Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr2
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: 61750188
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1877335 characters in sequence are not A, C, G, or T
File 149 of 186
Found at i:49262189 original size:22 final size:22
Alignment explanation
Indices: 49262163--49262206 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
49262153 AAAGACCTCC
* * *
49262163 TCTTTCAAATTTTAAAAGTAAA
1 TCTTTAAAAATTTAAAAATAAA
49262185 TCTTTAAAAATTTAAAAATAAA
1 TCTTTAAAAATTTAAAAATAAA
49262207 GTCAAAATAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.52, C:0.07, G:0.02, T:0.39
Consensus pattern (22 bp):
TCTTTAAAAATTTAAAAATAAA
Found at i:49265955 original size:10 final size:9
Alignment explanation
Indices: 49265939--49265963 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
49265929 AATAGGTGTA
49265939 ATTTTTTTT
1 ATTTTTTTT
49265948 ATTTTTTTT
1 ATTTTTTTT
49265957 ATTTTTT
1 ATTTTTT
49265964 ATGATTACAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (9 bp):
ATTTTTTTT
Found at i:49268979 original size:18 final size:16
Alignment explanation
Indices: 49268936--49268972 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
49268926 AATAAAATAA
*
49268936 AAATTGAAAATTATAT
1 AAATTAAAAATTATAT
49268952 AAATTAAAAATTATAT
1 AAATTAAAAATTATAT
49268968 AAATT
1 AAATT
49268973 GCAAAAAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (16 bp):
AAATTAAAAATTATAT
Found at i:49269402 original size:18 final size:18
Alignment explanation
Indices: 49269381--49269473 Score: 54
Period size: 17 Copynumber: 5.4 Consensus size: 18
49269371 TATTTTTTGA
49269381 ATATTTTTTTAATTTTAT
1 ATATTTTTTTAATTTTAT
* **
49269399 ATA-TATTTGCATTTT-T
1 ATATTTTTTTAATTTTAT
* *
49269415 ATATTTTTATAGTTATTAT
1 ATATTTTTTTAATT-TTAT
**
49269434 A-ATTTTCATAATTTT-T
1 ATATTTTTTTAATTTTAT
* *
49269450 ATA-ATTTTTATTTTTAT
1 ATATTTTTTTAATTTTAT
49269467 -TATTTTT
1 ATATTTTT
49269474 ATGGTTTTTA
Statistics
Matches: 54, Mismatches: 15, Indels: 13
0.66 0.18 0.16
Matches are distributed among these distances:
16 16 0.30
17 21 0.39
18 15 0.28
19 2 0.04
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.68
Consensus pattern (18 bp):
ATATTTTTTTAATTTTAT
Found at i:49269458 original size:9 final size:9
Alignment explanation
Indices: 49269409--49269460 Score: 70
Period size: 9 Copynumber: 5.9 Consensus size: 9
49269399 ATATATTTGC
49269409 ATTTTTAT-
1 ATTTTTATA
49269417 ATTTTTATA
1 ATTTTTATA
* *
49269426 GTTATTATA
1 ATTTTTATA
*
49269435 ATTTTCATA
1 ATTTTTATA
49269444 ATTTTTATA
1 ATTTTTATA
49269453 ATTTTTAT
1 ATTTTTAT
49269461 TTTTATTATT
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
8 8 0.22
9 29 0.78
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (9 bp):
ATTTTTATA
Found at i:49269481 original size:18 final size:18
Alignment explanation
Indices: 49269410--49269483 Score: 75
Period size: 18 Copynumber: 4.3 Consensus size: 18
49269400 TATATTTGCA
49269410 TTTTTAT-ATTTTTATAG
1 TTTTTATAATTTTTATAG
* * *
49269427 TTATTATAATTTTCATAA
1 TTTTTATAATTTTTATAG
49269445 TTTTTATAA-TTTT-TA-
1 TTTTTATAATTTTTATAG
* *
49269460 TTTTTATTATTTTTATGG
1 TTTTTATAATTTTTATAG
49269478 TTTTTA
1 TTTTTA
49269484 AATGAAAATA
Statistics
Matches: 46, Mismatches: 7, Indels: 7
0.77 0.12 0.12
Matches are distributed among these distances:
15 8 0.17
16 6 0.13
17 10 0.22
18 22 0.48
ACGTcount: A:0.26, C:0.01, G:0.04, T:0.69
Consensus pattern (18 bp):
TTTTTATAATTTTTATAG
Found at i:49269481 original size:24 final size:24
Alignment explanation
Indices: 49269409--49269483 Score: 80
Period size: 24 Copynumber: 3.0 Consensus size: 24
49269399 ATATATTTGC
49269409 ATTTTTA-TATTTTTATAGTTATTAT
1 ATTTTTATTATTTTTATAGTT-TT-T
* * *
49269434 AATTTTCATAATTTTTATAATTTTT
1 -ATTTTTATTATTTTTATAGTTTTT
*
49269459 ATTTTTATTATTTTTATGGTTTTT
1 ATTTTTATTATTTTTATAGTTTTT
49269483 A
1 A
49269484 AATGAAAATA
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
24 21 0.51
25 1 0.02
26 8 0.20
27 11 0.27
ACGTcount: A:0.27, C:0.01, G:0.04, T:0.68
Consensus pattern (24 bp):
ATTTTTATTATTTTTATAGTTTTT
Found at i:49274077 original size:15 final size:16
Alignment explanation
Indices: 49274057--49274090 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
49274047 ACTGAAGTTC
*
49274057 AACTTTAGATTTAT-A
1 AACTTTAAATTTATCA
49274072 AACTTTAAATTTATCA
1 AACTTTAAATTTATCA
49274088 AAC
1 AAC
49274091 ACTTCATCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.44, C:0.12, G:0.03, T:0.41
Consensus pattern (16 bp):
AACTTTAAATTTATCA
Found at i:49274558 original size:61 final size:61
Alignment explanation
Indices: 49274458--49274579 Score: 217
Period size: 61 Copynumber: 2.0 Consensus size: 61
49274448 AAATACCCTT
49274458 TCCCCACAAAAATTCCTCCCTTAGACAAAATAAACTTATCTGCCTCAAAAACAAGTTTGAA
1 TCCCCACAAAAATTCCTCCCTTAGACAAAATAAACTTATCTGCCTCAAAAACAAGTTTGAA
* * *
49274519 TCCCTACAAAAATTCCTCCCTTAGACAGAATAAACTTATCTGTCTCAAAAACAAGTTTGAA
1 TCCCCACAAAAATTCCTCCCTTAGACAAAATAAACTTATCTGCCTCAAAAACAAGTTTGAA
49274580 ACCAAATTTA
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
61 58 1.00
ACGTcount: A:0.40, C:0.26, G:0.07, T:0.26
Consensus pattern (61 bp):
TCCCCACAAAAATTCCTCCCTTAGACAAAATAAACTTATCTGCCTCAAAAACAAGTTTGAA
Found at i:49277132 original size:47 final size:47
Alignment explanation
Indices: 49277017--49277148 Score: 169
Period size: 46 Copynumber: 2.8 Consensus size: 47
49277007 TAATCTCACA
* * *
49277017 CATAATGAACTTGAAACGCAACTTAACGAGCTCGGGTG-TTCGCATC
1 CATAATGAACTTGGAACGCAACTTAACGAGTTCGGATGCTTCGCATC
* * *
49277063 CATAATGAACTCGGAACACAACTCAACGAGTTCGGATGCTT-GCATC
1 CATAATGAACTTGGAACGCAACTTAACGAGTTCGGATGCTTCGCATC
* *
49277109 CATAGGTGAACTTGGAACGCAACTTAACGAGTTCGAATGC
1 CATA-ATGAACTTGGAACGCAACTTAACGAGTTCGGATGC
49277149 CTCATAATTC
Statistics
Matches: 73, Mismatches: 11, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
46 41 0.56
47 32 0.44
ACGTcount: A:0.32, C:0.23, G:0.22, T:0.23
Consensus pattern (47 bp):
CATAATGAACTTGGAACGCAACTTAACGAGTTCGGATGCTTCGCATC
Found at i:49282033 original size:29 final size:28
Alignment explanation
Indices: 49281997--49282074 Score: 104
Period size: 29 Copynumber: 2.7 Consensus size: 28
49281987 TCATGAGATT
49281997 GGCACTAAGTGTGCGGGTTTAAATTGTACA
1 GGCACTAAGTGTGCGGGTTTAAA--GTACA
*
49282027 -GCACTAAGTGTGCGAGTTTAAAGTACA
1 GGCACTAAGTGTGCGGGTTTAAAGTACA
49282054 TGGCACTAAGTGTGCGTGGTT
1 -GGCACTAAGTGTGCG-GGTT
49282075 GATTATTAAG
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
27 5 0.12
29 35 0.81
30 3 0.07
ACGTcount: A:0.26, C:0.14, G:0.31, T:0.29
Consensus pattern (28 bp):
GGCACTAAGTGTGCGGGTTTAAAGTACA
Found at i:49282292 original size:174 final size:174
Alignment explanation
Indices: 49282027--49282354 Score: 602
Period size: 174 Copynumber: 1.9 Consensus size: 174
49282017 AAATTGTACA
*
49282027 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGTGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
* * *
49282092 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATTAAGGGTGCGACCTTATCGAGTCGA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACCTTACCGAGTCAA
49282157 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
131 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
*
49282201 GCACTAAGTGTGTGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
*
49282266 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACCTTACCGAGTCAA
49282331 TTTTGGACAGCGGAAAAGGTAAGT
131 TTTTGGACAGCGGAAAAGGTAAGT
49282355 ACCTTGAGTT
Statistics
Matches: 148, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
174 148 1.00
ACGTcount: A:0.30, C:0.14, G:0.24, T:0.31
Consensus pattern (174 bp):
GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACCTTACCGAGTCAA
TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
Found at i:49298844 original size:11 final size:11
Alignment explanation
Indices: 49298825--49298853 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
49298815 CAGTTTGTGA
49298825 AAAAT-AAAAT
1 AAAATAAAAAT
49298835 AAAATAAAAAT
1 AAAATAAAAAT
49298846 AAAATAAA
1 AAAATAAA
49298854 GAACACATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 5 0.28
11 13 0.72
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (11 bp):
AAAATAAAAAT
Found at i:49306622 original size:35 final size:35
Alignment explanation
Indices: 49306446--49306623 Score: 180
Period size: 35 Copynumber: 5.1 Consensus size: 35
49306436 CATGGAAAAT
* * * * *
49306446 TTATGACATGTAGGTATGGTGTTATCCATCCCGAG
1 TTATGAAACGTAGGTATGGTATTATCCATACTGAG
* *
49306481 TTATGACACGTAGGTATGGTATTATCCATACTAAG
1 TTATGAAACGTAGGTATGGTATTATCCATACTGAG
* * *
49306516 TTATGATATGTAGGTATGGTATTATCCATATTGAG
1 TTATGAAACGTAGGTATGGTATTATCCATACTGAG
* * *
49306551 CTAT-AATACGTAGGTATGGTATT-TCCTATCCCGAG
1 TTATGAA-ACGTAGGTATGGTATTATCC-ATACTGAG
** *
49306586 TTGCGAAACGTAGGTATGGTATTAACCATACTGAG
1 TTATGAAACGTAGGTATGGTATTATCCATACTGAG
49306621 TTA
1 TTA
49306624 CGAGTCGTGG
Statistics
Matches: 117, Mismatches: 22, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
34 4 0.03
35 109 0.93
36 4 0.03
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.35
Consensus pattern (35 bp):
TTATGAAACGTAGGTATGGTATTATCCATACTGAG
Found at i:49316129 original size:26 final size:26
Alignment explanation
Indices: 49316100--49316208 Score: 182
Period size: 26 Copynumber: 4.2 Consensus size: 26
49316090 TGGTACAAAT
49316100 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
49316126 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
49316152 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
49316178 TAATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
49316204 TGATA
1 TGATA
49316209 GGCATTTCAT
Statistics
Matches: 76, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 76 1.00
ACGTcount: A:0.34, C:0.07, G:0.23, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:49317870 original size:27 final size:26
Alignment explanation
Indices: 49317830--49317970 Score: 183
Period size: 27 Copynumber: 5.2 Consensus size: 26
49317820 AGGAAGCGTC
*
49317830 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCAC-ATTATCTGAT
*
49317857 CTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTCTGCCACAT-TATCTGAT
*
49317884 CTGGTGGCTATGCCACGATTATCTGAT
1 CTGGTGGCTCTGCCAC-ATTATCTGAT
*
49317911 CTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTCTGCCACAT-TATCTGAT
* *
49317938 CTGGTGGCTCTGCCACAATATTTGTAT
1 CTGGTGGCTCTGCCACATTATCTG-AT
49317965 CTGGTG
1 CTGGTG
49317971 ACTTCGTCAC
Statistics
Matches: 101, Mismatches: 9, Indels: 8
0.86 0.08 0.07
Matches are distributed among these distances:
26 9 0.09
27 90 0.89
28 2 0.02
ACGTcount: A:0.17, C:0.23, G:0.24, T:0.35
Consensus pattern (26 bp):
CTGGTGGCTCTGCCACATTATCTGAT
Found at i:49317912 original size:54 final size:53
Alignment explanation
Indices: 49317830--49317970 Score: 228
Period size: 54 Copynumber: 2.6 Consensus size: 53
49317820 AGGAAGCGTC
49317830 CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTATGCCAC-ATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
49317884 CTGGTGGCTATGCCACGATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTATGCCAC-ATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
* * *
49317938 CTGGTGGCTCTGCCACAATATTTGTATCTGGTG
1 CTGGTGGCTATGCCACATTATCTG-ATCTGGTG
49317971 ACTTCGTCAC
Statistics
Matches: 82, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
53 6 0.07
54 76 0.93
ACGTcount: A:0.17, C:0.23, G:0.24, T:0.35
Consensus pattern (53 bp):
CTGGTGGCTATGCCACATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
Found at i:49320571 original size:35 final size:35
Alignment explanation
Indices: 49320531--49320707 Score: 230
