Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A05
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 100714657
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3970000 characters in sequence are not A, C, G, or T
File 153 of 318
Found at i:47708110 original size:40 final size:40
Alignment explanation
Indices: 47708026--47708250 Score: 255
Period size: 40 Copynumber: 5.7 Consensus size: 40
47708016 TTGAATGATG
* * *
47708026 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAC-CAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAT
* *
47708065 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAT
* *
47708106 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
*
47708145 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AAT
* *
47708186 T-CGGGTTAAGTCCCAAAGGCATTTGTGCGAGTTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
* *
47708224 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
47708251 AACGAGGAGC
Statistics
Matches: 160, Mismatches: 17, Indels: 16
0.83 0.09 0.08
Matches are distributed among these distances:
38 2 0.01
39 34 0.21
40 111 0.69
41 13 0.08
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
Found at i:47716157 original size:40 final size:40
Alignment explanation
Indices: 47716073--47716297 Score: 237
Period size: 40 Copynumber: 5.7 Consensus size: 40
47716063 TTGAATGATG
* * *
47716073 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAC-CAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAT
* *
47716112 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAT
* * *
47716153 TCCGGGCTAAG-CCCGAAGGCATTGGTGCTAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
*
47716192 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AAT
* *
47716233 T-CGGGTTAAGTCCCAAAGGCATTTGTGCGAGTTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
* * *
47716271 AACCGGGCTATGTCCCGAAGGTATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
47716298 AACGAGGAGC
Statistics
Matches: 157, Mismatches: 20, Indels: 16
0.81 0.10 0.08
Matches are distributed among these distances:
38 2 0.01
39 33 0.21
40 109 0.69
41 13 0.08
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
Found at i:47720139 original size:25 final size:25
Alignment explanation
Indices: 47720118--47720166 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
47720108 TACGGCTCTT
*
47720118 ATGAGCTTCCTGTTACATGGCTCAC
1 ATGAGCTTCCCGTTACATGGCTCAC
*
47720143 ATGAGCTTCCCGTTATATGGCTCA
1 ATGAGCTTCCCGTTACATGGCTCA
47720167 GAAGAGCTCC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.20, C:0.27, G:0.20, T:0.33
Consensus pattern (25 bp):
ATGAGCTTCCCGTTACATGGCTCAC
Found at i:47720173 original size:25 final size:25
Alignment explanation
Indices: 47720120--47720187 Score: 75
Period size: 25 Copynumber: 2.7 Consensus size: 25
47720110 CGGCTCTTAT
* *
47720120 GAGCTTCCTGTTACATGGCTCACAT
1 GAGCTTCCCGTTACATGGCTCACAA
* *
47720145 GAGCTTCCCGTTATATGGCTCAGAA
1 GAGCTTCCCGTTACATGGCTCACAA
47720170 GAGC-TCCCGGTTTACATG
1 GAGCTTCCC-G-TTACATG
47720188 CTCGTATGAG
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
24 4 0.11
25 26 0.72
26 6 0.17
ACGTcount: A:0.21, C:0.26, G:0.24, T:0.29
Consensus pattern (25 bp):
GAGCTTCCCGTTACATGGCTCACAA
Found at i:47731234 original size:24 final size:23
Alignment explanation
Indices: 47731201--47731286 Score: 91
Period size: 24 Copynumber: 3.6 Consensus size: 23
47731191 TCCAGGCTAT
47731201 ATAACAGGAAGCTCATAAGAGCC
1 ATAACAGGAAGCTCATAAGAGCC
**
47731224 ATAATCAGGAAGCTCATGCGAGCC
1 ATAA-CAGGAAGCTCATAAGAGCC
* **
47731248 AATAACAGGTAGCTCCGAAGAGCC
1 -ATAACAGGAAGCTCATAAGAGCC
*
47731272 ATTAACGGGAAGCTC
1 A-TAACAGGAAGCTC
47731287 CGGATAACCA
Statistics
Matches: 51, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
23 5 0.10
24 42 0.82
25 4 0.08
ACGTcount: A:0.37, C:0.23, G:0.24, T:0.15
Consensus pattern (23 bp):
ATAACAGGAAGCTCATAAGAGCC
Found at i:47731386 original size:26 final size:26
Alignment explanation
Indices: 47731326--47731397 Score: 74
Period size: 26 Copynumber: 2.8 Consensus size: 26
47731316 GAGCCATATT
47731326 AGGAAGCTC-CAAAGAGCCATTAATC
1 AGGAAGCTCACAAAGAGCCATTAATC
** * * *
47731351 AAAAAACTCACAAAGATCCTTTAATC
1 AGGAAGCTCACAAAGAGCCATTAATC
* *
47731377 AGGAAGCTCACGAAGAACCAT
1 AGGAAGCTCACAAAGAGCCAT
47731398 ATATTGGGAC
Statistics
Matches: 35, Mismatches: 11, Indels: 1
0.74 0.23 0.02
Matches are distributed among these distances:
25 6 0.17
26 29 0.83
ACGTcount: A:0.44, C:0.24, G:0.15, T:0.17
Consensus pattern (26 bp):
AGGAAGCTCACAAAGAGCCATTAATC
Found at i:47739284 original size:25 final size:25
Alignment explanation
Indices: 47739256--47739444 Score: 77
Period size: 25 Copynumber: 7.6 Consensus size: 25
47739246 CTTATGACCA
47739256 TCCCGATATATGGCTCTCTTGAGCT
1 TCCCGATATATGGCTCTCTTGAGCT
* *
47739281 TCCC-ATTATTTGGCTCT-TGCGAGCT
1 TCCCGA-TATATGGCTCTCT-TGAGCT
** * *
47739306 TCCAAATA-ATTAGCTCTCATGAGCT
1 TCCCGATATA-TGGCTCTCTTGAGCT
* * **
47739331 TCTCGAT-TAATGGCTCTATAAAGCT
1 TCCCGATAT-ATGGCTCTCTTGAGCT
* * *
47739356 TCTCGATAT-TGGCTCGCATGAGCT
1 TCCCGATATATGGCTCTCTTGAGCT
** *
47739380 TCCCGAT-TACAGCTCT-TATAAGCT
1 TCCCGATATATGGCTCTCT-TGAGCT
* * * * * *
47739404 TCCTGTTACATGGCTCACATGAGCG
1 TCCCGATATATGGCTCTCTTGAGCT
*
47739429 TCCCGTTATATGGCTC
1 TCCCGATATATGGCTC
47739445 GAAAGAGCTT
Statistics
Matches: 115, Mismatches: 37, Indels: 24
0.65 0.21 0.14
Matches are distributed among these distances:
23 1 0.01
24 32 0.28
25 79 0.69
26 3 0.03
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (25 bp):
TCCCGATATATGGCTCTCTTGAGCT
Found at i:47739379 original size:24 final size:23
Alignment explanation
Indices: 47739318--47739386 Score: 66
Period size: 24 Copynumber: 2.8 Consensus size: 23
47739308 CAAATAATTA
47739318 GCTCTCATGAGCTTCTCGATTAATG
1 GCTC-CATGAGCTTCTCGA-TAATG
* * *
47739343 GCTCTATAAAGCTTCTCGATATTG
1 GCTCCAT-GAGCTTCTCGATAATG
*
47739367 GCTCGCATGAGCTTCCCGAT
1 GCTC-CATGAGCTTCTCGAT
47739387 TACAGCTCTT
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
24 20 0.56
25 16 0.44
ACGTcount: A:0.20, C:0.26, G:0.20, T:0.33
Consensus pattern (23 bp):
GCTCCATGAGCTTCTCGATAATG
Found at i:47743807 original size:21 final size:20
Alignment explanation
Indices: 47743778--47743824 Score: 60
Period size: 19 Copynumber: 2.3 Consensus size: 20
47743768 TTTAATTATT
47743778 TATTGTATATTATTTTTAAACA
1 TATTGTATA-T-TTTTTAAACA
*
47743800 TATT-TATATTTTTTAAATA
1 TATTGTATATTTTTTAAACA
47743819 TATTGT
1 TATTGT
47743825 TTCAACACAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 13 0.57
20 2 0.09
21 4 0.17
22 4 0.17
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.60
Consensus pattern (20 bp):
TATTGTATATTTTTTAAACA
Found at i:47744526 original size:18 final size:17
Alignment explanation
Indices: 47744486--47744522 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
47744476 AATGAGATTA
*
47744486 TTTAAAAATTAAATATT
1 TTTAAAAAATAAATATT
*
47744503 TTTAAAAAATAGATATT
1 TTTAAAAAATAAATATT
47744520 TTT
1 TTT
47744523 TAAAGAATTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (17 bp):
TTTAAAAAATAAATATT
Found at i:47748988 original size:45 final size:45
Alignment explanation
Indices: 47748936--47749023 Score: 149
Period size: 45 Copynumber: 2.0 Consensus size: 45
47748926 TATGTAATAT
*
47748936 GAACTCATTGAGCTGTGGTCTGAGTTCATGATATATGTGACATTC
1 GAACTCATTGAGCTGTGGTCTGAGTTCATGATATATATGACATTC
* *
47748981 GAACTCATTGAGTTGTGGTCTGAGTTCGTGATATATATGACAT
1 GAACTCATTGAGCTGTGGTCTGAGTTCATGATATATATGACAT
47749024 ATGTTTTGGA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.25, C:0.14, G:0.25, T:0.36
Consensus pattern (45 bp):
GAACTCATTGAGCTGTGGTCTGAGTTCATGATATATATGACATTC
Found at i:47751373 original size:27 final size:27
Alignment explanation
Indices: 47751342--47751438 Score: 90
Period size: 27 Copynumber: 3.6 Consensus size: 27
47751332 TATAGAGTAA
*
47751342 GCCATCAAGGCATTCCCTTCAGAGT-TT
1 GCCATGAAGGCATTCCCTTCAGA-TATT
* *
47751369 GCCATGAAGGCATTCCTTTCATATATT
1 GCCATGAAGGCATTCCCTTCAGATATT
* *
47751396 TCCATGAAGGCATTCCTTTC-GTATATT
1 GCCATGAAGGCATTCCCTTCAG-ATATT
* **
47751423 ACCACAAAGGCATTCC
1 GCCATGAAGGCATTCC
47751439 TTTTATAGCG
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
26 1 0.02
27 59 0.98
ACGTcount: A:0.26, C:0.27, G:0.15, T:0.32
Consensus pattern (27 bp):
GCCATGAAGGCATTCCCTTCAGATATT
Found at i:47751439 original size:27 final size:27
Alignment explanation
Indices: 47751375--47751441 Score: 98
Period size: 27 Copynumber: 2.5 Consensus size: 27
47751365 GTTTGCCATG
* **
47751375 AAGGCATTCCTTTCATATATTTCCATG
1 AAGGCATTCCTTTCATATATTACCACA
*
47751402 AAGGCATTCCTTTCGTATATTACCACA
1 AAGGCATTCCTTTCATATATTACCACA
47751429 AAGGCATTCCTTT
1 AAGGCATTCCTTT
47751442 TATAGCGTGT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.27, C:0.24, G:0.12, T:0.37
Consensus pattern (27 bp):
AAGGCATTCCTTTCATATATTACCACA
Found at i:47755744 original size:31 final size:30
Alignment explanation
Indices: 47755709--47755806 Score: 76
Period size: 31 Copynumber: 3.1 Consensus size: 30
47755699 GATTGGCTCA
47755709 TTGGTATGCTTTGGTTTGGTAGAATATGATG
1 TTGGTATG-TTTGGTTTGGTAGAATATGATG
* *
47755740 TTGGTATTTGTGTTGGTACTT-GT-GGATGTGA-G
1 TTGGTA--TGT-TTGGT--TTGGTAGAATATGATG
*
47755772 TTTGATATGATTTGGTTTGGTAGAATATGATG
1 -TTGGTATG-TTTGGTTTGGTAGAATATGATG
47755804 TTG
1 TTG
47755807 TAAGTATGTT
Statistics
Matches: 52, Mismatches: 5, Indels: 20
0.68 0.06 0.26
Matches are distributed among these distances:
29 2 0.04
30 2 0.04
31 22 0.42
32 4 0.08
33 18 0.35
34 2 0.04
35 2 0.04
ACGTcount: A:0.18, C:0.02, G:0.33, T:0.47
Consensus pattern (30 bp):
TTGGTATGTTTGGTTTGGTAGAATATGATG
Found at i:47756904 original size:58 final size:58
Alignment explanation
Indices: 47756834--47756949 Score: 232
Period size: 58 Copynumber: 2.0 Consensus size: 58
47756824 TAGATAAACG
47756834 TTTAATCTCGTTAAATGCGTAATGGATAATCATAGTCACATATTATTGGATTTTATCA
1 TTTAATCTCGTTAAATGCGTAATGGATAATCATAGTCACATATTATTGGATTTTATCA
47756892 TTTAATCTCGTTAAATGCGTAATGGATAATCATAGTCACATATTATTGGATTTTATCA
1 TTTAATCTCGTTAAATGCGTAATGGATAATCATAGTCACATATTATTGGATTTTATCA
47756950 GTATGAGGTA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.41
Consensus pattern (58 bp):
TTTAATCTCGTTAAATGCGTAATGGATAATCATAGTCACATATTATTGGATTTTATCA
Found at i:47759152 original size:20 final size:21
Alignment explanation
Indices: 47759119--47759157 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
47759109 GTCTTGCCCA
*
47759119 TTTTAAATATCTTTAATTATT
1 TTTTAAATAACTTTAATTATT
*
47759140 TTTTAAA-AACTTTCATTA
1 TTTTAAATAACTTTAATTA
47759158 AATTAATGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 9 0.56
21 7 0.44
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (21 bp):
TTTTAAATAACTTTAATTATT
Found at i:47761293 original size:35 final size:35
Alignment explanation
Indices: 47761252--47761323 Score: 126
Period size: 35 Copynumber: 2.1 Consensus size: 35
