Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A13
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: 109233746
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2708888 characters in sequence are not A, C, G, or T
File 70 of 332
Found at i:21288318 original size:7 final size:7
Alignment explanation
Indices: 21288276--21288351 Score: 65
Period size: 7 Copynumber: 11.6 Consensus size: 7
21288266 TAAATATAAA
21288276 AATA-AT
1 AATATAT
21288282 AATATA-
1 AATATAT
21288288 AATA-AT
1 AATATAT
21288294 AATATAT
1 AATATAT
*
21288301 -ATAAAAT
1 AAT-ATAT
*
21288308 AATACAT
1 AATATAT
*
21288315 AATAAAT
1 AATATAT
*
21288322 AATATGT
1 AATATAT
21288329 AATA-AT
1 AATATAT
21288335 AATATA-
1 AATATAT
21288341 AATATAT
1 AATATAT
21288348 AATA
1 AATA
21288352 GAATATAAAA
Statistics
Matches: 57, Mismatches: 6, Indels: 13
0.75 0.08 0.17
Matches are distributed among these distances:
5 1 0.02
6 25 0.44
7 29 0.51
8 2 0.04
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.34
Consensus pattern (7 bp):
AATATAT
Found at i:21288641 original size:30 final size:31
Alignment explanation
Indices: 21288607--21288665 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
21288597 AAAAACTGCC
* *
21288607 ATTAGGATTAAATT-GAAATTAAATAAAAAT
1 ATTAGGACTAAATTAGAAATAAAATAAAAAT
*
21288637 ATTAGGGCTAAATTAGAAATAAAATAAAA
1 ATTAGGACTAAATTAGAAATAAAATAAAA
21288666 CATAATTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 12 0.48
31 13 0.52
ACGTcount: A:0.58, C:0.02, G:0.12, T:0.29
Consensus pattern (31 bp):
ATTAGGACTAAATTAGAAATAAAATAAAAAT
Found at i:21290668 original size:176 final size:174
Alignment explanation
Indices: 21290258--21290705 Score: 547
Period size: 176 Copynumber: 2.5 Consensus size: 174
21290248 CGTAAATACA
* * * *
21290258 TGAAAGCCAAATCTGCTGTGTCTTCAATTTGCTCCTTGTGAACATAAGGATGCCAAATCATCTTG
1 TGAAAGTCAAATCTGCTATGTCTTCAATTTGCTTCTTGTGAACATAA-GAAGCCAAATCATCTTG
* ** * * * *
21290323 GATCTGCTTCAGTA-AAATCATTTGAAGGTTAGATCTGCTATGTATCTGCTCTTCATCGAAATGG
65 GATCTACTTCAGTATAAA-CACCTGAAGGTTAGACCTGCTATGTACCTGCTCTCCATCAAAATGG
* * * *
21290387 AGATGCGAGATCTGTTATCTTGGATCTGCTTTGGTGTGAGAACATC
129 AGATGCCAGATATGTTATCTTGGATCTGCTTTGATGTGAAAACATC
* * * * *
21290433 CGAAAGTCAAATCTGCTATGTCTTCGATTTGTTTCTTGTAAACACAAGAATGCCCAAATCATCTT
1 TGAAAGTCAAATCTGCTATGTCTTCAATTTGCTTCTTGTGAACATAAGAA-G-CCAAATCATCTT
* *
21290498 GGATCTACTTCAATATAAACACCTGAAGGTTAGACCTGCTATGTACCTGCTCTCCGTCAAAATGG
64 GGATCTACTTCAGTATAAACACCTGAAGGTTAGACCTGCTATGTACCTGCTCTCCATCAAAATGG
21290563 AGATGCCAGATATGTTATCTTGGATCTGCTTTGATGTGAAAACATC
129 AGATGCCAGATATGTTATCTTGGATCTGCTTTGATGTGAAAACATC
* * *
21290609 TGAAAGTCAGATCTGCTATGTCTTCAATTTGCTTCTCGTCGAAGATAGAGAAGCCAAATCTTGTT
1 TGAAAGTCAAATCTGCTATGTCTTCAATTTGCTTCTTGT-GAACATA-AGAAGCCAAATC-----
* *
21290674 ATCTTGGATCTACTTCAGTGTAAACACGTGAA
59 ATCTTGGATCTACTTCAGTATAAACACCTGAA
21290706 TGCCAGATCT
Statistics
Matches: 230, Mismatches: 33, Indels: 14
0.83 0.12 0.05
Matches are distributed among these distances:
174 2 0.01
175 40 0.17
176 147 0.64
177 8 0.03
178 4 0.02
181 29 0.13
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (174 bp):
TGAAAGTCAAATCTGCTATGTCTTCAATTTGCTTCTTGTGAACATAAGAAGCCAAATCATCTTGG
ATCTACTTCAGTATAAACACCTGAAGGTTAGACCTGCTATGTACCTGCTCTCCATCAAAATGGAG
ATGCCAGATATGTTATCTTGGATCTGCTTTGATGTGAAAACATC
Found at i:21292947 original size:40 final size:40
Alignment explanation
Indices: 21292771--21292993 Score: 236
Period size: 40 Copynumber: 5.6 Consensus size: 40
21292761 TCCTCGTTCA
* * * * *
21292771 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
21292810 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
21292850 ACTGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
21292890 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * * *
21292930 AAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
21292970 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
21292994 CAGCATTCAA
Statistics
Matches: 158, Mismatches: 22, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
39 37 0.23
40 113 0.72
41 8 0.05
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:21300103 original size:40 final size:40
Alignment explanation
Indices: 21300005--21300173 Score: 216
Period size: 39 Copynumber: 4.3 Consensus size: 40
21299995 TCCTCGTTCA
* * * *
21300005 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCACG
*
21300044 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCACG
* *
21300084 ACTGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCACG
* * * *
21300124 AATGCCTTCGGGACTTAA-CCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCACG
*
21300163 AAGGCCTTCGG
1 AATGCCTTCGG
21300174 ATCTTAATCC
Statistics
Matches: 116, Mismatches: 13, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
39 62 0.53
40 54 0.47
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCACG
Found at i:21300159 original size:79 final size:79
Alignment explanation
Indices: 21300003--21300226 Score: 236
Period size: 79 Copynumber: 2.8 Consensus size: 79
21299993 GCTCCTCGTT
* * * * * *
21300003 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACATAACCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACAATGCCTTCGGGACTTAACCCGGA
21300068 TTTAACAACTCGCA
66 TTTAACAACTCGCA
* *
21300082 CGACTGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAATGCCTTCGGGACTTAA-CCGG
1 CAAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC-AATGCCTTCGGGACTTAACCCGG
** *
21300146 ATTTAGTATCTCGCA
65 ATTTAACAACTCGCA
* * * * * * * *
21300161 CAAAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCACAAAGCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACAATGCCTTCGGGACTTAACCCG
21300225 GA
64 GA
21300227 CAGCATTCAA
Statistics
Matches: 120, Mismatches: 21, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
78 3 0.03
79 90 0.75
80 27 0.22
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.25
Consensus pattern (79 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACAATGCCTTCGGGACTTAACCCGGA
TTTAACAACTCGCA
Found at i:21300180 original size:39 final size:40
Alignment explanation
Indices: 21300003--21300226 Score: 204
Period size: 40 Copynumber: 5.7 Consensus size: 40
21299993 GCTCCTCGTT
* * * * * *
21300003 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAAGGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
* * *
21300043 C-AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCA
1 CAAAGGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
* **
21300082 CGACTGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
1 CAAAGGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
* * * *
21300122 CGAATGCCTTCGGGACTTAA-CCGGATTTAGTATCTCGCA
1 CAAAGGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
* * * * *
21300161 CAAAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCA
1 CAAAGGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCA
*
21300202 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAAGGCCTTCGGGACTTAACCCGGA
21300227 CAGCATTCAA
Statistics
Matches: 159, Mismatches: 20, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
38 3 0.02
39 65 0.41
40 80 0.50
41 11 0.07
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAAGGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
Found at i:21311468 original size:40 final size:40
Alignment explanation
Indices: 21311410--21311583 Score: 219
Period size: 40 Copynumber: 4.4 Consensus size: 40
21311400 TGATAACCGA
* * *
21311410 GCTAAGTCCCGAAGGCATTTGCGCTAGTGACTAGT-TCCGG
1 GCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-TATCCGG
*
21311450 GCCAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGG
1 GCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGG
*
21311490 GCTAAGTCCCGAAGGCATTGGTGCGAGTTACTATATCCGG
1 GCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGG
* * *
21311530 GCTATGTCCCGAAGGCATTCGAGCGAG-TAGCTATATCC-G
1 GCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATATCCGG
* *
21311569 GTTAAATCCCGAAGG
1 GCTAAGTCCCGAAGG
21311584 TACTTGGCTT
Statistics
Matches: 120, Mismatches: 12, Indels: 5
0.88 0.09 0.04
Matches are distributed among these distances:
39 16 0.13
40 104 0.87
ACGTcount: A:0.23, C:0.24, G:0.29, T:0.24
Consensus pattern (40 bp):
GCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGG
Found at i:21315988 original size:14 final size:14
Alignment explanation
Indices: 21315969--21316039 Score: 58
Period size: 14 Copynumber: 5.1 Consensus size: 14
21315959 TTAATATTTA
21315969 AATATAAAAATAAT
1 AATATAAAAATAAT
*
21315983 AATATAAATAACAAT
1 AATATAAA-AATAAT
21315998 -ATATATAAAATAAT
1 AATATA-AAAATAAT
*
21316012 ACATA-ATAAATAAT
1 A-ATATAAAAATAAT
* *
21316026 -ATGTAATAATAAT
1 AATATAAAAATAAT
21316039 A
1 A
21316040 TAAATATACA
Statistics
Matches: 45, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
12 2 0.04
13 7 0.16
14 25 0.56
15 8 0.18
16 3 0.07
ACGTcount: A:0.65, C:0.03, G:0.01, T:0.31
Consensus pattern (14 bp):
AATATAAAAATAAT
Found at i:21315993 original size:12 final size:12
Alignment explanation
Indices: 21315976--21316077 Score: 66
Period size: 12 Copynumber: 8.1 Consensus size: 12
21315966 TTAAATATAA
21315976 AAATAATAATAT
1 AAATAATAATAT
*
21315988 AAATAACAATAT
1 AAATAATAATAT
* *
21316000 ATATAAAATAATAC
1 A-A-ATAATAATAT
21316014 ATAATAAATAATAT
1 A-AAT-AATAATAT
*
21316028 GTAATAATAATAT
1 -AAATAATAATAT
21316041 AAAT-ATACA-AT
1 AAATAATA-ATAT
*
21316052 AGAAT-ATAAAAT
1 A-AATAATAATAT
21316064 AATATAATAATAT
1 AA-ATAATAATAT
21316077 A
1 A
21316078 GTAAAAAACA
Statistics
Matches: 72, Mismatches: 9, Indels: 17
0.73 0.09 0.17
Matches are distributed among these distances:
11 8 0.11
12 27 0.38
13 17 0.24
14 20 0.28
ACGTcount: A:0.64, C:0.03, G:0.02, T:0.31
Consensus pattern (12 bp):
AAATAATAATAT
Found at i:21316010 original size:17 final size:15
Alignment explanation
Indices: 21315969--21316052 Score: 53
Period size: 17 Copynumber: 5.1 Consensus size: 15
21315959 TTAATATTTA
*
21315969 AATATAAA-AATAAT
1 AATATAAATAACAAT
21315983 AATATAAATAACAAT
1 AATATAAATAACAAT
*
21315998 ATATATAAAATAATACAT
1 A-ATAT-AAATAACA-AT
*
21316016 AATAAATAATATGTAATAAT
1 AAT--ATAA-A--TAACAAT
21316036 AATATAAATATACAAT
1 AATATAAATA-ACAAT
21316052 A
1 A
21316053 GAATATAAAA
Statistics
Matches: 57, Mismatches: 3, Indels: 18
0.73 0.04 0.23
Matches are distributed among these distances:
14 8 0.14
15 8 0.14
16 9 0.16
17 10 0.18
18 9 0.16
19 3 0.05
20 5 0.09
21 5 0.09
ACGTcount: A:0.64, C:0.04, G:0.01, T:0.31
Consensus pattern (15 bp):
AATATAAATAACAAT
Found at i:21319676 original size:38 final size:38
Alignment explanation
Indices: 21319630--21319705 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
21319620 ACTACCAAAC
