Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009463.1 Hibiscus syriacus cultivar Beakdansim tig00113726_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: 3931635
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 20
Found at i:216223 original size:50 final size:51
Alignment explanation
Indices: 216136--216254 Score: 156
Period size: 50 Copynumber: 2.3 Consensus size: 51
216126 CAATACTTCT
*
216136 ATACTATGGTAAT-GATACCCCTTTCAGTATCGATACCA-TTT-ATATTCTGTG
1 ATAC-ATGGT-ATCGATACCCCTTTCAGTATCGATACCATTTTGACATTCTG-G
*
216187 TTAGCATGGTATCGATACCCC-TTCAGTATCGATACCATTTTGACATTCTGG
1 ATA-CATGGTATCGATACCCCTTTCAGTATCGATACCATTTTGACATTCTGG
216238 ATACATGGTATCGATAC
1 ATACATGGTATCGATAC
216255 TTCCCTTTGT
Statistics
Matches: 61, Mismatches: 3, Indels: 9
0.84 0.04 0.12
Matches are distributed among these distances:
50 32 0.52
51 21 0.34
52 8 0.13
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.36
Consensus pattern (51 bp):
ATACATGGTATCGATACCCCTTTCAGTATCGATACCATTTTGACATTCTGG
Found at i:220286 original size:2 final size:2
Alignment explanation
Indices: 220279--220323 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
220269 GAACTAGGGC
220279 AT AT AT AT AT AT AT AT AT -T 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
220320 AT AT
1 AT AT
220324 TGAGTAGTAA
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:221045 original size:17 final size:17
Alignment explanation
Indices: 221019--221051 Score: 50
Period size: 16 Copynumber: 1.9 Consensus size: 17
221009 ATATTATTTA
221019 TTTAATTATTTTTAAAAC
1 TTTAATTA-TTTTAAAAC
221037 TTTAA-TATTTTAAAA
1 TTTAATTATTTTAAAA
221052 TTAGTAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 8 0.53
17 2 0.13
18 5 0.33
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (17 bp):
TTTAATTATTTTAAAAC
Found at i:221827 original size:21 final size:21
Alignment explanation
Indices: 221776--221828 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
221766 ATTATGACTA
221776 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
221797 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
221818 TCGCAATGCGA
1 TCGCAATGCGA
221829 ATAAGTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:221843 original size:20 final size:21
Alignment explanation
Indices: 221818--221869 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
221808 TTTTCCCAAT
*
221818 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
221838 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
221859 TCGCAATGCGA
1 TCGCAATGCGA
221870 TACTGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:221848 original size:41 final size:42
Alignment explanation
Indices: 221803--221910 Score: 96
Period size: 41 Copynumber: 2.6 Consensus size: 42
221793 AATTTCGCGT
* *
221803 TGCGATTTTCCCAATTCGCAATGCGAATA-AGTA-AATCGCAA
1 TGCGATTTTCCAAATTCGCAATGCGAATACTG-ACAATCGCAA
* ** * *
221844 TGCGAATTTGGAAAATCGCAATGCG-ATACTGACTATCGCAA
1 TGCGATTTTCCAAATTCGCAATGCGAATACTGACAATCGCAA
* * *
221885 TGCAATTTTCCTAATTCGCATTGCGA
1 TGCGATTTTCCAAATTCGCAATGCGA
221911 TTTACATAGC
Statistics
Matches: 50, Mismatches: 14, Indels: 5
0.72 0.20 0.07
Matches are distributed among these distances:
40 4 0.08
41 46 0.92
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (42 bp):
TGCGATTTTCCAAATTCGCAATGCGAATACTGACAATCGCAA
Found at i:222449 original size:19 final size:19
Alignment explanation
Indices: 222411--222477 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
222401 TTCGAGAATG
*
222411 AAAATCGCAACACGGAAATA
1 AAAATCGCAACGC-GAAATA
**
222431 ACTATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
**
222450 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATA
222469 AAAATCGCA
1 AAAATCGCA
222478 TTGCGATTTC
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:0.25, G:0.15, T:0.10
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:222523 original size:33 final size:33
Alignment explanation
Indices: 222478--222641 Score: 181
Period size: 33 Copynumber: 4.9 Consensus size: 33
222468 CAAAATCGCA
222478 TTGCGA-TTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
222510 TTGGGATTTTCATTTCGCGTTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCGTTGCGA--TTC-TCTCG
222546 CATTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 --TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
** *
222581 TTGCGATAGTCATTTTGCGTTGCGA-T-TCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* ** *
222612 TTGAGATAGTCATTCCGCGTTGCGATTCTC
1 TTGCGATTTTCATTTCGCGTTGCGATTCTC
222642 ATTATCTCGT
Statistics
Matches: 114, Mismatches: 10, Indels: 15
0.82 0.07 0.11
Matches are distributed among these distances:
31 27 0.24
32 7 0.06
33 42 0.37
35 7 0.06
36 7 0.06
38 24 0.21
ACGTcount: A:0.12, C:0.22, G:0.23, T:0.43
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:222536 original size:19 final size:19
Alignment explanation
Indices: 222473--222666 Score: 127
Period size: 19 Copynumber: 11.1 Consensus size: 19
222463 GAAACCAAAA
*
222473 TCGCATTGCGA-TTTCATT
1 TCGCGTTGCGATTTTCATT
222491 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
222505 TCTCGTTGGGATTTTCATT
1 TCGCGTTGCGATTTTCATT
222524 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
222543 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
222562 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
222576 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
222595 TTGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
222609 T--CGTTGAGATAGTCATT
1 TCGCGTTGCGATTTTCATT
* *
222626 CCGCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATT
*
222645 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
222665 TC
1 TC
222667 AACCAAAAGA
Statistics
Matches: 137, Mismatches: 21, Indels: 35
0.71 0.11 0.18
Matches are distributed among these distances:
12 7 0.05
14 22 0.16
16 5 0.04
17 8 0.06
18 10 0.07
19 69 0.50
20 16 0.12
ACGTcount: A:0.13, C:0.22, G:0.21, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:222594 original size:71 final size:70
Alignment explanation
Indices: 222473--222607 Score: 225
Period size: 71 Copynumber: 1.9 Consensus size: 70
222463 GAAACCAAAA
* **
222473 TCGCATTGCGATTTCATTTCGCGTTGCGATTCTCTCGTTGGGATTTTCATTTCGCGTTGCGATTT
1 TCGCATTGCGATTTCATTTCGCGTTGCGATTCTCTCGTTGCGATAGTCATTTCGCGTTGCGATTT
222538 TCATT
66 TCATT
*
222543 TCGCATTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATAGTCATTTTGCGTTGCGATT
1 TCGCATTGCGA-TTTCATTTCGCGTTGCGATTCTCTCGTTGCGATAGTCATTTCGCGTTGCGATT
222608 CTCGTTGAGA
Statistics
Matches: 60, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
70 11 0.18
71 49 0.82
ACGTcount: A:0.12, C:0.21, G:0.22, T:0.44
Consensus pattern (70 bp):
TCGCATTGCGATTTCATTTCGCGTTGCGATTCTCTCGTTGCGATAGTCATTTCGCGTTGCGATTT
TCATT
Found at i:222614 original size:31 final size:31
Alignment explanation
Indices: 222548--222641 Score: 125
Period size: 31 Copynumber: 3.0 Consensus size: 31
222538 TCATTTCGCA
**
222548 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATAGTCATTTCGCGTTGCGA-T-TCTCG
*
222581 TTGCGATAGTCATTTTGCGTTGCGATTCTCG
1 TTGCGATAGTCATTTCGCGTTGCGATTCTCG
* *
222612 TTGAGATAGTCATTCCGCGTTGCGATTCTC
1 TTGCGATAGTCATTTCGCGTTGCGATTCTC
222642 ATTATCTCGT
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
31 32 0.58
32 1 0.02
33 22 0.40
ACGTcount: A:0.13, C:0.22, G:0.23, T:0.41
Consensus pattern (31 bp):
TTGCGATAGTCATTTCGCGTTGCGATTCTCG
Found at i:224787 original size:20 final size:20
Alignment explanation
Indices: 224764--224828 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 20
224754 TCATTCCTCG
224764 AGAGTCCCTCCCACCGTTCA
1 AGAGTCCCTCCCACCGTTCA
* * * * *
224784 AGAGGCCATGCCATCGTTGA
1 AGAGTCCCTCCCACCGTTCA
*
224804 AGAGATCCCTCCCACCATTCA
1 AGAG-TCCCTCCCACCGTTCA
224825 AGAG
1 AGAG
224829 CCCGATTCAC
Statistics
Matches: 33, Mismatches: 11, Indels: 1
0.73 0.24 0.02
Matches are distributed among these distances:
20 19 0.58
21 14 0.42
ACGTcount: A:0.26, C:0.35, G:0.20, T:0.18
Consensus pattern (20 bp):
AGAGTCCCTCCCACCGTTCA
Found at i:224789 original size:41 final size:42
Alignment explanation
Indices: 224712--224790 Score: 106
Period size: 41 Copynumber: 1.9 Consensus size: 42
224702 GACTCGCCTG
* * *
224712 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
* *
224754 TCATTCCTCGAGAGTCC-CTCCCACCGTTCAAGAGGCC
1 TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
224791 ATGCCATCGT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
41 17 0.53
42 15 0.47
ACGTcount: A:0.22, C:0.38, G:0.18, T:0.23
Consensus pattern (42 bp):
TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
Found at i:226173 original size:14 final size:14
Alignment explanation
Indices: 226154--226189 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
226144 GATTGTTTAA
226154 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
226168 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
226182 TGATTTGT
1 TGATTTGT
226190 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:226318 original size:19 final size:19
Alignment explanation
Indices: 226294--226340 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
226284 AAAAAGTACT
*
226294 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
226313 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
226332 ATCGCAACG
1 ATCGCAACG
226341 AGAGAATCGC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.45, C:0.21, G:0.21, T:0.13
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:226387 original size:19 final size:19
