Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A01
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: 115637255
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 5450143 characters in sequence are not A, C, G, or T
File 63 of 349
Found at i:18433708 original size:28 final size:28
Alignment explanation
Indices: 18433654--18433708 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
18433644 ACGGTTTGAA
*
18433654 TTATTTTTAACTAAGTTTTCTGTATTTT
1 TTATTTTTAACTAAGTTTTCTGGATTTT
18433682 TTATTTTTAGACTAAGTTTTC-GGATTT
1 TTATTTTTA-ACTAAGTTTTCTGGATTT
18433709 GATTTTGGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 14 0.56
29 11 0.44
ACGTcount: A:0.22, C:0.07, G:0.11, T:0.60
Consensus pattern (28 bp):
TTATTTTTAACTAAGTTTTCTGGATTTT
Found at i:18444978 original size:13 final size:13
Alignment explanation
Indices: 18444960--18444988 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
18444950 GTTAGTCTGT
18444960 TACTGTTTTGTTA
1 TACTGTTTTGTTA
18444973 TACTGTTTTGTTA
1 TACTGTTTTGTTA
18444986 TAC
1 TAC
18444989 AGGCTAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.17, C:0.10, G:0.14, T:0.59
Consensus pattern (13 bp):
TACTGTTTTGTTA
Found at i:18446104 original size:6 final size:6
Alignment explanation
Indices: 18446095--18446123 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
18446085 AAAATGAAAA
18446095 GAAAGG GAAAGG GAAAGG GAAAGG GAAAG
1 GAAAGG GAAAGG GAAAGG GAAAGG GAAAG
18446124 AACTACCCGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (6 bp):
GAAAGG
Found at i:18448883 original size:32 final size:31
Alignment explanation
Indices: 18448788--18448929 Score: 108
Period size: 32 Copynumber: 4.5 Consensus size: 31
18448778 TGGGAGACCT
* * *
18448788 ATTAAAATTTTCAAAAATTTTAGGA-GTTTT
1 ATTAAAATTTTCAAAAATTTTAGAAGGTATA
* **
18448818 ATGAAAATTTTCAAAAATTTTA-AGAGAACATA
1 ATTAAAATTTTCAAAAATTTTAGA-AG-GTATA
*
18448850 ATTAAAATTTTCAAAAAGTATTAGAAGGTATA
1 ATTAAAATTTTCAAAAA-TTTTAGAAGGTATA
* * * * * *
18448882 ATTAGACTTTTAAAAAATTTGAGAGGGTCTA
1 ATTAAAATTTTCAAAAATTTTAGAAGGTATA
*
18448913 ATTAAAACTTTTTAAAA
1 ATTAAAA-TTTTCAAAA
18448930 GCCTTAAGGG
Statistics
Matches: 86, Mismatches: 20, Indels: 10
0.74 0.17 0.09
Matches are distributed among these distances:
30 22 0.26
31 15 0.17
32 42 0.49
33 6 0.07
34 1 0.01
ACGTcount: A:0.46, C:0.05, G:0.11, T:0.37
Consensus pattern (31 bp):
ATTAAAATTTTCAAAAATTTTAGAAGGTATA
Found at i:18448992 original size:31 final size:31
Alignment explanation
Indices: 18448889--18448992 Score: 75
Period size: 31 Copynumber: 3.3 Consensus size: 31
18448879 ATAATTAGAC
*
18448889 TTTTAAAAAATTTGAGAGGGTCTAATTAAAACT
1 TTTTAAAAAATTT-A-AGGGTCTAATTAAAATT
*** ** * *
18448922 TTTTAAAAGCCTTAAGGG-AGAAATAAAGCTT
1 TTTTAAAAAATTTAAGGGTCTAATTAAA-ATT
***
18448953 TCCAAAAAAATTTAAGGGTCTAATTAAAATT
1 TTTTAAAAAATTTAAGGGTCTAATTAAAATT
18448984 TTTTAAAAA
1 TTTTAAAAA
18448993 TTTCAAATGA
Statistics
Matches: 48, Mismatches: 21, Indels: 6
0.64 0.28 0.08
Matches are distributed among these distances:
30 6 0.12
31 25 0.52
32 7 0.15
33 10 0.21
ACGTcount: A:0.45, C:0.08, G:0.13, T:0.34
Consensus pattern (31 bp):
TTTTAAAAAATTTAAGGGTCTAATTAAAATT
Found at i:18454196 original size:24 final size:24
Alignment explanation
Indices: 18454169--18454220 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
18454159 TTAGTAAGTC
*
18454169 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
18454193 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
18454217 AAAT
1 AAAT
18454221 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:18467632 original size:21 final size:20
Alignment explanation
Indices: 18467608--18467671 Score: 69
Period size: 21 Copynumber: 3.2 Consensus size: 20
18467598 TAGCCTTCGG
18467608 GCTTCCGTCTAGCACTTATGT
1 GCTTCCGT-TAGCACTTATGT
* * *
18467629 GCTTCAGTTAGC-CTT-CGG
1 GCTTCCGTTAGCACTTATGT
18467647 GCTTCCGTTTAGCACTTATGT
1 GCTTCCG-TTAGCACTTATGT
18467668 GCTT
1 GCTT
18467672 GAGCTAGACT
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
18 7 0.21
19 8 0.24
20 7 0.21
21 12 0.35
ACGTcount: A:0.12, C:0.27, G:0.22, T:0.39
Consensus pattern (20 bp):
GCTTCCGTTAGCACTTATGT
Found at i:18467633 original size:39 final size:39
Alignment explanation
Indices: 18467590--18467686 Score: 158
Period size: 39 Copynumber: 2.5 Consensus size: 39
18467580 GCTCTGGTGA
18467590 GCTTCAGTTAGCCTTCGGGCTTCCGTCTAGCACTTATGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTCTAGCACTTATGT
*
18467629 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTCTAGCACTTATGT
* * *
18467668 GCTTGAGCTAGACTTCGGG
1 GCTTCAGTTAGCCTTCGGG
18467687 TTTCAGATCA
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 54 1.00
ACGTcount: A:0.13, C:0.26, G:0.26, T:0.35
Consensus pattern (39 bp):
GCTTCAGTTAGCCTTCGGGCTTCCGTCTAGCACTTATGT
Found at i:18475425 original size:5 final size:5
Alignment explanation
Indices: 18475415--18475440 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
18475405 GAACAAATAT
18475415 ATTCG ATTCG ATTCG ATTCG ATTCG A
1 ATTCG ATTCG ATTCG ATTCG ATTCG A
18475441 ATTCCATCTC
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:0.23, C:0.19, G:0.19, T:0.38
Consensus pattern (5 bp):
ATTCG
Found at i:18475907 original size:33 final size:33
Alignment explanation
Indices: 18475840--18475907 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 33
18475830 TCAAGGCCGC
* *
18475840 CATCATAGTCTCAATGGCATCAGCCTTACCAGT
1 CATCATAGCCTCAATGGCATCAGCCCTACCAGT
* *
18475873 CATCATAGCCTCAATGGCATCATCCCTACTAGT
1 CATCATAGCCTCAATGGCATCAGCCCTACCAGT
18475906 CA
1 CA
18475908 GCTTTTCAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.28, C:0.32, G:0.13, T:0.26
Consensus pattern (33 bp):
CATCATAGCCTCAATGGCATCAGCCCTACCAGT
Found at i:18476561 original size:22 final size:24
Alignment explanation
Indices: 18476531--18476574 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
18476521 CTATCTAGAT
18476531 ATCAAATC-TCT-AAGATTACAGA
1 ATCAAATCTTCTAAAGATTACAGA
*
18476553 ATCATATCTTCTAAAGATTACA
1 ATCAAATCTTCTAAAGATTACA
18476575 TTTAATGTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
23 3 0.16
24 9 0.47
ACGTcount: A:0.43, C:0.18, G:0.07, T:0.32
Consensus pattern (24 bp):
ATCAAATCTTCTAAAGATTACAGA
Found at i:18483942 original size:31 final size:31
Alignment explanation
Indices: 18483899--18483960 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
18483889 TGTATTGATG
*
18483899 TATTAAATTATTTAAATATATTTTATCATTA
1 TATTAAATTATTTAAATATAATTTATCATTA
*
18483930 TATT-AATGTATTTAAATATAATTTATTATTA
1 TATTAAAT-TATTTAAATATAATTTATCATTA
18483961 GATTTAAGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 3 0.11
31 25 0.89
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (31 bp):
TATTAAATTATTTAAATATAATTTATCATTA
Found at i:18484633 original size:31 final size:30
Alignment explanation
Indices: 18484591--18484697 Score: 83
Period size: 31 Copynumber: 3.4 Consensus size: 30
18484581 AGTGGAAAAG
*
18484591 TTTGAGCAAAAATATAAATTTAAAAATTAGA
1 TTTGAGAAAAAATA-AAATTTAAAAATTAGA
* **
18484622 TTTGAGAAAAAA-AAAGCTCGTTTAGAAAACGAG-
1 TTTGAGAAAAAATAAA----ATTTA-AAAATTAGA
* *
18484655 TTTGAGCAAAAATAAAAACTTAAAAATTAGA
1 TTTGAGAAAAAAT-AAAATTTAAAAATTAGA
18484686 TTTGAGAAAAAA
1 TTTGAGAAAAAA
18484698 AAAGCTCGTT
Statistics
Matches: 58, Mismatches: 10, Indels: 16
0.69 0.12 0.19
Matches are distributed among these distances:
29 2 0.03
30 7 0.12
31 25 0.43
33 15 0.26
34 6 0.10
35 3 0.05
ACGTcount: A:0.54, C:0.06, G:0.14, T:0.26
Consensus pattern (30 bp):
TTTGAGAAAAAATAAAATTTAAAAATTAGA
Found at i:18484659 original size:33 final size:33
Alignment explanation
Indices: 18484609--18484722 Score: 114
Period size: 33 Copynumber: 3.5 Consensus size: 33
18484599 AAAATATAAA
*
18484609 TTTA-AAAATTAGATTTGAGAAAAAAAAAGCTCG
1 TTTAGAAAATGAG-TTTGAGAAAAAAAAAGCTCG
* *
18484642 TTTAGAAAACGAGTTTGAGCAAAAATAAAA--AC-
1 TTTAGAAAATGAGTTTGAG-AAAAA-AAAAGCTCG
*
18484674 -TTA-AAAATTAGATTTGAGAAAAAAAAAGCTCG
1 TTTAGAAAATGAG-TTTGAGAAAAAAAAAGCTCG
18484706 TTTAGAAAATGAGTTTG
1 TTTAGAAAATGAGTTTG
18484723 GCAATATATT
Statistics
Matches: 65, Mismatches: 7, Indels: 18
0.72 0.08 0.20
Matches are distributed among these distances:
29 4 0.06
30 11 0.17
31 10 0.15
33 18 0.28
34 18 0.28
35 4 0.06
ACGTcount: A:0.50, C:0.06, G:0.17, T:0.27
Consensus pattern (33 bp):
TTTAGAAAATGAGTTTGAGAAAAAAAAAGCTCG
Found at i:18484690 original size:64 final size:64
Alignment explanation
Indices: 18484589--18484726 Score: 242
Period size: 64 Copynumber: 2.2 Consensus size: 64
18484579 AAAGTGGAAA
* *
18484589 AGTTTGAGCAAAAATATAAATTTAAAAATTAGATTTGAGAAAAAAAAAGCTCGTTTAGAAAACG
1 AGTTTGAGCAAAAATAAAAACTTAAAAATTAGATTTGAGAAAAAAAAAGCTCGTTTAGAAAACG
*
18484653 AGTTTGAGCAAAAATAAAAACTTAAAAATTAGATTTGAGAAAAAAAAAGCTCGTTTAGAAAATG
1 AGTTTGAGCAAAAATAAAAACTTAAAAATTAGATTTGAGAAAAAAAAAGCTCGTTTAGAAAACG
18484717 AGTTTG-GCAA
1 AGTTTGAGCAA
18484727 TATATTTTTA
Statistics
Matches: 71, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
63 4 0.06
64 67 0.94
ACGTcount: A:0.51, C:0.07, G:0.17, T:0.26
Consensus pattern (64 bp):
AGTTTGAGCAAAAATAAAAACTTAAAAATTAGATTTGAGAAAAAAAAAGCTCGTTTAGAAAACG
Found at i:18494400 original size:2 final size:2
Alignment explanation
Indices: 18494393--18494424 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
18494383 AGTCATGTGA
18494393 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
18494425 TGGGTTTGGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:18497540 original size:14 final size:14
Alignment explanation
