Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold169
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: 2015121
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 45543 characters in sequence are not A, C, G, or T
File 13 of 14
Found at i:1815610 original size:11 final size:11
Alignment explanation
Indices: 1815594--1815635 Score: 66
Period size: 11 Copynumber: 3.7 Consensus size: 11
1815584 CCTTCTCTTC
1815594 AAAAAAAAGCA
1 AAAAAAAAGCA
1815605 AAAAAAAAGCA
1 AAAAAAAAGCA
*
1815616 AAAAAAAAACA
1 AAAAAAAAGCA
1815627 AAACAAAAA
1 AAA-AAAAA
1815636 AACAAAACAA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
11 24 0.83
12 5 0.17
ACGTcount: A:0.86, C:0.10, G:0.05, T:0.00
Consensus pattern (11 bp):
AAAAAAAAGCA
Found at i:1815612 original size:13 final size:11
Alignment explanation
Indices: 1815594--1815642 Score: 62
Period size: 11 Copynumber: 4.3 Consensus size: 11
1815584 CCTTCTCTTC
*
1815594 AAAAAAAAGCA
1 AAAAAAAAACA
*
1815605 AAAAAAAAGCA
1 AAAAAAAAACA
1815616 AAAAAAAAACAA
1 AAAAAAAAAC-A
1815628 AACAAAAAAACA
1 AA-AAAAAAACA
1815640 AAA
1 AAA
1815643 CAAAGAAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
11 21 0.60
12 6 0.17
13 8 0.23
ACGTcount: A:0.86, C:0.10, G:0.04, T:0.00
Consensus pattern (11 bp):
AAAAAAAAACA
Found at i:1815633 original size:16 final size:15
Alignment explanation
Indices: 1815604--1815652 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 15
1815594 AAAAAAAAGC
*
1815604 AAAAAAAAAGCAAAA
1 AAAAAAAAAACAAAA
1815619 AAAAAACAAAACAAAA
1 AAAAAA-AAAACAAAA
*
1815635 AAACAAAACAAAGAAAA
1 AAA-AAAA-AAACAAAA
1815652 A
1 A
1815653 GAGAGAAAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
15 6 0.21
16 12 0.41
17 11 0.38
ACGTcount: A:0.86, C:0.10, G:0.04, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAACAAAA
Found at i:1815643 original size:13 final size:13
Alignment explanation
Indices: 1815606--1815651 Score: 60
Period size: 13 Copynumber: 3.5 Consensus size: 13
1815596 AAAAAAGCAA
1815606 AAAAAAAGC-AAA-
1 AAAAAAA-CAAAAC
1815618 AAAAAAACAAAAC
1 AAAAAAACAAAAC
1815631 AAAAAAACAAAAC
1 AAAAAAACAAAAC
1815644 AAAGAAAA
1 AAA-AAAA
1815652 AGAGAGAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
11 1 0.03
12 10 0.32
13 16 0.52
14 4 0.13
ACGTcount: A:0.85, C:0.11, G:0.04, T:0.00
Consensus pattern (13 bp):
AAAAAAACAAAAC
Found at i:1816715 original size:55 final size:54
Alignment explanation
Indices: 1816635--1817442 Score: 938
Period size: 55 Copynumber: 14.4 Consensus size: 54
1816625 TTCCACTTTC
*
1816635 CAGTCCCCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTT
1 CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTT
1816689 CCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTT
1 -CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTT
1816744 CCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTT
1 -CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTT
* **
1816799 CCAGTCCTCAGAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTT
1 -CAGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCATTTT
* * **
1816854 CAGTCCTCAAAGAGCGGGACACATTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTT
1 CAGTCCTCAAAGAGCAGGACAC-----CTTTCAAAGCCCACACAAGTTGGTGGCATTTT
* * * * *
1816913 CAGTCCTCAAAAAGCGGGACGCCTTTTCTTTTAAAGCCCACCCAAGTTGGTGGCACCTTT
1 CAGTCCTCAAAGAGCAGGACACC-TTTC----AAAGCCCACACAAGTTGGTGGCA-TTTT
* * *
1816973 -AGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTT
1 CAGTCCTCAAAGAGCAGGA--C----ACCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTT
* *
1817033 CAGTCCTCAAAGAGCAGGACATCATTCAAAGCCCACACAAGTTGGTGGCATTTT
1 CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTT
* * *
1817087 CCAGCCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAGGTTGGTGGCATTTTT
1 -CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTT
* * *
1817143 CAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTT
1 CAGTCCTCAAAGAGCAGGA--C----ACCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTT
* * * *
1817204 CAGTCCCCAAAGAGCAGGACCCCTTTCGAAGCCCACACAAGTTGGTGTCATTTTT
1 CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTT
* * *
1817259 CAGTCCCCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGTATTTT
1 CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTT
*
1817313 CCAGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTT
1 -CAGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA-TTTT
* *
1817369 CAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACGAGTTGGTGGCACTTTT
1 CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTT
* * *
1817424 TACTCCTCAATGAGCAGGA
1 CAGTCCTCAAAGAGCAGGA
1817443 TACACTTTAT
Statistics
Matches: 667, Mismatches: 54, Indels: 64
0.85 0.07 0.08
Matches are distributed among these distances:
54 30 0.04
55 433 0.65
56 11 0.02
57 1 0.00
58 2 0.00
59 89 0.13
60 30 0.04
61 66 0.10
64 4 0.01
65 1 0.00
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.24
Consensus pattern (54 bp):
CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTT
Found at i:1816716 original size:27 final size:27
Alignment explanation
Indices: 1816686--1816771 Score: 68
Period size: 27 Copynumber: 3.1 Consensus size: 27
1816676 TTGGTGGCAT
1816686 TTTCCAGTCCTCAAAGAGCAGGACACC
1 TTTCCAGTCCTCAAAGAGCAGGACACC
* * * * ** *
1816713 TTTCAAAGCCCACACAAGTTGGTGG-CA-T
1 TTTC-CAGTCCTCA-AAG-AGCAGGACACC
1816741 TTTCCAGTCCTCAAAGAGCAGGACACC
1 TTTCCAGTCCTCAAAGAGCAGGACACC
1816768 TTTC
1 TTTC
1816772 AAAGCCCACA
Statistics
Matches: 40, Mismatches: 14, Indels: 10
0.62 0.22 0.16
Matches are distributed among these distances:
25 3 0.08
26 5 0.12
27 14 0.35
28 10 0.25
29 5 0.12
30 3 0.08
ACGTcount: A:0.28, C:0.30, G:0.19, T:0.23
Consensus pattern (27 bp):
TTTCCAGTCCTCAAAGAGCAGGACACC
Found at i:1818203 original size:21 final size:21
Alignment explanation
Indices: 1818179--1818256 Score: 147
Period size: 21 Copynumber: 3.7 Consensus size: 21
1818169 AATTTATCCA
1818179 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
1818200 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
1818221 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
1818242 AATGTATCGATACAT
1 AATGTATCGATACAT
1818257 CCTACAAATG
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 56 1.00
ACGTcount: A:0.33, C:0.10, G:0.19, T:0.37
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:1818267 original size:42 final size:43
Alignment explanation
Indices: 1818177--1818276 Score: 150
Period size: 42 Copynumber: 2.4 Consensus size: 43
1818167 AAAATTTATC
**
1818177 CAAATGTATCGATACATTTGTAGAATGTATCGATACATTTGTA
1 CAAATGTATCGATACATTTGTAGAATGTATCGATACATTCCTA
* *
1818220 -GAATGTATCGATACATTTGTGGAATGTATCGATACA-TCCTA
1 CAAATGTATCGATACATTTGTAGAATGTATCGATACATTCCTA
1818261 CAAATGTATCGATACA
1 CAAATGTATCGATACA
1818277 GGGTCCCAAC
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
41 3 0.06
42 48 0.94
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34
Consensus pattern (43 bp):
CAAATGTATCGATACATTTGTAGAATGTATCGATACATTCCTA
Found at i:1818336 original size:19 final size:19
Alignment explanation
Indices: 1818312--1818379 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
1818302 AATTCAACAA
1818312 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
1818331 TTTGTATCGAT--ATAA--
1 TTTGTATCGATACATAAGT
1818346 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
1818363 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
1818380 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 9 0.21
15 4 0.09
17 4 0.09
19 26 0.60
ACGTcount: A:0.35, C:0.10, G:0.15, T:0.40
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:1818350 original size:32 final size:32
Alignment explanation
Indices: 1818314--1818374 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
1818304 TTCAACAATT
*
1818314 TGTATCGATACATAAGTTTTGTATCGATATAA
1 TGTATCGATACATAAGTATTGTATCGATATAA
1818346 TGTATCGATACATAAGTATTGTATCGATA
1 TGTATCGATACATAAGTATTGTATCGATA
1818375 CATAATTAGC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.34, C:0.10, G:0.16, T:0.39
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATATAA
Found at i:1818437 original size:13 final size:13
Alignment explanation
Indices: 1818419--1818444 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1818409 CATTTTTCTG
1818419 TGTATCGATACAT
1 TGTATCGATACAT
1818432 TGTATCGATACAT
1 TGTATCGATACAT
1818445 GGATTTTTGT
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:1818441 original size:33 final size:32
Alignment explanation
Indices: 1818399--1818465 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 32
1818389 GCCAAGGAAA
*
1818399 TGTATCGATACAT-TTTTCTGTGTATCGATACAT
1 TGTATCGATACATGATTT-T-TGTATCGATACAT
1818432 TGTATCGATACATGGATTTTTGTATCGATACAT
1 TGTATCGATACAT-GATTTTTGTATCGATACAT
1818465 T
1 T
1818466 TGGAAATTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
33 27 0.87
34 1 0.03
35 3 0.10
ACGTcount: A:0.25, C:0.13, G:0.16, T:0.45
Consensus pattern (32 bp):
TGTATCGATACATGATTTTTGTATCGATACAT
Found at i:1820952 original size:27 final size:28
Alignment explanation
Indices: 1820903--1820978 Score: 84
Period size: 27 Copynumber: 2.8 Consensus size: 28
1820893 TTTCTTCACA
** *
1820903 ATCGGGGATACTCTGACCTCGTTA-ATC
1 ATCGGGGATACTCCAACCCCGTTATATC
*
1820930 ATCGGGGATACTCCAACCCCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTATATC
*
1820958 -TGAGGGGATACTCCAACCCCG
1 AT-CGGGGATACTCCAACCCCG
1820979 GTTTTATTGC
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
27 22 0.52
28 20 0.48
ACGTcount: A:0.22, C:0.30, G:0.22, T:0.25
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTATATC
Found at i:1821046 original size:52 final size:50
Alignment explanation
Indices: 1820962--1821131 Score: 132
Period size: 52 Copynumber: 3.3 Consensus size: 50
1820952 TATTTCTGAG
* *
1820962 GGGATACTCCAACCCCGGTTTTA-TTGCTAAAACACTAGTTTTTCCACAATC
1 GGGATACTCCAA-CCCGGTTTTATTTCCAAAAACACTA-TTTTTCCACAATC
* * * **
1821013 AGGGATACTCCAACCCTGGTTTTATTTTC-AAAAC-GTCAATTTTCCTTTAATC
1 -GGGATACTCCAACCC-GGTTTTATTTCCAAAAACACT-ATTTTTCC-ACAATC
* * *
1821065 GGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTT-CACAATC
1 -GGGATACTCCAAC-CCGGTTTTATTTCCAAAAACA-CTATTTTTCCACAATC
1821117 GAGGATACTCCAACC
1 G-GGATACTCCAACC
1821132 TCGTTATTTC
Statistics
Matches: 95, Mismatches: 14, Indels: 19
0.74 0.11 0.15
Matches are distributed among these distances:
51 12 0.13
52 68 0.72
53 10 0.11
54 5 0.05
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.32
Consensus pattern (50 bp):
GGGATACTCCAACCCGGTTTTATTTCCAAAAACACTATTTTTCCACAATC
Found at i:1821150 original size:28 final size:28
Alignment explanation
Indices: 1821114--1821190 Score: 100
Period size: 28 Copynumber: 2.8 Consensus size: 28
1821104 ATTTTTCACA
* * *
1821114 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
1821142 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
***
1821170 CGAGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
1821191 GCTTTATTCC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.23, C:0.34, G:0.19, T:0.23
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTACTTC
Found at i:1821159 original size:212 final size:212
Alignment explanation
Indices: 1820792--1821205 Score: 611
Period size: 212 Copynumber: 2.0 Consensus size: 212
1820782 TTCTCAATTC
* * *
1820792 TCCACAATCGGGGATATTCCAACTCCGATTTTCTTTTCAAAACACTAATTTTCTATAATCAGGGA
1 TCCACAATCAGGGATACTCCAACTCCGATTTTATTTTCAAAACACTAATTTTCTATAATCAGGGA
* * **
1820857 TACTCTAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGGGGATACTCTGACCT
