Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr3
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: 42799318
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.32
Warning! 891409 characters in sequence are not A, C, G, or T
File 59 of 141
Found at i:17585424 original size:24 final size:24
Alignment explanation
Indices: 17585397--17585448 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
17585387 TTAGTAAGTC
*
17585397 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
17585421 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
17585445 AAAT
1 AAAT
17585449 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:17587395 original size:24 final size:24
Alignment explanation
Indices: 17587368--17587419 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
17587358 TTAGTAAGTC
*
17587368 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
17587392 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
17587416 AAAT
1 AAAT
17587420 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:17588077 original size:16 final size:16
Alignment explanation
Indices: 17588056--17588088 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
17588046 GTGGCAGAAG
17588056 GAAAGCGCACCACGTA
1 GAAAGCGCACCACGTA
17588072 GAAAGCGCACCACGTA
1 GAAAGCGCACCACGTA
17588088 G
1 G
17588089 GACGAGCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.30, G:0.27, T:0.06
Consensus pattern (16 bp):
GAAAGCGCACCACGTA
Found at i:17592643 original size:20 final size:20
Alignment explanation
Indices: 17592618--17592684 Score: 98
Period size: 20 Copynumber: 3.4 Consensus size: 20
17592608 TGTTCCTTTT
*
17592618 ATTTATTCAATAAAATTCTA
1 ATTTATTCAATAAAATTCCA
*
17592638 ATTTATTCAATAAATTTCCA
1 ATTTATTCAATAAAATTCCA
*
17592658 ATTTATTCAATAAATTTCCA
1 ATTTATTCAATAAAATTCCA
*
17592678 TTTTATT
1 ATTTATT
17592685 AAACTTATTT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.39, C:0.12, G:0.00, T:0.49
Consensus pattern (20 bp):
ATTTATTCAATAAAATTCCA
Found at i:17602993 original size:19 final size:18
Alignment explanation
Indices: 17602971--17603011 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 18
17602961 GGCACAAAGA
17602971 TTTGTTTTCCTTTTTTG-TT
1 TTTGTTTT--TTTTTTGCTT
17602990 TTTGTTTTTTTTTTGCTT
1 TTTGTTTTTTTTTTGCTT
17603008 TTTG
1 TTTG
17603012 GTACAAAGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 7 0.33
18 6 0.29
19 8 0.38
ACGTcount: A:0.00, C:0.07, G:0.12, T:0.80
Consensus pattern (18 bp):
TTTGTTTTTTTTTTGCTT
Found at i:17603398 original size:14 final size:14
Alignment explanation
Indices: 17603379--17603408 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
17603369 ATACAATGAA
17603379 GCCAATGACTATTT
1 GCCAATGACTATTT
*
17603393 GCCAATGATTATTT
1 GCCAATGACTATTT
17603407 GC
1 GC
17603409 GTTTTTCATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.37
Consensus pattern (14 bp):
GCCAATGACTATTT
Found at i:17608781 original size:3 final size:3
Alignment explanation
Indices: 17608775--17608826 Score: 68
Period size: 3 Copynumber: 17.0 Consensus size: 3
17608765 AATAATAATA
* * *
17608775 ATT ATT ATT ATT ATT ATT ATA ATT ATT ATT ATT AATA ATA ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT
17608821 ATT ATT
1 ATT ATT
17608827 CATTCACTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
3 42 0.95
4 2 0.05
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:17614171 original size:43 final size:43
Alignment explanation
Indices: 17614101--17614206 Score: 115
Period size: 43 Copynumber: 2.5 Consensus size: 43
17614091 CAATACCAAC
** * ** *
17614101 GTCCCACACGTGGTCTTACATGTAATTACGTAGCGATGCCGCT
1 GTCCCACACAAGGTCTTACATGCAATTACAAAGCGATGCCACT
* **
17614144 GTCCCACACAAGGTCTTAC-TCGCAATTATAAATTGATGCCACT
1 GTCCCACACAAGGTCTTACAT-GCAATTACAAAGCGATGCCACT
17614187 GTCCCACACAAGGTCTTACA
1 GTCCCACACAAGGTCTTACA
17614207 CTGTAACACT
Statistics
Matches: 52, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
42 1 0.02
43 51 0.98
ACGTcount: A:0.26, C:0.29, G:0.18, T:0.26
Consensus pattern (43 bp):
GTCCCACACAAGGTCTTACATGCAATTACAAAGCGATGCCACT
Found at i:17620592 original size:67 final size:67
Alignment explanation
Indices: 17620492--17620777 Score: 258
Period size: 67 Copynumber: 4.3 Consensus size: 67
17620482 CCGTCGTAGG
* * *
17620492 CGAGCTATGGTCTTACACAACAT--ACCATGTGTTTATTGTCCTGGC-GAACTTTTTATGCTGCC
1 CGAGCTATGGTCTTACACAACATACACCA--TGTTTACTGTCCCGGCAG-ACTCTTTATGCTGCC
17620554 ATAGT
63 ATAGT
* * * *
17620559 CGAGCTATGGTCTTACACAACATACACCATGTTTATTGTCCCAGCAGACTCTCTATGTTGCCATA
1 CGAGCTATGGTCTTACACAACATACACCATGTTTACTGTCCCGGCAGACTCTTTATGCTGCCATA
17620624 GT
66 GT
* * * * * * *
17620626 TGAGCTTTGGTCTTACGCAACATACCCCGTGTTTACTCTCCCGACAGACTCTCTT-TGCTGCCAT
1 CGAGCTATGGTCTTACACAACATACACCATGTTTACTGTCCCGGCAGACTCT-TTATGCTGCCAT
*
17620690 AGC
65 AGT
* * * * * ** **
17620693 CGAACTATGATCATACATAACATAC-CTCATGTTTACTATCTTGGTGGACTCTTTATGCTGCCAT
1 CGAGCTATGGTCTTACACAACATACAC-CATGTTTACTGTCCCGGCAGACTCTTTATGCTGCCAT
*
17620757 ATT
65 AGT
*
17620760 CGAGTTATGGTCTTACAC
1 CGAGCTATGGTCTTACAC
17620778 CTTATACCTC
Statistics
Matches: 175, Mismatches: 38, Indels: 12
0.78 0.17 0.05
Matches are distributed among these distances:
66 3 0.02
67 166 0.95
68 2 0.01
69 4 0.02
ACGTcount: A:0.23, C:0.26, G:0.17, T:0.34
Consensus pattern (67 bp):
CGAGCTATGGTCTTACACAACATACACCATGTTTACTGTCCCGGCAGACTCTTTATGCTGCCATA
GT
Found at i:17625682 original size:11 final size:11
Alignment explanation
Indices: 17625666--17625691 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
17625656 TTACAATCTT
17625666 TTTTAAAAATA
1 TTTTAAAAATA
17625677 TTTTAAAAATA
1 TTTTAAAAATA
17625688 TTTT
1 TTTT
17625692 GAATATTTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (11 bp):
TTTTAAAAATA
Found at i:17631293 original size:32 final size:33
Alignment explanation
Indices: 17631257--17631318 Score: 108
Period size: 32 Copynumber: 1.9 Consensus size: 33
17631247 TATTTTTAGG
17631257 GATTGATTAGGATTTTATAGGATA-TTTTATGA
1 GATTGATTAGGATTTTATAGGATACTTTTATGA
*
17631289 GATTGATTAGGATTTTATGGGATACTTTTA
1 GATTGATTAGGATTTTATAGGATACTTTTA
17631319 AAAGGGGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
32 23 0.82
33 5 0.18
ACGTcount: A:0.29, C:0.02, G:0.23, T:0.47
Consensus pattern (33 bp):
GATTGATTAGGATTTTATAGGATACTTTTATGA
Found at i:17632163 original size:21 final size:21
Alignment explanation
Indices: 17632137--17632182 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
17632127 AAATGTAACT
17632137 GACTGGACTAACAGGACATTA
1 GACTGGACTAACAGGACATTA
* * *
17632158 GACTGGACTGACAGGATATTG
1 GACTGGACTAACAGGACATTA
17632179 GACT
1 GACT
17632183 AGATCCAAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.33, C:0.17, G:0.28, T:0.22
Consensus pattern (21 bp):
GACTGGACTAACAGGACATTA
Found at i:17634027 original size:78 final size:78
Alignment explanation
Indices: 17633940--17634173 Score: 450
Period size: 78 Copynumber: 3.0 Consensus size: 78
17633930 ACAGCTTCTA
17633940 AAAGAAACTCAAGAGCAATTCTTGAAGAAAAATTCAAAGAGAATTATTATTAACTCAATAAAACA
1 AAAGAAACTCAAGAGCAATTCTTGAAGAAAAATTCAAAGAGAATTATTATTAACTCAATAAAACA
17634005 TAAATCAATTGTG
66 TAAATCAATTGTG
17634018 AAAGAAACTCAAGAGCAATTCTTGAAGAAAAATTCAAAGAGAATTATTATTAACTCAATAAAACA
1 AAAGAAACTCAAGAGCAATTCTTGAAGAAAAATTCAAAGAGAATTATTATTAACTCAATAAAACA
17634083 TAAATCAATTGTG
66 TAAATCAATTGTG
*
17634096 AAAGAAACTCAAGAGCAATTCTTGAAGAAAAATTCAAAGAGAATTATTATTAACTCAAAAAAACA
1 AAAGAAACTCAAGAGCAATTCTTGAAGAAAAATTCAAAGAGAATTATTATTAACTCAATAAAACA
*
17634161 TAAATAAATTGTG
66 TAAATCAATTGTG
17634174 TGTATAACGG
Statistics
Matches: 154, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
78 154 1.00
ACGTcount: A:0.52, C:0.11, G:0.12, T:0.25
Consensus pattern (78 bp):
AAAGAAACTCAAGAGCAATTCTTGAAGAAAAATTCAAAGAGAATTATTATTAACTCAATAAAACA
TAAATCAATTGTG
Found at i:17637736 original size:33 final size:33
Alignment explanation
Indices: 17637699--17637849 Score: 116
Period size: 33 Copynumber: 4.5 Consensus size: 33
17637689 TACGGTGGTT
*
17637699 TCAGCAGTTAGCAACCACCAATGATTCGGGGAA
1 TCAGCACTTAGCAACCACCAATGATTCGGGGAA
* *
17637732 TCAGCACTTAGCAACCCCCTTCACATTTAAGATACGGTGGAA
1 TCAGCACTTAGCAA-CCAC--CA-A--T--GATTCGG-GGAA
* *
17637774 TCAGCACTTAGCAACCACCAATGAGTCGAGGAA
1 TCAGCACTTAGCAACCACCAATGATTCGGGGAA
* *
17637807 TTAGCACTTAGCAACC-CC-----TTGGGGGAA
1 TCAGCACTTAGCAACCACCAATGATTCGGGGAA
17637834 TCAGCACTTAGCAACC
1 TCAGCACTTAGCAACC
17637850 CCCTTTTTAT
Statistics
Matches: 97, Mismatches: 12, Indels: 24
0.73 0.09 0.18
Matches are distributed among these distances:
27 21 0.22
32 2 0.02
33 32 0.33
34 7 0.07
36 3 0.03
37 1 0.01
38 1 0.01
39 3 0.03
41 9 0.09
42 18 0.19
ACGTcount: A:0.32, C:0.28, G:0.21, T:0.20
Consensus pattern (33 bp):
TCAGCACTTAGCAACCACCAATGATTCGGGGAA
Found at i:17637785 original size:75 final size:75
Alignment explanation
Indices: 17637648--17637824 Score: 264
Period size: 75 Copynumber: 2.3 Consensus size: 75
17637638 TTAACCGTTA
* * * ** *
17637648 TCGGTGGATTCAGCACTTAGCAACCCCTTTCACATTTATGATACGGTGGTTTCAGCAGTTAGCAA
1 TCGG-GGAATCAGCACTTAGCAACCCCCTTCACATTTAAGATACGGTGGAATCAGCACTTAGCAA
*
17637713 CCACCAATGAT
65 CCACCAATGAG
17637724 TCGGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAGATACGGTGGAATCAGCACTTAGCAAC
1 TCGGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAGATACGGTGGAATCAGCACTTAGCAAC
17637789 CACCAATGAG
66 CACCAATGAG
* *
17637799 TCGAGGAATTAGCACTTAGCAACCCC
1 TCGGGGAATCAGCACTTAGCAACCCC
17637825 TTGGGGGAAT
Statistics
Matches: 92, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
75 88 0.96
76 4 0.04
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.24
Consensus pattern (75 bp):
TCGGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAGATACGGTGGAATCAGCACTTAGCAAC
CACCAATGAG
Found at i:17637841 original size:27 final size:31
Alignment explanation
Indices: 17637770--17637851 Score: 100
Period size: 27 Copynumber: 2.7 Consensus size: 31
17637760 AAGATACGGT
17637770 GGAATCAGCACTTAGCAACCACCAATGAGTCGA
1 GGAATCAGCACTTAGCAACC-CCAATGAG-CGA
* *
17637803 GGAATTAGCACTTAGCAACCCC-TTG-G-G-
1 GGAATCAGCACTTAGCAACCCCAATGAGCGA
17637830 GGAATCAGCACTTAGCAACCCC
1 GGAATCAGCACTTAGCAACCCC
17637852 CTTTTTATTC
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
27 21 0.46
28 1 0.02
30 1 0.02
31 2 0.04
32 2 0.04
33 19 0.41
ACGTcount: A:0.32, C:0.29, G:0.22, T:0.17
Consensus pattern (31 bp):
GGAATCAGCACTTAGCAACCCCAATGAGCGA
Found at i:17654083 original size:31 final size:31
Alignment explanation
Indices: 17654045--17654108 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
17654035 AAAACAAAAC