Indices: 18497521--18497554 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
18497511 GACATTTTTT
*
18497521 TTCTAATGATATTA
1 TTCTAATGATACTA
18497535 TTCTAATGATACTA
1 TTCTAATGATACTA
18497549 TTCTAA
1 TTCTAA
18497555 CATGTAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.35, C:0.12, G:0.06, T:0.47
Consensus pattern (14 bp):
TTCTAATGATACTA
Found at i:18498782 original size:64 final size:64
Alignment explanation
Indices: 18498666--18498789 Score: 205
Period size: 64 Copynumber: 1.9 Consensus size: 64
18498656 AATTAGATTA
** *
18498666 ATTACAACATTAAAACTTGGAACAAACTTTGTTGTCATAAATTAATTAATTGCAACATTATAAC
1 ATTACAACATTAAAACTTGGAACAAACTTTGTAATCATAAATTAAATAATTGCAACATTATAAC
18498730 ATTACAACATTAAAACTTGGAACAAACTTTGTAAT-ATAAATTAAATACATTGCAACATTA
1 ATTACAACATTAAAACTTGGAACAAACTTTGTAATCATAAATTAAATA-ATTGCAACATTA
18498790 AAACTTGGAA
Statistics
Matches: 56, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
63 11 0.20
64 45 0.80
ACGTcount: A:0.46, C:0.14, G:0.07, T:0.33
Consensus pattern (64 bp):
ATTACAACATTAAAACTTGGAACAAACTTTGTAATCATAAATTAAATAATTGCAACATTATAAC
Found at i:18498786 original size:48 final size:48
Alignment explanation
Indices: 18498728--18498820 Score: 168
Period size: 48 Copynumber: 1.9 Consensus size: 48
18498718 CAACATTATA
18498728 ACATTACAACATTAAAACTTGGAACAAACTTTGTAATATAAATTAAAT
1 ACATTACAACATTAAAACTTGGAACAAACTTTGTAATATAAATTAAAT
* *
18498776 ACATTGCAACATTAAAACTTGGAACGAACTTTGTAATATAAATTA
1 ACATTACAACATTAAAACTTGGAACAAACTTTGTAATATAAATTA
18498821 GGTACGTTGG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 43 1.00
ACGTcount: A:0.47, C:0.13, G:0.09, T:0.31
Consensus pattern (48 bp):
ACATTACAACATTAAAACTTGGAACAAACTTTGTAATATAAATTAAAT
Found at i:18503131 original size:19 final size:19
Alignment explanation
Indices: 18503091--18503132 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
18503081 CATAATTTAA
*
18503091 AATGAAAATTTTAAGAAAT
1 AATGAAAATTGTAAGAAAT
*
18503110 AATGAAAGTTGTAA-AAATT
1 AATGAAAATTGTAAGAAA-T
18503129 AATG
1 AATG
18503133 TTTTAAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 3 0.15
19 17 0.85
ACGTcount: A:0.55, C:0.00, G:0.14, T:0.31
Consensus pattern (19 bp):
AATGAAAATTGTAAGAAAT
Found at i:18503348 original size:21 final size:21
Alignment explanation
Indices: 18503300--18503348 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
18503290 AACAGTTTTA
*
18503300 ATAACGAAAGGACTTGATGAT
1 ATAACGTAAGGACTTGATGAT
18503321 ATAACGTAAGGACTTGATGAT
1 ATAACGTAAGGACTTGATGAT
18503342 ATAACGT
1 ATAACGT
18503349 CAATAGTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.41, C:0.10, G:0.22, T:0.27
Consensus pattern (21 bp):
ATAACGTAAGGACTTGATGAT
Found at i:18508022 original size:20 final size:20
Alignment explanation
Indices: 18507994--18508052 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 20
18507984 TTTTAAAATA
* *
18507994 AAGTGAAAATTATTTTAACC
1 AAGTCAAAATCATTTTAACC
* * *
18508014 AAGTCAAAATGATTTTCATC
1 AAGTCAAAATCATTTTAACC
*
18508034 AAGTTAAAATCATTTTAAC
1 AAGTCAAAATCATTTTAAC
18508053 ATATCAAAAT
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.44, C:0.12, G:0.08, T:0.36
Consensus pattern (20 bp):
AAGTCAAAATCATTTTAACC
Found at i:18508068 original size:39 final size:41
Alignment explanation
Indices: 18507994--18508079 Score: 115
Period size: 40 Copynumber: 2.1 Consensus size: 41
18507984 TTTTAAAATA
* * *
18507994 AAGTGAAAATTATTTTAACCAAGTCAAAATGATTTTC-ATC
1 AAGTTAAAATCATTTTAACCAAGTCAAAATGATTTTCAAAC
18508034 AAGTTAAAATCATTTTAA-CATA-TCAAAATGATTTTCAAAC
1 AAGTTAAAATCATTTTAACCA-AGTCAAAATGATTTTCAAAC
18508074 AAGTTA
1 AAGTTA
18508080 GAATTGCTCT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
39 16 0.39
40 25 0.61
ACGTcount: A:0.45, C:0.12, G:0.08, T:0.35
Consensus pattern (41 bp):
AAGTTAAAATCATTTTAACCAAGTCAAAATGATTTTCAAAC
Found at i:18508246 original size:20 final size:22
Alignment explanation
Indices: 18508223--18508262 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
18508213 TTTTACCGAT
18508223 ATCGATA-CTTTC-TAAAAATA
1 ATCGATACCTTTCTTAAAAATA
18508243 ATCGATACCTTTCTTAAAAA
1 ATCGATACCTTTCTTAAAAA
18508263 CGATACCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 5 0.28
22 6 0.33
ACGTcount: A:0.42, C:0.17, G:0.05, T:0.35
Consensus pattern (22 bp):
ATCGATACCTTTCTTAAAAATA
Found at i:18512193 original size:46 final size:46
Alignment explanation
Indices: 18512126--18512251 Score: 191
Period size: 46 Copynumber: 2.7 Consensus size: 46
18512116 AACCCGCCCC
**
18512126 TAAGTGAACTCGGACTCAACTCAACGAGCTCCGG-TGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAG-TCCGGACATTCGCATCCA
* *
18512172 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTCCGGACATTCGCATCCA
*
18512218 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTCCGGA
18512252 TGCTCAACCA
Statistics
Matches: 75, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
45 4 0.05
46 71 0.95
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.22
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTCCGGACATTCGCATCCA
Found at i:18512270 original size:46 final size:45
Alignment explanation
Indices: 18512128--18512270 Score: 148
Period size: 46 Copynumber: 3.1 Consensus size: 45
18512118 CCCGCCCCTA
* *
18512128 AGTGAACTCGGACTCAACTCAACGAGCTCCGG-TGTTC-GCATCCAT
1 AGTGAACTCGGACTCAACTCAACGAG-TTCGGATGTTCACCATCC-T
** **
18512173 AAGTGAACTCGGACTCAACTCAACGAGTTCGGACATT-TGCATCCAT
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGGATGTTCACCATCC-T
*
18512219 AAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCT
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGGATGTTC-ACCATCCT
18512266 AGTGA
1 AGTGA
18512271 CATGTCACTT
Statistics
Matches: 85, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
45 4 0.05
46 75 0.88
47 1 0.01
48 5 0.06
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (45 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGTTCACCATCCT
Found at i:18512707 original size:30 final size:30
Alignment explanation
Indices: 18512673--18512732 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
18512663 ATTTAATACG
18512673 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
18512703 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
18512733 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:18519777 original size:93 final size:93
Alignment explanation
Indices: 18519670--18519840 Score: 306
Period size: 93 Copynumber: 1.8 Consensus size: 93
18519660 GCCCCTAAGT
* *
18519670 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
18519735 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
* *
18519763 GAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
18519828 CGAGTTCGGATGC
66 CGAGTTCGGATGC
18519841 TCAACCATCC
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:18519837 original size:46 final size:46
Alignment explanation
Indices: 18519665--18519837 Score: 217
Period size: 46 Copynumber: 3.7 Consensus size: 46
18519655 AACCCGCCCC
* * * *
18519665 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
* *
18519711 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-ATTTGCATCCA
* *
18519759 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
18519804 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
18519838 TGCTCAACCA
Statistics
Matches: 108, Mismatches: 12, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
43 6 0.06
44 2 0.02
45 2 0.02
46 61 0.56
47 29 0.27
48 2 0.02
49 2 0.02
50 4 0.04
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
Found at i:18520294 original size:30 final size:30
Alignment explanation
Indices: 18520260--18520319 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
18520250 ATTTAATACG
18520260 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
18520290 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
18520320 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:18521567 original size:34 final size:34
Alignment explanation
Indices: 18521524--18521596 Score: 146
Period size: 34 Copynumber: 2.1 Consensus size: 34
18521514 TGATTATATC
18521524 CCCAAACTATCATTGATACTGAAAAGGGCTTAGG
1 CCCAAACTATCATTGATACTGAAAAGGGCTTAGG
18521558 CCCAAACTATCATTGATACTGAAAAGGGCTTAGG
1 CCCAAACTATCATTGATACTGAAAAGGGCTTAGG
18521592 CCCAA
1 CCCAA
18521597 GACCGTTCAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 39 1.00
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.22
Consensus pattern (34 bp):
CCCAAACTATCATTGATACTGAAAAGGGCTTAGG
Found at i:18543486 original size:18 final size:19
Alignment explanation
Indices: 18543459--18543494 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
18543449 ATCAATACCG
18543459 TTTTAAAAA-TATTGATAA
1 TTTTAAAAATTATTGATAA
*
18543477 TTTTATAAATTATTGATA
1 TTTTAAAAATTATTGATA
18543495 CTTATGAGAA
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:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (19 bp):
TTTTAAAAATTATTGATAA
Found at i:18543492 original size:19 final size:18
Alignment explanation
Indices: 18543459--18543494 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
18543449 ATCAATACCG
18543459 TTTTAAAAATATTGATAA
1 TTTTAAAAATATTGATAA
*
18543477 TTTTATAAATTATTGATA
1 TTTTA-AAAATATTGATA
18543495 CTTATGAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (18 bp):
TTTTAAAAATATTGATAA
Found at i:18544516 original size:22 final size:22
Alignment explanation
Indices: 18544491--18544563 Score: 119
Period size: 22 Copynumber: 3.3 Consensus size: 22
18544481 TAGCAATAAG
* *
18544491 GTGCTATATAGAGAGCACGAAT
1 GTGCTAAACAGAGAGCACGAAT
18544513 GTGCTAAACAGAGAGCACGAAT