47761242 TTTAGAGGTT
*
47761252 TAATTTCTCTTCTAGTTCTGTTTTTGGCGATAGAG
1 TAATTTCTCTTCTAGTTCTATTTTTGGCGATAGAG
*
47761287 TAATTTCTCTTCTAGTTTTATTTTTGGCGATAGAG
1 TAATTTCTCTTCTAGTTCTATTTTTGGCGATAGAG
47761322 TA
1 TA
47761324 TTGTGGTGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.19, C:0.12, G:0.18, T:0.50
Consensus pattern (35 bp):
TAATTTCTCTTCTAGTTCTATTTTTGGCGATAGAG
Found at i:47777824 original size:14 final size:14
Alignment explanation
Indices: 47777805--47777850 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 14
47777795 ATGGAAAGAA
*
47777805 AATTTTTGAATTAT
1 AATTTTTTAATTAT
47777819 AATTTTTTAATTTAAAT
1 AATTTTTTAA-TT--AT
47777836 AATTTTTTAATTAT
1 AATTTTTTAATTAT
47777850 A
1 A
47777851 TTTGTTTTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
14 12 0.43
15 2 0.07
16 2 0.07
17 12 0.43
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (14 bp):
AATTTTTTAATTAT
Found at i:47778891 original size:46 final size:47
Alignment explanation
Indices: 47778831--47779194 Score: 460
Period size: 46 Copynumber: 8.0 Consensus size: 47
47778821 TTTGACATGA
* * * * * * * *
47778831 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACAGTTTCATATCAGGC
** * *
47778877 TGCCATGGTATCTTTCAACCATGGTCTTATTCA-TTTCATGTCACGC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACAGTTTCATATCAGGC
*** *** * * *
47778923 TGCCATGGTATCTTTCAACCATGGTCTTATTTA-TTTCCCGTTATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACAGTTTCATATCAGGC
47778969 TGCCATGGTATCTTTCAACCATGGTCTTACAC-GTTTCATATCAGGC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACAGTTTCATATCAGGC
47779015 TGCCATGGTATCTTTCAACCATGGTCTTACAC-GTTTCATATCAGG-
1 TGCCATGGTATCTTTCAACCATGGTCTTACACAGTTTCATATCAGGC
47779060 TGCC-TGGTATCTTTCAACCATGGTCTTACAC-GTTTCATATCAGGC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACAGTTTCATATCAGGC
*
47779105 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACAGTTTCATATCAGGC
47779151 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACAGTTTCATATCAG
47779195 AGAGCACACT
Statistics
Matches: 291, Mismatches: 22, Indels: 10
0.90 0.07 0.03
Matches are distributed among these distances:
44 40 0.14
45 12 0.04
46 239 0.82
ACGTcount: A:0.21, C:0.24, G:0.16, T:0.39
Consensus pattern (47 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACAGTTTCATATCAGGC
Found at i:47778988 original size:92 final size:92
Alignment explanation
Indices: 47778831--47779194 Score: 509
Period size: 92 Copynumber: 4.0 Consensus size: 92
47778821 TTTGACATGA
* * * * *
47778831 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGTTGCCATGGTATCTTTCAA
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCATGTTGCCATGGTATCTTTCAA
** * *
47778895 CCATGGTCTTATTCATTTCATGTCACGC
65 CCATGGTCTTACACATTTCATATCAGGC
*** *** *
47778923 TGCCATGGTATCTTTCAACCATGGTCTTATTTATTTCCCGTTATGTTGCCATGGTATCTTTCAAC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTATCTTTCAAC
*
47778988 CATGGTCTTACACGTTTCATATCAGGC
66 CATGGTCTTACACATTTCATATCAGGC
* *
47779015 TGCCATGGTATCTTTCAACCATGGTCTTACACGTTTCATATCA-GGTGCC-TGGTATCTTTCAAC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTATCTTTCAAC
*
47779078 CATGGTCTTACACGTTTCATATCAGGC
66 CATGGTCTTACACATTTCATATCAGGC
*
47779105 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAAC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTATCTTTCAAC
47779170 CATGGTCTTACACATTTCATATCAG
66 CATGGTCTTACACATTTCATATCAG
47779195 AGAGCACACT
Statistics
Matches: 245, Mismatches: 24, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
90 83 0.34
91 14 0.06
92 148 0.60
ACGTcount: A:0.21, C:0.24, G:0.16, T:0.39
Consensus pattern (92 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTATCTTTCAAC
CATGGTCTTACACATTTCATATCAGGC
Found at i:47779081 original size:182 final size:184
Alignment explanation
Indices: 47778831--47779194 Score: 509
Period size: 182 Copynumber: 2.0 Consensus size: 184
47778821 TTTGACATGA
* * * * * *
47778831 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTCTGTCATGTTGCCATGGTATCTTTCAAC
1 TGCCATAGTATCTTTCAACCATGGTCTTACACAGTTTCTATCATGGTGCCATGGTATCTTTCAAC
** * *** *
47778896 CATGGTCTTATTCATTTCATGTCACGCTGCCATGGTATCTTTCAACCATGGTCTTATTTATTTCC
66 CATGGTCTTACACATTTCATATCACGCTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCA
* * * *
47778961 CGTTATGTTGCCATGGTATCTTTCAACCATGGTCTTACACGTTTCATATCAGGC
131 CATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
*
47779015 TGCCATGGTATCTTTCAACCATGGTCTTACAC-GTTTCATATCA-GGTGCC-TGGTATCTTTCAA
1 TGCCATAGTATCTTTCAACCATGGTCTTACACAGTTTC-TATCATGGTGCCATGGTATCTTTCAA
* *
47779077 CCATGGTCTTACACGTTTCATATCAGGCTGCCATGGTATCTTTCAACCATGGTCTTACACATTTC
65 CCATGGTCTTACACATTTCATATCACGCTGCCATGGTATCTTTCAACCATGGTCTTACACATTTC
*
47779142 ATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
130 ACATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
47779195 AGAGCACACT
Statistics
Matches: 158, Mismatches: 21, Indels: 4
0.86 0.11 0.02
Matches are distributed among these distances:
182 117 0.74
183 9 0.06
184 32 0.20
ACGTcount: A:0.21, C:0.24, G:0.16, T:0.39
Consensus pattern (184 bp):
TGCCATAGTATCTTTCAACCATGGTCTTACACAGTTTCTATCATGGTGCCATGGTATCTTTCAAC
CATGGTCTTACACATTTCATATCACGCTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCA
CATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
Found at i:47779096 original size:21 final size:21
Alignment explanation
Indices: 47779027--47779096 Score: 56
Period size: 21 Copynumber: 3.2 Consensus size: 21
47779017 CCATGGTATC
47779027 TTTCAACCATGGTCTTACACG
1 TTTCAACCATGGTCTTACACG
* *
47779048 TTTCATATCA-GGTGCCTGGTA-TC-
1 TTTCA-ACCATGGT--CT--TACACG
47779071 TTTCAACCATGGTCTTACACG
1 TTTCAACCATGGTCTTACACG
47779092 TTTCA
1 TTTCA
47779097 TATCAGGCTG
Statistics
Matches: 37, Mismatches: 4, Indels: 16
0.65 0.07 0.28
Matches are distributed among these distances:
19 2 0.05
20 1 0.03
21 15 0.41
22 6 0.16
23 10 0.27
24 1 0.03
25 2 0.05
ACGTcount: A:0.21, C:0.26, G:0.16, T:0.37
Consensus pattern (21 bp):
TTTCAACCATGGTCTTACACG
Found at i:47779224 original size:136 final size:133
Alignment explanation
Indices: 47778969--47779225 Score: 347
Period size: 136 Copynumber: 1.9 Consensus size: 133
47778959 CCCGTTATGT
*
47778969 TGCCATGGTATCTTTCAACCATGGTCTTACACGTTTCATATCAGGCTGCCATGGTATCTTTCAAC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGCTGCCATGGTATCTTTCAAC
* * *** **
47779034 CATGGTCTTACACGTTTCATATCAGGTGCCTGGTATCTTTCAACCATGGTCTTACACGTTTCATA
66 CATGGTCTTACACATTTCATATCAGGAGCC--G-ATCCCGCAACCATCATCTTACACGTTTCATA
47779099 TCAGGC
128 TCAGGC
*
47779105 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAAC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGCTGCCATGGTATCTTTCAAC
47779170 CATGGTCTTACACATTTCATATCAGAGAGCAC-ACTCCCGCGAACC-TCATCCTTACA
66 CATGGTCTTACACATTTCATATCAG-GAGC-CGA-TCCCGC-AACCATCAT-CTTACA
47779226 GTGGGATTAC
Statistics
Matches: 107, Mismatches: 9, Indels: 10
0.85 0.07 0.08
Matches are distributed among these distances:
134 1 0.01
135 5 0.05
136 97 0.91
137 3 0.03
138 1 0.01
ACGTcount: A:0.23, C:0.27, G:0.16, T:0.33
Consensus pattern (133 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGCTGCCATGGTATCTTTCAAC
CATGGTCTTACACATTTCATATCAGGAGCCGATCCCGCAACCATCATCTTACACGTTTCATATCA
GGC
Found at i:47781348 original size:11 final size:11
Alignment explanation
Indices: 47781332--47781371 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
47781322 ACTAAATAAT
47781332 TAATAATAAAA
1 TAATAATAAAA
47781343 TAATAATAAAA
1 TAATAATAAAA
*
47781354 TATATCATTAAAA
1 TA-AT-AATAAAA
47781367 TAATA
1 TAATA
47781372 TATATCTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
11 14 0.54
12 4 0.15
13 8 0.31
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.33
Consensus pattern (11 bp):
TAATAATAAAA
Found at i:47791944 original size:25 final size:25
Alignment explanation
Indices: 47791916--47791994 Score: 76
Period size: 25 Copynumber: 3.3 Consensus size: 25
47791906 CTAATGGCCA
47791916 ATGTGATGAATGTGAAAGTGTATAT
1 ATGTGATGAATGTGAAAGTGTATAT
* * ***
47791941 ATGTGAT-AAGGCCG-AA-TGGCCA-
1 ATGTGATGAATG-TGAAAGTGTATAT
47791963 ATGTGATGAATGTGAAAGTGTATAT
1 ATGTGATGAATGTGAAAGTGTATAT
47791988 ATGTGAT
1 ATGTGAT
47791995 AAGACCTAAT
Statistics
Matches: 39, Mismatches: 10, Indels: 10
0.66 0.17 0.17
Matches are distributed among these distances:
22 8 0.21
23 8 0.21
24 8 0.21
25 15 0.38
ACGTcount: A:0.34, C:0.05, G:0.29, T:0.32
Consensus pattern (25 bp):
ATGTGATGAATGTGAAAGTGTATAT
Found at i:47791944 original size:47 final size:47
Alignment explanation
Indices: 47791891--47792185 Score: 455
Period size: 47 Copynumber: 6.3 Consensus size: 47
47791881 ACAAGATATG
* *
47791891 TATATGTGACAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
47791938 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
* * *
47791985 TATATGTGATAAGACCTAATGGCCGATGTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
*
47792032 TATATGTGATGAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
** * * * * *
47792079 TATATAAGATAAGACCTAATGGCCGATGTGATGGATGTGAAGGTGTA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
*
47792126 TATATGTGATAAGGCCGAATGGCCAATGTGATGGATGTGAAAGTGTA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
*
47792173 TAAATGTGATAAG
1 TATATGTGATAAG
47792186 TCCCGAAGGG
Statistics
Matches: 224, Mismatches: 24, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
47 224 1.00
ACGTcount: A:0.34, C:0.08, G:0.29, T:0.28
Consensus pattern (47 bp):
TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
Found at i:47798304 original size:67 final size:68
Alignment explanation
Indices: 47798221--47798357 Score: 267
Period size: 68 Copynumber: 2.0 Consensus size: 68
47798211 AATACAACAG
47798221 TAAGATTTTGTA-TTTTTTTTTTCTGAATCGATCTCAAACATAAAAGCTTGGTTTTGCTCCCTCA
1 TAAGATTTTGTATTTTTTTTTTTCTGAATCGATCTCAAACATAAAAGCTTGGTTTTGCTCCCTCA
47798285 ATC
66 ATC
47798288 TAAGATTTTGTATTTTTTTTTTTCTGAATCGATCTCAAACATAAAAGCTTGGTTTTGCTCCCTCA
1 TAAGATTTTGTATTTTTTTTTTTCTGAATCGATCTCAAACATAAAAGCTTGGTTTTGCTCCCTCA
47798353 ATC
66 ATC
47798356 TA
1 TA
47798358 CGGATGCCTA
Statistics
Matches: 69, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
67 12 0.17
68 57 0.83
ACGTcount: A:0.26, C:0.18, G:0.12, T:0.45
Consensus pattern (68 bp):
TAAGATTTTGTATTTTTTTTTTTCTGAATCGATCTCAAACATAAAAGCTTGGTTTTGCTCCCTCA
ATC
Found at i:47800201 original size:20 final size:20
Alignment explanation
Indices: 47800163--47800201 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
47800153 ATATTTTTTT
*
47800163 AACTTTTTGAGTTTATAACA
1 AACTTTTTGACTTTATAACA
47800183 AACTTTCTTGACTTT-TAAC
1 AACTTT-TTGACTTTATAAC
47800202 TTTTTTCTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.31, C:0.15, G:0.08, T:0.46
Consensus pattern (20 bp):
AACTTTTTGACTTTATAACA
Found at i:47805423 original size:27 final size:28
Alignment explanation
Indices: 47805393--47805446 Score: 85
