Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008275.1 Hibiscus syriacus cultivar Beakdansim tig00110933_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: 1991061
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 8
Found at i:1786729 original size:20 final size:21
Alignment explanation
Indices: 1786704--1786755 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
1786694 TTTTCCCAAT
*
1786704 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGGAAA
* **
1786724 TCGCAACGCGAATTGGGGAAA
1 TCGCAATGCGAATTAAGGAAA
1786745 TCGCAATGCGA
1 TCGCAATGCGA
1786756 TACTTACTAT
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:0.37, C:0.19, G:0.27, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGGAAA
Found at i:1786834 original size:20 final size:20
Alignment explanation
Indices: 1786786--1786838 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
1786776 TAATACAAAA
* *
1786786 TCGCAACGAGATACTGACTT
1 TCGCAACGCGATTCTGACTT
1786806 TCGCAACGCGATTCTGACTT
1 TCGCAACGCGATTCTGACTT
1786826 TCGCAACGCGATT
1 TCGCAACGCGATT
1786839 TACATAGCGC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (20 bp):
TCGCAACGCGATTCTGACTT
Found at i:1787420 original size:19 final size:19
Alignment explanation
Indices: 1787398--1787576 Score: 145
Period size: 19 Copynumber: 10.1 Consensus size: 19
1787388 GAAACCAAAA
*
1787398 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1787417 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
1787431 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1787450 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1787469 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
1787483 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
1787502 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
1787516 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
1787535 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
1787555 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
1787575 TC
1 TC
1787577 AACCAAAAGA
Statistics
Matches: 129, Mismatches: 14, Indels: 34
0.73 0.08 0.19
Matches are distributed among these distances:
14 30 0.23
16 7 0.05
17 8 0.06
19 52 0.40
20 31 0.24
21 1 0.01
ACGTcount: A:0.12, C:0.24, G:0.21, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1787481 original size:52 final size:52
Alignment explanation
Indices: 1787398--1787514 Score: 207
Period size: 52 Copynumber: 2.2 Consensus size: 52
1787388 GAAACCAAAA
* **
1787398 TCGCATTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATAGTCATT
1787450 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATAGTCATT
1787502 TCGCGTTGCGATT
1 TCGCGTTGCGATT
1787515 CTCTCGTTGC
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 62 1.00
ACGTcount: A:0.11, C:0.23, G:0.22, T:0.44
Consensus pattern (52 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATAGTCATT
Found at i:1787490 original size:33 final size:33
Alignment explanation
Indices: 1787453--1787551 Score: 171
Period size: 33 Copynumber: 3.0 Consensus size: 33
1787443 TTTCATTTCG
**
1787453 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
1 CGTTGCGATAGTCATTTCGCGTTGCGATTCTCT
1787486 CGTTGCGATAGTCATTTCGCGTTGCGATTCTCT
1 CGTTGCGATAGTCATTTCGCGTTGCGATTCTCT
1787519 CGTTGCGATAGTCATTTCCGCGTTGCGATTCTC
1 CGTTGCGATAGTCATTT-CGCGTTGCGATTCTC
1787552 ATTATCTCGT
Statistics
Matches: 63, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
33 48 0.76
34 15 0.24
ACGTcount: A:0.11, C:0.25, G:0.23, T:0.40
Consensus pattern (33 bp):
CGTTGCGATAGTCATTTCGCGTTGCGATTCTCT
Found at i:1787491 original size:14 final size:14
Alignment explanation
Indices: 1787472--1787527 Score: 58
Period size: 14 Copynumber: 3.6 Consensus size: 14
1787462 TTTCATTTCG
1787472 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1787486 CGTTGCGATAGTCATTTCG
1 CGTTGCGAT--TC---TCT
1787505 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1787519 CGTTGCGAT
1 CGTTGCGAT
1787528 AGTCATTTCC
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 20 0.57
16 2 0.06
17 2 0.06
19 11 0.31
ACGTcount: A:0.11, C:0.25, G:0.25, T:0.39
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1789758 original size:42 final size:42
Alignment explanation
Indices: 1789657--1789832 Score: 199
Period size: 42 Copynumber: 4.2 Consensus size: 42
1789647 CCCGACTCGC
* * * * *
1789657 CTGTCATCCCTTAAGAGTCCACTCCTATCGTTGAAGAGGCCC
1 CTGTCATCCCTCAAGAGTCCCCTCCCATCGTTCAAGAGGCCA
* * * * *
1789699 CTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGTGGCCA
1 CTGTCATCCCTCAAGAGTCCCCTCCCATCGTTCAAGAGGCCA
* * * *
1789741 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCC
1 CTGTCATCCCTCAAGAGTCCCCTCCCATCGTTCAAGAGGCCA
* * *
1789783 CTATCATTCCTCGAGAGTCCCCTCCCATCGTTCAAGAGGCCA
1 CTGTCATCCCTCAAGAGTCCCCTCCCATCGTTCAAGAGGCCA
1789825 CTGTCATC
1 CTGTCATC
1789833 GTTGAAGAGG
Statistics
Matches: 106, Mismatches: 28, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
42 106 1.00
ACGTcount: A:0.20, C:0.37, G:0.18, T:0.25
Consensus pattern (42 bp):
CTGTCATCCCTCAAGAGTCCCCTCCCATCGTTCAAGAGGCCA
Found at i:1789820 original size:21 final size:21
Alignment explanation
Indices: 1789712--1789862 Score: 63
Period size: 21 Copynumber: 7.2 Consensus size: 21
1789702 TCATTCCTCG
*
1789712 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCATCGTTCA
* * * ** **
1789733 AGTGGCCACTGTCATCCCTCA
1 AGAGTCCCCTCCCATCGTTCA
* * *
1789754 AGAGTCCACTCCTATCGTTGA
1 AGAGTCCCCTCCCATCGTTCA
* ** * *
1789775 AGAGGCCCCTATCATTC-CTCG
1 AGAGTCCCCTCCCA-TCGTTCA
1789796 AGAGTCCCCTCCCATCGTTCA
1 AGAGTCCCCTCCCATCGTTCA
* * ** *
1789817 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCATCGTTCA
* *
1789838 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCATCGTTCA
1789859 AGAG
1 AGAG
1789863 CCCGATTCAC
Statistics
Matches: 86, Mismatches: 41, Indels: 7
0.64 0.31 0.05
Matches are distributed among these distances:
20 3 0.03
21 80 0.93
22 3 0.03
ACGTcount: A:0.22, C:0.36, G:0.19, T:0.23
Consensus pattern (21 bp):
AGAGTCCCCTCCCATCGTTCA
Found at i:1789841 original size:84 final size:84
Alignment explanation
Indices: 1789657--1789832 Score: 325
Period size: 84 Copynumber: 2.1 Consensus size: 84
1789647 CCCGACTCGC
*
1789657 CTGTCATCCCTTAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
*
1789722 CCCACCGTTCAAGTGGCCA
66 CCCACCGTTCAAGAGGCCA
1789741 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
*
1789806 CCCATCGTTCAAGAGGCCA
66 CCCACCGTTCAAGAGGCCA
1789825 CTGTCATC
1 CTGTCATC
1789833 GTTGAAGAGG
Statistics
Matches: 89, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
84 89 1.00
ACGTcount: A:0.20, C:0.37, G:0.18, T:0.25
Consensus pattern (84 bp):
CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
CCCACCGTTCAAGAGGCCA
Found at i:1789848 original size:42 final size:41
Alignment explanation
Indices: 1789657--1789862 Score: 157
Period size: 42 Copynumber: 4.9 Consensus size: 41
1789647 CCCGACTCGC
* * * *
1789657 CTGTCATCCCTT-AAGAGTCCACTCCTATCGTTGAAGAGGCCC
1 CTGTCAT-CCTTGAAGAGTCC-CTCCCACCGTTCAAGAGGCCA
* * *
1789699 CTATCATTCCTCG-AGAGTCCCCTCCCACCGTTCAAGTGGCCA
1 CTGTCA-TCCTTGAAGAGT-CCCTCCCACCGTTCAAGAGGCCA
* * * * * *
1789741 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCC
1 CTGTCATCCTTGAAGAGTCC-CTCCCACCGTTCAAGAGGCCA
* * *
1789783 CTATCATTCCTCG-AGAGTCCCCTCCCATCGTTCAAGAGGCCA
1 CTGTCA-TCCTTGAAGAGT-CCCTCCCACCGTTCAAGAGGCCA
* *
1789825 CTGTCATCGTTGAAGAGGTCCCTCCCACCATTCAAGAG
1 CTGTCATCCTTGAAGA-GTCCCTCCCACCGTTCAAGAG
1789863 CCCGATTCAC
Statistics
Matches: 127, Mismatches: 28, Indels: 18
0.73 0.16 0.10
Matches are distributed among these distances:
41 9 0.07
42 108 0.85
43 10 0.08
ACGTcount: A:0.21, C:0.36, G:0.18, T:0.24
Consensus pattern (41 bp):
CTGTCATCCTTGAAGAGTCCCTCCCACCGTTCAAGAGGCCA
Found at i:1789862 original size:84 final size:84
Alignment explanation
Indices: 1789657--1789862 Score: 270
Period size: 84 Copynumber: 2.5 Consensus size: 84
1789647 CCCGACTCGC
* * * * *
1789657 CTGTCATCCCTTAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCCACCATTCAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
*
1789722 CCCACCGTTCAAGTGGCCA
66 CCCACCGTTCAAGAGGCCA
* * * *
1789741 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCCACCATTCAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
*
1789806 CCCATCGTTCAAGAGGCCA
66 CCCACCGTTCAAGAGGCCA
** *
1789825 CTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CTGTCATCCCTCAAGA-GTCCACTCCCACCATTCAAGAG
1789863 CCCGATTCAC
Statistics
Matches: 111, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
