Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008155.1 Hibiscus syriacus cultivar Beakdansim tig00110721_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 962042
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 5
Found at i:518026 original size:42 final size:42
Alignment explanation
Indices: 517980--518157 Score: 138
Period size: 42 Copynumber: 4.3 Consensus size: 42
517970 TATCATCTCA
517980 CTCGAAAGACTTACAAATGACCCGAAGGATTTCATCATCATG
1 CTCGAAAGACTTACAAATGACCCGAAGGATTTCATCATCATG
* ** * *
518022 CTCGAAAGACTTAC---TGA--TGAATTTACTTCA-CTACTCTTCG
1 CTCGAAAGACTTACAAATGACCCGAA-GGATTTCATC-A-TCAT-G
* * * * *
518062 GT-G-AAGGCTTACAAATTATCCGAAGGATTTAATCATCATG
1 CTCGAAAGACTTACAAATGACCCGAAGGATTTCATCATCATG
** *
518102 CTCGAAAGACTTACTGATGGCCCGAAGGATTTCATCATCATG
1 CTCGAAAGACTTACAAATGACCCGAAGGATTTCATCATCATG
*
518144 CTCAAAAGACTTAC
1 CTCGAAAGACTTAC
518158 TGATGGCACT
Statistics
Matches: 101, Mismatches: 23, Indels: 24
0.68 0.16 0.16
Matches are distributed among these distances:
37 4 0.04
38 14 0.14
39 7 0.07
40 4 0.04
41 6 0.06
42 62 0.61
43 4 0.04
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (42 bp):
CTCGAAAGACTTACAAATGACCCGAAGGATTTCATCATCATG
Found at i:518158 original size:42 final size:42
Alignment explanation
Indices: 518081--518164 Score: 150
Period size: 42 Copynumber: 2.0 Consensus size: 42
518071 TACAAATTAT
*
518081 CCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGC
1 CCGAAGGATTTAATCATCATGCTCAAAAGACTTACTGATGGC
*
518123 CCGAAGGATTTCATCATCATGCTCAAAAGACTTACTGATGGC
1 CCGAAGGATTTAATCATCATGCTCAAAAGACTTACTGATGGC
518165 ACTTACTGAT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.26
Consensus pattern (42 bp):
CCGAAGGATTTAATCATCATGCTCAAAAGACTTACTGATGGC
Found at i:518170 original size:13 final size:13
Alignment explanation
Indices: 518152--518176 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
518142 TGCTCAAAAG
518152 ACTTACTGATGGC
1 ACTTACTGATGGC
518165 ACTTACTGATGG
1 ACTTACTGATGG
518177 GTTTGCTTCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (13 bp):
ACTTACTGATGGC
Found at i:518433 original size:41 final size:41
Alignment explanation
Indices: 518378--518484 Score: 133
Period size: 42 Copynumber: 2.6 Consensus size: 41
518368 CCCGAAGGTT
* * * *
518378 TTACGGATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGC
1 TTACAGATGGCCCGAAGGACTTATCATCATGCTCGAAAGAC
* * *
518419 TTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGAC
1 TTACAGATGGCCCGAAGGACTT-ATCATCATGCTCGAAAGAC
*
518461 TTACTGATGGCCCGAAGGACTTAT
1 TTACAGATGGCCCGAAGGACTTAT
518485 AAATTGTGAA
Statistics
Matches: 54, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
41 20 0.37
42 34 0.63
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.25
Consensus pattern (41 bp):
TTACAGATGGCCCGAAGGACTTATCATCATGCTCGAAAGAC
Found at i:518450 original size:214 final size:214
Alignment explanation
Indices: 518200--518601 Score: 678
Period size: 214 Copynumber: 1.9 Consensus size: 214
518190 CTCTTCGGTG
* *
518200 AAGGCTTACAAATTACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGACCGAAGG
1 AAGGCTTACAAATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGACCGAAGG
* *
518265 ACTTATAAATTGTGAAATTTAGAAAATCGCATTATTTGTTTTCAAAAATTTCATCTTCTCAAAAC
66 ACTTATAAATTGTGAAATTTAGAAAATCGCATTATTCGTTTTCAAAAATTCCATCTTCTCAAAAC
* *
518330 ATCGTTTTTCATTTTCAAATTCTTTTGAAAACATCTTACCCGAAGGTTTTACGGATGGCCCGAAG
131 ATCATTTTTCATTTTCAAATTCTTTTGAAAACATCTTACCCGAAGGTCTTACGGATGGCCCGAAG
518395 GACTTATCATCTTGCTCTA
196 GACTTATCATCTTGCTCTA
* *
518414 AAGGCTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGG
1 AAGGCTTACAAATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGACCGAAGG
* * * *
518479 ACTTATAAATTGTGAAATTTTGAAAATTGCATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAAC
66 ACTTATAAATTGTGAAATTTAGAAAATCGCATTATTCGTTTTCAAAAATTCCATCTTCTCAAAAC
* *
518544 ATCATTTTTTATTTTCAAATTCTTTTGAAAACATCTTACCCGAAGGTCTTATGGATGG
131 ATCATTTTTCATTTTCAAATTCTTTTGAAAACATCTTACCCGAAGGTCTTACGGATGG
518602 TTTGCTTCAC
Statistics
Matches: 174, Mismatches: 14, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
214 174 1.00
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.34
Consensus pattern (214 bp):
AAGGCTTACAAATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGACCGAAGG
ACTTATAAATTGTGAAATTTAGAAAATCGCATTATTCGTTTTCAAAAATTCCATCTTCTCAAAAC
ATCATTTTTCATTTTCAAATTCTTTTGAAAACATCTTACCCGAAGGTCTTACGGATGGCCCGAAG
GACTTATCATCTTGCTCTA
Found at i:524680 original size:6 final size:6
Alignment explanation
Indices: 524649--524678 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
524639 TGCTAATAAG
*
524649 AATGCA AATGCA AATGCA AATGCA CATGCA
1 AATGCA AATGCA AATGCA AATGCA AATGCA
524679 CAAGGTGTTA
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:0.20, G:0.17, T:0.17
Consensus pattern (6 bp):
AATGCA
Found at i:529071 original size:21 final size:21
Alignment explanation
Indices: 529046--529088 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
529036 TATTTTGATA
*
529046 TTATGTTTGATATTTATAAAT
1 TTATGTTTGATATATATAAAT
*
529067 TTATGTTTGATATATATTAAT
1 TTATGTTTGATATATATAAAT
529088 T
1 T
529089 AATTCAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.00, G:0.09, T:0.58
Consensus pattern (21 bp):
TTATGTTTGATATATATAAAT
Found at i:530665 original size:23 final size:23
Alignment explanation
Indices: 530627--530696 Score: 81
Period size: 23 Copynumber: 3.0 Consensus size: 23
530617 TAAAATATAA
*
530627 TATAA-TATTCTTATTTTCA-TAT
1 TATAATTATTATTATTTT-ATTAT
*
530649 TATAATTTTTATTATTTTATTAT
1 TATAATTATTATTATTTTATTAT
*
530672 TATTATTATTATTATTATTATTAT
1 TATAATTATTATTATT-TTATTAT
530696 T
1 T
530697 TTATTAAGTA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
22 6 0.15
23 27 0.66
24 8 0.20
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (23 bp):
TATAATTATTATTATTTTATTAT
Found at i:530671 original size:3 final size:3
Alignment explanation
Indices: 530646--530702 Score: 82
Period size: 3 Copynumber: 19.7 Consensus size: 3
530636 CTTATTTTCA
* *
530646 TAT TAT AAT TTT TAT TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
530693 TAT T-T TAT TA
1 TAT TAT TAT TA
530703 AGTAATTAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
2 4 0.08
3 44 0.92
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:530728 original size:32 final size:32
Alignment explanation
Indices: 530649--530765 Score: 112
Period size: 32 Copynumber: 3.7 Consensus size: 32
530639 ATTTTCATAT
* * * *
530649 TATAATT-TTTATTATTTTATTATTATTATTAT
1 TATAATTAATTATTATTTTATTA-AATAATTAA
* *
530681 TATTATT-ATTATTATTTTATTAAGTAATTAA
1 TATAATTAATTATTATTTTATTAAATAATTAA
* *
530712 TATAATTAATTCTTATTTTAATAAATAATTAA
1 TATAATTAATTATTATTTTATTAAATAATTAA
* * *
530744 TATAGTTTATTATAATTTTATT
1 TATAATTAATTATTATTTTATT
530766 TTAATAAAAT
Statistics
Matches: 69, Mismatches: 15, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
31 11 0.16
32 58 0.84
ACGTcount: A:0.38, C:0.01, G:0.02, T:0.60
Consensus pattern (32 bp):
TATAATTAATTATTATTTTATTAAATAATTAA
Found at i:530871 original size:20 final size:19
Alignment explanation
Indices: 530848--530904 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 19
530838 CATATATTAA
530848 ATAAATTAATCTAATATTTT
1 ATAAATTAAT-TAATATTTT
* *
530868 ATAAATATTATTATTATTTT
1 ATAAAT-TAATTAATATTTT
* *
530888 GTAAATTAAATAATATT
1 ATAAATTAATTAATATT
530905 ATTTATTGTA
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
19 8 0.27
20 19 0.63
21 3 0.10
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (19 bp):
ATAAATTAATTAATATTTT
Found at i:540546 original size:119 final size:119
Alignment explanation
Indices: 540335--540573 Score: 469
Period size: 119 Copynumber: 2.0 Consensus size: 119
540325 TCATTATCAA
540335 GAACCTACATGTTTGGGTATTCAAGATGTTGGATACCTAGTTTTTCGAGTACCAAAACAGTCGGT
1 GAACCTACATGTTTGGGTATTCAAGATGTTGGATACCTAGTTTTTCGAGTACCAAAACAGTCGGT
540400 TCGTGTCTCGACCTATGAAACTCGGGTACCTATAATTCGGGTCTTGCAAAACTT
66 TCGTGTCTCGACCTATGAAACTCGGGTACCTATAATTCGGGTCTTGCAAAACTT
540454 GAACCTACATGTTTGGGTATTCAAGATGTTGGATACCTAGTTTTTCGAGTACCAAAACAGTCGGT
1 GAACCTACATGTTTGGGTATTCAAGATGTTGGATACCTAGTTTTTCGAGTACCAAAACAGTCGGT
*
540519 TCGTGTCTCGACCTATTAAACTCGGGTACCTATAATTCGGGTCTTGCAAAACTT
66 TCGTGTCTCGACCTATGAAACTCGGGTACCTATAATTCGGGTCTTGCAAAACTT
540573 G
1 G
540574 GGTACTCGTT
Statistics
Matches: 119, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
119 119 1.00
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.32
Consensus pattern (119 bp):
GAACCTACATGTTTGGGTATTCAAGATGTTGGATACCTAGTTTTTCGAGTACCAAAACAGTCGGT
TCGTGTCTCGACCTATGAAACTCGGGTACCTATAATTCGGGTCTTGCAAAACTT
Found at i:543732 original size:10 final size:10
Alignment explanation
Indices: 543717--543790 Score: 50
Period size: 10 Copynumber: 7.6 Consensus size: 10
543707 CATTTAATAA
543717 ATAAACGAAC
1 ATAAACGAAC
543727 ATAAACGAAC
1 ATAAACGAAC
* *
543737 ACAAACATAAAC
1 ATAAAC--GAAC
*
543749 GA-ATACGAAC
1 -ATAAACGAAC
*
543759 ATAAATGAAC
1 ATAAACGAAC
543769 ----ACGAAC
1 ATAAACGAAC
543775 ATAAACGAAC
1 ATAAACGAAC
543785 ATAAAC
1 ATAAAC
543791 ATTGGAGACC
Statistics
Matches: 49, Mismatches: 7, Indels: 16
0.68 0.10 0.22
Matches are distributed among these distances:
6 5 0.10
9 1 0.02
10 36 0.73
12 6 0.12
13 1 0.02
