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 1 of 8
Found at i:1292 original size:91 final size:92
Alignment explanation
Indices: 1174--1628 Score: 834
Period size: 91 Copynumber: 5.0 Consensus size: 92
1164 TTGCTTAGTA
*
1174 AATTTATTC-GTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTG
1 AATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTG
1238 TC-TTGTTTTGTCTTTTGGTTGAAAGT
66 TCTTTGTTTTGTCTTTTGGTTGAAAGT
*
1264 AATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTATATTCTTTAACACTGTGAAATA-TATTTG
1 AATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTG
1328 TCTTTGTTTTGTCTTTTGGTTGAAAGT
66 TCTTTGTTTTGTCTTTTGGTTGAAAGT
1355 AATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTG
1 AATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTG
1420 TCTTTGTTTTGTCTTTTGGTTGAAAGT
66 TCTTTGTTTTGTCTTTTGGTTGAAAGT
*
1447 AATTTGTTCGGTTACTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA-TTG
1 AATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTG
1510 TCTTTGTTTTGTC-TTTGGTTGAAAGT
66 TCTTTGTTTTGTCTTTTGGTTGAAAGT
1536 AATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTG
1 AATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTG
1601 TC-TTGTTTTGTCTTTTGGTTGAAAGT
66 TCTTTGTTTTGTCTTTTGGTTGAAAGT
1627 AA
1 AA
1629 ATTTATCCAT
Statistics
Matches: 354, Mismatches: 5, Indels: 11
0.96 0.01 0.03
Matches are distributed among these distances:
89 70 0.20
90 44 0.12
91 150 0.42
92 90 0.25
ACGTcount: A:0.22, C:0.13, G:0.18, T:0.46
Consensus pattern (92 bp):
AATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTG
TCTTTGTTTTGTCTTTTGGTTGAAAGT
Found at i:1716 original size:19 final size:19
Alignment explanation
Indices: 1676--1803 Score: 116
Period size: 19 Copynumber: 7.3 Consensus size: 19
1666 TAGTTTACTT
* *
1676 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
1696 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
1715 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
1734 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
1748 TCGCAACGCGAAACC-AAA
1 TCGCAACGCGAAACCAAAA
*
1766 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
1780 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
1799 TCGCA
1 TCGCA
1804 TTGCGATTTT
Statistics
Matches: 88, Mismatches: 9, Indels: 23
0.73 0.08 0.19
Matches are distributed among these distances:
13 1 0.01
14 18 0.20
15 1 0.01
16 6 0.07
17 2 0.02
18 10 0.11
19 37 0.42
20 13 0.15
ACGTcount: A:0.45, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:1772 original size:32 final size:31
Alignment explanation
Indices: 1712--1803 Score: 130
Period size: 32 Copynumber: 2.8 Consensus size: 31
1702 CGCGAAACCA
**
1712 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAA-CCAAATCGCAACGAC
1744 AGAATCGCAACGCGAAACCAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAATCGCAACGAC
1776 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACC-AAATCGCA
1804 TTGCGATTTT
Statistics
Matches: 55, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
31 1 0.02
32 31 0.56
33 23 0.42
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (31 bp):
AAATCGCAACGCGAAACCAAATCGCAACGAC
Found at i:1821 original size:19 final size:19
Alignment explanation
Indices: 1799--1933 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
1789 GAAACCAAAA
*
1799 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1818 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
1834 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
1851 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
1867 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
1884 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
1903 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
1923 TCGTGTTGCGA
1 TCGCGTTGCGA
1934 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1840 original size:14 final size:14
Alignment explanation
Indices: 1821--1877 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1811 TTTCATTTCG
1821 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
1835 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
1852 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
1868 CGTTGCGATT
1 CGTTGCGATT
1878 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:1846 original size:33 final size:33
Alignment explanation
Indices: 1804--1896 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
1794 CAAAATCGCA
*
1804 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
1837 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
1870 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
1897 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:3843 original size:13 final size:14
Alignment explanation
Indices: 3827--3861 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
3817 ATTGTTTAAT
3827 TGATTTGT-AAAGA
1 TGATTTGTAAAAGA
*
3840 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
3854 TGATTTGT
1 TGATTTGT
3862 GTAATTGATG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.31, C:0.00, G:0.23, T:0.46
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:3984 original size:19 final size:19
Alignment explanation
Indices: 3968--4069 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
3958 AAAAATGACT
3968 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
3987 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
4006 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
4020 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
4039 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
4059 ATCGCAATGCG
1 ATCGCAATGCG
4070 TTTATAATTT
Statistics
Matches: 75, Mismatches: 2, Indels: 12
0.84 0.02 0.13
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 40 0.53
20 19 0.25
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:4122 original size:19 final size:19
Alignment explanation
Indices: 4098--4389 Score: 383
Period size: 19 Copynumber: 16.4 Consensus size: 19
4088 GATTATCTCG
4098 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
4117 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
4136 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
4150 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
4169 TTGCGATTTTCA-TTCGCA
1 TTGCGATTTTCATTTCGCA
4187 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
4206 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
4225 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
4244 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
4263 TTGCGA--TTC-TGTCG--
1 TTGCGATTTTCATTTCGCA
4277 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
4296 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
4315 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
4329 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
4349 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
4363 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
4382 TTGCGATT
1 TTGCGATT
4390 GTATTTTCCG
Statistics
Matches: 243, Mismatches: 8, Indels: 44
0.82 0.03 0.15
Matches are distributed among these distances:
14 29 0.12
16 24 0.10
17 20 0.08
18 21 0.09
19 137 0.56
20 12 0.05
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:4138 original size:52 final size:52
Alignment explanation
Indices: 4076--4389 Score: 321
Period size: 52 Copynumber: 5.9 Consensus size: 52
4066 TGCGTTTATA
*
4076 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTATTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
4128 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTATTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
4180 A-TTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA--TT-ATTTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
*
4236 ATTTCGCATTGCGATTTTAATTTCGCATTGCGA--TTC-TGTCG--TTGCGATTTTC
1 ATTTCGCATTGCGA--TT-ATTTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
*
4288 ATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTC
1 ATTTCGCATTGCGA--TT-ATTTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
* *
4340 ATTTCCGCATTGCGA-T-TTTCATGTTGGGATTTTCATTTCGCGTTGCGATT
1 ATTT-CGCATTGCGATTATTTC--GTTGCGATTTTCATTTCGCATTGCGATT
4390 GTATTTTCCG
Statistics
Matches: 239, Mismatches: 9, Indels: 27
0.87 0.03 0.10
Matches are distributed among these distances:
48 9 0.04
50 5 0.02
51 16 0.07
52 116 0.49
53 20 0.08
54 9 0.04
55 3 0.01
56 31 0.13
57 30 0.13
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.46
Consensus pattern (52 bp):
ATTTCGCATTGCGATTATTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:4245 original size:127 final size:122
Alignment explanation
Indices: 4098--4361 Score: 194
Period size: 127 Copynumber: 2.1 Consensus size: 122
4088 GATTATCTCG
*
4098 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA-TTC-TTTCG-TTGCGATTTT
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TGTCG--TTGCGATTTCATTTCGATTGCGATTTT
*
4160 CATTTCGCATTGCGATTTTCATTCGCATTGCGATTTTCATTT-CGCATTGCGATTTTCATTTCGC
61 CA-TTCGCATTGCGATTCTC-TTCG--TTGCGATTTTCATTTCCGCATTGCGATTTTCATTTCGC
4224 A
122 A
* * *
4225 TTGCGATTTTCATTTCGCATTGCGATTTTAATTTCGCATTGCGA-TTC-TGTCG-TTGCGATTTT
1 TTGCGATTTTCATTTCGCATTGCGA--TT-CTGTCG--TTGCGATTTCATTTCGATTGCGATTTT
* *
4287 CATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TCT-CG--TTGCGATTTTCATTTCC
61 CA-TTCGCATTGCGATTCTC--TTCG--TTGCGATTTTCATTTCCGCATTGCGATTTTCATTT-C
4346 GCA
120 GCA
4349 TTGCGATTTTCAT
1 TTGCGATTTTCAT
4362 GTTGGGATTT
Statistics
Matches: 130, Mismatches: 4, Indels: 9
0.91 0.03 0.06
Matches are distributed among these distances:
123 15 0.12
124 17 0.13
125 4 0.03
126 3 0.02
127 79 0.61
128 12 0.09
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.47
Consensus pattern (122 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTGTCGTTGCGATTTCATTTCGATTGCGATTTTCATTC
GCATTGCGATTCTCTTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATTTCGCA
Found at i:4333 original size:33 final size:33
Alignment explanation
Indices: 4117--4389 Score: 230
Period size: 33 Copynumber: 7.8 Consensus size: 33
4107 TCATTTCGCA
*
4117 TTGCGATTTTCATTTCGCATTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
4150 TTGCGATTTTCATTTCGCATTGCGATTTTCATTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTC--TCG
*
4185 CATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 --TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
