Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 135709677
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: 135709677
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 350 characters in sequence are not A, C, G, or T
File 396 of 438
Found at i:123433025 original size:23 final size:22
Alignment explanation
Indices: 123432970--123433026 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 22
123432960 TATAAAAAAT
123432970 AAAATTTAT-AATAAAATTTAA
1 AAAATTTATAAATAAAATTTAA
** *
123432991 AAAATCAAATAAATAAATTTTAA
1 AAAAT-TTATAAATAAAATTTAA
123433014 AAAGATTTATAAA
1 AAA-ATTTATAAA
123433027 ATTGTAAATA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
21 5 0.18
22 2 0.07
23 19 0.68
24 2 0.07
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (22 bp):
AAAATTTATAAATAAAATTTAA
Found at i:123433496 original size:16 final size:16
Alignment explanation
Indices: 123433477--123433511 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
123433467 AACCTAACCC
*
123433477 AAAAAAAA-ACAAAGA
1 AAAAAAAAGAAAAAGA
123433492 AAAAAAAAGAAAAAGA
1 AAAAAAAAGAAAAAGA
123433508 AAAA
1 AAAA
123433512 CCTACCAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.89, C:0.03, G:0.09, T:0.00
Consensus pattern (16 bp):
AAAAAAAAGAAAAAGA
Found at i:123436138 original size:12 final size:12
Alignment explanation
Indices: 123436121--123436156 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
123436111 ATTCATTTGA
123436121 CATTCATGCATT
1 CATTCATGCATT
123436133 CATTCATGCATT
1 CATTCATGCATT
*
123436145 CATTCATACATT
1 CATTCATGCATT
123436157 GCATATCCCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.28, C:0.25, G:0.06, T:0.42
Consensus pattern (12 bp):
CATTCATGCATT
Found at i:123441356 original size:70 final size:68
Alignment explanation
Indices: 123441237--123441658 Score: 399
Period size: 71 Copynumber: 6.2 Consensus size: 68
123441227 GAGTTAAGCC
*
123441237 TTTT-AATTTTTGTTTTTCAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGC
1 TTTTCAATTTTTG-TTTT--AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGGCACGC
123441301 TGAGGTA
62 TGAGGTA
* * * * *
123441308 TTTTCAATTTTTGTGTTTTAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGTTG
1 TTTTCAATTTTTGT-TTTAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGGCACGCTG
123441373 AGGTA
64 AGGTA
* *
123441378 TTTTTAATTTTTGTTTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCT
1 TTTTCAATTTTTGTTTT--AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGGCACGCT
123441443 GAGGTA
63 GAGGTA
* * * ** * * *
123441449 TTTTTAGTTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCT--------TTTA-
1 TTTTCAATTTTTGTTTTAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGCACGCTGAG
123441505 --A
66 GTA
** ** *
123441506 TTTT-TGTTTTTCA---AAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGCACGCTGAG
1 TTTTCAATTTTTGTTTTAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGCACGCTGAG
123441567 GTA
66 GTA
* *
123441570 TTTTCAATTTTTGTGTTTTAATTTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGC
1 TTTTCAA-TTTT-TGTTTTAA-ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGGCACGC
123441635 TGAGGTA
62 TGAGGTA
*
123441642 TTTTCAATTTCTGTTTT
1 TTTTCAATTTTTGTTTT
123441659 CAATTTACGT
Statistics
Matches: 287, Mismatches: 41, Indels: 47
0.77 0.11 0.13
Matches are distributed among these distances:
53 31 0.11
56 5 0.02
57 5 0.02
60 2 0.01
61 2 0.01
64 5 0.02
66 4 0.01
67 1 0.00
69 34 0.12
70 66 0.23
71 100 0.35
72 32 0.11
ACGTcount: A:0.24, C:0.14, G:0.22, T:0.39
Consensus pattern (68 bp):
TTTTCAATTTTTGTTTTAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGCACGCTGAG
GTA
Found at i:123441545 original size:122 final size:123
Alignment explanation
Indices: 123441379--123441624 Score: 381
Period size: 122 Copynumber: 2.0 Consensus size: 123
123441369 GTTGAGGTAT
123441379 TTTTAATTTTTGTTTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCTG
1 TTTTAATTTTTGTTTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTC-GGGCACGCTG
* *
123441444 AGGTATTTT-TA-GTTTATGTTTTAAATT-GACTCATATTGCGAGAGGTGAGTTAAGCC
65 AGGTATTTTCAATGTTTATGTTTTAAATTCAACTCATATTGCGAGAGGTGAGTTAAGCC
* *
123441500 TTTTAATTTTTGTTTTTCAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGCACGCTG
1 TTTTAATTTTTG-TTTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGCACGCTG
* * * *
123441565 AGGTATTTTCAATTTTTGTGTTTTAATTTCAACTCATATTGCGAGAGGTGAGTTGAGCC
65 AGGTATTTTCAATGTTTATGTTTTAAATTCAACTCATATTGCGAGAGGTGAGTTAAGCC
123441624 T
1 T
123441625 CAGGTCACGC
Statistics
Matches: 113, Mismatches: 8, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
121 31 0.27
122 41 0.36
123 13 0.12
124 28 0.25
ACGTcount: A:0.24, C:0.14, G:0.22, T:0.39
Consensus pattern (123 bp):
TTTTAATTTTTGTTTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGCACGCTGA
GGTATTTTCAATGTTTATGTTTTAAATTCAACTCATATTGCGAGAGGTGAGTTAAGCC
Found at i:123441548 original size:193 final size:204
Alignment explanation
Indices: 123441327--123441860 Score: 610
Period size: 193 Copynumber: 2.6 Consensus size: 204
123441317 TTTGTGTTTT
* * * *
123441327 AATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAATTTTTGT
1 AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTTTGT
* *
123441392 TTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCTGAGGTA-TT-TTT-
66 TTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTATTTC
**
123441454 AG-TTT-A-T-GTT-TT-A-AATTGACTCATATTGCGAGAGGT-GAGTT-AAGCCTTTTAATTT-
131 AGTTTTAATTAGTTGTTAAGAATCAACTCATATTGCGAGAGGTAG-GTTGAA-CCTTTTAATTTC
**
123441509 TTGTTTTTCAA
194 TACTTTTTCAA
* *
123441520 AATCAACTCATATTGCTAGAGGTGAGTTGAGCCTC-GGGCACGCTGAGGTATTTTCAATTTTTGT
1 AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTTTGT
* ** *
123441584 GTTTTAATTTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAA
66 -TTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTA-TTT--A
*
123441649 TTTCTGTTTTCAATTTACGTTGTTCAAGAATCAACTCATATTGCGAGAGGTAGGTTGAACCTTTT
127 TTTCAGTTTT-AA-TTA-GTTGTT-AAGAATCAACTCATATTGCGAGAGGTAGGTTGAACCTTTT
123441714 AATTTCTACTTTTTCAA
188 AATTTCTACTTTTTCAA
* *
123441731 AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGT
1 AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTTTGT
* * * * * *
123441796 TGTCAAAAAAATCAACTCGTATTGCGAGTGGCGAGTTGAGCCTCAGGTCACACGCCGAGGTATTT
66 TTTC---AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG--GCACGCTGAGGTATTT
123441861 TCAATTTCCG
Statistics
Matches: 284, Mismatches: 30, Indels: 32
0.82 0.09 0.09
Matches are distributed among these distances:
192 25 0.09
193 84 0.30
195 2 0.01
198 3 0.01
199 1 0.00
200 3 0.01
202 1 0.00
204 1 0.00
206 3 0.01
207 2 0.01
209 1 0.00
210 35 0.12
211 48 0.17
212 26 0.09
214 35 0.12
215 3 0.01
216 11 0.04
ACGTcount: A:0.26, C:0.16, G:0.22, T:0.35
Consensus pattern (204 bp):
AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTTTGT
TTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTATTTC
AGTTTTAATTAGTTGTTAAGAATCAACTCATATTGCGAGAGGTAGGTTGAACCTTTTAATTTCTA
CTTTTTCAA
Found at i:123441995 original size:74 final size:76
Alignment explanation
Indices: 123441889--123442033 Score: 224
Period size: 74 Copynumber: 1.9 Consensus size: 76
123441879 TTTTTGCCTT
*
123441889 TCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG--GACACG-CTGAGGTAATTT
1 TCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGATCACACGTC-GAGGTAATTT
123441951 CAATTTCTGTTG
65 CAATTTCTGTTG
* * *
123441963 TCAAAAAAGTCAACTCGTATTGCGAGAGGTGAGTTGAGCCTCAGATCACACGTCGAGGTATTTTC
1 TCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGATCACACGTCGAGGTAATTTC
123442028 AATTTC
66 AATTTC
123442034 CATTTTTCAA
Statistics
Matches: 64, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
74 42 0.66
76 21 0.33
77 1 0.02
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (76 bp):
TCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGATCACACGTCGAGGTAATTTC
AATTTCTGTTG
Found at i:123442001 original size:165 final size:166
Alignment explanation
Indices: 123441729--123442208 Score: 700
Period size: 165 Copynumber: 2.9 Consensus size: 166
123441719 CTACTTTTTC
123441729 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
* * *
123441794 GTTGTCAAAAAAATCAACTCGTATTGCGAGTGGCGAGTTGAGCCTCAGGTCACACGCCGAGGTAT
66 GTTGTCAAAAAAATCAACTCGTATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACGTCGAGGTAT
* *
123441859 TTTCAATTTCCGTTTTTCAATTTTTGCCTTTC-AAA
131 TTTCAATTTCCGTTTTTCAATTTCTGCATTTCAAAA
123441894 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
* *
123441959 GTTGTCAAAAAAGTCAACTCGTATTGCGAGAGGTGAGTTGAGCCTCAGATCACACGTCGAGGTAT
66 GTTGTCAAAAAAATCAACTCGTATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACGTCGAGGTAT
*
123442024 TTTCAATTTCCATTTTTCAATTTCTGCATTTCAAAAAAAAAAA
131 TTTCAATTTCCGTTTTTCAATTTCTGCATTTC-------AAAA
*
123442067 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
* * * * ** * *
123442132 GTTTTC--AAAATTCAACTCATATTGTGAGAAATGAGTTGAGCCTCAAG--ACACGTTGAGGTAT
66 GTTGTCAAAAAAATCAACTCGTATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACGTCGAGGTAT
*
123442193 TTTCAATTTCTGTTTT
131 TTTCAATTTCCGTTTT
123442209 CAAAAAATCA
Statistics
Matches: 287, Mismatches: 20, Indels: 12
0.90 0.06 0.04
Matches are distributed among these distances:
165 154 0.54
169 27 0.09
171 34 0.12
173 72 0.25
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.32
Consensus pattern (166 bp):
AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
GTTGTCAAAAAAATCAACTCGTATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACGTCGAGGTAT
TTTCAATTTCCGTTTTTCAATTTCTGCATTTCAAAA
Found at i:123442149 original size:72 final size:73
Alignment explanation
Indices: 123442065--123442571 Score: 406
Period size: 72 Copynumber: 6.5 Consensus size: 73
123442055 CAAAAAAAAA
*
123442065 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTCAATTT
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTCAATTT
123442130 CTGTTTTC
66 CTGTTTTC
* * ** ** *
123442138 -AAAATTCAACTCATATTGTGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTT
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTCAATTT
123442202 CTGTTTTC
66 CTGTTTTC
* * * ** *
123442210 AAAAAATCAACTTATATTGCGAGAGGTGAGTTGACCCTTGGCTCATGCGCTGAGCTATTTTCAAT
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACA--CGCTGAGGTATTTTCAAT
*
123442275 TTCTATCTTTC
64 TTCTGT-TTTC
* ** *
123442286 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGATCACACACTGAGGTATTTTTTC
1 -AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-G-GGACACGCTGAGGTA--TTTTC