84 107 0.96
85 4 0.04
ACGTcount: A:0.21, C:0.36, G:0.18, T:0.24
Consensus pattern (84 bp):
CTGTCATCCCTCAAGAGTCCACTCCCACCATTCAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
CCCACCGTTCAAGAGGCCA
Found at i:1791237 original size:14 final size:14
Alignment explanation
Indices: 1791218--1791253 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1791208 ATTGTTTAAT
1791218 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
1791232 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
1791246 TGATTTGT
1 TGATTTGT
1791254 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:1791437 original size:19 final size:19
Alignment explanation
Indices: 1791362--1791428 Score: 81
Period size: 19 Copynumber: 3.8 Consensus size: 19
1791352 AAAAAGTACT
*
1791362 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
1791381 ATCGCAA--CG--A-GAGA
1 ATCGCAACGCGAAATGAAA
1791395 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
1791414 ATCGCAACGCGAAAT
1 ATCGCAACGCGAAAT
1791429 TAAATTCGCG
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
14 10 0.24
15 1 0.02
16 2 0.05
17 2 0.05
18 1 0.02
19 25 0.61
ACGTcount: A:0.45, C:0.21, G:0.22, T:0.12
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:1791483 original size:20 final size:19
Alignment explanation
Indices: 1791433--1791486 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
1791423 CGAAATTAAA
** *
1791433 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATAGTAAT
*
1791452 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATAGTAAT
1791471 TTCCGCGTTGCGATAG
1 TT-CGCGTTGCGATAG
1791487 ACATTAAGAT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.17, C:0.20, G:0.24, T:0.39
Consensus pattern (19 bp):
TTCGCGTTGCGATAGTAAT
Found at i:1793775 original size:12 final size:12
Alignment explanation
Indices: 1793758--1793782 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1793748 TCTTCGGGGA
1793758 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1793770 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1793782 C
1 C
1793783 AAGATTATAT
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:1793991 original size:24 final size:24
Alignment explanation
Indices: 1793957--1794010 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1793947 CTGAAACATC
*
1793957 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
1793981 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
1794005 ATCAAA
1 ATCAAA
1794011 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:1794820 original size:20 final size:21
Alignment explanation
Indices: 1794795--1794846 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
1794785 TTTTCCTAAT
*
1794795 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
1794815 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
1794836 TCGCAATGCGA
1 TCGCAATGCGA
1794847 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:1794868 original size:20 final size:20
Alignment explanation
Indices: 1794835--1794908 Score: 69
Period size: 20 Copynumber: 3.6 Consensus size: 20
1794825 AATTTGGAAA
* *
1794835 ATCGCAATGCGATACTGACT
1 ATCGCAACGAGATACTGACT
* *
1794855 ATCGCAACGAGATAAT-ACAAA
1 ATCGCAACGAGATACTGAC--T
*
1794876 ATCGCAACGAGATTCTGACT
1 ATCGCAACGAGATACTGACT
*
1794896 TTCGCAACGAGAT
1 ATCGCAACGAGAT
1794909 TCTAAAAATC
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
19 2 0.05
20 25 0.58
21 14 0.33
22 2 0.05
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.22
Consensus pattern (20 bp):
ATCGCAACGAGATACTGACT
Found at i:1794877 original size:41 final size:40
Alignment explanation
Indices: 1794832--1794923 Score: 121
Period size: 41 Copynumber: 2.3 Consensus size: 40
1794822 GCGAATTTGG
*
1794832 AAAATCGCAATGCGATACTGACTATCGCAACGAGATAATA
1 AAAATCGCAATGAGATACTGACTATCGCAACGAGATAATA
* * * **
1794872 CAAAATCGCAACGAGATTCTGACTTTCGCAACGAGATTCTA
1 -AAAATCGCAATGAGATACTGACTATCGCAACGAGATAATA
1794913 AAAATCGCAAT
1 AAAATCGCAAT
1794924 CATCTTCAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
40 10 0.23
41 34 0.77
ACGTcount: A:0.40, C:0.22, G:0.16, T:0.22
Consensus pattern (40 bp):
AAAATCGCAATGAGATACTGACTATCGCAACGAGATAATA
Found at i:1794920 original size:20 final size:20
Alignment explanation
Indices: 1794855--1794922 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
1794845 GATACTGACT
**
1794855 ATCGCAACGAGATAATACAAA
1 ATCGCAACGAGATTCTA-AAA
* **
1794876 ATCGCAACGAGATTCTGACT
1 ATCGCAACGAGATTCTAAAA
*
1794896 TTCGCAACGAGATTCTAAAA
1 ATCGCAACGAGATTCTAAAA
1794916 ATCGCAA
1 ATCGCAA
1794923 TCATCTTCAA
Statistics
Matches: 37, Mismatches: 10, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
20 23 0.62
21 14 0.38
ACGTcount: A:0.41, C:0.22, G:0.16, T:0.21
Consensus pattern (20 bp):
ATCGCAACGAGATTCTAAAA
Found at i:1795161 original size:20 final size:20
Alignment explanation
Indices: 1795136--1795203 Score: 57
Period size: 20 Copynumber: 3.4 Consensus size: 20
1795126 CAACGGGGAA
1795136 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
** ***
1795156 ATCGCAATTCG-AAATGAAAA
1 ATCGCAACGCGAAAATG-GCT
* *
1795176 ATCACAACGCAAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
1795196 ATCGCAAC
1 ATCGCAAC
1795204 TAGAAAATCG
Statistics
Matches: 33, Mismatches: 13, Indels: 4
0.66 0.26 0.08
Matches are distributed among these distances:
19 5 0.15
20 23 0.70
21 5 0.15
ACGTcount: A:0.43, C:0.24, G:0.18, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGGCT
Found at i:1795254 original size:14 final size:14
Alignment explanation
Indices: 1795235--1795288 Score: 63
Period size: 14 Copynumber: 3.5 Consensus size: 14
1795225 GAAAATCGCA
1795235 TTGCGATTTTCTCG
1 TTGCGATTTTCTCG
1795249 TTGCGATTTTCATTTCG
1 TTGCGATTTTC---TCG
1795266 CATTGCGATTTTCTCG
1 --TTGCGATTTTCTCG
1795282 TTGCGAT
1 TTGCGAT
1795289 AGTCAGTTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 18 0.51
16 3 0.09
17 3 0.09
19 11 0.31
ACGTcount: A:0.11, C:0.20, G:0.20, T:0.48
Consensus pattern (14 bp):
TTGCGATTTTCTCG
Found at i:1795254 original size:33 final size:33
Alignment explanation
Indices: 1795217--1795287 Score: 88
Period size: 33 Copynumber: 2.2 Consensus size: 33
1795207 AAAATCGCAA
1795217 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
** ** **
1795250 TGCGATTTTCATTTCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
1795283 TGCGA
1 TGCGA
1795288 TAGTCAGTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.39
Consensus pattern (33 bp):
TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
Found at i:1795434 original size:14 final size:14
Alignment explanation
Indices: 1795415--1795451 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1795405 CATCAATTAA
1795415 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
1795429 ACAAATCATCTTTT
1 ACAAATCAACATTT
1795443 ACAAATCAA
1 ACAAATCAA
1795452 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:1797342 original size:20 final size:19
Alignment explanation
Indices: 1797319--1797386 Score: 82
Period size: 20 Copynumber: 3.5 Consensus size: 19
1797309 GAAACTTAAA
1797319 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCG-AAATGACT
*
1797339 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
1797359 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
1797378 ATCGCAACG
1 ATCGCAACG
1797387 ACAAAATCGC
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
19 14 0.34
20 26 0.63
21 1 0.02
ACGTcount: A:0.38, C:0.24, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:1797394 original size:14 final size:14
Alignment explanation
Indices: 1797375--1797465 Score: 83
Period size: 14 Copynumber: 5.9 Consensus size: 14
1797365 ATGCGAAATG
1797375 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
1797389 AAAATCGCAATGCGAAATG
1 AAAATCGCAA--CG--A-C
1797408 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
1797422 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
1797438 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
1797454 AAAATCGCAACG
1 AAAATCGCAACG
1797466 CGAAACACAA
Statistics
Matches: 64, Mismatches: 4, Indels: 18
0.74 0.05 0.21
Matches are distributed among these distances:
14 31 0.48
15 1 0.02
16 10 0.16
17 2 0.03
18 10 0.16
19 10 0.16
ACGTcount: A:0.48, C:0.23, G:0.18, T:0.11
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:1797450 original size:32 final size:33
Alignment explanation
Indices: 1797359--1797470 Score: 208
Period size: 33 Copynumber: 3.4 Consensus size: 33
1797349 GGAAATGGCT
