Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008523.1 Hibiscus syriacus cultivar Beakdansim tig00111392_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: 4657139
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 14 of 18
Found at i:3514290 original size:4 final size:4
Alignment explanation
Indices: 3514281--3514340 Score: 70
Period size: 4 Copynumber: 15.0 Consensus size: 4
3514271 CATAACGCAG
*
3514281 GTAT GTAT GTAT GTAT GTAT -TCAT GTAT TTAT -TGAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GT-AT GTAT GTAT GT-AT GTAT GTAT GTAT
*
3514329 GCAT GTAT GTAT
1 GTAT GTAT GTAT
3514341 AATCATGACA
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
3 2 0.04
4 45 0.92
5 2 0.04
ACGTcount: A:0.25, C:0.03, G:0.22, T:0.50
Consensus pattern (4 bp):
GTAT
Found at i:3523750 original size:149 final size:145
Alignment explanation
Indices: 3523484--3523774 Score: 483
Period size: 149 Copynumber: 2.0 Consensus size: 145
3523474 GTAGAAGACA
* * *
3523484 ATGATCAAGGTGATGCGGAAAAATGACTACCCTGGATTCGAAGAGATATAGTCATAGAAGTATAG
1 ATGATCAAGGTGATGAGGAAAAATGACTACCCGGGATTCGAAGAGATATAGCCATAGAAGTATAG
* * *
3523549 CAGAAGTATGCAAATAACTGATTTGGGATGTTAAGATTAAAGGCTTAATCAATAAGATTTGGGTT
66 CAAAAGTATGCAAATAACTGATTTGGGATATTAAGATTAAAGGCTTAATCAATAAGATTTGAGTT
3523614 TCCCTCCATGCCTCC
131 TCCCTCCATGCCTCC
*
3523629 ATGATCAAGGTGATGAGGAAAAATGACTACCCGGGATTTGAAGAGATATAGCCATAGAAAGAAGT
1 ATGATCAAGGTGATGAGGAAAAATGACTACCCGGGATTCGAAGAGATATAGCCAT----AGAAGT
3523694 ATAGCAAAAGTATGCAAATAACTGATTTGGGATATTAAGATTAAAGGCTTAATCAATAAGATTTG
62 ATAGCAAAAGTATGCAAATAACTGATTTGGGATATTAAGATTAAAGGCTTAATCAATAAGATTTG
3523759 AGTTTCCCTCCATGCC
127 AGTTTCCCTCCATGCC
3523775 CCTTTTCATT
Statistics
Matches: 135, Mismatches: 7, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
145 51 0.38
149 84 0.62
ACGTcount: A:0.37, C:0.14, G:0.22, T:0.27
Consensus pattern (145 bp):
ATGATCAAGGTGATGAGGAAAAATGACTACCCGGGATTCGAAGAGATATAGCCATAGAAGTATAG
CAAAAGTATGCAAATAACTGATTTGGGATATTAAGATTAAAGGCTTAATCAATAAGATTTGAGTT
TCCCTCCATGCCTCC
Found at i:3523907 original size:3 final size:3
Alignment explanation
Indices: 3523901--3523935 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
3523891 CTCCATCAAG
3523901 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
3523936 CATATAATCA
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:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:3532300 original size:21 final size:21
Alignment explanation
Indices: 3532276--3532322 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
3532266 TAATTTCTTC
3532276 TTCACCCTTCATTTATCATTG
1 TTCACCCTTCATTTATCATTG
3532297 TTCACCCTTCATTTATCATTG
1 TTCACCCTTCATTTATCATTG
3532318 TTCAC
1 TTCAC
3532323 ACATATATAT
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:0.19, C:0.30, G:0.04, T:0.47
Consensus pattern (21 bp):
TTCACCCTTCATTTATCATTG
Found at i:3534892 original size:16 final size:16
Alignment explanation
Indices: 3534871--3534918 Score: 62
Period size: 16 Copynumber: 2.9 Consensus size: 16
3534861 TAAGTTTGAA
3534871 AATAAT-ATAGATAAAT
1 AATAATAATA-ATAAAT
3534887 AATAATAATAATAAAT
1 AATAATAATAATAAAT
*
3534903 AATAATTAATGATAAA
1 AATAA-TAATAATAAA
3534919 GAACGAGTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
16 17 0.59
17 12 0.41
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (16 bp):
AATAATAATAATAAAT
Found at i:3541398 original size:27 final size:27
Alignment explanation
Indices: 3541346--3541401 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
3541336 TGTCAATCTA
* *
3541346 TTGTAAAATCAACACTATTCAAAAAAT
1 TTGTAAAATCAACACCAATCAAAAAAT
*
3541373 TTGTAAAATCAACACCAATAATAAAAAT
1 TTGTAAAATCAACACCAATCA-AAAAAT
3541401 T
1 T
3541402 AATGTGGTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
27 18 0.72
28 7 0.28
ACGTcount: A:0.54, C:0.14, G:0.04, T:0.29
Consensus pattern (27 bp):
TTGTAAAATCAACACCAATCAAAAAAT
Found at i:3541609 original size:23 final size:23
Alignment explanation
Indices: 3541583--3541646 Score: 103
Period size: 23 Copynumber: 2.8 Consensus size: 23
3541573 TGTACTTCTG
3541583 TGCTGAATCATTCAACACTGTTT
1 TGCTGAATCATTCAACACTGTTT
3541606 TGCTGAATCATTCAACACTGTTT
1 TGCTGAATCATTCAACACTGTTT
* *
3541629 TGATGAATCAGTC-ACACT
1 TGCTGAATCATTCAACACT
3541647 AAATCATTCA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
22 5 0.13
23 34 0.87
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.36
Consensus pattern (23 bp):
TGCTGAATCATTCAACACTGTTT
Found at i:3547325 original size:16 final size:16
Alignment explanation
Indices: 3547284--3547326 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
3547274 TGGTTAGTAA
3547284 TTAGCGGTTAGAAAAG
1 TTAGCGGTTAGAAAAG
**
3547300 TTAGTTGTTAGAAAAG
1 TTAGCGGTTAGAAAAG
*
3547316 TTTGCGGTTAG
1 TTAGCGGTTAG
3547327 TGGTTAGAAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.30, C:0.05, G:0.30, T:0.35
Consensus pattern (16 bp):
TTAGCGGTTAGAAAAG
Found at i:3547347 original size:21 final size:20
Alignment explanation
Indices: 3547299--3547378 Score: 79
Period size: 21 Copynumber: 3.8 Consensus size: 20
3547289 GGTTAGAAAA
*
3547299 GTTAGTTGTTAGAAAAGTTTGCG
1 GTTAG-TGTTAG-AAA-TTAGCG
*
3547322 GTTAGTGGTTAGAAATTAGTG
1 GTTAGT-GTTAGAAATTAGCG
*
3547343 GTTAGCAGTTAGAAATTAGCG
1 GTTAG-TGTTAGAAATTAGCG
*
3547364 GTTAGTGATAGAAAT
1 GTTAGTGTTAGAAAT
3547379 GTTAGTAGAG
Statistics
Matches: 49, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
20 8 0.16
21 27 0.55
22 4 0.08
23 10 0.20
ACGTcount: A:0.31, C:0.04, G:0.30, T:0.35
Consensus pattern (20 bp):
GTTAGTGTTAGAAATTAGCG
Found at i:3547637 original size:20 final size:20
Alignment explanation
Indices: 3547600--3547637 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
3547590 GTTAATTAAT
*
3547600 AAATAAAATAAAACATAACC
1 AAATAAAAGAAAACATAACC
3547620 AAATAAACAGAAAA-ATAA
1 AAATAAA-AGAAAACATAA
3547638 AAAACAGTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.74, C:0.11, G:0.03, T:0.13
Consensus pattern (20 bp):
AAATAAAAGAAAACATAACC
Found at i:3551725 original size:26 final size:24
Alignment explanation
Indices: 3551691--3551747 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 24
3551681 TTTCATCGAA
3551691 AAATATG-AATTGTACATGATTTATG
1 AAATATGAAATT-TAC-TGATTTATG
*
3551716 AAATCATGAAATTTACTGGTTTATG
1 AAAT-ATGAAATTTACTGATTTATG
*
3551741 AAGTATG
1 AAATATG
3551748 CATACCTGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
24 3 0.11
25 15 0.54
26 6 0.21
27 4 0.14
ACGTcount: A:0.39, C:0.05, G:0.18, T:0.39
Consensus pattern (24 bp):
AAATATGAAATTTACTGATTTATG
Found at i:3555107 original size:17 final size:15
Alignment explanation
Indices: 3555065--3555112 Score: 53
Period size: 15 Copynumber: 3.0 Consensus size: 15
3555055 CTCAAAGAAA
3555065 TAATATATTACAATTT
1 TAATATATTA-AATTT
3555081 TAAT-TATTAAATTAT
1 TAATATATTAAATT-T
3555096 TAATAATATTAACATTT
1 TAAT-ATATTAA-ATTT
3555113 AAATGTTGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
14 4 0.14
15 10 0.36
16 4 0.14
17 7 0.25
18 3 0.11
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (15 bp):
TAATATATTAAATTT
Found at i:3562804 original size:22 final size:21
Alignment explanation
Indices: 3562776--3562817 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3562766 TTCCTGTCGG
3562776 AAGAAAAAAAATGTATTTATTC
1 AAGAAAAAAAA-GTATTTATTC
**
3562798 AAGAAAATTAAGTATTTATT
1 AAGAAAAAAAAGTATTTATT
3562818 TATCTGATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.52, C:0.02, G:0.10, T:0.36
Consensus pattern (21 bp):
AAGAAAAAAAAGTATTTATTC
Found at i:3564157 original size:20 final size:20
Alignment explanation
Indices: 3564132--3564192 Score: 54
Period size: 19 Copynumber: 3.0 Consensus size: 20
3564122 AAAATTAGAC
3564132 TTAAAATAAAAAA-AATTAA
1 TTAAAATAAAAAACAATTAA
**
3564151 TTGAAAAATAAAGAAATTATTAA
1 TT--AAAATAAA-AAACAATTAA
*
3564174 -TCAAATAAAAAACAATTAA
1 TTAAAATAAAAAACAATTAA
3564193 ATTATTTAGC
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
19 10 0.29
20 7 0.21
21 8 0.24
22 4 0.12
23 5 0.15
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.26
Consensus pattern (20 bp):
TTAAAATAAAAAACAATTAA
Found at i:3565436 original size:57 final size:57
Alignment explanation
Indices: 3565373--3565483 Score: 186
Period size: 57 Copynumber: 1.9 Consensus size: 57
3565363 CTTTATATTT
* *
3565373 ATAATCTTCGAATTATGATTATAAATTATATTTAAAGACTCAAATAATGAATTTAAA
1 ATAATCTTAGAATTATGATTATAAATTATATCTAAAGACTCAAATAATGAATTTAAA
* *
3565430 ATAATCTTAGAATTATGATTATAAATTATGTCTAATGACTCAAATAATGAATTT
1 ATAATCTTAGAATTATGATTATAAATTATATCTAAAGACTCAAATAATGAATTT
3565484 GAATTATGAT
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
57 50 1.00
ACGTcount: A:0.45, C:0.07, G:0.08, T:0.40
Consensus pattern (57 bp):
ATAATCTTAGAATTATGATTATAAATTATATCTAAAGACTCAAATAATGAATTTAAA