21319630 ATGACATGAGAAATTAAGATGTAATTACACTCTATCAG
1 ATGACATGAGAAATTAAGATGTAATTACACTCTATCAG
21319668 ATGACATGAGAAATTAAGATGTAATTACACTCTATCAG
1 ATGACATGAGAAATTAAGATGTAATTACACTCTATCAG
21319706 TCAAACACAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.29
Consensus pattern (38 bp):
ATGACATGAGAAATTAAGATGTAATTACACTCTATCAG
Found at i:21323574 original size:24 final size:24
Alignment explanation
Indices: 21323547--21323595 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
21323537 AAATAAGATA
*
21323547 AGTAATTAATT-AGGTAATAATAAT
1 AGTAA-TAATTGAGGTAATAAAAAT
*
21323571 AGTAATAATTGAGTTAATAAAAAT
1 AGTAATAATTGAGGTAATAAAAAT
21323595 A
1 A
21323596 TATTAGTAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 5 0.23
24 17 0.77
ACGTcount: A:0.53, C:0.00, G:0.12, T:0.35
Consensus pattern (24 bp):
AGTAATAATTGAGGTAATAAAAAT
Found at i:21334324 original size:12 final size:12
Alignment explanation
Indices: 21334309--21334344 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
21334299 TTAGAAAACT
21334309 AATAAGAAGATA
1 AATAAGAAGATA
21334321 AATAA-AA-ATA
1 AATAAGAAGATA
21334331 AATAAGAAGATA
1 AATAAGAAGATA
21334343 AA
1 AA
21334345 GTGATTACAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 8 0.36
11 4 0.18
12 10 0.45
ACGTcount: A:0.72, C:0.00, G:0.11, T:0.17
Consensus pattern (12 bp):
AATAAGAAGATA
Found at i:21334391 original size:27 final size:27
Alignment explanation
Indices: 21334360--21334419 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
21334350 TACAAACTCG
*
21334360 AATAAAAACA-ACAATCAAAATAATAAA
1 AATAAAAACATA-AATCAAAATAAAAAA
* **
21334387 AATAACAACATAGTTCAAAATAAAAAA
1 AATAAAAACATAAATCAAAATAAAAAA
21334414 AATAAA
1 AATAAA
21334420 GAAGCCTCAC
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
27 26 0.96
28 1 0.04
ACGTcount: A:0.72, C:0.10, G:0.02, T:0.17
Consensus pattern (27 bp):
AATAAAAACATAAATCAAAATAAAAAA
Found at i:21340972 original size:76 final size:76
Alignment explanation
Indices: 21340879--21341033 Score: 310
Period size: 76 Copynumber: 2.0 Consensus size: 76
21340869 TTTTCTTAAG
21340879 TATTCTCTGACGGCTCCTTCTCCTTTTCTTATATTTGGTATATATAGGTATTAGAATGCCCGAAA
1 TATTCTCTGACGGCTCCTTCTCCTTTTCTTATATTTGGTATATATAGGTATTAGAATGCCCGAAA
21340944 AACCTAAAAAT
66 AACCTAAAAAT
21340955 TATTCTCTGACGGCTCCTTCTCCTTTTCTTATATTTGGTATATATAGGTATTAGAATGCCCGAAA
1 TATTCTCTGACGGCTCCTTCTCCTTTTCTTATATTTGGTATATATAGGTATTAGAATGCCCGAAA
21341020 AACCTAAAAAT
66 AACCTAAAAAT
21341031 TAT
1 TAT
21341034 GTTTTTTTCT
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 79 1.00
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.39
Consensus pattern (76 bp):
TATTCTCTGACGGCTCCTTCTCCTTTTCTTATATTTGGTATATATAGGTATTAGAATGCCCGAAA
AACCTAAAAAT
Found at i:21342295 original size:22 final size:23
Alignment explanation
Indices: 21342267--21342322 Score: 89
Period size: 22 Copynumber: 2.5 Consensus size: 23
21342257 TATATTTAGG
*
21342267 GAGAAAATACAATGGTTAA-GAA
1 GAGAAAATACAATAGTTAAGGAA
21342289 GAGAAAATACAATAGTTAAGGAA
1 GAGAAAATACAATAGTTAAGGAA
21342312 -AGAAAATACAA
1 GAGAAAATACAA
21342323 GACTATAAGA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
22 29 0.91
23 3 0.09
ACGTcount: A:0.59, C:0.05, G:0.20, T:0.16
Consensus pattern (23 bp):
GAGAAAATACAATAGTTAAGGAA
Found at i:21342334 original size:22 final size:21
Alignment explanation
Indices: 21342268--21342334 Score: 64
Period size: 22 Copynumber: 3.0 Consensus size: 21
21342258 ATATTTAGGG
*
21342268 AGAAAATACAATG-GTTAAGAA
1 AGAAAATACAA-GACTTAAGAA
* *
21342289 GAGAAAATACAATAGTTAAGGAA
1 -AGAAAATACAAGACTTAA-GAA
21342312 AGAAAATACAAGACTATAAGAA
1 AGAAAATACAAGACT-TAAGAA
21342334 A
1 A
21342335 TCTAAATCAT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
22 33 0.85
23 6 0.15
ACGTcount: A:0.60, C:0.06, G:0.18, T:0.16
Consensus pattern (21 bp):
AGAAAATACAAGACTTAAGAA
Found at i:21345005 original size:12 final size:12
Alignment explanation
Indices: 21344988--21345034 Score: 53
Period size: 12 Copynumber: 4.0 Consensus size: 12
21344978 TAAAGGCATC
21344988 AGAACTCCATAT
1 AGAACTCCATAT
*
21345000 AGAACT-CA-AA
1 AGAACTCCATAT
*
21345010 AGGAACTCCAAAT
1 A-GAACTCCATAT
21345023 AGAACTCCATAT
1 AGAACTCCATAT
21345035 TTAATCCCCA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
10 2 0.07
11 7 0.24
12 18 0.62
13 2 0.07
ACGTcount: A:0.47, C:0.23, G:0.11, T:0.19
Consensus pattern (12 bp):
AGAACTCCATAT
Found at i:21346468 original size:43 final size:42
Alignment explanation
Indices: 21346276--21346458 Score: 213
Period size: 43 Copynumber: 4.3 Consensus size: 42
21346266 TTATGTGGAA
* * ** *
21346276 AAACACCGTTATAGAACATGACAATTAGTAGCGCTTTTCCCAC
1 AAACGCCGCTATAGAACATGACCTTTAGCAGCG-TTTTCCCAC
* *
21346319 AAACGCCGATATAGAACATGACCTTTAACAGCGCTTTTCCCAC
1 AAACGCCGCTATAGAACATGACCTTTAGCAGCG-TTTTCCCAC
* * *
21346362 AAACGCCGCTATAGAGCATAACCTTTAGCAGCGCTTTCCCTAC
1 AAACGCCGCTATAGAACATGACCTTTAGCAGCGTTTTCCC-AC
* * *
21346405 AAATGCCACTATAGAACATGACCTTTAGCGGCGTTTTCCCCAC
1 AAACGCCGCTATAGAACATGACCTTTAGCAGCGTTTT-CCCAC
21346448 AAACGCCGCTA
1 AAACGCCGCTA
21346459 AAGGTCATGA
Statistics
Matches: 119, Mismatches: 19, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
42 6 0.05
43 110 0.92
44 3 0.03
ACGTcount: A:0.31, C:0.30, G:0.15, T:0.23
Consensus pattern (42 bp):
AAACGCCGCTATAGAACATGACCTTTAGCAGCGTTTTCCCAC
Found at i:21351928 original size:35 final size:35
Alignment explanation
Indices: 21351882--21351953 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
21351872 TAAAATAAAT
*
21351882 ATGATATCATCCTATTTCCCATTTCTTCTTTATTG
1 ATGATATCATCCTATTTCCCATTTCTTATTTATTG
21351917 ATGATATCATCCTATTTCCCATTTCTTATTTATTG
1 ATGATATCATCCTATTTCCCATTTCTTATTTATTG
21351952 AT
1 AT
21351954 TTTTTAGCCA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.22, C:0.21, G:0.06, T:0.51
Consensus pattern (35 bp):
ATGATATCATCCTATTTCCCATTTCTTATTTATTG
Found at i:21352824 original size:47 final size:46
Alignment explanation
Indices: 21352766--21352888 Score: 126
Period size: 47 Copynumber: 2.6 Consensus size: 46
21352756 GTGAGCTAGT
*
21352766 GTAAGATATGTCTAGGACATGCATCAGCCACAT-TATGAGAGCCAGTA
1 GTAAGACATGTCTAGGACATGCATCAGCCA-ATATATGAGAGCCAG-A
* * * *
21352813 -TAAGACCATGTCTAGGACATGGCATC-GGCATTGATATGAGTGCTAGA
1 GTAAGA-CATGTCTAGGACAT-GCATCAGCCAAT-ATATGAGAGCCAGA
*
21352860 GTAAGACATGTCTGGGACATGCATCAGCC
1 GTAAGACATGTCTAGGACATGCATCAGCC
21352889 TCGAGACGTA
Statistics
Matches: 63, Mismatches: 7, Indels: 12
0.77 0.09 0.15
Matches are distributed among these distances:
46 11 0.17
47 32 0.51
48 20 0.32
ACGTcount: A:0.31, C:0.20, G:0.26, T:0.24
Consensus pattern (46 bp):
GTAAGACATGTCTAGGACATGCATCAGCCAATATATGAGAGCCAGA
Found at i:21352913 original size:46 final size:45
Alignment explanation
Indices: 21352860--21352978 Score: 152
Period size: 46 Copynumber: 2.6 Consensus size: 45
21352850 GAGTGCTAGA
* *
21352860 GTAAGACATGTCTGGGACATGCATCAGCCT-CGAGACGTAAGTTAGT
1 GTAAGACATGTCTGGGACATGCATCAGACTACGAGACGT--GTCAGT
*
21352906 GTAAGACATGTCTGGGACATGCATC-GACTACGAGATGTGTCAGT
1 GTAAGACATGTCTGGGACATGCATCAGACTACGAGACGTGTCAGT
*
21352950 GTAAGACCATGTTTGGGACATGGCATCAG
1 GTAAGA-CATGTCTGGGACAT-GCATCAG
21352979 GACAGATATG
Statistics
Matches: 65, Mismatches: 4, Indels: 7
0.86 0.05 0.09
Matches are distributed among these distances:
44 11 0.17
45 16 0.25
46 37 0.57
47 1 0.02
ACGTcount: A:0.28, C:0.18, G:0.29, T:0.24
Consensus pattern (45 bp):
GTAAGACATGTCTGGGACATGCATCAGACTACGAGACGTGTCAGT
Found at i:21367457 original size:23 final size:23
Alignment explanation
Indices: 21367394--21367471 Score: 79
Period size: 23 Copynumber: 3.3 Consensus size: 23
21367384 GGACTCACAG
21367394 CAGCTCG-AATGAGCTTACCGATATAT
1 CAGCTCGTAA-GAGCTTACCG-T-T-T
* *
21367420 TAGCTCGTAAGAGCTTACTGTTT
1 CAGCTCGTAAGAGCTTACCGTTT
21367443 CAGCTCGTCAA-AGCTTACCGTTT
1 CAGCTCGT-AAGAGCTTACCGTTT
21367466 CAGCTC
1 CAGCTC
21367472 AATAGAGCTT
Statistics
Matches: 46, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
23 25 0.54
24 3 0.07
25 1 0.02
26 15 0.33
27 2 0.04
ACGTcount: A:0.24, C:0.26, G:0.19, T:0.31
Consensus pattern (23 bp):
CAGCTCGTAAGAGCTTACCGTTT
Found at i:21367480 original size:23 final size:23
Alignment explanation
Indices: 21367429--21367482 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
21367419 TTAGCTCGTA
* *
21367429 AGAGCTTACTGTTTCAGCTCGTC
1 AGAGCTTACCGTTTCAGCTCATC
*
21367452 AAAGCTTACCGTTTCAGCTCAAT-
1 AGAGCTTACCGTTTCAGCTC-ATC
21367475 AGAGCTTA
1 AGAGCTTA
21367483 GTGTCCATCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
23 25 0.96
24 1 0.04
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (23 bp):
AGAGCTTACCGTTTCAGCTCATC
Found at i:21367647 original size:20 final size:20
Alignment explanation
Indices: 21367622--21367662 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
21367612 CAATGAGCAT
21367622 AAATATTGTTTATATAGATG
1 AAATATTGTTTATATAGATG
*
21367642 AAATATTGTTTATATGGATG
1 AAATATTGTTTATATAGATG
21367662 A
1 A
21367663 GCCATTGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.17, T:0.44
Consensus pattern (20 bp):
AAATATTGTTTATATAGATG
Found at i:21367669 original size:20 final size:20
Alignment explanation
Indices: 21367626--21367672 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
21367616 GAGCATAAAT
*
21367626 ATTGTTTATATAGATGAAAT
1 ATTGTTTATATAGATGAAAC
* **
21367646 ATTGTTTATATGGATGAGCC
1 ATTGTTTATATAGATGAAAC
21367666 ATTGTTT
1 ATTGTTT
21367673 GCAAATGGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.04, G:0.19, T:0.47
Consensus pattern (20 bp):
ATTGTTTATATAGATGAAAC
Found at i:21368626 original size:43 final size:44
Alignment explanation
Indices: 21368546--21368630 Score: 136
Period size: 43 Copynumber: 1.9 Consensus size: 44
21368536 ATGAAGTCAG
21368546 TATGCTCCACACGATCTCACACACGAGCGTGTGACCGACCATCAA
1 TATGCTCCACACGATCT-ACACACGAGCGTGTGACCGACCATCAA
* *
21368591 TATGCTCCACACGGTCT-CACACGGGCGTGTGACCGACCAT
1 TATGCTCCACACGATCTACACACGAGCGTGTGACCGACCAT
21368631 GTGGTACAAG
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
43 22 0.58
45 16 0.42
ACGTcount: A:0.25, C:0.35, G:0.21, T:0.19
Consensus pattern (44 bp):
TATGCTCCACACGATCTACACACGAGCGTGTGACCGACCATCAA
Found at i:21371171 original size:21 final size:21
Alignment explanation
Indices: 21371134--21371173 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
21371124 ATTTCAGCAT
*
21371134 TTGAACATCATCTATTTACCA
1 TTGAACATCATCAATTTACCA
21371155 TTGAGACATCAT-AATTTAC
1 TTGA-ACATCATCAATTTAC
21371174 AATATGTAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.35, C:0.20, G:0.07, T:0.38
Consensus pattern (21 bp):
TTGAACATCATCAATTTACCA
Found at i:21373230 original size:22 final size:23
Alignment explanation
Indices: 21373204--21373254 Score: 72
