Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004862.1 Hibiscus syriacus cultivar Beakdansim tig00010968_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2846896
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 13
Found at i:1470446 original size:24 final size:24
Alignment explanation
Indices: 1470398--1470446 Score: 57
Period size: 24 Copynumber: 2.0 Consensus size: 24
1470388 AAAACATTAA
*
1470398 TTTAAGGTTATCTTTTGAGTGAAT
1 TTTAAGATTATCTTTTGAGTGAAT
1470422 TTTAAGATATATCATTTT-AGT-AAT
1 TTTAAGAT-TATC-TTTTGAGTGAAT
1470446 T
1 T
1470447 ATACGCGTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
24 11 0.50
25 7 0.32
26 4 0.18
ACGTcount: A:0.31, C:0.04, G:0.14, T:0.51
Consensus pattern (24 bp):
TTTAAGATTATCTTTTGAGTGAAT
Found at i:1470858 original size:92 final size:92
Alignment explanation
Indices: 1470701--1470873 Score: 231
Period size: 92 Copynumber: 1.9 Consensus size: 92
1470691 AACTTTCAAA
* * * * *** *
1470701 AAAGTATCGATTCTTTTTACAAAACGTATCTATACTTTCAACATATTAGGTAAATTTTATCGGTT
1 AAAGTATCGATCCTTTTTACAAAACGGATCGATACTTTCAACATATCAGGTAAACGCTACCGGTT
1470766 TTGTCATTTTTTTACCTGTTATATTGT
66 TTGTCATTTTTTTACCTGTTATATTGT
* *
1470793 AAAGTATCGATCCTTTTTATAAAA-GGATCGATACTTTCAATATATCAGGTAAAGCGCTACCGGT
1 AAAGTATCGATCCTTTTTACAAAACGGATCGATACTTTCAACATATCAGGTAAA-CGCTACCGGT
*
1470857 TTTGTTATTTTTTTACC
65 TTTGTCATTTTTTTACC
1470874 GGTTTTGTTA
Statistics
Matches: 69, Mismatches: 11, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
91 25 0.36
92 44 0.64
ACGTcount: A:0.29, C:0.14, G:0.13, T:0.44
Consensus pattern (92 bp):
AAAGTATCGATCCTTTTTACAAAACGGATCGATACTTTCAACATATCAGGTAAACGCTACCGGTT
TTGTCATTTTTTTACCTGTTATATTGT
Found at i:1470875 original size:20 final size:20
Alignment explanation
Indices: 1470850--1470893 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
1470840 GGTAAAGCGC
1470850 TACCGGTTTTGTTATTTTTT
1 TACCGGTTTTGTTATTTTTT
1470870 TACCGGTTTTGTTATTTTTT
1 TACCGGTTTTGTTATTTTTT
1470890 TACC
1 TACC
1470894 TGTTATATTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.11, C:0.14, G:0.14, T:0.61
Consensus pattern (20 bp):
TACCGGTTTTGTTATTTTTT
Found at i:1470898 original size:112 final size:112
Alignment explanation
Indices: 1470755--1470984 Score: 415
Period size: 112 Copynumber: 2.1 Consensus size: 112
1470745 ATTAGGTAAA
* *
1470755 TTTTATCGGTTTTGTCATTTTTTTACCTGTTATATTGTAAAGTATCGATCCTTTTTATAAAAGGA
1 TTTTACCGGTTTTGTCATTTTTTTACCTGTTATATTGTAAAGTATCGATCATTTTTATAAAAGGA
*
1470820 TCGATACTTTCAATATATCAGGTAAAGCGCTACCGGTTTTGTTATTT
66 TCGATACTTTCAATATATCAGGTAAAACGCTACCGGTTTTGTTATTT
* *
1470867 TTTTACCGGTTTTGTTATTTTTTTACCTGTTATATTGTAAAGTATCGATCATTTTTATAAAAGTA
1 TTTTACCGGTTTTGTCATTTTTTTACCTGTTATATTGTAAAGTATCGATCATTTTTATAAAAGGA
1470932 TCGATACTTTCAATATATCAGGTAAAACGCTACCGGTTTTGTTATTT
66 TCGATACTTTCAATATATCAGGTAAAACGCTACCGGTTTTGTTATTT
1470979 TTTTAC
1 TTTTAC
1470985 ATGTTATATT
Statistics
Matches: 113, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
112 113 1.00
ACGTcount: A:0.26, C:0.13, G:0.14, T:0.47
Consensus pattern (112 bp):
TTTTACCGGTTTTGTCATTTTTTTACCTGTTATATTGTAAAGTATCGATCATTTTTATAAAAGGA
TCGATACTTTCAATATATCAGGTAAAACGCTACCGGTTTTGTTATTT
Found at i:1471026 original size:91 final size:92
Alignment explanation
Indices: 1470870--1471167 Score: 490
Period size: 92 Copynumber: 3.2 Consensus size: 92
1470860 GTTATTTTTT
* *
1470870 TACCGGTTTTGTTATTTTTTTACCTGTTATATTGTAAAGTATCGATCATTTTTATAAAAGTATCG
1 TACCGGTTTTGTTATTTTTTTACCTGTTATATTGTAAAGTATCGATCCTTTTTATAAAAGGATCG
*
1470935 ATACTTTCAATATATCAGGTAAAACGC
66 ATACTTTCAATATATCAGGTAAAGCGC
*
1470962 TACCGGTTTTGTTATTTTTTTACATGTTATATT-TAAAGTATCGATCCTTTTTATAAAAGGATCG
1 TACCGGTTTTGTTATTTTTTTACCTGTTATATTGTAAAGTATCGATCCTTTTTATAAAAGGATCG
1471026 ATACTTTCAATATATCAGGTAAAGCGC
66 ATACTTTCAATATATCAGGTAAAGCGC
* * **
1471053 TACCGGTTTTGTTATTTTTTTACCGGTTATATTGTAAAATATTAATCCTTTTTATAAAAGGATCG
1 TACCGGTTTTGTTATTTTTTTACCTGTTATATTGTAAAGTATCGATCCTTTTTATAAAAGGATCG
*
1471118 ATACTTTCAATATATTAGGTAAAGCGC
66 ATACTTTCAATATATCAGGTAAAGCGC
* *
1471145 TACCGATTTTATTATTTTTTTAC
1 TACCGGTTTTGTTATTTTTTTAC
1471168 GTTTTATTGA
Statistics
Matches: 193, Mismatches: 12, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
91 86 0.45
92 107 0.55
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.45
Consensus pattern (92 bp):
TACCGGTTTTGTTATTTTTTTACCTGTTATATTGTAAAGTATCGATCCTTTTTATAAAAGGATCG
ATACTTTCAATATATCAGGTAAAGCGC
Found at i:1471051 original size:203 final size:204
Alignment explanation
Indices: 1470701--1471080 Score: 631
Period size: 203 Copynumber: 1.9 Consensus size: 204
1470691 AACTTTCAAA
* * *** *
1470701 AAAGTATCGATTCTTTTTACAAAACGTATCTATACTTTCAACATATTAGGTAAATTTTATCGGTT
1 AAAGTATCGATTCTTTTTACAAAACGTATCGATACTTTCAACATATCAGGTAAACGCTACCGGTT
*
1470766 TTGTCATTTTTTTACCTGTTATATTGTAAAGTATCGATCCTTTTTATAAAAGGATCGATACTTTC
66 TTGTCATTTTTTTACATGTTATATTGTAAAGTATCGATCCTTTTTATAAAAGGATCGATACTTTC
1470831 AATATATCAGGTAAAGCGCTACCGGTTTTGTTATTTTTTTACCGGTTTTGTTATTTTTTTACCTG
131 AATATATCAGGTAAAGCGCTACCGGTTTTGTTATTTTTTTACCGGTTTTGTTATTTTTTTACCTG
1470896 TTATATTGT
196 TTATATTGT
* *
1470905 AAAGTATCGA-TCATTTTTATAAAA-GTATCGATACTTTCAATATATCAGGTAAAACGCTACCGG
1 AAAGTATCGATTC-TTTTTACAAAACGTATCGATACTTTCAACATATCAGGT-AAACGCTACCGG
*
1470968 TTTTGTTATTTTTTTACATGTTATATT-TAAAGTATCGATCCTTTTTATAAAAGGATCGATACTT
64 TTTTGTCATTTTTTTACATGTTATATTGTAAAGTATCGATCCTTTTTATAAAAGGATCGATACTT
1471032 TCAATATATCAGGTAAAGCGCTACCGGTTTTGTTATTTTTTTACCGGTT
129 TCAATATATCAGGTAAAGCGCTACCGGTTTTGTTATTTTTTTACCGGTT
1471081 ATATTGTAAA
Statistics
Matches: 164, Mismatches: 10, Indels: 5
0.92 0.06 0.03
Matches are distributed among these distances:
203 111 0.68
204 53 0.32
ACGTcount: A:0.28, C:0.13, G:0.14, T:0.45
Consensus pattern (204 bp):
AAAGTATCGATTCTTTTTACAAAACGTATCGATACTTTCAACATATCAGGTAAACGCTACCGGTT
TTGTCATTTTTTTACATGTTATATTGTAAAGTATCGATCCTTTTTATAAAAGGATCGATACTTTC
AATATATCAGGTAAAGCGCTACCGGTTTTGTTATTTTTTTACCGGTTTTGTTATTTTTTTACCTG
TTATATTGT
Found at i:1471544 original size:24 final size:25
Alignment explanation
Indices: 1471517--1471585 Score: 76
Period size: 24 Copynumber: 2.9 Consensus size: 25
1471507 AGCATCAAAT
1471517 ACAATAA-AATAATATTATTTATTA
1 ACAATAAGAATAATATTATTTATTA
*
1471541 ACAA-AATAATAATATTATTT-TTA
1 ACAATAAGAATAATATTATTTATTA
1471564 A-AATATTAGAATAAT-TTATTTA
1 ACAATA--AGAATAATATTATTTA
1471586 ATATTATCTA
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
22 2 0.05
23 7 0.18
24 23 0.59
25 7 0.18
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.43
Consensus pattern (25 bp):
ACAATAAGAATAATATTATTTATTA
Found at i:1471618 original size:14 final size:14
Alignment explanation
Indices: 1471585--1471671 Score: 56
Period size: 14 Copynumber: 6.3 Consensus size: 14
1471575 TAATTTATTT
1471585 AATATTATCTATGT-A
1 AATATTAT-TAT-TAA
1471600 AATATTATTATTAA
1 AATATTATTATTAA
*
1471614 AATATTA-TATCTAT
1 AATATTATTAT-TAA
* * *
1471628 AATTTTATAAATAA
1 AATATTATTATTAA
* *
1471642 AA-ATTATGATTAT
1 AATATTATTATTAA
*
1471655 TATATT-TTATTAA
1 AATATTATTATTAA
1471668 AATA
1 AATA
1471672 AATTTGCAAT
Statistics
Matches: 55, Mismatches: 13, Indels: 10
0.71 0.17 0.13
Matches are distributed among these distances:
13 20 0.36
14 26 0.47
15 9 0.16
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.48
Consensus pattern (14 bp):
AATATTATTATTAA
Found at i:1471674 original size:29 final size:28
Alignment explanation
Indices: 1471601--1471675 Score: 70
Period size: 29 Copynumber: 2.7 Consensus size: 28
1471591 ATCTATGTAA
1471601 ATATTATTATTAAAAT--ATTATATCTAT
1 ATATT-TTATTAAAATAAATTATATCTAT
*
1471628 A-ATTTTA-TAAATAAAAATTATGAT-TATT
1 ATATTTTATTAAA-ATAAATTAT-ATCTA-T
1471656 ATATTTTATTAAAATAAATT
1 ATATTTTATTAAAATAAATT
1471676 TGCAATGTTA
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
24 4 0.10
25 4 0.10
26 3 0.08
27 8 0.21
28 4 0.10
29 12 0.31
30 4 0.10
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (28 bp):
ATATTTTATTAAAATAAATTATATCTAT
Found at i:1471824 original size:87 final size:86
Alignment explanation
Indices: 1471723--1471962 Score: 381
Period size: 87 Copynumber: 2.8 Consensus size: 86
1471713 ATAATATGCA
* *
1471723 ATATAAGCGTTACCTATTACATTATATAAACACTACCTAATATGTTATTGTGCTTGATAATGTTT
1 ATATAAGCGCTACCTATTACATTATATAAAC-CTACCTAATATGTTATTGTACTTGATAATGTTT
*
1471788 CCATTAATTAACCTATTTTATT
65 CCAGTAATTAACCTATTTTATT
1471810 ATATAAGCGCTACCTATTACATTATATAAACGCTACCTAATATGTTATTGTACTTGATAATGTTT
1 ATATAAGCGCTACCTATTACATTATATAAAC-CTACCTAATATGTTATTGTACTTGATAATGTTT
1471875 CCAGTAATTAACCTATTTTATT
65 CCAGTAATTAACCTATTTTATT
* * * * * *
1471897 ATATAAACGCTACCTATTACATTATATAAGCCTACCTAATTTGTTATTTTATTTGATAATATTTC
1 ATATAAGCGCTACCTATTACATTATATAAACCTACCTAATATGTTATTGTACTTGATAATGTTTC
1471962 C
66 C
1471963 GGTTGAATGA
Statistics
Matches: 143, Mismatches: 10, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
86 31 0.22
87 112 0.78
ACGTcount: A:0.33, C:0.16, G:0.08, T:0.43
Consensus pattern (86 bp):
ATATAAGCGCTACCTATTACATTATATAAACCTACCTAATATGTTATTGTACTTGATAATGTTTC
CAGTAATTAACCTATTTTATT
Found at i:1471833 original size:23 final size:23
Alignment explanation
Indices: 1471798--1471848 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
1471788 CCATTAATTA
** *
1471798 ACCTATTTTATTATATAAGCGCT
1 ACCTATTACATTATATAAACGCT
1471821 ACCTATTACATTATATAAACGCT
1 ACCTATTACATTATATAAACGCT
1471844 ACCTA
1 ACCTA
1471849 ATATGTTATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.35, C:0.22, G:0.06, T:0.37
Consensus pattern (23 bp):
ACCTATTACATTATATAAACGCT
Found at i:1471920 original size:23 final size:22
Alignment explanation
Indices: 1471885--1471934 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 22
1471875 CCAGTAATTA
**
1471885 ACCTATTTTATTATATAAACGCT
1 ACCTATTACATTATATAAAC-CT
*
1471908 ACCTATTACATTATATAAGCCT
1 ACCTATTACATTATATAAACCT
1471930 ACCTA
1 ACCTA
1471935 ATTTGTTATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 7 0.29
23 17 0.71
ACGTcount: A:0.36, C:0.22, G:0.04, T:0.38
Consensus pattern (22 bp):
ACCTATTACATTATATAAACCT
Found at i:1474108 original size:30 final size:29
Alignment explanation
Indices: 1474072--1474134 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 29
1474062 CCCGAAAAAT
1474072 CACCGGTGACCGA-TATATTTACCGATCTAA
1 CACCGGTGA--GATTATATTTACCGATCTAA
* **
1474102 CACCGGTTAGATTATATTTTTCGATCTAA
1 CACCGGTGAGATTATATTTACCGATCTAA
1474131 CACC
1 CACC
1474135 CGTAGCAGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
28 2 0.07
29 19 0.66
30 8 0.28
ACGTcount: A:0.29, C:0.25, G:0.14, T:0.32
Consensus pattern (29 bp):
CACCGGTGAGATTATATTTACCGATCTAA
Found at i:1474497 original size:17 final size:17
Alignment explanation
Indices: 1474456--1474501 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
1474446 TTTTAATATT
*
1474456 ATATATTTAATTTATTTA
1 ATAT-TTTACTTTATTTA
*
1474474 AGCATTTTACTTTATTTA
1 A-TATTTTACTTTATTTA
1474492 ATATTTTACT
1 ATATTTTACT
1474502 AATATAATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
17 8 0.33
18 14 0.58
19 2 0.08
ACGTcount: A:0.33, C:0.07, G:0.02, T:0.59
Consensus pattern (17 bp):
ATATTTTACTTTATTTA
Found at i:1476183 original size:18 final size:18
Alignment explanation
Indices: 1476160--1476194 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1476150 CAGCCACCGC
*
1476160 AGCCATTTATGATGTCGT
1 AGCCATATATGATGTCGT
1476178 AGCCATATATGATGTCG
1 AGCCATATATGATGTCG
1476195 CCGTCTTCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.34
Consensus pattern (18 bp):
AGCCATATATGATGTCGT
Found at i:1476665 original size:23 final size:23
Alignment explanation
Indices: 1476639--1476702 Score: 60
Period size: 24 Copynumber: 2.7 Consensus size: 23
1476629 TTGTATTTAC
1476639 TTTATTTTGTTAAATTGTAAT-TT
1 TTTATTTTGTTAAATT-TAATATT
**
1476662 TTTATTATT-TTTCATTTAATACTT
1 TTTATT-TTGTTAAATTTAATA-TT
*
1476686 TTTTTTTTGTTAAATTT
1 TTTATTTTGTTAAATTT
1476703 GTTGGACTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
22 4 0.12
23 13 0.41
24 15 0.47
ACGTcount: A:0.23, C:0.03, G:0.05, T:0.69
Consensus pattern (23 bp):
TTTATTTTGTTAAATTTAATATT
Found at i:1481071 original size:19 final size:20
Alignment explanation
