Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 132263754
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: 132263754
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 372 characters in sequence are not A, C, G, or T
File 22 of 433
Found at i:5898216 original size:23 final size:23
Alignment explanation
Indices: 5898190--5898234 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
5898180 CTAAAAACAA
5898190 GTTATAGTGAATTTATATTTGCC
1 GTTATAGTGAATTTATATTTGCC
5898213 GTTATAGTGAATTTATATTTGC
1 GTTATAGTGAATTTATATTTGC
5898235 TCGTAGTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.27, C:0.07, G:0.18, T:0.49
Consensus pattern (23 bp):
GTTATAGTGAATTTATATTTGCC
Found at i:5899893 original size:21 final size:22
Alignment explanation
Indices: 5899855--5899899 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
5899845 TACAGTTTTC
* *
5899855 AATGATAAAATTATCTTAACAT
1 AATGATAAAATGATCTTAAAAT
5899877 AATGATAAAA-GATCTTAAAAT
1 AATGATAAAATGATCTTAAAAT
5899898 AA
1 AA
5899900 ATTCAATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.56, C:0.07, G:0.07, T:0.31
Consensus pattern (22 bp):
AATGATAAAATGATCTTAAAAT
Found at i:5899943 original size:20 final size:20
Alignment explanation
Indices: 5899898--5899935 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
5899888 ATCTTAAAAT
5899898 AAATTCAATTTTGTACTTCA
1 AAATTCAATTTTGTACTTCA
5899918 AAATTCAATTTTGTACTT
1 AAATTCAATTTTGTACTT
5899936 GGAAATTCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.34, C:0.13, G:0.05, T:0.47
Consensus pattern (20 bp):
AAATTCAATTTTGTACTTCA
Found at i:5901675 original size:2 final size:2
Alignment explanation
Indices: 5901670--5901695 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5901660 ATATTCTTTT
5901670 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
5901696 AATTATAATT
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):
TA
Found at i:5911691 original size:6 final size:6
Alignment explanation
Indices: 5911680--5911714 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
5911670 CATAGCTCTA
5911680 ACAACT ACAACT ACAACT A-ACACT ACAACT ACAAC
1 ACAACT ACAACT ACAACT ACA-ACT ACAACT ACAAC
5911715 AACCATCAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
5 1 0.04
6 25 0.93
7 1 0.04
ACGTcount: A:0.51, C:0.34, G:0.00, T:0.14
Consensus pattern (6 bp):
ACAACT
Found at i:5911706 original size:18 final size:19
Alignment explanation
Indices: 5911677--5911714 Score: 69
Period size: 18 Copynumber: 2.1 Consensus size: 19
5911667 TGACATAGCT
5911677 CTAACAACTACAACTACAA
1 CTAACAACTACAACTACAA
5911696 CTAAC-ACTACAACTACAA
1 CTAACAACTACAACTACAA
5911714 C
1 C
5911715 AACCATCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.50, C:0.34, G:0.00, T:0.16
Consensus pattern (19 bp):
CTAACAACTACAACTACAA
Found at i:5912161 original size:27 final size:28
Alignment explanation
Indices: 5912131--5912184 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 28
5912121 GAGAGGCAGA
5912131 GGCTAATG-GACAGAGAG-GAAGGAGAAT
1 GGCTAATGTGA-AGAGAGTGAAGGAGAAT
**
5912158 GGCTGCTGTGAAGAGAGTGAAGGAGAA
1 GGCTAATGTGAAGAGAGTGAAGGAGAA
5912185 CGATAATTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 12 0.52
28 11 0.48
ACGTcount: A:0.37, C:0.07, G:0.43, T:0.13
Consensus pattern (28 bp):
GGCTAATGTGAAGAGAGTGAAGGAGAAT
Found at i:5921769 original size:25 final size:25
Alignment explanation
Indices: 5921738--5921786 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
5921728 CAAGCAAGCC
5921738 ATATCAGGAAGCTCACAAAGAGCTT
1 ATATCAGGAAGCTCACAAAGAGCTT
* * *
5921763 ATATCAGGATGTTCATAAAGAGCT
1 ATATCAGGAAGCTCACAAAGAGCT
5921787 GCAGCATGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.39, C:0.16, G:0.20, T:0.24
Consensus pattern (25 bp):
ATATCAGGAAGCTCACAAAGAGCTT
Found at i:5929161 original size:20 final size:20
Alignment explanation
Indices: 5929135--5929184 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
5929125 AGCAATGAAT
5929135 CTGTTCACCAAGAGATACAA
1 CTGTTCACCAAGAGATACAA
*
5929155 TTGTTCA--AA-AGATACAA
1 CTGTTCACCAAGAGATACAA
5929172 CTGTTCACCAAGA
1 CTGTTCACCAAGA
5929185 AACAAAACTA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
17 14 0.56
18 2 0.08
19 2 0.08
20 7 0.28
ACGTcount: A:0.40, C:0.22, G:0.14, T:0.24
Consensus pattern (20 bp):
CTGTTCACCAAGAGATACAA
Found at i:5951041 original size:15 final size:16
Alignment explanation
Indices: 5951021--5951057 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
5951011 CACTCTTTGG
5951021 TCTTTTCCTT-TCCTT
1 TCTTTTCCTTCTCCTT
*
5951036 TCTTTT-CTTCTCTTT
1 TCTTTTCCTTCTCCTT
5951051 TCTTTTC
1 TCTTTTC
5951058 TATTTGCTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
14 3 0.16
15 16 0.84
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (16 bp):
TCTTTTCCTTCTCCTT
Found at i:5951692 original size:15 final size:15
Alignment explanation
Indices: 5951663--5951699 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
5951653 TTCTTCTTCT
**
5951663 TCTTCTTCTTCCTCA
1 TCTTCTTCTAACTCA
5951678 TCTTCTTCTAACTCA
1 TCTTCTTCTAACTCA
5951693 TCTTCTT
1 TCTTCTT
5951700 GTTCCCAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.11, C:0.35, G:0.00, T:0.54
Consensus pattern (15 bp):
TCTTCTTCTAACTCA
Found at i:5951699 original size:3 final size:3
Alignment explanation
Indices: 5951649--5951686 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
5951639 GACTCAACAG
* *
5951649 CTT CTT CTT CTT CTT CTT CTT CTT CCT CAT CTT CTT CT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
5951687 AACTCATCTT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.03, C:0.37, G:0.00, T:0.61
Consensus pattern (3 bp):
CTT
Found at i:5951899 original size:2 final size:2
Alignment explanation
Indices: 5951894--5951918 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5951884 AAAAAAAAAA
5951894 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
5951919 CATAAATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5957875 original size:15 final size:14
Alignment explanation
Indices: 5957854--5957896 Score: 52
Period size: 15 Copynumber: 3.0 Consensus size: 14
5957844 TAACTAAAGC
5957854 ACTATTCTGAACAT
1 ACTATTCTGAACAT
5957868 AGCTATTCTTGAACA-
1 A-CTATTC-TGAACAT
*
5957883 ATTATTCTGAACAT
1 ACTATTCTGAACAT
5957897 GATAGCTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
13 6 0.24
14 6 0.24
15 7 0.28
16 6 0.24
ACGTcount: A:0.35, C:0.19, G:0.09, T:0.37
Consensus pattern (14 bp):
ACTATTCTGAACAT
Found at i:5959963 original size:22 final size:20
Alignment explanation
Indices: 5959913--5959969 Score: 62
Period size: 22 Copynumber: 2.8 Consensus size: 20
5959903 AGCCCACTCA
5959913 TATTATTTTATTTTAATATT
1 TATTATTTTATTTTAATATT
* *
5959933 TAATAATTTTATATTTTATATT
1 T-ATTATTTTAT-TTTAATATT
5959955 TATTGATTTT-TTTTA
1 TATT-ATTTTATTTTA
5959970 TACACTCATC
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
20 4 0.13
21 12 0.40
22 14 0.47
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (20 bp):
TATTATTTTATTTTAATATT
Found at i:5966833 original size:20 final size:19
Alignment explanation
Indices: 5966808--5966871 Score: 65
Period size: 19 Copynumber: 3.3 Consensus size: 19
5966798 TTAGTACGAT
5966808 AATTTTTATATTTTTTTAC
1 AATTTTTATATTTTTTTAC
* * *
5966827 AAATTTTAAATTTCTTTAC
1 AATTTTTATATTTTTTTAC
**
5966846 TTTTTTTATAATTTTTTTAC
1 AATTTTTAT-ATTTTTTTAC
*
5966866 GATTTT
1 AATTTT
5966872 ACAAAATTTT
Statistics
Matches: 34, Mismatches: 10, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
19 21 0.62
20 13 0.38
ACGTcount: A:0.27, C:0.06, G:0.02, T:0.66
Consensus pattern (19 bp):
AATTTTTATATTTTTTTAC
Found at i:5966889 original size:19 final size:19
Alignment explanation
Indices: 5966867--5966941 Score: 53
Period size: 20 Copynumber: 3.8 Consensus size: 19
5966857 TTTTTTTACG
5966867 ATTTTACAAAATTTTATAT
1 ATTTTACAAAATTTTATAT
* * *
5966886 ATTTTTTCTATATTTCTATAT
1 A-TTTTACAAAATTT-TATAT
* **
5966907 ATTTTATAATTTTTTATGAT
1 ATTTTACAAAATTTTAT-AT
*
5966927 -TTTTATAAAATTTTA
1 ATTTTACAAAATTTTA
5966942 CAATTTTTTT
Statistics
Matches: 44, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
19 17 0.39
20 21 0.48
21 6 0.14
ACGTcount: A:0.33, C:0.04, G:0.01, T:0.61
Consensus pattern (19 bp):
ATTTTACAAAATTTTATAT
Found at i:5966892 original size:21 final size:21
Alignment explanation
Indices: 5966868--5966911 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
5966858 TTTTTTACGA
*
5966868 TTTTACAAAATTT-TATATAT
1 TTTTTCAAAATTTCTATATAT
* *
5966888 TTTTTCTATATTTCTATATAT
1 TTTTTCAAAATTTCTATATAT
5966909 TTT
1 TTT
5966912 ATAATTTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.64
Consensus pattern (21 bp):
TTTTTCAAAATTTCTATATAT
Found at i:5966953 original size:30 final size:30
Alignment explanation
Indices: 5966849--5966978 Score: 126
Period size: 30 Copynumber: 4.4 Consensus size: 30
5966839 TCTTTACTTT
* *
5966849 TTTTATAATTTTTTTACGA-TTTTACAAAA
1 TTTTATAATTTTTTTATGATTTTTATAAAA
* *
5966878 TTTTATATATTTTTTCTAT-ATTTCTAT-ATA
1 TTTTATA-ATTTTTT-TATGATTTTTATAAAA
5966908 TTTTATAA-TTTTTTATGATTTTTATAAAA
1 TTTTATAATTTTTTTATGATTTTTATAAAA
* * * **
5966937 TTTTACAATTTTTTTATAATTTTTTTCTAA
1 TTTTATAATTTTTTTATGATTTTTATAAAA
5966967 TTTT-TAATTTTT
1 TTTTATAATTTTT
5966979 AAATATTTTT
Statistics
Matches: 83, Mismatches: 12, Indels: 12
0.78 0.11 0.11
Matches are distributed among these distances:
27 3 0.04
28 12 0.14
29 24 0.29
30 38 0.46
31 6 0.07
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.65
Consensus pattern (30 bp):
TTTTATAATTTTTTTATGATTTTTATAAAA
Found at i:5966975 original size:29 final size:28
Alignment explanation
Indices: 5966907--5967045 Score: 79
Period size: 29 Copynumber: 4.9 Consensus size: 28
5966897 ATTTCTATAT
* **
5966907 ATTTTATAA-TTTTTTATGATTTTTATAAA
1 ATTTT-TAATTTTTTTATAATTTTT-TTTA
*
5966936 ATTTTACAATTTTTTTATAATTTTTTTCTA
1 ATTTT-TAATTTTTTTATAATTTTTTT-TA
** *
5966966 ATTTTTAATTTTTAAATATTTTTTTATTA
1 ATTTTTAATTTTTTTATAATTTTTT-TTA
* * * * *
5966995 A-ATTTAATCATTTTTATAACTTTTATTG
1 ATTTTTAAT-TTTTTTATAATTTTTTTTA
*
5967023 ATTTTT-A-TTTTTTATCATTTTTT
1 ATTTTTAATTTTTTTATAATTTTTT
5967046 GCCACATGTC
Statistics
Matches: 84, Mismatches: 21, Indels: 13
0.71 0.18 0.11
Matches are distributed among these distances:
26 12 0.14
28 10 0.12
29 41 0.49
30 21 0.25
ACGTcount: A:0.29, C:0.04, G:0.01, T:0.66
Consensus pattern (28 bp):
ATTTTTAATTTTTTTATAATTTTTTTTA
Found at i:5967222 original size:90 final size:91
Alignment explanation
Indices: 5967118--5967298 Score: 222
Period size: 92 Copynumber: 2.0 Consensus size: 91
5967108 TTAAGTATCT
* * * * *
5967118 AATTTAGTGCAAAAAAAAAACATGGGTTTAATTAC-TTTTTTTGAAAAAGTTT-TAGTGCCTTTT
1 AATTGAGTGCAAAAAAAAAACATAGGCTTAACTACATTTTTTTGAAAAAGTTTGAAG-GCCTTTT
* *
5967181 TTATGCATTTTAAAAGTTCAAGTACCC
65 TGATGCATTGTAAAAGTTCAAGTACCC
* * * *
5967208 AATTGAGTGTAAAAAAAAACCATAGGCTTAACTACTATTTTTTTTAAAAAGTTTGAAGGTCTTTT
1 AATTGAGTGCAAAAAAAAAACATAGGCTTAACTAC-ATTTTTTTGAAAAAGTTTGAAGGCCTTTT
*
5967273 TGATGCATTGTGAAAGTTCAAGTACC
65 TGATGCATTGTAAAAGTTCAAGTACC
5967299 TAAGTAAATA
Statistics
Matches: 76, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
90 29 0.38
92 45 0.59
93 2 0.03
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.38
Consensus pattern (91 bp):
AATTGAGTGCAAAAAAAAAACATAGGCTTAACTACATTTTTTTGAAAAAGTTTGAAGGCCTTTTT
GATGCATTGTAAAAGTTCAAGTACCC
Found at i:5967314 original size:92 final size:89
Alignment explanation
Indices: 5967128--5967319 Score: 197
Period size: 92 Copynumber: 2.1 Consensus size: 89
