Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032245.1 Gossypioides kirkii chromosome KI_2_4
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: 41238926
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 6100 characters in sequence are not A, C, G, or T
File 126 of 132
Found at i:38909104 original size:17 final size:17
Alignment explanation
Indices: 38909084--38909121 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
38909074 GGGGATTTTT
38909084 ATTTAATATTA-ATTTAA
1 ATTTAATATTATA-TTAA
*
38909101 ATTTATTATTATATTAA
1 ATTTAATATTATATTAA
38909118 ATTT
1 ATTT
38909122 TTAATTGTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 18 0.95
18 1 0.05
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
ATTTAATATTATATTAA
Found at i:38911996 original size:38 final size:38
Alignment explanation
Indices: 38911954--38912031 Score: 138
Period size: 38 Copynumber: 2.1 Consensus size: 38
38911944 GATTCAATTG
*
38911954 GTTCCAAATAATTCATTCGAAAATTGGTTTAATTTTTA
1 GTTCCAAATAATTCACTCGAAAATTGGTTTAATTTTTA
*
38911992 GTTCCAAATAATTCACTCGACAATTGGTTTAATTTTTA
1 GTTCCAAATAATTCACTCGAAAATTGGTTTAATTTTTA
38912030 GT
1 GT
38912032 CTGAATCAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.32, C:0.13, G:0.12, T:0.44
Consensus pattern (38 bp):
GTTCCAAATAATTCACTCGAAAATTGGTTTAATTTTTA
Found at i:38914681 original size:32 final size:32
Alignment explanation
Indices: 38914644--38914708 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
38914634 ATTGGGAGTG
38914644 TTATCTACCTTAAGACTATTCTTTGTCAGTTA
1 TTATCTACCTTAAGACTATTCTTTGTCAGTTA
* *
38914676 TTATCTATCTTAAGACTATTCTTTGTCGGTTA
1 TTATCTACCTTAAGACTATTCTTTGTCAGTTA
38914708 T
1 T
38914709 CATGTGATGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.23, C:0.17, G:0.11, T:0.49
Consensus pattern (32 bp):
TTATCTACCTTAAGACTATTCTTTGTCAGTTA
Found at i:38916310 original size:3 final size:3
Alignment explanation
Indices: 38916302--38916329 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
38916292 AATTTAACAA
38916302 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
38916330 GTGTTGACAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:38920923 original size:21 final size:20
Alignment explanation
Indices: 38920893--38920931 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
38920883 CAATTCTATT
*
38920893 TTTATTATTATTTTTATTTA
1 TTTATTATTATTATTATTTA
38920913 TTTATTTATTATTATTATT
1 TTTA-TTATTATTATTATT
38920932 ATGAACATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (20 bp):
TTTATTATTATTATTATTTA
Found at i:38920979 original size:67 final size:66
Alignment explanation
Indices: 38920897--38921082 Score: 234
Period size: 67 Copynumber: 2.8 Consensus size: 66
38920887 TCTATTTTTA
*
38920897 TTATTATTTTTATTTATTTATTTATTATTATTAT-TATGAACATAAATAAATATAAAATAATATT
1 TTATT-TTATTATTTATTTATTTATTATTATTATATAT-AA-ATAAATAAATATAAAATAATATT
38920961 AATT
63 AATT
*
38920965 TTATTTTATTATTTATTTATTTATTATT-TTATGAATATAAATAAATAAATGTAAAATAATATTA
1 TTATTTTATTATTTATTTATTTATTATTATTAT--ATATAAATAAATAAATATAAAATAATATTA
38921029 ATT
64 ATT
* * * *
38921032 TT-GTTTATTTATTTATTTATTTATTGTTATAAATAAATAAATAAATAAATA
1 TTATTTTA-TTATTTATTTATTTATTATTAT-TATATATAAATAAATAAATA
38921083 ACAAACCAAA
Statistics
Matches: 105, Mismatches: 7, Indels: 13
0.84 0.06 0.10