Found at i:3565467 original size:45 final size:45
Alignment explanation
Indices: 3565439--3565528 Score: 144
Period size: 45 Copynumber: 2.0 Consensus size: 45
3565429 AATAATCTTA
*
3565439 GAATTATGATTATAAATTATGTCTAATGACTCAAATAATGAATTT
1 GAATTATGATTATAAATTATGTCTAATGAATCAAATAATGAATTT
* * *
3565484 GAATTATGATTATAAATTATGTCTAAAGACTCATATAATGAATTT
1 GAATTATGATTATAAATTATGTCTAATGAATCAAATAATGAATTT
3565529 AAAGAGAAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.42, C:0.07, G:0.11, T:0.40
Consensus pattern (45 bp):
GAATTATGATTATAAATTATGTCTAATGAATCAAATAATGAATTT
Found at i:3565704 original size:42 final size:43
Alignment explanation
Indices: 3565645--3565725 Score: 155
Period size: 42 Copynumber: 1.9 Consensus size: 43
3565635 TAAAGAGAAG
3565645 CCTTGGGAATCAAAAGGAC-AAAAAAAAAAGAATTCATTTTCT
1 CCTTGGGAATCAAAAGGACAAAAAAAAAAAGAATTCATTTTCT
3565687 CCTTGGGAATCAAAAGGACAAAAAAAAAAAGAATTCATT
1 CCTTGGGAATCAAAAGGACAAAAAAAAAAAGAATTCATT
3565726 ATGTACGTCA
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
42 19 0.50
43 19 0.50
ACGTcount: A:0.51, C:0.14, G:0.15, T:0.21
Consensus pattern (43 bp):
CCTTGGGAATCAAAAGGACAAAAAAAAAAAGAATTCATTTTCT
Found at i:3573124 original size:20 final size:21
Alignment explanation
Indices: 3573099--3573150 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
3573089 TTTTCCCAAT
*
3573099 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
3573119 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
3573140 TCGCAATGCGA
1 TCGCAATGCGA
3573151 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:3573164 original size:20 final size:20
Alignment explanation
Indices: 3573139--3573232 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
3573129 AATTGGGAAA
3573139 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
*
3573159 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
* * *
3573179 ATCGTAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* *
3573200 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACTGACT
* *
3573220 TTCGCAACGCGAT
1 ATCGCAATGCGAT
3573233 TTACATAGCG
Statistics
Matches: 60, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
19 2 0.03
20 44 0.73
21 12 0.20
22 2 0.03
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.24
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:3573837 original size:19 final size:19
Alignment explanation
Indices: 3573792--3573831 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
3573782 GAGATAATCC
*
3573792 CAACGCGAAATAAAAAACG
1 CAACGCGAAACAAAAAACG
*
3573811 CAACGCGAAACAAAAATCG
1 CAACGCGAAACAAAAAACG
3573830 CA
1 CA
3573832 TTGCGATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.55, C:0.25, G:0.15, T:0.05
Consensus pattern (19 bp):
CAACGCGAAACAAAAAACG
Found at i:3573857 original size:20 final size:20
Alignment explanation
Indices: 3573832--3573898 Score: 118
Period size: 20 Copynumber: 3.4 Consensus size: 20
3573822 AAAAATCGCA
3573832 TTGCGATTTTCATTTCGCGG
1 TTGCGATTTTCATTTCGCGG
*
3573852 TTGCGATTTTTATTTCGCGG
1 TTGCGATTTTCATTTCGCGG
3573872 TTGCGATTTTCATTTCGC-G
1 TTGCGATTTTCATTTCGCGG
3573891 TTGCGATT
1 TTGCGATT
3573899 GTCTGGTCGC
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
19 9 0.20
20 36 0.80
ACGTcount: A:0.10, C:0.18, G:0.24, T:0.48
Consensus pattern (20 bp):
TTGCGATTTTCATTTCGCGG
Found at i:3573918 original size:33 final size:33
Alignment explanation
Indices: 3573881--3573968 Score: 140
Period size: 33 Copynumber: 2.6 Consensus size: 33
3573871 GTTGCGATTT
* *
3573881 TCATTTCGCGTTGCGATTGTCTGGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
*
3573914 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
3573947 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
3573969 ATTATCTCGT
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 36 0.71
34 15 0.29
ACGTcount: A:0.11, C:0.25, G:0.25, T:0.39
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:3573970 original size:20 final size:20
Alignment explanation
Indices: 3573936--3573993 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
3573926 GCGATTCTCT
**
3573936 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTCTCATTTCCG
*
3573956 CGTTGCGATTCTCATTAT-CT
1 CGTTGCGATTCTCATT-TCCG
* *
3573976 CGTTGTGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
3573994 AACCAAAAGA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
19 1 0.03
20 29 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.45
Consensus pattern (20 bp):
CGTTGCGATTCTCATTTCCG
Found at i:3575593 original size:20 final size:20
Alignment explanation
Indices: 3575568--3575610 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
3575558 AATAGTTTCT
3575568 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
*
3575588 GAAAATGAAAATCGCAACGC
1 GAAAATGAAAATCGCAACAC
3575608 GAA
1 GAA
3575611 TTCGACTATC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.53, C:0.19, G:0.19, T:0.09
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:3575916 original size:22 final size:22
Alignment explanation
Indices: 3575888--3575931 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
3575878 GATGGAGATA
*
3575888 GACGGATTTTG-CTGGAGATGGG
1 GACGGATTTCGTC-GGAGATGGG
3575910 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
3575932 TGAGAGAGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 19 0.95
23 1 0.05
ACGTcount: A:0.18, C:0.11, G:0.45, T:0.25
Consensus pattern (22 bp):
GACGGATTTCGTCGGAGATGGG
Found at i:3576145 original size:20 final size:20
Alignment explanation
Indices: 3576119--3576232 Score: 120
Period size: 20 Copynumber: 5.7 Consensus size: 20
3576109 GATTATGTAT
3576119 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
3576139 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
3576159 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
* *** * *
3576179 TATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGA-AAGTCAG
* *
3576200 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
3576220 TATCGCATTGCGA
1 TATCGCGTTGCGA
3576233 TTTTCCCAAT
Statistics
Matches: 78, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
20 65 0.83
21 13 0.17
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:3576236 original size:41 final size:41
Alignment explanation
Indices: 3576099--3576234 Score: 148
Period size: 41 Copynumber: 3.3 Consensus size: 41
3576089 CGCTTTGAAA
* *
3576099 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATTATTTATTATCGCGTTGCGAAAGTCAGT
* * * * * *
3576140 ATCGCGTTGCGA-AAGTCAGTATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATTATTTATTATCGCGTTGCGAAAGTCAGT
* * * * *
3576180 ATCTCGTTGCGATTTTTTATTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTATTTATTATCGCGTTGCGAAAGTCAGT
3576221 ATCGCATTGCGATT
1 ATCGCATTGCGATT
3576235 TTCCCAATTC
Statistics
Matches: 75, Mismatches: 19, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
40 32 0.43
41 43 0.57
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (41 bp):
ATCGCATTGCGATTATTTATTATCGCGTTGCGAAAGTCAGT
Found at i:3576252 original size:41 final size:41
Alignment explanation
Indices: 3576222--3576314 Score: 141
Period size: 41 Copynumber: 2.3 Consensus size: 41
3576212 ATAGTCAGTA
* * *
3576222 TCGCATTGCGATTTTCCCAATTCGGGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTCACGTAT
* *
3576263 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTCACGTAT
3576304 TCGCATTGCGA
1 TCGCATTGCGA
3576315 ATTGGGAAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.17, C:0.24, G:0.19, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTCACGTAT
Found at i:3576253 original size:21 final size:21
Alignment explanation
Indices: 3576222--3576297 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
3576212 ATAGTCAGTA
*
3576222 TCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATTTTCCCAAT
* * **
3576243 TCGGGTTGCGA-TTTACTTAT
1 TCGCGTTGCGATTTTCCCAAT
*
3576263 TCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATTTTCCCAAT
3576284 TCGCGTTGCGATTT
1 TCGCGTTGCGATTT
3576298 ACTTATTCGC
Statistics
Matches: 43, Mismatches: 11, Indels: 2
0.77 0.20 0.04
Matches are distributed among these distances:
20 15 0.35
21 28 0.65
ACGTcount: A:0.16, C:0.24, G:0.20, T:0.41
Consensus pattern (21 bp):
TCGCGTTGCGATTTTCCCAAT
Found at i:3576271 original size:20 final size:20
Alignment explanation
Indices: 3576248--3576314 Score: 89
Period size: 20 Copynumber: 3.3 Consensus size: 20
3576238 CCAATTCGGG
3576248 TTGCGATTTACTTATTCGCA
1 TTGCGATTTACTTATTCGCA
* ** *
3576268 TTGCGATTTTCCCAATTCGCG
1 TTGCGA-TTTACTTATTCGCA
3576289 TTGCGATTTACTTATTCGCA
1 TTGCGATTTACTTATTCGCA
3576309 TTGCGA
1 TTGCGA
3576315 ATTGGGAAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 22 0.58
21 16 0.42
ACGTcount: A:0.18, C:0.22, G:0.18, T:0.42
Consensus pattern (20 bp):
