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
213188 TTTTTGAAAC
213198 AATACCAAAAGTTATGAGAT
1 AATACCAAAAGTTATGAGAT
213218 AATACCAAGAA-TTATGAGA-
1 AATACCAA-AAGTTATGAGAT
*
213237 AGTACCAAAA
1 AATACCAAAA
213247 ATATAAGGGA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
18 2 0.07
19 7 0.26
20 16 0.59
21 2 0.07
ACGTcount: A:0.53, C:0.12, G:0.14, T:0.20
Consensus pattern (20 bp):
AATACCAAAAGTTATGAGAT
Found at i:213340 original size:20 final size:19
Alignment explanation
Indices: 213312--213350 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
213302 TTTTACCAAA
213312 AAATAAAAAAAATGAAAAAT
1 AAAT-AAAAAAATGAAAAAT
* *
213332 AAATCAAAAATTGAAAAAT
1 AAATAAAAAAATGAAAAAT
213351 CTCAATAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.74, C:0.03, G:0.05, T:0.18
Consensus pattern (19 bp):
AAATAAAAAAATGAAAAAT
Found at i:213346 original size:19 final size:16
Alignment explanation
Indices: 213310--213350 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 16
213300 CATTTTACCA
213310 AAAAATAAAAAAAATG
1 AAAAATAAAAAAAATG
213326 AAAAATAAATCAAAAATTG
1 AAAAATAAA--AAAAA-TG
213345 AAAAAT
1 AAAAAT
213351 CTCAATAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 9 0.41
18 5 0.23
19 8 0.36
ACGTcount: A:0.76, C:0.02, G:0.05, T:0.17
Consensus pattern (16 bp):
AAAAATAAAAAAAATG
Found at i:219081 original size:17 final size:17
Alignment explanation
Indices: 219059--219091 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
219049 CAATGACATA
219059 TTTAGATTTCTCATTAG
1 TTTAGATTTCTCATTAG
219076 TTTAGATTTCTCATTA
1 TTTAGATTTCTCATTA
219092 TCCTTTCTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.12, G:0.09, T:0.55
Consensus pattern (17 bp):
TTTAGATTTCTCATTAG
Found at i:222503 original size:11 final size:11
Alignment explanation
Indices: 222481--222564 Score: 59
Period size: 11 Copynumber: 7.9 Consensus size: 11
222471 TTTTTTCTTT
222481 AATTAT-AAAA
1 AATTATAAAAA
222491 AATTATAAAAA
1 AATTATAAAAA
* *
222502 AAGTTTTTAAAA
1 AA-TTATAAAAA
** *
222514 TTTTATATAAA
1 AATTATAAAAA
222525 AATTAT---AA
1 AATTATAAAAA
222533 AATTATAAAAA
1 AATTATAAAAA
** *
222544 TTTTATATAAA
1 AATTATAAAAA
222555 AATTATAAAA
1 AATTATAAAA
222565 TTATAAAAAT
Statistics
Matches: 54, Mismatches: 15, Indels: 9
0.69 0.19 0.12
Matches are distributed among these distances:
8 8 0.15
10 6 0.11
11 33 0.61
12 7 0.13
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (11 bp):
AATTATAAAAA
Found at i:222531 original size:9 final size:9
Alignment explanation
Indices: 222519--222575 Score: 64
Period size: 8 Copynumber: 6.1 Consensus size: 9
222509 TAAAATTTTA
222519 TATAAAAAT
1 TATAAAAAT
222528 TAT-AAAAT
1 TATAAAAAT
222536 TATAAAAATTTT
1 TATAAAAA---T
222548 ATATAAAAAT
1 -TATAAAAAT
222558 TAT-AAAAT
1 TATAAAAAT
222566 TATAAAAAT
1 TATAAAAAT
222575 T
1 T
222576 TCCCAGATAT
Statistics
Matches: 42, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
