Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold82
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1057086
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.29
Warning! 131930 characters in sequence are not A, C, G, or T
File 2 of 3
Found at i:258 original size:22 final size:21
Alignment explanation
Indices: 185--260 Score: 80
Period size: 22 Copynumber: 3.5 Consensus size: 21
175 CTTTCGATAC
* *
185 TTCGCCTTAGCACCTTCGCAT
1 TTCGCCTTCGCAACTTCGCAT
* *
206 TTCGCCTTCACAACTTTGCACT
1 TTCGCCTTCGCAACTTCGCA-T
* *
228 CTCGGCTTCGCAACTTCGCATT
1 TTCGCCTTCGCAACTTCGCA-T
250 TTCGCCTTCGC
1 TTCGCCTTCGC
261 CTTTTTATGT
Statistics
Matches: 43, Mismatches: 11, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
21 16 0.37
22 27 0.63
ACGTcount: A:0.13, C:0.38, G:0.14, T:0.34
Consensus pattern (21 bp):
TTCGCCTTCGCAACTTCGCAT
Found at i:12415 original size:31 final size:31
Alignment explanation
Indices: 12374--12587 Score: 320
Period size: 31 Copynumber: 6.9 Consensus size: 31
12364 TATATTTTCC
12374 GTGTTAAGATAAATATCTGTAGAGATGTTCA
1 GTGTTAAGATAAATATCTGTAGAGATGTTCA
* * *
12405 GTATTAAGATAAATATCTATAGTGATGTTCA
1 GTGTTAAGATAAATATCTGTAGAGATGTTCA
*
12436 GTGTTAAGATAAACATCTGTAGAGATGTTCA
1 GTGTTAAGATAAATATCTGTAGAGATGTTCA
12467 GTGTTAAGATAAATATCTGTAGAGATGTTCA
1 GTGTTAAGATAAATATCTGTAGAGATGTTCA
* *
12498 GTGTTAAGATAAATATCTATAGTGATGTTCA
1 GTGTTAAGATAAATATCTGTAGAGATGTTCA
** * * * *
12529 GTGTTCTGAAAAATATCTATCGTGATGTTCA
1 GTGTTAAGATAAATATCTGTAGAGATGTTCA
12560 GTGTTAAGATAAATATCTGTAGAGATGT
1 GTGTTAAGATAAATATCTGTAGAGATGT
12588 CTAGTTGAGG
Statistics
Matches: 163, Mismatches: 20, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 163 1.00
ACGTcount: A:0.35, C:0.07, G:0.21, T:0.36
Consensus pattern (31 bp):
GTGTTAAGATAAATATCTGTAGAGATGTTCA
Found at i:12533 original size:93 final size:93
Alignment explanation
Indices: 12374--12587 Score: 356
Period size: 93 Copynumber: 2.3 Consensus size: 93
12364 TATATTTTCC
12374 GTGTTAAGATAAATATCTGTAGAGATGTTCAGTATTAAGATAAATATCTATAGTGATGTTCAGTG
1 GTGTTAAGATAAATATCTGTAGAGATGTTCAGTATTAAGATAAATATCTATAGTGATGTTCAGTG
* *
12439 TTAAGATAAACATCTGTAGAGATGTTCA
66 TTAAGAAAAACATCTATAGAGATGTTCA
*
12467 GTGTTAAGATAAATATCTGTAGAGATGTTCAGTGTTAAGATAAATATCTATAGTGATGTTCAGTG
1 GTGTTAAGATAAATATCTGTAGAGATGTTCAGTATTAAGATAAATATCTATAGTGATGTTCAGTG
** * * *
12532 TTCTGAAAAATATCTATCGTGATGTTCA
66 TTAAGAAAAACATCTATAGAGATGTTCA
12560 GTGTTAAGATAAATATCTGTAGAGATGT
1 GTGTTAAGATAAATATCTGTAGAGATGT
12588 CTAGTTGAGG
Statistics
Matches: 113, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
93 113 1.00
ACGTcount: A:0.35, C:0.07, G:0.21, T:0.36
Consensus pattern (93 bp):
GTGTTAAGATAAATATCTGTAGAGATGTTCAGTATTAAGATAAATATCTATAGTGATGTTCAGTG
TTAAGAAAAACATCTATAGAGATGTTCA
Found at i:13885 original size:32 final size:31
Alignment explanation
Indices: 13842--13998 Score: 233
Period size: 32 Copynumber: 4.9 Consensus size: 31
13832 ACAAAGATGT
*
13842 TAACACGTGTACCCCAAATTAGCAAGGCAATG
1 TAACAC-TGTACCCAAAATTAGCAAGGCAATG
*
13874 TAACACATGTACCCCAAATTAGCAAGGCAATG
1 TAACAC-TGTACCCAAAATTAGCAAGGCAATG
13906 TAACACATGTACCCAAAATTAGCAAGGCAATG
1 TAACAC-TGTACCCAAAATTAGCAAGGCAATG
*
13938 TAACATCTGTACCAAAAATTAGCAAGGCAATG
1 TAACA-CTGTACCCAAAATTAGCAAGGCAATG
*
13970 TAACATCTGTACCAAAAATTAGCAAGGCA
1 TAACA-CTGTACCCAAAATTAGCAAGGCA
13999 TTTCTTAAAA
Statistics
Matches: 121, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
32 120 0.99
33 1 0.01
ACGTcount: A:0.42, C:0.22, G:0.16, T:0.20
Consensus pattern (31 bp):
TAACACTGTACCCAAAATTAGCAAGGCAATG
Found at i:17502 original size:165 final size:165
Alignment explanation
Indices: 17170--17590 Score: 458
Period size: 165 Copynumber: 2.5 Consensus size: 165
17160 CATTAGAGTT
* * * *
17170 TACACAATTTGAGGATCCTTGCATAGTAATCTCACAAACTGTAGCATTATAGTTCTCGAGAAAAA
1 TACACTATTTGAGGATGCTTGCATAGTTATCTCACAAACTGAAGCATTATAGTTCTCGAGAAAAA
* * * * *
17235 -CTTTTTAAAAACATTTTCAATATATCTTTCTATGTTAAACTTTGAACCCCTCTTGGGGCCACAG
66 GATTTTT--AAACATTTTCCATATATATTTCTATGCTAAACTTTGAACACCTCTTGGGGCCACAG
* *
17299 TATTAGTCCAGTGCTAAAGTTTTAATTATTTGGAATC
129 TATTAGTCCAGTGCTAAAGTTTTAATAATTTCGAATC
* * * * * *
17336 TACATTATTTAAGGATGCTTGCCTAGTTATCTCACAAGCTGAAGCATTATAGTTCCCTAGAAAAA
1 TACACTATTTGAGGATGCTTGCATAGTTATCTCACAAACTGAAGCATTATAGTTCTCGAGAAAAA
* * * *
17401 GATTTTTCAACATTTTCCCTCTATATTTCTATGCTAAACTTTGAACACCTCTTGGGGCCCCAGTA
66 GATTTTTAAACATTTTCCATATATATTTCTATGCTAAACTTTGAACACCTCTTGGGGCCACAGTA
** **
17466 TTAGATTGAGAT-C-ACGGCTTTT-ATAATTTCGAATC
131 TTAG-TCCAG-TGCTAAAG-TTTTAATAATTTCGAATC
* * * * * *
17501 TACACTATTTGAGGGTGC-TGACGTAGTTATCTGACAAATTGATGCATTGTAGTTCTCGA-AAAG
1 TACACTATTTGAGGATGCTTG-CATAGTTATCTCACAAACTGAAGCATTATAGTTCTCGAGAAA-
17564 AAGATTTTTAAACATTTTCCATATATA
64 AAGATTTTTAAACATTTTCCATATATA
17591 CCGGTACTTC
Statistics
Matches: 210, Mismatches: 39, Indels: 13
0.80 0.15 0.05
Matches are distributed among these distances:
164 5 0.02
165 136 0.65
166 63 0.30
167 6 0.03
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (165 bp):
TACACTATTTGAGGATGCTTGCATAGTTATCTCACAAACTGAAGCATTATAGTTCTCGAGAAAAA
GATTTTTAAACATTTTCCATATATATTTCTATGCTAAACTTTGAACACCTCTTGGGGCCACAGTA
TTAGTCCAGTGCTAAAGTTTTAATAATTTCGAATC
Found at i:33852 original size:32 final size:32
Alignment explanation
Indices: 33807--34123 Score: 430
Period size: 32 Copynumber: 9.9 Consensus size: 32
33797 ACAAAGATGT
* *
33807 TAACACATATACCCAAAGTTAGCAAGGCTATG
1 TAACACATGTACCCAAAGTTAGCAAGGCAATG
33839 TAACACATGTACCCAAAGTTAGCAAGGCAATG
1 TAACACATGTACCCAAAGTTAGCAAGGCAATG
*
33871 TAACACATGTACCCAAAGTTAGCAAGGCTATG
1 TAACACATGTACCCAAAGTTAGCAAGGCAATG
**
33903 TAACACATGTGTCCAAAGTTAGCAAGGCAATG
1 TAACACATGTACCCAAAGTTAGCAAGGCAATG
33935 TAACACATGTACCCCAAA-TTAGCAAGGCAATG
1 TAACACATGTA-CCCAAAGTTAGCAAGGCAATG
*
33967 TAACACATGTACCCAAAATTAGCAAGGCAATG
1 TAACACATGTACCCAAAGTTAGCAAGGCAATG
*
33999 TAACACATGTACCCCAAA-TTAGCAAAGCAATG
1 TAACACATGTA-CCCAAAGTTAGCAAGGCAATG
** *
34031 TAACACATGTA-CC---GTCTTTCAAGTCCATAATG
1 TAACACATGTACCCAAAGT-TAGCAAG-GC--AATG
*
34063 TAACACATGTACCCAAAATTAGCAAGGCAATG
1 TAACACATGTACCCAAAGTTAGCAAGGCAATG
*
34095 TAACACATGTACCCAAAATTAGCAAGGCA
1 TAACACATGTACCCAAAGTTAGCAAGGCA
34124 TTTCTTAATA
Statistics
Matches: 256, Mismatches: 17, Indels: 24
0.86 0.06 0.08
Matches are distributed among these distances:
28 1 0.00
29 4 0.02
30 3 0.01
31 6 0.02
32 222 0.87
33 13 0.05
34 1 0.00
35 5 0.02
36 1 0.00
ACGTcount: A:0.40, C:0.23, G:0.16, T:0.21
Consensus pattern (32 bp):
TAACACATGTACCCAAAGTTAGCAAGGCAATG
Found at i:38007 original size:36 final size:33
Alignment explanation
Indices: 37964--38096 Score: 207
Period size: 32 Copynumber: 4.0 Consensus size: 33
37954 AGTCACCTAA
*
37964 TTTTTTTCAAAGCCCTTGAATTTGTACATCTATTTT
1 TTTTTTTCAAAGTCCTTGAATTTGTACATCTA---T
38000 TTTTTTTCAAAGTCCTTGAATTTGTACATCTA-
1 TTTTTTTCAAAGTCCTTGAATTTGTACATCTAT
*
38032 TTTTTTTCAAAGTCCTTGAATTTGTACACCTAT
1 TTTTTTTCAAAGTCCTTGAATTTGTACATCTAT
38065 TTTTTTT-AAAGTCCTTGAATTTGTACATCTAT
1 TTTTTTTCAAAGTCCTTGAATTTGTACATCTAT
38097 CTCAATAGTG
Statistics
Matches: 93, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
32 55 0.59
33 7 0.08
36 31 0.33
ACGTcount: A:0.24, C:0.16, G:0.09, T:0.51
Consensus pattern (33 bp):
TTTTTTTCAAAGTCCTTGAATTTGTACATCTAT
Found at i:38068 original size:68 final size:64
Alignment explanation
Indices: 37963--38096 Score: 214
Period size: 68 Copynumber: 2.0 Consensus size: 64
37953 AAGTCACCTA
*
37963 ATTTTTTTCAAAGCCCTTGAATTTGTACATCTATTTTTTTTTTTCAAAGTCCTTGAATTTGTACA
1 ATTTTTTTCAAAGCCCTTGAATTTGTACACCTA---TTTTTTTT-AAAGTCCTTGAATTTGTACA
38028 TCT
62 TCT
*
38031 ATTTTTTTCAAAGTCCTTGAATTTGTACACCTATTTTTTTTAAAGTCCTTGAATTTGTACATCT
1 ATTTTTTTCAAAGCCCTTGAATTTGTACACCTATTTTTTTTAAAGTCCTTGAATTTGTACATCT
38095 AT
1 AT
38097 CTCAATAGTG
Statistics
Matches: 64, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
64 25 0.39
65 8 0.12
68 31 0.48
ACGTcount: A:0.25, C:0.16, G:0.09, T:0.51
Consensus pattern (64 bp):
ATTTTTTTCAAAGCCCTTGAATTTGTACACCTATTTTTTTTAAAGTCCTTGAATTTGTACATCT
Found at i:39270 original size:26 final size:26
Alignment explanation
Indices: 39237--39290 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
39227 GGAACAGAAA
39237 ATTATTAATAAATAACGGATATGAAC
1 ATTATTAATAAATAACGGATATGAAC
* *
39263 ATTATTAATAAATGACGGATTTGAAC
1 ATTATTAATAAATAACGGATATGAAC
39289 AT
1 AT
39291 GTCCTTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.46, C:0.07, G:0.13, T:0.33
Consensus pattern (26 bp):
ATTATTAATAAATAACGGATATGAAC
Found at i:51223 original size:24 final size:24
Alignment explanation
Indices: 51191--51461 Score: 227
Period size: 24 Copynumber: 11.3 Consensus size: 24
51181 AAACTTTTAA
*
51191 TACA-TCATGATAGAGTTTTCATT
1 TACATTCATGATAGAGTTTTCAGT
51214 TACATTCATGATAGAGTTTTCAGT
1 TACATTCATGATAGAGTTTTCAGT
* *
51238 AACATTCATGAT--TGTTTTCAGT
1 TACATTCATGATAGAGTTTTCAGT
51260 TACATTCATGATAGAGTTTTCAGT
1 TACATTCATGATAGAGTTTTCAGT
* ** *
51284 AACATTTCA-G-TA-A-CATTCATGA
1 TACA-TTCATGATAGAGTTTTCA-GT
* * **
51306 TAGAGTTTTCA-GTTACGTAACATTTCAGT
1 TACA---TTCATGATA-G--AGTTTTCAGT
*
51335 TACATTCATAATAGAGTTTTCAGT
1 TACATTCATGATAGAGTTTTCAGT
* *
51359 TACATTTATAATAGAGTTTTCAGT
1 TACATTCATGATAGAGTTTTCAGT
*
51383 TACATTCATAATAGAG-TTTCAGT
1 TACATTCATGATAGAGTTTTCAGT
* *
51406 TACATTTATGGTAGAGTTTTCAGT
1 TACATTCATGATAGAGTTTTCAGT
* *
51430 TACATTCATAATAGAGTTTTCAAT
1 TACATTCATGATAGAGTTTTCAGT
*
51454 AACATTCA
1 TACATTCA
51462 CTTGTACAAT
Statistics
Matches: 204, Mismatches: 29, Indels: 29
0.78 0.11 0.11
Matches are distributed among these distances:
21 4 0.02
22 24 0.12
23 26 0.13
24 128 0.63
25 6 0.03
26 5 0.02
27 2 0.01
29 5 0.02
30 4 0.02
ACGTcount: A:0.32, C:0.13, G:0.14, T:0.41
Consensus pattern (24 bp):
TACATTCATGATAGAGTTTTCAGT
Found at i:51300 original size:35 final size:35
Alignment explanation
Indices: 51253--51365 Score: 154
Period size: 35 Copynumber: 3.1 Consensus size: 35
51243 TCATGATTGT
51253 TTTCAGTTACATTCATGATAGAGTTTTCAGTAACA
1 TTTCAGTTACATTCATGATAGAGTTTTCAGTAACA
*
51288 TTTCAGTAACATTCATGATAGAGTTTTCAGTTACGTAACA
1 TTTCAGTTACATTCATGATAGAGTTTTC----A-GTAACA
* *
51328 TTTCAGTTACATTCATAATAGAGTTTTCAGTTACA
1 TTTCAGTTACATTCATGATAGAGTTTTCAGTAACA
51363 TTT
1 TTT
51366 ATAATAGAGT
Statistics
Matches: 69, Mismatches: 4, Indels: 10
0.83 0.05 0.12
Matches are distributed among these distances:
35 35 0.51
36 1 0.01
39 1 0.01
40 32 0.46
ACGTcount: A:0.31, C:0.14, G:0.13, T:0.42
Consensus pattern (35 bp):
TTTCAGTTACATTCATGATAGAGTTTTCAGTAACA
Found at i:51340 original size:40 final size:40
Alignment explanation
Indices: 51253--51361 Score: 165
Period size: 40 Copynumber: 2.9 Consensus size: 40
51243 TCATGATTGT
51253 TTTCAGTTACATTCATGATAGAGTTTTC----A-GTAACA
1 TTTCAGTTACATTCATGATAGAGTTTTCAGTTACGTAACA
*
51288 TTTCAGTAACATTCATGATAGAGTTTTCAGTTACGTAACA
1 TTTCAGTTACATTCATGATAGAGTTTTCAGTTACGTAACA
*
51328 TTTCAGTTACATTCATAATAGAGTTTTCAGTTAC
1 TTTCAGTTACATTCATGATAGAGTTTTCAGTTAC
51362 ATTTATAATA
Statistics
Matches: 66, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
35 27 0.41
39 1 0.02
40 38 0.58
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.40
Consensus pattern (40 bp):
TTTCAGTTACATTCATGATAGAGTTTTCAGTTACGTAACA
Found at i:51421 original size:47 final size:47
Alignment explanation
Indices: 51328--51448 Score: 215
Period size: 47 Copynumber: 2.6 Consensus size: 47
51318 TTACGTAACA
51328 TTTCAGTTACATTCATAATAGAGTTTTCAGTTACATTTATAATAGAGT
1 TTTCAGTTACATTCATAATAGAG-TTTCAGTTACATTTATAATAGAGT
**
51376 TTTCAGTTACATTCATAATAGAGTTTCAGTTACATTTATGGTAGAGT
1 TTTCAGTTACATTCATAATAGAGTTTCAGTTACATTTATAATAGAGT
51423 TTTCAGTTACATTCATAATAGAGTTT
1 TTTCAGTTACATTCATAATAGAGTTT
51449 TCAATAACAT
Statistics
Matches: 71, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
47 48 0.68
48 23 0.32
ACGTcount: A:0.31, C:0.11, G:0.14, T:0.44
Consensus pattern (47 bp):
TTTCAGTTACATTCATAATAGAGTTTCAGTTACATTTATAATAGAGT
Found at i:51423 original size:71 final size:71