Alignment explanation
Indices: 226365--226514 Score: 80
Period size: 19 Copynumber: 8.7 Consensus size: 19
226355 CGAAATTAAA
226365 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
226384 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
226399 -CCTCGTTGCGA-TTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
226416 TTCGCATTGCGA-----AA
1 TTCGCGTTGCGATTTTCAT
226430 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
226449 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
226464 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
226482 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
226501 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
226515 AGACATTAAG
Statistics
Matches: 97, Mismatches: 19, Indels: 29
0.67 0.13 0.20
Matches are distributed among these distances:
14 29 0.30
15 3 0.03
16 3 0.03
17 6 0.06
18 8 0.08
19 38 0.39
20 10 0.10
ACGTcount: A:0.15, C:0.23, G:0.21, T:0.41
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:226411 original size:33 final size:32
Alignment explanation
Indices: 226369--226494 Score: 193
Period size: 33 Copynumber: 3.9 Consensus size: 32
226359 ATTAAATTCG
226369 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
*
226402 CGTTGCGA-TTTCATTTCGCATTGCGAAATT-CG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
226434 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
226467 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
226495 AGTAATTTCC
Statistics
Matches: 86, Mismatches: 2, Indels: 10
0.88 0.02 0.10
Matches are distributed among these distances:
31 3 0.03
32 26 0.30
33 54 0.63
34 3 0.03
ACGTcount: A:0.14, C:0.24, G:0.20, T:0.42
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:226456 original size:65 final size:66
Alignment explanation
Indices: 226362--226493 Score: 248
Period size: 65 Copynumber: 2.0 Consensus size: 66
226352 ACGCGAAATT
226362 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGA-TTTCATTTCGCATTGC
1 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
226426 G
66 G
*
226427 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
226492 G
66 G
226493 A
1 A
226494 TAGTAATTTC
Statistics
Matches: 65, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
65 47 0.72
66 18 0.28
ACGTcount: A:0.16, C:0.23, G:0.20, T:0.41
Consensus pattern (66 bp):
AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:228805 original size:12 final size:12
Alignment explanation
Indices: 228788--228812 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
228778 TCTTCGGGGA
228788 CTTTTTCTTCTT
1 CTTTTTCTTCTT
228800 CTTTTTCTTCTT
1 CTTTTTCTTCTT
228812 C
1 C
228813 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:229019 original size:24 final size:24
Alignment explanation
Indices: 228985--229038 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
228975 CTGAAACATC
*
228985 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
229009 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
229033 ATCAAA
1 ATCAAA
229039 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:229863 original size:20 final size:20
Alignment explanation
Indices: 229830--229908 Score: 61
Period size: 20 Copynumber: 3.9 Consensus size: 20
229820 AAATAAGTAA
* *
229830 ATCGCAATGCGATACTGACT
1 ATCGCAACGAGATACTGACT
* *
229850 ATCGCAACGAGATAAT-ACAAA
1 ATCGCAACGAGATACTGAC--T
*
229871 ATCGCAACGAGATTCTGACT
1 ATCGCAACGAGATACTGACT
* * *
229891 TTCGCAATGAGATTCTGA
1 ATCGCAACGAGATACTGA
229909 AAATCGCAAT
Statistics
Matches: 47, Mismatches: 9, Indels: 6
0.76 0.15 0.10
Matches are distributed among these distances:
19 2 0.04
20 29 0.62
21 14 0.30
22 2 0.04
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24
Consensus pattern (20 bp):
ATCGCAACGAGATACTGACT
Found at i:229915 original size:20 final size:20
Alignment explanation
Indices: 229868--229918 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
229858 GAGATAATAC
*
229868 AAAATCGCAACGAGATTCTG
1 AAAATCGCAATGAGATTCTG
***
229888 ACTTTCGCAATGAGATTCTG
1 AAAATCGCAATGAGATTCTG
229908 AAAATCGCAAT
1 AAAATCGCAAT
229919 CATCTTCAAA
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.25
Consensus pattern (20 bp):
AAAATCGCAATGAGATTCTG
Found at i:230152 original size:20 final size:20
Alignment explanation
Indices: 230127--230218 Score: 87
Period size: 20 Copynumber: 4.6 Consensus size: 20
230117 ATCGCAACGG
230127 GGAAATCGCAACGCGAAAAT
1 GGAAATCGCAACGCGAAAAT
*
230147 GGAAATCGCAACACGAAAAT
1 GGAAATCGCAACGCGAAAAT
** **
230167 GGCTATCGCAATTCG-AAAT
1 GGAAATCGCAACGCGAAAAT
* *
230186 GAAAAATTGCAACGCGAAAAT
1 G-GAAATCGCAACGCGAAAAT
**
230207 GGCTATCGCAAC
1 GGAAATCGCAAC
230219 TAGAAAATCG
Statistics
Matches: 55, Mismatches: 15, Indels: 4
0.74 0.20 0.05
Matches are distributed among these distances:
19 5 0.09
20 45 0.82
21 5 0.09
ACGTcount: A:0.42, C:0.21, G:0.22, T:0.15
Consensus pattern (20 bp):
GGAAATCGCAACGCGAAAAT
Found at i:230292 original size:19 final size:19
Alignment explanation
Indices: 230268--230312 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
230258 TTCTCGTTGT
*
230268 GATTTTCATTTTGCATTGC
1 GATTTTCATTTCGCATTGC
230287 GATTTTCATTTCGCATTGC
1 GATTTTCATTTCGCATTGC
230306 GATTTTC
1 GATTTTC
230313 TCGTTGCGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.16, C:0.18, G:0.16, T:0.51
Consensus pattern (19 bp):
GATTTTCATTTCGCATTGC
Found at i:232380 original size:20 final size:20
Alignment explanation
Indices: 232357--232406 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
232347 CTTAAAATCG
232357 CAACGCGAAAATGACTATCA
1 CAACGCGAAAATGACTATCA
* * * *
232377 CAACACGGAAATGGCTATCG
1 CAACGCGAAAATGACTATCA
*
232397 CAATGCGAAA
1 CAACGCGAAA
232407 TGCAAATCGC
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.42, C:0.24, G:0.20, T:0.14
Consensus pattern (20 bp):
CAACGCGAAAATGACTATCA
Found at i:232415 original size:19 final size:17
Alignment explanation
Indices: 232393--232456 Score: 53
Period size: 19 Copynumber: 3.7 Consensus size: 17
232383 GGAAATGGCT
232393 ATCGCAATGCGAAATGCAA
1 ATCGCAATGCGAAA--CAA
*
232412 ATCGCAA--CGACA-AA
1 ATCGCAATGCGAAACAA
232426 ATCGCAATGCGAAACACAA
1 ATCGCAATGCG-AA-ACAA
*
232445 ATCGCATTGCGA
1 ATCGCAATGCGA
232457 CTTTCATTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 11
0.73 0.06 0.22
Matches are distributed among these distances:
14 9 0.24
16 2 0.05
17 5 0.14
18 2 0.05
19 19 0.51
ACGTcount: A:0.42, C:0.25, G:0.19, T:0.14
Consensus pattern (17 bp):
ATCGCAATGCGAAACAA
Found at i:232487 original size:14 final size:14
Alignment explanation
Indices: 232470--232526 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
232460 TCATTTTGCA
232470 TTGCGATTTTGTCG
1 TTGCGATTTTGTCG
*
232484 TTGCGATTTTCATTTCG
1 TTGCGA-TTT--TGTCG
232501 CATTGCGATTTTGTCG
1 --TTGCGATTTTGTCG
*
232517 TTGCAATTTT
1 TTGCGATTTT
232527 CATTTCGCAT
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 15 0.43
15 3 0.09
16 4 0.11
17 4 0.11
18 3 0.09
19 6 0.17
ACGTcount: A:0.12, C:0.16, G:0.21, T:0.51
Consensus pattern (14 bp):
TTGCGATTTTGTCG
Found at i:232495 original size:33 final size:33
Alignment explanation
Indices: 232451--232542 Score: 157
Period size: 33 Copynumber: 2.8 Consensus size: 33
232441 ACAAATCGCA
* *
232451 TTGCGACTTTCATTTTGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
232484 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
*
232517 TTGCAATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
232543 AGCCATTTCC
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.14, C:0.18, G:0.20, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:232506 original size:19 final size:19
Alignment explanation
Indices: 232446--232542 Score: 79
Period size: 19 Copynumber: 5.6 Consensus size: 19
232436 GAAACACAAA
*
232446 TCGCATTGCGACTTTCATT
1 TCGCATTGCGATTTTCATT
* *
232465 TTGCATTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
232481 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
232498 TCGCATTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
*
232514 TCG--TTGCAATTTTCATT
1 TCGCATTGCGATTTTCATT
232531 TCGCATTGCGAT
1 TCGCATTGCGAT
232543 AGCCATTTCC
Statistics
Matches: 60, Mismatches: 8, Indels: 20
0.68 0.09 0.23
Matches are distributed among these distances:
14 11 0.18
15 6 0.10
16 7 0.12
17 8 0.13
18 6 0.10
19 22 0.37
ACGTcount: A:0.14, C:0.20, G:0.20, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:232549 original size:19 final size:19
Alignment explanation
Indices: 232527--232564 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
232517 TTGCAATTTT
232527 CATTTCGCA-TTGCGATAGC
1 CATTTC-CACTTGCGATAGC
232546 CATTTCCACGTTGCGATAG
1 CATTTCCAC-TTGCGATAG
232565 TCGTTTTCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 2 0.12
19 6 0.35
20 9 0.53
ACGTcount: A:0.21, C:0.26, G:0.21, T:0.32
Consensus pattern (19 bp):
CATTTCCACTTGCGATAGC
Found at i:233083 original size:18 final size:18
Alignment explanation
Indices: 233057--233101 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
233047 GTCGATCAGA
*
233057 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
233075 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
233093 TGATGGCTC
1 TGATGGCTC
233102 CCGAAGTAGA
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:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:234445 original size:20 final size:20
Alignment explanation
Indices: 234420--234461 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
234410 ATAGTTTCTA