Period size: 35 Copynumber: 5.1 Consensus size: 35
49320521 CATGGAAAAA
* *
49320531 TTATGACATGTAGGTATAGTATTATCCATACTGAG
1 TTATGACACGTAGGTATGGTATTATCCATACTGAG
49320566 TTATGACACGTAGGTATGGTATTATCCATACTGAG
1 TTATGACACGTAGGTATGGTATTATCCATACTGAG
* *
49320601 TTATGATACGTAGGTATGGTATTATCCATACTAAG
1 TTATGACACGTAGGTATGGTATTATCCATACTGAG
* * * * *
49320636 CTATAATACGTAGGTATGGCATT-TCCCATACCGAG
1 TTATGACACGTAGGTATGGTATTAT-CCATACTGAG
* * *
49320671 TTGTGAAACGTAGGTATGGTATTAACCATACTGAG
1 TTATGACACGTAGGTATGGTATTATCCATACTGAG
49320706 TT
1 TT
49320708 GTGAATCGTG
Statistics
Matches: 124, Mismatches: 16, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
34 1 0.01
35 123 0.99
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.34
Consensus pattern (35 bp):
TTATGACACGTAGGTATGGTATTATCCATACTGAG
Found at i:49325343 original size:44 final size:45
Alignment explanation
Indices: 49325248--49325381 Score: 144
Period size: 44 Copynumber: 3.0 Consensus size: 45
49325238 ACAGGACAAA
* * *
49325248 ACAGAAATGAGCCGTGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* *
49325294 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
* ** * * *
49325338 ACAGGAATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
49325382 CAGGATATTG
Statistics
Matches: 73, Mismatches: 13, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
44 36 0.49
45 1 0.01
46 36 0.49
ACGTcount: A:0.34, C:0.14, G:0.25, T:0.27
Consensus pattern (45 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:49329438 original size:34 final size:35
Alignment explanation
Indices: 49329394--49329460 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 35
49329384 CAGCAAAATG
* *
49329394 TTTTCCGTAAAATGA-TTTCTGAAAAATGTTTTAC
1 TTTTCCGTAAAATGACTTACTGAAAAATATTTTAC
* *
49329428 TTTTCTGTAAAATGACTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGACTTACTGAAAAATATTTT
49329461 CTGGTGTTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 14 0.50
35 14 0.50
ACGTcount: A:0.33, C:0.10, G:0.12, T:0.45
Consensus pattern (35 bp):
TTTTCCGTAAAATGACTTACTGAAAAATATTTTAC
Found at i:49329447 original size:20 final size:20
Alignment explanation
Indices: 49329409--49329448 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
49329399 CGTAAAATGA
**
49329409 TTTCTGAAAAATGTTTTACT
1 TTTCTGAAAAATGACTTACT
*
49329429 TTTCTGTAAAATGACTTACT
1 TTTCTGAAAAATGACTTACT
49329449 GGAAAATATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.30, C:0.12, G:0.10, T:0.47
Consensus pattern (20 bp):
TTTCTGAAAAATGACTTACT
Found at i:49337179 original size:13 final size:13
Alignment explanation
Indices: 49337161--49337188 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
49337151 TAAGGTGATA
49337161 TGGTTATTAGATG
1 TGGTTATTAGATG
49337174 TGGTTATTAGATG
1 TGGTTATTAGATG
49337187 TG
1 TG
49337189 ACATCTTAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.21, C:0.00, G:0.32, T:0.46
Consensus pattern (13 bp):
TGGTTATTAGATG
Found at i:49338641 original size:21 final size:19
Alignment explanation
Indices: 49338614--49338653 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 19
49338604 CTATTTTTTA
49338614 TAAAAAATATTTAAATATATTT
1 TAAAAAATA--TAAA-ATATTT
49338636 TAAAAAATATAAAATATT
1 TAAAAAATATAAAATATT
49338654 CTAGTATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 5 0.28
20 4 0.22
22 9 0.50
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
TAAAAAATATAAAATATTT
Found at i:49347965 original size:43 final size:42
Alignment explanation
Indices: 49347884--49347965 Score: 119
Period size: 43 Copynumber: 1.9 Consensus size: 42
49347874 TTGTGATTTG
* *
49347884 GGTTGGTTTGGGTTTGAAATTGATTCAGGAATCGATTAAGAA
1 GGTTGGTTTGGGTTAGAAATTGATTCAAGAATCGATTAAGAA
* *
49347926 GGTTGGTTTAGGGTTAGAAATTGATTCAATAATCTATTAA
1 GGTTGGTTT-GGGTTAGAAATTGATTCAAGAATCGATTAA
49347966 CAGGGTATAG
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
42 9 0.26
43 26 0.74
ACGTcount: A:0.30, C:0.05, G:0.27, T:0.38
Consensus pattern (42 bp):
GGTTGGTTTGGGTTAGAAATTGATTCAAGAATCGATTAAGAA
Found at i:49348163 original size:16 final size:16
Alignment explanation
Indices: 49348142--49348172 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
49348132 TTATTTTTTG
49348142 GATTTAGGGTTATTTC
1 GATTTAGGGTTATTTC
49348158 GATTTAGGGTTATTT
1 GATTTAGGGTTATTT
49348173 TGAGTTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.03, G:0.26, T:0.52
Consensus pattern (16 bp):
GATTTAGGGTTATTTC
Found at i:49348202 original size:18 final size:18
Alignment explanation
Indices: 49348179--49348260 Score: 103
Period size: 18 Copynumber: 4.6 Consensus size: 18
49348169 ATTTTGAGTT
49348179 ATTTCGATTTTAATTTTG
1 ATTTCGATTTTAATTTTG
* *
49348197 ATTTCGATTTCAATTTAG
1 ATTTCGATTTTAATTTTG
*
49348215 ATTTAGA-TTTAGATTTTG
1 ATTTCGATTTTA-ATTTTG
*
49348233 ATTTCGATTTTGATTTTG
1 ATTTCGATTTTAATTTTG
*
49348251 ATTTTGATTT
1 ATTTCGATTT
49348261 AGGGTTATTT
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
17 3 0.06
18 48 0.89
19 3 0.06
ACGTcount: A:0.23, C:0.05, G:0.13, T:0.59
Consensus pattern (18 bp):
ATTTCGATTTTAATTTTG
Found at i:49348205 original size:6 final size:6
Alignment explanation
Indices: 49348179--49348260 Score: 83
Period size: 6 Copynumber: 13.7 Consensus size: 6
49348169 ATTTTGAGTT
* * * ** * * *
49348179 ATTTCG ATTTTA ATTTTG ATTTCG ATTTCA ATTTAG ATTTAG ATTTAG
1 ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG
*
49348227 ATTTTG ATTTCG ATTTTG ATTTTG ATTTTG ATTT
1 ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG ATTT
49348261 AGGGTTATTT
Statistics
Matches: 66, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 66 1.00
ACGTcount: A:0.23, C:0.05, G:0.13, T:0.59
Consensus pattern (6 bp):
ATTTTG
Found at i:49348624 original size:62 final size:61
Alignment explanation
Indices: 49348527--49348658 Score: 221
Period size: 62 Copynumber: 2.2 Consensus size: 61
49348517 AAATGTTTGA
*
49348527 TTATTGTCTGCCATGTGCATGAAAAAAATGGTTGTGTTTGTATTAAATTATTTTTGTATTGG
1 TTATTGTCTGCCATGTGCATGAAAAAAATGGTTGTGTTCGTATTAAATTA-TTTTGTATTGG
* *
49348589 TTATTGTCTGCCATGTGCATGACAGAAATGGTTGTGTTCGTATTAAATTATTTTGTATTGG
1 TTATTGTCTGCCATGTGCATGAAAAAAATGGTTGTGTTCGTATTAAATTATTTTGTATTGG
49348650 TTA-TGTCTG
1 TTATTGTCTG
49348659 ATAGAAATGG
Statistics
Matches: 67, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
60 6 0.09
61 14 0.21
62 47 0.70
ACGTcount: A:0.23, C:0.08, G:0.22, T:0.46
Consensus pattern (61 bp):
TTATTGTCTGCCATGTGCATGAAAAAAATGGTTGTGTTCGTATTAAATTATTTTGTATTGG
Found at i:49348782 original size:15 final size:15
Alignment explanation
Indices: 49348762--49348806 Score: 63
Period size: 15 Copynumber: 3.0 Consensus size: 15
49348752 GAAAAAGAAA
49348762 TGTCTGGTAGTGATG
1 TGTCTGGTAGTGATG
*
49348777 TGTCTGGTAATGATG
1 TGTCTGGTAGTGATG
* *
49348792 TTTCTAGTAGTGATG
1 TGTCTGGTAGTGATG
49348807 CATTTGAAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.18, C:0.07, G:0.33, T:0.42
Consensus pattern (15 bp):
TGTCTGGTAGTGATG
Found at i:49351310 original size:21 final size:20
Alignment explanation
Indices: 49351286--49351356 Score: 58
Period size: 21 Copynumber: 3.5 Consensus size: 20
49351276 CAAGTGGTTG
49351286 CCCCAACTCAACAACAGGCTA
1 CCCCAACTC-ACAACAGGCTA
* *
49351307 CCCCAAATCAGCAAGAGAG-TA
1 CCCCAACTCA-CAACAG-GCTA
* *
49351328 CCCTAACT--CAACAGGCTG
1 CCCCAACTCACAACAGGCTA
49351346 CCCCAACTCAC
1 CCCCAACTCAC
49351357 CAAAAAGGTG
Statistics
Matches: 38, Mismatches: 7, Indels: 11
0.68 0.12 0.20
Matches are distributed among these distances:
17 1 0.03
18 13 0.34
20 2 0.05
21 21 0.55
22 1 0.03
ACGTcount: A:0.35, C:0.41, G:0.13, T:0.11
Consensus pattern (20 bp):
CCCCAACTCACAACAGGCTA
Found at i:49357154 original size:21 final size:21
Alignment explanation
Indices: 49357124--49357243 Score: 132
Period size: 21 Copynumber: 5.7 Consensus size: 21
49357114 CGAACACGCC
*
49357124 AACAGAAGCTCAAAAGAGCTT
1 AACAGAAGCTCAAAAGAGCTG
*
49357145 AACGGAAGCTCAAAAGAGCTG
1 AACAGAAGCTCAAAAGAGCTG
* **
49357166 AACAAAAGCTCGTAAGAGCTG
1 AACAGAAGCTCAAAAGAGCTG
* *
49357187 AACAGAAGCTCAAAAGATCTA
1 AACAGAAGCTCAAAAGAGCTG
* ** *
49357208 AACAAAAGCTCGTAAGAGCTA
1 AACAGAAGCTCAAAAGAGCTG
*
49357229 AACAAAAGCTCAAAA
1 AACAGAAGCTCAAAA
49357244 AAATTTGATC
Statistics
Matches: 82, Mismatches: 17, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 82 1.00
ACGTcount: A:0.49, C:0.19, G:0.19, T:0.12
Consensus pattern (21 bp):
AACAGAAGCTCAAAAGAGCTG
Found at i:49357183 original size:42 final size:42
Alignment explanation
Indices: 49357137--49357243 Score: 160
Period size: 42 Copynumber: 2.5 Consensus size: 42
49357127 AGAAGCTCAA
* * *
49357137 AAGAGCTTAACGGAAGCTCAAAAGAGCTGAACAAAAGCTCGT
1 AAGAGCTAAACAGAAGCTCAAAAGAGCTAAACAAAAGCTCGT
* *
49357179 AAGAGCTGAACAGAAGCTCAAAAGATCTAAACAAAAGCTCGT
1 AAGAGCTAAACAGAAGCTCAAAAGAGCTAAACAAAAGCTCGT
*
49357221 AAGAGCTAAACAAAAGCTCAAAA
1 AAGAGCTAAACAGAAGCTCAAAA
49357244 AAATTTGATC
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 59 1.00
ACGTcount: A:0.49, C:0.19, G:0.20, T:0.13
Consensus pattern (42 bp):
AAGAGCTAAACAGAAGCTCAAAAGAGCTAAACAAAAGCTCGT
Found at i:49361559 original size:29 final size:30
Alignment explanation
Indices: 49361503--49361561 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
49361493 TAATACATGT
*
49361503 ATGTATTTACTTATTATTGAAGTAATATTA
1 ATGTATTTACTTATTATTAAAGTAATATTA
* *
49361533 ATGTATTTA-TTATTATTAAATTGATATTA
1 ATGTATTTACTTATTATTAAAGTAATATTA
49361562 TATGGTAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 17 0.65
30 9 0.35
ACGTcount: A:0.37, C:0.02, G:0.08, T:0.53
Consensus pattern (30 bp):
ATGTATTTACTTATTATTAAAGTAATATTA
Found at i:49362363 original size:16 final size:16
Alignment explanation
Indices: 49362342--49362375 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
49362332 ATATATAGTT
49362342 AATTAATT-AAAATATG
1 AATTAATTGAAAA-ATG
49362358 AATTAATTGAAAAATG
1 AATTAATTGAAAAATG
49362374 AA
1 AA
49362376 AAGTGAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.59, C:0.00, G:0.09, T:0.32
Consensus pattern (16 bp):
AATTAATTGAAAAATG
Found at i:49362815 original size:19 final size:19
Alignment explanation
Indices: 49362793--49362844 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 19
49362783 AAATATTGAC
49362793 TGTTACTGAATAATTTAAT
1 TGTTACTGAATAATTTAAT
* *
49362812 TGTTACTGTAT-ATCTAAT
1 TGTTACTGAATAATTTAAT
* *
49362830 TTTTACTAAATAATT
1 TGTTACTGAATAATT
49362845 GACTGTTACT
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
18 14 0.54
19 12 0.46
ACGTcount: A:0.35, C:0.08, G:0.08, T:0.50
Consensus pattern (19 bp):
TGTTACTGAATAATTTAAT
Found at i:49362931 original size:18 final size:18
Alignment explanation
Indices: 49362870--49362933 Score: 74
Period size: 18 Copynumber: 3.6 Consensus size: 18
49362860 ACCGATCAAT
*
49362870 TGATTGATACCGAATAAC
1 TGATTGTTACCGAATAAC
* ** *
49362888 TGATTATTATTGAATAAT
1 TGATTGTTACCGAATAAC
49362906 TGATTGTTACCGAATAAC
1 TGATTGTTACCGAATAAC
*
49362924 TGACTGTTAC
1 TGATTGTTAC
49362934 TAAATAAATA
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (18 bp):
TGATTGTTACCGAATAAC
Found at i:49362940 original size:36 final size:36
Alignment explanation
Indices: 49362867--49362949 Score: 103
Period size: 36 Copynumber: 2.3 Consensus size: 36
49362857 ATAACCGATC
* * * *
49362867 AATTGATTGATACCGAATAACTGATTATTATTGAAT
1 AATTGATTGTTACCGAATAACTGACTATTACTAAAT
*
49362903 AATTGATTGTTACCGAATAACTGACTGTTACTAAAT
1 AATTGATTGTTACCGAATAACTGACTATTACTAAAT
* *
49362939 AAATAATTGTT
1 AATTGATTGTT
49362950 TTGATTGACT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.39
Consensus pattern (36 bp):
AATTGATTGTTACCGAATAACTGACTATTACTAAAT
Found at i:49368141 original size:21 final size:21
Alignment explanation
Indices: 49368115--49368185 Score: 83