* *
4223 CATTGCGATTTTCATTTCGCATTGCGATTTTAATTTCG
1 --TTGCGATTTTCATTTCGCATTGCGA--TT-CTCTCG
* * * * *
4261 CATTGCGATTCTGTCGTTGCG-ATTTTC-ATT-TCGCA
1 --TTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCG
4296 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
4329 TTGCGATTTTCATTTCCGCATTGCGATTTTCAT-G
1 TTGCGATTTTCATTT-CGCATTGCGATTCTC-TCG
* *
4363 TTGGGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATT
4390 GTATTTTCCG
Statistics
Matches: 205, Mismatches: 19, Indels: 32
0.80 0.07 0.12
Matches are distributed among these distances:
31 9 0.04
32 5 0.02
33 65 0.32
34 29 0.14
35 6 0.03
37 27 0.13
38 49 0.24
39 5 0.02
40 10 0.05
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:6676 original size:12 final size:12
Alignment explanation
Indices: 6659--6683 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
6649 TCTTCGGGGA
6659 CTTTTTCTTCTT
1 CTTTTTCTTCTT
6671 CTTTTTCTTCTT
1 CTTTTTCTTCTT
6683 C
1 C
6684 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:6891 original size:24 final size:24
Alignment explanation
Indices: 6857--6903 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
6847 CTGAAACATC
6857 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
6881 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
6904 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:7611 original size:20 final size:20
Alignment explanation
Indices: 7583--7948 Score: 433
Period size: 20 Copynumber: 18.4 Consensus size: 20
7573 AAATTTAAGT
* * * *
7583 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
7603 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
7623 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
7643 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
7663 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
7683 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
7703 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
7723 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
7743 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
7763 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
7783 GTTGC-AGTTTACGGATACGC
1 GTTGCGA-TTTACGGATACGC
7803 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
7823 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
7843 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
7863 GTTGCGA-TTACGGATACAC
1 GTTGCGATTTACGGATACGC
7882 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
7902 GTTGCGA-TTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
** *
7921 GTTGCGATTT-CATATTCGC
1 GTTGCGATTTACGGATACGC
7940 GTTGCGATT
1 GTTGCGATT
7949 ATGGAAAATC
Statistics
Matches: 305, Mismatches: 29, Indels: 25
0.85 0.08 0.07
Matches are distributed among these distances:
19 51 0.17
20 249 0.82
21 5 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.34
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:9007 original size:64 final size:64
Alignment explanation
Indices: 8906--9035 Score: 260
Period size: 64 Copynumber: 2.0 Consensus size: 64
8896 AAAGAAATAT
8906 TGGATCAAATAAAACTTAACGAAATGAATTTGAAAGCATCTCTAGAAGTCTTGTCTAACCAAAA
1 TGGATCAAATAAAACTTAACGAAATGAATTTGAAAGCATCTCTAGAAGTCTTGTCTAACCAAAA
8970 TGGATCAAATAAAACTTAACGAAATGAATTTGAAAGCATCTCTAGAAGTCTTGTCTAACCAAAA
1 TGGATCAAATAAAACTTAACGAAATGAATTTGAAAGCATCTCTAGAAGTCTTGTCTAACCAAAA
9034 TG
1 TG
9036 CAATTACAGA
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 66 1.00
ACGTcount: A:0.43, C:0.15, G:0.15, T:0.27
Consensus pattern (64 bp):
TGGATCAAATAAAACTTAACGAAATGAATTTGAAAGCATCTCTAGAAGTCTTGTCTAACCAAAA
Found at i:22760 original size:135 final size:135
Alignment explanation
Indices: 22519--22783 Score: 451
Period size: 135 Copynumber: 2.0 Consensus size: 135
22509 GAGTTCATGG
*
22519 ATATCTTGAGTGATTGAAAAAATACAAGAGAATTATAATTGCAGCATCAACATGACAAGAAAGAA
1 ATATCTTGAGTGATAGAAAAAATACAAGAGAATTATAATTGCAGCATCAACATGACAAGAAAGAA
* * *
22584 GCTATAAAATTTAAATTTTGGAGGAAGAGAATAAAG-GGGAAAAACATTTAAGCCCTATTTATGG
66 ACTATAAAATTTAAATTTTGGAGGAAGAAAATAAAGAGGAAAAAACATTTAAGCCCTATTTATGG
22648 CATTA
131 CATTA
* *
22653 ATATCTTGAGTGGTAGAAAAAAATACAAGAGAATTATAATTGCAGCATCACCATGACAAGAAAGA
1 ATATCTTGAGTGATAG-AAAAAATACAAGAGAATTATAATTGCAGCATCAACATGACAAGAAAGA
*
22718 AACTATAAAATTTAAATTTTGGAGGAAGAAAATAAAGAGGAAAAAACATTTAAGCTCTATTTATG
65 AACTATAAAATTTAAATTTTGGAGGAAGAAAATAAAGAGGAAAAAACATTTAAGCCCTATTTATG
22783 G
130 G
22784 GTACGGATGT
Statistics
Matches: 122, Mismatches: 7, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
134 14 0.11
135 82 0.67
136 26 0.21
ACGTcount: A:0.47, C:0.09, G:0.18, T:0.26
Consensus pattern (135 bp):
ATATCTTGAGTGATAGAAAAAATACAAGAGAATTATAATTGCAGCATCAACATGACAAGAAAGAA
ACTATAAAATTTAAATTTTGGAGGAAGAAAATAAAGAGGAAAAAACATTTAAGCCCTATTTATGG
CATTA
Found at i:28110 original size:26 final size:26
Alignment explanation
Indices: 28062--28114 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 26
28052 TTTAGAATTA
28062 TTATTATAATTTATTAAAATTAAAAT
1 TTATTATAATTTATTAAAATTAAAAT
* * *
28088 TTATT-TATTTTATTAAGATTTAAAT
1 TTATTATAATTTATTAAAATTAAAAT
28113 TT
1 TT
28115 TAATCAGGGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
25 19 0.79
26 5 0.21
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (26 bp):
TTATTATAATTTATTAAAATTAAAAT
Found at i:30339 original size:4 final size:4
Alignment explanation
Indices: 30332--31012 Score: 1189
Period size: 4 Copynumber: 171.8 Consensus size: 4
30322 AAGGTCGGTT
30332 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
30380 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
30428 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
30476 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
30524 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
30572 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
30620 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
30668 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
30716 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
* * *
30764 TATC TATC TATC TATC TATC TATC TATC TACC TATC TAAC TATC TACC
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
30812 TATC TA-C TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
* *
30859 TATC TATC TACC TATC TATC TATC TATC TATC TATC TACC TATC TATC
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
* *
30907 TATC TATC TA-C TA-C TATC TATC TACC TA-- TATC TATC TACC TA-C
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
* * * *
30950 TATC TACC TA-C TATC TACC TATAC TATC TACC TACC TATC TA-C TATAC
1 TATC TATC TATC TATC TATC TAT-C TATC TATC TATC TATC TATC TAT-C
30998 TATC TATC TATC TAT
1 TATC TATC TATC TAT
31013 ATCTATATAT
Statistics
Matches: 651, Mismatches: 17, Indels: 18
0.95 0.02 0.03
Matches are distributed among these distances:
2 2 0.00
3 18 0.03
4 623 0.96
5 8 0.01
ACGTcount: A:0.26, C:0.26, G:0.00, T:0.48
Consensus pattern (4 bp):
TATC
Found at i:31365 original size:181 final size:181
Alignment explanation
Indices: 31061--31598 Score: 1016
Period size: 175 Copynumber: 3.0 Consensus size: 181
31051 GAACGAGTGG
31061 CAAATAGTTAAGAAGTTAATTTTGTATGACGTTTCTTCAGGTACAAAGAAGCGTTGATGACCAGT
1 CAAATAGTTAAGAAGTTAATTTTGTATGACGTTTCTTCAGGTACAAAGAAGCGTTGATGACCAGT
31126 GTGTTGTTGTTGCAACATATGAAGGTGAGCATAATCACCTTCCCCCATCTCAAATGGAAGCAACA
66 GTGTTGTTGTTGCAACATATGAAGGTGAGCATAATCACCTTCCCCCATCTCAAATGGAAGCAACA
* *
31191 TCAGGTTCAAGCAGTTGCGTGGGTCTCAGTTCGGTCCATGTCGGTTCAGCC
131 TCGGGTTCAAGCAGTTGCGTGGGTCTCAGTTCGGTCCATGCCGGTTCAGCC
31242 CAAATAGTTAAGAAGTTAATTTTGTATGACGTTTCTTCAGGTACAAAGAAGCGTTGATGACCAGT
1 CAAATAGTTAAGAAGTTAATTTTGTATGACGTTTCTTCAGGTACAAAGAAGCGTTGATGACCAGT
31307 GTGTTGTTGTTGCAACATATGAAGGTGAGCATAATCACCTTCCCCCATCTCAAATGGAAGCAACA
66 GTGTTGTTGTTGCAACATATGAAGGTGAGCATAATCACCTTCCCCCATCTCAAATGGAAGCAACA
31372 TCGGGTTCAAGCAGTTGCGTGGGTCTCAGTTCGGTCCATGCCGGTT-----
131 TCGGGTTCAAGCAGTTGCGTGGGTCTCAGTTCGGTCCATGCCGGTTCAGCC
31418 C-AATAGTTAAGAAGTTAATTTTGTATGACGTTTCTTCAGGTACAAAGAAGCGTTGATGACCAGT
1 CAAATAGTTAAGAAGTTAATTTTGTATGACGTTTCTTCAGGTACAAAGAAGCGTTGATGACCAGT
31482 GTGTTGTTGTTGCAACATATGAAGGTGAGCATAATCACCTTCCCCCATCTCAAATGGAAGCAACA
66 GTGTTGTTGTTGCAACATATGAAGGTGAGCATAATCACCTTCCCCCATCTCAAATGGAAGCAACA
31547 TCGGGTTCAAGCAGTTGCGTGGGTCTCAGTTCGGTCCATGCCGGTTCAGCC
131 TCGGGTTCAAGCAGTTGCGTGGGTCTCAGTTCGGTCCATGCCGGTTCAGCC
31598 C
1 C
31599 CGGTCAAGTC
Statistics
Matches: 350, Mismatches: 2, Indels: 11
0.96 0.01 0.03
Matches are distributed among these distances:
175 174 0.50
176 1 0.00
180 1 0.00
181 174 0.50
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (181 bp):
CAAATAGTTAAGAAGTTAATTTTGTATGACGTTTCTTCAGGTACAAAGAAGCGTTGATGACCAGT
GTGTTGTTGTTGCAACATATGAAGGTGAGCATAATCACCTTCCCCCATCTCAAATGGAAGCAACA
TCGGGTTCAAGCAGTTGCGTGGGTCTCAGTTCGGTCCATGCCGGTTCAGCC
Found at i:33316 original size:68 final size:68
Alignment explanation
Indices: 33242--33374 Score: 239
Period size: 68 Copynumber: 2.0 Consensus size: 68
33232 GCATGCGTGT
*
33242 ATGTATGGAACTTTCATTACACGAAGTACCTGAACACATGTATTAGGTTATGCCTTGGATTCTTA
1 ATGTATGGAACTTTCATTACACGAAGTACCTGAACACATGTATTAGGTTATGCCTTAGATTCTTA
33307 TGC
66 TGC
* *
33310 ATGTATGGAACTTTCATTGCATGAAGTACCTGAACACATGTATTAGGTTATGCCTTAGATTCTTA
1 ATGTATGGAACTTTCATTACACGAAGTACCTGAACACATGTATTAGGTTATGCCTTAGATTCTTA
33375 GGAAGGAGGA
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
68 62 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.36
Consensus pattern (68 bp):
ATGTATGGAACTTTCATTACACGAAGTACCTGAACACATGTATTAGGTTATGCCTTAGATTCTTA
TGC
Found at i:35053 original size:4 final size:4
Alignment explanation
Indices: 35046--35219 Score: 348
Period size: 4 Copynumber: 43.5 Consensus size: 4
35036 CATGCGTACG
35046 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
35094 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
35142 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
35190 TACA TACA TACA TACA TACA TACA TACA TA
1 TACA TACA TACA TACA TACA TACA TACA TA
35220 TTATGTTGTC
Statistics
Matches: 170, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 170 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
TACA
Found at i:35446 original size:205 final size:202
Alignment explanation
Indices: 35174--35624 Score: 634
Period size: 205 Copynumber: 2.2 Consensus size: 202
35164 CATACATACA
* * * *