5967118 AATTTAGTGC
* * * * * *
5967128 AAAAAAAAAACATGGGTTTAATTACTTTTTTTGAAAAAGTTTTAGTGCCTTTTTTATGCATTTTA
1 AAAAAAAAAACATAGGCTTAACTACTTTTTTTGAAAAAGTTTAAGTGCCTTTTTGATGCATTGTA
* * * *
5967193 AAAGTTCAAGTACCCAATTGAGTGT
66 AAAGTTCAAGTACCCAAGTAAAT-A
* * *
5967218 AAAAAAAAACCATAGGCTTAACTACTATTTTTTTTAAAAAGTTTGAAG-GTCTTTTTGATGCATT
1 AAAAAAAAAACATAGGCTTAACTAC--TTTTTTTGAAAAAGTTT-AAGTGCCTTTTTGATGCATT
* *
5967282 GTGAAAGTTCAAGTACCTAAGTAAATA
63 GTAAAAGTTCAAGTACCCAAGTAAATA
5967309 AAAAAACAAAA
1 AAAAAA-AAAA
5967320 GTAGAGACTT
Statistics
Matches: 82, Mismatches: 16, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
90 21 0.26
91 6 0.07
92 53 0.65
93 2 0.02
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.35
Consensus pattern (89 bp):
AAAAAAAAAACATAGGCTTAACTACTTTTTTTGAAAAAGTTTAAGTGCCTTTTTGATGCATTGTA
AAAGTTCAAGTACCCAAGTAAATA
Found at i:5969363 original size:13 final size:13
Alignment explanation
Indices: 5969331--5969369 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
5969321 GGCTATTCGT
*
5969331 CTCAAATAAAATA
1 CTCAAATAAAAAA
* *
5969344 TTTAAATAAAAAA
1 CTCAAATAAAAAA
5969357 CTCAAATAAAAAA
1 CTCAAATAAAAAA
5969370 TAAAACTAGC
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.67, C:0.10, G:0.00, T:0.23
Consensus pattern (13 bp):
CTCAAATAAAAAA
Found at i:5969902 original size:19 final size:18
Alignment explanation
Indices: 5969880--5969915 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
5969870 CCAACCCCAA
5969880 ATATAGATACAGAATATAG
1 ATATAGATACAG-ATATAG
5969899 ATATAGATACAGATATA
1 ATATAGATACAGATATA
5969916 ACATGTTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.53, C:0.06, G:0.14, T:0.28
Consensus pattern (18 bp):
ATATAGATACAGATATAG
Found at i:5971148 original size:30 final size:30
Alignment explanation
Indices: 5971096--5971152 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
5971086 TCCGAACATT
*
5971096 GGGGCAAAAGTGCAAATATGTAAAAATTTA
1 GGGGCAAAAGTGAAAATATGTAAAAATTTA
*
5971126 GGGGTCAAAA-TGAAAATTTGTAAAAAT
1 GGGG-CAAAAGTGAAAATATGTAAAAAT
5971153 ATGATTTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 19 0.79
31 5 0.21
ACGTcount: A:0.47, C:0.05, G:0.23, T:0.25
Consensus pattern (30 bp):
GGGGCAAAAGTGAAAATATGTAAAAATTTA
Found at i:5971570 original size:31 final size:31
Alignment explanation
Indices: 5971533--5971679 Score: 215
Period size: 31 Copynumber: 4.7 Consensus size: 31
5971523 TGTGTAAAAT
*
5971533 GTGAAAAGTGGTAGCTTTGGCTACCTGATCA
1 GTGAAAAGTGGTAGCTTCGGCTACCTGATCA
5971564 GTGAAAAGTGGTAGCTTCGGCTACCTGATCA
1 GTGAAAAGTGGTAGCTTCGGCTACCTGATCA
* * *
5971595 GTGAAAAGTAGTAGCTTCGGCTTCCTGATTA
1 GTGAAAAGTGGTAGCTTCGGCTACCTGATCA
*
5971626 GTGAAAAGTGGTAGC-TCTAGCTACCTGATCA
1 GTGAAAAGTGGTAGCTTC-GGCTACCTGATCA
* *
5971657 GTGAATAGTGATAGCTTCGGCTA
1 GTGAAAAGTGGTAGCTTCGGCTA
5971680 TCGAATGTGA
Statistics
Matches: 103, Mismatches: 11, Indels: 4
0.87 0.09 0.03
Matches are distributed among these distances:
30 2 0.02
31 99 0.96
32 2 0.02
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.29
Consensus pattern (31 bp):
GTGAAAAGTGGTAGCTTCGGCTACCTGATCA
Found at i:5971723 original size:29 final size:29
Alignment explanation
Indices: 5971657--5971714 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
5971647 TACCTGATCA
* * * *
5971657 GTGAATAGTGATAGCTTCGGCTATCGAAT
1 GTGAAAAGGGATAGCTTCAGCTATCAAAT
5971686 GTGAAAAGGGATAGCTTCAGCTATCAAAT
1 GTGAAAAGGGATAGCTTCAGCTATCAAAT
5971715 TTAGAAAGGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.28
Consensus pattern (29 bp):
GTGAAAAGGGATAGCTTCAGCTATCAAAT
Found at i:5971768 original size:33 final size:33
Alignment explanation
Indices: 5971726--5971911 Score: 201
Period size: 33 Copynumber: 5.6 Consensus size: 33
5971716 TAGAAAGGAA
* * *
5971726 AGGTATACTTTGTGTAAACTATTTGAAAATGTT
1 AGGTATACTTTGTGTATACCATTTGAAAAGGTT
**
5971759 AGGTATACTTTGTGTATACCATTTGAAAAGGAA
1 AGGTATACTTTGTGTATACCATTTGAAAAGGTT
*
5971792 ATGTATACTTTGTGTATACCATTTGAAAAGGTT
1 AGGTATACTTTGTGTATACCATTTGAAAAGGTT
* **
5971825 AGGTATACTTTGTGTATACCATATGAAAAGGGA
1 AGGTATACTTTGTGTATACCATTTGAAAAGGTT
** * * * * **
5971858 ACATATACTTTTTGGATATCATATGAAAAGGAA
1 AGGTATACTTTGTGTATACCATTTGAAAAGGTT
* *
5971891 AGGTATATTTTGTGTGTACCA
1 AGGTATACTTTGTGTATACCA
5971912 CTCGGAAAGA
Statistics
Matches: 128, Mismatches: 25, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 128 1.00
ACGTcount: A:0.34, C:0.09, G:0.20, T:0.37
Consensus pattern (33 bp):
AGGTATACTTTGTGTATACCATTTGAAAAGGTT
Found at i:5971798 original size:66 final size:66
Alignment explanation
Indices: 5971719--5971911 Score: 233
Period size: 66 Copynumber: 2.9 Consensus size: 66
5971709 TCAAATTTAG
* * *
5971719 AAAGGAAAGGTATACTTTGTGTAAACTATTTGAAAATGTTAGGTATACTTTGTGTATACCATTTG
1 AAAGGAAAGGTATACTTTGTGTAAACCATTTGAAAAGGTTAGGTATACTTTGTGTATACCATATG
5971784 A
66 A
* *
5971785 AAAGGAAATGTATACTTTGTGTATACCATTTGAAAAGGTTAGGTATACTTTGTGTATACCATATG
1 AAAGGAAAGGTATACTTTGTGTAAACCATTTGAAAAGGTTAGGTATACTTTGTGTATACCATATG
5971850 A
66 A
* ** * * * * * ** * *
5971851 AAAGGGAACATATACTTTTTGGATATCATATGAAAAGGAAAGGTATATTTTGTGTGTACCA
1 AAAGGAAAGGTATACTTTGTGTAAACCATTTGAAAAGGTTAGGTATACTTTGTGTATACCA
5971912 CTCGGAAAGA
Statistics
Matches: 111, Mismatches: 16, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
66 111 1.00
ACGTcount: A:0.36, C:0.08, G:0.20, T:0.36
Consensus pattern (66 bp):
AAAGGAAAGGTATACTTTGTGTAAACCATTTGAAAAGGTTAGGTATACTTTGTGTATACCATATG
A
Found at i:5971890 original size:99 final size:99
Alignment explanation
Indices: 5971726--5971911 Score: 237
Period size: 99 Copynumber: 1.9 Consensus size: 99
5971716 TAGAAAGGAA
* * * ** ** * *
5971726 AGGTATACTTTGTGTAAACTATTTGAAAATGTTAGGTATACTTTGTGTATACCATTTGAAAAGGA
1 AGGTATACTTTGTGTAAACCATATGAAAAGGGAACATATACTTTGTGGATACCATATGAAAAGGA
*
5971791 AATGTATACTTTGTGTATACCATTTGAAAAGGTT
66 AAGGTATACTTTGTGTATACCATTTGAAAAGGTT
* * *
5971825 AGGTATACTTTGTGTATACCATATGAAAAGGGAACATATACTTTTTGGATATCATATGAAAAGGA
1 AGGTATACTTTGTGTAAACCATATGAAAAGGGAACATATACTTTGTGGATACCATATGAAAAGGA
* *
5971890 AAGGTATATTTTGTGTGTACCA
66 AAGGTATACTTTGTGTATACCA
5971912 CTCGGAAAGA
Statistics
Matches: 72, Mismatches: 15, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
99 72 1.00
ACGTcount: A:0.34, C:0.09, G:0.20, T:0.37
Consensus pattern (99 bp):
AGGTATACTTTGTGTAAACCATATGAAAAGGGAACATATACTTTGTGGATACCATATGAAAAGGA
AAGGTATACTTTGTGTATACCATTTGAAAAGGTT
Found at i:5975958 original size:38 final size:38
Alignment explanation
Indices: 5975916--5976004 Score: 103
Period size: 38 Copynumber: 2.4 Consensus size: 38
5975906 TAACCTAAAC
* *
5975916 CCCAAACCCAACTATCTATTAAAACCCAATACCCAAAA
1 CCCAAACCCAACTACCCATTAAAACCCAATACCCAAAA
*
5975954 CCCAAATCCCTAA--ACCCATTAAAACCCAATACTCAAAA
1 CCCAAA-CCC-AACTACCCATTAAAACCCAATACCCAAAA
*
5975992 CCCCAA-CCAACTA
1 CCCAAACCCAACTA
5976005 AACCCAAATT
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
35 2 0.05
36 2 0.05
37 1 0.02
38 33 0.77
39 3 0.07
40 2 0.05
ACGTcount: A:0.46, C:0.39, G:0.00, T:0.15
Consensus pattern (38 bp):
CCCAAACCCAACTACCCATTAAAACCCAATACCCAAAA
Found at i:5977109 original size:3 final size:3
Alignment explanation
Indices: 5977101--5977298 Score: 134
Period size: 3 Copynumber: 67.0 Consensus size: 3
5977091 TTTTTTACTT
5977101 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA GTGTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -T-TA
* * * *
5977148 -TA TTT TTA TTG TATA TGTA -TA TGTA -TA TATA TT- TATA CATA GTA
1 TTA TTA TTA TTA T-TA T-TA TTA T-TA TTA T-TA TTA T-TA -TTA TTA
* * *
5977192 TTA TT- TT- TTAA TTA CT- TTA TT- TTA ATA TTT TTA TTA -TA TTA
1 TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
**
5977233 -TA TT- TGC TT- TT- TGTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA
5977275 TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA
5977299 GTGTATATCT
Statistics
Matches: 159, Mismatches: 16, Indels: 40
0.74 0.07 0.19
Matches are distributed among these distances:
2 22 0.14
3 120 0.75
4 15 0.09
5 2 0.01
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:5977482 original size:77 final size:76
Alignment explanation
Indices: 5977401--5977625 Score: 190
Period size: 77 Copynumber: 3.0 Consensus size: 76
5977391 TGTGCCTTTT
5977401 GTATTTCAATATTATTATTATTATTAATATTAGTGTATA-TTTTATTATATATGTTTATGTATAT
1 GTATTTCAATATTATTATTATTATTAATATTAGTGTATATTTTTATTATATATG-TTATGTATAT
5977465 ATATTTATACATA
65 ATATTTATA-ATA
* * *
5977478 GTA-TT--AT-TT-TT-TTAATTACTT--TATT--TTTATATTTTTATTATATTATATT-TGCTT
1 GTATTTCAATATTATTATT-ATTA-TTAATATTAGTGTATATTTTTATTATA-TATGTTATG-TA
*
5977532 TTTATATTT-TAATA
62 TATATATTTATAATA
* * * * * *
5977546 CTATTACTATTAGTATTATTATTATTAATATTAGTGTATATTTTTATTAAATATG-TATATATAT
1 GTATTTC-AATATTATTATTATTATTAATATTAGTGTATATTTTTATTATATATGTTATGTATAT
5977610 ATATTTATATATA
65 ATATTTATA-ATA
5977623 GTA
1 GTA
5977626 CTATTTTTAA
Statistics
Matches: 114, Mismatches: 15, Indels: 38
0.68 0.09 0.23
Matches are distributed among these distances:
68 5 0.04
69 10 0.09
70 21 0.18
71 9 0.08
72 7 0.06
73 7 0.06
74 8 0.07
75 16 0.14
76 8 0.07
77 23 0.20
ACGTcount: A:0.33, C:0.03, G:0.05, T:0.59
Consensus pattern (76 bp):
GTATTTCAATATTATTATTATTATTAATATTAGTGTATATTTTTATTATATATGTTATGTATATA
TATTTATAATA
Found at i:5977510 original size:134 final size:138
Alignment explanation
Indices: 5977276--5977677 Score: 532
Period size: 134 Copynumber: 2.9 Consensus size: 138
5977266 TTATTATTAT
* *
5977276 TATTATTATTATTATTATTATTAGTGTATATCTTTATTGTATATGTATATGTATATATATTTATA
1 TATTATTATTATTATTAATATTAGTGTATAT-TTTATTATATATGT-TATGTATATATATTTATA
* * * *
5977341 CATAGTATTATTTTTTAATTATTTTATTTTAATATTTTTATTATATTATATGTGCCTTTTGTA-T
64 CATAGTATTATTTTTTAATTACTTTATTTTAATATTTTTATTATATTATATTTGCTTTTTATATT
5977405 T-T-C-A-A-
129 TATACTATAC
5977410 TATTATTATTATTATTAATATTAGTGTATATTTTATTATATATGTTTATGTATATATATTTATAC
1 TATTATTATTATTATTAATATTAGTGTATATTTTATTATATATG-TTATGTATATATATTTATAC
*
5977475 ATAGTATTATTTTTTTAATTACTTTATTTTTATATTTTTATTATATTATATTTGCTTTTTATATT
65 ATAGTATTA-TTTTTTAATTACTTTATTTTAATATTTTTATTATATTATATTTGCTTTTTATA-T
5977540 TTAATACTATTAC
128 TT-ATACTA-TAC
* *
5977553 TATTAGTATTATTATTATTAATATTAGTGTATATTTTTATTAAATATG-TATATATATATATTTA
1 TA-T--TATTATTATTATTAATATTAGTGTATA-TTTTATTATATATGTTATGTATATATATTTA
* * * *
5977617 TATATAGTACTA-TTTTTAATTACTTTATTTTAACATTATTATTATATTATATTTGCTTTTT
62 TACATAGTATTATTTTTTAATTACTTTATTTTAATATTTTTATTATATTATATTTGCTTTTT
5977678 TTTTGTGTAT
Statistics
Matches: 239, Mismatches: 14, Indels: 21
0.87 0.05 0.08
Matches are distributed among these distances:
133 40 0.17
134 79 0.33
136 2 0.01
138 1 0.00
139 1 0.00
140 1 0.00
142 1 0.00
143 48 0.20
144 1 0.00
145 25 0.10
146 27 0.11
147 13 0.05
ACGTcount: A:0.31, C:0.03, G:0.05, T:0.60
Consensus pattern (138 bp):
TATTATTATTATTATTAATATTAGTGTATATTTTATTATATATGTTATGTATATATATTTATACA
TAGTATTATTTTTTAATTACTTTATTTTAATATTTTTATTATATTATATTTGCTTTTTATATTTA
TACTATAC
Found at i:5977709 original size:143 final size:144
Alignment explanation
Indices: 5977112--5977713 Score: 714
Period size: 156 Copynumber: 4.2 Consensus size: 144
5977102 TATTATTATT
* *
5977112 ATTATTATTATTATTATTATTATTATTATTAGTGTATATTTTTATTGTATATGTATATGTATATA
1 ATTATTATTA-TATTATTATTATTAATATTAGTGTATATTTTTATTATATATGTATA-GTATATA
5977177 TATTTATACATAGTATTATTTTTTAATTACTTTATTTTAATATTTTTATTATATTATATTTGCTT
64 TATTTATACATAGTATTATTTTTTAATTACTTTATTTTAATATTTTTATTATATTATATTTGC-T
* *
5977242 TTTGTATTATTATTATTATTATT
128 TTT-TA-T-TT-TT-GTATT-TC
* *
5977265 ATTATTATTATTATTATTATTATTATTATTATTAGTGTATATCTTTATTGTATATGTATATGTAT
