Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 ID=Chr08-JGI_221_v2.0
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: 57128820
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 677448 characters in sequence are not A, C, G, or T
File 150 of 190
Found at i:43950321 original size:71 final size:70
Alignment explanation
Indices: 43950193--43950331 Score: 192
Period size: 71 Copynumber: 2.0 Consensus size: 70
43950183 ATCATGTTTC
*
43950193 AAAAAAAATGTCGTGTTTTAAAAATTTTCGTATTTCTAAAATTTCCCTGTTTTAAAAATTCCCGT
1 AAAAAAAATGTCGTGTTTCAAAAATTTTCGTATTTC-AAAATTTCCCTGTTTTAAAAATTCCCGT
43950258 GTTTTT
65 GTTTTT
* * *
43950264 AAAAAAAATGTCGTGTTTCAAAAATTTTCGTGTTT-ACAAA-TTCTCGTGTTTTCAAAAATTCTC
1 AAAAAAAATGTCGTGTTTCAAAAATTTTCGTATTTCA-AAATTTC-CCTGTTTT-AAAAATTCCC
43950327 GTGTT
63 GTGTT
43950332 AAAAAAAAAC
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
69 4 0.07
70 10 0.16
71 47 0.77
ACGTcount: A:0.32, C:0.13, G:0.12, T:0.43
Consensus pattern (70 bp):
AAAAAAAATGTCGTGTTTCAAAAATTTTCGTATTTCAAAATTTCCCTGTTTTAAAAATTCCCGTG
TTTTT
Found at i:43950336 original size:16 final size:16
Alignment explanation
Indices: 43950283--43950337 Score: 56
Period size: 16 Copynumber: 3.3 Consensus size: 16
43950273 GTCGTGTTTC
* *
43950283 AAAAATTTTCGTGTTT
1 AAAAATTCTCGTGTTA
* *
43950299 ACAAATTCTCGTGTTTTC
1 AAAAATTCTCGTG--TTA
43950317 AAAAATTCTCGTGTTA
1 AAAAATTCTCGTGTTA
43950333 AAAAA
1 AAAAA
43950338 AAACTTTCAT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
16 18 0.56
18 14 0.44
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.40
Consensus pattern (16 bp):
AAAAATTCTCGTGTTA
Found at i:43950338 original size:18 final size:18
Alignment explanation
Indices: 43950301--43950339 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
43950291 TCGTGTTTAC
***
43950301 AAATTCTCGTGTTTTCAA
1 AAATTCTCGTGTTAAAAA
43950319 AAATTCTCGTGTTAAAAA
1 AAATTCTCGTGTTAAAAA
43950337 AAA
1 AAA
43950340 ACTTTCATTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.41, C:0.13, G:0.10, T:0.36
Consensus pattern (18 bp):
AAATTCTCGTGTTAAAAA
Found at i:43962454 original size:76 final size:74
Alignment explanation
Indices: 43962330--43962959 Score: 632
Period size: 75 Copynumber: 8.3 Consensus size: 74
43962320 TCAAGAATTA
* * *
43962330 TATTTTTCAATTTTTGTTTTTCAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGGTC
1 TATTTTTAAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC
43962395 ACGCTGAGG
66 ACGCTGAGG
* *
43962404 TATTTTTAAATTGCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGTCTCGGG
1 TATTTTTAAATTTCTGTTTTTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG
*
43962469 TCACGCCGAGG
64 TCACGCTGAGG
* *
43962480 TATTTCTTTTAAATTT-T-TTTTTCAAAAATCAACTCACATTACGAGAGGTGAGTTGAGCCTCGG
1 TA--T-TTTTAAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG
43962543 GTCATC-CTGAGG
63 GTCA-CGCTGAGG
* * * * *
43962555 TA-TTTTCAATTTCTGTTTTTTAAAAAATCAACTCATATTGTGAGAGGTGAGTTGGGCCTCAGGT
1 TATTTTTAAATTTCTG-TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGT
43962619 CGCACGCTGAGG
65 --CACGCTGAGG
* *
43962631 TA-TTTTAAATTCCTGTTTTTCAAAAATCGACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC
1 TATTTTTAAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGT-
*
43962695 ACACGCCGAGG
65 -CACGCTGAGG
* * * *
43962706 TATTTTTCAATTACTACT-TTTTTAAAAAAAAAAGCAACTCATATTGCGAGAGGTGAGTTGAGCT
1 TATTTTTAAATT--T-CTGTTTTT----CAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
43962770 TCGGGTCACATG-TCGAGG
59 TCGGGTCAC--GCT-GAGG
* * * *
43962788 TATTTTTCAATTTTCTGTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTAAGCCTCAGGT
1 TATTTTT-AAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGT
43962853 CACGCTGAGG
65 CACGCTGAGG
* ** * * *
43962863 TA-TTTTCAATTAATG-TTTTCAAAAAAAAAAATAAACTCATAATCCGAGAGGTGAGTTGAGCCT
1 TATTTTTAAATTTCTGTTTTTC------AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
* * *
43962926 CGAGTCAAGCTGAGA
60 CGGGTCACGCTGAGG
*
43962941 TATTTTTTAATTTCT-TTTT
1 TATTTTTAAATTTCTGTTTT
43962960 CTTTTTCTTT
Statistics
Matches: 466, Mismatches: 56, Indels: 63
0.80 0.10 0.11
Matches are distributed among these distances:
71 9 0.02
72 6 0.01
73 5 0.01
74 65 0.14
75 111 0.24
76 82 0.18
77 46 0.10
78 54 0.12
79 23 0.05
80 5 0.01
81 6 0.01
82 51 0.11
83 3 0.01
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.35
Consensus pattern (74 bp):
TATTTTTAAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC
ACGCTGAGG
Found at i:43962509 original size:151 final size:149
Alignment explanation
Indices: 43962330--43962950 Score: 696
Period size: 149 Copynumber: 4.1 Consensus size: 149
43962320 TCAAGAATTA
* *
43962330 TATTTTTCAATTTTTGTTTTTCAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGGTC
1 TATTTTTTAAATTTTGTTTTTCAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGGTC
* *
43962395 ACGCTGAGGTATTTTTAAATTGCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTG
66 ACGCTGAGGTA-TTTTCAATTACTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTG
*
43962460 AGTCTCGGGTCACGCCGAGG
130 AGCCTCGGGTCACGCCGAGG
*
43962480 TATTTCTTTTAAATTTT-TTTTTCAAAAATCAACTCACATTACGAGAGGTGAGTTGAGCCTCGGG
1 TA-TT-TTTTAAATTTTGTTTTTCAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGG
* * *
43962544 TCATC-CTGAGGTATTTTCAATTTCTGTTTTT-TAAAAAATCAACTCATATTGTGAGAGGTGAGT
64 TCA-CGCTGAGGTATTTTCAATTACTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGT
* * *
43962607 TGGGCCTCAGGTCGCACGCTGAGG
128 TGAGCCTCGGGT--CACGCCGAGG
* * *
43962631 TA--TTTTAAATTCCTGTTTTTCAAAAATCGACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGT
1 TATTTTTTAAATT-TTGTTTTTCAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGGT
* * * *
43962694 CACACGCCGAGGTATTTTTCAATTACTACTTTTTTAAAAAAAAAAGCAACTCATATTGCGAGAGG
65 --CACGCTGAGGTA-TTTTCAATTACT--GTTTTT--CAAAAAAATCAACTCATATTGCGAGAGG
* *
43962759 TGAGTTGAGCTTCGGGTCACATGTCGAGG
123 TGAGTTGAGCCTCGGGTCAC--GCCGAGG
* * * * * *
43962788 TATTTTTCAATTTTCTGTTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTAAGCCTCAGGT
1 TATTTTTTAAATTT-TGTTTTTCAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGGT
* * * *
43962853 CACGCTGAGGTATTTTCAATTAATG-TTTTCAAAAAAAAAAATAAACTCATAATCCGAGAGGTGA
65 CACGCTGAGGTATTTTCAATTACTGTTTTTC----AAAAAAATCAACTCATATTGCGAGAGGTGA
* * * *
43962917 GTTGAGCCTCGAGTCAAGCTGAGA
126 GTTGAGCCTCGGGTCACGCCGAGG
43962941 TATTTTTTAA
1 TATTTTTTAA
43962951 TTTCTTTTTC
Statistics
Matches: 398, Mismatches: 48, Indels: 47
0.81 0.10 0.10
Matches are distributed among these distances:
147 9 0.02
148 1 0.00
149 84 0.21
150 19 0.05
151 79 0.20
152 21 0.05
153 17 0.04
154 5 0.01
155 43 0.11
156 11 0.03
157 56 0.14
159 53 0.13
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.34
Consensus pattern (149 bp):
TATTTTTTAAATTTTGTTTTTCAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGGTC
ACGCTGAGGTATTTTCAATTACTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGA
GCCTCGGGTCACGCCGAGG
Found at i:43963381 original size:30 final size:30
Alignment explanation
Indices: 43963322--43963379 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
43963312 ACAAAAAAAT
*
43963322 AAAAATTACGTTTTGGCCCCCAAACTTTTC
1 AAAAATTACGTTTTGACCCCCAAACTTTTC
* *
43963352 AAAAATTATGTTTT-ACCCCCTAACTTTT
1 AAAAATTACGTTTTGACCCCCAAACTTTT
43963380 TCTAAATTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 12 0.48
30 13 0.52
ACGTcount: A:0.31, C:0.24, G:0.07, T:0.38
Consensus pattern (30 bp):
AAAAATTACGTTTTGACCCCCAAACTTTTC
Found at i:43964073 original size:25 final size:25
Alignment explanation
Indices: 43964045--43964098 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
43964035 AGGAGGGAAG
* *
43964045 AAGAAAGGAGAGAAAA-AAATAGAAA
1 AAGAAAGAAAAGAAAATAAA-AGAAA
*
43964070 AAGAAAGAAAAGAAAATAAAATAAA
1 AAGAAAGAAAAGAAAATAAAAGAAA
43964095 AAGA
1 AAGA
43964099 TAAATAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 22 0.88
26 3 0.12
ACGTcount: A:0.76, C:0.00, G:0.19, T:0.06
Consensus pattern (25 bp):
AAGAAAGAAAAGAAAATAAAAGAAA
Found at i:43964105 original size:17 final size:17
Alignment explanation
Indices: 43964077--43964112 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
43964067 AAAAAGAAAG
43964077 AAAAGAAAAT-AAAATA
1 AAAAGAAAATAAAAATA
43964093 AAAAGATAAATAAAAATA
1 AAAAGA-AAATAAAAATA
43964111 AA
1 AA
43964113 TCAGTCGGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 6 0.33
17 4 0.22
18 8 0.44
ACGTcount: A:0.81, C:0.00, G:0.06, T:0.14
Consensus pattern (17 bp):
AAAAGAAAATAAAAATA
Found at i:43964893 original size:17 final size:17
Alignment explanation
Indices: 43964866--43964911 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 17
43964856 AAAAAAATCG
43964866 TGTTTCAAAAATTT-TCA
1 TGTTTC-AAAATTTCTCA
*
43964883 TGTCTTCAAAATTTCTCG
1 TGT-TTCAAAATTTCTCA
43964901 TGTTTCAAAAT
1 TGTTTCAAAAT
43964912 AATAATAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 18 0.69
18 8 0.31
ACGTcount: A:0.30, C:0.15, G:0.09, T:0.46
Consensus pattern (17 bp):
TGTTTCAAAATTTCTCA
Found at i:43965029 original size:32 final size:31
Alignment explanation
Indices: 43964968--43965029 Score: 72
Period size: 31 Copynumber: 2.0 Consensus size: 31
43964958 TTTCTTTTTT
***
43964968 AAAAAAAAAATTCGTGTTTTCATGTTTTTCA
1 AAAAAAAAAATTCGTGTTTTCAAAATTTTCA
43964999 AAAAAAAAAATCTCGTG-TTTCAAAAATTTTC
1 AAAAAAAAAAT-TCGTGTTTTC-AAAATTTTC
43965030 GTATTTTCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
31 15 0.58
32 11 0.42
ACGTcount: A:0.44, C:0.11, G:0.08, T:0.37
Consensus pattern (31 bp):
AAAAAAAAAATTCGTGTTTTCAAAATTTTCA
Found at i:43965053 original size:17 final size:18
Alignment explanation
Indices: 43965016--43965054 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
43965006 AAATCTCGTG
*
43965016 TTTCAAAAATTTTCGTAT
1 TTTCAAAAATTTTCATAT
*
43965034 TTTC-AAAATTTTCATGT
1 TTTCAAAAATTTTCATAT
43965051 TTTC
1 TTTC
43965055 GTGTTTTCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.28, C:0.13, G:0.05, T:0.54
Consensus pattern (18 bp):
TTTCAAAAATTTTCATAT
Found at i:43965122 original size:18 final size:18
Alignment explanation
Indices: 43965101--43965179 Score: 70
Period size: 19 Copynumber: 4.3 Consensus size: 18
43965091 AGTCGTGTTT
43965101 AAAAAATTTTATGTTTTC