Indices: 1481049--1481097 Score: 64
Period size: 22 Copynumber: 2.4 Consensus size: 20
1481039 AGATATTTAG
1481049 TTAGTTA-AGCTGTTGATAA
1 TTAGTTAGAGCTGTTGATAA
*
1481068 TTAGTTAGGCTGCTGTTGATAA
1 TTAGTTA-G-AGCTGTTGATAA
1481090 TTAGTTAG
1 TTAGTTAG
1481098 TTTGTTAGTG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
19 7 0.27
21 1 0.04
22 18 0.69
ACGTcount: A:0.27, C:0.06, G:0.24, T:0.43
Consensus pattern (20 bp):
TTAGTTAGAGCTGTTGATAA
Found at i:1485555 original size:22 final size:22
Alignment explanation
Indices: 1485524--1485568 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1485514 TTAGTTAAGC
*
1485524 TGTTGATAATTCGTTAGGTTGT
1 TGTTGATAATTAGTTAGGTTGT
* *
1485546 TGTTGTTAATTAGTTAGTTTGT
1 TGTTGATAATTAGTTAGGTTGT
1485568 T
1 T
1485569 AGTGAGGTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.18, C:0.02, G:0.24, T:0.56
Consensus pattern (22 bp):
TGTTGATAATTAGTTAGGTTGT
Found at i:1494854 original size:22 final size:22
Alignment explanation
Indices: 1494815--1494859 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
1494805 ATTTTAAATA
1494815 AAATAATTAAATTCATTATTTT
1 AAATAATTAAATTCATTATTTT
*
1494837 AAATAGATTGAATT-ATTATTTT
1 AAATA-ATTAAATTCATTATTTT
1494859 A
1 A
1494860 TTTTTGACCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.49
Consensus pattern (22 bp):
AAATAATTAAATTCATTATTTT
Found at i:1495669 original size:23 final size:24
Alignment explanation
Indices: 1495643--1495687 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
1495633 CCCAAAAATA
*
1495643 TAATGTT-ATTTTTAATAAAATTT
1 TAATGTTAAATTTTAATAAAATTT
* *
1495666 TAATTTTAAATTTTATTAAAAT
1 TAATGTTAAATTTTAATAAAAT
1495688 AACGTTTTGG
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 6 0.33
24 12 0.67
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (24 bp):
TAATGTTAAATTTTAATAAAATTT
Found at i:1497009 original size:16 final size:17
Alignment explanation
Indices: 1496984--1497017 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
1496974 CCGATGTGTT
1496984 ACATTGACTTTT-CAAA
1 ACATTGACTTTTACAAA
*
1497000 ACATTTACTTTTACAAA
1 ACATTGACTTTTACAAA
1497017 A
1 A
1497018 GAATGAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.41, C:0.18, G:0.03, T:0.38
Consensus pattern (17 bp):
ACATTGACTTTTACAAA
Found at i:1498967 original size:10 final size:10
Alignment explanation
Indices: 1498954--1498983 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
1498944 AAATTTACTT
1498954 CACTTTAACA
1 CACTTTAACA
1498964 CACTTTAACA
1 CACTTTAACA
1498974 CACTTTAACA
1 CACTTTAACA
1498984 TCCATATTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.40, C:0.30, G:0.00, T:0.30
Consensus pattern (10 bp):
CACTTTAACA
Found at i:1501498 original size:16 final size:17
Alignment explanation
Indices: 1501471--1501520 Score: 63
Period size: 16 Copynumber: 3.2 Consensus size: 17
1501461 CAGGCTAATA
1501471 TAATT-TTAAAAATATT
1 TAATTATTAAAAATATT
*
1501487 TAA-TATTTAAAATA-T
1 TAATTATTAAAAATATT
1501502 TAATTATTAAAAAT-TT
1 TAATTATTAAAAATATT
1501518 TAA
1 TAA
1501521 CAATATAGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
15 5 0.17
16 24 0.83
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TAATTATTAAAAATATT
Found at i:1505681 original size:42 final size:42
Alignment explanation
Indices: 1505635--1505858 Score: 124
Period size: 42 Copynumber: 5.5 Consensus size: 42
1505625 TAAAAATGCT
*
1505635 GCAATAGAGTTGACATATAGCGGCGTTTTTACAACAAACGTC
1 GCAATAGAGTTGACATATAGCGGCGTTTTTACAACAAACGCC
* *** * * **
1505677 GCAATAGTG-TGGTTTATTGCGACGTTTTTTTAACAAACGCC
1 GCAATAGAGTTGACATATAGCGGCGTTTTTACAACAAACGCC
* * * * *
1505718 GCAATAGAGTGGTAAAT-TAGCGGCGTTTATACCACAAATGCC
1 GCAATAGAGTTG-ACATATAGCGGCGTTTTTACAACAAACGCC
* * * *
1505760 GTAATAGA-TTAACATATAGTGGCG-TTTTAGCCA-AAACGCC
1 GCAATAGAGTTGACATATAGCGGCGTTTTTA-CAACAAACGCC
* * * * * * *
1505800 ACAATAGA-TCAGTAAAT-TAGCGGTGTTTATACCACAAATGCC
1 GCAATAGAGT-TG-ACATATAGCGGCGTTTTTACAACAAACGCC
1505842 GCAATAGA-TT-ACATATA
1 GCAATAGAGTTGACATATA
1505859 TAGTGGCATT
Statistics
Matches: 133, Mismatches: 40, Indels: 20
0.69 0.21 0.10
Matches are distributed among these distances:
39 3 0.02
40 22 0.17
41 52 0.39
42 55 0.41
43 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (42 bp):
GCAATAGAGTTGACATATAGCGGCGTTTTTACAACAAACGCC
Found at i:1505766 original size:83 final size:83
Alignment explanation
Indices: 1505612--1505766 Score: 188
Period size: 83 Copynumber: 1.9 Consensus size: 83
1505602 TGATACTTTA
* * * * * *
1505612 GCGACGTTTGTTGTAAAAATGCTGCAATAGAGTTGACATATAGCGGCGTTTTTACAACAAACGTC
1 GCGACGTTTGTTGTAAAAACGCCGCAATAGAGTGGAAATATAGCGGCGTTTATACAACAAACGCC
1505677 GCAATAGTGTGGTTTATT
66 GCAATAGTGTGGTTTATT
* * *
1505695 GCGACGTTT-TTTTAACAAACGCCGCAATAGAGTGGTAAAT-TAGCGGCGTTTATACCACAAATG
1 GCGACGTTTGTTGTAA-AAACGCCGCAATAGAGTGG-AAATATAGCGGCGTTTATACAACAAACG
*
1505758 CCGTAATAG
64 CCGCAATAG
1505767 ATTAACATAT
Statistics
Matches: 60, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
82 5 0.08
83 52 0.87
84 3 0.05
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (83 bp):
GCGACGTTTGTTGTAAAAACGCCGCAATAGAGTGGAAATATAGCGGCGTTTATACAACAAACGCC
GCAATAGTGTGGTTTATT
Found at i:1505828 original size:82 final size:83
Alignment explanation
Indices: 1505711--1505865 Score: 242
Period size: 82 Copynumber: 1.9 Consensus size: 83
1505701 TTTTTTTAAC
* * *
1505711 AAACGCCGCAATAGAGTGGTAAATTAGCGGCGTTTATACCACAAATGCCGTAATAGATTA-ACAT
1 AAACGCCACAATAGAGTAGTAAATTAGCGGCGTTTATACCACAAATGCCGCAATAGATTACACAT
1505775 ATAGTGGCGTTTTAGCCA
66 ATAGTGGCGTTTTAGCCA
* *
1505793 AAACGCCACAATAGA-TCAGTAAATTAGCGGTGTTTATACCACAAATGCCGCAATAGATTACATA
1 AAACGCCACAATAGAGT-AGTAAATTAGCGGCGTTTATACCACAAATGCCGCAATAGATTACACA
1505857 TATAGTGGC
65 TATAGTGGC
1505866 ATTTATTCTT
Statistics
Matches: 66, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
81 1 0.02
82 54 0.82
83 11 0.17
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.25
Consensus pattern (83 bp):
AAACGCCACAATAGAGTAGTAAATTAGCGGCGTTTATACCACAAATGCCGCAATAGATTACACAT
ATAGTGGCGTTTTAGCCA
Found at i:1505871 original size:42 final size:42
Alignment explanation
Indices: 1505739--1505871 Score: 132
Period size: 42 Copynumber: 3.2 Consensus size: 42
1505729 GTAAATTAGC
* *
1505739 GGCGTTTATACCACAAATGCCGTAATAGATTA-ACATATAGT
1 GGCGTTTATACCACAAATGCCGCAATAGATTACATATATAGT
* * * *
1505780 GGCGTTT-TAGCCA-AAACGCCACAATAGA-T-CAGTAAATTAGC
1 GGCGTTTATA-CCACAAATGCCGCAATAGATTACA-TATA-TAGT
*
1505821 GGTGTTTATACCACAAATGCCGCAATAGATTACATATATAGT
1 GGCGTTTATACCACAAATGCCGCAATAGATTACATATATAGT
*
1505863 GGCATTTAT
1 GGCGTTTAT
1505872 TCTTAAAACG
Statistics
Matches: 71, Mismatches: 13, Indels: 15
0.72 0.13 0.15
Matches are distributed among these distances:
39 2 0.03
40 16 0.23
41 22 0.31
42 25 0.35
43 4 0.06
44 2 0.03
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (42 bp):
GGCGTTTATACCACAAATGCCGCAATAGATTACATATATAGT
Found at i:1505932 original size:41 final size:41
Alignment explanation
Indices: 1505885--1505995 Score: 150
Period size: 41 Copynumber: 2.7 Consensus size: 41
1505875 TAAAACGCCG
* * * **
1505885 CAATAGTGATAATAAATAGTGGCGTTTTTAGACAAACGCTA
1 CAATAGTGTTAATCAATAGTGGCGTTTTTAGAAAAAAACTA
*
1505926 CAATAGTGTTAATCAATAGTGGCGTTTTTAGAAAAAAACTG
1 CAATAGTGTTAATCAATAGTGGCGTTTTTAGAAAAAAACTA
* *
1505967 CAATAGTTTTAATCAATAGTGGCTTTTTT
1 CAATAGTGTTAATCAATAGTGGCGTTTTT
1505996 TTTTGTATAA
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 62 1.00
ACGTcount: A:0.36, C:0.11, G:0.18, T:0.35
Consensus pattern (41 bp):
CAATAGTGTTAATCAATAGTGGCGTTTTTAGAAAAAAACTA
Found at i:1509242 original size:11 final size:11
Alignment explanation
Indices: 1509226--1509259 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
1509216 TTATTTGCAA
1509226 TTTCTTTATCT
1 TTTCTTTATCT
1509237 TTTCTTTATCT
1 TTTCTTTATCT
1509248 TTT-TTTAATCT
1 TTTCTTT-ATCT
1509259 T
1 T
1509260 ATTTTTAATC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 3 0.14
11 19 0.86
ACGTcount: A:0.12, C:0.15, G:0.00, T:0.74
Consensus pattern (11 bp):
TTTCTTTATCT
Found at i:1509264 original size:12 final size:11
Alignment explanation
Indices: 1509233--1509271 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
1509223 CAATTTCTTT
1509233 ATCTTTTCTTT-
1 ATCTTTT-TTTA
1509244 ATCTTTTTTTA
1 ATCTTTTTTTA
1509255 ATCTTATTTTTA
1 ATCTT-TTTTTA
1509267 ATCTT
1 ATCTT
1509272 GTTTCCAGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
10 3 0.12
11 12 0.46
12 11 0.42
ACGTcount: A:0.18, C:0.13, G:0.00, T:0.69
Consensus pattern (11 bp):
ATCTTTTTTTA
Found at i:1509633 original size:22 final size:22
Alignment explanation
Indices: 1509603--1509652 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
1509593 CTATTTTTTT
1509603 CAAAAAAAAAAACAAAAAAAGG
1 CAAAAAAAAAAACAAAAAAAGG
* *
1509625 CAAATAAAAAAACAAAAAAA-A
1 CAAAAAAAAAAACAAAAAAAGG
1509646 CAAAAAA
1 CAAAAAA
1509653 GCCAAAATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 6 0.24
22 19 0.76
ACGTcount: A:0.84, C:0.10, G:0.04, T:0.02
Consensus pattern (22 bp):
CAAAAAAAAAAACAAAAAAAGG
Found at i:1519663 original size:21 final size:21
Alignment explanation
Indices: 1519639--1519703 Score: 78
Period size: 21 Copynumber: 3.1 Consensus size: 21
1519629 CGGAAAATGA
**
1519639 AGCAAGGGAAGCAGAGAGAGC
1 AGCAAGGGAAGCAGCCAGAGC
*
1519660 AGC-AGCGGAAGCAGCCAGAGT
1 AGCAAG-GGAAGCAGCCAGAGC
*
1519681 AGCAACGGAAGCAGCCAGAGC
1 AGCAAGGGAAGCAGCCAGAGC
1519702 AG
1 AG
1519704 TAGTGAAAGC
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
20 2 0.05
21 34 0.92
22 1 0.03
ACGTcount: A:0.38, C:0.22, G:0.38, T:0.02
Consensus pattern (21 bp):
AGCAAGGGAAGCAGCCAGAGC
Found at i:1519780 original size:21 final size:21
Alignment explanation
Indices: 1519731--1519783 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
1519721 GAAGCACAGG
*
1519731 TAGCACAAAGAGAAGCAACGA
1 TAGCACAGAGAGAAGCAACGA
1519752 TAGCACAGAGAGAAGCAAC-A
1 TAGCACAGAGAGAAGCAACGA
*
1519772 TATCAACAGAGA
1 TAGC-ACAGAGA
1519784 TGTGAAGAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 4 0.14
21 25 0.86
ACGTcount: A:0.51, C:0.19, G:0.23, T:0.08
Consensus pattern (21 bp):
TAGCACAGAGAGAAGCAACGA
Found at i:1520372 original size:42 final size:43
Alignment explanation
Indices: 1520265--1520454 Score: 159
Period size: 43 Copynumber: 4.5 Consensus size: 43
1520255 CGATACAAAT
* * * * * * *
1520265 GCCGCTAAATCTGAAAACCTACTGCGACATTTGT-GGGAAAAC
1 GCCGCTAAATATCAACACCTTCTGCGGCGTTTGTAGGAAAAAC
* * * * * *
1520307 ACAGCTAAACATCATCACATTCTGCGGCGTTTGT-GGAAAAAT
1 GCCGCTAAATATCAACACCTTCTGCGGCGTTTGTAGGAAAAAC
* * * * *
1520349 GCCGCAAAATATCAAAACCTTCTGCGGCTTTTGTAAGTAAAAC
1 GCCGCTAAATATCAACACCTTCTGCGGCGTTTGTAGGAAAAAC
* * * *
1520392 GTCGCTAAATCTCAACACCTACTGCGGCGTTTGTAGGGAAAAC
1 GCCGCTAAATATCAACACCTTCTGCGGCGTTTGTAGGAAAAAC
*
1520435 GCCGCTAAACATCAACACCT
1 GCCGCTAAATATCAACACCT
1520455 ATTGCGACAT
Statistics
Matches: 112, Mismatches: 35, Indels: 1
0.76 0.24 0.01
Matches are distributed among these distances:
42 55 0.49
43 57 0.51
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (43 bp):
GCCGCTAAATATCAACACCTTCTGCGGCGTTTGTAGGAAAAAC
Found at i:1520418 original size:43 final size:43
Alignment explanation
Indices: 1520160--1520460 Score: 152
Period size: 43 Copynumber: 7.1 Consensus size: 43
1520150 CAGAATTTTA
* * * * *
1520160 GCGGCATTTGTATGG-AAACGCCACTAAATCTCAATACCTATT
1 GCGGCGTTTGTAAGGAAAACGCCGCTAAATCTCAACACCTACT
* * * ** * * *
1520202 ACGACATTT-TCAATAAAAACGCCGCTAATTCTCAACACTTATT
1 GCGGCGTTTGT-AAGGAAAACGCCGCTAAATCTCAACACCTACT
* * * * * *
1520245 GCGTCGTTT-T-CGATACAAATGCCGCTAAATCTGAAAACCTACT
1 GCGGCGTTTGTAAG-GA-AAACGCCGCTAAATCTCAACACCTACT
* * * * * * * *
1520288 GCGACATTTGT-GGGAAAACACAGCTAAA-CATCATCACATTCT
1 GCGGCGTTTGTAAGGAAAACGCCGCTAAATC-TCAACACCTACT
* * * * *
1520330 GCGGCGTTTGT--GGAAAAATGCCGCAAAATATCAAAACCTTCT
1 GCGGCGTTTGTAAGG-AAAACGCCGCTAAATCTCAACACCTACT
* * *
1520372 GCGGCTTTTGTAAGTAAAACGTCGCTAAATCTCAACACCTACT
1 GCGGCGTTTGTAAGGAAAACGCCGCTAAATCTCAACACCTACT
* *
1520415 GCGGCGTTTGTAGGGAAAACGCCGCTAAA-CATCAACACCTATT
1 GCGGCGTTTGTAAGGAAAACGCCGCTAAATC-TCAACACCTACT
1520458 GCG
1 GCG
1520461 ACATTTTTTG
Statistics
Matches: 192, Mismatches: 56, Indels: 21
