Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A05
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: 100714657
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3970000 characters in sequence are not A, C, G, or T
File 128 of 318
Found at i:39734028 original size:13 final size:13
Alignment explanation
Indices: 39734010--39734042 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
39734000 TTTAATATTC
39734010 AAAATT-TTTTATA
1 AAAATTATTTT-TA
39734023 AAAATTATTTTTA
1 AAAATTATTTTTA
39734036 AAAATTA
1 AAAATTA
39734043 AAAATTATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 15 0.79
14 4 0.21
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
AAAATTATTTTTA
Found at i:39734573 original size:12 final size:12
Alignment explanation
Indices: 39734556--39734589 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
39734546 CGACCAGCCC
39734556 ATATTAATTTTT
1 ATATTAATTTTT
*
39734568 ATATTATTTTTT
1 ATATTAATTTTT
39734580 ATA-TAATTTT
1 ATATTAATTTT
39734590 AAAATATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 6 0.30
12 14 0.70
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:39734747 original size:30 final size:30
Alignment explanation
Indices: 39734711--39734771 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
39734701 CAATTTAACA
*
39734711 AGCAAATGCCTCTAAAATAATAACAAAATT
1 AGCAAATGCCTCTAAAATAATAAAAAAATT
*
39734741 AGCAAATGCCTTTAAAATAATAAAAAAATT
1 AGCAAATGCCTCTAAAATAATAAAAAAATT
39734771 A
1 A
39734772 ACAATAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.56, C:0.13, G:0.07, T:0.25
Consensus pattern (30 bp):
AGCAAATGCCTCTAAAATAATAAAAAAATT
Found at i:39735516 original size:7 final size:7
Alignment explanation
Indices: 39735504--39735531 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
39735494 TAATGTTAGA
39735504 CTGCCTC
1 CTGCCTC
39735511 CTGCCTC
1 CTGCCTC
39735518 CTGCCTC
1 CTGCCTC
39735525 CTGCCTC
1 CTGCCTC
39735532 GGAGTCTTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.00, C:0.57, G:0.14, T:0.29
Consensus pattern (7 bp):
CTGCCTC
Found at i:39742519 original size:36 final size:36
Alignment explanation
Indices: 39742474--39742542 Score: 138
Period size: 36 Copynumber: 1.9 Consensus size: 36
39742464 ATATTAATAT
39742474 ATTTTTAAAAAATTTGAAAAGTCAAATCAAAATTAA
1 ATTTTTAAAAAATTTGAAAAGTCAAATCAAAATTAA
39742510 ATTTTTAAAAAATTTGAAAAGTCAAATCAAAAT
1 ATTTTTAAAAAATTTGAAAAGTCAAATCAAAAT
39742543 CCAAAATACA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.55, C:0.06, G:0.06, T:0.33
Consensus pattern (36 bp):
ATTTTTAAAAAATTTGAAAAGTCAAATCAAAATTAA
Found at i:39742865 original size:29 final size:29
Alignment explanation
Indices: 39742823--39742881 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
39742813 ACTAATGCAA
39742823 AGAATGAACTATGTTATGTATATTTTCCT
1 AGAATGAACTATGTTATGTATATTTTCCT
39742852 AGAATGAACTATGTTATGTATATTTTCCT
1 AGAATGAACTATGTTATGTATATTTTCCT
39742881 A
1 A
39742882 CTAACTCTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.32, C:0.10, G:0.14, T:0.44
Consensus pattern (29 bp):
AGAATGAACTATGTTATGTATATTTTCCT
Found at i:39747544 original size:10 final size:10
Alignment explanation
Indices: 39747531--39747572 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
39747521 AAAATTATAG
39747531 AATTTCTTTT
1 AATTTCTTTT
*
39747541 AATTCCTTTT
1 AATTTCTTTT
* *
39747551 ATTTTATTTT
1 AATTTCTTTT
39747561 -ATTTCTTTT
1 AATTTCTTTT
39747570 AAT
1 AAT
39747573 ATTATCCTTT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
9 7 0.28
10 18 0.72
ACGTcount: A:0.21, C:0.10, G:0.00, T:0.69
Consensus pattern (10 bp):
AATTTCTTTT
Found at i:39748409 original size:38 final size:36
Alignment explanation
Indices: 39748367--39748437 Score: 99
Period size: 38 Copynumber: 1.9 Consensus size: 36
39748357 TTTCACAATG
*
39748367 AGTTTT-AAATCCATCATTCTTTTTCATTCAATAATTTA
1 AGTTTTGAAAT-CATCA-TCATTTT-ATTCAATAATTTA
39748405 AGTTTTGAAATCATCATCATTTTATTCAATAAT
1 AGTTTTGAAATCATCATCATTTTATTCAATAAT
39748438 CTACATTATT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
36 10 0.32
37 6 0.19
38 11 0.35
39 4 0.13
ACGTcount: A:0.34, C:0.14, G:0.04, T:0.48
Consensus pattern (36 bp):
AGTTTTGAAATCATCATCATTTTATTCAATAATTTA
Found at i:39754086 original size:15 final size:16
Alignment explanation
Indices: 39754068--39754114 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 16
39754058 TGATAATGTA
39754068 AATAAC-AATAATACT
1 AATAACGAATAATACT
* *
39754083 AAT-ACTAATAATAAT
1 AATAACGAATAATACT
39754098 AATAACGAATAAT-CT
1 AATAACGAATAATACT
39754113 AA
1 AA
39754115 ATTTTCGAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 2 0.07
15 17 0.63
16 8 0.30
ACGTcount: A:0.60, C:0.11, G:0.02, T:0.28
Consensus pattern (16 bp):
AATAACGAATAATACT
Found at i:39754318 original size:3 final size:3
Alignment explanation
Indices: 39754310--39754337 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
39754300 TAAAATGGTT
39754310 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
39754338 TGTACAAGCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:39755821 original size:11 final size:11
Alignment explanation
Indices: 39755760--39755831 Score: 57
Period size: 11 Copynumber: 7.1 Consensus size: 11
39755750 CTTTTTAAAC
*
39755760 ATTATATATAT
1 ATTATGTATAT
39755771 ATT-T-T-TAT
1 ATTATGTATAT
*
39755779 ATTATGTCTAT
1 ATTATGTATAT
*
39755790 ATT-T-TATGT
1 ATTATGTATAT
* *
39755799 ATTTTTTA-AT
1 ATTATGTATAT
39755809 ATTATGTATAT
1 ATTATGTATAT
39755820 ATTATGTATAT
1 ATTATGTATAT
39755831 A
1 A
39755832 CTTTTAATAT
Statistics
Matches: 50, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
8 6 0.12
9 8 0.16
10 11 0.22
11 25 0.50
ACGTcount: A:0.33, C:0.01, G:0.06, T:0.60
Consensus pattern (11 bp):
ATTATGTATAT
Found at i:39755859 original size:23 final size:22
Alignment explanation
Indices: 39755816--39755866 Score: 66
Period size: 23 Copynumber: 2.3 Consensus size: 22
39755806 AATATTATGT
*
39755816 ATATATTATGTATATACTTTTA
1 ATATATTATATATATACTTTTA
* *
39755838 ATATCATTATATATTTATTTTTA
1 ATAT-ATTATATATATACTTTTA
39755861 ATATAT
1 ATATAT
39755867 ACGTATATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 6 0.24
23 19 0.76
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.57
Consensus pattern (22 bp):
ATATATTATATATATACTTTTA
Found at i:39756278 original size:13 final size:13
Alignment explanation
Indices: 39756260--39756284 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39756250 ATTATTATTA
39756260 TATATATTTCTTT
1 TATATATTTCTTT
39756273 TATATATTTCTT
1 TATATATTTCTT
39756285 ATTACTTCTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (13 bp):
TATATATTTCTTT
Found at i:39760177 original size:9 final size:9
Alignment explanation
Indices: 39760161--39760219 Score: 93
Period size: 9 Copynumber: 6.7 Consensus size: 9
39760151 ATCAACGCTT
39760161 TTGCATTCA
1 TTGCATTCA
*
39760170 TCGCATTCA
1 TTGCATTCA
39760179 TTGCATTCA
1 TTGCATTCA
*
39760188 TCGCATTCA
1 TTGCATTCA
39760197 TTGCATTCA
1 TTGCATTCA
39760206 TTGCATTCA
1 TTGCATTCA
39760215 -TGCAT
1 TTGCAT
39760220 CAGCATTGCA
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
8 5 0.11
9 41 0.89
ACGTcount: A:0.22, C:0.25, G:0.12, T:0.41
Consensus pattern (9 bp):
TTGCATTCA
Found at i:39771636 original size:3 final size:3
Alignment explanation
Indices: 39771613--39771652 Score: 50
Period size: 3 Copynumber: 14.3 Consensus size: 3
39771603 NNNNNNTATC
*
39771613 ATT ATT A-T ATT A-T ATT A-T ATT ATT ATT ATT TTT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
39771653 CGTATACATT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
2 6 0.19
3 26 0.81
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:39771651 original size:18 final size:16
Alignment explanation
Indices: 39771615--39771716 Score: 61
Period size: 18 Copynumber: 6.2 Consensus size: 16
39771605 NNNNTATCAT
*
39771615 TATTATATTA-TATTA
1 TATTATATTATTTTTA
39771630 TATTATTATTATTTTTA
1 TATTA-TATTATTTTTA
*
39771647 TTATTACGTATACATTTTTA
1 -TATTA--TAT-TATTTTTA
39771667 TATCTATATGTATTTTTA
1 TAT-TATAT-TATTTTTA
* *
39771685 TA-T-TGTTATTATTA
1 TATTATATTATTTTTA
39771699 TA-TATATT-TCTTTTA
1 TATTATATTAT-TTTTA
39771714 TAT
1 TAT
39771717 ATTTCTTATT
Statistics
Matches: 69, Mismatches: 9, Indels: 17
0.73 0.09 0.18
Matches are distributed among these distances:
14 11 0.16
15 16 0.23
16 6 0.09
17 4 0.06
18 17 0.25
19 6 0.09
20 9 0.13
ACGTcount: A:0.30, C:0.04, G:0.03, T:0.63
Consensus pattern (16 bp):
TATTATATTATTTTTA
Found at i:39771717 original size:13 final size:13
Alignment explanation
Indices: 39771699--39771723 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39771689 GTTATTATTA
39771699 TATATATTTCTTT
1 TATATATTTCTTT
39771712 TATATATTTCTT
1 TATATATTTCTT
39771724 ATTACTTCTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (13 bp):
TATATATTTCTTT
Found at i:39783629 original size:43 final size:43
Alignment explanation
Indices: 39783565--39783953 Score: 213
Period size: 43 Copynumber: 8.9 Consensus size: 43
39783555 AGAATTAGTG
* * *
39783565 AATTCACCAGACCTTAACCCCCTAAGCAGTAGGGTAACATGTTA
1 AATTCA-CAGATCTCAACCCCCTAAGCAGTAGGGTAACAGGTTA
*
39783609 AATTCACAGATCTCAACCCCCTAAGCAGTAGGGTAACAGGTTG
1 AATTCACAGATCTCAACCCCCTAAGCAGTAGGGTAACAGGTTA
* * * *
39783652 AATTCATAGATCTCAACCCCCTAAGCAGTAGGGAAATAGATTGA
1 AATTCACAGATCTCAACCCCCTAAGCAGTAGGGTAACAGGTT-A
* * ** * * *
39783696 AGATGAT-A-AG-CCTTAACCCTTTTATGCAGTAAGGTAACAGGCTAAA
1 A-AT--TCACAGATCTCAACCC-CCTAAGCAGTAGGGTAACAGG-T-TA
* * * * **
39783742 AATT-ACAGATCTTATCACCCTAAGCAGTAGGGAAACAGAGCGA
1 AATTCACAGATCTCAACCCCCTAAGCAGTAGGGTAACAG-GTTA
* * * * * *
39783785 AGA-TGA-AGAACCTTAAACCCCTAAGTAGTAGGGTAACAGGTTG
1 A-ATTCACAG-ATCTCAACCCCCTAAGCAGTAGGGTAACAGGTTA
* * * * *
39783828 AATTTACAGATCTCAGCCCCCTAAGCAGTAGGGAAACAGATCGA
1 AATTCACAGATCTCAACCCCCTAAGCAGTAGGGTAACAGGT-TA
* * *
39783872 AGATGAT-A-AG-CCTTAA-CCCCTAAGCAGTAGGGTAACAGGTTG
1 A-AT--TCACAGATCTCAACCCCCTAAGCAGTAGGGTAACAGGTTA
* * * *
39783914 AATTTATAGATCTTAACCCCCTTAAGCAGTAGGGAAACAG
1 AATTCACAGATCTCAACCCCC-TAAGCAGTAGGGTAACAG
39783954 ATCAGGAGTG
Statistics
Matches: 264, Mismatches: 57, Indels: 48
0.72 0.15 0.13
Matches are distributed among these distances:
39 1 0.00
40 1 0.00
41 4 0.02
42 7 0.03
43 133 0.50
44 80 0.30
45 31 0.12
46 5 0.02
47 2 0.01
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.22
Consensus pattern (43 bp):
AATTCACAGATCTCAACCCCCTAAGCAGTAGGGTAACAGGTTA
Found at i:39783807 original size:44 final size:45
Alignment explanation
Indices: 39783759--39783991 Score: 146
Period size: 43 Copynumber: 5.3 Consensus size: 45
39783749 GATCTTATCA
39783759 CCCTAAGCAGTAGGGAAACAGAGCGAAGATGA-AGAACCTTAAAC
1 CCCTAAGCAGTAGGGAAACAGAGCGAAGATGATAGAACCTTAAAC
* * * * * * * * **
39783803 CCCTAAGTAGTAGGGTAACAG-GTTGAA-TTTACAG-ATCTCAGCC
1 CCCTAAGCAGTAGGGAAACAGAG-CGAAGATGATAGAACCTTAAAC
* *
39783846 CCCTAAGCAGTAGGGAAACAGATCGAAGATGATA-AGCCTT-AAC
1 CCCTAAGCAGTAGGGAAACAGAGCGAAGATGATAGAACCTTAAAC
* * * * * *
39783889 CCCTAAGCAGTAGGGTAACAG-GTTGAA-TTTATAG-ATCTTAACC
1 CCCTAAGCAGTAGGGAAACAGAG-CGAAGATGATAGAACCTTAAAC
* * *
39783932 CCCTTAAGCAGTAGGGAAACAGATC-AGGAGTGAT-GAGCCTTAAAC
1 CCC-TAAGCAGTAGGGAAACAGAGCGAAGA-TGATAGAACCTTAAAC
* *
39783977 CCATAAGCAATAGGG
1 CCCTAAGCAGTAGGG
39783992 TCACAGGCTG
Statistics
Matches: 136, Mismatches: 40, Indels: 26
0.67 0.20 0.13
Matches are distributed among these distances:
42 7 0.05
43 60 0.44
44 58 0.43
45 11 0.08
ACGTcount: A:0.36, C:0.20, G:0.24, T:0.19
Consensus pattern (45 bp):
CCCTAAGCAGTAGGGAAACAGAGCGAAGATGATAGAACCTTAAAC
Found at i:39783865 original size:87 final size:86
Alignment explanation
Indices: 39783626--39784016 Score: 444
Period size: 87 Copynumber: 4.5 Consensus size: 86
39783616 AGATCTCAAC
* * *
39783626 CCCCTAAGCAGTAGGGTAACAGGTTGAATTCATAGATCTCAACCCCCTAAGCAGTAGGGAAATAG
1 CCCCTAAGCAGTAGGGTAACAGGTTGAATTTACAGATCTCAACCCCCTAAGCAGTAGGGAAACAG
*
39783691 ATTGAAGATGATAAGCCTTAA
66 ATCGAAGATGATAAGCCTTAA
* * * ** * * * *
39783712 CCCTTTTATGCAGTAAGGTAACAGGCTAAAAATTACAGATCTTATCACCCTAAGCAGTAGGGAAA
1 CCC--CTAAGCAGTAGGGTAACAGG-TTGAATTTACAGATCTCAACCCCCTAAGCAGTAGGGAAA
* *
39783777 CAGAGCGAAGATGA-AGAACCTTAAA
63 CAGATCGAAGATGATA-AGCCTT-AA
* *
39783802 CCCCTAAGTAGTAGGGTAACAGGTTGAATTTACAGATCTCAGCCCCCTAAGCAGTAGGGAAACAG
1 CCCCTAAGCAGTAGGGTAACAGGTTGAATTTACAGATCTCAACCCCCTAAGCAGTAGGGAAACAG
39783867 ATCGAAGATGATAAGCCTTAA
66 ATCGAAGATGATAAGCCTTAA
* *
39783888 CCCCTAAGCAGTAGGGTAACAGGTTGAATTTATAGATCTTAACCCCCTTAAGCAGTAGGGAAACA
1 CCCCTAAGCAGTAGGGTAACAGGTTGAATTTACAGATCTCAACCCCC-TAAGCAGTAGGGAAACA
* *
39783953 GATC-AGGAGTGATGAGCCTTAAA
65 GATCGAAGA-TGATAAGCCTT-AA
* * * * * *
39783976 CCCATAAGCAATAGGGTCACAGGCTGGAAATTACAAATCTC
1 CCCCTAAGCAGTAGGGTAACAGG-TTGAATTTACAGATCTC
39784017 TTCTCCCTGA
Statistics
Matches: 254, Mismatches: 41, Indels: 17
0.81 0.13 0.05
Matches are distributed among these distances:
86 51 0.20
87 82 0.32
88 57 0.22
89 59 0.23
90 5 0.02
ACGTcount: A:0.36, C:0.20, G:0.22, T:0.21
Consensus pattern (86 bp):
CCCCTAAGCAGTAGGGTAACAGGTTGAATTTACAGATCTCAACCCCCTAAGCAGTAGGGAAACAG
ATCGAAGATGATAAGCCTTAA
Found at i:39785791 original size:11 final size:11
Alignment explanation
Indices: 39785777--39785802 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
39785767 TGTTTTTTTT
39785777 TATATTATGTA
1 TATATTATGTA
39785788 TATATTATGTA
1 TATATTATGTA
39785799 TATA
1 TATA
39785803 CTTTTAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (11 bp):
TATATTATGTA
Found at i:39785808 original size:30 final size:30
Alignment explanation
Indices: 39785731--39785823 Score: 93
Period size: 30 Copynumber: 3.1 Consensus size: 30
39785721 CTTTTTAAAC
*
39785731 ATTATATATATATTTTTATATTATGTCTATAT
1 ATTATGTATATATTTTTATATTATG--TATAT
* *
39785763 TTTATGT-T-TTTTTTTATATTATGTATAT
1 ATTATGTATATATTTTTATATTATGTATAT
* *
39785791 ATTATGTATATACTTTTAATATCAT-TATAT
1 ATTATGTATATA-TTTTTATATTATGTATAT
39785821 ATT
1 ATT
39785824 TATTTTTAAT
Statistics
Matches: 51, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
28 11 0.22
29 1 0.02
30 23 0.45
31 11 0.22
32 5 0.10
ACGTcount: A:0.31, C:0.03, G:0.04, T:0.61
Consensus pattern (30 bp):
ATTATGTATATATTTTTATATTATGTATAT
Found at i:39785830 original size:23 final size:22
Alignment explanation
Indices: 39785787--39785836 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 22
39785777 TATATTATGT
*
39785787 ATATATTATGTATATACTTTTA
1 ATATATTATATATATACTTTTA
* *
39785809 ATATCATTATATATTTATTTTTA
1 ATAT-ATTATATATATACTTTTA
39785832 ATATA
1 ATATA
39785837 AACGTATATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 5 0.21
23 19 0.79
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (22 bp):
ATATATTATATATATACTTTTA
Found at i:39786252 original size:13 final size:13
Alignment explanation
Indices: 39786234--39786258 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39786224 ATTATTATTA
39786234 TATATATTTCTTT
1 TATATATTTCTTT
39786247 TATATATTTCTT
1 TATATATTTCTT
39786259 ATTACTTCTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (13 bp):
TATATATTTCTTT
Found at i:39787337 original size:3 final size:3
Alignment explanation
Indices: 39787331--39787384 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
39787321 TGGTTACGAC
39787331 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
39787379 AAT AAT
1 AAT AAT
39787385 TGAAGTTAAA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:39792907 original size:53 final size:53
Alignment explanation
Indices: 39792845--39792956 Score: 224
Period size: 53 Copynumber: 2.1 Consensus size: 53
39792835 TCTTATTAAA
39792845 TTTTTTATATAATTTTAAAAACTCTGTTTGCAATTTGATCTTAATGACATCAT
1 TTTTTTATATAATTTTAAAAACTCTGTTTGCAATTTGATCTTAATGACATCAT
39792898 TTTTTTATATAATTTTAAAAACTCTGTTTGCAATTTGATCTTAATGACATCAT
1 TTTTTTATATAATTTTAAAAACTCTGTTTGCAATTTGATCTTAATGACATCAT
39792951 TTTTTT
1 TTTTTT
39792957 GTCTCGAAAA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 59 1.00
ACGTcount: A:0.30, C:0.11, G:0.07, T:0.52
Consensus pattern (53 bp):
TTTTTTATATAATTTTAAAAACTCTGTTTGCAATTTGATCTTAATGACATCAT
Found at i:39792941 original size:26 final size:26
Alignment explanation
Indices: 39792859--39792941 Score: 69
Period size: 26 Copynumber: 3.2 Consensus size: 26
39792849 TTATATAATT
39792859 TTAAAAACTCTGTTTGCAATTTGATC
1 TTAAAAACTCTGTTTGCAATTTGATC
** *** * * *
39792885 TTAATGACATCAT-TTTTTTATATAATT
1 TTAAAAAC-TC-TGTTTGCAATTTGATC
39792912 TTAAAAACTCTGTTTGCAATTTGATC
1 TTAAAAACTCTGTTTGCAATTTGATC
39792938 TTAA
1 TTAA
39792942 TGACATCATT
Statistics
Matches: 38, Mismatches: 16, Indels: 6
0.63 0.27 0.10
Matches are distributed among these distances:
25 1 0.03
26 20 0.53
27 16 0.42
28 1 0.03
ACGTcount: A:0.33, C:0.12, G:0.08, T:0.47
Consensus pattern (26 bp):
TTAAAAACTCTGTTTGCAATTTGATC
Found at i:39793267 original size:13 final size:13
Alignment explanation
Indices: 39793249--39793273 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39793239 GAGTGAAAAT
39793249 ATCATTAATTTTC
1 ATCATTAATTTTC
39793262 ATCATTAATTTT
1 ATCATTAATTTT
39793274 TTAAAATGAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.12, G:0.00, T:0.56
Consensus pattern (13 bp):
ATCATTAATTTTC
Found at i:39793782 original size:22 final size:23
Alignment explanation
Indices: 39793724--39793783 Score: 56
Period size: 23 Copynumber: 2.7 Consensus size: 23
39793714 AGTGTTTGGG
39793724 AAATATTAAA-AT-AAATATATA
1 AAATATTAAATATAAAATATATA
* *
39793745 AAAAAGGT-AATGATAAAATAT-TA
1 AAATA-TTAAAT-ATAAAATATATA
39793768 AAATATTAAATATAAA
1 AAATATTAAATATAAA
39793784 TTACACTTCT
Statistics
Matches: 30, Mismatches: 4, Indels: 9
0.70 0.09 0.21
Matches are distributed among these distances:
21 6 0.20
22 7 0.23
23 11 0.37
24 6 0.20
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (23 bp):
AAATATTAAATATAAAATATATA
Found at i:39799173 original size:21 final size:22
Alignment explanation
Indices: 39799122--39799173 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 22
39799112 GAAAGAAGAT
39799122 TAAAT-TT-AACTAAAAATAAA
1 TAAATATTAAACTAAAAATAAA
* * *
39799142 TAAAAACTAAACTAAAAA-ATA
1 TAAATATTAAACTAAAAATAAA
39799163 TAAATATTAAA
1 TAAATATTAAA
39799174 AGCTAAATTA
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
20 4 0.16
21 12 0.48
22 9 0.36
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (22 bp):
TAAATATTAAACTAAAAATAAA
Found at i:39801156 original size:43 final size:42
Alignment explanation
Indices: 39801086--39801267 Score: 165
Period size: 43 Copynumber: 4.3 Consensus size: 42
39801076 TTATGTGGAA
* * * * * *
39801086 AAACGCCGTTATAGAACATTACATTTAGCGACGCTTTTTCCAC
1 AAACGCCGCTAAAGAACGTGACCTTTAGCGACGC-TTTCCCAC
*
39801129 AAACGCCGCTAAAGAACGTGACCTTTAGCGACGCTTTCCCCAT
1 AAACGCCGCTAAAGAACGTGACCTTTAGCGACGCTTT-CCCAC
*
39801172 AAACGCCACTAAAGAACGTGACCTTTAGCTG-CGCTTTCCCAC
1 AAACGCCGCTAAAGAACGTGACCTTTAGC-GACGCTTTCCCAC
** * *
39801214 AAACGTTGCTAAGAGAA--TGACCTTTAGC-AGCGCTTTTCTCAA
1 AAACGCCGCTAA-AGAACGTGACCTTTAGCGA-CGC-TTTCCCAC
*
39801256 AAACGCCACTAA
1 AAACGCCGCTAA
39801268 GGTCATGTTC
Statistics
Matches: 116, Mismatches: 17, Indels: 13
0.79 0.12 0.09
Matches are distributed among these distances:
41 14 0.12
42 31 0.27
43 70 0.60
44 1 0.01
ACGTcount: A:0.31, C:0.29, G:0.16, T:0.24
Consensus pattern (42 bp):
AAACGCCGCTAAAGAACGTGACCTTTAGCGACGCTTTCCCAC
Found at i:39801350 original size:42 final size:42
Alignment explanation
Indices: 39801269--39801350 Score: 103
Period size: 42 Copynumber: 2.0 Consensus size: 42
39801259 CGCCACTAAG
* * *
39801269 GTCATGTTCTTTAACGGCGTTTTAGTAAAAGCGCTGTTAAAA
1 GTCATGTTCTTTAACGGCGTTTTAGGAAAAACGCCGTTAAAA
**
39801311 GTCATGTTCTTTGGCGGCGTTTGT-GGAAAAACGCCGTTAA
1 GTCATGTTCTTTAACGGCGTTT-TAGGAAAAACGCCGTTAA
39801351 CTTTAGTAGA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
42 33 0.97
43 1 0.03
ACGTcount: A:0.24, C:0.16, G:0.26, T:0.34
Consensus pattern (42 bp):
GTCATGTTCTTTAACGGCGTTTTAGGAAAAACGCCGTTAAAA
Found at i:39801751 original size:66 final size:65
Alignment explanation
Indices: 39801623--39801756 Score: 162
Period size: 66 Copynumber: 2.0 Consensus size: 65
39801613 ATTCTGAAGC
* * ***
39801623 TGTAGCTGGAGTTCGTCATATTTTCTGCTTGCCTCTGCTTCCCTCGCTGCTACCTTTGCTTTAAG
1 TGTAGCTGGAGTTCGTCATATTTTCT-CTTGCCTCTACTTCCCTCGATGCTACCTCCACTTTAAG
39801688 T
65 T
* * *
39801689 TGTAGCTGGAGTTCTTCATATTTTCT-TTGAGCCTCTACTTCTCTCGATGCTGCCTCCACTTTAA
1 TGTAGCTGGAGTTCGTCATATTTTCTCTT--GCCTCTACTTCCCTCGATGCTACCTCCACTTTAA