35174 TACATACATACATACATACATACATACATACATACATACATACATATTATGTTGTCAAGCGAAGG
1 TACATACATACATACATACATACACACATACATACATACATACATATTATGTTATAAAGCCAAGG
* *
35239 CAAGTTTATTTTTCTTACATACATACATAACATAAATGCATACATGCGTACATATATCATTGTAG
66 CAAGTTTATTTTTCTTACATACATACATAACATAAATGCATACATGCATACATATACCATTGTAG
*
35304 GAGGGCTGTGCTTGTTTTTGTCAG-TCTTCATACTTCTTTATGTTATCAAGCCAAGGCAAGTTTC
131 GAGGGCTGTGCTTGTTTTTGGCAGTTCTTCATACTTCTTTATGTTATCAAGCCAAGGCAAGTTTC
35368 TTTTTCT
196 TTTTTCT
* * * * *
35375 TACATACATAACATTCATGCATACACACATATATGTACATACATACTTCTTTATGTTATAAAGCC
1 TACATACAT-ACATACATACATACACACATACA--TACATACATACAT-ATTATGTTATAAAGCC
* * * *
35440 AAGGCAAGTTTCTTTTTCTTACATGCATACATAACATAAATGCATACATGCATGCCTATACCATT
62 AAGGCAAGTTTATTTTTCTTACATACATACATAACATAAATGCATACATGCATACATATACCATT
* *
35505 TTGGGAGGGCTGTGCTTGTTTTTGGCAGTCTTCTTCATACTTCTTTATGTTATCAAGCCAAGGCA
127 GTAGGAGGGCTGTGCTTGTTTTTGGCAG--TTCTTCATACTTCTTTATGTTATCAAGCCAAGGCA
35570 AGTTTCTTTTTCT
190 AGTTTCTTTTTCT
* * * *
35583 TACATACACACATATATAACATACATACATACATGCATACAT
1 TACATACATACATACAT-ACATACACACATACATACATACAT
35625 TCTAAAAGAA
Statistics
Matches: 217, Mismatches: 25, Indels: 11
0.86 0.10 0.04
Matches are distributed among these distances:
201 9 0.04
202 19 0.09
204 12 0.06
205 96 0.44
206 8 0.04
207 6 0.03
208 67 0.31
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (202 bp):
TACATACATACATACATACATACACACATACATACATACATACATATTATGTTATAAAGCCAAGG
CAAGTTTATTTTTCTTACATACATACATAACATAAATGCATACATGCATACATATACCATTGTAG
GAGGGCTGTGCTTGTTTTTGGCAGTTCTTCATACTTCTTTATGTTATCAAGCCAAGGCAAGTTTC
TTTTTCT
Found at i:43240 original size:84 final size:84
Alignment explanation
Indices: 43097--43264 Score: 239
Period size: 84 Copynumber: 2.0 Consensus size: 84
43087 TGAACCTCAC
*
43097 ATATCTCAGGATATCCAACACCAAGATTACCAACATGCTAACCAGTGTATGCCAATTAAAACTCA
1 ATATCTCAGGATATCCAACACCAAAATTACCAACATGCTAACCAGTGTATGCCAATTAAAACTCA
43162 GCCTATGGAAG-CAAAGACT
66 GCCTATGGAAGTC-AAGACT
** * * * * * *
43181 ATATCTCAGGATATCCTGCACCAAAATTATCAACATGTTAGCCAGTGTATGGCAGTTAAACCTCA
1 ATATCTCAGGATATCCAACACCAAAATTACCAACATGCTAACCAGTGTATGCCAATTAAAACTCA
43246 GCCTATGGAAGTCAAGACT
66 GCCTATGGAAGTCAAGACT
43265 GAAGTCCCCA
Statistics
Matches: 74, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
84 73 0.99
85 1 0.01
ACGTcount: A:0.36, C:0.24, G:0.16, T:0.24
Consensus pattern (84 bp):
ATATCTCAGGATATCCAACACCAAAATTACCAACATGCTAACCAGTGTATGCCAATTAAAACTCA
GCCTATGGAAGTCAAGACT
Found at i:44755 original size:2 final size:2
Alignment explanation
Indices: 44748--44796 Score: 62
Period size: 2 Copynumber: 24.5 Consensus size: 2
44738 TCGTAGTCAT
* * * *
44748 TC TC TC TC TC TC TC TC TC TC TC CC TC CC TC CC TC CC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
44790 TC TC TC T
1 TC TC TC T
44797 ATATATATAT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.57, G:0.00, T:0.43
Consensus pattern (2 bp):
TC
Found at i:51250 original size:18 final size:18
Alignment explanation
Indices: 51227--51263 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
51217 AGTCTCGTTA
51227 AAAAACCTCTCTAGACCT
1 AAAAACCTCTCTAGACCT
51245 AAAAACCTCTCTAGACCT
1 AAAAACCTCTCTAGACCT
51263 A
1 A
51264 GTTGGGGGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.41, C:0.32, G:0.05, T:0.22
Consensus pattern (18 bp):
AAAAACCTCTCTAGACCT
Found at i:51351 original size:18 final size:18
Alignment explanation
Indices: 51328--51376 Score: 80
Period size: 18 Copynumber: 2.7 Consensus size: 18
51318 AAAGAACAAG
51328 ACCACAGAAGAAGAATCA
1 ACCACAGAAGAAGAATCA
*
51346 ACCACAGAAGACGAATCA
1 ACCACAGAAGAAGAATCA
*
51364 ACCACACAAGAAG
1 ACCACAGAAGAAG
51377 GAAAAAATGA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.53, C:0.27, G:0.16, T:0.04
Consensus pattern (18 bp):
ACCACAGAAGAAGAATCA
Found at i:62976 original size:4 final size:4
Alignment explanation
Indices: 62967--63005 Score: 51
Period size: 4 Copynumber: 9.5 Consensus size: 4
62957 AAATAGATGG
* *
62967 AGCC AGCC AGCC AGCC AGGCC AACC AGCT AGCC AGCC AG
1 AGCC AGCC AGCC AGCC A-GCC AGCC AGCC AGCC AGCC AG
63006 TGGCTGTCAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
4 26 0.87
5 4 0.13
ACGTcount: A:0.28, C:0.44, G:0.26, T:0.03
Consensus pattern (4 bp):
AGCC
Found at i:62993 original size:17 final size:17
Alignment explanation
Indices: 62968--63001 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
62958 AATAGATGGA
*
62968 GCCAGCCAGCCAGCCAG
1 GCCAACCAGCCAGCCAG
*
62985 GCCAACCAGCTAGCCAG
1 GCCAACCAGCCAGCCAG
63002 CCAGTGGCTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.26, C:0.44, G:0.26, T:0.03
Consensus pattern (17 bp):
GCCAACCAGCCAGCCAG
Found at i:64891 original size:30 final size:30
Alignment explanation
Indices: 64856--64914 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
64846 AACTTAAAAG
* *
64856 AGTTTTGCAATACTGAGATTTAAATAATTT
1 AGTTTTACAATACTGAAATTTAAATAATTT
64886 AGTTTTACAATACTGAAATTTAAATAATT
1 AGTTTTACAATACTGAAATTTAAATAATT
64915 CATACAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.42
Consensus pattern (30 bp):
AGTTTTACAATACTGAAATTTAAATAATTT
Found at i:64920 original size:26 final size:27
Alignment explanation
Indices: 64863--64923 Score: 70
Period size: 30 Copynumber: 2.2 Consensus size: 27
64853 AAGAGTTTTG
* *
64863 CAATACTGAGATTTAAATAATTTAGTTTTA
1 CAATACTGAAATTTAAATAATTCA---TTA
64893 CAATACTGAAATTTAAATAATTCA-TA
1 CAATACTGAAATTTAAATAATTCATTA
64919 CAATA
1 CAATA
64924 ACAATAATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
26 7 0.24
30 22 0.76
ACGTcount: A:0.46, C:0.10, G:0.07, T:0.38
Consensus pattern (27 bp):
CAATACTGAAATTTAAATAATTCATTA
Found at i:65014 original size:9 final size:9
Alignment explanation
Indices: 65000--65026 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
64990 ACATGTATTT
65000 AGTTTTATA
1 AGTTTTATA
65009 AGTTTTATA
1 AGTTTTATA
65018 AGTTTTATA
1 AGTTTTATA
65027 GAATAAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.11, T:0.56
Consensus pattern (9 bp):
AGTTTTATA
Found at i:65422 original size:19 final size:19
Alignment explanation
Indices: 65377--65435 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
65367 ACTTAAATCA
*
65377 AAATAATTAAAATAA-ATAT
1 AAATAATT-TAATAATATAT
65396 AAAT--TTTAATAATATAT
1 AAATAATTTAATAATATAT
*
65413 AAATAATTTATATGATATA-
1 AAATAATTTA-ATAATATAT
65432 AAAT
1 AAAT
65436 TAAATATCTA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
16 5 0.15
17 10 0.29
19 12 0.35
20 7 0.21
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (19 bp):
AAATAATTTAATAATATAT
Found at i:65468 original size:27 final size:23
Alignment explanation
Indices: 65431--65544 Score: 120
Period size: 27 Copynumber: 4.5 Consensus size: 23
65421 TATATGATAT
65431 AAAATTAAATATCTATAATATAATATTA
1 AAAATT-AATAT-T-TAAT-TAAT-TTA
*
65459 AAAATTAATATTTAATTTATTTAA
1 AAAATTAATATTTAATTAATTT-A
65483 AAAATTAATATTTATAATATAATATTA
1 AAAATTAATA-TT-TAAT-TAAT-TTA
*
65510 AAAATTAATATTTAATTTATTTA
1 AAAATTAATATTTAATTAATTTA
65533 AAAATTAATATT
1 AAAATTAATATT
65545 AAAATTAAAA
Statistics
Matches: 78, Mismatches: 3, Indels: 15
0.81 0.03 0.16
Matches are distributed among these distances:
23 17 0.22
24 17 0.22
25 10 0.13
26 7 0.09
27 19 0.24
28 8 0.10
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.46
Consensus pattern (23 bp):
AAAATTAATATTTAATTAATTTA
Found at i:65482 original size:23 final size:23
Alignment explanation
Indices: 65456--65544 Score: 124
Period size: 23 Copynumber: 3.7 Consensus size: 23
65446 TAATATAATA
65456 TTAAAAATTAATATTTAATTTAT
1 TTAAAAATTAATATTTAATTTAT
*
65479 TTAAAAAATTAATATTTATAATATAAT
1 TT-AAAAATTAATA-TT-TAAT-TTAT
65506 ATTAAAAATTAATATTTAATTTAT
1 -TTAAAAATTAATATTTAATTTAT
65530 TTAAAAATTAATATT
1 TTAAAAATTAATATT
65545 AAAATTAAAA
Statistics
Matches: 59, Mismatches: 2, Indels: 10
0.83 0.03 0.14
Matches are distributed among these distances:
23 17 0.29
24 14 0.24
25 6 0.10
26 6 0.10
27 14 0.24
28 2 0.03
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
TTAAAAATTAATATTTAATTTAT
Found at i:65493 original size:51 final size:50
Alignment explanation
Indices: 65431--65543 Score: 199
Period size: 51 Copynumber: 2.2 Consensus size: 50
65421 TATATGATAT
65431 AAAATTAAATATCTATAATATAATATTAAAAATTAATATTTAATTTATTTAA
1 AAAATT-AATATCTATAATATAATATTAAAAATTAATATTTAATTTATTT-A
*
65483 AAAATTAATATTTATAATATAATATTAAAAATTAATATTTAATTTATTTA
1 AAAATTAATATCTATAATATAATATTAAAAATTAATATTTAATTTATTTA
65533 AAAATTAATAT
1 AAAATTAATAT
65544 TAAAATTAAA
Statistics
Matches: 60, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
50 12 0.20
51 42 0.70
52 6 0.10
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (50 bp):
AAAATTAATATCTATAATATAATATTAAAAATTAATATTTAATTTATTTA
Found at i:65747 original size:82 final size:82
Alignment explanation
Indices: 65605--65774 Score: 277
Period size: 82 Copynumber: 2.1 Consensus size: 82
65595 GTTAGAAGAT
* * * *
65605 GTCTGCAGACATAAGGTCACGTCTGCGCCGCGCATACCACACGCAGACGTTAGAAGAGCTTCTGT
1 GTCTGCAGACATAAAGCCACGTCTGCGCCGCGCAGACCACACACAGACGTTAGAAGAGCTTCTGT
65670 CTTCTAAAAAACAAACG
66 CTTCTAAAAAACAAACG
* * *
65687 GTCTGCAGACATAAAGCCACGTCTGCGCCGCGCAGACCACGCACAGACGTTAGAATAGCTTTTGT
1 GTCTGCAGACATAAAGCCACGTCTGCGCCGCGCAGACCACACACAGACGTTAGAAGAGCTTCTGT
65752 CTTCTAAAAAACAAACG
66 CTTCTAAAAAACAAACG
65769 GTCTGC
1 GTCTGC
65775 GAAGCCTAAT
Statistics
Matches: 81, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
82 81 1.00
ACGTcount: A:0.30, C:0.28, G:0.22, T:0.20
Consensus pattern (82 bp):
GTCTGCAGACATAAAGCCACGTCTGCGCCGCGCAGACCACACACAGACGTTAGAAGAGCTTCTGT
CTTCTAAAAAACAAACG
Found at i:68209 original size:13 final size:13
Alignment explanation
Indices: 68191--68215 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
68181 TTTTAAATTA
68191 TTATATATTTTAT
1 TTATATATTTTAT
68204 TTATATATTTTA
1 TTATATATTTTA
68216 ATAATAATAT
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
TTATATATTTTAT
Found at i:68556 original size:100 final size:102
Alignment explanation
Indices: 68377--68580 Score: 335
Period size: 100 Copynumber: 2.0 Consensus size: 102
68367 AGCACCACAT
68377 TAAGATTTCCAAAGGATGTTCCCAAATGGGCGCCGGAATTGGAAACTCAGTTACATTTTTCTCCC
1 TAAGATTTCCAAAGGATGTTCCC-AATGGGCGCCGGAATTGGAAACTCAGTTACATTTTTCTCCC
*
68442 TCGTCATTATTATTTAAAGGTATAAT-AT-AAAATGTC
65 TCGTCATTACTATTTAAAGGTATAATGATAAAAATGTC
*
68478 TAAGATTTCCAAAGGATGTT-CC-ATGGGCGCCGGAATTGGAAAGTCAGAATTACATTTTTCTCC