1 AAAAAATTTTATGTTTTC
* **
43965119 -AAAACTTTCGTGTTTTC
1 AAAAAATTTTATGTTTTC
* *
43965136 AAAAATTTTTATGTTTTTA
1 AAAAAATTTTATG-TTTTC
**
43965155 AAAAAATTTTCGCGTTTTC
1 AAAAAATTTT-ATGTTTTC
43965174 AAAAAA
1 AAAAAA
43965180 ATATCTCGTG
Statistics
Matches: 47, Mismatches: 11, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
17 14 0.30
18 9 0.19
19 23 0.49
20 1 0.02
ACGTcount: A:0.38, C:0.09, G:0.08, T:0.46
Consensus pattern (18 bp):
AAAAAATTTTATGTTTTC
Found at i:43965217 original size:18 final size:18
Alignment explanation
Indices: 43965050--43965468 Score: 161
Period size: 17 Copynumber: 22.6 Consensus size: 18
43965040 AATTTTCATG
43965050 TTTTCGTGTTTTCAAAAAA
1 TTTTCGTGTTTTC-AAAAA
* *
43965069 TTCTCGTGTTTTTTTTAAAAA
1 TTTTCGTG---TTTTCAAAAA
*** *
43965090 AAGTCGTG-TTTAAAAAA
1 TTTTCGTGTTTTCAAAAA
*
43965107 TTTT-ATGTTTTC-AAAA
1 TTTTCGTGTTTTCAAAAA
*
43965123 CTTTCGTGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
** *
43965141 TTTTTATGTTTTTAAAAAAA
1 TTTTCGTG-TTTT-CAAAAA
*
43965161 TTTTCGCGTTTTCAAAAAAA
1 TTTTCGTGTTTTC--AAAAA
*
43965181 TATCTCGTG-TTTC--AAA
1 T-TTTCGTGTTTTCAAAAA
43965197 TTTTCGTGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
*
43965215 TTTCTCGT-ATTTCAAAAAAAATATCA
1 TTT-TCGTGTTTTC-----AAA-A--A
43965241 CTTTTCGTGTTTTCAAAAA
1 -TTTTCGTGTTTTCAAAAA
*
43965260 -TTTCTTGTATTTCAAAAA
1 TTTTCGTGT-TTTCAAAAA
** *
43965278 TATTCTCG-CATTTCAAAATTT
1 T-TT-TCGTGTTTTCAAAA--A
43965299 TTTAAATCGTG-TTTCAAAAAAA
1 TTT---TCGTGTTTTC--AAAAA
* *
43965321 ATGTCGTGTTTT-AAAAA
1 TTTTCGTGTTTTCAAAAA
*
43965338 TTTTCGTG-TTTCTAAAA
1 TTTTCGTGTTTTCAAAAA
* *
43965355 TTTCCCTGTTTT-AAAAA
1 TTTTCGTGTTTTCAAAAA
** *
43965372 TTCCCGTGTTTTTAAAAAA
1 TTTTCGTG-TTTTCAAAAA
* *
43965391 ATGTCGTG-TTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
*
43965408 TTTTCGTG-TTTCTAAAA
1 TTTTCGTGTTTTCAAAAA
*
43965425 TTTTCGTG-TTT-ACAAA
1 TTTTCGTGTTTTCAAAAA
*
43965441 TTCTCGTGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
*
43965459 TTCTCGTGTT
1 TTTTCGTGTT
43965469 AAAAAAAAAC
Statistics
Matches: 302, Mismatches: 55, Indels: 87
0.68 0.12 0.20
Matches are distributed among these distances:
15 6 0.02
16 30 0.10
17 93 0.31
18 49 0.16
19 43 0.14
20 27 0.09
21 19 0.06
22 15 0.05
23 3 0.01
24 5 0.02
26 5 0.02
27 7 0.02
ACGTcount: A:0.31, C:0.12, G:0.10, T:0.46
Consensus pattern (18 bp):
TTTTCGTGTTTTCAAAAA
Found at i:43965231 original size:17 final size:17
Alignment explanation
Indices: 43965177--43965231 Score: 51
Period size: 18 Copynumber: 3.2 Consensus size: 17
43965167 CGTTTTCAAA
* *
43965177 AAAATATCTCGTGTTTC
1 AAAATTTCTCGTATTTC
*
43965194 -AAATTT-TCGTGTTTTC
1 AAAATTTCTCGT-ATTTC
43965210 AAAAATTTCTCGTATTTC
1 -AAAATTTCTCGTATTTC
43965228 AAAA
1 AAAA
43965232 AAAATATCAC
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
15 4 0.13
16 9 0.29
17 4 0.13
18 10 0.32
19 4 0.13
ACGTcount: A:0.33, C:0.15, G:0.09, T:0.44
Consensus pattern (17 bp):
AAAATTTCTCGTATTTC
Found at i:43965419 original size:70 final size:69
Alignment explanation
Indices: 43965306--43965458 Score: 225
Period size: 70 Copynumber: 2.2 Consensus size: 69
43965296 TTTTTTAAAT
* *
43965306 CGTGTTTCAAAAAAAATGTCGTGTTTTAAAAATTTTCGTGTTTCTAAAATTTCCCTGTTTTAAAA
1 CGTGTTTTAAAAAAAATGTCGTGTTTCAAAAATTTTCGTGTTTCTAAAATTTCCCTG-TTTAAAA
43965371 ATTCC
65 ATTCC
* * * *
43965376 CGTGTTTTTAAAAAAATGTCGTGTTTCAAAAATTTTCGTGTTTCTAAAATTTTCGTGTTTACAAA
1 CGTGTTTTAAAAAAAATGTCGTGTTTCAAAAATTTTCGTGTTTCTAAAATTTCCCTGTTTAAAAA
*
43965441 TTCT
66 TTCC
*
43965445 CGTGTTTTCAAAAA
1 CGTGTTTTAAAAAA
43965459 TTCTCGTGTT
Statistics
Matches: 75, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
69 23 0.31
70 52 0.69
ACGTcount: A:0.31, C:0.13, G:0.12, T:0.44
Consensus pattern (69 bp):
CGTGTTTTAAAAAAAATGTCGTGTTTCAAAAATTTTCGTGTTTCTAAAATTTCCCTGTTTAAAAA
TTCC
Found at i:43965475 original size:18 final size:18
Alignment explanation
Indices: 43965438--43965476 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
43965428 TCGTGTTTAC
***
43965438 AAATTCTCGTGTTTTCAA
1 AAATTCTCGTGTTAAAAA
43965456 AAATTCTCGTGTTAAAAA
1 AAATTCTCGTGTTAAAAA
43965474 AAA
1 AAA
43965477 ACTTTCGTTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.41, C:0.13, G:0.10, T:0.36
Consensus pattern (18 bp):
AAATTCTCGTGTTAAAAA
Found at i:43970819 original size:13 final size:13
Alignment explanation
Indices: 43970801--43970825 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
43970791 ACCTTTTCGA
43970801 ATCTCAAAATACG
1 ATCTCAAAATACG
43970814 ATCTCAAAATAC
1 ATCTCAAAATAC
43970826 ATAGTTTTAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.24, G:0.04, T:0.24
Consensus pattern (13 bp):
ATCTCAAAATACG
Found at i:43971149 original size:3 final size:3
Alignment explanation
Indices: 43971141--43971165 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
43971131 AAAGGGTATA
43971141 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
43971166 TTATTATTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:43971311 original size:3 final size:3
Alignment explanation
Indices: 43971303--43971561 Score: 209
Period size: 3 Copynumber: 86.0 Consensus size: 3
43971293 ACATAGAAAT
43971303 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
* * * * *
43971351 ATA ATA ATA CAAA ATTA ATG GTA ATA ATC ATA ATA ATA TTA ATA ATA
1 ATA ATA ATA -ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * * * * * * *
43971398 TTA ATA AAA ATA GTA ATA ACA TTA ATA ATA ATT CTA ATA ATG ATG TTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * *
43971446 ATA GTA ATA A-A ATA ACA ATA A-A ACTA ATG ATA ATA ATG CTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA
* * * *
43971490 ATA ATA GTA AGA ATA ATA ATA ATA TTA ATA TTA ATA ATA AT- ATCA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A
* * * *
43971535 ACA ATA CTA ATA CTA CTA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
43971562 GTGTAATATT
Statistics
Matches: 197, Mismatches: 52, Indels: 14
0.75 0.20 0.05
Matches are distributed among these distances:
2 6 0.03
3 184 0.93
4 7 0.04
ACGTcount: A:0.58, C:0.05, G:0.04, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:43978641 original size:22 final size:22
Alignment explanation
Indices: 43978600--43978641 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
43978590 TTGGTTTTTT
* *
43978600 CTTTAAAAAAAATTATATTTGG
1 CTTTAAAAAAAATCACATTTGG
*
43978622 CTTTAAAAAATATCACATTT
1 CTTTAAAAAAAATCACATTT
43978642 AAAGGCAAGG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.45, C:0.10, G:0.05, T:0.40
Consensus pattern (22 bp):
CTTTAAAAAAAATCACATTTGG
Found at i:43978869 original size:21 final size:21
Alignment explanation
Indices: 43978843--43978895 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
43978833 GACTTAAAGA
* *
43978843 TTGGTTACTTGTGGGTCAACT
1 TTGGTTACTTATGGATCAACT
*
43978864 TTGGTTACTTATGGATCAAGT
1 TTGGTTACTTATGGATCAACT
43978885 TTGGTTACTTA
1 TTGGTTACTTA
43978896 CTAATCAAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.19, C:0.11, G:0.25, T:0.45
Consensus pattern (21 bp):
TTGGTTACTTATGGATCAACT
Found at i:43978902 original size:21 final size:21
Alignment explanation
Indices: 43978843--43978905 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
43978833 GACTTAAAGA
* ** *
43978843 TTGGTTACTTGTGGGTCAACT
1 TTGGTTACTTATGAATCAAGT
*
43978864 TTGGTTACTTATGGATCAAGT
1 TTGGTTACTTATGAATCAAGT
43978885 TTGGTTACTTACT-AATCAAGT
1 TTGGTTACTTA-TGAATCAAGT
43978906 AAAGTCACTT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
21 36 0.97
22 1 0.03
ACGTcount: A:0.22, C:0.13, G:0.22, T:0.43
Consensus pattern (21 bp):
TTGGTTACTTATGAATCAAGT
Found at i:43979923 original size:16 final size:16
Alignment explanation
Indices: 43979902--43979935 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
43979892 ATTTTAAAAA
*
43979902 AATTTAAGTTTTTTTT
1 AATTTAAATTTTTTTT
43979918 AATTTAAATTTTTTTT
1 AATTTAAATTTTTTTT
43979934 AA
1 AA
43979936 AAATAATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (16 bp):
AATTTAAATTTTTTTT
Found at i:44000708 original size:107 final size:105
Alignment explanation
Indices: 44000504--44000710 Score: 326
Period size: 107 Copynumber: 2.0 Consensus size: 105
44000494 TAATATTGAT
* * *
44000504 TGAAAGTTAAGAAGATATTTAGCTATTTGGTCGAACGAGAAATCGAAACCCGACACGTTAGGGCA
1 TGAAAGTTAAAAAGATATTTAGCTACTTGGTCGAACGAGAAATCGAAACCCGACACGTTAGCGCA
*
44000569 CGTTTTCTCGATTTTCCAAACGCAAAACATTGCCTCGTTC
66 CGTTTTCTCGATTTTCCAAAAGCAAAACATTGCCTCGTTC
*
44000609 TGAAAGTTTAAAAAGGATATTTTGCTACTTGGTCGAACGAGAAATCGAAACCC-AGCACGTTAGC
1 TGAAAG-TTAAAAA-GATATTTAGCTACTTGGTCGAACGAGAAATCGAAACCCGA-CACGTTAGC
*
44000673 GCACGTTTTCTCGATTTTCCAAAAGCAAAATATTGCCT
63 GCACGTTTTCTCGATTTTCCAAAAGCAAAACATTGCCT
44000711 TATTTAGAAA
Statistics
Matches: 93, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
105 6 0.06
106 7 0.08
107 80 0.86
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.28
Consensus pattern (105 bp):
TGAAAGTTAAAAAGATATTTAGCTACTTGGTCGAACGAGAAATCGAAACCCGACACGTTAGCGCA
CGTTTTCTCGATTTTCCAAAAGCAAAACATTGCCTCGTTC
Found at i:44001176 original size:25 final size:26
Alignment explanation
Indices: 44001148--44001196 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
44001138 ATATGGGTAT
*
44001148 ATATGAATTAT-ATATATAAAGGAAA
1 ATATGAATTATAAAATATAAAGGAAA
* *
44001173 ATATGGATTTTAAAATATAAAGGA
1 ATATGAATTATAAAATATAAAGGA
44001197 TATGCATATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 9 0.45
26 11 0.55
ACGTcount: A:0.53, C:0.00, G:0.14, T:0.33
Consensus pattern (26 bp):
ATATGAATTATAAAATATAAAGGAAA
Found at i:44001343 original size:29 final size:31
Alignment explanation
Indices: 44001284--44001371 Score: 85
Period size: 31 Copynumber: 3.0 Consensus size: 31
44001274 ATATACATTT
*
44001284 ATATATATATATATATATATATTAACAAAAC
1 ATATATATATATATATATATAGTAACAAAAC
* * *
44001315 ATATGTATATATATATATATGGT-A-GAAAC
1 ATATATATATATATATATATAGTAACAAAAC
* * *
44001344 GTATATATATTTA-ATGTATA-TAACAAAA
1 ATATATATATATATATATATAGTAACAAAA
44001372 TTAAGATTAA
Statistics
Matches: 45, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
27 1 0.02
28 6 0.13
29 17 0.38
30 1 0.02
31 20 0.44
ACGTcount: A:0.50, C:0.05, G:0.07, T:0.39
Consensus pattern (31 bp):
