Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: 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: 104050246
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4660000 characters in sequence are not A, C, G, or T
File 96 of 316
Found at i:29479697 original size:18 final size:18
Alignment explanation
Indices: 29479671--29479705 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
29479661 ATATAGTAAA
* *
29479671 GAAAGAAAGAAAGGAAAG
1 GAAACAAAGAAAAGAAAG
29479689 GAAACAAAGAAAAGAAA
1 GAAACAAAGAAAAGAAA
29479706 CAGAATGCTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.71, C:0.03, G:0.26, T:0.00
Consensus pattern (18 bp):
GAAACAAAGAAAAGAAAG
Found at i:29480611 original size:16 final size:15
Alignment explanation
Indices: 29480582--29480631 Score: 55
Period size: 15 Copynumber: 3.0 Consensus size: 15
29480572 TAATATAAAG
29480582 TGAATTGAAATATAT
1 TGAATTGAAATATAT
29480597 TGAATTGAGAATATAT
1 TGAATTGA-AATATAT
29480613 CTGATTAATTGAAATATAT
1 -TG---AATTGAAATATAT
29480632 ACTGATTGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
15 8 0.27
16 7 0.23
17 2 0.07
19 7 0.23
20 6 0.20
ACGTcount: A:0.44, C:0.02, G:0.14, T:0.40
Consensus pattern (15 bp):
TGAATTGAAATATAT
Found at i:29480624 original size:20 final size:20
Alignment explanation
Indices: 29480599--29480638 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
29480589 AAATATATTG
29480599 AATTGAGAATATAT-CTGATT
1 AATTGA-AATATATACTGATT
29480619 AATTGAAATATATACTGATT
1 AATTGAAATATATACTGATT
29480639 GAAAACTGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.42, C:0.05, G:0.12, T:0.40
Consensus pattern (20 bp):
AATTGAAATATATACTGATT
Found at i:29480867 original size:45 final size:45
Alignment explanation
Indices: 29480762--29480868 Score: 117
Period size: 45 Copynumber: 2.4 Consensus size: 45
29480752 TTATGTGTCG
* *
29480762 ATTACTGTTACTGTTACCGACTCGACAATTTGTGTGTCAAATTCT
1 ATTACTGTTACTGTTACAGACTCGACAATTTGTGTGTCAAATACT
* * * * **
29480807 ATTACCGTTATTGTTACAGATTC-AGCACTTTGTGTGTTGAATACT
1 ATTACTGTTACTGTTACAGACTCGA-CAATTTGTGTGTCAAATACT
*
29480852 ATTAATGTTACTGTTAC
1 ATTACTGTTACTGTTAC
29480869 TGCTACTGTT
Statistics
Matches: 50, Mismatches: 11, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
44 1 0.02
45 49 0.98
ACGTcount: A:0.25, C:0.17, G:0.16, T:0.42
Consensus pattern (45 bp):
ATTACTGTTACTGTTACAGACTCGACAATTTGTGTGTCAAATACT
Found at i:29481018 original size:18 final size:18
Alignment explanation
Indices: 29480995--29481052 Score: 80
Period size: 18 Copynumber: 3.2 Consensus size: 18
29480985 TAAATAAAGG
29480995 TACTAAATAACTGATTAT
1 TACTAAATAACTGATTAT
* *
29481013 TACTAAATAATTGACTAT
1 TACTAAATAACTGATTAT
* *
29481031 TACTGAATAACTGATTAA
1 TACTAAATAACTGATTAT
29481049 TACT
1 TACT
29481053 GATGACTGAC
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.43, C:0.12, G:0.07, T:0.38
Consensus pattern (18 bp):
TACTAAATAACTGATTAT
Found at i:29481053 original size:18 final size:18
Alignment explanation
Indices: 29480995--29481072 Score: 68
Period size: 18 Copynumber: 4.4 Consensus size: 18
29480985 TAAATAAAGG
* * *
29480995 TACTAAATAACTGATTAT
1 TACTGAATAACTGACTAA
* * *
29481013 TACTAAATAATTGACTAT
1 TACTGAATAACTGACTAA
*
29481031 TACTGAATAACTGATTAA
1 TACTGAATAACTGACTAA
* *
29481049 TACTG-ATGACTGACTGA
1 TACTGAATAACTGACTAA
29481066 TACTGAA
1 TACTGAA
29481073 GAATAAAGAT
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
17 14 0.28
18 36 0.72
ACGTcount: A:0.41, C:0.13, G:0.12, T:0.35
Consensus pattern (18 bp):
TACTGAATAACTGACTAA
Found at i:29483988 original size:22 final size:20
Alignment explanation
Indices: 29483963--29484005 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 20
29483953 CAAATGTTTT
*
29483963 AATTTTCTTCTTTCTGTTCTAA
1 AATTTGCTTC-TTCT-TTCTAA
*
29483985 AATTTGGTTCTTCTTTCTAA
1 AATTTGCTTCTTCTTTCTAA
29484005 A
1 A
29484006 CCTAAGTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 7 0.37
21 4 0.21
22 8 0.42
ACGTcount: A:0.21, C:0.16, G:0.07, T:0.56
Consensus pattern (20 bp):
AATTTGCTTCTTCTTTCTAA
Found at i:29484919 original size:18 final size:18
Alignment explanation
Indices: 29484885--29484936 Score: 50
Period size: 23 Copynumber: 2.6 Consensus size: 18
29484875 CTATAATGTT
*
29484885 TTTGTGTCGTACTCTGCC
1 TTTGTGGCGTACTCTGCC
29484903 TTTGTGGCGTATGCTGCAATGCC
1 TTTGTGGCGTA--CT-C--TGCC
29484926 TTTGTGGCGTA
1 TTTGTGGCGTA
29484937 TTCTACAATG
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 10 0.36
20 2 0.07
21 1 0.04
23 15 0.54
ACGTcount: A:0.10, C:0.21, G:0.29, T:0.40
Consensus pattern (18 bp):
TTTGTGGCGTACTCTGCC
Found at i:29484929 original size:23 final size:23
Alignment explanation
Indices: 29484899--29484955 Score: 96
Period size: 23 Copynumber: 2.5 Consensus size: 23
29484889 TGTCGTACTC
*
29484899 TGCCTTTGTGGCGTATGCTGCAA
1 TGCCTTTGTGGCGTATGCTACAA
*
29484922 TGCCTTTGTGGCGTATTCTACAA
1 TGCCTTTGTGGCGTATGCTACAA
29484945 TGCCTTTGTGG
1 TGCCTTTGTGG
29484956 TATGTAACAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.12, C:0.21, G:0.28, T:0.39
Consensus pattern (23 bp):
TGCCTTTGTGGCGTATGCTACAA
Found at i:29492989 original size:23 final size:23
Alignment explanation
Indices: 29492960--29493065 Score: 122
Period size: 23 Copynumber: 4.6 Consensus size: 23
29492950 AAGTTACTTA
*
29492960 CAATGCCTTTGTGGCGTATTTTG
1 CAATGCCTTTGTGGCGTATTCTG
* * * *
29492983 TAATGCCTTTGTGACATATTCTA
1 CAATGCCTTTGTGGCGTATTCTG
* *
29493006 CAATGCCTTTATGGCTTATTCTG
1 CAATGCCTTTGTGGCGTATTCTG
* * *
29493029 CAATACTTTTGTGGCGTGTTCTG
1 CAATGCCTTTGTGGCGTATTCTG
29493052 CAATGCCTTTGTGG
1 CAATGCCTTTGTGG
29493066 TAAGTTCTGT
Statistics
Matches: 66, Mismatches: 17, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 66 1.00
ACGTcount: A:0.17, C:0.19, G:0.22, T:0.42
Consensus pattern (23 bp):
CAATGCCTTTGTGGCGTATTCTG
Found at i:29494677 original size:22 final size:21
Alignment explanation
Indices: 29494629--29494677 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
29494619 ACATTTAAAC
* *
29494629 ATACATCTCATACATAATCAT
1 ATACATCTCATAAACAATCAT
*
29494650 AAACATCTCATATAACAATCAT
1 ATACATCTCATA-AACAATCAT
*
29494672 CTACAT
1 ATACAT
29494678 ATGTATCATC
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.45, C:0.24, G:0.00, T:0.31
Consensus pattern (21 bp):
ATACATCTCATAAACAATCAT
Found at i:29498985 original size:15 final size:15
Alignment explanation
Indices: 29498965--29498994 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
29498955 TTCATTTATA
29498965 CTCACAAATCATGTG
1 CTCACAAATCATGTG
29498980 CTCACAAATCATGTG
1 CTCACAAATCATGTG
29498995 TGTCTCTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.27, G:0.13, T:0.27
Consensus pattern (15 bp):
CTCACAAATCATGTG
Found at i:29499596 original size:24 final size:24
Alignment explanation
Indices: 29499536--29499629 Score: 75
Period size: 24 Copynumber: 3.8 Consensus size: 24
29499526 AAAAGGGTTA
* *
29499536 TAAAAATATG-AAAGATAAAGAAT
1 TAAAAAAATGAAAAGAGAAAGAAT
29499559 TAAGAAAAAT-AAAAGAGAAAGAAT
1 TAA-AAAAATGAAAAGAGAAAGAAT
* * *
29499583 TAAAAAGATGAAAAGTGAAATGTTGAT
1 TAAAAAAATGAAAAGAGAAA-G--AAT
* *
29499610 TATAAAAATGAAAAGTGAAA
1 TAAAAAAATGAAAAGAGAAA
29499630 TGTTGATTAT
Statistics
Matches: 58, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
23 8 0.14
24 29 0.50
25 1 0.02
27 20 0.34
ACGTcount: A:0.63, C:0.00, G:0.17, T:0.20
Consensus pattern (24 bp):
TAAAAAAATGAAAAGAGAAAGAAT
Found at i:29499611 original size:27 final size:27
Alignment explanation
Indices: 29499581--29499641 Score: 106
Period size: 27 Copynumber: 2.3 Consensus size: 27
29499571 AAGAGAAAGA
29499581 ATTA-AAAAGATGAAAAGTGAAATGTTG
1 ATTATAAAA-ATGAAAAGTGAAATGTTG
29499608 ATTATAAAAATGAAAAGTGAAATGTTG
1 ATTATAAAAATGAAAAGTGAAATGTTG
29499635 ATTATAA
1 ATTATAA
29499642 TGAATATCCA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
27 29 0.88
28 4 0.12
ACGTcount: A:0.52, C:0.00, G:0.18, T:0.30
Consensus pattern (27 bp):
ATTATAAAAATGAAAAGTGAAATGTTG
Found at i:29503872 original size:47 final size:47
Alignment explanation
Indices: 29503803--29503900 Score: 178
Period size: 47 Copynumber: 2.1 Consensus size: 47
29503793 GTATCTCATA
* *
29503803 TTAATATACAATGACTAATTTTTAACAATATAAATTAATGAAAAATT
1 TTAATATACAATGACTAATTTTTAACAATAAAAATAAATGAAAAATT
29503850 TTAATATACAATGACTAATTTTTAACAATAAAAATAAATGAAAAATT
1 TTAATATACAATGACTAATTTTTAACAATAAAAATAAATGAAAAATT
29503897 TTAA
1 TTAA
29503901 CAAAAAGATT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 49 1.00
ACGTcount: A:0.53, C:0.06, G:0.04, T:0.37
Consensus pattern (47 bp):
TTAATATACAATGACTAATTTTTAACAATAAAAATAAATGAAAAATT
Found at i:29522700 original size:56 final size:56
Alignment explanation
Indices: 29522612--29522771 Score: 230
Period size: 56 Copynumber: 2.9 Consensus size: 56
29522602 CCATGGCATC
* * * * *
29522612 GATATATGTGAGCCAGTAAGACCACATTTAGTACATTGGCATCGATATGTGATTTT
1 GATATATGTGTGCAAGTTAGACCACATCTAGTACGTTGGCATCGATATGTGATTTT
* * *
29522668 GATATATGTGTGCAAGTTAGAGCACATCTAGTACGTTGACATCGATATTTGATTTT
1 GATATATGTGTGCAAGTTAGACCACATCTAGTACGTTGGCATCGATATGTGATTTT
* *
29522724 GATATATGTGTGCGAGTTAGACCACGTCTAGTACGTTGGCATCGATAT
1 GATATATGTGTGCAAGTTAGACCACATCTAGTACGTTGGCATCGATAT
29522772 ATGTGGTTAC
Statistics
Matches: 92, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
56 92 1.00
ACGTcount: A:0.28, C:0.14, G:0.23, T:0.34
Consensus pattern (56 bp):
GATATATGTGTGCAAGTTAGACCACATCTAGTACGTTGGCATCGATATGTGATTTT
Found at i:29522810 original size:45 final size:42
Alignment explanation
Indices: 29522760--29522857 Score: 101
Period size: 41 Copynumber: 2.3 Consensus size: 42
29522750 TCTAGTACGT
29522760 TGGCATCGATATATGTGGTTACGAGTAAAACCATGTCTGGGACA-
1 TGGCATCGATAT-T-T-GTTACGAGTAAAACCATGTCTGGGACAG
* * * *
29522804 TCGGCATCG-TATTTGTTTCGTGTAAGACCCTGTCTGGGACAG
1 T-GGCATCGATATTTGTTACGAGTAAAACCATGTCTGGGACAG
*
29522846 TGTCATCGATAT
1 TGGCATCGATAT
29522858 GTGATTACAT
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
41 29 0.63
42 5 0.11
43 1 0.02
44 4 0.09
45 7 0.15
ACGTcount: A:0.23, C:0.18, G:0.27, T:0.32
Consensus pattern (42 bp):
TGGCATCGATATTTGTTACGAGTAAAACCATGTCTGGGACAG
Found at i:29523359 original size:15 final size:15
Alignment explanation
Indices: 29523319--29523360 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
29523309 AAGTATACGG
* *
29523319 ATTTGATTTACGTGA
1 ATTTGGTTTATGTGA
29523334 ATTTGGTTTATGTGA
1 ATTTGGTTTATGTGA
29523349 ATTTGGTTTATG
1 ATTTGGTTTATG
29523361 GATTTTCGAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.21, C:0.02, G:0.24, T:0.52
Consensus pattern (15 bp):
ATTTGGTTTATGTGA
Found at i:29527212 original size:17 final size:17
Alignment explanation
Indices: 29527190--29527224 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
29527180 ATTACTAACA
29527190 TGATTTATTTTCTATTT
1 TGATTTATTTTCTATTT
* *
29527207 TGATTTTTTTTGTATTT
1 TGATTTATTTTCTATTT
29527224 T
1 T
29527225 CTTAATGGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.14, C:0.03, G:0.09, T:0.74
Consensus pattern (17 bp):
TGATTTATTTTCTATTT
Found at i:29528887 original size:22 final size:20
Alignment explanation
Indices: 29528862--29528903 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 20
29528852 TGATTATCTC
29528862 ATTAATGAATGATGTAGTTTTG
1 ATTAATGAATGAT-TA-TTTTG
29528884 ATTAATGAATGATTATTTTG
1 ATTAATGAATGATTATTTTG
29528904 TTTAGCTAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 5 0.25
21 2 0.10
22 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.19, T:0.48
Consensus pattern (20 bp):
ATTAATGAATGATTATTTTG
Found at i:29529504 original size:70 final size:69
Alignment explanation
Indices: 29529405--29529591 Score: 221
Period size: 70 Copynumber: 2.7 Consensus size: 69
29529395 AAATTTTGGC
* * ** *
29529405 GTTGTGGTGAGATGTTAAATGAATAAAGTATTGGTGTTGTGGTAGGACATTACATGAATAAAGTA
1 GTTGTGGTGA-ATGTTAATTGAATGAAGTATCAGTGTTGTGGTAGGACATTAAATGAATAAAGTA
*
29529470 ACGGT
65 ACGAT
* * * *
29529475 GTTGTGGTGGAATGTTAATTGAATGAAGTACCAGTGTTGTGGTGGGGCATTAAATGAATGAAGTA
1 GTTGTGGT-GAATGTTAATTGAATGAAGTATCAGTGTTGTGGTAGGACATTAAATGAATAAAGTA
29529540 ACGAT
65 ACGAT
* * * *
29529545 GTTGTGGCAGAATGTTACTTGATTGAAGTATCAATGTTGTGGTAGGA
1 GTTGTGG-TGAATGTTAATTGAATGAAGTATCAGTGTTGTGGTAGGA
29529592 TGTTTATTGA
Statistics
Matches: 98, Mismatches: 17, Indels: 4
0.82 0.14 0.03
Matches are distributed among these distances:
70 96 0.98
71 2 0.02
ACGTcount: A:0.30, C:0.05, G:0.32, T:0.33
Consensus pattern (69 bp):
GTTGTGGTGAATGTTAATTGAATGAAGTATCAGTGTTGTGGTAGGACATTAAATGAATAAAGTAA
CGAT
Found at i:29529608 original size:35 final size:35
Alignment explanation