234420 AAAATGAAAATCGCAACACG
1 AAAATGAAAATCGCAACACG
** *
234440 AAAATGACTATCGCAACGCG
1 AAAATGAAAATCGCAACACG
234460 AA
1 AA
234462 TTTGACTATC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.50, C:0.21, G:0.17, T:0.12
Consensus pattern (20 bp):
AAAATGAAAATCGCAACACG
Found at i:234467 original size:20 final size:20
Alignment explanation
Indices: 234429--234477 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
234419 AAAAATGAAA
*
234429 ATCGCAACACGAAAATGACT
1 ATCGCAACGCGAAAATGACT
**
234449 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
234469 ATCGCAACG
1 ATCGCAACG
234478 AGAGAATCGC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.37, C:0.27, G:0.18, T:0.18
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:235057 original size:20 final size:19
Alignment explanation
Indices: 234951--235085 Score: 108
Period size: 20 Copynumber: 6.7 Consensus size: 19
234941 CGCTTTGAAA
*
234951 ATCGCATTGCGATTATGTATT
1 ATCGCATTGCGA-TA-GTAGT
* * *
234972 ATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATAGT-AGT
* *
234992 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGT-AGT
* * * *
235012 ATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGA--TAGTAGT
235033 ATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGATAGT-AGT
235053 ATCGCATTGCGATAGTTAGT
1 ATCGCATTGCGATAG-TAGT
235073 ATCGCATTGCGAT
1 ATCGCATTGCGAT
235086 TTTCCCAATT
Statistics
Matches: 96, Mismatches: 13, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
19 5 0.05
20 65 0.68
21 24 0.25
22 2 0.02
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.34
Consensus pattern (19 bp):
ATCGCATTGCGATAGTAGT
Found at i:235057 original size:61 final size:61
Alignment explanation
Indices: 234951--235088 Score: 186
Period size: 61 Copynumber: 2.3 Consensus size: 61
234941 CGCTTTGAAA
* * * *
234951 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
* * * * * *
235012 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTTAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
235073 ATCGCATTGCGATTTT
1 ATCGCATTGCGATTTT
235089 CCCAATTCGC
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 65 1.00
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.36
Consensus pattern (61 bp):
ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
Found at i:235104 original size:61 final size:61
Alignment explanation
Indices: 234951--235106 Score: 152
Period size: 61 Copynumber: 2.6 Consensus size: 61
234941 CGCTTTGAAA
* ** * * * *
234951 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGT
* * ** * * * * *
235012 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTTAGT
1 ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGT
235073 ATCGCATTGCGATTTTCCCAAT-TCGCGTTGCGAT
1 ATCGCATTGCGATTTT-CCAATATCGCGTTGCGAT
235107 TTACTTATTC
Statistics
Matches: 78, Mismatches: 16, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
61 76 0.97
62 2 0.03
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.35
Consensus pattern (61 bp):
ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGT
Found at i:235440 original size:2 final size:2
Alignment explanation
Indices: 235435--235481 Score: 78
Period size: 2 Copynumber: 24.0 Consensus size: 2
235425 ATAAATTATG
235435 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T 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
*
235476 TT AT AT
1 AT AT AT
235482 GTACTTATAT
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:235960 original size:38 final size:37
Alignment explanation
Indices: 235831--235963 Score: 108
Period size: 38 Copynumber: 3.5 Consensus size: 37
235821 CATTTGACCC
* * *
235831 GAGACAGTTTCTCTCGAAATAAAATTTTTATCTCACTT
1 GAGAAAGTTTC-CTTGAAACAAAATTTTTATCTCACTT
* * * * * * *
235869 GAGAAAAATTCCCTCGAAAC-AAA-TTTCATCTTAATC
1 GAG-AAAGTTTCCTTGAAACAAAATTTTTATCTCACTT
* *
235905 GAGACAGTTTCTTTTGAAACAAAATTTTTATCTCACTT
1 GAGAAAGTTTC-CTTGAAACAAAATTTTTATCTCACTT
235943 GAGAAAGTTTTCCTTGAAACA
1 GAGAAAG-TTTCCTTGAAACA
235964 TATTTCATCT
Statistics
Matches: 71, Mismatches: 19, Indels: 10
0.71 0.19 0.10
Matches are distributed among these distances:
35 5 0.07
36 18 0.25
37 6 0.08
38 33 0.46
39 9 0.13
ACGTcount: A:0.35, C:0.18, G:0.11, T:0.35
Consensus pattern (37 bp):
GAGAAAGTTTCCTTGAAACAAAATTTTTATCTCACTT
Found at i:235981 original size:74 final size:73
Alignment explanation
Indices: 235786--235984 Score: 222
Period size: 74 Copynumber: 2.7 Consensus size: 73
235776 AAAATATGTC
* * * *
235786 ATCTCACTTGAGACAATTTTCCTT-AAA-ATAAGGTTCATTTGACCCGAGACAGTTTCTCTCGAA
1 ATCTCACTTGAGA-AATTTTCCTTGAAACAT-A-TTTCATCTCACTCGAGACAGTTTCTCTCGAA
*
235849 ATAAAATTTTT
63 ACAAAATTTTT
* * * * * * * *
235860 ATCTCACTTGAGAAAAATTCCCTCGAAACAAATTTCATCTTAATCGAGACAGTTTCTTTTGAAAC
1 ATCTCACTTGAG-AAATTTTCCTTGAAACATATTTCATCTCACTCGAGACAGTTTCTCTCGAAAC
235925 AAAATTTTT
65 AAAATTTTT
235934 ATCTCACTTGAGAAAGTTTTCCTTGAAACATATTTCATCTCACTCGAGACA
1 ATCTCACTTGAGAAA-TTTTCCTTGAAACATATTTCATCTCACTCGAGACA
235985 ATATTTTTAC
Statistics
Matches: 103, Mismatches: 18, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
73 3 0.03
74 94 0.91
75 5 0.05
76 1 0.01
ACGTcount: A:0.34, C:0.20, G:0.11, T:0.35
Consensus pattern (73 bp):
ATCTCACTTGAGAAATTTTCCTTGAAACATATTTCATCTCACTCGAGACAGTTTCTCTCGAAACA
AAATTTTT
Found at i:237732 original size:24 final size:24
Alignment explanation
Indices: 237697--237743 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
237687 ACTATATACA
*
237697 TATTTTTACATATTTTATTTACCTC
1 TATTTTTACATAATTTA-TTACCTC
237722 TATTTTT-CATAATTTATTACCT
1 TATTTTTACATAATTTATTACCT
237744 TCCTTTTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 6 0.29
24 8 0.38
25 7 0.33
ACGTcount: A:0.26, C:0.15, G:0.00, T:0.60
Consensus pattern (24 bp):
TATTTTTACATAATTTATTACCTC
Found at i:237736 original size:25 final size:23
Alignment explanation
Indices: 237697--237743 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 23
237687 ACTATATACA
237697 TATTTTTACATATTTTATTTACCTC
1 TATTTTTACATA-TTTA-TTACCTC
237722 TATTTTT-CATAATTTATTACCT
1 TATTTTTACAT-ATTTATTACCT
237744 TCCTTTTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 6 0.29
24 7 0.33
25 8 0.38
ACGTcount: A:0.26, C:0.15, G:0.00, T:0.60
Consensus pattern (23 bp):
TATTTTTACATATTTATTACCTC
Found at i:237760 original size:8 final size:8
Alignment explanation
Indices: 237747--237782 Score: 63
Period size: 8 Copynumber: 4.4 Consensus size: 8
237737 ATTACCTTCC
237747 TTTTATAT
1 TTTTATAT
237755 TTTTATAT
1 TTTTATAT
237763 TTTTATAT
1 TTTTATAT
237771 TTTTATTAT
1 TTTTA-TAT
237780 TTT
1 TTT
237783 CTTCATTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 21 0.78
9 6 0.22
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (8 bp):
TTTTATAT
Found at i:237780 original size:9 final size:9
Alignment explanation
Indices: 237747--237831 Score: 61
Period size: 9 Copynumber: 9.2 Consensus size: 9
237737 ATTACCTTCC
237747 TTTTA-TAT
1 TTTTATTAT
237755 TTTTA-TAT
1 TTTTATTAT
237763 TTTTA-TAT
1 TTTTATTAT
237771 TTTTATTAT
1 TTTTATTAT
*
237780 TTTCT-TCAT
1 TTT-TATTAT
237789 TTATATATTTACT
1 TT-T-TA-TTA-T
237802 ATTTTATTAT
1 -TTTTATTAT
*
237812 TTTTATTAA
1 TTTTATTAT
*
237821 TTTTAGTAT
1 TTTTATTAT
237830 TT
1 TT
237832 ATATCCTTTT
Statistics
Matches: 64, Mismatches: 6, Indels: 13
0.77 0.07 0.16
Matches are distributed among these distances:
8 21 0.33
9 28 0.44
10 4 0.06
11 3 0.05
12 4 0.06
13 2 0.03
14 2 0.03
ACGTcount: A:0.25, C:0.04, G:0.01, T:0.71
Consensus pattern (9 bp):
TTTTATTAT
Found at i:237832 original size:41 final size:40
Alignment explanation
Indices: 237748--237835 Score: 108
Period size: 41 Copynumber: 2.2 Consensus size: 40
237738 TTACCTTCCT
* **
237748 TTTATATTTTTATATTTTTATATTTTTATTATTTTCTTCA
1 TTTATATATTTATATTTTTATATTTTTATTATTTTAGTCA
237788 TTTATATATTTACTA-TTTTATTATTTTTATTAATTTTAGT-A
1 TTTATATATTTA-TATTTTTA-TATTTTTATT-ATTTTAGTCA
237829 TTTATAT
1 TTTATAT
237836 CCTTTTGCAT
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
40 16 0.38
41 20 0.48
42 6 0.14
ACGTcount: A:0.26, C:0.03, G:0.01, T:0.69
Consensus pattern (40 bp):
TTTATATATTTATATTTTTATATTTTTATTATTTTAGTCA
Found at i:237864 original size:23 final size:22
Alignment explanation
Indices: 237822--237881 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 22
237812 TTTTATTAAT
* *
237822 TTTAGTATTTATATCCTTTTGCA
1 TTTACTATTTATAT-ATTTTGCA
* *
237845 TTTACTTTTTCATATATTTTGGA
1 TTTACTATTT-ATATATTTTGCA
237868 TTTACTATTTATAT
1 TTTACTATTTATAT
237882 TGTAATATAT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
22 4 0.13
23 23 0.74
24 4 0.13
ACGTcount: A:0.23, C:0.10, G:0.07, T:0.60
Consensus pattern (22 bp):
TTTACTATTTATATATTTTGCA
Found at i:242254 original size:30 final size:29
Alignment explanation
Indices: 242218--242280 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 29
242208 CATAAATATT
242218 AAATAAATC-AAAGAAAAAACATAAAAATAA
1 AAATAAATCAAAAGAAAAAA-A-AAAAATAA
* *
242248 AAATAAATCAAAAGGAGAAAAAAAAATAA
1 AAATAAATCAAAAGAAAAAAAAAAAATAA
242277 AAAT
1 AAAT
242281 TAAAAAATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
29 12 0.40
30 10 0.33
31 8 0.27
ACGTcount: A:0.76, C:0.05, G:0.06, T:0.13
Consensus pattern (29 bp):
AAATAAATCAAAAGAAAAAAAAAAAATAA
Found at i:242341 original size:21 final size:21
Alignment explanation
Indices: 242295--242341 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
242285 AAATTAAAGT
*
242295 AAAATCAAATAAAATAATATA
1 AAAATCAAATAAAATAATAGA
* *
242316 TAAATCAAAT-AAATCAATGGA