1797359 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1797392 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1797425 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
1797457 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
1797471 CACAAATCGC
Statistics
Matches: 78, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
32 29 0.37
33 49 0.63
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:1797478 original size:65 final size:66
Alignment explanation
Indices: 1797359--1797481 Score: 205
Period size: 65 Copynumber: 1.9 Consensus size: 66
1797349 GGAAATGGCT
* *
1797359 ATCGCAATGCGAAATGAAAATCGCAACGACAAAATCGCAATGCGAAATGAAAATCGCAACGACAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAAATCGCAACGCGAAATCAAAATCGCAACGACAA
1797424 A
66 A
1797425 ATCGCAATGCGAAATG-AAATCGCAACGACAAAATCGCAACGCGAAA-CACAAATCGCA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAAATCGCAACGCGAAATCA-AAATCGCA
1797482 TTGCGATTTT
Statistics
Matches: 54, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
64 1 0.02
65 37 0.69
66 16 0.30
ACGTcount: A:0.47, C:0.24, G:0.18, T:0.11
Consensus pattern (66 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAAATCGCAACGCGAAATCAAAATCGCAACGACAA
A
Found at i:1797518 original size:14 final size:14
Alignment explanation
Indices: 1797499--1797538 Score: 80
Period size: 14 Copynumber: 2.9 Consensus size: 14
1797489 TTTCATTTAG
1797499 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
1797513 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
1797527 CGTTGCGATTTT
1 CGTTGCGATTTT
1797539 CATTTCGCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.07, C:0.15, G:0.28, T:0.50
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:1797591 original size:20 final size:20
Alignment explanation
Indices: 1797539--1797582 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
1797529 TTGCGATTTT
*
1797539 CATTT-CGCATTGCGATAGC
1 CATTTCCGCGTTGCGATAGC
*
1797558 CATTTCCGCGTTGCGATAGT
1 CATTTCCGCGTTGCGATAGC
1797578 CATTT
1 CATTT
1797583 TCGTGTTGCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.18, C:0.25, G:0.20, T:0.36
Consensus pattern (20 bp):
CATTTCCGCGTTGCGATAGC
Found at i:1799464 original size:20 final size:20
Alignment explanation
Indices: 1799439--1799512 Score: 69
Period size: 20 Copynumber: 3.8 Consensus size: 20
1799429 AATAGTTTTT
*
1799439 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACGC
**
1799459 GAAAATGACTATCGCAACGC
1 GAAAATGAAAATCGCAACGC
** **
1799479 GAATTTGACTATCGCAACGC
1 GAAAATGAAAATCGCAACGC
*
1799499 GAAACT-AAAATCGC
1 GAAAATGAAAATCGC
1799513 GTTGCGATTT
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
19 6 0.13
20 39 0.87
ACGTcount: A:0.43, C:0.23, G:0.18, T:0.16
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACGC
Found at i:1799776 original size:22 final size:22
Alignment explanation
Indices: 1799746--1799789 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1799736 GATGGAGATA
*
1799746 GACGGATTTCGCCGGAGATGGG
1 GACGAATTTCGCCGGAGATGGG
*
1799768 GACGAATTTCGTCGGAGATGGG
1 GACGAATTTCGCCGGAGATGGG
1799790 TGAGAGAGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.16, G:0.43, T:0.20
Consensus pattern (22 bp):
GACGAATTTCGCCGGAGATGGG
Found at i:1800063 original size:20 final size:20
Alignment explanation
Indices: 1799957--1800091 Score: 121
Period size: 20 Copynumber: 6.7 Consensus size: 20
1799947 CGCTTTGAAA
*
1799957 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* * *
1799978 ATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATAGTCAGT
* *
1799998 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * * *
1800018 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTCAGT
*
1800039 ATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGATAGTCAGT
1800059 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
1800079 ATCGCATTGCGAT
1 ATCGCATTGCGAT
1800092 TTTCCCAATT
Statistics
Matches: 96, Mismatches: 14, Indels: 9
0.81 0.12 0.08
Matches are distributed among these distances:
19 5 0.05
20 66 0.69
21 23 0.24
22 2 0.02
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.33
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:1800063 original size:61 final size:61
Alignment explanation
Indices: 1799957--1800094 Score: 195
Period size: 61 Copynumber: 2.3 Consensus size: 61
1799947 CGCTTTGAAA
* * * *
1799957 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
* * * * *
1800018 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
1800079 ATCGCATTGCGATTTT
1 ATCGCATTGCGATTTT
1800095 CCCAATTCGC
Statistics
Matches: 66, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 66 1.00
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.35
Consensus pattern (61 bp):
ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
Found at i:1800111 original size:61 final size:61
Alignment explanation
Indices: 1799957--1800112 Score: 145
Period size: 61 Copynumber: 2.6 Consensus size: 61
1799947 CGCTTTGAAA
* ** * * * * *
1799957 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTCCAATATCGCGATGCGATAGTAAGAATCGCATTGCGAAAGTCAGT
* * ** * * *
1800018 ATCTCGTTGCGATTTTGTATTATCGC-ATTGCGATAGTAAGTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTTTCCAATATCGCGA-TGCGATAGTAAGAATCGCATTGCGAAAGTCAGT
1800079 ATCGCATTGCGATTTTCCCAAT-TCGCGATGCGAT
1 ATCGCATTGCGATTTT-CCAATATCGCGATGCGAT
1800113 TTACTTATTT
Statistics
Matches: 78, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
61 75 0.96
62 3 0.04
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (61 bp):
ATCGCATTGCGATTTTCCAATATCGCGATGCGATAGTAAGAATCGCATTGCGAAAGTCAGT
Found at i:1800653 original size:6 final size:6
Alignment explanation
Indices: 1800633--1800750 Score: 121
Period size: 6 Copynumber: 19.8 Consensus size: 6
1800623 ATAAGAAGTT
* * *
1800633 TTATTA -TATTG TTATTA TTATTA TTATTA TTATTG TTATTA TTATTT
1 TTATTA TTATTA TTATTA TTATTA TTATTA TTATTA TTATTA TTATTA
* * * * *
1800680 TTATTG TTATTA TTATTA TTATTG TTATTG TTATTA TTGTTA TTATTG
1 TTATTA TTATTA TTATTA TTATTA TTATTA TTATTA TTATTA TTATTA
* * * *
1800728 TTTTTG TTGTTA TTGTTA TTATT
1 TTATTA TTATTA TTATTA TTATT
1800751 TACTTGTCAG
Statistics
Matches: 95, Mismatches: 16, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
5 4 0.04
6 91 0.96
ACGTcount: A:0.23, C:0.00, G:0.08, T:0.69
Consensus pattern (6 bp):
TTATTA
Found at i:1800656 original size:9 final size:9
Alignment explanation
Indices: 1800633--1800750 Score: 121
Period size: 9 Copynumber: 13.2 Consensus size: 9
1800623 ATAAGAAGTT
1800633 TTATTA-TA
1 TTATTATTA
*
1800641 TTGTTATTA
1 TTATTATTA
1800650 TTATTATTA
1 TTATTATTA
*
1800659 TTATTATTG
1 TTATTATTA
1800668 TTATTATTA
1 TTATTATTA
* *
1800677 TTTTTATTG
1 TTATTATTA
1800686 TTATTATTA
1 TTATTATTA
*
1800695 TTATTATTG
1 TTATTATTA
*
1800704 TTATTGTTA
1 TTATTATTA
*
1800713 TTATTGTTA
1 TTATTATTA
* *
1800722 TTATTGTTT
1 TTATTATTA
* *
1800731 TTGTTGTTA
1 TTATTATTA
*
1800740 TTGTTATTA
1 TTATTATTA
1800749 TT
1 TT
1800751 TACTTGTCAG
Statistics
Matches: 94, Mismatches: 15, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
8 5 0.05
9 89 0.95
ACGTcount: A:0.23, C:0.00, G:0.08, T:0.69
Consensus pattern (9 bp):
TTATTATTA
Found at i:1800669 original size:24 final size:24
Alignment explanation
Indices: 1800644--1800750 Score: 142
Period size: 24 Copynumber: 4.5 Consensus size: 24
1800634 TATTATATTG
* * *
1800644 TTATTATTATTATTATTATTATTG
1 TTATTATTATTGTTATTGTTATTA
*
1800668 TTATTATTATTTTTATTGTTATTA
1 TTATTATTATTGTTATTGTTATTA
1800692 TTATTATTATTGTTATTGTTATTA
1 TTATTATTATTGTTATTGTTATTA
* * *
1800716 TTGTTATTATTGTTTTTGTTGTTA
1 TTATTATTATTGTTATTGTTATTA
*
1800740 TTGTTATTATT
1 TTATTATTATT
1800751 TACTTGTCAG
Statistics
Matches: 76, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 76 1.00
ACGTcount: A:0.22, C:0.00, G:0.08, T:0.69
Consensus pattern (24 bp):
TTATTATTATTGTTATTGTTATTA
Found at i:1807529 original size:30 final size:30
Alignment explanation
Indices: 1807495--1807575 Score: 135
Period size: 30 Copynumber: 2.6 Consensus size: 30
1807485 AAGGTTCGAC
1807495 GTGCTAATGCTACGATATTATCCAATGATT
1 GTGCTAATGCTACGATATTATCCAATGATT
*
1807525 GTGCTAATGCTACGATAGTATCCAATGATT
1 GTGCTAATGCTACGATATTATCCAATGATT
1807555 GTGCAATAATGCTACGATATT
1 GTGC--TAATGCTACGATATT
1807576 TTTATTTAAT
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
30 33 0.70
32 14 0.30
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.35
Consensus pattern (30 bp):
GTGCTAATGCTACGATATTATCCAATGATT
Found at i:1808549 original size:2 final size:2
Alignment explanation