Matches are distributed among these distances:
66 8 0.08
67 84 0.80
68 8 0.08
69 5 0.05
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.54
Consensus pattern (66 bp):
TTATTTTATTATTTATTTATTTATTATTATTATATATAAATAAATAAATATAAAATAATATTAAT
T
Found at i:38926123 original size:6 final size:6
Alignment explanation
Indices: 38926114--38926167 Score: 67
Period size: 6 Copynumber: 9.0 Consensus size: 6
38926104 TAAAAAATTA
*
38926114 AAAAAG -AAAA- AAAAAG AAAAAG AAAAGG AAAAAG AAGAAAAG AAAAAG
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG -A-AAAAG AAAAAG
38926162 AAAAAG
1 AAAAAG
38926168 GGGAGGTCGA
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
5 8 0.19
6 27 0.64
7 2 0.05
8 5 0.12
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:38926127 original size:17 final size:15
Alignment explanation
Indices: 38926092--38926167 Score: 71
Period size: 16 Copynumber: 4.7 Consensus size: 15
38926082 AAGAAATTTC
38926092 AAAAAAAAAAGATAAA
1 AAAAAAAAAAGA-AAA
*
38926108 AAATTAAAAAAGAAAA
1 AAA-AAAAAAAGAAAA
38926124 AAAAAGAAAAAGAAAA
1 AAAAA-AAAAAGAAAA
** *
38926140 GGAAAAAGAAGAAAA
1 AAAAAAAAAAGAAAA
38926155 GAAAAAGAAAAAG
1 -AAAAA-AAAAAG
38926168 GGGAGGTCGA
Statistics
Matches: 48, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
15 10 0.21
16 25 0.52
17 13 0.27
ACGTcount: A:0.82, C:0.00, G:0.14, T:0.04
Consensus pattern (15 bp):
AAAAAAAAAAGAAAA
Found at i:38926145 original size:20 final size:20
Alignment explanation
Indices: 38926114--38926167 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
38926104 TAAAAAATTA
*
38926114 AAAAAGAAAAAAAAAGAAAAAG
1 AAAAAG-AAAAAGAAG-AAAAG
*
38926136 AAAAGGAAAAAGAAGAAAAG
1 AAAAAGAAAAAGAAGAAAAG
38926156 AAAAAGAAAAAG
1 AAAAAGAAAAAG
38926168 GGGAGGTCGA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 16 0.55
21 8 0.28
22 5 0.17
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (20 bp):
AAAAAGAAAAAGAAGAAAAG
Found at i:38926151 original size:15 final size:14
Alignment explanation
Indices: 38926114--38926163 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
38926104 TAAAAAATTA
38926114 AAAAAGAA-AAAA-
1 AAAAAGAAGAAAAG
*
38926126 AAAGAAAAAGAAAAGG
1 AAA-AAGAAGAAAA-G
38926142 AAAAAGAAGAAAAG
1 AAAAAGAAGAAAAG
38926156 AAAAAGAA
1 AAAAAGAA
38926164 AAAGGGGAGG
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
12 3 0.09
13 4 0.12
14 13 0.41
15 9 0.28
16 3 0.09
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (14 bp):
AAAAAGAAGAAAAG
Found at i:38927157 original size:50 final size:50
Alignment explanation
Indices: 38927089--38927252 Score: 172
Period size: 50 Copynumber: 3.3 Consensus size: 50
38927079 TTTTTTACCT
* * *
38927089 CTAAAGTTATAGATGTGCAAATTGAAACTGCAATGACAAATCTCATACAC
1 CTAAAGCTGTAGAGGTGCAAATTGAAACTGCAATGACAAATCTCATACAC
* * *
38927139 CTAAAGCTGTGGAGGTGCAAATTG-AACCGCAATGGA-AAATCTCATATAC
1 CTAAAGCTGTAGAGGTGCAAATTGAAACTGCAAT-GACAAATCTCATACAC
* * * * *
38927188 CTAAAGCTGTAGAGGGGCAGAA-TGAAGCTGTAATGGCAAATCTCATTCAC
1 CTAAAGCTGTAGAGGTGCA-AATTGAAACTGCAATGACAAATCTCATACAC
* *
38927238 TTAAAGCTATAGAGG
1 CTAAAGCTGTAGAGG
38927253 AGAAGATTGA
Statistics
Matches: 94, Mismatches: 16, Indels: 8
0.80 0.14 0.07
Matches are distributed among these distances:
49 40 0.43
50 54 0.57
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.24
