Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009643.1 Hibiscus syriacus cultivar Beakdansim tig00117056_pilon, whole genome shotgun sequence
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: 8859806
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 41
Found at i:306417 original size:51 final size:51
Alignment explanation
Indices: 306355--306525 Score: 208
Period size: 52 Copynumber: 3.4 Consensus size: 51
306345 CATATTATCC
* *
306355 ATGT-GGGTATCTTGAAGGCTCACATCAGTATGAAAAGATAGAAGTAATTT
1 ATGTGGGGCATCTTGAAGGCTCACATCAGTATGAAAAGATAGAAGTAATCT
* * *
306405 ATGTGGGGTATCTTGAAGGCTCACATCAGCATGAAAA-ATAAAAAAGTAATCT
1 ATGTGGGGCATCTTGAAGGCTCACATCAGTATGAAAAGAT--AGAAGTAATCT
* * * *
306457 ATGTGGGGCATCTTGAAGGCTCACATTAGTATAAAAAGACAGAAG--A-CC
1 ATGTGGGGCATCTTGAAGGCTCACATCAGTATGAAAAGATAGAAGTAATCT
306505 ATGTGGGGCATCTTGAAGGCT
1 ATGTGGGGCATCTTGAAGGCT
306526 TACACCAGCA
Statistics
Matches: 107, Mismatches: 10, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
48 22 0.21
49 1 0.01
50 6 0.06
51 35 0.33
52 42 0.39
53 1 0.01
ACGTcount: A:0.36, C:0.13, G:0.25, T:0.26
Consensus pattern (51 bp):
ATGTGGGGCATCTTGAAGGCTCACATCAGTATGAAAAGATAGAAGTAATCT
Found at i:306474 original size:52 final size:50
Alignment explanation
Indices: 306355--306541 Score: 195
Period size: 51 Copynumber: 3.7 Consensus size: 50
306345 CATATTATCC
* * *
306355 ATGT-GGGTATCTTGAAGGCTCACATCAGTATGAAAAGAT-AGAAGTAATTT
1 ATGTGGGGCATCTTGAAGGCTCACATCAGCAT-AAAA-ATAAGAAGTAATCT
* *
306405 ATGTGGGGTATCTTGAAGGCTCACATCAGCATGAAAAATAAAAAAGTAATCT
1 ATGTGGGGCATCTTGAAGGCTCACATCAGCAT-AAAAAT-AAGAAGTAATCT
* * * *
306457 ATGTGGGGCATCTTGAAGGCTCACATTAGTATAAAAAGACAGAAG--A-CC
1 ATGTGGGGCATCTTGAAGGCTCACATCAGCATAAAAATA-AGAAGTAATCT
* *
306505 ATGTGGGGCATCTTGAAGGCTTACACCAGCATAAAAA
1 ATGTGGGGCATCTTGAAGGCTCACATCAGCATAAAAA
306542 GGTTGGGATA
Statistics
Matches: 120, Mismatches: 13, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
48 34 0.28
49 1 0.01
50 7 0.06
51 40 0.33
52 38 0.32
ACGTcount: A:0.37, C:0.14, G:0.24, T:0.25
Consensus pattern (50 bp):
ATGTGGGGCATCTTGAAGGCTCACATCAGCATAAAAATAAGAAGTAATCT
Found at i:306539 original size:48 final size:50
Alignment explanation
Indices: 306351--306542 Score: 192
Period size: 52 Copynumber: 3.8 Consensus size: 50
306341 GGTCCATATT
* * * * *
306351 ATCCATGT-GGGTATCTTGAAGGCTCACATCAGTATGAAAAGATAGAAGTA
1 ATCCATGTGGGGCATCTTGAAGGCTCACATCAGCATAAAAAGAAAAAAG-A
** * *
306401 ATTTATGTGGGGTATCTTGAAGGCTCACATCAGCATGAAAAATAAAAAAGTA
1 ATCCATGTGGGGCATCTTGAAGGCTCACATCAGCAT-AAAAAGAAAAAAG-A
* * * * *
306453 ATCTATGTGGGGCATCTTGAAGGCTCACATTAGTATAAAAAGACAGAAG-
1 ATCCATGTGGGGCATCTTGAAGGCTCACATCAGCATAAAAAGAAAAAAGA
* *
306502 A-CCATGTGGGGCATCTTGAAGGCTTACACCAGCATAAAAAG
1 ATCCATGTGGGGCATCTTGAAGGCTCACATCAGCATAAAAAG
306543 GTTGGGATAT
Statistics
Matches: 121, Mismatches: 19, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
48 35 0.29
49 1 0.01
50 6 0.05
51 36 0.30
52 43 0.36
ACGTcount: A:0.37, C:0.15, G:0.23, T:0.24
Consensus pattern (50 bp):
ATCCATGTGGGGCATCTTGAAGGCTCACATCAGCATAAAAAGAAAAAAGA
Found at i:308137 original size:108 final size:108
Alignment explanation
Indices: 307943--308145 Score: 286
Period size: 108 Copynumber: 1.9 Consensus size: 108
307933 CAGCTAATGT
* *
307943 GTTTTTTAGAAACTAAGTCTGATTTTCGGAAGTTTCTTGATCGTTTCAAATGAGTTTTCAAAGAA
1 GTTTTTAAGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATCGTTTCAAATGAGTTTTCAAAGAA
* *
308008 ATTAAGTCTGATTTTCAGAAGTTTCCTGATGATTTCACTATGA
66 ACTAAGTCCGATTTTCAGAAGTTTCCTGATGATTTCACTATGA
* *
308051 GTTTTTAAGAAACTAAGTCTGGTTTTCAGAAGTTTCTTGA-CGATTTTCAAATCTA-TTTT-AAA
1 GTTTTTAAGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATCG--TTTCAAAT-GAGTTTTCAAA
* *
308113 GAAACTAAGTCCGATTTTCTGAAGTTTCTTGAT
63 GAAACTAAGTCCGATTTTCAGAAGTTTCCTGAT
308146 TTTTCTCAAA
Statistics
Matches: 84, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
107 2 0.02
108 69 0.82
109 12 0.14
110 1 0.01
ACGTcount: A:0.29, C:0.12, G:0.17, T:0.42
Consensus pattern (108 bp):
GTTTTTAAGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATCGTTTCAAATGAGTTTTCAAAGAA
ACTAAGTCCGATTTTCAGAAGTTTCCTGATGATTTCACTATGA
Found at i:308155 original size:54 final size:53
Alignment explanation
Indices: 307950--308170 Score: 239
Period size: 54 Copynumber: 4.1 Consensus size: 53
307940 TGTGTTTTTT
* **
307950 AGAAACTAAGTCTGATTTTCGGAAGTTTCTTGATCGTTTCAAATGAGTTTTCAA
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATATTTTCAAATGAGTTTT-AA
* * * *
308004 AGAAATTAAGTCTGATTTTCAGAAGTTTCCTGATGA-TTTCACTATGAGTTTTTA
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGAT-ATTTTCA-AATGAGTTTTAA
* * *
308058 AGAAACTAAGTCTGGTTTTCAGAAGTTTCTTGACGATTTTCAAATCTA-TTTTAA
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGA-TATTTTCAAAT-GAGTTTTAA
* * * * *
308112 AGAAACTAAGTCCGATTTTCTGAAGTTTCTTGATTTTTCTCAAATGAATTTCAA
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATATTT-TCAAATGAGTTTTAA
308166 AGAAA
1 AGAAA
308171 TTAACCCTAA
Statistics
Matches: 140, Mismatches: 20, Indels: 14
0.80 0.11 0.08
Matches are distributed among these distances:
53 4 0.03
54 121 0.86
55 15 0.11
ACGTcount: A:0.32, C:0.13, G:0.16, T:0.40
Consensus pattern (53 bp):
AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATATTTTCAAATGAGTTTTAA
Found at i:308724 original size:99 final size:99
Alignment explanation
Indices: 308551--308770 Score: 354
Period size: 99 Copynumber: 2.2 Consensus size: 99
308541 ATAAGGAATG
* *
308551 AGAAGTTCATAATGAGAAGAATTTGTTCAACCTTAGCTCAATTCATCGCATATGGAGTTGAATTA
1 AGAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTCAATTCATCGCATATGGAGTTGAATCA
*
308616 ACAACACCTCACTCGAGGGATCAACATTTCCAGA
66 ACAACACCTCAATCGAGGGATCAACATTTCCAGA
* *
308650 AGAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGC-CTGATTCATCGCTTATGGAGTTGAATC
1 AGAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTC-AATTCATCGCATATGGAGTTGAATC
* *
308714 AGCAATACCTCAATCGAGGGATCAACATTTCCAGA
65 AACAACACCTCAATCGAGGGATCAACATTTCCAGA
308749 AG-AGTTCATAATGAGAAGAACT
1 AGAAGTTCATAATGAGAAGAACT
308771 CATCCAATGA
Statistics
Matches: 113, Mismatches: 7, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
98 21 0.19
99 92 0.81
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (99 bp):
AGAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTCAATTCATCGCATATGGAGTTGAATCA
ACAACACCTCAATCGAGGGATCAACATTTCCAGA
Found at i:308807 original size:137 final size:138
Alignment explanation
Indices: 308650--308908 Score: 423
Period size: 137 Copynumber: 1.9 Consensus size: 138
308640 CATTTCCAGA
* * *
308650 AGAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGC-CTGATTCATCGCTTATGGAGTTGAATC
1 AGAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTC-AAATCATCGCATATGGAGTTGAATC
*
308714 AGCAATACCTCAATCGAGGGATCAACATTTCCAGAAG-AGTTCATAATGAGAAGAACTCATCCAA
65 AGCAACACCTCAATCGAGGGATCAACATTTCCAGAAGAAGTTCATAATGAGAAGAACTCATCCAA
308778 TGAGGAAGG
130 TGAGGAAGG
* *
308787 AGAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTCAAATCATTGCATATGGAGTTGAGTCA
1 AGAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTCAAATCATCGCATATGGAGTTGAATCA
* *
308852 GCAACACCTCACTCGAGGGATCAATATTTCCAGAAGAAGTTCATAATGAGAAGAACT
66 GCAACACCTCAATCGAGGGATCAACATTTCCAGAAGAAGTTCATAATGAGAAGAACT
308909 TGTTCAACCT
Statistics
Matches: 112, Mismatches: 8, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
137 91 0.81
138 21 0.19
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.25
Consensus pattern (138 bp):
AGAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTCAAATCATCGCATATGGAGTTGAATCA
GCAACACCTCAATCGAGGGATCAACATTTCCAGAAGAAGTTCATAATGAGAAGAACTCATCCAAT
GAGGAAGG
Found at i:308911 original size:236 final size:236
Alignment explanation
Indices: 308498--309082 Score: 983
Period size: 236 Copynumber: 2.5 Consensus size: 236
308488 AATGAGGTGA
*
308498 ATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCCAATAAGGAATGAGAAGTTCATAA
1 ATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCCAATAAGGAAGGAGAAGTTCATAA
*
308563 TGAGAAGAATTTGTTCAACCTTAGCTCAATTCATCGCATATGGAGTTGAATTAACAACACCTCAC
66 TGAGAAGAATTTGTTCAACCTTAGCTCAATTCATCGCATATGGAGTTGAATCAACAACACCTCAC
*
308628 TCGAGGGATCAACATTTCCAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCCTGATT
131 TCGAGGGATCAACATTTCCAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCCCGATT
*
308693 CATCGCTTATGGAGTTGAATCAGCAATACCTCAATCGAGGG
196 CATCGCTTATGGAGTTGAATCAGCAACACCTCAATCGAGGG
*
308734 ATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCCAATGAGGAAGGAGAAGTTCATAA
1 ATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCCAATAAGGAAGGAGAAGTTCATAA
* * * * *
308799 TGAGAAGAACTTGTTCAACCTTAGCTCAAATCATTGCATATGGAGTTGAGTCAGCAACACCTCAC
66 TGAGAAGAATTTGTTCAACCTTAGCTCAATTCATCGCATATGGAGTTGAATCAACAACACCTCAC
*
308864 TCGAGGGATCAATATTTCCAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCCCGATT
131 TCGAGGGATCAACATTTCCAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCCCGATT
* *
308929 CGTCGCTTATGGAGTTGAATCAGTAACACCTCAATCGAGGG
196 CATCGCTTATGGAGTTGAATCAGCAACACCTCAATCGAGGG
* * * *
308970 ATTAACATTTTCAGAAGAGTTCATAATGAGAAGAACTCATCCGACA-AAGGGAGAAGAAGTTCAT
1 ATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCC-A-ATAAGGAAGGAGAAGTTCAT
*
309034 AATGAGAAGAATTTGTTCAACCTTAGCTCGATTCATCGCATATGGAGTT
64 AATGAGAAGAATTTGTTCAACCTTAGCTCAATTCATCGCATATGGAGTT
309083 CATAATGAGA
Statistics
Matches: 325, Mismatches: 22, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
236 263 0.81
237 61 0.19
238 1 0.00
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.26
Consensus pattern (236 bp):
ATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCCAATAAGGAAGGAGAAGTTCATAA
TGAGAAGAATTTGTTCAACCTTAGCTCAATTCATCGCATATGGAGTTGAATCAACAACACCTCAC
TCGAGGGATCAACATTTCCAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCCCGATT
CATCGCTTATGGAGTTGAATCAGCAACACCTCAATCGAGGG
Found at i:308958 original size:99 final size:99
Alignment explanation
Indices: 308787--309006 Score: 325
Period size: 99 Copynumber: 2.2 Consensus size: 99
308777 ATGAGGAAGG
* * *
308787 AGAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTCAAATCATTGCATATGGAGTTGAGTCA
1 AGAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCCCAAATCATCGCATATGGAGTTGAATCA
* *
308852 GCAACACCTCACTCGAGGGATCAATATTTCCAGA