Indices: 1808542--1808580 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1808532 TGATATTTCA
1808542 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 A
1808581 AAGTTAACAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1809344 original size:21 final size:23
Alignment explanation
Indices: 1809319--1809364 Score: 67
Period size: 25 Copynumber: 2.0 Consensus size: 23
1809309 AACCACTAAT
1809319 TTTTTTAT-TAAAATATACTTAC
1 TTTTTTATATAAAATATACTTAC
1809341 TTTTTTATAAATAAAATATACTTA
1 TTTTTTAT--ATAAAATATACTTA
1809365 TTTAAGTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 8 0.38
25 13 0.62
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (23 bp):
TTTTTTATATAAAATATACTTAC
Found at i:1811417 original size:22 final size:22
Alignment explanation
Indices: 1811366--1811426 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 22
1811356 TTTTTAATAA
* *
1811366 TTATGTCTTTATGACATGTTTT
1 TTATGTCTTTATAACATATTTT
*
1811388 TCTCTGTCTTTATAACATATTTT
1 T-TATGTCTTTATAACATATTTT
1811411 TTATGTCTTTATAACA
1 TTATGTCTTTATAACA
1811427 CGTTTTCGGT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
22 15 0.44
23 19 0.56
ACGTcount: A:0.23, C:0.13, G:0.08, T:0.56
Consensus pattern (22 bp):
TTATGTCTTTATAACATATTTT
Found at i:1811432 original size:22 final size:22
Alignment explanation
Indices: 1811366--1811432 Score: 89
Period size: 22 Copynumber: 3.0 Consensus size: 22
1811356 TTTTTAATAA
*
1811366 TTATGTCTTTATGACATGTTTT
1 TTATGTCTTTATAACATGTTTT
* *
1811388 TCTCTGTCTTTATAACATATTTT
1 T-TATGTCTTTATAACATGTTTT
*
1811411 TTATGTCTTTATAACACGTTTT
1 TTATGTCTTTATAACATGTTTT
1811433 CGGTCGTTTG
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
22 19 0.50
23 19 0.50
ACGTcount: A:0.21, C:0.13, G:0.09, T:0.57
Consensus pattern (22 bp):
TTATGTCTTTATAACATGTTTT
Found at i:1811833 original size:20 final size:20
Alignment explanation
Indices: 1811810--1811848 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1811800 ATATATTTAA
*
1811810 TTTATACATTTTATAATAAT
1 TTTAAACATTTTATAATAAT
* *
1811830 TTTAAATATTTTTTAATAA
1 TTTAAACATTTTATAATAA
1811849 AATTAACGGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (20 bp):
TTTAAACATTTTATAATAAT
Found at i:1812263 original size:12 final size:13
Alignment explanation
Indices: 1812237--1812261 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1812227 TATTATTAAA
1812237 AAATATATTTTTT
1 AAATATATTTTTT
1812250 AAATATATTTTT
1 AAATATATTTTT
1812262 AACTACGTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
AAATATATTTTTT
Found at i:1816946 original size:14 final size:14
Alignment explanation
Indices: 1816927--1816990 Score: 56
Period size: 14 Copynumber: 4.5 Consensus size: 14
1816917 GTCTGAACCT
*
1816927 AGTCAACTCGGCTG
1 AGTCAACTCGACTG
* *
1816941 AGTCAACTCGCCTA
1 AGTCAACTCGACTG
* *
1816955 AGTCAACCCGAATTG
1 AGTCAACTCG-ACTG
* *
1816970 AGTCAACTCGTCCG
1 AGTCAACTCGACTG
1816984 AGTCAAC
1 AGTCAAC
1816991 CCGTTGACTT
Statistics
Matches: 39, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
14 29 0.74
15 10 0.26
ACGTcount: A:0.28, C:0.31, G:0.20, T:0.20
Consensus pattern (14 bp):
AGTCAACTCGACTG
Found at i:1820539 original size:22 final size:23
Alignment explanation
Indices: 1820488--1820542 Score: 103
Period size: 23 Copynumber: 2.4 Consensus size: 23
1820478 ACATTTAAAA
1820488 TTTAGTCCTTTTATTCTTTTAGT
1 TTTAGTCCTTTTATTCTTTTAGT
1820511 TTTAGTCCTTTTATTCTTTTAG-
1 TTTAGTCCTTTTATTCTTTTAGT
1820533 TTTAGTCCTT
1 TTTAGTCCTT
1820543 CCATAATTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 10 0.31
23 22 0.69
ACGTcount: A:0.13, C:0.15, G:0.09, T:0.64
Consensus pattern (23 bp):
TTTAGTCCTTTTATTCTTTTAGT
Found at i:1821423 original size:38 final size:38
Alignment explanation
Indices: 1821372--1821446 Score: 123
Period size: 38 Copynumber: 2.0 Consensus size: 38
1821362 CTTGTATTGT
* *
1821372 TATTTGGGTATTGTGCTTGCTCTAGTTTGAGCAAAGGA
1 TATTTGGATATTGTGCTTGCTCTAATTTGAGCAAAGGA
*
1821410 TATTTGGATATTGTGCTTGTTCTAATTTGAGCAAAGG
1 TATTTGGATATTGTGCTTGCTCTAATTTGAGCAAAGG
1821447 GAATGTTACT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.23, C:0.09, G:0.27, T:0.41
Consensus pattern (38 bp):
TATTTGGATATTGTGCTTGCTCTAATTTGAGCAAAGGA
Found at i:1822126 original size:21 final size:21
Alignment explanation
Indices: 1822100--1822146 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
1822090 ATTTACCGTG
* *
1822100 ATTGCGGCCATCGTGGGCGCT
1 ATTGCGGCCATCGCGGACGCT
*
1822121 ATTGCGGCCGTCGCGGACGCT
1 ATTGCGGCCATCGCGGACGCT
1822142 ATTGC
1 ATTGC
1822147 AGCAGTCGCG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.11, C:0.30, G:0.36, T:0.23
Consensus pattern (21 bp):
ATTGCGGCCATCGCGGACGCT
Found at i:1822154 original size:21 final size:21
Alignment explanation
Indices: 1822117--1822157 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1822107 CCATCGTGGG
* *
1822117 CGCTATTGCGGCCGTCGCGGA
1 CGCTATTGCAGCAGTCGCGGA
1822138 CGCTATTGCAGCAGTCGCGG
1 CGCTATTGCAGCAGTCGCGG
1822158 GTAACTCGGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.12, C:0.32, G:0.37, T:0.20
Consensus pattern (21 bp):
CGCTATTGCAGCAGTCGCGGA
Found at i:1825055 original size:12 final size:12
Alignment explanation
Indices: 1825038--1825070 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
1825028 AACTTTTTTG
1825038 ATCTCATGATCT
1 ATCTCATGATCT
1825050 ATCTCATGATCT
1 ATCTCATGATCT
1825062 ATCTCATGA
1 ATCTCATGA
1825071 CTCATGACTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.27, C:0.24, G:0.09, T:0.39
Consensus pattern (12 bp):
ATCTCATGATCT
Found at i:1827568 original size:21 final size:21
Alignment explanation
Indices: 1827543--1827582 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1827533 GTCTGGTGAT
*
1827543 GAACCGAATTGAGTAGATGAC
1 GAACCCAATTGAGTAGATGAC
1827564 GAACCCAATTGAGTAGATG
1 GAACCCAATTGAGTAGATG
1827583 TTGCCTTCGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.38, C:0.15, G:0.28, T:0.20
Consensus pattern (21 bp):
GAACCCAATTGAGTAGATGAC
Found at i:1828415 original size:312 final size:304
Alignment explanation
Indices: 1827558--1828657 Score: 1283
Period size: 299 Copynumber: 3.7 Consensus size: 304
1827548 GAATTGAGTA
* * * *
1827558 GATGACGAACCCAATTGAGTAGATGTTGCCTTCGTCTTTGATAATGGTCGAGATTTGGAGGAAGA
1 GATGACGAACCCAATTGAGTAGATGTTTCCTTCGTCTTTGATAATCGTTGAGATTTCGAGGAAGA
** * * * * *
1827623 AGACTTGGCAAGGGAAGTTCTCTTCTT-T-CTTTTTCGTTTTTCCGTGACATTTAGAGGATCAAT
66 AGACTCAGCAATGGAAGTTCTCTTCTTCTCCTTTTTCGTTTCTCCGTAACATTTGGAAGATCAAT
* * *
1827686 GCAAGACTGGTTTCTCGTTTTCTCTGTTTCTGGTTCAGATCCCATTGATTGATCAATATCTGTAA
131 GCAAGACTGGTTTCTCATCTTCTCTGTTTCTGGTTCAGATCCCATTGATTGATCAATACCTGTAA
* * * * *
1827751 C--AA-AGT--TTAAA-TGATTTCGACTTTCTTATGTTAATGAGAATATTAAATATATTAATAAG
196 CAAAATAGTAATGAAATTGATTTCGACTTTGTTGTGTTCATGAGAATCTTAAATATATTAATAAG
*
1827810 AAATAATCATGCATGATGATCTTTATATTTTGAAGT-C--T-A-
261 AAATAATCATGCATGATGATCTCTATATTTTGAAGTACGTTGAC
* * * * * * * * *
1827849 G-TGACGAACCCAGTTGAGAAGATATTTTCTTCATCTTGGATAATCGTTTATATTTCGAAGAAGA
1 GATGACGAACCCAATTGAGTAGATGTTTCCTTCGTCTTTGATAATCGTTGAGATTTCGAGGAAGA
* ** * * *
1827913 AGAGTCAGCAATGGAAGAGCTCTTTCTTCTTCTTTTTCGTTTCTCTGCAACATTTGGAAGATCAA
66 AGACTCAGCAATGGAAGTTCTC-TTCTTCTCCTTTTTCGTTTCTCCGTAACATTTGGAAGATCAA
* * *
1827978 TGCAAGATTGGTTACTCATCTTCTCTGTTTCTGGTTCAGATCCCATTGATTGATCAATATCTGTA
130 TGCAAGACTGGTTTCTCATCTTCTCTGTTTCTGGTTCAGATCCCATTGATTGATCAATACCTGTA
* * * * * ** * *
1828043 ACAAAATATTAATGAAATTGACTTCAAATTTATTGTGTTTGTGAGAATTTTAAATATATTAGTAA
195 ACAAAATAGTAATGAAATTGATTTCGACTTTGTTGTGTTCATGAGAATCTTAAATATATTAATAA
1828108 GAAATAATCATGCATGAT-ACTCTCTATATTTTGAAGTCAAACTGATTGAGTC
260 GAAATAATCATGCATGATGA-TCTCTATATTTTGAAGT---AC-G-TTGA--C
* *
1828160 GATGACGAACCTAATTGAGTAGATGTTTCCTTCGTCTTCGATAATCGTTGAGATTTCGAGGAAGA
1 GATGACGAACCCAATTGAGTAGATGTTTCCTTCGTCTTTGATAATCGTTGAGATTTCGAGGAAGA
* * *
1828225 TGACTCAG-AAGTGGAAGTTCTCTTGCTTCTCCTTTTTCTTTTCTCCCTAACATTTGGAAGATCA
66 AGACTCAGCAA-TGGAAGTTCTCTT-CTTCTCCTTTTTCGTTTCTCCGTAACATTTGGAAGATCA
* * *
1828289 ATGCAAGACTGGTTTCTCATCTTCTCTGCTTCTGGTCCAGATCCCGTTGATTGATCAATACCTGT
129 ATGCAAGACTGGTTTCTCATCTTCTCTGTTTCTGGTTCAGATCCCATTGATTGATCAATACCTGT
* * *
1828354 AACATAATAGTAATGAAATTGATTTCGACTTTGTCGTGTTCTTGAGAATCTTAAATATATTAATA
194 AACAAAATAGTAATGAAATTGATTTCGACTTTGTTGTGTTCATGAGAATCTTAAATATATTAATA
* * *
1828419 AGAAATAATAATGTACGATGATCTCTATATTTTG-A--A-GTT--C
259 AGAAATAATCATGCATGATGATCTCTATATTTTGAAGTACGTTGAC
* *
1828459 GTTGACGAACCCAATTGAGTAGATGTTTCCTTCGTCTTTGACAATCGTTGAGATTTCGAGGAAGA
1 GATGACGAACCCAATTGAGTAGATGTTTCCTTCGTCTTTGATAATCGTTGAGATTTCGAGGAAGA
*