ATATATATATATATATATATAGTAACAAAAC
Found at i:44003249 original size:40 final size:40
Alignment explanation
Indices: 44003200--44003338 Score: 147
Period size: 40 Copynumber: 3.4 Consensus size: 40
44003190 CCACTATTAT
44003200 TTAGGGAGATAAGACTTGATACGATCTGATCCACTACTGC
1 TTAGGGAGATAAGACTTGATACGATCTGATCCACTACTGC
* ** * *
44003240 TTAGTGAGATAAGATCGGTTTCTTTCG-TCTGCTCCACTACTGC
1 TTAGGGAGATAAGA-C---TTGATACGATCTGATCCACTACTGC
**
44003283 TTAGGGAGATAAGACTTGATGTGATCT-ACTCCACTACTGC
1 TTAGGGAGATAAGACTTGATACGATCTGA-TCCACTACTGC
*
44003323 TTAGGGAGATAGGACT
1 TTAGGGAGATAAGACT
44003339 GGTGGCTTAA
Statistics
Matches: 81, Mismatches: 12, Indels: 12
0.77 0.11 0.11
Matches are distributed among these distances:
39 4 0.05
40 42 0.52
41 1 0.01
42 1 0.01
43 28 0.35
44 5 0.06
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (40 bp):
TTAGGGAGATAAGACTTGATACGATCTGATCCACTACTGC
Found at i:44003263 original size:83 final size:83
Alignment explanation
Indices: 44003159--44003333 Score: 246
Period size: 83 Copynumber: 2.1 Consensus size: 83
44003149 CTGTAACTTC
* * * *
44003159 AGGGAGATAGGATTGGTTTC-TTCTGTCTGCTCCACTATTATTTAGGGAGATAAGACTTGATACG
1 AGGGAGATAAGATCGGTTTCTTTC-GTCTGCTCCACTACTACTTAGGGAGATAAGACTTGATACG
44003223 ATCTGA-TCCACTACTGCTT
65 ATCT-ACTCCACTACTGCTT
* * **
44003242 AGTGAGATAAGATCGGTTTCTTTCGTCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGTGA
1 AGGGAGATAAGATCGGTTTCTTTCGTCTGCTCCACTACTACTTAGGGAGATAAGACTTGATACGA
44003307 TCTACTCCACTACTGCTT
66 TCTACTCCACTACTGCTT
44003325 AGGGAGATA
1 AGGGAGATA
44003334 GGACTGGTGG
Statistics
Matches: 81, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
82 1 0.01
83 77 0.95
84 3 0.04
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (83 bp):
AGGGAGATAAGATCGGTTTCTTTCGTCTGCTCCACTACTACTTAGGGAGATAAGACTTGATACGA
TCTACTCCACTACTGCTT
Found at i:44003361 original size:83 final size:83
Alignment explanation
Indices: 44003200--44003379 Score: 211
Period size: 83 Copynumber: 2.2 Consensus size: 83
44003190 CCACTATTAT
* ** *
44003200 TTAGGGAGATAAGACTTGATACGATCTGATCCACTACTGCTTAGTGAGATAAGATCGGTTTCTTT
1 TTAGGGAGATAAGACTTGATACGATCTGATCCACTACTGCTTAGGGAGATAAGATCGGTGGCTTA
** *
44003265 CGTCTGCTCCACTACTGC
66 AATCTACTCCACTACTGC
** *
44003283 TTAGGGAGATAAGACTTGATGTGATCT-ACTCCACTACTGCTTAGGGAGATAGGA-CTGGTGGCT
1 TTAGGGAGATAAGACTTGATACGATCTGA-TCCACTACTGCTTAGGGAGATAAGATC-GGTGGCT
*
44003346 TAAATCTACTTCACTACTGC
64 TAAATCTACTCCACTACTGC
* *
44003366 TTAGGAAGTTAAGA
1 TTAGGGAGATAAGA
44003380 TTCGCCGTCT
Statistics
Matches: 82, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
82 2 0.02
83 80 0.98
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31
Consensus pattern (83 bp):
TTAGGGAGATAAGACTTGATACGATCTGATCCACTACTGCTTAGGGAGATAAGATCGGTGGCTTA
AATCTACTCCACTACTGC
Found at i:44003367 original size:43 final size:40
Alignment explanation
Indices: 44003200--44003379 Score: 130
Period size: 43 Copynumber: 4.3 Consensus size: 40
44003190 CCACTATTAT
***
44003200 TTAGGGAGATAAGACTTGATACGATCTGA-TCCACTACTGC
1 TTAGGGAGATAAGACTTGATGTAATCT-ACTCCACTACTGC
* ** * ** *
44003240 TTAGTGAGATAAGATCGGTTTCTTTCGTCTGCTCCACTACTGC
1 TTAGGGAGATAAGA-C--TTGATGTAATCTACTCCACTACTGC
*
44003283 TTAGGGAGATAAGACTTGATGTGATCTACTCCACTACTGC
1 TTAGGGAGATAAGACTTGATGTAATCTACTCCACTACTGC
* * *
44003323 TTAGGGAGATAGGAC-TGGTGGCTTAAATCTACTTCACTACTGC
1 TTAGGGAGATAAGACTTGAT-G--T-AATCTACTCCACTACTGC
* *
44003366 TTAGGAAGTTAAGA
1 TTAGGGAGATAAGA
44003380 TTCGCCGTCT
Statistics
Matches: 110, Mismatches: 22, Indels: 13
0.76 0.15 0.09
Matches are distributed among these distances:
39 3 0.03
40 47 0.43
41 1 0.01
42 2 0.02
43 57 0.52
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31
Consensus pattern (40 bp):
TTAGGGAGATAAGACTTGATGTAATCTACTCCACTACTGC
Found at i:44003540 original size:86 final size:86
Alignment explanation
Indices: 44003412--44003936 Score: 649
Period size: 86 Copynumber: 5.8 Consensus size: 86
44003402 ACTACTGCTG
* * * * *
44003412 AGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCGCTACAACCGA-GAGAAGCAAGGCTTTGTTT
1 AGGAAGGCAAGATCTGCT-TCTTTAACCAGCTCCACTGCAACCGATG-GAGGCAAGGCTTTGTTT
*
44003476 TCGATCTGCTTCGCTGTTAATGC
64 TCGATCTGCTTCGCTGTTAACGC
*
44003499 AGGAAGGCAAGATCCGCTTCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTC
1 AGGAAGGCAAGATCTGCTTCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTC
*
44003564 GATCTGCTTCGCTGTTAATGC
66 GATCTGCTTCGCTGTTAACGC
* *
44003585 AGGAAGGCAAGATCTGCTTCTTTAACCAGCTCCACTACAACCGATGGAGGCAAGGCTTTATTTTC
1 AGGAAGGCAAGATCTGCTTCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTC
*
44003650 GATTTGCTTCGCTGTTAACGC
66 GATCTGCTTCGCTGTTAACGC
*
44003671 AGGATGGCAAGATCTGCTTCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTT
1 AGGAAGGCAAGATCTGCTTCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTG---TT
*
44003736 TATCTGCTTCGCTGTTAACTTCGCTGTTAACGC
63 T-TC-G-AT--CTG----CTTCGCTGTTAACGC
* *
44003769 AGGAAGGCAAGATCTGCTTCTTTAACCAGCTCCATTGCAACCGATGGAGGCAAGGCTTTATTTTC
1 AGGAAGGCAAGATCTGCTTCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTC
44003834 GATCTGCTTCACTGTTAACTTCGCTGTTAACGC
66 GA------T--CTG----CTTCGCTGTTAACGC
*
44003867 AGGAAGGCAAGATCTGCTTCTTTAACCAGCTCCACTGCAACCGATAGAGGCAAGGCTTTGTCTTT
1 AGGAAGGCAAGATCTGCTTCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGT-TTT
44003932 -GATCT
65 CGATCT
44003937 TCACTGATCT
Statistics
Matches: 394, Mismatches: 24, Indels: 37
0.87 0.05 0.08
Matches are distributed among these distances:
86 200 0.51
87 17 0.04
89 3 0.01
90 4 0.01
91 1 0.00
92 2 0.01
93 1 0.00
94 4 0.01
95 3 0.01
98 156 0.40
99 3 0.01
ACGTcount: A:0.23, C:0.25, G:0.23, T:0.29
Consensus pattern (86 bp):
AGGAAGGCAAGATCTGCTTCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTC
GATCTGCTTCGCTGTTAACGC
Found at i:44003593 original size:43 final size:43
Alignment explanation
Indices: 44003462--44003595 Score: 105
Period size: 43 Copynumber: 3.1 Consensus size: 43
44003452 ACCGAGAGAA
44003462 GCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAATGCAGGAAG
1 GCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAATGCAGGAAG
* ** ** * * * * * *
44003505 GCAA-GATCCGCTTCTTTAACCAGCTCCACTG-CAA-CCGATGG-AG
1 GCAAGGCTTTG-TT-TTCGATCTGCTTCGCTGTTAATGC-A-GGAAG
44003548 GCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAATGCAGGAAG
1 GCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAATGCAGGAAG
44003591 GCAAG
1 GCAAG
44003596 ATCTGCTTCT
Statistics
Matches: 61, Mismatches: 22, Indels: 16
0.62 0.22 0.16
Matches are distributed among these distances:
42 17 0.28
43 27 0.44
44 17 0.28
ACGTcount: A:0.22, C:0.23, G:0.26, T:0.29
Consensus pattern (43 bp):
GCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAATGCAGGAAG
Found at i:44003723 original size:43 final size:43
Alignment explanation
Indices: 44003503--44003724 Score: 113
Period size: 43 Copynumber: 5.2 Consensus size: 43
44003493 TAATGCAGGA
*
44003503 AGGCAAGATCCGCTTCTTTAACCAGCTCCACTGCAACCGATGG
1 AGGCAAGATCTGCTTCTTTAACCAGCTCCACTGCAACCGATGG
* * ** * * * * * *
44003546 AGGCAAGGCTTTG-TT-TTCGATCTGCTTCGCTGTTAA-TGCA-GG
1 AGGCAA-GATCTGCTTCTTTAACCAGCTCCACTG-CAACCG-ATGG
*
44003588 AAGGCAAGATCTGCTTCTTTAACCAGCTCCACTACAACCGATGG
1 -AGGCAAGATCTGCTTCTTTAACCAGCTCCACTGCAACCGATGG
* * * * * * *
44003632 AGGCAAG-GCT--TTATTT-TCGATTTGCTTCGCTGTTAA-CGCA-GG
1 AGGCAAGATCTGCTTCTTTAACCA---GCTCCACTG-CAACCG-ATGG
44003674 ATGGCAAGATCTGCTTCTTTAACCAGCTCCACTGCAACCGATGG
1 A-GGCAAGATCTGCTTCTTTAACCAGCTCCACTGCAACCGATGG
44003718 AGGCAAG
1 AGGCAAG
44003725 GCTTTGTTTT
Statistics
Matches: 122, Mismatches: 37, Indels: 40
0.61 0.19 0.20
Matches are distributed among these distances:
39 2 0.02
40 5 0.04
42 31 0.25
43 47 0.39
44 30 0.25
46 5 0.04
47 2 0.02
ACGTcount: A:0.24, C:0.26, G:0.23, T:0.27
Consensus pattern (43 bp):
AGGCAAGATCTGCTTCTTTAACCAGCTCCACTGCAACCGATGG
Found at i:44003759 original size:12 final size:12
Alignment explanation
Indices: 44003742--44003766 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
44003732 TTTTTATCTG
44003742 CTTCGCTGTTAA
1 CTTCGCTGTTAA
44003754 CTTCGCTGTTAA
1 CTTCGCTGTTAA
44003766 C
1 C
44003767 GCAGGAAGGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.28, G:0.16, T:0.40
Consensus pattern (12 bp):
CTTCGCTGTTAA
Found at i:44003825 original size:98 final size:98
Alignment explanation
Indices: 44003570--44003936 Score: 542
Period size: 98 Copynumber: 3.9 Consensus size: 98
44003560 TTTCGATCTG
* *
44003570 CTTCGCTGTTAATGCAGGAAGGCAAGATCTGCTTCTTTAACCAGCTCCACTACAACCGATGGAGG
1 CTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTTCTTTAACCAGCTCCACTGCAACCGATGGAGG
* *
44003635 CAAGGC------TTT-AT-T--TTCGAT-TT-G
66 CAAGGCTTTGTTTTTGATCTGCTTCGCTGTTAA
*
44003656 CTTCGCTGTTAACGCAGGATGGCAAGATCTGCTTCTTTAACCAGCTCCACTGCAACCGATGGAGG
1 CTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTTCTTTAACCAGCTCCACTGCAACCGATGGAGG
*
44003721 CAAGGCTTTGTTTTTTATCTGCTTCGCTGTTAA
66 CAAGGCTTTGTTTTTGATCTGCTTCGCTGTTAA
*
44003754 CTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTTCTTTAACCAGCTCCATTGCAACCGATGGAGG
1 CTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTTCTTTAACCAGCTCCACTGCAACCGATGGAGG
* * *
44003819 CAAGGCTTTATTTTCGATCTGCTTCACTGTTAA
66 CAAGGCTTTGTTTTTGATCTGCTTCGCTGTTAA
*
44003852 CTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTTCTTTAACCAGCTCCACTGCAACCGATAGAGG
1 CTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTTCTTTAACCAGCTCCACTGCAACCGATGGAGG
*
44003917 CAAGGCTTTGTCTTTGATCT
66 CAAGGCTTTGTTTTTGATCT
44003937 TCACTGATCT
Statistics
Matches: 253, Mismatches: 16, Indels: 12
0.90 0.06 0.04
Matches are distributed among these distances:
86 68 0.27
92 3 0.01
93 2 0.01
94 1 0.00
96 5 0.02
97 2 0.01
98 172 0.68
ACGTcount: A:0.23, C:0.25, G:0.22, T:0.31
Consensus pattern (98 bp):
CTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTTCTTTAACCAGCTCCACTGCAACCGATGGAGG
CAAGGCTTTGTTTTTGATCTGCTTCGCTGTTAA
Found at i:44005171 original size:6 final size:6
Alignment explanation
Indices: 44005160--44005190 Score: 53
Period size: 6 Copynumber: 5.0 Consensus size: 6
44005150 TTAGCCTCTC
44005160 CATTTT CATTTTT CATTTT CATTTT CATTTT
1 CATTTT CA-TTTT CATTTT CATTTT CATTTT