Period size: 21 Copynumber: 3.4 Consensus size: 21
49368105 CACGCCAAAA
49368115 AAAGCTCATAAGAGCTGAATG
1 AAAGCTCATAAGAGCTGAATG
*
49368136 AAAGCTCAAAAGAGCTGAAT-
1 AAAGCTCATAAGAGCTGAATG
* *
49368156 AGAAGCTCGTAAAAGCTGAATAG
1 A-AAGCTCATAAGAGCTGAAT-G
49368179 AAA-CTCA
1 AAAGCTCA
49368186 AAACTACTGA
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
20 1 0.02
21 38 0.90
22 2 0.05
23 1 0.02
ACGTcount: A:0.46, C:0.15, G:0.21, T:0.17
Consensus pattern (21 bp):
AAAGCTCATAAGAGCTGAATG
Found at i:49368196 original size:42 final size:42
Alignment explanation
Indices: 49368116--49368206 Score: 105
Period size: 42 Copynumber: 2.2 Consensus size: 42
49368106 ACGCCAAAAA
* *
49368116 AAGCTCATAAGAGCTGAATGAAAGCTCAAAAGAGCTGAATAG
1 AAGCTCATAAAAGCTGAATGAAAGCTCAAAAGAGCTGAACAG
* * *
49368158 AAGCTCGTAAAAGCTGAATAGAAA-CTCAAAACTA-CTGAACAT
1 AAGCTCATAAAAGCTGAAT-GAAAGCTCAAAA-GAGCTGAACAG
49368200 AAGCTCA
1 AAGCTCA
49368207 AAAGAGTTGA
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
42 36 0.88
43 5 0.12
ACGTcount: A:0.46, C:0.18, G:0.19, T:0.18
Consensus pattern (42 bp):
AAGCTCATAAAAGCTGAATGAAAGCTCAAAAGAGCTGAACAG
Found at i:49370360 original size:13 final size:13
Alignment explanation
Indices: 49370342--49370366 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
49370332 TTGCTAAGAG
49370342 ATAATATCCTATA
1 ATAATATCCTATA
49370355 ATAATATCCTAT
1 ATAATATCCTAT
49370367 TAAGAATCAA
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:0.44, C:0.16, G:0.00, T:0.40
Consensus pattern (13 bp):
ATAATATCCTATA
Found at i:49370374 original size:46 final size:46
Alignment explanation
Indices: 49370310--49370411 Score: 159
Period size: 46 Copynumber: 2.2 Consensus size: 46
49370300 TAATATCCTC
* * * * *
49370310 TAATGTCCCATTATGAATCAAATTGCTAAGAGATAATATCCTATAA
1 TAATATCCTATTAAGAATCAAATTGCTAAAAGAAAATATCCTATAA
49370356 TAATATCCTATTAAGAATCAAATTGCTAAAAGAAAATATCCTATAA
1 TAATATCCTATTAAGAATCAAATTGCTAAAAGAAAATATCCTATAA
49370402 TAATATCCTA
1 TAATATCCTA
49370412 ATAGATAACA
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 51 1.00
ACGTcount: A:0.45, C:0.15, G:0.08, T:0.32
Consensus pattern (46 bp):
TAATATCCTATTAAGAATCAAATTGCTAAAAGAAAATATCCTATAA
Found at i:49372183 original size:28 final size:28
Alignment explanation
Indices: 49372143--49372216 Score: 114
Period size: 28 Copynumber: 2.6 Consensus size: 28
49372133 GTTCAAATTG
* *
49372143 TATAGCACTAAGTGTGCGAGTTTGATTA
1 TATAGCACTAAGTGTGCGAGTTCGACTA
49372171 TATAGCACTAAGTGTGCGAGTTCGACTA
1 TATAGCACTAAGTGTGCGAGTTCGACTA
49372199 T-TAAGCACTAAGTGTGCG
1 TAT-AGCACTAAGTGTGCG
49372217 GGCTTATTAT
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
27 1 0.02
28 42 0.98
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.31
Consensus pattern (28 bp):
TATAGCACTAAGTGTGCGAGTTCGACTA
Found at i:49382997 original size:29 final size:32
Alignment explanation
Indices: 49382963--49383022 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 32
49382953 TTTTTGGTTA
49382963 AATTTTGT-TA-TTAATCCTTATA-TTTTATG
1 AATTTTGTATATTTAATCCTTATACTTTTATG
*
49382992 AATTTTGTATATTTAGTCCTTATACTTTTAT
1 AATTTTGTATATTTAATCCTTATACTTTTAT
49383023 TTGTTCAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 8 0.30
30 2 0.07
31 11 0.41
32 6 0.22
ACGTcount: A:0.27, C:0.08, G:0.07, T:0.58
Consensus pattern (32 bp):
AATTTTGTATATTTAATCCTTATACTTTTATG
Found at i:49383066 original size:30 final size:31
Alignment explanation
Indices: 49383003--49383085 Score: 95
Period size: 30 Copynumber: 2.8 Consensus size: 31
49382993 ATTTTGTATA
*
49383003 TTTAGTCCTTATACTTTT---ATTTGTTCAAT
1 TTTAGTCCTTATACTTTTCAAATTGGTT-AAT
49383032 TTTAGTCCTTATACTTTTCAAATTGGTT-AT
1 TTTAGTCCTTATACTTTTCAAATTGGTTAAT
*
49383062 TTTAGTCCCCT-TACTTTTCAAATT
1 TTTAGT-CCTTATACTTTTCAAATT
49383086 TTTAGTTTTA
Statistics
Matches: 48, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
29 18 0.38
30 21 0.44
31 3 0.06
32 6 0.12
ACGTcount: A:0.22, C:0.17, G:0.07, T:0.54
Consensus pattern (31 bp):
TTTAGTCCTTATACTTTTCAAATTGGTTAAT
Found at i:49388524 original size:60 final size:61
Alignment explanation
Indices: 49388420--49388597 Score: 229
Period size: 59 Copynumber: 3.0 Consensus size: 61
49388410 CATTTTGGGG
* * * *
49388420 CCTGAACTTGGCAACTT-TTTCCACATTGGGGCCT-GACTTTTTTTTTTGTTCAAGTTAGGC
1 CCTGAACTTGGCAA-TTATTCCCACATTGGGGCTTAAACTTTTTTTTTTGTCCAAGTTAGGC
* * * * *
49388480 CTTGAACTTGGCAATTATTCCCA-GTTGGGGTTTAAAC-TTCTTTTTTGGCCAAGTTAGGC
1 CCTGAACTTGGCAATTATTCCCACATTGGGGCTTAAACTTTTTTTTTTGTCCAAGTTAGGC
*
49388539 CCTGAACTTGGCAATTATTCCCACATTGGGGCTTGAACTTTTTTTTTTGTCCAAGTTAG
1 CCTGAACTTGGCAATTATTCCCACATTGGGGCTTAAACTTTTTTTTTTGTCCAAGTTAG
49388598 TAAAATCCTA
Statistics
Matches: 99, Mismatches: 15, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
59 50 0.51
60 31 0.31
61 18 0.18
ACGTcount: A:0.19, C:0.20, G:0.20, T:0.40
Consensus pattern (61 bp):
CCTGAACTTGGCAATTATTCCCACATTGGGGCTTAAACTTTTTTTTTTGTCCAAGTTAGGC
Found at i:49388644 original size:30 final size:31
Alignment explanation
Indices: 49388608--49388673 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 31
49388598 TAAAATCCTA
*
49388608 AAGTTTATGCCCCAATAAGGGAACAATTG-C
1 AAGTTTAGGCCCCAATAAGGGAACAATTGCC
* **
49388638 AAGTTTAGGTCCCAATGTGGGAACAATTGCC
1 AAGTTTAGGCCCCAATAAGGGAACAATTGCC
49388669 AAGTT
1 AAGTT
49388674 AAGGGTCTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 25 0.81
31 6 0.19
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.26
Consensus pattern (31 bp):
AAGTTTAGGCCCCAATAAGGGAACAATTGCC
Found at i:49392486 original size:3 final size:3
Alignment explanation
Indices: 49392478--49392502 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
49392468 GTGAGGAAAG
49392478 ATC ATC ATC ATC ATC ATC ATC ATC A
1 ATC ATC ATC ATC ATC ATC ATC ATC A
49392503 GTAAAAGAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.32, G:0.00, T:0.32
Consensus pattern (3 bp):
ATC
Found at i:49396991 original size:34 final size:33
Alignment explanation
Indices: 49396928--49396999 Score: 92
Period size: 34 Copynumber: 2.2 Consensus size: 33
49396918 TTTTGTATTG
* *
49396928 ATTTTTATTTTTTATATTTATGTTATTTTTTCA
1 ATTTTTATTTATTATATTTATCTTATTTTTTCA
* *
49396961 ATTTATTATTTATTATATTTATCCT-TTTTTTCC
1 ATTT-TTATTTATTATATTTATCTTATTTTTTCA
49396994 ATTTTT
1 ATTTTT
49397000 TTATAATTAC
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
32 2 0.06
33 15 0.44
34 17 0.50
ACGTcount: A:0.21, C:0.07, G:0.01, T:0.71
Consensus pattern (33 bp):
ATTTTTATTTATTATATTTATCTTATTTTTTCA
Found at i:49401115 original size:18 final size:18
Alignment explanation
Indices: 49401092--49401139 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
49401082 AGATTTTTAT
49401092 TTATAAATATGATAAATA
1 TTATAAATATGATAAATA
49401110 TTATAAATA--A-AAATA
1 TTATAAATATGATAAATA
49401125 TT-TAAAT-TGATAAAT
1 TTATAAATATGATAAAT
49401140 TCAATCTTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
14 5 0.19
15 8 0.30
16 5 0.19
18 9 0.33
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (18 bp):
TTATAAATATGATAAATA
Found at i:49402393 original size:3 final size:3
Alignment explanation
Indices: 49402372--49402417 Score: 53
Period size: 3 Copynumber: 16.3 Consensus size: 3
49402362 TTCATTTCGG
* *
49402372 GAA GAA -AA GAA GGA GAA GAA GAA -AA GAA G-A GAA GAA GAA GGA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
49402417 G
1 G
49402418 GAGGCGGCAC
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
2 6 0.17
3 30 0.83
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:49402398 original size:8 final size:8
Alignment explanation
Indices: 49402372--49402410 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
49402362 TTCATTTCGG
49402372 GAAGAAAA
1 GAAGAAAA
*
49402380 GAAGGAGAA
1 GAA-GAAAA
49402389 GAAGAAAA
1 GAAGAAAA
*
49402397 GAAGAGAA
1 GAAGAAAA
49402405 GAAGAA
1 GAAGAA
49402411 GGAGAAGGAG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
8 19 0.73
9 7 0.27
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (8 bp):
GAAGAAAA
Found at i:49402404 original size:22 final size:22
Alignment explanation
Indices: 49402373--49402416 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
49402363 TCATTTCGGG
*
49402373 AAGAAAAGAAGGAGAAGAAGAA
1 AAGAAAAGAAGAAGAAGAAGAA
* *
49402395 AAGAAGAGAAGAAGAAGGAGAA
1 AAGAAAAGAAGAAGAAGAAGAA
49402417 GGAGGCGGCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (22 bp):
AAGAAAAGAAGAAGAAGAAGAA
Found at i:49402486 original size:21 final size:20
Alignment explanation
Indices: 49402445--49402489 Score: 56
Period size: 22 Copynumber: 2.2 Consensus size: 20
49402435 GGAGGGAGGG
49402445 AAGA-AAAAAGAAGAAGAAA
1 AAGAGAAAAAGAAGAAGAAA
*
49402464 AAGAGAAAAAGAGGGAAGGAAA
1 AAGAGAAAAAGA-AGAA-GAAA
49402486 AAGA
1 AAGA
49402490 AGGGAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 4 0.18
20 7 0.32
21 3 0.14
22 8 0.36
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (20 bp):
AAGAGAAAAAGAAGAAGAAA
Found at i:49403186 original size:48 final size:50
Alignment explanation
Indices: 49403129--49403224 Score: 124
Period size: 50 Copynumber: 2.0 Consensus size: 50
49403119 AAAATCAGAG
* * *
49403129 TTATTTACT-AAATTAT-TAAAAAAATACTAAAAAAATACATTTTAAATA
1 TTATGTACTAAAATAATATAAAAAAATACGAAAAAAATACATTTTAAATA
* * *
49403177 TTATGTACTAAAATAATATAAAAAAATACGAAAATAGTATATTTTAAA
1 TTATGTACTAAAATAATATAAAAAAATACGAAAAAAATACATTTTAAA
49403225 AAATAAAATT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
48 8 0.20
49 6 0.15
50 26 0.65
ACGTcount: A:0.56, C:0.05, G:0.03, T:0.35
Consensus pattern (50 bp):
TTATGTACTAAAATAATATAAAAAAATACGAAAAAAATACATTTTAAATA
Found at i:49403443 original size:149 final size:149
Alignment explanation
Indices: 49403032--49404166 Score: 1588
Period size: 149 Copynumber: 7.6 Consensus size: 149
49403022 GCGAGTTTTT
* **
49403032 TACTAAAATAATATAAAAAATAAAATACGAAAATAGTATATTTTAAAAAATAAAATAAGAAAATT
1 TACTAAAATAATAT-AAAAATAAAATACGAAAATAATATATTTTAAAAAATAAAATCTGAAAATT
* * * * * * * *
49403097 TAAAAAATACAAATAAAGGGCCAAAATCAGAGTTATTTACTAAATTATTAAAAAAATACTAAAAA
65 AAAAAAATACCAACAAAGTGCCAAAATCAGGGTTATTTACTAAATTATTTAAAAAACACTAAAAT
* *
49403162 AATACATTTTAAATATTATG
130 AATACATTTGAAACATTATG
* *
49403182 TACTAAAATAATAT--AAA-AAAATACGAAAATAGTATATTTTAAAAAATAAAAT-TCAAAAATT
1 TACTAAAATAATATAAAAATAAAATACGAAAATAATATATTTTAAAAAATAAAATCT-GAAAATT
** * * ** *
49403243 TTAAAAATACAAAGAAAAAGCCAAAATCAGGGTTATTTACTAAACTATTTAAAAAACACTAAAAT
65 AAAAAAATACCAACAAAGTGCCAAAATCAGGGTTATTTACTAAATTATTTAAAAAACACTAAAAT
*
49403308 AATACATTTGAAATATTATG
130 AATACATTTGAAACATTATG
* *
49403328 TAATAAAATAATATAAAAAATAAAATACGAAAATAATATATTTTAAAAAATAAATTCTGAAAA-T
1 TACTAAAATAATAT-AAAAATAAAATACGAAAATAATATATTTTAAAAAATAAAATCTGAAAATT
*
49403392 AAAAAAATACCAACTAAGTGCCAAAATCAGGGTTATTTACTAAATTATTTAAAAAACACTAAAAT
65 AAAAAAATACCAACAAAGTGCCAAAATCAGGGTTATTTACTAAATTATTTAAAAAACACTAAAAT
49403457 AATACATTTGAAACATTATG
130 AATACATTTGAAACATTATG
* * *
49403477 TACTAAAATAATATAAAAAAATAAAATATGAAAATAGTATATTTTAAAAACTAAAATCTGAAAA-
1 TACTAAAATAATAT--AAAAATAAAATACGAAAATAATATATTTTAAAAAATAAAATCTGAAAAT
* * * * *
49403541 TAAAAAAATACTAACAAAGTGTCAAAATCAAGGTTATTTACTAAATTATTAAAAAAATACTAAAA
64 TAAAAAAATACCAACAAAGTGCCAAAATCAGGGTTATTTACTAAATTATTTAAAAAACACTAAAA
*
49403606 TAATACATTTGAAACATTATA
129 TAATACATTTGAAACATTATG
* * *
49403627 TACTAAAATAATATAAAAATAAAATACAAAAATAGTACATTTTAAAAAATAAAAT-TCGAAAATT
1 TACTAAAATAATATAAAAATAAAATACGAAAATAATATATTTTAAAAAATAAAATCT-GAAAATT
* * * * * *
49403691 TAAAAAATACAAACAAAGGGCGAAAATCAGGGTAATTTACTAAATTATTAAAAAAACACTAAAAT
65 AAAAAAATACCAACAAAGTGCCAAAATCAGGGTTATTTACTAAATTATTTAAAAAACACTAAAAT
49403756 AATACATTTGAAACATTATG
130 AATACATTTGAAACATTATG
*
49403776 TACTAAAATAATATAAAAATAAAATACGAAAATAATATATTTTAAAAAATAAATTCTGAAAA-TA
