Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D03
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: 50986338
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 218898 characters in sequence are not A, C, G, or T
File 45 of 170
Found at i:13118638 original size:16 final size:16
Alignment explanation
Indices: 13118591--13118629 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 16
13118581 GGCCTAAATG
*
13118591 ATTATTATCATTACTATT
1 ATTATTAT-ATT-TTATT
13118609 ATTATTATATTTTATT
1 ATTATTATATTTTATT
13118625 ATTAT
1 ATTAT
13118630 ATTTATTTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 9 0.45
17 3 0.15
18 8 0.40
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (16 bp):
ATTATTATATTTTATT
Found at i:13119299 original size:40 final size:42
Alignment explanation
Indices: 13119220--13119311 Score: 100
Period size: 42 Copynumber: 2.2 Consensus size: 42
13119210 TAAAGCTTTG
* * *
13119220 ATTTTTAAGAAAAATAGTGATTTTTAAAAAAAGAGAGTTTAT
1 ATTTTTAAAAAAAATAGTCATTTTTAAAAAAAGAGAGTTTAA
**
13119262 ATTTTTAAAAAAAATTAGTCA-TTTTAAAGGAA-A-AGTTTAA
1 ATTTTTAAAAAAAA-TAGTCATTTTTAAAAAAAGAGAGTTTAA
*
13119302 AATTTTAAAA
1 ATTTTTAAAA
13119312 CAAAGTTTTG
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
40 15 0.35
41 1 0.02
42 22 0.51
43 5 0.12
ACGTcount: A:0.50, C:0.01, G:0.11, T:0.38
Consensus pattern (42 bp):
ATTTTTAAAAAAAATAGTCATTTTTAAAAAAAGAGAGTTTAA
Found at i:13119397 original size:19 final size:19
Alignment explanation
Indices: 13119350--13119397 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
13119340 GAAATAAAGC
*
13119350 TTTT-ATTTTTAAGGAAAA
1 TTTTGATTTTTAAAGAAAA
**
13119368 TAGTGATTTTTTAAAGAAAA
1 TTTTGA-TTTTTAAAGAAAA
13119388 TTTTGATTTT
1 TTTTGATTTT
13119398 GCAAAAAAAC
Statistics
Matches: 23, Mismatches: 5, Indels: 3
0.74 0.16 0.10
Matches are distributed among these distances:
18 2 0.09
19 5 0.22
20 16 0.70
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.52
Consensus pattern (19 bp):
TTTTGATTTTTAAAGAAAA
Found at i:13126617 original size:18 final size:18
Alignment explanation
Indices: 13126594--13126629 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
13126584 ATTTAGAACA
13126594 ATTATAGTAATATTTTTC
1 ATTATAGTAATATTTTTC
13126612 ATTATAGTAATATTTTTC
1 ATTATAGTAATATTTTTC
13126630 TGAAAATATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.06, G:0.06, T:0.56
Consensus pattern (18 bp):
ATTATAGTAATATTTTTC
Found at i:13129351 original size:134 final size:134
Alignment explanation
Indices: 13129111--13129369 Score: 464
Period size: 134 Copynumber: 1.9 Consensus size: 134
13129101 TACTTATAAC
*
13129111 AAAATGACTCAACCTAAGTACATGCCATACTTAAACAAAATGAGATATATACAAATATTTCTGAG
1 AAAATGACTCAACCTAAATACATGCCATACTTAAACAAAATGAGATATATACAAATATTTCTGAG
* * *
13129176 TCGAGGGTCCACTTTCTGGACGCTAGAACTATTGCTTGAACTCTTATGAATCTATTATACATATG
66 TCGAGGGTCCACTTCCTGGACGCTAGAACTATTGCTTGAACTCTTAGGAACCTATTATACATATG
13129241 CCTA
131 CCTA
*
13129245 AAAATGACTTAACCTAAATACATGCCATACTTAAACAAAATGAGATATATACAAATATTTCTGAG
1 AAAATGACTCAACCTAAATACATGCCATACTTAAACAAAATGAGATATATACAAATATTTCTGAG
*
13129310 TCGAGGGTCCACTTCCTGGATGCTAGAACTATTGCTTGAACTCTTAGGAACCTATTATAC
66 TCGAGGGTCCACTTCCTGGACGCTAGAACTATTGCTTGAACTCTTAGGAACCTATTATAC
13129370 TTGCGCATGG
Statistics
Matches: 119, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
134 119 1.00
ACGTcount: A:0.36, C:0.19, G:0.14, T:0.30
Consensus pattern (134 bp):
AAAATGACTCAACCTAAATACATGCCATACTTAAACAAAATGAGATATATACAAATATTTCTGAG
TCGAGGGTCCACTTCCTGGACGCTAGAACTATTGCTTGAACTCTTAGGAACCTATTATACATATG
CCTA
Found at i:13135288 original size:49 final size:48
Alignment explanation
Indices: 13135214--13135400 Score: 196
Period size: 49 Copynumber: 3.8 Consensus size: 48
13135204 CGGTATCTGT
*
13135214 ATAAGATGGGCCACTAGTAGCGCATGTTAGTTGCTAACCAGATGGGCGA
1 ATAAGATGGGCCACTGGTAG-GCATGTTAGTTGCTAACCAGATGGGCGA
* * *
13135263 ATAAGGTGGGCCACTGGTAAGGCATGTTAGTTTCTAACCAGATTGGC-A
1 ATAAGATGGGCCACTGGT-AGGCATGTTAGTTGCTAACCAGATGGGCGA
** * * * *
13135311 GATGTGATAGACCATTGGTAGGGCATGTTAGTTGCTAACCAGATGGGTGA
1 -ATAAGATGGGCCACTGGTA-GGCATGTTAGTTGCTAACCAGATGGGCGA
* * * *
13135361 ATAAGGTGGGCCACTGATTGGACATGTTAGTTGGTAACCA
1 ATAAGATGGGCCACTGGTAGG-CATGTTAGTTGCTAACCA
13135401 TATTGGCTTG
Statistics
Matches: 111, Mismatches: 22, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
48 4 0.04
49 104 0.94
50 3 0.03
ACGTcount: A:0.27, C:0.16, G:0.31, T:0.26
Consensus pattern (48 bp):
ATAAGATGGGCCACTGGTAGGCATGTTAGTTGCTAACCAGATGGGCGA
Found at i:13135406 original size:98 final size:98
Alignment explanation
Indices: 13135230--13135449 Score: 284
Period size: 98 Copynumber: 2.2 Consensus size: 98
13135220 TGGGCCACTA
* *
13135230 GTAGCGCATGTTAGTTGCTAACCAGATGGGCGAATAAGGTGGGCCACTGGTAAGGCATGTTAGTT
1 GTAGGGCATGTTAGTTGCTAACCAGATGGGCGAATAAGGTGGGCCACTGATAAGGCATGTTAGTT
*
13135295 TCTAACCAGATTGGC-AGATGTGATAGACCAT-TG
66 GCTAACCAGATTGGCTAGA-GTGATAG-CCATCTG
* *
13135328 GTAGGGCATGTTAGTTGCTAACCAGATGGGTGAATAAGGTGGGCCACTGAT-TGGACATGTTAGT
1 GTAGGGCATGTTAGTTGCTAACCAGATGGGCGAATAAGGTGGGCCACTGATAAGG-CATGTTAGT
* * * * ***
13135392 TGGTAACCATATTGGCTTGAGTGCTAGGTTTCTG
65 TGCTAACCAGATTGGCTAGAGTGATAGCCATCTG
13135426 GTAGGGCATGTTAGTTGCTAACCA
1 GTAGGGCATGTTAGTTGCTAACCA
13135450 TGGCAAAGAG
Statistics
Matches: 107, Mismatches: 12, Indels: 6
0.86 0.10 0.05
Matches are distributed among these distances:
97 3 0.03
98 102 0.95
99 2 0.02
ACGTcount: A:0.25, C:0.15, G:0.31, T:0.29
Consensus pattern (98 bp):
GTAGGGCATGTTAGTTGCTAACCAGATGGGCGAATAAGGTGGGCCACTGATAAGGCATGTTAGTT
GCTAACCAGATTGGCTAGAGTGATAGCCATCTG
Found at i:13149811 original size:40 final size:40
Alignment explanation
Indices: 13149748--13149856 Score: 128
Period size: 40 Copynumber: 2.7 Consensus size: 40
13149738 GAAGTGCTCT
* * *
13149748 TGTTTGCACAACTGTGCCTCTGAATACACTTCGGTGTTCC
1 TGTTTGCACAACTATGCCCCTGAATACACTTCGGTGTCCC
* * *
13149788 TGTTTGCACAACTATGCCCCTGAATAAAATTTGGTGTCCC
1 TGTTTGCACAACTATGCCCCTGAATACACTTCGGTGTCCC
** * *
13149828 TGTTTGCACTTCGATGCCCCTGACTACAC
1 TGTTTGCACAACTATGCCCCTGAATACAC
13149857 GTATATGCCC
Statistics
Matches: 57, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 57 1.00
ACGTcount: A:0.20, C:0.28, G:0.18, T:0.33
Consensus pattern (40 bp):
TGTTTGCACAACTATGCCCCTGAATACACTTCGGTGTCCC
Found at i:13157896 original size:13 final size:13
Alignment explanation
Indices: 13157880--13157904 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13157870 ATAATTCAGT
13157880 AATATTTTTTAAA
1 AATATTTTTTAAA
13157893 AATATTTTTTAA
1 AATATTTTTTAA
13157905 TATATAATAA
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:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
AATATTTTTTAAA
Found at i:13158619 original size:12 final size:12
Alignment explanation
Indices: 13158602--13158626 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
13158592 AACAATTTGT
13158602 TACTTTTCTTGA
1 TACTTTTCTTGA
13158614 TACTTTTCTTGA
1 TACTTTTCTTGA
13158626 T
1 T
13158627 TATGATGCCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.16, G:0.08, T:0.60
Consensus pattern (12 bp):
TACTTTTCTTGA
Found at i:13162027 original size:41 final size:42
Alignment explanation
Indices: 13161982--13162134 Score: 188
Period size: 41 Copynumber: 3.7 Consensus size: 42
13161972 ACTTAATTAT
*
13161982 TCCCTAAATTACACATATGTGCCCCTGTTTGTACTTC-G-ATC
1 TCCCTAAATTGCACATATGTGCCCCTGTTTGTACTTCAGTA-C
13162023 TCCCTAAATTGCACATATGTGCCCCTGTTTGTACTTCAGTAC
1 TCCCTAAATTGCACATATGTGCCCCTGTTTGTACTTCAGTAC
* * * *
13162065 -CCCTGAATTGCACATTTATGCCCCTATTTGTACTTCAGTAC
1 TCCCTAAATTGCACATATGTGCCCCTGTTTGTACTTCAGTAC
* * * *
13162106 -CCCTAAATAGTACTTACGTGCCCCTGTTT
1 TCCCTAAATTGCACATATGTGCCCCTGTTT
13162135 ACACTCCGAT
Statistics
Matches: 97, Mismatches: 13, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
41 94 0.97
42 2 0.02
43 1 0.01
ACGTcount: A:0.22, C:0.29, G:0.13, T:0.36
Consensus pattern (42 bp):
TCCCTAAATTGCACATATGTGCCCCTGTTTGTACTTCAGTAC
Found at i:13162110 original size:20 final size:20
Alignment explanation
Indices: 13162044--13162110 Score: 64
Period size: 20 Copynumber: 3.3 Consensus size: 20
13162034 CACATATGTG
*
13162044 CCCCTGTTTGTACTTCAGTA
1 CCCCTATTTGTACTTCAGTA
* * * *
13162064 CCCCTGAATTGCACATTTA-TG
1 CCCCT-ATTTGTAC-TTCAGTA
13162085 CCCCTATTTGTACTTCAGTA
1 CCCCTATTTGTACTTCAGTA
13162105 CCCCTA
1 CCCCTA
13162111 AATAGTACTT
Statistics
Matches: 35, Mismatches: 9, Indels: 6
0.70 0.18 0.12
Matches are distributed among these distances:
19 3 0.09
20 18 0.51
21 11 0.31
22 3 0.09
ACGTcount: A:0.19, C:0.33, G:0.12, T:0.36
Consensus pattern (20 bp):
CCCCTATTTGTACTTCAGTA
Found at i:13173647 original size:35 final size:35
Alignment explanation
Indices: 13173562--13173682 Score: 125
Period size: 35 Copynumber: 3.5 Consensus size: 35
13173552 GTCGACTGGC
* *
13173562 CCTTCGGGGCAACACCGTGTAAATGGCATATAGGT
1 CCTTCGAGGCAACACCGTGTAAATGGTATATAGGT
* * ** * *
13173597 CATTTGAGGTGACACCGTATAAATGGTATATAAGT
1 CCTTCGAGGCAACACCGTGTAAATGGTATATAGGT
* * *
13173632 CCTTCGAGGCAACACCGTGCAAACGGTATACAGGT
1 CCTTCGAGGCAACACCGTGTAAATGGTATATAGGT
* *
13173667 CTTTCGGGGCAACACC
1 CCTTCGAGGCAACACC
13173683 TCAAAAGAGG
Statistics
Matches: 67, Mismatches: 19, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
35 67 1.00
ACGTcount: A:0.28, C:0.23, G:0.26, T:0.23
Consensus pattern (35 bp):
CCTTCGAGGCAACACCGTGTAAATGGTATATAGGT
Found at i:13180180 original size:14 final size:14
Alignment explanation
Indices: 13180161--13180189 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
13180151 AGTGTTGATT
13180161 TTACTATGTATATA
1 TTACTATGTATATA
13180175 TTACTATGTATATA
1 TTACTATGTATATA
13180189 T
1 T
13180190 ATATGTTGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.07, G:0.07, T:0.52
Consensus pattern (14 bp):
TTACTATGTATATA
Found at i:13181986 original size:18 final size:18
Alignment explanation
Indices: 13181965--13182006 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
13181955 GTAAGTTAGT
*
13181965 TTTTCAGTTTTCT-TGTTC
1 TTTTCAGTTTTATAT-TTC
*
13181983 TTTTAAGTTTTATATTTC
1 TTTTCAGTTTTATATTTC
13182001 TTTTCA
1 TTTTCA