39801753 GT
64 GT
39801755 TG
1 TG
39801757 AGCAATTTGC
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
64 2 0.03
66 56 0.97
ACGTcount: A:0.13, C:0.26, G:0.19, T:0.43
Consensus pattern (65 bp):
TGTAGCTGGAGTTCGTCATATTTTCTCTTGCCTCTACTTCCCTCGATGCTACCTCCACTTTAAGT
Found at i:39803535 original size:5 final size:5
Alignment explanation
Indices: 39803525--39803580 Score: 85
Period size: 5 Copynumber: 10.6 Consensus size: 5
39803515 TTAAGTATAT
39803525 TATTA TATTA TATTA TATTA TATTTA TATTTA TATTTA TATTA TATTA
1 TATTA TATTA TATTA TATTA TA-TTA TA-TTA TA-TTA TATTA TATTA
39803573 TATTA TAT
1 TATTA TAT
39803581 ATAAAAGAAA
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
5 33 0.66
6 17 0.34
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TATTA
Found at i:39804304 original size:18 final size:18
Alignment explanation
Indices: 39804273--39804307 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
39804263 GTGTGTTGAA
* *
39804273 TACTGTTACTGTTACTGC
1 TACTGCTACCGTTACTGC
39804291 TACTGCTACCGTTACTG
1 TACTGCTACCGTTACTG
39804308 ATTACTGATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.17, C:0.26, G:0.17, T:0.40
Consensus pattern (18 bp):
TACTGCTACCGTTACTGC
Found at i:39807526 original size:46 final size:46
Alignment explanation
Indices: 39807466--39807783 Score: 444
Period size: 46 Copynumber: 7.0 Consensus size: 46
39807456 TTTGACATGA
* * * ** * *
39807466 TGCCATAGTGTCTTTCAACTATGGTCTTACTTATTTTCA-GTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGT
** * * *
39807512 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGTCACGC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
39807558 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
39807604 TGCCATGGTATCTTTCAACTATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
** *
39807650 TGCCATGGTATCTTTCAACCATAATCTTACACATTTCATATTAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
39807696 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAAGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
39807742 TGCCATGGTATC-TT-AACCATGGTCTTACACATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
39807784 AGAGCACACT
Statistics
Matches: 249, Mismatches: 22, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
44 27 0.11
45 7 0.03
46 215 0.86
ACGTcount: A:0.24, C:0.23, G:0.14, T:0.39
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
Found at i:39809767 original size:14 final size:14
Alignment explanation
Indices: 39809731--39809776 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
39809721 GCTTTGTTTC
*
39809731 TTTATTTCTCTCC-T
1 TTTATTTC-CCCCTT
39809745 TTT-TTTCCCCCTT
1 TTTATTTCCCCCTT
*
39809758 TTTATTTCCCCTTT
1 TTTATTTCCCCCTT
39809772 TTTAT
1 TTTAT
39809777 ATATACACAC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
12 3 0.11
13 8 0.29
14 17 0.61
ACGTcount: A:0.07, C:0.28, G:0.00, T:0.65
Consensus pattern (14 bp):
TTTATTTCCCCCTT
Found at i:39811518 original size:30 final size:30
Alignment explanation
Indices: 39811484--39811546 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
39811474 ACTTAAGAAG
39811484 CAAATG-CTTCTAAAATAATAAAAAAATTAA
1 CAAATGCCTT-TAAAATAATAAAAAAATTAA
*
39811514 CAAATGCCTTTAAAATAATAAGAAAATTAA
1 CAAATGCCTTTAAAATAATAAAAAAATTAA
39811544 CAA
1 CAA
39811547 TAAAATAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 28 0.90
31 3 0.10
ACGTcount: A:0.59, C:0.11, G:0.05, T:0.25
Consensus pattern (30 bp):
CAAATGCCTTTAAAATAATAAAAAAATTAA
Found at i:39814836 original size:5 final size:5
Alignment explanation
Indices: 39814826--39814868 Score: 86
Period size: 5 Copynumber: 8.6 Consensus size: 5
39814816 AATAATTAAG
39814826 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TAT
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TAT
39814869 ATAAAAGAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 38 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATTA
Found at i:39815517 original size:12 final size:12
Alignment explanation
Indices: 39815500--39815524 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
39815490 GCCGACTACT
39815500 GTTACTGTTACC
1 GTTACTGTTACC
39815512 GTTACTGTTACC
1 GTTACTGTTACC
39815524 G
1 G
39815525 ATTCGACACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.24, G:0.20, T:0.40
Consensus pattern (12 bp):
GTTACTGTTACC
Found at i:39815552 original size:45 final size:45
Alignment explanation
Indices: 39815502--39815608 Score: 135
Period size: 45 Copynumber: 2.4 Consensus size: 45
39815492 CGACTACTGT
*
39815502 TACTGTTACCGTTACTGTTACCGATTC-GACACTTTGTGTGTCGAA
1 TACTGTTACCGTTACTGTTACAGATTCAG-CACTTTGTGTGTCGAA
* * * * *
39815547 TACTGTTACCGTTACTATTATAGATTCAGTATTTTGTGTGTTGAA
1 TACTGTTACCGTTACTGTTACAGATTCAGCACTTTGTGTGTCGAA
*
39815592 TACTGTTACTGTTACTG
1 TACTGTTACCGTTACTG
39815609 CTATTGCTAC
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
45 52 0.98
46 1 0.02
ACGTcount: A:0.21, C:0.17, G:0.19, T:0.43
Consensus pattern (45 bp):
TACTGTTACCGTTACTGTTACAGATTCAGCACTTTGTGTGTCGAA
Found at i:39829639 original size:19 final size:20
Alignment explanation
Indices: 39829602--39829639 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
39829592 ATATGATTAA
39829602 TAAAATTTTCATGTGAAATT
1 TAAAATTTTCATGTGAAATT
39829622 TAAACATTTT-AT-TGAAAT
1 TAAA-ATTTTCATGTGAAAT
39829640 AATATAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 6 0.35
20 6 0.35
21 5 0.29
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.45
Consensus pattern (20 bp):
TAAAATTTTCATGTGAAATT
Found at i:39833109 original size:22 final size:22
Alignment explanation
Indices: 39833081--39833130 Score: 91
Period size: 22 Copynumber: 2.3 Consensus size: 22
39833071 AACTATTGTA
39833081 CATATTAGATGAATTCAATAAT
1 CATATTAGATGAATTCAATAAT
*
39833103 CATATTAGATGAATTCAATAGT
1 CATATTAGATGAATTCAATAAT
39833125 CATATT
1 CATATT
39833131 TGATTCTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.42, C:0.10, G:0.10, T:0.38
Consensus pattern (22 bp):
CATATTAGATGAATTCAATAAT
Found at i:39835745 original size:15 final size:15
Alignment explanation
Indices: 39835725--39835754 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
39835715 TTCATTCTTT
39835725 TATGTTTTCTTTGTA
1 TATGTTTTCTTTGTA
39835740 TATGTTTTCTTTGTA
1 TATGTTTTCTTTGTA
39835755 GTAAGTTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.07, G:0.13, T:0.67
Consensus pattern (15 bp):
TATGTTTTCTTTGTA
Found at i:39835763 original size:15 final size:15
Alignment explanation
Indices: 39835728--39835762 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
39835718 ATTCTTTTAT
*
39835728 GTTTTCTTTGTATAT
1 GTTTTCTTTGTATAA
39835743 GTTTTCTTTGTAGTAA
1 GTTTTCTTTGTA-TAA
39835759 GTTT
1 GTTT
39835763 CATTGTAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 12 0.67
16 6 0.33
ACGTcount: A:0.14, C:0.06, G:0.17, T:0.63
Consensus pattern (15 bp):
GTTTTCTTTGTATAA
Found at i:39836095 original size:49 final size:51
Alignment explanation
Indices: 39835929--39836105 Score: 191
Period size: 52 Copynumber: 3.5 Consensus size: 51
39835919 GGATACTCGT
* * ** *
39835929 TGGCCTGCACATAGTACCACCCTTGT-AGTTAAAGCTA-CATTCTTCACAAAG
1 TGGCCTTCACATAGTACCACACTTGTGA-CCAAAACTATC-TTCTTCACAAAG
*
39835980 TGGCCTTCACATAGTACTACACTTGTGACCAAAACTATCTTTCTTCACAAAG
1 TGGCCTTCACATAGTACCACACTTGTGACCAAAACTATC-TTCTTCACAAAG
** * * *
39836032 TGGCCTTCTTATAGTACCATACTTGTGACC-AAGCTATC-TCTTCTCAAAG
1 TGGCCTTCACATAGTACCACACTTGTGACCAAAACTATCTTCTTCACAAAG
*
39836081 TGGCCTTCACATAGTACCACGCTTG
1 TGGCCTTCACATAGTACCACACTTG
39836106 AGTCACTAGT
Statistics
Matches: 107, Mismatches: 17, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
49 31 0.29
51 36 0.34
52 40 0.37
ACGTcount: A:0.27, C:0.28, G:0.15, T:0.31
Consensus pattern (51 bp):
TGGCCTTCACATAGTACCACACTTGTGACCAAAACTATCTTCTTCACAAAG
Found at i:39840375 original size:27 final size:27
Alignment explanation
Indices: 39840327--39840485 Score: 184
Period size: 27 Copynumber: 5.9 Consensus size: 27
39840317 GCGAGGCTGC
* *
39840327 CAGATATTGTGAC-GAAGTCACCAGATA
1 CAGATATTGTGGCAG-AGCCACCAGATA
39840354 CAGATATTGTGGCAGAGCCACCAGA-A
1 CAGATATTGTGGCAGAGCCACCAGATA
39840380 CAGATATATGTGGCAGAGCCACCAGAT-
1 CAGATAT-TGTGGCAGAGCCACCAGATA
* * *
39840407 CAAATAATCGTGGCATAGCCACCAGA-A
1 CAGAT-ATTGTGGCAGAGCCACCAGATA
39840434 CAGATATATGTGGCAGAGCCACCAGAT-
1 CAGATAT-TGTGGCAGAGCCACCAGATA
*
39840461 CAGATAATTGTGGCATAGCCACCAG
1 CAGAT-ATTGTGGCAGAGCCACCAG
39840486 GACGCTTCCT
Statistics
Matches: 115, Mismatches: 9, Indels: 16
0.82 0.06 0.11
Matches are distributed among these distances:
26 10 0.09
27 100 0.87
28 5 0.04
ACGTcount: A:0.35, C:0.23, G:0.24, T:0.18
Consensus pattern (27 bp):
CAGATATTGTGGCAGAGCCACCAGATA
Found at i:39840420 original size:54 final size:54
Alignment explanation
Indices: 39840345--39840485 Score: 239
Period size: 54 Copynumber: 2.6 Consensus size: 54
39840335 GTGACGAAGT
*
39840345 CACCAGATACAGAT-ATTGTGGCAGAGCCACCAGAACAGATATATGTGGCAGAGC
1 CACCAGAT-CAGATAATTGTGGCATAGCCACCAGAACAGATATATGTGGCAGAGC
* *
39840399 CACCAGATCAAATAATCGTGGCATAGCCACCAGAACAGATATATGTGGCAGAGC
1 CACCAGATCAGATAATTGTGGCATAGCCACCAGAACAGATATATGTGGCAGAGC
39840453 CACCAGATCAGATAATTGTGGCATAGCCACCAG
1 CACCAGATCAGATAATTGTGGCATAGCCACCAG
39840486 GACGCTTCCT
Statistics
Matches: 81, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
53 4 0.05
54 77 0.95
ACGTcount: A:0.35, C:0.24, G:0.23, T:0.17
Consensus pattern (54 bp):
CACCAGATCAGATAATTGTGGCATAGCCACCAGAACAGATATATGTGGCAGAGC
Found at i:39842103 original size:26 final size:26
Alignment explanation
Indices: 39842073--39842180 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
39842063 TGAAATTCCC
39842073 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
39842099 ATCATGGAACATTTACCTAACCTATT
1 ATCATGGAACATTTACCTAACCCATT
* *
39842125 ATCATGAAATATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
39842151 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
39842177 ATCA
1 ATCA
39842181 ATTTGTGTCA
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 76 1.00
ACGTcount: A:0.36, C:0.25, G:0.06, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:39849557 original size:32 final size:34
