Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold680
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: 1139231
ACGTcount: A:0.15, C:0.08, G:0.08, T:0.15
Warning! 618122 characters in sequence are not A, C, G, or T
File 4 of 4
Found at i:1003942 original size:28 final size:28
Alignment explanation
Indices: 1003868--1004033 Score: 111
Period size: 28 Copynumber: 5.9 Consensus size: 28
1003858 GTAGGCTTAA
* * *
1003868 ACTCAAATGCCCACTAACATGGGCTTTG
1 ACTCATATGCCAACTAATATGGGCTTTG
* * **
1003896 ACTCGTGTGCC-ACTGAATATGGGCTTCA
1 ACTCATATGCCAACT-AATATGGGCTTTG
* * *
1003924 ACTCATATGCCAATTAATATTGACTTTG
1 ACTCATATGCCAACTAATATGGGCTTTG
* * * * *
1003952 ACT-AAAGTGCTAGCTAGTATGGGCTTCG
1 ACTCATA-TGCCAACTAATATGGGCTTTG
* * *
1003980 ACTCTTATGCCAACTAATGTGAGCTTTG
1 ACTCATATGCCAACTAATATGGGCTTTG
* * *
1004008 ACTCAGATGCTAATTAATATGGGCTT
1 ACTCATATGCCAACTAATATGGGCTT
1004034 ACTTTTGATG
Statistics
Matches: 99, Mismatches: 35, Indels: 8
0.70 0.25 0.06
Matches are distributed among these distances:
27 5 0.05
28 91 0.92
29 3 0.03
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.32
Consensus pattern (28 bp):
ACTCATATGCCAACTAATATGGGCTTTG
Found at i:1003951 original size:56 final size:56
Alignment explanation
Indices: 1003861--1004012 Score: 137
Period size: 56 Copynumber: 2.7 Consensus size: 56
1003851 AACAAATGTA
* * * ** * **
1003861 GGCTTAAACTCAAATGCCCACTAACATGGGCTTTGACTCGTGTGCCA-CTGAATATG
1 GGCTTCAACTCATATGCCAACTAATGTGAGCTTTGACTCAAGTGCCAGCT-AATATG
* * * * *
1003917 GGCTTCAACTCATATGCCAATTAATATTGA-CTTTGACTAAAGTGCTAGCTAGTATG
1 GGCTTCAACTCATATGCCAACTAAT-GTGAGCTTTGACTCAAGTGCCAGCTAATATG
* *
1003973 GGCTTCGACTCTTATGCCAACTAATGTGAGCTTTGACTCA
1 GGCTTCAACTCATATGCCAACTAATGTGAGCTTTGACTCA
1004013 GATGCTAATT
Statistics
Matches: 76, Mismatches: 17, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
55 3 0.04
56 69 0.91
57 4 0.05
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (56 bp):
GGCTTCAACTCATATGCCAACTAATGTGAGCTTTGACTCAAGTGCCAGCTAATATG
Found at i:1004019 original size:56 final size:56
Alignment explanation
Indices: 1003911--1004033 Score: 142
Period size: 56 Copynumber: 2.2 Consensus size: 56
1003901 TGTGCCACTG
* * *
1003911 AATATGGGCTTCAACTCATATGCCAATTAATATTGACTTTGACTAAAGTGCTAGCT
1 AATATGGGCTTCAACTCATATGCCAACTAATAGTGACTTTGACTAAAGTGCTAACT
* * * * *
1003967 AGTATGGGCTTCGACTCTTATGCCAACTAAT-GTGAGCTTTGACT-CAGATGCTAATT
1 AATATGGGCTTCAACTCATATGCCAACTAATAGTGA-CTTTGACTAAAG-TGCTAACT
1004023 AATATGGGCTT
1 AATATGGGCTT
1004034 ACTTTTGATG
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
55 5 0.09
56 51 0.91
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (56 bp):
AATATGGGCTTCAACTCATATGCCAACTAATAGTGACTTTGACTAAAGTGCTAACT
Found at i:1004904 original size:18 final size:20
Alignment explanation
Indices: 1004862--1004898 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
1004852 ATTATCTTTC
*
1004862 ATTCATAAAAAAAAGGTACA
1 ATTCATAAAAAAAAGATACA
1004882 ATTCA-AAAAAAAAGATA
1 ATTCATAAAAAAAAGATA
1004899 GATTCATTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 11 0.69
20 5 0.31
ACGTcount: A:0.65, C:0.08, G:0.08, T:0.19
Consensus pattern (20 bp):
ATTCATAAAAAAAAGATACA
Found at i:1006200 original size:20 final size:21
Alignment explanation
Indices: 1006153--1006209 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 21
1006143 CATAAGTAAA
1006153 TGTATCGATACATACTTATAAT
1 TGTATCGATACATA-TTATAAT
* * *
1006175 TCTATCAATACAT-TTATCAT
1 TGTATCGATACATATTATAAT
1006195 TGTATCGATACATAT
1 TGTATCGATACATAT
1006210 GGGTTTTGAC
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
20 17 0.59
21 1 0.03
22 11 0.38
ACGTcount: A:0.35, C:0.16, G:0.07, T:0.42
Consensus pattern (21 bp):
TGTATCGATACATATTATAAT
Found at i:1008735 original size:79 final size:79
Alignment explanation
Indices: 1008645--1008946 Score: 417
Period size: 79 Copynumber: 3.8 Consensus size: 79
1008635 TTCCACCATC
* * **
1008645 AGGGATACTCCAACCCTGGTTTTATTTCTAAAACACCAATTTTTCATAATCGGGGATACTCCAAC
1 AGGGATACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTTCACCATCGGGGATACTCCAAC
1008710 CTTATTATTTCTGA
66 CTTATTATTTCTGA
*
1008724 AGGGATACTCCAACCCCAGTTTTATTTCTAAAACATCAATTTTTCACCATCGGGGATACTCCAAC
1 AGGGATACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTTCACCATCGGGGATACTCCAAC
* *
1008789 CTTATTATATCCGA
66 CTTATTATTTCTGA
* * * * *
1008803 GGGGATACTCCAACCTCGGTTTTATTTCTAAAACATCAAATTTTCACTATCGGGGATACTCCTAC
1 AGGGATACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTTCACCATCGGGGATACTCCAAC
** *
1008868 C-CGTTATTTCTAA
66 CTTATTATTTCTGA
* * * * *
1008881 AGGGATACTCCAACCCCGATTTTATTTTTAAAACATCGATTTTCCACCATCGAGGATACTCCAAC
1 AGGGATACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTTCACCATCGGGGATACTCCAAC
1008946 C
66 C
1008947 CCAGTTTTAT
Statistics
Matches: 195, Mismatches: 28, Indels: 1
0.87 0.12 0.00
Matches are distributed among these distances:
78 63 0.32
79 132 0.68
ACGTcount: A:0.29, C:0.25, G:0.13, T:0.33
Consensus pattern (79 bp):
AGGGATACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTTCACCATCGGGGATACTCCAAC
CTTATTATTTCTGA
Found at i:1008938 original size:157 final size:158
Alignment explanation
Indices: 1008646--1008946 Score: 457
Period size: 157 Copynumber: 1.9 Consensus size: 158
1008636 TCCACCATCA
*
1008646 GGGATACTCCAACCCTGGTTTTATTTCTAAAACACCAATTTTTCATAATCGGGGATACTCCAACC
1 GGGATACTCCAACCCTGGTTTTATTTCTAAAACACCAAATTTTCATAATCGGGGATACTCCAACC
* * *
1008711 TTATTATTTCTGAAGGGATACTCCAACCCCAGTTTTATTTCTAAAACATCAATTTTTCACCATCG
66 TCATTATTTCTAAAGGGATACTCCAACCCCAGTTTTATTTCTAAAACATCAATTTTCCACCATCG
*
1008776 GGGATACTCCAACCTTATTATATCCGAG
131 AGGATACTCCAACCTTATTATATCCGAG
* *
1008804 GGGATACTCCAA-CCTCGGTTTTATTTCTAAAACATCAAATTTTCACT-ATCGGGGATACTCCTA
1 GGGATACTCCAACCCT-GGTTTTATTTCTAAAACACCAAATTTTCA-TAATCGGGGATACTCCAA
* * *
1008867 CC-CGTTATTTCTAAAGGGATACTCCAACCCC-GATTTTATTTTTAAAACATCGATTTTCCACCA
64 CCTCATTATTTCTAAAGGGATACTCCAACCCCAG-TTTTATTTCTAAAACATCAATTTTCCACCA
1008930 TCGAGGATACTCCAACC
128 TCGAGGATACTCCAACC
1008947 CCAGTTTTAT
Statistics
Matches: 130, Mismatches: 10, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
156 1 0.01
157 72 0.55
158 56 0.43
159 1 0.01
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.33
Consensus pattern (158 bp):
GGGATACTCCAACCCTGGTTTTATTTCTAAAACACCAAATTTTCATAATCGGGGATACTCCAACC
TCATTATTTCTAAAGGGATACTCCAACCCCAGTTTTATTTCTAAAACATCAATTTTCCACCATCG
AGGATACTCCAACCTTATTATATCCGAG
Found at i:1008964 original size:51 final size:50
Alignment explanation
Indices: 1008881--1009013 Score: 191
Period size: 51 Copynumber: 2.6 Consensus size: 50
1008871 TTATTTCTAA
*
1008881 AGGGATACTCCAACCCCGATTTTATTTTTAAAACA-TCGATTTTCCACCATC
1 AGGGATACTCCAACCCCG-TTTTATTTCTAAAACACT-GATTTTCCACCATC
1008932 -GAGGATACTCCAACCCCAGTTTTATTTCTAAAACACTGATTTTCCACCATC
1 AG-GGATACTCCAACCCC-GTTTTATTTCTAAAACACTGATTTTCCACCATC
*
1008983 AGGGATACTCCAACCCCGTTAT-TTTCTAAAA
1 AGGGATACTCCAACCCCGTTTTATTTCTAAAA
1009014 AATACTTCAA
Statistics
Matches: 76, Mismatches: 2, Indels: 10
0.86 0.02 0.11
Matches are distributed among these distances:
49 9 0.12
50 5 0.07
51 59 0.78
52 3 0.04
ACGTcount: A:0.30, C:0.28, G:0.11, T:0.32
Consensus pattern (50 bp):
AGGGATACTCCAACCCCGTTTTATTTCTAAAACACTGATTTTCCACCATC
Found at i:1009035 original size:79 final size:78
Alignment explanation
Indices: 1008936--1009155 Score: 291
Period size: 79 Copynumber: 2.8 Consensus size: 78
1008926 ACCATCGAGG
*
1008936 ATACTCCAACCC-CAGTTTTATTTCTAAAACACTGATTTTCCACCATCAGGGATACTCCAACCCC
1 ATACTCCAACCCTGA-TTTTATTTCTAAAACACTGATTTTCCACCATC-GGGATACTCCAACCCC
*
1009000 GTTATTTTCTAAAAA
64 GTTATTTTCGAAAAA
* * * *
1009015 ATACTTCAA-CTTCGATTTTATTTCTAAAACATTGATTTTCCACCATCGGGGATACTCCAACCCT
1 ATACTCCAACCCT-GATTTTATTTCTAAAACACTGATTTTCCACCATC-GGGATACTCCAACCCC
* *
1009079 GTTATTTTCGAAGAG
64 GTTATTTTCGAAAAA
* *
1009094 ATACTCCAACCCTGATTTTATTTCTAAAACACTGATTTTTCATCATCGAGGATACTCCAACC
1 ATACTCCAACCCTGATTTTATTTCTAAAACACTGATTTTCCACCATCG-GGATACTCCAACC
1009156 TCTGATCCAT
Statistics
Matches: 123, Mismatches: 14, Indels: 8
0.85 0.10 0.06
Matches are distributed among these distances:
78 2 0.02
79 118 0.96
80 3 0.02
ACGTcount: A:0.30, C:0.26, G:0.10, T:0.34
Consensus pattern (78 bp):
ATACTCCAACCCTGATTTTATTTCTAAAACACTGATTTTCCACCATCGGGATACTCCAACCCCGT
TATTTTCGAAAAA
Found at i:1009053 original size:130 final size:129
Alignment explanation
Indices: 1008805--1009077 Score: 370
Period size: 130 Copynumber: 2.1 Consensus size: 129
1008795 ATATCCGAGG
* * * * *
1008805 GGATACTCCAACCTCGGTTTTATTTCTAAAACATCAAATTTTCACTATCGGGGATACTCCTACCC
1 GGATACTCCAACCCCAGTTTTATTTCTAAAACATCAAATTTTCACCATCAGGGATACTCCAACCC
** *
1008870 GTTATTTCTAAAGGGATACTCCAACCCCGATTTTATTTTTAAAACATCGATTTTCCACCATCGA
66 GTTATTTCTAAAGAAATACTCCAACCCCGATTTTATTTCTAAAACATCGATTTTCCACCATCGA
**
1008934 GGATACTCCAACCCCAGTTTTATTTCTAAAACA-CTGATTTTCCACCATCAGGGATACTCCAACC
1 GGATACTCCAACCCCAGTTTTATTTCTAAAACATCAAATTTT-CACCATCAGGGATACTCCAA-C
* ** *
1008998 CCGTTATTTTCTAAA-AAATACTTCAACTTCGATTTTATTTCTAAAACATTGATTTTCCACCATC
64 CCGTTA-TTTCTAAAGAAATACTCCAACCCCGATTTTATTTCTAAAACATCGATTTTCCACCATC
*
1009062 GG
128 GA
1009064 GGATACTCCAACCC
1 GGATACTCCAACCC
1009078 TGTTATTTTC
Statistics
Matches: 126, Mismatches: 15, Indels: 5
0.86 0.10 0.03
Matches are distributed among these distances:
128 6 0.05
129 48 0.38
130 64 0.51
131 8 0.06
ACGTcount: A:0.29, C:0.27, G:0.11, T:0.33
Consensus pattern (129 bp):
GGATACTCCAACCCCAGTTTTATTTCTAAAACATCAAATTTTCACCATCAGGGATACTCCAACCC
GTTATTTCTAAAGAAATACTCCAACCCCGATTTTATTTCTAAAACATCGATTTTCCACCATCGA
Found at i:1009149 original size:287 final size:287
Alignment explanation
Indices: 1008628--1009151 Score: 682
Period size: 287 Copynumber: 1.8 Consensus size: 287
1008618 TCTCTCAAAT
** * *
1008628 ATCGATTTTCCACCATCAGGGATACTCCAACCCTGGTTTTATTTCTAAAACACCAATTTTTCATA