Period size: 22 Copynumber: 2.3 Consensus size: 23
21373194 CTCTCCTATT
*
21373204 AATATAAATA-ATATATTAGATG
1 AATATAAATAGATATATCAGATG
21373226 AATAT-AATAGATATATCAGATG
1 AATATAAATAGATATATCAGATG
21373248 AAT-TAAA
1 AATATAAA
21373255 AAATTTAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
21 5 0.19
22 21 0.81
ACGTcount: A:0.55, C:0.02, G:0.10, T:0.33
Consensus pattern (23 bp):
AATATAAATAGATATATCAGATG
Found at i:21377320 original size:20 final size:20
Alignment explanation
Indices: 21377297--21377377 Score: 72
Period size: 21 Copynumber: 4.0 Consensus size: 20
21377287 GAATCAAGTT
21377297 AAACAATAAAGAATCGATTC
1 AAACAATAAAGAATCGATTC
* * *
21377317 AAACAATAATGAATCAAGTTT
1 AAACAATAAAGAATCGA-TTC
* * *
21377338 AAACAATGAACAATTGATTC
1 AAACAATAAAGAATCGATTC
* *
21377358 AAAGAAGCAAAGAATCGATT
1 AAACAA-TAAAGAATCGATT
21377378 TAAAACAACA
Statistics
Matches: 45, Mismatches: 14, Indels: 3
0.73 0.23 0.05
Matches are distributed among these distances:
20 22 0.49
21 23 0.51
ACGTcount: A:0.53, C:0.12, G:0.12, T:0.22
Consensus pattern (20 bp):
AAACAATAAAGAATCGATTC
Found at i:21377380 original size:41 final size:41
Alignment explanation
Indices: 21377295--21377426 Score: 122
Period size: 45 Copynumber: 3.1 Consensus size: 41
21377285 TTGAATCAAG
* * * * * *
21377295 TTAAACAATAAAGAATCGATTCAAACAA-TAATGAATCAAGT
1 TTAAACAATAAACAATTGATTCAAAGAAGCAAAGAATCGA-T
*
21377336 TTAAACAATGAACAATTGATTCAAAGAAGCAAAGAATCGAT
1 TTAAACAATAAACAATTGATTCAAAGAAGCAAAGAATCGAT
* * *
21377377 TTAAAACAACAATCATGAATTGATTCAAAGAAGCAAATAATCGAT
1 TT-AAACAATAA--A-CAATTGATTCAAAGAAGCAAAGAATCGAT
21377422 TTAAA
1 TTAAA
21377427 ACAACAATAA
Statistics
Matches: 75, Mismatches: 11, Indels: 7
0.81 0.12 0.08
Matches are distributed among these distances:
41 27 0.36
42 15 0.20
44 4 0.05
45 29 0.39
ACGTcount: A:0.52, C:0.12, G:0.11, T:0.24
Consensus pattern (41 bp):
TTAAACAATAAACAATTGATTCAAAGAAGCAAAGAATCGAT
Found at i:21377401 original size:45 final size:45
Alignment explanation
Indices: 21377349--21377517 Score: 211
Period size: 45 Copynumber: 3.8 Consensus size: 45
21377339 AACAATGAAC
* *
21377349 AATTGATTCAAAGAAGCAAAGAATCGATTTAAAACAACAATCATG
1 AATTGATTCAAAGAAGCAAATAATCGATTTAAAACAACAATAATG
21377394 AATTGATTCAAAGAAGCAAATAATCGATTTAAAACAACAATAATG
1 AATTGATTCAAAGAAGCAAATAATCGATTTAAAACAACAATAATG
** * *
21377439 AATCAATTCAAAAAAGCAAATAATCAATTTAAAACAACAA-AA--
1 AATTGATTCAAAGAAGCAAATAATCGATTTAAAACAACAATAATG
* * **
21377481 AATCT-ATTCAAAGAAGAAAAAAATTAATTTAAAACAA
1 AAT-TGATTCAAAGAAGCAAATAATCGATTTAAAACAA
21377518 GAAATTTAGT
Statistics
Matches: 112, Mismatches: 11, Indels: 5
0.88 0.09 0.04
Matches are distributed among these distances:
42 31 0.28
44 2 0.02
45 79 0.71
ACGTcount: A:0.57, C:0.12, G:0.08, T:0.22
Consensus pattern (45 bp):
AATTGATTCAAAGAAGCAAATAATCGATTTAAAACAACAATAATG
Found at i:21377422 original size:21 final size:20
Alignment explanation
Indices: 21377353--21377492 Score: 64
Period size: 21 Copynumber: 6.4 Consensus size: 20
21377343 ATGAACAATT
*
21377353 GATTCAAAGAAGCAAAGAATC
1 GATTCAAA-AAGCAAATAATC
* * *
21377374 GATTTAAAACAACAATCATGAATT
1 GATTCAAAA-AGCAA--AT-AATC
21377398 GATTCAAAGAAGCAAATAATC
1 GATTCAAA-AAGCAAATAATC
* *
21377419 GATTTAAAACAACAATAATGAATC
1 GATTCAAAA-AGC-A-AAT-AATC
*
21377443 AATTCAAAAAAGCAAATAATC
1 GATTC-AAAAAGCAAATAATC
* * * *
21377464 AATTTAAAACAACAAAAAATC
1 GATTCAAAA-AGCAAATAATC
*
21377485 TATTCAAA
1 GATTCAAA
21377493 GAAGAAAAAA
Statistics
Matches: 91, Mismatches: 17, Indels: 22
0.70 0.13 0.17
Matches are distributed among these distances:
20 6 0.07
21 46 0.51
22 6 0.07
23 5 0.05
24 23 0.25
25 5 0.05
ACGTcount: A:0.56, C:0.14, G:0.09, T:0.22
Consensus pattern (20 bp):
GATTCAAAAAGCAAATAATC
Found at i:21378564 original size:50 final size:50
Alignment explanation
Indices: 21378479--21378575 Score: 122
Period size: 50 Copynumber: 1.9 Consensus size: 50
21378469 GCGGATGTAA
* * * *
21378479 AGCCTTCAGGCTTGGAACTTGGTGCCCAGAAATGTTTTTGGAGGGATGAT
1 AGCCTTCAGGCTAGGAACTTGCTGCCAAGAAATGTTCTTGGAGGGATGAT
* ** *
21378529 AGCCTTCAGGCTAGGCACTTGCTGCCAAGGTATGTTCTTGGATGGAT
1 AGCCTTCAGGCTAGGAACTTGCTGCCAAGAAATGTTCTTGGAGGGAT
21378576 TAGCTCGTTG
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
50 39 1.00
ACGTcount: A:0.21, C:0.19, G:0.31, T:0.30
Consensus pattern (50 bp):
AGCCTTCAGGCTAGGAACTTGCTGCCAAGAAATGTTCTTGGAGGGATGAT
Found at i:21380201 original size:24 final size:27
Alignment explanation
Indices: 21380154--21380205 Score: 74
Period size: 24 Copynumber: 2.0 Consensus size: 27
21380144 AACCGAGGTA
21380154 AGTTCGTATGTTAAATAAGCTTTAATAT
1 AGTTCGTATGTTAAAT-AGCTTTAATAT
21380182 AGTT-GTAT-TTAAAT-GCTTTAATAT
1 AGTTCGTATGTTAAATAGCTTTAATAT
21380206 TGCATGAACT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
24 10 0.42
26 6 0.25
27 4 0.17
28 4 0.17
ACGTcount: A:0.35, C:0.06, G:0.13, T:0.46
Consensus pattern (27 bp):
AGTTCGTATGTTAAATAGCTTTAATAT
Found at i:21406562 original size:113 final size:113
Alignment explanation
Indices: 21406348--21406564 Score: 391
Period size: 113 Copynumber: 1.9 Consensus size: 113
21406338 CGTAAATTTC
* *
21406348 TCTAAACTCAAACTTGGAAAGTGATAAGGTTTTGTTTCCAAAACAGCATTAGGGAAACTAGTTGA
1 TCTAAACTCAAACTTGGAAAGTGATAAGGTTTTGTTTCCAAAACAACATTAGAGAAACTAGTTGA
* *
21406413 TAATGTGTCACTATGATTGCATATTTCAAGTTAAAAAAAAAAACCCGA
66 TAATGTGTCACAATGACTGCATATTTCAAGTTAAAAAAAAAAACCCGA
21406461 TCTAAACTCAAACTTGGAAAGTGATAAGGTTTTGTTTCCAAAACAACATTAGAGAAACTAGTTGA
1 TCTAAACTCAAACTTGGAAAGTGATAAGGTTTTGTTTCCAAAACAACATTAGAGAAACTAGTTGA
21406526 TAATGTGTC-CAATGACTGCATATTTCAAGTTAAAAAAAA
66 TAATGTGTCACAATGACTGCATATTTCAAGTTAAAAAAAA
21406565 CCCCCAGAAA
Statistics
Matches: 100, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
112 28 0.28
113 72 0.72
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.29
Consensus pattern (113 bp):
TCTAAACTCAAACTTGGAAAGTGATAAGGTTTTGTTTCCAAAACAACATTAGAGAAACTAGTTGA
TAATGTGTCACAATGACTGCATATTTCAAGTTAAAAAAAAAAACCCGA
Found at i:21407369 original size:81 final size:81
Alignment explanation
Indices: 21407234--21407389 Score: 294
Period size: 81 Copynumber: 1.9 Consensus size: 81
21407224 TGACAGGGTC
*
21407234 GGATCACATTATCAAGTAGGTTCCTATCCTTGTATATACATACATCATCTAATTATATAGTTTTA
1 GGATCACATTATCAAGTAGGTTCCTATCCTTGTATATACATACATCATCTAATTATATAATTTTA
*
21407299 TTCATTTCAGCATGTT
66 TCCATTTCAGCATGTT
21407315 GGATCACATTATCAAGTAGGTTCCTATCCTTGTATATACATACATCATCTAATTATATAATTTTA
1 GGATCACATTATCAAGTAGGTTCCTATCCTTGTATATACATACATCATCTAATTATATAATTTTA
21407380 TCCATTTCAG
66 TCCATTTCAG
21407390 TATGCTATTG
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
81 73 1.00
ACGTcount: A:0.31, C:0.18, G:0.10, T:0.41
Consensus pattern (81 bp):
GGATCACATTATCAAGTAGGTTCCTATCCTTGTATATACATACATCATCTAATTATATAATTTTA
TCCATTTCAGCATGTT
Found at i:21414600 original size:26 final size:26
Alignment explanation
Indices: 21414542--21414594 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
21414532 GGGCTTGGCT
21414542 CTAACATCACTCATAAGAAGAAGTTA
1 CTAACATCACTCATAAGAAGAAGTTA
*
21414568 CTAACATCACTCATGAGAAGAAGTTA
1 CTAACATCACTCATAAGAAGAAGTTA
21414594 C
1 C
21414595 AGACATATGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.43, C:0.21, G:0.13, T:0.23
Consensus pattern (26 bp):
CTAACATCACTCATAAGAAGAAGTTA
Found at i:21419906 original size:40 final size:40
Alignment explanation
Indices: 21419844--21420101 Score: 419
Period size: 40 Copynumber: 6.5 Consensus size: 40
21419834 AAGCCAAGTA
* * * * *
21419844 CCTTCGGGATTTA-ACCGGATATAGCTACTCGCTCGAATG
1 CCTTCGGGACTTAGCCCGGATATAGCAACTCGCACAAATG
* * *
21419883 CCTTCGGGACATAGCCCGGATATAGTAACTCGCACCAATG
1 CCTTCGGGACTTAGCCCGGATATAGCAACTCGCACAAATG
21419923 CCTTCGGGACTTAGCCCGGATATAGCAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGCAACTCGCACAAATG
21419963 CCTTCGGGACTTAGCCCGGATATAGCAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGCAACTCGCACAAATG
21420003 CCTTCGGGACTTAGCCCGGATATAGCAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGCAACTCGCACAAATG
* *
21420043 CCTTCGGGACTTAGCTCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGCAACTCGCACAAATG
21420083 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
21420102 TTATCATCCA
Statistics
Matches: 205, Mismatches: 13, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
39 11 0.05
40 194 0.95
ACGTcount: A:0.26, C:0.29, G:0.23, T:0.22
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGCAACTCGCACAAATG
Found at i:21422372 original size:30 final size:29
Alignment explanation
Indices: 21422333--21422390 Score: 98
Period size: 30 Copynumber: 2.0 Consensus size: 29
21422323 ATAGCCGAAG
*
21422333 CTAGTTAAATCGCACACTTAGTGCCAAAT
1 CTAGTTAAATCACACACTTAGTGCCAAAT
21422362 CTAGTTTAAATCACACACTTAGTGCCAAA
1 CTAG-TTAAATCACACACTTAGTGCCAAA
21422391 ACTTCCGTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 4 0.15
30 23 0.85
ACGTcount: A:0.36, C:0.24, G:0.12, T:0.28
Consensus pattern (29 bp):
CTAGTTAAATCACACACTTAGTGCCAAAT
Found at i:21433482 original size:30 final size:29
Alignment explanation
Indices: 21433448--21433506 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
21433438 GAATTAGATT
* *
21433448 AAATCAAAATTTCTTGTATAAAATTGCACA
1 AAATCAAAATTT-ATATATAAAATTGCACA
*
21433478 AAATCAAAGTTTATATATAAAATTGCACA
1 AAATCAAAATTTATATATAAAATTGCACA
21433507 TTAAACAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 15 0.58
30 11 0.42
ACGTcount: A:0.49, C:0.12, G:0.07, T:0.32
Consensus pattern (29 bp):
AAATCAAAATTTATATATAAAATTGCACA
Found at i:21439528 original size:49 final size:49
Alignment explanation
Indices: 21439437--21439562 Score: 139
Period size: 49 Copynumber: 2.6 Consensus size: 49
21439427 ATCAAAGTTG
* * *
21439437 ATGCCATGTCCCAGACAGGTCTTA-AGCTAACTTTTATATATCGAG-GCCG
1 ATGCCATGTCCCAGACAGGTCTTACA-CTAACTCTCATATATCG-GTGCCA
** * * *
21439486 ATGCTGTGTCCCAGACAGGTCTTACACTAGCTCTCATCTATCGGTGTCA
1 ATGCCATGTCCCAGACAGGTCTTACACTAACTCTCATATATCGGTGCCA
*
21439535 ATGCCATGTCCCAGATAGGTCTTACACT
1 ATGCCATGTCCCAGACAGGTCTTACACT
21439563 GACACACAAC
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
48 1 0.02
49 62 0.97
50 1 0.02
ACGTcount: A:0.24, C:0.27, G:0.20, T:0.29
Consensus pattern (49 bp):
ATGCCATGTCCCAGACAGGTCTTACACTAACTCTCATATATCGGTGCCA
Found at i:21448228 original size:42 final size:42
Alignment explanation
Indices: 21448189--21448376 Score: 241
Period size: 42 Copynumber: 4.4 Consensus size: 42
21448179 GGCACACGGT
21448189 CGTGTCTCTGCCCGTGTGTCACACACGGCCTAGACACACGCC
1 CGTGTCTCTGCCCGTGTGTCACACACGGCCTAGACACACGCC
* * * ** * **
21448231 CGTATCTTTACCTATGCGTCACACACGGCCTAGACACATACC
1 CGTGTCTCTGCCCGTGTGTCACACACGGCCTAGACACACGCC
** *
21448273 CGTGTCTCTGCCCGTGTGTCACACATAGCCTAGACACATGCC
1 CGTGTCTCTGCCCGTGTGTCACACACGGCCTAGACACACGCC
