Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009332.1 Hibiscus syriacus cultivar Beakdansim tig00113099_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: 474123
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 3
Found at i:1596 original size:94 final size:92
Alignment explanation
Indices: 1237--1605 Score: 632
Period size: 86 Copynumber: 4.1 Consensus size: 92
1227 TAGATTGCTT
* *
1237 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAAC-GTGTATTCTTTAACACTGTGAAATAGAT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATATAT
1301 TTGTCTTTG-TTTGTCTTTTGGTTGAA
66 TTGTCTTTGTTTTGTCTTTTGGTTGAA
1327 AGTAAA-TTGTTCGGTTGCTGCCAATT-TGCTAAACTGTGTATTC-TTAACACTGTG-AATATAT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATATAT
1388 TTGTCTTTGTTTTG--TTTTGGTTGAA
66 TTGTCTTTGTTTTGTCTTTTGGTTGAA
1413 AGTAAATTTG-TCGGTTGCTG-CAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATATAT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATATAT
1476 TTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTGTCTTTGTTTTGTCTTTTGGTTGAA
1503 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAAACTGTGTATTCTTTAACACTGTGAAATAGT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCT-AAACTGTGTATTCTTTAACACTGTGAAATA-T
1568 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
64 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
1597 AGTAAATTT
1 AGTAAATTT
1606 ATCCATTCAA
Statistics
Matches: 265, Mismatches: 2, Indels: 20
0.92 0.01 0.07
Matches are distributed among these distances:
85 5 0.02
86 44 0.17
87 29 0.11
88 44 0.17
89 27 0.10
90 27 0.10
91 10 0.04
92 10 0.04
93 30 0.11
94 39 0.15
ACGTcount: A:0.23, C:0.12, G:0.19, T:0.46
Consensus pattern (92 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATATAT
TTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:1689 original size:19 final size:19
Alignment explanation
Indices: 1649--1775 Score: 116
Period size: 19 Copynumber: 7.3 Consensus size: 19
1639 TAGTTTACTT
* *
1649 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
1669 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
1688 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
1707 TCGCAA--CG--A-C--AA
1 TCGCAACGCGAAACCAAAA
1719 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
1738 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
1752 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
1771 TCGCA
1 TCGCA
1776 TTGCGATTTC
Statistics
Matches: 88, Mismatches: 7, Indels: 25
0.73 0.06 0.21
Matches are distributed among these distances:
12 8 0.09
14 12 0.14
15 2 0.02
16 3 0.03
17 5 0.06
18 1 0.01
19 44 0.50
20 13 0.15
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:1724 original size:31 final size:32
Alignment explanation
Indices: 1685--1775 Score: 148
Period size: 31 Copynumber: 2.8 Consensus size: 32
1675 CGCGAAACCA
**
1685 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
1717 -AATCGCAACGCGAAACCAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
1748 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
1776 TTGCGATTTC
Statistics
Matches: 55, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
31 29 0.53
32 1 0.02
33 25 0.45
ACGTcount: A:0.46, C:0.29, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:1811 original size:14 final size:14
Alignment explanation
Indices: 1792--1848 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1782 TTTCATTTCG
1792 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
1806 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
1823 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
1839 CGTTGCGATT
1 CGTTGCGATT
1849 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:1823 original size:33 final size:33
Alignment explanation
Indices: 1776--1867 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
1766 CAAAATCGCA
*
1776 TTGCGA-TTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
1808 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
1841 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
1868 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
32 6 0.11
33 50 0.89
ACGTcount: A:0.11, C:0.21, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:1832 original size:19 final size:19
Alignment explanation
Indices: 1771--1904 Score: 119
Period size: 19 Copynumber: 7.6 Consensus size: 19
1761 GAAACCAAAA
*
1771 TCGCATTGCGA-TTTCATT
1 TCGCGTTGCGATTTTCATT
1789 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
1805 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
1822 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
1838 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
1855 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
1874 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
1894 TCGTGTTGCGA
1 TCGCGTTGCGA
1905 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 20
0.76 0.08 0.16
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
18 10 0.11
19 36 0.38
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:3798 original size:15 final size:14
Alignment explanation
Indices: 3760--3799 Score: 62
Period size: 14 Copynumber: 2.8 Consensus size: 14
3750 GATTGTTTAA
3760 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
*
3774 ATGATTTGTAAAAG
1 TTGATTTGTAAAAG
3788 TTGATTTTGTAA
1 TTGA-TTTGTAA
3800 TTGATGCGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 16 0.70
15 7 0.30
ACGTcount: A:0.35, C:0.00, G:0.20, T:0.45
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:3970 original size:20 final size:19
Alignment explanation
Indices: 3902--3984 Score: 113
Period size: 19 Copynumber: 4.6 Consensus size: 19
3892 AAAAATGACT
3902 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
3921 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
3935 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
3954 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
3974 ATCGCAATGCG
1 ATCGCAATGCG
3985 TTTATAATTC
Statistics
Matches: 56, Mismatches: 2, Indels: 12
0.80 0.03 0.17
Matches are distributed among these distances:
14 10 0.18
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 21 0.38
20 19 0.34
ACGTcount: A:0.43, C:0.18, G:0.24, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:4064 original size:51 final size:51
Alignment explanation
Indices: 3991--4247 Score: 396
Period size: 51 Copynumber: 5.0 Consensus size: 51
3981 TGCGTTTATA
*
3991 ATTCGCA-TGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
4041 ATTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
4092 ATTCGCATTGCGATT-TCCATTCGCATTGCGA-TTTCATTTCGCA-TGCGATTTTC
1 ATTCGCATTGCGATTCT-C--TCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
4145 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 A-TTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
4197 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTT
1 A-TTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTT
4248 CATGTTGGGA
Statistics
Matches: 193, Mismatches: 3, Indels: 19
0.90 0.01 0.09
Matches are distributed among these distances:
50 14 0.07
51 68 0.35
52 50 0.26
53 27 0.14
54 27 0.14
55 7 0.04
ACGTcount: A:0.15, C:0.23, G:0.18, T:0.45
Consensus pattern (51 bp):
ATTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:4135 original size:105 final size:104
Alignment explanation
Indices: 3992--4247 Score: 398
Period size: 105 Copynumber: 2.5 Consensus size: 104
3982 GCGTTTATAA
*
3992 TTCGCA-TGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCA-TTCGCATTGCGAT
1 TTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGAT
*
4055 TCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTCA-
66 TCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCAT
4093 TTCGCATTGCGATT-TCCATTCGCATTGCGA-TTTCATTTCGCA-TGCGATTTTCATTTCGCATT
1 TTCGCATTGCGATTCT-C--TCG--TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATT
4155 GCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCAT
61 GCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCAT
4199 TTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTT
1 TTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTT
4248 CATGTTGGGA
Statistics
Matches: 142, Mismatches: 1, Indels: 20
0.87 0.01 0.12
Matches are distributed among these distances:
101 7 0.05
102 14 0.10
103 8 0.06
104 21 0.15
105 70 0.49
106 21 0.15
107 1 0.01
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.45
Consensus pattern (104 bp):
TTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGAT
TCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCAT
Found at i:4250 original size:19 final size:19
Alignment explanation
Indices: 4011--4247 Score: 298
Period size: 18 Copynumber: 13.5 Consensus size: 19
4001 GATTATCTCG
4011 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
4030 TTGCGATTTTCA-TTCGCA
1 TTGCGATTTTCATTTCGCA
4048 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
4062 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
4081 TTGCGATTTTCA-TTCGCA
1 TTGCGATTTTCATTTCGCA
*
4099 TTGCGATTTCCA-TTCGCA
1 TTGCGATTTTCATTTCGCA
4117 TTGCGA-TTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
4135 -TGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
4153 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
4167 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
4186 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
4205 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
4219 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
4239 TTGCGATTT
1 TTGCGATTT
4248 CATGTTGGGA
Statistics
Matches: 192, Mismatches: 6, Indels: 39
0.81 0.03 0.16
Matches are distributed among these distances:
14 18 0.09
16 24 0.12
17 26 0.14
18 61 0.32
19 54 0.28
20 9 0.05
ACGTcount: A:0.14, C:0.23, G:0.17, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:4275 original size:32 final size:34
Alignment explanation
Indices: 4186--4278 Score: 115
Period size: 33 Copynumber: 2.8 Consensus size: 34
4176 TCATTTCGCA
4186 TTGCGATTTTCATTTCGC-ATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGATTGCGATTCTCTCG
4219 TTGCGATTTTCATTTC-CGCATTGCGATT-TCAT-G
1 TTGCGATTTTCATTTCGCG-ATTGCGATTCTC-TCG
* *
4252 TTGGGA-TTTCATTTCGCGTTTGCGATT
1 TTGCGATTTTCATTTCGCGATTGCGATT
4279 GTATTTTCCG
Statistics
Matches: 54, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
32 18 0.33
33 26 0.48
34 10 0.19
ACGTcount: A:0.13, C:0.20, G:0.20, T:0.46
Consensus pattern (34 bp):
TTGCGATTTTCATTTCGCGATTGCGATTCTCTCG
Found at i:4297 original size:105 final size:100
Alignment explanation
Indices: 3991--4278 Score: 322
Period size: 105 Copynumber: 2.8 Consensus size: 100
3981 TGCGTTTATA
*
3991 ATTCGCA-TGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTCGCATTGCGA-
1 ATTCGCATTGCGATT-TCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCA-T-G--TTGGGAT
4054 TTC-TTT-CGTTGCGATTTTCATTTCGCATTGCGATTTTC
61 TTCATTTCCGTTGCGATTTTCATTTCGCATTGCGATTTTC
* *