1 ATCGATTTTCCACCATCAGGGATACTCCAACCCCAGTTTTATTTCTAAAACACCAATTTTCCACA
* ** ***
1008693 ATCGGGGATACTCCAACCTTATTATTTCTGAAGGGATACTCCAACCCCAGTTTTATTTCTAAAAC
66 ATCAGGGATACTCCAACCCCATTATTTCTGAAAAAATACTCCAACCCCAGTTTTATTTCTAAAAC
* * * * *
1008758 ATCAATTTTTCACCATCGGGGATACTCCAACCTTATTATATCCGAGGGGATACTCCAACCTCGGT
131 ATCAATTTTCCACCATCGGGGATACTCCAACCCTATTATATCCGAAGAGATACTCCAACCTCGAT
*
1008823 TTTATTTCTAAAACATCAAATTTTCACTATCGGGGATACTCCTACCCGTTATTTCTAAAGGGATA
196 TTTATTTCTAAAACATCAAATTTTCACTATCGAGGATACTCCTACCCGTTATTTCTAAAGGGATA
1008888 CTCCAACCCCGATTTTATTTTTAAAAC
261 CTCCAACCCCGATTTTATTTTTAAAAC
**
1008915 ATCGATTTTCCACCATC-GAGGATACTCCAACCCCAGTTTTATTTCTAAAACACTGATTTTCCAC
1 ATCGATTTTCCACCATCAG-GGATACTCCAACCCCAGTTTTATTTCTAAAACACCAATTTTCCAC
* * * **
1008979 CATCAGGGATACTCCAACCCCGTTATTTTCT-AAAAAATACTTCAACTTC-GATTTTATTTCTAA
65 AATCAGGGATACTCCAACCCCATTA-TTTCTGAAAAAATACTCCAACCCCAG-TTTTATTTCTAA
** * * *
1009042 AACATTGATTTTCCACCATCGGGGATACTCCAACCCTGTTATTTTCGAAGAGATACTCCAACC-C
128 AACATCAATTTTCCACCATCGGGGATACTCCAACCCTATTATATCCGAAGAGATACTCCAACCTC
* *
1009106 TGATTTTATTTCTAAAACA-CTGATTTTTCA-TCATCGAGGATACTCC
193 -GATTTTATTTCTAAAACATC-AAATTTTCACT-ATCGAGGATACTCC
1009152 AACCTCTGAT
Statistics
Matches: 201, Mismatches: 30, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
286 5 0.02
287 191 0.95
288 5 0.02
ACGTcount: A:0.29, C:0.26, G:0.11, T:0.34
Consensus pattern (287 bp):
ATCGATTTTCCACCATCAGGGATACTCCAACCCCAGTTTTATTTCTAAAACACCAATTTTCCACA
ATCAGGGATACTCCAACCCCATTATTTCTGAAAAAATACTCCAACCCCAGTTTTATTTCTAAAAC
ATCAATTTTCCACCATCGGGGATACTCCAACCCTATTATATCCGAAGAGATACTCCAACCTCGAT
TTTATTTCTAAAACATCAAATTTTCACTATCGAGGATACTCCTACCCGTTATTTCTAAAGGGATA
CTCCAACCCCGATTTTATTTTTAAAAC
Found at i:1018028 original size:3 final size:3
Alignment explanation
Indices: 1018020--1018070 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
1018010 TATCAGCCAA
1018020 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1018068 ATT
1 ATT
1018071 CAAGTGTCAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1024156 original size:52 final size:51
Alignment explanation
Indices: 1024065--1024194 Score: 206
Period size: 52 Copynumber: 2.5 Consensus size: 51
1024055 CCCGAAATAT
* *
1024065 GAAAAGTTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGG
1 GAAAA-TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGG
* *
1024117 GCAAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGG
1 G-AAAATTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGG
1024169 GAAAATTGCCTGCATGTATCGATACA
1 GAAAATTGCCTGCATGTATCGATACA
1024195 AAGATCAGTG
Statistics
Matches: 72, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
51 24 0.33
52 45 0.62
53 3 0.04
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Consensus pattern (51 bp):
GAAAATTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGG
Found at i:1024207 original size:51 final size:50
Alignment explanation
Indices: 1024065--1024215 Score: 196
Period size: 52 Copynumber: 2.9 Consensus size: 50
1024055 CCCGAAATAT
*
1024065 GAAAAGTTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGG
1 GAAAA-TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGG
* * *
1024117 GCAAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGG
1 G-AAAATTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGG
*
1024169 GAAAATTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACAT
1 GAAAATTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACAT
1024216 TTGAGTAATG
Statistics
Matches: 88, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
50 2 0.02
51 38 0.43
52 45 0.51
53 3 0.03
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Consensus pattern (50 bp):
GAAAATTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGG
Found at i:1024292 original size:33 final size:33
Alignment explanation
Indices: 1024255--1024321 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1024245 AGTAGCTTAA
1024255 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
1024288 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
1024321 A
1 A
1024322 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:1024295 original size:13 final size:13
Alignment explanation
Indices: 1024277--1024301 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1024267 CAAAAAAATA
1024277 TGTATCGATACAT
1 TGTATCGATACAT
1024290 TGTATCGATACA
1 TGTATCGATACA
1024302 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1026209 original size:28 final size:28
Alignment explanation
Indices: 1026177--1026248 Score: 92
Period size: 28 Copynumber: 2.6 Consensus size: 28
1026167 GATAAAAATA
* *
1026177 GGGTTGGATTA-CCCCTTCAGAAATAACG
1 GGGTTGGAGTATCCCC-TCAAAAATAACG
*
1026205 GGGTTGGAGTATCTCCTCAAAAATAACG
1 GGGTTGGAGTATCCCCTCAAAAATAACG
*
1026233 GGGTTAGAGTATCCCC
1 GGGTTGGAGTATCCCC
1026249 AATGGTAGAA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
28 35 0.92
29 3 0.08
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.25
Consensus pattern (28 bp):
GGGTTGGAGTATCCCCTCAAAAATAACG
Found at i:1026302 original size:79 final size:78
Alignment explanation
Indices: 1026205--1026439 Score: 328
Period size: 79 Copynumber: 3.0 Consensus size: 78
1026195 AGAAATAACG
* *
1026205 GGGTTGGAGTATCTCCTCAAAAATAACGGGGTTAGAGTATCCCCAATGGTAGAAAATTGATGTTT
1 GGGTTGGAGTATCCCCTCAAAAATAACGGGGTTAGAGTATCCCCAATGGTAGAAAATCGATGTTT
*
1026270 TGGAAATAAAATC
66 TGAAAATAAAATC
* * * *
1026283 GGGTTTGGAGTATCCCCTCAAAAACAACGGGGTTAGAGTATTCCCGATTGT-GAAAAATCGATGT
1 GGG-TTGGAGTATCCCCTCAAAAATAACGGGGTTAGAGTATCCCCAATGGTAG-AAAATCGATGT
* **
1026347 TTTAAAAATAAAGCC
64 TTTGAAAATAAAATC
* *
1026362 GAGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATGGTAGAAAATCGATGTT
1 G-GGTTGGAGTATCCCCTCAAAAATAACGGGGTTAGAGTATCCCCAATGGTAGAAAATCGATGTT
1026427 TTGAAAATAAAAT
65 TTGAAAATAAAAT
1026440 TAGGGTTAGG
Statistics
Matches: 134, Mismatches: 19, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
78 4 0.03
79 127 0.95
80 3 0.02
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.27
Consensus pattern (78 bp):
GGGTTGGAGTATCCCCTCAAAAATAACGGGGTTAGAGTATCCCCAATGGTAGAAAATCGATGTTT
TGAAAATAAAATC
Found at i:1029356 original size:42 final size:42
Alignment explanation
Indices: 1029320--1029474 Score: 186
Period size: 42 Copynumber: 3.6 Consensus size: 42
1029310 CCTGTTTTTC
* *
1029320 GAGGACAAAGGAAAAAAGGAAATGAAGTGTGCCCTGTTCTTT
1 GAGGACAAAGGAAAAAAGGAAATGAAGTGTGACCTGCTCTTT
* * * * **
1029362 GAGGA-TAAGAGAGAAAAGAAAATAAAGTGTGTTCTGCTCTTT
1 GAGGACAAAG-GAAAAAAGGAAATGAAGTGTGACCTGCTCTTT
* *
1029404 GAGGACAGAGGGAAAAGAAGGAAATGAAATGTGACCTGCTCTTT
1 GAGGACA-AAGGAAAA-AAGGAAATGAAGTGTGACCTGCTCTTT
1029448 GAGGACAAAGGAAAAAAGGAAATGAAG
1 GAGGACAAAGGAAAAAAGGAAATGAAG
1029475 AAAGTAGCTT
Statistics
Matches: 92, Mismatches: 17, Indels: 8
0.79 0.15 0.07
Matches are distributed among these distances:
41 3 0.03
42 47 0.51
43 11 0.12
44 31 0.34
ACGTcount: A:0.43, C:0.09, G:0.30, T:0.19
Consensus pattern (42 bp):
GAGGACAAAGGAAAAAAGGAAATGAAGTGTGACCTGCTCTTT
Found at i:1029802 original size:62 final size:61
Alignment explanation
Indices: 1029490--1029929 Score: 372
Period size: 61 Copynumber: 7.2 Consensus size: 61
1029480 AGCTTGCACA
* ** * * *
1029490 TTGAGGACTAAAAGGTGCCACCAACTCATATGGGCTTT-AAA-AAATAGGTG-TCTTGCTCT
1 TTGAGGACTAAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAAGGCGTTC-TGCTCT
* * * *
1029549 TTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAAAGAAAACGTCCTACTC
1 TTGAGGACTAAAAAGTGCCACCAACTTGTGTGGGCTTTAAAA-G-AAAAAG---GCGTTCTGCTC
1029614 T
61 T
* * *
1029615 TTAAGGACTAAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAA-GTG-TCATGCTCT
1 TTGAGGACTAAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAAGGCGTTC-TGCTCT
* * * ** * *
1029675 TTGAGGACTAGAAAGTGCCACCAACTCGGGTGGGCTTTCTAA-AAAAAGGCATCCTGCTCT
1 TTGAGGACTAAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAAGGCGTTCTGCTCT
* ** * *
1029735 TTGAGGACTAAAAAGGTACCACCAGGTTATGTGGGCTTTGAAAGAAAAAGGCGTTCTGCTCT
1 TTGAGGACTAAAAA-GTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAAGGCGTTCTGCTCT
* * * ** * * *
1029797 CTGAGGATTAAAATGTGTTACCAACTCGTGTGGGCTTTAAAAGAAAAATGTG-TCTTGCTCT
1 TTGAGGACTAAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAAGGCGTTC-TGCTCT
** * * * * *
1029858 TTGAGGACTAAAGGGTGCCACTAACTCGTGTGGGCTTTGAAAAGAAAAAGGTGTCCTACTCT
1 TTGAGGACTAAAAAGTGCCACCAACTTGTGTGGGCTTT-AAAAGAAAAAGGCGTTCTGCTCT
*
1029920 TTGAGAACTA
1 TTGAGGACTA
1029930 GAGGGCTAAA
Statistics
Matches: 305, Mismatches: 60, Indels: 29
0.77 0.15 0.07
Matches are distributed among these distances:
59 40 0.13
60 67 0.22
61 86 0.28
62 54 0.18
63 6 0.02
64 4 0.01
65 1 0.00
66 46 0.15
67 1 0.00
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (61 bp):
TTGAGGACTAAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAAGGCGTTCTGCTCT
Found at i:1030957 original size:6 final size:6
Alignment explanation
Indices: 1030946--1030974 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
1030936 CACCAAGGTT
1030946 TTTTTG TTTTTG TTTTTG TTTTT- TTTTTG
1 TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG
1030975 GTAAAAGAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.23
6 17 0.77
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (6 bp):
TTTTTG
Found at i:1031218 original size:10 final size:11
Alignment explanation
Indices: 1031192--1031231 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
1031182 TTGTTGTTCC
*
1031192 TTTTTTATTTAT
1 TTTTTT-TTTAG
*
1031204 TTTTTTTTTTG
1 TTTTTTTTTAG
1031215 TTTTTTTTTAG
1 TTTTTTTTTAG
1031226 TTTTTT
1 TTTTTT
1031232 CATTTTTGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
11 19 0.76
12 6 0.24
ACGTcount: A:0.07, C:0.00, G:0.05, T:0.88
Consensus pattern (11 bp):
TTTTTTTTTAG
Found at i:1031231 original size:25 final size:26
Alignment explanation