1 TAAGATTTCCAAAGGATGTTCCCAATGGGCGCCGGAATTGGAAACTCAG--TTACATTTTTCTCC
68541 CTCGTCATTACTATTTAAAGGTATAATGATAAAAATGTC
64 CTCGTCATTACTATTTAAAGGTATAATGATAAAAATGTC
68580 T
1 T
68581 CTCATGTTTG
Statistics
Matches: 97, Mismatches: 2, Indels: 7
0.92 0.02 0.07
Matches are distributed among these distances:
98 24 0.25
100 42 0.43
101 22 0.23
102 9 0.09
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (102 bp):
TAAGATTTCCAAAGGATGTTCCCAATGGGCGCCGGAATTGGAAACTCAGTTACATTTTTCTCCCT
CGTCATTACTATTTAAAGGTATAATGATAAAAATGTC
Found at i:70487 original size:21 final size:20
Alignment explanation
Indices: 70462--70560 Score: 72
Period size: 21 Copynumber: 4.8 Consensus size: 20
70452 AATCAGTTTC
70462 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
70483 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
70504 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* * *
70524 CCAGAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
70545 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
70561 ACACATAAAT
Statistics
Matches: 59, Mismatches: 17, Indels: 5
0.73 0.21 0.06
Matches are distributed among these distances:
20 15 0.25
21 44 0.75
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:70553 original size:20 final size:20
Alignment explanation
Indices: 70528--70720 Score: 246
Period size: 20 Copynumber: 9.6 Consensus size: 20
70518 GATTTTCCAG
* ** *
70528 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
70548 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
70568 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
70588 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
70608 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
70628 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
70648 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
70668 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGTATCCGT-A
70689 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
70709 AATCGCAACGCG
1 AATCGCAACGCG
70721 ATTTTTAAAG
Statistics
Matches: 151, Mismatches: 17, Indels: 10
0.85 0.10 0.06
Matches are distributed among these distances:
19 1 0.01
20 131 0.87
21 19 0.13
ACGTcount: A:0.35, C:0.27, G:0.19, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:71304 original size:21 final size:21
Alignment explanation
Indices: 71237--71312 Score: 102
Period size: 21 Copynumber: 3.7 Consensus size: 21
71227 TGCAGAAGAG
71237 TCGCAACGAGAGAAATG-AAA
1 TCGCAACGAGAGAAATGAAAA
* **
71257 TCGCAACGTGA-AAATGACTA
1 TCGCAACGAGAGAAATGAAAA
71277 TCTGCAACGAGAGAAATGAAAA
1 TC-GCAACGAGAGAAATGAAAA
71299 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
71313 TCGCAACGCG
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
19 5 0.11
20 13 0.28
21 20 0.43
22 9 0.19
ACGTcount: A:0.46, C:0.17, G:0.24, T:0.13
Consensus pattern (21 bp):
TCGCAACGAGAGAAATGAAAA
Found at i:71316 original size:14 final size:14
Alignment explanation
Indices: 71297--71353 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
71287 GAGAAATGAA
71297 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
71311 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
71330 AATCGCAACGAGAG
1 AATCGCAACGAGAG
71344 AATCGCAACG
1 AATCGCAACG
71354 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:71327 original size:33 final size:33
Alignment explanation
Indices: 71289--71369 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
71279 TGCAACGAGA
71289 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
71322 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
**
71355 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
71370 TTGCGATTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.47, C:0.22, G:0.22, T:0.09
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:71335 original size:19 final size:19
Alignment explanation
Indices: 71248--71339 Score: 61
Period size: 19 Copynumber: 4.9 Consensus size: 19
71238 CGCAACGAGA
*
71248 GAAATG-AAATCGCAACGT
1 GAAATGAAAATCGCAACGC
** *
71266 GAAAATGACTATCTGCAACGAGA
1 G-AAATGAAAATC-GCAAC--GC
71289 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
71306 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
71322 GAAATGAAAATCGCAACG
1 GAAATGAAAATCGCAACG
71340 AGAGAATCGC
Statistics
Matches: 56, Mismatches: 8, Indels: 19
0.67 0.10 0.23
Matches are distributed among these distances:
14 10 0.18
15 1 0.02
16 2 0.04
17 1 0.02
18 2 0.04
19 17 0.30
20 3 0.05
21 9 0.16
22 9 0.16
23 2 0.04
ACGTcount: A:0.46, C:0.18, G:0.23, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:71412 original size:33 final size:33
Alignment explanation
Indices: 71370--71491 Score: 145
Period size: 33 Copynumber: 3.5 Consensus size: 33
71360 CAAAATCGCA
71370 TTGCGATTTTCATTTCGCGTTGCAATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCAATTCTCTCG
** *
71403 TTGCGATTTTTTTTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCAATTCTCTCG
*
71436 TTGCGATTTTCATTCTCTCGTTGCGACAGTCATTCTCTCG
1 TTGCGATTTTCATT-TCGCGTT--G-CA---ATTCTCTCG
71476 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
71492 AACCAAAAGA
Statistics
Matches: 75, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
33 42 0.56
34 6 0.08
36 1 0.01
37 1 0.01
39 2 0.03
40 23 0.31
ACGTcount: A:0.11, C:0.24, G:0.18, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCAATTCTCTCG
Found at i:71452 original size:20 final size:20
Alignment explanation
Indices: 71427--71489 Score: 99
Period size: 20 Copynumber: 3.1 Consensus size: 20
71417 TCGCGTTGCG
71427 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
***
71447 ATTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTC
71467 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
71487 ATT
1 ATT
71490 TCAACCAAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.13, C:0.25, G:0.16, T:0.46
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:73395 original size:15 final size:15
Alignment explanation
Indices: 73371--73401 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
73361 TTAAAATCAC
*
73371 AACGAGAGAATCGCA
1 AACGACAGAATCGCA
73386 AACGACAGAATCGCA
1 AACGACAGAATCGCA
73401 A
1 A
73402 CGCGAAACCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.23, G:0.23, T:0.06
Consensus pattern (15 bp):
AACGACAGAATCGCA
Found at i:73418 original size:19 final size:19
Alignment explanation
Indices: 73394--73452 Score: 83
Period size: 19 Copynumber: 3.4 Consensus size: 19
73384 CAAACGACAG
73394 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACCAA
73413 AATCGCAA--CG--A-CAA
1 AATCGCAACGCGAAACCAA
73427 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACCAA
73446 AATCGCA
1 AATCGCA
73453 TTGCGATTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 11 0.31
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 18 0.51
ACGTcount: A:0.47, C:0.31, G:0.15, T:0.07
Consensus pattern (19 bp):
AATCGCAACGCGAAACCAA
Found at i:73429 original size:14 final size:14
Alignment explanation
Indices: 73363--73436 Score: 58
Period size: 14 Copynumber: 4.9 Consensus size: 14
73353 CACGAAACTT
* *
73363 AAAATCACAACGAG
1 AAAATCGCAACGAC
*
73377 AGAATCGCAAACGAC
1 AAAATCGC-AACGAC
*
73392 AGAATCGCAACGCGAAACC
1 AAAATCGCAA--CG--A-C
73411 AAAATCGCAACGAC
1 AAAATCGCAACGAC
73425 AAAATCGCAACG
1 AAAATCGCAACG
73437 CGAAACCAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
14 21 0.42
15 14 0.28
16 2 0.04
17 2 0.04
18 1 0.02
19 10 0.20
ACGTcount: A:0.49, C:0.27, G:0.18, T:0.07
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:73431 original size:33 final size:33
Alignment explanation
Indices: 73379--73452 Score: 130
Period size: 33 Copynumber: 2.2 Consensus size: 33
73369 ACAACGAGAG
*
73379 AATCGCAAACGACAGAATCGCAACGCGAAACCAA
1 AATCGC-AACGACAAAATCGCAACGCGAAACCAA
73413 AATCGCAACGACAAAATCGCAACGCGAAACCAA
1 AATCGCAACGACAAAATCGCAACGCGAAACCAA
73446 AATCGCA
1 AATCGCA
73453 TTGCGATTTT
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
33 33 0.85
34 6 0.15
ACGTcount: A:0.47, C:0.30, G:0.16, T:0.07
Consensus pattern (33 bp):
AATCGCAACGACAAAATCGCAACGCGAAACCAA
Found at i:73470 original size:19 final size:19
Alignment explanation
Indices: 73448--73620 Score: 150
Period size: 19 Copynumber: 9.6 Consensus size: 19
73438 GAAACCAAAA
*
73448 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
73467 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
73481 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
73500 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
73516 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* **
73533 TCCCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
**
73552 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
* *
73571 TCTCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATT
*
73590 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
73610 TCGTGTTGCGA
1 TCGCGTTGCGA
73621 AAGTAAACTA
Statistics
Matches: 125, Mismatches: 18, Indels: 21
0.76 0.11 0.13
Matches are distributed among these distances:
14 17 0.14
16 8 0.06
17 8 0.06
19 80 0.64
20 12 0.10
ACGTcount: A:0.10, C:0.21, G:0.23, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:73489 original size:14 final size:14
Alignment explanation
Indices: 73470--73526 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
73460 TTTCATTTCG
73470 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
73484 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TCT
*
73501 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTCT
73517 CGTTGCGATT
1 CGTTGCGATT
73527 TTCATTTCCC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 16 0.44
16 7 0.19
17 7 0.19
19 6 0.17
ACGTcount: A:0.11, C:0.23, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:73495 original size:33 final size:33
Alignment explanation
Indices: 73453--73545 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
73443 CAAAATCGCA
73453 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
73486 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
73519 TTGCGATTTTCATTTCCCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
73546 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.11, C:0.23, G:0.20, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:73578 original size:38 final size:38
Alignment explanation