Period size: 27 Copynumber: 2.0 Consensus size: 28
47805383 TAATTTTCTC
47805393 ATAAAAATAT-TAAA-AAATCAGAAAAAA
1 ATAAAAATATATAAACAAATCA-AAAAAA
47805420 ATAAAAATATATAAACAAATCAAAAAA
1 ATAAAAATATATAAACAAATCAAAAAA
47805447 TTTATTAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
27 10 0.40
28 9 0.36
29 6 0.24
ACGTcount: A:0.74, C:0.06, G:0.02, T:0.19
Consensus pattern (28 bp):
ATAAAAATATATAAACAAATCAAAAAAA
Found at i:47805493 original size:19 final size:18
Alignment explanation
Indices: 47805459--47805507 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 18
47805449 TATTAAATAC
*
47805459 TAAAATTTATATAAACTTA
1 TAAAA-TTATAAAAACTTA
47805478 TTAAAATTATAAAAACTTA
1 -TAAAATTATAAAAACTTA
47805497 TAAATATTATA
1 TAAA-ATTATA
47805508 TATAATTAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 4 0.15
19 18 0.67
20 5 0.19
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (18 bp):
TAAAATTATAAAAACTTA
Found at i:47807696 original size:51 final size:51
Alignment explanation
Indices: 47807620--47807722 Score: 206
Period size: 51 Copynumber: 2.0 Consensus size: 51
47807610 AACCTTCCAT
47807620 GAAACATATTTTTAAAAAGCATAAAGATACTTCTCACCATATTATTTTGAA
1 GAAACATATTTTTAAAAAGCATAAAGATACTTCTCACCATATTATTTTGAA
47807671 GAAACATATTTTTAAAAAGCATAAAGATACTTCTCACCATATTATTTTGAA
1 GAAACATATTTTTAAAAAGCATAAAGATACTTCTCACCATATTATTTTGAA
47807722 G
1 G
47807723 GGTTATTATG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.43, C:0.14, G:0.09, T:0.35
Consensus pattern (51 bp):
GAAACATATTTTTAAAAAGCATAAAGATACTTCTCACCATATTATTTTGAA
Found at i:47812588 original size:16 final size:16
Alignment explanation
Indices: 47812559--47812601 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
47812549 CACACATAAT
*
47812559 GAGGGAGAGAGAGGGG
1 GAGGGGGAGAGAGGGG
*
47812575 GAGGGGGAGGGAGGGG
1 GAGGGGGAGAGAGGGG
47812591 GA-GGGGAGAGA
1 GAGGGGGAGAGA
47812602 TTTTGAACAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
15 8 0.33
16 16 0.67
ACGTcount: A:0.28, C:0.00, G:0.72, T:0.00
Consensus pattern (16 bp):
GAGGGGGAGAGAGGGG
Found at i:47814786 original size:14 final size:16
Alignment explanation
Indices: 47814757--47814791 Score: 56
Period size: 14 Copynumber: 2.3 Consensus size: 16
47814747 CCTTTATTTT
47814757 TATTTCACTCCCCGTA
1 TATTTCACTCCCCGTA
47814773 TATTTCA-T-CCCGTA
1 TATTTCACTCCCCGTA
47814787 TATTT
1 TATTT
47814792 TAGTAACTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 11 0.58
15 1 0.05
16 7 0.37
ACGTcount: A:0.20, C:0.29, G:0.06, T:0.46
Consensus pattern (16 bp):
TATTTCACTCCCCGTA
Found at i:47820693 original size:25 final size:24
Alignment explanation
Indices: 47820665--47820712 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 24
47820655 CTCGTGTACT
47820665 CTTATAA-CATATAATCCATGTAAAC
1 CTTATAACCATATAA--CATGTAAAC
47820690 CTTATAATCCATATAACATGTAA
1 CTTATAA-CCATATAACATGTAA
47820713 TTCATGTAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
25 14 0.67
27 7 0.33
ACGTcount: A:0.44, C:0.19, G:0.04, T:0.33
Consensus pattern (24 bp):
CTTATAACCATATAACATGTAAAC
Found at i:47821028 original size:23 final size:23
Alignment explanation
Indices: 47820940--47821028 Score: 103
Period size: 23 Copynumber: 3.9 Consensus size: 23
47820930 GGCTCCGTAA
*
47820940 AGCTGAAACGGTAAGCCCCTAA-
1 AGCTGAAACGGTAAGCCCATAAG
47820962 AGACTGAAACGGTAAGCTCCA-AAG
1 AG-CTGAAACGGTAAGC-CCATAAG
* * *
47820986 AGTTG-AACGATAAGCTCATAAG
1 AGCTGAAACGGTAAGCCCATAAG
47821008 AGCTGAAACGGTAAGCCCATA
1 AGCTGAAACGGTAAGCCCATA
47821029 CGAGTTGTGG
Statistics
Matches: 55, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
21 2 0.04
22 18 0.33
23 31 0.56
24 4 0.07
ACGTcount: A:0.39, C:0.21, G:0.24, T:0.16
Consensus pattern (23 bp):
AGCTGAAACGGTAAGCCCATAAG
Found at i:47829338 original size:43 final size:42
Alignment explanation
Indices: 47829224--47829354 Score: 149
Period size: 43 Copynumber: 3.0 Consensus size: 42
47829214 AATCGCTGCA
*
47829224 AAAGATCATGTTCTTTAGTG-GTATTTGTAGTAAGAA-TGCCGCT
1 AAAGATCATGTTCTTTAGTGCG--TTTGTGGTAA-AAGTGCCGCT
* *
47829267 AAAGATCATATTCTTTAGTGGCGATTGTGGTAAAAGTGCCGCT
1 AAAGATCATGTTCTTTAGT-GCGTTTGTGGTAAAAGTGCCGCT
* * *
47829310 AAAGATCATGTTCTTTAACTGCGTTTGTGGGAAAAGCGCCGCT
1 AAAGATCATGTTCTTT-AGTGCGTTTGTGGTAAAAGTGCCGCT
47829353 AA
1 AA
47829355 CATTAACAGA
Statistics
Matches: 76, Mismatches: 8, Indels: 8
0.83 0.09 0.09
Matches are distributed among these distances:
42 2 0.03
43 70 0.92
44 3 0.04
45 1 0.01
ACGTcount: A:0.28, C:0.15, G:0.24, T:0.33
Consensus pattern (42 bp):
AAAGATCATGTTCTTTAGTGCGTTTGTGGTAAAAGTGCCGCT
Found at i:47830926 original size:12 final size:12
Alignment explanation
Indices: 47830909--47830938 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
47830899 TCGTCTCTCG
47830909 CACACGGCCACC
1 CACACGGCCACC
*
47830921 CACACGGCCAGC
1 CACACGGCCACC
47830933 CACACG
1 CACACG
47830939 CCCGTGTGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.27, C:0.53, G:0.20, T:0.00
Consensus pattern (12 bp):
CACACGGCCACC
Found at i:47846138 original size:13 final size:13
Alignment explanation
Indices: 47846120--47846146 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
47846110 TCACTTGAAG
47846120 CCATCGCTTCATA
1 CCATCGCTTCATA
47846133 CCATCGCTTCATA
1 CCATCGCTTCATA
47846146 C
1 C
47846147 TCCGCCCTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.41, G:0.07, T:0.30
Consensus pattern (13 bp):
CCATCGCTTCATA
Found at i:47854915 original size:19 final size:19
Alignment explanation
Indices: 47854879--47854921 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
47854869 CCATTTTGTA
47854879 TAAATTGTAAAATAAGTGG
1 TAAATTGTAAAATAAGTGG
*
47854898 TAAATGTGTGAAAT-AGTGG
1 TAAAT-TGTAAAATAAGTGG
47854917 -AAATT
1 TAAATT
47854922 TGGGGTTGCT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 1 0.05
18 4 0.18
19 10 0.45
20 7 0.32
ACGTcount: A:0.44, C:0.00, G:0.23, T:0.33
Consensus pattern (19 bp):
TAAATTGTAAAATAAGTGG
Found at i:47855496 original size:46 final size:46
Alignment explanation
Indices: 47855350--47855668 Score: 238
Period size: 46 Copynumber: 6.7 Consensus size: 46
47855340 GGGTTATCGT
* * *
47855350 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGTCAC-ATTATGA
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGA-GATGA
* * *
47855396 GAGCTAGTGTAAGACCATGTCTGGGACATGACATCGGCATTGAGACGA
1 GAGCTAGTGTAAGA-CATGTCTGGGACATG-CATCGGCCTCGAGATGA
47855444 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGTA
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATG-A
* * * * * *
47855491 -AGCTAGTGTAAGATATGTCTAGGACATGCAT-TGACTACAAGATGT
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCT-CGAGATGA
* * *
47855536 G-TC-AGTGTAAGACCATGTCTGGGACATGGCATCGG-CACGGGTATGCGA
1 GAGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCTCGAG-AT--GA
* * * * * *
47855584 GAGCTAGAGTAATACCATGTCTGAGACATGGCGTCAGCCTCGATGACGA
1 GAGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCTCGA-GATGA
* *
47855633 TAG-TCAGTGTAAGACCAAGTCTGGGACATGGCATCG
1 GAGCT-AGTGTAAGA-CATGTCTGGGACAT-GCATCG
47855669 ACTCTCTACC
Statistics
Matches: 217, Mismatches: 39, Indels: 31
0.76 0.14 0.11
Matches are distributed among these distances:
44 9 0.04
45 18 0.08
46 69 0.32
47 32 0.15
48 26 0.12
49 31 0.14
50 27 0.12
51 4 0.02
52 1 0.00
ACGTcount: A:0.28, C:0.19, G:0.30, T:0.23
Consensus pattern (46 bp):
GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGA
Found at i:47855661 original size:49 final size:50
Alignment explanation
Indices: 47855536--47855667 Score: 144
Period size: 49 Copynumber: 2.7 Consensus size: 50
47855526 TACAAGATGT
* *
47855536 GTCAGTGTAAGACCATGTCTGGGACATGGCATCGGCACGGGTATGCGAGA
1 GTCAGTGTAAGACCATGTCTGGGACATGGCATCAGCACGCGTATGCGAGA
* * * * * *
47855586 G-CTAGAGTAATACCATGTCTGAGACATGGCGTCAGC-CTCG-ATGACGATA
1 GTC-AGTGTAAGACCATGTCTGGGACATGGCATCAGCACGCGTATG-CGAGA
*
47855635 GTCAGTGTAAGACCAAGTCTGGGACATGGCATC
1 GTCAGTGTAAGACCATGTCTGGGACATGGCATC
47855668 GACTCTCTAC
Statistics
Matches: 66, Mismatches: 13, Indels: 7
0.77 0.15 0.08
Matches are distributed among these distances:
48 3 0.05
49 33 0.50
50 30 0.45
ACGTcount: A:0.27, C:0.21, G:0.31, T:0.21
Consensus pattern (50 bp):
GTCAGTGTAAGACCATGTCTGGGACATGGCATCAGCACGCGTATGCGAGA
Found at i:47875581 original size:22 final size:22
Alignment explanation
Indices: 47875553--47875597 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
47875543 CTCATAACTT
*
47875553 ATTGAGCATTGGACATTGAATG
1 ATTGAGCATTAGACATTGAATG
*
47875575 ATTGAGCATTAGACATTTAATG
1 ATTGAGCATTAGACATTGAATG
47875597 A
1 A
47875598 CTAGTGGGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.36, C:0.09, G:0.22, T:0.33
Consensus pattern (22 bp):
ATTGAGCATTAGACATTGAATG
Found at i:47878782 original size:28 final size:28
Alignment explanation
Indices: 47878742--47878797 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
47878732 TTTCCTTACA
47878742 AAAACAAAATGAAAGGTATACGTGATGT
1 AAAACAAAATGAAAGGTATACGTGATGT
47878770 AAAACAAAATGAAAGGTATACGTGATGT
1 AAAACAAAATGAAAGGTATACGTGATGT
47878798 TGAGTGGTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.50, C:0.07, G:0.21, T:0.21
Consensus pattern (28 bp):
AAAACAAAATGAAAGGTATACGTGATGT
Found at i:47882481 original size:22 final size:22
Alignment explanation
Indices: 47882443--47882490 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 22
47882433 AGAAATTAAG
47882443 TAGAAAAGAAGTATGAATTGAGT
1 TAGAAAAGAAG-ATGAATTGAGT
*
47882466 TAGAAAAGTAAG-TGAATTTAGT
1 TAGAAAAG-AAGATGAATTGAGT
47882488 TAG
1 TAG
47882491 GATTAAATTG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 12 0.52
23 8 0.35
24 3 0.13
ACGTcount: A:0.46, C:0.00, G:0.25, T:0.29
Consensus pattern (22 bp):
TAGAAAAGAAGATGAATTGAGT
Found at i:47882826 original size:28 final size:28
Alignment explanation
Indices: 47882757--47882833 Score: 79
Period size: 28 Copynumber: 2.8 Consensus size: 28
47882747 ATTATGGAAT
47882757 TGAAAAG-GAAATTGAATTGATGATGGA
1 TGAAAAGTGAAATTGAATTGATGATGGA
* * * *
47882784 T-AAGTATTGATATTGAATTGTAT-ATTGA
1 TGAA-AAGTGAAATTGAATTG-ATGATGGA
47882812 TGAAAAGTGAAATTGAATTGAT
1 TGAAAAGTGAAATTGAATTGAT
47882834 TCGTATATGA
Statistics
Matches: 39, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
26 2 0.05
27 4 0.10
28 29 0.74
29 4 0.10
ACGTcount: A:0.42, C:0.00, G:0.23, T:0.35
Consensus pattern (28 bp):
TGAAAAGTGAAATTGAATTGATGATGGA
Found at i:47883008 original size:41 final size:39
Alignment explanation
Indices: 47882962--47883058 Score: 99
Period size: 38 Copynumber: 2.5 Consensus size: 39
47882952 TCGACCTTGA
* *
47882962 GTCGATGAGACACTGGGTGTCACTATTTTACTTCGGATAG
1 GTCGATGAGACACTGGGTGT-ACCACTTTACTTCGGATAG
* ** *
47883002 ATTCGATGAGGTACT-GG-GTACCACTTTACTTCGGCTAG
1 -GTCGATGAGACACTGGGTGTACCACTTTACTTCGGATAG
*
47883040 GCCGATGAGACACTGGGTG
1 GTCGATGAGACACTGGGTG
47883059 GCATTATATT
Statistics
Matches: 44, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