Alignment explanation
Indices: 51191--51461 Score: 216
Period size: 71 Copynumber: 3.8 Consensus size: 71
51181 AAACTTTTAA
* * * * * * *
51191 TACA-TCATGATAGAGTTTTCATTTACATTCATGATAGAGTTTTCAGTAACATTCATGATTG-TT
1 TACATTCATAATAGAGTTTTCAGTTACATTCATAATAGAGTTTTCAATAACATTCATAATAGAGT
51254 TTCAGT
66 TTCAGT
* * * **
51260 TACATTCATGATAGAGTTTTCAGTAACATTTCAGT-A-ACA---TTCATGATAGAGTTTTCAGTT
1 TACATTCATAATAGAGTTTTCAGTTACA-TTCA-TAATAGAGTTTTCA--ATA-A-CATTCA--T
* *
51320 ACGTA-ACATTTCAGT
58 A-ATAGA-GTTTCAGT
* * *
51335 TACATTCATAATAGAGTTTTCAGTTACATTTATAATAGAGTTTTCAGTTACATTCATAATAGAGT
1 TACATTCATAATAGAGTTTTCAGTTACATTCATAATAGAGTTTTCAATAACATTCATAATAGAGT
51400 TTCAGT
66 TTCAGT
* **
51406 TACATTTATGGTAGAGTTTTCAGTTACATTCATAATAGAGTTTTCAATAACATTCA
1 TACATTCATAATAGAGTTTTCAGTTACATTCATAATAGAGTTTTCAATAACATTCA
51462 CTTGTACAAT
Statistics
Matches: 158, Mismatches: 26, Indels: 34
0.72 0.12 0.16
Matches are distributed among these distances:
67 4 0.03
69 6 0.04
70 24 0.15
71 68 0.43
72 4 0.03
73 2 0.01
74 9 0.06
75 36 0.23
76 1 0.01
78 4 0.03
ACGTcount: A:0.32, C:0.13, G:0.14, T:0.41
Consensus pattern (71 bp):
TACATTCATAATAGAGTTTTCAGTTACATTCATAATAGAGTTTTCAATAACATTCATAATAGAGT
TTCAGT
Found at i:52505 original size:2 final size:2
Alignment explanation
Indices: 52500--52573 Score: 148
Period size: 2 Copynumber: 37.0 Consensus size: 2
52490 GAACCCCCCC
52500 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
52542 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
52574 GCTAATTATT
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 72 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:77002 original size:31 final size:31
Alignment explanation
Indices: 76949--77291 Score: 465
Period size: 31 Copynumber: 11.1 Consensus size: 31
76939 ATCGTTTGTA
* *
76949 TAATTATCAACAAAATTTGATGTTGAAATATTG
1 TAATTGTCAACAAAATATGATGTTGAAATA--G
* *
76982 TAATT-ACCAC-AAATATGATGTTGAAATAG
1 TAATTGTCAACAAAATATGATGTTGAAATAG
* *
77011 TAATTGTCCACAAAATTTGATGTTGAAATAG
1 TAATTGTCAACAAAATATGATGTTGAAATAG
* *
77042 TAATTGTCAACAAAATACGATGATGAAATAG
1 TAATTGTCAACAAAATATGATGTTGAAATAG
* *
77073 TAATTATCAACAAAATTTGATGTTGAAATAG
1 TAATTGTCAACAAAATATGATGTTGAAATAG
*
77104 TAATTGTCAACAAAATATCATGTTGAAATAG
1 TAATTGTCAACAAAATATGATGTTGAAATAG
* * * *
77135 TGATTGTCAAGAAAATGTCATGTTGAAATAG
1 TAATTGTCAACAAAATATGATGTTGAAATAG
*
77166 TAATTGTCAACAAAATATCATGTTGAAATAG
1 TAATTGTCAACAAAATATGATGTTGAAATAG
* *
77197 TAATTGTCAACAAAATATCATGTTAAAATAG
1 TAATTGTCAACAAAATATGATGTTGAAATAG
* * *
77228 TAATTGTCAAGAAAATGTCATGTTGAAATAG
1 TAATTGTCAACAAAATATGATGTTGAAATAG
77259 TAATTGTCAACAAAATATGATGTTGAAATAG
1 TAATTGTCAACAAAATATGATGTTGAAATAG
77290 TA
1 TA
77292 GGCTGGTCAA
Statistics
Matches: 279, Mismatches: 29, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
29 6 0.02
30 4 0.01
31 261 0.94
32 3 0.01
33 5 0.02
ACGTcount: A:0.44, C:0.08, G:0.15, T:0.33
Consensus pattern (31 bp):
TAATTGTCAACAAAATATGATGTTGAAATAG
Found at i:81934 original size:2 final size:2
Alignment explanation
Indices: 81927--81970 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
81917 ATATGAAAAT
81927 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
81969 TC
1 TC
81971 AAATATGAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:83328 original size:2 final size:2
Alignment explanation
Indices: 83321--83378 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
83311 CATGAAAAAT
83321 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
83363 TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC
83379 AGCCAATTAG
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:84046 original size:9 final size:9
Alignment explanation
Indices: 84030--84072 Score: 61
Period size: 9 Copynumber: 4.9 Consensus size: 9
84020 CTGGCCCTGT
*
84030 GTTTTTTTT
1 GTTTTTTTA
*
84039 GGTTTTTTA
1 GTTTTTTTA
84048 GTTTTTTTA
1 GTTTTTTTA
84057 G-TTTTTTA
1 GTTTTTTTA
84065 GTTTTTTT
1 GTTTTTTT
84073 GGGGAGGGGT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
8 8 0.27
9 22 0.73
ACGTcount: A:0.07, C:0.00, G:0.14, T:0.79
Consensus pattern (9 bp):
GTTTTTTTA
Found at i:84052 original size:7 final size:8
Alignment explanation
Indices: 84033--84071 Score: 60
Period size: 8 Copynumber: 4.8 Consensus size: 8
84023 GCCCTGTGTT
*
84033 TTTTTTGG
1 TTTTTTAG
84041 TTTTTTAG
1 TTTTTTAG
84049 TTTTTTTAG
1 -TTTTTTAG
84058 TTTTTTAG
1 TTTTTTAG
84066 TTTTTT
1 TTTTTT
84072 TGGGGAGGGG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
8 21 0.72
9 8 0.28
ACGTcount: A:0.08, C:0.00, G:0.13, T:0.79
Consensus pattern (8 bp):
TTTTTTAG
Found at i:84054 original size:17 final size:17
Alignment explanation
Indices: 84032--84074 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
84022 GGCCCTGTGT
84032 TTTTTTTGGTTTTTTAG
1 TTTTTTTGGTTTTTTAG
*
84049 TTTTTTTAGTTTTTTAG
1 TTTTTTTGGTTTTTTAG
84066 TTTTTTTGG
1 TTTTTTTGG
84075 GGAGGGGTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.07, C:0.00, G:0.16, T:0.77
Consensus pattern (17 bp):
TTTTTTTGGTTTTTTAG
Found at i:100643 original size:20 final size:22
Alignment explanation
Indices: 100606--100645 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
100596 GATTGTCACT
100606 GATTCTGAATTCATATTTTGCA
1 GATTCTGAATTCATATTTTGCA
100628 GATTCTGAA-T-ATATTTTG
1 GATTCTGAATTCATATTTTG
100646 GTTCTATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.44
21 1 0.06
22 9 0.50
ACGTcount: A:0.28, C:0.10, G:0.15, T:0.47
Consensus pattern (22 bp):
GATTCTGAATTCATATTTTGCA
Found at i:104571 original size:25 final size:25
Alignment explanation
Indices: 104542--104590 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
104532 TGAATAAAAA
*
104542 ATTAAAGCAAGATAAAAATGAAGAT
1 ATTAAAGCAAAATAAAAATGAAGAT
* **
104567 ATTAAATCAAAATAATTATGAAGA
1 ATTAAAGCAAAATAAAAATGAAGA
104591 CAAAAAAAAC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.59, C:0.04, G:0.12, T:0.24
Consensus pattern (25 bp):
ATTAAAGCAAAATAAAAATGAAGAT
Found at i:113554 original size:2 final size:2
Alignment explanation
Indices: 113547--113583 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
113537 GCAAAACGTG
113547 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
113584 CAAGGAAAAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:119533 original size:2 final size:2
Alignment explanation
Indices: 119526--119586 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
119516 GGTGAGACGC
119526 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
119568 CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT C
119587 GTAAACATTA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:121740 original size:2 final size:2
Alignment explanation
Indices: 121733--121774 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
121723 GCGACTTCAG
121733 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
121775 TTATGTCTGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:125129 original size:16 final size:16
Alignment explanation
Indices: 125103--125147 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
125093 ACCGTGCTGT
*
125103 AAGAGCCGGAGCTACG
1 AAGAGCCGGAGCCACG
* *
125119 AGGAGCAGGAGCCACG
1 AAGAGCCGGAGCCACG
125135 AAGAGCCGGAGCC
1 AAGAGCCGGAGCC
125148 GCGCTGAAAG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.31, C:0.27, G:0.40, T:0.02
Consensus pattern (16 bp):
AAGAGCCGGAGCCACG
Found at i:128679 original size:32 final size:31
Alignment explanation
Indices: 128637--129112 Score: 243
Period size: 32 Copynumber: 14.9 Consensus size: 31
128627 ATAGATATGT
* * *
128637 GTATATATACACTGTTTACACTTTGACATAGG
1 GTATAAATACA-TGTTTACACTTAGACAAAGG
* * *
128669 GTCTAAATACAATGTCTACACTTAGACAAAGT
1 GTATAAATAC-ATGTTTACACTTAGACAAAGG
* * *
128701 GTATAAATACAGGTGTTACACTTAGACACAGT
1 GTATAAATACATGT-TTACACTTAGACAAAGG
* * * * *
128733 CTTTAAATACAATGTTTTCACTAAGACAAAGT
1 GTATAAATAC-ATGTTTACACTTAGACAAAGG
* * * * * * *
128765 GTATAAATACAGGTGGTATACTTATATATAGT
1 GTATAAATACATGT-TTACACTTAGACAAAGG
* * * *
128797 CTTTAAATACAATGTTTACACTAAGACAAAGT
1 GTATAAATAC-ATGTTTACACTTAGACAAAGG
* * * * * *
128829 GTATAAATACAGGTGGTACACTTATATATAGT
1 GTATAAATACATGT-TTACACTTAGACAAAGG
* * * *
128861 CTTTAAATACAATGTTTACACTTAGACAGAGT
1 GTATAAATAC-ATGTTTACACTTAGACAAAGG
* * * * *
128893 GTATAAATACAGGTGTTACACTTATATATAGT
1 GTATAAATACATGT-TTACACTTAGACAAAGG
* * *
128925 CTTTAAATACAATGTTTACACTTAGACAAAGT
1 GTATAAATAC-ATGTTTACACTTAGACAAAGG
* * *
128957 GTATAAATACAGGTGTTACACTTAGACACAGT
1 GTATAAATACATGT-TTACACTTAGACAAAGG
* * * *
128989 CTTTAAATACAATGTTTACACTAAGACAAAGT
1 GTATAAATAC-ATGTTTACACTTAGACAAAGG
* * * * * * *
129021 GTATAAATACAGGTGGTATACTTATATATAGT
1 GTATAAATACATGT-TTACACTTAGACAAAGG
* * * * *
129053 CTTTAAATGCAATGTTTACACTTAGACAGAGT
1 GTATAAATAC-ATGTTTACACTTAGACAAAGG
129085 GTATAAATAC-TGGTGTTACACTTAGACA
1 GTATAAATACAT-GT-TTACACTTAGACA
129113 TAGTCTTTAA
Statistics
Matches: 337, Mismatches: 92, Indels: 30
0.73 0.20 0.07
Matches are distributed among these distances:
30 1 0.00
31 20 0.06
32 297 0.88
33 19 0.06
ACGTcount: A:0.38, C:0.14, G:0.15, T:0.33
Consensus pattern (31 bp):
GTATAAATACATGTTTACACTTAGACAAAGG
Found at i:128740 original size:64 final size:64
Alignment explanation
Indices: 128652--129172 Score: 726
Period size: 64 Copynumber: 8.2 Consensus size: 64
128642 TATACACTGT
* ** * *
128652 TTACACTTTGACATAGGGTCTAAATACAATGTCTACACTTAGACAAAGTGTATAAATACAGGTG
1 TTACACTTAGACATAGTCTTTAAATACAATGTTTACACTTAGACAAAGTGTATAAATACAGGTG
* * *
128716 TTACACTTAGACACAGTCTTTAAATACAATGTTTTCACTAAGACAAAGTGTATAAATACAGGTG
1 TTACACTTAGACATAGTCTTTAAATACAATGTTTACACTTAGACAAAGTGTATAAATACAGGTG
* * * * *
128780 GTATACTTATATATAGTCTTTAAATACAATGTTTACACTAAGACAAAGTGTATAAATACAGGTG
1 TTACACTTAGACATAGTCTTTAAATACAATGTTTACACTTAGACAAAGTGTATAAATACAGGTG
* * * *
128844 GTACACTTATATATAGTCTTTAAATACAATGTTTACACTTAGACAGAGTGTATAAATACAGGTG
1 TTACACTTAGACATAGTCTTTAAATACAATGTTTACACTTAGACAAAGTGTATAAATACAGGTG
* *
128908 TTACACTTATATATAGTCTTTAAATACAATGTTTACACTTAGACAAAGTGTATAAATACAGGTG
1 TTACACTTAGACATAGTCTTTAAATACAATGTTTACACTTAGACAAAGTGTATAAATACAGGTG
* *
128972 TTACACTTAGACACAGTCTTTAAATACAATGTTTACACTAAGACAAAGTGTATAAATACAGGTG
1 TTACACTTAGACATAGTCTTTAAATACAATGTTTACACTTAGACAAAGTGTATAAATACAGGTG
* * * * * * *
129036 GTATACTTATATATAGTCTTTAAATGCAATGTTTACACTTAGACAGAGTGTATAAATACTGGTG
1 TTACACTTAGACATAGTCTTTAAATACAATGTTTACACTTAGACAAAGTGTATAAATACAGGTG
** *
129100 TTACACTTAGACATAGTCTTTAAATACAATGTTTTTACTTAG----AGTGTATAAATACAGTTG
1 TTACACTTAGACATAGTCTTTAAATACAATGTTTACACTTAGACAAAGTGTATAAATACAGGTG
*
129160 TTACTCTTAGACA
1 TTACACTTAGACA
129173 AAGTATATGA
Statistics
Matches: 415, Mismatches: 42, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
60 28 0.07
64 387 0.93
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.34
Consensus pattern (64 bp):
TTACACTTAGACATAGTCTTTAAATACAATGTTTACACTTAGACAAAGTGTATAAATACAGGTG
Found at i:128962 original size:192 final size:192
Alignment explanation
Indices: 128672--129172 Score: 803
Period size: 192 Copynumber: 2.6 Consensus size: 192
128662 ACATAGGGTC
* * *
128672 TAAATACAATGTCTACACTTAGACAAAGTGTATAAATACAGGTGTTACACTTAGACACAGTCTTT
1 TAAATACAATGTTTACACTTAGACAGAGTGTATAAATACAGGTGTTACACTTAGACATAGTCTTT
* * * * *
128737 AAATACAATGTTTTCACTAAGACAAAGTGTATAAATACAGGTGGTATACTTATATATAGTCTTTA
66 AAATACAATGTTTTCACTTAGACAAAGTGTATAAATACAGGTGGTACACTTAGACACAGTCTTTA
128802 AATACAATGTTTACACTAAGACAAAGTGTATAAATACAGGTGGTACACTTATATATAGTCTT
131 AATACAATGTTTACACTAAGACAAAGTGTATAAATACAGGTGGTACACTTATATATAGTCTT
* *
128864 TAAATACAATGTTTACACTTAGACAGAGTGTATAAATACAGGTGTTACACTTATATATAGTCTTT
1 TAAATACAATGTTTACACTTAGACAGAGTGTATAAATACAGGTGTTACACTTAGACATAGTCTTT
* *
128929 AAATACAATGTTTACACTTAGACAAAGTGTATAAATACAGGTGTTACACTTAGACACAGTCTTTA
66 AAATACAATGTTTTCACTTAGACAAAGTGTATAAATACAGGTGGTACACTTAGACACAGTCTTTA
*
128994 AATACAATGTTTACACTAAGACAAAGTGTATAAATACAGGTGGTATACTTATATATAGTCTT
131 AATACAATGTTTACACTAAGACAAAGTGTATAAATACAGGTGGTACACTTATATATAGTCTT
* *