0.71 0.21 0.08
Matches are distributed among these distances:
41 4 0.02
42 65 0.34
43 120 0.62
44 3 0.02
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26
Consensus pattern (43 bp):
GCGGCGTTTGTAAGGAAAACGCCGCTAAATCTCAACACCTACT
Found at i:1520566 original size:12 final size:14
Alignment explanation
Indices: 1520530--1520566 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
1520520 CCCCGCTAAC
1520530 TTTAGCGGCGCTAT
1 TTTAGCGGCGCTAT
1520544 TTTCAGCGGCGCT-T
1 TTT-AGCGGCGCTAT
1520558 TTT-GCGGCG
1 TTTAGCGGCG
1520567 TTTGTCATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 6 0.27
14 7 0.32
15 9 0.41
ACGTcount: A:0.08, C:0.24, G:0.32, T:0.35
Consensus pattern (14 bp):
TTTAGCGGCGCTAT
Found at i:1521787 original size:31 final size:31
Alignment explanation
Indices: 1521747--1521906 Score: 284
Period size: 31 Copynumber: 5.2 Consensus size: 31
1521737 GGTCACAATA
*
1521747 TAAATTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
* *
1521778 TAAACTGTTCATATGTGCCTTCAAACATATA
1 TAAACTGTTCATATGTGCCTTTAAACATATG
*
1521809 TAAACTGTTCATATGTGGCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
1521840 TAAACTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
1521871 TAAACTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
1521902 TAAAC
1 TAAAC
1521907 CCTCGAATCT
Statistics
Matches: 122, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 122 1.00
ACGTcount: A:0.34, C:0.16, G:0.12, T:0.38
Consensus pattern (31 bp):
TAAACTGTTCATATGTGCCTTTAAACATATG
Found at i:1521870 original size:16 final size:16
Alignment explanation
Indices: 1521849--1521902 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
1521839 GTAAACTGTT
1521849 CATATGTGCCTTTAAA
1 CATATGTGCCTTTAAA
**
1521865 CATATGTAAACTGTT---
1 CATATGT-GCCT-TTAAA
1521880 CATATGTGCCTTTAAA
1 CATATGTGCCTTTAAA
1521896 CATATGT
1 CATATGT
1521903 AAACCCTCGA
Statistics
Matches: 29, Mismatches: 4, Indels: 10
0.67 0.09 0.23
Matches are distributed among these distances:
13 2 0.07
14 2 0.07
15 7 0.24
16 14 0.48
17 2 0.07
18 2 0.07
ACGTcount: A:0.31, C:0.17, G:0.13, T:0.39
Consensus pattern (16 bp):
CATATGTGCCTTTAAA
Found at i:1522523 original size:64 final size:65
Alignment explanation
Indices: 1522415--1522623 Score: 228
Period size: 64 Copynumber: 3.3 Consensus size: 65
1522405 TAATGAAGGT
* * ** * **
1522415 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAAGGTATTCGATGTAGT-ATTATTGCTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTAGTCATTATTAATGGG
* ** *
1522479 ATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGT-TTCATTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTAGTCATTATTAATGGG
* * * * **
1522543 ATGCATTGATGCACTACTTATGCATCGATGCATGAATTGCATTCGATGTATTTATT-TTAA-AAG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTAGTCATTATTAATGGG
1522606 AGTGCATCGATGCACTAC
1 A-TGCATCGATGCACTAC
1522624 CAATGCATTG
Statistics
Matches: 123, Mismatches: 19, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
63 3 0.02
64 115 0.93
65 5 0.04
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.33
Consensus pattern (65 bp):
ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTAGTCATTATTAATGGG
Found at i:1523565 original size:26 final size:26
Alignment explanation
Indices: 1523516--1523570 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
1523506 AATTCATACC
* *
1523516 TAATCCAAAGCAATCAATATTAATTA
1 TAATCCAAAGCAAACAATATTAATCA
*
1523542 TAATCCAAATCAAACAATGA-TAATCA
1 TAATCCAAAGCAAACAAT-ATTAATCA
1523568 TAA
1 TAA
1523571 ATTTGAATGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 24 0.96
27 1 0.04
ACGTcount: A:0.53, C:0.16, G:0.04, T:0.27
Consensus pattern (26 bp):
TAATCCAAAGCAAACAATATTAATCA
Found at i:1527208 original size:3 final size:3
Alignment explanation
Indices: 1527202--1527245 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
1527192 TTTGAATATG
1527202 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1527246 TTGTTATTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1528404 original size:25 final size:24
Alignment explanation
Indices: 1528362--1528408 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
1528352 TTAGTAATTG
* *
1528362 TTTTTAATTTTTATCTTTAATTTT
1 TTTTTAAATTTAATCTTTAATTTT
1528386 TTTTTAAATTTAATACTTTAATT
1 TTTTTAAATTTAAT-CTTTAATT
1528409 ATTGTTCTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.68
Consensus pattern (24 bp):
TTTTTAAATTTAATCTTTAATTTT
Found at i:1529994 original size:7 final size:7
Alignment explanation
Indices: 1529968--1530005 Score: 51
Period size: 7 Copynumber: 5.3 Consensus size: 7
1529958 GTACTAACCA
1529968 TTTTATT
1 TTTTATT
1529975 TTTCT-TAT
1 TTT-TAT-T
1529983 TTTTATT
1 TTTTATT
1529990 TTTTATT
1 TTTTATT
1529997 TTTTATT
1 TTTTATT
1530004 TT
1 TT
1530006 GCTCTAACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
7 22 0.79
8 6 0.21
ACGTcount: A:0.13, C:0.03, G:0.00, T:0.84
Consensus pattern (7 bp):
TTTTATT
Found at i:1532965 original size:12 final size:12
Alignment explanation
Indices: 1532938--1533013 Score: 59
Period size: 13 Copynumber: 6.2 Consensus size: 12
1532928 CTCATTTATT
*
1532938 AGAAAAAA-AGA
1 AGAAAAAAGAAA
1532949 A-AAAAAAGAAA
1 AGAAAAAAGAAA
1532960 AGAAAAAAGAAA
1 AGAAAAAAGAAA
*
1532972 GGAAAAAAAGATGAA
1 AG-AAAAAAGA--AA
1532987 A-AGAAAAAGAAAA
1 AGA-AAAAAG-AAA
*
1533000 AGAAAGAAGAAA
1 AGAAAAAAGAAA
1533012 AG
1 AG
1533014 GAATTAAATC
Statistics
Matches: 53, Mismatches: 4, Indels: 15
0.74 0.06 0.21
Matches are distributed among these distances:
10 6 0.11
11 4 0.08
12 16 0.30
13 17 0.32
14 7 0.13
15 3 0.06
ACGTcount: A:0.79, C:0.00, G:0.20, T:0.01
Consensus pattern (12 bp):
AGAAAAAAGAAA
Found at i:1532978 original size:33 final size:33
Alignment explanation
Indices: 1532941--1533013 Score: 80
Period size: 33 Copynumber: 2.2 Consensus size: 33
1532931 ATTTATTAGA
1532941 AAAAAAGA-AAAAAAAG-AAAAGAAAAAAGAAAGG
1 AAAAAAGAGAAAAAAAGAAAAAG-AAAAAGAAA-G
**
1532974 AAAAAA-AGATGAAAAGAAAAAGAAAAAGAAAG
1 AAAAAAGAGAAAAAAAGAAAAAGAAAAAGAAAG
1533006 AAGAAAAG
1 AA-AAAAG
1533014 GAATTAAATC
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
32 4 0.12
33 25 0.74
34 5 0.15
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.01
Consensus pattern (33 bp):
AAAAAAGAGAAAAAAAGAAAAAGAAAAAGAAAG
Found at i:1532982 original size:34 final size:32
Alignment explanation
Indices: 1532938--1533013 Score: 91
Period size: 34 Copynumber: 2.3 Consensus size: 32
1532928 CTCATTTATT
1532938 AGAAAAAAAGAAAAAAA-AGAAAAGAAAAAAGAA
1 AGAAAAAAAGAAAAAAAGA-AAAAG-AAAAAGAA
**
1532971 AGGAAAAAAAGATGAAAAGAAAAAGAAAAAGAA
1 A-GAAAAAAAGAAAAAAAGAAAAAGAAAAAGAA
*
1533004 AGAAGAAAAG
1 AGAAAAAAAG
1533014 GAATTAAATC
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
32 8 0.21
33 10 0.26
34 19 0.50
35 1 0.03
ACGTcount: A:0.79, C:0.00, G:0.20, T:0.01
Consensus pattern (32 bp):
AGAAAAAAAGAAAAAAAGAAAAAGAAAAAGAA
Found at i:1533009 original size:27 final size:27
Alignment explanation
Indices: 1532942--1533013 Score: 80
Period size: 27 Copynumber: 2.7 Consensus size: 27
1532932 TTTATTAGAA
*
1532942 AAAAAGAAAAAAAAGAAAAGAAAAAAG
1 AAAAAGAAAAAGAAGAAAAGAAAAAAG
*
1532969 AAAGGAA-AAAAAGATGAAAAG-AAAAAG
1 AAA--AAGAAAAAGAAGAAAAGAAAAAAG
1532996 AAAAAG--AAAGAAGAAAAG
1 AAAAAGAAAAAGAAGAAAAG
1533014 GAATTAAATC
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
24 11 0.28
25 2 0.05
27 12 0.31
28 12 0.31
29 2 0.05
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.01
Consensus pattern (27 bp):
AAAAAGAAAAAGAAGAAAAGAAAAAAG
Found at i:1534652 original size:52 final size:52
Alignment explanation
Indices: 1534545--1534726 Score: 260
Period size: 51 Copynumber: 3.5 Consensus size: 52
1534535 ATATGTGGAT
* * * * *
1534545 ATCTTGAAGGTTCACATCAACATG-AAAAGATAGAAGTAATCCATGTAGGGT
1 ATCTTGAAGGCTCACATCAGCATGAAAAAGACAGAAGTAATCCATGTGGGGC
*
1534596 ATCTTAAAGGCTCACATCAGCATGAAAAAGACAGAAGTAATCCATGTGGGGC
1 ATCTTGAAGGCTCACATCAGCATGAAAAAGACAGAAGTAATCCATGTGGGGC
* *
1534648 ATCTTGAAGGCTCATATCAGTATGAAAAAG-CAGAAGTAATCCATGTGGGGC
1 ATCTTGAAGGCTCACATCAGCATGAAAAAGACAGAAGTAATCCATGTGGGGC
* *
1534699 ATCTTGAAGGATCACACCAGCATGAAAA
1 ATCTTGAAGGCTCACATCAGCATGAAAA
1534727 GGTTGGGATA
Statistics
Matches: 117, Mismatches: 13, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
51 66 0.56
52 51 0.44
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.22
Consensus pattern (52 bp):
ATCTTGAAGGCTCACATCAGCATGAAAAAGACAGAAGTAATCCATGTGGGGC
Found at i:1535278 original size:54 final size:54
Alignment explanation
Indices: 1535192--1535297 Score: 167
Period size: 54 Copynumber: 2.0 Consensus size: 54
1535182 TACTGACAAG
* *
1535192 AAATCTTGGCAGAAGCCACAGGAAAAGATGAATGTGTTGACAAATGTTTTACGA
1 AAATCTGGGCAGAAGCCACAAGAAAAGATGAATGTGTTGACAAATGTTTTACGA
* * *
1535246 AAATCTGGGCAGAAGCCACAAGAAAGGTTGAATGTGTTGTCAAATGTTTTAC
1 AAATCTGGGCAGAAGCCACAAGAAAAGATGAATGTGTTGACAAATGTTTTAC
1535298 AAACCAGTGA
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 47 1.00
ACGTcount: A:0.37, C:0.13, G:0.25, T:0.25
Consensus pattern (54 bp):
AAATCTGGGCAGAAGCCACAAGAAAAGATGAATGTGTTGACAAATGTTTTACGA
Found at i:1536357 original size:73 final size:73
Alignment explanation
Indices: 1536164--1536371 Score: 344
Period size: 73 Copynumber: 2.8 Consensus size: 73
1536154 ACTTGAGATT
** * *
1536164 GCTGGAGAAAGTTTCACTTGAAATAGCAATTTATCTCACTTGAGATTACTTTTCTCAAAATAAAC
1 GCTGGAGAAAGTTTCACTTGAAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAC
1536229 TGTTTCTC
66 TGTTTCTC
* *
1536237 GCTGGAGAAAGTTTCACTTGAAATAGCAATTTATCTCACTTGAGATTGTTTTTATTAAAACAAAT
1 GCTGGAGAAAGTTTCACTTGAAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAC
1536302 TGTTTCTC
66 TGTTTCTC
* *
1536310 GCTTGAGAAAGTTTCACTCGAAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTAAAACA
1 GCTGGAGAAAGTTTCACTTGAAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTAAAACA
1536372 TTTCCAGAAG
Statistics
Matches: 126, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
73 126 1.00
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (73 bp):
GCTGGAGAAAGTTTCACTTGAAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAC
TGTTTCTC
Found at i:1536523 original size:123 final size:123
Alignment explanation
Indices: 1536368--1536696 Score: 514
Period size: 123 Copynumber: 2.7 Consensus size: 123
1536358 TTTTTCTTAA
* *
1536368 AACATTTCCAGAAGGAGTTCGTAATAAGAAGAACTCATCTGAAGAGTAAGAACAAGTTCATAATC
1 AACATTTCCACAAGGAGTTCGTAATAAGAAGAACTCATCTGAAGAGAAAGAACAAGTTCATAATC
* * * * *
1536433 TGAAGAACTTATTCAACCTTTTGCTCGACTTTATCGCAGAAGGAGATATAGCATCATC
66 TGAAGAACTTATTCAACCTTTTGCTCGAATCTATCGCACAAGGAGATAGAGCAGCATC
*
1536491 AACATTTGCACAAGGAGTTCGTAATAAGAAGAACTCATCTGAAGAGAAAGAACAAGTTCATAATC
1 AACATTTCCACAAGGAGTTCGTAATAAGAAGAACTCATCTGAAGAGAAAGAACAAGTTCATAATC
*
1536556 TGAATAACTTATTCAACCTTTTGCTCGAATCTATCGCACAAGGAGATAGAGCAGCATC
66 TGAAGAACTTATTCAACCTTTTGCTCGAATCTATCGCACAAGGAGATAGAGCAGCATC
* * * * *
1536614 AACATTTCCATAAGGAGTTCGTAATAAGAAGAACTCATCCGAATAGAAAGAAGAAGTTCATAATA
1 AACATTTCCACAAGGAGTTCGTAATAAGAAGAACTCATCTGAAGAGAAAGAACAAGTTCATAATC
* *
1536679 AGAAGAACTTGTTCAACC
66 TGAAGAACTTATTCAACC
1536697 AAAGCTTAAT
Statistics
Matches: 188, Mismatches: 18, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
123 188 1.00
ACGTcount: A:0.40, C:0.18, G:0.18, T:0.25
Consensus pattern (123 bp):
AACATTTCCACAAGGAGTTCGTAATAAGAAGAACTCATCTGAAGAGAAAGAACAAGTTCATAATC
TGAAGAACTTATTCAACCTTTTGCTCGAATCTATCGCACAAGGAGATAGAGCAGCATC
Found at i:1538328 original size:21 final size:19
Alignment explanation
Indices: 1538287--1538330 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 19
1538277 GTATATTTAG
**
1538287 TAATTTTTTTTTTTATCTT
1 TAATTTTTTTTTTTAAATT
1538306 TAATTTTATTTTTTTAAAATT
1 TAATTTT-TTTTTTT-AAATT
1538327 TAAT
1 TAAT
1538331 ACTTTAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 7 0.33
20 7 0.33
21 7 0.33
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.70
Consensus pattern (19 bp):
TAATTTTTTTTTTTAAATT
Found at i:1539752 original size:15 final size:15
Alignment explanation
Indices: 1539734--1539768 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1539724 TAAAAATGTA