ACGTcount: A:0.59, C:0.20, G:0.09, T:0.11
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:543745 original size:16 final size:16
Alignment explanation
Indices: 543724--543792 Score: 93
Period size: 16 Copynumber: 4.3 Consensus size: 16
543714 TAAATAAACG
543724 AACATAAACGAACACA
1 AACATAAACGAACACA
* *
543740 AACATAAACGAATACG
1 AACATAAACGAACACA
* *
543756 AACATAAATGAACACG
1 AACATAAACGAACACA
*
543772 AACATAAACGAACATA
1 AACATAAACGAACACA
543788 AACAT
1 AACAT
543793 TGGAGACCCT
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 46 1.00
ACGTcount: A:0.59, C:0.20, G:0.09, T:0.12
Consensus pattern (16 bp):
AACATAAACGAACACA
Found at i:543757 original size:32 final size:32
Alignment explanation
Indices: 543721--543783 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
543711 TAATAAATAA
543721 ACGAACATAAACGAACACAAACATAAACGAAT
1 ACGAACATAAACGAACACAAACATAAACGAAT
* *
543753 ACGAACATAAATGAACACGAACATAAACGAA
1 ACGAACATAAACGAACACAAACATAAACGAA
543784 CATAAACATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.59, C:0.21, G:0.11, T:0.10
Consensus pattern (32 bp):
ACGAACATAAACGAACACAAACATAAACGAAT
Found at i:544453 original size:14 final size:14
Alignment explanation
Indices: 544427--544458 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
544417 AACAAACATA
544427 AACGAACATAACTG
1 AACGAACATAACTG
544441 AACGAACATAACTG
1 AACGAACATAACTG
544455 AACG
1 AACG
544459 TTCACGAACG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.50, C:0.22, G:0.16, T:0.12
Consensus pattern (14 bp):
AACGAACATAACTG
Found at i:544457 original size:24 final size:24
Alignment explanation
Indices: 544383--544451 Score: 93
Period size: 24 Copynumber: 2.9 Consensus size: 24
544373 GATTAGCTTA
* *
544383 AACATAAATGAATGAACATAAACG
1 AACATAACTGAACGAACATAAACG
** *
544407 AACATAACCAAACAAACATAAACG
1 AACATAACTGAACGAACATAAACG
544431 AACATAACTGAACGAACATAA
1 AACATAACTGAACGAACATAA
544452 CTGAACGTTC
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.59, C:0.19, G:0.09, T:0.13
Consensus pattern (24 bp):
AACATAACTGAACGAACATAAACG
Found at i:547483 original size:43 final size:43
Alignment explanation
Indices: 547433--547530 Score: 124
Period size: 43 Copynumber: 2.3 Consensus size: 43
547423 CAATAGGTTA
* *
547433 AGATCTATAGCGGCGTTTTTGGAACAAACATCGCAAAAGGTCG
1 AGATCTATAGCGGCATTTTTGGAACAAACACCGCAAAAGGTCG
* * * * * *
547476 ATATCTATAACGGCATTTTTTGAATAAACGCCGTAAAAGGTCG
1 AGATCTATAGCGGCATTTTTGGAACAAACACCGCAAAAGGTCG
547519 AGATCTATAGCG
1 AGATCTATAGCG
547531 ACAAAATTTG
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.27
Consensus pattern (43 bp):
AGATCTATAGCGGCATTTTTGGAACAAACACCGCAAAAGGTCG
Found at i:548220 original size:21 final size:21
Alignment explanation
Indices: 548196--548252 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
548186 CAACAATAAC
548196 CATGAATCAAATGCTCGAAAG
1 CATGAATCAAATGCTCGAAAG
548217 CATGAATCAAATGCTCGAAAG
1 CATGAATCAAATGCTCGAAAG
*
548238 CATGAATCGAATGCT
1 CATGAATCAAATGCT
548253 AAAAAACAAC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.21
Consensus pattern (21 bp):
CATGAATCAAATGCTCGAAAG
Found at i:549846 original size:41 final size:40
Alignment explanation
Indices: 549769--549847 Score: 97
Period size: 41 Copynumber: 1.9 Consensus size: 40
549759 GTTTACATGA
* * * *
549769 AAAAAACGCCACTAATGTATGTGATTTTGTAGCGTTTTGC
1 AAAAAACGCCACTAATATATGGGATATCGTAGCGTTTTGC
549809 AAAAAACGCCACTATATATATGGGATATCGT-GACGTTTT
1 AAAAAACGCCACTA-ATATATGGGATATCGTAG-CGTTTT
549848 TTTAACATAA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
40 15 0.45
41 18 0.55
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Consensus pattern (40 bp):
AAAAAACGCCACTAATATATGGGATATCGTAGCGTTTTGC
Found at i:550717 original size:15 final size:17
Alignment explanation
Indices: 550692--550724 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
550682 ATAAAATATT
550692 AAAGAAAAAAT-ATAAA
1 AAAGAAAAAATAATAAA
550708 AAAG-AAAAATAATAAA
1 AAAGAAAAAATAATAAA
550724 A
1 A
550725 GGATCTCATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.82, C:0.00, G:0.06, T:0.12
Consensus pattern (17 bp):
AAAGAAAAAATAATAAA
Found at i:550853 original size:15 final size:15
Alignment explanation
Indices: 550807--550879 Score: 110
Period size: 15 Copynumber: 4.7 Consensus size: 15
550797 TGTGCAAATC
550807 CGGGTACCCGGATTTT
1 CGGGTACCC-GATTTT
*
550823 CGGGTACCAGGATTTT
1 CGGGTACC-CGATTTT
550839 CGGGTACCCGATTTT
1 CGGGTACCCGATTTT
550854 CGGGTACCCGATTTT
1 CGGGTACCCGATTTT
*
550869 CGGGTAACCGA
1 CGGGTACCCGA
550880 AACTTTCGGG
Statistics
Matches: 53, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
15 31 0.58
16 22 0.42
ACGTcount: A:0.16, C:0.25, G:0.30, T:0.29
Consensus pattern (15 bp):
CGGGTACCCGATTTT
Found at i:551670 original size:26 final size:26
Alignment explanation
Indices: 551641--551694 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
551631 ATCATTCTAG
* *
551641 TAGTTGGTTTGACCAACTAATTTGAT
1 TAGTTGATTTGACAAACTAATTTGAT
* *
551667 TAGTTGATTTGAGAAACTTATTTGAT
1 TAGTTGATTTGACAAACTAATTTGAT
551693 TA
1 TA
551695 ATTGTTTATG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.30, C:0.07, G:0.19, T:0.44
Consensus pattern (26 bp):
TAGTTGATTTGACAAACTAATTTGAT
Found at i:552481 original size:2 final size:2
Alignment explanation
Indices: 552474--552503 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
552464 AATTAAACAA
552474 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
552504 GACTAAAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:553951 original size:3 final size:3
Alignment explanation
Indices: 553943--553984 Score: 68
Period size: 3 Copynumber: 14.0 Consensus size: 3
553933 ATTTTATTTA
553943 AAT AAT AAT AAT AAT ATAT AAT AAT AAT AAT AAT AA- AAT AAT
1 AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT
553985 TTTAATGAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.05
3 32 0.86
4 3 0.08
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:554238 original size:76 final size:76
Alignment explanation
Indices: 554138--554847 Score: 1203
Period size: 76 Copynumber: 9.4 Consensus size: 76
554128 GGTCCTAAGA
* * * *
554138 AAACATCATGCACTGAAGGGCTTACAAATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
554203 AGGCTTTTTGG
66 AGGCTTTTTGG
* ** * *
554214 AAACATCATGCATTATAGGACTTACAGATGACCCTAAGGTTTTAAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
554279 AGGCTTTTTGG
66 AGGCTTTTTGG
*
554290 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
554355 AGGCTTTTTGG
66 AGGCTTTTTGG
*
554366 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAATATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
554431 AGGCTTTTTGG
66 AGGCTTTTTGG
554442 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
554507 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
554518 AAACATCATGCACTGTAGGACTTACATATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
554583 AGGCTTTTTGG
66 AGGCTTTTTGG
* * *
554594 AAACATCATGTATTGCAGGACTTACAGAT---CCTAAGGCTTTG-AAACATCAAAAATCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
554655 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
554666 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCTGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
554731 AGGCTTTTTGG
66 AGGCTTTTTGG
*
554742 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGTTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
554807 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
554818 AAACATCATGCACTGCAAGACTTAAAGATG
1 AAACATCATGCACTGCAGGACTTACAGATG
554848 TGGGAAATAG
Statistics
Matches: 600, Mismatches: 30, Indels: 8
0.94 0.05 0.01
Matches are distributed among these distances:
72 56 0.09
73 12 0.02
75 12 0.02
76 520 0.87
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24
Consensus pattern (76 bp):
AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGG
Found at i:555551 original size:22 final size:22
Alignment explanation
Indices: 555523--555599 Score: 145
Period size: 22 Copynumber: 3.5 Consensus size: 22
555513 AATAAAGCTT
555523 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
555545 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
555567 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
555589 TCATCTTTGAA
1 TCATCTTTGAA
555600 GAGTGTAGAT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 53 1.00
ACGTcount: A:0.40, C:0.14, G:0.12, T:0.34
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:560194 original size:16 final size:16
Alignment explanation
Indices: 560173--560231 Score: 88
Period size: 15 Copynumber: 3.8 Consensus size: 16
560163 CTTGATTCAA
560173 TTTTCCTTTTTTCTTT
1 TTTTCCTTTTTTCTTT
560189 TTTTCC-TTTTTCTTT
1 TTTTCCTTTTTTCTTT
560204 TTTTCCTTTTTGT-TTT
1 TTTTCCTTTTT-TCTTT
560220 TTTT-CTTTTTTC
1 TTTTCCTTTTTTC
560232 CTTCTCTTTC
Statistics
Matches: 40, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
14 1 0.03
15 21 0.52
16 17 0.43
17 1 0.03
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.81
Consensus pattern (16 bp):
TTTTCCTTTTTTCTTT
Found at i:560208 original size:31 final size:31
Alignment explanation
Indices: 560173--560231 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
560163 CTTGATTCAA
560173 TTTTCCTTTTT-TCTTTTTTTCCTTTTTCTTT
1 TTTTCCTTTTTGT-TTTTTTTCCTTTTTCTTT