Indices: 29529405--29529610 Score: 130
Period size: 35 Copynumber: 5.9 Consensus size: 35
29529395 AAATTTTGGC
* * ***
29529405 GTTGTGGT-GAGATGTTAAATGAATAAAGTATTGGT
1 GTTGTGGTAG-GATGTTAATTGAATGAAGTATCAAT
** * * **
29529440 GTTGTGGTAGGACATTACA-TGAATAAAGTAACGGT
1 GTTGTGGTAGGATGTTA-ATTGAATGAAGTATCAAT
* *
29529475 GTTGTGGT-GGAATGTTAATTGAATGAAGTACCAGT
1 GTTGTGGTAGG-ATGTTAATTGAATGAAGTATCAAT
* *** * * *
29529510 GTTGTGGTGGGGCATTAAATGAATGAAGTAACGAT
1 GTTGTGGTAGGATGTTAATTGAATGAAGTATCAAT
* * * *
29529545 GTTGTGGCAGAATGTTACTTGATTGAAGTATCAAT
1 GTTGTGGTAGGATGTTAATTGAATGAAGTATCAAT
* *
29529580 GTTGTGGTAGGATGTTTATTGAAAGAAGTAT
1 GTTGTGGTAGGATGTTAATTGAATGAAGTAT
29529611 TGGTATTGTG
Statistics
Matches: 133, Mismatches: 33, Indels: 10
0.76 0.19 0.06
Matches are distributed among these distances:
34 3 0.02
35 126 0.95
36 4 0.03
ACGTcount: A:0.31, C:0.05, G:0.31, T:0.34
Consensus pattern (35 bp):
GTTGTGGTAGGATGTTAATTGAATGAAGTATCAAT
Found at i:29529608 original size:70 final size:70
Alignment explanation
Indices: 29529439--29529609 Score: 191
Period size: 70 Copynumber: 2.4 Consensus size: 70
29529429 AAAGTATTGG
* * **
29529439 TGTTGTGGTAGGACATTACATGAATA-AAGTAACGGTGTTGTGGTGGAATGTTAATTGAATGAAG
1 TGTTGTGGTAGGACATTAAATGAA-AGAAGTAACGATGTTGTGGCAGAATGTTAATTGAATGAAG
*
29529503 TACCAG
65 TACCAA
* * * * *
29529509 TGTTGTGGTGGGGCATTAAATGAATGAAGTAACGATGTTGTGGCAGAATGTTACTTGATTGAAGT
1 TGTTGTGGTAGGACATTAAATGAAAGAAGTAACGATGTTGTGGCAGAATGTTAATTGAATGAAGT
*
29529574 ATCAA
66 ACCAA
** * *
29529579 TGTTGTGGTAGGATGTTTATTGAAAGAAGTA
1 TGTTGTGGTAGGACATTAAATGAAAGAAGTA
29529610 TTGGTATTGT
Statistics
Matches: 82, Mismatches: 18, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
70 82 1.00
ACGTcount: A:0.30, C:0.06, G:0.30, T:0.33
Consensus pattern (70 bp):
TGTTGTGGTAGGACATTAAATGAAAGAAGTAACGATGTTGTGGCAGAATGTTAATTGAATGAAGT
ACCAA
Found at i:29534864 original size:17 final size:18
Alignment explanation
Indices: 29534833--29534866 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
29534823 TATGTGGCCT
29534833 ACCCGTGTAGGCCTACAA
1 ACCCGTGTAGGCCTACAA
29534851 ACCCGTGT-GGCCTACA
1 ACCCGTGTAGGCCTACA
29534867 CGGCCCAAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.24, C:0.35, G:0.24, T:0.18
Consensus pattern (18 bp):
ACCCGTGTAGGCCTACAA
Found at i:29540250 original size:21 final size:21
Alignment explanation
Indices: 29540224--29540263 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
29540214 AACTCGAGCC
29540224 CCTCTACG-ACCCCTACCACGG
1 CCTCTA-GTACCCCTACCACGG
*
29540245 CCTCTAGTACCCCTTCCAC
1 CCTCTAGTACCCCTACCAC
29540264 AAGTACCACG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.17, C:0.53, G:0.10, T:0.20
Consensus pattern (21 bp):
CCTCTAGTACCCCTACCACGG
Found at i:29550933 original size:5 final size:5
Alignment explanation
Indices: 29550925--29550949 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
29550915 AGTAAATTAA
29550925 AACAT AACAT AACAT AACAT AACAT
1 AACAT AACAT AACAT AACAT AACAT
29550950 GCACAAGTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.20, G:0.00, T:0.20
Consensus pattern (5 bp):
AACAT
Found at i:29556061 original size:44 final size:43
Alignment explanation
Indices: 29555959--29556528 Score: 518
Period size: 44 Copynumber: 12.9 Consensus size: 43
29555949 GGGAGGTAAA
* * * * *
29555959 ATCTGCCATCTTCGATCTGCTTCGCTGCCAACTACAGGAAGGCAAG
1 ATCTGCTATCTTCGATCTACTTC-C-ACCAA-TATAGGAAGACAAG
* * * * * *
29556005 ATCTACAATCTTCGATCTACTTCACGCCAATACATGAAGATAAG
1 ATCTGCTATCTTCGATCTACTTC-CACCAATATAGGAAGACAAG
* * *
29556049 ATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAG
1 ATCTGCTATCTTCGATCTACTT--CCACCAATATAGGAAGACAAG
* * *
29556094 ATCTGC-ATCGTCGATCCACTTCCTACCAATATAGGAAGACAGG
1 ATCTGCTATCTTCGATCTACTTCC-ACCAATATAGGAAGACAAG
* * * *
29556137 ACCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAG
1 ATCTGCTATCTTCGATCTACTTC-CACCAATATAGGAAGACAAG
* * *
29556181 ATCTGCTTTCTGCGATCTACTTTGCCACCAATATGGGAAGACAAG
1 ATCTGCTATCTTCGATCTAC-TT-CCACCAATATAGGAAGACAAG
* * *
29556226 ATCTGC-ATCTTCGATCCACTTCCTACCAATATAGGAAGATAGG
1 ATCTGCTATCTTCGATCTACTTCC-ACCAATATAGGAAGACAAG
* * * *
29556269 ATCTGCTACCTTCGATCTACTTCACGCCAATACATGAAGACAAG
1 ATCTGCTATCTTCGATCTACTTC-CACCAATATAGGAAGACAAG
* * *
29556313 ATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAG
1 ATCTGCTATCTTCGATCTACTT--CCACCAATATAGGAAGACAAG
* * *
29556358 ATCTGC-ATCTTCGATCCACTTCCTACCAATATAGGAAGATAGG
1 ATCTGCTATCTTCGATCTACTTCC-ACCAATATAGGAAGACAAG
* * * *
29556401 ATCTGCTACCTTCGATCTACTTCACGCCAATACATGAAGACAAG
1 ATCTGCTATCTTCGATCTACTTC-CACCAATATAGGAAGACAAG
* * * *
29556445 ATCTACTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAG
1 ATCTGCTATCTTCGATCTACTT--CCACCAATATAGGAAGACAAG
* *
29556490 ATCTGC-ATCTTTGATCCACTTCCTACCAATATAGGAAGA
1 ATCTGCTATCTTCGATCTACTTCC-ACCAATATAGGAAGA
29556529 TAGGACCTAT
Statistics
Matches: 423, Mismatches: 83, Indels: 39
0.78 0.15 0.07
Matches are distributed among these distances:
42 8 0.02
43 81 0.19
44 214 0.51
45 95 0.22
46 25 0.06
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.27
Consensus pattern (43 bp):
ATCTGCTATCTTCGATCTACTTCCACCAATATAGGAAGACAAG
Found at i:29556131 original size:132 final size:132
Alignment explanation
Indices: 29555959--29556533 Score: 934
Period size: 132 Copynumber: 4.3 Consensus size: 132
29555949 GGGAGGTAAA
** * * * * * * *
29555959 ATCTGCCATCTTCGATCTGCTTCGCTGCCAACTACAGGAAGGCAAGATCTACAATCTTCGATCTA
1 ATCTG-CATCTTCGATCCACTTC-CTACCAA-TATAGGAAGACAGGATCTGCTACCTTCGATCTA
* * *
29556024 CTTCACGCCAATACATGAAGATAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAG
63 CTTCACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAG
29556089 ACAAG
128 ACAAG
* * *
29556094 ATCTGCATCGTCGATCCACTTCCTACCAATATAGGAAGACAGGACCTGCTATCTTCGATCTACTT
1 ATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGACAGGATCTGCTACCTTCGATCTACTT
*
29556159 CACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTTGCCACCAATATGGGAAGACA
66 CACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACA
29556224 AG
131 AG
*
29556226 ATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGATAGGATCTGCTACCTTCGATCTACTT
1 ATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGACAGGATCTGCTACCTTCGATCTACTT
29556291 CACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACA
66 CACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACA
29556356 AG
131 AG
*
29556358 ATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGATAGGATCTGCTACCTTCGATCTACTT
1 ATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGACAGGATCTGCTACCTTCGATCTACTT
*
29556423 CACGCCAATACATGAAGACAAGATCTACTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACA
66 CACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACA
29556488 AG
131 AG
* *
29556490 ATCTGCATCTTTGATCCACTTCCTACCAATATAGGAAGATAGGA
1 ATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGACAGGA
29556534 CCTATTTACG
Statistics
Matches: 419, Mismatches: 21, Indels: 3
0.95 0.05 0.01
Matches are distributed among these distances:
132 394 0.94
133 6 0.01
134 14 0.03
135 5 0.01
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.27
Consensus pattern (132 bp):
ATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGACAGGATCTGCTACCTTCGATCTACTT
CACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACA
AG
Found at i:29571642 original size:26 final size:26
Alignment explanation
Indices: 29571595--29571644 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
29571585 ATGTTTAAAA
*
29571595 ACTTTTTATTTATTATTTTTATTTTC
1 ACTTTTTATTTATTATTCTTATTTTC
*
29571621 ACTTTTATCTTTATTA-TCTTATTT
1 ACTTTT-TATTTATTATTCTTATTT
29571645 AAGTACTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 13 0.62
27 8 0.38
ACGTcount: A:0.20, C:0.10, G:0.00, T:0.70
Consensus pattern (26 bp):
ACTTTTTATTTATTATTCTTATTTTC
Found at i:29582274 original size:17 final size:17
Alignment explanation
Indices: 29582252--29582286 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
29582242 TTAATATGTG
29582252 ATATCAAAGAGGATAGA
1 ATATCAAAGAGGATAGA
29582269 ATATCAAAGAGGATAGA
1 ATATCAAAGAGGATAGA
29582286 A
1 A
29582287 GGATGATAAT
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:0.23, T:0.17
Consensus pattern (17 bp):
ATATCAAAGAGGATAGA
Found at i:29585556 original size:29 final size:29
Alignment explanation
Indices: 29585524--29585581 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
29585514 TGCTTAGGAA
29585524 TGATTATTTAAATATGTGAATGATTATAT
1 TGATTATTTAAATATGTGAATGATTATAT
29585553 TGATTATTTAAATATGTGAATGATTATAT
1 TGATTATTTAAATATGTGAATGATTATAT
29585582 AACTATACTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.38, C:0.00, G:0.14, T:0.48
Consensus pattern (29 bp):
TGATTATTTAAATATGTGAATGATTATAT
Found at i:29599791 original size:132 final size:131
Alignment explanation
Indices: 29599488--29600289 Score: 938
Period size: 132 Copynumber: 6.1 Consensus size: 131
29599478 ATGTAATTTT
* ** * *
29599488 AGGGAGA-AGAGATTTACAATCTTCAGCCTATTCCACTACTACTCAAGGAGACAAGGCTAGTGGC
1 AGGGAGATA-AGATCTACAATCTTCAGCCTGCTCCACTACTGCTCAGGGAGACAAGGCTAGTGGC
* * ** * * * * * *
29599552 TTAAATATGCTTCCCTACTGCCTCAGAAAAATAAGATT--CGCCTTCAATCTGCTCCATTGCTAC
65 TTAAATCTGCTTCCCTACTACCTCAGGGAGATAAGATTCCCGTCTTCGATCTGCTCCACTACTGC
29599615 TC
130 TC
*
29599617 AGGGAGATAAGATCTACAATCTTCAGCCTGCTCCACTACTGCTCAGGGAGACAAGGCTAGTGGTT
1 AGGGAGATAAGATCTACAATCTTCAGCCTGCTCCACTACTGCTCAGGGAGACAAGGCTAGTGGCT
* * *
29599682 TAAATCTAC-TCCCTTGCTACCTCAGGGAGATAAGATTCACCGTCTTCGATATGCTCCACTACTG
66 TAAATCTGCTTCCC-TACTACCTCAGGGAGATAAGATTC-CCGTCTTCGATCTGCTCCACTACTG
*
29599746 CTT
129 CTC
* * * * *
29599749 AGGGAGATAAGATTTACAATCTTCGGCCTGCTCCATTGCTGCTCAGGGAGATAAGGCTAGTGGCT
1 AGGGAGATAAGATCTACAATCTTCAGCCTGCTCCACTACTGCTCAGGGAGACAAGGCTAGTGGCT
* * * * * *
29599814 TAAATTTTCTTCCCTACTACCTC-GGGAAAATAATATT--CGCCTTCGATCTGCTTCACTACTGC
66 TAAATCTGCTTCCCTACTACCTCAGGG-AGATAAGATTCCCGTCTTCGATCTGCTCCACTACTGC
29599876 TC
130 TC
29599878 AGGGAGATAAGATCTACAATCTTCAGCCTGCTCCACTACTGCTCAGGGAGACAAGGCTAGTGGCT
1 AGGGAGATAAGATCTACAATCTTCAGCCTGCTCCACTACTGCTCAGGGAGACAAGGCTAGTGGCT
* * * *
29599943 TAAATCTGC-TCCCTTGCTACCTTAGGGAGATAAGATTCACTGTCTTCGATCTGCTCCACTATTG
66 TAAATCTGCTTCCC-TACTACCTCAGGGAGATAAGATTC-CCGTCTTCGATCTGCTCCACTACTG
*
29600007 CTT
129 CTC
* *
29600010 AGGGAGATAATATCTACAATCTTCAGCCTGCTCCACTACTGCTCAGGGAGATAAGGCTAGTGGCT
1 AGGGAGATAAGATCTACAATCTTCAGCCTGCTCCACTACTGCTCAGGGAGACAAGGCTAGTGGCT
* * * * *
29600075 TAAATCTGCTTCCCTACTACCTCAGGAAGATAAGATTCGCCATCTTTGATCTGCTCCACTGCTAC
66 TAAATCTGCTTCCCTACTACCTCAGGGAGATAAGATTC-CCGTCTTCGATCTGCTCCACTACTGC
29600140 TC
130 TC
* * * * *
29600142 AGGGAGATAAGATTTACAATCTTCAGCCTGTTCCACTGCTGCTCAGAGAGACAAGACTAGTGGCT
1 AGGGAGATAAGATCTACAATCTTCAGCCTGCTCCACTACTGCTCAGGGAGACAAGGCTAGTGGCT
* * * * * *
29600207 TAAATCTAC-TCCCTTGCTACCTCAGGGAGATAAGATTTTCCATCTCCGATCTGCTCCATTACTA
66 TAAATCTGCTTCCC-TACTACCTCAGGGAGATAAGA-TTCCCGTCTTCGATCTGCTCCACTACT-
*
29600271 CCTC
128 GCTC
* *
29600275 ATGAAGATAAGATCT
1 AGGGAGATAAGATCT
29600290 GTGAATTTAC
Statistics
Matches: 574, Mismatches: 83, Indels: 28
0.84 0.12 0.04
Matches are distributed among these distances:
128 8 0.01
129 187 0.33
130 4 0.01
131 7 0.01
132 343 0.60
133 25 0.04
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.28
Consensus pattern (131 bp):
AGGGAGATAAGATCTACAATCTTCAGCCTGCTCCACTACTGCTCAGGGAGACAAGGCTAGTGGCT
TAAATCTGCTTCCCTACTACCTCAGGGAGATAAGATTCCCGTCTTCGATCTGCTCCACTACTGCT
C
Found at i:29599924 original size:44 final size:44
Alignment explanation
Indices: 29599593--29600197 Score: 242
Period size: 44 Copynumber: 13.8 Consensus size: 44
29599583 TAAGATTCGC
* * * * *
29599593 CTTCAATCTGCTCCATTGCTACTCAGGGAGATAAGATCTACAAT
1 CTTCAGTCTGCTCCACTACTGCTCAGGGAGATAAGATCTACAGT
* * * **
29599637 CTTCAGCCTGCTCCACTACTGCTCAGGGAGACAAG-GCTAGTGGT
1 CTTCAGTCTGCTCCACTACTGCTCAGGGAGATAAGATCTA-CAGT
* * * * * *
29599681 -TTAAATCTACTCC-CTTGCTACCTCAGGGAGATAAGAT-TCACCGT
1 CTTCAGTCTGCTCCAC-TACT-GCTCAGGGAGATAAGATCT-ACAGT
* * * *
29599725 CTTC-GATATGCTCCACTACTGCTTAGGGAGATAAGATTTACAAT
1 CTTCAG-TCTGCTCCACTACTGCTCAGGGAGATAAGATCTACAGT
* * * * * ** *
29599769 CTTCGGCCTGCTCCATTGCTGCTCAGGGAGATAAG-GCTAGTGG
1 CTTCAGTCTGCTCCACTACTGCTCAGGGAGATAAGATCTACAGT
* * * * * * * *
29599812 CTTAAATTTTCTTCC-CTACTACCTC-GGGAAAATAATAT-T-C-GC
1 CTTCAGTCTGC-TCCACTACT-GCTCAGGG-AGATAAGATCTACAGT
* *
29599854 CTTC-GATCTGCTTCACTACTGCTCAGGGAGATAAGATCTACAAT
1 CTTCAG-TCTGCTCCACTACTGCTCAGGGAGATAAGATCTACAGT
* * * ** *
29599898 CTTCAGCCTGCTCCACTACTGCTCAGGGAGACAAG-GCTAGTGG
1 CTTCAGTCTGCTCCACTACTGCTCAGGGAGATAAGATCTACAGT