1539734 AAATTTAAATTACAG
1 AAATTTAAATTACAG
* *
1539749 AAATTTAGATTACTG
1 AAATTTAAATTACAG
1539764 AAATT
1 AAATT
1539769 AGGACTAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.49, C:0.06, G:0.09, T:0.37
Consensus pattern (15 bp):
AAATTTAAATTACAG
Found at i:1545511 original size:38 final size:36
Alignment explanation
Indices: 1545476--1545545 Score: 97
Period size: 37 Copynumber: 1.9 Consensus size: 36
1545466 TACAAATTGT
1545476 AAAATATTTATAT-ATTTTCTTTAAAAAAATTAAATTC
1 AAAATATTTATATAATTTT-TTT-AAAAAATTAAATTC
* *
1545513 ATAATATTTATATAATTTTTTTACAAAATTAAA
1 AAAATATTTATATAATTTTTTTAAAAAATTAAA
1545546 AATATAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
36 10 0.33
37 15 0.50
38 5 0.17
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (36 bp):
AAAATATTTATATAATTTTTTTAAAAAATTAAATTC
Found at i:1546670 original size:19 final size:20
Alignment explanation
Indices: 1546633--1546670 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
1546623 GGAAAAGAAT
1546633 ATTTCCGAATGAGAGAAAAC
1 ATTTCCGAATGAGAGAAAAC
1546653 ATTTCC-AA-GAGAAGAAAA
1 ATTTCCGAATGAG-AGAAAA
1546671 GTTCTTGAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 3 0.18
19 8 0.47
20 6 0.35
ACGTcount: A:0.50, C:0.13, G:0.18, T:0.18
Consensus pattern (20 bp):
ATTTCCGAATGAGAGAAAAC
Found at i:1550365 original size:58 final size:57
Alignment explanation
Indices: 1550251--1550366 Score: 133
Period size: 57 Copynumber: 2.0 Consensus size: 57
1550241 TTCAATACTT
*** * * * **
1550251 TCAAGAAATAAATCCAACAATTTTTTTATTTTTACAAGATAGAATCATACTTGATTC
1 TCAAGAAATAAATCCAACAATTTAAATATTTCTACAAAACAGAATCATACAAGATTC
* *
1550308 TCAAGAAATAAATTCAACGATTTAAATATCTTCTACAAAACAGAATCATACAAGATTC
1 TCAAGAAATAAATCCAACAATTTAAATAT-TTCTACAAAACAGAATCATACAAGATTC
1550366 T
1 T
1550367 ATGAAAATAA
Statistics
Matches: 48, Mismatches: 10, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
57 24 0.50
58 24 0.50
ACGTcount: A:0.44, C:0.16, G:0.07, T:0.34
Consensus pattern (57 bp):
TCAAGAAATAAATCCAACAATTTAAATATTTCTACAAAACAGAATCATACAAGATTC
Found at i:1550469 original size:58 final size:56
Alignment explanation
Indices: 1550266--1550480 Score: 139
Period size: 58 Copynumber: 3.7 Consensus size: 56
1550256 AAATAAATCC
* * * ** *
1550266 AACAATTTTTTTATTTTTACAAGATAGAATCATACTTGATTCTCAAG-AAAT-AAATT
1 AACAATTTATTTCTTTTTACAA-ACAGAATCATACAAGATTC-CATGAAAATAAAATT
* * * *
1550322 CAACGATTTAAATATC-TTCTACAAAACAGAATCATACAAGATTCTATGAAAATAAAATT
1 -AACAATTT--ATTTCTTTTTAC-AAACAGAATCATACAAGATTCCATGAAAATAAAATT
* * ** * * *
1550381 AATAATTTATTTCTTTTTACAGGATGGAATCGTTCAAGATTTCCATGAAAATAAATTT
1 AACAATTTATTTCTTTTTACA-AACAGAATCATACAAGA-TTCCATGAAAATAAAATT
* ** *
1550439 GACGTTTTATTTCTTTTTACAAACCAGAATCATATAAGATTC
1 AACAATTTATTTCTTTTTACAAA-CAGAATCATACAAGATTC
1550481 ATAGGAAAAT
Statistics
Matches: 118, Mismatches: 31, Indels: 18
0.71 0.19 0.11
Matches are distributed among these distances:
56 5 0.04
57 30 0.25
58 74 0.63
59 9 0.08
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (56 bp):
AACAATTTATTTCTTTTTACAAACAGAATCATACAAGATTCCATGAAAATAAAATT
Found at i:1554898 original size:29 final size:29
Alignment explanation
Indices: 1554819--1554899 Score: 78
Period size: 29 Copynumber: 2.8 Consensus size: 29
1554809 TGACTAAAAT
*
1554819 AAAAT-AAAAATAAAATAATAATTAAAGTAC
1 AAAATCAAAAATAAAATAA-AA-TAAAGGAC
* *
1554849 AAAATTAAACATATAAA-AAAATAAAGGAC
1 AAAATCAAAAATA-AAATAAAATAAAGGAC
1554878 AATAA-CAAAAATAAAATAAAAT
1 AA-AATCAAAAATAAAATAAAAT
1554900 TATAATTAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
28 3 0.07
29 20 0.47
30 9 0.21
31 8 0.19
32 3 0.07
ACGTcount: A:0.72, C:0.05, G:0.04, T:0.20
Consensus pattern (29 bp):
AAAATCAAAAATAAAATAAAATAAAGGAC
Found at i:1555029 original size:21 final size:22
Alignment explanation
Indices: 1554988--1555030 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
1554978 AATTAATGAC
1554988 TAACATGAAATAAAATAGAAAT
1 TAACATGAAATAAAATAGAAAT
* *
1555010 TAACATGCAA-AAAATCGAAAT
1 TAACATGAAATAAAATAGAAAT
1555031 AAAATAAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.60, C:0.09, G:0.09, T:0.21
Consensus pattern (22 bp):
TAACATGAAATAAAATAGAAAT
Found at i:1556384 original size:123 final size:123
Alignment explanation
Indices: 1556226--1556463 Score: 352
Period size: 123 Copynumber: 1.9 Consensus size: 123
1556216 GATGTTGATT
* * * * *
1556226 TATCTCCTTCTGTGGTATAATCGATGAAAATGTTGAATAAGTTCTTCAAATTATGAACTTTTTCT
1 TATCTCCTTCTGTGATAGAATAGATGAAAAGGTTGAATAAGTTCTTCAAATTATGAACTTCTTCT
* * * *
1556291 TTCTTTTCAGGTGAATTCTTCTTATTACGAACTCCTTTTGGAAATGTTGATGATGCTC
66 TCCTCTTCAGATGAATTCTTCTTATTACGAACTCCTTCTGGAAATGTTGATGATGCTC
* *
1556349 TATCTCCTTCTGTGATAGAGTAGA-GCAAAAGGTTGAATAAGTTCTTCAGATTATGAACTTCTTC
1 TATCTCCTTCTGTGATAGAATAGATG-AAAAGGTTGAATAAGTTCTTCAAATTATGAACTTCTTC
*
1556413 TTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCCTTCTGGAAATGTTGA
65 TTCCTCTTCAGATGAATTCTTCTTATTACGAACTCCTTCTGGAAATGTTGA
1556464 CCCATTGAGT
Statistics
Matches: 102, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
122 1 0.01
123 101 0.99
ACGTcount: A:0.26, C:0.17, G:0.16, T:0.41
Consensus pattern (123 bp):
TATCTCCTTCTGTGATAGAATAGATGAAAAGGTTGAATAAGTTCTTCAAATTATGAACTTCTTCT
TCCTCTTCAGATGAATTCTTCTTATTACGAACTCCTTCTGGAAATGTTGATGATGCTC
Found at i:1556525 original size:36 final size:35
Alignment explanation
Indices: 1556484--1556747 Score: 151
Period size: 36 Copynumber: 7.3 Consensus size: 35
1556474 GATGGAAATT
1556484 TTTGTTTCT-AGTGAAACTGTCTCAAGTGAGACAAA
1 TTTGTTT-TAAGTGAAACTGTCTCAAGTGAGACAAA
** ** * *
1556519 TCTTGTTTTAAGAAAAACAATCCCAAGTGAGATAAA
1 T-TTGTTTTAAGTGAAACTGTCTCAAGTGAGACAAA
** *
1556555 TTGATGTTTCGAGTGAAACTGTCTCAAGAGAGACAAA
1 TT--TGTTTTAAGTGAAACTGTCTCAAGTGAGACAAA
* * * *
1556592 TCTTGTTTTAAG-AAAAATAATCTCAAGTGAGATAAA
1 T-TTGTTTTAAGTGAAACT-GTCTCAAGTGAGACAAA
* * *
1556628 TTGATGTTTTGAGTGAAACTGTCTCAAGCGAGAGAAA
1 TT--TGTTTTAAGTGAAACTGTCTCAAGTGAGACAAA
* *** *
1556665 GTTTGTTTTAAG-AAAAAAATCTCAAGTGAGA-TAA
1 -TTTGTTTTAAGTGAAACTGTCTCAAGTGAGACAAA
* * * *
1556699 GTTGCTATTTCAAGTGAAACTTTTCTCAAGCGAGA-AAG
1 TTTG-T-TTT-AAGTGAAAC-TGTCTCAAGTGAGACAAA
1556737 TTTGTTTTAAG
1 TTTGTTTTAAG
1556748 AAAAATAATA
Statistics
Matches: 170, Mismatches: 44, Indels: 30
0.70 0.18 0.12
Matches are distributed among these distances:
33 3 0.02
34 3 0.02
35 28 0.16
36 63 0.37
37 51 0.30
38 22 0.13
ACGTcount: A:0.37, C:0.11, G:0.20, T:0.32
Consensus pattern (35 bp):
TTTGTTTTAAGTGAAACTGTCTCAAGTGAGACAAA
Found at i:1556762 original size:72 final size:73
Alignment explanation
Indices: 1556488--1556797 Score: 403
Period size: 73 Copynumber: 4.3 Consensus size: 73
1556478 GAAATTTTTG
* * * *
1556488 TTTCTAGTGAAACTGTCTCAAGTGAGACAAATCTTGTTTTAAGAAAAACAATCCCAAGTGAGATA
1 TTTCGAGTGAAACTGTCTCAAGCGAGACAAATCTTGTTTTAAGAAAAATAATCTCAAGTGAGATA
*
1556553 AATTGATG
66 AATTGATA
*
1556561 TTTCGAGTGAAACTGTCTCAAGAGAGACAAATCTTGTTTTAAGAAAAATAATCTCAAGTGAGATA
1 TTTCGAGTGAAACTGTCTCAAGCGAGACAAATCTTGTTTTAAGAAAAATAATCTCAAGTGAGATA
*
1556626 AATTGATG
66 AATTGATA
* *
1556634 TTTTGAGTGAAACTGTCTCAAGCGAGAGAAAGT-TTGTTTTAAGAAAAA-AATCTCAAGTGAGAT
1 TTTCGAGTGAAACTGTCTCAAGCGAGACAAA-TCTTGTTTTAAGAAAAATAATCTCAAGTGAGAT
* *
1556697 AAGTTGCTA
65 AAATTGATA
* * * * *
1556706 TTTCAAGTGAAACTTTTCTCAAGCGAGA-AAGT-TTGTTTTAAGAAAAATAATATCAAGTGAGAA
1 TTTCGAGTGAAAC-TGTCTCAAGCGAGACAAATCTTGTTTTAAGAAAAATAATCTCAAGTGAGAT
**
1556769 AAATTTCTA
65 AAATTGATA
*
1556778 TTTCGAGTGAAACTTTCTCA
1 TTTCGAGTGAAACTGTCTCA
1556798 GGAGAGACGT
Statistics
Matches: 215, Mismatches: 19, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
71 23 0.11
72 66 0.31
73 125 0.58
74 1 0.00
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.32
Consensus pattern (73 bp):
TTTCGAGTGAAACTGTCTCAAGCGAGACAAATCTTGTTTTAAGAAAAATAATCTCAAGTGAGATA
AATTGATA
Found at i:1556919 original size:6 final size:6
Alignment explanation
Indices: 1556905--1557307 Score: 783
Period size: 6 Copynumber: 67.5 Consensus size: 6
1556895 AAAATCATGG
*
1556905 ATGTAT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT
1 ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT
1556953 ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT
1 ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT
1557001 ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT
1 ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT
1557049 ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT
1 ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT
1557097 A--TGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT
1 ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT
1557143 ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT
1 ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT
1557191 ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT
1 ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT
1557239 ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT
1 ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT
1557287 ATGTGT ATGTGT ATGTGT ATG
1 ATGTGT ATGTGT ATGTGT ATG
1557308 CCGATGCATG
Statistics
Matches: 394, Mismatches: 1, Indels: 4
0.99 0.00 0.01
Matches are distributed among these distances:
4 4 0.01
6 390 0.99
ACGTcount: A:0.17, C:0.00, G:0.33, T:0.50
Consensus pattern (6 bp):
ATGTGT
Found at i:1559326 original size:88 final size:89
Alignment explanation
Indices: 1559219--1559389 Score: 229
Period size: 89 Copynumber: 1.9 Consensus size: 89
1559209 AAATAGTATA
* * * * *
1559219 ATAGGCTAGCTGAATATTATCCATAAAT-CGGGGCT-ATTAACCGACTGTTTTAGGGGGACAACT
1 ATAGGCTAGCTGAACATTATCCATAAATCCAGAG-TGATTAACCAACTGCTTTAGGGGGACAACT
1559282 CAAGCTTTATTGTATATATAATAAT
65 CAAGCTTTATTGTATATATAATAAT
* * **
1559307 ATAGGCTAGTTGAACATTATCCATAAATCCAGAGTGATTAACCAATTGCTTTAGGGGGTTAACTC
1 ATAGGCTAGCTGAACATTATCCATAAATCCAGAGTGATTAACCAACTGCTTTAGGGGGACAACTC
*
1559372 AATCTTTATTGTATATAT
66 AAGCTTTATTGTATATAT
1559390 CATGAGTATA
Statistics
Matches: 71, Mismatches: 10, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
88 27 0.38
89 44 0.62
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.35
Consensus pattern (89 bp):
ATAGGCTAGCTGAACATTATCCATAAATCCAGAGTGATTAACCAACTGCTTTAGGGGGACAACTC
AAGCTTTATTGTATATATAATAAT
Found at i:1562767 original size:2 final size:2
Alignment explanation
Indices: 1562760--1562816 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
1562750 ACTAAAGTAA
1562760 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1562802 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
1562817 GGGTATTTAT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1563139 original size:22 final size:20
Alignment explanation
Indices: 1563111--1563152 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 20
1563101 AATTAATGAC
1563111 TAACATGAAATAAAATAGAAAT
1 TAACATGAAA-AAAAT-GAAAT
*
1563133 TAACATGCAAAAAATGAAAT
1 TAACATGAAAAAAATGAAAT
1563153 AAAATAAAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 5 0.26
21 5 0.26
22 9 0.47
ACGTcount: A:0.62, C:0.07, G:0.10, T:0.21
Consensus pattern (20 bp):
TAACATGAAAAAAATGAAAT
Found at i:1563872 original size:20 final size:20
Alignment explanation
Indices: 1563842--1563890 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
1563832 AAAAATAAAA
*
1563842 TAAAGAATAAAATACCAAACTG
1 TAAA-AATAAAAGACCAAA-TG
1563864 -AAAAAT-AAAGACCAAATG
1 TAAAAATAAAAGACCAAATG
1563882 TAAAAATAA
1 TAAAAATAA
1563891 CATTTGCTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
18 2 0.08
19 15 0.62
20 4 0.17
21 3 0.12
ACGTcount: A:0.65, C:0.10, G:0.08, T:0.16
Consensus pattern (20 bp):
TAAAAATAAAAGACCAAATG
Found at i:1566570 original size:41 final size:41
Alignment explanation
Indices: 1566493--1566572 Score: 101
Period size: 41 Copynumber: 2.0 Consensus size: 41
1566483 AAGCAACTGT
*
1566493 AGGGGTGTCAGAAGCACCCAGGGGCGGCGGTAGGGCACTTC
1 AGGGGTGTCAGAAGCACCCAAGGGCGGCGGTAGGGCACTTC
* *
1566534 AGGGGCTG-CAGAAGACATCCAAGGGCGGCGG-CGGGCACT
1 AGGGG-TGTCAGAAG-CACCCAAGGGCGGCGGTAGGGCACT
1566573 GTTAGTGTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
41 18 0.53
42 16 0.47
ACGTcount: A:0.21, C:0.25, G:0.44, T:0.10
Consensus pattern (41 bp):