66 TACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCT
* * *
1820922 CGTTAATCATCGGGGATACTCCAACCCCGTTATTTCTGAGGGGATACTCCAACCCCGGTTTTATT
131 CGTTAATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTATT
*
1820987 GCTAAAACACTAGTTTT
196 CCTAAAACACTAGTTTT
* * * *
1821004 TCCACAATCAGGGATACTCCAAC-CCTGGTTTTATTTTCAAAAC-GTCAATTTTCCTTTAATCGG
1 TCCACAATCAGGGATACTCCAACTCC-GATTTTATTTTCAAAACACT-AATTTT-CTATAATCAG
*
1821067 GGATACTCCAACTCCGATTTTATTTCC-AAAAATACCAATTT-TTCACAATCGAGGATACTCCAA
63 GGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAA
*
1821130 CCTCGTTATTTCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTT
128 CCTCGTTA-ATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTT
1821195 TATTCCTAAAA
192 TATTCCTAAAA
1821206 TATTGATTTC
Statistics
Matches: 181, Mismatches: 17, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
211 30 0.17
212 117 0.65
213 34 0.19
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.32
Consensus pattern (212 bp):
TCCACAATCAGGGATACTCCAACTCCGATTTTATTTTCAAAACACTAATTTTCTATAATCAGGGA
TACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCT
CGTTAATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTATT
CCTAAAACACTAGTTTT
Found at i:1821257 original size:107 final size:108
Alignment explanation
Indices: 1820853--1821269 Score: 273
Period size: 107 Copynumber: 3.9 Consensus size: 108
1820843 TCTATAATCA
* * * * * **
1820853 GGGATACTCTAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGGGGATACTCTG
1 GGGATACTCCAACCCCGACTTTATTTCC-AAAAATACCAATTTC-TCACAATCGAGGATACTCCA
* * * * *
1820918 ACCTCGTTAATCATCGGGGATACTCCAA-CCCCGTTATTTCTGAG
64 ACCCCGTTATTTATCGGGGATACTCCAATCCCCGTTACTTCCGAG
** * * * * * *
1820962 GGGATACTCCAACCCCGGTTTTA-TTGCTAAAACACTAGTTTTTCCACAATC-AGGGATACTCCA
1 GGGATACTCCAACCCCGACTTTATTTCCAAAAATACCAATTTCT-CACAATCGA-GGATACTCCA
* * ***** * ** * *
1821025 ACCCTGGT-TTTATTTTCAAAACGT-CAATTTTCCTTTA-AT-C--G
64 ACCCCGTTATTTATCGGGGATAC-TCCAA-TCCCCGTTACTTCCGAG
* * *
1821066 GGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATCGAGGATACTCCAAC
1 GGGATACTCCAACCCCGACTTTATTTCCAAAAATACCAATTTCTCACAATCGAGGATACTCCAAC
*
1821131 CTCGTTATTTCATCGGGGATACTCCAA-CCCCGTTACTTCCGAG
66 CCCGTTATTT-ATCGGGGATACTCCAATCCCCGTTACTTCCGAG
* * *** * * *
1821174 GGGATACTCCAACCCCGGCTTTA-TTCCTAAAATATTGATTTCTCATAATTGGGGATACTCCAAC
1 GGGATACTCCAACCCCGACTTTATTTCCAAAAATACCAATTTCTCACAATCGAGGATACTCCAAC
1821238 CCCGTTATTT-TCGAAGGGATACTCCAATCCCC
66 CCCGTTATTTATCG--GGGATACTCCAATCCCC
1821270 ATTTTTTTTT
Statistics
Matches: 232, Mismatches: 59, Indels: 35
0.71 0.18 0.11
Matches are distributed among these distances:
104 49 0.21
105 24 0.10
106 19 0.08
107 87 0.38
108 33 0.14
109 20 0.09
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.31
Consensus pattern (108 bp):
GGGATACTCCAACCCCGACTTTATTTCCAAAAATACCAATTTCTCACAATCGAGGATACTCCAAC
CCCGTTATTTATCGGGGATACTCCAATCCCCGTTACTTCCGAG
Found at i:1821293 original size:79 final size:78
Alignment explanation
Indices: 1821144--1821346 Score: 212
Period size: 79 Copynumber: 2.6 Consensus size: 78
1821134 GTTATTTCAT
* * * *
1821144 CGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTATTCCTAAAATAT
1 CGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCAGCTTTATTCCT-AAATAT
* * *
1821209 TGATTTCTCATAAT
65 CGATTTCTCACAAC
* ** * *
1821223 TGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAATCCCCATTTTTTTTTCT-AATCA
1 CGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAA-CCCCAGCTTTATTCCTAAAT-A
1821287 TCGATTTCTCACAAC
64 TCGATTTCTCACAAC
* ** *
1821302 CGGGGATACTCCAGCCCTATTATTTTC-AAGGGAACACTCCAACCC
1 CGGGGATACTCCAACCCCGTTATTTTCGAAGGG-ATACTCCAACCC
1821347 TGTTATTATC
Statistics
Matches: 104, Mismatches: 17, Indels: 7
0.81 0.13 0.05
Matches are distributed among these distances:
78 11 0.11
79 82 0.79
80 11 0.11
ACGTcount: A:0.25, C:0.30, G:0.15, T:0.30
Consensus pattern (78 bp):
CGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCAGCTTTATTCCTAAATATC
GATTTCTCACAAC
Found at i:1824158 original size:21 final size:21
Alignment explanation
Indices: 1824134--1824178 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1824124 TTAAAAGTTA
1824134 CATT-TTTTCATCCAAAAAATG
1 CATTCTTTT-ATCCAAAAAATG
**
1824155 CATTCTTTTATCCAATCAATG
1 CATTCTTTTATCCAAAAAATG
1824176 CAT
1 CAT
1824179 CATTTCAACC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.33, C:0.22, G:0.04, T:0.40
Consensus pattern (21 bp):
CATTCTTTTATCCAAAAAATG
Found at i:1824439 original size:3 final size:3
Alignment explanation
Indices: 1824431--1824492 Score: 108
Period size: 3 Copynumber: 21.0 Consensus size: 3
1824421 GGATTAACAC
1824431 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
1824479 ATA A-A AAA ATA ATA
1 ATA ATA ATA ATA ATA
1824493 TTAGACACAA
Statistics
Matches: 57, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
2 2 0.04
3 55 0.96
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:1825074 original size:2 final size:2
Alignment explanation
Indices: 1825069--1825105 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1825059 TACATAACAA
1825069 AT 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 AT A
1825106 CACACACACA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1825346 original size:15 final size:14
Alignment explanation
Indices: 1825310--1825357 Score: 62
Period size: 14 Copynumber: 3.4 Consensus size: 14
1825300 TAATTTTTCT
1825310 AATTTATTTTTT-A
1 AATTTATTTTTTAA
*
1825323 AATATATTTTTTAA
1 AATTTATTTTTTAA
*
1825337 AATTTAATTTTTAA
1 AATTTATTTTTTAA
1825351 TAATTTA
1 -AATTTA
1825358 ATAATTTAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
13 11 0.37
14 13 0.43
15 6 0.20
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
AATTTATTTTTTAA
Found at i:1825347 original size:14 final size:14
Alignment explanation
Indices: 1825299--1825359 Score: 61
Period size: 14 Copynumber: 4.4 Consensus size: 14
1825289 TCATTTCATA
**
1825299 TTAATTTTTCTAAT
1 TTAATTTTTAAAAT
*
1825313 TT-ATTTTTTAAAT
1 TTAATTTTTAAAAT
* *
1825326 ATATTTTTTAAAAT
1 TTAATTTTTAAAAT
1825340 TTAATTTTTAATAAT
1 TTAATTTTTAA-AAT
1825355 TTAAT
1 TTAAT
1825360 AATTTAATAA
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
13 10 0.26
14 20 0.53
15 8 0.21
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (14 bp):
TTAATTTTTAAAAT
Found at i:1825359 original size:8 final size:8
Alignment explanation
Indices: 1825332--1825372 Score: 59
Period size: 8 Copynumber: 5.4 Consensus size: 8
1825322 AAATATATTT
1825332 TTTAA-AA
1 TTTAATAA
*
1825339 TTTAAT-T
1 TTTAATAA
1825346 TTTAATAA
1 TTTAATAA
1825354 TTTAATAA
1 TTTAATAA
1825362 TTTAATAA
1 TTTAATAA
1825370 TTT
1 TTT
1825373 TCTTTTATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
7 11 0.37
8 19 0.63
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (8 bp):
TTTAATAA
Found at i:1825846 original size:22 final size:21
Alignment explanation
Indices: 1825808--1825849 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
1825798 AAATTTTATT
1825808 TAAATTTAATTATAAAATATA
1 TAAATTTAATTATAAAATATA
1825829 TAAATATTAA-TATAAAA-ATA
1 TAAAT-TTAATTATAAAATATA
1825849 T
1 T
1825850 TTTTTTAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 4 0.20
21 12 0.60
22 4 0.20
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAATTTAATTATAAAATATA
Found at i:1825901 original size:90 final size:89
Alignment explanation
Indices: 1825795--1825962 Score: 293
Period size: 90 Copynumber: 1.9 Consensus size: 89
1825785 ATTCTTCAAA
1825795 TAAAAATTTTATTTAAATTTAATTATAAAATATATAAATATTAATATAAAAAT-ATTTTTTTAAT
1 TAAAAATTTTATTTAAATTTAATTATAAAATATATAAATATTAATATAAAAATAATTTTTTT-AT
*
1825859 ATTTTAAACTTTTAAAAGAGACTTG
65 AGTTTAAACTTTTAAAAGAGACTTG
*
1825884 TAAAAATTTTTATTTAAATTTTATTATAAAATATATAAATATTAATATAAAAATAATTTTTTTAT
1 TAAAAA-TTTTATTTAAATTTAATTATAAAATATATAAATATTAATATAAAAATAATTTTTTTAT
1825949 AGTTTAAACTTTTA
65 AGTTTAAACTTTTA
1825963 GGATTGGCTT
Statistics
Matches: 75, Mismatches: 2, Indels: 3
0.94 0.03 0.04
Matches are distributed among these distances:
89 6 0.08
90 61 0.81
91 8 0.11
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (89 bp):
TAAAAATTTTATTTAAATTTAATTATAAAATATATAAATATTAATATAAAAATAATTTTTTTATA
GTTTAAACTTTTAAAAGAGACTTG
Found at i:1827592 original size:23 final size:23
Alignment explanation
Indices: 1827566--1827614 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
1827556 GGAGATAAAA
1827566 TTTATTTATATTGTAATAAGACT
1 TTTATTTATATTGTAATAAGACT
1827589 TTTATTTATATTGTAATAAGACT
1 TTTATTTATATTGTAATAAGACT
1827612 TTT
1 TTT
1827615 TTTTTTAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.33, C:0.04, G:0.08, T:0.55
Consensus pattern (23 bp):
TTTATTTATATTGTAATAAGACT
Found at i:1829983 original size:2 final size:2
Alignment explanation
Indices: 1829974--1830144 Score: 99
Period size: 2 Copynumber: 93.5 Consensus size: 2
1829964 AATAAATAAA
* *
1829974 AT AT -T AT AT AT GAT AT AT AT -T AT GT AT AT AT -T AT AT -T GT
1 AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1830013 AT AT AT AT ACT AT AT AT AT -T AT -T AT AT -T AT -T AT AT AT AT
1 AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * *
1830052 AG CT GT TT AT AT AT AT TT AT AT -T A- AT AT A- 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
* * * *
1830091 A- AA AT AT AT A- AC AT A- AT AT AT A- AC AC AT A- AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1830127 AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT A
1830145 AAAGAAAAAA
Statistics
Matches: 135, Mismatches: 14, Indels: 40
0.71 0.07 0.21
Matches are distributed among these distances:
1 18 0.13
2 113 0.84
3 4 0.03
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1830016 original size:27 final size:28
Alignment explanation
Indices: 1829974--1830091 Score: 93
Period size: 29 Copynumber: 4.1 Consensus size: 28
1829964 AATAAATAAA
*
1829974 ATATTATATATG-ATATATAT-TATGTAT
1 ATATTATAT-TGTATATATATATATATAT
1830001 ATATTATATTGTATATATATACTATATAT
1 ATATTATATTGTATATATATA-TATATAT
* * *
1830030 ATTATTATATTAT-TATATATATAGCTGTTT
1 A-TATTATATTGTATATATATATA--TATAT
1830060 ATA-TATATT-TATATTAATATAATATATAT
1 ATATTATATTGTATA-T-ATAT-ATATATAT
1830089 ATA
1 ATA
1830092 AAATATATAA
Statistics
Matches: 75, Mismatches: 6, Indels: 18
0.76 0.06 0.18
Matches are distributed among these distances:
26 2 0.03
27 18 0.24
28 10 0.13
29 24 0.32
30 18 0.24
31 3 0.04
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.53
Consensus pattern (28 bp):
ATATTATATTGTATATATATATATATAT
Found at i:1830047 original size:45 final size:43
Alignment explanation
Indices: 1829974--1830091 Score: 116
Period size: 42 Copynumber: 2.7 Consensus size: 43
1829964 AATAAATAAA
* * *
1829974 ATAT-TATATATGATATATATTATGTATATATTATA-TTGTATATAT
1 ATATATATATATTAT-TATATTATATATATA-TATAGCTGT-T-TAT
1830019 ATACTATATATATTATTATATTAT-TATATATATAGCTGTTTAT
1 ATA-TATATATATTATTATATTATATATATATATAGCTGTTTAT
* * *
1830062 ATATATTTATATTAATATAATATATATATA
1 ATATATATATATTATTATATTATATATATA
1830092 AAATATATAA
Statistics
Matches: 64, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
42 17 0.27
43 12 0.19
44 5 0.08
45 12 0.19
46 9 0.14
47 9 0.14
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.53
Consensus pattern (43 bp):
ATATATATATATTATTATATTATATATATATATAGCTGTTTAT
Found at i:1830145 original size:25 final size:24
Alignment explanation
Indices: 1829974--1830145 Score: 103
Period size: 25 Copynumber: 7.4 Consensus size: 24
1829964 AATAAATAAA
*
1829974 ATAT-TAT-ATATGATATATATTAT
1 ATATATATAATATAATATATA-TAT
* * **
1829997 GTATATATTATATTGTATATATAT