44005191 TCATCTCTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 18 0.75
7 6 0.25
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.68
Consensus pattern (6 bp):
CATTTT
Found at i:44005174 original size:7 final size:7
Alignment explanation
Indices: 44005162--44005194 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
44005152 AGCCTCTCCA
44005162 TTTTCAT
1 TTTTCAT
44005169 TTTTCA-
1 TTTTCAT
44005175 TTTTCA-
1 TTTTCAT
44005181 TTTTCAT
1 TTTTCAT
44005188 TTTTCAT
1 TTTTCAT
44005195 CTCTCTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 12 0.48
7 13 0.52
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.70
Consensus pattern (7 bp):
TTTTCAT
Found at i:44005203 original size:19 final size:19
Alignment explanation
Indices: 44005160--44005203 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
44005150 TTAGCCTCTC
*
44005160 CATTTTCATTTTTCATTTT
1 CATTTTCATTTTTCATTCT
44005179 CATTTTCATTTTTCATCTCT
1 CATTTTCATTTTTCAT-TCT
44005199 C-TTTT
1 CATTTT
44005204 TTTTTTGAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 20 0.87
20 3 0.13
ACGTcount: A:0.14, C:0.20, G:0.00, T:0.66
Consensus pattern (19 bp):
CATTTTCATTTTTCATTCT
Found at i:44005596 original size:51 final size:47
Alignment explanation
Indices: 44005569--44005656 Score: 119
Period size: 45 Copynumber: 1.9 Consensus size: 47
44005559 TTTCATATTT
44005569 TTATTTTGACTTTGATTGATT-TCTC-TTTCTCTTTTTCTTTTTTTA
1 TTATTTTGACTTTGATTGATTCTCTCTTTTCTCTTTTTCTTTTTTTA
* ** *
44005614 TTATTTTGATTTTGATTTTTTCTCTCTTTTC-CTTTTCCTTTTT
1 TTATTTTGACTTTGATTGATTCTCTCTTTTCTCTTTTTCTTTTT
44005657 CGAATCGGAT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
45 18 0.49
46 15 0.41
47 4 0.11
ACGTcount: A:0.09, C:0.15, G:0.06, T:0.70
Consensus pattern (47 bp):
TTATTTTGACTTTGATTGATTCTCTCTTTTCTCTTTTTCTTTTTTTA
Found at i:44015184 original size:21 final size:21
Alignment explanation
Indices: 44015158--44015200 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
44015148 ATTGGGTGGA
44015158 TCAGCTCTTACGAGCTTCTGT
1 TCAGCTCTTACGAGCTTCTGT
* *
44015179 TCAGCTCTTATGAGCTTTTGT
1 TCAGCTCTTACGAGCTTCTGT
44015200 T
1 T
44015201 GGCGTATTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.14, C:0.23, G:0.19, T:0.44
Consensus pattern (21 bp):
TCAGCTCTTACGAGCTTCTGT
Found at i:44026778 original size:4 final size:4
Alignment explanation
Indices: 44026769--44026819 Score: 102
Period size: 4 Copynumber: 12.8 Consensus size: 4
44026759 TACAAACATA
44026769 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
44026817 TAT
1 TAT
44026820 TTGCAAAATA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 47 1.00
ACGTcount: A:0.25, C:0.00, G:0.24, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:44028734 original size:9 final size:9
Alignment explanation
Indices: 44028720--44028750 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
44028710 GTTAAACGAA
44028720 TCGAGTTAT
1 TCGAGTTAT
*
44028729 TCGAGTTAA
1 TCGAGTTAT
44028738 TCGAGTTAT
1 TCGAGTTAT
44028747 TCGA
1 TCGA
44028751 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:44029081 original size:30 final size:30
Alignment explanation
Indices: 44029047--44029104 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
44029037 AAACTTTTTA
*
44029047 TTTTCCCCCAAAATTTTTACTCCCTTCCAC
1 TTTTCCCCCAAAACTTTTACTCCCTTCCAC
* * *
44029077 TTTTCCCCTAAAACTTTTATTCTCTTCC
1 TTTTCCCCCAAAACTTTTACTCCCTTCC
44029105 CATCCCACCT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.19, C:0.36, G:0.00, T:0.45
Consensus pattern (30 bp):
TTTTCCCCCAAAACTTTTACTCCCTTCCAC
Found at i:44033265 original size:10 final size:10
Alignment explanation
Indices: 44033246--44033293 Score: 50
Period size: 10 Copynumber: 5.2 Consensus size: 10
44033236 TTCTTTTATT
44033246 AAAAAT-TAA
1 AAAAATATAA
44033255 AAAAATAT--
1 AAAAATATAA
*
44033263 -AAAATATAT
1 AAAAATATAA
*
44033272 AGAAATATAA
1 AAAAATATAA
44033282 AAAAATATAA
1 AAAAATATAA
44033292 AA
1 AA
44033294 TTTTATAAAG
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
7 7 0.22
9 6 0.19
10 19 0.59
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (10 bp):
AAAAATATAA
Found at i:44033265 original size:17 final size:18
Alignment explanation
Indices: 44033245--44033293 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 18
44033235 CTTCTTTTAT
44033245 TAAAAAT-TAAAAAAATA
1 TAAAAATATAAAAAAATA
* *
44033262 TAAAATATATAGAAATATA
1 TAAAA-ATATAAAAAAATA
*
44033281 AAAAAATATAAAA
1 TAAAAATATAAAA
44033294 TTTTATAAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 5 0.19
18 9 0.35
19 12 0.46
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.24
Consensus pattern (18 bp):
TAAAAATATAAAAAAATA
Found at i:44033540 original size:30 final size:30
Alignment explanation
Indices: 44033504--44033596 Score: 102
Period size: 29 Copynumber: 3.2 Consensus size: 30
44033494 GTTGTTAATT
44033504 TTTTTTATGATTTTTTATAAAATTTTACAA
1 TTTTTTATGATTTTTTATAAAATTTTACAA
*** *
44033534 TTTTTTATGA-TTTTTATAAAAAAAT-CTA
1 TTTTTTATGATTTTTTATAAAATTTTACAA
* *
44033562 TTTTTTAT-ATTTTTTATTAAAATTTAATAA
1 TTTTTTATGATTTTTTA-TAAAATTTTACAA
44033592 TTTTT
1 TTTTT
44033597 CTAAAATTTA
Statistics
Matches: 50, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
27 1 0.02
28 16 0.32
29 17 0.34
30 16 0.32
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.61
Consensus pattern (30 bp):
TTTTTTATGATTTTTTATAAAATTTTACAA
Found at i:44033595 original size:29 final size:28
Alignment explanation
Indices: 44033505--44033596 Score: 82
Period size: 30 Copynumber: 3.2 Consensus size: 28
44033495 TTGTTAATTT
*
44033505 TTTTTATGATTTTTTATAAAATTTTACAA
1 TTTTTATGATTTTTTATAAAA-TTTATAA
* *
44033534 TTTTTTATGATTTTTATAAAAAAATCTAT--
1 -TTTTTATGATTTTT-T-ATAAAATTTATAA
44033563 TTTTTAT-ATTTTTTATTAAAATTTAATAA
1 TTTTTATGATTTTTTA-TAAAATTT-ATAA
44033592 TTTTT
1 TTTTT
44033597 CTAAAATTTA
Statistics
Matches: 51, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
25 1 0.02
26 7 0.14
27 8 0.16
28 7 0.14
29 5 0.10
30 14 0.27
31 4 0.08
32 5 0.10
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (28 bp):
TTTTTATGATTTTTTATAAAATTTATAA
Found at i:44033611 original size:18 final size:19
Alignment explanation
Indices: 44033565--44033612 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
44033555 AAATCTATTT
* *
44033565 TTTATATTTTTTATTAAAA
1 TTTATAATTTTTACTAAAA
44033584 TTTAATAATTTTT-CTAAAA
1 TTT-ATAATTTTTACTAAAA
44033603 TTTATAATTT
1 TTTATAATTT
44033613 ATTATAATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 7 0.27
19 11 0.42
20 8 0.31
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (19 bp):
TTTATAATTTTTACTAAAA
Found at i:44033738 original size:87 final size:88
Alignment explanation
Indices: 44033642--44033816 Score: 244
Period size: 88 Copynumber: 2.0 Consensus size: 88
44033632 TTTTAATAAG
* * * *
44033642 AGTAGGGGCTTAATTGC-TTTTTTGAAAAATTTTGAGGGTCTTTTTGATGCATTTTGAGAGTTCA
1 AGTAAGGGCTTAATTGCTTTTTTTGAAAAAGTTTGAGGGCCTTTTTGATGCATTTTGAAAGTTCA
44033706 AGTACCCAATTGAGTGAAAAAAA
66 AGTACCCAATTGAGTGAAAAAAA
* **
44033729 AGTAAGGGCTTAATTGCTTTTTTTGAAGAAGTTTGAGGGCCTTTTTGATGTTTTTTGAAAGTTCA
1 AGTAAGGGCTTAATTGCTTTTTTTGAAAAAGTTTGAGGGCCTTTTTGATGCATTTTGAAAGTTCA
* * * *
44033794 CGTGCTCAATTGAGTGCAAAAAA
66 AGTACCCAATTGAGTGAAAAAAA
44033817 GGAGGGACTT
Statistics
Matches: 76, Mismatches: 11, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
87 16 0.21
88 60 0.79
ACGTcount: A:0.29, C:0.10, G:0.23, T:0.38
Consensus pattern (88 bp):
AGTAAGGGCTTAATTGCTTTTTTTGAAAAAGTTTGAGGGCCTTTTTGATGCATTTTGAAAGTTCA
AGTACCCAATTGAGTGAAAAAAA
Found at i:44036769 original size:2 final size:2
Alignment explanation
Indices: 44036756--44036794 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
44036746 GTGATACCCT
*
44036756 TC TC TC TT 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 TC TC T
44036795 TTAAATATTG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.46, G:0.00, T:0.54
Consensus pattern (2 bp):
TC
Found at i:44038015 original size:22 final size:22
Alignment explanation
Indices: 44037990--44038032 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
44037980 GACATGGCTA
44037990 ACGTACTAAGCTCTCATGTTTC
1 ACGTACTAAGCTCTCATGTTTC
44038012 ACGTACTAAGCTCTCATGTTT
1 ACGTACTAAGCTCTCATGTTT
44038033 GAACAATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.23, C:0.26, G:0.14, T:0.37
Consensus pattern (22 bp):
ACGTACTAAGCTCTCATGTTTC
Found at i:44038479 original size:60 final size:59
Alignment explanation
Indices: 44038298--44038479 Score: 192
Period size: 58 Copynumber: 3.1 Consensus size: 59
44038288 CTTTAGGATT
* * * *
44038298 TTCAAGGACC-AAATTGGACCCAAAAAAATTCAAGTCCCAATGTGGGAACATTTGCCAAA
1 TTCAAGG-CCTAACTTGGACCCAAAAAAATTCAAGCCCCAATGTGGGAACAATTACCAAA
* * ** *
44038357 TTCAAGGTCTAACTT-GA-CCAAAAAAAGTTC-AGACCCCTATGTGGGAACAATTATTAAG
1 TTCAAGGCCTAACTTGGACCCAAAAAAA-TTCAAG-CCCCAATGTGGGAACAATTACCAAA
* * *
44038415 TTCAAGGCCTAACTTGGACCCAAAAAATTTTCAAGCCCCAATGTGAGAAAAATTACCAAA
1 TTCAAGGCCTAACTTGGACCCAAAAAA-ATTCAAGCCCCAATGTGGGAACAATTACCAAA
44038475 TTCAA
1 TTCAA
44038480 ACCTCAAAAT
Statistics
Matches: 99, Mismatches: 17, Indels: 13
0.77 0.13 0.10
Matches are distributed among these distances:
57 11 0.11
58 38 0.38
59 13 0.13
60 35 0.35
61 2 0.02
ACGTcount: A:0.40, C:0.21, G:0.15, T:0.23
Consensus pattern (59 bp):
TTCAAGGCCTAACTTGGACCCAAAAAAATTCAAGCCCCAATGTGGGAACAATTACCAAA
Found at i:44047545 original size:19 final size:19
Alignment explanation
Indices: 44047523--44047566 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
44047513 AATTTCTAAA
44047523 AAAAATT-AAAATAATTT-T
1 AAAAATTAAAAAT-ATTTAT
*
44047541 TAAAATTAAAAATATTTAT
1 AAAAATTAAAAATATTTAT
44047560 AAAAATT
1 AAAAATT
44047567 CCAAAAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 10 0.45
19 12 0.55
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
AAAAATTAAAAATATTTAT
Found at i:44047557 original size:18 final size:18
Alignment explanation
Indices: 44047524--44047563 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
44047514 ATTTCTAAAA
*
44047524 AAAATTAAAATAATTTTT
1 AAAATTAAAATAATTTAT
44047542 AAAATTAAAA-ATATTTAT
1 AAAATTAAAATA-ATTTAT
44047560 AAAA
1 AAAA
44047564 ATTCCAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 1 0.05