AGGGGTGTCAGAAGCACCCAAGGGCGGCGGTAGGGCACTTC
Found at i:1569794 original size:21 final size:21
Alignment explanation
Indices: 1569770--1569809 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1569760 CACGTGCTCC
*
1569770 AATGCATGTTCCATTAAGTAT
1 AATGCATCTTCCATTAAGTAT
*
1569791 AATGCCTCTTCCATTAAGT
1 AATGCATCTTCCATTAAGT
1569810 GAGAACAACC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.38
Consensus pattern (21 bp):
AATGCATCTTCCATTAAGTAT
Found at i:1570114 original size:45 final size:45
Alignment explanation
Indices: 1570060--1570163 Score: 145
Period size: 45 Copynumber: 2.3 Consensus size: 45
1570050 ACCACACCAA
* * *
1570060 ACCGTGACAATGCGGATAGGATCACGTCCTTGGGAGCAATGGCTG
1 ACCGTGACAATGCGGATAGGACCACGTACTTGGGAGCAATGGCGG
* * * *
1570105 ACTGTGACAATGCGTATGGGACCACGTACTTTGGAGCAATGGCGG
1 ACCGTGACAATGCGGATAGGACCACGTACTTGGGAGCAATGGCGG
1570150 ACCGTGACAATGCG
1 ACCGTGACAATGCG
1570164 CATTGGGCTG
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 51 1.00
ACGTcount: A:0.25, C:0.22, G:0.33, T:0.20
Consensus pattern (45 bp):
ACCGTGACAATGCGGATAGGACCACGTACTTGGGAGCAATGGCGG
Found at i:1573561 original size:187 final size:184
Alignment explanation
Indices: 1573244--1573634 Score: 608
Period size: 187 Copynumber: 2.1 Consensus size: 184
1573234 TTTTCTAATT
* * * * *
1573244 TATATAA-AAATTAAATGTTTTTTAATTCAAAAAAAGTTTATAATTAATTTAAATAATATATAAT
1 TATATAATATATTTAATATTTTTTAATTAAAAAAAAGTTTACAATTAATTTAAATAATATATAAT
1573308 TATAAAATAAAAATTTCAGATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATT
66 TATAAAATAAAAATTTCAGATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATT
* *
1573373 GGATCTTAAATTATTAATTGGGTTTTAAATGGTTTGGGCTT-AGCCCATATGTTA
131 GGATCTTAAATTATTAATTGAGTTTTAAATGGTTTGAG-TTGAGCCCATATGTTA
1573427 TATATAATATATTTAATATTTTTTAATTAAAAAAATAGTTTACAATTAATTTAAATAATATATAA
1 TATATAATATATTTAATATTTTTTAATTAAAAAAA-AGTTTACAATTAATTTAAATAATATATAA
* * * *
1573492 TTATAAAATATAAAAATTTTATAT-AATTTTTTAAATTAATTAATATTGATTTACGTTTAAAATT
65 TTAT-AAA-ATAAAAATTTCAGATAAATTTTTT-AATTAATTAATATTGATTTAAGTTTAAAAGT
*
1573556 TATTGGATCTTAAATTATTAATTGAGTTTTAAATGGTTTGAGTTGAGTCCATATGTTA
127 TATTGGATCTTAAATTATTAATTGAGTTTTAAATGGTTTGAGTTGAGCCCATATGTTA
1573614 TATATAATATATTTAATATTT
1 TATATAATATATTTAATATTT
1573635 AAAATTTAAT
Statistics
Matches: 190, Mismatches: 12, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
183 7 0.04
184 23 0.12
185 32 0.17
186 13 0.07
187 115 0.61
ACGTcount: A:0.42, C:0.03, G:0.08, T:0.47
Consensus pattern (184 bp):
TATATAATATATTTAATATTTTTTAATTAAAAAAAAGTTTACAATTAATTTAAATAATATATAAT
TATAAAATAAAAATTTCAGATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATT
GGATCTTAAATTATTAATTGAGTTTTAAATGGTTTGAGTTGAGCCCATATGTTA
Found at i:1575929 original size:22 final size:22
Alignment explanation
Indices: 1575878--1575962 Score: 111
Period size: 22 Copynumber: 3.9 Consensus size: 22
1575868 ATGTGAAATT
* *
1575878 TGTCCTGAATGACCTCATGTATA
1 TGTCCCGAAGGACCT-ATGTATA
*
1575901 --TCCCGAAGGATCTATGTATA
1 TGTCCCGAAGGACCTATGTATA
1575921 TGTCCCGAAGGACCTATGTATA
1 TGTCCCGAAGGACCTATGTATA
*
1575943 TGTCCCGAATGACCTATGTA
1 TGTCCCGAAGGACCTATGTA
1575963 ACCCTCGAAT
Statistics
Matches: 55, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
20 7 0.13
21 10 0.18
22 38 0.69
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (22 bp):
TGTCCCGAAGGACCTATGTATA
Found at i:1578341 original size:17 final size:18
Alignment explanation
Indices: 1578304--1578341 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
1578294 ACCTATTTTG
*
1578304 GTATCGATACTCACTCCA
1 GTATCGATACTCACGCCA
*
1578322 GTATTGATACTCA-GCCA
1 GTATCGATACTCACGCCA
1578339 GTA
1 GTA
1578342 GTATCATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.29
Consensus pattern (18 bp):
GTATCGATACTCACGCCA
Found at i:1578971 original size:32 final size:33
Alignment explanation
Indices: 1578930--1579004 Score: 95
Period size: 32 Copynumber: 2.3 Consensus size: 33
1578920 TTTTAGTTGG
1578930 ACTGAAAGCAAACT-GAA-CTAAAATCAA-CCGAA
1 ACTGAAAGCAAACTCGAATC-AAAATCAACCCG-A
*
1578962 ACTGAAAGC-AACTCGAATCAAAATTAACCCGA
1 ACTGAAAGCAAACTCGAATCAAAATCAACCCGA
1578994 ACTGAAAGCAA
1 ACTGAAAGCAA
1579005 CACAAACCGA
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
31 4 0.11
32 29 0.76
33 5 0.13
ACGTcount: A:0.51, C:0.23, G:0.13, T:0.13
Consensus pattern (33 bp):
ACTGAAAGCAAACTCGAATCAAAATCAACCCGA
Found at i:1579022 original size:32 final size:32
Alignment explanation
Indices: 1578961--1579027 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 32
1578951 AATCAACCGA
* * * *
1578961 AACTGAAAGCAACTCGAATCAAAATTAACCCG
1 AACTGAAAGCAACACAAACCAAAAGTAACCCG
*
1578993 AACTGAAAGCAACACAAACCGAAAGTAACCCG
1 AACTGAAAGCAACACAAACCAAAAGTAACCCG
1579025 AAC
1 AAC
1579028 AAAAAATAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.49, C:0.27, G:0.13, T:0.10
Consensus pattern (32 bp):
AACTGAAAGCAACACAAACCAAAAGTAACCCG
Found at i:1579140 original size:3 final size:3
Alignment explanation
Indices: 1579134--1579169 Score: 54
Period size: 3 Copynumber: 11.7 Consensus size: 3
1579124 GTTGTTGTTG
*
1579134 TTA TTA TTA TTA TTA TTA TTA TTA TTG TTA TCTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TT
1579170 TTTAGCATTG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1580153 original size:43 final size:43
Alignment explanation
Indices: 1580080--1580330 Score: 172
Period size: 43 Copynumber: 5.9 Consensus size: 43
1580070 TTTCAACAAA
*** * *
1580080 AAAACGCCGCAATAGGTGACAACATATAGCGGCGTTTGTTGAG
1 AAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGTTGAG
* * * *
1580123 GAAACGCCGCAAAAGGTATTGATATTTAGCGGCGTTT-TTCAG
1 AAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGTTGAG
* * * *
1580165 AAAAAGACGCAATAGGTGTTGATATTTAACGGCATTTG--GCAG
1 AAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGTTG-AG
* * * *
1580207 ACAAACGCCGCAATAGGCGTTGATGTTTAGCGGCGTTTTCTTCA-
1 A-AAACGCCGCAATAGGTGTTGATATTTAGCGGCG-TTTGTTGAG
* * * * * ***
1580251 CAAACGCCGCAATAGATGTTTATTTTTAACGGCGTTT-TTCCT
1 AAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGTTGAG
* *
1580293 ACAAACGCCGTAGA-AGATGTTGATATTTAGCGGCGTTT
1 A-AAACGCCGCA-ATAGGTGTTGATATTTAGCGGCGTTT
1580331 TCCTACAAAC
Statistics
Matches: 162, Mismatches: 37, Indels: 18
0.75 0.17 0.08
Matches are distributed among these distances:
41 3 0.02
42 40 0.25
43 114 0.70
44 4 0.02
45 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.29
Consensus pattern (43 bp):
AAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGTTGAG
Found at i:1580213 original size:85 final size:84
Alignment explanation
Indices: 1580124--1580331 Score: 227
Period size: 86 Copynumber: 2.4 Consensus size: 84
1580114 TTTGTTGAGG
* *
1580124 AAACGCCGCAAAAGGTATTGATATTTAGCGGCGTTTTTCAGAAAAAGACGCAATAGGTGTTGATA
1 AAACGCCGCAAAAGGTGTTGATATTTAGCGGCGTTTTTCA-AAAAAGACGCAATAGATGTTGATA
1580189 TTTAACGGCATTTGGCAGAC
65 TTTAACGGCATTTGGCAGAC
* * * * * * *
1580209 AAACGCCGCAATAGGCGTTGATGTTTAGCGGCGTTTTCTTCACAAACGCCGCAATAGATGTTTAT
1 AAACGCCGCAAAAGGTGTTGATATTTAGCGGCG-TTT-TTCAAAAAAGACGCAATAGATGTTGAT
* * ** **
1580274 TTTTAACGGCGTTTTTCCTAC
64 ATTTAACGGCATTTGGCAGAC
* * *
1580295 AAACGCCGTAGAAGATGTTGATATTTAGCGGCGTTTT
1 AAACGCCGCAAAAGGTGTTGATATTTAGCGGCGTTTT
1580332 CCTACAAACA
Statistics
Matches: 100, Mismatches: 21, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
84 1 0.01
85 32 0.32
86 63 0.63
87 4 0.04
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.31
Consensus pattern (84 bp):
AAACGCCGCAAAAGGTGTTGATATTTAGCGGCGTTTTTCAAAAAAGACGCAATAGATGTTGATAT
TTAACGGCATTTGGCAGAC
Found at i:1580331 original size:43 final size:42
Alignment explanation
Indices: 1580124--1580340 Score: 186
Period size: 43 Copynumber: 5.1 Consensus size: 42
1580114 TTTGTTGAGG
* * * * *
1580124 AAACGCCGCAAAAGGTATTGATATTTAGCGGCGTTTTTC-AGA
1 AAACGCCGCAATAGATGTTGATATTTAGCGGCGTTTTCCTA-C
* * * * * * **
1580166 AAAAGACGCAATAGGTGTTGATATTTAACGGCATTTGGCAGAC
1 AAACGCCGCAATAGATGTTGATATTTAGCGGCGTTT-TCCTAC
** * *
1580209 AAACGCCGCAATAGGCGTTGATGTTTAGCGGCGTTTTCTTCAC
1 AAACGCCGCAATAGATGTTGATATTTAGCGGCGTTTTCCT-AC
* * *
1580252 AAACGCCGCAATAGATGTTTATTTTTAACGGCGTTTTTCCTAC
1 AAACGCCGCAATAGATGTTGATATTTAGCGGCG-TTTTCCTAC
*
1580295 AAACGCCGTAGA-AGATGTTGATATTTAGCGGCGTTTTCCTAC
1 AAACGCCGCA-ATAGATGTTGATATTTAGCGGCGTTTTCCTAC
1580337 AAAC
1 AAAC
1580341 AAAATTTTAG
Statistics
Matches: 141, Mismatches: 29, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
42 44 0.31
43 89 0.63
44 8 0.06
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.30
Consensus pattern (42 bp):
AAACGCCGCAATAGATGTTGATATTTAGCGGCGTTTTCCTAC
Found at i:1581898 original size:41 final size:40
Alignment explanation
Indices: 1581853--1582002 Score: 144
Period size: 41 Copynumber: 3.7 Consensus size: 40
1581843 TTAAAATCAA
1581853 TTGCGGCGTTTAC-AGAAAAACGCCACTAATGTATGACCCAT
1 TTGCGGCGTTT-CTAGAAAAACGCCACTAATGTA-GACCCAT
* * * * * *
1581894 TTGCGGCGTTTCTTGTAAAACGACACTATAAGCA-ACTC-T
1 TTGCGGCGTTTCTAGAAAAACGCCACTA-ATGTAGACCCAT
* *
1581933 ATTGCGGCGTTTATATAAAAACGCCACTAATGTACGACCCAT
1 -TTGCGGCGTTTCTAGAAAAACGCCACTAATGTA-GACCCAT
* *
1581975 TTGCGGCGTTTCTTGTAAAACGCCACTA
1 TTGCGGCGTTTCTAGAAAAACGCCACTA
1582003 TAAACAACTC
Statistics
Matches: 85, Mismatches: 18, Indels: 12
0.74 0.16 0.10
Matches are distributed among these distances:
39 4 0.05
40 27 0.32
41 50 0.59
42 4 0.05
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.28
Consensus pattern (40 bp):
TTGCGGCGTTTCTAGAAAAACGCCACTAATGTAGACCCAT
Found at i:1581944 original size:81 final size:81
Alignment explanation
Indices: 1581852--1582200 Score: 399
Period size: 82 Copynumber: 4.3 Consensus size: 81
1581842 GTTAAAATCA
* *
1581852 ATTGCGGCGTTTACAGAAAAACGCCACTAATGTATGACCCATTTGCGGCGTTTCTTGTAAAACGA
1 ATTGCGGCGTTTATATAAAAACGCCACTAATGTATGACCCATTTGCGGCGTTTCTTGTAAAACGA
*
1581917 CACTATAAGCAACTCT
66 CACTATAAACAACTCT
* *
1581933 ATTGCGGCGTTTATATAAAAACGCCACTAATGTACGACCCATTTGCGGCGTTTCTTGTAAAACGC
1 ATTGCGGCGTTTATATAAAAACGCCACTAATGTATGACCCATTTGCGGCGTTTCTTGTAAAACGA
1581998 CACTATAAACAACTCT
66 CACTATAAACAACTCT
* * * *
1582014 ATTGCGGCGTTTATATAAAAACACCACTAAAT-TACT-ACTC-TATTGCGGTGTTT-TTTTAGAA
1 ATTGCGGCGTTTATATAAAAACGCCACT-AATGTA-TGACCCAT-TTGCGGCGTTTCTTGT--AA
*
1582075 AACGTCACTATAAACAACTCT
61 AACGACACTATAAACAACTCT
* * * *
1582096 ATTGCGGCGTTTATATAAAAACGCCGCTAAAT-TACT-ACTC-TATTGCGGTGTTT-TTTTAGAA
1 ATTGCGGCGTTTATATAAAAACGCCACT-AATGTA-TGACCCAT-TTGCGGCGTTTCTTGT--AA
*
1582157 AACGTCACTATAAACAACTCT
61 AACGACACTATAAACAACTCT
**
1582178 ATTGCGATGTTTATATAAAAACG
1 ATTGCGGCGTTTATATAAAAACG
1582201 AAGCTAAATT
Statistics
Matches: 248, Mismatches: 15, Indels: 9
0.91 0.06 0.03
Matches are distributed among these distances:
80 4 0.02
81 118 0.48
82 126 0.51
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.31
Consensus pattern (81 bp):
ATTGCGGCGTTTATATAAAAACGCCACTAATGTATGACCCATTTGCGGCGTTTCTTGTAAAACGA
CACTATAAACAACTCT
Found at i:1582095 original size:41 final size:40
Alignment explanation
Indices: 1581910--1582200 Score: 266
Period size: 41 Copynumber: 7.2 Consensus size: 40
1581900 CGTTTCTTGT
* * *
1581910 AAAACGACACTATAAGCAACTCTATTGCGGCGTTTATATA
1 AAAACGCCACTATAAACAACTCTATTGCGGTGTTTATATA
** * * * * *
1581950 AAAACGCCACTAATGTACGAC-CCATTTGCGGCGTTTCT-TGT
1 AAAACGCCACT-ATAAACAACTCTA-TTGCGGTGTTTATAT-A
*
1581991 AAAACGCCACTATAAACAACTCTATTGCGGCGTTTATATA
1 AAAACGCCACTATAAACAACTCTATTGCGGTGTTTATATA
* * * *
1582031 AAAACACCACTA-AATTACTACTCTATTGCGGTGTTTTTTTA
1 AAAACGCCACTATAA--ACAACTCTATTGCGGTGTTTATATA
* *
1582072 GAAAACGTCACTATAAACAACTCTATTGCGGCGTTTATATA
1 -AAAACGCCACTATAAACAACTCTATTGCGGTGTTTATATA
* * * *
1582113 AAAACGCCGCTA-AATTACTACTCTATTGCGGTGTTTTTTTA
1 AAAACGCCACTATAA--ACAACTCTATTGCGGTGTTTATATA
* *
1582154 GAAAACGTCACTATAAACAACTCTATTGCGATGTTTATATA
1 -AAAACGCCACTATAAACAACTCTATTGCGGTGTTTATATA
1582195 AAAACG
1 AAAACG
1582201 AAGCTAAATT
Statistics
Matches: 201, Mismatches: 37, Indels: 26
0.76 0.14 0.10
Matches are distributed among these distances:
39 4 0.02
40 58 0.29
41 115 0.57
42 20 0.10
43 4 0.02
ACGTcount: A:0.34, C:0.21, G:0.14, T:0.31
Consensus pattern (40 bp):
AAAACGCCACTATAAACAACTCTATTGCGGTGTTTATATA