* *
123442351 AATTTATATTTTTC
61 AATTTCT-GTTTTC
* * *
123442365 AAAAAAATCAACTCACATTGCGAGATGTGAGTTGAGCCTCGGGTTACATG-TCGAGGTATTTTCA
1 -AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG--ACACGCT-GAGGTATTTTCA
**
123442429 AAATCTGTTTTTC
62 ATTTCTG-TTTTC
* * **
123442442 AAATTCTGTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTGGCTCACGTGCTGA
1 --A----------AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACAC--GCTGA
*
123442507 GCTATTTTCAATTTCTGTTTTTTTTTC
52 GGTATTTTCAATTTCTG-----TTTTC
123442534 AAAAAAATTCAACTCATATTGCGAGAGGTGAGTTGAGC
1 -AAAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGC
123442572 TTTTTAATTT
Statistics
Matches: 348, Mismatches: 53, Indels: 57
0.76 0.12 0.12
Matches are distributed among these distances:
72 64 0.18
73 33 0.09
75 21 0.06
76 4 0.01
77 57 0.16
78 5 0.01
79 64 0.18
80 1 0.00
81 5 0.01
82 29 0.08
86 2 0.01
88 54 0.16
89 1 0.00
91 2 0.01
92 6 0.02
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (73 bp):
AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTCAATTT
CTGTTTTC
Found at i:123442388 original size:79 final size:76
Alignment explanation
Indices: 123442064--123442781 Score: 427
Period size: 88 Copynumber: 9.0 Consensus size: 76
123442054 TCAAAAAAAA
** *
123442064 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-G-GGACACGCTGAGGTAATTTCAA
1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGATCACACGCTGAGGTATTTTCAA
123442127 TTTCTGTTTTC
66 TTTCTGTTTTC
* * ** * *
123442138 --AAAATTCAACTCATATTGTGAGAAATGAGTTGAGCCTCA-A-GACACGTTGAGGTATTTTCAA
1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGATCACACGCTGAGGTATTTTCAA
123442199 TTTCTGTTTTC
66 TTTCTGTTTTC
* * ** * ** *
123442210 -AAAAAATCAACTTATATTGCGAGAGGTGAGTTGACCCTTGGCTCATGCGCTGAGCTATTTTCAA
1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGATCACACGCTGAGGTATTTTCAA
*
123442274 TTTCTATCTTTC
66 TTTCTGT-TTTC
* *
123442286 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGATCACACACTGAGGTATTTTTTC
1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGATCACACGCTGAGGTA--TTTTC
* *
123442351 AATTTATATTTTTC
64 AATTTCT-GTTTTC
* * * * * *
123442365 AAAAAAATCAACTCACATTGCGAGATGTGAGTTGAGCCTCGGGTTACATG-TCGAGGTATTTTCA
1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGATCACACGCT-GAGGTATTTTCA
**
123442429 AAATCTGTTTTTC
65 ATTTCTG-TTTTC
* ** * **
123442442 AAATTCTGTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTGGCTCACGTGCTGA
1 -AA----------AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGATCACACGCTGA
*
123442507 GCTATTTTCAATTTCTGTTTTTTTTTC
55 GGTATTTTCAATTTCTG-----TTTTC
* * * * * *
123442534 AAAAAAATTCAACTCATATTGCGAGAGGTGAGTTGAGCTTTTTA-ATTTCTGCGAGAGTTGAGTT
1 AAAAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGC--CTCAGA--TC-AC-A-CGCTGAGGT
*
123442598 GAGTCTTTTAATTTCTGTTTTTC
58 -A-T-TTTCAATTTCTG-TTTTC
* **
123442621 --AAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCCAG-TCACA-TATCGAGGTATTTTC
1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT-CAGATCACACGCT-GAGGTATTTTC
**
123442682 AAAATCTGCTTTTC
64 AATTTCTG-TTTTC
** * *
123442696 AAGTTAAGTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGCGCTGA
1 ------A-----AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGATCACACGCTGA
*
123442761 GCTATTTTCAATTTCTGTTTT
55 GGTATTTTCAATTTCTGTTTT
123442782 TAATGTCTGT
Statistics
Matches: 503, Mismatches: 84, Indels: 101
0.73 0.12 0.15
Matches are distributed among these distances:
72 64 0.13
73 31 0.06
75 36 0.07
76 5 0.01
77 63 0.13
78 7 0.01
79 64 0.13
80 2 0.00
81 7 0.01
82 30 0.06
83 1 0.00
84 31 0.06
85 7 0.01
86 1 0.00
87 11 0.02
88 120 0.24
89 3 0.01
90 1 0.00
91 13 0.03
92 6 0.01
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.36
Consensus pattern (76 bp):
AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGATCACACGCTGAGGTATTTTCAA
TTTCTGTTTTC
Found at i:123442442 original size:14 final size:13
Alignment explanation
Indices: 123442423--123442458 Score: 54
Period size: 14 Copynumber: 2.7 Consensus size: 13
123442413 TGTCGAGGTA
123442423 TTTTCAAAATCTG
1 TTTTCAAAATCTG
*
123442436 TTTTTCAAATTCTG
1 -TTTTCAAAATCTG
123442450 TTTTCAAAA
1 TTTTCAAAA
123442459 ATCAACTCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.31, C:0.14, G:0.06, T:0.50
Consensus pattern (13 bp):
TTTTCAAAATCTG
Found at i:123442589 original size:30 final size:30
Alignment explanation
Indices: 123442553--123442614 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
123442543 CAACTCATAT
123442553 TGCGAGAGGTGAGTTGAG-CTTTTTAATTTC
1 TGCGAGAGGTGAGTTGAGTC-TTTTAATTTC
*
123442583 TGCGAGAGTTGAGTTGAGTCTTTTAATTTC
1 TGCGAGAGGTGAGTTGAGTCTTTTAATTTC
123442613 TG
1 TG
123442615 TTTTTCAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 29 0.97
31 1 0.03
ACGTcount: A:0.19, C:0.10, G:0.29, T:0.42
Consensus pattern (30 bp):
TGCGAGAGGTGAGTTGAGTCTTTTAATTTC
Found at i:123442715 original size:254 final size:248
Alignment explanation
Indices: 123442204--123442782 Score: 762
Period size: 254 Copynumber: 2.3 Consensus size: 248
123442194 TTCAATTTCT
* * *
123442204 GTTTTCAAAAAATCAACTTATATTGCGAGAGGTGAGTTGACCCTTGGCTCATGCGCTGAGCTATT
1 GTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGCGCTGAGCTATT
*
123442269 TTCAATTTC----TATCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGAT
66 TTCAATTTCTGTTTTTCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGAT
* *
123442330 CACACACTGAGGTATTTTTTCAATTTATATTTTTCAAAAAAATCAACTCACATTGCGAGATGTGA
131 CACACACTGAGGTATCTTTTCAATTTATATTTTTC-AAAAAATCAACTCACATTGCGAGAGGTGA
* ** * * * **
123442395 GTTGAGCCTCGGGTTACATGTCGAGGTATTTTCAAAATCTGTTTTTCAAATTCT
195 GTTGAACCTCCAGTCACATATCGAGGTATTTTCAAAATCTGCTTTTCAAATTAA
* *
123442449 GTTTTC-AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTGGCTCACGTGCTGAGCTATT
1 GTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGCGCTGAGCTATT
* *
123442513 TTCAATTTCTGTTTTTTTTTCAAAAAAATTCAACTCATATTGCGAGAGGTGAGTTGAGCTTTTTA
66 TTCAATTTCTGTTTTTCTTTCAAAAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGC--TTCA
* * * * * * *
123442578 -ATTTCTGCGAGAGTTGAGTTGAGTCTTTT-AATTTCTGTTTTTC-AAAAATCAACTCATATTGC
128 GA--TC-AC-ACA-CTGAGGT-A-TCTTTTCAATTTATATTTTTCAAAAAATCAACTCACATTGC
*
123442640 GAGAGGTGAGTTGAACCTCCAGTCACATATCGAGGTATTTTCAAAATCTGCTTTTCAAGTTAA
186 GAGAGGTGAGTTGAACCTCCAGTCACATATCGAGGTATTTTCAAAATCTGCTTTTCAAATTAA
123442703 G-TTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGCGCTGAGCTATT
1 GTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGCGCTGAGCTATT
123442767 TTCAATTTCTGTTTTT
66 TTCAATTTCTGTTTTT
123442783 AATGTCTGTT
Statistics
Matches: 291, Mismatches: 28, Indels: 21
0.86 0.08 0.06
Matches are distributed among these distances:
244 62 0.21
245 6 0.02
248 13 0.04
249 30 0.10
250 1 0.00
251 3 0.01
252 2 0.01
253 5 0.02
254 146 0.50
255 5 0.02
256 13 0.04
257 5 0.02
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.37
Consensus pattern (248 bp):
GTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGCGCTGAGCTATT
TTCAATTTCTGTTTTTCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGAT
CACACACTGAGGTATCTTTTCAATTTATATTTTTCAAAAAATCAACTCACATTGCGAGAGGTGAG
TTGAACCTCCAGTCACATATCGAGGTATTTTCAAAATCTGCTTTTCAAATTAA
Found at i:123443448 original size:17 final size:17
Alignment explanation
Indices: 123443428--123443464 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
123443418 AACCTAACCC
*
123443428 AAAAAAAAA-ACAAAGA
1 AAAAAAAAAGAAAAAGA
123443444 AAAAAAAAAGAAAAAGA
1 AAAAAAAAAGAAAAAGA
123443461 AAAA
1 AAAA
123443465 CCTACCAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.89, C:0.03, G:0.08, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAGAAAAAGA
Found at i:123443463 original size:11 final size:11
Alignment explanation
Indices: 123443431--123443464 Score: 50
Period size: 12 Copynumber: 2.9 Consensus size: 11
123443421 CTAACCCAAA
123443431 AAAAAAACAAAG
1 AAAAAAA-AAAG
123443443 AAAAAAAAAAG
1 AAAAAAAAAAG
123443454 AAAAAGAAAAA
1 AAAAA-AAAAA
123443465 CCTACCAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 9 0.43
12 12 0.57
ACGTcount: A:0.88, C:0.03, G:0.09, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:123443476 original size:13 final size:15
Alignment explanation
Indices: 123443460--123443492 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
123443450 AAAGAAAAAG
123443460 AAAAACCT-A-CCAA
1 AAAAACCTAACCCAA
123443473 AAAAACCTAACCCAA
1 AAAAACCTAACCCAA
123443488 AAAAA
1 AAAAA
123443493 AAAAGAAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 8 0.44
14 1 0.06
15 9 0.50
ACGTcount: A:0.67, C:0.27, G:0.00, T:0.06
Consensus pattern (15 bp):
AAAAACCTAACCCAA
Found at i:123446731 original size:21 final size:20
Alignment explanation
Indices: 123446707--123446749 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
123446697 TATTTTTTAA
* *
123446707 ATTTAAAAATTTATAAAATTT
1 ATTTAAAAA-GTATAAAAATT
*
123446728 ATTTTAAAAGTATAAAAATT
1 ATTTAAAAAGTATAAAAATT
123446748 AT
1 AT
123446750 AAAATATTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (20 bp):
ATTTAAAAAGTATAAAAATT
Found at i:123454162 original size:48 final size:49
Alignment explanation
Indices: 123453999--123454216 Score: 188
Period size: 48 Copynumber: 4.6 Consensus size: 49
123453989 TCCGTCAAGT
*
123453999 CGATGCCATGTCCCAGACATGGTCTTACACTGACTA-TTGA-AATCGAG-GC
1 CGATGCCATGTCCCAGACATGGTCTTACACTGAC-ACTT-ACTATCG-GTGC
* * * *
123454048 CGATGCCATGTCCCAAACACGGTCTTACACT-AGCTCTTACATATCCGTGC
1 CGATGCCATGTCCCAGACATGGTCTTACACTGA-CACTTAC-TATCGGTGC
* * *
123454098 TGATGCCATGTCCCAGACATGGTCTTACACTGACACCT-CTATAGGTGC
1 CGATGCCATGTCCCAGACATGGTCTTACACTGACACTTACTATCGGTGC
* * * * *
123454146 CAATGCCATGTCCCAGATATGGTCTTACACTAACAC--A-TCTC-GTAGT
1 CGATGCCATGTCCCAGACATGGTCTTACACTGACACTTACTATCGGT-GC
123454192 CGATG-CATGTCCCAGACAT-GTCTTA
1 CGATGCCATGTCCCAGACATGGTCTTA
123454217 TATTGGCTTA
Statistics
Matches: 140, Mismatches: 21, Indels: 21
0.77 0.12 0.12
Matches are distributed among these distances:
44 6 0.04
45 15 0.11
46 7 0.05
48 41 0.29
49 34 0.24
50 36 0.26
51 1 0.01
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.27
Consensus pattern (49 bp):
CGATGCCATGTCCCAGACATGGTCTTACACTGACACTTACTATCGGTGC
Found at i:123454341 original size:47 final size:46
Alignment explanation
Indices: 123454192--123454358 Score: 153
Period size: 46 Copynumber: 3.6 Consensus size: 46
123454182 ATCTCGTAGT
* ** * *
123454192 CGATGCATGTCCCAGACATGTCTTATATTGGCT-TACATCGTGAGGA