129056 TAAATGCAATGTTTACACTTAGACAGAGTGTATAAATACTGGTGTTACACTTAGACATAGTCTTT
1 TAAATACAATGTTTACACTTAGACAGAGTGTATAAATACAGGTGTTACACTTAGACATAGTCTTT
* * * *
129121 AAATACAATGTTTTTACTTAG----AGTGTATAAATACAGTTGTTACTCTTAGACA
66 AAATACAATGTTTTCACTTAGACAAAGTGTATAAATACAGGTGGTACACTTAGACA
129173 AAGTATATGA
Statistics
Matches: 288, Mismatches: 21, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
188 29 0.10
192 259 0.90
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.34
Consensus pattern (192 bp):
TAAATACAATGTTTACACTTAGACAGAGTGTATAAATACAGGTGTTACACTTAGACATAGTCTTT
AAATACAATGTTTTCACTTAGACAAAGTGTATAAATACAGGTGGTACACTTAGACACAGTCTTTA
AATACAATGTTTACACTAAGACAAAGTGTATAAATACAGGTGGTACACTTATATATAGTCTT
Found at i:129168 original size:28 final size:29
Alignment explanation
Indices: 129137--129199 Score: 74
Period size: 32 Copynumber: 2.1 Consensus size: 29
129127 AATGTTTTTA
*
129137 CTTAG-AGTGTATAAATACAGTTGTTACT
1 CTTAGAAGTATATAAATACAGTTGTTACT
*
129165 CTTAGACAAAGTATATGAATACAGTTGTTACT
1 CTTAG---AAGTATATAAATACAGTTGTTACT
129197 CTT
1 CTT
129200 CGACATAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 5 0.17
32 24 0.83
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.38
Consensus pattern (29 bp):
CTTAGAAGTATATAAATACAGTTGTTACT
Found at i:129187 original size:32 final size:32
Alignment explanation
Indices: 129146--129226 Score: 110
Period size: 32 Copynumber: 2.5 Consensus size: 32
129136 ACTTAGAGTG
129146 TATAAATACAGTTGTTACTCTTAGACA-AAGTA
1 TATAAATACAGTTGTTACTCTTAGACATAA-TA
* * *
129178 TATGAATACAGTTGTTACTCTTCGACATAATT
1 TATAAATACAGTTGTTACTCTTAGACATAATA
*
129210 TATAAATACATTTGTTA
1 TATAAATACAGTTGTTA
129227 AACTTTTAGT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
32 41 0.95
33 2 0.05
ACGTcount: A:0.37, C:0.12, G:0.11, T:0.40
Consensus pattern (32 bp):
TATAAATACAGTTGTTACTCTTAGACATAATA
Found at i:129205 original size:92 final size:92
Alignment explanation
Indices: 128876--129249 Score: 233
Period size: 96 Copynumber: 4.0 Consensus size: 92
128866 AATACAATGT
* * * * * *
128876 TTACACTTAGACAGAGTGTATAAATACAGGTGTTACACTTATATATAGTCTT-TAAATACA-ATG
1 TTACACTTAGACAAAGTATATAAATACAGGTGTTACACTTAGACATAAT-TTATAAATACATTTG
* *
128939 TTTACACTTAGACAAAGTGTATAAATACAGGTG
65 -TTAAACTTAG----AGTGTATAAATACAGTTG
* * * * * * **
128972 TTACACTTAGACACAGTCTTTAAATACA-ATGTTTACACTAAGACA-AAGTGTATAAATACAGGT
1 TTACACTTAGACAAAGTATATAAATACAGGTG-TTACACTTAGACATAA-TTTATAAATACATTT
* * * * * * *
129035 GGTATACTTATATATAGTCTTTAAATGCA-ATG
64 GTTAAAC---T-TAGAGTGTATAAATACAGTTG
* * * *
129067 TTTACACTTAGACAGAGTGTATAAATACTGGTGTTACACTTAGACATAGTCTT-TAAATACAATG
1 -TTACACTTAGACAAAGTATATAAATACAGGTGTTACACTTAGACATAAT-TTATAAATAC-AT-
*
129131 TT-TT-TACTTAGAGTGTATAAATACAGTTG
62 TTGTTAAACTTAGAGTGTATAAATACAGTTG
* * * * *
129160 TTACTCTTAGACAAAGTATATGAATACAGTTGTTACTCTTCGACATAATTTATAAATACATTTGT
1 TTACACTTAGACAAAGTATATAAATACAGGTGTTACACTTAGACATAATTTATAAATACATTTGT
**
129225 TAAACTTTTAGTGTATAAATACAGT
66 TAAACTTAGAGTGTATAAATACAGT
129250 GTTTTCACTT
Statistics
Matches: 215, Mismatches: 45, Indels: 40
0.72 0.15 0.13
Matches are distributed among these distances:
90 2 0.01
91 6 0.03
92 80 0.37
93 3 0.01
95 6 0.03
96 106 0.49
97 8 0.04
98 1 0.00
99 1 0.00
100 2 0.01
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.36
Consensus pattern (92 bp):
TTACACTTAGACAAAGTATATAAATACAGGTGTTACACTTAGACATAATTTATAAATACATTTGT
TAAACTTAGAGTGTATAAATACAGTTG
Found at i:141905 original size:12 final size:12
Alignment explanation
Indices: 141888--141912 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
141878 CAGTATTACC
141888 TGATTTTTTTTT
1 TGATTTTTTTTT
141900 TGATTTTTTTTT
1 TGATTTTTTTTT
141912 T
1 T
141913 TAATATTACA
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:0.08, C:0.00, G:0.08, T:0.84
Consensus pattern (12 bp):
TGATTTTTTTTT
Found at i:149086 original size:1 final size:1
Alignment explanation
Indices: 149080--149120 Score: 73
Period size: 1 Copynumber: 41.0 Consensus size: 1
149070 GATATATGTC
*
149080 TTTTTTTATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
149121 ACAAAATCTC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
1 38 1.00
ACGTcount: A:0.02, C:0.00, G:0.00, T:0.98
Consensus pattern (1 bp):
T
Found at i:153564 original size:2 final size:2
Alignment explanation
Indices: 153559--153605 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
153549 GTCTTATCCT
153559 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
153601 GA GA G
1 GA GA G
153606 TTTGATTTGC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:166684 original size:38 final size:38
Alignment explanation
Indices: 166607--166684 Score: 111
Period size: 38 Copynumber: 2.1 Consensus size: 38
166597 TTGTGATACT
* ***
166607 GACAGACAGACAGACAGACAGTGTAGAGACAGTTGAGA
1 GACAGACAGACAGACAGACAGTGGAGAGACAGGACAGA
*
166645 GACAGACAGACAGACAGATAGTGGAGAGACAGGACAGA
1 GACAGACAGACAGACAGACAGTGGAGAGACAGGACAGA
166683 GA
1 GA
166685 GTGAGACAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.44, C:0.15, G:0.33, T:0.08
Consensus pattern (38 bp):
GACAGACAGACAGACAGACAGTGGAGAGACAGGACAGA
Found at i:172137 original size:18 final size:19
Alignment explanation
Indices: 172114--172151 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
172104 ATGTATATGT
172114 AACTAT-TGCATATATGAG
1 AACTATATGCATATATGAG
172132 AACTATAAATGCATATATGA
1 AACTAT--ATGCATATATGA
172152 TATATATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 6 0.35
21 11 0.65
ACGTcount: A:0.45, C:0.11, G:0.13, T:0.32
Consensus pattern (19 bp):
AACTATATGCATATATGAG
Found at i:175500 original size:15 final size:15
Alignment explanation
Indices: 175480--175509 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
175470 AAAGTTACTC
175480 TGCATGATTGTCAGT
1 TGCATGATTGTCAGT
*
175495 TGCATGGTTGTCAGT
1 TGCATGATTGTCAGT
175510 CTTTCAGTCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.13, G:0.30, T:0.40
Consensus pattern (15 bp):
TGCATGATTGTCAGT
Found at i:175667 original size:2 final size:2
Alignment explanation
Indices: 175660--175734 Score: 116
Period size: 2 Copynumber: 38.0 Consensus size: 2
175650 CTGATGTAAG
* * *
175660 GA GA GA GA GA GA GA CA GA CA GA GA GA GC GA GA GA GA G- GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
175701 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
175735 TACAGGATAA
Statistics
Matches: 66, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
1 1 0.02
2 65 0.98
ACGTcount: A:0.48, C:0.04, G:0.48, T:0.00
Consensus pattern (2 bp):
GA
Found at i:175955 original size:2 final size:2
Alignment explanation
Indices: 175948--176024 Score: 50
Period size: 2 Copynumber: 39.0 Consensus size: 2
175938 TCTGAAATCA
* * * * *
175948 AG AG AG AG AG AG AG AG AG GG AG AG AA AG AG AC AG AA AG AC AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
* * * *
175990 AG -G AT AG AG AG AC AG AG CA- AG AC AT AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG -AG AG AG AG AG AG AG AG AG
176025 GTGGGGGCAA
Statistics
Matches: 55, Mismatches: 17, Indels: 6
0.71 0.22 0.08
Matches are distributed among these distances:
1 2 0.04
2 52 0.95
3 1 0.02
ACGTcount: A:0.51, C:0.06, G:0.40, T:0.03
Consensus pattern (2 bp):
AG
Found at i:176092 original size:2 final size:2
Alignment explanation
Indices: 176087--176137 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
176077 TTGTAGATCT
176087 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
176129 GA GA GA GA G
1 GA GA GA GA G
176138 TAGAAATTGG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:183334 original size:2 final size:2
Alignment explanation
Indices: 183327--183379 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
183317 ATTATTTCAT
183327 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
183369 TC TC TC TC TC T
1 TC TC TC TC TC T
183380 GAGTGATCAA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:183340 original size:24 final size:24
Alignment explanation
Indices: 183283--183364 Score: 75
Period size: 24 Copynumber: 3.4 Consensus size: 24
183273 TCTCTCCCTT
*
183283 TCTCTCCCTCATTCATTCATTCTC
1 TCTCTCTCTCATTCATTCATTCTC
183307 TCTCAT-TCTCATT-ATTTCATTCTC
1 TCTC-TCTCTCATTCA-TTCATTCTC
183331 TCTCTCTCTC-TCTC-TCTC-TCTCTC
1 TCTCTCTCTCAT-TCAT-TCAT-TCTC
183355 TCTCTCTCTC
1 TCTCTCTCTC
183365 TCTCTCTCTC
Statistics
Matches: 50, Mismatches: 1, Indels: 14
0.77 0.02 0.22
Matches are distributed among these distances:
23 5 0.10
24 44 0.88
25 1 0.02
ACGTcount: A:0.09, C:0.41, G:0.00, T:0.50
Consensus pattern (24 bp):
TCTCTCTCTCATTCATTCATTCTC
Found at i:204190 original size:29 final size:29
Alignment explanation
Indices: 204156--204242 Score: 140
Period size: 29 Copynumber: 3.0 Consensus size: 29
204146 TGTATGTGTC
204156 CATGAGTATAAATAGAAGGCTTATGTTAA
1 CATGAGTATAAATAGAAGGCTTATGTTAA
*
204185 CATGAGTTTAAATAGAAGGCTTATGTTAA
1 CATGAGTATAAATAGAAGGCTTATGTTAA
**
204214 TGTGAGTATAAATAGAAGGC-TATGTTAA
1 CATGAGTATAAATAGAAGGCTTATGTTAA
204242 C
1 C
204243 TTGTATTCTA
Statistics
Matches: 53, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
28 8 0.15
29 45 0.85
ACGTcount: A:0.39, C:0.07, G:0.22, T:0.32
Consensus pattern (29 bp):
CATGAGTATAAATAGAAGGCTTATGTTAA
Found at i:207290 original size:7 final size:7
Alignment explanation
Indices: 207273--207302 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
207263 ATTTGTTTTG
207273 TTTTG-T
1 TTTTGTT
207279 TTTTGTT
1 TTTTGTT
207286 TTTTGTT
1 TTTTGTT
207293 TTTTGTT
1 TTTTGTT
207300 TTT
1 TTT
207303 GCTTACCTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 5 0.22
7 18 0.78
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (7 bp):
TTTTGTT
Found at i:213763 original size:11 final size:9
Alignment explanation
Indices: 213739--213768 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
213729 TCCTTATGAT
213739 AATATATAC
1 AATATATAC
213748 AATATATAC
1 AATATATAC
213757 AATATATAC
1 AATATATAC
213766 AAT
1 AAT
213769 TGTCATAGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.57, C:0.10, G:0.00, T:0.33
Consensus pattern (9 bp):
AATATATAC
Found at i:220289 original size:2 final size:2
Alignment explanation
Indices: 220284--220347 Score: 121
Period size: 2 Copynumber: 32.5 Consensus size: 2
220274 TGTGTCACAA
220284 TC TC TC TC TC TC TC TC TC -C TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
220325 TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC T
220348 GACGGAGGAG
Statistics
Matches: 61, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 60 0.98
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:227562 original size:22 final size:22
Alignment explanation
Indices: 227546--227619 Score: 139
Period size: 22 Copynumber: 3.4 Consensus size: 22
227536 TACTAGCATA
227546 GCTGATATATAAAACTAATATT
1 GCTGATATATAAAACTAATATT
227568 GCTGATATATAAAACTAATATT
1 GCTGATATATAAAACTAATATT
*
227590 GCTGATATATAAAACTAAAATT
1 GCTGATATATAAAACTAATATT
227612 GCTGATAT
1 GCTGATAT
227620 CGTGAGCTTT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 51 1.00
ACGTcount: A:0.45, C:0.09, G:0.11, T:0.35
Consensus pattern (22 bp):
GCTGATATATAAAACTAATATT
Found at i:227765 original size:38 final size:38
Alignment explanation
Indices: 227714--227792 Score: 133
Period size: 38 Copynumber: 2.1 Consensus size: 38
227704 GTGTAAGTCA
*
227714 TTCACAATGTAAAAATG-TTGACCTATATTTTACAATCG
1 TTCACAATGTAAAAATGCTT-ACCTATAGTTTACAATCG
227752 TTCACAATGTAAAAATGCTTACCTATAGTTTACAATCG
1 TTCACAATGTAAAAATGCTTACCTATAGTTTACAATCG
227790 TTC
1 TTC
227793 GTTTTTAGAG
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
38 37 0.95
39 2 0.05
ACGTcount: A:0.35, C:0.18, G:0.10, T:0.37
Consensus pattern (38 bp):
TTCACAATGTAAAAATGCTTACCTATAGTTTACAATCG
Found at i:234117 original size:2 final size:2
Alignment explanation
Indices: 234112--234153 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
234102 TGTGTTAATT
234112 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