1828524 AGACTCAGCAATGGAAGTGT-TCTTCCTTCTCCTTTTTCGTTTCTCCGTAACATTTGAAAGATCA
66 AGACTCAGCAATGGAAGT-TCTCTT-CTTCTCCTTTTTCGTTTCTCCGTAACATTTGGAAGATCA
* * * * * * *
1828588 GTGCAAGACTGTTTTCCCGTATTCTCTGTTTCTGGTTCAGATCCTACTGATTGATCAATACCTGT
129 ATGCAAGACTGGTTTCTCATCTTCTCTGTTTCTGGTTCAGATCCCATTGATTGATCAATACCTGT
1828653 AACAA
194 AACAA
1828658 GGTCGTATAG
Statistics
Matches: 681, Mismatches: 100, Indels: 48
0.82 0.12 0.06
Matches are distributed among these distances:
290 66 0.10
291 6 0.01
292 1 0.00
293 91 0.13
295 2 0.00
296 2 0.00
298 5 0.01
299 247 0.36
300 3 0.00
303 3 0.00
304 1 0.00
306 1 0.00
307 1 0.00
308 1 0.00
311 6 0.01
312 244 0.36
313 1 0.00
ACGTcount: A:0.28, C:0.16, G:0.18, T:0.38
Consensus pattern (304 bp):
GATGACGAACCCAATTGAGTAGATGTTTCCTTCGTCTTTGATAATCGTTGAGATTTCGAGGAAGA
AGACTCAGCAATGGAAGTTCTCTTCTTCTCCTTTTTCGTTTCTCCGTAACATTTGGAAGATCAAT
GCAAGACTGGTTTCTCATCTTCTCTGTTTCTGGTTCAGATCCCATTGATTGATCAATACCTGTAA
CAAAATAGTAATGAAATTGATTTCGACTTTGTTGTGTTCATGAGAATCTTAAATATATTAATAAG
AAATAATCATGCATGATGATCTCTATATTTTGAAGTACGTTGAC
Found at i:1828507 original size:611 final size:604
Alignment explanation
Indices: 1827314--1828657 Score: 1650
Period size: 611 Copynumber: 2.2 Consensus size: 604
1827304 AGATCTGGAT
** * *
1827314 ATGGAAGTTCTCTTCTTTCTCCTTTTTCATTTCT-TCGTAACATTTGAAAGATCAGTGCAAGACT
1 ATGGAAGAGCTCTTCCTTCTCCTTTTTCGTTTCTCT-GTAACATTTGAAAGATCAGTGCAAGACT
* * * *
1827378 GATTTTTTATCTCCTCTGTTGT-TGGTTCAGATCCCATCGATTGATCAATACCTGTAACAAAATA
65 GATTTCTCATCTTCTCTGTT-TCTGGTTCAGATCCCATTGATTGATCAATACCTGTAACAAAATA
* * * * *
1827442 GTACTAAATTAATTTCGAGTTTGTTGAGTTCATGAATATCTTTAATACATTAATAAGAAATAATC
129 GTAATAAATTAACTTCAAATTTATTGAGTTCATGAATATCTTTAATACATTAATAAGAAATAATC
1827507 ATGCATGATGATCTCTATATTTTAATGTCTGGTGATGAACCGAATTGAGTAGATGACGAACCCAA
194 ATGCATGATGATCTCTATATTTTAATGTC----GA-GAACCGAATTGAGTAGATGACGAACCCAA
* * * **
1827572 TTGAGTAGATGTTGCCTTCGTCTTTGATAATGGTCGAGATTTGGAGGAAGAAGACTTGGCAAGGG
254 TTGAGTAGATGTTGCCTTCGTCTTCGATAATCGTCGAGATTTCGAGGAAGAAGACTCAGCAAGGG
* * *
1827637 AAGTTCTCTTCTTTCTTTTTCGTTTTTCCGTGACATTTAGAGGATCAATGCAAGACTGGTTTCTC
319 AAGTTCTCTTCTTTCTTTTTCGTTTTTCCCTAACATTTAGAAGATCAATGCAAGACTGGTTTCTC
* * * * * *
1827702 GTTTTCTCTGTTTCTGGTTCAGATCCCATTGATTGATCAATATCTGTAACAAAGTTTAAATGATT
384 ATCTTCTCTGCTTCTGGTCCAGATCCCATTGATTGATCAATACCTGTAACAAAGTTGAAATGATT
* * *
1827767 TCGACTTTCTTATGTTAATGAGAATATTAAATATATTAATAAGAAATAATCATGCATGATGATCT
449 TCGACTTTCTCATGTTAATGAGAATATTAAATATATTAATAAGAAATAATAATGCACGATGATCT
* * * *
1827832 TTATATTTTGAAGTCTAGTGACGAACCCAGTTGAGAAGATATTTTCTTCATCTTGGATAATCGTT
514 CTATATTTTGAAGTCTAGTGACGAACCCAATTGAGAAGATATTTCCTTCATCTTGGACAATCGTT
* * *
1827897 TATATTTCGAAGAAGAAGAGTCAGCA
579 GAGATTTCGAAGAAGAAGACTCAGCA
* * * * * *
1827923 ATGGAAGAGCTCTTTCTTCTTCTTTTTCGTTTCTCTGCAACATTTGGAAGATCAATGCAAGATTG
1 ATGGAAGAGCTCTTCCTTCTCCTTTTTCGTTTCTCTGTAACATTTGAAAGATCAGTGCAAGACTG
* * * *
1827988 GTTACTCATCTTCTCTGTTTCTGGTTCAGATCCCATTGATTGATCAATATCTGTAACAAAATATT
66 ATTTCTCATCTTCTCTGTTTCTGGTTCAGATCCCATTGATTGATCAATACCTGTAACAAAATAGT
* * ** * *
1828053 AATGAAATTGACTTCAAATTTATTGTGTTTGTGAGA-AT-TTTAAATATATTAGTAAGAAATAAT
131 AAT-AAATTAACTTCAAATTTATTGAGTTCATGA-ATATCTTT-AATACATTAATAAGAAATAAT
* * *
1828116 CATGCATGAT-ACTCTCTATATTTTGAA-GTC-A-AACTG-ATTGAGTCGATGACGAACCTAATT
193 CATGCATGATGA-TCTCTATATTTT-AATGTCGAGAACCGAATTGAGTAGATGACGAACCCAATT
* * *
1828176 GAGTAGATGTTTCCTTCGTCTTCGATAATCGTTGAGATTTCGAGGAAGATGACTCAG-AAGTGGA
256 GAGTAGATGTTGCCTTCGTCTTCGATAATCGTCGAGATTTCGAGGAAGAAGACTCAGCAAG-GGA
*
1828240 AGTTCTCTTGCTTCTCCTTTTTC-TTTTCTCCCTAACATTTGGAAGATCAATGCAAGACTGGTTT
320 AGTTCTCTT-CTT-T-CTTTTTCGTTTT-TCCCTAACATTTAGAAGATCAATGCAAGACTGGTTT
*
1828304 CTCATCTTCTCTGCTTCTGGTCCAGATCCCGTTGATTGATCAATACCTGTAACATAATAGTAATG
381 CTCATCTTCTCTGCTTCTGGTCCAGATCCCATTGATTGATCAATACCTGTAAC--AA-AGT--TG
* * ** * *
1828369 AAATTGATTTCGACTTTGTCGTGTTCTTGAGAATCTTAAATATATTAATAAGAAATAATAATGTA
441 AAA-TGATTTCGACTTTCTCATGTTAATGAGAATATTAAATATATTAATAAGAAATAATAATGCA
* * * * *
1828434 CGATGATCTCTATATTTTGAAGT-TCGTTGACGAACCCAATTGAGTAGATGTTTCCTTCGTCTTT
505 CGATGATCTCTATATTTTGAAGTCTAG-TGACGAACCCAATTGAGAAGATATTTCCTTCATCTTG
*
1828498 GACAATCGTTGAGATTTCGAGGAAGAAGACTCAGCA
569 GACAATCGTTGAGATTTCGAAGAAGAAGACTCAGCA
* * *
1828534 ATGGAAGTGTTCTTCCTTCTCCTTTTTCGTTTCTCCGTAACATTTGAAAGATCAGTGCAAGACTG
1 ATGGAAGAGCTCTTCCTTCTCCTTTTTCGTTTCTCTGTAACATTTGAAAGATCAGTGCAAGACTG
* * * * * *
1828599 TTTTCCCGTATTCTCTGTTTCTGGTTCAGATCCTACTGATTGATCAATACCTGTAACAA
66 ATTTCTCATCTTCTCTGTTTCTGGTTCAGATCCCATTGATTGATCAATACCTGTAACAA
1828658 GGTCGTATAG
Statistics
Matches: 626, Mismatches: 90, Indels: 36
0.83 0.12 0.05
Matches are distributed among these distances:
601 3 0.00
602 83 0.13
603 7 0.01
604 5 0.01
605 87 0.14
607 2 0.00
608 4 0.01
609 114 0.18
610 75 0.12
611 246 0.39
ACGTcount: A:0.28, C:0.16, G:0.18, T:0.38
Consensus pattern (604 bp):
ATGGAAGAGCTCTTCCTTCTCCTTTTTCGTTTCTCTGTAACATTTGAAAGATCAGTGCAAGACTG
ATTTCTCATCTTCTCTGTTTCTGGTTCAGATCCCATTGATTGATCAATACCTGTAACAAAATAGT
AATAAATTAACTTCAAATTTATTGAGTTCATGAATATCTTTAATACATTAATAAGAAATAATCAT
GCATGATGATCTCTATATTTTAATGTCGAGAACCGAATTGAGTAGATGACGAACCCAATTGAGTA
GATGTTGCCTTCGTCTTCGATAATCGTCGAGATTTCGAGGAAGAAGACTCAGCAAGGGAAGTTCT
CTTCTTTCTTTTTCGTTTTTCCCTAACATTTAGAAGATCAATGCAAGACTGGTTTCTCATCTTCT
CTGCTTCTGGTCCAGATCCCATTGATTGATCAATACCTGTAACAAAGTTGAAATGATTTCGACTT
TCTCATGTTAATGAGAATATTAAATATATTAATAAGAAATAATAATGCACGATGATCTCTATATT
TTGAAGTCTAGTGACGAACCCAATTGAGAAGATATTTCCTTCATCTTGGACAATCGTTGAGATTT
CGAAGAAGAAGACTCAGCA
Found at i:1839444 original size:14 final size:14
Alignment explanation
Indices: 1839425--1839458 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
1839415 CGATGACGGC
1839425 AGCTATAGCTTCAA
1 AGCTATAGCTTCAA
1839439 AGCTATAGCTTCAA
1 AGCTATAGCTTCAA
1839453 AGCTAT
1 AGCTAT
1839459 GAAAATAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.35, C:0.21, G:0.15, T:0.29
Consensus pattern (14 bp):
AGCTATAGCTTCAA
Found at i:1843277 original size:29 final size:31
Alignment explanation
Indices: 1843244--1843304 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
1843234 ATATTTTTAT
1843244 TCAATGGAAACCAT-A-ATAGGATTATATAA
1 TCAATGGAAACCATAATATAGGATTATATAA
1843273 TCAATGGAAACCATAATATAGGATTATATAA
1 TCAATGGAAACCATAATATAGGATTATATAA
1843304 T
1 T
1843305 AAAGATAAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 14 0.47
30 1 0.03
31 15 0.50
ACGTcount: A:0.48, C:0.10, G:0.13, T:0.30
Consensus pattern (31 bp):
TCAATGGAAACCATAATATAGGATTATATAA
Found at i:1847279 original size:223 final size:223
Alignment explanation
Indices: 1846885--1847331 Score: 828
Period size: 223 Copynumber: 2.0 Consensus size: 223
1846875 CTGCATCGTT
1846885 GTGCATTTCCACTTTTGCTCAATTTCACTAACATGGATTCCCAAAGCACCAGATTACTTGAACCA
1 GTGCATTTCCACTTTTGCTCAATTTCACTAACATGGATTCCCAAAGCACCAGATTACTTGAACCA
*
1846950 GAAAGGAAACCAGGCATGAATGTATAAGGAATGATTCAATCTTTTCCATTTTAACTGAACCATAA
66 GAAAGGAAACCAGGCATGAATGTATAAGGAATGATTCAATCTTTTCCATTTCAACTGAACCATAA
1847015 GTGCTTGGCCATGACCGCTGTGGAACCAGCCTACTAGCCTCTGCAAAGG-AAT-CCCCATAGGTA
131 GTGCTTGGCCATGACCGCTGTGGAACCAGCCTACTAGCCTCTGC-AAGGAAATCCCCCATAGGTA
1847078 ACCCCTTCTATATTCCCCACAGCCCAATC
195 ACCCCTTCTATATTCCCCACAGCCCAATC
1847107 GTGCATTTCCACTTTTGCTCAATTTCACTAACATGGATTCCCAAAGCACCATGATTACTTGAACC
1 GTGCATTTCCACTTTTGCTCAATTTCACTAACATGGATTCCCAAAGCACCA-GATTACTTGAACC
1847172 AGAAAGGAAACCAGGCATGAATGTATAAGGAATGATTCAATCTTTTCCATTTCAACTGAACCATA
65 AGAAAGGAAACCAGGCATGAATGTATAAGGAATGATTCAATCTTTTCCATTTCAACTGAACCATA
1847237 AGTGCTTGGCCATGACCGCTGTGGGAACCAGCCTAC-AGCCTCTGCAAGGAAATCCCCCCATAGG
130 AGTGCTTGGCCATGACCGCTGT-GGAACCAGCCTACTAGCCTCTGCAAGGAAAT-CCCCCATAGG
1847301 TAACCCCTTCTATATTCCCCACAGCCCAATC
193 TAACCCCTTCTATATTCCCCACAGCCCAATC
1847332 TTTGGTCCAA
Statistics
Matches: 219, Mismatches: 1, Indels: 7
0.96 0.00 0.03
Matches are distributed among these distances:
222 55 0.25
223 111 0.51
224 13 0.06
225 40 0.18
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (223 bp):
GTGCATTTCCACTTTTGCTCAATTTCACTAACATGGATTCCCAAAGCACCAGATTACTTGAACCA
GAAAGGAAACCAGGCATGAATGTATAAGGAATGATTCAATCTTTTCCATTTCAACTGAACCATAA
GTGCTTGGCCATGACCGCTGTGGAACCAGCCTACTAGCCTCTGCAAGGAAATCCCCCATAGGTAA
CCCCTTCTATATTCCCCACAGCCCAATC
Found at i:1863036 original size:40 final size:40
Alignment explanation
Indices: 1862985--1863064 Score: 124
Period size: 40 Copynumber: 2.0 Consensus size: 40
1862975 TTCTTTATTA
* *
1862985 TTAGGCTACAATTATTTCCATAGAGAAAATAGAGTACGTT
1 TTAGGCCACAATTATTTCCATAGAGAAAACAGAGTACGTT
* *
1863025 TTAGGCCACAATTATTTCTATGGAGAAAACAGAGTACGTT
1 TTAGGCCACAATTATTTCCATAGAGAAAACAGAGTACGTT