1 CGATGCATGTCCCAGACATGTCTTACATTGGCTCT-CATAATGTGGC
* * * *
123454238 CGATGCATGTCCTAGACATGTCTTACACTAGCTCTCGTTTCAA--T-GC
1 CGATGCATGTCCCAGACATGTCTTACATTGGCTCTC--AT-AATGTGGC
*
123454284 CGGTGCCATGTCCCAGACATGATCTTACATTGGCTCTCATAATGTGGC
1 CGATG-CATGTCCCAGACATG-TCTTACATTGGCTCTCATAATGTGGC
*
123454332 CGATGCATGTCCCAGACATGTTTTACA
1 CGATGCATGTCCCAGACATGTCTTACA
123454359 CTAGCATACA
Statistics
Matches: 96, Mismatches: 16, Indels: 18
0.74 0.12 0.14
Matches are distributed among these distances:
45 2 0.02
46 42 0.44
47 31 0.32
48 21 0.22
ACGTcount: A:0.23, C:0.26, G:0.21, T:0.31
Consensus pattern (46 bp):
CGATGCATGTCCCAGACATGTCTTACATTGGCTCTCATAATGTGGC
Found at i:123470251 original size:45 final size:45
Alignment explanation
Indices: 123470187--123470278 Score: 184
Period size: 45 Copynumber: 2.0 Consensus size: 45
123470177 TAAGATGTAC
123470187 ATTGCCCTCAATGTACAAAGATAGATGTTAGAGTATAAAAATAAG
1 ATTGCCCTCAATGTACAAAGATAGATGTTAGAGTATAAAAATAAG
123470232 ATTGCCCTCAATGTACAAAGATAGATGTTAGAGTATAAAAATAAG
1 ATTGCCCTCAATGTACAAAGATAGATGTTAGAGTATAAAAATAAG
123470277 AT
1 AT
123470279 AGGGAGAGAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.45, C:0.11, G:0.17, T:0.27
Consensus pattern (45 bp):
ATTGCCCTCAATGTACAAAGATAGATGTTAGAGTATAAAAATAAG
Found at i:123474981 original size:27 final size:27
Alignment explanation
Indices: 123474943--123475005 Score: 117
Period size: 27 Copynumber: 2.3 Consensus size: 27
123474933 ATCATCTCCT
*
123474943 CGTCACCTACTCTAAGTACCAATTTAC
1 CGTCACCCACTCTAAGTACCAATTTAC
123474970 CGTCACCCACTCTAAGTACCAATTTAC
1 CGTCACCCACTCTAAGTACCAATTTAC
123474997 CGTCACCCA
1 CGTCACCCA
123475006 TGCCAATTAC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.29, C:0.38, G:0.08, T:0.25
Consensus pattern (27 bp):
CGTCACCCACTCTAAGTACCAATTTAC
Found at i:123484724 original size:17 final size:18
Alignment explanation
Indices: 123484692--123484726 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
123484682 CGTGTGGTTC
123484692 ACCCGTGTGAGCCCACAT
1 ACCCGTGTGAGCCCACAT
123484710 ACCCGTGTG-GCCCACAT
1 ACCCGTGTGAGCCCACAT
123484727 GGCCCAATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.20, C:0.40, G:0.23, T:0.17
Consensus pattern (18 bp):
ACCCGTGTGAGCCCACAT
Found at i:123486171 original size:11 final size:11
Alignment explanation
Indices: 123486155--123486182 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
123486145 ATTGTAGACC
123486155 ATAAAAATAAA
1 ATAAAAATAAA
123486166 ATAAAAATAAA
1 ATAAAAATAAA
123486177 ATAAAA
1 ATAAAA
123486183 TTTTTTCTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (11 bp):
ATAAAAATAAA
Found at i:123491852 original size:18 final size:19
Alignment explanation
Indices: 123491823--123491864 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 19
123491813 TTATTACTTA
*
123491823 AAAAATATAAAAAATATTT
1 AAAAATATAAAAAAAATTT
123491842 AAAAATA-AAAAAAAATTT
1 AAAAATATAAAAAAAATTT
123491860 AAAAA
1 AAAAA
123491865 GTTCCACACA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 15 0.68
19 7 0.32
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (19 bp):
AAAAATATAAAAAAAATTT
Found at i:123493893 original size:12 final size:12
Alignment explanation
Indices: 123493876--123493914 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
123493866 AAGTTAAGAA
123493876 AGAAAAAGAAAG
1 AGAAAAAGAAAG
123493888 AGAAAAAGAAAG
1 AGAAAAAGAAAG
*
123493900 A-AAGAAGAAATG
1 AGAAAAAGAAA-G
123493912 AGA
1 AGA
123493915 GACACACGAC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
11 8 0.33
12 15 0.62
13 1 0.04
ACGTcount: A:0.72, C:0.00, G:0.26, T:0.03
Consensus pattern (12 bp):
AGAAAAAGAAAG
Found at i:123493916 original size:26 final size:22
Alignment explanation
Indices: 123493871--123493914 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 22
123493861 ATGCAAAGTT
123493871 AAGAAAGAAAAAGAAAGAGAAA
1 AAGAAAGAAAAAGAAAGAGAAA
123493893 AAGAAAGAAAGAAGAAATGAGA
1 AAGAAAGAAA-AAGAAA-GAGA
123493915 GACACACGAC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 10 0.50
23 6 0.30
24 4 0.20
ACGTcount: A:0.73, C:0.00, G:0.25, T:0.02
Consensus pattern (22 bp):
AAGAAAGAAAAAGAAAGAGAAA
Found at i:123508777 original size:20 final size:18
Alignment explanation
Indices: 123508730--123508831 Score: 58
Period size: 20 Copynumber: 5.8 Consensus size: 18
123508720 CAAGATAAAA
123508730 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
123508747 ATTAAGA-TAATCATTCTAAT
1 ATTAA-ATTAAT-ATT-TAAT
*
123508767 ATTAAATTAATA--AAAT
1 ATTAAATTAATATTTAAT
*
123508783 ACT--ATTAATA--TAAGT
1 ATTAAATTAATATTTAA-T
*
123508798 ATTAAATTTAATATTAAACT
1 ATTAAA-TTAATATTTAA-T
*
123508818 ATTAAAATAATATT
1 ATTAAATTAATATT
123508832 ATTTTTGGAA
Statistics
Matches: 67, Mismatches: 7, Indels: 20
0.71 0.07 0.21
Matches are distributed among these distances:
14 9 0.13
15 3 0.04
16 5 0.07
17 9 0.13
18 7 0.10
19 12 0.18
20 22 0.33
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.42
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:123508819 original size:32 final size:32
Alignment explanation
Indices: 123508735--123508832 Score: 96
Period size: 32 Copynumber: 3.1 Consensus size: 32
123508725 TAAAAATTAA
* * *
123508735 ATTAAATTTAATATTAAGA-TAATCATTCTAAT
1 ATTAAATTTAATATTAAGACT-ATTAATATAAT
* *
123508767 ATTAAA-TTAATA-AAATACTATTAATATAAGT
1 ATTAAATTTAATATTAAGACTATTAATATAA-T
*
123508798 ATTAAATTTAATATTAA-ACTATTAAAATAAT
1 ATTAAATTTAATATTAAGACTATTAATATAAT
123508829 ATTA
1 ATTA
123508833 TTTTTGGAAT
Statistics
Matches: 55, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
30 10 0.18
31 19 0.35
32 24 0.44
33 2 0.04
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.42
Consensus pattern (32 bp):
ATTAAATTTAATATTAAGACTATTAATATAAT
Found at i:123510826 original size:27 final size:28
Alignment explanation
Indices: 123510796--123510888 Score: 102
Period size: 27 Copynumber: 3.4 Consensus size: 28
123510786 GATTACCTTG
*
123510796 TGTTTATTGTCCCTG-TGGACTACCCCA
1 TGTTTACTGTCCCTGATGGACTACCCCA
* * *
123510823 TGTTTACTAT-CTTGATGGACTACCCTA
1 TGTTTACTGTCCCTGATGGACTACCCCA
* *
123510850 TGTTTACTGTTCC-GATTGACTACCCCA
1 TGTTTACTGTCCCTGATGGACTACCCCA
*
123510877 TGTTTATTGTCC
1 TGTTTACTGTCC
123510889 TAGCAGACTA
Statistics
Matches: 54, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
26 3 0.06
27 50 0.93
28 1 0.02
ACGTcount: A:0.17, C:0.26, G:0.16, T:0.41
Consensus pattern (28 bp):
TGTTTACTGTCCCTGATGGACTACCCCA
Found at i:123522200 original size:21 final size:21
Alignment explanation
Indices: 123522175--123522223 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
123522165 TGTCTTATAT
123522175 ACTTAATAAATATTTAATTAA
1 ACTTAATAAATATTTAATTAA
* * ** *
123522196 TCTTATTTTATTTTTAATTAA
1 ACTTAATAAATATTTAATTAA
123522217 ACTTAAT
1 ACTTAAT
123522224 TAGATTAATG
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (21 bp):
ACTTAATAAATATTTAATTAA
Found at i:123522451 original size:20 final size:20
Alignment explanation
Indices: 123522428--123522467 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
123522418 TTATACTGAC
*
123522428 CTTGTAAATATTAAATAATA
1 CTTGTAAATACTAAATAATA
123522448 CTTGTAAATACTAAATAATA
1 CTTGTAAATACTAAATAATA
123522468 TTTACGGACT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.50, C:0.07, G:0.05, T:0.38
Consensus pattern (20 bp):
CTTGTAAATACTAAATAATA
Found at i:123525161 original size:22 final size:21
Alignment explanation
Indices: 123525126--123525183 Score: 53
Period size: 22 Copynumber: 2.7 Consensus size: 21
123525116 AAAGGATATC
* * *
123525126 TACAAATTAAATCTCTAAGAT
1 TACAAATCATATCTCTAAAAT
123525147 TACAAAATCATATCTTCTAAAAT
1 TAC-AAATCATATC-TCTAAAAT
* *
123525170 TGCATATCATATCT
1 TACAAATCATATCT
123525184 AAGATTGCAA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
21 4 0.13
22 17 0.57
23 9 0.30
ACGTcount: A:0.43, C:0.17, G:0.03, T:0.36
Consensus pattern (21 bp):
TACAAATCATATCTCTAAAAT
Found at i:123525190 original size:19 final size:19
Alignment explanation
Indices: 123525162--123525252 Score: 125
Period size: 19 Copynumber: 4.9 Consensus size: 19
123525152 AATCATATCT
*
123525162 TCTAAAATTGCATATCATA
1 TCTAAGATTGCATATCATA
123525181 TCTAAGATTGCA-ATCATA
1 TCTAAGATTGCATATCATA
*
123525199 TATAAGATTG--TATCATA
1 TCTAAGATTGCATATCATA
*
123525216 TCTAAGATTGCATATCACA
1 TCTAAGATTGCATATCATA
*
123525235 ACTAAGATTGCATATCAT
1 TCTAAGATTGCATATCAT
123525253 TGAAGATTAT
Statistics
Matches: 63, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
17 15 0.24
18 15 0.24
19 33 0.52
ACGTcount: A:0.40, C:0.15, G:0.10, T:0.35
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:123529379 original size:32 final size:34
Alignment explanation
Indices: 123529343--123529407 Score: 89
Period size: 32 Copynumber: 2.0 Consensus size: 34
123529333 TAACAGTGGT
*
123529343 ACTGGGCCAGAGCCC-TT-TTCAGATTACAATAA
1 ACTGGGCCAGAGCCCATTATTCAGATAACAATAA
**
123529375 ACTGGGCCTTAGCCCATTATTCAGATAACAATA
1 ACTGGGCCAGAGCCCATTATTCAGATAACAATA
123529408 TGGCCCATAG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 13 0.46
33 2 0.07
34 13 0.46
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26
Consensus pattern (34 bp):
ACTGGGCCAGAGCCCATTATTCAGATAACAATAA
Found at i:123532985 original size:26 final size:26
Alignment explanation
Indices: 123532949--123533056 Score: 207
Period size: 26 Copynumber: 4.2 Consensus size: 26
123532939 TGAAATTCTC
123532949 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
123532975 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
123533001 ATCATGAAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
123533027 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
123533053 ATCA
1 ATCA
123533057 ATTTGTATCA
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 80 1.00
ACGTcount: A:0.36, C:0.27, G:0.06, T:0.31
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:123535104 original size:18 final size:18
Alignment explanation
Indices: 123535081--123535135 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
123535071 AGAAGTTGTA
123535081 GGAAATCATGGACTAATT
1 GGAAATCATGGACTAATT
* *
123535099 GGAAATTATTG--T-A--
1 GGAAATCATGGACTAATT
123535112 GGAAATCATGGACTAATT
1 GGAAATCATGGACTAATT
123535130 GGAAAT
1 GGAAAT
123535136 TTTCTCTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 10
0.67 0.10 0.24
Matches are distributed among these distances:
13 9 0.32
15 2 0.07
16 2 0.07
18 15 0.54
ACGTcount: A:0.40, C:0.07, G:0.24, T:0.29
Consensus pattern (18 bp):
GGAAATCATGGACTAATT
Found at i:123535114 original size:31 final size:31