1 GTGCTAAACAGAGAGCACGAAT
*
18544535 GTGCTAAACAGAGAGCACTAAT
1 GTGCTAAACAGAGAGCACGAAT
18544557 GTGCTAA
1 GTGCTAA
18544564 TAATCAGATA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 48 1.00
ACGTcount: A:0.38, C:0.16, G:0.26, T:0.19
Consensus pattern (22 bp):
GTGCTAAACAGAGAGCACGAAT
Found at i:18548041 original size:20 final size:19
Alignment explanation
Indices: 18548018--18548087 Score: 68
Period size: 20 Copynumber: 3.5 Consensus size: 19
18548008 CAAGTGAAAA
18548018 TCAACCAAGTCAAAATGATT
1 TCAA-CAAGTCAAAATGATT
* *
18548038 TCAATCAAGTTAAAATCATT
1 TCAA-CAAGTCAAAATGATT
* *
18548058 TTAACACGTCAAAATGATTT
1 TCAACAAGTCAAAATGA-TT
18548078 TCAAACAAGT
1 TC-AACAAGT
18548088 TAGAATTGCT
Statistics
Matches: 39, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
19 10 0.26
20 23 0.59
21 6 0.15
ACGTcount: A:0.44, C:0.17, G:0.09, T:0.30
Consensus pattern (19 bp):
TCAACAAGTCAAAATGATT
Found at i:18548077 original size:19 final size:20
Alignment explanation
Indices: 18548023--18548078 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
18548013 GAAAATCAAC
*
18548023 CAAGTCAAAATGATTTCAAT
1 CAAGTCAAAATGATTTTAAT
* *
18548043 CAAGTTAAAATCATTTTAA-
1 CAAGTCAAAATGATTTTAAT
*
18548062 CACGTCAAAATGATTTT
1 CAAGTCAAAATGATTTT
18548079 CAAACAAGTT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.43, C:0.14, G:0.09, T:0.34
Consensus pattern (20 bp):
CAAGTCAAAATGATTTTAAT
Found at i:18551451 original size:16 final size:16
Alignment explanation
Indices: 18551430--18551465 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
18551420 TAGTAGACAT
18551430 TATAATAT-AGTTAACA
1 TATAATATCA-TTAACA
18551446 TATAATATCATTAACA
1 TATAATATCATTAACA
18551462 TATA
1 TATA
18551466 TGAAATTACA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 18 0.95
17 1 0.05
ACGTcount: A:0.50, C:0.08, G:0.03, T:0.39
Consensus pattern (16 bp):
TATAATATCATTAACA
Found at i:18554575 original size:57 final size:57
Alignment explanation
Indices: 18554454--18554573 Score: 163
Period size: 57 Copynumber: 2.1 Consensus size: 57
18554444 TTCTCATTTT
*
18554454 CATTTTCATTTCCATTTTGGAGAAAACCACATTCATTTCCAAATGATTTTATTTCTC
1 CATTTTCATTTCCATTTTGGAGAAAACCACAATCATTTCCAAATGATTTTATTTCTC
* **
18554511 CATTTTCATTTTCC-TTTTGGAGATAACCTTAATCATTTCCAAATG-TTTCATATTTCTC
1 CATTTTCA-TTTCCATTTTGGAGAAAACCACAATCATTTCCAAATGATTT--TATTTCTC
18554569 CATTT
1 CATTT
18554574 CACCATTTCT
Statistics
Matches: 56, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
56 3 0.05
57 35 0.62
58 18 0.32
ACGTcount: A:0.26, C:0.21, G:0.07, T:0.47
Consensus pattern (57 bp):
CATTTTCATTTCCATTTTGGAGAAAACCACAATCATTTCCAAATGATTTTATTTCTC
Found at i:18560362 original size:29 final size:29
Alignment explanation
Indices: 18560330--18560410 Score: 92
Period size: 29 Copynumber: 2.8 Consensus size: 29
18560320 AATTTCACAT
* *
18560330 ACCTGTATCTGGCCCATTAGGTCTAAATC
1 ACCTGTATCTGGCCCATTAGGCCCAAATC
*
18560359 ACCTGCATAC-GGCCCATTAGGCCCAAATC
1 ACCTGTAT-CTGGCCCATTAGGCCCAAATC
* * *
18560388 ACATTTATATGGCCCATTAGGCC
1 ACCTGTATCTGGCCCATTAGGCC
18560411 TAGTCACATT
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
29 42 0.98
30 1 0.02
ACGTcount: A:0.26, C:0.31, G:0.17, T:0.26
Consensus pattern (29 bp):
ACCTGTATCTGGCCCATTAGGCCCAAATC
Found at i:18560677 original size:16 final size:16
Alignment explanation
Indices: 18560636--18560678 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
18560626 GTAGCCAAAC
18560636 TTTCGGCTTTTCAGCA
1 TTTCGGCTTTTCAGCA
**
18560652 TTTCAACTTTTC-GACA
1 TTTCGGCTTTTCAG-CA
18560668 TTTCGGCTTTT
1 TTTCGGCTTTT
18560679 ACCGATACAT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
15 1 0.05
16 21 0.95
ACGTcount: A:0.14, C:0.23, G:0.14, T:0.49
Consensus pattern (16 bp):
TTTCGGCTTTTCAGCA
Found at i:18561790 original size:16 final size:16
Alignment explanation
Indices: 18561763--18561812 Score: 64
Period size: 16 Copynumber: 3.1 Consensus size: 16
18561753 AAAAATTCAA
*
18561763 GATTTCGGGATTTTTG
1 GATTTCGAGATTTTTG
*
18561779 GATTTTGAGATTTTTG
1 GATTTCGAGATTTTTG
* *
18561795 GGTTTCGGGATTTTTG
1 GATTTCGAGATTTTTG
18561811 GA
1 GA
18561813 GCATTACATA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.14, C:0.04, G:0.32, T:0.50
Consensus pattern (16 bp):
GATTTCGAGATTTTTG
Found at i:18563203 original size:30 final size:30
Alignment explanation
Indices: 18563156--18563212 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
18563146 AGACTAATTA
*
18563156 CACACGGGCTGAGCACACGCCCATGTGAGG
1 CACACAGGCTGAGCACACGCCCATGTGAGG
18563186 CACACAGGCT-AGCCACACGCCCATGTG
1 CACACAGGCTGAG-CACACGCCCATGTG
18563213 GCAGCCCGTG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
29 2 0.08
30 23 0.92
ACGTcount: A:0.25, C:0.37, G:0.28, T:0.11
Consensus pattern (30 bp):
CACACAGGCTGAGCACACGCCCATGTGAGG
Found at i:18565789 original size:166 final size:167
Alignment explanation
Indices: 18565506--18565829 Score: 465
Period size: 166 Copynumber: 1.9 Consensus size: 167
18565496 CTTCACATAG
** * * * *
18565506 ACACTACGAGTTTCTAGCAATGTTGTTTGGGCTAACCAATGCCCAATCCACTTTTATGGATTTGA
1 ACACTACGAGTTTCTAGCAATGTCATTTGGACTAAACAACGCCCAATCCACTTTTATGGATCTGA
** * * * *
18565571 TGAACATAATTTTTCATTTGTATTTTTATAGATTTTTTGTTGTGTTCATAGATTATATATTTATC
66 TGAACATAATTTTTCATTTGTATTTGGATAAATTTGTTGTTGTGTTCATAGATGATATATTAATC
18565636 TACTC-AAAAAATAAAAATGATCATGATCAGCATCTA
131 TACTCAAAAAAATAAAAATGATCATGATCAGCATCTA
* * *
18565672 ACACTAGGGGTTTCTAGTAATGTCATTTGGACTAAACAACGCCCAATCCACTTTTATGGATCTGA
1 ACACTACGAGTTTCTAGCAATGTCATTTGGACTAAACAACGCCCAATCCACTTTTATGGATCTGA
18565737 TGAACATAATTTTTCATGTT-TATTTGGATAAATTTGTTGTTGT-TATCATAGATGATATATTAA
66 TGAACATAATTTTTCAT-TTGTATTTGGATAAATTTGTTGTTGTGT-TCATAGATGATATATTAA
*
18565800 TCTACTCAAAAAAATGAAAATGATCATGAT
129 TCTACTCAAAAAAATAAAAATGATCATGAT
18565830 TAGTGTCTAA
Statistics
Matches: 139, Mismatches: 16, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
165 1 0.01
166 115 0.83
167 23 0.17
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.39
Consensus pattern (167 bp):
ACACTACGAGTTTCTAGCAATGTCATTTGGACTAAACAACGCCCAATCCACTTTTATGGATCTGA
TGAACATAATTTTTCATTTGTATTTGGATAAATTTGTTGTTGTGTTCATAGATGATATATTAATC
TACTCAAAAAAATAAAAATGATCATGATCAGCATCTA
Found at i:18566030 original size:162 final size:163
Alignment explanation
Indices: 18565759--18566088 Score: 599
Period size: 162 Copynumber: 2.0 Consensus size: 163
18565749 TTCATGTTTA
18565759 TTTGGATAAATTTGTTGTTGTTATCATAGATGATATATTAATCTACTCAAAAAAATGAAAATGAT
1 TTTGGATAAATTTGTTGTTGTTATCATAGATGATATATTAATCTACTCAAAAAAATGAAAATGAT
* *
18565824 CATGATTAGTGTCTAAGAGTTTTACTACAAACCTTGCAAGAAAAATAATTGTTTTCAAAAGTCTA
66 CATGATTAGTATCTAAGAGTTTTACAACAAACCTTGCAAGAAAAATAATTGTTTTCAAAAGTCTA
18565889 CAAATGTGAGTTCTGGCTACGAGAAGTGAGATT
131 CAAATGTGAGTTCTGGCTACGAGAAGTGAGATT
*
18565922 TTTGGATAAATTTGTTGTTGTTTTCATAGATGATATATTAATCTACTC-AAAAAATGAAAATGAT
1 TTTGGATAAATTTGTTGTTGTTATCATAGATGATATATTAATCTACTCAAAAAAATGAAAATGAT
*
18565986 CATGATTAGTATCTAATAGTTTTACAACAAACCTTGCAAGAAAAATAATTGTTTTCAAAAGTCTA
66 CATGATTAGTATCTAAGAGTTTTACAACAAACCTTGCAAGAAAAATAATTGTTTTCAAAAGTCTA
* *
18566051 CAAATGTGAGTTTTGGCTACGAGAAGTGGGATT
131 CAAATGTGAGTTCTGGCTACGAGAAGTGAGATT
18566084 TTTGG
1 TTTGG
18566089 GTTACCTAAT
Statistics
Matches: 161, Mismatches: 6, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
162 114 0.71
163 47 0.29
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.36
Consensus pattern (163 bp):
TTTGGATAAATTTGTTGTTGTTATCATAGATGATATATTAATCTACTCAAAAAAATGAAAATGAT
CATGATTAGTATCTAAGAGTTTTACAACAAACCTTGCAAGAAAAATAATTGTTTTCAAAAGTCTA
CAAATGTGAGTTCTGGCTACGAGAAGTGAGATT
Found at i:18569718 original size:19 final size:19
Alignment explanation
Indices: 18569694--18569730 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
18569684 TCTATAAATA
18569694 TCAGCTTGTGTGAGCAATG
1 TCAGCTTGTGTGAGCAATG
18569713 TCAGCTTGTGTGAGCAAT
1 TCAGCTTGTGTGAGCAAT
18569731 ATAGTCTCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (19 bp):
TCAGCTTGTGTGAGCAATG
Found at i:18580152 original size:12 final size:12
Alignment explanation
Indices: 18580137--18580163 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
18580127 GTCACACACA
18580137 GCCTACCACATG
1 GCCTACCACATG
18580149 GCCTACCACATG
1 GCCTACCACATG
18580161 GCC
1 GCC
18580164 GTGTGGTGTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.22, C:0.44, G:0.19, T:0.15
Consensus pattern (12 bp):
GCCTACCACATG
Found at i:18587499 original size:21 final size:21
Alignment explanation
Indices: 18587467--18587507 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
18587457 GAACAATTGG
18587467 TGTATAGGCTAAGAA-AGGCCT
1 TGTATAGGCTAA-AACAGGCCT
18587488 TGTAT-GGCCTAAAACAGGCC
1 TGTATAGG-CTAAAACAGGCC
18587508 CCTCGAGCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.32, C:0.20, G:0.27, T:0.22
Consensus pattern (21 bp):
TGTATAGGCTAAAACAGGCCT
Found at i:18595911 original size:45 final size:45
Alignment explanation
Indices: 18595847--18595935 Score: 160
Period size: 45 Copynumber: 2.0 Consensus size: 45
18595837 CCACACTAAT
* *
18595847 ATGTAGCCGAAGCTACCACTGATATGTAGCCGAAGCTACCACTGG
1 ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTGG
18595892 ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTG
1 ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTG
18595936 ATCAAGAACA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.31, C:0.27, G:0.22, T:0.19
Consensus pattern (45 bp):
ATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTACCACTGG
Found at i:18595935 original size:23 final size:23
Alignment explanation