Found at i:1582115 original size:82 final size:82
Alignment explanation
Indices: 1581910--1582230 Score: 420
Period size: 82 Copynumber: 3.9 Consensus size: 82
1581900 CGTTTCTTGT
* * * * *
1581910 AAAACGACACTATAAGCAACTCTATTGCGGCGTTTATATAAAAACGCCACT-AATGTACGAC-CC
1 AAAACGTCACTATAAACAACTCTATTGCGGCGTTTATATAAAAACACCACTAAAT-TACTACTCT
* *
1581973 ATTTGCGGCG-TTTCTT-G
65 A-TTGCGGTGTTTTTTTAG
*
1581990 TAAAACGCCACTATAAACAACTCTATTGCGGCGTTTATATAAAAACACCACTAAATTACTACTCT
1 -AAAACGTCACTATAAACAACTCTATTGCGGCGTTTATATAAAAACACCACTAAATTACTACTCT
1582055 ATTGCGGTGTTTTTTTAG
65 ATTGCGGTGTTTTTTTAG
* *
1582073 AAAACGTCACTATAAACAACTCTATTGCGGCGTTTATATAAAAACGCCGCTAAATTACTACTCTA
1 AAAACGTCACTATAAACAACTCTATTGCGGCGTTTATATAAAAACACCACTAAATTACTACTCTA
1582138 TTGCGGTGTTTTTTTAG
66 TTGCGGTGTTTTTTTAG
** * *
1582155 AAAACGTCACTATAAACAACTCTATTGCGATGTTTATATAAAAACGA--AGCTAAATTACCACCC
1 AAAACGTCACTATAAACAACTCTATTGCGGCGTTTATATAAAAAC-ACCA-CTAAATTACTACTC
*
1582218 TATTGCGGAGTTT
64 TATTGCGGTGTTT
1582231 GTTGAAAAAA
Statistics
Matches: 217, Mismatches: 17, Indels: 11
0.89 0.07 0.04
Matches are distributed among these distances:
81 60 0.28
82 156 0.72
83 1 0.00
ACGTcount: A:0.34, C:0.21, G:0.14, T:0.31
Consensus pattern (82 bp):
AAAACGTCACTATAAACAACTCTATTGCGGCGTTTATATAAAAACACCACTAAATTACTACTCTA
TTGCGGTGTTTTTTTAG
Found at i:1582902 original size:20 final size:19
Alignment explanation
Indices: 1582864--1582932 Score: 65
Period size: 20 Copynumber: 3.8 Consensus size: 19
1582854 ATATAAAAGA
1582864 AAAATAAAAT-AAAA-T--
1 AAAATAAAATAAAAATTAG
1582879 AAAATAAAATAAAAATTAG
1 AAAATAAAATAAAAATTAG
* * *
1582898 AAAAAAAAATTAAAGATTTG
1 AAAATAAAA-TAAAAATTAG
*
1582918 TAAATAAAATAAAAA
1 AAAATAAAATAAAAA
1582933 CAAATGCATA
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
15 10 0.23
16 4 0.09
17 1 0.02
19 13 0.30
20 15 0.35
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.22
Consensus pattern (19 bp):
AAAATAAAATAAAAATTAG
Found at i:1582906 original size:5 final size:5
Alignment explanation
Indices: 1582864--1582892 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
1582854 ATATAAAAGA
1582864 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
1582893 ATTAGAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:1582992 original size:37 final size:37
Alignment explanation
Indices: 1582922--1582993 Score: 92
Period size: 38 Copynumber: 1.9 Consensus size: 37
1582912 GATTTGTAAA
**
1582922 TAAAATAAAAACAAATGCATAGTAAACCTAGAAAATAG
1 TAAAATAAAAACAAAT-CATAGTAAACAAAGAAAATAG
*
1582960 TAAAATAAAAACAAA-CTATAGTGAACAAAGAAAA
1 TAAAATAAAAACAAATC-ATAGTAAACAAAGAAAA
1582994 AGTGAACATA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
36 1 0.03
37 14 0.47
38 15 0.50
ACGTcount: A:0.64, C:0.10, G:0.10, T:0.17
Consensus pattern (37 bp):
TAAAATAAAAACAAATCATAGTAAACAAAGAAAATAG
Found at i:1584898 original size:14 final size:14
Alignment explanation
Indices: 1584870--1584912 Score: 59
Period size: 14 Copynumber: 3.0 Consensus size: 14
1584860 CCAAAGCAAC
1584870 CCAATCTGAAATGAT
1 CCAATCTG-AATGAT
*
1584885 TCAATCTGAATGAT
1 CCAATCTGAATGAT
*
1584899 CCAATCCGAATGAT
1 CCAATCTGAATGAT
1584913 ATGATTGTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
14 18 0.72
15 7 0.28
ACGTcount: A:0.37, C:0.21, G:0.14, T:0.28
Consensus pattern (14 bp):
CCAATCTGAATGAT
Found at i:1587001 original size:19 final size:19
Alignment explanation
Indices: 1586977--1587081 Score: 102
Period size: 19 Copynumber: 5.2 Consensus size: 19
1586967 GCGATTTTGA
*
1586977 AAAATGTATTGCGATAGTT
1 AAAATGTGTTGCGATAGTT
1586996 AAAATGTGTTGCGATAGTT
1 AAAATGTGTTGCGATAGTT
* *
1587015 ACAATGTGTTGCGAGAGTTT
1 AAAATGTGTTGCGATAG-TT
*
1587035 AAAAAACGTGTTGTTGCGATAGTG
1 --AAAA--TG-TGTTGCGATAGTT
* *
1587059 AAAAAGTGTTGCGATAGTG
1 AAAATGTGTTGCGATAGTT
1587078 AAAA
1 AAAA
1587082 ATCCAAAATA
Statistics
Matches: 73, Mismatches: 7, Indels: 12
0.79 0.08 0.13
Matches are distributed among these distances:
19 50 0.68
20 3 0.04
22 7 0.10
24 3 0.04
25 10 0.14
ACGTcount: A:0.35, C:0.07, G:0.27, T:0.31
Consensus pattern (19 bp):
AAAATGTGTTGCGATAGTT
Found at i:1587404 original size:6 final size:6
Alignment explanation
Indices: 1587373--1587402 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
1587363 CCGCCGTCCC
*
1587373 GTCGTG GTCGTG GTCGTG GTCGTG ATCGTG
1 GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG
1587403 ATATTTTAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.03, C:0.17, G:0.47, T:0.33
Consensus pattern (6 bp):
GTCGTG
Found at i:1594718 original size:36 final size:35
Alignment explanation
Indices: 1594674--1594820 Score: 231
Period size: 36 Copynumber: 4.1 Consensus size: 35
1594664 CATCCTTCCA
*
1594674 TTCGACTTGAGTCGGAAGTGCCGATGCTTCTTTCTG
1 TTCGACTTGAATCGGAAGTGCCGATGCTTCTTTC-G
*
1594710 TTCGACTTGAATCGGAAGTGCCGATGCTTCATTGCG
1 TTCGACTTGAATCGGAAGTGCCGATGCTTC-TTTCG
*
1594746 TTCGACTTGAATCGGAAGTGCCGATGCTTCCTTCCG
1 TTCGACTTGAATCGGAAGTGCCGATGCTT-CTTTCG
1594782 TTCGACTTGAATCGGAAGTGCCGATGCTTTCTTTCG
1 TTCGACTTGAATCGGAAGTGCCGATGC-TTCTTTCG
1594818 TTC
1 TTC
1594821 TTCTTATTCA
Statistics
Matches: 104, Mismatches: 4, Indels: 6
0.91 0.04 0.05
Matches are distributed among these distances:
36 98 0.94
37 6 0.06
ACGTcount: A:0.16, C:0.24, G:0.26, T:0.34
Consensus pattern (35 bp):
TTCGACTTGAATCGGAAGTGCCGATGCTTCTTTCG
Found at i:1597122 original size:13 final size:13
Alignment explanation
Indices: 1597104--1597190 Score: 56
Period size: 13 Copynumber: 6.6 Consensus size: 13
1597094 AATCAAAGAA
1597104 AAATAAAATAAAT
1 AAATAAAATAAAT
*
1597117 ACATAACAA-AAAT
1 AAATAA-AATAAAT
1597130 AAAT-AAATAAA-
1 AAATAAAATAAAT
*
1597141 AAGTAAAAATAAA-
1 AAAT-AAAATAAAT
*
1597154 AAATTAAATTAAATT
1 AAA-TAAAATAAA-T
* *
1597169 AAATTAAAGAAAT
1 AAATAAAATAAAT
1597182 GAAATAAAA
1 -AAATAAAA
1597191 AATGGATTGC
Statistics
Matches: 57, Mismatches: 9, Indels: 15
0.70 0.11 0.19
Matches are distributed among these distances:
11 5 0.09
12 4 0.07
13 29 0.51
14 16 0.28
15 3 0.05
ACGTcount: A:0.72, C:0.02, G:0.03, T:0.22
Consensus pattern (13 bp):
AAATAAAATAAAT
Found at i:1597148 original size:21 final size:21
Alignment explanation
Indices: 1597098--1597157 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
1597088 CTAAAAAATC
1597098 AAAGAAAAATAAAATAAATACA
1 AAAGAAAAAT-AAATAAATACA
* *
1597120 TAACAAAAATAAATAAATA-A
1 AAAGAAAAATAAATAAATACA
1597140 AAAGTAAAAATAAA-AAAT
1 AAAG-AAAAATAAATAAAT
1597158 TAAATTAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
20 7 0.21
21 18 0.55
22 8 0.24
ACGTcount: A:0.77, C:0.03, G:0.03, T:0.17
Consensus pattern (21 bp):
AAAGAAAAATAAATAAATACA
Found at i:1600897 original size:45 final size:45
Alignment explanation
Indices: 1600817--1600933 Score: 119
Period size: 45 Copynumber: 2.6 Consensus size: 45
1600807 TAGTTATAAT
* * *
1600817 ATTGACTTATCTTCACAAGAAATTCAATAAGGACAACACTAAAAG
1 ATTGACTCATCTTCACAAGAAAGTCAAGAAGGACAACACTAAAAG
* * * *
1600862 ATTGACTCATCTTCACGAGAAAGTCAAGGAA-GACAACATTGAAAT
1 ATTGACTCATCTTCACAAGAAAGTCAA-GAAGGACAACACTAAAAG
* * * *
1600907 AATGACTCCTCTGCACTAGAAAGTCAA
1 ATTGACTCATCTTCACAAGAAAGTCAA
1600934 TAATAACAAT
Statistics
Matches: 60, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
45 58 0.97
46 2 0.03
ACGTcount: A:0.43, C:0.20, G:0.15, T:0.23
Consensus pattern (45 bp):
ATTGACTCATCTTCACAAGAAAGTCAAGAAGGACAACACTAAAAG
Found at i:1601001 original size:38 final size:38
Alignment explanation
Indices: 1600950--1602216 Score: 1595
Period size: 38 Copynumber: 33.2 Consensus size: 38
1600940 CAATACTGAG
*
1600950 AGATTGACTTCTCTTCATGAGGAAGTCAAGAATAACAA
1 AGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAA
** *
1600988 AGATTGACTTCTCTTCATAAGGAAGTAAAGAATAACAA
1 AGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAA
1601026 AGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAA
1 AGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAA
1601064 AGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAA
1 AGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAA
* * *
1601102 A-ACATGACTTCTCTTCATGAGGAAGTCAAGAATAAAAA
1 AGA-TTGACTTCTCTTCACGAGGAAGTCAAGAATAACAA
* *
1601140 AGAATGACTTCTCTTCACGAGGAAGTCAAGAATAAAAA
1 AGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAA
* * *
1601178 AGATTGACTTCTCTTCACGAGGAATTAAAAAATAACAA
1 AGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAA
* *
1601216 AGACTGACTTCTCTTCACGAGAAAGTCAAGAATAACAA
1 AGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAA
** *
1601254 AGACCGATTTCTCTTCACGAGGAAGTCAAGAATAACAA
1 AGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAA
* *
1601292 AGATGGTA-TTCTCTTCACGAGAAAGTCAAGAATAACAA
1 AGATTG-ACTTCTCTTCACGAGGAAGTCAAGAATAACAA
*
1601330 AGATTGACTTCTCTTCACGAGGAAGTCAATAATAACAA
1 AGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAA
* * *
1601368 ATATTGATTTCTCTTCATGAGGAAGTCAAGAATAACAA
1 AGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAA
* *
1601406 AGATTGACTTCTCTTCTCGAGGAAGTTAAGAATAACAA
1 AGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAA
*
1601444 AGATTGACTTCTC-T--CGAGGAAGTTAAGAATAACAA
1 AGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAA
* *
1601479 AGATTGACTTCTCTTCATGAGAAAGTCAAGAATAACAA
1 AGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAA
* *
1601517 AGCTTGAATTCTCTTCACGAGGAAGTCAAGAATAACAA
1 AGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAA
* *
1601555 AGATTAACTTCTCTTCATGAGGAAGTCAAGAATAACAA
1 AGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAA
** *
1601593 AGA-TGACTTCTCTGAACGAGGAAGTAAAGAATAACAA
1 AGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAA
* * *
1601630 AGATTGTA-TTCTCTTCCCAAGGAAGTCAAGAATAATAA
1 AGATTG-ACTTCTCTTCACGAGGAAGTCAAGAATAACAA
*
1601668 CA-ATTGACTTCTCTTCACGAGGAAGTCAAGAATAATAA
1 -AGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAA
** * *
1601706 AGGCTGACTTCTCTTCTCGAGGAAGTTAAGAATAACAA
1 AGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAA
* *
1601744 AGATTGAC-TCATCTTCACAAGGAAGTTAAGAATAACAA
1 AGATTGACTTC-TCTTCACGAGGAAGTCAAGAATAACAA
* * *
1601782 AGATTGACTTTTCTTCTCAAGGAAGTCAATAATAAGTCAAGAATAACAA
1 AGATTGACTTCTC-T-TC-ACG-AG-------GAAGTCAAGAATAACAA
* * *
1601831 AGATTGACTCCTCTTCACGAGGAAGTCAGGAATAAAAA
1 AGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAA
* *
1601869 AGATTGACTTCACTTCACGAGAAAGTCAAGAATAACAA
1 AGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAA
**
1601907 AGATTGACTTCTCTTCACGAATAAGTCAAGAATAA-AA
1 AGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAA
*
1601944 AGATTGACTTCTCTTCACGAAGAAGTCAAGAATAACAA
1 AGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAA
* * *
1601982 AGATTAACTTATCTTCATGAGGAAGTCAAGAATAACAA
1 AGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAA
* *
1602020 AGATTGACTTCTTTTC-CTGAGGAAGTCAAGAATAAAAA
1 AGATTGACTTCTCTTCAC-GAGGAAGTCAAGAATAACAA
*
1602058 AGATTGACTTCTCTTC-CTAAGGAAGTCAAGAATAACAA
1 AGATTGACTTCTCTTCAC-GAGGAAGTCAAGAATAACAA
* * * * * *
1602096 AGGTTAACTCCTATTTATGAGGAAGTCAAGAATAACAA
1 AGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAA
* ** * * * *
1602134 AGATTAACGCCTTTTCGCGAGGGAGTCAGGAATAACAA
1 AGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAA
* *
1602172 AGATTGACTTCTCTTCACGAGGAAGTTAAGAATAACGA
1 AGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAA
1602210 AGATTGA
1 AGATTGA
1602217 AAATTGACTC
Statistics
Matches: 1075, Mismatches: 126, Indels: 56
0.86 0.10 0.04
Matches are distributed among these distances:
35 34 0.03
36 1 0.00
37 75 0.07
38 921 0.86
39 6 0.01
40 2 0.00
41 1 0.00
42 2 0.00
45 2 0.00
46 2 0.00
47 2 0.00
48 1 0.00
49 26 0.02
ACGTcount: A:0.41, C:0.16, G:0.18, T:0.25
Consensus pattern (38 bp):
AGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAA
Found at i:1601865 original size:49 final size:49
Alignment explanation
Indices: 1601766--1601865 Score: 137
Period size: 49 Copynumber: 2.0 Consensus size: 49
1601756 CTTCACAAGG
* ** * *
1601766 AAGTTAAGAATAACAAAGATTGACTTTTCTTCTCAAGGAAGTCAATAAT
1 AAGTCAAGAATAACAAAGATTGACTCCTCTTCACAAGGAAGTCAAGAAT
* *
1601815 AAGTCAAGAATAACAAAGATTGACTCCTCTTCACGAGGAAGTCAGGAAT
1 AAGTCAAGAATAACAAAGATTGACTCCTCTTCACAAGGAAGTCAAGAAT