234154 ATGACTAATC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:236938 original size:14 final size:14
Alignment explanation
Indices: 236919--236963 Score: 81
Period size: 14 Copynumber: 3.2 Consensus size: 14
236909 CAACGTCAAC
*
236919 GTTTACAGTAAACA
1 GTTTACAGTAGACA
236933 GTTTACAGTAGACA
1 GTTTACAGTAGACA
236947 GTTTACAGTAGACA
1 GTTTACAGTAGACA
236961 GTT
1 GTT
236964 GACAACAACT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.31
Consensus pattern (14 bp):
GTTTACAGTAGACA
Found at i:248801 original size:2 final size:2
Alignment explanation
Indices: 248794--248820 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
248784 AAAGTCGTAA
248794 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 C
248821 NTCGGCAAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:250076 original size:2 final size:2
Alignment explanation
Indices: 250069--250114 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
250059 AAAGTCGTAA
250069 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
250111 CT CT
1 CT CT
250115 TTTTAGGCAG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:270277 original size:36 final size:36
Alignment explanation
Indices: 270230--270300 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
270220 TTTGTCACCA
270230 TCTGTGGCTTCTCCTTCATGTCCCTTCCCGCTTTTT
1 TCTGTGGCTTCTCCTTCATGTCCCTTCCCGCTTTTT
* *
270266 TCTGTGGCTTCTCCTTCATGTTCCTTCCTGCTTTT
1 TCTGTGGCTTCTCCTTCATGTCCCTTCCCGCTTTT
270301 GTTTTTAGTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.03, C:0.34, G:0.14, T:0.49
Consensus pattern (36 bp):
TCTGTGGCTTCTCCTTCATGTCCCTTCCCGCTTTTT
Found at i:272301 original size:2 final size:2
Alignment explanation
Indices: 272283--272417 Score: 135
Period size: 2 Copynumber: 67.5 Consensus size: 2
272273 TCTATCATTA
* * * * * *
272283 TC TC TC TT TC TC CC TC TC TC TC TC TT TT TA TG TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* * * * * * *
272325 TC TC TT TA TG TC TC TC TC TC TC TC TC TT TT TA TG TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* *
272367 TC TC TC TC TC TC TC TT TC TC TC TC TC TC TC TC TT TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
272409 TC TC TC TC T
1 TC TC TC TC T
272418 TCATTTGAAA
Statistics
Matches: 113, Mismatches: 20, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 113 1.00
ACGTcount: A:0.02, C:0.40, G:0.02, T:0.56
Consensus pattern (2 bp):
TC
Found at i:272323 original size:24 final size:24
Alignment explanation
Indices: 272291--272417 Score: 154
Period size: 24 Copynumber: 5.5 Consensus size: 24
272281 TATCTCTCTT
*
272291 TCTCCCTCTCTCTCTCTTTTTATG
1 TCTCTCTCTCTCTCTCTTTTTATG
272315 --TCTCTCTCTCTCTC--TTTATG
1 TCTCTCTCTCTCTCTCTTTTTATG
272335 TCTCTCTCTCTCTCTCTTTTTATG
1 TCTCTCTCTCTCTCTCTTTTTATG
* * * *
272359 TCTCTCTCTCTCTCTCTCTCTCTT
1 TCTCTCTCTCTCTCTCTTTTTATG
* * *
272383 TCTCTCTCTCTCTCTCTTTCTCTC
1 TCTCTCTCTCTCTCTCTTTTTATG
272407 TCTCTCTCTCT
1 TCTCTCTCTCT
272418 TCATTTGAAA
Statistics
Matches: 92, Mismatches: 7, Indels: 8
0.86 0.07 0.07
Matches are distributed among these distances:
20 6 0.07
22 27 0.29
24 59 0.64
ACGTcount: A:0.02, C:0.40, G:0.02, T:0.55
Consensus pattern (24 bp):
TCTCTCTCTCTCTCTCTTTTTATG
Found at i:273930 original size:1 final size:1
Alignment explanation
Indices: 273924--273954 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
273914 CCAGTATGAT
273924 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
273955 TCCCGCCGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:274401 original size:4 final size:4
Alignment explanation
Indices: 274392--274479 Score: 131
Period size: 4 Copynumber: 22.0 Consensus size: 4
274382 AAATGTCAGC
* *
274392 CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTGT CTGT
1 CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT
* * *
274440 CTGT CTGT CTCT GTCT CTCT CTCT CTCT CTCT CTCT CTCT
1 CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT
274480 TAAACATCAT
Statistics
Matches: 80, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 80 1.00
ACGTcount: A:0.00, C:0.44, G:0.06, T:0.50
Consensus pattern (4 bp):
CTCT
Found at i:274401 original size:6 final size:6
Alignment explanation
Indices: 274392--274479 Score: 131
Period size: 6 Copynumber: 14.7 Consensus size: 6
274382 AAATGTCAGC
* *
274392 CTCTCT CTCTCT CTCTCT CTCTCT CTCTCT CTCTCT CTCTCT GTCTGT
1 CTCTCT CTCTCT CTCTCT CTCTCT CTCTCT CTCTCT CTCTCT CTCTCT
* * *
274440 CTGTCT GTCTCT GTCTCT CTCTCT CTCTCT CTCTCT CTCT
1 CTCTCT CTCTCT CTCTCT CTCTCT CTCTCT CTCTCT CTCT
274480 TAAACATCAT
Statistics
Matches: 74, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 74 1.00
ACGTcount: A:0.00, C:0.44, G:0.06, T:0.50
Consensus pattern (6 bp):
CTCTCT
Found at i:278099 original size:63 final size:63
Alignment explanation
Indices: 277999--278120 Score: 217
Period size: 63 Copynumber: 1.9 Consensus size: 63
277989 GGGACGCAAC
277999 ACTCCTTCCAACGACACTGAGAATAAAACTGGGGATACAGGGTCGACAACTGTTCCCCAGTCG
1 ACTCCTTCCAACGACACTGAGAATAAAACTGGGGATACAGGGTCGACAACTGTTCCCCAGTCG
* * *
278062 ACTCCTTCCAACGATACTGAGAATAAAACTTGTGATACAGGGTCGACAACTGTTCCCCA
1 ACTCCTTCCAACGACACTGAGAATAAAACTGGGGATACAGGGTCGACAACTGTTCCCCA
278121 ACCAACATGT
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
63 56 1.00
ACGTcount: A:0.31, C:0.28, G:0.20, T:0.21
Consensus pattern (63 bp):
ACTCCTTCCAACGACACTGAGAATAAAACTGGGGATACAGGGTCGACAACTGTTCCCCAGTCG
Found at i:286455 original size:4 final size:4
Alignment explanation
Indices: 286448--286497 Score: 73
Period size: 4 Copynumber: 12.5 Consensus size: 4
286438 CGTCAGTTCT
* * *
286448 TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCCG TCCG TCCG TCTG TCTG
1 TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG
286496 TC
1 TC
286498 CTACTTCAGT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 44 1.00
ACGTcount: A:0.00, C:0.32, G:0.24, T:0.44
Consensus pattern (4 bp):
TCTG
Found at i:303149 original size:57 final size:57
Alignment explanation
Indices: 303088--303250 Score: 263
Period size: 57 Copynumber: 2.9 Consensus size: 57
303078 TCTGGAACTG
*
303088 ACTACTACTCACCATCATAGAACCTCAGAGAGTCGTACATACAGTACATTAGTACTA
1 ACTACTACTCACCATCATAGAACCTCAGAGAGTCGTACACACAGTACATTAGTACTA
* * **
303145 ACTACTACTCACCATCATAGAACCCCAGAGCGTTATACACACAGTACATTAGTACTA
1 ACTACTACTCACCATCATAGAACCTCAGAGAGTCGTACACACAGTACATTAGTACTA
* *
303202 ACTACTACTCAACGTCATAGAACCTCAGAGAGTCGTACACACAGTACAT
1 ACTACTACTCACCATCATAGAACCTCAGAGAGTCGTACACACAGTACAT
303251 ATACACTGTA
Statistics
Matches: 95, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
57 95 1.00
ACGTcount: A:0.37, C:0.28, G:0.12, T:0.23
Consensus pattern (57 bp):
ACTACTACTCACCATCATAGAACCTCAGAGAGTCGTACACACAGTACATTAGTACTA
Found at i:303595 original size:71 final size:65
Alignment explanation
Indices: 303479--303661 Score: 226
Period size: 71 Copynumber: 2.8 Consensus size: 65
303469 GAAACCACAG
* *
303479 TAACTACTAAACTTACCATCATAGAACCTCAGATAGTCGTACACACAGTACATATACATGTATAT
1 TAACTACTATACTTACCATCATAGAACCTCAGAGAGTCGTACACACAGTACATATAC----AT-T
303544 AAGTAA
61 -AGTAA
* * *
303550 TAACTACTATACTTACCATCATAGAACCTCAGGGAGTCGTACACACAGTACATGTACATTAGTAC
1 TAACTACTATACTTACCATCATAGAACCTCAGAGAGTCGTACACACAGTACATATACATTAGTAA
* * *
303615 TCACTAC--TACTCACCGTCATAGAACCTCAGAGAGTCGTACACACAGT
1 TAACTACTATACTTACCATCATAGAACCTCAGAGAGTCGTACACACAGT
303662 CCGCCCCCTC
Statistics
Matches: 103, Mismatches: 9, Indels: 8
0.86 0.08 0.07
Matches are distributed among these distances:
63 37 0.36
65 10 0.10
66 1 0.01
67 2 0.02
71 53 0.51
ACGTcount: A:0.37, C:0.25, G:0.13, T:0.25
Consensus pattern (65 bp):
TAACTACTATACTTACCATCATAGAACCTCAGAGAGTCGTACACACAGTACATATACATTAGTAA
Found at i:303793 original size:19 final size:20
Alignment explanation
Indices: 303769--303813 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
303759 ATCACAAATN
303769 TTTGCTTAATGCTTG-TTGC
1 TTTGCTTAATGCTTGCTTGC
**
303788 TTTGCTTTTTGCTTGCTTGC
1 TTTGCTTAATGCTTGCTTGC
303808 -TTGCTT
1 TTTGCTT
303814 TTGTTGGGGG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 19 0.83
20 4 0.17
ACGTcount: A:0.04, C:0.18, G:0.20, T:0.58
Consensus pattern (20 bp):
TTTGCTTAATGCTTGCTTGC
Found at i:303814 original size:19 final size:19
Alignment explanation
Indices: 303778--303815 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
303768 NTTTGCTTAA
303778 TGCTTGTTGCTTTGCTTTT
1 TGCTTGTTGCTTTGCTTTT
303797 TGCTTGCTTGC-TTGCTTTT
1 TGCTTG-TTGCTTTGCTTTT
303816 GTTGGGGGCG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.00, C:0.18, G:0.21, T:0.61
Consensus pattern (19 bp):
TGCTTGTTGCTTTGCTTTT
Found at i:305801 original size:57 final size:57
Alignment explanation
Indices: 305711--306106 Score: 441
Period size: 57 Copynumber: 7.0 Consensus size: 57
305701 TAAAGGAGAA
* *
305711 AGTATATAAGTACCAACTACTACTTACCATCATAGAAACTCAGAGAGTCGTACACAC
1 AGTATATTAGTACTAACTACTACTTACCATCATAGAAACTCAGAGAGTCGTACACAC
* * * * *
305768 AGTATATAAGTACCAACTACTACTTACCCTCATAGAATCTCCGAGAGTCGTACACAC
1 AGTATATTAGTACTAACTACTACTTACCATCATAGAAACTCAGAGAGTCGTACACAC
* * * * *
305825 AGTACATTTGTACTAACTACTACTCACCGTCATAGAACCTCAGAGAGTCGTACACAC
1 AGTATATTAGTACTAACTACTACTTACCATCATAGAAACTCAGAGAGTCGTACACAC
* * * *
305882 AGTATATTAGTACTAGCTACTACTTACTATCATAGAACCCCAGAGAGTCGTACACAC
1 AGTATATTAGTACTAACTACTACTTACCATCATAGAAACTCAGAGAGTCGTACACAC
* * * * *
305939 AGTACATTAGTACTAACTACTACTCACCATCATAG-GAC-C------TTGAACACAC
1 AGTATATTAGTACTAACTACTACTTACCATCATAGAAACTCAGAGAGTCGTACACAC
* *
305988 AGTATATTAGTACTAGCTACTACTTACCATCATAGAACCTCAGAGAGTCGTACATGCACAC
1 AGTATATTAGTACTAACTACTACTTACCATCATAGAAACTCAGAGAGTCGT--A--CACAC
* * * *
306049 AGTACATTAGTAATAACTACTACTCACCATCATA-AAACCTCAGGGAGTCGTACACAC
1 AGTATATTAGTACTAACTACTACTTACCATCATAGAAA-CTCAGAGAGTCGTACACAC
306106 A
1 A
306107 ATCCGCCCCC
Statistics
Matches: 287, Mismatches: 39, Indels: 26
0.82 0.11 0.07
Matches are distributed among these distances:
49 40 0.14
50 1 0.00
51 1 0.00
55 1 0.00
56 1 0.00
57 192 0.67
59 2 0.01
60 2 0.01
61 47 0.16
ACGTcount: A:0.36, C:0.26, G:0.13, T:0.24
Consensus pattern (57 bp):
AGTATATTAGTACTAACTACTACTTACCATCATAGAAACTCAGAGAGTCGTACACAC
Found at i:305928 original size:114 final size:114
Alignment explanation
Indices: 305719--306106 Score: 515
Period size: 114 Copynumber: 3.4 Consensus size: 114
305709 AAAGTATATA
* * * * * *
305719 AGTACCAACTACTACTTACCATCATAGAAACTCAGAGAGTCGTACACACAGTATATAAGTACCAA
1 AGTACTAACTACTACTCACCATCATAGAACCTCAGAGAGTCGTACACACAGTATATTAGTACTAG
* *
305784 CTACTACTTACCCTCATAGAATCTCC-GAGAGTCGTACACACAGTACATT
66 CTACTACTTACCATCATAGAA-CCCCAGAGAGTCGTACACACAGTACATT
* *
305833 TGTACTAACTACTACTCACCGTCATAGAACCTCAGAGAGTCGTACACACAGTATATTAGTACTAG
1 AGTACTAACTACTACTCACCATCATAGAACCTCAGAGAGTCGTACACACAGTATATTAGTACTAG
*
305898 CTACTACTTACTATCATAGAACCCCAGAGAGTCGTACACACAGTACATT
66 CTACTACTTACCATCATAGAACCCCAGAGAGTCGTACACACAGTACATT
* *
305947 AGTACTAACTACTACTCACCATCATAGGACCT-------T-GAACACACAGTATATTAGTACTAG
1 AGTACTAACTACTACTCACCATCATAGAACCTCAGAGAGTCGTACACACAGTATATTAGTACTAG
*
306004 CTACTACTTACCATCATAGAACCTCAGAGAGTCGTACATGCACACAGTACATT
66 CTACTACTTACCATCATAGAACCCCAGAGAGTCGT--A--CACACAGTACATT
* * *
306057 AGTAATAACTACTACTCACCATCATAAAACCTCAGGGAGTCGTACACACA
1 AGTACTAACTACTACTCACCATCATAGAACCTCAGAGAGTCGTACACACA
306107 ATCCGCCCCC
Statistics
Matches: 240, Mismatches: 21, Indels: 22
0.85 0.07 0.08
Matches are distributed among these distances:
106 56 0.23
107 1 0.00
108 1 0.00
110 42 0.17
113 3 0.01
114 128 0.53
117 1 0.00
118 8 0.03
ACGTcount: A:0.36, C:0.27, G:0.13, T:0.24
Consensus pattern (114 bp):
AGTACTAACTACTACTCACCATCATAGAACCTCAGAGAGTCGTACACACAGTATATTAGTACTAG
CTACTACTTACCATCATAGAACCCCAGAGAGTCGTACACACAGTACATT
Found at i:305986 original size:49 final size:49
Alignment explanation
Indices: 305933--306027 Score: 154
Period size: 49 Copynumber: 1.9 Consensus size: 49
305923 AGAGAGTCGT
*
305933 ACACACAGTACATTAGTACTAACTACTACTCACCATCATAGGACCTTGA
