Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009581.1 Hibiscus syriacus cultivar Beakdansim tig00116958_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: 2551150
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 13
Found at i:1222991 original size:41 final size:41
Alignment explanation
Indices: 1222882--1223038 Score: 126
Period size: 41 Copynumber: 3.9 Consensus size: 41
1222872 AAATGACCAA
* **
1222882 CAAAATCGCAACGCGAA-ATAAAAATCGCAACGCGA-TCCC
1 CAAAATCGCAACGCGAATATCAAAATCGCAACGCGATTTTC
* ** * *
1222921 CAGAATCGCAAATC-AGTTTCCAAAATCGCAACGCGATTCTT-
1 CAAAATCGCAACGCGAATAT-CAAAATCGCAACGCGATT-TTC
* * * **
1222962 GAAAATCGCAATGCG-ATAGTCAAATTCGCATTGCGATTTTC
1 CAAAATCGCAACGCGAATA-TCAAAATCGCAACGCGATTTTC
*
1223003 CAAAATCGCAACGCGAATATGAAAATCGCAACGCGA
1 CAAAATCGCAACGCGAATATCAAAATCGCAACGCGA
1223039 ACACATAAAT
Statistics
Matches: 87, Mismatches: 23, Indels: 14
0.70 0.19 0.11
Matches are distributed among these distances:
38 1 0.01
39 12 0.14
40 17 0.20
41 53 0.61
42 4 0.05
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.19
Consensus pattern (41 bp):
CAAAATCGCAACGCGAATATCAAAATCGCAACGCGATTTTC
Found at i:1223048 original size:20 final size:20
Alignment explanation
Indices: 1223025--1223198 Score: 118
Period size: 20 Copynumber: 8.7 Consensus size: 20
1223015 GCGAATATGA
1223025 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTAAC-CAT
* * *
1223045 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTAACCAT
* * *
1223065 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTAACCAT
****
1223085 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTAACCAT
* * *
1223105 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTAACCAT
* * **
1223125 ATATCGCAACGCGTATCGGT
1 AAATCGCAACGCGTAACCAT
* *
1223145 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGTAA-CCAT
* *
1223165 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTAACCAT
1223186 AAATCGCAACGCG
1 AAATCGCAACGCG
1223199 ATATTTAAAG
Statistics
Matches: 126, Mismatches: 24, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
19 2 0.02
20 107 0.85
21 15 0.12
22 2 0.02
ACGTcount: A:0.34, C:0.25, G:0.20, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTAACCAT
Found at i:1223069 original size:40 final size:39
Alignment explanation
Indices: 1223005--1223199 Score: 183
Period size: 40 Copynumber: 4.9 Consensus size: 39
1222995 CGATTTTCCA
* ** *
1223005 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACAT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAAC-CAT
* * * *
1223045 AAATCGCAATGCGTATCCGTAAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCG-AACCAT
** * * *
1223085 AAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCG-AACCAT
* * ** *
1223125 ATATCGCAACGCGTATCGGTAAATCGCAACGATAATACAT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAA-CCAT
1223165 AAAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 -AAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1223200 TATTTAAAGC
Statistics
Matches: 127, Mismatches: 25, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
39 1 0.01
40 94 0.74
41 32 0.25
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.19
Consensus pattern (39 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAACCAT
Found at i:1223090 original size:60 final size:60
Alignment explanation
Indices: 1223005--1223198 Score: 244
Period size: 60 Copynumber: 3.2 Consensus size: 60
1222995 CGATTTTCCA
* ** * *
1223005 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAATGCGTATCCGT
* * ***
1223065 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAATGCGTATCCGT
* * ** *
1223125 ATATCGCAACGCGTATCGGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAATGCGTATCCGT
1223186 AAATCGCAACGCG
1 AAATCGCAACGCG
1223199 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 81 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.20
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAATGCGTATCCGT
Found at i:1223617 original size:32 final size:33
Alignment explanation
Indices: 1223579--1223648 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
1223569 TTCACTTAGA
1223579 TTTCATTTCGCGTTACGA-TCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
1223611 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1223644 TTTCA
1 TTTCA
1223649 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
32 16 0.46
33 19 0.54
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.47
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:1223771 original size:19 final size:19
Alignment explanation
Indices: 1223728--1223832 Score: 76
Period size: 19 Copynumber: 5.7 Consensus size: 19
1223718 TGCAGAAGAG
* *
1223728 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAG--AGATGACAA
**
1223749 TCGCAACGAGAGATGACTG
1 TCGCAACGAGAGATGACAA
* *
1223768 TCGCAACGCGAAATGACAA
1 TCGCAACGAGAGATGACAA
1223787 TCGCAAC--GAGA-G--AA
1 TCGCAACGAGAGATGACAA
* * *
1223801 TCGCAACGCGAAATGAAAA
1 TCGCAACGAGAGATGACAA
1223820 TCGCAACGAGAGA
1 TCGCAACGAGAGA
1223833 ATCGCAACGC
Statistics
Matches: 67, Mismatches: 12, Indels: 12
0.74 0.13 0.13
Matches are distributed among these distances:
14 9 0.13
16 4 0.06
17 4 0.06
19 40 0.60
21 10 0.15
ACGTcount: A:0.43, C:0.21, G:0.25, T:0.11
Consensus pattern (19 bp):
TCGCAACGAGAGATGACAA
Found at i:1223804 original size:14 final size:14
Alignment explanation
Indices: 1223785--1223841 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1223775 GCGAAATGAC
1223785 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
1223799 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
1223818 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1223832 AATCGCAACG
1 AATCGCAACG
1223842 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:1223810 original size:33 final size:33
Alignment explanation
Indices: 1223740--1223857 Score: 164
Period size: 33 Copynumber: 3.4 Consensus size: 33
1223730 GCAACGAGAT
1223740 AAATGAAAATCGCAACGAGAGATGACTGTCGCAACGCG
1 AAATGAAAATCGCAACGAGAGA--A---TCGCAACGCG
*
1223778 AAATGACAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1223811 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
**
1223844 AAACCAAAATCGCA
1 AAATGAAAATCGCA
1223858 TTGCGATTTT
Statistics
Matches: 76, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
33 54 0.71
36 1 0.01
38 21 0.28
ACGTcount: A:0.44, C:0.23, G:0.23, T:0.10
Consensus pattern (33 bp):
AAATGAAAATCGCAACGAGAGAATCGCAACGCG
Found at i:1223894 original size:14 final size:14
Alignment explanation
Indices: 1223875--1223964 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
1223865 TTTTATTTCG
1223875 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1223889 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1223908 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1223922 CGTTGCGATTGTCATTTCG
1 CGTTGCGA-T-TC---TCT
1223941 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1223955 CGTTGCGATT
1 CGTTGCGATT
1223965 TTCATTTCAA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 30 0.48
15 1 0.02
16 5 0.08
17 5 0.08
18 1 0.02
19 20 0.32
ACGTcount: A:0.09, C:0.24, G:0.23, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1223900 original size:33 final size:33
Alignment explanation
Indices: 1223858--1223972 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
1223848 CAAAATCGCA
*
1223858 TTGCGATTTTTATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1223891 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
1223924 TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1223957 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
1223973 AACCAAAAGA
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 79 1.00
ACGTcount: A:0.10, C:0.23, G:0.21, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:1223913 original size:19 final size:19
Alignment explanation
Indices: 1223853--1223950 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
1223843 GAAACCAAAA
* *
1223853 TCGCATTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
1223872 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
1223886 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1223905 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
1223919 TCTCGTTGCGATTGTCATT
1 TCGCGTTGCGATTTTCATT
1223938 TCGCGTTGCGATT
1 TCGCGTTGCGATT
1223951 CTCTCGTTGC
Statistics
Matches: 62, Mismatches: 7, Indels: 20
0.70 0.08 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 5 0.08
19 32 0.52
ACGTcount: A:0.10, C:0.22, G:0.22, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1225830 original size:93 final size:93
Alignment explanation
Indices: 1225671--1225953 Score: 541
Period size: 93 Copynumber: 3.1 Consensus size: 93
1225661 TAGATTGCTT
*
1225671 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1225736 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1225764 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1225829 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
1225857 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTTTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1225922 TTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1225949 AGTAA
1 AGTAA
1225954 TGCAATCCAT
Statistics
Matches: 188, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
92 6 0.03
93 182 0.97
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:1226026 original size:20 final size:19
Alignment explanation
