Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr9
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: 91122320
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2661692 characters in sequence are not A, C, G, or T
File 139 of 279
Found at i:45070543 original size:21 final size:21
Alignment explanation
Indices: 45070501--45070543 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
45070491 GCAACTAGAT
* *
45070501 CCACAACCACCACATCAACAG
1 CCACAACAACCACAACAACAG
*
45070522 CCACAACAACCACAACAGCAG
1 CCACAACAACCACAACAACAG
45070543 C
1 C
45070544 AGCAAAGTCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.44, C:0.47, G:0.07, T:0.02
Consensus pattern (21 bp):
CCACAACAACCACAACAACAG
Found at i:45070758 original size:15 final size:15
Alignment explanation
Indices: 45070717--45070772 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
45070707 GATGATGCAA
*
45070717 CAGCAGCAGCAGCAG
1 CAGCAGCAGCAACAG
* ***
45070732 CGGCAATTGCAACAG
1 CAGCAGCAGCAACAG
45070747 CAGCAGCAGCAACCA-
1 CAGCAGCAGCAA-CAG
45070762 CAGCAGCAGCA
1 CAGCAGCAGCA
45070773 GCAAATGCAG
Statistics
Matches: 31, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
15 29 0.94
16 2 0.06
ACGTcount: A:0.36, C:0.34, G:0.27, T:0.04
Consensus pattern (15 bp):
CAGCAGCAGCAACAG
Found at i:45070768 original size:21 final size:21
Alignment explanation
Indices: 45070720--45070775 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
45070710 GATGCAACAG
* ***
45070720 CAGCAGCAGCAGCGGCAATTG
1 CAGCAGCAGCAGCAGCAACCA
*
45070741 CAACAGCAGCAGCAGCAACCA
1 CAGCAGCAGCAGCAGCAACCA
45070762 CAGCAGCAGCAGCA
1 CAGCAGCAGCAGCA
45070776 AATGCAGAGG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.36, C:0.34, G:0.27, T:0.04
Consensus pattern (21 bp):
CAGCAGCAGCAGCAGCAACCA
Found at i:45071263 original size:3 final size:3
Alignment explanation
Indices: 45071248--45071447 Score: 118
Period size: 3 Copynumber: 66.7 Consensus size: 3
45071238 TTACATGAAC
* ** * **
45071248 CAG CAG CAA CAG CAG CAG CAG CAG CAG CAG TTG CAA TTG CAG CAG CAG
1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG
* * ** * *
45071296 CAG CAA CAA CAG CAG CAG TTG CA- CTTG CAG CAG CAG CAG CAG CAA
1 CAG CAG CAG CAG CAG CAG CAG CAG C-AG CAG CAG CAG CAG CAG CAG
* * ** ** ** * * *
45071341 CAA CAA CAG CAG CAG TTG CAG TTG CAG CAG CAG TTG CAT CAT CAG CAA
1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG
* * *
45071389 CAA CAG CTG CAG CAG CAG CAG TTA- CAG CAG CAG CAG CCA- CAG CAG
1 CAG CAG CAG CAG CAG CAG CAG -CAG CAG CAG CAG CAG -CAG CAG CAG
45071434 CAG CAG CAG CAG CA
1 CAG CAG CAG CAG CA
45071448 AGAAACAACT
Statistics
Matches: 149, Mismatches: 42, Indels: 12
0.73 0.21 0.06
Matches are distributed among these distances:
2 4 0.03
3 141 0.95
4 4 0.03
ACGTcount: A:0.34, C:0.30, G:0.26, T:0.10
Consensus pattern (3 bp):
CAG
Found at i:45071297 original size:36 final size:36
Alignment explanation
Indices: 45071250--45071342 Score: 150
Period size: 36 Copynumber: 2.6 Consensus size: 36
45071240 ACATGAACCA
* *
45071250 GCAGCAACAGCAGCAGCAGCAGCAGCAGTTGCAATT
1 GCAGCAGCAGCAGCAGCAACAGCAGCAGTTGCAATT
* *
45071286 GCAGCAGCAGCAGCAACAACAGCAGCAGTTGCACTT
1 GCAGCAGCAGCAGCAGCAACAGCAGCAGTTGCAATT
45071322 GCAGCAGCAGCAGCAGCAACA
1 GCAGCAGCAGCAGCAGCAACA
45071343 ACAACAGCAG
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 52 1.00
ACGTcount: A:0.34, C:0.30, G:0.27, T:0.09
Consensus pattern (36 bp):
GCAGCAGCAGCAGCAGCAACAGCAGCAGTTGCAATT
Found at i:45071387 original size:36 final size:36
Alignment explanation
Indices: 45071250--45071373 Score: 149
Period size: 36 Copynumber: 3.3 Consensus size: 36
45071240 ACATGAACCA
* * *
45071250 GCAGCAACAGCAGCAGCAGCAGCAGCAGTTGCAATT
1 GCAGCAGCAGCAGCAACAACAGCAGCAGTTGCAATT
*
45071286 GCAGCAGCAGCAGCAACAACAGCAGCAGTTGCACTT
1 GCAGCAGCAGCAGCAACAACAGCAGCAGTTGCAATT
*
45071322 GCAGCAGCAGCAGCAGCAACAACAACAGCAGCAGTTGCAGTT
1 ---GCAGCAGCAGCAG---CAACAACAGCAGCAGTTGCAATT
45071364 GCAGCAGCAG
1 GCAGCAGCAG
45071374 TTGCATCATC
Statistics
Matches: 77, Mismatches: 5, Indels: 9
0.85 0.05 0.10
Matches are distributed among these distances:
36 32 0.42
39 23 0.30
42 22 0.29
ACGTcount: A:0.34, C:0.29, G:0.27, T:0.10
Consensus pattern (36 bp):
GCAGCAGCAGCAGCAACAACAGCAGCAGTTGCAATT
Found at i:45072679 original size:6 final size:6
Alignment explanation
Indices: 45072668--45072694 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
45072658 GATCGTGATG
45072668 GATGGA GATGGA GATGGA GATGGA GAT
1 GATGGA GATGGA GATGGA GATGGA GAT
45072695 AGAATTGGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.48, T:0.19
Consensus pattern (6 bp):
GATGGA
Found at i:45083496 original size:1 final size:1
Alignment explanation
Indices: 45083490--45083514 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
45083480 TGAGAGGCAG
45083490 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
45083515 GAGACCACAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:45083906 original size:22 final size:24
Alignment explanation
Indices: 45083880--45083927 Score: 82
Period size: 22 Copynumber: 2.1 Consensus size: 24
45083870 TACTGTCCAA
45083880 TTTCTGCATAGCTAAA-TAAT-AT
1 TTTCTGCATAGCTAAATTAATCAT
45083902 TTTCTGCATAGCTAAATTAATCAT
1 TTTCTGCATAGCTAAATTAATCAT
45083926 TT
1 TT
45083928 CATCTATGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 16 0.67
23 4 0.17
24 4 0.17
ACGTcount: A:0.33, C:0.15, G:0.08, T:0.44
Consensus pattern (24 bp):
TTTCTGCATAGCTAAATTAATCAT
Found at i:45087244 original size:29 final size:30
Alignment explanation
Indices: 45087200--45087261 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 30
45087190 TTTTTGTTTA
*
45087200 AAATAATTATGAAAAATATGTATTAAA-CAT
1 AAATAATTATGAAAAATATATA-TAAATCAT
*
45087230 AAATAA-TATGTAAAATATATATAAATCAT
1 AAATAATTATGAAAAATATATATAAATCAT
45087259 AAA
1 AAA
45087262 ATAAAATTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 4 0.14
29 19 0.66
30 6 0.21
ACGTcount: A:0.60, C:0.03, G:0.05, T:0.32
Consensus pattern (30 bp):
AAATAATTATGAAAAATATATATAAATCAT
Found at i:45099748 original size:21 final size:21
Alignment explanation
Indices: 45099718--45099765 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
45099708 AAAATCTCGA
*
45099718 TTCAACTGATTTTTTAGCCAG
1 TTCAATTGATTTTTTAGCCAG
*
45099739 TTCAATTGATTTTTTAGCCGG
1 TTCAATTGATTTTTTAGCCAG
45099760 TTCAAT
1 TTCAAT
45099766 ATGTTCATAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.23, C:0.17, G:0.15, T:0.46
Consensus pattern (21 bp):
TTCAATTGATTTTTTAGCCAG
Found at i:45103733 original size:17 final size:17
Alignment explanation
Indices: 45103711--45103743 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
45103701 CGAAACCCTG
45103711 AGTTTGTTCTGTTTTCT
1 AGTTTGTTCTGTTTTCT
*
45103728 AGTTTGTTCTTTTTTC
1 AGTTTGTTCTGTTTTC
45103744 CTTCTTTTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.06, C:0.12, G:0.15, T:0.67
Consensus pattern (17 bp):
AGTTTGTTCTGTTTTCT
Found at i:45121394 original size:23 final size:22
Alignment explanation
Indices: 45121365--45121410 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 22
45121355 ATGCTTAAAA
45121365 TATTATATTT-TAATTATTTATGT
1 TATTATATTTAT-ATTA-TTATGT
45121388 TATTATATTTATATTATTATGT
1 TATTATATTTATATTATTATGT
45121410 T
1 T
45121411 GTAACATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 7 0.32
23 14 0.64
24 1 0.05
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.65
Consensus pattern (22 bp):
TATTATATTTATATTATTATGT
Found at i:45134820 original size:21 final size:21
Alignment explanation
Indices: 45134796--45134863 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 21
45134786 TTAAATCTAT
*
45134796 TTTAATTATAATTAATTCGGA
1 TTTAATTATAATTAATTCGAA
* * *
45134817 TTTAA-T-TAA-TAAATCTAT
1 TTTAATTATAATTAATTCGAA
45134835 TTTAATTATAATTAATTCGAA
1 TTTAATTATAATTAATTCGAA
*
45134856 TCTAATTA
1 TTTAATTA
45134864 ATTATTGGAT
Statistics
Matches: 36, Mismatches: 8, Indels: 6
0.72 0.16 0.12
Matches are distributed among these distances:
18 10 0.28
19 4 0.11
20 4 0.11
21 18 0.50
ACGTcount: A:0.41, C:0.06, G:0.04, T:0.49
Consensus pattern (21 bp):
TTTAATTATAATTAATTCGAA
Found at i:45134830 original size:39 final size:39
Alignment explanation
Indices: 45134787--45134865 Score: 140
Period size: 39 Copynumber: 2.0 Consensus size: 39
45134777 AGTTTTTCTT
* *
45134787 TAAATCTATTTTAATTATAATTAATTCGGATTTAATTAA
1 TAAATCTATTTTAATTATAATTAATTCGAATCTAATTAA
45134826 TAAATCTATTTTAATTATAATTAATTCGAATCTAATTAA
1 TAAATCTATTTTAATTATAATTAATTCGAATCTAATTAA
45134865 T
1 T
45134866 TATTGGATCA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.42, C:0.06, G:0.04, T:0.48
Consensus pattern (39 bp):
TAAATCTATTTTAATTATAATTAATTCGAATCTAATTAA
Found at i:45136406 original size:13 final size:14
Alignment explanation
Indices: 45136390--45136425 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
45136380 CAATCTCATA
45136390 TCTCAATTTCAA-T
1 TCTCAATTTCAATT
45136403 TCTCAA-TTCAATT
1 TCTCAATTTCAATT
45136416 TCTC-ATTTCA
1 TCTCAATTTCA
45136426 TTCCAATAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 6 0.29
13 15 0.71
ACGTcount: A:0.28, C:0.25, G:0.00, T:0.47
Consensus pattern (14 bp):
TCTCAATTTCAATT
Found at i:45136415 original size:18 final size:19
Alignment explanation