* * * * * *
29599941 CTTAAATCTGCTCC-CTTGCTACCTTAGGGAGATAAGAT-TCACTGT
1 CTTCAGTCTGCTCCAC-TACT-GCTCAGGGAGATAAGATCT-ACAGT
* * * *
29599986 CTTC-GATCTGCTCCACTATTGCTTAGGGAGATAATATCTACAAT
1 CTTCAG-TCTGCTCCACTACTGCTCAGGGAGATAAGATCTACAGT
* * ** *
29600030 CTTCAGCCTGCTCCACTACTGCTCAGGGAGATAAG-GCTAGTGG
1 CTTCAGTCTGCTCCACTACTGCTCAGGGAGATAAGATCTACAGT
* * * * **
29600073 CTTAAATCTGCTTCC-CTACTACCTCAGGAAGATAAGATTCGCCA-T
1 CTTCAGTCTGC-TCCACTACT-GCTCAGGGAGATAAGA-TCTACAGT
* * * * *
29600118 CTT-TGATCTGCTCCACTGCTACTCAGGGAGATAAGATTTACAAT
1 CTTCAG-TCTGCTCCACTACTGCTCAGGGAGATAAGATCTACAGT
* * * * *
29600162 CTTCAGCCTGTTCCACTGCTGCTCAGAGAGACAAGA
1 CTTCAGTCTGCTCCACTACTGCTCAGGGAGATAAGA
29600198 CTAGTGGCTT
Statistics
Matches: 400, Mismatches: 124, Indels: 74
0.67 0.21 0.12
Matches are distributed among these distances:
41 12 0.03
42 18 0.05
43 65 0.16
44 256 0.64
45 46 0.12
46 3 0.01
ACGTcount: A:0.25, C:0.26, G:0.20, T:0.29
Consensus pattern (44 bp):
CTTCAGTCTGCTCCACTACTGCTCAGGGAGATAAGATCTACAGT
Found at i:29599957 original size:261 final size:261
Alignment explanation
Indices: 29599486--29600243 Score: 1158
Period size: 261 Copynumber: 2.9 Consensus size: 261
29599476 CAATGTAATT
** * * *
29599486 TTAGGGAGA-AGAGATTTACAATCTTCAGCCTATTCCACTACTACTCAAGGAGACAAGGCTAGTG
1 TTAGGGAGATA-AGATTTACAATCTTCAGCCTGCTCCACTACTGCTCAGGGAGATAAGGCTAGTG
* * * *
29599550 GCTTAAATATGCTTCCCTACTGCCTCAGAAAAATAAGATTCGCCTTCAATCTGCTCCATTGCTAC
65 GCTTAAATATGCTTCCCTACTACCTCAGGAAAATAAGATTCGCCTTCGATCTGCTCCACTGCTAC
29599615 TCAGGGAGATAAGATCTACAATCTTCAGCCTGCTCCACTACTGCTCAGGGAGACAAGGCTAGTGG
130 TCAGGGAGATAAGATCTACAATCTTCAGCCTGCTCCACTACTGCTCAGGGAGACAAGGCTAGTGG
*
29599680 TTTAAATCTACTCCCTTGCTACCTCAGGGAGATAAGATTCACCGTCTTCGATATGCTCCACTACT
195 CTTAAATCTACTCCCTTGCTACCTCAGGGAGATAAGATTCACCGTCTTCGATATGCTCCACTACT
29599745 GC
260 GC
* * *
29599747 TTAGGGAGATAAGATTTACAATCTTCGGCCTGCTCCATTGCTGCTCAGGGAGATAAGGCTAGTGG
1 TTAGGGAGATAAGATTTACAATCTTCAGCCTGCTCCACTACTGCTCAGGGAGATAAGGCTAGTGG
* * * * * * *
29599812 CTTAAATTTTCTTCCCTACTACCTCGGGAAAATAATATTCGCCTTCGATCTGCTTCACTACTGCT
66 CTTAAATATGCTTCCCTACTACCTCAGGAAAATAAGATTCGCCTTCGATCTGCTCCACTGCTACT
29599877 CAGGGAGATAAGATCTACAATCTTCAGCCTGCTCCACTACTGCTCAGGGAGACAAGGCTAGTGGC
131 CAGGGAGATAAGATCTACAATCTTCAGCCTGCTCCACTACTGCTCAGGGAGACAAGGCTAGTGGC
* * * * *
29599942 TTAAATCTGCTCCCTTGCTACCTTAGGGAGATAAGATTCACTGTCTTCGATCTGCTCCACTATTG
196 TTAAATCTACTCCCTTGCTACCTCAGGGAGATAAGATTCACCGTCTTCGATATGCTCCACTACTG
29600007 C
261 C
* *
29600008 TTAGGGAGATAATATCTACAATCTTCAGCCTGCTCCACTACTGCTCAGGGAGATAAGGCTAGTGG
1 TTAGGGAGATAAGATTTACAATCTTCAGCCTGCTCCACTACTGCTCAGGGAGATAAGGCTAGTGG
* * *
29600073 CTTAAATCTGCTTCCCTACTACCTCAGGAAGATAAGATTCGCCATCTTTGATCTGCTCCACTGCT
66 CTTAAATATGCTTCCCTACTACCTCAGGAAAATAAGATTCG-C--CTTCGATCTGCTCCACTGCT
* * * * *
29600138 ACTCAGGGAGATAAGATTTACAATCTTCAGCCTGTTCCACTGCTGCTCAGAGAGACAAGACTAGT
128 ACTCAGGGAGATAAGATCTACAATCTTCAGCCTGCTCCACTACTGCTCAGGGAGACAAGGCTAGT
29600203 GGCTTAAATCTACTCCCTTGCTACCTCAGGGAGATAAGATT
193 GGCTTAAATCTACTCCCTTGCTACCTCAGGGAGATAAGATT
29600244 TTCCATCTCC
Statistics
Matches: 447, Mismatches: 46, Indels: 5
0.90 0.09 0.01
Matches are distributed among these distances:
261 330 0.74
262 2 0.00
264 115 0.26
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.28
Consensus pattern (261 bp):
TTAGGGAGATAAGATTTACAATCTTCAGCCTGCTCCACTACTGCTCAGGGAGATAAGGCTAGTGG
CTTAAATATGCTTCCCTACTACCTCAGGAAAATAAGATTCGCCTTCGATCTGCTCCACTGCTACT
CAGGGAGATAAGATCTACAATCTTCAGCCTGCTCCACTACTGCTCAGGGAGACAAGGCTAGTGGC
TTAAATCTACTCCCTTGCTACCTCAGGGAGATAAGATTCACCGTCTTCGATATGCTCCACTACTG
C
Found at i:29609239 original size:40 final size:40
Alignment explanation
Indices: 29609202--29609466 Score: 351
Period size: 40 Copynumber: 6.7 Consensus size: 40
29609192 GCTACTCGTT
*
29609202 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
29609242 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
*
29609282 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* *
29609322 CAAATGCCTTC-GGATCTTAGTCCGGATTTAGTAACTCGTA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAACTCGCA
* *
29609362 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * *
29609401 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
29609442 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
29609467 CATCATTCAA
Statistics
Matches: 201, Mismatches: 17, Indels: 14
0.87 0.07 0.06
Matches are distributed among these distances:
38 2 0.01
39 35 0.17
40 149 0.74
41 15 0.07
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:29617281 original size:40 final size:40
Alignment explanation
Indices: 29617237--29617501 Score: 342
Period size: 40 Copynumber: 6.7 Consensus size: 40
29617227 GCTACTCGTT
* *
29617237 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTAGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
29617277 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
*
29617317 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* *
29617357 CAAATGCCTTC-GGATCTTAGTCCGGATTTAGTAACTCGTA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAACTCGCA
* *
29617397 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * *
29617436 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
29617477 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
29617502 CATCATTCAA
Statistics
Matches: 200, Mismatches: 18, Indels: 14
0.86 0.08 0.06
Matches are distributed among these distances:
38 2 0.01
39 35 0.17
40 148 0.74
41 15 0.08
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:29625837 original size:24 final size:24
Alignment explanation
Indices: 29625810--29625860 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
29625800 TAGCCAGTTC
29625810 TTCTTGCATCT-ATGTTTGCATCTG
1 TTCTTGCATCTCAT-TTTGCATCTG
* *
29625834 TTCTTGCATTTCCTTTTGCATCTG
1 TTCTTGCATCTCATTTTGCATCTG
29625858 TTC
1 TTC
29625861 CAACCTTTCC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 23 0.96
25 1 0.04
ACGTcount: A:0.10, C:0.24, G:0.14, T:0.53
Consensus pattern (24 bp):
TTCTTGCATCTCATTTTGCATCTG
Found at i:29625869 original size:24 final size:24
Alignment explanation
Indices: 29625824--29625870 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
29625814 TGCATCTATG
***
29625824 TTTGCATCTGTTCTTGCATTTCCT
1 TTTGCATCTGTTCCAACATTTCCT
*
29625848 TTTGCATCTGTTCCAACCTTTCC
1 TTTGCATCTGTTCCAACATTTCC
29625871 AATTTTTTAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.11, C:0.30, G:0.11, T:0.49
Consensus pattern (24 bp):
TTTGCATCTGTTCCAACATTTCCT
Found at i:29629747 original size:17 final size:16
Alignment explanation
Indices: 29629727--29629766 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 16
29629717 TAGATAGAAT
29629727 ATAAAAAATAATATATA
1 ATAAAAAA-AATATATA
29629744 ATAAATAAAAATATATA
1 ATAAA-AAAAATATATA
29629761 ATAAAA
1 ATAAAA
29629767 TAACTTGATG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 1 0.05
17 18 0.82
18 3 0.14
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (16 bp):
ATAAAAAAAATATATA
Found at i:29629768 original size:22 final size:20
Alignment explanation
Indices: 29629730--29629769 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
29629720 ATAGAATATA
*
29629730 AAAAATAATATATAATAAAT
1 AAAAATAATATAAAATAAAT
29629750 AAAAATATATAATAAAATAA
1 AAAAATA-AT-ATAAAATAA
29629770 CTTGATGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
21 2 0.12
22 8 0.47
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (20 bp):
AAAAATAATATAAAATAAAT
Found at i:29634381 original size:3 final size:3
Alignment explanation
Indices: 29634373--29634405 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
29634363 TGAATTGCAA
29634373 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
29634406 GAAATTAAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:29638306 original size:49 final size:47
Alignment explanation
Indices: 29638222--29638679 Score: 700
Period size: 47 Copynumber: 9.6 Consensus size: 47
29638212 TATTTGAATA
* * *
29638222 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGGCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
29638269 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
29638318 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
29638365 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATG
29638414 AATGTGAAAGTGTATACATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTAT--ATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
29638463 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
29638510 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATAGCCGATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATG
29638559 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* * * * * *
29638606 AATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
29638653 GATGTGAAAGTGTATAAATGTGATAAG
1 AATGTGAAAGTGTATATATGTGATAAG
29638680 TCCCGAAGGG
Statistics
Matches: 380, Mismatches: 23, Indels: 16
0.91 0.05 0.04
Matches are distributed among these distances:
47 200 0.53
49 180 0.47
ACGTcount: A:0.33, C:0.08, G:0.30, T:0.29
Consensus pattern (47 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
Found at i:29638330 original size:96 final size:96
Alignment explanation
Indices: 29638222--29638679 Score: 721
Period size: 96 Copynumber: 4.8 Consensus size: 96
29638212 TATTTGAATA
*
29638222 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGGCAATGTGATGAATGTGAAAGTGTATATA
1 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATA
29638287 TATGTGATAAGGCCTAATGGCCGATGTGATG
66 TATGTGATAAGGCCTAATGGCCGATGTGATG
29638318 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATA
1 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATA
29638383 TATGTGATAAGGCCTAATGGCCGATGTGATG
66 TATGTGATAAGGCCTAATGGCCGATGTGATG
* *
29638414 AATGTGAAAGTGTATACATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TA
1 AATGTGAAAGTGTAT--ATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATA
* *
29638477 TATATGTGATAAGGCCGAATGGCCAATGTGATG
64 TATATGTGATAAGGCCTAATGGCCGATGTGATG
* * *
29638510 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTG--TA
1 AATGTGAAAGTG--TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATA
29638573 TATATGTGATAAGGCCTAATGGCCGATGTGATG
64 TATATGTGATAAGGCCTAATGGCCGATGTGATG
* * * * *
29638606 AATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTATA-A
1 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATA
29638670 -ATGTGATAAG
66 TATGTGATAAG
29638680 TCCCGAAGGG
Statistics
Matches: 340, Mismatches: 16, Indels: 14
0.92 0.04 0.04
Matches are distributed among these distances:
94 49 0.14
95 1 0.00
96 245 0.72
98 45 0.13
ACGTcount: A:0.33, C:0.08, G:0.30, T:0.29
Consensus pattern (96 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATA
TATGTGATAAGGCCTAATGGCCGATGTGATG
Found at i:29646729 original size:27 final size:27
Alignment explanation
Indices: 29646689--29646744 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
29646679 AACATGTCAG
*
29646689 GAAAGAAAAGCCTTTTTGGCGTAA-CAT
1 GAAAGAAAAGCCTTTGTGGCG-AATCAT
*
29646716 GAAAGAAAATCCTTTGTGGCGAATCAT
1 GAAAGAAAAGCCTTTGTGGCGAATCAT
29646743 GA
1 GA
29646745 TATGGAAGCC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 2 0.08
27 24 0.92
ACGTcount: A:0.38, C:0.14, G:0.23, T:0.25
Consensus pattern (27 bp):
GAAAGAAAAGCCTTTGTGGCGAATCAT
Found at i:29649237 original size:56 final size:56
Alignment explanation
Indices: 29649190--29649324 Score: 252
Period size: 56 Copynumber: 2.4 Consensus size: 56
29649180 CTTACTTGTG
*
29649190 CACATATATCGGAATCACATATCGATGGCAACGTATTAAACGTGGTCTTACTCGCA
1 CACATATATCGGAATCACATATCGATGCCAACGTATTAAACGTGGTCTTACTCGCA
29649246 CACATATATCGGAATCACATATCGATGCCAACGTATTAAACGTGGTCTTACTCGCA
1 CACATATATCGGAATCACATATCGATGCCAACGTATTAAACGTGGTCTTACTCGCA
*
29649302 CATATATATCGGAATCACATATC
1 CACATATATCGGAATCACATATC
29649325 ACAAGTCGAA
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
56 77 1.00
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.27
Consensus pattern (56 bp):
CACATATATCGGAATCACATATCGATGCCAACGTATTAAACGTGGTCTTACTCGCA
Found at i:29655155 original size:13 final size:13
Alignment explanation
Indices: 29655137--29655207 Score: 106
Period size: 13 Copynumber: 5.5 Consensus size: 13
29655127 AAATTTTTCC
29655137 AAAGCACTTCTCA
1 AAAGCACTTCTCA
29655150 AAAGCACTTCTCA
1 AAAGCACTTCTCA
*
29655163 AAAGTACTTCTCA
1 AAAGCACTTCTCA
*
29655176 AAAGCACTTCTCT
1 AAAGCACTTCTCA
* *
29655189 ACAGCACTTTTCA
1 AAAGCACTTCTCA
29655202 AAAGCA
1 AAAGCA
29655208 ATGAAGAACT
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 51 1.00