17654045 ACAACAACAATTCCAAGCCTAAAACTAACTA
1 ACAACAACAATTCCAAGCCTAAAACTAACTA
17654076 ACAACAACAATTCCAAGCCTAAAACTAACTA
1 ACAACAACAATTCCAAGCCTAAAACTAACTA
17654107 AC
1 AC
17654109 CCGAAACACG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.52, C:0.30, G:0.03, T:0.16
Consensus pattern (31 bp):
ACAACAACAATTCCAAGCCTAAAACTAACTA
Found at i:17654843 original size:28 final size:28
Alignment explanation
Indices: 17654812--17654868 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
17654802 ACTAAGACAT
17654812 TGGATCAAAACACTAGGAAAGTAAAATG
1 TGGATCAAAACACTAGGAAAGTAAAATG
* *
17654840 TGGATCAAAACATTAGGCAAGTAAAATG
1 TGGATCAAAACACTAGGAAAGTAAAATG
17654868 T
1 T
17654869 AAGTATATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.47, C:0.11, G:0.21, T:0.21
Consensus pattern (28 bp):
TGGATCAAAACACTAGGAAAGTAAAATG
Found at i:17660467 original size:21 final size:21
Alignment explanation
Indices: 17660441--17660511 Score: 56
Period size: 21 Copynumber: 3.4 Consensus size: 21
17660431 CAGAAGCTTG
17660441 AAAGCTAAACAAAAGCTCGTA
1 AAAGCTAAACAAAAGCTCGTA
* **
17660462 AAAGCTGAACTGTAA-CTCG-A
1 AAAGCTAAAC-AAAAGCTCGTA
* *
17660482 AAGAGCTAAACAGAAGCTCATA
1 AA-AGCTAAACAAAAGCTCGTA
*
17660504 AGAGCTAA
1 AAAGCTAA
17660512 TTCACCCAAT
Statistics
Matches: 38, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
20 5 0.13
21 29 0.76
22 4 0.11
ACGTcount: A:0.48, C:0.18, G:0.18, T:0.15
Consensus pattern (21 bp):
AAAGCTAAACAAAAGCTCGTA
Found at i:17663441 original size:2 final size:2
Alignment explanation
Indices: 17663434--17663458 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
17663424 AGAAGATAGA
17663434 GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT G
17663459 CACGTTTGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.52, T:0.48
Consensus pattern (2 bp):
GT
Found at i:17664868 original size:51 final size:51
Alignment explanation
Indices: 17664780--17664921 Score: 149
Period size: 51 Copynumber: 2.8 Consensus size: 51
17664770 CCATGACGAC
* * * * * *
17664780 GGTATATAGCGTAAGACCATGGATGAAAAATGTTATGGTAGTCTAGTATAA
1 GGTATATAGTGTAAGACCATGGATGAAAGACGCTATGGCAATCTAGTATAA
** * * *
17664831 GGTATATAGTGTAAGACCATATATGAAAGACGCTATGGCAATTTGGTATGA
1 GGTATATAGTGTAAGACCATGGATGAAAGACGCTATGGCAATCTAGTATAA
** * *
17664882 GGTACGTAGTGTAAGACCATGGATGAAAGACACCATGGCA
1 GGTATATAGTGTAAGACCATGGATGAAAGACGCTATGGCA
17664922 GCATGGTACA
Statistics
Matches: 74, Mismatches: 17, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
51 74 1.00
ACGTcount: A:0.36, C:0.11, G:0.27, T:0.26
Consensus pattern (51 bp):
GGTATATAGTGTAAGACCATGGATGAAAGACGCTATGGCAATCTAGTATAA
Found at i:17664936 original size:51 final size:51
Alignment explanation
Indices: 17664837--17664936 Score: 119
Period size: 51 Copynumber: 2.0 Consensus size: 51
17664827 ATAAGGTATA
* * * ** **
17664837 TAGTGTAAGACCATATATGAAAGACGCTATGGCAATTTGGTATGAGGTACG
1 TAGTGTAAGACCATAGATGAAAGACACCATGGCAACATGGTACAAGGTACG
* *
17664888 TAGTGTAAGACCATGGATGAAAGACACCATGGCAGCATGGTACAAGGTA
1 TAGTGTAAGACCATAGATGAAAGACACCATGGCAACATGGTACAAGGTA
17664937 TAAGGTATAC
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
51 40 1.00
ACGTcount: A:0.35, C:0.14, G:0.28, T:0.23
Consensus pattern (51 bp):
TAGTGTAAGACCATAGATGAAAGACACCATGGCAACATGGTACAAGGTACG
Found at i:17667816 original size:22 final size:22
Alignment explanation
Indices: 17667773--17667816 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
17667763 GATATTTTAT
* *
17667773 TGTTGTAATTGAGGTGTATAAA
1 TGTTGTAATAGAGATGTATAAA
17667795 TGTTGTTAATAGAGATGT-TAAA
1 TGTTG-TAATAGAGATGTATAAA
17667817 GTGCTACAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.34, C:0.00, G:0.25, T:0.41
Consensus pattern (22 bp):
TGTTGTAATAGAGATGTATAAA
Found at i:17667906 original size:23 final size:23
Alignment explanation
Indices: 17667871--17667923 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 23
17667861 TAAGTATCGC
17667871 AAATTGA-ATTG-TTTAGTTGCTGG
1 AAATTGAGATTGTTTTA-TTGCT-G
17667894 AAATTGAGA-TGTTTTATTGCTG
1 AAATTGAGATTGTTTTATTGCTG
*
17667916 TAATTGAG
1 AAATTGAG
17667924 GTGTATAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
22 8 0.30
23 14 0.52
24 5 0.19
ACGTcount: A:0.28, C:0.04, G:0.25, T:0.43
Consensus pattern (23 bp):
AAATTGAGATTGTTTTATTGCTG
Found at i:17667952 original size:138 final size:138
Alignment explanation
Indices: 17667704--17667967 Score: 467
Period size: 138 Copynumber: 1.9 Consensus size: 138
17667694 TCTGTCTTAA
17667704 GTTGTAAATTGAAGTGTTTTAAGTACTGCAAATTGAATTATTTAGTTGCTGGAAATTGAGATATT
1 GTTGTAAATTGAAGTGTTTTAAGTACTGCAAATTGAATTATTTAGTTGCTGGAAATTGAGATATT
*
17667769 TTATTGTTGTAATTGAGGTGTATAAATGTTGTTAATAGAGATGTTAAAGTGCTACAAATTAAAGT
66 TTATTGCTGTAATTGAGGTGTATAAATGTTGTTAATAGAGATGTTAAAGTGCTACAAATTAAAGT
17667834 GTTTAAAT
131 GTTTAAAT
* *
17667842 GTTGTAAATTGAAGTGTTTTAAGTA-TCGCAAATTGAATTGTTTAGTTGCTGGAAATTGAGATGT
1 GTTGTAAATTGAAGTGTTTTAAGTACT-GCAAATTGAATTATTTAGTTGCTGGAAATTGAGATAT
* *
17667906 TTTATTGCTGTAATTGAGGTGTATAAATGTTGTTAATAGAGATGTTAAAGTGTTGCAAATTA
65 TTTATTGCTGTAATTGAGGTGTATAAATGTTGTTAATAGAGATGTTAAAGTGCTACAAATTA
17667968 CTGAAGCTCT
Statistics
Matches: 120, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
137 1 0.01
138 119 0.99
ACGTcount: A:0.33, C:0.04, G:0.22, T:0.41
Consensus pattern (138 bp):
GTTGTAAATTGAAGTGTTTTAAGTACTGCAAATTGAATTATTTAGTTGCTGGAAATTGAGATATT
TTATTGCTGTAATTGAGGTGTATAAATGTTGTTAATAGAGATGTTAAAGTGCTACAAATTAAAGT
GTTTAAAT
Found at i:17669679 original size:24 final size:25
Alignment explanation
Indices: 17669652--17669734 Score: 65
Period size: 23 Copynumber: 3.6 Consensus size: 25
17669642 TTTATAGTAT
* *
17669652 TATATATTATGATTTT-TT-AATTCA
1 TATATATAATAATTTTATTAAATT-A
17669676 TATA-ATAATAATTTTATTAAA-T-
1 TATATATAATAATTTTATTAAATTA
17669698 TATATAT--T-ATTTTATTAAATTA
1 TATATATAATAATTTTATTAAATTA
*
17669720 TATTTAATAATAATT
1 TATAT-ATAATAATT
17669735 ATGTTAAAAT
Statistics
Matches: 47, Mismatches: 3, Indels: 16
0.71 0.05 0.24
Matches are distributed among these distances:
20 11 0.23
21 2 0.04
22 8 0.17
23 13 0.28
24 7 0.15
25 3 0.06
26 3 0.06
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (25 bp):
TATATATAATAATTTTATTAAATTA
Found at i:17669711 original size:20 final size:19
Alignment explanation
Indices: 17669629--17669722 Score: 71
Period size: 20 Copynumber: 4.4 Consensus size: 19
17669619 AATAAAGTAG
*
17669629 ATTATATATTATTTTTATAGT
1 ATTATATATTATTTTT-TA-A
*
17669650 ATTATATATTATGATTTTTTA
1 ATTATATATTAT--TTTTTAA
17669671 ATTCATATAATAATAATTTTATTAA
1 ATT-ATAT-AT--T-ATTTT-TTAA
17669696 ATTATATATTATTTTATTAA
1 ATTATATATTATTTT-TTAA
17669716 ATTATAT
1 ATTATAT
17669723 TTAATAATAA
Statistics
Matches: 62, Mismatches: 3, Indels: 17
0.76 0.04 0.21
Matches are distributed among these distances:
20 17 0.27
21 16 0.26
22 5 0.08
23 8 0.13
24 7 0.11
25 7 0.11
26 2 0.03
ACGTcount: A:0.39, C:0.01, G:0.02, T:0.57
Consensus pattern (19 bp):
ATTATATATTATTTTTTAA
Found at i:17669800 original size:58 final size:57
Alignment explanation
Indices: 17669692--17669802 Score: 170
Period size: 58 Copynumber: 1.9 Consensus size: 57
17669682 AATAATTTTA
*
17669692 TTAAATTATATATTATTTTATTAAATTATATTTAATAATAATTATGTTAAAATATAG
1 TTAAATTATATATTATTTTATTAAATTATATTTAATAATAATTATATTAAAATATAG
* *
17669749 TTAAATTATTTATTATTTTTATTAAATTATTTTTAATAATAATCT-TATTAAAAT
1 TTAAATTATATATTA-TTTTATTAAATTATATTTAATAATAAT-TATATTAAAAT
17669803 TTAATACCAA
Statistics
Matches: 49, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
57 14 0.29
58 34 0.69
59 1 0.02
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.54
Consensus pattern (57 bp):
TTAAATTATATATTATTTTATTAAATTATATTTAATAATAATTATATTAAAATATAG
Found at i:17669982 original size:16 final size:16
Alignment explanation
Indices: 17669961--17670015 Score: 83
Period size: 16 Copynumber: 3.4 Consensus size: 16
17669951 TGAGTTACTG
*
17669961 ATTACAGCTTTATTCC
1 ATTACAGCTCTATTCC
* *
17669977 ATTACAACTCTATTCA
1 ATTACAGCTCTATTCC
17669993 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCC
17670009 ATTACAG
1 ATTACAG
17670016 TGAACCAAAC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.31, C:0.25, G:0.05, T:0.38
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:17677747 original size:14 final size:14
Alignment explanation
Indices: 17677724--17677757 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
17677714 TACAATCTCC
17677724 AAATAATAACAATA
1 AAATAATAACAATA
*
17677738 AAATAGTAACAATA
1 AAATAATAACAATA
*
17677752 TAATAA
1 AAATAA
17677758 CGAAACGATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.68, C:0.06, G:0.03, T:0.24
Consensus pattern (14 bp):
AAATAATAACAATA
Found at i:17681004 original size:12 final size:11
Alignment explanation
Indices: 17680976--17681005 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
17680966 GATTTTTTAA
17680976 TTTTTAAGAAT
1 TTTTTAAGAAT
17680987 TTTTTAAGAAT
1 TTTTTAAGAAT
17680998 TTATTTAA
1 TT-TTTAA
17681006 TTAAAATTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.72
12 5 0.28
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.57
Consensus pattern (11 bp):
TTTTTAAGAAT
Found at i:17688588 original size:20 final size:19
Alignment explanation
Indices: 17688564--17688612 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
17688554 GGCAAAGTAC
17688564 CGATATCTTGAGAAAGGTAT
1 CGATA-CTTGAGAAAGGTAT
* * *
17688584 TGATACCTTCAGCAAGGTAT
1 CGATA-CTTGAGAAAGGTAT
17688604 CGATACTTG
1 CGATACTTG
17688613 TTAAATTAAA
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
19 3 0.13
20 20 0.87
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (19 bp):
CGATACTTGAGAAAGGTAT
Found at i:17691284 original size:6 final size:6
Alignment explanation
Indices: 17691273--17691301 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
17691263 TATATGTCTA
17691273 TTGTAT TTGTAT TTGTAT TTGTAT TTGTA
1 TTGTAT TTGTAT TTGTAT TTGTAT TTGTA
17691302 ATGGTACACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.00, G:0.17, T:0.66
Consensus pattern (6 bp):
TTGTAT
Found at i:17694645 original size:84 final size:84
Alignment explanation
Indices: 17694504--17694760 Score: 496
Period size: 84 Copynumber: 3.1 Consensus size: 84
17694494 GCAGCAACCC
*
17694504 AATAGTTAAGCACTTACTCCTTCTCCTAGCACAACTAAGTTTAAACCACTCCATTCCTAAGTCTC
1 AATAGTTAAGCACTTACTCATTCTCCTAGCACAACTAAGTTTAAACCACTCCATTCCTAAGTCTC
17694569 TTTCATTTTATTTCAACAG
66 TTTCATTTTATTTCAACAG
17694588 AATAGTTAAGCACTTACTCATTCTCCTAGCACAACTAAGTTTAAACCACTCCATTCCTAAGTCTC
1 AATAGTTAAGCACTTACTCATTCTCCTAGCACAACTAAGTTTAAACCACTCCATTCCTAAGTCTC
17694653 TTTCATTTTATTTCAACAG
