Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr2
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: 41236440
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2030548 characters in sequence are not A, C, G, or T
File 106 of 106
Found at i:41140891 original size:24 final size:24
Alignment explanation
Indices: 41140859--41140908 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
41140849 AGCGCCAGCA
*
41140859 CCAACACCAACTCTAACTCCAACT
1 CCAACACCAACTCCAACTCCAACT
* *
41140883 CCAACACCAATTCCAATTCCAACT
1 CCAACACCAACTCCAACTCCAACT
41140907 CC
1 CC
41140909 GAATCCTCCA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.36, C:0.46, G:0.00, T:0.18
Consensus pattern (24 bp):
CCAACACCAACTCCAACTCCAACT
Found at i:41141048 original size:15 final size:15
Alignment explanation
Indices: 41141030--41141077 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
41141020 TCCTCTTCCT
41141030 CCTCCTCTTCCACCA
1 CCTCCTCTTCCACCA
**
41141045 CCTCCTGCAGCC-CCA
1 CCTCCT-CTTCCACCA
*
41141060 CCTCCTATTCCACCA
1 CCTCCTCTTCCACCA
41141075 CCT
1 CCT
41141078 GTTCCAAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
14 2 0.08
15 21 0.81
16 3 0.12
ACGTcount: A:0.15, C:0.58, G:0.04, T:0.23
Consensus pattern (15 bp):
CCTCCTCTTCCACCA
Found at i:41141244 original size:49 final size:49
Alignment explanation
Indices: 41141188--41141287 Score: 200
Period size: 49 Copynumber: 2.0 Consensus size: 49
41141178 TGCCACTTAC
41141188 CCCTCCTCCAACTCCAAAGCCCCCACCATGGCCTGAACCACCACCACCA
1 CCCTCCTCCAACTCCAAAGCCCCCACCATGGCCTGAACCACCACCACCA
41141237 CCCTCCTCCAACTCCAAAGCCCCCACCATGGCCTGAACCACCACCACCA
1 CCCTCCTCCAACTCCAAAGCCCCCACCATGGCCTGAACCACCACCACCA
41141286 CC
1 CC
41141288 ACCACCACCT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 51 1.00
ACGTcount: A:0.26, C:0.56, G:0.08, T:0.10
Consensus pattern (49 bp):
CCCTCCTCCAACTCCAAAGCCCCCACCATGGCCTGAACCACCACCACCA
Found at i:41142651 original size:2 final size:2
Alignment explanation
Indices: 41142644--41142685 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
41142634 AGTGGNACTA
41142644 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
41142686 ATATATATAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:41142690 original size:2 final size:2
Alignment explanation
Indices: 41142685--41142717 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
41142675 TCTCTCTCTC
*
41142685 TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
41142718 CAGTTTTTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:41143115 original size:526 final size:525
Alignment explanation
Indices: 41142168--41143166 Score: 1989
Period size: 526 Copynumber: 1.9 Consensus size: 525
41142158 AAAAAAATAA
41142168 ATATATATATATATACATATATATCAGTTTTTTGTTGATTCTCTTTGGGAAGAAATTTAGCCATG
1 ATATATATATATATACATATATATCAGTTTTTTGTTGATTCTCTTTGGGAAGAAATTTAGCCATG
41142233 CACGCATGCGTGTAGGTGGAAATGCATTGCAAGCAATATCCAGTGATTAAGTATAAGGAGGCCTT
66 CACGCATGCGTGTAGGTGGAAATGCATTGCAAGCAATATCCAGTGATTAAGTATAAGGAGGCCTT
41142298 GCCCATTCAGATATGTCCAAGTGCCAGCTAGTCAACTCCGCCAACATTTAAAAACTACCAGCATT
131 GCCCATTCAGATATGTCCAAGTGCCAGCTAGTCAACTCCGCCAACATTTAAAAACTACCAGCATT
41142363 TATGCAGTCGTACCTAGAATTTAGGTTTTCGCACTGCAAGTGAGTGCACATTGGAATTCAGAACC
196 TATGCAGTCGTACCTAGAATTTAGGTTTTCGCACTGCAAGTGAGTGCACATTGGAATTCAGAACC
41142428 ATTTTTTTCCAATTTAATTAGTTGATGCAGAGGATGGTGATTGATAATGTGGTGACTTTATCAAA
261 ATTTTTTTCCAATTTAATTAGTTGATGCAGAGGATGGTGATTGATAATGTGGTGACTTTATCAAA
41142493 GTTATCAAAATCATACCCGACAATGACTTATTCAAGATTTCGAGTTAATAGTTCAACAATATTTT
326 GTTATCAAAATCATACCCGACAATGACTTATTCAAGATTTCGAGTTAATAGTTCAACAATATTTT
41142558 GATCATTCAATTTAATTAACATTGAAATAATAAAAAATATTTTAAATGTTTGACTCGTGAAAGCA
391 GATCATTCAATTTAATTAACATTGAAATAATAAAAAATATTTTAAATGTTTGACTCGTGAAAGCA
41142623 ATATTTAACTCAGTGGNACTACTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTAT
456 ATATTTAACTCAGTGG-ACTACTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTAT
41142688 ATATAT
520 ATATAT
41142694 ATATATATATATATACATATATATCAGTTTTTTGTTGATTCTCTTTGGGAAGAAATTTAGCCATG
1 ATATATATATATATACATATATATCAGTTTTTTGTTGATTCTCTTTGGGAAGAAATTTAGCCATG
41142759 CACGCATGCGTGTAGGTGGAAATGCATTGCAAGCAATATCCAGTGATTAAGTATAAGGAGGCCTT
66 CACGCATGCGTGTAGGTGGAAATGCATTGCAAGCAATATCCAGTGATTAAGTATAAGGAGGCCTT
41142824 GCCCATTCAGATATGTCCAAGTGCCAGCTAGTCAACTCCGCCAACATTTAAAAACTACCAGCATT
131 GCCCATTCAGATATGTCCAAGTGCCAGCTAGTCAACTCCGCCAACATTTAAAAACTACCAGCATT
41142889 TATGCAGTCGTACCTAGAATTTAGGTTTTCGCACTGCAAGTGAGTGCACATTGGAATTCAGAACC
196 TATGCAGTCGTACCTAGAATTTAGGTTTTCGCACTGCAAGTGAGTGCACATTGGAATTCAGAACC
41142954 ATTTTTTTCCAATTTAATTAGTTGATGCAGAGGATGGTGATTGATAATGTGGTGACTTTATCAAA
261 ATTTTTTTCCAATTTAATTAGTTGATGCAGAGGATGGTGATTGATAATGTGGTGACTTTATCAAA
41143019 GTTATCAAAATCATACCCGACAATGACTTATTCAAGATTTCGAGTTAATAGTTCAACAATATTTT
326 GTTATCAAAATCATACCCGACAATGACTTATTCAAGATTTCGAGTTAATAGTTCAACAATATTTT
41143084 GATCATTCAATTTAATTAACATTGAAATAATAAAAAATATTTTAAATGTTTGACTCGTGAAAGCA
391 GATCATTCAATTTAATTAACATTGAAATAATAAAAAATATTTTAAATGTTTGACTCGTGAAAGCA
41143149 ATATTTAACTCAGTGGAC
456 ATATTTAACTCAGTGGAC
41143167 CGAATAATAT
Statistics
Matches: 473, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
525 2 0.00
526 471 1.00
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.34
Consensus pattern (525 bp):
ATATATATATATATACATATATATCAGTTTTTTGTTGATTCTCTTTGGGAAGAAATTTAGCCATG
CACGCATGCGTGTAGGTGGAAATGCATTGCAAGCAATATCCAGTGATTAAGTATAAGGAGGCCTT
GCCCATTCAGATATGTCCAAGTGCCAGCTAGTCAACTCCGCCAACATTTAAAAACTACCAGCATT
TATGCAGTCGTACCTAGAATTTAGGTTTTCGCACTGCAAGTGAGTGCACATTGGAATTCAGAACC
ATTTTTTTCCAATTTAATTAGTTGATGCAGAGGATGGTGATTGATAATGTGGTGACTTTATCAAA
GTTATCAAAATCATACCCGACAATGACTTATTCAAGATTTCGAGTTAATAGTTCAACAATATTTT
GATCATTCAATTTAATTAACATTGAAATAATAAAAAATATTTTAAATGTTTGACTCGTGAAAGCA
ATATTTAACTCAGTGGACTACTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTATA
TATAT
Found at i:41143793 original size:5 final size:5
Alignment explanation
Indices: 41143783--41143807 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
41143773 ACCGTTAACG
41143783 ATACA ATACA ATACA ATACA ATACA
1 ATACA ATACA ATACA ATACA ATACA
41143808 GTCTACAGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.20, G:0.00, T:0.20
Consensus pattern (5 bp):
ATACA
Found at i:41151875 original size:15 final size:16
Alignment explanation
Indices: 41151857--41151891 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
41151847 TCGTTCGGAT
*
41151857 TTTTTTCC-TATTAAG
1 TTTTTTCCTTATAAAG
41151872 TTTTTTCCTTATAAAG
1 TTTTTTCCTTATAAAG
41151888 TTTT
1 TTTT
41151892 AACGAAACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.20, C:0.11, G:0.06, T:0.63
Consensus pattern (16 bp):
TTTTTTCCTTATAAAG
Found at i:41152176 original size:23 final size:23
Alignment explanation
Indices: 41152150--41152195 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
41152140 TCTTTCTTTC
41152150 CTTTAATTGTTT-TTTCAAGTTAT
1 CTTT-ATTGTTTCTTTCAAGTTAT
* *
41152173 CTTTATTTTTTCTTTTAAGTTAT
1 CTTTATTGTTTCTTTCAAGTTAT
41152196 ATTCTCATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.20, C:0.09, G:0.07, T:0.65
Consensus pattern (23 bp):
CTTTATTGTTTCTTTCAAGTTAT
Found at i:41152704 original size:15 final size:15
Alignment explanation
Indices: 41152674--41152713 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 15
41152664 CTAATTACAG
*
41152674 TAAAACTTTTATAAAT
1 TAAAA-TTTGATAAAT
41152690 TAAAATTTGATAAAT
1 TAAAATTTGATAAAT
41152705 TAATAATTT
1 TAA-AATTT
41152714 TGATTAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 12 0.55
16 10 0.45
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (15 bp):
TAAAATTTGATAAAT
Found at i:41152729 original size:16 final size:17