* *
21448315 CATGTCTCTACCCGTGTGTCACACACGGCCTAGACACACGCC
1 CGTGTCTCTGCCCGTGTGTCACACACGGCCTAGACACACGCC
21448357 CGTGTGTCTCTGCCCGTGTG
1 C--GTGTCTCTGCCCGTGTG
21448377 GACAATATAA
Statistics
Matches: 120, Mismatches: 24, Indels: 2
0.82 0.16 0.01
Matches are distributed among these distances:
42 105 0.88
44 15 0.12
ACGTcount: A:0.19, C:0.37, G:0.21, T:0.23
Consensus pattern (42 bp):
CGTGTCTCTGCCCGTGTGTCACACACGGCCTAGACACACGCC
Found at i:21449162 original size:47 final size:48
Alignment explanation
Indices: 21449093--21449272 Score: 161
Period size: 49 Copynumber: 3.7 Consensus size: 48
21449083 AGGGTATGAT
* ** *
21449093 GTCGATGCCATGTCCCGGACATGCTCTTACACTGGCTCATC-CATCAA
1 GTCGAGGCCATGTCCCAAACATGGTCTTACACTGGCTCATCACATCAA
* * *
21449140 GTCGAGGCCATGTCCCAAACATGGTCTTACACTGACT-ATCGAAATCGAG
1 GTCGAGGCCATGTCCCAAACATGGTCTTACACTGGCTCATC-ACATC-AA
* * * * *
21449189 GCCGACGCCATGTCTCAAACATGGTCTTACACTAGCTC-TCACAT-ATCC
1 GTCGAGGCCATGTCCCAAACATGGTCTTACACTGGCTCATCACATCA--A
*
21449237 GTGACGAGGCCATGTCCCAGACATGGTCTTACACTG
1 GT--CGAGGCCATGTCCCAAACATGGTCTTACACTG
21449273 AAACCTCTAT
Statistics
Matches: 106, Mismatches: 19, Indels: 13
0.77 0.14 0.09
Matches are distributed among these distances:
46 4 0.04
47 32 0.30
48 7 0.07
49 35 0.33
50 28 0.26
ACGTcount: A:0.24, C:0.31, G:0.21, T:0.24
Consensus pattern (48 bp):
GTCGAGGCCATGTCCCAAACATGGTCTTACACTGGCTCATCACATCAA
Found at i:21449308 original size:48 final size:45
Alignment explanation
Indices: 21449246--21449363 Score: 150
Period size: 48 Copynumber: 2.6 Consensus size: 45
21449236 CGTGACGAGG
*
21449246 CCATGTCCCAGACATGGTCTTACACTGAAACCTCTATACGT-GCCGAT
1 CCATGTCCCAGACATGGTCTTACACTGAAACATCT-T--GTAGCCGAT
*
21449293 CCCATGTCCCAGACATGGTCTTACACTGACACATCTTGTAGCCGAT
1 -CCATGTCCCAGACATGGTCTTACACTGAAACATCTTGTAGCCGAT
* *
21449339 GCATGTCCAAGACAT-GTCTTACACT
1 CCATGTCCCAGACATGGTCTTACACT
21449364 AGCTTACGTC
Statistics
Matches: 65, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
44 10 0.15
45 15 0.23
46 6 0.09
47 1 0.02
48 33 0.51
ACGTcount: A:0.25, C:0.31, G:0.17, T:0.26
Consensus pattern (45 bp):
CCATGTCCCAGACATGGTCTTACACTGAAACATCTTGTAGCCGAT
Found at i:21454547 original size:11 final size:11
Alignment explanation
Indices: 21454531--21454560 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
21454521 AAATTAGCCG
21454531 AAATCCAACTA
1 AAATCCAACTA
21454542 AAATCCAACTA
1 AAATCCAACTA
21454553 AAATCCAA
1 AAATCCAA
21454561 AGACAAAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.57, C:0.27, G:0.00, T:0.17
Consensus pattern (11 bp):
AAATCCAACTA
Found at i:21464464 original size:6 final size:6
Alignment explanation
Indices: 21464445--21464483 Score: 51
Period size: 6 Copynumber: 6.3 Consensus size: 6
21464435 TGTTAATGAA
* *
21464445 TTCATT TCTCATT TTCATT TTCAGT TTCATT TCCATT TT
1 TTCATT T-TCATT TTCATT TTCATT TTCATT TTCATT TT
21464484 GAGAAAACCA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
6 22 0.79
7 6 0.21
ACGTcount: A:0.15, C:0.21, G:0.03, T:0.62
Consensus pattern (6 bp):
TTCATT
Found at i:21464532 original size:57 final size:59
Alignment explanation
Indices: 21464469--21464586 Score: 161
Period size: 58 Copynumber: 2.0 Consensus size: 59
21464459 TCATTTTCAG
*
21464469 TTTCATTTCCATTTT-GAGAAAACCACATTAATTT-TCAAATG-ATTCCATTTTCTCCAT
1 TTTCATTTCCATTTTGGAGAAAACCACAATAATTTCTCAAATGTATTCCA-TTTCTCCAT
* * * *
21464526 TTTCATTTTCATTTTGGAGAAAACCATAATAATTTCTTAAATGTTTTCCATTTCTCCAT
1 TTTCATTTCCATTTTGGAGAAAACCACAATAATTTCTCAAATGTATTCCATTTCTCCAT
21464585 TT
1 TT
21464587 CTATTCATTC
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
57 14 0.26
58 17 0.32
59 17 0.32
60 5 0.09
ACGTcount: A:0.29, C:0.19, G:0.06, T:0.47
Consensus pattern (59 bp):
TTTCATTTCCATTTTGGAGAAAACCACAATAATTTCTCAAATGTATTCCATTTCTCCAT
Found at i:21467355 original size:27 final size:27
Alignment explanation
Indices: 21467325--21467378 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
21467315 GCATGTAGAG
21467325 AACCAAGCATTACAGAACTCTCTCTCT
1 AACCAAGCATTACAGAACTCTCTCTCT
* **
21467352 AACCAAGTATTGTAGAACTCTCTCTCT
1 AACCAAGCATTACAGAACTCTCTCTCT
21467379 TTCTCTTTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.31, C:0.30, G:0.09, T:0.30
Consensus pattern (27 bp):
AACCAAGCATTACAGAACTCTCTCTCT
Found at i:21470531 original size:24 final size:24
Alignment explanation
Indices: 21470499--21470547 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
21470489 AAAGTAATAG
21470499 CCAGTCCCCATTCCCATGGTCGGC
1 CCAGTCCCCATTCCCATGGTCGGC
21470523 CCAGTCCCCATTCCCATGGTCGGC
1 CCAGTCCCCATTCCCATGGTCGGC
21470547 C
1 C
21470548 ATGCTTGGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.12, C:0.47, G:0.20, T:0.20
Consensus pattern (24 bp):
CCAGTCCCCATTCCCATGGTCGGC
Found at i:21484999 original size:39 final size:39
Alignment explanation
Indices: 21484939--21485022 Score: 132
Period size: 39 Copynumber: 2.2 Consensus size: 39
21484929 ACGATAGGGG
21484939 CCTTCACGTGTCTAACACCACACACTACACTTTTTTCAT
1 CCTTCACGTGTCTAACACCACACACTACACTTTTTTCAT
* * *
21484978 CCTTCACGTGTCTACCGCCACACATTACACTTTTTTCAT
1 CCTTCACGTGTCTAACACCACACACTACACTTTTTTCAT
*
21485017 TCTTCA
1 CCTTCA
21485023 TTGTATTAAC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.23, C:0.36, G:0.06, T:0.36
Consensus pattern (39 bp):
CCTTCACGTGTCTAACACCACACACTACACTTTTTTCAT
Found at i:21485171 original size:15 final size:15
Alignment explanation
Indices: 21485151--21485182 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
21485141 CAAATTTGAA
21485151 AACCTCGTGAAATCG
1 AACCTCGTGAAATCG
21485166 AACCTCGTGAAATCG
1 AACCTCGTGAAATCG
21485181 AA
1 AA
21485183 TCGTCTTCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.19
Consensus pattern (15 bp):
AACCTCGTGAAATCG
Found at i:21493856 original size:26 final size:26
Alignment explanation
Indices: 21493827--21493934 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
21493817 TGGTACAAAT
*
21493827 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATATTCCA
*
21493853 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATATTCCA
21493879 TGATAATGGGTTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATATTCCA
* *
21493905 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATATTCCA
21493931 TGAT
1 TGAT
21493935 GGGCATTTCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.33, C:0.07, G:0.23, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATATTCCA
Found at i:21498995 original size:48 final size:49
Alignment explanation
Indices: 21498929--21499023 Score: 131
Period size: 48 Copynumber: 2.0 Consensus size: 49
21498919 ACTGGTAGTT
* *
21498929 CACACACCCGTGTCTATTTAACAGA-T-TGCAACACGGCCTAAGCCACAC
1 CACACACCCATGTCTATTTAACAGACTCT-AAACACGGCCTAAGCCACAC
* *
21498977 CACACGCCCATGTCTATTTAGCAGACTCTAAACACGGCCTAAGCCAC
1 CACACACCCATGTCTATTTAACAGACTCTAAACACGGCCTAAGCCAC
21499024 CTTACACGGG
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
48 22 0.54
49 18 0.44
50 1 0.02
ACGTcount: A:0.31, C:0.36, G:0.15, T:0.19
Consensus pattern (49 bp):
CACACACCCATGTCTATTTAACAGACTCTAAACACGGCCTAAGCCACAC
Found at i:21499049 original size:13 final size:13
Alignment explanation
Indices: 21499027--21499065 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
21499017 AAGCCACCTT
21499027 ACACGGGCGTGTC
1 ACACGGGCGTGTC
*
21499040 ACACGAGCGTGTC
1 ACACGGGCGTGTC
21499053 ACACGGGCGTGTC
1 ACACGGGCGTGTC
21499066 CCTGTCAAGC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.18, C:0.31, G:0.36, T:0.15
Consensus pattern (13 bp):
ACACGGGCGTGTC
Found at i:21505154 original size:40 final size:40
Alignment explanation
Indices: 21505092--21505346 Score: 354
Period size: 40 Copynumber: 6.4 Consensus size: 40
21505082 AAGCCAAGTA
* * * *
21505092 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTCGAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
* * ** *
21505131 CCTTCGGGACATAGCCCGGATATAGTAATTCATACCAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
21505171 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACCAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
21505211 CCTTCGGGACTTAGCCCGGATATAGTAACTCACACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
21505251 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
21505291 CCTTCGGGACTTAGCCCGGA-ACTAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
21505331 CCTTCGGGACTTAGCC
1 CCTTCGGGACTTAGCC
21505347 TGGTTATCAT
Statistics
Matches: 196, Mismatches: 17, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
39 13 0.07
40 183 0.93
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:21513643 original size:43 final size:43
Alignment explanation
Indices: 21513595--21513783 Score: 281
Period size: 43 Copynumber: 4.4 Consensus size: 43
21513585 ATATAAAAAG
*
21513595 ACGCCGCTAAAGGTCATGACCTTTAGCGGCGCTTTCCCCACAA
1 ACGCCGCTAAAGGTCATGACCTTTAGCGACGCTTTCCCCACAA
* *
21513638 ACGCCGCTAAAGGTCATGACCTATAGCGACGCTTTCCCCACGA
1 ACGCCGCTAAAGGTCATGACCTTTAGCGACGCTTTCCCCACAA
* * *
21513681 ATGCCGCTATAA-ATCATGACCTTTAGCGACGCTTTCCCCCCAA
1 ACGCCGCTA-AAGGTCATGACCTTTAGCGACGCTTTCCCCACAA
* *
21513724 ACGCCACTAAAGGTCATGACCTTTAGCGACGCTTTCCCCAAAA
1 ACGCCGCTAAAGGTCATGACCTTTAGCGACGCTTTCCCCACAA
*
21513767 ACGCCGCTAAAAGTCAT
1 ACGCCGCTAAAGGTCAT
21513784 AAAATTTTTA
Statistics
Matches: 129, Mismatches: 15, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
42 2 0.02
43 125 0.97
44 2 0.02
ACGTcount: A:0.27, C:0.34, G:0.18, T:0.21
Consensus pattern (43 bp):
ACGCCGCTAAAGGTCATGACCTTTAGCGACGCTTTCCCCACAA
Found at i:21518179 original size:6 final size:7
Alignment explanation
Indices: 21518157--21518187 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
21518147 ATTTAAGTTC
*
21518157 TTTATTT
1 TTTAATT
21518164 TTTAATT
1 TTTAATT
21518171 TTTAATT
1 TTTAATT
21518178 TTTAATT
1 TTTAATT
21518185 TTT
1 TTT
21518188 TGAATATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (7 bp):
TTTAATT
Found at i:21518212 original size:8 final size:8
Alignment explanation
Indices: 21518160--21518212 Score: 54
Period size: 8 Copynumber: 6.4 Consensus size: 8
21518150 TAAGTTCTTT
*
21518160 ATTTTTTA
1 ATTTTTAA
21518168 ATTTTT-A
1 ATTTTTAA
21518175 ATTTTTAA
1 ATTTTTAA
*
21518183 TTTTTTGAA
1 ATTTTT-AA
21518192 TATTTTTATA
1 -ATTTTTA-A
21518202 ATTTTTAA
1 ATTTTTAA
21518210 ATT
1 ATT
21518213 ATCATATAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
7 7 0.18
8 16 0.41
9 10 0.26
10 6 0.15
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (8 bp):
ATTTTTAA
Found at i:21518696 original size:21 final size:21
Alignment explanation
Indices: 21518657--21518747 Score: 65
Period size: 21 Copynumber: 4.3 Consensus size: 21
21518647 CAATTGCACA
*
21518657 CTAAATCCTAAACCCTAAACC