66 TTTCATTTTATTTCAACAG
*
17694672 AATAGTTAAGCACTTACTCATTCTCCTAGCACAACTAAGTTTAAACCACTCCATTCCTAAGTCTT
1 AATAGTTAAGCACTTACTCATTCTCCTAGCACAACTAAGTTTAAACCACTCCATTCCTAAGTCTC
17694737 TTTCATTTTATTTCAACAG
66 TTTCATTTTATTTCAACAG
17694756 AATAG
1 AATAG
17694761 GGAAATTACC
Statistics
Matches: 171, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
84 171 1.00
ACGTcount: A:0.31, C:0.26, G:0.07, T:0.36
Consensus pattern (84 bp):
AATAGTTAAGCACTTACTCATTCTCCTAGCACAACTAAGTTTAAACCACTCCATTCCTAAGTCTC
TTTCATTTTATTTCAACAG
Found at i:17700719 original size:3 final size:3
Alignment explanation
Indices: 17700711--17700745 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
17700701 TGTAATATTC
17700711 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
17700746 ATTAAAAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:17702632 original size:14 final size:15
Alignment explanation
Indices: 17702610--17702686 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
17702600 CAATCAAACA
17702610 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
17702624 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
17702639 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
17702659 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
* *
17702673 ACGGAAAAT-ATTTT
1 CCAGAAAATCATTTT
17702687 ACTGGCAATC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 21 0.42
15 15 0.30
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.43, C:0.14, G:0.09, T:0.34
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:17702651 original size:20 final size:20
Alignment explanation
Indices: 17702626--17702665 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
17702616 AATATTTTCC
*
17702626 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
17702646 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
17702666 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:17702671 original size:34 final size:35
Alignment explanation
Indices: 17702614--17702680 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
17702604 CAAACACCAG
*
17702614 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
17702649 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
17702681 TATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:17713948 original size:31 final size:31
Alignment explanation
Indices: 17713873--17713938 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 31
17713863 ATTATTAAAT
*
17713873 TATTCAAAAATTTTCATTTAAGTCATTGGAC
1 TATTCAAAATTTTTCATTTAAGTCATTGGAC
*
17713904 TATTCAAAATTTTTTATTTAAGTCATTAGG-C
1 TATTCAAAATTTTTCATTTAAGTCATT-GGAC
17713935 TATT
1 TATT
17713939 AAGTTTTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
31 30 0.94
32 2 0.06
ACGTcount: A:0.33, C:0.11, G:0.09, T:0.47
Consensus pattern (31 bp):
TATTCAAAATTTTTCATTTAAGTCATTGGAC
Found at i:17715497 original size:22 final size:22
Alignment explanation
Indices: 17715472--17715518 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
17715462 TAGTACAGAT
* * *
17715472 ATAATAGCATAATGGTAGCAAA
1 ATAACAGCAAAATGGCAGCAAA
*
17715494 ATAACAGCAAAATGGCAGTAAA
1 ATAACAGCAAAATGGCAGCAAA
17715516 ATA
1 ATA
17715519 GAAGTAAAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.53, C:0.11, G:0.17, T:0.19
Consensus pattern (22 bp):
ATAACAGCAAAATGGCAGCAAA
Found at i:17743043 original size:6 final size:7
Alignment explanation
Indices: 17743026--17743050 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
17743016 GCAAAAGGAG
17743026 GGGGGAA
1 GGGGGAA
17743033 GGGGGAA
1 GGGGGAA
17743040 GGGGGAA
1 GGGGGAA
17743047 GGGG
1 GGGG
17743051 TTTTGGGTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.76, T:0.00
Consensus pattern (7 bp):
GGGGGAA
Found at i:17745916 original size:21 final size:21
Alignment explanation
Indices: 17745892--17745937 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
17745882 ATTATTGAAT
17745892 AAAATAATAGATTAAAAGAAG
1 AAAATAATAGATTAAAAGAAG
17745913 AAAATAATAGATTAAAAGAAG
1 AAAATAATAGATTAAAAGAAG
17745934 AAAA
1 AAAA
17745938 GGAAAATGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.70, C:0.00, G:0.13, T:0.17
Consensus pattern (21 bp):
AAAATAATAGATTAAAAGAAG
Found at i:17746294 original size:29 final size:29
Alignment explanation
Indices: 17746259--17746316 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
17746249 ATTACTCTTG
17746259 TAATTAGAAGAAATTGTAATTCCCTAGGT
1 TAATTAGAAGAAATTGTAATTCCCTAGGT
17746288 TAATTAGAAGAAATTGTAATTCCCTAGGT
1 TAATTAGAAGAAATTGTAATTCCCTAGGT
17746317 ATGTTTAGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.34
Consensus pattern (29 bp):
TAATTAGAAGAAATTGTAATTCCCTAGGT
Found at i:17747491 original size:112 final size:110
Alignment explanation
Indices: 17747293--17747696 Score: 571
Period size: 112 Copynumber: 3.7 Consensus size: 110
17747283 GAAATTCAAG
* * * * *
17747293 AGGATATTTGGCTATTCGGTTAAATGAGAAAAATCGACACCCAGCACCTTAGGGCACGTTTTCTC
1 AGGATATTTAGCCATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCACGTTTTCTC
*
17747358 GAATTTCCCAAATGCAAAACATTGCCTTATTTCGAAAATTTTTTAA
66 GAATTTCCCAAAAGCAAAACATTGCCTTATTT-GAAAATTTTTTAA
* *
17747404 ACGGATATTTAGCCATTTGGTTGAACGAGAAAAATCGATACCCAGCACCTTAGGGCACGTTCTCT
1 A-GGATATTTAGCCATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCACGTTTTCT
* *
17747469 CGAATTTCCCAAACGCAAAACATTGCCTTATTTGAAAGGTTTTTT-A
65 CGAATTTCCCAAAAGCAAAACATTGCCTTATTTGAAA-ATTTTTTAA
* * * * *
17747515 AGGAT-TTTAAGCCATTTGGTTGAATGAAAAAAATCGACACCCAGTACCTTAAGGCATGTTTTCT
1 AGGATATTT-AGCCATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCACGTTTTCT
* *
17747579 CGAATTT-CCAAAAGCAAAACATTGCCTTATTTTAAAATTTTTGAA
65 CGAATTTCCCAAAAGCAAAACATTGCCTTATTTGAAAATTTTTTAA
* * *
17747624 AGGATATTCAGCTATTTGGTTGAACGAGAAAAATCGACACTCAGCACCTTAGGGCACGTTTTCTC
1 AGGATATTTAGCCATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCACGTTTTCTC
17747689 GAATTTCC
66 GAATTTCC
17747697 TGACAAAACT
Statistics
Matches: 259, Mismatches: 28, Indels: 13
0.86 0.09 0.04
Matches are distributed among these distances:
108 5 0.02
109 91 0.35
110 62 0.24
111 7 0.03
112 94 0.36
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Consensus pattern (110 bp):
AGGATATTTAGCCATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCACGTTTTCTC
GAATTTCCCAAAAGCAAAACATTGCCTTATTTGAAAATTTTTTAA
Found at i:17747644 original size:109 final size:109
Alignment explanation
Indices: 17747293--17747696 Score: 560
Period size: 109 Copynumber: 3.7 Consensus size: 109
17747283 GAAATTCAAG
* * * * *
17747293 AGGATATTTGGCTATTCGGTTAAATGAGAAAAATCGACACCCAGCACCTTAGGGCACGTTTTCTC
1 AGGATATTTAGCCATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCACGTTTTCTC
*
17747358 GAATTTCCCAAATGCAAAACATTGCCTTATTTCGAAAATTTTTTAA
66 GAATTTCCCAAAAGCAAAACATTGCCTTATTT-GAAAA-TTTTTAA
* *
17747404 ACGGATATTTAGCCATTTGGTTGAACGAGAAAAATCGATACCCAGCACCTTAGGGCACGTTCTCT
1 A-GGATATTTAGCCATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCACGTTTTCT
* * *
17747469 CGAATTTCCCAAACGCAAAACATTGCCTTATTTGAAAGGTTTTTTA
65 CGAATTTCCCAAAAGCAAAACATTGCCTTATTTGAAA-ATTTTTAA
* * * * *
17747515 AGGAT-TTTAAGCCATTTGGTTGAATGAAAAAAATCGACACCCAGTACCTTAAGGCATGTTTTCT
1 AGGATATTT-AGCCATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCACGTTTTCT
*
17747579 CGAATTT-CCAAAAGCAAAACATTGCCTTATTTTAAAATTTTTGAA
65 CGAATTTCCCAAAAGCAAAACATTGCCTTATTTGAAAATTTTT-AA
* * *
17747624 AGGATATTCAGCTATTTGGTTGAACGAGAAAAATCGACACTCAGCACCTTAGGGCACGTTTTCTC
1 AGGATATTTAGCCATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCACGTTTTCTC
17747689 GAATTTCC
66 GAATTTCC
17747697 TGACAAAACT
Statistics
Matches: 258, Mismatches: 29, Indels: 13
0.86 0.10 0.04
Matches are distributed among these distances:
108 5 0.02
109 91 0.35
110 62 0.24
111 12 0.05
112 88 0.34
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Consensus pattern (109 bp):
AGGATATTTAGCCATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCACGTTTTCTC
GAATTTCCCAAAAGCAAAACATTGCCTTATTTGAAAATTTTTAA
Found at i:17749685 original size:24 final size:22
Alignment explanation
Indices: 17749657--17749703 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 22
17749647 CATCGACTTT
*
17749657 ATAATATTTAGATTTACAGTTTAA
1 ATAATATATAGATTTA-A-TTTAA
*
17749681 ATAATATATAGCTTTAATTTAA
1 ATAATATATAGATTTAATTTAA
17749703 A
1 A
17749704 AACTTATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 6 0.29
23 1 0.05
24 14 0.67
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (22 bp):
ATAATATATAGATTTAATTTAA
Found at i:17750959 original size:28 final size:28
Alignment explanation
Indices: 17750923--17750979 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
17750913 TAATTTTTTC
* *
17750923 TTTAATCCAATGTGTAATGACTAATTTG
1 TTTAATCCAATGTGAAAGGACTAATTTG
17750951 TTTAATCCAATGTGAAAGGACTAATTTG
1 TTTAATCCAATGTGAAAGGACTAATTTG
17750979 T
1 T
17750980 CTAACTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.33, C:0.11, G:0.16, T:0.40
Consensus pattern (28 bp):
TTTAATCCAATGTGAAAGGACTAATTTG
Found at i:17752143 original size:25 final size:25
Alignment explanation
Indices: 17752109--17752158 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
17752099 AAGCCCAACT
17752109 CCTCAGCCACCGTCACTGCTTGGAG
1 CCTCAGCCACCGTCACTGCTTGGAG
17752134 CCTCAGCCACCGTCACTGCTTGGAG
1 CCTCAGCCACCGTCACTGCTTGGAG
17752159 GCATGTTTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.16, C:0.40, G:0.24, T:0.20
Consensus pattern (25 bp):
CCTCAGCCACCGTCACTGCTTGGAG
Found at i:17758032 original size:60 final size:60
Alignment explanation
Indices: 17757950--17758071 Score: 183
Period size: 60 Copynumber: 2.0 Consensus size: 60
17757940 TGTATGAATA
* * * * *
17757950 TTGTAATTATTTTATAATTAATTTGTTAGTAATTTAGGATTATGTTATAAATTTTTGTGT
1 TTGTAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTAAGCTATAAATTCTTGTGT
17758010 TTGTAATTA-TTTAAAATTTAATTTATTAGTAATTTAGGATTAAGCTATAAATTCTTGTGT
1 TTGTAATTATTTTAAAA-TTAATTTATTAGTAATTTAGGATTAAGCTATAAATTCTTGTGT
17758070 TT
1 TT
17758072 AGTTTAGTAT
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
59 6 0.11
60 50 0.89
ACGTcount: A:0.32, C:0.02, G:0.12, T:0.54
Consensus pattern (60 bp):
TTGTAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTAAGCTATAAATTCTTGTGT
Found at i:17758212 original size:16 final size:15
Alignment explanation
Indices: 17758191--17758225 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
17758181 CATTTCATTC
17758191 TTATATAATGTAACTT
1 TTATATAATGTAA-TT
*
17758207 TTATATTATGTAATT
1 TTATATAATGTAATT
17758222 TTAT
1 TTAT
17758226 TTGATTTTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.34, C:0.03, G:0.06, T:0.57