1 AAAATCAAATAAAAT-AATAGA
242337 AAAAT
1 AAAAT
242342 GTAAAAATAA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.66, C:0.06, G:0.04, T:0.23
Consensus pattern (21 bp):
AAAATCAAATAAAATAATAGA
Found at i:242393 original size:16 final size:14
Alignment explanation
Indices: 242364--242397 Score: 50
Period size: 16 Copynumber: 2.3 Consensus size: 14
242354 ATAAATAAAT
242364 AAATAAAGGAAAAG
1 AAATAAAGGAAAAG
242378 AAATCAAAGAGAAAAG
1 AAAT-AAAG-GAAAAG
242394 AAAT
1 AAAT
242398 GAAATAAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 4 0.22
15 4 0.22
16 10 0.56
ACGTcount: A:0.71, C:0.03, G:0.18, T:0.09
Consensus pattern (14 bp):
AAATAAAGGAAAAG
Found at i:244047 original size:165 final size:163
Alignment explanation
Indices: 243852--244203 Score: 413
Period size: 164 Copynumber: 2.1 Consensus size: 163
243842 ACTCGACAGT
* * * ** *
243852 TTTGTTGACAGATAGCCCTTCTTGCCTTGAGCTATGATGTAAGCTTGAT-TTTCCTCTG-AGTTA
1 TTTGTTGA-AGATAACCCTTCTAGCCTTGAGCTATGATGTAA--ATGATGTGCCCTC-GAAGCTA
* * * *
243915 AATGTAATC-AAACTAGAAGGTCTTTGGCATATATCCCTTCTCGACTTAAGCTATATTGCAAATG
62 AATGTAATCGAAA-TAGAAGGTCTTTCGCAGATAGCCCTTCTCGACTGAAGCTATATTGCAAATG
* * * *
243979 ATTTGCCTTGGAGCTGAGCGTAGTCGAACTTGCAGGTC
126 ATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTA
* * *
244017 TTTGTTGATAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTAAGT
1 TTTGTTGA-AGATAACCCTTCTAGCCTTGAGCTATGATGTAAATGATGTGCCCTCGAAGCTAAAT
* * * * *
244082 GTAATCGAAATCGAGGGTCTTTCGCAGATAGCCTTTCTGGACTGAAGCTATGTTGCAAATGATGT
65 GTAATCGAAATAGAAGGTCTTTCGCAGATAGCCCTTCTCGACTGAAGCTATATTGCAAATGATGT
244147 GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTA
130 GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTA
244181 TTTGGTTGGAAGATAACCCTTCT
1 TTT-GTT-GAAGATAACCCTTCT
244204 CGACTTAATT
Statistics
Matches: 159, Mismatches: 23, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
163 5 0.03
164 96 0.60
165 56 0.35
166 2 0.01
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (163 bp):
TTTGTTGAAGATAACCCTTCTAGCCTTGAGCTATGATGTAAATGATGTGCCCTCGAAGCTAAATG
TAATCGAAATAGAAGGTCTTTCGCAGATAGCCCTTCTCGACTGAAGCTATATTGCAAATGATGTG
CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTA
Found at i:244229 original size:84 final size:82
Alignment explanation
Indices: 243949--244268 Score: 284
Period size: 84 Copynumber: 3.9 Consensus size: 82
243939 TGGCATATAT
* * * * *
243949 CCCTTCTCGACTTAAGCTATATTGCAAATGATTTGCCTTGGAGCTGAGCGTAGTCGAACTTGCAG
1 CCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTAAGCGTAGTCGAACTCGAAG
*
244014 GTCTTTGTTGATAGATAA
66 GTATTTGTTGA-AGATAA
* * * * * * * * * * * *
244032 CCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTAAGTGTAATCGAAATCGAG
1 CCCTTCTCGACTTAAGCTATACTGCAAATGATGTG-CCTTGGAGCTAAGCGTAGTCGAACTCGAA
* * * *
244097 GGT-CTT-TCGCAGATAG
65 GGTATTTGTTGAAGATAA
* * * ** *
244113 CCTTTCTGGACTGAAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
1 CCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTAAGCGTAGTCGAACTCGAAG
244178 GTATTTGGTTGGAAGATAA
66 GTATTT-GTT-GAAGATAA
** * * * *
244197 CCCTTCTCGACTTAATTTATACTACAAATGATGTGTCTTGGAGCTAAGGGTAGTTGAACTCGAAG
1 CCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTAAGCGTAGTCGAACTCGAAG
244262 GTATTTG
66 GTATTTG
244269 GTGGGCACGA
Statistics
Matches: 180, Mismatches: 52, Indels: 10
0.74 0.21 0.04
Matches are distributed among these distances:
80 25 0.14
81 34 0.19
82 2 0.01
83 31 0.17
84 88 0.49
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (82 bp):
CCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTAAGCGTAGTCGAACTCGAAG
GTATTTGTTGAAGATAA
Found at i:244597 original size:110 final size:110
Alignment explanation
Indices: 244377--244811 Score: 639
Period size: 110 Copynumber: 4.0 Consensus size: 110
244367 ATCCAAATAT
* * * *
244377 TTGTGCTGTTTCGAGGCCAATATCCTTCGCCGTGAAGTTGAAATTGACTC----TGAAACTCG-A
1 TTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACT-GAA
* ** *
244437 AAGTTATTTGTTGACAGCCAACCGCCCCTTCGCTGTGAAGTTGAGT
65 AAGTTATTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGC
* *
244483 TTGTGTTGTCTCGAGCCCAATATCCTTCACTGTGAAGTTGAAATTGACTCTGAATGAAACT-AAA
1 TTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAA
244547 ATGTTATTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGC
66 A-GTTATTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGC
* * *
244593 TTGTGTTGTCTCGAGTCCAATATCATTTGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAA
1 TTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAA
* *
244658 AGTTATTTGTTGACAGTTAGTCGCCCCTTCGCTGTGAAGTTGAAC
66 AGTTATTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGC
*
244703 TTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAATGAAACTGAAA
1 TTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAA
* **
244768 AGTTGTTTGTTGACAGTCAGTCGCCCCTTCTATGTGAAGTTGAG
66 AGTTATTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAG
244812 TTGAACTGGA
Statistics
Matches: 297, Mismatches: 25, Indels: 10
0.89 0.08 0.03
Matches are distributed among these distances:
106 45 0.15
109 3 0.01
110 245 0.82
111 4 0.01
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.34
Consensus pattern (110 bp):
TTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAA
AGTTATTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGC
Found at i:245328 original size:32 final size:32
Alignment explanation
Indices: 245244--245320 Score: 100
Period size: 32 Copynumber: 2.4 Consensus size: 32
245234 CATCATAATT
* * * *
245244 TTGAATCCCCGAAGATGCCCCAATATTCGATG
1 TTGAATCTCCAAAAATGCCCCAACATTCGATG
*
245276 TTGAATCTCCAAAAATGCCCCAACATTTGATG
1 TTGAATCTCCAAAAATGCCCCAACATTCGATG
*
245308 TTGAATCTTCAAA
1 TTGAATCTCCAAA
245321 GGTGCCCCCA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.32, C:0.25, G:0.14, T:0.29
Consensus pattern (32 bp):
TTGAATCTCCAAAAATGCCCCAACATTCGATG
Found at i:246425 original size:12 final size:12
Alignment explanation
Indices: 246398--246468 Score: 61
Period size: 14 Copynumber: 5.3 Consensus size: 12
246388 TCTTTCTTCA
*
246398 TTTTTTCCTTTGT
1 TTTTTTTCTTT-T
246411 TTTTGTTTCTTTTT
1 TTTT-TTTC-TTTT
246425 TTTATTTTCTCTTT
1 TTT-TTTTCT-TTT
*
246439 GCTTTTTTCTTTGT
1 -TTTTTTTCTTT-T
246453 TTTTTTTCTTTT
1 TTTTTTTCTTTT
246465 TTTT
1 TTTT
246469 CTTTTTGTTC
Statistics
Matches: 49, Mismatches: 3, Indels: 13
0.75 0.05 0.20
Matches are distributed among these distances:
12 5 0.10
13 17 0.35
14 21 0.43
15 6 0.12
ACGTcount: A:0.01, C:0.11, G:0.06, T:0.82
Consensus pattern (12 bp):
TTTTTTTCTTTT
Found at i:246479 original size:9 final size:9
Alignment explanation
Indices: 246410--246479 Score: 59
Period size: 9 Copynumber: 7.1 Consensus size: 9
246400 TTTTCCTTTG
246410 TTTTTGTTTC
1 TTTTT-TTTC
*
246420 TTTTTTTTA
1 TTTTTTTTC
246429 TTTTCTCTTTGC
1 TTTT-T-TTT-C
*
246441 TTTTTTCTTTG
1 -TTTTT-TTTC
246452 TTTTTTTTC
1 TTTTTTTTC
246461 TTTTTTTTC
1 TTTTTTTTC
*
246470 TTTTTGTTC
1 TTTTTTTTC
246479 T
1 T
246480 GATTGGATCT
Statistics
Matches: 51, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
9 28 0.55
10 11 0.22
11 3 0.06
12 5 0.10
13 4 0.08
ACGTcount: A:0.01, C:0.11, G:0.06, T:0.81
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:246923 original size:17 final size:17
Alignment explanation
Indices: 246901--246935 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
246891 CATGTTCAAA
246901 TGAACAACTCAATGCCT
1 TGAACAACTCAATGCCT
246918 TGAACAACTCAATGCCT
1 TGAACAACTCAATGCCT
246935 T
1 T
246936 AATGGTATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.34, C:0.29, G:0.11, T:0.26
Consensus pattern (17 bp):
TGAACAACTCAATGCCT
Found at i:251048 original size:21 final size:21
Alignment explanation
Indices: 250994--251056 Score: 72
Period size: 21 Copynumber: 2.9 Consensus size: 21
250984 ATTCCCCTGT
250994 GGGGGGAATCGGTTCCCCTTCAA
1 GGGGGGAATCGGTT-CCC-TCAA
* *
251017 AGGGGGAATCGGTTCCCTCAG
1 GGGGGGAATCGGTTCCCTCAA
* *
251038 GGGGGGGATCGATTCCCTC
1 GGGGGGAATCGGTTCCCTC
251057 TGTACCAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
21 19 0.54
22 3 0.09
23 13 0.37
ACGTcount: A:0.16, C:0.25, G:0.38, T:0.21
Consensus pattern (21 bp):
GGGGGGAATCGGTTCCCTCAA
Found at i:256374 original size:11 final size:11
Alignment explanation
Indices: 256358--256387 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
256348 AAATACTTTG
256358 TAAAATTATTT
1 TAAAATTATTT
256369 TAAAATTATTT
1 TAAAATTATTT
*
256380 TAAGATTA
1 TAAAATTA
256388 AAACTTAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (11 bp):
TAAAATTATTT
Found at i:258465 original size:3 final size:3
Alignment explanation
Indices: 258457--258484 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
258447 AAGAAAAAAC
258457 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
258485 ATCAAAAGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:258509 original size:5 final size:5
Alignment explanation
Indices: 258499--258554 Score: 58
Period size: 5 Copynumber: 10.8 Consensus size: 5
258489 AAAGGAGAAA
** **
258499 AAAAT AAAAT AAAAT AAAAAAT AAAGG AAAAT AAAGG AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT --AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
258551 AAAA
1 AAAA
258555 AATATATCAA
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
5 36 0.88
7 5 0.12
ACGTcount: A:0.79, C:0.00, G:0.07, T:0.14
Consensus pattern (5 bp):
AAAAT
Found at i:258525 original size:32 final size:33
Alignment explanation
Indices: 258459--258549 Score: 96
Period size: 32 Copynumber: 2.7 Consensus size: 33