37 10 0.23
38 18 0.41
39 3 0.07
40 2 0.05
41 11 0.25
ACGTcount: A:0.22, C:0.20, G:0.30, T:0.29
Consensus pattern (39 bp):
GTCGATGAGACACTGGGTGTACCACTTTACTTCGGATAG
Found at i:47890005 original size:16 final size:16
Alignment explanation
Indices: 47889986--47890029 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
47889976 ATTTTTGGGT
* *
47889986 ACTTATTTTTTTTATC
1 ACTTATTTTTTTCAGC
*
47890002 ACTTATTATTTTCAGC
1 ACTTATTTTTTTCAGC
47890018 ACTTAATTTTTT
1 ACTT-ATTTTTT
47890030 AGTTTTCAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
16 17 0.74
17 6 0.26
ACGTcount: A:0.23, C:0.14, G:0.02, T:0.61
Consensus pattern (16 bp):
ACTTATTTTTTTCAGC
Found at i:47892481 original size:57 final size:58
Alignment explanation
Indices: 47892328--47892481 Score: 165
Period size: 57 Copynumber: 2.7 Consensus size: 58
47892318 CCACATATCA
* ** * * *
47892328 TATAACAGGATTACTTGTCCAAGCTAAAT-CTTGTTT-TCAACATATGCTCATAAGAGTT
1 TATATCAGGATTACCAGTCCAGGCTAAATCCTT-TTTGT-AACATATGCTCAGAAGAGCT
* * *
47892386 TA-ATCAGGATTACCCGTCCAGGCTAAATCCTATCTGTAA-ATATGCTCAAGAAG-GCT
1 TATATCAGGATTACCAGTCCAGGCTAAATCCTTTTTGTAACATATGCTC-AGAAGAGCT
47892442 TATATCAGGATTACCAGTCCAGGCTAAATCCTTTTTGTAA
1 TATATCAGGATTACCAGTCCAGGCTAAATCCTTTTTGTAA
47892482 TGAGGTCAAT
Statistics
Matches: 81, Mismatches: 11, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
56 12 0.15
57 64 0.79
58 5 0.06
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (58 bp):
TATATCAGGATTACCAGTCCAGGCTAAATCCTTTTTGTAACATATGCTCAGAAGAGCT
Found at i:47897168 original size:47 final size:47
Alignment explanation
Indices: 47897110--47897240 Score: 172
Period size: 47 Copynumber: 2.8 Consensus size: 47
47897100 GTGCAAATAA
* * * *
47897110 TACCTTGATTTGGCAATGGGCCATGATATAGGTATTTTGAGAGGAGT
1 TACCTTGATTTGGCTACGGGCCATGGTATAGGTATTTTGAGAGAAGT
* * * * *
47897157 TACCTTGATTTGGCTACGGGGCATGGTATAGGTACTCTGGGATAAGT
1 TACCTTGATTTGGCTACGGGCCATGGTATAGGTATTTTGAGAGAAGT
*
47897204 TACCTTGATTTGGCTACGGGTCATGGTATAGGTATTT
1 TACCTTGATTTGGCTACGGGCCATGGTATAGGTATTT
47897241 ATCGATTGTG
Statistics
Matches: 72, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
47 72 1.00
ACGTcount: A:0.22, C:0.13, G:0.30, T:0.35
Consensus pattern (47 bp):
TACCTTGATTTGGCTACGGGCCATGGTATAGGTATTTTGAGAGAAGT
Found at i:47901569 original size:22 final size:22
Alignment explanation
Indices: 47901528--47901569 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
47901518 ACATAAGCAT
*
47901528 TCAATTATATTAGCACAATAAA
1 TCAATTATATCAGCACAATAAA
* *
47901550 TCAATTATATCGGCATAATA
1 TCAATTATATCAGCACAATA
47901570 CATCTATGGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.45, C:0.14, G:0.07, T:0.33
Consensus pattern (22 bp):
TCAATTATATCAGCACAATAAA
Found at i:47903104 original size:47 final size:45
Alignment explanation
Indices: 47903036--47903349 Score: 152
Period size: 47 Copynumber: 6.7 Consensus size: 45
47903026 GACGAGGGCT
* * *
47903036 AGTGTAAGACATGTTTCGGACATGCATCAGCCACATTATGATCACC
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCACATGATGAT-ACC
* * * *
47903082 AGTGTAAGACCATGTCTGGGACATGGCATCAGCGTAGA-GATAAGTGCC
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCAGC-CACATGATGA-TACC
* * * *
47903130 AGTGAAAGACATGTCTGGGACATGCCTCGGCCTCAATGATGATAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCAC-ATGATGATA-CC
* * * * * * *
47903177 AATGTAAGACGTGTCTGGGACATGCATC-GACTA-AGCGCTG-TGCT
1 AGTGTAAGACATGTCTGGGACATGCATCAG-CCACA-TGATGATACC
* * * * *
47903221 AGTGTAAGACATGTTTGGGACATGTATCAG-CACTTATATATGAGAGCT
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCAC--AT-GATGATA-CC
* * ** * *
47903269 AGTGTAAGACCATGTCTGGGACATAGAATCGGCCTTTATAATGATTGCC
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCAGCC-ACATGATGA-TACC
*
47903318 AGTGTAAGACCATGTTTGGGACATGGCATCAG
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCAG
47903350 TAACTTAGCC
Statistics
Matches: 199, Mismatches: 48, Indels: 39
0.70 0.17 0.14
Matches are distributed among these distances:
43 1 0.01
44 25 0.13
45 3 0.02
46 24 0.12
47 57 0.29
48 32 0.16
49 49 0.25
50 7 0.04
51 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.27, T:0.25
Consensus pattern (45 bp):
AGTGTAAGACATGTCTGGGACATGCATCAGCCACATGATGATACC
Found at i:47903151 original size:94 final size:93
Alignment explanation
Indices: 47902988--47903292 Score: 300
Period size: 94 Copynumber: 3.3 Consensus size: 93
47902978 TGTGAGAGCT
* * * * *
47902988 AGTGTAAGACCATGTCTAGGACATGGCATCGACATTGAGACGAGGGCTAGTGTAAGACATGTTTC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGAC-TAGAGA-TAGTGCTAGTGTAAGACATGTTTG
47903053 GGACATGCATCAGCCAC-ATTATGATCA-CC
64 GGACATGCATCAGCCACTATTATGAT-AGCC
* * *
47903082 AGTGTAAGACCATGTCTGGGACATGGCATC-AGCGTAGAGATAAGTGCCAGTGAAAGACATGTCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGA-C-TAGAGAT-AGTGCTAGTGTAAGACATGTTT
* * * * *
47903146 GGGACATGCCTCGGCCTCAATGATGATAGCC
63 GGGACATGCATCAGCCACTATTATGATAGCC
* * * *
47903177 AATGTAAGA-CGTGTCTGGGACAT-GCATCGACTAAGCGCT-GTGCTAGTGTAAGACATGTTTGG
1 AGTGTAAGACCATGTCTGGGACATGGCATCGACT-AGAGATAGTGCTAGTGTAAGACATGTTTGG
* * *
47903239 GACATGTATCAG-CACTTATATATGAGAGCT
65 GACATGCATCAGCCAC-TAT-TATGATAGCC
47903269 AGTGTAAGACCATGTCTGGGACAT
1 AGTGTAAGACCATGTCTGGGACAT
47903293 AGAATCGGCC
Statistics
Matches: 172, Mismatches: 30, Indels: 19
0.78 0.14 0.09
Matches are distributed among these distances:
90 2 0.01
91 31 0.18
92 16 0.09
93 24 0.14
94 82 0.48
95 17 0.10
ACGTcount: A:0.29, C:0.19, G:0.28, T:0.24
Consensus pattern (93 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGACTAGAGATAGTGCTAGTGTAAGACATGTTTGGG
ACATGCATCAGCCACTATTATGATAGCC
Found at i:47903322 original size:49 final size:49
Alignment explanation
Indices: 47903221--47903342 Score: 151
Period size: 49 Copynumber: 2.5 Consensus size: 49
47903211 GCGCTGTGCT
* *
47903221 AGTGTAAGA-CATGTTTGGGACATGTATCAGCACTTATATATGAGAGCT
1 AGTGTAAGACCATGTTTGGGACATGAATCAGCACTTATATATGAGAGCC
* * **
47903269 AGTGTAAGACCATGTCTGGGACATAGAATCGGC-CTT-TATAATGATTGCC
1 AGTGTAAGACCATGTTTGGGACAT-GAATCAGCACTTATAT-ATGAGAGCC
47903318 AGTGTAAGACCATGTTTGGGACATG
1 AGTGTAAGACCATGTTTGGGACATG
47903343 GCATCAGTAA
Statistics
Matches: 64, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
48 13 0.20
49 45 0.70
50 6 0.09
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.30
Consensus pattern (49 bp):
AGTGTAAGACCATGTTTGGGACATGAATCAGCACTTATATATGAGAGCC
Found at i:47903554 original size:20 final size:20
Alignment explanation
Indices: 47903529--47903568 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
47903519 GTAGATGGTA
47903529 ATGAGTAAGTCAAGTTATGC
1 ATGAGTAAGTCAAGTTATGC
47903549 ATGAGTAAGTCAAGTTATGC
1 ATGAGTAAGTCAAGTTATGC
47903569 TTACCTTTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.10, G:0.25, T:0.30
Consensus pattern (20 bp):
ATGAGTAAGTCAAGTTATGC
Found at i:47910597 original size:47 final size:45
Alignment explanation
Indices: 47910522--47910840 Score: 219
Period size: 47 Copynumber: 6.8 Consensus size: 45
47910512 GGGTTATGTA
* * * *
47910522 AGAGCTAATGTAAGACCATGTTTAGGACAAGGCATCGGCATTAAGACG
1 AGAGCTAGTGTAAGA-CATGTCTGGGAC-ATGCATCGGC-TTAAGACG
* * ** *
47910570 AGGGCTAGTGTAAGACATGTCTGGGACATGCATCAGCTATATTATG
1 AGAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCT-TAAGACG
** * * * * *
47910616 ATCGCTAGTGTAAGACATGTTTGAGACATGGCATTGGCGTTGAGATG
1 AGAGCTAGTGTAAGACATGTCTGGGACAT-GCATCGGC-TTAAGACG
* * * * * * *
47910663 AGTGCCAGTGTAAGACATGTTTGGGACATGCCTCGGCCTCGATGATG
1 AGAGCTAGTGTAAGACATGTCTGGGACATGCATCGG-CT-TAAGACG
* * *
47910710 ATAGCCAGTGTAAGACATGTCTGGGACATGCATCAGC-TAAGCAC-
1 AGAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCTTAAG-ACG
* * * *
47910754 TGTGCTAGTGTAAGACATGTCTGGGACATGCATCAGCACTTATATACG
1 AGAGCTAGTGTAAGACATGTCTGGGACATGCATC-G-GCTTA-AGACG
*
47910802 AGAGCTACTGTAAGACCATGTCTGGGACATGGCATCGGC
1 AGAGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGC
47910841 CACGATGATG
Statistics
Matches: 212, Mismatches: 46, Indels: 26
0.75 0.16 0.09
Matches are distributed among these distances:
44 32 0.15
45 2 0.01
46 45 0.21
47 85 0.40
48 28 0.13
49 15 0.07
50 5 0.02
ACGTcount: A:0.28, C:0.18, G:0.29, T:0.25
Consensus pattern (45 bp):
AGAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCTTAAGACG
Found at i:47910822 original size:140 final size:141
Alignment explanation
Indices: 47910576--47910886 Score: 382
Period size: 140 Copynumber: 2.2 Consensus size: 141
47910566 GACGAGGGCT
** *
47910576 AGTGTAAGACATGTCTGGGACATGCATCAGCTATATTATGATCGCTAGTGTAAGACATGTTTGAG
1 AGTGTAAGACATGTCTGGGACATGCATCAGCTATAGCATGATCGCTAGTGTAAGACATGTCTGAG
** * * * * * *
47910641 ACATGGCATTGGCGTTGAGATGAGTGCCAGTGTAAGACATGTTTGGGACAT-GCCTCGGCCTCGA
66 ACATGGCATCAGCCTTGAGATGAGAGCCACTGTAAGACATGTCTGGGACATGGCATCGGCCACGA
47910705 TGATGATAGCC
131 TGATGATAGCC
*
47910716 AGTGTAAGACATGTCTGGGACATGCATCAGCTA-AGCACTG-T-GCTAGTGTAAGACATGTCTGG
1 AGTGTAAGACATGTCTGGGACATGCATCAGCTATAGCA-TGATCGCTAGTGTAAGACATGTCTGA
* *
47910778 GACAT-GCATCAGCACTT-ATATACGAGAGCTACTGTAAGACCATGTCTGGGACATGGCATCGGC
65 GACATGGCATCAGC-CTTGAGAT--GAGAGCCACTGTAAGA-CATGTCTGGGACATGGCATCGGC
47910841 CACGATGATGATAGCC
126 CACGATGATGATAGCC
*
47910857 AGTGTAAGACCTTGTCTGGGACATGGCATC
1 AGTGTAAGA-CATGTCTGGGACAT-GCATC
47910887 GGTAACTTAG
Statistics
Matches: 148, Mismatches: 15, Indels: 13
0.84 0.09 0.07
Matches are distributed among these distances:
137 9 0.06
138 26 0.18
139 16 0.11
140 48 0.32
141 31 0.21
142 13 0.09
143 5 0.03
ACGTcount: A:0.27, C:0.19, G:0.28, T:0.26
Consensus pattern (141 bp):
AGTGTAAGACATGTCTGGGACATGCATCAGCTATAGCATGATCGCTAGTGTAAGACATGTCTGAG
ACATGGCATCAGCCTTGAGATGAGAGCCACTGTAAGACATGTCTGGGACATGGCATCGGCCACGA
TGATGATAGCC
Found at i:47923382 original size:47 final size:47
Alignment explanation
Indices: 47923316--47923446 Score: 172
Period size: 47 Copynumber: 2.8 Consensus size: 47
47923306 GTGCAAATAA
* * *
47923316 TACCTTGATTTGGCAATGGGCCATGATATAGGTATTTTGAGAGGAGT
1 TACCTTGATTTGGCTATGGGCCATGGTATAGGTATTTTGAGAGAAGT
* * * * *
47923363 TACCTTGATTTGGCTATGGGGCATGGTATAGGTACTCTGGGATAAGT
1 TACCTTGATTTGGCTATGGGCCATGGTATAGGTATTTTGAGAGAAGT
* *
47923410 TACCTTGATTTGGCTACGGGTCATGGTATAGGTATTT
1 TACCTTGATTTGGCTATGGGCCATGGTATAGGTATTT
47923447 ATCGATTGTG
Statistics
Matches: 72, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
47 72 1.00
ACGTcount: A:0.22, C:0.12, G:0.30, T:0.36
Consensus pattern (47 bp):
TACCTTGATTTGGCTATGGGCCATGGTATAGGTATTTTGAGAGAAGT
Found at i:47927760 original size:22 final size:22
Alignment explanation
Indices: 47927735--47927776 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
47927725 ACATAAGCAT
47927735 TCAATTATATTAGCACAATAAA
1 TCAATTATATTAGCACAATAAA
* *
47927757 TCAATTATATTGGCATAATA
1 TCAATTATATTAGCACAATA
47927777 CATCTATGGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.45, C:0.12, G:0.07, T:0.36
Consensus pattern (22 bp):
TCAATTATATTAGCACAATAAA