*
560204 TTTTCCTTTTTGTTTTTTTTCTTTTTTC
1 TTTTCCTTTTTGTTTTTTTTCCTTTTTC
560232 CTTCTCTTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 25 0.96
32 1 0.04
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.81
Consensus pattern (31 bp):
TTTTCCTTTTTGTTTTTTTTCCTTTTTCTTT
Found at i:560544 original size:2 final size:2
Alignment explanation
Indices: 560537--560569 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
560527 ACAATAAAGG
560537 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
560570 GGATAAATGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:562798 original size:37 final size:37
Alignment explanation
Indices: 562757--562827 Score: 92
Period size: 37 Copynumber: 1.9 Consensus size: 37
562747 TAAATGCGAA
*
562757 AATGCATAA-ATGCCAAAAA-TAAGAATGCAAAATGTGC
1 AATGCA-AAGATG-CAAAAAGTAAGAATACAAAATGTGC
*
562794 AATGCAAAGATGTAAAAAGTAAGAATACAAAATG
1 AATGCAAAGATGCAAAAAGTAAGAATACAAAATG
562828 AAAATGCATA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
36 7 0.23
37 23 0.77
ACGTcount: A:0.55, C:0.10, G:0.17, T:0.18
Consensus pattern (37 bp):
AATGCAAAGATGCAAAAAGTAAGAATACAAAATGTGC
Found at i:562842 original size:21 final size:21
Alignment explanation
Indices: 562818--562857 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
562808 AAAAGTAAGA
562818 ATACAAAATGAAAATGCATAG
1 ATACAAAATGAAAATGCATAG
*
562839 ATACAAAATGTAAATGCAT
1 ATACAAAATGAAAATGCAT
562858 GTATGAAAAG
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):
ATACAAAATGAAAATGCATAG
Found at i:565702 original size:2 final size:2
Alignment explanation
Indices: 565695--565740 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
565685 TTTAAAGAAA
565695 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
565737 AT AT
1 AT AT
565741 CTTAACATAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:565864 original size:21 final size:21
Alignment explanation
Indices: 565809--565864 Score: 51
Period size: 21 Copynumber: 2.6 Consensus size: 21
565799 GCTCTTTCCT
* *
565809 TAAAATAAATAAATAAATATTAA
1 TAAAAT-AATTAA-AAATAATAA
*
565832 TAAAATATTTAAAAATAATAA
1 TAAAATAATTAAAAATAATAA
565853 -AAAATAGATTAA
1 TAAAATA-ATTAA
565865 TATATATAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
20 6 0.21
21 12 0.43
22 4 0.14
23 6 0.21
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (21 bp):
TAAAATAATTAAAAATAATAA
Found at i:566131 original size:2 final size:2
Alignment explanation
Indices: 566124--566157 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
566114 AATTAAACAA
566124 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
566158 GACTAAAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:567600 original size:3 final size:3
Alignment explanation
Indices: 567592--567645 Score: 65
Period size: 3 Copynumber: 18.0 Consensus size: 3
567582 ATTTTATTTA
* * *
567592 AAT AAT AAT AAT AAT ATAT AAT ATT AAT ATT AAT ATT AAT AAT AAT
1 AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT
567638 AA- AAT AAT
1 AAT AAT AAT
567646 TTTAATGAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
2 2 0.05
3 38 0.88
4 3 0.07
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
AAT
Found at i:568994 original size:20 final size:21
Alignment explanation
Indices: 568969--569020 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 21
568959 GATAAATTTA
*
568969 TTAATAATTTTTATAA-TCTT
1 TTAATAATTTTTATAAGTATT
* *
568989 TTAATAAATTTAATAAGTATT
1 TTAATAATTTTTATAAGTATT
569010 TT-ATAATTTTT
1 TTAATAATTTTT
569021 TAAATTTTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
20 21 0.81
21 5 0.19
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (21 bp):
TTAATAATTTTTATAAGTATT
Found at i:568996 original size:32 final size:31
Alignment explanation
Indices: 568936--569023 Score: 90
Period size: 31 Copynumber: 2.8 Consensus size: 31
568926 CTAGATAATA
* * *
568936 TAATAATTATTTTATAGT-ATTTAGATAAATT
1 TAATAAGTATTTTATAATCTTTTA-ATAAATT
*
568967 TATTAA-TAATTTTTATAATCTTTTAATAAATT
1 TAATAAGT-A-TTTTATAATCTTTTAATAAATT
*
568999 TAATAAGTATTTTATAATTTTTTAA
1 TAATAAGTATTTTATAATCTTTTAA
569024 ATTTTATTGA
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
30 1 0.02
31 21 0.44
32 21 0.44
33 5 0.10
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (31 bp):
TAATAAGTATTTTATAATCTTTTAATAAATT
Found at i:569015 original size:31 final size:29
Alignment explanation
Indices: 568936--569027 Score: 89
Period size: 32 Copynumber: 3.0 Consensus size: 29
568926 CTAGATAATA
* *
568936 TAATAATTATTTTATAGTATTTAGATAAATT
1 TAATAA-TATTTTATAATTTTTA-ATAAATT
*
568967 TATTAATAATTTTTATAATCTTTTAATAAATT
1 TAATAAT-A-TTTTATAAT-TTTTAATAAATT
568999 TAATAAGTATTTTATAATTTTT--TAAATT
1 TAATAA-TATTTTATAATTTTTAATAAATT
569027 T
1 T
569028 TATTGACGAA
Statistics
Matches: 53, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
28 7 0.13
30 5 0.09
31 15 0.28
32 21 0.40
33 5 0.09
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.55
Consensus pattern (29 bp):
TAATAATATTTTATAATTTTTAATAAATT
Found at i:569504 original size:18 final size:18
Alignment explanation
Indices: 569462--569504 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
569452 TCGAGTATTG
* * *
569462 ATATATTTGTGAATTGAA
1 ATATAATTGAGAATTAAA
569480 A-ATAATTGAGAATTAAA
1 ATATAATTGAGAATTAAA
569497 ATATAATT
1 ATATAATT
569505 TTTTTTAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 14 0.67
18 7 0.33
ACGTcount: A:0.49, C:0.00, G:0.12, T:0.40
Consensus pattern (18 bp):
ATATAATTGAGAATTAAA
Found at i:569773 original size:20 final size:20
Alignment explanation
Indices: 569748--569823 Score: 66
Period size: 20 Copynumber: 3.7 Consensus size: 20
569738 TCAATAAAGT
569748 TTAAAAAATTATTAAATTTA
1 TTAAAAAATTATTAAATTTA
* *
569768 TTAAAATATTA-TAAAATTA
1 TTAAAAAATTATTAAATTTA
* *
569787 TTAATAAATTTATCTAAATACTA
1 TTAA-AAAATTAT-TAAAT-TTA
569810 -TAAAATAATTATTA
1 TTAAAA-AATTATTA
569824 TATTATCGAA
Statistics
Matches: 44, Mismatches: 7, Indels: 9
0.73 0.12 0.15
Matches are distributed among these distances:
19 11 0.25
20 15 0.34
21 4 0.09
22 12 0.27
23 2 0.05
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (20 bp):
TTAAAAAATTATTAAATTTA
Found at i:569798 original size:31 final size:31
Alignment explanation
Indices: 569749--569820 Score: 94
Period size: 31 Copynumber: 2.4 Consensus size: 31
569739 CAATAAAGTT
* *
569749 TAAAA-AATTATTAAATTTAT-TAAAATATTA
1 TAAAATAATTAATAAATTTATCT-AAATACTA
*
569779 TAAAATTATTAATAAATTTATCTAAATACTA
1 TAAAATAATTAATAAATTTATCTAAATACTA
569810 TAAAATAATTA
1 TAAAATAATTA
569821 TTATATTATC
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
30 5 0.14
31 30 0.83
32 1 0.03
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.42
Consensus pattern (31 bp):
TAAAATAATTAATAAATTTATCTAAATACTA
Found at i:590064 original size:18 final size:18
Alignment explanation
Indices: 590035--590093 Score: 68
Period size: 18 Copynumber: 3.3 Consensus size: 18
590025 ATAATATAAG
590035 TTTATA-TATAAACTATA
1 TTTATATTATAAACTATA
590052 TTTATATTATAAACTATA
1 TTTATATTATAAACTATA
* *
590070 -TAATTATTATAAGCTATA
1 TTTA-TATTATAAACTATA
*
590088 TATATA
1 TTTATA
590094 AATTGTGTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
17 8 0.23
18 26 0.74
19 1 0.03
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.47
Consensus pattern (18 bp):
TTTATATTATAAACTATA
Found at i:590131 original size:13 final size:13
Alignment explanation
Indices: 590103--590154 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
590093 AAATTGTGTT
* *
590103 TATATGAACTACA
1 TATATAAACTATA
*
590116 TATATAAATTATA
1 TATATAAACTATA
*
590129 TATGTAAACTATA
1 TATATAAACTATA
590142 TACGTATAAACTA
1 TA--TATAAACTA
590155 AAAAAAGTAT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
13 23 0.74
15 8 0.26
ACGTcount: A:0.48, C:0.10, G:0.06, T:0.37
Consensus pattern (13 bp):
TATATAAACTATA
Found at i:590331 original size:27 final size:27
Alignment explanation
Indices: 590297--590355 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 27
590287 ATTTAGAGGG
*
590297 AAATTGGGAAATTTTGA-GAAAATTGGA
1 AAATTGGG-AATTTAGAGGAAAATTGGA
*
590324 AAATTGGGAATTTAGAGGGAAATTGGA
1 AAATTGGGAATTTAGAGGAAAATTGGA
590351 AAATT
1 AAATT
590356 TAGAGAGAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 7 0.24
27 22 0.76
ACGTcount: A:0.44, C:0.00, G:0.27, T:0.29
Consensus pattern (27 bp):
AAATTGGGAATTTAGAGGAAAATTGGA
Found at i:590338 original size:46 final size:47
Alignment explanation
Indices: 590279--590380 Score: 143
Period size: 46 Copynumber: 2.2 Consensus size: 47
590269 ATTTTATTTT
* * * * *
590279 ATTTGAGAATTTAGAGGGAAATTGGGAAATTTTGAGAAAATTGGAAA
1 ATTTGGGAATTTAGAGGGAAATTGGAAAATTTAGAGAAAATAGAAAA
*
590326 A-TTGGGAATTTAGAGGGAAATTGGAAAATTTAGAGAGAATAGAAAA
1 ATTTGGGAATTTAGAGGGAAATTGGAAAATTTAGAGAAAATAGAAAA
590372 ATTTGGGAA
1 ATTTGGGAA
590381 GTTGGGGCTA
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
46 40 0.83
47 8 0.17
ACGTcount: A:0.44, C:0.00, G:0.28, T:0.27
Consensus pattern (47 bp):
ATTTGGGAATTTAGAGGGAAATTGGAAAATTTAGAGAAAATAGAAAA
Found at i:590709 original size:21 final size:21
Alignment explanation
Indices: 590657--590703 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
590647 GTTTCCAGAT
590657 TCGCAACGCGAACTTCGACTA
1 TCGCAACGCGAACTTCGACTA
590678 TCGCAACGCGAACTTCGACTA