Indices: 73448--73604 Score: 145
Period size: 33 Copynumber: 4.4 Consensus size: 38
73438 GAAACCAAAA
* *
73448 TCGCATTGCGATTTTCATTTCGCGTTGCGATTCTC---
1 TCGCGTTGCGATTTTCATTTCCCGTTGCGATTCTCATT
* * *
73483 T--CGTTGCGATTTTCATTTCGCATTGCGA-T-TC-TG
1 TCGCGTTGCGATTTTCATTTCCCGTTGCGATTCTCATT
* **
73516 T--CGTTGCGATTTTCATTTCCCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATTTCCCGTTGCGATTCTCATT
** *
73552 TCGCGTTGCGATTTTGGTTTCTCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATTTCCCGTTGCGATTCTCATT
73590 TCGCGTTGCGATTTT
1 TCGCGTTGCGATTTT
73605 AAGTTTCGTG
Statistics
Matches: 103, Mismatches: 12, Indels: 11
0.82 0.10 0.09
Matches are distributed among these distances:
31 2 0.02
32 1 0.01
33 51 0.50
34 1 0.01
35 2 0.02
36 2 0.02
38 44 0.43
ACGTcount: A:0.10, C:0.22, G:0.22, T:0.46
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCATTTCCCGTTGCGATTCTCATT
Found at i:75558 original size:13 final size:14
Alignment explanation
Indices: 75533--75567 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
75523 ATTGTTTAAT
75533 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
75547 TGATTTGT-AAAGT
1 TGATTTGTAAAAGA
75560 TGATTTGT
1 TGATTTGT
75568 GTAATTGATG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.31, C:0.00, G:0.23, T:0.46
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:75690 original size:20 final size:18
Alignment explanation
Indices: 75673--75788 Score: 122
Period size: 19 Copynumber: 6.7 Consensus size: 18
75663 AAAAATGACT
75673 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATG-AA
75693 ATCGCAATGCGAAATGAA
1 ATCGCAATGCGAAATGAA
*
75711 ATCGCAA--CGAGA-G-A
1 ATCGCAATGCGAAATGAA
75725 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATG-AA
75744 ATCGCAATGCGGAAATGAA
1 ATCGCAATGC-GAAATGAA
*
75763 ATCGCAA--CGAGA-G-A
1 ATCGCAATGCGAAATGAA
75777 ATCGCAATGCGA
1 ATCGCAATGCGA
75789 TTTTCATTTC
Statistics
Matches: 85, Mismatches: 3, Indels: 20
0.79 0.03 0.19
Matches are distributed among these distances:
14 16 0.19
15 2 0.02
16 14 0.16
17 2 0.02
18 9 0.11
19 26 0.31
20 16 0.19
ACGTcount: A:0.43, C:0.18, G:0.25, T:0.14
Consensus pattern (18 bp):
ATCGCAATGCGAAATGAA
Found at i:75801 original size:52 final size:52
Alignment explanation
Indices: 75673--75788 Score: 216
Period size: 52 Copynumber: 2.2 Consensus size: 52
75663 AAAAATGACT
75673 ATCGCAATGCGGAAATGAAAATCGCAATGC-GAAATGAAATCGCAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAATGCGGAAATGAAATCGCAACGAGAGA
75725 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAATCGCAACGAGAGA
75777 ATCGCAATGCGA
1 ATCGCAATGCGA
75789 TTTTCATTTC
Statistics
Matches: 63, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
51 19 0.30
52 44 0.70
ACGTcount: A:0.43, C:0.18, G:0.25, T:0.14
Consensus pattern (52 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAATCGCAACGAGAGA
Found at i:75806 original size:19 final size:19
Alignment explanation
Indices: 75778--75934 Score: 199
Period size: 19 Copynumber: 8.7 Consensus size: 19
75768 AACGAGAGAA
*
75778 TCGCAATGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
75797 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
75816 TCCGCATTGCGA--TTC-TC
1 T-CGCATTGCGATTTTCATT
75833 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
75850 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
75869 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
75888 TCCGCATTGCGATTTTCA--
1 T-CGCATTGCGATTTTCATT
*
75906 T-G--TTGGGATTTTCATT
1 TCGCATTGCGATTTTCATT
75922 TCGCATTGCGATT
1 TCGCATTGCGATT
75935 CTCTCGTTGC
Statistics
Matches: 121, Mismatches: 5, Indels: 24
0.81 0.03 0.16
Matches are distributed among these distances:
14 17 0.14
16 7 0.06
17 7 0.06
18 4 0.03
19 60 0.50
20 26 0.21
ACGTcount: A:0.15, C:0.22, G:0.18, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:75847 original size:53 final size:52
Alignment explanation
Indices: 75784--75948 Score: 214
Period size: 53 Copynumber: 3.1 Consensus size: 52
75774 AGAATCGCAA
75784 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTT-CGCATTGCGATTCTCTCGT
*
75837 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCAT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TCT-CG--T
*
75895 TGCGATTTTCA--T-G--TTGGGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
75942 TGCGATT
1 TGCGATT
75949 GTAATTTTCG
Statistics
Matches: 103, Mismatches: 3, Indels: 18
0.83 0.02 0.15
Matches are distributed among these distances:
47 8 0.08
49 2 0.02
50 2 0.02
51 3 0.03
52 10 0.10
53 57 0.55
54 3 0.03
55 3 0.03
56 3 0.03
58 12 0.12
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (52 bp):
TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
Found at i:75865 original size:72 final size:72
Alignment explanation
Indices: 75778--75934 Score: 271
Period size: 72 Copynumber: 2.2 Consensus size: 72
75768 AACGAGAGAA
*
75778 TCGCAATGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTC-TCGTTGCGA
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCAT-GTTGCGA
75842 TTTTCATT
65 TTTTCATT
* *
75850 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTTTCATGTTGGGAT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCATGTTGCGAT
75915 TTTCATT
66 TTTCATT
75922 TCGCATTGCGATT
1 TCGCATTGCGATT
75935 CTCTCGTTGC
Statistics
Matches: 81, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
72 80 0.99
73 1 0.01
ACGTcount: A:0.15, C:0.22, G:0.18, T:0.45
Consensus pattern (72 bp):
TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCATGTTGCGAT
TTTCATT
Found at i:75956 original size:53 final size:53
Alignment explanation
Indices: 75802--75967 Score: 187
Period size: 53 Copynumber: 3.1 Consensus size: 53
75792 TCATTTCGCA
* * *
75802 TTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA--
1 TTGCGATTTTCATTT-CGCATTGCGATTCTCTCGTTGCGATTGTAATTT-TCATG
* * **
75855 TTGCGATTTTCATTTCGCATTGCGATT-T-TCATTTCCGCATTGCGATTTTCATG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTC-GTTGCG-ATTGTAATTTTCATG
* *
75908 TTGGGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTGTAATTTTCGTG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTGTAATTTTCATG
75961 TTGCGAT
1 TTGCGAT
75968 AGTCAAATGC
Statistics
Matches: 94, Mismatches: 13, Indels: 12
0.79 0.11 0.10
Matches are distributed among these distances:
50 2 0.02
51 7 0.07
52 19 0.20
53 59 0.63
54 5 0.05
55 2 0.02
ACGTcount: A:0.14, C:0.20, G:0.19, T:0.46
Consensus pattern (53 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTGTAATTTTCATG
Found at i:76345 original size:20 final size:20
Alignment explanation
Indices: 76317--76507 Score: 233
Period size: 20 Copynumber: 9.6 Consensus size: 20
76307 AAATTTCAGT
* * * *
76317 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
76337 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
76357 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
76377 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
76397 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
76417 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
76437 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
76457 GTTGCTATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
76477 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
76497 GTTGCGATTTA
1 GTTGCGATTTA
76508 TGTGTTCGCG
Statistics
Matches: 151, Mismatches: 16, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
19 3 0.02
20 146 0.97
21 2 0.01
ACGTcount: A:0.20, C:0.18, G:0.26, T:0.36
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:76517 original size:20 final size:21
Alignment explanation
Indices: 76494--76545 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 21
76484 TTTACGGATA
* *
76494 CGCGTTGCGATTTAT-GTGTT
1 CGCGTTGCGATTTATCATATT
*
76514 CGCGTTGCG-TTTTTCATATT
1 CGCGTTGCGATTTATCATATT
76534 CGCGTTGCGATT
1 CGCGTTGCGATT
76546 CTGGGAAATC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 4 0.15
20 21 0.78
21 2 0.07
ACGTcount: A:0.10, C:0.19, G:0.27, T:0.44
Consensus pattern (21 bp):
CGCGTTGCGATTTATCATATT
Found at i:79418 original size:31 final size:30
Alignment explanation
Indices: 79383--79484 Score: 80
Period size: 31 Copynumber: 3.3 Consensus size: 30
79373 TAAACTAGTT
79383 ATTAAACTTTTTAATCGGTTATAAAATAATC
1 ATTAAACTTTTTAAT-GGTTATAAAATAATC
* * * *
79414 ATTAAATTTTATCTAATTGTTACAACAT-ATC
1 ATTAAACTTT-T-TAATGGTTATAAAATAATC
* * * *
79445 ATCAAACTTATCAAAGTGTTATAAAATAATC
1 ATTAAACTTTTTAATG-GTTATAAAATAATC
*
79476 CTTAAACTT
1 ATTAAACTT
79485 ATAAAATTTC
Statistics
Matches: 53, Mismatches: 14, Indels: 8
0.71 0.19 0.11
Matches are distributed among these distances:
29 2 0.04
30 9 0.17
31 29 0.55
32 9 0.17
33 4 0.08
ACGTcount: A:0.42, C:0.13, G:0.05, T:0.40
Consensus pattern (30 bp):
ATTAAACTTTTTAATGGTTATAAAATAATC
Found at i:79486 original size:31 final size:31
Alignment explanation
Indices: 79400--79486 Score: 95
Period size: 31 Copynumber: 2.8 Consensus size: 31
79390 TTTTTAATCG
* * *
79400 GTTATAAAATAATCATTAAATTTTATCTAATT
1 GTTATAAAATAATCATTAAA-CTTATCAAAGT
* * *
79432 GTTACAACAT-ATCATCAAACTTATCAAAGT
1 GTTATAAAATAATCATTAAACTTATCAAAGT
*
79462 GTTATAAAATAATCCTTAAACTTAT
1 GTTATAAAATAATCATTAAACTTAT
79487 AAAATTTCAT
Statistics
Matches: 44, Mismatches: 10, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
30 16 0.36
31 20 0.45
32 8 0.18
ACGTcount: A:0.44, C:0.13, G:0.05, T:0.39
Consensus pattern (31 bp):
GTTATAAAATAATCATTAAACTTATCAAAGT
Found at i:86748 original size:2 final size:2
Alignment explanation
Indices: 86743--86770 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
86733 CCTCTCTCCC
86743 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
86771 ACATATTTAA
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):
TA
Found at i:88563 original size:34 final size:32
Alignment explanation
Indices: 88522--88623 Score: 100
Period size: 34 Copynumber: 3.1 Consensus size: 32
88512 TTACTCCAAC
88522 TAAAATATCTTTTAATATTCAAATTTAAACAGA
1 TAAAATATCTTTTAATATTCAAATTTAAA-AGA
*
88555 TAATAATATCTTTTAAT-TTAAAATATTCAAAAGA
1 TAA-AATATCTTTTAATATTCAAAT-TT-AAAAGA
** *
88589 TAAAATCA-CTTTTTCTATTCAAACTTAAATAGA
1 TAAAAT-ATCTTTTAATATTCAAATTTAAA-AGA
88622 TA
1 TA
88624 TTATTTTAAT
Statistics
Matches: 58, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
32 3 0.05
33 25 0.43
34 27 0.47
35 3 0.05
ACGTcount: A:0.47, C:0.10, G:0.03, T:0.40