Found at i:47929244 original size:47 final size:46
Alignment explanation
Indices: 47929187--47929412 Score: 162
Period size: 47 Copynumber: 4.8 Consensus size: 46
47929177 ATCGGGTTAT
* *
47929187 GTGAGAGCTAGTGTAAGACCATGTCTAGGACATGGCATCGACATTGA
1 GTGAGAGCCAGTGTAAGA-CATGTCTGGGACATGGCATCGACATTGA
* * *
47929234 GTGAGGGCTAGTGTAAGACATGTTTGGGACAT-GCATCAGCCACATT-A
1 GTGAGAGCCAGTGTAAGACATGTCTGGGACATGGCATC-G--ACATTGA
* * *
47929281 -TGATCA-CCAGTGTAAGACCATGTCTGGGACATGGCATC-AGCGTAGA
1 GTGA-GAGCCAGTGTAAGA-CATGTCTGGGACATGGCATCGA-CATTGA
* * * *
47929327 GATGAGTGCCAGTGTAAGACATGTCTGGGACAT-GCCTCGGCCTCAATGA
1 G-TGAGAGCCAGTGTAAGACATGTCTGGGACATGGCATC-G--ACATTGA
* * *
47929376 -TGATAGCCAGTGTAAGACGTGTTTGGGACAT-GCATCG
1 GTGAGAGCCAGTGTAAGACATGTCTGGGACATGGCATCG
47929413 GCTAAGCGCT
Statistics
Matches: 143, Mismatches: 21, Indels: 31
0.73 0.11 0.16
Matches are distributed among these distances:
44 1 0.01
45 7 0.05
46 32 0.22
47 76 0.53
48 24 0.17
49 3 0.02
ACGTcount: A:0.27, C:0.19, G:0.30, T:0.24
Consensus pattern (46 bp):
GTGAGAGCCAGTGTAAGACATGTCTGGGACATGGCATCGACATTGA
Found at i:47929414 original size:47 final size:47
Alignment explanation
Indices: 47929243--47929556 Score: 252
Period size: 47 Copynumber: 6.6 Consensus size: 47
47929233 AGTGAGGGCT
* *
47929243 AGTGTAAGACATGTTTGGGACATGCATCAGCCAC-ATTATGATCA-CC
1 AGTGTAAGACATGTTTGGGACATGCATCAGCCTCAATGATGAT-AGCC
* *
47929289 AGTGTAAGACCATGTCTGGGACATGGCATCAGCGT-AGA-GATGAGT-GCC
1 AGTGTAAGA-CATGTTTGGGACAT-GCATCAGCCTCA-ATGATGA-TAGCC
* * *
47929337 AGTGTAAGACATGTCTGGGACATGCCTCGGCCTCAATGATGATAGCC
1 AGTGTAAGACATGTTTGGGACATGCATCAGCCTCAATGATGATAGCC
* * * * *
47929384 AGTGTAAGACGTGTTTGGGACATGCATC-GGCT-AAGCGCTG-T-GCT
1 AGTGTAAGACATGTTTGGGACATGCATCAGCCTCAA-TGATGATAGCC
* * * *
47929428 AGTGTAAGACATGTTTGGGACATGTATCAGCACTTATAT-ATGAGAGCT
1 AGTGTAAGACATGTTTGGGACATGCATCAGC-CTCA-ATGATGATAGCC
* * * * *
47929476 AGTGTAAGACCATGTCTGGGACATAGAATCGGCCTCGATAATGATAGCC
1 AGTGTAAGA-CATGTTTGGGACAT-GCATCAGCCTCAATGATGATAGCC
*
47929525 AGTGTAAGACCATGTTTAGGACATGGCATCAG
1 AGTGTAAGA-CATGTTTGGGACAT-GCATCAG
47929557 TAACTTAGCC
Statistics
Matches: 217, Mismatches: 32, Indels: 35
0.76 0.11 0.12
Matches are distributed among these distances:
44 28 0.13
45 4 0.02
46 28 0.13
47 62 0.29
48 38 0.18
49 51 0.24
50 6 0.03
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.25
Consensus pattern (47 bp):
AGTGTAAGACATGTTTGGGACATGCATCAGCCTCAATGATGATAGCC
Found at i:47929508 original size:141 final size:141
Alignment explanation
Indices: 47929289--47929554 Score: 351
Period size: 139 Copynumber: 1.9 Consensus size: 141
47929279 TATGATCACC
*
47929289 AGTGTAAGACCATGTCTGGGACATGGCATCAGCGTAGAGATGAGTGCCAGTGTAAGACATGTCTG
1 AGTGTAAGACCATGTCTGGGACATGGCATCAGCGTAGAGATGAGAGCCAGTGTAAGACATGTCTG
** * * *
47929354 GGACATGCCTCGGCCTCAATGATGATAGCCAGTGTAAGA-CGTGTTTGGGACAT-GCATCGGCTA
66 GGACATGAATCGGCCTCAATAATGATAGCCAGTGTAAGACCATGTTTAGGACATGGCATCGGCTA
47929417 AGCGCTGTGCT
131 AGCGCTGTGCT
* * * * * *
47929428 AGTGTAAGA-CATGTTTGGGACAT-GTATCAGCACTTATATATGAGAGCTAGTGTAAGACCATGT
1 AGTGTAAGACCATGTCTGGGACATGGCATCAG--CGTAGAGATGAGAGCCAGTGTAAGA-CATGT
*
47929491 CTGGGACATAGAATCGGCCTCGATAATGATAGCCAGTGTAAGACCATGTTTAGGACATGGCATC
63 CTGGGACAT-GAATCGGCCTCAATAATGATAGCCAGTGTAAGACCATGTTTAGGACATGGCATC
47929555 AGTAACTTAG
Statistics
Matches: 108, Mismatches: 13, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
137 6 0.06
138 13 0.12
139 29 0.27
140 14 0.13
141 29 0.27
142 12 0.11
143 5 0.05
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.25
Consensus pattern (141 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCAGCGTAGAGATGAGAGCCAGTGTAAGACATGTCTG
GGACATGAATCGGCCTCAATAATGATAGCCAGTGTAAGACCATGTTTAGGACATGGCATCGGCTA
AGCGCTGTGCT
Found at i:47936733 original size:47 final size:45
Alignment explanation
Indices: 47936658--47937024 Score: 220
Period size: 47 Copynumber: 7.8 Consensus size: 45
47936648 GGGTTATGTA
* * * *
47936658 AGAGCTAATGTAAGACCATGTTTAGGACATGGCATCGGCATTAAGACG
1 AGAGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGC-TTAAGATG
* * * **
47936706 AGGGCTAGTGTAAGACATGTATGGGACATGCATCAGCTATATTATG
1 AGAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCT-TAAGATG
** * * * *
47936752 ATCGCTAGTGTAAGACATGTTTGAGACATGGCATTGGCGTAGAGATG
1 AGAGCTAGTGTAAGACATGTCTGGGACAT-GCATCGGCTTA-AGATG
* * * * * *
47936799 AGTGCCAGTGTAAGACATGTTTGGGACATGCCTCGGCCTCGATGATG
1 AGAGCTAGTGTAAGACATGTCTGGGACATGCATCGG-CT-TAAGATG
* * *
47936846 ATAGCCAGTGTAAGACGTGTCTGGGACATGCATCGGC-TAAGCACT-
1 AGAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCTTAAG-A-TG
* * * *
47936891 -GTGCTAGTGTAAGACATGTCTGGGACATGCATCAGCACTTATATACG
1 AGAGCTAGTGTAAGACATGTCTGGGACATGCATC-G-GCTTA-AGATG
** * *
47936938 AGAGCTACAGTAAGACCATGTCTGGGACATGGCCTCGGC-CACGATGATG
1 AGAGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCTTA--A-GATG
* *
47936987 ATAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGG
1 AGAGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGG
47937025 TAACTTAGCC
Statistics
Matches: 248, Mismatches: 54, Indels: 33
0.74 0.16 0.10
Matches are distributed among these distances:
44 31 0.12
45 3 0.01
46 46 0.19
47 86 0.35
48 28 0.11
49 50 0.20
50 4 0.02
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.24
Consensus pattern (45 bp):
AGAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCTTAAGATG
Found at i:47937000 original size:49 final size:47
Alignment explanation
Indices: 47936712--47937024 Score: 225
Period size: 47 Copynumber: 6.6 Consensus size: 47
47936702 GACGAGGGCT
* * * * * * *
47936712 AGTGTAAGACATGTATGGGACATGCATCAGCTA-TATTATGATCGCT
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCACGATGATGATAGCC
* * * *
47936758 AGTGTAAGACATGTTTGAGACATGGCATTGGCGTA-GA-GATGAGT-GCC
1 AGTGTAAGACATGTCTGGGACAT-GCATCGGC-CACGATGATGA-TAGCC
* * *
47936805 AGTGTAAGACATGTTTGGGACATGCCTCGGCCTCGATGATGATAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCACGATGATGATAGCC
* * *
47936852 AGTGTAAGACGTGTCTGGGACATGCATCGGCTA--A-GCACTG-T-GCT
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCACGATG-A-TGATAGCC
* * * *
47936896 AGTGTAAGACATGTCTGGGACATGCATCAG-CACTTAT-ATACGAGAGCT
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCAC-GATGAT--GATAGCC
** *
47936944 ACAGTAAGACCATGTCTGGGACATGGCCTCGGCCACGATGATGATAGCC
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCACGATGATGATAGCC
47936993 AGTGTAAGACCATGTCTGGGACATGGCATCGG
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGG
47937025 TAACTTAGCC
Statistics
Matches: 215, Mismatches: 32, Indels: 37
0.76 0.11 0.13
Matches are distributed among these distances:
43 1 0.00
44 32 0.15
45 4 0.02
46 34 0.16
47 70 0.33
48 14 0.07
49 48 0.22
50 7 0.03
51 5 0.02
ACGTcount: A:0.27, C:0.19, G:0.29, T:0.25
Consensus pattern (47 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCCACGATGATGATAGCC
Found at i:47939681 original size:19 final size:19
Alignment explanation
Indices: 47939650--47939688 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
47939640 ATAAACTCCA
47939650 ATTTAACCCAAAA-TATTT
1 ATTTAACCCAAAATTATTT
*
47939668 ATTTTACCCAAAAATTATTT
1 ATTTAACCC-AAAATTATTT
47939688 A
1 A
47939689 AAACCATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 8 0.44
19 4 0.22
20 6 0.33
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.41
Consensus pattern (19 bp):
ATTTAACCCAAAATTATTT
Found at i:47949041 original size:41 final size:40
Alignment explanation
Indices: 47948944--47949052 Score: 105
Period size: 41 Copynumber: 2.7 Consensus size: 40
47948934 TGATATTTTG
* *
47948944 ATCTGCATTCTGTATCTGATTGGGCTGAGGCTCTAATATAT
1 ATCTG-ATTCTGTATCTGACTGGGCTAAGGCTCTAATATAT
* *
47948985 -TCCTGACTCTGTATCTGAGCTGGGCTAAGGC-CTTAATTTAT
1 AT-CTGATTCTGTATCTGA-CTGGGCTAAGGCTC-TAATATAT
* * *
47949026 ATCTGATTCTATATCTGAATGGACTAA
1 ATCTGATTCTGTATCTGACTGGGCTAA
47949053 CGCCCACACT
Statistics
Matches: 56, Mismatches: 8, Indels: 9
0.77 0.11 0.12
Matches are distributed among these distances:
40 21 0.38
41 34 0.61
42 1 0.02
ACGTcount: A:0.24, C:0.18, G:0.20, T:0.38
Consensus pattern (40 bp):
ATCTGATTCTGTATCTGACTGGGCTAAGGCTCTAATATAT
Found at i:47967272 original size:41 final size:40
Alignment explanation
Indices: 47967215--47967313 Score: 110
Period size: 41 Copynumber: 2.5 Consensus size: 40
47967205 TATTCTGTAT
* * *
47967215 CTGATTGGGCTGAGGCCCTAATATAT-TCCTAACTCTGTAC
1 CTGAGTGGGCTAAGGCCCTAATATATAT-CTAACTCTATAC
* * * *
47967255 CTGAGCTGGGCTAAGGCCCTAATTTATATCTGATTCTATAT
1 CTGAG-TGGGCTAAGGCCCTAATATATATCTAACTCTATAC
47967296 CTGAGTGGGCTAAGGCCC
1 CTGAGTGGGCTAAGGCCC
47967314 ATACTGATTC
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
40 17 0.34
41 32 0.64
42 1 0.02
ACGTcount: A:0.22, C:0.23, G:0.23, T:0.31
Consensus pattern (40 bp):
CTGAGTGGGCTAAGGCCCTAATATATATCTAACTCTATAC
Found at i:47970050 original size:17 final size:17
Alignment explanation
Indices: 47970030--47970064 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
47970020 ATTGAACATA
*
47970030 ATAATAAATATATTCTT
1 ATAATAAAGATATTCTT
47970047 ATAATAAAGATATTCTT
1 ATAATAAAGATATTCTT
47970064 A
1 A
47970065 CTTCTAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.43
Consensus pattern (17 bp):
ATAATAAAGATATTCTT
Found at i:47979398 original size:20 final size:20
Alignment explanation
Indices: 47979365--47979417 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
47979355 AAGCACCATT
*
47979365 AGCT-CTTTAATGCACCAGC
1 AGCTCCTTTATTGCACCAGC
47979384 AGCTCCTTTATTGCACCAGC
1 AGCTCCTTTATTGCACCAGC
*
47979404 AACTCCTTTATTGC
1 AGCTCCTTTATTGC
47979418 TGGTTTTTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 4 0.13
20 27 0.87
ACGTcount: A:0.23, C:0.32, G:0.13, T:0.32
Consensus pattern (20 bp):
AGCTCCTTTATTGCACCAGC
Found at i:47986062 original size:45 final size:46
Alignment explanation
Indices: 47986003--47986089 Score: 115
Period size: 46 Copynumber: 1.9 Consensus size: 46
47985993 TTACGCTAGC
47986003 ACATCTCGTAGCCGACGCATAT-CCAGACATGTCTGACACTGACTA
1 ACATCTCGTAGCCGACGCATATCCCAGACATGTCTGACACTGACTA
* * * *
47986048 ACATCTCG-AGGCCGATGCTTGTCCCAGACATGTCTTACACTG
1 ACATCTCGTA-GCCGACGCATATCCCAGACATGTCTGACACTG
47986090 GCGCACATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
44 1 0.03
45 17 0.47
46 18 0.50
ACGTcount: A:0.25, C:0.31, G:0.20, T:0.24
Consensus pattern (46 bp):
ACATCTCGTAGCCGACGCATATCCCAGACATGTCTGACACTGACTA
Found at i:47991773 original size:45 final size:44
Alignment explanation
Indices: 47991681--47991793 Score: 158
Period size: 45 Copynumber: 2.5 Consensus size: 44
47991671 CATGCCAATA
* *
47991681 CATGTCCCAGACATGTCTTACACTAGCACATCTCGTGGCCGACG
1 CATGTCCCAGACATGTCTTACACTAACACATCTCGAGGCCGACG
*
47991725 CATGT-CCAGACATGT-TTGACACTAACTAACATCTCGAGGCCGATG
1 CATGTCCCAGACATGTCTT-ACACTAAC--ACATCTCGAGGCCGACG
47991770 CATGTCCCAGACATGTCTTACACT
1 CATGTCCCAGACATGTCTTACACT
47991794 GGCACACATA
Statistics
Matches: 61, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