8 16 0.38
9 16 0.38
10 1 0.02
12 1 0.02
13 8 0.19
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (9 bp):
TATAAAAAT
Found at i:222597 original size:38 final size:30
Alignment explanation
Indices: 222510--222576 Score: 134
Period size: 30 Copynumber: 2.2 Consensus size: 30
222500 AAAAGTTTTT
222510 AAAATTTTATATAAAAATTATAAAATTATA
1 AAAATTTTATATAAAAATTATAAAATTATA
222540 AAAATTTTATATAAAAATTATAAAATTATA
1 AAAATTTTATATAAAAATTATAAAATTATA
222570 AAAATTT
1 AAAATTT
222577 CCCAGATATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (30 bp):
AAAATTTTATATAAAAATTATAAAATTATA
Found at i:225794 original size:24 final size:24
Alignment explanation
Indices: 225767--225816 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
225757 AGTTTGATTG
225767 AAATGATAAAATTAAGTTAAGGAA
1 AAATGATAAAATTAAGTTAAGGAA
225791 AAATGATAAAATTAAGTTAAGGAA
1 AAATGATAAAATTAAGTTAAGGAA
225815 AA
1 AA
225817 CTATGATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.60, C:0.00, G:0.16, T:0.24
Consensus pattern (24 bp):
AAATGATAAAATTAAGTTAAGGAA
Found at i:237041 original size:81 final size:81
Alignment explanation
Indices: 236914--237070 Score: 305
Period size: 81 Copynumber: 1.9 Consensus size: 81
236904 AAAGAAAGCA
236914 TAGTGATTTCTTATTGGTTGCTTGAGGAGAATGGAGGTGGCAACAATGAAGGTGCAAAATATCAT
1 TAGTGATTTCTTATTGGTTGCTTGAGGAGAATGGAGGTGGCAACAATGAAGGTGCAAAATATCAT
236979 GAAAGTTTAGAAAGGT
66 GAAAGTTTAGAAAGGT
*
236995 TAGTGATTTCTTGTTGGTTGCTTGAGGAGAATGGAGGTGGCAACAATGAAGGTGCAAAATATCAT
1 TAGTGATTTCTTATTGGTTGCTTGAGGAGAATGGAGGTGGCAACAATGAAGGTGCAAAATATCAT
237060 GAAAGTTTAGA
66 GAAAGTTTAGA
237071 TTTTTAACTA
Statistics
Matches: 75, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
81 75 1.00
ACGTcount: A:0.32, C:0.08, G:0.30, T:0.30
Consensus pattern (81 bp):
TAGTGATTTCTTATTGGTTGCTTGAGGAGAATGGAGGTGGCAACAATGAAGGTGCAAAATATCAT
GAAAGTTTAGAAAGGT
Found at i:245419 original size:2 final size:2
Alignment explanation
Indices: 245412--245438 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
245402 CATCATTTAT
245412 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 T
245439 TAGATTTTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:282027 original size:25 final size:26
Alignment explanation
Indices: 281999--282063 Score: 73
Period size: 25 Copynumber: 2.6 Consensus size: 26
281989 GAGGTAAGAA
*
281999 ATTTCTAAATTA-TAA-TTTTTAATTT
1 ATTT-TAAATTATTAACTCTTTAATTT
*
282024 A-TTTAATTTATTAACTCTTTAATTT
1 ATTTTAAATTATTAACTCTTTAATTT
*
282049 ATTTTAAATTGTTAA
1 ATTTTAAATTATTAA
282064 TATTTTATAC
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
23 6 0.18
24 5 0.15
25 11 0.33
26 11 0.33
ACGTcount: A:0.35, C:0.05, G:0.02, T:0.58
Consensus pattern (26 bp):
ATTTTAAATTATTAACTCTTTAATTT
Found at i:282070 original size:26 final size:24
Alignment explanation
Indices: 282004--282070 Score: 73