Alignment explanation
Indices: 123535076--123535136 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
123535066 TTTGTAGAAG
123535076 TTGTAGGAAATCATGGACTAATTGGAAATTA
1 TTGTAGGAAATCATGGACTAATTGGAAATTA
123535107 TTGTAGGAAATCATGGACTAATTGGAAATT
1 TTGTAGGAAATCATGGACTAATTGGAAATT
123535137 TTCTCTTTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.38, C:0.07, G:0.23, T:0.33
Consensus pattern (31 bp):
TTGTAGGAAATCATGGACTAATTGGAAATTA
Found at i:123535471 original size:16 final size:16
Alignment explanation
Indices: 123535452--123535482 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
123535442 TTTCACTAAA
123535452 ATCATTTAATAAATTC
1 ATCATTTAATAAATTC
*
123535468 ATCATTTAATGAATT
1 ATCATTTAATAAATT
123535483 AAAAGCTTCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.10, G:0.03, T:0.45
Consensus pattern (16 bp):
ATCATTTAATAAATTC
Found at i:123535991 original size:30 final size:30
Alignment explanation
Indices: 123535957--123536017 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
123535947 TAACTATCAA
123535957 AACGTTAAAATTTTATGACGAAACTTTAAT
1 AACGTTAAAATTTTATGACGAAACTTTAAT
123535987 AACGTTAAAATTTTATGACGAAACTTTAAT
1 AACGTTAAAATTTTATGACGAAACTTTAAT
123536017 A
1 A
123536018 CTAACTTAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.44, C:0.10, G:0.10, T:0.36
Consensus pattern (30 bp):
AACGTTAAAATTTTATGACGAAACTTTAAT
Found at i:123537870 original size:25 final size:25
Alignment explanation
Indices: 123537842--123537899 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
123537832 AGTTGTAAAA
* *
123537842 GGTAAGCTCATACAACCTGAATATC
1 GGTAAACTCATACAACCTAAATATC
* * *
123537867 GGTAAACTCATGCGAGCTAAATATC
1 GGTAAACTCATACAACCTAAATATC
123537892 GGTAAACT
1 GGTAAACT
123537900 TTCTCAAGAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.36, C:0.21, G:0.19, T:0.24
Consensus pattern (25 bp):
GGTAAACTCATACAACCTAAATATC
Found at i:123540713 original size:47 final size:46
Alignment explanation
Indices: 123540643--123540771 Score: 143
Period size: 47 Copynumber: 2.8 Consensus size: 46
123540633 TTGCAAGTAA
* * * *
123540643 TACCTTAATTTGGCTACTGGCCATGGTATAGGTA-TTCAGAGAGGAGT
1 TACCTTGATTTGGCTAC-GGCCATGGTATAAGTACTCCAGA-AGAAGT
* * *
123540690 TACCTTGATTTGGTTACGAGCCATGATATAAGTACTCCAGAATAAGT
1 TACCTTGATTTGGCTACG-GCCATGGTATAAGTACTCCAGAAGAAGT
* *
123540737 TACCTTGATTTGGCTACGGCTATGGTATATGTACT
1 TACCTTGATTTGGCTACGGCCATGGTATAAGTACT
123540772 TATCGATTGA
Statistics
Matches: 69, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
46 15 0.22
47 49 0.71
48 5 0.07
ACGTcount: A:0.26, C:0.16, G:0.23, T:0.34
Consensus pattern (46 bp):
TACCTTGATTTGGCTACGGCCATGGTATAAGTACTCCAGAAGAAGT
Found at i:123546685 original size:17 final size:18
Alignment explanation
Indices: 123546665--123546702 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
123546655 TGGCATGCCA
123546665 ATTGTATTAAAAT-ATTT
1 ATTGTATTAAAATAATTT
*
123546682 ATTGTATTAAATTAATTT
1 ATTGTATTAAAATAATTT
123546700 ATT
1 ATT
123546703 AATAAAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.55
Consensus pattern (18 bp):
ATTGTATTAAAATAATTT
Found at i:123547030 original size:12 final size:12
Alignment explanation
Indices: 123547013--123547045 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
123547003 CGACCCGCCC
123547013 ATATTAATTTTT
1 ATATTAATTTTT
123547025 ATATT-ATTTTT
1 ATATTAATTTTT
123547036 ATA-TAATTTT
1 ATATTAATTTT
123547046 AAAATATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 14 0.70
12 5 0.25
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:123547213 original size:30 final size:30
Alignment explanation
Indices: 123547169--123547231 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
123547159 ATTTAACAAG
*
123547169 CAAATGCTTCTAAAATAATAACAAAATTAA
1 CAAATGCTTCTAAAATAATAAAAAAATTAA
123547199 CAAATGTCTT-TAAAATAATAAAAAAATTAA
1 CAAATG-CTTCTAAAATAATAAAAAAATTAA
123547229 CAA
1 CAA
123547232 TAAAATAAGT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 28 0.90
31 3 0.10
ACGTcount: A:0.59, C:0.11, G:0.03, T:0.27
Consensus pattern (30 bp):
CAAATGCTTCTAAAATAATAAAAAAATTAA
Found at i:123549206 original size:32 final size:32
Alignment explanation
Indices: 123549165--123549231 Score: 116
Period size: 32 Copynumber: 2.1 Consensus size: 32
123549155 CGTTTATTAG
*
123549165 TTTTGAAATCTTTCTAACATCCTTGTATAATT
1 TTTTGAAATCTTTCTAACATCCCTGTATAATT
*
123549197 TTTTGAAATCTTTCTTACATCCCTGTATAATT
1 TTTTGAAATCTTTCTAACATCCCTGTATAATT
123549229 TTT
1 TTT
123549232 CAGCTTATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.25, C:0.16, G:0.06, T:0.52
Consensus pattern (32 bp):
TTTTGAAATCTTTCTAACATCCCTGTATAATT
Found at i:123559292 original size:17 final size:17
Alignment explanation
Indices: 123559267--123559313 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
123559257 TAATTTTTCG
123559267 AAAAA-TATTTTTACAA
1 AAAAATTATTTTTACAA
**
123559283 AAAAATTATTTAAACAA
1 AAAAATTATTTTTACAA
*
123559300 AAAATTTTATTTTT
1 AAAA-ATTATTTTT
123559314 TGAAAAATAA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
16 5 0.21
17 13 0.54
18 6 0.25
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (17 bp):
AAAAATTATTTTTACAA
Found at i:123560902 original size:27 final size:29
Alignment explanation
Indices: 123560841--123560902 Score: 76
Period size: 27 Copynumber: 2.2 Consensus size: 29
123560831 AAAATAATAA
123560841 AAATATATTATATGATATAATAGCTTAGT
1 AAATATATTATATGATATAATAGCTTAGT
* *
123560870 ATATAT-TTATAT-ATATAATA-CTATATT
1 AAATATATTATATGATATAATAGCT-TAGT
123560897 AAATAT
1 AAATAT
123560903 GTGTGAAACT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
26 2 0.07
27 16 0.55
28 6 0.21
29 5 0.17
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (29 bp):
AAATATATTATATGATATAATAGCTTAGT
Found at i:123561084 original size:20 final size:19
Alignment explanation
Indices: 123561049--123561098 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
123561039 TAGTAAAAAT
*
123561049 AATATAATATATATATCGTAA
1 AATAT-ATA-ATATATCATAA
*
123561070 AATGATATAATATATTATAA
1 AAT-ATATAATATATCATAA
123561090 AATATATAA
1 AATATATAA
123561099 ATAAAATGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
19 6 0.23
20 12 0.46
21 6 0.23
22 2 0.08
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (19 bp):
AATATATAATATATCATAA
Found at i:123561095 original size:34 final size:32
Alignment explanation
Indices: 123561067--123561143 Score: 88
Period size: 32 Copynumber: 2.4 Consensus size: 32
123561057 ATATATATCG
123561067 TAAAATGATATAATATATTATAAAATATATAAA
1 TAAAATG-TATAATATATTATAAAATATATAAA
123561100 TAAAATGTATAATA-ATGTA-AATAATATGATAAA
1 TAAAATGTATAATATAT-TATAA-AATAT-ATAAA
*
123561133 TAATATG-ATAA
1 TAAAATGTATAA
123561144 ATAATAAAGA
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
31 4 0.10
32 18 0.45
33 18 0.45
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.35
Consensus pattern (32 bp):
TAAAATGTATAATATATTATAAAATATATAAA
Found at i:123561098 original size:19 final size:20
Alignment explanation
Indices: 123561035--123561098 Score: 60
Period size: 24 Copynumber: 3.1 Consensus size: 20
123561025 AGTAATATAA
*
123561035 AATATAGTA-AAAATAATAT
1 AATATATTATAAAATAATAT
*
123561054 AATATATATATCGTAAAATGATAT
1 AATATAT-TA---TAAAATAATAT
123561078 AATATATTATAAAAT-ATAT
1 AATATATTATAAAATAATAT
123561097 AA
1 AA
123561099 ATAAAATGTA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
19 12 0.32
20 8 0.21
23 2 0.05
24 16 0.42
ACGTcount: A:0.58, C:0.02, G:0.05, T:0.36
Consensus pattern (20 bp):
AATATATTATAAAATAATAT
Found at i:123561111 original size:32 final size:33
Alignment explanation
Indices: 123561067--123561148 Score: 91
Period size: 33 Copynumber: 2.5 Consensus size: 33
123561057 ATATATATCG
123561067 TAAAATGATATAATATAT-TATAA-AATAT-ATAAA
1 TAAAATG-TATAATA-ATGTA-AATAATATGATAAA
123561100 TAAAATGTATAATAATGTAAATAATATGATAAA
1 TAAAATGTATAATAATGTAAATAATATGATAAA
*
123561133 TAATATG-ATAAATAAT
1 TAAAATGTAT-AATAAT
123561149 AAAGATAATA
Statistics
Matches: 44, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
31 4 0.09
32 16 0.36
33 24 0.55
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (33 bp):
TAAAATGTATAATAATGTAAATAATATGATAAA
Found at i:123561121 original size:21 final size:21
Alignment explanation
Indices: 123561096--123561136 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
123561086 ATAAAATATA
123561096 TAAATAAAATG-TATAATAATG
1 TAAATAAAATGATA-AATAATG
*
123561117 TAAATAATATGATAAATAAT
1 TAAATAAAATGATAAATAAT
123561137 ATGATAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.34
Consensus pattern (21 bp):
TAAATAAAATGATAAATAATG
Found at i:123561123 original size:12 final size:13
Alignment explanation
Indices: 123561108--123561156 Score: 68
Period size: 12 Copynumber: 4.0 Consensus size: 13
123561098 AATAAAATGT
123561108 ATAATAATG-TAA
1 ATAATAATGATAA
123561120 ATAAT-ATGATAA
1 ATAATAATGATAA
123561132 ATAAT-ATGATAA
1 ATAATAATGATAA
*
123561144 ATAATAAAGATAA
1 ATAATAATGATAA
123561157 TATATATTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
11 3 0.09
12 25 0.74
13 6 0.18
ACGTcount: A:0.61, C:0.00, G:0.08, T:0.31
Consensus pattern (13 bp):
ATAATAATGATAA
Found at i:123561156 original size:21 final size:21
Alignment explanation
Indices: 123561090--123561159 Score: 56
Period size: 21 Copynumber: 3.2 Consensus size: 21
123561080 TATATTATAA
*
123561090 AATAT-ATAAATAA-AATGTAT
1 AATATGATAAATAATAAAG-AT
*
123561110 AATAATG-TAAATAATATGATAAAT
1 AAT-ATGATAAATAATA--A-AGAT
123561134 AATATGATAAATAATAAAGAT
1 AATATGATAAATAATAAAGAT
123561155 AATAT
1 AATAT
123561160 ATATTATTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 13
0.71 0.05 0.23
Matches are distributed among these distances:
20 3 0.08
21 17 0.43
22 2 0.05
23 3 0.08
24 15 0.38
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (21 bp):
AATATGATAAATAATAAAGAT
Found at i:123561157 original size:33 final size:32
Alignment explanation
Indices: 123561067--123561162 Score: 90
Period size: 33 Copynumber: 2.9 Consensus size: 32
123561057 ATATATATCG
* *
123561067 TAAAATGATATAATATATTATAA-AATATATAAA
1 TAAAATG-TATAATA-ATGAAAATAATATATAAA
*
123561100 TAAAATGTATAATAATGTAAATAATATGATAAA
1 TAAAATGTATAATAATGAAAATAATAT-ATAAA
*
123561133 TAATATG-ATAAATAAT-AAAGATAATATATA
1 TAAAATGTAT-AATAATGAAA-ATAATATATA
123561163 TTATTTTTAT
Statistics
Matches: 54, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
31 4 0.07
32 19 0.35
33 31 0.57
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.34