TTGCGATTTACTTATTCGCA
Found at i:3579030 original size:2 final size:2
Alignment explanation
Indices: 3579023--3579063 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
3579013 TAGTATGAAA
3579023 AT AT AT AT 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 AT AT AT AT A
3579064 GTTGATTAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3582413 original size:2 final size:2
Alignment explanation
Indices: 3582406--3582460 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
3582396 TACAGAAATA
3582406 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
3582448 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
3582461 ACAATATAAT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3584706 original size:17 final size:18
Alignment explanation
Indices: 3584666--3584705 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
3584656 ATTATAATTC
3584666 TTTTTAAAAAATTATATA
1 TTTTTAAAAAATTATATA
*
3584684 TTTTTAAAACA-TATATTA
1 TTTTTAAAAAATTATA-TA
3584702 TTTT
1 TTTT
3584706 ATAATTATCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (18 bp):
TTTTTAAAAAATTATATA
Found at i:3585111 original size:27 final size:25
Alignment explanation
Indices: 3585081--3585150 Score: 68
Period size: 27 Copynumber: 2.6 Consensus size: 25
3585071 ATAATTGATA
3585081 AATAAATAAATTAATAAATATTTTTT
1 AATAAA-AAATTAATAAATATTTTTT
* *
3585107 CAATAAAAACTTCAATTAATATTTTTT
1 -AATAAAAAATT-AATAAATATTTTTT
*
3585134 ATTAAAAACAATTAATA
1 AAT-AAAA-AATTAATA
3585151 TAATTATTCT
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
26 6 0.17
27 26 0.74
28 3 0.09
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (25 bp):
AATAAAAAATTAATAAATATTTTTT
Found at i:3601482 original size:254 final size:252
Alignment explanation
Indices: 3601004--3601490 Score: 635
Period size: 257 Copynumber: 1.9 Consensus size: 252
3600994 AAAATACCCA
* *
3601004 ACCCGACCCGAAAAGAAAATATAATTTTACATTATATATTTAGGTATAATTACAATAATATCCCT
1 ACCCGACCCGAAAAGAAAATATAATTTTACATTATATATTTAGGAATAATTACAATAATACCCCT
*
3601069 TTATATATAATTTTTTTCAATTAAGTCACTGTTTTTATTGAATATTTTTTTATTATTATTTCAGG
66 CTATATATAATTTTTTTCAATTAAGTCACTGTTTTTATTGAATATTTTTTTATTATTATTTCAGG
* * * *
3601134 TCGGGTCGGGTTTATTATTTATATATTCGGGTCGGGTTGGGTGAAACATTATTTTGGTCGGATCG
131 TAGGGTCGGGTTTATAATTTATATATTCGGGTCGGGTCGGGTGAAACATTATTCTGGTCGGATCG
* * ***
3601199 GGTCGATTTTTTTAAGTGTGATATTCGGGTCGGATCGGGTTCGGATTTAGGGTGAAAAAT
196 GATCGAGTTCCCT-A-TGT-ATATTCGGGTCGGATCGGGTTCGGATTTAGGGTGAAAAAT
* *
3601259 ACCCGACCCGAAAA-AATATATAATTTTACATTATATATTTAGGAATAATTATAATAATACCCCT
1 ACCCGACCCGAAAAGAAAATATAATTTTACATTATATATTTAGGAATAATTACAATAATACCCCT
3601323 CTATATATAA-TTTTTTCAATTAAGTCACTGTTTTTATTGAATAAAAATATTTTTT-TTATTATT
66 CTATATATAATTTTTTTCAATTAAGTCACTGTTTTTATTGAAT----AT-TTTTTTATTATTATT
* * * **
3601386 TCGGGTAGGGTTGGGTTTCTAATTTATATATTCGGGTCGGGTCGGGTGAAATTTTATTCTGGTCG
126 TCAGGTAGGGTCGGGTTTATAATTTATATATTCGGGTCGGGTCGGGTGAAACATTATTCTGGTCG
* * *
3601451 GGTCTTGGATGGAGGTTCCCT-TGT-T-TTCGGGTCGGGTCGG
191 GATC--GGATCGA-GTTCCCTATGTATATTCGGGTCGGATCGG
3601491 TGGACCAAAA
Statistics
Matches: 202, Mismatches: 22, Indels: 17
0.84 0.09 0.07
Matches are distributed among these distances:
253 32 0.16
254 69 0.34
255 15 0.07
257 72 0.36
258 6 0.03
259 5 0.02
260 3 0.01
ACGTcount: A:0.27, C:0.11, G:0.20, T:0.42
Consensus pattern (252 bp):
ACCCGACCCGAAAAGAAAATATAATTTTACATTATATATTTAGGAATAATTACAATAATACCCCT
CTATATATAATTTTTTTCAATTAAGTCACTGTTTTTATTGAATATTTTTTTATTATTATTTCAGG
TAGGGTCGGGTTTATAATTTATATATTCGGGTCGGGTCGGGTGAAACATTATTCTGGTCGGATCG
GATCGAGTTCCCTATGTATATTCGGGTCGGATCGGGTTCGGATTTAGGGTGAAAAAT
Found at i:3602943 original size:30 final size:30
Alignment explanation
Indices: 3602908--3602982 Score: 105
Period size: 30 Copynumber: 2.5 Consensus size: 30
3602898 ACCAACGTGA
* *
3602908 ACCGTTGGAATTTGGTTGCACCCCACTTGC
1 ACCGTTGGAATTGGGTTGAACCCCACTTGC
* *
3602938 GCCGTTGGAATTGGGTTGAACCCCATTTGC
1 ACCGTTGGAATTGGGTTGAACCCCACTTGC
*
3602968 ACCATTGGAATTGGG
1 ACCGTTGGAATTGGG
3602983 ATGATCCACG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.19, C:0.24, G:0.28, T:0.29
Consensus pattern (30 bp):
ACCGTTGGAATTGGGTTGAACCCCACTTGC
Found at i:3602999 original size:30 final size:29
Alignment explanation
Indices: 3602942--3603008 Score: 71
Period size: 30 Copynumber: 2.2 Consensus size: 29
3602932 ACTTGCGCCG
* * *
3602942 TTGGAATTGGGTTGAACCCCATTTGCACC
1 TTGGAATTGGGATGAACCACATATGCACC
* *
3602971 ATTGGAATTGGGATGATCCACGTATGCACC
1 -TTGGAATTGGGATGAACCACATATGCACC
3603001 TCTGGAAT
1 T-TGGAAT
3603009 CGGTTTGAAG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
29 1 0.03
30 30 0.97
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (29 bp):
TTGGAATTGGGATGAACCACATATGCACC
Found at i:3603036 original size:30 final size:30
Alignment explanation
Indices: 3603002--3603077 Score: 91
Period size: 30 Copynumber: 2.5 Consensus size: 30
3602992 GTATGCACCT
* * *
3603002 CTGGAATCGGTTTGAAGCC-CGTCTGCATCG
1 CTGGAATCGGGTTGAA-CCTCGTATGAATCG
* *
3603032 CTGGAATCGGGCTGAACCTCGTATGAATGG
1 CTGGAATCGGGTTGAACCTCGTATGAATCG
3603062 CTGGAATCGGGTTGAA
1 CTGGAATCGGGTTGAA
3603078 AACGAGGTCC
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
29 2 0.05
30 37 0.95
ACGTcount: A:0.21, C:0.21, G:0.33, T:0.25
Consensus pattern (30 bp):
CTGGAATCGGGTTGAACCTCGTATGAATCG
Found at i:3603177 original size:30 final size:30
Alignment explanation
Indices: 3603063--3603167 Score: 174
Period size: 30 Copynumber: 3.5 Consensus size: 30
3603053 TATGAATGGC
*
3603063 TGGAATCGGGTTGAAAACGAGGTCCACCTT
1 TGGAATTGGGTTGAAAACGAGGTCCACCTT
3603093 TGGAATTGGGTTGAAAACGAGGTCCACCTT
1 TGGAATTGGGTTGAAAACGAGGTCCACCTT
* **
3603123 TGGATTTGGGTTGAAAACGAGGTCCACCGA
1 TGGAATTGGGTTGAAAACGAGGTCCACCTT
3603153 TGGAATTGGGTTGAA
1 TGGAATTGGGTTGAA
3603168 TCAGAGGTCC
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 70 1.00
ACGTcount: A:0.27, C:0.15, G:0.32, T:0.26
Consensus pattern (30 bp):
TGGAATTGGGTTGAAAACGAGGTCCACCTT
Found at i:3606239 original size:36 final size:36
Alignment explanation
Indices: 3606192--3606269 Score: 156
Period size: 36 Copynumber: 2.2 Consensus size: 36
3606182 CAGCTCCAAC
3606192 TGCATCACTGGAATTTGCTTTAATCCCATTCTCATG
1 TGCATCACTGGAATTTGCTTTAATCCCATTCTCATG
3606228 TGCATCACTGGAATTTGCTTTAATCCCATTCTCATG
1 TGCATCACTGGAATTTGCTTTAATCCCATTCTCATG
3606264 TGCATC
1 TGCATC
3606270 GTCGACTCTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 42 1.00
ACGTcount: A:0.22, C:0.26, G:0.14, T:0.38
Consensus pattern (36 bp):
TGCATCACTGGAATTTGCTTTAATCCCATTCTCATG
Found at i:3613004 original size:15 final size:15
Alignment explanation
Indices: 3612954--3613033 Score: 54
Period size: 15 Copynumber: 5.1 Consensus size: 15
3612944 TTCAAACTAA
3612954 TATATATTTTAATTT
1 TATATATTTTAATTT
* *
3612969 TTTATATTTTAGTTT
1 TATATATTTTAATTT
* *
3612984 GATATATTTTTTACTTT
1 --TATATATTTTAATTT
*
3613001 TATA-ATTTTATAAATT
1 TATATA-TTT-TAATTT
*
3613017 TATTCTATTTTAATTT
1 TA-TATATTTTAATTT
3613033 T
1 T
3613034 TTAAAATTTC
Statistics
Matches: 49, Mismatches: 10, Indels: 11
0.70 0.14 0.16
Matches are distributed among these distances:
15 20 0.41
16 12 0.24
17 16 0.33
18 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.66
Consensus pattern (15 bp):
TATATATTTTAATTT
Found at i:3613017 original size:25 final size:25
Alignment explanation
Indices: 3612964--3613038 Score: 75
Period size: 24 Copynumber: 3.1 Consensus size: 25
3612954 TATATATTTT
* *
3612964 AATTTTTTA-TATTTTAGTTTGATA
1 AATTTTTTACTATTTTAATTTTATA
*
3612988 TATTTTTTACT-TTTATAATTTTATA
1 AATTTTTTACTATTT-TAATTTTATA
* *
3613013 AATTTATT-CTATTTTAATTTTTTA
1 AATTTTTTACTATTTTAATTTTATA
3613037 AA
1 AA
3613039 ATTTCATTCT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
24 24 0.57
25 18 0.43
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.64
Consensus pattern (25 bp):
AATTTTTTACTATTTTAATTTTATA
Found at i:3614266 original size:16 final size:16
Alignment explanation
Indices: 3614245--3614278 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3614235 TATTTTAAAA
* *
3614245 AAATAATTATATAATT
1 AAATAAATATAAAATT
3614261 AAATAAATATAAAATT
1 AAATAAATATAAAATT
3614277 AA
1 AA
3614279 TTCATAACAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
AAATAAATATAAAATT
Found at i:3617544 original size:24 final size:26
Alignment explanation
Indices: 3617523--3617570 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 26
3617513 TTTTATATGA
3617523 TTTCAT-T-AAAATATTAAAATATAT
1 TTTCATCTAAAAATATTAAAATATAT
*
3617547 TTTGATCTAAAAATATT-AAATATA
1 TTTCATCTAAAAATATTAAAATATA
3617571 AAATTTTCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 5 0.24
25 8 0.38
26 8 0.38
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (26 bp):
TTTCATCTAAAAATATTAAAATATAT
Found at i:3619157 original size:15 final size:15