1 TACTAAAATAATATAAAAATAAAATACGAAAATAATATATTTTAAAAAATAAAATCTGAAAATTA
*
49403840 AAAAAATACCAACTAAGTGCCAAAATCAGGGTTATTTACTAAATTATTTAAAAAACACTAAAATA
66 AAAAAATACCAACAAAGTGCCAAAATCAGGGTTATTTACTAAATTATTTAAAAAACACTAAAATA
49403905 ATACATTTGAAACATTATG
131 ATACATTTGAAACATTATG
* ** **
49403924 TACTAAAATAATATAAAAATAAAATACAAAAATAATATATTTTAAAAAATAAAATCCAAAAACAA
1 TACTAAAATAATATAAAAATAAAATACGAAAATAATATATTTTAAAAAATAAAATCTGAAAATTA
* * *
49403989 AAAAAATACCAACAAAGTACCAAAATCAGGGTTATTTATTAAATTAATATAAAAAACACTAAAAT
66 AAAAAATACCAACAAAGTGCCAAAATCAGGGTTATTTACTAAATT-ATTTAAAAAACACTAAAAT
*
49404054 AATACA-TT-ACAATATTATG
130 AATACATTTGA-AACATTATG
*
49404073 TACTAAAATAATATAAAAAATAAAATACGAAAATAATATATTTTAAAAAATAAAATCTGAAAATA
1 TACTAAAATAATAT-AAAAATAAAATACGAAAATAATATATTTTAAAAAATAAAATCTGAAAATT
* * *
49404138 AAAAAAATACCAATAGAGGGCCAAAATCA
65 AAAAAAATACCAACAAAGTGCCAAAATCA
49404167 CCGAACAAAA
Statistics
Matches: 892, Mismatches: 79, Indels: 28
0.89 0.08 0.03
Matches are distributed among these distances:
146 129 0.14
147 4 0.00
148 180 0.20
149 293 0.33
150 285 0.32
151 1 0.00
ACGTcount: A:0.58, C:0.08, G:0.06, T:0.28
Consensus pattern (149 bp):
TACTAAAATAATATAAAAATAAAATACGAAAATAATATATTTTAAAAAATAAAATCTGAAAATTA
AAAAAATACCAACAAAGTGCCAAAATCAGGGTTATTTACTAAATTATTTAAAAAACACTAAAATA
ATACATTTGAAACATTATG
Found at i:49403899 original size:447 final size:447
Alignment explanation
Indices: 49403032--49404166 Score: 1750
Period size: 447 Copynumber: 2.5 Consensus size: 447
49403022 GCGAGTTTTT
* *
49403032 TACTAAAATAATATAAAAAATAAAATACGAAAATAGTATATTTTAAAAAATAAAATAAGAAAATT
1 TACTAAAATAATATAAAAAATAAAATACGAAAATAGTATATTTTAAAAAATAAAATCAGAAAACT
* * *
49403097 TAAAAAATACAAATAAAGGGCCAAAATC-AGAGTTATTTACTAAATTATTAAAAAAATACTAAAA
66 AAAAAAATACAAACAAAGTGCCAAAATCAAG-GTTATTTACTAAATTATTAAAAAAATACTAAAA
*
49403161 AAATACATTTTAAATATTATGTACTAAAATAATAT--AAA-AAAATACGAAAATAGTATATTTTA
130 TAATACA-TTTAAATATTATGTACTAAAATAATATAAAAATAAAATACGAAAATAGTATATTTTA
* * * ** *
49403223 AAAAATAAAATTCAAAAATTTTAAAAATACAAAGAAAAAGCCAAAATCAGGGTTATTTACTAAAC
194 AAAAATAAAATTCGAAAATTTAAAAAATACAAACAAAGGGCCAAAATCAGGGTAATTTACTAAAC
* *
49403288 TATTTAAAAAACACTAAAATAATACATTTGAAATATTATGTAATAAAATAATATAAAAAATAAAA
259 TATTAAAAAAACACTAAAATAATACATTTGAAACATTATGTAATAAAATAATATAAAAAATAAAA
49403353 TACGAAAATAATATATTTTAAAAAATAAATTCTGAAAATAAAAAAATACCAACTAAGTGCCAAAA
324 TACGAAAATAATATATTTTAAAAAATAAATTCTGAAAATAAAAAAATACCAACTAAGTGCCAAAA
49403418 TCAGGGTTATTTACTAAATTATTTAAAAAACACTAAAATAATACATTTGAAACATTATG
389 TCAGGGTTATTTACTAAATTATTTAAAAAACACTAAAATAATACATTTGAAACATTATG
* * *
49403477 TACTAAAATAATATAAAAAAATAAAATATGAAAATAGTATATTTTAAAAACTAAAATCTGAAAA-
1 TACTAAAATAATAT-AAAAAATAAAATACGAAAATAGTATATTTTAAAAAATAAAATCAGAAAAC
* *
49403541 TAAAAAAATACTAACAAAGTGTCAAAATCAAGGTTATTTACTAAATTATTAAAAAAATACTAAAA
65 TAAAAAAATACAAACAAAGTGCCAAAATCAAGGTTATTTACTAAATTATTAAAAAAATACTAAAA
* * * *
49403606 TAATACATTTGAAACATTATATACTAAAATAATATAAAAATAAAATACAAAAATAGTACATTTTA
130 TAATACATTT-AAATATTATGTACTAAAATAATATAAAAATAAAATACGAAAATAGTATATTTTA
* *
49403671 AAAAATAAAATTCGAAAATTTAAAAAATACAAACAAAGGGCGAAAATCAGGGTAATTTACTAAAT
194 AAAAATAAAATTCGAAAATTTAAAAAATACAAACAAAGGGCCAAAATCAGGGTAATTTACTAAAC
*
49403736 TATTAAAAAAACACTAAAATAATACATTTGAAACATTATGTACTAAAATAATAT-AAAAATAAAA
259 TATTAAAAAAACACTAAAATAATACATTTGAAACATTATGTAATAAAATAATATAAAAAATAAAA
49403800 TACGAAAATAATATATTTTAAAAAATAAATTCTGAAAATAAAAAAATACCAACTAAGTGCCAAAA
324 TACGAAAATAATATATTTTAAAAAATAAATTCTGAAAATAAAAAAATACCAACTAAGTGCCAAAA
49403865 TCAGGGTTATTTACTAAATTATTTAAAAAACACTAAAATAATACATTTGAAACATTATG
389 TCAGGGTTATTTACTAAATTATTTAAAAAACACTAAAATAATACATTTGAAACATTATG
* *
49403924 TACTAAAATAATAT-AAAAATAAAATACAAAAATAATATATTTTAAAAAATAAAATCCA-AAAAC
1 TACTAAAATAATATAAAAAATAAAATACGAAAATAGTATATTTTAAAAAATAAAAT-CAGAAAAC
* * * * * * *
49403987 AAAAAAAATACCAACAAAGTACCAAAATCAGGGTTATTTATTAAATTAATATAAAAAACACTAAA
65 TAAAAAAATACAAACAAAGTGCCAAAATCAAGGTTATTTACTAAATTATTA-AAAAAATACTAAA
*
49404052 ATAATACA-TTACAATATTATGTACTAAAATAATATAAAAAATAAAATACGAAAATAATATATTT
129 ATAATACATTTA-AATATTATGTACTAAAATAATAT-AAAAATAAAATACGAAAATAGTATATTT
** * * *
49404116 TAAAAAATAAAA-TCTGAAAATAAAAAAAATACCAATAGAGGGCCAAAATCA
192 TAAAAAATAAAATTC-GAAAATTTAAAAAATACAAACAAAGGGCCAAAATCA
49404167 CCGAACAAAA
Statistics
Matches: 629, Mismatches: 49, Indels: 22
0.90 0.07 0.03
Matches are distributed among these distances:
444 3 0.00
445 141 0.22
446 117 0.19
447 238 0.38
448 130 0.21
ACGTcount: A:0.58, C:0.08, G:0.06, T:0.28
Consensus pattern (447 bp):
TACTAAAATAATATAAAAAATAAAATACGAAAATAGTATATTTTAAAAAATAAAATCAGAAAACT
AAAAAAATACAAACAAAGTGCCAAAATCAAGGTTATTTACTAAATTATTAAAAAAATACTAAAAT
AATACATTTAAATATTATGTACTAAAATAATATAAAAATAAAATACGAAAATAGTATATTTTAAA
AAATAAAATTCGAAAATTTAAAAAATACAAACAAAGGGCCAAAATCAGGGTAATTTACTAAACTA
TTAAAAAAACACTAAAATAATACATTTGAAACATTATGTAATAAAATAATATAAAAAATAAAATA
CGAAAATAATATATTTTAAAAAATAAATTCTGAAAATAAAAAAATACCAACTAAGTGCCAAAATC
AGGGTTATTTACTAAATTATTTAAAAAACACTAAAATAATACATTTGAAACATTATG
Found at i:49410629 original size:16 final size:16
Alignment explanation
Indices: 49410608--49410682 Score: 64
Period size: 16 Copynumber: 4.5 Consensus size: 16
49410598 ATAGTCTTTT
49410608 ACTAACAATAATAATA
1 ACTAACAATAATAATA
49410624 ACTAACAATAATAACTA
1 ACTAACAATAATAA-TA
* *
49410641 A-AAACAAAAATTAATAAA
1 ACTAACAATAA-TAAT--A
*
49410659 AATCAACAATAATAATA
1 ACT-AACAATAATAATA
49410676 AC-AACAA
1 ACTAACAA
49410683 AAACAGAATA
Statistics
Matches: 48, Mismatches: 5, Indels: 13
0.73 0.08 0.20
Matches are distributed among these distances:
15 5 0.10
16 22 0.46
17 8 0.17
18 2 0.04
19 4 0.08
20 7 0.15
ACGTcount: A:0.67, C:0.13, G:0.00, T:0.20
Consensus pattern (16 bp):
ACTAACAATAATAATA
Found at i:49410635 original size:13 final size:13
Alignment explanation
Indices: 49410617--49410641 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
49410607 TACTAACAAT
49410617 AATAATAACTAAC
1 AATAATAACTAAC
49410630 AATAATAACTAA
1 AATAATAACTAA
49410642 AAACAAAAAT
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:0.64, C:0.12, G:0.00, T:0.24
Consensus pattern (13 bp):
AATAATAACTAAC
Found at i:49410636 original size:39 final size:39
Alignment explanation
Indices: 49410535--49410637 Score: 120
Period size: 39 Copynumber: 2.6 Consensus size: 39
49410525 TAATAAAAAT
* * *
49410535 CAATAATAATAACTAACAATAATTAGGGTTTTTTACTAA
1 CAATAATAATAACTAACAATAATAAGAGTCTTTTACTAA
* * *
49410574 CAATAATAACCAAC-AATC-CTAATAATAGTCTTTTACTAA
1 CAATAATAA-TAACTAA-CAATAATAAGAGTCTTTTACTAA
49410613 CAATAATAATAACTAACAATAATAA
1 CAATAATAATAACTAACAATAATAA
49410638 CTAAAAACAA
Statistics
Matches: 52, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
38 4 0.08
39 44 0.85
40 4 0.08
ACGTcount: A:0.50, C:0.15, G:0.04, T:0.31
Consensus pattern (39 bp):
CAATAATAATAACTAACAATAATAAGAGTCTTTTACTAA
Found at i:49416962 original size:31 final size:31
Alignment explanation
Indices: 49416924--49416988 Score: 130
Period size: 31 Copynumber: 2.1 Consensus size: 31
49416914 GGAGAATATT
49416924 GAAAAAAAATTCGATGATTTTCATTCAAAAA
1 GAAAAAAAATTCGATGATTTTCATTCAAAAA
49416955 GAAAAAAAATTCGATGATTTTCATTCAAAAA
1 GAAAAAAAATTCGATGATTTTCATTCAAAAA
49416986 GAA
1 GAA
49416989 CATTGGCATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.52, C:0.09, G:0.11, T:0.28
Consensus pattern (31 bp):
GAAAAAAAATTCGATGATTTTCATTCAAAAA
Found at i:49421384 original size:5 final size:5
Alignment explanation
Indices: 49421373--49421404 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
49421363 AAAGTTTATG
49421373 TAAAA -AAAA -AAAA TAAAA TAAAA TAAAA TAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAA
49421405 GAACTCACAG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 8 0.31
5 18 0.69
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (5 bp):
TAAAA
Found at i:49427957 original size:11 final size:11
Alignment explanation
Indices: 49427923--49428028 Score: 60
Period size: 11 Copynumber: 9.2 Consensus size: 11
49427913 AATCGTTTGT
49427923 TTATTTA-TTA
1 TTATTTATTTA
49427933 TTATTTAAACTTTA
1 TTATTT--A-TTTA
49427947 TTAGTTT-TTTA
1 TTA-TTTATTTA
*
49427958 TTATTTCTTTA
1 TTATTTATTTA
49427969 TTATTTATTTA
1 TTATTTATTTA
*
49427980 TT-TGCTTATTAA
1 TTAT--TTATTTA
*
49427992 TTCTTTTATTTA
1 TT-ATTTATTTA
49428004 -T-TTTATTTTA
1 TTATTTA-TTTA
49428014 TTTTATTTATTTA
1 --TTATTTATTTA
49428027 TT
1 TT
49428029 TTTGTAATTG
Statistics
Matches: 78, Mismatches: 3, Indels: 29
0.71 0.03 0.26
Matches are distributed among these distances:
9 4 0.05
10 14 0.18
11 26 0.33
12 15 0.19
13 5 0.06
14 11 0.14
15 3 0.04
ACGTcount: A:0.24, C:0.04, G:0.02, T:0.71
Consensus pattern (11 bp):
TTATTTATTTA
Found at i:49427978 original size:4 final size:4
Alignment explanation
Indices: 49427954--49428029 Score: 59
Period size: 4 Copynumber: 18.8 Consensus size: 4
49427944 TTATTAGTTT
* * * *
49427954 TTTA -TTA TTTC TTTA -TTA TTTA TTTA TTTG CTTA TTAA TTCT- TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT-TA TTTA
49428000 TTTA TTTTA TTTTA TTTTA TTTA TTTA TTT
1 TTTA -TTTA -TTTA -TTTA TTTA TTTA TTT
49428030 TTGTAATTGG
Statistics
Matches: 59, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
3 7 0.12
4 38 0.64
5 14 0.24
ACGTcount: A:0.21, C:0.04, G:0.01, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:49428009 original size:9 final size:9
Alignment explanation
Indices: 49427995--49428029 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
49427985 TTATTAATTC
49427995 TTTTATTTA
1 TTTTATTTA
49428004 TTTTATTTTA
1 TTTTA-TTTA
49428014 TTTTATTTA
1 TTTTATTTA
49428023 -TTTATTT
1 TTTTATTT
49428030 TTGTAATTGG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
8 7 0.28
9 9 0.36
10 9 0.36
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTTATTTA
Found at i:49428031 original size:19 final size:19
Alignment explanation
Indices: 49427922--49428031 Score: 66
Period size: 19 Copynumber: 5.7 Consensus size: 19
49427912 AAATCGTTTG
* *
49427922 TTTATTTATTATTATTTAAA
1 TTTATTTATTTTTATTT-TA
*
49427942 CTTTA-TTAGTTTTT-TATTA
1 -TTTATTTA-TTTTTATTTTA
*
49427961 TTTCTTTATTATTTA-TTTA
1 TTTATTTATT-TTTATTTTA
** * *
49427980 TTTGCTTATTAATTCTTTTA
1 TTTATTTATT-TTTATTTTA
49428000 TTTATTT-TATTTTATTTTA
1 TTTATTTAT-TTTTATTTTA
49428019 TTTATTTATTTTT
1 TTTATTTATTTTT
49428032 GTAATTGGCT
Statistics
Matches: 69, Mismatches: 13, Indels: 16
0.70 0.13 0.16
Matches are distributed among these distances:
18 5 0.07
19 40 0.58
20 16 0.23
21 8 0.12
ACGTcount: A:0.23, C:0.04, G:0.02, T:0.72
Consensus pattern (19 bp):
TTTATTTATTTTTATTTTA
Found at i:49428051 original size:5 final size:5
Alignment explanation
Indices: 49427995--49428030 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
49427985 TTATTAATTC
49427995 TTTTA -TTTA TTTTA TTTTA TTTTA -TTTA -TTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
49428031 TGTAATTGGC
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 12 0.41
5 17 0.59
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:49431596 original size:43 final size:43
Alignment explanation
Indices: 49431530--49431641 Score: 179
Period size: 43 Copynumber: 2.6 Consensus size: 43
49431520 CCGGCATTAC
* * * *
49431530 GCCTACTAGGCACGAAGGCCCGAATACAGATCATCGGTATGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGTACGAA
49431573 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGTACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGTACGAA
*
49431616 GCCTGCTAGGCACGAAGGCCCTAATA
1 GCCTGCTAGGCACGAAGGCCCGAATA
49431642 TAATACCAGC
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 64 1.00
ACGTcount: A:0.30, C:0.29, G:0.26, T:0.14
Consensus pattern (43 bp):
GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGTACGAA
Found at i:49431682 original size:38 final size:38