Alignment explanation
Indices: 39849521--39849585 Score: 80
Period size: 34 Copynumber: 2.0 Consensus size: 34
39849511 TAACAGTGGT
*
39849521 ACTGGACCAGAG-CCCTT-TTTAGATTACAATAA
1 ACTGGACCAGAGCCCCTTATTTAGATAACAATAA
* **
39849553 ACTGGGCCTTAGCCCCTTATTTAGATAACAATA
1 ACTGGACCAGAGCCCCTTATTTAGATAACAATA
39849586 TGGCCCATAG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
32 9 0.33
33 5 0.19
34 13 0.48
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.29
Consensus pattern (34 bp):
ACTGGACCAGAGCCCCTTATTTAGATAACAATAA
Found at i:39849930 original size:25 final size:27
Alignment explanation
Indices: 39849893--39849945 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
39849883 TCAAACATGC
39849893 ATTTAAGTCAATTTAAC-CCTAGGGGT
1 ATTTAAGTCAATTTAACTCCTAGGGGT
* *
39849919 ATTTCAGT-AATTTATCTCCTAGGGGT
1 ATTTAAGTCAATTTAACTCCTAGGGGT
39849945 A
1 A
39849946 AAACTGTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.28, C:0.15, G:0.19, T:0.38
Consensus pattern (27 bp):
ATTTAAGTCAATTTAACTCCTAGGGGT
Found at i:39851423 original size:26 final size:26
Alignment explanation
Indices: 39851387--39851468 Score: 155
Period size: 26 Copynumber: 3.2 Consensus size: 26
39851377 TGAAATTTCA
39851387 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
39851413 ATCATGAAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
39851439 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
39851465 ATCA
1 ATCA
39851469 ATTTGTATCA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 54 1.00
ACGTcount: A:0.37, C:0.27, G:0.06, T:0.30
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:39852285 original size:33 final size:36
Alignment explanation
Indices: 39852221--39852292 Score: 87
Period size: 33 Copynumber: 2.1 Consensus size: 36
39852211 GTAAGTGTTC
*
39852221 TAATACTATATCATATATACACATGCATTTTTCATAT
1 TAATACTATATCATATATACACATG-ATTTTTAATAT
* *
39852258 TAATA-TATAT-ATATATATATATG-TTTTTAATAT
1 TAATACTATATCATATATACACATGATTTTTAATAT
39852291 TA
1 TA
39852293 TATTATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
33 11 0.34
35 11 0.34
36 5 0.16
37 5 0.16
ACGTcount: A:0.40, C:0.08, G:0.03, T:0.49
Consensus pattern (36 bp):
TAATACTATATCATATATACACATGATTTTTAATAT
Found at i:39852287 original size:27 final size:27
Alignment explanation
Indices: 39852257--39852320 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 27
39852247 ATTTTTCATA
39852257 TTAATA-TATATATAT-ATATATATGTTT
1 TTAATATTATAT-TATCATATATATG-TT
*
39852284 TTAATATTATATTATCATGTATATGTT
1 TTAATATTATATTATCATATATATGTT
39852311 TTAATATTAT
1 TTAATATTAT
39852321 TAGCTATCTA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
27 21 0.62
28 13 0.38
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.56
Consensus pattern (27 bp):
TTAATATTATATTATCATATATATGTT
Found at i:39852504 original size:21 final size:21
Alignment explanation
Indices: 39852462--39852504 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
39852452 AATATAAATA
* *
39852462 TATATATACATCATATAGGTT
1 TATATACACATCATACAGGTT
* *
39852483 TATATACATATCATACATGTT
1 TATATACACATCATACAGGTT
39852504 T
1 T
39852505 CATTATTTTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.37, C:0.12, G:0.07, T:0.44
Consensus pattern (21 bp):
TATATACACATCATACAGGTT
Found at i:39858324 original size:45 final size:45
Alignment explanation
Indices: 39858273--39858375 Score: 127
Period size: 46 Copynumber: 2.3 Consensus size: 45
39858263 GAGTCATGGT
* * *
39858273 CGGTAAGCTCTTTCGAGCTG-AATAGTAAGCTCTATTGAGCTGAAA
1 CGGTAAGCTCTTT-GAGCTGAAACAGTAAGCTCCAATGAGCTGAAA
**
39858318 CGGTAAGCTCCAATGAGCTGAAACAGTAAGCTCCAATGAGCTGAAA
1 CGGTAAGCT-CTTTGAGCTGAAACAGTAAGCTCCAATGAGCTGAAA
*
39858364 CGATAAGCTCTT
1 CGGTAAGCTCTT
39858376 AAGAGCTATG
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
45 16 0.33
46 32 0.67
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.24
Consensus pattern (45 bp):
CGGTAAGCTCTTTGAGCTGAAACAGTAAGCTCCAATGAGCTGAAA
Found at i:39858327 original size:23 final size:23
Alignment explanation
Indices: 39858273--39858382 Score: 111
Period size: 23 Copynumber: 4.8 Consensus size: 23
39858263 GAGTCATGGT
*
39858273 CGGTAAGCTCT-TTCGAGCTGAATA
1 CGGTAAGCTCTAAT-GAGCTGAA-A
*
39858297 --GTAAGCTCTATTGAGCTGAAA
1 CGGTAAGCTCTAATGAGCTGAAA
*
39858318 CGGTAAGCTCCAATGAGCTGAAA
1 CGGTAAGCTCTAATGAGCTGAAA
* *
39858341 CAGTAAGCTCCAATGAGCTGAAA
1 CGGTAAGCTCTAATGAGCTGAAA
*
39858364 CGATAAGCTCTTAA-GAGCT
1 CGGTAAGCTC-TAATGAGCT
39858383 ATGGTGAGTT
Statistics
Matches: 76, Mismatches: 6, Indels: 9
0.84 0.07 0.10
Matches are distributed among these distances:
21 1 0.01
22 17 0.22
23 56 0.74
24 2 0.03
ACGTcount: A:0.33, C:0.20, G:0.24, T:0.24
Consensus pattern (23 bp):
CGGTAAGCTCTAATGAGCTGAAA
Found at i:39858349 original size:46 final size:45
Alignment explanation
Indices: 39858287--39858373 Score: 129
Period size: 46 Copynumber: 1.9 Consensus size: 45
39858277 AAGCTCTTTC
* * * *
39858287 GAGCTGAATAGTAAGCTCTATTGAGCTGAAACGGTAAGCTCCAAT
1 GAGCTGAACAGTAAGCTCCAATGAGCTGAAACGATAAGCTCCAAT
39858332 GAGCTGAAACAGTAAGCTCCAATGAGCTGAAACGATAAGCTC
1 GAGCTG-AACAGTAAGCTCCAATGAGCTGAAACGATAAGCTC
39858374 TTAAGAGCTA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
45 6 0.16
46 31 0.84
ACGTcount: A:0.36, C:0.20, G:0.24, T:0.21
Consensus pattern (45 bp):
GAGCTGAACAGTAAGCTCCAATGAGCTGAAACGATAAGCTCCAAT
Found at i:39861413 original size:28 final size:27
Alignment explanation
Indices: 39861369--39861423 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 27
39861359 AACATTTGAC
*
39861369 AAGTTTAGGTACAAAATTAGATAAAAAA
1 AAGTTCAGGTACAAAATTAGA-AAAAAA
*
39861397 AAGTTCAGGTATC-AAATTGGAAAAAAA
1 AAGTTCAGGTA-CAAAATTAGAAAAAAA
39861424 TGTTAAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 6 0.25
28 17 0.71
29 1 0.04
ACGTcount: A:0.55, C:0.05, G:0.16, T:0.24
Consensus pattern (27 bp):
AAGTTCAGGTACAAAATTAGAAAAAAA
Found at i:39861445 original size:31 final size:29
Alignment explanation
Indices: 39861409--39861504 Score: 79
Period size: 29 Copynumber: 3.2 Consensus size: 29
39861399 GTTCAGGTAT
39861409 CAAATTGGAAAAAAATGTTAAATTTAAATAC
1 CAAATTGGAAAAAAA--TTAAATTTAAATAC
* * *
39861440 CAAATTGTGTAAAAAAA-T-AGTTTAGATAT
1 CAAATTG-G-AAAAAAATTAAATTTAAATAC
* *
39861469 CAAATTAGAAAAAAAAATCAAATTTAAATAC
1 CAAATT-G-GAAAAAAATTAAATTTAAATAC
39861500 CAAAT
1 CAAAT
39861505 GTTATGTTAA
Statistics
Matches: 51, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
29 21 0.41
30 2 0.04
31 20 0.39
32 1 0.02
33 7 0.14
ACGTcount: A:0.56, C:0.07, G:0.08, T:0.28
Consensus pattern (29 bp):
CAAATTGGAAAAAAATTAAATTTAAATAC
Found at i:39861474 original size:60 final size:59
Alignment explanation
Indices: 39861390--39861504 Score: 167
Period size: 60 Copynumber: 1.9 Consensus size: 59
39861380 CAAAATTAGA
* * ** *
39861390 TAAAAAAAAGTTCAGGTATCAAATTGGAAAAAAATGTTAAATTTAAATACCAAATTGTG
1 TAAAAAAAAGTTCAGATATCAAATTAGAAAAAAAAATCAAATTTAAATACCAAATTGTG
*
39861449 TAAAAAAATAGTTTAGATATCAAATTAGAAAAAAAAATCAAATTTAAATACCAAAT
1 TAAAAAAA-AGTTCAGATATCAAATTAGAAAAAAAAATCAAATTTAAATACCAAAT
39861505 GTTATGTTAA
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
59 8 0.16
60 41 0.84
ACGTcount: A:0.56, C:0.07, G:0.10, T:0.28
Consensus pattern (59 bp):
TAAAAAAAAGTTCAGATATCAAATTAGAAAAAAAAATCAAATTTAAATACCAAATTGTG
Found at i:39862019 original size:19 final size:19
Alignment explanation
Indices: 39861978--39862048 Score: 70
Period size: 19 Copynumber: 3.7 Consensus size: 19
39861968 TAATTCTTAA
*
39861978 AAAAATATATAAAAAATTAT
1 AAAAATATAT-AAAAATTTT
* *
39861998 AAAAATACATAAATATTTT
1 AAAAATATATAAAAATTTT
* * *
39862017 AAAAAAAGATAAAAAATTT
1 AAAAATATATAAAAATTTT
*
39862036 AAATATATATAAA
1 AAAAATATATAAA
39862049 TTACATTGTA
Statistics
Matches: 41, Mismatches: 10, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
19 32 0.78
20 9 0.22
ACGTcount: A:0.68, C:0.01, G:0.01, T:0.30
Consensus pattern (19 bp):
AAAAATATATAAAAATTTT
Found at i:39863080 original size:24 final size:24
Alignment explanation
Indices: 39863053--39863104 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
39863043 TTACTAAGTC
*
39863053 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
39863077 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
39863101 AAAT
1 AAAT
39863105 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:39865048 original size:24 final size:24
Alignment explanation
Indices: 39865021--39865072 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
39865011 TTAGTAAGTC
*
39865021 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
39865045 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
39865069 AAAT
1 AAAT
39865073 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:39869106 original size:25 final size:27
Alignment explanation
Indices: 39869069--39869121 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
39869059 TCAAACATGC
39869069 ATTTAGGTCAATTTAAC-CCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
* *
39869095 ATTTCGGT-AATTTATCTCCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
39869121 A
1 A
39869122 AAACTGTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.38
Consensus pattern (27 bp):
ATTTAGGTCAATTTAACTCCTAGGGGT
Found at i:39870631 original size:26 final size:25
Alignment explanation
Indices: 39870600--39870654 Score: 101
Period size: 26 Copynumber: 2.2 Consensus size: 25
39870590 TGAAATGCCC
39870600 ATCATGGAACATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAA-CCATT
39870626 ATCATGGAACATTTACCTAACCATT
1 ATCATGGAACATTTACCTAACCATT
39870651 ATCA
1 ATCA
39870655 ATTTTTATCA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
25 9 0.31
26 20 0.69
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.33
Consensus pattern (25 bp):
ATCATGGAACATTTACCTAACCATT
Found at i:39882565 original size:25 final size:27
Alignment explanation
Indices: 39882528--39882580 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
39882518 TCAAACATGC
39882528 ATTTAGGTCAATTTAAC-CCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
* *
39882554 ATTTCGGT-AATTTATCTCCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
39882580 A
1 A