Indices: 1226001--1226110 Score: 78
Period size: 19 Copynumber: 6.3 Consensus size: 19
1225991 TAGTTTACTT
**
1226001 TCGCAACACGAAAGTTAAAA
1 TCGCAACACGAAA-CCAAAA
*
1226021 TCGCAACGCGAAACCAAAA
1 TCGCAACACGAAACCAAAA
*
1226040 TCGC-A-ACG--A-CAGAA
1 TCGCAACACGAAACCAAAA
*
1226054 TCGCAACGCGAAACCAAAA
1 TCGCAACACGAAACCAAAA
*
1226073 TCGC-A-ACG--A-CAAGA
1 TCGCAACACGAAACCAAAA
*
1226087 TCGCAACGCGAAACCAAAA
1 TCGCAACACGAAACCAAAA
1226106 TCGCA
1 TCGCA
1226111 TTGCGATTTT
Statistics
Matches: 69, Mismatches: 11, Indels: 21
0.68 0.11 0.21
Matches are distributed among these distances:
14 16 0.23
15 4 0.06
16 4 0.06
17 4 0.06
18 4 0.06
19 25 0.36
20 12 0.17
ACGTcount: A:0.45, C:0.29, G:0.17, T:0.08
Consensus pattern (19 bp):
TCGCAACACGAAACCAAAA
Found at i:1226041 original size:19 final size:19
Alignment explanation
Indices: 1226017--1226110 Score: 100
Period size: 19 Copynumber: 5.5 Consensus size: 19
1226007 CACGAAAGTT
1226017 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAACC
1226036 AAAATCGCAA--CG--A-C
1 AAAATCGCAACGCGAAACC
*
1226050 AGAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAACC
1226069 AAAATCGCAA--CG--A-C
1 AAAATCGCAACGCGAAACC
*
1226083 AAGATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAACC
1226102 AAAATCGCA
1 AAAATCGCA
1226111 TTGCGATTTT
Statistics
Matches: 61, Mismatches: 4, Indels: 20
0.72 0.05 0.24
Matches are distributed among these distances:
14 20 0.33
15 2 0.03
16 4 0.07
17 4 0.07
18 2 0.03
19 29 0.48
ACGTcount: A:0.47, C:0.30, G:0.17, T:0.06
Consensus pattern (19 bp):
AAAATCGCAACGCGAAACC
Found at i:1226061 original size:33 final size:32
Alignment explanation
Indices: 1226018--1226110 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 32
1226008 ACGAAAGTTA
1226018 AAATCGCAACGCGAAACCAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
1226050 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
1226083 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
1226111 TTGCGATTTT
Statistics
Matches: 59, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
32 2 0.03
33 57 0.97
ACGTcount: A:0.46, C:0.30, G:0.17, T:0.06
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:1226128 original size:19 final size:19
Alignment explanation
Indices: 1226106--1226239 Score: 119
Period size: 19 Copynumber: 7.6 Consensus size: 19
1226096 GAAACCAAAA
*
1226106 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1226125 TCGCGTTGCGA--TTC--T
1 TCGCGTTGCGATTTTCATT
1226140 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
1226157 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
1226173 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
1226190 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
1226209 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
1226229 TCGTGTTGCGA
1 TCGCGTTGCGA
1226240 AAGTAAACTA
Statistics
Matches: 93, Mismatches: 10, Indels: 23
0.74 0.08 0.18
Matches are distributed among these distances:
13 8 0.09
14 7 0.08
15 5 0.05
16 5 0.05
17 10 0.11
19 46 0.49
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:1226152 original size:32 final size:33
Alignment explanation
Indices: 1226111--1226202 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
1226101 CAAAATCGCA
1226111 TTGCGATTTTCATTTCGCGTTGCGATTCT-TCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
1226143 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
1226176 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
1226203 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
32 28 0.49
33 29 0.51
ACGTcount: A:0.11, C:0.21, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:1228174 original size:14 final size:14
Alignment explanation
Indices: 1228155--1228190 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1228145 CTTATTTAAT
1228155 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
1228169 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
1228183 TGATTTGT
1 TGATTTGT
1228191 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1228313 original size:19 final size:19
Alignment explanation
Indices: 1228297--1228403 Score: 214
Period size: 19 Copynumber: 5.6 Consensus size: 19
1228287 AAAAATGACT
1228297 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1228316 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1228335 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1228354 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1228373 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1228392 ATCGCAATGCGA
1 ATCGCAATGCGA
1228404 TTTTCATTTC
Statistics
Matches: 88, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 88 1.00
ACGTcount: A:0.46, C:0.17, G:0.21, T:0.16
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1228415 original size:19 final size:19
Alignment explanation
Indices: 1228393--1228701 Score: 359
Period size: 19 Copynumber: 17.7 Consensus size: 19
1228383 GAAATGAAAA
*
1228393 TCGCAATGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1228412 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
1228428 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1228445 TCGCATTGCGA--TTC--T
1 TCGCATTGCGATTTTCATT
1228460 TCG--TTGCGA-TTTCATT
1 TCGCATTGCGATTTTCATT
1228476 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1228495 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1228514 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1228533 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1228552 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1228571 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
1228587 TCG--TTGCGA-TTTCATT
1 TCGCATTGCGATTTTCATT
1228603 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1228622 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
1228638 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1228655 TCCGCATTGCGATTTTCA--
1 T-CGCATTGCGATTTTCATT
*
1228673 T-G--TTGGGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1228689 TCGCGTTGCGATT
1 TCGCATTGCGATT
1228702 GTAATTTCCG
Statistics
Matches: 254, Mismatches: 9, Indels: 54
0.80 0.03 0.17
Matches are distributed among these distances:
13 6 0.02
14 32 0.13
15 7 0.03
16 28 0.11
17 19 0.07
18 15 0.06
19 135 0.53
20 12 0.05
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:1228550 original size:57 final size:52
Alignment explanation
Indices: 1228393--1228673 Score: 408
Period size: 51 Copynumber: 5.3 Consensus size: 52
1228383 GAAATGAAAA
*
1228393 TCGCAATGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
* * * * *
1228445 TCGCATTGCGATTCTTCGTTGCG-ATTTC-ATT-TCGCATTGCGATTTTCATT
1 TCGCATTGCGATT-TTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
*
1228495 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATT
1228552 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGA-TTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1228603 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1228655 TCCGCATTGCGATTTTCAT
1 T-CGCATTGCGATTTTCAT
1228674 GTTGGGATTT
Statistics
Matches: 205, Mismatches: 13, Indels: 21
0.86 0.05 0.09
Matches are distributed among these distances:
49 7 0.03
50 34 0.17
51 55 0.27
52 30 0.15
53 26 0.13
54 4 0.02
55 5 0.02
57 44 0.21
ACGTcount: A:0.15, C:0.23, G:0.17, T:0.46
Consensus pattern (52 bp):
TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:1231000 original size:12 final size:12
Alignment explanation
Indices: 1230983--1231007 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1230973 TCTTCGGGGA
1230983 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1230995 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1231007 C
1 C
1231008 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:1231216 original size:24 final size:24
Alignment explanation
Indices: 1231182--1231228 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1231172 CTGAAACATC
1231182 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
1231206 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
1231229 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:1231937 original size:20 final size:20
Alignment explanation
Indices: 1231909--1232118 Score: 206
Period size: 20 Copynumber: 10.5 Consensus size: 20
1231899 AAATTTCAGT
* * *
1231909 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
1231929 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
1231949 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
1231969 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
1231989 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* **
1232009 GTTGCGATATACGGAAACGC
1 GTTGCGATTTACGGATTCGC
* *
1232029 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
* *
1232049 GTTGCGATTTACAGATACGC
1 GTTGCGATTTACGGATTCGC
* *
1232069 ATTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
1232089 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
1232109 GTTGCGATTT
1 GTTGCGATTT
1232119 TGGAAAATCG
Statistics
Matches: 162, Mismatches: 26, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
20 161 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:1232135 original size:21 final size:20
Alignment explanation
Indices: 1232085--1232182 Score: 79
Period size: 20 Copynumber: 4.8 Consensus size: 20
1232075 ATTTATGTGT
* * * *
1232085 TCGCGTTGCGATTTTCATAT
1 TCGCATTGCGATTTTGAAAA
*
1232105 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTT-GAAAA