1863065 GACCCATTCA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.31
Consensus pattern (40 bp):
TTAGGCCACAATTATTTCCATAGAGAAAACAGAGTACGTT
Found at i:1864660 original size:2 final size:2
Alignment explanation
Indices: 1864653--1864682 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1864643 GCCTTGTACT
1864653 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
1864683 AAAGCTGAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1872712 original size:18 final size:20
Alignment explanation
Indices: 1872670--1872714 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 20
1872660 AAAAATAATC
*
1872670 AATTTTAATATTAATTTTTT
1 AATTTTAATATTAATTTTTA
*
1872690 TATTTTAA-A-TAATTTTTA
1 AATTTTAATATTAATTTTTA
1872708 AATTTTA
1 AATTTTA
1872715 TAAGTCTGGC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 14 0.64
19 1 0.05
20 7 0.32
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
AATTTTAATATTAATTTTTA
Found at i:1876872 original size:3 final size:3
Alignment explanation
Indices: 1876864--1876888 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1876854 TTTGACCCTG
1876864 CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT C
1876889 CTCTCTTAGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:1878250 original size:18 final size:18
Alignment explanation
Indices: 1878227--1878261 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
1878217 TAGTGATTTT
1878227 ATAATTTAATTTATATTA
1 ATAATTTAATTTATATTA
1878245 ATAATTTAATTTATATT
1 ATAATTTAATTTATATT
1878262 CTTAAAATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
ATAATTTAATTTATATTA
Found at i:1880402 original size:40 final size:40
Alignment explanation
Indices: 1880356--1880436 Score: 135
Period size: 40 Copynumber: 2.0 Consensus size: 40
1880346 TATTGATACA
* *
1880356 GTGATGTTGTGTTTTACAGTACTTATATATTACTGTCACT
1 GTGATGTTGTGTTTTACAATACTTATATATTACTGACACT
*
1880396 GTGATGTTGTGTTTTACAATACTTGTATATTACTGACACT
1 GTGATGTTGTGTTTTACAATACTTATATATTACTGACACT
1880436 G
1 G
1880437 GCACTGAAAG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.23, C:0.12, G:0.19, T:0.46
Consensus pattern (40 bp):
GTGATGTTGTGTTTTACAATACTTATATATTACTGACACT
Found at i:1882140 original size:2 final size:2
Alignment explanation
Indices: 1882133--1882184 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
1882123 GTCCACCAAT
1882133 TA TA 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 TA TA
1882175 TA TA TA TA TA
1 TA TA TA TA TA
1882185 ATGTCCCTAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1890276 original size:6 final size:6
Alignment explanation
Indices: 1890266--1890350 Score: 143
Period size: 6 Copynumber: 14.2 Consensus size: 6
1890256 TTCAGACACT
* * *
1890266 ACTGGT ACTGGT ATTGGC ACTGGC ACTGGC ACTGGC ACTGGC ACTGGC
1 ACTGGC ACTGGC ACTGGC ACTGGC ACTGGC ACTGGC ACTGGC ACTGGC
1890314 ACTGGC ACTGGC ACTGGC ACTGGC ACTGGC ACTGGC A
1 ACTGGC ACTGGC ACTGGC ACTGGC ACTGGC ACTGGC A
1890351 GCAGTATTTT
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 76 1.00
ACGTcount: A:0.18, C:0.29, G:0.33, T:0.20
Consensus pattern (6 bp):
ACTGGC
Found at i:1903251 original size:15 final size:16
Alignment explanation
Indices: 1903231--1903263 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1903221 ACCTGTCTGT
1903231 TCACAATG-GGTGTTG
1 TCACAATGAGGTGTTG
*
1903246 TCACAATGATGTGTTG
1 TCACAATGAGGTGTTG
1903262 TC
1 TC
1903264 TCCATTTGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.21, C:0.15, G:0.27, T:0.36
Consensus pattern (16 bp):
TCACAATGAGGTGTTG
Found at i:1916516 original size:70 final size:70
Alignment explanation
Indices: 1916403--1916544 Score: 275
Period size: 70 Copynumber: 2.0 Consensus size: 70
1916393 TATTCCTAGA
*
1916403 GATATGGCCACATATCTGATAAAGTTACTGCAATTTGAAGAAATTTGTTCATATAATTTGGTACT
1 GATATGGCCACATATCTGATAAAGTTACTGCAATTTGAAGAAATTTGTTCATAAAATTTGGTACT
1916468 ATGGC
66 ATGGC
1916473 GATATGGCCACATATCTGATAAAGTTACTGCAATTTGAAGAAATTTGTTCATAAAATTTGGTACT
1 GATATGGCCACATATCTGATAAAGTTACTGCAATTTGAAGAAATTTGTTCATAAAATTTGGTACT
1916538 ATGGC
66 ATGGC
1916543 GA
1 GA
1916545 AAGCAAGACA
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
70 71 1.00
ACGTcount: A:0.34, C:0.13, G:0.19, T:0.35
Consensus pattern (70 bp):
GATATGGCCACATATCTGATAAAGTTACTGCAATTTGAAGAAATTTGTTCATAAAATTTGGTACT
ATGGC
Found at i:1919263 original size:28 final size:29
Alignment explanation
Indices: 1919216--1919273 Score: 75
Period size: 28 Copynumber: 2.0 Consensus size: 29
1919206 AAAATAATAA
*
1919216 TTTAAAAAAAAACTTCAAATC-CTAAAAT
1 TTTAAAAAAAAACTCCAAATCTCTAAAAT
*
1919244 TTTAAAAAAAAA-TCCAAAATCTTTAAAAT
1 TTTAAAAAAAAACTCC-AAATCTCTAAAAT
1919273 T
1 T
1919274 CTAATTCTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 2 0.08
28 17 0.65
29 7 0.27
ACGTcount: A:0.57, C:0.12, G:0.00, T:0.31
Consensus pattern (29 bp):
TTTAAAAAAAAACTCCAAATCTCTAAAAT
Found at i:1919271 original size:20 final size:21
Alignment explanation
Indices: 1919232--1919271 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
1919222 AAAAAACTTC
1919232 AAATCCTAAAATTTTAAAAAA
1 AAATCCTAAAATTTTAAAAAA
1919253 AAATCC-AAAATCTTTAAAA
1 AAATCCTAAAAT-TTTAAAA
1919272 TTCTAATTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (21 bp):
AAATCCTAAAATTTTAAAAAA
Found at i:1927159 original size:2 final size:2
Alignment explanation
Indices: 1927139--1927188 Score: 66
Period size: 2 Copynumber: 25.5 Consensus size: 2
1927129 TCATCCTATC
* *
1927139 AT AT AT -T AT AC AT AA 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
*
1927180 AT AG AT AT A
1 AT AT AT AT A
1927189 AAGAAAAATT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (2 bp):
AT
Found at i:1929934 original size:2 final size:2
Alignment explanation
Indices: 1929927--1930021 Score: 138
Period size: 2 Copynumber: 47.5 Consensus size: 2
1929917 GCAGAAAAGG
1929927 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
* * *
1929969 AT AT AT AT AT AT AT AT AG A- AA AGG AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT
*
1930011 AT AC AT AT AT A
1 AT AT AT AT AT A
1930022 AGCATTGACA
Statistics
Matches: 86, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
1 1 0.01
2 84 0.98
3 1 0.01
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.44
Consensus pattern (2 bp):
AT
Found at i:1930803 original size:12 final size:12
Alignment explanation
Indices: 1930788--1930870 Score: 53
Period size: 12 Copynumber: 6.9 Consensus size: 12
1930778 TAATCATAAA
*
1930788 AATATTAATTAT
1 AATATAAATTAT
1930800 AATATAAATTAT
1 AATATAAATTAT
* *
1930812 AA-A-ATATCAT
1 AATATAAATTAT
* *
1930822 AAAGATAGATTTAT
1 -AATATA-AATTAT
*
1930836 AATGTAAATTAT
1 AATATAAATTAT
* *
1930848 AATATTAATTAA
1 AATATAAATTAT
*
1930860 AATATATATTA
1 AATATAAATTA
1930871 ATATTTGTGT
Statistics
Matches: 53, Mismatches: 14, Indels: 8
0.71 0.19 0.11
Matches are distributed among these distances:
10 5 0.09
11 3 0.06
12 37 0.70
13 5 0.09
14 3 0.06
ACGTcount: A:0.54, C:0.01, G:0.04, T:0.41
Consensus pattern (12 bp):
AATATAAATTAT
Found at i:1930844 original size:36 final size:38
Alignment explanation
Indices: 1930772--1930849 Score: 106
Period size: 36 Copynumber: 2.1 Consensus size: 38
1930762 AATGAGAAGA
*
1930772 ATAAAATAATCATAAAAATATTAATTATAATATAAATT
1 ATAAAATAATCATAAAAATATGAATTATAATATAAATT
* * *
1930810 ATAAAAT-ATCATAAAGATA-GATTTATAATGTAAATT
1 ATAAAATAATCATAAAAATATGAATTATAATATAAATT
1930846 ATAA
1 ATAA
1930850 TATTAATTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
36 18 0.50
37 11 0.31
38 7 0.19
ACGTcount: A:0.58, C:0.03, G:0.04, T:0.36
Consensus pattern (38 bp):
ATAAAATAATCATAAAAATATGAATTATAATATAAATT
Found at i:1931032 original size:13 final size:13
Alignment explanation
Indices: 1931014--1931040 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1931004 ATAAAATGAT
1931014 ATGTTGAGATGTG
1 ATGTTGAGATGTG
1931027 ATGTTGAGATGTG
1 ATGTTGAGATGTG
1931040 A
1 A
1931041 CATTAAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.26, C:0.00, G:0.37, T:0.37
Consensus pattern (13 bp):
ATGTTGAGATGTG
Found at i:1935855 original size:2 final size:2
Alignment explanation
Indices: 1935848--1935884 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1935838 AATCATAATC
1935848 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 A
1935885 ATCTTATAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1937665 original size:14 final size:14
Alignment explanation
Indices: 1937646--1937672 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1937636 TATGACCATC
1937646 GTTCGGAGCGTGGT
1 GTTCGGAGCGTGGT