Indices: 1031192--1031242 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
1031182 TTGTTGTTCC
* **
1031192 TTTTTTATTTATTTTTTTTTTTGTTT
1 TTTTTTAGTTATTTTCATTTTTGTTT
1031218 TTTTTTAGTT-TTTTCATTTTTGTTT
1 TTTTTTAGTTATTTTCATTTTTGTTT
1031243 CTCTTGTGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 13 0.59
26 9 0.41
ACGTcount: A:0.08, C:0.02, G:0.06, T:0.84
Consensus pattern (26 bp):
TTTTTTAGTTATTTTCATTTTTGTTT
Found at i:1032022 original size:39 final size:39
Alignment explanation
Indices: 1031979--1032057 Score: 140
Period size: 39 Copynumber: 2.0 Consensus size: 39
1031969 AAACAAGTAG
*
1031979 ATTTTCTTGATATTTGCACAAAATAGGCAAGAAGAGTGC
1 ATTTTCTTGATATTTGCACAAAATAGGCAAGAAAAGTGC
*
1032018 ATTTTCTTGATATTTGCATAAAATAGGCAAGAAAAGTGC
1 ATTTTCTTGATATTTGCACAAAATAGGCAAGAAAAGTGC
1032057 A
1 A
1032058 AGGATTTCCA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.38, C:0.11, G:0.19, T:0.32
Consensus pattern (39 bp):
ATTTTCTTGATATTTGCACAAAATAGGCAAGAAAAGTGC
Found at i:1036242 original size:27 final size:28
Alignment explanation
Indices: 1036192--1036262 Score: 126
Period size: 27 Copynumber: 2.6 Consensus size: 28
1036182 GATAAAAACG
1036192 GGGTTGGAGTACCCCCTCAGAAATAACA
1 GGGTTGGAGTACCCCCTCAGAAATAACA
1036220 GGGTTGGAGTACCCCC-CAGAAATAACA
1 GGGTTGGAGTACCCCCTCAGAAATAACA
*
1036247 GGGTTGGAGTATCCCC
1 GGGTTGGAGTACCCCC
1036263 AATGGTGAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 26 0.62
28 16 0.38
ACGTcount: A:0.28, C:0.25, G:0.28, T:0.18
Consensus pattern (28 bp):
GGGTTGGAGTACCCCCTCAGAAATAACA
Found at i:1036459 original size:79 final size:77
Alignment explanation
Indices: 1036220--1036451 Score: 250
Period size: 78 Copynumber: 3.0 Consensus size: 77
1036210 AGAAATAACA
* * *
1036220 GGGTTGGAGTACCCCCCAGAAATAACAGGGTTGGAGTATCCCCAATGGTGAAAAATCAATGTTTT
1 GGGTTGGAGTATCCCCTAGAAATAACAGGGTTGGAGTAT-CCCGATGGTGAAAAATCAATGTTTT
* *
1036285 GGAAATAGAACCG
65 GAAAATAAAACCG
* * ** * * *
1036298 GAGTTTGAGTATCTTCTCGAAAATAACAAGGTTGGAGTATCCCGATTGTGAAAAATCAATGTTTT
1 GGGTTGGAGTATCCCCTAG-AAATAACAGGGTTGGAGTATCCCGATGGTGAAAAATCAATGTTTT
*
1036363 -AGAAATAAAGCCG
65 GA-AAATAAAACCG
* * * * *
1036376 GGGTTGGAGTATCCCCTTAGAAATAACGGGGCTGAAGTATCTCCGATGGTGGAAAATCGATGTTT
1 GGGTTGGAGTATCCCC-TAGAAATAACAGGGTTGGAGTATC-CCGATGGTGAAAAATCAATGTTT
1036441 TGAAAATAAAA
64 TGAAAATAAAA
1036452 TTGGGGTTAG
Statistics
Matches: 123, Mismatches: 26, Indels: 9
0.78 0.16 0.06
Matches are distributed among these distances:
78 73 0.59
79 49 0.40
80 1 0.01
ACGTcount: A:0.34, C:0.15, G:0.25, T:0.26
Consensus pattern (77 bp):
GGGTTGGAGTATCCCCTAGAAATAACAGGGTTGGAGTATCCCGATGGTGAAAAATCAATGTTTTG
AAAATAAAACCG
Found at i:1038790 original size:50 final size:50
Alignment explanation
Indices: 1038697--1038828 Score: 183
Period size: 50 Copynumber: 2.6 Consensus size: 50
1038687 AAAAATGCTT
* * * * **
1038697 GAATATATCGATACATTGAGAAATGTATCAATACTTCTAGGTAAAACCTA
1 GAATGTATCGATACAATGAAAAATGTATCGATAAATCTAGGTAAAACCTA
* *
1038747 GAATGTATCAATACAATGAAAAATGTATCGATAAATCTGGGTAAAACCTA
1 GAATGTATCGATACAATGAAAAATGTATCGATAAATCTAGGTAAAACCTA
*
1038797 GAATGTATCGATACAATGAAGAATGTATCGAT
1 GAATGTATCGATACAATGAAAAATGTATCGAT
1038829 TAAAATTGTA
Statistics
Matches: 72, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
50 72 1.00
ACGTcount: A:0.43, C:0.12, G:0.17, T:0.28
Consensus pattern (50 bp):
GAATGTATCGATACAATGAAAAATGTATCGATAAATCTAGGTAAAACCTA
Found at i:1041029 original size:3 final size:3
Alignment explanation
Indices: 1041023--1041054 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
1041013 CAGCCAAATT
1041023 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1041055 CAAGTATCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1044427 original size:2 final size:2
Alignment explanation
Indices: 1044422--1044464 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1044412 TATATATAGC
1044422 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1044464 G
1 G
1044465 GTCATCAGAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1044579 original size:76 final size:76
Alignment explanation
Indices: 1044453--1044601 Score: 289
Period size: 76 Copynumber: 2.0 Consensus size: 76
1044443 AGAGAGAGAG
1044453 AGAGAGAGAGAGGTCATCAGAACCTGATATTTTGATGATTTCATAACTGTTAGAACTGTGATATA
1 AGAGAGAGAGAGGTCATCAGAACCTGATATTTTGATGATTTCATAACTGTTAGAACTGTGATATA
1044518 TACATATAAAT
66 TACATATAAAT
1044529 AGAGAGAGAGAGGTCATCAGAACCTGATATTTTGATGATTTCATAACTGTTAGAACTGTGATATA
1 AGAGAGAGAGAGGTCATCAGAACCTGATATTTTGATGATTTCATAACTGTTAGAACTGTGATATA
*
1044594 TATATATA
66 TACATATA
1044602 TATGGAGACA
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
76 72 1.00
ACGTcount: A:0.38, C:0.10, G:0.20, T:0.32
Consensus pattern (76 bp):
AGAGAGAGAGAGGTCATCAGAACCTGATATTTTGATGATTTCATAACTGTTAGAACTGTGATATA
TACATATAAAT
Found at i:1046061 original size:15 final size:15
Alignment explanation
Indices: 1046041--1046132 Score: 69
Period size: 15 Copynumber: 6.0 Consensus size: 15
1046031 TAAAAAAAAG
1046041 TAAAAAATTTAAATT
1 TAAAAAATTTAAATT
*
1046056 TAAAAAATTTGAATT
1 TAAAAAATTTAAATT
* *
1046071 CAAAATAGTTT-AATT
1 TAAAA-AATTTAAATT
* * *
1046086 TGAAATAGTTTGAATT
1 T-AAAAAATTTAAATT
*
1046102 TAAAAAATTCAAATT
1 TAAAAAATTTAAATT
* *
1046117 CGAAAAAATTCAAATT
1 -TAAAAAATTTAAATT
1046133 CAAGAGAGTC
Statistics
Matches: 63, Mismatches: 10, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
15 37 0.59
16 26 0.41
ACGTcount: A:0.52, C:0.04, G:0.07, T:0.37
Consensus pattern (15 bp):
TAAAAAATTTAAATT
Found at i:1046124 original size:16 final size:16
Alignment explanation
Indices: 1046103--1046133 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1046093 GTTTGAATTT
1046103 AAAAAATTCAAATTCG
1 AAAAAATTCAAATTCG
1046119 AAAAAATTCAAATTC
1 AAAAAATTCAAATTC
1046134 AAGAGAGTCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.58, C:0.13, G:0.03, T:0.26
Consensus pattern (16 bp):
AAAAAATTCAAATTCG
Found at i:1050240 original size:18 final size:18
Alignment explanation
Indices: 1050217--1050275 Score: 59
Period size: 18 Copynumber: 3.2 Consensus size: 18
1050207 AATTATTTAA
1050217 AAATTAATTTTATATAAT
1 AAATTAATTTTATATAAT
**
1050235 AAATTAATCATATAT-AT
1 AAATTAATTTTATATAAT
1050252 AAATATATATTTTA-ATAAAT
1 AAAT-TA-ATTTTATAT-AAT
1050272 AAAT
1 AAAT
1050276 ATATTAAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
17 6 0.18
18 17 0.52
19 4 0.12
20 6 0.18
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (18 bp):
AAATTAATTTTATATAAT
Found at i:1050271 original size:16 final size:16
Alignment explanation
Indices: 1050227--1050293 Score: 59
Period size: 16 Copynumber: 4.2 Consensus size: 16
1050217 AAATTAATTT
*
1050227 TATA-TAATAAATTAA
1 TATATTAATAAATAAA
*
1050242 TCATA-TATATAAATATA
1 T-ATATTA-ATAAATAAA
*
1050259 TATTTTAATAAATAAA
1 TATATTAATAAATAAA
1050275 TATATTAA-AAATAACA
1 TATATTAATAAATAA-A
1050291 TAT
1 TAT
1050294 TATAGTAAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
15 7 0.16
16 26 0.60
17 10 0.23
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (16 bp):
TATATTAATAAATAAA
Found at i:1050446 original size:16 final size:16
Alignment explanation
Indices: 1050427--1050461 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1050417 ATTCGAAAAT
* *
1050427 ATTCAAACTTCAATAA
1 ATTCAAACCTAAATAA
1050443 ATTCAAACCTAAATAA
1 ATTCAAACCTAAATAA
1050459 ATT
1 ATT
1050462 TTAAAAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.51, C:0.17, G:0.00, T:0.31
Consensus pattern (16 bp):
ATTCAAACCTAAATAA
Found at i:1050493 original size:16 final size:16
Alignment explanation
Indices: 1050463--1050501 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
1050453 AAATAAATTT
*
1050463 TAAAA-AATTTTAATA
1 TAAAATAATTTAAATA
1050478 TAAAATAATTTAAATA
1 TAAAATAATTTAAATA
1050494 TAAAATAA
1 TAAAATAA
1050502 CCTAATTCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 5 0.23
16 17 0.77
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
TAAAATAATTTAAATA
Found at i:1050844 original size:40 final size:39
Alignment explanation
Indices: 1050800--1050903 Score: 102
Period size: 41 Copynumber: 2.5 Consensus size: 39
1050790 TATAAAATTA
*
1050800 AATTAATTT-TATAAATTTTATATTTTTTTATATTATTTAC
1 AATT-ATTTATATAAATTTTATATTTTATTAT-TTATTTAC
* *
1050840 AATTATTTAATTTAATTTTTATATTTTATTATTTATTTAC
1 AATTATTT-ATATAAATTTTATATTTTATTATTTATTTAC
*
1050880 GTAAGTTATGTATATCAAATTTTA
1 --AA-TTATTTATAT-AAATTTTA
1050904 AATAAATAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
39 4 0.08
40 12 0.23
41 19 0.37
42 5 0.10
43 12 0.23
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.60
Consensus pattern (39 bp):
AATTATTTATATAAATTTTATATTTTATTATTTATTTAC
Found at i:1051116 original size:2 final size:2
Alignment explanation
Indices: 1051109--1051167 Score: 68
Period size: 2 Copynumber: 30.5 Consensus size: 2
1051099 TTAGTTTTAC
* * *
1051109 AT AT AT AT AT AT AT AT AT AT AA AT AA AT AT -T TT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
1051149 AT AT AT AT AT AA AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
1051168 AACTATTTTC
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
1 2 0.04
2 46 0.96
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1052317 original size:19 final size:18
Alignment explanation
Indices: 1052269--1052340 Score: 56
Period size: 19 Copynumber: 3.8 Consensus size: 18
1052259 ATAAAAAATT
1052269 AAAAATAAAAAAAATCAGA
1 AAAAATAAAAAAAATCA-A
* * **
1052288 AAAATTCAAAACGATCAA
1 AAAAATAAAAAAAATCAA
1052306 AAAAATAAAAAATAAT-AA
1 AAAAATAAAAAA-AATCAA
*
1052324 TAAAAAAACAAAAAAAT
1 -AAAAATA-AAAAAAAT
1052341 GATGATGGTT
Statistics
Matches: 41, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
18 12 0.29
19 24 0.59
20 5 0.12
ACGTcount: A:0.76, C:0.07, G:0.03, T:0.14
Consensus pattern (18 bp):
AAAAATAAAAAAAATCAA
Found at i:1053158 original size:13 final size:13