Consensus pattern (15 bp):
TTATATAATGTAATT
Found at i:17760044 original size:90 final size:90
Alignment explanation
Indices: 17759891--17760173 Score: 548
Period size: 90 Copynumber: 3.1 Consensus size: 90
17759881 AATTGATGTC
17759891 AGCATAATAGAGTACCGATTAAATATATTATAAAATTAAAAAAGCTAAGTAATGTAAAAAGTTAA
1 AGCATAATAGAGTACCGATTAAATATATTATAAAATTAAAAAAGCTAAGTAATGTAAAAAGTTAA
17759956 AGTATGTAGATTAAATCTTAAGTTA
66 AGTATGTAGATTAAATCTTAAGTTA
17759981 AGCATAATAGAGTACCGATTAAATATATTATAAAATTAAAAAAGCTAAGTAATGTAAAAAGTTAA
1 AGCATAATAGAGTACCGATTAAATATATTATAAAATTAAAAAAGCTAAGTAATGTAAAAAGTTAA
17760046 AGTATGTAGATTAAATCTTAAGTTA
66 AGTATGTAGATTAAATCTTAAGTTA
17760071 AGCATAATAGAGTACCGATTAAATATATTATAAAATTAAAAAAGCTAAGTAATGTAAAAAGTTAA
1 AGCATAATAGAGTACCGATTAAATATATTATAAAATTAAAAAAGCTAAGTAATGTAAAAAGTTAA
17760136 AGTATGTAGATTAAATCTTAAGTTTA
66 AGTATGTAGATTAAATCTTAAG-TTA
*
17760162 GGCATAATAGAG
1 AGCATAATAGAG
17760174 GTGTAAGTGT
Statistics
Matches: 191, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
90 177 0.93
91 14 0.07
ACGTcount: A:0.49, C:0.06, G:0.14, T:0.31
Consensus pattern (90 bp):
AGCATAATAGAGTACCGATTAAATATATTATAAAATTAAAAAAGCTAAGTAATGTAAAAAGTTAA
AGTATGTAGATTAAATCTTAAGTTA
Found at i:17785744 original size:25 final size:25
Alignment explanation
Indices: 17785690--17785772 Score: 71
Period size: 25 Copynumber: 3.3 Consensus size: 25
17785680 TTCATGTACA
17785690 GGTATGCTCA-TGCGAGCTGT-GAATC
1 GGTATGCTCACT-CGAGCTGTAG-ATC
* *
17785715 AGTATGCTCACTCGAACTGTAGATC
1 GGTATGCTCACTCGAGCTGTAGATC
* * * * *
17785740 GGTATTCTCTCACGAGCTATAAATC
1 GGTATGCTCACTCGAGCTGTAGATC
17785765 GGTATGCT
1 GGTATGCT
17785773 TACATGAGCT
Statistics
Matches: 46, Mismatches: 10, Indels: 4
0.77 0.17 0.07
Matches are distributed among these distances:
25 44 0.96
26 2 0.04
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.30
Consensus pattern (25 bp):
GGTATGCTCACTCGAGCTGTAGATC
Found at i:17796146 original size:36 final size:35
Alignment explanation
Indices: 17796099--17796171 Score: 101
Period size: 36 Copynumber: 2.1 Consensus size: 35
17796089 AATCCGAGAG
* * *
17796099 GGAAAGAGCACTGTAAGGCTATTACTCTCAGGAGT
1 GGAAAGAGCACTGTAAAGCCATCACTCTCAGGAGT
*
17796134 NGGAAAGAGCACTGTAAAGCCATCACTCTTAGGAGT
1 -GGAAAGAGCACTGTAAAGCCATCACTCTCAGGAGT
17796170 GG
1 GG
17796172 TAAACAAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
35 2 0.06
36 31 0.94
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (35 bp):
GGAAAGAGCACTGTAAAGCCATCACTCTCAGGAGT
Found at i:17809068 original size:24 final size:25
Alignment explanation
Indices: 17809041--17809217 Score: 77
Period size: 25 Copynumber: 7.1 Consensus size: 25
17809031 AGATCTTTCA
*
17809041 AGCCATAATCAGGAAGCTCAT-GTG
1 AGCCATAATCAGGAAGCTCATAGAG
* *
17809065 AGCCA-ATATCGGGAAGCTAATGAGAG
1 AGCCATA-ATCAGGAAGCTCAT-AGAG
* *
17809091 AGCCTTAAATCAGGAAGCTCGTA-AG
1 AGCCAT-AATCAGGAAGCTCATAGAG
* * *
17809116 AGCCATATGTCGGGATGCTCATA-AG
1 AGCCATA-ATCAGGAAGCTCATAGAG
* * **
17809141 AGCTA-AATGACGGGAAGCTTGT-GAG
1 AGCCATAAT--CAGGAAGCTCATAGAG
*
17809166 AGCCAAATATC-GAGAAGCTCA-AGAG
1 AGCCATA-ATCAG-GAAGCTCATAGAG
*
17809191 AGCCA-ATATCAGGATGCTCAT-GAG
1 AGCCATA-ATCAGGAAGCTCATAGAG
17809215 AGC
1 AGC
17809218 TAAAAACGGG
Statistics
Matches: 117, Mismatches: 21, Indels: 30
0.70 0.12 0.18
Matches are distributed among these distances:
23 2 0.02
24 38 0.32
25 55 0.47
26 8 0.07
27 13 0.11
28 1 0.01
ACGTcount: A:0.35, C:0.19, G:0.28, T:0.19
Consensus pattern (25 bp):
AGCCATAATCAGGAAGCTCATAGAG
Found at i:17809135 original size:25 final size:25
Alignment explanation
Indices: 17809103--17809173 Score: 79
Period size: 25 Copynumber: 2.8 Consensus size: 25
17809093 CCTTAAATCA
* *
17809103 GGAAGCTCGTAAGAGCCATATGTCG
1 GGAAGCTCGTAAGAGCCAAATGACG
* * *
17809128 GGATGCTCATAAGAGCTAAATGACG
1 GGAAGCTCGTAAGAGCCAAATGACG
* *
17809153 GGAAGCTTGTGAGAGCCAAAT
1 GGAAGCTCGTAAGAGCCAAAT
17809174 ATCGAGAAGC
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.32, C:0.17, G:0.31, T:0.20
Consensus pattern (25 bp):
GGAAGCTCGTAAGAGCCAAATGACG
Found at i:17809191 original size:25 final size:24
Alignment explanation
Indices: 17809163--17809217 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 24
17809153 GGAAGCTTGT
17809163 GAGAGCCAAATATC-GAGAAGCTCAA
1 GAGAGCC-AATATCAG-GAAGCTCAA
* *
17809188 GAGAGCCAATATCAGGATGCTCAT
1 GAGAGCCAATATCAGGAAGCTCAA
17809212 GAGAGC
1 GAGAGC
17809218 TAAAAACGGG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 19 0.70
25 8 0.30
ACGTcount: A:0.38, C:0.20, G:0.27, T:0.15
Consensus pattern (24 bp):
GAGAGCCAATATCAGGAAGCTCAA
Found at i:17817054 original size:25 final size:25
Alignment explanation
Indices: 17817026--17817073 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
17817016 AGTCATACGT
* *
17817026 CGGGATGCTCATAAGAGCTAAATGA
1 CGGGAAGCTCATAAGAGCCAAATGA
* *
17817051 CGGGAAGCTTATGAGAGCCAAAT
1 CGGGAAGCTCATAAGAGCCAAAT
17817074 ATCGAGAAGC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.35, C:0.17, G:0.29, T:0.19
Consensus pattern (25 bp):
CGGGAAGCTCATAAGAGCCAAATGA
Found at i:17832790 original size:80 final size:79
Alignment explanation
Indices: 17832645--17832816 Score: 188
Period size: 80 Copynumber: 2.2 Consensus size: 79
17832635 ATGTCTGGGC
* **
17832645 TAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTTGTGCGAG
1 TAAGTCCCGAAGGCTTTGTGCTAAGTGACCATAACCGGACTAAGATCCGAAGGCATTTGAACGAG
17832710 TTA-CTAAATCCGGGT
66 -TAGCTAAATCC-GGT
* * * * *
17832725 TAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAACCGGGCTATG-TCCCGAAGGCATTTGAACG
1 TAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAACCGGACTAAGAT-CCGAAGGCATTTGAACG
*
17832788 AGTAGCTATATCCGGT
64 AGTAGCTAAATCCGGT
* *
17832804 TAAATTCCGAAGG
1 TAAGTCCCGAAGG
17832817 TACGTGATTT
Statistics
Matches: 78, Mismatches: 11, Indels: 7
0.81 0.11 0.07
Matches are distributed among these distances:
79 17 0.22
80 54 0.69
81 7 0.09
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.26
Consensus pattern (79 bp):
TAAGTCCCGAAGGCTTTGTGCTAAGTGACCATAACCGGACTAAGATCCGAAGGCATTTGAACGAG
TAGCTAAATCCGGT
Found at i:17832797 original size:40 final size:40
Alignment explanation
Indices: 17832641--17832783 Score: 175
Period size: 40 Copynumber: 3.6 Consensus size: 40
17832631 AATGATGTCT
* * * *
17832641 GGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAACC
*
17832681 GGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTA-AATCC
1 GGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATAA-CC
*
17832721 GGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACC
*
17832761 GGGCTATGTCCCGAAGGCATTTG
1 GGGCTAAGTCCCGAAGGCATTTG
17832784 AACGAGTAGC
Statistics
Matches: 89, Mismatches: 9, Indels: 10
0.82 0.08 0.09
Matches are distributed among these distances:
39 2 0.02
40 77 0.87
41 10 0.11
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACC
Found at i:17835735 original size:19 final size:18
Alignment explanation
Indices: 17835711--17835776 Score: 60
Period size: 19 Copynumber: 3.4 Consensus size: 18
17835701 ATCCCTAATC
17835711 GTACTTGCGTGCCCCTATT
1 GTACTT-CGTGCCCCTATT
* * *
17835730 GTACTTCGGTACCCATAATC
1 GTACTTC-GTGCCCCT-ATT
*
17835750 GCACTTACGTGCCCCTATT
1 GTACTT-CGTGCCCCTATT
17835769 GTACTTCG
1 GTACTTCG
17835777 GTACTCTTGA
Statistics
Matches: 36, Mismatches: 8, Indels: 7
0.71 0.16 0.14
Matches are distributed among these distances:
18 3 0.08
19 19 0.53
20 13 0.36
21 1 0.03
ACGTcount: A:0.17, C:0.32, G:0.18, T:0.33
Consensus pattern (18 bp):
GTACTTCGTGCCCCTATT
Found at i:17835761 original size:39 final size:39
Alignment explanation
Indices: 17835706--17835780 Score: 132
Period size: 39 Copynumber: 1.9 Consensus size: 39
17835696 ATTATATCCC
* *
17835706 TAATCGTACTTGCGTGCCCCTATTGTACTTCGGTACCCA
1 TAATCGCACTTACGTGCCCCTATTGTACTTCGGTACCCA
17835745 TAATCGCACTTACGTGCCCCTATTGTACTTCGGTAC
1 TAATCGCACTTACGTGCCCCTATTGTACTTCGGTAC
17835781 TCTTGATAGC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.19, C:0.31, G:0.17, T:0.33
Consensus pattern (39 bp):
TAATCGCACTTACGTGCCCCTATTGTACTTCGGTACCCA
Found at i:17835793 original size:39 final size:39
Alignment explanation
Indices: 17835713--17835794 Score: 119
Period size: 39 Copynumber: 2.1 Consensus size: 39
17835703 CCCTAATCGT
* *
17835713 ACTTGCGTGCCCCTATTGTACTTCGGTACCCATAATCGC
1 ACTTACGTGCCCCTATTGTACTTCGGTACCCATAATAGC
* * *
17835752 ACTTACGTGCCCCTATTGTACTTCGGTACTCTTGATAGC
1 ACTTACGTGCCCCTATTGTACTTCGGTACCCATAATAGC
17835791 ACTT
1 ACTT
17835795 CTGTACCATG
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.18, C:0.30, G:0.17, T:0.34
Consensus pattern (39 bp):
ACTTACGTGCCCCTATTGTACTTCGGTACCCATAATAGC
Found at i:17839584 original size:31 final size:28
Alignment explanation
Indices: 17839524--17839586 Score: 72
Period size: 28 Copynumber: 2.1 Consensus size: 28
17839514 TTAATTTTCG
* *
17839524 AGTTTGGGGAAAAATGTAATTATGCAAA
1 AGTTTAGGGAAAAATATAATTATGCAAA
*
17839552 AGTTTAGGGACAAAATTATAATTTTGACAAA
1 AGTTTAGGGA-AAAA-TATAATTATG-CAAA
17839583 AGTT
1 AGTT
17839587 GAGTTGAAGC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
28 9 0.31
29 4 0.14
30 8 0.28
31 8 0.28
ACGTcount: A:0.43, C:0.05, G:0.21, T:0.32
Consensus pattern (28 bp):
AGTTTAGGGAAAAATATAATTATGCAAA
Found at i:17840118 original size:51 final size:50
Alignment explanation
Indices: 17840055--17840439 Score: 387
Period size: 51 Copynumber: 7.6 Consensus size: 50
17840045 ATTGATGAAT
* * * *
17840055 ACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAATAATGGTC
1 ACGTGTGTAGTACTATGTGAAGGCTACTATGTGTACCGATAAAT-TTGGTC
* * * * * * *
17840106 ACATGTGTAGTACTAAGTGAAGGCTACAATATGTACCTAGAAGCTTTGGTC
1 ACGTGTGTAGTACTATGTGAAGGCTACTATGTGTACCGATAA-ATTTGGTC
* * * * * *
17840157 ACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATCAATGATGGTC
1 ACGTGTGTAGTACTATGTGAAGGCTACTATGTGTACCGATAAAT-TTGGTC
* * * * *
17840208 ACATGTGTAGTACTAAGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGTC
1 ACGTGTGTAGTACTATGTGAAGGCTACTATGTGTACCGATAA-ATTTGGTC
* * * * *
17840259 ACGTGTGTAGTACTGTGAGAAGGCTACTATGTGAATCGATAAATGATGGTC
1 ACGTGTGTAGTACTATGTGAAGGCTACTATGTGTACCGATAAAT-TTGGTC
* * *
17840310 ACATGTGTAGTACTAAGTGAAGGCTACTATGTGTACCGA-AAATCTTTGATC
1 ACGTGTGTAGTACTATGTGAAGGCTACTATGTGTACCGATAAA--TTTGGTC
* * *
17840361 ACGTGTGTAGTACTATGTGAAGGCTACTATGTGAACCG-TAAAACTTGATC
1 ACGTGTGTAGTACTATGTGAAGGCTACTATGTGTACCGAT-AAATTTGGTC
17840411 ACGTGTGTAGTACTATGTGAAGGCTACTA
1 ACGTGTGTAGTACTATGTGAAGGCTACTA
17840440 CGTTTATCGA
Statistics
Matches: 269, Mismatches: 57, Indels: 17