1 TCGCAACGCGAACTTCGACTA
590699 TCGCA
1 TCGCA
590704 TTGCGATTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.28, C:0.34, G:0.19, T:0.19
Consensus pattern (21 bp):
TCGCAACGCGAACTTCGACTA
Found at i:590744 original size:21 final size:20
Alignment explanation
Indices: 590722--591059 Score: 410
Period size: 21 Copynumber: 16.2 Consensus size: 20
590712 TACATATTCG
590722 CGTTGCGATAG-TCCAAGTT
1 CGTTGCGATAGCTCCAAGTT
* **
590741 CGCGTTGCAAT-TTTCCAAGTT
1 --CGTTGCGATAGCTCCAAGTT
590762 CGTTGCGATAGTCTCCAAGTT
1 CGTTGCGATAG-CTCCAAGTT
*
590783 CGTTGCTATAGTCTCCAAGTT
1 CGTTGCGATAG-CTCCAAGTT
*
590804 CGTTGCGATAGTCTCCAAATT
1 CGTTGCGATAG-CTCCAAGTT
* *
590825 GGTTGCGATAGTCTCCAAATT
1 CGTTGCGATAG-CTCCAAGTT
*
590846 CATTGCGATAGTCTCCAAGTT
1 CGTTGCGATAG-CTCCAAGTT
590867 CGTTGCGATAGTCTCCAAGTT
1 CGTTGCGATAG-CTCCAAGTT
590888 CGTTGCGATAGTCTCCAAGTT
1 CGTTGCGATAG-CTCCAAGTT
590909 CGTTGCGATAGTCTCCAAGTT
1 CGTTGCGATAG-CTCCAAGTT
*
590930 CGTTGCGATAGTCTCCAAATT
1 CGTTGCGATAG-CTCCAAGTT
*
590951 CGTTGCGATAGTCTCCAACTT
1 CGTTGCGATAG-CTCCAAGTT
*
590972 CGTTGCGATAGTCTCTAAGTT
1 CGTTGCGATAG-CTCCAAGTT
*
590993 CGTTGCGATAGTCTCCAAATT
1 CGTTGCGATAG-CTCCAAGTT
591014 CGTTGCGATAGTCTCCAAGTT
1 CGTTGCGATAG-CTCCAAGTT
591035 CGTTGCGATAGTCTCCAAGTT
1 CGTTGCGATAG-CTCCAAGTT
591056 CGTT
1 CGTT
591060 ATTGCATTTG
Statistics
Matches: 294, Mismatches: 20, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
19 8 0.03
21 286 0.97
ACGTcount: A:0.20, C:0.23, G:0.22, T:0.34
Consensus pattern (20 bp):
CGTTGCGATAGCTCCAAGTT
Found at i:590800 original size:42 final size:42
Alignment explanation
Indices: 590722--591059 Score: 531
Period size: 42 Copynumber: 8.1 Consensus size: 42
590712 TACATATTCG
* *
590722 CGTTGCGATAG--TCCAAGTTCGCGTTGC-A-ATTTTCCAAGTT
1 CGTTGCGATAGTCTCCAAGTT--CGTTGCGATAGTCTCCAAGTT
*
590762 CGTTGCGATAGTCTCCAAGTTCGTTGCTATAGTCTCCAAGTT
1 CGTTGCGATAGTCTCCAAGTTCGTTGCGATAGTCTCCAAGTT
* * *
590804 CGTTGCGATAGTCTCCAAATTGGTTGCGATAGTCTCCAAATT
1 CGTTGCGATAGTCTCCAAGTTCGTTGCGATAGTCTCCAAGTT
*
590846 CATTGCGATAGTCTCCAAGTTCGTTGCGATAGTCTCCAAGTT
1 CGTTGCGATAGTCTCCAAGTTCGTTGCGATAGTCTCCAAGTT
590888 CGTTGCGATAGTCTCCAAGTTCGTTGCGATAGTCTCCAAGTT
1 CGTTGCGATAGTCTCCAAGTTCGTTGCGATAGTCTCCAAGTT
* *
590930 CGTTGCGATAGTCTCCAAATTCGTTGCGATAGTCTCCAACTT
1 CGTTGCGATAGTCTCCAAGTTCGTTGCGATAGTCTCCAAGTT
* *
590972 CGTTGCGATAGTCTCTAAGTTCGTTGCGATAGTCTCCAAATT
1 CGTTGCGATAGTCTCCAAGTTCGTTGCGATAGTCTCCAAGTT
591014 CGTTGCGATAGTCTCCAAGTTCGTTGCGATAGTCTCCAAGTT
1 CGTTGCGATAGTCTCCAAGTTCGTTGCGATAGTCTCCAAGTT
591056 CGTT
1 CGTT
591060 ATTGCATTTG
Statistics
Matches: 276, Mismatches: 18, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
40 17 0.06
41 1 0.00
42 258 0.93
ACGTcount: A:0.20, C:0.23, G:0.22, T:0.34
Consensus pattern (42 bp):
CGTTGCGATAGTCTCCAAGTTCGTTGCGATAGTCTCCAAGTT
Found at i:590830 original size:63 final size:63
Alignment explanation
Indices: 590722--591059 Score: 540
Period size: 63 Copynumber: 5.4 Consensus size: 63
590712 TACATATTCG
* * *
590722 CGTTGCGATAG--TCCAAGTTCGCGTTGC-A-ATTTTCCAAGTTCGTTGCGATAGTCTCCAAGTT
1 CGTTGCGATAGTCTCCAAGTT--CGTTGCGATAGTCTCCAAATTCGTTGCGATAGTCTCCAAGTT
* * *
590783 CGTTGCTATAGTCTCCAAGTTCGTTGCGATAGTCTCCAAATTGGTTGCGATAGTCTCCAAATT
1 CGTTGCGATAGTCTCCAAGTTCGTTGCGATAGTCTCCAAATTCGTTGCGATAGTCTCCAAGTT
* *
590846 CATTGCGATAGTCTCCAAGTTCGTTGCGATAGTCTCCAAGTTCGTTGCGATAGTCTCCAAGTT
1 CGTTGCGATAGTCTCCAAGTTCGTTGCGATAGTCTCCAAATTCGTTGCGATAGTCTCCAAGTT
*
590909 CGTTGCGATAGTCTCCAAGTTCGTTGCGATAGTCTCCAAATTCGTTGCGATAGTCTCCAACTT
1 CGTTGCGATAGTCTCCAAGTTCGTTGCGATAGTCTCCAAATTCGTTGCGATAGTCTCCAAGTT
*
590972 CGTTGCGATAGTCTCTAAGTTCGTTGCGATAGTCTCCAAATTCGTTGCGATAGTCTCCAAGTT
1 CGTTGCGATAGTCTCCAAGTTCGTTGCGATAGTCTCCAAATTCGTTGCGATAGTCTCCAAGTT
591035 CGTTGCGATAGTCTCCAAGTTCGTT
1 CGTTGCGATAGTCTCCAAGTTCGTT
591060 ATTGCATTTG
Statistics
Matches: 256, Mismatches: 17, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
61 16 0.06
62 1 0.00
63 239 0.93
ACGTcount: A:0.20, C:0.23, G:0.22, T:0.34
Consensus pattern (63 bp):
CGTTGCGATAGTCTCCAAGTTCGTTGCGATAGTCTCCAAATTCGTTGCGATAGTCTCCAAGTT
Found at i:591640 original size:6 final size:6
Alignment explanation
Indices: 591629--591653 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
591619 CCGTCTCGTC
591629 TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG T
591654 AATACGTGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.48, T:0.36
Consensus pattern (6 bp):
TCGTGG
Found at i:591772 original size:21 final size:21
Alignment explanation
Indices: 591746--591949 Score: 329
Period size: 21 Copynumber: 9.7 Consensus size: 21
591736 TGCGATTTTG
*
591746 GACTATCACAACGAATTTGGA
1 GACTATCGCAACGAATTTGGA
591767 GACTATCGCAACGAATTTGGA
1 GACTATCGCAACGAATTTGGA
*
591788 GACTATCGCAACGAACTTGGA
1 GACTATCGCAACGAATTTGGA
591809 GACTATCGCAACGAATTTGGA
1 GACTATCGCAACGAATTTGGA
* *
591830 CACTATCGCAACGAACTTGGA
1 GACTATCGCAACGAATTTGGA
591851 GACTATCGCAACGAATTTGGA
1 GACTATCGCAACGAATTTGGA
591872 GACTATCGCAACGAATTTGGA
1 GACTATCGCAACGAATTTGGA
*
591893 GACTAAT-GCAACGAACTTGGA
1 GACT-ATCGCAACGAATTTGGA
* *
591914 GACTATCGCAACGCACTTGGA
1 GACTATCGCAACGAATTTGGA
591935 GACTATCGCAACGAA
1 GACTATCGCAACGAA
591950 CTTGAAAATC
Statistics
Matches: 171, Mismatches: 10, Indels: 4
0.92 0.05 0.02
Matches are distributed among these distances:
20 2 0.01
21 167 0.98
22 2 0.01
ACGTcount: A:0.34, C:0.22, G:0.23, T:0.21
Consensus pattern (21 bp):
GACTATCGCAACGAATTTGGA
Found at i:592301 original size:24 final size:25
Alignment explanation
Indices: 592266--592312 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
592256 ATATGTATGT
*
592266 ATATAAACTATATA-TGTATAAACA
1 ATATAAAATATATAGTGTATAAACA
*
592290 ATATAAAATATATAGTTTATAAA
1 ATATAAAATATATAGTGTATAAA
592313 TTATAATTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.36
Consensus pattern (25 bp):
ATATAAAATATATAGTGTATAAACA
Found at i:592332 original size:29 final size:32
Alignment explanation
Indices: 592299--592357 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
592289 AATATAAAAT
*
592299 ATATAGT-T-TATAAAT-TATAATTTATATTA
1 ATATAGTATATATAAATGTATAATTAATATTA
*
592328 ATATAGTATATATATATGTATAATTAATAT
1 ATATAGTATATATAAATGTATAATTAATAT
592358 AAGTAATCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 7 0.28
30 1 0.04
31 6 0.24
32 11 0.44
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (32 bp):
ATATAGTATATATAAATGTATAATTAATATTA
Found at i:592353 original size:26 final size:28
Alignment explanation
Indices: 592324--592377 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
592314 TATAATTTAT
*
592324 ATTAATAT-AGT-ATATATATATGTATA
1 ATTAATATAAGTAATATATATATATATA
*
592350 ATTAATATAAGTAATCTATATATATATA
1 ATTAATATAAGTAATATATATATATATA
592378 TATATGCATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 8 0.33
27 3 0.12
28 13 0.54
ACGTcount: A:0.48, C:0.02, G:0.06, T:0.44
Consensus pattern (28 bp):
ATTAATATAAGTAATATATATATATATA
Found at i:592396 original size:2 final size:2
Alignment explanation
Indices: 592245--592382 Score: 55
Period size: 2 Copynumber: 72.5 Consensus size: 2
592235 CTTTTAATTT
* * * * *
592245 TA TA TA TA TA TA TA TG TA TG TA TA TA AA CTA TA TA TG TA TA AA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
* * * * *
592288 CA -A TA TA -A AA TA TA TA GTT TA TA AA T- TA TA -A TT TA TA T-
1 TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA
*
592326 TA -A TA TA GTA TA TA TA TA TG TA TA -A T- TA -A TA TA -A GTA -A
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
*
592364 TC TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
592383 GCATAAACTA
Statistics
Matches: 100, Mismatches: 21, Indels: 30
0.66 0.14 0.20
Matches are distributed among these distances:
1 11 0.11
2 84 0.84
3 5 0.05
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (2 bp):
TA
Found at i:592396 original size:38 final size:40
Alignment explanation
Indices: 592328--592403 Score: 104
Period size: 38 Copynumber: 1.9 Consensus size: 40
592318 ATTTATATTA
* *
592328 ATATAGTATATATATATGTATAATTAATAT-AAGTAATCT
1 ATATAGTATATATATATGCATAACTAATATAAAGTAATCT
592367 ATATA-TATATATATATGCATAAACT-ATATAAAGTAAT
1 ATATAGTATATATATATGCAT-AACTAATATAAAGTAAT
592404 AAAATATGTA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
38 18 0.55
39 15 0.45
ACGTcount: A:0.49, C:0.04, G:0.07, T:0.41
Consensus pattern (40 bp):
ATATAGTATATATATATGCATAACTAATATAAAGTAATCT
Found at i:592521 original size:22 final size:22
Alignment explanation
Indices: 592496--592539 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
592486 CTTATAGTGC
* *
592496 ATATATGTATAAACTATGTATA
1 ATATATATATAAACTATATATA
*
592518 ATATATATATAACCTATATATA
1 ATATATATATAAACTATATATA
592540 GAAACTATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.48, C:0.07, G:0.05, T:0.41
Consensus pattern (22 bp):
ATATATATATAAACTATATATA
Found at i:592643 original size:14 final size:14
Alignment explanation
Indices: 592624--592663 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
592614 TAGTTTATAG
*
592624 AAACCCTAAACTTT
1 AAACCCTAAACTCT
592638 AAACCCTAAACTCT
1 AAACCCTAAACTCT
*
592652 AAACCTTAAACT
1 AAACCCTAAACT
592664 ATATATGTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.45, C:0.30, G:0.00, T:0.25
Consensus pattern (14 bp):
AAACCCTAAACTCT