Alignment explanation
Indices: 49431634--49431741 Score: 137
Period size: 38 Copynumber: 2.8 Consensus size: 38
49431624 GGCACGAAGG
* * *
49431634 CCCTAATATAATACCAGCACTAGGCCTGCGGGATTTAT
1 CCCTGATATAATACCAGCACTAAGCCTGCGGGATTTAA
49431672 CCCTGATATAATACCAGCA-TGAAGCCTGCGGGATTTAA
1 CCCTGATATAATACCAGCACT-AAGCCTGCGGGATTTAA
* ** *
49431710 CCCGGATATTTTACCAGCACGAAGCCTGCGGG
1 CCCTGATATAATACCAGCACTAAGCCTGCGGG
49431742 TCTTTAAGCC
Statistics
Matches: 61, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
37 1 0.02
38 60 0.98
ACGTcount: A:0.28, C:0.27, G:0.22, T:0.23
Consensus pattern (38 bp):
CCCTGATATAATACCAGCACTAAGCCTGCGGGATTTAA
Found at i:49438374 original size:62 final size:63
Alignment explanation
Indices: 49438286--49438410 Score: 180
Period size: 62 Copynumber: 2.0 Consensus size: 63
49438276 AAGGATTTTT
* * *
49438286 TGCATGTTGCTCTAAAAAGCTTCTAAATAGTATAAGGACCTGAAACAGGACCACTAGTTAGAA
1 TGCATATTGCTCTAAAAAGCTTCTAAATAGTACAAGGACCTGAAACAGGACCACTAGTCAGAA
* * * *
49438349 TGCATATTGCTCT-GAAAGCTTCTAAATGGTACAAGGACTTGAAACGGGACCACTAGTCAGAA
1 TGCATATTGCTCTAAAAAGCTTCTAAATAGTACAAGGACCTGAAACAGGACCACTAGTCAGAA
49438411 CTAACCAAAT
Statistics
Matches: 55, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
62 43 0.78
63 12 0.22
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.25
Consensus pattern (63 bp):
TGCATATTGCTCTAAAAAGCTTCTAAATAGTACAAGGACCTGAAACAGGACCACTAGTCAGAA
Found at i:49438865 original size:44 final size:44
Alignment explanation
Indices: 49438798--49439661 Score: 335
Period size: 44 Copynumber: 18.9 Consensus size: 44
49438788 CATTATGGCA
**
49438798 AATCTTATCTCCCTGAAAATGCAGTGGAGCAGATTGAAGTCACT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTCACT
* * *
49438842 AATCTTATGC-CCCTGAAGTTGCAGCGG-GATAGATTGAAGTTATCATGGT
1 AATCTTAT-CTCCCTGAAGTTGCAGTGGAG-CAGATTGAAG---TCA--CT
* * * *
49438891 GAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCCACA
1 -AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTCACT
* * * * * *
49438936 AATCCTATAC-CCTTGAAGTTACAATGG-GACGGATTGAAGTTATCACCAC
1 AATCTTAT-CTCCCTGAAGTTGCAGTGGAG-CAGATTGAAG---TCA-C-T
* * * * * *
49438985 AGATCTTATCTCCCTGAAGTTACAGTGGAGTAGATTAAAAATTACA
1 A-ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT-GAAGTCACT
* ** * * * **
49439031 AACCTTATCTTTCTGAAGTTGCAGTAGAGCAGGTTAAAGTTGC-
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTCACT
* * * * * *
49439074 AAGTCTTATCTCCTTGAAGTTGTAGTGAAGCAGACTAAAGAT-AGCG
1 AA-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG-TCA-CT
* * * *
49439120 AATCTTATTTCCCTGAAGTTGCAGTGGAACAGATTGAAGCTATAAATTAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG---T-CA--CT
* * * *
49439170 AGATCTTATCTCTCTGAAGTTGCAATAGAGCATATT-ATAG-CA--
1 A-ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGA-AGTCACT
* * * *
49439212 AA-CTTTATCTCCATGAAGTTGTAGTGGAGCAGGTTGAAGTTA-T
1 AATC-TTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTCACT
** * * **
49439255 AAGTCTTATCTCCCTGAAGTTGCAGTAAAGCAGACTGAAGATAAAG
1 AA-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG-TCACT
* * * * * *
49439301 AATCTTATTTCTCTGAAGTTGCAGTGGAACAAATTGAAGCTATAAATT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG---T-CACT
* * ** *
49439349 AGATATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAACCACA
1 --A-ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTCACT
* * * * *
49439396 AACCTTATCTCCCTAAAGTTGCAGTGGAGCAGGTTAAAAGTTAC-
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT-GAAGTCACT
** *
49439440 AGATCTTATCTCCCTGAAGTTGCAGTGGAATAGATCGAAGAT-AGC-
1 A-ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG-TCA-CT
* * * * *
49439485 AAACTTTATCTCCCTGTAGTTGTAGTGGAGCAGATTGAAAATAGGCTACA
1 AATC-TTATCTCCCTGAAGTTGCAGTGGAGCAGATTG---A-AGTC-ACT
* * *
49439535 AATCTTATCTCCCTGAAGTTGCAGTGGAGAAAATTAAAG-CTAC-
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTC-ACT
* * * *
49439578 ACA-CATTATCTCCCTGAAGTTACAGTGGAGTAAATTGAAGACAC-
1 A-ATC-TTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTCACT
* * * *
49439622 ATATCTTATCTCCCTAAATTTGCAATGGAGTAGATTGAAG
1 A-ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG
49439662 CTACAAGTTT
Statistics
Matches: 622, Mismatches: 136, Indels: 124
0.71 0.15 0.14
Matches are distributed among these distances:
40 1 0.00
41 27 0.04
42 3 0.00
43 8 0.01
44 230 0.37
45 162 0.26
46 7 0.01
47 13 0.02
48 6 0.01
49 35 0.06
50 63 0.10
51 67 0.11
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (44 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTCACT
Found at i:49438896 original size:94 final size:94
Alignment explanation
Indices: 49438747--49439023 Score: 286
Period size: 94 Copynumber: 2.9 Consensus size: 94
49438737 GAGAAACCAT
* * * * * *
49438747 AAATCCAATACCCCTGAGGATGCAGTGGGATGGATTGAAATCATTATGGCAAATCTTATCTCCCT
1 AAATCCTATACCCCTGAAGTTGCAGTGGGATGGATTGAAGTTATCATGGCAAATCTTATCTCCCT
* *
49438812 GAAA-ATGCAGTGGAGCAGATTGAAGTCAC
66 -AAAGATGCAGTGGAGCAGATTAAAGCCAC
* * * * * **
49438841 TAATCTTATGCCCCTGAAGTTGCAGCGGGATAGATTGAAGTTATCATGGTGAATCTTATCTCCCT
1 AAATCCTATACCCCTGAAGTTGCAGTGGGATGGATTGAAGTTATCATGGCAAATCTTATCTCCCT
*
49438906 AAAGTTGCAGTGGAGCAGATTAAAGCCAC
66 AAAGATGCAGTGGAGCAGATTAAAGCCAC
* * * * *** *
49438935 AAATCCTATACCCTTGAAGTTACAATGGGACGGATTGAAGTTATCACCACAGATCTTATCTCCCT
1 AAATCCTATACCCCTGAAGTTGCAGTGGGATGGATTGAAGTTATCATGGCAAATCTTATCTCCCT
* * * *
49439000 GAAGTTACAGTGGAGTAGATTAAA
66 AAAGATGCAGTGGAGCAGATTAAA
49439024 AATTACAAAC
Statistics
Matches: 148, Mismatches: 34, Indels: 2
0.80 0.18 0.01
Matches are distributed among these distances:
93 3 0.02
94 145 0.98
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.27
Consensus pattern (94 bp):
AAATCCTATACCCCTGAAGTTGCAGTGGGATGGATTGAAGTTATCATGGCAAATCTTATCTCCCT
AAAGATGCAGTGGAGCAGATTAAAGCCAC
Found at i:49439187 original size:51 final size:50
Alignment explanation
Indices: 49439119--49439386 Score: 168
Period size: 51 Copynumber: 5.7 Consensus size: 50
49439109 TAAAGATAGC
* *
49439119 GAATCTTATTTCCCTGAAGTTGCAGTGGAACAGATTGAAGCTATAAATTA
1 GAATCTTATCTCTCTGAAGTTGCAGTGGAACAGATTGAAGCTATAAATTA
* * * * *
49439169 TAGATCTTATCTCTCTGAAGTTGCAATAGAGCATATT-ATAGC-----A--A
1 GA-ATCTTATCTCTCTGAAGTTGCAGTGGAACAGATTGA-AGCTATAAATTA
* * * *
49439213 -ACT-TTATCTC-CATGAAGTTGTAGTGGAGCAGGTTGAAG-T-T--A-TA
1 GAATCTTATCTCTC-TGAAGTTGCAGTGGAACAGATTGAAGCTATAAATTA
* * * *
49439256 -AGTCTTATCTCCCTGAAGTTGCAGT-AAAGCAGACTGAAG--AT-AA--A
1 GAATCTTATCTCTCTGAAGTTGCAGTGGAA-CAGATTGAAGCTATAAATTA
* *
49439300 GAATCTTATTTCTCTGAAGTTGCAGTGGAACAAATTGAAGCTATAAATTA
1 GAATCTTATCTCTCTGAAGTTGCAGTGGAACAGATTGAAGCTATAAATTA
*
49439350 GATATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATT
1 GA-ATCTTATCTCTCTGAAGTTGCAGTGGAACAGATT
49439387 AAAACCACAA
Statistics
Matches: 170, Mismatches: 28, Indels: 39
0.72 0.12 0.16
Matches are distributed among these distances:
40 1 0.01
41 26 0.15
42 3 0.02
43 5 0.03
44 29 0.17
45 32 0.19
46 3 0.02
47 2 0.01
48 2 0.01
50 5 0.03
51 62 0.36
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32
Consensus pattern (50 bp):
GAATCTTATCTCTCTGAAGTTGCAGTGGAACAGATTGAAGCTATAAATTA
Found at i:49439261 original size:181 final size:182
Alignment explanation
Indices: 49438985--49439607 Score: 614
Period size: 181 Copynumber: 3.4 Consensus size: 182
49438975 TTATCACCAC
* * * * * * *
49438985 AGATCTTATCTCCCTGAAGTTACAGTGGAGTAGATTAAAAATTACAAACCTTATCTTTC-TGAAG
1 AGATCTTATCTCTCTGAAGTTGCAATAGAGCAGATT-AAAA-CACAAACCTTATC-TCCATGAAG
* * * * *
49439049 TTGCAGTAGAGCAGGTTAAAGTTGCAAGTCTTATCTCCTTGAAGTTGTAGTGAAGCAGACTAAAG
63 TTGCAGTGGAGCAGGTTAAAGTT-AAAGTCTTATCTCCCTGAAGTTGCAGTGAAGCAGACTGAAG
*
49439114 ATAGCGAATCTTATTTCCCTGAAGTTGCAGTGGAACAGATTGAAGCTATAAATTAT
127 ATAGCGAATCTTATTTCCCTGAAGTTGCAGTGGAACAGATTGAAGCTATAAATTAG
* * * *
49439170 AGATCTTATCTCTCTGAAGTTGCAATAGAGCATATT-ATA-GCAAACTTTATCTCCATGAAGTTG
1 AGATCTTATCTCTCTGAAGTTGCAATAGAGCAGATTAAAACACAAACCTTATCTCCATGAAGTTG
* * *
49439233 TAGTGGAGCAGGTTGAAGTTATAAGTCTTATCTCCCTGAAGTTGCAGTAAAGCAGACTGAAGATA
66 CAGTGGAGCAGGTTAAAGTTA-AAGTCTTATCTCCCTGAAGTTGCAGTGAAGCAGACTGAAGATA
** * *
49439298 AAGAATCTTATTTCTCTGAAGTTGCAGTGGAACAAATTGAAGCTATAAATTAG
130 GCGAATCTTATTTCCCTGAAGTTGCAGTGGAACAGATTGAAGCTATAAATTAG
* * * * *
49439351 ATATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAACCACAAACCTTATCTCCCTAAAGTT
1 AGATCTTATCTCTCTGAAGTTGCAATAGAGCAGATTAAAA-CACAAACCTTATCTCCATGAAGTT
* *
49439416 GCAGTGGAGCAGGTTAAAAGTTACAGATCTTATCTCCCTGAAGTTGCAGTGGAA-TAGA-TCGAA
65 GCAGTGGAGCAGGTT-AAAGTTAAAG-TCTTATCTCCCTGAAGTTGCAGT-GAAGCAGACT-GAA
* * * * * * *** *
49439479 GATAGC-AAACTTTATCTCCCTGTAGTTGTAGTGGAGCAGATTGAA--AATAGGCTAC
126 GATAGCGAATC-TTATTTCCCTGAAGTTGCAGTGGAACAGATTGAAGCTATAAATTAG
* * * * * * * * * *
49439534 AAATCTTATCTCCCTGAAGTTGCAGTGGAGAAAATTAAAGCTACACACATTATCTCCCTGAAGTT
1 AGATCTTATCTCTCTGAAGTTGCAATAGAGCAGATTAAAAC-ACAAACCTTATCTCCATGAAGTT
*
49439599 ACAGTGGAG
65 GCAGTGGAG
49439608 TAAATTGAAG
Statistics
Matches: 367, Mismatches: 60, Indels: 24
0.81 0.13 0.05
Matches are distributed among these distances:
180 2 0.01
181 154 0.42
182 3 0.01
183 70 0.19
184 39 0.11
185 97 0.26
186 2 0.01
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.30
Consensus pattern (182 bp):
AGATCTTATCTCTCTGAAGTTGCAATAGAGCAGATTAAAACACAAACCTTATCTCCATGAAGTTG
CAGTGGAGCAGGTTAAAGTTAAAGTCTTATCTCCCTGAAGTTGCAGTGAAGCAGACTGAAGATAG
CGAATCTTATTTCCCTGAAGTTGCAGTGGAACAGATTGAAGCTATAAATTAG
Found at i:49439339 original size:45 final size:50
Alignment explanation
Indices: 49439258--49439379 Score: 139
Period size: 45 Copynumber: 2.5 Consensus size: 50
49439248 AAGTTATAAG
* * *
49439258 TCTTATCTCCCTGAAGTTGCAGT-AAAGCAGACTGAAG-AT-AA-AGA-A
1 TCTTATCTCTCTGAAGTTGCAGTGGAAGCAAACTGAAGCATAAATAGATA
* *
49439303 TCTTATTTCTCTGAAGTTGCAGTGGAA-CAAATTGAAGCTATAAATTAGATA
1 TCTTATCTCTCTGAAGTTGCAGTGGAAGCAAACTGAAGC-ATAAA-TAGATA
49439354 TCTTATCTCTCTGAAGTTGCAGTGGA
1 TCTTATCTCTCTGAAGTTGCAGTGGA
49439380 GCAGATTAAA
Statistics
Matches: 64, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
45 29 0.45
46 2 0.03
47 2 0.03
48 2 0.03
50 3 0.05
51 26 0.41
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.32
Consensus pattern (50 bp):
TCTTATCTCTCTGAAGTTGCAGTGGAAGCAAACTGAAGCATAAATAGATA
Found at i:49439461 original size:89 final size:88
Alignment explanation
Indices: 49438983--49439607 Score: 411
Period size: 89 Copynumber: 6.9 Consensus size: 88
49438973 AGTTATCACC
* * **
49438983 ACAGATCTTATCTCCCTGAAGTTACAGTGGAGTAGATTAAAAATTACAAACCTTATCTTTCTGAA
1 ACAGATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT-AAAA-TACAAACCTTATCTCCCTGAA
*
49439048 GTTGCAGTAGAGCAGGTT-AAAGTT
64 GTTGCAGTGGAGCAGGTTAAAAGTT
* * * * * * * *
49439072 GCA-AGTCTTATCTCCTTGAAGTTGTAGTGAAGCAGACTAAAGATAGCGAATCTTATTTCCCTGA
1 ACAGA-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAA-ATA-CAAACCTTATCTCCCTGA
* * *
49439136 AGTTGCAGTGGAACAGATTGAAGCTATAAATT
63 AGTTGCAGTGGAGCAGGTT--A---A-AAGTT
* * * * * * *
49439168 ATAGATCTTATCTCTCTGAAGTTGCAATAGAGCATATT---ATAGCAAACTTTATCTCCATGAAG
1 ACAGATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATA-CAAACCTTATCTCCCTGAAG
* *
49439230 TTGTAGTGGAGCAGGTT-GAAGTT
65 TTGCAGTGGAGCAGGTTAAAAGTT
* ** * * * * * *
49439253 ATA-AGTCTTATCTCCCTGAAGTTGCAGTAAAGCAGACTGAAGATAAAGAATCTTATTTCTCTGA
1 ACAGA-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TTAAAATACA-AACCTTATCTCCCTGA
* *
49439317 AGTTGCAGTGGAACAAATTGAAGCTATAAA-TT
63 AGTTGCAGTGGAGC--A--G--GTTA-AAAGTT
* * * * *
49439349 AGATATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAACCACAAACCTTATCTCCCTAAAG
1 ACAGATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAA-TACAAACCTTATCTCCCTGAAG
49439414 TTGCAGTGGAGCAGGTTAAAAGTT
65 TTGCAGTGGAGCAGGTTAAAAGTT