* * **
1232126 TCGCAATGCGAATTTGACTA
1 TCGCATTGCGATTTTGAAAA
*
1232146 TCGCATTGCGATTTTCAAGAA
1 TCGCATTGCGATTTTGAA-AA
*
1232167 TCGCGTTGCGATTTTG
1 TCGCATTGCGATTTTG
1232183 GAAACTGATT
Statistics
Matches: 61, Mismatches: 15, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
20 32 0.52
21 29 0.48
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (20 bp):
TCGCATTGCGATTTTGAAAA
Found at i:1232177 original size:41 final size:41
Alignment explanation
Indices: 1232085--1232182 Score: 110
Period size: 41 Copynumber: 2.4 Consensus size: 41
1232075 ATTTATGTGT
* * *
1232085 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGATTTTGATATTCGCATTGCGATTTTGCAAAA
** *
1232126 TCGCAATGCGAATTTGACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGATTTTGA-TATTCGCATTGCGATTTTGCAA-AA
1232167 TCGCGTTGCGATTTTG
1 TCGCGTTGCGATTTTG
1232183 GAAACTGATT
Statistics
Matches: 46, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
40 2 0.04
41 42 0.91
42 2 0.04
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (41 bp):
TCGCGTTGCGATTTTGATATTCGCATTGCGATTTTGCAAAA
Found at i:1234323 original size:6 final size:6
Alignment explanation
Indices: 1234312--1234396 Score: 134
Period size: 6 Copynumber: 14.2 Consensus size: 6
1234302 GACACGTATT
* * *
1234312 ACCACG ACCACG ACCACG ACCACG ACCACG ACCTCG ACCTCG ACCTCG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
*
1234360 ACCACG ACCACG ACCACG ACCACG ACCATG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG A
1234397 GCCGAGCCGA
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 75 1.00
ACGTcount: A:0.31, C:0.48, G:0.16, T:0.05
Consensus pattern (6 bp):
ACCACG
Found at i:1234404 original size:5 final size:5
Alignment explanation
Indices: 1234394--1234432 Score: 60
Period size: 5 Copynumber: 7.8 Consensus size: 5
1234384 ACCATGACCA
* *
1234394 CGAGC CGAGC CGAGC CGTGC CGTGC CGAGC CGAGC CGAG
1 CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAG
1234433 ACGGACGGAC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.15, C:0.38, G:0.41, T:0.05
Consensus pattern (5 bp):
CGAGC
Found at i:1240184 original size:6 final size:6
Alignment explanation
Indices: 1240173--1240215 Score: 68
Period size: 6 Copynumber: 7.2 Consensus size: 6
1240163 CAAACAGTCC
* *
1240173 ACCACT ACCACT ACCACG ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG A
1240216 GCCGAGCCGA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.35, C:0.49, G:0.12, T:0.05
Consensus pattern (6 bp):
ACCACG
Found at i:1243230 original size:46 final size:46
Alignment explanation
Indices: 1243175--1243277 Score: 188
Period size: 46 Copynumber: 2.2 Consensus size: 46
1243165 ACTAAAAATC
1243175 TATTAAGGGAATCATTTCAAGATCAGAGAATGTTCAAGAAAACAAT
1 TATTAAGGGAATCATTTCAAGATCAGAGAATGTTCAAGAAAACAAT
1243221 TATTAAGGGAATCATTTCAAGATCAGAGAATGTTCAAGAAAACAAT
1 TATTAAGGGAATCATTTCAAGATCAGAGAATGTTCAAGAAAACAAT
*
1243267 TAATTATGGGA
1 T-ATTAAGGGA
1243278 TCTTTAAATT
Statistics
Matches: 55, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
46 47 0.85
47 8 0.15
ACGTcount: A:0.45, C:0.10, G:0.18, T:0.27
Consensus pattern (46 bp):
TATTAAGGGAATCATTTCAAGATCAGAGAATGTTCAAGAAAACAAT
Found at i:1244187 original size:27 final size:26
Alignment explanation
Indices: 1244157--1244247 Score: 137
Period size: 27 Copynumber: 3.4 Consensus size: 26
1244147 GGTAGTTCTG
* *
1244157 TATTACTGAGCTTTTTGAAGCTCACTC
1 TATTACTCA-CTTTTCGAAGCTCACTC
1244184 TATTACTCACCTTTTCGAAGCTCACTC
1 TATTACTCA-CTTTTCGAAGCTCACTC
1244211 TATTACTCACATTTTCGAAGCTCACTC
1 TATTACTCAC-TTTTCGAAGCTCACTC
1244238 TATTACTCAC
1 TATTACTCAC
1244248 CTTTGCAGGT
Statistics
Matches: 60, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
26 1 0.02
27 59 0.98
ACGTcount: A:0.24, C:0.29, G:0.09, T:0.38
Consensus pattern (26 bp):
TATTACTCACTTTTCGAAGCTCACTC
Found at i:1248060 original size:64 final size:64
Alignment explanation
Indices: 1247988--1248196 Score: 251
Period size: 64 Copynumber: 3.3 Consensus size: 64
1247978 CGATCCATTG
**
1247988 GTAGTGCATCGATGCA-CTCTTTTAA-AATAAAAACATCGAATGCAATTCATGCATCGATGCATA
1 GTAGTGCATCGATGCATC-CCATTAATAAT-AAAACATCGAATGCAATTCATGCATCGATGCATA
1248051 A
64 A
* ** *
1248052 GTAGTGCATCGATGCATCCCATTAATAATGAAACATCGAATGCAATTGGTGTATCGATGCATAA
1 GTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCATGCATCGATGCATAA
* * * * ** * * *
1248116 GAAGTGCATCGATGCATCCCATCAATAATAATACATCGAATACCTTTTATGCACCGATGCATCA
1 GTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCATGCATCGATGCATAA
1248180 GTAGTGCATCGATGCAT
1 GTAGTGCATCGATGCAT
1248197 ACCTTCATTA
Statistics
Matches: 124, Mismatches: 19, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
64 120 0.97
65 4 0.03
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (64 bp):
GTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCATGCATCGATGCATAA
Found at i:1254165 original size:64 final size:64
Alignment explanation
Indices: 1254095--1254315 Score: 225
Period size: 64 Copynumber: 3.5 Consensus size: 64
1254085 TTGAAGGTGT
* ** * *
1254095 ATCGATGCATTGGTAGTGCATCGATGCA-CTCTTTTAA-AATAAAAATATCGAATGCAATTCATG
1 ATCGATGCATAGGTAGTGCATCGATGCATC-CCATTAATAAT-AAAACATCGAATGCAATTCATA
1254158 C
64 C
* * **
1254159 ATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATGAAACATCGAATGCAATTGGTAC
1 ATCGATGCATAGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCATAC
* * * ** * *
1254223 ATCGATGCATAAGG-AGTGCATCGATGCATCCCATCAATAATAATACATCGAATACCTTTTATGC
1 ATCGATGCAT-AGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCATAC
*
1254287 ACCGATGCATCA-GTAGTGCATCGATGCAT
1 ATCGATGCAT-AGGTAGTGCATCGATGCAT
1254316 ACCTTCATTA
Statistics
Matches: 132, Mismatches: 21, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
63 1 0.01
64 125 0.95
65 6 0.05
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (64 bp):
ATCGATGCATAGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCATAC
Found at i:1254822 original size:15 final size:15
Alignment explanation
Indices: 1254804--1254836 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
1254794 GAGGGTATAA
1254804 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGATG
1254819 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGATG
1254834 TAG
1 TAG
1254837 GGGTCCTACG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.15, C:0.18, G:0.33, T:0.33
Consensus pattern (15 bp):
TAGTCCTTCGGGATG
Found at i:1258331 original size:58 final size:58
Alignment explanation
Indices: 1258269--1258407 Score: 145
Period size: 59 Copynumber: 2.4 Consensus size: 58
1258259 GATAATGCGA
* * **
1258269 ATAGTCGGGAATCATTTTATAACTTTTAATAGTCGATGACTCAACAAAATAATGTCTT
1 ATAGTCGGGAATCATTTTATAACTTTTAATAATCGATGACTCAACAAAACAAAATCTT
*** ** * *
1258327 ATAGTCAATAGATCATTTCGTAACTTTTAATAATCGGTGACTCAACAAAGCAAAATCTT
1 ATAGTCGGGA-ATCATTTTATAACTTTTAATAATCGATGACTCAACAAAACAAAATCTT
1258386 ATAGTCGGAGAA-CATTTATATA
1 ATAGTCGG-GAATCATTT-TATA
1258408 TTTTACTCCT
Statistics
Matches: 62, Mismatches: 16, Indels: 5
0.75 0.19 0.06
Matches are distributed among these distances:
58 12 0.19
59 49 0.79
60 1 0.02
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.34
Consensus pattern (58 bp):
ATAGTCGGGAATCATTTTATAACTTTTAATAATCGATGACTCAACAAAACAAAATCTT
Found at i:1258386 original size:59 final size:59
Alignment explanation
Indices: 1258279--1258391 Score: 154
Period size: 59 Copynumber: 1.9 Consensus size: 59
1258269 ATAGTCGGGA
* * * **
1258279 ATCATTTTATAACTTTTAATAGTCGATGACTCAACAAAATAATGTCTTATAGTCAATAG
1 ATCATTTCATAACTTTTAATAATCGATGACTCAACAAAACAAAATCTTATAGTCAATAG
* * *
1258338 ATCATTTCGTAACTTTTAATAATCGGTGACTCAACAAAGCAAAATCTTATAGTC
1 ATCATTTCATAACTTTTAATAATCGATGACTCAACAAAACAAAATCTTATAGTC
1258392 GGAGAACATT
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
59 46 1.00
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.35
Consensus pattern (59 bp):
ATCATTTCATAACTTTTAATAATCGATGACTCAACAAAACAAAATCTTATAGTCAATAG
Found at i:1258590 original size:4 final size:4
Alignment explanation
Indices: 1258581--1258607 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1258571 AAAGAATTAT
1258581 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1258608 GAGAAAAGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:1261171 original size:19 final size:17
Alignment explanation
Indices: 1261139--1261173 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
1261129 TTAGTCAAGT
1261139 TAACTAAATTTATTTTA
1 TAACTAAATTTATTTTA
1261156 TAACTCAAACTTTATTTT
1 TAACT-AAA-TTTATTTT
1261174 TACATTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 3 0.19
19 8 0.50
ACGTcount: A:0.37, C:0.11, G:0.00, T:0.51
Consensus pattern (17 bp):
TAACTAAATTTATTTTA
Found at i:1267570 original size:2 final size:2
Alignment explanation
Indices: 1267563--1267603 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1267553 GGATATTCTT
1267563 TA 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 TA T
1267604 GTAACACTCT
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1271306 original size:27 final size:27
Alignment explanation
Indices: 1271276--1271365 Score: 171
Period size: 27 Copynumber: 3.3 Consensus size: 27
1271266 TTATGTTGTC
1271276 TAATAATGTAATTATTATATTTATATA
1 TAATAATGTAATTATTATATTTATATA
*
1271303 TAATAATGTAATCATTATATTTATATA
1 TAATAATGTAATTATTATATTTATATA
1271330 TAATAATGTAATTATTATATTTATATA
1 TAATAATGTAATTATTATATTTATATA
1271357 TAATAATGT
1 TAATAATGT
1271366 TGTCTAAGAA
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 61 1.00