1 ATTATTATTA-TATTATTATTATTA--A-TATTAGTGTATATTTTTATTATATATGTATA-GTAT
* *
5977330 ATATATTTATACATAGTATTATTTTTTAATTATTTTATTTTAATATTTTTATTATATTATATGTG
61 ATATATTTATACATAGTATTATTTTTTAATTACTTTATTTTAATATTTTTATTATATTATATTTG
*
5977395 C------CTTTTGTATTTC
126 CTTTTTATTTTTGTATTTC
*
5977408 A--A-TA-T-TATTATTATTATTAATATTAGTGTATA-TTTTATTATATATGTTTATGTATATAT
1 ATTATTATTATATTATTATTATTAATATTAGTGTATATTTTTATTATATATGTATA-GTATATAT
*
5977467 ATTTATACATAGTATTATTTTTTTAATTACTTTATTTTTATATTTTTATTATATTATATTTGCTT
65 ATTTATACATAGTATTA-TTTTTTAATTACTTTATTTTAATATTTTTATTATATTATATTTGCTT
* * *
5977532 TTTATATTT-TAATAC
129 TTTATTTTTGTATTTC
* *
5977547 TATTACTATTAGTATTATTATTATTAATATTAGTGTATATTTTTATTAAATATGTATA-TATATA
1 -ATTATTATTA-TATTATTATTATTAATATTAGTGTATATTTTTATTATATATGTATAGTATATA
* * * *
5977611 TATTTATATATAGTACTA-TTTTTAATTACTTTATTTTAACATTATTATTATATTATATTTGCTT
64 TATTTATACATAGTATTATTTTTTAATTACTTTATTTTAATATTTTTATTATATTATATTTGCTT
5977675 TTT-TTTTGTGTATTTC
129 TTTATTTT-TGTATTTC
* *
5977691 ATTATTATTGCTAGTATTATTAT
1 ATTATTATT-ATATTATTATTAT
5977714 CATTATCATC
Statistics
Matches: 398, Mismatches: 30, Indels: 52
0.83 0.06 0.11
Matches are distributed among these distances:
133 41 0.10
134 54 0.14
135 1 0.00
137 14 0.04
139 5 0.01
140 6 0.02
141 1 0.00
142 4 0.01
143 70 0.18
144 9 0.02
145 24 0.06
146 29 0.07
147 16 0.04
153 25 0.06
156 99 0.25
ACGTcount: A:0.31, C:0.03, G:0.05, T:0.61
Consensus pattern (144 bp):
ATTATTATTATATTATTATTATTAATATTAGTGTATATTTTTATTATATATGTATAGTATATATA
TTTATACATAGTATTATTTTTTAATTACTTTATTTTAATATTTTTATTATATTATATTTGCTTTT
TATTTTTGTATTTC
Found at i:5989689 original size:47 final size:47
Alignment explanation
Indices: 5989623--5989776 Score: 168
Period size: 47 Copynumber: 3.3 Consensus size: 47
5989613 ATTGCTTCCA
*
5989623 TATAAGACCATATCCGGGATATGGCATCGGTGTGATATGTGCTACTG
1 TATAAGACCATATCTGGGATATGGCATCGGTGTGATATGTGCTACTG
* * *
5989670 TATAAGACCATATCTGGGATATGGCATCAGTGTGATATGTGAT-CCG
1 TATAAGACCATATCTGGGATATGGCATCGGTGTGATATGTGCTACTG
* ** * *
5989716 TGTAAGACCATGGCTGGGCTATGGCCTCGGTATGTGATATGTGACTA-TG
1 TATAAGACCATATCTGGGATATGGCATCGG--TGTGATATGTG-CTACTG
**
5989765 TGCAAGACCATA
1 TATAAGACCATA
5989777 GTTTTACTAT
Statistics
Matches: 89, Mismatches: 14, Indels: 6
0.82 0.13 0.06
Matches are distributed among these distances:
46 26 0.29
47 40 0.45
48 11 0.12
49 12 0.13
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.29
Consensus pattern (47 bp):
TATAAGACCATATCTGGGATATGGCATCGGTGTGATATGTGCTACTG
Found at i:5989739 original size:46 final size:47
Alignment explanation
Indices: 5989569--5989759 Score: 170
Period size: 47 Copynumber: 4.0 Consensus size: 47
5989559 AATATGATTT
* * * *
5989569 CCGTATAAGACCATAGCTGGGCTATGGCTTCGGAGAGATGTGATAT-TGCTT
1 CCGTATAAGACCATAGCTGGGATATGGCATC---G-G-TGTGATATGTGATA
* * * *
5989620 CCATATAAGACCATATCCGGGATATGGCATCGGTGTGATATGTGCTA
1 CCGTATAAGACCATAGCTGGGATATGGCATCGGTGTGATATGTGATA
* * *
5989667 CTGTATAAGACCATATCTGGGATATGGCATCAGTGTGATATGTGAT-
1 CCGTATAAGACCATAGCTGGGATATGGCATCGGTGTGATATGTGATA
* * * *
5989713 CCGTGTAAGACCATGGCTGGGCTATGGCCTCGGTATGTGATATGTGA
1 CCGTATAAGACCATAGCTGGGATATGGCATCGG--TGTGATATGTGA
5989760 CTATGTGCAA
Statistics
Matches: 119, Mismatches: 18, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
46 34 0.29
47 46 0.39
48 13 0.11
51 26 0.22
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.29
Consensus pattern (47 bp):
CCGTATAAGACCATAGCTGGGATATGGCATCGGTGTGATATGTGATA
Found at i:5993847 original size:77 final size:77
Alignment explanation
Indices: 5993486--5994626 Score: 1217
Period size: 78 Copynumber: 14.8 Consensus size: 77
5993476 GGTATCCTGA
* *
5993486 TATTTTT-ATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAATTGAGCCTCGGGT
1 TATTTTTAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGT
* *
5993550 CACATGCCGAGG
66 CACACGCTGAGG
* * * *
5993562 TATTTTCAATTTAC---ATTTCAAAAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCGGG
1 TATTTTTAATTT-CTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG
5993624 TCACACGCTGAGG
65 TCACACGCTGAGG
* * * * * **
5993637 TATTTTTAGTCTCTATTTTTCAAAAAAAAACAACTCATATTGCGAGAGGTGAGTTAAGCCTCAAA
1 TATTTTTAATTTCTGTTTTTC-AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG
* * *
5993702 TTACGCACTGAGG
65 TCACACGCTGAGG
* * ***
5993715 TATTTTCAATTTATGTTTCAAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG
1 TATTTTTAATTTCTGTTT-TTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG
*
5993780 TCACATGCTGAGG
65 TCACACGCTGAGG
* **
5993793 TATTTTTAGTTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAAT
1 TATTTTTAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGT
* * *
5993858 CACGCACT-AAG
66 CACACGCTGAGG
* *** * *
5993869 TATTTTCAATTTAC-GTTTCAAAAAAAAATCAACTCATATTGAGAGAGGTGAGTTGAGCCT-TGA
1 TATTTTTAATTT-CTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG-
5993932 GTCACACGCTGAGG
64 GTCACACGCTGAGG
* * **
5993946 TATTTTTAGTCTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAAT
1 TATTTTTAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGT
* * *
5994011 CACGCACTGAGA
66 CACACGCTGAGG
* *** *
5994023 TATTTTCAATTTAC-GTTTCAAAAAAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTC-GA
1 TATTTTTAATTT-CTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG-
*
5994086 GTCACACGTTGAGG
64 GTCACACGCTGAGG
* * * * * *
5994100 TAATTTTAGTTTCTATTTTTCAAAAAAAGTCAACTCATATTACGAGAGGTGAGTTGACCCTCAGA
1 TATTTTTAATTTCTGTTTTTCAAAAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG
5994165 TCACACGCTGAGG
65 TCACACGCTGAGG
* * **
5994178 TATTTTTAGTCTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAAT
1 TATTTTTAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGT
* * *
5994243 CACGCACTGAGA
66 CACACGCTGAGG
* *** *
5994255 TATTTTCAATTTAC-GTTTCAAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG
1 TATTTTTAATTT-CTGTTT-TTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG
*
5994319 GTCACACGTTGAGG
64 GTCACACGCTGAGG
* * * * * *
5994333 TAATTTTAGTTTCTATTTTTCAAAAAAAGTCAACTCATATTACGAGAGGTGAGTTGACCCTCGGG
1 TATTTTTAATTTCTGTTTTTCAAAAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG
5994398 TCACACGCTGAGG
65 TCACACGCTGAGG
* * * * *
5994411 TATTTTTAGTTTCTATCTTTCAAAAAAAGTCAACTCATATTACGAGAGGTGAGTTGACCCTC-GG
1 TATTTTTAATTTCTGTTTTTCAAAAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG
5994475 TTCACACGCTGAGG
65 -TCACACGCTGAGG
* * * ** *
5994489 TATCTTCAATTTATG-TTTAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGAT
1 TATTTTTAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGT
***
5994553 CACGTACTGAGG
66 CACACGCTGAGG
* * * * **
5994565 TATTTTCAATTTATGTTTTTTTCAAAAAAATCGACTCATTTTGCGAGAAATGAGTTGAGCCT
1 TATTTTTAATTTCTG--TTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
5994627 TTTAGTCTCT
Statistics
Matches: 887, Mismatches: 152, Indels: 49
0.82 0.14 0.05
Matches are distributed among these distances:
74 1 0.00
75 65 0.07
76 124 0.14
77 275 0.31
78 383 0.43
79 39 0.04
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (77 bp):
TATTTTTAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGT
CACACGCTGAGG
Found at i:5994183 original size:155 final size:154
Alignment explanation
Indices: 5993486--5994626 Score: 1352
Period size: 155 Copynumber: 7.4 Consensus size: 154
5993476 GGTATCCTGA
* * * *
5993486 TATTTTTA-TTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAATTGAGCCTCGGGT
1 TATTTTTAGTTTCTATTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGAT
* * * *
5993550 CACATGCCGAGGTATTTTCAATTTACATTTC--AAAAAAATCAACTCATATTGTGAGAGGTGAGT
66 CACACGCTGAGGTATTTTCAATTTACGTTTCAAAAAAAAATCAACTCATATTGCGAGAGGTGAGT
*
5993613 TGAGCCTCGGGTCACACGCTGAGG
131 TGAGCCTCGAGTCACACGCTGAGG
* * * *
5993637 TATTTTTAGTCTCTATTTTTCAAAAAAAAACAACTCATATTGCGAGAGGTGAGTTAAGCCTCAAA
1 TATTTTTAGTTTCTATTTTTC-AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGA
* * * *
5993702 TTACGCACTGAGGTATTTTCAATTTATGTTTCAAAAAAAAAATCAACTCATATTGCGAGAGGTGA
65 TCACACGCTGAGGTATTTTCAATTTACGTTTC-AAAAAAAAATCAACTCATATTGCGAGAGGTGA
*
5993767 GTTGAGCCTC-AGGTCACATGCTGAGG
129 GTTGAGCCTCGA-GTCACACGCTGAGG
* *
5993793 TATTTTTAGTTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAAT
1 TATTTTTAGTTTCTATTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGAT
* * * *
5993858 CACGCACT-AAGTATTTTCAATTTACGTTTCAAAAAAAAATCAACTCATATTGAGAGAGGTGAGT
66 CACACGCTGAGGTATTTTCAATTTACGTTTCAAAAAAAAATCAACTCATATTGCGAGAGGTGAGT
*
5993922 TGAGCCTTGAGTCACACGCTGAGG
131 TGAGCCTCGAGTCACACGCTGAGG
* * *
5993946 TATTTTTAGTCTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAAT
1 TATTTTTAGTTTCTATTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGAT
* * * *
5994011 CACGCACTGAGATATTTTCAATTTACGTTTCAAAAAAAAATCAACTCATATTGCTAGAGGTGAGT
66 CACACGCTGAGGTATTTTCAATTTACGTTTCAAAAAAAAATCAACTCATATTGCGAGAGGTGAGT
*
5994076 TGAGCCTCGAGTCACACGTTGAGG
131 TGAGCCTCGAGTCACACGCTGAGG
* * *
5994100 TAATTTTAGTTTCTATTTTTCAAAAAAAGTCAACTCATATTACGAGAGGTGAGTTGACCCTCAGA
1 TATTTTTAGTTTCTATTTTTCAAAAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGA
* * * ***
5994165 TCACACGCTGAGGTATTTTTAGTCT-CTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGA
65 TCACACGCTGAGGTATTTTCAATTTAC-GTTTCAAAAAAAAATCAACTCATATTGCGAGAGGTGA
* * * * *
5994229 GTTGAGCCTCAAATCACGCACTGAGA
129 GTTGAGCCTCGAGTCACACGCTGAGG
* * ** *
5994255 TATTTTCA-ATT-TACGTTTCAAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCG
1 TATTTTTAGTTTCTATTTTTC---AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCA
* * * ** * *
5994318 GGTCACACGTTGAGGTAATTTT-AGTTTCTATTTTTC-AAAAAAAGTCAACTCATATTACGAGAG
63 GATCACACGCTGAGGT-ATTTTCA-ATT-TACGTTTCAAAAAAAAATCAACTCATATTGCGAGAG
* *
5994381 GTGAGTTGACCCTCGGGTCACACGCTGAGG
125 GTGAGTTGAGCCTCGAGTCACACGCTGAGG
* * * * *
5994411 TATTTTTAGTTTCTATCTTTCAAAAAAAGTCAACTCATATTACGAGAGGTGAGTTGACCCTCGGT
1 TATTTTTAGTTTCTATTTTTCAAAAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGA
* *
5994476 TCACACGCTGAGGTATCTTCAATTTATGTTT-AAAAAAAAATCAACTCATATTGCGAGAGGTGAG
65 TCACACGCTGAGGTATTTTCAATTTACGTTTCAAAAAAAAATCAACTCATATTGCGAGAGGTGAG
***
5994540 TTGAGCCTC-AGATCACGTACTGAGG
130 TTGAGCCTCGAG-TCACACGCTGAGG
* * * * * * **
5994565 TATTTTCAATTTATGTTTTTTTCAAAAAAATCGACTCATTTTGCGAGAAATGAGTTGAGCCT
1 TATTTT-TAGTT-TCTATTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
5994627 TTTAGTCTCT
Statistics
Matches: 854, Mismatches: 111, Indels: 46
0.84 0.11 0.05
Matches are distributed among these distances:
151 8 0.01
152 10 0.01
153 194 0.23
154 183 0.21
155 248 0.29
156 199 0.23
157 6 0.01
158 6 0.01
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (154 bp):
TATTTTTAGTTTCTATTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGAT
CACACGCTGAGGTATTTTCAATTTACGTTTCAAAAAAAAATCAACTCATATTGCGAGAGGTGAGT
TGAGCCTCGAGTCACACGCTGAGG
Found at i:5995270 original size:38 final size:38
Alignment explanation
Indices: 5995228--5995316 Score: 105
Period size: 38 Copynumber: 2.4 Consensus size: 38
5995218 TAACCTAAAC
*
5995228 CCCAAACCCAACTATCCATTAAAACCCAATA-TCCAAAA
1 CCCAAACCCAACTACCCATTAAAACCCAATACT-CAAAA
5995266 CCCAAATCCCTAA--ACCCATTAAAACCCAATACTCAAAA
1 CCCAAA-CCC-AACTACCCATTAAAACCCAATACTCAAAA
*
5995304 CCCCAA-CCAACTA
1 CCCAAACCCAACTA
5995317 AACCCAAATT
Statistics
Matches: 44, Mismatches: 2, Indels: 11
0.77 0.04 0.19
Matches are distributed among these distances:
35 2 0.05
36 2 0.05
37 1 0.02
38 33 0.75
39 4 0.09
40 2 0.05
ACGTcount: A:0.46, C:0.39, G:0.00, T:0.15
Consensus pattern (38 bp):
CCCAAACCCAACTACCCATTAAAACCCAATACTCAAAA
Found at i:5996407 original size:7 final size:7