Period size: 26 Copynumber: 2.7 Consensus size: 24
281994 AAGAAATTTC
282004 TAAATTA-TAATTTTTAATTTATT
1 TAAATTATTAATTTTTAATTTATT
* *
282027 TAATTTATTAACTCTTTAATTTATTT
1 TAAATTATTAA-TTTTTAATTTA-TT
*
282053 TAAATTGTTAATATTTTA
1 TAAATTATTAAT-TTTTA
282071 TACTAATTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
23 6 0.17
24 3 0.09
25 11 0.31
26 15 0.43
ACGTcount: A:0.36, C:0.03, G:0.01, T:0.60
Consensus pattern (24 bp):
TAAATTATTAATTTTTAATTTATT
Found at i:282969 original size:18 final size:18
Alignment explanation
Indices: 282946--282989 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
282936 GCAAGCTGAA
*
282946 GAAGAAGAATAAGATCCT
1 GAAGAAGAAGAAGATCCT
282964 GAAGAAGAAGAAGATCCT
1 GAAGAAGAAGAAGATCCT
*
282982 GATGAAGA
1 GAAGAAGA
282990 TCCTATGGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.50, C:0.09, G:0.27, T:0.14
Consensus pattern (18 bp):
GAAGAAGAAGAAGATCCT
Found at i:282987 original size:21 final size:21
Alignment explanation
Indices: 282941--282989 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 21
282931 CAACAGCAAG
* *
282941 CTGAAGAAGAAGAATAAGATC
1 CTGATGAAGAAGAAGAAGATC
282962 C---TGAAGAAGAAGAAGATC
1 CTGATGAAGAAGAAGAAGATC
282980 CTGATGAAGA
1 CTGATGAAGA
282990 TCCTATGGTA
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
18 16 0.70
21 7 0.30
ACGTcount: A:0.49, C:0.10, G:0.27, T:0.14
Consensus pattern (21 bp):
CTGATGAAGAAGAAGAAGATC
Found at i:286558 original size:15 final size:15
Alignment explanation
Indices: 286530--286565 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
286520 GAATATAGTT
286530 TTAACTTTAACTTAGA
1 TTAA-TTTAACTTAGA
*
286546 TTAATTTAGCTTAGA
1 TTAATTTAACTTAGA
286561 TTAAT
1 TTAAT
286566 ACTTTAGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 15 0.79
16 4 0.21
ACGTcount: A:0.36, C:0.08, G:0.08, T:0.47
Consensus pattern (15 bp):
TTAATTTAACTTAGA
Found at i:305193 original size:21 final size:20
Alignment explanation
Indices: 305159--305199 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
305149 AGATTCAAAG
* *
305159 ACTAATGCTACCCATTCATT
1 ACTAATGCAACCCAATCATT
305179 ACTAATGCAATCCCAATCATT
1 ACTAATGCAA-CCCAATCATT
305200 CATTCAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.34, C:0.29, G:0.05, T:0.32
Consensus pattern (20 bp):
ACTAATGCAACCCAATCATT
Found at i:305500 original size:17 final size:17
Alignment explanation
Indices: 305463--305510 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
305453 ATTAGAATGG
305463 AAATGCAACTACAATAC
1 AAATGCAACTACAATAC
305480 AAATG-AACTAACAAGTA-
1 AAATGCAACT-ACAA-TAC
*
305497 AAATGCAACGACAA
1 AAATGCAACTACAA
305511 CTAAAATAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
16 4 0.15
17 18 0.67
18 5 0.19
ACGTcount: A:0.56, C:0.19, G:0.10, T:0.15
Consensus pattern (17 bp):
AAATGCAACTACAATAC
Found at i:311532 original size:11 final size:11
Alignment explanation