Consensus pattern (50 bp):
CTAAAGCTGTAGAGGTGCAAATTGAAACTGCAATGACAAATCTCATACAC
Found at i:38927494 original size:44 final size:42
Alignment explanation
Indices: 38927438--38927563 Score: 125
Period size: 44 Copynumber: 3.0 Consensus size: 42
38927428 ATTGAAGACC
38927438 ATCCGATCTTTTACCTCGATCATGGGGCAGATTGAAGAAATGAA
1 ATCCGATCTTTTACC-CGATCATGGGGCAGATTGAAGAAAT-AA
* * * **
38927482 ATCCAATCTTTTACCCTAAC-TAGAGGGCAAGATTGAAG--A-CC
1 ATCCGATCTTTTACCCGATCAT-G-GGGC-AGATTGAAGAAATAA
38927523 ATCCGATCTTTTACCCCGATCATGGGGCAGATTGAAGAAAT
1 ATCCGATCTTTTA-CCCGATCATGGGGCAGATTGAAGAAAT
38927564 CCAATCTTTT
Statistics
Matches: 66, Mismatches: 8, Indels: 17
0.73 0.09 0.19
Matches are distributed among these distances:
40 9 0.14
41 16 0.24
42 8 0.12
43 6 0.09
44 18 0.27
45 9 0.14
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (42 bp):
ATCCGATCTTTTACCCGATCATGGGGCAGATTGAAGAAATAA
Found at i:38927635 original size:80 final size:80
Alignment explanation
Indices: 38927318--38927607 Score: 454
Period size: 80 Copynumber: 3.6 Consensus size: 80
38927308 AGTTACAACC
* * * *
38927318 TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAAACCATCCGGTCTTTTACCCCGATAATGG
1 TCCAATCTTTTACCCTAACTAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGG
*
38927383 GGTAGATTGAAGAAA
66 GGCAGATTGAAGAAA
* * * *
38927398 TCCAATCTTTTACCCTAACCAGATGGCAAAATTGAAGACCATCCGATCTTTTACCTCGATCATGG
1 TCCAATCTTTTACCCTAACTAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGG
38927463 GGCAGATTGAAGAAATGAAA
66 GGCAGATT---G-AA-GAAA
38927483 TCCAATCTTTTACCCTAACTAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGG
1 TCCAATCTTTTACCCTAACTAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGG
38927548 GGCAGATTGAAGAAA
66 GGCAGATTGAAGAAA
38927563 TCCAATCTTTTACCCTAACTAGAGGGCAAGATTGAAGACCATCCG
1 TCCAATCTTTTACCCTAACTAGAGGGCAAGATTGAAGACCATCCG
38927608 TGTAACATCC
Statistics
Matches: 194, Mismatches: 11, Indels: 10
0.90 0.05 0.05
Matches are distributed among these distances:
80 115 0.59
81 2 0.01
82 1 0.01
83 1 0.01
84 2 0.01
85 73 0.38
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.25
Consensus pattern (80 bp):
TCCAATCTTTTACCCTAACTAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGG
GGCAGATTGAAGAAA
Found at i:38929270 original size:23 final size:22
Alignment explanation
Indices: 38929241--38929362 Score: 127
Period size: 23 Copynumber: 5.4 Consensus size: 22
38929231 CTAGCGCATT
*
38929241 TACTGTTTCGCACTTTGTGTGCT
1 TACTGTTT-GCACTTTGTGTGCC
*
38929264 TACTGTTTCGCACCTTGTGTGCC
1 TACTGTTT-GCACTTTGTGTGCC
* * *
38929287 TACTGATTTGCGCTATGTGCGCC
1 TACTG-TTTGCACTTTGTGTGCC
* *
38929310 TACTGATTGCACTGTGTGTGCC
1 TACTGTTTGCACTTTGTGTGCC
* *
38929332 TACTGGATTGCACTTTGTGTGCT
1 TACT-GTTTGCACTTTGTGTGCC
38929355 TACTGTTT
1 TACTGTTT
38929363 CCCCAGCACT
Statistics
Matches: 84, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
22 20 0.24
23 61 0.73
24 3 0.04
ACGTcount: A:0.11, C:0.23, G:0.24, T:0.42
Consensus pattern (22 bp):
TACTGTTTGCACTTTGTGTGCC
Found at i:38929359 original size:45 final size:46
Alignment explanation
Indices: 38929241--38929359 Score: 138
Period size: 45 Copynumber: 2.6 Consensus size: 46
38929231 CTAGCGCATT
*
38929241 TACTG-TTTCGCACTTTGTGTGCTTACTGTTTCGCACCTTGTGTGCC