39882581 AAACTATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.38
Consensus pattern (27 bp):
ATTTAGGTCAATTTAACTCCTAGGGGT
Found at i:39884090 original size:26 final size:26
Alignment explanation
Indices: 39884060--39884115 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
39884050 TGAAATGCCC
39884060 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
39884086 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
39884112 ATCA
1 ATCA
39884116 ATTTTTACCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.36, C:0.27, G:0.07, T:0.30
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:39885032 original size:2 final size:2
Alignment explanation
Indices: 39885025--39885057 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
39885015 TTTGTACCTT
39885025 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
39885058 AAGATGTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:39888554 original size:16 final size:15
Alignment explanation
Indices: 39888520--39888555 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
39888510 ATTTTTTTTT
39888520 AAAAAGTCGATTTCC
1 AAAAAGTCGATTTCC
39888535 AAAAAGTCGATTTCC
1 AAAAAGTCGATTTCC
39888550 AAAAAG
1 AAAAAG
39888556 GTTTTGACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.47, C:0.17, G:0.14, T:0.22
Consensus pattern (15 bp):
AAAAAGTCGATTTCC
Found at i:39891136 original size:36 final size:36
Alignment explanation
Indices: 39891088--39891160 Score: 112
Period size: 36 Copynumber: 2.0 Consensus size: 36
39891078 AACTTTTGTC
**
39891088 TAAATTCTAATTTAGCCCCTAAATGGAGACTAACTT
1 TAAATTCTAATTTAGCCCCTAAACCGAGACTAACTT
39891124 TAAATT-TCAATTTAGCCCCTAAACCGAGACTAACTT
1 TAAATTCT-AATTTAGCCCCTAAACCGAGACTAACTT
39891160 T
1 T
39891161 TATTCTTCAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
35 1 0.03
36 33 0.97
ACGTcount: A:0.36, C:0.22, G:0.10, T:0.33
Consensus pattern (36 bp):
TAAATTCTAATTTAGCCCCTAAACCGAGACTAACTT
Found at i:39891623 original size:20 final size:22
Alignment explanation
Indices: 39891585--39891624 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
39891575 TTTCGTTTGC
39891585 TTTGTTTCTCTTATTCATTTCT
1 TTTGTTTCTCTTATTCATTTCT
39891607 TTTGTTTC-CTT-TTCATTT
1 TTTGTTTCTCTTATTCATTT
39891625 ATTATTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 3 0.17
22 8 0.44
ACGTcount: A:0.07, C:0.17, G:0.05, T:0.70
Consensus pattern (22 bp):
TTTGTTTCTCTTATTCATTTCT
Found at i:39891801 original size:14 final size:15
Alignment explanation
Indices: 39891777--39891822 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
39891767 ATAAATATCT
39891777 TATAATATAATTATAA
1 TATAAT-TAATTATAA
39891793 TA-AATTAATT-TAA
1 TATAATTAATTATAA
*
39891806 TATAATTTATTACTAA
1 TATAATTAATTA-TAA
39891822 T
1 T
39891823 TCGTATATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
13 5 0.19
14 12 0.46
15 3 0.12
16 6 0.23
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (15 bp):
TATAATTAATTATAA
Found at i:39897261 original size:26 final size:26
Alignment explanation
Indices: 39897225--39897334 Score: 184
Period size: 26 Copynumber: 4.2 Consensus size: 26
39897215 CATGAAATTC
39897225 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
39897251 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
39897277 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
* *
39897303 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
39897329 TTATCA
1 TTATCA
39897335 ATTTGTATCA
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 82 1.00
ACGTcount: A:0.36, C:0.25, G:0.05, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:39901013 original size:27 final size:22
Alignment explanation
Indices: 39900976--39901034 Score: 84
Period size: 22 Copynumber: 2.7 Consensus size: 22
39900966 TCCCCTGTTC
* *
39900976 TTCTCTGTTTCGTTTGC-TTTGT
1 TTCTCTTTTTCATTT-CTTTTGT
39900998 TTCTCTTTTTCATTTCTTTTGT
1 TTCTCTTTTTCATTTCTTTTGT
39901020 TTCTCTTTTTCATTT
1 TTCTCTTTTTCATTT
39901035 ATTATTTATT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
21 1 0.03
22 33 0.97
ACGTcount: A:0.03, C:0.19, G:0.08, T:0.69
Consensus pattern (22 bp):
TTCTCTTTTTCATTTCTTTTGT
Found at i:39901211 original size:14 final size:15
Alignment explanation
Indices: 39901187--39901232 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
39901177 ATAAATATCT
39901187 TATAATATAATTATAA
1 TATAAT-TAATTATAA
39901203 TA-AATTAATT-TAA
1 TATAATTAATTATAA
*
39901216 TATAATTTATTACTAA
1 TATAATTAATTA-TAA
39901232 T
1 T
39901233 TCGTATATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
13 5 0.19
14 12 0.46
15 3 0.12
16 6 0.23
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (15 bp):
TATAATTAATTATAA
Found at i:39902981 original size:179 final size:179
Alignment explanation
Indices: 39902674--39903018 Score: 595
Period size: 179 Copynumber: 1.9 Consensus size: 179
39902664 AATAACCATT
* * *
39902674 TAGGTCGTCAAGTATTTTTTTAATATAAAACTCAATAGCGATTGGATTTTTACAATTTAGTCTCT
1 TAGGTCATCAAGTATTTTTCTAATATAAAACTCAATAGCAATTGGATTTTTACAATTTAGTCTCT
39902739 GAACTTTAATTAATAAATTTTTCGATTAAATTTCTGAACCAATCTTTAATATATTTTCATACTAA
66 GAACTTTAATTAATAAATTTTTCGATTAAATTTCTGAACCAATCTTTAATATATTTTCATACTAA
39902804 CTCCATAAAACCTCTTATTATAATCTCACGGACTTGATTAATTGCCAAC
131 CTCCATAAAACCTCTTATTATAATCTCACGGACTTGATTAATTGCCAAC
* *
39902853 TAGGTCATCAAGTA-TTTTCTAATATGAAACTCAATAGCAATTGGATTTTTATAATTTAGTCTCT
1 TAGGTCATCAAGTATTTTTCTAATATAAAACTCAATAGCAATTGGATTTTTACAATTTAGTCTCT
* *
39902917 GAACTTTAATTAACT-ATTTTTCTCGGTTAAATTTCTGAACCAATCTTTAATATATTTTCATACT
66 GAACTTTAATTAA-TAAATTTT-TCGATTAAATTTCTGAACCAATCTTTAATATATTTTCATACT
39902981 AACTCCATAAAACCTCTTATTATAATCTCACGGACTTG
129 AACTCCATAAAACCTCTTATTATAATCTCACGGACTTG
39903019 GTTTATAGAA
Statistics
Matches: 157, Mismatches: 7, Indels: 4
0.93 0.04 0.02
Matches are distributed among these distances:
178 64 0.41
179 93 0.59
ACGTcount: A:0.33, C:0.17, G:0.09, T:0.41
Consensus pattern (179 bp):
TAGGTCATCAAGTATTTTTCTAATATAAAACTCAATAGCAATTGGATTTTTACAATTTAGTCTCT
GAACTTTAATTAATAAATTTTTCGATTAAATTTCTGAACCAATCTTTAATATATTTTCATACTAA
CTCCATAAAACCTCTTATTATAATCTCACGGACTTGATTAATTGCCAAC
Found at i:39913205 original size:21 final size:21
Alignment explanation
Indices: 39913176--39913215 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
39913166 TTGCAACAAA
* *
39913176 CAGCTAAAATAACCCAATATT
1 CAGCAAAAAGAACCCAATATT
39913197 CAGCAAAAAGAACCCAATA
1 CAGCAAAAAGAACCCAATA
39913216 AATTTTAAAT
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:0.53, C:0.25, G:0.07, T:0.15
Consensus pattern (21 bp):
CAGCAAAAAGAACCCAATATT
Found at i:39916974 original size:69 final size:68
Alignment explanation
Indices: 39916884--39917012 Score: 163
Period size: 69 Copynumber: 1.9 Consensus size: 68
39916874 AGGTTTTATC
* * * *
39916884 GTTGTAATTGAGGTGCATAAATGTTGTTAATTG-TGATGT-TAAAGTGCTGCAAATTGAAGTATT
1 GTTGTAATTGAAGTGCATAAATGTTGTAAATTGAAG-TGTCT-AAGTACTGCAAATTGAAGTATT
39916947 AAAGT
64 AAAGT
**
39916952 GTTGTAAATTGAAGTGTTTAAATGTTGTAAATTGAAGTGTCTAAGTACTGCAAATTGAAGT
1 GTTGT-AATTGAAGTGCATAAATGTTGTAAATTGAAGTGTCTAAGTACTGCAAATTGAAGT
39917013 GTTTAGTTGC
Statistics
Matches: 52, Mismatches: 6, Indels: 5
0.83 0.10 0.08
Matches are distributed among these distances:
68 5 0.10
69 45 0.87
70 2 0.04
ACGTcount: A:0.33, C:0.05, G:0.24, T:0.38
Consensus pattern (68 bp):
GTTGTAATTGAAGTGCATAAATGTTGTAAATTGAAGTGTCTAAGTACTGCAAATTGAAGTATTAA
AGT
Found at i:39917013 original size:23 final size:22
Alignment explanation
Indices: 39916920--39917032 Score: 93
Period size: 23 Copynumber: 4.9 Consensus size: 22
39916910 TTAATTGTGA
39916920 TGTTAAAGTGCTGCAAATTGAAG
1 TGTT-AAGTGCTGCAAATTGAAG
* * *
39916943 TATTAAAGTGTTGTAAATTGAAG
1 TGTT-AAGTGCTGCAAATTGAAG
* * *
39916966 TGTTTAAATGTTGTAAATTGAAG
1 TG-TTAAGTGCTGCAAATTGAAG
*
39916989 TGTCTAAGTACTGCAAATTGAAG
1 TGT-TAAGTGCTGCAAATTGAAG
*
39917012 TGTTTAGTTGCTAG-AAATTGA
1 TGTTAAG-TGCT-GCAAATTGA
39917033 GATATTTTGT
Statistics
Matches: 75, Mismatches: 11, Indels: 8
0.80 0.12 0.09
Matches are distributed among these distances:
22 4 0.05
23 68 0.91
24 3 0.04
ACGTcount: A:0.35, C:0.05, G:0.23, T:0.37
Consensus pattern (22 bp):
TGTTAAGTGCTGCAAATTGAAG
Found at i:39920364 original size:15 final size:16
Alignment explanation
Indices: 39920330--39920366 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
39920320 ATATACTAGA
*
39920330 ATAACAGATTATTCAG
1 ATAACAGATTAGTCAG
39920346 -TAACAGATT-GTCAG
1 ATAACAGATTAGTCAG
39920360 ATAACAG
1 ATAACAG
39920367 TTTCAATGTC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
14 4 0.21
15 15 0.79
ACGTcount: A:0.43, C:0.14, G:0.16, T:0.27
Consensus pattern (16 bp):
ATAACAGATTAGTCAG
Found at i:39921747 original size:27 final size:28
Alignment explanation
Indices: 39921692--39921750 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
39921682 ATAACATTTG
*
39921692 AAAAGTTTAGGTACCAAATTAGATAAAA
1 AAAAGTTTAGGTACCAAATTAGAGAAAA
* * *
39921720 AAAAGTTTATGTATCAAATTAGGGAAAA
1 AAAAGTTTAGGTACCAAATTAGAGAAAA
39921748 AAA
1 AAA
39921751 TGTCAAGTTC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.54, C:0.05, G:0.15, T:0.25
Consensus pattern (28 bp):
AAAAGTTTAGGTACCAAATTAGAGAAAA
Found at i:39921839 original size:28 final size:26
Alignment explanation
Indices: 39921799--39921853 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 26
39921789 AAAAAGTATC
*
39921799 AAGTTCAGGTACCAAATTAGGTAAAAAA
1 AAGTTCAGATACCAAATTA-G-AAAAAA
*
39921827 AAGTTTAGATACCAAATTAGAAAAAA
1 AAGTTCAGATACCAAATTAGAAAAAA
39921853 A
1 A
39921854 TGTCAAGGCT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 7 0.28
27 1 0.04
28 17 0.68
ACGTcount: A:0.55, C:0.09, G:0.15, T:0.22
Consensus pattern (26 bp):
AAGTTCAGATACCAAATTAGAAAAAA
Found at i:39923191 original size:21 final size:22
Alignment explanation
Indices: 39923135--39923192 Score: 55
Period size: 21 Copynumber: 2.6 Consensus size: 22
39923125 TGCCTTTTAC
**
39923135 ATTAAAATATTATTTTTTAATTT
1 ATTAAAATATTATTCATT-ATTT
** *
39923158 ATTAGTATTTTATTCATT-TTT
1 ATTAAAATATTATTCATTATTT
39923179 ATTAAAATATTATT
1 ATTAAAATATTATT
39923193 TTTATATTGA
Statistics
Matches: 27, Mismatches: 8, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
21 14 0.52
23 13 0.48