Alignment explanation
Indices: 3619117--3619180 Score: 60
Period size: 15 Copynumber: 4.3 Consensus size: 15
3619107 TTGAAAAATA
*
3619117 AATTACTAG-AATTTA
1 AATTAC-AGAAATTTG
*
3619132 AATTACTGAAATTTG
1 AATTACAGAAATTTG
*
3619147 AATTACAGAAAAATT-
1 AATTACAG-AAATTTG
*
3619162 AATTACTGAAATTTG
1 AATTACAGAAATTTG
3619177 AATT
1 AATT
3619181 CTGAAAAATG
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
14 6 0.15
15 29 0.73
16 5 0.12
ACGTcount: A:0.47, C:0.06, G:0.09, T:0.38
Consensus pattern (15 bp):
AATTACAGAAATTTG
Found at i:3619175 original size:45 final size:44
Alignment explanation
Indices: 3619109--3619197 Score: 117
Period size: 45 Copynumber: 2.0 Consensus size: 44
3619099 TTGGTTTTTT
**
3619109 GAAAAATAAATTACTAGAATTTAAATTACTGAAATTTGAATTACA
1 GAAAAATAAATTACTAGAATTTAAATT-CTGAAAAATGAATTACA
* *
3619154 GAAAAATTAATTACT-GAAATTTGAATTCTGAAAAATGAATTACA
1 GAAAAATAAATTACTAG-AATTTAAATTCTGAAAAATGAATTACA
3619198 TTTCTAGAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
44 16 0.41
45 23 0.59
ACGTcount: A:0.51, C:0.07, G:0.10, T:0.33
Consensus pattern (44 bp):
GAAAAATAAATTACTAGAATTTAAATTCTGAAAAATGAATTACA
Found at i:3619192 original size:14 final size:15
Alignment explanation
Indices: 3619132--3619196 Score: 69
Period size: 15 Copynumber: 4.4 Consensus size: 15
3619122 CTAGAATTTA
**
3619132 AATTACTGAAATTTG
1 AATTACTGAAAAATG
* *
3619147 AATTACAGAAAAATT
1 AATTACTGAAAAATG
**
3619162 AATTACTGAAATTTG
1 AATTACTGAAAAATG
3619177 AATT-CTGAAAAATG
1 AATTACTGAAAAATG
3619191 AATTAC
1 AATTAC
3619197 ATTTCTAGAA
Statistics
Matches: 39, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
14 12 0.31
15 27 0.69
ACGTcount: A:0.48, C:0.08, G:0.11, T:0.34
Consensus pattern (15 bp):
AATTACTGAAAAATG
Found at i:3619569 original size:23 final size:23
Alignment explanation
Indices: 3619520--3619582 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
3619510 GTGTTATATT
* **
3619520 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAATATATTAATTAAA
*
3619543 ATATTTTAAATATCTTAATTAAA
1 ATATTTTAAATATATTAATTAAA
3619566 ATATTATTTAAATATAT
1 ATA-T-TTTAAATATAT
3619583 AAATAATATT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
23 22 0.67
24 1 0.03
25 10 0.30
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.49
Consensus pattern (23 bp):
ATATTTTAAATATATTAATTAAA
Found at i:3619610 original size:19 final size:20
Alignment explanation
Indices: 3619560--3619615 Score: 53
Period size: 20 Copynumber: 2.8 Consensus size: 20
3619550 AAATATCTTA
3619560 ATTAAA-ATATTATTTAAAT
1 ATTAAATATATTATTTAAAT
* *
3619579 ATATAAATAATATTA-TTCATT
1 AT-TAAAT-ATATTATTTAAAT
*
3619600 ATTAAATATATAATTT
1 ATTAAATATATTATTT
3619616 TTTTATTATA
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
19 7 0.23
20 11 0.37
21 6 0.20
22 6 0.20
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (20 bp):
ATTAAATATATTATTTAAAT
Found at i:3619969 original size:42 final size:41
Alignment explanation
Indices: 3619922--3620036 Score: 162
Period size: 40 Copynumber: 2.8 Consensus size: 41
3619912 ATTACGTTCA
*
3619922 GGAAAACCAATTACGTGAAACAAACAATGGAAAATATTTTCC
1 GGAAAACGAATTACGTGAAACAAAC-ATGGAAAATATTTTCC
* * *
3619964 GGAAAACGAATTACATGAAACAAACACGGAAAACATTTTCC
1 GGAAAACGAATTACGTGAAACAAACATGGAAAATATTTTCC
*
3620005 -AAAAACGAATTACGTGAAACAAACAT-GAAAAT
1 GGAAAACGAATTACGTGAAACAAACATGGAAAAT
3620037 TCGGAGAAAA
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
39 5 0.08
40 23 0.35
41 14 0.22
42 23 0.35
ACGTcount: A:0.51, C:0.17, G:0.14, T:0.18
Consensus pattern (41 bp):
GGAAAACGAATTACGTGAAACAAACATGGAAAATATTTTCC
Found at i:3621888 original size:27 final size:27
Alignment explanation
Indices: 3621850--3621905 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
3621840 CTCCCCCTCT
3621850 CAACCTATCCCTGTCATAATCCAAAAA
1 CAACCTATCCCTGTCATAATCCAAAAA
3621877 CAACCTATCCCTGTCATAATCCAAAAA
1 CAACCTATCCCTGTCATAATCCAAAAA
3621904 CA
1 CA
3621906 GATGAAGGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.41, C:0.34, G:0.04, T:0.21
Consensus pattern (27 bp):
CAACCTATCCCTGTCATAATCCAAAAA
Found at i:3623963 original size:22 final size:23
Alignment explanation
Indices: 3623929--3623971 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
3623919 ATATAATAAA
3623929 TAATATTATTTAT-TATAAAAACT
1 TAATATTATTTATCT-TAAAAACT
3623952 TAATATTA-TTATCTTAAAAA
1 TAATATTATTTATCTTAAAAA
3623972 TATTAGAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.47
Consensus pattern (23 bp):
TAATATTATTTATCTTAAAAACT
Found at i:3624231 original size:42 final size:41
Alignment explanation
Indices: 3624156--3624235 Score: 103
Period size: 39 Copynumber: 1.9 Consensus size: 41
3624146 TAGACTATTA
3624156 TATTAAAATTAAATACATAAATAATATAATTTATTATATAT
1 TATTAAAATTAAATACATAAATAATATAATTTATTATATAT
3624197 TATTAAAA-TAAA-A-ATATAATAATATCATATTTTATTATA
1 TATTAAAATTAAATACATA-AATAATAT-A-A-TTTATTATA
3624236 ATATAACTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
38 3 0.09
39 9 0.26
40 5 0.14
41 9 0.26
42 9 0.26
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (41 bp):
TATTAAAATTAAATACATAAATAATATAATTTATTATATAT
Found at i:3624232 original size:32 final size:32
Alignment explanation
Indices: 3624172--3624322 Score: 87
Period size: 32 Copynumber: 4.5 Consensus size: 32
3624162 AATTAAATAC
* *
3624172 ATAAATAATATAATTTATTATATATTATTAAA
1 ATAAATAATATAATATATCATATATTATTAAA
*
3624204 ATAAA-AATATAATAATATCATATTTTATTATAA
1 ATAAATAATATAAT-ATATCATATATTATTA-AA
* * *
3624237 TATAACTATATATATAATA-ATAATAATAATAATAATA
1 -ATAA--ATA-ATATAATATATCAT-ATATTATTAA-A
* *
3624274 AT-AATAATATTACTATATCATATTATATTTTAAA
1 ATAAATAATA-TAATATATCATA-TAT-TATTAAA
*
3624308 AT-ATTAATA-AATATA
1 ATAAATAATATAATATA
3624323 CTTTAATTAC
Statistics
Matches: 92, Mismatches: 14, Indels: 26
0.70 0.11 0.20
Matches are distributed among these distances:
31 8 0.09
32 26 0.28
33 10 0.11
34 19 0.21
35 5 0.05
36 8 0.09
37 9 0.10
38 7 0.08
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (32 bp):
ATAAATAATATAATATATCATATATTATTAAA
Found at i:3624258 original size:3 final size:3
Alignment explanation
Indices: 3624250--3624282 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
3624240 AACTATATAT
3624250 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
3624283 TTACTATATC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:3626728 original size:18 final size:16
Alignment explanation
Indices: 3626694--3626737 Score: 52
Period size: 18 Copynumber: 2.6 Consensus size: 16
3626684 ATTCAATTAT
*
3626694 AATTATATTTTAAAAC
1 AATTAAATTTTAAAAC
3626710 AATTAACATTTTAAAAAC
1 AATTAA-ATTTT-AAAAC
*
3626728 ATTTAAATTT
1 AATTAAATTT
3626738 AATTTATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 5 0.21
17 9 0.38
18 10 0.42
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (16 bp):
AATTAAATTTTAAAAC
Found at i:3628037 original size:13 final size:15
Alignment explanation
Indices: 3628009--3628041 Score: 52
Period size: 13 Copynumber: 2.3 Consensus size: 15
3627999 TAATTTATGC
3628009 TTAAAACAATTAAAT
1 TTAAAACAATTAAAT
3628024 TTAAAA-AA-TAAAT
1 TTAAAACAATTAAAT
3628037 TTAAA
1 TTAAA
3628042 TTTACTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 10 0.56
14 2 0.11
15 6 0.33
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (15 bp):
TTAAAACAATTAAAT
Found at i:3634338 original size:2 final size:2
Alignment explanation
Indices: 3634331--3634368 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
3634321 ATTTGTATCC
3634331 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3634369 AGCAAATTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3635038 original size:20 final size:20
Alignment explanation
Indices: 3635013--3635105 Score: 96
Period size: 21 Copynumber: 4.5 Consensus size: 20
3635003 TTTTCCCAAT
3635013 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
3635033 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGTAAA
3635053 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGTAAA
* ** *
3635074 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
3635095 TCGCAATGCGA
1 TCGCAATGCGA
3635106 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:3635055 original size:41 final size:41
Alignment explanation
Indices: 3635010--3635105 Score: 183
Period size: 41 Copynumber: 2.3 Consensus size: 41
3635000 CGATTTTCCC
3635010 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
3635051 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
*
3635092 AAATCGCAATGCGA
1 AATTCGCAATGCGA
3635106 TACTGACTAT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.19
Consensus pattern (41 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
Found at i:3635059 original size:21 final size:20
Alignment explanation
Indices: 3635013--3635105 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