Alignment explanation
Indices: 41152680--41152732 Score: 60
Period size: 17 Copynumber: 3.3 Consensus size: 17
41152670 ACAGTAAAAC
41152680 TTTT-ATAAATTAA-AA
1 TTTTGATAAATTAATAA
41152695 -TTTGATAAATTAATAA
1 TTTTGATAAATTAATAA
*
41152711 TTTTGATTAAA-TAATAT
1 TTTTGA-TAAATTAATAA
41152728 TTTTG
1 TTTTG
41152733 CTCAGTCCCA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
14 3 0.09
15 9 0.27
16 2 0.06
17 15 0.45
18 4 0.12
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (17 bp):
TTTTGATAAATTAATAA
Found at i:41158451 original size:2 final size:2
Alignment explanation
Indices: 41158444--41158475 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
41158434 TAATAACATG
41158444 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
41158476 CAANNNNNNN
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:41158519 original size:2 final size:2
Alignment explanation
Indices: 41158512--41158543 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
41158502 NNNNNNNNNN
41158512 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
41158544 ACAAATAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:41183442 original size:236 final size:236
Alignment explanation
Indices: 41183018--41183464 Score: 598
Period size: 236 Copynumber: 1.9 Consensus size: 236
41183008 ATTCTTGCCA
*
41183018 CAGATTCCTAAAACAAGAGTATGCTTTAGATTTATTAAATTAAAAAATTTTAATATTGTGGGTAG
1 CAGATTCCTAAAACAAGAGTATGCTTCAGATTTATTAAATTAAAAAATTTTAATATTGTGGGTAG
* * * * * * * * * *
41183083 TTCGGCTGTTTCTGAAGAAAGTGAAGAACAACTTGTAGGCTTTAAAGAGGGGATCCAAACAGTTA
66 TGCGGCTGTTTCTGAAGAAAATGAAGAAAAAATTGCAGGCATAAAACAGGGAATCCAAACAGTGA
* * * *
41183148 AATTTCTATTCAAAAAGTTCCCTTAACATGCAATGGTCAATTCATGCTAGACTATGACACTAATA
131 AATTTCGATTCAAAAAGTTCCCTTAACATGCAATGGTCAATTCATACCAGAATATGACACTAATA
41183213 AGTCTAAAGAGCATCAAGTAACAGTTTTCGAATTGTTGTTG
196 AGTCTAAAGAGCATCAAGTAACAGTTTTCGAATTGTTGTTG
* * *
41183254 CAGATTCTTAGAACAAGAGTATGCTTCAGATTTCTTAAATT-AAAAATTTTAATATTGTTGGGTA
1 CAGATTCCTAAAACAAGAGTATGCTTCAGATTTATTAAATTAAAAAATTTTAATATTG-TGGGTA
* * *
41183318 GTGGGGTTGTTTCTGAAGAAAATGAAGAAAAAATTGCAGGCATAAAATCA-GGAAT-GAAATC-G
65 GTGCGGCTGTTTCTGAAGAAAATGAAGAAAAAATTGCAGGCATAAAA-CAGGGAATCCAAA-CAG
* *
41183380 TGAAATTTCGATTCAAAGAG-TCTCTTAACATGCAATGGTCAATTCAAATACCAGAATATGACAC
128 TGAAATTTCGATTCAAAAAGTTCCCTTAACATGCAATGGTCAATTC--ATACCAGAATATGACAC
*
41183444 TAATAAGTGTAAAGAGCATCA
191 TAATAAGTCTAAAGAGCATCA
41183465 TGTCCGAGTT
Statistics
Matches: 182, Mismatches: 24, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
234 24 0.13
235 37 0.20
236 120 0.66
237 1 0.01
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.31
Consensus pattern (236 bp):
CAGATTCCTAAAACAAGAGTATGCTTCAGATTTATTAAATTAAAAAATTTTAATATTGTGGGTAG
TGCGGCTGTTTCTGAAGAAAATGAAGAAAAAATTGCAGGCATAAAACAGGGAATCCAAACAGTGA
AATTTCGATTCAAAAAGTTCCCTTAACATGCAATGGTCAATTCATACCAGAATATGACACTAATA
AGTCTAAAGAGCATCAAGTAACAGTTTTCGAATTGTTGTTG
Found at i:41206766 original size:2 final size:2
Alignment explanation
Indices: 41206761--41206846 Score: 124
Period size: 2 Copynumber: 43.0 Consensus size: 2
41206751 ATACACACAC
41206761 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
41206802 AT NAT GA- AT AT AT AT AT AT AT GA- 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
41206843 AT AT
1 AT AT
41206847 GTCGGAGACT
Statistics
Matches: 78, Mismatches: 1, Indels: 10
0.88 0.01 0.11
Matches are distributed among these distances:
1 3 0.04
2 71 0.91
3 4 0.05
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:41209930 original size:11 final size:11
Alignment explanation
Indices: 41209882--41209951 Score: 60
Period size: 10 Copynumber: 6.6 Consensus size: 11
41209872 CTTGAGAAAA
41209882 CTTAAAAAA-C
1 CTTAAAAAATC
*
41209892 CTT-AAAATTC
1 CTTAAAAAATC
41209902 CTTAAAAAGA-C
1 CTTAAAAA-ATC
*
41209913 CCT-AAAAATC
1 CTTAAAAAATC
41209923 CTT-AAAAATGC
1 CTTAAAAAAT-C
41209934 CTTAAAAAATC
1 CTTAAAAAATC
*
41209945 TTTAAAA
1 CTTAAAA
41209952 TCGGCAATAG
Statistics
Matches: 49, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
9 5 0.10
10 20 0.41
11 18 0.37
12 6 0.12
ACGTcount: A:0.51, C:0.19, G:0.03, T:0.27
Consensus pattern (11 bp):
CTTAAAAAATC
Found at i:41209939 original size:21 final size:20
Alignment explanation
Indices: 41209882--41209951 Score: 77
Period size: 21 Copynumber: 3.4 Consensus size: 20
41209872 CTTGAGAAAA
* *
41209882 CTTAAAAAACCTTAAAATTC
1 CTTAAAAAGCCTTAAAAATC
*
41209902 CTTAAAAAGACCCTAAAAATC
1 CTTAAAAAG-CCTTAAAAATC
41209923 CTTAAAAATGCCTTAAAAAATC
1 CTTAAAAA-GCCTT-AAAAATC
*
41209945 TTTAAAA
1 CTTAAAA
41209952 TCGGCAATAG
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
20 8 0.19
21 20 0.48
22 14 0.33
ACGTcount: A:0.51, C:0.19, G:0.03, T:0.27
Consensus pattern (20 bp):
CTTAAAAAGCCTTAAAAATC
Found at i:41209991 original size:11 final size:10
Alignment explanation
Indices: 41209975--41210076 Score: 71
Period size: 10 Copynumber: 9.9 Consensus size: 10
41209965 ATTAAGAAAA
41209975 TTAAAAATCTC
1 TTAAAAATC-C
*
41209986 TTAAAAA-CA
1 TTAAAAATCC
*
41209995 TAAAAAATCC
1 TTAAAAATCC
* *
41210005 TTCAAATTCC
1 TTAAAAATCC
41210015 TTGAAAAATCTC
1 TT-AAAAATC-C
* *
41210027 TAAAAAAACC
1 TTAAAAATCC
* *
41210037 TTAAATAGCC
1 TTAAAAATCC
*
41210047 TTAAAAGTACC
1 TTAAAAAT-CC
*
41210058 TTAAAAATGC
1 TTAAAAATCC
41210068 TTAAAAATC
1 TTAAAAATC
41210077 TATAAAAAAA
Statistics
Matches: 68, Mismatches: 19, Indels: 9
0.71 0.20 0.09
Matches are distributed among these distances:
9 6 0.09
10 33 0.49
11 27 0.40
12 2 0.03
ACGTcount: A:0.50, C:0.18, G:0.04, T:0.28
Consensus pattern (10 bp):
TTAAAAATCC
Found at i:41210285 original size:22 final size:21
Alignment explanation
Indices: 41210256--41210339 Score: 65
Period size: 21 Copynumber: 4.2 Consensus size: 21
41210246 AAAGGATTCT
41210256 AAAA-ATCCTTTAAAAAACCTA
1 AAAATATCC-TTAAAAAACCTA
*
41210277 AAAATATCCTTAAAAATCCTA
1 AAAATATCCTTAAAAAACCTA
41210298 ATAAATAAT--TTAAAAAA--TA
1 A-AAAT-ATCCTTAAAAAACCTA
* *
41210317 AAAATCT-CTT-AAAAACATA
1 AAAATATCCTTAAAAAACCTA
41210336 AAAA
1 AAAA
41210340 ATACTTCAAA
Statistics
Matches: 54, Mismatches: 3, Indels: 14
0.76 0.04 0.20
Matches are distributed among these distances:
17 6 0.11
18 6 0.11
19 9 0.17
21 23 0.43
22 8 0.15
23 2 0.04
ACGTcount: A:0.61, C:0.13, G:0.00, T:0.26
Consensus pattern (21 bp):
AAAATATCCTTAAAAAACCTA
Found at i:41210289 original size:21 final size:20
Alignment explanation
Indices: 41210265--41210331 Score: 68
Period size: 21 Copynumber: 3.4 Consensus size: 20
41210255 TAAAAATCCT
41210265 TTAAAAAACCTAAAAATATCC
1 TTAAAAAACCTAAAAATAT-C
*
41210286 TTAAAAATCCTAATAAATAAT-
1 TTAAAAAACCTAA-AAAT-ATC
*
41210307 TTAAAAAA--TAAAAATCTC
1 TTAAAAAACCTAAAAATATC
41210325 TTAAAAA
1 TTAAAAA
41210332 CATAAAAAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
17 1 0.03
18 11 0.28
19 3 0.08
21 19 0.47
22 4 0.10
23 2 0.05
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (20 bp):
TTAAAAAACCTAAAAATATC
Found at i:41210295 original size:10 final size:10
Alignment explanation
Indices: 41210255--41210530 Score: 85
Period size: 10 Copynumber: 27.1 Consensus size: 10
41210245 AAAAGGATTC
41210255 TAAAAATCCTT
1 TAAAAATCC-T
*
41210266 TAAAAAACCT
1 TAAAAATCCT
*
41210276 AAAAATATCCT
1 TAAAA-ATCCT
41210287 TAAAAATCCT
1 TAAAAATCCT
41210297 AATAAATAAT--T
1 --TAAA-AATCCT
*
41210308 TAAAAA---A
1 TAAAAATCCT
41210315 TAAAAATCTCT
1 TAAAAATC-CT
*
41210326 TAAAAA-CAT
1 TAAAAATCCT
* *
41210335 AAAAAATACT
1 TAAAAATCCT
** *
41210345 TCAAATTTCTT
1 T-AAAAATCCT
41210356 TAAAAAT-CT
1 TAAAAATCCT
41210365 CTAAAAATCCT
1 -TAAAAATCCT
**
41210376 TAACTATCCT
1 TAAAAATCCT
*
41210386 GAAAAAGAT-CT
1 -TAAAA-ATCCT