1 ACACACAGTACATTAGTACTAACTACTACTCACCATCATAGAACCTTGA
* * *
305982 ACACACAGTATATTAGTACTAGCTACTACTTACCATCATAGAACCT
1 ACACACAGTACATTAGTACTAACTACTACTCACCATCATAGAACCT
306028 CAGAGAGTCG
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
49 42 1.00
ACGTcount: A:0.37, C:0.27, G:0.09, T:0.26
Consensus pattern (49 bp):
ACACACAGTACATTAGTACTAACTACTACTCACCATCATAGAACCTTGA
Found at i:305992 original size:106 final size:108
Alignment explanation
Indices: 305876--306082 Score: 355
Period size: 106 Copynumber: 1.9 Consensus size: 108
305866 AGAGAGTCGT
*
305876 ACACACAGTATATTAGTACTAGCTACTACTTACTATCATAGAACCCCAGAGAGTCGT-A-CACAC
1 ACACACAGTATATTAGTACTAGCTACTACTTACCATCATAGAACCCCAGAGAGTCGTAAGCACAC
*
305939 AGTACATTAGTACTAACTACTACTCACCATCATAGGACCTTGA
66 AGTACATTAGTAATAACTACTACTCACCATCATAGGACCTTGA
*
305982 ACACACAGTATATTAGTACTAGCTACTACTTACCATCATAGAACCTCAGAGAGTCGTACATGCAC
1 ACACACAGTATATTAGTACTAGCTACTACTTACCATCATAGAACCCCAGAGAGTCGTA-A-GCAC
306047 ACAGTACATTAGTAATAACTACTACTCACCATCATA
64 ACAGTACATTAGTAATAACTACTACTCACCATCATA
306083 AAACCTCAGG
Statistics
Matches: 94, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
106 55 0.59
108 1 0.01
110 38 0.40
ACGTcount: A:0.37, C:0.26, G:0.12, T:0.26
Consensus pattern (108 bp):
ACACACAGTATATTAGTACTAGCTACTACTTACCATCATAGAACCCCAGAGAGTCGTAAGCACAC
AGTACATTAGTAATAACTACTACTCACCATCATAGGACCTTGA
Found at i:306059 original size:61 final size:61
Alignment explanation
Indices: 305983--306102 Score: 186
Period size: 61 Copynumber: 2.0 Consensus size: 61
305973 GGACCTTGAA
* * * * *
305983 CACACAGTATATTAGTACTAGCTACTACTTACCATCATAGAACCTCAGAGAGTCGTACATG
1 CACACAGTACATTAGTAATAACTACTACTCACCATCATAAAACCTCAGAGAGTCGTACATG
*
306044 CACACAGTACATTAGTAATAACTACTACTCACCATCATAAAACCTCAGGGAGTCGTACA
1 CACACAGTACATTAGTAATAACTACTACTCACCATCATAAAACCTCAGAGAGTCGTACA
306103 CACAATCCGC
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
61 53 1.00
ACGTcount: A:0.37, C:0.26, G:0.13, T:0.24
Consensus pattern (61 bp):
CACACAGTACATTAGTAATAACTACTACTCACCATCATAAAACCTCAGAGAGTCGTACATG
Found at i:312297 original size:2 final size:2
Alignment explanation
Indices: 312290--312343 Score: 101
Period size: 2 Copynumber: 27.5 Consensus size: 2
312280 TACATGTAAG
312290 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC -C TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
312331 TC TC TC TC TC TC T
1 TC TC TC TC TC TC T
312344 GTTGCCTATA
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 50 0.98
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:315782 original size:14 final size:14
Alignment explanation
Indices: 315765--315793 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
315755 CTGCCCTAGA
315765 TTTTTAAATGAATT
1 TTTTTAAATGAATT
315779 TTTTTAAATGAATT
1 TTTTTAAATGAATT
315793 T
1 T
315794 CTACTGATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (14 bp):
TTTTTAAATGAATT
Found at i:324285 original size:26 final size:26
Alignment explanation
Indices: 324249--324412 Score: 114
Period size: 28 Copynumber: 5.8 Consensus size: 26
324239 ATATGTGTTG
324249 TATTCTGTAAATATGACGGACATTTA
1 TATTCTGTAAATATGACGGACATTTA
* *
324275 TATTCTGTAAATATAACGGACAAACATGTA
1 TATTCTGTAAATATGACGG----ACATTTA
*
324305 GATGTCATTTGTAAATATGACGGACATTTA
1 TAT-TC---TGTAAATATGACGGACATTTA
* ** *
324335 TGTTCTGTAAATATGACGGACGTAGATG
1 TATTCTGTAAATATGACGGAC--ATTTA
*
324363 TCATT-TGTAAATATGACGGACATTGATG
1 T-ATTCTGTAAATATGACGGACATT--TA
* *
324391 TGTTCTGTAAATATGATGGACA
1 TATTCTGTAAATATGACGGACA
324413 AAATTAGAGT
Statistics
Matches: 109, Mismatches: 15, Indels: 26
0.73 0.10 0.17
Matches are distributed among these distances:
26 35 0.32
27 2 0.02
28 38 0.35
29 4 0.04
30 15 0.14
31 2 0.02
34 13 0.12
ACGTcount: A:0.34, C:0.11, G:0.20, T:0.35
Consensus pattern (26 bp):
TATTCTGTAAATATGACGGACATTTA
Found at i:324347 original size:60 final size:58
Alignment explanation
Indices: 324254--324414 Score: 222
Period size: 60 Copynumber: 2.8 Consensus size: 58
324244 TGTTGTATTC
* *
324254 TGTAAATATGACGGACATTTATATTCTGTAAATATAACGGACAAACATGTAGATGTCATT
1 TGTAAATATGACGGACATTTATGTTCTGTAAATATGACGGACAAAC--GTAGATGTCATT
324314 TGTAAATATGACGGACATTTATGTTCTGTAAATATGACGG----ACGTAGATGTCATT
1 TGTAAATATGACGGACATTTATGTTCTGTAAATATGACGGACAAACGTAGATGTCATT
* *
324368 TGTAAATATGACGGACATTGATGTGTTCTGTAAATATGATGGACAAA
1 TGTAAATATGACGGACATT--TATGTTCTGTAAATATGACGGACAAA
324415 ATTAGAGTAT
Statistics
Matches: 91, Mismatches: 4, Indels: 12
0.85 0.04 0.11
Matches are distributed among these distances:
54 31 0.34
56 21 0.23
60 39 0.43
ACGTcount: A:0.35, C:0.11, G:0.20, T:0.34
Consensus pattern (58 bp):
TGTAAATATGACGGACATTTATGTTCTGTAAATATGACGGACAAACGTAGATGTCATT
Found at i:324380 original size:28 final size:27
Alignment explanation
Indices: 324303--324412 Score: 123
Period size: 28 Copynumber: 4.0 Consensus size: 27
324293 GACAAACATG
324303 TAGATGTCATTTGTAAATATGACGGACA
1 TAGATGT-ATTTGTAAATATGACGGACA
** * *
324331 TTTATGT-TCTGTAAATATGACGGACG
1 TAGATGTATTTGTAAATATGACGGACA
324357 TAGATGTCATTTGTAAATATGACGGACA
1 TAGATGT-ATTTGTAAATATGACGGACA
* * *
324385 TTGATGTGTTCTGTAAATATGATGGACA
1 TAGATGTATT-TGTAAATATGACGGACA
324413 AAATTAGAGT
Statistics
Matches: 68, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
26 22 0.32
27 2 0.03
28 44 0.65
ACGTcount: A:0.32, C:0.10, G:0.23, T:0.35
Consensus pattern (27 bp):
TAGATGTATTTGTAAATATGACGGACA
Found at i:338080 original size:81 final size:81
Alignment explanation
Indices: 337945--338155 Score: 386
Period size: 81 Copynumber: 2.6 Consensus size: 81
337935 CAAAGATTTG
* *
337945 TAAGTTTAGGTCGCCCTTTGAAAAACAGGAAGAATATCTTGACAAATAGATCTATGTTTATGTAT
1 TAAGTTTAGGACGCCCTTTGAAAAACAGGAAGAATATCTTGACAAATAGATCTATGTTCATGTAT
338010 TATAGAATAAGAAAAC
66 TATAGAATAAGAAAAC
338026 TAAGTTTAGGACGCCCTTTGAAAAACAGGAAGAATATCTTGACAAATAGATCTATGTTCATGTAT
1 TAAGTTTAGGACGCCCTTTGAAAAACAGGAAGAATATCTTGACAAATAGATCTATGTTCATGTAT
*
338091 TATAGTATAAGAAAAC
66 TATAGAATAAGAAAAC
*
338107 TAAGTTTAGGACGCCCTTTGAAAAACAGGAACAATATCTTGACAAATAG
1 TAAGTTTAGGACGCCCTTTGAAAAACAGGAAGAATATCTTGACAAATAG
338156 GTTTAGGTAT
Statistics
Matches: 126, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
81 126 1.00
ACGTcount: A:0.41, C:0.13, G:0.18, T:0.29
Consensus pattern (81 bp):
TAAGTTTAGGACGCCCTTTGAAAAACAGGAAGAATATCTTGACAAATAGATCTATGTTCATGTAT
TATAGAATAAGAAAAC
Found at i:345954 original size:19 final size:20
Alignment explanation
Indices: 345918--345955 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
345908 CCGATGAGCG
**
345918 AATTGTTTACAATCTTTGAC
1 AATTGTTTACAAAATTTGAC
345938 AATT-TTTACAAAATTTGA
1 AATTGTTTACAAAATTTGA
345956 ACCGAGTCCT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.37, C:0.11, G:0.08, T:0.45
Consensus pattern (20 bp):
AATTGTTTACAAAATTTGAC
Found at i:350495 original size:2 final size:2
Alignment explanation
Indices: 350488--350562 Score: 150
Period size: 2 Copynumber: 37.5 Consensus size: 2
350478 TTCTTGATAT
350488 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
350530 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
350563 CGCGTTTGTT
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 73 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:351781 original size:23 final size:22
Alignment explanation
Indices: 351755--351874 Score: 96
Period size: 23 Copynumber: 5.2 Consensus size: 22
351745 TTCTTGATTA
*
351755 TTATTATTATGATATTTATTAAT
1 TTATTATTAT-TTATTTATTAAT
* * *
351778 TTATTCTTATTTTATCTATTTATT
1 TTATTATTA-TTTATTTA-TTAAT
* * *
351802 TTTTTATTATCTATTTATTTAT
1 TTATTATTATTTATTTATTAAT
* *
351824 TTCATTTTTTTTTATTTATTAAT
1 TT-ATTATTATTTATTTATTAAT
* *
351847 TTTTTTTTATTTATTTATTTAAT
1 TTATTATTATTTATTTA-TTAAT
351870 TTATT
1 TTATT
351875 TGTTGTTTTT
Statistics
Matches: 75, Mismatches: 18, Indels: 8
0.74 0.18 0.08
Matches are distributed among these distances:
22 18 0.24
23 45 0.60
24 12 0.16
ACGTcount: A:0.24, C:0.03, G:0.01, T:0.72
Consensus pattern (22 bp):
TTATTATTATTTATTTATTAAT
Found at i:351798 original size:19 final size:19
Alignment explanation
Indices: 351776--351821 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 19
351766 ATATTTATTA
351776 ATTTATTCTTATT-TTATCT
1 ATTTATT-TTATTATTATCT
*
351795 ATTTATTTTTTTATTATCT
1 ATTTATTTTATTATTATCT
351814 ATTTATTT
1 ATTTATTT
351822 ATTTCATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 4 0.16
19 21 0.84
ACGTcount: A:0.22, C:0.07, G:0.00, T:0.72
Consensus pattern (19 bp):
ATTTATTTTATTATTATCT
Found at i:351807 original size:27 final size:27
Alignment explanation
Indices: 351788--351843 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
351778 TTATTCTTAT
351788 TTTATCTATTTATTTTTTTATTATCTA
1 TTTATCTATTTATTTTTTTATTATCTA
* *
351815 TTTATTTATTTCATTTTTTT-TTATTTA
1 TTTATCTATTT-ATTTTTTTATTATCTA
351842 TT
1 TT
351844 AATTTTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
27 18 0.69
28 8 0.31
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.75
Consensus pattern (27 bp):
TTTATCTATTTATTTTTTTATTATCTA
Found at i:351837 original size:19 final size:18
Alignment explanation
Indices: 351796--351892 Score: 90
Period size: 18 Copynumber: 5.3 Consensus size: 18
351786 ATTTTATCTA
* * *
351796 TTTATTTTTTTATTATCTA
1 TTTATTTATTTATT-TTTT
351815 TTTATTTATTTCATTTTTT
1 TTTATTTATTT-ATTTTTT
*
351834 TTTATTTATTAATTTTTT
1 TTTATTTATTTATTTTTT
**
351852 TTTATTTATTTA-TTTAA
1 TTTATTTATTTATTTTTT
*
351869 TTTATTTGTTGT-TTTTTT
1 TTTATTTATT-TATTTTTT
351887 TTTATT
1 TTTATT
351893 GTTTTTTTTG
Statistics
Matches: 65, Mismatches: 10, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
17 12 0.18
18 28 0.43
19 22 0.34
20 3 0.05
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.77
Consensus pattern (18 bp):
TTTATTTATTTATTTTTT
Found at i:351848 original size:27 final size:26
Alignment explanation
Indices: 351794--351892 Score: 91
Period size: 27 Copynumber: 3.8 Consensus size: 26
351784 TTATTTTATC
* *
351794 TATTTATTTTTTTATTATCTATTTATT
1 TATTTATTTTTTT-TTATTTATTAATT
351821 TATTTCATTTTTTTTTATTTATTAA--
1 TATTT-ATTTTTTTTTATTTATTAATT
*
351846 T-TTT-TTTTTATTTATTTATTTAATT
1 TATTTATTTTTTTTTATTTA-TTAATT
*
351871 TATTTGTTGTTTTTTT-TTTATT
1 TATTTATT-TTTTTTTATTTATT
351893 GTTTTTTTTG
Statistics
Matches: 61, Mismatches: 4, Indels: 15
0.76 0.05 0.19
Matches are distributed among these distances:
22 13 0.21
23 4 0.07
24 3 0.05
25 2 0.03
26 5 0.08
27 20 0.33
28 14 0.23
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.77
Consensus pattern (26 bp):
TATTTATTTTTTTTTATTTATTAATT
Found at i:351871 original size:5 final size:4
Alignment explanation
Indices: 351767--351875 Score: 93
Period size: 4 Copynumber: 27.2 Consensus size: 4
351757 ATTATTATGA
* * * *
351767 TATT TATT AATT TATTCT TATTT TATC TATT TATT TTTT TA-T TATC TATT
1 TATT TATT TATT TA-T-T TA-TT TATT TATT TATT TATT TATT TATT TATT
*
351817 TATT TATT TCATT T-TT T-TT TATT TATT AATT T-TT T-TT TATT TATT
1 TATT TATT T-ATT TATT TATT TATT TATT TATT TATT TATT TATT TATT
351862 TATT TAATT TATT T
1 TATT T-ATT TATT T
351876 GTTGTTTTTT
Statistics
Matches: 88, Mismatches: 10, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
3 15 0.17
4 56 0.64
5 12 0.14
6 5 0.06
ACGTcount: A:0.23, C:0.04, G:0.00, T:0.73
Consensus pattern (4 bp):
TATT
Found at i:351884 original size:49 final size:47
Alignment explanation
Indices: 351767--351901 Score: 132
Period size: 49 Copynumber: 2.9 Consensus size: 47
351757 ATTATTATGA
* * * *
351767 TATTTATTAATTT-ATTCTTATTTTATCTATT-TATTTTTTTATTATC
1 TATTTATTTATTTCATTGTT-TTTTATTTATTATTTTTTTTTATTATC
* *
351813 TATTTATTTATTTCATTTTTTTTTATTTATTAATTTTTTTTTATTTATT
1 TATTTATTTATTTCATTGTTTTTTATTTATT-ATTTTTTTTTA-TTATC
* * *
351862 TATTTAATTTATTT-GTTGTTTTTTTTTTATTGTTTTTTTT
1 TATTT-ATTTATTTCATTGTTTTTTATTTATTATTTTTTTT
351902 GGCTGCTCAC
Statistics
Matches: 75, Mismatches: 9, Indels: 8
0.82 0.10 0.09
Matches are distributed among these distances:
46 22 0.29
47 5 0.07
48 17 0.23
49 23 0.31
50 8 0.11