3635003 TTTTCCCAAT
*
3635013 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGGAAA
* **
3635033 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGGAAA
*
3635053 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGGAAA
* **
3635074 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGG-AAA
3635095 TCGCAATGCGA
1 TCGCAATGCGA
3635106 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 29 0.50
21 29 0.50
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGGAAA
Found at i:3635136 original size:41 final size:41
Alignment explanation
Indices: 3635091--3635168 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 41
3635081 GCGAATTGGG
* * * *
3635091 AAAATCGCAATGCGATACTGACTATCTCAATGCGATAATAA
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATAA
* *
3635132 AAAATCGCAACGAGATACTTACTTTCGCAACGCGATA
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATA
3635169 CTGACTTTCG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 31 1.00
ACGTcount: A:0.40, C:0.22, G:0.15, T:0.23
Consensus pattern (41 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATAA
Found at i:3635184 original size:20 final size:20
Alignment explanation
Indices: 3635136--3635187 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
3635126 TAATAAAAAA
* *
3635136 TCGCAACGAGATACTTACTT
1 TCGCAACGCGATACTGACTT
3635156 TCGCAACGCGATACTGACTT
1 TCGCAACGCGATACTGACTT
3635176 TCGCAACGCGAT
1 TCGCAACGCGAT
3635188 TTACTTAGCG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.27, C:0.29, G:0.19, T:0.25
Consensus pattern (20 bp):
TCGCAACGCGATACTGACTT
Found at i:3635747 original size:19 final size:19
Alignment explanation
Indices: 3635709--3635775 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
3635699 TTCGAGAATG
*
3635709 AAAATCGCAAAGCGGAAATA
1 AAAATCGCAACGC-GAAATA
**
3635729 ACTATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
**
3635748 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATA
3635767 AAAATCGCA
1 AAAATCGCA
3635776 TTGCGATTTT
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
19 30 0.75
20 10 0.25
ACGTcount: A:0.49, C:0.24, G:0.16, T:0.10
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:3635793 original size:19 final size:19
Alignment explanation
Indices: 3635771--3635935 Score: 134
Period size: 19 Copynumber: 9.1 Consensus size: 19
3635761 GAAACCAAAA
*
3635771 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
3635790 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
3635809 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
3635828 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * **
3635842 TCTCGTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
3635861 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * **
3635875 TCTCATTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
* *
3635894 TCCGCGTTGCAATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
3635914 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
3635934 TC
1 TC
3635936 AACCAAAAGA
Statistics
Matches: 116, Mismatches: 18, Indels: 24
0.73 0.11 0.15
Matches are distributed among these distances:
14 18 0.16
16 4 0.03
17 5 0.04
19 60 0.52
20 28 0.24
21 1 0.01
ACGTcount: A:0.13, C:0.24, G:0.19, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:3635827 original size:38 final size:33
Alignment explanation
Indices: 3635776--3635910 Score: 144
Period size: 33 Copynumber: 3.9 Consensus size: 33
3635766 CAAAATCGCA
*
3635776 TTGCGATTTTCATTTCGCGTTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCGTTGCGA--TTC---TCTCG
3635814 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* ** *
3635847 TCGCGATAGTCATTTCGCGTTGCGATTCTCTCA
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
** *
3635880 TTGCGATAGTCATTTCCGCGTTGCAATTCTC
1 TTGCGATTTTCATTT-CGCGTTGCGATTCTC
3635911 ATTATCTCGT
Statistics
Matches: 89, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
33 47 0.53
34 14 0.16
36 3 0.03
38 25 0.28
ACGTcount: A:0.13, C:0.24, G:0.21, T:0.42
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:3635912 original size:20 final size:20
Alignment explanation
Indices: 3635889--3635935 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
3635879 ATTGCGATAG
3635889 TCATTTCCGCGTTGCAATTC
1 TCATTTCCGCGTTGCAATTC
* * *
3635909 TCATTAT-CTCGTTGCGATTT
1 TCATT-TCCGCGTTGCAATTC
3635929 TCATTTC
1 TCATTTC
3635936 AACCAAAAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
19 1 0.05
20 20 0.91
21 1 0.05
ACGTcount: A:0.15, C:0.26, G:0.13, T:0.47
Consensus pattern (20 bp):
TCATTTCCGCGTTGCAATTC
Found at i:3637992 original size:42 final size:42
Alignment explanation
Indices: 3637932--3638054 Score: 115
Period size: 42 Copynumber: 2.9 Consensus size: 42
3637922 GCCCGACTCG
* * *
3637932 CCTATCATCCATCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCATCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* *
3637974 CCTATCATTCC-TCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCA-TCCATCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * ** * *
3638016 ACTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CCTATCATCCATCAAGA-GTCCACTCCCACCGTTCAAGAG
3638055 CCCGATTCAC
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 2 0.03
42 58 0.87
43 7 0.10
ACGTcount: A:0.24, C:0.36, G:0.18, T:0.23
Consensus pattern (42 bp):
CCTATCATCCATCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:3638012 original size:21 final size:21
Alignment explanation
Indices: 3637988--3638054 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
3637978 TCATTCCTCG
3637988 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
3638009 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
3638030 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
3638051 AGAG
1 AGAG
3638055 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:3639427 original size:14 final size:14
Alignment explanation
Indices: 3639408--3639443 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
3639398 ATTGTTTAAT
3639408 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
3639422 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
3639436 TGATTTGT
1 TGATTTGT
3639444 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:3639612 original size:19 final size:19
Alignment explanation
Indices: 3639550--3639603 Score: 90
Period size: 20 Copynumber: 2.8 Consensus size: 19
3639540 AAAAAGTACT
*
3639550 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
3639569 ATCGCAACGCGAAAATGAAA
1 ATCGCAACGCG-AAATGAAA
3639589 ATCGCAACGCGAAAT
1 ATCGCAACGCGAAAT
3639604 TAAATTCGCG
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
19 14 0.42
20 19 0.58
ACGTcount: A:0.46, C:0.20, G:0.20, T:0.13
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:3639630 original size:19 final size:19
Alignment explanation
Indices: 3639608--3639725 Score: 76
Period size: 19 Copynumber: 6.7 Consensus size: 19
3639598 CGAAATTAAA
3639608 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
3639627 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
3639642 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
3639660 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
3639675 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
3639693 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
3639712 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
3639726 GGACATTAAG
Statistics
Matches: 73, Mismatches: 15, Indels: 21
0.67 0.14 0.19
Matches are distributed among these distances:
14 17 0.23
16 6 0.08
17 6 0.08
19 34 0.47
20 10 0.14
ACGTcount: A:0.14, C:0.24, G:0.20, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:3639654 original size:33 final size:33
Alignment explanation
Indices: 3639612--3639705 Score: 179
Period size: 33 Copynumber: 2.8 Consensus size: 33
3639602 ATTAAATTCG
3639612 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
*
3639645 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
3639678 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
3639706 AGTAATTTCC
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 60 1.00
ACGTcount: A:0.13, C:0.24, G:0.19, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
Found at i:3642014 original size:12 final size:12
Alignment explanation
Indices: 3641997--3642021 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3641987 TCTTCGGGGA
3641997 CTTTTTCTTCTT
1 CTTTTTCTTCTT
3642009 CTTTTTCTTCTT
1 CTTTTTCTTCTT
3642021 C
1 C
3642022 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:3643925 original size:20 final size:20
Alignment explanation
Indices: 3643900--3643956 Score: 96
Period size: 20 Copynumber: 2.9 Consensus size: 20
3643890 TTCATTTGAC
*
3643900 TATCGCAATGCGAAAATGGT
1 TATCGCAACGCGAAAATGGT