Indices: 18595847--18595936 Score: 146
Period size: 23 Copynumber: 4.0 Consensus size: 23
18595837 CCACACTAAT
*
18595847 ATGTAGCCGAAGCTACCACTGAT
1 ATGTAGCCGAAGCTACCACTGAA
*
18595870 ATGTAGCCGAAGCTACCACTG-G
1 ATGTAGCCGAAGCTACCACTGAA
*
18595892 ATGTAGCCAAAGCTACCACTGAA
1 ATGTAGCCGAAGCTACCACTGAA
18595915 ATGTAGCCGAAGCTACCACTGA
1 ATGTAGCCGAAGCTACCACTGA
18595937 TCAAGAACAC
Statistics
Matches: 62, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
22 20 0.32
23 42 0.68
ACGTcount: A:0.32, C:0.27, G:0.22, T:0.19
Consensus pattern (23 bp):
ATGTAGCCGAAGCTACCACTGAA
Found at i:18597463 original size:20 final size:20
Alignment explanation
Indices: 18597425--18597465 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
18597415 CATGAACAAT
**
18597425 TTTGTGCCTACTAACACTAA
1 TTTGTGCCTAAAAACACTAA
*
18597445 TTTGTGCCTAAAAAGACTAA
1 TTTGTGCCTAAAAACACTAA
18597465 T
1 T
18597466 GGCTGATGCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.34, C:0.20, G:0.12, T:0.34
Consensus pattern (20 bp):
TTTGTGCCTAAAAACACTAA
Found at i:18602371 original size:29 final size:29
Alignment explanation
Indices: 18602306--18602386 Score: 130
Period size: 29 Copynumber: 2.8 Consensus size: 29
18602296 ACGGCCAGGT
18602306 ACATGGGCATGTG-GCTAGGCCGTGTGAGCC
1 ACATGGGCATGTGAG--AGGCCGTGTGAGCC
18602336 ACA-GGGCATGTGAGAGGCCGTGTGAGCC
1 ACATGGGCATGTGAGAGGCCGTGTGAGCC
18602364 ACATGGGCATGTGAGAGGCCGTG
1 ACATGGGCATGTGAGAGGCCGTG
18602387 CGACTGGCCG
Statistics
Matches: 49, Mismatches: 0, Indels: 5
0.91 0.00 0.09
Matches are distributed among these distances:
28 17 0.35
29 28 0.57
30 4 0.08
ACGTcount: A:0.20, C:0.21, G:0.42, T:0.17
Consensus pattern (29 bp):
ACATGGGCATGTGAGAGGCCGTGTGAGCC
Found at i:18609164 original size:28 final size:28
Alignment explanation
Indices: 18609124--18609180 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
18609114 CCTACAATCA
18609124 AATCTAATTTACTTTTTAATTAACATAC
1 AATCTAATTTACTTTTTAATTAACATAC
18609152 AATCTAATTTACTTTTTAATTAACATAC
1 AATCTAATTTACTTTTTAATTAACATAC
18609180 A
1 A
18609181 GAGACTAGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.40, C:0.14, G:0.00, T:0.46
Consensus pattern (28 bp):
AATCTAATTTACTTTTTAATTAACATAC
Found at i:18614329 original size:25 final size:26
Alignment explanation
Indices: 18614289--18614345 Score: 80
Period size: 25 Copynumber: 2.2 Consensus size: 26
18614279 TTTATTTTAT
*
18614289 TTTGGGTTTTATTTTTGTTTTATTGG
1 TTTGGGTTTTATTTTTGGTTTATTGG
*
18614315 TTTGGG-TTTATTTTTGGTTTGTTGG
1 TTTGGGTTTTATTTTTGGTTTATTGG
*
18614340 TCTGGG
1 TTTGGG
18614346 CCAAAATTGG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
25 22 0.79
26 6 0.21
ACGTcount: A:0.05, C:0.02, G:0.30, T:0.63
Consensus pattern (26 bp):
TTTGGGTTTTATTTTTGGTTTATTGG
Found at i:18614870 original size:43 final size:44
Alignment explanation
Indices: 18614533--18615233 Score: 294
Period size: 44 Copynumber: 15.6 Consensus size: 44
18614523 CTTTGATTTA
* * * *
18614533 CTCCACTGCAACTTCAGGGAGATAAGAATCGTAACTTCAACCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTTAATCTG
* * * * ** *
18614577 CTCTACTACAACTTTAGGGAGATGAGGTTTGTGACTTTAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTTAATCTG
* * * *
18614621 CTCCATTGCAACTTCAGGGAGATAAAATTTTCCATGGTAGA-TTTGATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGA-----C-TTGTA-ACTTTAATCTG
* * * * * ** * * *
18614671 AC-CTACTACGACTTCAGAGG-TATAGGGTTTATAGCTTTAATCTA
1 -CTCCACTGCAACTTCAG-GGAGATAAGACTTGTAACTTTAATCTG
* * * * ** *
18614715 CTCTATTGCAACTTCAGAGAGATAAGATTTGCTATTTTTAGTCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTG-TAACTTTAATCTG
* * *
18614760 TTCCACTACAACTTCAGGGAGATAAGACTTGTAACTTCAA-CTTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTTAATC-TG
* * *
18614804 CTCCACTGCATCTTCAGGAAGATAGGACTTGT-ACTTTAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTTAATCTG
* * * *
18614847 CTCCACTGTAACTTTAGGGAGATAAGATTCGCCATGGTAGA-TTTGATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGA-----C-TTGTA-ACTTTAATCTG
* * * * ** * * *
18614897 AC-CTACTGCGACTTCAGAGG-TATAGGGTTTATAGCTTTAATCTA
1 -CTCCACTGCAACTTCAG-GGAGATAAGACTTGTAACTTTAATCTG
* * * * * * * *
18614941 CTCTACTACAACCTGAGAGAGATAAGATTTGCT-ATTTTCAGTCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTG-TAACTTT-AATCTG
* * * * *
18614986 TTCCACTGCAACTTCAGGGAGATAAAACTTGTAACTTCAACCCG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTTAATCTG
* * * * *
18615030 CTCCACTGCATCTTCAAGGAGATAGGACTTGT-ACTTCAACCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTTAATCTG
* * ** * **
18615073 CCCCACTGCAACTTCAGGGGGATAAGGTTTGCTATCTTCGATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTG-TAACTTTAATCTG
* * * * *
18615118 TTCCACTGCAACTTCAGGAATATAAGA-TCTGTGACTTCAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACT-TGTAACTTTAATCTG
* * * *
18615162 CTCCGCTGCAACTTCAGAGAGACAAGA-TT-TACGACTTAAAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGTA--ACTT-TAATCTG
*
18615207 CTCCACTGTAACTTCAGGGAGATAAGA
1 CTCCACTGCAACTTCAGGGAGATAAGA
18615234 TTCACTATGG
Statistics
Matches: 474, Mismatches: 146, Indels: 73
0.68 0.21 0.11
Matches are distributed among these distances:
42 1 0.00
43 70 0.15
44 218 0.46
45 125 0.26
48 1 0.00
49 3 0.01
50 48 0.10
51 8 0.02
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (44 bp):
CTCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTTAATCTG
Found at i:18614936 original size:226 final size:225
Alignment explanation
Indices: 18614534--18615098 Score: 835
Period size: 226 Copynumber: 2.5 Consensus size: 225
18614524 TTTGATTTAC
* * * * * *
18614534 TCCACTGCAACTTCAGGGAGATAAGAATCGTAACTTCAACCTGCTCTACTACAACTTTAGGGAGA
1 TCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTCAACCTGCTCCACTGCATCTTCA-GGAGA
* * * **
18614599 TGAGG-TTTGTGACTTTAATCTGCTCCATTGCAACTTCAGGGAGATAAAATTTTCCATGGTAGAT
65 T-AGGACTTGT-ACTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCCATGGTAGAT
* * *
18614663 TTGATCTGACCTACTACGACTTCAGAGGTATAGGGTTTATAGCTTTAATCTACTCTATTGCAACT
128 TTGATCTGACCTACTACGACTTCAGAGGTATAGGGTTTATAGCTTTAATCTACTCTACTACAACC
*
18614728 TCAGAGAGATAAGATTTGCTATTTTTAGTCTGT
193 TCAGAGAGATAAGATTTGCTATTTTCAGTCTGT
* *
18614761 TCCACTACAACTTCAGGGAGATAAGACTTGTAACTTCAACTTGCTCCACTGCATCTTCAGGAAGA
1 TCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTCAACCTGCTCCACTGCATCTTCAGG-AGA
* *
18614826 TAGGACTTGTACTTTAATCTGCTCCACTGTAACTTTAGGGAGATAAGATTCGCCATGGTAGATTT
65 TAGGACTTGTACTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCCATGGTAGATTT
* *
18614891 GATCTGACCTACTGCGACTTCAGAGGTATAGGGTTTATAGCTTTAATCTACTCTACTACAACCTG
130 GATCTGACCTACTACGACTTCAGAGGTATAGGGTTTATAGCTTTAATCTACTCTACTACAACCTC
18614956 AGAGAGATAAGATTTGCTATTTTCAGTCTGT
195 AGAGAGATAAGATTTGCTATTTTCAGTCTGT
* *
18614987 TCCACTGCAACTTCAGGGAGATAAAACTTGTAACTTCAACCCGCTCCACTGCATCTTCAAGGAGA
1 TCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTCAACCTGCTCCACTGCATCTTC-AGGAGA
* * * *
18615052 TAGGACTTGTACTTCAACCTGCCCCACTGCAACTTCAGGGGGATAAG
65 TAGGACTTGTACTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAG
18615099 GTTTGCTATC
Statistics
Matches: 304, Mismatches: 31, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
226 242 0.80
227 62 0.20
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.31
Consensus pattern (225 bp):
TCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTCAACCTGCTCCACTGCATCTTCAGGAGAT
AGGACTTGTACTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCCATGGTAGATTTG
ATCTGACCTACTACGACTTCAGAGGTATAGGGTTTATAGCTTTAATCTACTCTACTACAACCTCA
GAGAGATAAGATTTGCTATTTTCAGTCTGT
Found at i:18615143 original size:45 final size:44
Alignment explanation
Indices: 18614977--18615234 Score: 177
Period size: 45 Copynumber: 5.8 Consensus size: 44
18614967 ATTTGCTATT
* * * * *
18614977 TTCAGTCTGTTCCACTGCAACTTCAGGGAGATAA-AACTTGTAAC
1 TTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATC-TGTGAC
* * * *
18615021 TTCAACCCGCTCCACTGCATCTTCAAGG-AGATAGGA-CT-TGTAC
1 TTCAATCTGCTCCACTGCAACTTC-AGGAAGATAAGATCTGTG-AC
* * ** * *
18615064 TTCAACCTGCCCCACTGCAACTTCAGGGGGATAAGGTTTGCT-ATC
1 TTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATCTG-TGA-C
* * *
18615109 TTCGATCTGTTCCACTGCAACTTCAGGAATATAAGATCTGTGAC
1 TTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATCTGTGAC
* * * **
18615153 TTCAATCTGCTCCGCTGCAACTTCA-GAGAGACAAGATTTACGAC
1 TTCAATCTGCTCCACTGCAACTTCAGGA-AGATAAGATCTGTGAC
* * *
18615197 TTAAAATCTGCTCCACTGTAACTTCAGGGAGATAAGAT
1 TT-CAATCTGCTCCACTGCAACTTCAGGAAGATAAGAT
18615235 TCACTATGGT
Statistics
Matches: 166, Mismatches: 36, Indels: 23
0.74 0.16 0.10
Matches are distributed among these distances:
42 4 0.02
43 31 0.19
44 64 0.39
45 65 0.39
46 2 0.01
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (44 bp):
TTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATCTGTGAC
Found at i:18624191 original size:23 final size:22
Alignment explanation
Indices: 18624140--18624191 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
18624130 CCTCGTCTTT
*
18624140 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
18624162 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
18624185 TTCTTTT
1 TTCTTTT
18624192 TCAATTTCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:18624200 original size:12 final size:12
Alignment explanation
Indices: 18624149--18624203 Score: 51
Period size: 12 Copynumber: 4.6 Consensus size: 12
18624139 TTTCTTTTGT
18624149 TTCTTTTTCTAAC
1 TTCTTTTTC-AAC
* *
18624162 -TCATTTTC-TC
1 TTCTTTTTCAAC
18624172 TTCTTTCTTCAAC
1 TTCTTT-TTCAAC
*
18624185 TTCTTTTTCAAT