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (22 bp):
ATTAAAATATTATTCATTATTT
Found at i:39924254 original size:43 final size:40
Alignment explanation
Indices: 39924171--39924258 Score: 104
Period size: 43 Copynumber: 2.1 Consensus size: 40
39924161 AAAAAAAAGT
** *
39924171 TTAGGTATTAAATTAAAAAAAATCAAGTTCATGTATCAAA
1 TTAGGTATTAAATTAAAAAAAATCAAGTTCAAATACCAAA
* *
39924211 TTAGGTATTAAATTAAGAAAAAATGTTAAGTTTAAATACCAAA
1 TTAGGTATTAAATTAA-AAAAAA--TCAAGTTCAAATACCAAA
39924254 TTAGG
1 TTAGG
39924259 GGAAAAAAGC
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
40 16 0.40
41 6 0.15
43 18 0.45
ACGTcount: A:0.49, C:0.06, G:0.12, T:0.33
Consensus pattern (40 bp):
TTAGGTATTAAATTAAAAAAAATCAAGTTCAAATACCAAA
Found at i:39926147 original size:11 final size:11
Alignment explanation
Indices: 39926131--39926155 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
39926121 TTATTTTGAA
39926131 TTTAATTTAAT
1 TTTAATTTAAT
39926142 TTTAATTTAAT
1 TTTAATTTAAT
39926153 TTT
1 TTT
39926156 TTATTTGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TTTAATTTAAT
Found at i:39926150 original size:16 final size:17
Alignment explanation
Indices: 39926123--39926154 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
39926113 TGAGAGTATT
39926123 ATTTTGAATTTAATTTA
1 ATTTTGAATTTAATTTA
39926140 ATTTT-AATTTAATTT
1 ATTTTGAATTTAATTT
39926155 TTTATTTGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (17 bp):
ATTTTGAATTTAATTTA
Found at i:39927665 original size:55 final size:53
Alignment explanation
Indices: 39927576--39927679 Score: 131
Period size: 55 Copynumber: 1.9 Consensus size: 53
39927566 AATATTATTA
*
39927576 ATAATTATTTTTAAACATTATTATTATTTTTAATACGTGCATATATATTATGTGTAT
1 ATAATTATTTTTAAACATTATTATTATTTCTAATA--TG--TATATATTATGTGTAT
* *
39927633 ATAATTGTTTTT-AATATTA-TATTATTTCTAATATGTATATATTATGT
1 ATAATTATTTTTAAACATTATTATTATTTCTAATATGTATATATTATGT
39927680 ATTTATCTCT
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
51 12 0.27
53 2 0.05
55 13 0.30
56 6 0.14
57 11 0.25
ACGTcount: A:0.35, C:0.04, G:0.07, T:0.55
Consensus pattern (53 bp):
ATAATTATTTTTAAACATTATTATTATTTCTAATATGTATATATTATGTGTAT
Found at i:39927677 original size:25 final size:24
Alignment explanation
Indices: 39927646--39927720 Score: 71
Period size: 23 Copynumber: 3.0 Consensus size: 24
39927636 ATTGTTTTTA
*
39927646 ATATTATATTATTTCTAATATGTAT
1 ATATTATATTATTTCTAATA-CTAT
*
39927671 ATATTATGTATTTATCTCTAATACTAT
1 ATATTA--TA-TTATTTCTAATACTAT
* *
39927698 ACATTGTA-TATTTCTAATACTAT
1 ATATTATATTATTTCTAATACTAT
39927721 TATGCTATTA
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
23 14 0.33
25 8 0.19
27 9 0.21
28 11 0.26
ACGTcount: A:0.35, C:0.09, G:0.04, T:0.52
Consensus pattern (24 bp):
ATATTATATTATTTCTAATACTAT
Found at i:39927746 original size:3 final size:3
Alignment explanation
Indices: 39927733--39927847 Score: 119
Period size: 3 Copynumber: 38.7 Consensus size: 3
39927723 TGCTATTACC
* *
39927733 ATT ACT ATT ATT ATT ATT ATT ATT ACTT A-T ATT ATT ATC ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT
* * * * * *
39927778 ATC ATT ATG ATTT ATT ACT -TT ATT ATT ATC ATT ATT ACT ACT ATT
1 ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
39927823 A-T ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
39927848 ATTTTTACCC
Statistics
Matches: 93, Mismatches: 14, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
2 5 0.05
3 83 0.89
4 5 0.05
ACGTcount: A:0.33, C:0.07, G:0.01, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:39927827 original size:23 final size:23
Alignment explanation
Indices: 39927793--39927850 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 23
39927783 TATGATTTAT
39927793 TACT-TTATTATTATCATTATTAC
1 TACTATTA-TATTATCATTATTAC
* *
39927816 TACTATTATATTATTATTATTAT
1 TACTATTATATTATCATTATTAC
*
39927839 TATTATTATATT
1 TACTATTATATT
39927851 TTTACCCATT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
23 28 0.90
24 3 0.10
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (23 bp):
TACTATTATATTATCATTATTAC
Found at i:39930134 original size:19 final size:19
Alignment explanation
Indices: 39930110--39930155 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
39930100 CTTCCTTTCT
*
39930110 TTTGCATT-CATTTCATGCA
1 TTTGCATTGCATTGCAT-CA
*
39930129 TTTGCATTGCATTGCATTA
1 TTTGCATTGCATTGCATCA
39930148 TTTGCATT
1 TTTGCATT
39930156 AGACTTTCCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.20, C:0.17, G:0.13, T:0.50
Consensus pattern (19 bp):
TTTGCATTGCATTGCATCA
Found at i:39932798 original size:3 final size:3
Alignment explanation
Indices: 39932792--39932834 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
39932782 CAAATCCTAA
39932792 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
39932835 TCATGGAAAG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:39934677 original size:66 final size:66
Alignment explanation
Indices: 39934557--39934688 Score: 210
Period size: 66 Copynumber: 2.0 Consensus size: 66
39934547 ATTCATATGT
* * * * *
39934557 CATTCATAACATATCTAATTAGGAGCATTTGATTCATTTCGATCATAGCCTCCTAATTATTTGAC
1 CATTCATAACACATCTAATTAGGAGCATTTGATTCATTTCAATCACAGCATCCTAATCATTTGAC
39934622 A
66 A
*
39934623 CATTCATAACACATCTAGTTAGGAGCATTTGATTCATTTCAATCACAGCATCCTAATCATTTGAC
1 CATTCATAACACATCTAATTAGGAGCATTTGATTCATTTCAATCACAGCATCCTAATCATTTGAC
39934688 A
66 A
39934689 TAAGCATAGA
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
66 60 1.00
ACGTcount: A:0.33, C:0.21, G:0.11, T:0.36
Consensus pattern (66 bp):
CATTCATAACACATCTAATTAGGAGCATTTGATTCATTTCAATCACAGCATCCTAATCATTTGAC
A
Found at i:39934929 original size:89 final size:88
Alignment explanation
Indices: 39934746--39934961 Score: 276
Period size: 89 Copynumber: 2.5 Consensus size: 88
39934736 CAGTGAATTC
* * *
39934746 ACAAGCCTTAACCCCCTAAGCAGTAGGGCAACAGGCTG-AATTGACAGATCTTAATCCTCTAAGC
1 ACAAGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTGAAATTGACAGATCTTAATCCCCTAAAC
* **
39934810 AGTAGGGAAACAGATCGAAGGTA
66 AGTAGGGAAACAGATCAAAGACA
* *
39934833 ACAAGCCTTGACCCCCTAAGCAGTAGGGTAACAGGCTGAAGATTTG-CAGATC-TCATCACCCTA
1 ACAAGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTGAA-A-TTGACAGATCTTAATC-CCCTA
*
39934896 AACAGTAGGGAAACAGATCAAAGACG
63 AACAGTAGGGAAACAGATCAAAGACA
* * *
39934922 GCGAGCCTTAACCCCCTAAGCAGTAGAGTAACAGGCTGAA
1 ACAAGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTGAA
39934962 TTACAAATCA
Statistics
Matches: 112, Mismatches: 13, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
87 36 0.32
88 5 0.04
89 68 0.61
90 3 0.03
ACGTcount: A:0.35, C:0.25, G:0.23, T:0.17
Consensus pattern (88 bp):
ACAAGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTGAAATTGACAGATCTTAATCCCCTAAAC
AGTAGGGAAACAGATCAAAGACA
Found at i:39935115 original size:45 final size:44
Alignment explanation
Indices: 39935016--39935535 Score: 232
Period size: 45 Copynumber: 11.5 Consensus size: 44
39935006 CCATAGCAGA
* * * * *
39935016 CTCCTTGAAGTTTCAGTGGAGTAGATTGAAAT-CACAAGTCTTAT
1 CTCCCTGAAGTTGCAGTGGAGCAGACT-AAATACACAAATCTTAT
*
39935060 CTCCCTGAAGTTGCAGTGGAGCAGACTAAATATAGCAAATCTTAT
1 CTCCCTGAAGTTGCAGTGGAGCAGACTAAATACA-CAAATCTTAT
* * * * * *
39935105 TTCCTTGAAGTTGCAGTGGAACAGATTGAAGCTATAAATCATAGATCTCAT
1 CTCCCTGAAGTTGCAGTGGAGCAGACT-AA---ATACA-CA-A-ATCTTAT
* * * * *
39935156 CTCTCTGAAGTTGCAGTAGAGAAGA-T-CA-ACACAAGTCTTAT
1 CTCCCTGAAGTTGCAGTGGAGCAGACTAAATACACAAATCTTAT
* * *
39935197 CTCCCTGAAGTTACAGTGGAGCAGACTAAAGATAGCAAATCTTAT
1 CTCCCTGAAGTTGCAGTGGAGCAGACTAAATACA-CAAATCTTAT
* * * * * *
39935242 TTCCCTGAAGTTGCAGTGGAACAAATTGAAGCTATAAACCATAGATCTCAT
1 CTCCCTGAAGTTGCAGTGGAGCAGACT-AA---ATACA-CA-A-ATCTTAT
* * * * * *
39935293 CTCTCTGAAGATGTAGTAGAGCAGA-T-CA-ACACAAGTCTTAT
1 CTCCCTGAAGTTGCAGTGGAGCAGACTAAATACACAAATCTTAT
* * * * * * *
39935334 CTCTCTAAAGTTGCAGTGGAGTAGACTAAAGAAAGAAAATTTTAT
1 CTCCCTGAAGTTGCAGTGGAGCAGACTAAATACA-CAAATCTTAT
* * * * * *
39935379 TTCACTGAAGTTGCAGTGGAACAGATTGAAGCTATAAACCACAGATCTCAT
1 CTCCCTGAAGTTGCAGTGGAGCAGACT-AA---AT--A-CACAAATCTTAT
* * * * *
39935430 CTCTCTGAAGATGCAGTAGAGCAGA-T-CA-ACACAAGTCTTAT
1 CTCCCTGAAGTTGCAGTGGAGCAGACTAAATACACAAATCTTAT
* * * *
39935471 CTCCCTGAAGTTGTAGTGGAGCAGACTAAAGAAAACAAGTCTTAT
1 CTCCCTGAAGTTGCAGTGGAGCAGACTAAA-TACACAAATCTTAT
* *
39935516 TTCCCTGAAGTCGCAGTGGA
1 CTCCCTGAAGTTGCAGTGGA
39935536 ACATATTGAA
Statistics
Matches: 353, Mismatches: 90, Indels: 65
0.69 0.18 0.13
Matches are distributed among these distances:
41 81 0.23
42 6 0.02
43 11 0.03
44 32 0.09
45 123 0.35
46 6 0.02
49 12 0.03
50 5 0.01
51 76 0.22
52 1 0.00
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.27
Consensus pattern (44 bp):
CTCCCTGAAGTTGCAGTGGAGCAGACTAAATACACAAATCTTAT
Found at i:39935243 original size:137 final size:137
Alignment explanation
Indices: 39935048--39935596 Score: 846
Period size: 137 Copynumber: 4.0 Consensus size: 137
39935038 AGATTGAAAT
* * *
39935048 CACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAATATAGCAAATCTTATTTCCTTGA
1 CACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGAAAGCAAATCTTATTTCCCTGA
* * * *
39935113 AGTTGCAGTGGAACAGATTGAAGCTATAAATCATAGATCTCATCTCTCTGAAGTTGCAGTAGAGA
66 AGTTGCAGTGGAACAGATTGAAGCTATAAACCACAGATCTCATCTCTCTGAAGATGCAGTAGAGC
39935178 AGATCAA
131 AGATCAA
* *
39935185 CACAAGTCTTATCTCCCTGAAGTTACAGTGGAGCAGACTAAAGATAGCAAATCTTATTTCCCTGA
1 CACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGAAAGCAAATCTTATTTCCCTGA
* * *
39935250 AGTTGCAGTGGAACAAATTGAAGCTATAAACCATAGATCTCATCTCTCTGAAGATGTAGTAGAGC
66 AGTTGCAGTGGAACAGATTGAAGCTATAAACCACAGATCTCATCTCTCTGAAGATGCAGTAGAGC
39935315 AGATCAA
131 AGATCAA
* * * * * *
39935322 CACAAGTCTTATCTCTCTAAAGTTGCAGTGGAGTAGACTAAAGAAAGAAAATTTTATTTCACTGA
1 CACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGAAAGCAAATCTTATTTCCCTGA
39935387 AGTTGCAGTGGAACAGATTGAAGCTATAAACCACAGATCTCATCTCTCTGAAGATGCAGTAGAGC
66 AGTTGCAGTGGAACAGATTGAAGCTATAAACCACAGATCTCATCTCTCTGAAGATGCAGTAGAGC
39935452 AGATCAA
131 AGATCAA
* * *
39935459 CACAAGTCTTATCTCCCTGAAGTTGTAGTGGAGCAGACTAAAGAAAACAAGTCTTATTTCCCTGA
1 CACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGAAAGCAAATCTTATTTCCCTGA
* * ** * *
39935524 AGTCGCAGTGGAACATATTGAAGCTATAAATAAACAGATCTTATCTCTCTGAAGTTGCAGTAGAG