ACGTcount: A:0.19, C:0.03, G:0.02, T:0.76
Consensus pattern (47 bp):
TATTTATTTATTTCATTGTTTTTTATTTATTATTTTTTTTTATTATC
Found at i:351892 original size:18 final size:17
Alignment explanation
Indices: 351815--351901 Score: 77
Period size: 18 Copynumber: 4.9 Consensus size: 17
351805 TTATTATCTA
351815 TTTATTTATTTCATTTTTT
1 TTTATTTATTT--TTTTTT
*
351834 TTTATTTATTAATTTTTT
1 TTTATTTATT-TTTTTTT
* **
351852 TTTATTTATTTATTTAA
1 TTTATTTATTTTTTTTT
*
351869 TTTATTTGTTGTTTTTTT
1 TTTATTTATT-TTTTTTT
351887 TTTATTGT-TTTTTTT
1 TTTATT-TATTTTTTT
351902 GGCTGCTCAC
Statistics
Matches: 56, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
17 17 0.30
18 28 0.50
19 11 0.20
ACGTcount: A:0.16, C:0.01, G:0.03, T:0.79
Consensus pattern (17 bp):
TTTATTTATTTTTTTTT
Found at i:352623 original size:2 final size:2
Alignment explanation
Indices: 352616--352652 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
352606 TCATAAAATG
352616 CT CT CT 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 CT CT CT C
352653 CATGGTGACA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:365398 original size:2 final size:2
Alignment explanation
Indices: 365391--365429 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
365381 AACTCACTCA
365391 CT CT CT CT 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 CT CT CT CT C
365430 CTGCAGGTGG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:393712 original size:5 final size:5
Alignment explanation
Indices: 393702--393760 Score: 50
Period size: 5 Copynumber: 11.8 Consensus size: 5
393692 AGCGAGTATC
* * *
393702 CAAAA CAAAA CAACA CAACAA C-AAA C-AAA CGAAA CAAAA CAAACA AAAAA
1 CAAAA CAAAA CAAAA CAA-AA CAAAA CAAAA CAAAA CAAAA CAAA-A CAAAA
*
393752 TAAAA CAAA
1 CAAAA CAAA
393761 GAAAATCTCA
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
4 7 0.16
5 32 0.71
6 6 0.13
ACGTcount: A:0.75, C:0.22, G:0.02, T:0.02
Consensus pattern (5 bp):
CAAAA
Found at i:400701 original size:19 final size:19
Alignment explanation
Indices: 400654--400707 Score: 81
Period size: 19 Copynumber: 2.8 Consensus size: 19
400644 GGACCAATCT
400654 CCCAAATGGGATATAATAG
1 CCCAAATGGGATATAATAG
***
400673 CCCGTTTGGGATATAATAG
1 CCCAAATGGGATATAATAG
400692 CCCAAATGGGATATAA
1 CCCAAATGGGATATAA
400708 ATTTAAAGTG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.37, C:0.17, G:0.22, T:0.24
Consensus pattern (19 bp):
CCCAAATGGGATATAATAG
Found at i:400750 original size:16 final size:15
Alignment explanation
Indices: 400727--400755 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
400717 GCAAATAATA
400727 AAAATTTTTGATTTT
1 AAAATTTTTGATTTT
400742 AAAATTTTTGATTT
1 AAAATTTTTGATTT
400756 GAATCCGCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (15 bp):
AAAATTTTTGATTTT
Found at i:406417 original size:8 final size:8
Alignment explanation
Indices: 406404--406429 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
406394 TGATAATAAA
406404 AACAAAAT
1 AACAAAAT
406412 AACAAAAT
1 AACAAAAT
406420 AACAAAAT
1 AACAAAAT
406428 AA
1 AA
406430 TAACAGTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.77, C:0.12, G:0.00, T:0.12
Consensus pattern (8 bp):
AACAAAAT
Found at i:417739 original size:4 final size:4
Alignment explanation
Indices: 417667--417781 Score: 131
Period size: 4 Copynumber: 28.8 Consensus size: 4
417657 CCAAGTGCTC
* * * * * *
417667 CTCT CTCT GTCT GTCT GTCT CTCT CTGT CTCT CTCT CTCT GTCT GTCT
1 CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT
* * * * *
417715 GTCT GTCT GTCT GTCT GTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT
1 CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT
417763 CTCT CTCT CTCT CTCT CTC
1 CTCT CTCT CTCT CTCT CTC
417782 CAATCTTACA
Statistics
Matches: 105, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 105 1.00
ACGTcount: A:0.00, C:0.41, G:0.10, T:0.50
Consensus pattern (4 bp):
CTCT
Found at i:417985 original size:4 final size:4
Alignment explanation
Indices: 417976--418043 Score: 118
Period size: 4 Copynumber: 17.0 Consensus size: 4
417966 AGTAACACAA
*
417976 GAAT GAAT GAAT AAAT GAAT GAAT GAAT GAAT GAAT GAAT GAAT GAAT
1 GAAT GAAT GAAT GAAT GAAT GAAT GAAT GAAT GAAT GAAT GAAT GAAT
*
418024 GAAT GAAT GAAT GGAT GAAT
1 GAAT GAAT GAAT GAAT GAAT
418044 TCACTTATTT
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.25, T:0.25
Consensus pattern (4 bp):
GAAT
Found at i:420158 original size:18 final size:18
Alignment explanation
Indices: 420135--420169 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
420125 CGGTGCCAAA
420135 TACTCCGTTTTCGGAGTT
1 TACTCCGTTTTCGGAGTT
*
420153 TACTCCTTTTTCGGAGT
1 TACTCCGTTTTCGGAGT
420170 CCGCCCAGAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.11, C:0.23, G:0.20, T:0.46
Consensus pattern (18 bp):
TACTCCGTTTTCGGAGTT
Found at i:423345 original size:1 final size:1
Alignment explanation
Indices: 423339--423368 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
423329 AAAGCTCATT
423339 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
423369 CCCCCCCCCC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:423472 original size:1 final size:1
Alignment explanation
Indices: 423466--423513 Score: 78
Period size: 1 Copynumber: 48.0 Consensus size: 1
423456 TGAAAAGGGG
**
423466 AAAAAAAAAAAATCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
423514 GCCGACCTAC
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 44 1.00
ACGTcount: A:0.96, C:0.02, G:0.00, T:0.02
Consensus pattern (1 bp):
A
Found at i:427704 original size:7 final size:7
Alignment explanation
Indices: 427690--427734 Score: 72
Period size: 7 Copynumber: 6.4 Consensus size: 7
427680 CTTCGTCCGT
427690 CGTCGTG
1 CGTCGTG
*
427697 CGTTGTG
1 CGTCGTG
427704 CGTCGTG
1 CGTCGTG
427711 CGTCGTG
1 CGTCGTG
*
427718 CGCCGTG
1 CGTCGTG
427725 CGTCGTG
1 CGTCGTG
427732 CGT
1 CGT
427735 TAACAATTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 34 1.00
ACGTcount: A:0.00, C:0.29, G:0.42, T:0.29
Consensus pattern (7 bp):
CGTCGTG
Found at i:428522 original size:168 final size:168
Alignment explanation
Indices: 427939--429020 Score: 1562
Period size: 168 Copynumber: 6.5 Consensus size: 168
427929 CATGTGAGGA
* * * * * **
427939 AAAAACTGAATGCATGGTTATGATGTCCATGAGGCCCTCTACCAAAATTGTGAAATTTATGGTCC
1 AAAAACTAAATGCATGATTATGATGTCCATGAAGCCCTCTACCTAAATTGTGAAATTCATGACCC
* *
428004 CTGGGTCAGGGGTTCTGGCTCTAGGGTGGGGCCAATATGGCCATATAGTAAAAATGTATTAAAAT
66 CTGGGTCAGGGGTTCAGGCTCTAGGGTGGGGCCAATATGGCCAAATAGTAAAAATGTATT-AAAT
428069 CTTAGAAAATCTTCTTCTCTACTCCCATATATATTTGTT
130 CTTAGAAAATCTTCTTCTCTACTCCCATATATATTTGTT
* *
428108 AAAAACTAAATGCATGGTTATGATGTCCATGAAGCCCTCTACCTTAATTGTGAAATTCATGACCC
1 AAAAACTAAATGCATGATTATGATGTCCATGAAGCCCTCTACCTAAATTGTGAAATTCATGACCC
428173 CTGGGTCAGGGGTTCAGGCTCTAGGGTGGGGCCAATATGGCCAAATAGTAAAAATGTATTAAATC
66 CTGGGTCAGGGGTTCAGGCTCTAGGGTGGGGCCAATATGGCCAAATAGTAAAAATGTATTAAATC
428238 -T------TCTTC-TCTACTA-T--CATATATATTTGTT
131 TTAGAAAATCTTCTTCT-CTACTCCCATATATATTTGTT
* * * *
428266 AAAAGCTAAATGCATGATAATGATGTCCATGAAGCCCTCAACGTAAATTGTGAAATTCATGACCC
1 AAAAACTAAATGCATGATTATGATGTCCATGAAGCCCTCTACCTAAATTGTGAAATTCATGACCC
** * * * * *
428331 CTTTGTTAGGTGTTCATGCTCTAGGGTGGGGCCAATTTGGCCATATAGTAAAAATGTATTAAATC
66 CTGGGTCAGGGGTTCAGGCTCTAGGGTGGGGCCAATATGGCCAAATAGTAAAAATGTATTAAATC
*
428396 TTAGAAAATCTTCTTCTCTACTCTCATATATATTTGTT
131 TTAGAAAATCTTCTTCTCTACTCCCATATATATTTGTT
*
428434 AAATACTAAATGCATGATTATGATGTCCATGAAGCCCTCTACCTAAATTGTGAAATTCATGACCC
1 AAAAACTAAATGCATGATTATGATGTCCATGAAGCCCTCTACCTAAATTGTGAAATTCATGACCC
428499 CTGGGTCAGGGGTTCAGGCTCTAGGGTGGGGCCAATATGGCCAAATAGTAAAAATGTATTAAATC
66 CTGGGTCAGGGGTTCAGGCTCTAGGGTGGGGCCAATATGGCCAAATAGTAAAAATGTATTAAATC
*
428564 TTAGAAAATCTTCTTCTCTACTCTCATATATATTTGTT
131 TTAGAAAATCTTCTTCTCTACTCCCATATATATTTGTT
* *
428602 AAATACTAAATGCATGATTATGATGTCCATTAAGCCCTCTACCTAAATTGTGAAATTCATGACCC
1 AAAAACTAAATGCATGATTATGATGTCCATGAAGCCCTCTACCTAAATTGTGAAATTCATGACCC
428667 CTGGGTCAGGGGTTCAGGCTCTAGGGTGGGGCCAATATGGCCAAATAGTAAAAATGTATTAAATC
66 CTGGGTCAGGGGTTCAGGCTCTAGGGTGGGGCCAATATGGCCAAATAGTAAAAATGTATTAAATC
428732 TTAGAAAATCTTCTTCTCTACTCCCATATATATTTGTT
131 TTAGAAAATCTTCTTCTCTACTCCCATATATATTTGTT
* *
428770 AAAAACTAAATGCATGATTATGATGTCCATGAGGCTCTCTA-CTAAAATTGTGAAATTCATGACC
1 AAAAACTAAATGCATGATTATGATGTCCATGAAGCCCTCTACCT-AAATTGTGAAATTCATGACC
** * * * *
428834 CCTTTGTTAGGTGTTCATGCTCTAGGGTGGGGCCAATATGGCCATATAGTAAAAATG-ATTTAAA
65 CCTGGGTCAGGGGTTCAGGCTCTAGGGTGGGGCCAATATGGCCAAATAGTAAAAATGTA-TTAAA
* * * * ** **
428898 TCTTAAAAAATCTTCTTCTCTACTCCCACACATGTGGGCA
129 TCTTAGAAAATCTTCTTCTCTACTCCCATATATATTTGTT
* * * * * * * *
428938 AAAAACTGAATACATGGTTATGATATCCA-CAATCTCCTTTACCTAAATTGTGAAATTCATGGCC
1 AAAAACTAAATGCATGATTATGATGTCCATGAAGC-CCTCTACCTAAATTGTGAAATTCATGACC
429002 CCTGGGTCAGGGGTTCAGG
65 CCTGGGTCAGGGGTTCAGG
429021 ACATGGGGGG
Statistics
Matches: 828, Mismatches: 69, Indels: 33
0.89 0.07 0.04
Matches are distributed among these distances:
158 131 0.16
159 1 0.00
160 4 0.00
161 8 0.01
165 8 0.01
166 4 0.00
167 6 0.01
168 548 0.66
169 118 0.14
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.32
Consensus pattern (168 bp):
AAAAACTAAATGCATGATTATGATGTCCATGAAGCCCTCTACCTAAATTGTGAAATTCATGACCC
CTGGGTCAGGGGTTCAGGCTCTAGGGTGGGGCCAATATGGCCAAATAGTAAAAATGTATTAAATC
TTAGAAAATCTTCTTCTCTACTCCCATATATATTTGTT
Found at i:449735 original size:134 final size:134
Alignment explanation
Indices: 449486--450837 Score: 1410
Period size: 134 Copynumber: 10.1 Consensus size: 134
449476 NNNNNNNNNN
* * *
449486 TTTTTTGAAAATTTTAAATTTAATTAAATCGTGTTTAAATTACCTCAGACTAATTTTTAAACATA
1 TTTTTTAAAAATTTTAAATTTAATTAAATCGTGTTAAAATGACCTCAGACTAATTTTTAAACATA
*
449551 ATATCTAAGTTGCGCTTAGAATTCTGCGTCTAATGACATCTGTCTCGAATTAATTGAATGAATTT
66 ATATCTAAGTTGCGCTTAGAATTCTGCGTCTAATGACATCTTTCTCGAATTAATTGAATGAATTT
*
449616 TCAA
131 TAAA
* * * **
449620 TTTTTTGAAAATTTTAAATTTAATTAAATCAG-GTTAAAATGAGCTGAGACTAATTTAAAAACAT
1 TTTTTTAAAAATTTTAAATTTAATTAAATC-GTGTTAAAATGACCTCAGACTAATTTTTAAACAT
* * * * * * *
449684 AATATTTAAGTTACGCTTACAATTCTGCGTCTGATGACATCGTTT-TTGAATTGATCGAATGAAT
65 AATATCTAAGTTGCGCTTAGAATTCTGCGTCTAATGACATC-TTTCTCGAATTAATTGAATGAAT
*
449748 TTTAAT
129 TTTAAA
* * * * * * * *
449754 TTTTTTAAAAATTTTAAACTCATTTAAATCGCGTTAAAATGATCTCTGACTAATTTTAAAACATG
1 TTTTTTAAAAATTTTAAATTTAATTAAATCGTGTTAAAATGACCTCAGACTAATTTTTAAACATA
* * * * * *
449819 ATATCTAAGTTGTGCTTAGAATTCTGCGTCCATTGACATCCTTCTCGAATTGATTGGATGAATTT
66 ATATCTAAGTTGCGCTTAGAATTCTGCGTCTAATGACATCTTTCTCGAATTAATTGAATGAATTT
*
449884 AAAA
131 TAAA
** * * * * ** * * *
449888 AATTTCAAAAATTTTAATTTTATTTAAATCGCGTTAAAATGACCTCAGACTTGTTTTGAATCATG
1 TTTTTTAAAAATTTTAAATTTAATTAAATCGTGTTAAAATGACCTCAGACTAATTTTTAAACATA
* * * * * * ** * * **
449953 ATAACTTAGTTGTGCTTACAATTCTGCGTCTAAGGACATCTTTGTTAAATTGATTGGATGGTTTT
66 ATATCTAAGTTGCGCTTAGAATTCTGCGTCTAATGACATCTTTCTCGAATTAATTGAATGAATTT
450018 TAAA
131 TAAA
** * * * *
450022 TTTTTGGAAAATTTTAAATTTAATTAAATCGTGTTTAAATTACCTCAGATTAATTTTTAAACATC
1 TTTTTTAAAAATTTTAAATTTAATTAAATCGTGTTAAAATGACCTCAGACTAATTTTTAAACATA
450087 ATATCTAAGTTGCGCTTAGAATTCTGCGTCTAATGACATCTTTCTCGAATTAATTGAATGAATTT
66 ATATCTAAGTTGCGCTTAGAATTCTGCGTCTAATGACATCTTTCTCGAATTAATTGAATGAA-TT
*
450152 TTAAT
130 TTAAA
* * * * * **
450157 TTTTTTTAAAATTTTAGATTTAATTAAATCATGTTAAAATGAGCTGAGACTAATTTAAAAACATA
1 TTTTTTAAAAATTTTAAATTTAATTAAATCGTGTTAAAATGACCTCAGACTAATTTTTAAACATA
* * * * * * *
450222 ATATTTAAGTTACGCTTACAATTCTGCGTCTGATGACATCTTTTTCG-AGTAGATCGAATGAATT
66 ATATCTAAGTTGCGCTTAGAATTCTGCGTCTAATGACATCTTTCTCGAATTA-ATTGAATGAATT
450286 TTAAA
130 TTAAA
* * * * * ** * *
450291 TTTTTCAAAAAATTTAAACTCATTTAAATCGCATTAAAATGACCTCACACTAATTTTAAAACATA
1 TTTTTTAAAAATTTTAAATTTAATTAAATCGTGTTAAAATGACCTCAGACTAATTTTTAAACATA
* * * * *
450356 ATATCTAAGTTGCGCTTTA-AATTCTGCATCTAATAACATCTTTCTCGAAATGATTGGATGAATT
66 ATATCTAAGTTGCGC-TTAGAATTCTGCGTCTAATGACATCTTTCTCGAATTAATTGAATGAATT
*
450420 CTAAA
130 TTAAA