Indices: 311504--311537 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
311494 AATAGGGGTC
* *
311504 TGATAAACTTC
1 TGATAATCTTT
311515 TGATAATCTTT
1 TGATAATCTTT
311526 TGATAATCTTT
1 TGATAATCTTT
311537 T
1 T
311538 TCATGATCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.29, C:0.12, G:0.09, T:0.50
Consensus pattern (11 bp):
TGATAATCTTT
Found at i:313743 original size:24 final size:23
Alignment explanation
Indices: 313706--313752 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
313696 AAGAGTTAAT
*
313706 TTGTCAACGAAAATATAAAATAAA
1 TTGTCAAAGAAAAT-TAAAATAAA
* *
313730 TTGTCAAAGCAAATTAAGATAAA
1 TTGTCAAAGAAAATTAAAATAAA
313753 ATTAATAGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.55, C:0.09, G:0.11, T:0.26
Consensus pattern (23 bp):
TTGTCAAAGAAAATTAAAATAAA
Found at i:316080 original size:26 final size:26
Alignment explanation
Indices: 316051--316126 Score: 67
Period size: 26 Copynumber: 3.2 Consensus size: 26
316041 ACCTTACTAG
316051 TATGGCCAATTCCAAACCCGTTAGTC
1 TATGGCCAATTCCAAACCCGTTAGTC
* * *
316077 TAT-G-C---TCCTAA-CC-TTACTAG
1 TATGGCCAATTCCAAACCCGTTAGT-C
316097 TATGGCCAATTCCAAACCCGTTAGTC
1 TATGGCCAATTCCAAACCCGTTAGTC
316123 TATG
1 TATG
316127 TAATGTCATA
Statistics
Matches: 36, Mismatches: 6, Indels: 16
0.62 0.10 0.28
Matches are distributed among these distances:
19 4 0.11
20 5 0.14
21 6 0.17
22 1 0.03
24 1 0.03
25 6 0.17
26 9 0.25
27 4 0.11
ACGTcount: A:0.26, C:0.29, G:0.14, T:0.30
Consensus pattern (26 bp):
TATGGCCAATTCCAAACCCGTTAGTC
Found at i:316087 original size:46 final size:46
Alignment explanation
Indices: 316034--316126 Score: 186
Period size: 46 Copynumber: 2.0 Consensus size: 46
316024 GCTTCCAAAA
316034 GCTCCTAACCTTACTAGTATGGCCAATTCCAAACCCGTTAGTCTAT
1 GCTCCTAACCTTACTAGTATGGCCAATTCCAAACCCGTTAGTCTAT
316080 GCTCCTAACCTTACTAGTATGGCCAATTCCAAACCCGTTAGTCTAT
1 GCTCCTAACCTTACTAGTATGGCCAATTCCAAACCCGTTAGTCTAT
316126 G
1 G
316127 TAATGTCATA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.26, C:0.30, G:0.14, T:0.30
Consensus pattern (46 bp):
GCTCCTAACCTTACTAGTATGGCCAATTCCAAACCCGTTAGTCTAT
Found at i:316114 original size:25 final size:25
Alignment explanation
Indices: 316040--316114 Score: 63
Period size: 25 Copynumber: 3.2 Consensus size: 25
316030 AAAAGCTCCT
316040 AACCTTACTAGTATGGCCAATTCCA
1 AACCTTACTAGTATGGCCAATTCCA
* * *
316065 AACCCGTTAGT-CTAT-G-C---TCCT
1 AA-CC-TTACTAGTATGGCCAATTCCA
316086 AACCTTACTAGTATGGCCAATTCCA
1 AACCTTACTAGTATGGCCAATTCCA
316111 AACC
1 AACC
316115 CGTTAGTCTA
Statistics
Matches: 36, Mismatches: 6, Indels: 16
0.62 0.10 0.28
Matches are distributed among these distances:
19 4 0.11
20 5 0.14
21 6 0.17
22 1 0.03
24 1 0.03
25 10 0.28
26 5 0.14
27 4 0.11
ACGTcount: A:0.29, C:0.31, G:0.12, T:0.28
Consensus pattern (25 bp):
AACCTTACTAGTATGGCCAATTCCA
Found at i:320908 original size:19 final size:20
Alignment explanation
Indices: 320882--320926 Score: 69