13182007 ATTATTTTCA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 19 0.95
19 1 0.05
ACGTcount: A:0.14, C:0.12, G:0.07, T:0.67
Consensus pattern (18 bp):
TTTTCAGTTTTATATTTC
Found at i:13185358 original size:19 final size:19
Alignment explanation
Indices: 13185331--13185370 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
13185321 TAAAACTTTT
*
13185331 ATTATACTTTTCTATTCTA
1 ATTAAACTTTTCTATTCTA
* *
13185350 ATTAAACTTTTTTTTTCTA
1 ATTAAACTTTTCTATTCTA
13185369 AT
1 AT
13185371 AAAAAATAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.28, C:0.12, G:0.00, T:0.60
Consensus pattern (19 bp):
ATTAAACTTTTCTATTCTA
Found at i:13189326 original size:25 final size:25
Alignment explanation
Indices: 13189285--13189358 Score: 96
Period size: 25 Copynumber: 2.9 Consensus size: 25
13189275 TCTCATCCCT
*
13189285 ATTTT-ACCCAGTAAAAATTTTGACG
1 ATTTTAACCCGGT-AAAATTTTGACG
*
13189310 ATTTTAACCCGGTAAAATTTTGATG
1 ATTTTAACCCGGTAAAATTTTGACG
*
13189335 ATTTTACCCCTGGTAAAATTTTGA
1 ATTTTAACCC-GGTAAAATTTTGA
13189359 GAAAATATAT
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
25 25 0.57
26 19 0.43
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.39
Consensus pattern (25 bp):
ATTTTAACCCGGTAAAATTTTGACG
Found at i:13191513 original size:18 final size:17
Alignment explanation
Indices: 13191486--13191524 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
13191476 TATCTTTGCA
* *
13191486 TTTTTCTTTTCTATTTCT
1 TTTTTATTTTCT-TTTAT
13191504 TTTTTATTTTCTTTTAT
1 TTTTTATTTTCTTTTAT
13191521 TTTT
1 TTTT
13191525 ATCCATTTGC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.08, C:0.10, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTTTATTTTCTTTTAT
Found at i:13200274 original size:26 final size:26
Alignment explanation
Indices: 13200224--13200275 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
13200214 AATCTAAAAT
*
13200224 TTAGAAATATTTATTTTTTTGTGATA
1 TTAGAAATATTTATTTTATTGTGATA
13200250 TTAGAAATATTTATTTTGATT-TGATA
1 TTAGAAATATTTATTTT-ATTGTGATA
13200276 GTTAAGATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 22 0.92
27 2 0.08
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.56
Consensus pattern (26 bp):
TTAGAAATATTTATTTTATTGTGATA
Found at i:13201135 original size:18 final size:18
Alignment explanation
Indices: 13201101--13201136 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
13201091 ACTAAAGTTT
*
13201101 TATTTTAATATTCTTATA
1 TATTTTAATATTATTATA
*
13201119 TATTTTAATTTTATTATA
1 TATTTTAATATTATTATA
13201137 CACATTTTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (18 bp):
TATTTTAATATTATTATA
Found at i:13202511 original size:25 final size:25
Alignment explanation
Indices: 13202475--13202535 Score: 79
Period size: 25 Copynumber: 2.4 Consensus size: 25
13202465 TAAAAATGAA
*
13202475 ATTTATTATTATAT-TTTTTGAAATT
1 ATTTATTTTTATATATTTTT-AAATT
13202500 ATTTATTTTTATATATTTTTAAATT
1 ATTTATTTTTATATATTTTTAAATT
*
13202525 ATATATATTTT
1 ATTTAT-TTTT
13202536 CAACAATCAT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
25 23 0.72
26 9 0.28
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.66
Consensus pattern (25 bp):
ATTTATTTTTATATATTTTTAAATT
Found at i:13202576 original size:29 final size:30
Alignment explanation
Indices: 13202526--13202590 Score: 71
Period size: 30 Copynumber: 2.2 Consensus size: 30
13202516 TTTTAAATTA
* *
13202526 TATATATTTTCAACAATCATTT-TTTATTCT
1 TATATATTTTCAAAAATCATTTATGTATT-T
* *
13202556 TATATTTTTTTAAAAAT-ATTTATGTATTT
1 TATATATTTTCAAAAATCATTTATGTATTT
13202585 TATATA
1 TATATA
13202591 ATTATTTGAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
29 10 0.34
30 19 0.66
ACGTcount: A:0.34, C:0.06, G:0.02, T:0.58
Consensus pattern (30 bp):
TATATATTTTCAAAAATCATTTATGTATTT
Found at i:13208847 original size:26 final size:27
Alignment explanation
Indices: 13208812--13208862 Score: 86
Period size: 26 Copynumber: 1.9 Consensus size: 27
13208802 AACCACCACA
13208812 CTTTATCTTTTCTCCTCCACCCTTTCT
1 CTTTATCTTTTCTCCTCCACCCTTTCT
*
13208839 CTTT-TCTTTTCTTCTCCACCCTTT
1 CTTTATCTTTTCTCCTCCACCCTTT
13208863 GTTAGTGTCC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 19 0.83
27 4 0.17
ACGTcount: A:0.06, C:0.39, G:0.00, T:0.55
Consensus pattern (27 bp):
CTTTATCTTTTCTCCTCCACCCTTTCT
Found at i:13223516 original size:33 final size:33
Alignment explanation
Indices: 13223459--13223586 Score: 141
Period size: 33 Copynumber: 3.9 Consensus size: 33
13223449 GACTTACCTC
* * *
13223459 GTGTTTACTGT-CTAGACAGGCTATCTCTATTTT
1 GTGTTTACTGTCCCAG-CAGACTATCTCTGTTTT
* *
13223492 GTGCTTACTGTCCCAGCAGACTATCTTTGTTTT
1 GTGTTTACTGTCCCAGCAGACTATCTCTGTTTT
* * * * *
13223525 GTGTTTATTGTCCCAACGGACTATCTTTGTTCT
1 GTGTTTACTGTCCCAGCAGACTATCTCTGTTTT
*
13223558 GTGTTTACTGTCTCAGCAGACTATCTCTG
1 GTGTTTACTGTCCCAGCAGACTATCTCTG
13223587 AGGATGCCAT
Statistics
Matches: 79, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
33 76 0.96
34 3 0.04
ACGTcount: A:0.16, C:0.22, G:0.19, T:0.43
Consensus pattern (33 bp):
GTGTTTACTGTCCCAGCAGACTATCTCTGTTTT
Found at i:13223705 original size:58 final size:58
Alignment explanation
Indices: 13223637--13223749 Score: 172
Period size: 58 Copynumber: 1.9 Consensus size: 58
13223627 TATCTGACCG
* *
13223637 CCATAGCGTCTTTCATCCATGGTCTTACACCGTATACCTTATACCTTATACCATGGCA
1 CCATAACGTCTTTCATCCATGGTCTTACACCATATACCTTATACCTTATACCATGGCA
* * * *
13223695 CCATAACGTCTTTCATCCATGGTTTTACTCTATATACCTTTTACCTTATACCATG
1 CCATAACGTCTTTCATCCATGGTCTTACACCATATACCTTATACCTTATACCATG
13223750 CTGCAATGGT
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
58 49 1.00
ACGTcount: A:0.24, C:0.29, G:0.10, T:0.37
Consensus pattern (58 bp):
CCATAACGTCTTTCATCCATGGTCTTACACCATATACCTTATACCTTATACCATGGCA
Found at i:13227460 original size:22 final size:23
Alignment explanation
Indices: 13227432--13227503 Score: 73
Period size: 21 Copynumber: 3.3 Consensus size: 23
13227422 AGGTCGTGCT
*
13227432 CGTGTGAGATAGGCCACAT-GTC
1 CGTGTGAGATAGGTCACATAGTC
* * *
13227454 CGTGTGAG-TGGGTCAGATGGT-
1 CGTGTGAGATAGGTCACATAGTC
13227475 CGTGTG-GATAGGTCACATAG-C
1 CGTGTGAGATAGGTCACATAGTC
13227496 CGTGTGAG
1 CGTGTGAG
13227504 CAAACCATGT
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
20 1 0.03
21 28 0.70
22 11 0.28
ACGTcount: A:0.19, C:0.17, G:0.39, T:0.25
Consensus pattern (23 bp):
CGTGTGAGATAGGTCACATAGTC
Found at i:13229980 original size:24 final size:24
Alignment explanation
Indices: 13229906--13229982 Score: 63
Period size: 23 Copynumber: 3.3 Consensus size: 24
13229896 ACTTTCTTTT
* * * *
13229906 TGTTTTA-TTATAGTTTTGGTTAG
1 TGTTTTATTTATAATTTAGATTAA
*
13229929 TGTTTTA-TTATAATTTAGTTTAA
1 TGTTTTATTTATAATTTAGATTAA
*
13229952 -CTTTTATTTTATAATTTA-ATTAA
1 TGTTTTA-TTTATAATTTAGATTAA
13229975 TGTTTTAT
1 TGTTTTAT
13229983 AATATAAAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
22 5 0.11
23 24 0.55
24 15 0.34
ACGTcount: A:0.26, C:0.01, G:0.10, T:0.62
Consensus pattern (24 bp):
TGTTTTATTTATAATTTAGATTAA
Found at i:13234287 original size:25 final size:25
Alignment explanation
Indices: 13234257--13234367 Score: 82
Period size: 25 Copynumber: 4.5 Consensus size: 25
13234247 AGCCCTCCCT
13234257 TGAGCCATATAACAGGAAGCTCATG
1 TGAGCCATATAACAGGAAGCTCATG
** ** * *
13234282 TGAGCCATGGAATGGGAAGCTTATC
1 TGAGCCATATAACAGGAAGCTCATG
* * * * *
13234307 CGGGCTATATAACAAGAAGCTCATA
1 TGAGCCATATAACAGGAAGCTCATG
* **
13234332 AGAGCCATA-ATTAGGAAGCTCATG
1 TGAGCCATATAACAGGAAGCTCATG
13234356 TGAGCCA-ATAAC
1 TGAGCCATATAAC
13234368 GAGTAGCTCT
Statistics
Matches: 59, Mismatches: 26, Indels: 3
0.67 0.30 0.03
Matches are distributed among these distances:
23 1 0.02
24 18 0.31
25 40 0.68
ACGTcount: A:0.36, C:0.19, G:0.24, T:0.21
Consensus pattern (25 bp):
TGAGCCATATAACAGGAAGCTCATG
Found at i:13234400 original size:25 final size:25
Alignment explanation
Indices: 13234357--13234500 Score: 68
Period size: 25 Copynumber: 5.8 Consensus size: 25
13234347 AAGCTCATGT
* *
13234357 GAGCCAATAA-CGAGTAGCTCTGAA
1 GAGCCATTAATCGAGAAGCTCTGAA
* *
13234381 GAGCCATTAATCGAGAAGCTCCGGA
1 GAGCCATTAATCGAGAAGCTCTGAA
* * * *
13234406 TAGCCA-TATATGGGGAAG-T-TCAA
1 GAGCCATTA-ATCGAGAAGCTCTGAA
* *
13234429 GCGAGCCA-T-ATCGGGAAGCTCTGGA
1 --GAGCCATTAATCGAGAAGCTCTGAA
* **
13234454 GAGCCATTAATC-AGGAAGTTCACAAA
1 GAGCCATTAATCGA-GAAGCTC-TGAA
*
13234480 GAGCCTTTAATCGAGAAGCTC
1 GAGCCATTAATCGAGAAGCTC
13234501 ACAAAGAACC
Statistics
Matches: 88, Mismatches: 21, Indels: 20
0.68 0.16 0.16
Matches are distributed among these distances:
23 15 0.17
24 14 0.16
25 40 0.45
26 18 0.20
27 1 0.01
ACGTcount: A:0.33, C:0.21, G:0.26, T:0.19
Consensus pattern (25 bp):
GAGCCATTAATCGAGAAGCTCTGAA
Found at i:13234483 original size:26 final size:26
Alignment explanation
Indices: 13234453--13234512 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
13234443 GAAGCTCTGG
*
13234453 AGAGCCATTAATC-AGGAAGTTCACAA
1 AGAGCCATTAATCGA-GAAGCTCACAA
*
13234479 AGAGCCTTTAATCGAGAAGCTCACAA
1 AGAGCCATTAATCGAGAAGCTCACAA
*
13234505 AGAACCAT
1 AGAGCCAT
13234513 ATAACAAGAC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 28 0.97
27 1 0.03
ACGTcount: A:0.42, C:0.22, G:0.18, T:0.18
Consensus pattern (26 bp):
AGAGCCATTAATCGAGAAGCTCACAA
Found at i:13240835 original size:17 final size:18
Alignment explanation
Indices: 13240808--13240846 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
13240798 AATATGTTCG
*
13240808 ATTATTTTTAAAAATTTA
1 ATTATTTTTAAAAAATTA
13240826 ATTA-TTTTAAAAAATTA
1 ATTATTTTTAAAAAATTA
13240843 ATTA
1 ATTA
13240847 AAATTAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
ATTATTTTTAAAAAATTA
Found at i:13249600 original size:31 final size:31
Alignment explanation
Indices: 13249553--13249619 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 31
13249543 ATTACAAAAT
13249553 AGTTATTGAACAATTCAAAAAATTTCATTTA
1 AGTTATTGAACAATTCAAAAAATTTCATTTA
* * ** *
13249584 AGTTGTTGAACTATTCAAAAGTTTTTATTTA
1 AGTTATTGAACAATTCAAAAAATTTCATTTA
13249615 AGTTA
1 AGTTA
13249620 CTAAATTGTT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.39, C:0.07, G:0.10, T:0.43
Consensus pattern (31 bp):
AGTTATTGAACAATTCAAAAAATTTCATTTA