1 CTAAATCATAAACCCTAAACC
** **
21518678 CTAAATCATAAACTTTAAAATA
1 CTAAATCATAAACCCT-AAACC
* * *
21518700 GTAACTCATAAACCTTAAACC
1 CTAAATCATAAACCCTAAACC
* * *
21518721 CTTAACCATATACCCTAAACC
1 CTAAATCATAAACCCTAAACC
*
21518742 GTAAAT
1 CTAAAT
21518748 GCTAAACTAT
Statistics
Matches: 50, Mismatches: 19, Indels: 2
0.70 0.27 0.03
Matches are distributed among these distances:
21 34 0.68
22 16 0.32
ACGTcount: A:0.45, C:0.27, G:0.02, T:0.25
Consensus pattern (21 bp):
CTAAATCATAAACCCTAAACC
Found at i:21518914 original size:14 final size:14
Alignment explanation
Indices: 21518905--21518934 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
21518895 ATTAACTTTG
21518905 AACCCCTAACTCTT
1 AACCCCTAACTCTT
*
21518919 AACCCCTAACCCTT
1 AACCCCTAACTCTT
21518933 AA
1 AA
21518935 ACCATAAACC
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:0.33, C:0.43, G:0.00, T:0.23
Consensus pattern (14 bp):
AACCCCTAACTCTT
Found at i:21518945 original size:36 final size:36
Alignment explanation
Indices: 21518905--21518980 Score: 107
Period size: 36 Copynumber: 2.1 Consensus size: 36
21518895 ATTAACTTTG
** *
21518905 AACCCCTAACTCTTAACCCCTAACCCTTAAACCATA
1 AACCCCTAAAGCTTAAACCCTAACCCTTAAACCATA
* *
21518941 AACCCCTAAAGCTTAAACCCTGACCCTTAAACTATA
1 AACCCCTAAAGCTTAAACCCTAACCCTTAAACCATA
21518977 AACC
1 AACC
21518981 ATAAAACATA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.38, C:0.38, G:0.03, T:0.21
Consensus pattern (36 bp):
AACCCCTAAAGCTTAAACCCTAACCCTTAAACCATA
Found at i:21519073 original size:14 final size:14
Alignment explanation
Indices: 21519047--21519085 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
21519037 TCATAAACCT
*
21519047 TAAACCCTTAATCA
1 TAAACCCTAAATCA
* *
21519061 TATACCCTAAATCG
1 TAAACCCTAAATCA
21519075 TAAACCCTAAA
1 TAAACCCTAAA
21519086 CTATAATGAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.44, C:0.28, G:0.03, T:0.26
Consensus pattern (14 bp):
TAAACCCTAAATCA
Found at i:21519582 original size:40 final size:40
Alignment explanation
Indices: 21519499--21519646 Score: 142
Period size: 40 Copynumber: 3.7 Consensus size: 40
21519489 ATAATTTTTT
* * * * * *
21519499 GCGGCGTTTTTTTAAAAAGTGCCGCTAAAG-GTGACCTATA
1 GCGGCATTTTTCTAAAAAGCGCCGCTAATGCTTGATCT-TA
21519539 GCGGC-TTTTTCTAAAAAGCGCCGCTAATGCTTGATCTTCA
1 GCGGCATTTTTCTAAAAAGCGCCGCTAATGCTTGATCTT-A
* * *
21519579 GCGGC-GTTTTGTAAAAAACGCCGCTAATGCTTGATCTTTA
1 GCGGCATTTTTCTAAAAAGCGCCGCTAATGCTTGATC-TTA
*
21519619 GCGGCATTTTTCATTAAAA-CGCCGCTAA
1 GCGGCATTTTTC-TAAAAAGCGCCGCTAA
21519647 AAACGCCGCT
Statistics
Matches: 92, Mismatches: 11, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
39 22 0.24
40 50 0.54
41 15 0.16
42 5 0.05
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.31
Consensus pattern (40 bp):
GCGGCATTTTTCTAAAAAGCGCCGCTAATGCTTGATCTTA
Found at i:21519651 original size:12 final size:12
Alignment explanation
Indices: 21519634--21519662 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
21519624 ATTTTTCATT
21519634 AAAACGCCGCTA
1 AAAACGCCGCTA
21519646 AAAACGCCGCTA
1 AAAACGCCGCTA
21519658 AAAAC
1 AAAAC
21519663 CTGTTTTGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.48, C:0.31, G:0.14, T:0.07
Consensus pattern (12 bp):
AAAACGCCGCTA
Found at i:21530498 original size:43 final size:43
Alignment explanation
Indices: 21530448--21530640 Score: 237
Period size: 43 Copynumber: 4.5 Consensus size: 43
21530438 TATCCTATAT
* * * *
21530448 ATGGTCTTACATGTTATCA-AATATCGATGCCACTGTCCCAGAC
1 ATGGTCTTACACGTAATCACAATA-CAATGCCAATGTCCCAGAC
* * ** * * *
21530491 AAGGTCTTATACAAAATCA-TATAGCGATGCCAATGTCTCAGAC
1 ATGGTCTTACACGTAATCACAATA-CAATGCCAATGTCCCAGAC
21530534 ATGGTCTTACACGTAATCACAATACAATGCCAATGTCCCAGAC
1 ATGGTCTTACACGTAATCACAATACAATGCCAATGTCCCAGAC
*
21530577 ATGGTCTTACACGTAATCACAACACAATGCCAATGTCCCAGAC
1 ATGGTCTTACACGTAATCACAATACAATGCCAATGTCCCAGAC
*
21530620 ATGGTCTTACATGTAATCACA
1 ATGGTCTTACACGTAATCACA
21530641 TCTAGGTAAT
Statistics
Matches: 130, Mismatches: 19, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
43 127 0.98
44 3 0.02
ACGTcount: A:0.34, C:0.25, G:0.15, T:0.26
Consensus pattern (43 bp):
ATGGTCTTACACGTAATCACAATACAATGCCAATGTCCCAGAC
Found at i:21532704 original size:38 final size:38
Alignment explanation
Indices: 21532655--21532732 Score: 156
Period size: 38 Copynumber: 2.1 Consensus size: 38
21532645 GAATAAGAGA
21532655 AAACAATGGAAGGAATAGTGCAAGGCCATCACTCTCAG
1 AAACAATGGAAGGAATAGTGCAAGGCCATCACTCTCAG
21532693 AAACAATGGAAGGAATAGTGCAAGGCCATCACTCTCAG
1 AAACAATGGAAGGAATAGTGCAAGGCCATCACTCTCAG
21532731 AA
1 AA
21532733 GTGGGACACA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.41, C:0.21, G:0.23, T:0.15
Consensus pattern (38 bp):
AAACAATGGAAGGAATAGTGCAAGGCCATCACTCTCAG
Found at i:21533801 original size:36 final size:36
Alignment explanation
Indices: 21533754--21533845 Score: 139
Period size: 36 Copynumber: 2.6 Consensus size: 36
21533744 GAATCTTTGG
* * * *
21533754 ATTTAAAATATGCATATTTGAAACCTTTACTGTAAT
1 ATTTAAAATATGCATATTTGAAACATTTACCGCAAC
*
21533790 ATTTAAAATATGCATATTTGAAACATTTGCCGCAAC
1 ATTTAAAATATGCATATTTGAAACATTTACCGCAAC
21533826 ATTTAAAATATGCATATTTG
1 ATTTAAAATATGCATATTTG
21533846 GGAGACAACA
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 51 1.00
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (36 bp):
ATTTAAAATATGCATATTTGAAACATTTACCGCAAC
Found at i:21548876 original size:55 final size:55
Alignment explanation
Indices: 21548749--21548880 Score: 156
Period size: 55 Copynumber: 2.4 Consensus size: 55
21548739 CCAAACCAAT
* * * * *
21548749 ACGGGCGTGCGACACGTCCGTGTTCTGAAACCGTGGGCAAACCTATCAATTTAGC
1 ACGGGTGTGTGACACGCCCGTGTTCTAAAACCGTAGGCAAACCTATCAATTTAGC
*** * * *
21548804 ACGGGTGTGTCTTACGCCCGTGTTTTAAAACCGTAGGCTAACCTGTCAATTTAGC
1 ACGGGTGTGTGACACGCCCGTGTTCTAAAACCGTAGGCAAACCTATCAATTTAGC
*
21548859 ACGGGTGTTTGACACGCCCGTG
1 ACGGGTGTGTGACACGCCCGTG
21548881 CCTAGCCCCC
Statistics
Matches: 62, Mismatches: 15, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
55 62 1.00
ACGTcount: A:0.21, C:0.26, G:0.27, T:0.26
Consensus pattern (55 bp):
ACGGGTGTGTGACACGCCCGTGTTCTAAAACCGTAGGCAAACCTATCAATTTAGC
Found at i:21552508 original size:47 final size:45
Alignment explanation
Indices: 21552390--21552558 Score: 200
Period size: 47 Copynumber: 3.7 Consensus size: 45
21552380 GGATGGTTGA
*** * *
21552390 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATG-GA-TGC
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTC-GGAATGTAACTAC
* *
21552434 GAATGTCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAAATGTAACTAG
1 GCA--TCCGAACTCGTTGAGTTGAGTCCGAGTTCG-G-AATGTAACTAC
21552483 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCGGAATGTAACTAC
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCGGAATGTAACTAC
*
21552528 GCAT-CGAGCTCGTTGAGTTGAGTCCGAGTTC
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTC
21552559 ACTTATGGGC
Statistics
Matches: 109, Mismatches: 10, Indels: 12
0.83 0.08 0.09
Matches are distributed among these distances:
44 28 0.26
45 14 0.13
46 30 0.28
47 33 0.30
48 1 0.01
49 3 0.03
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.28
Consensus pattern (45 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCGGAATGTAACTAC
Found at i:21552555 original size:44 final size:47
Alignment explanation
Indices: 21552439--21552558 Score: 201
Period size: 47 Copynumber: 2.6 Consensus size: 47
21552429 GATGCGAATG
*
21552439 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAAATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAAATGTAACTACGCA
21552486 TCCGAACTCGTTGAGTTGAGTCCGAGTTCG-G-AATGTAACTACGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAAATGTAACTACGCA
*
21552531 T-CGAGCTCGTTGAGTTGAGTCCGAGTTC
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC
21552559 ACTTATGGGC
Statistics
Matches: 71, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
44 26 0.37
45 14 0.20
46 1 0.01
47 30 0.42
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (47 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAAATGTAACTACGCA
Found at i:21560028 original size:46 final size:45
Alignment explanation
Indices: 21559977--21560106 Score: 158
Period size: 46 Copynumber: 2.8 Consensus size: 45
21559967 ATGGTTGAGC
21559977 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGA-T-GCGA
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGACTAG-GA
* * * *
21560021 ATGTCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGAATGTAACTAGGC
1 A--TCCGAACTCGTTGAGTTGAGTCCGAGTTCACT-TATG-GACTAGGA
21560069 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
21560107 GCGGGTTACA
Statistics
Matches: 72, Mismatches: 7, Indels: 13
0.78 0.08 0.14
Matches are distributed among these distances:
44 1 0.01
45 1 0.01
46 64 0.89
47 2 0.03
48 3 0.04
49 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (45 bp):
ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGACTAGGA
Found at i:21572132 original size:29 final size:28
Alignment explanation
Indices: 21572085--21572212 Score: 148
Period size: 28 Copynumber: 4.5 Consensus size: 28
21572075 CATGAGATTG
* * **
21572085 GCACTAAGTATGCGGGTTTAAATTGCATA
1 GCACTAAGTGTGCGAGTTT-AATTATATA
* *
21572114 GCACTAAGTGTGCAAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTAATTATATA
* *
21572142 GCACTAAGTGTGCGAGTTTGATTATGTAA
1 GCACTAAGTGTGCGAGTTTAATTATAT-A
*
21572171 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTAATTATATA
*
21572199 ACACTAAGTGTGCG
1 GCACTAAGTGTGCG
21572213 GACTTACTAT
Statistics
Matches: 88, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
28 45 0.51
29 43 0.49
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTAATTATATA
Found at i:21572151 original size:28 final size:28
Alignment explanation
Indices: 21572111--21572212 Score: 168
Period size: 28 Copynumber: 3.6 Consensus size: 28
21572101 TTTAAATTGC
*
21572111 ATAGCACTAAGTGTGCAAGTTTGATTAT
1 ATAGCACTAAGTGTGCGAGTTTGATTAT
21572139 ATAGCACTAAGTGTGCGAGTTTGATTAT
1 ATAGCACTAAGTGTGCGAGTTTGATTAT
*
21572167 GTAAGCACTAAGTGTGCGAGTTTGATTAT
1 AT-AGCACTAAGTGTGCGAGTTTGATTAT
*
21572196 ATAACACTAAGTGTGCG
1 ATAGCACTAAGTGTGCG
21572213 GACTTACTAT
Statistics
Matches: 69, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
28 42 0.61
29 27 0.39
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (28 bp):
ATAGCACTAAGTGTGCGAGTTTGATTAT
Found at i:21591898 original size:39 final size:39
Alignment explanation
Indices: 21591852--21591976 Score: 151
Period size: 39 Copynumber: 3.2 Consensus size: 39
21591842 GTATTGCAAC
* *
21591852 ATATGCTTGAATGTTATATGATTAAATGAGTATTGTGAT
1 ATATGCTTGAATGTTATGTGATTATATGAGTATTGTGAT
* * * *
21591891 ATGTGCTTGAACGTTACGTAATTATATGAGTATTGTGAT