66 AGTTGCAGTGGAACAGATTGAAGCTATAAA-CCACAGATCTCATCTCTCTGAAGATGCAGTAGAG
39935589 CAGATCAA
130 CAGATCAA
39935597 AATAAACTTT
Statistics
Matches: 377, Mismatches: 34, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
137 339 0.90
138 38 0.10
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (137 bp):
CACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGAAAGCAAATCTTATTTCCCTGA
AGTTGCAGTGGAACAGATTGAAGCTATAAACCACAGATCTCATCTCTCTGAAGATGCAGTAGAGC
AGATCAA
Found at i:39937199 original size:3 final size:3
Alignment explanation
Indices: 39937186--39937288 Score: 95
Period size: 3 Copynumber: 34.7 Consensus size: 3
39937176 TGCTATTACC
* * *
39937186 ATT ACT ATT ATT ATT ATT ATT ACTT A-T ATT ATT ATC ATT ATT ATC
1 ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT
* * * * *
39937231 ATT ATG ATTT ATT ACT -TT ATT ATT ATC ATT ATT ACT ACT ATT A-T
1 ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
39937275 ATT ATT ATT ATT AT
1 ATT ATT ATT ATT AT
39937289 ATTTTTACCC
Statistics
Matches: 81, Mismatches: 14, Indels: 10
0.77 0.13 0.10
Matches are distributed among these distances:
2 5 0.06
3 71 0.88
4 5 0.06
ACGTcount: A:0.33, C:0.08, G:0.01, T:0.58
Consensus pattern (3 bp):
ATT
Found at i:39937277 original size:23 final size:23
Alignment explanation
Indices: 39937243--39937287 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
39937233 TATGATTTAT
39937243 TACTTTATTATTATCATTATTAC
1 TACTTTATTATTATCATTATTAC
*
39937266 TACTATTA-TATTATTATTATTA
1 TACT-TTATTATTATCATTATTA
39937288 TATTTTTACC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 17 0.85
24 3 0.15
ACGTcount: A:0.33, C:0.09, G:0.00, T:0.58
Consensus pattern (23 bp):
TACTTTATTATTATCATTATTAC
Found at i:39946485 original size:125 final size:125
Alignment explanation
Indices: 39946272--39946522 Score: 475
Period size: 125 Copynumber: 2.0 Consensus size: 125
39946262 TGATTTCATG
* *
39946272 ACTGGTGGAGGTGGGAGCCTTAATCGGCTAGTGATGTTCCAGCATGATGTTGAGTTTGGGGGTTG
1 ACTGGTGGAGGTGGGAGCCTCAATCGGCTAGTGATATTCCAGCATGATGTTGAGTTTGGGGGTTG
*
39946337 TAATACCATGGGAGTATTGATAAAATTGTTGATATGATTTGTACTGATAGGGATTTTGCT
66 TAATACCATGGGAGTATTGATAAAATTATTGATATGATTTGTACTGATAGGGATTTTGCT
39946397 ACTGGTGGAGGTGGGAGCCTCAATCGGCTAGTGATATTCCAGCATGATGTTGAGTTTGGGGGTTG
1 ACTGGTGGAGGTGGGAGCCTCAATCGGCTAGTGATATTCCAGCATGATGTTGAGTTTGGGGGTTG
39946462 TAATACCATGGGAGTATTGATAAAATTATTGATATGATTTGTACTGATAGGGATTTTGCT
66 TAATACCATGGGAGTATTGATAAAATTATTGATATGATTTGTACTGATAGGGATTTTGCT
39946522 A
1 A
39946523 GTTTTAAGGT
Statistics
Matches: 123, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
125 123 1.00
ACGTcount: A:0.24, C:0.10, G:0.31, T:0.35
Consensus pattern (125 bp):
ACTGGTGGAGGTGGGAGCCTCAATCGGCTAGTGATATTCCAGCATGATGTTGAGTTTGGGGGTTG
TAATACCATGGGAGTATTGATAAAATTATTGATATGATTTGTACTGATAGGGATTTTGCT
Found at i:39951736 original size:24 final size:25
Alignment explanation
Indices: 39951677--39951741 Score: 82
Period size: 24 Copynumber: 2.7 Consensus size: 25
39951667 TATATAATAT
*
39951677 AATAATATATAATAACA-TGATGTAA
1 AATAATATATAATAA-ATTGATGAAA
39951702 AATAATA-ATAATAAATTG-TGAAA
1 AATAATATATAATAAATTGATGAAA
*
39951725 AATAAGATATAATAAAT
1 AATAATATATAATAAAT
39951742 AATAATATAT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
23 11 0.31
24 18 0.50
25 7 0.19
ACGTcount: A:0.60, C:0.02, G:0.08, T:0.31
Consensus pattern (25 bp):
AATAATATATAATAAATTGATGAAA
Found at i:39951815 original size:17 final size:17
Alignment explanation
Indices: 39951793--39951834 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
39951783 AAAGTAAGGT
39951793 AAAAAATATCA-ATATAA
1 AAAAAATAT-ATATATAA
*
39951810 AAAAAATATATATATAC
1 AAAAAATATATATATAA
39951827 AAAAAATA
1 AAAAAATA
39951835 AACATAGGGC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 1 0.04
17 22 0.96
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (17 bp):
AAAAAATATATATATAA
Found at i:39953855 original size:205 final size:206
Alignment explanation
Indices: 39953409--39954610 Score: 1517
Period size: 205 Copynumber: 5.8 Consensus size: 206
39953399 CTACTTCTTT
* * * *
39953409 GATTTGTTCTCTGACAATACAGAGATGACAAATCGTCTTAGATTTGCTTCATCATAAGTACGTGA
1 GATTTGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATTTGCTTCATCGTAAGCACGTGA
* *
39953474 AAGCCAAATCAGCTATGTCTTTGACTTGTTCCTTGTAAGCACAAGGATGCCAAATCATCTTGGAT
66 AAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAATCATCTTGGAT
* * * *
39953539 CTTGCTTCAGTCTAATCGTCTGAAGGTCAGATCTGCTATGTATCTGCTCTCCATTGAAGTGGAGA
131 CTTGCTTCAGTCTAAACATCTGAAGGTCAGATCTGCTATGTGTCTGCTCTCCATCGAAGTGGAGA
* *
39953604 TGCCAGATTTT
196 TGCCAGACTTC
* * *
39953615 GATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGTTTCAAT-GTAAGCACGTG
1 GATTTGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATTTGCTTC-ATCGTAAGCACGTG
* * * * *
39953679 AAAGCCAAATCAGCTATGTCTTCGATTTGCTCATTGTAAGCGCAAGGATGCCATACCATCTTGGA
65 AAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAATCATCTTGGA
* * * ** * * **
39953744 TC-TACTTCAGTATAAACATCCGAAGGTTGGATCTGCTATGTGTCTGCCCACTGTCGAAGTGGAG
130 TCTTGCTTCAGTCTAAACATCTGAAGGTCAGATCTGCTATGTGTCTGCTCTCCATCGAAGTGGAG
39953808 ATGCCAGACTTC
195 ATGCCAGACTTC
* * *
39953820 -AGTTTGTTCTCTGATAATACAGAGATGCCAAATCATCTTAGATTTGCTTCATCGTAAGCACGTG
1 GA-TTTGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATTTGCTTCATCGTAAGCACGTG
* * * *
39953884 AAAACCAAATCAGCTATGTCTTTGACTTGTTCCTTGTAAGCACAAGGATGCCAAATCATCTTGGT
65 AAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAATCATCTTGGA
* * * * *
39953949 TCTTGCTTCAGTCTAATCGTCTGAAGGTCAGATCTACTATGTATCTGCTCTCCATTGAAGTGGAG
130 TCTTGCTTCAGTCTAAACATCTGAAGGTCAGATCTGCTATGTGTCTGCTCTCCATCGAAGTGGAG
* *
39954014 ATGCCAGATTTT
195 ATGCCAGACTTC
* * * *
39954026 AATTTGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATTTGTTTCAACGTAAACACGTGA
1 GATTTGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATTTGCTTCATCGTAAGCACGTGA
* * * *
39954091 AAGCCAAATCAGCTATGTCTTCTATTTGTTCCTTGTAAACACAAGGATACCAAACCATCTTGGAT
66 AAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAATCATCTTGGAT
* * * * * *
39954156 C-CGCTTCAG-CATAAACATCCGAAGG-CGAGATCTGCTATATGTCTGTTCTCTATCAAAGTGGA
131 CTTGCTTCAGTC-TAAACATCTGAAGGTC-AGATCTGCTATGTGTCTGCTCTCCATCGAAGTGGA
39954218 GATGCCAGACTTC
194 GATGCCAGACTTC
* * *
39954231 GATTTGTTCTCTAACAATACAGAGACGACAAATCATCTTAGATTTGCTTCATCGTAAACACGTGG
1 GATTTGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATTTGCTTCATCGTAAGCACGTGA
* * * ** * * **
39954296 AAGCCAAATCAGCTATATCTTCGATCTGCTCCCCGCTGAA-TACAGAGAGATAAGATC-TGTCAT
66 AAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTG-T-AAGCACA-AG-GAT--G-CCAAATCAT
* * *
39954359 CTAGGATC-TGCTTCAG-CGTAAACATCTGAAGGTGAGATCTGCTATGTGTCTGC-CTTCCATCA
124 CTTGGATCTTGCTTCAGTC-TAAACATCTGAAGGTCAGATCTGCTATGTGTCTGCTC-TCCATCG
*
39954421 AAGTGGAAATGCCAGACTTC
187 AAGTGGAGATGCCAGACTTC
39954441 GATTTGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATTTGCTTCATCGTAAGCACGTGA
1 GATTTGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATTTGCTTCATCGTAAGCACGTGA
* *
39954506 AAGCCAAATCAGCTATGTCTTTGATTTGTTCCTTGTAAGCCCAAGGATGCCAAATCATCTTGGAT
66 AAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAATCATCTTGGAT
* *
39954571 CTTGCTTCAGTCTAATCGTCTGAAGGTCAGATCTGCTATG
131 CTTGCTTCAGTCTAAACATCTGAAGGTCAGATCTGCTATG
39954611 CTGCGGCCTA
Statistics
Matches: 851, Mismatches: 125, Indels: 40
0.84 0.12 0.04
Matches are distributed among these distances:
204 6 0.01
205 332 0.39
206 326 0.38
207 11 0.01
208 7 0.01
209 4 0.00
210 164 0.19
211 1 0.00
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.31
Consensus pattern (206 bp):
GATTTGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATTTGCTTCATCGTAAGCACGTGA
AAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAATCATCTTGGAT
CTTGCTTCAGTCTAAACATCTGAAGGTCAGATCTGCTATGTGTCTGCTCTCCATCGAAGTGGAGA
TGCCAGACTTC
Found at i:39954173 original size:411 final size:411
Alignment explanation
Indices: 39953409--39954580 Score: 1642
Period size: 411 Copynumber: 2.8 Consensus size: 411
39953399 CTACTTCTTT
* * *
39953409 GATTTGTTCTCTGACAATACAGAGATGACAAATCGTCTTAGATTTGCTTCATCATAAGTACGTGA
1 GATTTGTTCTCTGACAATACAGAGATGACAAATCATCTTAGATTTGCTTCATCGTAAGCACGTGA
39953474 AAGCCAAATCAGCTATGTCTTTGACTTGTTCCTTGTAAGCACAAGGATGCCAAATCATCTTGGAT
66 AAGCCAAATCAGCTATGTCTTTGACTTGTTCCTTGTAAGCACAAGGATGCCAAATCATCTTGGAT
39953539 CTTGCTTCAGTCTAATCGTCTGAAGGTCAGATCTGCTATGTATCTGCTCTCCATTGAAGTGGAGA
131 CTTGCTTCAGTCTAATCGTCTGAAGGTCAGATCTGCTATGTATCTGCTCTCCATTGAAGTGGAGA
* * *
39953604 TGCCAGATTTTGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGTTTCAATG
196 TGCCAGATTTTGATTTGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATTTGTTTCAACG
* * * * *
39953669 TAAGCACGTGAAAGCCAAATCAGCTATGTCTTCGATTTGCTCATTGTAAGCGCAAGGATGCCATA
261 TAAGCACGTGAAAGCCAAATCAGCTATGTCTTCTATTTGTTCCTTGTAAGCACAAGGATGCCAAA
* * * * *
39953734 CCATCTTGGATCTACTTCAGTATAAACATCCGAAGGTTG-GATCTGCTATGTGTCTGCCCACTGT
326 CCATCTTGGATCTGCTTCAGCATAAACATCCGAAGG-CGAGATCTGCTATATGTCTGCCCACTAT
*
39953798 CGAAGTGGAGATGCCAGACTTC
390 CAAAGTGGAGATGCCAGACTTC
* *
39953820 -AGTTTGTTCTCTGATAATACAGAGATGCCAAATCATCTTAGATTTGCTTCATCGTAAGCACGTG
1 GA-TTTGTTCTCTGACAATACAGAGATGACAAATCATCTTAGATTTGCTTCATCGTAAGCACGTG
* *
39953884 AAAACCAAATCAGCTATGTCTTTGACTTGTTCCTTGTAAGCACAAGGATGCCAAATCATCTTGGT
65 AAAGCCAAATCAGCTATGTCTTTGACTTGTTCCTTGTAAGCACAAGGATGCCAAATCATCTTGGA
*
39953949 TCTTGCTTCAGTCTAATCGTCTGAAGGTCAGATCTACTATGTATCTGCTCTCCATTGAAGTGGAG
130 TCTTGCTTCAGTCTAATCGTCTGAAGGTCAGATCTGCTATGTATCTGCTCTCCATTGAAGTGGAG
*
39954014 ATGCCAGATTTTAATTTGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATTTGTTTCAAC
195 ATGCCAGATTTTGATTTGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATTTGTTTCAAC
* * *
39954079 GTAAACACGTGAAAGCCAAATCAGCTATGTCTTCTATTTGTTCCTTGTAAACACAAGGATACCAA
260 GTAAGCACGTGAAAGCCAAATCAGCTATGTCTTCTATTTGTTCCTTGTAAGCACAAGGATGCCAA
* ** *
39954144 ACCATCTTGGATCCGCTTCAGCATAAACATCCGAAGGCGAGATCTGCTATATGTCTGTTCTCTAT
325 ACCATCTTGGATCTGCTTCAGCATAAACATCCGAAGGCGAGATCTGCTATATGTCTGCCCACTAT
39954209 CAAAGTGGAGATGCCAGACTTC
390 CAAAGTGGAGATGCCAGACTTC
* * * *
39954231 GATTTGTTCTCTAACAATACAGAGACGACAAATCATCTTAGATTTGCTTCATCGTAAACACGTGG