** * * * *
49439438 ACAGATCTTATCTCCCTGAAGTTGCAGTGGAATAGATCGAAGATAGCAAACTTTATCTCCCTGTA
1 ACAGATCTTATCTCCCTGAAGTTGCAGTGGAGCAGAT-TAAAATA-CAAACCTTATCTCCCTGAA
* * *
49439503 GTTGTAGTGGAGCAGATTGAAAATAGGCT
64 GTTGCAGTGGAGCAGGTT--AAA-A-GTT
* * * * * *
49439532 ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGAAAATTAAAGCTACACACATTATCTCCCTGAAG
1 ACAGATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAA-ATACAAACCTTATCTCCCTGAAG
*
49439597 TTACAGTGGAG
65 TTGCAGTGGAG
49439608 TAAATTGAAG
Statistics
Matches: 410, Mismatches: 91, Indels: 66
0.72 0.16 0.12
Matches are distributed among these distances:
84 1 0.00
85 34 0.08
86 1 0.00
88 10 0.02
89 123 0.30
90 35 0.09
91 2 0.00
92 36 0.09
93 31 0.08
94 37 0.09
95 32 0.08
96 64 0.16
97 4 0.01
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (88 bp):
ACAGATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATACAAACCTTATCTCCCTGAAGT
TGCAGTGGAGCAGGTTAAAAGTT
Found at i:49439675 original size:44 final size:44
Alignment explanation
Indices: 49439353--49439696 Score: 221
Period size: 44 Copynumber: 7.7 Consensus size: 44
49439343 TAAATTAGAT
* * * * * * *
49439353 ATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAACCACAA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGTAAATTGAAGCTACAC
* * * ** * * *
49439397 ACCTTATCTCCCTAAAGTTGCAGTGGAGCAGGTTAAAAGTTACAG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGTAAATT-GAAGCTACAC
* * * *
49439442 ATCTTATCTCCCTGAAGTTGCAGTGGAATAGATCGAAGATAGCA-
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGTAAATTGAAGCTA-CAC
* * * * * *
49439486 AACTTTATCTCCCTGTAGTTGTAGTGGAGCAGATTGAAAATAGGCTACAA
1 ATC-TTATCTCCCTGAAGTTGCAGTGGAGTAAATTG---A-A-GCTACAC
* *
49439536 ATCTTATCTCCCTGAAGTTGCAGTGGAGAAAATTAAAGCTACAC
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGTAAATTGAAGCTACAC
* *
49439580 A-CATTATCTCCCTGAAGTTACAGTGGAGTAAATTGAAGAC-ACAT
1 ATC-TTATCTCCCTGAAGTTGCAGTGGAGTAAATTGAAG-CTACAC
* * * *
49439624 ATCTTATCTCCCTAAATTTGCAATGGAGTAGATTGAAGCTACA-
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGTAAATTGAAGCTACAC
* * *
49439667 AGTTTTATCT-CTTGGAAGTTGTAGTGGAGT
1 A-TCTTATCTCCCT-GAAGTTGCAGTGGAGT
49439697 GGATCGAAGC
Statistics
Matches: 240, Mismatches: 45, Indels: 30
0.76 0.14 0.10
Matches are distributed among these distances:
43 5 0.02
44 132 0.55
45 66 0.28
46 1 0.00
48 1 0.00
49 30 0.12
50 5 0.02
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.30
Consensus pattern (44 bp):
ATCTTATCTCCCTGAAGTTGCAGTGGAGTAAATTGAAGCTACAC
Found at i:49441077 original size:3 final size:3
Alignment explanation
Indices: 49441069--49441100 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
49441059 TAATCCTCTT
49441069 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
49441101 TACTATTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:49441218 original size:3 final size:3
Alignment explanation
Indices: 49441203--49441253 Score: 75
Period size: 3 Copynumber: 16.7 Consensus size: 3
49441193 TATTTAAACT
* *
49441203 TTA TTA GTTA TTA TTA TTA TTA TTA TCA TCA TTA TTA TTA TTA TTA
1 TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
49441249 TTA TT
1 TTA TT
49441254 TATTTCTTTA
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
3 42 0.93
4 3 0.07
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:49441305 original size:23 final size:22
Alignment explanation
Indices: 49441237--49441306 Score: 61
Period size: 23 Copynumber: 3.0 Consensus size: 22
49441227 ATCATCATTA
*
49441237 TTATTATTATTATTATTTATTTCT
1 TTATT-TTCTTATTATTTATTT-T
* *
49441261 TTATTTTCTTATTAATTCTTTT
1 TTATTTTCTTATTATTTATTTT
*
49441283 ATTTTTTTCATT-TTATTTATTTT
1 -TTATTTTC-TTATTATTTATTTT
49441306 T
1 T
49441307 ATAATTGGCT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
22 2 0.05
23 29 0.76
24 7 0.18
ACGTcount: A:0.20, C:0.06, G:0.00, T:0.74
Consensus pattern (22 bp):
TTATTTTCTTATTATTTATTTT
Found at i:49441441 original size:21 final size:21
Alignment explanation
Indices: 49441417--49441460 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
49441407 TTATTCATCA
49441417 TTATTATTAATATTAATGTTG
1 TTATTATTAATATTAATGTTG
* **
49441438 TTATTATTATTATTGTTGTTG
1 TTATTATTAATATTAATGTTG
49441459 TT
1 TT
49441461 GTTGTTGTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.25, C:0.00, G:0.11, T:0.64
Consensus pattern (21 bp):
TTATTATTAATATTAATGTTG
Found at i:49441443 original size:18 final size:18
Alignment explanation
Indices: 49441420--49441457 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
49441410 TTCATCATTA
49441420 TTATTAATATTAATGTTG
1 TTATTAATATTAATGTTG
* *
49441438 TTATTATTATTATTGTTG
1 TTATTAATATTAATGTTG
49441456 TT
1 TT
49441458 GTTGTTGTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.26, C:0.00, G:0.11, T:0.63
Consensus pattern (18 bp):
TTATTAATATTAATGTTG
Found at i:49441456 original size:3 final size:3
Alignment explanation
Indices: 49441450--49441475 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
49441440 ATTATTATTA
49441450 TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TT
49441476 ATTTACATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:49443171 original size:17 final size:17
Alignment explanation
Indices: 49443149--49443182 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
49443139 TGAATATTTC
49443149 CTTGTTCTAAGAGATAG
1 CTTGTTCTAAGAGATAG
49443166 CTTGTTCTAAGAGATAG
1 CTTGTTCTAAGAGATAG
49443183 GAGTATACCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.12, G:0.24, T:0.35
Consensus pattern (17 bp):
CTTGTTCTAAGAGATAG
Found at i:49446933 original size:27 final size:27
Alignment explanation
Indices: 49446902--49447079 Score: 187
Period size: 27 Copynumber: 6.6 Consensus size: 27
49446892 TAAATTGTAC
*
49446902 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGAATTGACTATGT
* * *
49446929 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGAATTGACTATGT
* *
49446955 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGAATTGACTATGT
* *
49446983 GGCACTAAGTGTGCGAGATGGACTATGT
1 AGCACTAAGTGTGCGA-ATTGACTATGT
* * * *
49447011 GGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGAATTGACTATGT
* * *
49447038 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAATTGACTATGT
*
49447065 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
49447080 GGCTCAATAA
Statistics
Matches: 127, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
27 103 0.81
28 24 0.19
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.29
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAATTGACTATGT
Found at i:49447018 original size:82 final size:81
Alignment explanation
Indices: 49446903--49447058 Score: 215
Period size: 82 Copynumber: 1.9 Consensus size: 81
49446893 AAATTGTACA
* * * *
49446903 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGAATGGACTATGTGGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
49446967 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
49446984 GCACTAAGTGTGCGAGATGGACTATGTGGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-ATGGACTATGTGGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
49447049 TGCGAGTTGA
65 TGCGAATTGA
49447059 TTATATAGCA
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
81 15 0.23
82 49 0.75
83 1 0.02
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.28
Consensus pattern (81 bp):
GCACTAAGTGTGCGAATGGACTATGTGGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:49447070 original size:82 final size:81
Alignment explanation
Indices: 49446899--49447079 Score: 211
Period size: 82 Copynumber: 2.2 Consensus size: 81
49446889 GATTAAATTG
* * * *
49446899 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGAATGGACTATGTGGCACTAAGTGTGCGAAATGAATACGATGCACTAA
49446964 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
49446980 TGCGGCACTAAGTGTGCGAGATGGACTATGTGGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-ATGGACTATGTGGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
49447044 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
49447062 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
49447080 GGCTCAATAA
Statistics
Matches: 82, Mismatches: 16, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
81 18 0.22
82 64 0.78
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.29
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGAATGGACTATGTGGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:49452584 original size:24 final size:22
Alignment explanation
Indices: 49452557--49452604 Score: 62
Period size: 21 Copynumber: 2.1 Consensus size: 22
49452547 ATTTATCAAG
49452557 ATAAATATTAGATTAAATTTAATA
1 ATAAA-ATT-GATTAAATTTAATA
*
49452581 AT-AAATTGATTAAGTTTAATA
1 ATAAAATTGATTAAATTTAATA
49452602 ATA
1 ATA
49452605 GTTGAACTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
21 15 0.68
22 3 0.14
23 2 0.09
24 2 0.09
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (22 bp):
ATAAAATTGATTAAATTTAATA
Found at i:49453020 original size:15 final size:15
Alignment explanation
Indices: 49453000--49453038 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
49452990 TATTTTCCGT
*
49453000 TGTGTTTTTCAAATC
1 TGTGTTTTTCAAACC
*
49453015 TGTGTTTTCCAAACC
1 TGTGTTTTTCAAACC
49453030 TG-GTTTTTC
1 TGTGTTTTTC
49453039 CAACATGCCA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 6 0.29
15 15 0.71
ACGTcount: A:0.15, C:0.18, G:0.15, T:0.51
Consensus pattern (15 bp):
TGTGTTTTTCAAACC
Found at i:49454410 original size:58 final size:56
Alignment explanation
Indices: 49454340--49454479 Score: 165
Period size: 58 Copynumber: 2.4 Consensus size: 56
49454330 TTATTATAGA
* * * * *
49454340 AAGGATTTAGCCTGGATGGGTAATTCTGATATAATCCC-TCTCGAGCATATGTTACAAT
1 AAGGATTTAGCCTGGATTGGTAATCCTAAT-TAAGCCCTTCT-GAGCATACGTTAC-AT
* * *
49454398 TAGGATTTAGCCTGGACTTGGTAATCCTAATTAAGCTCTTCTGAGCATACGTTACGT
1 AAGGATTTAGCCTGGA-TTGGTAATCCTAATTAAGCCCTTCTGAGCATACGTTACAT
49454455 AAGGATTTAGCCTGGATTGGTAATC
1 AAGGATTTAGCCTGGATTGGTAATC
49454480 TTGTAATACG
Statistics
Matches: 71, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
56 9 0.13
57 16 0.23
58 32 0.45
59 14 0.20
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.34
Consensus pattern (56 bp):
AAGGATTTAGCCTGGATTGGTAATCCTAATTAAGCCCTTCTGAGCATACGTTACAT
Found at i:49456868 original size:4 final size:4
Alignment explanation
Indices: 49456859--49456891 Score: 59
Period size: 4 Copynumber: 8.5 Consensus size: 4
49456849 GTTTGGTAGG
49456859 AGAA AGAA AGAA AGAA AGAA AGAA AGAA A-AA AG
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AG
49456892 TCTGGCGTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.11
4 25 0.89
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:49461158 original size:13 final size:13
Alignment explanation
Indices: 49461140--49461169 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
49461130 ATAAATCATT
49461140 TAATTTAGATTCA
1 TAATTTAGATTCA
49461153 TAATTTAGATTCA
1 TAATTTAGATTCA
49461166 TAAT
1 TAAT
49461170 CAATCCTGGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.47
Consensus pattern (13 bp):
TAATTTAGATTCA
Found at i:49465214 original size:3 final size:3
Alignment explanation
Indices: 49465206--49465318 Score: 67
Period size: 3 Copynumber: 37.7 Consensus size: 3
49465196 TGGTTATTTG
49465206 TTA TTA TTA TT- TTA TT- TT- TCTA GTTA TTA TTTA TTTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA T-TA -TTA TTA -TTA -TTA TTA TTA TTA
* * * * *
49465252 TTC TCA TTA TTA TTA TTA TTA TTAA TT- TTC TTT TTA TTT TTA GTT-
1 TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA -TTA
* *
49465297 TTA TTA TCA TTA GT- TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TT
49465319 CTTTATGTTA
Statistics