258449 GAAAAAACAT
*
258459 AATAATAATAATAATAATAATAATAAATCAAAAGGAGA
1 AATAA-AATAA-AATAA-AATAAAAAAT-AAAAGGA-A
258497 AA-AAAATAAAATAAAATAAAAAAT-AAAGGAA
1 AATAAAATAAAATAAAATAAAAAATAAAAGGAA
**
258528 AATAAAGGAAAATAAAATAAAA
1 AATAAAATAAAATAAAATAAAA
258550 TAAAAAATAT
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
31 3 0.06
32 23 0.47
34 9 0.18
35 5 0.10
36 5 0.10
37 2 0.04
38 2 0.04
ACGTcount: A:0.74, C:0.01, G:0.08, T:0.18
Consensus pattern (33 bp):
AATAAAATAAAATAAAATAAAAAATAAAAGGAA
Found at i:263333 original size:2 final size:2
Alignment explanation
Indices: 263326--263353 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
263316 AAATATTTGG
263326 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
263354 CCAAAAGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:270946 original size:17 final size:16
Alignment explanation
Indices: 270924--270957 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
270914 ATGGAGATAA
*
270924 AGAATGAGTAGGAAATG
1 AGAATGAG-AGAAAATG
270941 AGAATGAGAGAAAATG
1 AGAATGAGAGAAAATG
270957 A
1 A
270958 AGAGAAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.53, C:0.00, G:0.32, T:0.15
Consensus pattern (16 bp):
AGAATGAGAGAAAATG
Found at i:274819 original size:18 final size:18
Alignment explanation
Indices: 274796--274836 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
274786 CAACGGTCAA
*
274796 TGGTCAACGGGTTGGGTC
1 TGGTCAACGGGTCGGGTC
274814 TGGTCAACGGGTCGGGTC
1 TGGTCAACGGGTCGGGTC
*
274832 AGGTC
1 TGGTC
274837 GGGTCAACGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.12, C:0.20, G:0.44, T:0.24
Consensus pattern (18 bp):
TGGTCAACGGGTCGGGTC
Found at i:284563 original size:2 final size:2
Alignment explanation
Indices: 284556--284609 Score: 101
Period size: 2 Copynumber: 27.5 Consensus size: 2
284546 ACTTTATTTT
284556 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
284597 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
284610 TAAAAAATAA
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 50 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:285208 original size:42 final size:42
Alignment explanation
Indices: 285149--285235 Score: 174
Period size: 42 Copynumber: 2.1 Consensus size: 42
285139 ATATGTTTTC
285149 ATCAATAATATAATTTAAATAATAATGAGTCAAAGTTAAAAA
1 ATCAATAATATAATTTAAATAATAATGAGTCAAAGTTAAAAA
285191 ATCAATAATATAATTTAAATAATAATGAGTCAAAGTTAAAAA
1 ATCAATAATATAATTTAAATAATAATGAGTCAAAGTTAAAAA
285233 ATC
1 ATC
285236 TGGAAAAAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.56, C:0.06, G:0.07, T:0.31
Consensus pattern (42 bp):
ATCAATAATATAATTTAAATAATAATGAGTCAAAGTTAAAAA
Found at i:285229 original size:21 final size:21
Alignment explanation
Indices: 285163--285230 Score: 77
Period size: 21 Copynumber: 3.2 Consensus size: 21
285153 ATAATATAAT
285163 TTAAATAATAATGAGTCAAAG
1 TTAAATAATAATGAGTCAAAG
* * *
285184 TTAAAAAATCAAT-AAT-ATAAT
1 TTAAATAAT-AATGAGTCA-AAG
285205 TTAAATAATAATGAGTCAAAG
1 TTAAATAATAATGAGTCAAAG
285226 TTAAA
1 TTAAA
285231 AAATCTGGAA
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
20 4 0.11
21 29 0.78
22 4 0.11
ACGTcount: A:0.56, C:0.04, G:0.09, T:0.31
Consensus pattern (21 bp):
TTAAATAATAATGAGTCAAAG
Found at i:286797 original size:16 final size:17
Alignment explanation
Indices: 286757--286794 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
286747 TCAATGTCTC
*
286757 AAAAATATAAGATGCAT
1 AAAAATATAAGATCCAT
*
286774 AAAAATATAATATCCAT
1 AAAAATATAAGATCCAT
286791 AAAA
1 AAAA
286795 TATCCAACAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.63, C:0.08, G:0.05, T:0.24
Consensus pattern (17 bp):
AAAAATATAAGATCCAT
Found at i:288507 original size:14 final size:15
Alignment explanation
Indices: 288488--288517 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
288478 TATAAGGAAA
288488 AAAATAAT-GTATAT
1 AAAATAATAGTATAT
288502 AAAATAATAGTATAT
1 AAAATAATAGTATAT
288517 A
1 A
288518 TATATACACA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (15 bp):
AAAATAATAGTATAT
Found at i:288671 original size:2 final size:2
Alignment explanation
Indices: 288666--288714 Score: 80
Period size: 2 Copynumber: 24.5 Consensus size: 2
288656 ACGTGCGCGC
*
288666 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
288708 AT GT AT A
1 AT AT AT A
288715 AACATGGATC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (2 bp):
AT
Found at i:288902 original size:7 final size:7
Alignment explanation
Indices: 288890--288927 Score: 76
Period size: 7 Copynumber: 5.4 Consensus size: 7
288880 GCCTAAATTT
288890 GAAAAAG
1 GAAAAAG
288897 GAAAAAG
1 GAAAAAG
288904 GAAAAAG
1 GAAAAAG
288911 GAAAAAG
1 GAAAAAG
288918 GAAAAAG
1 GAAAAAG
288925 GAA
1 GAA
288928 GGGTTTCTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (7 bp):
GAAAAAG
Found at i:291429 original size:39 final size:39
Alignment explanation
Indices: 291374--291491 Score: 182
Period size: 39 Copynumber: 3.0 Consensus size: 39
291364 GATACCATTT
*
291374 CAACCCAATACCTAGTCTTGTCAAAACTCCTTGGGAAGA
1 CAACCCAATATCTAGTCTTGTCAAAACTCCTTGGGAAGA
* * *
291413 CAACCCAATATATAGTCTTGTCAAAATTCCTTGGGAATA
1 CAACCCAATATCTAGTCTTGTCAAAACTCCTTGGGAAGA
* *
291452 GAACGCAATATCTAGTCTTGTCAAAACTCCTTGGGAAGA
1 CAACCCAATATCTAGTCTTGTCAAAACTCCTTGGGAAGA
291491 C
1 C
291492 CACTTGATGT
Statistics
Matches: 69, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 69 1.00
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.26
Consensus pattern (39 bp):
CAACCCAATATCTAGTCTTGTCAAAACTCCTTGGGAAGA
Found at i:294719 original size:130 final size:129
Alignment explanation
Indices: 294499--294743 Score: 334
Period size: 129 Copynumber: 1.9 Consensus size: 129
294489 TTAACTGCCA
* *
294499 ATTTGGAGGCTTTCAGCTTCGAATCTGGAAAAACGGACTGCGGAATCAAACTCAGGACGTCAAAA
1 ATTTAGAGGCTTTCAGCTTCGAATCTGGAAAAAC-AACTGCGGAATCAAACTCAGGACGTCAAAA
*
294564 AATAATATAAAATGTCTTTTCAAAAAATTTGACTTTTTGGTCAA-AGTCAACGGGTTTGACTAAT
65 AATAATATAAAATGACTTTTCAAAAAA-TTGACTTTTTGGTCAACAGTCAACGGGTTTGACTAAT
294628 G
129 G
* * * * **
294629 ATTTAGAGGCTTTCAGGTTCGAATTTGGAAAATA-AACTTCGGATTCAAACTCAGGACGTTGAAA
1 ATTTAGAGGCTTTCAGCTTCGAATCTGGAAAA-ACAACTGCGGAATCAAACTCAGGACGTCAAAA
* *
294693 AA-CATATAATATGACTTTTCGAAAAAATTGACTTTTTGGTCAACAGTCAAC
65 AATAATATAAAATGACTTTTC-AAAAAATTGACTTTTTGGTCAACAGTCAAC
294744 AGGTCGGGTC
Statistics
Matches: 101, Mismatches: 11, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
128 31 0.31
129 40 0.40
130 29 0.29
131 1 0.01
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.30
Consensus pattern (129 bp):
ATTTAGAGGCTTTCAGCTTCGAATCTGGAAAAACAACTGCGGAATCAAACTCAGGACGTCAAAAA
ATAATATAAAATGACTTTTCAAAAAATTGACTTTTTGGTCAACAGTCAACGGGTTTGACTAATG
Found at i:301853 original size:18 final size:18
Alignment explanation
Indices: 301830--301877 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
301820 CAAAGTCAAC
301830 GGTCAACGGGTCA-GTTCG
1 GGTCAACGGGTCAGGTT-G
* *
301848 GGTCAACAGATCAGGTTG
1 GGTCAACGGGTCAGGTTG
*
301866 TGTCAACGGGTC
1 GGTCAACGGGTC
301878 GAATCAGGTC
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
18 21 0.88
19 3 0.12
ACGTcount: A:0.21, C:0.21, G:0.35, T:0.23
Consensus pattern (18 bp):
GGTCAACGGGTCAGGTTG
Found at i:303001 original size:20 final size:19
Alignment explanation
Indices: 302959--303007 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
302949 ATTCTAACAA
*
302959 TTTCCTCAAAAGTTCTATT
1 TTTCCTCAAAAGTTCAATT
302978 TTTCCTCTAAAA-TTCAATT
1 TTTCCTC-AAAAGTTCAATT
302997 CTTTCTCTCAA
1 -TTTC-CTCAA
303008 CTTCATTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 13 0.50
20 10 0.38
21 3 0.12
ACGTcount: A:0.27, C:0.24, G:0.02, T:0.47
Consensus pattern (19 bp):
TTTCCTCAAAAGTTCAATT
Found at i:306579 original size:24 final size:24
Alignment explanation
Indices: 306547--306592 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
306537 CATATAAATT
*
306547 TGCACCGAAGTGCCACGTAGAATA
1 TGCACCGAAGTGCCACATAGAATA
306571 TGCACCGAAGTGCCACATAGAA
1 TGCACCGAAGTGCCACATAGAA
306593 ATGTCAAGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.35, C:0.26, G:0.24, T:0.15
Consensus pattern (24 bp):
TGCACCGAAGTGCCACATAGAATA
Found at i:306630 original size:23 final size:23
Alignment explanation
Indices: 306604--306685 Score: 74
Period size: 23 Copynumber: 3.6 Consensus size: 23
306594 TGTCAAGAAT
* *
306604 GACCACATAGATATGTCCCAAAG
1 GACCACGTAGAAATGTCCCAAAG
* * *
306627 GACCGCGTAGAAATGTTCCGAAG
1 GACCACGTAGAAATGTCCCAAAG
* *** *
306650 GACCACGTAGAATTGTCGTGAAT
1 GACCACGTAGAAATGTCCCAAAG
306673 GACCACGTAGAAA
1 GACCACGTAGAAA
306686 CCTCGACTCT
Statistics
Matches: 47, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 47 1.00
ACGTcount: A:0.35, C:0.22, G:0.24, T:0.18
Consensus pattern (23 bp):
GACCACGTAGAAATGTCCCAAAG
Found at i:313521 original size:24 final size:23
Alignment explanation
Indices: 313489--313536 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 23
313479 TATAAATTTA
**
313489 CACCAAAGTGCTGCGTAGAATATG
1 CACCAAAGTGCCACGTAGAA-ATG
313513 CACCAAAGTGCCACGTAGAAATG
1 CACCAAAGTGCCACGTAGAAATG
313536 C
1 C
313537 CCTAGAGGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 4 0.18
24 18 0.82
ACGTcount: A:0.35, C:0.25, G:0.23, T:0.17
Consensus pattern (23 bp):
CACCAAAGTGCCACGTAGAAATG
Found at i:313549 original size:23 final size:22
Alignment explanation
Indices: 313504--313625 Score: 86
Period size: 23 Copynumber: 5.3 Consensus size: 22
313494 AAGTGCTGCG
*
313504 TAGAATATGCACCAAAGTG-CCACG
1 TAGAA-ATGC-CCAAAG-GACCACA