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.50
Consensus pattern (27 bp):
TAATAATGTAATTATTATATTTATATA
Found at i:1271378 original size:27 final size:26
Alignment explanation
Indices: 1271276--1271379 Score: 86
Period size: 27 Copynumber: 3.8 Consensus size: 26
1271266 TTATGTTGTC
*
1271276 TAATAATGTAAT-TATTATATTTATATA
1 TAATAATGTAATCTA--AAATTTATATA
* *
1271303 TAATAATGTAATCATTATATTTATATA
1 TAATAATGTAATC-TAAAATTTATATA
*
1271330 TAATAATGTAAT-TATTATATTTATATA
1 TAATAATGTAATCTA--AAATTTATATA
**
1271357 TAATAATGTTGTCTAAGAATTTA
1 TAATAATGTAATCTAA-AATTTA
1271380 GGGGTGTTCA
Statistics
Matches: 66, Mismatches: 5, Indels: 12
0.80 0.06 0.14
Matches are distributed among these distances:
25 1 0.02
26 1 0.02
27 61 0.92
28 2 0.03
29 1 0.02
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (26 bp):
TAATAATGTAATCTAAAATTTATATA
Found at i:1271517 original size:2 final size:2
Alignment explanation
Indices: 1271510--1271536 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1271500 TAAATGAAAT
1271510 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1271537 CTTTGGTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1273207 original size:2 final size:2
Alignment explanation
Indices: 1273202--1273230 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1273192 ATATATATAT
1273202 AG AG 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 AG AG A
1273231 CAACAGAAAT
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1282552 original size:2 final size:2
Alignment explanation
Indices: 1282545--1282572 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1282535 TCTGAAATGC
1282545 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
1282573 TATTTCAAGG
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:1290919 original size:22 final size:24
Alignment explanation
Indices: 1290875--1290919 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 24
1290865 TTTAGGTGAC
*
1290875 AAAAATAAATTATCAATAGAAGAT
1 AAAAATAAATTATAAATAGAAGAT
*
1290899 AAAAA-AAATTA-AAATATAAGA
1 AAAAATAAATTATAAATAGAAGA
1290920 GTTTGAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 8 0.42
23 6 0.32
24 5 0.26
ACGTcount: A:0.69, C:0.02, G:0.07, T:0.22
Consensus pattern (24 bp):
AAAAATAAATTATAAATAGAAGAT
Found at i:1295936 original size:111 final size:109
Alignment explanation
Indices: 1295694--1295944 Score: 265
Period size: 110 Copynumber: 2.3 Consensus size: 109
1295684 TTTTTTTTTT
* * *
1295694 GATGATTTGGTGCTTAATCATAGGTCATTGATCTAGTTAATCTAGTTTCTTGCTGAAATTTCTTT
1 GATGATTTGATGCTTAATCATA-GTCAATGATCTAGTTAATCTAGTTTCTTGCTGAAATTTATTT
* * * * ** * *
1295759 CTTTCTTCACTTGTTAGGTACATTACAATGTTCACTTAGTGTTTT
65 CTTTATTCAATTATCAGGTACATTACAATACTCAATTAGTGTTTG
* * *
1295804 GAT-AGTTTGATACTTAATCATAGTTCAATGTTC-AGTTAATCTAGTTTTCTTGTTGAAATTTAT
1 GATGA-TTTGATGCTTAATCATAG-TCAATGATCTAGTTAATCTAG-TTTCTTGCTGAAATTTAT
* *
1295867 TTCTTTATTACAATTATCATGTACATTACAATACTCAATTCGT-TTTGG
63 TTCTTTATT-CAATTATCAGGTACATTACAATACTCAATTAGTGTTT-G
*
1295915 GATGATTTGATGCTTCATCATAAGTCAATG
1 GATGATTTGATGCTTAATCAT-AGTCAATG
1295945 CGTGGTACAG
Statistics
Matches: 116, Mismatches: 18, Indels: 13
0.79 0.12 0.09
Matches are distributed among these distances:
109 13 0.11
110 52 0.45
111 48 0.41
112 3 0.03
ACGTcount: A:0.26, C:0.14, G:0.15, T:0.46
Consensus pattern (109 bp):
GATGATTTGATGCTTAATCATAGTCAATGATCTAGTTAATCTAGTTTCTTGCTGAAATTTATTTC
TTTATTCAATTATCAGGTACATTACAATACTCAATTAGTGTTTG
Found at i:1306569 original size:18 final size:17
Alignment explanation
Indices: 1306544--1306591 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 17
1306534 CTGGACTGAT
* *
1306544 TTGGTAAGTTGGACTAG
1 TTGGTAAGCTGAACTAG
1306561 TTGGATAAGCTGAACTAG
1 TTGG-TAAGCTGAACTAG
*
1306579 TTTGGTGAGCTGA
1 -TTGGTAAGCTGA
1306592 GCCAGACGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 4 0.15
18 18 0.69
19 4 0.15
ACGTcount: A:0.25, C:0.08, G:0.33, T:0.33
Consensus pattern (17 bp):
TTGGTAAGCTGAACTAG
Found at i:1310285 original size:59 final size:60
Alignment explanation
Indices: 1310193--1310319 Score: 159
Period size: 59 Copynumber: 2.1 Consensus size: 60
1310183 TTGGAGGATC
* * * * * * * *
1310193 ATAGTTTAGTGATGAAATTAGAATGTTTAAAAGTTTAAGGGCTAA-TTAGAATG-AGAGTT
1 ATAGTTTGGGGATGAAATTAAAATATTGAAAAGTTTAAGGACCAATTTAAAATGAAGA-TT
1310252 ATAGTTTGGGGATGAAATTAAAATATTGAAAAGTTTAAGGACCAATTTAAAATGAAGATT
1 ATAGTTTGGGGATGAAATTAAAATATTGAAAAGTTTAAGGACCAATTTAAAATGAAGATT
1310312 ATAGTTTG
1 ATAGTTTG
1310320 AAAACATATA
Statistics
Matches: 58, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
59 38 0.66
60 17 0.29
61 3 0.05
ACGTcount: A:0.41, C:0.02, G:0.22, T:0.35
Consensus pattern (60 bp):
ATAGTTTGGGGATGAAATTAAAATATTGAAAAGTTTAAGGACCAATTTAAAATGAAGATT
Found at i:1310454 original size:13 final size:11
Alignment explanation
Indices: 1310436--1310484 Score: 55
Period size: 12 Copynumber: 4.3 Consensus size: 11
1310426 TCAAAAAATT
1310436 ATTAATTATATA
1 ATTAATTATA-A
1310448 CATTAATTATAA
1 -ATTAATTATAA
1310460 ATTAAATTATAA
1 ATT-AATTATAA
*
1310472 AAT-ATTATAA
1 ATTAATTATAA
1310482 ATT
1 ATT
1310485 TTAATTTTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
10 9 0.27
11 3 0.09
12 11 0.33
13 10 0.30
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (11 bp):
ATTAATTATAA
Found at i:1312462 original size:61 final size:61
Alignment explanation
Indices: 1312367--1312488 Score: 244
Period size: 61 Copynumber: 2.0 Consensus size: 61
1312357 TCGTAATGGC
1312367 GGTAAATGAGACATGACCGAAAACGCGACTTCGATTTGAATCCCTAGGATTTACATTAGGT
1 GGTAAATGAGACATGACCGAAAACGCGACTTCGATTTGAATCCCTAGGATTTACATTAGGT
1312428 GGTAAATGAGACATGACCGAAAACGCGACTTCGATTTGAATCCCTAGGATTTACATTAGGT
1 GGTAAATGAGACATGACCGAAAACGCGACTTCGATTTGAATCCCTAGGATTTACATTAGGT
1312489 TTTATCTTGG
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 61 1.00
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.26
Consensus pattern (61 bp):
GGTAAATGAGACATGACCGAAAACGCGACTTCGATTTGAATCCCTAGGATTTACATTAGGT
Found at i:1313086 original size:37 final size:37
Alignment explanation
Indices: 1313036--1313109 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
1313026 GTCCGAGAAA
1313036 TTGATTTGGTGCACCTTTACCTAATGTACTTAGGGAT
1 TTGATTTGGTGCACCTTTACCTAATGTACTTAGGGAT
1313073 TTGATTTGGTGCACCTTTACCTAATGTACTTAGGGAT
1 TTGATTTGGTGCACCTTTACCTAATGTACTTAGGGAT
1313110 GATCATTGGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.22, C:0.16, G:0.22, T:0.41
Consensus pattern (37 bp):
TTGATTTGGTGCACCTTTACCTAATGTACTTAGGGAT
Found at i:1315444 original size:185 final size:185
Alignment explanation
Indices: 1315132--1315498 Score: 698
Period size: 185 Copynumber: 2.0 Consensus size: 185
1315122 TTTAAAATAT
*
1315132 AAATAATTTTATAAAATATTATAAATCATCACCATTTAAAACAATAATTTTACAGAAAAAGTCAT
1 AAATAATTTTATAAAATATTATAAATCATCACCATTTAAAACAATAATTTTACAAAAAAAGTCAT
1315197 CAAATACACCACATAAGATTTTGAAATGATCAAAAACACATCAAAAAATATCAAATGATAATTAA
66 CAAATACACCACATAAGATTTTGAAATGATCAAAAACACATCAAAAAATATCAAATGATAATTAA
* *
1315262 TATACATAATTATATTATGTAATTTAATGCAAGAATAATTTATAAAAAATATAAA
131 TATACATAATTATATTATATAATTTAATACAAGAATAATTTATAAAAAATATAAA
*
1315317 AAATAATTTTATAAGATATTATAAATCATCACCATTTAAAACAATAATTTTACAAAAAAAGTCAT
1 AAATAATTTTATAAAATATTATAAATCATCACCATTTAAAACAATAATTTTACAAAAAAAGTCAT
1315382 CAAATACACCACATAAGATTTTGAAATGATCAAAAACACATCAAAAAATATCAAATGATAATTAA
66 CAAATACACCACATAAGATTTTGAAATGATCAAAAACACATCAAAAAATATCAAATGATAATTAA
1315447 TATACATAATTATATTATATAATTTAATACAAGAATAATTTATAAAAAATAT
131 TATACATAATTATATTATATAATTTAATACAAGAATAATTTATAAAAAATAT
1315499 TTAAAAATTT
Statistics
Matches: 178, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
185 178 1.00
ACGTcount: A:0.54, C:0.10, G:0.04, T:0.32
Consensus pattern (185 bp):
AAATAATTTTATAAAATATTATAAATCATCACCATTTAAAACAATAATTTTACAAAAAAAGTCAT
CAAATACACCACATAAGATTTTGAAATGATCAAAAACACATCAAAAAATATCAAATGATAATTAA
TATACATAATTATATTATATAATTTAATACAAGAATAATTTATAAAAAATATAAA
Found at i:1317759 original size:18 final size:17
Alignment explanation
Indices: 1317730--1317773 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
1317720 ATACTGCGTC
1317730 TTAAATTAATTTTAAATAT
1 TTAAA-TAATTTTAAAT-T
*
1317749 TTAAATAATTTTTAATT
1 TTAAATAATTTTAAATT
*
1317766 TAAAATAA
1 TTAAATAA
1317774 ACAGTTAACA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 8 0.35
18 10 0.43
19 5 0.22
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TTAAATAATTTTAAATT
Found at i:1317912 original size:22 final size:21
Alignment explanation
Indices: 1317868--1317912 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
1317858 ATATATATTA
* **
1317868 AAATTTATTTTTAAAAAGTTG
1 AAATTTATTTTAAAAAACATG
1317889 AAATATTATTTTAAAAAACATG
1 AAAT-TTATTTTAAAAAACATG
1317911 AA
1 AA
1317913 TTAGAAAGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.51, C:0.02, G:0.07, T:0.40
Consensus pattern (21 bp):
AAATTTATTTTAAAAAACATG
Found at i:1322240 original size:6 final size:6
Alignment explanation
Indices: 1322229--1322262 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
1322219 AGAAACAGCC
* *
1322229 GAAAAT GAAAAT GAAAAT AAAAAT TAAAAT GAAA
1 GAAAAT GAAAAT GAAAAT GAAAAT GAAAAT GAAA
1322263 GAGTCATACC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.71, C:0.00, G:0.12, T:0.18
Consensus pattern (6 bp):
GAAAAT
Found at i:1325379 original size:20 final size:19
Alignment explanation
Indices: 1325339--1325383 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
1325329 TAATTTTATT