Alignment explanation
Indices: 1053140--1053172 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
1053130 CAGAAGAACG
1053140 ACAACACCAAGCA
1 ACAACACCAAGCA
1053153 ACAACACCAAGCA
1 ACAACACCAAGCA
*
1053166 ACCACAC
1 ACAACAC
1053173 GGCAACATAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.52, C:0.42, G:0.06, T:0.00
Consensus pattern (13 bp):
ACAACACCAAGCA
Found at i:1054339 original size:79 final size:79
Alignment explanation
Indices: 1054091--1054444 Score: 410
Period size: 79 Copynumber: 4.5 Consensus size: 79
1054081 TATTCAAAAA
* *
1054091 CAAAATACCGATTTTTCACAATTGGGGATACTCCAATCC-CGTTATTTCCGAGGGGATACTCCAA
1 CAAAATACCGATTTTTCACAATCGGGGATACTCCAA-CCTCGTTATTTCTGAGGGGATACTCCAA
1054155 CCTCGGTTTTATTTC
65 CCTCGGTTTTATTTC
** * * *
1054170 TGATATACCAATTTTTCACCATCGGGGATACTCCAACCTCGTTATTT-TCGA-GGGATACTCCAA
1 CAAAATACCGATTTTTCACAATCGGGGATACTCCAACCTCGTTATTTCT-GAGGGGATACTCCAA
1054233 CCTCGGTTTTATTTC
65 CCTCGGTTTTATTTC
* * * * * *
1054248 CATAACATCGATTTTCCACAATCAGGGATACTCTAATCCT-GTTATTTCTGAGGGGATACTCCAA
1 CAAAATACCGATTTTTCACAATCGGGGATACTCCAA-CCTCGTTATTTCTGAGGGGATACTCCAA
* *
1054312 CCCCGATTTTATTTC
65 CCTCGGTTTTATTTC
* * * * *
1054327 TAAAATACCGATTTTCCACCATCGGGGATACTCCAACCTCGTTATTTTTGAGAGGATACTCCAAC
1 CAAAATACCGATTTTTCACAATCGGGGATACTCCAACCTCGTTATTTCTGAGGGGATACTCCAAC
* * *
1054392 CTTTGTTTTTTTTTC
66 C-TCGGTTTTATTTC
** *
1054407 CAAAATATTGATTTTTCACAATCGGGGATACCCCAACC
1 CAAAATACCGATTTTTCACAATCGGGGATACTCCAACC
1054445 CTATTTTCAA
Statistics
Matches: 229, Mismatches: 39, Indels: 13
0.81 0.14 0.05
Matches are distributed among these distances:
78 66 0.29
79 122 0.53
80 41 0.18
ACGTcount: A:0.26, C:0.25, G:0.15, T:0.34
Consensus pattern (79 bp):
CAAAATACCGATTTTTCACAATCGGGGATACTCCAACCTCGTTATTTCTGAGGGGATACTCCAAC
CTCGGTTTTATTTC
Found at i:1055335 original size:13 final size:13
Alignment explanation
Indices: 1055317--1055341 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1055307 CAATTCCTCA
1055317 TGTATCGATACAT
1 TGTATCGATACAT
1055330 TGTATCGATACA
1 TGTATCGATACA
1055342 ATGTGCCATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1055339 original size:33 final size:33
Alignment explanation
Indices: 1055297--1055361 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
1055287 TTTGAGACAA
1055297 TGTATCGATACAAT-TCCTCATGTATCGATACAT
1 TGTATCGATACAATGTCC-CATGTATCGATACAT
*
1055330 TGTATCGATACAATGTGCCATGTATCGATACA
1 TGTATCGATACAATGTCCCATGTATCGATACA
1055362 AACTGTGGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 28 0.93
34 2 0.07
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.34
Consensus pattern (33 bp):
TGTATCGATACAATGTCCCATGTATCGATACAT
Found at i:1055436 original size:20 final size:19
Alignment explanation
Indices: 1055391--1055440 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
1055381 CTGCCAGTTT
*
1055391 CATGTATCGATACAATGAA
1 CATGTATCGATACAAAGAA
1055410 CATGTATCGATACAAAGCATA
1 CATGTATCGATACAAAG-A-A
1055431 -ATGTATCGAT
1 CATGTATCGAT
1055441 CCATCTAGAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 16 0.57
20 11 0.39
21 1 0.04
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.28
Consensus pattern (19 bp):
CATGTATCGATACAAAGAA
Found at i:1057894 original size:13 final size:13
Alignment explanation
Indices: 1057875--1057914 Score: 71
Period size: 13 Copynumber: 3.1 Consensus size: 13
1057865 ATAGTAACCC
1057875 ATGTATCGATACA
1 ATGTATCGATACA
*
1057888 TTGTATCGATACA
1 ATGTATCGATACA
1057901 ATGTATCGATACA
1 ATGTATCGATACA
1057914 A
1 A
1057915 AGAACATTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.33
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1061257 original size:17 final size:17
Alignment explanation
Indices: 1061235--1061268 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1061225 AGTAGAATTG
1061235 CTACCAATGGTGCTGAT
1 CTACCAATGGTGCTGAT
1061252 CTACCAATGGTGCTGAT
1 CTACCAATGGTGCTGAT
1061269 TCCTTCAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.29
Consensus pattern (17 bp):
CTACCAATGGTGCTGAT
Found at i:1064139 original size:33 final size:33
Alignment explanation
Indices: 1064096--1064160 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
1064086 TTTGAGACAA
*
1064096 TGTATTGATACAAT-TCCTCATGTATCGATACAT
1 TGTATGGATACAATGTCC-CATGTATCGATACAT
*
1064129 TGTATGGATACAATGTGCCATGTATCGATACA
1 TGTATGGATACAATGTCCCATGTATCGATACA
1064161 AACAGTGGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 27 0.93
34 2 0.07
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Consensus pattern (33 bp):
TGTATGGATACAATGTCCCATGTATCGATACAT
Found at i:1064234 original size:19 final size:19
Alignment explanation
Indices: 1064190--1064245 Score: 85
Period size: 19 Copynumber: 2.9 Consensus size: 19
1064180 CTGCCAGTTT
**
1064190 CATGTATCGATACAATTGTG
1 CATGTATCGATACAA-TGAA
1064210 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
1064229 CATGTATCGATACAATG
1 CATGTATCGATACAATG
1064246 TATCGATGCA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
19 19 0.56
20 15 0.44
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.30
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:1069854 original size:79 final size:79
Alignment explanation
Indices: 1069752--1069955 Score: 239
Period size: 79 Copynumber: 2.6 Consensus size: 79
1069742 ATAATAACGG
* * * * * *
1069752 GGTTGGAGTATCCCCTTGAAAATAACGAGGTTGGAGTATCCCCGGTTGTGAAAAATCGATGATTA
1 GGTTGGAGTATCCCCTTGGAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATCAATCATTA
**
1069817 GGAAATAAAATTG-
66 GGAAATAAAACCGA
* * * * *
1069830 GGATTTGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATCTTT
1 GG-TTGGAGTATCCCCTTGGAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATCAATCATT
* *
1069895 TGGAAATAAAGCCGA
65 AGGAAATAAAACCGA
**
1069910 GGTTGGAGTATCCCCTTGGAGGTAACGGGGTTGGAGTATCCCCGAT
1 GGTTGGAGTATCCCCTTGGAAATAACGGGGTTGGAGTATCCCCGAT
1069956 GAAATAACGA
Statistics
Matches: 104, Mismatches: 20, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
78 2 0.02
79 100 0.96
80 2 0.02
ACGTcount: A:0.29, C:0.16, G:0.28, T:0.26
Consensus pattern (79 bp):
GGTTGGAGTATCCCCTTGGAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATCAATCATTA
GGAAATAAAACCGA
Found at i:1069942 original size:28 final size:28
Alignment explanation
Indices: 1069907--1069983 Score: 93
Period size: 28 Copynumber: 2.8 Consensus size: 28
1069897 GAAATAAAGC
* **
1069907 CGAGGTTGGAGTATCCCC-TTGGAGGTAA
1 CGAGGTTGGAGTATCCCCGAT-GAAATAA
*
1069935 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGAGGTTGGAGTATCCCCGATGAAATAA
*
1069963 CGAGGTTGGAGTATCCTCGAT
1 CGAGGTTGGAGTATCCCCGAT
1069984 TGTGAAAAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
28 41 0.98
29 1 0.02
ACGTcount: A:0.23, C:0.18, G:0.34, T:0.25
Consensus pattern (28 bp):
CGAGGTTGGAGTATCCCCGATGAAATAA
Found at i:1070060 original size:52 final size:51
Alignment explanation
Indices: 1069967--1070216 Score: 265
Period size: 52 Copynumber: 4.9 Consensus size: 51
1069957 AAATAACGAG
* * *
1069967 GTTGGAGTATCCTCGATTGT-GAAAAATAGTGTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCTCGATTATGGAAAATTAGTGTTTTAGAAATAAAATCGGA
* * * *
1070017 GTTGGAGTATCCTCGATTAAAGGAAAATTGGTGTTTT-GAAAATAAAACCGGG
1 GTTGGAGTATCCTCGATT-ATGGAAAATTAGTGTTTTAG-AAATAAAATCGGA
* * * *
1070069 GTTGAAGTATCC-CTAATAGTGGAAAATTAGTGTTTTAGAAATAAAA-CCGA
1 GTTGGAGTATCCTCGATTA-TGGAAAATTAGTGTTTTAGAAATAAAATCGGA
* * * * * *
1070119 GGATTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTAGAAATAAAATCGGG
1 -G-TTGGAGTATCCTCGATTATGGAAAATTAGTGTTTTAGAAATAAAATCGGA
*
1070172 GTTGAAGTATCCTCGATTATGGAAAATTAGTGTTTTAGAAATAAA
1 GTTGGAGTATCCTCGATTATGGAAAATTAGTGTTTTAGAAATAAA
1070217 TAGACACCAT
Statistics
Matches: 163, Mismatches: 28, Indels: 17
0.78 0.13 0.08
Matches are distributed among these distances:
50 21 0.13
51 66 0.40
52 71 0.44
53 5 0.03
ACGTcount: A:0.36, C:0.09, G:0.24, T:0.31
Consensus pattern (51 bp):
GTTGGAGTATCCTCGATTATGGAAAATTAGTGTTTTAGAAATAAAATCGGA
Found at i:1070147 original size:103 final size:103
Alignment explanation
Indices: 1069966--1070216 Score: 307
Period size: 103 Copynumber: 2.4 Consensus size: 103
1069956 GAAATAACGA
* * * *
1069966 GGTTGGAGTATCCTCG-AT-TGTGAAAAATAGTGTTTTGGAAATAAAATCGGAGTTGGAGTATCC
1 GGTTGAAGTATCCTCGAATATG-GAAAATTAGTGTTTTAGAAATAAAACCGGAGTTGGAGTATCC
* * *
1070029 TCGATTAAAGGAAAATTGGTGTTTT-GAAAATAAAACCGG
65 CCGATTAAAGAAAAATTGGTATTTTAG-AAATAAAACCGG
*
1070068 GGTTGAAGTATCC-CTAATAGTGGAAAATTAGTGTTTTAGAAATAAAACC-GAGGATTGGAGTAT
1 GGTTGAAGTATCCTCGAATA-TGGAAAATTAGTGTTTTAGAAATAAAACCGGA-G-TTGGAGTAT
** *
1070131 CCCCGATT-GTGAAAAATTGGTATTTTAGAAATAAAATCGG
63 CCCCGATTAAAGAAAAATTGGTATTTTAGAAATAAAACCGG
*
1070171 GGTTGAAGTATCCTCGATTATGGAAAATTAGTGTTTTAGAAATAAA
1 GGTTGAAGTATCCTCGAATATGGAAAATTAGTGTTTTAGAAATAAA
1070217 TAGACACCAT
Statistics
Matches: 129, Mismatches: 13, Indels: 13
0.83 0.08 0.08
Matches are distributed among these distances:
101 1 0.01
102 16 0.12
103 89 0.69
104 23 0.18
ACGTcount: A:0.36, C:0.09, G:0.24, T:0.31
Consensus pattern (103 bp):
GGTTGAAGTATCCTCGAATATGGAAAATTAGTGTTTTAGAAATAAAACCGGAGTTGGAGTATCCC
CGATTAAAGAAAAATTGGTATTTTAGAAATAAAACCGG
Found at i:1070932 original size:55 final size:54
Alignment explanation
Indices: 1070845--1071591 Score: 710
Period size: 55 Copynumber: 13.4 Consensus size: 54
1070835 AAGTGAATCT
* * *
1070845 TGCTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAGGTGTCC
1 TGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCC
* * ** *
1070900 TGCTCTTTGAGGATTGAAAGGTGCCACTAACTCATGTGGGCTTTGAAAAGAAAAGGCATCC
1 TGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTT-----G-AAAGGCGTCC
* * *
1070961 TGCTCTTTGAGGACTGGAAACTGCAACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCC
1 TGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTG-AAAG-----GCGTCC