ACGTcount: A:0.38, C:0.28, G:0.08, T:0.25
Consensus pattern (13 bp):
AAAGCACTTCTCA
Found at i:29669037 original size:29 final size:28
Alignment explanation
Indices: 29669005--29669062 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 28
29668995 TAATTGTTCT
*
29669005 AAATCATTTTATATATTATATTATTTTAA
1 AAATCATTTTACATATTA-ATTATTTTAA
* *
29669034 AAATCATTTTGCATATTAATTGTTTTAA
1 AAATCATTTTACATATTAATTATTTTAA
29669062 A
1 A
29669063 TTATTTTATA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 10 0.38
29 16 0.62
ACGTcount: A:0.40, C:0.05, G:0.03, T:0.52
Consensus pattern (28 bp):
AAATCATTTTACATATTAATTATTTTAA
Found at i:29669272 original size:14 final size:14
Alignment explanation
Indices: 29669199--29669276 Score: 54
Period size: 14 Copynumber: 5.4 Consensus size: 14
29669189 CCTTTTTATT
29669199 TTTTTTATT-TTTA
1 TTTTTTATTCTTTA
*
29669212 -TTTTTACTCTTTTA
1 TTTTTTATTC-TTTA
** *
29669226 TTACTTATTC-TAA
1 TTTTTTATTCTTTA
29669239 TCTTTTTCATATCATTTA
1 T-TTTTT-AT-TC-TTTA
29669257 TTTTTTATTCTTTA
1 TTTTTTATTCTTTA
29669271 TTTTTT
1 TTTTTT
29669277 TAGACATATC
Statistics
Matches: 49, Mismatches: 8, Indels: 15
0.68 0.11 0.21
Matches are distributed among these distances:
12 7 0.14
13 3 0.06
14 17 0.35
15 10 0.20
16 4 0.08
17 5 0.10
18 3 0.06
ACGTcount: A:0.18, C:0.10, G:0.00, T:0.72
Consensus pattern (14 bp):
TTTTTTATTCTTTA
Found at i:29672880 original size:19 final size:19
Alignment explanation
Indices: 29672856--29672900 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
29672846 AACGCCTTTT
*
29672856 TGCATT-CACTACATGCATC
1 TGCATTACACTACAT-CATA
*
29672875 TGCATTACATTACATCATA
1 TGCATTACACTACATCATA
29672894 TGCATTA
1 TGCATTA
29672901 AAGTCCATCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.31, C:0.24, G:0.09, T:0.36
Consensus pattern (19 bp):
TGCATTACACTACATCATA
Found at i:29676400 original size:37 final size:37
Alignment explanation
Indices: 29676350--29676428 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 37
29676340 TTATTACGAA
* * * *
29676350 GTCTTACCCGGACATAATCTCCACATGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
29676387 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
29676424 GTCTT
1 GTCTT
29676429 TAGAGCTCGG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.25
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:29676625 original size:47 final size:47
Alignment explanation
Indices: 29676547--29677102 Score: 934
Period size: 47 Copynumber: 11.7 Consensus size: 47
29676537 CCCTTCGGGA
* * * * * *
29676547 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
29676594 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
29676641 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
29676688 CTTATCACATATATACACTTTCACATTCATCACATCGACCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
29676735 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
29676784 CTTATCACATATATACACTTTCACAGTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
29676831 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTGGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
29676878 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
29676927 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
29676974 CTTATCACATATATACGCTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
29677021 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
29677068 CTTATCACATATATGCA-TGTTCACATCCATCACAT
1 CTTATCACATATATACACT-TTCACATTCATCACAT
29677103 AGAATCCTAA
Statistics
Matches: 484, Mismatches: 20, Indels: 10
0.94 0.04 0.02
Matches are distributed among these distances:
46 1 0.00
47 391 0.81
49 92 0.19
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:29676803 original size:143 final size:141
Alignment explanation
Indices: 29676547--29677102 Score: 934
Period size: 143 Copynumber: 3.9 Consensus size: 141
29676537 CCCTTCGGGA
* * * * * * * *
29676547 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
29676612 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
29676677 GGCCATTAGGC
131 GGCCATTAGGC
*
29676688 CTTATCACATATATACACTTTCACATTCATCACATCGACCATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATAC
*
29676753 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACAGTCATCACA
64 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
29676818 TCGGCCATTAGGC
129 TCGGCCATTAGGC
*
29676831 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTGGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATAC
29676896 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
64 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
29676961 TCGGCCATTAGGC
129 TCGGCCATTAGGC
*
29676974 CTTATCACATATATACGCTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
* *
29677039 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATGCA-TGTTCACATCCATCACAT
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACT-TTCACATTCATCACAT
29677103 AGAATCCTAA
Statistics
Matches: 395, Mismatches: 17, Indels: 6
0.94 0.04 0.01
Matches are distributed among these distances:
140 1 0.00
141 116 0.29
143 278 0.70
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (141 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
GGCCATTAGGC
Found at i:29676881 original size:190 final size:190
Alignment explanation
Indices: 29676547--29677102 Score: 933
Period size: 190 Copynumber: 2.9 Consensus size: 190
29676537 CCCTTCGGGA
* * * * * * *
29676547 CTTATCACAT-T-TATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
29676610 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
66 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
29676675 TCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGACCATTAGGC
131 TCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGACCATTAGGC
29676735 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
*
29676800 ACTTTCACAGTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
66 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
* *
29676865 TCGGCCATTGGGCCTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
131 TCGGCCATTAGGCCTTATCAC--ATATATACACTTTCACATTCATCACATCGACCATTAGGC
29676927 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
*
29676990 GCTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
66 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
* *
29677055 TCGGCCATTAGGCCTTATCACATATATGCA-TGTTCACATCCATCACAT
131 TCGGCCATTAGGCCTTATCACATATATACACT-TTCACATTCATCACAT
29677103 AGAATCCTAA
Statistics
Matches: 348, Mismatches: 15, Indels: 10
0.93 0.04 0.03
Matches are distributed among these distances:
187 1 0.00
188 33 0.09
189 1 0.00
190 267 0.77
192 46 0.13
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (190 bp):
CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
TCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGACCATTAGGC
Found at i:29685620 original size:44 final size:44
Alignment explanation
Indices: 29685572--29685851 Score: 171
Period size: 44 Copynumber: 6.3 Consensus size: 44
29685562 AGCCACTAGC
29685572 CTTATCTCCCTGAGGTAGCAAGAGAGCAGACTAATGATTGTAGT
1 CTTATCTCCCTGAGGTAGCAAGAGAGCAGACTAATGATTGTAGT
* *
29685616 CTTATCTTCCTGAGGTAGCAAG-GAAGCAGACTGAA-GATTGCAGAT
1 CTTATCTCCCTGAGGTAGCAAGAG-AGCAGACT-AATGATTGTAG-T
* * * * * * * * *
29685661 TTTATCTCGCTCAGATAGCAACAGAGCAGATCGAA-GATGGAAAAT
1 CTTATCTCCCTGAGGTAGCAAGAGAGCAGA-CTAATGATTG-TAGT
* * ** **** *
29685706 CTTATCTTCC-GAGGTAGCAGGAGAGCAGA-TTTTAGCCACTAGC
1 CTTATCTCCCTGAGGTAGCAAGAGAGCAGACTAAT-GATTGTAGT
* * *
29685749 CTTATCTTCCC-GAGGTAGCGAGGGAGCAGGCTAATGATTGTAGT
1 CTTATC-TCCCTGAGGTAGCAAGAGAGCAGACTAATGATTGTAGT
* * * *
29685793 CTTATCTTCCTGAGGTA--AAGACGGAGCAGACTAAAGATGGTAAAT
1 CTTATCTCCCTGAGGTAGCAAGA--GAGCAGACTAATGATTGT-AGT
29685838 CTTATCTCCCTGAG
1 CTTATCTCCCTGAG
29685852 CAGCAGTGGA
Statistics
Matches: 173, Mismatches: 49, Indels: 27
0.69 0.20 0.11
Matches are distributed among these distances:
42 2 0.01
43 11 0.06
44 101 0.58
45 56 0.32
46 3 0.02
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.26
Consensus pattern (44 bp):
CTTATCTCCCTGAGGTAGCAAGAGAGCAGACTAATGATTGTAGT
Found at i:29685974 original size:44 final size:44
Alignment explanation
Indices: 29685926--29686084 Score: 178
Period size: 44 Copynumber: 3.6 Consensus size: 44
29685916 AGCCACCAGC
29685926 CTTATCTTCCTGAGGTAGCAAGGGAGTAGGCCGAAAATTGTAGT
1 CTTATCTTCCTGAGGTAGCAAGGGAGTAGGCCGAAAATTGTAGT
* * *
29685970 CTTATCTTCTTGAGGTAGCAAGGGAGCAGGTC-AAGAATTGTTA-T
1 CTTATCTTCCTGAGGTAGCAAGGGAGTAGGCCGAA-AATTG-TAGT
** * * * *
29686014 CTTATCTTTTTGAGGTAGCAAGGAAGTAGACTGAAGATTGTAGAT
1 CTTATCTTCCTGAGGTAGCAAGGGAGTAGGCCGAAAATTGTAG-T
* *
29686059 CTTATCTTCCCGAGGTAGTAAGGGAG
1 CTTATCTTCCTGAGGTAGCAAGGGAG
29686085 CAGATTTTAG
Statistics
Matches: 95, Mismatches: 15, Indels: 9
0.80 0.13 0.08
Matches are distributed among these distances:
43 4 0.04
44 65 0.68
45 26 0.27
ACGTcount: A:0.28, C:0.14, G:0.28, T:0.30
Consensus pattern (44 bp):
CTTATCTTCCTGAGGTAGCAAGGGAGTAGGCCGAAAATTGTAGT
Found at i:29686063 original size:177 final size:175
Alignment explanation
Indices: 29685525--29686114 Score: 619
Period size: 177 Copynumber: 3.3 Consensus size: 175
29685515 AAAAATGACA
29685525 AATCTTATCTTCCCGAGGTAGCAAGGGAGCAGATTTTAGCCACTAGCCTTATCTCCCTGAGGTAG
1 AATCTTATCTTCCCGAGGTAGCAAGGGAGCAGATTTTAGCCACTAGCCTTATCTCCCTGAGGTAG
* * * *
29685590 CAAGAGAGCAGACTAATGATTGTAGTCTTATCTTCCTGAGGTAGCAAGGAAGCAGACTGAAGATT
66 CAAGGGAGCAGGCTAATGATTGTAGTCTTATCTTCCTGAGGTAGCAAGGGAGCAGACTAAAGATT
* * * * * * *
29685655 GCAGATTTTATCTCGCTCAGATAGCAA-CAGAGCAGA-TCGAAGATGG
131 GTA-ATCTTATCTCCCTGAGGTAGCAAGGA-AGCAGACT-GAAGATTG
29685701 AAAATCTTATCTT-CCGAGGTAGC-AGGAGAGCAGATTTTAGCCACTAGCCTTATCTTCCC-GAG
1 --AATCTTATCTTCCCGAGGTAGCAAGG-GAGCAGATTTTAGCCACTAGCCTTATC-TCCCTGAG
*
29685763 GTAGCGAGGGAGCAGGCTAATGATTGTAGTCTTATCTTCCTGAGGTA--AAGACGGAGCAGACTA
62 GTAGCAAGGGAGCAGGCTAATGATTGTAGTCTTATCTTCCTGAGGTAGCAAG--GGAGCAGACTA
* * * *
29685826 AAGATGGTAAATCTTATCTCCCTGA-GCAGC-AGTGGAGCAGATCGGAGACGA-TG
125 AAGATTGT-AATCTTATCTCCCTGAGGTAGCAAG-GAAGCAGA-CTGA-A-GATTG
* * * * *
29685879 AATCTTATCTTCCCAAGGTAACAGGGGAGCAGATTTTAGCCACCAGCCTTATCTTCCTGAGGTAG
1 AATCTTATCTTCCCGAGGTAGCAAGGGAGCAGATTTTAGCCACTAGCCTTATCTCCCTGAGGTAG
* * * * * *
29685944 CAAGGGAGTAGGCCGAA-AATTGTAGTCTTATCTTCTTGAGGTAGCAAGGGAGCAG-GTCAAGAA
66 CAAGGGAGCAGG-CTAATGATTGTAGTCTTATCTTCCTGAGGTAGCAAGGGAGCAGACTAAAG-A
* *** *
29686007 TTGTTATCTTATCTTTTTGAGGTAGCAAGGAAGTAGACTGAAGATTG
129 TTGTAATCTTATCTCCCTGAGGTAGCAAGGAAGCAGACTGAAGATTG
* * *
29686054 TAGATCTTATCTTCCCGAGGTAGTAAGGGAGCAGATTTTAGCCACAAGTCTTATCTCCCTG
1 -A-ATCTTATCTTCCCGAGGTAGCAAGGGAGCAGATTTTAGCCACTAGCCTTATCTCCCTG
29686115 CAGTTACAGT
Statistics
Matches: 345, Mismatches: 44, Indels: 47
0.79 0.10 0.11
Matches are distributed among these distances:
174 2 0.01
175 7 0.02
176 46 0.13
177 260 0.75
178 25 0.07
179 5 0.01
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.26
Consensus pattern (175 bp):
AATCTTATCTTCCCGAGGTAGCAAGGGAGCAGATTTTAGCCACTAGCCTTATCTCCCTGAGGTAG
CAAGGGAGCAGGCTAATGATTGTAGTCTTATCTTCCTGAGGTAGCAAGGGAGCAGACTAAAGATT
GTAATCTTATCTCCCTGAGGTAGCAAGGAAGCAGACTGAAGATTG
Found at i:29697700 original size:224 final size:224
Alignment explanation
Indices: 29697301--29697742 Score: 706
Period size: 224 Copynumber: 2.0 Consensus size: 224
29697291 GTCTACTGAA
* * * *
29697301 TTTGTGATTAGAGTGTCAAACCCTGGGGCCGGTGTGTTATGGTTGAGAAGGTGTGTAAGAATTGT
1 TTTGTGATTAGAGTGTCAAACCCTGAGGCCGGTGTGATATGGTTGAGAAGGTATATAAGAATTGT
* *
29697366 CCTTTAATAGTTTGAGATCTGTGCTTTCCGACTGATTTGATGTTACTACCATTTGCTGAGTTCAA
66 CCTTTAATAGTTCGAGATCTGTGCTTTCCAACTGATTTGATGTTACTACCATTTGCTGAGTTCAA
* * * *
29697431 ATTAATTCTGGGTATGGATTGGTTGACTTTAGATGATACTGTTGTAAATTGCAAAAGAAAGACCA
131 ATTAATTCTGGCTATGGATGGGCTGACTTTACATGATACTGTTGTAAATTGCAAAAGAAAGACCA
29697496 TTGATCTATGGAACCAGAATAATACTAAG
196 TTGATCTATGGAACCAGAATAATACTAAG
* * *
29697525 TTTGTGATTAGAGTGTCAAACCCTTAGGCTGGTGTGATATGGTTGATAAGGTATATAAGAATTGT
1 TTTGTGATTAGAGTGTCAAACCCTGAGGCCGGTGTGATATGGTTGAGAAGGTATATAAGAATTGT
* * *
29697590 CCTTTAATGGTTCGAGATCTGTTCTTTCCAACTGATTTGATGTTACTACCATTTGTTGAGTTCAA
66 CCTTTAATAGTTCGAGATCTGTGCTTTCCAACTGATTTGATGTTACTACCATTTGCTGAGTTCAA
* *
29697655 CTTAATTCTGGCTATGGATGGGCTGACTTTACATGATGA-TGTTGTAAATTGTAAAAGAAAGACC
131 ATTAATTCTGGCTATGGATGGGCTGACTTTACATGAT-ACTGTTGTAAATTGCAAAAGAAAGACC
29697719 ATTGATCTATGGAACCAGAATAAT
195 ATTGATCTATGGAACCAGAATAAT
29697743 GAAGTCATTC
Statistics
Matches: 199, Mismatches: 18, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
224 198 0.99
225 1 0.01