1937660 GTTCGGAGCGTGG
1 GTTCGGAGCGTGG
1937673 AGACGACGCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.15, G:0.52, T:0.26
Consensus pattern (14 bp):
GTTCGGAGCGTGGT
Found at i:1943844 original size:127 final size:127
Alignment explanation
Indices: 1942853--1943835 Score: 1619
Period size: 127 Copynumber: 7.7 Consensus size: 127
1942843 GTACTATTCA
*
1942853 CGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTTAGAGAATATGTTATCATTACCC
1 CGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTACCC
*** * *
1942918 TATTATGTCACTTATGTCCCCCGGGAACTATTCATATCAATACCTATTATTCCTTAGGGGAT
66 TATTATGTCACTTATGTCCCCCGGGAACTAAGGATGTCAATACCTATTATTCCTTAGGGGAC
* * * * *
1942980 CGTGAAGGCGCTTTCCCGGGGGTGCGCATTCCATTATTTTGTCAGAGAATATTTTATCATTACCT
1 CGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTACCC
* *** *
1943045 TATTATGTCACTTATGTCCCCCTGGAACTATTCATGTCAATACATATTATTCCTTAGGGGAC
66 TATTATGTCACTTATGTCCCCCGGGAACTAAGGATGTCAATACCTATTATTCCTTAGGGGAC
* *
1943107 CATGAAGGCGCGTTCCCGGGGG-GCGTCTTCCATTATTTTGTCAGAGAATATGTTATCATTACCC
1 CGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTACCC
* *
1943171 TATTATGTCACTTATGTCCCCCGAGAACTAAGGATGTCAATACTTATTATTCCTTAGGGGAC
66 TATTATGTCACTTATGTCCCCCGGGAACTAAGGATGTCAATACCTATTATTCCTTAGGGGAC
*
1943233 CGTGAAGGCGCGTTCCCAGGGGG-GCACCTTCCATTATTTTGTCAGAGAATATGTTATCATTACC
1 CGTGAAGGCGCGTTCCC-GGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTACC
*
1943297 CTATTATGTCACTTATGTCCCCCGGGAACTAAGGATGTCAATACCTATTATTCCTTAAGGGAC
65 CTATTATGTCACTTATGTCCCCCGGGAACTAAGGATGTCAATACCTATTATTCCTTAGGGGAC
*
1943360 CGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGATAATATGTTATCATTACCC
1 CGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTACCC
*
1943425 TATTATGTCACTTATGTCCCCCGGGAACTAAGGATGTCAATACCTATTATTCATTAGGGGAC
66 TATTATGTCACTTATGTCCCCCGGGAACTAAGGATGTCAATACCTATTATTCCTTAGGGGAC
*
1943487 CGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCTATTATTTTGTCAGAGAATATGTTATCATTACCC
1 CGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTACCC
1943552 TATTATGTCACTTATGTCCCCCGGGAACTAAGGATGTCAATACCTATTATTCCTTAGGGGAC
66 TATTATGTCACTTATGTCCCCCGGGAACTAAGGATGTCAATACCTATTATTCCTTAGGGGAC
**
1943614 CGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTATTC
1 CGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTACCC
* * *
1943679 TATTATGTCACTTATGTCCCCCGGGAACTAAGGATGTCAGTACATATTATTCCTTATGGGAC
66 TATTATGTCACTTATGTCCCCCGGGAACTAAGGATGTCAATACCTATTATTCCTTAGGGGAC
* ** * *
1943741 CATGAAGGCGCGTTATCGGGGGGGCGCCTTCCATTATTTTGTCAGAGAATATATTATCATTACCC
1 CGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTACCC
*
1943806 TATTAGGTCACTTATGTCCCCCGGGAACTA
66 TATTATGTCACTTATGTCCCCCGGGAACTA
1943836 TTCATGTCAC
Statistics
Matches: 805, Mismatches: 49, Indels: 4
0.94 0.06 0.00
Matches are distributed among these distances:
126 115 0.14
127 690 0.86
ACGTcount: A:0.23, C:0.23, G:0.22, T:0.33
Consensus pattern (127 bp):
CGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTACCC
TATTATGTCACTTATGTCCCCCGGGAACTAAGGATGTCAATACCTATTATTCCTTAGGGGAC
Found at i:1944024 original size:23 final size:23
Alignment explanation
Indices: 1943976--1944025 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
1943966 TGAAGTTTGA
* * *
1943976 ATAAATTAGATAAAATGTTATGG
1 ATAAATTAAATAAAATGTGAAGG
1943999 ATAAATTAAAT-AAATGTGAAGTG
1 ATAAATTAAATAAAATGTGAAG-G
1944022 ATAA
1 ATAA
1944026 GTTTATTGTG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 8 0.35
23 15 0.65
ACGTcount: A:0.52, C:0.00, G:0.16, T:0.32
Consensus pattern (23 bp):
ATAAATTAAATAAAATGTGAAGG
Found at i:1944286 original size:34 final size:34
Alignment explanation
Indices: 1944248--1944345 Score: 151
Period size: 34 Copynumber: 2.9 Consensus size: 34
1944238 TTTAATGTTG
* *
1944248 AATTTCGAATACTATAATTTATATTTTAAATTTA
1 AATTTTGAATACTATAATTTGTATTTTAAATTTA
* * *
1944282 AATTTTGAATAATATTATTTGTATTTTAATTTTA
1 AATTTTGAATACTATAATTTGTATTTTAAATTTA
1944316 AATTTTGAATACTATAATTTGTATTTTAAA
1 AATTTTGAATACTATAATTTGTATTTTAAA
1944346 AACATTTATT
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 56 1.00
ACGTcount: A:0.39, C:0.03, G:0.05, T:0.53
Consensus pattern (34 bp):
AATTTTGAATACTATAATTTGTATTTTAAATTTA
Found at i:1944901 original size:21 final size:20
Alignment explanation
Indices: 1944870--1944938 Score: 84
Period size: 21 Copynumber: 3.3 Consensus size: 20
1944860 GTATAAAACT
* *
1944870 CTGCAGGCTAGGCATGTAAC
1 CTGCGGGCTAGGAATGTAAC
*
1944890 CTGGCGGGCTAGGAATATAACC
1 CT-GCGGGCTAGGAATGTAA-C
1944912 CTGCGGGCTAGGAATGTAACC
1 CTGCGGGCTAGGAATGTAA-C
1944933 CTGCGG
1 CTGCGG
1944939 AGATGACATA
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
20 2 0.05
21 38 0.88
22 3 0.07
ACGTcount: A:0.23, C:0.25, G:0.33, T:0.19
Consensus pattern (20 bp):
CTGCGGGCTAGGAATGTAAC
Found at i:1944962 original size:42 final size:42
Alignment explanation
Indices: 1944916--1945013 Score: 106
Period size: 42 Copynumber: 2.3 Consensus size: 42
1944906 ATAACCCTGC
* * *
1944916 GGGCTAGGAATGTAACCCTGCGGAGATGACATATGAACTGGT
1 GGGCTAGGCATGTAACCCTGAGGAGATGACATATGAACTGGA
* * * * * *
1944958 GGGCTTGGCATATACCCCTGAGGAGATGGCATCTGAAGTGGA
1 GGGCTAGGCATGTAACCCTGAGGAGATGACATATGAACTGGA
*
1945000 GGGCTGGGCATGTA
1 GGGCTAGGCATGTA
1945014 CCATTGTGGC
Statistics
Matches: 45, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.24, C:0.17, G:0.37, T:0.21
Consensus pattern (42 bp):
GGGCTAGGCATGTAACCCTGAGGAGATGACATATGAACTGGA
Found at i:1946612 original size:25 final size:23
Alignment explanation
Indices: 1946566--1946623 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 23
1946556 ATAAATTCAT
1946566 AATAAAT-TTAAATTAAACATAA
1 AATAAATATTAAATTAAACATAA
**
1946588 CAATAAATATTAACATTAATTATAA
1 -AATAAATATTAA-ATTAAACATAA
*
1946613 AAAAAATATTA
1 AATAAATATTA
1946624 TCATATCGCT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
23 7 0.23
24 14 0.47
25 9 0.30
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (23 bp):
AATAAATATTAAATTAAACATAA
Found at i:1946786 original size:30 final size:30
Alignment explanation
Indices: 1946720--1946815 Score: 90
Period size: 30 Copynumber: 3.3 Consensus size: 30
1946710 TAATTAGCAC
* * *
1946720 AAAAAATAATTA-ATTAATA-AATTTAAAT
1 AAAAAATAATTATATAAATATTATTTTAAT
*
1946748 AAATAATAATTATATAAATATTATTTTAAT
1 AAAAAATAATTATATAAATATTATTTTAAT
* * *
1946778 AAAAAATAA-TATTTATATAATTATATTAAT
1 AAAAAATAATTATATAAAT-ATTATTTTAAT
*
1946808 ATAAAATA
1 AAAAAATA
1946816 TAATAACTAT
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
28 11 0.20
29 13 0.23
30 32 0.57
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (30 bp):
AAAAAATAATTATATAAATATTATTTTAAT
Found at i:1947402 original size:21 final size:21
Alignment explanation
Indices: 1947373--1947414 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1947363 GTAAAAAAAA
* *
1947373 ATACTTAAAAAATTATTATTT
1 ATACCTAAAAAATTAATATTT
*
1947394 ATACCTAAAATATTAATATTT
1 ATACCTAAAAAATTAATATTT
1947415 TTTAACATAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (21 bp):
ATACCTAAAAAATTAATATTT
Found at i:1950212 original size:3 final size:3
Alignment explanation
Indices: 1950204--1950233 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
1950194 ACACACACAC
1950204 ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA
1 ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA
1950234 TTTTAGGAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.33, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:1951800 original size:31 final size:32
Alignment explanation
Indices: 1951741--1951811 Score: 90
Period size: 31 Copynumber: 2.2 Consensus size: 32
1951731 AAATAATACG
* *
1951741 TCATCATTTTAAATGTTGCGGCACATGTCACA
1 TCATCATATTAAATGTTGCGACACATGTCACA
* * *
1951773 TTATCATATTAAATGTT-TGACACATGTCACG
1 TCATCATATTAAATGTTGCGACACATGTCACA
1951804 TCATCATA
1 TCATCATA
1951812 CAATTAAATG
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
31 18 0.55
32 15 0.45
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.37
Consensus pattern (32 bp):
TCATCATATTAAATGTTGCGACACATGTCACA
Found at i:1952747 original size:6 final size:6
Alignment explanation
Indices: 1952736--1952762 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
1952726 AGGACTAAAC
1952736 TATAGT TATAGT TATAGT TATAGT TAT
1 TATAGT TATAGT TATAGT TATAGT TAT
1952763 GTTTAGGAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (6 bp):
TATAGT
Found at i:1953823 original size:27 final size:27
Alignment explanation
Indices: 1953769--1953828 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
1953759 GGTCAATCCG
* * *