* *
1071022 TGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGCGTCC
1 TGCTCTTTGAGGACTG-AAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCC
*
1071077 TGCTCTTTGAGGACTGAAAGGTGCCACTAACTTGTGTGGGCTTTGAAAGGCGTCC
1 TGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCC
*
1071132 TGCTCTTTAAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCC
1 TGCTCTTTGAGGACTG-AAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCC
*
1071187 TGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAACAGCATCC
1 TGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTG-AAAG-----GCGTCC
* * *
1071248 TGCTCTTTGAGGACTGGAAAATGCCACCAACTTGCGTGGGCTTTGAAAGGCATCC
1 TGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCC
* *
1071303 TACTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTT-ATAAGGCGTCC
1 TGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTGA-AAGGCGTCC
* * *** * * *
1071358 TACTCTTTGAGGACTGGAAAATG-------CTT-TGAAAAG----AAAAAGCATCC
1 TGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTG-TGGGCTTTGAAAGGCGTCC
* ** * *
1071402 TGCTCTTTGAGGACTGGAAAATGCCATTAACTTGTGTGGGCTTTAAAAGGCATCC
1 TGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCC
* * *
1071457 TACTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGGGTCC
1 TGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCC
*
1071512 TGCTCTTTGAGGACTGAAAGGTGCCACTAACTTGTGTGGGCTTTGAAAGGAAAAGGCGTCC
1 TGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTT-----G-AAAGGCGTCC
1071573 TGCTCTTTGAGGACTGAAA
1 TGCTCTTTGAGGACTGAAA
1071592 AGTGAAAGGG
Statistics
Matches: 596, Mismatches: 50, Indels: 86
0.81 0.07 0.12
Matches are distributed among these distances:
44 29 0.05
45 1 0.00
47 2 0.00
48 4 0.01
51 4 0.01
52 2 0.00
54 14 0.02
55 350 0.59
56 13 0.02
60 11 0.02
61 158 0.27
62 8 0.01
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.27
Consensus pattern (54 bp):
TGCTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCC
Found at i:1071251 original size:171 final size:169
Alignment explanation
Indices: 1070845--1071592 Score: 825
Period size: 171 Copynumber: 4.5 Consensus size: 169
1070835 AAGTGAATCT
* * *
1070845 TGCTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTTG-AAAG----GTGTCCTGCTC
1 TGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAGCGTCCTGCTC
* * ** *
1070905 TTTGAGGATTGAAAGGTGCCACTAACTCATGTGGGCTTTGAAAAGAAAAGGCATCCTGCTCTTTG
66 TTTGAGGACTGAAA-ATGCCACTAACTTGTGTGGGCTTT-----G-AAAGGCATCCTACTCTTTG
* * * *
1070970 AGGACTGGAAACTGCAACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCC
124 AGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTG-AAAG-----GCGTCC
*
1071022 TGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTT-AAAAG----GCGTCCTGCTC
1 TGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAGCGTCCTGCTC
* * * *
1071082 TTTGAGGACTGAAAGGTGCCACTAACTTGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTAAGGACT
66 TTTGAGGACTGAAA-ATGCCACTAACTTGTGTGGGCTTTGAAAGGCATCCTACTCTTTGAGGACT
1071147 -GAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCC
130 AGAAAA-TGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCC
* *
1071187 TGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAACAGCATCCTGCT
1 TGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAA-AGCGTCCTGCT
* *
1071252 CTTTGAGGACTGGAAAATGCCACCAACTTGCGTGGGCTTTGAAAGGCATCCTACTCTTTGAGGAC
65 CTTTGAGGACT-GAAAATGCCACTAACTTGTGTGGGCTTTGAAAGGCATCCTACTCTTTGAGGAC
1071317 TAGAAAATGCCACCAACTTGTGTGGGCTTT-ATAAGGCGTCC
129 TAGAAAATGCCACCAACTTGTGTGGGCTTTGA-AAGGCGTCC
* * *
1071358 TACTCTTTGAGGACT-----G-G--A--AA-----AT--GCTTTGAAAAGAAAAAGCATCCTGCT
1 TGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAAG-AAAAGCGTCCTGCT
* *
1071406 CTTTGAGGACTGGAAAATGCCATTAACTTGTGTGGGCTTTAAAAGGCATCCTACTCTTTGAGGAC
65 CTTTGAGGACT-GAAAATGCCACTAACTTGTGTGGGCTTTGAAAGGCATCCTACTCTTTGAGGAC
* *
1071471 TGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGGGTCC
129 TAGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCC
* * *
1071512 TGCTCTTTGAGGACTGAAAGGTGCCACTAACTTGTGTGGGCTTTGAAAGGAAAAGGCGTCCTGCT
1 TGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAA-GCGTCCTGCT
1071577 CTTTGAGGACTGAAAA
65 CTTTGAGGACTGAAAA
1071593 GTGAAAGGGG
Statistics
Matches: 507, Mismatches: 33, Indels: 69
0.83 0.05 0.11
Matches are distributed among these distances:
154 134 0.26
155 4 0.01
156 1 0.00
159 1 0.00
160 1 0.00
161 2 0.00
162 1 0.00
163 1 0.00
164 2 0.00
165 48 0.09
166 6 0.01
169 1 0.00
170 18 0.04
171 186 0.37
172 10 0.02
177 91 0.18
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.27
Consensus pattern (169 bp):
TGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAGCGTCCTGCTC
TTTGAGGACTGAAAATGCCACTAACTTGTGTGGGCTTTGAAAGGCATCCTACTCTTTGAGGACTA
GAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCC
Found at i:1071468 original size:99 final size:99
Alignment explanation
Indices: 1071297--1071480 Score: 314
Period size: 99 Copynumber: 1.9 Consensus size: 99
1071287 GCTTTGAAAG
* *
1071297 GCATCCTACTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTATAAGGCGTCCTACT
1 GCATCCTACTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGCATCCTACT
1071362 CTTTGAGGACTGGAAAATGCTTTGAAAAGAAAAA
66 CTTTGAGGACTGGAAAATGCTTTGAAAAGAAAAA
* * **
1071396 GCATCCTGCTCTTTGAGGACTGGAAAATGCCATTAACTTGTGTGGGCTTTAAAAGGCATCCTACT
1 GCATCCTACTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGCATCCTACT
1071461 CTTTGAGGACTGGAAAATGC
66 CTTTGAGGACTGGAAAATGC
1071481 CACCAACTTG
Statistics
Matches: 79, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
99 79 1.00
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (99 bp):
GCATCCTACTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGCATCCTACT
CTTTGAGGACTGGAAAATGCTTTGAAAAGAAAAA
Found at i:1071512 original size:154 final size:154
Alignment explanation
Indices: 1071226--1071527 Score: 516
Period size: 154 Copynumber: 2.0 Consensus size: 154
1071216 ACTTGTGTGG
*
1071226 GCTTTGAAAAGAAACAGCATCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGCGTGGGCTT
1 GCTTTGAAAAGAAAAAGCATCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGCGTGGGCTT
*
1071291 TGAAAGGCATCCTACTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTATAAGGCGT
66 TAAAAGGCATCCTACTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTATAAGGCGT
1071356 CCTACTCTTTGAGGACTGGAAAAT
131 CCTACTCTTTGAGGACTGGAAAAT
** *
1071380 GCTTTGAAAAGAAAAAGCATCCTGCTCTTTGAGGACTGGAAAATGCCATTAACTTGTGTGGGCTT
1 GCTTTGAAAAGAAAAAGCATCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGCGTGGGCTT
* *
1071445 TAAAAGGCATCCTACTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGA-AAGGGG
66 TAAAAGGCATCCTACTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTT-ATAAGGCG
*
1071509 TCCTGCTCTTTGAGGACTG
130 TCCTACTCTTTGAGGACTG
1071528 AAAGGTGCCA
Statistics
Matches: 139, Mismatches: 8, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
154 138 0.99
155 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.27
Consensus pattern (154 bp):
GCTTTGAAAAGAAAAAGCATCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGCGTGGGCTT
TAAAAGGCATCCTACTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTATAAGGCGT
CCTACTCTTTGAGGACTGGAAAAT
Found at i:1072564 original size:1 final size:1
Alignment explanation
Indices: 1072558--1072647 Score: 63
Period size: 1 Copynumber: 90.0 Consensus size: 1
1072548 TTCTTTTCTC
* * * * * ** * *
1072558 TTTTTTTTTCTTTGTTTTGTCTTTTTTTTGTTTTTTTTGGTTTTTTTTTTTGTTTTTTGTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
** * *
1072623 TTTTGCTTTTGTTTTTGTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
1072648 AGAAGATAAG
Statistics
Matches: 66, Mismatches: 23, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 66 1.00
ACGTcount: A:0.00, C:0.03, G:0.11, T:0.86
Consensus pattern (1 bp):
T
Found at i:1072575 original size:11 final size:10
Alignment explanation
Indices: 1072558--1072647 Score: 94
Period size: 11 Copynumber: 8.8 Consensus size: 10
1072548 TTCTTTTCTC
1072558 TTTTTTTTT-
1 TTTTTTTTTG
* *
1072567 CTTTGTTTTG
1 TTTTTTTTTG
1072577 TCTTTTTTTTG
1 T-TTTTTTTTG
*
1072588 TTTTTTTTGG
1 TTTTTTTTTG
1072598 TTTTTTTTT-
1 TTTTTTTTTG
*
1072607 TTGTTTTTTG
1 TTTTTTTTTG
1072617 TTTTTTTTTTG
1 -TTTTTTTTTG
1072628 CTTTTGTTTTTG
1 -TTTT-TTTTTG
1072640 TTTTTTTT
1 TTTTTTTT
1072648 AGAAGATAAG
Statistics
Matches: 67, Mismatches: 9, Indels: 9
0.79 0.11 0.11
Matches are distributed among these distances:
9 15 0.22
10 20 0.30
11 26 0.39
12 6 0.09
ACGTcount: A:0.00, C:0.03, G:0.11, T:0.86
Consensus pattern (10 bp):
TTTTTTTTTG
Found at i:1072584 original size:19 final size:17
Alignment explanation
Indices: 1072559--1072645 Score: 84
Period size: 18 Copynumber: 4.6 Consensus size: 17
1072549 TCTTTTCTCT
1072559 TTTTTTTTCTTTGTTTTG
1 TTTTTTTT-TTTGTTTTG
*
1072577 TCTTTTTTTTGTTTTTTTTGG
1 --TTTTTTTT-TTTGTTTT-G
*
1072598 TTTTTTTTTTTGTTTTT
1 TTTTTTTTTTTGTTTTG
1072615 TGTTTTTTTTTTGCTTTTG
1 T-TTTTTTTTTTG-TTTTG
1072634 TTTTTGTTTTTT
1 TTTTT-TTTTTT
1072646 TTAGAAGATA
Statistics
Matches: 58, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
17 1 0.02
18 22 0.38
19 19 0.33
20 15 0.26
21 1 0.02
ACGTcount: A:0.00, C:0.03, G:0.11, T:0.85
Consensus pattern (17 bp):
TTTTTTTTTTTGTTTTG
Found at i:1072644 original size:20 final size:18
Alignment explanation
Indices: 1072558--1072646 Score: 99
Period size: 20 Copynumber: 4.7 Consensus size: 18
1072548 TTCTTTTCTC
1072558 TTTTTTTTTCTTTGTTTTG
1 TTTTTTTTT-TTTGTTTTG
*
1072577 TCTTTTTTTTGTTTTTTTTG
1 T-TTTTTTTT-TTTGTTTTG
*
1072597 GTTTTTTTTTTTGTTTT-
1 TTTTTTTTTTTTGTTTTG
1072614 TTGTTTTTTTTTTGCTTTTG
1 TT-TTTTTTTTTTG-TTTTG
1072634 TTTTTGTTTTTTT
1 TTTTT-TTTTTTT
1072647 TAGAAGATAA
Statistics
Matches: 60, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
17 1 0.02
18 18 0.30