Period size: 18 Copynumber: 2.4 Consensus size: 20
320872 TTATTTCCAT
320882 TTTCTTTTTTTTTT-C-TTA
1 TTTCTTTTTTTTTTCCATTA
320900 TTTCTTTTTTTTTTCCATTA
1 TTTCTTTTTTTTTTCCATTA
320920 -TTCTTTT
1 TTTCTTTT
320927 CTTCCTCATT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.56
19 8 0.32
20 3 0.12
ACGTcount: A:0.07, C:0.13, G:0.00, T:0.80
Consensus pattern (20 bp):
TTTCTTTTTTTTTTCCATTA
Found at i:320926 original size:18 final size:18
Alignment explanation
Indices: 320875--320926 Score: 63
Period size: 19 Copynumber: 2.9 Consensus size: 18
320865 AAAAAATTTA
320875 TTTCCATT-TTCTTTTTT
1 TTTCCATTATTCTTTTTT
*
320892 TTTTC-TTATTTCTTTTTTT
1 TTTCCATTA-TTC-TTTTTT
320911 TTTCCATTATTCTTTT
1 TTTCCATTATTCTTTT
320927 CTTCCTCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
16 2 0.07
17 4 0.14
18 7 0.24
19 13 0.45
20 3 0.10
ACGTcount: A:0.08, C:0.15, G:0.00, T:0.77
Consensus pattern (18 bp):
TTTCCATTATTCTTTTTT
Found at i:322037 original size:6 final size:6
Alignment explanation
Indices: 322008--322060 Score: 52
Period size: 6 Copynumber: 8.0 Consensus size: 6
321998 GGGAAATAAT
*
322008 AAAAGA AAAGGA AAAAGGAA AAAATGA AAAAGA AAAAGAA AAATAGA AAAAGA
1 AAAAGA AAAAGA AAAA-G-A AAAA-GA AAAAGA AAAAG-A AAA-AGA AAAAGA
322061 GATTATGACA
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
6 18 0.45
7 14 0.35
8 8 0.20
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.04
Consensus pattern (6 bp):
AAAAGA
Found at i:322043 original size:20 final size:20
Alignment explanation
Indices: 322011--322060 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
322001 AAATAATAAA
*
322011 AGAAAAGGAAAAAGGAAAAA-
1 AGAAAAAGAAAAA-GAAAAAT
322031 ATGAAAAAGAAAAAGAAAAAT
1 A-GAAAAAGAAAAAGAAAAAT
322052 AGAAAAAGA
1 AGAAAAAGA
322061 GATTATGACA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
20 15 0.56
21 12 0.44
ACGTcount: A:0.76, C:0.00, G:0.20, T:0.04
Consensus pattern (20 bp):
AGAAAAAGAAAAAGAAAAAT
Found at i:322055 original size:14 final size:13
Alignment explanation
Indices: 322008--322060 Score: 54
Period size: 14 Copynumber: 3.9 Consensus size: 13
321998 GGGAAATAAT
*
322008 AAAAGAAAAGGAA
1 AAAAGAAAAAGAA
*
322021 AAAGGAAAAA-ATGA
1 AAAAGAAAAAGA--A
322035 AAAAGAAAAAGAA
1 AAAAGAAAAAGAA
322048 AAATAGAAAAAGA
1 AAA-AGAAAAAGA
322061 GATTATGACA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
12 1 0.03
13 12 0.36
14 19 0.58
15 1 0.03
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.04
Consensus pattern (13 bp):
AAAAGAAAAAGAA
Found at i:322712 original size:27 final size:27
Alignment explanation
Indices: 322673--322724 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
322663 TGTCCACTTC
*
322673 TCCCAGATCGGTACCTAAATTTTTTTG
1 TCCCAGATCGGTACCTAAACTTTTTTG
* *
322700 TCCCAGATTGGTACCTGAACTTTTT
1 TCCCAGATCGGTACCTAAACTTTTT
322725 CTCCTTCAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.21, C:0.23, G:0.15, T:0.40