Indices: 45136377--45136417 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
45136367 TGGTTCATGT
45136377 TTTCAATCTCATATCTCAA
1 TTTCAATCTCATATCTCAA
45136396 TTTCAATTCTCA-AT-TCAA
1 TTTCAA-TCTCATATCTCAA
45136414 TTTC
1 TTTC
45136418 TCATTTCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 8 0.38
20 5 0.24
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTCAATCTCATATCTCAA
Found at i:45136607 original size:39 final size:38
Alignment explanation
Indices: 45136540--45136674 Score: 101
Period size: 39 Copynumber: 3.4 Consensus size: 38
45136530 ACCAATATGG
* * *
45136540 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATATTTGA
1 CACCCAGTGCCTCATCGGCTAG-CCGAAGAAATATTTGA
* * * *
45136579 CACCCAGTGTCTCATCGGCCTAGCCGAAGTAA-AGTTGG
1 CACCCAGTGCCTCATCGG-CTAGCCGAAGAAATATTTGA
* * * * *
45136617 TACCCAGTACCTCATCGAATCTATCCGAAGAAATATAGTGA
1 CACCCAGTGCCTCATCG--GCTAGCCGAAGAAATAT-TTGA
*
45136658 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
45136675 ACTCGAGGTC
Statistics
Matches: 73, Mismatches: 18, Indels: 8
0.74 0.18 0.08
Matches are distributed among these distances:
38 18 0.25
39 35 0.48
40 4 0.05
41 16 0.22
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (38 bp):
CACCCAGTGCCTCATCGGCTAGCCGAAGAAATATTTGA
Found at i:45136940 original size:18 final size:19
Alignment explanation
Indices: 45136914--45136952 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
45136904 TTTCAATTCA
45136914 ATTCAAATAATCAATATAT
1 ATTCAAATAATCAATATAT
*
45136933 ATTC-AATATTCAATATAT
1 ATTCAAATAATCAATATAT
45136951 AT
1 AT
45136953 ATCTATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (19 bp):
ATTCAAATAATCAATATAT
Found at i:45138290 original size:12 final size:12
Alignment explanation
Indices: 45138273--45138313 Score: 66
Period size: 12 Copynumber: 3.5 Consensus size: 12
45138263 TTTACTTATT
45138273 TATATAATATAA
1 TATATAATATAA
45138285 TATATAATATAA
1 TATATAATATAA
*
45138297 TA-ATAATTTAA
1 TATATAATATAA
45138308 TATATA
1 TATATA
45138314 TATTTTAACA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
11 10 0.37
12 17 0.63
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
TATATAATATAA
Found at i:45140016 original size:13 final size:13
Alignment explanation
Indices: 45139990--45140056 Score: 82
Period size: 13 Copynumber: 5.2 Consensus size: 13
45139980 CTAGTATGAC
45139990 AATATTTTTAAAA
1 AATATTTTTAAAA
* *
45140003 AATGTTTTTGAAA
1 AATATTTTTAAAA
* * *
45140016 AATGTTGTGAAAA
1 AATATTTTTAAAA
45140029 AATATTTTTAAAA
1 AATATTTTTAAAA
45140042 AATA-TTTTAAAA
1 AATATTTTTAAAA
45140054 AAT
1 AAT
45140057 TTTAGTTTAA
Statistics
Matches: 46, Mismatches: 8, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
12 11 0.24
13 35 0.76
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.42
Consensus pattern (13 bp):
AATATTTTTAAAA
Found at i:45140339 original size:33 final size:30
Alignment explanation
Indices: 45140263--45140347 Score: 86
Period size: 33 Copynumber: 2.8 Consensus size: 30
45140253 TTTTTTAAGC
*
45140263 AATA-AATATT-AATTATTTATAAAATTTA
1 AATATAATATTAAATTATTTTTAAAATTTA
* *
45140291 ATTAGAATATATAAATTATATTTTAAATATTTA
1 AATATAATAT-TAAATTAT-TTTTAAA-ATTTA
45140324 AATATAACTATTAAA-TATTTTTAA
1 AATATAA-TATTAAATTATTTTTAA
45140348 TTAGCATTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
28 3 0.06
29 5 0.11
30 1 0.02
31 12 0.26
32 9 0.19
33 14 0.30
34 3 0.06
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (30 bp):
AATATAATATTAAATTATTTTTAAAATTTA
Found at i:45146814 original size:12 final size:12
Alignment explanation
Indices: 45146797--45146821 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
45146787 ATTCTATGTT
45146797 TGAAAATAAGAA
1 TGAAAATAAGAA
45146809 TGAAAATAAGAA
1 TGAAAATAAGAA
45146821 T
1 T
45146822 ACCATAAAAA
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:0.64, C:0.00, G:0.16, T:0.20
Consensus pattern (12 bp):
TGAAAATAAGAA
Found at i:45149542 original size:6 final size:6
Alignment explanation
Indices: 45149531--45149577 Score: 85
Period size: 6 Copynumber: 7.8 Consensus size: 6
45149521 AGAAATATTC
*
45149531 CCAAAT CCAAAT CCAAAT TCAAAT CCAAAT CCAAAT CCAAAT CCAAA
1 CCAAAT CCAAAT CCAAAT CCAAAT CCAAAT CCAAAT CCAAAT CCAAA
45149578 ACCATATATT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.51, C:0.32, G:0.00, T:0.17
Consensus pattern (6 bp):
CCAAAT
Found at i:45158489 original size:16 final size:15
Alignment explanation
Indices: 45158446--45158491 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 15
45158436 TTTTAAATAG
45158446 TTTAAAAGTATTTTA
1 TTTAAAAGTATTTTA
*
45158461 TTTAACAATTATTTTA
1 TTTAA-AAGTATTTTA
*
45158477 TTTCGAAAGTATTTT
1 TTT-AAAAGTATTTT
45158492 TTATCCCAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
15 5 0.19
16 20 0.77
17 1 0.04
ACGTcount: A:0.35, C:0.04, G:0.07, T:0.54
Consensus pattern (15 bp):
TTTAAAAGTATTTTA
Found at i:45168216 original size:17 final size:17
Alignment explanation
Indices: 45168190--45168222 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
45168180 AAAAAAGAAG
45168190 GAAAAAAGAACAAACTA
1 GAAAAAAGAACAAACTA
*
45168207 GAAAACAGAACAAACT
1 GAAAAAAGAACAAACT
45168223 CAGGGTTTCG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.67, C:0.15, G:0.12, T:0.06
Consensus pattern (17 bp):
GAAAAAAGAACAAACTA
Found at i:45170245 original size:2 final size:2
Alignment explanation
Indices: 45170240--45170275 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
45170230 CCTATAATCT
45170240 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
45170276 TTAATTAAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:45173435 original size:5 final size:5
Alignment explanation
Indices: 45173425--45173468 Score: 58
Period size: 5 Copynumber: 9.2 Consensus size: 5
45173415 GATTATGTTC
45173425 TTATA TTATA TTATTA TTA-A -TATA TTATA TTATA TTATA -TATA T
1 TTATA TTATA TTA-TA TTATA TTATA TTATA TTATA TTATA TTATA T
45173469 ACATAAAACA
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
3 2 0.06
4 6 0.17
5 22 0.63
6 5 0.14
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TTATA
Found at i:45173450 original size:19 final size:19
Alignment explanation
Indices: 45173426--45173468 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
45173416 ATTATGTTCT
45173426 TATATTATATTATTATTA-A
1 TATATTATATTA-TATTATA
45173445 TATATTATATTATATTATA
1 TATATTATATTATATTATA
45173464 TATAT
1 TATAT
45173469 ACATAAAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 5 0.22
19 18 0.78
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TATATTATATTATATTATA
Found at i:45173498 original size:15 final size:15
Alignment explanation
Indices: 45173478--45173519 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
45173468 TACATAAAAC
*
45173478 AAAAGAAAGAATAGA
1 AAAAGAAAGAAAAGA
45173493 AAAAGAAAGAAAAGA
1 AAAAGAAAGAAAAGA
*
45173508 AACAGAATAGAA
1 AAAAGAA-AGAA
45173520 GAGACGAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 20 0.83
16 4 0.17
ACGTcount: A:0.74, C:0.02, G:0.19, T:0.05
Consensus pattern (15 bp):
AAAAGAAAGAAAAGA
Found at i:45173576 original size:4 final size:4
Alignment explanation
Indices: 45173569--45173596 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
45173559 GAGAAGGAAG
45173569 GAAA GAAA GAAA GAAA GAAA GAAA GAAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA
45173597 AAGAAAAAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:45174141 original size:29 final size:30
Alignment explanation
Indices: 45174082--45174139 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
45174072 TCCGAGCTTT
*
45174082 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* *
45174112 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
45174140 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:45174369 original size:13 final size:13
Alignment explanation
Indices: 45174351--45174382 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
45174341 TTTCCAGCAA
45174351 TTATGAATTTATT
1 TTATGAATTTATT
45174364 TTATGAATTTATT
1 TTATGAATTTATT
*
45174377 TGATGA
1 TTATGA
45174383 TGATCTAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:45174590 original size:50 final size:50
Alignment explanation
Indices: 45174484--45174718 Score: 283
Period size: 50 Copynumber: 4.6 Consensus size: 50
45174474 TAAAGAGATG
* *
45174484 CCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATGAGAGGTC
1 CCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CC--GAGA-C--GAGAGGTC
*
45174540 CCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACGAGAGGTC
1 CCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACGAGAGGTC
* * *
45174590 CCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTC
1 CCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACGAGAGGTC
* * * * **
45174640 CCCTATAAGACCATGTCTAGGACATGGCATGGGCACC-ATCACGAGAACATC
1 CCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACGAG-AGGTC
45174691 CCATGTAAGACCATGTCTGGGACATGGC
1 CCATGTAAGACCATGTCTGGGACATGGC
45174719 TTTGGCATGT
Statistics
Matches: 158, Mismatches: 19, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
49 1 0.01
50 90 0.57
51 28 0.18
52 1 0.01
53 3 0.02
55 2 0.01
56 33 0.21
ACGTcount: A:0.26, C:0.25, G:0.29, T:0.20
Consensus pattern (50 bp):
CCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACGAGAGGTC
Found at i:45174665 original size:100 final size:104
Alignment explanation
Indices: 45174484--45174726 Score: 343
Period size: 100 Copynumber: 2.3 Consensus size: 104
45174474 TAAAGAGATG
*
45174484 CCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATGAGAGGTCCCCTGTAAG
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC---AGATCATGAGAGGTCCCCTATAAG
* * **
45174549 ACCATGTCTGGGACATGGCATGGGCACCGA-GACGAG-AGGTC
63 ACCATGTCTAGGACATGGCATGGGCACC-ATCACGAGAACATC
* *
45174590 CCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC-GA-GATGAGAGGTCCCCTATAAGACC
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTATAAGACC
45174652 ATGTCTAGGACATGGCATGGGCACCATCACGAGAACATC
66 ATGTCTAGGACATGGCATGGGCACCATCACGAGAACATC
*
45174691 CCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
45174727 GTTATTATCA
Statistics
Matches: 126, Mismatches: 8, Indels: 10
0.88 0.06 0.07
Matches are distributed among these distances:
99 1 0.01
100 50 0.40
101 39 0.31
105 2 0.02
106 34 0.27
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.21
Consensus pattern (104 bp):
CCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTATAAGACC
ATGTCTAGGACATGGCATGGGCACCATCACGAGAACATC
Found at i:45177316 original size:18 final size:18
Alignment explanation
Indices: 45177295--45177333 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
45177285 ACAATAAAAA
* *
45177295 TAATTTTTTTTATTATTT
1 TAATATTTTTCATTATTT
*
45177313 TAATATTTTTCATTTTTT
1 TAATATTTTTCATTATTT
45177331 TAA
1 TAA
45177334 GAAAACAATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.72
Consensus pattern (18 bp):
TAATATTTTTCATTATTT
Found at i:45179354 original size:2 final size:2
Alignment explanation
Indices: 45179347--45179377 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
45179337 TGAGAAACCC
45179347 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 A
45179378 TTTTTATATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:45188042 original size:26 final size:26
Alignment explanation
Indices: 45188012--45188062 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
45188002 TTCAAAGAAT
*
45188012 TTTGATCTCTGTTGAAAAATAATTCA
1 TTTGATATCTGTTGAAAAATAATTCA
*
45188038 TTTGATATCTGTTGACAAATAATTC
1 TTTGATATCTGTTGAAAAATAATTC
45188063 TTAAAAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.43
Consensus pattern (26 bp):
TTTGATATCTGTTGAAAAATAATTCA
Found at i:45202984 original size:21 final size:21
Alignment explanation
Indices: 45202960--45202999 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
45202950 ATATTTTTTA
*
45202960 AAGTTAAAAGTCAAAACTATT
1 AAGTTAAAAGGCAAAACTATT
45202981 AAGTTAAAAGGCAAAACTA
1 AAGTTAAAAGGCAAAACTA
45203000 CATTATTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.55, C:0.10, G:0.12, T:0.23
Consensus pattern (21 bp):
AAGTTAAAAGGCAAAACTATT
Found at i:45221365 original size:21 final size:22
Alignment explanation
Indices: 45221341--45221413 Score: 71
Period size: 23 Copynumber: 3.4 Consensus size: 22
45221331 TTTAACAAAG
45221341 TTATAATATTTTTTTATAA-TT
1 TTATAATATTTTTTTATAATTT
*
45221362 TTAT-ATA-ATTTTTATAATTTT
1 TTATAATATTTTTTTATAA-TTT
* *
45221383 TTATAATATTTTTCATATTATTT
1 TTATAATATTTTT-TTATAATTT
*
45221406 TTAAAATA
1 TTATAATA
45221414 CAAATTTTAT
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
19 9 0.21
20 3 0.07
21 10 0.24
22 3 0.07
23 13 0.31
24 4 0.10
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (22 bp):
TTATAATATTTTTTTATAATTT
Found at i:45221374 original size:41 final size:43
Alignment explanation
Indices: 45221290--45221375 Score: 108
Period size: 41 Copynumber: 2.0 Consensus size: 43
45221280 ACCTTCAAAA
*
45221290 TAACAAATATATATATATTTCTTTTATAATCTTCATAACTTTT
1 TAACAAATATATATATATTTCTTTTATAATCTTCATAAATTTT
*
45221333 TAACAAAGT-TATA-ATATTT-TTTTATAAT-TTTATATAATTTT
1 TAACAAA-TATATATATATTTCTTTTATAATCTTCATA-AATTTT
45221374 TA
1 TA
45221376 TAATTTTTTA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
40 5 0.13
41 16 0.41
42 6 0.15
43 11 0.28
44 1 0.03
ACGTcount: A:0.38, C:0.07, G:0.01, T:0.53
Consensus pattern (43 bp):
TAACAAATATATATATATTTCTTTTATAATCTTCATAAATTTT
Found at i:45221375 original size:19 final size:18
Alignment explanation
Indices: 45221351--45221492 Score: 82
Period size: 17 Copynumber: 7.7 Consensus size: 18
45221341 TTATAATATT
45221351 TTTTTATAATTTTATATAA
1 TTTTTATAATTTTATA-AA
45221370 TTTTTATAATTTTTTATAATA
1 TTTTTATAA--TTTTATAA-A
45221391 TTTTTCATATTATTTT-TAAA
1 TTTTT-ATA--ATTTTATAAA
* **
45221411 -ATACA-AATTTTATAAA
1 TTTTTATAATTTTATAAA
*
45221427 TTTTCTATAATTTTCA-CAA
1 TTTT-TATAATTTT-ATAAA
* *
45221446 TTTTTA-ATTTATTAT-AT
1 TTTTTATAATT-TTATAAA
*
45221463 TTTTTATAAATTTA-AAA
1 TTTTTATAATTTTATAAA
45221480 TTTTTATAATTTT
1 TTTTTATAATTTT
45221493 TTTTCTATAT
Statistics
Matches: 95, Mismatches: 13, Indels: 32
0.68 0.09 0.23
Matches are distributed among these distances:
15 5 0.05
16 4 0.04
17 29 0.31
18 8 0.08
19 22 0.23
20 3 0.03
21 16 0.17
22 7 0.07
24 1 0.01
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.61
Consensus pattern (18 bp):
TTTTTATAATTTTATAAA
Found at i:45221377 original size:9 final size:9
Alignment explanation
Indices: 45221351--45221493 Score: 76
Period size: 10 Copynumber: 14.6 Consensus size: 9
45221341 TTATAATATT
45221351 TTTTTATAA
1 TTTTTATAA
45221360 TTTTATATAA
1 TTTT-TATAA
45221370 TTTTTATAA
1 TTTTTATAA
45221379 TTTTTTATAATA
1 -TTTTTAT-A-A
45221391 TTTTTCATATTA
1 TTTTT-ATA--A
45221403 TTTTTAAAATACAA
1 TTTTT---AT--AA
*
45221417 ATTTTATAAA
1 TTTTTAT-AA
45221427 TTTTCTATAA
1 TTTT-TATAA
* *
45221437 TTTTCACAA
1 TTTTTATAA
45221446 -TTTT-TAA
1 TTTTTATAA
*
45221453 TTTATTATAT
1 TTT-TTATAA
45221463 TTTTTATAA
1 TTTTTATAA
* *
45221472 -ATTTAAAA
1 TTTTTATAA
45221480 TTTTTATAA
1 TTTTTATAA
45221489 TTTTT
1 TTTTT
45221494 TTTCTATATT
Statistics
Matches: 105, Mismatches: 14, Indels: 30
0.70 0.09 0.20
Matches are distributed among these distances:
7 2 0.02
8 11 0.10
9 30 0.29
10 32 0.30
11 12 0.11
12 10 0.10
14 7 0.07
16 1 0.01
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (9 bp):
TTTTTATAA
Found at i:45221455 original size:35 final size:34
Alignment explanation
Indices: 45221419--45221485 Score: 82
Period size: 35 Copynumber: 2.0 Consensus size: 34
45221409 AAATACAAAT
* *
45221419 TTTA-TAAATTTTCTATAATTTTCACAATTTTTAA
1 TTTATTAAATTTTCTATAAATTT-AAAATTTTTAA
* *
45221453 TTTATTATATTTTTTATAAATTTAAAATTTTTA
1 TTTATTAAATTTTCTATAAATTTAAAATTTTTA
45221486 TAATTTTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
34 13 0.46
35 15 0.54
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (34 bp):
TTTATTAAATTTTCTATAAATTTAAAATTTTTAA
Found at i:45221493 original size:26 final size:25
Alignment explanation
Indices: 45221419--45221493 Score: 69
Period size: 26 Copynumber: 2.8 Consensus size: 25
45221409 AAATACAAAT
* *
45221419 TTTATAAATTTTCTATAATTTTCACAA
1 TTTA-AAATTTT-TATAATTTTTAAAA
** *
45221446 TTTTTAATTTATTATATTTTTTATAAA
1 TTTAAAATTT-TTATAATTTTTA-AAA
45221473 TTTAAAATTTTTATAATTTTT
1 TTTAAAATTTTTATAATTTTT
45221494 TTTCTATATT
Statistics
Matches: 38, Mismatches: 8, Indels: 5
0.75 0.16 0.10
Matches are distributed among these distances:
26 24 0.63
27 14 0.37
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (25 bp):
TTTAAAATTTTTATAATTTTTAAAA
Found at i:45221580 original size:31 final size:31
Alignment explanation
Indices: 45221545--45221604 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 31
45221535 TGTTAAAAAT
*
45221545 TCTTATAAAATAA-TTAAAAACTCAATTAAGA
1 TCTTAAAAAATAATTTAAAAAC-CAATTAAGA
45221576 TCTTAAAAAATAATTTAAAAACCAATTAA
1 TCTTAAAAAATAATTTAAAAACCAATTAA
45221605 ACAGTCACGT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 19 0.70
32 8 0.30
ACGTcount: A:0.57, C:0.10, G:0.02, T:0.32
Consensus pattern (31 bp):
TCTTAAAAAATAATTTAAAAACCAATTAAGA
Found at i:45225418 original size:7 final size:7
Alignment explanation
Indices: 45225408--45225441 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
45225398 CATAATATAT
45225408 AACCTTG
1 AACCTTG
45225415 AACCCTTG
1 AA-CCTTG
45225423 AACCTTG
1 AACCTTG
*
45225430 AGCCTTG
1 AACCTTG
45225437 AACCT
1 AACCT
45225442 AAACATGTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.26, C:0.32, G:0.15, T:0.26
Consensus pattern (7 bp):
AACCTTG
Found at i:45228496 original size:36 final size:36
Alignment explanation
Indices: 45228452--45228523 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
45228442 ATGGCCTGAG
45228452 TGACACTGTACTCTGTCTCAGCCCTGAATTGACGCC
1 TGACACTGTACTCTGTCTCAGCCCTGAATTGACGCC
*
45228488 TGACACTGTACTCTGTCTCAGCCCTGAATTGCCGCC
1 TGACACTGTACTCTGTCTCAGCCCTGAATTGACGCC
45228524 ACAAAGATTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.18, C:0.35, G:0.19, T:0.28
Consensus pattern (36 bp):
TGACACTGTACTCTGTCTCAGCCCTGAATTGACGCC
Found at i:45230740 original size:50 final size:50
Alignment explanation
Indices: 45230665--45230764 Score: 173
Period size: 50 Copynumber: 2.0 Consensus size: 50
45230655 ATCCCAATTT
*
45230665 ACATTAGCATCTACAAAAACAATTAAAAAAATCCACATGTATCCAGTCCA
1 ACATTAGCATCTACAAAAACAATTAAAAAAATCCACATCTATCCAGTCCA
* *
45230715 ACATTAGCATCTGCAAAAACAATTAAAAATATCCACATCTATCCAGTCCA