*
313528 TAGAAATGCCCTAGAGGACCACA
1 TAGAAATGCCC-AAAGGACCACA
*
313551 TAGATATAT-CCCAAAGGACCGCA
1 TAGA-A-ATGCCCAAAGGACCACA
**
313574 TAGAAATGTCCCAAAGGACCATG
1 TAGAAATG-CCCAAAGGACCACA
* * *
313597 TAGAATTGCCCCGAATGACCACA
1 TAGAAATG-CCCAAAGGACCACA
313620 TAGAAA
1 TAGAAA
313626 CCTTGACTCT
Statistics
Matches: 78, Mismatches: 14, Indels: 13
0.74 0.13 0.12
Matches are distributed among these distances:
21 2 0.03
22 4 0.05
23 61 0.78
24 9 0.12
25 2 0.03
ACGTcount: A:0.39, C:0.25, G:0.20, T:0.16
Consensus pattern (22 bp):
TAGAAATGCCCAAAGGACCACA
Found at i:313735 original size:16 final size:17
Alignment explanation
Indices: 313714--313754 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
313704 CATAGCTTAT
313714 ATCACATAGA-CATATA
1 ATCACATAGATCATATA
*
313730 ATCACATAGATCATGTA
1 ATCACATAGATCATATA
313747 A-CACATAG
1 ATCACATAG
313755 GATGAAATGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 17 0.74
17 6 0.26
ACGTcount: A:0.46, C:0.20, G:0.10, T:0.24
Consensus pattern (17 bp):
ATCACATAGATCATATA
Found at i:315812 original size:23 final size:23
Alignment explanation
Indices: 315785--315849 Score: 60
Period size: 23 Copynumber: 2.8 Consensus size: 23
315775 CCACAGCTAA
315785 TATAAATGCACCAAAGTGCCACG
1 TATAAATGCACCAAAGTGCCACG
* * * * *
315808 TATAATTACACCGTAA-TACCGCG
1 TATAAATGCACC-AAAGTGCCACG
*
315831 TAGAAATGCACCAAAGTGC
1 TATAAATGCACCAAAGTGC
315850 TATATAAGGT
Statistics
Matches: 30, Mismatches: 10, Indels: 4
0.68 0.23 0.09
Matches are distributed among these distances:
22 2 0.07
23 26 0.87
24 2 0.07
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.20
Consensus pattern (23 bp):
TATAAATGCACCAAAGTGCCACG
Found at i:316886 original size:2 final size:2
Alignment explanation
Indices: 316879--316906 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
316869 TTATGTTCAC
316879 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
316907 CAATGATTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:322853 original size:24 final size:22
Alignment explanation
Indices: 322804--322858 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 22
322794 ATAAAGGTAA
322804 GCATCGATGCATTCTACAGTGT
1 GCATCGATGCATTCTACAGTGT
322826 --ATCGATGCATTCCTTA-ACGTGT
1 GCATCGATGCATT-C-TACA-GTGT
322848 GCATCGATGCA
1 GCATCGATGCA
322859 CTACCTGCGC
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
20 11 0.39
21 2 0.07
22 6 0.21
24 9 0.32
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.31
Consensus pattern (22 bp):
GCATCGATGCATTCTACAGTGT
Found at i:322972 original size:21 final size:21
Alignment explanation
Indices: 322946--322993 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
322936 TATTTGGGAG
322946 TGCATCGATACACATTGAAGA
1 TGCATCGATACACATTGAAGA
322967 TGCATCGATACACATTGAAGA
1 TGCATCGATACACATTGAAGA
322988 TGCATC
1 TGCATC
322994 AATGCATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.25
Consensus pattern (21 bp):
TGCATCGATACACATTGAAGA
Found at i:328075 original size:17 final size:17
Alignment explanation
Indices: 328050--328085 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
328040 ACGGTTAGGG
328050 TTAGAGATTTGAGATTT
1 TTAGAGATTTGAGATTT
* *
328067 TTAGGGATTTGTGATTT
1 TTAGAGATTTGAGATTT
328084 TT
1 TT
328086 TTGTAATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.22, C:0.00, G:0.25, T:0.53
Consensus pattern (17 bp):
TTAGAGATTTGAGATTT
Found at i:328117 original size:14 final size:13
Alignment explanation
Indices: 328100--328149 Score: 59
Period size: 13 Copynumber: 3.8 Consensus size: 13
328090 AATTTTAGAA
328100 AAATAGTTTTTTAT
1 AAATA-TTTTTTAT
328114 AAATATTTTTT-T
1 AAATATTTTTTAT
*
328126 AAA-ATTTCTTTAA
1 AAATATTT-TTTAT
328139 AAATATTTTTT
1 AAATATTTTTT
328150 TAATTACCAG
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
11 4 0.12
12 7 0.22
13 12 0.38
14 9 0.28
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (13 bp):
AAATATTTTTTAT
Found at i:328151 original size:14 final size:14
Alignment explanation
Indices: 328098--328152 Score: 62
Period size: 14 Copynumber: 4.1 Consensus size: 14
328088 GTAATTTTAG
*
328098 AAAAATAGTTTTTT
1 AAAAATATTTTTTT
*
328112 ATAAATATTTTTTT
1 AAAAATATTTTTTT
*
328126 --AAA-ATTTCTTT
1 AAAAATATTTTTTT
328137 AAAAATATTTTTTT
1 AAAAATATTTTTTT
328151 AA
1 AA
328153 TTACCAGAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
11 7 0.21
12 3 0.09
13 3 0.09
14 21 0.62
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (14 bp):
AAAAATATTTTTTT
Found at i:329506 original size:6 final size:6
Alignment explanation
Indices: 329495--329543 Score: 98
Period size: 6 Copynumber: 8.2 Consensus size: 6
329485 CCACGTGTAC
329495 GGATTT GGATTT GGATTT GGATTT GGATTT GGATTT GGATTT GGATTT
1 GGATTT GGATTT GGATTT GGATTT GGATTT GGATTT GGATTT GGATTT
329543 G
1 G
329544 AGTGTTTTTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 43 1.00
ACGTcount: A:0.16, C:0.00, G:0.35, T:0.49
Consensus pattern (6 bp):
GGATTT
Found at i:330823 original size:23 final size:23
Alignment explanation
Indices: 330796--330843 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
330786 TTTAAGTACA
* *
330796 ATAATATATTAGGTAGCGCTTAT
1 ATAATATAATAGATAGCGCTTAT
*
330819 ATAATGTAATAGATAGCGCTTAT
1 ATAATATAATAGATAGCGCTTAT
330842 AT
1 AT
330844 TGACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.38, C:0.08, G:0.17, T:0.38
Consensus pattern (23 bp):
ATAATATAATAGATAGCGCTTAT
Found at i:332079 original size:112 final size:112
Alignment explanation
Indices: 331604--332174 Score: 831
Period size: 111 Copynumber: 5.1 Consensus size: 112
331594 AATACTTATA
* * * *
331604 ATAAAGTATCGACACTATCAACATATCCGGTAGCTCTTTACCTGTTTTGTCATTTATAGACCGAT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* * *
331669 TTTATTATTTTTTTTACCTGTTTTATTATTATGGATCGATACATTTTT
66 TTTGTCA-TTTTTTTACCTGTTATATTATTATGGATCGATACATTTTT
* * * * *
331717 ATAAAGTATCGATACTATCAACATATCCGGTAGCGCTTTACTTGTTTTGTCATTTATAGACCAGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
*
331782 TTTGTCA-TTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTATTATGGATCGATACATTTTT
* *
331828 ATAAAGTATCGACACTTTCAATATATTCGGTAACGCTTTACCTGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* *
331893 TTTATCATTTTTTTA-CTGTTATATTATTATAGATCGATACATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTATTATGGATCGATACATTTTT
* *
331939 ATAAAGTATCGACATTTTCAATATATCCGGTAGCGCTTTACCTGTTATGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* ** * * * *
332004 TTTGTTATTTTTTTATTTGTTATATTGTTACGGATAGATACGTTTTT
66 TTTGTCATTTTTTTACCTGTTATATTATTATGGATCGATACATTTTT
* * *
332051 ATAAAGTATTGACACTTTCAATATATCCGGTAGCGCTTTATCTGTTTTGTCATTTATAGACCGAT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* * *
332116 TTTGTCATTTTTTTACTTGTTATATTATTATGGATCAATATATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTATTATGGATCGATACATTTTT
332163 ATAAAGTATCGA
1 ATAAAGTATCGA
332175 TATAAATCGA
Statistics
Matches: 411, Mismatches: 45, Indels: 5
0.89 0.10 0.01
Matches are distributed among these distances:
111 204 0.50
112 142 0.35
113 65 0.16
ACGTcount: A:0.26, C:0.14, G:0.13, T:0.47
Consensus pattern (112 bp):
ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
TTTGTCATTTTTTTACCTGTTATATTATTATGGATCGATACATTTTT
Found at i:338995 original size:88 final size:88
Alignment explanation
Indices: 338785--338995 Score: 264
Period size: 88 Copynumber: 2.4 Consensus size: 88
338775 AAATATGGCA
* * *
338785 TTTTGACCTTAAAATGAAACGTTGAGGGTCAGAATACTATAAGAAAAAGAATAAGGTTCAAAGTA
1 TTTTTACCCTAAAATGAAACGTT-AGGGTCAAAATACTATAAGAAAAAGAATAAGGTTCAAAGTA
*
338850 ATTATTTGGCCAAACATTTGGGAC
65 ATTATTTGACCAAACATTTGGGAC
* * * * *
338874 TTTTTCCCCTAAAATGAAATGTTATGG-CTAAAATACTATAGGTAAAAGAATAAAGG-TCAAAGT
1 TTTTTACCCTAAAATGAAACGTTAGGGTC-AAAATACTATAAGAAAAAGAAT-AAGGTTCAAAGT
* * *
338937 AATTATTTGATCAAATATTTGGGAT
64 AATTATTTGACCAAACATTTGGGAC
*
338962 TTTTTACCCTACAATGAAACGTTAGGGTCAAAAT
1 TTTTTACCCTAAAATGAAACGTTAGGGTCAAAAT
338996 GCTAAAAAAA
Statistics
Matches: 103, Mismatches: 16, Indels: 7
0.82 0.13 0.06
Matches are distributed among these distances:
87 1 0.01
88 78 0.76
89 24 0.23
ACGTcount: A:0.40, C:0.11, G:0.18, T:0.31
Consensus pattern (88 bp):
TTTTTACCCTAAAATGAAACGTTAGGGTCAAAATACTATAAGAAAAAGAATAAGGTTCAAAGTAA
TTATTTGACCAAACATTTGGGAC
Found at i:340458 original size:2 final size:2
Alignment explanation
Indices: 340453--340481 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
340443 TATTTAAACG
340453 TA TA TA 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 TA T
340482 CAATCATATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:346974 original size:164 final size:166
Alignment explanation
Indices: 346699--347024 Score: 638
Period size: 164 Copynumber: 2.0 Consensus size: 166
346689 CAACTTTTCC
346699 CACGTCTCTTCAAACCTGTAAGAAAACACACACAAAAACAATAGATTATTTATAACAAAGAAGAA
1 CACGTCTCTTCAAACCTGTAAGAAAACACACACAAAAACAATAGATTATTTATAACAAAGAAGAA
346764 AATAATGAAGAGGGTGTGTGCGTTGTTAAGAACCTGTTCTGTTGGCTATTTTATTCCATTGTCCT
66 AATAATGAAGAGGGTGTGTGCGTTGTTAAGAACCTGTTCTGTTGGCTATTTTATTCCATTGTCCT
346829 TTTCCATGGACCTTGACATAATCAATGAGTAAGTTG
131 TTTCCATGGACCTTGACATAATCAATGAGTAAGTTG
346865 CACGTCTCTTCAAACCTGTAAGAAAACACACACAAAAACAATAGATTATTTATAAC-AA-AAGAA
1 CACGTCTCTTCAAACCTGTAAGAAAACACACACAAAAACAATAGATTATTTATAACAAAGAAGAA
346928 AATAATGAAGAGGGTGTGTGCGTTGTTAAGAACCTGTTCTGTTGGCTATTTTATTCCATTGTCCT
66 AATAATGAAGAGGGTGTGTGCGTTGTTAAGAACCTGTTCTGTTGGCTATTTTATTCCATTGTCCT
346993 TTTCCATGGACCTTGACATAATCAATGAGTAA