Consensus pattern (27 bp):
TCCCAGATCGGTACCTAAACTTTTTTG
Found at i:322850 original size:14 final size:14
Alignment explanation
Indices: 322831--322877 Score: 64
Period size: 14 Copynumber: 3.5 Consensus size: 14
322821 TGTCATAATC
322831 TCTTTTTCTATTTT
1 TCTTTTTCTATTTT
322845 TCTTTTTCTA--TT
1 TCTTTTTCTATTTT
322857 TCATTTTTC-ATTTT
1 TC-TTTTTCTATTTT
322871 TCTTTTT
1 TCTTTTT
322878 TCCTTTTCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
12 5 0.17
13 11 0.37
14 14 0.47
ACGTcount: A:0.09, C:0.15, G:0.00, T:0.77
Consensus pattern (14 bp):
TCTTTTTCTATTTT
Found at i:322852 original size:6 final size:6
Alignment explanation
Indices: 322831--322889 Score: 55
Period size: 6 Copynumber: 9.0 Consensus size: 6
322821 TGTCATAATC
* *
322831 TCTTTT TCTATTTT TCTTTT TCTATT TCATTTT TCATTTT TCTTTTT TCCTTT
1 TCTTTT TC--TTTT TCTTTT TCTTTT TC-TTTT TC-TTTT TC-TTTT TCTTTT
322884 TCTTTT
1 TCTTTT
322890 ATTATTTCTC
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
6 21 0.47
7 18 0.40
8 6 0.13
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.76
Consensus pattern (6 bp):
TCTTTT
Found at i:322869 original size:12 final size:12
Alignment explanation
Indices: 322831--322898 Score: 50
Period size: 14 Copynumber: 5.2 Consensus size: 12
322821 TGTCATAATC
322831 TCTTTTTCTATTTT
1 TCTTTTTCTA--TT
322845 TCTTTTTCTATT
1 TCTTTTTCTATT
*
322857 TCATTTTTCATTTT
1 TC-TTTTTC-TATT
322871 TCTTTTTTCCT-TT
1 TC-TTTTT-CTATT
322884 TCTTTTAT-TATT
1 TCTTTT-TCTATT
322896 TCT
1 TCT
322899 CGTTCCCATC
Statistics
Matches: 47, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
11 1 0.02
12 13 0.28
13 11 0.23
14 21 0.45
15 1 0.02
ACGTcount: A:0.09, C:0.16, G:0.00, T:0.75
Consensus pattern (12 bp):
TCTTTTTCTATT
Found at i:322878 original size:14 final size:13
Alignment explanation
Indices: 322831--322889 Score: 57
Period size: 13 Copynumber: 4.5 Consensus size: 13
322821 TGTCATAATC
*
322831 TCTTTTTCTATTTT
1 TCTTTTT-TCTTTT
*
322845 TC-TTTTTCTATT
1 TCTTTTTTCTTTT
*
322857 TCATTTTTCATTTT
1 TCTTTTTTC-TTTT
*
322871 TCTTTTTTCCTTT
1 TCTTTTTTCTTTT
322884 TCTTTT
1 TCTTTT
322890 ATTATTTCTC
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
12 6 0.16
13 19 0.50
14 13 0.34
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.76
Consensus pattern (13 bp):
TCTTTTTTCTTTT
Found at i:322996 original size:27 final size:27
Alignment explanation
Indices: 322944--322997 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
322934 TCCTCAGCCC
*
322944 TTTTCCAACCCTAACCACCTCCAACAT
1 TTTTCCAACCCTAACCACCGCCAACAT
* * *
322971 TTTTCCAACCCTAGCCGCCGCTAACAT
1 TTTTCCAACCCTAACCACCGCCAACAT
322998 GCACAATAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.26, C:0.43, G:0.06, T:0.26
Consensus pattern (27 bp):
TTTTCCAACCCTAACCACCGCCAACAT
Found at i:323189 original size:21 final size:21
Alignment explanation