1 ACATTAGCATCTACAAAAACAATTAAAAAAATCCACATCTATCCAGTCCA
45230765 CCTTGTTGAG
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 47 1.00
ACGTcount: A:0.46, C:0.25, G:0.06, T:0.23
Consensus pattern (50 bp):
ACATTAGCATCTACAAAAACAATTAAAAAAATCCACATCTATCCAGTCCA
Found at i:45235305 original size:137 final size:138
Alignment explanation
Indices: 45235058--45235332 Score: 448
Period size: 137 Copynumber: 2.0 Consensus size: 138
45235048 ACAGCTAAAC
* *
45235058 AAATGAAATCAATTATGGAATGCGTTACATTCAAAATAACAATAAACAAAATATGGATATAACAC
1 AAATGAAATCAATTATGGAATGAGTTACATTCAAAATAACAATAAACAAAAGATGGATATAACAC
* *
45235123 TAGCTACAAAAGTAATGTAACAATATCATGTGGTAACAAGTTCACATGAAAGTG-AGATATGAAA
66 TAACTACAAAAGTAATGTAACAATATCATGTAGTAACAAGTTCACATGAAAGTGCA-ATATGAAA
*
45235187 GATATGCCA
130 GACATGCCA
* *
45235196 AAATGAAATCATTTATGGCATGAGTTACATTCAAAATAACAAT-AACAAAAGATGGATATAACAC
1 AAATGAAATCAATTATGGAATGAGTTACATTCAAAATAACAATAAACAAAAGATGGATATAACAC
45235260 TAACTACAAAAGTAACT-TAACAATATCATGTAGTAACAAGTTCACATGAAAGTGCAATATGAAA
66 TAACTACAAAAGTAA-TGTAACAATATCATGTAGTAACAAGTTCACATGAAAGTGCAATATGAAA
45235324 GACATGCCA
130 GACATGCCA
45235333 TTTTCTGAAA
Statistics
Matches: 128, Mismatches: 7, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
137 86 0.67
138 42 0.33
ACGTcount: A:0.48, C:0.13, G:0.14, T:0.24
Consensus pattern (138 bp):
AAATGAAATCAATTATGGAATGAGTTACATTCAAAATAACAATAAACAAAAGATGGATATAACAC
TAACTACAAAAGTAATGTAACAATATCATGTAGTAACAAGTTCACATGAAAGTGCAATATGAAAG
ACATGCCA
Found at i:45239232 original size:14 final size:15
Alignment explanation
Indices: 45239194--45239254 Score: 61
Period size: 15 Copynumber: 4.0 Consensus size: 15
45239184 TTTAATTATT
* *
45239194 TAAAAATTATAAAATA
1 TAAAAATTACAATA-A
*
45239210 TAAATAATTAAAATAA
1 TAAA-AATTACAATAA
*
45239226 T-AAAATTACTATAA
1 TAAAAATTACAATAA
45239240 TAAAAATTACAATAA
1 TAAAAATTACAATAA
45239255 CGGTGCTACC
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
14 10 0.26
15 14 0.37
16 6 0.16
17 8 0.21
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (15 bp):
TAAAAATTACAATAA
Found at i:45239239 original size:23 final size:23
Alignment explanation
Indices: 45239194--45239246 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
45239184 TTTAATTATT
*
45239194 TAAAAATTATAAAATATAAATAA
1 TAAAAATAATAAAATATAAATAA
* *
45239217 TTAAAATAATAAAAT-TACTATAA
1 TAAAAATAATAAAATATA-AATAA
45239240 TAAAAAT
1 TAAAAAT
45239247 TACAATAACG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
22 2 0.08
23 23 0.92
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (23 bp):
TAAAAATAATAAAATATAAATAA
Found at i:45246422 original size:16 final size:15
Alignment explanation
Indices: 45246401--45246430 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
45246391 AAAATGTGAA
45246401 AAACAAAAAGAAAAAC
1 AAACAAAAA-AAAAAC
45246417 AAACAAAAAAAAAA
1 AAACAAAAAAAAAA
45246431 GCTTACAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.87, C:0.10, G:0.03, T:0.00
Consensus pattern (15 bp):
AAACAAAAAAAAAAC
Found at i:45250953 original size:7 final size:7
Alignment explanation
Indices: 45250941--45250979 Score: 60
Period size: 7 Copynumber: 5.4 Consensus size: 7
45250931 CTTCTTCTTC
45250941 TTTTTGT
1 TTTTTGT
45250948 TTTTTGT
1 TTTTTGT
45250955 TTTTTGT
1 TTTTTGT
*
45250962 TTTTTTT
1 TTTTTGT
45250969 TTTTTGGT
1 TTTTT-GT
45250977 TTT
1 TTT
45250980 GGGTTTAAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
7 25 0.86
8 4 0.14
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (7 bp):
TTTTTGT
Found at i:45251558 original size:19 final size:20
Alignment explanation
Indices: 45251520--45251564 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
45251510 GGTTTTTTTT
* *
45251520 TTAAATTACATATGATAAAA
1 TTAAATTACAAATAATAAAA
45251540 TTAAATT-CAAATAATAAAA
1 TTAAATTACAAATAATAAAA
*
45251559 TAAAAT
1 TTAAAT
45251565 ACATAAACAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.33
Consensus pattern (20 bp):
TTAAATTACAAATAATAAAA
Found at i:45251875 original size:14 final size:14
Alignment explanation
Indices: 45251834--45251877 Score: 79
Period size: 14 Copynumber: 3.1 Consensus size: 14
45251824 GGAAGTGAAA
*
45251834 AAGTAATAGTTAAA
1 AAGTAATAGTTAAG
45251848 AAGTAATAGTTAAG
1 AAGTAATAGTTAAG
45251862 AAGTAATAGTTAAG
1 AAGTAATAGTTAAG
45251876 AA
1 AA
45251878 CAGATATAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.55, C:0.00, G:0.18, T:0.27
Consensus pattern (14 bp):
AAGTAATAGTTAAG
Found at i:45252728 original size:15 final size:16
Alignment explanation
Indices: 45252698--45252728 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
45252688 TTAAGAAGTT
45252698 AATTTAATTATTAATA
1 AATTTAATTATTAATA
45252714 AATTTAATT-TTAATA
1 AATTTAATTATTAATA
45252729 GCCAAATAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
AATTTAATTATTAATA
Found at i:45254629 original size:41 final size:41
Alignment explanation
Indices: 45254561--45254842 Score: 307
Period size: 41 Copynumber: 6.9 Consensus size: 41
45254551 GCGTTTGTCT
* * * * * *
45254561 AAAACGCCACTAAAAGCTAAACTATAGCGGCGTTTTTGGCA
1 AAAACGCCACTAAAAACTGATCAATAGCGGCGTTTTTAGCC
* * *
45254602 AAAACACCACTAAAAACTGGTCAATAGCGGCGTTTTTGGCC
1 AAAACGCCACTAAAAACTGATCAATAGCGGCGTTTTTAGCC
* *
45254643 AAAACGCCACTAAAAACTGGTCAATAGCGGCGTTTTTCGCC
1 AAAACGCCACTAAAAACTGATCAATAGCGGCGTTTTTAGCC
* * * *
45254684 -AAACGCCACTAAAAGCTGATCAATAGCGGCATTTTAATCC
1 AAAACGCCACTAAAAACTGATCAATAGCGGCGTTTTTAGCC
* * * *
45254724 CAAACGCCACTAAAAACTAATCAATTGCGGCGTTTTTATCC
1 AAAACGCCACTAAAAACTGATCAATAGCGGCGTTTTTAGCC
* * *** *
45254765 CAAACGCCACAAAAAACTGATCAATTTTGGCGTTTTTATCC
1 AAAACGCCACTAAAAACTGATCAATAGCGGCGTTTTTAGCC
*
45254806 AAAACGCCACTAAAAACT-AACTAATAGCGGCGTTTTT
1 AAAACGCCACTAAAAACTGATC-AATAGCGGCGTTTTT
45254843 GGTCCAAACG
Statistics
Matches: 209, Mismatches: 30, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
40 36 0.17
41 173 0.83
ACGTcount: A:0.35, C:0.24, G:0.16, T:0.24
Consensus pattern (41 bp):
AAAACGCCACTAAAAACTGATCAATAGCGGCGTTTTTAGCC
Found at i:45254670 original size:82 final size:81
Alignment explanation
Indices: 45254561--45254854 Score: 338
Period size: 82 Copynumber: 3.6 Consensus size: 81
45254551 GCGTTTGTCT
* * * * *
45254561 AAAACGCCACTAAAAGCTAAACTATAGCGGCGTTTTTGGCAAAAACACCACTAAAAACTGGTCAA
1 AAAACGCCACTAAAAACTAAACAATAGCGGCGTTTTTGGC-CAAACGCCACTAAAAACTGATCAA
**
45254626 TAGCGGCGTTTTTGGCC
65 TAGCGGCGTTTTTATCC
*** * *
45254643 AAAACGCCACTAAAAACTGGTCAATAGCGGCGTTTTTCGCCAAACGCCACTAAAAGCTGATCAAT
1 AAAACGCCACTAAAAACTAAACAATAGCGGCGTTTTTGGCCAAACGCCACTAAAAACTGATCAAT
* *
45254708 AGCGGCATTTTAATCC
66 AGCGGCGTTTTTATCC
* * * ** *
45254724 CAAACGCCACTAAAAACTAATCAATTGCGGCGTTTTTATCCCAAACGCCACAAAAAACTGATCAA
1 AAAACGCCACTAAAAACTAAACAATAGCGGCGTTTTT-GGCCAAACGCCACTAAAAACTGATCAA
***
45254789 TTTTGGCGTTTTTATCC
65 TAGCGGCGTTTTTATCC
45254806 AAAACGCCACTAAAAACT-AACTAATAGCGGCGTTTTTGGTCCAAACGCC
1 AAAACGCCACTAAAAACTAAAC-AATAGCGGCGTTTTTGG-CCAAACGCC
45254855 GCAAAAAGTT
Statistics
Matches: 177, Mismatches: 32, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
81 68 0.38
82 109 0.62
ACGTcount: A:0.35, C:0.25, G:0.16, T:0.23
Consensus pattern (81 bp):
AAAACGCCACTAAAAACTAAACAATAGCGGCGTTTTTGGCCAAACGCCACTAAAAACTGATCAAT
AGCGGCGTTTTTATCC
Found at i:45254861 original size:122 final size:123
Alignment explanation
Indices: 45254561--45254854 Score: 337
Period size: 122 Copynumber: 2.4 Consensus size: 123
45254551 GCGTTTGTCT
* * **
45254561 AAAACGCCACTAAAAGCTAAACT-ATAGCGGCGTTTTTGG-CAAAAACACCACTAAAAACTGGTC
1 AAAACGCCACTAAAAGCT-AACTAATAGCGGCGTTTTTGGTC-CAAACGCCACTAAAAACTAATC
* * * *
45254624 AATAGCGGCGTTTTTGGCCAAAACGCCACTAAAAACTGGTCAATAGCGGCGTTTTTCGCC
64 AATAGCGGCGTTTTTAGCCAAAACGCCACAAAAAACTGATCAATAGCGGCGTTTTTAGCC
* * **
45254684 -AAACGCCACTAAAAGCTGA-TCAATAGCGGC-ATTTTAATCCCAAACGCCACTAAAAACTAATC
1 AAAACGCCACTAAAAGCTAACT-AATAGCGGCGTTTTTGGT-CCAAACGCCACTAAAAACTAATC
* * * *** *
45254746 AATTGCGGCGTTTTTATCCCAAACGCCACAAAAAACTGATCAATTTTGGCGTTTTTATCC
64 AATAGCGGCGTTTTTAGCCAAAACGCCACAAAAAACTGATCAATAGCGGCGTTTTTAGCC
*
45254806 AAAACGCCACTAAAAACTAACTAATAGCGGCGTTTTTGGTCCAAACGCC
1 AAAACGCCACTAAAAGCTAACTAATAGCGGCGTTTTTGGTCCAAACGCC
45254855 GCAAAAAGTT
Statistics
Matches: 140, Mismatches: 24, Indels: 14
0.79 0.13 0.08
Matches are distributed among these distances:
120 1 0.01
121 5 0.04
122 92 0.66
123 36 0.26
124 6 0.04
ACGTcount: A:0.35, C:0.25, G:0.16, T:0.23
Consensus pattern (123 bp):
AAAACGCCACTAAAAGCTAACTAATAGCGGCGTTTTTGGTCCAAACGCCACTAAAAACTAATCAA
TAGCGGCGTTTTTAGCCAAAACGCCACAAAAAACTGATCAATAGCGGCGTTTTTAGCC
Found at i:45255943 original size:54 final size:54
Alignment explanation
Indices: 45255877--45255985 Score: 209
Period size: 54 Copynumber: 2.0 Consensus size: 54
45255867 TTTTTAAATT
*
45255877 AAATTCTAATTATAAAATTCGTGAGCACTTTAAAATTTATAGCCTCATGATTAA
1 AAATTATAATTATAAAATTCGTGAGCACTTTAAAATTTATAGCCTCATGATTAA
45255931 AAATTATAATTATAAAATTCGTGAGCACTTTAAAATTTATAGCCTCATGATTAA
1 AAATTATAATTATAAAATTCGTGAGCACTTTAAAATTTATAGCCTCATGATTAA
45255985 A
1 A
45255986 TATTGAAATT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.42, C:0.12, G:0.09, T:0.37
Consensus pattern (54 bp):
AAATTATAATTATAAAATTCGTGAGCACTTTAAAATTTATAGCCTCATGATTAA
Found at i:45260904 original size:23 final size:23
Alignment explanation