1 ATATATATAATATAATATATATAT
* *
1830021 ACTATATATATTATTATAT-TAT-T
1 A-TATATATAATATAATATATATAT
* * *
1830044 ATATATATAGCTGT-TTATATATAT
1 ATATATATA-ATATAATATATATAT
*
1830068 TTATAT-TAATATAATATATATAT
1 ATATATATAATATAATATATATAT
* * *
1830091 AAAATATATAACATAATATATA-AC
1 -ATATATATAATATAATATATATAT
*
1830115 ACATA-ATAATAT-ATATATATAT
1 ATATATATAATATAATATATATAT
1830137 ATA-ATATAA
1 ATATATATAA
1830146 AAGAAAAAAA
Statistics
Matches: 116, Mismatches: 22, Indels: 23
0.72 0.14 0.14
Matches are distributed among these distances:
21 8 0.07
22 26 0.22
23 25 0.22
24 20 0.17
25 37 0.32
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (24 bp):
ATATATATAATATAATATATATAT
Found at i:1832532 original size:2 final size:2
Alignment explanation
Indices: 1832525--1832559 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1832515 TAGAAACACT
1832525 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1832560 TTTCCTGAGG
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:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1836805 original size:10 final size:10
Alignment explanation
Indices: 1836790--1836819 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
1836780 TATTCTTCAC
1836790 ACACGACACA
1 ACACGACACA
*
1836800 ACACGACACG
1 ACACGACACA
1836810 ACACGACACA
1 ACACGACACA
1836820 GATGTGTGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.47, C:0.40, G:0.13, T:0.00
Consensus pattern (10 bp):
ACACGACACA
Found at i:1838018 original size:21 final size:21
Alignment explanation
Indices: 1837993--1838054 Score: 63
Period size: 24 Copynumber: 2.8 Consensus size: 21
1837983 CAAATTACTA
1837993 TTTATATAATAAAATAATATT
1 TTTATATAATAAAATAATATT
* *
1838014 TTTATTTAAAATAAAAATATTATT
1 TTTA--TATAAT-AAAATAATATT
1838038 TTT-TAATAATAAAATAA
1 TTTAT-ATAATAAAATAA
1838055 ACTTTCTAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
21 11 0.33
22 4 0.12
23 5 0.15
24 13 0.39
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
TTTATATAATAAAATAATATT
Found at i:1839222 original size:5 final size:5
Alignment explanation
Indices: 1839212--1839245 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
1839202 AACAAATGAT
* *
1839212 AAAGA AAAGA AAGGA AAAGA AAAGA AAGGA AAAG
1 AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAG
1839246 GCTAATAGCA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (5 bp):
AAAGA
Found at i:1839232 original size:15 final size:15
Alignment explanation
Indices: 1839212--1839245 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
1839202 AACAAATGAT
1839212 AAAGAAAAGAAAGGA
1 AAAGAAAAGAAAGGA
1839227 AAAGAAAAGAAAGGA
1 AAAGAAAAGAAAGGA
1839242 AAAG
1 AAAG
1839246 GCTAATAGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (15 bp):
AAAGAAAAGAAAGGA
Found at i:1839940 original size:2 final size:2
Alignment explanation
Indices: 1839933--1839993 Score: 70
Period size: 2 Copynumber: 31.0 Consensus size: 2
1839923 AAACATTAAA
* * * * *
1839933 AT AT AT AT AT AG AT AC CT AC AT AC AT A- 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
1839974 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
1839994 CAATCACATA
Statistics
Matches: 48, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
1 1 0.02
2 47 0.98
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.43
Consensus pattern (2 bp):
AT
Found at i:1845711 original size:29 final size:29
Alignment explanation
Indices: 1845669--1845727 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
1845659 GAGTTAAAGA
1845669 AAGACTAGAATCTGGTACACATACATTCC
1 AAGACTAGAATCTGGTACACATACATTCC
1845698 AAGACTAGAATCTGGTACACATACATTCC
1 AAGACTAGAATCTGGTACACATACATTCC
1845727 A
1 A
1845728 GGTGCTCTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.39, C:0.24, G:0.14, T:0.24
Consensus pattern (29 bp):
AAGACTAGAATCTGGTACACATACATTCC
Found at i:1847073 original size:24 final size:24
Alignment explanation
Indices: 1847027--1847073 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
1847017 CGCAGGGGGA
*
1847027 GGAGGTGCTTGAGTCGGTAGAGGT
1 GGAGGTGCTTGAATCGGTAGAGGT
* * *
1847051 GGAGGTGGTTGAATTGGTGGAGG
1 GGAGGTGCTTGAATCGGTAGAGG
1847074 CGGTGGAGGT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.17, C:0.04, G:0.53, T:0.26
Consensus pattern (24 bp):
GGAGGTGCTTGAATCGGTAGAGGT
Found at i:1854147 original size:27 final size:27
Alignment explanation
Indices: 1854094--1854216 Score: 110
Period size: 27 Copynumber: 4.7 Consensus size: 27
1854084 TGTACAGCTA
* *
1854094 TGTGTGCAGCTAGGTGCTGT---GAGT
1 TGTGTACAGCTATGTGCTGTAAGGAGT
*
1854118 TGTGTACAACTATGTGCTGTAAGGAGT
1 TGTGTACAGCTATGTGCTGTAAGGAGT
** **
1854145 TGTGTACAGCTATGTG-TACAACTAGGT
1 TGTGTACAGCTATGTGCTGTAAGGA-GT
* *
1854172 TGTGTATAGCTATGTGCTGTGAGGAGT
1 TGTGTACAGCTATGTGCTGTAAGGAGT
* *
1854199 TGTGTGCAGCTAGGTGCT
1 TGTGTACAGCTATGTGCT
1854217 ATTCTAGAAA
Statistics
Matches: 77, Mismatches: 17, Indels: 7
0.76 0.17 0.07
Matches are distributed among these distances:
24 17 0.22
26 4 0.05
27 53 0.69
28 3 0.04
ACGTcount: A:0.20, C:0.12, G:0.34, T:0.34
Consensus pattern (27 bp):
TGTGTACAGCTATGTGCTGTAAGGAGT
Found at i:1854479 original size:68 final size:68
Alignment explanation
Indices: 1854365--1854499 Score: 218
Period size: 68 Copynumber: 2.0 Consensus size: 68
1854355 ATTAGTTCTT
* * *
1854365 TTCTTTTTTTTTGGCCTTAATTGTCAAATGTTTGGTGAAGTTTCTTGGCCTTTATTGCCATCACC
1 TTCTGTTTTTCTGGCCTTAATTGTCAAATATTTGGTGAAGTTTCTTGGCCTTTATTGCCATCACC
1854430 ATA
66 ATA
*
1854433 TTCTGTTTTTCTGGCCTTAATTG-CTAGATATTTGGTGAAGTTTCTTGGCCTTTATTGCCATCAC
1 TTCTGTTTTTCTGGCCTTAATTGTC-AAATATTTGGTGAAGTTTCTTGGCCTTTATTGCCATCAC
1854497 CAT
65 CAT
1854500 TTTTCTGTCT
Statistics
Matches: 62, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
67 1 0.02
68 61 0.98
ACGTcount: A:0.17, C:0.19, G:0.17, T:0.47
Consensus pattern (68 bp):
TTCTGTTTTTCTGGCCTTAATTGTCAAATATTTGGTGAAGTTTCTTGGCCTTTATTGCCATCACC
ATA
Found at i:1859065 original size:24 final size:25
Alignment explanation
Indices: 1859038--1859100 Score: 74
Period size: 24 Copynumber: 2.5 Consensus size: 25
1859028 TGTACAGCTA
*
1859038 TGTGTGCAGCTAGGTGCTGT-GAGT
1 TGTGTACAGCTAGGTGCTGTAGAGT
* *
1859062 TGTGTACAACTATGTGCTGTAAGGAGT
1 TGTGTACAGCTAGGTGCTGT-A-GAGT
1859089 TGTGTACAGCTA
1 TGTGTACAGCTA
1859101 TATGTACAGC
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
24 17 0.53
27 15 0.47
ACGTcount: A:0.21, C:0.13, G:0.33, T:0.33
Consensus pattern (25 bp):
TGTGTACAGCTAGGTGCTGTAGAGT
Found at i:1859066 original size:36 final size:36
Alignment explanation
Indices: 1859025--1859151 Score: 119
Period size: 36 Copynumber: 3.8 Consensus size: 36
1859015 GTGTGAGGAA
* *
1859025 TTGTGTACAGCTATGTGTGCAGCTAGGTGCTGTGAG
1 TTGTGTACAGCTATGTGTACAGCTAGGTGATGTGAG
* *
1859061 TTGTGTACAACTA--TGT---GCT--GT-AAG-GAG
1 TTGTGTACAGCTATGTGTACAGCTAGGTGATGTGAG
* *
1859088 TTGTGTACAGCTATATGTACAGCTAGGTGGTGTGAG
1 TTGTGTACAGCTATGTGTACAGCTAGGTGATGTGAG
* *
1859124 TTGTGTACAGCTAGGTGTACAACTAGGT
1 TTGTGTACAGCTATGTGTACAGCTAGGT
1859152 TGTGTATAGC
Statistics
Matches: 73, Mismatches: 9, Indels: 18
0.73 0.09 0.18
Matches are distributed among these distances:
27 15 0.21
28 1 0.01
29 5 0.07
31 3 0.04
32 3 0.04
34 5 0.07
35 1 0.01
36 40 0.55
ACGTcount: A:0.22, C:0.13, G:0.32, T:0.33
Consensus pattern (36 bp):
TTGTGTACAGCTATGTGTACAGCTAGGTGATGTGAG
Found at i:1859154 original size:63 final size:63
Alignment explanation
Indices: 1859025--1859164 Score: 174
Period size: 63 Copynumber: 2.2 Consensus size: 63
1859015 GTGTGAGGAA
* * * ** *
1859025 TTGTGTACAGCTATGTGTGCAGCTAGGTGCTGTGAGTTGTGTACAACTATGTGCTGTAAGGAG
1 TTGTGTACAGCTATATGTACAGCTAGGTGCTGTGAGTTGTGTACAACTAGGTGCTACAACGAG
* * *
1859088 TTGTGTACAGCTATATGTACAGCTAGGTGGTGTGAGTTGTGTACAGCTAGGTG-TACAACTAGG
1 TTGTGTACAGCTATATGTACAGCTAGGTGCTGTGAGTTGTGTACAACTAGGTGCTACAACGA-G
*
1859151 TTGTGTATAGCTAT
1 TTGTGTACAGCTAT
1859165 GTGCTGTGAG
Statistics
Matches: 66, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
62 4 0.06
63 62 0.94
ACGTcount: A:0.22, C:0.12, G:0.31, T:0.34
Consensus pattern (63 bp):
TTGTGTACAGCTATATGTACAGCTAGGTGCTGTGAGTTGTGTACAACTAGGTGCTACAACGAG
Found at i:1861920 original size:32 final size:32
Alignment explanation
Indices: 1861832--1861922 Score: 80
Period size: 32 Copynumber: 2.9 Consensus size: 32
1861822 TTTAATTTAT
* * *
1861832 ATTAATTATATATTTAATG-A-ATTAGATAA-A
1 ATTATTTATAAATTTAATGAACATTA-AAAATA
* * *
1861862 ATTATTTATAAATTTGATTAATATTAAAAATA
1 ATTATTTATAAATTTAATGAACATTAAAAATA
* *
1861894 ATTATTTTTAAATTTAATGACCATTAAAA
1 ATTATTTATAAATTTAATGAACATTAAAA
1861923 TGTTTCAATC
Statistics
Matches: 48, Mismatches: 10, Indels: 4
0.77 0.16 0.06
Matches are distributed among these distances:
30 15 0.31
31 4 0.08
32 29 0.60
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.45
Consensus pattern (32 bp):
ATTATTTATAAATTTAATGAACATTAAAAATA
Found at i:1862085 original size:16 final size:18
Alignment explanation
Indices: 1862061--1862098 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 18
1862051 AAATATTTTT
1862061 ATATATAAAA-TTAA-AA
1 ATATATAAAATTTAATAA
*
1862077 ATATTTAAAATTTAATAA
1 ATATATAAAATTTAATAA
1862095 ATAT
1 ATAT
1862099 GAAATGACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 9 0.47
17 4 0.21
18 6 0.32
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
ATATATAAAATTTAATAA
Found at i:1862591 original size:16 final size:17
Alignment explanation
Indices: 1862570--1862608 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
1862560 TTAAACATAT
1862570 TTTTTAAAAATTTAA-A
1 TTTTTAAAAATTTAATA
**
1862586 TTTTTATTAATTTAATA
1 TTTTTAAAAATTTAATA
1862603 TTTTTA
1 TTTTTA
1862609 TTAGGTTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 13 0.65
17 7 0.35
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTTTAAAAATTTAATA
Found at i:1862605 original size:17 final size:16
Alignment explanation
Indices: 1862578--1862611 Score: 59
Period size: 17 Copynumber: 2.1 Consensus size: 16
1862568 ATTTTTTAAA
1862578 AATTTAAATTTTTATT
1 AATTTAAATTTTTATT
1862594 AATTTAATATTTTTATT
1 AATTTAA-ATTTTTATT
1862611 A
1 A
1862612 GGTTTAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
AATTTAAATTTTTATT
Found at i:1862679 original size:30 final size:30
Alignment explanation
Indices: 1862643--1862700 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
1862633 TATTTTTAGA
* *
1862643 TTTATATTAT-AATATTATATAGATATATTC
1 TTTATATGATAAAAATTATATA-ATATATTC
1862673 TTTATATGATAAAAATTATATAATATAT
1 TTTATATGATAAAAATTATATAATATAT
1862701 AAAATTAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 15 0.60
31 10 0.40
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.50
Consensus pattern (30 bp):
TTTATATGATAAAAATTATATAATATATTC
Found at i:1862704 original size:18 final size:20
Alignment explanation
Indices: 1862675--1862722 Score: 57
Period size: 18 Copynumber: 2.5 Consensus size: 20
1862665 ATATATTCTT
1862675 TATATGATAAAAATT-ATATA
1 TATAT-ATAAAAATTAATATA
1862695 -ATATAT-AAAATTAATATA
1 TATATATAAAAATTAATATA
1862713 TATTATATAA
1 TA-TATATAA
1862723 TTATAAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
17 6 0.25
18 7 0.29
19 5 0.21
20 5 0.21
21 1 0.04
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (20 bp):
TATATATAAAAATTAATATA
Found at i:1863073 original size:17 final size:17
Alignment explanation
Indices: 1863026--1863080 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 17
1863016 TAAAGATGTA
*
1863026 AATATTTTTATTGAATA
1 AATATTTTTATTGAATT
* * *
1863043 AAGA-ATTAATTGAATT
1 AATATTTTTATTGAATT
1863059 AATATTTTTATTGAATT
1 AATATTTTTATTGAATT
*
1863076 GATAT
1 AATAT