3643920 TATCGCAACGCGAAAATGGT
1 TATCGCAACGCGAAAATGGT
*
3643940 TATCGCAACGAGAAAAT
1 TATCGCAACGCGAAAAT
3643957 CGCAATGCGA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.39, C:0.18, G:0.23, T:0.21
Consensus pattern (20 bp):
TATCGCAACGCGAAAATGGT
Found at i:3644016 original size:19 final size:19
Alignment explanation
Indices: 3643975--3644038 Score: 93
Period size: 19 Copynumber: 3.6 Consensus size: 19
3643965 GAAATGAAAA
3643975 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
3643991 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
3644008 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
3644027 TCGCATTGCGAT
1 TCGCATTGCGAT
3644039 ATTCTCGTTG
Statistics
Matches: 43, Mismatches: 0, Indels: 7
0.86 0.00 0.14
Matches are distributed among these distances:
14 11 0.26
16 3 0.07
17 3 0.07
19 26 0.60
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:3644178 original size:14 final size:14
Alignment explanation
Indices: 3644159--3644195 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
3644149 CATCAATTAA
3644159 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
3644173 ACAAATCATCTTTT
1 ACAAATCAACATTT
3644187 ACAAATCAA
1 ACAAATCAA
3644196 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:3646098 original size:20 final size:19
Alignment explanation
Indices: 3646063--3646129 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
3646053 GAAACTTAAA
3646063 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
3646082 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
3646102 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
3646121 ATCGCAACG
1 ATCGCAACG
3646130 ACAAAATCGC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 24 0.59
20 17 0.41
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:3646137 original size:14 final size:14
Alignment explanation
Indices: 3646118--3646206 Score: 81
Period size: 14 Copynumber: 5.9 Consensus size: 14
3646108 ATGCGAAATG
3646118 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
3646132 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
3646148 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
*
3646164 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
3646180 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
3646196 -AAATCGCAACG
1 AAAATCGCAACG
3646207 CGAAACACAA
Statistics
Matches: 63, Mismatches: 4, Indels: 17
0.75 0.05 0.20
Matches are distributed among these distances:
13 11 0.17
14 19 0.30
16 15 0.24
18 18 0.29
ACGTcount: A:0.47, C:0.26, G:0.18, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:3646160 original size:32 final size:32
Alignment explanation
Indices: 3646102--3646211 Score: 195
Period size: 32 Copynumber: 3.4 Consensus size: 32
3646092 GGAAATGGCT
*
3646102 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
3646135 ATCGCAACGCGAAATGAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAATCGCAACGACAAA
3646167 ATCGCAACGCGAAATGAAATCGCAACGAC-AA
1 ATCGCAACGCGAAATGAAATCGCAACGACAAA
3646198 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
3646212 CACAAATCGC
Statistics
Matches: 76, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
31 16 0.21
32 45 0.59
33 15 0.20
ACGTcount: A:0.46, C:0.25, G:0.19, T:0.10
Consensus pattern (32 bp):
ATCGCAACGCGAAATGAAATCGCAACGACAAA
Found at i:3646199 original size:18 final size:18
Alignment explanation
Indices: 3646113--3646199 Score: 77
Period size: 18 Copynumber: 5.2 Consensus size: 18
3646103 TCGCAATGCG
3646113 AAATGAAAATCGCAACGAC
1 AAATG-AAATCGCAACGAC
3646132 --A--AAATCGCAACG-C
1 AAATGAAATCGCAACGAC
3646145 GAAATGAAATCGCAACGAC
1 -AAATGAAATCGCAACGAC
3646164 --A--AAATCGCAACG-C
1 AAATGAAATCGCAACGAC
3646177 GAAATGAAATCGCAACGAC
1 -AAATGAAATCGCAACGAC
3646196 AAAT
1 AAAT
3646200 CGCAACGCGA
Statistics
Matches: 56, Mismatches: 0, Indels: 25
0.69 0.00 0.31
Matches are distributed among these distances:
13 2 0.04
14 22 0.39
16 3 0.05
17 1 0.02
18 26 0.46
19 2 0.04
ACGTcount: A:0.49, C:0.23, G:0.17, T:0.10
Consensus pattern (18 bp):
AAATGAAATCGCAACGAC
Found at i:3646240 original size:19 final size:17
Alignment explanation
Indices: 3646218--3646313 Score: 78
Period size: 19 Copynumber: 5.6 Consensus size: 17
3646208 GAAACACAAA
3646218 TCGCATTGCGATTTTCATT
1 TCGC-TTGCGA-TTTCATT
*
3646237 TCGCGTTGCGATTT--TG
1 TCGC-TTGCGATTTCATT
3646253 TCG-TTGCGATTTCATT
1 TCGCTTGCGATTTCATT
*
3646269 TCGCGTTGCGATTT--TG
1 TCGC-TTGCGATTTCATT
3646285 TCG-TTGCGATTTTCATT
1 TCGCTTGCGA-TTTCATT
3646302 TCGCATTGCGAT
1 TCGC-TTGCGAT
3646314 AGCCATTTCC
Statistics
Matches: 63, Mismatches: 5, Indels: 19
0.72 0.06 0.22
Matches are distributed among these distances:
14 15 0.24
15 3 0.05
16 12 0.19
17 4 0.06
18 13 0.21
19 16 0.25
ACGTcount: A:0.11, C:0.20, G:0.23, T:0.46
Consensus pattern (17 bp):
TCGCTTGCGATTTCATT
Found at i:3646259 original size:14 final size:14
Alignment explanation
Indices: 3646240--3646297 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
3646230 TTTCATTTCG
3646240 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
3646254 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
3646270 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
3646286 CGTTGCGATTTT
1 CGTTGCGATTTT
3646298 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:3646304 original size:33 final size:33
Alignment explanation
Indices: 3646223--3646313 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
3646213 ACAAATCGCA
3646223 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
3646256 TTGCGA-TTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
*
3646288 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCGTTGCGAT
3646314 AGCCATTTCC
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 32 0.57
33 24 0.43
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
Found at i:3646332 original size:20 final size:19
Alignment explanation
Indices: 3646298--3646352 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
3646288 TTGCGATTTT
*
3646298 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
3646317 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
3646337 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
3646353 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:3646851 original size:18 final size:18
Alignment explanation
Indices: 3646825--3646869 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
3646815 GTCGATCAGA
*
3646825 TGATGGCTCTAGGTGAGG
1 TGATGGCTCTAGGCGAGG
*
3646843 TGATAGCTCTAGGCGAGG
1 TGATGGCTCTAGGCGAGG
3646861 TGATGGCTC
1 TGATGGCTC
3646870 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.18, C:0.16, G:0.40, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTAGGCGAGG
Found at i:3648212 original size:20 final size:20
Alignment explanation
Indices: 3648187--3648224 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3648177 AATAGTTTCT
3648187 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
3648207 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
3648225 GAGAGAATCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:3648513 original size:22 final size:22
Alignment explanation
Indices: 3648488--3648531 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
3648478 GATTTAGATA
3648488 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
3648510 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
3648532 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:3648744 original size:20 final size:20
Alignment explanation
Indices: 3648719--3648812 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
3648709 GATTATGTAT
3648719 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
3648739 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
* *** * *
3648759 TATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGA-AAGTCAG
* *
3648780 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
3648800 TATCGCATTGCGA
1 TATCGCGTTGCGA
3648813 TTTTCTCAAT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:3648784 original size:41 final size:42
Alignment explanation
Indices: 3648739--3648874 Score: 118
Period size: 41 Copynumber: 3.3 Consensus size: 42
3648729 CGAAAGTCAG
* * * *
3648739 TATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTAT
1 TATCGCGTTGCGAAAGTAAGTATCGCATTGCGATTTTCTCAA
* * *
3648780 TATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCTCAA
1 TATCGCGTTGCGAAAGTAAGTATCGCATTGCGATTTTCTCAA
** ** * *
3648822 T-TCGCGTTGCG-ATTTACTTATTCGCATTGCGAATTTCCCAA
1 TATCGCGTTGCGAAAGTAAGTA-TCGCATTGCGATTTTCTCAA
3648863 T-TCGCGTTGCGA
1 TATCGCGTTGCGA
3648875 TTTACTTATT
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
40 3 0.04
41 70 0.92
42 3 0.04
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.38
Consensus pattern (42 bp):
TATCGCGTTGCGAAAGTAAGTATCGCATTGCGATTTTCTCAA