Indices: 45260874--45260923 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
45260864 AACATTAATC
45260874 AAATGTATGAATTGCAGCCCTTT
1 AAATGTATGAATTGCAGCCCTTT
45260897 AAATGTATGAATTGCAGCCCTTT
1 AAATGTATGAATTGCAGCCCTTT
45260920 AAAT
1 AAAT
45260924 AAACTTGAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (23 bp):
AAATGTATGAATTGCAGCCCTTT
Found at i:45261469 original size:241 final size:241
Alignment explanation
Indices: 45261046--45261480 Score: 789
Period size: 241 Copynumber: 1.8 Consensus size: 241
45261036 ATGAATTAAT
*
45261046 TTTATTACCATGTAGCTTGCTTGTCCATTAAAATTACAACAATAGCTCACCTTCTCTCCAACCTT
1 TTTATTACCATGTAGCTTGCTTGTCCATTAAAATTACAACAATAGCTCACCTTCTCTCCAACATT
*
45261111 ATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTAACCGGTTGCCTTATATTGAG
66 ATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTAACCGGTTGCCTTATATCGAG
* *
45261176 CTGTAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACATATGATGAATCTTAAAAAATTC
131 CTGTAAGATATAATGGATCCTCCCTAAGTGTAACAACACCACATATGATGAATCTTAAAAAATTC
45261241 AAAAAGACTTGAAAAAAGTTCTATCGAGCTCATTTACTATTGAATA
196 AAAAAGACTTGAAAAAAGTTCTATCGAGCTCATTTACTATTGAATA
*
45261287 TTTATTACCATGTAGCTTGCTTGTCCATTAAAATTACAACAATAGCTGACCTTCTCTCCAACATT
1 TTTATTACCATGTAGCTTGCTTGTCCATTAAAATTACAACAATAGCTCACCTTCTCTCCAACATT
* * *
45261352 TTTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAG
66 ATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTAACCGGTTGCCTTATATCGAG
*
45261417 CTGTAAGATATAATGGATCCTCCCTAAGTGTAACAACACCACGTATGATGAATCTTAAAAAATT
131 CTGTAAGATATAATGGATCCTCCCTAAGTGTAACAACACCACATATGATGAATCTTAAAAAATT
45261481 ACTATATTCA
Statistics
Matches: 185, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
241 185 1.00
ACGTcount: A:0.34, C:0.19, G:0.14, T:0.33
Consensus pattern (241 bp):
TTTATTACCATGTAGCTTGCTTGTCCATTAAAATTACAACAATAGCTCACCTTCTCTCCAACATT
ATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTAACCGGTTGCCTTATATCGAG
CTGTAAGATATAATGGATCCTCCCTAAGTGTAACAACACCACATATGATGAATCTTAAAAAATTC
AAAAAGACTTGAAAAAAGTTCTATCGAGCTCATTTACTATTGAATA
Found at i:45261623 original size:9 final size:9
Alignment explanation
Indices: 45261600--45261736 Score: 130
Period size: 9 Copynumber: 14.6 Consensus size: 9
45261590 ATTGATCATT
*
45261600 ACTTAAATA
1 ACTTACATA
*
45261609 AATTACATA
1 ACTTACATA
45261618 ACTTACATA
1 ACTTACATA
* *
45261627 ACTCATATA
1 ACTTACATA
45261636 ACTTACATA
1 ACTTACATA
*
45261645 ATTTACATAACA
1 ACTTACAT---A
45261657 ACTTACATA
1 ACTTACATA
*
45261666 ACTCACATA
1 ACTTACATA
*
45261675 ACTCACATA
1 ACTTACATA
45261684 ACTTACATA
1 ACTTACATA
*
45261693 ATTTACATA
1 ACTTACATA
*
45261702 ACTCACATA
1 ACTTACATA
*
45261711 ACGTACATAACA
1 ACTTACAT---A
45261723 ACTTACATA
1 ACTTACATA
45261732 ACTTA
1 ACTTA
45261737 ACTAATACAT
Statistics
Matches: 105, Mismatches: 17, Indels: 12
0.78 0.13 0.09
Matches are distributed among these distances:
9 89 0.85
12 16 0.15
ACGTcount: A:0.47, C:0.22, G:0.01, T:0.31
Consensus pattern (9 bp):
ACTTACATA
Found at i:45261685 original size:48 final size:48
Alignment explanation
Indices: 45261611--45261703 Score: 168
Period size: 48 Copynumber: 1.9 Consensus size: 48
45261601 CTTAAATAAA
* *
45261611 TTACATAACTTACATAACTCATATAACTTACATAATTTACATAACAAC
1 TTACATAACTCACATAACTCACATAACTTACATAATTTACATAACAAC
45261659 TTACATAACTCACATAACTCACATAACTTACATAATTTACATAAC
1 TTACATAACTCACATAACTCACATAACTTACATAATTTACATAAC
45261704 TCACATAACG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 43 1.00
ACGTcount: A:0.45, C:0.23, G:0.00, T:0.32
Consensus pattern (48 bp):
TTACATAACTCACATAACTCACATAACTTACATAATTTACATAACAAC
Found at i:45261736 original size:48 final size:46
Alignment explanation
Indices: 45261613--45261721 Score: 150
Period size: 48 Copynumber: 2.3 Consensus size: 46
45261603 TAAATAAATT
* * *
45261613 ACATAACTTACATAACTCATATAACTTACATAATTTACATAACAACTT
1 ACATAACTCACATAACTCACATAACTTACATAATTTACAT-A-AACTC
45261661 ACATAACTCACATAACTCACATAACTTACATAATTTACAT-AACTC
1 ACATAACTCACATAACTCACATAACTTACATAATTTACATAAACTC
45261706 ACATAACGT-ACATAAC
1 ACATAAC-TCACATAAC
45261722 AACTTACATA
Statistics
Matches: 57, Mismatches: 3, Indels: 5
0.88 0.05 0.08
Matches are distributed among these distances:
45 18 0.32
46 1 0.02
48 38 0.67
ACGTcount: A:0.46, C:0.24, G:0.01, T:0.29
Consensus pattern (46 bp):
ACATAACTCACATAACTCACATAACTTACATAATTTACATAAACTC
Found at i:45267785 original size:43 final size:41
Alignment explanation
Indices: 45267738--45267870 Score: 167
Period size: 43 Copynumber: 3.1 Consensus size: 41
45267728 TCTGCCAAAA
** *
45267738 TTAGCGGCGTTTGTAGAAAAAGCGGCGCTAAAAGCCTTGACCT
1 TTAGCGGCGTTT-TCCAAAAA-CGCCGCTAAAAGCCTTGACCT
*
45267781 TTAGCGGCGCTTTTCCCACAAACGCCGCTAAAAGCCTTGACCT
1 TTAGCGGCG-TTTT-CCAAAAACGCCGCTAAAAGCCTTGACCT
*
45267824 TTAGCGGCGTTTTTCCAACAAACGCCGCTAAAAGTCTTGACCT
1 TTAGCGGCG-TTTTCCAA-AAACGCCGCTAAAAGCCTTGACCT
45267867 TTAG
1 TTAG
45267871 AAGCCTTGAC
Statistics
Matches: 80, Mismatches: 7, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
42 3 0.04
43 70 0.88
44 7 0.09
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.26
Consensus pattern (41 bp):
TTAGCGGCGTTTTCCAAAAACGCCGCTAAAAGCCTTGACCT
Found at i:45268727 original size:23 final size:24
Alignment explanation
Indices: 45268693--45268743 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 24
45268683 ATCTTTTATC
* *
45268693 ATAATT-ATTTAAAGTCTATTTTA
1 ATAATTAATTAAAAATCTATTTTA
45268716 ATAATTAATTAAAAAATCTATTTTA
1 ATAATTAATT-AAAAATCTATTTTA
45268741 ATA
1 ATA
45268744 TCTATAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 6 0.25
24 3 0.12
25 15 0.62
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (24 bp):
ATAATTAATTAAAAATCTATTTTA
Found at i:45270360 original size:28 final size:26
Alignment explanation
Indices: 45270317--45270371 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 26
45270307 AAAACAATAT
*
45270317 AAAATATAAAAATTTACTGTTTTTAA
1 AAAATATAAAAATTTAATGTTTTTAA
*
45270343 AAAATATTAGAAATTTTAATGTTTTTAA
1 AAAATA-TA-AAAATTTAATGTTTTTAA
45270371 A
1 A
45270372 TTTTTAGGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 6 0.24
27 2 0.08
28 17 0.68
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (26 bp):
AAAATATAAAAATTTAATGTTTTTAA
Found at i:45270530 original size:25 final size:26
Alignment explanation
Indices: 45270488--45270539 Score: 79
Period size: 25 Copynumber: 2.0 Consensus size: 26
45270478 TTAAACTTTG
* *
45270488 ATTTATAAAATTTTAAAAATATTAAA
1 ATTTATAAAATTTAAAAAATAGTAAA
45270514 ATTTAT-AAATTTAAAAAATAGTAAA
1 ATTTATAAAATTTAAAAAATAGTAAA
45270539 A
1 A
45270540 ATTTGTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 18 0.75
26 6 0.25
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (26 bp):
ATTTATAAAATTTAAAAAATAGTAAA
Found at i:45270540 original size:26 final size:26
Alignment explanation
Indices: 45270488--45270543 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
45270478 TTAAACTTTG
* *
45270488 ATTTATAAAATTTTAAAAATATTAAA
1 ATTTATAAAATTTAAAAAATATAAAA
45270514 ATTTAT-AAATTTAAAAAATAGTAAAA
1 ATTTATAAAATTTAAAAAATA-TAAAA
45270540 ATTT
1 ATTT
45270544 GTTTTTTGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
25 13 0.48
26 14 0.52
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (26 bp):
ATTTATAAAATTTAAAAAATATAAAA
Found at i:45275068 original size:7 final size:7
Alignment explanation
Indices: 45275056--45275082 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
45275046 CGACATTGAC
45275056 TTTAAAA
1 TTTAAAA
45275063 TTTAAAA
1 TTTAAAA
45275070 TTTAAAA
1 TTTAAAA
45275077 TTTAAA
1 TTTAAA
45275083 CACGTGTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
TTTAAAA
Found at i:45276086 original size:18 final size:18
Alignment explanation
Indices: 45276065--45276099 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
45276055 GTAATATTCA
*
45276065 TTTATTCAGTATCAGTCG
1 TTTATTCAGTAACAGTCG
*
45276083 TTTATTCTGTAACAGTC
1 TTTATTCAGTAACAGTC
45276100 AATTATTCAA
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:0.23, C:0.17, G:0.14, T:0.46
Consensus pattern (18 bp):
TTTATTCAGTAACAGTCG
Found at i:45279141 original size:47 final size:47
Alignment explanation
Indices: 45279034--45279224 Score: 186
Period size: 47 Copynumber: 3.9 Consensus size: 47
45279024 AATGTGATTT
* * * *
45279034 CCGTATAAGACCATAGCTGGGCTATGGCTTCGGACAAATGTGATATGTGCTT
1 CCGTATAAGACCATATCTGGGATATGGCATCGG-----TGTGATATGTGCTA
*
45279086 CCGTATAAGACCATATCCGGGATATGGCATCGGTGTGATATGTGCTA
1 CCGTATAAGACCATATCTGGGATATGGCATCGGTGTGATATGTGCTA
* * * *
45279133 CTGTATAAGACCATATTTGGGATATGGCATCAGTGTGATATGTGAT-
1 CCGTATAAGACCATATCTGGGATATGGCATCGGTGTGATATGTGCTA
* ** * *
45279179 CCGTGTAAGACCATGGCTGGGTTATGGCCTCGGTATGTGATATGTG
1 CCGTATAAGACCATATCTGGGATATGGCATCGG--TGTGATATGTG
45279225 ACTATGTGCA
Statistics
Matches: 119, Mismatches: 18, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
46 25 0.21
47 54 0.45
48 11 0.09
52 29 0.24
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.30
Consensus pattern (47 bp):
CCGTATAAGACCATATCTGGGATATGGCATCGGTGTGATATGTGCTA
Found at i:45279257 original size:95 final size:93
Alignment explanation
Indices: 45279072--45279242 Score: 211
Period size: 93 Copynumber: 1.8 Consensus size: 93
45279062 TTCGGACAAA
* *
45279072 TGTGATATGTGCTTCCGTATAAGACCATATCCGGGATATGGCATCGGTGTGATATGTGCTACTGT