Alignment explanation
Indices: 5996392--5996478 Score: 70
Period size: 6 Copynumber: 14.0 Consensus size: 7
5996382 TTTGCTGTTC
5996392 TATTATT
1 TATTATT
*
5996399 TATTTTT
1 TATTATT
**
5996406 TA-CGTT
1 TATTATT
5996412 TATTA-T
1 TATTATT
5996418 TATTA-T
1 TATTATT
5996424 TATTA-T
1 TATTATT
5996430 TATTA-T
1 TATTATT
5996436 TATTA-T
1 TATTATT
5996442 TATTA-T
1 TATTATT
5996448 TATTA-T
1 TATTATT
5996454 TATTA-T
1 TATTATT
5996460 TATTA-T
1 TATTATT
5996466 TATTA-T
1 TATTATT
5996472 TATTATT
1 TATTATT
5996479 ATTGTTAGTG
Statistics
Matches: 73, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
6 64 0.88
7 9 0.12
ACGTcount: A:0.30, C:0.01, G:0.01, T:0.68
Consensus pattern (7 bp):
TATTATT
Found at i:5996415 original size:20 final size:22
Alignment explanation
Indices: 5996378--5996418 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
5996368 CCTTTTAATC
*
5996378 ATTTTTTGCTGTTCTATTATTT
1 ATTTTTTACTGTTCTATTATTT
5996400 ATTTTTTAC-GTT-TATTATT
1 ATTTTTTACTGTTCTATTATT
5996419 ATTATTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
21 3 0.17
22 8 0.44
ACGTcount: A:0.17, C:0.07, G:0.07, T:0.68
Consensus pattern (22 bp):
ATTTTTTACTGTTCTATTATTT
Found at i:5996417 original size:3 final size:3
Alignment explanation
Indices: 5996411--5997300 Score: 234
Period size: 3 Copynumber: 298.3 Consensus size: 3
5996401 TTTTTTACGT
5996411 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
5996459 TTA TTA TTA TTA TTA TTA TTA TTG TTA GTGTA -TA TTT TTA TTG TATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -T-TA TTA TTA TTA TTA T-TA
* *
5996506 TGTA -TA TGTA -TA TATA TT- TATA CATA ATA TTA TT- TT- TTAA TTA
1 T-TA TTA T-TA TTA T-TA TTA T-TA -TTA TTA TTA TTA TTA TT-A TTA
* * * ** *
5996549 CT- TTA TT- TTA ATA TTT TTA TTA -TA TTA -TA TT- TGCC TTT TGTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA T-TA
* *
5996591 TT- TCA ATA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
5996638 GTGTA -TA TT- TTA TTG TATA TGTA -TA TGTA -TA TATA TT- TATA CATA
1 -T-TA TTA TTA TTA TTA T-TA T-TA TTA T-TA TTA T-TA TTA T-TA -TTA
* * *
5996683 GTA TTA TT- TT- TTAA TTA CT- TTA TT- TTA ATA TT- TTA TTA -TA
1 TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
** * *
5996723 TTA -TA TT- TGC TT- TT- TGTA TT- TCA ATA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA
* *
5996764 TTA TTA TTA TTA TTA TTA TTA TTA GTGTA -TA TTT TTA TTG TATA TGTA
1 TTA TTA TTA TTA TTA TTA TTA TTA -T-TA TTA TTA TTA TTA T-TA T-TA
* * * *
5996812 -TA TGTA -TA TATA TT- TATA CATA GTA TTA TTT TTA TTA CT- TTA TT-
1 TTA T-TA TTA T-TA TTA T-TA -TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * ** * * *
5996856 TTA ATA TTT TTA TTA -TA TTA -TA TT- TGCC TTT TGTA TT- TCA ATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA T-TA TTA TTA TTA
* * *
5996899 TTG TTA CTA TTA TTA TTA TTA TTA TTA TTA TTA ATA TTA GTGTA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -T-TA TTA
* * *
5996945 TT- TTA TTG TATA TGTA -TA TGTA -TA TATA TT- TATA CATA GTA TTA
1 TTA TTA TTA T-TA T-TA TTA T-TA TTA T-TA TTA T-TA -TTA TTA TTA
* * *
5996989 TT- TT- TTAA TTA CT- TTA TT- TTA ATA TTT TTA TTA -TA TTA -TA
1 TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * *
5997029 TGTGCC TTT TGTA TT- TCA ATA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 T-T--A TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
5997077 TTA TTA TTA TTA TTA TTA TTA TTA GTGTA -TA TT- TTA TTA TATA TGTA
1 TTA TTA TTA TTA TTA TTA TTA TTA -T-TA TTA TTA TTA TTA T-TA T-TA
* * * *
5997124 -TA TGTA -TA TATA TT- TATA CATA GTA TTA TT- TTT TTAA TTA CT-
1 TTA T-TA TTA T-TA TTA T-TA -TTA TTA TTA TTA TTA TT-A TTA TTA
* * ** *
5997166 TTA TT- TTA ATA TTT TTA TTA -TA TTA -TA TT- TGC TTT TTA -TA TT-
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * *
5997208 TCA ATA CTA TTA CTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
5997256 TTA ATA TTA GTGTA -TA TTT TTA TTA TATA TGTA TATA TATA TTA T
1 TTA TTA TTA -T-TA TTA TTA TTA TTA T-TA T-TA T-TA T-TA TTA T
5997301 ATATAGTACT
Statistics
Matches: 660, Mismatches: 116, Indels: 222
0.66 0.12 0.22
Matches are distributed among these distances:
2 108 0.16
3 445 0.67
4 93 0.14
5 13 0.02
6 1 0.00
ACGTcount: A:0.31, C:0.03, G:0.05, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:5996945 original size:300 final size:305
Alignment explanation
Indices: 5996442--5997412 Score: 1440
Period size: 300 Copynumber: 3.1 Consensus size: 305
5996432 TTATTATTAT
*
5996442 TATTATTATTATTATTATTATTATTATTATTATTATTATTGTTAGTGTATATTTTTATTGTATAT
1 TATTATTATTATTATTATTATTATTATTATTATTATTATTATTAGTGTATATTTTTATTGTATAT
*
5996507 GTATATGTATATATATTTATACATAATATTATTTTTTAATTACTTTATTTTAATATTTTTATTAT
66 GTATATGTATATATATTTATACATAGTATTATTTTTTAATTACTTTATTTTAATATTTTTATTAT
*
5996572 ATTATATTTGCCTTTTGTATTTCAATATTATTATTATTATTATTATTATTATTATTATTATTATT
131 ATTATATTTGCCTTTTGTATTTCAATATTATTACTATTATTATTATTATTATTATTATTATTATT
5996637 AGTGTATATTTTATTGTATATGTATATGTATATATATTTATACATAGTATTATTTTTTAATTACT
196 AGTGTATATTTTATTGTATATGTATATGTATATATATTTATACATAGTATTATTTTTTAATTACT
5996702 TTATTTTAATATTTTATTATATTATATTTGCTTTTTGTATTTC-A
261 TTATTTTAATATTTTATTATATTATATTTGCTTTTTGTATTTCTA
5996746 -A-TATTATTATTATTATTATTATTATTATTATTATTATTATTAGTGTATATTTTTATTGTATAT
1 TATTATTATTATTATTATTATTATTATTATTATTATTATTATTAGTGTATATTTTTATTGTATAT
5996809 GTATATGTATATATATTTATACATAGTATTA-TTTTT-ATTACTTTATTTTAATATTTTTATTAT
66 GTATATGTATATATATTTATACATAGTATTATTTTTTAATTACTTTATTTTAATATTTTTATTAT
* *
5996872 ATTATATTTGCCTTTTGTATTTCAATATTGTTACTATTATTATTATTATTATTATTATTAATATT
131 ATTATATTTGCCTTTTGTATTTCAATATTATTACTATTATTATTATTATTATTATTATTATTATT
5996937 AGTGTATATTTTATTGTATATGTATATGTATATATATTTATACATAGTATTATTTTTTAATTACT
196 AGTGTATATTTTATTGTATATGTATATGTATATATATTTATACATAGTATTATTTTTTAATTACT
* *
5997002 TTATTTTAATATTTTTATTATATTATATGTGCCTTTTGTATTTCAATATTATTA
261 TTATTTTAATA-TTTTATTATATTATATTTGCTTTTTGTATTTC--------TA
*
5997056 TTATTATTATTATTATTATTATTATTATTATTATTATTATTATTAGTGTATA-TTTTATTATATA
1 -TATTATTATTATTATTATTATTATTATTATTATTATTATTATTAGTGTATATTTTTATTGTATA
5997120 TGTATATGTATATATATTTATACATAGTATTATTTTTTTAATTACTTTATTTTAATATTTTTATT
65 TGTATATGTATATATATTTATACATAGTATTA-TTTTTTAATTACTTTATTTTAATATTTTTATT
* * *
5997185 ATATTATATTTGCTTTTTATATTTCAATACTATTACTATTATTATTATTATTATTATTATTATTA
129 ATATTATATTTGCCTTTTGTATTTCAATATTATTACTATTATTATTATTATTATTATTATTATTA
* * * * * * *
5997250 TTATTATTAATATTAGTGTATATTTTTATTATATATGTATATATATATTATATATAGTACTA-TT
194 TTAGT-GT-ATATT--T-TAT-TGTATA-TGTATATGTATATATAT-TTATACATAGTATTATTT
* *
5997314 TTTAATTACTTTATTTTAACATTATTATTATATTATATTTGCTTTTT-T-TTGTGTA
251 TTTAATTACTTTATTTTAATATT-TTATTATATTATATTTGCTTTTTGTATT-TCTA
** * * * *
5997369 T-TTCATTATTATTGCTAGTATTATTATCATTATCATCATTATTA
1 TATT-ATTATTATTATTATTATTATTATTATTATTATTATTATTA
5997413 ACATATACAT
Statistics
Matches: 610, Mismatches: 30, Indels: 46
0.89 0.04 0.07
Matches are distributed among these distances:
300 165 0.27
301 35 0.06
302 91 0.15
303 1 0.00
310 1 0.00
311 2 0.00
312 79 0.13
313 50 0.08
314 5 0.01
315 89 0.15
316 1 0.00
317 5 0.01
319 1 0.00
320 5 0.01
321 8 0.01
322 59 0.10
323 13 0.02
ACGTcount: A:0.31, C:0.04, G:0.05, T:0.61
Consensus pattern (305 bp):
TATTATTATTATTATTATTATTATTATTATTATTATTATTATTAGTGTATATTTTTATTGTATAT
GTATATGTATATATATTTATACATAGTATTATTTTTTAATTACTTTATTTTAATATTTTTATTAT
ATTATATTTGCCTTTTGTATTTCAATATTATTACTATTATTATTATTATTATTATTATTATTATT
AGTGTATATTTTATTGTATATGTATATGTATATATATTTATACATAGTATTATTTTTTAATTACT
TTATTTTAATATTTTATTATATTATATTTGCTTTTTGTATTTCTA
Found at i:5997105 original size:163 final size:162
Alignment explanation
Indices: 5996897--5997360 Score: 740
Period size: 164 Copynumber: 2.9 Consensus size: 162
5996887 TGTATTTCAA
* *
5996897 TATTGTTACTATTATTATTATTATTATTATTATTAATATTAGTGTATATTTTATTGTATATGTAT
1 TATTATTATTATTATTATTATTATTATTATTATTAATATTAGTGTATATTTTATT-TATATGTAT
5996962 ATGTATATATATTTATACATAGTATTATTTTTTAATTACTTTATTTTAATATTTTTATTATATTA
65 ATGTATATATATTTATACATAGTATTATTTTTTAATTACTTTATTTTAATATTTTTATTATATTA
* * * * *
5997027 TATGTGCCTTTTGTATTTCAATATTATTATTAT
130 TATTTGCTTTTTATATTTCAATACTATTACTAT
*
5997060 TATTATTATTATTATTATTATTATTATTATTATTATTATTAGTGTATATTTTATTATATATGTAT
1 TATTATTATTATTATTATTATTATTATTATTATTAATATTAGTGTATATTTTATT-TATATGTAT
5997125 ATGTATATATATTTATACATAGTATTATTTTTTTAATTACTTTATTTTAATATTTTTATTATATT
65 ATGTATATATATTTATACATAGTATTA-TTTTTTAATTACTTTATTTTAATATTTTTATTATATT
5997190 ATATTTGCTTTTTATATTTCAATACTATTACTAT
129 ATATTTGCTTTTTATATTTCAATACTATTACTAT
*
5997224 TATTATTATTATTATTATTATTATTATTATTATTAATATTAGTGTATA--TT-TTTAT-TATATA
1 TATTATTATTATTATTATTATTATTATTATTATTAATATTAGTGTATATTTTATTTATATGTATA
* * * *
5997285 TGTATATATATATTATATATAGTACTA-TTTTTAATTACTTTATTTTAACATTATTATTATATTA
66 TGTATATATAT-TTATACATAGTATTATTTTTTAATTACTTTATTTTAATATTTTTATTATATTA
5997349 TATTTGCTTTTT
130 TATTTGCTTTTT
5997361 TTTGTGTATT
Statistics
Matches: 284, Mismatches: 15, Indels: 9
0.92 0.05 0.03
Matches are distributed among these distances:
158 47 0.17
159 16 0.06
160 16 0.06
161 2 0.01
162 2 0.01
163 88 0.31
164 113 0.40
ACGTcount: A:0.32, C:0.03, G:0.05, T:0.60
Consensus pattern (162 bp):
TATTATTATTATTATTATTATTATTATTATTATTAATATTAGTGTATATTTTATTTATATGTATA
TGTATATATATTTATACATAGTATTATTTTTTAATTACTTTATTTTAATATTTTTATTATATTAT
ATTTGCTTTTTATATTTCAATACTATTACTAT
Found at i:6000232 original size:31 final size:31
Alignment explanation
Indices: 6000197--6000369 Score: 201
Period size: 31 Copynumber: 5.6 Consensus size: 31
6000187 GTACAATGTA
* *
6000197 AAAAGTGGTAGCTTTGGCTACCTAATCAGTG
1 AAAAGTGGTAGCTTCGGCTACCTGATCAGTG
*
6000228 AAAAGTGGTAGCTTCGGTTACCTGATCAGTG
1 AAAAGTGGTAGCTTCGGCTACCTGATCAGTG
* *
6000259 AAAAGTAGTAGCTTCGGCTACCTGATTAGTG
1 AAAAGTGGTAGCTTCGGCTACCTGATCAGTG
* * *
6000290 AAAAGTGGTAGCTCCAGTTACCTGATCAGTG
1 AAAAGTGGTAGCTTCGGCTACCTGATCAGTG
* * *
6000321 AATAGTGATAGCTTCGGCTATC-GA--ATGTG
1 AAAAGTGGTAGCTTCGGCTACCTGATCA-GTG
6000350 AAAAG-GGATAGCTTCGGCTA
1 AAAAGTGG-TAGCTTCGGCTA
6000370 TCAAATTTGG
Statistics
Matches: 121, Mismatches: 19, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
28 2 0.02
29 19 0.16
30 2 0.02
31 98 0.81
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (31 bp):
AAAAGTGGTAGCTTCGGCTACCTGATCAGTG
Found at i:6000383 original size:29 final size:29
Alignment explanation
Indices: 6000318--6000384 Score: 89
Period size: 29 Copynumber: 2.3 Consensus size: 29
6000308 TACCTGATCA
* * *
6000318 GTGAATAGTGATAGCTTCGGCTATCGAAT
1 GTGAAAAGGGATAGCTTCGGCTATCAAAT
6000347 GTGAAAAGGGATAGCTTCGGCTATCAAAT
1 GTGAAAAGGGATAGCTTCGGCTATCAAAT
* *
6000376 TTGGAAAGG
1 GTGAAAAGG
6000385 AAAGGTATAT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.31, C:0.12, G:0.30, T:0.27
Consensus pattern (29 bp):
GTGAAAAGGGATAGCTTCGGCTATCAAAT
Found at i:6000411 original size:33 final size:33
Alignment explanation
Indices: 6000374--6000503 Score: 188
Period size: 33 Copynumber: 3.9 Consensus size: 33
6000364 CGGCTATCAA
* * *
6000374 ATTTGGAAAGGAAAGGTATATTTTGTGTATACT
1 ATTTGAAAAGGAAAGGTATACTTTGTGTATACC
* ** *
6000407 ATTTGAAAATGTTAGGTATACTTTGTATATACC
1 ATTTGAAAAGGAAAGGTATACTTTGTGTATACC
*
6000440 ATTTGAAAAGGAAATGTATACTTTGTGTATACC
1 ATTTGAAAAGGAAAGGTATACTTTGTGTATACC
6000473 ATTTGAAAAGGAAAGGTATACTTTGTGTATA
1 ATTTGAAAAGGAAAGGTATACTTTGTGTATA
6000504 TGTGACAGCC
Statistics
Matches: 84, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 84 1.00
ACGTcount: A:0.35, C:0.06, G:0.20, T:0.38
Consensus pattern (33 bp):
ATTTGAAAAGGAAAGGTATACTTTGTGTATACC
Found at i:6001898 original size:2 final size:2