1601864 AA
1 AA
1601866 AAAAGATTGA
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
49 44 1.00
ACGTcount: A:0.43, C:0.15, G:0.17, T:0.25
Consensus pattern (49 bp):
AAGTCAAGAATAACAAAGATTGACTCCTCTTCACAAGGAAGTCAAGAAT
Found at i:1601895 original size:87 final size:84
Alignment explanation
Indices: 1601728--1602031 Score: 309
Period size: 75 Copynumber: 3.8 Consensus size: 84
1601718 CTTCTCGAGG
* * * * * *
1601728 AAGTTAAGAATAACAAAGATTGACTCATCTTCACAAGGAAGTTAAGAATAACAAAGATTGACTTT
1 AAGTCAAGAATAACAAAGATTGACTCCTCTTCACGAGGAAGTCAAGAATAAAAAAGATTGACTTC
*
1601793 TCTTCTCAAGGAAGTCAATAAT
66 TCTTCAC-A-GAAGTCAA-AAT
*
1601815 AAGTCAAGAATAACAAAGATTGACTCCTCTTCACGAGGAAGTCAGGAATAAAAAAGATTGACTTC
1 AAGTCAAGAATAACAAAGATTGACTCCTCTTCACGAGGAAGTCAAGAATAAAAAAGATTGACTTC
*
1601880 ACTTCAC-G-AG-----A-
66 TCTTCACAGAAGTCAAAAT
* **
1601891 AAGTCAAGAATAACAAAGATTGACTTCTCTTCACGAATAAGTCAAGAAT-AAAAAGATTGACTTC
1 AAGTCAAGAATAACAAAGATTGACTCCTCTTCACGAGGAAGTCAAGAATAAAAAAGATTGACTTC
1601955 TCTTCAC-GAAG-------
66 TCTTCACAGAAGTCAAAAT
* ** * *
1601966 AAGTCAAGAATAACAAAGATTAACTTATCTTCATGAGGAAGTCAAGAATAACAAAGATTGACTTC
1 AAGTCAAGAATAACAAAGATTGACTCCTCTTCACGAGGAAGTCAAGAATAAAAAAGATTGACTTC
1602031 T
66 T
1602032 TTTCCTGAGG
Statistics
Matches: 195, Mismatches: 20, Indels: 15
0.85 0.09 0.07
Matches are distributed among these distances:
75 66 0.34
76 62 0.32
77 1 0.01
83 2 0.01
84 1 0.01
87 63 0.32
ACGTcount: A:0.43, C:0.16, G:0.16, T:0.25
Consensus pattern (84 bp):
AAGTCAAGAATAACAAAGATTGACTCCTCTTCACGAGGAAGTCAAGAATAAAAAAGATTGACTTC
TCTTCACAGAAGTCAAAAT
Found at i:1603461 original size:44 final size:43
Alignment explanation
Indices: 1603386--1603518 Score: 124
Period size: 43 Copynumber: 3.0 Consensus size: 43
1603376 TATTCCCAGA
*
1603386 TGATATGGACCTTTAAAAAATGTCCCAACATTTATTATTTCTTGC
1 TGATATGGACC-TTCAAAAATG-CCCAACATTTATTATTTCTTGC
* * * * *
1603431 TGATATGGGCCTTCAAAAATGCCCTAACA-TTAATACTTCTGGA
1 TGATATGGACCTTCAAAAATGCCC-AACATTTATTATTTCTTGC
** * * *
1603474 TGATACAGACCTTCAAAAGTGCCCCAACATTCATCATTTCTTGC
1 TGATATGGACCTTCAAAAATG-CCCAACATTTATTATTTCTTGC
1603518 T
1 T
1603519 CCAGCACTAA
Statistics
Matches: 69, Mismatches: 16, Indels: 7
0.75 0.17 0.08
Matches are distributed among these distances:
43 34 0.49
44 25 0.36
45 10 0.14
ACGTcount: A:0.31, C:0.23, G:0.13, T:0.34
Consensus pattern (43 bp):
TGATATGGACCTTCAAAAATGCCCAACATTTATTATTTCTTGC
Found at i:1610185 original size:20 final size:20
Alignment explanation
Indices: 1610149--1610215 Score: 89
Period size: 21 Copynumber: 3.2 Consensus size: 20
1610139 CTGGTTACTA
*
1610149 TTGTTCACTATTATTGGTATG
1 TTGTTCCCTA-TATTGGTATG
1610170 TTGTTCCCTATATTGGTATG
1 TTGTTCCCTATATTGGTATG
* *
1610190 TTGTTCCCTGGTATTGGTCTG
1 TTGTTCCCT-ATATTGGTATG
1610211 TTGTT
1 TTGTT
1610216 TTCTTTCTCC
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
20 19 0.45
21 23 0.55
ACGTcount: A:0.12, C:0.13, G:0.22, T:0.52
Consensus pattern (20 bp):
TTGTTCCCTATATTGGTATG
Found at i:1610992 original size:25 final size:23
Alignment explanation
Indices: 1610946--1611005 Score: 59
Period size: 24 Copynumber: 2.5 Consensus size: 23
1610936 ATTAAATACT
* * *
1610946 TATATTTATATTTGTTTTCAAACC
1 TATA-TTATATTTATTTCCAAAAC
1610970 ATATATTATATTTATCTTCCAAAAC
1 -TATATTATATTTAT-TTCCAAAAC
1610995 TATATT-TATTT
1 TATATTATATTT
1611006 TCAAAACTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
23 5 0.16
24 15 0.48
25 11 0.35
ACGTcount: A:0.33, C:0.12, G:0.02, T:0.53
Consensus pattern (23 bp):
TATATTATATTTATTTCCAAAAC
Found at i:1611012 original size:18 final size:19
Alignment explanation
Indices: 1610976--1611016 Score: 66
Period size: 18 Copynumber: 2.2 Consensus size: 19
1610966 AACCATATAT
1610976 TATATTTATCTTCCAAAAC
1 TATATTTATCTTCCAAAAC
*
1610995 TATATTTAT-TTTCAAAAC
1 TATATTTATCTTCCAAAAC
1611013 TATA
1 TATA
1611017 CTATATATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 12 0.57
19 9 0.43
ACGTcount: A:0.39, C:0.15, G:0.00, T:0.46
Consensus pattern (19 bp):
TATATTTATCTTCCAAAAC
Found at i:1611023 original size:25 final size:25
Alignment explanation
Indices: 1610995--1611069 Score: 70
Period size: 24 Copynumber: 3.1 Consensus size: 25
1610985 CTTCCAAAAC
1610995 TATATTTATTTTCAAAACTATACTA
1 TATATTTATTTTCAAAACTATACTA
*
1611020 TATATATATTTTTC-AAAC-ACT-CTA
1 TATATTTA-TTTTCAAAACTA-TACTA
*
1611044 TA-CTTTATATTTCAAAACTATA-TA
1 TATATTTAT-TTTCAAAACTATACTA
1611068 TA
1 TA
1611070 GTATACATAT
Statistics
Matches: 41, Mismatches: 3, Indels: 13
0.72 0.05 0.23
Matches are distributed among these distances:
22 1 0.02
23 7 0.17
24 15 0.37
25 13 0.32
26 5 0.12
ACGTcount: A:0.40, C:0.13, G:0.00, T:0.47
Consensus pattern (25 bp):
TATATTTATTTTCAAAACTATACTA
Found at i:1611074 original size:22 final size:22
Alignment explanation
Indices: 1611016--1611074 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 22
1611006 TCAAAACTAT
*
1611016 ACTATATATATATTTTTCAAAC
1 ACTATATATATATATTTCAAAC
* *
1611038 ACTCTATACTTTATATTTCAAA-
1 ACTATATA-TATATATTTCAAAC
1611060 ACTATATATAGTATA
1 ACTATATATA-TATA
1611075 CATATATATA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
21 1 0.03
22 18 0.60
23 11 0.37
ACGTcount: A:0.41, C:0.14, G:0.02, T:0.44
Consensus pattern (22 bp):
ACTATATATATATATTTCAAAC
Found at i:1611117 original size:15 final size:16
Alignment explanation
Indices: 1611088--1611121 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1611078 ATATATAACC
1611088 AAAATAAAATAAAACA
1 AAAATAAAATAAAACA
*
1611104 AAAATAAACT-AAACA
1 AAAATAAAATAAAACA
1611119 AAA
1 AAA
1611122 GAAAACTCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.79, C:0.09, G:0.00, T:0.12
Consensus pattern (16 bp):
AAAATAAAATAAAACA
Found at i:1611662 original size:45 final size:45
Alignment explanation
Indices: 1611579--1611675 Score: 133
Period size: 45 Copynumber: 2.2 Consensus size: 45
1611569 AATCCGAAAG
* *
1611579 ATTGACTCCTCTTTACGAGAAAGTCAATAAGGAAAACACTAAAAT
1 ATTGACTCCTCTTCACGAGAAAGTCAAGAAGGAAAACACTAAAAT
* *
1611624 ATTGACTCCTCTTCACGAGAAAGTCAAGGAA-GATAACACTGAAAT
1 ATTGACTCCTCTTCACGAGAAAGTCAA-GAAGGAAAACACTAAAAT
*
1611669 GTTGACT
1 ATTGACT
1611676 GACTCCTATT
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
45 44 0.96
46 2 0.04
ACGTcount: A:0.40, C:0.19, G:0.16, T:0.25
Consensus pattern (45 bp):
ATTGACTCCTCTTCACGAGAAAGTCAAGAAGGAAAACACTAAAAT
Found at i:1612433 original size:45 final size:44
Alignment explanation
Indices: 1612329--1612506 Score: 248
Period size: 44 Copynumber: 4.0 Consensus size: 44
1612319 ATACCATGAG
* * **
1612329 TGGCACCTTTCTGCCAATAATGTACCATTATATATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
* * *
1612373 TGGCACATTTCTGCCAATAATGCATCGTTATGTATTTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCA-TTTTCATTTA
* *
1612418 TGGCACCTTTATGCCAATAATGCACCGTTATGCATTTTCATTTC
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
* *
1612462 TGACATCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
1612506 T
1 T
1612507 TTTAGAGCAG
Statistics
Matches: 119, Mismatches: 14, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
44 79 0.66
45 40 0.34
ACGTcount: A:0.25, C:0.21, G:0.12, T:0.42
Consensus pattern (44 bp):
TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
Found at i:1612433 original size:89 final size:88
Alignment explanation
Indices: 1612329--1612506 Score: 250
Period size: 89 Copynumber: 2.0 Consensus size: 88
1612319 ATACCATGAG
* * * *
1612329 TGGCACCTTTCTGCCAATAATGTACCATTATATATTTTCATTTATGGCA-CATTTCTGCCAATAA
1 TGGCACCTTTATGCCAATAATGCACCATTATACATTTTCATTTATGACATC-TTTCTGCCAATAA
* *
1612393 TGCATCGTTATGTATTTTTCATTTA
65 TGCACCGTTATGCA-TTTTCATTTA
* * *
1612418 TGGCACCTTTATGCCAATAATGCACCGTTATGCATTTTCATTTCTGACATCTTTCTGCCAATAAT
1 TGGCACCTTTATGCCAATAATGCACCATTATACATTTTCATTTATGACATCTTTCTGCCAATAAT
1612483 GCACCGTTATGCATTTTCATTTA
66 GCACCGTTATGCATTTTCATTTA
1612506 T
1 T
1612507 TTTAGAGCAG
Statistics
Matches: 79, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
88 11 0.14
89 67 0.85
90 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.12, T:0.42
Consensus pattern (88 bp):
TGGCACCTTTATGCCAATAATGCACCATTATACATTTTCATTTATGACATCTTTCTGCCAATAAT
GCACCGTTATGCATTTTCATTTA
Found at i:1613476 original size:15 final size:17
Alignment explanation
Indices: 1613440--1613478 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
1613430 AAATCATTCA
1613440 TCTCTTAGTTTTAATCC
1 TCTCTTAGTTTTAATCC
1613457 TCTCTTAGTTTTAATCC
1 TCTCTTAGTTTTAATCC
1613474 TCTCT
1 TCTCT
1613479 AACCCTTCCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.15, C:0.26, G:0.05, T:0.54
Consensus pattern (17 bp):
TCTCTTAGTTTTAATCC
Found at i:1615072 original size:73 final size:75
Alignment explanation
Indices: 1614917--1615064 Score: 196
Period size: 73 Copynumber: 2.0 Consensus size: 75
1614907 TATATATATT
*
1614917 AATATTATATTTTATCTTTGTATTCTAGTTTAAATAGATGTTAGTATTTCAATTAGGATTTAGGA
1 AATATTATATTTTATCTTTGTATTCTAGTTTAAATAGATGTTAGTATTTCAATTAGGATATAGGA
1614982 TATTATTTTA
66 TATTATTTTA
* * * * *
1614992 AATATTATTTTTTATC-TT-TATTTTAGTTTAAATAG-TTTTAAGTTTTTTAATTAGGATAATA-
1 AATATTATATTTTATCTTTGTATTCTAGTTTAAATAGATGTT-AGTATTTCAATTAGGAT-ATAG
1615053 GATATTATTTTA
64 GATATTATTTTA
1615065 TGAATTATCT
Statistics
Matches: 65, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
72 3 0.05
73 43 0.66
74 4 0.06
75 15 0.23
ACGTcount: A:0.32, C:0.03, G:0.10, T:0.55
Consensus pattern (75 bp):
AATATTATATTTTATCTTTGTATTCTAGTTTAAATAGATGTTAGTATTTCAATTAGGATATAGGA
TATTATTTTA
Found at i:1615721 original size:18 final size:18
Alignment explanation
Indices: 1615698--1615740 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
1615688 CTTTAGATCA
1615698 TTTATTTAATTATT-TTCT
1 TTTATTTAATTATTATT-T
*
1615716 TTTATTTAATTCTTATTT
1 TTTATTTAATTATTATTT
1615734 TTTATTT
1 TTTATTT
1615741 TTAAAACAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 21 0.91
19 2 0.09
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTATTTAATTATTATTT
Found at i:1623325 original size:86 final size:86
Alignment explanation
Indices: 1623131--1623595 Score: 556
Period size: 86 Copynumber: 5.4 Consensus size: 86
1623121 AAGAACATCT
* * * * * **
1623131 CACATAACTTTCCCGTGAAGGGGAGTCATCAAAATATAATCTCACCTGGTTCAGA-TCGTGAATA
1 CACATGACTTTCCCGTGAAGGGGAGTCATCCAAAGATAATCTCACCTGGTTCAGACCCGCGAAGG
* *
1623195 TGAACCACCTTAAGAATATAC
66 GGAACCACCTGAAGAATATAC
** * * * * *
1623216 CGTATAACTTTCCCATGAAGGGGAGTTATCCAAAGATAATCTCACATGGTTCAGACCCGCGAATG
1 CACATGACTTTCCCGTGAAGGGGAGTCATCCAAAGATAATCTCACCTGGTTCAGACCCGCGAAGG
*
1623281 GGAACCACCTGAAGAATGTAC
66 GGAACCACCTGAAGAATATAC
* *
1623302 CACATGATTTTCCCGTGAAGGGGAGTCATCCAAAGATCATCTCACCTGGTTCAGACCCGCGAAGG
1 CACATGACTTTCCCGTGAAGGGGAGTCATCCAAAGATAATCTCACCTGGTTCAGACCCGCGAAGG
* *
1623367 GGAGCCACCTGAGGAATATAC
66 GGAACCACCTGAAGAATATAC
* * * * *
1623388 CACATTACTTTCCTGTGAAGGGGAGTCATCAAAAGATAATCTTACCTGGTTTAGACCCGCGAAGG
1 CACATGACTTTCCCGTGAAGGGGAGTCATCCAAAGATAATCTCACCTGGTTCAGACCCGCGAAGG
*
1623453 GGAACCACATGAAGAATATAC
66 GGAACCACCTGAAGAATATAC
* * * * * * *
1623474 CACATGACTTTCCCATGAAGGGGAGTCATCCAAATATCATCTCAACTGGTCCATACCCGTGAAGG
1 CACATGACTTTCCCGTGAAGGGGAGTCATCCAAAGATAATCTCACCTGGTTCAGACCCGCGAAGG
*
1623539 GGAACTACCTGAAGAATATAC
66 GGAACCACCTGAAGAATATAC
* * * *
1623560 CA-ATTGGCTTTCCCGTGAAAGGAAGTCATCTAAAGA
1 CACA-TGACTTTCCCGTGAAGGGGAGTCATCCAAAGA
1623596 ATTATGACCG
Statistics
Matches: 323, Mismatches: 55, Indels: 3
0.85 0.14 0.01
Matches are distributed among these distances:
85 49 0.15
86 274 0.85
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.23
Consensus pattern (86 bp):
CACATGACTTTCCCGTGAAGGGGAGTCATCCAAAGATAATCTCACCTGGTTCAGACCCGCGAAGG
GGAACCACCTGAAGAATATAC
Found at i:1624373 original size:76 final size:78
Alignment explanation
Indices: 1624245--1624394 Score: 207
Period size: 76 Copynumber: 1.9 Consensus size: 78
1624235 TATATATGAA
** *
1624245 TATTATATTTTATCTTTGTATTCTAGTTTAAATAGATGTTAGTATTTCAATTAGGATTTAGGATA
1 TATTATATTTTATCTTTGTATTCTAGTTTAAATAGATGTTAGTATTTCAATTAGGATAAAAGATA
1624310 TTATTTTAAATAT
66 TTATTTTAAATAT
* * * *
1624323 TATTTTATTTTATCTTTGT-TT-TAGTTTAAATAG-TTTTAAGTGTTTTAATTAGGATAAAAGAT
