Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001711.1 Hibiscus syriacus cultivar Beakdansim tig00003454_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 4148933
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 13
Found at i:3462780 original size:33 final size:33
Alignment explanation
Indices: 3462631--3462780 Score: 118
Period size: 31 Copynumber: 4.6 Consensus size: 33
3462621 CTTTATTTAT
*
3462631 TTATTTTTCTCTCTTTTTCCTTCTTTT-TTTCTCTT
1 TTATTTTTCTCT-TTTTT-C-TCTTTTCTTTCTCTC
* * *
3462666 TCTATTTTTCTTATTTTTTTCTTTTTTCTTT-TTTC
1 T-TATTTTTC-T-CTTTTTTCTCTTTTCTTTCTCTC
* *
3462701 -T-TTTTT-TCTTTTTTCTTTTTTCTTTCTTTC
1 TTATTTTTCTCTTTTTTCTCTTTTCTTTCTCTC
*
3462731 TT-TTTTTCT-TTCTTTCTCTTTTCTTT-TCTC
1 TTATTTTTCTCTTTTTTCTCTTTTCTTTCTCTC
3462761 TTATTTTTCTCTTATTTTCT
1 TTATTTTTCTCTT-TTTTCT
3462781 ACTTCAAGTG
Statistics
Matches: 96, Mismatches: 9, Indels: 22
0.76 0.07 0.17
Matches are distributed among these distances:
29 17 0.18
30 10 0.10
31 28 0.29
32 8 0.08
33 6 0.06
35 8 0.08
36 12 0.12
37 6 0.06
38 1 0.01
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.78
Consensus pattern (33 bp):
TTATTTTTCTCTTTTTTCTCTTTTCTTTCTCTC
Found at i:3475602 original size:3 final size:3
Alignment explanation
Indices: 3475594--3475629 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
3475584 GTAAATAATT
*
3475594 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAG TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3475630 AGACCCAAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:3478660 original size:14 final size:14
Alignment explanation
Indices: 3478641--3478669 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
3478631 CGACTCGCCC
3478641 CGGGGTACGACTCA
1 CGGGGTACGACTCA
3478655 CGGGGTACGACTCA
1 CGGGGTACGACTCA
3478669 C
1 C
3478670 ATTCAGCAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.31, G:0.34, T:0.14
Consensus pattern (14 bp):
CGGGGTACGACTCA
Found at i:3478750 original size:2 final size:2
Alignment explanation
Indices: 3478743--3478794 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
3478733 TCCCATGAAG
3478743 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3478785 AT AT AT AT AT
1 AT AT AT AT AT
3478795 GTGTTTCATA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3487914 original size:40 final size:40
Alignment explanation
Indices: 3487788--3488013 Score: 129
Period size: 40 Copynumber: 5.7 Consensus size: 40
3487778 CATAAATTTA
* * * * *
3487788 GGTGTGTACCTCATACAATACATCACATCGCTTATAATTG
1 GGTGTGTACCCCGTACAATACATCACATTGCTTGTAGTTG
* * ** * * *
3487828 GGTGTATATCATGTACAATACATCACCACTTTC-T-TATTTA
1 GGTGTGTACCCCGTACAATACATCA-CA-TTGCTTGTAGTTG
* * *
3487868 GATGTGTACCCCGTACGATACATCATATTGCTTGTAGTTG
1 GGTGTGTACCCCGTACAATACATCACATTGCTTGTAGTTG
** ** * * * *
3487908 GGTGTGTGTCTTGTACAATACATCACCA--CCTTCATATTTA
1 GGTGTGTACCCCGTACAATACATCA-CATTGCTT-GTAGTTG
* * *
3487948 GATGTGTACCCCATATAATACATCAGC-TTGCTTGTAGTTG
1 GGTGTGTACCCCGTACAATACATCA-CATTGCTTGTAGTTG
*
3487988 GGTGTGTATCCCGTACAATACATCAC
1 GGTGTGTACCCCGTACAATACATCAC
3488014 CACCTTTATA
Statistics
Matches: 132, Mismatches: 46, Indels: 17
0.68 0.24 0.09
Matches are distributed among these distances:
38 3 0.02
39 6 0.05
40 114 0.86
41 7 0.05
42 2 0.02
ACGTcount: A:0.27, C:0.22, G:0.17, T:0.35
Consensus pattern (40 bp):
GGTGTGTACCCCGTACAATACATCACATTGCTTGTAGTTG
Found at i:3487923 original size:80 final size:80
Alignment explanation
Indices: 3487783--3488094 Score: 362
Period size: 80 Copynumber: 3.9 Consensus size: 80
3487773 CTACTCATAA
* * * * * * **
3487783 ATTTAGGTGTGTACCTCATACAATACATCACATCGCTTATAATTGGGTGTATATCATGTACAATA
1 ATTTAGATGTGTACCCCATACAATACATCATATTGCTTATAGTTGGGTGTGTATCCCGTACAATA
*
3487848 CATCACCACTTTCTT
66 CATCACCACTTTCAT
* * * * **
3487863 ATTTAGATGTGTACCCCGTACGATACATCATATTGCTTGTAGTTGGGTGTGTGTCTTGTACAATA
1 ATTTAGATGTGTACCCCATACAATACATCATATTGCTTATAGTTGGGTGTGTATCCCGTACAATA
*
3487928 CATCACCACCTTCAT
66 CATCACCACTTTCAT
* ** *
3487943 ATTTAGATGTGTACCCCATATAATACATCAGCTTGCTTGTAGTTGGGTGTGTATCCCGTACAATA
1 ATTTAGATGTGTACCCCATACAATACATCATATTGCTTATAGTTGGGTGTGTATCCCGTACAATA
3488008 CATCACCACCTTT-AT
66 CATCACCA-CTTTCAT
* * *
3488023 ATTTAGATGTCTA-CCC-TACATGATACATCATCTTGC-TATAGTTGGGTGTGTATCCCATACAA
1 ATTTAGATGTGTACCCCATACA--ATACATCATATTGCTTATAGTTGGGTGTGTATCCCGTACAA
3488085 TACATCACCA
64 TACATCACCA
3488095 TTTTATTTAA
Statistics
Matches: 202, Mismatches: 27, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
78 3 0.01
79 37 0.18
80 159 0.79
81 3 0.01
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.35
Consensus pattern (80 bp):
ATTTAGATGTGTACCCCATACAATACATCATATTGCTTATAGTTGGGTGTGTATCCCGTACAATA
CATCACCACTTTCAT
Found at i:3491088 original size:74 final size:79
Alignment explanation
Indices: 3490904--3491161 Score: 240
Period size: 74 Copynumber: 3.3 Consensus size: 79
3490894 TAATTGGGTA
* * * * * * ** * * **
3490904 TGTATCTCGTACACTACATCACCACTTTCTTATTTAGATATGTACCCCGTACGATAAAAAATCTT
1 TGTATCCCGTACAATATATCACCACCTTCATATTTAGATGTGTACCCCACATGATACATCATCTT
* *
3490969 G-TTTGAAGTTGGGTG
66 GCTAT--AGTTAGGTG
** * *** *
3490984 TGTATCCTATACAATACATCACCACCTTCATATTTAGATGTGTACCCTGTATGATGCATCATCTT
1 TGTATCCCGTACAATATATCACCACCTTCATATTTAGATGTGTACCCCACATGATACATCATCTT
3491049 GC-AT-G-T-GGT-
66 GCTATAGTTAGGTG
*
3491058 TGTATCCCGTACAATATATCACCAGCTTCATATTTAGATGTGTACCCCACATGATACATCATCTT
1 TGTATCCCGTACAATATATCACCACCTTCATATTTAGATGTGTACCCCACATGATACATCATCTT
3491123 GCTATAGTTAGGTG
66 GCTATAGTTAGGTG
* *
3491137 TGTATCCCGTATAATATATAACCAC
1 TGTATCCCGTACAATATATCACCAC
3491162 TTTATTTAAA
Statistics
Matches: 147, Mismatches: 25, Indels: 13
0.79 0.14 0.07
Matches are distributed among these distances:
74 59 0.40
75 5 0.03
76 2 0.01
77 2 0.01
78 3 0.02
79 22 0.15
80 54 0.37
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.35
Consensus pattern (79 bp):
TGTATCCCGTACAATATATCACCACCTTCATATTTAGATGTGTACCCCACATGATACATCATCTT
GCTATAGTTAGGTG
Found at i:3491601 original size:80 final size:80
Alignment explanation
Indices: 3491462--3491850 Score: 385
Period size: 79 Copynumber: 4.9 Consensus size: 80
3491452 GTTGACGTAA
* *
3491462 TTAGGTGTGTACCCCGTATGATACATCA-CATTGCTTATAATTGGGTGTGTATCCCATACAATAC
1 TTAGATGTGTACCCCGTATGATACATCATC-TTGCTTATAGTTGGGTGTGTATCCCATACAATAC
* *
3491526 ATCACCACTTTCTTAT
65 ATCACCACCTTCATAT
* * * * * ** *
3491542 TTAGATGTGTACCCCTTATTATACATCATCTTTCTTGTAGTTGGGTGTATATCTTATACAATAGA
1 TTAGATGTGTACCCCGTATGATACATCATCTTGCTTATAGTTGGGTGTGTATCCCATACAATACA
* *
3491607 TTACCATCTTCATAT
66 TCACCACCTTCATAT
* * * * * *
3491622 CTAGATGTATACCCCGT-TGATATATTATCTTGCTTGTAGTTGGGTGTGTATCCCGTACAATACA
1 TTAGATGTGTACCCCGTATGATACATCATCTTGCTTATAGTTGGGTGTGTATCCCATACAATACA
*
3491686 TCATCACCTTCATAT
66 TCACCACCTTCATAT
* * * ** * * **
3491701 TTAAATCTGTACACCACACGATACATAATCTTGC-TATAGTTGGGTGTGTATCCTGTACAATACA
1 TTAGATGTGTACCCCGTATGATACATCATCTTGCTTATAGTTGGGTGTGTATCCCATACAATACA
3491765 TCACCACCTTCATAT
66 TCACCACCTTCATAT
** * ** *
3491780 TTAGATGTGTACCCAC--ACAATAAATCATCTTGC-TATAGTTGGGTGTGTATCCCGCACAATCC
1 TTAGATGTGTACCC-CGTATGATACATCATCTTGCTTATAGTTGGGTGTGTATCCCATACAAT-A
3491842 CATCACCAC
64 CATCACCAC
3491851 TTTATTTAAA
Statistics
Matches: 254, Mismatches: 51, Indels: 9
0.81 0.16 0.03
Matches are distributed among these distances:
78 39 0.15
79 122 0.48
80 92 0.36
81 1 0.00
ACGTcount: A:0.27, C:0.23, G:0.14, T:0.36
Consensus pattern (80 bp):
TTAGATGTGTACCCCGTATGATACATCATCTTGCTTATAGTTGGGTGTGTATCCCATACAATACA
TCACCACCTTCATAT
Found at i:3491765 original size:39 final size:39
Alignment explanation
Indices: 3491714--3491839 Score: 105
Period size: 39 Copynumber: 3.2 Consensus size: 39
3491704 AATCTGTACA
*
3491714 CCACACGATACATAATCTTGCTATAGTTGGGTGTGTATC
1 CCACACAATACATAATCTTGCTATAGTTGGGTGTGTATC
*** * * * *
3491753 CTGTACAATACATCACCACCTT-C-ATATTTAGATGTGTA-C
1 CCACACAATACAT-A--ATCTTGCTATAGTTGGGTGTGTATC
* *
3491792 CCACACAATAAATCATCTTGCTATAGTTGGGTGTGTATC
1 CCACACAATACATAATCTTGCTATAGTTGGGTGTGTATC
*
3491831 CCGCACAAT
1 CCACACAAT
3491840 CCCATCACCA
Statistics
Matches: 63, Mismatches: 18, Indels: 12
0.68 0.19 0.13
Matches are distributed among these distances:
36 4 0.06
37 1 0.02
38 12 0.19
39 28 0.44
40 13 0.21
41 1 0.02
42 4 0.06
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.32
Consensus pattern (39 bp):
CCACACAATACATAATCTTGCTATAGTTGGGTGTGTATC
Found at i:3495323 original size:26 final size:26
Alignment explanation
Indices: 3495268--3495324 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
3495258 TACTTATATA
** *
3495268 ATATAGCTTTTGAAAATATATGTAAT
1 ATATAGCTTTTGAAAATATACATAAC
3495294 ATATA-CTATTTGAAAATATACATAAC
1 ATATAGCT-TTTGAAAATATACATAAC
3495320 ATATA
1 ATATA
3495325 TAATATATAG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 2 0.07
26 25 0.93
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.39
Consensus pattern (26 bp):
ATATAGCTTTTGAAAATATACATAAC
Found at i:3495357 original size:33 final size:33
Alignment explanation
Indices: 3495284--3495389 Score: 105
Period size: 35 Copynumber: 3.3 Consensus size: 33
3495274 CTTTTGAAAA
* * * *
3495284 TATATGTAATATATACTATTTGAAAATATACATAA
1 TATATATAATATATAGTTTTTGAAAATAT--ATAG
*
3495319 CATATATAATATATAGTTTTTGAAAATATATAG
1 TATATATAATATATAGTTTTTGAAAATATATAG
*
3495352 TATATAT-AT-TATAG-TTTTGAAAAAATAT-G
1 TATATATAATATATAGTTTTTGAAAATATATAG
3495381 -ATATATAAT
1 TATATATAAT
3495390 TTTTTAATAT
Statistics
Matches: 63, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
28 6 0.10
29 3 0.05
30 13 0.21
31 5 0.08
32 2 0.03
33 9 0.14
35 25 0.40
ACGTcount: A:0.47, C:0.03, G:0.08, T:0.42
Consensus pattern (33 bp):
TATATATAATATATAGTTTTTGAAAATATATAG
Found at i:3495384 original size:28 final size:32
Alignment explanation
Indices: 3495320--3495387 Score: 90
Period size: 30 Copynumber: 2.2 Consensus size: 32
3495310 TATACATAAC
*
3495320 ATATATAATATATAGTTTTTGAAAATATATAGT
1 ATATAT-ATATATAGTTTTTGAAAAAATATAGT
3495353 ATATATAT-TATAG-TTTTGAAAAAATAT-G-
1 ATATATATATATAGTTTTTGAAAAAATATAGT
3495381 ATATATA
1 ATATATA
3495388 ATTTTTTAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
28 7 0.21
29 1 0.03
30 13 0.38
31 5 0.15
32 2 0.06
33 6 0.18
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.44
Consensus pattern (32 bp):
ATATATATATATAGTTTTTGAAAAAATATAGT
Found at i:3495387 original size:23 final size:22
Alignment explanation
Indices: 3495353--3495432 Score: 61
Period size: 23 Copynumber: 3.4 Consensus size: 22
3495343 AATATATAGT
3495353 ATATATATTATAGTTTTGAAAAA
1 ATATATA-TATAGTTTTGAAAAA
* * *
3495376 ATATGATATATAATTTTTTAATATAT
1 ATAT-ATATAT-AGTTTTGAA-A-AA
*
3495402 ATATATATATAGTTTTTGAAAAT
1 ATATATATATAG-TTTTGAAAAA
*
3495425 ATTTATAT
1 ATATATAT
3495433 GTAATCTAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
23 16 0.35
24 12 0.26
25 13 0.28
26 5 0.11
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (22 bp):
ATATATATATAGTTTTGAAAAA
Found at i:3495409 original size:25 final size:25
Alignment explanation
Indices: 3495352--3495432 Score: 80
Period size: 25 Copynumber: 3.4 Consensus size: 25
3495342 AAATATATAG
*
3495352 TATATATAT-TAT-AGTTTTGAAAA
1 TATATATATATATAATTTTTGAAAA
* *
3495375 -A-ATATGATATATAATTTTTTAATA
1 TATATAT-ATATATAATTTTTGAAAA
*
3495399 TATATATATATATAGTTTTTGAAAA
1 TATATATATATATAATTTTTGAAAA
*
3495424 TATTTATAT
1 TATATATAT
3495433 GTAATCTAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 8
0.75 0.11 0.13
Matches are distributed among these distances:
21 4 0.09
22 3 0.07
23 3 0.07
24 8 0.17
25 24 0.52
26 4 0.09
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (25 bp):
TATATATATATATAATTTTTGAAAA
Found at i:3497158 original size:20 final size:20
Alignment explanation
Indices: 3497133--3497171 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
3497123 CTTTAGTGAA
3497133 TCCAATTATAATAAGGTATG
1 TCCAATTATAATAAGGTATG
3497153 TCCAATTATAATAAGGTAT
1 TCCAATTATAATAAGGTAT
3497172 ACCCATGTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.41, C:0.10, G:0.13, T:0.36
Consensus pattern (20 bp):
TCCAATTATAATAAGGTATG
Found at i:3499090 original size:21 final size:21
Alignment explanation
Indices: 3499066--3499112 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
3499056 AAGGTCGAAT
*
3499066 GGTTTGTGTACCTAAGGCCAG
1 GGTTTATGTACCTAAGGCCAG
3499087 GGTTTATGTACCTAAGGCCAG
1 GGTTTATGTACCTAAGGCCAG
3499108 GGTTT
1 GGTTT
3499113 TTATAATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.19, C:0.17, G:0.32, T:0.32
Consensus pattern (21 bp):
GGTTTATGTACCTAAGGCCAG
Found at i:3501182 original size:20 final size:21
Alignment explanation
Indices: 3501134--3501186 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
3501124 ATGCCAAAAT
* *
3501134 GGTATCGGTACCATAGTATATA
1 GGTATCGATACCATAG-ATAGA
*
3501156 AGTATCGATACCATAG-TAGA
1 GGTATCGATACCATAGATAGA
3501176 GGTATCGATAC
1 GGTATCGATAC