18 19 0.95
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
AAAATTAAAATAATTTAT
Found at i:44055008 original size:14 final size:15
Alignment explanation
Indices: 44054982--44055011 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
44054972 TCAAAATATT
44054982 AAATAATTATGTTTA
1 AAATAATTATGTTTA
44054997 AAATAATT-TGTTTA
1 AAATAATTATGTTTA
44055011 A
1 A
44055012 CTTTTTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (15 bp):
AAATAATTATGTTTA
Found at i:44063291 original size:3 final size:3
Alignment explanation
Indices: 44063283--44063353 Score: 142
Period size: 3 Copynumber: 23.7 Consensus size: 3
44063273 TAGCATGTAA
44063283 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
44063331 AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AA
44063354 CAAACAAAAA
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 68 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:44065681 original size:31 final size:31
Alignment explanation
Indices: 44065643--44065704 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
44065633 AGGCAAATTA
44065643 CAAGAGTAATTGAATCCTAATAAAACTCTTT
1 CAAGAGTAATTGAATCCTAATAAAACTCTTT
44065674 CAAGAGTAATTGAATCCTAATAAAACTCTTT
1 CAAGAGTAATTGAATCCTAATAAAACTCTTT
44065705 AAAATTATCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.42, C:0.16, G:0.10, T:0.32
Consensus pattern (31 bp):
CAAGAGTAATTGAATCCTAATAAAACTCTTT
Found at i:44071255 original size:12 final size:12
Alignment explanation
Indices: 44071238--44071294 Score: 51
Period size: 12 Copynumber: 4.4 Consensus size: 12
44071228 AGTAGGCAAC
44071238 TTTTTTTTGCGG
1 TTTTTTTTGCGG
*
44071250 TTTTTTTTTGCGCTTT
1 -TTTTTTTTGCG---G
*
44071266 TTTTTTTTGCCG
1 TTTTTTTTGCGG
*
44071278 TTTTTTTTGCGC
1 TTTTTTTTGCGG
44071290 TTTTT
1 TTTTT
44071295 GCTTTTTTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
12 15 0.42
13 11 0.31
15 10 0.28
ACGTcount: A:0.00, C:0.12, G:0.16, T:0.72
Consensus pattern (12 bp):
TTTTTTTTGCGG
Found at i:44071256 original size:13 final size:13
Alignment explanation
Indices: 44071238--44071294 Score: 62
Period size: 13 Copynumber: 4.3 Consensus size: 13
44071228 AGTAGGCAAC
44071238 TTTTTTTTGCGGT
1 TTTTTTTTGCGGT
*
44071251 TTTTTTTTGCGCTTT
1 TTTTTTTTGCG--GT
*
44071266 TTTTTTTTGCCG-
1 TTTTTTTTGCGGT
*
44071278 TTTTTTTTGCGCT
1 TTTTTTTTGCGGT
44071291 TTTT
1 TTTT
44071295 GCTTTTTTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
12 10 0.28
13 15 0.42
15 11 0.31
ACGTcount: A:0.00, C:0.12, G:0.16, T:0.72
Consensus pattern (13 bp):
TTTTTTTTGCGGT
Found at i:44071258 original size:15 final size:15
Alignment explanation
Indices: 44071238--44071285 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
44071228 AGTAGGCAAC
44071238 TTTTTTTTGCGG--T
1 TTTTTTTTGCGGTTT
*
44071251 TTTTTTTTGCGCTTT
1 TTTTTTTTGCGGTTT
*
44071266 TTTTTTTTGCCGTTT
1 TTTTTTTTGCGGTTT
44071281 TTTTT
1 TTTTT
44071286 GCGCTTTTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
13 11 0.37
15 19 0.63
ACGTcount: A:0.00, C:0.10, G:0.15, T:0.75
Consensus pattern (15 bp):
TTTTTTTTGCGGTTT
Found at i:44071281 original size:27 final size:28
Alignment explanation
Indices: 44071238--44071294 Score: 98
Period size: 27 Copynumber: 2.1 Consensus size: 28
44071228 AGTAGGCAAC
*
44071238 TTTTTTTTGCGGTTTTTTTTTGCGCTTT
1 TTTTTTTTGCCGTTTTTTTTTGCGCTTT
44071266 TTTTTTTTGCCG-TTTTTTTTGCGCTTT
1 TTTTTTTTGCCGTTTTTTTTTGCGCTTT
44071293 TT
1 TT
44071295 GCTTTTTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
27 17 0.61
28 11 0.39
ACGTcount: A:0.00, C:0.12, G:0.16, T:0.72
Consensus pattern (28 bp):
TTTTTTTTGCCGTTTTTTTTTGCGCTTT
Found at i:44071300 original size:28 final size:28
Alignment explanation
Indices: 44071241--44071301 Score: 88
Period size: 27 Copynumber: 2.2 Consensus size: 28
44071231 AGGCAACTTT
* *
44071241 TTTTTGCGGTTTTTTTTTGCGCTTTTTT
1 TTTTTGCCGTTTTTTTTTGCGCTTTTTC
44071269 TTTTTGCCG-TTTTTTTTGCGCTTTTTGC
1 TTTTTGCCGTTTTTTTTTGCGCTTTTT-C
44071297 TTTTT
1 TTTTT
44071302 TTTAAAGAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 17 0.57
28 13 0.43
ACGTcount: A:0.00, C:0.13, G:0.16, T:0.70
Consensus pattern (28 bp):
TTTTTGCCGTTTTTTTTTGCGCTTTTTC
Found at i:44071847 original size:31 final size:31
Alignment explanation
Indices: 44071812--44071873 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
44071802 AAGCAAATTA
44071812 CAAGAGTAATTGAATCCTAACAAAACTCTTT
1 CAAGAGTAATTGAATCCTAACAAAACTCTTT
*
44071843 CAAGAGTAATTGAATCCTAATAAAACTCTTT
1 CAAGAGTAATTGAATCCTAACAAAACTCTTT
44071874 AAAATTATCT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.42, C:0.18, G:0.10, T:0.31
Consensus pattern (31 bp):
CAAGAGTAATTGAATCCTAACAAAACTCTTT
Found at i:44073979 original size:6 final size:6
Alignment explanation
Indices: 44073968--44074029 Score: 54
Period size: 6 Copynumber: 9.7 Consensus size: 6
44073958 TTTAGCATTT
**
44073968 TTTTAA TTTTAA TTTTAA TTTTAATA TTTTTGT TTTTAA -TTTAA TTGTTACA
1 TTTTAA TTTTAA TTTTAA TTTT-A-A -TTTTAA TTTTAA TTTTAA TT-TTA-A
44074020 TTTTAA TTTT
1 TTTTAA TTTT
44074030 TCTTTTGTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 12
0.74 0.06 0.19
Matches are distributed among these distances:
5 5 0.11
6 26 0.57
7 7 0.15
8 4 0.09
9 4 0.09
ACGTcount: A:0.27, C:0.02, G:0.03, T:0.68
Consensus pattern (6 bp):
TTTTAA
Found at i:44073996 original size:20 final size:20
Alignment explanation
Indices: 44073973--44074029 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
44073963 CATTTTTTTA
44073973 ATTTTAATTTTAATTTTAAT
1 ATTTTAATTTTAATTTTAAT
**
44073993 ATTTTTGTTTTTAA-TTTAAT
1 A-TTTTAATTTTAATTTTAAT
*
44074013 -TGTTACATTTTAATTTT
1 ATTTTA-ATTTTAATTTT
44074030 TCTTTTGTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
18 3 0.10
19 6 0.21
20 10 0.34
21 10 0.34
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.67
Consensus pattern (20 bp):
ATTTTAATTTTAATTTTAAT
Found at i:44073997 original size:26 final size:26
Alignment explanation
Indices: 44073967--44074029 Score: 67
Period size: 27 Copynumber: 2.4 Consensus size: 26
44073957 ATTTAGCATT
*
44073967 TTTTTAATTTTAATTTTAATT-TTAATA
1 TTTTTAATTTTAA-TTTAATTGTT-ACA
**
44073994 TTTTTGTTTTTAATTTAATTGTTACA
1 TTTTTAATTTTAATTTAATTGTTACA
44074020 -TTTTAATTTT
1 TTTTTAATTTT
44074030 TCTTTTGTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
25 8 0.27
26 9 0.30
27 13 0.43
ACGTcount: A:0.27, C:0.02, G:0.03, T:0.68
Consensus pattern (26 bp):
TTTTTAATTTTAATTTAATTGTTACA
Found at i:44074030 original size:26 final size:27
Alignment explanation
Indices: 44073968--44074030 Score: 69
Period size: 26 Copynumber: 2.4 Consensus size: 27
44073958 TTTAGCATTT
*
44073968 TTTTAA-TTTTAATTTTAATTTTAATA
1 TTTTAATTTTTAATTTTAATTTTAACA
**
44073994 TTTTTGTTTTTAA-TTTAATTGTT-ACA
1 TTTTAATTTTTAATTTTAATT-TTAACA
44074020 TTTTAATTTTT
1 TTTTAATTTTT
44074031 CTTTTGTTTG
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
26 22 0.73
27 8 0.27
ACGTcount: A:0.27, C:0.02, G:0.03, T:0.68
Consensus pattern (27 bp):
TTTTAATTTTTAATTTTAATTTTAACA
Found at i:44082317 original size:13 final size:12
Alignment explanation
Indices: 44082299--44082332 Score: 50
Period size: 13 Copynumber: 2.7 Consensus size: 12
44082289 TTTTATTTAT
44082299 TAAAAAAAATTAA
1 TAAAAAAAA-TAA
44082312 TAAAAATAAATAA
1 TAAAAA-AAATAA
44082325 TAAAAAAA
1 TAAAAAAA
44082333 TGGTCAACAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 2 0.10
13 15 0.75
14 3 0.15
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (12 bp):
TAAAAAAAATAA
Found at i:44086935 original size:5 final size:5
Alignment explanation
Indices: 44086927--44087018 Score: 121
Period size: 5 Copynumber: 17.8 Consensus size: 5
44086917 TATTTAGTTT
44086927 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
* * * *
44086977 ATATA TTATATT ATATT ATATA ATAAA ATAAA ATACTA ATAT
1 ATATA --ATATA ATATA ATATA ATATA ATATA ATA-TA ATAT
44087019 TTAAAACATA
Statistics
Matches: 80, Mismatches: 4, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
5 72 0.90
6 4 0.05
7 4 0.05
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (5 bp):
ATATA
Found at i:44098061 original size:29 final size:29
Alignment explanation
Indices: 44097986--44098061 Score: 98
Period size: 29 Copynumber: 2.6 Consensus size: 29
44097976 ACGATAATGC
* *
44097986 AAGTGACTAAAACGTAGTATTTCAAACGT
1 AAGTGACTAAAACGTAATATTTCAAACAT
* * *
44098015 AAGTAACTAAAACATAATATTTTAAACAT
1 AAGTGACTAAAACGTAATATTTCAAACAT
*
44098044 AAGTGACTAAAATGTAAT
1 AAGTGACTAAAACGTAAT
44098062 CTGAGTCAAA
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.49, C:0.11, G:0.12, T:0.29
Consensus pattern (29 bp):
AAGTGACTAAAACGTAATATTTCAAACAT
Found at i:44111489 original size:5 final size:5
Alignment explanation
Indices: 44111476--44111507 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
44111466 ACATATTATG
*
44111476 TAAAC TAAAA TAAAA TAAAA TAAAA TAAAA TA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TA
44111508 TTCTAATATT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.22
Consensus pattern (5 bp):
TAAAA
Found at i:44112500 original size:27 final size:27
Alignment explanation
Indices: 44112470--44112522 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
44112460 AAAAATTGAC
44112470 TAAAA-AAGAGTTGTGCTAATTTTATTT
1 TAAAACAA-AGTTGTGCTAATTTTATTT
44112497 TAAAACAAAGTTGTGCTAATTTTATT
1 TAAAACAAAGTTGTGCTAATTTTATT
44112523 AATGTAAAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 23 0.92
28 2 0.08
ACGTcount: A:0.38, C:0.06, G:0.13, T:0.43
Consensus pattern (27 bp):
TAAAACAAAGTTGTGCTAATTTTATTT
Found at i:44115712 original size:22 final size:22
Alignment explanation
Indices: 44115667--44115785 Score: 125
Period size: 22 Copynumber: 5.3 Consensus size: 22
44115657 ATGTCATAGC
*
44115667 TCACATAGGTCAT-AGTTTGCATA
1 TCACAT-GG-CATAAGTTCGCATA
44115690 TCACATGGCATATA-TTCGCATA
1 TCACATGGCATA-AGTTCGCATA
* * *
44115712 TCACTTTAGCATAAGTTCGTATA
1 TCAC-ATGGCATAAGTTCGCATA
* * *
44115735 TCACATGACATAGGTTCACATA
1 TCACATGGCATAAGTTCGCATA
44115757 TCACATGGCATAAGTTCGCATA
1 TCACATGGCATAAGTTCGCATA
44115779 TCACATG
1 TCACATG
44115786 ACAATCACAC
Statistics
Matches: 79, Mismatches: 13, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