ACGTcount: A:0.28, C:0.13, G:0.23, T:0.36
Consensus pattern (224 bp):
TTTGTGATTAGAGTGTCAAACCCTGAGGCCGGTGTGATATGGTTGAGAAGGTATATAAGAATTGT
CCTTTAATAGTTCGAGATCTGTGCTTTCCAACTGATTTGATGTTACTACCATTTGCTGAGTTCAA
ATTAATTCTGGCTATGGATGGGCTGACTTTACATGATACTGTTGTAAATTGCAAAAGAAAGACCA
TTGATCTATGGAACCAGAATAATACTAAG
Found at i:29710315 original size:24 final size:23
Alignment explanation
Indices: 29710282--29710339 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 23
29710272 AGTTGAAAAG
29710282 TATAA-AATAAAATAAATAATGATA
1 TATAATAATAAAAT-AAT-ATGATA
*
29710306 -ATAATAATAAAATGATATGATA
1 TATAATAATAAAATAATATGATA
29710328 TATATATAATAA
1 TATA-ATAATAA
29710340 TGTTTGATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
22 6 0.20
23 9 0.30
24 15 0.50
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (23 bp):
TATAATAATAAAATAATATGATA
Found at i:29710692 original size:49 final size:48
Alignment explanation
Indices: 29710610--29710767 Score: 273
Period size: 49 Copynumber: 3.2 Consensus size: 48
29710600 CTTACTTTGA
*
29710610 GAATGTGAAAGTG-TATATATGTGATAAGGCCTAATGGCCGATGTGAT
1 GAATGTGAAAGTGTTATATATGTGATAGGGCCTAATGGCCGATGTGAT
29710657 GAATGTGAAAGTGTATATATATGTGATAGGGCCTAATGGCCGATGTGAT
1 GAATGTGAAAGTGT-TATATATGTGATAGGGCCTAATGGCCGATGTGAT
29710706 GAATGTGAAAGTGTGTATATATGTGATAGGGCCTAATGGCCGATGTGAT
1 GAATGTGAAAGTGT-TATATATGTGATAGGGCCTAATGGCCGATGTGAT
29710755 GAATGTGATAAGT
1 GAATGTGA-AAGT
29710768 CCCGAAGGGC
Statistics
Matches: 106, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
47 13 0.12
49 89 0.84
50 4 0.04
ACGTcount: A:0.31, C:0.08, G:0.31, T:0.30
Consensus pattern (48 bp):
GAATGTGAAAGTGTTATATATGTGATAGGGCCTAATGGCCGATGTGAT
Found at i:29710943 original size:37 final size:37
Alignment explanation
Indices: 29710885--29710963 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 37
29710875 CCGAGCTCTA
* * *
29710885 AAGACCCGATGACTACATGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACATGTGGAGATTATGTCCGGGT
* *
29710922 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACATGTGGAGATTATGTCCGGGT
29710959 AAGAC
1 AAGAC
29710964 TTCGTAATAA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACATGTGGAGATTATGTCCGGGT
Found at i:29716298 original size:38 final size:38
Alignment explanation
Indices: 29716247--29716366 Score: 143
Period size: 38 Copynumber: 3.1 Consensus size: 38
29716237 TTTAAACTTA
* *
29716247 GATATAACACCAGCACTAGGCCTGCGGGATTTAAGCCG
1 GATATAATACCAGCACTAAGCCTGCGGGATTTAAGCCG
* *
29716285 GATATAATACCAGCACGAAGCCTGCGGGATTTAACCCG
1 GATATAATACCAGCACTAAGCCTGCGGGATTTAAGCCG
* * *
29716323 GATATAATTCTAGCA-TATAGCCTGCGGGTCTTTAAGCTCG
1 GATATAATACCAGCACTA-AGCCTGCGGG-ATTTAAGC-CG
29716363 GATA
1 GATA
29716367 CACATCAAAT
Statistics
Matches: 70, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
37 1 0.01
38 57 0.81
39 6 0.09
40 6 0.09
ACGTcount: A:0.29, C:0.23, G:0.24, T:0.23
Consensus pattern (38 bp):
GATATAATACCAGCACTAAGCCTGCGGGATTTAAGCCG
Found at i:29718888 original size:48 final size:48
Alignment explanation
Indices: 29718817--29719036 Score: 204
Period size: 48 Copynumber: 4.6 Consensus size: 48
29718807 TGATATGTGT
* *
29718817 GCTAGTGTAAGACCATGTCTGGGACATGGCATCAACCACATTG-CGTGA
1 GCTAGTGTAAGACCATGTCTGGGACATGGCAT-ATCCACATTGACGAGA
* ** *
29718865 GCTAGTGTAAGGCCATGTCTGGGACATGGC--ATCGGCATCGAC-ATCTGA
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATATCCACATTGACGA---GA
* * *
29718913 TCCAGTGTAAGACCATGTCTGGGACATGG-A-ATCGACATTGAGACGAGA
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATATCCACATT--GACGAGA
* * *
29718961 GCTAGTGTCAGACCATGTCTGGGACATGGCAT-TGGCA-TTGTGACGAGA
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATAT-CCACAT-TGACGAGA
29719009 GCTAGTGTAAGACCATGTCTGGGACATG
1 GCTAGTGTAAGACCATGTCTGGGACATG
29719037 CCTTGACATG
Statistics
Matches: 142, Mismatches: 18, Indels: 24
0.77 0.10 0.13
Matches are distributed among these distances:
45 6 0.04
46 1 0.01
48 126 0.89
49 3 0.02
50 5 0.04
51 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.23
Consensus pattern (48 bp):
GCTAGTGTAAGACCATGTCTGGGACATGGCATATCCACATTGACGAGA
Found at i:29718984 original size:96 final size:95
Alignment explanation
Indices: 29718820--29719180 Score: 269
Period size: 96 Copynumber: 3.8 Consensus size: 95
29718810 TATGTGTGCT
* *
29718820 AGTGTAAGACCATGTCTGGGACATGGCATCAACCACATTGCGTGAGCTAGTGTAAGGCCATGTCT
1 AGTGTAAGACCATGTCTGGGACATGGCA-CAACCACATTGCGAGAGCTAGTGTAAGACCATGTCT
* *
29718885 GGGACATGGCATCGGCATCGACATC-TGATCC
65 GGGACATGGCATCGGCATCGACA-CGAGAGCC
* * *
29718916 AGTGTAAGACCATGTCTGGGACATGG-A-ATCGACATTGAGACGAGAGCTAGTGTCAGACCATGT
1 AGTGTAAGACCATGTCTGGGACATGGCACAACCACATT--G-CGAGAGCTAGTGTAAGACCATGT
* * ** *
29718979 CTGGGACATGGCATTGGCATTGTGACGAGAGCT
63 CTGGGACATGGCATCGGCATCGACACGAGAGCC
*** * * *
29719012 AGTGTAAGACCATGTCTGGGACAT-GC-C-TTGACA-T--GTGAGCCAGTATAAGACCATGTCTG
1 AGTGTAAGACCATGTCTGGGACATGGCACAACCACATTGCGAGAGCTAGTGTAAGACCATGTCTG
* * * * * * * *
29719071 GGGCTTAGCATTGGCATTGAGACGAGCGCT
66 GGACATGGCATCGGCATCGACACGAGAGCC
* * * * * *
29719101 AGTGCAAGACTATGTCTAGGATATGGCATCAGCCTCGACA-T--GTGAGCTAGTGTAAGACCATG
1 AGTGTAAGACCATGTCTGGGACATGGCA-CA-AC-C-ACATTGCGAGAGCTAGTGTAAGACCATG
29719163 TCTGGGACATGGCATCGG
62 TCTGGGACATGGCATCGG
29719181 TAATTTACCC
Statistics
Matches: 217, Mismatches: 35, Indels: 26
0.78 0.13 0.09
Matches are distributed among these distances:
89 66 0.30
90 2 0.01
92 1 0.00
93 7 0.03
94 1 0.00
95 9 0.04
96 131 0.60
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.24
Consensus pattern (95 bp):
AGTGTAAGACCATGTCTGGGACATGGCACAACCACATTGCGAGAGCTAGTGTAAGACCATGTCTG
GGACATGGCATCGGCATCGACACGAGAGCC
Found at i:29719103 original size:89 final size:92
Alignment explanation
Indices: 29718970--29719177 Score: 251
Period size: 89 Copynumber: 2.2 Consensus size: 92
29718960 AGCTAGTGTC
* * *
29718970 AGACCATGTCTGGGACATGGCATTGGCATTGTGACGAGAGCTAGTGTAAGACCATGTCT-GG-GA
1 AGACCATGTCTGGGACATAGCATTGGCATTGAGACGAGAGCTAGTGCAAGACCATGTCTAGGAGA
*
29719033 CAT-GCCTTGACATGTGAGCCAGTATA
66 CATAGCCTCGACATGTGAGCCAGTATA
* * * *
29719059 AGACCATGTCTGGGGCTTAGCATTGGCATTGAGACGAGCGCTAGTGCAAGACTATGTCTAGGATA
1 AGACCATGTCTGGGACATAGCATTGGCATTGAGACGAGAGCTAGTGCAAGACCATGTCTAGG--A
* * *
29719124 TGGCATCAGCCTCGACATGTGAGCTAGTGTA
64 -GACAT-AGCCTCGACATGTGAGCCAGTATA
*
29719155 AGACCATGTCTGGGACATGGCAT
1 AGACCATGTCTGGGACATAGCAT
29719178 CGGTAATTTA
Statistics
Matches: 98, Mismatches: 14, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
89 52 0.53
90 2 0.02
94 4 0.04
96 40 0.41
ACGTcount: A:0.25, C:0.20, G:0.30, T:0.25
Consensus pattern (92 bp):
AGACCATGTCTGGGACATAGCATTGGCATTGAGACGAGAGCTAGTGCAAGACCATGTCTAGGAGA
CATAGCCTCGACATGTGAGCCAGTATA
Found at i:29719127 original size:137 final size:140
Alignment explanation
Indices: 29718817--29719173 Score: 350
Period size: 137 Copynumber: 2.5 Consensus size: 140
29718807 TGATATGTGT
* * * * *
29718817 GCTAGTGTAAGACCATGTCTGGGACATGGCATCA--A-CCACATTGCGTGAGCTAGTGTAAGGCC
1 GCTAGTGTCAGACCATGTCTAGGACATGGCATCAGCATCGACA---CGAGAGCTAGTGTAAGACC
* * *
29718879 ATGTCTGGGACATGGCATCGGCATCGACATCTGATCCAGTGTAAGACCATGTCTGGGACATGGAA
63 ATGTCTGGGACAT-G-A-C-GCATCGACATCTGAGCCAGTATAAGACCATGTCTGGGACATAGAA
29718944 TCGACATTGAGACGAGA
124 TCGACATTGAGACGAGA
* ** * **
29718961 GCTAGTGTCAGACCATGTCTGGGACATGGCATTGGCATTGTGACGAGAGCTAGTGTAAGACCATG
1 GCTAGTGTCAGACCATGTCTAGGACATGGCATCAGCATCGACACGAGAGCTAGTGTAAGACCATG
* * * * * * *
29719026 TCTGGGACATG-C-C-TTGACATGTGAGCCAGTATAAGACCATGTCTGGGGCTTAGCATTGGCAT
66 TCTGGGACATGACGCATCGACATCTGAGCCAGTATAAGACCATGTCTGGGACATAGAATCGACAT
*
29719088 TGAGACGAGC
131 TGAGACGAGA
* * * * *
29719098 GCTAGTG-CAAGACTATGTCTAGGATATGGCATCAGCCTCGACATGTGAGCTAGTGTAAGACCAT
1 GCTAGTGTC-AGACCATGTCTAGGACATGGCATCAGCATCGACACGAGAGCTAGTGTAAGACCAT
29719162 GTCTGGGACATG
65 GTCTGGGACATG
29719174 GCATCGGTAA
Statistics
Matches: 178, Mismatches: 31, Indels: 15
0.79 0.14 0.07
Matches are distributed among these distances:
136 1 0.01
137 111 0.62
138 1 0.01
140 1 0.01
143 1 0.01
144 61 0.34
146 1 0.01
147 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.24
Consensus pattern (140 bp):
GCTAGTGTCAGACCATGTCTAGGACATGGCATCAGCATCGACACGAGAGCTAGTGTAAGACCATG
TCTGGGACATGACGCATCGACATCTGAGCCAGTATAAGACCATGTCTGGGACATAGAATCGACAT
TGAGACGAGA
Found at i:29731490 original size:46 final size:46
Alignment explanation
Indices: 29731341--29731516 Score: 169
Period size: 46 Copynumber: 3.8 Consensus size: 46
29731331 GGGTTATTGT
* * * * * ** *
29731341 GAGCTAGTGTAAGGCATGTCTGGGACATGCATTGACCA-CATTATGA
1 GAGCCAGTGTAAGACATGTCTGGGACATGCATCG-GCATTAAGACGA
*
29731387 GAGTCAGTGTAAGACCATGTCTGGGACATGACATCGGCATTAAGACGA
1 GAGCCAGTGTAAGA-CATGTCTGGGACATG-CATCGGCATTAAGACGA
* *
29731435 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCT-AGACGTA
1 GAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCAT-TAAGACG-A
* *
29731482 -AGCCAGTGTAAGACATGTTTGGGACATACATCGGC
1 GAGCCAGTGTAAGACATGTCTGGGACATGCATCGGC
29731517 TATGAGATGT
Statistics
Matches: 110, Mismatches: 15, Indels: 10
0.81 0.11 0.07
Matches are distributed among these distances:
46 56 0.51
47 34 0.31
48 20 0.18
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.23
Consensus pattern (46 bp):
GAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCATTAAGACGA
Found at i:29734237 original size:28 final size:27
Alignment explanation
Indices: 29734180--29734331 Score: 232
Period size: 27 Copynumber: 5.6 Consensus size: 27
29734170 TAAATTGTGC
* *
29734180 AGCACTAAGTGTGCGAATTGAATATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
29734207 AGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAG-TTGACTATGT
29734235 AGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
*
29734262 AGCACTAAGTGTGCGAGTATGATTATGT
1 AGCACTAAGTGTGCGAGT-TGACTATGT
* *
29734290 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGTTGACTATGT
*
29734317 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
29734332 GACTTAATAT
Statistics
Matches: 118, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
27 66 0.56
28 52 0.44
ACGTcount: A:0.28, C:0.13, G:0.29, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGTTGACTATGT
Found at i:29734245 original size:55 final size:55
Alignment explanation
Indices: 29734180--29734331 Score: 241
Period size: 55 Copynumber: 2.8 Consensus size: 55
29734170 TAAATTGTGC
* *
29734180 AGCACTAAGTGTGCGAATTGAATATGTAGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAGTTGAATATGTAGCACTAAGTGTGCGAGTATGACTATGT
* *
29734235 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTATGATTATGT
1 AGCACTAAGTGTGCGAGTTGAATATGTAGCACTAAGTGTGCGAGTATGACTATGT
* * *
29734290 AGCACTAAGTGTGCGAGTTGATTATATAGCACTGAGTGTGCG
1 AGCACTAAGTGTGCGAGTTGAATATGTAGCACTAAGTGTGCG
29734332 GACTTAATAT
Statistics
Matches: 90, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
55 90 1.00
ACGTcount: A:0.28, C:0.13, G:0.29, T:0.30
Consensus pattern (55 bp):
AGCACTAAGTGTGCGAGTTGAATATGTAGCACTAAGTGTGCGAGTATGACTATGT
Found at i:29739493 original size:24 final size:24
Alignment explanation
Indices: 29739401--29739529 Score: 75
Period size: 24 Copynumber: 5.3 Consensus size: 24
29739391 TCTGCTCTTT
* *
29739401 CGAGCT-ATGAATAGTAAGCTCCTC
1 CGAGCTGA-GAATAGTAAGCTCATA
* *
29739425 CTGAGCTGAGGACAGTAAGCTC-TA
1 C-GAGCTGAGAATAGTAAGCTCATA
* * * *
29739449 TTGATCT-AAAACAGTAAGCTCATA
1 -CGAGCTGAGAATAGTAAGCTCATA
*
29739473 CGAGCTGAGAATAGTAAGCTCTTA
1 CGAGCTGAGAATAGTAAGCTCATA
* * *
29739497 CGAGTTGATATATCGGTAAGCTCATA
1 CGAGCTGAGA-AT-AGTAAGCTCATA
*
29739523 TGAGCTG
1 CGAGCTG
29739530 TGGTGAGTCC
Statistics
Matches: 80, Mismatches: 18, Indels: 12
0.73 0.16 0.11
Matches are distributed among these distances:
23 16 0.20
24 30 0.38
25 18 0.22
26 16 0.20
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (24 bp):
CGAGCTGAGAATAGTAAGCTCATA
Found at i:29744165 original size:37 final size:37
Alignment explanation
Indices: 29744101--29744183 Score: 103
Period size: 37 Copynumber: 2.2 Consensus size: 37
29744091 TATACCTCAG
* *
29744101 AATTTTTCAATTTTTACAAAATAGTCCCTAAAATTCA
1 AATTTTACAATTTTTACAAAATAGTCCCTAAAATCCA
* ** *
29744138 AATTTTACAATTTTTACGATTTTGTCCCTAAAATCCA
1 AATTTTACAATTTTTACAAAATAGTCCCTAAAATCCA
*
29744175 AAATTTACA
1 AATTTTACA
29744184 CAATATTACA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.39, C:0.17, G:0.04, T:0.41
Consensus pattern (37 bp):
AATTTTACAATTTTTACAAAATAGTCCCTAAAATCCA
Found at i:29747907 original size:42 final size:43
Alignment explanation
Indices: 29747857--29747962 Score: 119
Period size: 42 Copynumber: 2.5 Consensus size: 43
29747847 TGATATTTAT
*