66 GCAACACCTCAATCGAGGGATCAACATTTCCAGA
* * * *
308886 AGAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCCCGATTCGTCGCTTATGGAGTTGAATCA
1 AGAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCCCAAATCATCGCATATGGAGTTGAATCA
* * *
308951 GTAACACCTCAATCGAGGGATTAACATTTTCAGA
66 GCAACACCTCAATCGAGGGATCAACATTTCCAGA
308985 AG-AGTTCATAATGAGAAGAACT
1 AGAAGTTCATAATGAGAAGAACT
309007 CATCCGACAA
Statistics
Matches: 109, Mismatches: 12, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
98 20 0.18
99 89 0.82
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.27
Consensus pattern (99 bp):
AGAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCCCAAATCATCGCATATGGAGTTGAATCA
GCAACACCTCAATCGAGGGATCAACATTTCCAGA
Found at i:309142 original size:20 final size:20
Alignment explanation
Indices: 309080--309143 Score: 51
Period size: 20 Copynumber: 3.2 Consensus size: 20
309070 CGCATATGGA
*
309080 GTTCATAATGAGAGGAACTT
1 GTTCATAATGAGAAGAACTT
* * ***
309100 -ATC-TAATGAGGGAGAAGAA
1 GTTCATAATGA-GAAGAACTT
309119 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
309139 GTTCA
1 GTTCA
309144 ACCTTAACTT
Statistics
Matches: 30, Mismatches: 11, Indels: 6
0.64 0.23 0.13
Matches are distributed among these distances:
18 6 0.20
19 6 0.20
20 12 0.40
21 6 0.20
ACGTcount: A:0.39, C:0.09, G:0.25, T:0.27
Consensus pattern (20 bp):
GTTCATAATGAGAAGAACTT
Found at i:313045 original size:16 final size:15
Alignment explanation
Indices: 312998--313049 Score: 61
Period size: 16 Copynumber: 3.4 Consensus size: 15
312988 ATTTTATAAA
312998 AAAAC-AAATAATTT
1 AAAACTAAATAATTT
* *
313012 AAAATTAAATTAACTT
1 AAAACTAAA-TAATTT
313028 AAACACTAAATAATTT
1 AAA-ACTAAATAATTT
313044 AAAACT
1 AAAACT
313050 GATATGACCC
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
14 4 0.13
15 6 0.19
16 16 0.52
17 5 0.16
ACGTcount: A:0.60, C:0.10, G:0.00, T:0.31
Consensus pattern (15 bp):
AAAACTAAATAATTT
Found at i:314516 original size:29 final size:29
Alignment explanation
Indices: 314473--314555 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
314463 CTCACCTAAC
314473 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
314503 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
314532 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
314556 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:319285 original size:29 final size:29
Alignment explanation
Indices: 319242--319324 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
319232 CTCACCTAAC
319242 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
319272 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
319301 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
319325 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:321495 original size:215 final size:215
Alignment explanation
Indices: 321120--321551 Score: 792
Period size: 215 Copynumber: 2.0 Consensus size: 215
321110 CAGTAGCTAT
*
321120 CCATAATTTCCATATTAGTGTTGGCCCACAAACGTCAGTGTCTTTAATGTTTACAGAGTTCTGGG
1 CCATAATTTCCATATTAGTGTTGGCCCACAAACGTCAGTGTCTTTAATGATTACAGAGTTCTGGG
321185 CAATAAGATGACACACTGGGCATCCAGGATTAATTCTACATTGCTTCATAACCACAATAATTGTT
66 CAATAAGATGACACACTGGGCATCCAGGATTAATTCTACATTGCTTCATAACCACAATAATTGTT
* * * *
321250 TAACAAAAATACGAGGAGAATAGTCAGATCAGAAAATCGTGAGATGTGTTAATGGCGGCTGAACT
131 TAACAAAAATACGAAGAGAATAGCCAGATCAGAAAATCGTGAGATGCGTTAATGGCGGCTAAACT
321315 TGAAGAAGAAAAGGAGAGTA
196 TGAAGAAGAAAAGGAGAGTA
*
321335 CCATAATTTCCATATTAGTGTTGGCCCACAAACGTCAGTGTCTTTAATGATTACAGAGTTTTGGG
1 CCATAATTTCCATATTAGTGTTGGCCCACAAACGTCAGTGTCTTTAATGATTACAGAGTTCTGGG
321400 CAATAAGATGACACACTGGGCATCCAGGATTAATTCTACATTGCTTCATAACCACAATAATTGTT
66 CAATAAGATGACACACTGGGCATCCAGGATTAATTCTACATTGCTTCATAACCACAATAATTGTT
* *
321465 TAACAAAATTACGAAGAGAATAGCCAGATCAGAAAATGGTGAGATGCGTTAATGGCGGCTAAACT
131 TAACAAAAATACGAAGAGAATAGCCAGATCAGAAAATCGTGAGATGCGTTAATGGCGGCTAAACT
321530 TGAAGAAGAAAAGGAGAGTA
196 TGAAGAAGAAAAGGAGAGTA
321550 CC
1 CC
321552 TATACAGAGG
Statistics
Matches: 209, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
215 209 1.00
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.27
Consensus pattern (215 bp):
CCATAATTTCCATATTAGTGTTGGCCCACAAACGTCAGTGTCTTTAATGATTACAGAGTTCTGGG
CAATAAGATGACACACTGGGCATCCAGGATTAATTCTACATTGCTTCATAACCACAATAATTGTT
TAACAAAAATACGAAGAGAATAGCCAGATCAGAAAATCGTGAGATGCGTTAATGGCGGCTAAACT
TGAAGAAGAAAAGGAGAGTA
Found at i:324096 original size:14 final size:14
Alignment explanation
Indices: 324077--324106 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
324067 TTCGGTAATG
*
324077 CGGTTTTTTCAGTT
1 CGGTTTGTTCAGTT
324091 CGGTTTGTTCAGTT
1 CGGTTTGTTCAGTT
324105 CG
1 CG
324107 TCAGTTTTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.07, C:0.17, G:0.27, T:0.50
Consensus pattern (14 bp):
CGGTTTGTTCAGTT
Found at i:326388 original size:19 final size:20
Alignment explanation
Indices: 326366--326403 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
326356 TCTCAACTAA
*
326366 AATTTATCA-TAAAATAAAT
1 AATTCATCATTAAAATAAAT
*
326385 AATTCATGATTAAAATAAA
1 AATTCATCATTAAAATAAA
326404 ATAAAAATGA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 7 0.44
20 9 0.56
ACGTcount: A:0.58, C:0.05, G:0.03, T:0.34
Consensus pattern (20 bp):
AATTCATCATTAAAATAAAT
Found at i:328150 original size:18 final size:18
Alignment explanation
Indices: 328127--328161 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
328117 TCGGTTCTTC
*
328127 CGACCGGTAAAACCAATT
1 CGACCGATAAAACCAATT
*
328145 CGACCGATTAAACCAAT
1 CGACCGATAAAACCAAT
328162 AATCGGTAAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.29, G:0.14, T:0.17
Consensus pattern (18 bp):
CGACCGATAAAACCAATT
Found at i:328390 original size:23 final size:23
Alignment explanation
Indices: 328355--328400 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
328345 GGCGATTTTC
*
328355 CCGATATATCACCGGTAATATTA
1 CCGATATAACACCGGTAATATTA
* *
328378 CCGATGTAACACCGGTCATATTA
1 CCGATATAACACCGGTAATATTA
328401 TATTTCCCGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.33, C:0.24, G:0.15, T:0.28
Consensus pattern (23 bp):
CCGATATAACACCGGTAATATTA
Found at i:328529 original size:50 final size:49
Alignment explanation
Indices: 328431--328556 Score: 155
Period size: 50 Copynumber: 2.5 Consensus size: 49
328421 TTAGCAGTAA
** *
328431 AGCGCGCCCCTGCACCGCGCTATACGATGATTTGGAGTCACGTGGGGTAT
1 AGCGCGCCCCTGCA-CGCGCTATACGATGAGCTGGAGCCACGTGGGGTAT
* *
328481 AGCGCGCCCCCTGCACTGCGCTATACGGTGAGCTGGTGCCACGT-GGGTAT
1 AGCGCG-CCCCTGCAC-GCGCTATACGATGAGCTGGAGCCACGTGGGGTAT
328531 AGCGCGGCCCCTGCAGCGCGCTATAC
1 AGCGC-GCCCCTGCA-CGCGCTATAC
328557 CTGTATATCT
Statistics
Matches: 67, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
50 35 0.52
51 32 0.48
ACGTcount: A:0.16, C:0.33, G:0.33, T:0.19
Consensus pattern (49 bp):
AGCGCGCCCCTGCACGCGCTATACGATGAGCTGGAGCCACGTGGGGTAT
Found at i:328579 original size:50 final size:51
Alignment explanation
Indices: 328431--328587 Score: 144
Period size: 50 Copynumber: 3.1 Consensus size: 51
328421 TTAGCAGTAA
* * ** ** *
328431 AGCGC-GCCCCTGCACCGCGCTATACGATGATTTGGAGTCACGTGGGGTAT
1 AGCGCGGCCCCTGCACTGCGCTATACGGTGAGATGCTGACACGTGGGGTAT
* * * *
328481 AGCGCGCCCCCTGCACTGCGCTATACGGTGAGCTGGTGCCACGT-GGGTAT
1 AGCGCGGCCCCTGCACTGCGCTATACGGTGAGATGCTGACACGTGGGGTAT
* *
328531 AGCGCGGCCCCTGCAGC-GCGCTATAC-CTGTATAT-CTGACACGTGGGGTAT
1 AGCGCGGCCCCTGCA-CTGCGCTATACGGTG-AGATGCTGACACGTGGGGTAT
328581 AGCGCGG
1 AGCGCGG
328588 TGCAGGGGGC
Statistics
Matches: 90, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
49 9 0.10
50 49 0.54
51 32 0.36
ACGTcount: A:0.17, C:0.30, G:0.33, T:0.20
Consensus pattern (51 bp):
AGCGCGGCCCCTGCACTGCGCTATACGGTGAGATGCTGACACGTGGGGTAT
Found at i:328708 original size:12 final size:10
Alignment explanation
Indices: 328667--328707 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
328657 TTTATCACAC
328667 CAAATTCTCT
1 CAAATTCTCT
328677 CAAATTCTCT
1 CAAATTCTCT
328687 -AAATTTCTCT
1 CAAA-TTCTCT
*
328697 CAAATACTCT
1 CAAATTCTCT
328707 C
1 C
328708 TTTTTAAGGT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 3 0.11
10 22 0.79
11 3 0.11
ACGTcount: A:0.32, C:0.29, G:0.00, T:0.39
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:328756 original size:13 final size:14
Alignment explanation
Indices: 328728--328756 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
328718 ATATTTTATA
328728 ATATTTTTACTATT
1 ATATTTTTACTATT
328742 ATATTTTTACT-TT
1 ATATTTTTACTATT
328755 AT
1 AT
328757 TTAATATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.27
14 11 0.73
ACGTcount: A:0.28, C:0.07, G:0.00, T:0.66
Consensus pattern (14 bp):
ATATTTTTACTATT
Found at i:331296 original size:48 final size:49
Alignment explanation
Indices: 331225--331343 Score: 170
Period size: 49 Copynumber: 2.4 Consensus size: 49
331215 TATACAAAAT
* *
331225 GCGGTACATGCCCCGCGCTATATAAAA-TGTCAGGAGTAAAGGTAT-GTC
1 GCGGTACCTGCCCCGCGCTATATAAAATTATCAGGAGTAAAGGTATAG-C
*
331273 GCGGTACCTGCCCCGCGCTATATAAAATTATTAGGAGTAAAGGTATAGC
1 GCGGTACCTGCCCCGCGCTATATAAAATTATCAGGAGTAAAGGTATAGC
**
331322 GCGGTACCTGATCCGCGCTATA
1 GCGGTACCTGCCCCGCGCTATA
331344 CCCCTACGTG
Statistics
Matches: 64, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
48 26 0.41
49 37 0.58
50 1 0.02
ACGTcount: A:0.28, C:0.23, G:0.26, T:0.24
Consensus pattern (49 bp):
GCGGTACCTGCCCCGCGCTATATAAAATTATCAGGAGTAAAGGTATAGC
Found at i:331463 original size:51 final size:50
Alignment explanation
Indices: 331355--331479 Score: 144
Period size: 51 Copynumber: 2.5 Consensus size: 50
331345 CCCTACGTGG
* * **
331355 CGTATAGCGCGCTGCAGGGGCCGCGCTATACCCACGTGGCGCCAGCTCAC
1 CGTATAGCGCGGTGCAGGGGGCGCGCTATACCCACGTGGCGCCAAATCAC
* * *
331405 CGAATAGCGCGGTTCAGGGGGCGCGCTATACCCCACGTGGCGCCAAAT-ATT
1 CGTATAGCGCGGTGCAGGGGGCGCGCTATA-CCCACGTGGCGCCAAATCA-C
**
331456 CGTATAGCATGGTGCAGGGGGCGC
1 CGTATAGCGCGGTGCAGGGGGCGC
331480 TTTACTGCTA
Statistics
Matches: 62, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
50 27 0.44
51 35 0.56
ACGTcount: A:0.18, C:0.31, G:0.34, T:0.16
Consensus pattern (50 bp):
CGTATAGCGCGGTGCAGGGGGCGCGCTATACCCACGTGGCGCCAAATCAC
Found at i:332231 original size:9 final size:9
Alignment explanation
Indices: 332217--332266 Score: 55
Period size: 9 Copynumber: 5.3 Consensus size: 9
332207 GCTGCTGGAA