*
41210397 TAAAAATACT
1 TAAAAATCCT
*
41210407 TCAAAAT-CT
1 TAAAAATCCT
41210416 ATAAAAAAT-CT
1 -T-AAAAATCCT
* *
41210427 TTAAAATGCT
1 TAAAAATCCT
*
41210437 TCAAAAGAT-TT
1 T-AAAA-ATCCT
*
41210448 TAAAAATCTTT
1 TAAAAATC-CT
*
41210459 TAAAAATAACT
1 TAAAAAT-CCT
41210470 TACAAAA-CCT
1 TA-AAAATCCT
41210480 TAAAAAT-C-
1 TAAAAATCCT
* *
41210488 TATAAATTTCT
1 TA-AAAATCCT
41210499 TAAAAATCCT
1 TAAAAATCCT
*
41210509 TTAAAATACCT
1 TAAAAAT-CCT
41210520 TAAAAATCCT
1 TAAAAATCCT
41210530 T
1 T
41210531 TGAAATCTAT
Statistics
Matches: 199, Mismatches: 37, Indels: 59
0.67 0.13 0.20
Matches are distributed among these distances:
7 6 0.03
8 4 0.02
9 31 0.16
10 73 0.37
11 70 0.35
12 12 0.06
13 3 0.02
ACGTcount: A:0.51, C:0.15, G:0.01, T:0.32
Consensus pattern (10 bp):
TAAAAATCCT
Found at i:41210521 original size:21 final size:20
Alignment explanation
Indices: 41210476--41210536 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 20
41210466 AACTTACAAA
*
41210476 ACCTTAAAAAT-CTATAAAT
1 ACCTTAAAAATCCTTTAAAT
**
41210495 TTCTTAAAAATCCTTTAAAAT
1 ACCTTAAAAATCCTTT-AAAT
41210516 ACCTTAAAAATCCTTTGAAAT
1 ACCTTAAAAATCCTTT-AAAT
41210537 CTATAAACAA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
19 9 0.26
20 3 0.09
21 22 0.65
ACGTcount: A:0.46, C:0.16, G:0.02, T:0.36
Consensus pattern (20 bp):
ACCTTAAAAATCCTTTAAAT
Found at i:41210541 original size:50 final size:51
Alignment explanation
Indices: 41210447--41210543 Score: 135
Period size: 50 Copynumber: 1.9 Consensus size: 51
41210437 TCAAAAGATT
*
41210447 TTAAAAATCTTTTAAAAATAACTTACAAAACCTTAAAAATCTATAAATTTC
1 TTAAAAATCCTTTAAAAATAACTTACAAAACCTTAAAAATCTATAAATTTC
* **
41210498 TTAAAAATCCTTT-AAAATACCTTA-AAAATCCTTTGAAATCTATAAA
1 TTAAAAATCCTTTAAAAATAACTTACAAAA-CCTTAAAAATCTATAAA
41210544 CAAAACTTAA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
49 4 0.10
50 25 0.61
51 12 0.29
ACGTcount: A:0.49, C:0.14, G:0.01, T:0.35
Consensus pattern (51 bp):
TTAAAAATCCTTTAAAAATAACTTACAAAACCTTAAAAATCTATAAATTTC
Found at i:41210724 original size:21 final size:19
Alignment explanation
Indices: 41210673--41210847 Score: 59
Period size: 21 Copynumber: 8.4 Consensus size: 19
41210663 AATTTATTGC
41210673 AAAATCTCTAAAAAACCTTA
1 AAAATCT-TAAAAAACCTTA
41210693 AATATAT-TTAAAAAGACCTTA
1 AA-A-ATCTTAAAAA-ACCTTA
41210714 AAAATGCTT--AAAACTCTAGTGA
1 AAAAT-CTTAAAAAAC-CT--T-A
* * *
41210736 AAAAGCTTTAAAAATCCCTA
1 AAAATC-TTAAAAAACCTTA
* * * *
41210756 AAAAGACTTTACAAATCTTTTA
1 AAAA-TC-TTAAAAAAC-CTTA
*
41210778 AAAATGACTTAAAAACCCTTA
1 AAAAT--CTTAAAAAACCTTA
* ** *
41210799 AAAATCAATAAAATCCCTTG
1 AAAATC-TTAAAAAACCTTA
41210819 AAAATCTTAGAAAACACCTTA
1 AAAATCTTA-AAAA-ACCTTA
41210840 AAAATCTT
1 AAAATCTT
41210848 TTGAAATTCA
Statistics
Matches: 118, Mismatches: 18, Indels: 37
0.68 0.10 0.21
Matches are distributed among these distances:
18 2 0.02
19 10 0.08
20 33 0.28
21 45 0.38
22 22 0.19
23 2 0.02
24 4 0.03
ACGTcount: A:0.50, C:0.17, G:0.05, T:0.28
Consensus pattern (19 bp):
AAAATCTTAAAAAACCTTA
Found at i:41210810 original size:20 final size:19
Alignment explanation
Indices: 41210787--41210845 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 19
41210777 AAAAATGACT
41210787 TAAAAACCCTTAAAAATCAA
1 TAAAAACCCTTAAAAATC-A
* * *
41210807 TAAAATCCCTTGAAAATCT
1 TAAAAACCCTTAAAAATCA
41210826 TAGAAAACACCTTAAAAATC
1 TA-AAAAC-CCTTAAAAATC
41210846 TTTTGAAATT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
19 2 0.06
20 20 0.62
21 10 0.31
ACGTcount: A:0.53, C:0.20, G:0.03, T:0.24
Consensus pattern (19 bp):
TAAAAACCCTTAAAAATCA
Found at i:41211035 original size:21 final size:20
Alignment explanation
Indices: 41211002--41211048 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
41210992 GAAAAATCTC
* *
41211002 TAAAAAACCTTAA-ATATCCT
1 TAAAAAACATTAACA-ATACT
41211022 TAAAAAGACATTAACAATACT
1 TAAAAA-ACATTAACAATACT
41211043 TAAAAA
1 TAAAAA
41211049 TCTATGAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 6 0.26
21 16 0.70
22 1 0.04
ACGTcount: A:0.57, C:0.15, G:0.02, T:0.26
Consensus pattern (20 bp):
TAAAAAACATTAACAATACT
Found at i:41211079 original size:21 final size:21
Alignment explanation
Indices: 41211040--41211101 Score: 54
Period size: 21 Copynumber: 2.9 Consensus size: 21
41211030 CATTAACAAT
*
41211040 ACTTAAAAATCTATGAAAAA-A
1 ACTTAAAAATTTAT-AAAAAGA
* *
41211061 CCTTAAAAATTTCTAAAAAGA
1 ACTTAAAAATTTATAAAAAGA
* *
41211082 ATTTAAAAATATTTTAAAAA
1 ACTTAAAAAT-TTATAAAAA
41211102 TGACTTATAA
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
20 5 0.15
21 20 0.61
22 8 0.24
ACGTcount: A:0.58, C:0.08, G:0.03, T:0.31
Consensus pattern (21 bp):
ACTTAAAAATTTATAAAAAGA
Found at i:41211390 original size:10 final size:10
Alignment explanation
Indices: 41211377--41211496 Score: 59
Period size: 10 Copynumber: 11.6 Consensus size: 10
41211367 ATTCATGAAA
41211377 AAAAATCCTT
1 AAAAATCCTT
*
41211387 AAAAATTCTTT
1 AAAAA-TCCTT
*
41211398 AAAAGA-CATT
1 AAAA-ATCCTT
**
41211408 AAAAATATTTT
1 AAAAAT-CCTT
* *
41211419 AAAAGTAACTT
1 AAAAAT-CCTT
41211430 ACAAAA-CCTT
1 A-AAAATCCTT
*
41211440 AAAAATCCAT
1 AAAAATCCTT
41211450 -AAAATCCCTT
1 AAAAAT-CCTT
*
41211460 GAAAATCCTT
1 AAAAATCCTT
41211470 GAAAACA-CCTT
1 -AAAA-ATCCTT
*
41211481 AAAAATCCTC
1 AAAAATCCTT
41211491 AAAAAT
1 AAAAAT
41211497 ACATGAAAAA
Statistics
Matches: 86, Mismatches: 13, Indels: 22
0.71 0.11 0.18
Matches are distributed among these distances:
9 11 0.13
10 39 0.45
11 31 0.36
12 5 0.06
ACGTcount: A:0.52, C:0.17, G:0.03, T:0.28
Consensus pattern (10 bp):
AAAAATCCTT
Found at i:41211412 original size:34 final size:33
Alignment explanation
Indices: 41211342--41211412 Score: 79
Period size: 34 Copynumber: 2.1 Consensus size: 33
41211332 AAATATCGTT
* **
41211342 AAAAAAACCTTGAAAATACTTAAAAATTCATGA
1 AAAAAAACCTTAAAAATACTTAAAAAGACATGA
* * *
41211375 AAAAAAATCCTTAAAAATTCTTTAAAAGACATTA
1 AAAAAAA-CCTTAAAAATACTTAAAAAGACATGA
41211409 AAAA
1 AAAA
41211413 TATTTTAAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
33 7 0.23
34 24 0.77
ACGTcount: A:0.59, C:0.11, G:0.04, T:0.25
Consensus pattern (33 bp):
AAAAAAACCTTAAAAATACTTAAAAAGACATGA
Found at i:41211474 original size:21 final size:20
Alignment explanation
Indices: 41211435--41211494 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
41211425 AACTTACAAA
*
41211435 ACCTTAAAAATCCATAAAATC
1 ACCTTAAAAATCCTTAAAA-C
*
41211456 -CCTTGAAAATCCTTGAAAAC
1 ACCTTAAAAATCCTT-AAAAC
*
41211476 ACCTTAAAAATCCTCAAAA
1 ACCTTAAAAATCCTTAAAA
41211495 ATACATGAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
20 17 0.52
21 16 0.48
ACGTcount: A:0.48, C:0.25, G:0.03, T:0.23
Consensus pattern (20 bp):
ACCTTAAAAATCCTTAAAAC
Found at i:41211677 original size:20 final size:20
Alignment explanation
Indices: 41211603--41211677 Score: 62
Period size: 21 Copynumber: 3.7 Consensus size: 20
41211593 TAATAAATAA
41211603 TTAAAAAA-ATTAAAAATCT
1 TTAAAAAACATTAAAAATCT
*
41211622 CTTAAAAAACATAAAAAATCAT
1 -TTAAAAAACATTAAAAATC-T
* *** *
41211644 TCAAATTCCTTTAAAAATCT
1 TTAAAAAACATTAAAAATCT
*
41211664 TTAAAAAACCTTAA
1 TTAAAAAACATTAA
41211678 TTATCCTTAA
Statistics
Matches: 41, Mismatches: 12, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
20 18 0.44
21 22 0.54
22 1 0.02
ACGTcount: A:0.56, C:0.13, G:0.00, T:0.31
Consensus pattern (20 bp):
TTAAAAAACATTAAAAATCT
Found at i:41211776 original size:9 final size:10
Alignment explanation
Indices: 41211759--41211785 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
41211749 TAAAAGTCTT
41211759 TTAAAAAAAC
1 TTAAAAAAAC
41211769 TTAAAAAAAC
1 TTAAAAAAAC
41211779 TTAAAAA
1 TTAAAAA
41211786 TCAAAAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.70, C:0.07, G:0.00, T:0.22