21 3 0.04
22 52 0.66
23 24 0.30
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.32
Consensus pattern (22 bp):
TCACATGGCATAAGTTCGCATA
Found at i:44115737 original size:45 final size:44
Alignment explanation
Indices: 44115667--44115788 Score: 138
Period size: 45 Copynumber: 2.7 Consensus size: 44
44115657 ATGTCATAGC
* * * *
44115667 TCACATAGGTCAT-AGTTTGCATATCACATGGCATATATTCGCATA
1 TCACATA-G-CATAAGTTCGCATATCACATGACATAGATTCACATA
* * *
44115712 TCACTTTAGCATAAGTTCGTATATCACATGACATAGGTTCACATA
1 TCAC-ATAGCATAAGTTCGCATATCACATGACATAGATTCACATA
*
44115757 TCACATGGCATAAGTTCGCATATCACATGACA
1 TCACATAGCATAAGTTCGCATATCACATGACA
44115789 ATCACACAAT
Statistics
Matches: 65, Mismatches: 10, Indels: 5
0.81 0.12 0.06
Matches are distributed among these distances:
44 28 0.43
45 35 0.54
46 2 0.03
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.31
Consensus pattern (44 bp):
TCACATAGCATAAGTTCGCATATCACATGACATAGATTCACATA
Found at i:44116083 original size:23 final size:25
Alignment explanation
Indices: 44116053--44116154 Score: 101
Period size: 24 Copynumber: 4.3 Consensus size: 25
44116043 TCACATATAA
44116053 GGTGATA-GGG-TT-CACATGTCACT
1 GGTGATAGGGGTTTACACATGT-ACT
44116076 GGTGATAGGGGTTTACACATG-ACT
1 GGTGATAGGGGTTTACACATGTACT
* * *
44116100 GGTGATAAGGGTTTGCACATGT-TT
1 GGTGATAGGGGTTTACACATGTACT
*
44116124 GGTGATAGGGG-TT-CACATGTATCA
1 GGTGATAGGGGTTTACACATGTA-CT
44116148 GGTGATA
1 GGTGATA
44116155 AGTGGTTATA
Statistics
Matches: 67, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
22 7 0.10
23 9 0.13
24 43 0.64
25 2 0.03
26 6 0.09
ACGTcount: A:0.24, C:0.12, G:0.33, T:0.31
Consensus pattern (25 bp):
GGTGATAGGGGTTTACACATGTACT
Found at i:44116588 original size:21 final size:20
Alignment explanation
Indices: 44116564--44116629 Score: 50
Period size: 20 Copynumber: 3.4 Consensus size: 20
44116554 CCCTAAATAT
44116564 CATCTAATTACAAGTCTGAAC
1 CATC-AATTACAAGTCTGAAC
** * *
44116585 CATCAATTTTAA--AT--AT
1 CATCAATTACAAGTCTGAAC
44116601 CATCTAATTACAAGTCTGAAC
1 CATC-AATTACAAGTCTGAAC
44116622 CATCAATT
1 CATCAATT
44116630 TTATCTAATT
Statistics
Matches: 32, Mismatches: 8, Indels: 11
0.63 0.16 0.22
Matches are distributed among these distances:
16 5 0.16
17 6 0.19
18 1 0.03
19 1 0.03
20 10 0.31
21 9 0.28
ACGTcount: A:0.39, C:0.21, G:0.06, T:0.33
Consensus pattern (20 bp):
CATCAATTACAAGTCTGAAC
Found at i:44116598 original size:37 final size:37
Alignment explanation
Indices: 44116557--44116632 Score: 152
Period size: 37 Copynumber: 2.1 Consensus size: 37
44116547 TCATACACCC
44116557 TAAATATCATCTAATTACAAGTCTGAACCATCAATTT
1 TAAATATCATCTAATTACAAGTCTGAACCATCAATTT
44116594 TAAATATCATCTAATTACAAGTCTGAACCATCAATTT
1 TAAATATCATCTAATTACAAGTCTGAACCATCAATTT
44116631 TA
1 TA
44116633 TCTAATTACA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.41, C:0.18, G:0.05, T:0.36
Consensus pattern (37 bp):
TAAATATCATCTAATTACAAGTCTGAACCATCAATTT
Found at i:44119679 original size:44 final size:44
Alignment explanation
Indices: 44119628--44119728 Score: 114
Period size: 44 Copynumber: 2.3 Consensus size: 44
44119618 ATTTTACTGC
* * **
44119628 CAATGGCTGTGGACACAAAACAAAATGTCGCAGATGGAATCTG-
1 CAATGGCTGTGGACACAAAACAAAATATCACAGATCAAATCTGT
** * *
44119671 CATATGGCTGTGGGTACATAACAAAATATTACAGATCAAATCTGT
1 CA-ATGGCTGTGGACACAAAACAAAATATCACAGATCAAATCTGT
44119716 CAATGGCTGTGGA
1 CAATGGCTGTGGA
44119729 AGCACAACAT
Statistics
Matches: 47, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
43 2 0.04
44 43 0.91
45 2 0.04
ACGTcount: A:0.36, C:0.17, G:0.24, T:0.24
Consensus pattern (44 bp):
CAATGGCTGTGGACACAAAACAAAATATCACAGATCAAATCTGT
Found at i:44122731 original size:22 final size:23
Alignment explanation
Indices: 44122685--44122734 Score: 68
Period size: 22 Copynumber: 2.2 Consensus size: 23
44122675 AAAAATATCT
44122685 TTAAAATAATATTTATTATTTTG
1 TTAAAATAATATTTATTATTTTG
*
44122708 TTAAAATAATGA-TT-TTGTTTTG
1 TTAAAATAAT-ATTTATTATTTTG
44122730 TTAAA
1 TTAAA
44122735 GAAATTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 12 0.48
23 12 0.48
24 1 0.04
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (23 bp):
TTAAAATAATATTTATTATTTTG
Found at i:44128121 original size:12 final size:13
Alignment explanation
Indices: 44128102--44128139 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
44128092 AAGATTGTTT
44128102 CAAAAAAAGTAAA
1 CAAAAAAAGTAAA
44128115 CAAAAAAAG-AAA
1 CAAAAAAAGTAAA
* *
44128127 CATAAAAACTAAA
1 CAAAAAAAGTAAA
44128140 ATTAAACTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
12 10 0.45
13 12 0.55
ACGTcount: A:0.76, C:0.11, G:0.05, T:0.08
Consensus pattern (13 bp):
CAAAAAAAGTAAA
Found at i:44128159 original size:19 final size:19
Alignment explanation
Indices: 44128118--44128164 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
44128108 AAGTAAACAA
*
44128118 AAAAAGAAACATAAAAACT
1 AAAAATAAACATAAAAACT
* *
44128137 AAAATTAAACTTAAAAA-T
1 AAAAATAAACATAAAAACT
44128155 AAAAAATAAA
1 -AAAAATAAA
44128165 AAGAAAGAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
18 1 0.04
19 22 0.96
ACGTcount: A:0.74, C:0.06, G:0.02, T:0.17
Consensus pattern (19 bp):
AAAAATAAACATAAAAACT
Found at i:44129661 original size:25 final size:24
Alignment explanation
Indices: 44129633--44129680 Score: 78
Period size: 25 Copynumber: 2.0 Consensus size: 24
44129623 GTTCTGTGGT
44129633 AAAGGATGAATTGACGGTAAAATGC
1 AAAGGATGAATTGACGG-AAAATGC
*
44129658 AAAGGATGAATTGATGGAAAATG
1 AAAGGATGAATTGACGGAAAATG
44129681 TACCCAAGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 6 0.27
25 16 0.73
ACGTcount: A:0.46, C:0.04, G:0.29, T:0.21
Consensus pattern (24 bp):
AAAGGATGAATTGACGGAAAATGC
Found at i:44132830 original size:16 final size:17
Alignment explanation
Indices: 44132806--44132837 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
44132796 TTAAATTAAC
44132806 TAAATTAATTTCTCAAT
1 TAAATTAATTTCTCAAT
44132823 TAAA-TAATTTCTCAA
1 TAAATTAATTTCTCAA
44132838 CTGAATTCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.44, C:0.12, G:0.00, T:0.44
Consensus pattern (17 bp):
TAAATTAATTTCTCAAT
Found at i:44132831 original size:20 final size:20
Alignment explanation
Indices: 44132788--44132829 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
44132778 TTATTTAACC
*
44132788 AATTAATTTTAAATTAACTA
1 AATTAATTTTAAATTAAATA
*
44132808 AATTAATTTCTCAATTAAATA
1 AATTAATTT-TAAATTAAATA
44132829 A
1 A
44132830 TTTCTCAACT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (20 bp):
AATTAATTTTAAATTAAATA
Found at i:44136136 original size:24 final size:24
Alignment explanation
Indices: 44136094--44136145 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
44136084 AATCAAAGTC
** *
44136094 AAATATATTATGTTAATAAATGCT
1 AAATATATTATACTAATAAATACT
*
44136118 AAATATATTATACTCATAAATACT
1 AAATATATTATACTAATAAATACT
44136142 AAAT
1 AAAT
44136146 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.50, C:0.08, G:0.04, T:0.38
Consensus pattern (24 bp):
AAATATATTATACTAATAAATACT
Found at i:44141005 original size:20 final size:20
Alignment explanation
Indices: 44140926--44141070 Score: 80
Period size: 20 Copynumber: 6.7 Consensus size: 20
44140916 GAAGGAGAGG
*
44140926 GAAAGAAGAAGAAAGAAAGAAA
1 GAAAGAAGAAG-AAGGAA-AAA
44140948 GAAAAGGAA-AAGAGAGGAAATAAA
1 G-AAA-GAAGAAGA-AGG-AA-AAA
*
44140972 GAAA-AAGAAGGAAGGAAAAG
1 GAAAGAAGAA-GAAGGAAAAA
* *
44140992 GAAAGGAGAAGAAGAAAAAA
1 GAAAGAAGAAGAAGGAAAAA
*
44141012 GAAAGAAAAAGAAGGAAAGAAAA
1 GAAAGAAGAAGAAGG--A-AAAA
**
44141035 GGAAATG-AGAAGAGAAAAAAAA
1 -GAAA-GAAGAAGA-AGGAAAAA
44141057 GAAAGAAGAAGAAG
1 GAAAGAAGAAGAAG
44141071 AAGGGAGGAA
Statistics
Matches: 96, Mismatches: 13, Indels: 30
0.69 0.09 0.22
Matches are distributed among these distances:
20 28 0.29
21 18 0.19
22 12 0.12
23 18 0.19
24 18 0.19
25 2 0.02
ACGTcount: A:0.69, C:0.00, G:0.30, T:0.01
Consensus pattern (20 bp):
GAAAGAAGAAGAAGGAAAAA
Found at i:44141024 original size:44 final size:44
Alignment explanation
Indices: 44140926--44141070 Score: 168
Period size: 44 Copynumber: 3.3 Consensus size: 44
44140916 GAAGGAGAGG
* * * * **
44140926 GAAAGAAGAAGAAAGAAAG-AAAGAAAAGGAAAAG-AGAGGAAA
1 GAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAGAAGAAAAAA
* *
44140968 TAAAGAAAAAGAAGGAAGGAAAAGGAAAGGAGAAGAAGAAAAAA
1 GAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAGAAGAAAAAA
* *
44141012 GAAAGAAAAAGAAGGAAAGAAAAGGAAATGAGAAGAGAAAAAAAA
1 GAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAGA-AGAAAAAA
*
44141057 GAAAGAAGAAGAAG
1 GAAAGAAAAAGAAG
44141071 AAGGGAGGAA
Statistics
Matches: 87, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
42 15 0.17
43 13 0.15
44 39 0.45
45 20 0.23
ACGTcount: A:0.69, C:0.00, G:0.30, T:0.01
Consensus pattern (44 bp):
GAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAGAAGAAAAAA
Found at i:44141027 original size:72 final size:75
Alignment explanation
Indices: 44140928--44141095 Score: 188
Period size: 72 Copynumber: 2.3 Consensus size: 75
44140918 AGGAGAGGGA
* * * * *
44140928 AAGAAGAAGAAAGAAAGAAAGAAAAGGAAA-AGAGAGGAAAT-A-AAGA-AAAAGAAGGAAGGAA
1 AAGAAGAAAAAAGAAAGAAA-AAAAGGAAAGA-AAAGGAAATGAGAAGAGAAAAAAAAGAAAGAA
*
44140989 -AAGGA-AAGGAG
64 GAAGAAGAAGG-G
44141000 AAGAAGAAAAAAGAAAGAAAAAGAAGGAAAGAAAAGGAAATGAGAAGAGAAAAAAAAGAAAGAAG
1 AAGAAGAAAAAAGAAAGAAAAA-AAGGAAAGAAAAGGAAATGAGAAGAGAAAAAAAAGAAAGAAG
44141065 AAGAAGAAGGG
65 AAGAAGAAGGG
*
44141076 AGGAAGAAAAAAGAAA-AAAA
1 AAGAAGAAAAAAGAAAGAAAA
44141096 GGTAATTTTT
Statistics
Matches: 82, Mismatches: 7, Indels: 11
0.82 0.07 0.11
Matches are distributed among these distances:
71 2 0.02
72 34 0.41
73 2 0.02
74 4 0.05
75 16 0.20
76 20 0.24
77 4 0.05
ACGTcount: A:0.70, C:0.00, G:0.29, T:0.01
Consensus pattern (75 bp):
AAGAAGAAAAAAGAAAGAAAAAAAGGAAAGAAAAGGAAATGAGAAGAGAAAAAAAAGAAAGAAGA
AGAAGAAGGG
Found at i:44141082 original size:76 final size:81
Alignment explanation
Indices: 44140927--44141095 Score: 201
Period size: 82 Copynumber: 2.1 Consensus size: 81
44140917 AAGGAGAGGG
* *
44140927 AAAG-AAGAAGAAAGAAAGAAAGAAAAGGAAAAGAGAGGAAATAAAGAAAAAGAAGGAAGGAAAA
1 AAAGAAAGAA-AAAGAAAGAAAGAAAAGGAAAAGAGA-GAAAGAAAGAAAAAGAAAGAAGGAAAA
44140991 GGAAAGGAGAAGAAGAAA
64 GGAAAGGAGAAGAAGAAA
* * *