1 TGTGATATGTGCATCCGTATAAGACCATAGCCGGGATATGGCATCGGTGTGATATGTGCTACTGT
*
45279137 ATAAGACCATATTTGGGATATGGCATCAG
66 ACAAGACCATATTT-GGATATGGCATCAG
* * * * *
45279166 TGTGATATGTG-ATCCGTGTAAGACCATGGCTGGGTTATGGCCTCGGTATGTGATATGTGACTA-
1 TGTGATATGTGCATCCGTATAAGACCATAGCCGGGATATGGCATCGG--TGTGATATGTG-CTAC
*
45279229 TGTGCAAGACCATA
63 TGTACAAGACCATA
45279243 GTTTTACTAT
Statistics
Matches: 65, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
93 28 0.43
94 11 0.17
95 23 0.35
96 3 0.05
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.32
Consensus pattern (93 bp):
TGTGATATGTGCATCCGTATAAGACCATAGCCGGGATATGGCATCGGTGTGATATGTGCTACTGT
ACAAGACCATATTTGGATATGGCATCAG
Found at i:45288068 original size:3 final size:3
Alignment explanation
Indices: 45288060--45288085 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
45288050 TGATTGGTAC
45288060 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
45288086 GACAACAACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:45291016 original size:47 final size:47
Alignment explanation
Indices: 45290907--45291017 Score: 127
Period size: 47 Copynumber: 2.4 Consensus size: 47
45290897 CCGGGATAAG
* * *
45290907 CACATAGTGCTTCATCGGAATAAATCCGGAACTTTAACATTATAGTA
1 CACATAGTGCTTCATCGGAACAAATCCGAAACTTTAACAGTATAGTA
* * * *
45290954 CATAAAGTACTTCATCGGAACAAATCCGAAACTTTAACAGTAGTCG-A
1 CACATAGTGCTTCATCGGAACAAATCCGAAACTTTAACAGTA-TAGTA
45291001 CACATAGTG-TCTCATCG
1 CACATAGTGCT-TCATCG
45291018 ACTCAATGTC
Statistics
Matches: 52, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
46 1 0.02
47 49 0.94
48 2 0.04
ACGTcount: A:0.36, C:0.22, G:0.15, T:0.27
Consensus pattern (47 bp):
CACATAGTGCTTCATCGGAACAAATCCGAAACTTTAACAGTATAGTA
Found at i:45292520 original size:25 final size:25
Alignment explanation
Indices: 45292480--45292531 Score: 70
Period size: 26 Copynumber: 2.1 Consensus size: 25
45292470 ATATTTTATT
*
45292480 AAATAAAAAAATTT-AAAATATAAA
1 AAATAAAAAAATTTAAAAACATAAA
*
45292504 AAATCAAATAAATTTAAAAACATAAA
1 AAAT-AAAAAAATTTAAAAACATAAA
45292530 AA
1 AA
45292532 CAAATATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 4 0.17
25 9 0.38
26 11 0.46
ACGTcount: A:0.73, C:0.04, G:0.00, T:0.23
Consensus pattern (25 bp):
AAATAAAAAAATTTAAAAACATAAA
Found at i:45298504 original size:50 final size:49
Alignment explanation
Indices: 45298446--45298544 Score: 180
Period size: 50 Copynumber: 2.0 Consensus size: 49
45298436 AAAAAAAAAA
45298446 AACCCAGAAACCTATCATCATGGGGAAAGAGGGGGGGAACTTACTGTGG
1 AACCCAGAAACCTATCATCATGGGGAAAGAGGGGGGGAACTTACTGTGG
*
45298495 NAACCCAGAAACCTATCATCATGGGGAAAGAGTGGGGGAACTTACTGTGG
1 -AACCCAGAAACCTATCATCATGGGGAAAGAGGGGGGGAACTTACTGTGG
45298545 TGTCCCACAT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.32, C:0.18, G:0.31, T:0.17
Consensus pattern (49 bp):
AACCCAGAAACCTATCATCATGGGGAAAGAGGGGGGGAACTTACTGTGG
Found at i:45299011 original size:24 final size:23
Alignment explanation
Indices: 45298964--45299012 Score: 71
Period size: 24 Copynumber: 2.1 Consensus size: 23
45298954 TATATAAGTT
*
45298964 TTAATTTTATATAATTATACATA
1 TTAATTTTATATAAGTATACATA
*
45298987 TTAATTTTAATTTAAGTATACATA
1 TTAATTTT-ATATAAGTATACATA
45299011 TT
1 TT
45299013 TAAAGAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 8 0.35
24 15 0.65
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.53
Consensus pattern (23 bp):
TTAATTTTATATAAGTATACATA
Found at i:45307913 original size:21 final size:21
Alignment explanation
Indices: 45307874--45307913 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
45307864 CGCCCCTCGG
* *
45307874 TTTTTTTTTCCATTGTTTTTC
1 TTTTTCTTTCCATTATTTTTC
*
45307895 TTTTTCTTTCCTTTATTTT
1 TTTTTCTTTCCATTATTTT
45307914 ACTTGCTTTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.05, C:0.15, G:0.03, T:0.78
Consensus pattern (21 bp):
TTTTTCTTTCCATTATTTTTC
Found at i:45314061 original size:53 final size:54
Alignment explanation
Indices: 45313969--45314075 Score: 189
Period size: 53 Copynumber: 2.0 Consensus size: 54
45313959 ATGGGCTTTA
*
45313969 GTGTTGGCAATTATTATTTTTTTCATTGGTGGAGCCTTTTGACATTTTCTACTT
1 GTGTTGGCAATTATTATTTTTTTCATGGGTGGAGCCTTTTGACATTTTCTACTT
*
45314023 GTGTTGGCAATTATT-TTTTTTTCGTGGGTGGAGCCTTTTGACATTTTCTACTT
1 GTGTTGGCAATTATTATTTTTTTCATGGGTGGAGCCTTTTGACATTTTCTACTT
45314076 TTATATTATC
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
53 36 0.71
54 15 0.29
ACGTcount: A:0.15, C:0.13, G:0.21, T:0.51
Consensus pattern (54 bp):
GTGTTGGCAATTATTATTTTTTTCATGGGTGGAGCCTTTTGACATTTTCTACTT
Found at i:45314283 original size:60 final size:60
Alignment explanation
Indices: 45314190--45314309 Score: 231
Period size: 60 Copynumber: 2.0 Consensus size: 60
45314180 ACTGATAATG
45314190 AAGAGCGGCTTCTAGATGGAAGGAAATCAAGGTATACATATTTCTATTGAAGTTGAAAAA
1 AAGAGCGGCTTCTAGATGGAAGGAAATCAAGGTATACATATTTCTATTGAAGTTGAAAAA
*
45314250 AAGAGCGTCTTCTAGATGGAAGGAAATCAAGGTATACATATTTCTATTGAAGTTGAAAAA
1 AAGAGCGGCTTCTAGATGGAAGGAAATCAAGGTATACATATTTCTATTGAAGTTGAAAAA
45314310 GGGATATGAG
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 59 1.00
ACGTcount: A:0.40, C:0.10, G:0.23, T:0.28
Consensus pattern (60 bp):
AAGAGCGGCTTCTAGATGGAAGGAAATCAAGGTATACATATTTCTATTGAAGTTGAAAAA
Found at i:45314295 original size:32 final size:32
Alignment explanation
Indices: 45314199--45314295 Score: 80
Period size: 30 Copynumber: 3.2 Consensus size: 32
45314189 GAAGAGCGGC
45314199 TTCTAGATGGAAGGAAATCAAGGTATACATAT
1 TTCTAGATGGAAGGAAATCAAGGTATACATAT
* * * * * *
45314231 TTCT--ATTGAAGTTGAAA-AAAAG-A-GCGT-C
1 TTCTAGATGGAAG--GAAATCAAGGTATACATAT
45314259 TTCTAGATGGAAGGAAATCAAGGTATACATAT
1 TTCTAGATGGAAGGAAATCAAGGTATACATAT
45314291 TTCTA
1 TTCTA
45314296 TTGAAGTTGA
Statistics
Matches: 45, Mismatches: 12, Indels: 16
0.62 0.16 0.22
Matches are distributed among these distances:
28 8 0.18
29 5 0.11
30 14 0.31
31 5 0.11
32 13 0.29
ACGTcount: A:0.39, C:0.10, G:0.21, T:0.30
Consensus pattern (32 bp):
TTCTAGATGGAAGGAAATCAAGGTATACATAT
Found at i:45320547 original size:14 final size:14
Alignment explanation
Indices: 45320528--45320555 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
45320518 AAATCCTACT
45320528 TAATATGATCGACA
1 TAATATGATCGACA
45320542 TAATATGATCGACA
1 TAATATGATCGACA
45320556 GATGAGATCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (14 bp):
TAATATGATCGACA
Found at i:45324116 original size:22 final size:22
Alignment explanation
Indices: 45324091--45324143 Score: 106
Period size: 22 Copynumber: 2.4 Consensus size: 22
45324081 AAGTTAATTA
45324091 TATTTTTACAAAAATACTTATG
1 TATTTTTACAAAAATACTTATG
45324113 TATTTTTACAAAAATACTTATG
1 TATTTTTACAAAAATACTTATG
45324135 TATTTTTAC
1 TATTTTTAC
45324144 CATTTCTATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.38, C:0.09, G:0.04, T:0.49
Consensus pattern (22 bp):
TATTTTTACAAAAATACTTATG
Found at i:45328977 original size:62 final size:62
Alignment explanation
Indices: 45328901--45329023 Score: 201
Period size: 62 Copynumber: 2.0 Consensus size: 62
45328891 GATAATAATA
*** * *
45328901 ACTCCGTCGATAACAATAACTAATTTTTTAAAACACAATGAAAATTGAATCTCTAATCTCAG
1 ACTCCGTCGATAACAATAACTAATCACTTAAAACACAACGAAAATTAAATCTCTAATCTCAG
45328963 ACTCCGTCGATAACAATAACTAATCACTTAAAACACAACGAAAATTAAATCTCTAATCTCA
1 ACTCCGTCGATAACAATAACTAATCACTTAAAACACAACGAAAATTAAATCTCTAATCTCA
45329024 TAATTAAGAG
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
62 56 1.00
ACGTcount: A:0.44, C:0.22, G:0.07, T:0.28
Consensus pattern (62 bp):
ACTCCGTCGATAACAATAACTAATCACTTAAAACACAACGAAAATTAAATCTCTAATCTCAG
Found at i:45329193 original size:10 final size:10
Alignment explanation
Indices: 45329178--45329220 Score: 54
Period size: 10 Copynumber: 4.4 Consensus size: 10
45329168 GGACTGAATG
45329178 TTATAAATAA
1 TTATAAATAA
45329188 TTATAAATAA
1 TTATAAATAA
*
45329198 -TACAAATAA
1 TTATAAATAA
45329207 TTATATAA-AA
1 TTATA-AATAA
45329217 TTAT
1 TTAT
45329221 GTATGTCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
9 8 0.28
10 19 0.66
11 2 0.07
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (10 bp):
TTATAAATAA
Found at i:45335395 original size:13 final size:13
Alignment explanation
Indices: 45335323--45335394 Score: 101
Period size: 13 Copynumber: 5.5 Consensus size: 13
45335313 TTTAGCAATA
45335323 CTTTTGAAAAGTG
1 CTTTTGAAAAGTG
*
45335336 CTTTTGAAAAATG
1 CTTTTGAAAAGTG
45335349 CTTTTGAAAAGTG
1 CTTTTGAAAAGTG
*
45335362 C-TGTGCAAAAGTG
1 CTTTTG-AAAAGTG
*
45335375 CTTTTGAGAAGTG
1 CTTTTGAAAAGTG
45335388 CTTTTGA
1 CTTTTGA
45335395 GTGTTTAGCA
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
12 3 0.06
13 46 0.88
14 3 0.06
ACGTcount: A:0.29, C:0.10, G:0.24, T:0.38
Consensus pattern (13 bp):
CTTTTGAAAAGTG
Found at i:45339870 original size:21 final size:21
Alignment explanation
Indices: 45339827--45339871 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
45339817 TATTTACATA
*
45339827 TTTAAATATAAATATATGATT
1 TTTAAATATAAATATAAGATT
*
45339848 TTTAAATATGAAATA-AAGTTT
1 TTTAAATAT-AAATATAAGATT
45339869 TTT
1 TTT
45339872 TAAGAGGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (21 bp):
TTTAAATATAAATATAAGATT
Found at i:45341118 original size:31 final size:31
Alignment explanation
Indices: 45341065--45341127 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 31