Consensus pattern (10 bp):
TTAAAAAAAC
Found at i:41211980 original size:20 final size:19
Alignment explanation
Indices: 41211917--41211982 Score: 62
Period size: 19 Copynumber: 3.4 Consensus size: 19
41211907 GTAAAAGCCT
* *
41211917 TAAAAAATTCTTAAAATTCG
1 TAAAAAATTCTTAAAA-ACA
* *
41211937 TAATAAATTATTAAAAA-A
1 TAAAAAATTCTTAAAAACA
*
41211955 TTAAAAATTTCTTAAAAACA
1 -TAAAAAATTCTTAAAAACA
41211975 TAAAAAAT
1 TAAAAAAT
41211983 AATTCAAATT
Statistics
Matches: 36, Mismatches: 8, Indels: 5
0.73 0.16 0.10
Matches are distributed among these distances:
19 21 0.58
20 15 0.42
ACGTcount: A:0.59, C:0.06, G:0.02, T:0.33
Consensus pattern (19 bp):
TAAAAAATTCTTAAAAACA
Found at i:41212129 original size:21 final size:21
Alignment explanation
Indices: 41212037--41212129 Score: 77
Period size: 22 Copynumber: 4.4 Consensus size: 21
41212027 TGAAAGGACT
41212037 TTAAAAATG-CTTAAAAAT-C
1 TTAAAAATGACTTAAAAATCC
*
41212056 TATAAAAA-AACCCTTAAAAATCC
1 T-TAAAAATGA--CTTAAAAATCC
* *
41212079 TTAAAAA-GACTTTAAAAGTCTT
1 TTAAAAATGAC-TTAAAAATC-C
*
41212101 TTAAAAATGACTTAAAAAACC
1 TTAAAAATGACTTAAAAATCC
41212122 TTAAAAAT
1 TTAAAAAT
41212130 CAATAAAAGC
Statistics
Matches: 59, Mismatches: 7, Indels: 14
0.74 0.09 0.17
Matches are distributed among these distances:
19 1 0.02
20 7 0.12
21 16 0.27
22 30 0.51
23 5 0.08
ACGTcount: A:0.54, C:0.13, G:0.04, T:0.29
Consensus pattern (21 bp):
TTAAAAATGACTTAAAAATCC
Found at i:41212136 original size:20 final size:20
Alignment explanation
Indices: 41212113--41212168 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
41212103 AAAAATGACT
41212113 TAAAAAACCTTAAAAATCAA
1 TAAAAAACCTTAAAAATCAA
** * **
41212133 TAAAAGCCCTTGAAAATCTT
1 TAAAAAACCTTAAAAATCAA
41212153 TAAAAATACCTTAAAA
1 TAAAAA-ACCTTAAAA
41212169 CTCTTTTGAA
Statistics
Matches: 27, Mismatches: 8, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
20 20 0.74
21 7 0.26
ACGTcount: A:0.55, C:0.16, G:0.04, T:0.25
Consensus pattern (20 bp):
TAAAAAACCTTAAAAATCAA
Found at i:41212167 original size:73 final size:75
Alignment explanation
Indices: 41212037--41212201 Score: 192
Period size: 73 Copynumber: 2.2 Consensus size: 75
41212027 TGAAAGGACT
** * *
41212037 TTAAAAATGCTTAAAAATCTATAAAAAAACCCTTAAAAATCCTTAAAAAGACTTTAAAAGTCTTT
1 TTAAAAAACCTTAAAAATCTATAAAAAAACCCTTAAAAATCCTTAAAAAGACCTTAAAACTCTTT
*
41212102 TAAAAAT-GAC
66 T-AAAATCAAC
* * * * *
41212112 TTAAAAAACCTTAAAAATC-A-ATAAAAGCCCTTGAAAATCTTTAAAAATACCTTAAAACTCTTT
1 TTAAAAAACCTTAAAAATCTATAAAAAAACCCTTAAAAATCCTTAAAAAGACCTTAAAACTCTTT
*
41212175 TGAAATCAAC
66 TAAAATCAAC
*
41212185 TTAAAAACCCTTAAAAA
1 TTAAAAAACCTTAAAAA
41212202 GGCTTAGAAT
Statistics
Matches: 77, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
72 4 0.05
73 55 0.71
74 1 0.01
75 17 0.22
ACGTcount: A:0.52, C:0.16, G:0.04, T:0.28
Consensus pattern (75 bp):
TTAAAAAACCTTAAAAATCTATAAAAAAACCCTTAAAAATCCTTAAAAAGACCTTAAAACTCTTT
TAAAATCAAC
Found at i:41212427 original size:22 final size:21
Alignment explanation
Indices: 41212394--41212452 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
41212384 AAAAATGTTA
* *
41212394 AAAAAACCTTAAAAA-GATTTT
1 AAAAAACTTTAAAAATGA-CTT
*
41212415 AAAAATCTTTTAAAAATGACTT
1 AAAAAAC-TTTAAAAATGACTT
41212437 AAAAAACTTTAAAAAT
1 AAAAAACTTTAAAAAT
41212453 CCATAAAATC
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
21 15 0.47
22 15 0.47
23 2 0.06
ACGTcount: A:0.58, C:0.08, G:0.03, T:0.31
Consensus pattern (21 bp):
AAAAAACTTTAAAAATGACTT
Found at i:41212732 original size:46 final size:45
Alignment explanation
Indices: 41212655--41212743 Score: 106
Period size: 46 Copynumber: 2.0 Consensus size: 45
41212645 AAATTTCATG
* * *
41212655 AAAAATCTATAAAAAACCTGAAATATCCTTCAAAGGGCCTTAATT
1 AAAAATCAATAAAAAACCTGAAAAATCCTTCAAAAGGCCTTAATT
* * * *
41212700 AAAAATCAATGAAAAAACTTTAAAAATGCTTCAAAAGGCTTTAA
1 AAAAATCAAT-AAAAAACCTGAAAAATCCTTCAAAAGGCCTTAA
41212744 AATTCTTTTA
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
45 9 0.25
46 27 0.75
ACGTcount: A:0.51, C:0.15, G:0.09, T:0.26
Consensus pattern (45 bp):
AAAAATCAATAAAAAACCTGAAAAATCCTTCAAAAGGCCTTAATT
Found at i:41212899 original size:21 final size:22
Alignment explanation
Indices: 41212856--41212906 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
41212846 TAGAATGACT
*
41212856 TTAAATATCCTTAAAAAAACCC
1 TTAAAAATCCTTAAAAAAACCC
* **
41212878 -TAAAAATCCTTATAAATGCCC
1 TTAAAAATCCTTAAAAAAACCC
41212899 TTAAAAAT
1 TTAAAAAT
41212907 TTTTAAAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 17 0.71
22 7 0.29
ACGTcount: A:0.49, C:0.20, G:0.02, T:0.29
Consensus pattern (22 bp):
TTAAAAATCCTTAAAAAAACCC
Found at i:41213150 original size:10 final size:10
Alignment explanation
Indices: 41213127--41213156 Score: 51
Period size: 11 Copynumber: 2.9 Consensus size: 10
41213117 AACTCCCTCG
41213127 AAAATCCTTA
1 AAAATCCTTA
41213137 AAAATACCTTA
1 AAAAT-CCTTA
41213148 AAAATCCTT
1 AAAATCCTT
41213157 TGAAATTCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.50, C:0.20, G:0.00, T:0.30
Consensus pattern (10 bp):
AAAATCCTTA
Found at i:41213201 original size:21 final size:21
Alignment explanation
Indices: 41213177--41213226 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
41213167 GAAAAAAACA
* * * *
41213177 TAAAAATGCTTAGAATGACCT
1 TAAAAATCCTTAAAAAGACCC
*
41213198 TAAACATCCTTAAAAAGACCC
1 TAAAAATCCTTAAAAAGACCC
41213219 TAAAAATC
1 TAAAAATC
41213227 TTTACAAATG
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.48, C:0.20, G:0.08, T:0.24
Consensus pattern (21 bp):
TAAAAATCCTTAAAAAGACCC
Found at i:41213457 original size:21 final size:22
Alignment explanation
Indices: 41213433--41213478 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
41213423 AAAAATCCAT
* *
41213433 AAAATCTCTTGAAATTCC-TTG
1 AAAATATCTTGAAAATCCTTTG
*
41213454 AAAATATCTTTAAAATCCTTTG
1 AAAATATCTTGAAAATCCTTTG
41213476 AAA
1 AAA
41213479 TTCATGAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.41, C:0.15, G:0.07, T:0.37
Consensus pattern (22 bp):
AAAATATCTTGAAAATCCTTTG
Found at i:41213495 original size:32 final size:32
Alignment explanation
Indices: 41213423--41213501 Score: 81
Period size: 32 Copynumber: 2.5 Consensus size: 32
41213413 AAAAAACTTT
** *
41213423 AAAAATCCATAAAATCTCTTGAAATTCCTTGA
1 AAAAATCTTTAAAATCTCTTGAAATTCCATGA
*
41213455 AAATATCTTTAAAATC-CTTTGAAATT-CATGAA
1 AAAAATCTTTAAAATCTC-TTGAAATTCCATG-A
*
41213487 AAAAATCTTAAAAAT
1 AAAAATCTTTAAAAT
41213502 GCTTAGAATG
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
31 4 0.10
32 35 0.90
ACGTcount: A:0.48, C:0.14, G:0.05, T:0.33
Consensus pattern (32 bp):
AAAAATCTTTAAAATCTCTTGAAATTCCATGA
Found at i:41213661 original size:21 final size:20
Alignment explanation
Indices: 41213637--41213696 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 20
41213627 CTTTCAAATT
41213637 CCTTGAAAAATCTTTAAAA-AA
1 CCTT-AAAAATC-TTAAAAGAA
*
41213658 CCTTAAATATCCTTAAAAGAA
1 CCTTAAAAAT-CTTAAAAGAA
41213679 CCTTAAAAATGCTTAAAA
1 CCTTAAAAAT-CTTAAAA
41213697 CTCTATAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
20 11 0.32
21 23 0.68
ACGTcount: A:0.50, C:0.17, G:0.05, T:0.28
Consensus pattern (20 bp):
CCTTAAAAATCTTAAAAGAA
Found at i:41214175 original size:31 final size:32
Alignment explanation
Indices: 41214123--41214182 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 32
41214113 AGTCGCTTAA
*
41214123 AAATCCATGAAAACACCTTAAAAA-ACTTTTG
1 AAATCCATGAAAAAACCTTAAAAATACTTTTG
**
41214154 AAATCCATGAAAAAATGTTAAAAATACTT
1 AAATCCATGAAAAAACCTTAAAAATACTT
41214183 AGAATGACCT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 21 0.84
32 4 0.16