Matches: 88, Mismatches: 12, Indels: 20
0.73 0.10 0.17
Matches are distributed among these distances:
2 10 0.11
3 63 0.72
4 14 0.16
5 1 0.01
ACGTcount: A:0.25, C:0.04, G:0.03, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:49465234 original size:20 final size:18
Alignment explanation
Indices: 49465199--49465271 Score: 78
Period size: 18 Copynumber: 4.0 Consensus size: 18
49465189 ATTTATTTGG
*
49465199 TTATTTGTTATTATTATT
1 TTATTTATTATTATTATT
*
49465217 TTATTTTTCTAGTTATTA-T
1 TTATTTAT-TA-TTATTATT
49465236 TTATTTATTATTATTATT
1 TTATTTATTATTATTATT
*
49465254 CTCA-TTATTATTATTATT
1 -TTATTTATTATTATTATT
49465272 ATTAATTTTC
Statistics
Matches: 48, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
17 6 0.12
18 24 0.50
19 12 0.25
20 6 0.12
ACGTcount: A:0.25, C:0.04, G:0.03, T:0.68
Consensus pattern (18 bp):
TTATTTATTATTATTATT
Found at i:49465382 original size:14 final size:14
Alignment explanation
Indices: 49465353--49465391 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
49465343 CCTCATTATA
*
49465353 GTTATTTT-TATTT
1 GTTATTTTATTTTT
49465366 GTTATTTTATTTTT
1 GTTATTTTATTTTT
49465380 GTTATTCTTATT
1 GTTATT-TTATT
49465392 ATCATTTGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 8 0.35
14 10 0.43
15 5 0.22
ACGTcount: A:0.15, C:0.03, G:0.08, T:0.74
Consensus pattern (14 bp):
GTTATTTTATTTTT
Found at i:49465407 original size:20 final size:20
Alignment explanation
Indices: 49465384--49465422 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
49465374 ATTTTTGTTA
49465384 TTCTTATTATCATTTGTTTC
1 TTCTTATTATCATTTGTTTC
* *
49465404 TTCTTCTTATTATTTGTTT
1 TTCTTATTATCATTTGTTT
49465423 TAATGTTGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.13, C:0.13, G:0.05, T:0.69
Consensus pattern (20 bp):
TTCTTATTATCATTTGTTTC
Found at i:49465470 original size:21 final size:21
Alignment explanation
Indices: 49465420--49465462 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
49465410 TTATTATTTG
* *
49465420 TTTTAA-TGTTGTTATTATTA
1 TTTTAATTTTTGTCATTATTA
49465440 TTTTAATTTTTGTCATT-TTA
1 TTTTAATTTTTGTCATTATTA
49465460 TTT
1 TTT
49465463 CTCATTTTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.21, C:0.02, G:0.07, T:0.70
Consensus pattern (21 bp):
TTTTAATTTTTGTCATTATTA
Found at i:49471454 original size:57 final size:58
Alignment explanation
Indices: 49471368--49471487 Score: 161
Period size: 57 Copynumber: 2.1 Consensus size: 58
49471358 AGAAATGGTG
* * *
49471368 AATGAAGAAATAGGAAACTTTTGGAAATGATTATGGTTTTCCCTAAAACGAAATTGAA
1 AATGAAGAAATAGGAAACATTTGGAAATGAATATGGTTTTCCCTAAAACGAAAATGAA
* * * * *
49471426 AATGGAGAAAT-GGAATCATTTGGAAATGAATGTGGTTTTCTCTAAAATGAAAATGAA
1 AATGAAGAAATAGGAAACATTTGGAAATGAATATGGTTTTCCCTAAAACGAAAATGAA
49471483 AATGA
1 AATGA
49471488 CTTGAAAAAT
Statistics
Matches: 53, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
57 43 0.81
58 10 0.19
ACGTcount: A:0.43, C:0.07, G:0.21, T:0.29
Consensus pattern (58 bp):
AATGAAGAAATAGGAAACATTTGGAAATGAATATGGTTTTCCCTAAAACGAAAATGAA
Found at i:49475218 original size:40 final size:39
Alignment explanation
Indices: 49475151--49475233 Score: 132
Period size: 40 Copynumber: 2.1 Consensus size: 39
49475141 ACCCAAGTAT
49475151 CTTCGGGATTTAGCCGGATATAACAACTCGCACAAATGC
1 CTTCGGGATTTAGCCGGATATAACAACTCGCACAAATGC
*
49475190 CTTCGGG-TCTTAGCCCGGATATAGCAACTCGCACAAATGC
1 CTTCGGGAT-TTAG-CCGGATATAACAACTCGCACAAATGC
49475230 CTTC
1 CTTC
49475234 NNNNNNNNNN
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
38 1 0.02
39 11 0.27
40 29 0.71
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.24
Consensus pattern (39 bp):
CTTCGGGATTTAGCCGGATATAACAACTCGCACAAATGC
Found at i:49484520 original size:27 final size:27
Alignment explanation
Indices: 49484473--49484539 Score: 91
Period size: 26 Copynumber: 2.4 Consensus size: 27
49484463 ATTCAGCTAG
*
49484473 GACACATTAAAACAAGTAAT-AACTAA
1 GACATATTAAAACAAGTAATAAACTAA
49484499 GACATATTAAACACAAGTAATAAACTAA
1 GACATATTAAA-ACAAGTAATAAACTAA
49484527 GACACATATTAAA
1 G--ACATATTAAA
49484540 TTCAGCTGTA
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
26 10 0.28
27 9 0.25
28 7 0.19
30 10 0.28
ACGTcount: A:0.57, C:0.15, G:0.07, T:0.21
Consensus pattern (27 bp):
GACATATTAAAACAAGTAATAAACTAA
Found at i:49489100 original size:10 final size:10
Alignment explanation
Indices: 49489085--49489119 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
49489075 TTAATGAGCT
49489085 GAAAATTCCA
1 GAAAATTCCA
*
49489095 GAAAATTTCAA
1 GAAAA-TTCCA
49489106 GAAAATTCCA
1 GAAAATTCCA
49489116 GAAA
1 GAAA
49489120 GCTTCTGCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
10 13 0.59
11 9 0.41
ACGTcount: A:0.54, C:0.14, G:0.11, T:0.20
Consensus pattern (10 bp):
GAAAATTCCA
Found at i:49490967 original size:22 final size:22
Alignment explanation
Indices: 49490939--49490992 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 22
49490929 AAAAGAGTTT
*
49490939 ATGGGGACAAGGTCTGTAAATG
1 ATGGGGACAAGGTCTGCAAATG
*
49490961 ATGGGGACAAGGTCTGCAAGTG
1 ATGGGGACAAGGTCTGCAAATG
*
49490983 ATGTGGACAA
1 ATGGGGACAA
49490993 CTTCTTATGG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.31, C:0.11, G:0.37, T:0.20
Consensus pattern (22 bp):
ATGGGGACAAGGTCTGCAAATG
Found at i:49495943 original size:12 final size:11
Alignment explanation
Indices: 49495926--49495969 Score: 61
Period size: 12 Copynumber: 3.7 Consensus size: 11
49495916 CAAAGAAAAA
49495926 AATAAAATAACT
1 AATAAAATAA-T
49495938 AATAAAATGAAT
1 AATAAAAT-AAT
49495950 AATAACAATAAT
1 AATAA-AATAAT
49495962 AATAAAAT
1 AATAAAAT
49495970 CTAAATTTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
11 3 0.10
12 22 0.73
13 5 0.17
ACGTcount: A:0.68, C:0.05, G:0.02, T:0.25
Consensus pattern (11 bp):
AATAAAATAAT
Found at i:49504761 original size:46 final size:46
Alignment explanation
Indices: 49504592--49504810 Score: 146
Period size: 46 Copynumber: 4.8 Consensus size: 46
49504582 CACTGCTGTT
* * * *
49504592 ATGTGAGCCAGTGTAAGACATGTCTAGGACATGCATCAGCCAC-ATT
1 ATGTAAGCCAGTGTAAGACATGTCTAGGACATGCATCGGCCTCGA-G
* * * * * *
49504638 ATGAAATGCTAGTGTAAGACATGT-TTGAGATATGCATCGGCATTGAG
1 ATGTAA-GCCAGTGTAAGACATGTCTAG-GACATGCATCGGCCTCGAG
* * * * *
49504685 ACG-AGAGCTAGTGTAAGATATGTTTGGGACATGCATCGGCCTCGAG
1 ATGTA-AGCCAGTGTAAGACATGTCTAGGACATGCATCGGCCTCGAG
* * *
49504731 ATGTAAGCCAGTGCAAGACATGTCTAGGACAT-CTATCAG-CTATGAG
1 ATGTAAGCCAGTGTAAGACATGTCTAGGACATGC-ATCGGCCT-CGAG
* * *
49504777 ACGT--GCTAGTGTAAGACATGTCTGGGACATGCAT
1 ATGTAAGCCAGTGTAAGACATGTCTAGGACATGCAT
49504811 TGGCATCAGT
Statistics
Matches: 136, Mismatches: 28, Indels: 20
0.74 0.15 0.11
Matches are distributed among these distances:
44 25 0.18
45 4 0.03
46 73 0.54
47 33 0.24
48 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.27, T:0.26
Consensus pattern (46 bp):
ATGTAAGCCAGTGTAAGACATGTCTAGGACATGCATCGGCCTCGAG
Found at i:49510266 original size:46 final size:46
Alignment explanation
Indices: 49510194--49510321 Score: 163
Period size: 46 Copynumber: 2.8 Consensus size: 46
49510184 CACTACTGTT
49510194 ATGTGAGCCAGTGTAAGACATGTCTGGGACATGAATCGACCT-CAAG
1 ATGT-AGCCAGTGTAAGACATGTCTGGGACATGAATCGACCTACAAG
* * *
49510240 ATGTAAGCCAGTGTAAGACATGTCTGGGACATGTATC-AGCTACGAG
1 ATGT-AGCCAGTGTAAGACATGTCTGGGACATGAATCGACCTACAAG
* * *
49510286 ATGT-GCTAGTGTAAGAAATGTCTGGGACATGCATCG
1 ATGTAGCCAGTGTAAGACATGTCTGGGACATGAATCG
49510322 GCACAGATAT
Statistics
Matches: 73, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
44 28 0.38
45 3 0.04
46 42 0.58
ACGTcount: A:0.30, C:0.17, G:0.29, T:0.24
Consensus pattern (46 bp):
ATGTAGCCAGTGTAAGACATGTCTGGGACATGAATCGACCTACAAG
Found at i:49512405 original size:45 final size:44
Alignment explanation
Indices: 49512329--49513481 Score: 277
Period size: 45 Copynumber: 24.8 Consensus size: 44
49512319 TCGTAGCTTT
* * *
49512329 AATCTGTTCCACTGCAACTTCAAGGAAATAAGATTCGCTATCTTC
1 AATCTCTT-CACTGCAACTTCAGGGAGATAAGATTCGCTATCTTC
* * *
49512374 AATCTACTTCACTGCAACATT-AGGGAGATAAGATTTGTAACTTGTAGCTTT
1 AATCT-CTTCACTGCAAC-TTCAGGGAGATAAGATTCG---C---TATCTTC
* *
49512425 AATCTGTTCCACTGCAACTTCAGGG-GAATAAGATTCGCTATATTC
1 AATCTCTT-CACTGCAACTTCAGGGAG-ATAAGATTCGCTATCTTC
* * * * * *
49512470 AATCTGCTCCACTGCAACTTTAGGGACATAAGATTTGTAACTTGTAGCTTT
1 AATCT-CTTCACTGCAACTTCAGGGAGATAAGATTCG---C---TATCTTC
* *
49512521 AATCTGTTCCACTGCAACTTCAGGG-GAATAAGATTCGCTATATTC
1 AATCTCTT-CACTGCAACTTCAGGGAG-ATAAGATTCGCTATCTTC
* * * * * *
49512566 AATCTGCTCCACTGCAACTTTAGGGACATAAGATTTGTAACTTGTAGCTTT
1 AATCT-CTTCACTGCAACTTCAGGGAGATAAGATTCG---C---TATCTTC
* * * **
49512617 AATCTGTTCCACTGCAACTTCAGGAAAATAAGATTTTCTATCTTC
1 AATCTCTT-CACTGCAACTTCAGGGAGATAAGATTCGCTATCTTC
* * * *
49512662 AATCTACTCCACTGTAACTTCAGGGAGATAAGATTCGCTATGGTAAATTT
1 AATCT-CTTCACTGCAACTTCAGGGAGATAAGATTCGCTA---T--CTTC
** * * * *
49512712 AATC-CGACCTACTGCAACTTCAGAGG-TATAGGACTTGTGACTTGTATCTTT
1 AATCTC-TTC-ACTGCAACTTCAG-GGAGATAAGA-TT-CG-C---TATCTTC
* * * * *
49512763 AATCTATTCCACTACAAATTCAGGGAAATAAGATTTGCTATCTTC
1 AATCTCTT-CACTGCAACTTCAGGGAGATAAGATTCGCTATCTTC
* * * * * *
49512808 AATCTGC-TCTACTGCAACCTCAAGGAGATTAGATTTGTAACTTGTAGCTTT
1 AATCT-CTTC-ACTGCAACTTCAGGGAGATAAGATTCG---C---TATCTTC
* * * * * *
49512859 AATATATTCCACTGTAACTTCAGAGAAATAAGATTCGTTATCTTC
1 AATCTCTT-CACTGCAACTTCAGGGAGATAAGATTCGCTATCTTC
* * * *
49512904 AATCCGCTCCACTGCAACTTCAGGGAGATAAGATTTGCAAAT-TT-
1 AAT-CTCTTCACTGCAACTTCAGGGAGATAAGATTCGC-TATCTTC
* * * * * ** *
49512948 GATCTACTCCACTGTAACTTTAGGGAGATAA-AATCTG-TAAATTT
1 AATCT-CTTCACTGCAACTTCAGGGAGATAAGATTC-GCTATCTTC
* * * *
49512992 AATCTATTTCACTGTAACTTCAGGGAGATAAGATTTTTAATTTG-TATCTTT
1 AATCT-CTTCACTGCAACTTCAGGGAGATAAG-------ATTCGCTATCTTC
* * * * *
49513043 AATCTATTCCACTACAAC-TCTAAGGAAATAAGATTAGCTATCTTC
1 AATCTCTT-CACTGCAACTTC-AGGGAGATAAGATTCGCTATCTTC
* * * *
49513088 AGTCTGCTCCACTGCAACTTCAGGGAAATAAGATTCACTATCTTC
1 AATCT-CTTCACTGCAACTTCAGGGAGATAAGATTCGCTATCTTC
* * * *
49513133 AATTTGCTCCACTACAACTTCAGGGAGATAAGACTT-G-TAACTTC
1 AATCT-CTTCACTGCAACTTCAGGGAGATAAGA-TTCGCTATCTTC
* * * * ** *
49513177 AACCTGCTTCACTTCAACTTCAAGGAGATAAGCTT-TATAGC-T-
1 AATCT-CTTCACTGCAACTTCAGGGAGATAAGATTCGCTATCTTC
* * * *
49513219 AATTTGC-TCTACTACAACTTCAGGGAGATAAGATTTG-TGA-CTTT
1 AATCT-CTTC-ACTGCAACTTCAGGGAGATAAGATTCGCT-ATCTTC
* ** * * *
49513263 AATCTACTCCACTATAACTTCAAGGAGATAAAATTCGCCACGATGACTTC
1 AATCT-CTTCACTGCAACTTCAGGGAGATAAGATTCG---CTAT--CTTC
* * * * ** *
49513313 AATCTGTCCCAATGTAACTTCAGGG-GTATGAA-ATT-TTTAACTTC
1 AATCTCT-TCACTGCAACTTCAGGGAG-AT-AAGATTCGCTATCTTC
* * * * * *
49513357 AATCTACTCCACTACAACTTCAGGGAGATAAGATTTGTTATTTTT
1 AATCT-CTTCACTGCAACTTCAGGGAGATAAGATTCGCTATCTTC
* * * * *
49513402 AACCTGCTTCACTACAACTTTAGGGAGATAAGTTTTG-TGA-CTTC
1 AATCT-CTTCACTGCAACTTCAGGGAGATAAGATTCGCT-ATCTTC
*
49513446 AATCTACTCCACTGCAACTTCAGGGAGATAAGATTC
1 AATCT-CTTCACTGCAACTTCAGGGAGATAAGATTC
49513482 ACCATAATGA
Statistics
Matches: 822, Mismatches: 186, Indels: 201
0.68 0.15 0.17
Matches are distributed among these distances:
41 2 0.00
42 30 0.04
43 12 0.01
44 182 0.22
45 305 0.37
46 16 0.02
47 1 0.00
48 10 0.01
49 6 0.01
50 65 0.08
51 184 0.22
52 5 0.01
53 2 0.00
56 2 0.00
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (44 bp):
AATCTCTTCACTGCAACTTCAGGGAGATAAGATTCGCTATCTTC
Found at i:49512408 original size:96 final size:96
Alignment explanation
Indices: 49512275--49512696 Score: 632
Period size: 96 Copynumber: 4.4 Consensus size: 96
49512265 GATTTGTCAC
* * * *
49512275 TTCAATGTACTCCACAGCAA-TTTCAGGGAGATCAGATTTGTAACTCGTAGCTTTAATCTGTTCC
1 TTCAATCTACTCCACTGCAACTTT-AGGGAGATAAGATTTGTAACTTGTAGCTTTAATCTGTTCC
*
49512339 ACTGCAACTTCAAGGAAATAAGATTCGCTATC
65 ACTGCAACTTCAAGGAAATAAGATTCGCTATA
* *
49512371 TTCAATCTACTTCACTGCAACATTAGGGAGATAAGATTTGTAACTTGTAGCTTTAATCTGTTCCA