29747857 GTGTAAGACCATGTCTGGGACA-TCGGCATCG-TATTTGATTTC
1 GTGTAAGACCATGTCTGGGACAGT-GGCATCGATATTTGATTAC
* *
29747899 GTGTAAGACCCTGTTTAGGG-CAGTGGCATCGATATTTGATTAC
1 GTGTAAGACCATGTCT-GGGACAGTGGCATCGATATTTGATTAC
* * *
29747942 ATGTAAAACCACGTCTGGGAC
1 GTGTAAGACCATGTCTGGGAC
29747963 GTTGACATTG
Statistics
Matches: 52, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
42 26 0.50
43 26 0.50
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.30
Consensus pattern (43 bp):
GTGTAAGACCATGTCTGGGACAGTGGCATCGATATTTGATTAC
Found at i:29755104 original size:43 final size:42
Alignment explanation
Indices: 29754988--29755105 Score: 121
Period size: 43 Copynumber: 2.8 Consensus size: 42
29754978 GATTTGAGAT
* * * *
29754988 TTACGTGTAAGACCATGTTTGGGACATCGGCATCATATTTGG
1 TTACGTGTAAGACCATGTCTGGGACGTTGGCATCATATTTGA
** * *
29755030 TTTTGTGTAAGACCCTGTCTGGGGCAG-TGGCATCAATATTTGA
1 TTACGTGTAAGACCATGTCTGGGAC-GTTGGCATC-ATATTTGA
* *
29755073 TTACATGTAAGACCATATCTGGGACGTTGGCAT
1 TTACGTGTAAGACCATGTCTGGGACGTTGGCAT
29755106 TGTACGAGCT
Statistics
Matches: 59, Mismatches: 14, Indels: 5
0.76 0.18 0.06
Matches are distributed among these distances:
42 27 0.46
43 32 0.54
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.33
Consensus pattern (42 bp):
TTACGTGTAAGACCATGTCTGGGACGTTGGCATCATATTTGA
Found at i:29757082 original size:26 final size:24
Alignment explanation
Indices: 29757050--29757102 Score: 70
Period size: 24 Copynumber: 2.1 Consensus size: 24
29757040 AAATTTTTAT
29757050 CAAATTAATCATTTAAAATCATCCAC
1 CAAATTAATCA--TAAAATCATCCAC
* *
29757076 CAAATTATTCATAAAATCATTCAC
1 CAAATTAATCATAAAATCATCCAC
29757100 CAA
1 CAA
29757103 TCATATTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 15 0.60
26 10 0.40
ACGTcount: A:0.47, C:0.23, G:0.00, T:0.30
Consensus pattern (24 bp):
CAAATTAATCATAAAATCATCCAC
Found at i:29761365 original size:6 final size:6
Alignment explanation
Indices: 29761354--29761425 Score: 76
Period size: 6 Copynumber: 11.8 Consensus size: 6
29761344 AACCAAAATG
* *
29761354 AGAATC AGAATC AAAATC AGTAA-C AGAATC AGAATC AGAATC AGAATT
1 AGAATC AGAATC AGAATC AG-AATC AGAATC AGAATC AGAATC AGAATC
*
29761402 AG-GTGAC AGAATC AGAATC AGAAT
1 AGAAT--C AGAATC AGAATC AGAAT
29761426 GTGAATGCAA
Statistics
Matches: 55, Mismatches: 6, Indels: 10
0.77 0.08 0.14
Matches are distributed among these distances:
5 3 0.05
6 47 0.85
7 4 0.07
8 1 0.02
ACGTcount: A:0.50, C:0.14, G:0.18, T:0.18
Consensus pattern (6 bp):
AGAATC
Found at i:29761368 original size:18 final size:18
Alignment explanation
Indices: 29761333--29761400 Score: 75
Period size: 18 Copynumber: 3.8 Consensus size: 18
29761323 AAGAAACATT
** *
29761333 ATCAGAATTGGAACCAAA
1 ATCAGAATCAGAATCAAA
*
29761351 ATGAGAATCAGAATCAAA
1 ATCAGAATCAGAATCAAA
*
29761369 ATCAGTAA-CAGAATCAGA
1 ATCAG-AATCAGAATCAAA
29761387 ATCAGAATCAGAAT
1 ATCAGAATCAGAAT
29761401 TAGGTGACAG
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
17 2 0.05
18 38 0.90
19 2 0.05
ACGTcount: A:0.51, C:0.15, G:0.16, T:0.18
Consensus pattern (18 bp):
ATCAGAATCAGAATCAAA
Found at i:29761414 original size:31 final size:30
Alignment explanation
Indices: 29761354--29761425 Score: 108
Period size: 31 Copynumber: 2.4 Consensus size: 30
29761344 AACCAAAATG
29761354 AGAATCAGAATCAAAATCAGTAACAGAATC
1 AGAATCAGAATCAAAATCAGTAACAGAATC
* * *
29761384 AGAATCAGAATCAGAATTAGGTGACAGAATC
1 AGAATCAGAATCAAAATCA-GTAACAGAATC
29761415 AGAATCAGAAT
1 AGAATCAGAAT
29761426 GTGAATGCAA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
30 17 0.45
31 21 0.55
ACGTcount: A:0.50, C:0.14, G:0.18, T:0.18
Consensus pattern (30 bp):
AGAATCAGAATCAAAATCAGTAACAGAATC
Found at i:29761613 original size:27 final size:27
Alignment explanation
Indices: 29761543--29761616 Score: 73
Period size: 27 Copynumber: 2.8 Consensus size: 27
29761533 AGCATGGCTG
* *
29761543 CCAGAA-CAGAT-ATCGTGACAGAGTCA
1 CCAGAATCAGATAAT-GTGGCAGAGCCA
* *
29761569 CCAG-ATACACATATTGTGGCAGAGCCA
1 CCAGAAT-CAGATAATGTGGCAGAGCCA
29761596 CCAGAATCAGATAATGTGGCA
1 CCAGAATCAGATAATGTGGCA
29761617 AACCCACCTA
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
25 1 0.03
26 4 0.11
27 30 0.79
28 3 0.08
ACGTcount: A:0.36, C:0.23, G:0.23, T:0.18
Consensus pattern (27 bp):
CCAGAATCAGATAATGTGGCAGAGCCA
Found at i:29761966 original size:27 final size:26
Alignment explanation
Indices: 29761927--29762009 Score: 121
Period size: 27 Copynumber: 3.1 Consensus size: 26
29761917 TCGATCGGTC
* *
29761927 AACAGATATTGTGACAGAGTCACCAG
1 AACAGATATTGTGGCAGAGCCACCAG
29761953 ATACAGATATTGTGGCAGAGCCACCAG
1 A-ACAGATATTGTGGCAGAGCCACCAG
*
29761980 AACAGATATTTGTGGCATAGCCACCAG
1 AACAGATA-TTGTGGCAGAGCCACCAG
29762007 AAC
1 AAC
29762010 GCTTCCTCCA
Statistics
Matches: 52, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
26 8 0.15
27 44 0.85
ACGTcount: A:0.36, C:0.22, G:0.23, T:0.19
Consensus pattern (26 bp):
AACAGATATTGTGGCAGAGCCACCAG
Found at i:29762238 original size:27 final size:27
Alignment explanation
Indices: 29762208--29762395 Score: 232
Period size: 27 Copynumber: 7.0 Consensus size: 27
29762198 GCGGCAAAAT
* * * *
29762208 GGTAATTTTACCCCACAAAGGTATCTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
29762235 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
29762262 GATATTTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* **
29762289 GATAATTCTACCCTACGGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
29762316 GGTAATTCTACCCTATAAGGGTATTTT
1 GGTAATTCTACCCTACAAGGGTATTTC
* * *
29762343 AGTAATTCTACCCTATAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
29762370 GGTAATTCTACCCTACAGGGGTATTT
1 GGTAATTCTACCCTACAAGGGTATTT
29762396 TAGTAATTTC
Statistics
Matches: 140, Mismatches: 21, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 140 1.00
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.35
Consensus pattern (27 bp):
GGTAATTCTACCCTACAAGGGTATTTC
Found at i:29762396 original size:54 final size:54
Alignment explanation
Indices: 29762208--29762403 Score: 259
Period size: 54 Copynumber: 3.6 Consensus size: 54
29762198 GCGGCAAAAT
* * * * **
29762208 GGTAATTTTACCCCACAAAGGTATCTCGGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTTAGTAATTCTACCCTACAGGGGTATTTC
* * * *
29762262 GATATTTCTACCCTACAAGGGTA-TTTCGATAATTCTACCCTACGGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTTAG-TAATTCTACCCTACAGGGGTATTTC
* *
29762316 GGTAATTCTACCCTATAAGGGTATTTTAGTAATTCTACCCTATAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTTAGTAATTCTACCCTACAGGGGTATTTC
*
29762370 GGTAATTCTACCCTACAGGGGTATTTTAGTAATT
1 GGTAATTCTACCCTACAAGGGTATTTTAGTAATT
29762404 TCACAATTGA
Statistics
Matches: 123, Mismatches: 17, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
53 2 0.02
54 117 0.95
55 4 0.03
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.36
Consensus pattern (54 bp):
GGTAATTCTACCCTACAAGGGTATTTTAGTAATTCTACCCTACAGGGGTATTTC
Found at i:29762442 original size:27 final size:27
Alignment explanation
Indices: 29762412--29762832 Score: 464
Period size: 27 Copynumber: 15.7 Consensus size: 27
29762402 TTTCACAATT
**
29762412 GAGGGTAAAACAGTAATTCTGTAAATC
1 GAGGGTAAAATGGTAATTCTGTAAATC
*
29762439 GAGGGTAAAATGATAATT-TCGTAAATC
1 GAGGGTAAAATGGTAATTCT-GTAAATC
* *** *
29762466 GAGTGTAAACCAGTAATTCTATAAATC
1 GAGGGTAAAATGGTAATTCTGTAAATC
* * **
29762493 GA-GGTAAAACGGTAATTTTACAAATC
1 GAGGGTAAAATGGTAATTCTGTAAATC
*
29762519 GAGGGTAAAATAGTAATTCTGTAAATC
1 GAGGGTAAAATGGTAATTCTGTAAATC
* *
29762546 AAGGGTAAAATAGTAATTCTGTAAA-C
1 GAGGGTAAAATGGTAATTCTGTAAATC
* *
29762572 TGAGGGTAAAACGATAATTCTGTAAATC
1 -GAGGGTAAAATGGTAATTCTGTAAATC
29762600 GAGGGTAAAATGGTAATTCTGTAAA-C
1 GAGGGTAAAATGGTAATTCTGTAAATC
* *
29762626 TGAGGGTAAAACGATAATTCTGTAAATC
1 -GAGGGTAAAATGGTAATTCTGTAAATC
* * * ** *
29762654 GAGGGGAAAAT-ATGAATTTTACAAATT
1 GAGGGTAAAATGGT-AATTCTGTAAATC
29762681 GAGGGTAAAATGGTAATTCTGTAAA-C
1 GAGGGTAAAATGGTAATTCTGTAAATC
*
29762707 TGAGGGTAAAATAGTAATTCTGTAAA-C
1 -GAGGGTAAAATGGTAATTCTGTAAATC
29762734 TGAGGGTAAAATGGTAATTCTGTAAATC
1 -GAGGGTAAAATGGTAATTCTGTAAATC
*
29762762 AAGGGTAAAATGGTAATTCTGTAAA-C
1 GAGGGTAAAATGGTAATTCTGTAAATC
29762788 TGAGGGTAAAATGGTAATT-TGTAAATC
1 -GAGGGTAAAATGGTAATTCTGTAAATC
*
29762815 GAGGGTAAAACGGTAATT
1 GAGGGTAAAATGGTAATT
29762833 TTAAAATTAA
Statistics
Matches: 336, Mismatches: 45, Indels: 27
0.82 0.11 0.07
Matches are distributed among these distances:
26 50 0.15
27 281 0.84
28 5 0.01
ACGTcount: A:0.40, C:0.08, G:0.23, T:0.29
Consensus pattern (27 bp):
GAGGGTAAAATGGTAATTCTGTAAATC
Found at i:29762877 original size:25 final size:25
Alignment explanation
Indices: 29762848--29762927 Score: 89
Period size: 25 Copynumber: 3.4 Consensus size: 25
29762838 ATTAAATATC
*
29762848 GTAATCGGGGTAAAACGGTAATTCT
1 GTAATCGAGGTAAAACGGTAATTCT
*
29762873 GTAATCGAGGTAAAAC-ATAA-T-T
1 GTAATCGAGGTAAAACGGTAATTCT
*
29762895 -AAAT-GAGGTAAAACGGTAATTCT
1 GTAATCGAGGTAAAACGGTAATTCT
29762918 GTAAATCGAG
1 GT-AATCGAG
29762928 AGTACTTTGG
Statistics
Matches: 44, Mismatches: 5, Indels: 11
0.73 0.08 0.18
Matches are distributed among these distances:
20 10 0.23
21 6 0.14
22 2 0.05
23 2 0.05
24 3 0.07
25 18 0.41
26 3 0.07
ACGTcount: A:0.40, C:0.10, G:0.24, T:0.26
Consensus pattern (25 bp):
GTAATCGAGGTAAAACGGTAATTCT
Found at i:29764950 original size:30 final size:29
Alignment explanation
Indices: 29764914--29765032 Score: 132
Period size: 30 Copynumber: 3.9 Consensus size: 29
29764904 AAGAAACATT
* * *
29764914 ATCAGAATTGGAACCAAAATGAGAATCAGA
1 ATCAGAATTGTAA-CAGAATCAGAATCAGA
*
29764944 ATCAGAATCAGTAACAGAATCAGAATCAGA
1 ATCAGAAT-TGTAACAGAATCAGAATCAGA
29764974 ATCA-ATATTAGTAACAGAATCAGAATCAGA
1 ATCAGA-ATT-GTAACAGAATCAGAATCAGA
*
29765004 ATCAGAATTAGGTGACAGAATCAGAATCA
1 ATCAGAATT--GTAACAGAATCAGAATCA
29765033 AATGTGAATG
Statistics
Matches: 77, Mismatches: 7, Indels: 9
0.83 0.08 0.10
Matches are distributed among these distances:
29 1 0.01
30 55 0.71
31 21 0.27
ACGTcount: A:0.49, C:0.14, G:0.18, T:0.19
Consensus pattern (29 bp):
ATCAGAATTGTAACAGAATCAGAATCAGA
Found at i:29765031 original size:6 final size:6
Alignment explanation
Indices: 29764935--29765011 Score: 97
Period size: 6 Copynumber: 12.8 Consensus size: 6
29764925 AACCAAAATG
*
29764935 AGAATC AGAATC AGAATC AGTAA-C AGAATC AGAATC AGAATC A-ATATT
1 AGAATC AGAATC AGAATC AG-AATC AGAATC AGAATC AGAATC AGA-ATC
29764983 AGTAA-C AGAATC AGAATC AGAATC AGAAT
1 AG-AATC AGAATC AGAATC AGAATC AGAAT
29765012 TAGGTGACAG
Statistics
Matches: 63, Mismatches: 2, Indels: 12
0.82 0.03 0.16
Matches are distributed among these distances:
5 5 0.08
6 54 0.86
7 3 0.05
8 1 0.02
ACGTcount: A:0.51, C:0.14, G:0.16, T:0.19
Consensus pattern (6 bp):
AGAATC
Found at i:29765189 original size:27 final size:26
Alignment explanation
Indices: 29765152--29765217 Score: 78
Period size: 27 Copynumber: 2.5 Consensus size: 26
29765142 CAGCATGGTG
*
29765152 CCAGAACAGATATCATGACAGAGTCA
1 CCAGAACAGATATCATGACAGAGCCA
** *
29765178 CCAGATACAGATATTGTGGCAGAGCCA
1 CCAGA-ACAGATATCATGACAGAGCCA
29765205 CCAGAATCAGATA
1 CCAGAA-CAGATA
29765218 ATGTGGCAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
26 6 0.18
27 28 0.82
ACGTcount: A:0.39, C:0.23, G:0.21, T:0.17
Consensus pattern (26 bp):
CCAGAACAGATATCATGACAGAGCCA
Found at i:29765222 original size:27 final size:27
Alignment explanation
Indices: 29765170--29765225 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
29765160 GATATCATGA
* *
29765170 CAGAGTCACCAGATACAGATATTGTGG
1 CAGAGCCACCAGATACAGATAATGTGG
29765197 CAGAGCCACCAGA-ATCAGATAATGTGG
1 CAGAGCCACCAGATA-CAGATAATGTGG
29765224 CA
1 CA
29765226 AACCCACCTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 1 0.04
27 25 0.96
ACGTcount: A:0.36, C:0.21, G:0.25, T:0.18
Consensus pattern (27 bp):
CAGAGCCACCAGATACAGATAATGTGG
Found at i:29765232 original size:27 final size:27
Alignment explanation
Indices: 29765176--29765233 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
29765166 ATGACAGAGT
* * *
29765176 CACCAGATACAGATATTGTGGCAGAGC
1 CACCAGATACAGATAATGTGGCAAACC
29765203 CACCAGA-ATCAGATAATGTGGCAAACC
1 CACCAGATA-CAGATAATGTGGCAAACC
29765230 CACC
1 CACC
29765234 TAACAGATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 1 0.04
27 26 0.96
ACGTcount: A:0.36, C:0.28, G:0.21, T:0.16
Consensus pattern (27 bp):
CACCAGATACAGATAATGTGGCAAACC
Found at i:29765557 original size:27 final size:26
Alignment explanation
Indices: 29765516--29765595 Score: 97
Period size: 27 Copynumber: 3.0 Consensus size: 26
29765506 ATCGGTCAAT
* *
29765516 AGATATTGTGACAGAGTCACCAGATAC
1 AGATATTGTGGCAGAGCCACCAGA-AC