Consensus pattern (32 bp):
TAAAATGTATAATAATGAAAATAATATATAAA
Found at i:123564712 original size:18 final size:19
Alignment explanation
Indices: 123564691--123564728 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
123564681 ATTTTAAAAA
123564691 TATATAAAT-TTTGGAATT
1 TATATAAATATTTGGAATT
*
123564709 TATATAAATATTTTGAATT
1 TATATAAATATTTGGAATT
123564728 T
1 T
123564729 GAAAAATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.39, C:0.00, G:0.08, T:0.53
Consensus pattern (19 bp):
TATATAAATATTTGGAATT
Found at i:123564769 original size:20 final size:20
Alignment explanation
Indices: 123564717--123564769 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 20
123564707 TTTATATAAA
123564717 TATTTTGAA-TTTGAAAAAT
1 TATTTTGAATTTTGAAAAAT
*
123564736 TATTTTAAAATTTTG-AAAAT
1 TATTTT-GAATTTTGAAAAAT
123564756 TATTTTGAACTTTT
1 TATTTTGAA-TTTT
123564770 TTATAATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
19 8 0.28
20 17 0.59
21 4 0.14
ACGTcount: A:0.38, C:0.02, G:0.08, T:0.53
Consensus pattern (20 bp):
TATTTTGAATTTTGAAAAAT
Found at i:123573769 original size:46 final size:44
Alignment explanation
Indices: 123573664--123573771 Score: 135
Period size: 44 Copynumber: 2.4 Consensus size: 44
123573654 TGTCTTTGAC
** * * *
123573664 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
123573708 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
*
123573754 ATGGACTTATATGGCTCA
1 ATGGACTTACATGGCTCA
123573772 TTTCTGTTCT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 33 0.60
46 22 0.40
ACGTcount: A:0.30, C:0.22, G:0.14, T:0.34
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:123576727 original size:26 final size:26
Alignment explanation
Indices: 123576676--123576728 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
123576666 ATCTCCCTGA
** **
123576676 GTAAGGTTCAGGAGTTCCCTTTTATG
1 GTAAGGTTCAGGAACTCCCTCCTATG
123576702 GTAAGGTTCAGGAACTCCCTCCTATG
1 GTAAGGTTCAGGAACTCCCTCCTATG
123576728 G
1 G
123576729 GCATCCACGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (26 bp):
GTAAGGTTCAGGAACTCCCTCCTATG
Found at i:123577403 original size:17 final size:17
Alignment explanation
Indices: 123577378--123577418 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
123577368 TCGCAGTCTC
* *
123577378 TCTCTGTTTTGCTACAG
1 TCTCAGTTTTACTACAG
123577395 TCTCAGTTTTACTACAG
1 TCTCAGTTTTACTACAG
*
123577412 TTTCAGT
1 TCTCAGT
123577419 ATATACTGCC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.17, C:0.22, G:0.15, T:0.46
Consensus pattern (17 bp):
TCTCAGTTTTACTACAG
Found at i:123577482 original size:25 final size:24
Alignment explanation
Indices: 123577410--123577482 Score: 58
Period size: 25 Copynumber: 2.9 Consensus size: 24
123577400 GTTTTACTAC
* * *
123577410 AGTTTCAGTATATACTGCCTAGAGT
1 AGTTTCAGAATATACT-ACTACAGT
* *
123577435 -GTTTTCACAGTATACTACTTACAGT
1 AG-TTTCAGAATATACTAC-TACAGT
123577460 AGTTTCAGAATATACTATCTACA
1 AGTTTCAGAATATACTA-CTACA
123577483 ATATTTTTAA
Statistics
Matches: 37, Mismatches: 7, Indels: 8
0.71 0.13 0.15
Matches are distributed among these distances:
24 2 0.05
25 33 0.89
26 2 0.05
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.37
Consensus pattern (24 bp):
AGTTTCAGAATATACTACTACAGT
Found at i:123582513 original size:41 final size:41
Alignment explanation
Indices: 123582457--123582551 Score: 151
Period size: 41 Copynumber: 2.4 Consensus size: 41
123582447 GGTAGGGAAG
123582457 GGGAATAAAAG-TTTTTTTTTTT--GGGGGGGGAAGTGAGA
1 GGGAATAAAAGTTTTTTTTTTTTGAGGGGGGGGAAGTGAGA
123582495 GGGAATAAAAGTTTTTTTTTTTTGAGGGGGGGGAAGTGAGA
1 GGGAATAAAAGTTTTTTTTTTTTGAGGGGGGGGAAGTGAGA
*
123582536 GAGAAGTAAAAGTTTT
1 GGGAA-TAAAAGTTTT
123582552 GGGAAAAAAA
Statistics
Matches: 52, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
38 11 0.21
39 11 0.21
41 20 0.38
42 10 0.19
ACGTcount: A:0.29, C:0.00, G:0.37, T:0.34
Consensus pattern (41 bp):
GGGAATAAAAGTTTTTTTTTTTTGAGGGGGGGGAAGTGAGA
Found at i:123587005 original size:2 final size:2
Alignment explanation
Indices: 123586998--123587052 Score: 51
Period size: 2 Copynumber: 28.5 Consensus size: 2
123586988 TGGTTTAATG
** * *
123586998 AT AT AT AT AT AT AT AT AT AT AT GC AT GT GT AT AT -T 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
*
123587039 AT AT -T AT AT TT AT A
1 AT AT AT AT AT AT AT A
123587053 AGTTAAATAA
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
1 2 0.05
2 41 0.95
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.51
Consensus pattern (2 bp):
AT
Found at i:123587531 original size:30 final size:30
Alignment explanation
Indices: 123587497--123587559 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
123587487 ATTTATTTTA
123587497 TTGTTAATTTTCTTATTATTTTA-AAGGCAT
1 TTGTTAATTTTCTTATTATTTTAGAA-GCAT
*
123587527 TTGTTAATTTTTTTATTATTTTAGAAGCAT
1 TTGTTAATTTTCTTATTATTTTAGAAGCAT
123587557 TTG
1 TTG
123587560 CTTGTTAAGT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 29 0.94
31 2 0.06
ACGTcount: A:0.25, C:0.05, G:0.11, T:0.59
Consensus pattern (30 bp):
TTGTTAATTTTCTTATTATTTTAGAAGCAT
Found at i:123589463 original size:31 final size:31
Alignment explanation
Indices: 123589420--123589481 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
123589410 GGTGATGTTA
* *
123589420 AAATTTGTAATGGTATGTACCTAGGAAGTCT
1 AAATTTGCAATGGCATGTACCTAGGAAGTCT
123589451 AAATTTGCAATGGCATGTACCTAGGAAGTCT
1 AAATTTGCAATGGCATGTACCTAGGAAGTCT
123589482 TTGTTTGAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.32, C:0.13, G:0.23, T:0.32
Consensus pattern (31 bp):
AAATTTGCAATGGCATGTACCTAGGAAGTCT
Found at i:123594259 original size:30 final size:30
Alignment explanation
Indices: 123594189--123594250 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
123594179 GGTACTCAGT
*
123594189 ACGGTGGAGGTGAGTCATCCCAAGTTCGGC
1 ACGGTGAAGGTGAGTCATCCCAAGTTCGGC
*
123594219 ACGGTGAAGGTGAGTCATCCCAAGTTTGGC
1 ACGGTGAAGGTGAGTCATCCCAAGTTCGGC
123594249 AC
1 AC
123594251 TTTTAAGGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.23, C:0.23, G:0.34, T:0.21
Consensus pattern (30 bp):
ACGGTGAAGGTGAGTCATCCCAAGTTCGGC
Found at i:123597078 original size:93 final size:93
Alignment explanation
Indices: 123596966--123597136 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
123596956 GCCCATAAGT
* *
123596966 GAACTCGGACTCAACTCAACGAGCTCGGTCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
123597031 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
123597059 GAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
123597124 CGAGTTCGGATGC
66 CGAGTTCGGATGC
123597137 TCAACCATCC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.27, C:0.30, G:0.22, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:123597152 original size:46 final size:46
Alignment explanation
Indices: 123596958--123597138 Score: 235
Period size: 46 Copynumber: 3.9 Consensus size: 46
123596948 TGTAACCCGC
* *
123596958 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG-TCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGAT-GCTCGCAT
*
123597004 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATG-CTCG---CAT
* * *
123597054 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCGCAT
123597097 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTC
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTC
123597139 AACCATCCTA
Statistics
Matches: 117, Mismatches: 10, Indels: 16
0.82 0.07 0.11
Matches are distributed among these distances:
43 3 0.03
44 1 0.01
45 2 0.02
46 72 0.62
47 33 0.28
48 2 0.02
49 1 0.01
50 3 0.03
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.22
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCGCAT
Found at i:123625919 original size:31 final size:31
Alignment explanation
Indices: 123625853--123625920 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
123625843 CTGACAGTGT
* *
123625853 CCCTCCTCCTACTAGTGTCGCCTAACAAAGG
1 CCCTCCTCCTACTAGCGTCGCCTAACAAAGA
* * * *
123625884 CCCTCCTCCTACTGGCGTCGCCTGATAGAGA
1 CCCTCCTCCTACTAGCGTCGCCTAACAAAGA
123625915 CCCTCC
1 CCCTCC
123625921 AACCTTGGTG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.18, C:0.43, G:0.18, T:0.22
Consensus pattern (31 bp):
CCCTCCTCCTACTAGCGTCGCCTAACAAAGA
Found at i:123626823 original size:6 final size:6
Alignment explanation
Indices: 123626812--123626875 Score: 62
Period size: 6 Copynumber: 11.0 Consensus size: 6
123626802 AAATATTGTG
* * **
123626812 ATAATT ATAATT ATAATT ATAATT -TAATTT AAAATT ATTATT -TAAAA
1 ATAATT ATAATT ATAATT ATAATT ATAA-TT ATAATT ATAATT ATAATT
123626859 ATAATT ATAATT -TAATT
1 ATAATT ATAATT ATAATT
123626876 TTGAAATTAT
Statistics
Matches: 47, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
5 10 0.21
6 35 0.74
7 2 0.04
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
ATAATT
Found at i:123630672 original size:49 final size:49
Alignment explanation
Indices: 123630567--123630848 Score: 220
Period size: 49 Copynumber: 5.8 Consensus size: 49
123630557 GGGCTAAGTT
*
123630567 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTTTCATATAGCGAG
1 GCCGATGCCATGTCCCAGACA-GGTCTTACACTGGCTCTCATATAGCGAG
* * *
123630617 GCCGATGCCATGTCCCATACAGGTCTTACACTGGCTCTCATCTATCG-G
1 GCCGATGCCATGTCCCAGACAGGTCTTACACTGGCTCTCATATAGCGAG
* * * *
123630665 TGTCGATGCCATGTCCCAGACAGGTCTTACACTAGCT-TGTATATCGCGAG
1 -GCCGATGCCATGTCCCAGACAGGTCTTACACTGGCTCT-CATATAGCGAG
* * * * * * ** * *
123630715 GCCGATG-CATATTCAAGACATGTCTTACACTAGCTCT--TGTCTCAAT
1 GCCGATGCCATGTCCCAGACAGGTCTTACACTGGCTCTCATATAGCGAG
* * * * **
123630761 GCCGATG-CATGTCCTAGACATGTCTTACACTCGCT-TAAATATCTCGAG
1 GCCGATGCCATGTCCCAGACAGGTCTTACACTGGCTCT-CATATAGCGAG
* * * *
123630809 GCCGATG-CATGTCCCAAACATGTCTTATACTAGCTCTCAT
1 GCCGATGCCATGTCCCAGACAGGTCTTACACTGGCTCTCAT
123630849 GCTGTGGTTG
Statistics
Matches: 192, Mismatches: 32, Indels: 18
0.79 0.13 0.07
Matches are distributed among these distances:
45 1 0.01
46 36 0.19
48 65 0.34
49 69 0.36
50 21 0.11
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.29
Consensus pattern (49 bp):
GCCGATGCCATGTCCCAGACAGGTCTTACACTGGCTCTCATATAGCGAG
Found at i:123630782 original size:46 final size:47
Alignment explanation
Indices: 123630567--123630888 Score: 249
Period size: 46 Copynumber: 6.7 Consensus size: 47
123630557 GGGCTAAGTT
* * **
123630567 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTTTCATATAGCGAG
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTAGCTCT-ATATCTCGAG
* * * * *
123630617 GCCGATGCCATGTCCCATACAGGTCTTACACTGGCTCTCATCTATCG-G