1 TACTGATTT-GCACTTTGTGTGCTTACTGATTCGCACCTTGTGTGCC
* * * *
38929287 TACTGATTTGCGCTATGTGCGCCTACTGATT-GCA-CTGTGTGTGCC
1 TACTGATTTGCACTTTGTGTGCTTACTGATTCGCACCT-TGTGTGCC
38929332 TACTGGA-TTGCACTTTGTGTGCTTACTG
1 TACT-GATTTGCACTTTGTGTGCTTACTG
38929360 TTTCCCCAGC
Statistics
Matches: 61, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
44 2 0.03
45 32 0.52
46 24 0.39
47 3 0.05
ACGTcount: A:0.12, C:0.24, G:0.24, T:0.40
Consensus pattern (46 bp):
TACTGATTTGCACTTTGTGTGCTTACTGATTCGCACCTTGTGTGCC
Found at i:38930347 original size:80 final size:80
Alignment explanation
Indices: 38930210--38930902 Score: 1131
Period size: 80 Copynumber: 8.7 Consensus size: 80
38930200 AGGTGTTACA
* * *
38930210 ATCCGATCTTTTACCTCGATTATGGGGTAGATTGAAGAAATCTAATCTTTTACCCTAACCAGAGG
1 ATCCGATCTTTTACCCCGATCATGGGGCAGATTGAAGAAATCTAATCTTTTACCCTAACCAGAGG
38930275 GCAAGATTGAAGACC
66 GCAAGATTGAAGACC
* *
38930290 ATCTGATCTTTTACCCCGATCATGGGGCAGATTGAAGAAATCCAATCTTTTACCCTAACCAGAGG
1 ATCCGATCTTTTACCCCGATCATGGGGCAGATTGAAGAAATCTAATCTTTTACCCTAACCAGAGG
38930355 GCAAGATTGAAGACC
66 GCAAGATTGAAGACC
* ** *
38930370 ATCCGATCTTTTACCCCAATCATAAGGCAGATTGAAGAAATCTAATCTTTTATCCTAACCAGAGG
1 ATCCGATCTTTTACCCCGATCATGGGGCAGATTGAAGAAATCTAATCTTTTACCCTAACCAGAGG
*
38930435 GCAAGATTAAAGACC
66 GCAAGATTGAAGACC
*
38930450 ATCCGATCTTTTACCCCGATTATGGGGCAGATTGAAGAAATCTAATCTTTTACCCTAACCAGAGG
1 ATCCGATCTTTTACCCCGATCATGGGGCAGATTGAAGAAATCTAATCTTTTACCCTAACCAGAGG
38930515 GCAAGATTGAAGACC
66 GCAAGATTGAAGACC
* *
38930530 ATCCGATCTTTTACCCCAATCATGGGGCAGATTGAAGAAATCCAATCTTTTACCCTAACCAGAGG
1 ATCCGATCTTTTACCCCGATCATGGGGCAGATTGAAGAAATCTAATCTTTTACCCTAACCAGAGG
38930595 GCAAGATTGAAGACC
66 GCAAGATTGAAGACC
* * *
38930610 ATCCGATCTTTTACTCCGATCATGGGGCAAATTGAAGAAATCTAATCTTTTACCCTAACTAGAGG
1 ATCCGATCTTTTACCCCGATCATGGGGCAGATTGAAGAAATCTAATCTTTTACCCTAACCAGAGG
*
38930675 GCAAGATTAAAGACC
66 GCAAGATTGAAGACC
* *
38930690 ATCCGATCTTTTACCCCGATCATGAGGCAGATTGAAGAAATCTAATC-TTTACCCTAACTAGAGG
1 ATCCGATCTTTTACCCCGATCATGGGGCAGATTGAAGAAATCTAATCTTTTACCCTAACCAGAGG
38930754 GCAAGATTGAAGACC
66 GCAAGATTGAAGACC
* *
38930769 ATCCGATCTTTTACCCTGATCATGTGGCAGATTGAAGAAATCTAATCTTTTACCCTAACCAGAGG
1 ATCCGATCTTTTACCCCGATCATGGGGCAGATTGAAGAAATCTAATCTTTTACCCTAACCAGAGG
38930834 GC-AGATTGAAGACC
66 GCAAGATTGAAGACC
* * * *
38930848 ATCAGATCTCTTACCCCGACCATGGGGTAGATTGAA-ACAATCTAATCTTTTACCC
1 ATCCGATCTTTTACCCCGATCATGGGGCAGATTGAAGA-AATCTAATCTTTTACCC
38930903 CTAAAGTTAT
Statistics
Matches: 571, Mismatches: 40, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
78 1 0.00
79 135 0.24
80 435 0.76
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (80 bp):
ATCCGATCTTTTACCCCGATCATGGGGCAGATTGAAGAAATCTAATCTTTTACCCTAACCAGAGG
GCAAGATTGAAGACC
Found at i:38930955 original size:50 final size:50
Alignment explanation
Indices: 38930891--38931025 Score: 216
Period size: 50 Copynumber: 2.7 Consensus size: 50
38930881 GAAACAATCT
* * * *
38930891 AATCTTTTACCCCTAAAGTTATAAAGGGGCAGATTGAAGCTACAAAACCA
1 AATCTTATACCCCTAAAATAATAGAGGGGCAGATTGAAGCTACAAAACCA
*
38930941 AATCTTATAGCCCTAAAATAATAGAGGGGCAGATTGAAGCTACAAAACCA
1 AATCTTATACCCCTAAAATAATAGAGGGGCAGATTGAAGCTACAAAACCA
*
38930991 AATCTTATACCCCTAAAATAATAGAGGGGTAGATT
1 AATCTTATACCCCTAAAATAATAGAGGGGCAGATT
38931026 AAAACTCACA
Statistics