Found at i:13256736 original size:50 final size:52
Alignment explanation
Indices: 13256655--13256759 Score: 160
Period size: 50 Copynumber: 2.1 Consensus size: 52
13256645 ACAAATACAA
*
13256655 AAAATTAAATACACAAGTATAATTTACTGATAAAAGAATAAGCGTTAGTATG
1 AAAATTAAATACACAAGTATAATTCACTGATAAAAGAATAAGCGTTAGTATG
* * *
13256707 AAAATTATATACA-AA-TATAATTCATTGATAAAAGAATAAGTGTTAGTATG
1 AAAATTAAATACACAAGTATAATTCACTGATAAAAGAATAAGCGTTAGTATG
13256757 AAA
1 AAA
13256760 TAAACATGTG
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
50 35 0.71
51 2 0.04
52 12 0.24
ACGTcount: A:0.51, C:0.06, G:0.12, T:0.30
Consensus pattern (52 bp):
AAAATTAAATACACAAGTATAATTCACTGATAAAAGAATAAGCGTTAGTATG
Found at i:13256840 original size:17 final size:18
Alignment explanation
Indices: 13256818--13256856 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
13256808 AGTGATTCCT
* *
13256818 ATAATT-AATTTATTAAA
1 ATAATTAAATTCATAAAA
13256835 ATAATTAAATTCATAAAA
1 ATAATTAAATTCATAAAA
13256853 ATAA
1 ATAA
13256857 AATATAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (18 bp):
ATAATTAAATTCATAAAA
Found at i:13259455 original size:42 final size:42
Alignment explanation
Indices: 13259408--13259504 Score: 106
Period size: 43 Copynumber: 2.3 Consensus size: 42
13259398 TTATATTGAA
* *
13259408 GAATAAAGCCTAGAATTAG-AAAACAAAAGTAATATGTTTAAT
1 GAATAAAACCTAGAA-GAGTAAAACAAAAGTAATATGTTTAAT
* * *
13259450 GAATAAAAACTTAGCAGAGTTAAACAAAAGTAATATGTTTAAT
1 GAAT-AAAACCTAGAAGAGTAAAACAAAAGTAATATGTTTAAT
* *
13259493 AAATAAACCCTA
1 GAATAAAACCTA
13259505 ATTTTTTTAT
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
42 12 0.27
43 33 0.73
ACGTcount: A:0.53, C:0.09, G:0.12, T:0.26
Consensus pattern (42 bp):
GAATAAAACCTAGAAGAGTAAAACAAAAGTAATATGTTTAAT
Found at i:13260975 original size:26 final size:26
Alignment explanation
Indices: 13260939--13260997 Score: 82
Period size: 26 Copynumber: 2.3 Consensus size: 26
13260929 CTAGTGAGCT
13260939 TGAGTTTAAGTGGGTCAAAGGACCCC
1 TGAGTTTAAGTGGGTCAAAGGACCCC
* * * *
13260965 TGAGTTTAAGTGGTTCAGAGGACTCT
1 TGAGTTTAAGTGGGTCAAAGGACCCC
13260991 TGAGTTT
1 TGAGTTT
13260998 GTGTAACATC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.24, C:0.14, G:0.31, T:0.32
Consensus pattern (26 bp):
TGAGTTTAAGTGGGTCAAAGGACCCC
Found at i:13267128 original size:41 final size:41
Alignment explanation
Indices: 13267066--13267185 Score: 150
Period size: 41 Copynumber: 2.9 Consensus size: 41
13267056 TGATCGAATG
* *
13267066 TAATACAGACTTTACGTCTAGCAGGCTTGATGCCGGTGAAA
1 TAATTCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAA
*
13267107 TAATTCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGATA
1 TAATTCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAA
* * * * * * *
13267148 CATTTCGGACTATAGGTCTAGCAGGCTAAAAGCCGGTG
1 TAATTCAGACTTTACGTCTAGCAGGCTTAATGCCGGTG
13267186 TACTGAATCA
Statistics
Matches: 69, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 69 1.00
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.28
Consensus pattern (41 bp):
TAATTCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAA
Found at i:13267570 original size:25 final size:25
Alignment explanation
Indices: 13267539--13267613 Score: 97
Period size: 25 Copynumber: 3.2 Consensus size: 25
13267529 TGTATATATC
13267539 TATTCGAATGTATGTATTAGCTATG
1 TATTCGAATGTATGTATTAGCTATG
*
13267564 TATTCGAA--TATGTA-TA--TATA
1 TATTCGAATGTATGTATTAGCTATG
*
13267584 TATTCGAATGTAGGTATTAGCTATG
1 TATTCGAATGTATGTATTAGCTATG
13267609 TATTC
1 TATTC
13267614 AGGTAAAAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
20 11 0.26
22 7 0.17
23 8 0.19
25 16 0.38
ACGTcount: A:0.31, C:0.08, G:0.17, T:0.44
Consensus pattern (25 bp):
TATTCGAATGTATGTATTAGCTATG
Found at i:13267573 original size:45 final size:45
Alignment explanation
Indices: 13267524--13267613 Score: 162
Period size: 45 Copynumber: 2.0 Consensus size: 45
13267514 TGTATATGAT
* *
13267524 GAATATGTATATATCTATTCGAATGTATGTATTAGCTATGTATTC
1 GAATATGTATATATATATTCGAATGTAGGTATTAGCTATGTATTC
13267569 GAATATGTATATATATATTCGAATGTAGGTATTAGCTATGTATTC
1 GAATATGTATATATATATTCGAATGTAGGTATTAGCTATGTATTC
13267614 AGGTAAAAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.32, C:0.08, G:0.17, T:0.43
Consensus pattern (45 bp):
GAATATGTATATATATATTCGAATGTAGGTATTAGCTATGTATTC
Found at i:13267589 original size:20 final size:20
Alignment explanation
Indices: 13267524--13267592 Score: 75
Period size: 20 Copynumber: 3.2 Consensus size: 20
13267514 TGTATATGAT
*
13267524 GAATATGTATATATCTATTC
1 GAATATGTATATATATATTC
*
13267544 GAATGTATGTATTAGCTATGTATTC
1 GAA--TATGTA-TA--TATATATTC
13267569 GAATATGTATATATATATTC
1 GAATATGTATATATATATTC
13267589 GAAT
1 GAAT
13267593 GTAGGTATTA
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
20 15 0.36
22 8 0.19
23 8 0.19
25 11 0.26
ACGTcount: A:0.35, C:0.07, G:0.14, T:0.43
Consensus pattern (20 bp):
GAATATGTATATATATATTC
Found at i:13271619 original size:58 final size:58
Alignment explanation
Indices: 13271554--13271677 Score: 232
Period size: 58 Copynumber: 2.2 Consensus size: 58
13271544 AAATTCAAAG
13271554 AAAGATTTGTATCTGTTGCAGATAATAACTATAATATTCAAATCAGAATATTATTATA
1 AAAGATTTGTATCTGTTGCAGATAATAACTATAATATTCAAATCAGAATATTATTATA
13271612 AAAGATTTGTATCTGTTGCAGATAATAACTATAATATTCAAATCAGAATATTATTATA
1 AAAGATTTGTATCTGTTGCAGATAATAACTATAATATTCAAATCAGAATATTATTATA
*
13271670 CAA-ATTTG
1 AAAGATTTG
13271678 GAAAAATAAA
Statistics
Matches: 65, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
57 5 0.08
58 60 0.92
ACGTcount: A:0.43, C:0.09, G:0.10, T:0.38
Consensus pattern (58 bp):
AAAGATTTGTATCTGTTGCAGATAATAACTATAATATTCAAATCAGAATATTATTATA
Found at i:13274523 original size:22 final size:22
Alignment explanation
Indices: 13274498--13274541 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
13274488 AACATAACAC
13274498 ATCATGTTCTCTAGTATGCATA
1 ATCATGTTCTCTAGTATGCATA
13274520 ATCATGTTCTCTAGTATGCATA
1 ATCATGTTCTCTAGTATGCATA
13274542 CATATATCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.27, C:0.18, G:0.14, T:0.41
Consensus pattern (22 bp):
ATCATGTTCTCTAGTATGCATA
Found at i:13287508 original size:50 final size:50
Alignment explanation
Indices: 13287384--13287627 Score: 240
Period size: 50 Copynumber: 4.7 Consensus size: 50
13287374 GGTAAAGAGA
* ** *
13287384 TCCCATGTAAGACCATGTCTGGGACATGGCTTTGGAATCATTGAGATTATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGG---CACCGAG---ATGAGAAG
*
13287440 TCCCATGTAAGACTATGTCTGGGACATGGCGTTGGCACCGAGATGAGAAG
1 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAAG
* *
13287490 TCTCATGTAAGACCATGTCTGGGACATGGCGTTGGCACAGAGATGAG-AG
1 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAAG
** * * * *
13287539 ATCCCCCCGTAAGACCATGTCTGGGACATGGC-ATGGTCACCTATATGAGAAC
1 -T-CCCATGTAAGACCATGTCTGGGACATGGCGTTGG-CACCGAGATGAGAAG
* * * *
13287591 TCTCATGTAAGACCATATCTGGGATATGGCATTGGCA
1 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA
13287628 GTACAAGAAA
Statistics
Matches: 161, Mismatches: 22, Indels: 16
0.81 0.11 0.08
Matches are distributed among these distances:
49 2 0.01
50 81 0.50
51 39 0.24
52 1 0.01
53 5 0.03
56 33 0.20
ACGTcount: A:0.27, C:0.20, G:0.28, T:0.25
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAAG
Found at i:13287595 original size:101 final size:103
Alignment explanation
Indices: 13287387--13287627 Score: 292
Period size: 101 Copynumber: 2.3 Consensus size: 103
13287377 AAAGAGATCC
* * * *
13287387 CATGTAAGACCATGTCTGGGACATGGCTTTGGAATCATTGAGATTATGAGAGGTCCCATGTAAGA
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCATCA-TGAG--TATGAGAGATCCCACGTAAGA
* * *
13287452 CTATGTCTGGGACATGGCGTTGGCACCGAGATGAGAAGTCT
63 CCATGTCTGGGACATGGCGATGGCACCGAGATGAGAACTCT
* *
13287493 CATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CA-GAG-ATGAGAGATCCCCCCGTAAGACC
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCATCATGAGTATGAGAGAT-CCCACGTAAGACC
* *
13287555 ATGTCTGGGACATGGC-ATGGTCACCTATATGAGAACTCT
65 ATGTCTGGGACATGGCGATGG-CACCGAGATGAGAACTCT
* *
13287594 CATGTAAGACCATATCTGGGATATGGCATTGGCA
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCA
13287628 GTACAAGAAA
Statistics
Matches: 120, Mismatches: 13, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
100 11 0.09
101 72 0.60
103 3 0.03
105 2 0.02
106 32 0.27
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (103 bp):
CATGTAAGACCATGTCTGGGACATGGCATTGGCATCATGAGTATGAGAGATCCCACGTAAGACCA
TGTCTGGGACATGGCGATGGCACCGAGATGAGAACTCT
Found at i:13294733 original size:24 final size:24
Alignment explanation
Indices: 13294700--13294746 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
13294690 TGAAAATATA
13294700 GTTTGACGGGACTGTAAACACGAG
1 GTTTGACGGGACTGTAAACACGAG
* *
13294724 GTTTGCCGGGATTGTAAACACGA
1 GTTTGACGGGACTGTAAACACGA
13294747 AAAAATGAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.28, C:0.17, G:0.32, T:0.23
Consensus pattern (24 bp):
GTTTGACGGGACTGTAAACACGAG
Found at i:13298503 original size:31 final size:34
Alignment explanation
Indices: 13298430--13298508 Score: 92
Period size: 35 Copynumber: 2.4 Consensus size: 34
13298420 TAATAACTTT
*
13298430 AATATTAAATTAATAAAATATTTATATACAAAATA
1 AATATTAAATTAATAAAATATCTATATA-AAAATA
* *
13298465 AACATTAAATTAATAATATA-CTAT-T-AAAATA
1 AATATTAAATTAATAAAATATCTATATAAAAATA
*
13298496 AGTATTAAATTAA
1 AATATTAAATTAA
13298509 GCTTAATATT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
31 17 0.44
33 1 0.03
34 3 0.08
35 18 0.46
ACGTcount: A:0.58, C:0.04, G:0.01, T:0.37
Consensus pattern (34 bp):
AATATTAAATTAATAAAATATCTATATAAAAATA
Found at i:13323195 original size:40 final size:39
Alignment explanation
Indices: 13323132--13323212 Score: 108
Period size: 40 Copynumber: 2.1 Consensus size: 39
13323122 GACGTGGACA
* * * *
13323132 CAAATCGCGCTTATGTGGGCGCGATTTGTTACCACGTCAG
1 CAAAGCGCGCTGACGTGGACGCGATTTGTTACCACGT-AG
*
13323172 CAAAGCGCGCTGACGTGGACGCGATTTGTTGCCACGTAG
1 CAAAGCGCGCTGACGTGGACGCGATTTGTTACCACGTAG
13323211 CA
1 CA
13323213 CGCCCTTGGG
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
39 4 0.11
40 32 0.89
ACGTcount: A:0.21, C:0.26, G:0.30, T:0.23