Alignment explanation
Indices: 6001891--6001926 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
6001881 TGACTAGAGA
6001891 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
6001927 GCATATGGTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6002416 original size:2 final size:2
Alignment explanation
Indices: 6002405--6002440 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
6002395 GCTAATGTGT
6002405 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
6002441 GTGCATGATA
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:6004208 original size:41 final size:41
Alignment explanation
Indices: 6004151--6004300 Score: 221
Period size: 41 Copynumber: 3.7 Consensus size: 41
6004141 TCGAGGTTTA
6004151 AATCCGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGTCAT
1 AATCCGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGTCAT
6004192 AATCCGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGTCAT
1 AATCCGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGTCAT
* * * * * * * *
6004233 AA-CCGAACCTAGTTTCGAAGGGCCTTCGGGCCAATGTCAT
1 AATCCGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGTCAT
6004273 AATCCGAGCTTGGTCTCGAAGGGCTTTT
1 AATCCGAGCTTGGTCTCGAAGGGCTTTT
6004301 TGAGTCAGCG
Statistics
Matches: 94, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
40 32 0.34
41 62 0.66
ACGTcount: A:0.21, C:0.23, G:0.28, T:0.28
Consensus pattern (41 bp):
AATCCGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGTCAT
Found at i:6005956 original size:39 final size:39
Alignment explanation
Indices: 6005913--6006042 Score: 208
Period size: 39 Copynumber: 3.3 Consensus size: 39
6005903 GGGTGTGACA
6005913 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
6005952 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
* * *
6005991 TTATATCCGGGCTAAAGTCCCGTAGGC-TTTGTGCTGGTA
1 TTATATCCGGGCT-AAGTCCCGAAGGCATTCGTGCTGGTG
*
6006030 TTATATCCAGGCT
1 TTATATCCGGGCT
6006043 TAAAGTCCTG
Statistics
Matches: 86, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
39 74 0.86
40 12 0.14
ACGTcount: A:0.18, C:0.22, G:0.28, T:0.31
Consensus pattern (39 bp):
TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
Found at i:6006060 original size:40 final size:39
Alignment explanation
Indices: 6005913--6006069 Score: 192
Period size: 39 Copynumber: 4.0 Consensus size: 39
6005903 GGGTGTGACA
*
6005913 TTATATCCGGGCT-AAGTCCCGAAGGCATTCGTGCTGGTG
1 TTATATCCGGGCTAAAGTCCCGAAGGC-TTTGTGCTGGTG
*
6005952 TTATATCCGGGCT-AAGTCCCGAAGGCATTCGTGCTGGTG
1 TTATATCCGGGCTAAAGTCCCGAAGGC-TTTGTGCTGGTG
* *
6005991 TTATATCCGGGCTAAAGTCCCGTAGGCTTTGTGCTGGTA
1 TTATATCCGGGCTAAAGTCCCGAAGGCTTTGTGCTGGTG
* * * * *
6006030 TTATATCCAGGCTTAAAGTCCTGCATGCTTTGTGGTGGTG
1 TTATATCCGGGC-TAAAGTCCCGAAGGCTTTGTGCTGGTG
6006070 ATTGGATTTG
Statistics
Matches: 107, Mismatches: 9, Indels: 3
0.90 0.08 0.03
Matches are distributed among these distances:
39 73 0.68
40 34 0.32
ACGTcount: A:0.18, C:0.21, G:0.29, T:0.32
Consensus pattern (39 bp):
TTATATCCGGGCTAAAGTCCCGAAGGCTTTGTGCTGGTG
Found at i:6007705 original size:33 final size:33
Alignment explanation
Indices: 6007662--6007735 Score: 121
Period size: 33 Copynumber: 2.2 Consensus size: 33
6007652 GAGTGTTACA
*
6007662 GTATACCATATGAAAAGGGAAGGTATACTTTGT
1 GTATACCATATGAAAAGGAAAGGTATACTTTGT
*
6007695 GTATATCATATGAAAAGGAAAGGTATACTTTGT
1 GTATACCATATGAAAAGGAAAGGTATACTTTGT
*
6007728 GTGTACCA
1 GTATACCA
6007736 CTCGGAAAGA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.36, C:0.09, G:0.23, T:0.31
Consensus pattern (33 bp):
GTATACCATATGAAAAGGAAAGGTATACTTTGT
Found at i:6013067 original size:3 final size:3
Alignment explanation
Indices: 6013055--6013107 Score: 99
Period size: 3 Copynumber: 18.0 Consensus size: 3
6013045 AGCATACATT
6013055 ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
6013102 ATA ATA
1 ATA ATA
6013108 TACTATGATA
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 47 0.96
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:6013588 original size:16 final size:16
Alignment explanation
Indices: 6013552--6013589 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
6013542 AATTATATTC
6013552 AATAATTTTATAGATT
1 AATAATTTTATAGATT
*
6013568 TATAATTTTATTA-ATT
1 AATAATTTTA-TAGATT
6013584 AATAAT
1 AATAAT
6013590 ATATTATGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
16 17 0.89
17 2 0.11
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (16 bp):
AATAATTTTATAGATT
Found at i:6013783 original size:110 final size:110
Alignment explanation
Indices: 6013654--6013877 Score: 448
Period size: 110 Copynumber: 2.0 Consensus size: 110
6013644 CTTCACATTA
6013654 ATATATTATCATATTAACTAATATTAATTTTATTATTATCACATAATAATATTAATAAATTATTA
1 ATATATTATCATATTAACTAATATTAATTTTATTATTATCACATAATAATATTAATAAATTATTA
6013719 TTCTAAATTCTAATGTTAATTTAATAATATAATTAACAATAAAAG
66 TTCTAAATTCTAATGTTAATTTAATAATATAATTAACAATAAAAG
6013764 ATATATTATCATATTAACTAATATTAATTTTATTATTATCACATAATAATATTAATAAATTATTA
1 ATATATTATCATATTAACTAATATTAATTTTATTATTATCACATAATAATATTAATAAATTATTA
6013829 TTCTAAATTCTAATGTTAATTTAATAATATAATTAACAATAAAAG
66 TTCTAAATTCTAATGTTAATTTAATAATATAATTAACAATAAAAG
6013874 ATAT
1 ATAT
6013878 TCTAATTAGA
Statistics
Matches: 114, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
110 114 1.00
ACGTcount: A:0.47, C:0.06, G:0.02, T:0.45
Consensus pattern (110 bp):
ATATATTATCATATTAACTAATATTAATTTTATTATTATCACATAATAATATTAATAAATTATTA
TTCTAAATTCTAATGTTAATTTAATAATATAATTAACAATAAAAG
Found at i:6013827 original size:30 final size:30
Alignment explanation
Indices: 6013657--6013830 Score: 115
Period size: 30 Copynumber: 6.1 Consensus size: 30
6013647 CACATTAATA
* *
6013657 TATTATCATATTAACTAATATTAATTTTAT
1 TATTATCACATTAACTAATATTAATATTAT
*
6013687 TATTATCACA-TAA-TAATATTAATA-AAT
1 TATTATCACATTAACTAATATTAATATTAT
* * *
6013714 TATTATTCTAAATT--CTAATGTTAAT-TTAA
1 TATTA-TC-ACATTAACTAATATTAATATTAT
* * *
6013743 TAATAT-A-ATTAAC-AATA-AAAGA-TA-
1 TATTATCACATTAACTAATATTAATATTAT
* *
6013767 TATTATCATATTAACTAATATTAATTTTAT
1 TATTATCACATTAACTAATATTAATATTAT
6013797 TATTATCACA-TAA-TAATATTAATAAATTAT
1 TATTATCACATTAACTAATATTAAT--ATTAT
6013827 TATT
1 TATT
6013831 CTAAATTCTA
Statistics
Matches: 111, Mismatches: 17, Indels: 32
0.69 0.11 0.20
Matches are distributed among these distances:
24 5 0.05
25 8 0.07
26 10 0.09
27 12 0.11
28 25 0.23
29 24 0.22
30 27 0.24
ACGTcount: A:0.46, C:0.06, G:0.01, T:0.47
Consensus pattern (30 bp):
TATTATCACATTAACTAATATTAATATTAT
Found at i:6016625 original size:6 final size:6
Alignment explanation
Indices: 6016616--6016640 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
6016606 TTTAAATTTT
6016616 ATATTA ATATTA ATATTA ATATTA A
1 ATATTA ATATTA ATATTA ATATTA A
6016641 ATGAATCTAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
ATATTA
Found at i:6020803 original size:19 final size:19
Alignment explanation
Indices: 6020768--6020805 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
6020758 TTAATCATAT
*
6020768 ATTTAATTATTTGTTTTTA
1 ATTTAATTAGTTGTTTTTA
6020787 ATTTAATTTAGTT-TTTTTA
1 ATTTAA-TTAGTTGTTTTTA
6020806 GTTTTTTAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.68
Consensus pattern (19 bp):
ATTTAATTAGTTGTTTTTA
Found at i:6021482 original size:26 final size:24
Alignment explanation
Indices: 6021453--6021500 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 24
6021443 AATTAATTAT
6021453 TTTTAAAATTAAAAATATATAAAAAA
1 TTTTAAAA-TAAAAATAT-TAAAAAA
6021479 TTTTAAAATAAAAATATTAAAA
1 TTTTAAAATAAAAATATTAAAA
6021501 TTCTAAAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 5 0.23
25 9 0.41
26 8 0.36
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (24 bp):
TTTTAAAATAAAAATATTAAAAAA
Found at i:6031212 original size:39 final size:40
Alignment explanation
Indices: 6031169--6031253 Score: 118
Period size: 39 Copynumber: 2.1 Consensus size: 40
6031159 TCAAATACAT
6031169 TTAAAACAAATATTAAAACAAGAAACAAA-TAAAAATATA
1 TTAAAACAAATATTAAAACAAGAAACAAATTAAAAATATA
* * * *
6031208 TTAAAACAATTCTTAAAACAATATACAAATTAAAAATATA
1 TTAAAACAAATATTAAAACAAGAAACAAATTAAAAATATA
*
6031248 ATAAAA
1 TTAAAA
6031254 ATTGATTATA
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
39 25 0.62
40 15 0.38
ACGTcount: A:0.66, C:0.08, G:0.01, T:0.25
Consensus pattern (40 bp):
TTAAAACAAATATTAAAACAAGAAACAAATTAAAAATATA
Found at i:6031297 original size:23 final size:23
Alignment explanation
Indices: 6031269--6031313 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
6031259 TTATATTAAA
* *
6031269 ATTAAAATTAAAATATAAATATG
1 ATTAAAAATAAAAAATAAATATG
*
6031292 ATTAAAAATAAAAAATATATAT
1 ATTAAAAATAAAAAATAAATAT
6031314 ATTTAGTATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (23 bp):
ATTAAAAATAAAAAATAAATATG
Found at i:6034646 original size:76 final size:76
Alignment explanation
Indices: 6034559--6034749 Score: 256
Period size: 76 Copynumber: 2.5 Consensus size: 76
6034549 AAATAAACCA
* * * * *
6034559 ACAATGTTTTGCACCTAGCGCTAGTCGGATAAATCGACGATATCAAATGTGTGCCCAGTACTAAT
1 ACAATGATTTGCACCCAGCGCTAGTCGGATAAACCGACGATATCAAATGTATGCCCAGCACTAAT
*
6034624 CAGATAGACTG
66 CAGATAGACCG
* * * *
6034635 ACAATGATTTGCACCCAGCACTAGTTGGATAAACCGACGATATCAAATGTATGCCTAGCACTAGT
1 ACAATGATTTGCACCCAGCGCTAGTCGGATAAACCGACGATATCAAATGTATGCCCAGCACTAAT
**
6034700 TGGATAGACCG
66 CAGATAGACCG
*
6034711 ACAATGATTTGCACCCAGCGCTAGTCAGATAAAACCGAC
1 ACAATGATTTGCACCCAGCGCTAGTCGGAT-AAACCGAC
6034750 AATTACATAC
Statistics
Matches: 99, Mismatches: 15, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
76 91 0.92
77 8 0.08
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.24
Consensus pattern (76 bp):
ACAATGATTTGCACCCAGCGCTAGTCGGATAAACCGACGATATCAAATGTATGCCCAGCACTAAT
CAGATAGACCG
Found at i:6049073 original size:54 final size:54
Alignment explanation
Indices: 6049013--6049168 Score: 167
Period size: 52 Copynumber: 2.9 Consensus size: 54
6049003 ACCAGTATTT
* * *
6049013 AAAAAAATTAAATTTTTTTGTACCTGATGCCAGCCATTAGAAGGCCAGAACAAA
1 AAAAAAATTAAATTTTTTGGTACCTGGTGCCGGCCATTAGAAGGCCAGAACAAA
** * * * * *
6049067 AAAAAAATTTAAA--TACTGGTAGTCTGGTGCTGGCCATTAAAAGGGCAG--CACA
1 AAAAAAA-TTAAATTTTTTGGTA-CCTGGTGCCGGCCATTAGAAGGCCAGAACAAA
*
6049119 AAAAAATTTAAATTTTTTGGTACCTGGTGCCGGCCATTAGAAGGCCAGAA
1 AAAAAAATTAAATTTTTTGGTACCTGGTGCCGGCCATTAGAAGGCCAGAA
6049169 TTTTTTTTTT
Statistics
Matches: 79, Mismatches: 17, Indels: 12
0.73 0.16 0.11
Matches are distributed among these distances:
51 5 0.06
52 31 0.39
53 11 0.14
54 27 0.34
55 5 0.06
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.26
Consensus pattern (54 bp):
AAAAAAATTAAATTTTTTGGTACCTGGTGCCGGCCATTAGAAGGCCAGAACAAA
Found at i:6054505 original size:58 final size:58
Alignment explanation
Indices: 6054444--6054643 Score: 223
Period size: 55 Copynumber: 3.6 Consensus size: 58
6054434 TTCAAAAAAT
* * * *
6054444 GATTGCTTATATGTTTAAATCAATTGTTATGGTGGAATACTTCTTCTTCTTTTGAATT
1 GATTGTTTATATGTTTAAATCTATTGTTATGTTGGAATACTTCTTCTTCTTTTGAATC
* * * * *
6054502 GATTGTTTATATGTTTAAATCGACTATTATGTTGGAATGCTGC-T-TT-TTTTGAATC
1 GATTGTTTATATGTTTAAATCTATTGTTATGTTGGAATACTTCTTCTTCTTTTGAATC
* * * * *
6054557 AATTGTTTATAAGTTTAAATCTATTGTTATATTGAAATA--T-TACTTCTTTTGAATC
1 GATTGTTTATATGTTTAAATCTATTGTTATGTTGGAATACTTCTTCTTCTTTTGAATC
*
6054612 GATTGTTTGTATGTTTAAATCTATTGTTATGT
1 GATTGTTTATATGTTTAAATCTATTGTTATGT
6054644 AGTATGTCTA
Statistics
Matches: 117, Mismatches: 22, Indels: 9
0.79 0.15 0.06
Matches are distributed among these distances:
54 2 0.02
55 76 0.65
56 2 0.02
57 1 0.01
58 36 0.31