1863081 CTGATTTATA
Statistics
Matches: 29, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
16 12 0.41
17 17 0.59
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.49
Consensus pattern (17 bp):
AATATTTTTATTGAATT
Found at i:1864308 original size:6 final size:6
Alignment explanation
Indices: 1864299--1864323 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1864289 TTTTTCTCCA
1864299 TTTTTC TTTTTC TTTTTC TTTTTC T
1 TTTTTC TTTTTC TTTTTC TTTTTC T
1864324 GGCTGGTAGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTTC
Found at i:1864407 original size:12 final size:12
Alignment explanation
Indices: 1864390--1864430 Score: 73
Period size: 12 Copynumber: 3.4 Consensus size: 12
1864380 CTCCTCCCCT
*
1864390 TTATTCTTCTAG
1 TTATTCCTCTAG
1864402 TTATTCCTCTAG
1 TTATTCCTCTAG
1864414 TTATTCCTCTAG
1 TTATTCCTCTAG
1864426 TTATT
1 TTATT
1864431 GATGTCTCTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.17, C:0.20, G:0.07, T:0.56
Consensus pattern (12 bp):
TTATTCCTCTAG
Found at i:1870256 original size:22 final size:20
Alignment explanation
Indices: 1870207--1870262 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 20
1870197 AAAAACCCAG
*
1870207 AATGTATCGACACAATAAGA
1 AATGTATCGATACAATAAGA
1870227 AATGTATCGATACAATTATA-A
1 AATGTATCGATACAA-TA-AGA
1870248 ACATGTATCGATACA
1 A-ATGTATCGATACA
1870263 TTTCCTTGGC
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 14 0.44
21 4 0.12
22 14 0.44
ACGTcount: A:0.46, C:0.14, G:0.12, T:0.27
Consensus pattern (20 bp):
AATGTATCGATACAATAAGA
Found at i:1871428 original size:52 final size:51
Alignment explanation
Indices: 1871306--1871458 Score: 175
Period size: 52 Copynumber: 3.0 Consensus size: 51
1871296 AGATGACAAG
* * * * *
1871306 AATGATAAAGGTGCCAATATGCTAATTCACGA-CAGCGATATTGGGCTTAAG
1 AATGA-AAAAGTGCCAATATGCTGATTCAAGACCAGCGATATTGGACTTAAA
*
1871357 AAT-AATAAAGATGCCAATATGCTGATTCAAGACCAGCGATATTGAACTTAAA
1 AATGAA-AAAG-TGCCAATATGCTGATTCAAGACCAGCGATATTGGACTTAAA
* * *
1871409 AATGACAAAAGTGCTAATATGTTGATTCAAGGCCAGCGATATTGGACTTA
1 AATGA-AAAAGTGCCAATATGCTGATTCAAGACCAGCGATATTGGACTTA
1871459 GAGATGGTAA
Statistics
Matches: 87, Mismatches: 10, Indels: 9
0.82 0.09 0.08
Matches are distributed among these distances:
49 1 0.01
50 4 0.05
51 22 0.25
52 54 0.62
53 5 0.06
54 1 0.01
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.26
Consensus pattern (51 bp):
AATGAAAAAGTGCCAATATGCTGATTCAAGACCAGCGATATTGGACTTAAA
Found at i:1871487 original size:52 final size:52
Alignment explanation
Indices: 1871372--1871551 Score: 153
Period size: 52 Copynumber: 3.5 Consensus size: 52
1871362 TAAAGATGCC
* **
1871372 AATATGCTGATTCAAGACCAGCGATATTGAACTTAAAAATGACAAAAGTGCT
1 AATATGCTGATTCAAGGCCAGCGATATTGAACTTAAAAATGACAAAAGTAAT
* * * * ** *
1871424 AATATGTTGATTCAAGGCCAGCGATATTGGACTTAGAGATGGTAAAGGTAAT
1 AATATGCTGATTCAAGGCCAGCGATATTGAACTTAAAAATGACAAAAGTAAT
* * * * * * * * * *
1871476 AATGTGCTGATTCAAGGCCAACAACATCGGACTTGAAGATGAAAAAAGTGAT
1 AATATGCTGATTCAAGGCCAGCGATATTGAACTTAAAAATGACAAAAGTAAT
* * *
1871528 AATATGCTAATTTAGGGCCAGCGA
1 AATATGCTGATTCAAGGCCAGCGA
1871552 CATTAGACTT
Statistics
Matches: 100, Mismatches: 28, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
52 100 1.00
ACGTcount: A:0.38, C:0.14, G:0.23, T:0.25
Consensus pattern (52 bp):
AATATGCTGATTCAAGGCCAGCGATATTGAACTTAAAAATGACAAAAGTAAT
Found at i:1871854 original size:32 final size:32
Alignment explanation
Indices: 1871699--1871855 Score: 131
Period size: 32 Copynumber: 4.8 Consensus size: 32
1871689 GCTACCAATG
*
1871699 TGTGTGGGCTTTTGAG-AAGGTTGCCATCAACT
1 TGTGTGGGC-TTTGAGAAAGGTTGCCACCAACT
* * * * **
1871731 TGTATAGGCTTTGA-AGAAGATTGTCACCGGCT
1 TGTGTGGGCTTTGAGA-AAGGTTGCCACCAACT
* * * *
1871763 TTTGTGAGCTTTAGAGAAAGGTTGCTATCGAA-T
1 TGTGTGGGCTTT-GAGAAAGGTTGCCA-CCAACT
*
1871796 TGTGTGGGCTTTTGAGAAAGGATGCCACCAACT
1 TGTGTGGGC-TTTGAGAAAGGTTGCCACCAACT
*
1871829 TGTGTGGGCTGTGAGAAAGGTTGCCAC
1 TGTGTGGGCTTTGAGAAAGGTTGCCAC
1871856 TGACTTGTTA
Statistics
Matches: 94, Mismatches: 24, Indels: 14
0.71 0.18 0.11
Matches are distributed among these distances:
31 5 0.05
32 45 0.48
33 39 0.41
34 5 0.05
ACGTcount: A:0.23, C:0.15, G:0.31, T:0.31
Consensus pattern (32 bp):
TGTGTGGGCTTTGAGAAAGGTTGCCACCAACT
Found at i:1872063 original size:16 final size:16
Alignment explanation
Indices: 1872034--1872085 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
1872024 AAGGTTATAT
1872034 TTATTCATTTTATTTTGA
1 TTATT-ATTTTATTTT-A
*
1872052 TTATTA-TTTATTTAA
1 TTATTATTTTATTTTA
*
1872067 TTTTTATTTTATTTTA
1 TTATTATTTTATTTTA
1872083 TTA
1 TTA
1872086 AAAATCATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 6 0.21
16 17 0.59
17 1 0.03
18 5 0.17
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.71
Consensus pattern (16 bp):
TTATTATTTTATTTTA
Found at i:1872084 original size:21 final size:21
Alignment explanation
Indices: 1872034--1872080 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
1872024 AAGGTTATAT
* *
1872034 TTATTCATTTTATTTTGATTA
1 TTATTTATTTAATTTTGATTA
*
1872055 TTATTTATTTAATTTTTATT-
1 TTATTTATTTAATTTTGATTA
1872075 TTATTT
1 TTATTT
1872081 TATTAAAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 6 0.26
21 17 0.74
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.72
Consensus pattern (21 bp):
TTATTTATTTAATTTTGATTA
Found at i:1873296 original size:10 final size:11
Alignment explanation
Indices: 1873276--1873300 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1873266 TTTGGCTTAA
1873276 TTTTTCTTTTT
1 TTTTTCTTTTT
1873287 TTTTTCTTTTT
1 TTTTTCTTTTT
1873298 TTT
1 TTT
1873301 GGAAGCTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTTCTTTTT
Found at i:1873871 original size:21 final size:21
Alignment explanation
Indices: 1873825--1873865 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1873815 CTGATGTAAT
1873825 ATGAATTTAATAAAATATTTG
1 ATGAATTTAATAAAATATTTG
*
1873846 ATGAATTTTA-AAAAT-TTTG
1 ATGAATTTAATAAAATATTTG
1873865 A
1 A
1873866 ATTGAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 5 0.26
20 5 0.26
21 9 0.47
ACGTcount: A:0.46, C:0.00, G:0.10, T:0.44
Consensus pattern (21 bp):
ATGAATTTAATAAAATATTTG
Found at i:1875304 original size:44 final size:45
Alignment explanation
Indices: 1875240--1875428 Score: 183
Period size: 44 Copynumber: 4.3 Consensus size: 45
1875230 AAATGTAATA
* * * *
1875240 AGTTCGACCAAGGCT-GAACCATCACGTCGAACGAAGATGAAAAA
1 AGTTTGACCAGGGCTAGAACCATCACGTCAAACGAAGATGAAAAG
* **
1875284 AGTTTGACCAGGGCTA-AACCATCACGTCAAA-TAAGAATGAATGG
1 AGTTTGACCAGGGCTAGAACCATCACGTCAAACGAAG-ATGAAAAG
* * *
1875328 AGTTTGACCA-AGCTAGAACCATCACATCAAATGATAG-TGAAAAG
1 AGTTTGACCAGGGCTAGAACCATCACGTCAAACGA-AGATGAAAAG
* * * *
1875372 GGTTCGACCAGGG-TAAGAACCATCACGTCAAACCAAAATGAAAAG
1 AGTTTGACCAGGGCT-AGAACCATCACGTCAAACGAAGATGAAAAG
1875417 AGTTTGACCAGG
1 AGTTTGACCAGG
1875429 TATAGTTAAA
Statistics
Matches: 116, Mismatches: 21, Indels: 15
0.76 0.14 0.10
Matches are distributed among these distances:
43 7 0.06
44 71 0.61
45 36 0.31
46 2 0.02
ACGTcount: A:0.40, C:0.20, G:0.22, T:0.17
Consensus pattern (45 bp):
AGTTTGACCAGGGCTAGAACCATCACGTCAAACGAAGATGAAAAG
Found at i:1875425 original size:89 final size:88
Alignment explanation
Indices: 1875240--1875426 Score: 211
Period size: 88 Copynumber: 2.1 Consensus size: 88
1875230 AAATGTAATA
* * * *
1875240 AGTTCGACCAAGGCTGAACCATCACGTCGAACGAAGATGAAAAAAGTTTGACCAGGGCTAAACCA
1 AGTTTGACCAAGGCTGAACCATCACATCAAACGAAGATGAAAAAAGTTCGACCAGGGCTAAACCA
* **
1875305 TCACGTCAAATAAGAATGAATGG
66 TCACGTCAAACAAGAATGAAAAG
* **
1875328 AGTTTGACCAA-GCTAGAACCATCACATCAAATGATAG-TGAAAAGGGTTCGACCAGGG-TAAGA
1 AGTTTGACCAAGGCT-GAACCATCACATCAAACGA-AGATGAAAAAAGTTCGACCAGGGCT-A-A
1875390 ACCATCACGTCAAACCAA-AATGAAAAG
62 ACCATCACGTCAAA-CAAGAATGAAAAG
1875417 AGTTTGACCA
1 AGTTTGACCA
1875427 GGTATAGTTA
Statistics
Matches: 84, Mismatches: 10, Indels: 9
0.82 0.10 0.09
Matches are distributed among these distances:
87 4 0.05
88 44 0.52
89 34 0.40
90 2 0.02
ACGTcount: A:0.41, C:0.20, G:0.21, T:0.18
Consensus pattern (88 bp):
AGTTTGACCAAGGCTGAACCATCACATCAAACGAAGATGAAAAAAGTTCGACCAGGGCTAAACCA
TCACGTCAAACAAGAATGAAAAG
Found at i:1875456 original size:35 final size:35
Alignment explanation
Indices: 1875408--1875484 Score: 109
Period size: 35 Copynumber: 2.2 Consensus size: 35
1875398 GTCAAACCAA
* * **
1875408 AATGAAAAGAGTTTGACCAGGTATAGTTAAATGGG
1 AATGAAAAAAGTTTGACCAGGTATAGTCAAACAGG
*
1875443 AATGAAAAAAGTTTGACTAGGTATAGTCAAACAGG
1 AATGAAAAAAGTTTGACCAGGTATAGTCAAACAGG
1875478 AATGAAA
1 AATGAAA
1875485 TGAATTTGAC
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.45, C:0.06, G:0.25, T:0.23
Consensus pattern (35 bp):
AATGAAAAAAGTTTGACCAGGTATAGTCAAACAGG
Found at i:1875493 original size:35 final size:34
Alignment explanation
Indices: 1875408--1875496 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 34
1875398 GTCAAACCAA
* * * **
1875408 AATGAAAAGAGTTTGACCAGGTATAGTTAAATGGG
1 AATG-AAAGAATTTGACTAGGTATAGTCAAACAGG
*
1875443 AATGAAAAAAGTTTGACTAGGTATAGTCAAACAGG
1 AATGAAAGAA-TTTGACTAGGTATAGTCAAACAGG
1875478 AATGAAATGAATTTGACTA
1 AATGAAA-GAATTTGACTA
1875497 TAGTCAAATA
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
34 4 0.09
35 39 0.87
36 2 0.04
ACGTcount: A:0.44, C:0.07, G:0.24, T:0.26
Consensus pattern (34 bp):
AATGAAAGAATTTGACTAGGTATAGTCAAACAGG
Found at i:1885985 original size:274 final size:274
Alignment explanation
Indices: 1885490--1886022 Score: 1021
Period size: 274 Copynumber: 1.9 Consensus size: 274
1885480 AAGGCTCAGA
1885490 CTAATTGTTCGTCTATAGGGATTTTCAATAGTAGAGCCACATGTCCGTATTTTGCTATAAACTGG
1 CTAATTGTTCGTCTATAGGGATTTTCAATAGTAGAGCCACATGTCCGTATTTTGCTATAAACTGG
*
1885555 GCTCGCTTAGCGTTACACCAACCTTCCCATATATGCACCAATTTGGACAAATTATTCTATTTGAG
66 GCTCGCTTAGCGTTACACCAACCTTCCCATATATGCACCAATTCGGACAAATTATTCTATTTGAG
1885620 GTCCAAGTTAGTGATCTTCAGTAGTCTCGGTACAAAGTCCCCCGGTATACAGTCCCCTTATTTTT
131 GTCCAAGTTAGTGATCTTCAGTAGTCTCGGTACAAAGTCCCCCGGTATACAGTCCCCTTATTTTT
1885685 TTTGATTTAATTTGAACTCCGTAACATAATAATTCCATATAATAAAACATAGCAATAAGTAAAAG
196 TTTGATTTAATTTGAACTCCGTAACATAATAATTCCATATAATAAAACATAGCAATAAGTAAAAG
1885750 AGCCACATGTCCGT
261 AGCCACATGTCCGT
* *
1885764 CTAATTGTTCGTTTATAGGGATTTTCAATAGTAGAGCCACATGTCTGTATTTTGCTATAAACTGG
1 CTAATTGTTCGTCTATAGGGATTTTCAATAGTAGAGCCACATGTCCGTATTTTGCTATAAACTGG
1885829 GCTCGCTTAGCGTTACACCAACCTTCCCATATATGCACCAATTCGGACAAATTATTCTATTTGAG
66 GCTCGCTTAGCGTTACACCAACCTTCCCATATATGCACCAATTCGGACAAATTATTCTATTTGAG
*
1885894 GTCCAAGTTAGTGATCTTTAGTAGTCTCGGTACAAAGTCCCCCGGTATACAGTCCCCTTATTTTT
131 GTCCAAGTTAGTGATCTTCAGTAGTCTCGGTACAAAGTCCCCCGGTATACAGTCCCCTTATTTTT
*
1885959 TTTGATTTAATTTGAACTCTGTAACATAATAATTCCATATAATAAAACATAGCAATAAGTAAAA
196 TTTGATTTAATTTGAACTCCGTAACATAATAATTCCATATAATAAAACATAGCAATAAGTAAAA
1886023 ATACCACAAA
Statistics
Matches: 254, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
274 254 1.00
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.34
Consensus pattern (274 bp):
CTAATTGTTCGTCTATAGGGATTTTCAATAGTAGAGCCACATGTCCGTATTTTGCTATAAACTGG
GCTCGCTTAGCGTTACACCAACCTTCCCATATATGCACCAATTCGGACAAATTATTCTATTTGAG
GTCCAAGTTAGTGATCTTCAGTAGTCTCGGTACAAAGTCCCCCGGTATACAGTCCCCTTATTTTT
TTTGATTTAATTTGAACTCCGTAACATAATAATTCCATATAATAAAACATAGCAATAAGTAAAAG
AGCCACATGTCCGT
Found at i:1889521 original size:51 final size:51
Alignment explanation
Indices: 1889408--1889525 Score: 139
Period size: 51 Copynumber: 2.3 Consensus size: 51
1889398 ATTTCCGATG
* ** *
1889408 GGATACTCCAACCCCGGTTTTATTTTTAAAACATCAATTTTCCATAATCAA
1 GGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTCCATAATCAA
* * * * *
1889459 AGATAAC-CCAACTCTGATTTTATTTCCAAAACACCAATTTTTCATAATCGA
1 GGAT-ACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTCCATAATCAA
1889510 GGATACTCCAACCCCG
1 GGATACTCCAACCCCG
1889526 TTATTTCCGA
Statistics
Matches: 53, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
50 2 0.04
51 49 0.92
52 2 0.04
ACGTcount: A:0.34, C:0.26, G:0.08, T:0.31
Consensus pattern (51 bp):
GGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTCCATAATCAA
Found at i:1889633 original size:79 final size:78
Alignment explanation
Indices: 1889497--1889834 Score: 275
Period size: 79 Copynumber: 4.3 Consensus size: 78
1889487 AAACACCAAT
* * * * * *
1889497 TTTTCATAATCGAGGATACTCCAACCCCGTTATTTCCGAGAGGACACTCTAAACCCGGTATTATT
1 TTTTCATAATCGAGGATACTCCAACCCCATTATTTTCGAGGGGATACTCCAACCCCGGTATTATT
*
1889562 TCTAAAATATTGA
66 TCTAAAACATTGA
* * * * **
1889575 TTTCTCATAATCGGGGATACTCTAACCCCATTATTTTGGCGGGGATACTCCAACCCCGGCCTTAT
1 TTT-TCATAATCGAGGATACTCCAACCCCATTATTTTCGAGGGGATACTCCAACCCCGGTATTAT
* *
1889640 TTCTAAAGCATCGA
65 TTCTAAAACATTGA
** * * * *
1889654 TTTTCCACCATCGAGTATACTCCAATCCCAGTTATTTTCGAGGGGATACTCCAACCCCGATTTTA
1 TTTT-CATAATCGAGGATACTCCAACCCCA-TTATTTTCGAGGGGATACTCCAACCCCGGTATTA
1889719 TTT-TCAAAACATTGA
64 TTTCT-AAAACATTGA
* * ** * * * * ** *
1889734 TTTTCTATAATC-AGGGATACTCTAACTCTGTTATTTCCAAGGGGATATTCCAACCTCTATTTTA
1 TTTTC-ATAATCGA-GGATACTCCAACCCCATTATTTTCGAGGGGATACTCCAACCCCGGTATTA
* * *
1889798 TTTCCAGAACATCGA
64 TTTCTAAAACATTGA
*
1889813 TTTTCTATAATCGGGGATACTC
1 TTTTC-ATAATCGAGGATACTC
1889835 TAGCCCCGTT
Statistics
Matches: 207, Mismatches: 45, Indels: 15
0.78 0.17 0.06
Matches are distributed among these distances:
78 4 0.02
79 145 0.70
80 58 0.28
ACGTcount: A:0.27, C:0.24, G:0.14, T:0.34
Consensus pattern (78 bp):
TTTTCATAATCGAGGATACTCCAACCCCATTATTTTCGAGGGGATACTCCAACCCCGGTATTATT
TCTAAAACATTGA
Found at i:1889833 original size:159 final size:157
Alignment explanation
Indices: 1889466--1889834 Score: 359
Period size: 159 Copynumber: 2.3 Consensus size: 157
1889456 CAAAGATAAC
* * *
1889466 CCAA-CTCTGATTTTATTTCCAAAACACCAATTTT-TCATAATCGAGGATACTCCAACCCCGTTA
1 CCAACCTCT-ATTTTATTTCC-AAACATCGATTTTCT-ATAATCGAGGATACTCCAACCCAGTTA
* * * *
1889529 TTTCCGAGAGGACACTCTAAACCCGGTATTATTTCTAAAATATTGATTTCTCATAATCGGGGATA
63 TTTCCGAGAGGACACTCCAAACCCGATATTATTTCTAAAACATTGATTTCTCATAATCAGGGATA
****
1889594 CTCTAACCCCATTATTTTGGCGGGGATACT
128 CTCTAACCCCATTATTTCCAAGGGGATACT
* **** * * ** *
1889624 CCAACCCCGGCCTTATTTCTAAAGCATCGATTTTCCACCATCGAGTATACTCCAATCCCAGTTAT
1 CCAACCTCTATTTTATTTCCAAA-CATCGATTTTCTATAATCGAGGATACTCCAA-CCCAGTTAT
* * * * *
1889689 TTTCGAGGGGATACTCCAACCCCGATTTTATTT-TCAAAACATTGATTT-TCTATAATCAGGGAT
64 TTCCGAGAGGACACTCCAAACCCGATATTATTTCT-AAAACATTGATTTCTC-ATAATCAGGGAT
* ** *
1889752 ACTCTAACTCTGTTATTTCCAAGGGGATATT
127 ACTCTAACCCCATTATTTCCAAGGGGATACT
*
1889783 CCAACCTCTATTTTATTTCCAGAACATCGATTTTCTATAATCGGGGATACTC
1 CCAACCTCTATTTTATTTCCA-AACATCGATTTTCTATAATCGAGGATACTC
1889835 TAGCCCCGTT
Statistics
Matches: 163, Mismatches: 41, Indels: 13
0.75 0.19 0.06
Matches are distributed among these distances:
157 3 0.02
158 38 0.23
159 120 0.74
160 2 0.01
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.34
Consensus pattern (157 bp):
CCAACCTCTATTTTATTTCCAAACATCGATTTTCTATAATCGAGGATACTCCAACCCAGTTATTT
CCGAGAGGACACTCCAAACCCGATATTATTTCTAAAACATTGATTTCTCATAATCAGGGATACTC
TAACCCCATTATTTCCAAGGGGATACT
Found at i:1889861 original size:79 final size:77
Alignment explanation
Indices: 1889703--1889861 Score: 167
Period size: 79 Copynumber: 2.0 Consensus size: 77
1889693 GAGGGGATAC
* * *
1889703 TCCAACCCCGATTTTATTTTCAAAACATTGATTTTCTATAATCAGGGATACTCTAACTCTGTTAT
1 TCCAACCCCGATTTTATTTCCAAAACATCGATTTTCTATAATCAGGGATACTCTAACCCTGTTAT
** *
1889768 TTCCAAGGGGATAT
66 CCCCAA--GAATAT
* * * * *
1889782 TCCAACCTCTATTTTATTTCCAGAACATCGATTTTCTATAATCGGGGATACTCTAGCCCCGTTGT
1 TCCAACCCCGATTTTATTTCCAAAACATCGATTTTCTATAATCAGGGATACTCTA-ACCC--TGT
1889847 TATCCCCAA-AATAT
63 TATCCCCAAGAATAT
1889861 T
1 T
1889862 AAATTTTTCG
Statistics
Matches: 66, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
79 54 0.82
80 2 0.03
82 10 0.15
ACGTcount: A:0.28, C:0.23, G:0.12, T:0.37
Consensus pattern (77 bp):
TCCAACCCCGATTTTATTTCCAAAACATCGATTTTCTATAATCAGGGATACTCTAACCCTGTTAT
CCCCAAGAATAT
Found at i:1891925 original size:4 final size:4
Alignment explanation
Indices: 1891916--1891946 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
1891906 TTTTGAGGTG
1891916 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
1891947 GTTTTGTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:1900517 original size:21 final size:21
Alignment explanation
Indices: 1900491--1900567 Score: 102
Period size: 21 Copynumber: 3.7 Consensus size: 21
1900481 AAATTATCCA
*
1900491 AATGTATCGATATATTTGTAG
1 AATGTATCGATACATTTGTAG
*
1900512 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
* *
1900533 AATGTATCGATACA-TTCTACA
1 AATGTATCGATACATTTGTA-G
1900554 AATGTATCGATACA
1 AATGTATCGATACA
1900568 GGGTCCCAAC
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
20 3 0.06
21 47 0.94
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.36
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:1900628 original size:19 final size:18
Alignment explanation
Indices: 1900603--1900699 Score: 88
Period size: 19 Copynumber: 5.8 Consensus size: 18
1900593 ATTTCAGCGA
1900603 TTTGTATCGATACATAAG
1 TTTGTATCGATACATAAG
1900621 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
1900637 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
1900653 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
*
1900669 --TGTATTGATACATAAG
1 TTTGTATCGATACATAAG
1900685 TTTTGTATCGATACA
1 -TTTGTATCGATACA
1900700 ATGTATCGCT
Statistics
Matches: 64, Mismatches: 2, Indels: 25
0.70 0.02 0.27
Matches are distributed among these distances:
13 21 0.33
15 4 0.06
17 4 0.06
18 1 0.02
19 34 0.53
ACGTcount: A:0.33, C:0.11, G:0.18, T:0.38
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:1900641 original size:32 final size:32
Alignment explanation
Indices: 1900605--1900707 Score: 188
Period size: 32 Copynumber: 3.2 Consensus size: 32
1900595 TTCAGCGATT
1900605 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
1900637 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
* *
1900669 TGTATTGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
1900701 TGTATCG
1 TGTATCG
1900708 CTAGGAAGCT
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 68 1.00
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:1900642 original size:13 final size:13
Alignment explanation
Indices: 1900624--1900680 Score: 51
Period size: 13 Copynumber: 3.9 Consensus size: 13
1900614 ACATAAGTGT
1900624 TGTATCGATACAA
1 TGTATCGATACAA
1900637 TGTATCGATACATAA
1 TGTATCGATAC--AA
1900652 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
*
1900669 TGTATTGATACA
1 TGTATCGATACA
1900681 TAAGTTTTGT
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
13 22 0.59
15 2 0.05
17 2 0.05
19 11 0.30
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1900769 original size:13 final size:13
Alignment explanation
Indices: 1900751--1900776 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1900741 CATTTTTCTG
1900751 TGTATCGATACAT
1 TGTATCGATACAT
1900764 TGTATCGATACAT
1 TGTATCGATACAT
1900777 CTATTCTTTG
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:1900794 original size:34 final size:33
Alignment explanation
Indices: 1900731--1900797 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 33
1900721 GCCAAGGAAA
* *
1900731 TGTATTGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATTATTCTGTGTATCGATACAT
*
1900764 TGTATCGATACATCTATTCTTTGTATCGATACAT
1 TGTATCGATACAT-TATTCTGTGTATCGATACAT
1900798 CTAGGAAGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 12 0.40
34 18 0.60
ACGTcount: A:0.25, C:0.15, G:0.13, T:0.46
Consensus pattern (33 bp):
TGTATCGATACATTATTCTGTGTATCGATACAT
Found at i:1903198 original size:52 final size:52
Alignment explanation
Indices: 1903141--1903579 Score: 288
Period size: 52 Copynumber: 8.4 Consensus size: 52
1903131 CAATTCTCTG
* *
1903141 CAATCGGGGATATTCCATCTCCGATTTTATTTTCAAAACACCAATTTTTCCA
1 CAATCGGGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTTTCCA
* * **
1903193 CAATCGGGGATACTCCAACCCCGATTTTATTTTTAAAACACCAATTTTTCTT
1 CAATCGGGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTTTCCA
* *
1903245 TAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAAGCACCAATTTTT-CA
1 CAATCGGGGATACTCCAACTCCGATTTTATTTTC-AAAA-CACCAATTTTTCCA
* * * ** * * * *
1903298 CAATTGGGGATACTCCAACCCCG--TTAATCATCGGGGATACTCCAACCCTATTATTTC-
1 CAATCGGGGATACTCCAACTCCGATTTTATTTTC---AAAACACCAA---T-TT-TTCCA
* * * * *** *
1903355 CGA--GGGGATACTCCAACCCCTG-CTTTATTCTT-AAAATATTGATTTCT-CA
1 CAATCGGGGATACTCCAACTCC-GATTTTATT-TTCAAAACACCAATTTTTCCA
* * * * * *
1903404 TAATGGGGGATACTCCAACCCCGGTTTTA-TTGCTAAAACACTAATTTTTCCA
1 CAATCGGGGATACTCCAACTCCGATTTTATTTTC-AAAACACCAATTTTTCCA
* * * **
1903456 CAATCGGGGACACTCCAAC-CTCGGTTTTATTTTTAAAACACCAATTTTTCTT
1 CAATCGGGGATACTCCAACTC-CGATTTTATTTTCAAAACACCAATTTTTCCA
* * * * *
1903508 TAATCGGGGATACTCTAGCTCCGATTTTATTTCCAAAAACACCAATTTTTTCA
1 CAATCGGGGATACTCCAACTCCGATTTTATTTTC-AAAACACCAATTTTTCCA
*
1903561 CAATCGAGGATACTCCAAC
1 CAATCGGGGATACTCCAAC
1903580 CTCGTTATTT
Statistics
Matches: 298, Mismatches: 65, Indels: 47
0.73 0.16 0.11
Matches are distributed among these distances:
48 1 0.00
49 3 0.01
50 4 0.01
51 39 0.13
52 147 0.49
53 59 0.20
54 14 0.05
55 18 0.06
56 3 0.01
57 8 0.03
58 2 0.01
ACGTcount: A:0.29, C:0.25, G:0.13, T:0.33
Consensus pattern (52 bp):
CAATCGGGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTTTCCA
Found at i:1903742 original size:79 final size:79
Alignment explanation
Indices: 1903593--1903797 Score: 207
Period size: 79 Copynumber: 2.6 Consensus size: 79
1903583 GTTATTTCAT
** * * *
1903593 CGGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTTCAACCCCGGCTTTATTCCCAAAATAT
1 CGGGGATACTCCAACCCCGTTATTTCTGAGGGGATACTCCAACCCCGACTTTATTCCCAAAATAT
* * *
1903658 TGATTTCTCATAAT
66 CGATTTCTCACAAC
** * * * * *
1903672 TTGGGATACTCCAACCCCGTTATTTCTGAGGGGATACTCCAATCCCGATTTTTTTTCC-TAATCA
1 CGGGGATACTCCAACCCCGTTATTTCTGAGGGGATACTCCAACCCCGACTTTATTCCCAAAAT-A
1903736 TCGATTTCTCACAAC
65 TCGATTTCTCACAAC
* * * *
1903751 CGGGGATACTCCAGCCCCGTCATTT-TCAAGGGGACACTCCAACCCCG
1 CGGGGATACTCCAACCCCGTTATTTCT-GAGGGGATACTCCAACCCCG
1903798 TTATTATCTC
Statistics
Matches: 102, Mismatches: 22, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
78 4 0.04
79 98 0.96
ACGTcount: A:0.23, C:0.31, G:0.17, T:0.28
Consensus pattern (79 bp):
CGGGGATACTCCAACCCCGTTATTTCTGAGGGGATACTCCAACCCCGACTTTATTCCCAAAATAT
CGATTTCTCACAAC
Found at i:1906762 original size:11 final size:11
Alignment explanation
Indices: 1906745--1906778 Score: 50
Period size: 12 Copynumber: 2.9 Consensus size: 11
1906735 ATCTTCTTTT
1906745 AAAAAAAACAAC
1 AAAAAAAA-AAC
1906757 AAAAAAAAAAC
1 AAAAAAAAAAC
1906768 AAAACAAAAAA
1 AAAA-AAAAAA
1906779 AGAGATAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 7 0.33
12 14 0.67
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAC
Found at i:1906764 original size:14 final size:14
Alignment explanation
Indices: 1906745--1906779 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
1906735 ATCTTCTTTT
1906745 AAAAAAAACAACAA-
1 AAAAAAAACAA-AAC
1906759 AAAAAAAACAAAAC
1 AAAAAAAACAAAAC
1906773 AAAAAAA
1 AAAAAAA
1906780 GAGATAAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 2 0.10
14 18 0.90