19 16 0.27
20 25 0.42
ACGTcount: A:0.00, C:0.03, G:0.11, T:0.85
Consensus pattern (18 bp):
TTTTTTTTTTTTGTTTTG
Found at i:1082958 original size:4 final size:4
Alignment explanation
Indices: 1082949--1082977 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
1082939 AAAACAAAAC
1082949 AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
1082978 CCTCAAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:1085153 original size:79 final size:79
Alignment explanation
Indices: 1085027--1085251 Score: 256
Period size: 79 Copynumber: 2.8 Consensus size: 79
1085017 TGAGAAATTT
* * * *
1085027 AATATTTTGGAGATAATAA-CGGGGTTGGAGTATCCCCTTGAAAATAACGGGGTTGGAGTATCCC
1 AATATTTAGGAAATAA-AACCGGGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCC
* *
1085091 CGGCTGTGAAAAATC
65 CGACTATGAAAAATC
* * * *
1085106 GATGA-TTAGGAAATAAAATCGGGATTGGAGTATTCCCTCGGAAATAACGGGGTTGGAGTATCCC
1 AAT-ATTTAGGAAATAAAACCGGGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCC
* * *
1085170 CAATTATGAGAAATC
65 CGACTATGAAAAATC
* * ** *
1085185 AATATTTTGGAAATAAAGCCGGGGTTGGAGTATCCCCTCGGAGGTAATGGGGTTGGAGTATCCCC
1 AATATTTAGGAAATAAAACCGGGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCC
1085250 GA
66 GA
1085252 TGAAATAACG
Statistics
Matches: 121, Mismatches: 22, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
78 3 0.02
79 117 0.97
80 1 0.01
ACGTcount: A:0.30, C:0.15, G:0.29, T:0.26
Consensus pattern (79 bp):
AATATTTAGGAAATAAAACCGGGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCC
GACTATGAAAAATC
Found at i:1085218 original size:51 final size:51
Alignment explanation
Indices: 1085153--1085328 Score: 144
Period size: 51 Copynumber: 3.4 Consensus size: 51
1085143 TCGGAAATAA
1085153 CGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGGAAATAAAGC
1 CGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGGAAATAAAGC
* * *** * * ***
1085204 CGGGGTTGGAGTATCCCCTCGGAGGTAATG-GGGTTGGAGTATCCCCGATGAAAT-AA--
1 CGGGGTTGGAGTAT-CCC-C--A-ATTATGAGAAAT-CAATAT-TTTG--GAAATAAAGC
*
1085260 CGAGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGGAAATAAAGC
1 CGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGGAAATAAAGC
1085311 CGGGGTTGGAGTATCCCC
1 CGGGGTTGGAGTATCCCC
1085329 TCGGAGGTAA
Statistics
Matches: 90, Mismatches: 22, Indels: 26
0.65 0.16 0.19
Matches are distributed among these distances:
48 5 0.06
49 2 0.02
50 1 0.01
51 39 0.43
52 6 0.07
53 1 0.01
54 1 0.01
55 6 0.07
56 21 0.23
57 1 0.01
58 2 0.02
59 5 0.06
ACGTcount: A:0.30, C:0.16, G:0.28, T:0.26
Consensus pattern (51 bp):
CGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGGAAATAAAGC
Found at i:1085257 original size:107 final size:107
Alignment explanation
Indices: 1085125--1085434 Score: 464
Period size: 107 Copynumber: 2.9 Consensus size: 107
1085115 GAAATAAAAT
* *
1085125 CGGGATTGGAGTATTCCCTCG--GAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAAT
1 CGGGGTTGGAGTA-TCCC-CGATGAAATAACGAGGTTGGAGTATCCCCAATTATGAGAAATCAAT
1085188 ATTTTGGAAATAAAGCCGGGGTTGGAGTATCCCCTCGGAGGTAA
64 ATTTTGGAAATAAAGCCGGGGTTGGAGTATCCCCTCGGAGGTAA
*
1085232 TGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCCCAATTATGAGAAATCAATAT
1 CGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCCCAATTATGAGAAATCAATAT
1085297 TTTGGAAATAAAGCCGGGGTTGGAGTATCCCCTCGGAGGTAA
66 TTTGGAAATAAAGCCGGGGTTGGAGTATCCCCTCGGAGGTAA
* * * * * *
1085339 CGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCTCGATTGTGA-AAAACTAGTG
1 CGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCCCAATTATGAGAAATC-AATA
** *
1085403 TTTTGGAAATAAAATCGGAGTTGGAGTATCCC
65 TTTTGGAAATAAAGCCGGGGTTGGAGTATCCC
1085435 TGATTAAAGG
Statistics
Matches: 187, Mismatches: 13, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
105 2 0.01
106 8 0.04
107 177 0.95
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.26
Consensus pattern (107 bp):
CGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCCCAATTATGAGAAATCAATAT
TTTGGAAATAAAGCCGGGGTTGGAGTATCCCCTCGGAGGTAA
Found at i:1085367 original size:28 final size:28
Alignment explanation
Indices: 1085311--1085387 Score: 91
Period size: 28 Copynumber: 2.8 Consensus size: 28
1085301 GAAATAAAGC
*** **
1085311 CGGGGTTGGAGTATCCCCTCGGAGGTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
1085339 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
* *
1085367 CGAGGTTGGAGTATCCTCGAT
1 CGGGGTTGGAGTATCCCCGAT
1085388 TGTGAAAAAC
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 42 1.00
ACGTcount: A:0.22, C:0.19, G:0.35, T:0.23
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:1085509 original size:103 final size:101
Alignment explanation
Indices: 1085372--1085655 Score: 361
Period size: 103 Copynumber: 2.8 Consensus size: 101
1085362 AATAACGAGG
* * * * * *
1085372 TTGGAGTATCCTCGATTGTGAAAAACTAGTGTTTTGGAAATAAAATCGGAGTTGGAGTATCCCTG
1 TTGGAGTATCCCCGATTGTGGAAAATTAGTGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCTG
*
1085437 ATTAAAGGAAAATTGGTGTTTTAAAAATAAAACCGGGA
66 ATTAAA--AAAATTGGTATTTTAAAAATAAAACCGGGA
* * *
1085475 TTGGAGTATCCCCAATTGTGGAAAATTAGTGTTTTATAAATAAAACCGGGGGTTGGAGTTTCCCT
1 TTGGAGTATCCCCGATTGTGGAAAATTAGTGTTTTAGAAATAAAACC-GGGGTTGGAGTATCCCT
* * * *
1085540 GATTGTAAAAAATTGGTATTTTAGAAATAAAATCGGGG
65 GATT-AAAAAAATTGGTATTTTAAAAATAAAACCGGGA
* * *
1085578 TTAGAGTATCCCCGATTATGGAAAATTAGTGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCCG
1 TTGGAGTATCCCCGATTGTGGAAAATTAGTGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCTG
*
1085643 ATTATGAAAAATT
66 ATTA-AAAAAATT
1085656 ACGAAACTTA
Statistics
Matches: 156, Mismatches: 22, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
102 26 0.17
103 109 0.70
104 19 0.12
105 2 0.01
ACGTcount: A:0.35, C:0.11, G:0.24, T:0.31
Consensus pattern (101 bp):
TTGGAGTATCCCCGATTGTGGAAAATTAGTGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCTG
ATTAAAAAAATTGGTATTTTAAAAATAAAACCGGGA
Found at i:1085516 original size:51 final size:51
Alignment explanation
Indices: 1085370--1085656 Score: 331
Period size: 51 Copynumber: 5.6 Consensus size: 51
1085360 GAAATAACGA
* * * * *
1085370 GGTTGGAGTATCCTCGATTGTGAAAAACTAGTGTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTAGAAATAAAACCGG
* * * * * *
1085421 AGTTGGAGTATCCCTGATTAAAGGAAAATTGGTGTTTTAAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT-ATGAAAAATTAGTGTTTTAGAAATAAAACCGG
* * * * *
1085473 GATTGGAGTATCCCCAATTGTGGAAAATTAGTGTTTTATAAATAAAACCGGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTAGAAATAAAACC-GG
* * * * * * *
1085525 GGTTGGAGTTTCCCTGATTGTAAAAAATTGGTATTTTAGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTAGAAATAAAACCGG
* *
1085576 GGTTAGAGTATCCCCGATTATGGAAAATTAGTGTTTTAGAAATAAAACCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTAGAAATAAAACCGG
1085627 GGTTGGAGTATCCCCGATTATGAAAAATTA
1 GGTTGGAGTATCCCCGATTATGAAAAATTA
1085657 CGAAACTTAA
Statistics
Matches: 194, Mismatches: 40, Indels: 4
0.82 0.17 0.02
Matches are distributed among these distances:
51 114 0.59
52 80 0.41
ACGTcount: A:0.34, C:0.10, G:0.24, T:0.31
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTAGAAATAAAACCGG
Found at i:1088014 original size:13 final size:13
Alignment explanation
Indices: 1087996--1088021 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1087986 ACAAAGATCG
1087996 ATGTATCGATACA
1 ATGTATCGATACA
1088009 ATGTATCGATACA
1 ATGTATCGATACA
1088022 TTCTACAAAT
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1088098 original size:19 final size:21
Alignment explanation
Indices: 1088074--1088123 Score: 77
Period size: 19 Copynumber: 2.5 Consensus size: 21
1088064 AGCGATACAC
*
1088074 TGTATCGATACA-TTACT-TA
1 TGTATCGATACATTTACTGAA
1088093 TGTATCGATACATTTACTGAA
1 TGTATCGATACATTTACTGAA
1088114 TGTATCGATA
1 TGTATCGATA
1088124 AAAATTATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
19 12 0.43
20 5 0.18
21 11 0.39
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.40
Consensus pattern (21 bp):
TGTATCGATACATTTACTGAA
Found at i:1090657 original size:32 final size:32
Alignment explanation
Indices: 1090621--1090682 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 32
1090611 TAGCCAAACT
* *
1090621 TGTATCGATACAC-CAAAGTATGTATCGATAAA
1 TGTATCGATACACAAAAAAT-TGTATCGATAAA
1090653 TGTATCGATACACAAAAAATTGTATCGATA
1 TGTATCGATACACAAAAAATTGTATCGATA
1090683 CATTGGCTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
32 23 0.85
33 4 0.15
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.29
Consensus pattern (32 bp):
TGTATCGATACACAAAAAATTGTATCGATAAA
Found at i:1096857 original size:13 final size:13
Alignment explanation
Indices: 1096839--1096877 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
1096829 ACATTTTTCT
1096839 TTGTATCGATACA
1 TTGTATCGATACA
1096852 TTGTATCGATACA
1 TTGTATCGATACA
*
1096865 CTGTATCGATACA
1 TTGTATCGATACA
1096878 GGGGGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1097041 original size:20 final size:20
Alignment explanation
Indices: 1096998--1097043 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
1096988 AAATCTTTTG
1096998 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
1097019 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
1097039 CAAAA
1 CAAAA
1097044 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:1099447 original size:13 final size:13
Alignment explanation
Indices: 1099429--1099454 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1099419 ACACCAAAGT
1099429 ATGTATCGATACA
1 ATGTATCGATACA
1099442 ATGTATCGATACA
1 ATGTATCGATACA
1099455 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1099454 original size:33 final size:33
Alignment explanation
Indices: 1099410--1099474 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
1099400 TAGCCAAACT
* *
1099410 TGTATCAATACAC-CAAAGTATGTATCGATACAA