1325339 TAAAAAAAAATCTTAAATC
1 TAAAAAAAAATCTTAAATC
*
1325358 TAAAAGAAAA-CTCTAAACTC
1 TAAAAAAAAATCT-TAAA-TC
1325378 TAAAAA
1 TAAAAA
1325384 CCTTAATTCC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 2 0.09
19 13 0.59
20 7 0.32
ACGTcount: A:0.62, C:0.13, G:0.02, T:0.22
Consensus pattern (19 bp):
TAAAAAAAAATCTTAAATC
Found at i:1326198 original size:2 final size:2
Alignment explanation
Indices: 1326187--1326222 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
1326177 TAAAGTTCTT
1326187 TA TA -A 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 T
1326223 TTACACACAC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1337538 original size:31 final size:29
Alignment explanation
Indices: 1337461--1337539 Score: 81
Period size: 30 Copynumber: 2.6 Consensus size: 29
1337451 ACGACCCTTG
1337461 GGTAGGCTC-TACGGCCCCGAGATCTTCTT
1 GGTAGGCTCTTA-GGCCCCGAGATCTTCTT
* *
1337490 AGGTAGGCCCTGT-GGCCCCGAGATTTTTCTT
1 -GGTAGGCTCT-TAGGCCCCGAGA-TCTTCTT
1337521 GGATAGGCTCTTAGGCCCC
1 GG-TAGGCTCTTAGGCCCC
1337540 AATGTGCTCC
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
30 21 0.51
31 19 0.46
32 1 0.02
ACGTcount: A:0.14, C:0.29, G:0.29, T:0.28
Consensus pattern (29 bp):
GGTAGGCTCTTAGGCCCCGAGATCTTCTT
Found at i:1339222 original size:22 final size:22
Alignment explanation
Indices: 1339194--1339239 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
1339184 ATCATTTTTT
1339194 GTAGGAAGATGGGAAATAATAC
1 GTAGGAAGATGGGAAATAATAC
1339216 GTAGGAAGATGGGAAATAATAC
1 GTAGGAAGATGGGAAATAATAC
1339238 GT
1 GT
1339240 TGGGAAAGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.43, C:0.04, G:0.33, T:0.20
Consensus pattern (22 bp):
GTAGGAAGATGGGAAATAATAC
Found at i:1345633 original size:27 final size:28
Alignment explanation
Indices: 1345590--1345642 Score: 81
Period size: 27 Copynumber: 1.9 Consensus size: 28
1345580 CCAGGGCTTT
* *
1345590 GGGGTATTTTAGGTTATTTCATATTTTA
1 GGGGTAATTTAGGTTATTTCACATTTTA
1345618 GGGGTAATTT-GGTTATTTCACATTT
1 GGGGTAATTTAGGTTATTTCACATTT
1345643 CATGGGTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 14 0.61
28 9 0.39
ACGTcount: A:0.21, C:0.06, G:0.23, T:0.51
Consensus pattern (28 bp):
GGGGTAATTTAGGTTATTTCACATTTTA
Found at i:1345649 original size:27 final size:28
Alignment explanation
Indices: 1345590--1345650 Score: 79
Period size: 27 Copynumber: 2.2 Consensus size: 28
1345580 CCAGGGCTTT
* * *
1345590 GGGGTATTTTAGGTTATTTCATATTTTA
1 GGGGTAATTTAGGTTATTTCACATTTCA
1345618 GGGGTAATTT-GGTTATTTCACATTTCA
1 GGGGTAATTTAGGTTATTTCACATTTCA
*
1345645 TGGGTA
1 GGGGTA
1345651 TTTCAGTCAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 20 0.69
28 9 0.31
ACGTcount: A:0.21, C:0.07, G:0.25, T:0.48
Consensus pattern (28 bp):
GGGGTAATTTAGGTTATTTCACATTTCA
Found at i:1346445 original size:19 final size:19
Alignment explanation
Indices: 1346417--1346468 Score: 86
Period size: 19 Copynumber: 2.7 Consensus size: 19
1346407 CGGCACGGTC
*
1346417 CAGATTGGTCCAACCGATT
1 CAGATCGGTCCAACCGATT
1346436 CAGATCGGTCCAACCGATT
1 CAGATCGGTCCAACCGATT
*
1346455 CAGATCGGTTCAAC
1 CAGATCGGTCCAAC
1346469 ATGTCAATAG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.23
Consensus pattern (19 bp):
CAGATCGGTCCAACCGATT
Found at i:1347261 original size:21 final size:21
Alignment explanation
Indices: 1347232--1347284 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
1347222 ATTCTGACTA
1347232 TCGCATTGCGA-TTTCCTAAAT
1 TCGCATTGCGATTTTCCT-AAT
*
1347253 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCCTAAT
*
1347274 TCGCAATGCGA
1 TCGCATTGCGA
1347285 ATACGTAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 22 0.79
22 6 0.21
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCTAAT
Found at i:1347299 original size:20 final size:20
Alignment explanation
Indices: 1347274--1347387 Score: 156
Period size: 20 Copynumber: 5.7 Consensus size: 20
1347264 TTTTCCTAAT
1347274 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* ** *
1347294 TCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAA-TACGTAAA
* *
1347315 TCACAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
1347335 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
1347355 TCGCAATGCAAATACGTAAA
1 TCGCAATGCGAATACGTAAA
1347375 TCGCAATGCGAAT
1 TCGCAATGCGAAT
1347388 TTGACTATCG
Statistics
Matches: 79, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
20 65 0.82
21 14 0.18
ACGTcount: A:0.39, C:0.20, G:0.19, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:1347325 original size:21 final size:21
Alignment explanation
Indices: 1347274--1347410 Score: 122
Period size: 20 Copynumber: 6.8 Consensus size: 21
1347264 TTTTCCTAAT
*
1347274 TCGCAATGCGAA-TACGTAAA
1 TCGCAATGCGAATTACGAAAA
* **
1347294 TCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAATTACGAAAA
* *
1347315 TCACAATGCG-ATTACGTAAA
1 TCGCAATGCGAATTACGAAAA
*
1347335 TCGCAATGCGAA-TACGTAAA
1 TCGCAATGCGAATTACGAAAA
* *
1347355 TCGCAATGC-AAATACGTAAA
1 TCGCAATGCGAATTACGAAAA
* **
1347375 TCGCAATGCGAATT-TGACTA
1 TCGCAATGCGAATTACGAAAA
*
1347395 TCGCAATGCGATTTAC
1 TCGCAATGCGAATTAC
1347411 ATAGCGCCAT
Statistics
Matches: 95, Mismatches: 17, Indels: 9
0.79 0.14 0.07
Matches are distributed among these distances:
19 2 0.02
20 76 0.80
21 17 0.18
ACGTcount: A:0.37, C:0.20, G:0.19, T:0.23
Consensus pattern (21 bp):
TCGCAATGCGAATTACGAAAA
Found at i:1347398 original size:40 final size:39
Alignment explanation
Indices: 1347274--1347405 Score: 165
Period size: 40 Copynumber: 3.3 Consensus size: 39
1347264 TTTTCCTAAT
*
1347274 TCGCAATGCGAATACGTAAATCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAATACGTAAATCGCAATGCGAATTT-G-AAA
* * **
1347315 TCACAATGCGATTACGTAAATCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAATCGCAATGCGAATTTG-AAA
* *
1347355 TCGCAATGCAAATACGTAAATCGCAATGCGAATTTGACTA
1 TCGCAATGCGAATACGTAAATCGCAATGCGAATTTGA-AA
1347395 TCGCAATGCGA
1 TCGCAATGCGA
1347406 TTTACATAGC
Statistics
Matches: 77, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
39 1 0.01
40 46 0.60
41 30 0.39
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.22
Consensus pattern (39 bp):
TCGCAATGCGAATACGTAAATCGCAATGCGAATTTGAAA
Found at i:1348068 original size:20 final size:20
Alignment explanation
Indices: 1347980--1348069 Score: 92
Period size: 20 Copynumber: 4.5 Consensus size: 20
1347970 GCGATTCTGT
1347980 CGTTGCGATTTTCA-TTTCG
1 CGTTGCGATTTTCATTTTCG
** **
1347999 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATTTTCATTTTCG
** *
1348019 CGTTGCGATAGTCATTTTCA
1 CGTTGCGATTTTCATTTTCG
*
1348039 TGTTGCGATTTTCATTTTCG
1 CGTTGCGATTTTCATTTTCG
*
1348059 TGTTGCGATTT
1 CGTTGCGATTT
1348070 AAAGTTTTAG
Statistics
Matches: 60, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
19 12 0.20
20 48 0.80
ACGTcount: A:0.16, C:0.18, G:0.22, T:0.44
Consensus pattern (20 bp):
CGTTGCGATTTTCATTTTCG
Found at i:1349961 original size:20 final size:20
Alignment explanation
Indices: 1349936--1350027 Score: 139
Period size: 20 Copynumber: 4.6 Consensus size: 20
1349926 AGAATAGTTT
1349936 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
1349956 ACTATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
1349976 ACTATCGCAATGTGAAAATG
1 ACTATCGCAATGCGAAAATG
**
1349996 ACTATCGCAATGCGAATTTG
1 ACTATCGCAATGCGAAAATG
*
1350016 ACTATCGAAATG
1 ACTATCGCAATG
1350028 AAAGAATCGC
Statistics
Matches: 65, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 65 1.00
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.23
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:1350045 original size:21 final size:19
Alignment explanation
Indices: 1350021--1350063 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
1350011 ATTTGACTAT
1350021 CGAAATGAAAGAATCGCAATG
1 CGAAATG-AA-AATCGCAATG
*
1350042 CGAAATGAAAATCGCATTG
1 CGAAATGAAAATCGCAATG
1350061 CGA
1 CGA
1350064 TTCTCTCGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 12 0.57
20 2 0.10
21 7 0.33
ACGTcount: A:0.44, C:0.16, G:0.23, T:0.16
Consensus pattern (19 bp):
CGAAATGAAAATCGCAATG
Found at i:1350710 original size:18 final size:19
Alignment explanation
Indices: 1350671--1350712 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 19
1350661 CTCACCTGTC
1350671 ATCGTTCAAGAGGCCTCCCCT
1 ATCGTTCAAGAGG-C-CCCCT
1350692 ATCGTTCAAGAGG-CCCCT
1 ATCGTTCAAGAGGCCCCCT
1350710 ATC
1 ATC
1350713 ATCCCTCAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
21 13 0.62
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.24
Consensus pattern (19 bp):
ATCGTTCAAGAGGCCCCCT
Found at i:1352150 original size:14 final size:14
Alignment explanation
Indices: 1352131--1352166 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1352121 ATTGTTTAAT
1352131 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
1352145 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
1352159 TGATTTGT
1 TGATTTGT
1352167 TTAATTGACG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1352356 original size:34 final size:33
Alignment explanation
Indices: 1352292--1352357 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
1352282 ATGACTATCG
1352292 CAACGAGAGAATCGCAATGCGAAATGAAAATCA
1 CAACGAGAGAATCGCAATGCGAAATGAAAATCA
*
1352325 CAACGAGTGAATCGCAATGCGAAAATGAAAATC
1 CAACGAGAGAATCGCAATGCG-AAATGAAAATC
1352358 GTAACGCGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 20 0.65
34 11 0.35
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (33 bp):
CAACGAGAGAATCGCAATGCGAAATGAAAATCA