ACGTcount: A:0.26, C:0.08, G:0.15, T:0.51
Consensus pattern (58 bp):
GATTGTTTATATGTTTAAATCTATTGTTATGTTGGAATACTTCTTCTTCTTTTGAATC
Found at i:6061549 original size:18 final size:19
Alignment explanation
Indices: 6061526--6061575 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 19
6061516 TTATACTTAA
6061526 AATATTTTAATTTAATTT-
1 AATATTTTAATTTAATTTC
* *
6061544 AATATTTAAATTTAGTTTC
1 AATATTTTAATTTAATTTC
*
6061563 AATA-ATTAATTTA
1 AATATTTTAATTTA
6061576 GTATTTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 23 0.85
19 4 0.15
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (19 bp):
AATATTTTAATTTAATTTC
Found at i:6061896 original size:58 final size:58
Alignment explanation
Indices: 6061833--6061948 Score: 223
Period size: 58 Copynumber: 2.0 Consensus size: 58
6061823 CATTATAACC
6061833 AAACTAAAATACTAAATAATATATTAACTCTTTACGTATAGATATTTGGTCCAAGTTA
1 AAACTAAAATACTAAATAATATATTAACTCTTTACGTATAGATATTTGGTCCAAGTTA
*
6061891 AAACTAAAATACTAAATAATATATTAACTCTTTACGTATAGATATTTGGTTCAAGTTA
1 AAACTAAAATACTAAATAATATATTAACTCTTTACGTATAGATATTTGGTCCAAGTTA
6061949 TCCTCTCTCA
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 57 1.00
ACGTcount: A:0.43, C:0.11, G:0.09, T:0.37
Consensus pattern (58 bp):
AAACTAAAATACTAAATAATATATTAACTCTTTACGTATAGATATTTGGTCCAAGTTA
Found at i:6066966 original size:113 final size:113
Alignment explanation
Indices: 6066768--6066995 Score: 357
Period size: 113 Copynumber: 2.0 Consensus size: 113
6066758 ATAGCTTCCC
* * * *
6066768 TAACTTCATAATTGGCTCATAAGCACTAACTAATAAAATTTACAATCTCACTTATCAGATTTAGT
1 TAACTTCACAATTGGCTCATAAGCACTAAATAATAAAATTTACAAGCTCACTTATCAAATTTAGT
* *
6066833 GATCTCGAATCACTGTTTCCGACACCATTGAAAATTGAGCTGTTACAT
66 GATCTCGAATCACTGTTTCCGACACAATTGAAAATTGAGCTATTACAT
* *
6066881 TAACTTCACAATTGGCTCATAAGCACTAAATAATAAAATTTACAAGCTCATTTGTCAAATTTAGT
1 TAACTTCACAATTGGCTCATAAGCACTAAATAATAAAATTTACAAGCTCACTTATCAAATTTAGT
* * *
6066946 GATCTCGAATCACTGTTTCCGATACAATTGAAAGTTGGGCTATTACAT
66 GATCTCGAATCACTGTTTCCGACACAATTGAAAATTGAGCTATTACAT
6066994 TA
1 TA
6066996 TATGTGTTGT
Statistics
Matches: 104, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
113 104 1.00
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.34
Consensus pattern (113 bp):
TAACTTCACAATTGGCTCATAAGCACTAAATAATAAAATTTACAAGCTCACTTATCAAATTTAGT
GATCTCGAATCACTGTTTCCGACACAATTGAAAATTGAGCTATTACAT
Found at i:6071740 original size:4 final size:4
Alignment explanation
Indices: 6071715--6071756 Score: 50
Period size: 4 Copynumber: 10.5 Consensus size: 4
6071705 AATTAAAATA
* *
6071715 AAAG AAAT AAAG AAATG AAAG AAAG AAA- AAGG AAAG AAAG AA
1 AAAG AAAG AAAG AAA-G AAAG AAAG AAAG AAAG AAAG AAAG AA
6071757 GGCCACGGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
3 2 0.06
4 26 0.81
5 4 0.12
ACGTcount: A:0.74, C:0.00, G:0.21, T:0.05
Consensus pattern (4 bp):
AAAG
Found at i:6072849 original size:6 final size:6
Alignment explanation
Indices: 6072838--6072870 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
6072828 TGTGTACCGC
*
6072838 TACTGT TACTGT TACTGT TATTGT TACTGT TAC
1 TACTGT TACTGT TACTGT TACTGT TACTGT TAC
6072871 CCTTACGGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.18, C:0.15, G:0.15, T:0.52
Consensus pattern (6 bp):
TACTGT
Found at i:6073059 original size:18 final size:18
Alignment explanation
Indices: 6073002--6073061 Score: 50
Period size: 18 Copynumber: 3.3 Consensus size: 18
6072992 GACTGTCTGC
* *
6073002 TACTGAATAATTGACTAT
1 TACTGAATAAATGAATAT
** * *
6073020 TACAAAATAAACGATTGA-
1 TACTGAATAAATGAAT-AT
6073038 TACTGAATAAATGAATAT
1 TACTGAATAAATGAATAT
6073056 TACTGA
1 TACTGA
6073062 TTAACCGATT
Statistics
Matches: 31, Mismatches: 9, Indels: 4
0.70 0.20 0.09
Matches are distributed among these distances:
17 1 0.03
18 29 0.94
19 1 0.03
ACGTcount: A:0.47, C:0.10, G:0.12, T:0.32
Consensus pattern (18 bp):
TACTGAATAAATGAATAT
Found at i:6074498 original size:18 final size:18
Alignment explanation
Indices: 6074462--6074500 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
6074452 GAAATATTTA
*
6074462 TTTTGATGTTTTTAGTAT
1 TTTTGATGTTTATAGTAT
6074480 TTTTGATGTATTATA-TAT
1 TTTTGATGT-TTATAGTAT
6074498 TTT
1 TTT
6074501 AAAATTATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.21, C:0.00, G:0.13, T:0.67
Consensus pattern (18 bp):
TTTTGATGTTTATAGTAT
Found at i:6076997 original size:29 final size:29
Alignment explanation
Indices: 6076927--6076985 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
6076917 CAAGGTCATT
6076927 TGACAAAGCATAAATTTAAGTTACTTTCG
1 TGACAAAGCATAAATTTAAGTTACTTTCG
6076956 TGACAAAGCATAAATTTAAGTTACTTTCG
1 TGACAAAGCATAAATTTAAGTTACTTTCG
6076985 T
1 T
6076986 AATGGCCTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.36
Consensus pattern (29 bp):
TGACAAAGCATAAATTTAAGTTACTTTCG
Found at i:6077678 original size:2 final size:2
Alignment explanation
Indices: 6077671--6077696 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
6077661 GTAATTTTTC
6077671 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
6077697 AAAGGACTAA
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):
TA
Found at i:6086554 original size:91 final size:89
Alignment explanation
Indices: 6086442--6086621 Score: 231
Period size: 89 Copynumber: 2.0 Consensus size: 89
6086432 TTTAGTTCAA
* * *
6086442 GTTAGGCCCTGGACTTGGCAACTTTTCTC-ACATTTGGGCTTGAACATTTTTGTTGTCCGAA-TT
1 GTTAGGACCTGGACTTGGCAAC-TTTCTCAACATTGGGGCCTGAAC-TTTTT-TTGTCC-AAGTT
* *
6086505 AGGTCCTAAACTTGACAATTATTCTCAC
62 AAGCCCTAAACTTGACAATTATTCTCAC
*
6086533 GTTAGGACTTGGACTCT-GCAACTTTCTCAACATTGGGGCCTGAACTTTTTTTGTCCAAGTTAAG
1 GTTAGGACCTGGACT-TGGCAACTTTCTCAACATTGGGGCCTGAACTTTTTTTGTCCAAGTTAAG
*
6086597 CCCTAAACTTGACAATTGTTCTCAC
65 CCCTAAACTTGACAATTATTCTCAC
6086622 ATTGAACCCT
Statistics
Matches: 79, Mismatches: 7, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
88 2 0.03
89 33 0.42
90 11 0.14
91 32 0.41
92 1 0.01
ACGTcount: A:0.23, C:0.23, G:0.18, T:0.36
Consensus pattern (89 bp):
GTTAGGACCTGGACTTGGCAACTTTCTCAACATTGGGGCCTGAACTTTTTTTGTCCAAGTTAAGC
CCTAAACTTGACAATTATTCTCAC
Found at i:6086578 original size:152 final size:149
Alignment explanation
Indices: 6086351--6086624 Score: 347
Period size: 152 Copynumber: 1.8 Consensus size: 149
6086341 TTTGTTTAAG
* * * *
6086351 TTAGGTCCTAAATTTGCCAATTATTCTCACATTGGGACTTGGACTAGACAACTTTTCCCACATTG
1 TTAGGTCCTAAACTTGACAATTATTCTCACATTAGGACTTGGACTAGACAACTTTTCCAACATTG
* * * ** *
6086416 GGATATGAACTTCTTTTTTAGTTCAAGTTAGGCCCTGGACTTGGCAACTT-TTCTCACATTTGGG
66 GGACATGAAC-T-TTTTTT-GTCCAAGTTAAGCCCTAAACTTGACAA-TTGTTCTCACATTTGGG
6086480 CTTGAACATTTTTGTTGTCCGAA
127 CTTGAACATTTTTGTTGTCCGAA
* *
6086503 TTAGGTCCTAAACTTGACAATTATTCTCACGTTAGGACTTGGACTCTG-CAAC-TTTCTCAACAT
1 TTAGGTCCTAAACTTGACAATTATTCTCACATTAGGACTTGGACT-AGACAACTTTTC-CAACAT
* *
6086566 TGGGGCCTGAACTTTTTTTGTCCAAGTTAAGCCCTAAACTTGACAATTGTTCTCACATT
64 TGGGACATGAACTTTTTTTGTCCAAGTTAAGCCCTAAACTTGACAATTGTTCTCACATT
6086625 GAACCCTGAG
Statistics
Matches: 105, Mismatches: 14, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
148 2 0.02
149 32 0.30
150 6 0.06
151 5 0.05
152 59 0.56
153 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.17, T:0.37
Consensus pattern (149 bp):
TTAGGTCCTAAACTTGACAATTATTCTCACATTAGGACTTGGACTAGACAACTTTTCCAACATTG
GGACATGAACTTTTTTTGTCCAAGTTAAGCCCTAAACTTGACAATTGTTCTCACATTTGGGCTTG
AACATTTTTGTTGTCCGAA
Found at i:6088052 original size:41 final size:41
Alignment explanation
Indices: 6087945--6088228 Score: 324
Period size: 41 Copynumber: 7.0 Consensus size: 41
6087935 TTGTAAAATG
* ** *
6087945 CAGAGCAATAGCGGCGTCTTAC-CAAAAACGCCGTTAAAAA-
1 CAGAGCAATAGCGGCG-CTTTCTGTAAAACGCCGCTAAAAAC
* *
6087985 CAGAGCAATAGCGGC-ATTTTTGGTAAAACGCCGCTAAAAAC
1 CAGAGCAATAGCGGCGCTTTCT-GTAAAACGCCGCTAAAAAC
6088026 CAGAGCAATAGCGGCGCTTTCTGTAAAACGCCGCTAAAAAC
1 CAGAGCAATAGCGGCGCTTTCTGTAAAACGCCGCTAAAAAC
* * *
6088067 CAAAGCAATAGCGGCGCTTTCAGTAAAACGCCACTAAAAAC
1 CAGAGCAATAGCGGCGCTTTCTGTAAAACGCCGCTAAAAAC
* *
6088108 TAGAGCAATAGCGGCGCTTT-TGGTAAAATGCCGCTAAAAAC
1 CAGAGCAATAGCGGCGCTTTCT-GTAAAACGCCGCTAAAAAC
* * * * * *
6088149 CAGAGCATTATCGACGTTTTCGGTAAAACGCCACTAAAAAC
1 CAGAGCAATAGCGGCGCTTTCTGTAAAACGCCGCTAAAAAC
* ** *
6088190 CAGAGCATTAGCGGCGCTTTCAATAAAACACCGCTAAAA
1 CAGAGCAATAGCGGCGCTTTCTGTAAAACGCCGCTAAAA
6088229 GTCATTTAAC
Statistics
Matches: 207, Mismatches: 31, Indels: 11
0.83 0.12 0.04
Matches are distributed among these distances:
38 2 0.01
40 30 0.14
41 171 0.83
42 4 0.02
ACGTcount: A:0.37, C:0.24, G:0.20, T:0.18
Consensus pattern (41 bp):
CAGAGCAATAGCGGCGCTTTCTGTAAAACGCCGCTAAAAAC
Found at i:6088113 original size:82 final size:82
Alignment explanation
Indices: 6087945--6088228 Score: 358
Period size: 82 Copynumber: 3.5 Consensus size: 82
6087935 TTGTAAAATG
* ** * * *
6087945 CAGAGCAATAGCGGCGTCTTAC-CAAAAACGCCGTTAAAAA-CAGAGCAATAGCGGCATTTTTGG
1 CAGAGCAATAGCGGCG-CTTTCTGTAAAACGCCGCTAAAAACCAGAGCAATAGCGGCGTTTTCGG
*
6088008 TAAAACGCCGCTAAAAAC
65 TAAAACGCCACTAAAAAC
* * *
6088026 CAGAGCAATAGCGGCGCTTTCTGTAAAACGCCGCTAAAAACCAAAGCAATAGCGGCGCTTTCAGT
1 CAGAGCAATAGCGGCGCTTTCTGTAAAACGCCGCTAAAAACCAGAGCAATAGCGGCGTTTTCGGT
6088091 AAAACGCCACTAAAAAC
66 AAAACGCCACTAAAAAC
* * * * *
6088108 TAGAGCAATAGCGGCGCTTT-TGGTAAAATGCCGCTAAAAACCAGAGCATTATCGACGTTTTCGG
1 CAGAGCAATAGCGGCGCTTTCT-GTAAAACGCCGCTAAAAACCAGAGCAATAGCGGCGTTTTCGG
6088172 TAAAACGCCACTAAAAAC
65 TAAAACGCCACTAAAAAC
* ** *
6088190 CAGAGCATTAGCGGCGCTTTCAATAAAACACCGCTAAAA
1 CAGAGCAATAGCGGCGCTTTCTGTAAAACGCCGCTAAAA
6088229 GTCATTTAAC
Statistics
Matches: 175, Mismatches: 24, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
80 4 0.02
81 32 0.18
82 139 0.79
ACGTcount: A:0.37, C:0.24, G:0.20, T:0.18
Consensus pattern (82 bp):
CAGAGCAATAGCGGCGCTTTCTGTAAAACGCCGCTAAAAACCAGAGCAATAGCGGCGTTTTCGGT
AAAACGCCACTAAAAAC
Found at i:6088144 original size:123 final size:121
Alignment explanation
Indices: 6087948--6088228 Score: 375
Period size: 123 Copynumber: 2.3 Consensus size: 121
6087938 TAAAATGCAG
* * *
6087948 AGCAATAGCGGCGTCTTACCA-AAAACGCCGTTAAAAACAGAGCAATAGCGGCATTTTTGGTAAA
1 AGCAATAGCGGCG-CTT-TCATAAAACGCCGCTAAAAACAGAGCAATAGCGGCACTTTTGGTAAA
* * *
6088012 ACGCCGCTAAAAACCAGAGCAATAGCGGCGCTTTCTGTAAAACGCCGCTAAAAACCAA
64 ACGCCGCTAAAAACCAGAGCAATAGCGACGCTTTCGGTAAAACGCCACTAAAAACCAA
* *
6088070 AGCAATAGCGGCGCTTTCAGTAAAACGCCACTAAAAACTAGAGCAATAGCGGCGCTTTTGGTAAA
1 AGCAATAGCGGCGCTTTCA-TAAAACGCCGCTAAAAAC-AGAGCAATAGCGGCACTTTTGGTAAA
* * * * *
6088135 ATGCCGCTAAAAACCAGAGCATTATCGACGTTTTCGGTAAAACGCCACTAAAAACCAG
64 ACGCCGCTAAAAACCAGAGCAATAGCGACGCTTTCGGTAAAACGCCACTAAAAACCAA
* *
6088193 AGCATTAGCGGCGCTTTCAATAAAACACCGCTAAAA
1 AGCAATAGCGGCGCTTTC-ATAAAACGCCGCTAAAA
6088229 GTCATTTAAC
Statistics
Matches: 139, Mismatches: 16, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
120 2 0.01
121 3 0.02
122 28 0.20
123 105 0.76
124 1 0.01
ACGTcount: A:0.37, C:0.24, G:0.20, T:0.19
Consensus pattern (121 bp):
AGCAATAGCGGCGCTTTCATAAAACGCCGCTAAAAACAGAGCAATAGCGGCACTTTTGGTAAAAC
GCCGCTAAAAACCAGAGCAATAGCGACGCTTTCGGTAAAACGCCACTAAAAACCAA
Found at i:6088471 original size:7 final size:7
Alignment explanation
Indices: 6088460--6088523 Score: 56
Period size: 7 Copynumber: 9.0 Consensus size: 7
6088450 TTTTTTTTTG
*
6088460 GGTTTAG
1 GGTTTAA
6088467 GGTTTAA
1 GGTTTAA
**
6088474 TTTTTAA
1 GGTTTAA
6088481 GGTTTAA
1 GGTTTAA
* *
6088488 GGTCTAT
1 GGTTTAA
*
6088495 GGTTTAG
1 GGTTTAA
*
6088502 GGTTTTAT
1 GG-TTTAA
6088510 GGTTTAA
1 GGTTTAA
6088517 GGTTTAA
1 GGTTTAA
6088524 TGGCCATGGG
Statistics