Consensus pattern (32 bp):
TAAAATATCTTTTAATATTCAAATTTAAAAGA
Found at i:88593 original size:67 final size:66
Alignment explanation
Indices: 88522--88743 Score: 190
Period size: 62 Copynumber: 3.4 Consensus size: 66
88512 TTACTCCAAC
* *
88522 TAAAATATCTTTTAATATTCAAATTTAAACAGATAATAATATCTTTTAATTTAAAATATTCAAAA
1 TAAAATATCTTTTAATATTCAAATTTAAATAGATAATAATA-CTTTTAATTTGAAATATTCAAAA
88587 GA
65 GA
** *
88589 TAAAATCA-CTTTTTCTATTCAAACTTAAATAGAT-AT--TA-TTTTAATTTGAAATATTCAAAA
1 TAAAAT-ATCTTTTAATATTCAAATTTAAATAGATAATAATACTTTTAATTTGAAATATTCAAAA
88649 GGA
65 -GA
* * * * * * * *
88652 TATATTATC-TTTAACATTCAAAGTTAAATAGGTAACAAATAACTTTTAATTTGATATATT-TAA
1 TAAAATATCTTTTAATATTCAAATTTAAATAGATAA-TAAT-ACTTTTAATTTGAAATATTCAAA
88715 AGA
64 AGA
* *
88718 -ATAATTATCTCATTAATATTCAAATT
1 TA-AAATATCT-TTTAATATTCAAATT
88744 AAAAATATCC
Statistics
Matches: 124, Mismatches: 19, Indels: 23
0.75 0.11 0.14
Matches are distributed among these distances:
62 41 0.33
63 8 0.06
64 2 0.02
65 1 0.01
66 11 0.09
67 32 0.26
68 29 0.23
ACGTcount: A:0.45, C:0.09, G:0.05, T:0.41
Consensus pattern (66 bp):
TAAAATATCTTTTAATATTCAAATTTAAATAGATAATAATACTTTTAATTTGAAATATTCAAAAG
A
Found at i:91401 original size:2 final size:2
Alignment explanation
Indices: 91394--91434 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
91384 ACTTCTTTAT
91394 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
91435 TATTTTGAAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:95027 original size:20 final size:20
Alignment explanation
Indices: 94999--95042 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
94989 ATTAAGTGCC
*
94999 TGCCCATTTG-AAGGACCACT
1 TGCCAATTTGCAAGG-CCACT
*
95019 TGCCAATTTGCAAGGCTACT
1 TGCCAATTTGCAAGGCCACT
95039 TGCC
1 TGCC
95043 CTACACGGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.27
Consensus pattern (20 bp):
TGCCAATTTGCAAGGCCACT
Found at i:98604 original size:15 final size:16
Alignment explanation
Indices: 98578--98607 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
98568 TTTTTATTTG
98578 AAAATTATTTAAAATT
1 AAAATTATTTAAAATT
98594 AAAATTA-TTAAAAT
1 AAAATTATTTAAAAT
98608 ATTTTAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
AAAATTATTTAAAATT
Found at i:98955 original size:74 final size:74
Alignment explanation
Indices: 98779--99029 Score: 207
Period size: 76 Copynumber: 3.4 Consensus size: 74
98769 AAAAAATTGG
* ** *
98779 AAAACATATATATTATATAG---TTTAAAAAAAAGCATTGTGGAAATATATAT-ATA-ATTTTTG
1 AAAACATATATAATATATAGATTTTTAAAAAAAA-CATT-TTAAAATATATATAATATAATTTTG
* *
98839 AAAGCATTTTCG
64 AAAACATTTT-A
* * *
98851 AAAACATATATATTATATAGTTTTTATAAAAAAAACATTTTAAAATATATATAATATAATTTCCG
1 AAAACATATATAATATATAGATTTT-TAAAAAAAACATTTTAAAATATATATAATATAATTT-TG
98916 AAAACATTTTA
64 AAAACATTTTA
* * * *
98927 AAAATATGTATAATATATA-ATTTTT-AAAAAAACAGTTTGAAAAATATTTATAATATATAGTTT
1 AAAACATATATAATATATAGATTTTTAAAAAAAACA-TTT-TAAAATATATATAATATA-A-TTT
*
98990 TTAAAACATTTT-
62 TGAAAACATTTTA
* *
99002 AAAAC-TATATAGTATAT-GATTTTGAAAA
1 AAAACATATATAATATATAGATTTTTAAAA
99030 CATTTTTTAG
Statistics
Matches: 148, Mismatches: 18, Indels: 23
0.78 0.10 0.12
Matches are distributed among these distances:
72 20 0.14
73 9 0.06
74 30 0.20
75 36 0.24
76 40 0.27
77 13 0.09
ACGTcount: A:0.49, C:0.05, G:0.07, T:0.39
Consensus pattern (74 bp):
AAAACATATATAATATATAGATTTTTAAAAAAAACATTTTAAAATATATATAATATAATTTTGAA
AACATTTTA
Found at i:98970 original size:40 final size:39
Alignment explanation
Indices: 98916--98995 Score: 124
Period size: 40 Copynumber: 2.0 Consensus size: 39
98906 ATAATTTCCG
*
98916 AAAACATTTTAAAAATATGTATAATATATAATTTTTAAA
1 AAAACATTTGAAAAATATGTATAATATATAATTTTTAAA
* *
98955 AAAACAGTTTGAAAAATATTTATAATATATAGTTTTTAAA
1 AAAACA-TTTGAAAAATATGTATAATATATAATTTTTAAA
98995 A
1 A
98996 CATTTTAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
39 6 0.16
40 31 0.84
ACGTcount: A:0.53, C:0.03, G:0.05, T:0.40
Consensus pattern (39 bp):
AAAACATTTGAAAAATATGTATAATATATAATTTTTAAA
Found at i:99030 original size:34 final size:36
Alignment explanation
Indices: 98882--99035 Score: 124
Period size: 34 Copynumber: 4.3 Consensus size: 36
98872 TTTTATAAAA
*
98882 AAAACATTTT-AAAATA-TAT-ATAATATAA-TTTCCG
1 AAAACATTTTAAAAATATTATAAT-ATATAAGTTT-TG
* *
98916 AAAACATTTTAAAAATATGTATAATATATAATTTTTAAA
1 AAAACATTTTAAAAATAT-TATAATATATAAGTTTT--G
* *
98955 AAAACAGTTTGAAAAATATTTATAATATAT-AGTTTTT
1 AAAACA-TTTTAAAAATA-TTATAATATATAAGTTTTG
* * *
98992 AAAACATTTTAAAACTA-TATAGTATATGA-TTTTG
1 AAAACATTTTAAAAATATTATAATATATAAGTTTTG
99026 AAAACATTTT
1 AAAACATTTT
99036 TTAGAAAGTA
Statistics
Matches: 101, Mismatches: 9, Indels: 20
0.78 0.07 0.15
Matches are distributed among these distances:
34 33 0.33
35 7 0.07
36 9 0.09
37 15 0.15
38 5 0.05
39 11 0.11
40 20 0.20
41 1 0.01
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.41
Consensus pattern (36 bp):
AAAACATTTTAAAAATATTATAATATATAAGTTTTG
Found at i:99054 original size:36 final size:32
Alignment explanation
Indices: 98979--99054 Score: 82
Period size: 34 Copynumber: 2.2 Consensus size: 32
98969 AATATTTATA
*
98979 ATATATA-GTTTTTAAAACATTTTAAAACTAT
1 ATATATATGTTTTGAAAACATTTTAAAACTAT
*
99010 ATAGTATATGATTTTGAAAACATTTTTTAGAAAGTAT
1 ATA-TATATG-TTTTGAAAACA--TTTTA-AAACTAT
99047 ATATATAT
1 ATATATAT
99055 AATATAATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
31 3 0.08
32 4 0.11
33 1 0.03
34 10 0.27
36 10 0.27
37 9 0.24
ACGTcount: A:0.43, C:0.04, G:0.08, T:0.45
Consensus pattern (32 bp):
ATATATATGTTTTGAAAACATTTTAAAACTAT
Found at i:99618 original size:13 final size:13
Alignment explanation
Indices: 99602--99631 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
99592 CGAATTGAGT
99602 TTTTAAATTTTAA
1 TTTTAAATTTTAA
*
99615 TTTTAATTTTTAA
1 TTTTAAATTTTAA
99628 TTTT
1 TTTT
99632 CGCAATTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTTAAATTTTAA
Found at i:101273 original size:25 final size:26
Alignment explanation
Indices: 101221--101274 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
101211 GTTAGTTTTT
* *
101221 AAGTTTGAGTCAAATTAAAATTTAAA
1 AAGTTCGAGTCAAATTAAAAATTAAA
101247 AAGTTCGAGTC-AATTGAAAAATTAAA
1 AAGTTCGAGTCAAATT-AAAAATTAAA
101273 AA
1 AA
101275 TCCAACTGAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 4 0.16
26 21 0.84
ACGTcount: A:0.52, C:0.06, G:0.13, T:0.30
Consensus pattern (26 bp):
AAGTTCGAGTCAAATTAAAAATTAAA
Found at i:101553 original size:2 final size:2
Alignment explanation
Indices: 101546--101625 Score: 153
Period size: 2 Copynumber: 40.5 Consensus size: 2
101536 TACCACTACA
101546 AT AT AT AT AT AT AT AT AT AT -T 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
101587 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
101626 ACTTCAATTA
Statistics
Matches: 77, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 76 0.99
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:102493 original size:12 final size:13
Alignment explanation
Indices: 102465--102502 Score: 53
Period size: 12 Copynumber: 3.1 Consensus size: 13
102455 TAGAGAATAT
*
102465 TAATCATGTACAA
1 TAATCATGTATAA
102478 TAATCATGT-TAA
1 TAATCATGTATAA
102490 TAAT-ATGTATAA
1 TAATCATGTATAA
102502 T
1 T
102503 TATTTTTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
11 4 0.17
12 10 0.43
13 9 0.39
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.39
Consensus pattern (13 bp):
TAATCATGTATAA
Found at i:104564 original size:2 final size:2
Alignment explanation
Indices: 104559--104594 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
104549 TCACACATTT
104559 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
104595 ACATATACAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:107411 original size:27 final size:27
Alignment explanation
Indices: 107358--107411 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 27
107348 TCATTTTAAT
* * *
107358 TATCTATCGTTAAAAAATTAACTATAA
1 TATCTATCATTAAAAAATAAACCATAA
107385 TATC-ATCATTAAAAAATAAGACCATAA
1 TATCTATCATTAAAAAATAA-ACCATAA
107412 GAATGAGTAG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 13 0.57
27 10 0.43
ACGTcount: A:0.52, C:0.13, G:0.04, T:0.31
Consensus pattern (27 bp):
TATCTATCATTAAAAAATAAACCATAA
Found at i:107920 original size:60 final size:60
Alignment explanation
Indices: 107834--107970 Score: 161
Period size: 60 Copynumber: 2.3 Consensus size: 60
107824 TAAATTGATT
* * * *
107834 AAAAAATATTTTAGGTACCTAAATGAAAGGAT-T-GTATATTTTAGGTACCTATTTTGATCC
1 AAAAAATATTTTAGGTACCTAAATGAAA-AATATAGTATACTTTAGATACCTACTTTGA-CC
* * *
107894 AAAAAATATTTTAGGTACTTGAATGAAAAATATAGTATACTTTAGATACCTACTTTGACT
1 AAAAAATATTTTAGGTACCTAAATGAAAAATATAGTATACTTTAGATACCTACTTTGACC
* *
107954 AAACAATAATTTAGGTA
1 AAAAAATATTTTAGGTA
107971 TTTAGATAAA
Statistics
Matches: 66, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
59 2 0.03
60 43 0.65
61 21 0.32
ACGTcount: A:0.41, C:0.09, G:0.13, T:0.36
Consensus pattern (60 bp):
AAAAAATATTTTAGGTACCTAAATGAAAAATATAGTATACTTTAGATACCTACTTTGACC
Found at i:107984 original size:61 final size:61
Alignment explanation
Indices: 107834--107999 Score: 142
Period size: 60 Copynumber: 2.7 Consensus size: 61
107824 TAAATTGATT
* * * * ** * * *
107834 AAAAAATATTTTAGGTACCTAAATGAAAGGAT-TGTATATTTTAGGTACCTATTTTGATCC
1 AAAAAATAATTTAGGTACTTGAATAAAAAAATATGTATACTTTAGATACCTACTTTGATCC
* * *
107894 AAAAAATATTTTAGGTACTTGAAT-GAAAAATATAGTATACTTTAGATACCTACTTTGA-CT
1 AAAAAATAATTTAGGTACTTGAATAAAAAAATAT-GTATACTTTAGATACCTACTTTGATCC
* *
107954 AAACAATAATTTAGGTA-TTTAGATAAAAAAAATATGATATACTTTA
1 AAAAAATAATTTAGGTACTTGA-AT-AAAAAAATATG-TATACTTTA
108000 TATAATTATT
Statistics
Matches: 87, Mismatches: 13, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
59 7 0.08
60 41 0.47
61 22 0.25
62 17 0.20
ACGTcount: A:0.43, C:0.08, G:0.12, T:0.37
Consensus pattern (61 bp):
AAAAAATAATTTAGGTACTTGAATAAAAAAATATGTATACTTTAGATACCTACTTTGATCC
Found at i:113438 original size:12 final size:13
Alignment explanation
Indices: 113408--113441 Score: 52
Period size: 12 Copynumber: 2.6 Consensus size: 13
113398 TTATTTTATA
113408 TTAAATAATAAATT
1 TTAAA-AATAAATT
113422 TTAAAAATAAA-T
1 TTAAAAATAAATT
113434 TTAAAAAT
1 TTAAAAAT
113442 TATTTCACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 9 0.45
13 6 0.30
14 5 0.25
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
TTAAAAATAAATT