Found at i:1352394 original size:19 final size:19
Alignment explanation
Indices: 1352372--1352497 Score: 163
Period size: 19 Copynumber: 6.8 Consensus size: 19
1352362 CGCGAAACTA
*
1352372 ATTTCGCGTTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
1352391 ATTTTCGCATTGCGA--TTC
1 A-TTTCGCATTGCGATTTTC
*
1352409 A-CTCG--TTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
1352425 ATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
* *
1352444 ATTTTGCATTTCGATTTTC
1 ATTTCGCATTGCGATTTTC
*
1352463 ATTTCGTATTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
1352482 ATTTCGCATTGCGATT
1 ATTTCGCATTGCGATT
1352498 CTCTCATTGC
Statistics
Matches: 92, Mismatches: 9, Indels: 12
0.81 0.08 0.11
Matches are distributed among these distances:
14 6 0.07
16 7 0.08
17 3 0.03
18 4 0.04
19 60 0.65
20 12 0.13
ACGTcount: A:0.15, C:0.20, G:0.17, T:0.48
Consensus pattern (19 bp):
ATTTCGCATTGCGATTTTC
Found at i:1352529 original size:20 final size:20
Alignment explanation
Indices: 1352504--1352595 Score: 123
Period size: 20 Copynumber: 4.6 Consensus size: 20
1352494 GATTCTCTCA
1352504 TTGCGATAGTCATTTCCGCG
1 TTGCGATAGTCATTTCCGCG
* *
1352524 TTGCGATAGTCAATTCCGCA
1 TTGCGATAGTCATTTCCGCG
* *
1352544 TTGCGATAGTCATTTCTGTG
1 TTGCGATAGTCATTTCCGCG
*
1352564 TTGCGATAGTTATATT-CGCG
1 TTGCGATAGTCAT-TTCCGCG
1352584 TTGCGATAGTCA
1 TTGCGATAGTCA
1352596 AATGAATGTC
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
20 59 0.97
21 2 0.03
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.37
Consensus pattern (20 bp):
TTGCGATAGTCATTTCCGCG
Found at i:1352557 original size:40 final size:40
Alignment explanation
Indices: 1352502--1352595 Score: 136
Period size: 40 Copynumber: 2.4 Consensus size: 40
1352492 GCGATTCTCT
1352502 CATTGCGATAGTCATTTCCGCGTTGCGATAGTCA-ATTCCG
1 CATTGCGATAGTCATTTCCGCGTTGCGATAGTCATATT-CG
* * *
1352542 CATTGCGATAGTCATTTCTGTGTTGCGATAGTTATATTCG
1 CATTGCGATAGTCATTTCCGCGTTGCGATAGTCATATTCG
*
1352582 CGTTGCGATAGTCA
1 CATTGCGATAGTCA
1352596 AATGAATGTC
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
40 46 0.94
41 3 0.06
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.36
Consensus pattern (40 bp):
CATTGCGATAGTCATTTCCGCGTTGCGATAGTCATATTCG
Found at i:1355070 original size:24 final size:24
Alignment explanation
Indices: 1355019--1355070 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
1355009 ATCTGAGTAT
** *
1355019 TGACCAAGATCAAAGTCCGGGTAT
1 TGACCAAGATCAAAGTCCGAATAC
* *
1355043 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTCCGAATAC
1355067 TGAC
1 TGAC
1355071 TAGTACTCAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.23
Consensus pattern (24 bp):
TGACCAAGATCAAAGTCCGAATAC
Found at i:1356022 original size:20 final size:20
Alignment explanation
Indices: 1355918--1356024 Score: 117
Period size: 20 Copynumber: 5.3 Consensus size: 20
1355908 CAGAATCTCG
1355918 TTGCGATTTACAG-ATTCGCA
1 TTGCGATTTAC-GTATTCGCA
*
1355938 TTGCGATTTACGTAATCGCA
1 TTGCGATTTACGTATTCGCA
* *
1355958 TTGCGATTTACGTAATCACA
1 TTGCGATTTACGTATTCGCA
* ** * *
1355978 TTGCGATTTTCCAAATTCACG
1 TTGCGA-TTTACGTATTCGCA
1355999 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
1356019 TTGCGA
1 TTGCGA
1356025 ATTAGGAAAA
Statistics
Matches: 73, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
19 1 0.01
20 57 0.78
21 15 0.21
ACGTcount: A:0.24, C:0.21, G:0.19, T:0.36
Consensus pattern (20 bp):
TTGCGATTTACGTATTCGCA
Found at i:1356045 original size:21 final size:21
Alignment explanation
Indices: 1356021--1356061 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1356011 TATTCGCATT
1356021 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* *
1356042 GCGAATTTGGGAAATCGCAA
1 GCGAATTAGGAAAATCGCAA
1356062 TACGATAGTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.39, C:0.17, G:0.27, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:1357052 original size:6 final size:6
Alignment explanation
Indices: 1357041--1357065 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1357031 ATTTGACAAA
1357041 ATATCT ATATCT ATATCT ATATCT A
1 ATATCT ATATCT ATATCT ATATCT A
1357066 GCTATATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.16, G:0.00, T:0.48
Consensus pattern (6 bp):
ATATCT
Found at i:1358160 original size:31 final size:30
Alignment explanation
Indices: 1358102--1358160 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
1358092 GTATACAAAT
* **
1358102 AGTCCTCCGATTATAGGGGATGTTTTGTCA
1 AGTCCTCCAATTATAGGACATGTTTTGTCA
1358132 AGTCCTCCAATTATAGGACACTGTTTTGT
1 AGTCCTCCAATTATAGGACA-TGTTTTGT
1358161 TAAATATAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 17 0.68
31 8 0.32
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.37
Consensus pattern (30 bp):
AGTCCTCCAATTATAGGACATGTTTTGTCA
Found at i:1363320 original size:24 final size:24
Alignment explanation
Indices: 1363222--1363323 Score: 116
Period size: 24 Copynumber: 4.2 Consensus size: 24
1363212 ATTTCCGATT
* * *
1363222 TGAATTATGTTATGATACCTGACA
1 TGAATTCTGATATGATACTTGACA
* *
1363246 TGGATTCTGATATGATACTTGACC
1 TGAATTCTGATATGATACTTGACA
***
1363270 TGGAATT-TGATCCAATACTTGACA
1 T-GAATTCTGATATGATACTTGACA
1363294 TGAATTCTGATATGATACTTGACA
1 TGAATTCTGATATGATACTTGACA
1363318 TGAATT
1 TGAATT
1363324 ATGTTTTGAT
Statistics
Matches: 63, Mismatches: 13, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
23 5 0.08
24 54 0.86
25 4 0.06
ACGTcount: A:0.31, C:0.14, G:0.18, T:0.37
Consensus pattern (24 bp):
TGAATTCTGATATGATACTTGACA
Found at i:1363511 original size:2 final size:2
Alignment explanation
Indices: 1363504--1363553 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
1363494 GGTAGTGTTC
1363504 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1363546 AT AT AT AT
1 AT AT AT AT
1363554 GTTTTAAAAG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1385087 original size:2 final size:2
Alignment explanation
Indices: 1385080--1385119 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1385070 AAAGGTAATA
1385080 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1385120 TAATAATTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1392957 original size:18 final size:18
Alignment explanation
Indices: 1392931--1392978 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
1392921 GGTCATAACT
*
1392931 CGACTCGTTGACCCGACC
1 CGACACGTTGACCCGACC
1392949 CGACACGTTGACCCGACC
1 CGACACGTTGACCCGACC
1392967 CGACACGTTGAC
1 CGACACGTTGAC
1392979 TGACGTTGAC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.21, C:0.42, G:0.23, T:0.15
Consensus pattern (18 bp):
CGACACGTTGACCCGACC
Found at i:1394853 original size:182 final size:183
Alignment explanation
Indices: 1394567--1394934 Score: 614
Period size: 182 Copynumber: 2.0 Consensus size: 183
1394557 AATTAAATGT
*
1394567 TTTTTAATTAAAAAAAAGTTTATAATTAATTTAAATAATATATAATTATAAAATAAAAATTTCAG
1 TTTTTAATTAAAAAAAAGTTTACAATTAATTTAAATAATATATAATTATAAAATAAAAATTTCAG
* *
1394632 ATAAAATTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTGGATCTTAAATTATTAATT
66 ATAAAATTTTTAATTAATTAATATTGATTTAGCTTTAAAAGTTATTAGATCTTAAATTATTAATT
* *
1394697 GGGTTTTAAATGGTTTGAGCTTAGCCCATATGTTATATATAATATATATAATA
131 GGGTTTTAAATGGTTTGAGCTGAGCCCATATGTTATATATAATATATATAAAA
*
1394750 TTTTTAATTAAAAAAACAGTTTACAATTAATTTAAATAATATA-AATTATAAAATAAAAATTTTA
1 TTTTTAATTAAAAAAA-AGTTTACAATTAATTTAAATAATATATAATTATAAAATAAAAATTTCA
* * *
1394814 TAT-AATTTTTTAATTAATTAATATTGATTTAGCTTTAAAAGTTATTATATCTTAAATTATTAAT
65 GATAAAATTTTTAATTAATTAATATTGATTTAGCTTTAAAAGTTATTAGATCTTAAATTATTAAT
* *
1394878 TGGGTTTTAAATGGTTTGGGCTGAGCCCATATGTTATATATAATATATTTAAAA
130 TGGGTTTTAAATGGTTTGAGCTGAGCCCATATGTTATATATAATATATATAAAA
1394932 TTT
1 TTT
1394935 AATTTCGGTT
Statistics
Matches: 173, Mismatches: 11, Indels: 3
0.93 0.06 0.02
Matches are distributed among these distances:
182 110 0.64
183 38 0.22
184 25 0.14
ACGTcount: A:0.42, C:0.04, G:0.09, T:0.45
Consensus pattern (183 bp):
TTTTTAATTAAAAAAAAGTTTACAATTAATTTAAATAATATATAATTATAAAATAAAAATTTCAG
ATAAAATTTTTAATTAATTAATATTGATTTAGCTTTAAAAGTTATTAGATCTTAAATTATTAATT
GGGTTTTAAATGGTTTGAGCTGAGCCCATATGTTATATATAATATATATAAAA
Found at i:1396197 original size:24 final size:23
Alignment explanation
Indices: 1396165--1396250 Score: 91
Period size: 24 Copynumber: 3.6 Consensus size: 23
1396155 TTCCGACTTA
*
1396165 AATTCTGTTCTGATACATTACCTG
1 AATTCTGTTCTGATAC-TTATCTG
* *
1396189 AATTCTGTTCTGATTTCTGATCTG
1 AATTCTGTTCTGA-TACTTATCTG
* *
1396213 GATTCTGTTCTAATATCTTATCTG
1 AATTCTGTTCTGATA-CTTATCTG
*
1396237 AATTCTGTTTTGAT
1 AATTCTGTTCTGAT
1396251 TTCTGATATC
Statistics
Matches: 50, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
23 1 0.02
24 47 0.94
25 2 0.04
ACGTcount: A:0.21, C:0.16, G:0.14, T:0.49
Consensus pattern (23 bp):
AATTCTGTTCTGATACTTATCTG
Found at i:1396201 original size:12 final size:12
Alignment explanation
Indices: 1396186--1396255 Score: 63
Period size: 12 Copynumber: 5.8 Consensus size: 12
1396176 GATACATTAC
1396186 CTGAATTCTGTT
1 CTGAATTCTGTT
* *
1396198 CTGATTTCTGAT
1 CTGAATTCTGTT
*
1396210 CTGGATTCTGTT
1 CTGAATTCTGTT
1396222 CT-AATATCT-TAT
1 CTGAAT-TCTGT-T
1396234 CTGAATTCTGTT
1 CTGAATTCTGTT
* *
1396246 TTGATTTCTG
1 CTGAATTCTG
1396256 ATATCTCCGT
Statistics
Matches: 46, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
11 3 0.07
12 39 0.85
13 4 0.09
ACGTcount: A:0.17, C:0.16, G:0.16, T:0.51
Consensus pattern (12 bp):
CTGAATTCTGTT
Found at i:1396238 original size:48 final size:48