Found at i:3648813 original size:20 final size:20
Alignment explanation
Indices: 3648699--3648813 Score: 88
Period size: 20 Copynumber: 5.7 Consensus size: 20
3648689 CGCTTTGAAA
*
3648699 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* *
3648720 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
3648740 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * ** * *
3648760 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
3648781 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
3648801 ATCGCATTGCGAT
1 ATCGCATTGCGAT
3648814 TTTCTCAATT
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
19 2 0.03
20 50 0.66
21 24 0.32
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.36
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:3648846 original size:20 final size:20
Alignment explanation
Indices: 3648802--3648894 Score: 105
Period size: 21 Copynumber: 4.5 Consensus size: 20
3648792 ATAGTCAGTA
*
3648802 TCGCATTGCGATTTTCTCAAT
1 TCGCATTGCGATTTACT-AAT
* *
3648823 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTAAT
* *
3648843 TCGCATTGCGAATTTCCCAAT
1 TCGCATTGCG-ATTTACTAAT
* *
3648864 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTAAT
3648884 TCGCATTGCGA
1 TCGCATTGCGA
3648895 ATTGGGAAAA
Statistics
Matches: 59, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
20 28 0.47
21 31 0.53
ACGTcount: A:0.18, C:0.24, G:0.18, T:0.40
Consensus pattern (20 bp):
TCGCATTGCGATTTACTAAT
Found at i:3648875 original size:41 final size:41
Alignment explanation
Indices: 3648802--3648897 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 41
3648792 ATAGTCAGTA
* *
3648802 TCGCATTGCGATTTTCTCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
3648843 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
3648884 TCGCATTGCGAATT
1 TCGCATTGCGAATT
3648898 GGGAAAATCG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.19, C:0.23, G:0.18, T:0.41
Consensus pattern (41 bp):
TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:3649292 original size:13 final size:15
Alignment explanation
Indices: 3649264--3649296 Score: 52
Period size: 13 Copynumber: 2.3 Consensus size: 15
3649254 TAATTTATGC
3649264 TTAAAACAATTAAAT
1 TTAAAACAATTAAAT
3649279 TTAAAA-AA-TAAAT
1 TTAAAACAATTAAAT
3649292 TTAAA
1 TTAAA
3649297 TTTACTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 10 0.56
14 2 0.11
15 6 0.33
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (15 bp):
TTAAAACAATTAAAT
Found at i:3661010 original size:20 final size:20
Alignment explanation
Indices: 3660985--3661067 Score: 121
Period size: 20 Copynumber: 4.2 Consensus size: 20
3660975 CCAAATTCGG
* * *
3660985 AACGCGAATATGTAAATCGC
1 AACGCGAATTTGGAAATCAC
*
3661005 AACGCGAATTTGGAAATCAT
1 AACGCGAATTTGGAAATCAC
*
3661025 AACGCGAATTTGGAAATCCC
1 AACGCGAATTTGGAAATCAC
3661045 AACGCGAATTTGGAAATCAC
1 AACGCGAATTTGGAAATCAC
3661065 AAC
1 AAC
3661068 ACAGAAGTCA
Statistics
Matches: 56, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 56 1.00
ACGTcount: A:0.40, C:0.20, G:0.19, T:0.20
Consensus pattern (20 bp):
AACGCGAATTTGGAAATCAC
Found at i:3661638 original size:20 final size:20
Alignment explanation
Indices: 3661613--3661718 Score: 194
Period size: 20 Copynumber: 5.3 Consensus size: 20
3661603 AAACTTAAAT
*
3661613 TCGCAACACGAACATGAAAA
1 TCGCAACGCGAACATGAAAA
3661633 TCGCAACGCGAACATGAAAA
1 TCGCAACGCGAACATGAAAA
3661653 TCGCAACGCGAACATGAAAA
1 TCGCAACGCGAACATGAAAA
*
3661673 TCGCAACGTGAACATGAAAA
1 TCGCAACGCGAACATGAAAA
3661693 TCGCAACGCGAACATGAAAA
1 TCGCAACGCGAACATGAAAA
3661713 TCGCAA
1 TCGCAA
3661719 TGCGTTGCGA
Statistics
Matches: 83, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 83 1.00
ACGTcount: A:0.45, C:0.25, G:0.19, T:0.11
Consensus pattern (20 bp):
TCGCAACGCGAACATGAAAA
Found at i:3674899 original size:3 final size:3
Alignment explanation
Indices: 3674887--3674922 Score: 54
Period size: 3 Copynumber: 11.7 Consensus size: 3
3674877 AAACGAATAA
*
3674887 TAT TAG TAT TAT TAAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TA
3674923 CTTGTATTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:3680222 original size:24 final size:24
Alignment explanation
Indices: 3680161--3680229 Score: 66
Period size: 24 Copynumber: 2.9 Consensus size: 24
3680151 AAGTACAAAA
* * *
3680161 CAGAGTCCATGTTAAGTATCATAT
1 CAGAATCCATGTCAAATATCATAT
* * * *
3680185 AAAAATTCAGGTCAAATATCATAT
1 CAGAATCCATGTCAAATATCATAT
*
3680209 CAGAATCCATGTCAAAAATCA
1 CAGAATCCATGTCAAATATCA
3680230 GATAAACTAT
Statistics
Matches: 33, Mismatches: 12, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.43, C:0.17, G:0.12, T:0.28
Consensus pattern (24 bp):
CAGAATCCATGTCAAATATCATAT
Found at i:3680969 original size:29 final size:28
Alignment explanation
Indices: 3680927--3681000 Score: 87
Period size: 29 Copynumber: 2.5 Consensus size: 28
3680917 GTCAAACATT
3680927 TTACACAAATAGCACCCTTTTTA-AAATAA
1 TTAC-CAAATAGCACCC-TTTTAGAAATAA
*
3680956 TTACCAATATAGCACCCTTTTAGAATTAA
1 TTACCAA-ATAGCACCCTTTTAGAAATAA
*
3680985 TTCCCAAAATAGCACC
1 TTACC-AAATAGCACC
3681001 AAAACCAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
28 8 0.20
29 30 0.75
30 2 0.05
ACGTcount: A:0.41, C:0.24, G:0.05, T:0.30
Consensus pattern (28 bp):
TTACCAAATAGCACCCTTTTAGAAATAA
Found at i:3681049 original size:13 final size:13
Alignment explanation
Indices: 3681031--3681060 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
3681021 GAATAGCACC
3681031 GGTCAACGGGTCG
1 GGTCAACGGGTCG
3681044 GGTCAACGGGTCG
1 GGTCAACGGGTCG
3681057 GGTC
1 GGTC
3681061 GTGACCGGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.13, C:0.23, G:0.47, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:3687134 original size:24 final size:24
Alignment explanation
Indices: 3687096--3687165 Score: 86
Period size: 24 Copynumber: 2.9 Consensus size: 24
3687086 CAAAACAGAG
* *
3687096 TCCATGTCAAGTATCATATAAAAA
1 TCCAGGTCAAATATCATATAAAAA
* * *
3687120 TTCAGGTCAAATATCATATCAGAA
1 TCCAGGTCAAATATCATATAAAAA
*
3687144 TCCAGGTCAAATATCAGATAAA
1 TCCAGGTCAAATATCATATAAA
3687166 CTATTTATAT
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.44, C:0.17, G:0.11, T:0.27
Consensus pattern (24 bp):
TCCAGGTCAAATATCATATAAAAA
Found at i:3687899 original size:29 final size:28
Alignment explanation
Indices: 3687857--3687930 Score: 87
Period size: 29 Copynumber: 2.5 Consensus size: 28
3687847 GTCAAACATT
3687857 TTACACAAATAGCACCCTTTTTA-AAATAA
1 TTAC-CAAATAGCACCC-TTTTAGAAATAA
*
3687886 TTACCAATATAGCACCCTTTTAGAATTAA
1 TTACCAA-ATAGCACCCTTTTAGAAATAA
*
3687915 TTCCCAAAATAGCACC
1 TTACC-AAATAGCACC
3687931 AAAACCAAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
28 8 0.20
29 30 0.75
30 2 0.05
ACGTcount: A:0.41, C:0.24, G:0.05, T:0.30
Consensus pattern (28 bp):
TTACCAAATAGCACCCTTTTAGAAATAA
Found at i:3689062 original size:29 final size:29
Alignment explanation
Indices: 3688995--3689062 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
3688985 CATTTTACAC
*
3688995 AAATAGCACCCTTTTTAAAATAATTACCA
1 AAATAGCACCCTTTTCAAAATAATTACCA
* * * *
3689024 ATATAGCACCCTTTTCGAATTAATTCCCA
1 AAATAGCACCCTTTTCAAAATAATTACCA
*
3689053 AAATAACACC
1 AAATAGCACC
3689063 AAAACCAAAT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.41, C:0.25, G:0.04, T:0.29
Consensus pattern (29 bp):
AAATAGCACCCTTTTCAAAATAATTACCA
Found at i:3689110 original size:13 final size:13
Alignment explanation
Indices: 3689092--3689121 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
3689082 GAATAGCACC
3689092 GGTCAACGGGTCG
1 GGTCAACGGGTCG
3689105 GGTCAACGGGTCG
1 GGTCAACGGGTCG
3689118 GGTC
1 GGTC
3689122 GTGACTGGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.13, C:0.23, G:0.47, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:3689148 original size:11 final size:11
Alignment explanation
Indices: 3689132--3689170 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
3689122 GTGACTGGTC
3689132 AAACCGGTTCA
1 AAACCGGTTCA
3689143 AAACCGGTT--
1 AAACCGGTTCA
3689152 AAACCGG-TCA
1 AAACCGGTTCA
3689162 AAACCGGTT
1 AAACCGGTT
3689171 TCCAGCGTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
8 1 0.04
9 7 0.28
10 7 0.28
11 10 0.40
ACGTcount: A:0.36, C:0.26, G:0.21, T:0.18
Consensus pattern (11 bp):
AAACCGGTTCA
Found at i:3689164 original size:19 final size:20
Alignment explanation
Indices: 3689132--3689170 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
3689122 GTGACTGGTC
3689132 AAACCGGTTCAAAACCGGTT
1 AAACCGGTTCAAAACCGGTT
3689152 AAACCGG-TCAAAACCGGTT
1 AAACCGGTTCAAAACCGGTT
3689171 TCCAGCGTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.36, C:0.26, G:0.21, T:0.18
Consensus pattern (20 bp):
AAACCGGTTCAAAACCGGTT
Found at i:3690233 original size:7 final size:7
Alignment explanation