** ** * * * * *
450425 --TTAAAAAGAAAATTAAATTTAATTAAATCGTGTTTAAGTGACATAAGAATAATTTTTAAACAT
1 TTTTTTAAA-AATTTTAAATTTAATTAAATCGTGTTAAAATGACCTCAGACTAATTTTTAAACAT
* * * * ** *
450488 GATATCTAAGTTGTGCTTACAATTCTGCGTCTAATGACATCTTTGTTAAATTGATTTG-ATG-AT
65 AATATCTAAGTTGCGCTTAGAATTCTGCGTCTAATGACATCTTTCTCGAATT-AATTGAATGAAT
*
450551 CTT-AA
129 TTTAAA
* * * *
450556 TTTTATGAAAATTTTAAATTTAATTAAATCGTGTTTAAATGACATCAGACTAATTTTTAAACATA
1 TTTTTTAAAAATTTTAAATTTAATTAAATCGTGTTAAAATGACCTCAGACTAATTTTTAAACATA
* * *
450621 ATATCTAAGTTGCGCTTTGAATTCTGCGTCTAATGACATCTTTCTCGAAATGATTTG-ATGAATT
66 ATATCTAAGTTGCGCTTAGAATTCTGCGTCTAATGACATCTTTCTCG-AATTAATTGAATGAATT
*
450685 TTGAA
130 TTAAA
** * * * * *
450690 TTTTCAAAAAAATTTAAATTTAATTAAATCGTGTTTAAATTACATCAGAATAATTTTTAAACATA
1 TTTTTTAAAAATTTTAAATTTAATTAAATCGTGTTAAAATGACCTCAGACTAATTTTTAAACATA
* * * *
450755 ATATCTAAGTTGCGCTTAGAATTCTGCGTCTAACGACATCTTTCTCGAAATGATTGGATGAATTT
66 ATATCTAAGTTGCGCTTAGAATTCTGCGTCTAATGACATCTTTCTCGAATTAATTGAATGAATTT
450820 TAAA
131 TAAA
450824 TTTTTTAAAAATTT
1 TTTTTTAAAAATTT
450838 AAAAAAATTT
Statistics
Matches: 1006, Mismatches: 195, Indels: 34
0.81 0.16 0.03
Matches are distributed among these distances:
131 2 0.00
132 110 0.11
133 105 0.10
134 671 0.67
135 118 0.12
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.41
Consensus pattern (134 bp):
TTTTTTAAAAATTTTAAATTTAATTAAATCGTGTTAAAATGACCTCAGACTAATTTTTAAACATA
ATATCTAAGTTGCGCTTAGAATTCTGCGTCTAATGACATCTTTCTCGAATTAATTGAATGAATTT
TAAA
Found at i:451041 original size:62 final size:62
Alignment explanation
Indices: 450919--451110 Score: 210
Period size: 66 Copynumber: 3.0 Consensus size: 62
450909 AATCTAGTTA
* * * *
450919 TTATTATTATTATTAAGGTCTTCCGT-TTCCAACGGAAGA-CCTTAT-TGTTTTCGTACTGTTTC
1 TTATTATTATTATTAAGGTCTTCCGTCTT-CAGCGGAAGACCCTTCTAT-TATTC-TAATGTTTC
*
450981 TTATTATTATTATTAAGGTCTTCCGTCTTCAGCGGAAGACCCTTCTATTATTCTATTGTTTC
1 TTATTATTATTATTAAGGTCTTCCGTCTTCAGCGGAAGACCCTTCTATTATTCTAATGTTTC
* * * * *
451043 TTTTTCACTTTTCTTATTAGGGTATTCCGTCTTCAGCGGAAGACCCTTCTATTATTGTAATGTTT
1 TTATT-A---TTATTATTAAGGTCTTCCGTCTTCAGCGGAAGACCCTTCTATTATTCTAATGTTT
451108 C
62 C
451109 TT
1 TT
451111 TTTCACTTTT
Statistics
Matches: 113, Mismatches: 10, Indels: 10
0.85 0.08 0.08
Matches are distributed among these distances:
62 47 0.42
63 12 0.11
64 1 0.01
66 53 0.47
ACGTcount: A:0.20, C:0.19, G:0.14, T:0.47
Consensus pattern (62 bp):
TTATTATTATTATTAAGGTCTTCCGTCTTCAGCGGAAGACCCTTCTATTATTCTAATGTTTC
Found at i:451077 original size:66 final size:66
Alignment explanation
Indices: 450990--451120 Score: 226
Period size: 66 Copynumber: 2.0 Consensus size: 66
450980 CTTATTATTA
* *
450990 TTATTAAGGTCTTCCGTCTTCAGCGGAAGACCCTTCTATTATTCTATTGTTTCTTTTTCACTTTT
1 TTATTAAGGTATTCCGTCTTCAGCGGAAGACCCTTCTATTATTCTAATGTTTCTTTTTCACTTTT
451055 C
66 C
* *
451056 TTATTAGGGTATTCCGTCTTCAGCGGAAGACCCTTCTATTATTGTAATGTTTCTTTTTCACTTTT
1 TTATTAAGGTATTCCGTCTTCAGCGGAAGACCCTTCTATTATTCTAATGTTTCTTTTTCACTTTT
451121 TTTTTTATTC
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 61 1.00
ACGTcount: A:0.18, C:0.21, G:0.14, T:0.48
Consensus pattern (66 bp):
TTATTAAGGTATTCCGTCTTCAGCGGAAGACCCTTCTATTATTCTAATGTTTCTTTTTCACTTTT
C
Found at i:452406 original size:2 final size:2
Alignment explanation
Indices: 452399--452458 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
452389 TACATACAGA
452399 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
452441 CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT
452459 TTTGTTACAA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:460820 original size:437 final size:435
Alignment explanation
Indices: 460071--461121 Score: 1437
Period size: 437 Copynumber: 2.4 Consensus size: 435
460061 TCCAACAAAA
* * *
460071 TCAAGAAAAAGGGGCTGGCCCCTT-TATTGAGGGGCCAAGACAC-CTGTAAACTCTGTTACAAAT
1 TCAAGAAAAAGGGGCTGGCCCCTTAAATT-AGGGGCCAAGACACTC-GTAAACTCTATTTCAAAT
* * * *
460134 AACTTAAAAACGATTTAGATTTTGTAATGCTTTATAGAAGCAAAGTTGTTGATCGTCACAATATC
64 AACTTAAAAATGA-TAAGATTTTGTAATGCATTATAGAAGCAAAGTTGTTGATCGTAACAATATC
* * *
460199 TGTCAGGAAAAATTATTGCCACGCCCATTTGTTACGTAATTAGGGATTTTTAGGGGCCAAAGTAC
128 TTTCAGGAAAAATCATTGCCACGCCCATTTATTACGTAATTAGGGATTTTTAGGGGCCAAAGTAC
* * *
460264 TGAAACTTTGACGCAATATATCTAGAGAAGGAGACATATCTTGTTAAGCATTGTAGAAGAGAAAA
193 TGAAACTTTGACACAATATATCTAAAGAAGGAGACATATCTTGTTAAGCATTGTAAAAGAGAAAA
* * * * * *
460329 TGCTTGCATTGATGATTCTCATCGATTCCATCAATGAAAATACCAATTTCTGTCCCCTTTAGGGA
258 TGCTTGCATTGATGATTCTAATCGATTCCATCAATCAAAACACCAATATCTGTCCCCATTAAGGA
* * *
460394 TCAAGCGGGCTGGCCCCTTAAATATTCAAACATTTGTATCTCAAAAATGATAAACAATTTTAAAT
323 TCAAGAGGGCTGGCCCCTAAAATATTCAAACAATTGTATCTCAAAAATGATAAACAATTTTAAAT
* * *
460459 AAATTTTAGAACAAAAAATGTTAGAATTTGTAAGACCTTTCGATTGAAT
388 AAATGTAAGAAC-AAAAATGTTAGAATTTGTAAGACCTTTCGACTGAAT
* *
460508 TCAAGAAAAGGGGGCTGGCCCCTTAAATTAGGGGCCAAGACACTCGTAAACTCTATTTCAGATAA
1 TCAAGAAAAAGGGGCTGGCCCCTTAAATTAGGGGCCAAGACACTCGTAAACTCTATTTCAAATAA
460573 CTTAAAAATGATAACGATTTCT-TAATGCATTATAGAAGCAAAGTTGTTGATCGTAACAATATCT
66 CTTAAAAATGATAA-GATTT-TGTAATGCATTATAGAAGCAAAGTTGTTGATCGTAACAATATCT
460637 TTCAGGAAAAATCATTGCCACGCCCATTTATTACGTAATTAGGGATTTTTAGGGGCCAAAGTACT
129 TTCAGGAAAAATCATTGCCACGCCCATTTATTACGTAATTAGGGATTTTTAGGGGCCAAAGTACT
* * * * *
460702 TAAACTTTGACACAATATATCTAAAGAAGGAGACATATTTTGTTTAGCTTTGTAAAAGATAAAAT
194 GAAACTTTGACACAATATATCTAAAGAAGGAGACATATCTTGTTAAGCATTGTAAAAGAGAAAAT
*
460767 GCTTGCGTTGATGATTCTAATCGATTCCATCAATCAAAACACCAATATCTGTCCCCATTAAGGAT
259 GCTTGCATTGATGATTCTAATCGATTCCATCAATCAAAACACCAATATCTGTCCCCATTAAGGAT
* * * *
460832 CTAGAGGGCTGGCCCCTAAAATATTCAATCAATTGTATCTCAAAAATGATCAACAATTTTAGATA
324 CAAGAGGGCTGGCCCCTAAAATATTCAAACAATTGTATCTCAAAAATGATAAACAATTTTAAATA
** * *
460897 CGTGTAATAACAAAAATGTTAGAATTTGTGAGACCTTTCGACTGAAT
389 AATGTAAGAACAAAAATGTTAGAATTTGTAAGACCTTTCGACTGAAT
* * * * * *
460944 TCAAGAAAAAGGGGCTGGACCCTTAAATTAGGGGCCAAGCCACTCGTAAAGTCTTTTTCACATAC
1 TCAAGAAAAAGGGGCTGGCCCCTTAAATTAGGGGCCAAGACACTCGTAAACTCTATTTCAAATAA
* * * ** * * *
461009 CTTAAAAATAATCAAGATTTTGTAATGCATTACAAAAATAAAGTTTTTGATCATAATAATATCAG
66 CTTAAAAATGAT-AAGATTTTGTAATGCATTATAGAAGCAAAGTTGTTGATCGTAACAATATC--
* * * * * *
461074 TTT--GTAAAACTCATTGCCACACCCATTGATGACGTAATTATGGATTTT
128 TTTCAGGAAAAATCATTGCCACGCCCATTTATTACGTAATTAGGGATTTT
461122 ATGGGACTAA
Statistics
Matches: 544, Mismatches: 62, Indels: 17
0.87 0.10 0.03
Matches are distributed among these distances:
435 1 0.00
436 183 0.34
437 352 0.65
438 8 0.01
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.31
Consensus pattern (435 bp):
TCAAGAAAAAGGGGCTGGCCCCTTAAATTAGGGGCCAAGACACTCGTAAACTCTATTTCAAATAA
CTTAAAAATGATAAGATTTTGTAATGCATTATAGAAGCAAAGTTGTTGATCGTAACAATATCTTT
CAGGAAAAATCATTGCCACGCCCATTTATTACGTAATTAGGGATTTTTAGGGGCCAAAGTACTGA
AACTTTGACACAATATATCTAAAGAAGGAGACATATCTTGTTAAGCATTGTAAAAGAGAAAATGC
TTGCATTGATGATTCTAATCGATTCCATCAATCAAAACACCAATATCTGTCCCCATTAAGGATCA
AGAGGGCTGGCCCCTAAAATATTCAAACAATTGTATCTCAAAAATGATAAACAATTTTAAATAAA
TGTAAGAACAAAAATGTTAGAATTTGTAAGACCTTTCGACTGAAT
Found at i:462506 original size:16 final size:16
Alignment explanation
Indices: 462485--462522 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
462475 TAGTAATCAC
*
462485 TCTGTCCGTCCGTCCT
1 TCTGTCCGTCCGTCCG
462501 TCTGTCCGTCCGTCCG
1 TCTGTCCGTCCGTCCG
462517 TCTGTC
1 TCTGTC
462523 ACTCTTCCGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.00, C:0.42, G:0.21, T:0.37
Consensus pattern (16 bp):
TCTGTCCGTCCGTCCG
Found at i:465744 original size:37 final size:37
Alignment explanation
Indices: 465690--465763 Score: 112
Period size: 37 Copynumber: 2.0 Consensus size: 37
465680 TATATGCTGC
* *
465690 TTATTTATGTCAACATGCAACTTAGTTATGTTCACAT
1 TTATTTATGTCAACATGCAACTTAATAATGTTCACAT
**
465727 TTATTTATGTCGGCATGCAACTTAATAATGTTCACAT
1 TTATTTATGTCAACATGCAACTTAATAATGTTCACAT
465764 GCTACTTATT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.30, C:0.16, G:0.12, T:0.42
Consensus pattern (37 bp):
TTATTTATGTCAACATGCAACTTAATAATGTTCACAT
Found at i:465805 original size:21 final size:21
Alignment explanation
Indices: 465689--465879 Score: 94
Period size: 21 Copynumber: 9.0 Consensus size: 21
465679 CTATATGCTG
*
465689 CTTATTTATG-TCAACATGCAA
1 CTTAGTTATGTTC-ACATGCAA
465710 CTTAGTTATGTTCACAT----
1 CTTAGTTATGTTCACATGCAA
* *
465727 -TTATTTATG-TCGGCATGCAA
1 CTTAGTTATGTTC-ACATGCAA
* * *
465747 CTTAATAATGTTCACATGCTA
1 CTTAGTTATGTTCACATGCAA
**
465768 CTTA-TTCA-AATCGACATGCAA
1 CTTAGTT-ATGTTC-ACATGCAA
465789 CTTAGTTATGTTTACATGCTACATGCAA
1 CTTAGTTATG--T---T-C-ACATGCAA
465817 CTTAGTTATGTTCACATGCAA
1 CTTAGTTATGTTCACATGCAA
** ** *
465838 GATAAATATGTTGACATGCAA
1 CTTAGTTATGTTCACATGCAA
*
465859 CTTAGTTATGTTCATATGCAA
1 CTTAGTTATGTTCACATGCAA
465880 GATAAATATG
Statistics
Matches: 127, Mismatches: 25, Indels: 36
0.68 0.13 0.19
Matches are distributed among these distances:
15 2 0.02
16 11 0.09
20 3 0.02
21 82 0.65
22 7 0.06
23 1 0.01
26 1 0.01
27 1 0.01
28 19 0.15
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (21 bp):
CTTAGTTATGTTCACATGCAA
Found at i:465813 original size:28 final size:28
Alignment explanation
Indices: 465781--465835 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
465771 ATTCAAATCG
*
465781 ACATGCAACTTAGTTATGTTTACATGCT
1 ACATGCAACTTAGTTATGTTCACATGCT
465809 ACATGCAACTTAGTTATGTTCACATGC
1 ACATGCAACTTAGTTATGTTCACATGC
465836 AAGATAAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.36
Consensus pattern (28 bp):
ACATGCAACTTAGTTATGTTCACATGCT
Found at i:465868 original size:42 final size:42
Alignment explanation
Indices: 465809--465892 Score: 159
Period size: 42 Copynumber: 2.0 Consensus size: 42
465799 TTTACATGCT
465809 ACATGCAACTTAGTTATGTTCACATGCAAGATAAATATGTTG
1 ACATGCAACTTAGTTATGTTCACATGCAAGATAAATATGTTG
*
465851 ACATGCAACTTAGTTATGTTCATATGCAAGATAAATATGTTG
1 ACATGCAACTTAGTTATGTTCACATGCAAGATAAATATGTTG
465893 CATATCGTCA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.35
Consensus pattern (42 bp):
ACATGCAACTTAGTTATGTTCACATGCAAGATAAATATGTTG
Found at i:465889 original size:21 final size:21
Alignment explanation
Indices: 465823--465891 Score: 84
Period size: 21 Copynumber: 3.3 Consensus size: 21
465813 GCAACTTAGT
465823 TATGTTCACATGCAAGATAAA
1 TATGTTCACATGCAAGATAAA
* ** **
465844 TATGTTGACATGCAACTTAGT
1 TATGTTCACATGCAAGATAAA
*
465865 TATGTTCATATGCAAGATAAA
1 TATGTTCACATGCAAGATAAA
465886 TATGTT
1 TATGTT
465892 GCATATCGTC
Statistics
Matches: 37, Mismatches: 11, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.36
Consensus pattern (21 bp):
TATGTTCACATGCAAGATAAA
Found at i:465984 original size:21 final size:21
Alignment explanation
Indices: 465924--465977 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
465914 TAACATAATT
465924 AAGTTGCATGTCGACATAAAG
1 AAGTTGCATGTCGACATAAAG
*
465945 AAATTGCATGTCGACATAAAG
1 AAGTTGCATGTCGACATAAAG
*
465966 AAGTCGCATGTC
1 AAGTTGCATGTC
465978 ATCATAATCA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.37, C:0.17, G:0.22, T:0.24
Consensus pattern (21 bp):
AAGTTGCATGTCGACATAAAG
Found at i:466104 original size:21 final size:21
Alignment explanation
Indices: 466047--466104 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 21
466037 ATTGCATTTT
*
466047 TCTTGCATGTCAACATAATTA
1 TCTTGCATGTCAACATAACTA
* * **
466068 TGTTGCAAGTTGACATAACTA
1 TCTTGCATGTCAACATAACTA
466089 TCTTGCATGTCAACAT
1 TCTTGCATGTCAACAT
466105 GCTTATCTTA
Statistics
Matches: 28, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.31, C:0.19, G:0.14, T:0.36
Consensus pattern (21 bp):
TCTTGCATGTCAACATAACTA
Found at i:466111 original size:21 final size:21
Alignment explanation
Indices: 466047--466120 Score: 69
Period size: 21 Copynumber: 3.5 Consensus size: 21
466037 ATTGCATTTT
*
466047 TCTTGCATGTCAACATAATTA
1 TCTTGCATGTCAACATACTTA
* * **
466068 TGTTGCAAGTTGACATAAC-TA
1 TCTTGCATGTCAACAT-ACTTA
*
466089 TCTTGCATGTCAACATGCTTA
1 TCTTGCATGTCAACATACTTA
*
466110 TCTTACATGTC
1 TCTTGCATGTC
466121 CGCATATTTG
Statistics