ACGTcount: A:0.52, C:0.15, G:0.07, T:0.27
Consensus pattern (32 bp):
AAATCCATGAAAAAACCTTAAAAATACTTTTG
Found at i:41214195 original size:21 final size:21
Alignment explanation
Indices: 41214171--41214246 Score: 66
Period size: 21 Copynumber: 3.6 Consensus size: 21
41214161 TGAAAAAATG
41214171 TTAAAAATACTTAGAATGACC
1 TTAAAAATACTTAGAATGACC
* * *
41214192 TTAAACATCCTTAGAAAGATCC
1 TTAAAAATACTTAGAATGA-CC
* *
41214214 -TAAAAATTCTTAAAAATG-CC
1 TTAAAAATACTT-AGAATGACC
*
41214234 ATAAAAATACTTA
1 TTAAAAATACTTA
41214247 AAATTCGTAA
Statistics
Matches: 44, Mismatches: 8, Indels: 7
0.75 0.14 0.12
Matches are distributed among these distances:
20 3 0.07
21 35 0.80
22 6 0.14
ACGTcount: A:0.49, C:0.16, G:0.07, T:0.29
Consensus pattern (21 bp):
TTAAAAATACTTAGAATGACC
Found at i:41214334 original size:20 final size:19
Alignment explanation
Indices: 41214189--41214348 Score: 61
Period size: 20 Copynumber: 8.0 Consensus size: 19
41214179 ACTTAGAATG
*
41214189 ACCTTAAACATCCTTAGAAA
1 ACCTTAAAAATCCTTA-AAA
*
41214209 GATCC-TAAAAATTCTTAAAA
1 -A-CCTTAAAAATCCTTAAAA
* *
41214229 ATGCCATAAAAATACTTAAAA
1 A--CCTTAAAAATCCTTAAAA
** * **
41214250 TTCGTAATAAATAATTAAAA
1 ACCTTAA-AAATCCTTAAAA
** * *
41214270 AAATTAAAAATATCTTGAAA
1 ACCTTAAAAAT-CCTTAAAA
* * *
41214290 ACATTAAAAATTCTTCAAAT
1 ACCTTAAAAATCCTT-AAAA
* *
41214310 TCCTTGAAAAATCTTTAAAA
1 ACCTT-AAAAATCCTTAAAA
*
41214330 ACCTTAAATATCCTTAAAA
1 ACCTTAAAAATCCTTAAAA
41214349 GGATCTGAAA
Statistics
Matches: 106, Mismatches: 26, Indels: 16
0.72 0.18 0.11
Matches are distributed among these distances:
19 25 0.24
20 46 0.43
21 33 0.31
22 2 0.02
ACGTcount: A:0.51, C:0.14, G:0.04, T:0.31
Consensus pattern (19 bp):
ACCTTAAAAATCCTTAAAA
Found at i:41214805 original size:32 final size:33
Alignment explanation
Indices: 41214769--41214846 Score: 94
Period size: 32 Copynumber: 2.5 Consensus size: 33
41214759 AAAAATCCAT
*
41214769 AAAATCTCTTGAAAATCCTTG-AAAGCAA-CTTA
1 AAAATCTCTTGAAAATCCATGAAAAG-AACCTTA
*
41214801 AAAATCTTTTG-AAATCCATGAAAAGAACCTTA
1 AAAATCTCTTGAAAATCCATGAAAAGAACCTTA
41214833 AAAAT-TCTT-AAAAT
1 AAAATCTCTTGAAAAT
41214847 GACCTTAAAC
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
31 17 0.43
32 23 0.57
ACGTcount: A:0.47, C:0.15, G:0.08, T:0.29
Consensus pattern (33 bp):
AAAATCTCTTGAAAATCCATGAAAAGAACCTTA
Found at i:41214845 original size:21 final size:21
Alignment explanation
Indices: 41214821--41214901 Score: 76
Period size: 21 Copynumber: 3.8 Consensus size: 21
41214811 GAAATCCATG
41214821 AAAAGAACCTTAAAAATTCTT
1 AAAAGAACCTTAAAAATTCTT
* *
41214842 AAAATG-ACCTTAAACATGCTT
1 AAAA-GAACCTTAAAAATTCTT
* *
41214863 AAAAAAACCCTAAAAATTCTT
1 AAAAGAACCTTAAAAATTCTT
*
41214884 GAAAA-AGCCTTAGAAAAT
1 -AAAAGAACCTTA-AAAAT
41214902 CTTTACAATT
Statistics
Matches: 48, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
21 38 0.79
22 10 0.21
ACGTcount: A:0.52, C:0.16, G:0.07, T:0.25
Consensus pattern (21 bp):
AAAAGAACCTTAAAAATTCTT
Found at i:41215049 original size:21 final size:21
Alignment explanation
Indices: 41215025--41215073 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
41215015 TTAAAAATGC
*
41215025 TTAAAAATTCATAAAAAAACT
1 TTAAAAATCCATAAAAAAACT
* * *
41215046 TTAAAAATCCTTTAAAAGACT
1 TTAAAAATCCATAAAAAAACT
41215067 TTAAAAA
1 TTAAAAA
41215074 CCTTTAAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.57, C:0.10, G:0.02, T:0.31
Consensus pattern (21 bp):
TTAAAAATCCATAAAAAAACT
Found at i:41215050 original size:31 final size:31
Alignment explanation
Indices: 41215015--41215090 Score: 80
Period size: 31 Copynumber: 2.4 Consensus size: 31
41215005 TAAAAGGATC
**
41215015 TTAAAAATGCTTAAAAATTCATAAAAAAACT
1 TTAAAAATGCTTAAAAAGACATAAAAAAACT
* * * * *
41215046 TTAAAAATCCTTTAAAAGACTTTAAAAACCT
1 TTAAAAATGCTTAAAAAGACATAAAAAAACT
41215077 TTAAAAATGACTTA
1 TTAAAAATG-CTTA
41215091 GGAAACCTTA
Statistics
Matches: 35, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
31 32 0.91
32 3 0.09
ACGTcount: A:0.53, C:0.12, G:0.04, T:0.32
Consensus pattern (31 bp):
TTAAAAATGCTTAAAAAGACATAAAAAAACT
Found at i:41215083 original size:21 final size:22
Alignment explanation
Indices: 41215036--41215089 Score: 76
Period size: 21 Copynumber: 2.5 Consensus size: 22
41215026 TAAAAATTCA
*
41215036 TAAAAAAACTTTAAAAATCCTT
1 TAAAAAGACTTTAAAAATCCTT
41215058 T-AAAAGACTTTAAAAA-CCTT
1 TAAAAAGACTTTAAAAATCCTT
41215078 TAAAAATGACTT
1 TAAAAA-GACTT
41215090 AGGAAACCTT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 5 0.17
21 18 0.62
22 6 0.21
ACGTcount: A:0.52, C:0.13, G:0.04, T:0.31
Consensus pattern (22 bp):
TAAAAAGACTTTAAAAATCCTT
Found at i:41215384 original size:9 final size:10
Alignment explanation
Indices: 41215359--41215585 Score: 65
Period size: 10 Copynumber: 21.6 Consensus size: 10
41215349 CAAAAGAACA
*
41215359 TTAAAAATGC
1 TTAAAAATCC
41215369 TTAAAAATCC
1 TTAAAAATCC
41215379 TTAAAAAAAT-C
1 TT--AAAAATCC
**
41215390 TTAAAAATGT
1 TTAAAAATCC
*
41215400 TTCAAAAGA-CT
1 TT-AAAA-ATCC
*
41215411 TTAAAAATCTT
1 TTAAAAATC-C
*
41215422 TTAAAAATAAC
1 TTAAAAAT-CC
41215433 TTACAAAA-CC
1 TTA-AAAATCC
41215443 TTAAAAATCC
1 TTAAAAATCC
* * *
41215453 AT-CAAATACT
1 TTAAAAAT-CC
41215463 TTGAAAACA-CC
1 TT-AAAA-ATCC
*
41215474 ATAAAAATCC
1 TTAAAAATCC
*
41215484 TTTAAAAT-C
1 TTAAAAATCC
*
41215493 TATAAAAAAAACC
1 T-T--AAAAATCC
*
41215506 TTAAAAATGC
1 TTAAAAATCC
*
41215516 TT-AAAATGACT
1 TTAAAAAT--CC
*
41215527 TTAAACATCC
1 TTAAAAATCC
41215537 TTAAAAAGATCC
1 TT-AAAA-ATCC
41215549 -TAAAAATCC
1 TTAAAAATCC
* *
41215558 TTGAAAATGTC
1 TTAAAAAT-CC
*
41215569 TTAAAAAATCT
1 TT-AAAAATCC
41215580 TTAAAA
1 TTAAAA
41215586 TTCGTAATAA
Statistics
Matches: 161, Mismatches: 29, Indels: 54
0.66 0.12 0.22
Matches are distributed among these distances:
9 27 0.17
10 65 0.40
11 35 0.22
12 31 0.19
13 3 0.02
ACGTcount: A:0.52, C:0.15, G:0.04, T:0.30
Consensus pattern (10 bp):
TTAAAAATCC
Found at i:41215406 original size:21 final size:21
Alignment explanation
Indices: 41215361--41215449 Score: 67
Period size: 21 Copynumber: 4.1 Consensus size: 21
41215351 AAAGAACATT
*
41215361 AAAAATGCTTAAAAATCCTTAA
1 AAAAAT-CTTAAAAATCTTTAA
* *
41215383 AAAAATCTTAAAAATGTTTCA
1 AAAAATCTTAAAAATCTTTAA
*
41215404 AAAGA-CTTTAAAAATCTTTTAA
1 AAAAATC-TTAAAAATC-TTTAA
*
41215426 AAATAA-CTTACAAAA-CCTTAA
1 AAA-AATCTTA-AAAATCTTTAA
41215447 AAA
1 AAA
41215450 TCCATCAAAT
Statistics
Matches: 55, Mismatches: 8, Indels: 9
0.76 0.11 0.12
Matches are distributed among these distances:
20 1 0.02
21 31 0.56
22 17 0.31
23 6 0.11
ACGTcount: A:0.55, C:0.12, G:0.03, T:0.29
Consensus pattern (21 bp):
AAAAATCTTAAAAATCTTTAA
Found at i:41215501 original size:22 final size:22
Alignment explanation
Indices: 41215476--41215521 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
41215466 AAAACACCAT
* *
41215476 AAAAATCCTTTAAAAT-CTATAA
1 AAAAAACCTTAAAAATGCT-TAA
41215498 AAAAAACCTTAAAAATGCTTAA
1 AAAAAACCTTAAAAATGCTTAA
41215520 AA
1 AA
41215522 TGACTTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 19 0.90
23 2 0.10
ACGTcount: A:0.59, C:0.13, G:0.02, T:0.26
Consensus pattern (22 bp):
AAAAAACCTTAAAAATGCTTAA
Found at i:41215530 original size:21 final size:21
Alignment explanation
Indices: 41215506--41215586 Score: 74
Period size: 21 Copynumber: 3.8 Consensus size: 21
41215496 AAAAAAAACC
*
41215506 TTAAAAATGCTTAAAATGACT
1 TTAAAAATCCTTAAAATGACT
* *
41215527 TTAAACATCCTTAAAAAGA-T
1 TTAAAAATCCTTAAAATGACT
* *
41215547 CCTAAAAATCCTTGAAAATGTCT
1 -TTAAAAATCCTT-AAAATGACT
* *
41215570 TAAAAAATCTTTAAAAT
1 TTAAAAATCCTTAAAAT
41215587 TCGTAATAAA
Statistics
Matches: 47, Mismatches: 10, Indels: 6
0.75 0.16 0.10
Matches are distributed among these distances:
20 1 0.02
21 31 0.66
22 14 0.30
23 1 0.02
ACGTcount: A:0.48, C:0.14, G:0.06, T:0.32
Consensus pattern (21 bp):
TTAAAAATCCTTAAAATGACT
Found at i:41215694 original size:21 final size:20
Alignment explanation
Indices: 41215652--41215706 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 20
41215642 AAATTCTTTG
41215652 AAAAAT-CTATAAAAAACCTT
1 AAAAATGCT-TAAAAAACCTT
* * *
41215672 AAATATTCTTAAAAAGACTTT
1 AAAAATGCTTAAAAA-ACCTT
41215693 AAAAATGCTTAAAA
1 AAAAATGCTTAAAA
41215707 GCCCATTAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 11 0.38
21 18 0.62
ACGTcount: A:0.56, C:0.11, G:0.04, T:0.29
Consensus pattern (20 bp):
AAAAATGCTTAAAAAACCTT
Found at i:41217294 original size:11 final size:10
Alignment explanation
Indices: 41217212--41217305 Score: 55
Period size: 11 Copynumber: 8.9 Consensus size: 10
41217202 TTAAAAGGTT
*
41217212 CTTAAAAATG
1 CTTAAAAATA
*
41217222 CTTCAAAATA
1 CTTAAAAATA
*
41217232 -TGTGAAAAAAA
1 CT-T-AAAAATA
*
41217243 CCTTAAAAATC
1 -CTTAAAAATA
*
41217254 CTTAAAAAGA
1 CTTAAAAATA
41217264 CTTTAAAAATA
1 C-TTAAAAATA
* *
41217275 TTTTTAAAATGA
1 -CTTAAAAAT-A
*
41217287 CTTAAAAATC
1 CTTAAAAATA
41217297 CTTAAAAAT
1 CTTAAAAAT
41217306 TCATAAAATC
Statistics
Matches: 63, Mismatches: 14, Indels: 14
0.69 0.15 0.15
Matches are distributed among these distances:
9 1 0.02
10 27 0.43
11 32 0.51
12 2 0.03
13 1 0.02
ACGTcount: A:0.52, C:0.12, G:0.05, T:0.31
Consensus pattern (10 bp):
CTTAAAAATA
Found at i:41217300 original size:10 final size:10
Alignment explanation
Indices: 41217287--41217598 Score: 81
Period size: 10 Copynumber: 30.1 Consensus size: 10
41217277 TTTAAAATGA
41217287 CTTAAAAATC
1 CTTAAAAATC
*
41217297 CTTAAAAATT
1 CTTAAAAATC
*
41217307 CAT-AAAATC
1 CTTAAAAATC
* *
41217316 TCTTGAAATTC
1 -CTTAAAAATC
*
41217327 TTTGAAAACA-C
1 CTT-AAAA-ATC
*
41217338 TTTAAAAATC
1 CTTAAAAATC
*
41217348 CTTTCAAAA--
1 C-TTAAAAATC
*
41217357 CTATGAAAAAAAC
1 CT-T-AA-AAATC
*
41217370 CTTAAAAATG
1 CTTAAAAATC
41217380 CTTAGAATAA-C
1 CTTA-AA-AATC
* *
41217391 CTTGAACATC
1 CTTAAAAATC
41217401 CTTAAAAAGATC
1 CTT-AAAA-ATC
41217413 C-TAAAAATC
1 CTTAAAAATC
*
41217422 CTTGAAAATGC
1 CTTAAAAAT-C
41217433 CTTAAAAAATC
1 CTT-AAAAATC
* *
41217444 CTTCAAAATT
1 CTTAAAAATC
* *
41217454 CGTAATAAATT
1 CTTAA-AAATC
*
41217465 ATTAAGAAA--
1 CTTAA-AAATC
*
41217474 ATTAAAAATC
1 CTTAAAAATC
*
41217484 CACTAAAAA--
1 C-TTAAAAATC
*
41217493 CATAAAAGATC
1 CTTAAAA-ATC
* *
41217504 CTTCAAATTC
1 CTTAAAAATC
41217514 CTTGAAAAATC
1 CTT-AAAAATC
*
41217525 TTTAAAAAAT-
1 CTT-AAAAATC
* *
41217535 CTTAAATATT
1 CTTAAAAATC
41217545 CTTAAAAGAT-
1 CTTAAAA-ATC
* *
41217555 TTTAAAAAATG
1 CTT-AAAAATC
41217566 CTTAAAAATC
1 CTTAAAAATC
*
41217576 CATATAAAAAAC
1 C-T-TAAAAATC
41217588 CTTAAAAATC
1 CTTAAAAATC
41217598 C
1 C
41217599 AAGAAAAGAT
Statistics
Matches: 224, Mismatches: 45, Indels: 66
0.67 0.13 0.20
Matches are distributed among these distances:
8 9 0.04
9 25 0.11
10 84 0.38
11 84 0.38
12 20 0.09
13 2 0.01
ACGTcount: A:0.49, C:0.16, G:0.05, T:0.30
Consensus pattern (10 bp):
CTTAAAAATC
Found at i:41217810 original size:7 final size:7
Alignment explanation
Indices: 41217789--41217880 Score: 98
Period size: 7 Copynumber: 13.0 Consensus size: 7
41217779 AGAGAGATAA
*
41217789 TTTAGGA
1 TTTAGGG
*
41217796 TTTGGGG
1 TTTAGGG
41217803 TTTAGGG
1 TTTAGGG
41217810 TTTAGGGG
1 TTTA-GGG
*
41217818 ATTAGGG
1 TTTAGGG
41217825 TTT-GGG
1 TTTAGGG
*
41217831 -GTAGGGG
1 TTTA-GGG
41217838 TTTAGGG
1 TTTAGGG
41217845 TTTAGGG
1 TTTAGGG
*
41217852 GTTAGGG
1 TTTAGGG
41217859 TTTAAGGG
1 TTT-AGGG
41217867 TTTAGGG
1 TTTAGGG
41217874 TTTAGGG
1 TTTAGGG
41217881 GTCAAGGGTT
Statistics
Matches: 71, Mismatches: 9, Indels: 10
0.79 0.10 0.11
Matches are distributed among these distances:
5 1 0.01
6 3 0.04
7 52 0.73
8 15 0.21
ACGTcount: A:0.15, C:0.00, G:0.47, T:0.38
Consensus pattern (7 bp):
TTTAGGG
Found at i:41217822 original size:15 final size:15
Alignment explanation
Indices: 41217789--41217882 Score: 102
Period size: 15 Copynumber: 6.1 Consensus size: 15
41217779 AGAGAGATAA
*
41217789 TTTAGGATTT-GGGG
1 TTTAGGGTTTAGGGG
41217803 TTTAGGGTTTAGGGG
1 TTTAGGGTTTAGGGG
*
41217818 ATTAGGGTTTGGGGTAGGGG
1 TTTAGGG-TT----TAGGGG
41217838 TTTAGGGTTTAGGGG
1 TTTAGGGTTTAGGGG
*
41217853 -TTAGGGTTTAAGGG
1 TTTAGGGTTTAGGGG
41217867 TTTAGGGTTTAGGGG
1 TTTAGGGTTTAGGGG
41217882 T
1 T
41217883 CAAGGGTTAG
Statistics
Matches: 68, Mismatches: 5, Indels: 13
0.79 0.06 0.15
Matches are distributed among these distances:
14 22 0.32
15 30 0.44
16 2 0.03
19 2 0.03
20 12 0.18
ACGTcount: A:0.15, C:0.00, G:0.47, T:0.38
Consensus pattern (15 bp):
TTTAGGGTTTAGGGG
Found at i:41217827 original size:22 final size:22
Alignment explanation
Indices: 41217800--41217897 Score: 114
Period size: 22 Copynumber: 4.6 Consensus size: 22
41217790 TTAGGATTTG
*
41217800 GGGTTTAGGGTTTAGGGGATTA
1 GGGTTTAGGGTTTAGGGGTTTA
*
41217822 GGGTTT-GGG-GTAGGGGTTTA
1 GGGTTTAGGGTTTAGGGGTTTA
*
41217842 GGGTTTAGGGGTTA-GGGTTTAA
1 GGGTTTAGGGTTTAGGGGTTT-A
**
41217864 GGGTTTAGGGTTTAGGGGTCAA
1 GGGTTTAGGGTTTAGGGGTTTA
41217886 GGG-TTAGGGTTT
1 GGGTTTAGGGTTT
41217898 TTTTTTTTTT
Statistics
Matches: 66, Mismatches: 6, Indels: 9
0.81 0.07 0.11
Matches are distributed among these distances:
20 15 0.23
21 21 0.32
22 26 0.39
23 4 0.06
ACGTcount: A:0.15, C:0.01, G:0.48, T:0.36
Consensus pattern (22 bp):
GGGTTTAGGGTTTAGGGGTTTA
Found at i:41217888 original size:15 final size:14
Alignment explanation
Indices: 41217790--41217897 Score: 87
Period size: 14 Copynumber: 7.6 Consensus size: 14
41217780 GAGAGATAAT
*
41217790 TTAGGATTT-GGGG
1 TTAGGGTTTAGGGG
41217803 TTTAGGGTTTAGGGG
1 -TTAGGGTTTAGGGG
41217818 ATTAGGGTTT-GGGG
1 -TTAGGGTTTAGGGG
*
41217832 -TAGGGGTTTAGGGT
1 TTA-GGGTTTAGGGG
* *
41217846 TTAGGGGTTAGGGT
1 TTAGGGTTTAGGGG
*
41217860 TTAAGGGTTTAGGGT
1 TT-AGGGTTTAGGGG
* * *
41217875 TTAGGGGTCAAGGG
1 TTAGGGTTTAGGGG
41217889 TTAGGGTTT
1 TTAGGGTTT
41217898 TTTTTTTTTT
Statistics
Matches: 78, Mismatches: 11, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
12 2 0.03
13 6 0.08
14 42 0.54
15 28 0.36
ACGTcount: A:0.16, C:0.01, G:0.46, T:0.37
Consensus pattern (14 bp):
TTAGGGTTTAGGGG
Found at i:41219184 original size:7 final size:7
Alignment explanation
Indices: 41219174--41219398 Score: 169
Period size: 7 Copynumber: 32.7 Consensus size: 7
41219164 TTAGCCTCCA
41219174 AGGGTTT
1 AGGGTTT
41219181 AGGGTTT
1 AGGGTTT
*
41219188 AAGGTTT
1 AGGGTTT
41219195 AGGGTTT
1 AGGGTTT
41219202 AGGGTTT
1 AGGGTTT
*
41219209 AGGGGTT
1 AGGGTTT
41219216 AGGG-TT
1 AGGGTTT
*
41219222 GGGGTTT
1 AGGGTTT
41219229 AGGGTTT
1 AGGGTTT
41219236 AGGTGTTT
1 AGG-GTTT
*
41219244 AAGGTTT
1 AGGGTTT
*
41219251 GGGGTTT
1 AGGGTTT
*
41219258 -GGGGTT
1 AGGGTTT
41219264 AGGGTTT
1 AGGGTTT
*
41219271 AGGGGTT
1 AGGGTTT
*
41219278 AGGG-GT
1 AGGGTTT
41219284 AGGGGTTT
1 A-GGGTTT
*
41219292 GGGGTTT
1 AGGGTTT
*
41219299 GGGGTTT
1 AGGGTTT
*
41219306 GGGGTTT
1 AGGGTTT
41219313 -GGGTTT
1 AGGGTTT
*
41219319 GGGGTTT
1 AGGGTTT
* *
41219326 GGGGGTTG
1 -AGGGTTT
*
41219334 GGGGTTT
1 AGGGTTT
41219341 AGGG--T
1 AGGGTTT
*
41219346 AGGGGTT
1 AGGGTTT
*
41219353 ATGGTTT
1 AGGGTTT
*
41219360 GGGGTTT
1 AGGGTTT
*
41219367 GGGGTTT
1 AGGGTTT
*
41219374 -TGGTTT
1 AGGGTTT
*
41219380 TGAGG-TT
1 AG-GGTTT
41219387 AGGGTTT
1 AGGGTTT
41219394 AGGGT
1 AGGGT
41219399 AGGGGTTGGG
Statistics
Matches: 182, Mismatches: 24, Indels: 24
0.79 0.10 0.10
Matches are distributed among these distances:
5 5 0.03
6 25 0.14
7 137 0.75
8 15 0.08
ACGTcount: A:0.10, C:0.00, G:0.50, T:0.40
Consensus pattern (7 bp):
AGGGTTT
Found at i:41219231 original size:34 final size:35