3501187 TATGGAGTCT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 13 0.48
22 14 0.52
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.28
Consensus pattern (21 bp):
GGTATCGATACCATAGATAGA
Found at i:3501684 original size:55 final size:54
Alignment explanation
Indices: 3501505--3501745 Score: 250
Period size: 54 Copynumber: 4.4 Consensus size: 54
3501495 ATTATTGAAT
*
3501505 GGCACTATATGTGTGCAAAAGCTAAGAAATTCATAATAAGTTTATGAATTTTTGTATG
1 GGCACT-T-TGTGTGC-AAA-CTAAGAAATTCATAATAAGTTTATGAATTTTCGTATG
* *
3501563 GGCACTTTGTATGCAAACTAAGAAATTCAAAATAAGTTTATGAATTTTCGTATG
1 GGCACTTTGTGTGCAAACTAAGAAATTCATAATAAGTTTATGAATTTTCGTATG
* * * *
3501617 GGCACTTTGTGTGCAAAACAAAGAAATTCATAATAAGTTTATGAATTTCCATATT
1 GGCACTTTGTGTGC-AAACTAAGAAATTCATAATAAGTTTATGAATTTTCGTATG
* * ** * * * * * *
3501672 GGTAGTGGGTGTGCAACCCACGTAAATT-ATAATAAGTTTGTGAATTATCGTATT
1 GGCACTTTGTGTGCAAACTAAG-AAATTCATAATAAGTTTATGAATTTTCGTATG
**
3501726 GGCACTACGTGTGCAAACTA
1 GGCACTTTGTGTGCAAACTA
3501746 TAGAGTTTAT
Statistics
Matches: 155, Mismatches: 26, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
54 89 0.57
55 53 0.34
56 6 0.04
57 1 0.01
58 6 0.04
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.34
Consensus pattern (54 bp):
GGCACTTTGTGTGCAAACTAAGAAATTCATAATAAGTTTATGAATTTTCGTATG
Found at i:3501706 original size:109 final size:110
Alignment explanation
Indices: 3501505--3501742 Score: 264
Period size: 109 Copynumber: 2.2 Consensus size: 110
3501495 ATTATTGAAT
* *** *
3501505 GGCACTATATGTGTGCAAAAGCTAAGAAATTCATAATAAGTTTATGAATTTTTGTATGGGCACTT
1 GGCACT-T-TGTGTGCAAAAGCAAAGAAATTCATAATAAGTTTATGAATTTCCATATGGGCACTG
* * *
3501570 TGTATGCAAACTAAGAAATTCAAAATAAGTTTATGAATTTTCGTATG
64 GGTATGCAAACCAAGAAATTCAAAATAAGTTTATGAATTATCGTATG
* * *
3501617 GGCACTTTGTGTGCAAAA-CAAAGAAATTCATAATAAGTTTATGAATTTCCATATTGGTAGTGGG
1 GGCACTTTGTGTGCAAAAGCAAAGAAATTCATAATAAGTTTATGAATTTCCATATGGGCACTGGG
* * * * * *
3501681 TGTGCAACCCACGTAAATT-ATAATAAGTTTGTGAATTATCGTATT
66 TATGCAAACCAAG-AAATTCAAAATAAGTTTATGAATTATCGTATG
**
3501726 GGCACTACGTGTGCAAA
1 GGCACTTTGTGTGCAAA
3501743 CTATAGAGTT
Statistics
Matches: 106, Mismatches: 19, Indels: 5
0.82 0.15 0.04
Matches are distributed among these distances:
109 83 0.78
110 16 0.15
111 1 0.01
112 6 0.06
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.34
Consensus pattern (110 bp):
GGCACTTTGTGTGCAAAAGCAAAGAAATTCATAATAAGTTTATGAATTTCCATATGGGCACTGGG
TATGCAAACCAAGAAATTCAAAATAAGTTTATGAATTATCGTATG
Found at i:3502036 original size:46 final size:45
Alignment explanation
Indices: 3501961--3502047 Score: 147
Period size: 46 Copynumber: 1.9 Consensus size: 45
3501951 TTAGATGAAG
*
3501961 AACAATGCATAATTGCATGAAAGGATGCCATAAATGAAAATGTAT
1 AACAATGCATAATTGCATGAAAGGATGCCACAAATGAAAATGTAT
*
3502006 AACAATGCATAATTGGCATGTAAGGATGCCACAAATGAAAAT
1 AACAATGCATAATT-GCATGAAAGGATGCCACAAATGAAAAT
3502048 ACATAATGAT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
45 14 0.36
46 25 0.64
ACGTcount: A:0.46, C:0.13, G:0.18, T:0.23
Consensus pattern (45 bp):
AACAATGCATAATTGCATGAAAGGATGCCACAAATGAAAATGTAT
Found at i:3506438 original size:18 final size:18
Alignment explanation
Indices: 3506417--3506459 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
3506407 GTTATTTTTA
*
3506417 AAATAAAAGATAA-CAATT
1 AAATAAAAGA-AATCAAAT
3506435 AAATAAAAGAAATCAAAT
1 AAATAAAAGAAATCAAAT
3506453 AAATAAA
1 AAATAAA
3506460 TAAATTAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 2 0.09
18 21 0.91
ACGTcount: A:0.72, C:0.05, G:0.05, T:0.19
Consensus pattern (18 bp):
AAATAAAAGAAATCAAAT
Found at i:3514424 original size:16 final size:18
Alignment explanation
Indices: 3514394--3514427 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
3514384 ATTAAAAAGG
3514394 TATAATAAAATAAATAAT
1 TATAATAAAATAAATAAT
3514412 TATAA-AAAA-AAATAAT
1 TATAATAAAATAAATAAT
3514428 AAATATTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (18 bp):
TATAATAAAATAAATAAT
Found at i:3514499 original size:18 final size:18
Alignment explanation
Indices: 3514478--3514517 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
3514468 ATTGTTTTTA
* *
3514478 AAATAAAAGATAACAATT
1 AAATAAAAGAAAACAAAT
3514496 AAATAAAAGAAAACAAAT
1 AAATAAAAGAAAACAAAT
3514514 AAAT
1 AAAT
3514518 TAATTAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.72, C:0.05, G:0.05, T:0.17
Consensus pattern (18 bp):
AAATAAAAGAAAACAAAT
Found at i:3515082 original size:12 final size:12
Alignment explanation
Indices: 3515067--3515093 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
3515057 TACCTAAAAT
3515067 AATAATATTCTA
1 AATAATATTCTA
3515079 AATAATATTCTA
1 AATAATATTCTA
3515091 AAT
1 AAT
3515094 CCTAATTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (12 bp):
AATAATATTCTA
Found at i:3515101 original size:72 final size:77
Alignment explanation
Indices: 3515017--3515208 Score: 243
Period size: 72 Copynumber: 2.6 Consensus size: 77
3515007 TTAAACATCT
* * *
3515017 TAAATCCTAATTAAAACACTTAAAA-CTATTTAAACTAAAATACCT-AAA-ATA-ATAATAT-TC
1 TAAATCCTAATTAAAACACTTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATA
* *
3515077 TAAATAATATTC
66 AAAATAATATCC
3515089 TAAATCCTAATTAAAACAC-TAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATA
1 TAAATCCTAATTAAAACACTTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATA
3515153 AAAATAATATCC
66 AAAATAATATCC
* * * * **
3515165 TAAAACTTAATTAAAATACTCAAAATATATTTAAACTAAAATAC
1 TAAATCCTAATTAAAACACTTAAAACCTATTTAAACTAAAATAC
3515209 AAAGAAAAAT
Statistics
Matches: 103, Mismatches: 11, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
71 5 0.05
72 39 0.38
73 3 0.03
74 2 0.02
75 6 0.06
76 27 0.26
77 21 0.20
ACGTcount: A:0.56, C:0.14, G:0.01, T:0.30
Consensus pattern (77 bp):
TAAATCCTAATTAAAACACTTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATA
AAAATAATATCC
Found at i:3515223 original size:76 final size:75
Alignment explanation
Indices: 3515017--3515243 Score: 232
Period size: 76 Copynumber: 3.1 Consensus size: 75
3515007 TTAAACATCT
* * * **
3515017 TAAATCCTAATTAAAACACTTAAAAC-TATTTAAACTAAAATACCT--AAAATA-ATAATATTCT
1 TAAAACCTAATTAAAACAC-TAAAACATATTTAAACTAAAATACCTAAAAAAAAGATAAAATTAA
*
3515078 AAATAATATTC
65 AAATAATATCC
* * *
3515089 TAAATCCTAATTAAAACACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAA
1 TAAAACCTAATTAAAACACTAAAACATATTTAAACTAAAATACCTAAAAAAAAGATAAAAT-TAA
3515154 AAATAATATCC
65 AAATAATATCC
* * * * * *
3515165 TAAAACTTAATTAAAATACTCAAAATATATTTAAACTAAAATA-C-AAAGAAAAATATAAAGTTT
1 TAAAACCTAATTAAAACACT-AAAACATATTTAAACTAAAATACCTAAA-AAAAAGATAAAATTA
*
3515228 AAAATATTATCC
64 AAAATAATATCC
3515240 TAAA
1 TAAA
3515244 CTTGAGTTTA
Statistics
Matches: 132, Mismatches: 16, Indels: 11
0.83 0.10 0.07
Matches are distributed among these distances:
71 6 0.05
72 38 0.29
74 4 0.03
75 25 0.19
76 39 0.30
77 20 0.15
ACGTcount: A:0.56, C:0.13, G:0.01, T:0.30
Consensus pattern (75 bp):
TAAAACCTAATTAAAACACTAAAACATATTTAAACTAAAATACCTAAAAAAAAGATAAAATTAAA
AATAATATCC
Found at i:3516156 original size:3 final size:3
Alignment explanation
Indices: 3516148--3516192 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
3516138 AAATAATTTT
3516148 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3516193 AGACCCAGAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:3516678 original size:137 final size:137
Alignment explanation
Indices: 3516427--3516718 Score: 311
Period size: 137 Copynumber: 2.1 Consensus size: 137
3516417 CTATCTAAGG
* * * * * * *
3516427 GATGAGGAGATATGGTCAGTCGATGAAATGGTTCCTACGTGATGAGGATGATTATGCATCTTTAG
1 GATGAGGAGATCTGGTCAGTAGATGAAAGGGTTCATACGTGATAAGGATGATTAGGCATATTTAG
* * * * *
3516492 GGATAATGTTGATAACACGGTTTCTACGTGATGAGGACGATTGGATATCTAGGGGTAACATGACT
66 GGATAATGTTGATAACACGATTTCTACGTGATGAAGACGATTAGATATCTAAGGGTAACACGACT
*
3516557 CCTATGT
131 CCTACGT
* ** *
3516564 GATGAGGAGATCTGGTCGGTAGATGCCAGGGTTCATATGTGATAAGGATGATT-GGCCATATTTA
1 GATGAGGAGATCTGGTCAGTAGATGAAAGGGTTCATACGTGATAAGGATGATTAGG-CATATTTA
* * * * * *
3516628 GGGATAATGTTTATAACACGA-TTCTTATGTGATGAAGACG-TCTAGTTATCTAAGGTTGACGCG
65 GGGATAATGTTGATAACACGATTTC-TACGTGATGAAGACGAT-TAGATATCTAAGGGTAACACG
**
3516691 GTTCCTACGT
128 ACTCCTACGT
3516701 GATGAGGAGATCTGGTCA
1 GATGAGGAGATCTGGTCA
3516719 TAGTTGATGA
Statistics
Matches: 126, Mismatches: 26, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
136 5 0.04
137 121 0.96
ACGTcount: A:0.27, C:0.13, G:0.29, T:0.31
Consensus pattern (137 bp):
GATGAGGAGATCTGGTCAGTAGATGAAAGGGTTCATACGTGATAAGGATGATTAGGCATATTTAG
GGATAATGTTGATAACACGATTTCTACGTGATGAAGACGATTAGATATCTAAGGGTAACACGACT
CCTACGT
Found at i:3517464 original size:15 final size:15
Alignment explanation
Indices: 3517427--3517536 Score: 84
Period size: 16 Copynumber: 7.1 Consensus size: 15
3517417 TTTATTTATT
3517427 TTTCTCTTTTTT-TC
1 TTTCTCTTTTTTCTC
*
3517441 CTTCT-TTTTTTCTC
1 TTTCTCTTTTTTCTC
*
3517455 TTTCTCTTTTTTCTTA
1 TTTCTCTTTTTTC-TC
* *
3517471 TTTTTCTTCTTTTTTC
1 TTTCTCTT-TTTTCTC
3517487 TTTCTTTCTTTTTTCT-
1 TTTC--TCTTTTTTCTC
*
3517503 TTCTTTCTTTTTTCT-
1 TT-TCTCTTTTTTCTC
3517518 TTTCTCTTATTTTTCTC
1 TTTCTC-T-TTTTTCTC
3517535 TT
1 TT
3517537 ATTTTCTTCT
Statistics
Matches: 76, Mismatches: 10, Indels: 17
0.74 0.10 0.17
Matches are distributed among these distances:
13 6 0.08
14 13 0.17
15 20 0.26
16 21 0.28
17 12 0.16
18 4 0.05
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTCTCTTTTTTCTC
Found at i:3517465 original size:36 final size:36
Alignment explanation
Indices: 3517425--3517547 Score: 113
Period size: 33 Copynumber: 3.6 Consensus size: 36
3517415 TATTTATTTA
3517425 TTTTTCTCTT-TTTTTCCTTCTTTTTT-TCTCTTTCT
1 TTTTTCTCTTATTTTT-CTTCTTTTTTCTCTCTTTCT
*
3517460 CTTTTT-TCTTATTTTTCTTCTTTTTTCTTTCTTTC-
1 -TTTTTCTCTTATTTTTCTTCTTTTTTCTCTCTTTCT
* * *
3517495 TTTTT-TCTT-TCTTTCTT-TTTTCTTTTCTC-TT-A
1 TTTTTCTCTTATTTTTCTTCTTTT-TTCTCTCTTTCT
3517527 TTTTTCTCTTA-TTTTCTTCTT
1 TTTTTCTCTTATTTTTCTTCTT
3517548 CAAGTGTAAT
Statistics
Matches: 75, Mismatches: 5, Indels: 16
0.78 0.05 0.17
Matches are distributed among these distances:
32 11 0.15
33 22 0.29
34 11 0.15
35 14 0.19
36 17 0.23
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.77
Consensus pattern (36 bp):
TTTTTCTCTTATTTTTCTTCTTTTTTCTCTCTTTCT
Found at i:3517486 original size:56 final size:53
Alignment explanation
Indices: 3517425--3517543 Score: 141
Period size: 56 Copynumber: 2.1 Consensus size: 53
3517415 TATTTATTTA
* *
3517425 TTTTTCTCTTT-TTTTCCTTCTTTTTTTCTCTTTCTCTTTTTTCTTATTTTTCTTCT
1 TTTTTCTCTTTCTTTT--TTCTTTCTTTCT-TTTCTCTTTTCTCTTATTTTTC-TCT
*
3517481 TTTTTCTTTCTTTCTTTTTTCTTTCTTTCTTTTTTCTTTTCTCTTATTTTTCTCT
1 TTTTTC--TCTTTCTTTTTTCTTTCTTTCTTTTCTCTTTTCTCTTATTTTTCTCT
3517536 TATTTTCT
1 T-TTTTCT
3517544 TCTTCAAGTG
Statistics
Matches: 56, Mismatches: 3, Indels: 10
0.81 0.04 0.14
Matches are distributed among these distances:
54 1 0.02
55 4 0.07
56 31 0.55
57 11 0.20
58 5 0.09
59 4 0.07
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.77
Consensus pattern (53 bp):
TTTTTCTCTTTCTTTTTTCTTTCTTTCTTTTCTCTTTTCTCTTATTTTTCTCT
Found at i:3517487 original size:7 final size:7
Alignment explanation
Indices: 3517446--3517530 Score: 84
Period size: 7 Copynumber: 11.9 Consensus size: 7
3517436 TTTTCCTTCT
3517446 TTTTTTC
1 TTTTTTC
*
3517453 TCTTTCTC
1 T-TTTTTC
3517461 TTTTTTC
1 TTTTTTC
*
3517468 -TTATT-
1 TTTTTTC
*
3517473 TTTCTTC
1 TTTTTTC
3517480 TTTTTTC
1 TTTTTTC
3517487 TTTCTTTC
1 TTT-TTTC
3517495 TTTTTTC
1 TTTTTTC
3517502 TTTCTTTC
1 TTT-TTTC
3517510 TTTTTTC
1 TTTTTTC
*
3517517 TTTTCTC
1 TTTTTTC
3517524 TTATTTT
1 TT-TTTT
3517531 TCTCTTATTT
Statistics
Matches: 65, Mismatches: 7, Indels: 11
0.78 0.08 0.13
Matches are distributed among these distances:
6 8 0.12
7 34 0.52
8 23 0.35
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (7 bp):
TTTTTTC
Found at i:3517492 original size:46 final size:48
Alignment explanation
Indices: 3517422--3517518 Score: 137
Period size: 46 Copynumber: 2.0 Consensus size: 48
3517412 CTTTATTTAT
3517422 TTATTTTTCTCTTTTTTTCCTTCTTT-TTTTCTCTTTC-TCTTTTTTC
1 TTATTTTTCTCTTTTTTTCCTTCTTTCTTTTCTCTTTCTTCTTTTTTC
* *
3517468 TTATTTTTCT-TCTTTTTTCTTTCTTTCTTTTTTCTTTCTTTCTTTTTTC
1 TTATTTTTCTCT-TTTTTTCCTTCTTTCTTTTCTCTTTC-TTCTTTTTTC
3517517 TT
1 TT
3517519 TTCTCTTATT
Statistics
Matches: 45, Mismatches: 2, Indels: 5
0.87 0.04 0.10
Matches are distributed among these distances:
45 1 0.02
46 23 0.51
47 10 0.22
49 11 0.24
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (48 bp):
TTATTTTTCTCTTTTTTTCCTTCTTTCTTTTCTCTTTCTTCTTTTTTC
Found at i:3517531 original size:11 final size:10
Alignment explanation
Indices: 3517425--3517543 Score: 76
Period size: 11 Copynumber: 10.7 Consensus size: 10
3517415 TATTTATTTA
3517425 TTTTTCTCTT
1 TTTTTCTCTT
3517435 TTTTTCCTTCTT
1 TTTTT-C-TCTT
3517447 TTTTTCTCTTT
1 TTTTTCTC-TT
*
3517458 CTCTTTTTTCTT
1 -T-TTTTCTCTT
3517470 ATTTTTCTTCTT