Consensus pattern (39 bp):
CAAAGCGCGCTGACGTGGACGCGATTTGTTACCACGTAG
Found at i:13323273 original size:21 final size:22
Alignment explanation
Indices: 13323248--13323290 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
13323238 TTTTTCCCAT
*
13323248 GTTA-GGTTTTTGGTTTTTAGG
1 GTTAGGGTTTATGGTTTTTAGG
13323269 GTTAGGGTTTATGGTTTTTAGG
1 GTTAGGGTTTATGGTTTTTAGG
13323291 ATTTTTAGGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.12, C:0.00, G:0.35, T:0.53
Consensus pattern (22 bp):
GTTAGGGTTTATGGTTTTTAGG
Found at i:13331039 original size:23 final size:23
Alignment explanation
Indices: 13331020--13331063 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
13331010 TAAATTTTGA
13331020 ATTATTTAGTGATAATATTTACG
1 ATTATTTAGTGATAATATTTACG
13331043 ATTATTTAGTGATAATATTTA
1 ATTATTTAGTGATAATATTTA
13331064 AGAAAAATCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.36, C:0.02, G:0.11, T:0.50
Consensus pattern (23 bp):
ATTATTTAGTGATAATATTTACG
Found at i:13331040 original size:13 final size:13
Alignment explanation
Indices: 13331022--13331063 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
13331012 AATTTTGAAT
13331022 TATTTAGTGATAA
1 TATTTAGTGATAA
*
13331035 TATTTA-CGAT--
1 TATTTAGTGATAA
13331045 TATTTAGTGATAA
1 TATTTAGTGATAA
13331058 TATTTA
1 TATTTA
13331064 AGAAAAATCT
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
10 6 0.25
11 3 0.12
12 3 0.12
13 12 0.50
ACGTcount: A:0.36, C:0.02, G:0.12, T:0.50
Consensus pattern (13 bp):
TATTTAGTGATAA
Found at i:13331943 original size:31 final size:30
Alignment explanation
Indices: 13331907--13331975 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 30
13331897 TAAAAAATAT
* *
13331907 TTTATTTATCCATTTATTTTATTTTTTAAAA
1 TTTATTTATCCATTT-TTTCATTTTTGAAAA
* * *
13331938 TTTATTTTTTCATTTTTTCATTTTTGAATA
1 TTTATTTATCCATTTTTTCATTTTTGAAAA
13331968 TTT-TTTAT
1 TTTATTTAT
13331976 TTTATTTTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
29 4 0.12
30 15 0.47
31 13 0.41
ACGTcount: A:0.23, C:0.06, G:0.01, T:0.70
Consensus pattern (30 bp):
TTTATTTATCCATTTTTTCATTTTTGAAAA
Found at i:13331983 original size:30 final size:29
Alignment explanation
Indices: 13331923--13331985 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 29
13331913 TATCCATTTA
*
13331923 TTTTATTTTTTAAAATTTATTTTTTCATT
1 TTTTATTTTTGAAAATTTATTTTTTCATT
* *
13331952 TTTTCATTTTTGAATATTT-TTTATTTTATT
1 TTTT-ATTTTTGAAAATTTATTT-TTTCATT
13331982 TTTT
1 TTTT
13331986 GTATTTCCTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
29 7 0.24
30 22 0.76
ACGTcount: A:0.21, C:0.03, G:0.02, T:0.75
Consensus pattern (29 bp):
TTTTATTTTTGAAAATTTATTTTTTCATT
Found at i:13338490 original size:17 final size:15
Alignment explanation
Indices: 13338462--13338501 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 15
13338452 ACTACGTTTG
13338462 AAAAAAATAAAATACA
1 AAAAAAATAAAATA-A
13338478 AAAAAAATAAAAATAA
1 AAAAAAAT-AAAATAA
*
13338494 ATAAAAAT
1 AAAAAAAT
13338502 GTATATTGGG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 16 0.73
17 6 0.27
ACGTcount: A:0.82, C:0.03, G:0.00, T:0.15
Consensus pattern (15 bp):
AAAAAAATAAAATAA
Found at i:13339104 original size:23 final size:23
Alignment explanation
Indices: 13339078--13339124 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
13339068 TAAATTTTGA
*
13339078 ATTATTTAGGGATAATATTTAGG
1 ATTATTTAGGGATAATACTTAGG
* *
13339101 ATTATTTAGTGATAGTACTTAGG
1 ATTATTTAGGGATAATACTTAGG
13339124 A
1 A
13339125 AAAATCTAGC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.34, C:0.02, G:0.21, T:0.43
Consensus pattern (23 bp):
ATTATTTAGGGATAATACTTAGG
Found at i:13342089 original size:97 final size:97
Alignment explanation
Indices: 13341923--13342117 Score: 381
Period size: 97 Copynumber: 2.0 Consensus size: 97
13341913 GTTTATTATC
13341923 TCCATCTTGTACTCTTCGTTGGTTTGCCGAATTAGTAAAATTTTCTTTGCCTGTAGTTTTTATTC
1 TCCATCTTGTACTCTTCGTTGGTTTGCCGAATTAGTAAAATTTTCTTTGCCTGTAGTTTTTATTC
13341988 TTTTCAGAGGAGTTTTTCATATAATATTTGGG
66 TTTTCAGAGGAGTTTTTCATATAATATTTGGG
*
13342020 TCCATCTTGTACTCTTCGTTGGTTTGCCGAATTAGTAAAGTTTTCTTTGCCTGTAGTTTTTATTC
1 TCCATCTTGTACTCTTCGTTGGTTTGCCGAATTAGTAAAATTTTCTTTGCCTGTAGTTTTTATTC
13342085 TTTTCAGAGGAGTTTTTCATATAATATTTGGG
66 TTTTCAGAGGAGTTTTTCATATAATATTTGGG
13342117 T
1 T
13342118 TCGATCTTCT
Statistics
Matches: 97, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
97 97 1.00
ACGTcount: A:0.19, C:0.14, G:0.18, T:0.49
Consensus pattern (97 bp):
TCCATCTTGTACTCTTCGTTGGTTTGCCGAATTAGTAAAATTTTCTTTGCCTGTAGTTTTTATTC
TTTTCAGAGGAGTTTTTCATATAATATTTGGG
Found at i:13344761 original size:23 final size:25
Alignment explanation
Indices: 13344706--13344761 Score: 89
Period size: 26 Copynumber: 2.3 Consensus size: 25
13344696 CATGCCCACA
13344706 TAATAAACAAATTGTATGCTAAAACG
1 TAATAAACAAATTGTATGCT-AAACG
13344732 TAATAAACAAATTGTATGCT-AA-G
1 TAATAAACAAATTGTATGCTAAACG
13344755 TAATAAA
1 TAATAAA
13344762 GCTCGGGTGA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
23 8 0.27
24 2 0.07
26 20 0.67
ACGTcount: A:0.52, C:0.09, G:0.11, T:0.29
Consensus pattern (25 bp):
TAATAAACAAATTGTATGCTAAACG
Found at i:13346050 original size:13 final size:13
Alignment explanation
Indices: 13346032--13346056 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13346022 GAATTAATAT
13346032 GTGTGAAAATTTC
1 GTGTGAAAATTTC
13346045 GTGTGAAAATTT
1 GTGTGAAAATTT
13346057 TATCGTTTGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.04, G:0.24, T:0.40
Consensus pattern (13 bp):
GTGTGAAAATTTC
Found at i:13347219 original size:44 final size:42
Alignment explanation
Indices: 13347146--13347252 Score: 128
Period size: 44 Copynumber: 2.5 Consensus size: 42
13347136 AGGATTCTGA
* *
13347146 TATATGA-TATCGTGTAAGAGCACGTCTGGGACGTTGGCATCG
1 TATATGATTA-CGTGTAAGACCACGTCTGGGACATTGGCATCG
* *
13347188 -ATTTGAGATTTACGTGTAAGACCATGTCTGGGACATTGGCATCG
1 TATAT--GA-TTACGTGTAAGACCACGTCTGGGACATTGGCATCG
13347232 TATATGATTACGTGTAAGACC
1 TATATGATTACGTGTAAGACC
13347253 TTATCCAAGA
Statistics
Matches: 55, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
41 3 0.05
42 14 0.25
43 4 0.07
44 29 0.53
45 5 0.09
ACGTcount: A:0.26, C:0.16, G:0.27, T:0.31
Consensus pattern (42 bp):
TATATGATTACGTGTAAGACCACGTCTGGGACATTGGCATCG
Found at i:13351899 original size:6 final size:6
Alignment explanation
Indices: 13351877--13351911 Score: 52
Period size: 6 Copynumber: 5.5 Consensus size: 6
13351867 TTTCTTATGA
13351877 TTTCAT TTATCCAT TTTCAT TTTCAT TTTCAT TTT
1 TTTCAT TT-T-CAT TTTCAT TTTCAT TTTCAT TTT
13351912 AGAGAAATCT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 20 0.74
7 2 0.07
8 5 0.19
ACGTcount: A:0.17, C:0.17, G:0.00, T:0.66
Consensus pattern (6 bp):
TTTCAT
Found at i:13351918 original size:62 final size:63
Alignment explanation
Indices: 13351825--13351957 Score: 148
Period size: 62 Copynumber: 2.1 Consensus size: 63
13351815 ATTTCCAAGT
* * *
13351825 CATTTTCATTTTTCTTTTTCTTTTTGAAGAAAACCACATCTATTTCT-TATGATT-TCATTTATC
1 CATTTTCATTTTTCATTTTCTTTTAGAAGAAAACCA-ATCT-TTTCTAAATGATTCTCATTTATC
* * * *
13351888 CATTTTCA-TTTTCATTTTCATTTTAG-AGAAATCTAATCTTTTCTAAATGTTTCTCATTTCTC
1 CATTTTCATTTTTCATTTTC-TTTTAGAAGAAAACCAATCTTTTCTAAATGATTCTCATTTATC
13351950 CATTTTCA
1 CATTTTCA
13351958 CCATTTCTAT
Statistics
Matches: 60, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
60 5 0.08
61 9 0.15
62 33 0.55
63 13 0.22
ACGTcount: A:0.24, C:0.18, G:0.05, T:0.53
Consensus pattern (63 bp):
CATTTTCATTTTTCATTTTCTTTTAGAAGAAAACCAATCTTTTCTAAATGATTCTCATTTATC
Found at i:13354128 original size:23 final size:23
Alignment explanation
Indices: 13354076--13354136 Score: 63
Period size: 23 Copynumber: 2.6 Consensus size: 23
13354066 TTTATACTTA
13354076 AATTATACCTTAATTAAGCTTAATT
1 AATTATA--TTAATTAAGCTTAATT
*
13354101 AATTAGT-TTAATTAAGACTTTATT
1 AATTA-TATTAATTAAG-CTTAATT
13354125 -ATTATATTAATT
1 AATTATATTAATT
13354137 TATCTATTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
22 1 0.03
23 19 0.59
24 6 0.19
25 5 0.16
26 1 0.03
ACGTcount: A:0.39, C:0.07, G:0.05, T:0.49
Consensus pattern (23 bp):
AATTATATTAATTAAGCTTAATT
Found at i:13357430 original size:85 final size:86
Alignment explanation
Indices: 13357195--13357419 Score: 285
Period size: 85 Copynumber: 2.6 Consensus size: 86
13357185 CTTAAGGGTG
* * *
13357195 CAAAAAG-CCCTCAAACTTTTTCAAAAGAAGTAATTAAGTCCCTGCTTTTTTTATTCACTCATTT
1 CAAAAAGACCCTCAAACTTTTTCAAAAAAAG-AATTAAGCCCCTGC---TTTTATTCACTCAATT
*
13357259 GGGCACTTGAACTTTCAAAATGCAT
62 AGGCACTTGAACTTTCAAAATGCAT
* * * *
13357284 CAAAAA-AGCTCTCAAACTTTTTCAAAAAAA-AATTAAGCCCTTACTTTTTTTCACTCAATTAGG
1 CAAAAAGA-CCCTCAAACTTTTTCAAAAAAAGAATTAAGCCCCTGCTTTTATTCACTCAATTAGG
* *
13357347 TACTTGGACTTTCAAAATGCAT
65 CACTTGAACTTTCAAAATGCAT
13357369 CAAAAAGACCCTCAAACTTTTTCAAAAAAAGCAATTAAGCCCCTGCTTTTA
1 CAAAAAGACCCTCAAACTTTTTCAAAAAAAG-AATTAAGCCCCTGCTTTTA
13357420 CTAAAAATTA
Statistics
Matches: 117, Mismatches: 14, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
85 63 0.54
86 1 0.01
87 16 0.14
88 11 0.09
89 6 0.05
90 20 0.17
ACGTcount: A:0.36, C:0.22, G:0.09, T:0.32
Consensus pattern (86 bp):
CAAAAAGACCCTCAAACTTTTTCAAAAAAAGAATTAAGCCCCTGCTTTTATTCACTCAATTAGGC
ACTTGAACTTTCAAAATGCAT
Found at i:13357908 original size:10 final size:10
Alignment explanation
Indices: 13357895--13357947 Score: 67
Period size: 10 Copynumber: 5.4 Consensus size: 10
13357885 TTTTAATAAA
13357895 TTTTAAATTT
1 TTTTAAATTT
13357905 TTTTAAATTT
1 TTTTAAATTT
13357915 TTATTAAATTT
1 TT-TTAAATTT
13357926 TTTT--ATTT
1 TTTTAAATTT
13357934 TTTCT-AATTT
1 TTT-TAAATTT
13357944 TTTT
1 TTTT
13357948 TCTAATTTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
8 7 0.17
9 2 0.05
10 21 0.52
11 10 0.25
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.74
Consensus pattern (10 bp):
TTTTAAATTT
Found at i:13357948 original size:19 final size:19
Alignment explanation
Indices: 13357900--13357948 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
13357890 ATAAATTTTA
*
13357900 AATTTTTTTAAATTTTTATT
1 AATTTTTTT-TATTTTTATT
*
13357920 AAATTTTTTTATTTTT-TCT
1 AATTTTTTTTATTTTTAT-T