1 GCCGATG-CATGTCCCAGACATGTCTTACACTAGCTCT-ATATCTCGAG
* * * *
123630665 TGTCGATGCCATGTCCCAGACAGGTCTTACACTAGCTTGTATATCGCGAG
1 -GCCGATG-CATGTCCCAGACATGTCTTACACTAGC-TCTATATCTCGAG
* * * * * *
123630715 GCCGATGCATATTCAAGACATGTCTTACACTAGCTCT-TGTCTCAAT
1 GCCGATGCATGTCCCAGACATGTCTTACACTAGCTCTATATCTCGAG
* *
123630761 GCCGATGCATGTCCTAGACATGTCTTACACTCGCT-TAAATATCTCGAG
1 GCCGATGCATGTCCCAGACATGTCTTACACTAGCTCT--ATATCTCGAG
* * * *
123630809 GCCGATGCATGTCCCAAACATGTCTTATACTAGCTCTCAT-GCT-GTG
1 GCCGATGCATGTCCCAGACATGTCTTACACTAGCTCT-ATATCTCGAG
** * *
123630855 GTTGATGCATATCCCAGATATGTCTTACACTAGC
1 GCCGATGCATGTCCCAGACATGTCTTACACTAGC
123630889 ACACATATCA
Statistics
Matches: 223, Mismatches: 42, Indels: 18
0.79 0.15 0.06
Matches are distributed among these distances:
45 1 0.00
46 66 0.30
47 4 0.02
48 63 0.28
49 66 0.30
50 23 0.10
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.29
Consensus pattern (47 bp):
GCCGATGCATGTCCCAGACATGTCTTACACTAGCTCTATATCTCGAG
Found at i:123630862 original size:94 final size:95
Alignment explanation
Indices: 123630570--123630888 Score: 319
Period size: 94 Copynumber: 3.3 Consensus size: 95
123630560 CTAAGTTGCC
* ** * *
123630570 GATGCCATGTCCCAGACATGGTCTTACACTGGCTTTCATATAGCGAGGCCGATGCCATGTCCCAT
1 GATGCCATGTCCCAGACAT-GTCTTACACTAGCTTAAATATCGCGAGGCCGATG-CATGTCCCAA
* *
123630635 ACAGGTCTTACACTGGCTCTCAT-CTATCGGTGT
64 ACATGTCTTACACTAGCTCTCATGCTAT-GGT-T
* ** * *
123630668 CGATGCCATGTCCCAGACAGGTCTTACACTAGCTTGTATATCGCGAGGCCGATGCATAT-TCAAG
1 -GATGCCATGTCCCAGACATGTCTTACACTAGCTTAAATATCGCGAGGCCGATGCATGTCCCAA-
**
123630732 ACATGTCTTACACTAGCTCT--TGTCTCAAT-GCC
64 ACATGTCTTACACTAGCTCTCATG-CT--ATGGTT
* * *
123630764 GATG-CATGTCCTAGACATGTCTTACACTCGCTTAAATATCTCGAGGCCGATGCATGTCCCAAAC
1 GATGCCATGTCCCAGACATGTCTTACACTAGCTTAAATATCGCGAGGCCGATGCATGTCCCAAAC
* *
123630828 ATGTCTTATACTAGCTCTCATGCTGTGGTT
66 ATGTCTTACACTAGCTCTCATGCTATGGTT
* *
123630858 GATG-CATATCCCAGATATGTCTTACACTAGC
1 GATGCCATGTCCCAGACATGTCTTACACTAGC
123630889 ACACATATCA
Statistics
Matches: 183, Mismatches: 28, Indels: 23
0.78 0.12 0.10
Matches are distributed among these distances:
93 1 0.01
94 93 0.51
95 10 0.05
96 4 0.02
97 25 0.14
98 30 0.16
99 20 0.11
ACGTcount: A:0.23, C:0.27, G:0.20, T:0.29
Consensus pattern (95 bp):
GATGCCATGTCCCAGACATGTCTTACACTAGCTTAAATATCGCGAGGCCGATGCATGTCCCAAAC
ATGTCTTACACTAGCTCTCATGCTATGGTT
Found at i:123644001 original size:49 final size:48
Alignment explanation
Indices: 123643941--123644137 Score: 158
Period size: 49 Copynumber: 4.1 Consensus size: 48
123643931 TCTCAAACAT
123643941 GGTCTTACACTGGCTTTCATATGGCGAGGTCGATGCCATGTCCCAGACA
1 GGTCTTACACTGGCTTTCATAT-GCGAGGTCGATGCCATGTCCCAGACA
* * * *
123643990 GGTCTTACACTGGCTCTCATCAAT-CG-GTGTCAATGGCATGTCCCAGAGA
1 GGTCTTACACTGGCTTTCAT--ATGCGAG-GTCGATGCCATGTCCCAGACA
* * * * * *
123644039 GGTCTTACACTGGC--ACACA-ACAAGCT-GACGCCATGTCCCAGACA
1 GGTCTTACACTGGCTTTCATATGCGAGGTCGATGCCATGTCCCAGACA
* * *
123644083 GGTCTTACATTGGCTTGT-ATATCGCGAGGCCGATG-CATGTCCTAGACA
1 GGTCTTACACTGGCTT-TCATAT-GCGAGGTCGATGCCATGTCCCAGACA
*
123644131 TGTCTTA
1 GGTCTTA
123644138 AACTAGCTCT
Statistics
Matches: 115, Mismatches: 22, Indels: 23
0.72 0.14 0.14
Matches are distributed among these distances:
44 27 0.23
45 3 0.03
46 3 0.03
47 2 0.02
48 22 0.19
49 56 0.49
51 2 0.02
ACGTcount: A:0.23, C:0.27, G:0.24, T:0.26
Consensus pattern (48 bp):
GGTCTTACACTGGCTTTCATATGCGAGGTCGATGCCATGTCCCAGACA
Found at i:123644176 original size:46 final size:45
Alignment explanation
Indices: 123644110--123644236 Score: 168
Period size: 46 Copynumber: 2.8 Consensus size: 45
123644100 TATATCGCGA
* * *
123644110 GGCCGATGCATGTCCTAGACATGTCTTAAACTAGCTCT-TGTCTCAAT
1 GGCCAATGCATGTCCCAGACATGTCTTACACTAGCTCTATGT-T--AT
123644157 -GCCAATGCATGTCCCAGACATGTCTTACACTAGCTCTCATGTTAT
1 GGCCAATGCATGTCCCAGACATGTCTTACACTAGCTCT-ATGTTAT
*
123644202 GGCTAATGCATGTCCCAGACATGTCTTACACTAGC
1 GGCCAATGCATGTCCCAGACATGTCTTACACTAGC
123644237 ACACATATCA
Statistics
Matches: 73, Mismatches: 4, Indels: 7
0.87 0.05 0.08
Matches are distributed among these distances:
45 2 0.03
46 67 0.92
47 1 0.01
48 3 0.04
ACGTcount: A:0.24, C:0.28, G:0.18, T:0.30
Consensus pattern (45 bp):
GGCCAATGCATGTCCCAGACATGTCTTACACTAGCTCTATGTTAT
Found at i:123655566 original size:35 final size:35
Alignment explanation
Indices: 123655479--123655558 Score: 108
Period size: 35 Copynumber: 2.3 Consensus size: 35
123655469 GTATATCTAT
*
123655479 ATCTGTATCTAAGATGGGCTTAGGCCCAAATATGT
1 ATCTGTATCTAAGATGGGCTTAGGCCCAAATATGC
* * *
123655514 ATTTGTATCTGAA-ATGGGCTTGGGCCCGAATATGC
1 ATCTGTATCT-AAGATGGGCTTAGGCCCAAATATGC
123655549 ATCTGTATCT
1 ATCTGTATCT
123655559 CTGATGGGGT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
35 37 0.95
36 2 0.05
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (35 bp):
ATCTGTATCTAAGATGGGCTTAGGCCCAAATATGC
Found at i:123658612 original size:26 final size:26
Alignment explanation
Indices: 123658583--123658656 Score: 94
Period size: 26 Copynumber: 2.8 Consensus size: 26
123658573 CTCGTTATAT
**
123658583 GGCTCTTCATGAGCTTCCCTATTAAA
1 GGCTCTTTGTGAGCTTCCCTATTAAA
***
123658609 GGCTCTTTGTGAGCTTCTGGATTAAA
1 GGCTCTTTGTGAGCTTCCCTATTAAA
*
123658635 GGCTCTTTGTGAGCTTTCCTAT
1 GGCTCTTTGTGAGCTTCCCTAT
123658657 ATGGCTCGCT
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.18, C:0.22, G:0.22, T:0.39
Consensus pattern (26 bp):
GGCTCTTTGTGAGCTTCCCTATTAAA
Found at i:123658819 original size:25 final size:24
Alignment explanation
Indices: 123658723--123658834 Score: 82
Period size: 25 Copynumber: 4.5 Consensus size: 24
123658713 TTCGGAGTTA
* *
123658723 CCTGTTATTGGCTCGCATGAGCTT
1 CCTGTTAATGGCTCACATGAGCTT
* **
123658747 TCTGATT-ATGGCTCTTATGAGCTT
1 CCTG-TTAATGGCTCACATGAGCTT
** * * *
123658771 CCTGTTATACAGCCCAGATAAGCTT
1 CCTGTTA-ATGGCTCACATGAGCTT
123658796 CCTGTTACATGGCTCACATGAGCTT
1 CCTGTTA-ATGGCTCACATGAGCTT
*
123658821 TCTGTTATATGGCT
1 CCTGTTA-ATGGCT
123658835 TGAGAGAGGG
Statistics
Matches: 66, Mismatches: 19, Indels: 5
0.73 0.21 0.06
Matches are distributed among these distances:
23 2 0.03
24 20 0.30
25 44 0.67
ACGTcount: A:0.19, C:0.23, G:0.21, T:0.38
Consensus pattern (24 bp):
CCTGTTAATGGCTCACATGAGCTT
Found at i:123661618 original size:2 final size:2
Alignment explanation
Indices: 123661611--123661635 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
123661601 TCTGATTCAT
123661611 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
123661636 CAATTCACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:123668750 original size:20 final size:19
Alignment explanation
Indices: 123668704--123668756 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
123668694 ATGCATATTT
123668704 AATTATTTATA-TTTAATA
1 AATTATTTATATTTTAATA
*
123668722 ATATAATTTATTATTTTAATA
1 A-ATTATTTA-TATTTTAATA
123668743 AATTATTTAATATT
1 AATTATTT-ATATT
123668757 ACAATTTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
18 1 0.03
19 7 0.24
20 12 0.41
21 9 0.31
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
AATTATTTATATTTTAATA
Found at i:123668751 original size:33 final size:31
Alignment explanation
Indices: 123668713--123668775 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
123668703 TAATTATTTA
*
123668713 TATTTAATAATATAATTTATTATTTTAATAAAT
1 TATTTAATAATACAA-TT-TTATTTTAATAAAT
*
123668746 TATTTAATATTACAATTTTATTTTAATAAA
1 TATTTAATAATACAATTTTATTTTAATAAA
123668776 AAATTAACAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 13 0.46
32 2 0.07
33 13 0.46
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (31 bp):
TATTTAATAATACAATTTTATTTTAATAAAT
Found at i:123670541 original size:7 final size:7
Alignment explanation
Indices: 123670531--123670571 Score: 75
Period size: 7 Copynumber: 6.0 Consensus size: 7
123670521 TATAAATATA
123670531 AATTATT
1 AATTATT
123670538 AATTATT
1 AATTATT
123670545 AATTA-T
1 AATTATT
123670551 AATTATT
1 AATTATT
123670558 AATTATT
1 AATTATT
123670565 AATTATT
1 AATTATT
123670572 TTTTAATTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 6 0.18
7 27 0.82
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
AATTATT
Found at i:123670556 original size:20 final size:20
Alignment explanation
Indices: 123670531--123670570 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
123670521 TATAAATATA
123670531 AATTATTAATTATTAATTAT
1 AATTATTAATTATTAATTAT
123670551 AATTATTAATTATTAATTAT
1 AATTATTAATTATTAATTAT
123670571 TTTTTAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
AATTATTAATTATTAATTAT
Found at i:123675748 original size:17 final size:18
Alignment explanation
Indices: 123675708--123675751 Score: 65
Period size: 17 Copynumber: 2.5 Consensus size: 18
123675698 AGTAAAGTAA
123675708 ATTTT-GTTTATTATTTT
1 ATTTTAGTTTATTATTTT
123675725 ATTTTTAGTTTATT-TTTT
1 A-TTTTAGTTTATTATTTT
123675743 ATTTTAGTT
1 ATTTTAGTT
123675752 GGGGGAAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 9 0.36
18 9 0.36
19 7 0.28
ACGTcount: A:0.18, C:0.00, G:0.07, T:0.75
Consensus pattern (18 bp):
ATTTTAGTTTATTATTTT
Found at i:123678292 original size:23 final size:24
Alignment explanation
Indices: 123678265--123678309 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
123678255 AAAATCAAAT
*
123678265 GAGC-ACATACACAAAATTTAGCA
1 GAGCAACAGACACAAAATTTAGCA
123678288 GAGCAACAGACACAAAATTTAG
1 GAGCAACAGACACAAAATTTAG
123678310 TTGAACGGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.49, C:0.20, G:0.16, T:0.16
Consensus pattern (24 bp):
GAGCAACAGACACAAAATTTAGCA
Found at i:123679468 original size:60 final size:60
Alignment explanation
Indices: 123679349--123679465 Score: 175
Period size: 60 Copynumber: 2.0 Consensus size: 60
123679339 CAACAATTTA
* * * *
123679349 TAACTTAATCCTAAATTACTAATAATTTAATTTTAAAATAATTACAAACACAAAAAAATT
1 TAACATAATCCTAAATTACTAACAATTTAATTTTAAAATAATTAAAAAAACAAAAAAATT
123679409 TAACATAATCCTAAATTACTAACAA-TT-ATTTTAAAATAATTATAAAAAACAAAAAAA
1 TAACATAATCCTAAATTACTAACAATTTAATTTTAAAATAATTA-AAAAAACAAAAAAA
123679466 ATTACATTCA
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
58 15 0.29
59 14 0.27
60 23 0.44
ACGTcount: A:0.56, C:0.11, G:0.00, T:0.32
Consensus pattern (60 bp):
TAACATAATCCTAAATTACTAACAATTTAATTTTAAAATAATTAAAAAAACAAAAAAATT
Found at i:123679656 original size:23 final size:23
Alignment explanation
Indices: 123679627--123679687 Score: 70
Period size: 23 Copynumber: 2.6 Consensus size: 23
123679617 TACATTACCT
123679627 TTTTTTTTCTTCTTC-TTCTCTTC
1 TTTTTTTTCTTCTTCTTTCTC-TC
* *
123679650 TTTTTTTTTTTCTCCTTTCTCTC