1 -TTTTTC-TCTT
*
3517482 TTTTCTTTCTT
1 TTTT-TCTCTT
*
3517493 TCTTTTTTCTT
1 T-TTTTCTCTT
* *
3517504 TCTTTCTTTTT
1 TTTTTC-TCTT
3517515 TCTTTTCTCTT
1 T-TTTTCTCTT
3517526 ATTTTTCTCTT
1 -TTTTTCTCTT
*
3517537 ATTTTCT
1 TTTTTCT
3517544 TCTTCAAGTG
Statistics
Matches: 88, Mismatches: 10, Indels: 22
0.73 0.08 0.18
Matches are distributed among these distances:
10 16 0.18
11 40 0.45
12 26 0.30
13 6 0.07
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.77
Consensus pattern (10 bp):
TTTTTCTCTT
Found at i:3530298 original size:3 final size:3
Alignment explanation
Indices: 3530290--3530325 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
3530280 GTAAATAATT
* *
3530290 TAA TAA TAA TAA TAA TAA TAA TAG TAA TAG TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3530326 AGACCTAGAC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:3533656 original size:2 final size:2
Alignment explanation
Indices: 3533649--3533692 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
3533639 TCCCATGAAG
3533649 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3533691 AT
1 AT
3533693 GCATGTTTCA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3542034 original size:80 final size:79
Alignment explanation
Indices: 3541946--3542212 Score: 342
Period size: 80 Copynumber: 3.4 Consensus size: 79
3541936 CTTATAATTT
** *
3541946 GGTGTATATCATGTACAATACATCACCACTTTCTTATTTAGATGTGTACCCCGTACGATACATCA
1 GGTGTATATCCCGTACAATACATCACCACTTTCATATTTAGATGTGTACCCC-TACGATACATCA
*
3542011 TATTGCTTGTAGTTG
65 TCTTGCTTGTAGTTG
* ** * * *
3542026 GGTATATATCTTGTACAATACATCACCACCTTCATATTTATATGTGTACCCCATACAATACATCA
1 GGTGTATATCCCGTACAATACATCACCACTTTCATATTTAGATGTGTACCCC-TACGATACATCA
3542091 TCTTGCTTGTAGTTG
65 TCTTGCTTGTAGTTG
*
3542106 GGTGTGTATCCCGTACAATACATCACCACCTTT-ATATTTAGATGTGTA-CCCTACATGATACAT
1 GGTGTATATCCCGTACAATACATCACCA-CTTTCATATTTAGATGTGTACCCCTAC--GATACAT
*
3542169 CATCTTGC-TATAGTTG
63 CATCTTGCTTGTAGTTG
* *
3542185 GGTGTGTATCCCATACAATACATCACCA
1 GGTGTATATCCCGTACAATACATCACCA
3542213 TTTTATTTAA
Statistics
Matches: 167, Mismatches: 17, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
78 3 0.02
79 37 0.22
80 124 0.74
81 3 0.02
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.36
Consensus pattern (79 bp):
GGTGTATATCCCGTACAATACATCACCACTTTCATATTTAGATGTGTACCCCTACGATACATCAT
CTTGCTTGTAGTTG
Found at i:3542083 original size:40 final size:39
Alignment explanation
Indices: 3542039--3542212 Score: 120
Period size: 40 Copynumber: 4.4 Consensus size: 39
3542029 ATATATCTTG
*
3542039 TACAATACATCACCACCTTCATATTTATATGTGTACCCCA
1 TACAATACATCACCACCTT-ATATTTAGATGTGTACCCCA
*** * * * * * *
3542079 TACAATACATCATCTTGCTTGTAGTTGGGTGTGTATCCCG
1 TACAATACATCA-CCACCTTATATTTAGATGTGTACCCCA
3542119 TACAATACATCACCACCTTTATATTTAGATGTGTA-CCC-
1 TACAATACATCACCACC-TTATATTTAGATGTGTACCCCA
*** * * * *
3542157 TACATGATACATCATCTTGC-TATAGTTGGGTGTGTATCCCA
1 TACA--ATACATCA-CCACCTTATATTTAGATGTGTACCCCA
3542198 TACAATACATCACCA
1 TACAATACATCACCA
3542213 TTTTATTTAA
Statistics
Matches: 102, Mismatches: 25, Indels: 16
0.71 0.17 0.11
Matches are distributed among these distances:
38 5 0.05
39 26 0.25
40 61 0.60
41 10 0.10
ACGTcount: A:0.29, C:0.25, G:0.13, T:0.34
Consensus pattern (39 bp):
TACAATACATCACCACCTTATATTTAGATGTGTACCCCA
Found at i:3542083 original size:160 final size:157
Alignment explanation
Indices: 3541908--3542212 Score: 382
Period size: 160 Copynumber: 1.9 Consensus size: 157
3541898 TAAATTTAGG
* * *
3541908 TGTGTACCTCATACAATACATCGCATC-GCTTATAATTTGGTGTATATCATGTACAATACATCAC
1 TGTGTACCCCATACAATACAT--CATCTGCTTATAATTGGGTGTATATCACGTACAATACATCAC
* *
3541972 CA-CTTTCTTATTTAGATGTGTACCCCGTAC-GATACATCATATTGCTTGTAGTTGGGTATATAT
64 CACCTTT-ATATTTAGATGTGTA-CCC-TACAGATACATCATATTGC-TATAGTTGGGTATATAT
***
3542035 CTTGTACAATACATCACCACCTTCATATTTATA
125 CCCATACAATACATCACCACCTTCATATTTATA
* * * *
3542068 TGTGTACCCCATACAATACATCATCTTGCTTGTAGTTGGGTGTGTATCCCGTACAATACATCACC
1 TGTGTACCCCATACAATACATCATC-TGCTTATAATTGGGTGTATATCACGTACAATACATCACC
* * *
3542133 ACCTTTATATTTAGATGTGTACCCTACATGATACATCATCTTGCTATAGTTGGGTGTGTATCCCA
65 ACCTTTATATTTAGATGTGTACCCTACA-GATACATCATATTGCTATAGTTGGGTATATATCCCA
3542198 TACAATACATCACCA
129 TACAATACATCACCA
3542213 TTTTATTTAA
Statistics
Matches: 125, Mismatches: 15, Indels: 11
0.83 0.10 0.07
Matches are distributed among these distances:
158 7 0.06
159 33 0.26
160 81 0.65
161 4 0.03
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.36
Consensus pattern (157 bp):
TGTGTACCCCATACAATACATCATCTGCTTATAATTGGGTGTATATCACGTACAATACATCACCA
CCTTTATATTTAGATGTGTACCCTACAGATACATCATATTGCTATAGTTGGGTATATATCCCATA
CAATACATCACCACCTTCATATTTATA
Found at i:3545269 original size:74 final size:79
Alignment explanation
Indices: 3545059--3545343 Score: 240
Period size: 80 Copynumber: 3.6 Consensus size: 79
3545049 ACCCGGTACA
* * * * * * * * * *
3545059 ATACATCAACTTGTTTATAATTGGGTATGTATCTCGTACACTACATCACCACTTTCTTATTTAGA
1 ATACATCATCTTG-CTATAGTTAGGTGTGTATCCCGTACAATATATCACCACCTTCATATTTAGA
* ** *
3545124 TATGTACCCCGTACG
65 TGTGTACCCCACATG
* ** * * * *
3545139 ATAAAAAATCTTTCT-TGAAGTTGGGTGTGTATCCTGTACAATACATCACCACCTTCATATTTAG
1 ATACATCATCTTGCTAT--AGTTAGGTGTGTATCCCGTACAATATATCACCACCTTCATATTTAG
***
3545203 ATGTGTACCCTGTATG
64 ATGTGTACCCCACATG
* * *
3545219 ATGCATCATTTTGCT-T-G-T-GGT-TGTATCCCGTACAATATATCACCAGCTTCATATTTAGAT
1 ATACATCATCTTGCTATAGTTAGGTGTGTATCCCGTACAATATATCACCACCTTCATATTTAGAT
3545279 GTGTACCCCACATG
66 GTGTACCCCACATG
* *
3545293 ATACATCATCTTGCTATAGTTAGGTGTGTATCCCGTATAATATATAACCAC
1 ATACATCATCTTGCTATAGTTAGGTGTGTATCCCGTACAATATATCACCAC
3545344 TTTATTTAAA
Statistics
Matches: 165, Mismatches: 33, Indels: 15
0.77 0.15 0.07
Matches are distributed among these distances:
74 60 0.36
75 4 0.02
76 2 0.01
77 2 0.01
78 4 0.02
79 23 0.14
80 70 0.42
ACGTcount: A:0.28, C:0.21, G:0.15, T:0.36
Consensus pattern (79 bp):
ATACATCATCTTGCTATAGTTAGGTGTGTATCCCGTACAATATATCACCACCTTCATATTTAGAT
GTGTACCCCACATG
Found at i:3545783 original size:80 final size:80
Alignment explanation
Indices: 3545644--3546032 Score: 414
Period size: 79 Copynumber: 4.9 Consensus size: 80
3545634 GTTGACGTAA
*
3545644 TTAGGTGTGTACCCCGTATGATACATCA-CATTGCTTATCA-TTGGGTGTGTATCCCATACAATA
1 TTAGATGTGTACCCCGTATGATACATCATC-TTGCTTAT-AGTTGGGTGTGTATCCCATACAATA
** *
3545707 CATCACCATTTTCTTAT
64 CATCACCACCTTCATAT
* * * * * ** *
3545724 TTAGATGTGTACCCCTTATTATACATCATCTTTCTTGTAGTTGGGTGTATATCTTATACAATAGA
1 TTAGATGTGTACCCCGTATGATACATCATCTTGCTTATAGTTGGGTGTGTATCCCATACAATACA
*
3545789 TCACCATCTTCATAT
66 TCACCACCTTCATAT
* * * * *
3545804 CTAGATGTGTACCCCGT-TGATATATTATCTTGCTTGTAGTTGGGTGTGTATCCCGTACAATACA
1 TTAGATGTGTACCCCGTATGATACATCATCTTGCTTATAGTTGGGTGTGTATCCCATACAATACA
3545868 TCACCACCTTCATAT
66 TCACCACCTTCATAT
* * ** * *
3545883 TTAAATTTGTACCCCACACGATACATCATCTTGC-TATAGTTGGGTGTGTATCCCGTACAATACA
1 TTAGATGTGTACCCCGTATGATACATCATCTTGCTTATAGTTGGGTGTGTATCCCATACAATACA
3545947 TCACCACCTTCATAT
66 TCACCACCTTCATAT
* ** * ** *
3545962 TTAAATGTGTACCCAC--ACAATAAATCATCTTGC-TATAGTTGGGTGTGTATCCCGCACAATCC
1 TTAGATGTGTACCC-CGTATGATACATCATCTTGCTTATAGTTGGGTGTGTATCCCATACAAT-A
3546024 CATCACCAC
64 CATCACCAC
3546033 TTTATTTGAA
Statistics
Matches: 267, Mismatches: 37, Indels: 11
0.85 0.12 0.03
Matches are distributed among these distances:
78 41 0.15
79 131 0.49
80 94 0.35
81 1 0.00
ACGTcount: A:0.26, C:0.24, G:0.14, T:0.36
Consensus pattern (80 bp):
TTAGATGTGTACCCCGTATGATACATCATCTTGCTTATAGTTGGGTGTGTATCCCATACAATACA
TCACCACCTTCATAT
Found at i:3545949 original size:39 final size:39
Alignment explanation
Indices: 3545903--3546021 Score: 118
Period size: 39 Copynumber: 3.1 Consensus size: 39
3545893 ACCCCACACG
*
3545903 ATACATCATCTTGCTATAGTTGGGTGTGTATCCCGTACA
1 ATACATCATCTTGCTATAGTTGGGTGTGTATCCCGCACA
* * *** *
3545942 ATACATCACCACCTT-C-ATATTTAAATGTGTA-CCCACACA
1 ATACAT---CATCTTGCTATAGTTGGGTGTGTATCCCGCACA
*
3545981 ATAAATCATCTTGCTATAGTTGGGTGTGTATCCCGCACA
1 ATACATCATCTTGCTATAGTTGGGTGTGTATCCCGCACA
3546020 AT
1 AT
3546022 CCCATCACCA
Statistics
Matches: 60, Mismatches: 14, Indels: 12
0.70 0.16 0.14
Matches are distributed among these distances:
36 5 0.08
37 1 0.02
38 11 0.18
39 26 0.43
40 11 0.18
41 1 0.02
42 5 0.08
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.33
Consensus pattern (39 bp):
ATACATCATCTTGCTATAGTTGGGTGTGTATCCCGCACA
Found at i:3549522 original size:2 final size:2
Alignment explanation
Indices: 3549517--3549545 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3549507 TAACTTTTTA
3549517 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3549546 GGTTTTGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3551283 original size:20 final size:20
Alignment explanation
Indices: 3551254--3551293 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
3551244 ACTTTAGTGA
3551254 GTCCAATTATAATAAGGTAT
1 GTCCAATTATAATAAGGTAT
*
3551274 GTCCAGTTATAATAAGGTAT
1 GTCCAATTATAATAAGGTAT
3551294 ACCTATGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.35
Consensus pattern (20 bp):
GTCCAATTATAATAAGGTAT
Found at i:3553176 original size:2 final size:2
Alignment explanation
Indices: 3553169--3553203 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3553159 TGTTATTCAA
3553169 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3553204 ATAACATTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3554747 original size:176 final size:175
Alignment explanation
Indices: 3554429--3554755 Score: 521
Period size: 176 Copynumber: 1.9 Consensus size: 175
3554419 ATCCCATAAC
3554429 TTTTCATAATTATCGATTTGGTCCCCCAACTTTCAAAAAATTATAGATTGGCCCAAAAAATTTCT
1 TTTTCATAATTATCGATTTGGTCCCCCAACTTTCAAAAAATTATAGATTGGCCCAAAAAATTTCT
* * *
3554494 AAGGCTTATAAAATCTTTCTAATATCATTTCTAAGAAACATGAAAATTTTTCAAAATTTTCTCCT
66 AAGGCTTATAAAACCTTTCTAATATCATTTCTAAGAAACATGAAAATTTTTCAAAAATTTCTCCC
*
3554559 ATCATTTTCCTCAAGGTCGAATTGTTTGTGTACCTAAGGCCAGGG
131 ATCATCTTCCTCAAGGTCGAATTGTTTGTGTACCTAAGGCCAGGG
* * **
3554604 TTTTTATAATTATCGATTTGGTCCCCCAACTTTCATAAAATTATAGATTGGCCCCAAAATTTTTC
1 TTTTCATAATTATCGATTTGGTCCCCCAACTTTCAAAAAATTATAGATTGG-CCCAAAAAATTTC
* * **
3554669 TAAGGCTTGTAAAGCCTTTCTAATATCATTTCTAAGAAACATGAATTTTTTTCAAAAAATTTC-C
65 TAAGGCTTATAAAACCTTTCTAATATCATTTCTAAGAAACATGAAAATTTTTC-AAAAATTTCTC
3554733 CCATCATCTTCCTCAAGGTCGAA
129 CCATCATCTTCCTCAAGGTCGAA
3554756 CGGTTTATCT
Statistics
Matches: 138, Mismatches: 12, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
175 49 0.36
176 81 0.59
177 8 0.06
ACGTcount: A:0.32, C:0.19, G:0.11, T:0.38
Consensus pattern (175 bp):
TTTTCATAATTATCGATTTGGTCCCCCAACTTTCAAAAAATTATAGATTGGCCCAAAAAATTTCT
AAGGCTTATAAAACCTTTCTAATATCATTTCTAAGAAACATGAAAATTTTTCAAAAATTTCTCCC
ATCATCTTCCTCAAGGTCGAATTGTTTGTGTACCTAAGGCCAGGG
Found at i:3557304 original size:55 final size:55
Alignment explanation
Indices: 3557145--3557304 Score: 223
Period size: 54 Copynumber: 2.9 Consensus size: 55
3557135 ATTACCGAAT
* *
3557145 GGCACTATATGTGTGCACAAGCTAAGAAATTCATAATAAGTTTATGAATTTTTGTATG
1 GGCACT-T-TGTGTGCA-AAACTAAGAAATTCATAATAAGTTTATGAATTTTCGTATG
** *
3557203 GGCACTTTGCATGC-AAACTAAGAAATTCAGAATAAGTTTATGAATTTTCGTATG
1 GGCACTTTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTTCGTATG
* *
3557257 GGCACTTTGTGTGCAAAACAAAGAAATTCATAATAAGTTTATAAATTT
1 GGCACTTTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTT
3557305 CCATATTGGT
Statistics
Matches: 91, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
54 49 0.54
55 30 0.33
56 5 0.05
57 1 0.01
58 6 0.07
ACGTcount: A:0.37, C:0.11, G:0.17, T:0.34
Consensus pattern (55 bp):
GGCACTTTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTTCGTATG
Found at i:3557677 original size:46 final size:45
Alignment explanation
Indices: 3557602--3557688 Score: 129
Period size: 46 Copynumber: 1.9 Consensus size: 45
3557592 TTAGATGAAG
* *
3557602 AACAATGCATAATTGTATGAAAGGATGCCATAAATGAAAATGTAT
1 AACAATGCATAATTGCATGAAAGGATGCCACAAATGAAAATGTAT
* *
3557647 AACAGTGCATAATTGGCATGTAAGGATGCCACAAATGAAAAT
1 AACAATGCATAATT-GCATGAAAGGATGCCACAAATGAAAAT
3557689 ACATAATGAT
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
45 13 0.35
46 24 0.65
ACGTcount: A:0.45, C:0.11, G:0.20, T:0.24
Consensus pattern (45 bp):
AACAATGCATAATTGCATGAAAGGATGCCACAAATGAAAATGTAT
Found at i:3559461 original size:2 final size:2
Alignment explanation
Indices: 3559454--3559482 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3559444 TGTCAGAAAG
3559454 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3559483 GTTTTGTGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3562428 original size:55 final size:55
Alignment explanation
Indices: 3562338--3562610 Score: 313
Period size: 55 Copynumber: 5.0 Consensus size: 55
3562328 TGTCACTATA
*
3562338 TGTGTGCAAAAGCTAAGAAATTCATAATAAGTTTATCAATTTCCGTATGGGCACTT
1 TGTGTGCAAAA-CTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTT
**
3562394 TGTGTGCAAAACTAAGAAATTCATAA-ACTTTTTATGAATTTCTC-TAT-GGCACTT
1 TGTGTGCAAAACTAAGAAATTCATAATA-AGTTTATGAATTTC-CGTATGGGCACTT
* * *
3562448 TGTGTGCAAAACTAAGACATTCGTAATAAGTTTATGAATTTCCGTATGAGCACTT
1 TGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTT
* * * * * *
3562503 TGTGTGCAAAACTAATAAATTCATAATAAGTTTATGAATTTTCGTATTGGTAGTG
1 TGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTT
* * * * * *
3562558 GGTGTGC-AACCCACGTAAATT-ATAATAAGTTTATGAATTACCGTATTGGCACT
1 TGTGTGCAAAACTAAG-AAATTCATAATAAGTTTATGAATTTCCGTATGGGCACT
3562611 ACATGTGCAA
Statistics
Matches: 185, Mismatches: 26, Indels: 14
0.82 0.12 0.06
Matches are distributed among these distances:
53 1 0.01
54 79 0.43
55 93 0.50
56 12 0.06
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (55 bp):
TGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTT
Found at i:3562541 original size:109 final size:110
Alignment explanation
Indices: 3562338--3562543 Score: 326
Period size: 109 Copynumber: 1.9 Consensus size: 110
3562328 TGTCACTATA
*
3562338 TGTGTGCAAAAGCTAAGAAATTCATAATAAGTTTATCAATTTCCGTATGGGCACTTTGTGTGCAA
1 TGTGTGCAAAAGCTAAGAAATTCATAATAAGTTTATCAATTTCCGTATGAGCACTTTGTGTGCAA
**
3562403 AACTAAGAAATTCATAAACTTTTTATGAATTTCTCTATGGCACTT
66 AACTAAGAAATTCATAAACAGTTTATGAATTTCTCTATGGCACTT
* * *
3562448 TGTGTGCAAAA-CTAAGACATTCGTAATAAGTTTATGAATTTCCGTATGAGCACTTTGTGTGCAA
1 TGTGTGCAAAAGCTAAGAAATTCATAATAAGTTTATCAATTTCCGTATGAGCACTTTGTGTGCAA
*
3562512 AACTAATAAATTCATAATA-AGTTTATGAATTT
66 AACTAAGAAATTCATAA-ACAGTTTATGAATTT
3562544 TCGTATTGGT
Statistics
Matches: 88, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
109 76 0.86
110 12 0.14
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.36
Consensus pattern (110 bp):
TGTGTGCAAAAGCTAAGAAATTCATAATAAGTTTATCAATTTCCGTATGAGCACTTTGTGTGCAA
AACTAAGAAATTCATAAACAGTTTATGAATTTCTCTATGGCACTT
Found at i:3562584 original size:109 final size:109
Alignment explanation
Indices: 3562339--3562603 Score: 313
Period size: 109 Copynumber: 2.4 Consensus size: 109
3562329 GTCACTATAT
* * *
3562339 GTGTGCAAAAGCTAAGAAATTCATAATAAGTTTATCAATTTCCGTATGGGCACTTTGTGTGCAAA
1 GTGTGCAAAA-CCAAGAAATTCATAATAAGTTTATGAATTTCCGTATGAGCACTTTGTGTGCAAA
** **
3562404 ACTAAGAAATTCATAAACTTTTTATGAATTTCTCTATGGCACTTT
65 ACTAAGAAATTCATAAACAGTTTATGAATTTCTCTATGGCACTGG
* * *
3562449 GTGTGCAAAACTAAGACATTCGTAATAAGTTTATGAATTTCCGTATGAGCACTTTGTGTGCAAAA
1 GTGTGCAAAACCAAGAAATTCATAATAAGTTTATGAATTTCCGTATGAGCACTTTGTGTGCAAAA
* * *
3562514 CTAATAAATTCATAATA-AGTTTATGAATTT-TCGTATTGGTAGTGG
66 CTAAGAAATTCATAA-ACAGTTTATGAATTTCTC-TA-TGGCACTGG
* * *
3562559 GTGTGC-AACCCACGTAAATT-ATAATAAGTTTATGAATTACCGTAT
1 GTGTGCAAAACCAAG-AAATTCATAATAAGTTTATGAATTTCCGTAT
3562604 TGGCACTACA
Statistics
Matches: 134, Mismatches: 17, Indels: 9
0.84 0.11 0.06
Matches are distributed among these distances:
108 2 0.01
109 106 0.79
110 26 0.19
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.36
Consensus pattern (109 bp):
GTGTGCAAAACCAAGAAATTCATAATAAGTTTATGAATTTCCGTATGAGCACTTTGTGTGCAAAA
CTAAGAAATTCATAAACAGTTTATGAATTTCTCTATGGCACTGG
Found at i:3566118 original size:20 final size:21
Alignment explanation
Indices: 3566072--3566129 Score: 75
Period size: 22 Copynumber: 2.8 Consensus size: 21
3566062 GTGAACAGTA
3566072 GGGGAATCAGTTCCCTGTTGGG
1 GGGGAATCAGTTCCCTGTT-GG
3566094 GGGGAATC-GATTCCCTGTT-G
1 GGGGAATCAG-TTCCCTGTTGG
*
3566114 GGGGAATCAGTACCCT
1 GGGGAATCAGTTCCCT
3566130 AAAATTATTC
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
20 14 0.42
21 2 0.06
22 17 0.52
ACGTcount: A:0.17, C:0.21, G:0.36, T:0.26
Consensus pattern (21 bp):
GGGGAATCAGTTCCCTGTTGG
Found at i:3566649 original size:44 final size:44
Alignment explanation
Indices: 3566580--3566686 Score: 169
Period size: 44 Copynumber: 2.4 Consensus size: 44
3566570 TAAATTTTTT
* *
3566580 TTTATCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAATATA
1 TTTACCATTTAT-CCATAAGCTCGTAAGCTTATTTTACCAATACA
3566625 TTTACCATTTATCCATAAGCTCGTAAGCTTATTTTACCAATACA
1 TTTACCATTTATCCATAAGCTCGTAAGCTTATTTTACCAATACA
* *
3566669 CTAACCATTTATCCATAA
1 TTTACCATTTATCCATAA
3566687 TGTTGAAAAC
Statistics
Matches: 58, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
44 47 0.81
45 11 0.19
ACGTcount: A:0.33, C:0.22, G:0.06, T:0.39
Consensus pattern (44 bp):
TTTACCATTTATCCATAAGCTCGTAAGCTTATTTTACCAATACA
Found at i:3575507 original size:22 final size:22
Alignment explanation
Indices: 3575471--3575523 Score: 90
Period size: 22 Copynumber: 2.4 Consensus size: 22
3575461 GAAGGAACCT
3575471 ATTCCCCCCCAAGGGGGTACCG
1 ATTCCCCCCCAAGGGGGTACCG
3575493 ATTTCCCCCCC-AGGGGGTACCG
1 A-TTCCCCCCCAAGGGGGTACCG
3575515 ATTCCCCCC
1 ATTCCCCCC
3575524 ACTGTTCAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
21 8 0.27
22 13 0.43
23 9 0.30
ACGTcount: A:0.15, C:0.45, G:0.23, T:0.17
Consensus pattern (22 bp):
ATTCCCCCCCAAGGGGGTACCG
Found at i:3576287 original size:45 final size:45
Alignment explanation
Indices: 3576223--3576317 Score: 163
Period size: 45 Copynumber: 2.1 Consensus size: 45
3576213 TAACTCAACA
*
3576223 CATAAGCTAGTAAGTTTATTTTTACCAATACACTTGCCATTATTC
1 CATAAGCTAGTAAGCTTATTTTTACCAATACACTTGCCATTATTC
* *
3576268 CATAAGCTCGTAAGCTTATTTTTACCAATATACTTGCCATTATTC
1 CATAAGCTAGTAAGCTTATTTTTACCAATACACTTGCCATTATTC
3576313 CATAA
1 CATAA
3576318 CCATATATCA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.32, C:0.21, G:0.08, T:0.39
Consensus pattern (45 bp):
CATAAGCTAGTAAGCTTATTTTTACCAATACACTTGCCATTATTC
Found at i:3576524 original size:59 final size:58
Alignment explanation
Indices: 3576390--3576526 Score: 139
Period size: 59 Copynumber: 2.3 Consensus size: 58
3576380 ATAAGCACCG
* * * * **
3576390 TAGTGCTATCCCGAGTATGACACATAAGGTTGTATCCACCACCTGTACTAGGTATCCTT
1 TAGTG-TATCCCGAATATGACACATAAGGTCGTACCCACCACATACACTAGGTATCCTT
* ** * * *
3576449 AAGTACAGTCCAGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTT
1 TAGTGTA-TCCCGAATATGACACATAAGGTCGTACCCACCACATACACTAGGTATCCTT
3576508 TAGTGTATTCCCGAATATG
1 TAGTGTA-TCCCGAATATG
3576527 CAGCTTGCTG
Statistics
Matches: 60, Mismatches: 17, Indels: 2
0.76 0.22 0.03
Matches are distributed among these distances:
58 1 0.02
59 59 0.98
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.28
Consensus pattern (58 bp):
TAGTGTATCCCGAATATGACACATAAGGTCGTACCCACCACATACACTAGGTATCCTT
Found at i:3589156 original size:15 final size:15
Alignment explanation
Indices: 3589138--3589176 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
3589128 TAAAGGAATG
3589138 AAATTTAAATGTTGA
1 AAATTTAAATGTTGA
3589153 AAATTTAAATGTTGA
1 AAATTTAAATGTTGA
3589168 AAATTTAAA
1 AAATTTAAA
3589177 AGGCAAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.51, C:0.00, G:0.10, T:0.38
Consensus pattern (15 bp):
AAATTTAAATGTTGA
Found at i:3589156 original size:29 final size:29
Alignment explanation
Indices: 3589095--3589157 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 29
3589085 GAAATATCAG
* *
3589095 AAATTAAAGGATTGAAATGTAAATACTGG
1 AAATTAAAGGAATGAAATGTAAATACTGA
* **
3589124 AAATTAAAGGAATGAAATTTAAATGTTGA
1 AAATTAAAGGAATGAAATGTAAATACTGA
3589153 AAATT
1 AAATT
3589158 TAAATGTTGA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.51, C:0.02, G:0.17, T:0.30
Consensus pattern (29 bp):
AAATTAAAGGAATGAAATGTAAATACTGA
Found at i:3592536 original size:20 final size:20
Alignment explanation
Indices: 3592513--3592561 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
3592503 CTTAAAATCA
3592513 TTTTTCAAAACT-TCATTTTG
1 TTTTTCAAAA-TATCATTTTG
* *
3592533 TTTTTCGAAATATGATTTTG
1 TTTTTCAAAATATCATTTTG
3592553 -TTTTCAAAA
1 TTTTTCAAAA
3592562 GAAAATCATT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 9 0.36
20 16 0.64
ACGTcount: A:0.29, C:0.10, G:0.08, T:0.53
Consensus pattern (20 bp):
TTTTTCAAAATATCATTTTG
Found at i:3593336 original size:13 final size:13
Alignment explanation
Indices: 3593320--3593345 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3593310 TTCATCTTGA
3593320 AGTTGGCTTGTTC
1 AGTTGGCTTGTTC
3593333 AGTTGGCTTGTTC
1 AGTTGGCTTGTTC
3593346 CTTTATGGGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.08, C:0.15, G:0.31, T:0.46
Consensus pattern (13 bp):
AGTTGGCTTGTTC
Found at i:3597214 original size:22 final size:22
Alignment explanation
Indices: 3597184--3597249 Score: 105
Period size: 22 Copynumber: 3.0 Consensus size: 22
3597174 CACGTCAACA
* *
3597184 GCCATGTTGTTGTTGGTCAGCC
1 GCCACGTTGTCGTTGGTCAGCC
*
3597206 TCCACGTTGTCGTTGGTCAGCC
1 GCCACGTTGTCGTTGGTCAGCC
3597228 GCCACGTTGTCGTTGGTCAGCC
1 GCCACGTTGTCGTTGGTCAGCC
3597250 ACCATGTCAC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.09, C:0.29, G:0.30, T:0.32
Consensus pattern (22 bp):
GCCACGTTGTCGTTGGTCAGCC
Found at i:3597257 original size:19 final size:20
Alignment explanation
Indices: 3597195--3597257 Score: 65
Period size: 22 Copynumber: 3.0 Consensus size: 20
3597185 CCATGTTGTT
*
3597195 GTTGGTCAGCCTCCACGTTGTC
1 GTTGGTCAGCCACCAC--TGTC
*
3597217 GTTGGTCAGCCGCCACGTTGTC
1 GTTGGTCAGCCACCAC--TGTC
3597239 GTTGGTCAGCCACCA-TGTC
1 GTTGGTCAGCCACCACTGTC
3597258 ACCGTCCACT
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
19 4 0.10
22 35 0.90
ACGTcount: A:0.11, C:0.32, G:0.29, T:0.29
Consensus pattern (20 bp):
GTTGGTCAGCCACCACTGTC
Found at i:3597647 original size:30 final size:30
Alignment explanation
Indices: 3597610--3597739 Score: 215
Period size: 30 Copynumber: 4.3 Consensus size: 30
3597600 AATATTAATA
*
3597610 ATTCAGATCTTATGGGAACATATCAAACAG
1 ATTCAGATCCTATGGGAACATATCAAACAG
*
3597640 ATCCAGATCCTATGGGAACATATCAAACAG
1 ATTCAGATCCTATGGGAACATATCAAACAG
3597670 ATTCAGATCCTATGGGAACATATCAAACAG
1 ATTCAGATCCTATGGGAACATATCAAACAG
** *
3597700 ATTCAGATCCTATGAAAACAGATCAAACAG
1 ATTCAGATCCTATGGGAACATATCAAACAG
3597730 ATTCAGATCC
1 ATTCAGATCC
3597740 AAGATCCTAT
Statistics
Matches: 94, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 94 1.00
ACGTcount: A:0.41, C:0.21, G:0.15, T:0.23
Consensus pattern (30 bp):
ATTCAGATCCTATGGGAACATATCAAACAG
Found at i:3599066 original size:21 final size:21
Alignment explanation
Indices: 3599042--3599097 Score: 112
Period size: 21 Copynumber: 2.7 Consensus size: 21
3599032 TATTCAATAG
3599042 AGAAAATATTAATATTTCAGA
1 AGAAAATATTAATATTTCAGA
3599063 AGAAAATATTAATATTTCAGA
1 AGAAAATATTAATATTTCAGA
3599084 AGAAAATATTAATA
1 AGAAAATATTAATA
3599098 ATCCATATCC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.55, C:0.04, G:0.09, T:0.32
Consensus pattern (21 bp):
AGAAAATATTAATATTTCAGA
Found at i:3605692 original size:19 final size:20
Alignment explanation
Indices: 3605668--3605713 Score: 78
Period size: 19 Copynumber: 2.4 Consensus size: 20
3605658 CATTGGTTCT
3605668 CATTTTTCT-ACAGGAATTG
1 CATTTTTCTCACAGGAATTG
3605687 CATTTTT-TCACAGGAATTG
1 CATTTTTCTCACAGGAATTG
3605706 CATTTTTC
1 CATTTTTC
3605714 CGACAATTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
18 1 0.04
19 24 0.96
ACGTcount: A:0.24, C:0.17, G:0.13, T:0.46
Consensus pattern (20 bp):
CATTTTTCTCACAGGAATTG
Found at i:3611711 original size:192 final size:191
Alignment explanation
Indices: 3611414--3611800 Score: 469
Period size: 192 Copynumber: 2.0 Consensus size: 191
3611404 ACTTTTCTAT
* * **
3611414 ATAACGTCACTATATAATTGATATTCAATGACAATTAATTCTGTCACTAAATTATGTAAAATTTC
1 ATAACGTCACTATATAATTGATATTCAATGAAAATTAATTCTATCACTAAATTAAATAAAATTTC
* * * * *
3611479 ATTATTGATGATTTATGTCATCACATATAATACATTAAAATCAACATATATGTG-ATGAAAGAGA
66 ATTACTGATGAATTATATCATCACAAATAATACATTAAAATCAACATATATATGAAT-AAAGAGA
* * *
3611543 TATTGTCACATTTTTAGTGACAAT-ATAAAT-GTTACCTAATAATATTATGAATGA-CATTTATG
130 TA--GTCACATTTTTAATGA-AATAATAAATCATTAACTAATAATATTATGAATGATCA-TTATG
3611605 C
191 C
* * * * *
3611606 ATAACGTCACTTTATAATTTATATTCTATGAAAATTAGTTAC-ATCACTAAATTAAATAAGATTT
1 ATAACGTCACTATATAATTGATATTCAATGAAAATTAATT-CTATCACTAAATTAAATAAAATTT
* ** *
3611670 CATTACTGATTAATTATATTGTCACAAATAATACATTAAAATCAACTTATATATGAATAAAGAGA
65 CATTACTGATGAATTATATCATCACAAATAATACATTAAAATCAACATATATATGAATAAAGAGA
* * *
3611735 TAGTCACATTTTTAATGAGATAATATATCATTAACTAATAATATTATGAATGATGATTATGC
130 TAGTCACATTTTTAATGAAATAATAAATCATTAACTAATAATATTATGAATGATCATTATGC
3611797 ATAA
1 ATAA
3611801 AATCACCATA
Statistics
Matches: 166, Mismatches: 24, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
189 2 0.01
190 20 0.12
191 32 0.19
192 109 0.66
193 3 0.02
ACGTcount: A:0.42, C:0.11, G:0.09, T:0.38
Consensus pattern (191 bp):
ATAACGTCACTATATAATTGATATTCAATGAAAATTAATTCTATCACTAAATTAAATAAAATTTC
ATTACTGATGAATTATATCATCACAAATAATACATTAAAATCAACATATATATGAATAAAGAGAT
AGTCACATTTTTAATGAAATAATAAATCATTAACTAATAATATTATGAATGATCATTATGC
Found at i:3611829 original size:14 final size:15
Alignment explanation
Indices: 3611803--3611831 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
3611793 ATGCATAAAA
3611803 TCACCATATATAATG
1 TCACCATATATAATG
3611818 TCACCA-ATATAATG