Found at i:592794 original size:20 final size:20
Alignment explanation
Indices: 592771--592888 Score: 51
Period size: 20 Copynumber: 6.3 Consensus size: 20
592761 ATAGTTAATA
592771 TATATAACCTATAGTATATG
1 TATATAACCTATAGTATATG
* * *
592791 --TAT-ACATATA-AACTATA
1 TATATAACCTATAGTA-TATG
* * *
592808 TATGTAACTTATAGTACATG
1 TATATAACCTATAGTATATG
*
592828 TATGTATAAACTAT-GTATA-G
1 TA--TATAACCTATAGTATATG
* *
592848 TATAT-A--TAAACTATAT-
1 TATATAACCTATAGTATATG
592864 -ATATAACCTATAGTATATG
1 TATATAACCTATAGTATATG
592883 TATATA
1 TATATA
592889 TACAATCTAT
Statistics
Matches: 68, Mismatches: 16, Indels: 28
0.61 0.14 0.25
Matches are distributed among these distances:
15 6 0.09
16 6 0.09
17 10 0.15
18 14 0.21
19 2 0.03
20 18 0.26
21 5 0.07
22 7 0.10
ACGTcount: A:0.43, C:0.08, G:0.08, T:0.40
Consensus pattern (20 bp):
TATATAACCTATAGTATATG
Found at i:592836 original size:35 final size:36
Alignment explanation
Indices: 592768--592846 Score: 97
Period size: 37 Copynumber: 2.2 Consensus size: 36
592758 ACAATAGTTA
*
592768 ATATATATAACCTATAGTATATGTATACATATAAACT
1 ATATATATAACCTATAGTACATGTATA-ATATAAACT
* * *
592805 ATATATGTAACTTATAGTACATGTAT-GTATAAACT
1 ATATATATAACCTATAGTACATGTATAATATAAACT
*
592840 ATGTATA
1 ATATATA
592847 GTATATATAA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
35 13 0.36
37 23 0.64
ACGTcount: A:0.43, C:0.09, G:0.09, T:0.39
Consensus pattern (36 bp):
ATATATATAACCTATAGTACATGTATAATATAAACT
Found at i:592860 original size:55 final size:56
Alignment explanation
Indices: 592769--592934 Score: 210
Period size: 57 Copynumber: 2.9 Consensus size: 56
592759 CAATAGTTAA
* *
592769 TATATATAACCTATAGTATATGTATACATATAAACTATATATGTAACTTATAGTACATG
1 TATATATAAACTAT-GTATATGTAT--ATATAAACTATATATGTAACCTATAGTACATG
* * *
592828 TATGTATAAACTATGTATA-GTATATATAAACTATATATATAACCTATAGTATATG
1 TATATATAAACTATGTATATGTATATATAAACTATATATGTAACCTATAGTACATG
* *
592883 TATATATACAATCTATTTATATGT-TATATAAACAATATATGTAACCTATAGT
1 TATATATA-AA-CTATGTATATGTATATATAAACTATATATGTAACCTATAGT
592935 TTATAAACAA
Statistics
Matches: 95, Mismatches: 9, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
55 36 0.38
56 2 0.02
57 38 0.40
58 7 0.07
59 12 0.13
ACGTcount: A:0.43, C:0.09, G:0.08, T:0.40
Consensus pattern (56 bp):
TATATATAAACTATGTATATGTATATATAAACTATATATGTAACCTATAGTACATG
Found at i:592866 original size:13 final size:13
Alignment explanation
Indices: 592848--592881 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
592838 CTATGTATAG
592848 TATATATAAACTA
1 TATATATAAACTA
*
592861 TATATATAACCTA
1 TATATATAAACTA
592874 TAGTATAT
1 TA-TATAT
592882 GTATATATAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 14 0.74
14 5 0.26
ACGTcount: A:0.47, C:0.09, G:0.03, T:0.41
Consensus pattern (13 bp):
TATATATAAACTA
Found at i:592886 original size:24 final size:23
Alignment explanation
Indices: 592859--592912 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
592849 ATATATAAAC
*
592859 TATATATATAACCTATAGTATATG
1 TATATATACAACCTAT-GTATATG
* *
592883 TATATATACAATCTATTTATATG
1 TATATATACAACCTATGTATATG
592906 T-TATATA
1 TATATATA
592913 AACAATATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 6 0.22
23 7 0.26
24 14 0.52
ACGTcount: A:0.41, C:0.07, G:0.06, T:0.46
Consensus pattern (23 bp):
TATATATACAACCTATGTATATG
Found at i:593200 original size:31 final size:30
Alignment explanation
Indices: 593029--593213 Score: 126
Period size: 31 Copynumber: 5.8 Consensus size: 30
593019 TAATGTACTA
* * *
593029 TATAATTTATATTAATGTTAATTATCTTAAC
1 TATAATTTATATTAATATTAATT-TATAAAC
593060 TATAATTTATATTAATATAGTATATAGTTTATAAAC
1 TATAATTTATATT-A-ATA-T-TA-A-TTTATAAAC
*
593096 TAT-A-CTATATTAATATT-ATTTATATTAAC
1 TATAATTTATATTAATATTAATTTATA--AAC
* *
593125 TATAGTTTACAATCTATACTATATAATTTAT-AAC
1 TATAATTTA-TAT-TA-A-TAT-TAATTTATAAAC
*
593159 ATATAGTTTATATTAATATTAATGTTATAAAC
1 -TATAATTTATATTAATATTAAT-TTATAAAC
*
593191 TATATTTTATATTAATATTAATT
1 TATAATTTATATTAATATTAATT
593214 ACAAATTATA
Statistics
Matches: 126, Mismatches: 9, Indels: 39
0.72 0.05 0.22
Matches are distributed among these distances:
27 6 0.05
28 1 0.01
29 6 0.05
30 6 0.05
31 44 0.35
32 10 0.08
33 7 0.06
34 13 0.10
35 15 0.12
36 10 0.08
37 8 0.06
ACGTcount: A:0.42, C:0.05, G:0.03, T:0.50
Consensus pattern (30 bp):
TATAATTTATATTAATATTAATTTATAAAC
Found at i:593251 original size:16 final size:16
Alignment explanation
Indices: 593232--593288 Score: 91
Period size: 16 Copynumber: 3.6 Consensus size: 16
593222 TAAACTTATT
593232 ATATTAATATAAGTTA
1 ATATTAATATAAGTTA
593248 ATATTAATATTAA-TT-
1 ATATTAATA-TAAGTTA
593263 ATATTAATATAAGTTA
1 ATATTAATATAAGTTA
593279 ATATTAATAT
1 ATATTAATAT
593289 TAATTATATT
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
14 3 0.08
15 11 0.29
16 21 0.55
17 3 0.08
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (16 bp):
ATATTAATATAAGTTA
Found at i:593254 original size:6 final size:6
Alignment explanation
Indices: 593228--593292 Score: 56
Period size: 6 Copynumber: 12.2 Consensus size: 6
593218 ATTATAAACT
*
593228 TATT-A TATTAA TA-TAA -GTTAA TATTAA TATT-A -ATT-A TATTAA
1 TATTAA TATTAA TATTAA TATTAA TATTAA TATTAA TATTAA TATTAA
*
593270 TA-TAA -GTTAA TATTAA TATTAA T
1 TATTAA TATTAA TATTAA TATTAA T
593293 TATATTTCAC
Statistics
Matches: 49, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
4 4 0.08
5 20 0.41
6 25 0.51
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (6 bp):
TATTAA
Found at i:593267 original size:31 final size:31
Alignment explanation
Indices: 593229--593298 Score: 140
Period size: 31 Copynumber: 2.3 Consensus size: 31
593219 TTATAAACTT
593229 ATTATATTAATATAAGTTAATATTAATATTA
1 ATTATATTAATATAAGTTAATATTAATATTA
593260 ATTATATTAATATAAGTTAATATTAATATTA
1 ATTATATTAATATAAGTTAATATTAATATTA
593291 ATTATATT
1 ATTATATT
593299 TCACTGTTTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (31 bp):
ATTATATTAATATAAGTTAATATTAATATTA
Found at i:593831 original size:29 final size:29
Alignment explanation
Indices: 593768--593834 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 29
593758 ATTTTATTAA
*
593768 TTTTATTAAATAATTTTATATAATAGGTAT
1 TTTTATTAAATAA-TTTATATAATAGATAT
*
593798 ATTTATTAATATAA-TTATCATAATA-ATAT
1 TTTTATTAA-ATAATTTAT-ATAATAGATAT
593827 TTTTATTA
1 TTTTATTA
593835 TAACATTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
29 14 0.44
30 14 0.44
31 4 0.12
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (29 bp):
TTTTATTAAATAATTTATATAATAGATAT
Found at i:594002 original size:46 final size:46
Alignment explanation
Indices: 593937--594034 Score: 144
Period size: 46 Copynumber: 2.1 Consensus size: 46
593927 TAATATATAA
* *
593937 GTCAGGTAAATGTTAGATCAGGTCATTAGCAAGTC-AATCATTTACAG
1 GTCA-GTAAATGTTAGATCA-GTCATTAACAAGGCGAATCATTTACAG
*
593984 GTCAGTAAATGTTAGATCAGTCATTAACAAGGCGGATCATTTACAG
1 GTCAGTAAATGTTAGATCAGTCATTAACAAGGCGAATCATTTACAG
594030 GTCAG
1 GTCAG
594035 GTTAAAAACA
Statistics
Matches: 47, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
45 12 0.26
46 31 0.66
47 4 0.09
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.29
Consensus pattern (46 bp):
GTCAGTAAATGTTAGATCAGTCATTAACAAGGCGAATCATTTACAG
Found at i:594047 original size:16 final size:16
Alignment explanation
Indices: 594026--594080 Score: 74
Period size: 16 Copynumber: 3.4 Consensus size: 16
594016 CGGATCATTT
594026 ACAGGTCAGGTTAAAA
1 ACAGGTCAGGTTAAAA
* * *
594042 ACAGGTCATGTTCATA
1 ACAGGTCAGGTTAAAA
*
594058 ACAGGTCAGGTTGAAA
1 ACAGGTCAGGTTAAAA
594074 ACAGGTC
1 ACAGGTC
594081 GGGTAATACC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.36, C:0.16, G:0.25, T:0.22
Consensus pattern (16 bp):
ACAGGTCAGGTTAAAA
Found at i:607114 original size:21 final size:21
Alignment explanation
Indices: 607088--607143 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
607078 GGGAGCGTCA
*
607088 GTGCATCGATGCATACACTAG
1 GTGCATCGGTGCATACACTAG
607109 GTGCATCGGTGCATACACTAG
1 GTGCATCGGTGCATACACTAG
607130 GTGCATCGGTGCAT
1 GTGCATCGGTGCAT
607144 CAACTGTAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.23, C:0.23, G:0.29, T:0.25
Consensus pattern (21 bp):
GTGCATCGGTGCATACACTAG
Found at i:610090 original size:21 final size:21
Alignment explanation
Indices: 610048--610091 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
610038 TTTCTGGGCT
* *
610048 AGGGGAATCGATAGCCATTCA
1 AGGGGAATCGATACCCACTCA
*
610069 AGGGGAATCGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
610090 AG
1 AG
610092 CGAACATGGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.32, C:0.25, G:0.27, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:611975 original size:103 final size:103
Alignment explanation
Indices: 611750--611966 Score: 398
Period size: 103 Copynumber: 2.1 Consensus size: 103
611740 GTCGAGGGTC
611750 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* * *
611815 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTATTAAGGAATGA
611853 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
611918 TTGATCCCTAGTATATGTATATGATTATTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTATTAAGGAATGA
611956 TATGTGGTCCT
1 TATGTGGTCCT
611967 AATGGACATT
Statistics
Matches: 110, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 110 1.00
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.36