44141009 AAAGAAAGAAAAAGAAGGAAAGAAAAGGAAATGAGA-AGAGAAA-AAAAAGAAAGAA-GAAGAA-
1 AAAGAAAGAAAAAGAAAGAAAGAAAAGGAAAAGAGAGAAAGAAAGAAAAAGAAAGAAGGAA-AAG
*
44141070 G-AAGG-GAGGAAGAAA
65 GAAAGGAGAAGAAGAAA
44141085 AAAGAAA-AAAA
1 AAAGAAAGAAAA
44141096 GGTAATTTTT
Statistics
Matches: 79, Mismatches: 6, Indels: 11
0.82 0.06 0.11
Matches are distributed among these distances:
75 4 0.05
76 16 0.20
77 4 0.05
78 4 0.05
79 13 0.16
80 5 0.06
82 28 0.35
83 5 0.06
ACGTcount: A:0.70, C:0.00, G:0.29, T:0.01
Consensus pattern (81 bp):
AAAGAAAGAAAAAGAAAGAAAGAAAAGGAAAAGAGAGAAAGAAAGAAAAAGAAAGAAGGAAAAGG
AAAGGAGAAGAAGAAA
Found at i:44141925 original size:24 final size:24
Alignment explanation
Indices: 44141898--44141944 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
44141888 TTTTTAAAAA
44141898 TTCAAA-AATAAT-TAATACAAATAT
1 TTCAAACAA-AATGTAATA-AAATAT
44141922 TTCAAACAAAATGTAATAAAATA
1 TTCAAACAAAATGTAATAAAATA
44141945 ATATAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 14 0.67
25 7 0.33
ACGTcount: A:0.60, C:0.09, G:0.02, T:0.30
Consensus pattern (24 bp):
TTCAAACAAAATGTAATAAAATAT
Found at i:44142040 original size:322 final size:323
Alignment explanation
Indices: 44141427--44142200 Score: 1302
Period size: 322 Copynumber: 2.4 Consensus size: 323
44141417 AATGGTATAT
44141427 TTAATAAATTTCAAACATAATGCACTGAAATAAAGTAAAATTATAAAATTAGAAATTATGATATT
1 TTAATAAATTTCAAACATAATGCACTGAAATAAAGTAAAATTATAAAATTAGAAATTATGATATT
* * *
44141492 TTTTAAAATAATAAAATATGGAGAAAAAAATACGAACAAATGACCGAAGTAAGAGTGTTTTACTT
66 TTTTAAAATAATAAAATACGGAGAAAAAAATACGAACAAATGACAGAAGTAAGAGTATTTTACTT
* *
44141557 TTACTAACTTTTTTAAAAATTCAAAAGTAATTAATACAAATATTTCAAACAAAATGTACTAAAAA
131 TTACTAACTTTTTTAAAAATTCAAAAATAATTAATACAAATATTTCAAACAAAATGTAATAAAAA
*
44141622 AATATAAAATAATAAAATACAAAAATAATATATTTTTATTGAAAGTAATAAAATTCGGGAGAATA
196 AATATAAAATAATAAAATACAAAAATAATATATTTTTATTGAAAGTAATAAAATTCGGGAAAATA
* *
44141687 GTACGAGCAAAGAGCAGGAATAAGGTTTTTTTACACTAAATTAA-TTTAAAAAACACACTAAA
261 ATACAAGCAAAGAGCAGGAATAAGGTTTTTTTACACTAAATTAATTTTAAAAAACACACTAAA
*
44141749 TTAATAAATTTCAAACATAATGCATTGAAATAAAGTAAAATTATAAAATTAGAAATTATGATATT
1 TTAATAAATTTCAAACATAATGCACTGAAATAAAGTAAAATTATAAAATTAGAAATTATGATATT
* *
44141814 TTTTAAAATAATAAAATGCGGAGAAAAAAATACGAACAAATGGCAGAAGTAAGAGTATTTTACTT
66 TTTTAAAATAATAAAATACGGAGAAAAAAATACGAACAAATGACAGAAGTAAGAGTATTTTACTT
*
44141879 TTACTAACTTTTTTAAAAATTCAAAAATAATTAATACAAATATTTCAAACAAAATGTAATAAAAT
131 TTACTAACTTTTTTAAAAATTCAAAAATAATTAATACAAATATTTCAAACAAAATGTAATAAAAA
* * *
44141944 AATATAAAATAATAAAATACGAAAATAATAT-TTTTTATTGAGAGTAATAAAATTTGGGAAAATA
196 AATATAAAATAATAAAATACAAAAATAATATATTTTTATTGAAAGTAATAAAATTCGGGAAAATA
* *
44142008 ATACAAGCAAAGAG-AGGGATAATGGTTTTTTTTACACTAAATTAATTTTAAAAAACGCACTAAA
261 ATACAAGCAAAGAGCAGGAATAA-GG-TTTTTTTACACTAAATTAATTTTAAAAAACACACTAAA
* **
44142072 TTAATAAATTTCAAACATAATGCACTGAAATAATGTATTATTATAAAATTAGAAATTATGATATT
1 TTAATAAATTTCAAACATAATGCACTGAAATAAAGTAAAATTATAAAATTAGAAATTATGATATT
* * *
44142137 TTTTAAAGTAATAAAATACGGAGAAAAAAATACGAACAAATGACTGAAGTAAGAGTTTTTTACT
66 TTTTAAAATAATAAAATACGGAGAAAAAAATACGAACAAATGACAGAAGTAAGAGTATTTTACT
44142201 AACTTTTTTT
Statistics
Matches: 423, Mismatches: 26, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
320 7 0.02
321 44 0.10
322 235 0.56
323 137 0.32
ACGTcount: A:0.51, C:0.07, G:0.10, T:0.32
Consensus pattern (323 bp):
TTAATAAATTTCAAACATAATGCACTGAAATAAAGTAAAATTATAAAATTAGAAATTATGATATT
TTTTAAAATAATAAAATACGGAGAAAAAAATACGAACAAATGACAGAAGTAAGAGTATTTTACTT
TTACTAACTTTTTTAAAAATTCAAAAATAATTAATACAAATATTTCAAACAAAATGTAATAAAAA
AATATAAAATAATAAAATACAAAAATAATATATTTTTATTGAAAGTAATAAAATTCGGGAAAATA
ATACAAGCAAAGAGCAGGAATAAGGTTTTTTTACACTAAATTAATTTTAAAAAACACACTAAA
Found at i:44147800 original size:27 final size:27
Alignment explanation
Indices: 44147770--44147863 Score: 136
Period size: 27 Copynumber: 3.5 Consensus size: 27
44147760 TGACACAAGT
44147770 GGTGCCGCCTATGGGAAAGGCACCTTC
1 GGTGCCGCCTATGGGAAAGGCACCTTC
* *
44147797 GGTGCCGCCTATGGGAAAGACACCTTT
1 GGTGCCGCCTATGGGAAAGGCACCTTC
* *
44147824 GGTGCCGCCCAT-GGAAATGGCACCATC
1 GGTGCCGCCTATGGGAAA-GGCACCTTC
44147851 GGTGCCGCCTATG
1 GGTGCCGCCTATG
44147864 AGATACCCTC
Statistics
Matches: 58, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
26 5 0.09
27 53 0.91
ACGTcount: A:0.19, C:0.30, G:0.32, T:0.19
Consensus pattern (27 bp):
GGTGCCGCCTATGGGAAAGGCACCTTC
Found at i:44149254 original size:26 final size:26
Alignment explanation
Indices: 44149212--44149261 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 26
44149202 ACCATGATAT
44149212 TAAAATTTATACTTTTAT-TATTTTA
1 TAAAATTTATACTTTTATATATTTTA
44149237 TAAAATTTTATA-TATTTATATATTT
1 TAAAA-TTTATACT-TTTATATATTT
44149262 ATTTTATATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 6 0.27
26 11 0.50
27 5 0.23
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (26 bp):
TAAAATTTATACTTTTATATATTTTA
Found at i:44149747 original size:10 final size:10
Alignment explanation
Indices: 44149734--44149768 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
44149724 AAATCCTTTT
44149734 AATTATTAAA
1 AATTATTAAA
44149744 AATTATTAAA
1 AATTATTAAA
*
44149754 AATCA-TAAA
1 AATTATTAAA
44149763 AATTAT
1 AATTAT
44149769 AATTTTTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
9 8 0.36
10 14 0.64
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (10 bp):
AATTATTAAA
Found at i:44153020 original size:23 final size:23
Alignment explanation
Indices: 44152994--44153090 Score: 142
Period size: 23 Copynumber: 4.3 Consensus size: 23
44152984 TAAGTGCCAA
44152994 ACTGATATGTAGCCGAAGCTACC
1 ACTGATATGTAGCCGAAGCTACC
** *
44153017 ACTGATACATAGCCG-TGCTACC
1 ACTGATATGTAGCCGAAGCTACC
*
44153039 ACTGAAATGTAGCCGAAGCTACC
1 ACTGATATGTAGCCGAAGCTACC
*
44153062 ACTGATATGTAGCCGTAGCTACC
1 ACTGATATGTAGCCGAAGCTACC
44153085 ACTGAT
1 ACTGAT
44153091 CAATAACACT
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
22 18 0.28
23 46 0.72
ACGTcount: A:0.30, C:0.27, G:0.21, T:0.23
Consensus pattern (23 bp):
ACTGATATGTAGCCGAAGCTACC
Found at i:44153058 original size:45 final size:46
Alignment explanation
Indices: 44152994--44153089 Score: 158
Period size: 45 Copynumber: 2.1 Consensus size: 46
44152984 TAAGTGCCAA
*
44152994 ACTGATATGTAGCCGAAGCTACCACTGATACATAGCCGT-GCTACC
1 ACTGAAATGTAGCCGAAGCTACCACTGATACATAGCCGTAGCTACC
**
44153039 ACTGAAATGTAGCCGAAGCTACCACTGATATGTAGCCGTAGCTACC
1 ACTGAAATGTAGCCGAAGCTACCACTGATACATAGCCGTAGCTACC
44153085 ACTGA
1 ACTGA
44153090 TCAATAACAC
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
45 36 0.77
46 11 0.23
ACGTcount: A:0.30, C:0.27, G:0.21, T:0.22
Consensus pattern (46 bp):
ACTGAAATGTAGCCGAAGCTACCACTGATACATAGCCGTAGCTACC
Found at i:44161581 original size:33 final size:34
Alignment explanation
Indices: 44161538--44161609 Score: 137
Period size: 33 Copynumber: 2.1 Consensus size: 34
44161528 CATATAATTC
44161538 TTTTTCTTACCCTTTGAACTAAAACAATTTTTAA
1 TTTTTCTTACCCTTTGAACTAAAACAATTTTTAA
44161572 TTTTT-TTACCCTTTGAACTAAAACAATTTTTAA
1 TTTTTCTTACCCTTTGAACTAAAACAATTTTTAA
44161605 TTTTT
1 TTTTT
44161610 AATGAAACTT
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 33 0.87
34 5 0.13
ACGTcount: A:0.31, C:0.15, G:0.03, T:0.51
Consensus pattern (34 bp):
TTTTTCTTACCCTTTGAACTAAAACAATTTTTAA
Found at i:44166096 original size:2 final size:2
Alignment explanation
Indices: 44166089--44166119 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
44166079 TATAGATTAG
44166089 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
44166120 CTTCTTCTAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:44166893 original size:2 final size:2
Alignment explanation
Indices: 44166886--44166919 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
44166876 TTTTCTTCTC
44166886 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
44166920 TTGTTCAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:44169947 original size:21 final size:21
Alignment explanation
Indices: 44169923--44169963 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
44169913 TATAATTTTT
*
44169923 TTTTATTTATCAATATATATA
1 TTTTATTTATCAAAATATATA
44169944 TTTTATTTATCAAAATATAT
1 TTTTATTTATCAAAATATAT
44169964 CAAAAAAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56
Consensus pattern (21 bp):
TTTTATTTATCAAAATATATA
Found at i:44170170 original size:11 final size:11
Alignment explanation
Indices: 44170154--44170184 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
44170144 GTTGCTGCGG
44170154 AAAAGAAGAGA
1 AAAAGAAGAGA
*
44170165 AAAAGAGGAGA
1 AAAAGAAGAGA
44170176 AAAAGAAGA
1 AAAAGAAGA
44170185 TATTTTTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (11 bp):
AAAAGAAGAGA
Found at i:44170245 original size:19 final size:21
Alignment explanation
Indices: 44170207--44170245 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
44170197 AATAATTAAT
*
44170207 TATATTGTTGTTATTATTTTG
1 TATATTGTTGTTAATATTTTG
44170228 TATATT-TTG-TAATATTTT
1 TATATTGTTGTTAATATTTT
44170246 TTGTTTTACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 3 0.18
21 6 0.35
ACGTcount: A:0.23, C:0.00, G:0.10, T:0.67
Consensus pattern (21 bp):
TATATTGTTGTTAATATTTTG
Found at i:44170307 original size:3 final size:3
Alignment explanation
Indices: 44170291--44170325 Score: 52
Period size: 3 Copynumber: 11.3 Consensus size: 3
44170281 AAAATAATAG
*
44170291 TAT TAGT TAG TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT T
44170326 GTTGTTGTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:44170330 original size:3 final size:3
Alignment explanation
Indices: 44170324--44170361 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
44170314 ATTATTATTA
44170324 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
44170362 AGTATTAAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:44174120 original size:24 final size:24
Alignment explanation
Indices: 44174093--44174140 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
44174083 AGGTTTTTTT
44174093 TATATATTTTGGTAAATAAAAAAA
1 TATATATTTTGGTAAATAAAAAAA
44174117 TATATATTTTGGTAAATAAAAAAA
1 TATATATTTTGGTAAATAAAAAAA
44174141 ACTTATAACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (24 bp):
TATATATTTTGGTAAATAAAAAAA