1 TCACCATATATAATG
3611832 GAAAAACCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.41, C:0.21, G:0.07, T:0.31
Consensus pattern (15 bp):
TCACCATATATAATG
Found at i:3613671 original size:41 final size:43
Alignment explanation
Indices: 3613593--3613683 Score: 150
Period size: 41 Copynumber: 2.1 Consensus size: 43
3613583 CAAACAAACT
*
3613593 GTTTTTCTTTTGTTTTTTAATTTGGACTTCCGTATACATATCA
1 GTTTTTCTTTTGTTTTTTAATTTGGACTTCCATATACATATCA
3613636 GTTTTTCTTTTGTTTTTT-A-TTGGACTTCCATATACATATCA
1 GTTTTTCTTTTGTTTTTTAATTTGGACTTCCATATACATATCA
3613677 GTGTTTT
1 GT-TTTT
3613684 ACAAAATTTT
Statistics
Matches: 46, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
41 23 0.50
42 5 0.11
43 18 0.39
ACGTcount: A:0.18, C:0.13, G:0.12, T:0.57
Consensus pattern (43 bp):
GTTTTTCTTTTGTTTTTTAATTTGGACTTCCATATACATATCA
Found at i:3613733 original size:19 final size:19
Alignment explanation
Indices: 3613709--3613748 Score: 64
Period size: 19 Copynumber: 2.1 Consensus size: 19
3613699 ATAATGTATG
3613709 AAACAG-AGAAAACAAGCTA
1 AAACAGAAG-AAACAAGCTA
3613728 AAACAGAAGAAACAAGCTA
1 AAACAGAAGAAACAAGCTA
3613747 AA
1 AA
3613749 TATTAACTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 18 0.90
20 2 0.10
ACGTcount: A:0.65, C:0.15, G:0.15, T:0.05
Consensus pattern (19 bp):
AAACAGAAGAAACAAGCTA
Found at i:3614540 original size:26 final size:24
Alignment explanation
Indices: 3614511--3614570 Score: 70
Period size: 22 Copynumber: 2.5 Consensus size: 24
3614501 TATTAAAAAT
*
3614511 AATAATAATATTTGAAAGGTAAGTGA
1 AATAATAATATTT--AAGGAAAGTGA
*
3614537 AATAATAATA--TATGGAAAGTGA
1 AATAATAATATTTAAGGAAAGTGA
3614559 AATAATAATATT
1 AATAATAATATT
3614571 ATTAATTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
22 19 0.63
24 1 0.03
26 10 0.33
ACGTcount: A:0.53, C:0.00, G:0.15, T:0.32
Consensus pattern (24 bp):
AATAATAATATTTAAGGAAAGTGA
Found at i:3616684 original size:21 final size:20
Alignment explanation
Indices: 3616655--3616706 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
3616645 ACTGTGCAAT
* *
3616655 GGATTGATCCTTCGGGGAAAA
1 GGATCGATCCTT-GAGGAAAA
3616676 GGATCGATCCCTTGAGGAAAA
1 GGATCGAT-CCTTGAGGAAAA
*
3616697 TGATCGATCC
1 GGATCGATCC
3616707 CTCGAAAGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 2 0.07
21 21 0.78
22 4 0.15
ACGTcount: A:0.29, C:0.19, G:0.29, T:0.23
Consensus pattern (20 bp):
GGATCGATCCTTGAGGAAAA
Found at i:3616722 original size:21 final size:21
Alignment explanation
Indices: 3616671--3616729 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
3616661 ATCCTTCGGG
* *
3616671 GAAAAGGATCGATCCCTTGAG
1 GAAAAGGATCGATCCCTCGAA
*
3616692 GAAAATGATCGATCCCTCGAA
1 GAAAAGGATCGATCCCTCGAA
*
3616713 -AGAAAGGATCAATCCCT
1 GA-AAAGGATCGATCCCT
3616730 TCATTGTTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
20 1 0.03
21 31 0.97
ACGTcount: A:0.37, C:0.22, G:0.22, T:0.19
Consensus pattern (21 bp):
GAAAAGGATCGATCCCTCGAA
Found at i:3629993 original size:21 final size:21
Alignment explanation
Indices: 3629967--3630017 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
3629957 GCATTTCTCA
*
3629967 AAGTCATCTCCAGAAACAGAG
1 AAGTCATCCCCAGAAACAGAG
*
3629988 AAGTCATCCCCAGAAACGGAG
1 AAGTCATCCCCAGAAACAGAG
3630009 AAGTCATCC
1 AAGTCATCC
3630018 ATAAAGATTC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.39, C:0.27, G:0.20, T:0.14
Consensus pattern (21 bp):
AAGTCATCCCCAGAAACAGAG
Found at i:3632151 original size:71 final size:71
Alignment explanation
Indices: 3632035--3632173 Score: 269
Period size: 71 Copynumber: 2.0 Consensus size: 71
3632025 TTTAATTAGA
*
3632035 GCTAATAGGACATTCATAAGTACATGCCACTAAACTAAGTCAAAAATTACATTATAGGATGTCTT
1 GCTAATAGGACATTCATAAGTACATGCAACTAAACTAAGTCAAAAATTACATTATAGGATGTCTT
3632100 ACTAGT
66 ACTAGT
3632106 GCTAATAGGACATTCATAAGTACATGCAACTAAACTAAGTCAAAAATTACATTATAGGATGTCTT
1 GCTAATAGGACATTCATAAGTACATGCAACTAAACTAAGTCAAAAATTACATTATAGGATGTCTT
3632171 ACT
66 ACT
3632174 GATATTATAA
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 67 1.00
ACGTcount: A:0.40, C:0.17, G:0.14, T:0.29
Consensus pattern (71 bp):
GCTAATAGGACATTCATAAGTACATGCAACTAAACTAAGTCAAAAATTACATTATAGGATGTCTT
ACTAGT
Found at i:3632714 original size:54 final size:53
Alignment explanation
Indices: 3632653--3633353 Score: 758
Period size: 54 Copynumber: 13.2 Consensus size: 53
3632643 TTACGTGGGG
*
3632653 TGCACACATAATGCCAATACAGAAATTCATAAATTAATTATGAATTTCTTAGGT
1 TGCACACATAGTGCCAATACAGAAATTCATAAATT-ATTATGAATTTCTTAGGT
* * * * *
3632707 TGTACACACAGTGCCAATACAAAAATTTATAAACTAATTATGAATTTCTTAGGT
1 TGCACACATAGTGCCAATACAGAAATTCATAAA-TTATTATGAATTTCTTAGGT
* * * * * **
3632761 TGCATACATAGTGGCAATA-A-AATTTCATAAACTAATTATGAATTTATTAAAT
1 TGCACACATAGTGCCAATACAGAAATTCATAAA-TTATTATGAATTTCTTAGGT
* * *
3632813 TG--CAC--AGTACCAATACAGAAATTCATAAACTTATTATGAATTTCTGAAGT
1 TGCACACATAGTGCCAATACAGAAATTCATAAA-TTATTATGAATTTCTTAGGT
* * * * * * **
3632863 TGCACACACATTGTCAATACATAAATTCAAAAACTTATTATGAA-TTATTAACT
1 TGCACACATAGTGCCAATACAGAAATTCATAAA-TTATTATGAATTTCTTAGGT
* * *
3632916 TGTACACACAGTGCCAATACAGAAATTCATAAACTAATTATGAATTTCTTAGGT
1 TGCACACATAGTGCCAATACAGAAATTCATAAA-TTATTATGAATTTCTTAGGT
*
3632970 TGCACACATAGTACCAATAC-GAAAATTCATAAAATTATTATGAATTTCTTAGGT
1 TGCACACATAGTGCCAATACAG-AAATTCAT-AAATTATTATGAATTTCTTAGGT
* * *
3633024 TGTACAC--AGTGCCAATACGGAAATTCATAAACTTATTATGAATTTATTAGGT
1 TGCACACATAGTGCCAATACAGAAATTCATAAA-TTATTATGAATTTCTTAGGT
* * *
3633076 TGCACACATAGTGCCAATGCCGAAATTCATAAACTAATTATGAATTTCTTAGGT
1 TGCACACATAGTGCCAATACAGAAATTCATAAA-TTATTATGAATTTCTTAGGT
* * *
3633130 TGCACACACAGTGCCAATACGGAAATTCATAAACTAATTATGAATTTCTTAGGT
1 TGCACACATAGTGCCAATACAGAAATTCATAAA-TTATTATGAATTTCTTAGGT
** *
3633184 TGCACACATAGTGCCAATAGGGAAATTCATAAACTTATTATGAAATTCTTAGGT
1 TGCACACATAGTGCCAATACAGAAATTCATAAA-TTATTATGAATTTCTTAGGT
* * *
3633238 TGCACACATAGTGTCAGTACAAAAATTCATAAACTTATTATGAATTTCTT-GAGT
1 TGCACACATAGTGCCAATACAGAAATTCATAAA-TTATTATGAATTTCTTAG-GT
* * ** *
3633292 TGCGCACACAGTGCCAATATGGAAATTCATAAACTTATTATGAATTTCTTAAGT
1 TGCACACATAGTGCCAATACAGAAATTCATAAA-TTATTATGAATTTCTTAGGT
3633346 TGCACACA
1 TGCACACA
3633354 GAGCCATTCG
Statistics
Matches: 557, Mismatches: 74, Indels: 32
0.84 0.11 0.05
Matches are distributed among these distances:
48 8 0.01
49 1 0.00
50 31 0.06
51 3 0.01
52 75 0.13
53 48 0.09
54 387 0.69
55 4 0.01
ACGTcount: A:0.39, C:0.16, G:0.13, T:0.33
Consensus pattern (53 bp):
TGCACACATAGTGCCAATACAGAAATTCATAAATTATTATGAATTTCTTAGGT
Found at i:3633193 original size:108 final size:108
Alignment explanation
Indices: 3632653--3633353 Score: 868
Period size: 108 Copynumber: 6.6 Consensus size: 108
3632643 TTACGTGGGG
* *
3632653 TGCACACATAATGCCAATACAGAAATTCATAAA-TTAATTATGAATTTCTTAGGTTGTACACACA
1 TGCACACATAGTGCCAATACAGAAATTCATAAACTT-ATTATGAATTTCTTAGGTTGCACACACA
* *
3632717 GTGCCAATACAAAAATTTATAAACTAATTATGAATTTCTTAGGT
65 GTGCCAATACAGAAATTCATAAACTAATTATGAATTTCTTAGGT
* * * * * **
3632761 TGCATACATAGTGGCAATA-A-AATTTCATAAACTAATTATGAATTTATTAAATTG----CACAG
1 TGCACACATAGTGCCAATACAGAAATTCATAAACTTATTATGAATTTCTTAGGTTGCACACACAG
* * * *
3632820 TACCAATACAGAAATTCATAAACTTATTATGAATTTCTGAAGT
66 TGCCAATACAGAAATTCATAAACTAATTATGAATTTCTTAGGT
* * * * * * ** *
3632863 TGCACACACATTGTCAATACATAAATTCAAAAACTTATTATGAA-TTATTAACTTGTACACACAG
1 TGCACACATAGTGCCAATACAGAAATTCATAAACTTATTATGAATTTCTTAGGTTGCACACACAG
3632927 TGCCAATACAGAAATTCATAAACTAATTATGAATTTCTTAGGT
66 TGCCAATACAGAAATTCATAAACTAATTATGAATTTCTTAGGT
* * *
3632970 TGCACACATAGTACCAATAC-GAAAATTCATAAAATTATTATGAATTTCTTAGGTTG--TACACA
1 TGCACACATAGTGCCAATACAG-AAATTCATAAACTTATTATGAATTTCTTAGGTTGCACACACA
* * *
3633032 GTGCCAATACGGAAATTCATAAACTTATTATGAATTTATTAGGT
65 GTGCCAATACAGAAATTCATAAACTAATTATGAATTTCTTAGGT
* * *
3633076 TGCACACATAGTGCCAATGCCGAAATTCATAAACTAATTATGAATTTCTTAGGTTGCACACACAG
1 TGCACACATAGTGCCAATACAGAAATTCATAAACTTATTATGAATTTCTTAGGTTGCACACACAG
*
3633141 TGCCAATACGGAAATTCATAAACTAATTATGAATTTCTTAGGT
66 TGCCAATACAGAAATTCATAAACTAATTATGAATTTCTTAGGT
** * *
3633184 TGCACACATAGTGCCAATAGGGAAATTCATAAACTTATTATGAAATTCTTAGGTTGCACACATAG
1 TGCACACATAGTGCCAATACAGAAATTCATAAACTTATTATGAATTTCTTAGGTTGCACACACAG
* * * *
3633249 TGTCAGTACAAAAATTCATAAACTTATTATGAATTTCTT-GAGT
66 TGCCAATACAGAAATTCATAAACTAATTATGAATTTCTTAG-GT
* * ** *
3633292 TGCGCACACAGTGCCAATATGGAAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACA
1 TGCACACATAGTGCCAATACAGAAATTCATAAACTTATTATGAATTTCTTAGGTTGCACACA
3633354 GAGCCATTCG
Statistics
Matches: 517, Mismatches: 63, Indels: 26
0.85 0.10 0.04
Matches are distributed among these distances:
102 57 0.11
103 11 0.02
104 19 0.04
106 123 0.24
107 84 0.16
108 223 0.43
ACGTcount: A:0.39, C:0.16, G:0.13, T:0.33
Consensus pattern (108 bp):
TGCACACATAGTGCCAATACAGAAATTCATAAACTTATTATGAATTTCTTAGGTTGCACACACAG
TGCCAATACAGAAATTCATAAACTAATTATGAATTTCTTAGGT
Found at i:3633287 original size:162 final size:162
Alignment explanation
Indices: 3632653--3633353 Score: 866
Period size: 162 Copynumber: 4.4 Consensus size: 162
3632643 TTACGTGGGG
* * * *
3632653 TGCACACATAATGCCAATACAGAAATTCATAAA-TTAATTATGAATTTCTTAGGTTGTACACACA
1 TGCACACACAGTGCCAATACGGAAATTCATAAACTT-ATTATGAATTTCTTAGGTTGCACACACA
* * * * * * *
3632717 GTGCCAATACAAAAATTTATAAACTAATTATGAATTTCTTAGGTTGCATACATAGTGGCAAT--A
65 GTGCCAATACAGAAATTCATAAACTTATTATGAAATTATTAGGTTGCACACATAGTGCCAATACA
* * **
3632780 AAATTTCATAAACTAATTATGAATTTATTAAAT
130 AAAATTCATAAACTAATTATGAATTTCTTAGGT
* * * * *
3632813 TG----CACAGTACCAATACAGAAATTCATAAACTTATTATGAATTTCTGAAGTTGCACACACAT
1 TGCACACACAGTGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTAGGTTGCACACACAG
* * * ** * * *
3632874 TGTCAATACATAAATTCAAAAACTTATTATG-AATTATTAACTTGTACACACAGTGCCAATACAG
66 TGCCAATACAGAAATTCATAAACTTATTATGAAATTATTAGGTTGCACACATAGTGCCAATACAA
3632938 AAATTCATAAACTAATTATGAATTTCTTAGGT
131 AAATTCATAAACTAATTATGAATTTCTTAGGT
* * * * *
3632970 TGCACACATAGTACCAATACGAAAATTCATAAAATTATTATGAATTTCTTAGGTTG--TACACAG
1 TGCACACACAGTGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTAGGTTGCACACACAG
* * * **
3633033 TGCCAATACGGAAATTCATAAACTTATTATGAATTTATTAGGTTGCACACATAGTGCCAATGCCG
66 TGCCAATACAGAAATTCATAAACTTATTATGAAATTATTAGGTTGCACACATAGTGCCAATACAA
3633098 AAATTCATAAACTAATTATGAATTTCTTAGGT
131 AAATTCATAAACTAATTATGAATTTCTTAGGT
* *
3633130 TGCACACACAGTGCCAATACGGAAATTCATAAACTAATTATGAATTTCTTAGGTTGCACACATAG
1 TGCACACACAGTGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTAGGTTGCACACACAG
** * * *
3633195 TGCCAATAGGGAAATTCATAAACTTATTATGAAATTCTTAGGTTGCACACATAGTGTCAGTACAA
66 TGCCAATACAGAAATTCATAAACTTATTATGAAATTATTAGGTTGCACACATAGTGCCAATACAA
*
3633260 AAATTCATAAACTTATTATGAATTTCTT-GAGT
131 AAATTCATAAACTAATTATGAATTTCTTAG-GT
* * *
3633292 TGCGCACACAGTGCCAATATGGAAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACA
1 TGCACACACAGTGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTAGGTTGCACACA
3633354 GAGCCATTCG
Statistics
Matches: 466, Mismatches: 64, Indels: 20
0.85 0.12 0.04
Matches are distributed among these distances:
155 21 0.05
156 75 0.16
157 33 0.07
159 32 0.07
160 111 0.24
161 45 0.10
162 149 0.32
ACGTcount: A:0.39, C:0.16, G:0.13, T:0.33
Consensus pattern (162 bp):
TGCACACACAGTGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTAGGTTGCACACACAG
TGCCAATACAGAAATTCATAAACTTATTATGAAATTATTAGGTTGCACACATAGTGCCAATACAA
AAATTCATAAACTAATTATGAATTTCTTAGGT
Found at i:3638137 original size:53 final size:52
Alignment explanation
Indices: 3638080--3638185 Score: 142
Period size: 53 Copynumber: 2.0 Consensus size: 52
3638070 ACATAGTGTT
* *
3638080 AATACTGAAATTCAT-AACTTATTATGAATTTCTTAAGTTCCACACACAGTGCC
1 AATACGGAAATTCATAAACTTATTAT-AAATTCTTAAGTTCCACACACA-TGCC
* * *
3638133 AATACGGGAATTCATAAACTTATTATAAATTCTTAAGTTGCACAGACATGCC
1 AATACGGAAATTCATAAACTTATTATAAATTCTTAAGTTCCACACACATGCC
3638185 A
1 A
3638186 TTCGGTAAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
52 5 0.11
53 32 0.68
54 10 0.21
ACGTcount: A:0.38, C:0.19, G:0.11, T:0.32
Consensus pattern (52 bp):
AATACGGAAATTCATAAACTTATTATAAATTCTTAAGTTCCACACACATGCC
Found at i:3642025 original size:53 final size:54
Alignment explanation
Indices: 3641933--3642053 Score: 199
Period size: 53 Copynumber: 2.3 Consensus size: 54
3641923 TTTGAGGTTT
* *
3641933 CACACATAGTGCCAATACTGAAATTCATAAACTTATTATGAATTTCTTAAGATG
1 CACACACAGTGCCAATACTAAAATTCATAAACTTATTATGAATTTCTTAAGATG
* *
3641987 CACACACAATGCCAATAC-AAAATTCATAAACTTATTATGAATTTCTTAAGTTG
1 CACACACAGTGCCAATACTAAAATTCATAAACTTATTATGAATTTCTTAAGATG
3642040 CACACACAGTGCCA
1 CACACACAGTGCCA
3642054 TTCGTAAATG
Statistics
Matches: 62, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
53 46 0.74
54 16 0.26
ACGTcount: A:0.40, C:0.21, G:0.10, T:0.30
Consensus pattern (54 bp):
CACACACAGTGCCAATACTAAAATTCATAAACTTATTATGAATTTCTTAAGATG
Found at i:3644083 original size:36 final size:36
Alignment explanation
Indices: 3644036--3644115 Score: 151