Alignment explanation
Indices: 41219174--41219440 Score: 212
Period size: 34 Copynumber: 7.8 Consensus size: 35
41219164 TTAGCCTCCA
* **
41219174 AGGGTTTAGGGTTTAAGGTTTAGGGTTTAGGGTTT
1 AGGGGTTAGGGTTTGGGGTTTAGGGTTTAGGGTTT
41219209 AGGGGTTAGGG-TTGGGGTTTAGGGTTTAGGTGTTT
1 AGGGGTTAGGGTTTGGGGTTTAGGGTTTAGG-GTTT
* * * *
41219244 AAGGTTTGGGGTTTGGGG-TTAGGGTTTAGGGGTT
1 AGGGGTTAGGGTTTGGGGTTTAGGGTTTAGGGTTT
* *
41219278 AGGGG-TAGGGGTTTGGGGTTTGGGGTTTGGGGTTT
1 AGGGGTTA-GGGTTTGGGGTTTAGGGTTTAGGGTTT
* * **
41219313 -GGGTTTGGGGTTTGGGGGTTGGGGGTTTAGGG--T
1 AGGGGTTAGGGTTT-GGGGTTTAGGGTTTAGGGTTT
* * *
41219346 AGGGGTTATGGTTTGGGGTTTGGGGTTT-TGGTTT
1 AGGGGTTAGGGTTTGGGGTTTAGGGTTTAGGGTTT
* * * **
41219380 TGAGGTTAGGGTTTAGGG--TAGGGGTTGGGGGTTT
1 AGGGGTTAGGGTTTGGGGTTTA-GGGTTTAGGGTTT
* *
41219414 -GGGGTTAGGGGTTGGGGGTTGAGGGTT
1 AGGGGTTA-GGGTTTGGGGTTTAGGGTT
41219441 GGGTTAGGGT
Statistics
Matches: 185, Mismatches: 33, Indels: 28
0.75 0.13 0.11
Matches are distributed among these distances:
32 3 0.02
33 26 0.14
34 80 0.43
35 69 0.37
36 7 0.04
ACGTcount: A:0.09, C:0.00, G:0.52, T:0.39
Consensus pattern (35 bp):
AGGGGTTAGGGTTTGGGGTTTAGGGTTTAGGGTTT
Found at i:41219262 original size:48 final size:48
Alignment explanation
Indices: 41219175--41219496 Score: 210
Period size: 48 Copynumber: 6.8 Consensus size: 48
41219165 TAGCCTCCAA
* *
41219175 GGGTTTAGGGTTTAAGGTTTAGGGTTTAGGGTTTAGGGGTTAGGG-TTG
1 GGGTTTAGGGTTTAGGGTTTAGGGTTTGGGGTTT-GGGGTTAGGGTTTG
*
41219223 GGGTTTAGGGTTTAGGTGTTTAAGGTTTGGGGTTTGGGGTTAGGGTTTAG
1 GGGTTTAGGGTTTAGG-GTTTAGGGTTTGGGGTTTGGGGTTAGGGTTT-G
* * *
41219273 GGG-TTAGGG-GTAGGGGTTTGGGGTTTGGGGTTTGGGGTTTGGGTTTG
1 GGGTTTAGGGTTTA-GGGTTTAGGGTTTGGGGTTTGGGGTTAGGGTTTG
** * * *
41219320 GGGTTT--GG----GGGTTGGGGGTTTAGGG-TAGGGGTTATGGTTTG
1 GGGTTTAGGGTTTAGGGTTTAGGGTTTGGGGTTTGGGGTTAGGGTTTG
* * * * * *
41219361 GGGTTTGGGGTTT-TGGTTTTGAGG-TTAGGGTTTAGGG-TAGGGGTTGG
1 GGGTTTAGGGTTTAGGGTTTAG-GGTTTGGGGTTTGGGGTTA-GGGTTTG
* * * *
41219408 GGGTTT-GGGGTTAGGGGTTGGGGGTTGAGGG-TT-GGGTTAGGGTTTGG
1 GGGTTTAGGGTTTAGGGTTTAGGGTTTG-GGGTTTGGGGTTAGGGTTT-G
* * *
41219455 GGGTTT-GGGTTTTGGGGATTTGGGGGTTTGGGGTTGGGGGTT
1 GGGTTTAGGG-TTTAGGG-TTT-AGGGTTTGGGGTTTGGGGTT
41219497 CNAAGAGATT
Statistics
Matches: 221, Mismatches: 30, Indels: 43
0.75 0.10 0.15
Matches are distributed among these distances:
41 19 0.09
42 15 0.07
43 2 0.01
46 30 0.14
47 42 0.19
48 65 0.29
49 31 0.14
50 12 0.05
51 5 0.02
ACGTcount: A:0.08, C:0.00, G:0.53, T:0.39
Consensus pattern (48 bp):
GGGTTTAGGGTTTAGGGTTTAGGGTTTGGGGTTTGGGGTTAGGGTTTG
Found at i:41219361 original size:47 final size:48
Alignment explanation
Indices: 41219308--41219493 Score: 152
Period size: 47 Copynumber: 3.9 Consensus size: 48
41219298 TGGGGTTTGG
41219308 GGTTT-GGGTTTGGGGTTTGGGGGTTGGGGGTTTAGGGTAGGGGTTAT
1 GGTTTGGGGTTTGGGGTTTGGGGGTTGGGGGTTTAGGGTAGGGGTTAT
* * * * *
41219355 GGTTTGGGGTTTGGGGTTT-TGGTTTTGAGG-TTAGGGTTTA-GGG-TAGG
1 GGTTTGGGGTTTGGGGTTTGGGGGTTGGGGGTTTAGGG--TAGGGGTTA-T
* * * * *
41219402 GGTTGGGGGTTTGGGG-TTAGGGGTTGGGGGTTGAGGGT-TGGGTTAG
1 GGTTTGGGGTTTGGGGTTTGGGGGTTGGGGGTTTAGGGTAGGGGTTAT
* * * *
41219448 GGTTTGGGGGTTTGGGTTTTGGGGATTTGGGGGTTTGGGGTTGGGG
1 GGTTT-GGGGTTTGGGGTTTGGGG-GTTGGGGGTTTAGGGTAGGGG
41219494 GTTCNAAGAG
Statistics
Matches: 109, Mismatches: 18, Indels: 21
0.74 0.12 0.14
Matches are distributed among these distances:
46 19 0.17
47 49 0.45
48 25 0.23
49 13 0.12
50 3 0.03
ACGTcount: A:0.06, C:0.00, G:0.56, T:0.38
Consensus pattern (48 bp):
GGTTTGGGGTTTGGGGTTTGGGGGTTGGGGGTTTAGGGTAGGGGTTAT
Found at i:41219410 original size:7 final size:7
Alignment explanation
Indices: 41219400--41219496 Score: 81
Period size: 7 Copynumber: 13.9 Consensus size: 7
41219390 GTTTAGGGTA
41219400 GGGGTTG
1 GGGGTTG
*
41219407 GGGGTTT
1 GGGGTTG
*
41219414 GGGGTTA
1 GGGGTTG
41219421 GGGGTTG
1 GGGGTTG
41219428 GGGGTTG
1 GGGGTTG
*
41219435 AGGGTT-
1 GGGGTTG
*
41219441 -GGGTTA
1 GGGGTTG
*
41219447 GGGTTTG
1 GGGGTTG
41219454 GGGGTTTG
1 GGGG-TTG
**
41219462 GGTTTTG
1 GGGGTTG
*
41219469 GGGATTTG
1 GGG-GTTG
*
41219477 GGGGTTT
1 GGGGTTG
41219484 GGGGTTG
1 GGGGTTG
41219491 GGGGTT
1 GGGGTT
41219497 CNAAGAGATT
Statistics
Matches: 73, Mismatches: 13, Indels: 8
0.78 0.14 0.09
Matches are distributed among these distances:
5 5 0.07
7 56 0.77
8 12 0.16
ACGTcount: A:0.04, C:0.00, G:0.60, T:0.36
Consensus pattern (7 bp):
GGGGTTG
Found at i:41219419 original size:14 final size:14
Alignment explanation
Indices: 41219175--41219496 Score: 213
Period size: 14 Copynumber: 23.4 Consensus size: 14
41219165 TAGCCTCCAA
* *
41219175 GGGTTTAGGGTTTA
1 GGGTTTGGGGTTTG
* * *
41219189 AGGTTTAGGGTTTA
1 GGGTTTGGGGTTTG
*
41219203 GGGTTTAGGGG-TTA
1 GGGTTT-GGGGTTTG
*
41219217 GGG-TTGGGGTTTA
1 GGGTTTGGGGTTTG
* *
41219230 GGGTTTAGGTGTTTA
1 GGGTTT-GGGGTTTG
*
41219245 AGGTTTGGGGTTTG
1 GGGTTTGGGGTTTG
*
41219259 GGG-TTAGGGTTTAG
1 GGGTTTGGGGTTT-G
* *
41219273 GGGTTAGGGG-TAG
1 GGGTTTGGGGTTTG
41219286 GGGTTTGGGGTTTG
1 GGGTTTGGGGTTTG
41219300 GGGTTTGGGGTTT-
1 GGGTTTGGGGTTTG
41219313 GGGTTTGGGGTTTGG
1 GGGTTTGGGGTTT-G
* *
41219328 GGGTTGGGGGTTTA
1 GGGTTTGGGGTTTG
*
41219342 GGG-TAGGGGTTAT-
1 GGGTTTGGGGTT-TG
41219355 -GGTTTGGGGTTTG
1 GGGTTTGGGGTTTG
* *
41219368 GGGTTTTGGTTTTG
1 GGGTTTGGGGTTTG
* * *
41219382 AGG-TTAGGGTTTA
1 GGGTTTGGGGTTTG
* *
41219395 GGG-TAGGGGTTGG
1 GGGTTTGGGGTTTG
*
41219408 GGGTTTGGGGTTAG
1 GGGTTTGGGGTTTG
*
41219422 GGG-TTGGGGGTTG
1 GGGTTTGGGGTTTG
*
41219435 AGGG-TT-GGG-TTA
1 -GGGTTTGGGGTTTG
41219447 GGGTTTGGGGGTTTG
1 GGGTTT-GGGGTTTG
*
41219462 GGTTTTGGGGATTTGG
1 GGGTTTGGGG-TTT-G
*
41219478 GGGTTTGGGGTTGG
1 GGGTTTGGGGTTTG
41219492 GGGTT
1 GGGTT
41219497 CNAAGAGATT
Statistics
Matches: 249, Mismatches: 38, Indels: 42
0.76 0.12 0.13
Matches are distributed among these distances:
11 3 0.01
12 11 0.04
13 82 0.33
14 100 0.40
15 43 0.17
16 10 0.04
ACGTcount: A:0.08, C:0.00, G:0.53, T:0.39
Consensus pattern (14 bp):
GGGTTTGGGGTTTG
Found at i:41219444 original size:26 final size:28
Alignment explanation
Indices: 41219190--41219496 Score: 138
Period size: 27 Copynumber: 11.1 Consensus size: 28
41219180 TAGGGTTTAA
* * *
41219190 GGTTTAGGGTTTAGGGTTTAGGGGTT-AG
1 GGTTT-GGGGTTAGGGGTTGGGGGTTGAG
* * * * *
41219218 GG-TTGGGGTTTAGGGTTTAGGTGTTTAA
1 GGTTTGGGG-TTAGGGGTTGGGGGTTGAG
* * *
41219246 GGTTTGGGGTTTGGGGTT-AGGGTTTAGG
1 GGTTTGGGGTTAGGGGTTGGGGGTTGA-G
* *
41219274 GGTTAGGGG-TAGGGGTTTGGGGTTTG-G
1 GGTTTGGGGTTAGGGG-TTGGGGGTTGAG
* * * *
41219301 GGTTTGGGGTTTGGGTTTGGGGTTTGGG
1 GGTTTGGGGTTAGGGGTTGGGGGTTGAG
* * *
41219329 GGTTGGGGGTTTA-GGG-TAGGGGTT-AT
1 GGTTTGGGG-TTAGGGGTTGGGGGTTGAG
* * **
41219355 GGTTTGGGGTTTGGGGTTTTGGTTTTGA-
1 GGTTTGGGGTTAGGGG-TTGGGGGTTGAG
* * * *
41219383 GGTTAGGGTTTA-GGG-TAGGGGTTGGG
1 GGTTTGGGGTTAGGGGTTGGGGGTTGAG
41219409 GGTTTGGGGTTAGGGGTTGGGGGTTGAG
1 GGTTTGGGGTTAGGGGTTGGGGGTTGAG
*
41219437 GG-TT-GGGTTAGGGTTTGGGGGTTTG-G
1 GGTTTGGGGTTAGGGGTTGGGGG-TTGAG
* * * *
41219463 GTTTTGGGGATTTGGGGGTTTGGGGTTGGG
1 GGTTTGGGG--TTAGGGGTTGGGGGTTGAG
41219493 GGTT
1 GGTT
41219497 CNAAGAGATT
Statistics
Matches: 212, Mismatches: 45, Indels: 42
0.71 0.15 0.14
Matches are distributed among these distances:
25 8 0.04
26 42 0.20
27 66 0.31
28 65 0.31
29 16 0.08
30 15 0.07
ACGTcount: A:0.07, C:0.00, G:0.54, T:0.39
Consensus pattern (28 bp):
GGTTTGGGGTTAGGGGTTGGGGGTTGAG
Found at i:41220456 original size:35 final size:33
Alignment explanation
Indices: 41220333--41220458 Score: 103
Period size: 35 Copynumber: 3.7 Consensus size: 33
41220323 TTAGGTGTTG
* * * *
41220333 GGTTTTAGTTGATCTTGTGAAAAATCATTGTTGTA
1 GGTTTTGGTTGAGCTTTTGAAAAACCATTG-TG-A
* *
41220368 GGTTGTGGTTGAGCCTTTGAAAAACCACTT-TGA