1 TATTATATTTTATCTTTGTATTCTAGTTTAAATAGATGTT-AGTATTTCAATTAGGATAAAAGAT
1624385 ATTATTTTAA
65 ATTATTTTAA
1624395 GAATTACCTT
Statistics
Matches: 64, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
75 3 0.05
76 41 0.64
77 2 0.03
78 18 0.28
ACGTcount: A:0.32, C:0.03, G:0.11, T:0.54
Consensus pattern (78 bp):
TATTATATTTTATCTTTGTATTCTAGTTTAAATAGATGTTAGTATTTCAATTAGGATAAAAGATA
TTATTTTAAATAT
Found at i:1625047 original size:18 final size:19
Alignment explanation
Indices: 1625024--1625067 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
1625014 CTTTAGATCA
1625024 TTTATTTAATTATT-TTCT
1 TTTATTTAATTATTATTCT
* *
1625042 TTTATTTAATTCTTATTTT
1 TTTATTTAATTATTATTCT
1625061 TTTATTT
1 TTTATTT
1625068 TAAAAACAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 13 0.57
19 10 0.43
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.75
Consensus pattern (19 bp):
TTTATTTAATTATTATTCT
Found at i:1625168 original size:22 final size:22
Alignment explanation
Indices: 1625108--1625160 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
1625098 TTTATTACTA
* *
1625108 TTATTTATTA-TA-TTTCTCTT
1 TTATTTATTATTATTTTTTGTT
1625128 TTATTTATTATTATTTTTTGTT
1 TTATTTATTATTATTTTTTGTT
1625150 TTATTT-TTATT
1 TTATTTATTATT
1625161 TTCTTTTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 10 0.34
21 7 0.24
22 12 0.41
ACGTcount: A:0.19, C:0.04, G:0.02, T:0.75
Consensus pattern (22 bp):
TTATTTATTATTATTTTTTGTT
Found at i:1625260 original size:42 final size:42
Alignment explanation
Indices: 1625164--1625260 Score: 101
Period size: 42 Copynumber: 2.3 Consensus size: 42
1625154 TTTTATTTTC
* * *
1625164 TTTTTTAACATTTTTTCATATTTTATTATTTTTCTTTTATTA
1 TTTTTTAAAATTTCTTCATATTTTATTATTTTTCTTTTAATA
**
1625206 -AATTTAATAATTTCTTCAT-TTATT-TTATTTTTTCTTTTAATA
1 TTTTTTAA-AATTTCTTCATATT-TTATTA-TTTTTCTTTTAATA
1625248 TTTTTTAAAATTT
1 TTTTTTAAAATTT
1625261 AATATTTCAT
Statistics
Matches: 44, Mismatches: 7, Indels: 8
0.75 0.12 0.14
Matches are distributed among these distances:
41 10 0.23
42 29 0.66
43 5 0.11
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.68
Consensus pattern (42 bp):
TTTTTTAAAATTTCTTCATATTTTATTATTTTTCTTTTAATA
Found at i:1627238 original size:56 final size:56
Alignment explanation
Indices: 1627177--1627620 Score: 637
Period size: 56 Copynumber: 8.0 Consensus size: 56
1627167 CCCACTACCA
*
1627177 ATACGAAAATTCATAAACTTATTATGAATTTCTTAGCTTTTGCACACAAAGTTCCC
1 ATACGAAAATTCATAAACTTATTATGAATTTCTTAGCTTTTGCACACAAAGTGCCC
* * * **
1627233 ATACGAAATTTCATAAACTTATTATGAATTTTTTAGC-TTTGAACAGGAAGTGCCC
1 ATACGAAAATTCATAAACTTATTATGAATTTCTTAGCTTTTGCACACAAAGTGCCC
* * * * *
1627288 ATACGGAAATTCATAAACTCATTATAAATTTCTTAGCTTTTACACACCAAGTGCCC
1 ATACGAAAATTCATAAACTTATTATGAATTTCTTAGCTTTTGCACACAAAGTGCCC
* *
1627344 ATACGAAAATTCATAAACTTATTATGAATTTCTTAGCTTTTGCACACAATGCGCCC
1 ATACGAAAATTCATAAACTTATTATGAATTTCTTAGCTTTTGCACACAAAGTGCCC
*
1627400 ATAC-AGAAATTCATAAACTTATTATGAATTTCTTAGCTTTTGCACACAAATTGCCC
1 ATACGA-AAATTCATAAACTTATTATGAATTTCTTAGCTTTTGCACACAAAGTGCCC
* * *
1627456 ATATGGAAATTCATAAACTTATTATGAATTTCTTAGCTTTTGCACACAAAGTTCCC
1 ATACGAAAATTCATAAACTTATTATGAATTTCTTAGCTTTTGCACACAAAGTGCCC
* * *
1627512 ATACGGAAATTCATAAACTCATTATGAATTTCTTAG-TTTTGCACATAAAGTGCCC
1 ATACGAAAATTCATAAACTTATTATGAATTTCTTAGCTTTTGCACACAAAGTGCCC
* *
1627567 ATAC-AGAAATTCATAAACTTATTATGAATTTCTTAG-TTTTGCACGCATAGTGCC
1 ATACGA-AAATTCATAAACTTATTATGAATTTCTTAGCTTTTGCACACAAAGTGCC
1627621 ATTTGGTAAT
Statistics
Matches: 346, Mismatches: 38, Indels: 9
0.88 0.10 0.02
Matches are distributed among these distances:
55 112 0.32
56 234 0.68
ACGTcount: A:0.35, C:0.19, G:0.11, T:0.35
Consensus pattern (56 bp):
ATACGAAAATTCATAAACTTATTATGAATTTCTTAGCTTTTGCACACAAAGTGCCC
Found at i:1627554 original size:167 final size:168
Alignment explanation
Indices: 1627177--1627620 Score: 680
Period size: 167 Copynumber: 2.7 Consensus size: 168
1627167 CCCACTACCA
*
1627177 ATACGAAAATTCATAAACTTATTATGAATTTCTTAGCTTTTGCACACAAAGTTCCCATAC-GAAA
1 ATACGAAAATTCATAAACTTATTATGAATTTCTTAGCTTTTGCACACAAAGTGCCCATACAGAAA
* * **
1627241 TTTCATAAACTTATTATGAATTTTTTAGC-TTTGAACAGGAAGTGCCCATACGGAAATTCATAAA
66 -TTCATAAACTTATTATGAATTTCTTAGCTTTTGCACACAAAGTGCCCATACGGAAATTCATAAA
*
1627305 CTCATTATAAATTTCTTAGCTTTTACACACCAAGTGCCC
130 CTCATTATAAATTTCTTAGCTTTTACACACAAAGTGCCC
* *
1627344 ATACGAAAATTCATAAACTTATTATGAATTTCTTAGCTTTTGCACACAATGCGCCCATACAGAAA
1 ATACGAAAATTCATAAACTTATTATGAATTTCTTAGCTTTTGCACACAAAGTGCCCATACAGAAA
* *
1627409 TTCATAAACTTATTATGAATTTCTTAGCTTTTGCACACAAATTGCCCATATGGAAATTCATAAAC
66 TTCATAAACTTATTATGAATTTCTTAGCTTTTGCACACAAAGTGCCCATACGGAAATTCATAAAC
* * * *
1627474 TTATTATGAATTTCTTAGCTTTTGCACACAAAGTTCCC
131 TCATTATAAATTTCTTAGCTTTTACACACAAAGTGCCC
* * *
1627512 ATACGGAAATTCATAAACTCATTATGAATTTCTTAG-TTTTGCACATAAAGTGCCCATACAGAAA
1 ATACGAAAATTCATAAACTTATTATGAATTTCTTAGCTTTTGCACACAAAGTGCCCATACAGAAA
* *
1627576 TTCATAAACTTATTATGAATTTCTTAG-TTTTGCACGCATAGTGCC
66 TTCATAAACTTATTATGAATTTCTTAGCTTTTGCACACAAAGTGCC
1627621 ATTTGGTAAT
Statistics
Matches: 253, Mismatches: 22, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
166 15 0.06
167 136 0.54
168 102 0.40
ACGTcount: A:0.35, C:0.19, G:0.11, T:0.35
Consensus pattern (168 bp):
ATACGAAAATTCATAAACTTATTATGAATTTCTTAGCTTTTGCACACAAAGTGCCCATACAGAAA
TTCATAAACTTATTATGAATTTCTTAGCTTTTGCACACAAAGTGCCCATACGGAAATTCATAAAC
TCATTATAAATTTCTTAGCTTTTACACACAAAGTGCCC
Found at i:1633090 original size:56 final size:56
Alignment explanation
Indices: 1632974--1633563 Score: 809
Period size: 56 Copynumber: 10.6 Consensus size: 56
1632964 ACCATTACAA
* * *
1632974 AAATTCATAAACTTATTATGAATTTCTTAG-TTTTGCACACAAATTGCACATATGG
1 AAATTCATAAACTTATTATGAATTTCTTAGCTTTTGCACACAAAGTGCCCATACGG
*
1633029 AAATTCATAAACTTATTATGAATTTCTTAGCTTTTGCACACAAAGTTCCCATACGG
1 AAATTCATAAACTTATTATGAATTTCTTAGCTTTTGCACACAAAGTGCCCATACGG
*
1633085 AAATTCATAAACTTATTATGAATTTCTTAGCTTTTGCACACAAAGTGACCATACGG
1 AAATTCATAAACTTATTATGAATTTCTTAGCTTTTGCACACAAAGTGCCCATACGG
** **
1633141 AAATTCATAAACTTATTATGAATTTCTTAGC-TTTGCACA-AGAA-TTTCCATACAA
1 AAATTCATAAACTTATTATGAATTTCTTAGCTTTTGCACACA-AAGTGCCCATACGG
* * **
1633195 AAATTCATAAACTTATTATGAATATCTTAGGTTTTGCACACAAAGTGCCCATACAA
1 AAATTCATAAACTTATTATGAATTTCTTAGCTTTTGCACACAAAGTGCCCATACGG
* * * *
1633251 AAATTCATAAACTTGTTACGAATTTCTTAGCTTTTGTACACAAAGTCCCCATACGG
1 AAATTCATAAACTTATTATGAATTTCTTAGCTTTTGCACACAAAGTGCCCATACGG
1633307 AAATTCATAAACTTATTATGAATTTCTTAGCTTTTGCACACAAAGTGCCCATACGG
1 AAATTCATAAACTTATTATGAATTTCTTAGCTTTTGCACACAAAGTGCCCATACGG
* *
1633363 AAATTCATAAACTTATTATGAATTTCTTAGCTTTTACACACAAAGTACCCATACGG
1 AAATTCATAAACTTATTATGAATTTCTTAGCTTTTGCACACAAAGTGCCCATACGG
* * **
1633419 AAATTCATAAACTCATTATGAATTCCTTAG-TTTTGCACGTAAAGTGCCCATACGG
1 AAATTCATAAACTTATTATGAATTTCTTAGCTTTTGCACACAAAGTGCCCATACGG
* * * *** * *
1633474 AAATTCAAAAACTAATTATGAATTTCTTA-ATTTTGCATGTAAAGTGCCCAAACAG
1 AAATTCATAAACTTATTATGAATTTCTTAGCTTTTGCACACAAAGTGCCCATACGG
**
1633529 AAATTCATAATAAGT-TTATGAATTTCTTAG-TTTTG
1 AAATTCATAA-ACTTATTATGAATTTCTTAGCTTTTG
1633564 TACGCATAGT
Statistics
Matches: 483, Mismatches: 44, Indels: 16
0.89 0.08 0.03
Matches are distributed among these distances:
54 37 0.08
55 147 0.30
56 299 0.62
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.35
Consensus pattern (56 bp):
AAATTCATAAACTTATTATGAATTTCTTAGCTTTTGCACACAAAGTGCCCATACGG
Found at i:1633313 original size:222 final size:222
Alignment explanation
Indices: 1632969--1633563 Score: 833
Period size: 222 Copynumber: 2.7 Consensus size: 222
1632959 CCACTACCAT
* * *
1632969 TACAAAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAATTGCACATATGGAAATT
1 TACAAAAATTCATAAACTTATTATGAA-TTCTTAGTTTTGCACACAAAGTGCCCATACGGAAATT
*
1633034 CATAAACTTATTATGAATTTCTTAGCTTTTGCACACAAAGTTCCCATACGGAAATTCATAAACTT
65 CATAAACTTATTATGAATTTCTTAGCTTTTGCACACAAAGTCCCCATACGGAAATTCATAAACTT
1633099 ATTATGAATTTCTTAGCTTTTGCACACAAAGTGACCATACGGAAATTCATAAACTTATTATGAAT
130 ATTATGAATTTCTTAGCTTTTGCACACAAAGTGACCATACGGAAATTCATAAACTTATTATGAAT
* **
1633164 TTCTTAGC-TTTGCACA-AGAA-TTTCCA
195 TTCTTAGCTTTTACACACA-AAGTACCCA
**
1633190 TACAAAAATTCATAAACTTATTATGAATATCTTAGGTTTTGCACACAAAGTGCCCATACAAAAAT
1 TACAAAAATTCATAAACTTATTATGAAT-TCTTA-GTTTTGCACACAAAGTGCCCATACGGAAAT
* * *
1633255 TCATAAACTTGTTACGAATTTCTTAGCTTTTGTACACAAAGTCCCCATACGGAAATTCATAAACT
64 TCATAAACTTATTATGAATTTCTTAGCTTTTGCACACAAAGTCCCCATACGGAAATTCATAAACT
*
1633320 TATTATGAATTTCTTAGCTTTTGCACACAAAGTGCCCATACGGAAATTCATAAACTTATTATGAA
129 TATTATGAATTTCTTAGCTTTTGCACACAAAGTGACCATACGGAAATTCATAAACTTATTATGAA
1633385 TTTCTTAGCTTTTACACACAAAGTACCCA
194 TTTCTTAGCTTTTACACACAAAGTACCCA
** * **
1633414 TACGGAAATTCATAAACTCATTATGAATTCCTTAGTTTTGCACGTAAAGTGCCCATACGGAAATT
1 TACAAAAATTCATAAACTTATTATGAATT-CTTAGTTTTGCACACAAAGTGCCCATACGGAAATT
* * * *** * * * **
1633479 CAAAAACTAATTATGAATTTCTTA-ATTTTGCATGTAAAGTGCCCAAACAGAAATTCATAATAAG
65 CATAAACTTATTATGAATTTCTTAGCTTTTGCACACAAAGTCCCCATACGGAAATTCATAA-ACT
1633543 T-TTATGAATTTCTTAG-TTTTG
129 TATTATGAATTTCTTAGCTTTTG
1633564 TACGCATAGT
Statistics
Matches: 333, Mismatches: 34, Indels: 14
0.87 0.09 0.04
Matches are distributed among these distances:
220 1 0.00
221 37 0.11
222 202 0.61
223 59 0.18
224 34 0.10
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.35
Consensus pattern (222 bp):
TACAAAAATTCATAAACTTATTATGAATTCTTAGTTTTGCACACAAAGTGCCCATACGGAAATTC
ATAAACTTATTATGAATTTCTTAGCTTTTGCACACAAAGTCCCCATACGGAAATTCATAAACTTA
TTATGAATTTCTTAGCTTTTGCACACAAAGTGACCATACGGAAATTCATAAACTTATTATGAATT
TCTTAGCTTTTACACACAAAGTACCCA
Found at i:1633510 original size:278 final size:276
Alignment explanation
Indices: 1632969--1633566 Score: 869
Period size: 278 Copynumber: 2.2 Consensus size: 276
1632959 CCACTACCAT
* * * *
1632969 TACAAAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAATTGCACATATGGAAATT
1 TACAAAAATTCATAAACTT-TTATGAATTTCTTAGTTTTGTACACAAAGTCCACATACGGAAATT
*
1633034 CATAAACTTATTATGAATTTCTTAGCTTTTGCACACAAAGTTCCCATACGGAAATTCATAAACTT
65 CATAAACTTATTATGAATTTCTTAGCTTTTGCACACAAAGTGCCCATACGGAAATTCATAAACTT
* *
1633099 ATTATGAATTTCTTAGCTTTTGCACACAAAGTGACCATACGGAAATTCATAAACTTATTATGAAT
130 ATTATGAATTTCTTAGCTTTTACACACAAAGTGACCATACGGAAATTCATAAACTCATTATGAAT
* ** * * *
1633164 TTCTTAGCTTTGCACAAGAATTTCCATACAAAAATTCATAAACTTATTATGAATATCTTAGGTTT
195 TCCTTAGCTTTGCACAAGAATGCCCATACAAAAATTCAAAAACTAATTATGAATATCTTAGATTT
1633229 TGCACACAAAGTGCCCA
260 TGCACACAAAGTGCCCA
* *
1633246 TACAAAAATTCATAAACTTGTTACGAATTTCTTAGCTTTTGTACACAAAGTCCCCATACGGAAAT
1 TACAAAAATTCATAAACTT-TTATGAATTTCTTAG-TTTTGTACACAAAGTCCACATACGGAAAT
1633311 TCATAAACTTATTATGAATTTCTTAGCTTTTGCACACAAAGTGCCCATACGGAAATTCATAAACT
64 TCATAAACTTATTATGAATTTCTTAGCTTTTGCACACAAAGTGCCCATACGGAAATTCATAAACT
1633376 TATTATGAATTTCTTAGCTTTTACACACAAAGT-ACCCATACGGAAATTCATAAACTCATTATGA
129 TATTATGAATTTCTTAGCTTTTACACACAAAGTGA-CCATACGGAAATTCATAAACTCATTATGA
* * ** *
1633440 ATTCCTTAGTTTTGCACGTAA-AGTGCCCATACGGAAATTCAAAAACTAATTATGAATTTCTTA-
193 ATTCCTTAGCTTTGCAC--AAGAATGCCCATACAAAAATTCAAAAACTAATTATGAATATCTTAG
***
1633503 ATTTTGCATGTAAAGTGCCCA
256 ATTTTGCACACAAAGTGCCCA
* * **
1633524 AACAGAAATTCATAATAAGTTTATGAATTTCTTAGTTTTGTAC
1 TACAAAAATTCATAA-ACTTTTATGAATTTCTTAGTTTTGTAC
1633567 GCATAGTACC
Statistics
Matches: 287, Mismatches: 29, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
277 42 0.15
278 207 0.72
279 36 0.13
280 2 0.01
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.35
Consensus pattern (276 bp):
TACAAAAATTCATAAACTTTTATGAATTTCTTAGTTTTGTACACAAAGTCCACATACGGAAATTC
ATAAACTTATTATGAATTTCTTAGCTTTTGCACACAAAGTGCCCATACGGAAATTCATAAACTTA
TTATGAATTTCTTAGCTTTTACACACAAAGTGACCATACGGAAATTCATAAACTCATTATGAATT
CCTTAGCTTTGCACAAGAATGCCCATACAAAAATTCAAAAACTAATTATGAATATCTTAGATTTT
GCACACAAAGTGCCCA
Found at i:1639128 original size:21 final size:21
Alignment explanation
Indices: 1639098--1639137 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1639088 TCGATAACCA
*
1639098 CATCAATATCGATACTAATTG
1 CATCAATATCAATACTAATTG
*
1639119 CATCAGTATCAATACTAAT
1 CATCAATATCAATACTAAT
1639138 CATCATAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.40, C:0.20, G:0.07, T:0.33
Consensus pattern (21 bp):
CATCAATATCAATACTAATTG
Done.