Matches: 78, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 78 1.00
ACGTcount: A:0.41, C:0.18, G:0.17, T:0.24
Consensus pattern (50 bp):
AATCTTATACCCCTAAAATAATAGAGGGGCAGATTGAAGCTACAAAACCA
Found at i:38931579 original size:63 final size:64
Alignment explanation
Indices: 38931485--38931638 Score: 231
Period size: 67 Copynumber: 2.4 Consensus size: 64
38931475 TTCTTATCAT
38931485 TTTTATTTATTTATTTATTATTATTTTTATGAACATAAATAAAT-A-TAAAATAATATTAATTTT
1 TTTTA-TTATTTATTTATTATTA-TTTTATGAACATAAATAAATAAGTAAAATAATATTAATTTT
38931548 A
64 A
*
38931549 TTTTATTATTTATTTATTTATTATTTTATGAATATAAATAAATAAATGTAAAATAATATTAATTT
1 TTTTATTATTTATTTA-TTATTATTTTATGAACATAAATAAAT-AA-GTAAAATAATATTAATTT
*
38931614 TG
63 TA
38931616 TTTTATTATTTATTTATTATTAT
1 TTTTATTATTTATTTATTATTAT
38931639 AAACAAATAA
Statistics
Matches: 83, Mismatches: 2, Indels: 8
0.89 0.02 0.09
Matches are distributed among these distances:
63 30 0.36
64 11 0.13
65 1 0.01
66 7 0.08
67 34 0.41
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.57
Consensus pattern (64 bp):
TTTTATTATTTATTTATTATTATTTTATGAACATAAATAAATAAGTAAAATAATATTAATTTTA
Found at i:38931649 original size:63 final size:66
Alignment explanation
Indices: 38931487--38931655 Score: 202
Period size: 67 Copynumber: 2.6 Consensus size: 66
38931477 CTTATCATTT
****
38931487 TTATTTATTTATTTATTATT-ATTTTTATGAACATAAATAAATATAAAATAATATTAATTTTATT
1 TTATTTATTTATTTATTATTAAACAATAT-AA-ATAAATAAATATAAAATAATATTAATTTTATT
38931551 TTA
64 TTA
* ** * *
38931554 TTATTTATTTATTTATTATTTTATGAATATAAATAAATAAATGTAAAATAATATTAATTTTGTTT
1 TTATTTATTTATTTATTA-TTAAACAATATAAATAAATAAATATAAAATAATATTAATTTTATTT
38931619 TA
65 TA
38931621 TTATTTATTTA-TTATTA-TAAACAA-ATAAATAAATA
1 TTATTTATTTATTTATTATTAAACAATATAAATAAATA
38931656 TCAAACCAAA
Statistics
Matches: 92, Mismatches: 8, Indels: 8
0.85 0.07 0.07
Matches are distributed among these distances:
63 11 0.12
64 4 0.04
66 6 0.07
67 62 0.67
68 4 0.04
69 5 0.05
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (66 bp):
TTATTTATTTATTTATTATTAAACAATATAAATAAATAAATATAAAATAATATTAATTTTATTTT
A
Found at i:38933870 original size:18 final size:19
Alignment explanation
Indices: 38933847--38933882 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
38933837 AGATCAAAAA
38933847 ATCAATTTAA-AAATAAAC
1 ATCAATTTAATAAATAAAC
38933865 ATCAATTTAATAAATAAA
1 ATCAATTTAATAAATAAA
38933883 TTCTTAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.61, C:0.08, G:0.00, T:0.31
Consensus pattern (19 bp):
ATCAATTTAATAAATAAAC
Found at i:38934238 original size:15 final size:15
Alignment explanation
Indices: 38934218--38934256 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
38934208 CAAAGCTTTG
38934218 AAGATTAAAAGTAGA
1 AAGATTAAAAGTAGA
38934233 AAGATTAAAAGTAGA
1 AAGATTAAAAGTAGA
*
38934248 AATATTAAA
1 AAGATTAAA
38934257 TTTTAAATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.62, C:0.00, G:0.15, T:0.23
Consensus pattern (15 bp):
AAGATTAAAAGTAGA
Found at i:38936782 original size:21 final size:23
Alignment explanation
Indices: 38936756--38936802 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
38936746 TAACCGTTAA
*
38936756 TTTCTT-AAAAGGATCGATT-TT
1 TTTCTTCAAAAGGATCAATTCTT
*
38936777 TTTCTTCAAAATGATCAATTCTT
1 TTTCTTCAAAAGGATCAATTCTT
38936800 TTT
1 TTT