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTATTAAGGAATGA
Found at i:612010 original size:23 final size:23
Alignment explanation
Indices: 611977--612051 Score: 100
Period size: 23 Copynumber: 3.3 Consensus size: 23
611967 AATGGACATT
611977 ATTATAT--GGCACTACGGTGCA
1 ATTATATGCGGCACTACGGTGCA
* *
611998 ATTCTATGCGGCACTCCGGTGCA
1 ATTATATGCGGCACTACGGTGCA
* *
612021 ATTATATGTGGCACTTCGGTGCA
1 ATTATATGCGGCACTACGGTGCA
612044 ATTATATG
1 ATTATATG
612052 AGCTGTGGTG
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
21 6 0.13
23 41 0.87
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (23 bp):
ATTATATGCGGCACTACGGTGCA
Found at i:619603 original size:29 final size:30
Alignment explanation
Indices: 619543--619625 Score: 84
Period size: 29 Copynumber: 2.8 Consensus size: 30
619533 TCAAAAACTA
619543 AATTATGAAAT-TATAAAAATTA-GGGACTCT
1 AATTAT-AAATATA-AAAAATTAGGGGACTCT
*
619573 AATTATAAATATAAAAAATTAGGGGTC-CT
1 AATTATAAATATAAAAAATTAGGGGACTCT
* * *
619602 AATTATATATACAGAAAATT-GGGG
1 AATTATAAATATAAAAAATTAGGGG
619626 CCCTTTATTC
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
28 4 0.09
29 31 0.66
30 12 0.26
ACGTcount: A:0.47, C:0.06, G:0.16, T:0.31
Consensus pattern (30 bp):
AATTATAAATATAAAAAATTAGGGGACTCT
Found at i:623475 original size:22 final size:22
Alignment explanation
Indices: 623450--623492 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
623440 TCATCAGTGT
623450 AATTTACCTAATTATTTTCTGC
1 AATTTACCTAATTATTTTCTGC
*
623472 AATTTACCTGATTATTTTCTG
1 AATTTACCTAATTATTTTCTG
623493 TATTATTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.26, C:0.16, G:0.07, T:0.51
Consensus pattern (22 bp):
AATTTACCTAATTATTTTCTGC
Found at i:624250 original size:27 final size:27
Alignment explanation
Indices: 624216--624279 Score: 74
Period size: 27 Copynumber: 2.4 Consensus size: 27
624206 CATAAAACAT
*
624216 ATATTTTTAGATGAAAATAAAAATAAA
1 ATATTTTTAAATGAAAATAAAAATAAA
* ** *
624243 ATATTTTTAAATTAAGTTAATAATAAA
1 ATATTTTTAAATGAAAATAAAAATAAA
*
624270 ATATATTTAA
1 ATATTTTTAA
624280 TAAGTTAACA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.41
Consensus pattern (27 bp):
ATATTTTTAAATGAAAATAAAAATAAA
Found at i:624279 original size:22 final size:24
Alignment explanation
Indices: 624254--624326 Score: 71
Period size: 24 Copynumber: 3.0 Consensus size: 24
624244 TATTTTTAAA
624254 TTAAGTTAATAATAAAATA-TATT
1 TTAAGTTAATAATAAAATATTATT
*
624277 TAATAAGTTAA-CATAAAATATT-TT
1 T--TAAGTTAATAATAAAATATTATT
624301 TTAAGTTAATATATTTAAAATATTAT
1 TTAAGTTAATA-A--TAAAATATTAT
624327 GAATTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
22 8 0.20
23 1 0.03
24 12 0.30
25 9 0.22
26 9 0.22
27 1 0.03
ACGTcount: A:0.49, C:0.01, G:0.04, T:0.45
Consensus pattern (24 bp):
TTAAGTTAATAATAAAATATTATT
Found at i:624292 original size:27 final size:27
Alignment explanation
Indices: 624237--624311 Score: 83
Period size: 27 Copynumber: 3.0 Consensus size: 27
624227 TGAAAATAAA
*
624237 AATAAAATATTTTTAAATTAAGTTAAT
1 AATAAAATATATTTAAATTAAGTTAAT
624264 AATAAAATATATTT-AA-TAAGTTAA-
1 AATAAAATATATTTAAATTAAGTTAAT
*
624288 CATAAAATAT-TTT---TTAAGTTAAT
1 AATAAAATATATTTAAATTAAGTTAAT
624311 A
1 A
624312 TATTTAAAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
22 8 0.19
23 3 0.07
24 9 0.21
25 8 0.19
26 2 0.05
27 13 0.30
ACGTcount: A:0.52, C:0.01, G:0.04, T:0.43
Consensus pattern (27 bp):
AATAAAATATATTTAAATTAAGTTAAT
Found at i:628468 original size:33 final size:33
Alignment explanation
Indices: 628431--628529 Score: 162
Period size: 33 Copynumber: 3.0 Consensus size: 33
628421 ATTTGGCTAG
628431 TTGGAAAATTCATCTTGGTTGGTGGCCAACTTA
1 TTGGAAAATTCATCTTGGTTGGTGGCCAACTTA
* *
628464 TTGGAAAATTCATCTTGTTTGGTGGGCAACTTA
1 TTGGAAAATTCATCTTGGTTGGTGGCCAACTTA
*
628497 TTGGAAAATTCATCTTTGGTAGGTGGCCAACTT
1 TTGGAAAATTCATC-TTGGTTGGTGGCCAACTT
628530 TGCATATGGG
Statistics
Matches: 60, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
33 45 0.75
34 15 0.25
ACGTcount: A:0.24, C:0.14, G:0.24, T:0.37
Consensus pattern (33 bp):
TTGGAAAATTCATCTTGGTTGGTGGCCAACTTA
Found at i:630089 original size:22 final size:22
Alignment explanation
Indices: 630061--630108 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
630051 TGGTCATTAG
630061 TGTAATTTACCTAATTATTTTC
1 TGTAATTTACCTAATTATTTTC
*
630083 TGTAATTTACCTGATTATTTTC
1 TGTAATTTACCTAATTATTTTC
630105 TGTA
1 TGTA
630109 TTATTTTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.25, C:0.12, G:0.08, T:0.54
Consensus pattern (22 bp):
TGTAATTTACCTAATTATTTTC
Found at i:630260 original size:30 final size:30
Alignment explanation
Indices: 630224--630332 Score: 191
Period size: 30 Copynumber: 3.6 Consensus size: 30
630214 CGAATATAGA
*
630224 TCGCCAGGTGATCTGGGTGACCAATGAAGG
1 TCGCCAGGTGATCTGGGCGACCAATGAAGG
630254 TCGCCAGGTGATCTGGGCGACCAATGAAGG
1 TCGCCAGGTGATCTGGGCGACCAATGAAGG
*
630284 TCGCCAGGTGGTCTGGGCGACCAATGAAGG
1 TCGCCAGGTGATCTGGGCGACCAATGAAGG
*
630314 TCGCCAGGTGGTCTGGGCG
1 TCGCCAGGTGATCTGGGCG
630333 CCATGCCGTT
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 77 1.00
ACGTcount: A:0.19, C:0.23, G:0.39, T:0.18
Consensus pattern (30 bp):
TCGCCAGGTGATCTGGGCGACCAATGAAGG
Found at i:630567 original size:49 final size:50
Alignment explanation
Indices: 630507--630607 Score: 186
Period size: 50 Copynumber: 2.0 Consensus size: 50
630497 TTTATCCTAT
*
630507 TTTAGTATGTATTTATTTT-AAATTGATTATTGGGATATCTTGTTTTGTA
1 TTTAGTATGTATTTATTTTAAAACTGATTATTGGGATATCTTGTTTTGTA
630556 TTTAGTATGTATTTATTTTAAAACTGATTATTGGGATATCTTGTTTTGTA
1 TTTAGTATGTATTTATTTTAAAACTGATTATTGGGATATCTTGTTTTGTA
630606 TT
1 TT
630608 CAATAATTTT
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
49 19 0.38
50 31 0.62
ACGTcount: A:0.25, C:0.03, G:0.16, T:0.56
Consensus pattern (50 bp):
TTTAGTATGTATTTATTTTAAAACTGATTATTGGGATATCTTGTTTTGTA
Found at i:631857 original size:31 final size:31
Alignment explanation
Indices: 631820--631883 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
631810 AAAAAACACA
*
631820 TAAGATATGGTCACCTTT-GTATTTATTTAAT
1 TAAGATATAGTCA-CTTTCGTATTTATTTAAT
*
631851 TAAGATATAGTCACTTTCGTTTTTATTTAAT
1 TAAGATATAGTCACTTTCGTATTTATTTAAT
631882 TA
1 TA
631884 GGATGTGATA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 4 0.13
31 26 0.87
ACGTcount: A:0.30, C:0.09, G:0.11, T:0.50
Consensus pattern (31 bp):
TAAGATATAGTCACTTTCGTATTTATTTAAT
Found at i:632060 original size:27 final size:27
Alignment explanation
Indices: 632030--632091 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 27
632020 TAAATCATAA
*
632030 ATTTTTAGATGAAAATAAAAATAAAAT
1 ATTTTTAAATGAAAATAAAAATAAAAT
* ** *
632057 ATTTTTAAATTAAGTTAATAATAAAAT
1 ATTTTTAAATGAAAATAAAAATAAAAT
*
632084 ATATTTAA
1 ATTTTTAA
632092 TAAGTTAACA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (27 bp):
ATTTTTAAATGAAAATAAAAATAAAAT
Found at i:632109 original size:24 final size:25
Alignment explanation
Indices: 632049--632125 Score: 84
Period size: 24 Copynumber: 3.0 Consensus size: 25
632039 TGAAAATAAA
*
632049 AATAAAATATTTTTAAATTAAGTTAAT
1 AATAAAATATATTT-AA-TAAGTTAAT
632076 AATAAAATATATTTAATAAGTTAA-
1 AATAAAATATATTTAATAAGTTAAT
* * **
632100 CATAAAATATGTTTTTTAAGTTAAT
1 AATAAAATATATTTAATAAGTTAAT
632125 A
1 A
632126 TATTTAAAAT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
24 20 0.47
25 8 0.19
26 2 0.05
27 13 0.30
ACGTcount: A:0.51, C:0.01, G:0.05, T:0.43
Consensus pattern (25 bp):
AATAAAATATATTTAATAAGTTAAT
Found at i:634070 original size:2 final size:2
Alignment explanation
Indices: 634063--634107 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
634053 TCTCCAAGCT
634063 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
634105 TC T
1 TC T
634108 TGTTTTTATT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:639405 original size:71 final size:71
Alignment explanation
Indices: 639254--639394 Score: 200
Period size: 71 Copynumber: 2.0 Consensus size: 71
639244 GACTAAATCG
* * *
639254 AAATATAAATAAGTATGGGCGAATTTCATATACAAATATAACTTTAAGGACAAAGTTGAAGTAAA
1 AAATATAAATAAGTATGGGCGAATTTCATAGACAAATATAACTTTAAGGACAAAATTGAAGCAAA
639319 TTGAAA
66 TTGAAA
*
639325 AAATATAAATAAGTATGGGTC-AATTTCATAGACAAATATAATTTTAAGGACTAAAATT-AA-CA
1 AAATATAAATAAGTATGGG-CGAATTTCATAGACAAATATAACTTTAAGGAC-AAAATTGAAGCA
639387 AATT-AAA
64 AATTGAAA
639394 A
1 A
639395 TTTAAATAAA
Statistics
Matches: 64, Mismatches: 4, Indels: 6
0.86 0.05 0.08
Matches are distributed among these distances:
69 4 0.06
70 5 0.08
71 49 0.77
72 6 0.09
ACGTcount: A:0.51, C:0.07, G:0.13, T:0.29
Consensus pattern (71 bp):
AAATATAAATAAGTATGGGCGAATTTCATAGACAAATATAACTTTAAGGACAAAATTGAAGCAAA
TTGAAA
Found at i:639537 original size:2 final size:2
Alignment explanation
Indices: 639523--639708 Score: 62
Period size: 2 Copynumber: 95.5 Consensus size: 2
639513 ACAAATTTAG
*
639523 TA TA TA CTA -A TA TA TA TA TA TA TA -A GTA TA CT- TA TA T- TT
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA TA -TA TA TA TA TA
* * *
639562 TA -A GTT TA TA TA TA -A TA TT TA TA TA -A GTA TA CA T- TA TA CT-
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA -TA
* * *
639602 TA TA TA TA TA GTA TA -A TA TT TA TA -A TA TA CA T- TA TA CA TA
1 TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
639642 TA GTA TA TA TA TA CT- TC TA AA TA TA TA -A TA TA -A GTA TT TA