4092 ATTCGCATTGCGATTTCCATTCGCATTGCGA-TTTCATTTCGCA-TGCGATTTTCAT-TTCGCAT
1 ATTCGCATTGCGATTT-C--TCG--TTGCGATTTTCATTTCGCATTGCGATTTTCATGTTGGGAT
*
4154 TGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
61 TTC-ATT-TC-CGTTGCGATTTTCATTTCGCATTGCGATTTTC
4197 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGA-TTTCATGTTGGGATTT
1 A-TTCGCATTGCGATT-TCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATGTTGGGATTT
4261 CATTTCGCGTTTGCGATT
63 CATTTC-CG-TTGCGATT
4279 GTATTTTCCG
Statistics
Matches: 160, Mismatches: 8, Indels: 35
0.79 0.04 0.17
Matches are distributed among these distances:
99 3 0.02
100 2 0.01
101 8 0.05
102 16 0.10
103 14 0.09
104 38 0.24
105 57 0.36
106 21 0.13
107 1 0.01
ACGTcount: A:0.15, C:0.22, G:0.18, T:0.45
Consensus pattern (100 bp):
ATTCGCATTGCGATTTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATGTTGGGATTTCAT
TTCCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:6562 original size:12 final size:12
Alignment explanation
Indices: 6545--6569 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
6535 TCTTCGGGGA
6545 CTTTTTCTTCTT
1 CTTTTTCTTCTT
6557 CTTTTTCTTCTT
1 CTTTTTCTTCTT
6569 C
1 C
6570 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:6776 original size:24 final size:24
Alignment explanation
Indices: 6742--6788 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
6732 CTGAAACATC
6742 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
6766 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
6789 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:7491 original size:20 final size:20
Alignment explanation
Indices: 7463--7851 Score: 455
Period size: 20 Copynumber: 19.4 Consensus size: 20
7453 AAATTTCAGT
* * * *
7463 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
* *
7483 GTTGCGATTTACGGATTCTC
1 GTTGCGATTTACGGATACGC
* * *
7503 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
7523 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
7543 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
7563 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
7583 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
7603 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
7623 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
7643 GTTGCGA-TTACGGATACAC
1 GTTGCGATTTACGGATACGC
7662 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* * *
7682 GTTGCGATTTTATGTATTA-TC
1 GTTGCGA-TTTACGGA-TACGC
7703 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
7723 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
7743 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
7763 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
7783 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
7803 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
7823 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
7843 GTTGCGATT
1 GTTGCGATT
7852 ATTGAAAATC
Statistics
Matches: 325, Mismatches: 34, Indels: 20
0.86 0.09 0.05
Matches are distributed among these distances:
19 24 0.07
20 281 0.86
21 18 0.06
22 2 0.01
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:9634 original size:15 final size:15
Alignment explanation
Indices: 9611--9640 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
9601 ATGAGGCTGG
9611 AATTACAACAACAAC
1 AATTACAACAACAAC
*
9626 AATTCCAACAACAAC
1 AATTACAACAACAAC
9641 TATGAGAAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.30, G:0.00, T:0.13
Consensus pattern (15 bp):
AATTACAACAACAAC
Found at i:22143 original size:11 final size:11
Alignment explanation
Indices: 22127--22160 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
22117 GTAATAATGT
22127 TGTCGCAAAGG
1 TGTCGCAAAGG
22138 TGTCGCAAAGG
1 TGTCGCAAAGG
*
22149 TGTTGCAAAGG
1 TGTCGCAAAGG
22160 T
1 T
22161 ATTGAAAATC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.26, C:0.15, G:0.35, T:0.24
Consensus pattern (11 bp):
TGTCGCAAAGG
Found at i:25002 original size:13 final size:13
Alignment explanation
Indices: 24984--25022 Score: 71
Period size: 13 Copynumber: 3.1 Consensus size: 13
24974 CGAATTTGAA
24984 GAAACGGACTTCG
1 GAAACGGACTTCG
24997 GAAACGGACTTCG
1 GAAACGGACTTCG
25010 GAAACGGA-TTCG
1 GAAACGGACTTCG
25022 G
1 G
25023 GACGTCGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 5 0.19
13 21 0.81
ACGTcount: A:0.31, C:0.21, G:0.33, T:0.15
Consensus pattern (13 bp):
GAAACGGACTTCG
Found at i:25158 original size:5 final size:5
Alignment explanation
Indices: 25148--25190 Score: 70
Period size: 5 Copynumber: 8.8 Consensus size: 5
25138 AACGGCCAAC
*
25148 GGTCG GGTCG GGTC- AGTCG GGTCG GGTCG GGTCG GGTCG GGTC
1 GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG GGTC
25191 AGACCGGTCA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
4 3 0.09
5 32 0.91
ACGTcount: A:0.02, C:0.21, G:0.56, T:0.21
Consensus pattern (5 bp):
GGTCG
Found at i:25205 original size:9 final size:9
Alignment explanation
Indices: 25187--25243 Score: 60
Period size: 9 Copynumber: 6.1 Consensus size: 9
25177 GGTCGGGTCG
*
25187 GGTCAGACC
1 GGTCAAACC
25196 GGTCAAACC
1 GGTCAAACC
*
25205 GGTTCAGACC
1 GG-TCAAACC
*
25215 GGTCAAACT
1 GGTCAAACC
*
25224 GGTTCGAACC
1 GG-TCAAACC
25234 GGTCAAACC
1 GGTCAAACC
25243 G
1 G
25244 ATTTCCAGCC
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
9 24 0.62
10 15 0.38
ACGTcount: A:0.26, C:0.30, G:0.28, T:0.16
Consensus pattern (9 bp):
GGTCAAACC
Found at i:25211 original size:19 final size:19
Alignment explanation
Indices: 25189--25243 Score: 85
Period size: 19 Copynumber: 2.9 Consensus size: 19
25179 TCGGGTCGGG
25189 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
*
25208 TCAGACCGGTCAAACTGGT
1 TCAGACCGGTCAAACCGGT
25227 TC-GAACCGGTCAAACCG
1 TCAG-ACCGGTCAAACCG
25244 ATTTCCAGCC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
18 1 0.03
19 32 0.97
ACGTcount: A:0.27, C:0.31, G:0.25, T:0.16
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGGT
Found at i:32363 original size:13 final size:14
Alignment explanation
Indices: 32345--32374 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
32335 GTCAAAGGAA
32345 GTCAACGGTCAA-G
1 GTCAACGGTCAACG
32358 GTCAACGGTCAACG
1 GTCAACGGTCAACG
32372 GTC
1 GTC
32375 GGGTCGGGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.27, C:0.27, G:0.30, T:0.17
Consensus pattern (14 bp):
GTCAACGGTCAACG
Found at i:32367 original size:7 final size:7
Alignment explanation
Indices: 32345--32374 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
32335 GTCAAAGGAA
32345 GTCAACG
1 GTCAACG
32352 GTCAA-G
1 GTCAACG
32358 GTCAACG
1 GTCAACG
32365 GTCAACG
1 GTCAACG
32372 GTC
1 GTC
32375 GGGTCGGGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.27, C:0.27, G:0.30, T:0.17
Consensus pattern (7 bp):
GTCAACG
Found at i:32381 original size:5 final size:5
Alignment explanation
Indices: 32371--32403 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
32361 AACGGTCAAC
*
32371 GGTCG GGTCG GGTC- AGTCG GGTCG GGTCG GGTC
1 GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG GGTC
32404 AGATCGGTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
4 3 0.12
5 22 0.88
ACGTcount: A:0.03, C:0.21, G:0.55, T:0.21
Consensus pattern (5 bp):
GGTCG
Found at i:32389 original size:14 final size:14
Alignment explanation
Indices: 32372--32398 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
32362 ACGGTCAACG
32372 GTCGGGTCGGGTCA
1 GTCGGGTCGGGTCA
32386 GTCGGGTCGGGTC
1 GTCGGGTCGGGTC
32399 GGGTCAGATC
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:0.04, C:0.22, G:0.52, T:0.22
Consensus pattern (14 bp):
GTCGGGTCGGGTCA
Found at i:32393 original size:19 final size:20
Alignment explanation
Indices: 32371--32410 Score: 73
Period size: 19 Copynumber: 2.0 Consensus size: 20
32361 AACGGTCAAC
32371 GGTCGGGTCGGGTCAG-TCG
1 GGTCGGGTCGGGTCAGATCG
32390 GGTCGGGTCGGGTCAGATCG
1 GGTCGGGTCGGGTCAGATCG
32410 G
1 G
32411 TCAAACCGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.07, C:0.20, G:0.53, T:0.20
Consensus pattern (20 bp):
GGTCGGGTCGGGTCAGATCG
Found at i:32671 original size:107 final size:107
Alignment explanation
Indices: 32503--32717 Score: 412
Period size: 107 Copynumber: 2.0 Consensus size: 107
32493 AAACCGGTCA
32503 AACCGGTTTACAACCCTCCACTCTCCCTGCGGCGGCGCGTGCGGCGCGTGAGGCCTCCTCCGGGG
1 AACCGGTTTACAACCCTCCACTCTCCCTGCGGCGGCGCGTGCGGCGCGTGAGGCCTCCTCCGGGG
32568 GTCTAAAGATTCCGAAAAATTTTCTAAAAATTATTTTAAGCG
66 GTCTAAAGATTCCGAAAAATTTTCTAAAAATTATTTTAAGCG
* *
32610 AACCGGTTTCCAACCCTCCACTCTCCTTGCGGCGGCGCGTGCGGCGCGTGAGGCCTCCTCCGGGG
1 AACCGGTTTACAACCCTCCACTCTCCCTGCGGCGGCGCGTGCGGCGCGTGAGGCCTCCTCCGGGG
32675 GTCTAAAGATTCCGAAAAATTTTCTAAAAATTATTTTAAGCG
66 GTCTAAAGATTCCGAAAAATTTTCTAAAAATTATTTTAAGCG
32717 A
1 A
32718 TTTCGAGATA
Statistics
Matches: 106, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
107 106 1.00
ACGTcount: A:0.22, C:0.29, G:0.24, T:0.25
Consensus pattern (107 bp):
AACCGGTTTACAACCCTCCACTCTCCCTGCGGCGGCGCGTGCGGCGCGTGAGGCCTCCTCCGGGG
GTCTAAAGATTCCGAAAAATTTTCTAAAAATTATTTTAAGCG
Found at i:41893 original size:43 final size:42
Alignment explanation
Indices: 41853--41946 Score: 125
Period size: 43 Copynumber: 2.2 Consensus size: 42
41843 TTGTGGAAAA
* * * *
41853 AAACGCCGCAAAAGATTGGATCTATAGCGTCGCTTTTGGAAC
1 AAACGCCGCAAAAGATCGAATCTATAACATCGCTTTTGGAAC
* *
41895 AAATGCCCGCAAAAGATCGAATCTATAACATCGTTTTTGGAAC
1 AAACG-CCGCAAAAGATCGAATCTATAACATCGCTTTTGGAAC
41938 AAACGCCGC
1 AAACGCCGC
41947 TAATTACCGT
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
42 8 0.18
43 36 0.82
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.22
Consensus pattern (42 bp):
AAACGCCGCAAAAGATCGAATCTATAACATCGCTTTTGGAAC
Found at i:46376 original size:29 final size:32
Alignment explanation
Indices: 46326--46417 Score: 82
Period size: 32 Copynumber: 3.0 Consensus size: 32
46316 ACCTAAGGGA
* ** *
46326 ACATCTTAGGGCCTGAGAGCCTACCCAAGAA-
1 ACATCTCAGGGCCACAGGGCCTACCCAAGAAC
* * *
46357 A-GT-TCAGGGCCACGGGGCCTACCTAAGAAC
1 ACATCTCAGGGCCACAGGGCCTACCCAAGAAC
* *
46387 ACATCTTAGGGCCGCAGGGCCTACCCAAGAA
1 ACATCTCAGGGCCACAGGGCCTACCCAAGAA
46418 TGATCTCAGG
Statistics
Matches: 46, Mismatches: 12, Indels: 5
0.73 0.19 0.08
Matches are distributed among these distances:
29 20 0.43
30 2 0.04
31 2 0.04
32 22 0.48
ACGTcount: A:0.29, C:0.30, G:0.26, T:0.14
Consensus pattern (32 bp):
ACATCTCAGGGCCACAGGGCCTACCCAAGAAC
Found at i:57257 original size:12 final size:12
Alignment explanation
Indices: 57240--57267 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
57230 AATTTGCCAA
57240 GCAAGATCAGAG
1 GCAAGATCAGAG
57252 GCAAGATCAGAG
1 GCAAGATCAGAG
57264 GCAA
1 GCAA
57268 TATCCTGCAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.43, C:0.18, G:0.32, T:0.07
Consensus pattern (12 bp):
GCAAGATCAGAG
Found at i:71759 original size:21 final size:20
Alignment explanation
Indices: 71735--71785 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
71725 TTTGAGTTGA
* *
71735 TTAAAACATTTATAAAGTGTT
1 TTAAAACATGTATAAA-TCTT
**
71756 TTAAAATGTGTATAAATCTT