13357939 AATTTTTTTT
1 AATTTTTTTT
13357949 CTAATTTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
18 1 0.04
19 16 0.64
20 8 0.32
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.73
Consensus pattern (19 bp):
AATTTTTTTTATTTTTATT
Found at i:13357956 original size:11 final size:12
Alignment explanation
Indices: 13357931--13357957 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
13357921 AATTTTTTTA
13357931 TTTTTTCTAATT
1 TTTTTTCTAATT
13357943 TTTTTTCTAATT
1 TTTTTTCTAATT
13357955 TTT
1 TTT
13357958 AATAAGAGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.15, C:0.07, G:0.00, T:0.78
Consensus pattern (12 bp):
TTTTTTCTAATT
Found at i:13358062 original size:85 final size:88
Alignment explanation
Indices: 13357966--13358183 Score: 257
Period size: 86 Copynumber: 2.5 Consensus size: 88
13357956 TTAATAAGAG
* * *
13357966 TAGGGGCTTAATTGCTTTTTTGAAAAATTTTGAGGGTC-TTTTTGATGCATTTTGAAAGTTCAA-
1 TAGGGGCTTAATTGCTTTTTTGAAAAAGTTTGAGGG-CATTTTTGATACATTTTGAAAGCTCAAG
*
13358029 GTAC-CTTGAATG-AAAAAAAAAA
65 GTACAATTGAATGCAAAAAAAAAA
* *
13358051 TAGGGGCTTAATTGCTTTTTTTGAATAAGTTTGAGGGCATTTTTTATACATTTTGAAAGCTCAAG
1 TAGGGGCTTAATTGC-TTTTTTGAAAAAGTTTGAGGGCATTTTTGATACATTTTGAAAGCTCAAG
* *
13358116 TGTTCAATTGAGTGCAAAAAAAAAA
65 -GTACAATTGAATGCAAAAAAAAAA
* * * *
13358141 GAGGGGCTCAATTGCTTTTTTAAAAAAAGTTTGGGGGC-TTTTT
1 TAGGGGCTTAATTGCTTTTTT-GAAAAAGTTTGAGGGCATTTTT
13358184 ACACCCTTAA
Statistics
Matches: 113, Mismatches: 13, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
85 16 0.14
86 41 0.36
88 3 0.03
89 17 0.15
90 36 0.32
ACGTcount: A:0.32, C:0.09, G:0.22, T:0.38
Consensus pattern (88 bp):
TAGGGGCTTAATTGCTTTTTTGAAAAAGTTTGAGGGCATTTTTGATACATTTTGAAAGCTCAAGG
TACAATTGAATGCAAAAAAAAAA
Found at i:13358094 original size:86 final size:88
Alignment explanation
Indices: 13357966--13358183 Score: 264
Period size: 90 Copynumber: 2.5 Consensus size: 88
13357956 TTAATAAGAG
* * *
13357966 TAGGGGCTTAATTGC-TTTTTTGAAAAATTTTGAGGGTCTTTTTGATGCATTTTGAAAGTTCAA-
1 TAGGGGCTTAATTGCTTTTTTTGAAAAAGTTTGAGGG-CTTTTTGATACATTTTGAAAGCTCAAG
*
13358029 GTAC-CTTGAATG-AAAAAAAAAA
65 GTACAATTGAATGCAAAAAAAAAA
* *
13358051 TAGGGGCTTAATTGCTTTTTTTGAATAAGTTTGAGGGCATTTTTTATACATTTTGAAAGCTCAAG
1 TAGGGGCTTAATTGCTTTTTTTGAAAAAGTTTGAGGGC-TTTTTGATACATTTTGAAAGCTCAAG
* *
13358116 TGTTCAATTGAGTGCAAAAAAAAAA
65 -GTACAATTGAATGCAAAAAAAAAA
* * ** *
13358141 GAGGGGCTCAATTGCTTTTTTAAAAAAAGTTTGGGGGCTTTTT
1 TAGGGGCTTAATTGCTTTTTTTGAAAAAGTTTGAGGGCTTTTT
13358184 ACACCCTTAA
Statistics
Matches: 113, Mismatches: 14, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
85 16 0.14
86 41 0.36
88 3 0.03
89 11 0.10
90 42 0.37
ACGTcount: A:0.32, C:0.09, G:0.22, T:0.38
Consensus pattern (88 bp):
TAGGGGCTTAATTGCTTTTTTTGAAAAAGTTTGAGGGCTTTTTGATACATTTTGAAAGCTCAAGG
TACAATTGAATGCAAAAAAAAAA
Found at i:13358264 original size:20 final size:19
Alignment explanation
Indices: 13358241--13358280 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
13358231 CATATTAAAT
13358241 AGTTTAAAAATAATTTTTAA
1 AGTTTAAAAA-AATTTTTAA
* *
13358261 AGTTTTAAAAAGTTTTTAA
1 AGTTTAAAAAAATTTTTAA
13358280 A
1 A
13358281 AAACGTATAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.45
Consensus pattern (19 bp):
AGTTTAAAAAAATTTTTAA
Found at i:13359074 original size:31 final size:33
Alignment explanation
Indices: 13359036--13359117 Score: 105
Period size: 31 Copynumber: 2.5 Consensus size: 33
13359026 TTTTTGGATC
13359036 AATTTGGTACCTGAACTTGGCA-CTTTCT-CCT
1 AATTTGGTACCTGAACTTGGCATCTTTCTCCCT
* * * *
13359067 AATTTGGTACTTGAGCTTGGCATTTTTTTCCCT
1 AATTTGGTACCTGAACTTGGCATCTTTCTCCCT
*
13359100 AATTTGGTACCTAAACTT
1 AATTTGGTACCTGAACTT
13359118 TTTTTAGGCT
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
31 20 0.48
32 4 0.10
33 18 0.43
ACGTcount: A:0.21, C:0.21, G:0.16, T:0.43
Consensus pattern (33 bp):
AATTTGGTACCTGAACTTGGCATCTTTCTCCCT
Found at i:13359351 original size:23 final size:21
Alignment explanation
Indices: 13359306--13359358 Score: 61
Period size: 23 Copynumber: 2.4 Consensus size: 21
13359296 TATTATTTGA
**
13359306 ATTTTTAAAATTTATAATTAT
1 ATTTTTAAAATTTATAAAAAT
*
13359327 ATATTTTAGAATTTTATAAAAAT
1 AT-TTTTA-AAATTTATAAAAAT
13359350 ATTTTTAAA
1 ATTTTTAAA
13359359 CCTTTTTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 4 0.15
22 10 0.37
23 13 0.48
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (21 bp):
ATTTTTAAAATTTATAAAAAT
Found at i:13359414 original size:20 final size:20
Alignment explanation
Indices: 13359368--13359415 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
13359358 ACCTTTTTTA
13359368 ATTATTTTTATATATTATAT
1 ATTATTTTTATATATTATAT
* *
13359388 ATGATTTTTATAT-TTTTAT
1 ATTATTTTTATATATTATAT
13359407 ATTTATTTT
1 A-TTATTTT
13359416 AAATAAACCT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 6 0.25
20 18 0.75
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (20 bp):
ATTATTTTTATATATTATAT
Found at i:13365646 original size:17 final size:18
Alignment explanation
Indices: 13365624--13365658 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
13365614 ATAACGGTAC
13365624 GTCAGCA-AGATACATAT
1 GTCAGCACAGATACATAT
*
13365641 GTCAGCACAGCTACATAT
1 GTCAGCACAGATACATAT
13365659 TATTATTCGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.37, C:0.23, G:0.17, T:0.23
Consensus pattern (18 bp):
GTCAGCACAGATACATAT
Found at i:13369187 original size:18 final size:17
Alignment explanation
Indices: 13369160--13369203 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
13369150 CTTGTTAATC
**
13369160 ATTTTTTACATTTTTTA
1 ATTTTTTACAAATTTTA
13369177 ATTTTTGTACAAATTTTA
1 ATTTTT-TACAAATTTTA
13369195 ATGTTTTTA
1 AT-TTTTTA
13369204 ATAATTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 6 0.26
18 13 0.57
19 4 0.17
ACGTcount: A:0.27, C:0.05, G:0.05, T:0.64
Consensus pattern (17 bp):
ATTTTTTACAAATTTTA
Found at i:13371383 original size:12 final size:12
Alignment explanation
Indices: 13371366--13371390 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
13371356 AGTCTGTAAG
13371366 AAAATTTATTTT
1 AAAATTTATTTT
13371378 AAAATTTATTTT
1 AAAATTTATTTT
13371390 A
1 A
13371391 TGGTCTACCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
AAAATTTATTTT
Found at i:13372607 original size:24 final size:25
Alignment explanation
Indices: 13372555--13372601 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
13372545 TAGCCCTTTT
* *
13372555 GAGCTTCCCGTTATATAGTTCTTGC
1 GAGCTTCCCGTTATACAGCTCTTGC
13372580 GAGCTTCCCGTTA-ACAGCTCTT
1 GAGCTTCCCGTTATACAGCTCTT
13372602 CGGAGCATCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.17, C:0.28, G:0.19, T:0.36
Consensus pattern (25 bp):
GAGCTTCCCGTTATACAGCTCTTGC
Found at i:13372788 original size:25 final size:25
Alignment explanation
Indices: 13372760--13372814 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
13372750 TGGCTCACTT
*
13372760 GAGCTT-CCGAATATATGGCTATTCG
1 GAGCTTCCCGAATA-ATGGCTATTCA
* *
13372785 GAGCTTCCCGATTAATGGCTCTTCA
1 GAGCTTCCCGAATAATGGCTATTCA
13372810 GAGCT
1 GAGCT
13372815 ACTCGTTATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 20 0.77
26 6 0.23
ACGTcount: A:0.22, C:0.24, G:0.24, T:0.31
Consensus pattern (25 bp):
GAGCTTCCCGAATAATGGCTATTCA
Found at i:13372841 original size:49 final size:50
Alignment explanation
Indices: 13372786--13372912 Score: 136
Period size: 49 Copynumber: 2.6 Consensus size: 50
13372776 GGCTATTCGG
* * **
13372786 AGCTTCCCGATTAATGGCTCTTCA-GAGCTACTCGTTAT-TGGCTTGCATA
1 AGCTTCCCGATTAATGGCTCTT-ATGAGCTACCCGTTATATAGCCCGCATA
* *
13372835 AGCTTCCCGATT-ATGGCTCTTATGAGCTTCCCGTTATATAGCCCGGATA
1 AGCTTCCCGATTAATGGCTCTTATGAGCTACCCGTTATATAGCCCGCATA
**
13372884 AGCTTCCC-ATTACATGGCTCACATGAGCT
1 AGCTTCCCGATTA-ATGGCTCTTATGAGCT
13372913 TTCTGTTATA
Statistics
Matches: 66, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
47 1 0.02
48 24 0.36
49 27 0.41
50 14 0.21
ACGTcount: A:0.21, C:0.27, G:0.20, T:0.32
Consensus pattern (50 bp):
AGCTTCCCGATTAATGGCTCTTATGAGCTACCCGTTATATAGCCCGCATA
Found at i:13377663 original size:21 final size:23
Alignment explanation
Indices: 13377639--13377686 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 23
13377629 TTGGAATTAT
13377639 ATTTTATTT-TTTTA-ATTAAAA
1 ATTTTATTTATTTTACATTAAAA
13377660 ATTTTATTTATTTTATCATTAAAA
1 ATTTTATTTATTTTA-CATTAAAA
13377684 ATT
1 ATT
13377687 AATCTTTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
21 9 0.38
22 5 0.21
24 10 0.42
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (23 bp):
ATTTTATTTATTTTACATTAAAA
Found at i:13387235 original size:21 final size:21
Alignment explanation
Indices: 13387200--13387269 Score: 79
Period size: 21 Copynumber: 3.3 Consensus size: 21
13387190 CTTCAATCCC
*
13387200 CAATTTCAAATTTTATATTTT
1 CAATTTCAAATTTTAAATTTT
13387221 CAATCTTCAAA-TTTAAATTTT
1 CAAT-TTCAAATTTTAAATTTT
** *
13387242 CAATTTTTAATTTTTAATTTT
1 CAATTTCAAATTTTAAATTTT
*
13387263 GAATTTC
1 CAATTTC
13387270 CAATCCTCAA
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
20 4 0.10
21 31 0.76
22 6 0.15
ACGTcount: A:0.33, C:0.10, G:0.01, T:0.56
Consensus pattern (21 bp):
CAATTTCAAATTTTAAATTTT
Found at i:13387246 original size:7 final size:7
Alignment explanation
Indices: 13387203--13387273 Score: 54
Period size: 7 Copynumber: 10.0 Consensus size: 7
13387193 CAATCCCCAA
13387203 TTTCAAAT
1 TTTC-AAT
13387211 TTT-ATAT
1 TTTCA-AT
13387218 TTTCAAT
1 TTTCAAT
* *
13387225 CTTCAAA
1 TTTCAAT
*
13387232 TTTAAAT
1 TTTCAAT
13387239 TTTCAAT
1 TTTCAAT
*
13387246 TTTTAAT
1 TTTCAAT
*
13387253 TTTTAAT
1 TTTCAAT
*
13387260 TTTGAAT
1 TTTCAAT
*
13387267 TTCCAAT
1 TTTCAAT
13387274 CCTCAATCCT
Statistics
Matches: 51, Mismatches: 10, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
6 1 0.02
7 46 0.90
8 4 0.08
ACGTcount: A:0.32, C:0.10, G:0.01, T:0.56
Consensus pattern (7 bp):
TTTCAAT
Found at i:13387247 original size:28 final size:28
Alignment explanation
Indices: 13387184--13387248 Score: 71
Period size: 28 Copynumber: 2.3 Consensus size: 28
13387174 ATTCTCAATC
* *
13387184 TTCAATCTTCAATCCCCAATTTCAAATT
1 TTCAATTTTCAATCCCAAATTTCAAATT
*