1 TTCAATCTACTCCACTGCAACTTTAGGGAGATAAGATTTGTAACTTGTAGCTTTAATCTGTTCCA
* *
49512436 CTGCAACTTCAGGGGAATAAGATTCGCTATA
66 CTGCAACTTCAAGGAAATAAGATTCGCTATA
* *
49512467 TTCAATCTGCTCCACTGCAACTTTAGGGACATAAGATTTGTAACTTGTAGCTTTAATCTGTTCCA
1 TTCAATCTACTCCACTGCAACTTTAGGGAGATAAGATTTGTAACTTGTAGCTTTAATCTGTTCCA
* *
49512532 CTGCAACTTCAGGGGAATAAGATTCGCTATA
66 CTGCAACTTCAAGGAAATAAGATTCGCTATA
* *
49512563 TTCAATCTGCTCCACTGCAACTTTAGGGACATAAGATTTGTAACTTGTAGCTTTAATCTGTTCCA
1 TTCAATCTACTCCACTGCAACTTTAGGGAGATAAGATTTGTAACTTGTAGCTTTAATCTGTTCCA
** *
49512628 CTGCAACTTC-AGGAAAATAAGATTTTCTATC
66 CTGCAACTTCAAGG-AAATAAGATTCGCTATA
* *
49512659 TTCAATCTACTCCACTGTAACTTCAGGGAGATAAGATT
1 TTCAATCTACTCCACTGCAACTTTAGGGAGATAAGATT
49512697 CGCTATGGTA
Statistics
Matches: 302, Mismatches: 22, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
95 2 0.01
96 298 0.99
97 2 0.01
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.33
Consensus pattern (96 bp):
TTCAATCTACTCCACTGCAACTTTAGGGAGATAAGATTTGTAACTTGTAGCTTTAATCTGTTCCA
CTGCAACTTCAAGGAAATAAGATTCGCTATA
Found at i:49512973 original size:44 final size:44
Alignment explanation
Indices: 49512856--49513480 Score: 192
Period size: 44 Copynumber: 13.9 Consensus size: 44
49512846 AACTTGTAGC
* * * * * **
49512856 TTTAATATATTCCACTGTAACTTCAGAGAAATAAGATTCG-TTA
1 TTTAATCTACTCCACTGTAACTTCAGGGAGATAAGATTTGCAAA
** *
49512899 TCTTCAATCCGCTCCACTGCAACTTCAGGGAGATAAGATTTGCAAA
1 T-TT-AATCTACTCCACTGTAACTTCAGGGAGATAAGATTTGCAAA
* * * * *
49512945 TTTGATCTACTCCACTGTAACTTTAGGGAGATAAAATCTGTAAA
1 TTTAATCTACTCCACTGTAACTTCAGGGAGATAAGATTTGCAAA
* * **
49512989 TTTAATCTATTTCACTGTAACTTCAGGGAGATAAGATTTTTAATTTGTA
1 TTTAATCTACTCCACTGTAACTTCAGGGAGATAAGATTTGCAA-----A
* ** * * * *
49513038 TCTTTAATCTATTCCACTACAAC-TCTAAGGAAATAAGATTAGC-TA
1 --TTTAATCTACTCCACTGTAACTTC-AGGGAGATAAGATTTGCAAA
* * * * *
49513083 TCTTCAGTCTGCTCCACTGCAACTTCAGGGAAATAAGA-TT-CACTA
1 T-TT-AATCTACTCCACTGTAACTTCAGGGAGATAAGATTTGCA-AA
* * ** * * *
49513128 TCTTCAATTTGCTCCACTACAACTTCAGGGAGATAAGACTTGTAAC
1 T-TT-AATCTACTCCACTGTAACTTCAGGGAGATAAGATTTGCAAA
* * * * * * *
49513174 TTCAACCTGCTTCACT-TCAACTTCAAGGAGATAAGCTTT--ATA
1 TTTAATCTACTCCACTGT-AACTTCAGGGAGATAAGATTTGCAAA
** * * * ** ** *
49513216 GCTAATTTGCTCTACTACAACTTCAGGGAGATAAGATTTGTGAC
1 TTTAATCTACTCCACTGTAACTTCAGGGAGATAAGATTTGCAAA
* * * *
49513260 TTTAATCTACTCCACTATAACTTCAAGGAGATAAAATTCGCCACGATGA
1 TTTAATCTACTCCACTGTAACTTCAGGGAGATAAGATTTG-CA--A--A
* * * ** *
49513309 CTTCAATCT-GTCCCAATGTAACTTCAGGG-GTATGAA-ATTTTTAAC
1 -TTTAATCTACT-CCACTGTAACTTCAGGGAG-AT-AAGATTTGCAAA
* ** * **
49513354 TTCAATCTACTCCACTACAACTTCAGGGAGATAAGATTTGTTATT
1 TTTAATCTACTCCACTGTAACTTCAGGGAGATAAGATTTG-CAAA
* * * ** * * ** *
49513399 TTTAACCTGCTTCACTACAACTTTAGGGAGATAAGTTTTGTGAC
1 TTTAATCTACTCCACTGTAACTTCAGGGAGATAAGATTTGCAAA
* *
49513443 TTCAATCTACTCCACTGCAACTTCAGGGAGATAAGATT
1 TTTAATCTACTCCACTGTAACTTCAGGGAGATAAGATT
49513481 CACCATAATG
Statistics
Matches: 433, Mismatches: 114, Indels: 69
0.70 0.19 0.11
Matches are distributed among these distances:
42 29 0.07
43 5 0.01
44 193 0.45
45 132 0.30
46 7 0.02
47 3 0.01
49 4 0.01
50 28 0.06
51 32 0.07
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.33
Consensus pattern (44 bp):
TTTAATCTACTCCACTGTAACTTCAGGGAGATAAGATTTGCAAA
Found at i:49513119 original size:96 final size:94
Alignment explanation
Indices: 49512753--49513122 Score: 317
Period size: 96 Copynumber: 3.9 Consensus size: 94
49512743 GACTTGTGAC
* * *
49512753 TTGTATCTTTAATCTATTCCACTACAAATTCAGGGAAATAAGATTTGCTATCTTCAATCTGCTCT
1 TTGTATCTTTAATCTATTCCACTACAACTT-AAGGAAATAAGA-TTGCTATCTTCAATCTGCTCC
* * * * *
49512818 ACTGCAACCTCAAGGAGATTAGATTTGTAAC
64 ACTGCAACTTCAGGGAGATAAGATTTCTAAT
* * ** * * *
49512849 TTGTAGCTTTAATATATTCCACTGTAACTTCAGAGAAATAAGATTCGTTATCTTCAATCCGCTCC
1 TTGTATCTTTAATCTATTCCACTACAACTTAAG-GAAATAAGATT-GCTATCTTCAATCTGCTCC
*
49512914 ACTGCAACTTCAGGGAGATAAGATTTGCAAAT
64 ACTGCAACTTCAGGGAGATAAGATTT-CTAAT
** * * * ** * ** *
49512946 TTG-ATC--T-A-C---TCCACTGTAACTTTAGGGAGATAAAATCTG-TAAATTTAATCTATTTC
1 TTGTATCTTTAATCTATTCCACTACAAC-TTAAGGAAATAAGAT-TGCTATCTTCAATCTGCTCC
* *
49513002 ACTGTAACTTCAGGGAGATAAGATTTTTAAT
64 ACTGCAACTTCAGGGAGATAAGATTTCTAAT
*
49513033 TTGTATCTTTAATCTATTCCACTACAACTCTAAGGAAATAAGATTAGCTATCTTCAGTCTGCTCC
1 TTGTATCTTTAATCTATTCCACTACAACT-TAAGGAAATAAGATT-GCTATCTTCAATCTGCTCC
*
49513098 ACTGCAACTTCAGGGAAATAAGATT
64 ACTGCAACTTCAGGGAGATAAGATT
49513123 CACTATCTTC
Statistics
Matches: 212, Mismatches: 46, Indels: 32
0.73 0.16 0.11
Matches are distributed among these distances:
87 6 0.03
88 38 0.18
89 20 0.09
90 5 0.02
91 1 0.00
92 1 0.00
93 1 0.00
94 3 0.01
95 24 0.11
96 108 0.51
97 5 0.02
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.35
Consensus pattern (94 bp):
TTGTATCTTTAATCTATTCCACTACAACTTAAGGAAATAAGATTGCTATCTTCAATCTGCTCCAC
TGCAACTTCAGGGAGATAAGATTTCTAAT
Found at i:49513242 original size:86 final size:86
Alignment explanation
Indices: 49513133--49513293 Score: 243
Period size: 86 Copynumber: 1.9 Consensus size: 86
49513123 CACTATCTTC
* *
49513133 AATTTGCTCCACTACAACTTCAGGGAGATAAGACTTGTAACTTCAACCTGCTTCACT-TCAACTT
1 AATTTGCTCCACTACAACTTCAGGGAGATAAGACTTGTAACTTCAACCTACTCCACTAT-AACTT
49513197 CAAGGAGATAAGCTTTATAGCT
65 CAAGGAGATAAGCTTTATAGCT
* * * * *
49513219 AATTTGCTCTACTACAACTTCAGGGAGATAAGATTTGTGACTTTAATCTACTCCACTATAACTTC
1 AATTTGCTCCACTACAACTTCAGGGAGATAAGACTTGTAACTTCAACCTACTCCACTATAACTTC
49513284 AAGGAGATAA
66 AAGGAGATAA
49513294 AATTCGCCAC
Statistics
Matches: 67, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
86 66 0.99
87 1 0.01
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.31
Consensus pattern (86 bp):
AATTTGCTCCACTACAACTTCAGGGAGATAAGACTTGTAACTTCAACCTACTCCACTATAACTTC
AAGGAGATAAGCTTTATAGCT
Found at i:49520167 original size:3 final size:3
Alignment explanation
Indices: 49520131--49520186 Score: 62
Period size: 3 Copynumber: 18.7 Consensus size: 3
49520121 CAAAGAAAAA
* *
49520131 AAT AA- AAT AACT AAT AA- AAT GAAT AAT AAC AAT AAT AGT AAT AAT
1 AAT AAT AAT AA-T AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT
49520176 AAT AAT AAT AA
1 AAT AAT AAT AA
49520187 AATCTAAATT
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
2 4 0.09
3 35 0.78
4 6 0.13
ACGTcount: A:0.66, C:0.04, G:0.04, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:49525017 original size:14 final size:14
Alignment explanation
Indices: 49524998--49525025 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
49524988 AAAGTATGCC
49524998 CCCTTGAATGATTA
1 CCCTTGAATGATTA
49525012 CCCTTGAATGATTA
1 CCCTTGAATGATTA
49525026 TATTTCTAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.36
Consensus pattern (14 bp):
CCCTTGAATGATTA
Found at i:49527227 original size:42 final size:42
Alignment explanation
Indices: 49527168--49527331 Score: 172
Period size: 42 Copynumber: 3.9 Consensus size: 42
49527158 TTAGGGTTAC
* *
49527168 TGAGATTAT-ATGTAAGACCATATTTGGGATATGGCATCTATA
1 TGAGATT-TCATGTAAGACCATATCTGGGATATGGCATCGATA
*
49527210 TGAGATTTCATGTAAGACTC-TATCTAGGATATGGCATCGATA
1 TGAGATTTCATGTAAGAC-CATATCTGGGATATGGCATCGATA
* * *
49527252 TGAGATTTCGTATAAGACCATAGCT-GGACTATTGGCATCGATA
1 TGAGATTTCATGTAAGACCATATCTGGGA-TA-TGGCATCGATA
** * * *
49527295 CAAGATTACATGTAAAACCATATCTGAGATATGGCAT
1 TGAGATTTCATGTAAGACCATATCTGGGATATGGCAT
49527332 TGGTATGGTG
Statistics
Matches: 102, Mismatches: 14, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
41 5 0.05
42 63 0.62
43 32 0.31
44 2 0.02
ACGTcount: A:0.34, C:0.14, G:0.21, T:0.32
Consensus pattern (42 bp):
TGAGATTTCATGTAAGACCATATCTGGGATATGGCATCGATA
Found at i:49528737 original size:17 final size:17
Alignment explanation
Indices: 49528715--49528747 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
49528705 ACACACGGGC
49528715 GTGTGTCTAGGCCGTGT
1 GTGTGTCTAGGCCGTGT
49528732 GTGTGTCTAGGCCGTG
1 GTGTGTCTAGGCCGTG
49528748 AGTGACATAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.06, C:0.18, G:0.42, T:0.33
Consensus pattern (17 bp):
GTGTGTCTAGGCCGTGT
Found at i:49530139 original size:27 final size:27
Alignment explanation
Indices: 49530101--49530156 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
49530091 AGAGGATACA
49530101 ATTAAAATAATATATTAATTGAATTTC
1 ATTAAAATAATATATTAATTGAATTTC
49530128 ATTAAAATAATATATTAATTGAATTTC
1 ATTAAAATAATATATTAATTGAATTTC
49530155 AT
1 AT
49530157 ACAAGTTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.45
Consensus pattern (27 bp):
ATTAAAATAATATATTAATTGAATTTC
Found at i:49538367 original size:26 final size:27
Alignment explanation
Indices: 49538327--49538377 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
49538317 AAGCTATTTG
*
49538327 GCAGACTGTCCATTGGCGAACTGTCAA
1 GCAGACAGTCCATTGGCGAACTGTCAA
* *
49538354 GCAGACAG-CCATTGGTGGACTGTC
1 GCAGACAGTCCATTGGCGAACTGTC
49538378 CAAATGTGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 14 0.67
27 7 0.33
ACGTcount: A:0.24, C:0.25, G:0.29, T:0.22
Consensus pattern (27 bp):
GCAGACAGTCCATTGGCGAACTGTCAA
Found at i:49544317 original size:16 final size:17
Alignment explanation
Indices: 49544282--49544322 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
49544272 TTAAATGTGC
* *
49544282 TATGACATGATATGAAA
1 TATGATATGATATAAAA
49544299 TATGATATGATA-AAAA
1 TATGATATGATATAAAA
49544315 TATGATAT
1 TATGATAT
49544323 AAGATATGCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 11 0.50
17 11 0.50
ACGTcount: A:0.49, C:0.02, G:0.15, T:0.34
Consensus pattern (17 bp):
TATGATATGATATAAAA
Found at i:49544322 original size:5 final size:5
Alignment explanation
Indices: 49544227--49544310 Score: 51
Period size: 5 Copynumber: 15.6 Consensus size: 5
49544217 TGGGGGTAGT
* * * *
49544227 ATATG ATATG ATATG ATACG ATATG AGTTATG ATAAG ATAAG ATATTAA
1 ATATG ATATG ATATG ATATG ATATG A--TATG ATATG ATATG ATA-T-G
* * *
49544276 ATGTG CTATG ACATG ATATG AAATATG ATATG ATA
1 ATATG ATATG ATATG ATATG --ATATG ATATG ATA
49544311 AAAATATGAT
Statistics
Matches: 61, Mismatches: 12, Indels: 12
0.72 0.14 0.14
Matches are distributed among these distances:
5 48 0.79
6 1 0.02
7 12 0.20
ACGTcount: A:0.43, C:0.04, G:0.19, T:0.35
Consensus pattern (5 bp):
ATATG
Found at i:49552218 original size:18 final size:18
Alignment explanation
Indices: 49552195--49552251 Score: 78
Period size: 18 Copynumber: 3.2 Consensus size: 18
49552185 CCCAACTACT
*
49552195 GTATACGTGAACAGTACC
1 GTATACGTGAATAGTACC
* **
49552213 GTATACATGAATAGTGTC
1 GTATACGTGAATAGTACC
49552231 GTATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
49552249 GTA
1 GTA
49552252 GTATGGGTAT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.28
Consensus pattern (18 bp):
GTATACGTGAATAGTACC
Found at i:49552617 original size:21 final size:21
Alignment explanation
Indices: 49552593--49552633 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
49552583 GCCTGCCATT
*
49552593 CCAAAGTTGTTTATATTATAG
1 CCAAAGTTCTTTATATTATAG
49552614 CCAAAGTTCTTTATATTATA
1 CCAAAGTTCTTTATATTATA
49552634 TAAATTAAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.34, C:0.12, G:0.10, T:0.44
Consensus pattern (21 bp):
CCAAAGTTCTTTATATTATAG
Found at i:49555299 original size:42 final size:42
Alignment explanation
Indices: 49555251--49555337 Score: 174
Period size: 42 Copynumber: 2.1 Consensus size: 42
49555241 AATTTAGGCA
49555251 TTTCAAGTTTTATAATATATCACTCATGATAAATTAAACTTC
1 TTTCAAGTTTTATAATATATCACTCATGATAAATTAAACTTC
49555293 TTTCAAGTTTTATAATATATCACTCATGATAAATTAAACTTC
1 TTTCAAGTTTTATAATATATCACTCATGATAAATTAAACTTC
49555335 TTT
1 TTT
49555338 TTCTTTGTAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.37, C:0.14, G:0.05, T:0.45
Consensus pattern (42 bp):
TTTCAAGTTTTATAATATATCACTCATGATAAATTAAACTTC
Done.