1 ATATGCTTGAATGTTATGTGATTATATGAGTATTGTGAT
* * * * *
21591930 ATATTCTTAAATGTTATGTGATTATATGTGTAATGTGGT
1 ATATGCTTGAATGTTATGTGATTATATGAGTATTGTGAT
21591969 ATATGCTT
1 ATATGCTT
21591977 AAAAGTGAAT
Statistics
Matches: 70, Mismatches: 16, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
39 70 1.00
ACGTcount: A:0.30, C:0.05, G:0.21, T:0.45
Consensus pattern (39 bp):
ATATGCTTGAATGTTATGTGATTATATGAGTATTGTGAT
Found at i:21594241 original size:17 final size:17
Alignment explanation
Indices: 21594221--21594279 Score: 73
Period size: 17 Copynumber: 3.4 Consensus size: 17
21594211 CATTCAAATA
21594221 AATCCAAAATTAATAAT
1 AATCCAAAATTAATAAT
** *
21594238 AATCCATCATTAATATGAA
1 AATCCAAAATTAATA--AT
21594257 AATCCAAAATTAATAAT
1 AATCCAAAATTAATAAT
21594274 AATCCA
1 AATCCA
21594280 TCATTAATAT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
17 20 0.59
19 14 0.41
ACGTcount: A:0.54, C:0.15, G:0.02, T:0.29
Consensus pattern (17 bp):
AATCCAAAATTAATAAT
Found at i:21594262 original size:19 final size:19
Alignment explanation
Indices: 21594238--21594295 Score: 75
Period size: 19 Copynumber: 3.2 Consensus size: 19
21594228 AATTAATAAT
21594238 AATCCATCATTAATATGAA
1 AATCCATCATTAATATGAA
** *
21594257 AATCCAAAATTAATA--AT
1 AATCCATCATTAATATGAA
21594274 AATCCATCATTAATATGAA
1 AATCCATCATTAATATGAA
21594293 AAT
1 AAT
21594296 TTAAGGATTT
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
17 14 0.45
19 17 0.55
ACGTcount: A:0.52, C:0.14, G:0.03, T:0.31
Consensus pattern (19 bp):
AATCCATCATTAATATGAA
Found at i:21594266 original size:36 final size:36
Alignment explanation
Indices: 21594220--21594295 Score: 152
Period size: 36 Copynumber: 2.1 Consensus size: 36
21594210 TCATTCAAAT
21594220 AAATCCAAAATTAATAATAATCCATCATTAATATGA
1 AAATCCAAAATTAATAATAATCCATCATTAATATGA
21594256 AAATCCAAAATTAATAATAATCCATCATTAATATGA
1 AAATCCAAAATTAATAATAATCCATCATTAATATGA
21594292 AAAT
1 AAAT
21594296 TTAAGGATTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.54, C:0.13, G:0.03, T:0.30
Consensus pattern (36 bp):
AAATCCAAAATTAATAATAATCCATCATTAATATGA
Found at i:21594285 original size:17 final size:17
Alignment explanation
Indices: 21594229--21594288 Score: 75
Period size: 17 Copynumber: 3.4 Consensus size: 17
21594219 TAAATCCAAA
21594229 ATTAATAATAATCCATC
1 ATTAATAATAATCCATC
* **
21594246 ATTAATATGAAAATCCAAA
1 ATTAATA--ATAATCCATC
21594265 ATTAATAATAATCCATC
1 ATTAATAATAATCCATC
21594282 ATTAATA
1 ATTAATA
21594289 TGAAAATTTA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
17 21 0.60
19 14 0.40
ACGTcount: A:0.52, C:0.13, G:0.02, T:0.33
Consensus pattern (17 bp):
ATTAATAATAATCCATC
Found at i:21599921 original size:27 final size:27
Alignment explanation
Indices: 21599864--21599925 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 27
21599854 ATAATATTTG
** *
21599864 TGTTTAATGTCCCGATGGACTACCCCC
1 TGTTTAACATCCCGATGGACTACCCCA
* * *
21599891 TGTTTAACATCCCGTTGGACTATCCTA
1 TGTTTAACATCCCGATGGACTACCCCA
21599918 TGTTTAAC
1 TGTTTAAC
21599926 GTCTTGCTAG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.21, C:0.27, G:0.16, T:0.35
Consensus pattern (27 bp):
TGTTTAACATCCCGATGGACTACCCCA
Found at i:21604755 original size:13 final size:13
Alignment explanation
Indices: 21604737--21604765 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
21604727 ACCATTTAAG
21604737 GGCACACGCCCAA
1 GGCACACGCCCAA
21604750 GGCACACGCCCAA
1 GGCACACGCCCAA
21604763 GGC
1 GGC
21604766 CCAAGGCCGT
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:0.28, C:0.45, G:0.28, T:0.00
Consensus pattern (13 bp):
GGCACACGCCCAA
Found at i:21606839 original size:27 final size:27
Alignment explanation
Indices: 21606799--21606852 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
21606789 TCATACAACC
* *
21606799 CATGTAATATTAATTTAACATTCAATT
1 CATGTAACAATAATTTAACATTCAATT
**
21606826 CATGTAACAATAATTTTCCATTCAATT
1 CATGTAACAATAATTTAACATTCAATT
21606853 TCACATAACA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.39, C:0.15, G:0.04, T:0.43
Consensus pattern (27 bp):
CATGTAACAATAATTTAACATTCAATT
Found at i:21609442 original size:46 final size:46
Alignment explanation
Indices: 21609389--21609561 Score: 139
Period size: 47 Copynumber: 3.7 Consensus size: 46
21609379 AGACTATTAT
*
21609389 GAGCTAGTGTAAGA-CATGTCTAGGACAT-GCATCAGCCACATTAAGA
1 GAGCTAGTGTAAGACCATGT-TGGGACATGGCATCAG-CACATTAAGA
*
21609435 GAGCTAGTGTAAGACCATGTTCGGGACATGGCATC-G-GCATTGAGACGA
1 GAGCTAGTGTAAGACCATGTT-GGGACATGGCATCAGCACATT-A-A-GA
* * * *
21609483 GAGCTACTGTAAGA-CATGTTTGAGACAT-GCATAAGCTACGAGT-A-A
1 GAGCTAGTGTAAGACCATG-TTGGGACATGGCATCAGC-AC-ATTAAGA
21609528 -AGCTAGTGTAAGACCATGTCTGGGACATGGCATC
1 GAGCTAGTGTAAGACCATGT-TGGGACATGGCATC
21609562 GGCATCCTAC
Statistics
Matches: 103, Mismatches: 10, Indels: 28
0.73 0.07 0.20
Matches are distributed among these distances:
44 13 0.13
45 16 0.16
46 24 0.23
47 25 0.24
48 22 0.21
49 1 0.01
50 2 0.02
ACGTcount: A:0.31, C:0.18, G:0.28, T:0.23
Consensus pattern (46 bp):
GAGCTAGTGTAAGACCATGTTGGGACATGGCATCAGCACATTAAGA
Found at i:21609494 original size:48 final size:47
Alignment explanation
Indices: 21609432--21609566 Score: 138
Period size: 44 Copynumber: 2.9 Consensus size: 47
21609422 AGCCACATTA
21609432 AGAGAGCTAGTGTAAGACCATGTTCGGGACATGGCATCGGCATTGA-G
1 AGAGAGCTAGTGTAAGACCATGTTCGGGACATGGCATCGGCATT-ACG
* * * **
21609479 ACGAGAGCTACTGTAAGA-CATGTTTGAGACAT-GCATAAGC--TACG
1 A-GAGAGCTAGTGTAAGACCATGTTCGGGACATGGCATCGGCATTACG
*
21609523 AGTAAAGCTAGTGTAAGACCATG-TCTGGGACATGGCATCGGCAT
1 AG-AGAGCTAGTGTAAGACCATGTTC-GGGACATGGCATCGGCAT
21609567 CCTACCCCAT
Statistics
Matches: 69, Mismatches: 11, Indels: 15
0.73 0.12 0.16
Matches are distributed among these distances:
43 2 0.03
44 17 0.25
45 10 0.14
46 12 0.17
47 13 0.19
48 15 0.22
ACGTcount: A:0.30, C:0.18, G:0.30, T:0.22
Consensus pattern (47 bp):
AGAGAGCTAGTGTAAGACCATGTTCGGGACATGGCATCGGCATTACG
Found at i:21616668 original size:19 final size:18
Alignment explanation
Indices: 21616635--21616672 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
21616625 TAATATTAGT
*
21616635 TAAACATGTTTAATTAAA
1 TAAACATGATTAATTAAA
21616653 TAAACTATGATTAATTAAA
1 TAAAC-ATGATTAATTAAA
21616672 T
1 T
21616673 TTTTTAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.39
Consensus pattern (18 bp):
TAAACATGATTAATTAAA
Found at i:21619380 original size:24 final size:24
Alignment explanation
Indices: 21619348--21619395 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
21619338 TGCTTAAGGG
21619348 TTGGATTGTATAAGTTTCAAAAGT
1 TTGGATTGTATAAGTTTCAAAAGT
21619372 TTGGATTGTATAAGTTTCAAAAGT
1 TTGGATTGTATAAGTTTCAAAAGT
21619396 GATCATTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.04, G:0.21, T:0.42
Consensus pattern (24 bp):
TTGGATTGTATAAGTTTCAAAAGT
Found at i:21626906 original size:6 final size:6
Alignment explanation
Indices: 21626895--21626923 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
21626885 TGTGTATGGT
21626895 TTTTTA TTTTTA TTTTTA TTTTTA TTTTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTT
21626924 TGCTTCTGCT
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:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTTA
Found at i:21631686 original size:2 final size:2
Alignment explanation
Indices: 21631679--21631705 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
21631669 ACCTAAAAAG
21631679 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA G
21631706 CTGCAGGAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:21639194 original size:32 final size:26
Alignment explanation
Indices: 21639133--21639272 Score: 217
Period size: 26 Copynumber: 5.2 Consensus size: 26
21639123 TGATACAAAT
*
21639133 TGATAATGGGTTAGATAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
21639159 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
21639185 TGATAATGATAATGAGTTAGGTAAATGTTCCA
1 TGATAATG-----G-GTTAGGTAAATGTTCCA
21639217 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
21639243 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
21639269 TGAT
1 TGAT
21639273 GGGAATTTCA
Statistics
Matches: 107, Mismatches: 1, Indels: 12
0.89 0.01 0.10
Matches are distributed among these distances:
26 80 0.75
27 1 0.01
31 1 0.01
32 25 0.23
ACGTcount: A:0.33, C:0.07, G:0.25, T:0.35
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:21639204 original size:58 final size:58
Alignment explanation
Indices: 21639133--21639250 Score: 218
Period size: 58 Copynumber: 2.0 Consensus size: 58
21639123 TGATACAAAT
*
21639133 TGATAATGGGTTAGATAAATGTTCCATGATAATGGGTTAGGTAAATGTTCCATGATAA
1 TGATAATGAGTTAGATAAATGTTCCATGATAATGGGTTAGGTAAATGTTCCATGATAA
*
21639191 TGATAATGAGTTAGGTAAATGTTCCATGATAATGGGTTAGGTAAATGTTCCATGATAA
1 TGATAATGAGTTAGATAAATGTTCCATGATAATGGGTTAGGTAAATGTTCCATGATAA
21639249 TG
1 TG
21639251 GGTTAGGTAA
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.34, C:0.07, G:0.25, T:0.35
Consensus pattern (58 bp):
TGATAATGAGTTAGATAAATGTTCCATGATAATGGGTTAGGTAAATGTTCCATGATAA
Found at i:21642484 original size:12 final size:12
Alignment explanation
Indices: 21642463--21642505 Score: 77
Period size: 12 Copynumber: 3.6 Consensus size: 12
21642453 ACTCGGGGAA
21642463 GAGGCCGTGGTC
1 GAGGCCGTGGTC
*
21642475 GAGGCTGTGGTC
1 GAGGCCGTGGTC
21642487 GAGGCCGTGGTC
1 GAGGCCGTGGTC
21642499 GAGGCCG
1 GAGGCCG
21642506 AGGTAGTACT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.09, C:0.23, G:0.51, T:0.16
Consensus pattern (12 bp):
GAGGCCGTGGTC
Found at i:21647410 original size:26 final size:26
Alignment explanation
Indices: 21647381--21647462 Score: 155
Period size: 26 Copynumber: 3.2 Consensus size: 26
21647371 TGATACAAAT
*
21647381 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
21647407 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
21647433 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
21647459 TGAT
1 TGAT
21647463 GGGAATTTCA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 55 1.00
ACGTcount: A:0.30, C:0.06, G:0.27, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:21651529 original size:29 final size:29
Alignment explanation
Indices: 21651496--21651552 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
21651486 TCAACATAAT
* *
21651496 TATTG-ATATAACATTATTTTATATTTATA
1 TATTGTATATAAAATTA-ATTATATTTATA
21651525 TATTGTATATAAAATTAATTATATTTAT
1 TATTGTATATAAAATTAATTATATTTAT
21651553 TCAATATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 15 0.60
30 10 0.40
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (29 bp):
TATTGTATATAAAATTAATTATATTTATA
Found at i:21654187 original size:15 final size:15
Alignment explanation
Indices: 21654167--21654197 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