Period size: 36 Copynumber: 2.2 Consensus size: 36
3644026 CCTCAATCTA
3644036 TTCATCTTCTACTTATACAATTCTTATCATAAAATT
1 TTCATCTTCTACTTATACAATTCTTATCATAAAATT
*
3644072 TTCATCTTCTACTTATACAGTTCTTATCATAAAATT
1 TTCATCTTCTACTTATACAATTCTTATCATAAAATT
3644108 TTCATCTT
1 TTCATCTT
3644116 TCTATCTCAA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 43 1.00
ACGTcount: A:0.30, C:0.20, G:0.01, T:0.49
Consensus pattern (36 bp):
TTCATCTTCTACTTATACAATTCTTATCATAAAATT
Found at i:3646988 original size:54 final size:54
Alignment explanation
Indices: 3646930--3647474 Score: 619
Period size: 54 Copynumber: 10.1 Consensus size: 54
3646920 TTACGTGGGG
* * * * *** * *
3646930 TGCACACATAGTGCGAATATGGAAATTAATAAAAGAAATATGAATTTCTTAGGT
1 TGCACACATAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAGT
* * * * *
3646984 TGCACATACAGTGCCAATATGAAAAGTCATAAACTTATTAAGAATTTCTTAAGT
1 TGCACACATAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAGT
* * * * * *
3647038 TACACATATAGTGCCAATACGGAAATTCACAACCTCATTATGAATTTCTTAAGT
1 TGCACACATAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAGT
* * * * * * * * *
3647092 TGTACAGACATTGCCAATACAAAAATTCATTAACTAATTTTGAATTTCTTAGGT
1 TGCACACATAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAGT
* * * *
3647146 TGCACTCATAGTGACAATACGAAAATTCATAAGCTTATTATGAATTTCTTAGGT
1 TGCACACATAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAGT
* ** * * *
3647200 TG--CACATAATGCCAATATAAAAATTCATAAAC-TATTATGTATATCTTATGT
1 TGCACACATAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAGT
* *
3647251 TGCACACATAGTGCCAATATGGAAATTCATAAACTTATTATGAATTTCTTAAGT
1 TGCACACATAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAGT
* * *
3647305 TGCACACATAGTGCCAATACGAAAATTCATAAACTAATTATGAATTTATTAGGT
1 TGCACACATAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAGT
3647359 TGCACACATAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAGT
1 TGCACACATAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAGT
* * * * *
3647413 TCCACAGATAGTGCCAATGCAAAAATTCATAAACTTCTTATGAATTTCTTAAGT
1 TGCACACATAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAGT
*
3647467 TGCTCACA
1 TGCACACA
3647475 CAGCACCATT
Statistics
Matches: 412, Mismatches: 76, Indels: 6
0.83 0.15 0.01
Matches are distributed among these distances:
51 18 0.04
52 24 0.06
53 27 0.07
54 343 0.83
ACGTcount: A:0.39, C:0.16, G:0.12, T:0.33
Consensus pattern (54 bp):
TGCACACATAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAGT
Found at i:3647457 original size:267 final size:267
Alignment explanation
Indices: 3646976--3647469 Score: 700
Period size: 267 Copynumber: 1.9 Consensus size: 267
3646966 AATATGAATT
*
3646976 TCTTAGGTTGCACATACAGTGCCAATATGAAAAGTCATAAACTTATTAAGAATTTCTTAAGTTAC
1 TCTTAGGTTGCACACACAGTGCCAATATGAAAAGTCATAAACTTATTAAGAATTTCTTAAGTTAC
* * * * * * * *
3647041 ACATATAGTGCCAATACGGAAATTCACAACCTCATTATGAATTTCTTAAGTTGTACAGACATTGC
66 ACACATAGTGCCAATACGAAAATTCACAAACTAATTATGAATTTATTAAGTTGCACACACAGTGC
* * * * * *
3647106 CAATACAAAAATTCATTAACTAATTTTGAATTTCTTAGGTTGCACTCATAGTGACAATACGAAAA
131 CAATACAAAAATTCATAAACTAATTATGAATTTCTTAAGTTCCACACATAGTGACAATACAAAAA
* *
3647171 TTCATAAGCTTATTATGAATTTCTTAGGTTGCACATAATGCCAATATAAAAATTCATAAACTATT
196 TTCATAAACTTATTATGAATTTCTTAAGTTGCACATAATGCCAATATAAAAATTCATAAACTATT
3647236 ATGTATA
261 ATGTATA
* * * * * *
3647243 TCTTATGTTGCACACATAGTGCCAATATGGAAATTCATAAACTTATTATGAATTTCTTAAGTTGC
1 TCTTAGGTTGCACACACAGTGCCAATATGAAAAGTCATAAACTTATTAAGAATTTCTTAAGTTAC
* * *
3647308 ACACATAGTGCCAATACGAAAATTCATAAACTAATTATGAATTTATTAGGTTGCACACATAGTGC
66 ACACATAGTGCCAATACGAAAATTCACAAACTAATTATGAATTTATTAAGTTGCACACACAGTGC
* * * * *
3647373 CAATACGAAAATTCATAAACTTATTATGAATTTCTTAAGTTCCACAGATAGTGCCAATGCAAAAA
131 CAATACAAAAATTCATAAACTAATTATGAATTTCTTAAGTTCCACACATAGTGACAATACAAAAA
*
3647438 TTCATAAACTTCTTATGAATTTCTTAAGTTGC
196 TTCATAAACTTATTATGAATTTCTTAAGTTGC
3647470 TCACACAGCA
Statistics
Matches: 195, Mismatches: 32, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
267 195 1.00
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.34
Consensus pattern (267 bp):
TCTTAGGTTGCACACACAGTGCCAATATGAAAAGTCATAAACTTATTAAGAATTTCTTAAGTTAC
ACACATAGTGCCAATACGAAAATTCACAAACTAATTATGAATTTATTAAGTTGCACACACAGTGC
CAATACAAAAATTCATAAACTAATTATGAATTTCTTAAGTTCCACACATAGTGACAATACAAAAA
TTCATAAACTTATTATGAATTTCTTAAGTTGCACATAATGCCAATATAAAAATTCATAAACTATT
ATGTATA
Found at i:3650518 original size:19 final size:18
Alignment explanation
Indices: 3650494--3650538 Score: 72
Period size: 18 Copynumber: 2.4 Consensus size: 18
3650484 CATTGGTTCT
3650494 CATTTTTCTACAGGAATTG
1 CATTTTTC-ACAGGAATTG
*
3650513 CATTTTTCATAGGAATTG
1 CATTTTTCACAGGAATTG
3650531 CATTTTTC
1 CATTTTTC
3650539 CAACAATTAC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 17 0.68
19 8 0.32
ACGTcount: A:0.24, C:0.16, G:0.13, T:0.47
Consensus pattern (18 bp):
CATTTTTCACAGGAATTG
Found at i:3651827 original size:20 final size:20
Alignment explanation
Indices: 3651802--3651842 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
3651792 TATTTATACC
*
3651802 AAATGCAACTATATGCTCCT
1 AAATGCAACTATATGATCCT
*
3651822 AAATGCATCTATATGATCCT
1 AAATGCAACTATATGATCCT
3651842 A
1 A
3651843 TATGAGCTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.37, C:0.22, G:0.10, T:0.32
Consensus pattern (20 bp):
AAATGCAACTATATGATCCT
Found at i:3655084 original size:77 final size:78
Alignment explanation
Indices: 3654950--3655104 Score: 303
Period size: 77 Copynumber: 2.0 Consensus size: 78
3654940 AGATTGTTGC
3654950 AGCATTACAAGAGCGTCAACAAAGATGTTTTCCAAGTGACATTGAAATCACTAAATCGCATTGAA
1 AGCATTACAAGAGCGTCAACAAAGATGTTTTCCAAGTGACATTGAAATCACTAAATCGCATTGAA
3655015 AAGAAAAATGCAA
66 AAGAAAAATGCAA
3655028 AGCATT-CAAGAGCGTCAACAAAGATGTTTTCCAAGTGACATTGAAATCACTAAATCGCATTGAA
1 AGCATTACAAGAGCGTCAACAAAGATGTTTTCCAAGTGACATTGAAATCACTAAATCGCATTGAA
3655092 AAGAAAAATGCAA
66 AAGAAAAATGCAA
3655105 CGTAGACCCC
Statistics
Matches: 77, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
77 71 0.92
78 6 0.08
ACGTcount: A:0.45, C:0.17, G:0.17, T:0.22
Consensus pattern (78 bp):
AGCATTACAAGAGCGTCAACAAAGATGTTTTCCAAGTGACATTGAAATCACTAAATCGCATTGAA
AAGAAAAATGCAA
Found at i:3661946 original size:9 final size:8
Alignment explanation
Indices: 3661923--3661960 Score: 58
Period size: 8 Copynumber: 4.8 Consensus size: 8
3661913 ACATGCTTCC
3661923 CCCTTTTT
1 CCCTTTTT
*
3661931 CTCTTTTT
1 CCCTTTTT
3661939 CCCTTTTT
1 CCCTTTTT
3661947 CCCTTTTT
1 CCCTTTTT
*
3661955 CTCTTT
1 CCCTTT
3661961 GCAGTTTGCT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
8 27 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (8 bp):
CCCTTTTT
Found at i:3665799 original size:13 final size:13
Alignment explanation
Indices: 3665776--3665814 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
3665766 AATGACGCTC
*
3665776 AATGCGCGTCATA
1 AATGTGCGTCATA
*
3665789 AATGTGTGTCATA
1 AATGTGCGTCATA
3665802 AATGTGCGTCATA
1 AATGTGCGTCATA
3665815 GATTTATGAC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (13 bp):
AATGTGCGTCATA
Found at i:3669961 original size:8 final size:7
Alignment explanation
Indices: 3669920--3669983 Score: 51
Period size: 7 Copynumber: 8.9 Consensus size: 7
3669910 GATTTAATAA
3669920 AATAAAT
1 AATAAAT
*
3669927 TATATAAT
1 AATA-AAT
3669935 AATAAAT
1 AATAAAT
3669942 AA-AAA-
1 AATAAAT
*
3669947 AGTAAAT
1 AATAAAT
3669954 AATGAAAT
1 AAT-AAAT
3669962 AATAAAT
1 AATAAAT
*
3669969 AGTAATAGT
1 AATAA-A-T
3669978 AATAAA
1 AATAAA
3669984 GATAAAAGGG
Statistics
Matches: 45, Mismatches: 6, Indels: 11
0.73 0.10 0.18
Matches are distributed among these distances:
5 1 0.02
6 6 0.13
7 18 0.40
8 15 0.33
9 5 0.11
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.28
Consensus pattern (7 bp):
AATAAAT
Found at i:3672723 original size:5 final size:5
Alignment explanation
Indices: 3672713--3672829 Score: 83
Period size: 5 Copynumber: 22.8 Consensus size: 5
3672703 TGCTCAGAGA
* * * * *
3672713 AAAAT AAAAT AAAAT TAATT AAAAT AAAAT -AAAT AGAAT GAAAAT TAAGT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT -AAAAT AAAAT
**** * *
3672763 TTGCT AAAAAT AAAAT AAAAAT TAAAC AAAAT AAAAT GAAAAT AAAAT
1 AAAAT -AAAAT AAAAT -AAAAT AAAAT AAAAT AAAAT -AAAAT AAAAT
*
3672811 GAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAA
3672830 AATATAATAA
Statistics
Matches: 86, Mismatches: 21, Indels: 10
0.74 0.18 0.09
Matches are distributed among these distances:
4 4 0.05
5 67 0.78
6 15 0.17
ACGTcount: A:0.70, C:0.02, G:0.05, T:0.23
Consensus pattern (5 bp):
AAAAT
Found at i:3672756 original size:20 final size:20
Alignment explanation
Indices: 3672713--3672844 Score: 57
Period size: 20 Copynumber: 6.8 Consensus size: 20
3672703 TGCTCAGAGA
* *
3672713 AAAATAAAATAAAATTAATT
1 AAAATAAAATAAAATGAATG
3672733 AAAATAAAAT-AAATAGAATG
1 AAAATAAAATAAAAT-GAATG
* * * * *
3672753 AAAATTAAGT---TTG-CTA
1 AAAATAAAATAAAATGAATG
* **
3672769 AAAATAAAATAAAAATTAAAC
1 AAAATAAAAT-AAAATGAATG
*
3672790 AAAATAAAATGAAAATAAAATG
1 AAAATAAAAT-AAAAT-GAATG
3672812 -AAATAAAATAAAAT-AA--
1 AAAATAAAATAAAATGAATG
*
3672828 AAAATATAATAAAATGA
1 AAAATAAAATAAAATGA
3672845 GTCGCCTCCC
Statistics
Matches: 84, Mismatches: 19, Indels: 20
0.68 0.15 0.16
Matches are distributed among these distances:
16 9 0.11
17 14 0.17
18 4 0.05
19 4 0.05
20 27 0.32
21 24 0.29
22 2 0.02
ACGTcount: A:0.70, C:0.02, G:0.05, T:0.23
Consensus pattern (20 bp):
AAAATAAAATAAAATGAATG
Found at i:3672783 original size:11 final size:11
Alignment explanation
Indices: 3672767--3672842 Score: 70
Period size: 10 Copynumber: 7.1 Consensus size: 11
3672757 TTAAGTTTGC
3672767 TAAAAATAAAA
1 TAAAAATAAAA
*
3672778 TAAAAATTAAA
1 TAAAAATAAAA
*
3672789 -CAAAATAAAA
1 TAAAAATAAAA
*
3672799 TGAAAATAAAA
1 TAAAAATAAAA
*
3672810 T-GAAATAAAA
1 TAAAAATAAAA
3672820 T-AAAATAAAA
1 TAAAAATAAAA
3672830 -AATATAATAAAA
1 TAA-A-AATAAAA
3672842 T
1 T
3672843 GAGTCGCCTC
Statistics
Matches: 54, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
10 26 0.48
11 21 0.39
12 7 0.13
ACGTcount: A:0.75, C:0.01, G:0.03, T:0.21
Consensus pattern (11 bp):
TAAAAATAAAA
Found at i:3672830 original size:21 final size:21
Alignment explanation
Indices: 3672769--3672842 Score: 85
Period size: 21 Copynumber: 3.5 Consensus size: 21
3672759 AAGTTTGCTA
* *
3672769 AAAATAAAATAAAAATTAAAC
1 AAAATAAAATAAAAATAAAAT
*
3672790 AAAATAAAATGAAAATAAAAT
1 AAAATAAAATAAAAATAAAAT
* *
3672811 GAAATAAAATAAAATAAAAAAT
1 AAAATAAAATAAAA-ATAAAAT
*
3672833 ATAATAAAAT
1 AAAATAAAAT
3672843 GAGTCGCCTC
Statistics
Matches: 44, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
21 30 0.68
22 14 0.32
ACGTcount: A:0.76, C:0.01, G:0.03, T:0.20
Consensus pattern (21 bp):
AAAATAAAATAAAAATAAAAT
Found at i:3673814 original size:12 final size:12
Alignment explanation
Indices: 3673787--3673835 Score: 55
Period size: 12 Copynumber: 4.0 Consensus size: 12
3673777 CATTTCATTA
*
3673787 TATCTGTTTTTTT
1 TATCT-TTTATTT
3673800 TATCTTTTATTT
1 TATCTTTTATTT
3673812 TATCTTTATATTT
1 TATCTTT-TATTT
*
3673825 TAAC-TTTATTT
1 TATCTTTTATTT
3673836 CACCACACGC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
11 5 0.15
12 15 0.45
13 13 0.39
ACGTcount: A:0.18, C:0.08, G:0.02, T:0.71
Consensus pattern (12 bp):
TATCTTTTATTT
Found at i:3673826 original size:13 final size:13
Alignment explanation
Indices: 3673797--3673833 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
3673787 TATCTGTTTT
3673797 TTTTATCTTT-TA
1 TTTTATCTTTATA
3673809 TTTTATCTTTATA
1 TTTTATCTTTATA
*
3673822 TTTTAACTTTAT
1 TTTTATCTTTAT
3673834 TTCACCACAC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 10 0.43
13 13 0.57
ACGTcount: A:0.22, C:0.08, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTTATCTTTATA
Found at i:3676419 original size:11 final size:11
Alignment explanation
Indices: 3676403--3676431 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
3676393 TTGTAACTCA
3676403 TTTTCCTTGAT
1 TTTTCCTTGAT
3676414 TTTTCCTTGAT
1 TTTTCCTTGAT
3676425 TTTTCCT
1 TTTTCCT
3676432 AGTGAGAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.07, C:0.21, G:0.07, T:0.66
Consensus pattern (11 bp):
TTTTCCTTGAT
Found at i:3676822 original size:21 final size:21
Alignment explanation
Indices: 3676798--3676848 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 21
3676788 TAAGGGAAAT
*
3676798 GATCGATCCCT-TACCAAAAAG
1 GATCGATCCCTCGACC-AAAAG
* * *
3676819 GATCAATCTCTCGACCGAAAG
1 GATCGATCCCTCGACCAAAAG
3676840 GATCGATCC
1 GATCGATCC
3676849 TAAACTCTTT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
21 20 0.87
22 3 0.13
ACGTcount: A:0.33, C:0.29, G:0.18, T:0.20
Consensus pattern (21 bp):
GATCGATCCCTCGACCAAAAG
Found at i:3676894 original size:21 final size:21
Alignment explanation
Indices: 3676870--3676915 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
3676860 TTATGTAATG
*
3676870 GATCGATCCCTTAGAGAAAAT