Indices: 3690211--3690254 Score: 61
Period size: 7 Copynumber: 6.3 Consensus size: 7
3690201 TCTTGTAATG
3690211 AACCCTA
1 AACCCTA
* *
3690218 AATCTTA
1 AACCCTA
*
3690225 AACCATA
1 AACCCTA
3690232 AACCCTA
1 AACCCTA
3690239 AACCCTA
1 AACCCTA
3690246 AACCCTA
1 AACCCTA
3690253 AA
1 AA
3690255 TTGTACTTAC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.48, C:0.34, G:0.00, T:0.18
Consensus pattern (7 bp):
AACCCTA
Found at i:3690502 original size:7 final size:7
Alignment explanation
Indices: 3690475--3690512 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
3690465 TCTTTGCAAC
3690475 AAACCCT
1 AAACCCT
*
3690482 AAACCAT
1 AAACCCT
*
3690489 AAGCCCT
1 AAACCCT
3690496 AAACCCT
1 AAACCCT
3690503 AAACCCT
1 AAACCCT
3690510 AAA
1 AAA
3690513 TCCGATTATG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.47, C:0.37, G:0.03, T:0.13
Consensus pattern (7 bp):
AAACCCT
Found at i:3690513 original size:174 final size:167
Alignment explanation
Indices: 3690223--3690543 Score: 509
Period size: 167 Copynumber: 1.9 Consensus size: 167
3690213 CCCTAAATCT
* * *
3690223 TAAACCATAAACCCTAAACCCTAAACCCTAAATTGTACTTACCTCATAAATCGATACAAAGTCGG
1 TAAACCATAAACCATAAACCCTAAACCCTAAATTATACTTACCTCATAAATCGATACAAAGTCGA
*
3690288 TTAATTAATGTCTTTGCAATAAACCCTAAACTATAAACCCTAAAACCTAAATCCGATTATGTGAT
66 TTAATTAATGTCTTTGCAACAAACCCTAAACTATAAACCCTAAAACCTAAATCCGATTATGTGAT
3690353 AGAGGTTAAGTTATGCAAAATGATGTTATGTGACTCC
131 AGAGGTTAAGTTATGCAAAATGATGTTATGTGACTCC
*
3690390 TAAATCATAAACCATAAACCCTAAACCCTAAATTATACTTACCTCATAAATCGATACCAAA-TCG
1 TAAACCATAAACCATAAACCCTAAACCCTAAATTATACTTACCTCATAAATCGATA-CAAAGTCG
*
3690454 ATTAATTAATGTCTTTGCAACAAACCCTAAACCATAAGCCCTAAACCCTAAACCCTAAATCCGAT
65 ATTAATTAATGTCTTTGCAACAAACCCTAAA-C-T-A----TAAACCCTAAAACCTAAATCCGAT
3690519 TATGTGATAGAGGTTAAGTTATGCA
123 TATGTGATAGAGGTTAAGTTATGCA
3690544 CAGGAAGGTA
Statistics
Matches: 140, Mismatches: 6, Indels: 9
0.90 0.04 0.06
Matches are distributed among these distances:
167 85 0.61
168 5 0.04
169 1 0.01
170 1 0.01
174 48 0.34
ACGTcount: A:0.40, C:0.22, G:0.10, T:0.28
Consensus pattern (167 bp):
TAAACCATAAACCATAAACCCTAAACCCTAAATTATACTTACCTCATAAATCGATACAAAGTCGA
TTAATTAATGTCTTTGCAACAAACCCTAAACTATAAACCCTAAAACCTAAATCCGATTATGTGAT
AGAGGTTAAGTTATGCAAAATGATGTTATGTGACTCC
Found at i:3692602 original size:11 final size:11
Alignment explanation
Indices: 3692586--3692612 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
3692576 GCTCAAAGTT
3692586 GAGCTTCAATC
1 GAGCTTCAATC
3692597 GAGCTTCAATC
1 GAGCTTCAATC
3692608 GAGCT
1 GAGCT
3692613 CGAGTTTCGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.26
Consensus pattern (11 bp):
GAGCTTCAATC
Found at i:3698527 original size:12 final size:12
Alignment explanation
Indices: 3698510--3698535 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3698500 ATGAAAGCAC
3698510 AAGCAATTGAGG
1 AAGCAATTGAGG
3698522 AAGCAATTGAGG
1 AAGCAATTGAGG
3698534 AA
1 AA
3698536 ACAACACAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.08, G:0.31, T:0.15
Consensus pattern (12 bp):
AAGCAATTGAGG
Found at i:3703826 original size:32 final size:31
Alignment explanation
Indices: 3703790--3703866 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 31
3703780 CGGGGCCGTG
*
3703790 GGGCCTACCTAAGAACACATCTTAGGGCCACA
1 GGGCCTACCTAAGAA-ACATCTCAGGGCCACA
** ** *
3703822 GGGCCTACCCGAGAATGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAAACATCTCAGGGCCACA
*
3703853 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
3703867 GTCACATTAG
Statistics
Matches: 36, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
31 23 0.64
32 13 0.36
ACGTcount: A:0.29, C:0.31, G:0.26, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAGGGCCACA
Found at i:3703849 original size:63 final size:63
Alignment explanation
Indices: 3703743--3703866 Score: 151
Period size: 63 Copynumber: 2.0 Consensus size: 63
3703733 CCCTAAGGGA
** * * ** *
3703743 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCGTGGGGCCTACCTAAGAAC
1 ACATCTTAGGGCCACAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
* *
3703806 ACATCTTAGGGCCACAGGGCCTACCCGAGA-ATGATCTCAGGGCCGCAGAGCCTACCTAAGA
1 ACATCTTAGGGCCACAGAGCCTACCCAAGATA-GATCTCAGGGCCGCAGAGCCTACCTAAGA
3703867 GTCACATTAG
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
62 1 0.02
63 50 0.98
ACGTcount: A:0.27, C:0.29, G:0.27, T:0.17
Consensus pattern (63 bp):
ACATCTTAGGGCCACAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:3704752 original size:7 final size:7
Alignment explanation
Indices: 3704736--3704772 Score: 65
Period size: 7 Copynumber: 5.3 Consensus size: 7
3704726 GTCAAAGGAA
3704736 GTCAACG
1 GTCAACG
*
3704743 GTCAATG
1 GTCAACG
3704750 GTCAACG
1 GTCAACG
3704757 GTCAACG
1 GTCAACG
3704764 GTCAACG
1 GTCAACG
3704771 GT
1 GT
3704773 TGGGTCGGGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.27, C:0.24, G:0.30, T:0.19
Consensus pattern (7 bp):
GTCAACG
Found at i:3704785 original size:17 final size:17
Alignment explanation
Indices: 3704763--3704820 Score: 62
Period size: 17 Copynumber: 3.3 Consensus size: 17
3704753 AACGGTCAAC
* *
3704763 GGTCAACGGTTGGGTCG
1 GGTCAACAGTCGGGTCG
3704780 GGTCAACAGTCGGGTCG
1 GGTCAACAGTCGGGTCG
**
3704797 GGTCCGGTCAGTCGGGTCG
1 GGT-C-AACAGTCGGGTCG
3704816 GGTCA
1 GGTCA
3704821 TTCCGGTTCA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
17 18 0.53
18 2 0.06
19 14 0.41
ACGTcount: A:0.12, C:0.22, G:0.45, T:0.21
Consensus pattern (17 bp):
GGTCAACAGTCGGGTCG
Found at i:3704838 original size:19 final size:19
Alignment explanation
Indices: 3704823--3704906 Score: 96
Period size: 20 Copynumber: 4.3 Consensus size: 19
3704813 TCGGGTCATT
3704823 CCGGTTCAGACCGGTCAAA
1 CCGGTTCAGACCGGTCAAA
3704842 CCGGTTCAGACCGGTCAAA
1 CCGGTTCAGACCGGTCAAA
* * *
3704861 CCGGTTTAAAACTGGTCAAA
1 CCGG-TTCAGACCGGTCAAA
* * *
3704881 CCGGTTTAAAACTGGTCAAA
1 CCGG-TTCAGACCGGTCAAA
3704901 CCGGTT
1 CCGGTT
3704907 TTCCAGCAGC
Statistics
Matches: 61, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
19 25 0.41
20 36 0.59
ACGTcount: A:0.29, C:0.26, G:0.24, T:0.21
Consensus pattern (19 bp):
CCGGTTCAGACCGGTCAAA
Found at i:3704854 original size:10 final size:10
Alignment explanation
Indices: 3704823--3704906 Score: 68
Period size: 9 Copynumber: 8.6 Consensus size: 10
3704813 TCGGGTCATT
*
3704823 CCGGTTCAGA
1 CCGGTTCAAA
3704833 CCGG-TCAAA
1 CCGGTTCAAA
*
3704842 CCGGTTCAGA
1 CCGGTTCAAA
3704852 CCGG-TCAAA
1 CCGGTTCAAA
*
3704861 CCGGTTTAAAA
1 CCGG-TTCAAA
*
3704872 CTGG-TCAAA
1 CCGGTTCAAA
*
3704881 CCGGTTTAAAA
1 CCGG-TTCAAA
*
3704892 CTGG-TCAAA
1 CCGGTTCAAA
3704901 CCGGTT
1 CCGGTT
3704907 TTCCAGCAGC
Statistics
Matches: 57, Mismatches: 11, Indels: 12
0.71 0.14 0.15
Matches are distributed among these distances:
9 30 0.53
10 13 0.23
11 14 0.25
ACGTcount: A:0.29, C:0.26, G:0.24, T:0.21
Consensus pattern (10 bp):
CCGGTTCAAA
Found at i:3704879 original size:20 final size:20
Alignment explanation
Indices: 3704835--3704907 Score: 112
Period size: 20 Copynumber: 3.7 Consensus size: 20
3704825 GGTTCAGACC
* * *
3704835 GGTCAAACCGG-TTCAGACC
1 GGTCAAACCGGTTTAAAACT
3704854 GGTCAAACCGGTTTAAAACT
1 GGTCAAACCGGTTTAAAACT
3704874 GGTCAAACCGGTTTAAAACT
1 GGTCAAACCGGTTTAAAACT
3704894 GGTCAAACCGGTTT
1 GGTCAAACCGGTTT
3704908 TCCAGCAGCT
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
19 11 0.22
20 39 0.78
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.23
Consensus pattern (20 bp):
GGTCAAACCGGTTTAAAACT
Found at i:3711191 original size:32 final size:31
Alignment explanation
Indices: 3711155--3711231 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
3711145 CGGGGCCGTG
*
3711155 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAA-ACATCTCAGGGCCGCA
** **
3711187 GGGCCTACCCGAGAATGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAAACATCTCAGGGCCGCA
*
3711218 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
3711232 GTCACATTAG
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
31 24 0.65
32 13 0.35
ACGTcount: A:0.27, C:0.31, G:0.27, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAGGGCCGCA
Found at i:3711214 original size:63 final size:63
Alignment explanation
Indices: 3711108--3711231 Score: 153
Period size: 63 Copynumber: 2.0 Consensus size: 63
3711098 CCCTAAGGGA
* * ** *
3711108 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCGTGGGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
* *
3711171 ACATCTTAGGGCC-GCAGGGCCTACCCGAGA-ATGATCTCAGGGCCGCAGAGCCTACCTAAGA
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAGATA-GATCTCAGGGCCGCAGAGCCTACCTAAGA
3711232 GTCACATTAG
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
62 2 0.04
63 50 0.96
ACGTcount: A:0.26, C:0.29, G:0.28, T:0.17
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Done.