1 TTAAAACATGTATAAATCTT
71776 TTAAAACATG
1 TTAAAACATG
71786 AAACACACTA
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
20 11 0.46
21 13 0.54
ACGTcount: A:0.43, C:0.06, G:0.10, T:0.41
Consensus pattern (20 bp):
TTAAAACATGTATAAATCTT
Found at i:73136 original size:10 final size:10
Alignment explanation
Indices: 73121--73151 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
73111 AATGTTATAC
73121 TTTTTCATTT
1 TTTTTCATTT
73131 TTTTTCA-TT
1 TTTTTCATTT
73140 TTTTTCATTT
1 TTTTTCATTT
73150 TT
1 TT
73152 ATCTTTGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.10, C:0.10, G:0.00, T:0.81
Consensus pattern (10 bp):
TTTTTCATTT
Found at i:73141 original size:9 final size:9
Alignment explanation
Indices: 73121--73151 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
73111 AATGTTATAC
73121 TTTTTCATTT
1 TTTTTCA-TT
73131 TTTTTCATT
1 TTTTTCATT
73140 TTTTTCATT
1 TTTTTCATT
73149 TTT
1 TTT
73152 ATCTTTGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 14 0.67
10 7 0.33
ACGTcount: A:0.10, C:0.10, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTTTCATT
Found at i:74291 original size:18 final size:18
Alignment explanation
Indices: 74265--74309 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
74255 GAAAAGATTT
74265 TAAAATAAATAATAATA-
1 TAAAATAAATAATAATAG
*
74282 TAATAATAAATAATAGTAG
1 TAA-AATAAATAATAATAG
74301 TAAAATAAA
1 TAAAATAAA
74310 AAGGGGTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 3 0.12
18 19 0.76
19 3 0.12
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (18 bp):
TAAAATAAATAATAATAG
Found at i:75027 original size:71 final size:75
Alignment explanation
Indices: 74946--75135 Score: 259
Period size: 76 Copynumber: 2.6 Consensus size: 75
74936 TAAAACATCT
*
74946 TAAATCCTAATTAAAACACTTAAAA-CTATTTAAACTAAAATACCTAAAA-AATA-AT-ATT-T-
1 TAAATCCTAATTAAAATAC-TAAAACCTATTTAAACTAAAATACCTAAAACAA-AGATAATTATA
75005 AAAATAATA-CTC
64 AAAATAATATC-C
75017 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAATTATAA
1 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGAT-AATTATAA
75082 AAATAATATCC
65 AAATAATATCC
* * *
75093 TAAAACTTAATTTAAATACTAAAACCTATTTAAACTAAAATAC
1 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATAC
75136 AAAGATAAAA
Statistics
Matches: 107, Mismatches: 4, Indels: 11
0.88 0.03 0.09
Matches are distributed among these distances:
70 5 0.05
71 43 0.40
72 4 0.04
74 3 0.03
75 1 0.01
76 50 0.47
77 1 0.01
ACGTcount: A:0.55, C:0.14, G:0.01, T:0.30
Consensus pattern (75 bp):
TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAATTATAAA
AATAATATCC
Found at i:75159 original size:76 final size:70
Alignment explanation
Indices: 74946--75171 Score: 231
Period size: 76 Copynumber: 3.1 Consensus size: 70
74936 TAAAACATCT
* * **
74946 TAAATCCTAATTAAAACACTTAAAA-CTATTTAAACTAAAATACCTAAAAAATAATATTTAAAAT
1 TAAAACCTAATTAAAATAC-TAAAACCTATTTAAACTAAAATACAAAAAAAATAAT-TTTAAAAT
75010 AATA-CTC
64 AATATC-C
* *
75017 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAATTATAA
1 TAAAACCTAATTAAAATACTAAAACCTATTTAAACTAAAATA-C-AAAA-AAA-AT-AATT-TTA
75082 AAATAATATCC
60 AAATAATATCC
* *
75093 TAAAACTTAATTTAAATACTAAAACCTATTTAAACTAAAATACAAAGATAAAATATATTGTTTAA
1 TAAAACCTAATTAAAATACTAAAACCTATTTAAACTAAAATACAAA-A-AAAATA-A-T-TTTAA
*
75158 AATATTATCC
61 AATAATATCC
75168 TAAA
1 TAAA
75172 CTTGAGTTTA
Statistics
Matches: 133, Mismatches: 10, Indels: 20
0.82 0.06 0.12
Matches are distributed among these distances:
70 5 0.04
71 35 0.26
72 1 0.01
73 3 0.02
74 9 0.07
75 25 0.19
76 54 0.41
77 1 0.01
ACGTcount: A:0.55, C:0.13, G:0.01, T:0.31
Consensus pattern (70 bp):
TAAAACCTAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAAAAAATAATTTTAAAATAA
TATCC
Found at i:76913 original size:5 final size:5
Alignment explanation
Indices: 76903--76950 Score: 53
Period size: 5 Copynumber: 9.6 Consensus size: 5
76893 TGTTCAGAGA
* * *
76903 AAAAT AAAAT AAAAT TAATT AAAAT AAAAT -AAAT AGAAT GAAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT -AAAAT AAA
76951 GTTTGCTAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
4 4 0.11
5 27 0.77
6 4 0.11
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.23
Consensus pattern (5 bp):
AAAAT
Found at i:76946 original size:20 final size:20
Alignment explanation
Indices: 76903--76950 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
76893 TGTTCAGAGA
* *
76903 AAAATAAAATAAAATTAATT
1 AAAATAAAATAAAATGAATG
76923 AAAATAAAAT-AAATAGAATG
1 AAAATAAAATAAAAT-GAATG
76943 AAAATAAA
1 AAAATAAA
76951 GTTTGCTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 4 0.16
20 21 0.84
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.23
Consensus pattern (20 bp):
AAAATAAAATAAAATGAATG
Found at i:76996 original size:27 final size:26
Alignment explanation
Indices: 76958--77010 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
76948 AAAGTTTGCT
*
76958 AAAAAAATAAAATAAAAATAAAATGGA
1 AAAAAAAAAAAAT-AAAATAAAATGGA
*
76985 AAAAATAAAAAAATAAAATGAAATGG
1 AAAAA-AAAAAAATAAAATAAAATGG
77011 GTTGCCTCCC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 16 0.70
28 7 0.30
ACGTcount: A:0.75, C:0.00, G:0.09, T:0.15
Consensus pattern (26 bp):
AAAAAAAAAAAATAAAATAAAATGGA
Found at i:82276 original size:12 final size:13
Alignment explanation
Indices: 82255--82289 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
82245 AAGATTTAAA
82255 AATAAATAATAAT
1 AATAAATAATAAT
82268 AAT-AATAAT-AT
1 AATAAATAATAAT
82279 AATAAATAATA
1 AATAAATAATA
82290 GTAGTAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
11 5 0.25
12 12 0.60
13 3 0.15
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AATAAATAATAAT
Found at i:82301 original size:21 final size:21
Alignment explanation
Indices: 82253--82302 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
82243 AAAAGATTTA
82253 AAAATAAATAATAATAATAAT
1 AAAATAAATAATAATAATAAT
* * *
82274 AATAT-AATAAATAATAGTAGT
1 AAAATAAAT-AATAATAATAAT
82295 AAAATAAA
1 AAAATAAA
82303 AAAGGGTTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
20 3 0.13
21 18 0.78
22 2 0.09
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (21 bp):
AAAATAAATAATAATAATAAT
Found at i:83068 original size:72 final size:74
Alignment explanation
Indices: 82948--83138 Score: 235
Period size: 76 Copynumber: 2.6 Consensus size: 74
82938 TAAAACATCT
* * * * *
82948 TAAATCCTAATTAAAACACTTAAAACTATTTAAACTAAAATACGT-AA-AAACATAATAT-TTAT
1 TAAATCCTAATTAAAATAC-TAAAACTATTTAAACTAAAATACCTAAACAAACATAAAATATAAA
*
83010 AATAATATTC
65 AATAATATCC
* *
83020 TAAATCCTAATTAAAATACTAAAATCTATTTAAAGTAAAATACCTAAAACAAAGATAAAATATAA
1 TAAATCCTAATTAAAATACTAAAA-CTATTTAAACTAAAATACCT-AAACAAACATAAAATATAA
83085 AAATAATATCC
64 AAATAATATCC
* *
83096 TAAAACTTAATTAAAATACTAAAACCTATTTAAACTAAAATAC
1 TAAATCCTAATTAAAATACTAAAA-CTATTTAAACTAAAATAC
83139 AAAGATAAAA
Statistics
Matches: 102, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
71 5 0.05
72 36 0.35
74 2 0.02
75 9 0.09
76 50 0.49
ACGTcount: A:0.55, C:0.13, G:0.02, T:0.30
Consensus pattern (74 bp):
TAAATCCTAATTAAAATACTAAAACTATTTAAACTAAAATACCTAAACAAACATAAAATATAAAA
ATAATATCC
Found at i:83164 original size:76 final size:74
Alignment explanation
Indices: 82948--83175 Score: 232
Period size: 76 Copynumber: 3.1 Consensus size: 74
82938 TAAAACATCT
* * *
82948 TAAATCCTAATTAAAACACTTAAAACTATTTAAACTAAAATAC---G-TAAAAACATAATATTTA
1 TAAAACCTAATTAAAATAC-TAAAACTATTTAAACTAAAATACAAAGATAAAAATATAAT-TTTA
* *
83009 TAATAATATTC
64 AAATAATATCC
* * * * * * *
83020 TAAATCCTAATTAAAATACTAAAATCTATTTAAAGTAAAATACCTAAA-ACAAAGATAAAATATA
1 TAAAACCTAATTAAAATACTAAAA-CTATTTAAACTAAAATA-C-AAAGATAAAAATATAATTTT
83084 AAAATAATATCC
63 AAAATAATATCC
*
83096 TAAAACTTAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAGATAAAAATATAATGTTTA
1 TAAAACCTAATTAAAATACTAAAA-CTATTTAAACTAAAATACAAAGATAAAAATATAAT-TTTA
*
83161 AAATATTATCC
64 AAATAATATCC
83172 TAAA
1 TAAA
83176 CTTGAGTTTA
Statistics
Matches: 127, Mismatches: 20, Indels: 14
0.79 0.12 0.09
Matches are distributed among these distances:
71 5 0.04
72 34 0.27
73 1 0.01
74 3 0.02
75 11 0.09
76 65 0.51
77 8 0.06
ACGTcount: A:0.56, C:0.11, G:0.02, T:0.31
Consensus pattern (74 bp):
TAAAACCTAATTAAAATACTAAAACTATTTAAACTAAAATACAAAGATAAAAATATAATTTTAAA
ATAATATCC
Found at i:86169 original size:26 final size:26
Alignment explanation
Indices: 86140--86190 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
86130 CATTCAAATT
*
86140 TATGATTATCATTGTTTGATTCGGAC
1 TATGATTATCATTGATTGATTCGGAC
*
86166 TATGATTATTATTGATTGATTCGGA
1 TATGATTATCATTGATTGATTCGGA
86191 TTAGGTTATG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.25, C:0.08, G:0.20, T:0.47
Consensus pattern (26 bp):
TATGATTATCATTGATTGATTCGGAC
Found at i:87743 original size:13 final size:13
Alignment explanation
Indices: 87725--87750 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
87715 ACTTGTAGAA
87725 TCATCCATACATC
1 TCATCCATACATC
87738 TCATCCATACATC
1 TCATCCATACATC
87751 ATATCTAACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.38, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATCCATACATC
Found at i:103940 original size:28 final size:28
Alignment explanation
Indices: 103907--103987 Score: 126
Period size: 28 Copynumber: 2.9 Consensus size: 28
103897 ATACTATAGG
*
103907 GTTCTATGTGGTCCTTCGGGATATATGT
1 GTTCTATGTGGTCCTTCGGGACATATGT
* *
103935 GTTCTACGTGGTCCTTCAGGACATATGT
1 GTTCTATGTGGTCCTTCGGGACATATGT
*
103963 GTTCTATGTGGTCCTTCGTGACATA
1 GTTCTATGTGGTCCTTCGGGACATA
103988 GTGGTCCTTC
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 47 1.00
ACGTcount: A:0.16, C:0.19, G:0.26, T:0.40
Consensus pattern (28 bp):
GTTCTATGTGGTCCTTCGGGACATATGT
Found at i:105843 original size:119 final size:119
Alignment explanation
Indices: 105628--105898 Score: 427
Period size: 119 Copynumber: 2.3 Consensus size: 119
105618 ACTAAAATGA
*
105628 TATCGATACTAATTAGTATAGTAGTACCGATACTCTAAGTGGTGGTACCGATACTACCTTTTTGG
1 TATCGATACTACTTAGTATAGTAGTACCGATACTCTAAGTGGTGGTACCGATACTACCTTTTTGG
* *
105693 TTTTGAATCCGTCAAAATTCCAAAATTCTAAAATGGTACCGATACTATACA-CAG
66 CTTTGAATCCGTCAAAATTCCAAAATACTAAAATGGTACCGATACTATACATC-G
*
105747 TATCGATACTACTTAGTATAGTAGTATCGATACTCTAAGTGGTGGTACCGATACTACCTTTTTGG
1 TATCGATACTACTTAGTATAGTAGTACCGATACTCTAAGTGGTGGTACCGATACTACCTTTTTGG
* ** *
105812 CTTTGAATCCGTCAAAATTCGAGTATACTAAAATGGTACCGATACTATATATCG
66 CTTTGAATCCGTCAAAATTCCAAAATACTAAAATGGTACCGATACTATACATCG
* * *
105866 TATCGATACTACTGAATATAGTAGTGCCGATAC
1 TATCGATACTACTTAGTATAGTAGTACCGATAC
105899 CCTCGTGACA
Statistics
Matches: 139, Mismatches: 12, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
119 138 0.99
120 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (119 bp):
TATCGATACTACTTAGTATAGTAGTACCGATACTCTAAGTGGTGGTACCGATACTACCTTTTTGG
CTTTGAATCCGTCAAAATTCCAAAATACTAAAATGGTACCGATACTATACATCG
Found at i:108596 original size:47 final size:45
Alignment explanation
Indices: 108485--108626 Score: 163
Period size: 47 Copynumber: 3.3 Consensus size: 45