1 GATCGATCCCTCAGAGAAAAT
*
3676891 GATCGATCGCTCAGAGAAAAT
1 GATCGATCCCTCAGAGAAAAT
3676912 GATC
1 GATC
3676916 AATTCCTTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.37, C:0.20, G:0.22, T:0.22
Consensus pattern (21 bp):
GATCGATCCCTCAGAGAAAAT
Found at i:3677568 original size:278 final size:276
Alignment explanation
Indices: 3677073--3677626 Score: 1081
Period size: 278 Copynumber: 2.0 Consensus size: 276
3677063 CTTGACCCGA
3677073 GTCCTAAGGAGACACTAATGCTAGGTGACCCAGGTATTCCTTATGTATTGTAAGTAAAGAGGGGT
1 GTCCTAAGGAGACACTAATGCTAGGTGACCCAGGTATTCCTTATGTATTGTAAGTAAAGAGGGGT
3677138 GTGAGTTCTGCGATGCTGTATGACCCCCTACATCATGATACTTACTGTTTTCTTGAGTGTTGCAA
66 GTGAGTTCTGCGATGCTGTATGACCCCCTACATCATGATACTTACTGTTTTCTTGAGTGTTGCAA
3677203 TTGCTCATAACTATAATGTATTATGCTTATATGTTAAATGCATGTAGTACAACTTGGTTATTTTT
131 TTGCTCATAACTATAATGTATTATGCTTATATGTTAAATGCATGTAGTACAACTTGGTTATTTTT
3677268 GGTGTCATTAAGCTTGTAAGCTCAGCGTATGAAATGTGTTTCTGTGCATAGGTTAGTAGGTTCCA
196 GGTGTCATTAAGCTTGTAAGCTCAGCGTATGAAATGTGTTTCTGTGCATAGGTTAGTAGGTTCCA
3677333 GCTAAGGAGCTCTTCG
261 GCTAAGGAGCTCTTCG
3677349 GTCCTAAGGAGACACTAATGCTAGGTGACCCAGGTATTCCTTATGTATTGTAAGTAAAGAGGGGT
1 GTCCTAAGGAGACACTAATGCTAGGTGACCCAGGTATTCCTTATGTATTGTAAGTAAAGAGGGGT
*
3677414 GTGAGTTCTGCGATGCTGTATGACCCGAGCTACATCATGATACTTACTGTTTTCTTGAGTGTTGC
66 GTGAGTTCTGCGATGCTGTATGACCC--CCTACATCATGATACTTACTGTTTTCTTGAGTGTTGC
3677479 AATTGCTCATAACTATAATGTATTATGCTTATATGTTAAATGCATGTAGTACAACTTGGTTATTT
129 AATTGCTCATAACTATAATGTATTATGCTTATATGTTAAATGCATGTAGTACAACTTGGTTATTT
3677544 TTGGTGTCATTAAGCTTGTAAGCTCAGCGTATGAAATGTGTTTCTGTGCATAGGTTAGTAGGTTC
194 TTGGTGTCATTAAGCTTGTAAGCTCAGCGTATGAAATGTGTTTCTGTGCATAGGTTAGTAGGTTC
3677609 CAGCTAAGGAGCTCTTCG
259 CAGCTAAGGAGCTCTTCG
3677627 CTAGACTTGG
Statistics
Matches: 275, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
276 91 0.33
278 184 0.67
ACGTcount: A:0.25, C:0.16, G:0.23, T:0.36
Consensus pattern (276 bp):
GTCCTAAGGAGACACTAATGCTAGGTGACCCAGGTATTCCTTATGTATTGTAAGTAAAGAGGGGT
GTGAGTTCTGCGATGCTGTATGACCCCCTACATCATGATACTTACTGTTTTCTTGAGTGTTGCAA
TTGCTCATAACTATAATGTATTATGCTTATATGTTAAATGCATGTAGTACAACTTGGTTATTTTT
GGTGTCATTAAGCTTGTAAGCTCAGCGTATGAAATGTGTTTCTGTGCATAGGTTAGTAGGTTCCA
GCTAAGGAGCTCTTCG
Found at i:3686444 original size:21 final size:21
Alignment explanation
Indices: 3686420--3686477 Score: 57
Period size: 20 Copynumber: 2.8 Consensus size: 21
3686410 TACTCAGGTG
3686420 AGTATCAATACCCATGGGTC-C
1 AGTATCAATACCCATGGG-CAC
* * *
3686441 AGTATCGATA-CTATTGGCAC
1 AGTATCAATACCCATGGGCAC
*
3686461 AGTACCAATACCCATGG
1 AGTATCAATACCCATGG
3686478 TGAATTTCGG
Statistics
Matches: 28, Mismatches: 7, Indels: 4
0.72 0.18 0.10
Matches are distributed among these distances:
19 1 0.04
20 14 0.50
21 13 0.46
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.24
Consensus pattern (21 bp):
AGTATCAATACCCATGGGCAC
Found at i:3693419 original size:42 final size:41
Alignment explanation
Indices: 3693320--3693423 Score: 120
Period size: 42 Copynumber: 2.5 Consensus size: 41
3693310 GTACCTACAG
*
3693320 GTTCCGGTTTCGGATCCCAATTTTTAAGAACAGGTTGAACAT
1 GTTCC-GTTTCGGTTCCCAATTTTTAAGAACAGGTTGAACAT
* * * *
3693362 GTTCCGATTCTGGTTCCCCATTTTTAGGAACCGG-TGCAACAT
1 GTTCCGTTTC-GGTTCCCAATTTTTAAGAACAGGTTG-AACAT
3693404 GTTCCGCTTTCGGTTCCCAA
1 GTTCCG-TTTCGGTTCCCAA
3693424 AAAAATAAGC
Statistics
Matches: 52, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
41 6 0.12
42 43 0.83
43 3 0.06
ACGTcount: A:0.20, C:0.25, G:0.21, T:0.34
Consensus pattern (41 bp):
GTTCCGTTTCGGTTCCCAATTTTTAAGAACAGGTTGAACAT
Found at i:3701738 original size:45 final size:45
Alignment explanation
Indices: 3701675--3702269 Score: 847
Period size: 45 Copynumber: 13.2 Consensus size: 45
3701665 TATACTTTAT
3701675 TTTCATTTATGGCATCCTTTCATGTCGATAATGCACTGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGTCGATAATGCACTGTTATGCA
* * *
3701720 TTTTATTTATGGCATCCTTTCAT-ACAGATAATGCACCGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGTC-GATAATGCACTGTTATGCA
* * *
3701765 TTACATTTATGGGATCCTTTCATGTCGATAATGCATTGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGTCGATAATGCACTGTTATGCA
* ** *
3701810 TTTTATTTATGGCATCCTTTCATACCGATAATGCACCGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGTCGATAATGCACTGTTATGCA
*
3701855 TTTCATTTATGGCATCCTTTCATGTCGATAATGCACCGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGTCGATAATGCACTGTTATGCA
** *
3701900 TTTCATTTATGGCATTATTTCATGTCGATAATGCACCGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGTCGATAATGCACTGTTATGCA
* * *
3701945 TTTCATTTATGGCATCCTTTCAT-TCTGATAATACA-TCGTTGTGTA
1 TTTCATTTATGGCATCCTTTCATGTC-GATAATGCACT-GTTATGCA
* * * *
3701990 TTTCATTTATGGCAACATTTCATGCCGATAATGCATTGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGTCGATAATGCACTGTTATGCA
*
3702035 TTTCATTTATGGCATCCTTTCATGTCGATAATGCACCGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGTCGATAATGCACTGTTATGCA
*
3702080 TTTCATTTATGGCTTCCTTTCATGTCGATAATGCACCT-TTATGCA
1 TTTCATTTATGGCATCCTTTCATGTCGATAATGCA-CTGTTATGCA
** *
3702125 TTTCATTTATACCATCCTTTCATGCCGATAATGCACTGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGTCGATAATGCACTGTTATGCA
* * *
3702170 TTTCATTTATGCCATCCTTTCATGTTGATAATACACTGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGTCGATAATGCACTGTTATGCA
* *
3702215 TTTCATTTATGGCATCATTTCATGTCGATAATGCACCGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGTCGATAATGCACTGTTATGCA
3702260 TTTCATTTAT
1 TTTCATTTAT
3702270 TATCCCAAAG
Statistics
Matches: 489, Mismatches: 53, Indels: 16
0.88 0.09 0.03
Matches are distributed among these distances:
44 5 0.01
45 480 0.98
46 4 0.01
ACGTcount: A:0.24, C:0.20, G:0.14, T:0.42
Consensus pattern (45 bp):
TTTCATTTATGGCATCCTTTCATGTCGATAATGCACTGTTATGCA
Found at i:3707323 original size:45 final size:45
Alignment explanation
Indices: 3707263--3708056 Score: 559
Period size: 45 Copynumber: 18.2 Consensus size: 45
3707253 TATACTTTAT
* *
3707263 TTTCATTTATAGCATCCTTTCATGCCGATAATGCACTGTTATTCA
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACTGTTATGCA
* * *
3707308 TTTCAGTTATGGCATCCTTTCATGCTGATAATGCACCGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACTGTTATGCA
* * *
3707353 TTTCATTTATGGCATCCTTTCATACCGATAAAGCATTGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACTGTTATGCA
3707398 TTTCATTTATGGCATCCTTTCATGCCGATAAT--A-TGCTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACTG-TTATGCA
* * *
3707441 TTTCATTTATGGCATACTTTCATGTCGATAATGCGCCT-TTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGC-ACTGTTATGCA
* * *
3707486 TTTCATTTATGGCATCATTTCATGTCGATAATGCA-TCCTT-T-CA
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACT-GTTATGCA
* * * *
3707529 TGTCGA-TAAT-GCA-CCGTT-ATG-C-AT-GT-CA-T-TTATGGCA
1 TTTC-ATTTATGGCATCCTTTCATGCCGATAATGCACTGTTAT-GCA
* ** * * * **
3707566 --TCCTTTCAT-GC-T--GATAATGTACCG-TTATGCA-TTTTATTTA
1 TTTCATTT-ATGGCATCCTTTCATG--CCGATAATGCACTGTTATGCA
** * ** * * * **
3707606 TGGCAACCTTTCATGTCGAT-AATGCA--CCG-TTATGCA-TTTTATTTA
1 TTTC-A--TTT-ATGGC-ATCCTTTCATGCCGATAATGCACTGTTATGCA
** * * **
3707651 TGGCATTCAT---A------CATGCCAATAATGCACCATTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACTGTTATGCA
* * *
3707687 TTTCATTTATGGCATCCTTTCATGTCGATAATGCACCGTTGTGCA
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACTGTTATGCA
* * *
3707732 TTTCATTTATGGCATACTTTCATGCCTATAATGCACCGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACTGTTATGCA
* * * *
3707777 TCTCATTTATGACATCCTTTCATGTCGATAATGCACCGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACTGTTATGCA
*
3707822 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACTGTTATGCA
* ** **
3707867 TTTCATTTATGGCATCATTTCATGTTGATAATGCACCATTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACTGTTATGCA
* * **
3707912 TTTCATTTATGGTATCCTTTCATGTCGATAATGCACCATTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACTGTTATGCA
* **
3707957 TTTCATTTATGGCATCATTTCATGTTGATAATGCACTGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACTGTTATGCA
* * * * **
3708002 TTTCTTTTATGGCATCCATTCATGCTGATAATACACCATTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACTGTTATGCA
3708047 TTTCATTTAT
1 TTTCATTTAT
3708057 TATCCCAAAG
Statistics
Matches: 622, Mismatches: 83, Indels: 88
0.78 0.10 0.11
Matches are distributed among these distances:
32 2 0.00
34 6 0.01
35 13 0.02
36 19 0.03
37 4 0.01
38 4 0.01
39 3 0.00
40 7 0.01
41 9 0.01
42 8 0.01
43 47 0.08
44 3 0.00
45 493 0.79
46 1 0.00
47 1 0.00
48 1 0.00
49 1 0.00
ACGTcount: A:0.24, C:0.21, G:0.14, T:0.41
Consensus pattern (45 bp):
TTTCATTTATGGCATCCTTTCATGCCGATAATGCACTGTTATGCA
Found at i:3707483 original size:88 final size:89
Alignment explanation
Indices: 3707263--3707517 Score: 345
Period size: 88 Copynumber: 2.9 Consensus size: 89
3707253 TATACTTTAT
* * *
3707263 TTTCATTTATAGCATCCTTTCATGCCGATAATGCACTGTTATTCATTTCAGTTATGGCATCCTTT
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACTGTTATGCATTTCATTTATGGCATCCTTT
*
3707328 CATGCTGATAATGCACCGTTATGCA
66 CATGCCGATAAT-CACCGTTATGCA
* * *
3707353 TTTCATTTATGGCATCCTTTCATACCGATAAAGCATTGTTATGCATTTCATTTATGGCATCCTTT
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACTGTTATGCATTTCATTTATGGCATCCTTT
*
3707418 CATGCCGATAAT-A-TGCTTATGCA
66 CATGCCGATAATCACCG-TTATGCA
* * * *
3707441 TTTCATTTATGGCATACTTTCATGTCGATAATGCGCCT-TTATGCATTTCATTTATGGCATCATT
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGC-ACTGTTATGCATTTCATTTATGGCATCCTT
*
3707505 TCATGTCGATAAT
65 TCATGCCGATAAT
3707518 GCATCCTTTC
Statistics
Matches: 147, Mismatches: 16, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
87 1 0.01
88 75 0.51
89 1 0.01
90 70 0.48
ACGTcount: A:0.24, C:0.20, G:0.14, T:0.42
Consensus pattern (89 bp):
TTTCATTTATGGCATCCTTTCATGCCGATAATGCACTGTTATGCATTTCATTTATGGCATCCTTT
CATGCCGATAATCACCGTTATGCA
Found at i:3707507 original size:133 final size:134
Alignment explanation
Indices: 3707263--3708056 Score: 619
Period size: 135 Copynumber: 6.1 Consensus size: 134
3707253 TATACTTTAT
* *
3707263 TTTCATTTATAGCATCCTTTCATGCCGATAATGCACTGTTATTCATTTCAGTTATGGCATCCTTT
1 TTTCATTTATAGCATCCTTTCATGCCGATAAT-CACTGTTATGCATTTCAGTTATGGCATACTTT
*
3707328 CATGCTGATAATGCACCGTTATGCATTTCATTTATGGCATCCTTTCATACCGATAAAGCATTGTT
65 CATGCTGATAATGCACCGTTATGCATTTCATTTATGGCATCATTTCATACCGATAAAGCATTGTT
3707393 ATGCA
130 ATGCA
* *
3707398 TTTCATTTATGGCATCCTTTCATGCCGATAAT-A-TGCTTATGCATTTCATTTATGGCATACTTT
1 TTTCATTTATAGCATCCTTTCATGCCGATAATCACTG-TTATGCATTTCAGTTATGGCATACTTT
* * ** * **
3707461 CATG-TCGATAATGCGCCTTTATGCATTTCATTTATGGCATCATTTCATGTCGATAATGCATCCT
65 CATGCT-GATAATGCACCGTTATGCATTTCATTTATGGCATCATTTCATACCGATAAAGCATTGT
3707525 T-T-CA
129 TATGCA
* * * * *
3707529 TGTCGA-TAAT-GCA-CCGTT-ATG-C-AT-GTCA-T-TTATG-------G-CAT--C---CTTT
1 TTTC-ATTTATAGCATCCTTTCATGCCGATAATCACTGTTATGCATTTCAGTTATGGCATACTTT
* * * * ** * **
3707572 CATGCTGATAATGTACCGTTATGCATTTTATTTATGGCAACCTTTCATGTCGATAATGCACCGTT
65 CATGCTGATAATGCACCGTTATGCATTTCATTTATGGCATCATTTCATACCGATAAAGCATTGTT
3707637 ATGCA
130 ATGCA
* * * * * * ** * *
3707642 TTTTATTTATGGCATTCATACATGCCAATAATGCACCATTATGCATTTCATTTATGGCATCCTTT
1 TTTCATTTATAGCATCCTTTCATGCCGATAAT-CACTGTTATGCATTTCAGTTATGGCATACTTT
* * * * **
3707707 CATG-TCGATAATGCACCGTTGTGCATTTCATTTATGGCAT-ACTTTCATGCCTATAATGCACCG
65 CATGCT-GATAATGCACCGTTATGCATTTCATTTATGGCATCA-TTTCATACCGATAAAGCATTG
3707770 TTATGCA
128 TTATGCA
* * * * *
3707777 TCTCATTTAT-GACATCCTTTCATGTCGATAATGCACCGTTATGCATTTCATTTATGGCATCCTT
1 TTTCATTTATAG-CATCCTTTCATGCCGATAAT-CACTGTTATGCATTTCAGTTATGGCATACTT
* *** * ***
3707841 TCATGCCGATAATGCACCGTTATGCATTTCATTTATGGCATCATTTCATGTTGATAATGCACCAT
64 TCATGCTGATAATGCACCGTTATGCATTTCATTTATGGCATCATTTCATACCGATAAAGCATTGT
3707906 TATGCA
129 TATGCA
* * * ** *
3707912 TTTCATTTATGGTATCCTTTCATGTCGATAATGCACCATTATGCATTTCATTTATGGCAT-CATT
1 TTTCATTTATAGCATCCTTTCATGCCGATAAT-CACTGTTATGCATTTCAGTTATGGCATAC-TT
* * * * * **
3707976 TCATGTTGATAATGCACTGTTATGCATTTCTTTTATGGCATCCA-TTCATGCTGATAATA-CACC
64 TCATGCTGATAATGCACCGTTATGCATTTCATTTATGGCAT-CATTTCATACCGATAA-AGCATT
*
3708039 ATTATGCA
127 GTTATGCA
3708047 TTTCATTTAT
1 TTTCATTTAT
3708057 TATCCCAAAG
Statistics
Matches: 554, Mismatches: 66, Indels: 78
0.79 0.09 0.11
Matches are distributed among these distances:
111 59 0.11
112 3 0.01
113 7 0.01
114 4 0.01
115 2 0.00
116 5 0.01
117 1 0.00
118 2 0.00
119 1 0.00
120 2 0.00
122 5 0.01
124 5 0.01
125 1 0.00
126 4 0.01
127 1 0.00
128 3 0.01
129 4 0.01
130 5 0.01
131 8 0.01
132 6 0.01
133 80 0.14
134 3 0.01
135 339 0.61
136 4 0.01
ACGTcount: A:0.24, C:0.21, G:0.14, T:0.41
Consensus pattern (134 bp):
TTTCATTTATAGCATCCTTTCATGCCGATAATCACTGTTATGCATTTCAGTTATGGCATACTTTC
ATGCTGATAATGCACCGTTATGCATTTCATTTATGGCATCATTTCATACCGATAAAGCATTGTTA
TGCA
Found at i:3707527 original size:21 final size:21
Alignment explanation
Indices: 3707497--3707584 Score: 83
Period size: 21 Copynumber: 4.0 Consensus size: 21