1 TTTTTTTTCTTCTTCTTTCTCTC
*
123679673 TTTTCTTTCTCTCTT
1 TTTTTTTTCT-TCTT
123679688 TCGGTGTGTG
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
23 23 0.74
24 8 0.26
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (23 bp):
TTTTTTTTCTTCTTCTTTCTCTC
Found at i:123679661 original size:26 final size:28
Alignment explanation
Indices: 123679626--123679680 Score: 78
Period size: 26 Copynumber: 2.0 Consensus size: 28
123679616 ATACATTACC
*
123679626 TTTTTTTTTCTTC-TTCT-TCTCTTCTT
1 TTTTTTTTTCTCCTTTCTCTCTCTTCTT
*
123679652 TTTTTTTTTCTCCTTTCTCTCTTTTCTT
1 TTTTTTTTTCTCCTTTCTCTCTCTTCTT
123679680 T
1 T
123679681 CTCTCTTTCG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 12 0.48
27 4 0.16
28 9 0.36
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (28 bp):
TTTTTTTTTCTCCTTTCTCTCTCTTCTT
Found at i:123679682 original size:13 final size:13
Alignment explanation
Indices: 123679664--123679688 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
123679654 TTTTTTTCTC
123679664 CTTTCTCTCTTTT
1 CTTTCTCTCTTTT
123679677 CTTTCTCTCTTT
1 CTTTCTCTCTTT
123679689 CGGTGTGTGG
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:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (13 bp):
CTTTCTCTCTTTT
Found at i:123684189 original size:59 final size:59
Alignment explanation
Indices: 123684097--123684216 Score: 240
Period size: 59 Copynumber: 2.0 Consensus size: 59
123684087 CTCCGATGGC
123684097 CACATGAGCGTGTGTCGTGGTACATGGCCGAATGGATTTGGGAAATTAGGGTTCCAGGA
1 CACATGAGCGTGTGTCGTGGTACATGGCCGAATGGATTTGGGAAATTAGGGTTCCAGGA
123684156 CACATGAGCGTGTGTCGTGGTACATGGCCGAATGGATTTGGGAAATTAGGGTTCCAGGA
1 CACATGAGCGTGTGTCGTGGTACATGGCCGAATGGATTTGGGAAATTAGGGTTCCAGGA
123684215 CA
1 CA
123684217 ATTTTAAAGC
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 61 1.00
ACGTcount: A:0.24, C:0.16, G:0.35, T:0.25
Consensus pattern (59 bp):
CACATGAGCGTGTGTCGTGGTACATGGCCGAATGGATTTGGGAAATTAGGGTTCCAGGA
Found at i:123684930 original size:14 final size:14
Alignment explanation
Indices: 123684911--123684961 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
123684901 TGAATTGGTG
123684911 CATCCGCATTCATA
1 CATCCGCATTCATA
*
123684925 CATCCGCATACATA
1 CATCCGCATTCATA
* *
123684939 AATCTGCATAT-ATA
1 CATCCGCAT-TCATA
*
123684953 CATCTGCAT
1 CATCCGCAT
123684962 ATAAAGTATT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
14 31 1.00
ACGTcount: A:0.33, C:0.29, G:0.08, T:0.29
Consensus pattern (14 bp):
CATCCGCATTCATA
Found at i:123684962 original size:14 final size:14
Alignment explanation
Indices: 123684922--123684964 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 14
123684912 ATCCGCATTC
* *
123684922 ATACATCCGCATAC
1 ATACATCTGCATAT
*
123684936 ATAAATCTGCATAT
1 ATACATCTGCATAT
123684950 ATACATCTGCATAT
1 ATACATCTGCATAT
123684964 A
1 A
123684965 AAGTATTTTG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.40, C:0.23, G:0.07, T:0.30
Consensus pattern (14 bp):
ATACATCTGCATAT
Found at i:123686414 original size:12 final size:12
Alignment explanation
Indices: 123686399--123686451 Score: 54
Period size: 12 Copynumber: 4.5 Consensus size: 12
123686389 AGTTATCAAT
123686399 TTATTATTATAA
1 TTATTATTATAA
**
123686411 TTATTATTATGG
1 TTATTATTATAA
*
123686423 TTTTTATT-TAA
1 TTATTATTATAA
* *
123686434 ATATTATTATTA
1 TTATTATTATAA
123686446 TTATTA
1 TTATTA
123686452 AATAAAATAA
Statistics
Matches: 31, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
11 7 0.23
12 24 0.77
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (12 bp):
TTATTATTATAA
Found at i:123686722 original size:3 final size:3
Alignment explanation
Indices: 123686708--123686770 Score: 62
Period size: 3 Copynumber: 22.0 Consensus size: 3
123686698 AAATAGATAT
* *
123686708 TTA TTA TAA TTA TTA TTA -TA GTT- TTA -TA TTA -AA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA
*
123686750 TTA TTA TTA CTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA
123686771 AAATAATTTA
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
2 7 0.14
3 41 0.84
4 1 0.02
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:123686904 original size:3 final size:3
Alignment explanation
Indices: 123686896--123686950 Score: 69
Period size: 3 Copynumber: 18.7 Consensus size: 3
123686886 ATGAATTAAA
*
123686896 TAT TAT TAT TA- TAT TAT T-T TAT TAT TAT AAT GTAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT
*
123686940 TAA TAT TAT TA
1 TAT TAT TAT TA
123686951 ACTAACATAT
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
2 4 0.09
3 39 0.87
4 2 0.04
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:123686919 original size:16 final size:17
Alignment explanation
Indices: 123686896--123686950 Score: 76
Period size: 16 Copynumber: 3.1 Consensus size: 17
123686886 ATGAATTAAA
123686896 TATTATTATTATATTAT
1 TATTATTATTATATTAT
123686913 T-TTATTATTATAATGTAT
1 TATTATTATTAT-AT-TAT
123686931 TATTATTATTAATATTAT
1 TATTATTATT-ATATTAT
123686949 TA
1 TA
123686951 ACTAACATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
16 10 0.29
17 3 0.09
18 9 0.26
19 10 0.29
20 2 0.06
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (17 bp):
TATTATTATTATATTAT
Found at i:123686920 original size:19 final size:19
Alignment explanation
Indices: 123686896--123686949 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
123686886 ATGAATTAAA
123686896 TATTATTATTATATTATTT
1 TATTATTATTATATTATTT
123686915 TATTATTA-TA-ATGTA--T
1 TATTATTATTATAT-TATTT
123686931 TATTATTATTAATATTATT
1 TATTATTATT-ATATTATT
123686950 AACTAACATA
Statistics
Matches: 29, Mismatches: 0, Indels: 11
0.73 0.00 0.28
Matches are distributed among these distances:
16 9 0.31
17 3 0.10
18 7 0.24
19 10 0.34
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (19 bp):
TATTATTATTATATTATTT
Found at i:123687013 original size:17 final size:17
Alignment explanation
Indices: 123686993--123687025 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
123686983 AAGTAAAATA
*
123686993 AGAAAAGAAACAGAAGG
1 AGAAAACAAACAGAAGG
123687010 AGAAAACAAACAGAAG
1 AGAAAACAAACAGAAG
123687026 TTTTCGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.67, C:0.09, G:0.24, T:0.00
Consensus pattern (17 bp):
AGAAAACAAACAGAAGG
Found at i:123687412 original size:17 final size:17
Alignment explanation
Indices: 123687377--123687417 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
123687367 AATTAAGTGA
123687377 AATATGAAAAGAAATTG
1 AATATGAAAAGAAATTG
*
123687394 AATA-GAAATGAAATATG
1 AATATGAAAAGAAAT-TG
123687411 AAT-TGAA
1 AATATGAA
123687418 TTATAAAAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 9 0.43
17 12 0.57
ACGTcount: A:0.59, C:0.00, G:0.17, T:0.24
Consensus pattern (17 bp):
AATATGAAAAGAAATTG
Found at i:123688684 original size:128 final size:129
Alignment explanation
Indices: 123688504--123688752 Score: 385
Period size: 128 Copynumber: 1.9 Consensus size: 129
123688494 CCGCGCTTTA
* * * *
123688504 AAAAACACGAGTGAAATTCCATAGGAATATTCGATTATTTTGATCAAACGGGAAATCGAAACCTA
1 AAAAACACGAGTAAAATTCCAAAGGAATATTCGATTATTTTGAACAAACGGGAAATCGAAACCCA
*
123688569 GCACGATAGGACACTATTCCCCGAATTTCCCAACATC-AGATATTGCC-TTGTTTTAGTGTTTGG
66 GCACGATAGGACACTATTCCCCGAATTTCCAAACATCGA-ATATTGCCTTTGTTTTAGTGTTTGG
* * *
123688632 AAAAACACGAGTAAAATTCTAAAGGAATATTTGATTATTTTGAACAAACGGGAAATTGAAACCCA
1 AAAAACACGAGTAAAATTCCAAAGGAATATTCGATTATTTTGAACAAACGGGAAATCGAAACCCA
**
123688697 GCACGATAGGGTACTATTCCCCGAATTTCCAAACATCGAATATTGCCTTTGTTTTA
66 GCACGATAGGACACTATTCCCCGAATTTCCAAACATCGAATATTGCCTTTGTTTTA
123688753 ATGAATCTTC
Statistics
Matches: 109, Mismatches: 10, Indels: 3
0.89 0.08 0.02
Matches are distributed among these distances:
128 100 0.92
129 9 0.08
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.29
Consensus pattern (129 bp):
AAAAACACGAGTAAAATTCCAAAGGAATATTCGATTATTTTGAACAAACGGGAAATCGAAACCCA
GCACGATAGGACACTATTCCCCGAATTTCCAAACATCGAATATTGCCTTTGTTTTAGTGTTTGG
Found at i:123690808 original size:21 final size:21
Alignment explanation
Indices: 123690747--123690808 Score: 58
Period size: 20 Copynumber: 3.0 Consensus size: 21
123690737 TTTTTAGCAG
*
123690747 GTACGGAGTGCGT-GGCGT-GT
1 GTACGGAG-GCGTGGGCGTGGC
* *
123690767 GTACGGGGGCCGTGTGC-TGGC
1 GTACGGAGG-CGTGGGCGTGGC
123690788 GTACGGAGGCGTGGGCGTGGC
1 GTACGGAGGCGTGGGCGTGGC
123690809 TGTGGCGCCA
Statistics
Matches: 33, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
19 1 0.03
20 17 0.52
21 15 0.45
ACGTcount: A:0.08, C:0.19, G:0.53, T:0.19
Consensus pattern (21 bp):
GTACGGAGGCGTGGGCGTGGC
Found at i:123692258 original size:39 final size:39
Alignment explanation
Indices: 123692210--123692351 Score: 205
Period size: 39 Copynumber: 3.6 Consensus size: 39
123692200 ACTCTGATGA
*
123692210 GCTTCAGTTAGCCTTCGGGCTTCAGTTTAGCACTTTTGT
1 GCTTCAGTTAGCCTTCGGGCTTCAGTTTAGCACTTATGT
* * *
123692249 GCGTT-AGTTAGCCTTCGGGCTTCCGTTTAACACTTCTGT
1 GC-TTCAGTTAGCCTTCGGGCTTCAGTTTAGCACTTATGT
*
123692288 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
1 GCTTCAGTTAGCCTTCGGGCTTCAGTTTAGCACTTATGT
* *
123692327 GCTTCAGCTAGACTTCGGGCTTCAG
1 GCTTCAGTTAGCCTTCGGGCTTCAG
123692352 ATGACGATGT
Statistics
Matches: 93, Mismatches: 8, Indels: 4
0.89 0.08 0.04
Matches are distributed among these distances:
38 2 0.02
39 89 0.96
40 2 0.02
ACGTcount: A:0.13, C:0.25, G:0.24, T:0.37
Consensus pattern (39 bp):
GCTTCAGTTAGCCTTCGGGCTTCAGTTTAGCACTTATGT
Found at i:123692291 original size:21 final size:21
Alignment explanation
Indices: 123692228--123692331 Score: 78
Period size: 21 Copynumber: 5.2 Consensus size: 21
123692218 TAGCCTTCGG
* *
123692228 GCTTCAGTTTAGCACTTTTGT
1 GCTTCCGTTTAGCACTTCTGT
* *
123692249 GCGTT-AG-TTAGC-CTTC-GG
1 GC-TTCCGTTTAGCACTTCTGT
*
123692267 GCTTCCGTTTAACACTTCTGT
1 GCTTCCGTTTAGCACTTCTGT
* *
123692288 GCTTCAG-TTAGC-CTTC-GG
1 GCTTCCGTTTAGCACTTCTGT
*
123692306 GCTTCCGTTTAGCACTTATGT
1 GCTTCCGTTTAGCACTTCTGT
123692327 GCTTC
1 GCTTC
123692332 AGCTAGACTT
Statistics
Matches: 64, Mismatches: 11, Indels: 16
0.70 0.12 0.18
Matches are distributed among these distances:
17 2 0.03
18 11 0.17
19 16 0.25
20 16 0.25
21 17 0.27
22 2 0.03
ACGTcount: A:0.12, C:0.25, G:0.22, T:0.40
Consensus pattern (21 bp):
GCTTCCGTTTAGCACTTCTGT
Found at i:123709344 original size:44 final size:46
Alignment explanation
Indices: 123709291--123709383 Score: 109
Period size: 44 Copynumber: 2.0 Consensus size: 46
123709281 TTATTATTGA
* *
123709291 TTTTAAAAAACTTGAAATGTATA-TTTGAAA-TATTTTATAATATT
1 TTTTAAAAAACTTGAAATATATATTTTGAAATTATTTTATAAAATT
* * * *