45341055 AACAAAAAAG
* *
45341065 CCATTTCCCCTCCCCCATTTTCTTTCTTTTT
1 CCATTTCCCCTCCCCCATTTTCTCTCTCTTT
* *
45341096 CCATTT-CCTTCCCCCTTCTTTCTCTCTCTTT
1 CCATTTCCCCTCCCCCAT-TTTCTCTCTCTTT
45341127 C
1 C
45341128 TCTCTCAATC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 9 0.33
31 18 0.67
ACGTcount: A:0.05, C:0.44, G:0.00, T:0.51
Consensus pattern (31 bp):
CCATTTCCCCTCCCCCATTTTCTCTCTCTTT
Found at i:45348432 original size:63 final size:63
Alignment explanation
Indices: 45348333--45348458 Score: 243
Period size: 63 Copynumber: 2.0 Consensus size: 63
45348323 TTCAAACGAC
45348333 TTGATCAATTATAGAAAAGATGATAGCCATTCCTATGAGATTCTTAACAGCCATGAACAGCAT
1 TTGATCAATTATAGAAAAGATGATAGCCATTCCTATGAGATTCTTAACAGCCATGAACAGCAT
*
45348396 TTGATCAATTATAGAAAAGATGATAGCCATTTCTATGAGATTCTTAACAGCCATGAACAGCAT
1 TTGATCAATTATAGAAAAGATGATAGCCATTCCTATGAGATTCTTAACAGCCATGAACAGCAT
45348459 ACCTTCATCC
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 62 1.00
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.29
Consensus pattern (63 bp):
TTGATCAATTATAGAAAAGATGATAGCCATTCCTATGAGATTCTTAACAGCCATGAACAGCAT
Found at i:45357621 original size:17 final size:16
Alignment explanation
Indices: 45357599--45357665 Score: 64
Period size: 17 Copynumber: 4.0 Consensus size: 16
45357589 TAAAAAAGAA
*
45357599 TTAATATGTTCAAAATT
1 TTAATATATT-AAAATT
*
45357616 TTAATATATTTAAATATA
1 TTAATATA-TTAAA-ATT
45357634 TTAAGTATATTAAAATT
1 TTAA-TATATTAAAATT
*
45357651 TTAA-ATTTTAAAATT
1 TTAATATATTAAAATT
45357666 GGTTATACTC
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
15 10 0.23
17 16 0.37
18 13 0.30
19 4 0.09
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.49
Consensus pattern (16 bp):
TTAATATATTAAAATT
Found at i:45357711 original size:17 final size:17
Alignment explanation
Indices: 45357685--45357748 Score: 67
Period size: 17 Copynumber: 3.6 Consensus size: 17
45357675 CAACATTTTC
*
45357685 TTTAACATATTTAAAAT
1 TTTAATATATTTAAAAT
*
45357702 TTTAATATATTTAAAAAA
1 TTTAATATATTT-AAAAT
*
45357720 TTTAACT-TTTTTAAAAT
1 TTTAA-TATATTTAAAAT
45357737 TTTAAATATATT
1 TTT-AATATATT
45357749 AAATATATTT
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
17 19 0.50
18 18 0.47
19 1 0.03
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (17 bp):
TTTAATATATTTAAAAT
Found at i:45357791 original size:9 final size:9
Alignment explanation
Indices: 45357772--45357853 Score: 61
Period size: 9 Copynumber: 9.8 Consensus size: 9
45357762 TCTCTTTACC
45357772 TATTAAAATA
1 TATT-AAATA
45357782 TATTAAATA
1 TATTAAATA
45357791 TATTAAA-A
1 TATTAAATA
*
45357799 T-TTCAATA
1 TATTAAATA
*
45357807 TATTTAA-A
1 TATTAAATA
45357815 -A--AAATA
1 TATTAAATA
*
45357821 TATTGAATA
1 TATTAAATA
45357830 TATTAAA-A
1 TATTAAATA
* *
45357838 TTTTTAATA
1 TATTAAATA
45357847 TATTAAA
1 TATTAAA
45357854 ATTTTAAAAT
Statistics
Matches: 56, Mismatches: 9, Indels: 15
0.70 0.11 0.19
Matches are distributed among these distances:
5 2 0.04
6 1 0.02
7 6 0.11
8 11 0.20
9 32 0.57
10 4 0.07
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (9 bp):
TATTAAATA
Found at i:45357830 original size:39 final size:39
Alignment explanation
Indices: 45357776--45357854 Score: 124
Period size: 39 Copynumber: 2.0 Consensus size: 39
45357766 TTTACCTATT
45357776 AAAATATATTAAATATATTAAAA-TTTCAATATATTTAAA
1 AAAATATATTAAATATATTAAAATTTTCAATATA-TTAAA
* *
45357815 AAAATATATTGAATATATTAAAATTTTTAATATATTAAA
1 AAAATATATTAAATATATTAAAATTTTCAATATATTAAA
45357854 A
1 A
45357855 TTTTAAAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
39 28 0.76
40 9 0.24
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (39 bp):
AAAATATATTAAATATATTAAAATTTTCAATATATTAAA
Found at i:45357848 original size:17 final size:17
Alignment explanation
Indices: 45357772--45357861 Score: 74
Period size: 17 Copynumber: 4.9 Consensus size: 17
45357762 TCTCTTTACC
45357772 TATTAAAATATATTAAATA
1 TATTAAAAT-T-TTAAATA
*
45357791 TATTAAAA-TTTCAATA
1 TATTAAAATTTTAAATA
*
45357807 TATTTAAAAAAATATATTGAATA
1 TA-TT---AAAAT-T-TTAAATA
*
45357830 TATTAAAATTTTTAATA
1 TATTAAAATTTTAAATA
45357847 TATTAAAATTTTAAA
1 TATTAAAATTTTAAA
45357862 ATTGGTTATA
Statistics
Matches: 60, Mismatches: 4, Indels: 16
0.75 0.05 0.20
Matches are distributed among these distances:
16 8 0.13
17 23 0.38
18 1 0.02
19 13 0.22
20 4 0.07
22 3 0.05
23 8 0.13
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (17 bp):
TATTAAAATTTTAAATA
Found at i:45357927 original size:63 final size:63
Alignment explanation
Indices: 45357843--45357966 Score: 187
Period size: 63 Copynumber: 2.0 Consensus size: 63
45357833 TAAAATTTTT
* *
45357843 AATATATTAAAATTTTAAAATTGGTTATAATTAACATTTTTTAATATATTT-ATTTTTAAAAA
1 AATATATCAAAATATTAAAATTGGTTATAATTAACATTTTTTAATATATTTAATTTTTAAAAA
* *
45357905 AATATATCAAATATATTAAAATTGGTTATACTTAACCTTTTTTAATATATTTAAATTTTTAA
1 AATATATCAAA-ATATTAAAATTGGTTATAATTAACATTTTTTAATATATTT-AATTTTTAA
45357967 TATATTTAAA
Statistics
Matches: 55, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
62 10 0.18
63 37 0.67
65 8 0.15
ACGTcount: A:0.44, C:0.04, G:0.03, T:0.49
Consensus pattern (63 bp):
AATATATCAAAATATTAAAATTGGTTATAATTAACATTTTTTAATATATTTAATTTTTAAAAA
Found at i:45357965 original size:17 final size:17
Alignment explanation
Indices: 45357943--45357976 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
45357933 TACTTAACCT
45357943 TTTTTAATATATTTAAA
1 TTTTTAATATATTTAAA
45357960 TTTTTAATATATTTAAA
1 TTTTTAATATATTTAAA
45357977 AAAATTAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TTTTTAATATATTTAAA
Found at i:45357985 original size:35 final size:35
Alignment explanation
Indices: 45357946--45358016 Score: 90
Period size: 36 Copynumber: 2.0 Consensus size: 35
45357936 TTAACCTTTT
*
45357946 TTAA-TATATTTAAATTTTTAATATATTTAAAAAAA
1 TTAATTATATTTAAATTTTAAATATA-TTAAAAAAA
* * *
45357981 TTAATTTTTTTTAAATTTTAAATATATTAAGAAAA
1 TTAATTATATTTAAATTTTAAATATATTAAAAAAA
45358016 T
1 T
45358017 CTTTTTTGTC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
35 13 0.42
36 18 0.58
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (35 bp):
TTAATTATATTTAAATTTTAAATATATTAAAAAAA
Found at i:45358051 original size:13 final size:13
Alignment explanation
Indices: 45358033--45358092 Score: 54
Period size: 13 Copynumber: 4.7 Consensus size: 13
45358023 TGTCTTTACC
45358033 TATTAAATATATA
1 TATTAAATATATA
45358046 TATTAAATATAT-
1 TATTAAATATATA
*
45358058 TA--AAATTTTAATA
1 TATTAAA-TAT-ATA
*
45358071 TATTTAATATATA
1 TATTAAATATATA
*
45358084 TATTTAATA
1 TATTAAATA
45358093 GGTAAAGACA
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
10 3 0.08
11 2 0.05
12 4 0.10
13 26 0.67
14 2 0.05
15 2 0.05
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
TATTAAATATATA
Found at i:45358171 original size:17 final size:17
Alignment explanation
Indices: 45358149--45358182 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
45358139 AATTAATTTT
45358149 TTTAAATATATTAAAAA
1 TTTAAATATATTAAAAA
45358166 TTTAAATATATTAAAAA
1 TTTAAATATATTAAAAA
45358183 AGGTTAAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TTTAAATATATTAAAAA
Found at i:45358238 original size:63 final size:63
Alignment explanation
Indices: 45358159--45358282 Score: 187
Period size: 63 Copynumber: 2.0 Consensus size: 63
45358149 TTTAAATATA
* *
45358159 TTAAAAATTTAAATATATTAAAAAAGGTTAAGTATAACCAATTTTAATATATTTGATATATTTTT
1 TTAAAAA-TTAAATATATTAAAAAAGGTTAAGTATAACCAATTTTAAAAT-TTTAATATATTTTT
* *
45358224 TTAAAAA-TAAATATATTAAAAAATGTTAATTATAACCAATTTTAAAATTTTAATATATT
1 TTAAAAATTAAATATATTAAAAAAGGTTAAGTATAACCAATTTTAAAATTTTAATATATT
45358283 AAAAATTTTA
Statistics
Matches: 55, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
62 10 0.18
63 38 0.69
65 7 0.13
ACGTcount: A:0.49, C:0.03, G:0.04, T:0.44
Consensus pattern (63 bp):
TTAAAAATTAAATATATTAAAAAAGGTTAAGTATAACCAATTTTAAAATTTTAATATATTTTT
Found at i:45358289 original size:17 final size:17
Alignment explanation
Indices: 45358267--45358353 Score: 68
Period size: 17 Copynumber: 4.7 Consensus size: 17
45358257 AACCAATTTT
45358267 AAAATTTTAATATATTA
1 AAAATTTTAATATATTA
45358284 AAAATTTTAATATATTCA
1 AAAATTTTAATATATT-A
*
45358302 ATATATTTTTTTAAATATATT-
1 A-A-A--ATTTT-AATATATTA
*
45358323 GAAATTTTAATATATTTA
1 AAAATTTTAATATA-TTA
*
45358341 ATATATTTTAATA
1 A-AAATTTTAATA
45358354 GGTAAAGAGA
Statistics
Matches: 56, Mismatches: 5, Indels: 16
0.73 0.06 0.21
Matches are distributed among these distances:
16 6 0.11
17 22 0.39
18 2 0.04
19 12 0.21
20 2 0.04
22 4 0.07
23 8 0.14
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (17 bp):
AAAATTTTAATATATTA
Found at i:45358328 original size:39 final size:39
Alignment explanation
Indices: 45358271--45358349 Score: 124
Period size: 39 Copynumber: 2.0 Consensus size: 39
45358261 AATTTTAAAA
45358271 TTTTAATATATTAAAAATTTTAATATATTCAATATATTT
1 TTTTAATATATTAAAAATTTTAATATATTCAATATATTT
* *
45358310 TTTTAAATATATT-GAAATTTTAATATATTTAATATATTT
1 TTTT-AATATATTAAAAATTTTAATATATTCAATATATTT
45358349 T
1 T
45358350 AATAGGTAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
39 29 0.78
40 8 0.22
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (39 bp):
TTTTAATATATTAAAAATTTTAATATATTCAATATATTT
Found at i:45358342 original size:9 final size:9