0.78 0.17 0.05
Matches are distributed among these distances:
50 40 0.15
51 223 0.83
52 6 0.02
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.30
Consensus pattern (50 bp):
ACGTGTGTAGTACTATGTGAAGGCTACTATGTGTACCGATAAATTTGGTC
Found at i:17840231 original size:102 final size:102
Alignment explanation
Indices: 17840055--17840437 Score: 579
Period size: 102 Copynumber: 3.8 Consensus size: 102
17840045 ATTGATGAAT
* *
17840055 ACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAATAATGGTCACATGTGTAGTACT
1 ACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTACT
* *
17840120 AAGTGAAGGCTACAATATGTACCTAGAAGCTTTGGTC
66 AAGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGTC
*
17840157 ACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATCAATGATGGTCACATGTGTAGTACT
1 ACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTACT
17840222 AAGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGTC
66 AAGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGTC
* *
17840259 ACGTGTGTAGTACTGTGAGAAGGCTACTATGTGAATCGATAAATGATGGTCACATGTGTAGTACT
1 ACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTACT
* * * *
17840324 AAGTGAAGGCTACTATGTGTACCGAAAATCTTTGATC
66 AAGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGTC
* * * *** * *
17840361 ACGTGTGTAGTACTATGTGAAGGCTACTATGTGAACCG-TAAAACTTGATCACGTGTGTAGTACT
1 ACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTACT
*
17840425 ATGTGAAGGCTAC
66 AAGTGAAGGCTAC
17840438 TACGTTTATC
Statistics
Matches: 260, Mismatches: 21, Indels: 1
0.92 0.07 0.00
Matches are distributed among these distances:
101 33 0.13
102 227 0.87
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.30
Consensus pattern (102 bp):
ACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTACT
AAGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGTC
Found at i:17840476 original size:152 final size:153
Alignment explanation
Indices: 17840206--17840482 Score: 344
Period size: 152 Copynumber: 1.8 Consensus size: 153
17840196 TCAATGATGG
* * *
17840206 TCACATGTGTAGTACTAAGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGTCACGTGTGTAGTA
1 TCACATGTGTAGTACTAAGTGAAGGCTACAATGTGAACCGAGAAACTTTGATCACGTGTGTAGTA
* * * ** * * *
17840271 CTGTGAGAAGGCTACTATGTGAATCGATAAATGATGGTCACATGTGTAGTACTAAGTGAAGGCTA
66 CTATGAGAAGGCTACTACGTGAATCGATAAATAAAAGTAACATGGGCAGTACTAAGTGAAGGCTA
17840336 CTATGTGTACCGAAAATCTTTGA
131 CTATGTGTACCGAAAATCTTTGA
* * *
17840359 TCACGTGTGTAGTACTATGTGAAGGCTACTATGTGAACCGTA-AAAC-TTGATCACGTGTGTAGT
1 TCACATGTGTAGTACTAAGTGAAGGCTACAATGTGAACCG-AGAAACTTTGATCACGTGTGTAGT
* ** * *
17840422 ACTATGTGAAGGCTACTACGTTTATCGA-ATGATAAAAGTAACATGGGCAGTACTATGTGAA
65 ACTATGAGAAGGCTACTACGTGAATCGATA-AATAAAAGTAACATGGGCAGTACTAAGTGAA
17840483 AAACCCCAAA
Statistics
Matches: 103, Mismatches: 19, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
151 1 0.01
152 62 0.60
153 39 0.38
154 1 0.01
ACGTcount: A:0.31, C:0.14, G:0.25, T:0.30
Consensus pattern (153 bp):
TCACATGTGTAGTACTAAGTGAAGGCTACAATGTGAACCGAGAAACTTTGATCACGTGTGTAGTA
CTATGAGAAGGCTACTACGTGAATCGATAAATAAAAGTAACATGGGCAGTACTAAGTGAAGGCTA
CTATGTGTACCGAAAATCTTTGA
Found at i:17845925 original size:12 final size:12
Alignment explanation
Indices: 17845908--17845941 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
17845898 CGTTACCTGA
*
17845908 CCTAGCACATGG
1 CCTAGCACACGG
17845920 CCTAGCACACGG
1 CCTAGCACACGG
*
17845932 CCTGGCACAC
1 CCTAGCACAC
17845942 AAGCATCTGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.24, C:0.41, G:0.24, T:0.12
Consensus pattern (12 bp):
CCTAGCACACGG
Found at i:17845997 original size:42 final size:42
Alignment explanation
Indices: 17845926--17846033 Score: 144
Period size: 42 Copynumber: 2.6 Consensus size: 42
17845916 ATGGCCTAGC
* * * * * *
17845926 ACACGGCCTGGCACACAAGCATCTGGGTTCATTTCGAAGGGT
1 ACACGGCCTGGCACACGAGCGTGTAGGTTCATTTCAAAAGGT
*
17845968 ACACGGCCAGGCACACGAGCGTGTAGGTTCATTTCAAAAGGT
1 ACACGGCCTGGCACACGAGCGTGTAGGTTCATTTCAAAAGGT
*
17846010 ACACGGCCTGGCACACGGGCGTGT
1 ACACGGCCTGGCACACGAGCGTGT
17846034 GGCTTGGCCA
Statistics
Matches: 57, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 57 1.00
ACGTcount: A:0.24, C:0.27, G:0.31, T:0.19
Consensus pattern (42 bp):
ACACGGCCTGGCACACGAGCGTGTAGGTTCATTTCAAAAGGT
Found at i:17852025 original size:24 final size:24
Alignment explanation
Indices: 17851971--17852035 Score: 62
Period size: 24 Copynumber: 2.7 Consensus size: 24
17851961 GGATCATCTC
17851971 ATATATATATCAAA-ATTATAACATT
1 ATATA-ATAT-AAATATTATAACATT
*
17851996 ACATAATATAAATATTATAAACATT
1 ATATAATATAAATATTAT-AACATT
* *
17852021 -TATAAAATAGATATT
1 ATATAATATAAATATT
17852036 TAATGAGATA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
23 3 0.09
24 21 0.62
25 10 0.29
ACGTcount: A:0.54, C:0.06, G:0.02, T:0.38
Consensus pattern (24 bp):
ATATAATATAAATATTATAACATT
Found at i:17856446 original size:25 final size:26
Alignment explanation
Indices: 17856396--17856446 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
17856386 AGTTGTAGAG
*
17856396 AGAAAATTCTCTGAAGAGATTATTCT
1 AGAAAATTCTCTAAAGAGATTATTCT
* *
17856422 AGAAAATT-TCTAAAGATATTTTTCT
1 AGAAAATTCTCTAAAGAGATTATTCT
17856447 TATTTACAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 14 0.64
26 8 0.36
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (26 bp):
AGAAAATTCTCTAAAGAGATTATTCT
Found at i:17857054 original size:19 final size:19
Alignment explanation
Indices: 17857030--17857067 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
17857020 CCTTCCAAAT
17857030 GGTAAGCTGTTAATAGCGA
1 GGTAAGCTGTTAATAGCGA
17857049 GGTAAGCTGTTAATAGCGA
1 GGTAAGCTGTTAATAGCGA
17857068 TCAAGGACAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.11, G:0.32, T:0.26
Consensus pattern (19 bp):
GGTAAGCTGTTAATAGCGA
Found at i:17858286 original size:41 final size:41
Alignment explanation
Indices: 17858222--17858392 Score: 211
Period size: 41 Copynumber: 4.2 Consensus size: 41
17858212 TTTATGAGAA
* *
17858222 AAACACCGTAAAA-GGTGAGCAATAGTGGCGTTTTTGGTCC
1 AAACGCCGTAAAATGTTGAGCAATAGTGGCGTTTTTGGTCC
* *
17858262 AAACGCCGTAAAATGTTGAGCAATAGTGGCATTTTTTGTCC
1 AAACGCCGTAAAATGTTGAGCAATAGTGGCGTTTTTGGTCC
*
17858303 AAACGCCGCAAAAAT-TTGAGCAATAGTGGCGTTTTTGGTCC
1 AAACGCCG-TAAAATGTTGAGCAATAGTGGCGTTTTTGGTCC
* *** ** *
17858344 AAACACTACAAAACATTGAGCAATAGTGGCGTTTTGGGTCC
1 AAACGCCGTAAAATGTTGAGCAATAGTGGCGTTTTTGGTCC
17858385 AAACGCCG
1 AAACGCCG
17858393 CGAATATGAT
Statistics
Matches: 112, Mismatches: 16, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
40 16 0.14
41 91 0.81
42 5 0.04
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26
Consensus pattern (41 bp):
AAACGCCGTAAAATGTTGAGCAATAGTGGCGTTTTTGGTCC
Found at i:17858335 original size:82 final size:82
Alignment explanation
Indices: 17858237--17858393 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 82
17858227 CCGTAAAAGG
* ** ** **
17858237 TGAGCAATAGTGGCGTTTTTGGTCCAAACGCCGTAAAATGTTGAGCAATAGTGGCATTTTTTGTC
1 TGAGCAATAGTGGCGTTTTTGGTCCAAACACCACAAAACATTGAGCAATAGTGGCATTTTGGGTC
17858302 CAAACGCCGCAAAAATT
66 CAAACGCCGCAAAAATT
* *
17858319 TGAGCAATAGTGGCGTTTTTGGTCCAAACACTACAAAACATTGAGCAATAGTGGCGTTTTGGGTC
1 TGAGCAATAGTGGCGTTTTTGGTCCAAACACCACAAAACATTGAGCAATAGTGGCATTTTGGGTC
17858384 CAAACGCCGC
66 CAAACGCCGC
17858394 GAATATGATT
Statistics
Matches: 66, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
82 66 1.00
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (82 bp):
TGAGCAATAGTGGCGTTTTTGGTCCAAACACCACAAAACATTGAGCAATAGTGGCATTTTGGGTC
CAAACGCCGCAAAAATT
Found at i:17859543 original size:116 final size:114
Alignment explanation
Indices: 17859403--17859771 Score: 343
Period size: 116 Copynumber: 3.2 Consensus size: 114
17859393 ATTAAAAGAA
** * *
17859403 TGCAAAACGTTGTCATTTGTAGCTGTGTTTTTAGTGGCGTTTTGACTAAAACACCGCAAAAGGTT
1 TGCAAAACAATGTCATTT-TAGCTGTGTTTTTAGTGGCGTTTTCACTAAAACACCGCAAAAGGAT
* *
17859468 ATGCGTTAGTGGCGTTTTCACCAAAAACACCGCAAATATGTATTAAGAGTT
65 ATGCGTTAGTGGCGTTTTCACAAAAAACACCGTAAATATGT-TTAAGAGTT
* * * * * *
17859519 TGCAAAACAATGTCGTTTTCAGCTGCGCTTTTGGTGGCGCTTTCACTAAAACACCACAAAAGGAT
1 TGCAAAACAATGTCATTTT-AGCTGTGTTTTTAGTGGCGTTTTCACTAAAACACCGCAAAAGGAT
* * *
17859584 ATGCGTTAGTGGCGTTTTCATAAAAAAAAACGCCGTGAATATGGTTTAAGAGTT
65 ATGCGTTAGTGGCGTTTTC---ACAAAAAACACCGTAAATAT-GTTTAAGAGTT
* * * * * * ** *
17859638 TGC-AAA-AATTTAACATTTTTATCTACT-TTTTTAATGGCATTTTTACTAAAAGGCTGCAAAAG
1 TGCAAAACAATGT--CA-TTTTAGCT-GTGTTTTTAGTGGCGTTTTCACTAAAACACCGCAAAAG
**
17859700 GATATAAGTTAGT-G-GTTTTCACAAAAAACACCGTAAATATGCTTTAAGAGTT
62 GATATGCGTTAGTGGCGTTTTCACAAAAAACACCGTAAATATG-TTTAAGAGTT
**
17859752 TGCAAAACGTTGTCATTTTA
1 TGCAAAACAATGTCATTTTA
17859772 AGCTACATTT
Statistics
Matches: 203, Mismatches: 38, Indels: 27
0.76 0.14 0.10
Matches are distributed among these distances:
113 6 0.03
114 32 0.16
115 4 0.02
116 74 0.36
117 10 0.05
118 4 0.02
119 67 0.33
120 6 0.03
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.33
Consensus pattern (114 bp):
TGCAAAACAATGTCATTTTAGCTGTGTTTTTAGTGGCGTTTTCACTAAAACACCGCAAAAGGATA
TGCGTTAGTGGCGTTTTCACAAAAAACACCGTAAATATGTTTAAGAGTT
Found at i:17859960 original size:25 final size:22
Alignment explanation
Indices: 17859906--17859962 Score: 60
Period size: 25 Copynumber: 2.4 Consensus size: 22
17859896 CACGATTTCA
*
17859906 TTTCCCCAATTTCCCAACTTCT
1 TTTCCCCAATTTCCCAACTTAT
*
17859928 TTTCCCCCAATTTCCCCCAAGTTAT
1 TTT-CCCCAATTT--CCCAACTTAT
17859953 TCTTCCCCAA
1 T-TTCCCCAA
17859963 ATTATTTTCC
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
22 3 0.10
23 9 0.31
25 15 0.52
26 2 0.07
ACGTcount: A:0.19, C:0.42, G:0.02, T:0.37
Consensus pattern (22 bp):
TTTCCCCAATTTCCCAACTTAT
Found at i:17859974 original size:14 final size:14
Alignment explanation
Indices: 17859937--17859976 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 14
17859927 TTTTCCCCCA
* *
17859937 ATTTCCCCCAAGTT
1 ATTTTCCCCAAATT
17859951 ATTCTTCCCCAAATT
1 ATT-TTCCCCAAATT
17859966 ATTTTCCCCAA
1 ATTTTCCCCAA
17859977 TTTCCCAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 11 0.48
15 12 0.52
ACGTcount: A:0.25, C:0.35, G:0.03, T:0.38
Consensus pattern (14 bp):
ATTTTCCCCAAATT
Found at i:17860640 original size:33 final size:33
Alignment explanation
Indices: 17860598--17860665 Score: 118
Period size: 33 Copynumber: 2.1 Consensus size: 33
17860588 CATCTATGTT
*
17860598 ATTCGAGTTAAATGAGATGAGTGTTCGGTATGA
1 ATTCGAGTTAAATGAGATGAGTGTTAGGTATGA
*
17860631 ATTCGAGTTAAATGAGATTAGTGTTAGGTATGA
1 ATTCGAGTTAAATGAGATGAGTGTTAGGTATGA
17860664 AT
1 AT