Indices: 323164--323214 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
323154 TGCTCCAATA
323164 TCGTCACCGTATGTTTCAGTG
1 TCGTCACCGTATGTTTCAGTG
323185 TCGTCACCGTATGTTTCAGTG
1 TCGTCACCGTATGTTTCAGTG
*
323206 TCGTTACCG
1 TCGTCACCG
323215 ATCAGAGAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.14, C:0.25, G:0.24, T:0.37
Consensus pattern (21 bp):
TCGTCACCGTATGTTTCAGTG
Found at i:328344 original size:25 final size:25
Alignment explanation
Indices: 328310--328363 Score: 108
Period size: 25 Copynumber: 2.2 Consensus size: 25
328300 GTCTCTTGTA
328310 AGAGTCGTCGGGACACATACAACTT
1 AGAGTCGTCGGGACACATACAACTT
328335 AGAGTCGTCGGGACACATACAACTT
1 AGAGTCGTCGGGACACATACAACTT
328360 AGAG
1 AGAG
328364 CAATCCTACC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.33, C:0.22, G:0.26, T:0.19
Consensus pattern (25 bp):
AGAGTCGTCGGGACACATACAACTT
Found at i:331750 original size:25 final size:23
Alignment explanation
Indices: 331708--331762 Score: 67
Period size: 25 Copynumber: 2.3 Consensus size: 23
331698 TGAGAAAAAC
331708 TCGATTT-AAAAAATAAAATTAA
1 TCGATTTGAAAAAATAAAATTAA
* *
331730 TGGATTTGAAAAAATAAAAAATTAT
1 TCGATTTGAAAAAAT--AAAATTAA
331755 TCGATTTG
1 TCGATTTG
331763 GTGAATTAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 6 0.22
23 7 0.26
25 14 0.52
ACGTcount: A:0.51, C:0.04, G:0.11, T:0.35
Consensus pattern (23 bp):
TCGATTTGAAAAAATAAAATTAA
Found at i:332086 original size:22 final size:21
Alignment explanation
Indices: 332061--332112 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
332051 TAACATGAAA
*
332061 TTAATTATATCATA-ATAATATT
1 TTAATT-TAACATATATAA-ATT
*
332083 TTAATTTAACATATTTAAATT
1 TTAATTTAACATATATAAATT
332104 TTAATTTAA
1 TTAATTTAA
332113 TTCAAATAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 18 0.67
22 9 0.33
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (21 bp):
TTAATTTAACATATATAAATT
Found at i:341033 original size:3 final size:3
Alignment explanation
Indices: 341027--341068 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
341017 TTTTTGTCAT
341027 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
341069 ACAGTCGGGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:342120 original size:33 final size:31
Alignment explanation
Indices: 342051--342122 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 31
342041 AGAAACGACA
* * *
342051 GAAAAATTTGGGGGAGAGAAAAGTCAAAATT
1 GAAAATTTTGGGGGAGAGAAAAGTAAAAAGT
*
342082 G-AAATTTTGGAGGGGGAGAAAAGTAAAAAAGT
1 GAAAATTTTGG-GGGAGAGAAAAGT-AAAAAGT
342114 GAAAATTTT
1 GAAAATTTT
342123 TTTTTAATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
30 8 0.24
31 13 0.38
32 6 0.18
33 7 0.21
ACGTcount: A:0.47, C:0.01, G:0.29, T:0.22
Consensus pattern (31 bp):
GAAAATTTTGGGGGAGAGAAAAGTAAAAAGT
Found at i:346350 original size:15 final size:15
Alignment explanation
Indices: 346330--346359 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