21654157 TCAAATAAAC
21654167 TGTAAAATATGAAAT
1 TGTAAAATATGAAAT
21654182 TGTAAAATATGAAAT
1 TGTAAAATATGAAAT
21654197 T
1 T
21654198 TGGTCGTCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.13, T:0.35
Consensus pattern (15 bp):
TGTAAAATATGAAAT
Found at i:21657212 original size:16 final size:16
Alignment explanation
Indices: 21657191--21657223 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
21657181 AGTAATGAAA
21657191 TTAGTTTTGACTAAAG
1 TTAGTTTTGACTAAAG
21657207 TTAGTTTTGACTAAAG
1 TTAGTTTTGACTAAAG
21657223 T
1 T
21657224 ATAACATTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.06, G:0.18, T:0.45
Consensus pattern (16 bp):
TTAGTTTTGACTAAAG
Found at i:21657553 original size:40 final size:40
Alignment explanation
Indices: 21657486--21657729 Score: 307
Period size: 40 Copynumber: 6.1 Consensus size: 40
21657476 ACCCAAGTAT
*
21657486 CTTCGGGAT-TTAG-CCGGATATAACAACTCGCACAAATGC
1 CTTCGGG-TCTTAGCCCGGATATAGCAACTCGCACAAATGC
*
21657525 CCTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
* * * *
21657565 CTTCGGGTCTTAGCCCAGATATAATC-ACTAGCATAAATGC
1 CTTCGGGTCTTAGCCCGGATAT-AGCAACTCGCACAAATGC
* * *
21657605 CTTTGGGACATAGCCCGGATATAGCAACTCGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
* * *
21657645 CTTCGGGTCTTAGCCCGGATATAATC-ACTAGCATAAATGC
1 CTTCGGGTCTTAGCCCGGATAT-AGCAACTCGCACAAATGC
* *
21657685 CTTCGGGACATAGCCCGGATATAGCAACTCGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
21657725 CTTCG
1 CTTCG
21657730 AATCTTAGTC
Statistics
Matches: 174, Mismatches: 25, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
38 1 0.01
39 14 0.08
40 155 0.89
41 4 0.02
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (40 bp):
CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
Found at i:21657737 original size:80 final size:80
Alignment explanation
Indices: 21657486--21657729 Score: 386
Period size: 80 Copynumber: 3.1 Consensus size: 80
21657476 ACCCAAGTAT
* * * * *
21657486 CTTCGGGAT-TTAG-CCGGATATAA-CAACTCGCACAAATGCCCTCGGGTCTTAGCCCGGATATA
1 CTTCGGG-TCTTAGCCCGGATATAATC-ACTAGCATAAATGCCTTCGGGACATAGCCCGGATATA
21657548 GCAACTCGCACAAATGC
64 GCAACTCGCACAAATGC
* *
21657565 CTTCGGGTCTTAGCCCAGATATAATCACTAGCATAAATGCCTTTGGGACATAGCCCGGATATAGC
1 CTTCGGGTCTTAGCCCGGATATAATCACTAGCATAAATGCCTTCGGGACATAGCCCGGATATAGC
21657630 AACTCGCACAAATGC
66 AACTCGCACAAATGC
21657645 CTTCGGGTCTTAGCCCGGATATAATCACTAGCATAAATGCCTTCGGGACATAGCCCGGATATAGC
1 CTTCGGGTCTTAGCCCGGATATAATCACTAGCATAAATGCCTTCGGGACATAGCCCGGATATAGC
21657710 AACTCGCACAAATGC
66 AACTCGCACAAATGC
21657725 CTTCG
1 CTTCG
21657730 AATCTTAGTC
Statistics
Matches: 153, Mismatches: 9, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
78 1 0.01
79 11 0.07
80 140 0.92
81 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (80 bp):
CTTCGGGTCTTAGCCCGGATATAATCACTAGCATAAATGCCTTCGGGACATAGCCCGGATATAGC
AACTCGCACAAATGC
Found at i:21660394 original size:43 final size:43
Alignment explanation
Indices: 21660346--21660485 Score: 153
Period size: 42 Copynumber: 3.3 Consensus size: 43
21660336 CATATCCGGA
* *
21660346 TATGGTCTTACATGTAATCTCATATTGATGCCAATAGCCCA-AC
1 TATGGTCTTACACGTAATATCATATTGATGCC-ATAGCCCAGAC
** * * *
21660389 TATGGTCTTACACAAAATTTCGTATCGATGCCAT-GTCCCAGAC
1 TATGGTCTTACACGTAATATCATATTGATGCCATAG-CCCAGAC
* *
21660432 -ATGGTCTTACACGTAATATCATACTGATGCCATATCCCAGA-
1 TATGGTCTTACACGTAATATCATATTGATGCCATAGCCCAGAC
21660473 TATGGTCTTACAC
1 TATGGTCTTACAC
21660486 ATATTCTCAT
Statistics
Matches: 80, Mismatches: 13, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
41 1 0.01
42 51 0.64
43 28 0.35
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.31
Consensus pattern (43 bp):
TATGGTCTTACACGTAATATCATATTGATGCCATAGCCCAGAC
Found at i:21674685 original size:310 final size:308
Alignment explanation
Indices: 21674089--21674808 Score: 703
Period size: 310 Copynumber: 2.4 Consensus size: 308
21674079 TTTTATTTTG
* * * *
21674089 CACATTTTAATCTATT-TTTTTTATTTTAACACCATATATATTTTATGTGTTATTATTAATTAGT
1 CACAATTTAATCTATTATTTTTTATTTTAACAACATACATATTTCATGTGTTATTATTAATTAGT
* * * *
21674153 TTCAAACCATACATTTAATTATTTATTGTATGTTATTTTTAACCACAAATTTATATTCTAAATAC
66 TTCAAACAATACATTTAATTATTTATTGTATATTATTTTTAAACACAAATTTACATTCTAAATAC
* * * * * * *
21674218 GTGGTTTTCATACGCATATGCGTTTATAGAGTTTCTAGTATTAATAATATTGTTAATTGAATTGG
131 GTGGTTTTCACACACATATACATTGATAGAATTTCTA-TATAAATAATATTGTTAATTGAATTGG
* * * * * * * * *
21674283 TGTAATAAATTAACTCGACACCAACTCATGGTTGATGACAACACCATAATCAATAAATGTATTCA
195 TGTAATAAATTAACTCAAAACAAACTAAAGATTGATGACAACACCATAATAAACAAATATATTCA
* * * *
21674348 TTTAATATTTTTAATTTGATATATTTATGTGCTTAAAATTCATTTTACT
260 TTTAATATTTTAAATCTAATATATTTATATGCTTAAAATTCATTTTACT
* * * *
21674397 CGCAATTTAATCTATTATTTTTTCATTTTAACAGCATACATATTTCACGTGCTATTATTAATTAG
1 CACAATTTAATCTATTATTTTTT-ATTTTAACAACATACATATTTCATGTGTTATTATTAATTAG
* * * * *
21674462 TTTCAAACTATA-AGTTTCATTATTTATTGTATTTTATTTTTAAACACATATTTGCATTCTAAAT
65 TTTCAAACAATACA-TTTAATTATTTATTGTATATTATTTTTAAACACAAATTTACATTCTAAAT
* * *
21674526 ATGTGG-TTTC-CACACATATACAAAATTGATAGAAATTTCT-TATAAATAATGTTGTTGATTGA
129 ACGTGGTTTTCACACACATATAC---ATTGATAG-AATTTCTATATAAATAATATTGTTAATTGA
* ** * *** * *
21674588 GTTGGTGTCGTAAATTAACTTAAAACAAACTAAAGATTGATGACAACATTGTGATAAACAATTAT
190 ATTGGTGTAATAAATTAACTCAAAACAAACTAAAGATTGATGACAACACCATAATAAACAAATAT
* * * ** * *
21674653 ATTTA-TTAGGTATTTTAAATCTAATGTATTTATATTTTTAAATTTCGTTTTACT
255 ATTCATTTA-ATATTTTAAATCTAATATATTTATATGCTTAAAATTCATTTTACT
* *
21674707 CACAATTT-A---A-TA--TTTTATTTTAATAACTTACATATTTCATGTGTTATTATTAATTA-T
1 CACAATTTAATCTATTATTTTTTATTTTAACAACATACATATTTCATGTGTTATTATTAATTAGT
* * * * *
21674764 TTCAACCAATATATTTTATTATTTATTATATATTATTTTTGAACA
66 TTCAAACAATACATTTAATTATTTATTGTATATTATTTTTAAACA
21674809 TATTTCTATA
Statistics
Matches: 338, Mismatches: 65, Indels: 25
0.79 0.15 0.06
Matches are distributed among these distances:
301 38 0.11
302 36 0.11
303 4 0.01
305 2 0.01
306 1 0.00
308 22 0.07
309 15 0.04
310 208 0.62
311 6 0.02
312 6 0.02
ACGTcount: A:0.34, C:0.11, G:0.09, T:0.46
Consensus pattern (308 bp):
CACAATTTAATCTATTATTTTTTATTTTAACAACATACATATTTCATGTGTTATTATTAATTAGT
TTCAAACAATACATTTAATTATTTATTGTATATTATTTTTAAACACAAATTTACATTCTAAATAC
GTGGTTTTCACACACATATACATTGATAGAATTTCTATATAAATAATATTGTTAATTGAATTGGT
GTAATAAATTAACTCAAAACAAACTAAAGATTGATGACAACACCATAATAAACAAATATATTCAT
TTAATATTTTAAATCTAATATATTTATATGCTTAAAATTCATTTTACT
Found at i:21675921 original size:21 final size:21
Alignment explanation
Indices: 21675895--21675938 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
21675885 TCTACAGTGA
21675895 CCACAATAGCATCCGTTATGT
1 CCACAATAGCATCCGTTATGT
21675916 CCACAATAGCATCCGTTATGT
1 CCACAATAGCATCCGTTATGT
21675937 CC
1 CC
21675939 GTAATCGCGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.27, C:0.32, G:0.14, T:0.27
Consensus pattern (21 bp):
CCACAATAGCATCCGTTATGT
Found at i:21677247 original size:39 final size:39
Alignment explanation
Indices: 21677188--21677365 Score: 284
Period size: 39 Copynumber: 4.6 Consensus size: 39
21677178 ATCGTGATCT
** * *
21677188 GAAGCCCGAAATCTAGCTGAAGCATATAAGTGCTAAACG
1 GAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAACG
*
21677227 AAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAACG
1 GAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAACG
* *
21677266 GAAGCCTGGAGGCTAACTGAAGCACATAAGTGCTAAACG
1 GAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAACG
*
21677305 GAAGCCCGGAGGCTAACTGAAGCACATAAGTGCTAAACG
1 GAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAACG
21677344 GAAGCCCGAAGGCTAACTGAAG
1 GAAGCCCGAAGGCTAACTGAAG
21677366 TTCATCAGAG
Statistics
Matches: 129, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 129 1.00
ACGTcount: A:0.38, C:0.22, G:0.26, T:0.14
Consensus pattern (39 bp):
GAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAACG
Found at i:21677545 original size:27 final size:27
Alignment explanation
Indices: 21677507--21677560 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
21677497 AATTTACCGT
21677507 CAATTCATCTTTTTCACTGAAAGATTG
1 CAATTCATCTTTTTCACTGAAAGATTG
21677534 CAATTCATCTTTTTCACTGAAAGATTG
1 CAATTCATCTTTTTCACTGAAAGATTG
21677561 TACTCATTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.30, C:0.19, G:0.11, T:0.41
Consensus pattern (27 bp):
CAATTCATCTTTTTCACTGAAAGATTG
Found at i:21679792 original size:29 final size:30
Alignment explanation
Indices: 21679715--21679789 Score: 141
Period size: 30 Copynumber: 2.5 Consensus size: 30
21679705 AAAATTATAA
21679715 TTTTATAATTTTTAAATGATTAAATCAAAT
1 TTTTATAATTTTTAAATGATTAAATCAAAT
21679745 TTTTATAATTTTTAAATGATTAAATCAAAT
1 TTTTATAATTTTTAAATGATTAAATCAAAT
*
21679775 TTTTATTATTTTTAA
1 TTTTATAATTTTTAA
21679790 TGAGACCAAA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 44 1.00
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.55
Consensus pattern (30 bp):
TTTTATAATTTTTAAATGATTAAATCAAAT
Found at i:21686901 original size:43 final size:42
Alignment explanation
Indices: 21686754--21686902 Score: 124
Period size: 42 Copynumber: 3.5 Consensus size: 42
21686744 ATGTGATTCG
* * * * * *
21686754 TGTAAGACCACGTTTGGGACGTTGACATCGATTTTTGATTTACA
1 TGTAAGACCTCGTCTGGGACATTGGCATCGA-TATTGA-GTACA
* * *
21686798 TGTAAAACCAT-GTCTGGGACATTGGCATCG-TATATGAGTTCG
1 TGTAAGACC-TCGTCTGGGACATTGGCATCGATAT-TGAGTACA
* *
21686840 TGTAAGACCTTGTCTGGGACAATGGCATCGATAGTTGA-TCACA
1 TGTAAGACCTCGTCTGGGACATTGGCATCGATA-TTGAGT-ACA
21686883 TGTAAGACCTCGTCTGGGAC
1 TGTAAGACCTCGTCTGGGAC
21686903 GTAGGCATTG
Statistics
Matches: 85, Mismatches: 14, Indels: 13
0.76 0.12 0.12
Matches are distributed among these distances:
41 1 0.01
42 31 0.36
43 28 0.33
44 25 0.29
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.31
Consensus pattern (42 bp):
TGTAAGACCTCGTCTGGGACATTGGCATCGATATTGAGTACA
Found at i:21686910 original size:43 final size:42
Alignment explanation
Indices: 21686754--21686910 Score: 106
Period size: 43 Copynumber: 3.7 Consensus size: 42
21686744 ATGTGATTCG
* * * * * *
21686754 TGTAAGACCACGTTTGGGACGTTGACATCGATTTTTGATTTACA
1 TGTAAGACCTCGTCTGGGACGTAGGCATCGA-TATTGA-GTACA
* * * * *
21686798 TGTAAAACCAT-GTCTGGGACATTGGCATCG-TATATGAGTTCG
1 TGTAAGACC-TCGTCTGGGACGTAGGCATCGATAT-TGAGTACA
* *
21686840 TGTAAGACCTTGTCTGGGAC-AATGGCATCGATAGTTGA-TCACA
1 TGTAAGACCTCGTCTGGGACGTA-GGCATCGATA-TTGAGT-ACA
21686883 TGTAAGACCTCGTCTGGGACGTAGGCAT
1 TGTAAGACCTCGTCTGGGACGTAGGCAT
21686911 TGTACGAGCT
Statistics
Matches: 89, Mismatches: 16, Indels: 17
0.73 0.13 0.14
Matches are distributed among these distances:
41 1 0.01
42 29 0.33
43 33 0.37
44 26 0.29
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.31
Consensus pattern (42 bp):
TGTAAGACCTCGTCTGGGACGTAGGCATCGATATTGAGTACA