1 TTCTTTTTCAAC
18624197 TTCTTTT
1 TTCTTTT
18624204 CTGTTTCACA
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
10 1 0.03
11 4 0.12
12 22 0.65
13 7 0.21
ACGTcount: A:0.13, C:0.24, G:0.00, T:0.64
Consensus pattern (12 bp):
TTCTTTTTCAAC
Found at i:18624210 original size:17 final size:18
Alignment explanation
Indices: 18624185--18624222 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
18624175 TTTCTTCAAC
* *
18624185 TTCTTTTTCA-ATTTCTT
1 TTCTGTTTCACATTCCTT
18624202 TTCTGTTTCACATTCCTT
1 TTCTGTTTCACATTCCTT
18624220 TTC
1 TTC
18624223 ACTCTCAATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.11, C:0.24, G:0.03, T:0.63
Consensus pattern (18 bp):
TTCTGTTTCACATTCCTT
Found at i:18625489 original size:26 final size:26
Alignment explanation
Indices: 18625460--18625509 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
18625450 GCTGAATCTT
18625460 TTTTTAAATTTTTATTGA-ATTTTGTA
1 TTTTTAAATTTTT-TTGACATTTTGTA
**
18625486 TTTTTTGATTTTTTTGACATTTTG
1 TTTTTAAATTTTTTTGACATTTTG
18625510 ACTGATTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 4 0.19
26 17 0.81
ACGTcount: A:0.20, C:0.02, G:0.10, T:0.68
Consensus pattern (26 bp):
TTTTTAAATTTTTTTGACATTTTGTA
Found at i:18631590 original size:25 final size:26
Alignment explanation
Indices: 18631555--18631611 Score: 80
Period size: 25 Copynumber: 2.2 Consensus size: 26
18631545 TTTATTTTAT
*
18631555 TTTGGGTTTTATTTTTGTTTTATTGG
1 TTTGGGTTTTATTTTTGGTTTATTGG
*
18631581 TTTGGG-TTTATTTTTGGTTTGTTGG
1 TTTGGGTTTTATTTTTGGTTTATTGG
*
18631606 TCTGGG
1 TTTGGG
18631612 CCAAAATTGG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
25 22 0.79
26 6 0.21
ACGTcount: A:0.05, C:0.02, G:0.30, T:0.63
Consensus pattern (26 bp):
TTTGGGTTTTATTTTTGGTTTATTGG
Found at i:18633247 original size:20 final size:20
Alignment explanation
Indices: 18633224--18633299 Score: 64
Period size: 20 Copynumber: 3.6 Consensus size: 20
18633214 ATAATAAGAT
18633224 AATAATAATGAGAATAAA-AA
1 AATAATAATGA-AATAAATAA
* *
18633244 AATAAAAATGAAATAAATAC
1 AATAATAATGAAATAAATAA
* *
18633264 AATAATAAAGGAATAATAAATGA
1 AATAAT-AATG-A-AATAAATAA
*
18633287 AATAATAAAGAAA
1 AATAATAATGAAA
18633300 ATTCTAGTGA
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
19 6 0.13
20 18 0.40
21 4 0.09
22 4 0.09
23 13 0.29
ACGTcount: A:0.70, C:0.01, G:0.09, T:0.20
Consensus pattern (20 bp):
AATAATAATGAAATAAATAA
Found at i:18633248 original size:23 final size:22
Alignment explanation
Indices: 18633216--18633295 Score: 60
Period size: 23 Copynumber: 3.6 Consensus size: 22
18633206 CGAAATATAT
*
18633216 AATAAGATAATAATAATGAGAATA
1 AATAAAATAATAA-AATGA-AATA
18633240 AA-AAAAT-A-AAAATGAAATA
1 AATAAAATAATAAAATGAAATA
* *
18633259 AATACAATAAT-AAAGGAATAATA
1 AATAAAATAATAAAATG-A-AATA
*
18633282 AATGAAATAATAAA
1 AATAAAATAATAAA
18633296 GAAAATTCTA
Statistics
Matches: 45, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
19 6 0.13
20 9 0.20
21 7 0.16
22 2 0.04
23 17 0.38
24 4 0.09
ACGTcount: A:0.69, C:0.01, G:0.09, T:0.21
Consensus pattern (22 bp):
AATAAAATAATAAAATGAAATA
Found at i:18633258 original size:28 final size:30
Alignment explanation
Indices: 18633227--18633293 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 30
18633217 ATAAGATAAT
*
18633227 AATAATGAGAATAA-AAA-AATAA-AAATGA
1 AATAAT-ACAATAATAAAGAATAATAAATGA
18633255 AATAAATACAATAATAAAGGAATAATAAATGA
1 AAT-AATACAATAATAAA-GAATAATAAATGA
18633287 AATAATA
1 AATAATA
18633294 AAGAAAATTC
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
28 9 0.27
29 6 0.18
31 9 0.27
32 9 0.27
ACGTcount: A:0.69, C:0.01, G:0.09, T:0.21
Consensus pattern (30 bp):
AATAATACAATAATAAAGAATAATAAATGA
Found at i:18633301 original size:12 final size:11
Alignment explanation
Indices: 18633264--18633299 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
18633254 AAATAAATAC
*
18633264 AATAATAAAGG
1 AATAATAAAGA
18633275 AATAATAAATGA
1 AATAATAAA-GA
18633287 AATAATAAAGA
1 AATAATAAAGA
18633298 AA
1 AA
18633300 ATTCTAGTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 13 0.57
12 10 0.43
ACGTcount: A:0.69, C:0.00, G:0.11, T:0.19
Consensus pattern (11 bp):
AATAATAAAGA
Found at i:18633389 original size:3 final size:3
Alignment explanation
Indices: 18633381--18633562 Score: 132
Period size: 3 Copynumber: 62.7 Consensus size: 3
18633371 ATGGTTTAAA
* * * *
18633381 AAT AAT AAT GAT AAT AAT AAT AAT AGT AAT AAT AAT CAT ACT -AT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * ** *
18633428 GAT AGT AAT AAT GGT AA- AAT AAT AAT AAT GAT AAT AAT AAT AA- AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * *
18633474 -AT AA- AA- AAT -TT AGCA- AAT GAT AAT AAT AAT ATT GAT AAT AAAT
1 AAT AAT AAT AAT AAT A--AT AAT AAT AAT AAT AAT AAT AAT AAT -AAT
*
18633517 AAT AAT AGT AA- AAT AAT AAT AAT AAT AAT AAT AAT AACT AA- AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT
18633561 AA
1 AA
18633563 CTAAAAAGGA
Statistics
Matches: 138, Mismatches: 28, Indels: 26
0.72 0.15 0.14
Matches are distributed among these distances:
2 17 0.12
3 114 0.83
4 7 0.05
ACGTcount: A:0.60, C:0.02, G:0.06, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:18640469 original size:21 final size:21
Alignment explanation
Indices: 18640445--18640485 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
18640435 ACGTGACAAG
*
18640445 TTAACTGGCCACGTCAGCTAA
1 TTAACTAGCCACGTCAGCTAA
*
18640466 TTAACTAGCCATGTCAGCTA
1 TTAACTAGCCACGTCAGCTA
18640486 TTCCGTTAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.27
Consensus pattern (21 bp):
TTAACTAGCCACGTCAGCTAA
Found at i:18641169 original size:12 final size:12
Alignment explanation
Indices: 18641152--18641184 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
18641142 CCGACCTTCC
18641152 ATATTAATTTTT
1 ATATTAATTTTT
18641164 ATATT-ATTTTT
1 ATATTAATTTTT
18641175 ATA-TAATTTT
1 ATATTAATTTT
18641185 AAAATATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 14 0.70
12 5 0.25
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:18641447 original size:22 final size:22
Alignment explanation
Indices: 18641399--18641447 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
18641389 ATATCCAAAC
*
18641399 AATAACAACAAAATAGTAGCAA
1 AATAACAACAAAATAGTAACAA
* * * *
18641421 CATAATAATAAAATGGTAACAA
1 AATAACAACAAAATAGTAACAA
18641443 AATAA
1 AATAA
18641448 GGAGAAAACA
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.63, C:0.10, G:0.08, T:0.18
Consensus pattern (22 bp):
AATAACAACAAAATAGTAACAA
Found at i:18648101 original size:29 final size:28
Alignment explanation
Indices: 18648064--18648118 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
18648054 AGTGGTATAC
18648064 TTTTTAAATAATTTGAATAATTTTTAAT
1 TTTTTAAATAATTTGAATAATTTTTAAT
* **
18648092 TTTTTAAAATATTTTTTATAATTTTTA
1 TTTTT-AAATAATTTGAATAATTTTTA
18648119 TTGAAATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 5 0.22
29 18 0.78
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (28 bp):
TTTTTAAATAATTTGAATAATTTTTAAT
Found at i:18654991 original size:4 final size:4
Alignment explanation
Indices: 18654982--18655007 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
18654972 CCTACTTTCT
18654982 CATA CATA CATA CATA CATA CATA CA
1 CATA CATA CATA CATA CATA CATA CA
18655008 CTTCAGCTAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.50, C:0.27, G:0.00, T:0.23
Consensus pattern (4 bp):
CATA
Found at i:18659820 original size:3 final size:3
Alignment explanation
Indices: 18659812--18659859 Score: 71
Period size: 3 Copynumber: 15.7 Consensus size: 3
18659802 ATTTAGGCCT
18659812 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT- TTCA TCTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A T-TA TTA TTA TTA
18659858 TT
1 TT
18659860 TATTTATTCA
Statistics
Matches: 42, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.05
3 36 0.86
4 3 0.07
5 1 0.02
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:18659852 original size:25 final size:25
Alignment explanation
Indices: 18659811--18659875 Score: 84
Period size: 25 Copynumber: 2.7 Consensus size: 25
18659801 TATTTAGGCC
18659811 TTTA-TTATT-AT-TATTATTATTA
1 TTTATTTATTCATCTATTATTATTA
*
18659833 -TTATTATTTTCATCTATTATTATTA
1 TTTATT-TATTCATCTATTATTATTA
18659858 TTTATTTATTCATCTATT
1 TTTATTTATTCATCTATT
18659876 TGTTTATCAC
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
21 3 0.08
22 1 0.03
23 3 0.08
24 2 0.06
25 22 0.61
26 5 0.14
ACGTcount: A:0.28, C:0.06, G:0.00, T:0.66
Consensus pattern (25 bp):
TTTATTTATTCATCTATTATTATTA
Found at i:18659992 original size:3 final size:3
Alignment explanation
Indices: 18659948--18659981 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
18659938 TTGTTCCTAC
*
18659948 TAT TAT TAT GAAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT
18659982 CACATTATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 26 0.93
4 2 0.07
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:18660204 original size:11 final size:11
Alignment explanation
Indices: 18660188--18660212 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
18660178 TATGACTATT
18660188 ATAGTACATTA
1 ATAGTACATTA
18660199 ATAGTACATTA
1 ATAGTACATTA
18660210 ATA
1 ATA
18660213 CTATCATAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.48, C:0.08, G:0.08, T:0.36
Consensus pattern (11 bp):
ATAGTACATTA
Found at i:18660686 original size:11 final size:11
Alignment explanation
Indices: 18660670--18660700 Score: 55
Period size: 10 Copynumber: 2.9 Consensus size: 11
18660660 AGGGATCGTA
18660670 TTTTAATTTTT
1 TTTTAATTTTT