38936803 GTTTGAACTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 6 0.27
22 11 0.50
23 5 0.23
ACGTcount: A:0.28, C:0.13, G:0.09, T:0.51
Consensus pattern (23 bp):
TTTCTTCAAAAGGATCAATTCTT
Found at i:38953054 original size:24 final size:23
Alignment explanation
Indices: 38953023--38953090 Score: 64
Period size: 27 Copynumber: 2.8 Consensus size: 23
38953013 GCTGTTTTGA
38953023 TGTTTTTTTTACTATTTTGATGC
1 TGTTTTTTTTACTATTTTGATGC
** *
38953046 TGTTGTTTTTATTGTTATTTTTGCTGC
1 TG-T-TTTTT-TTACTA-TTTTGATGC
*
38953073 TGTTTTTGTTACTATTTT
1 TGTTTTTTTTACTATTTT
38953091 TGTTGATTTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
23 6 0.17
24 5 0.14
25 9 0.26
26 5 0.14
27 10 0.29
ACGTcount: A:0.10, C:0.07, G:0.15, T:0.68
Consensus pattern (23 bp):
TGTTTTTTTTACTATTTTGATGC
Found at i:38953067 original size:27 final size:26
Alignment explanation
Indices: 38953037--38953134 Score: 81
Period size: 27 Copynumber: 3.6 Consensus size: 26
38953027 TTTTTTACTA
38953037 TTTTGATGCTGTTGTTTTTATTGTTAT
1 TTTTGATGCTGTT-TTTTTATTGTTAT
* * *
38953064 TTTTGCTGCTGTTTTTGTTACTATT-T
1 TTTTGATGCTGTTTTT-TTATTGTTAT
**
38953090 TTGTTGATTTTGTTATTGTTTTATTGTTAT
1 TT-TTGATGCTG-T-TT-TTTTATTGTTAT
*
38953120 TTTTGCTGCTGTTTT
1 TTTTGATGCTGTTTT
38953135 GGTTATTATT
Statistics
Matches: 54, Mismatches: 11, Indels: 13
0.69 0.14 0.17
Matches are distributed among these distances:
26 7 0.13
27 26 0.48
28 2 0.04
29 14 0.26
30 5 0.09
ACGTcount: A:0.09, C:0.06, G:0.17, T:0.67
Consensus pattern (26 bp):
TTTTGATGCTGTTTTTTTATTGTTAT
Found at i:38953091 original size:24 final size:24
Alignment explanation
Indices: 38953023--38953092 Score: 77
Period size: 24 Copynumber: 2.8 Consensus size: 24
38953013 GCTGTTTTGA
* *
38953023 TGTTTTTTTTACTATTTTGATGCTGT
1 TGTTTTTATTACTATTTT--TGCTGC
**
38953049 TGTTTTTATTGTTATTTTTGCTGC
1 TGTTTTTATTACTATTTTTGCTGC
*
38953073 TGTTTTTGTTACTATTTTTG
1 TGTTTTTATTACTATTTTTG
38953093 TTGATTTTGT
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
24 22 0.59
26 15 0.41
ACGTcount: A:0.10, C:0.07, G:0.16, T:0.67
Consensus pattern (24 bp):
TGTTTTTATTACTATTTTTGCTGC
Found at i:38953213 original size:11 final size:11
Alignment explanation
Indices: 38953174--38953217 Score: 54
Period size: 11 Copynumber: 4.1 Consensus size: 11
38953164 TTTTATGCGT
*
38953174 TTTTACTATTA
1 TTTTAATATTA
*
38953185 TTTTACTATT-
1 TTTTAATATTA
38953195 TTTTAATATTA
1 TTTTAATATTA
*
38953206 TTTGAATATTA
1 TTTTAATATTA
38953217 T
1 T
38953218 AGAACTTATG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
10 9 0.30
11 21 0.70
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.64
Consensus pattern (11 bp):
TTTTAATATTA
Found at i:38953215 original size:21 final size:21
Alignment explanation
Indices: 38953173--38953215 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
38953163 TTTTTATGCG
* * *
38953173 TTTTTACTATTATTTTACTAT
1 TTTTTAATATTATTTGAATAT
38953194 TTTTTAATATTATTTGAATAT
1 TTTTTAATATTATTTGAATAT
38953215 T
1 T
38953216 ATAGAACTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.65
Consensus pattern (21 bp):
TTTTTAATATTATTTGAATAT
Found at i:38974832 original size:46 final size:45
Alignment explanation
Indices: 38974775--38974865 Score: 119
Period size: 46 Copynumber: 2.0 Consensus size: 45
38974765 AGGGAAATAA
* *