Found at i:115371 original size:2 final size:2
Alignment explanation
Indices: 115364--115392 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
115354 TTGATTTGTT
115364 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
115393 TCATTTTAAT
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:118982 original size:12 final size:12
Alignment explanation
Indices: 118965--118989 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
118955 TTTAATTAAA
118965 AAAAAATAAAAT
1 AAAAAATAAAAT
118977 AAAAAATAAAAT
1 AAAAAATAAAAT
118989 A
1 A
118990 CTTCAAGTAT
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:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (12 bp):
AAAAAATAAAAT
Found at i:136421 original size:30 final size:30
Alignment explanation
Indices: 136373--136510 Score: 195
Period size: 30 Copynumber: 4.6 Consensus size: 30
136363 TTTAACACCC
* * * * *
136373 ATATCTGAATTTCTTATTAGTACTTGAGCT
1 ATATCCGATTTTCATATTAGTACTTAAACT
* * *
136403 ATATTCGATTTTCATATTAGTACTTGAGCT
1 ATATCCGATTTTCATATTAGTACTTAAACT
*
136433 ATATTCGATTTTCATATTAGTACTTAAACT
1 ATATCCGATTTTCATATTAGTACTTAAACT
136463 ATATCCGATTTTCATATTAGTACTTAAACT
1 ATATCCGATTTTCATATTAGTACTTAAACT
136493 ATATCCGATTTTCATATT
1 ATATCCGATTTTCATATT
136511 GGAATGTGAG
Statistics
Matches: 101, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 101 1.00
ACGTcount: A:0.30, C:0.14, G:0.09, T:0.46
Consensus pattern (30 bp):
ATATCCGATTTTCATATTAGTACTTAAACT
Found at i:139654 original size:30 final size:30
Alignment explanation
Indices: 139618--139838 Score: 307
Period size: 30 Copynumber: 7.4 Consensus size: 30
139608 AACTATCCTA
* *
139618 ATTTTCATATTAGTACTTAAACTACATCAG
1 ATTTTCATATTAGTACTTAAACTATATCCG
* *
139648 ATTTTCATATTAGTACTTAAGCTATATCCT
1 ATTTTCATATTAGTACTTAAACTATATCCG
* ** *
139678 ATTTTTATATTAGTACTTAATGTATACCCG
1 ATTTTCATATTAGTACTTAAACTATATCCG
* * *
139708 ATTTTCATATTAGTACTTAAACCATAACTG
1 ATTTTCATATTAGTACTTAAACTATATCCG
* * * *
139738 AATTTCATATTAGTACTTAAGCTGTATTCG
1 ATTTTCATATTAGTACTTAAACTATATCCG
139768 ATTTTCATATTAGTACTTAAACTATATCCG
1 ATTTTCATATTAGTACTTAAACTATATCCG
139798 ATTTTCATATTAGTACTTAAACTATATCCG
1 ATTTTCATATTAGTACTTAAACTATATCCG
139828 ATTTTCATATT
1 ATTTTCATATT
139839 GGAATGTGTG
Statistics
Matches: 165, Mismatches: 26, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 165 1.00
ACGTcount: A:0.33, C:0.15, G:0.08, T:0.44
Consensus pattern (30 bp):
ATTTTCATATTAGTACTTAAACTATATCCG
Found at i:145859 original size:31 final size:32
Alignment explanation
Indices: 145824--145884 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
145814 TTTTGATTCT
145824 CCCTTATT-TTCTATGGTAATTATACTTTGCC
1 CCCTTATTATTCTATGGTAATTATACTTTGCC
* * *
145855 CCCTTATTATTTTGTGGTAATTATATTTTG
1 CCCTTATTATTCTATGGTAATTATACTTTG
145885 TCTTATTGAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 8 0.31
32 18 0.69
ACGTcount: A:0.20, C:0.16, G:0.11, T:0.52
Consensus pattern (32 bp):
CCCTTATTATTCTATGGTAATTATACTTTGCC
Found at i:148616 original size:16 final size:16
Alignment explanation
Indices: 148591--148629 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
148581 AGCAATGGCC
148591 ATTTTT-AGTTATGTA
1 ATTTTTCAGTTATGTA
148606 ATTTTTCAGTTATGTA
1 ATTTTTCAGTTATGTA
148622 ATTTTTCA
1 ATTTTTCA
148630 ACTTCTGACA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 6 0.26
16 17 0.74
ACGTcount: A:0.26, C:0.05, G:0.10, T:0.59
Consensus pattern (16 bp):
ATTTTTCAGTTATGTA
Found at i:170904 original size:21 final size:21
Alignment explanation
Indices: 170878--170917 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
170868 CAGAACCCCA
*
170878 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
170899 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
170918 TCAAAGGAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:179789 original size:16 final size:16
Alignment explanation
Indices: 179754--179789 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
179744 TAAAGGGAGT
* *
179754 AAGTATTCTTTAGTGT
1 AAGTATTCTTTAATGC
179770 AAGTATTCTTTAATGC
1 AAGTATTCTTTAATGC
179786 AAGT
1 AAGT
179790 GTTGAAACCC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.31, C:0.08, G:0.17, T:0.44
Consensus pattern (16 bp):
AAGTATTCTTTAATGC
Found at i:183520 original size:19 final size:18
Alignment explanation
Indices: 183475--183522 Score: 62
Period size: 19 Copynumber: 2.7 Consensus size: 18
183465 ATCAAATTTG
183475 TTAT-TTAACGACCGTTA
1 TTATGTTAACGACCGTTA
*
183492 TTATGATAACAGACCGTTA
1 TTATGTTAAC-GACCGTTA
*
183511 TTCTGTTAACGA
1 TTATGTTAACGA
183523 TATGTTATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 4 0.15
18 6 0.23
19 16 0.62
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.38
Consensus pattern (18 bp):
TTATGTTAACGACCGTTA
Found at i:193459 original size:13 final size:13
Alignment explanation
Indices: 193441--193479 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 13
193431 TATTTTTTTT
193441 AAAAAAAAAGTAA
1 AAAAAAAAAGTAA
193454 AAAAAAATAAG-AA
1 AAAAAAA-AAGTAA
193467 AAAGAAAAAAGTA
1 AAA-AAAAAAGTA
193480 TTCTCTCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
13 15 0.65
14 8 0.35
ACGTcount: A:0.82, C:0.00, G:0.10, T:0.08
Consensus pattern (13 bp):
AAAAAAAAAGTAA
Found at i:197332 original size:43 final size:43
Alignment explanation
Indices: 197271--197353 Score: 121
Period size: 43 Copynumber: 1.9 Consensus size: 43
197261 ATCAAATTAG
* * *
197271 GTATTTTTGGTCAAAAAGGGTAAATGGGAAAAAGGATTGAGTA
1 GTATTTGTGGTCAAAAAGGGGAAATAGGAAAAAGGATTGAGTA
* *
197314 GTATTTGTGGTCAAAAAGGGGAAATAGGAACACGGATTGA
1 GTATTTGTGGTCAAAAAGGGGAAATAGGAAAAAGGATTGA
197354 CCATGCAAGA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 35 1.00
ACGTcount: A:0.39, C:0.05, G:0.31, T:0.25
Consensus pattern (43 bp):
GTATTTGTGGTCAAAAAGGGGAAATAGGAAAAAGGATTGAGTA
Found at i:200294 original size:30 final size:30
Alignment explanation
Indices: 200258--200320 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
200248 CTTCAGCAGA
200258 TTTGCATGGAAGCTTGGAGCTCTCGGCGTC
1 TTTGCATGGAAGCTTGGAGCTCTCGGCGTC
* *
200288 TTTGCATGGAAGGTTGGATCTCTCGGCGTC
1 TTTGCATGGAAGCTTGGAGCTCTCGGCGTC
200318 TTT
1 TTT
200321 AACACAATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.13, C:0.21, G:0.32, T:0.35
Consensus pattern (30 bp):
TTTGCATGGAAGCTTGGAGCTCTCGGCGTC
Found at i:200549 original size:23 final size:24
Alignment explanation
Indices: 200518--200579 Score: 110
Period size: 24 Copynumber: 2.7 Consensus size: 24
200508 GGGTTGAGCA
200518 GGGG-CTGCACGTCTGCATGT-GG
1 GGGGCCTGCACGTCTGCATGTGGG
200540 GGGGCCTGCACGTCTGCATGTGGG
1 GGGGCCTGCACGTCTGCATGTGGG
200564 GGGGCCTGCACGTCTG
1 GGGGCCTGCACGTCTG
200580 TATCATGCAA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
22 4 0.11
23 16 0.42
24 18 0.47
ACGTcount: A:0.08, C:0.26, G:0.45, T:0.21
Consensus pattern (24 bp):
GGGGCCTGCACGTCTGCATGTGGG
Found at i:203186 original size:31 final size:31
Alignment explanation
Indices: 203134--203193 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
203124 TTCCAACACC
*
203134 TTTCTTTTACTTTTGCATTGTTTTCAATCCA
1 TTTCTTTTACTTTTGCATTGTTTTAAATCCA
* *
203165 TTTCTTTTGCTTTT-TATTTGTTTTAAATC
1 TTTCTTTTACTTTTGCA-TTGTTTTAAATC
203194 AAATAAGTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 1 0.04
31 24 0.96
ACGTcount: A:0.15, C:0.15, G:0.07, T:0.63
Consensus pattern (31 bp):
TTTCTTTTACTTTTGCATTGTTTTAAATCCA
Found at i:217396 original size:6 final size:6
Alignment explanation
Indices: 217385--217437 Score: 70
Period size: 6 Copynumber: 8.3 Consensus size: 6
217375 CTTCAGCCAC
*
217385 GAGGAA GAGGAA GACGAGAAA GAGGAA GAGGAA GAGGAA GTGGAA GAGGAA
1 GAGGAA GAGGAA GA-G-G-AA GAGGAA GAGGAA GAGGAA GAGGAA GAGGAA
217436 GA
1 GA
217438 CCAGCTACCA
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
6 34 0.81
7 2 0.05
8 2 0.05
9 4 0.10
ACGTcount: A:0.49, C:0.02, G:0.47, T:0.02
Consensus pattern (6 bp):
GAGGAA
Found at i:217542 original size:2 final size:2
Alignment explanation
Indices: 217505--217533 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
217495 TCAGTGTGTA
217505 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 A
217534 GCCTATATAG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:217685 original size:29 final size:29
Alignment explanation
Indices: 217643--217731 Score: 124
Period size: 29 Copynumber: 3.1 Consensus size: 29
217633 TACCGGGGGT
*
217643 AGGTCGCCATGCACGCCCGGCGACCTACC
1 AGGTCGCCATGCACGCCCAGCGACCTACC
***
217672 AGGTCGCCATGCACGCCCAGCGACCTGGT
1 AGGTCGCCATGCACGCCCAGCGACCTACC
* *
217701 AGGTCGCCATGCATGCCCTGCGACCTACC
1 AGGTCGCCATGCACGCCCAGCGACCTACC
217730 AG
1 AG
217732 CCAACGACCT
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 51 1.00
ACGTcount: A:0.18, C:0.40, G:0.28, T:0.13
Consensus pattern (29 bp):
AGGTCGCCATGCACGCCCAGCGACCTACC
Found at i:217761 original size:10 final size:10
Alignment explanation
Indices: 217746--217803 Score: 55
Period size: 10 Copynumber: 5.6 Consensus size: 10
217736 CGACCTCCAT
217746 GCCCATGCAC
1 GCCCATGCAC
217756 GCCCATGCAC
1 GCCCATGCAC
*
217766 GCCCAT-CTC
1 GCCCATGCAC
* *
217775 GCCAAAGGAGCAC
1 GCC-CA--TGCAC
217788 GCCCATGCAC
1 GCCCATGCAC
217798 GCCCAT
1 GCCCAT
217804 CCATGCCCTG
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
9 5 0.13
10 27 0.71
12 1 0.03
13 5 0.13
ACGTcount: A:0.22, C:0.47, G:0.21, T:0.10
Consensus pattern (10 bp):
GCCCATGCAC
Found at i:218086 original size:29 final size:29
Alignment explanation
Indices: 218025--218108 Score: 96
Period size: 29 Copynumber: 2.9 Consensus size: 29
218015 ATGAATCCTT
** * **
218025 GGTCGCCCCGAGTGCATGGCGACCTCCTT
1 GGTCGCCGGGAGTGCATGGCGACCTACGA
* *
218054 GGTCGCCGGGCGTGCATGGCGACCTAGGA
1 GGTCGCCGGGAGTGCATGGCGACCTACGA
*
218083 GGTCGCTGGGAGTGCATGGCGACCTA
1 GGTCGCCGGGAGTGCATGGCGACCTA
218109 TGGTTGGGTT
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 46 1.00
ACGTcount: A:0.13, C:0.30, G:0.39, T:0.18
Consensus pattern (29 bp):
GGTCGCCGGGAGTGCATGGCGACCTACGA
Found at i:218274 original size:2 final size:2
Alignment explanation
Indices: 218267--218294 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
218257 GAGTTTAGCC
218267 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
218295 ATTGATGTTG
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):
TA
Found at i:224295 original size:25 final size:25
Alignment explanation