Matches: 45, Mismatches: 11, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
7 39 0.87
8 6 0.13
ACGTcount: A:0.22, C:0.02, G:0.28, T:0.48
Consensus pattern (7 bp):
GGTTTAA
Found at i:6088512 original size:15 final size:15
Alignment explanation
Indices: 6088462--6088526 Score: 62
Period size: 14 Copynumber: 4.5 Consensus size: 15
6088452 TTTTTTTGGG
* *
6088462 TTTAGGGTTTAA-TT
1 TTTATGGTTTAAGGT
*
6088476 TTTAAGGTTTAAGG-
1 TTTATGGTTTAAGGT
* *
6088490 TCTATGGTTTAGGGT
1 TTTATGGTTTAAGGT
6088505 TTTATGGTTTAAGGT
1 TTTATGGTTTAAGGT
*
6088520 TTAATGG
1 TTTATGG
6088527 CCATGGGAAT
Statistics
Matches: 41, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
14 22 0.54
15 19 0.46
ACGTcount: A:0.22, C:0.02, G:0.28, T:0.49
Consensus pattern (15 bp):
TTTATGGTTTAAGGT
Found at i:6089135 original size:15 final size:15
Alignment explanation
Indices: 6089111--6089189 Score: 65
Period size: 15 Copynumber: 5.2 Consensus size: 15
6089101 TAAATCAAAA
*
6089111 TAAAAATAAAAATAT
1 TAAAATTAAAAATAT
6089126 TAAAATTAAAAA-AT
1 TAAAATTAAAAATAT
*
6089140 TAAAAAATTAAAAAATAA
1 T--AAAATT-AAAAATAT
* *
6089158 AAAAATT-AAAATTT
1 TAAAATTAAAAATAT
6089172 TAAAAATTAAAAAT-T
1 T-AAAATTAAAAATAT
6089187 TAA
1 TAA
6089190 TATTTTAGTC
Statistics
Matches: 52, Mismatches: 6, Indels: 13
0.73 0.08 0.18
Matches are distributed among these distances:
14 10 0.19
15 19 0.37
16 17 0.33
17 5 0.10
18 1 0.02
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
TAAAATTAAAAATAT
Found at i:6089138 original size:8 final size:8
Alignment explanation
Indices: 6089127--6089189 Score: 83
Period size: 8 Copynumber: 8.0 Consensus size: 8
6089117 TAAAAATATT
6089127 AAAATTAA
1 AAAATTAA
6089135 AAAATTAA
1 AAAATTAA
6089143 AAAATTAA
1 AAAATTAA
*
6089151 AAAATAAA
1 AAAATTAA
6089159 AAAATT-A
1 AAAATTAA
* *
6089166 AAATTTTA
1 AAAATTAA
6089174 AAAATTAA
1 AAAATTAA
*
6089182 AAATTTAA
1 AAAATTAA
6089190 TATTTTAGTC
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
7 6 0.12
8 42 0.88
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (8 bp):
AAAATTAA
Found at i:6089185 original size:16 final size:16
Alignment explanation
Indices: 6089111--6089187 Score: 79
Period size: 16 Copynumber: 5.0 Consensus size: 16
6089101 TAAATCAAAA
*
6089111 TAAAAA-TAAAAATAT
1 TAAAAATTAAAAATTT
*
6089126 T-AAAATTAAAAAATT
1 TAAAAATTAAAAATTT
* * *
6089141 AAAAAATTAAAAAATA
1 TAAAAATTAAAAATTT
*
6089157 AAAAAATT-AAAATTT
1 TAAAAATTAAAAATTT
6089172 TAAAAATTAAAAATTT
1 TAAAAATTAAAAATTT
6089188 AATATTTTAG
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
14 4 0.08
15 20 0.38
16 28 0.54
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
TAAAAATTAAAAATTT
Found at i:6089194 original size:23 final size:23
Alignment explanation
Indices: 6089112--6089196 Score: 91
Period size: 23 Copynumber: 3.7 Consensus size: 23
6089102 AAATCAAAAT
* *
6089112 AAAAATAAAAATATT-AAAATTA
1 AAAAATTAAAATTTTAAAAATTA
* * *
6089134 AAAAATTAAAAAATTAAAAAATAA
1 AAAAATT-AAAATTTTAAAAATTA
6089158 AAAAATTAAAATTTTAAAAATTA
1 AAAAATTAAAATTTTAAAAATTA
* *
6089181 AAAATTTAATATTTTA
1 AAAAATTAAAATTTTA
6089197 GTCCATATTT
Statistics
Matches: 51, Mismatches: 10, Indels: 3
0.80 0.16 0.05
Matches are distributed among these distances:
22 6 0.12
23 32 0.63
24 13 0.25
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (23 bp):
AAAAATTAAAATTTTAAAAATTA
Found at i:6089296 original size:20 final size:16
Alignment explanation
Indices: 6089291--6089369 Score: 51
Period size: 14 Copynumber: 4.9 Consensus size: 16
6089281 AAAATATATG
6089291 TTAAAAATGAAAAAAAA
1 TTAAAAAT-AAAAAAAA
*
6089308 TTAAACAAT-AAAAGAA
1 TTAAA-AATAAAAAAAA
6089324 --AAAAATAAAAAATATA
1 TTAAAAATAAAAAA-A-A
6089340 TGTTAAAAAT-AAAAAAA
1 --TTAAAAATAAAAAAAA
*
6089357 -TAAAATTAAAAAA
1 TTAAAAATAAAAAA
6089370 TAGTGGCGTT
Statistics
Matches: 50, Mismatches: 3, Indels: 20
0.68 0.04 0.27
Matches are distributed among these distances:
13 3 0.06
14 13 0.26
15 6 0.12
16 7 0.14
17 6 0.12
18 4 0.08
19 5 0.10
20 6 0.12
ACGTcount: A:0.75, C:0.01, G:0.04, T:0.20
Consensus pattern (16 bp):
TTAAAAATAAAAAAAA
Found at i:6093611 original size:3 final size:3
Alignment explanation
Indices: 6093603--6093839 Score: 99
Period size: 3 Copynumber: 76.7 Consensus size: 3
6093593 GAATTAAATA
** *
6093603 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TGC TGT TAT CT-T TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT
* * * * *
6093648 TAT TAT TAC TAT TGT TAT TAC TACT TCCAT TAT TTT TAT T-T CTAAC
1 TAT TAT TAT TAT TAT TAT TAT TA-T T--AT TAT TAT TAT TAT -T-AT
* * ** *
6093694 TAT TAT TTT TAT GTAT ATAT TAT TAT T-T ATAT CAT CGT TAT TAT TAC
1 TAT TAT TAT TAT -TAT -TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT
* * * * *
6093741 TAT TAT TAAA TAT CT-T TAT TAT TAC TAT TAT TTT TGT TCCT T-T TAT
1 TAT TAT T-AT TAT -TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT
* * * * *
6093787 TAT TGTT TAT CAT CAT TA- TAT TAT TAT TAT TAC TCT TAT TAT TAT
1 TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
6093832 TAT CAT TA
1 TAT TAT TA
6093840 CTTCTTTTTT
Statistics
Matches: 176, Mismatches: 40, Indels: 36
0.70 0.16 0.14
Matches are distributed among these distances:
2 8 0.05
3 148 0.84
4 17 0.10
5 2 0.01
6 1 0.01
ACGTcount: A:0.28, C:0.09, G:0.03, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:6095997 original size:19 final size:19
Alignment explanation
Indices: 6095975--6096015 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
6095965 TTTATTGATA
6095975 TTTTTA-TATTTAATCTAG
1 TTTTTATTATTTAATCTAG
* *
6095993 TTTTTATTATTTATTTTAG
1 TTTTTATTATTTAATCTAG
6096012 TTTT
1 TTTT
6096016 GATTCTAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.22, C:0.02, G:0.05, T:0.71
Consensus pattern (19 bp):
TTTTTATTATTTAATCTAG
Found at i:6096338 original size:43 final size:43
Alignment explanation
Indices: 6096277--6096374 Score: 160
Period size: 43 Copynumber: 2.3 Consensus size: 43
6096267 TTTTGAATTT
* * *
6096277 ATGACCTTTAGCGGCGTTTGTGGGAAAAGTGCCGCTAAAGGCC
1 ATGACCTTTAGCGACGTTTGTGGGAAAAGCGCAGCTAAAGGCC
*
6096320 ATGACCTTTAGCGACGTTTGTGGGAAAAGCGCAGCTAAAGGTC
1 ATGACCTTTAGCGACGTTTGTGGGAAAAGCGCAGCTAAAGGCC
6096363 ATGACCTTTAGC
1 ATGACCTTTAGC
6096375 TGCGTTTTTT
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 51 1.00
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.24
Consensus pattern (43 bp):
ATGACCTTTAGCGACGTTTGTGGGAAAAGCGCAGCTAAAGGCC
Found at i:6097047 original size:7 final size:7
Alignment explanation
Indices: 6097035--6097111 Score: 82
Period size: 7 Copynumber: 11.0 Consensus size: 7
6097025 TTAAAAAAGT
6097035 AATTGAG
1 AATTGAG
6097042 AATTGAG
1 AATTGAG
6097049 AATTGAG
1 AATTGAG
*
6097056 ACTTGAG
1 AATTGAG
* *
6097063 ACTTGAA
1 AATTGAG
*
6097070 AATTGAA
1 AATTGAG
*
6097077 AATTGAA
1 AATTGAG
*
6097084 AATTGAA
1 AATTGAG
6097091 AATTGAG
1 AATTGAG
*
6097098 AAATGAG
1 AATTGAG
*
6097105 GATTGAG
1 AATTGAG
6097112 GGTCGAGTAT
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
7 63 1.00
ACGTcount: A:0.45, C:0.03, G:0.25, T:0.27
Consensus pattern (7 bp):
AATTGAG
Found at i:6097770 original size:2 final size:2
Alignment explanation
Indices: 6097763--6097791 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
6097753 GCAAATCATG
6097763 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
6097792 TTAAAAAGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6098740 original size:2 final size:2
Alignment explanation
Indices: 6098733--6098768 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
6098723 GTCACCGTAC
* *
6098733 AT AT AT AT AT AC AT AC 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
6098769 GGGTAAACTA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:6099871 original size:20 final size:20
Alignment explanation
Indices: 6099846--6099885 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
6099836 ATATGAAAGA
6099846 ACAAAAGGGAAGTGGATGAT
1 ACAAAAGGGAAGTGGATGAT
6099866 ACAAAAGGGAAGTGGATGAT
1 ACAAAAGGGAAGTGGATGAT
6099886 TTAATTAGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.45, C:0.05, G:0.35, T:0.15
Consensus pattern (20 bp):
ACAAAAGGGAAGTGGATGAT
Found at i:6107511 original size:46 final size:45
Alignment explanation
Indices: 6107451--6107677 Score: 276
Period size: 46 Copynumber: 5.0 Consensus size: 45
6107441 TTTGACATAA
* * * * * *
6107451 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTCTGTCACGC
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCA-TTTCTATCAGGT
* ** *
6107497 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCCCGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTT-CTATCAGGT
* *
6107543 TGCTATGGTATCTTTCAACCATGGTCTTATTCATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTC-TATCAGGT
* *
6107589 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCTATCAGGT
6107634 TGCCATGGTATCTTTCAACCATGGTCTTA-TACATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACT-CATTTC-TATCAG
6107678 AGAGCACACT
Statistics
Matches: 160, Mismatches: 17, Indels: 8
0.86 0.09 0.04
Matches are distributed among these distances:
45 46 0.29
46 114 0.71
ACGTcount: A:0.21, C:0.23, G:0.15, T:0.41
Consensus pattern (45 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCTATCAGGT
Found at i:6108082 original size:24 final size:23
Alignment explanation
Indices: 6108050--6108098 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
6108040 ATCAGGTAGT
6108050 TCACAAAGAACCATATCGGGAAGC
1 TCACAAAGAACC-TATCGGGAAGC
* *
6108074 TCACGAAGAGCCTATCGGGAAGC
1 TCACAAAGAACCTATCGGGAAGC
6108097 TC
1 TC
6108099 CGGATAGCCA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 13 0.57
24 10 0.43
ACGTcount: A:0.35, C:0.27, G:0.24, T:0.14
Consensus pattern (23 bp):
TCACAAAGAACCTATCGGGAAGC
Found at i:6108093 original size:23 final size:23
Alignment explanation
Indices: 6108063--6108156 Score: 75
Period size: 23 Copynumber: 4.0 Consensus size: 23
6108053 CAAAGAACCA
6108063 TATCGGGAAGCTCACGAAGAGCC
1 TATCGGGAAGCTCACGAAGAGCC
* *
6108086 TATCGGGAAGCTC-CGGATAGCC
1 TATCGGGAAGCTCACGAAGAGCC
* * * *
6108108 ATATTTTGGGAAGTTCAAG-CGAGCAC
1 -TA--TCGGGAAGCTCACGAAGAGC-C
*
6108134 TATCGGAAAGCTCACGAAGAGCC
1 TATCGGGAAGCTCACGAAGAGCC
6108157 ATATATCGAA
Statistics
Matches: 53, Mismatches: 12, Indels: 12
0.69 0.16 0.16
Matches are distributed among these distances:
22 7 0.13
23 26 0.49
24 4 0.08
25 14 0.26
26 2 0.04
ACGTcount: A:0.30, C:0.23, G:0.29, T:0.18
Consensus pattern (23 bp):
TATCGGGAAGCTCACGAAGAGCC
Found at i:6108119 original size:48 final size:49
Alignment explanation
Indices: 6108067--6108160 Score: 111
Period size: 48 Copynumber: 1.9 Consensus size: 49
6108057 GAACCATATC
* * * *
6108067 GGGAAGCTCACGAAGAGC-CTATCGGGAAGCTC-CGGATAGCCATATTTT
1 GGGAAGCTCAAG-AGAGCACTATCGGAAAGCTCACGAAGAGCCATATTTT
* *
6108115 GGGAAGTTCAAGCGAGCACTATCGGAAAGCTCACGAAGAGCCATAT
1 GGGAAGCTCAAGAGAGCACTATCGGAAAGCTCACGAAGAGCCATAT
6108161 ATCGAACACT
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
47 4 0.11
48 23 0.61
49 11 0.29
ACGTcount: A:0.31, C:0.22, G:0.29, T:0.18
Consensus pattern (49 bp):
GGGAAGCTCAAGAGAGCACTATCGGAAAGCTCACGAAGAGCCATATTTT
Found at i:6108273 original size:24 final size:23
Alignment explanation
Indices: 6108214--6108274 Score: 70
Period size: 23 Copynumber: 2.6 Consensus size: 23
6108204 GATCACAATC
6108214 TATCGGGACGCTCTGAAGAGCTA
1 TATCGGGACGCTCTGAAGAGCTA
* * *
6108237 TAACGGGAAGCTC-GAGAGGGCTAA
1 TATCGGGACGCTCTGA-AGAGCT-A
6108261 TATCGGGACGCTCT
1 TATCGGGACGCTCT
6108275 TTCGAGCTAT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