Matches: 40, Mismatches: 11, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
20 1 0.03
21 38 0.95
22 1 0.03
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (21 bp):
TCTTGCATGTCAACATACTTA
Found at i:472029 original size:24 final size:24
Alignment explanation
Indices: 471983--472034 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
471973 TCTATCTCAC
471983 CTTTAAGTTCTGTTTTCAGTTCAGT
1 CTTTAAGTTCTGTTTTCAGTTCA-T
* * *
472008 CTTTAA-TTCTTTTTTTATTTCAT
1 CTTTAAGTTCTGTTTTCAGTTCAT
472031 CTTT
1 CTTT
472035 GATTGCGGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 5 0.21
24 13 0.54
25 6 0.25
ACGTcount: A:0.15, C:0.15, G:0.08, T:0.62
Consensus pattern (24 bp):
CTTTAAGTTCTGTTTTCAGTTCAT
Found at i:478526 original size:381 final size:382
Alignment explanation
Indices: 477821--478585 Score: 1505
Period size: 381 Copynumber: 2.0 Consensus size: 382
477811 AAGTGTTTAA
*
477821 ATTGACAAGACCTTTCATTTGAAATCATAAAAAGGGGCTGGCCCTTTAAATAAGGGGCTGAGGGG
1 ATTGACAAGACCTTTCATTTGAAATCATAAAAAGGGACTGGCCCTTTAAATAAGGGGCTGAGGGG
477886 GCCCTTAAGTCTTTTTATGATCACTTTTTACCGTGAAATATTTTGTGATACGTTATAGAAGCAAT
66 GCCCTTAAGTCTTTTTATGATCACTTTTTACCGTGAAATATTTTGTGATACGTTATAGAAGCAAT
477951 TATGTTCATTCTAACGTTATTCACCTATACATGGCAACCATTTACTTCTGTGTTACGTAGTTAGG
131 TATGTTCATTCTAACGTTATTCACCTATACATGGCAACCATTTACTTCTGTGTTACGTAGTTAGG
478016 GAGTTTAAAGGGCCAGAAGTCCAAAACTTTGATGCTCAATATCTCAAAATAGAGGAAAATTTTGA
196 GAGTTTAAAGGGCCAGAAGTCCAAAACTTTGATGCTCAATATCTCAAAATAGAGGAAAATTTTGA
*
478081 TAAGCCATATTGAACAAAGGATGCTCAAAATATTGAGCTTAACATTCTGTAACCATAGTTTCTTT
261 TAAGCCATATTGAACAAAGGATGCTCAAAATATTGAGCTTAACATTCTGTAACCATAATTTCTTT
478146 GTTATGCGGTCTTCAAAAGGAGTTACA-GGTCGGCCCCTTAAAACGACCCTCTCAAG
326 GTTATGCGGTCTTCAAAAGGAGTTACAGGGTCGGCCCCTTAAAACGACCCTCTCAAG
478202 ATTGACAAGACCTTTCATTTGAAATCATAAAAAGGGACTGGCCCTTTAAATAAGGGGCTGAGGGG
1 ATTGACAAGACCTTTCATTTGAAATCATAAAAAGGGACTGGCCCTTTAAATAAGGGGCTGAGGGG
478267 GCCCTTAAGTCTTTTTATGATCACTTTTTACCGTGAAATATTTTGTGATACGTTATAGAAGCAAT
66 GCCCTTAAGTCTTTTTATGATCACTTTTTACCGTGAAATATTTTGTGATACGTTATAGAAGCAAT
478332 TATGTTCATTCTAACGTTATTCACCTATACATGGCAACCATTTACTTCTGTGTTACGTAGTTAGG
131 TATGTTCATTCTAACGTTATTCACCTATACATGGCAACCATTTACTTCTGTGTTACGTAGTTAGG
478397 GAGTTTAAAGGGCCAGAAGTCCAAAACTTTGATGCTCAATATCTCAAAATAGAGGAAAATTTTGA
196 GAGTTTAAAGGGCCAGAAGTCCAAAACTTTGATGCTCAATATCTCAAAATAGAGGAAAATTTTGA
478462 TAAGCCATATTGAACAAAGGATGCTCAAAATATTGAGCTTAACATTCTGTAACCATAATTTCTTT
261 TAAGCCATATTGAACAAAGGATGCTCAAAATATTGAGCTTAACATTCTGTAACCATAATTTCTTT
478527 GTTATGCGGTCTTCAAAAGGAGTTACAGGGTCGGCCCCTTAAAACGACCCTCTCAAG
326 GTTATGCGGTCTTCAAAAGGAGTTACAGGGTCGGCCCCTTAAAACGACCCTCTCAAG
478584 AT
1 AT
478586 ATCTCGAGAA
Statistics
Matches: 381, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
381 350 0.92
382 31 0.08
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Consensus pattern (382 bp):
ATTGACAAGACCTTTCATTTGAAATCATAAAAAGGGACTGGCCCTTTAAATAAGGGGCTGAGGGG
GCCCTTAAGTCTTTTTATGATCACTTTTTACCGTGAAATATTTTGTGATACGTTATAGAAGCAAT
TATGTTCATTCTAACGTTATTCACCTATACATGGCAACCATTTACTTCTGTGTTACGTAGTTAGG
GAGTTTAAAGGGCCAGAAGTCCAAAACTTTGATGCTCAATATCTCAAAATAGAGGAAAATTTTGA
TAAGCCATATTGAACAAAGGATGCTCAAAATATTGAGCTTAACATTCTGTAACCATAATTTCTTT
GTTATGCGGTCTTCAAAAGGAGTTACAGGGTCGGCCCCTTAAAACGACCCTCTCAAG
Found at i:480773 original size:442 final size:437
Alignment explanation
Indices: 479681--481105 Score: 1787
Period size: 442 Copynumber: 3.3 Consensus size: 437
479671 TCACAAGTCG
* * * *
479681 TTTTC-TTTAAAATCAAGAAAAAAGGGCTTGCCCCTCAAATAAGGGGACAAACAGGCTCTAAAGT
1 TTTTCATTTGAAATCAAGAAAAAGGGGCTGGCCCCTCAAATTAGGGGACAAA-AGGCTCTAAAGT
* * *
479745 CTTTAATCTGTAGCCCTTTACTGAGAGATATTTTGTGAAATGTTATATAAGCAAATATGTTTAT-
65 CTTTAATCTATAGCCCTTTACTGAGAGATATTTTGTGAAATGTTATAGAAGCAAATGTGTTTATC
* * * * *
479809 CTCACAGTAATGTATCAAGGCAATGTATTGATTTTGTTATGTATTACGTAATTAAGGGTTTTTAG
130 CT-ACAGTTATGTATCAAAGCAATGTAATGATTTTGTCATGTGTTACGTAATTAAGGGTTTTTAG
* * * *
479874 GGGCCAAAAGTCCAAAATTTCGATCACCCATATCTCAGAAAGGAATATTTTTTTGTAATGCAGTA
194 GGGCCAAAAGTCCAAAATTTTGATCACCCATATCTCAGAAAGGAAAAATATTTTGTAATGCAGTA
* * * *
479939 CAGAAGAAAAGTTGTTTAAAATGATTTTCTCAACAAAATGCAACCTTCAAAATTTCGTTAAACGG
259 CAGAAGAAAAATTGTTTAAAATGATGTTCTTAACAATATGCAACCTTCAAAATTTCGTTAAACGG
* * * *
480004 CCCCTAAAAGGAGATAATGGACCGGCCCCTAAAACCTTCTTTCTCATATATCTCCAGAACGGTCA
324 CCCCTATAAGGAGATAAGGGATCGGCCCCTAAAACCTTCTTTCTCATATATCTCCAGAACGGTAA
* * *
480069 C-GAATATCTAAACACTTGTTGAACAAAATGTGTTCATAATTAAATGATC
389 CAGAATTTCTAAACACTTGTTTAACAAAATGTGTTCAGAATTAAAT-ATC
* *** *
480118 TTTT-ATTTGATATCAAGAAAAAGGGGCTGAATCCTCAAATTAGGGGACCAAAGGGCTCTGAAA-
1 TTTTCATTTGAAATCAAGAAAAAGGGGCTGGCCCCTCAAATTAGGGGA-CAAAAGGCTCT-AAAG
*
480181 TCTTTAATCTGTAGCCCTTTACTGAGAGATATTTTGTGAAATGTTATAGAAGCAAATGTGTTTAT
64 TCTTTAATCTATAGCCCTTTACTGAGAGATATTTTGTGAAATGTTATAGAAGCAAATGTGTTTAT
* * *
480246 CTTACAGTTATGTATTC-ACGCAATGTAATGATTTTATCATGTGTTACGTAATTAAGGGTTTTTA
129 CCTACAGTTATGTA-TCAAAGCAATGTAATGATTTTGTCATGTGTTACGTAATTAAGGGTTTTTA
* * * * * *
480310 GGGGCCAAAAGTCCAAAATTTTAATCATCTATATCTCAGAAAGGAAAACTATTTTGTTATGCAGA
193 GGGGCCAAAAGTCCAAAATTTTGATCACCCATATCTCAGAAAGGAAAAATATTTTGTAATGCAGT
*
480375 ACAGAAGAAAAATTGTTTAAAATGATGTTCTTAACAATATGTC-ACCTTTAAAATTTCGTTAAAC
258 ACAGAAGAAAAATTGTTTAAAATGATGTTCTTAACAATATG-CAACCTTCAAAATTTCGTTAAAC
* * * *
480439 GACCCCTATAAGGAGGTAAGGGATCGGCCCGTATAACCTTCTTTCTCATATATCTCCAGAACGGT
322 GGCCCCTATAAGGAGATAAGGGATCGGCCCCTAAAACCTTCTTTCTCATATATCTCCAGAACGGT
* * * * *
480504 AACAAATTGAATTTCTAAATACTTGTTTAACATAATTTGTTTAGAATTAAATAAC
387 AAC--A--GAATTTCTAAACACTTGTTTAACAAAATGTGTTCAGAATTAAATATC
** *
480559 TTTTCATTTGAAATCAAGAAAAAGGGGCTGGCCCCTTTAATTAGGGGATTAAAAGGCTCTAAAGT
1 TTTTCATTTGAAATCAAGAAAAAGGGGCTGGCCCCTCAAATTAGGGGA-CAAAAGGCTCTAAAGT
* * * * * * * * *
480624 CTTTTATCTATAACCATTTATTGAGGGTTATTTTGTGAAATGCTAAAGAAGCAAATGTCTTTATC
65 CTTTAATCTATAGCCCTTTACTGAGAGATATTTTGTGAAATGTTATAGAAGCAAATGTGTTTATC
* * **
480689 CTACATTTATGTATCAAAGCAATGTAATGGTTTTGTCATGTGTTTTGTAATT-AGGGTATTTTAG
130 CTACAGTTATGTATCAAAGCAATGTAATGATTTTGTCATGTGTTACGTAATTAAGGGT-TTTTAG
* ** * *
480753 GGACCAAAAAACCCAAATTTTGATCACCCATATCTCAGAAAGGAAAAATATTTTGAAATGCAGTA
194 GGGCCAAAAGTCCAAAATTTTGATCACCCATATCTCAGAAAGGAAAAATATTTTGTAATGCAGTA
* * * *
480818 CAGAAGAAAAATTGTTTAAAATGATGTTCCTAACAATATACAACCTTCAACATTTCGTCAAACGG
259 CAGAAGAAAAATTGTTTAAAATGATGTTCTTAACAATATGCAACCTTCAAAATTTCGTTAAACGG
* * * *
480883 CCCCTATAAAGAGATAAGGGATCGGCCCCTAAAACCTTCTTCCTCAAATATCTCTAGAACGGTAA
324 CCCCTATAAGGAGATAAGGGATCGGCCCCTAAAACCTTCTTTCTCATATATCTCCAGAACGGTAA
* * *
480948 C-GAATTTCTAAACACTTG-TTGACAAAATGTGTCCAGAATTAAATGTC
389 CAGAATTTCTAAACACTTGTTTAACAAAATGTGTTCAGAATTAAATATC
* * * *
480995 CTTTCATTTG-AATCCAAGAAAAAGGGACTGGCCCCTTAAATTAGGGTATC-AAAGAGCTCTAAA
1 TTTTCATTTGAAAT-CAAGAAAAAGGGGCTGGCCCCTCAAATTAGGGGA-CAAAAG-GCTCTAAA
* * *
481058 ATCTTTAATCTATAGCCCTTTAATGAGAGCA-ATTTTGTGAAAGGTTAT
63 GTCTTTAATCTATAGCCCTTTACTGAGAG-ATATTTTGTGAAATGTTAT
481106 TAAAGCTAGA
Statistics
Matches: 848, Mismatches: 121, Indels: 39
0.84 0.12 0.04
Matches are distributed among these distances:
435 7 0.01
436 108 0.13
437 348 0.41
438 11 0.01
441 17 0.02
442 357 0.42
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Consensus pattern (437 bp):
TTTTCATTTGAAATCAAGAAAAAGGGGCTGGCCCCTCAAATTAGGGGACAAAAGGCTCTAAAGTC
TTTAATCTATAGCCCTTTACTGAGAGATATTTTGTGAAATGTTATAGAAGCAAATGTGTTTATCC
TACAGTTATGTATCAAAGCAATGTAATGATTTTGTCATGTGTTACGTAATTAAGGGTTTTTAGGG
GCCAAAAGTCCAAAATTTTGATCACCCATATCTCAGAAAGGAAAAATATTTTGTAATGCAGTACA
GAAGAAAAATTGTTTAAAATGATGTTCTTAACAATATGCAACCTTCAAAATTTCGTTAAACGGCC
CCTATAAGGAGATAAGGGATCGGCCCCTAAAACCTTCTTTCTCATATATCTCCAGAACGGTAACA
GAATTTCTAAACACTTGTTTAACAAAATGTGTTCAGAATTAAATATC
Found at i:481499 original size:72 final size:66
Alignment explanation
Indices: 481417--481685 Score: 421
Period size: 66 Copynumber: 4.0 Consensus size: 66
481407 TGTCTAGTTA
* *
481417 TTATTAGGGTCTTCCGTCTTCAGCGGAAGACCCTTCTATTATTCTGTTGTTTCTTTTTCAATTTT
1 TTATTAGGGTCTTCCGTCTTCAGCGGAAGACCCTTCTATTATTCTATTGTTTCTTTTTCACTTTT
481482 C
66 C
*
481483 GTATTATTATTAGGGTCTTCCGTCTTCAGCGGAAGACTCTTCTATTATTCTATTGTTTCTTTTTC
1 ------TTATTAGGGTCTTCCGTCTTCAGCGGAAGACCCTTCTATTATTCTATTGTTTCTTTTTC
481548 ACTTTTC
60 ACTTTTC
*
481555 TTATTAGGGTCTTCCGTCTTCAGCGGAAGACTCTTCTATTATTCTATTGTTTCTTTTTCACTTTT
1 TTATTAGGGTCTTCCGTCTTCAGCGGAAGACCCTTCTATTATTCTATTGTTTCTTTTTCACTTTT
481620 C
66 C
* * *
481621 TTATTAGGGTCTTCCGTCTTCAGCGGAAGACCCTTCTATTATTGTAATGTTTCTTTTTCAGTTTT
1 TTATTAGGGTCTTCCGTCTTCAGCGGAAGACCCTTCTATTATTCTATTGTTTCTTTTTCACTTTT
481686 TTTTTTCTTT
Statistics
Matches: 190, Mismatches: 7, Indels: 6
0.94 0.03 0.03
Matches are distributed among these distances:
66 127 0.67
72 63 0.33
ACGTcount: A:0.16, C:0.20, G:0.15, T:0.49
Consensus pattern (66 bp):
TTATTAGGGTCTTCCGTCTTCAGCGGAAGACCCTTCTATTATTCTATTGTTTCTTTTTCACTTTT
C
Found at i:481565 original size:138 final size:132
Alignment explanation
Indices: 481417--481685 Score: 421
Period size: 138 Copynumber: 2.0 Consensus size: 132
481407 TGTCTAGTTA
*
481417 TTATTAGGGTCTTCCGTCTTCAGCGGAAGACCCTTCTATTATTCTGTTGTTTCTTTTTCAATTTT
1 TTATTAGGGTCTTCCGTCTTCAGCGGAAGACCCTTCTATTATTCTATTGTTTCTTTTTCAATTTT
* *
481482 CGTATTATTATTAGGGTCTTCCGTCTTCAGCGGAAGACTCTTCTATTATTCTATTGTTTCTTTTT
66 C------TTATTAGGGTCTTCCGTCTTCAGCGGAAGACCCTTCTATTATTCTAATGTTTCTTTTT
481547 CACTTTTC
125 CACTTTTC
* *
481555 TTATTAGGGTCTTCCGTCTTCAGCGGAAGACTCTTCTATTATTCTATTGTTTCTTTTTCACTTTT
1 TTATTAGGGTCTTCCGTCTTCAGCGGAAGACCCTTCTATTATTCTATTGTTTCTTTTTCAATTTT
* *
481620 CTTATTAGGGTCTTCCGTCTTCAGCGGAAGACCCTTCTATTATTGTAATGTTTCTTTTTCAGTTT
66 CTTATTAGGGTCTTCCGTCTTCAGCGGAAGACCCTTCTATTATTCTAATGTTTCTTTTTCACTTT
481685 T
131 T
481686 TTTTTTCTTT
Statistics
Matches: 124, Mismatches: 7, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
132 61 0.49
138 63 0.51
ACGTcount: A:0.16, C:0.20, G:0.15, T:0.49
Consensus pattern (132 bp):
TTATTAGGGTCTTCCGTCTTCAGCGGAAGACCCTTCTATTATTCTATTGTTTCTTTTTCAATTTT
CTTATTAGGGTCTTCCGTCTTCAGCGGAAGACCCTTCTATTATTCTAATGTTTCTTTTTCACTTT
TC
Found at i:482130 original size:166 final size:165
Alignment explanation
Indices: 481856--482403 Score: 738
Period size: 166 Copynumber: 3.3 Consensus size: 165
481846 TAAAAAAGTT
* * * * *
481856 CTTGTCCACGTATCTCCTCAAAAACGAGCAATGATAGAAAGCTGAAATTTTCAGGAATGAAAAAG
1 CTTGTCCACGCATCTCCTCAAAAACGAGCAAAGATAGAAAGCTGAAATTTTTAGGAATGATAGAG
* * *
481921 GACATGAATGTCTGGCCTCACGAGGAAAATAATTGTCCGGAAATTCCGAGTACGGAAGCTAACTG
66 GACATGAACGTCTAGCCTCACGAGGAAAATAATTGTCCGGAAATTCCGAGTACGGAAGCTAACTA
481986 GGGTCAAAATATAGGACACGTTTTAGACGAGAACTC
131 GGGTCAAAATATAGGACACGTTTTAGACGA-AACTC
* *
482022 CTTGTCCACGCATCCCCTCAAAAACGAGCAAAGATAGAAAGCTGAAATTTTTAGGAATGATAGCG
1 CTTGTCCACGCATCTCCTCAAAAACGAGCAAAGATAGAAAGCTGAAATTTTTAGGAATGATAGAG
* * *
482087 GACACGATA-GTCTAGCCTCACGAAGAAAATGATTGTCCGGAAATTCCGAGTACGGAAGCTAACT
66 GACATGA-ACGTCTAGCCTCACGAGGAAAATAATTGTCCGGAAATTCCGAGTACGGAAGCTAACT
*
482151 TGGGTCAAAATATAGGACACGTTTTAGACGAAAACTC
130 AGGGTCAAAATATAGGACACGTTTTAGACG-AAACTC
* * * * * * * *
482188 CTTGTCCACGCATTTCCTCAAGAACAAGCAATGATAGAAAGCTGAAATTGTTCGAAATGATAGAT
1 CTTGTCCACGCATCTCCTCAAAAACGAGCAAAGATAGAAAGCTGAAATTTTTAGGAATGATAGAG
* * * * *
482253 GACATGAACGTATAGCCTCACGAGGAAAATCATTGTCTGGAAATTCCGAGTACGGAAGCTAGCCA
66 GACATGAACGTCTAGCCTCACGAGGAAAATAATTGTCCGGAAATTCCGAGTACGGAAGCTAACTA
* * * *
482318 GGGTCAATATATAGGACACGTTTTCGACGAAATTT
131 GGGTCAAAATATAGGACACGTTTTAGACGAAACTC
* * * * *
482353 TTTGTCCACGCATTTCCTCAAAAATGAGTAAAGATGGAAAGCTGAAATTTT
1 CTTGTCCACGCATCTCCTCAAAAACGAGCAAAGATAGAAAGCTGAAATTTT
482404 ACAGATTGGT
Statistics
Matches: 337, Mismatches: 42, Indels: 7
0.87 0.11 0.02
Matches are distributed among these distances:
165 48 0.14
166 287 0.85
167 2 0.01
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.24
Consensus pattern (165 bp):
CTTGTCCACGCATCTCCTCAAAAACGAGCAAAGATAGAAAGCTGAAATTTTTAGGAATGATAGAG
GACATGAACGTCTAGCCTCACGAGGAAAATAATTGTCCGGAAATTCCGAGTACGGAAGCTAACTA
GGGTCAAAATATAGGACACGTTTTAGACGAAACTC
Done.