38974775 AAACCTAATATAATAAGGAAAATAACTAAAACAAAAACTCTTAATT
1 AAACCTAATATAATAAAGAAAATAAATAAAACAAAAACTC-TAATT
* * * *
38974821 AAACCTGATATAATAAAGAAATTAAATAAATCTAAAACTCTAATT
1 AAACCTAATATAATAAAGAAAATAAATAAAACAAAAACTCTAATT
38974866 GCAATAAAGT
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
45 5 0.13
46 34 0.87
ACGTcount: A:0.57, C:0.12, G:0.04, T:0.26
Consensus pattern (45 bp):
AAACCTAATATAATAAAGAAAATAAATAAAACAAAAACTCTAATT
Found at i:38997636 original size:90 final size:85
Alignment explanation
Indices: 38997485--38997659 Score: 296
Period size: 90 Copynumber: 2.0 Consensus size: 85
38997475 TGTACATAAA
38997485 GTCGAACATGTTATATCCTTATGGCTTAGCAACCCTTCTTTTATTATGCCATGTCGTCTTTGATA
1 GTCGAACATGTTATATCCTTATGGCTTAGCAACCCTTCTTTTATTATGCCATGTCGTCTTTGATA
38997550 ATAGCGAGCCGTGTAATTTT
66 ATAGCGAGCCGTGTAATTTT
38997570 GTCGAACATGTTATATCCTTATGGCTTGCTCAGCAACCCTTTCTTTTATTATGCCATGTCGTCTT
1 GTCGAACATGTTATATCCTTATGGC-T--T-AGCAACCC-TTCTTTTATTATGCCATGTCGTCTT
*
38997635 TGATAATCGCGAGCCGTGTAATTTT
61 TGATAATAGCGAGCCGTGTAATTTT
38997660 ATGTTGTGCT
Statistics
Matches: 84, Mismatches: 1, Indels: 5
0.93 0.01 0.06
Matches are distributed among these distances:
85 25 0.30
86 1 0.01
88 1 0.01
89 8 0.10
90 49 0.58
ACGTcount: A:0.21, C:0.21, G:0.18, T:0.40
Consensus pattern (85 bp):
GTCGAACATGTTATATCCTTATGGCTTAGCAACCCTTCTTTTATTATGCCATGTCGTCTTTGATA
ATAGCGAGCCGTGTAATTTT
Found at i:39003235 original size:13 final size:13
Alignment explanation
Indices: 39003219--39003244 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
39003209 ATTTCGGCTC
39003219 TTAAAATTTAAAT
1 TTAAAATTTAAAT
39003232 TTAAAATTTAAAT
1 TTAAAATTTAAAT
39003245 GAACATATCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
TTAAAATTTAAAT
Found at i:39003867 original size:24 final size:24
Alignment explanation
Indices: 39003813--39003867 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 24
39003803 ATAATATTTG
*
39003813 ATACCTAAACAAATGTCAAGTTTAG
1 ATACC-AAACAAATGTCAAGTTTAA
**
39003838 GCACCAAA-AAATGTCAAGTTTTAA
1 ATACCAAACAAATGTCAAG-TTTAA
39003862 ATACCA
1 ATACCA
39003868 TTTCTTCACG
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
23 10 0.42
24 11 0.46
25 3 0.12
ACGTcount: A:0.45, C:0.18, G:0.11, T:0.25
Consensus pattern (24 bp):
ATACCAAACAAATGTCAAGTTTAA
Found at i:39003945 original size:39 final size:39
Alignment explanation
Indices: 39003891--39003969 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
39003881 AGCCAAATAG
39003891 ACATTATATTTAGAATCATCAGAAAGGACCTTAATAATC
1 ACATTATATTTAGAATCATCAGAAAGGACCTTAATAATC
39003930 ACATTATATTTAGAATCATCAGAAAGGACCTTAATAATC
1 ACATTATATTTAGAATCATCAGAAAGGACCTTAATAATC
39003969 A
1 A
39003970 TACTTTTCCA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.44, C:0.15, G:0.10, T:0.30
Consensus pattern (39 bp):
ACATTATATTTAGAATCATCAGAAAGGACCTTAATAATC
Found at i:39007880 original size:33 final size:33
Alignment explanation
Indices: 39007838--39007904 Score: 100
Period size: 33 Copynumber: 2.0 Consensus size: 33
39007828 TCATCTCCTA
**
39007838 AAAAGTCATAC-AAAGTCATTTTGGTTACTTTAG
1 AAAAGTCATACTAAA-TCATTAGGGTTACTTTAG
39007871 AAAAGTCATACTAAATCATTAGGGTTACTTTAG
1 AAAAGTCATACTAAATCATTAGGGTTACTTTAG
39007904 A
1 A
39007905 TAAACTAAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
33 28 0.90
34 3 0.10