17860666 ATATGTATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.32, C:0.04, G:0.28, T:0.35
Consensus pattern (33 bp):
ATTCGAGTTAAATGAGATGAGTGTTAGGTATGA
Found at i:17860929 original size:17 final size:17
Alignment explanation
Indices: 17860907--17860942 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
17860897 GTCCCAGGAA
17860907 CTTGCAGCCTCTACTTC
1 CTTGCAGCCTCTACTTC
*
17860924 CTTGCAGCCTTTACTTC
1 CTTGCAGCCTCTACTTC
17860941 CT
1 CT
17860943 AGTGAACTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.11, C:0.39, G:0.11, T:0.39
Consensus pattern (17 bp):
CTTGCAGCCTCTACTTC
Found at i:17861397 original size:24 final size:24
Alignment explanation
Indices: 17861370--17861422 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
17861360 TATTTGTATA
17861370 ATATTTGTAACTAAAATTAATATT
1 ATATTTGTAACTAAAATTAATATT
*
17861394 ATATTTGTATCTAAAATTAATATT
1 ATATTTGTAACTAAAATTAATATT
17861418 ATATT
1 ATATT
17861423 ATAAAATACT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.49
Consensus pattern (24 bp):
ATATTTGTAACTAAAATTAATATT
Found at i:17862651 original size:13 final size:13
Alignment explanation
Indices: 17862633--17862665 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
17862623 TAATTAAAGG
17862633 GTTAAAATTTAAA
1 GTTAAAATTTAAA
17862646 GTTAAAATTTAAA
1 GTTAAAATTTAAA
*
17862659 GATAAAA
1 GTTAAAA
17862666 ATCATAACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.58, C:0.00, G:0.09, T:0.33
Consensus pattern (13 bp):
GTTAAAATTTAAA
Found at i:17862761 original size:9 final size:9
Alignment explanation
Indices: 17862747--17862816 Score: 74
Period size: 9 Copynumber: 8.0 Consensus size: 9
17862737 AACTTTGGAT
17862747 CATAACTTA
1 CATAACTTA
17862756 CATAACTTA
1 CATAACTTA
17862765 CATAACTTA
1 CATAACTTA
17862774 CATAA--TA
1 CATAACTTA
*
17862781 CATAA-ATA
1 CATAACTTA
* * *
17862789 TATATCATA
1 CATAACTTA
17862798 TCATAACTTA
1 -CATAACTTA
17862808 CATAACTTA
1 CATAACTTA
17862817 TGTAATATAT
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
7 7 0.13
8 5 0.09
9 35 0.66
10 6 0.11
ACGTcount: A:0.47, C:0.19, G:0.00, T:0.34
Consensus pattern (9 bp):
CATAACTTA
Found at i:17868818 original size:43 final size:43
Alignment explanation
Indices: 17868771--17868986 Score: 269
Period size: 43 Copynumber: 5.0 Consensus size: 43
17868761 AGAACATGAC
* *
17868771 CTTTAGCAGCGTTTATGGGGAAAGCGCTGCTAAAGGTCATGAT
1 CTTTAGCAGCGTTTGTGGGGAAAGCGCTGCTAAAGGTCATGTT
** * *
17868814 CTTTAGCAGCGTTTGTGGAAAAAGCTCCGCTAAAGGTCATGTT
1 CTTTAGCAGCGTTTGTGGGGAAAGCGCTGCTAAAGGTCATGTT
*
17868857 CTATAGC-GACGTTTGTGGGGAAAGCGCTGCTAAAGGTCATGTT
1 CTTTAGCAG-CGTTTGTGGGGAAAGCGCTGCTAAAGGTCATGTT
* * * *
17868900 CTTTAGCCGCATTTGTGGGGAAAGCGCCGCTAAAGATCA-GTT
1 CTTTAGCAGCGTTTGTGGGGAAAGCGCTGCTAAAGGTCATGTT
*
17868942 CTTTAGCAGCGTTTGT-GGGAAAG-GTGTCGCTAAAGGTCATGTT
1 CTTTAGCAGCGTTTGTGGGGAAAGCG-CT-GCTAAAGGTCATGTT
17868985 CT
1 CT
17868987 ATAACGGCAT
Statistics
Matches: 148, Mismatches: 20, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
40 1 0.01
41 7 0.05
42 28 0.19
43 111 0.75
44 1 0.01
ACGTcount: A:0.24, C:0.18, G:0.30, T:0.29
Consensus pattern (43 bp):
CTTTAGCAGCGTTTGTGGGGAAAGCGCTGCTAAAGGTCATGTT
Found at i:17872173 original size:17 final size:15
Alignment explanation
Indices: 17872151--17872185 Score: 52
Period size: 17 Copynumber: 2.2 Consensus size: 15
17872141 TTTTTAACAT
17872151 AAATTAAATCAAATTCA
1 AAATTAAAT-AAATT-A
17872168 AAATTAAATAAATTA
1 AAATTAAATAAATTA
17872183 AAA
1 AAA
17872186 AAATTATGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 4 0.22
16 5 0.28
17 9 0.50
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.29
Consensus pattern (15 bp):
AAATTAAATAAATTA
Found at i:17872187 original size:17 final size:17
Alignment explanation
Indices: 17872151--17872186 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
17872141 TTTTTAACAT
*
17872151 AAATTAAATCAAATTCA
1 AAATTAAATCAAATTAA
17872168 AAATTAAAT-AAATTAA
1 AAATTAAATCAAATTAA
17872184 AAA
1 AAA
17872187 AATTATGGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.28
Consensus pattern (17 bp):
AAATTAAATCAAATTAA
Found at i:17872223 original size:83 final size:83
Alignment explanation
Indices: 17872136--17872303 Score: 318
Period size: 83 Copynumber: 2.0 Consensus size: 83
17872126 ATTATTATTC
17872136 TTTTATTTTTAACATAAATTAAATCAAATTCAAAATTAAATAAATTAAAAAAATTATGGTTGCCT
1 TTTTATTTTTAACATAAATTAAATCAAATTCAAAATTAAATAAATTAAAAAAATTATGGTTGCCT
*
17872201 CCCAAAAAGCGCTTTTGT
66 CCCAAAAAACGCTTTTGT
*
17872219 TTTTATTTTTAACATAAATTAAATTAAATTCAAAATTAAATAAATTAAAAAAATTATGGTTGCCT
1 TTTTATTTTTAACATAAATTAAATCAAATTCAAAATTAAATAAATTAAAAAAATTATGGTTGCCT
17872284 CCCAAAAAACGCTTTTGT
66 CCCAAAAAACGCTTTTGT
17872302 TT
1 TT
17872304 AATGTCGTTA
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
83 83 1.00
ACGTcount: A:0.43, C:0.11, G:0.07, T:0.39
Consensus pattern (83 bp):
TTTTATTTTTAACATAAATTAAATCAAATTCAAAATTAAATAAATTAAAAAAATTATGGTTGCCT
CCCAAAAAACGCTTTTGT
Found at i:17872256 original size:17 final size:15
Alignment explanation
Indices: 17872234--17872268 Score: 52
Period size: 17 Copynumber: 2.2 Consensus size: 15
17872224 TTTTTAACAT
17872234 AAATTAAATTAAATTCA
1 AAATTAAA-TAAATT-A
17872251 AAATTAAATAAATTA
1 AAATTAAATAAATTA
17872266 AAA
1 AAA
17872269 AAATTATGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 4 0.22
16 6 0.33
17 8 0.44
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (15 bp):
AAATTAAATAAATTA
Found at i:17872270 original size:17 final size:17
Alignment explanation
Indices: 17872234--17872269 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
17872224 TTTTTAACAT
*
17872234 AAATTAAATTAAATTCA
1 AAATTAAATTAAATTAA
17872251 AAATTAAA-TAAATTAA
1 AAATTAAATTAAATTAA
17872267 AAA
1 AAA
17872270 AATTATGGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (17 bp):
AAATTAAATTAAATTAA
Found at i:17874885 original size:25 final size:26
Alignment explanation
Indices: 17874844--17874913 Score: 90
Period size: 25 Copynumber: 2.8 Consensus size: 26
17874834 TCATGTACAT
* *
17874844 GTATGCTCATACAAGCTGTGA-ATCG
1 GTATGCTCACACGAGCTGTGAGATCG
* *
17874869 GTTTGCTCACTCGAGCTGT-AGATCG
1 GTATGCTCACACGAGCTGTGAGATCG
17874894 GTATGCTCACACGAGCTGTG
1 GTATGCTCACACGAGCTGTG
17874914 GGTCGAAACG
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
24 1 0.03
25 36 0.97
ACGTcount: A:0.21, C:0.23, G:0.27, T:0.29
Consensus pattern (26 bp):
GTATGCTCACACGAGCTGTGAGATCG
Found at i:17882674 original size:25 final size:25
Alignment explanation
Indices: 17882574--17882668 Score: 106
Period size: 25 Copynumber: 3.8 Consensus size: 25
17882564 TCATGTACAT
*
17882574 GTATGCTCATACGAGCTGTGAATTG
1 GTATGCTCATACGAGCTGTGAATCG
*
17882599 GTATGCTCACT-CGAGTTGT-AGATCG
1 GTATGCTCA-TACGAGCTGTGA-ATCG
*
17882624 GTATGCTC-TCACGAGCTATGAATCG
1 GTATGCTCAT-ACGAGCTGTGAATCG
*
17882649 GTATGCTCATACAAGCTGTG
1 GTATGCTCATACGAGCTGTG
17882669 GGTCGGAACA
Statistics
Matches: 58, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
23 1 0.02
24 1 0.02
25 53 0.91
26 3 0.05
ACGTcount: A:0.23, C:0.20, G:0.26, T:0.31
Consensus pattern (25 bp):
GTATGCTCATACGAGCTGTGAATCG
Found at i:17888125 original size:18 final size:18
Alignment explanation
Indices: 17888090--17888131 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
17888080 ACATAACTTT
*
17888090 TAAAAATAAAAACTAAAA
1 TAAAAATAAAAACAAAAA
*
17888108 TAAAAATAAAACCAAAAA
1 TAAAAATAAAAACAAAAA
*
17888126 GAAAAA
1 TAAAAA
17888132 AACAGACAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.79, C:0.07, G:0.02, T:0.12
Consensus pattern (18 bp):
TAAAAATAAAAACAAAAA
Found at i:17888479 original size:14 final size:15
Alignment explanation
Indices: 17888440--17888481 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
17888430 TTTTAACATA
*
17888440 ATTATTATTAAATAT
1 ATTATAATTAAATAT
17888455 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
17888469 A-TATAATTTAATA
1 ATTATAATTAAATA
17888482 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:17888544 original size:61 final size:61
Alignment explanation
Indices: 17888479--17888666 Score: 179
Period size: 61 Copynumber: 3.1 Consensus size: 61
17888469 ATATAATTTA
*
17888479 ATAAAATTCTTAATATTCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACT
1 ATAAAATTCTTAATATTCAATATTCTTATATGAATTTACTAAAATCATAATATATGATACT
* * * * * * ** * * * * *
17888540 ATAAAA-T-ATAAT-TTAACATAATTATTAT-TAAATATATTTTAATTAAAAAATATAAT-TT
1 ATAAAATTCTTAATATTCA-AT-ATTCTTATATGAATTTACTAAAATCATAATATATGATACT
*
17888598 AATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTAAAATCATAATATATGATACT
1 -ATAAAATTCTTAATATTCAATATTCTTATATGAATTTACTAAAATCATAATATATGATACT
17888660 ATAAAAT
1 ATAAAAT
17888667 ATAATTTGAA
Statistics
Matches: 92, Mismatches: 27, Indels: 16
0.68 0.20 0.12
Matches are distributed among these distances:
58 4 0.04
59 31 0.34
60 16 0.17
61 38 0.41
62 3 0.03
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.42
Consensus pattern (61 bp):
ATAAAATTCTTAATATTCAATATTCTTATATGAATTTACTAAAATCATAATATATGATACT
Found at i:17888604 original size:16 final size:18
Alignment explanation
Indices: 17888569--17888604 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
17888559 AATTATTATT
*
17888569 AAATATATTTTAATTAAA
1 AAATATAATTTAATTAAA
17888587 AAATATAATTTAA-TAAA
1 AAATATAATTTAATTAAA
17888604 A
1 A
17888605 TTCTTAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
AAATATAATTTAATTAAA
Found at i:17888651 original size:59 final size:59
Alignment explanation
Indices: 17888469--17888652 Score: 157
Period size: 59 Copynumber: 3.1 Consensus size: 59
17888459 TAATTAAAAT
* *
17888469 ATATAATTTAATAAAATTCTTAATATTCAATATTCTTATATGAATTTACTCAAATCATA
1 ATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTAAAATCATA
* * * * * * *
17888528 ATAT-ATGATACTATAAAATATAATTTAA-CAT-AATTATTATTAAATAT-ATTTTAATTAAA--
1 ATATAAT-TTA--ATAAAAT-T--CTTAATAATCAA-TATTCTT--ATATGAATTTACTAAAATC
17888587 A-A
57 ATA
17888589 ATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTAAAATCATA
1 ATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTAAAATCATA
17888648 ATATA
1 ATATA
17888653 TGATACTATA
Statistics
Matches: 94, Mismatches: 15, Indels: 32
0.67 0.11 0.23
Matches are distributed among these distances:
55 4 0.04
56 13 0.14
57 8 0.09
58 6 0.06
59 19 0.20
61 14 0.15
62 6 0.06
63 7 0.07
64 13 0.14
65 4 0.04
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.43
Consensus pattern (59 bp):
ATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTAAAATCATA
Found at i:17888710 original size:59 final size:58
Alignment explanation
Indices: 17888527--17888715 Score: 163