332217 ACCGGTTTG
1 ACCGGTTTG
*
332226 ACCGGTTTCA
1 ACCGGTTT-G
*
332236 ACCGGTTCG
1 ACCGGTTTG
332245 AACCGGTTTG
1 -ACCGGTTTG
*
332255 ACCGGTCTG
1 ACCGGTTTG
332264 ACC
1 ACC
332267 CGACCGACCC
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
9 19 0.56
10 15 0.44
ACGTcount: A:0.16, C:0.30, G:0.28, T:0.26
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:332240 original size:19 final size:18
Alignment explanation
Indices: 332216--332266 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 18
332206 GGCTGCTGGA
332216 AACCGGTTTGACCGGTTT
1 AACCGGTTTGACCGGTTT
*
332234 CAACCGGTTCGAACCGGTTT
1 -AACCGGTTTG-ACCGGTTT
* *
332254 GACCGGTCTGACC
1 AACCGGTTTGACC
332267 CGACCGACCC
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
18 3 0.11
19 16 0.59
20 8 0.30
ACGTcount: A:0.18, C:0.29, G:0.27, T:0.25
Consensus pattern (18 bp):
AACCGGTTTGACCGGTTT
Found at i:332295 original size:22 final size:22
Alignment explanation
Indices: 332270--332336 Score: 98
Period size: 22 Copynumber: 3.0 Consensus size: 22
332260 TCTGACCCGA
332270 CCGACCCGACCCGACCGTTGAC
1 CCGACCCGACCCGACCGTTGAC
* * * *
332292 CCGAACCAACCGGACCGTTAAC
1 CCGACCCGACCCGACCGTTGAC
332314 CCGACCCGACCCGACCGTTGAC
1 CCGACCCGACCCGACCGTTGAC
332336 C
1 C
332337 GTTGACCGTT
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.22, C:0.48, G:0.21, T:0.09
Consensus pattern (22 bp):
CCGACCCGACCCGACCGTTGAC
Found at i:338166 original size:20 final size:21
Alignment explanation
Indices: 338141--338179 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
338131 GGCTGCTGGA
338141 AACCGGTT-TAACCGGTTTTC
1 AACCGGTTCTAACCGGTTTTC
*
338161 AACCGGTTCTGACCGGTTT
1 AACCGGTTCTAACCGGTTT
338180 GACCTGTCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.18, C:0.26, G:0.23, T:0.33
Consensus pattern (21 bp):
AACCGGTTCTAACCGGTTTTC
Found at i:338227 original size:17 final size:18
Alignment explanation
Indices: 338187--338232 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
338177 TTTGACCTGT
*
338187 CTGACCCAACCGATCGAC
1 CTGACCCGACCGATCGAC
* *
338205 CCGACCCGACCG-TTGAC
1 CTGACCCGACCGATCGAC
338222 CTGACCCGACC
1 CTGACCCGACC
338233 CGACCGTTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
17 14 0.58
18 10 0.42
ACGTcount: A:0.22, C:0.48, G:0.20, T:0.11
Consensus pattern (18 bp):
CTGACCCGACCGATCGAC
Found at i:338227 original size:22 final size:22
Alignment explanation
Indices: 338201--338260 Score: 102
Period size: 22 Copynumber: 2.7 Consensus size: 22
338191 CCCAACCGAT
*
338201 CGACCCGACCCGACCGTTGACC
1 CGACCCGACCCGACCGTTAACC
*
338223 TGACCCGACCCGACCGTTAACC
1 CGACCCGACCCGACCGTTAACC
338245 CGACCCGACCCGACCG
1 CGACCCGACCCGACCG
338261 GACCGTTGAT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.20, C:0.50, G:0.22, T:0.08
Consensus pattern (22 bp):
CGACCCGACCCGACCGTTAACC
Found at i:339868 original size:23 final size:23
Alignment explanation
Indices: 339838--339889 Score: 95
Period size: 23 Copynumber: 2.3 Consensus size: 23
339828 ATATAGTCTG
339838 ACCGGTGTTAGATCAGTAATATT
1 ACCGGTGTTAGATCAGTAATATT
*
339861 ACCGGTGTTAGATCGGTAATATT
1 ACCGGTGTTAGATCAGTAATATT
339884 ACCGGT
1 ACCGGT
339890 CACTGGTGAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.27, C:0.15, G:0.25, T:0.33
Consensus pattern (23 bp):
ACCGGTGTTAGATCAGTAATATT
Found at i:347660 original size:20 final size:21
Alignment explanation
Indices: 347635--347674 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
347625 GAATCCTGGC
347635 AAAGAGCAT-TGAAATACAGT
1 AAAGAGCATCTGAAATACAGT
*
347655 AAAGAGGATCCTGAAATACA
1 AAAGAGCAT-CTGAAATACA
347675 TCAAAGGGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
22 9 0.53
ACGTcount: A:0.50, C:0.12, G:0.20, T:0.17
Consensus pattern (21 bp):
AAAGAGCATCTGAAATACAGT
Found at i:349744 original size:30 final size:31
Alignment explanation
Indices: 349708--349771 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
349698 AAGTGATTAG
* *
349708 ATAAAAATAT-TTTAAAATTTAATGACTAAA
1 ATAAAAATATAGTTAAAATTGAATGACTAAA
* *
349738 ATAAAAATATAGTTAAAGTTGAATGATTAAA
1 ATAAAAATATAGTTAAAATTGAATGACTAAA
349769 ATA
1 ATA
349772 TAATTTACAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 10 0.34
31 19 0.66
ACGTcount: A:0.56, C:0.02, G:0.08, T:0.34
Consensus pattern (31 bp):
ATAAAAATATAGTTAAAATTGAATGACTAAA
Found at i:353566 original size:22 final size:24
Alignment explanation
Indices: 353511--353571 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 24
353501 ATAATTTGCT
*
353511 TTTATGACATGTTTT-TTTCTGTC
1 TTTATGATATGTTTTCTTTCTGTC
*
353534 TTTATTATATGTTTTCTTT-TGTC
1 TTTATGATATGTTTTCTTTCTGTC
*
353557 TTT-TGGTATGTTTTC
1 TTTATGATATGTTTTC
353572 GGTCGTTTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
22 10 0.30
23 20 0.61
24 3 0.09
ACGTcount: A:0.11, C:0.10, G:0.13, T:0.66
Consensus pattern (24 bp):
TTTATGATATGTTTTCTTTCTGTC
Found at i:362113 original size:14 final size:14
Alignment explanation
Indices: 362059--362115 Score: 51
Period size: 14 Copynumber: 3.9 Consensus size: 14
362049 TTGATTTTTT
362059 GAAAATTGAATTATG
1 GAAAA-TGAATTATG
*
362074 AAAAATGAATTATTG
1 GAAAATGAATTA-TG
** * *
362089 GAATTTAAATTCTG
1 GAAAATGAATTATG
362103 GAAAATGAATTAT
1 GAAAATGAATTAT
362116 ATTTCTAGAA
Statistics
Matches: 31, Mismatches: 10, Indels: 3
0.70 0.23 0.07
Matches are distributed among these distances:
14 18 0.58
15 13 0.42
ACGTcount: A:0.47, C:0.02, G:0.16, T:0.35
Consensus pattern (14 bp):
GAAAATGAATTATG
Found at i:362340 original size:26 final size:27
Alignment explanation
Indices: 362306--362356 Score: 70
Period size: 26 Copynumber: 1.9 Consensus size: 27
362296 ATTATAAACT
*
362306 TAATATTA-TTATTTTTAAAATATTAAA
1 TAATATTATTTATTATT-AAATATTAAA
362333 TAAT-TTATTTATTATTAAATATTA
1 TAATATTATTTATTATTAAATATTA
362357 TTTTTATAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 11 0.50
27 11 0.50
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (27 bp):
TAATATTATTTATTATTAAATATTAAA
Found at i:362362 original size:19 final size:19
Alignment explanation
Indices: 362312--362363 Score: 52
Period size: 19 Copynumber: 2.6 Consensus size: 19
362302 AACTTAATAT
*
362312 TATTATTTTTAAAATATTAAA
1 TATTATTTTT--ATTATTAAA
*
362333 TAATT-TATTTATTATTAAA
1 T-ATTATTTTTATTATTAAA
362352 TATTATTTTTAT
1 TATTATTTTTAT
362364 AATTTTATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
18 3 0.12
19 15 0.58
21 5 0.19
22 3 0.12
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TATTATTTTTATTATTAAA
Found at i:362509 original size:23 final size:23
Alignment explanation
Indices: 362460--362510 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
362450 GTGTTATATT
**
362460 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAAAATATTAATTAAA
*
362483 ATATTTTAAATATCATT-ATTAAA
1 ATATTTTAAAAAT-ATTAATTAAA
362506 ATATT
1 ATATT
362511 ATTAGATTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 21 0.88
24 3 0.12
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (23 bp):
ATATTTTAAAAATATTAATTAAA
Found at i:362709 original size:30 final size:32
Alignment explanation
Indices: 362675--362735 Score: 99
Period size: 30 Copynumber: 2.0 Consensus size: 32
362665 AATATAATTG
*
362675 ATTATTTTATTAT-AATATTAA-AAATATTAT
1 ATTATATTATTATAAATATTAATAAATATTAT
362705 ATTATATTATTATAAATATTAATAAATATTA
1 ATTATATTATTATAAATATTAATAAATATTA
362736 GTAAATATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
30 12 0.43
31 8 0.29
32 8 0.29
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (32 bp):
ATTATATTATTATAAATATTAATAAATATTAT
Found at i:362729 original size:10 final size:10
Alignment explanation
Indices: 362688--362744 Score: 55
Period size: 10 Copynumber: 5.6 Consensus size: 10
362678 ATTTTATTAT
362688 AATATTAA-A
1 AATATTAATA
362697 AATATT-ATA
1 AATATTAATA
*
362706 TTATATTATTATA
1 -AATATTA--ATA
362719 AATATTAATA
1 AATATTAATA
*
362729 AATATTAGTA
1 AATATTAATA
362739 AATATT
1 AATATT
362745 TTAATAATTA
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
8 1 0.03
9 7 0.17
10 23 0.57
12 6 0.15
13 3 0.08
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.46
Consensus pattern (10 bp):
AATATTAATA
Found at i:362748 original size:22 final size:22
Alignment explanation
Indices: 362677--362759 Score: 73
Period size: 22 Copynumber: 3.8 Consensus size: 22
362667 TATAATTGAT
* *
362677 TATTTTATTATAATATTAAAAA
1 TATTTTAATATAATATTATAAA
* * *
362699 TATTATATTATATTATTATAAA
1 TATTTTAATATAATATTATAAA
362721 TA--TTAATA-AATATTAGTAAA
1 TATTTTAATATAATATTA-TAAA
362741 TATTTTAATAATTAATATT
1 TATTTTAAT-A-TAATATT
362760 TTGATTAAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
19 6 0.12
20 10 0.20
22 26 0.53
23 1 0.02
25 6 0.12
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (22 bp):
TATTTTAATATAATATTATAAA
Found at i:363013 original size:42 final size:42
Alignment explanation
Indices: 362957--363046 Score: 144
Period size: 42 Copynumber: 2.1 Consensus size: 42
362947 TTCCTCCATC
* *
362957 CAAACACTGGAAAACATTTTACGGAAGACGAATTACATGAAA
1 CAAACACAGGAAAACATTTTACGGAAAACGAATTACATGAAA
* *
362999 CAAACACAGGAAAACATTTTTCGGAAAACGAATTACGTGAAA
1 CAAACACAGGAAAACATTTTACGGAAAACGAATTACATGAAA
363041 CAAACA
1 CAAACA
363047 TGAGATTTCG
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.49, C:0.18, G:0.16, T:0.18
Consensus pattern (42 bp):
CAAACACAGGAAAACATTTTACGGAAAACGAATTACATGAAA
Found at i:363410 original size:21 final size:20
Alignment explanation
Indices: 363370--363409 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
363360 TGATTAATAG
363370 GTGCAAATTTATGTTTAAAA
1 GTGCAAATTTATGTTTAAAA
*
363390 GTGCTAATCTTAT-TTTAAAA
1 GTGCAAAT-TTATGTTTAAAA
363410 ATATGTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.38, C:0.07, G:0.12, T:0.42
Consensus pattern (20 bp):
GTGCAAATTTATGTTTAAAA
Found at i:365913 original size:5 final size:5
Alignment explanation
Indices: 365903--365931 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
365893 CTCTCACACC
365903 ACCAA ACCAA ACCAA ACCAA ACCAA ACCA
1 ACCAA ACCAA ACCAA ACCAA ACCAA ACCA
365932 TTCTACTAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.59, C:0.41, G:0.00, T:0.00
Consensus pattern (5 bp):
ACCAA
Found at i:379734 original size:15 final size:15
Alignment explanation
Indices: 379710--379740 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