18660681 TTTTAA-TTTT
1 TTTTAATTTTT
18660691 TTTTAATTTT
1 TTTTAATTTT
18660701 CGACATTAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.53
11 9 0.47
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (11 bp):
TTTTAATTTTT
Found at i:18662343 original size:16 final size:16
Alignment explanation
Indices: 18662322--18662389 Score: 118
Period size: 16 Copynumber: 4.2 Consensus size: 16
18662312 TTTGGTTCGC
18662322 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
*
18662338 TGTATTGGATTAGAGA
1 TGTATTGGATTAGAGG
18662354 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
*
18662370 TGTACTGGATTAGAGG
1 TGTATTGGATTAGAGG
18662386 TGTA
1 TGTA
18662390 ATAGCAAATC
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 49 1.00
ACGTcount: A:0.26, C:0.01, G:0.35, T:0.37
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:18662646 original size:18 final size:17
Alignment explanation
Indices: 18662625--18662659 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
18662615 TTATTATTAA
*
18662625 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
18662643 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
18662660 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:18662766 original size:18 final size:17
Alignment explanation
Indices: 18662745--18662779 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
18662735 TTATTATTAA
*
18662745 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
18662763 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
18662780 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:18662803 original size:37 final size:37
Alignment explanation
Indices: 18662762--18662936 Score: 95
Period size: 38 Copynumber: 4.5 Consensus size: 37
18662752 TTAATTAAAA
18662762 TATATAATTTAATAAAATTCTTAATAATTAATATTCT
1 TATATAATTTAATAAAATTCTTAATAATTAATATTCT
* * * * * *
18662799 TATATTAATTTACTGAAA-TCATAAT-ATATGATACTGT
1 TATA-TAATTTAATAAAATTCTTAATAAT-TAATATTCT
* * * * ***
18662836 AAATATAAATTAACATAATTATTATTAAATATATTTTAAT-TAAAA
1 -TATAT-AATTTA-ATAA-AATTCTT-AATA-A--TTAATAT-TCT
18662881 TATATAATTTAATAAAATTCTTAATAATTAATATTCT
1 TATATAATTTAATAAAATTCTTAATAATTAATATTCT
*
18662918 TATATTAATTTACTAAAAT
1 TATA-TAATTTAATAAAAT
18662937 CATAATATAT
Statistics
Matches: 97, Mismatches: 26, Indels: 29
0.64 0.17 0.19
Matches are distributed among these distances:
36 2 0.02
37 26 0.27
38 33 0.34
39 3 0.03
40 5 0.05
41 7 0.07
42 7 0.07
43 5 0.05
44 5 0.05
45 3 0.03
46 1 0.01
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.46
Consensus pattern (37 bp):
TATATAATTTAATAAAATTCTTAATAATTAATATTCT
Found at i:18662821 original size:120 final size:120
Alignment explanation
Indices: 18662608--18663109 Score: 979
Period size: 120 Copynumber: 4.2 Consensus size: 120
18662598 ATCATATTTA
18662608 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
18662673 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
18662728 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
18662793 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGT-AAATATAAATT
66 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
18662847 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
*
18662912 TATTCTTATATTAATTTACTAAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
18662967 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
18663032 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
*
18663087 AACATAATAATTATTAAATATAT
1 AACATAATTATTATTAAATATAT
18663110 AACTTGAAAA
Statistics
Matches: 378, Mismatches: 3, Indels: 2
0.99 0.01 0.01
Matches are distributed among these distances:
119 118 0.31
120 260 0.69
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (120 bp):
AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
Found at i:18662885 original size:18 final size:17
Alignment explanation
Indices: 18662864--18662898 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
18662854 TTATTATTAA
*
18662864 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
18662882 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
18662899 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:18663005 original size:18 final size:17
Alignment explanation
Indices: 18662984--18663018 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
18662974 TTATTATTAA
*
18662984 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
18663002 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
18663019 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:18663027 original size:239 final size:240
Alignment explanation
Indices: 18662608--18663109 Score: 979
Period size: 239 Copynumber: 2.1 Consensus size: 240
18662598 ATCATATTTA
18662608 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
*
18662673 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATTAACATAATTA
66 TATTCTTATATTAATTTACTAAAATCATAATATATGATACTGTAAAATATAAATTAACATAATTA
18662738 TTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATA
131 TTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATA
18662803 TTAATTTACTGAAATCATAATATATGATACTGT-AAATATAAATT
196 TTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
18662847 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
18662912 TATTCTTATATTAATTTACTAAAATCATAATATATGATACTGTAAAATATAAATTAACATAATTA
66 TATTCTTATATTAATTTACTAAAATCATAATATATGATACTGTAAAATATAAATTAACATAATTA
18662977 TTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATA
131 TTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATA
18663042 TTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
196 TTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
*
18663087 AACATAATAATTATTAAATATAT
1 AACATAATTATTATTAAATATAT
18663110 AACTTGAAAA
Statistics
Matches: 260, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
239 227 0.87
240 33 0.13
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (240 bp):
AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
TATTCTTATATTAATTTACTAAAATCATAATATATGATACTGTAAAATATAAATTAACATAATTA
TTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATA
TTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
Found at i:18666213 original size:21 final size:21
Alignment explanation
Indices: 18666170--18666225 Score: 85
Period size: 21 Copynumber: 2.6 Consensus size: 21
18666160 AAGCAGATGG
*
18666170 AGCCACTGCAAATAAATTATAT
1 AGCCACTGCAAA-CAATTATAT
*
18666192 AGCCACTGCAAACAATTGTAT
1 AGCCACTGCAAACAATTATAT
18666213 AGCCACTGCAAAC
1 AGCCACTGCAAAC
18666226 GGGGGAAACT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
21 20 0.62
22 12 0.38
ACGTcount: A:0.41, C:0.25, G:0.12, T:0.21
Consensus pattern (21 bp):
AGCCACTGCAAACAATTATAT
Found at i:18667337 original size:15 final size:15
Alignment explanation
Indices: 18667317--18667432 Score: 62
Period size: 15 Copynumber: 7.5 Consensus size: 15
18667307 AACATGGTAC
18667317 AGAAACAGAAAATAG
1 AGAAACAGAAAATAG
*
18667332 AGAAACA-AAAA-ACC
1 AGAAACAGAAAATA-G
**
18667346 A-CTACAGAAAATAG
1 AGAAACAGAAAATAG
* *
18667360 AGGAACA-AAACATGGTAC
1 AGAAACAGAAA-A---TAG
18667378 AGAAACAGAAAATAG
1 AGAAACAGAAAATAG
*
18667393 AGAAACA-AAACATGGTAC
1 AGAAACAGAAA-A---TAG
18667411 AGAAACAGAAAATAG
1 AGAAACAGAAAATAG
18667426 AGAAACA
1 AGAAACA
18667433 TAAAGCAGAC
Statistics
Matches: 76, Mismatches: 11, Indels: 28
0.66 0.10 0.24
Matches are distributed among these distances:
13 4 0.05
14 16 0.21
15 31 0.41
18 19 0.25
19 6 0.08
ACGTcount: A:0.62, C:0.13, G:0.17, T:0.08
Consensus pattern (15 bp):
AGAAACAGAAAATAG
Found at i:18667339 original size:33 final size:33
Alignment explanation
Indices: 18667297--18667432 Score: 185
Period size: 33 Copynumber: 4.3 Consensus size: 33
18667287 AAAAATGGCA
*
18667297 AGAGGAACAAAACATGGTACAGAAACAGAAAAT
1 AGAGAAACAAAACATGGTACAGAAACAGAAAAT
**
18667330 AGAGAAACAAAA-A----ACCA-CTACAGAAAAT
1 AGAGAAACAAAACATGGTA-CAGAAACAGAAAAT
*
18667358 AGAGGAACAAAACATGGTACAGAAACAGAAAAT
1 AGAGAAACAAAACATGGTACAGAAACAGAAAAT
18667391 AGAGAAACAAAACATGGTACAGAAACAGAAAAT
1 AGAGAAACAAAACATGGTACAGAAACAGAAAAT
18667424 AGAGAAACA
1 AGAGAAACA
18667433 TAAAGCAGAC
Statistics
Matches: 89, Mismatches: 7, Indels: 14
0.81 0.06 0.13
Matches are distributed among these distances:
28 21 0.24
29 3 0.03
32 3 0.03
33 62 0.70
ACGTcount: A:0.60, C:0.13, G:0.18, T:0.08
Consensus pattern (33 bp):
AGAGAAACAAAACATGGTACAGAAACAGAAAAT
Found at i:18667416 original size:18 final size:18
Alignment explanation
Indices: 18667363--18667417 Score: 64
Period size: 18 Copynumber: 3.2 Consensus size: 18
18667353 AAAATAGAGG
18667363 AACAAAACATGGTACAGA
1 AACAAAACATGGTACAGA
*
18667381 AACAGAAA-A---TAGAGA
1 AACA-AAACATGGTACAGA
18667396 AACAAAACATGGTACAGA
1 AACAAAACATGGTACAGA
18667414 AACA
1 AACA
18667418 GAAAATAGAG
Statistics
Matches: 30, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
14 3 0.10
15 10 0.33
18 14 0.47
19 3 0.10
ACGTcount: A:0.60, C:0.15, G:0.16, T:0.09
Consensus pattern (18 bp):
AACAAAACATGGTACAGA
Found at i:18668614 original size:26 final size:26
Alignment explanation
Indices: 18668556--18668608 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
18668546 TAAATAATGC
**
18668556 TTAATTAAAATTTAAGTTTTTATACA
1 TTAATTAAAATTTAAGTTTAAATACA
18668582 TTAATTAAAATTTAA-TTTAAATTACA
1 TTAATTAAAATTTAAGTTTAAA-TACA
18668608 T
1 T
18668609 ATATTACAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 4 0.17
26 20 0.83
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (26 bp):
TTAATTAAAATTTAAGTTTAAATACA
Found at i:18669102 original size:15 final size:15
Alignment explanation