1 TGTATCAATACACAAAAAAT-TGTATCGATACAA
*
1099443 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCAATACACAAAAAATTGTATCGATACA
1099475 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 24 0.86
34 4 0.14
ACGTcount: A:0.43, C:0.17, G:0.12, T:0.28
Consensus pattern (33 bp):
TGTATCAATACACAAAAAATTGTATCGATACAA
Found at i:1105710 original size:32 final size:32
Alignment explanation
Indices: 1105669--1105729 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
1105659 TACAAGCCAA
*
1105669 TGTATCGATACA-ATTTTTGTGTATCGATATAT
1 TGTATCGATACATA-CTTTGTGTATCGATATAT
1105701 TGTATCGATACATACTTTGTGTATCGATA
1 TGTATCGATACATACTTTGTGTATCGATA
1105730 CAAGTTTGGC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
32 26 0.96
33 1 0.04
ACGTcount: A:0.28, C:0.11, G:0.16, T:0.44
Consensus pattern (32 bp):
TGTATCGATACATACTTTGTGTATCGATATAT
Found at i:1109640 original size:52 final size:52
Alignment explanation
Indices: 1109555--1109679 Score: 205
Period size: 52 Copynumber: 2.4 Consensus size: 52
1109545 ATATGAAAAG
* * *
1109555 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATATATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
* *
1109607 TTGCCTGCATGTATCAATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
1109659 TTGCCTGCATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
1109680 AAGATCAGTG
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.37
Consensus pattern (52 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
Found at i:1109692 original size:52 final size:51
Alignment explanation
Indices: 1109555--1109700 Score: 195
Period size: 52 Copynumber: 2.8 Consensus size: 51
1109545 ATATGAAAAG
* *
1109555 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATATATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
* * *
1109607 TTGCCTGCATGTATCAATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
*
1109659 TTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACAT
1 TTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACAT
1109701 GTGAGTAATG
Statistics
Matches: 83, Mismatches: 9, Indels: 4
0.86 0.09 0.04
Matches are distributed among these distances:
51 2 0.02
52 81 0.98
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAAT
Found at i:1109782 original size:33 final size:33
Alignment explanation
Indices: 1109740--1109809 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
1109730 GGCAGTAGCT
1109740 TACATTGTATCGATACAAAAAAATATGTATCGA
1 TACATTGTATCGATACAAAAAAATATGTATCGA
* ***
1109773 TACATTGTATCGATACAACATTTTATGTATCGA
1 TACATTGTATCGATACAAAAAAATATGTATCGA
1109806 TACA
1 TACA
1109810 AATCGTTGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.34
Consensus pattern (33 bp):
TACATTGTATCGATACAAAAAAATATGTATCGA
Found at i:1109783 original size:13 final size:13
Alignment explanation
Indices: 1109765--1109789 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1109755 CAAAAAAATA
1109765 TGTATCGATACAT
1 TGTATCGATACAT
1109778 TGTATCGATACA
1 TGTATCGATACA
1109790 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1111920 original size:13 final size:13
Alignment explanation
Indices: 1111904--1111936 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
1111894 CCCCTGTACT
*
1111904 GATACAGTGTATC
1 GATACAATGTATC
1111917 GATACAATGTATC
1 GATACAATGTATC
1111930 GATACAA
1 GATACAA
1111937 AGAAAAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.27
Consensus pattern (13 bp):
GATACAATGTATC
Found at i:1117561 original size:71 final size:71
Alignment explanation
Indices: 1117445--1117621 Score: 329
Period size: 71 Copynumber: 2.5 Consensus size: 71
1117435 TTCCCGTGTG
1117445 AATGTATCGATACAATTTTTGATGTATCGATACATATTTGAAAATATAGCCGTTTCTAGCCGTTA
1 AATGTATCGATACAATTTTTGATGTATCGATACATATTTGAAAATATAGCCGTTTCTAGCCGTTA
1117510 CAAGCC
66 CAAGCC
*
1117516 AATGTATCGATACAATTTTTGATGTATCGATACATATTTGAAAATATAGCCGTTTCTAGCTGTTA
1 AATGTATCGATACAATTTTTGATGTATCGATACATATTTGAAAATATAGCCGTTTCTAGCCGTTA
1117581 CAAGCC
66 CAAGCC
1117587 AATGTATCGATACAATTTTTTG-TGTATCGATACAT
1 AATGTATCGATACAA-TTTTTGATGTATCGATACAT
1117622 TGTATCGATA
Statistics
Matches: 104, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
71 98 0.94
72 6 0.06
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.37
Consensus pattern (71 bp):
AATGTATCGATACAATTTTTGATGTATCGATACATATTTGAAAATATAGCCGTTTCTAGCCGTTA
CAAGCC
Found at i:1117627 original size:13 final size:13
Alignment explanation
Indices: 1117609--1117634 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1117599 CAATTTTTTG
1117609 TGTATCGATACAT
1 TGTATCGATACAT
1117622 TGTATCGATACAT
1 TGTATCGATACAT
1117635 ACTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1117646 original size:32 final size:33
Alignment explanation
Indices: 1117589--1117652 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
1117579 TACAAGCCAA
**
1117589 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTTGTGTATCGATACAT
1117622 TGTATCGATAC-ATACTTTGTGTATCGATACA
1 TGTATCGATACAATACTTTGTGTATCGATACA
1117653 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (33 bp):
TGTATCGATACAATACTTTGTGTATCGATACAT
Found at i:1118812 original size:28 final size:29
Alignment explanation
Indices: 1118780--1119131 Score: 361
Period size: 28 Copynumber: 12.5 Consensus size: 29
1118770 CAACGTTCTC
1118780 CAAAGCCCACGAGTC-GATGGCA-CCTTTT
1 CAAAGCCCACGAGTCAG-TGGCACCCTTTT
* * * *
1118808 CAAAGCACACAAGTCAGTGACAACCTTTT
1 CAAAGCCCACGAGTCAGTGGCACCCTTTT
1118837 -AAAGCCCACGAGTCAGTGGCACCCTTTT
1 CAAAGCCCACGAGTCAGTGGCACCCTTTT
*
1118865 -AAAGCCTACGAGTCAGTGGCA-CCTTTT
1 CAAAGCCCACGAGTCAGTGGCACCCTTTT
*
1118892 CAAAGCCCACGACTCAGTGGCACCCTTTT
1 CAAAGCCCACGAGTCAGTGGCACCCTTTT
* * * *
1118921 -TAAGCCCACAAGTCAGTGGCATCC-TTC
1 CAAAGCCCACGAGTCAGTGGCACCCTTTT
* *
1118948 CAATGCCCACGAGTCAGTGGTA-CCTTTT
1 CAAAGCCCACGAGTCAGTGGCACCCTTTT
* ** * *
1118976 CAAAGCCTATAAGTTAGTGGCACTCTTTT
1 CAAAGCCCACGAGTCAGTGGCACCCTTTT
* *
1119005 -AAAGCCCAAGAGTTAGTGGCACCCTTTT
1 CAAAGCCCACGAGTCAGTGGCACCCTTTT
*
1119033 -AAAGCCCACGAGTCAGTGGCATCCTTTT
1 CAAAGCCCACGAGTCAGTGGCACCCTTTT
* *
1119061 -AAAGCCCATGAGTTAGTGGCA-CCTTTT
1 CAAAGCCCACGAGTCAGTGGCACCCTTTT
* * *
1119088 CAAAGCCCATGAGTCAATGGCATCC-TTT
1 CAAAGCCCACGAGTCAGTGGCACCCTTTT
*
1119116 CAAAAGCCCACAAGTC
1 C-AAAGCCCACGAGTC
1119132 GATGGTACCC
Statistics
Matches: 274, Mismatches: 40, Indels: 19
0.82 0.12 0.06
Matches are distributed among these distances:
27 16 0.06
28 226 0.82
29 32 0.12
ACGTcount: A:0.28, C:0.29, G:0.19, T:0.24
Consensus pattern (29 bp):
CAAAGCCCACGAGTCAGTGGCACCCTTTT
Found at i:1118842 original size:56 final size:56
Alignment explanation
Indices: 1118781--1119215 Score: 375
Period size: 56 Copynumber: 7.6 Consensus size: 56
1118771 AACGTTCTCC
* *
1118781 AAAGCCCACGAGTC-GATGGCA-CCTTTTCAAAGCACACAAGTCAGTGACAACCTTTT
1 AAAGCCCACGAGTCAG-TGGCACCCTTTT-AAAGCCCACAAGTCAGTGGCAACCTTTT
* *
1118837 AAAGCCCACGAGTCAGTGGCACCCTTTTAAAGCCTACGAGTCAGTGGC-ACCTTTT
1 AAAGCCCACGAGTCAGTGGCACCCTTTTAAAGCCCACAAGTCAGTGGCAACCTTTT
* * * **
1118892 CAAAGCCCACGACTCAGTGGCACCCTTTTTAAGCCCACAAGTCAGTGGCATCCTTCC
1 -AAAGCCCACGAGTCAGTGGCACCCTTTTAAAGCCCACAAGTCAGTGGCAACCTTTT
* * * * *
1118949 AATGCCCACGAGTCAGTGGTA-CCTTTTCAAAGCCTATAAGTTAGTGGC-ACTCTTTT
1 AAAGCCCACGAGTCAGTGGCACCCTTTT-AAAGCCCACAAGTCAGTGGCAAC-CTTTT
* * * *
1119005 AAAGCCCAAGAGTTAGTGGCACCCTTTTAAAGCCCACGAGTCAGTGGCATCCTTTT
1 AAAGCCCACGAGTCAGTGGCACCCTTTTAAAGCCCACAAGTCAGTGGCAACCTTTT
* * ** * * *
1119061 AAAGCCCATGAGTTAGTGGCA-CCTTTTCAAAGCCCATGAGTCAATGGCATCCTTTCA
1 AAAGCCCACGAGTCAGTGGCACCCTTTT-AAAGCCCACAAGTCAGTGGCAACCTTT-T
* * * * *
1119118 AAAGCCCACAAGTC-GATGGTACCCTTCTGAAGCCCACACAAG-CTGGTGGCAACCTTTCT
1 AAAGCCCACGAGTCAG-TGGCACCCTTTTAAAG-CC-CACAAGTC-AGTGGCAACCTTT-T
* *
1119177 CAAAGCCCACACAAGTCAGTGGCAACCCTTCT-AAGCCCA
1 -AAAG-CC-CACGAGTCAGTGGC-ACCCTTTTAAAGCCCA
1119216 ATGTCTTTGG
Statistics
Matches: 312, Mismatches: 47, Indels: 36
0.79 0.12 0.09
Matches are distributed among these distances:
55 20 0.06
56 200 0.64
57 36 0.12
58 8 0.03
59 15 0.05
60 6 0.02
61 4 0.01
62 14 0.04
63 9 0.03
ACGTcount: A:0.28, C:0.30, G:0.19, T:0.23
Consensus pattern (56 bp):
AAAGCCCACGAGTCAGTGGCACCCTTTTAAAGCCCACAAGTCAGTGGCAACCTTTT
Found at i:1118886 original size:84 final size:83
Alignment explanation
Indices: 1118781--1119131 Score: 400
Period size: 84 Copynumber: 4.2 Consensus size: 83
1118771 AACGTTCTCC
* *
1118781 AAAGCCCACGAGTC-GATGGCACCTTTTCAAAGCACACAAGTCAGTGACAACCTTTTAAAGCCCA
1 AAAGCCCACGAGTCAG-TGGCACCTTTTCAAAGCCCACAAGTCAGTGGC-ACCTTTTAAAGCCCA
1118845 CGAGTCAGTGGCACCCTTTT
64 CGAGTCAGTGGCACCCTTTT
* * * *
1118865 AAAGCCTACGAGTCAGTGGCACCTTTTCAAAGCCCACGACTCAGTGGCACCCTTTTTAAGCCCAC
1 AAAGCCCACGAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCA-CCTTTTAAAGCCCAC
* * **
1118930 AAGTCAGTGGCATCCTTCC
65 GAGTCAGTGGCACCCTTTT
* * * * * *
1118949 AATGCCCACGAGTCAGTGGTACCTTTTCAAAGCCTATAAGTTAGTGGCACTCTTTTAAAGCCCAA
1 AAAGCCCACGAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCAC-CTTTTAAAGCCCAC
*
1119014 GAGTTAGTGGCACCCTTTT
65 GAGTCAGTGGCACCCTTTT
** *
1119033 AAAGCCCACGAGTCAGTGGCATCCTTTT-AAAGCCCATGAGTTAGTGGCACCTTTTCAAAGCCCA
1 AAAGCCCACGAGTCAGTGGCA-CCTTTTCAAAGCCCACAAGTCAGTGGCACCTTTT-AAAGCCCA
* * * *
1119097 TGAGTCAATGGCATCCTTTCA
64 CGAGTCAGTGGCACCCTTT-T
*
1119118 AAAGCCCACAAGTC
1 AAAGCCCACGAGTC
1119132 GATGGTACCC
Statistics
Matches: 226, Mismatches: 35, Indels: 11
0.83 0.13 0.04
Matches are distributed among these distances:
83 7 0.03
84 199 0.88
85 20 0.09
ACGTcount: A:0.28, C:0.29, G:0.19, T:0.24
Consensus pattern (83 bp):
AAAGCCCACGAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCACCTTTTAAAGCCCACG
AGTCAGTGGCACCCTTTT
Found at i:1119215 original size:30 final size:31
Alignment explanation
Indices: 1119138--1119215 Score: 97
Period size: 32 Copynumber: 2.5 Consensus size: 31
1119128 AGTCGATGGT
* *
1119138 ACCCTTCTGAAGCCCACACAAGCTGGTGGCA