Found at i:21697594 original size:43 final size:43
Alignment explanation
Indices: 21697485--21697614 Score: 122
Period size: 43 Copynumber: 3.0 Consensus size: 43
21697475 ATATCGTACA
* * * ** *
21697485 ATGCCAACGTCCCAGACGTGGTCTTATATGTAATCACATATTG
1 ATGCCAACGTCCCGGACATGGTCTTACACATAATCACATATCG
* *
21697528 ATGCC-ACTGTCCCAGG-CAGGGTCTTACACATAATCACTTATCG
1 ATGCCAAC-GTCCC-GGACATGGTCTTACACATAATCACATATCG
* *
21697571 ATGCCAACATCCCGGACATGGTCTTACACA-AGAACACATATCG
1 ATGCCAACGTCCCGGACATGGTCTTACACATA-ATCACATATCG
21697614 A
1 A
21697615 AAATCCTATG
Statistics
Matches: 70, Mismatches: 12, Indels: 10
0.76 0.13 0.11
Matches are distributed among these distances:
42 5 0.07
43 62 0.89
44 3 0.04
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.25
Consensus pattern (43 bp):
ATGCCAACGTCCCGGACATGGTCTTACACATAATCACATATCG
Found at i:21700946 original size:42 final size:43
Alignment explanation
Indices: 21700845--21700989 Score: 156
Period size: 43 Copynumber: 3.4 Consensus size: 43
21700835 AGCTCGTACA
* * *
21700845 ATGCCAACGTCCTAGAC-GTGGTCTTACATGTAAA-CAAATATTG
1 ATGCCAACGTCCCAGACAG-GGTCTTACACGTAAATCAAATA-CG
*
21700888 ATGCC-ACTATCCCAGACAGGGTCTTACACG-AAATCAAATACG
1 ATGCCAAC-GTCCCAGACAGGGTCTTACACGTAAATCAAATACG
* *
21700930 ATGCCAACGTCCCAGACATGGTCTTACAGGTAAATCATAAGT-CG
1 ATGCCAACGTCCCAGACAGGGTCTTACACGTAAATCA-AA-TACG
21700974 ATGCCAACGTCCCAGA
1 ATGCCAACGTCCCAGA
21700990 TGTAGTCTTA
Statistics
Matches: 88, Mismatches: 7, Indels: 13
0.81 0.06 0.12
Matches are distributed among these distances:
42 30 0.34
43 36 0.41
44 21 0.24
45 1 0.01
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.22
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACAGGGTCTTACACGTAAATCAAATACG
Found at i:21715295 original size:3 final size:3
Alignment explanation
Indices: 21715281--21715453 Score: 92
Period size: 3 Copynumber: 59.0 Consensus size: 3
21715271 AAATTGAATC
* * *
21715281 TAA TAC TAA TAA TAA -AA -AA TAA TAA TAA GAA TAA TAA -AA T-A CAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* ** * * * * **
21715325 TAA -AA TAA TAG TAA TCC TAA -AA AAA TAC TAA GAA TAC TAA TGT TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
21715371 TAA TAA AAA GAA TAA TAA TAA CAA TAA TAA TAGA TAA TAA -AA GTAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA -TAA
* * *
21715417 AAA AAA T-A TAA TAA TAAA TGA TAA TAA TAAA TAA TAA
1 TAA TAA TAA TAA TAA T-AA TAA TAA TAA T-AA TAA TAA
21715454 AAAAAAAGAG
Statistics
Matches: 127, Mismatches: 32, Indels: 22
0.70 0.18 0.12
Matches are distributed among these distances:
2 15 0.12
3 101 0.80
4 11 0.09
ACGTcount: A:0.65, C:0.04, G:0.05, T:0.26
Consensus pattern (3 bp):
TAA
Found at i:21715419 original size:40 final size:40
Alignment explanation
Indices: 21715372--21715462 Score: 107
Period size: 43 Copynumber: 2.2 Consensus size: 40
21715362 TAATGTTAAT
*
21715372 AATAAAAAGA-ATAATAATAACA-ATAATAATAGATAATAA
1 AATAAAAAGATATAATAATAA-AGATAATAATAAATAATAA
*
21715411 AAGTAAAAAAAATATAATAATAAATGATAATAATAAATAATAA
1 AA-T-AAAAAGATATAATAATAAA-GATAATAATAAATAATAA
21715454 AA-AAAAAGA
1 AATAAAAAGA
21715463 GGCAAATGGT
Statistics
Matches: 44, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
39 2 0.05
40 7 0.16
41 7 0.16
42 10 0.23
43 18 0.41
ACGTcount: A:0.71, C:0.01, G:0.05, T:0.22
Consensus pattern (40 bp):
AATAAAAAGATATAATAATAAAGATAATAATAAATAATAA
Found at i:21717431 original size:40 final size:40
Alignment explanation
Indices: 21717357--21717528 Score: 190
Period size: 40 Copynumber: 4.3 Consensus size: 40
21717347 GATAACCAGA
* * * *
21717357 CTAAGATCCGAAGGCATTCGTGCGAGTTGCTATATCCGGG
1 CTAAGACCCGAAGGCATTTGTGCTAGTTGTTATATCCGGG
* * *
21717397 CTATGTCCCGAAGGCATTTATGCTAG-TGATTATATCCGGG
1 CTAAGACCCGAAGGCATTTGTGCTAGTTG-TTATATCCGGG
* *
21717437 CTAAGACCTGAAGGCATTTGTG-TGAGTTGCTATATCCGGG
1 CTAAGACCCGAAGGCATTTGTGCT-AGTTGTTATATCCGGG
* *
21717477 CTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT-CTGG
1 CTAAGACCCGAAGGCATTTGTGCTAGTTGTTATATCCGGG
21717516 CTAA-ATCCCGAAG
1 CTAAGA-CCCGAAG
21717529 ATACTTGGGT
Statistics
Matches: 111, Mismatches: 16, Indels: 11
0.80 0.12 0.08
Matches are distributed among these distances:
38 1 0.01
39 17 0.15
40 91 0.82
41 2 0.02
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.28
Consensus pattern (40 bp):
CTAAGACCCGAAGGCATTTGTGCTAGTTGTTATATCCGGG
Found at i:21717490 original size:80 final size:80
Alignment explanation
Indices: 21717357--21717528 Score: 226
Period size: 80 Copynumber: 2.2 Consensus size: 80
21717347 GATAACCAGA
* * *
21717357 CTAAGATCCGAAGGCATTCGTGCGAGTTGCTATATCCGGGCTATGTCCCGAAGGCATTTATGCTA
1 CTAAGATCCGAAGGCATTCGTGCGAGTTGCTATATCCGGGCTAAGACCCGAAGGCATTTATGCGA
21717422 G-TGATTATATCCGGG
66 GTTG-TTATATCCGGG
* * *
21717437 CTAAGA-CCTGAAGGCATTTGTGTGAGTTGCTATATCCGGGCTAAGACCCGAAGGCATTTGTGCG
1 CTAAGATCC-GAAGGCATTCGTGCGAGTTGCTATATCCGGGCTAAGACCCGAAGGCATTTATGCG
*
21717501 AGTTGTTATAT-CTGG
65 AGTTGTTATATCCGGG
21717516 CTAA-ATCCCGAAG
1 CTAAGAT-CCGAAG
21717529 ATACTTGGGT
Statistics
Matches: 81, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
78 1 0.01
79 13 0.16
80 65 0.80
81 2 0.02
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.28
Consensus pattern (80 bp):
CTAAGATCCGAAGGCATTCGTGCGAGTTGCTATATCCGGGCTAAGACCCGAAGGCATTTATGCGA
GTTGTTATATCCGGG
Found at i:21723806 original size:42 final size:42
Alignment explanation
Indices: 21723747--21723832 Score: 172
Period size: 42 Copynumber: 2.0 Consensus size: 42
21723737 AGACAACTCC
21723747 TTCTTATTCCTCAATGTAACTACCTTAATATGCTCTTTTGGA
1 TTCTTATTCCTCAATGTAACTACCTTAATATGCTCTTTTGGA
21723789 TTCTTATTCCTCAATGTAACTACCTTAATATGCTCTTTTGGA
1 TTCTTATTCCTCAATGTAACTACCTTAATATGCTCTTTTGGA
21723831 TT
1 TT
21723833 GGGCTTAGTG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.23, C:0.21, G:0.09, T:0.47
Consensus pattern (42 bp):
TTCTTATTCCTCAATGTAACTACCTTAATATGCTCTTTTGGA
Found at i:21724038 original size:127 final size:128
Alignment explanation
Indices: 21723806--21724059 Score: 492
Period size: 127 Copynumber: 2.0 Consensus size: 128
21723796 TCCTCAATGT
21723806 AACTACCTTAATATGCTCTTTTGGATTGGGCTTAGTGTTACTAGGTAAGCTGCCTTGCTGTCGTT
1 AACTACCTTAATATGCTCTTTTGGATTGGGCTTAGTGTTACTAGGTAAGCTGCCTTGCTGTCGTT
21723871 CTGAAAACAGTTTAGCTAGCTGCCCAATCTAATTTTTGAGCCCATGAATTGATGCTTGCTTAC
66 CTGAAAACAGTTTAGCTAGCTGCCCAATCTAATTTTTGAGCCCATGAATTGATGCTTGCTTAC
*
21723934 AACTA-CTTAATATGCTCTTTTGGATTGGGCTTAGTGTTACTAGGTAAGCTGCCTTGCTGTCTTT
1 AACTACCTTAATATGCTCTTTTGGATTGGGCTTAGTGTTACTAGGTAAGCTGCCTTGCTGTCGTT
21723998 CTGAAAACAGTTTAGCTAGCTGCCCAATCTAATTTTTGAGCCCATGAATTGATGCTTGCTTA
66 CTGAAAACAGTTTAGCTAGCTGCCCAATCTAATTTTTGAGCCCATGAATTGATGCTTGCTTA
21724060 TTTTTCAAAA
Statistics
Matches: 125, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
127 120 0.96
128 5 0.04
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.37
Consensus pattern (128 bp):
AACTACCTTAATATGCTCTTTTGGATTGGGCTTAGTGTTACTAGGTAAGCTGCCTTGCTGTCGTT
CTGAAAACAGTTTAGCTAGCTGCCCAATCTAATTTTTGAGCCCATGAATTGATGCTTGCTTAC
Found at i:21725433 original size:23 final size:23
Alignment explanation
Indices: 21725387--21725433 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
21725377 AAAAGAAAAT
* * * *
21725387 ACAAAAATATAAAATTTAATTAA
1 ACAAAAAAATAAAAGTAAAATAA
21725410 ACAAAAAAATAAAAGTAAAATAA
1 ACAAAAAAATAAAAGTAAAATAA
21725433 A
1 A
21725434 AAATGGCTAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.72, C:0.04, G:0.02, T:0.21
Consensus pattern (23 bp):
ACAAAAAAATAAAAGTAAAATAA
Found at i:21732018 original size:17 final size:18
Alignment explanation
Indices: 21731996--21732037 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
21731986 TTTAGTTTAG
*
21731996 ATTTTAAATTTTAT-TAA
1 ATTTTAAATTTTATAGAA
**
21732013 ATTTTATGTTTTATAGAA
1 ATTTTAAATTTTATAGAA
21732031 ATTTTAA
1 ATTTTAA
21732038 TACTCTAGAA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (18 bp):
ATTTTAAATTTTATAGAA
Found at i:21732968 original size:35 final size:35
Alignment explanation
Indices: 21732906--21732991 Score: 106
Period size: 35 Copynumber: 2.5 Consensus size: 35
21732896 TTTTATTTGT
*
21732906 TTTA-ATTATATAATTAATGATATTTAAA-TATAA
1 TTTATATTATATAATTAATGATAATTAAATTATAA
*
21732939 TTTATATTATATGAATTTATGATAATTAAATTATAA
1 TTTATATTATAT-AATTAATGATAATTAAATTATAA
* *
21732975 -TGATATTATATTATTAA
1 TTTATATTATATAATTAA
21732992 ATAAATCAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
33 4 0.09
34 11 0.24
35 25 0.56
36 5 0.11
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (35 bp):
TTTATATTATATAATTAATGATAATTAAATTATAA
Found at i:21732977 original size:25 final size:23
Alignment explanation
Indices: 21732933--21732993 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 23
21732923 TGATATTTAA
*
21732933 ATATAATTTATATTATATGA-ATTT
1 ATATAA-TTAAATTATATGATA-TT
21732957 ATGATAATTAAATTATAATGATATT
1 AT-ATAATTAAATTAT-ATGATATT
*
21732982 ATATTATTAAAT
1 ATATAATTAAAT
21732994 AAATCAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
24 19 0.59
25 12 0.38
26 1 0.03
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (23 bp):
ATATAATTAAATTATATGATATT
Found at i:21734397 original size:45 final size:45
Alignment explanation
Indices: 21734323--21734419 Score: 113
Period size: 45 Copynumber: 2.2 Consensus size: 45
21734313 GCCGACTACT
* * * *
21734323 GTTATTGTTACCGATTCGACATTTTGTGTGTCGAATACTATTACC
1 GTTATTGTTACAGATTCAACACTTAGTGTGTCGAATACTATTACC
* * * * *
21734368 GTTATTGTTATAGATTCAACACTTAGTGTGTTGAATATTGTTACT
1 GTTATTGTTACAGATTCAACACTTAGTGTGTCGAATACTATTACC
21734413 GTTATTG
1 GTTATTG
21734420 CTACCGTTAT
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.24, C:0.12, G:0.19, T:0.45
Consensus pattern (45 bp):
GTTATTGTTACAGATTCAACACTTAGTGTGTCGAATACTATTACC
Found at i:21766927 original size:30 final size:30
Alignment explanation
Indices: 21766893--21767058 Score: 83
Period size: 30 Copynumber: 5.2 Consensus size: 30
21766883 GACCTGAATG
*
21766893 CATGTTTGACTGTTACTATTTACTGCATGC
1 CATGTTTGACTATTACTATTTACTGCATGC
* *
21766923 CATG-TT-ATTATTATCTGATAAGGTTGACCTGAATG-
1 CATGTTTGACTATTA-CT-AT----TT-A-CTGCATGC
21766958 CATGTTTGACTATTACTATTTACTGCATGC
1 CATGTTTGACTATTACTATTTACTGCATGC
* *
21766988 CATG-TT-ATTATTATCTGATAAGGTTGACTTGAATG-
1 CATGTTTGACTATTA-CT-AT----TT-AC-TGCATGC
*
21767023 CATGTTTGACTGTTACTATTTACTGCATGC
1 CATGTTTGACTATTACTATTTACTGCATGC
*
21767053 TATGTT
1 CATGTT
21767059 ATTATTATTT
Statistics
Matches: 103, Mismatches: 11, Indels: 44
0.65 0.07 0.28
Matches are distributed among these distances:
28 11 0.11
29 19 0.18
30 20 0.19
31 4 0.04
34 4 0.04
35 15 0.15
36 19 0.18
37 11 0.11
ACGTcount: A:0.24, C:0.15, G:0.17, T:0.43
Consensus pattern (30 bp):
CATGTTTGACTATTACTATTTACTGCATGC
Done.