13387212 TT-ATATTTTCAATCTTCAAATTT-AAATT
1 TTCA-ATTTTCAATC-CCAAATTTCAAATT
13387240 TTCAATTTT
1 TTCAATTTT
13387249 TAATTTTTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
27 1 0.03
28 23 0.74
29 7 0.23
ACGTcount: A:0.32, C:0.18, G:0.00, T:0.49
Consensus pattern (28 bp):
TTCAATTTTCAATCCCAAATTTCAAATT
Found at i:13387253 original size:14 final size:14
Alignment explanation
Indices: 13387200--13387273 Score: 60
Period size: 14 Copynumber: 5.3 Consensus size: 14
13387190 CTTCAATCCC
*
13387200 CAATTTCAAATTTT
1 CAATTTTAAATTTT
* *
13387214 -ATATTTTCAATCTT
1 CA-ATTTTAAATTTT
*
13387228 CAAATTTAAATTTT
1 CAATTTTAAATTTT
*
13387242 CAATTTTTAATTTT
1 CAATTTTAAATTTT
* * *
13387256 TAATTTTGAATTTC
1 CAATTTTAAATTTT
13387270 CAAT
1 CAAT
13387274 CCTCAATCCT
Statistics
Matches: 46, Mismatches: 12, Indels: 4
0.74 0.19 0.06
Matches are distributed among these distances:
13 1 0.02
14 44 0.96
15 1 0.02
ACGTcount: A:0.34, C:0.11, G:0.01, T:0.54
Consensus pattern (14 bp):
CAATTTTAAATTTT
Found at i:13387373 original size:38 final size:38
Alignment explanation
Indices: 13387329--13387410 Score: 164
Period size: 38 Copynumber: 2.2 Consensus size: 38
13387319 CTCTTTGGTT
13387329 TTATTCTTTTCTTATAAAATTTTAAATGGCAAATCAAC
1 TTATTCTTTTCTTATAAAATTTTAAATGGCAAATCAAC
13387367 TTATTCTTTTCTTATAAAATTTTAAATGGCAAATCAAC
1 TTATTCTTTTCTTATAAAATTTTAAATGGCAAATCAAC
13387405 TTATTC
1 TTATTC
13387411 GTTTGGATGA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 44 1.00
ACGTcount: A:0.35, C:0.13, G:0.05, T:0.46
Consensus pattern (38 bp):
TTATTCTTTTCTTATAAAATTTTAAATGGCAAATCAAC
Found at i:13388003 original size:8 final size:8
Alignment explanation
Indices: 13387990--13388025 Score: 72
Period size: 8 Copynumber: 4.5 Consensus size: 8
13387980 ATTTATCAAC
13387990 TTTTATTA
1 TTTTATTA
13387998 TTTTATTA
1 TTTTATTA
13388006 TTTTATTA
1 TTTTATTA
13388014 TTTTATTA
1 TTTTATTA
13388022 TTTT
1 TTTT
13388026 GAATTTCTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 28 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (8 bp):
TTTTATTA
Found at i:13390464 original size:22 final size:22
Alignment explanation
Indices: 13390423--13390464 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
13390413 TTAGAATTAT
*
13390423 AATTTTAATTATGTTTAATTGA
1 AATTTTAATTATGTTCAATTGA
13390445 AATTTTAATTAT-TTACAATT
1 AATTTTAATTATGTT-CAATT
13390465 CAATACAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.55
Consensus pattern (22 bp):
AATTTTAATTATGTTCAATTGA
Found at i:13393798 original size:2 final size:2
Alignment explanation
Indices: 13393793--13393845 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
13393783 TCACAACCAT
13393793 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
13393835 CA CA CA CA CA C
1 CA CA CA CA CA C
13393846 TCATTCCCTG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.51, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:13394505 original size:9 final size:9
Alignment explanation
Indices: 13394491--13394519 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
13394481 TGAATTTTAC
13394491 AATTTGAAT
1 AATTTGAAT
13394500 AATTTGAAT
1 AATTTGAAT
13394509 AATTTGAAT
1 AATTTGAAT
13394518 AA
1 AA
13394520 CATATTTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.41
Consensus pattern (9 bp):
AATTTGAAT
Found at i:13403053 original size:11 final size:13
Alignment explanation
Indices: 13403037--13403070 Score: 54
Period size: 11 Copynumber: 2.8 Consensus size: 13
13403027 AATTTTACGG
13403037 AAAAATTTCG-T-
1 AAAAATTTCGTTC
13403048 AAAAATTTCGTTC
1 AAAAATTTCGTTC
13403061 AAAAATTTCG
1 AAAAATTTCG
13403071 ACGTTTGGGC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 10 0.48
12 1 0.05
13 10 0.48
ACGTcount: A:0.44, C:0.12, G:0.09, T:0.35
Consensus pattern (13 bp):
AAAAATTTCGTTC
Found at i:13404683 original size:40 final size:39
Alignment explanation
Indices: 13404639--13404822 Score: 181
Period size: 40 Copynumber: 4.6 Consensus size: 39
13404629 AAGTGAATAT
* * *
13404639 ATCCGGATTAAGATCCGAAGGCCTTTGTGCGAGATACTAA
1 ATCCGGGTTAAG-TCCGAAGGCATTCGTGCGAGATACTAA
* *
13404679 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAA
1 ATCCGGGTTAAGT-CCGAAGGCATTCGTGCGAGATACTAA
* * **
13404719 ATCCGGGTTAAGTCTCGAAGGCAGTCGTGCGAGTTGTTAA
1 ATCCGGGTTAAGTC-CGAAGGCATTCGTGCGAGATACTAA
* * *
13404759 ATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAA
1 ATCCGGGTTAAGT-CCGAAGGCATTCGTGCGAGATACTAA
* * *
13404798 AACCGGGCTATGTCCCGAAGGCATT
1 ATCCGGGTTAAGT-CCGAAGGCATT
13404823 TGAACGAGGA
Statistics
Matches: 127, Mismatches: 14, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
39 36 0.28
40 90 0.71
41 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (39 bp):
ATCCGGGTTAAGTCCGAAGGCATTCGTGCGAGATACTAA
Found at i:13404738 original size:80 final size:78
Alignment explanation
Indices: 13404600--13404824 Score: 234
Period size: 80 Copynumber: 2.8 Consensus size: 78
13404590 TTGAATGCTG
* * * * * * *
13404600 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATATCCGGATTAAGATCCGAAGGCCTTT
1 TCCGGGTTAAGTCCCGAAGGCATTGTGC-GAGTTAATAAATCCGGGTTAAG-TCCGAAGGCATTT
13404665 GTGCGAGATACTAAA
64 GTGCGAGATACTAAA
* * *
13404680 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCTCGAAGGCAGTC
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGTTAATAAATCCGGGTTAAGTC-CGAAGGCATTT
* **
13404745 GTGCGAGTTGTTAAA
64 GTGCGAGATACTAAA
* * * * * *
13404760 TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTAATAAATCCGGGTTAAGT-CCGAAGGCATTTG
13404825 AACGAGGAGC
Statistics
Matches: 121, Mismatches: 21, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
79 34 0.28
80 83 0.69
81 4 0.03
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.27
Consensus pattern (78 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTAATAAATCCGGGTTAAGTCCGAAGGCATTTGT
GCGAGATACTAAA
Found at i:13407284 original size:26 final size:26
Alignment explanation
Indices: 13407248--13407299 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
13407238 TGAATAAAAC
13407248 GGGGTTGCTAAGTGCTGATTCCCTGA
1 GGGGTTGCTAAGTGCTGATTCCCTGA
13407274 GGGGTTGCTAAGTGCTGATTCCCTGA
1 GGGGTTGCTAAGTGCTGATTCCCTGA
13407300 ATTATTGACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.15, C:0.19, G:0.35, T:0.31
Consensus pattern (26 bp):
GGGGTTGCTAAGTGCTGATTCCCTGA
Found at i:13407425 original size:85 final size:84
Alignment explanation
Indices: 13407311--13407511 Score: 260
Period size: 85 Copynumber: 2.4 Consensus size: 84
13407301 TTATTGACTC
* * ** *
13407311 TAAAGGTGGTTGCTAAGTGCTGATCCCACCGTATTTTTAATTGTGAAATGAGTTGCTA-GATGTT
1 TAAAGGTGGTTGCTAAGTGCTGATTCCACCGAATCCTTAATTGTGAAAGGAGTTGCTATG-TGTT
** *
13407375 GATTCCCCGTATCGTTGAAT
65 GATTCCCCGTATCACTAAAT
*
13407395 ATAAAGGTGGTTGCTAAGTGCTGATTCCACCGAATCCTTAATTGTGAAAGGGGTTGCTATGTGTT
1 -TAAAGGTGGTTGCTAAGTGCTGATTCCACCGAATCCTTAATTGTGAAAGGAGTTGCTATGTGTT
13407460 GATTCCCCGTATCACTAAAT
65 GATTCCCCGTATCACTAAAT
* * * *
13407480 TTATGGTGGTTGCTAAGTGCGGAATCCACCGA
1 TAAAGGTGGTTGCTAAGTGCTGATTCCACCGA
13407512 GTAACGGATA
Statistics
Matches: 102, Mismatches: 13, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
84 28 0.27
85 73 0.72
86 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.34
Consensus pattern (84 bp):
TAAAGGTGGTTGCTAAGTGCTGATTCCACCGAATCCTTAATTGTGAAAGGAGTTGCTATGTGTTG
ATTCCCCGTATCACTAAAT
Found at i:13407452 original size:43 final size:42
Alignment explanation
Indices: 13407276--13407499 Score: 156
Period size: 43 Copynumber: 5.3 Consensus size: 42
13407266 TTCCCTGAGG
* ** * * *
13407276 GGTTGCTAAGTGCTGATTCCCTGAATTATTGACTCTAAAGGT
1 GGTTGCTAAGTGCTGATTCCCCGAATCCTTAATTGTAAAGGT
* * **
13407318 GGTTGCTAAGTGCTGATCCCACCGTATTTTTAATTGTGAAA--T
1 GGTTGCTAAGTGCTGATTCC-CCGAATCCTTAATTGT-AAAGGT
* * * *
13407360 GAGTTGCT-AGATGTTGATTCCCCGTATCGTTGAA-TATAAAGGT
1 G-GTTGCTAAG-TGCTGATTCCCCGAATCCTT-AATTGTAAAGGT
13407403 GGTTGCTAAGTGCTGATTCCACCGAATCCTTAATTGTGAAAGG-
1 GGTTGCTAAGTGCTGATTCC-CCGAATCCTTAATTGT-AAAGGT
* * * * *
13407446 GGTTGCTATGTGTTGATTCCCCGTATCACTAAATT-T-ATGGT
1 GGTTGCTAAGTGCTGATTCCCCGAATC-CTTAATTGTAAAGGT
13407487 GGTTGCTAAGTGC
1 GGTTGCTAAGTGC
13407500 GGAATCCACC
Statistics
Matches: 146, Mismatches: 23, Indels: 27
0.74 0.12 0.14
Matches are distributed among these distances:
40 3 0.02
41 14 0.10
42 57 0.39
43 64 0.44
44 8 0.05
ACGTcount: A:0.23, C:0.17, G:0.25, T:0.36
Consensus pattern (42 bp):
GGTTGCTAAGTGCTGATTCCCCGAATCCTTAATTGTAAAGGT
Found at i:13411017 original size:28 final size:29
Alignment explanation
Indices: 13410985--13411043 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
13410975 TCCTTTTTGT
*
13410985 TTTTA-TTTATAACATTTGAATGCATGGA
1 TTTTATTTTATAACATTTGAATGCAAGGA
13411013 TTTTATTTTATAACATTTGAATGCAAGGA
1 TTTTATTTTATAACATTTGAATGCAAGGA
13411042 TT
1 TT
13411044 AAGGATTGAT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
28 5 0.17
29 24 0.83
ACGTcount: A:0.32, C:0.07, G:0.14, T:0.47
Consensus pattern (29 bp):
TTTTATTTTATAACATTTGAATGCAAGGA
Found at i:13414315 original size:28 final size:29
Alignment explanation
Indices: 13414255--13414318 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
13414245 TAGGGTCCTG
* *
13414255 ATTAAATTAGTTCCTTTATTATTAAATAG
1 ATTAAATTAGTTCCTTTACTATTAAATAA
*
13414284 ATTAATTTAG-TCCTTATACTATTAAA-AA
1 ATTAAATTAGTTCCTT-TACTATTAAATAA
13414312 ATTAAAT
1 ATTAAAT
13414319 AAGATAAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
28 12 0.40
29 18 0.60
ACGTcount: A:0.42, C:0.08, G:0.05, T:0.45
Consensus pattern (29 bp):
ATTAAATTAGTTCCTTTACTATTAAATAA
Found at i:13416725 original size:26 final size:26
Alignment explanation
Indices: 13416689--13416743 Score: 101
Period size: 26 Copynumber: 2.1 Consensus size: 26
13416679 TAAGATTTTG
*
13416689 ATTTTGATTTCTGTTATCTCCTTTAC
1 ATTTAGATTTCTGTTATCTCCTTTAC
13416715 ATTTAGATTTCTGTTATCTCCTTTAC
1 ATTTAGATTTCTGTTATCTCCTTTAC
13416741 ATT
1 ATT
13416744 GATAAATAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.18, C:0.18, G:0.07, T:0.56
Consensus pattern (26 bp):
ATTTAGATTTCTGTTATCTCCTTTAC
Found at i:13420731 original size:13 final size:13
Alignment explanation