379700 ACTGATGATC
379710 ATTATAAATAATAAT
1 ATTATAAATAATAAT
*
379725 ATTATTAATAATAAT
1 ATTATAAATAATAAT
379740 A
1 A
379741 AAAACACGGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
ATTATAAATAATAAT
Found at i:380318 original size:31 final size:30
Alignment explanation
Indices: 380237--380314 Score: 102
Period size: 31 Copynumber: 2.5 Consensus size: 30
380227 ACCCCTAAGT
* *
380237 TTTAGATAAAACACTAATTTGACTCTTGAAC
1 TTTAGATAAAATA-TAATTTGACTCTTAAAC
* *
380268 TTTAGACAAGATATTAATTTGACTCTTAAAC
1 TTTAGATAAAATA-TAATTTGACTCTTAAAC
380299 TTTAGATAAAATATAA
1 TTTAGATAAAATATAA
380315 ATTTAACACA
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
30 3 0.08
31 37 0.93
ACGTcount: A:0.42, C:0.12, G:0.09, T:0.37
Consensus pattern (30 bp):
TTTAGATAAAATATAATTTGACTCTTAAAC
Found at i:382035 original size:35 final size:35
Alignment explanation
Indices: 381987--382062 Score: 116
Period size: 35 Copynumber: 2.2 Consensus size: 35
381977 AAAATAGTCC
* *
381987 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
* *
382022 TTAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
382057 TCAATT
1 TCAATT
382063 AAATTCAATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.39, C:0.22, G:0.01, T:0.37
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
Found at i:382605 original size:130 final size:130
Alignment explanation
Indices: 382459--382706 Score: 415
Period size: 130 Copynumber: 1.9 Consensus size: 130
382449 TATTTATATA
* * **
382459 ATCAATTTGGTCCTAAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAACTAATCATTTAACCAGGATCTGACATGTG
* *
382524 TTAGCACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCC
66 TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCC
382589 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAACTAATCATTTAACCAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAACTAATCATTTAACCAGGATCTGACATGTG
* * *
382654 TTAACACATGATCATGATATATGTTATTGGTGACACATGTCACCACCTAATTA
66 TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTA
382707 GAAGAAAATT
Statistics
Matches: 109, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
130 109 1.00
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.35
Consensus pattern (130 bp):
ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAACTAATCATTTAACCAGGATCTGACATGTG
TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCC
Found at i:382737 original size:130 final size:129
Alignment explanation
Indices: 382473--382737 Score: 291
Period size: 130 Copynumber: 2.0 Consensus size: 129
382463 ATTTGGTCCT
* * ** *
382473 AAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTGTTAGCACATGATCA
1 AAATTAAATAAAATTTAATAAACTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
* *** * * **** *
382538 TGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCCATCAATTTGGTCCT
66 TGACACATGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCCATCAAAGAAGT-CA
382603 AAATTAAATAAAATTTAATAAACTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
1 AAATTAAATAAAATTTAATAAACTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
* * * **
382668 TGATATATGTTATTGGTGACACATGTCACCACCTAATTAGAAGAAAATTAAGTTA-CAAAGAAGT
66 TGACACATGTCATTGGTGACACATGTCACCACCTAATT--AAGAAAA-TAAGCCATCAAAGAAGT
382732 -A
128 CA
382733 AAATT
1 AAATT
382738 TGGGTCTTGG
Statistics
Matches: 111, Mismatches: 21, Indels: 6
0.80 0.15 0.04
Matches are distributed among these distances:
130 99 0.89
132 8 0.07
133 4 0.04
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.33
Consensus pattern (129 bp):
AAATTAAATAAAATTTAATAAACTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
TGACACATGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCCATCAAAGAAGTCA
Found at i:383063 original size:28 final size:27
Alignment explanation
Indices: 383032--383094 Score: 63
Period size: 28 Copynumber: 2.3 Consensus size: 27
383022 AGTTGATACA
*
383032 ATATTTTAAAAGAATAAATTTAAGATTT
1 ATATTTTAAAA-AATAAATTTAAGAATT
** * *
383060 ATATATTTTTAAACTAAATTTAATAATT
1 ATAT-TTTAAAAAATAAATTTAAGAATT
383088 ATATTTT
1 ATATTTT
383095 TCATATATAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
27 3 0.10
28 21 0.72
29 5 0.17
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (27 bp):
ATATTTTAAAAAATAAATTTAAGAATT
Found at i:383196 original size:16 final size:18
Alignment explanation
Indices: 383175--383208 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
383165 ATTTCTTATT
383175 AAAAATA-AAAT-ATTCA
1 AAAAATATAAATGATTCA
383191 AAAAATATAAATGATTCA
1 AAAAATATAAATGATTCA
383209 TACATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAAATATAAATGATTCA
Found at i:395607 original size:17 final size:17
Alignment explanation
Indices: 395585--395621 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
395575 ATAATAAAAG
395585 TAAATTTTTGCATTTTA
1 TAAATTTTTGCATTTTA
395602 TAAATTTTTGCATTTTA
1 TAAATTTTTGCATTTTA
395619 TAA
1 TAA
395622 TCAAAGTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.57
Consensus pattern (17 bp):
TAAATTTTTGCATTTTA
Found at i:400118 original size:25 final size:25
Alignment explanation
Indices: 400090--400141 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
400080 CGCTAATAAC
400090 AGATAACAACTTCAATTACTAAAAA
1 AGATAACAACTTCAATTACTAAAAA
400115 AGATAACAACTTCAATTACTAAAAA
1 AGATAACAACTTCAATTACTAAAAA
400140 AG
1 AG
400142 GACAAAGTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.56, C:0.15, G:0.06, T:0.23
Consensus pattern (25 bp):
AGATAACAACTTCAATTACTAAAAA
Found at i:400584 original size:20 final size:20
Alignment explanation
Indices: 400559--400636 Score: 80
Period size: 18 Copynumber: 4.2 Consensus size: 20
400549 ACGTTTTATA
400559 TTTTTA-AAAAACTTTTATTT
1 TTTTTATAAAAA-TTTTATTT
400579 TTTTTATAAAAA--TTATTT
1 TTTTTATAAAAATTTTATTT
400597 TTTTTATAAAAA--TTATTT
1 TTTTTATAAAAATTTTATTT
*
400615 TTTTGT-TAAAAA-TCTATTT
1 TTTT-TATAAAAATTTTATTT
400634 TTT
1 TTT
400637 AAAAATCTTC
Statistics
Matches: 54, Mismatches: 1, Indels: 7
0.87 0.02 0.11
Matches are distributed among these distances:
18 34 0.63
19 9 0.17
20 6 0.11
21 5 0.09
ACGTcount: A:0.35, C:0.03, G:0.01, T:0.62
Consensus pattern (20 bp):
TTTTTATAAAAATTTTATTT
Found at i:400632 original size:19 final size:18
Alignment explanation
Indices: 400573--400636 Score: 103
Period size: 18 Copynumber: 3.5 Consensus size: 18
400563 TAAAAAACTT
400573 TTATTTTTTTTATAAAAA
1 TTATTTTTTTTATAAAAA
400591 TTATTTTTTTTATAAAAA
1 TTATTTTTTTTATAAAAA
400609 TTATTTTTTTGT-TAAAAA
1 TTATTTTTTT-TATAAAAA
400627 TCTATTTTTT
1 T-TATTTTTT
400637 AAAAATCTTC
Statistics
Matches: 44, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
18 35 0.80
19 9 0.20
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.64
Consensus pattern (18 bp):
TTATTTTTTTTATAAAAA
Found at i:400640 original size:15 final size:16
Alignment explanation
Indices: 400615--400644 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
400605 AAAATTATTT
400615 TTTTGTTAAAAATCTA
1 TTTTGTTAAAAATCTA
400631 TTTT-TTAAAAATCT
1 TTTTGTTAAAAATCT
400645 TCATAATATC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.37, C:0.07, G:0.03, T:0.53
Consensus pattern (16 bp):
TTTTGTTAAAAATCTA
Found at i:400959 original size:19 final size:20
Alignment explanation
Indices: 400923--400960 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
400913 CGAAAATGTA
*
400923 GATAATAATTGGAGATGATC
1 GATAATAATTGAAGATGATC
400943 GATAATAA-TGAAGATGAT
1 GATAATAATTGAAGATGAT
400961 AATTGGAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.45, C:0.03, G:0.24, T:0.29
Consensus pattern (20 bp):
GATAATAATTGAAGATGATC
Found at i:400968 original size:32 final size:29
Alignment explanation
Indices: 400883--400982 Score: 130
Period size: 29 Copynumber: 3.3 Consensus size: 29
400873 TGGTGGTCAT
*
400883 TCGACAATGAAGATAATAATTGGAGATGA
1 TCGAAAATGAAGATAATAATTGGAGATGA
*
400912 TCGAAAATGTAGATAATAATTGGAGATGA
1 TCGAAAATGAAGATAATAATTGGAGATGA
*
400941 TCGATAATAATGAAGATGATAATTGGAGATGA
1 TCG--AA-AATGAAGATAATAATTGGAGATGA
400973 TC-AACAATGA
1 TCGAA-AATGA
400983 CTGGAAATGA
Statistics
Matches: 63, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
29 37 0.59
31 2 0.03
32 24 0.38
ACGTcount: A:0.45, C:0.06, G:0.23, T:0.26
Consensus pattern (29 bp):
TCGAAAATGAAGATAATAATTGGAGATGA
Found at i:408567 original size:76 final size:76
Alignment explanation
Indices: 408486--408638 Score: 306
Period size: 76 Copynumber: 2.0 Consensus size: 76
408476 TTACGATTTG
408486 TTTGTTTGTTCTTACTTTTATTCGGTTAATTTGATATAATTAAATATTATCAATTTGTATTTCTA
1 TTTGTTTGTTCTTACTTTTATTCGGTTAATTTGATATAATTAAATATTATCAATTTGTATTTCTA
408551 ATTTTAACCAA
66 ATTTTAACCAA
408562 TTTGTTTGTTCTTACTTTTATTCGGTTAATTTGATATAATTAAATATTATCAATTTGTATTTCTA
1 TTTGTTTGTTCTTACTTTTATTCGGTTAATTTGATATAATTAAATATTATCAATTTGTATTTCTA
408627 ATTTTAACCAA
66 ATTTTAACCAA
408638 T
1 T
408639 AATTTCAAGT
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 77 1.00
ACGTcount: A:0.29, C:0.09, G:0.08, T:0.54
Consensus pattern (76 bp):
TTTGTTTGTTCTTACTTTTATTCGGTTAATTTGATATAATTAAATATTATCAATTTGTATTTCTA
ATTTTAACCAA
Found at i:414166 original size:24 final size:24
Alignment explanation
Indices: 414118--414166 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
414108 AATCGATAAT
* *
414118 TAATTGAAAATTAATAACAATATA
1 TAATTGAAAATTAACAACAAAATA
* *
414142 TAATTGAAAATTAACGAGAAAATA
1 TAATTGAAAATTAACAACAAAATA
414166 T
1 T
414167 GGAAAATAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.57, C:0.04, G:0.08, T:0.31
Consensus pattern (24 bp):
TAATTGAAAATTAACAACAAAATA
Found at i:423390 original size:2 final size:2
Alignment explanation
Indices: 423383--423407 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
423373 ACCGCCCCCG
423383 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
423408 GCTCTTCAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:423555 original size:2 final size:2
Alignment explanation
Indices: 423550--423579 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
423540 AGTCATCCTA
423550 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
423580 TCCAAACTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:425334 original size:28 final size:28
Alignment explanation
Indices: 425279--425341 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 28
425269 ATAAAACCAA