108475 TTTATTGGTT
108485 AATAAATGGTAAG--TA-TG-T-AAATAAGCTTACGAGCTTAT-G
1 AATAAATGGTAAGTATATTGATAAAATAAGCTTACGAGCTTATGG
* *
108524 AAT-AATGGCAAGTATATTGATAAAATAAGCTTATGAGCTTATGG
1 AATAAATGGTAAGTATATTGATAAAATAAGCTTACGAGCTTATGG
* * *
108568 AATTTAAATGGTAAGTATTTTGGTAAAATAAGCTTACGAGCTTTTGG
1 AA--TAAATGGTAAGTATATTGATAAAATAAGCTTACGAGCTTATGG
*
108615 GATAAATGGTAA
1 AATAAATGGTAA
108627 AAGATTTTAT
Statistics
Matches: 86, Mismatches: 8, Indels: 12
0.81 0.08 0.11
Matches are distributed among these distances:
38 8 0.09
39 3 0.03
40 2 0.02
41 2 0.02
42 1 0.01
43 19 0.22
44 3 0.03
45 10 0.12
46 1 0.01
47 37 0.43
ACGTcount: A:0.39, C:0.06, G:0.21, T:0.33
Consensus pattern (45 bp):
AATAAATGGTAAGTATATTGATAAAATAAGCTTACGAGCTTATGG
Found at i:115579 original size:12 final size:14
Alignment explanation
Indices: 115562--115593 Score: 50
Period size: 12 Copynumber: 2.4 Consensus size: 14
115552 GAATTAACTA
115562 AATTTTTT-TA-AT
1 AATTTTTTATATAT
115574 AATTTTTTATATAT
1 AATTTTTTATATAT
115588 AATTTT
1 AATTTT
115594 AATATACTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 8 0.44
13 2 0.11
14 8 0.44
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
AATTTTTTATATAT
Found at i:120245 original size:21 final size:22
Alignment explanation
Indices: 120204--120256 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
120194 AGTTCCACCG
*
120204 GGTATCAATACCCTCCACATA-
1 GGTATCGATACCCTCCACATAT
*
120225 GGTATCGATACCTCTTC-CATAT
1 GGTATCGATACC-CTCCACATAT
120247 GGTATCGATA
1 GGTATCGATA
120257 TTATTAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 15 0.54
22 13 0.46
ACGTcount: A:0.28, C:0.26, G:0.15, T:0.30
Consensus pattern (22 bp):
GGTATCGATACCCTCCACATAT
Found at i:123505 original size:32 final size:32
Alignment explanation
Indices: 123419--123511 Score: 104
Period size: 30 Copynumber: 3.0 Consensus size: 32
123409 TCCCGAAGGA
*
123419 CCTATCCATATGTTCCG-AAGAACATAGGTAAT
1 CCTATCCATATGTCCCGAAAG-ACATAGGTAAT
* **
123451 --TGTTTATATGTCCC-AAATGACATAGGTAAT
1 CCTATCCATATGTCCCGAAA-GACATAGGTAAT
123481 CCTATCCATATGTCCCGAAAGACATAGGTAA
1 CCTATCCATATGTCCCGAAAGACATAGGTAA
123512 CCCTCGACTC
Statistics
Matches: 49, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
30 23 0.47
31 1 0.02
32 22 0.45
33 3 0.06
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.29
Consensus pattern (32 bp):
CCTATCCATATGTCCCGAAAGACATAGGTAAT
Found at i:124444 original size:21 final size:22
Alignment explanation
Indices: 124403--124478 Score: 77
Period size: 21 Copynumber: 3.5 Consensus size: 22
124393 AGTTCCACCG
* *
124403 GGTATCAATACC-CTCCATATA
1 GGTATCGATACCTCTTCATATA
124424 GGTATCGATACCTCTTC-TATA
1 GGTATCGATACCTCTTCATATA
* * *
124445 TGTTATCGATA-CTTTTCATACA
1 -GGTATCGATACCTCTTCATATA
124467 GGTATCGATACC
1 GGTATCGATACC
124479 CCATATATCA
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
21 29 0.64
22 16 0.36
ACGTcount: A:0.28, C:0.24, G:0.13, T:0.36
Consensus pattern (22 bp):
GGTATCGATACCTCTTCATATA
Found at i:127794 original size:32 final size:30
Alignment explanation
Indices: 127715--127803 Score: 115
Period size: 32 Copynumber: 2.9 Consensus size: 30
127705 AAATGACCTA
** *
127715 TCCATATGTTTCGAAGAACATAGGTAATTG
1 TCCATATGTCCCGAAGGACATAGGTAATTG
* *
127745 TCTATATGTCCCAAAGGACATAGGTAATCATG
1 TCCATATGTCCCGAAGGACATAGGTAAT--TG
127777 TCCATATGTCCCGAAGGACATAGGTAA
1 TCCATATGTCCCGAAGGACATAGGTAA
127804 CCCTCGAATC
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
30 23 0.46
32 27 0.54
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (30 bp):
TCCATATGTCCCGAAGGACATAGGTAATTG
Found at i:127921 original size:15 final size:15
Alignment explanation
Indices: 127901--127932 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
127891 GTCACAAAGG
*
127901 CACATAGTTTCTTAT
1 CACATAGCTTCTTAT
127916 CACATAGCTTCTTAT
1 CACATAGCTTCTTAT
127931 CA
1 CA
127933 TATCATTCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.28, C:0.25, G:0.06, T:0.41
Consensus pattern (15 bp):
CACATAGCTTCTTAT
Found at i:128721 original size:21 final size:20
Alignment explanation
Indices: 128679--128751 Score: 69
Period size: 21 Copynumber: 3.6 Consensus size: 20
128669 AAGTTCCACC
* *
128679 AGGTATCGATACCCTCCACAT
1 AGGTATCGATACTCTTC-CAT
128700 AGGTATCGATACGTCTTCCAT
1 AGGTATCGATAC-TCTTCCAT
*
128721 ATGGTA-CGATACTGTT-CAT
1 A-GGTATCGATACTCTTCCAT
*
128740 ACGTATCGATAC
1 AGGTATCGATAC
128752 CCCATACATC
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
18 3 0.07
19 10 0.22
20 3 0.07
21 22 0.49
22 7 0.16
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.30
Consensus pattern (20 bp):
AGGTATCGATACTCTTCCAT
Found at i:133846 original size:71 final size:71
Alignment explanation
Indices: 133765--134056 Score: 226
Period size: 71 Copynumber: 4.2 Consensus size: 71
133755 ATTTTCCTCA
* * * *
133765 AAACAAAATTTCATCTCTCTTGAGATATTTTCCCTTGAAAATTTACATGTCACTCGAGACAATTT
1 AAACAAAATTTCATCTCACATGAGATATTTTCCCTTGAAAATTTACTTCTCACTCGAGACAATTT
133830 CTCTTG
66 CTCTTG
* * * ** *
133836 AAATAAAATTTCATCTCACATGTGATATTTT-CCTTGAATACTTTTTTTCTCATTCGAG---A--
1 AAACAAAATTTCATCTCACATGAGATATTTTCCCTTGAA-AATTTACTTCTCACTCGAGACAATT
133895 -CTC--G
65 TCTCTTG
* * * * * * ** *
133899 AAACAAAATTTCATCTCTCTTTAAATATTTTCCCTTTAATATTTACGCCTCACTCGAGACAGTTT
1 AAACAAAATTTCATCTCACATGAGATATTTTCCCTTGAAAATTTACTTCTCACTCGAGACAATTT
133964 CTCTTG
66 CTCTTG
* * * * ** * * *
133970 AAACAAAATTTTATCTCACATGTGGTATTTTTCCTTG-AAATTTTTTGTCCCACTCGAGATAGTT
1 AAACAAAATTTCATCTCACATGAGATATTTTCCCTTGAAAATTTACT-TCTCACTCGAGACAATT
*
134034 TCTCTCG
65 TCTCTTG
*
134041 AAATAAAATTTCATCT
1 AAACAAAATTTCATCT
134057 TATGTTTTCT
Statistics
Matches: 166, Mismatches: 44, Indels: 22
0.72 0.19 0.09
Matches are distributed among these distances:
63 38 0.23
64 6 0.04
65 3 0.02
68 1 0.01
69 3 0.02
70 12 0.07
71 103 0.62
ACGTcount: A:0.29, C:0.21, G:0.09, T:0.41
Consensus pattern (71 bp):
AAACAAAATTTCATCTCACATGAGATATTTTCCCTTGAAAATTTACTTCTCACTCGAGACAATTT
CTCTTG
Found at i:134027 original size:134 final size:134
Alignment explanation
Indices: 133765--134028 Score: 379
Period size: 134 Copynumber: 2.0 Consensus size: 134
133755 ATTTTCCTCA
* **
133765 AAACAAAATTTCATCTCTCTTGAGATATTTTCCCTTGAAAATTTACATGTCACTCGAGACAATTT
1 AAACAAAATTTCATCTCTCTTGAAATATTTTCCCTTGAAAATTTACACCTCACTCGAGACAATTT
* * *
133830 CTCTTGAAATAAAATTTCATCTCACATGTGATATTTTCCTTGAATACTTTTTTTCTCATTCGAGA
66 CTCTTGAAACAAAATTTCATCTCACATGTGATATTTTCCTTGAATACTTTTTTTCCCACTCGAGA
133895 CTCG
131 CTCG
* * * * *
133899 AAACAAAATTTCATCTCTCTTTAAATATTTTCCCTTTAATATTTACGCCTCACTCGAGACAGTTT
1 AAACAAAATTTCATCTCTCTTGAAATATTTTCCCTTGAAAATTTACACCTCACTCGAGACAATTT
* *
133964 CTCTTGAAACAAAATTTTATCTCACATGTGGTATTTTTCCTTGAA-A-TTTTTTGTCCCACTCGA
66 CTCTTGAAACAAAATTTCATCTCACATGTGATA-TTTTCCTTGAATACTTTTTT-TCCCACTCGA
134027 GA
129 GA
134029 TAGTTTCTCT
Statistics
Matches: 115, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
133 6 0.05
134 98 0.85
135 11 0.10
ACGTcount: A:0.29, C:0.21, G:0.09, T:0.41
Consensus pattern (134 bp):
AAACAAAATTTCATCTCTCTTGAAATATTTTCCCTTGAAAATTTACACCTCACTCGAGACAATTT
CTCTTGAAACAAAATTTCATCTCACATGTGATATTTTCCTTGAATACTTTTTTTCCCACTCGAGA
CTCG
Found at i:142995 original size:27 final size:27
Alignment explanation
Indices: 142957--143008 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
142947 TTGAACTCAG
142957 CTTTAGACTTTTCAAATCAAATCAAAA
1 CTTTAGACTTTTCAAATCAAATCAAAA
*
142984 CTTTAGACTTTTCAAATCTAATCAA
1 CTTTAGACTTTTCAAATCAAATCAA
143009 GATCAATAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.40, C:0.19, G:0.04, T:0.37
Consensus pattern (27 bp):
CTTTAGACTTTTCAAATCAAATCAAAA
Found at i:150360 original size:31 final size:30
Alignment explanation
Indices: 150304--150456 Score: 142
Period size: 31 Copynumber: 5.2 Consensus size: 30
150294 CTAGTCTAAA
150304 CTTATCTTAACATTAAAAATATATATTTTATT
1 CTTATCTTAAC-TT-AAAATATATATTTTATT
*
150336 CTTATCTTAACTTAAATATTTATATTTTATT
1 CTTATCTTAACTTAAA-ATATATATTTTATT
*
150367 CTTATTTTAACTTATAAA-ATATA-TTT-TT
1 CTTATCTTAACTTA-AAATATATATTTTATT
*
150395 -TTA--TTAACTTTAAAA-A-ATAATTTATT
1 CTTATCTTAAC-TTAAAATATATATTTTATT
* * *
150421 CTTACCTTAGCTTAAATATTTATATTTTATT
1 CTTATCTTAACTTAAA-ATATATATTTTATT
150452 CTTAT
1 CTTAT
150457 AATATTTCAA
Statistics
Matches: 103, Mismatches: 7, Indels: 23
0.77 0.05 0.17
Matches are distributed among these distances:
24 3 0.03
25 12 0.12
26 5 0.05
27 6 0.06
28 7 0.07
29 8 0.08
30 7 0.07
31 42 0.41
32 13 0.13
ACGTcount: A:0.36, C:0.09, G:0.01, T:0.54
Consensus pattern (30 bp):
CTTATCTTAACTTAAAATATATATTTTATT
Found at i:150529 original size:28 final size:28
Alignment explanation
Indices: 150476--150546 Score: 74
Period size: 26 Copynumber: 2.5 Consensus size: 28
150466 ACATTCAAAT
*
150476 AAAAATTAAATAT-ATTTTAAAATT-AA
1 AAAAATAAAATATAATTTTAAAATTAAA
* *
150502 AAAAATAAAATATACATTTTTAATTTAAA
1 AAAAATAAAATATA-ATTTTAAAATTAAA
*
150531 ATAAAATAATATATAA
1 A-AAAATAAAATATAA
150547 ATATATTAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
26 12 0.32
28 9 0.24
29 4 0.11
30 12 0.32
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (28 bp):
AAAAATAAAATATAATTTTAAAATTAAA
Found at i:150557 original size:25 final size:25
Alignment explanation
Indices: 150529--150578 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
150519 TTTTAATTTA
*
150529 AAAT-AAAATAATATATAAATATATT
1 AAATAAAAATAAGA-ATAAATATATT
150554 AAATAAAAATAAGAATAAATATATT
1 AAATAAAAATAAGAATAAATATATT
150579 TTTATGTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 15 0.65
26 8 0.35
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (25 bp):
AAATAAAAATAAGAATAAATATATT
Found at i:150685 original size:14 final size:14
Alignment explanation
Indices: 150662--150702 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
150652 AAGAATGTAA
150662 TAAATGTAATAAGT
1 TAAATGTAATAAGT
*
150676 TAAATATAATAAGT
1 TAAATGTAATAAGT
150690 TAGAATGTAATAA
1 TA-AATGTAATAA
150703 TAGTTAAGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 15 0.62
15 9 0.38
ACGTcount: A:0.54, C:0.00, G:0.12, T:0.34
Consensus pattern (14 bp):
TAAATGTAATAAGT
Found at i:150773 original size:29 final size:29
Alignment explanation
Indices: 150472--150815 Score: 121
Period size: 30 Copynumber: 11.7 Consensus size: 29
150462 TTCAACATTC
* * * *
150472 AAATAAAAATTAAATATATTTTAAAATT-
1 AAATAAGAATAAAATATATTTTTAAGTTA
*
150500 AAA-AA-AATAAAATATACATTTTTAATTTA
1 AAATAAGAATAAAATAT--ATTTTTAAGTTA
* * * *
150529 AAATAA-AATAATATATAAATATATTAAATAA
1 AAATAAGAATAA-A-ATATAT-TTTTAAGTTA
*
150560 AAATAAGAAT-AAATATATTTTTATGTTA
1 AAATAAGAATAAAATATATTTTTAAGTTA
* * * *
150588 AAA-AAGGGATAAATTATATTTAATAATTTA
1 AAATAA-GAATAAAATATATTT-TTAAGTTA
** * * * *
150618 AGGTAAGACTATAATATATTTAATAATTTA
1 AAATAAGAATAAAATATATTT-TTAAGTTA
** ** * **
150648 ATTTAAGAATGTAATAAATGTAATAAGTTA
1 AAATAAGAATAAAATATAT-TTTTAAGTTA
* * * * **
150678 AATATAATAAGTTAGAATGTAATAAT-AGTTA
1 AA-ATAAGAA--TAAAATATATTTTTAAGTTA
* * *
150709 AGATAAAAAATTAAATATATTTTTAAGTTA
1 AAAT-AAGAATAAAATATATTTTTAAGTTA