Indices: 13420715--13420743 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
13420705 CCAAATTACA
13420715 TACAATAATTAAT
1 TACAATAATTAAT
13420728 TACAATAATTAAT
1 TACAATAATTAAT
13420741 TAC
1 TAC
13420744 CATTGATTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.38
Consensus pattern (13 bp):
TACAATAATTAAT
Found at i:13423617 original size:20 final size:20
Alignment explanation
Indices: 13423589--13423642 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
13423579 TGTTGGAGTT
* *
13423589 TGAATCGATTTAAACAATAA
1 TGAACCGATTCAAACAATAA
13423609 TGAACCGATTCAAACAATAA
1 TGAACCGATTCAAACAATAA
** *
13423629 ACAATCGATTCAAA
1 TGAACCGATTCAAA
13423643 GAAGCAAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.50, C:0.17, G:0.09, T:0.24
Consensus pattern (20 bp):
TGAACCGATTCAAACAATAA
Found at i:13424612 original size:32 final size:31
Alignment explanation
Indices: 13424561--13424621 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 31
13424551 TCTTCTTTTT
* *
13424561 AGCTAAATTTGACCCTCAACCATTTTAAAATG
1 AGCTAAATTTGACCATCAACC-TTCTAAAATG
* *
13424593 AGCTGAATTTGGCCATCAACCTTCTAAAA
1 AGCTAAATTTGACCATCAACCTTCTAAAA
13424622 AAAAGTCAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
31 7 0.28
32 18 0.72
ACGTcount: A:0.36, C:0.23, G:0.11, T:0.30
Consensus pattern (31 bp):
AGCTAAATTTGACCATCAACCTTCTAAAATG
Found at i:13428339 original size:63 final size:62
Alignment explanation
Indices: 13428146--13428349 Score: 214
Period size: 63 Copynumber: 3.3 Consensus size: 62
13428136 AATATCTCTC
* * * *
13428146 ACACGGCCTGGACATATGCCCATGTCCCTGGCCCATATGACTC-GAATTTACAAAAAATGAGTT
1 ACACGGCCTGGACACA-GCCCATGTCCCTGGCCCGTGTGACTCTG-ATTCACAAAAAATGAGTT
** * * * **
13428209 ACATAGCCTGAACACAGGCCTATGTCCTTGATCCGTGTGACTCTGATTCACAAAAAATGAGTT
1 ACACGGCCTGGACACA-GCCCATGTCCCTGGCCCGTGTGACTCTGATTCACAAAAAATGAGTT
* * * *
13428272 ACACGGCCTGGACACACGTCCGTGTCCCTGGCCCGTGTGACTCTGAGTCACAAATAATGAGTT
1 ACACGGCCTGGACACA-GCCCATGTCCCTGGCCCGTGTGACTCTGATTCACAAAAAATGAGTT
*
13428335 ACACGGACT-GACACA
1 ACACGGCCTGGACACA
13428350 TAGCCGTGTA
Statistics
Matches: 115, Mismatches: 25, Indels: 3
0.80 0.17 0.02
Matches are distributed among these distances:
62 6 0.05
63 108 0.94
64 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.23
Consensus pattern (62 bp):
ACACGGCCTGGACACAGCCCATGTCCCTGGCCCGTGTGACTCTGATTCACAAAAAATGAGTT
Found at i:13429981 original size:13 final size:13
Alignment explanation
Indices: 13429963--13429987 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13429953 GCAATTATAT
13429963 ATTTATTTAATGA
1 ATTTATTTAATGA
13429976 ATTTATTTAATG
1 ATTTATTTAATG
13429988 TTGACTCAAG
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:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (13 bp):
ATTTATTTAATGA
Found at i:13430148 original size:50 final size:50
Alignment explanation
Indices: 13430094--13430224 Score: 190
Period size: 50 Copynumber: 2.6 Consensus size: 50
13430084 GAGGTCCCAT
*
13430094 GTAAGACCATGTCTGGGATATGGCATTGGCACCGAGATGAGAAGTCCCCC
1 GTAAGACCATGTCTGGGATATGGCATTGGCACCGAGATGAGAACTCCCCC
* * * * **
13430144 GTAAGACCATGTCTGGGACATGACATGGGCACCGATATGAGAACTCCCTT
1 GTAAGACCATGTCTGGGATATGGCATTGGCACCGAGATGAGAACTCCCCC
*
13430194 GTAAGACCATATCTGGGATATGGCATTGGCA
1 GTAAGACCATGTCTGGGATATGGCATTGGCA
13430225 GTACAAGAAA
Statistics
Matches: 70, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
50 70 1.00
ACGTcount: A:0.27, C:0.22, G:0.28, T:0.22
Consensus pattern (50 bp):
GTAAGACCATGTCTGGGATATGGCATTGGCACCGAGATGAGAACTCCCCC
Found at i:13439145 original size:31 final size:31
Alignment explanation
Indices: 13439110--13439641 Score: 387
Period size: 31 Copynumber: 17.4 Consensus size: 31
13439100 TCATATATAA
* *
13439110 TTATACATTACTGAAATTAATTTATATATGG
1 TTATACATTGCTGAAATTAATTTGTATATGG
* *
13439141 TTATACGTTG-TTAACATTGAA-TTGTATATGG
1 TTATACATTGCTGAA-ATT-AATTTGTATATGG
* *
13439172 ATATA-AGTTGCTG-AATTAATTCGTATATGG
1 TTATACA-TTGCTGAAATTAATTTGTATATGG
* * *
13439202 TTGTACATTGCTGAAATTTATTTGTATATGA
1 TTATACATTGCTGAAATTAATTTGTATATGG
* * *
13439233 TTATACATT-ATCGAAATTGATTTGTATATGA
1 TTATACATTGCT-GAAATTAATTTGTATATGG
** * * **
13439264 AGATA-AGTTGCCG-AATTAATTCGTATATAA
1 TTATACA-TTGCTGAAATTAATTTGTATATGG
**
13439294 TTATACATTTTTGAAATTAATTTGTATATGG
1 TTATACATTGCTGAAATTAATTTGTATATGG
*
13439325 TTATACATTGTTGAAATTGAA-TTGTATATGG
1 TTATACATTGCTGAAATT-AATTTGTATATGG
* *
13439356 ATATA-AGTTGCTG-AATTAATTCGTATATGG
1 TTATACA-TTGCTGAAATTAATTTGTATATGG
* * *
13439386 TTGTACGTTGCTGAAATTTATTTGTATATGG
1 TTATACATTGCTGAAATTAATTTGTATATGG
* * * *
13439417 TTATACATT-ATCAAAATTGATTTGTATATGA
1 TTATACATTGCT-GAAATTAATTTGTATATGG
** * * *
13439448 AGATA-AGTTGC-CAAATTGATTTGTATATGA
1 TTATACA-TTGCTGAAATTAATTTGTATATGG
*
13439478 TTATACTTTGCTGAAATTAATTTGTATATGG
1 TTATACATTGCTGAAATTAATTTGTATATGG
*
13439509 TTATACATTGTTGAAATTGAA-TTGTATATGG
1 TTATACATTGCTGAAATT-AATTTGTATATGG
* * * * *
13439540 ATATA-AGTTACCG-AATTAATTCGTATATGA
1 TTATACA-TTGCTGAAATTAATTTGTATATGG
* * * ** *
13439570 TTATACATTGCCGAACTTGATTCATATATAG
1 TTATACATTGCTGAAATTAATTTGTATATGG
* * *
13439601 TTATACATTGCCG-AATTGATTTGTATATGA
1 TTATACATTGCTGAAATTAATTTGTATATGG
13439631 TTATACATTGC
1 TTATACATTGC
13439642 GGACTTTGAT
Statistics
Matches: 398, Mismatches: 76, Indels: 55
0.75 0.14 0.10
Matches are distributed among these distances:
29 6 0.02
30 141 0.35
31 244 0.61
32 7 0.02
ACGTcount: A:0.33, C:0.07, G:0.16, T:0.43
Consensus pattern (31 bp):
TTATACATTGCTGAAATTAATTTGTATATGG
Found at i:13439399 original size:184 final size:184
Alignment explanation
Indices: 13439087--13439630 Score: 826
Period size: 184 Copynumber: 3.0 Consensus size: 184
13439077 GATATATATA
* * * *
13439087 TTGCCGAATTAATTCATATATAATTATACATTACTGAAATTAATTTATATATGGTTATACGTTGT
1 TTGCCGAATTAATTCGTATATAATTATACATTTCTGAAATTAATTTGTATATGGTTATACATTGT
13439152 T-AACATTGAATTGTATATGGATATAAGTTGCTGAATTAATTCGTATATGGTTGTACATTGCTGA
66 TGAA-ATTGAATTGTATATGGATATAAGTTGCTGAATTAATTCGTATATGGTTGTACATTGCTGA
13439216 AATTTATTTGTATATGATTATACATTATCGAAATTGATTTGTATATGAAGATAAG
130 AATTTATTTGTATATGATTATACATTATCGAAATTGATTTGTATATGAAGATAAG
*
13439271 TTGCCGAATTAATTCGTATATAATTATACATTTTTGAAATTAATTTGTATATGGTTATACATTGT
1 TTGCCGAATTAATTCGTATATAATTATACATTTCTGAAATTAATTTGTATATGGTTATACATTGT
*
13439336 TGAAATTGAATTGTATATGGATATAAGTTGCTGAATTAATTCGTATATGGTTGTACGTTGCTGAA
66 TGAAATTGAATTGTATATGGATATAAGTTGCTGAATTAATTCGTATATGGTTGTACATTGCTGAA
* *
13439401 ATTTATTTGTATATGGTTATACATTATCAAAATTGATTTGTATATGAAGATAAG
131 ATTTATTTGTATATGATTATACATTATCGAAATTGATTTGTATATGAAGATAAG
* * * *
13439455 TTGCCAAATTGATTTGTATATGATTATAC-TTTGCTGAAATTAATTTGTATATGGTTATACATTG
1 TTGCCGAATTAATTCGTATATAATTATACATTT-CTGAAATTAATTTGTATATGGTTATACATTG
* * * * *
13439519 TTGAAATTGAATTGTATATGGATATAAGTTACCGAATTAATTCGTATATGATTATACATTGCCGA
65 TTGAAATTGAATTGTATATGGATATAAGTTGCTGAATTAATTCGTATATGGTTGTACATTGCTGA
* * ** **
13439584 ACTTGATTCATATAT-AGTTATACATTGCCG-AATTGATTTGTATATGA
130 AATTTATTTGTATATGA-TTATACATTATCGAAATTGATTTGTATATGA
13439631 TTATACATTG
Statistics
Matches: 330, Mismatches: 27, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
183 20 0.06
184 308 0.93
185 2 0.01
ACGTcount: A:0.33, C:0.07, G:0.16, T:0.43
Consensus pattern (184 bp):
TTGCCGAATTAATTCGTATATAATTATACATTTCTGAAATTAATTTGTATATGGTTATACATTGT
TGAAATTGAATTGTATATGGATATAAGTTGCTGAATTAATTCGTATATGGTTGTACATTGCTGAA
ATTTATTTGTATATGATTATACATTATCGAAATTGATTTGTATATGAAGATAAG
Found at i:13439576 original size:61 final size:61
Alignment explanation
Indices: 13439111--13439684 Score: 395
Period size: 61 Copynumber: 9.4 Consensus size: 61
13439101 CATATATAAT
* * * *
13439111 TATACATTACTGAAATTAATTTATATATGGTTATACGTTG-TTAACATTGAATTGTATATGGA
1 TATACATTGCTG-AATTAATTTGTATATGGTTATACATTGCTGAA-ATTGAATTGTATATGGA
* * * *
13439173 TATA-AGTTGCTGAATTAATTCGTATATGGTTGTACATTGCTGAAATTTATTTGTATAT-GA
1 TATACA-TTGCTGAATTAATTTGTATATGGTTATACATTGCTGAAATTGAATTGTATATGGA
* * *** * *
13439233 TTATACATT-ATCGAAATTGATTTGTATATGAAGATA-AGTTGCCG-AATT-AATTCGTATAT-A
1 -TATACATTGCT-G-AATTAATTTGTATATGGTTATACA-TTGCTGAAATTGAATT-GTATATGG
13439293 A
61 A
** *
13439294 TTATACATTTTTGAAATTAATTTGTATATGGTTATACATTGTTGAAATTGAATTGTATATGGA
1 -TATACATTGCTG-AATTAATTTGTATATGGTTATACATTGCTGAAATTGAATTGTATATGGA
* * * * * *
13439357 TATA-AGTTGCTGAATTAATTCGTATATGGTTGTACGTTGCTGAAATTTATTTGTATATGGT
1 TATACA-TTGCTGAATTAATTTGTATATGGTTATACATTGCTGAAATTGAATTGTATATGGA
* ** * *** * *
13439418 TATACATTATCAAAATTGATTTGTATATGAAGATA-AGTTGC-CAAATTGATTTGTATAT-GA
1 TATACATT-GCTGAATTAATTTGTATATGGTTATACA-TTGCTGAAATTGAATTGTATATGGA
* *
13439478 TTATACTTTGCTGAAATTAATTTGTATATGGTTATACATTGTTGAAATTGAATTGTATATGGA
1 -TATACATTGCTG-AATTAATTTGTATATGGTTATACATTGCTGAAATTGAATTGTATATGGA
* * * * * * * * *
13439541 TATA-AGTTACCGAATTAATTCGTATATGATTATACATTGCCGAACTTG-ATTCATATATAGT
1 TATACA-TTGCTGAATTAATTTGTATATGGTTATACATTGCTGAAATTGAATT-GTATATGGA
* * * * ** *
13439602 TATACATTGCCGAATTGATTTGTATATGATTATACATTGCGGACTTTG-ATTCGTATATGAA
1 TATACATTGCTGAATTAATTTGTATATGGTTATACATTGCTGAAATTGAATT-GTATATGGA
* * *
13439663 TATATATTGTTGAATTGATTTG
1 TATACATTGCTGAATTAATTTG
13439685 AGCATTAGAT
Statistics
Matches: 404, Mismatches: 83, Indels: 51
0.75 0.15 0.09
Matches are distributed among these distances:
60 11 0.03
61 285 0.71
62 101 0.25
63 7 0.02
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.44
Consensus pattern (61 bp):
TATACATTGCTGAATTAATTTGTATATGGTTATACATTGCTGAAATTGAATTGTATATGGA
Found at i:13439654 original size:92 final size:91
Alignment explanation
Indices: 13439087--13439684 Score: 655
Period size: 92 Copynumber: 6.5 Consensus size: 91
13439077 GATATATATA
* * * * *
13439087 TTGCCGAATTAATTCATATATAATTATACATTACTGAAATTAATTTATATATGGTTATACGTTGT
1 TTGCCGAATTAATTCGTATATGATTATACATTGCTGAAATTAATTTGTATATGGTTATACATTGT
* *
13439152 -TAACATTGAATTGTATATGGATATAAG
66 CGAA-ATTGATTTGTATAT-GATATAAG
* * * * * *
13439179 TTGCTGAATTAATTCGTATATGGTTGTACATTGCTGAAATTTATTTGTATATGATTATACATTAT
1 TTGCCGAATTAATTCGTATATGATTATACATTGCTGAAATTAATTTGTATATGGTTATACATTGT
*
13439244 CGAAATTGATTTGTATATGAAGATAAG
66 CGAAATTGATTTGTATATG-ATATAAG
* **
13439271 TTGCCGAATTAATTCGTATATAATTATACATTTTTGAAATTAATTTGTATATGGTTATACATTGT