22 2 0.07
23 16 0.53
24 12 0.40
ACGTcount: A:0.26, C:0.21, G:0.33, T:0.20
Consensus pattern (23 bp):
TATCGGGACGCTCTGAAGAGCTA
Found at i:6113565 original size:33 final size:31
Alignment explanation
Indices: 6113519--6113580 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 31
6113509 CTTGTCTTTA
* *
6113519 ATTTAATTTAATAATAATAAATAATAAATATCT
1 ATTTAATTAAATAAT--TAAATAAAAAATATCT
*
6113552 ATTTACTTAAATAATTAAATAAAAAATAT
1 ATTTAATTAAATAATTAAATAAAAAATAT
6113581 TACAATTGTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 13 0.50
33 13 0.50
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.40
Consensus pattern (31 bp):
ATTTAATTAAATAATTAAATAAAAAATATCT
Found at i:6114698 original size:26 final size:26
Alignment explanation
Indices: 6114669--6114721 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
6114659 TATACTCAAT
6114669 TTAGATCAATCTCTCCTCTAAAACTC
1 TTAGATCAATCTCTCCTCTAAAACTC
*
6114695 TTAGATCAATCTCTCCTCTGAAACTC
1 TTAGATCAATCTCTCCTCTAAAACTC
6114721 T
1 T
6114722 CCCATTGAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.28, C:0.30, G:0.06, T:0.36
Consensus pattern (26 bp):
TTAGATCAATCTCTCCTCTAAAACTC
Found at i:6114997 original size:30 final size:30
Alignment explanation
Indices: 6114954--6115013 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
6114944 AATTATTTAA
* * *
6114954 TTATTTTATAAAAATAAAATTTAATACTTT
1 TTATTATACAAAAATAAAATTCAATACTTT
6114984 TTATTATACAAAAATAAAATTCAATACTTT
1 TTATTATACAAAAATAAAATTCAATACTTT
6115014 GTTTTTGTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (30 bp):
TTATTATACAAAAATAAAATTCAATACTTT
Found at i:6116968 original size:4 final size:4
Alignment explanation
Indices: 6116959--6116993 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
6116949 TACTCCTCAG
6116959 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTA
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTA
6116994 CAATAATCTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.49
Consensus pattern (4 bp):
GTAT
Found at i:6122392 original size:51 final size:51
Alignment explanation
Indices: 6122331--6122456 Score: 180
Period size: 51 Copynumber: 2.5 Consensus size: 51
6122321 TAATAAAACG
* * * *
6122331 AATACATTTTTTAATATGTGATGTGATGTGATTTTATATAATATTAAAAAT
1 AATATATTTTTTAATATGTGATGTAATGTAATTTTATATAATACTAAAAAT
* *
6122382 AATATCTTTTTTAATATGTGATGTAATGTAATTTTATATAATACTAAGAAT
1 AATATATTTTTTAATATGTGATGTAATGTAATTTTATATAATACTAAAAAT
* *
6122433 AATGTATCTTTTAATATGTGATGT
1 AATATATTTTTTAATATGTGATGT
6122457 TTTAATATGT
Statistics
Matches: 66, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 66 1.00
ACGTcount: A:0.37, C:0.03, G:0.12, T:0.48
Consensus pattern (51 bp):
AATATATTTTTTAATATGTGATGTAATGTAATTTTATATAATACTAAAAAT
Found at i:6122459 original size:15 final size:15
Alignment explanation
Indices: 6122441--6122471 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
6122431 ATAATGTATC
6122441 TTTTAATATGTGATG
1 TTTTAATATGTGATG
6122456 TTTTAATATGTGATG
1 TTTTAATATGTGATG
6122471 T
1 T
6122472 GATGTGATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.19, T:0.55
Consensus pattern (15 bp):
TTTTAATATGTGATG
Found at i:6138636 original size:16 final size:17
Alignment explanation
Indices: 6138606--6138639 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
6138596 AATTTTTTAG
*
6138606 ATTAATTTTTATTTAAA
1 ATTAAATTTTATTTAAA
6138623 ATTAAATTTT-TTTAAA
1 ATTAAATTTTATTTAAA
6138639 A
1 A
6138640 CATAATACAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTAAATTTTATTTAAA
Found at i:6138894 original size:26 final size:27
Alignment explanation
Indices: 6138861--6138921 Score: 74
Period size: 28 Copynumber: 2.3 Consensus size: 27
6138851 TTTTGGATTA
6138861 ATTATTTA-ATATA-AA-TATATATAATT
1 ATTATTTACATATATAATTA-ATATAA-T
6138887 ATTATTTATCATATATAATTAATATAAT
1 ATTATTTA-CATATATAATTAATATAAT
6138915 ATTATTT
1 ATTATTT
6138922 TTTAACATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
26 8 0.26
28 13 0.42
29 8 0.26
30 2 0.06
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (27 bp):
ATTATTTACATATATAATTAATATAAT
Found at i:6144008 original size:12 final size:14
Alignment explanation
Indices: 6143991--6144022 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
6143981 ATAACGTACT
6143991 AAATTAT-GTA-AA
1 AAATTATAGTATAA
6144003 AAATTATAGTATAA
1 AAATTATAGTATAA
6144017 AAATTA
1 AAATTA
6144023 AATTTCAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.39
13 3 0.17
14 8 0.44
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.34
Consensus pattern (14 bp):
AAATTATAGTATAA
Found at i:6145773 original size:25 final size:25
Alignment explanation
Indices: 6145740--6145787 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
6145730 TTAAATTAAC
6145740 TATTATATATTA-CTTATTTTAAAAT
1 TATTATATA-TACCTTATTTTAAAAT
*
6145765 TATTTTATATACCTTATTTTAAA
1 TATTATATATACCTTATTTTAAA
6145788 CCCATTTTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 2 0.10
25 19 0.90
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (25 bp):
TATTATATATACCTTATTTTAAAAT
Found at i:6149118 original size:44 final size:44
Alignment explanation
Indices: 6149068--6149157 Score: 180
Period size: 44 Copynumber: 2.0 Consensus size: 44
6149058 GTGACTCGTT
6149068 ATATGTTTCACTTTCATAACCTGTCTACATCTGCTACCGATACC
1 ATATGTTTCACTTTCATAACCTGTCTACATCTGCTACCGATACC
6149112 ATATGTTTCACTTTCATAACCTGTCTACATCTGCTACCGATACC
1 ATATGTTTCACTTTCATAACCTGTCTACATCTGCTACCGATACC
6149156 AT
1 AT
6149158 CTCTTATTCT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.26, C:0.29, G:0.09, T:0.37
Consensus pattern (44 bp):
ATATGTTTCACTTTCATAACCTGTCTACATCTGCTACCGATACC
Found at i:6152984 original size:27 final size:27
Alignment explanation
Indices: 6152954--6153042 Score: 106
Period size: 27 Copynumber: 3.3 Consensus size: 27
6152944 TTCAAAGAGC
* *
6152954 CACTATCACTGAGTTGCATTGAAGTGT
1 CACTATCACTGACTTGCATCGAAGTGT
* * *
6152981 CACTATCATTGACTTGCACCAAAGTGT
1 CACTATCACTGACTTGCATCGAAGTGT
* * *
6153008 CATTATCACTAATTTGCATCGAAGTGT
1 CACTATCACTGACTTGCATCGAAGTGT
6153035 CACTATCA
1 CACTATCA
6153043 TTATGCACGC
Statistics
Matches: 50, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 50 1.00
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.33
Consensus pattern (27 bp):
CACTATCACTGACTTGCATCGAAGTGT
Found at i:6165840 original size:19 final size:20
Alignment explanation
Indices: 6165816--6165853 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
6165806 GAAACTCGCA
6165816 AAGGAAA-AAAAAAATTAAT
1 AAGGAAATAAAAAAATTAAT
*
6165835 AAGGAAATAAAAACATTAA
1 AAGGAAATAAAAAAATTAA
6165854 AAAAGAAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.71, C:0.03, G:0.11, T:0.16
Consensus pattern (20 bp):
AAGGAAATAAAAAAATTAAT
Found at i:6169688 original size:27 final size:27
Alignment explanation
Indices: 6169658--6169712 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
6169648 ATTTTTTTAT
6169658 CACAACGAAAAATTTAAATTTTGAAAA
1 CACAACGAAAAATTTAAATTTTGAAAA
6169685 CACAACGAAAAATTTAAATTTTGAAAA
1 CACAACGAAAAATTTAAATTTTGAAAA
6169712 C
1 C
6169713 TAAGTCAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.55, C:0.13, G:0.07, T:0.25
Consensus pattern (27 bp):
CACAACGAAAAATTTAAATTTTGAAAA
Found at i:6176720 original size:24 final size:24
Alignment explanation
Indices: 6176567--6176725 Score: 207
Period size: 24 Copynumber: 6.8 Consensus size: 24
6176557 GAGGCATGCT
*
6176567 CAGCAACAACAGCAGCAGCAACAA
1 CAGCAACAGCAGCAGCAGCAACAA
* * *
6176591 CAACAACAGCAGCA--A-CAGCAG
1 CAGCAACAGCAGCAGCAGCAACAA
*
6176612 CAGCAGCAGCAGCAGCAGCAACAA
1 CAGCAACAGCAGCAGCAGCAACAA
6176636 CAGCAACAGCAGCAGCAGCAACAA
1 CAGCAACAGCAGCAGCAGCAACAA
6176660 CAGCAACAGCAGCAGCAGCAACAA
1 CAGCAACAGCAGCAGCAGCAACAA
* * *
6176684 CAACAACAACAGCAACAGCAACAA
1 CAGCAACAGCAGCAGCAGCAACAA
* *
6176708 CAGCAGCCGCAGCAGCAG
1 CAGCAACAGCAGCAGCAG
6176726 TCTCCCCAGC
Statistics
Matches: 115, Mismatches: 17, Indels: 6
0.83 0.12 0.04
Matches are distributed among these distances:
21 16 0.14
22 1 0.01
23 1 0.01
24 97 0.84
ACGTcount: A:0.46, C:0.34, G:0.20, T:0.00
Consensus pattern (24 bp):
CAGCAACAGCAGCAGCAGCAACAA
Found at i:6176738 original size:3 final size:3
Alignment explanation
Indices: 6176576--6176725 Score: 120
Period size: 3 Copynumber: 50.0 Consensus size: 3
6176566 TCAGCAACAA
* * * * *
6176576 CAG CAG CAG CAA CAA CAA CAA CAG CAG CAA CAG CAG CAG CAG CAG CAG
1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG
* * * * * *
6176624 CAG CAG CAA CAA CAG CAA CAG CAG CAG CAG CAA CAA CAG CAA CAG CAG
1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG
* * * * * * * * *
6176672 CAG CAG CAA CAA CAA CAA CAA CAG CAA CAG CAA CAA CAG CAG CCG CAG
1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG
6176720 CAG CAG
1 CAG CAG
6176726 TCTCCCCAGC
Statistics
Matches: 127, Mismatches: 20, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 127 1.00
ACGTcount: A:0.45, C:0.34, G:0.21, T:0.00
Consensus pattern (3 bp):
CAG
Found at i:6177517 original size:13 final size:14
Alignment explanation
Indices: 6177484--6177530 Score: 71
Period size: 14 Copynumber: 3.4 Consensus size: 14
6177474 GGTAGGTTTG
6177484 TTTGATCTCTTTCA
1 TTTGATCTCTTTCA
6177498 TTTGATCTC-TT-A
1 TTTGATCTCTTTCA
6177510 TATTGATCTCTTTCA
1 T-TTGATCTCTTTCA
6177525 TTTGAT
1 TTTGAT
6177531 GCTTCTCTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
12 2 0.07
13 10 0.33
14 16 0.53
15 2 0.07
ACGTcount: A:0.17, C:0.17, G:0.09, T:0.57
Consensus pattern (14 bp):
TTTGATCTCTTTCA
Found at i:6178495 original size:6 final size:6
Alignment explanation
Indices: 6178484--6178534 Score: 56
Period size: 6 Copynumber: 9.2 Consensus size: 6
6178474 TGGCTCAGTT
* *
6178484 GCAACA GCAACA G---CA GCAACT GCAACA ACAACA GCAACA GCAACA
1 GCAACA GCAACA GCAACA GCAACA GCAACA GCAACA GCAACA GCAACA
6178529 G-AACA G
1 GCAACA G
6178535 TAGCTCACAG
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
3 3 0.08
5 5 0.13
6 30 0.79
ACGTcount: A:0.49, C:0.31, G:0.18, T:0.02
Consensus pattern (6 bp):
GCAACA
Found at i:6184290 original size:2 final size:2
Alignment explanation
Indices: 6184285--6184311 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
6184275 TACCTTAATA
6184285 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
6184312 AATAACTGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6187687 original size:40 final size:40
Alignment explanation
Indices: 6187624--6187704 Score: 135
Period size: 40 Copynumber: 2.0 Consensus size: 40
6187614 TTTTATGCTT
*
6187624 GTTTTGCTATATGCAACTCTGTAATTATCAAAGAACAAAG
1 GTTTTACTATATGCAACTCTGTAATTATCAAAGAACAAAG
* *
6187664 GTTTTACTATATGCAGCTTTGTAATTATCAAAGAACAAAG
1 GTTTTACTATATGCAACTCTGTAATTATCAAAGAACAAAG
6187704 G
1 G
6187705 GTTGTCTACA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (40 bp):
GTTTTACTATATGCAACTCTGTAATTATCAAAGAACAAAG
Found at i:6188050 original size:52 final size:52
Alignment explanation
Indices: 6187972--6188071 Score: 155
Period size: 52 Copynumber: 1.9 Consensus size: 52
6187962 AAAAATTGGT
* * * *
6187972 GTAAATTACTGAATAATCTGACAATTACATATAGTGTGCCATATGTACTGGC
1 GTAAATAACGGAATAACCTGACAATTACATATAGTATGCCATATGTACTGGC
*
6188024 GTAAATAACGGAATAACCTGACAATTACATATGGTATGCCATATGTAC
1 GTAAATAACGGAATAACCTGACAATTACATATAGTATGCCATATGTAC
6188072 CTTATACTAG
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 43 1.00
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.30
Consensus pattern (52 bp):
GTAAATAACGGAATAACCTGACAATTACATATAGTATGCCATATGTACTGGC
Done.