** *
150739 TGATAAGATTAAAATATATTTTTAAGTTA
1 AAATAAGAATAAAATATATTTTTAAGTTA
* * *
150768 AAATAAAAACAAAATA-A-TTTTAGGTTA
1 AAATAAGAATAAAATATATTTTTAAGTTA
*
150795 AAATAAGAATAAAATAGATTT
1 AAATAAGAATAAAATATATTT
150816 AATAATTTAG
Statistics
Matches: 238, Mismatches: 58, Indels: 39
0.71 0.17 0.12
Matches are distributed among these distances:
26 9 0.04
27 27 0.11
28 26 0.11
29 60 0.25
30 68 0.29
31 33 0.14
32 10 0.04
33 5 0.02
ACGTcount: A:0.55, C:0.01, G:0.07, T:0.37
Consensus pattern (29 bp):
AAATAAGAATAAAATATATTTTTAAGTTA
Found at i:150816 original size:27 final size:27
Alignment explanation
Indices: 150720--150815 Score: 93
Period size: 27 Copynumber: 3.4 Consensus size: 27
150710 GATAAAAAAT
* ** *
150720 TAAATATATTTTTAAGTTATGATAAGAT
1 TAAA-ATAATTTTAAGTTAAAATAAGAA
*
150748 TAAAATATATTTTTAAGTTAAAATAAAAA
1 TAAAATA-A-TTTTAAGTTAAAATAAGAA
* *
150777 CAAAATAATTTTAGGTTAAAATAAGAA
1 TAAAATAATTTTAAGTTAAAATAAGAA
150804 TAAAATAGATTT
1 TAAAATA-ATTT
150816 AATAATTTAG
Statistics
Matches: 56, Mismatches: 9, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
27 26 0.46
28 9 0.16
29 21 0.38
ACGTcount: A:0.52, C:0.01, G:0.08, T:0.39
Consensus pattern (27 bp):
TAAAATAATTTTAAGTTAAAATAAGAA
Found at i:162746 original size:28 final size:28
Alignment explanation
Indices: 162700--162754 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
162690 GTCGTTGCTT
162700 TCAAGCACTAACTCAACAACATAATATC
1 TCAAGCACTAACTCAACAACATAATATC
** * *
162728 TCAAGCACTGGCTCGACAAGATAATAT
1 TCAAGCACTAACTCAACAACATAATAT
162755 AAACAGAGAG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.42, C:0.25, G:0.11, T:0.22
Consensus pattern (28 bp):
TCAAGCACTAACTCAACAACATAATATC
Found at i:163435 original size:20 final size:20
Alignment explanation
Indices: 163410--163487 Score: 111
Period size: 20 Copynumber: 3.9 Consensus size: 20
163400 GCGATTTTCC
*
163410 GACTATCGCAACGCAATTCT
1 GACTATCGCAACGCGATTCT
163430 GACTATCGCAACGCGATTCT
1 GACTATCGCAACGCGATTCT
* *
163450 GACTGTCGCAACGCGATGCT
1 GACTATCGCAACGCGATTCT
* *
163470 GACTGTCGCAATGCGATT
1 GACTATCGCAACGCGATT
163488 TTCAAAGCGC
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 53 1.00
ACGTcount: A:0.24, C:0.28, G:0.23, T:0.24
Consensus pattern (20 bp):
GACTATCGCAACGCGATTCT
Found at i:164172 original size:20 final size:20
Alignment explanation
Indices: 164068--164174 Score: 119
Period size: 20 Copynumber: 5.5 Consensus size: 20
164058 AGAATCTCAA
*
164068 TGCGATTTT-AGTTTCGCGT
1 TGCGATTTTCATTTTCGCGT
164087 TGCGATTTTCA-TTTCGCGT
1 TGCGATTTTCATTTTCGCGT
** **
164106 TGCGATAGTCAAATTCGCGT
1 TGCGATTTTCATTTTCGCGT
** *
164126 TGCGATAGTCATTTTCGTGT
1 TGCGATTTTCATTTTCGCGT
*
164146 TGCGATTTTCATTTTCGTGT
1 TGCGATTTTCATTTTCGCGT
164166 TGCGATTTT
1 TGCGATTTT
164175 AAGTTTCATA
Statistics
Matches: 78, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
19 26 0.33
20 52 0.67
ACGTcount: A:0.14, C:0.17, G:0.23, T:0.46
Consensus pattern (20 bp):
TGCGATTTTCATTTTCGCGT
Found at i:166092 original size:20 final size:20
Alignment explanation
Indices: 166067--166114 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
166057 ATAGTTTACT
166067 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
**
166087 TCGCAACGCGAATTTGACTA
1 TCGCAACGCGAAAATGACTA
166107 TCGCAACG
1 TCGCAACG
166115 AAAGAATCAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.33, C:0.27, G:0.21, T:0.19
Consensus pattern (20 bp):
TCGCAACGCGAAAATGACTA
Found at i:166182 original size:20 final size:20
Alignment explanation
Indices: 166157--166226 Score: 97
Period size: 20 Copynumber: 3.5 Consensus size: 20
166147 GCGATTCTCT
*
166157 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAATTTCG
*
166177 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAATTTCG
* *
166197 CATTGCGATAGTC-ATTTTG
1 CGTTGCGATAGTCAATTTCG
166216 CGTTGCGATAG
1 CGTTGCGATAG
166227 CCATTCGTGT
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
19 14 0.32
20 30 0.68
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.36
Consensus pattern (20 bp):
CGTTGCGATAGTCAATTTCG
Found at i:166825 original size:21 final size:21
Alignment explanation
Indices: 166734--166838 Score: 86
Period size: 21 Copynumber: 5.0 Consensus size: 21
166724 GACTCACCTG
* *
166734 TCATTGTTCAAGAGGCCTCCCC
1 TCATCGTTCAAGAGGCC-CCTC
*
166756 T-ATCGTTCAAGAGGCCCCTA
1 TCATCGTTCAAGAGGCCCCTC
** *
166776 TCATCCCTCAAGAGTCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* * * *
166797 CCACCGTTCAAGAGGCCACTG
1 TCATCGTTCAAGAGGCCCCTC
* *
166818 TCATCGTTGAAGAGGTCCCTC
1 TCATCGTTCAAGAGGCCCCTC
166839 CCAACATTCT
Statistics
Matches: 62, Mismatches: 20, Indels: 3
0.73 0.24 0.04
Matches are distributed among these distances:
20 3 0.05
21 58 0.94
22 1 0.02
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.24
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:166831 original size:42 final size:42
Alignment explanation
Indices: 166759--166841 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 42
166749 CCTCCCCTAT
*
166759 CGTTCAAGAGGCCCCTATCATCCCTCAAGA-GTCCCCTCCCAC
1 CGTTCAAGAGGCCACTATCATCCCTCAAGAGGT-CCCTCCCAC
* ** *
166801 CGTTCAAGAGGCCACTGTCATCGTTGAAGAGGTCCCTCCCA
1 CGTTCAAGAGGCCACTATCATCCCTCAAGAGGTCCCTCCCA
166842 ACATTCTAGA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
42 33 0.94
43 2 0.06
ACGTcount: A:0.22, C:0.39, G:0.19, T:0.20
Consensus pattern (42 bp):
CGTTCAAGAGGCCACTATCATCCCTCAAGAGGTCCCTCCCAC
Found at i:168141 original size:14 final size:14
Alignment explanation
Indices: 168104--168165 Score: 61
Period size: 14 Copynumber: 4.3 Consensus size: 14
168094 TTGCTTGTTT
*
168104 AATTGATTTATAAA
1 AATTGATTTGTAAA
168118 AATTGATTTGTAAA
1 AATTGATTTGTAAA
* *
168132 AGTTGATTTGTTTAA
1 AATTGATTTG-TAAA
* *
168147 TATTGATGTGTAAA
1 AATTGATTTGTAAA
168161 TAATT
1 -AATT
168166 CTTATTTGTG
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
14 25 0.66
15 13 0.34
ACGTcount: A:0.39, C:0.00, G:0.15, T:0.47
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:168317 original size:20 final size:20
Alignment explanation
Indices: 168264--168317 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
168254 AGGTACACTT
* **
168264 TCGCAACGCTAAACTCAAAA
1 TCGCAACGCGAAAGACAAAA
*
168284 TCGCAATGCGAAAGACAAAA
1 TCGCAACGCGAAAGACAAAA
168304 TCGCAACGCGAAAG
1 TCGCAACGCGAAAG
168318 TCAATTCGTG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.44, C:0.26, G:0.19, T:0.11
Consensus pattern (20 bp):
TCGCAACGCGAAAGACAAAA
Found at i:168378 original size:34 final size:34
Alignment explanation
Indices: 168331--168576 Score: 113
Period size: 40 Copynumber: 6.7 Consensus size: 34
168321 ATTCGTGTTA
* *
168331 CGATAGTCTAATACGCTTTGCGATTTTCTCGTTG
1 CGATAGTCAAATACGCGTTGCGATTTTCTCGTTG
* * **
168365 CGATAGTCAAATACCCGTTACGATAATCAAATTCGAGTTG
1 CGATAGTCAAATACGCGTTGCGAT--T----TTCTCGTTG
* * *
168405 CGATACTCAAATTCGCGTTGGGATTTTCTCGTTG
1 CGATAGTCAAATACGCGTTGCGATTTTCTCGTTG
168439 CGATAGTCAAATA-GTCGTTGCGATAATCAAATTCGT-GTTG
1 CGATAGTCAAATACG-CGTTGCGAT--T----TTC-TCGTTG
* *
168479 CGATAGACAAATTCGCGTTGCGATAGTCATAT-TCGTGTTG
1 CGATAGTCAAATACGCGTTGCGAT--T--T-TCTC--GTTG
* * *
168519 CAATAGTCAAATTCGCGTTGCGATTTT-TGAGTTG
1 CGATAGTCAAATACGCGTTGCGATTTTCT-CGTTG
* * *
168553 CGATAATCAAATTCGCATTGCGAT
1 CGATAGTCAAATACGCGTTGCGAT
168577 AATCAAATTC
Statistics
Matches: 166, Mismatches: 26, Indels: 40
0.72 0.11 0.17
Matches are distributed among these distances:
33 1 0.01
34 71 0.43
35 2 0.01
36 3 0.02
37 1 0.01
38 4 0.02
39 1 0.01
40 81 0.49
41 2 0.01
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (34 bp):
CGATAGTCAAATACGCGTTGCGATTTTCTCGTTG
Found at i:168408 original size:20 final size:20
Alignment explanation
Indices: 168360--168624 Score: 216
Period size: 20 Copynumber: 13.8 Consensus size: 20
168350 GCGATTTTCT
* * *
168360 CGTTGCGATAGTCAAATACC
1 CGTTGCGATAATCAAATTCG
*
168380 CGTTACGATAATCAAATTCG
1 CGTTGCGATAATCAAATTCG
* *
168400 AGTTGCGATACTCAAATTCG
1 CGTTGCGATAATCAAATTCG
* *
168420 CGTTGGGAT--T----TTCT
1 CGTTGCGATAATCAAATTCG
* *
168434 CGTTGCGATAGTCAAA-TAG
1 CGTTGCGATAATCAAATTCG
168453 TCGTTGCGATAATCAAATTCG
1 -CGTTGCGATAATCAAATTCG
*
168474 TGTTGCGATAGA-CAAATTCG
1 CGTTGCGATA-ATCAAATTCG
* *
168494 CGTTGCGATAGTCATATTCG
1 CGTTGCGATAATCAAATTCG
* * *
168514 TGTTGCAATAGTCAAATTCG
1 CGTTGCGATAATCAAATTCG
*
168534 CGTTGCGAT--T----TTTG
1 CGTTGCGATAATCAAATTCG
*
168548 AGTTGCGATAATCAAATTCG
1 CGTTGCGATAATCAAATTCG
*
168568 CATTGCGATAATCAAATTCG
1 CGTTGCGATAATCAAATTCG
*
168588 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAATCAAATTCG
* *
168608 TGTTGCGATATTCAAAT
1 CGTTGCGATAATCAAAT
168625 GAATGTGTAA
Statistics
Matches: 196, Mismatches: 33, Indels: 32
0.75 0.13 0.12
Matches are distributed among these distances:
14 22 0.11
16 2 0.01
18 2 0.01
19 1 0.01
20 166 0.85
21 3 0.02
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.33
Consensus pattern (20 bp):
CGTTGCGATAATCAAATTCG
Found at i:168441 original size:74 final size:74
Alignment explanation
Indices: 168320--168502 Score: 267
Period size: 74 Copynumber: 2.5 Consensus size: 74
168310 CGCGAAAGTC
* * * *
168320 AATTCGTGTTACGATAGTCTAATACGCTTTGCGATTTTCTCGTTGCGATAGTCAAATACCCGTTA
1 AATTCGTGTTGCGATAGTCAAATTCGCGTTGCGATTTTCTCGTTGCGATAGTCAAATACCCGTTA
168385 CGATAATCA
66 CGATAATCA
* * * ** *
168394 AATTCGAGTTGCGATACTCAAATTCGCGTTGGGATTTTCTCGTTGCGATAGTCAAATAGTCGTTG
1 AATTCGTGTTGCGATAGTCAAATTCGCGTTGCGATTTTCTCGTTGCGATAGTCAAATACCCGTTA
168459 CGATAATCA
66 CGATAATCA
*
168468 AATTCGTGTTGCGATAGACAAATTCGCGTTGCGAT
1 AATTCGTGTTGCGATAGTCAAATTCGCGTTGCGAT
168503 AGTCATATTC
Statistics
Matches: 95, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
74 95 1.00
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (74 bp):
AATTCGTGTTGCGATAGTCAAATTCGCGTTGCGATTTTCTCGTTGCGATAGTCAAATACCCGTTA
CGATAATCA
Found at i:168529 original size:114 final size:113
Alignment explanation
Indices: 168360--168624 Score: 345
Period size: 114 Copynumber: 2.3 Consensus size: 113
168350 GCGATTTTCT
* * * *
168360 CGTTGCGATAGTCAAATACCCGTTACGATAATCAAATTCGAGTTGCGATACTCAAATTCGCGTTG
1 CGTTGCGATAGTCAAATTCGCGTTGCGATAATCAAATTCGAGTTGCAATACTCAAATTCGCGTTG
* * *
168425 GGATTTTCT-CGTTGCGATAGTCAAATAGTCG-TTGCGATAATCAAATTCG
66 CGATTTT-TGAGTTGCGATAATCAAAT--TCGATTGCGATAATCAAATTCG
* * * * * *
168474 TGTTGCGATAGACAAATTCGCGTTGCGATAGTCATATTCGTGTTGCAATAGTCAAATTCGCGTTG
1 CGTTGCGATAGTCAAATTCGCGTTGCGATAATCAAATTCGAGTTGCAATACTCAAATTCGCGTTG
168539 CGATTTTTGAGTTGCGATAATCAAATTCGCATTGCGATAATCAAATTCG
66 CGATTTTTGAGTTGCGATAATCAAATTCG-ATTGCGATAATCAAATTCG
* *
168588 CGTTGCGATAGTCAAATTCGTGTTGCGATATTCAAAT
1 CGTTGCGATAGTCAAATTCGCGTTGCGATAATCAAAT
168625 GAATGTGTAA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
112 3 0.02
113 1 0.01
114 126 0.97
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.33
Consensus pattern (113 bp):
CGTTGCGATAGTCAAATTCGCGTTGCGATAATCAAATTCGAGTTGCAATACTCAAATTCGCGTTG
CGATTTTTGAGTTGCGATAATCAAATTCGATTGCGATAATCAAATTCG
Found at i:168553 original size:74 final size:74
Alignment explanation