Period size: 66 Copynumber: 3.2 Consensus size: 58
17888517 CTCAAATCAT
*
17888527 AATATATGATACTATAAAATATAATTTAACATAATTATTATTAAATATATTTTAATTAA
1 AATATATGATACTATAAAATATAATTTAA-ATAATTAATATTAAATATATTTTAATTAA
** * * * ** *
17888586 AA-A-AT-ATA--ATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTAAAATCA
1 AATATATGATACTATAAAATATAATT-TAAATAATTAATATT-AAATAT--ATTT--T--AATTA
*
17888646 T
58 A
17888647 AATATATGATACTATAAAATATAATTTGAAATAATTAATATTAAATATATTTTAATTAA
1 AATATATGATACTATAAAATATAATTT-AAATAATTAATATTAAATATATTTTAATTAA
17888706 AATATATGAT
1 AATATATGAT
17888716 TTAATAAAAT
Statistics
Matches: 97, Mismatches: 19, Indels: 28
0.67 0.13 0.19
Matches are distributed among these distances:
54 20 0.21
55 6 0.06
56 3 0.03
57 6 0.06
58 1 0.01
59 17 0.18
61 7 0.07
62 1 0.01
63 6 0.06
64 3 0.03
65 5 0.05
66 22 0.23
ACGTcount: A:0.51, C:0.04, G:0.03, T:0.42
Consensus pattern (58 bp):
AATATATGATACTATAAAATATAATTTAAATAATTAATATTAAATATATTTTAATTAA
Found at i:17888735 original size:120 final size:120
Alignment explanation
Indices: 17888431--17888726 Score: 522
Period size: 120 Copynumber: 2.5 Consensus size: 120
17888421 TTAATCATAT
* *
17888431 TTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATATT
1 TTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAAT
*
17888496 CAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAA
66 CAATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAA
*
17888551 TTTAACATAATTATTATTAAATATATTTTAATTAAAAAATATAATTTAATAAAATTCTTAATAAT
1 TTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAAT
17888616 CAATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAA
66 CAATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAA
* *
17888671 TTTGAA-ATAATTAATATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
1 TTT-AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATT
17888727 TAAAATAATT
Statistics
Matches: 168, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
120 166 0.99
121 2 0.01
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (120 bp):
TTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAAT
CAATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAA
Found at i:17888777 original size:47 final size:46
Alignment explanation
Indices: 17888708--17889039 Score: 198
Period size: 47 Copynumber: 7.3 Consensus size: 46
17888698 TTAATTAAAA
*
17888708 TATATG-ATTTAATAAAATTTAAAATAATTATAACTAATAAATTTTCT
1 TATATGAATTT-ATATAATTTAAAATAATTATAA-TAATAAATTTTCT
* * *
17888755 TATATGAATTTGTATAATTTAAAATAATTAT--TATTAAATATAAT-T
1 TATATGAATTTATATAATTTAAAATAATTATAATAATAAAT-T-TTCT
* * * *
17888800 TA-AT-AATAATATATAATTTCATAA-AATTCTTGATAATAAATTTTCT
1 TATATGAAT-TTATATAATTT-AAAATAATT-ATAATAATAAATTTTCT
* *
17888846 TATATGAATTTATATAATTTAAAATAA-T-TAATATTAAATATAAT-T
1 TATATGAATTTATATAATTTAAAATAATTATAATAATAAAT-T-TTCT
* * * *
17888891 TA-AT-AATGATATATAATTTCATAA-AATTCTTGATAATAAATTTTCT
1 TATATGAAT-TTATATAATTT-AAAATAATT-ATAATAATAAATTTTCT
* *
17888937 TATATGAATTTATATAATTTAAAATAA-T-TAATATTAAATATAAT-T
1 TATATGAATTTATATAATTTAAAATAATTATAATAATAAAT-T-TTCT
* * * *
17888982 TA-AT-AATGATATATAATTTCATAA-AATTCTTAATAATAAATGTTCT
1 TATATGAAT-TTATATAATTT-AAAATAATT-ATAATAATAAATTTTCT
17889028 TATATGAATTTA
1 TATATGAATTTA
17889040 CTAAAATCAT
Statistics
Matches: 221, Mismatches: 31, Indels: 66
0.69 0.10 0.21
Matches are distributed among these distances:
43 9 0.04
44 68 0.31
45 27 0.12
46 22 0.10
47 82 0.37
48 13 0.06
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.46
Consensus pattern (46 bp):
TATATGAATTTATATAATTTAAAATAATTATAATAATAAATTTTCT
Found at i:17888838 original size:91 final size:91
Alignment explanation
Indices: 17888742--17889039 Score: 551
Period size: 91 Copynumber: 3.3 Consensus size: 91
17888732 TAATTATAAC
* *
17888742 TAATAAATTTTCTTATATGAATTTGTATAATTTAAAATAATTATTATTAAATATAATTTAATAAT
1 TAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAATTTAATAAT
*
17888807 AATATATAATTTCATAAAATTCTTGA
66 GATATATAATTTCATAAAATTCTTGA
17888833 TAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAATTTAATAAT
1 TAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAATTTAATAAT
17888898 GATATATAATTTCATAAAATTCTTGA
66 GATATATAATTTCATAAAATTCTTGA
17888924 TAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAATTTAATAAT
1 TAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAATTTAATAAT
*
17888989 GATATATAATTTCATAAAATTCTTAA
66 GATATATAATTTCATAAAATTCTTGA
*
17889015 TAATAAATGTTCTTATATGAATTTA
1 TAATAAATTTTCTTATATGAATTTA
17889040 CTAAAATCAT
Statistics
Matches: 202, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
91 202 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (91 bp):
TAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAATTTAATAAT
GATATATAATTTCATAAAATTCTTGA
Found at i:17892150 original size:6 final size:6
Alignment explanation
Indices: 17892139--17892168 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
17892129 TAGTTTGAAC
17892139 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
17892169 TTTCGTATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
ATTTAA
Found at i:17892968 original size:13 final size:13
Alignment explanation
Indices: 17892950--17892974 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17892940 ATCAAATTTG
17892950 TATGTACTCTTTA
1 TATGTACTCTTTA
17892963 TATGTACTCTTT
1 TATGTACTCTTT
17892975 CACTAATAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.16, G:0.08, T:0.56
Consensus pattern (13 bp):
TATGTACTCTTTA
Found at i:17895960 original size:33 final size:34
Alignment explanation
Indices: 17895894--17895969 Score: 109
Period size: 34 Copynumber: 2.3 Consensus size: 34
17895884 AGGTTTAGGG
*
17895894 TTAAGGTTAGTTTAAAGTTTAAGAAAAAAATAAA
1 TTAAGGTTTGTTTAAAGTTTAAGAAAAAAATAAA
**
17895928 TTAAGGTTTGTTTAGGGTTTAAG-AAAAAATAAA
1 TTAAGGTTTGTTTAAAGTTTAAGAAAAAAATAAA
*
17895961 TTAGGGTTT
1 TTAAGGTTT
17895970 AGGGTTTAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
33 18 0.47
34 20 0.53
ACGTcount: A:0.43, C:0.00, G:0.20, T:0.37
Consensus pattern (34 bp):
TTAAGGTTTGTTTAAAGTTTAAGAAAAAAATAAA
Found at i:17895969 original size:29 final size:32
Alignment explanation
Indices: 17895910--17895978 Score: 99
Period size: 29 Copynumber: 2.2 Consensus size: 32
17895900 TTAGTTTAAA
17895910 GTTTAAGAAAAAAATAAATTAAGGTTTGTTTAGG
1 GTTTAAGAAAAAAATAAATTAAGG--TGTTTAGG
17895944 GTTTAAG-AAAAAATAAATT-AGG-GTTTAGG
1 GTTTAAGAAAAAAATAAATTAAGGTGTTTAGG
17895973 GTTTAA
1 GTTTAA
17895979 ATTTTTTAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
29 13 0.37
32 3 0.09
33 12 0.34
34 7 0.20
ACGTcount: A:0.43, C:0.00, G:0.22, T:0.35
Consensus pattern (32 bp):
GTTTAAGAAAAAAATAAATTAAGGTGTTTAGG
Found at i:17899495 original size:59 final size:59
Alignment explanation
Indices: 17899422--17900355 Score: 1678
Period size: 59 Copynumber: 15.8 Consensus size: 59
17899412 TAACTCCTAA
*
17899422 TTTATTAAATGAAACAATATAAAAATAAATTGTACAAACATATTCAAAAGAACTATTAT
1 TTTATTAAACGAAACAATATAAAAATAAATTGTACAAACATATTCAAAAGAACTATTAT
17899481 TTTATTAAACGAAACAATATAAAAATAAATTGTACAAACATATTCAAAAGAACT-TCTAT
1 TTTATTAAACGAAACAATATAAAAATAAATTGTACAAACATATTCAAAAGAACTAT-TAT
* * * *
17899540 TTTATTAAATGAAACAATATAAAAATAAATTGCACAAAAATATTTAAAAGAACT-TCTAT
1 TTTATTAAACGAAACAATATAAAAATAAATTGTACAAACATATTCAAAAGAACTAT-TAT
* *
17899599 TTTATTAAATGAAACAATATAAAAATAATTTGTACAAACATATTCAAAAGAACTATTAT
1 TTTATTAAACGAAACAATATAAAAATAAATTGTACAAACATATTCAAAAGAACTATTAT
17899658 TTTATTAAACGAAACAATATAAAAATAAATTGTACAAACATATTCAAAAGAACTATTAT
1 TTTATTAAACGAAACAATATAAAAATAAATTGTACAAACATATTCAAAAGAACTATTAT
17899717 TTTATTAAACGAAACAATATAAAAATAAATTGTACAAACATATTCAAAAGAACTATTAT
1 TTTATTAAACGAAACAATATAAAAATAAATTGTACAAACATATTCAAAAGAACTATTAT
17899776 TTTATTAAACGAAACAATATAAAAATAAATTGTACAAACATATTCAAAAGAACTATTAT
1 TTTATTAAACGAAACAATATAAAAATAAATTGTACAAACATATTCAAAAGAACTATTAT
17899835 TTTATTAAACGAAACAATATAAAAATAAATTGTACAAACATATTCAAAAGAACTATTAT
1 TTTATTAAACGAAACAATATAAAAATAAATTGTACAAACATATTCAAAAGAACTATTAT
17899894 TTTATTAAACGAAACAATATAAAAATAAATTGTACAAACATATTCAAAAGAACTATTAT
1 TTTATTAAACGAAACAATATAAAAATAAATTGTACAAACATATTCAAAAGAACTATTAT
17899953 TTTATTAAACGAAACAATATAAAAATAAATTGTACAAACATATTCAAAAGAACTATTAT
1 TTTATTAAACGAAACAATATAAAAATAAATTGTACAAACATATTCAAAAGAACTATTAT
17900012 TTTATTAAACGAAACAATATAAAAATAAATTGTACAAACATATTCAAAAGAACTATTAT
1 TTTATTAAACGAAACAATATAAAAATAAATTGTACAAACATATTCAAAAGAACTATTAT
17900071 TTTATTAAACGAAACAATATAAAAATAAATTGTACAAACATATTCAAAAGAACTATTAT
1 TTTATTAAACGAAACAATATAAAAATAAATTGTACAAACATATTCAAAAGAACTATTAT
17900130 TTTATTAAACGAAACAATATAAAAATAAATTGTACAAACATATTCAAAAGAACTATTAT
1 TTTATTAAACGAAACAATATAAAAATAAATTGTACAAACATATTCAAAAGAACTATTAT
17900189 TTTATTAAACGAAACAATATAAAAATAAATTGTACAAACATATTCAAAAGAACT-TCTAT
1 TTTATTAAACGAAACAATATAAAAATAAATTGTACAAACATATTCAAAAGAACTAT-TAT
* * * *
17900248 TTTATTAAATGAAACAATATAAAAATAAATTGCACAAAAATATTTAAAAGAACT-TCTAT
1 TTTATTAAACGAAACAATATAAAAATAAATTGTACAAACATATTCAAAAGAACTAT-TAT
* * *
17900307 TTTATTAAATGAAACAATATAAAAATAATTTGTACAAAAATATTCAAAA
1 TTTATTAAACGAAACAATATAAAAATAAATTGTACAAACATATTCAAAA
17900356 ATAAATCAAT
Statistics
Matches: 854, Mismatches: 18, Indels: 6
0.97 0.02 0.01
Matches are distributed among these distances:
58 2 0.00
59 851 1.00
60 1 0.00
ACGTcount: A:0.54, C:0.10, G:0.05, T:0.31
Consensus pattern (59 bp):
TTTATTAAACGAAACAATATAAAAATAAATTGTACAAACATATTCAAAAGAACTATTAT
Found at i:17902278 original size:31 final size:31
Alignment explanation
Indices: 17902241--17902302 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
17902231 GAAATTATAA
* *
17902241 AAAAATATTAATTAA-ATTACAAAAATGAAAT
1 AAAAATATTAAATAATATTA-AAAAATAAAAT
17902272 AAAAATATTAAATAATATTAAAAAATAAAAT
1 AAAAATATTAAATAATATTAAAAAATAAAAT
17902303 TAACCGTTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 24 0.86
32 4 0.14
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.29
Consensus pattern (31 bp):
AAAAATATTAAATAATATTAAAAAATAAAAT
Found at i:17903105 original size:26 final size:24
Alignment explanation
Indices: 17903055--17903110 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 24
17903045 TGTATTTAAA
17903055 ATATTATTTTTATTATAATTATAG
1 ATATTATTTTTATTATAATTATAG
* *
17903079 ATATTATTTCTTAATTATATTTGTAG
1 ATATTATTT-TT-ATTATAATTATAG
17903105 ATATTA
1 ATATTA
17903111 AAATCTTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 9 0.32
25 2 0.07
26 17 0.61
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.57
Consensus pattern (24 bp):
ATATTATTTTTATTATAATTATAG
Found at i:17903121 original size:26 final size:25
Alignment explanation