3707487 TTCATTTATG
*
3707497 GCATCATTTCATGTCGATAAT
1 GCATCCTTTCATGTCGATAAT
3707518 GCATCCTTTCATGTCGATAAT
1 GCATCCTTTCATGTCGATAAT
*
3707539 GCA-CCGTTATGCATGTC-ATTTAT
1 GCATCC-TT-T-CATGTCGA-TAAT
3707562 GGCATCCTTTCATG-CTGATAAT
1 -GCATCCTTTCATGTC-GATAAT
3707584 G
1 G
3707585 TACCGTTATG
Statistics
Matches: 56, Mismatches: 3, Indels: 16
0.75 0.04 0.21
Matches are distributed among these distances:
20 2 0.04
21 27 0.48
22 9 0.16
23 11 0.20
24 5 0.09
25 2 0.04
ACGTcount: A:0.24, C:0.22, G:0.17, T:0.38
Consensus pattern (21 bp):
GCATCCTTTCATGTCGATAAT
Found at i:3707531 original size:66 final size:66
Alignment explanation
Indices: 3707452--3707584 Score: 205
Period size: 66 Copynumber: 2.0 Consensus size: 66
3707442 TTCATTTATG
* * *
3707452 GCATACTTTCATGTCGATAATGCGCCTTTATGCATTTCATTTATGGCATCATTTCATG-TCGATA
1 GCATACTTTCATGTCGATAATGCACCGTTATGCATGTCATTTATGGCATCATTTCATGCT-GATA
3707516 AT
65 AT
* *
3707518 GCATCCTTTCATGTCGATAATGCACCGTTATGCATGTCATTTATGGCATCCTTTCATGCTGATAA
1 GCATACTTTCATGTCGATAATGCACCGTTATGCATGTCATTTATGGCATCATTTCATGCTGATAA
3707583 T
66 T
3707584 G
1 G
3707585 TACCGTTATG
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
66 60 0.98
67 1 0.02
ACGTcount: A:0.23, C:0.21, G:0.17, T:0.39
Consensus pattern (66 bp):
GCATACTTTCATGTCGATAATGCACCGTTATGCATGTCATTTATGGCATCATTTCATGCTGATAA
T
Found at i:3707565 original size:111 final size:109
Alignment explanation
Indices: 3707409--3707631 Score: 306
Period size: 111 Copynumber: 2.0 Consensus size: 109
3707399 TTCATTTATG
* *
3707409 GCATCCTTTCATGCCGATAATATGCTTATGCATTTCATTTATGGCATACTTTCATG-TCGATAAT
1 GCATCCTTTCATGCCGATAATACGCTTATGCATGTCATTTATGGCATACTTTCATGCT-GATAAT
* * *
3707473 GCGCCTTTATGCATTTCATTTATGGCATCATTTCATGTCGATAAT
65 GCACCGTTATGCATTTCATTTATGGCAACATTTCATGTCGATAAT
* *
3707518 GCATCCTTTCATGTCGATAATGCAC-CGTTATGCATGTCATTTATGGCATCCTTTCATGCTGATA
1 GCATCCTTTCATGCCGATAAT--ACGC-TTATGCATGTCATTTATGGCATACTTTCATGCTGATA
* * *
3707582 ATGTACCGTTATGCATTTTATTTATGGCAACCTTTCATGTCGATAAT
63 ATGCACCGTTATGCATTTCATTTATGGCAACATTTCATGTCGATAAT
3707629 GCA
1 GCA
3707632 CCGTTATGCA
Statistics
Matches: 100, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
109 20 0.20
110 1 0.01
111 78 0.78
112 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.16, T:0.40
Consensus pattern (109 bp):
GCATCCTTTCATGCCGATAATACGCTTATGCATGTCATTTATGGCATACTTTCATGCTGATAATG
CACCGTTATGCATTTCATTTATGGCAACATTTCATGTCGATAAT
Found at i:3707629 original size:90 final size:90
Alignment explanation
Indices: 3707518--3708056 Score: 794
Period size: 90 Copynumber: 6.0 Consensus size: 90
3707508 TGTCGATAAT
*
3707518 GCATCCTTTCATGTCGATAATGCACCGTTATGCATGTCATTTATGGCATCCTTTCATGCTGATAA
1 GCATCCTTTCATGTCGATAATGCACCGTTATGCATTTCATTTATGGCATCCTTTCATGCTGATAA
* * *
3707583 TGTACCGTTATGCATTTTATTTATG
66 TGCACCATTATGCATTTCATTTATG
* * * * * **
3707608 GCAACCTTTCATGTCGATAATGCACCGTTATGCATTTTATTTATGGCATTCATACATGCCAATAA
1 GCATCCTTTCATGTCGATAATGCACCGTTATGCATTTCATTTATGGCATCCTTTCATGCTGATAA
3707673 TGCACCATTATGCATTTCATTTATG
66 TGCACCATTATGCATTTCATTTATG
* *
3707698 GCATCCTTTCATGTCGATAATGCACCGTTGTGCATTTCATTTATGGCATACTTTCATGCCT-ATA
1 GCATCCTTTCATGTCGATAATGCACCGTTATGCATTTCATTTATGGCATCCTTTCATG-CTGATA
* *
3707762 ATGCACCGTTATGCATCTCATTTATG
65 ATGCACCATTATGCATTTCATTTATG
* *
3707788 ACATCCTTTCATGTCGATAATGCACCGTTATGCATTTCATTTATGGCATCCTTTCATGCCGATAA
1 GCATCCTTTCATGTCGATAATGCACCGTTATGCATTTCATTTATGGCATCCTTTCATGCTGATAA
*
3707853 TGCACCGTTATGCATTTCATTTATG
66 TGCACCATTATGCATTTCATTTATG
* * * *
3707878 GCATCATTTCATGTTGATAATGCACCATTATGCATTTCATTTATGGTATCCTTTCATG-TCGATA
1 GCATCCTTTCATGTCGATAATGCACCGTTATGCATTTCATTTATGGCATCCTTTCATGCT-GATA
3707942 ATGCACCATTATGCATTTCATTTATG
65 ATGCACCATTATGCATTTCATTTATG
* * * * *
3707968 GCATCATTTCATGTTGATAATGCACTGTTATGCATTTCTTTTATGGCATCCATTCATGCTGATAA
1 GCATCCTTTCATGTCGATAATGCACCGTTATGCATTTCATTTATGGCATCCTTTCATGCTGATAA
*
3708033 TACACCATTATGCATTTCATTTAT
66 TGCACCATTATGCATTTCATTTAT
3708057 TATCCCAAAG
Statistics
Matches: 407, Mismatches: 38, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
89 1 0.00
90 404 0.99
91 2 0.00
ACGTcount: A:0.24, C:0.21, G:0.14, T:0.40
Consensus pattern (90 bp):
GCATCCTTTCATGTCGATAATGCACCGTTATGCATTTCATTTATGGCATCCTTTCATGCTGATAA
TGCACCATTATGCATTTCATTTATG
Found at i:3707673 original size:156 final size:154
Alignment explanation
Indices: 3707364--3707676 Score: 432
Period size: 156 Copynumber: 2.0 Consensus size: 154
3707354 TTCATTTATG
** *
3707364 GCATCCTTTCATACCGATAAAGCATTGTTATGCATTTCATTTATGGCATCCTTTCATGCCGATAA
1 GCATCCTTTCATACCGATAAAGCACCGTTATGCATGTCATTTATGGCATCCTTTCATGCCGATAA
* * *
3707429 TATGCTTATGCATTTCATTTATGGCATACTTTCATGTCGATAATGCGCCTTTATGCATTTCATTT
66 TATCCTTATGCATTTCATTTATGGCATACTTTCATGTCGATAATGCACCGTTATGCATTTCATTT
* * *
3707494 ATGGCATCATTTCATGTCGATAAT
131 ATGGCATCATTACATGCCAATAAT
** * *
3707518 GCATCCTTTCATGTCGATAATGCACCGTTATGCATGTCATTTATGGCATCCTTTCATGCTGATAA
1 GCATCCTTTCATACCGATAAAGCACCGTTATGCATGTCATTTATGGCATCCTTTCATGCCGATAA
* * *
3707583 TGTACCGTTATGCATTTTATTTATGGCA-ACCTTTCATGTCGATAATGCACCGTTATGCATTTTA
66 TAT-CC-TTATGCATTTCATTTATGGCATA-CTTTCATGTCGATAATGCACCGTTATGCATTTCA
3707647 TTTATGGCATTCA-TACATGCCAATAAT
128 TTTATGGCA-TCATTACATGCCAATAAT
3707674 GCA
1 GCA
3707677 CCATTATGCA
Statistics
Matches: 139, Mismatches: 16, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
154 60 0.43
155 2 0.01
156 74 0.53
157 3 0.02
ACGTcount: A:0.25, C:0.20, G:0.15, T:0.40
Consensus pattern (154 bp):
GCATCCTTTCATACCGATAAAGCACCGTTATGCATGTCATTTATGGCATCCTTTCATGCCGATAA
TATCCTTATGCATTTCATTTATGGCATACTTTCATGTCGATAATGCACCGTTATGCATTTCATTT
ATGGCATCATTACATGCCAATAAT
Found at i:3710016 original size:22 final size:22
Alignment explanation
Indices: 3709988--3710046 Score: 118
Period size: 22 Copynumber: 2.7 Consensus size: 22
3709978 TACTGAAGGG
3709988 AGTATCGATACCATAGTGTAGA
1 AGTATCGATACCATAGTGTAGA
3710010 AGTATCGATACCATAGTGTAGA
1 AGTATCGATACCATAGTGTAGA
3710032 AGTATCGATACCATA
1 AGTATCGATACCATA
3710047 CTAGGGGTAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.27
Consensus pattern (22 bp):
AGTATCGATACCATAGTGTAGA
Found at i:3710471 original size:54 final size:54
Alignment explanation
Indices: 3710392--3710949 Score: 722
Period size: 54 Copynumber: 10.3 Consensus size: 54
3710382 GTACTATCAA
* * * * *
3710392 CACTAAGTGTGTAACCCATGGAATTCATAATATGTTTATGAATGATCGTATCAG
1 CACTAAGTGTGCAACCCACGGAATTCATAATATGTTTATGAACGACCGTATCGG
* ** *
3710446 TACTAAGTGTGCAACCCACAAAATTCATAATATATTTATGAACGACCGTATCGG
1 CACTAAGTGTGCAACCCACGGAATTCATAATATGTTTATGAACGACCGTATCGG
* * *
3710500 CACTAAGTGTGCAACCCACGGAATTCGTAATATGTTTATGAACGACTGTCTCGG
1 CACTAAGTGTGCAACCCACGGAATTCATAATATGTTTATGAACGACCGTATCGG
*
3710554 CACTAAGTGTGCAACCCACGGAATTCATAATTTGTTTATGAACGACCGTATCGG
1 CACTAAGTGTGCAACCCACGGAATTCATAATATGTTTATGAACGACCGTATCGG
* *
3710608 CACTAAGTGTGCAACCCATGGAATTCATAATATGTTTATGAACGACCATATCGG
1 CACTAAGTGTGCAACCCACGGAATTCATAATATGTTTATGAACGACCGTATCGG
* *
3710662 CACTAAGTGTGCAGCCCACGGAATTCATAATATGTTTATGAACGATCGTATCGG
1 CACTAAGTGTGCAACCCACGGAATTCATAATATGTTTATGAACGACCGTATCGG
* * * * *
3710716 CACTAATTGTGCAACCCACAGAATTCATAATATATTTATGAATGACCATATCGG
1 CACTAAGTGTGCAACCCACGGAATTCATAATATGTTTATGAACGACCGTATCGG
* * * * *
3710770 CACTAAGTGTGCAACCCACGAAATTCATAATATGATTATGAACTACTGTATTGG
1 CACTAAGTGTGCAACCCACGGAATTCATAATATGTTTATGAACGACCGTATCGG
* ** ** * **
3710824 CACTAAGTGTGCAACCTACATAATTCATAATAAATTAATGAACGATTGTATCGG
1 CACTAAGTGTGCAACCCACGGAATTCATAATATGTTTATGAACGACCGTATCGG
* *** * *
3710878 CACTAAGTGTGCAACCAATAAAATTCATAATATATTTATGAATGACCGTATCGG
1 CACTAAGTGTGCAACCCACGGAATTCATAATATGTTTATGAACGACCGTATCGG
*
3710932 CAC-AACGTGTGCACCCCA
1 CACTAA-GTGTGCAACCCA
3710950 ACAAACTTAT
Statistics
Matches: 439, Mismatches: 64, Indels: 2
0.87 0.13 0.00
Matches are distributed among these distances:
53 2 0.00
54 437 1.00
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (54 bp):
CACTAAGTGTGCAACCCACGGAATTCATAATATGTTTATGAACGACCGTATCGG
Found at i:3712575 original size:14 final size:14
Alignment explanation
Indices: 3712556--3712585 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3712546 TTTAGCATTA
*
3712556 ATTGCTATAAAGTT
1 ATTGCTACAAAGTT
3712570 ATTGCTACAAAGTT
1 ATTGCTACAAAGTT
3712584 AT
1 AT
3712586 CGAGTCTTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.37, C:0.10, G:0.13, T:0.40
Consensus pattern (14 bp):
ATTGCTACAAAGTT
Found at i:3716190 original size:18 final size:18
Alignment explanation
Indices: 3716167--3716208 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
3716157 TTCAAAAATT
*
3716167 GTATCGATATTGAAGGAA
1 GTATCGATACTGAAGGAA
*
3716185 GTATCGGTACTGAAGGAA
1 GTATCGATACTGAAGGAA
*
3716203 ATATCG
1 GTATCG
3716209 GTACCATAGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.36, C:0.10, G:0.29, T:0.26
Consensus pattern (18 bp):
GTATCGATACTGAAGGAA
Found at i:3716209 original size:18 final size:18
Alignment explanation
Indices: 3716177--3716212 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
3716167 GTATCGATAT
*
3716177 TGAAGGAAGTATCGGTAC
1 TGAAGGAAATATCGGTAC
3716195 TGAAGGAAATATCGGTAC
1 TGAAGGAAATATCGGTAC
3716213 CATAGTATAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.36, C:0.11, G:0.31, T:0.22
Consensus pattern (18 bp):
TGAAGGAAATATCGGTAC
Found at i:3716699 original size:54 final size:54
Alignment explanation
Indices: 3716577--3716990 Score: 550
Period size: 54 Copynumber: 7.7 Consensus size: 54
3716567 ATATGTGTAT
* * *
3716577 TATCGACACAAAGTGTGCAACCCACGAAATTCATAATATG-TTATGAACGACTG
1 TATCGGCACTAAGTGTGCAACCCACGAAATTCATAATATGTTTATGAACGACCG
* *
3716630 TATCAGCACTAAGTGTGCAACCCACGGAATTCATAATATGTTTATGAACGACCG
1 TATCGGCACTAAGTGTGCAACCCACGAAATTCATAATATGTTTATGAACGACCG
*
3716684 TATCGGCACTAAGTGTGCAACCCACGAAATTCATAATATGTTTATGAACGACCA
1 TATCGGCACTAAGTGTGCAACCCACGAAATTCATAATATGTTTATGAACGACCG
* * * * *
3716738 TATCGGCACTAAGTGTGTAACCCACGGAATTCATAAAATGTTTATGAAAGACTG
1 TATCGGCACTAAGTGTGCAACCCACGAAATTCATAATATGTTTATGAACGACCG
* * * *
3716792 TATCGACACTAAGTGTTCAACCCAC-ATAATTCATAATATGTTTATGAATGATCG
1 TATCGGCACTAAGTGTGCAACCCACGA-AATTCATAATATGTTTATGAACGACCG
* *
3716846 TATCGGCACTAAGTGTGCAACCCACGAAATTCATAATAAGCTTATGAACGACCG
1 TATCGGCACTAAGTGTGCAACCCACGAAATTCATAATATGTTTATGAACGACCG
* * *
3716900 TATCGGCACTAAGTATGCAACCCA-TAGAATTCATAATATGTTTATGAACGATCG
1 TATCGGCACTAAGTGTGCAACCCACGA-AATTCATAATATGTTTATGAACGACCG
* * *
3716954 TATCTGCACTACGTATGC-ACCCTAACGAAATT-ATAAT
1 TATCGGCACTAAGTGTGCAACCC--ACGAAATTCATAAT
3716991 GTTATGAAAA
Statistics
Matches: 318, Mismatches: 36, Indels: 13
0.87 0.10 0.04
Matches are distributed among these distances:
53 41 0.13
54 270 0.85
55 6 0.02
56 1 0.00
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (54 bp):
TATCGGCACTAAGTGTGCAACCCACGAAATTCATAATATGTTTATGAACGACCG
Found at i:3726319 original size:12 final size:12
Alignment explanation
Indices: 3726302--3726327 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3726292 TAACTCCAAG
3726302 GAATTAGTATTA
1 GAATTAGTATTA
3726314 GAATTAGTATTA
1 GAATTAGTATTA
3726326 GA
1 GA
3726328 GGAATAAGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.19, T:0.38
Consensus pattern (12 bp):
GAATTAGTATTA
Found at i:3733425 original size:39 final size:39
Alignment explanation
Indices: 3733382--3733461 Score: 99
Period size: 39 Copynumber: 2.1 Consensus size: 39
3733372 TACTTTCACA
* *
3733382 TTTCAGATTCAGAAATCA-CTTTCATATTCAGAACTCATT
1 TTTCAGATTCAGAAATCATC-TTCAAATTCAAAACTCATT
* * *
3733421 TTTCATATTCATAACTCATCTTCAAATTCAAAACTCATT
1 TTTCAGATTCAGAAATCATCTTCAAATTCAAAACTCATT
3733460 TT
1 TT
3733462 CATAATCATA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
39 34 0.97
40 1 0.03
ACGTcount: A:0.34, C:0.21, G:0.04, T:0.41
Consensus pattern (39 bp):
TTTCAGATTCAGAAATCATCTTCAAATTCAAAACTCATT
Found at i:3733449 original size:19 final size:19
Alignment explanation
Indices: 3733382--3733473 Score: 78
Period size: 19 Copynumber: 4.8 Consensus size: 19
3733372 TACTTTCACA
* * * *
3733382 TTTCAGATTCAGAAATCAC
1 TTTCAAATTCATAACTCAT
* *
3733401 TTTCATATTCAGAACTCATT
1 TTTCAAATTCATAACTCA-T
*
3733421 TTTCATATTCATAACTCAT
1 TTTCAAATTCATAACTCAT
* *
3733440 CTTCAAATTCAAAACTCAT
1 TTTCAAATTCATAACTCAT
3733459 TTTCATAA-TCATAAC
1 TTTCA-AATTCATAAC
3733474 CCAATGTATA
Statistics
Matches: 62, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
19 43 0.69
20 19 0.31
ACGTcount: A:0.36, C:0.22, G:0.03, T:0.39
Consensus pattern (19 bp):
TTTCAAATTCATAACTCAT
Found at i:3750876 original size:13 final size:13
Alignment explanation
Indices: 3750855--3750885 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
3750845 AAATGGTAAT
3750855 AAAAAAAATTAAC
1 AAAAAAAATTAAC
*
3750868 AAAATAAATTAAC
1 AAAAAAAATTAAC
3750881 AAAAA
1 AAAAA
3750886 GTCCAACCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.77, C:0.06, G:0.00, T:0.16
Consensus pattern (13 bp):
AAAAAAAATTAAC
Done.