42 2 0.03
43 17 0.28
44 5 0.08
45 20 0.33
46 15 0.25
47 2 0.03
ACGTcount: A:0.26, C:0.31, G:0.19, T:0.25
Consensus pattern (44 bp):
CATGTCCCAGACATGTCTTACACTAACACATCTCGAGGCCGACG
Found at i:47999933 original size:14 final size:15
Alignment explanation
Indices: 47999914--47999950 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
47999904 CGTGTTTTAA
47999914 AAAAATAATAA-AAG
1 AAAAATAATAATAAG
47999928 AAAAATAA-AATAAG
1 AAAAATAATAATAAG
*
47999942 ATAAATAAT
1 AAAAATAAT
47999951 CTAATTTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
13 2 0.10
14 18 0.90
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.19
Consensus pattern (15 bp):
AAAAATAATAATAAG
Found at i:48000313 original size:13 final size:13
Alignment explanation
Indices: 48000295--48000319 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
48000285 TACCCTATTT
48000295 TTGCACGGCCGTA
1 TTGCACGGCCGTA
48000308 TTGCACGGCCGT
1 TTGCACGGCCGT
48000320 GTTTCGTCCG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.32, G:0.32, T:0.24
Consensus pattern (13 bp):
TTGCACGGCCGTA
Found at i:48010543 original size:13 final size:13
Alignment explanation
Indices: 48010525--48010549 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
48010515 GGGCGTTACC
48010525 ACGGCCGTACAAT
1 ACGGCCGTACAAT
48010538 ACGGCCGTACAA
1 ACGGCCGTACAA
48010550 AAATAGGGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.32, G:0.24, T:0.12
Consensus pattern (13 bp):
ACGGCCGTACAAT
Found at i:48013924 original size:29 final size:29
Alignment explanation
Indices: 48013889--48014042 Score: 238
Period size: 29 Copynumber: 5.3 Consensus size: 29
48013879 GAAAGCATGA
* *
48013889 ATATGAATGTGATTTGGGCCTAATGAGCT
1 ATATGAATGTGATTTGGGCCTAATGGGCC
48013918 ATATGAATGTGATTTGGGCCTAATGGGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
48013947 ATATGAATGTGATTTGGGCCTAATGGGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
*
48013976 ATACGAATGTGATTTGGGCCTAATGGGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
* * *
48014005 ATATGAATGAGA-TTGGGCCTAGTGGGCT
1 ATATGAATGTGATTTGGGCCTAATGGGCC
*
48014033 ATATGCATGT
1 ATATGAATGT
48014043 ATGTAGACTT
Statistics
Matches: 116, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
28 22 0.19
29 94 0.81
ACGTcount: A:0.25, C:0.13, G:0.31, T:0.31
Consensus pattern (29 bp):
ATATGAATGTGATTTGGGCCTAATGGGCC
Found at i:48025649 original size:13 final size:15
Alignment explanation
Indices: 48025619--48025650 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
48025609 AAAAGGGAAA
48025619 AAAAGAATTAGTAAT
1 AAAAGAATTAGTAAT
48025634 AAAA-AATTAG-AAT
1 AAAAGAATTAGTAAT
48025647 AAAA
1 AAAA
48025651 TTTAAATTGC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 7 0.41
14 6 0.35
15 4 0.24
ACGTcount: A:0.69, C:0.00, G:0.09, T:0.22
Consensus pattern (15 bp):
AAAAGAATTAGTAAT
Found at i:48028174 original size:28 final size:29
Alignment explanation
Indices: 48028095--48028218 Score: 171
Period size: 28 Copynumber: 4.3 Consensus size: 29
48028085 GAAAGCATGA
*
48028095 ATATGAATGTGATTTGGGCTTAATGGGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
* *
48028124 ATATGAAGGTGATTTGGGTCTAATGGGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
*
48028153 ATA-AAATGTGATTTGGGCCTAATGGGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
* *
48028181 ATATGAATGAGATTT-GGCCTAGTGGGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
*
48028209 ATATGCATGT
1 ATATGAATGT
48028219 ATGTAGACTT
Statistics
Matches: 83, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
28 45 0.54
29 38 0.46
ACGTcount: A:0.26, C:0.12, G:0.31, T:0.31
Consensus pattern (29 bp):
ATATGAATGTGATTTGGGCCTAATGGGCC
Found at i:48028195 original size:57 final size:56
Alignment explanation
Indices: 48028100--48028211 Score: 170
Period size: 57 Copynumber: 2.0 Consensus size: 56
48028090 CATGAATATG
* * *
48028100 AATGTGATTTGGGCTTAATGGGCCATATGAAGGTGATTTGGGTCTAATGGGCCATAA
1 AATGTGATTTGGGCCTAATGGGCCATATGAAGGAGATTT-GGCCTAATGGGCCATAA
* *
48028157 AATGTGATTTGGGCCTAATGGGCCATATGAATGAGATTTGGCCTAGTGGGCCATA
1 AATGTGATTTGGGCCTAATGGGCCATATGAAGGAGATTTGGCCTAATGGGCCATA
48028212 TGCATGTATG
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
56 14 0.28
57 36 0.72
ACGTcount: A:0.26, C:0.12, G:0.31, T:0.30
Consensus pattern (56 bp):
AATGTGATTTGGGCCTAATGGGCCATATGAAGGAGATTTGGCCTAATGGGCCATAA
Found at i:48035805 original size:27 final size:27
Alignment explanation
Indices: 48035743--48035835 Score: 87
Period size: 27 Copynumber: 3.4 Consensus size: 27
48035733 AATACTTTAG
* *
48035743 TTTACCAAATTACTAAAATACCCTCGA
1 TTTACAAAATTACCAAAATACCCTCGA
* ** * *
48035770 CTTGTAAAATTACCAAAGTACCCCCGA
1 TTTACAAAATTACCAAAATACCCTCGA
****
48035797 TTTACAAAATTACCGTTTTACCCTCGA
1 TTTACAAAATTACCAAAATACCCTCGA
48035824 TTTACAAAATTA
1 TTTACAAAATTA
48035836 TTGAAATACC
Statistics
Matches: 51, Mismatches: 15, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
27 51 1.00
ACGTcount: A:0.38, C:0.25, G:0.06, T:0.31
Consensus pattern (27 bp):
TTTACAAAATTACCAAAATACCCTCGA
Found at i:48035861 original size:27 final size:27
Alignment explanation
Indices: 48035839--48035943 Score: 101
Period size: 27 Copynumber: 3.9 Consensus size: 27
48035829 AAAATTATTG
48035839 AAATACCAC-TATAGGATAGAATTACTA
1 AAATACC-CTTATAGGATAGAATTACTA
* *
48035866 AAATACCCTTGTAGGGTAGAATTAC-A
1 AAATACCCTTATAGGATAGAATTACTA
* * * *
48035892 AAATACCCTTGTAGGGTAGAAATACTG
1 AAATACCCTTATAGGATAGAATTACTA
48035919 AAATACCCCTGTA-AGG-TAGAATTAC
1 AAATA-CCCT-TATAGGATAGAATTAC
48035944 CGAGATACCC
Statistics
Matches: 68, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
26 26 0.38
27 34 0.50
28 7 0.10
29 1 0.01
ACGTcount: A:0.41, C:0.16, G:0.17, T:0.26
Consensus pattern (27 bp):
AAATACCCTTATAGGATAGAATTACTA
Found at i:48035901 original size:26 final size:27
Alignment explanation
Indices: 48035850--48035970 Score: 145
Period size: 27 Copynumber: 4.5 Consensus size: 27
48035840 AATACCACTA
*
48035850 TAGGATAGAATTACTAAAATACCCTTG
1 TAGGGTAGAATTACTAAAATACCCTTG
48035877 TAGGGTAGAATTAC-AAAATACCCTTG
1 TAGGGTAGAATTACTAAAATACCCTTG
* * *
48035903 TAGGGTAGAAATACTGAAATACCCCTG
1 TAGGGTAGAATTACTAAAATACCCTTG
* ** *
48035930 TAAGGTAGAATTACCGAGATACCCTTG
1 TAGGGTAGAATTACTAAAATACCCTTG
* *
48035957 TGGGGTAAAATTAC
1 TAGGGTAGAATTAC
48035971 CATTTTGCCC
Statistics
Matches: 81, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
26 25 0.31
27 56 0.69
ACGTcount: A:0.37, C:0.16, G:0.21, T:0.26
Consensus pattern (27 bp):
TAGGGTAGAATTACTAAAATACCCTTG
Found at i:48035923 original size:53 final size:54
Alignment explanation
Indices: 48035850--48035967 Score: 150
Period size: 53 Copynumber: 2.2 Consensus size: 54
48035840 AATACCACTA
* * * *
48035850 TAGGATAGAATTACTAAAATACCCTTGTAGGGTAGAATTA-CAAAATACCCTTG
1 TAGGGTAGAAATACTAAAATACCCCTGTAAGGTAGAATTACCAAAATACCCTTG
* * *
48035903 TAGGGTAGAAATACTGAAATACCCCTGTAAGGTAGAATTACCGAGATACCCTTG
1 TAGGGTAGAAATACTAAAATACCCCTGTAAGGTAGAATTACCAAAATACCCTTG
*
48035957 TGGGGTA-AAAT
1 TAGGGTAGAAAT
48035968 TACCATTTTG
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
53 39 0.70
54 17 0.30
ACGTcount: A:0.37, C:0.15, G:0.21, T:0.26
Consensus pattern (54 bp):
TAGGGTAGAAATACTAAAATACCCCTGTAAGGTAGAATTACCAAAATACCCTTG
Found at i:48036134 original size:16 final size:16
Alignment explanation
Indices: 48036113--48036144 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
48036103 CAAATATGGG
*
48036113 CATGACATTTTGCATA
1 CATGACATGTTGCATA
48036129 CATGACATGTTGCATA
1 CATGACATGTTGCATA
48036145 GGTTGGGATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (16 bp):
CATGACATGTTGCATA
Found at i:48036374 original size:20 final size:20
Alignment explanation
Indices: 48036327--48036374 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
48036317 CAAAGGTTGT
*
48036327 GTGCCGTTATTATGGGCTTC
1 GTGCCGATATTATGGGCTTC
** *
48036347 GTATCGATATTGTGGGCTTC
1 GTGCCGATATTATGGGCTTC
48036367 GTGCCGAT
1 GTGCCGAT
48036375 TATAGACCCG
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.12, C:0.19, G:0.31, T:0.38
Consensus pattern (20 bp):
GTGCCGATATTATGGGCTTC
Found at i:48036617 original size:25 final size:25
Alignment explanation
Indices: 48036589--48036652 Score: 83
Period size: 25 Copynumber: 2.6 Consensus size: 25
48036579 CATTCACATT
*
48036589 CTGATTCTGATTCTGTTACCTGATA
1 CTGATTCTGATTCTGTCACCTGATA
* *
48036614 CTGATTCTAATTCTGTCACCTGATT
1 CTGATTCTGATTCTGTCACCTGATA
* *
48036639 CTCATTTTGATTCT
1 CTGATTCTGATTCT
48036653 AGTTCTGATA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.19, C:0.22, G:0.12, T:0.47
Consensus pattern (25 bp):
CTGATTCTGATTCTGTCACCTGATA
Found at i:48036670 original size:18 final size:17
Alignment explanation
Indices: 48036649--48036682 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
48036639 CTCATTTTGA
48036649 TTCTAGTTCTGATAATGT
1 TTCTAGTTCTG-TAATGT
*
48036667 TTCTTGTTCTGTAATG
1 TTCTAGTTCTGTAATG
48036683 GGCTAAGGCC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.18, C:0.12, G:0.18, T:0.53
Consensus pattern (17 bp):
TTCTAGTTCTGTAATGT
Found at i:48056892 original size:13 final size:13
Alignment explanation
Indices: 48056871--48056910 Score: 71
Period size: 13 Copynumber: 3.1 Consensus size: 13
48056861 AGAGTAATCG
*
48056871 CACATGGGCGTGT
1 CACACGGGCGTGT
48056884 CACACGGGCGTGT
1 CACACGGGCGTGT
48056897 CACACGGGCGTGT
1 CACACGGGCGTGT
48056910 C
1 C
48056911 CTTGTCGAGC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.15, C:0.30, G:0.38, T:0.17
Consensus pattern (13 bp):
CACACGGGCGTGT
Found at i:48058961 original size:21 final size:21
Alignment explanation
Indices: 48058935--48058979 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
48058925 GACACATATG
48058935 ACAAAATACTCAAAGCCCTAT
1 ACAAAATACTCAAAGCCCTAT
48058956 ACAAAATACTCAAAGCCCTAT
1 ACAAAATACTCAAAGCCCTAT
48058977 ACA
1 ACA
48058980 TGCCATTAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.49, C:0.29, G:0.04, T:0.18
Consensus pattern (21 bp):
ACAAAATACTCAAAGCCCTAT
Found at i:48080542 original size:21 final size:20
Alignment explanation
Indices: 48080516--48080562 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 20
48080506 AACTGAATTA
48080516 CCTAACTAGCCTTAACTAACT
1 CCTAACTA-CCTTAACTAACT
48080537 CCT-A--ACCTTAACTAACT
1 CCTAACTACCTTAACTAACT
*
48080554 CTTAACTAC
1 CCTAACTAC
48080563 AACCTACAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 7
0.73 0.03 0.23
Matches are distributed among these distances:
17 14 0.64
18 2 0.09
20 3 0.14
21 3 0.14
ACGTcount: A:0.34, C:0.34, G:0.02, T:0.30
Consensus pattern (20 bp):
CCTAACTACCTTAACTAACT
Found at i:48080547 original size:17 final size:17
Alignment explanation
Indices: 48080525--48080559 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
48080515 ACCTAACTAG
48080525 CCTTAACTAACTCCTAA
1 CCTTAACTAACTCCTAA
*
48080542 CCTTAACTAACTCTTAA
1 CCTTAACTAACTCCTAA