Alignment explanation
Indices: 1396166--1396257 Score: 141
Period size: 48 Copynumber: 1.9 Consensus size: 48
1396156 TCCGACTTAA
*
1396166 ATTCTGTTCTGATACATTACCTGAATTCTGTTCTGATTTCTGATCTGG
1 ATTCTGTTCTAATACATTACCTGAATTCTGTTCTGATTTCTGATCTGG
* *
1396214 ATTCTGTTCTAATATC-TTATCTGAATTCTGTTTTGATTTCTGAT
1 ATTCTGTTCTAATA-CATTACCTGAATTCTGTTCTGATTTCTGAT
1396258 ATCTCCGTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
48 39 0.98
49 1 0.03
ACGTcount: A:0.20, C:0.16, G:0.14, T:0.50
Consensus pattern (48 bp):
ATTCTGTTCTAATACATTACCTGAATTCTGTTCTGATTTCTGATCTGG
Found at i:1398353 original size:6 final size:6
Alignment explanation
Indices: 1398342--1398382 Score: 75
Period size: 6 Copynumber: 7.0 Consensus size: 6
1398332 AAAAGATAGT
1398342 ACGACC ACGACC ACGACC ACGACC ACGACC ACGACC -CGACC
1 ACGACC ACGACC ACGACC ACGACC ACGACC ACGACC ACGACC
1398383 TGAGACGGAC
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.14
6 30 0.86
ACGTcount: A:0.32, C:0.51, G:0.17, T:0.00
Consensus pattern (6 bp):
ACGACC
Found at i:1398886 original size:6 final size:6
Alignment explanation
Indices: 1398870--1398937 Score: 129
Period size: 6 Copynumber: 11.5 Consensus size: 6
1398860 GTCTGTCTCG
1398870 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1398917 GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGT
1398938 AATACGTGTC
Statistics
Matches: 62, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 5 0.08
6 57 0.92
ACGTcount: A:0.00, C:0.16, G:0.51, T:0.32
Consensus pattern (6 bp):
GGTCGT
Found at i:1399076 original size:41 final size:41
Alignment explanation
Indices: 1399031--1399119 Score: 151
Period size: 41 Copynumber: 2.2 Consensus size: 41
1399021 CAACGAATTT
* *
1399031 TCGCAACGAATTTGGAAAATCGTAACGACAACTGTAGACTA
1 TCGCAACGAATTTCGAAAATCGCAACGACAACTGTAGACTA
*
1399072 TCGCAACGAATTTCGAAAATCGCAACGATAACTGTAGACTA
1 TCGCAACGAATTTCGAAAATCGCAACGACAACTGTAGACTA
1399113 TCGCAAC
1 TCGCAAC
1399120 ACGAACTGAA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 45 1.00
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.21
Consensus pattern (41 bp):
TCGCAACGAATTTCGAAAATCGCAACGACAACTGTAGACTA
Found at i:1399079 original size:22 final size:22
Alignment explanation
Indices: 1399049--1399127 Score: 67
Period size: 22 Copynumber: 3.7 Consensus size: 22
1399039 AATTTGGAAA
*
1399049 ATCGTAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
* * **
1399071 ATCGCAACG--AA-TTTCGAAA
1 ATCGCAACGACAACTGTAGACT
*
1399090 ATCGCAACGATAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
1399112 ATCGCAAC-ACGAACTG
1 ATCGCAACGAC-AACTG
1399128 AAAAATCGCA
Statistics
Matches: 43, Mismatches: 10, Indels: 8
0.70 0.16 0.13
Matches are distributed among these distances:
19 13 0.30
20 2 0.05
21 3 0.07
22 25 0.58
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.20
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Found at i:1399131 original size:41 final size:42
Alignment explanation
Indices: 1399045--1399181 Score: 131
Period size: 41 Copynumber: 3.3 Consensus size: 42
1399035 AACGAATTTG
* * * *
1399045 GAAAATCGTAACGACAACTGTAGACTATCGC-A-ACGAATTTC
1 GAAAATCGCAACGATAACTGTAGACTATCGCAACACGAA-ATA
*
1399086 GAAAATCGCAACGATAACTGTAGACTATCGCAACACGAACT-
1 GAAAATCGCAACGATAACTGTAGACTATCGCAACACGAAATA
* * * *
1399127 GAAAAATCGCAACG-TGATTTTCA-ACTATCGCAACGCGAAATA
1 G-AAAATCGCAACGATAACTGT-AGACTATCGCAACACGAAATA
1399169 GAAAATCGCAACG
1 GAAAATCGCAACG
1399182 CGAACTGAAA
Statistics
Matches: 83, Mismatches: 8, Indels: 10
0.82 0.08 0.10
Matches are distributed among these distances:
41 62 0.75
42 16 0.19
43 5 0.06
ACGTcount: A:0.41, C:0.23, G:0.18, T:0.19
Consensus pattern (42 bp):
GAAAATCGCAACGATAACTGTAGACTATCGCAACACGAAATA
Found at i:1399137 original size:20 final size:20
Alignment explanation
Indices: 1399112--1399212 Score: 87
Period size: 20 Copynumber: 5.0 Consensus size: 20
1399102 ACTGTAGACT
*
1399112 ATCGCAACACGAACTGAAAA
1 ATCGCAACGCGAACTGAAAA
* ** * **
1399132 ATCGCAACGTGATTTTCAACT
1 ATCGCAACGCGA-ACTGAAAA
*
1399153 ATCGCAACGCGAAAT-AGAAA
1 ATCGCAACGCGAACTGA-AAA
1399173 ATCGCAACGCGAACTGAAAA
1 ATCGCAACGCGAACTGAAAA
* *
1399193 ATCGCAACGCAAAATGAAAA
1 ATCGCAACGCGAACTGAAAA
1399213 GATAAGGAAA
Statistics
Matches: 63, Mismatches: 15, Indels: 6
0.75 0.18 0.07
Matches are distributed among these distances:
19 1 0.02
20 47 0.75
21 15 0.24
ACGTcount: A:0.46, C:0.23, G:0.17, T:0.15
Consensus pattern (20 bp):
ATCGCAACGCGAACTGAAAA
Found at i:1399140 original size:61 final size:59
Alignment explanation
Indices: 1399071--1399201 Score: 138
Period size: 61 Copynumber: 2.2 Consensus size: 59
1399061 ACTGTAGACT
* * **
1399071 ATCGCAACGAATTTCGAA-AATCGCAACGATAACTGTAGACTATCGCAACACGAACTGAAAA
1 ATCGCAACGAATTTC-AACAATCGCAACGAGAA--ATAGAAAATCGCAACACGAACTGAAAA
* * * *
1399132 ATCGCAACGTGATTTTCAACTATCGCAACGCGAAATAGAAAATCGCAACGCGAACTGAAAA
1 ATCGCAAC--GAATTTCAACAATCGCAACGAGAAATAGAAAATCGCAACACGAACTGAAAA
1399193 ATCGCAACG
1 ATCGCAACG
1399202 CAAAATGAAA
Statistics
Matches: 59, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
59 1 0.02
61 39 0.66
62 2 0.03
63 17 0.29
ACGTcount: A:0.41, C:0.24, G:0.18, T:0.18
Consensus pattern (59 bp):
ATCGCAACGAATTTCAACAATCGCAACGAGAAATAGAAAATCGCAACACGAACTGAAAA
Found at i:1401657 original size:2 final size:2
Alignment explanation
Indices: 1401650--1401677 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1401640 ACGAACTTTA
1401650 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
1401678 GCGCTTTGAA
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:1404114 original size:23 final size:23
Alignment explanation
Indices: 1404087--1404144 Score: 116
Period size: 23 Copynumber: 2.5 Consensus size: 23
1404077 TGCCGATGAC
1404087 ATGCATAATTAAGTGTACTTATT
1 ATGCATAATTAAGTGTACTTATT
1404110 ATGCATAATTAAGTGTACTTATT
1 ATGCATAATTAAGTGTACTTATT
1404133 ATGCATAATTAA
1 ATGCATAATTAA
1404145 CCTGTAACCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.38, C:0.09, G:0.12, T:0.41
Consensus pattern (23 bp):
ATGCATAATTAAGTGTACTTATT
Found at i:1407380 original size:24 final size:24
Alignment explanation
Indices: 1407320--1407382 Score: 63
Period size: 26 Copynumber: 2.5 Consensus size: 24
1407310 ATAACATTTT
* * *
1407320 TTCATTTTCTTATAGTTTTATAAA
1 TTCATTTTCTTAAAATTTTAAAAA
* *
1407344 TTTATCCTCTCTTAAAATTTTAAAAA
1 TTCAT--TTTCTTAAAATTTTAAAAA
1407370 TTCATTTTCTTAA
1 TTCATTTTCTTAA
1407383 CATAAAATTT
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
24 11 0.37
26 19 0.63
ACGTcount: A:0.32, C:0.13, G:0.02, T:0.54
Consensus pattern (24 bp):
TTCATTTTCTTAAAATTTTAAAAA
Found at i:1410771 original size:24 final size:24
Alignment explanation
Indices: 1410743--1410847 Score: 86
Period size: 24 Copynumber: 4.4 Consensus size: 24
1410733 GAATATTTTA
*
1410743 TCTGATTTCCGATTTGAATTCTGT
1 TCTGATTTCCGATCTGAATTCTGT
* * * *
1410767 TCTGA-TACCTGACCTGGATTATGT
1 TCTGATTTCC-GATCTGAATTCTGT
** *
1410791 TCTGATTTCTTATCTGGATTCTGT
1 TCTGATTTCCGATCTGAATTCTGT
* **
1410815 TCTGATATCTTATCTGAATTCTGT
1 TCTGATTTCCGATCTGAATTCTGT
*
1410839 TTTGATTTC
1 TCTGATTTC
1410848 TAATATCTCC
Statistics
Matches: 65, Mismatches: 14, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
23 3 0.05
24 60 0.92
25 2 0.03
ACGTcount: A:0.17, C:0.17, G:0.16, T:0.50
Consensus pattern (24 bp):
TCTGATTTCCGATCTGAATTCTGT
Found at i:1418263 original size:21 final size:21
Alignment explanation
Indices: 1418237--1418283 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
1418227 AGCCAATTGG
1418237 TACCCATTCAATGAGAATCGA
1 TACCCATTCAATGAGAATCGA
*
1418258 TACCCATTCAATGGGAATCGA
1 TACCCATTCAATGAGAATCGA
1418279 TACCC
1 TACCC
1418284 CCTCAACCGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.34, C:0.28, G:0.15, T:0.23
Consensus pattern (21 bp):
TACCCATTCAATGAGAATCGA
Found at i:1418289 original size:21 final size:21
Alignment explanation
Indices: 1418237--1418289 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
1418227 AGCCAATTGG
*
1418237 TACCCATTCAATGAGAATCGA
1 TACCCACTCAATGAGAATCGA
* *
1418258 TACCCATTCAATGGGAATCGA
1 TACCCACTCAATGAGAATCGA
*
1418279 TACCCCCTCAA
1 TACCCACTCAA
1418290 CCGAACCAGA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.34, C:0.30, G:0.13, T:0.23
Consensus pattern (21 bp):
TACCCACTCAATGAGAATCGA
Found at i:1419916 original size:23 final size:23
Alignment explanation
Indices: 1419890--1419953 Score: 101
Period size: 23 Copynumber: 2.8 Consensus size: 23
1419880 AATTATTATA
*
1419890 TGGCACTACGGTGTAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
1419913 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
* *
1419936 TGGCACTTCGGTACAATT
1 TGGCACTACGGTGCAATT
1419954 TATATAAGCT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.22, C:0.23, G:0.25, T:0.30
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTACG
Found at i:1423339 original size:21 final size:21
Alignment explanation
Indices: 1423278--1423333 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
1423268 TCTGGGCTAG
1423278 GGGAATCGGTACCCATTCAAT
1 GGGAATCGGTACCCATTCAAT
1423299 GGGAATCGGTACCCATTCAAT
1 GGGAATCGGTACCCATTCAAT
*
1423320 GGGAATCGATACCC
1 GGGAATCGGTACCC
1423334 CCTCAACCGA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.29, C:0.25, G:0.25, T:0.21
Consensus pattern (21 bp):
GGGAATCGGTACCCATTCAAT
Found at i:1423394 original size:22 final size:22
Alignment explanation
Indices: 1423368--1423427 Score: 120