Indices: 224261--224310 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
224251 CGATGATGAT
224261 GATTAAGATGAGGGAACAAGAAATA
1 GATTAAGATGAGGGAACAAGAAATA
224286 GATTAAGATGAGGGAACAAGAAATA
1 GATTAAGATGAGGGAACAAGAAATA
224311 CAAAGGAGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.52, C:0.04, G:0.28, T:0.16
Consensus pattern (25 bp):
GATTAAGATGAGGGAACAAGAAATA
Found at i:228500 original size:75 final size:75
Alignment explanation
Indices: 228382--228602 Score: 212
Period size: 75 Copynumber: 2.9 Consensus size: 75
228372 AATGTGGATA
* * * * *
228382 GGTACTAGGAACGAAAAATTAGAATACAAATTATTACTCGTATGCACACATTTTACCATGAATGT
1 GGTACTAGAAACGAAAAATTAGAATACAAATCACTACTCGTATGAACAAATTTTACCATGAATGT
228447 GGATCGATTC
66 GGATCGATTC
* * * * *
228457 GGTACTAGAAATGAAAAATTAGAATATAAATCACTATTTGTATGAACAAATTTTATCATGAATGT
1 GGTACTAGAAACGAAAAATTAGAATACAAATCACTACTCGTATGAACAAATTTTACCATGAATGT
* *
228522 GGGTCG-GTC
66 GGATCGATTC
* * * * * * * * * *
228531 TGGTACCAGGAACAAAAAATTAGAATGCCAATCGCCT-CCCATATAAACAAATTTTATCATGAAT
1 -GGTACTAGAAACGAAAAATTAGAATACAAATC-ACTACTCGTATGAACAAATTTTACCATGAAT
228595 GTGGATCG
64 GTGGATCG
228603 GTCTGATACT
Statistics
Matches: 118, Mismatches: 26, Indels: 4
0.80 0.18 0.03
Matches are distributed among these distances:
74 2 0.02
75 114 0.97
76 2 0.02
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29
Consensus pattern (75 bp):
GGTACTAGAAACGAAAAATTAGAATACAAATCACTACTCGTATGAACAAATTTTACCATGAATGT
GGATCGATTC
Found at i:241514 original size:24 final size:24
Alignment explanation
Indices: 241468--241516 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
241458 AAGGGGGAAA
*
241468 TCTAGTGATAAACAGATATTTTTT
1 TCTAGTGATAAACAGATAATTTTT
* * *
241492 TCTAGTGATAGACCGTTAATTTTT
1 TCTAGTGATAAACAGATAATTTTT
241516 T
1 T
241517 TTTCTATCGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.29, C:0.10, G:0.14, T:0.47
Consensus pattern (24 bp):
TCTAGTGATAAACAGATAATTTTT
Found at i:252672 original size:13 final size:13
Alignment explanation
Indices: 252654--252678 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
252644 AATTTTTTTT
252654 AAAAAATCTAAAG
1 AAAAAATCTAAAG
252667 AAAAAATCTAAA
1 AAAAAATCTAAA
252679 ATTTCTTAAA
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:0.72, C:0.08, G:0.04, T:0.16
Consensus pattern (13 bp):
AAAAAATCTAAAG
Found at i:254381 original size:32 final size:32
Alignment explanation
Indices: 254293--254382 Score: 112
Period size: 32 Copynumber: 2.8 Consensus size: 32
254283 ATAATAATAA
* *
254293 AGTTTGATAAG-TATAAGGATCATTTTGTAAT
1 AGTTTGATAAGTTTTAATGATCATTTTGTAAT
*
254324 AGTTTGATAAGTTTTAATGACCATTTTGTAAT
1 AGTTTGATAAGTTTTAATGATCATTTTGTAAT
* *
254356 AGTTTGGTAAAG-TTTAGTGATCATTTT
1 AGTTTGAT-AAGTTTTAATGATCATTTT
254383 ATAACTTTTA
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
31 11 0.22
32 37 0.73
33 3 0.06
ACGTcount: A:0.31, C:0.04, G:0.19, T:0.46
Consensus pattern (32 bp):
AGTTTGATAAGTTTTAATGATCATTTTGTAAT
Found at i:259253 original size:2 final size:2
Alignment explanation
Indices: 259246--259272 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
259236 ACTAAAAACA
259246 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 A
259273 GAGAGAGAGA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:259277 original size:2 final size:2
Alignment explanation
Indices: 259272--259296 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
259262 ATATATATAT
259272 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
259297 ATCGATAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:260629 original size:3 final size:3
Alignment explanation
Indices: 260611--260662 Score: 54
Period size: 3 Copynumber: 17.3 Consensus size: 3
260601 GCTGTTAGAT
* *
260611 GAA GAA GAT GAT GAA GAA GAA GAA GAA GACA -AA GATA G-A GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GA-A GAA GA-A GAA GAA GAA
260656 GAA GAA G
1 GAA GAA G
260663 GTGATGATGG
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
2 3 0.07
3 37 0.86
4 3 0.07
ACGTcount: A:0.60, C:0.02, G:0.33, T:0.06
Consensus pattern (3 bp):
GAA
Found at i:268238 original size:3 final size:3
Alignment explanation
Indices: 268230--268314 Score: 66
Period size: 3 Copynumber: 28.7 Consensus size: 3
268220 CTGTAATATG
* * * *
268230 TAA TAA TAA TATT TAT TAA TAA AAA T-A TAA TAA TAA TAG TAA TAA
1 TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * *
268275 TTA TAA CAA TTA TAA TAA TTA TAA TAA TAA AAA TAA -AA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
268315 GGCAAAAATT
Statistics
Matches: 63, Mismatches: 16, Indels: 6
0.74 0.19 0.07
Matches are distributed among these distances:
2 4 0.06
3 57 0.90
4 2 0.03
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:268677 original size:58 final size:58
Alignment explanation
Indices: 268584--268699 Score: 187
Period size: 58 Copynumber: 2.0 Consensus size: 58
268574 TGAAAATGTG
* *
268584 GATGCTAATATATCTCCTTCTATGATAGATTATACAAAAGGTTGAACAAGCTCTTCTC
1 GATGCTAATATATCTCCTTCTATGATAGATCATACAAAAGGTTGAACAAACTCTTCTC
* * *
268642 GATGCTAATCTATCTCCTTCTGTGATAGATCATACAAAAGGTTGAACAAATTCTTCTC
1 GATGCTAATATATCTCCTTCTATGATAGATCATACAAAAGGTTGAACAAACTCTTCTC
268700 ATTATGAACT
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
58 53 1.00
ACGTcount: A:0.32, C:0.20, G:0.14, T:0.34
Consensus pattern (58 bp):
GATGCTAATATATCTCCTTCTATGATAGATCATACAAAAGGTTGAACAAACTCTTCTC
Found at i:268875 original size:124 final size:124
Alignment explanation
Indices: 268649--269250 Score: 821
Period size: 124 Copynumber: 5.0 Consensus size: 124
268639 CTCGATGCTA
**
268649 ATCTATCTCCTTCTGTGATAGA-TCATAC-AAAAGGTTGAACAAATTCTTCTCATTATGAACTTC
1 ATCTATCTCCTTCTGTGATAGAGTCATACAAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTC
*
268712 TTCTT-CTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGTTG
66 TTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAAC-TTCTCTGGAAAAGTTGATGTTG
*
268771 ATCTATCTCCTTCTGTGATAGAGTCATGCAAAAA-GTTGAACAAGCTCTTCTCATTATGAACTTC
1 ATCTATCTCCTTCTGTGATAGAGTCATACAAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTC
268835 TTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTTCTCTGGAAAAGTTGATGTTG
66 TTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAAC-TTCTCTGGAAAAGTTGATGTTG
*
268895 ATCTATCTCCTTCTGTGATAGAGTCATGCAAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTC
1 ATCTATCTCCTTCTGTGATAGAGTCATACAAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTC
* *
268960 TTCTTCCTTCTTAAGATGAGTTATTCTTATTATGAACTTCTCTGGAAAAGTTGATGTTG
66 TTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTCTCTGGAAAAGTTGATGTTG
*
269019 ATCTATCTCCTTCTGTGATAGAGTCATACAAAAAGGTTAAACAAGCTCTTCTCATTATGAACTTC
1 ATCTATCTCCTTCTGTGATAGAGTCATACAAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTC
*
269084 TTCTTCATTCTTCAGATGAG---TTCTTATTATGAACTTCTTCTGG-AAA----A-GTTG
66 TTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTC-TCTGGAAAAGTTGATGTTG
* *** * * ** *
269135 ATCCA--T-C--GAATGAT-GAATTCAAAC-AAAAGGTTTGAACAAATTCTTCTCATTATGAATT
1 ATCTATCTCCTTCTGTGATAG-AGTCATACAAAAAGG-TTGAACAAGCTCTTCTCATTATGAACT
* * *
269193 TCTTCTTCCTTCTTCAGACGAGTTCTTCTTATTATGAACTCTTTCTGGAAATGTTGAT
64 TCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACT-TCTCTGGAAAAGTTGAT
269251 CCATCAAATG
Statistics
Matches: 439, Mismatches: 24, Indels: 36
0.88 0.05 0.07
Matches are distributed among these distances:
110 7 0.02
111 53 0.12
113 1 0.00
114 21 0.05
115 3 0.01
116 8 0.02
117 1 0.00
119 1 0.00
121 20 0.05
122 27 0.06
123 38 0.09
124 194 0.44
125 65 0.15
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.40
Consensus pattern (124 bp):
ATCTATCTCCTTCTGTGATAGAGTCATACAAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTC
TTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTCTCTGGAAAAGTTGATGTTG
Found at i:269181 original size:111 final size:112
Alignment explanation
Indices: 269065--269268 Score: 313
Period size: 114 Copynumber: 1.8 Consensus size: 112
269055 TTAAACAAGC
*
269065 TCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAG-TTCTTATTATGAACT-TCTTCTGGA
1 TCTTCTCATTATGAACTTCTTCTTCATTCTTCAGACGAGTTTCTTATTATGAACTCT-TTCTGGA
*
269128 AAAGTTGATCCATCGAATGATGAATTCAAACAAAAGGTTTGAACAAAT
65 AAAGTTGATCCATCAAATGATGAATTCAAACAAAAGGTTTGAACAAAT
* *
269176 TCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGACGAGTTCTTCTTATTATGAACTCTTTCTGG
1 TCTTCTCATTATGAACTTCTTCTTCATTCTTCAGACGAG-T-TTCTTATTATGAACTCTTTCTGG
* *
269241 AAATGTTGATCCATCAAATGATGGATTC
64 AAAAGTTGATCCATCAAATGATGAATTC
269269 GAATCTTTGC
Statistics
Matches: 83, Mismatches: 6, Indels: 5
0.88 0.06 0.05
Matches are distributed among these distances:
111 36 0.43
114 46 0.55
115 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.13, T:0.41
Consensus pattern (112 bp):
TCTTCTCATTATGAACTTCTTCTTCATTCTTCAGACGAGTTTCTTATTATGAACTCTTTCTGGAA
AAGTTGATCCATCAAATGATGAATTCAAACAAAAGGTTTGAACAAAT
Found at i:270439 original size:18 final size:18
Alignment explanation
Indices: 270416--270450 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
270406 TATGTGAAAC
*
270416 AAATTGAATTTTAAAAAT
1 AAATTGAATTTCAAAAAT
270434 AAATTGAATTTCAAAAA
1 AAATTGAATTTCAAAAA
270451 GATAAACTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.57, C:0.03, G:0.06, T:0.34
Consensus pattern (18 bp):
AAATTGAATTTCAAAAAT
Found at i:270858 original size:9 final size:9
Alignment explanation
Indices: 270825--270863 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
270815 TTTTCCCTTA
270825 TTTTTTTCT
1 TTTTTTTCT
* *
270834 TCTTTCTTCA
1 T-TTTTTTCT
270844 TTTTTTTCT
1 TTTTTTTCT
270853 TTTTTTTCT
1 TTTTTTTCT
270862 TT
1 TT
270864 CTTCTTCAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
9 18 0.72
10 7 0.28
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (9 bp):
TTTTTTTCT
Found at i:281384 original size:26 final size:26
Alignment explanation
Indices: 281337--281398 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 26
281327 AAAATGAAAC
* *
281337 ATTATTAAAATAATATACATATAAAT
1 ATTATGAAAATAATATACATATAAAA
*
281363 ATTATGAAAATAATA-AGTATATAAAA
1 ATTATGAAAATAATATA-CATATAAAA
*
281389 ATTTTGAAAA
1 ATTATGAAAA
281399 GAAAGAATTA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
25 1 0.03
26 30 0.97
ACGTcount: A:0.58, C:0.02, G:0.05, T:0.35
Consensus pattern (26 bp):
ATTATGAAAATAATATACATATAAAA
Done.