**
425279 AAATAATAATATTAATAATATAGTATAT
1 AAATAATAATATTAATAATATACAATAT
*
425307 AAATAATAATATT-ATTATATAACAATAT
1 AAATAATAATATTAATAATAT-ACAATAT
425335 -AATAATA
1 AAATAATA
425342 CTATATATAC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
27 13 0.42
28 18 0.58
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (28 bp):
AAATAATAATATTAATAATATACAATAT
Found at i:429683 original size:31 final size:31
Alignment explanation
Indices: 429645--429706 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
429635 GGTTGAATTC
*
429645 AGGGGTCAAATTGATATTTCAGCTAAAGTTT
1 AGGGGTCAAAATGATATTTCAGCTAAAGTTT
* * *
429676 AGGGGTCAAAATGATGTTTTATCTAAAGTTT
1 AGGGGTCAAAATGATATTTCAGCTAAAGTTT
429707 GAGGTCTAAC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.32, C:0.08, G:0.23, T:0.37
Consensus pattern (31 bp):
AGGGGTCAAAATGATATTTCAGCTAAAGTTT
Found at i:429874 original size:31 final size:30
Alignment explanation
Indices: 429811--429874 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
429801 AACGGTTCAA
* *
429811 TGACTAAAATGTAACAATCGATAATATAAG
1 TGACTAAAATGTAACAATCAATAACATAAG
* *
429841 TGACTAAAATGTAATAACTTAATAACATAAG
1 TGACTAAAATGTAACAA-TCAATAACATAAG
429872 TGA
1 TGA
429875 TCAAAAATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 16 0.55
31 13 0.45
ACGTcount: A:0.50, C:0.09, G:0.12, T:0.28
Consensus pattern (30 bp):
TGACTAAAATGTAACAATCAATAACATAAG
Found at i:431737 original size:23 final size:23
Alignment explanation
Indices: 431711--431756 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
431701 TAAATGTATC
*
431711 TTAATTGCATTAATAATT-TTTAT
1 TTAAATGC-TTAATAATTGTTTAT
*
431734 TTAAATGCTTAATATTTGTTTAT
1 TTAAATGCTTAATAATTGTTTAT
431757 GTTTTATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.57
Consensus pattern (23 bp):
TTAAATGCTTAATAATTGTTTAT
Found at i:432136 original size:24 final size:24
Alignment explanation
Indices: 432090--432142 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
432080 TAGAAAATTT
* *
432090 AAAAACATAATATAATTATAATACC
1 AAAAACATAATATAATAAGAATA-C
432115 AAAAACA-AATATAATAAGAATAC
1 AAAAACATAATATAATAAGAATAC
432138 AAAAA
1 AAAAA
432143 TCCCAAATCA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 6 0.23
24 13 0.50
25 7 0.27
ACGTcount: A:0.68, C:0.09, G:0.02, T:0.21
Consensus pattern (24 bp):
AAAAACATAATATAATAAGAATAC
Found at i:434807 original size:2 final size:2
Alignment explanation
Indices: 434802--434862 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
434792 TGAAAAAAAG
434802 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
434844 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
434863 GATCTATAAG
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:435460 original size:116 final size:117
Alignment explanation
Indices: 435308--435540 Score: 459
Period size: 117 Copynumber: 2.0 Consensus size: 117
435298 TAAACTTGAA
435308 GTCATCACTGACCATTTGAGTTAGGTAGAATCAAACACCTATAGAATCGAATTT-AAAAAAAAAA
1 GTCATCACTGACCATTTGAGTTAGGTAGAATCAAACACCTATAGAATCGAATTTAAAAAAAAAAA
435372 TTGAAGTTCACATTTCATTAGAGAAACATTTTGAAAGAGTTCAAATGTCAGT
66 TTGAAGTTCACATTTCATTAGAGAAACATTTTGAAAGAGTTCAAATGTCAGT
435424 GTCATCACTGACCATTTGAGTTAGGTAGAATCAAACACCTATAGAATCGAATTTAAAAAAAAAAA
1 GTCATCACTGACCATTTGAGTTAGGTAGAATCAAACACCTATAGAATCGAATTTAAAAAAAAAAA
435489 TTGAAGTTCACATTTCATTAGAGAAACATTTTGAAAGAGTTCAAATGTCAGT
66 TTGAAGTTCACATTTCATTAGAGAAACATTTTGAAAGAGTTCAAATGTCAGT
435541 TACACAGAAG
Statistics
Matches: 116, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
116 54 0.47
117 62 0.53
ACGTcount: A:0.42, C:0.14, G:0.15, T:0.29
Consensus pattern (117 bp):
GTCATCACTGACCATTTGAGTTAGGTAGAATCAAACACCTATAGAATCGAATTTAAAAAAAAAAA
TTGAAGTTCACATTTCATTAGAGAAACATTTTGAAAGAGTTCAAATGTCAGT
Found at i:437746 original size:23 final size:23
Alignment explanation
Indices: 437720--437779 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 23
437710 ATAAAGTACT
*
437720 AAATATAATTATTAA-TTAGTTAA
1 AAATATAATT-TTAATTTAATTAA
*
437743 AAATATAAATTTAATTTAATTAA
1 AAATATAATTTTAATTTAATTAA
*
437766 AAGTATAATATTTA
1 AAATATAAT-TTTA
437780 TAAAATATTA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
22 4 0.13
23 23 0.74
24 4 0.13
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.43
Consensus pattern (23 bp):
AAATATAATTTTAATTTAATTAA
Found at i:439000 original size:2 final size:2
Alignment explanation
Indices: 438995--439047 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
438985 TTCTATTAAT
438995 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
439037 TA TA TA TA TA T
1 TA TA TA TA TA T
439048 TATGTTGTGA
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:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:439610 original size:22 final size:22
Alignment explanation
Indices: 439585--439627 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
439575 GATTTTTAAG
439585 TAATTTATAA-TTATATGTTTTT
1 TAATTTATAATTTA-ATGTTTTT
439607 TAATTTATAATTTAATGTTTT
1 TAATTTATAATTTAATGTTTT
439628 ATAAATTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 17 0.85
23 3 0.15
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.63
Consensus pattern (22 bp):
TAATTTATAATTTAATGTTTTT
Found at i:439923 original size:23 final size:23
Alignment explanation
Indices: 439894--439946 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
439884 TTATTGATAA
439894 TATAATT-TTATATCCTTAA-TTTT
1 TATAATTCTTATAT-C-TAATTTTT
439917 TATAATTTCTTATATCTAATTTTT
1 TATAA-TTCTTATATCTAATTTTT
439941 TATAAT
1 TATAAT
439947 AAATTCTTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
23 9 0.33
24 12 0.44
25 6 0.22
ACGTcount: A:0.32, C:0.08, G:0.00, T:0.60
Consensus pattern (23 bp):
TATAATTCTTATATCTAATTTTT
Found at i:446406 original size:30 final size:30
Alignment explanation
Indices: 446367--446517 Score: 104
Period size: 30 Copynumber: 5.0 Consensus size: 30
446357 TCGACTTATT
*
446367 AAATATATTTTTATCTTTATTTTAACTTAA
1 AAATATATTTTTATCTTTATATTAACTTAA
* * *
446397 AAATGTATTTTGT-TC-TTATGTTATCTTTAA
1 AAATATATTTT-TATCTTTATATTAAC-TTAA
*
446427 AGATATA-TTTTATCCTTT-TATTAACTTAA
1 AAATATATTTTTAT-CTTTATATTAACTTAA
446456 AAA-ATATATTTTAT-TGTTA-ACTTTAACTTCAA
1 AAATATAT-TTTTATCT-TTATA--TTAACTT-AA
446488 ATAATATATTTTGT-TCTTT-TATTAACTTAA
1 A-AATATATTTT-TATCTTTATATTAACTTAA
446518 TATAATAATA
Statistics
Matches: 96, Mismatches: 8, Indels: 34
0.70 0.06 0.25
Matches are distributed among these distances:
28 5 0.05
29 21 0.22
30 35 0.36
31 17 0.18
32 3 0.03
33 9 0.09
34 6 0.06
ACGTcount: A:0.34, C:0.08, G:0.04, T:0.54
Consensus pattern (30 bp):
AAATATATTTTTATCTTTATATTAACTTAA
Found at i:446636 original size:60 final size:59
Alignment explanation
Indices: 446559--446685 Score: 157
Period size: 59 Copynumber: 2.1 Consensus size: 59
446549 ATATATATAT
* * * * * * *
446559 ATATATATTTGAAGTTAAGATAATAGGGAAATATATTTTTTAAGTTAATAA-AAGAATAAA
1 ATATATTTTTAAAGTTAAAATAAGAAGAAAATATA-TTTTTAAGTTAA-AATAAAAATAAA
*
446619 ATATATTTTTAAAGTTAAAATAAGAATAAAATATATTTTTAAGTTAAAATAAAAATAAA
1 ATATATTTTTAAAGTTAAAATAAGAAGAAAATATATTTTTAAGTTAAAATAAAAATAAA
446678 ATATATTT
1 ATATATTT
446686 AATATGTTGA
Statistics
Matches: 58, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
58 2 0.03
59 28 0.48
60 28 0.48
ACGTcount: A:0.53, C:0.00, G:0.09, T:0.39
Consensus pattern (59 bp):
ATATATTTTTAAAGTTAAAATAAGAAGAAAATATATTTTTAAGTTAAAATAAAAATAAA
Found at i:446657 original size:29 final size:30
Alignment explanation
Indices: 446587--446722 Score: 163
Period size: 30 Copynumber: 4.5 Consensus size: 30
446577 GATAATAGGG
446587 AAATATATTTTTTAAGTTAATAA-AAGAATA
1 AAATATATTTTTTAAGTTAA-AATAAGAATA
*
446617 AAATATATTTTTAAAGTTAAAATAAGAATA
1 AAATATATTTTTTAAGTTAAAATAAGAATA
*
446647 AAATATA-TTTTTAAGTTAAAATAAAAATA
1 AAATATATTTTTTAAGTTAAAATAAGAATA
** *
446676 AAATATATTTAATATGTTGAATAA-AA-AATA
1 AAATATATTTTTTAAGTT-AA-AATAAGAATA
446706 AAATATATATTTTTAAG
1 AAATATAT-TTTTTAAG
446723 CTTAGGATAT
Statistics
Matches: 92, Mismatches: 9, Indels: 9
0.84 0.08 0.08
Matches are distributed among these distances:
29 29 0.32
30 52 0.57
31 9 0.10
32 2 0.02
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (30 bp):
AAATATATTTTTTAAGTTAAAATAAGAATA
Found at i:446706 original size:59 final size:58
Alignment explanation
Indices: 446587--446718 Score: 155
Period size: 59 Copynumber: 2.2 Consensus size: 58
446577 GATAATAGGG
*
446587 AAATATATTTTTTAAGTTAATAAAAGAATAAAATATATTTTTAAAGTTAAAATAAGAATA
1 AAATATA-TTTTTAAGTTAATAAAAAAATAAAATATA-TTTTAAAGTTAAAATAAGAATA
446647 AAATATATTTTTAAGTTAA-AATAAAAATAAAATATA-TTTAATATGTTGAATAA-AA-AATA
1 AAATATATTTTTAAGTTAATAA-AAAAATAAAATATATTTTAA-A-GTT-AA-AATAAGAATA
446706 AAATATATATTTT
1 AAATATAT-TTTT
446719 TAAGCTTAGG
Statistics
Matches: 65, Mismatches: 1, Indels: 12
0.83 0.01 0.15
Matches are distributed among these distances:
57 5 0.08
58 3 0.05
59 40 0.62
60 15 0.23
61 2 0.03
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.39
Consensus pattern (58 bp):
AAATATATTTTTAAGTTAATAAAAAAATAAAATATATTTTAAAGTTAAAATAAGAATA
Found at i:449977 original size:45 final size:45
Alignment explanation
Indices: 449895--449983 Score: 124
Period size: 45 Copynumber: 2.0 Consensus size: 45
449885 CAGTGATGTT
*
449895 TGCAGCCGGCTGTGGGGCTCTAGTACTAGTACATGGACCATGCAA
1 TGCAGCCGGCTGAGGGGCTCTAGTACTAGTACATGGACCATGCAA
* * * * *
449940 TGCAGCTGGCTGAGGGGCTTTATTACTCGTACTTGGACCATGCA
1 TGCAGCCGGCTGAGGGGCTCTAGTACTAGTACATGGACCATGCA
449984 GAAAAGCACA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.20, C:0.24, G:0.30, T:0.26
Consensus pattern (45 bp):
TGCAGCCGGCTGAGGGGCTCTAGTACTAGTACATGGACCATGCAA
Found at i:460433 original size:17 final size:17
Alignment explanation
Indices: 460408--460443 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
460398 TCCCACACGA
*
460408 ACGTGGTTTTAAAATTG
1 ACGTAGTTTTAAAATTG
460425 ACGTAGTTTTAAAATTG
1 ACGTAGTTTTAAAATTG
460442 AC
1 AC
460444 CTAAAATGTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.33, C:0.08, G:0.19, T:0.39
Consensus pattern (17 bp):
ACGTAGTTTTAAAATTG
Found at i:461620 original size:18 final size:18
Alignment explanation
Indices: 461593--461648 Score: 76
Period size: 18 Copynumber: 2.9 Consensus size: 18
461583 GTCTTTTATA
*
461593 TTTATATTTATTTTTATTT
1 TTTAT-TTTATTATTATTT
461612 TTTATTTTATTATTATTT
1 TTTATTTTATTATTATTT
461630 TTTATTATTAATTATTATT