1 GGTTTTGGTTGAGCTTTTGAAAAACCA-TTGTGA
* **
41220401 -GTCTTGGTTGAGCTCGTGAAAAACCATTGTGAAA
1 GGTTTTGGTTGAGCTTTTGAAAAACCATTGTG--A
*
41220435 GGTTTTGGTTCAGCTTTTGAAAAA
1 GGTTTTGGTTGAGCTTTTGAAAAA
41220459 TCACTTTGGG
Statistics
Matches: 71, Mismatches: 15, Indels: 10
0.74 0.16 0.10
Matches are distributed among these distances:
31 2 0.03
32 23 0.32
33 1 0.01
34 3 0.04
35 40 0.56
36 2 0.03
ACGTcount: A:0.26, C:0.11, G:0.25, T:0.37
Consensus pattern (33 bp):
GGTTTTGGTTGAGCTTTTGAAAAACCATTGTGA
Found at i:41220506 original size:67 final size:67
Alignment explanation
Indices: 41220330--41220517 Score: 209
Period size: 67 Copynumber: 2.8 Consensus size: 67
41220320 AAGTTAGGTG
** * * * *
41220330 TTGGGTTTTAGTTGATCTTGTGAAAAATCATTGTTG-TAGGTTGTGGTTGAGCCTTTGAAAAACC
1 TTGGGTTTTAGTTGATCCCGTGAAAAACCATTG-TGAAAGGTTTTGGTTCAGCCTTTGAAAAACC
41220394 ACT
65 ACT
* * * * * * *
41220397 TTGAGTCTTGGTTGAGCTCGTGAAAAACCATTGTGAAAGGTTTTGGTTCAGCTTTTGAAAAATCA
1 TTGGGTTTTAGTTGATCCCGTGAAAAACCATTGTGAAAGGTTTTGGTTCAGCCTTTGAAAAACCA
41220462 CT
66 CT
* *
41220464 TTGGGTTTTAGTTGATCCCG-GTAAAAACCATTGTGAAAGGTTTTGTTTAAGCCT
1 TTGGGTTTTAGTTGATCCCGTG-AAAAACCATTGTGAAAGGTTTTGGTTCAGCCT
41220518 GGTAAAAGCC
Statistics
Matches: 100, Mismatches: 19, Indels: 4
0.81 0.15 0.03
Matches are distributed among these distances:
66 3 0.03
67 97 0.97
ACGTcount: A:0.25, C:0.12, G:0.24, T:0.38
Consensus pattern (67 bp):
TTGGGTTTTAGTTGATCCCGTGAAAAACCATTGTGAAAGGTTTTGGTTCAGCCTTTGAAAAACCA
CT
Found at i:41227535 original size:6 final size:6
Alignment explanation
Indices: 41227526--41227815 Score: 245
Period size: 6 Copynumber: 46.3 Consensus size: 6
41227516 TTTTTTGGTT
41227526 GGTTTA GGTTT- GGTTTA GGTTTA GGTTTA GGTTTA -GTTTA GGTTTA
1 GGTTTA GGTTTA GGTTTA GGTTTA GGTTTA GGTTTA GGTTTA GGTTTA
* * *
41227572 -GTTTA -GTTTA GGGTTA GG-TTA GGGTTA GG-TTA GGGTTA GG-TTA
1 GGTTTA GGTTTA GGTTTA GGTTTA GGTTTA GGTTTA GGTTTA GGTTTA
* * * *
41227615 GGGTTTA GGGTTTA GGGTTA GGGTTTA GTTTTG GGTTTA GGGTTTA GGGTTA
1 -GGTTTA -GGTTTA GGTTTA -GGTTTA GGTTTA GGTTTA -GGTTTA GGTTTA
*
41227667 GGGTTAA GGGTTTA GGGTTTA GGGNTTTTA GGTTTTA GGTTTTA GGTTTTA
1 -GGTTTA -GGTTTA -GGTTTA -GG--TTTA GG-TTTA GG-TTTA GG-TTTA
* *
41227718 GGTTTTA GGTTTA GGTTTA GGTTTA GGTTTA TGTTTA GGGTTA GTGTTTA
1 GG-TTTA GGTTTA GGTTTA GGTTTA GGTTTA GGTTTA GGTTTA G-GTTTA
*
41227768 GGGTTTA GGGTTTA GG-TTA GGGTTTA GGGTTTA GGGTTTA GGGTTA GG
1 -GGTTTA -GGTTTA GGTTTA -GGTTTA -GGTTTA -GGTTTA GGTTTA GG
41227816 GGGTAGGGTT
Statistics
Matches: 252, Mismatches: 16, Indels: 32
0.84 0.05 0.11
Matches are distributed among these distances:
5 36 0.14
6 107 0.42
7 102 0.40
8 3 0.01
9 4 0.02
ACGTcount: A:0.16, C:0.00, G:0.38, T:0.46
Consensus pattern (6 bp):
GGTTTA
Found at i:41227862 original size:15 final size:14
Alignment explanation
Indices: 41227821--41227988 Score: 210
Period size: 15 Copynumber: 11.5 Consensus size: 14
41227811 TTAGGGGGTA
* *
41227821 GGGTTTAGGGTTTA
1 GGGTTTTGGGTTTG
*
41227835 GGGTTTTGGGTTTT
1 GGGTTTTGGGTTTG
41227849 GGGTTTTGGGGTTTG
1 GGGTTTT-GGGTTTG
41227864 GGGTTTTTGGGTTTG
1 GGG-TTTTGGGTTTG
41227879 GGGTTTTTGGGTTTG
1 GGG-TTTTGGGTTTG
41227894 GGGTTTTTGGGTTTG
1 GGG-TTTTGGGTTTG
41227909 GGGTTTTTGGGTTTG
1 GGG-TTTTGGGTTTG
41227924 GGGTTTTTGGGTTTG
1 GGG-TTTTGGGTTTG
* *
41227939 GGGTTTTTGGTTTT
1 GGGTTTTGGGTTTG
41227953 GGGTTTTGGGTTTTG
1 GGGTTTTGGG-TTTG
* *
41227968 GGGTTTAGGGTTTA
1 GGGTTTTGGGTTTG
41227982 GGGTTTT
1 GGGTTTT
41227989 TTTAGGGTTT
Statistics
Matches: 141, Mismatches: 10, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
14 46 0.33
15 91 0.65
16 4 0.03
ACGTcount: A:0.02, C:0.00, G:0.45, T:0.52
Consensus pattern (14 bp):
GGGTTTTGGGTTTG
Found at i:41227880 original size:6 final size:7
Alignment explanation
Indices: 41227526--41228029 Score: 364
Period size: 7 Copynumber: 75.7 Consensus size: 7
41227516 TTTTTTGGTT
41227526 GGTTTA-
1 GGTTTAG
41227532 GGTTT--
1 GGTTTAG
41227537 GGTTTA-
1 GGTTTAG
41227543 GGTTTA-
1 GGTTTAG
41227549 GGTTTA-
1 GGTTTAG
41227555 GGTTTA-
1 GGTTTAG
41227561 -GTTTA-
1 GGTTTAG
41227566 GGTTTA-
1 GGTTTAG
41227572 -GTTTA-
1 GGTTTAG
41227577 -GTTTAG
1 GGTTTAG
41227583 GG-TTA-
1 GGTTTAG
41227588 GG-TTAG
1 GGTTTAG
41227594 GG-TTA-
1 GGTTTAG
41227599 GG-TTAG
1 GGTTTAG
41227605 GG-TTA-
1 GGTTTAG
41227610 GG-TTAG
1 GGTTTAG
41227616 GGTTTAG
1 GGTTTAG
41227623 GGTTTAG
1 GGTTTAG
41227630 GG-TTAG
1 GGTTTAG
41227636 GGTTTA-
1 GGTTTAG
*
41227642 -GTTTTG
1 GGTTTAG
41227648 GGTTTAG
1 GGTTTAG
41227655 GGTTTAG
1 GGTTTAG
41227662 GG-TTAG
1 GGTTTAG
*
41227668 GGTTAAG
1 GGTTTAG
41227675 GGTTTAG
1 GGTTTAG
41227682 GGTTTAG
1 GGTTTAG
41227689 GGNTTTTAG
1 GG--TTTAG
*
41227698 GTTTTAG
1 GGTTTAG
*
41227705 GTTTTAG
1 GGTTTAG
*
41227712 GTTTTAG
1 GGTTTAG
*
41227719 GTTTTA-
1 GGTTTAG
41227725 GGTTTA-
1 GGTTTAG
41227731 GGTTTA-
1 GGTTTAG
41227737 GGTTTA-
1 GGTTTAG
41227743 GGTTTA-
1 GGTTTAG
*
41227749 TGTTTAG
1 GGTTTAG
41227756 GG-TTAG
1 GGTTTAG
*
41227762 TGTTTAG
1 GGTTTAG
41227769 GGTTTAG
1 GGTTTAG
41227776 GGTTTA-
1 GGTTTAG
41227782 GG-TTAG
1 GGTTTAG
41227788 GGTTTAG
1 GGTTTAG
41227795 GGTTTAG
1 GGTTTAG
41227802 GGTTTAG
1 GGTTTAG
41227809 GG-TTAG
1 GGTTTAG
**
41227815 GGGGTAG
1 GGTTTAG
41227822 GGTTTAG
1 GGTTTAG
41227829 GGTTTAG
1 GGTTTAG
*
41227836 GGTTTTG
1 GGTTTAG
*
41227843 GGTTTTG
1 GGTTTAG
*
41227850 GGTTTTGG
1 GG-TTTAG
*
41227858 GGTTTGG
1 GGTTTAG
*
41227865 GGTTTTTG
1 GG-TTTAG
*
41227873 GGTTTGG
1 GGTTTAG
*
41227880 GGTTTTTG
1 GG-TTTAG
*
41227888 GGTTTGG
1 GGTTTAG
*
41227895 GGTTTTTG
1 GG-TTTAG
*
41227903 GGTTTGG
1 GGTTTAG
*
41227910 GGTTTTTG
1 GG-TTTAG
*
41227918 GGTTTGG
1 GGTTTAG
*
41227925 GGTTTTTG
1 GG-TTTAG
*
41227933 GGTTTGG
1 GGTTTAG
**
41227940 GGTTTTT
1 GGTTTAG
*
41227947 GGTTTTG
1 GGTTTAG
*
41227954 GGTTTTG
1 GGTTTAG
*
41227961 GGTTTTGG
1 GG-TTTAG
41227969 GGTTTAG
1 GGTTTAG
41227976 GGTTTAG
1 GGTTTAG
41227983 GGTTT--
1 GGTTTAG
*
41227988 -TTTTAG
1 GGTTTAG
41227994 GGTTTTTTAG
1 GG---TTTAG
41228004 GGTTTAG
1 GGTTTAG
41228011 GGTTTAG
1 GGTTTAG
41228018 GGTTTAG
1 GGTTTAG
41228025 GGTTT
1 GGTTT
41228030 TTTTTTTTTT
Statistics
Matches: 434, Mismatches: 32, Indels: 63
0.82 0.06 0.12
Matches are distributed among these distances:
4 3 0.01
5 42 0.10
6 98 0.23
7 236 0.54
8 42 0.10
9 6 0.01
10 7 0.02
ACGTcount: A:0.11, C:0.00, G:0.40, T:0.48
Consensus pattern (7 bp):
GGTTTAG
Found at i:41227994 original size:11 final size:11
Alignment explanation
Indices: 41227978--41228008 Score: 55
Period size: 10 Copynumber: 2.9 Consensus size: 11
41227968 GGGTTTAGGG
41227978 TTTAGGGTTTT
1 TTTAGGGTTTT
41227989 TTTAGGG-TTT
1 TTTAGGGTTTT
41227999 TTTAGGGTTT
1 TTTAGGGTTT
41228009 AGGGTTTAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.53
11 9 0.47
ACGTcount: A:0.10, C:0.00, G:0.29, T:0.61
Consensus pattern (11 bp):
TTTAGGGTTTT
Found at i:41228033 original size:1 final size:1
Alignment explanation
Indices: 41228027--41228063 Score: 74
Period size: 1 Copynumber: 37.0 Consensus size: 1
41228017 GGGTTTAGGG
41228027 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
41228064 ATGCTGGAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 36 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:41235392 original size:7 final size:7
Alignment explanation
Indices: 41235382--41235415 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
41235372 TTTTTATAGC
41235382 GGGTTTA
1 GGGTTTA
41235389 GGGTTTA
1 GGGTTTA
41235396 GGGTTTA
1 GGGTTTA
41235403 GGGTTTA
1 GGGTTTA
41235410 GGGTTT
1 GGGTTT
41235416 TTTTTTTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.12, C:0.00, G:0.44, T:0.44
Consensus pattern (7 bp):
GGGTTTA
Done.