Indices: 18669082--18669147 Score: 55
Period size: 14 Copynumber: 4.3 Consensus size: 15
18669072 ACTACAAAAC
18669082 ATTTATTATTAATAT
1 ATTTATTATTAATAT
*
18669097 ATTTATAATTGTAATAAAT
1 ATTTATTA-T-TAAT--AT
*
18669116 ATTTATTATTAAAAT
1 ATTTATTATTAATAT
*
18669131 A-TTAATATTAA-AT
1 ATTTATTATTAATAT
18669144 ATTT
1 ATTT
18669148 TCAACAATAT
Statistics
Matches: 42, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
13 3 0.07
14 11 0.26
15 10 0.24
16 1 0.02
17 7 0.17
18 1 0.02
19 9 0.21
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (15 bp):
ATTTATTATTAATAT
Found at i:18675352 original size:17 final size:17
Alignment explanation
Indices: 18675330--18675363 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
18675320 ATCCACTAAT
*
18675330 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
18675347 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
18675364 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:18679989 original size:17 final size:17
Alignment explanation
Indices: 18679967--18680000 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
18679957 ATCCACTAAT
*
18679967 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
18679984 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
18680001 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:18682298 original size:13 final size:13
Alignment explanation
Indices: 18682277--18682331 Score: 56
Period size: 13 Copynumber: 4.2 Consensus size: 13
18682267 AAATTTTTCC
18682277 AAAGCACTTCTCA
1 AAAGCACTTCTCA
*
18682290 AAAGTACTTCTCA
1 AAAGCACTTCTCA
* * *
18682303 AAAACACTTTTCC
1 AAAGCACTTCTCA
* *
18682316 ACAGCACTTTTCA
1 AAAGCACTTCTCA
18682329 AAA
1 AAA
18682332 ACAATAAAGA
Statistics
Matches: 33, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
13 33 1.00
ACGTcount: A:0.40, C:0.27, G:0.05, T:0.27
Consensus pattern (13 bp):
AAAGCACTTCTCA
Found at i:18682310 original size:26 final size:26
Alignment explanation
Indices: 18682281--18682334 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 26
18682271 TTTTCCAAAG
*
18682281 CACTTCTCAAAAGTACTTCTCAAAAA
1 CACTTCTCAAAAGCACTTCTCAAAAA
* * * *
18682307 CACTTTTCCACAGCACTTTTCAAAAA
1 CACTTCTCAAAAGCACTTCTCAAAAA
18682333 CA
1 CA
18682335 ATAAAGAACT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.39, C:0.30, G:0.04, T:0.28
Consensus pattern (26 bp):
CACTTCTCAAAAGCACTTCTCAAAAA
Found at i:18684637 original size:26 final size:24
Alignment explanation
Indices: 18684608--18684663 Score: 58
Period size: 26 Copynumber: 2.2 Consensus size: 24
18684598 TGTTTCTTGT
* *
18684608 TTTAATATTTTTTTAAATGTATTTGA
1 TTTAATATATTTTAAAAT-T-TTTGA
* *
18684634 TTTATTATATTTTAAAATTTTTTA
1 TTTAATATATTTTAAAATTTTTGA
18684658 TTTAAT
1 TTTAAT
18684664 GAAATAAGCT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
24 9 0.36
25 1 0.04
26 15 0.60
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (24 bp):
TTTAATATATTTTAAAATTTTTGA
Found at i:18685437 original size:29 final size:29
Alignment explanation
Indices: 18685403--18685508 Score: 90
Period size: 29 Copynumber: 3.7 Consensus size: 29
18685393 ATATTACTGC
* *
18685403 TATTATTATGTTTCTATTTATATTTATTT
1 TATTATTATATTTCTATTTATATTTATAT
* * * * *
18685432 TGTTATTCTAATACTA-TTATTATTTATCT
1 TATTATTATATTTCTATTTA-TATTTATAT
* * *
18685461 AATTATTAT-TTATCTATTTATATTTCTAC
1 TATTATTATATT-TCTATTTATATTTATAT
18685490 TATTATTATATTTCTATTT
1 TATTATTATATTTCTATTT
18685509 GTTATATTTT
Statistics
Matches: 58, Mismatches: 15, Indels: 8
0.72 0.19 0.10
Matches are distributed among these distances:
28 4 0.07
29 49 0.84
30 5 0.09
ACGTcount: A:0.27, C:0.08, G:0.02, T:0.63
Consensus pattern (29 bp):
TATTATTATATTTCTATTTATATTTATAT
Found at i:18685467 original size:15 final size:15
Alignment explanation
Indices: 18685447--18685498 Score: 63
Period size: 15 Copynumber: 3.5 Consensus size: 15
18685437 TTCTAATACT
18685447 ATTATTATTTATCTA
1 ATTATTATTTATCTA
18685462 ATTATTATTTATCTA
1 ATTATTATTTATCTA
* *
18685477 TTTA-TATTTCTACT-
1 ATTATTATTTAT-CTA
18685491 ATTATTAT
1 ATTATTAT
18685499 ATTTCTATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
14 9 0.28
15 23 0.72
ACGTcount: A:0.31, C:0.08, G:0.00, T:0.62
Consensus pattern (15 bp):
ATTATTATTTATCTA
Found at i:18685515 original size:15 final size:15
Alignment explanation
Indices: 18685478--18685523 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 15
18685468 ATTTATCTAT
18685478 TTATATTTCTACTATTA
1 TTATATTTCTA-T-TTA
*
18685495 TTATATTTCTATTTG
1 TTATATTTCTATTTA
*
18685510 TTATATTTTTATTT
1 TTATATTTCTATTT
18685524 CTATTTATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
15 15 0.56
16 1 0.04
17 11 0.41
ACGTcount: A:0.24, C:0.07, G:0.02, T:0.67
Consensus pattern (15 bp):
TTATATTTCTATTTA
Found at i:18685558 original size:87 final size:86
Alignment explanation
Indices: 18685392--18685558 Score: 191
Period size: 87 Copynumber: 1.9 Consensus size: 86
18685382 ACTATTTTAA
* * *
18685392 TATATTACTGCTATTATTATGTTTCTATTTATATTTATTTTGTTATTCTAATACTATTATTATTT
1 TATATTACTACTATTATTATATTTCTATTTATATTTATTTTGTTATTCTAATACTAATATTATTT
*
18685457 ATCTAATTATTATTTATCTATT
66 ATC-AATTAGTATTTATCTATT
*
18685479 TATATTTCTACTATTATTATATTTCTATTTGTTATATTT-TTATT-TCTATT-TATATACTAATA
1 TATATTACTACTATTATTATATTTCTA--T-TTATATTTATT-TTGT-TATTCTA-ATACTAATA
18685541 TTATTT-TC-ATTAGTATTT
60 TTATTTATCAATTAGTATTT
18685559 TTCTTATATA
Statistics
Matches: 69, Mismatches: 5, Indels: 12
0.80 0.06 0.14
Matches are distributed among these distances:
87 33 0.48
89 8 0.12
90 28 0.41
ACGTcount: A:0.28, C:0.08, G:0.03, T:0.62
Consensus pattern (86 bp):
TATATTACTACTATTATTATATTTCTATTTATATTTATTTTGTTATTCTAATACTAATATTATTT
ATCAATTAGTATTTATCTATT
Found at i:18685696 original size:25 final size:25
Alignment explanation
Indices: 18685668--18685762 Score: 66
Period size: 25 Copynumber: 3.7 Consensus size: 25
18685658 CTCATTTCAA
18685668 ATTTTTATACATTATTTATTTTAAT
1 ATTTTTATACATTATTTATTTTAAT
* * * *
18685693 ATTTTCATATATTATGTATTTCAAACT
1 ATTTTTATACATTATTTATTT-TAA-T
* * *
18685720 TTTTTTCAGACATTATATATTTTGAAT
1 ATTTTT-ATACATTATTTATTTT-AAT
* *
18685747 -TATTTATATATTATTT
1 ATTTTTATACATTATTT
18685763 TTAAAGAGTT
Statistics
Matches: 52, Mismatches: 14, Indels: 8
0.70 0.19 0.11
Matches are distributed among these distances:
25 26 0.50
26 6 0.12
27 6 0.12
28 14 0.27
ACGTcount: A:0.32, C:0.06, G:0.03, T:0.59
Consensus pattern (25 bp):
ATTTTTATACATTATTTATTTTAAT
Found at i:18685763 original size:21 final size:22
Alignment explanation
Indices: 18685733--18685786 Score: 58
Period size: 23 Copynumber: 2.5 Consensus size: 22
18685723 TTTCAGACAT
**
18685733 TATA-TATTTTGAATTA-TTTA
1 TATATTATTTTGAAAGAGTTTA
*
18685753 TATATTATTTTTAAAGAGTTTTA
1 TATATTATTTTGAAAGAG-TTTA
18685776 TATATTATTTT
1 TATATTATTTT
18685787 ATCTTGAATG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 4 0.14
21 9 0.32
23 15 0.54
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (22 bp):
TATATTATTTTGAAAGAGTTTA
Found at i:18697787 original size:15 final size:15
Alignment explanation
Indices: 18697767--18697795 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
18697757 TTACCAGACA
18697767 TGGATAATGAAAAAT
1 TGGATAATGAAAAAT
18697782 TGGATAATGAAAAA
1 TGGATAATGAAAAA
18697796 CAAGTCACTC
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:0.55, C:0.00, G:0.21, T:0.24
Consensus pattern (15 bp):
TGGATAATGAAAAAT
Found at i:18700567 original size:39 final size:39
Alignment explanation
Indices: 18700513--18700590 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 39
18700503 AGGTCATGAT
18700513 TGTCATGGTGTCATCTCAAGTCTTAAAGGCTCAGTATAC
1 TGTCATGGTGTCATCTCAAGTCTTAAAGGCTCAGTATAC
*
18700552 TGTCATGGTGTCATCTCAAGTCTTGAAGGCTCAGTATAC
1 TGTCATGGTGTCATCTCAAGTCTTAAAGGCTCAGTATAC
18700591 CCTCTGTGCA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.24, C:0.21, G:0.22, T:0.33
Consensus pattern (39 bp):
TGTCATGGTGTCATCTCAAGTCTTAAAGGCTCAGTATAC
Found at i:18700895 original size:50 final size:50
Alignment explanation
Indices: 18700832--18700927 Score: 138
Period size: 50 Copynumber: 1.9 Consensus size: 50
18700822 CAGCAAATAC
* * *
18700832 ATGGTCCAAAGAGCGAAACTTGGTTTCAAGTTACGGAAATAAGTCTCATT
1 ATGGTCCAAAGAGCAAAACTTGGTTTCAAGTTACAGAAAGAAGTCTCATT
* * *
18700882 ATGGTCCATAGAGCAAAATTTTGTTTCAAGTTACAGAAAGAAGTCT
1 ATGGTCCAAAGAGCAAAACTTGGTTTCAAGTTACAGAAAGAAGTCT
18700928 AAATTAAACA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
50 40 1.00
ACGTcount: A:0.35, C:0.15, G:0.21, T:0.29
Consensus pattern (50 bp):
ATGGTCCAAAGAGCAAAACTTGGTTTCAAGTTACAGAAAGAAGTCTCATT
Found at i:18702212 original size:17 final size:17
Alignment explanation
Indices: 18702190--18702224 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
18702180 CAAAGTAAAA
18702190 AACAGATATGAAGATAT
1 AACAGATATGAAGATAT
18702207 AACAGATATGAAGATAT
1 AACAGATATGAAGATAT
18702224 A
1 A
18702225 TGCACTTGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (17 bp):
AACAGATATGAAGATAT
Found at i:18706220 original size:2 final size:2
Alignment explanation
Indices: 18706213--18706243 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
18706203 AATAATCGAC
18706213 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
18706244 ACCTACCCTA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:18707362 original size:50 final size:50
Alignment explanation
Indices: 18707303--18707417 Score: 151
Period size: 50 Copynumber: 2.3 Consensus size: 50
18707293 CTACTTATTT
* * *
18707303 GGCCGAATATGCAAGAT-CAAGAATAATATCACATATGTACATATCTATAA