1 GATTTGTTCTCTGACAATACAGAGATGACAAATCATCTTAGATTTGCTTCATCGTAAGCACGTGA
* * * ** * * **
39954296 AAGCCAAATCAGCTATATCTTCGA-TCTGCTCCCCGCTGAA-TACAGAGAGATAAGATC-TGTCA
66 AAGCCAAATCAGCTATGTCTTTGACT-TGTTCCTTG-T-AAGCACA-AG-GAT--G-CCAAATCA
* * * * * *
39954358 TCTAGGATC-TGCTTCAG-CGTAAACATCTGAAGGTGAGATCTGCTATGTGTCTGC-CTTCCATC
123 TCTTGGATCTTGCTTCAGTC-TAATCGTCTGAAGGTCAGATCTGCTATGTATCTGCTC-TCCATT
* * * *
39954420 AAAGTGGAAATGCCAGACTTCGATTTGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATT
186 GAAGTGGAGATGCCAGATTTTGATTTGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATT
* * *
39954485 TGCTTCATCGTAAGCACGTGAAAGCCAAATCAGCTATGTCTT-TGATTTGTTCCTTGTAAGCCCA
251 TGTTTCAACGTAAGCACGTGAAAGCCAAATCAGCTATGTCTTCT-ATTTGTTCCTTGTAAGCACA
*
39954549 AGGATGCCAAATCATCTTGGATCTTGCTTCAG
315 AGGATGCCAAACCATCTTGGATC-TGCTTCAG
39954581 TCTAATCGTC
Statistics
Matches: 679, Mismatches: 67, Indels: 25
0.88 0.09 0.03
Matches are distributed among these distances:
410 3 0.00
411 461 0.68
412 5 0.01
413 4 0.01
414 6 0.01
415 181 0.27
416 18 0.03
417 1 0.00
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.31
Consensus pattern (411 bp):
GATTTGTTCTCTGACAATACAGAGATGACAAATCATCTTAGATTTGCTTCATCGTAAGCACGTGA
AAGCCAAATCAGCTATGTCTTTGACTTGTTCCTTGTAAGCACAAGGATGCCAAATCATCTTGGAT
CTTGCTTCAGTCTAATCGTCTGAAGGTCAGATCTGCTATGTATCTGCTCTCCATTGAAGTGGAGA
TGCCAGATTTTGATTTGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATTTGTTTCAACG
TAAGCACGTGAAAGCCAAATCAGCTATGTCTTCTATTTGTTCCTTGTAAGCACAAGGATGCCAAA
CCATCTTGGATCTGCTTCAGCATAAACATCCGAAGGCGAGATCTGCTATATGTCTGCCCACTATC
AAAGTGGAGATGCCAGACTTC
Found at i:39957993 original size:28 final size:28
Alignment explanation
Indices: 39957953--39958008 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
39957943 TTGTCTGAGT
39957953 CAACTTCAATTCCTTTTTCACTTACTAC
1 CAACTTCAATTCCTTTTTCACTTACTAC
*
39957981 CAACTTCAATTCCTTTTTCGCTTACTAC
1 CAACTTCAATTCCTTTTTCACTTACTAC
39958009 GAAGCCTAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.23, C:0.32, G:0.02, T:0.43
Consensus pattern (28 bp):
CAACTTCAATTCCTTTTTCACTTACTAC
Found at i:39962676 original size:15 final size:15
Alignment explanation
Indices: 39962634--39962683 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
39962624 ATAACTTTGA
*
39962634 ATGCAAATG-ATGTG
1 ATGCAAATGCATGAG
39962648 ATG-AAATGCTATGAG
1 ATGCAAATGC-ATGAG
39962663 ATGCAAATGCATGA-
1 ATGCAAATGCATGAG
39962677 ATGCAAA
1 ATGCAAA
39962684 AAGAATATCG
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
13 5 0.16
14 10 0.31
15 11 0.34
16 6 0.19
ACGTcount: A:0.42, C:0.10, G:0.24, T:0.24
Consensus pattern (15 bp):
ATGCAAATGCATGAG
Found at i:39963331 original size:13 final size:13
Alignment explanation
Indices: 39963299--39963323 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39963289 GATACTTGTG
39963299 CCCTTTTGTAATA
1 CCCTTTTGTAATA
39963312 CCCTTTTGTAAT
1 CCCTTTTGTAAT
39963324 GCTCTTTTAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.24, G:0.08, T:0.48
Consensus pattern (13 bp):
CCCTTTTGTAATA
Found at i:39966736 original size:19 final size:19
Alignment explanation
Indices: 39966708--39966746 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
39966698 ATATACATAA
39966708 AAAATAAAAA-ATATAGAAT
1 AAAATAAAAATATATA-AAT
*
39966727 AAAATGAAAATATATAAAT
1 AAAATAAAAATATATAAAT
39966746 A
1 A
39966747 TTATAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (19 bp):
AAAATAAAAATATATAAAT
Found at i:39966926 original size:24 final size:24
Alignment explanation
Indices: 39966835--39966949 Score: 95
Period size: 24 Copynumber: 5.0 Consensus size: 24
39966825 GTAAAAACAA
39966835 TATATATAAATAAT-TA-AATAAAT
1 TATATA-AAATAATATATAATAAAT
*
39966858 ATATAATATAATAATATATAATAAAAT
1 -TAT-ATAAAATAATATATAAT-AAAT
39966885 TATATAAAATAATA-ATAATAAAT
1 TATATAAAATAATATATAATAAAT
* *
39966908 TGTGA-AAAATAAGATATAATAAA-
1 TAT-ATAAAATAATATATAATAAAT
39966931 TA-AT--AAT-ATATATAATAAA
1 TATATAAAATAATATATAATAAA
39966950 ATGATCTTAT
Statistics
Matches: 78, Mismatches: 6, Indels: 19
0.76 0.06 0.18
Matches are distributed among these distances:
19 11 0.14
20 3 0.04
21 1 0.01
23 15 0.19
24 23 0.29
25 15 0.19
26 6 0.08
27 4 0.05
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.35
Consensus pattern (24 bp):
TATATAAAATAATATATAATAAAT
Found at i:39967002 original size:15 final size:15
Alignment explanation
Indices: 39966982--39967019 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
39966972 AAAAGTAAGG
39966982 TAAAAAATATCA-ATA
1 TAAAAAATAT-ATATA
39966997 TAAAAAATATATATA
1 TAAAAAATATATATA
39967012 TACAAAAA
1 TA-AAAAA
39967020 ATAAACATAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 1 0.05
15 15 0.71
16 5 0.24
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.26
Consensus pattern (15 bp):
TAAAAAATATATATA
Found at i:39968523 original size:12 final size:12
Alignment explanation
Indices: 39968506--39968533 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
39968496 TGTTCTTTTT
39968506 CTTTTTCAATGA
1 CTTTTTCAATGA
39968518 CTTTTTCAATGA
1 CTTTTTCAATGA
39968530 CTTT
1 CTTT
39968534 CTTGATCTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.21, C:0.18, G:0.07, T:0.54
Consensus pattern (12 bp):
CTTTTTCAATGA
Found at i:39969219 original size:11 final size:11
Alignment explanation
Indices: 39969203--39969252 Score: 55
Period size: 11 Copynumber: 4.3 Consensus size: 11
39969193 CATACTCATA
39969203 TTTTTTTGAAT
1 TTTTTTTGAAT
* *
39969214 TTTTTTCGTAT
1 TTTTTTTGAAT
39969225 TTTTTTTGAAACTT
1 TTTTTTTG-AA--T
39969239 TTTTTTTGAAT
1 TTTTTTTGAAT
39969250 TTT
1 TTT
39969253 ACTTGAGTCA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
11 20 0.62
12 1 0.03
13 2 0.06
14 9 0.28
ACGTcount: A:0.16, C:0.04, G:0.08, T:0.72
Consensus pattern (11 bp):
TTTTTTTGAAT
Found at i:39979778 original size:22 final size:20
Alignment explanation
Indices: 39979738--39979786 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
39979728 CAATTTAAAA
39979738 TATAAAAATTTATTAATATG
1 TATAAAAATTTATTAATATG
* *
39979758 TATATAAATTTATTAATATA
1 TATAAAAATTTATTAATATG
*
39979778 TGTAAAAAT
1 TATAAAAAT
39979787 AACTTTTACG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (20 bp):
TATAAAAATTTATTAATATG
Found at i:39979899 original size:20 final size:20
Alignment explanation
Indices: 39979874--39979913 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
39979864 AAATATTTTC
39979874 AGTAAATCATTTTTCAGAAA
1 AGTAAATCATTTTTCAGAAA
39979894 AGTAAATCATTTTTCAGAAA
1 AGTAAATCATTTTTCAGAAA
39979914 TCATTTTCCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.45, C:0.10, G:0.10, T:0.35
Consensus pattern (20 bp):
AGTAAATCATTTTTCAGAAA
Found at i:39986987 original size:20 final size:20
Alignment explanation
Indices: 39986954--39986992 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
39986944 TGTATCGCCA
* *
39986954 ATTATATTTTTTATGATTAC
1 ATTATATATATTATGATTAC
*
39986974 ATTATATATATTATTATTA
1 ATTATATATATTATGATTA
39986993 TTAAATCATA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.59
Consensus pattern (20 bp):
ATTATATATATTATGATTAC
Found at i:39987503 original size:16 final size:17
Alignment explanation
Indices: 39987482--39987515 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
39987472 ATTTTTTTTG
*
39987482 CTTTATAT-GTATTATT
1 CTTTATATCGTAGTATT
39987498 CTTTATATCGTAGTATT
1 CTTTATATCGTAGTATT
39987515 C
1 C
39987516 ATTTTTTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.24, C:0.12, G:0.09, T:0.56
Consensus pattern (17 bp):
CTTTATATCGTAGTATT
Found at i:39991481 original size:128 final size:128
Alignment explanation
Indices: 39991310--39991609 Score: 388
Period size: 128 Copynumber: 2.3 Consensus size: 128
39991300 CATGAAAAAC
* * * * * * * * *
39991310 CGAAACCCAACACAGTAGGGCACGATTCCTCGAATTTCTAAACATTGAAC-TTGCCTTGTTTTAG
1 CGAAACCCAGCACGGTAGGGCACGATTCCTCAAATCTCCAAACATCGAACATTACCTTGTTGTAA
* *
39991374 AATTTAAAAAAAACACGAGTGAAGTTCTAAAGGAATATTTGATTATTTTGAACAAA-AGGACAAT
66 AATTT-AAAAAAACACGAGTGAAATTCTAAAGGAATATTCGATTATTTTGAACAAACAGGA-AAT
*
39991438 CGAAACCCAGTACGGTAGGGCACGATTCCTCAAATCTCCAAACATCGAACATTACCTTGTTGTAA
1 CGAAACCCAGCACGGTAGGGCACGATTCCTCAAATCTCCAAACATCGAACATTACCTTGTTGTAA
* * *
39991503 AATTTAGAAAAACATGAGTGAAATTCTAAAGGAATATTCGATTATTTTGAACAAACGGGAAAT
66 AATTTAAAAAAACACGAGTGAAATTCTAAAGGAATATTCGATTATTTTGAACAAACAGGAAAT
* * * * *
39991566 AGAAACCCAGCACGATAGGGCACTATTCCCCTAATCTCCAAACA
1 CGAAACCCAGCACGGTAGGGCACGATTCCTCAAATCTCCAAACA
39991610 CCAAATATTG
Statistics
Matches: 149, Mismatches: 21, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
128 130 0.87
129 19 0.13
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.25
Consensus pattern (128 bp):
CGAAACCCAGCACGGTAGGGCACGATTCCTCAAATCTCCAAACATCGAACATTACCTTGTTGTAA
AATTTAAAAAAACACGAGTGAAATTCTAAAGGAATATTCGATTATTTTGAACAAACAGGAAAT
Found at i:39996487 original size:26 final size:26
Alignment explanation
Indices: 39996451--39996504 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
39996441 ACAGTTTTCG
39996451 TAAAATCAACCTATTCCCATAATTCT
1 TAAAATCAACCTATTCCCATAATTCT
39996477 TAAAATCAACCTATTCCCATAATTCT
1 TAAAATCAACCTATTCCCATAATTCT
39996503 TA
1 TA
39996505 CAAAAAAGGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.39, C:0.26, G:0.00, T:0.35
Consensus pattern (26 bp):
TAAAATCAACCTATTCCCATAATTCT
Found at i:39996940 original size:13 final size:15
Alignment explanation
Indices: 39996911--39996945 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
39996901 CGTAAGAACA
39996911 ATTTTCAAGCTATAT
1 ATTTTCAAGCTATAT
39996926 ATTTTC-AGCATATAT
1 ATTTTCAAGC-TATAT
39996941 ATTTT
1 ATTTT
39996946 TTTTGCTCAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 3 0.16
15 16 0.84
ACGTcount: A:0.31, C:0.11, G:0.06, T:0.51
Consensus pattern (15 bp):
ATTTTCAAGCTATAT
Found at i:39999852 original size:19 final size:19
Alignment explanation
Indices: 39999828--39999865 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
39999818 AAAATTACGT
39999828 ATTTAAAATATAA-ATATAA
1 ATTTAAAA-ATAATATATAA
39999847 ATTTAAAAATAATATATAA
1 ATTTAAAAATAATATATAA
39999866 TAAATAACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
ATTTAAAAATAATATATAA
Done.