1 TTGCCGAATTAATTCGTATATGATTATACATTGCTGAAATTAATTTGTATATGGTTATACATTGT
* *
13439336 TGAAATTGAATTGTATATGGATATAAG
66 CGAAATTGATTTGTATAT-GATATAAG
* * * * * *
13439363 TTGCTGAATTAATTCGTATATGGTTGTACGTTGCTGAAATTTATTTGTATATGGTTATACATTAT
1 TTGCCGAATTAATTCGTATATGATTATACATTGCTGAAATTAATTTGTATATGGTTATACATTGT
* *
13439428 CAAAATTGATTTGTATATGAAGATAAG
66 CGAAATTGATTTGTATATG-ATATAAG
* * * *
13439455 TTGCCAAATTGATTTGTATATGATTATACTTTGCTGAAATTAATTTGTATATGGTTATACATTGT
1 TTGCCGAATTAATTCGTATATGATTATACATTGCTGAAATTAATTTGTATATGGTTATACATTGT
* *
13439520 TGAAATTGAATTGTATATGGATATAAG
66 CGAAATTGATTTGTATAT-GATATAAG
* * * * ** * *
13439547 TTACCGAATTAATTCGTATATGATTATACATTGCCGAACTTGATTCATATATAGTTATACATTGC
1 TTGCCGAATTAATTCGTATATGATTATACATTGCTGAAATTAATTTGTATATGGTTATACATTGT
13439612 CG-AATTGATTTGTATATGATTATACA-
66 CGAAATTGATTTGTATATGA-TATA-AG
* * * * * * *
13439638 TTGCGGACTTTGATTCGTATATGAATATATATTGTTG-AATTGATTTG
1 TTGCCGA-ATTAATTCGTATATGATTATACATTGCTGAAATTAATTTG
13439685 AGCATTAGAT
Statistics
Matches: 421, Mismatches: 77, Indels: 17
0.82 0.15 0.03
Matches are distributed among these distances:
90 2 0.00
91 32 0.08
92 383 0.91
93 4 0.01
ACGTcount: A:0.33, C:0.07, G:0.16, T:0.43
Consensus pattern (91 bp):
TTGCCGAATTAATTCGTATATGATTATACATTGCTGAAATTAATTTGTATATGGTTATACATTGT
CGAAATTGATTTGTATATGATATAAG
Found at i:13439658 original size:31 final size:30
Alignment explanation
Indices: 13439558--13439671 Score: 131
Period size: 31 Copynumber: 3.7 Consensus size: 30
13439548 TACCGAATTA
*
13439558 ATTCGTATATGATTATACATTGCCGAACTTG
1 ATTCGTATATGATTATACATTG-CGGACTTG
* * *
13439589 ATTCATATAT-AGTTATACATTGCCGAATTG
1 ATTCGTATATGA-TTATACATTGCGGACTTG
*
13439619 ATTTGTATATGATTATACATTGCGGACTTTG
1 ATTCGTATATGATTATACATTGCGGAC-TTG
* *
13439650 ATTCGTATATGAATATATATTG
1 ATTCGTATATGATTATACATTG
13439672 TTGAATTGAT
Statistics
Matches: 69, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
30 27 0.39
31 42 0.61
ACGTcount: A:0.31, C:0.11, G:0.16, T:0.42
Consensus pattern (30 bp):
ATTCGTATATGATTATACATTGCGGACTTG
Found at i:13439913 original size:41 final size:41
Alignment explanation
Indices: 13439805--13439926 Score: 131
Period size: 43 Copynumber: 2.9 Consensus size: 41
13439795 GAGGTGTGAT
* *
13439805 TTCGTGTAAGACCATGTCTGGGACATTGGCATCGAAGTAAGAA
1 TTCGTGTAAGACCTTGTCTGGGACATTGGCATCG-A-TATGAA
**
13439848 AACGTGTAAGA-CTATGTCTGGGACATTGGCATCGTATATG-A
1 TTCGTGTAAGACCT-TGTCTGGGACATTGGCATCG-ATATGAA
* * *
13439889 TTCGTATAAGACCTTGTCTAGGACAGTGGCATCGATAT
1 TTCGTGTAAGACCTTGTCTGGGACATTGGCATCGATAT
13439927 TCGTTAACAT
Statistics
Matches: 67, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
40 4 0.06
41 27 0.40
42 6 0.09
43 30 0.45
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.29
Consensus pattern (41 bp):
TTCGTGTAAGACCTTGTCTGGGACATTGGCATCGATATGAA
Found at i:13443915 original size:20 final size:21
Alignment explanation
Indices: 13443878--13443920 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 21
13443868 CTTCTTTTTG
13443878 AATTTTTATGAACA-TTTTAT
1 AATTTTTATGAACATTTTTAT
* **
13443898 AATTTTTTTGAATGTTTTTAT
1 AATTTTTATGAACATTTTTAT
13443919 AA
1 AA
13443921 AATTTAAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.33, C:0.02, G:0.07, T:0.58
Consensus pattern (21 bp):
AATTTTTATGAACATTTTTAT
Found at i:13447180 original size:23 final size:23
Alignment explanation
Indices: 13447153--13447203 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
13447143 AAACATATGT
*
13447153 AATTTTGTACTTTTATTTTTAAG
1 AATTTTGTACCTTTATTTTTAAG
* * *
13447176 AATTTAGTCCCTTTATTTTTTAG
1 AATTTTGTACCTTTATTTTTAAG
13447199 -ATTTT
1 AATTTT
13447204 AAAATTCAAG
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
22 4 0.17
23 19 0.83
ACGTcount: A:0.24, C:0.08, G:0.08, T:0.61
Consensus pattern (23 bp):
AATTTTGTACCTTTATTTTTAAG
Found at i:13447447 original size:16 final size:16
Alignment explanation
Indices: 13447428--13447460 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
13447418 ATGGAATAAG
13447428 GTTGTAAT-GAACTAGA
1 GTTGTAATAGAA-TAGA
13447444 GTTGTAATAGAATAGA
1 GTTGTAATAGAATAGA
13447460 G
1 G
13447461 CTATAATGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.81
17 3 0.19
ACGTcount: A:0.39, C:0.03, G:0.27, T:0.30
Consensus pattern (16 bp):
GTTGTAATAGAATAGA
Found at i:13447753 original size:15 final size:15
Alignment explanation
Indices: 13447710--13447778 Score: 59
Period size: 15 Copynumber: 4.5 Consensus size: 15
13447700 TTTTTTACTA
* **
13447710 AATAAAATTTAATAA
1 AATAAAATATAATTT
*
13447725 AATAATATATAATTT
1 AATAAAATATAATTT
13447740 AATAAAATATAATTATT
1 AATAAAATATAA-T-TT
*
13447757 ATTAAAATATGAA-TT
1 AATAAAATAT-AATTT
13447772 AATAAAA
1 AATAAAA
13447779 ATTATAATAT
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
15 30 0.68
16 1 0.02
17 11 0.25
18 2 0.05
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (15 bp):
AATAAAATATAATTT
Found at i:13462801 original size:13 final size:14
Alignment explanation
Indices: 13462783--13462817 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
13462773 AAAGATATAA
13462783 ATATATTT-CTTTT
1 ATATATTTACTTTT
13462796 ATATATTTACTTTT
1 ATATATTTACTTTT
*
13462810 AAATATTT
1 ATATATTT
13462818 TAATATACCC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (14 bp):
ATATATTTACTTTT
Found at i:13463505 original size:45 final size:44
Alignment explanation
Indices: 13463455--13463558 Score: 120
Period size: 44 Copynumber: 2.3 Consensus size: 44
13463445 AACATTTTTC
* ** * *
13463455 TATTTTTGAAATTTTGACCTATTATTTTAAATTTT-TAGAATTTA
1 TATTTTTGAAATTTTAAAAT-TTATTATAAATTTTCTAGAATGTA
* *
13463499 TAATTTTTAAAAATTTAAAATTTATTATAAATTTTCTAGAATGTA
1 T-ATTTTTGAAATTTTAAAATTTATTATAAATTTTCTAGAATGTA
13463544 TATTTTTGAAATTTT
1 TATTTTTGAAATTTT
13463559 CTAGAATTTA
Statistics
Matches: 49, Mismatches: 9, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
44 26 0.53
45 23 0.47
ACGTcount: A:0.37, C:0.03, G:0.06, T:0.55
Consensus pattern (44 bp):
TATTTTTGAAATTTTAAAATTTATTATAAATTTTCTAGAATGTA
Found at i:13463513 original size:17 final size:16
Alignment explanation
Indices: 13463480--13463532 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 16
13463470 GACCTATTAT
*
13463480 TTTAAATTTTT-AGAA
1 TTTAAATTTTTAAAAA
13463495 TTTATAATTTTTAAAAA
1 TTTA-AATTTTTAAAAA
*
13463512 TTTAAAATTTATTATAAA
1 TTT-AAATTT-TTAAAAA
13463530 TTT
1 TTT
13463533 TCTAGAATGT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
15 4 0.12
16 7 0.22
17 11 0.34
18 10 0.31
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (16 bp):
TTTAAATTTTTAAAAA
Found at i:13464222 original size:20 final size:20
Alignment explanation
Indices: 13464197--13464237 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
13464187 AAATAACAAC
13464197 ATCTATAGT-TTTATATTATT
1 ATCTATA-TATTTATATTATT
*
13464217 ATCTATATATTTTTATTATT
1 ATCTATATATTTATATTATT
13464237 A
1 A
13464238 AATTTAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 1 0.05
20 18 0.95
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.61
Consensus pattern (20 bp):
ATCTATATATTTATATTATT
Found at i:13466393 original size:31 final size:31
Alignment explanation
Indices: 13466354--13466424 Score: 110
Period size: 31 Copynumber: 2.3 Consensus size: 31
13466344 AAAAGTTACA
*
13466354 ATTT-AGTCACTGAAC-TATTCAAAATTTTTC
1 ATTTAAGTCACTG-ACTTATTCAAAAGTTTTC
13466384 ATTTAAGTCACTGACTTATTCAAAAGTTTTC
1 ATTTAAGTCACTGACTTATTCAAAAGTTTTC
13466415 ATTTAAGTCA
1 ATTTAAGTCA
13466425 TTGGGATGTT
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
30 6 0.16
31 32 0.84
ACGTcount: A:0.34, C:0.15, G:0.08, T:0.42
Consensus pattern (31 bp):
ATTTAAGTCACTGACTTATTCAAAAGTTTTC
Found at i:13468092 original size:17 final size:18
Alignment explanation
Indices: 13468072--13468105 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
13468062 AGAAAAAAAA
13468072 TATTTT-TTTCAAAAATC
1 TATTTTCTTTCAAAAATC
*
13468089 TATTTTCTTTTAAAAAT
1 TATTTTCTTTCAAAAAT
13468106 TAAATAAATC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.35, C:0.09, G:0.00, T:0.56
Consensus pattern (18 bp):
TATTTTCTTTCAAAAATC
Found at i:13468321 original size:72 final size:70
Alignment explanation
Indices: 13468185--13468322 Score: 152
Period size: 74 Copynumber: 1.9 Consensus size: 70
13468175 TCAAATGAAT
** * * *
13468185 ATTAAAACTAATAAAATCTGTTTCGGGATTTTCCCACCGTTTAACAGATTTTATTAGATTTTATT
1 ATTAAAACTAATAAAATCCATTTCGGGATTTTCCCACCGCTCAACAGATTTTATTACA-TTTATT
13468250 TCCAAA
65 TCCAAA
* * * *
13468256 ATTAAAAGTAAATAAAATCCATTTTGGGATTTATTCCCACCGCTCAACGGATTTTATTCCA-TTA
1 ATTAAAACT-AATAAAATCCATTTCGGGA-TT-TTCCCACCGCTCAACAGATTTTATTACATTTA
13468320 TTT
63 TTT
13468323 TAATTCTATT
Statistics
Matches: 55, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
71 8 0.15
72 22 0.40
73 2 0.04
74 23 0.42
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.40
Consensus pattern (70 bp):
ATTAAAACTAATAAAATCCATTTCGGGATTTTCCCACCGCTCAACAGATTTTATTACATTTATTT
CCAAA
Found at i:13468477 original size:79 final size:79
Alignment explanation
Indices: 13468354--13468600 Score: 287
Period size: 79 Copynumber: 3.1 Consensus size: 79
13468344 AATTAAAGGT
* * * * * * * *
13468354 AAATAAAATCCATTTCTAGAGTGACTCCCGCCGTTTAACGATTTTATTCCAAATTTTGTTTTATT
1 AAATAAAATCCGTTTCCAGATTGATTCCCACCATTCAACAATTTTATTCCAAATTTTGTTTTATT
*
13468419 TCCAAAAATGAGTA
66 TCCAAAAACGAGTA
* * *
13468433 AAATAAAATCTGTTTCCAGATTGATTCCCACCATTCAACAATTTTGTTCCACATTTTGTTTTATT
1 AAATAAAATCCGTTTCCAGATTGATTCCCACCATTCAACAATTTTATTCCAAATTTTGTTTTA-T
*
13468498 TTTCAAAAACGAGTA
65 TTCCAAAAACGAGTA
*** * * * ** *
13468513 AAATAAAATCCGTTTTGGGATTGATTCTCGCCGTTCAATGATTTTATTCTAAATTTTGTTTTATT
1 AAATAAAATCCGTTTCCAGATTGATTCCCACCATTCAACAATTTTATTCCAAATTTTGTTTTATT
13468578 TCCAAAAACGAGTA
66 TCCAAAAACGAGTA
13468592 AAATAAAAT
1 AAATAAAAT
13468601 TCATTTCGGG
Statistics
Matches: 141, Mismatches: 26, Indels: 2
0.83 0.15 0.01
Matches are distributed among these distances:
79 76 0.54
80 65 0.46
ACGTcount: A:0.34, C:0.16, G:0.11, T:0.39
Consensus pattern (79 bp):
AAATAAAATCCGTTTCCAGATTGATTCCCACCATTCAACAATTTTATTCCAAATTTTGTTTTATT
TCCAAAAACGAGTA
Done.