48080559 C
1 C
48080560 TACAACCTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.34, C:0.34, G:0.00, T:0.31
Consensus pattern (17 bp):
CCTTAACTAACTCCTAA
Found at i:48083318 original size:40 final size:40
Alignment explanation
Indices: 48083269--48083450 Score: 287
Period size: 40 Copynumber: 4.6 Consensus size: 40
48083259 TATTCGAATG
* *
48083269 ATATTCGGGCTAAGTCCCGAAGGCTTTTGTGCTAATGACT
1 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTATTGACT
48083309 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTATTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTATTGACT
48083349 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTATTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTATTGACT
* * *
48083389 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTA-TTGACT
*
48083429 ATATCC-GGCTAAATCCCGAAGG
1 ATATCCGGGCTAAGTCCCGAAGG
48083451 TACTTGGGTT
Statistics
Matches: 134, Mismatches: 7, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
39 14 0.10
40 117 0.87
41 3 0.02
ACGTcount: A:0.23, C:0.23, G:0.26, T:0.29
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTATTGACT
Found at i:48099186 original size:25 final size:23
Alignment explanation
Indices: 48099120--48099204 Score: 62
Period size: 25 Copynumber: 3.4 Consensus size: 23
48099110 ATTCATATTC
48099120 AGGAATGCTCATGTGAGCATATAA
1 AGGAA-GCTCATGTGAGCATATAA
* * *
48099144 ACGGGTAGCTCTTTTGAGCCATATAA
1 A--GGAAGCTCATGTGAG-CATATAA
*
48099170 TAGGAAGCTCATGTGAGTCATGTAA
1 -AGGAAGCTCATGTGAG-CATATAA
*
48099195 CGGAAAGCTC
1 AGG-AAGCTC
48099205 TTGCAAGCCA
Statistics
Matches: 47, Mismatches: 9, Indels: 9
0.72 0.14 0.14
Matches are distributed among these distances:
24 3 0.06
25 33 0.70
26 10 0.21
27 1 0.02
ACGTcount: A:0.32, C:0.16, G:0.26, T:0.26
Consensus pattern (23 bp):
AGGAAGCTCATGTGAGCATATAA
Found at i:48099303 original size:76 final size:74
Alignment explanation
Indices: 48099217--48099389 Score: 192
Period size: 74 Copynumber: 2.3 Consensus size: 74
48099207 GCAAGCCAAA
* * * *
48099217 TATCGGGAAGCTTATGCGAGCCAA-TATTG-GATAGCTC-TAAAGAGCCATTAATCGGGAAACTC
1 TATCGGGAAGCTCAGGAGAGCCAATTATTGAGA-AGCTCATAAA-AGCCATAAAT-GGGAAACTC
*
48099279 ATGAGAGAGCCTTT
63 A--AGAGAGCCATT
* *
48099293 TATCGGGAAGCTCCGGAGAGCCAATTATTGAGAAGCTCATACAAGCCATAAATGGGAAACTCAAG
1 TATCGGGAAGCTCAGGAGAGCCAATTATTGAGAAGCTCATAAAAGCCATAAATGGGAAACTCAAG
48099358 AGAGCCATT
66 AGAGCCATT
*
48099367 AATCGGGAAGCTC-GTGAGAGCCA
1 TATCGGGAAGCTCAG-GAGAGCCA
48099390 TATAACGGGA
Statistics
Matches: 85, Mismatches: 8, Indels: 10
0.83 0.08 0.10
Matches are distributed among these distances:
73 1 0.01
74 30 0.35
76 30 0.35
77 19 0.22
78 5 0.06
ACGTcount: A:0.34, C:0.20, G:0.26, T:0.21
Consensus pattern (74 bp):
TATCGGGAAGCTCAGGAGAGCCAATTATTGAGAAGCTCATAAAAGCCATAAATGGGAAACTCAAG
AGAGCCATT
Found at i:48099377 original size:49 final size:52
Alignment explanation
Indices: 48099257--48099412 Score: 128
Period size: 49 Copynumber: 3.1 Consensus size: 52
48099247 ATAGCTCTAA
* * * ** * **
48099257 AGAGCCATTAATCGGGAAACTCATGAGAGAGCCTTTTATCGGGAAGCTCCGG
1 AGAGCCATTAATCGGGAAGCTCATGACAGAGCCATAAATCGGGAAACTCAAG
* *
48099309 AGAGCCAATT-ATTGAGAAGCTCAT-ACA-AGCCATAAAT-GGGAAACTCAAG
1 AGAGCC-ATTAATCGGGAAGCTCATGACAGAGCCATAAATCGGGAAACTCAAG
* * *
48099358 AGAGCCATTAATCGGGAAGCTCGTG--AGAGCCATATAA-CGGGATACTCATG
1 AGAGCCATTAATCGGGAAGCTCATGACAGAGCCATA-AATCGGGAAACTCAAG
48099408 AGAGC
1 AGAGC
48099413 TAAATAACGA
Statistics
Matches: 83, Mismatches: 15, Indels: 14
0.74 0.13 0.12
Matches are distributed among these distances:
48 4 0.05
49 33 0.40
50 24 0.29
51 2 0.02
52 17 0.20
53 3 0.04
ACGTcount: A:0.35, C:0.20, G:0.26, T:0.19
Consensus pattern (52 bp):
AGAGCCATTAATCGGGAAGCTCATGACAGAGCCATAAATCGGGAAACTCAAG
Found at i:48099385 original size:25 final size:24
Alignment explanation
Indices: 48099257--48099586 Score: 178
Period size: 25 Copynumber: 13.2 Consensus size: 24
48099247 ATAGCTCTAA
*
48099257 AGAGCCATTAATCGGGAAACTCATGAG
1 AGAGCCATTAA-CGGGAAGCTCAT--G
* * **
48099284 AGAGCCTTTTATCGGGAAGCTCCGG
1 AGAGCC-ATTAACGGGAAGCTCATG
** *
48099309 AGAGCCAATTATTGAGAAGCTCAT-
1 AGAGCC-ATTAACGGGAAGCTCATG
* * * * *
48099333 ACAAGCCATAAATGGGAAACTCAAG
1 A-GAGCCATTAACGGGAAGCTCATG
*
48099358 AGAGCCATTAATCGGGAAGCTCGTG
1 AGAGCCATTAA-CGGGAAGCTCATG
48099383 AGAGCCATATAACGGGATA-CTCATG
1 AGAGCCAT-TAACGGGA-AGCTCATG
* * * * *
48099408 AGAGCTAAATAACGAGAAGCTCGTA
1 AGAGC-CATTAACGGGAAGCTCATG
* *
48099433 AGAGTCATATAACGGGAAGCTCGTG
1 AGAGCCAT-TAACGGGAAGCTCATG
*
48099458 AGAGCCATATAACGGGATGCTCATG
1 AGAGCCAT-TAACGGGAAGCTCATG
* * * * *
48099483 AGAGCTAAATAACGAGAAGCTCGTA
1 AGAGC-CATTAACGGGAAGCTCATG
* *
48099508 AGAGTCATATAACGGGATGCTCATG
1 AGAGCCAT-TAACGGGAAGCTCATG
* * *
48099533 AAAGCTAAATAACGGGAAGCTCATG
1 AGAGC-CATTAACGGGAAGCTCATG
* * * *
48099558 AAAGCCTATTATCGGGACGCTCATA
1 AGAGCC-ATTAACGGGAAGCTCATG
48099583 AGAG
1 AGAG
48099587 TTGTGGTGTA
Statistics
Matches: 229, Mismatches: 61, Indels: 28
0.72 0.19 0.09
Matches are distributed among these distances:
24 24 0.10
25 180 0.79
26 7 0.03
27 15 0.07
28 3 0.01
ACGTcount: A:0.36, C:0.18, G:0.26, T:0.19
Consensus pattern (24 bp):
AGAGCCATTAACGGGAAGCTCATG
Found at i:48099457 original size:75 final size:75
Alignment explanation
Indices: 48099370--48099558 Score: 308
Period size: 75 Copynumber: 2.5 Consensus size: 75
48099360 AGCCATTAAT
48099370 CGGGAAGCTCGTGAGAGCCATATAACGGGATACTCATGAGAGCTAAATAACGAGAAGCTCGTAAG
1 CGGGAAGCTCGTGAGAGCCATATAACGGGATACTCATGAGAGCTAAATAACGAGAAGCTCGTAAG
48099435 AGTCATATAA
66 AGTCATATAA
*
48099445 CGGGAAGCTCGTGAGAGCCATATAACGGGATGCTCATGAGAGCTAAATAACGAGAAGCTCGTAAG
1 CGGGAAGCTCGTGAGAGCCATATAACGGGATACTCATGAGAGCTAAATAACGAGAAGCTCGTAAG
48099510 AGTCATATAA
66 AGTCATATAA
* * * * *
48099520 CGGGATGCTCATGAAAGCTAAATAACGGGA-AGCTCATGA
1 CGGGAAGCTCGTGAGAGCCATATAACGGGATA-CTCATGA
48099559 AAGCCTATTA
Statistics
Matches: 106, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
75 106 1.00
ACGTcount: A:0.37, C:0.17, G:0.28, T:0.19
Consensus pattern (75 bp):
CGGGAAGCTCGTGAGAGCCATATAACGGGATACTCATGAGAGCTAAATAACGAGAAGCTCGTAAG
AGTCATATAA
Found at i:48106620 original size:8 final size:8
Alignment explanation
Indices: 48106607--48106638 Score: 64
Period size: 8 Copynumber: 4.0 Consensus size: 8
48106597 GCATAGGCAT
48106607 AGGCATAG
1 AGGCATAG
48106615 AGGCATAG
1 AGGCATAG
48106623 AGGCATAG
1 AGGCATAG
48106631 AGGCATAG
1 AGGCATAG
48106639 GCAGGATGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.38, C:0.12, G:0.38, T:0.12
Consensus pattern (8 bp):
AGGCATAG
Found at i:48108893 original size:19 final size:19
Alignment explanation
Indices: 48108869--48108910 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
48108859 TCATATTTAT
48108869 TAAAAA-AATAAAAAAATTG
1 TAAAAATAAT-AAAAAATTG
*
48108888 TAAAAATCATAAAAAATTG
1 TAAAAATAATAAAAAATTG
48108907 TAAA
1 TAAA
48108911 CATTTTTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 19 0.90
20 2 0.10
ACGTcount: A:0.69, C:0.02, G:0.05, T:0.24
Consensus pattern (19 bp):
TAAAAATAATAAAAAATTG
Found at i:48113170 original size:422 final size:423
Alignment explanation
Indices: 48112379--48113202 Score: 1362
Period size: 422 Copynumber: 2.0 Consensus size: 423
48112369 TTTGAGAAGA
*
48112379 GAATGTTTGTTTTCAACCCAAAAGAATAGAAAATTATTTCTAGTTTATGTGATTGATTCAATTTG
1 GAATGTTTGTTTTCAACCCAAAAGAAAAGAAAATTATTTCTAGTTTATGTGATTGATTCAATTTG
* *
48112444 ATCGAGCTTACATTCAAGGCTATTTGTGGAACAAGAATAGCGGAGAAGACCGTTTGGTTGAAAGC
66 ATCGAGCTCACACTCAAGGCTATTTGTGGAACAAGAATAGCGGAGAAGACCGTTTGGTTGAAAGC
* ** * * * *
48112509 CGGGGATGACATGGATTTGTCTATCCAAAATCACTGGTATGATTTCAGCATAGGATTTATTGCTA
131 CGGAGACAACATGCATTCGTCTATCCAAAATCACAGGTACGATTTCAGCATAGGATTTATTGCTA
* * *
48112574 TAAATATCACAAATCAGATTGGTTTTCAAAATTTTTATTTTTCATTGTGCAAGAAAACCATTTTC
196 TAAATATCACAAATCAGATTGGTTTTCAAAATTTTTATTTTCCATTATGAAAGAAAACCATTTTC
* * *
48112639 AAACCGAATTTTTTCCAACATCCCTTTTAACGAAGGTTCAATATCTTCATAAAATTAGTGGAATG
261 AAACCGAATTTTTTCCAACACCCCTTTTAACGAAGGTTCAATATCTTCATAAAAATAGTGGAATA
* *
48112704 AAGTCAAGCCCTTTAAGAAGGAGAGCTCCTCATGTAGGAGAACAAATCTCATCAAAAGATATTAA
326 AAATCAAGCCCTTTAAGAAGGAGAGCTCCTCATGTAGAAGAACAAATCTCATCAAAAGATATTAA
48112769 AATGTTAGTAGACTAAATCTCATAAAAATAGTG
391 AATGTTAGTAGACTAAATCTCATAAAAATAGTG
* * *
48112802 GAATGTTTGTTTTCACCCCAAAAGAAAAGAAAATTATTTCTAGTTTATGTGTTTGATTCGATTTG
1 GAATGTTTGTTTTCAACCCAAAAGAAAAGAAAATTATTTCTAGTTTATGTGATTGATTCAATTTG
*
48112867 ATCGAGCTCACGCTCAAGGCTATTTGTGGAACAAGAATAGCGGAGAAGACCGTTTGGTTGAAAGC
66 ATCGAGCTCACACTCAAGGCTATTTGTGGAACAAGAATAGCGGAGAAGACCGTTTGGTTGAAAGC
* * * * * *
48112932 TGGAGACAATATTCATTCGTTTATCCAAAATCACAGGTACGATTTCAGTATAGGGTTTATTGCTA
131 CGGAGACAACATGCATTCGTCTATCCAAAATCACAGGTACGATTTCAGCATAGGATTTATTGCTA
48112997 -AAATATCACAAATCAGATTGGTTTTCAAAATTTTTATTTTCCATTATGAAAGAAAACCATTTTC
196 TAAATATCACAAATCAGATTGGTTTTCAAAATTTTTATTTTCCATTATGAAAGAAAACCATTTTC
* *
48113061 AAACCGGATTTTTTCCAACACCCCTTTTAACGAAGGTTCAATATCTTCATAAAAATGGTGGAATA
261 AAACCGAATTTTTTCCAACACCCCTTTTAACGAAGGTTCAATATCTTCATAAAAATAGTGGAATA
*
48113126 AAATGAAGCCCTTTAAGAAGGAGAGCTCCTCATGTAGAAGAACAAATCTCATCAAAAGATATTAA
326 AAATCAAGCCCTTTAAGAAGGAGAGCTCCTCATGTAGAAGAACAAATCTCATCAAAAGATATTAA
48113191 AATGTTAGTAGA
391 AATGTTAGTAGA
48113203 ACAAAATAAC
Statistics
Matches: 370, Mismatches: 31, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
422 195 0.53
423 175 0.47
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.32
Consensus pattern (423 bp):
GAATGTTTGTTTTCAACCCAAAAGAAAAGAAAATTATTTCTAGTTTATGTGATTGATTCAATTTG
ATCGAGCTCACACTCAAGGCTATTTGTGGAACAAGAATAGCGGAGAAGACCGTTTGGTTGAAAGC
CGGAGACAACATGCATTCGTCTATCCAAAATCACAGGTACGATTTCAGCATAGGATTTATTGCTA
TAAATATCACAAATCAGATTGGTTTTCAAAATTTTTATTTTCCATTATGAAAGAAAACCATTTTC
AAACCGAATTTTTTCCAACACCCCTTTTAACGAAGGTTCAATATCTTCATAAAAATAGTGGAATA
AAATCAAGCCCTTTAAGAAGGAGAGCTCCTCATGTAGAAGAACAAATCTCATCAAAAGATATTAA
AATGTTAGTAGACTAAATCTCATAAAAATAGTG
Found at i:48114831 original size:27 final size:27
Alignment explanation
Indices: 48114801--48114918 Score: 119
Period size: 27 Copynumber: 4.4 Consensus size: 27
48114791 CTTCATGGAG
* * *
48114801 GCTTCTTTTTCATAGATAGCCACAAAA
1 GCTTCCTTTTCATAGATCGCCACAAAT
* *
48114828 GCTTCCTTTTCATAGCTCGCCTCAAAT
1 GCTTCCTTTTCATAGATCGCCACAAAT
* * *
48114855 GTTTCCTTTTCATAGCTCGCCTCAAAT
1 GCTTCCTTTTCATAGATCGCCACAAAT
* ** *
48114882 GTTTCCTTTTCATAGATCGTTACAAAG
1 GCTTCCTTTTCATAGATCGCCACAAAT
*
48114909 GCTTCTTTTT
1 GCTTCCTTTT
48114919 TCTGGCATGC
Statistics
Matches: 78, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 78 1.00
ACGTcount: A:0.22, C:0.25, G:0.12, T:0.41
Consensus pattern (27 bp):
GCTTCCTTTTCATAGATCGCCACAAAT
Found at i:48129703 original size:9 final size:10
Alignment explanation
Indices: 48129696--48129752 Score: 55
Period size: 11 Copynumber: 5.5 Consensus size: 10
48129686 ACGAGAAAAC
48129696 AAAGAAAAGA
1 AAAGAAAAGA
48129706 AAAGAAAAAGCA
1 AAAG-AAAAG-A
*
48129718 AAAGAAGA-A