*
29765543 AGATATTGTGGCAGAGCCACTAGAAC
1 AGATATTGTGGCAGAGCCACCAGAAC
* *
29765569 AGATATTTATGGCATAGCCACCAGAAC
1 AGATA-TTGTGGCAGAGCCACCAGAAC
29765596 GCTTCCTCCG
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
26 7 0.15
27 39 0.85
ACGTcount: A:0.36, C:0.20, G:0.23, T:0.21
Consensus pattern (26 bp):
AGATATTGTGGCAGAGCCACCAGAAC
Found at i:29765849 original size:27 final size:27
Alignment explanation
Indices: 29765811--29765978 Score: 230
Period size: 27 Copynumber: 6.3 Consensus size: 27
29765801 TACCCCAAAA
*
29765811 GGTATCTCGGTAATTCTACCCTACAGG
1 GGTATTTCGGTAATTCTACCCTACAGG
* *
29765838 GGTATTTCGGTATTTCTACCCTACAAG
1 GGTATTTCGGTAATTCTACCCTACAGG
*
29765865 GGTATTTCGATAATTCTACCCTAC-GG
1 GGTATTTCGGTAATTCTACCCTACAGG
* * *
29765891 GGTATTTCAGTAATTCTACCCTATAAG
1 GGTATTTCGGTAATTCTACCCTACAGG
** *
29765918 GGTATTTTAGTAATTCTACCCTATAGG
1 GGTATTTCGGTAATTCTACCCTACAGG
*
29765945 GGTATTTCGGTAATTCTACCCTATAGG
1 GGTATTTCGGTAATTCTACCCTACAGG
29765972 GGTATTT
1 GGTATTT
29765979 TAGTAATTTC
Statistics
Matches: 126, Mismatches: 14, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
26 22 0.17
27 104 0.83
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.37
Consensus pattern (27 bp):
GGTATTTCGGTAATTCTACCCTACAGG
Found at i:29765881 original size:54 final size:54
Alignment explanation
Indices: 29765793--29765978 Score: 243
Period size: 53 Copynumber: 3.5 Consensus size: 54
29765783 GGGGTAAAAT
* * * * *
29765793 GGTAATTTTACCCCA-AAAGGTATCTCGGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTATAAGGGTATTTCGATAATTCTACCCTACAGGGGTATTTC
* *
29765846 GGTATTTCTACCCTACAAGGGTATTTCGATAATTCTACCCTAC-GGGGTATTTC
1 GGTAATTCTACCCTATAAGGGTATTTCGATAATTCTACCCTACAGGGGTATTTC
* * *
29765899 AGTAATTCTACCCTATAAGGGTATTT-TAGTAATTCTACCCTATAGGGGTATTTC
1 GGTAATTCTACCCTATAAGGGTATTTCGA-TAATTCTACCCTACAGGGGTATTTC
*
29765953 GGTAATTCTACCCTATAGGGGTATTT
1 GGTAATTCTACCCTATAAGGGTATTT
29765979 TAGTAATTTC
Statistics
Matches: 117, Mismatches: 13, Indels: 5
0.87 0.10 0.04
Matches are distributed among these distances:
52 1 0.01
53 58 0.50
54 58 0.50
ACGTcount: A:0.25, C:0.20, G:0.19, T:0.36
Consensus pattern (54 bp):
GGTAATTCTACCCTATAAGGGTATTTCGATAATTCTACCCTACAGGGGTATTTC
Found at i:29765921 original size:80 final size:81
Alignment explanation
Indices: 29765811--29765986 Score: 237
Period size: 80 Copynumber: 2.2 Consensus size: 81
29765801 TACCCCAAAA
* * * * *
29765811 GGTATCTCGGTAATTCTACCCTACAGGGGTATTTCGGTATTTCTACCCTACAAGGGTATTTCGAT
1 GGTATTTCAGTAATTCTACCCTACAAGGGTATTTCAGTAATTCTACCCTACAAGGGTATTTCGAT
*
29765876 AATTCTACCCTA-CGG
66 AATTCTACCCTATAGG
* * * * *
29765891 GGTATTTCAGTAATTCTACCCTATAAGGGTATTTTAGTAATTCTACCCTATAGGGGTATTTCGGT
1 GGTATTTCAGTAATTCTACCCTACAAGGGTATTTCAGTAATTCTACCCTACAAGGGTATTTCGAT
29765956 AATTCTACCCTATAGG
66 AATTCTACCCTATAGG
*
29765972 GGTATTTTAGTAATT
1 GGTATTTCAGTAATT
29765987 TCACAATTGA
Statistics
Matches: 83, Mismatches: 12, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
80 67 0.81
81 16 0.19
ACGTcount: A:0.24, C:0.19, G:0.19, T:0.38
Consensus pattern (81 bp):
GGTATTTCAGTAATTCTACCCTACAAGGGTATTTCAGTAATTCTACCCTACAAGGGTATTTCGAT
AATTCTACCCTATAGG
Found at i:29766001 original size:107 final size:107
Alignment explanation
Indices: 29765820--29766015 Score: 245
Period size: 107 Copynumber: 1.8 Consensus size: 107
29765810 AGGTATCTCG
* * *
29765820 GTAATTCTACCCTACAGGGGTATTTCGGTATTTCTACCCTACAAGGGTATTTCGATAATTCTACC
1 GTAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCCTACAAGGGTATTTAGATAATTCTACA
* ***
29765885 CTACGGGGTATTTCAGTAATTCTACCCTATAAGGGTATTTTA
66 ATACGGGGTAAAACAGTAATTCTACCCTATAAGGGTATTTTA
* * *
29765927 GTAATTCTACCCTATAGGGGTATTTCGGTAATTCTACCCTATAGGGGTATTTTAG-TAATT-TCA
1 GTAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCCTACAAGGGTA-TTTAGATAATTCT-A
*
29765990 CAAT-TGAGGGTAAAACAGTAATTCTA
64 CAATACG-GGGTAAAACAGTAATTCTA
29766016 TAAATGAGGG
Statistics
Matches: 75, Mismatches: 11, Indels: 6
0.82 0.12 0.07
Matches are distributed among these distances:
106 2 0.03
107 69 0.92
108 4 0.05
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (107 bp):
GTAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCCTACAAGGGTATTTAGATAATTCTACA
ATACGGGGTAAAACAGTAATTCTACCCTATAAGGGTATTTTA
Found at i:29766010 original size:80 final size:80
Alignment explanation
Indices: 29765851--29766015 Score: 190
Period size: 80 Copynumber: 2.1 Consensus size: 80
29765841 ATTTCGGTAT
* **
29765851 TTCTACCCTACAAGGGTATTTCGATAATTCTACCCTACGGGGTATTTCAGTAATTCTACCCTATA
1 TTCTACCCTACAAGGGTATTTCGATAATTCTACCCTAAGGGGTATTTCAGTAATTCTACAATATA
****
29765916 AGGGTATTTTAGTAA
66 AGGGTAAAACAGTAA
* * * *
29765931 TTCTACCCTATAGGGGTATTTCGGTAATTCTACCCTATAGGGGTATTTTAGTAATT-TCACAAT-
1 TTCTACCCTACAAGGGTATTTCGATAATTCTACCCTA-AGGGGTATTTCAGTAATTCT-ACAATA
*
29765994 TGAGGGTAAAACAGTAA
64 TAAGGGTAAAACAGTAA
29766011 TTCTA
1 TTCTA
29766016 TAAATGAGGG
Statistics
Matches: 71, Mismatches: 12, Indels: 4
0.82 0.14 0.05
Matches are distributed among these distances:
80 52 0.73
81 19 0.27
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (80 bp):
TTCTACCCTACAAGGGTATTTCGATAATTCTACCCTAAGGGGTATTTCAGTAATTCTACAATATA
AGGGTAAAACAGTAA
Found at i:29766064 original size:27 final size:27
Alignment explanation
Indices: 29765995--29766531 Score: 553
Period size: 27 Copynumber: 20.1 Consensus size: 27
29765985 TTTCACAATT
*
29765995 GAGGGTAAAACAGTAATTCTATAAAT-
1 GAGGGTAAAACAGTAATTCTGTAAATC
* *
29766021 GAGGGTAAAAC-GATAATTTTGTAAACC
1 GAGGGTAAAACAG-TAATTCTGTAAATC
*
29766048 GAGGGT-AAACTAGTAATTCTATAAATC
1 GAGGGTAAAAC-AGTAATTCTGTAAATC
* * **
29766075 GAGGGTAAAA-GGTAATTTTACAAATC
1 GAGGGTAAAACAGTAATTCTGTAAATC
* *
29766101 GAGGGTAAAATAGTAATTCTATAAATC
1 GAGGGTAAAACAGTAATTCTGTAAATC
29766128 GAGGGTAAAACAGTAATTCTGTAAA-C
1 GAGGGTAAAACAGTAATTCTGTAAATC
*
29766154 TGAGGGTAAAAC-GATAATTCTATAAATC
1 -GAGGGTAAAACAG-TAATTCTGTAAATC
**
29766182 GAGGGTAAAATGGTAATTCTGTAAA-C
1 GAGGGTAAAACAGTAATTCTGTAAATC
*
29766208 TGAGGGTAAAACGGTAATTCTGTAAATC
1 -GAGGGTAAAACAGTAATTCTGTAAATC
* ** *
29766236 GAGGGTAAAACAGTAATTTTACAAATT
1 GAGGGTAAAACAGTAATTCTGTAAATC
*
29766263 GAGGGTAAAACGGTAATTCTGTAAATC
1 GAGGGTAAAACAGTAATTCTGTAAATC
* * *
29766290 AAGGGT-AAATAGTAATTCTGTTAA-C
1 GAGGGTAAAACAGTAATTCTGTAAATC
* **
29766315 TAAGGGTAAAATGGTAATTCTGTAAATC
1 -GAGGGTAAAACAGTAATTCTGTAAATC
**
29766343 GAGGGTAAAATGGTAATTCTGTAAA-C
1 GAGGGTAAAACAGTAATTCTGTAAATC
*
29766369 TGAGGGTAAAACGGTAATTCTGTAAATC
1 -GAGGGTAAAACAGTAATTCTGTAAATC
* * * **
29766397 GATGGTAAAACGGTAATTTTAAAAATC
1 GAGGGTAAAACAGTAATTCTGTAAATC
*
29766424 GA-GGTAAAAC-GATAATTCTATAAATC
1 GAGGGTAAAACAG-TAATTCTGTAAATC
29766450 GAGGGTAAAAC-GTAATTCTGTAAATC
1 GAGGGTAAAACAGTAATTCTGTAAATC
* **
29766476 GAGGGTAAAACAGTAATTTTACAAAT-
1 GAGGGTAAAACAGTAATTCTGTAAATC
* *
29766502 GAGGGTAAAACGGTAATTCTATAAATC
1 GAGGGTAAAACAGTAATTCTGTAAATC
29766529 GAG
1 GAG
29766532 AGTACTTTGG
Statistics
Matches: 441, Mismatches: 49, Indels: 41
0.83 0.09 0.08
Matches are distributed among these distances:
25 3 0.01
26 142 0.32
27 287 0.65
28 9 0.02
ACGTcount: A:0.41, C:0.09, G:0.22, T:0.28
Consensus pattern (27 bp):
GAGGGTAAAACAGTAATTCTGTAAATC
Found at i:29768552 original size:6 final size:6
Alignment explanation
Indices: 29768541--29768642 Score: 95
Period size: 6 Copynumber: 16.8 Consensus size: 6
29768531 AACCAAAATG
* *
29768541 AGAATC AGAATC AGAATC AGTAA-C AGAACC AGAATC AGAATC A-ATATT
1 AGAATC AGAATC AGAATC AG-AATC AGAATC AGAATC AGAATC AGA-ATC
* *
29768589 AGTAA-C AGAATC AGAATC AGAATC AGAATT AG-GTGAC AGAATC AGAATC
1 AG-AATC AGAATC AGAATC AGAATC AGAATC AGAAT--C AGAATC AGAATC
29768638 AGAAT
1 AGAAT
29768643 GTGAATGCAA
Statistics
Matches: 80, Mismatches: 7, Indels: 18
0.76 0.07 0.17
Matches are distributed among these distances:
5 6 0.08
6 67 0.84
7 5 0.06
8 2 0.03
ACGTcount: A:0.49, C:0.15, G:0.18, T:0.19
Consensus pattern (6 bp):
AGAATC
Found at i:29768556 original size:30 final size:29
Alignment explanation
Indices: 29768520--29768642 Score: 131
Period size: 30 Copynumber: 4.1 Consensus size: 29
29768510 AAGAAACATT
* * *
29768520 ATCAGAATTGGAACCAAAATGAGAATCAGA
1 ATCAGAATTGTAA-CAGAATCAGAATCAGA
* *
29768550 ATCAGAATCAGTAACAGAACCAGAATCAGA
1 ATCAGAAT-TGTAACAGAATCAGAATCAGA
29768580 ATCA-ATATTAGTAACAGAATCAGAATCAGA
1 ATCAGA-ATT-GTAACAGAATCAGAATCAGA
*
29768610 ATCAGAATTAGGTGACAGAATCAGAATCAGA
1 ATCAGAATT--GTAACAGAATCAGAATCAGA
29768641 AT
1 AT
29768643 GTGAATGCAA
Statistics
Matches: 79, Mismatches: 9, Indels: 9
0.81 0.09 0.09
Matches are distributed among these distances:
29 1 0.01
30 53 0.67
31 25 0.32
ACGTcount: A:0.49, C:0.15, G:0.18, T:0.19
Consensus pattern (29 bp):
ATCAGAATTGTAACAGAATCAGAATCAGA
Found at i:29768797 original size:27 final size:26
Alignment explanation
Indices: 29768760--29768825 Score: 78
Period size: 27 Copynumber: 2.5 Consensus size: 26
29768750 AGCATGGTTG
*
29768760 CCAGAACAGATATCATGACAGAGTCA
1 CCAGAACAGATATCATGACAGAGCCA
** *
29768786 CCAGATACAGATATTGTGGCAGAGCCA
1 CCAGA-ACAGATATCATGACAGAGCCA
29768813 CCAGAATCAGATA
1 CCAGAA-CAGATA
29768826 ATGTGGCAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
26 6 0.18
27 28 0.82
ACGTcount: A:0.39, C:0.23, G:0.21, T:0.17
Consensus pattern (26 bp):
CCAGAACAGATATCATGACAGAGCCA
Found at i:29768830 original size:27 final size:27
Alignment explanation
Indices: 29768778--29768833 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
29768768 GATATCATGA
* *
29768778 CAGAGTCACCAGATACAGATATTGTGG
1 CAGAGCCACCAGATACAGATAATGTGG
29768805 CAGAGCCACCAGA-ATCAGATAATGTGG
1 CAGAGCCACCAGATA-CAGATAATGTGG
29768832 CA
1 CA
29768834 AACCCACCTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 1 0.04
27 25 0.96
ACGTcount: A:0.36, C:0.21, G:0.25, T:0.18
Consensus pattern (27 bp):
CAGAGCCACCAGATACAGATAATGTGG
Found at i:29768840 original size:27 final size:27
Alignment explanation
Indices: 29768784--29768841 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
29768774 ATGACAGAGT
* * *
29768784 CACCAGATACAGATATTGTGGCAGAGC
1 CACCAGATACAGATAATGTGGCAAACC
29768811 CACCAGA-ATCAGATAATGTGGCAAACC
1 CACCAGATA-CAGATAATGTGGCAAACC
29768838 CACC
1 CACC
29768842 TAACAGGATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 1 0.04
27 26 0.96
ACGTcount: A:0.36, C:0.28, G:0.21, T:0.16
Consensus pattern (27 bp):
CACCAGATACAGATAATGTGGCAAACC
Found at i:29769167 original size:27 final size:26
Alignment explanation
Indices: 29769126--29769205 Score: 97
Period size: 27 Copynumber: 3.0 Consensus size: 26
29769116 ATCGGTCAAT
* *
29769126 AGATATTGTGACAGAGTCACCAGATAC
1 AGATATTGTGGCAGAGCCACCAGA-AC
*
29769153 AGATATTGTGGCAGAGCCACTAGAAC
1 AGATATTGTGGCAGAGCCACCAGAAC
* *
29769179 AGATATTTATGGCATAGCCACCAGAAC
1 AGATA-TTGTGGCAGAGCCACCAGAAC
29769206 GCTTCCTCCG
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
26 7 0.15
27 39 0.85
ACGTcount: A:0.36, C:0.20, G:0.23, T:0.21
Consensus pattern (26 bp):
AGATATTGTGGCAGAGCCACCAGAAC
Found at i:29769434 original size:27 final size:27
Alignment explanation
Indices: 29769404--29769590 Score: 205
Period size: 27 Copynumber: 7.0 Consensus size: 27
29769394 GGGGTAAAAT
* * * * *
29769404 GGTAATTTTACCCCAAAAAGGTATCTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
29769431 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
29769458 GGT-ATTTTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* **
29769484 GATAATTCTACCCTACGGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* * *
29769511 AGTAATTCTACCCTATAAGGGTATTTT
1 GGTAATTCTACCCTACAAGGGTATTTC
* * *
29769538 AGTAATTCTACCCTATAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
29769565 GGTAATTCTACCCTATAGGGGTATTT
1 GGTAATTCTACCCTACAAGGGTATTT
29769591 TAGTAATTTC
Statistics
Matches: 138, Mismatches: 21, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
26 23 0.17
27 115 0.83
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.36
Consensus pattern (27 bp):
GGTAATTCTACCCTACAAGGGTATTTC
Found at i:29769465 original size:53 final size:54
Alignment explanation
Indices: 29769404--29769590 Score: 232
Period size: 54 Copynumber: 3.5 Consensus size: 54
29769394 GGGGTAAAAT
* * * *
29769404 GGTAATTTTACCCCAAAAAGGTATCTCGGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTAAAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTC
* * * *
29769458 GGT-ATTTTACCCTACAAGGGTATTTCGATAATTCTACCCTACGGGGGTATTTC
1 GGTAATTCTACCCTAAAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTC
* * ** *
29769511 AGTAATTCTACCCTATAAGGGTATTTTAGTAATTCTACCCTATAGGGGTATTTC
1 GGTAATTCTACCCTAAAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTC
* *
29769565 GGTAATTCTACCCTATAGGGGTATTT
1 GGTAATTCTACCCTAAAAGGGTATTT
29769591 TAGTAATTTC
Statistics
Matches: 116, Mismatches: 16, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
53 46 0.40
54 70 0.60
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.36
Consensus pattern (54 bp):
GGTAATTCTACCCTAAAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTC
Found at i:29769546 original size:54 final size:54
Alignment explanation
Indices: 29769432--29769598 Score: 248
Period size: 54 Copynumber: 3.1 Consensus size: 54
29769422 AGGTATCTCG
* * *
29769432 GTAATTCTACCCTACAGGGGTATTTCGGT-ATTTTACCCTACAAGGGTA-TTTC
1 GTAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCCTATAAGGGTATTTTA
* *
29769484 GATAATTCTACCCTACGGGGGTATTTCAGTAATTCTACCCTATAAGGGTATTTTA
1 G-TAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCCTATAAGGGTATTTTA
* *
29769539 GTAATTCTACCCTATAGGGGTATTTCGGTAATTCTACCCTATAGGGGTATTTTA
1 GTAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCCTATAAGGGTATTTTA
29769593 GTAATT
1 GTAATT
29769599 TCACAATTGA
Statistics
Matches: 103, Mismatches: 9, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
52 1 0.01
53 26 0.25
54 72 0.70
55 4 0.04
ACGTcount: A:0.25, C:0.18, G:0.19, T:0.38
Consensus pattern (54 bp):
GTAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCCTATAAGGGTATTTTA
Found at i:29769596 original size:27 final size:27
Alignment explanation
Indices: 29769423--29769598 Score: 212
Period size: 27 Copynumber: 6.6 Consensus size: 27
29769413 ACCCCAAAAA
* *
29769423 GGTATCTCGGTAATTCTACCCTACAGG
1 GGTATTTCAGTAATTCTACCCTACAGG
* * *
29769450 GGTATTTCGGT-ATTTTACCCTACAAG
1 GGTATTTCAGTAATTCTACCCTACAGG
*
29769476 GGTATTTC-GATAATTCTACCCTACGGG
1 GGTATTTCAG-TAATTCTACCCTACAGG
* *
29769503 GGTATTTCAGTAATTCTACCCTATAAG
1 GGTATTTCAGTAATTCTACCCTACAGG
* *
29769530 GGTATTTTAGTAATTCTACCCTATAGG
1 GGTATTTCAGTAATTCTACCCTACAGG
* *
29769557 GGTATTTCGGTAATTCTACCCTATAGG
1 GGTATTTCAGTAATTCTACCCTACAGG
*
29769584 GGTATTTTAGTAATT
1 GGTATTTCAGTAATT
29769599 TCACAATTGA
Statistics
Matches: 131, Mismatches: 15, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
25 1 0.01
26 22 0.17
27 107 0.82
28 1 0.01
ACGTcount: A:0.24, C:0.18, G:0.20, T:0.38
Consensus pattern (27 bp):
GGTATTTCAGTAATTCTACCCTACAGG
Found at i:29769633 original size:27 final size:27
Alignment explanation
Indices: 29769607--29770149 Score: 601
Period size: 27 Copynumber: 20.1 Consensus size: 27
29769597 TTTCACAATT
* *
29769607 GAGGGTAAAACAGTAATTCTATAAATT
1 GAGGGTAAAACGGTAATTCTATAAATC
* * * *
29769634 GAGGGTAAAACGATAATTTTGTAAACC
1 GAGGGTAAAACGGTAATTCTATAAATC
*
29769661 GAGGGT-AAACTAGTAATTCTATAAATC
1 GAGGGTAAAAC-GGTAATTCTATAAATC
* * *
29769688 GAGGGTAAAATGGTAATTTTACAAATC
1 GAGGGTAAAACGGTAATTCTATAAATC
**
29769715 GAGGGTAAAATAGTAATTCTATAAATC
1 GAGGGTAAAACGGTAATTCTATAAATC
* *
29769742 GAGGGTAAAACAGTAATTCTGTAAA-C
1 GAGGGTAAAACGGTAATTCTATAAATC
*
29769768 TGAGGGTAAAACGATAATTCTATAAATC
1 -GAGGGTAAAACGGTAATTCTATAAATC
* *
29769796 GAGGGTAAAATGGTAATTCTGTAAA-C
1 GAGGGTAAAACGGTAATTCTATAAATC
*
29769822 TGAGGGTAAAACGGTAATTCTGTAAATC
1 -GAGGGTAAAACGGTAATTCTATAAATC
* * * *
29769850 GAGGGTAAAACAGTAATTTTACAAATT
1 GAGGGTAAAACGGTAATTCTATAAATC
*
29769877 GAGGGTAAAACGGTAATTCTGTAAATC
1 GAGGGTAAAACGGTAATTCTATAAATC
* ** * *
29769904 AAGGGTAAAATAGTAATTCTGTTAA-C
1 GAGGGTAAAACGGTAATTCTATAAATC
* * *
29769930 TAAGGGTAAAATGGTAATTCTGTAAATC
1 -GAGGGTAAAACGGTAATTCTATAAATC
* *
29769958 GAGGGTAAAATGGTAATTCTGTAAA-C
1 GAGGGTAAAACGGTAATTCTATAAATC
*
29769984 TGAGGGTAAAACGGTAATTCTGTAAATC
1 -GAGGGTAAAACGGTAATTCTATAAATC
* * * *
29770012 GATGGTAAAACGATAATTTTAAAAATC
1 GAGGGTAAAACGGTAATTCTATAAATC
*
29770039 GAGGGTAAAACGATAATTCTATAAATC
1 GAGGGTAAAACGGTAATTCTATAAATC
*
29770066 GAGGGTAAAACGGTAATTCTGTAAATC
1 GAGGGTAAAACGGTAATTCTATAAATC
** * * *
29770093 GAGGGTAAAATAGTAATTTTACAAATT
1 GAGGGTAAAACGGTAATTCTATAAATC
29770120 GAGGGTAAAACGGTAATTCTATAAATC
1 GAGGGTAAAACGGTAATTCTATAAATC
29770147 GAG
1 GAG
29770150 AGTACTTTGG
Statistics
Matches: 440, Mismatches: 66, Indels: 20
0.84 0.13 0.04
Matches are distributed among these distances:
26 8 0.02
27 425 0.97
28 7 0.02
ACGTcount: A:0.41, C:0.09, G:0.22, T:0.28
Consensus pattern (27 bp):
GAGGGTAAAACGGTAATTCTATAAATC
Found at i:29771549 original size:17 final size:17
Alignment explanation
Indices: 29771509--29771551 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
29771499 GAATAAAAAT
*
29771509 AAAAATAAACACCTAAA
1 AAAAATAAACAACTAAA
29771526 AAGAAATAAA-AACTAAA
1 AA-AAATAAACAACTAAA
29771543 GAAAAATAA
1 -AAAAATAA
29771552 TTTCTCCCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 14 0.61
18 9 0.39
ACGTcount: A:0.74, C:0.09, G:0.05, T:0.12
Consensus pattern (17 bp):
AAAAATAAACAACTAAA
Found at i:29793014 original size:6 final size:6
Alignment explanation
Indices: 29792998--29793070 Score: 51
Period size: 6 Copynumber: 12.2 Consensus size: 6
29792988 CCTTTTTTTA
* * *
29792998 TTTATT CTTATT TTTA-T TTTA-T TTTATT TTATTTAT TTTATT TTTAGT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TT-TAT-T TTTATT TTTATT
* * * *
29793046 TTTCTT TTGACT TTTATT TTCATT T
1 TTTATT TTTATT TTTATT TTTATT T
29793071 CAATTTTATT
Statistics
Matches: 51, Mismatches: 13, Indels: 6
0.73 0.19 0.09
Matches are distributed among these distances:
5 10 0.20
6 34 0.67
7 4 0.08
8 3 0.06
ACGTcount: A:0.16, C:0.05, G:0.03, T:0.75
Consensus pattern (6 bp):
TTTATT
Found at i:29793019 original size:5 final size:5
Alignment explanation
Indices: 29792993--29793090 Score: 78
Period size: 5 Copynumber: 18.8 Consensus size: 5
29792983 ATCCTCCTTT
29792993 TTTTA -TTTA TTCTTA TTTTTA TTTTA TTTTA TTTTA -TTTA TTTTA TTTTTA
1 TTTTA TTTTA TT-TTA -TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA -TTTTA
* *
29793044 GTTTTC TTTTGA CTTTTA TTTTCA TTTCAA TTTTA --TTA TTTTA TTTT
1 -TTTTA TTTT-A -TTTTA TTTT-A TTT-TA TTTTA TTTTA TTTTA TTTT
29793091 GAAAGACATA
Statistics
Matches: 77, Mismatches: 5, Indels: 22
0.74 0.05 0.21
Matches are distributed among these distances:
3 3 0.04
4 8 0.10
5 36 0.47
6 24 0.31
7 6 0.08
ACGTcount: A:0.18, C:0.05, G:0.02, T:0.74
Consensus pattern (5 bp):
TTTTA
Found at i:29793031 original size:31 final size:33
Alignment explanation
Indices: 29792993--29793064 Score: 105
Period size: 31 Copynumber: 2.2 Consensus size: 33
29792983 ATCCTCCTTT
29792993 TTTTATTTATTCTTATTTTTA-TTTTATTTT-A-
1 TTTTATTTATT-TTATTTTTAGTTTTATTTTGAC
*
29793024 TTTTATTTATTTTATTTTTAGTTTTCTTTTGAC
1 TTTTATTTATTTTATTTTTAGTTTTATTTTGAC
29793057 TTTTATTT
1 TTTTATTT
29793065 TCATTTCAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
30 9 0.24
31 19 0.51
32 1 0.03
33 8 0.22
ACGTcount: A:0.17, C:0.04, G:0.03, T:0.76
Consensus pattern (33 bp):
TTTTATTTATTTTATTTTTAGTTTTATTTTGAC
Found at i:29793034 original size:9 final size:9
Alignment explanation
Indices: 29792993--29793040 Score: 60
Period size: 9 Copynumber: 4.9 Consensus size: 9
29792983 ATCCTCCTTT
29792993 TTTTATTTA
1 TTTTATTTA
29793002 TTCTTATTTTTA
1 TT-TTA--TTTA
29793014 TTTTATTTTA
1 TTTTA-TTTA
29793024 TTTTATTTA
1 TTTTATTTA
29793033 TTTTATTT
1 TTTTATTT
29793041 TTAGTTTTCT
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
9 14 0.39
10 13 0.36
11 3 0.08
12 6 0.17
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTTATTTA
Found at i:29793155 original size:13 final size:13
Alignment explanation
Indices: 29793137--29793161 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29793127 CCATTTTCTG
29793137 GTATTTCTAACAA
1 GTATTTCTAACAA
29793150 GTATTTCTAACA
1 GTATTTCTAACA
29793162 GACTTCCAAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.08, T:0.40
Consensus pattern (13 bp):
GTATTTCTAACAA
Found at i:29796902 original size:30 final size:30
Alignment explanation
Indices: 29796858--29796917 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
29796848 CACAGCCGAC
* *
29796858 CATACATCCGGTAGACACGCCCGTGTGTCT
1 CATACATCCAGTAGACACGCCCATGTGTCT
* *
29796888 CATACGTCCAGTAGACATGCCCATGTGTCT
1 CATACATCCAGTAGACACGCCCATGTGTCT
29796918 AGGCTGTGTC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.22, C:0.32, G:0.22, T:0.25
Consensus pattern (30 bp):
CATACATCCAGTAGACACGCCCATGTGTCT
Found at i:29798149 original size:40 final size:40
Alignment explanation
Indices: 29798105--29798181 Score: 129
Period size: 40 Copynumber: 1.9 Consensus size: 40
29798095 TTAGTGCCAC
*
29798105 ATATAGCCGAAGCTAT-TCCAATTCGCACACTAAGTGCTTT
1 ATATAGCCGAAGCTATCT-CAAATCGCACACTAAGTGCTTT
29798145 ATATAGCCGAAGCTATCTCAAATCGCACACTAAGTGC
1 ATATAGCCGAAGCTATCTCAAATCGCACACTAAGTGC
29798182 CAAACATAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
40 34 0.97
41 1 0.03
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.26
Consensus pattern (40 bp):
ATATAGCCGAAGCTATCTCAAATCGCACACTAAGTGCTTT
Found at i:29803859 original size:29 final size:29
Alignment explanation
Indices: 29803798--29803946 Score: 255
Period size: 29 Copynumber: 5.2 Consensus size: 29
29803788 TACATGCATG
*
29803798 CATATGGCCCATTAGGCCC-AATCTCATT
1 CATATGGCCCATTAGGCCCAAATCACATT
29803826 CATATGGCCCATTAGGCCCAAATCACATT
1 CATATGGCCCATTAGGCCCAAATCACATT
29803855 CATATGGCCCATTAGGCCCAAATCACATT
1 CATATGGCCCATTAGGCCCAAATCACATT
*
29803884 CATATGGCCCATTAGGCCCAAATTACATT
1 CATATGGCCCATTAGGCCCAAATCACATT
* *
29803913 CATATGGTCCATTAGACCCAAATCACATT
1 CATATGGCCCATTAGGCCCAAATCACATT
29803942 CATAT
1 CATAT
29803947 TCATGCTGTC
Statistics
Matches: 115, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
28 19 0.17
29 96 0.83
ACGTcount: A:0.31, C:0.30, G:0.13, T:0.27
Consensus pattern (29 bp):
CATATGGCCCATTAGGCCCAAATCACATT
Found at i:29804175 original size:15 final size:16
Alignment explanation
Indices: 29804155--29804184 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
29804145 TTGTAACCAA
29804155 ACTTTT-AGCTTTTCG
1 ACTTTTCAGCTTTTCG
29804170 ACTTTTCAGCTTTTC
1 ACTTTTCAGCTTTTC
29804185 AGCATTTCGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.13, C:0.23, G:0.10, T:0.53
Consensus pattern (16 bp):
ACTTTTCAGCTTTTCG
Found at i:29811740 original size:41 final size:41
Alignment explanation
Indices: 29811671--29811755 Score: 127
Period size: 41 Copynumber: 2.1 Consensus size: 41
29811661 CAACGCTGGA
29811671 ATAGAGTTACGAGGCATTACCGGATAACACACCTCATTCAC
1 ATAGAGTTACGAGGCATTACCGGATAACACACCTCATTCAC
* * *
29811712 ATAGGGTTATGAGGCGTTACCAGG-TAACACACCTCATTCAC
1 ATAGAGTTACGAGGCATTACC-GGATAACACACCTCATTCAC
29811753 ATA
1 ATA
29811756 CATATATGTA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
41 38 0.95
42 2 0.05
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.24
Consensus pattern (41 bp):
ATAGAGTTACGAGGCATTACCGGATAACACACCTCATTCAC
Found at i:29813350 original size:39 final size:40
Alignment explanation
Indices: 29813296--29813371 Score: 111
Period size: 39 Copynumber: 1.9 Consensus size: 40
29813286 TTAATGCCAC
*
29813296 ATATAGCCGAAGCTAT-TCCAATTCGCACA-TAAGTGCTTT
1 ATATAGCCAAAGCTATCTCCAATT-GCACACTAAGTGCTTT
*
29813335 ATATAGCCAAAGCTATCTCGAATTGCACACTAAGTGC
1 ATATAGCCAAAGCTATCTCCAATTGCACACTAAGTGC
29813372 CAAACATAGT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
39 20 0.61
40 13 0.39
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.28
Consensus pattern (40 bp):
ATATAGCCAAAGCTATCTCCAATTGCACACTAAGTGCTTT
Found at i:29816842 original size:18 final size:18
Alignment explanation
Indices: 29816827--29816865 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
29816817 TAGGCCATAT
*
29816827 TATAACCTTATACCATTA
1 TATAACCATATACCATTA
*
29816845 TATGACCATATACCATTA
1 TATAACCATATACCATTA
29816863 TAT
1 TAT
29816866 GCTATGTCCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.21, G:0.03, T:0.38
Consensus pattern (18 bp):
TATAACCATATACCATTA
Found at i:29821088 original size:26 final size:26
Alignment explanation
Indices: 29821059--29821110 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
29821049 CTTTCACGAT
29821059 GAGGTTAAGTCTCCTTTGCCAATCAA
1 GAGGTTAAGTCTCCTTTGCCAATCAA
29821085 GAGGTTAAGTCTCCTTTGCCAATCAA
1 GAGGTTAAGTCTCCTTTGCCAATCAA
29821111 TCTTACCTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (26 bp):
GAGGTTAAGTCTCCTTTGCCAATCAA
Found at i:29823075 original size:6 final size:6
Alignment explanation
Indices: 29823064--29823099 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
29823054 ATTGCATGAA
29823064 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
1 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
29823100 CTGTCTTTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (6 bp):
ATGTAT
Done.