131 TTTCCATGGACCTTGACATAATCAATGAGTAA
347025 TTTGTCTTCC
Statistics
Matches: 160, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
164 102 0.64
165 2 0.01
166 56 0.35
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (166 bp):
CACGTCTCTTCAAACCTGTAAGAAAACACACACAAAAACAATAGATTATTTATAACAAAGAAGAA
AATAATGAAGAGGGTGTGTGCGTTGTTAAGAACCTGTTCTGTTGGCTATTTTATTCCATTGTCCT
TTTCCATGGACCTTGACATAATCAATGAGTAAGTTG
Found at i:352700 original size:23 final size:23
Alignment explanation
Indices: 352674--352742 Score: 63
Period size: 23 Copynumber: 3.1 Consensus size: 23
352664 AAAAATGATT
* *
352674 TTAAAAATTATATATTTTAAAAA
1 TTAAAAATTAAATAATTTAAAAA
*
352697 TTAAAATTTAAATAATTT-AAAA
1 TTAAAAATTAAATAATTTAAAAA
**
352719 TT--TTATCTAAATAATTTAAAAA
1 TTAAAAAT-TAAATAATTTAAAAA
352741 TT
1 TT
352743 CATTTTTGAT
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
20 1 0.03
21 10 0.26
22 12 0.32
23 15 0.39
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (23 bp):
TTAAAAATTAAATAATTTAAAAA
Found at i:352716 original size:16 final size:14
Alignment explanation
Indices: 352673--352721 Score: 53
Period size: 16 Copynumber: 3.2 Consensus size: 14
352663 TAAAAATGAT
*
352673 TTTAAAAATTATATAT
1 TTTAAAAATTA-A-AA
352689 TTTAAAAATTAAAA
1 TTTAAAAATTAAAA
352703 TTTAAATAATTTAAAA
1 TTTAAA-AA-TTAAAA
352719 TTT
1 TTT
352722 TATCTAAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
14 7 0.23
15 3 0.10
16 20 0.67
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
TTTAAAAATTAAAA
Found at i:354285 original size:31 final size:32
Alignment explanation
Indices: 354250--354336 Score: 92
Period size: 31 Copynumber: 2.8 Consensus size: 32
354240 GACTATTTGG
* *
354250 ATATTGA-TCAGATCCGAAAAT-AACTGATCGA
1 ATATTGATTC-GACCCGAAAATCAACCGATCGA
*
354281 ATATTGATTCGACCCGAAAATCAACCGATCTA
1 ATATTGATTCGACCCGAAAATCAACCGATCGA
**
354313 AT-TTGACCCGACCCG-AAATCAACC
1 ATATTGATTCGACCCGAAAATCAACC
354337 AATCTGATAT
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
30 9 0.18
31 28 0.57
32 12 0.24
ACGTcount: A:0.38, C:0.25, G:0.14, T:0.23
Consensus pattern (32 bp):
ATATTGATTCGACCCGAAAATCAACCGATCGA
Found at i:357038 original size:25 final size:25
Alignment explanation
Indices: 357009--357085 Score: 108
Period size: 25 Copynumber: 3.2 Consensus size: 25
356999 AACGGTCAAC
357009 GGTCAACGGTCGGGTCGGGTCGTCG
1 GGTCAACGGTCGGGTCGGGTCGTCG
357034 GGTCAACGGTCGGGTC-GG--GTC-
1 GGTCAACGGTCGGGTCGGGTCGTCG
*
357055 GGTCAACGGTCGGGTCGGGTCAGCCG
1 GGTCAACGGTCGGGTCGGGTC-GTCG
357081 GGTCA
1 GGTCA
357086 GACCGGTCAA
Statistics
Matches: 46, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
21 16 0.35
22 5 0.11
24 2 0.04
25 18 0.39
26 5 0.11
ACGTcount: A:0.10, C:0.25, G:0.47, T:0.18
Consensus pattern (25 bp):
GGTCAACGGTCGGGTCGGGTCGTCG
Found at i:357047 original size:12 final size:12
Alignment explanation
Indices: 357030--357070 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
357020 GGGTCGGGTC
357030 GTCGGGTCAACG
1 GTCGGGTCAACG
*
357042 GTCGGGTC--GG
1 GTCGGGTCAACG
357052 GTC-GGTCAACG
1 GTCGGGTCAACG
357063 GTCGGGTC
1 GTCGGGTC
357071 GGGTCAGCCG
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
9 4 0.17
10 4 0.17
11 4 0.17
12 12 0.50
ACGTcount: A:0.10, C:0.24, G:0.46, T:0.20
Consensus pattern (12 bp):
GTCGGGTCAACG
Found at i:357052 original size:17 final size:17
Alignment explanation
Indices: 357030--357076 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 17
357020 GGGTCGGGTC
357030 GTCGGGTCAACGGTCGG
1 GTCGGGTCAACGGTCGG
357047 GTCGGGTCGGTCAACGGTCGG
1 GTC--G--GGTCAACGGTCGG
357068 GTCGGGTCA
1 GTCGGGTCA
357077 GCCGGGTCAG
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
17 8 0.31
19 2 0.08
21 16 0.62
ACGTcount: A:0.11, C:0.23, G:0.47, T:0.19
Consensus pattern (17 bp):
GTCGGGTCAACGGTCGG
Found at i:357107 original size:19 final size:20
Alignment explanation
Indices: 357078--357150 Score: 91
Period size: 19 Copynumber: 3.8 Consensus size: 20
357068 GTCGGGTCAG
*
357078 CCGGGTCAG-ACCGGTCAAA
1 CCGGTTCAGAACCGGTCAAA
*
357097 TCGGTTCAG-ACCGGTCAAA
1 CCGGTTCAGAACCGGTCAAA
357116 CCGGTTC-GAACCGGTCGAAA
1 CCGGTTCAGAACCGGTC-AAA
357136 CCGG-TCAGAACCGGT
1 CCGGTTCAGAACCGGT
357151 TGAAAACCGG
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
18 1 0.02
19 32 0.67
20 15 0.31
ACGTcount: A:0.25, C:0.30, G:0.30, T:0.15
Consensus pattern (20 bp):
CCGGTTCAGAACCGGTCAAA
Found at i:357120 original size:9 final size:9
Alignment explanation
Indices: 357081--357150 Score: 68
Period size: 10 Copynumber: 7.3 Consensus size: 9
357071 GGGTCAGCCG
*
357081 GGTCAGACC
1 GGTCAAACC
*
357090 GGTCAAATC
1 GGTCAAACC
*
357099 GGTTCAGACC
1 GG-TCAAACC
357109 GGTCAAACC
1 GGTCAAACC
*
357118 GGTTCGAACC
1 GG-TCAAACC
357128 GGTCGAAACC
1 GGTC-AAACC
357138 GGTCAGAACC
1 GGTCA-AACC
357148 GGT
1 GGT
357151 TGAAAACCGG
Statistics
Matches: 50, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
9 20 0.40
10 30 0.60
ACGTcount: A:0.26, C:0.29, G:0.30, T:0.16
Consensus pattern (9 bp):
GGTCAAACC
Found at i:357155 original size:20 final size:20
Alignment explanation
Indices: 357113--357161 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 20
357103 CAGACCGGTC
357113 AAACCGGTTCGAACCGGTCG-
1 AAACCGG-TCGAACCGGTCGA
*
357133 AAACCGGTCAGAACCGGTTGA
1 AAACCGGTC-GAACCGGTCGA
357154 AAACCGGT
1 AAACCGGT
357162 TTCCAGCAGC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 2 0.08
20 16 0.62
21 8 0.31
ACGTcount: A:0.31, C:0.27, G:0.29, T:0.14
Consensus pattern (20 bp):
AAACCGGTCGAACCGGTCGA
Found at i:364354 original size:17 final size:17
Alignment explanation
Indices: 364334--364371 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
364324 GAAAGTCAAC
364334 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
364351 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
364368 GGTC
1 GGTC
364372 GGTCGGGTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.11, C:0.24, G:0.47, T:0.18
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:364408 original size:20 final size:20
Alignment explanation
Indices: 364383--364428 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
364373 GTCGGGTCAG
364383 ACCGGTTC-GAACCGGTCGAA
1 ACCGGTTCAGAACCGGT-GAA
*
364403 ACCGG-TCAGAACCGGTTAA
1 ACCGGTTCAGAACCGGTGAA
364422 ACCGGTT
1 ACCGGTT
364429 TCCAGCAACC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 9 0.39
20 14 0.61
ACGTcount: A:0.26, C:0.28, G:0.28, T:0.17
Consensus pattern (20 bp):
ACCGGTTCAGAACCGGTGAA
Found at i:366177 original size:58 final size:57
Alignment explanation
Indices: 366114--366225 Score: 136
Period size: 57 Copynumber: 1.9 Consensus size: 57
366104 CAACTCTTTT
*
366114 ATTAATATAAATAAATAAATATTAA-TAAAATATTTATCTAAAAATAATAAAAAATTAG
1 ATTAATATAAAT-AATAAATA-AAAGTAAAATATTTATCTAAAAATAATAAAAAATTAG
* ** * * *
366172 ATTAATATATATAATTGATAAAAGTAAAATATTTATTTAAAAATATTAGAAAAT
1 ATTAATATAAATAATAAATAAAAGTAAAATATTTATCTAAAAATAATAAAAAAT
366226 GGACATCCAG
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
56 2 0.04
57 33 0.72
58 11 0.24
ACGTcount: A:0.59, C:0.01, G:0.04, T:0.37
Consensus pattern (57 bp):
ATTAATATAAATAATAAATAAAAGTAAAATATTTATCTAAAAATAATAAAAAATTAG
Found at i:367628 original size:3 final size:3
Alignment explanation
Indices: 367622--367720 Score: 78
Period size: 3 Copynumber: 33.3 Consensus size: 3
367612 ATTATTTATT
* * * *
367622 TAA TAA TAA TAT TAA -AA TAAA TATT TAT TAA TAA TAA TAA TAT TAA
1 TAA TAA TAA TAA TAA TAA T-AA TA-A TAA TAA TAA TAA TAA TAA TAA
* * * * *
367668 TAA TAT TAT TAT TAA TAT TAA TAA TGA TAA T-A TAA TAA T-A TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
367714 TAA TAA T
1 TAA TAA T
367721 TAAAAATAAA
Statistics
Matches: 79, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
2 6 0.08
3 68 0.86
4 5 0.06
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (3 bp):
TAA
Found at i:368263 original size:122 final size:122
Alignment explanation
Indices: 367937--368263 Score: 566
Period size: 122 Copynumber: 2.7 Consensus size: 122
367927 ATAGAAAAAA
*
367937 TTGAACAAGCTCTTCTCATTATGAACTTCTTTTCCTTTTTCAGATGAGTTCTTCTCATTATGAAC
1 TTGAACAAGCTCTTCTCATTATGAACTTCTTTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC
*
368002 ACTTCTGGAAATATTAATGTTGATCTATCTCCTTCTGTGATAGAGTCATGCAAAAGG
66 ACTTCTGGAAATATTGATGTTGATCTATCTCCTTCTGTGATAGAGTCATGCAAAAGG
*
368059 TTGAACAAGCTCTTCTCATTATGATCTTCTTTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC
1 TTGAACAAGCTCTTCTCATTATGAACTTCTTTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC
368124 ACTTCTGGAAATATTGATGTTGATCTATCTCCTTCTGTGATAGAGTCATGCAAAAGG
66 ACTTCTGGAAATATTGATGTTGATCTATCTCCTTCTGTGATAGAGTCATGCAAAAGG
* * *
368181 TTGAACAATCTATTCCCATTATGAACTTCTTTTTCC-TCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAGCTCTTCTCATTATGAACTTC-TTTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
* *
368245 CACTTCTGGTAATGTTGAT
65 CACTTCTGGAAATATTGAT
368264 CCATCAAGTG
Statistics
Matches: 195, Mismatches: 9, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
122 189 0.97
123 6 0.03
ACGTcount: A:0.25, C:0.20, G:0.14, T:0.41
Consensus pattern (122 bp):
TTGAACAAGCTCTTCTCATTATGAACTTCTTTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC
ACTTCTGGAAATATTGATGTTGATCTATCTCCTTCTGTGATAGAGTCATGCAAAAGG
Found at i:368404 original size:113 final size:112
Alignment explanation
Indices: 368173--368502 Score: 430
Period size: 113 Copynumber: 2.9 Consensus size: 112
368163 ATAGAGTCAT
* * * * *