1 ACCCTTCTAAAGCCCACACAAGCTAGTGGCA
*
1119169 ACCTTTCTCAAAGCCCACACAAG-TCAGTGGCA
1 ACCCTTCT-AAAGCCCACACAAGCT-AGTGGCA
1119201 ACCCTTCT-AAGCCCA
1 ACCCTTCTAAAGCCCA
1119216 ATGTCTTTGG
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
30 7 0.17
31 8 0.20
32 26 0.63
ACGTcount: A:0.28, C:0.37, G:0.17, T:0.18
Consensus pattern (31 bp):
ACCCTTCTAAAGCCCACACAAGCTAGTGGCA
Found at i:1119461 original size:62 final size:62
Alignment explanation
Indices: 1119283--1119510 Score: 216
Period size: 62 Copynumber: 3.7 Consensus size: 62
1119273 AGTATCGCTA
* *
1119283 GCCTTGAATCAGCATATTGGCACCTTTATCAGTT-TTCTCATC-TTCAAGCCCGATGTCGTTA
1 GCCTTGAATCAGCATATTGGCACCTTTATC-GTTCTTCTCATCTTTCAAGCCCGATATCGTTG
* * * * * * * * * *
1119344 GCCTTAAATCAACACACTAGTACTTTTCAAACCTTCTT-TC-T-TTT-AAGCCCAATATCGTTG
1 GCCTTGAATCAGCATATTGGCACCTTT--ATCGTTCTTCTCATCTTTCAAGCCCGATATCGTTG
*
1119404 GCCTTGAATCAGCATATTGGCACCTTTATCGTTCTTCTCATCTTTCAAGCCCGATATCGCTG
1 GCCTTGAATCAGCATATTGGCACCTTTATCGTTCTTCTCATCTTTCAAGCCCGATATCGTTG
* * * * * *
1119466 GCCGTGAATCAGCATATCGACACATTTATCATTCTTCGCATCTTT
1 GCCTTGAATCAGCATATTGGCACCTTTATCGTTCTTCTCATCTTT
1119511 AAGTCCAAAG
Statistics
Matches: 130, Mismatches: 29, Indels: 15
0.75 0.17 0.09
Matches are distributed among these distances:
58 7 0.05
59 2 0.02
60 34 0.26
61 26 0.20
62 57 0.44
63 4 0.03
ACGTcount: A:0.23, C:0.27, G:0.14, T:0.36
Consensus pattern (62 bp):
GCCTTGAATCAGCATATTGGCACCTTTATCGTTCTTCTCATCTTTCAAGCCCGATATCGTTG
Found at i:1119665 original size:61 final size:61
Alignment explanation
Indices: 1119505--1119640 Score: 254
Period size: 61 Copynumber: 2.2 Consensus size: 61
1119495 CATTCTTCGC
*
1119505 ATCTTTAAGTCCAAAGTCACTGATCTTGAATCAACACATTGGCACTCTTCTCATCTTTATT
1 ATCTTTAAGTCCAAAGTCACTGATCTTGAATCAACACATTGGCACTATTCTCATCTTTATT
*
1119566 ATCTTTAAGTCCAAAGTCACTGATCTTGAATCAACACATTGGCACTATTCTCCTCTTTATT
1 ATCTTTAAGTCCAAAGTCACTGATCTTGAATCAACACATTGGCACTATTCTCATCTTTATT
1119627 ATCTTTAAGTCCAA
1 ATCTTTAAGTCCAA
1119641 GCCTTGATTC
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
61 73 1.00
ACGTcount: A:0.29, C:0.24, G:0.10, T:0.38
Consensus pattern (61 bp):
ATCTTTAAGTCCAAAGTCACTGATCTTGAATCAACACATTGGCACTATTCTCATCTTTATT
Found at i:1119858 original size:85 final size:85
Alignment explanation
Indices: 1119676--1119836 Score: 195
Period size: 85 Copynumber: 1.9 Consensus size: 85
1119666 CTTGGAGATT
* * * *
1119676 TTCTTAC-CCTTGTTGACTTGTCGGCTTTGTCCTCGGTCAACCATTCCTCTATTTGTTTACTTGT
1 TTCTTACTCCTAGGTGACCTGTCGGCTTTGTCCTCGGTCAACCATTCCTCTATTTGTTTACTTAT
* *
1119740 CGACTTTGTCCCTCGTAGAC
66 CGACCTTGTCCCTCATAGAC
* *
1119760 TTCTTACTCCTAGGTGACCTGTTGGCTTTG-CCTCCGGTCAACCATTCC-CATCTTTGTTTAAC-
1 TTCTTACTCCTAGGTGACCTGTCGGCTTTGTCCT-CGGTCAACCATTCCTC-TATTTGTTT-ACT
1119822 TATCGACCTTGTCCC
63 TATCGACCTTGTCCC
1119837 CAATAAGCTT
Statistics
Matches: 66, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
84 11 0.17
85 53 0.80
86 2 0.03
ACGTcount: A:0.13, C:0.30, G:0.16, T:0.40
Consensus pattern (85 bp):
TTCTTACTCCTAGGTGACCTGTCGGCTTTGTCCTCGGTCAACCATTCCTCTATTTGTTTACTTAT
CGACCTTGTCCCTCATAGAC
Found at i:1120333 original size:18 final size:20
Alignment explanation
Indices: 1120307--1120354 Score: 59
Period size: 18 Copynumber: 2.6 Consensus size: 20
1120297 AAAATCAAAG
*
1120307 AAATCAAAAAAT-TTAAAAA
1 AAATCAAAAAATAATAAAAA
1120326 AAAT-AAAAAATAAT-AAAA
1 AAATCAAAAAATAATAAAAA
1120344 AAA-CAAAAAAT
1 AAATCAAAAAAT
1120355 GATGATGGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 21 0.81
19 5 0.19
ACGTcount: A:0.79, C:0.04, G:0.00, T:0.17
Consensus pattern (20 bp):
AAATCAAAAAATAATAAAAA
Found at i:1120510 original size:15 final size:15
Alignment explanation
Indices: 1120492--1120529 Score: 60
Period size: 15 Copynumber: 2.5 Consensus size: 15
1120482 AGGGGGACAA
1120492 CAATGAAATGG-ATAG
1 CAATGAAATGGCAT-G
1120507 CAATGAAATGGCATG
1 CAATGAAATGGCATG
1120522 CAATGAAA
1 CAATGAAA
1120530 GGAAGAGACA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 20 0.91
16 2 0.09
ACGTcount: A:0.47, C:0.11, G:0.24, T:0.18
Consensus pattern (15 bp):
CAATGAAATGGCATG
Found at i:1122425 original size:28 final size:25
Alignment explanation
Indices: 1122386--1122437 Score: 77
Period size: 28 Copynumber: 2.0 Consensus size: 25
1122376 TCCACCATCG
1122386 GAGGTACTCCAACCCTATTATTTTTGA
1 GAGGTACTCCAACCCTA--ATTTTTGA
1122413 GAGGATACTCCAACCCTAATTTTTG
1 GAGG-TACTCCAACCCTAATTTTTG
1122438 TTTCCAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
26 7 0.29
27 4 0.17
28 13 0.54
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.35
Consensus pattern (25 bp):
GAGGTACTCCAACCCTAATTTTTGA
Found at i:1122474 original size:80 final size:77
Alignment explanation
Indices: 1122206--1122480 Score: 291
Period size: 79 Copynumber: 3.5 Consensus size: 77
1122196 TTTACGTCTG
* *
1122206 AAATACCGATTTTTCACCATCGAGGATACTCCAA-CCTCGTTATTTTTGAGGGGATACTCCAACC
1 AAATATCGATTTTTCACAATCG-GGATACTCCAACCCT-GTTATTTTTGAGGGGATACTCCAA-C
1122270 CCGATTTTATTTCCA
63 CCGATTTTATTTCCA
* * * * * * * *
1122285 AAACATCAATTTTTCACAATCAGGGATACTCTAATCCTGTTATTTCTAAGGGGATCCTCCAATAC
1 AAATATCGATTTTTCACAATC-GGGATACTCCAACCCTGTTATTTTTGAGGGGATACTCCAA-CC
*
1122350 CGATTTTATTTCTA
64 CGATTTTATTTCCA
* * * * *
1122364 AAATATCGATTTTCCACCATCGGAGGTACTCCAACCCTATTATTTTTGAGAGGATACTCCAACCC
1 AAATATCGATTTTTCACAATCGG-GATACTCCAACCCTGTTATTTTTGAGGGGATACTCCAACCC
* *
1122429 TAATTTTTGTTTCCA
65 -GA-TTTTATTTCCA
*
1122444 AAATATTGATTTTTCACAATCGGGCATACTCCAACCC
1 AAATATCGATTTTTCACAATCGGG-ATACTCCAACCC
1122481 CGTTTTTCAA
Statistics
Matches: 159, Mismatches: 31, Indels: 11
0.79 0.15 0.05
Matches are distributed among these distances:
78 4 0.03
79 111 0.70
80 44 0.28
ACGTcount: A:0.29, C:0.25, G:0.12, T:0.34
Consensus pattern (77 bp):
AAATATCGATTTTTCACAATCGGGATACTCCAACCCTGTTATTTTTGAGGGGATACTCCAACCCG
ATTTTATTTCCA
Found at i:1126713 original size:21 final size:20
Alignment explanation
Indices: 1126684--1126726 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1126674 GGCTAGTATG
*
1126684 GGGACTGCCCGGTTGCGACCT
1 GGGACTG-CCGGTCGCGACCT
*
1126705 GGGAGTGCCGGTCGCGACCT
1 GGGACTGCCGGTCGCGACCT
1126725 GG
1 GG
1126727 TGGTGCTGCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.09, C:0.30, G:0.44, T:0.16
Consensus pattern (20 bp):
GGGACTGCCGGTCGCGACCT
Found at i:1127185 original size:13 final size:13
Alignment explanation
Indices: 1127167--1127218 Score: 86
Period size: 13 Copynumber: 4.0 Consensus size: 13
1127157 ATAATCCCCC
1127167 TGTATCGATACAA
1 TGTATCGATACAA
*
1127180 TGTATCGATACAG
1 TGTATCGATACAA
1127193 TGTATCGATACAA
1 TGTATCGATACAA
*
1127206 TATATCGATACAA
1 TGTATCGATACAA
1127219 AGAAAAATGT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 36 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1133187 original size:13 final size:13
Alignment explanation
Indices: 1133169--1133194 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1133159 CAATTTTTTG
1133169 TGTATCGATACAT
1 TGTATCGATACAT
1133182 TGTATCGATACAT
1 TGTATCGATACAT
1133195 ACTTTGGTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1133205 original size:33 final size:33
Alignment explanation
Indices: 1133149--1133213 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
1133139 TACAAGCCAA
* * *
1133149 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATCTTTGGTGTATCAATACAT
1133182 TGTATCGATAC-ATACTTTGGTGTATCAATACA
1 TGTATCGATACAAT-CTTTGGTGTATCAATACA
1133214 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 2 0.07
33 26 0.93
ACGTcount: A:0.29, C:0.14, G:0.15, T:0.42
Consensus pattern (33 bp):
TGTATCGATACAATCTTTGGTGTATCAATACAT
Found at i:1134527 original size:35 final size:35
Alignment explanation
Indices: 1134482--1134553 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
1134472 TAAATGGAAT
1134482 ATATACGAGAAGGAATTTATTTACACCTATGTAAA
1 ATATACGAGAAGGAATTTATTTACACCTATGTAAA
1134517 ATATACGAGAAGGAATTTATTTACACCTATGTAAA
1 ATATACGAGAAGGAATTTATTTACACCTATGTAAA
1134552 AT
1 AT
1134554 TAAATAAATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.43, C:0.11, G:0.14, T:0.32
Consensus pattern (35 bp):
ATATACGAGAAGGAATTTATTTACACCTATGTAAA
Found at i:1135719 original size:19 final size:20
Alignment explanation
Indices: 1135666--1135720 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
1135656 CTGCCAGTTT
*
1135666 CATGTATCGATACAATTAAG
1 CATGTATCGATACAATGAAG
* * *
1135686 TATGTATCAAAACAATGAA-
1 CATGTATCGATACAATGAAG
1135705 CATGTATCGATACAAT
1 CATGTATCGATACAAT
1135721 ATATCGATAC
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
19 13 0.46
20 15 0.54
ACGTcount: A:0.44, C:0.15, G:0.13, T:0.29
Consensus pattern (20 bp):
CATGTATCGATACAATGAAG
Found at i:1136392 original size:17 final size:17
Alignment explanation
Indices: 1136370--1136435 Score: 60
Period size: 17 Copynumber: 3.6 Consensus size: 17
1136360 TTCATTTTAG
1136370 TACTCCCCCTTAATAAC
1 TACTCCCCCTTAATAAC
* ** *
1136387 TACTCCCCTTTTTTGTTATC
1 TACTCCCC---CTTAATAAC
1136407 GTACTCCCCCTTAATAAC
1 -TACTCCCCCTTAATAAC
1136425 TACTCCCCCTT
1 TACTCCCCCTT
1136436 TTTGTTAACC
Statistics
Matches: 37, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
17 19 0.51
18 5 0.14
20 5 0.14
21 8 0.22
ACGTcount: A:0.20, C:0.39, G:0.03, T:0.38
Consensus pattern (17 bp):
TACTCCCCCTTAATAAC
Found at i:1136420 original size:38 final size:38
Alignment explanation
Indices: 1136369--1136442 Score: 139
Period size: 38 Copynumber: 1.9 Consensus size: 38
1136359 TTTCATTTTA
*
1136369 GTACTCCCCCTTAATAACTACTCCCCTTTTTTGTTATC
1 GTACTCCCCCTTAATAACTACTCCCCCTTTTTGTTATC
1136407 GTACTCCCCCTTAATAACTACTCCCCCTTTTTGTTA
1 GTACTCCCCCTTAATAACTACTCCCCCTTTTTGTTA
1136443 ACCCTCTTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.19, C:0.35, G:0.05, T:0.41
Consensus pattern (38 bp):
GTACTCCCCCTTAATAACTACTCCCCCTTTTTGTTATC
Done.