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (14 bp):
AAAAAAAACAAAAC
Found at i:1906766 original size:16 final size:16
Alignment explanation
Indices: 1906745--1906779 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
1906735 ATCTTCTTTT
1906745 AAAAAAAAC--AACAA
1 AAAAAAAACAAAACAA
1906759 AAAAAAAACAAAACAA
1 AAAAAAAACAAAACAA
1906775 AAAAA
1 AAAAA
1906780 GAGATAAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 9 0.47
16 10 0.53
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (16 bp):
AAAAAAAACAAAACAA
Found at i:1907856 original size:61 final size:61
Alignment explanation
Indices: 1907761--1907921 Score: 245
Period size: 61 Copynumber: 2.6 Consensus size: 61
1907751 TTTCTCCTTT
**
1907761 CACTT-TTCAGTCCTCAAAGAGCAGGGTGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGG
1 CACTTCTT-AGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGG
* *
1907822 CACTTCTTAGTCCTCAAAGAGCAAGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTTG
1 CACTTCTTAGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGG
*
1907883 CACTTCCTAGTCCTCAAAGAGCAGGACG-CTCTCTCCTTT
1 CACTTCTTAGTCCTCAAAGAGCAGGACGCCT-TCTCCTTT
1907922 CACCCTTTAG
Statistics
Matches: 92, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
60 2 0.02
61 88 0.96
62 2 0.02
ACGTcount: A:0.24, C:0.30, G:0.18, T:0.28
Consensus pattern (61 bp):
CACTTCTTAGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGG
Found at i:1908239 original size:61 final size:61
Alignment explanation
Indices: 1907925--1908554 Score: 570
Period size: 61 Copynumber: 10.6 Consensus size: 61
1907915 CTCCTTTCAC
* *
1907925 CCTT-TAGTCCTCAAAGAGCAGGATGCC-TTT-C----AAAGCCCACACCAGTTGGTGGCA
1 CCTTCTAGTCCTCAAAGAGCAAGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
** * * * *
1907979 TTTTCCAGTCCTCAAAGAGCAGGACGCC-TTT-C----AAAGCCCACACAAGCTGGTGGCA
1 CCTTCTAGTCCTCAAAGAGCAAGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
** ** *
1908034 CCTTC-AGTTATCAAAGAGCAAGACACTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
1 CCTTCTAGTCCTCAAAGAGCAAGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * *
1908094 CTTTGCTAGTCCTCAAAGAGTAGGATGCCTTTTCCTTTTAAAGCCCACTACAAGTTGGT-GCA
1 CCTT-CTAGTCCTCAAAGAGCAAGATGCCTTTTCCTTTTAAAGCCCAC-ACAAGTTGGTGGCA
* * * * *
1908156 CTTTTCTATTCCTCAAAGAGTAAGACGTCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
1 C-CTTCTAGTCCTCAAAGAGCAAGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * * *
1908218 CCTTCTAGTCCTTAAAAAGTAAGATG-CTTTCTCCTTTTAAAGACCAC-CAAGTTGGTGGCA
1 CCTTCTAGTCCTCAAAGAGCAAGATGCCTTT-TCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * * * * *
1908278 -CTTTTCAGTCCTCAAGGAGCATGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGT-ACA
1 CCTTCT-AGTCCTCAAAGAGCAAGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * * *
1908338 CCTTCTAGTCCTCAAAGAGCATGATG-CTTTCTCCTTTTAAAGACCACACAAGTTAGTGGTA
1 CCTTCTAGTCCTCAAAGAGCAAGATGCCTTT-TCCTTTTAAAGCCCACACAAGTTGGTGGCA
* *
1908399 TCTT-TCAGTCCTTAAAGAGCAAGATG--TTTTCTCTTTGTAAAGCCCACACAAGTTGGTGGCA
1 CCTTCT-AGTCCTCAAAGAGCAAGATGCCTTTTC-CTTT-TAAAGCCCACACAAGTTGGTGGCA
* * * * * *
1908460 CCTTCCAGTCCTCAAAGAGTAGGATGCCTTTT-CTTTTCAAAGTCCACACGAGTTGGTGACA
1 CCTTCTAGTCCTCAAAGAGCAAGATGCCTTTTCCTTTT-AAAGCCCACACAAGTTGGTGGCA
** * * *
1908521 TGTTTTAGTCCTCAAAGAGCAGGATGCTTTTTCC
1 CCTTCTAGTCCTCAAAGAGCAAGATGCCTTTTCC
1908555 GTCTCTTATT
Statistics
Matches: 479, Mismatches: 70, Indels: 46
0.81 0.12 0.08
Matches are distributed among these distances:
54 19 0.04
55 52 0.11
56 1 0.00
59 9 0.02
60 124 0.26
61 175 0.37
62 82 0.17
63 17 0.04
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.30
Consensus pattern (61 bp):
CCTTCTAGTCCTCAAAGAGCAAGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
Found at i:1908325 original size:121 final size:122
Alignment explanation
Indices: 1907950--1908541 Score: 631
Period size: 121 Copynumber: 4.9 Consensus size: 122
1907940 GAGCAGGATG
* * ** * * *
1907950 CCTTTCAAAGCCCACACCAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACGCC-TTT-C--
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGTAGGATGCCTTTTCCTT
* * * ** * * *
1908011 --AAAGCCCACACAAGCTGGTGGCAC-CTTCAGTTATCAAAGAGCAAGACACTTTTT
66 TTAAAGACCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAAGACGCCTTCT
*
1908065 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTGCTAGTCCTCAAAGAGTAGGATGCCTTTTCCT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTT-CTAGTCCTCAAAGAGTAGGATGCCTTTTCCT
* * * * *
1908130 TTTAAAGCCCACTACAAGTTGGT-GCACTTTTCTATTCCTCAAAGAGTAAGACGTCTTTT
65 TTTAAAGACCAC-ACAAGTTGGTGGCACTTTTC-AGTCCTCAAAGAGCAAGACGCCTTCT
* * *
1908189 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTTAAAAAGTAAGATG-CTTTCTCCT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGTAGGATGCCTTT-TCCT
* *
1908253 TTTAAAGACCAC-CAAGTTGGTGGCACTTTTCAGTCCTCAAGGAGCATGACGCCTTCT
65 TTTAAAGACCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAAGACGCCTTCT
* * *
1908310 CCTTTTAAAGCCCACACAAGTTGGT-ACACCTTCTAGTCCTCAAAGAGCATGATG-CTTTCTCCT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGTAGGATGCCTTT-TCCT
* * * * **
1908373 TTTAAAGACCACACAAGTTAGTGGTA-TCTTTCAGTCCTTAAAGAGCAAGATGTTTTCT
65 TTTAAAGACCACACAAGTTGGTGGCACT-TTTCAGTCCTCAAAGAGCAAGACGCCTTCT
*
1908431 -CTTTGTAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGTAGGATGCCTTTT-CT
1 CCTTT-TAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGTAGGATGCCTTTTCCT
* * * *
1908494 TTTCAAAGTCCACACGAGTTGGTGACA-TGTTTTAGTCCTCAAAGAGCA
65 TTT-AAAGACCACACAAGTTGGTGGCACT-TTTCAGTCCTCAAAGAGCA
1908542 GGATGCTTTT
Statistics
Matches: 408, Mismatches: 51, Indels: 29
0.84 0.10 0.06
Matches are distributed among these distances:
115 30 0.07
116 21 0.05
117 3 0.01
118 1 0.00
120 50 0.12
121 114 0.28
122 88 0.22
123 50 0.12
124 51 0.12
ACGTcount: A:0.27, C:0.26, G:0.18, T:0.30
Consensus pattern (122 bp):
CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGTAGGATGCCTTTTCCTT
TTAAAGACCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAAGACGCCTTCT
Found at i:1908616 original size:45 final size:44
Alignment explanation
Indices: 1908565--1908712 Score: 133
Period size: 46 Copynumber: 3.3 Consensus size: 44
1908555 GTCTCTTATT
1908565 TGTCCTCAAAGAGCAGGACACATTTCATTTCCTTCTTTTCCCTTC
1 TGTCCTCAAAGAGCAGGAC-CATTTCATTTCCTTCTTTTCCCTTC
* * **
1908610 TGTCCTCAAAGAGTAGGATTCCTTTTTTTTTCC-T-TTTT-CCTT-
1 TGTCCTCAAAGAGCAGGA--CCATTTCATTTCCTTCTTTTCCCTTC
* * * *
1908652 TGTCCTCAAAGAGCGGGACGCACTTCATTTCTTTCTTTTCCTTTC
1 TGTCCTCAAAGAGCAGGAC-CATTTCATTTCCTTCTTTTCCCTTC
**
1908697 TAGTTTTCAAAGAGCA
1 T-GTCCTCAAAGAGCA
1908713 TGACGCACTT
Statistics
Matches: 80, Mismatches: 15, Indels: 15
0.73 0.14 0.14
Matches are distributed among these distances:
40 1 0.01
41 7 0.09
42 17 0.21
43 8 0.10
44 7 0.09
45 19 0.24
46 20 0.25
47 1 0.01
ACGTcount: A:0.19, C:0.26, G:0.14, T:0.42
Consensus pattern (44 bp):
TGTCCTCAAAGAGCAGGACCATTTCATTTCCTTCTTTTCCCTTC
Found at i:1908733 original size:87 final size:87
Alignment explanation
Indices: 1908563--1908833 Score: 202
Period size: 87 Copynumber: 3.2 Consensus size: 87
1908553 CCGTCTCTTA
* *
1908563 TTTGTCCTCAAAGAGCAGGACACATTTCATTTCCTTCTTTTCCCTTCTGTCCTCAAAGAGTAGGA
1 TTTGTCCTCAAAGAGCAGGACACACTTCATTTCCTTCTTTTCCCTTCTGTCCTCAAAGAGCAGGA
** * *
1908628 TTCCTTTTTTTTTCCTTTTTCC
66 CGCCTTTTATTCTCCTTTTTCC
* * * * ** *
1908650 TTTGTCCTCAAAGAGCGGGACGCACTTCATTTCTTTCTTTTCCTTTCTAGTTTTCAAAGAGCATG
1 TTTGTCCTCAAAGAGCAGGACACACTTCATTTCCTTCTTTTCCCTTCT-GTCCTCAAAGAGCAGG
1908715 ACGCAC-TTTATTCT-CTTTTT--
65 ACGC-CTTTTATTCTCCTTTTTCC
* * * * * * * **
1908735 TTT-TCTTCAAAAAGCAGGACACATTTAAATTCC-T-TTTT-CCTT-TGTCTTCAAAGGGCACCA
1 TTTGTCCTCAAAGAGCAGGACACACTTCATTTCCTTCTTTTCCCTTCTGTCCTCAAAGAGCAGGA
* *
1908795 TGCATTTTATT-TCCTTTTTCCC
66 CGCCTTTTATTCTCCTTTTT-CC
* * *
1908817 TTAGTCCCCAAGGAGCA
1 TTTGTCCTCAAAGAGCA
1908834 AGACCCATTT
Statistics
Matches: 143, Mismatches: 33, Indels: 20
0.73 0.17 0.10
Matches are distributed among these distances:
78 1 0.01
79 27 0.19
80 1 0.01
81 3 0.02
82 6 0.04
83 10 0.07
84 22 0.15
85 3 0.02
87 49 0.34
88 20 0.14
89 1 0.01
ACGTcount: A:0.20, C:0.25, G:0.13, T:0.42
Consensus pattern (87 bp):
TTTGTCCTCAAAGAGCAGGACACACTTCATTTCCTTCTTTTCCCTTCTGTCCTCAAAGAGCAGGA
CGCCTTTTATTCTCCTTTTTCC
Found at i:1911939 original size:28 final size:28
Alignment explanation
Indices: 1911898--1911970 Score: 110
Period size: 28 Copynumber: 2.6 Consensus size: 28
1911888 TGTCACAATC
1911898 AGGATACTCTAACCCCATCATTTCCGAG
1 AGGATACTCTAACCCCATCATTTCCGAG
* **
1911926 AGGATACTCCAACCCTGTCATTTCCGAG
1 AGGATACTCTAACCCCATCATTTCCGAG
*
1911954 GGGATACTCTAACCCCA
1 AGGATACTCTAACCCCA
1911971 GTTTTATTTC
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.27, C:0.33, G:0.16, T:0.23
Consensus pattern (28 bp):
AGGATACTCTAACCCCATCATTTCCGAG
Found at i:1912090 original size:28 final size:28
Alignment explanation
Indices: 1912053--1912129 Score: 82
Period size: 28 Copynumber: 2.8 Consensus size: 28
1912043 ATTTTTCACA
* * *
1912053 ATCGGGGATACTCTAACCCCTTTATTTC
1 ATCGGAGATACTCCAACCCCGTTATTTC
*
1912081 ATCGGAGATACTCCAACCTCGTTATTTC
1 ATCGGAGATACTCCAACCCCGTTATTTC
*** *
1912109 CGAGGAGATACTCCAAACCCG
1 ATCGGAGATACTCCAACCCCG
1912130 GCATTATTTT
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.26, C:0.30, G:0.17, T:0.27
Consensus pattern (28 bp):
ATCGGAGATACTCCAACCCCGTTATTTC
Found at i:1912137 original size:159 final size:157
Alignment explanation
Indices: 1911884--1912169 Score: 355
Period size: 159 Copynumber: 1.8 Consensus size: 157
1911874 CCAAAATACT
1911884 AATTTGTCACAATCAGGATACTCTAACCCCATCATTTCCGAGAGGATACTCCAACCCTGTCATTT
1 AATTTGTCACAATCAGGATACTCTAACCCCATCATTTCCGAGAGGATACTCCAACCCTGTCATTT
* * * **
1911949 CCGAGGGGATACTCTAACCCCAGTTTTATTTCTAAAACTACCAATTT-TCCACAATCGGGGATAA
66 CCGAGGAGATACTCCAAACCCAGCATTATTTCTAAAA-TACCAATTTCT-CACAATCGGGGATAA
1912013 TTCAACTCTGATTTTATTTTCAAAACATC
129 TTCAACTCTGATTTTATTTTCAAAACATC
* * * * *
1912042 AATTTTTCACAATCGGGGATACTCTAACCCCTTTATTTCATCG-GA-GATACTCCAA-CCTCGTT
1 AATTTGTCACAATC-AGGATACTCTAACCCCATCATTTC--CGAGAGGATACTCCAACCCT-GTC
* * ***
1912104 ATTTCCGAGGAGATACTCCAAACCCGGCATTATTTTTAAAATATTGATTTCTCACAATCGGGGAT
62 ATTTCCGAGGAGATACTCCAAACCCAGCATTATTTCTAAAATACCAATTTCTCACAATCGGGGAT
1912169 A
127 A
1912170 CTCCAACCCC
Statistics
Matches: 108, Mismatches: 15, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
158 36 0.33
159 68 0.63
160 2 0.02
161 2 0.02
ACGTcount: A:0.30, C:0.25, G:0.13, T:0.32
Consensus pattern (157 bp):
AATTTGTCACAATCAGGATACTCTAACCCCATCATTTCCGAGAGGATACTCCAACCCTGTCATTT
CCGAGGAGATACTCCAAACCCAGCATTATTTCTAAAATACCAATTTCTCACAATCGGGGATAATT
CAACTCTGATTTTATTTTCAAAACATC
Found at i:1912177 original size:79 final size:78
Alignment explanation
Indices: 1912081--1912362 Score: 260
Period size: 79 Copynumber: 3.6 Consensus size: 78
1912071 CCTTTATTTC
* * * *
1912081 ATCGGAGATACTCCAACCTCGTTATTTCCGAGGAGATACTCCAAACCCGGCATTATTTTTAAAAT
1 ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGCATTATTTTTAAAAT
*
1912146 ATTGATTTCTCACA
66 ATCGATTT-TCACA
* ** * * * *
1912160 ATCGGGGATACTCCAACCCCATTATTTTAGCGGGGATACTCCAACCCCGGCCTTATTTCTAAAGT
1 ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGCATTATTTTTAAAAT
*
1912225 ATCGATTTTCCACG
66 ATCGATTTT-CACA
* * * * * *** * *
1912239 ATCGGGGATATTTCAACCCCGTTATTTTCAAGGGGATACTCTAACCCCGATTTTATTTTCAAAAC
1 ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGCATTATTTTTAAAAT
*
1912304 ATCGATTTTCTATA
66 ATCGATTTTC-ACA
** * ** *
1912318 ATCAAGGATACTCCAACCCTGTTATTT-CGAAAGGATATTCCAACC
1 ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACC
1912363 TTGATTTTAT
Statistics
Matches: 162, Mismatches: 39, Indels: 5
0.79 0.19 0.02
Matches are distributed among these distances:
78 15 0.09
79 147 0.91
ACGTcount: A:0.28, C:0.25, G:0.15, T:0.32
Consensus pattern (78 bp):
ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGCATTATTTTTAAAAT
ATCGATTTTCACA
Found at i:1924807 original size:12 final size:13
Alignment explanation
Indices: 1924790--1924822 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
1924780 CCTTCTTTTT
1924790 AAAAAAAC-AACA
1 AAAAAAACAAACA
1924802 AAAAAAACAAAACA
1 AAAAAAAC-AAACA
1924816 AAAAAAA
1 AAAAAAA
1924823 AGAGAGAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 8 0.42
14 11 0.58
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAAACAAACA
Found at i:1925902 original size:61 final size:61
Alignment explanation
Indices: 1925816--1925950 Score: 189
Period size: 61 Copynumber: 2.2 Consensus size: 61
1925806 CTTTTCAGTT
* * *
1925816 CTCAAAGAGCAGGGCGCCTTCTCCTTTTAAAGCCCACACAAGCTGGTGGCACTTCCTACTC
1 CTCAAAGAGCAGGACGCCTTATCCTTTTAAAGCCCACACAAGCTGGTAGCACTTCCTACTC
* * * * * *
1925877 TTCAAAGAGTAGGACGCCTTATCCTTTTAAAGCCCATACAAGTTGGTAGCACTTTCTAGTC
1 CTCAAAGAGCAGGACGCCTTATCCTTTTAAAGCCCACACAAGCTGGTAGCACTTCCTACTC
1925938 CTCAAAGAGCAGG
1 CTCAAAGAGCAGG
1925951 GCGCTCTCTC
Statistics
Matches: 63, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
61 63 1.00
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (61 bp):
CTCAAAGAGCAGGACGCCTTATCCTTTTAAAGCCCACACAAGCTGGTAGCACTTCCTACTC
Found at i:1926041 original size:55 final size:54
Alignment explanation
Indices: 1925975--1926100 Score: 155
Period size: 55 Copynumber: 2.3 Consensus size: 54
1925965 CACCCTTTAG
* * **
1925975 TCCTCAAAGAGCAGGACGCCTTTCAAAACCCACACCAG-TTGGTGGTATTTTCCAA
1 TCCTCAAAGAGCAGGACGCCTTTCAAAACCCACACAAGCTT-GTGGCACCTT-CAA
* * * *
1926030 TCCTCAAAGAGCATGATGCCTTTCAAAGCCCACACAAGCTTGTGGCACCTTCAG
1 TCCTCAAAGAGCAGGACGCCTTTCAAAACCCACACAAGCTTGTGGCACCTTCAA
1926084 TCCTCAAAGAGCAGGAC
1 TCCTCAAAGAGCAGGAC
1926101 ACATTTTCCT
Statistics
Matches: 60, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
54 17 0.28
55 41 0.68
56 2 0.03
ACGTcount: A:0.29, C:0.30, G:0.19, T:0.21
Consensus pattern (54 bp):
TCCTCAAAGAGCAGGACGCCTTTCAAAACCCACACAAGCTTGTGGCACCTTCAA
Found at i:1926207 original size:122 final size:122
Alignment explanation
Indices: 1926048--1926521 Score: 608
Period size: 122 Copynumber: 3.9 Consensus size: 122
1926038 GAGCATGATG
*
1926048 CCTTTCAAAGCCCACACAAGCTT-GTGGCACCTT-CAGTCCTCAAAGAGCAGGACACATTT-TCC
1 CCTTTCAAAGCCCACACAAG-TTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGACGC-TTTCTCC
*
1926110 TTTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGTAGGACGTCTTTT
64 TTTTAAAGACCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGTAGGAC-TCTTTT
* * *
1926170 CCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTCCAGTCCTCAAAGAGCAAGATGCTTTCTCCTT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGACGCTTTCTCCTT
* * * ** * *
1926234 TTAAAGACCACACAAGTTAGTGGCACTTTTC-AATCCTCAAGGAGCCGGACACATTCT
66 TTAAAGACCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGTAGGACTC-TTTT
* * *
1926291 CTTTTTAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGATGCTTTCTCCTT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGACGCTTTCTCCTT
** * *
1926356 TTAAAGACCACACAAGTTGGTGGCAC-CATCTAGTCTTCAAAGAGTAGGA-TGTTTT
66 TTAAAGACCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGTAGGACTCTTTT
*
1926411 CTCTTTGCAAAGCCCACACAAGTTGGTGGCACCTTACAGTCCTCAAAGAGCAGGACGCCTTT-T-
1 C-CTTT-CAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGACG-CTTTCTC
* *
1926474 CTTTTCAAAGTCCACACGAGTTGGTGGCACTTTT-TAGTCCTCAAAGAG
63 CTTTT-AAAGACCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAG
1926522 CTAGACACCT
Statistics
Matches: 307, Mismatches: 34, Indels: 22
0.85 0.09 0.06
Matches are distributed among these distances:
120 5 0.02
121 64 0.21
122 233 0.76
123 5 0.02
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.28
Consensus pattern (122 bp):
CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGACGCTTTCTCCTT
TTAAAGACCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGTAGGACTCTTTT
Found at i:1926305 original size:183 final size:182
Alignment explanation
Indices: 1926048--1926522 Score: 627
Period size: 183 Copynumber: 2.6 Consensus size: 182
1926038 GAGCATGATG
* *
1926048 CCTTTCAAAGCCCACACAAGCTTGTGGCACCTTCAGTCCTCAAAGAGCAGGACACATTTTCCTTT
1 CCTTTCAAAGCCCACACAAG-TTGTGGCACTTTCAGTCCTCAAAGAGCAGGACACATTTTCTTTT
*
1926113 TAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGTAGGACGTCTTT-TCCTTTTA
65 TAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACG-CTTTCTCCTTTTA
* *
1926177 AAGCCCACACAAGTTGGTGGCA-CTTCCAGTCCTCAAAGAGCAAGATGCTTTCT
129 AAGACCACACAAGTTGGTGGCACCATCCAGTCCTCAAAGAGCAAGATGCTTTCT
* * * * * *
1926230 CCTTTTAAAGACCACACAAGTTAGTGGCACTTTTCAATCCTCAAGGAGCCGGACACATTCTCTTT
1 CCTTTCAAAGCCCACACAAGTT-GTGGCAC-TTTCAGTCCTCAAAGAGCAGGACACATTTTCTTT
* * *
1926295 TTAAAGCCCACACAAGTTGGTGGCAC-CTTCCAGTCCTCAAAGAGCAGGATGCTTTCTCCTTTTA
64 TTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACGCTTTCTCCTTTTA
* * * * *
1926359 AAGACCACACAAGTTGGTGGCACCATCTAGTCTTCAAAGAGTAGGATGTTTTCT
129 AAGACCACACAAGTTGGTGGCACCATCCAGTCCTCAAAGAGCAAGATGCTTTCT
* * *
1926413 -CTTTGCAAAGCCCACACAAGTTGGTGGCACCTTACAGTCCTCAAAGAGCAGGACGCCTTTTCTT
1 CCTTT-CAAAGCCCACACAAGTT-GTGGCA-CTTTCAGTCCTCAAAGAGCAGGACACATTTTCTT
* * *
1926477 TTCAAAGTCCACACGAGTTGGTGGCACTTTT-TAGTCCTCAAAGAGC
63 TTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGC
1926523 TAGACACCTT
Statistics
Matches: 252, Mismatches: 34, Indels: 13
0.84 0.11 0.04
Matches are distributed among these distances:
181 6 0.02
182 79 0.31
183 164 0.65
184 3 0.01
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.28
Consensus pattern (182 bp):
CCTTTCAAAGCCCACACAAGTTGTGGCACTTTCAGTCCTCAAAGAGCAGGACACATTTTCTTTTT
AAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACGCTTTCTCCTTTTAAA
GACCACACAAGTTGGTGGCACCATCCAGTCCTCAAAGAGCAAGATGCTTTCT
Found at i:1926306 original size:61 final size:60
Alignment explanation
Indices: 1926048--1926522 Score: 530
Period size: 61 Copynumber: 7.8 Consensus size: 60
1926038 GAGCATGATG
* * *
1926048 CCTTTCAAAGCCCACACAAGCTT-GTGGCACCTTCAGTCCTCAAAGAGCAGGACACATTT-T
1 CCTTTTAAAGCCCACACAAG-TTGGTGGCACTTTCAGTCCTCAAAGAGCAGGACGC-TTTCT
*
1926108 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGTAGGACGTCTTT-T
1 CCTTTTAAAGCCCACACAAGTTGGTGGCAC-TTTC-AGTCCTCAAAGAGCAGGACG-CTTTCT
* * *
1926170 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCAGTCCTCAAAGAGCAAGATGCTTTCT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCAGTCCTCAAAGAGCAGGACGCTTTCT
* * * * * * *
1926230 CCTTTTAAAGACCACACAAGTTAGTGGCACTTTTCAATCCTCAAGGAGCCGGACACATTCT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCAC-TTTCAGTCCTCAAAGAGCAGGACGCTTTCT
* * *
1926291 CTTTTTAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGATGCTTTCT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTTCAGTCCTCAAAGAGCAGGACGCTTTCT
* ** * * * *
1926352 CCTTTTAAAGACCACACAAGTTGGTGGCACCATCTAGTCTTCAAAGAGTAGGATGTTTTCT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTC-AGTCCTCAAAGAGCAGGACGCTTTCT
* *
1926413 -CTTTGCAAAGCCCACACAAGTTGGTGGCACCTTACAGTCCTCAAAGAGCAGGACGCCTTT-T
1 CCTTT-TAAAGCCCACACAAGTTGGTGGCA-CTTTCAGTCCTCAAAGAGCAGGACG-CTTTCT
* * *
1926474 -CTTTTCAAAGTCCACACGAGTTGGTGGCACTTTTTAGTCCTCAAAGAGC
1 CCTTTT-AAAGCCCACACAAGTTGGTGGCAC-TTTCAGTCCTCAAAGAGC
1926523 TAGACACCTT
Statistics
Matches: 352, Mismatches: 50, Indels: 25
0.82 0.12 0.06
Matches are distributed among these distances:
59 6 0.02
60 79 0.22
61 208 0.59
62 58 0.16
63 1 0.00
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.28
Consensus pattern (60 bp):
CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCAGTCCTCAAAGAGCAGGACGCTTTCT
Found at i:1926659 original size:85 final size:85
Alignment explanation
Indices: 1926531--1926686 Score: 208
Period size: 85 Copynumber: 1.8 Consensus size: 85
1926521 GCTAGACACC
* * *
1926531 TTTTTTTTTCTCCTTTGTCCTCAAAAAGCAGGACACATTTCATTTCCTTCTTTTCCCTTTT-GTC
1 TTTTTTTTTCTCCTTTATCCTCAAAAAGCAGGACACACTTCATTTCCTTATTTTCCCTTTTAGTC
1926595 CTCAAAGAATAAGATGCCTT
66 CTCAAAGAATAAGATGCCTT
* * * *
1926615 TTTTTCTTTTTTCCTTTATCCTCAAAGAGC-GAGACGCACTTCATTTCCTTATTTTCCTTTTTAG
1 TTTTT-TTTTCTCCTTTATCCTCAAAAAGCAG-GACACACTTCATTTCCTTATTTTCCCTTTTAG
*
1926679 TTCTCAAA
64 TCCTCAAA
1926687 AAGCAGGATG
Statistics
Matches: 61, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
84 6 0.10
85 47 0.77
86 8 0.13
ACGTcount: A:0.21, C:0.24, G:0.09, T:0.46
Consensus pattern (85 bp):
TTTTTTTTTCTCCTTTATCCTCAAAAAGCAGGACACACTTCATTTCCTTATTTTCCCTTTTAGTC
CTCAAAGAATAAGATGCCTT
Found at i:1926775 original size:41 final size:40
Alignment explanation
Indices: 1926700--1926789 Score: 108
Period size: 41 Copynumber: 2.2 Consensus size: 40
1926690 CAGGATGCAA
*
1926700 CCTTTTTCCTTTTCTTCAAAAAGCAGGACACATTTAAATT
1 CCTTTTTCCTTTTCTTCAAAAAGCACGACACATTTAAATT
** ** * *
1926740 CCTTTTTCCTTTGTCTTCAAAGGGCACGATGCATTTTATTT
1 CCTTTTTCCTTT-TCTTCAAAAAGCACGACACATTTAAATT
1926781 CCTTTTTCC
1 CCTTTTTCC
1926790 CTTAGTCCCC
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
40 12 0.29
41 30 0.71
ACGTcount: A:0.21, C:0.24, G:0.10, T:0.44
Consensus pattern (40 bp):
CCTTTTTCCTTTTCTTCAAAAAGCACGACACATTTAAATT
Found at i:1929966 original size:51 final size:51
Alignment explanation
Indices: 1929909--1930005 Score: 167
Period size: 51 Copynumber: 1.9 Consensus size: 51
1929899 CCAACCCCAG
1929909 TTTTATTTCTAAAACACCAATTTTTCACAATCGGGGATAATCCAACTCTGA
1 TTTTATTTCTAAAACACCAATTTTTCACAATCGGGGATAATCCAACTCTGA
* * *
1929960 TTTTATTTTTAAAATACCAATTTTTCACAATCGGGGATACTCCAAC
1 TTTTATTTCTAAAACACCAATTTTTCACAATCGGGGATAATCCAAC
1930006 CCTGTTATTT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
51 43 1.00
ACGTcount: A:0.33, C:0.21, G:0.09, T:0.37
Consensus pattern (51 bp):
TTTTATTTCTAAAACACCAATTTTTCACAATCGGGGATAATCCAACTCTGA
Found at i:1930153 original size:78 final size:74
Alignment explanation
Indices: 1930023--1930297 Score: 221
Period size: 78 Copynumber: 3.5 Consensus size: 74
1930013 TTTCATCAAA
** * * *
1930023 GATACTCCAACCTTATTATTTTTGATGGGATACTCCAAACCCGGCATTATTTCAAAAATATTGAT
1 GATACTCCAACCCCATTA-TTTTG-GGGGATACTCC-AACCCGACATTATTTC-AAAACATTGAT
1930088 TTCTTACAATCAGG
62 TT-TTACAATCAGG
* ** *
1930102 GATACTCCAACCCCATTATTTTGGCGGGATACTCCAACCTCGACCTTATTTCTAAGGCATTAATT
1 GATACTCCAACCCCATTATTTTGG-GGGATACTCCAACC-CGACATTATTTC-AAAACATTGATT
1930167 TTT-CATGATC-GG
63 TTTACA--ATCAGG
* * **
1930179 AGATACTCCAATCCCGTTATTTTCGAGGGGATACTCCAACCCGATTTTATTTTCAAAACATTGAT
1 -GATACTCCAACCCCATTATTTT-G-GGGGATACTCCAACCCGACATTA-TTTCAAAACATTGAT
*
1930244 TTTCTATAATCAGG
62 TTT-TACAATCAGG
*** *
1930258 GATACTCCAACCTTGTTATTTTCGAGGGGATATTCCAACC
1 GATACTCCAACCCCATTATTTT-G-GGGGATACTCCAACC
1930298 TCAATTTTAT
Statistics
Matches: 163, Mismatches: 22, Indels: 23
0.78 0.11 0.11
Matches are distributed among these distances:
76 2 0.01
77 8 0.05
78 113 0.69
79 38 0.23
80 2 0.01
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.35
Consensus pattern (74 bp):
GATACTCCAACCCCATTATTTTGGGGGATACTCCAACCCGACATTATTTCAAAACATTGATTTTT
ACAATCAGG
Found at i:1930324 original size:157 final size:157
Alignment explanation
Indices: 1930038--1930325 Score: 343
Period size: 157 Copynumber: 1.8 Consensus size: 157
1930028 TCCAACCTTA
* * * *
1930038 TTATTTTTGATGGGATACTCCAAACCCGGCATTATTTCAAAAATATTGATTTCTTACAATCAGGG
1 TTATTTTCGAGGGGATACTCCAAACCCGACATTATTTCAAAAACATTGATTTCTTACAATCAGGG