123709335 TTTTTAAAAATTTTAAATATATATTTTTGAAATTATTTTTTAAAATT
1 TTTTAAAAAACTTGAAATATATA-TTTTGAAATTATTTTATAAAATT
123709382 TT
1 TT
123709384 AAATATATAT
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
44 19 0.47
46 7 0.17
47 14 0.35
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.54
Consensus pattern (46 bp):
TTTTAAAAAACTTGAAATATATATTTTGAAATTATTTTATAAAATT
Found at i:123709360 original size:35 final size:35
Alignment explanation
Indices: 123709320--123709401 Score: 123
Period size: 35 Copynumber: 2.3 Consensus size: 35
123709310 TATATTTGAA
123709320 ATATTTTATAATATT-TTTTTAAAAATTTTAAATAT
1 ATATTTT-TAATATTATTTTTAAAAATTTTAAATAT
*
123709355 ATATTTTTGAA-ATTATTTTTTAAAATTTTAAATAT
1 ATATTTTT-AATATTATTTTTAAAAATTTTAAATAT
123709390 ATATTTTTAATA
1 ATATTTTTAATA
123709402 ATATAAAACA
Statistics
Matches: 43, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
34 6 0.14
35 37 0.86
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.57
Consensus pattern (35 bp):
ATATTTTTAATATTATTTTTAAAAATTTTAAATAT
Found at i:123709361 original size:23 final size:23
Alignment explanation
Indices: 123709290--123709362 Score: 62
Period size: 22 Copynumber: 3.3 Consensus size: 23
123709280 TTTATTATTG
* * * *
123709290 ATTTTAAAAAACTTGAAATGTAT
1 ATTTTTAAAAATTTTAAATATAT
* *
123709313 A-TTTGAAATATTTTATAATAT-T
1 ATTTTTAAAAATTTTA-AATATAT
123709335 -TTTTTAAAAATTTTAAATATAT
1 ATTTTTAAAAATTTTAAATATAT
123709357 ATTTTT
1 ATTTTT
123709363 GAAATTATTT
Statistics
Matches: 39, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
21 5 0.13
22 24 0.62
23 10 0.26
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.52
Consensus pattern (23 bp):
ATTTTTAAAAATTTTAAATATAT
Found at i:123709382 original size:22 final size:22
Alignment explanation
Indices: 123709359--123709399 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
123709349 AAATATATAT
123709359 TTTTGAAAT-TAT-TTTTTAAAA
1 TTTT-AAATATATATTTTTAAAA
123709380 TTTTAAATATATATTTTTAA
1 TTTTAAATATATATTTTTAA
123709400 TAATATAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.22
21 7 0.39
22 7 0.39
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (22 bp):
TTTTAAATATATATTTTTAAAA
Found at i:123709508 original size:21 final size:23
Alignment explanation
Indices: 123709453--123709514 Score: 76
Period size: 21 Copynumber: 2.8 Consensus size: 23
123709443 TTTATTATTA
*
123709453 GTTTTATAATATTTTAAATGTAT
1 GTTTTATAATATTTTTAATGTAT
* *
123709476 CTTTGA-AATATTTTTAAT-T-T
1 GTTTTATAATATTTTTAATGTAT
123709496 GTTTTATAATATTTTTAAT
1 GTTTTATAATATTTTTAAT
123709515 ATTTTTAATT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
20 5 0.15
21 13 0.39
22 11 0.33
23 4 0.12
ACGTcount: A:0.32, C:0.02, G:0.06, T:0.60
Consensus pattern (23 bp):
GTTTTATAATATTTTTAATGTAT
Found at i:123709516 original size:9 final size:9
Alignment explanation
Indices: 123709482--123709530 Score: 55
Period size: 9 Copynumber: 5.2 Consensus size: 9
123709472 GTATCTTTGA
123709482 AATATTTTT
1 AATATTTTT
*
123709491 AATTTGTTTTAT
1 AA--TATTTT-T
123709503 AATATTTTT
1 AATATTTTT
123709512 AATATTTTT
1 AATATTTTT
123709521 AAT-TTTTT
1 AATATTTTT
123709529 AA
1 AA
123709531 AAATATATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
8 7 0.20
9 15 0.43
10 5 0.14
11 5 0.14
12 3 0.09
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (9 bp):
AATATTTTT
Found at i:123709653 original size:122 final size:122
Alignment explanation
Indices: 123709420--123709650 Score: 310
Period size: 122 Copynumber: 1.9 Consensus size: 122
123709410 CATTTAAATA
*
123709420 TTTTAAAGATATGACCTTTCAAATTTATTATTAGTTTTATAATATTTTAAATGTATCTTTGAAAT
1 TTTTAAAGATATGACATTTCAAATTTATTATTAGTTTTATAATATTTTAAATGTATCTTTGAAAT
** **
123709485 ATTTTTAATTTGTTTTATAATATTTTTAATATTTTTAATTTTTTAAAAATATATTAT
66 ATTTTTAATTTGTAATATAATATTTTTAATATGATTAATTTTTTAAAAATATATTAT
* *
123709542 TTTTAAAGATATGACATTTCAAATTTATTATTTGTTTTATAATATTTTAAATGCATAT-TTTTAA
1 TTTTAAAGATATGACATTTCAAATTTATTATTAGTTTTATAATATTTTAAATG--TATCTTTGAA
123709606 A-ATTTTTAAAATTT-TAAATATAAT-TTTTATAA-ATGATTAATTTTT
64 ATATTTTT--AATTTGT-AATATAATATTTT-TAATATGATTAATTTTT
123709651 AAATTAATTT
Statistics
Matches: 96, Mismatches: 7, Indels: 11
0.84 0.06 0.10
Matches are distributed among these distances:
122 57 0.59
123 22 0.23
124 17 0.18
ACGTcount: A:0.37, C:0.03, G:0.05, T:0.55
Consensus pattern (122 bp):
TTTTAAAGATATGACATTTCAAATTTATTATTAGTTTTATAATATTTTAAATGTATCTTTGAAAT
ATTTTTAATTTGTAATATAATATTTTTAATATGATTAATTTTTTAAAAATATATTAT
Found at i:123712857 original size:30 final size:30
Alignment explanation
Indices: 123712815--123712917 Score: 116
Period size: 30 Copynumber: 3.4 Consensus size: 30
123712805 GGTTACTCTA
* *
123712815 GGTGAAATGAACTCGAACCACCTATGTCTG
1 GGTGATATGAACTCGAACCACCCATGTCTG
* * *
123712845 GTTGATATGAACTCGAAGCGCCCATGTCTG
1 GGTGATATGAACTCGAACCACCCATGTCTG
* ** *
123712875 GGTGATATGAACTTGAACCGTCCATGTCCG
1 GGTGATATGAACTCGAACCACCCATGTCTG
*
123712905 AGTGATATGAACT
1 GGTGATATGAACT
123712918 GCTCTGCGAC
Statistics
Matches: 62, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 62 1.00
ACGTcount: A:0.27, C:0.21, G:0.25, T:0.26
Consensus pattern (30 bp):
GGTGATATGAACTCGAACCACCCATGTCTG
Found at i:123715743 original size:14 final size:14
Alignment explanation
Indices: 123715724--123715750 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
123715714 ATCTTTAAAA
123715724 ATAATTTAAAAATC
1 ATAATTTAAAAATC
123715738 ATAATTTAAAAAT
1 ATAATTTAAAAAT
123715751 TATATGTAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (14 bp):
ATAATTTAAAAATC
Found at i:123715865 original size:20 final size:19
Alignment explanation
Indices: 123715825--123715904 Score: 90
Period size: 20 Copynumber: 4.1 Consensus size: 19
123715815 TTGAAAGGTC
* **
123715825 ATATTTTTAAAATTTTTAA
1 ATATATTTAAAATTTAAAA
123715844 ATAT-TTTATATAATTTAAAA
1 ATATATTTA-A-AATTTAAAA
123715864 ATATATTTAAAATTTTAAAA
1 ATATATTTAAAA-TTTAAAA
123715884 ATAATATTTAAAATTTAAAA
1 AT-ATATTTAAAATTTAAAA
123715904 A
1 A
123715905 AATAATTTCA
Statistics
Matches: 54, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
18 4 0.07
19 7 0.13
20 29 0.54
21 14 0.26
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
ATATATTTAAAATTTAAAA
Found at i:123715884 original size:21 final size:20
Alignment explanation
Indices: 123715842--123715905 Score: 78
Period size: 21 Copynumber: 3.1 Consensus size: 20
123715832 TAAAATTTTT
123715842 AAATAT-TTTATATAATTT-AA
1 AAATATATTTA-A-AATTTAAA
*
123715862 AAATATATTTAAAATTTTAA
1 AAATATATTTAAAATTTAAA
123715882 AAATAATATTTAAAATTTAAA
1 AAAT-ATATTTAAAATTTAAA
123715903 AAA
1 AAA
123715906 ATAATTTCAA
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
19 5 0.12
20 13 0.32
21 22 0.55
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
AAATATATTTAAAATTTAAA
Found at i:123718003 original size:9 final size:9
Alignment explanation
Indices: 123717989--123718023 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
123717979 TGCTTTGAAT
123717989 TTTTGGTAC
1 TTTTGGTAC
123717998 TTTTGGTAC
1 TTTTGGTAC
*
123718007 TTTTGATAC
1 TTTTGGTAC
123718016 TTTGTGGT
1 TTT-TGGT
123718024 TGTGTGATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 20 0.87
10 3 0.13
ACGTcount: A:0.11, C:0.09, G:0.23, T:0.57
Consensus pattern (9 bp):
TTTTGGTAC
Found at i:123722859 original size:8 final size:7
Alignment explanation
Indices: 123722835--123722867 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
123722825 AAACTTTCAA
123722835 AAAATAT
1 AAAATAT
123722842 AAAATAT
1 AAAATAT
123722849 AAAATAT
1 AAAATAT
*
123722856 TAAA-AT
1 AAAATAT
123722862 AAAATA
1 AAAATA
123722868 AATATTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
6 5 0.22
7 18 0.78
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (7 bp):
AAAATAT
Found at i:123724093 original size:20 final size:20
Alignment explanation
Indices: 123724061--123724126 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 20
123724051 TAAAATATAT
*
123724061 TAAA-TTTATTATTTTAACA
1 TAAATTTTAATATTTTAACA
*
123724080 TAAATTTTAATATTTTTAATA
1 TAAATTTTAATA-TTTTAACA
*
123724101 TAATTTTAATAATTATTTTAACA
1 TAAATTT--TAA-TATTTTAACA
123724124 TAA
1 TAA
123724127 TTTAAAAATG
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
19 4 0.11
20 6 0.16
21 13 0.34
23 13 0.34
24 2 0.05
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (20 bp):
TAAATTTTAATATTTTAACA
Found at i:123739320 original size:37 final size:36
Alignment explanation
Indices: 123739270--123739402 Score: 124
Period size: 37 Copynumber: 3.6 Consensus size: 36
123739260 CAAATCTTAT
*
123739270 CGTTATATTGAATGAAGCTCAATCGAGCAACTCATAC
1 CGTTATACTGAATGAAGCTCAATCGAGCAACTC-TAC
* *
123739307 CGTTATACTGAATGGAGCTCAATTGAGCAAAC-CTTAC
1 CGTTATACTGAATGAAGCTCAATCGAGC-AACTC-TAC
* * * * * *
123739344 TGTTATACTGAATGATGTTCAATCAAGAAAATTCTAC
1 CGTTATACTGAATGAAGCTCAATCGAG-CAACTCTAC
* *
123739381 TGTAATACTGAATGAAGCTCAA
1 CGTTATACTGAATGAAGCTCAA
123739403 ACGACTAGAA
Statistics
Matches: 78, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
37 74 0.95
38 4 0.05
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.29
Consensus pattern (36 bp):
CGTTATACTGAATGAAGCTCAATCGAGCAACTCTAC
Found at i:123742924 original size:32 final size:33
Alignment explanation
Indices: 123742888--123742959 Score: 128
Period size: 32 Copynumber: 2.2 Consensus size: 33
123742878 ATGTTGTTTC
123742888 TTCTTATTCAAGTAGAACTCTTGTGA-TTCTTT
1 TTCTTATTCAAGTAGAACTCTTGTGATTTCTTT
*
123742920 TTCTTATTCAAGTAGAACTCTTGTGATTTTTTT
1 TTCTTATTCAAGTAGAACTCTTGTGATTTCTTT
123742953 TTCTTAT
1 TTCTTAT
123742960 ATATAGGGGC
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
32 26 0.68
33 12 0.32
ACGTcount: A:0.21, C:0.14, G:0.11, T:0.54
Consensus pattern (33 bp):
TTCTTATTCAAGTAGAACTCTTGTGATTTCTTT
Found at i:123746781 original size:61 final size:61
Alignment explanation
Indices: 123746713--123746838 Score: 164
Period size: 61 Copynumber: 2.1 Consensus size: 61
123746703 CCTAAATATG
* ** * * *
123746713 AAAAATTCAACAAATTT-AGTCTTCAATATTTACAATTTTTTTCATTTTAGTTCAAATTCTA
1 AAAAATTCAACAAATTTGA-CCTTCAATATTTACAAAATTTTTCAATTTAATTCAAATCCTA
* *
123746774 AAAAATTCAATAAATTTGACCTTCAATATTTACAAAATTTTTCAATTTAATTCTAATCCTA
1 AAAAATTCAACAAATTTGACCTTCAATATTTACAAAATTTTTCAATTTAATTCAAATCCTA
123746835 AAAA
1 AAAA
123746839 TATCCAAAAA
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
61 55 0.98
62 1 0.02
ACGTcount: A:0.42, C:0.13, G:0.02, T:0.42
Consensus pattern (61 bp):
AAAAATTCAACAAATTTGACCTTCAATATTTACAAAATTTTTCAATTTAATTCAAATCCTA
Done.