Period size: 22 Copynumber: 2.7 Consensus size: 22
1423358 AATGTCATAG
1423368 GGGAACCGATTCCCCCACAGTA
1 GGGAACCGATTCCCCCACAGTA
1423390 GGGAACCGATTCCCCCACAGTA
1 GGGAACCGATTCCCCCACAGTA
1423412 GGGAACCGATTCCCCC
1 GGGAACCGATTCCCCC
1423428 TCTAAAGGAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.25, C:0.38, G:0.23, T:0.13
Consensus pattern (22 bp):
GGGAACCGATTCCCCCACAGTA
Found at i:1424991 original size:23 final size:23
Alignment explanation
Indices: 1424961--1425024 Score: 101
Period size: 23 Copynumber: 2.8 Consensus size: 23
1424951 CATTATTATA
*
1424961 TGGCACTACTGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
*
1424984 TGGCACTACGGTGTAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
*
1425007 TGGCACTTCGGTGCAATT
1 TGGCACTACGGTGCAATT
1425025 TATATGAGTT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.20, C:0.23, G:0.25, T:0.31
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTACG
Found at i:1434234 original size:31 final size:32
Alignment explanation
Indices: 1434199--1434269 Score: 90
Period size: 32 Copynumber: 2.2 Consensus size: 32
1434189 TAAAAGTCAA
* * *
1434199 TTTATAGTAATTTGAT-GAATTTAATGATTAT
1 TTTATAATAATTTGATAAAATTTAATGACTAT
* *
1434230 TTTATAATGATTTGATAAAATTTAATGACTGT
1 TTTATAATAATTTGATAAAATTTAATGACTAT
1434262 TTTATAAT
1 TTTATAAT
1434270 TGTTTATAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
31 14 0.41
32 20 0.59
ACGTcount: A:0.37, C:0.01, G:0.11, T:0.51
Consensus pattern (32 bp):
TTTATAATAATTTGATAAAATTTAATGACTAT
Found at i:1434257 original size:32 final size:32
Alignment explanation
Indices: 1434199--1434296 Score: 94
Period size: 31 Copynumber: 3.1 Consensus size: 32
1434189 TAAAAGTCAA
* * *
1434199 TTTATAGTAATTTGAT-GAATTTAATGATTAT
1 TTTATAATGATTTGATAAAATTTAATGATTAT
* *
1434230 TTTATAATGATTTGATAAAATTTAATGACTGT
1 TTTATAATGATTTGATAAAATTTAATGATTAT
* * *
1434262 TTTATAATTG-TTT-ATAAATTTTGATGGTTAT
1 TTTATAA-TGATTTGATAAAATTTAATGATTAT
1434293 TTTA
1 TTTA
1434297 CATTTTTAAA
Statistics
Matches: 55, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
31 31 0.56
32 22 0.40
33 2 0.04
ACGTcount: A:0.34, C:0.01, G:0.12, T:0.53
Consensus pattern (32 bp):
TTTATAATGATTTGATAAAATTTAATGATTAT
Found at i:1434860 original size:11 final size:11
Alignment explanation
Indices: 1434844--1434905 Score: 70
Period size: 11 Copynumber: 5.5 Consensus size: 11
1434834 GAGACTCGAA
1434844 CTCGATTCAAG
1 CTCGATTCAAG
*
1434855 CTCGATTTTAAG
1 CTCGA-TTCAAG
*
1434867 CTTGATTCAAG
1 CTCGATTCAAG
* *
1434878 TTCGATTTTAAG
1 CTCGA-TTCAAG
1434890 CTCGATTCAAG
1 CTCGATTCAAG
1434901 CTCGA
1 CTCGA
1434906 ATCTTAGCCA
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
11 23 0.56
12 18 0.44
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.35
Consensus pattern (11 bp):
CTCGATTCAAG
Found at i:1434877 original size:23 final size:23
Alignment explanation
Indices: 1434844--1434905 Score: 106
Period size: 23 Copynumber: 2.7 Consensus size: 23
1434834 GAGACTCGAA
1434844 CTCGATTCAAGCTCGATTTTAAG
1 CTCGATTCAAGCTCGATTTTAAG
* *
1434867 CTTGATTCAAGTTCGATTTTAAG
1 CTCGATTCAAGCTCGATTTTAAG
1434890 CTCGATTCAAGCTCGA
1 CTCGATTCAAGCTCGA
1434906 ATCTTAGCCA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.35
Consensus pattern (23 bp):
CTCGATTCAAGCTCGATTTTAAG
Found at i:1436254 original size:7 final size:7
Alignment explanation
Indices: 1436242--1436323 Score: 60
Period size: 7 Copynumber: 11.7 Consensus size: 7
1436232 AATCGGATTA
1436242 AGGGTTT
1 AGGGTTT
1436249 AGGGTTT
1 AGGGTTT
1436256 AGGGTTT
1 AGGGTTT
*
1436263 ATAGG-TT
1 A-GGGTTT
1436270 AGGGTTT
1 AGGGTTT
1436277 -GGGATTT
1 AGGG-TTT
**
1436284 AAAGTTT
1 AGGGTTT
* *
1436291 ATGGTTC
1 AGGGTTT
**
1436298 ATAGTTT
1 AGGGTTT
1436305 AGGGTTT
1 AGGGTTT
*
1436312 AGGATTT
1 AGGGTTT
1436319 AGGGT
1 AGGGT
1436324 GTAATCTAAC
Statistics
Matches: 58, Mismatches: 13, Indels: 8
0.73 0.16 0.10
Matches are distributed among these distances:
6 5 0.09
7 50 0.86
8 3 0.05
ACGTcount: A:0.21, C:0.01, G:0.35, T:0.43
Consensus pattern (7 bp):
AGGGTTT
Found at i:1436307 original size:35 final size:35
Alignment explanation
Indices: 1436252--1436319 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
1436242 AGGGTTTAGG
* *
1436252 GTTTAGGGTTTATAGGTTAGGGTTTGGGATTTAAA
1 GTTTAGGGTTCATAGGTTAGGGTTTAGGATTTAAA
* *
1436287 GTTTATGGTTCATAGTTTAGGGTTTAGGATTTA
1 GTTTAGGGTTCATAGGTTAGGGTTTAGGATTTA
1436320 GGGTGTAATC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.22, C:0.01, G:0.31, T:0.46
Consensus pattern (35 bp):
GTTTAGGGTTCATAGGTTAGGGTTTAGGATTTAAA
Found at i:1436422 original size:7 final size:7
Alignment explanation
Indices: 1436394--1436456 Score: 65
Period size: 7 Copynumber: 9.1 Consensus size: 7
1436384 AATTAGATTA
1436394 AGGGTTT
1 AGGGTTT
*
1436401 AGGGCTT
1 AGGGTTT
*
1436408 AGGATTT
1 AGGGTTT
*
1436415 ATGGTTT
1 AGGGTTT
1436422 AGGGTTT
1 AGGGTTT
**
1436429 -GGAATT
1 AGGGTTT
*
1436435 AAGGTTT
1 AGGGTTT
1436442 AGGGTTT
1 AGGGTTT
1436449 AGGGTTT
1 AGGGTTT
1436456 A
1 A
1436457 ATCTAACATG
Statistics
Matches: 43, Mismatches: 12, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
6 4 0.09
7 39 0.91
ACGTcount: A:0.21, C:0.02, G:0.37, T:0.41
Consensus pattern (7 bp):
AGGGTTT
Found at i:1436442 original size:20 final size:20
Alignment explanation
Indices: 1436390--1436448 Score: 73
Period size: 20 Copynumber: 2.9 Consensus size: 20
1436380 ATATAATTAG
*
1436390 ATTAAGGGTTTAGGGCTTAGGA
1 ATTAA-GGTTTAGGG-TTTGGA
* *
1436412 TTTATGGTTTAGGGTTTGGA
1 ATTAAGGTTTAGGGTTTGGA
1436432 ATTAAGGTTTAGGGTTT
1 ATTAAGGTTTAGGGTTT
1436449 AGGGTTTAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
20 20 0.62
21 9 0.28
22 3 0.09
ACGTcount: A:0.22, C:0.02, G:0.34, T:0.42
Consensus pattern (20 bp):
ATTAAGGTTTAGGGTTTGGA
Found at i:1436590 original size:19 final size:18
Alignment explanation
Indices: 1436566--1436609 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
1436556 TGAGGGTAGT
1436566 TATATTATAGAATATTTTA
1 TATATTATAGAA-ATTTTA
* *
1436585 TATATTTTTGAAATTTTA
1 TATATTATAGAAATTTTA
1436603 TA-ATTAT
1 TATATTAT
1436610 CAATAATGTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 4 0.18
18 8 0.36
19 10 0.45
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.57
Consensus pattern (18 bp):
TATATTATAGAAATTTTA
Found at i:1437544 original size:23 final size:23
Alignment explanation
Indices: 1437518--1437608 Score: 83
Period size: 23 Copynumber: 3.9 Consensus size: 23
1437508 CTAATAGCGT
*
1437518 AAACATATTCGTTTAATGTTCGC
1 AAACATGTTCGTTTAATGTTCGC
**
1437541 AAACATGTTCGTTTATATGTTCAT
1 AAACATGTTCGTTTA-ATGTTCGC
** ** *
1437565 AAATGTGTTTATTTAGTGTTCGC
1 AAACATGTTCGTTTAATGTTCGC
* *
1437588 AAACATTTTCGTTTAACGTTC
1 AAACATGTTCGTTTAATGTTC
1437609 ATTTAATATT
Statistics
Matches: 50, Mismatches: 17, Indels: 2
0.72 0.25 0.03
Matches are distributed among these distances:
23 33 0.66
24 17 0.34
ACGTcount: A:0.27, C:0.14, G:0.14, T:0.44
Consensus pattern (23 bp):
AAACATGTTCGTTTAATGTTCGC
Found at i:1437686 original size:30 final size:30
Alignment explanation
Indices: 1437650--1437720 Score: 124
Period size: 30 Copynumber: 2.4 Consensus size: 30
1437640 TATTTGCAAG
1437650 TTAAAAATTTATTCGTTTACAAATACCATA
1 TTAAAAATTTATTCGTTTACAAATACCATA
* *
1437680 TTAAAAATTTATTCGTTTATAAATATCATA
1 TTAAAAATTTATTCGTTTACAAATACCATA
1437710 TTAAAAATTTA
1 TTAAAAATTTA
1437721 AACGAACACA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.45, C:0.08, G:0.03, T:0.44
Consensus pattern (30 bp):
TTAAAAATTTATTCGTTTACAAATACCATA
Found at i:1437824 original size:13 final size:13
Alignment explanation
Indices: 1437806--1437833 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1437796 ACTCATTTAC
1437806 CCTATGATAATAA
1 CCTATGATAATAA
1437819 CCTATGATAATAA
1 CCTATGATAATAA
1437832 CC
1 CC
1437834 AAAGTGAGAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.43, C:0.21, G:0.07, T:0.29
Consensus pattern (13 bp):
CCTATGATAATAA
Found at i:1438933 original size:6 final size:6
Alignment explanation
Indices: 1438922--1438951 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
1438912 TTAGCCGTCC
1438922 GATCAG GATCAG GATCAG GATCAG GATCAG
1 GATCAG GATCAG GATCAG GATCAG GATCAG
1438952 TAAAAAATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.33, C:0.17, G:0.33, T:0.17
Consensus pattern (6 bp):
GATCAG
Found at i:1441424 original size:2 final size:2
Alignment explanation
Indices: 1441417--1441442 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1441407 TTCATGTATC
1441417 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
1441443 TATTGTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1443188 original size:60 final size:60
Alignment explanation
Indices: 1443067--1443223 Score: 154
Period size: 60 Copynumber: 2.6 Consensus size: 60
1443057 ACTTTTATTT
* * * ** * **
1443067 TAAATTAGTCTTTAAACTTTAGAATATTCTAATTTTATTCCTAGATTATGATTCTCATTC
1 TAAATTAGTCCTTAAACTTTTGAATATTCTAATTTCAACCCTAAATTATGACCCTCATTC
* * * *
1443127 TAAATCAGTCCTTAAACTTTTGAAAATTCTGATTTCAACCCTAAATTATGACCCTCTTTC
1 TAAATTAGTCCTTAAACTTTTGAATATTCTAATTTCAACCCTAAATTATGACCCTCATTC
* ** *
1443187 TATATTAGTCC-CCAACTTTTGAATATTCCCAATTTCA
1 TAAATTAGTCCTTAAACTTTTGAATATT-CTAATTTCA
1443224 TCCACATTAT
Statistics
Matches: 77, Mismatches: 19, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
59 13 0.17
60 64 0.83
ACGTcount: A:0.31, C:0.20, G:0.06, T:0.43
Consensus pattern (60 bp):
TAAATTAGTCCTTAAACTTTTGAATATTCTAATTTCAACCCTAAATTATGACCCTCATTC
Done.