* * * *
1930103 ATACTCCAACCCCATTATTTTGGCGGGATACTCCAACCTCGACCTTATTTCTAAGGCATTAATTT
66 ATACTCCAACCCCATTATTTTGGCGGGATACTCCAACCTCAACCTTATTTCCAAGACATCAATTT
1930168 TTCATGATCGGAGATACTCCAATCCCG
131 TTCATGATCGGAGATACTCCAATCCCG
** *
1930195 TTATTTTCGAGGGGATACTCC-AACCCGATTTTATTTTC-AAAACATTGATTT-TCTATAATCAG
1 TTATTTTCGAGGGGATACTCCAAACCCGACATTA-TTTCAAAAACATTGATTTCT-TACAATCAG
*** * **
1930257 GGATACTCCAACCTTGTTATTTTCGAG-GGGATATTCCAACCTCAATTTTATTTCC-AGAACATC
64 GGATACTCCAACCCCATTATTTT-G-GCGGGATACTCCAACCTCAACCTTATTTCCAAG-ACATC
1930320 AATTTT
126 AATTTT
1930326 CTATAATCGA
Statistics
Matches: 109, Mismatches: 17, Indels: 10
0.80 0.12 0.07
Matches are distributed among these distances:
155 1 0.01
156 51 0.47
157 56 0.51
158 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.36
Consensus pattern (157 bp):
TTATTTTCGAGGGGATACTCCAAACCCGACATTATTTCAAAAACATTGATTTCTTACAATCAGGG
ATACTCCAACCCCATTATTTTGGCGGGATACTCCAACCTCAACCTTATTTCCAAGACATCAATTT
TTCATGATCGGAGATACTCCAATCCCG
Found at i:1930343 original size:79 final size:78
Alignment explanation
Indices: 1930095--1930345 Score: 244
Period size: 78 Copynumber: 3.2 Consensus size: 78
1930085 GATTTCTTAC
* * * ** * *
1930095 AATCAGGGATACTCCAACCCCATTATTTT-G-GCGGGATACTCCAACCTCGACCTTATTTCTAAG
1 AATCAGGGATACTCCAATCCCGTTATTTTCGAG-GGGATACTCCAACC-CAATTTTATTTCCAAA
* *
1930158 GCATTAATTTT-TCAT
64 ACATCAATTTTCT-AT
* * *
1930173 GATC-GGAGATACTCCAATCCCGTTATTTTCGAGGGGATACTCCAACCCGATTTTATTTTCAAAA
1 AATCAGG-GATACTCCAATCCCGTTATTTTCGAGGGGATACTCCAACCCAATTTTATTTCCAAAA
**
1930237 CATTGATTTTCTAT
65 CATCAATTTTCTAT
* * *
1930251 AATCAGGGATACTCCAA-CCTTGTTATTTTCGAGGGGATATTCCAACCTCAATTTTATTTCCAGA
1 AATCAGGGATACTCCAATCC-CGTTATTTTCGAGGGGATACTCCAACC-CAATTTTATTTCCAAA
1930315 ACATCAATTTTCTAT
64 ACATCAATTTTCTAT
1930330 AATC-GAGGATACTCCA
1 AATCAG-GGATACTCCA
1930346 GCCCCATTGT
Statistics
Matches: 147, Mismatches: 18, Indels: 15
0.82 0.10 0.08
Matches are distributed among these distances:
77 4 0.03
78 84 0.57
79 58 0.39
80 1 0.01
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.34
Consensus pattern (78 bp):
AATCAGGGATACTCCAATCCCGTTATTTTCGAGGGGATACTCCAACCCAATTTTATTTCCAAAAC
ATCAATTTTCTAT
Found at i:1933360 original size:17 final size:17
Alignment explanation
Indices: 1933338--1933409 Score: 135
Period size: 17 Copynumber: 4.2 Consensus size: 17
1933328 TCGAGTTATG
1933338 GACATCCGAATGTCTGT
1 GACATCCGAATGTCTGT
*
1933355 GACATCCGAATGTCTAT
1 GACATCCGAATGTCTGT
1933372 GACATCCGAATGTCTGT
1 GACATCCGAATGTCTGT
1933389 GACATCCGAATGTCTGT
1 GACATCCGAATGTCTGT
1933406 GACA
1 GACA
1933410 GAAGGGAAAG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 53 1.00
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.28
Consensus pattern (17 bp):
GACATCCGAATGTCTGT
Found at i:1936448 original size:148 final size:147
Alignment explanation
Indices: 1936157--1936450 Score: 337
Period size: 148 Copynumber: 2.0 Consensus size: 147
1936147 GGAAAAACCA
* * * *
1936157 AACCTATCCCTAATACGTACCCTTGGCATAGAAATAACTCGATAGTTTCACAGGACTAGGTTTCA
1 AACCTATCCCTAATACGTACCCTCGGCATAGAAACAACTCGATAATTTCAAAGGACTAGGTTT-A
* * * * *
1936222 AGGAAAAATGCTATAGGTCCCTAAGGTTTGCCATCGACTTAGAAGTGCCCGATAATCCTAGAGAA
65 AGGAAAAATGCTAAAGGTCCCTAAGGTCTACCATCGACTTAAAAGTGCCAGATAATCCTAGAGAA
1936287 CTTGAAAAAGTAAAAGTG
130 CTTGAAAAAGTAAAAGTG
*
1936305 AACCTA-CGCCTAATACGTACCCTCGGCATAGAAACGACTCTG-TAATTTCATAAGG-CTAGGTT
1 AACCTATC-CCTAATACGTACCCTCGGCATAGAAACAACTC-GATAATTTCA-AAGGACTAGGTT
* * * * *
1936367 T-GGGAAAAATGTTAAAGAGTCTCTAAGGTCTACCATCGACTTAAAAGTGCCTAG-TGATCTTAG
63 TAAGGAAAAATGCTAAAG-GTCCCTAAGGTCTACCATCGACTTAAAAGTGCC-AGATAATCCTAG
* *
1936430 AGGACTTGCAAAATGTAAAAG
126 AGAACTTG-AAAAAGTAAAAG
1936451 GATGACAAAC
Statistics
Matches: 123, Mismatches: 17, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
146 13 0.11
147 44 0.36
148 62 0.50
149 4 0.03
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.26
Consensus pattern (147 bp):
AACCTATCCCTAATACGTACCCTCGGCATAGAAACAACTCGATAATTTCAAAGGACTAGGTTTAA
GGAAAAATGCTAAAGGTCCCTAAGGTCTACCATCGACTTAAAAGTGCCAGATAATCCTAGAGAAC
TTGAAAAAGTAAAAGTG
Found at i:1936709 original size:16 final size:18
Alignment explanation
Indices: 1936680--1936720 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
1936670 AGAAAATTTA
1936680 TTTATTA-TGATTA-TCC
1 TTTATTATTGATTATTCC
*
1936696 TTTATTATTG-TTATTTC
1 TTTATTATTGATTATTCC
1936713 TTTATTAT
1 TTTATTAT
1936721 ATATAAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 10 0.45
17 12 0.55
ACGTcount: A:0.22, C:0.07, G:0.05, T:0.66
Consensus pattern (18 bp):
TTTATTATTGATTATTCC
Found at i:1939881 original size:16 final size:17
Alignment explanation
Indices: 1939860--1939919 Score: 72
Period size: 16 Copynumber: 3.7 Consensus size: 17
1939850 CTAGTATTTA
1939860 GGAATTAATGGTTTA-T
1 GGAATTAATGGTTTAGT
1939876 GGAATTAATGG-TTAGT
1 GGAATTAATGGTTTAGT
**
1939892 GGTGTTAATGG-TTAGT
1 GGAATTAATGGTTTAGT
*
1939908 GGAGTTAATGGT
1 GGAATTAATGGT
1939920 CAGTATGATG
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
15 3 0.08
16 36 0.92
ACGTcount: A:0.27, C:0.00, G:0.33, T:0.40
Consensus pattern (17 bp):
GGAATTAATGGTTTAGT
Found at i:1944248 original size:16 final size:16
Alignment explanation
Indices: 1944219--1944288 Score: 68
Period size: 16 Copynumber: 4.4 Consensus size: 16
1944209 TAGGAATTAG
**
1944219 TGGTTAGTGGAGTTAA
1 TGGTTAGTAAAGTTAA
*
1944235 TGGTCAGTAAAGTTAA
1 TGGTTAGTAAAGTTAA
* **
1944251 TGGTTAATAGTGTTAA
1 TGGTTAGTAAAGTTAA
* *
1944267 CGGTTAGCAAAGTTAA
1 TGGTTAGTAAAGTTAA
1944283 TGGTTA
1 TGGTTA
1944289 ATGTGATGTT
Statistics
Matches: 41, Mismatches: 13, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
16 41 1.00
ACGTcount: A:0.31, C:0.04, G:0.29, T:0.36
Consensus pattern (16 bp):
TGGTTAGTAAAGTTAA
Found at i:1944266 original size:32 final size:32
Alignment explanation
Indices: 1944230--1944290 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
1944220 GGTTAGTGGA
* *
1944230 GTTAATGGTCAGTAAAGTTAATGGTTAATAGT
1 GTTAACGGTCAGCAAAGTTAATGGTTAATAGT
*
1944262 GTTAACGGTTAGCAAAGTTAATGGTTAAT
1 GTTAACGGTCAGCAAAGTTAATGGTTAAT
1944291 GTGATGTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.34, C:0.05, G:0.25, T:0.36
Consensus pattern (32 bp):
GTTAACGGTCAGCAAAGTTAATGGTTAATAGT
Found at i:1947805 original size:32 final size:32
Alignment explanation
Indices: 1947709--1947806 Score: 110
Period size: 32 Copynumber: 3.1 Consensus size: 32
1947699 TGATGAATTG
* * *
1947709 AACATAAATATTCATAAATTTAATTAATATTA
1 AACATAATTACTCATAAATTTAACTAATATTA
* *
1947741 AACAAAATTACT-AGTAAATTTAACAAATATTA
1 AACATAATTACTCA-TAAATTTAACTAATATTA
*
1947773 AACATAATTACTCATAAATTTGA-TAATCATTA
1 AACATAATTACTCATAAATTTAACTAAT-ATTA
1947805 AA
1 AA
1947807 AAATTTCAGC
Statistics
Matches: 55, Mismatches: 8, Indels: 6
0.80 0.12 0.09
Matches are distributed among these distances:
31 4 0.07
32 50 0.91
33 1 0.02
ACGTcount: A:0.53, C:0.09, G:0.02, T:0.36
Consensus pattern (32 bp):
AACATAATTACTCATAAATTTAACTAATATTA
Found at i:1953444 original size:4 final size:4
Alignment explanation
Indices: 1953435--1953461 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1953425 GTACTCAAAG
1953435 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1953462 CAAGAGCTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:1953744 original size:18 final size:18
Alignment explanation
Indices: 1953721--1953756 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1953711 GAATTAAATT
1953721 GAATCCCATTCATTTTTA
1 GAATCCCATTCATTTTTA
1953739 GAATCCCATTCATTTTTA
1 GAATCCCATTCATTTTTA
1953757 AAATATGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.22, G:0.06, T:0.44
Consensus pattern (18 bp):
GAATCCCATTCATTTTTA
Found at i:1954069 original size:42 final size:37
Alignment explanation
Indices: 1953988--1954059 Score: 135
Period size: 37 Copynumber: 1.9 Consensus size: 37
1953978 ATTTTTCATC
*
1953988 TTCCTAGCCTTCGACGCAAGAAAAGAAATTGTATATT
1 TTCCTAGCCTTCGACCCAAGAAAAGAAATTGTATATT
1954025 TTCCTAGCCTTCGACCCAAGAAAAGAAATTGTATA
1 TTCCTAGCCTTCGACCCAAGAAAAGAAATTGTATA
1954060 CATTCTTTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.28
Consensus pattern (37 bp):
TTCCTAGCCTTCGACCCAAGAAAAGAAATTGTATATT
Found at i:1954360 original size:22 final size:21
Alignment explanation
Indices: 1954318--1954387 Score: 65
Period size: 22 Copynumber: 3.2 Consensus size: 21
1954308 TAAATATATT
1954318 AATAATATTAAA-ATATAATAAA
1 AATAATA-TAAATATA-AATAAA
1954340 AATAAT-TATAATATAATATAAA
1 AATAATATA-AATATAA-ATAAA
*
1954362 ATATGATATAAATATAAA-AAA
1 A-ATAATATAAATATAAATAAA
1954383 AATAA
1 AATAA
1954388 ACATAACCTA
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
20 5 0.12
21 7 0.17
22 16 0.39
23 11 0.27
24 2 0.05
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.31
Consensus pattern (21 bp):
AATAATATAAATATAAATAAA
Found at i:1954555 original size:7 final size:6
Alignment explanation
Indices: 1954519--1954551 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
1954509 TTTATTTCTA
1954519 TTAAAT TTAAAT TTAAA- -TAAAT TTAAAT TTAAA
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAA
1954552 ATTTTTAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
4 4 0.16
6 21 0.84
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (6 bp):
TTAAAT
Found at i:1954989 original size:12 final size:12
Alignment explanation
Indices: 1954974--1955005 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
1954964 TTTGATAAAA
1954974 TATTTTTTTATT
1 TATTTTTTTATT
*
1954986 TATTTATTTATT
1 TATTTTTTTATT
1954998 TATTTTTT
1 TATTTTTT
1955006 CATTGTTTGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (12 bp):
TATTTTTTTATT
Found at i:1955586 original size:20 final size:20
Alignment explanation
Indices: 1955542--1955592 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
1955532 TAAAATTTTT
*
1955542 AAAATTTTAATTTTAATTTA
1 AAAATTTAAATTTTAATTTA
*
1955562 TAAATTTAAATTATT-ATTTA
1 AAAATTTAAATT-TTAATTTA
1955582 AAAATATTAAA
1 AAAAT-TTAAA
1955593 AATTATTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 19 0.73
21 7 0.27
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
AAAATTTAAATTTTAATTTA
Found at i:1955629 original size:14 final size:14
Alignment explanation
Indices: 1955606--1955646 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
1955596 TATTAAATAT
*
1955606 ATTTTTATAATTAA
1 ATTTTAATAATTAA
1955620 ATTTTAATAA--AA
1 ATTTTAATAATTAA
*
1955632 ATTTTATTAATTAA
1 ATTTTAATAATTAA
1955646 A
1 A
1955647 AATAATATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
12 11 0.48
14 12 0.52
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
ATTTTAATAATTAA
Found at i:1955851 original size:14 final size:15
Alignment explanation
Indices: 1955827--1955857 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
1955817 ACAATTACTC
1955827 TTTTATATTTAAATA
1 TTTTATATTTAAATA
1955842 TTTT-TATTTAAATA
1 TTTTATATTTAAATA
1955856 TT
1 TT
1955858 ACATATAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
TTTTATATTTAAATA
Found at i:1955975 original size:26 final size:26
Alignment explanation
Indices: 1955926--1955988 Score: 83
Period size: 25 Copynumber: 2.4 Consensus size: 26
1955916 CTAAGCGTTG
*
1955926 TTTTAAAAATATAATTTATTAAAAT-
1 TTTTAAAAATATAATTCATTAAAATA
* *
1955951 TTTTAAATATTTATATTCATTAAAATA
1 TTTTAAAAATATA-ATTCATTAAAATA
1955978 TTTTAAAAATA
1 TTTTAAAAATA
1955989 ATTTATTATT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
25 11 0.35
26 11 0.35
27 9 0.29
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (26 bp):
TTTTAAAAATATAATTCATTAAAATA
Done.