1 TA -TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
*
639682 -A GTG TA TA TA TA TA TA TA TA TA TA TA T
1 TA -TA TA TA TA TA TA TA TA TA TA TA TA T
639709 TCGAGAGACT
Statistics
Matches: 137, Mismatches: 20, Indels: 54
0.65 0.09 0.26
Matches are distributed among these distances:
1 16 0.12
2 109 0.80
3 12 0.09
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (2 bp):
TA
Found at i:639592 original size:21 final size:19
Alignment explanation
Indices: 639568--639708 Score: 83
Period size: 18 Copynumber: 7.3 Consensus size: 19
639558 ATTTTAAGTT
639568 TATATATAATATTTATATAA
1 TATATATAATATTTATAT-A
* * *
639588 GTATACATTATACTTATATA
1 -TATATATAATATTTATATA
639608 TATAGTATAATATTTATA-A
1 TATA-TATAATATTTATATA
* * **
639627 TATACATTATACATATAGTA
1 TATATATAATATTTATA-TA
* * *
639647 TATATATACT-TCTAAATA
1 TATATATAATATTTATATA
*
639665 TATAATATAAGTATTTA-AGTG
1 TAT-ATATAA-TATTTATA-TA
*
639686 TATATAT-ATATATATATA
1 TATATATAATATTTATATA
639704 TATAT
1 TATAT
639709 TCGAGAGACT
Statistics
Matches: 91, Mismatches: 21, Indels: 19
0.69 0.16 0.15
Matches are distributed among these distances:
18 25 0.27
19 19 0.21
20 25 0.27
21 22 0.24
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.46
Consensus pattern (19 bp):
TATATATAATATTTATATA
Found at i:639631 original size:38 final size:41
Alignment explanation
Indices: 639520--639654 Score: 138
Period size: 40 Copynumber: 3.3 Consensus size: 41
639510 AAAACAAATT
* * *
639520 TAGTATATACTAATATATATATATATAAGTATAC-TTATA-TTT
1 TAGTATATA-T-ATA-ATATTTATATAAGTATACATTATACATA
* *
639562 TAAGTTTATATATAATATTTATATAAGTATACATTATACTTA
1 T-AGTATATATATAATATTTATATAAGTATACATTATACATA
639604 TA-TATATAGTATAATA-TT-TATAA-TATACATTATACATA
1 TAGTATATA-TATAATATTTATATAAGTATACATTATACATA
639642 TAGTATATATATA
1 TAGTATATATATA
639655 CTTCTAAATA
Statistics
Matches: 83, Mismatches: 5, Indels: 14
0.81 0.05 0.14
Matches are distributed among these distances:
38 20 0.24
39 11 0.13
40 24 0.29
41 16 0.19
42 5 0.06
43 7 0.08
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.47
Consensus pattern (41 bp):
TAGTATATATATAATATTTATATAAGTATACATTATACATA
Found at i:640644 original size:24 final size:24
Alignment explanation
Indices: 640617--640681 Score: 103
Period size: 24 Copynumber: 2.7 Consensus size: 24
640607 AATAAAACAT
640617 AATCCAGGTCAAGTATTCGATCAG
1 AATCCAGGTCAAGTATTCGATCAG
* *
640641 AATCCAGGTCAAATATCCGATCAG
1 AATCCAGGTCAAGTATTCGATCAG
*
640665 AATCCAGGTCAGGTATT
1 AATCCAGGTCAAGTATT
640682 ATAATATAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.25
Consensus pattern (24 bp):
AATCCAGGTCAAGTATTCGATCAG
Found at i:641835 original size:18 final size:18
Alignment explanation
Indices: 641814--641854 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
641804 CTTCCATCCG
*
641814 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
641832 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
*
641850 GTCTT
1 ATCTT
641855 TTTGAACAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.27, C:0.17, G:0.02, T:0.54
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:643128 original size:20 final size:21
Alignment explanation
Indices: 643091--643130 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
643081 AAATTAAGTT
643091 AAATGAATTTTAAGATTTTAC
1 AAATGAATTTTAAGATTTTAC
643112 AAATG-ATTTTACA-ATTTTA
1 AAATGAATTTTA-AGATTTTA
643131 TATTCGATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.45
Consensus pattern (21 bp):
AAATGAATTTTAAGATTTTAC
Found at i:643373 original size:19 final size:19
Alignment explanation
Indices: 643349--643387 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
643339 TCGAATGCAT
643349 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
643368 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
643387 T
1 T
643388 GAATATTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:643512 original size:64 final size:65
Alignment explanation
Indices: 643335--643497 Score: 222
Period size: 65 Copynumber: 2.5 Consensus size: 65
643325 GAATTAATTG
* * * *
643335 AACATCGAATGCATTCCATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAA
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTTCAA
* ** **
643400 AACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCAC-CAGGCTATTTTTC-
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATA-TTTTCA
643463 A
65 A
643464 AACATCGAATGCATTTCATGCATCGATGCACACT
1 AACATCGAATGCATTTCATGCATCGATGCACACT
643498 TGGTGCACCG
Statistics
Matches: 85, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
64 36 0.42
65 49 0.58
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.27
Consensus pattern (65 bp):
AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTTCAA
Found at i:644458 original size:17 final size:17
Alignment explanation
Indices: 644436--644479 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
644426 AATAGTCAAG
*
644436 CATCCAAATATCATAAA
1 CATCCAAATAACATAAA
*
644453 CATCCAAACAAACATAAA
1 CATCCAAA-TAACATAAA
644471 CATCCAAAT
1 CATCCAAAT
644480 CAAAAAGTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 8 0.35
18 15 0.65
ACGTcount: A:0.55, C:0.27, G:0.00, T:0.18
Consensus pattern (17 bp):
CATCCAAATAACATAAA
Found at i:644470 original size:18 final size:19
Alignment explanation
Indices: 644447--644483 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
644437 ATCCAAATAT
644447 CATAAACATCCAAA-CAAA
1 CATAAACATCCAAATCAAA
644465 CATAAACATCCAAATCAAA
1 CATAAACATCCAAATCAAA
644484 AAGTTTAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.59, C:0.27, G:0.00, T:0.14
Consensus pattern (19 bp):
CATAAACATCCAAATCAAA
Found at i:652278 original size:64 final size:64
Alignment explanation
Indices: 652225--652387 Score: 211
Period size: 65 Copynumber: 2.5 Consensus size: 64
652215 CGGTGCACCA
* *
652225 AGTGTGCAACGATGCATGAAATGCATTCGATGTTTGAAAAATAGCCTG-GTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTG-AAAATAGCCAGAGTGCATCGATGCATGG
** * **
652289 CTTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATAGCCAGAGTGCATCGATGCATGG
* * *
652354 AGAGTGCATCGGTGCATGGAATGCATTCGATGTT
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTT
652388 CAATTAATTC
Statistics
Matches: 84, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
64 38 0.45
65 46 0.55
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.29
Consensus pattern (64 bp):
AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCAGAGTGCATCGATGCATGG
Found at i:652359 original size:19 final size:19
Alignment explanation
Indices: 652335--652385 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
652325 GAAAATATTC
652335 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
652354 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
652373 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
652386 TTCAATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:652625 original size:20 final size:20
Alignment explanation
Indices: 652602--652643 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
652592 TTGAATCGAA
652602 TATAAAAT-TGTAAAATCATT
1 TATAAAATCT-TAAAATCATT
*
652622 TATAAAATCTTAAATTCATT
1 TATAAAATCTTAAAATCATT
652642 TA
1 TA
652644 ACTTAATTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 19 0.95
21 1 0.05
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.43
Consensus pattern (20 bp):
TATAAAATCTTAAAATCATT
Found at i:655188 original size:24 final size:24
Alignment explanation
Indices: 655169--655256 Score: 97
Period size: 24 Copynumber: 3.7 Consensus size: 24
655159 AACAAAACAT
*
655169 AATCCAGGTCAAGTATCAAATCAA
1 AATCCAGGTCAAGTATCAAATCAG
* * *
655193 AATTCAGGTCAACTATTC-GATCAG
1 AATCCAGGTCAAGTA-TCAAATCAG
**
655217 AATCCAGGTCAAGTATCCGATCAG
1 AATCCAGGTCAAGTATCAAATCAG
*
655241 AATCCAGGTCAGGTAT
1 AATCCAGGTCAAGTAT
655257 TATAATATAA
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
23 2 0.04
24 51 0.93
25 2 0.04
ACGTcount: A:0.36, C:0.22, G:0.18, T:0.24
Consensus pattern (24 bp):
AATCCAGGTCAAGTATCAAATCAG
Found at i:656420 original size:18 final size:18
Alignment explanation
Indices: 656397--656431 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
656387 TTCCATCCAG
*
656397 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
656415 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
656432 GTCCTTTCGA
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:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:659592 original size:28 final size:29
Alignment explanation
Indices: 659524--659613 Score: 98
Period size: 28 Copynumber: 3.1 Consensus size: 29
659514 TGTTTTCTTT
*
659524 TTTTATT-GGTTTT-TA-TTTTATTTGTTA
1 TTTTATTATGTTTTCTATTTTTATTT-TTA
*
659551 TATATATATATGTTTTCTATTTTTA-TTTTA
1 T-TTTAT-TATGTTTTCTATTTTTATTTTTA
*
659581 TTTTATTATGTTTTTTATTTTTATTTTTA
1 TTTTATTATGTTTTCTATTTTTATTTTTA
659610 TTTT
1 TTTT
659614 TATTTTCTTT
Statistics
Matches: 53, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
27 1 0.02
28 20 0.38
29 14 0.26
30 9 0.17
31 4 0.08
32 5 0.09
ACGTcount: A:0.19, C:0.01, G:0.06, T:0.74
Consensus pattern (29 bp):
TTTTATTATGTTTTCTATTTTTATTTTTA
Found at i:659625 original size:6 final size:6
Alignment explanation
Indices: 659563--659619 Score: 66
Period size: 6 Copynumber: 9.7 Consensus size: 6