1953769 ACCCGACCCAAAAATTTTACATCATTC
1 ACCCGACCCAAAAAATATACACCATTC
* *
1953796 ACCCGACCCAAAAAATATATACCCTTC
1 ACCCGACCCAAAAAATATACACCATTC
1953823 ACCCGA
1 ACCCGA
1953829 TCAGAACCTA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.38, C:0.37, G:0.05, T:0.20
Consensus pattern (27 bp):
ACCCGACCCAAAAAATATACACCATTC
Found at i:1961627 original size:69 final size:71
Alignment explanation
Indices: 1961536--1961671 Score: 170
Period size: 72 Copynumber: 1.9 Consensus size: 71
1961526 TACAGTGCGT
* * *
1961536 TTTACTGATAAACGCCACTATAGAT-GA-CTATTGCGACGTTTTTTAA-AAAACGCCACTATTAT
1 TTTACTGATAAACGCCACTATAGATGGATCTATTGCGACGTTTGTCAAGAAAACACCACTATTAT
1961598 TGAGGC
66 TGAGGC
* * * * *
1961604 TTTATTGATAAAACGTCATTATAGATGGATTTATTGCGGCGTTTGTCAAGAAAACACCACTATTA
1 TTTACTGAT-AAACGCCACTATAGATGGATCTATTGCGACGTTTGTCAAGAAAACACCACTATTA
1961669 TTG
65 TTG
1961672 CCCCAAAATC
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
68 8 0.14
69 14 0.25
70 2 0.04
71 15 0.27
72 17 0.30
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Consensus pattern (71 bp):
TTTACTGATAAACGCCACTATAGATGGATCTATTGCGACGTTTGTCAAGAAAACACCACTATTAT
TGAGGC
Found at i:1963252 original size:17 final size:15
Alignment explanation
Indices: 1963220--1963263 Score: 52
Period size: 17 Copynumber: 2.7 Consensus size: 15
1963210 ATATATTTGT
1963220 TTATAATTATAATTTTA
1 TTATAATTAT--TTTTA
1963237 TTCATACATTATTTTTA
1 TT-ATA-ATTATTTTTA
1963254 TTATAATTAT
1 TTATAATTAT
1963264 ATAAATATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
15 5 0.20
16 3 0.12
17 9 0.36
18 3 0.12
19 5 0.20
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (15 bp):
TTATAATTATTTTTA
Found at i:1965966 original size:21 final size:24
Alignment explanation
Indices: 1965931--1965980 Score: 79
Period size: 23 Copynumber: 2.2 Consensus size: 24
1965921 AATAGAGTAA
1965931 ATTAAAATATAGAT-AA-AAATAT
1 ATTAAAATATAGATAAATAAATAT
1965953 ATTAAAAT-TAGATAAATAAATAT
1 ATTAAAATATAGATAAATAAATAT
1965976 ATTAA
1 ATTAA
1965981 TTTTTTTGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
21 5 0.19
22 10 0.38
23 11 0.42
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (24 bp):
ATTAAAATATAGATAAATAAATAT
Found at i:1970595 original size:12 final size:12
Alignment explanation
Indices: 1970580--1970625 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
1970570 CGGTTTTTTT
*
1970580 ACCGGATAAAAA
1 ACCGGTTAAAAA
1970592 ACCGGTTTGAAAAAA
1 ACCGG-TT--AAAAA
1970607 ACCGGTTAAAAA
1 ACCGGTTAAAAA
1970619 ACCGGTT
1 ACCGGTT
1970626 TTTATCCGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
12 17 0.57
13 1 0.03
14 2 0.07
15 10 0.33
ACGTcount: A:0.46, C:0.17, G:0.20, T:0.17
Consensus pattern (12 bp):
ACCGGTTAAAAA
Found at i:1970607 original size:15 final size:13
Alignment explanation
Indices: 1970586--1970626 Score: 57
Period size: 12 Copynumber: 3.1 Consensus size: 13
1970576 TTTTACCGGA
1970586 TAAAAAACCGGTT
1 TAAAAAACCGGTT
1970599 TGAAAAAAACCGG-T
1 T--AAAAAACCGGTT
1970613 TAAAAAACCGGTT
1 TAAAAAACCGGTT
1970626 T
1 T
1970627 TTATCCGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 10 0.40
13 3 0.12
14 2 0.08
15 10 0.40
ACGTcount: A:0.46, C:0.15, G:0.17, T:0.22
Consensus pattern (13 bp):
TAAAAAACCGGTT
Found at i:1972942 original size:21 final size:21
Alignment explanation
Indices: 1972918--1972957 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1972908 TTTATTTTAT
1972918 AACTTTATTTCAATTATCGTA
1 AACTTTATTTCAATTATCGTA
*
1972939 AACTTTGTTTCAATTATCG
1 AACTTTATTTCAATTATCG
1972958 AACTTGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (21 bp):
AACTTTATTTCAATTATCGTA
Found at i:1973005 original size:33 final size:33
Alignment explanation
Indices: 1972952--1973050 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
1972942 TTTGTTTCAA
1972952 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1972984 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* * *
1973017 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1973050 T
1 T
1973051 ATGTTGAGTT
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 11 0.17
33 52 0.83
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.45
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:1973079 original size:13 final size:13
Alignment explanation
Indices: 1973036--1973090 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
1973026 TTGGAAGTAT
1973036 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
1973049 TTATGTTGAGTT-AA
1 TTAAG-T-ATTTCAA
1973063 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
1973076 TTAAGTATTTGAA
1 TTAAGTATTTCAA
1973089 TT
1 TT
1973091 TATCGAACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.49
Consensus pattern (13 bp):
TTAAGTATTTCAA
Found at i:1973511 original size:15 final size:15
Alignment explanation
Indices: 1973486--1973541 Score: 67
Period size: 15 Copynumber: 3.6 Consensus size: 15
1973476 ATCTGGAATA
*
1973486 TTAAAATCGGTTTTT
1 TTAAAACCGGTTTTT
*
1973501 TTATAACCGGTTTTT
1 TTAAAACCGGTTTTT
*
1973516 TAAAAAAACCGGTTTTT
1 T--TAAAACCGGTTTTT
1973533 TTAAAACCG
1 TTAAAACCG
1973542 AAACCGGTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
15 21 0.62
17 13 0.38
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.43
Consensus pattern (15 bp):
TTAAAACCGGTTTTT
Found at i:1973550 original size:21 final size:18
Alignment explanation
Indices: 1973505--1973538 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1973495 GTTTTTTTAT
1973505 AACCGG-TTTTTTAAAAA
1 AACCGGTTTTTTTAAAAA
1973522 AACCGGTTTTTTTAAAA
1 AACCGGTTTTTTTAAAA
1973539 CCGAAACCGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (18 bp):
AACCGGTTTTTTTAAAAA
Found at i:1974743 original size:25 final size:22
Alignment explanation
Indices: 1974702--1974748 Score: 67
Period size: 25 Copynumber: 2.0 Consensus size: 22
1974692 ACAATGATTT
1974702 TTTAATAAAAAATAATTTCTAAA
1 TTTAATAAAAAATAATTT-TAAA
1974725 TTTAATATTAAAAATAATTTTAAA
1 TTTAATA--AAAAATAATTTTAAA
1974749 AAAATAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 7 0.32
24 4 0.18
25 11 0.50
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (22 bp):
TTTAATAAAAAATAATTTTAAA
Found at i:1976272 original size:18 final size:18
Alignment explanation
Indices: 1976235--1976273 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
1976225 TTTAAAAATA
*
1976235 ACATAAATATAAAGCGAT
1 ACATAAATATAAAGCAAT
* *
1976253 ACATTAATATAAATCAAT
1 ACATAAATATAAAGCAAT
1976271 ACA
1 ACA
1976274 GTTACATATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.56, C:0.13, G:0.05, T:0.26
Consensus pattern (18 bp):
ACATAAATATAAAGCAAT
Found at i:1981791 original size:85 final size:85
Alignment explanation
Indices: 1981648--1981817 Score: 322
Period size: 85 Copynumber: 2.0 Consensus size: 85
1981638 GTATTGGAAT
*
1981648 TTGTACAAGGTAAGAAGATGAACTTTTAATTGTATGAGCTGATGTATTAATAGATAATGGATGGT
1 TTGTACAAGGTAAGAAGATGAACGTTTAATTGTATGAGCTGATGTATTAATAGATAATGGATGGT
1981713 CCCAAGAATTGAGACTTTTA
66 CCCAAGAATTGAGACTTTTA
*
1981733 TTGTACAAGGTAAGAAGATGAACGTTTAATTGTATGGGCTGATGTATTAATAGATAATGGATGGT
1 TTGTACAAGGTAAGAAGATGAACGTTTAATTGTATGAGCTGATGTATTAATAGATAATGGATGGT
1981798 CCCAAGAATTGAGACTTTTA
66 CCCAAGAATTGAGACTTTTA
1981818 GATTTACTTT
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
85 83 1.00
ACGTcount: A:0.35, C:0.08, G:0.24, T:0.34
Consensus pattern (85 bp):
TTGTACAAGGTAAGAAGATGAACGTTTAATTGTATGAGCTGATGTATTAATAGATAATGGATGGT
CCCAAGAATTGAGACTTTTA
Found at i:1983996 original size:2 final size:2
Alignment explanation
Indices: 1983989--1984015 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1983979 CAATACCCCG
1983989 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 T
1984016 CCGTTATCTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1984181 original size:22 final size:22
Alignment explanation
Indices: 1984156--1984205 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
1984146 AATGGAACGA
* *
1984156 TTCAGCGCCGAATGTTGAACCG
1 TTCAACGCCGAATGCTGAACCG
**
1984178 TTCAACGTTGAATGCTGAACCG
1 TTCAACGCCGAATGCTGAACCG
1984200 TTCAAC
1 TTCAAC
1984206 ATTCAGCGTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.26
Consensus pattern (22 bp):
TTCAACGCCGAATGCTGAACCG
Found at i:1984504 original size:17 final size:17
Alignment explanation
Indices: 1984482--1984515 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1984472 TTCATACAGA
1984482 GCCATTGAATCATTCAG
1 GCCATTGAATCATTCAG
1984499 GCCATTGAATCATTCAG
1 GCCATTGAATCATTCAG
1984516 TGCTTAATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (17 bp):
GCCATTGAATCATTCAG
Done.