1 GGCCGAATATGCAAGATCCAA-AATAACATCACATAAGTACATACCTATAA
* * **
18707353 GGCCGAATATGCAAGTTCCAATATAACATCACATAAGTACATACCTATGT
1 GGCCGAATATGCAAGATCCAAAATAACATCACATAAGTACATACCTATAA
18707403 GGCCGAATATGCAAG
1 GGCCGAATATGCAAG
18707418 GTCATTTAAC
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
50 54 0.95
51 3 0.05
ACGTcount: A:0.40, C:0.19, G:0.17, T:0.24
Consensus pattern (50 bp):
GGCCGAATATGCAAGATCCAAAATAACATCACATAAGTACATACCTATAA
Found at i:18709086 original size:19 final size:18
Alignment explanation
Indices: 18709055--18709099 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
18709045 CAAGCTTAAT
18709055 ATTAAATTAATTAAGATTTA
1 ATTAAA-TAATTAAG-TTTA
*
18709075 GTTAAATAATTAAGTTTA
1 ATTAAATAATTAAGTTTA
18709093 ATTAAAT
1 ATTAAAT
18709100 GTTAAACTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 10 0.43
19 8 0.35
20 5 0.22
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (18 bp):
ATTAAATAATTAAGTTTA
Found at i:18715316 original size:12 final size:12
Alignment explanation
Indices: 18715296--18715325 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
18715286 TATGGTTAAT
*
18715296 TTCTTTAGCAGC
1 TTCTGTAGCAGC
18715308 TTCTGTAGCAGC
1 TTCTGTAGCAGC
18715320 TTCTGT
1 TTCTGT
18715326 TGTTTGTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.13, C:0.23, G:0.20, T:0.43
Consensus pattern (12 bp):
TTCTGTAGCAGC
Found at i:18715971 original size:91 final size:91
Alignment explanation
Indices: 18715839--18716046 Score: 274
Period size: 91 Copynumber: 2.3 Consensus size: 91
18715829 TTGATTTTAG
* *
18715839 TAAATTCATATAAGAACATTTTATTATTAACAATTTCATGAAATTATATATCACTATTAAATTAT
1 TAAATTCATATAAGAA-AATTTATTATCAACAATTTCATGAAATTATATATCACTATTAAATTAT
* *
18715904 ATTTAAT-ATTAATTATTTTAAATTGTA
65 ATGTAATAATT-ATTATTTTAAATTATA
* * * * *
18715931 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTTTATATTATTATTAAATTATA
1 TAAATTCATATAAGAAAATTTATTATCAACAATTTCATGAAATTATATATCACTATTAAATTATA
18715996 TGTAATAATTATTATTTTAAATTATA
66 TGTAATAATTATTATTTTAAATTATA
* * * *
18716022 CAAATTCATAAAATATAATTTATTA
1 TAAATTCATATAAGAAAATTTATTA
18716047 GTTATAATTA
Statistics
Matches: 102, Mismatches: 13, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
91 83 0.81
92 19 0.19
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATCAACAATTTCATGAAATTATATATCACTATTAAATTATA
TGTAATAATTATTATTTTAAATTATA
Found at i:18716095 original size:16 final size:17
Alignment explanation
Indices: 18716076--18716107 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
18716066 TTATTAAATC
18716076 ATATATTTAA-ATTAAA
1 ATATATTTAATATTAAA
18716092 ATATATTTAATATTAA
1 ATATATTTAATATTAA
18716108 TTATTTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATATATTTAATATTAAA
Found at i:18716171 original size:66 final size:63
Alignment explanation
Indices: 18716100--18716312 Score: 203
Period size: 59 Copynumber: 3.4 Consensus size: 63
18716090 AAATATATTT
18716100 AATATTAATTATTTAA-AATTTTATTTTATAGTATCATATATTATGATTTGAGTAAATTCATATA
1 AATATTAATTA-TTAAGAATTTTA--TTA-AGTATCATATATTATGATTTGAGTAAATTCATATA
18716164 AG
62 AG
* * * * * * *
18716166 AATATTAATTATTAAGAATTTTATTAAAT-TC-TATATTTTAATTAT-ATTATATTTA-ATAAT
1 AATATTAATTATTAAGAATTTTATTAAGTATCATATATTATGATT-TGAGTAAATTCATATAAG
* * *
18716226 AATTATGTTATT-TT-A-TATTTTA--CAGTATCATATATTATGATTTGAGTAAATTCATATAAG
1 AA-TAT-TAATTATTAAGAATTTTATTAAGTATCATATATTATGATTTGAGTAAATTCATATAAG
18716286 AATATTAATTATTAAGAATTTTATTAA
1 AATATTAATTATTAAGAATTTTATTAA
18716313 ATTATATATT
Statistics
Matches: 114, Mismatches: 20, Indels: 29
0.70 0.12 0.18
Matches are distributed among these distances:
57 2 0.02
58 7 0.06
59 28 0.25
60 14 0.12
61 28 0.25
62 7 0.06
63 3 0.03
64 3 0.03
65 4 0.04
66 18 0.16
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (63 bp):
AATATTAATTATTAAGAATTTTATTAAGTATCATATATTATGATTTGAGTAAATTCATATAAG
Found at i:18716186 original size:120 final size:120
Alignment explanation
Indices: 18716062--18716354 Score: 475
Period size: 120 Copynumber: 2.4 Consensus size: 120
18716052 AATTATTTTA
* *
18716062 AATTTTATTAAATCATATATTTAAATTAAAATATATTTAATATTAATTAT-TTAAAATTT-TATT
1 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATGTT--AATTTATATT
*
18716125 TTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
64 TTACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
* * *
18716182 AATTTTATTAAATTC-TATATTTTAATTATATTATATTTAATAATAATTATGTTATTTTATATTT
1 AATTTTATTAAA-TCATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTT
18716246 TACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
65 TACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
*
18716302 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTT
1 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATGTT
18716355 TAAATATGAT
Statistics
Matches: 160, Mismatches: 9, Indels: 8
0.90 0.05 0.05
Matches are distributed among these distances:
119 5 0.03
120 151 0.94
121 4 0.03
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (120 bp):
AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTT
ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:18716331 original size:18 final size:17
Alignment explanation
Indices: 18716303--18716337 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
18716293 ATTATTAAGA
*
18716303 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
18716320 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
18716338 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:18716456 original size:147 final size:143
Alignment explanation
Indices: 18716291--18716559 Score: 459
Period size: 147 Copynumber: 1.9 Consensus size: 143
18716281 ATAAGAATAT
* *
18716291 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAAATATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
18716356 AAATATGATTAAATTATTTATTATTGATATTAATAATCTTATTAAAATTTAAATAA-AATAATTT
66 AAATATGATTAAATTATTTATTATTGATA-T--T-AT-TTATTAAAATTTAAATAACAATAATTT
18716420 ACCAAAACAAATTTCTGC
126 ACCAAAACAAATTTCTGC
18716438 TAATTATTAAGAATTTTATTAAAATATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAAATATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
*
18716503 AAATATGATTAAATTATTTATTTTTGATATTATTTATTAAAATTTAAATAACAATAA
66 AAATATGATTAAATTATTTATTATTGATATTATTTATTAAAATTTAAATAACAATAA
18716560 CAATAATCAT
Statistics
Matches: 118, Mismatches: 3, Indels: 6
0.93 0.02 0.05
Matches are distributed among these distances:
142 18 0.15
143 7 0.06
144 1 0.01
146 1 0.01
147 91 0.77
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (143 bp):
TAATTATTAAGAATTTTATTAAAATATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
AAATATGATTAAATTATTTATTATTGATATTATTTATTAAAATTTAAATAACAATAATTTACCAA
AACAAATTTCTGC
Found at i:18716485 original size:16 final size:17
Alignment explanation
Indices: 18716450--18716484 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
18716440 ATTATTAAGA
18716450 ATTTTATTAAAATATAT
1 ATTTTATTAAAATATAT
18716467 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
18716485 TAAATAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:18716729 original size:45 final size:44
Alignment explanation
Indices: 18716640--18716734 Score: 131
Period size: 45 Copynumber: 2.1 Consensus size: 44
18716630 TTACACCTCT
*
18716640 ATTACATTCAACCAAACACAGTTTTACTATTACGCCTCTATTCC
1 ATTACATTCAACCAAACACAGTTTTACTATTACACCTCTATTCC
*
18716684 ATTACATTCAACC-AA-ACAGTTAATTTGCTATTACACCTCTATTCC
1 ATTACATTCAACCAAACACAG-T--TTTACTATTACACCTCTATTCC
18716729 ATTACA
1 ATTACA
18716735 CCTCTAATCC
Statistics
Matches: 46, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
42 4 0.09
43 3 0.07
44 13 0.28
45 26 0.57
ACGTcount: A:0.34, C:0.27, G:0.04, T:0.35
Consensus pattern (44 bp):
ATTACATTCAACCAAACACAGTTTTACTATTACACCTCTATTCC
Found at i:18716762 original size:16 final size:16
Alignment explanation
Indices: 18716715--18716764 Score: 82
Period size: 16 Copynumber: 3.1 Consensus size: 16
18716705 AATTTGCTAT
* *
18716715 TACACCTCTATTCCAT
1 TACACCTCTAATCCAA
18716731 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
18716747 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
18716763 TA
1 TA
18716765 GAGCGAACTC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.34, C:0.36, G:0.00, T:0.30
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:18729474 original size:17 final size:17
Alignment explanation
Indices: 18729439--18729529 Score: 55
Period size: 17 Copynumber: 5.3 Consensus size: 17
18729429 TAATCAAACC
*
18729439 TTGAACTTAAGAATGTT
1 TTGAACTTAAGAATATT
18729456 TTGAACTTAAAGAA-ATT
1 TTGAACTT-AAGAATATT
* *
18729473 TT-AGGCTTAAGTGAA-AAT
1 TTGA-ACTTAA--GAATATT
* *
18729491 TTGAACTTAAGCATGTT
1 TTGAACTTAAGAATATT
*
18729508 TTAAACTTAAGTAA-ATT
1 TTGAACTTAAG-AATATT
18729525 TTGAA
1 TTGAA
18729530 TTTGAGTAAA
Statistics
Matches: 56, Mismatches: 11, Indels: 14
0.69 0.14 0.17
Matches are distributed among these distances:
16 5 0.09
17 32 0.57
18 18 0.32
19 1 0.02
ACGTcount: A:0.40, C:0.07, G:0.15, T:0.38
Consensus pattern (17 bp):
TTGAACTTAAGAATATT
Found at i:18731260 original size:30 final size:30
Alignment explanation
Indices: 18731224--18731292 Score: 111
Period size: 30 Copynumber: 2.3 Consensus size: 30
18731214 TGCAGGACAC
18731224 AATAAATTGTTTTAATCTATCATGTAATTG
1 AATAAATTGTTTTAATCTATCATGTAATTG
* **
18731254 AATAAATTATTTTAATCTATTGTGTAATTG
1 AATAAATTGTTTTAATCTATCATGTAATTG
18731284 AATAAATTG
1 AATAAATTG
18731293 ACAAATATCT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.39, C:0.04, G:0.10, T:0.46
Consensus pattern (30 bp):
AATAAATTGTTTTAATCTATCATGTAATTG
Done.