659553 TATATATATG
*
659563 TTTTCTA TTTTTA -TTTTA -TTTTA TTATGT- TTTTTA TTTTTA TTTTTA
1 TTTT-TA TTTTTA TTTTTA TTTTTA TT-TTTA TTTTTA TTTTTA TTTTTA
659610 TTTTTA TTTT
1 TTTTTA TTTT
659620 CTTTTTTTCT
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
5 12 0.27
6 27 0.60
7 6 0.13
ACGTcount: A:0.16, C:0.02, G:0.02, T:0.81
Consensus pattern (6 bp):
TTTTTA
Found at i:659625 original size:12 final size:13
Alignment explanation
Indices: 659563--659626 Score: 62
Period size: 12 Copynumber: 4.9 Consensus size: 13
659553 TATATATATG
659563 TTTTCTATTTTTA
1 TTTTCTATTTTTA
*
659576 TTTTAT-TTTATTA
1 TTTTCTATTT-TTA
*
659589 TGTTTTTTATTTTTA
1 --TTTTCTATTTTTA
659604 TTTT-TATTTTTA
1 TTTTCTATTTTTA
659616 TTTTCT-TTTTT
1 TTTTCTATTTTT
659627 TCTTTGTTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 11
0.77 0.04 0.19
Matches are distributed among these distances:
12 20 0.45
13 13 0.30
15 8 0.18
16 3 0.07
ACGTcount: A:0.14, C:0.03, G:0.02, T:0.81
Consensus pattern (13 bp):
TTTTCTATTTTTA
Found at i:659625 original size:18 final size:19
Alignment explanation
Indices: 659563--659648 Score: 69
Period size: 18 Copynumber: 4.8 Consensus size: 19
659553 TATATATATG
659563 TTTTCTATTTTTA-TTTTA
1 TTTTCTATTTTTATTTTTA
*
659581 -TTT-TATTATGT-TTTTTA
1 TTTTCTATT-TTTATTTTTA
659598 TTTT-TATTTTTATTTTTA
1 TTTTCTATTTTTATTTTTA
* *
659616 TTTTCT-TTTTT-TCTTTG
1 TTTTCTATTTTTATTTTTA
* *
659633 TTTTATATTTATATTT
1 TTTTCTATTTTTATTT
659649 ATATGTTATC
Statistics
Matches: 54, Mismatches: 7, Indels: 13
0.73 0.09 0.18
Matches are distributed among these distances:
16 4 0.07
17 21 0.39
18 26 0.48
19 3 0.06
ACGTcount: A:0.15, C:0.03, G:0.02, T:0.79
Consensus pattern (19 bp):
TTTTCTATTTTTATTTTTA
Found at i:659637 original size:40 final size:40
Alignment explanation
Indices: 659534--659650 Score: 112
Period size: 40 Copynumber: 2.9 Consensus size: 40
659524 TTTTATTGGT
* * *
659534 TTTTATTTTATT-TGTTATATATATATATGTTTTCTATTTTTA
1 TTTTATTTTATTATGTT-T-TTTATATTTATTTT-TATTTTTA
*
659576 TTTTATTTTATTATGTTTTTTATTTTTATTTTTATTTTTA
1 TTTTATTTTATTATGTTTTTTATATTTATTTTTATTTTTA
* * * *
659616 TTTTCTTTTTTTCT-TTGTTTTATATTTATATTTAT
1 TTTTATTTTATTATGTT-TTTTATATTTATTTTTAT
659651 ATGTTATCTT
Statistics
Matches: 64, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
39 2 0.03
40 35 0.55
41 10 0.16
42 13 0.20
43 4 0.06
ACGTcount: A:0.19, C:0.03, G:0.03, T:0.75
Consensus pattern (40 bp):
TTTTATTTTATTATGTTTTTTATATTTATTTTTATTTTTA
Found at i:659642 original size:30 final size:30
Alignment explanation
Indices: 659563--659648 Score: 79
Period size: 30 Copynumber: 2.9 Consensus size: 30
659553 TATATATATG
* * * *
659563 TTTTCTATTTTTA-TTTTA-TTTTATTATG
1 TTTTTTATCTTTATTTTTATTTTTATTTTC
*
659591 TTTTTTATTTTTATTTTTATTTTTATTTTC
1 TTTTTTATCTTTATTTTTATTTTTATTTTC
* *
659621 TTTTTT-TCTTTGTTTTATATTTATATTT
1 TTTTTTATCTTTATTTT-TATTTTTATTT
659649 ATATGTTATC
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
28 12 0.24
29 13 0.27
30 24 0.49
ACGTcount: A:0.15, C:0.03, G:0.02, T:0.79
Consensus pattern (30 bp):
TTTTTTATCTTTATTTTTATTTTTATTTTC
Found at i:659671 original size:36 final size:35
Alignment explanation
Indices: 659598--659673 Score: 84
Period size: 36 Copynumber: 2.1 Consensus size: 35
659588 ATGTTTTTTA
* * *
659598 TTTTTATTTTTATTTTTATTTTCTTTTTTTCTTTG
1 TTTTTATTTATATTTATATTTTCTTTTTTTCTCTG
659633 TTTTATATTTATATTTATATGTTATC-TTTTTTC-CTG
1 TTTT-TATTTATATTTATAT-TT-TCTTTTTTTCTCTG
659669 TTTTT
1 TTTTT
659674 CTTGTTTTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
35 5 0.14
36 19 0.54
37 9 0.26
38 2 0.06
ACGTcount: A:0.13, C:0.07, G:0.04, T:0.76
Consensus pattern (35 bp):
TTTTTATTTATATTTATATTTTCTTTTTTTCTCTG
Found at i:663942 original size:16 final size:16
Alignment explanation
Indices: 663899--663954 Score: 60
Period size: 16 Copynumber: 3.4 Consensus size: 16
663889 TTGGAATGTT
*
663899 TCTGAGGGAATT-AGAA
1 TCTGAAGGAATTGA-AA
663915 TCTGTAAAGGAATTGAAA
1 TCTG--AAGGAATTGAAA
*
663933 TCTGAAGGAATTGGAA
1 TCTGAAGGAATTGAAA
663949 TCTGAA
1 TCTGAA
663955 TCTGAAACCT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
16 21 0.60
18 13 0.37
19 1 0.03
ACGTcount: A:0.39, C:0.07, G:0.27, T:0.27
Consensus pattern (16 bp):
TCTGAAGGAATTGAAA
Found at i:664320 original size:34 final size:34
Alignment explanation
Indices: 664278--664353 Score: 143
Period size: 34 Copynumber: 2.2 Consensus size: 34
664268 CCACCCGACT
664278 CGACCCGAGAACAAGGGAACCTCCACCCGAGACC
1 CGACCCGAGAACAAGGGAACCTCCACCCGAGACC
*
664312 CGACCCGAGAACAAGGGAACCTCCACCTGAGACC
1 CGACCCGAGAACAAGGGAACCTCCACCCGAGACC
664346 CGACCCGA
1 CGACCCGA
664354 CCTGAATATA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 41 1.00
ACGTcount: A:0.32, C:0.41, G:0.24, T:0.04
Consensus pattern (34 bp):
CGACCCGAGAACAAGGGAACCTCCACCCGAGACC
Found at i:664346 original size:29 final size:32
Alignment explanation
Indices: 664267--664353 Score: 111
Period size: 34 Copynumber: 2.6 Consensus size: 32
664257 GTTGGGTTGG
**
664267 TCCACCCGACTCGACCCGAGAACAAGGGAACC
1 TCCACCCGAGACGACCCGAGAACAAGGGAACC
664299 TCCACCCGAGACCCGACCCGAGAACAAGGGAACC
1 TCCACCCGAGA--CGACCCGAGAACAAGGGAACC
*
664333 TCCACCTGAGACCCGACCCGA
1 TCCACCCGAGA--CGACCCGA
664354 CCTGAATATA
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
32 9 0.18
34 41 0.82
ACGTcount: A:0.30, C:0.43, G:0.22, T:0.06
Consensus pattern (32 bp):
TCCACCCGAGACGACCCGAGAACAAGGGAACC
Found at i:664594 original size:32 final size:34
Alignment explanation
Indices: 664532--664599 Score: 104
Period size: 32 Copynumber: 2.0 Consensus size: 34
664522 TTTTCACCCT
*
664532 AAACCCGAACCCGACCCGAATATCACACTTAAAAA
1 AAACCCGAACCCGACCCG-ATATCAAACTTAAAAA
664567 AAACCC-AACCCGACCCG-TATCAAACTTAAAAA
1 AAACCCGAACCCGACCCGATATCAAACTTAAAAA
664599 A
1 A
664600 TCCCGACCTG
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
32 15 0.47
34 11 0.34
35 6 0.19
ACGTcount: A:0.47, C:0.34, G:0.07, T:0.12
Consensus pattern (34 bp):
AAACCCGAACCCGACCCGATATCAAACTTAAAAA
Found at i:665439 original size:58 final size:58
Alignment explanation
Indices: 665346--665487 Score: 232
Period size: 58 Copynumber: 2.4 Consensus size: 58
665336 CAGTTTTCAA
* *
665346 ATTCGCAACTC-GATTCTCCAAATTCGCAACACTAATTACCGATATAGGTAAACTCAACT
1 ATTCGCAACTCAG-TT-TTCAAATTCGCAACACTAATTACCGATATAGGTAAACACAACT
*
665405 ATTCGCAACTCAGTTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACACAACT
1 ATTCGCAACTCAGTTTTCAAATTCGCAACACTAATTACCGATATAGGTAAACACAACT
665463 ATTCGCAACTCAGTTTTCAAATTCG
1 ATTCGCAACTCAGTTTTCAAATTCG
665488 TAACTCAGAT
Statistics
Matches: 79, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
58 65 0.82
59 13 0.16
60 1 0.01
ACGTcount: A:0.35, C:0.25, G:0.11, T:0.29
Consensus pattern (58 bp):
ATTCGCAACTCAGTTTTCAAATTCGCAACACTAATTACCGATATAGGTAAACACAACT
Found at i:665492 original size:20 final size:20
Alignment explanation
Indices: 665463--665511 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
665453 AAACACAACT
*
665463 ATTCGCAACTCAGTTTTCAA
1 ATTCGCAACTCAGATTTCAA
*
665483 ATTCGTAACTCAGATTTCAA
1 ATTCGCAACTCAGATTTCAA
*
665503 ATTCACAAC
1 ATTCGCAAC
665512 ACGAATTTCG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.35, C:0.24, G:0.08, T:0.33
Consensus pattern (20 bp):
ATTCGCAACTCAGATTTCAA
Found at i:666108 original size:41 final size:40
Alignment explanation
Indices: 666060--666157 Score: 124
Period size: 41 Copynumber: 2.4 Consensus size: 40
666050 AAAACGAAAT
* * **
666060 TCGCGTTGCGAATTTGAAAATTGTGTTGCGAATTTGGAGAA
1 TCGCGTTGCGAATTTGAAAACTGTGTTGCGAAATCAGAG-A
* * *
666101 TCGCGTTGCAAATTTGGAAACTGTGTTGCGAAATCAGAGT
1 TCGCGTTGCGAATTTGAAAACTGTGTTGCGAAATCAGAGA
666141 TCGCGTTGCGAATTTGA
1 TCGCGTTGCGAATTTGA
666158 GATCGCATTG
Statistics
Matches: 48, Mismatches: 9, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
40 15 0.31
41 33 0.69
ACGTcount: A:0.26, C:0.13, G:0.29, T:0.33
Consensus pattern (40 bp):
TCGCGTTGCGAATTTGAAAACTGTGTTGCGAAATCAGAGA
Found at i:666114 original size:21 final size:21
Alignment explanation
Indices: 666055--666175 Score: 81
Period size: 20 Copynumber: 6.0 Consensus size: 21
666045 TTGCGAAAAC
*
666055 GAAATTCGCGTTGCGAATTT-
1 GAAAATCGCGTTGCGAATTTG
* *
666075 GAAAATTGTGTTGCGAATTTG
1 GAAAATCGCGTTGCGAATTTG
* *
666096 GAGAATCGCGTTGCAAATTTG
1 GAAAATCGCGTTGCGAATTTG
* * * **
666117 GAAACT-GTGTTGCGAAATCA
1 GAAAATCGCGTTGCGAATTTG
**
666137 G-AGTTCGCGTTGCGAATTT-
1 GAAAATCGCGTTGCGAATTTG
* *
666156 G-AGATCGCATTGCGAATTTG
1 GAAAATCGCGTTGCGAATTTG
666176 TTGGTTATTT
Statistics
Matches: 77, Mismatches: 21, Indels: 6
0.74 0.20 0.06
Matches are distributed among these distances:
19 19 0.25
20 37 0.48
21 21 0.27
ACGTcount: A:0.26, C:0.13, G:0.28, T:0.32
Consensus pattern (21 bp):
GAAAATCGCGTTGCGAATTTG
Found at i:666298 original size:26 final size:28
Alignment explanation
Indices: 666260--666316 Score: 64
Period size: 26 Copynumber: 2.1 Consensus size: 28
666250 TTTTCCCTAT
* **
666260 TTTAAATATCTAATTTAAAAA-AATA-A
1 TTTAAATAACTAAAATAAAAACAATATA
*
666286 TTTAAGTAACTAAAATAAAAACAATATA
1 TTTAAATAACTAAAATAAAAACAATATA
666314 TTT
1 TTT
666317 TTAAATATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
26 17 0.68
27 4 0.16
28 4 0.16
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.37
Consensus pattern (28 bp):
TTTAAATAACTAAAATAAAAACAATATA
Done.