Indices: 168475--168616 Score: 214
Period size: 74 Copynumber: 1.9 Consensus size: 74
168465 TCAAATTCGT
* * * *
168475 GTTGCGATAGA-CAAATTCGCGTTGCGATAGTCATATTCGTGTTGCAATAGTCAAATTCGCGTTG
1 GTTGCGATA-ATCAAATTCGCATTGCGATAATCAAATTCGCGTTGCAATAGTCAAATTCGCGTTG
168539 CGATTTTTGA
65 CGATTTTTGA
* *
168549 GTTGCGATAATCAAATTCGCATTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGTGTTGC
1 GTTGCGATAATCAAATTCGCATTGCGATAATCAAATTCGCGTTGCAATAGTCAAATTCGCGTTGC
168614 GAT
66 GAT
168617 ATTCAAATGA
Statistics
Matches: 61, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
73 1 0.02
74 60 0.98
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.34
Consensus pattern (74 bp):
GTTGCGATAATCAAATTCGCATTGCGATAATCAAATTCGCGTTGCAATAGTCAAATTCGCGTTGC
GATTTTTGA
Found at i:168845 original size:139 final size:139
Alignment explanation
Indices: 168595--168863 Score: 511
Period size: 139 Copynumber: 1.9 Consensus size: 139
168585 TCGCGTTGCG
*
168595 ATAGTCAAATTCGTGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCA
1 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCA
*
168660 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTAACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
168725 AAACACATA
131 AAACACATA
168734 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCA
1 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCA
*
168799 TAGCAATTTTCAAACTCAAGTAACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTAACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
168864 TACAACGTTT
Statistics
Matches: 127, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
139 127 1.00
ACGTcount: A:0.43, C:0.15, G:0.13, T:0.29
Consensus pattern (139 bp):
ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCA
TAGCAATGTTCAAACTCAAGTAACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
AAACACATA
Found at i:170241 original size:15 final size:15
Alignment explanation
Indices: 170221--170255 Score: 56
Period size: 13 Copynumber: 2.5 Consensus size: 15
170211 TCATATAACT
170221 AACAAAAAATGAGTC
1 AACAAAAAATGAGTC
170236 AAC--AAAATGAGTC
1 AACAAAAAATGAGTC
170249 AACAAAA
1 AACAAAA
170256 TTATATGATT
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
13 13 0.72
15 5 0.28
ACGTcount: A:0.63, C:0.14, G:0.11, T:0.11
Consensus pattern (15 bp):
AACAAAAAATGAGTC
Found at i:170244 original size:13 final size:13
Alignment explanation
Indices: 170226--170256 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
170216 TAACTAACAA
170226 AAAATGAGTCAAC
1 AAAATGAGTCAAC
170239 AAAATGAGTCAAC
1 AAAATGAGTCAAC
170252 AAAAT
1 AAAAT
170257 TATATGATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.58, C:0.13, G:0.13, T:0.16
Consensus pattern (13 bp):
AAAATGAGTCAAC
Found at i:170948 original size:20 final size:20
Alignment explanation
Indices: 170884--170951 Score: 84
Period size: 20 Copynumber: 3.4 Consensus size: 20
170874 GAAATTCAGT
* *
170884 GTTGCGACAGTCAGAATCGC
1 GTTGCGATAGTCAGAATTGC
*
170904 GTTACGATAGTCAGAATCT-C
1 GTTGCGATAGTCAGAAT-TGC
170924 GTTGCGATAGTCAGAATTGC
1 GTTGCGATAGTCAGAATTGC
*
170944 ATTGCGAT
1 GTTGCGAT
170952 TTACATATTC
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
19 1 0.02
20 40 0.98
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.28
Consensus pattern (20 bp):
GTTGCGATAGTCAGAATTGC
Found at i:170965 original size:20 final size:20
Alignment explanation
Indices: 170942--171031 Score: 180
Period size: 20 Copynumber: 4.5 Consensus size: 20
170932 AGTCAGAATT
170942 GCATTGCGATTTACATATTC
1 GCATTGCGATTTACATATTC
170962 GCATTGCGATTTACATATTC
1 GCATTGCGATTTACATATTC
170982 GCATTGCGATTTACATATTC
1 GCATTGCGATTTACATATTC
171002 GCATTGCGATTTACATATTC
1 GCATTGCGATTTACATATTC
171022 GCATTGCGAT
1 GCATTGCGAT
171032 AGTCGAAAAA
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 70 1.00
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.39
Consensus pattern (20 bp):
GCATTGCGATTTACATATTC
Found at i:170969 original size:40 final size:40
Alignment explanation
Indices: 170925--171031 Score: 146
Period size: 40 Copynumber: 2.7 Consensus size: 40
170915 CAGAATCTCG
170925 TTGCGATAGT-CAGAATT-GCATTGCGATTTACATATTCGCA
1 TTGCGAT-GTACA-AATTCGCATTGCGATTTACATATTCGCA
* *
170965 TTGCGATTTACATATTCGCATTGCGATTTACATATTCGCA
1 TTGCGATGTACAAATTCGCATTGCGATTTACATATTCGCA
* *
171005 TTGCGATTTACATATTCGCATTGCGAT
1 TTGCGATGTACAAATTCGCATTGCGAT
171032 AGTCGAAAAA
Statistics
Matches: 63, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
39 4 0.06
40 59 0.94
ACGTcount: A:0.25, C:0.19, G:0.18, T:0.38
Consensus pattern (40 bp):
TTGCGATGTACAAATTCGCATTGCGATTTACATATTCGCA
Found at i:171052 original size:22 final size:22
Alignment explanation
Indices: 171027--171078 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
171017 TATTCGCATT
171027 GCGATAGTCGAAAAATCGCAAC
1 GCGATAGTCGAAAAATCGCAAC
* * * *
171049 GCGA-ATTTGGAAAATCGCAAT
1 GCGATAGTCGAAAAATCGCAAC
171070 GCGATAGTC
1 GCGATAGTC
171079 AGAATCGCGT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
21 17 0.74
22 6 0.26
ACGTcount: A:0.37, C:0.19, G:0.25, T:0.19
Consensus pattern (22 bp):
GCGATAGTCGAAAAATCGCAAC
Found at i:172147 original size:24 final size:24
Alignment explanation
Indices: 172120--172169 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
172110 TATATCCAAA
*
172120 ATCAAAACATAATCCAGGTCAAGT
1 ATCAAAACAAAATCCAGGTCAAGT
* * *
172144 ATCAGATCAAAATCTAGGTCAAGT
1 ATCAAAACAAAATCCAGGTCAAGT
172168 AT
1 AT
172170 TCGATCAGAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.44, C:0.18, G:0.14, T:0.24
Consensus pattern (24 bp):
ATCAAAACAAAATCCAGGTCAAGT
Found at i:172194 original size:24 final size:24
Alignment explanation
Indices: 172130--172188 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
172120 ATCAAAACAT
*
172130 AATCCAGGTCAAGTA-TCAGATCAA
1 AATCTAGGTCAAGTATTC-GATCAA
*
172154 AATCTAGGTCAAGTATTCGATCAG
1 AATCTAGGTCAAGTATTCGATCAA
172178 AATCTAGGTCA
1 AATCTAGGTCA
172189 GTTATTATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
24 30 0.94
25 2 0.06
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Consensus pattern (24 bp):
AATCTAGGTCAAGTATTCGATCAA
Found at i:176387 original size:27 final size:27
Alignment explanation
Indices: 176325--176435 Score: 197
Period size: 27 Copynumber: 4.1 Consensus size: 27
176315 CTAACAATCT
176325 AACATTAGTTTAAAGATTTTATTAAAAA
1 AACATTAGTTTAAAGATTTTATT-AAAA
176353 AACATTAGTTTAAAGATTTTATTAAAA
1 AACATTAGTTTAAAGATTTTATTAAAA
176380 AACATTAGTTTAAAGATTTTATTAAAA
1 AACATTAGTTTAAAGATTTTATTAAAA
176407 AACATTAGTTTAAAGATTTTCA-TAAAA
1 AACATTAGTTTAAAGATTTT-ATTAAAA
176434 AA
1 AA
176436 GATCATAAAC
Statistics
Matches: 82, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
27 58 0.71
28 24 0.29
ACGTcount: A:0.50, C:0.05, G:0.07, T:0.39
Consensus pattern (27 bp):
AACATTAGTTTAAAGATTTTATTAAAA
Found at i:178511 original size:114 final size:114
Alignment explanation
Indices: 178362--178809 Score: 596
Period size: 114 Copynumber: 3.9 Consensus size: 114
178352 AAAAATATAT
* ** *
178362 ATACTTTCAACATATCAGGTAATTTTTTA-TCGGTTTTGTCATAATGAAACTGATTTTGTCATAT
1 ATACTTTCAACATATCAAGTAGCTCTTTACT-GGTTTTGTCATAATGAAACTGATTTTGTCATAT
** *
178426 TTTTATATGTTATATTGTAAAATATCGATACATTTTAATAAAAATGATCA
65 TTTTACCTGTTATATTGTAAAATATCGATACATTTTTATAAAAATGATCA
* *
178476 ATACTTTCAACATATTAAGCAGCTCTTTACTGGTTTTGTCATAATGAAACTGATTTTGTCATATT
1 ATACTTTCAACATATCAAGTAGCTCTTTACTGGTTTTGTCATAATGAAACTGATTTTGTCATATT
* * * *
178541 TTTACTTGTTATATTGTAAAGTATCGATACATTTTTATAAAAAGGATTA
66 TTTACCTGTTATATTGTAAAATATCGATACATTTTTATAAAAATGATCA
* * *
178590 ATACTTTCAACATATCAGGTAGCTCTTTACTGATTTTGTCATAATGAAACTGGTTTTGTCATATT
1 ATACTTTCAACATATCAAGTAGCTCTTTACTGGTTTTGTCATAATGAAACTGATTTTGTCATATT
* * * * *
178655 TTTACCTGTTATATTGTAAAATATCGATATAATTCTAT-AAAGT-ATCG
66 TTTACCTGTTATATTGTAAAATATCGATACATTTTTATAAAAATGATCA
* ** * *
178702 ATACTTTCAACATATCATGTAGCTCTTTACCAGTTTTGTCATAGTGAAACTGATTTTTTTTCATA
1 ATACTTTCAACATATCAAGTAGCTCTTTACTGGTTTTGTCATAATGAAACTGA--TTTTGTCATA
* *
178767 TTTTTACCTGTTATATTGTAAAGTATCGATATATTTTTATAAA
64 TTTTTACCTGTTATATTGTAAAATATCGATACATTTTTATAAA
178810 GTATCGACAC
Statistics
Matches: 294, Mismatches: 36, Indels: 7
0.87 0.11 0.02
Matches are distributed among these distances:
112 49 0.17
113 3 0.01
114 239 0.81
115 3 0.01
ACGTcount: A:0.32, C:0.12, G:0.11, T:0.45
Consensus pattern (114 bp):
ATACTTTCAACATATCAAGTAGCTCTTTACTGGTTTTGTCATAATGAAACTGATTTTGTCATATT
TTTACCTGTTATATTGTAAAATATCGATACATTTTTATAAAAATGATCA
Found at i:179087 original size:75 final size:74
Alignment explanation
Indices: 178905--179078 Score: 260
Period size: 75 Copynumber: 2.4 Consensus size: 74
178895 AACATATCCG
* *
178905 GTAGGTAGTTTAATGTAATAGGTAGTCCCTA-TTTGTTTTACCGTTTACATTATTAATAACCTTA
1 GTAGGTATTTTAATGTAATAGGTAGTCCCTATTTTGTTTTACCGTTTACATTATTAACAACCTTA
*
178969 AAAAAACCT
66 AAAAAACCA
* * * *
178978 GTAGGTATTTTAATGTAATAGGTAATGCCTATTTTTTTTTACTGTTTACATTATTAACAACCTTC
1 GTAGGTATTTTAATGTAATAGGTAGTCCCTATTTTGTTTTACCGTTTACATTATTAACAACCTT-
*
179043 AAAAAAACGA
65 AAAAAAACCA
179053 GTAGGTATTTTAATGTAATAGGTAGT
1 GTAGGTATTTTAATGTAATAGGTAGT
179079 TTAAATTTTG
Statistics
Matches: 90, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
73 28 0.31
74 29 0.32
75 33 0.37
ACGTcount: A:0.33, C:0.11, G:0.15, T:0.41
Consensus pattern (74 bp):
GTAGGTATTTTAATGTAATAGGTAGTCCCTATTTTGTTTTACCGTTTACATTATTAACAACCTTA
AAAAAACCA
Found at i:181247 original size:32 final size:33
Alignment explanation
Indices: 181202--181272 Score: 108
Period size: 33 Copynumber: 2.2 Consensus size: 33
181192 TTTATTTTAC
* *
181202 TCGGGTCGTG-TTTTTTAAGTGTGATATTCGAG
1 TCGGGTCGGGTTTTTTTAAGTGTAATATTCGAG
*
181234 TCGGGTCGGGTTTTTTTAAGTGTAATATTCGGG
1 TCGGGTCGGGTTTTTTTAAGTGTAATATTCGAG
181267 TCGGGT
1 TCGGGT
181273 TTGGGTTTAG
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
32 9 0.26
33 26 0.74
ACGTcount: A:0.14, C:0.10, G:0.34, T:0.42
Consensus pattern (33 bp):
TCGGGTCGGGTTTTTTTAAGTGTAATATTCGAG
Found at i:181462 original size:287 final size:283
Alignment explanation
Indices: 180947--181463 Score: 792
Period size: 287 Copynumber: 1.8 Consensus size: 283
180937 TTTTGGTCGG
*
180947 GTCGGGTCAGTTTTTTTAAGTGTGATATTCGGGTCGGGTCGAGTTCGGGTTTAAGGTGAAAAATA
1 GTCGGGTCAGTTTTTTTAAGTGTAATATTCGGGTCGGGT---GTTCGGGTTTAAGGTGAAAAATA
*
181012 CCCGACCCGAAAATATATATAATTTTACCTTATATATTTAGCAATAATTACAATAATACCCCTCT
63 CCCGACCCGAAAAAATATATAATTTTACCTTATATATTTAGCAATAATTACAATAATACCCCTCT
* *
181077 CTATATAATTTTTTTTCAATTAAGTCACTGTTTTTATTGAATAAAAATAATTTTTTTATTATTTC
128 ATATATAATTTTTTTTCAATTAAGTCAATGTTTTTATTGAATAAAAATAATTTTTTTATTATTTC
*
181142 TGGTCGGGTCGGGTCGAATTTCTAATTCATATATTCGGGTCGGGTGAAACTTTATTTTACTCGGG
193 TGGTCGGGTCGAGTCGAATTTCTAATTCATATATTCGGGTCGGGTGAAACTTTATTTTACTCGGG
181207 TCGTGTTTTTTAAGTGTGATATTCGA
258 TCGTGTTTTTTAAGTGTGATATTCGA
* *
181233 GTCGGGTCGGGTTTTTTTAAGTGTAATATTCGGGTCGGGT-TT-GGGTTTAGGGTGAAAAA-ACC
1 GTCGGGTC-AGTTTTTTTAAGTGTAATATTCGGGTCGGGTGTTCGGGTTTAAGGTGAAAAATA--
*
181295 CGGACCTGACCCGAAAAAATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCC
63 C---CC-GACCCGAAAAAATATATAATTTTACCTTATATATTTAGCAATAATTACAATAATACCC
181360 CTCTATATATAA-TTTTTTTCAATTAAGTCAATGTTTTTATTGAATAAAAATAATTTTTTTTATT
124 CTCTATATATAATTTTTTTTCAATTAAGTCAATGTTTTTATTGAATAAAAATAA-TTTTTTTATT
* **
181424 ATTT-TGTGTCGTGTCGAGTCGGGTTTCTAATTCATATATT
188 ATTTCTG-GTCGGGTCGAGTCGAATTTCTAATTCATATATT
181464 GAATAAAAAT
Statistics
Matches: 211, Mismatches: 11, Indels: 17
0.88 0.05 0.07
Matches are distributed among these distances:
281 1 0.00
282 16 0.08
283 3 0.01
286 52 0.25
287 139 0.66
ACGTcount: A:0.28, C:0.13, G:0.18, T:0.41
Consensus pattern (283 bp):
GTCGGGTCAGTTTTTTTAAGTGTAATATTCGGGTCGGGTGTTCGGGTTTAAGGTGAAAAATACCC
GACCCGAAAAAATATATAATTTTACCTTATATATTTAGCAATAATTACAATAATACCCCTCTATA
TATAATTTTTTTTCAATTAAGTCAATGTTTTTATTGAATAAAAATAATTTTTTTATTATTTCTGG
TCGGGTCGAGTCGAATTTCTAATTCATATATTCGGGTCGGGTGAAACTTTATTTTACTCGGGTCG
TGTTTTTTAAGTGTGATATTCGA
Found at i:182875 original size:17 final size:17
Alignment explanation
Indices: 182853--182886 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
182843 GCTCTCTCTC
*
182853 GGCCACACCCTGGTGGT
1 GGCCACACCCGGGTGGT
182870 GGCCACACCCGGGTGGT
1 GGCCACACCCGGGTGGT
182887 AGGGTGGCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.12, C:0.35, G:0.38, T:0.15
Consensus pattern (17 bp):
GGCCACACCCGGGTGGT
Found at i:185072 original size:12 final size:12
Alignment explanation
Indices: 185053--185084 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
185043 ACATATCATT
185053 TCATTATTCTTA
1 TCATTATTCTTA
*
185065 TTATTATTCTTA
1 TCATTATTCTTA
185077 TCATTATT
1 TCATTATT
185085 AGCATTATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.25, C:0.12, G:0.00, T:0.62
Consensus pattern (12 bp):
TCATTATTCTTA
Found at i:185368 original size:18 final size:18
Alignment explanation
Indices: 185342--185394 Score: 72
Period size: 18 Copynumber: 2.9 Consensus size: 18
185332 GCACTTAACT
*
185342 TGTCTCGAAAGACCACTA
1 TGTCCCGAAAGACCACTA
*
185360 TGTCCCGAAGGACCACTA
1 TGTCCCGAAAGACCACTA
185378 TGTCCC-AAAGGACCACT
1 TGTCCCGAAA-GACCACT
185395 CCTTAAGAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
17 2 0.06
18 29 0.94
ACGTcount: A:0.30, C:0.32, G:0.19, T:0.19
Consensus pattern (18 bp):
TGTCCCGAAAGACCACTA
Found at i:195711 original size:40 final size:39
Alignment explanation
Indices: 195663--195751 Score: 101
Period size: 40 Copynumber: 2.2 Consensus size: 39
195653 TAGATTACAC
*
195663 ATATATATATGTTA-ATTTTCATTATCTGTTTTA-TTAATTT
1 ATATATATAT-TTACATTTT-ATTATAT-TTTTATTTAATTT
* *
195703 ATATATATATTTACTATTTTTTTATATTTTTATTTATTTT
1 ATATATATATTTAC-ATTTTATTATATTTTTATTTAATTT
195743 ATATATATA
1 ATATATATA
195752 CATATATACA
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
39 8 0.19
40 30 0.70
41 5 0.12
ACGTcount: A:0.31, C:0.03, G:0.02, T:0.63
Consensus pattern (39 bp):
ATATATATATTTACATTTTATTATATTTTTATTTAATTT
Found at i:195728 original size:19 final size:18
Alignment explanation
Indices: 195691--195748 Score: 55
Period size: 17 Copynumber: 3.1 Consensus size: 18
195681 TCATTATCTG
*
195691 TTTTATTAATTTATATATA
1 TTTTATTTATTT-TATATA
*
195710 TATTTACTATTTTTTTATAT-
1 T-TTTA-T-TTATTTTATATA
195730 TTTTATTTATTTTATATA
1 TTTTATTTATTTTATATA
195748 T
1 T
195749 ATACATATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
17 10 0.31
18 2 0.06
19 5 0.16
20 5 0.16
21 6 0.19
22 4 0.12
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (18 bp):
TTTTATTTATTTTATATA
Found at i:198358 original size:28 final size:29
Alignment explanation
Indices: 198316--198418 Score: 131
Period size: 29 Copynumber: 3.6 Consensus size: 29
198306 AAAAATAATA
* * *
198316 TTTTGATATATTACAATAAAGACCAAAAC
1 TTTTTATAAATTACAAAAAAGACCAAAAC
198345 -TTTTATAAATTACAAACAAATG-CC-AAAC
1 TTTTTATAAATTACAAA-AAA-GACCAAAAC
*
198373 TTTTTATAAATTACAAAAAATACCAAAAC
1 TTTTTATAAATTACAAAAAAGACCAAAAC
198402 TTTTTATAAATTACAAA
1 TTTTTATAAATTACAAA
198419 TGCCAAAAAA
Statistics
Matches: 65, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
28 22 0.34
29 42 0.65
30 1 0.02
ACGTcount: A:0.50, C:0.14, G:0.03, T:0.33
Consensus pattern (29 bp):
TTTTTATAAATTACAAAAAAGACCAAAAC
Found at i:206361 original size:3 final size:3
Alignment explanation
Indices: 206355--206388 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
206345 GTCAAAAAAA
*
206355 TAT TAT TA- AAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
206389 ATACAAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 1 0.04
3 27 0.96
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:208041 original size:2 final size:2
Alignment explanation
Indices: 208036--208063 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
208026 ATTAATTCGA
208036 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
208064 TAATTAAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:208375 original size:2 final size:2
Alignment explanation
Indices: 208368--208406 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
208358 TATTTTATTT
208368 TA TA TA TA TA 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 TA TA TA TA TA T
208407 TATGATTCAG
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:208871 original size:15 final size:16
Alignment explanation
Indices: 208836--208879 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
208826 GCAGACCAGC
208836 TTTTGTCTTAAAAATGA
1 TTTT-TCTTAAAAATGA
*
208853 TTTTTCTTAAAATTG-
1 TTTTTCTTAAAAATGA
208868 TTTTT-TTAAAAA
1 TTTTTCTTAAAAA
208880 GACGATTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 6 0.24
15 5 0.20
16 10 0.40
17 4 0.16
ACGTcount: A:0.34, C:0.05, G:0.07, T:0.55
Consensus pattern (16 bp):
TTTTTCTTAAAAATGA
Found at i:215606 original size:2 final size:2
Alignment explanation
Indices: 215599--215659 Score: 83
Period size: 2 Copynumber: 31.0 Consensus size: 2
215589 TAAATTAATT
215599 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TGA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA
215641 -A TA TGA TA TA -A TA TA TA TA
1 TA TA T-A TA TA TA TA TA TA TA
215660 AACGACATAG
Statistics
Matches: 54, Mismatches: 0, Indels: 10
0.84 0.00 0.16
Matches are distributed among these distances:
1 3 0.06
2 48 0.89
3 3 0.06
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (2 bp):
TA
Found at i:217259 original size:19 final size:20
Alignment explanation
Indices: 217237--217277 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
217227 CTGTGTAATG
*
217237 ATGA-TTTTCGAATGATTAC
1 ATGATTTTTCCAATGATTAC
217256 ATGATTTTTTCCAATGATTAC
1 ATGA-TTTTTCCAATGATTAC
217277 A
1 A
217278 AGATATCACT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 4 0.21
21 15 0.79
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.44
Consensus pattern (20 bp):
ATGATTTTTCCAATGATTAC
Found at i:218059 original size:18 final size:19
Alignment explanation
Indices: 218023--218059 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
218013 TGGAACGTGG
218023 GGGGAATCGGTACTCCCTAT
1 GGGGAATCGGTA-TCCCTAT
218043 GGGGAATCGGT-TCCCTA
1 GGGGAATCGGTATCCCTA
218060 AGTGTAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
20 11 0.65
ACGTcount: A:0.19, C:0.24, G:0.32, T:0.24
Consensus pattern (19 bp):
GGGGAATCGGTATCCCTAT
Found at i:218991 original size:16 final size:18
Alignment explanation
Indices: 218970--219008 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
218960 ATGTCTTTTT
218970 AAAAAT-AATTTTAAGA-
1 AAAAATCAATTTTAAGAC
*
218986 AAAAATCATTTTTAAGAC
1 AAAAATCAATTTTAAGAC
219004 AAAAA
1 AAAAA
219009 GCTGGTCTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 6 0.30
17 9 0.45
18 5 0.25
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.28
Consensus pattern (18 bp):
AAAAATCAATTTTAAGAC
Found at i:219430 original size:2 final size:2
Alignment explanation
Indices: 219423--219478 Score: 98
Period size: 2 Copynumber: 29.0 Consensus size: 2
219413 CAAGGGTAAT
219423 TA TA TA TA TA TA -A TA TA TA -A 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
219463 TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA
219479 AACAGTAAAG
Statistics
Matches: 52, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
1 2 0.04
2 50 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:221149 original size:3 final size:3
Alignment explanation
Indices: 221141--221193 Score: 72
Period size: 3 Copynumber: 17.7 Consensus size: 3
221131 AATATTGTAA
* *
221141 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT ACT -AT AGT ATAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT
221186 AAT AAT AA
1 AAT AAT AA
221194 ATATAATATA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
2 1 0.02
3 41 0.93
4 2 0.05
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:221199 original size:12 final size:13
Alignment explanation
Indices: 221140--221201 Score: 67
Period size: 12 Copynumber: 4.8 Consensus size: 13
221130 AAATATTGTA
221140 AAATAATAATAAT
1 AAATAATAATAAT
221153 -AATAATAATAAT
1 AAATAATAATAAT
*
221165 -AATAATAATACT
1 AAATAATAATAAT
*
221177 ATAGTATATAATAAT
1 A-AATA-ATAATAAT
221192 AAAT-ATAATA
1 AAATAATAATA
221202 TATATTTTAA
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
12 29 0.69
14 5 0.12
15 8 0.19
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.34
Consensus pattern (13 bp):
AAATAATAATAAT
Found at i:221206 original size:9 final size:10
Alignment explanation
Indices: 221141--221206 Score: 63
Period size: 9 Copynumber: 7.0 Consensus size: 10
221131 AATATTGTAA
221141 AATAATA-AT
1 AATAATATAT
221150 AATAATA-AT
1 AATAATATAT
221159 AATAATA-AT
1 AATAATATAT
221168 AATAATACTAT
1 AATAATA-TAT
*
221179 AGT-ATATAAT
1 AATAATAT-AT
221189 AATAA-ATAT
1 AATAATATAT
221198 AAT-ATATAT
1 AATAATATAT
221207 TTTAATCCCA
Statistics
Matches: 50, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
8 1 0.02
9 35 0.70
10 9 0.18
11 5 0.10
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (10 bp):
AATAATATAT
Found at i:221730 original size:181 final size:182
Alignment explanation
Indices: 221385--221789 Score: 672
Period size: 181 Copynumber: 2.2 Consensus size: 182
221375 CATTTTGCCC
* * * *
221385 GAAGGTCTTATGGTTGCCT-GAAGGACTTAAAAAATCAAGAAACCACTGAAGGCTTAGTTTCTTA
1 GAAGGTCTTATGGATGGCTCGAAGGACTTAAAAAATCAAGAAACCACCGAAGGCTCAGTTTCTTA
221449 AATCTCATTTGAAAACATCCTGCACTGAAGGTCTTACGGATGGCCCAAAGGACTTAAAAAATCAA
66 AATCTCATTTGAAAACATCCTGCACTGAAGGTCTTACGGATGGCCCAAAGGACTTAAAAAATCAA
221514 GAAACCCCCGAAGGCTCAGTTTCTTAAATCTCATTTGAAAACATCCTGCACT
131 GAAACCCCCGAAGGCTCAGTTTCTTAAATCTCATTTGAAAACATCCTGCACT
* *
221566 GAAGGTCTTACGGATGGCTCGAAGGACTTAAAAAATCAAGAAACCCCCGAAGGCTCAGTTTCTTA
1 GAAGGTCTTATGGATGGCTCGAAGGACTTAAAAAATCAAGAAACCACCGAAGGCTCAGTTTCTTA
* * *
221631 AATCTTATTTGAAAACATCCTGCACTGAAGGTCTTACGGATGGTCCGAAGGACTT-AAAAATCAA
66 AATCTCATTTGAAAACATCCTGCACTGAAGGTCTTACGGATGGCCCAAAGGACTTAAAAAATCAA
* * *
221695 GAAACCCCCGAAGGCTCAGTTTTTTAGATCTCATTTGAAAACATCTTGCACT
131 GAAACCCCCGAAGGCTCAGTTTCTTAAATCTCATTTGAAAACATCCTGCACT
*
221747 GAAGGTCTTATGGATGGCCCGAAGGACTT-AAAAATCAAGAAAC