Indices: 17903064--17903122 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 25
17903054 AATATTATTT
**
17903064 TTATTATAATTATAGATATTATTTC
1 TTATTATAATTATAGATATTAAATC
* *
17903089 TTAATTATATTTGTAGATATTAAAATC
1 TT-ATTATAATTATAGATATT-AAATC
17903116 TTATTAT
1 TTATTAT
17903123 TTTATTTTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
25 2 0.07
26 21 0.75
27 5 0.18
ACGTcount: A:0.37, C:0.03, G:0.05, T:0.54
Consensus pattern (25 bp):
TTATTATAATTATAGATATTAAATC
Found at i:17905475 original size:31 final size:31
Alignment explanation
Indices: 17905437--17905498 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
17905427 GTAAGGGTTA
*
17905437 ATTTCATTTTT-TAATATTATTTAATATTTTT
1 ATTTCATTTTTGTAAT-TTAATTAATATTTTT
17905468 ATTTCATTTTTGTAATTTAATTAATATTTTT
1 ATTTCATTTTTGTAATTTAATTAATATTTTT
17905499 TTATAATTTC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 25 0.86
32 4 0.14
ACGTcount: A:0.29, C:0.03, G:0.02, T:0.66
Consensus pattern (31 bp):
ATTTCATTTTTGTAATTTAATTAATATTTTT
Found at i:17905604 original size:76 final size:78
Alignment explanation
Indices: 17905480--17905633 Score: 231
Period size: 76 Copynumber: 2.0 Consensus size: 78
17905470 TTCATTTTTG
* * *
17905480 TAATTTAATTAATATTTTTTTATAATTTCTTTATAACAGTCAGTAGATCAAGTGCTACAATGTTT
1 TAATTTAATTAATATTTTTATATAATTTCATTATAACAGTCAGTAGATCAAGTGCTACAATGCTT
17905545 TATTCGTAATATA
66 TATTCGTAATATA
** * *
17905558 TAATTTAATTAATATTTTTATA-AATTT-ATTATAACAGTTGGTAGATCGAGTGTTACAATGCTT
1 TAATTTAATTAATATTTTTATATAATTTCATTATAACAGTCAGTAGATCAAGTGCTACAATGCTT
17905621 TATTCGTAATATA
66 TATTCGTAATATA
17905634 CCTGGTCCTC
Statistics
Matches: 69, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
76 43 0.62
77 5 0.07
78 21 0.30
ACGTcount: A:0.35, C:0.08, G:0.10, T:0.47
Consensus pattern (78 bp):
TAATTTAATTAATATTTTTATATAATTTCATTATAACAGTCAGTAGATCAAGTGCTACAATGCTT
TATTCGTAATATA
Found at i:17907586 original size:59 final size:59
Alignment explanation
Indices: 17907494--17907673 Score: 326
Period size: 59 Copynumber: 3.1 Consensus size: 59
17907484 ATTGATTTAT
17907494 TTTTGAATATTTTTGTA-AAAGTTATTTTTATATTGTTTCATTTAATAAAATAAAATTTC
1 TTTTGAATATTTTTGTACAAA-TTATTTTTATATTGTTTCATTTAATAAAATAAAATTTC
17907553 TTTTGAATATTTTTGTACAAATTATTTTTATATTGTTTCATTTAATAAAATAAAATTTC
1 TTTTGAATATTTTTGTACAAATTATTTTTATATTGTTTCATTTAATAAAATAAAATTTC
* *
17907612 TTTTGAATATTTTTGTACAAATTATTTTTATATTGTTTCATTTAATAAAATAGAAGTTC
1 TTTTGAATATTTTTGTACAAATTATTTTTATATTGTTTCATTTAATAAAATAAAATTTC
17907671 TTT
1 TTT
17907674 ATAACTCGTT
Statistics
Matches: 118, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
59 115 0.97
60 3 0.03
ACGTcount: A:0.34, C:0.04, G:0.07, T:0.54
Consensus pattern (59 bp):
TTTTGAATATTTTTGTACAAATTATTTTTATATTGTTTCATTTAATAAAATAAAATTTC
Found at i:17912499 original size:69 final size:70
Alignment explanation
Indices: 17912385--17912520 Score: 202
Period size: 69 Copynumber: 2.0 Consensus size: 70
17912375 CCATTTTCCA
*
17912385 TACCAACCATAACCATCTAAGAAGAAATCATATTCTTTCCAATCAAATCTGTCCAACATCATATT
1 TACCAACCATAACCATATAAGAAGAAATCATATTCTTTCCAATCAAATCTGTCCAACATCATATT
17912450 AGGCT
66 AGGCT
* * * * * *
17912455 TACCAACCATAATCATATAA-AAGTAGTCATATTCTTTCCCATCAAATCTGTCTAACATCTTATT
1 TACCAACCATAACCATATAAGAAGAAATCATATTCTTTCCAATCAAATCTGTCCAACATCATATT
17912519 AG
66 AG
17912521 AGAAAGAAAA
Statistics
Matches: 59, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
69 41 0.69
70 18 0.31
ACGTcount: A:0.38, C:0.24, G:0.07, T:0.32
Consensus pattern (70 bp):
TACCAACCATAACCATATAAGAAGAAATCATATTCTTTCCAATCAAATCTGTCCAACATCATATT
AGGCT
Found at i:17916307 original size:16 final size:16
Alignment explanation
Indices: 17916280--17916322 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
17916270 TTAACCCAAA
17916280 ATAAATTGAATTAAAATT
1 ATAAATT-AATT-AAATT
*
17916298 A-AAATTAATTATATT
1 ATAAATTAATTAAATT
17916313 ATAAATTAAT
1 ATAAATTAAT
17916323 ATTCATAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 5 0.22
16 12 0.52
17 5 0.22
18 1 0.04
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (16 bp):
ATAAATTAATTAAATT
Found at i:17916307 original size:21 final size:22
Alignment explanation
Indices: 17916277--17916321 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
17916267 TATTTAACCC
17916277 AAAATAAATTGA-ATTA-AAATT
1 AAAATAAATT-ATATTATAAATT
*
17916298 AAAATTAATTATATTATAAATT
1 AAAATAAATTATATTATAAATT
17916320 AA
1 AA
17916322 TATTCATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 1 0.05
21 13 0.62
22 7 0.33
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (22 bp):
AAAATAAATTATATTATAAATT
Found at i:17919460 original size:24 final size:24
Alignment explanation
Indices: 17919378--17919513 Score: 132
Period size: 25 Copynumber: 5.5 Consensus size: 24
17919368 ACGAGCTATG
* *
17919378 AATCGGTATGCTCTCATGAGCTAGA
1 AATCGGTAAGCTCTCACGAGCT-GA
* *
17919403 AATCAGTAAGCGCAT-ACGAGCTGA
1 AATCGGTAAGCTC-TCACGAGCTGA
17919427 GAATCGGTAAGCTCTCACGAGCTGA
1 -AATCGGTAAGCTCTCACGAGCTGA
*
17919452 AATCGGTAAGCTCAT-ACGAGCTTA
1 AATCGGTAAGCTC-TCACGAGCTGA
* * *
17919476 GAATCGATAAGCTTTCATGAGCTGA
1 -AATCGGTAAGCTCTCACGAGCTGA
*
17919501 AATCGATAAGCTC
1 AATCGGTAAGCTC
17919514 ATAAGAGCTC
Statistics
Matches: 93, Mismatches: 12, Indels: 13
0.79 0.10 0.11
Matches are distributed among these distances:
24 37 0.40
25 55 0.59
26 1 0.01
ACGTcount: A:0.32, C:0.21, G:0.24, T:0.24
Consensus pattern (24 bp):
AATCGGTAAGCTCTCACGAGCTGA
Found at i:17919473 original size:49 final size:48
Alignment explanation
Indices: 17919362--17919522 Score: 214
Period size: 49 Copynumber: 3.3 Consensus size: 48
17919352 GTACATGTAT
* *
17919362 GCTCATACGAGCTATGAATCGGTATGCTCTCATGAGCTAGAAATCAGTAA
1 GCTCATACGAGCTA-GAATCGGTAAGCTCTCATGAGCT-GAAATCGGTAA
* *
17919412 GCGCATACGAGCTGAGAATCGGTAAGCTCTCACGAGCTGAAATCGGTAA
1 GCTCATACGAGCT-AGAATCGGTAAGCTCTCATGAGCTGAAATCGGTAA
* * *
17919461 GCTCATACGAGCTTAGAATCGATAAGCTTTCATGAGCTGAAATCGATAA
1 GCTCATACGAGC-TAGAATCGGTAAGCTCTCATGAGCTGAAATCGGTAA
*
17919510 GCTCATAAGAGCT
1 GCTCATACGAGCT
17919523 CTGGTGTGCC
Statistics
Matches: 99, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
48 1 0.01
49 63 0.64
50 34 0.34
51 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.24
Consensus pattern (48 bp):
GCTCATACGAGCTAGAATCGGTAAGCTCTCATGAGCTGAAATCGGTAA
Found at i:17926385 original size:3 final size:3
Alignment explanation
Indices: 17926377--17927178 Score: 1604
Period size: 3 Copynumber: 267.3 Consensus size: 3
17926367 GGGTGGAGTA
17926377 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
17926425 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
17926473 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
17926521 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
17926569 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
17926617 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
17926665 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
17926713 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
17926761 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
17926809 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
17926857 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
17926905 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
17926953 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
17927001 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
17927049 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
17927097 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
17927145 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
17927179 ATCTTTGTAC
Statistics
Matches: 799, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 799 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:17927979 original size:3 final size:3
Alignment explanation
Indices: 17927971--17928002 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
17927961 ATGGTTTTAT
*
17927971 ATA ATA ATA ATA ATA ATA ATA GTA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
17928003 TAGCTTAAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:17935756 original size:25 final size:25
Alignment explanation
Indices: 17935722--17935770 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
17935712 CAAGCCCATT
* * *
17935722 TTCATAGCTCGTGTGAGCATACTTA
1 TTCAAAGCTCATGTGAGCACACTTA
17935747 TTCAAAGCTCATGTGAGCACACTT
1 TTCAAAGCTCATGTGAGCACACTT
17935771 TGTGTGAGCT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.33
Consensus pattern (25 bp):
TTCAAAGCTCATGTGAGCACACTTA
Found at i:17938104 original size:16 final size:16
Alignment explanation
Indices: 17938083--17938117 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
17938073 TCTATAGTTG
*
17938083 ATATTCAAATATTTAA
1 ATATTCAAAAATTTAA
*
17938099 ATATTCAAAAATTTTA
1 ATATTCAAAAATTTAA
17938115 ATA
1 ATA
17938118 GAATCCCGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (16 bp):
ATATTCAAAAATTTAA
Found at i:17943121 original size:46 final size:48
Alignment explanation
Indices: 17943045--17943187 Score: 168
Period size: 47 Copynumber: 3.0 Consensus size: 48
17943035 CAACCCTGTT
* * *
17943045 TTGGACAGCAATTATTCATCAAATTGGACAGCAAT-AATATGCTCTAAA
1 TTGGACAGC-ATTATACATCAAATTGGACAGCAATAAATATACTCAAAA
* * *
17943093 -TGGGCAGCATTATACATCAAATTAGACAGC-TTAAATATACTCAAAA
1 TTGGACAGCATTATACATCAAATTGGACAGCAATAAATATACTCAAAA
* * *
17943139 TTGGACAGCATTATACATTAAAATGGACAGC-ATCAATATACTCAAAA
1 TTGGACAGCATTATACATCAAATTGGACAGCAATAAATATACTCAAAA
17943186 TT
1 TT
17943188 TATAACACAA
Statistics
Matches: 81, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
45 1 0.01
46 31 0.38
47 49 0.60
ACGTcount: A:0.42, C:0.17, G:0.13, T:0.28
Consensus pattern (48 bp):
TTGGACAGCATTATACATCAAATTGGACAGCAATAAATATACTCAAAA
Found at i:17943165 original size:22 final size:22
Alignment explanation
Indices: 17943046--17943171 Score: 85
Period size: 23 Copynumber: 5.5 Consensus size: 22
17943036 AACCCTGTTT
* *
17943046 TGGACAGCAATTATTCATCAAAT
1 TGGACAGC-ATTATACATCAAAA
* *
17943069 TGGACAGCAATAATATGC-TCTAAA
1 TGGACAGC-AT--TATACATCAAAA
* *
17943093 TGGGCAGCATTATACATCAAAT
1 TGGACAGCATTATACATCAAAA
* *
17943115 TAGACAGC-TTAAATATACTCAAAA
1 TGGACAGCATT--ATACA-TCAAAA
*
17943139 TTGGACAGCATTATACATTAAAA
1 -TGGACAGCATTATACATCAAAA
17943162 TGGACAGCAT
1 TGGACAGCAT
17943172 CAATATACTC
Statistics
Matches: 81, Mismatches: 14, Indels: 17
0.72 0.12 0.15
Matches are distributed among these distances:
21 6 0.07
22 20 0.25
23 22 0.27
24 20 0.25
25 11 0.14
26 2 0.02
ACGTcount: A:0.41, C:0.17, G:0.15, T:0.27
Consensus pattern (22 bp):
TGGACAGCATTATACATCAAAA
Done.