346320 AAAATTGAAT
346330 AATATCGAAGCTAAC
1 AATATCGAAGCTAAC
346345 AATATCGAAGCTAAC
1 AATATCGAAGCTAAC
346360 TTCTTTGTCG
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:0.47, C:0.20, G:0.13, T:0.20
Consensus pattern (15 bp):
AATATCGAAGCTAAC
Found at i:360947 original size:15 final size:14
Alignment explanation
Indices: 360915--360957 Score: 52
Period size: 15 Copynumber: 3.0 Consensus size: 14
360905 GTAAGGAATT
360915 TAAAA-TAACATAAA
1 TAAAAGTAA-ATAAA
*
360929 TAAAAGTGAAATAAT
1 TAAAAGT-AAATAAA
360944 TAAAAGTAAATAAA
1 TAAAAGTAAATAAA
360958 GTAATGCATC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
14 11 0.44
15 12 0.48
16 2 0.08
ACGTcount: A:0.67, C:0.02, G:0.07, T:0.23
Consensus pattern (14 bp):
TAAAAGTAAATAAA
Found at i:369542 original size:48 final size:48
Alignment explanation
Indices: 369486--369661 Score: 244
Period size: 48 Copynumber: 3.7 Consensus size: 48
369476 AAGGAGGAAG
* * *
369486 ATGTGGCCATTTATGGAAAATATGTAGTAGTTCATTTGCAAAGTGACT
1 ATGTGGCCATTTATGGAAAATATGTAGCAGTTCATCTACAAAGTGACT
* *
369534 ATGTGGCCATTTATGGTAAATATGCAGCAGTTCATCTACAAAGTGACT
1 ATGTGGCCATTTATGGAAAATATGTAGCAGTTCATCTACAAAGTGACT
* * *
369582 ATGTGGCCATTTATGAAAAATATGTAGCAGTTCATCTAAAAAGTGAAT
1 ATGTGGCCATTTATGGAAAATATGTAGCAGTTCATCTACAAAGTGACT
* * * *
369630 ATGTAGCCATTTATGGCAATTATGTGGCAGTT
1 ATGTGGCCATTTATGGAAAATATGTAGCAGTT
369662 TTACGATAAA
Statistics
Matches: 113, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
48 113 1.00
ACGTcount: A:0.32, C:0.12, G:0.22, T:0.34
Consensus pattern (48 bp):
ATGTGGCCATTTATGGAAAATATGTAGCAGTTCATCTACAAAGTGACT
Found at i:394632 original size:18 final size:18
Alignment explanation
Indices: 394609--394653 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
394599 TCAGTCATTT
*
394609 GAAAAAGAAACAAAATGA
1 GAAAAAGAAACAAAAAGA
* *
394627 GAAAAAGGAAGAAAAAGA
1 GAAAAAGAAACAAAAAGA
394645 -AAAAAGAAA
1 GAAAAAGAAA
394654 AAAGTTTGGT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
17 8 0.35
18 15 0.65
ACGTcount: A:0.76, C:0.02, G:0.20, T:0.02
Consensus pattern (18 bp):
GAAAAAGAAACAAAAAGA
Found at i:397785 original size:75 final size:75
Alignment explanation
Indices: 397662--397809 Score: 278
Period size: 75 Copynumber: 2.0 Consensus size: 75
397652 TCTGGAAGAG
*
397662 GAGATGCTTTCAATCCTAAAGCATTGTCATAATGCTCCTTATGGAGGTCATTTCCGTGGCATGAG
1 GAGATGCTTTCAATCCTAAAGCATTGTCATAATGCTCCTTATGGAGGTCATTTCCGTGGAATGAG
397727 AACTGCTGTT
66 AACTGCTGTT
*
397737 GAGATGCTTTCAATCCTAAAGCATTGTCATGATGCTCCTTATGGAGGTCATTTCCGTGGAATGAG
1 GAGATGCTTTCAATCCTAAAGCATTGTCATAATGCTCCTTATGGAGGTCATTTCCGTGGAATGAG
397802 AACTGCTG
66 AACTGCTG
397810 CTAAAGTTCT
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
75 71 1.00
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (75 bp):
GAGATGCTTTCAATCCTAAAGCATTGTCATAATGCTCCTTATGGAGGTCATTTCCGTGGAATGAG
AACTGCTGTT
Done.