1 GAAGGTCTTATGGATGGCTCGAAGGACTTAAAAAATCAAGAAAC
221790 TCTTGAAAAT
Statistics
Matches: 209, Mismatches: 14, Indels: 3
0.92 0.06 0.01
Matches are distributed among these distances:
180 14 0.07
181 101 0.48
182 94 0.45
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.25
Consensus pattern (182 bp):
GAAGGTCTTATGGATGGCTCGAAGGACTTAAAAAATCAAGAAACCACCGAAGGCTCAGTTTCTTA
AATCTCATTTGAAAACATCCTGCACTGAAGGTCTTACGGATGGCCCAAAGGACTTAAAAAATCAA
GAAACCCCCGAAGGCTCAGTTTCTTAAATCTCATTTGAAAACATCCTGCACT
Found at i:221748 original size:90 final size:91
Alignment explanation
Indices: 221385--221789 Score: 663
Period size: 91 Copynumber: 4.5 Consensus size: 91
221375 CATTTTGCCC
* * * * * *
221385 GAAGGTCTTATGG-TTGCCTGAAGGACTTAAAAAATCAAGAAACCACTGAAGGCTTAGTTTCTTA
1 GAAGGTCTTACGGATGGCCCGAAGGACTTAAAAAATCAAGAAACCCCCGAAGGCTCAGTTTCTTA
221449 AATCTCATTTGAAAACATCCTGCACT
66 AATCTCATTTGAAAACATCCTGCACT
*
221475 GAAGGTCTTACGGATGGCCCAAAGGACTTAAAAAATCAAGAAACCCCCGAAGGCTCAGTTTCTTA
1 GAAGGTCTTACGGATGGCCCGAAGGACTTAAAAAATCAAGAAACCCCCGAAGGCTCAGTTTCTTA
221540 AATCTCATTTGAAAACATCCTGCACT
66 AATCTCATTTGAAAACATCCTGCACT
*
221566 GAAGGTCTTACGGATGGCTCGAAGGACTTAAAAAATCAAGAAACCCCCGAAGGCTCAGTTTCTTA
1 GAAGGTCTTACGGATGGCCCGAAGGACTTAAAAAATCAAGAAACCCCCGAAGGCTCAGTTTCTTA
*
221631 AATCTTATTTGAAAACATCCTGCACT
66 AATCTCATTTGAAAACATCCTGCACT
* *
221657 GAAGGTCTTACGGATGGTCCGAAGGACTT-AAAAATCAAGAAACCCCCGAAGGCTCAGTTTTTTA
1 GAAGGTCTTACGGATGGCCCGAAGGACTTAAAAAATCAAGAAACCCCCGAAGGCTCAGTTTCTTA
* *
221721 GATCTCATTTGAAAACATCTTGCACT
66 AATCTCATTTGAAAACATCCTGCACT
*
221747 GAAGGTCTTATGGATGGCCCGAAGGACTT-AAAAATCAAGAAAC
1 GAAGGTCTTACGGATGGCCCGAAGGACTTAAAAAATCAAGAAAC
221790 TCTTGAAAAT
Statistics
Matches: 296, Mismatches: 18, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
90 110 0.37
91 186 0.63
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.25
Consensus pattern (91 bp):
GAAGGTCTTACGGATGGCCCGAAGGACTTAAAAAATCAAGAAACCCCCGAAGGCTCAGTTTCTTA
AATCTCATTTGAAAACATCCTGCACT
Found at i:221865 original size:58 final size:54
Alignment explanation
Indices: 221818--222238 Score: 175
Period size: 43 Copynumber: 8.8 Consensus size: 54
221808 ATTTCTTAAA
*
221818 TTGTCACCAAGGAACCCCTACATATCACGTTGGTCCCTCAAGTGCTCATCAAAT
1 TTGTCACCAAGGAACCCCTACATATCACGATGGTCCCTCAAGTGCTCATCAAAT
**
221872 TTGTCTTCAAGGAACCCCTACATATCACGATGGTCCCTCAA------A-C---T
1 TTGTCACCAAGGAACCCCTACATATCACGATGGTCCCTCAAGTGCTCATCAAAT
* * **
221916 TT-TCATCAAGAAACCCCTACATATCACGATGG----T----T--TC-TCAAGC
1 TTGTCACCAAGGAACCCCTACATATCACGATGGTCCCTCAAGTGCTCATCAAAT
*
221958 TTGTCATCAAGGAACCCCTACATATCACGATGGTCCCTCAA--G--C-T----T
1 TTGTCACCAAGGAACCCCTACATATCACGATGGTCCCTCAAGTGCTCATCAAAT
* * *
222003 TT-T-ATCAAGAAACCCCTACATATCACGATGGTCCTTCAAGCTTG-TCATCAAAT
1 TTGTCACCAAGGAACCCCTACATATCACGATGGTCCCTCAAG--TGCTCATCAAAT
* ** *
222056 TTTTCGTCAAGGAACCCCTACATATCACGACGGTCCCTCAA--G--------AT
1 TTGTCACCAAGGAACCCCTACATATCACGATGGTCCCTCAAGTGCTCATCAAAT
* * * **
222100 TT-TCATCAAGAAACCCCTACATATCGCGATGGTTTCTCAA--GCT--T----T
1 TTGTCACCAAGGAACCCCTACATATCACGATGGTCCCTCAAGTGCTCATCAAAT
**
222145 TCCTCA--AA-GAACCCCTACATATCACGATGG-CCCTTCAAGCTTG-TCATCAAAT
1 TTGTCACCAAGGAACCCCTACATATCACGATGGTCCC-TCAAG--TGCTCATCAAAT
* *
222197 TTGTCATCAAGGAACCCCTACATATCACGACGGTCCCTCAAG
1 TTGTCACCAAGGAACCCCTACATATCACGATGGTCCCTCAAG
222239 CTTTTCATCA
Statistics
Matches: 292, Mismatches: 28, Indels: 93
0.71 0.07 0.23
Matches are distributed among these distances:
39 2 0.01
42 3 0.01
43 148 0.51
44 10 0.03
45 4 0.01
46 4 0.01
47 4 0.01
48 3 0.01
49 3 0.01
51 1 0.00
52 5 0.02
53 3 0.01
54 41 0.14
55 58 0.20
56 3 0.01
ACGTcount: A:0.29, C:0.30, G:0.14, T:0.27
Consensus pattern (54 bp):
TTGTCACCAAGGAACCCCTACATATCACGATGGTCCCTCAAGTGCTCATCAAAT
Found at i:221931 original size:43 final size:43
Alignment explanation
Indices: 221878--222301 Score: 420
Period size: 43 Copynumber: 9.3 Consensus size: 43
221868 AAATTTGTCT
* *
221878 TCAAGGAACCCCTACATATCACGATGGTCCCTCAAACTTTTCA
1 TCAAGAAACCCCTACATATCACGATGGTCCCTCAAGCTTTTCA
** *
221921 TCAAGAAACCCCTACATATCACGATGGTTTCTCAAGCTTGTCA
1 TCAAGAAACCCCTACATATCACGATGGTCCCTCAAGCTTTTCA
* *
221964 TCAAGGAACCCCTACATATCACGATGGTCCCTCAAGCTTTTTA
1 TCAAGAAACCCCTACATATCACGATGGTCCCTCAAGCTTTTCA
*
222007 TCAAGAAACCCCTACATATCACGATGGTCCTTCAAGCTTGTCATCAAA
1 TCAAGAAACCCCTACATATCACGATGGTCCCTCAAGCTT-T--TC--A
* * *
222055 TTTTTCGTCAAGGAACCCCTACATATCACGACGGTCCCTCAAGATTTTCA
1 -------TCAAGAAACCCCTACATATCACGATGGTCCCTCAAGCTTTTCA
* ** *
222105 TCAAGAAACCCCTACATATCGCGATGGTTTCTCAAGCTTTTCC
1 TCAAGAAACCCCTACATATCACGATGGTCCCTCAAGCTTTTCA
222148 TCAA-AGAACCCCTACATATCACGATGG-CCCTTCAAGCTTGTCATCAAATTTGTCA
1 TCAAGA-AACCCCTACATATCACGATGGTCCC-TCAA----G----C---TTT-TCA
* *
222203 TCAAGGAACCCCTACATATCACGACGGTCCCTCAAGCTTTTCA
1 TCAAGAAACCCCTACATATCACGATGGTCCCTCAAGCTTTTCA
** *
222246 TCAAGAAACCCCTACATATCACGATGGTTTCTCAAGCTTTTCT
1 TCAAGAAACCCCTACATATCACGATGGTCCCTCAAGCTTTTCA
222289 TCAAGAAACCCCT
1 TCAAGAAACCCCT
222302 GAAAATCAGG
Statistics
Matches: 318, Mismatches: 35, Indels: 56
0.78 0.09 0.14
Matches are distributed among these distances:
42 2 0.01
43 231 0.73
44 4 0.01
46 1 0.00
47 2 0.01
48 1 0.00
50 1 0.00
51 2 0.01
52 2 0.01
54 4 0.01
55 65 0.20
56 3 0.01
ACGTcount: A:0.29, C:0.30, G:0.13, T:0.27
Consensus pattern (43 bp):
TCAAGAAACCCCTACATATCACGATGGTCCCTCAAGCTTTTCA
Found at i:222084 original size:55 final size:53
Alignment explanation
Indices: 222001--222249 Score: 189
Period size: 55 Copynumber: 5.0 Consensus size: 53
221991 TCCCTCAAGC
* *
222001 TTTTTATCAAGAAACCCCTACATATCACGATGGTCCTTCAAGCTTGTCATCAAA
1 TTTTCATCAAGGAACCCCTACATATCACGATGGTCCTTCAAGCTT-TCATCAAA
* * *
222055 TTTTTCGTCAAGGAACCCCTACATATCACGACGGT-C--C---C--TCA--AGA
1 -TTTTCATCAAGGAACCCCTACATATCACGATGGTCCTTCAAGCTTTCATCAAA
* * *
222099 TTTTCATCAAGAAACCCCTACATATCGCGATGGT-TTCTCAAGCTTT--TC---
1 TTTTCATCAAGGAACCCCTACATATCACGATGGTCCT-TCAAGCTTTCATCAAA
* *
222147 ----C-TCAAAGAACCCCTACATATCACGATGGCCCTTCAAGCTTGTCATCAAA
1 TTTTCATCAAGGAACCCCTACATATCACGATGGTCCTTCAAGCTT-TCATCAAA
* *
222196 TTTGTCATCAAGGAACCCCTACATATCACGACGGTCCCTCAAGCTTTTCATCAA
1 TTT-TCATCAAGGAACCCCTACATATCACGATGGTCCTTCAAGC-TTTCATCAA
222250 GAAACCCCTA
Statistics
Matches: 151, Mismatches: 19, Indels: 48
0.69 0.09 0.22
Matches are distributed among these distances:
43 62 0.41
44 5 0.03
46 6 0.04
49 2 0.01
51 1 0.01
52 1 0.01
54 2 0.01
55 70 0.46
56 2 0.01
ACGTcount: A:0.29, C:0.30, G:0.13, T:0.29
Consensus pattern (53 bp):
TTTTCATCAAGGAACCCCTACATATCACGATGGTCCTTCAAGCTTTCATCAAA
Found at i:222096 original size:141 final size:140
Alignment explanation
Indices: 221909--222301 Score: 608
Period size: 141 Copynumber: 2.8 Consensus size: 140
221899 CGATGGTCCC
* * * ** * *
221909 TCAAACTTTTCATCAAGAAACCCCTACATATCACGATGGTTTCTCAAGCTTGTCATCAAGGAACC
1 TCAAATTTTTCATCAAGGAACCCCTACATATCACGACGGTCCCTCAAGCTTTTCATCAAGAAACC
** *
221974 CCTACATATCACGATGGTCCCTCAAGCTTTTTATCAAGAAACCCCTACATATCACGATGGTCCTT
66 CCTACATATCACGATGGTTTCTCAAGCTTTTT-TCAAGAAACCCCTACATATCACGATGGCCCTT
222039 CAAGCTTGTCA
130 CAAGCTTGTCA
* *
222050 TCAAATTTTTCGTCAAGGAACCCCTACATATCACGACGGTCCCTCAAGATTTTCATCAAGAAACC
1 TCAAATTTTTCATCAAGGAACCCCTACATATCACGACGGTCCCTCAAGCTTTTCATCAAGAAACC
* *
222115 CCTACATATCGCGATGGTTTCTCAAGCTTTTCCTCAA-AGAACCCCTACATATCACGATGGCCCT
66 CCTACATATCACGATGGTTTCTCAAGCTTTT-TTCAAGA-AACCCCTACATATCACGATGGCCCT
222179 TCAAGCTTGTCA
129 TCAAGCTTGTCA
*
222191 TCAAATTTGTCATCAAGGAACCCCTACATATCACGACGGTCCCTCAAGCTTTTCATCAAGAAACC
1 TCAAATTTTTCATCAAGGAACCCCTACATATCACGACGGTCCCTCAAGCTTTTCATCAAGAAACC
222256 CCTACATATCACGATGGTTTCTCAAGCTTTTCTTCAAGAAACCCCT
66 CCTACATATCACGATGGTTTCTCAAGCTTTT-TTCAAGAAACCCCT
222302 GAAAATCAGG
Statistics
Matches: 230, Mismatches: 19, Indels: 6
0.90 0.07 0.02
Matches are distributed among these distances:
140 1 0.00
141 228 0.99
142 1 0.00
ACGTcount: A:0.29, C:0.30, G:0.13, T:0.28
Consensus pattern (140 bp):
TCAAATTTTTCATCAAGGAACCCCTACATATCACGACGGTCCCTCAAGCTTTTCATCAAGAAACC
CCTACATATCACGATGGTTTCTCAAGCTTTTTTCAAGAAACCCCTACATATCACGATGGCCCTTC
AAGCTTGTCA
Found at i:222172 original size:184 final size:183
Alignment explanation
Indices: 221825--222186 Score: 577
Period size: 184 Copynumber: 2.0 Consensus size: 183
221815 AAATTGTCAC
* * *
221825 CAAGGAACCCCTACATATCACGTTGGTCCCTCAAGTGCTCATCAAATTTGTCTTCAAGGAACCCC
1 CAAGAAACCCCTACATATCACGATGGTCCCTCAAGTGCTCATCAAATTTGTCGTCAAGGAACCCC
*
221890 TACATATCACGATGGTCCCTCAAACTTTTCATCAAGAAACCCCTACATATCACGATGGTTTCTCA
66 TACATATCACGACGGTCCCTCAAACTTTTCATCAAGAAACCCCTACATATCACGATGGTTTCTCA
*
221955 AGCTTGTCATCAAGGAACCCCTACATATCACGATGGTCCC-TCAAGCTTTTTAT
131 AGCTTGTCATCAAAGAACCCCTACATATCACGATGG-CCCTTCAAGCTTTTTAT
* *
222008 CAAGAAACCCCTACATATCACGATGGTCCTTCAAGCTTG-TCATCAAATTTTTCGTCAAGGAACC
1 CAAGAAACCCCTACATATCACGATGGTCCCTCAAG--TGCTCATCAAATTTGTCGTCAAGGAACC
*
222072 CCTACATATCACGACGGTCCCTCAAGA-TTTTCATCAAGAAACCCCTACATATCGCGATGGTTTC
64 CCTACATATCACGACGGTCCCTCAA-ACTTTTCATCAAGAAACCCCTACATATCACGATGGTTTC
* *
222136 TCAAGCTTTTCCTCAAAGAACCCCTACATATCACGATGGCCCTTCAAGCTT
128 TCAAGCTTGTCATCAAAGAACCCCTACATATCACGATGGCCCTTCAAGCTT
222187 GTCATCAAAT
Statistics
Matches: 165, Mismatches: 10, Indels: 7
0.91 0.05 0.04
Matches are distributed among these distances:
183 35 0.21
184 127 0.77
185 3 0.02
ACGTcount: A:0.29, C:0.30, G:0.14, T:0.27
Consensus pattern (183 bp):
CAAGAAACCCCTACATATCACGATGGTCCCTCAAGTGCTCATCAAATTTGTCGTCAAGGAACCCC
TACATATCACGACGGTCCCTCAAACTTTTCATCAAGAAACCCCTACATATCACGATGGTTTCTCA
AGCTTGTCATCAAAGAACCCCTACATATCACGATGGCCCTTCAAGCTTTTTAT
Found at i:222284 original size:98 final size:98
Alignment explanation
Indices: 222093--222272 Score: 274
Period size: 98 Copynumber: 1.8 Consensus size: 98
222083 CGACGGTCCC
* * ** *
222093 TCAAGATTTTCATCAAGAAACCCCTACATATCGCGATGGTTTCTCAAGCTTTTCCTCAAAGAACC
1 TCAAGATTTTCATCAAGAAACCCCTACATATCACGACGGTCCCTCAAGCTTTTCATCAAAGAACC
222158 CCTACATATCACGATGGCCCTTCAAGCTTGTCA
66 CCTACATATCACGATGGCCCTTCAAGCTTGTCA
*
222191 TCAA-ATTTGTCATCAAGGAACCCCTACATATCACGACGGTCCCTCAAGCTTTTCATC-AAGAAA
1 TCAAGATTT-TCATCAAGAAACCCCTACATATCACGACGGTCCCTCAAGCTTTTCATCAAAG-AA
222254 CCCCTACATATCACGATGG
64 CCCCTACATATCACGATGG
222273 TTTCTCAAGC
Statistics
Matches: 74, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
97 7 0.09
98 67 0.91
ACGTcount: A:0.30, C:0.30, G:0.13, T:0.27
Consensus pattern (98 bp):
TCAAGATTTTCATCAAGAAACCCCTACATATCACGACGGTCCCTCAAGCTTTTCATCAAAGAACC
CCTACATATCACGATGGCCCTTCAAGCTTGTCA
Found at i:222375 original size:39 final size:39
Alignment explanation
Indices: 222322--222399 Score: 93
Period size: 39 Copynumber: 2.0 Consensus size: 39
222312 CTTAGTTTCT
*
222322 AAAAATATTGTGTTTCGAGCGAAACTATCTCAAGCGAGA
1 AAAAATATTGTGTTTCAAGCGAAACTATCTCAAGCGAGA
* * * * * *
222361 AAAAATCTTTTGTTTCAAGTGAAATTGTCTCAAGGGAGA
1 AAAAATATTGTGTTTCAAGCGAAACTATCTCAAGCGAGA
222400 CTGTCTCAAT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
39 32 1.00
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.29
Consensus pattern (39 bp):
AAAAATATTGTGTTTCAAGCGAAACTATCTCAAGCGAGA
Done.