368173 GCAAAAGGTTGAACAATCTATTCCCATTATGAACTTCTTTTTCC-TCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAAAAAT-TCTTCTCATTATGAACTTCTTATGCCTTCTTCAGATGAGTTCTTCTC
* * * * *
368237 ATTATGAACACT-TCTGGTAATGTTGATCCATCAAGTGATGTATTAAA
65 ATTATGAACTCTACCTGGCAATGTTGATCCATCGAGTGATGAATTAAA
* * * *
368284 GCGAAAGGTTGAATAAATTCTTCTCATTATGAACTTCTTCTGCCTTCTTCAGATGTGTTTTTCTC
1 GCAAAAGGTTGAA-AAATTCTTCTCATTATGAACTTCTTATGCCTTCTTCAGATGAGTTCTTCTC
**
368349 ATTATGAACTCTACCTGGCAATGTTGATCCATCGAGTGATGAATTTGA
65 ATTATGAACTCTACCTGGCAATGTTGATCCATCGAGTGATGAATTAAA
* * *
368397 GTAAAAGGTTGAACAAATTCTTCTCATTATAAACTTCTTATGCCTTCTTCATATGAGTTCTTCTC
1 GCAAAAGGTTGAA-AAATTCTTCTCATTATGAACTTCTTATGCCTTCTTCAGATGAGTTCTTCTC
* *
368462 ATTATGAACTCTACTTGGCAATGTTGATCCATTGAGTGATG
65 ATTATGAACTCTACCTGGCAATGTTGATCCATCGAGTGATG
368503 GATTCAAATC
Statistics
Matches: 191, Mismatches: 25, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
111 34 0.18
112 32 0.17
113 125 0.65
ACGTcount: A:0.27, C:0.18, G:0.16, T:0.39
Consensus pattern (112 bp):
GCAAAAGGTTGAAAAATTCTTCTCATTATGAACTTCTTATGCCTTCTTCAGATGAGTTCTTCTCA
TTATGAACTCTACCTGGCAATGTTGATCCATCGAGTGATGAATTAAA
Found at i:370071 original size:11 final size:11
Alignment explanation
Indices: 370050--370129 Score: 53
Period size: 10 Copynumber: 7.5 Consensus size: 11
370040 TTCACTCATT
370050 TTTTTCATTTTA
1 TTTTTC-TTTTA
370062 TTTTTCTTTTA
1 TTTTTCTTTTA
*
370073 TTATTT-TTTCA
1 TT-TTTCTTTTA
*
370084 TTATT-TTTT-
1 TTTTTCTTTTA
* *
370093 TCTTTC-TTTC
1 TTTTTCTTTTA
370103 TTTTTCTTTT-
1 TTTTTCTTTTA
*
370113 TCTTTCTTTTCA
1 TTTTTCTTTT-A
370125 TTTTT
1 TTTTT
370130 TTCTTCAAGC
Statistics
Matches: 54, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
9 6 0.11
10 19 0.35
11 16 0.30
12 13 0.24
ACGTcount: A:0.09, C:0.12, G:0.00, T:0.79
Consensus pattern (11 bp):
TTTTTCTTTTA
Found at i:370098 original size:16 final size:14
Alignment explanation
Indices: 370089--370122 Score: 50
Period size: 16 Copynumber: 2.3 Consensus size: 14
370079 TTTCATTATT
370089 TTTTTCTTTCTTTC
1 TTTTTCTTTCTTTC
370103 TTTTTCTTTTTCTTTC
1 TTTTTC--TTTCTTTC
370119 TTTT
1 TTTT
370123 CATTTTTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 6 0.33
16 12 0.67
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (14 bp):
TTTTTCTTTCTTTC
Found at i:370102 original size:20 final size:20
Alignment explanation
Indices: 370048--370131 Score: 75
Period size: 20 Copynumber: 4.1 Consensus size: 20
370038 CTTTCACTCA
370048 TTTT-TTTCATTTT-ATTTTT
1 TTTTCTTTC-TTTTCATTTTT
* *
370067 CTTTTATTATTTTTTCATTATTT
1 -TTTTCTT-TCTTTTCATT-TTT
*
370090 TTTTCTTTC-TTTCTTTTTCT
1 TTTTCTTTCTTTTCATTTT-T
370110 TTTTCTTTCTTTTCATTTTT
1 TTTTCTTTCTTTTCATTTTT
370130 TT
1 TT
370132 CTTCAAGCAT
Statistics
Matches: 53, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
19 2 0.04
20 23 0.43
21 15 0.28
22 10 0.19
23 3 0.06
ACGTcount: A:0.08, C:0.12, G:0.00, T:0.80
Consensus pattern (20 bp):
TTTTCTTTCTTTTCATTTTT
Found at i:370128 original size:16 final size:16
Alignment explanation
Indices: 370048--370134 Score: 60
Period size: 15 Copynumber: 5.7 Consensus size: 16
370038 CTTTCACTCA
* *
370048 TTTT-TTTCATTTTAT
1 TTTTCTTTCTTTTTCT
*
370063 TTTTCTTT-TATTAT-T
1 TTTTCTTTCT-TTTTCT
* *
370078 TTTTCATTATTTTT-T
1 TTTTCTTTCTTTTTCT
370093 TCTTTCTTTCTTTTTCT
1 T-TTTCTTTCTTTTTCT
*
370110 TTTTCTTTC-TTTTCA
1 TTTTCTTTCTTTTTCT
370125 TTTT-TTTCTT
1 TTTTCTTTCTT
370135 CAAGCATAAT
Statistics
Matches: 59, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
14 4 0.07
15 27 0.46
16 26 0.44
17 2 0.03
ACGTcount: A:0.08, C:0.13, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTTCTTTCTTTTTCT
Found at i:380783 original size:28 final size:28
Alignment explanation
Indices: 380743--380797 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
380733 ACATTAATAA
*
380743 AATAATATAATATAAATATTATGAAAAT
1 AATAATATAATATAAAAATTATGAAAAT
*
380771 AATAAGTAT-ATATAAAAATTTTGAAAA
1 AATAA-TATAATATAAAAATTATGAAAA
380798 AAAAAATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 21 0.88
29 3 0.12
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (28 bp):
AATAATATAATATAAAAATTATGAAAAT
Found at i:382904 original size:3 final size:3
Alignment explanation
Indices: 382898--382977 Score: 83
Period size: 3 Copynumber: 26.0 Consensus size: 3
382888 ATTATTTATT
*
382898 TAA TAA TAA TAA TAT TAA TAA T-A TATA TATA TATA TATA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA-A TA-A TA-A TA-A TAA TAA TAA
* *
382946 TAA TAT TAA TAA TAA TAA TAA T-A TAA AAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
382978 ATGGATGAAG
Statistics
Matches: 68, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
2 4 0.06
3 49 0.72
4 15 0.22
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:385442 original size:19 final size:17
Alignment explanation
Indices: 385406--385438 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
385396 AATAATTCAC
385406 TCAACCTTCTTTTCTCA
1 TCAACCTTCTTTTCTCA
*
385423 TCAACCTTCTCTTCTC
1 TCAACCTTCTTTTCTC
385439 TCATGTCAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.39, G:0.00, T:0.45
Consensus pattern (17 bp):
TCAACCTTCTTTTCTCA
Found at i:390894 original size:23 final size:23
Alignment explanation
Indices: 390860--390920 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 23
390850 CTCATATAAA
390860 TGCACCGA-AGTGCCACGTAGAAT
1 TGCACC-ATAGTGCCACGTAGAAT
*
390883 TGCACCATAGTGCCGCGTAGAAT
1 TGCACCATAGTGCCACGTAGAAT
*
390906 TGCACCGTAGTGCCA
1 TGCACCATAGTGCCA
390921 TATAATAATG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
22 1 0.03
23 33 0.97
ACGTcount: A:0.26, C:0.28, G:0.26, T:0.20
Consensus pattern (23 bp):
TGCACCATAGTGCCACGTAGAAT
Found at i:397912 original size:17 final size:19
Alignment explanation
Indices: 397890--397925 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
397880 CGAGAACCCC
397890 CTTTCA-CTCT-TATCTCT
1 CTTTCACCTCTATATCTCT
397907 CTTTCACCTCTATATCTCT
1 CTTTCACCTCTATATCTCT
397926 ATAAGAAACC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.35
18 4 0.24
19 7 0.41
ACGTcount: A:0.14, C:0.36, G:0.00, T:0.50
Consensus pattern (19 bp):
CTTTCACCTCTATATCTCT
Found at i:398702 original size:3 final size:3
Alignment explanation
Indices: 398694--398759 Score: 91
Period size: 3 Copynumber: 21.7 Consensus size: 3
398684 ATTTCGTTAT
398694 TAA TAA TAA -AA TTAA TAA TAA TAA TAA TAA TAGA TTAA TAA TAA TAA
1 TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TA-A -TAA TAA TAA TAA
398741 TAA TAA TAA TAA -AA TAA TA
1 TAA TAA TAA TAA TAA TAA TA
398760 TTTTTGGTAG
Statistics
Matches: 58, Mismatches: 0, Indels: 10
0.85 0.00 0.15
Matches are distributed among these distances:
2 4 0.07
3 48 0.83
4 4 0.07
5 2 0.03
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:398734 original size:23 final size:22
Alignment explanation
Indices: 398694--398759 Score: 102
Period size: 23 Copynumber: 3.1 Consensus size: 22
398684 ATTTCGTTAT
398694 TAATAATAA-AATTAATAATAA
1 TAATAATAATAATTAATAATAA
398715 TAATAATAATAGATTAATAATAA
1 TAATAATAATA-ATTAATAATAA
398738 TAATAATAATAA-TAA-AATAA
1 TAATAATAATAATTAATAATAA
398758 TA
1 TA
398760 TTTTTGGTAG
Statistics
Matches: 43, Mismatches: 0, Indels: 5
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.16
21 12 0.28
22 2 0.05
23 22 0.51
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (22 bp):
TAATAATAATAATTAATAATAA
Found at i:399329 original size:135 final size:134
Alignment explanation
Indices: 398961--399415 Score: 585
Period size: 134 Copynumber: 3.4 Consensus size: 134
398951 GGTCTGGTCG
* * **
398961 TCTAAGGGTGACACGAGTCCTACGTGATGAGGAGATCTGGTCGGGGGATGACACAACTCATACAA
1 TCTAGGGGTGACACGACTCCTACGTGATGAGGAGATCTGGTCGGGGGATGACACAACTCATACGT
* * *
399026 GATGAAGAGTTCTGGCCATCTTTAGGAAGGGTGATAACATGGTTCCTACGTAATAAGGAC-ATAT
66 GATGAAGAGTTCTGGCCATCTTTAGGAAGGGTGATAACACGGTTCCTACGTGATAAGGACGA-CT
399090 GGTTA
130 GGTTA
* * *
399095 TCTAGGGGTGACAC-AGCTCCTACGTGATGAGGAGATATGGTCGGGGGATGACACAATTTATACG
1 TCTAGGGGTGACACGA-CTCCTACGTGATGAGGAGATCTGGTCGGGGGATGACACAACTCATACG
* * *
399159 TGATAAAGAGTTCTGGCCATCTTTAGGAAGGGTGATAGA-ACGGTTCCTATGTGATAAGAACGAC
65 TGATGAAGAGTTCTGGCCATCTTTAGGAAGGGTGATA-ACACGGTTCCTACGTGATAAGGACGAC
399223 TGGTTA
129 TGGTTA
* * * * * **
399229 TCTAGGGGGTGACACGAATCCTACGTGATGAAGAGACCTCGTCGGGGAATGACATGACTCATACG
1 TCTA-GGGGTGACACGACTCCTACGTGATGAGGAGATCTGGTCGGGGGATGACACAACTCATACG
* * * * * * *
399294 TGTTGAAGAGTTCTAGCCATCTTTAGCAAGAGTGATAACACGATTCTTACGTGATGAGGACGACT
65 TGATGAAGAGTTCTGGCCATCTTTAGGAAGGGTGATAACACGGTTCCTACGTGATAAGGACGACT
399359 GGTTA
130 GGTTA
* *
399364 TCTA-GGGTGACACGTCTCCTACGTGATGAGGGGATCTGGTCGGGGGATGACA
1 TCTAGGGGTGACACGACTCCTACGTGATGAGGAGATCTGGTCGGGGGATGACA
399416 TGGTTTCTAC
Statistics
Matches: 275, Mismatches: 40, Indels: 13
0.84 0.12 0.04
Matches are distributed among these distances:
133 42 0.15
134 120 0.44
135 112 0.41
136 1 0.00
ACGTcount: A:0.28, C:0.17, G:0.30, T:0.25
Consensus pattern (134 bp):
TCTAGGGGTGACACGACTCCTACGTGATGAGGAGATCTGGTCGGGGGATGACACAACTCATACGT
GATGAAGAGTTCTGGCCATCTTTAGGAAGGGTGATAACACGGTTCCTACGTGATAAGGACGACTG
GTTA
Found at i:399503 original size:29 final size:29
Alignment explanation
Indices: 399461--399518 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
399451 AGGGATAATG
* * *
399461 GTTTCAAGAGAAACCGATTCAAAGATGAT
1 GTTTCAAAAGAAACAGACTCAAAGATGAT
399490 GTTTCAAAAGAAACAGACTCAAAGATGAT
1 GTTTCAAAAGAAACAGACTCAAAGATGAT
399519 TTTGTTAAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.45, C:0.14, G:0.19, T:0.22
Consensus pattern (29 bp):
GTTTCAAAAGAAACAGACTCAAAGATGAT
Done.