1 AAAGAAAAGA
48129727 AAAGAAAATGA
1 AAAGAAAA-GA
48129738 AATA-AAAAGA
1 AA-AGAAAAGA
48129748 AAAGA
1 AAAGA
48129753 GAGGCAAAAG
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
9 9 0.23
10 9 0.23
11 15 0.38
12 6 0.15
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (10 bp):
AAAGAAAAGA
Found at i:48129720 original size:6 final size:5
Alignment explanation
Indices: 48129696--48129752 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
48129686 ACGAGAAAAC
*
48129696 AAAGA AAAGA AAAGAA AAAGCA AAAGA AGA-A AAAGA AAATGA AATA-A
1 AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA AAAGA AAA-GA AA-AGA
48129743 AAAGA AAAGA
1 AAAGA AAAGA
48129753 GAGGCAAAAG
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
4 4 0.09
5 25 0.57
6 14 0.32
7 1 0.02
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (5 bp):
AAAGA
Found at i:48129727 original size:15 final size:14
Alignment explanation
Indices: 48129696--48129752 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
48129686 ACGAGAAAAC
48129696 AAAGAAAAGAAAAGAA
1 AAAGAAAAG--AAGAA
48129712 AAAGCAAAAGAAGAA
1 AAAG-AAAAGAAGAA
*
48129727 AAAGAAAATGAAATAA
1 AAAGAAAA-G-AAGAA
48129743 AAAGAAAAGA
1 AAAGAAAAGA
48129753 GAGGCAAAAG
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
14 5 0.14
15 11 0.30
16 16 0.43
17 5 0.14
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (14 bp):
AAAGAAAAGAAGAA
Found at i:48129893 original size:18 final size:19
Alignment explanation
Indices: 48129857--48129895 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
48129847 TTTGAGAGAG
*
48129857 AAAAAGAATGTGAATAAGA
1 AAAAAGAATGTGAAAAAGA
*
48129876 AAAAAGAGTG-GAAAAAGA
1 AAAAAGAATGTGAAAAAGA
48129894 AA
1 AA
48129896 TTGAGATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.67, C:0.00, G:0.23, T:0.10
Consensus pattern (19 bp):
AAAAAGAATGTGAAAAAGA
Found at i:48131453 original size:25 final size:25
Alignment explanation
Indices: 48131419--48131468 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
48131409 GCAATCTAGT
48131419 TGCTTGAGCTAAACCGAGCTTACTC
1 TGCTTGAGCTAAACCGAGCTTACTC
48131444 TGCTTGAGCTAAACCGAGCTTACTC
1 TGCTTGAGCTAAACCGAGCTTACTC
48131469 CTAGCTTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.28
Consensus pattern (25 bp):
TGCTTGAGCTAAACCGAGCTTACTC
Found at i:48131565 original size:30 final size:30
Alignment explanation
Indices: 48131489--48131574 Score: 86
Period size: 30 Copynumber: 2.9 Consensus size: 30
48131479 TTCAACTCAC
* *
48131489 GAGCTAAACCTTAGCTCAACTTCAGCTTAG
1 GAGCTAAACCTTAGCTCAACTTTAGCTAAG
* * *
48131519 GAGTTTAACCTCAGCTCAACTTTAGCTCAAG
1 GAGCTAAACCTTAGCTCAACTTTAGCT-AAG
* *
48131550 G-GCTAAAGCTTAGCTC-ATTTTAGCT
1 GAGCTAAACCTTAGCTCAACTTTAGCT
48131575 TAAACTCGAT
Statistics
Matches: 45, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
29 8 0.18
30 34 0.76
31 3 0.07
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.30
Consensus pattern (30 bp):
GAGCTAAACCTTAGCTCAACTTTAGCTAAG
Found at i:48142605 original size:14 final size:14
Alignment explanation
Indices: 48142577--48142614 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
48142567 TCGAGATTAC
48142577 AAAACAAC-A-TTT
1 AAAACAACTAGTTT
48142589 AAAACAACTAGTTT
1 AAAACAACTAGTTT
48142603 AAAACAACTAGT
1 AAAACAACTAGT
48142615 GGACAAACGG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 8 0.33
13 1 0.04
14 15 0.62
ACGTcount: A:0.55, C:0.16, G:0.05, T:0.24
Consensus pattern (14 bp):
AAAACAACTAGTTT
Found at i:48145275 original size:37 final size:37
Alignment explanation
Indices: 48145234--48145306 Score: 110
Period size: 37 Copynumber: 2.0 Consensus size: 37
48145224 CTAAAAAGAC
*
48145234 AAAAGACGAAGATGAACAGTAATGATTCTCTGCAAAG
1 AAAAGACGAAGATGAACAATAATGATTCTCTGCAAAG
* * *
48145271 AAAAGATGGAGATGAACAATAATGATTCTTTGCAAA
1 AAAAGACGAAGATGAACAATAATGATTCTCTGCAAA
48145307 AATTCTTCCA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.47, C:0.11, G:0.21, T:0.22
Consensus pattern (37 bp):
AAAAGACGAAGATGAACAATAATGATTCTCTGCAAAG
Found at i:48145675 original size:23 final size:23
Alignment explanation
Indices: 48145622--48145677 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
48145612 TTTGTTTTCA
48145622 AAAATTTAAA-TTCAAAACAATT
1 AAAATTTAAATTTCAAAACAATT
* *
48145644 CAAATTTAAATTTTCAAAA-ATTT
1 AAAATTTAAA-TTTCAAAACAATT
48145667 AAAATTTAAAT
1 AAAATTTAAAT
48145678 CCATTTGTCC
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
22 10 0.34
23 12 0.41
24 7 0.24
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (23 bp):
AAAATTTAAATTTCAAAACAATT
Found at i:48149085 original size:15 final size:15
Alignment explanation
Indices: 48149065--48149121 Score: 59
Period size: 15 Copynumber: 3.9 Consensus size: 15
48149055 AAAAGCGTTT
48149065 TTTAATATTTAAATA
1 TTTAATATTTAAATA
48149080 TTTAATATTATAAAT-
1 TTTAATATT-TAAATA
*
48149095 TTCT-ATTTTTAAA-A
1 TT-TAATATTTAAATA
48149109 TTTAA-ATTTAAAT
1 TTTAATATTTAAAT
48149122 TTTTTATTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 11
0.73 0.04 0.23
Matches are distributed among these distances:
13 7 0.20
14 7 0.20
15 15 0.43
16 6 0.17
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (15 bp):
TTTAATATTTAAATA
Found at i:48149127 original size:22 final size:21
Alignment explanation
Indices: 48149065--48149125 Score: 68
Period size: 22 Copynumber: 2.8 Consensus size: 21
48149055 AAAAGCGTTT
* *
48149065 TTTAATATTTAAATATTTAATA
1 TTTAA-ATTTAAATTTTTAAAA
**
48149087 TTATAAATTTCTATTTTTAAAA
1 TT-TAAATTTAAATTTTTAAAA
48149109 TTTAAATTTAAATTTTT
1 TTTAAATTTAAATTTTT
48149126 TATTTTCAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
21 13 0.41
22 16 0.50
23 3 0.09
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (21 bp):
TTTAAATTTAAATTTTTAAAA
Found at i:48149538 original size:18 final size:18
Alignment explanation
Indices: 48149515--48149553 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
48149505 TATAATTTTA
*
48149515 AAATATA-TATAATACATC
1 AAATATACTA-AAAACATC
48149533 AAATATACTAAAAACATC
1 AAATATACTAAAAACATC
48149551 AAA
1 AAA
48149554 ATAAATATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 17 0.89
19 2 0.11
ACGTcount: A:0.62, C:0.13, G:0.00, T:0.26
Consensus pattern (18 bp):
AAATATACTAAAAACATC
Found at i:48149587 original size:22 final size:22
Alignment explanation
Indices: 48149562--48149630 Score: 81
Period size: 22 Copynumber: 3.2 Consensus size: 22
48149552 AAATAAATAT
48149562 TTTTCAACAAATTGAAAATAAA
1 TTTTCAACAAATTGAAAATAAA
* *
48149584 TTTT-AAAAAATATGTAAAT--A
1 TTTTCAACAAAT-TGAAAATAAA
48149604 TTTTCCAACAAATTGAAAATAAA
1 TTTT-CAACAAATTGAAAATAAA
48149627 TTTT
1 TTTT
48149631 AAAAAATATT
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
20 5 0.13
21 12 0.32
22 16 0.42
23 5 0.13
ACGTcount: A:0.51, C:0.07, G:0.04, T:0.38
Consensus pattern (22 bp):
TTTTCAACAAATTGAAAATAAA
Found at i:48149603 original size:43 final size:43
Alignment explanation
Indices: 48149555--48149639 Score: 161
Period size: 43 Copynumber: 2.0 Consensus size: 43
48149545 AACATCAAAA
*
48149555 TAAATATTTTTCAACAAATTGAAAATAAATTTTAAAAAATATG
1 TAAATATTTTCCAACAAATTGAAAATAAATTTTAAAAAATATG
48149598 TAAATATTTTCCAACAAATTGAAAATAAATTTTAAAAAATAT
1 TAAATATTTTCCAACAAATTGAAAATAAATTTTAAAAAATAT
48149640 TTATACTTAA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.54, C:0.06, G:0.04, T:0.36
Consensus pattern (43 bp):
TAAATATTTTCCAACAAATTGAAAATAAATTTTAAAAAATATG
Found at i:48150571 original size:19 final size:20
Alignment explanation
Indices: 48150530--48150574 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
48150520 AAAATTTTAG
48150530 AAAAT-TAAAAAAATCATTC
1 AAAATATAAAAAAATCATTC
* *
48150549 AAAATATAAAAATAT-ATTT
1 AAAATATAAAAAAATCATTC
48150568 AAAATAT
1 AAAATAT
48150575 GAAATATTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 15 0.65
20 8 0.35
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.31
Consensus pattern (20 bp):
AAAATATAAAAAAATCATTC
Found at i:48150635 original size:20 final size:19
Alignment explanation
Indices: 48150602--48150645 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
48150592 TTCAAAATTA
48150602 TAAAAATGTAAAAAAATATT
1 TAAAAATGTAAAAAAATA-T
* * *
48150622 TAAAAATTTTAAAATATAT
1 TAAAAATGTAAAAAAATAT
48150641 TAAAA
1 TAAAA
48150646 TCATAAGTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (19 bp):
TAAAAATGTAAAAAAATAT
Found at i:48150775 original size:30 final size:30
Alignment explanation
Indices: 48150741--48150797 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
48150731 TTTTATTTAC
*
48150741 AAATTATTAAATGT-TTTTTATAATTTTAAT
1 AAATT-TTAAATATATTTTTATAATTTTAAT
48150771 AAATTTTAAATATATTTTTATAATTTT
1 AAATTTTAAATATATTTTTATAATTTT
48150798 TACATTTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
29 7 0.28
30 18 0.72
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (30 bp):
AAATTTTAAATATATTTTTATAATTTTAAT
Found at i:48150867 original size:15 final size:16
Alignment explanation
Indices: 48150849--48150886 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
48150839 TTCAATTATT
*
48150849 TTATTTTTGTAAT-TA
1 TTATTTTTATAATGTA
48150864 TTATTTTTATAATGTA
1 TTATTTTTATAATGTA
48150880 -TATTTTT
1 TTATTTTT
48150887 TTTTCTATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 19 0.90
16 2 0.10
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.68
Consensus pattern (16 bp):
TTATTTTTATAATGTA
Found at i:48151127 original size:29 final size:29
Alignment explanation
Indices: 48151074--48151129 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
48151064 AAAAATATAC
* * * *
48151074 TTTAAATACCAAATTGAACCCATAAATTT
1 TTTAAATACCAAAATAAAACAATAAATTT
48151103 TTTAAATACCAAAATAAAACAATAAAT
1 TTTAAATACCAAAATAAAACAATAAAT
48151130 ATACTTCAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.54, C:0.14, G:0.02, T:0.30
Consensus pattern (29 bp):
TTTAAATACCAAAATAAAACAATAAATTT
Found at i:48151457 original size:19 final size:18
Alignment explanation
Indices: 48151432--48151486 Score: 58
Period size: 18 Copynumber: 2.9 Consensus size: 18
48151422 CCGCAACAGT
48151432 AAAAAAAAACACTGAAAAAG
1 AAAAAAAAA-ACT-AAAAAG
*
48151452 AAAAAAAAAACTAAAAAT
1 AAAAAAAAAACTAAAAAG
*
48151470 AAAACTAAAAA-TAAAAA
1 AAAA-AAAAAACTAAAAA
48151487 ATGGGTCATG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
18 15 0.47
19 8 0.25
20 9 0.28
ACGTcount: A:0.80, C:0.07, G:0.04, T:0.09
Consensus pattern (18 bp):
AAAAAAAAAACTAAAAAG
Found at i:48151467 original size:12 final size:12
Alignment explanation
Indices: 48151452--48151486 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
48151442 ACTGAAAAAG
48151452 AAAAAAAAAACT
1 AAAAAAAAAACT
*
48151464 AAAAATAAAACT
1 AAAAAAAAAACT
48151476 AAAAATAAAAA
1 AAAAA-AAAAA
48151487 ATGGGTCATG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
12 16 0.80
13 4 0.20
ACGTcount: A:0.83, C:0.06, G:0.00, T:0.11
Consensus pattern (12 bp):
AAAAAAAAAACT
Done.