Alignment explanation
Indices: 45358272--45358353 Score: 61
Period size: 9 Copynumber: 9.8 Consensus size: 9
45358262 ATTTTAAAAT
45358272 TTTAATATA
1 TTTAATATA
* *
45358281 TTAAAAAT-
1 TTTAATATA
45358289 TTTAATATA
1 TTTAATATA
*
45358298 TTCAATATA
1 TTTAATATA
45358307 TTT--T-T-
1 TTTAATATA
*
45358312 TTAAATATA
1 TTTAATATA
*
45358321 TTGAA-AT-
1 TTTAATATA
45358328 TTTAATATA
1 TTTAATATA
45358337 TTTAATATA
1 TTTAATATA
45358346 TTTTAATA
1 -TTTAATA
45358354 GGTAAAGAGA
Statistics
Matches: 56, Mismatches: 9, Indels: 15
0.70 0.11 0.19
Matches are distributed among these distances:
5 2 0.04
6 1 0.02
7 6 0.11
8 11 0.20
9 29 0.52
10 7 0.12
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (9 bp):
TTTAATATA
Found at i:45358434 original size:17 final size:17
Alignment explanation
Indices: 45358377--45358526 Score: 78
Period size: 17 Copynumber: 8.6 Consensus size: 17
45358367 AAATATATTT
45358377 AATATATTTAAAATTTTA
1 AATATA-TTAAAATTTTA
* *
45358395 AA-AAAGTTAAATTTTTTA
1 AATATA-TTAAA-ATTTTA
45358413 AATATATTAAAATTTTA
1 AATATATTAAAATTTTA
* * *
45358430 AATATGTTAAAGAAAATGTTG
1 AATATATT----AAAATTTTA
* *
45358451 AGTATA--ACCAATTTTA
1 AATATATTA-AAATTTTA
45358467 AA-AT-TTAAAATTTT-
1 AATATATTAAAATTTTA
*
45358481 AATATACTTAATATATTTA
1 AATATA-TTAAAAT-TTTA
*
45358500 AATATATTAAAATTTTG
1 AATATATTAAAATTTTA
*
45358517 AACATATTAA
1 AATATATTAA
45358527 TTCTTTTTTA
Statistics
Matches: 99, Mismatches: 19, Indels: 29
0.67 0.13 0.20
Matches are distributed among these distances:
14 2 0.02
15 11 0.11
16 7 0.07
17 37 0.37
18 23 0.23
19 8 0.08
21 11 0.11
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.43
Consensus pattern (17 bp):
AATATATTAAAATTTTA
Found at i:45358439 original size:9 final size:9
Alignment explanation
Indices: 45358367--45358440 Score: 55
Period size: 9 Copynumber: 8.3 Consensus size: 9
45358357 AAAGAGAAAA
45358367 AAATATATTT
1 AAATAT-TTT
45358377 -AATATATTT
1 AAATAT-TTT
45358386 AAA-ATTTT
1 AAATATTTT
* **
45358394 AAAAAAGTT
1 AAATATTTT
*
45358403 AAATTTTTT
1 AAATATTTT
*
45358412 AAATATATT
1 AAATATTTT
45358421 AAA-ATTTT
1 AAATATTTT
*
45358429 AAATATGTT
1 AAATATTTT
45358438 AAA
1 AAA
45358441 GAAAATGTTG
Statistics
Matches: 51, Mismatches: 10, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
8 13 0.25
9 36 0.71
10 2 0.04
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (9 bp):
AAATATTTT
Found at i:45358527 original size:35 final size:33
Alignment explanation
Indices: 45358463--45358527 Score: 87
Period size: 35 Copynumber: 1.9 Consensus size: 33
45358453 TATAACCAAT
*
45358463 TTTAAAATTTAAAATTTTAATATACTTAATATA
1 TTTAAAATTTAAAATTTTAACATACTTAATATA
45358496 TTTAAATATATTAAAATTTTGAACATA-TTAAT
1 TTTAAA-AT-TTAAAATTTT-AACATACTTAAT
45358528 TCTTTTTTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 6 0.21
34 2 0.07
35 15 0.54
36 5 0.18
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.48
Consensus pattern (33 bp):
TTTAAAATTTAAAATTTTAACATACTTAATATA
Found at i:45358900 original size:17 final size:17
Alignment explanation
Indices: 45358864--45358899 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
45358854 ATACATTTTC
45358864 TTTAACATATTTAAAAT
1 TTTAACATATTTAAAAT
*
45358881 TTTAATATATTT-AAAT
1 TTTAACATATTTAAAAT
45358897 TTT
1 TTT
45358900 TTTAAGTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.56
Consensus pattern (17 bp):
TTTAACATATTTAAAAT
Found at i:45359103 original size:34 final size:35
Alignment explanation
Indices: 45359065--45359132 Score: 104
Period size: 34 Copynumber: 2.0 Consensus size: 35
45359055 TTATACTTAA
45359065 AATTTTTTAA-TATATTTAAAATTTT-AATATATTT
1 AATTTTTTAAGT-TATTTAAAATTTTAAATATATTT
*
45359099 AATTTTTTAAGTTTTTTAAAATTTTAAATATATT
1 AATTTTTTAAGTTATTTAAAATTTTAAATATATT
45359133 AAGAAAATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
34 22 0.71
35 9 0.29
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (35 bp):
AATTTTTTAAGTTATTTAAAATTTTAAATATATTT
Found at i:45359134 original size:17 final size:18
Alignment explanation
Indices: 45359019--45359132 Score: 90
Period size: 17 Copynumber: 6.1 Consensus size: 18
45359009 ATTTAGTTTT
*
45359019 TTTAAATATATTAAATATA
1 TTTAAA-ATTTTAAATATA
45359038 -TTAAAATTTTAAATTAGTTA
1 TTTAAAATTTTAAA-TA--TA
*
45359058 TACTTAAAATTTTTTAATATA
1 T--TTAAAA-TTTTAAATATA
45359079 TTTAAAATTTT-AATATA
1 TTTAAAATTTTAAATATA
** * *
45359096 TTTAATTTTTTAAGT-TT
1 TTTAAAATTTTAAATATA
45359113 TTTAAAATTTTAAATATA
1 TTTAAAATTTTAAATATA
45359131 TT
1 TT
45359133 AAGAAAATTT
Statistics
Matches: 76, Mismatches: 10, Indels: 19
0.72 0.10 0.18
Matches are distributed among these distances:
17 35 0.46
18 16 0.21
19 6 0.08
20 2 0.03
21 3 0.04
23 8 0.11
24 6 0.08
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.54
Consensus pattern (18 bp):
TTTAAAATTTTAAATATA
Found at i:45359226 original size:19 final size:20
Alignment explanation
Indices: 45359194--45359232 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
45359184 AATTTTAAAA
*
45359194 TTAATTATACTTAACATTTT
1 TTAATTATACTTAAAATTTT
*
45359214 TTAA-TATATTTAAAATTTT
1 TTAATTATACTTAAAATTTT
45359233 AAAAAAACTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.56
Consensus pattern (20 bp):
TTAATTATACTTAAAATTTT
Found at i:45361842 original size:6 final size:6
Alignment explanation
Indices: 45361828--45361857 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
45361818 ATTCTTTTCA
*
45361828 AAGTTG AAGTAG AAGTAG AAGTAG AAGTAG
1 AAGTAG AAGTAG AAGTAG AAGTAG AAGTAG
45361858 GACAACGTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.47, C:0.00, G:0.33, T:0.20
Consensus pattern (6 bp):
AAGTAG
Found at i:45364977 original size:20 final size:20
Alignment explanation
Indices: 45364952--45364996 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
45364942 CAGTTAATTG
45364952 TGAAGACATCTTTAAACTCT
1 TGAAGACATCTTTAAACTCT
45364972 TGAAGACATCTTTAAACTCT
1 TGAAGACATCTTTAAACTCT
45364992 TGAAG
1 TGAAG
45364997 CAACTCAACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.33
Consensus pattern (20 bp):
TGAAGACATCTTTAAACTCT
Found at i:45372862 original size:23 final size:23
Alignment explanation
Indices: 45372836--45372884 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
45372826 GCTCCAATAT
*
45372836 TAACAACAATGAC-AATAATAGAA
1 TAACAACAATAACAAATAA-AGAA
45372859 TAACAACAATAACAAATAAAGAA
1 TAACAACAATAACAAATAAAGAA
45372882 TAA
1 TAA
45372885 TAATGATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 19 0.79
24 5 0.21
ACGTcount: A:0.65, C:0.12, G:0.06, T:0.16
Consensus pattern (23 bp):
TAACAACAATAACAAATAAAGAA
Found at i:45377853 original size:22 final size:23
Alignment explanation
Indices: 45377813--45377857 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
45377803 TTCTAATCTA
45377813 TAATTTTTATTTATGAAAATTGT
1 TAATTTTTATTTATGAAAATTGT
45377836 TAATTTTT-TTTCAT-AAAATTGT
1 TAATTTTTATTT-ATGAAAATTGT
45377858 GATTCAAACT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 11 0.52
23 10 0.48
ACGTcount: A:0.33, C:0.02, G:0.07, T:0.58
Consensus pattern (23 bp):
TAATTTTTATTTATGAAAATTGT
Found at i:45384502 original size:21 final size:21
Alignment explanation
Indices: 45384477--45384519 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
45384467 AATATATTTT
*
45384477 TATTTAAA-TTTAATTATAAAA
1 TATTTAAACATTAA-TATAAAA
45384498 TATTTAAACATTAATATAAAA
1 TATTTAAACATTAATATAAAA
45384519 T
1 T
45384520 TATATATCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (21 bp):
TATTTAAACATTAATATAAAA
Found at i:45384612 original size:27 final size:28
Alignment explanation
Indices: 45384576--45384634 Score: 77
Period size: 27 Copynumber: 2.1 Consensus size: 28
45384566 AATAGAATTT
45384576 TATATATATTT-AAAATTAATAATATTAA
1 TATATATATTTGAAAA-TAATAATATTAA
* *
45384604 TATAT-TATTTGTAAATATTAATATTAA
1 TATATATATTTGAAAATAATAATATTAA
45384631 TATA
1 TATA
45384635 AAATTGAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 20 0.71
28 8 0.29
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (28 bp):
TATATATATTTGAAAATAATAATATTAA
Found at i:45384930 original size:20 final size:20
Alignment explanation
Indices: 45384907--45385151 Score: 132
Period size: 20 Copynumber: 12.2 Consensus size: 20
45384897 TAACGGTTAC
*
45384907 CAATAATTCTAAGGATTTAT
1 CAATAATTCTAACGATTTAT
45384927 CAATATATT-TAACGATTTAT
1 CAATA-ATTCTAACGATTTAT
* * *
45384947 CAATATTTCTAAGGATATAT
1 CAATAATTCTAACGATTTAT
*
45384967 CAAT-ATATCTAACAATTTGCA-
1 CAATAAT-TCTAACGATTT--AT
* *
45384988 AAAAAATT-TAACGATTTAT
1 CAATAATTCTAACGATTTAT
* * *
45385007 CAATAATTGTAACAATTTAC
1 CAATAATTCTAACGATTTAT
* *
45385027 CAA-AATATCTAACGATTGAC
1 CAATAAT-TCTAACGATTTAT
* * *
45385047 CAATAATTTTAAAGATTTAC
1 CAATAATTCTAACGATTTAT
* *
45385067 CAA-AATTTCTAAAGATTTAC
1 CAATAA-TTCTAACGATTTAT
*
45385087 CAATATATTGT-ACGATTT-T
1 CAATA-ATTCTAACGATTTAT
**
45385106 CCAA-AATTTCTAATAATTTAT
1 -CAATAA-TTCTAACGATTTAT
* *
45385127 CAA-AATATCTAATGATTTAC
1 CAATAAT-TCTAACGATTTAT
45385147 CAATA
1 CAATA
45385152 TTTATGAGAC
Statistics
Matches: 176, Mismatches: 30, Indels: 37
0.72 0.12 0.15
Matches are distributed among these distances:
18 2 0.01
19 19 0.11
20 136 0.77
21 15 0.09
22 4 0.02
ACGTcount: A:0.43, C:0.13, G:0.06, T:0.38
Consensus pattern (20 bp):
CAATAATTCTAACGATTTAT
Done.