1 TTTATT-TT-ATTATTATT
461649 AACTATTATT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
18 18 0.53
19 7 0.21
20 9 0.26
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (18 bp):
TTTATTTTATTATTATTT
Found at i:461626 original size:3 final size:3
Alignment explanation
Indices: 461600--461662 Score: 55
Period size: 3 Copynumber: 22.0 Consensus size: 3
461590 ATATTTATAT
*
461600 TTA TTT TTA TT- TT- TTA TT- TTA TTA TTA TT- TT- TTA TTA TTAA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A
*
461641 TTA TTA TTAA CTA TTA TTA TTA
1 TTA TTA TT-A TTA TTA TTA TTA
461663 ATTTTACATA
Statistics
Matches: 51, Mismatches: 4, Indels: 10
0.78 0.06 0.15
Matches are distributed among these distances:
2 10 0.20
3 36 0.71
4 5 0.10
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:461636 original size:13 final size:13
Alignment explanation
Indices: 461603--461649 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
461593 TTTATATTTA
461603 TTTTTATT-TT-T
1 TTTTTATTATTAT
461614 TATTTTATTATTAT
1 T-TTTTATTATTAT
*
461628 TTTTTATTATTAA
1 TTTTTATTATTAT
*
461641 TTATTATTA
1 TTTTTATTA
461650 ACTATTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
11 1 0.03
12 7 0.23
13 21 0.68
14 2 0.06
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (13 bp):
TTTTTATTATTAT
Found at i:461649 original size:10 final size:10
Alignment explanation
Indices: 461620--461659 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
461610 TTTTTATTTT
*
461620 ATTATTATTT
1 ATTATTATTA
*
461630 TTTATTATTA
1 ATTATTATTA
461640 ATTATTATTA
1 ATTATTATTA
*
461650 ACTATTATTA
1 ATTATTATTA
461660 TTAATTTTAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (10 bp):
ATTATTATTA
Found at i:479090 original size:14 final size:15
Alignment explanation
Indices: 479065--479105 Score: 57
Period size: 14 Copynumber: 2.8 Consensus size: 15
479055 AAAAATAACC
*
479065 AAATATATAAATATT
1 AAATAAATAAATATT
*
479080 TAA-AAATAAATATT
1 AAATAAATAAATATT
479094 AAATAAATAAAT
1 AAATAAATAAAT
479106 TACAAATTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
14 12 0.55
15 10 0.45
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
AAATAAATAAATATT
Found at i:484426 original size:113 final size:113
Alignment explanation
Indices: 484228--484448 Score: 433
Period size: 113 Copynumber: 2.0 Consensus size: 113
484218 TGGGTATGAG
*
484228 GATATGACCCTCAAATGACCTTCCTAATACATGAAAGAACTTTAAAAATAAATAAATAGAGATGC
1 GATATGACCCTCAAATGACCTTCCAAATACATGAAAGAACTTTAAAAATAAATAAATAGAGATGC
484293 TTGTGTCAAATAGATACTCGGATTTGACACTTCCACCCAAGTCAAATA
66 TTGTGTCAAATAGATACTCGGATTTGACACTTCCACCCAAGTCAAATA
484341 GATATGACCCTCAAATGACCTTCCAAATACATGAAAGAACTTTAAAAATAAATAAATAGAGATGC
1 GATATGACCCTCAAATGACCTTCCAAATACATGAAAGAACTTTAAAAATAAATAAATAGAGATGC
484406 TTGTGTCAAATAGATACTCGGATTTGACACTTCCACCCAAGTC
66 TTGTGTCAAATAGATACTCGGATTTGACACTTCCACCCAAGTC
484449 TGAGTGACGT
Statistics
Matches: 107, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
113 107 1.00
ACGTcount: A:0.40, C:0.20, G:0.14, T:0.26
Consensus pattern (113 bp):
GATATGACCCTCAAATGACCTTCCAAATACATGAAAGAACTTTAAAAATAAATAAATAGAGATGC
TTGTGTCAAATAGATACTCGGATTTGACACTTCCACCCAAGTCAAATA
Found at i:486668 original size:23 final size:24
Alignment explanation
Indices: 486612--486683 Score: 83
Period size: 23 Copynumber: 3.0 Consensus size: 24
486602 TCAAATAAAC
*
486612 ATATTCGTGAACATATAAACGAAT
1 ATATTCGTGAATATATAAACGAAT
**
486636 ATGGTCGTGAATAT-TAAACGAAT
1 ATATTCGTGAATATATAAACGAAT
*
486659 ATATTTGTGAATATAAATAAACGAA
1 ATATTCGTGAATAT--ATAAACGAA
486684 CACAAACACG
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
23 20 0.51
24 11 0.28
26 8 0.21
ACGTcount: A:0.46, C:0.08, G:0.15, T:0.31
Consensus pattern (24 bp):
ATATTCGTGAATATATAAACGAAT
Found at i:486753 original size:30 final size:31
Alignment explanation
Indices: 486696--486755 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
486686 CAAACACGAT
* * *
486696 CTTAAAAATTAAACAATCTGGACATGAACAC
1 CTTAAAAAATAAACAATATGAACATGAACAC
486727 CTTAAAAAATAAACAA-ATGAACATGAACA
1 CTTAAAAAATAAACAATATGAACATGAACA
486756 TCACCTTGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 11 0.42
31 15 0.58
ACGTcount: A:0.55, C:0.17, G:0.08, T:0.20
Consensus pattern (31 bp):
CTTAAAAAATAAACAATATGAACATGAACAC
Found at i:487113 original size:12 final size:12
Alignment explanation
Indices: 487084--487125 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
487074 TTATGTCATG
*
487084 ATAAATTATATTA
1 ATAATTTATA-TA
*
487097 A-AATTTATGTA
1 ATAATTTATATA
487108 ATAATTTATATA
1 ATAATTTATATA
487120 ATAATT
1 ATAATT
487126 AAGTTTTTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
11 3 0.12
12 21 0.84
13 1 0.04
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (12 bp):
ATAATTTATATA
Found at i:491382 original size:26 final size:24
Alignment explanation
Indices: 491337--491384 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
491327 TTTGAATTAA
* *
491337 TTATTTAAAAAATTATAGGAATAT
1 TTATTTAAAAAACTAAAGGAATAT
491361 TTATATTAAAAAACTAGAAGGAAT
1 TTAT-TTAAAAAACTA-AAGGAAT
491385 GATAATAATG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 4 0.20
25 10 0.50
26 6 0.30
ACGTcount: A:0.52, C:0.02, G:0.10, T:0.35
Consensus pattern (24 bp):
TTATTTAAAAAACTAAAGGAATAT
Found at i:492776 original size:2 final size:2
Alignment explanation
Indices: 492769--492801 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
492759 ATGAAATTCC
*
492769 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
492802 AAATGATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:494627 original size:2 final size:2
Alignment explanation
Indices: 494620--494657 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
494610 CTCAAAATAA
494620 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
494658 GTTAATCTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:500201 original size:21 final size:20
Alignment explanation
Indices: 500171--500214 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 20
500161 AAAATTATTT
500171 AAATATTTTTTAATAATTTATA
1 AAATATTTTTTAAT-A-TTATA
500193 AAATATTTTTT-ATATTATA
1 AAATATTTTTTAATATTATA
500212 AAA
1 AAA
500215 AAGCTATACC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 8 0.36
20 1 0.05
21 2 0.09
22 11 0.50
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
AAATATTTTTTAATATTATA
Found at i:502476 original size:3 final size:3
Alignment explanation
Indices: 502470--502512 Score: 59
Period size: 3 Copynumber: 14.0 Consensus size: 3
502460 TATATACATG
* *
502470 TTA TTA TAA ATA TTA TTTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA
502513 ATTCTATTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
3 32 0.91
4 3 0.09
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:507677 original size:106 final size:106
Alignment explanation
Indices: 507492--508553 Score: 1586
Period size: 106 Copynumber: 10.4 Consensus size: 106
507482 ATTTTGCTCG
507492 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
507557 CGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTC
66 CGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTC
* * *
507598 AGAGCCAATTTCAACTTCACAGCGAATGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
* * *
507663 CGAAGGGACCGCTGGTTGTCAAAAAACAACTTCTCAATTTC
66 CGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTC
* * *
507704 AGAGCCAATTTCAAGTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTTATGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
*
507769 CGAAGGGACCGTTGGTTGTCAATAAACAATTT--C----T-
66 CGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTC
507803 -----CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
507863 CGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTC
66 CGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTC
* * * *
507904 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACATGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
*
507969 CGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTC
66 CGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTC
*
508010 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
*
508075 CGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTC
66 CGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTC
* *
508116 AGAGCCAATTTTAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACAA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
*
508181 CGAAGGGACCGCTGGTTGTC----AAC--TGAT---AATTTC
66 CGAAGGGACCGCTGGTTGTCAATAAACAAT-TTCCCAATTTC
508214 ----CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
*
508275 CGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTC
66 CGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTC
*
508316 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
*
508381 CGAATGGACCGCTGGTTGTCAAT--A-AA-----CAATTTC
66 CGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTC
*
508414 ----CCAATTTCAACTTCACAACGAAGGATATTGGACTCCATACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
* * *
508475 CGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAGTTCC
66 CGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTC
** *
508516 AGAGCCAATTTCAACTTCACGTCGGAGGATATTGGACT
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACT
508554 TGGAATAATA
Statistics
Matches: 871, Mismatches: 47, Indels: 76
0.88 0.05 0.08
Matches are distributed among these distances:
94 247 0.28
96 2 0.00
97 2 0.00
98 16 0.02
99 1 0.00
100 2 0.00
101 1 0.00
102 14 0.02
103 2 0.00
104 2 0.00
106 582 0.67
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
CGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTC
Found at i:507852 original size:200 final size:200
Alignment explanation
Indices: 507492--508553 Score: 1631
Period size: 200 Copynumber: 5.2 Consensus size: 200
507482 ATTTTGCTCG
507492 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
507557 CGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCG
66 CGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCA-A--C---TTC-A---CA-A-CG
* * *
507622 AATGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAAA
119 AAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATA
*
507687 AACAACTTCTCAATTTC
184 AACAACTTCCCAATTTC
* * *
507704 AGAGCCAATTTCAAGTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTTATGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
* *
507769 CGAAGGGACCGTTGGTTGTCAATAAACAATTTCTCAATTTCAACTTCACAACGAAGGATATTGGA
66 CGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAACTTCACAACGAAGGATATTGGA
*
507834 CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCA
131 CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCA
507899 ATTTC
196 ATTTC
* * * *
507904 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACATGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
*
507969 CGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCG
66 CGAAGGGACCGCTGGTTGTCAAT--A-AA-----CAATTTC----CCAATTTCAACTTCACAACG
508034 AAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATA
119 AAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATA
508099 AACAACTTCCCAATTTC
184 AACAACTTCCCAATTTC
* *
508116 AGAGCCAATTTTAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACAA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
* *
508181 CGAAGGGACCGCTGGTTGTCAACT-GATAATTTCCCAATTTCAACTTCACAACGAAGGATATTGG
66 CGAAGGGACCGCTGGTTGTCAA-TAAACAATTTCCCAATTTCAACTTCACAACGAAGGATATTGG
508245 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
130 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
508310 AATTTC
195 AATTTC
*
508316 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
*
508381 CGAATGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAACTTCACAACGAAGGATATTGGA
66 CGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAACTTCACAACGAAGGATATTGGA
* * *
508446 CTCCATACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCA
131 CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCA
* *
508511 GTTCC
196 ATTTC
** *
508516 AGAGCCAATTTCAACTTCACGTCGGAGGATATTGGACT
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACT
508554 TGGAATAATA
Statistics
Matches: 792, Mismatches: 44, Indels: 40
0.90 0.05 0.05
Matches are distributed among these distances:
199 1 0.00
200 482 0.61
201 1 0.00
202 3 0.00
203 2 0.00
204 6 0.01
205 1 0.00
206 3 0.00
208 7 0.01
209 2 0.00
211 1 0.00
212 282 0.36
213 1 0.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (200 bp):
AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
CGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAACTTCACAACGAAGGATATTGGA
CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCA
ATTTC
Found at i:507868 original size:43 final size:43
Alignment explanation
Indices: 507713--507868 Score: 123
Period size: 43 Copynumber: 3.4 Consensus size: 43
507703 CAGAGCCAAT
*
507713 TTCAAGTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
1 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
* ** ** ** * * * *
507756 TTCAACTTTATGACGAAGGGACCGTTGGTTGTCAATAAACAATTTCTCAAT
1 TTCAACTTCACAACGAA-GGA-TATTGG-ACTC--CAGACAA---CGCAAG
507807 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
1 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
*
507850 TTCAACTTCACGACGAAGG
1 TTCAACTTCACAACGAAGG
507869 GACCGCTGGT
Statistics
Matches: 81, Mismatches: 24, Indels: 16
0.67 0.20 0.13
Matches are distributed among these distances:
43 35 0.43
44 3 0.04
45 4 0.05
46 7 0.09
48 7 0.09
49 4 0.05
50 3 0.04
51 18 0.22
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24
Consensus pattern (43 bp):
TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
Found at i:508050 original size:306 final size:306
Alignment explanation
Indices: 507496--508553 Score: 1694
Period size: 306 Copynumber: 3.5 Consensus size: 306
507486 TGCTCGAGAG
507496 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
*
507561 GGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAATG
66 GGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGG
*
507626 ATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAAAAACA
131 ATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACA
* * *
507691 ACTTCTCAATTTCAGAGCCAATTTCAAGTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
196 ACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAG
* * *
507756 TTCAACTTTATGACGAAGGGACCGTTGGTTGTCAATAAACAATTTC
261 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTC
*
507802 TCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
507867 GGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGG
66 GGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGG
* *
507932 ATATTGGACTCAAGACAACACATGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACA
131 ATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACA
507997 ACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAG
196 ACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAG
508062 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTC
261 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAT--A-AA-----CAATTTC
* *
508116 AGAGCCAATTTTAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACAA
1 ----CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
* *
508181 CGAAGGGACCGCTGGTTGTC----AAC--TGAT---AATTTC----CCAATTTCAACTTCACAAC
62 CGAAGGGACCGCTGGTTGTCAATAAACAAT-TTCCCAATTTCAGAGCCAATTTCAACTTCACAGC
*
508233 GAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAT
126 GAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAT
508298 AAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAAC
191 AAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAAC
*
508363 GCAAGTTCAACTTCACGACGAATGGACCGCTGGTTGTCAATAAACAATTTC
256 GCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTC
*
508414 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCATACAACGCAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
* * * *
508479 GGGACCGCTGGTTGTCAACAAACAATTTCCCAGTTCCAGAGCCAATTTCAACTTCAC-GTCGGAG
66 GGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAG-CGAAG
508543 GATATTGGACT
130 GATATTGGACT
508554 TGGAATAATA
Statistics
Matches: 697, Mismatches: 28, Indels: 54
0.89 0.04 0.07
Matches are distributed among these distances:
294 78 0.11
298 10 0.01
299 1 0.00
300 1 0.00
302 4 0.01
303 2 0.00
304 1 0.00
306 501 0.72
308 1 0.00
309 2 0.00
310 6 0.01
312 1 0.00
313 1 0.00
314 10 0.01
318 78 0.11
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.23
Consensus pattern (306 bp):
CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
GGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGG
ATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACA
ACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAG
TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTC
Found at i:508480 original size:43 final size:43
Alignment explanation
Indices: 508325--508480 Score: 134
Period size: 43 Copynumber: 3.4 Consensus size: 43
508315 CAGAGCCAAT
*
508325 TTCAACTTCAC-AGCGAAGGATATTGGACTCCAGACAACGCAAG
1 TTCAACTTCACGA-CGAAGGATATTGGACTCCATACAACGCAAG
*** ** * * *
508368 TTCAACTTCACGACGAATGGACCGCTGGTTGTCAATAAACAATTTCCCAAT
1 TTCAACTTCACGACGAA-GGA-TATTGG-ACTCCAT--ACAA---CGCAAG
*
508419 TTCAACTTCACAACGAAGGATATTGGACTCCATACAACGCAAG
1 TTCAACTTCACGACGAAGGATATTGGACTCCATACAACGCAAG
508462 TTCAACTTCACGACGAAGG
1 TTCAACTTCACGACGAAGG
508481 GACCGCTGGT
Statistics
Matches: 85, Mismatches: 19, Indels: 18
0.70 0.16 0.15
Matches are distributed among these distances:
43 37 0.44
44 4 0.05
45 3 0.04
46 7 0.08
48 8 0.09
49 3 0.04
50 3 0.04
51 20 0.24
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (43 bp):
TTCAACTTCACGACGAAGGATATTGGACTCCATACAACGCAAG
Found at i:508852 original size:3 final size:3
Alignment explanation
Indices: 508846--508881 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
508836 TATATACATG
* *
508846 TTA TTA TAA ATA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
508882 ATTCTATTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:510181 original size:21 final size:21
Alignment explanation
Indices: 510134--510177 Score: 72
Period size: 20 Copynumber: 2.1 Consensus size: 21
510124 AGGTTCACCA
510134 ATTATTATTGTTTTTTATTTT
1 ATTATTATTGTTTTTTATTTT
*
510155 ATTATTATT-TTTTTTCTTTT
1 ATTATTATTGTTTTTTATTTT
510175 ATT
1 ATT
510178 TATTTAACAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.77
Consensus pattern (21 bp):
ATTATTATTGTTTTTTATTTT
Found at i:511589 original size:2 final size:2
Alignment explanation
Indices: 511582--511649 Score: 129
Period size: 2 Copynumber: 34.5 Consensus size: 2
511572 AGTTTGAGCT
511582 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
511623 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
511650 TTTAATACTT
Statistics
Matches: 65, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 64 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:517523 original size:21 final size:21
Alignment explanation
Indices: 517499--517562 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 21
517489 GCAAATTTGC
517499 GTTGCATTTCGCGTTGCGATA
1 GTTGCATTTCGCGTTGCGATA
* **
517520 GTTGAAAATCGCGTTGCGAT-
1 GTTGCATTTCGCGTTGCGATA
* *
517540 -TTCCCATTTTGCGTTGCGATA
1 GTT-GCATTTCGCGTTGCGATA
517561 GT
1 GT
517563 CTACAATGTC
Statistics
Matches: 32, Mismatches: 8, Indels: 5
0.71 0.18 0.11
Matches are distributed among these distances:
19 2 0.06
20 12 0.38
21 17 0.53
22 1 0.03
ACGTcount: A:0.17, C:0.19, G:0.27, T:0.38
Consensus pattern (21 bp):
GTTGCATTTCGCGTTGCGATA
Found at i:517576 original size:41 final size:41
Alignment explanation
Indices: 517503--517607 Score: 126
Period size: 41 Copynumber: 2.6 Consensus size: 41
517493 ATTTGCGTTG
* *
517503 CATTTCGCGTTGCGATAGT-TGAAAATCGCGTTGCGATTTCC
1 CATTTTGCGTTGCGATAGTCT-ACAATCGCGTTGCGATTTCC
*
517544 CATTTTGCGTTGCGATAGTCTACAAT-GTCGTTGCGATTTTC
1 CATTTTGCGTTGCGATAGTCTACAATCG-CGTTGCGATTTCC
**
517585 CAAATT-CGTTGCGATAGTCTACA
1 CATTTTGCGTTGCGATAGTCTACA
517608 GTTGTTGTTG
Statistics
Matches: 57, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
40 18 0.32
41 38 0.67
42 1 0.02
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.36
Consensus pattern (41 bp):
CATTTTGCGTTGCGATAGTCTACAATCGCGTTGCGATTTCC
Found at i:517614 original size:19 final size:20
Alignment explanation
Indices: 517552--517634 Score: 62
Period size: 19 Copynumber: 4.1 Consensus size: 20
517542 CCCATTTTGC
*
517552 GTTGCGATAGTCTACAATGTC
1 GTTGCGATAGTCTAC-ATGTT
** * * *
517573 GTTGCGATTTTCCAAAT-TC
1 GTTGCGATAGTCTACATGTT
517592 GTTGCGATAGTCTACAGTTGTT
1 GTTGCGATAGTCTACA--TGTT