Found at i:44174958 original size:34 final size:35
Alignment explanation
Indices: 44174884--44175014 Score: 128
Period size: 39 Copynumber: 3.7 Consensus size: 35
44174874 AAAAAAAATA
* *
44174884 CCTTTTCTT-TTCTTT-TTCTTTT-TCCT-TCCTTC
1 CCTTTTCTTCTTCTTTCTT-TTTTCTCTTCTCCTTT
*
44174916 CCTCTTCTTCTTC-TTCTTTTTTCTCTTCTCCTTT
1 CCTTTTCTTCTTCTTTCTTTTTTCTCTTCTCCTTT
* *
44174950 CTTTTTCTTTCCTTCTTTCTTTCTTTTTTCTTCTCCTTT
1 CCTTTTC-TT-CTTCTTTC-TT-TTTTCTCTTCTCCTTT
44174989 CCTTTTCTTCTTCTTTCTTTCTTTCT
1 CCTTTTCTTCTTCTTTCTTT-TTTCT
44175015 TTTTTTCTCT
Statistics
Matches: 81, Mismatches: 8, Indels: 16
0.77 0.08 0.15
Matches are distributed among these distances:
32 14 0.17
33 8 0.10
34 10 0.12
35 3 0.04
36 10 0.12
37 11 0.14
38 4 0.05
39 21 0.26
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (35 bp):
CCTTTTCTTCTTCTTTCTTTTTTCTCTTCTCCTTT
Found at i:44174960 original size:4 final size:4
Alignment explanation
Indices: 44174929--44175073 Score: 103
Period size: 4 Copynumber: 36.8 Consensus size: 4
44174919 CTTCTTCTTC
* *
44174929 TTCT TT-T TTCT CTTC- TCCT TTC- TT-T TTCT TTCC TTCT TTCT TTCT
1 TTCT TTCT TTCT -TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT
*
44174974 TT-T TTCT TCTCCT TTCCT TT-T CTTC- TTCT TTCT TTCT TTCT TTTT
1 TTCT TTCT T-T-CT TT-CT TTCT -TTCT TTCT TTCT TTCT TTCT TTCT
* *
44175019 TTCT CTTC- TCCT TTCCTT TTCT TTCC TTC- TT-T TTCT TTCT TTCT TTCT
1 TTCT -TTCT TTCT TT-C-T TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT
44175067 TTCT TTC
1 TTCT TTC
44175074 CCTCTCCATC
Statistics
Matches: 115, Mismatches: 9, Indels: 34
0.73 0.06 0.22
Matches are distributed among these distances:
3 22 0.19
4 72 0.63
5 15 0.13
6 6 0.05
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (4 bp):
TTCT
Found at i:44174992 original size:44 final size:45
Alignment explanation
Indices: 44174892--44175071 Score: 183
Period size: 44 Copynumber: 3.9 Consensus size: 45
44174882 TACCTTTTCT
* *
44174892 TTTCTTTTTCTTTTTCCTTCCTTCCCTCTTCTTCTTCTTCTTTT-TTCT-C
1 TTTCCTTTTCTTTTTCTTTCCTT--CT-TTC-T-TTCTT-TTTTCTTCTCC
44174941 TTCTCC-TTTCTTTTTCTTTCCTTCTTTCTTTCTTTTTTCTTCTCC
1 TT-TCCTTTTCTTTTTCTTTCCTTCTTTCTTTCTTTTTTCTTCTCC
* * *
44174986 TTTCCTTTTCTTCTTCTTTCTTTCTTTCTTT-TTTTCTCTTCTCC
1 TTTCCTTTTCTTTTTCTTTCCTTCTTTCTTTCTTTTTTCTTCTCC
44175030 TTTCCTTTTCTTTCCTTCTTT--TTCTTTCTTTCTTTCTTTCTT
1 TTTCCTTTTCTTT--TTCTTTCCTTCTTTCTTTCTTT-TTTCTT
44175072 TCCCTCTCCA
Statistics
Matches: 116, Mismatches: 7, Indels: 19
0.82 0.05 0.13
Matches are distributed among these distances:
43 4 0.03
44 46 0.40
45 30 0.26
46 14 0.12
47 2 0.02
49 18 0.16
50 2 0.02
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (45 bp):
TTTCCTTTTCTTTTTCTTTCCTTCTTTCTTTCTTTTTTCTTCTCC
Found at i:44175040 original size:34 final size:36
Alignment explanation
Indices: 44174898--44175071 Score: 139
Period size: 37 Copynumber: 4.9 Consensus size: 36
44174888 TTCTTTTCTT
* *
44174898 TTTCTTTTTCCT-TCCTTCCCTCTT-CTTCTTC-TTC
1 TTTCTTTTTCTTCTCCTTTCCT-TTCCTTCTTCTTTC
* * *
44174932 TTT-TTTCTCTTCTCCTTTCTTTTTCTTTCCTTCTTTC
1 TTTCTTTTTCTTCTCCTTTC-CTTTCCTT-CTTCTTTC
*
44174969 TTTCTTTTTTCTTCTCCTTTCCTTTTCTTCTTCTTTC
1 TTTC-TTTTTCTTCTCCTTTCCTTTCCTTCTTCTTTC
* *
44175006 TTTCTTTCTTTTTTTCTCTTCTCCTTTCCTT-TTCTTTC
1 TTTCTTT-TTCTTCTC-CTT-TCCTTTCCTTCTTCTTTC
* *
44175044 CTTCTTTTTCTT-T-CTTT-CTTTCTTTCTT
1 TTTCTTTTTCTTCTCCTTTCCTTTCCTTCTT
44175072 TCCCTCTCCA
Statistics
Matches: 114, Mismatches: 15, Indels: 23
0.75 0.10 0.15
Matches are distributed among these distances:
32 7 0.06
33 9 0.08
34 14 0.12
35 3 0.03
36 8 0.07
37 28 0.25
38 21 0.18
39 24 0.21
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (36 bp):
TTTCTTTTTCTTCTCCTTTCCTTTCCTTCTTCTTTC
Found at i:44175153 original size:27 final size:27
Alignment explanation
Indices: 44175115--44175184 Score: 115
Period size: 27 Copynumber: 2.6 Consensus size: 27
44175105 CCCCAATAAA
44175115 CATTGGTGCCGCCAATGG-TATTGGCAC
1 CATTGGTGCCGCCAATGGCT-TTGGCAC
44175142 CATTGGTGCCGCCAATGGCTTTGGCAC
1 CATTGGTGCCGCCAATGGCTTTGGCAC
*
44175169 CTTTGGTGCCGCCAAT
1 CATTGGTGCCGCCAAT
44175185 CTCATTGGCG
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
27 40 0.98
28 1 0.02
ACGTcount: A:0.16, C:0.29, G:0.29, T:0.27
Consensus pattern (27 bp):
CATTGGTGCCGCCAATGGCTTTGGCAC
Found at i:44175192 original size:27 final size:27
Alignment explanation
Indices: 44175115--44175193 Score: 106
Period size: 27 Copynumber: 2.9 Consensus size: 27
44175105 CCCCAATAAA
44175115 CATTGGTGCCGCCAATGGT-ATTGGCAC
1 CATTGGTGCCGCCAAT-GTCATTGGCAC
* *
44175142 CATTGGTGCCGCCAATGGCTTTGGCAC
1 CATTGGTGCCGCCAATGTCATTGGCAC
* *
44175169 CTTTGGTGCCGCCAATCTCATTGGC
1 CATTGGTGCCGCCAATGTCATTGGC
44175194 GTGACCAAGG
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
26 1 0.02
27 44 0.98
ACGTcount: A:0.15, C:0.29, G:0.28, T:0.28
Consensus pattern (27 bp):
CATTGGTGCCGCCAATGTCATTGGCAC
Found at i:44178856 original size:3 final size:3
Alignment explanation
Indices: 44178850--44178875 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
44178840 CGTTGCTTGC
44178850 GTT GTT GTT GTT GTT GTT GTT GTT GT
1 GTT GTT GTT GTT GTT GTT GTT GTT GT
44178876 CGTCGGGAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.35, T:0.65
Consensus pattern (3 bp):
GTT
Found at i:44183071 original size:19 final size:20
Alignment explanation
Indices: 44183049--44183089 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
44183039 ATATTTGTAT
*
44183049 TTTATAATGA-TTAATTTTA
1 TTTATAATGATTTAAATTTA
*
44183068 TTTATAATTATTTAAATTTA
1 TTTATAATGATTTAAATTTA
44183088 TT
1 TT
44183090 GTTTTTATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (20 bp):
TTTATAATGATTTAAATTTA
Found at i:44187090 original size:19 final size:20
Alignment explanation
Indices: 44187068--44187112 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 20
44187058 ATATGTAATA
44187068 TTAGATATG-GTATGCAATC
1 TTAGATATGAGTATGCAATC
*
44187087 TTAGATATGATTTATGCAATC
1 TTAGATATGA-GTATGCAATC
44187108 TTAGA
1 TTAGA
44187113 AGATATGATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 9 0.39
21 14 0.61
ACGTcount: A:0.33, C:0.09, G:0.18, T:0.40
Consensus pattern (20 bp):
TTAGATATGAGTATGCAATC
Found at i:44187459 original size:3 final size:3
Alignment explanation
Indices: 44187451--44187490 Score: 62
Period size: 3 Copynumber: 13.3 Consensus size: 3
44187441 TGTTATTAAG
* *
44187451 ATT ATT ATT ATT GTT ATT ATT ATC ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
44187491 CTATATATAC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:44187460 original size:12 final size:12
Alignment explanation
Indices: 44187443--44187490 Score: 53
Period size: 12 Copynumber: 4.0 Consensus size: 12
44187433 GATTTTCTTG
*
44187443 TTATTAAGATTA
1 TTATTATGATTA
44187455 TTATTATTG-TTA
1 TTATTA-TGATTA
*
44187467 TTATTATCATTA
1 TTATTATGATTA
*
44187479 TTATTATTATTA
1 TTATTATGATTA
44187491 CTATATATAC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
11 1 0.03
12 29 0.94
13 1 0.03
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.60
Consensus pattern (12 bp):
TTATTATGATTA
Found at i:44187464 original size:21 final size:20
Alignment explanation
Indices: 44187409--44187490 Score: 67
Period size: 21 Copynumber: 3.9 Consensus size: 20
44187399 TCTTTTGTAT
*
44187409 TTATTATTTATTTTTATTAAA
1 TTATTA-TTATTGTTATTAAA
*
44187430 TTTGATT-TTCTTGTTATTAAGA
1 -TT-ATTATTATTGTTATTAA-A
*
44187452 TTATTATTATTGTTATTATTA
1 TTATTATTATTGTTATTA-AA
* *
44187473 TCATTATTATTATTATTA
1 TTATTATTATTGTTATTA
44187491 CTATATATAC
Statistics
Matches: 50, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
20 3 0.06
21 41 0.82
22 3 0.06
23 3 0.06
ACGTcount: A:0.29, C:0.02, G:0.05, T:0.63
Consensus pattern (20 bp):
TTATTATTATTGTTATTAAA
Found at i:44187651 original size:17 final size:17
Alignment explanation
Indices: 44187620--44187663 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
44187610 CATAACTTTT
*
44187620 ATATACA-TATATATAC
1 ATATACATTTTATATAC
*
44187636 ATTTACATTTTATATAC
1 ATATACATTTTATATAC
44187653 ATATACATTTT
1 ATATACATTTT
44187664 TTATTTCCTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 6 0.25
17 18 0.75
ACGTcount: A:0.41, C:0.11, G:0.00, T:0.48
Consensus pattern (17 bp):
ATATACATTTTATATAC
Found at i:44191488 original size:15 final size:15
Alignment explanation
Indices: 44191468--44191501 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
44191458 TTGCCCAAAA
44191468 AAAAGATGGCGCAAT
1 AAAAGATGGCGCAAT
44191483 AAAAGATGGCGCAAT
1 AAAAGATGGCGCAAT
44191498 AAAA
1 AAAA
44191502 AATTAAAAAA
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:0.53, C:0.12, G:0.24, T:0.12
Consensus pattern (15 bp):
AAAAGATGGCGCAAT
Found at i:44193177 original size:88 final size:88
Alignment explanation
Indices: 44193024--44193531 Score: 791
Period size: 88 Copynumber: 5.8 Consensus size: 88
44193014 GTGAAGATAA
* * * *
44193024 CAGATCTTACCTTCCTGCACCGACAGCGTAGCAGATCGAAGACACCAACCTTGCCTCCTTGGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
* * *
44193089 GTAGCGAAGTAGGTTAAAAATAG
66 GCAGCGGAGCAGGTTAAAAATAG
* * * * * * * *
44193112 TAGATCTTGCATTCCTGCACTGACAGCGAAGCAAATCGAAAACACTAGCATTGCCTCCCTAGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
*
44193177 GCAGCGGAGCAGGTTAAAAATAA
66 GCAGCGGAGCAGGTTAAAAATAG
*
44193200 CAGATCTTGCCTTCCTGCACCGACAGTGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
* * *
44193265 GTAACGGAGCAGGTTAAAAATAC
66 GCAGCGGAGCAGGTTAAAAATAG
* *
44193288 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAACCTTGCCTCCATGGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
44193353 GCAGCGGAGCAGGTTAAAAATAG
66 GCAGCGGAGCAGGTTAAAAATAG
*
44193376 CAGATCTTCCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
44193441 GCAGCGGAGCAGGTTAAAAATAG
66 GCAGCGGAGCAGGTTAAAAATAG
* *
44193464 CAGATATTGCCTTCCTGCACCGACAGTGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
44193529 GCA
66 GCA
44193532 CCGACAGCGA
Statistics
Matches: 380, Mismatches: 40, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
88 380 1.00
ACGTcount: A:0.28, C:0.28, G:0.24, T:0.20
Consensus pattern (88 bp):
CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
GCAGCGGAGCAGGTTAAAAATAG
Done.