*
517614 GTTGCGAAAGTCTACA-GTT
1 GTTGCGATAGTCTACATGTT
517633 GT
1 GT
517635 CGTTGCGATT
Statistics
Matches: 49, Mismatches: 10, Indels: 8
0.73 0.15 0.12
Matches are distributed among these distances:
19 19 0.39
20 2 0.04
21 12 0.24
22 16 0.33
ACGTcount: A:0.22, C:0.17, G:0.24, T:0.37
Consensus pattern (20 bp):
GTTGCGATAGTCTACATGTT
Found at i:517619 original size:22 final size:22
Alignment explanation
Indices: 517551--517643 Score: 95
Period size: 22 Copynumber: 4.4 Consensus size: 22
517541 TCCCATTTTG
*
517551 CGTTGCGATAGTCTACA-ATGT
1 CGTTGCGATAGTCTACAGTTGT
* * **
517572 CGTTGCGAT--TTTCCAAAT-T
1 CGTTGCGATAGTCTACAGTTGT
517591 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
* *
517613 TGTTGCGAAAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
517635 CGTTGCGAT
1 CGTTGCGAT
517644 TTTCCAAATT
Statistics
Matches: 58, Mismatches: 10, Indels: 7
0.77 0.13 0.09
Matches are distributed among these distances:
19 14 0.24
20 2 0.03
21 14 0.24
22 28 0.48
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGTTGT
Found at i:517753 original size:6 final size:6
Alignment explanation
Indices: 517742--517770 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
517732 GACACGTATT
517742 ACCACG ACCACG ACCACG ACCACG ACCAC
1 ACCACG ACCACG ACCACG ACCACG ACCAC
517771 CCCCTTTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.52, G:0.14, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:518247 original size:6 final size:6
Alignment explanation
Indices: 518225--518273 Score: 84
Period size: 6 Copynumber: 8.5 Consensus size: 6
518215 GTCCGTCTCG
518225 GGTCG- GGTCGT -GTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
518271 GGT
1 GGT
518274 AATACGTGTC
Statistics
Matches: 42, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
5 10 0.24
6 32 0.76
ACGTcount: A:0.00, C:0.16, G:0.51, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:518425 original size:43 final size:41
Alignment explanation
Indices: 518397--518587 Score: 134
Period size: 41 Copynumber: 4.8 Consensus size: 41
518387 ACTGTAGACT
518397 ATCGCAACGCGATTTTCAACTATCGCAACGCGAACTGGAAA
1 ATCGCAACGCGATTTTCAACTATCGCAACGCGAACTGGAAA
*
518438 ATCGCAACGCGA--TT----T-TCGCAA--CGAATTTGGAAA
1 ATCGCAACGCGATTTTCAACTATCGCAACGCGAA-CTGGAAA
* * *
518471 ATCGCAACGACAACTGT-AGACTATCGCAACGCGAACTGGAAA
1 ATCGCAACG-CGATTTTCA-ACTATCGCAACGCGAACTGGAAA
** ** * ** ** *
518513 ATCGCAACGCGAAATGGAA-AATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACTATCGCAACGCGAACTGGAA-A
*
518554 ATCGCAACGCGATTTTCAATTATCGCAACGCGAA
1 ATCGCAACGCGATTTTCAACTATCGCAACGCGAA
518588 ATGCAACGCA
Statistics
Matches: 115, Mismatches: 21, Indels: 27
0.71 0.13 0.17
Matches are distributed among these distances:
32 4 0.03
33 15 0.13
34 8 0.07
35 1 0.01
36 1 0.01
39 2 0.02
40 16 0.14
41 36 0.31
42 28 0.24
43 4 0.03
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.20
Consensus pattern (41 bp):
ATCGCAACGCGATTTTCAACTATCGCAACGCGAACTGGAAA
Found at i:518443 original size:20 final size:20
Alignment explanation
Indices: 518418--518544 Score: 101
Period size: 20 Copynumber: 6.6 Consensus size: 20
518408 ATTTTCAACT
518418 ATCGCAACGCGAACTGGAAA
1 ATCGCAACGCGAACTGGAAA
*
518438 ATCGCAACGCG-A-T----T
1 ATCGCAACGCGAACTGGAAA
* *
518452 TTCGCAA--CGAATTTGGAAA
1 ATCGCAACGCGAA-CTGGAAA
**
518471 ATCGCAACGAC-AACTGTAGACT
1 ATCGCAACG-CGAACTG--GAAA
518493 ATCGCAACGCGAACTGGAAA
1 ATCGCAACGCGAACTGGAAA
*
518513 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAACTGGAAA
518533 ATCGCAACGCGA
1 ATCGCAACGCGA
518545 TTTTCAACTA
Statistics
Matches: 84, Mismatches: 10, Indels: 26
0.70 0.08 0.22
Matches are distributed among these distances:
12 2 0.02
13 1 0.01
14 6 0.07
15 1 0.01
18 1 0.01
19 7 0.08
20 46 0.55
21 3 0.04
22 17 0.20
ACGTcount: A:0.38, C:0.24, G:0.23, T:0.15
Consensus pattern (20 bp):
ATCGCAACGCGAACTGGAAA
Found at i:518471 original size:96 final size:95
Alignment explanation
Indices: 518354--518549 Score: 320
Period size: 96 Copynumber: 2.1 Consensus size: 95
518344 TTTTAACTAT
** * *
518354 TTTTCGCAACGAATTTAGAAAATCGCAACGACAACTGTAGACTATCGCAACGCGATTTTCAACTA
1 TTTTCGCAACGAATTTAGAAAATCGCAACGACAACTGTAGACTATCGCAACGCGAACTGCAA-AA
*
518419 TCGCAACGCGAACTGGAAAATCGCAACGCGA
65 TCGCAACGCGAAATGGAAAATCGCAACGCGA
* *
518450 TTTTCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTATCGCAACGCGAACTGGAAAAT
1 TTTTCGCAACGAATTTAGAAAATCGCAACGACAACTGTAGACTATCGCAACGCGAACTGCAAAAT
518515 CGCAACGCGAAATGGAAAATCGCAACGCGA
66 CGCAACGCGAAATGGAAAATCGCAACGCGA
518545 TTTTC
1 TTTTC
518550 AACTATCGCA
Statistics
Matches: 93, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
95 36 0.39
96 57 0.61
ACGTcount: A:0.36, C:0.24, G:0.20, T:0.20
Consensus pattern (95 bp):
TTTTCGCAACGAATTTAGAAAATCGCAACGACAACTGTAGACTATCGCAACGCGAACTGCAAAAT
CGCAACGCGAAATGGAAAATCGCAACGCGA
Found at i:518559 original size:21 final size:21
Alignment explanation
Indices: 518533--518586 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
518523 GAAATGGAAA
518533 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
*
518554 ATCGCAACGCGATTTTCAATT
1 ATCGCAACGCGATTTTCAACT
518575 ATCGCAACGCGA
1 ATCGCAACGCGA
518587 AATGCAACGC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.26
Consensus pattern (21 bp):
ATCGCAACGCGATTTTCAACT
Found at i:519234 original size:23 final size:23
Alignment explanation
Indices: 519208--519276 Score: 102
Period size: 23 Copynumber: 3.0 Consensus size: 23
519198 CACCACAGCT
*
519208 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* *
519231 CGTAGAATTGCACCGGAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCA
*
519254 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
519277 TATAATAATG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.26, C:0.26, G:0.28, T:0.20
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:519530 original size:30 final size:30
Alignment explanation
Indices: 519486--519555 Score: 104
Period size: 30 Copynumber: 2.3 Consensus size: 30
519476 ACATAATTTG
* * *
519486 TATCACGTAAACATATTATTTTCATACCTT
1 TATCACATAAACATATCATTTCCATACCTT
*
519516 TATCACATAGACATATCATTTCCATACCTT
1 TATCACATAAACATATCATTTCCATACCTT
519546 TATCACATAA
1 TATCACATAA
519556 CTCATATAAC
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.36, C:0.23, G:0.03, T:0.39
Consensus pattern (30 bp):
TATCACATAAACATATCATTTCCATACCTT
Found at i:520019 original size:63 final size:67
Alignment explanation
Indices: 519882--520019 Score: 155
Period size: 63 Copynumber: 2.1 Consensus size: 67
519872 GCCATTTTCA
519882 TCTTTTAATGGAGGTATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATGT
1 TCTTTTAATGGAGG-ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATGT
519947 TTG
65 TTG
* * ** *
519950 T-ATTTAATGG-GG-TGCATCGATGCACT-C-CTTATGCATCGATGCATCGATGGC-ATTCGATG
1 TCTTTTAATGGAGGATGCATCGATGCACTACAC-CATGCATCGATGCATAAAT-CCTATTCGATG
520009 TTT-
64 TTTG
520012 TCTTTTAA
1 TCTTTTAA
520020 ATTAATGCAT
Statistics
Matches: 61, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
62 2 0.03
63 33 0.54
64 15 0.25
66 2 0.03
67 8 0.13
68 1 0.02
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.36
Consensus pattern (67 bp):
TCTTTTAATGGAGGATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATGTT
TG
Found at i:524825 original size:31 final size:31
Alignment explanation
Indices: 524787--524847 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
524777 ATAAAATTTT
*
524787 ATATGAATAGATTTATAAAATCTAATATGTG
1 ATATGAATAGATTTATAAAATATAATATGTG
524818 ATATGAATAGATTTATAAAATATAATATGT
1 ATATGAATAGATTTATAAAATATAATATGT
524848 TAAATAAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.48, C:0.02, G:0.11, T:0.39
Consensus pattern (31 bp):
ATATGAATAGATTTATAAAATATAATATGTG
Found at i:524858 original size:31 final size:31
Alignment explanation
Indices: 524792--524860 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
524782 ATTTTATATG
* * *
524792 AATAGATTTATAAAATCTAATATGTGATATG
1 AATAGATTTATAAAATATAATATGTGAAATA
*
524823 AATAGATTTATAAAATATAATATGTTAAATA
1 AATAGATTTATAAAATATAATATGTGAAATA
524854 AATAGAT
1 AATAGAT
524861 AGATTAATAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.51, C:0.01, G:0.10, T:0.38
Consensus pattern (31 bp):
AATAGATTTATAAAATATAATATGTGAAATA
Found at i:531817 original size:2 final size:2
Alignment explanation
Indices: 531810--531885 Score: 152
Period size: 2 Copynumber: 38.0 Consensus size: 2
531800 CGGGCTAGGA
531810 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
531852 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
531886 TTGTAAAATC
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 74 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:535332 original size:2 final size:2
Alignment explanation
Indices: 535325--535355 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
535315 ACAAAATTAC
535325 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
535356 CTGTATTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:554837 original size:75 final size:75
Alignment explanation
Indices: 554744--554890 Score: 276
Period size: 75 Copynumber: 2.0 Consensus size: 75
554734 TATAAGTTCG
* *
554744 TTGTCTCTTAAAATTTTATAAATTTATTCTCTAACATAAAATCATGTAGAGTTTAAAATCATGTA
1 TTGTCTCTTAAAATTTTATAAATTCATTCCCTAACATAAAATCATGTAGAGTTTAAAATCATGTA
554809 TACATCCTCA
66 TACATCCTCA
554819 TTGTCTCTTAAAATTTTATAAATTCATTCCCTAACATAAAATCATGTAGAGTTTAAAATCATGTA
1 TTGTCTCTTAAAATTTTATAAATTCATTCCCTAACATAAAATCATGTAGAGTTTAAAATCATGTA
554884 TACATCC
66 TACATCC
554891 CTGAACTCTA
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
75 70 1.00
ACGTcount: A:0.37, C:0.16, G:0.07, T:0.40
Consensus pattern (75 bp):
TTGTCTCTTAAAATTTTATAAATTCATTCCCTAACATAAAATCATGTAGAGTTTAAAATCATGTA
TACATCCTCA
Found at i:556461 original size:29 final size:29
Alignment explanation
Indices: 556404--556462 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
556394 TCCCAACACA
*
556404 TAGGTCGCCATGCCCTCCGGACGATCTTG
1 TAGGTCGCCATGCCCTCCGGACGACCTTG
* *
556433 TAGGTCGTCATGCCCTCTGTG-CGACCTTG
1 TAGGTCGCCATGCCCTCCG-GACGACCTTG
556462 T
1 T
556463 CGCCATGCAC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 25 0.96
30 1 0.04
ACGTcount: A:0.12, C:0.32, G:0.27, T:0.29
Consensus pattern (29 bp):
TAGGTCGCCATGCCCTCCGGACGACCTTG
Done.