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.34
Consensus pattern (33 bp):
AAAAGTCATACTAAATCATTAGGGTTACTTTAG
Found at i:39015370 original size:21 final size:21
Alignment explanation
Indices: 39015346--39015393 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
39015336 AATCAGCTCG
*
39015346 AAAAA-AAAGAGAATCTAAGT
1 AAAAATAAAAAGAATCTAAGT
*
39015366 AAAAATAAAAAGAATTTAAGT
1 AAAAATAAAAAGAATCTAAGT
39015387 AAAAATA
1 AAAAATA
39015394 TAGTTTCAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 5 0.20
21 20 0.80
ACGTcount: A:0.69, C:0.02, G:0.10, T:0.19
Consensus pattern (21 bp):
AAAAATAAAAAGAATCTAAGT
Found at i:39028775 original size:21 final size:22
Alignment explanation
Indices: 39028749--39028794 Score: 69
Period size: 21 Copynumber: 2.1 Consensus size: 22
39028739 ATATTATTTT
39028749 AAACCCAAATCCC-TTT-AAATA
1 AAACCCAAA-CCCTTTTAAAATA
39028770 AAACCCAAACCCTTTTAAAATA
1 AAACCCAAACCCTTTTAAAATA
39028792 AAA
1 AAA
39028795 ACGCAAGCCC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 3 0.13
21 12 0.52
22 8 0.35
ACGTcount: A:0.52, C:0.26, G:0.00, T:0.22
Consensus pattern (22 bp):
AAACCCAAACCCTTTTAAAATA
Found at i:39031927 original size:21 final size:21
Alignment explanation
Indices: 39031901--39031948 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
39031891 TTTGAAACTA
39031901 TATTTTTACTTAAATTCTCTT
1 TATTTTTACTTAAATTCTCTT
* *
39031922 TATTTTTACTTAGATTTTCTT
1 TATTTTTACTTAAATTCTCTT
39031943 T-TTTTT
1 TATTTTT
39031949 CGGGCTGATT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 5 0.20
21 20 0.80
ACGTcount: A:0.19, C:0.10, G:0.02, T:0.69
Consensus pattern (21 bp):
TATTTTTACTTAAATTCTCTT
Found at i:39034151 original size:76 final size:76
Alignment explanation
Indices: 39034041--39034190 Score: 282
Period size: 76 Copynumber: 2.0 Consensus size: 76
39034031 GAGGGTATGA
*
39034041 GAGAGAGAAAGGGTTCACGGGCTAAAATATTTTCCTTGGAAATATAATCTGTGATAAGTCTGTTG
1 GAGAGAGAAAGGGTTCACGGGCTAAAATATTTTCCTTGGAAATATAATCCGTGATAAGTCTGTTG
39034106 GTATTGGCAGC
66 GTATTGGCAGC
39034117 GAGAGAGAAAGGGTTCACGGGCTAAAATATTTTCCTTGGAAATATAATCCGTGATAAGTCTGTTG
1 GAGAGAGAAAGGGTTCACGGGCTAAAATATTTTCCTTGGAAATATAATCCGTGATAAGTCTGTTG
*
39034182 GTGTTGGCA
66 GTATTGGCA
39034191 AGTAAGGGTC
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
76 72 1.00
ACGTcount: A:0.30, C:0.12, G:0.28, T:0.30
Consensus pattern (76 bp):
GAGAGAGAAAGGGTTCACGGGCTAAAATATTTTCCTTGGAAATATAATCCGTGATAAGTCTGTTG
GTATTGGCAGC
Found at i:39051192 original size:12 final size:13
Alignment explanation
Indices: 39051162--39051195 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
39051152 TATAACGAGA
39051162 AAATCAATTTTTGT
1 AAAT-AATTTTTGT
39051176 AAATAATTTTTGT
1 AAATAATTTTTGT
39051189 -AATAATT
1 AAATAATT
39051196 CTTTATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 7 0.35
13 9 0.45
14 4 0.20
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (13 bp):
AAATAATTTTTGT
Found at i:39051417 original size:32 final size:32
Alignment explanation
Indices: 39051362--39051463 Score: 127
Period size: 32 Copynumber: 3.2 Consensus size: 32
39051352 TTTTTCTGAA
* *
39051362 TAATCATCT-ATAAATAGACATAATTATTCAAG
1 TAAT-ATCTCATAAATATATATAATTATTCAAG
*
39051394 TAATATCTCTTAAATATATATAATTATTCAAG
1 TAATATCTCATAAATATATATAATTATTCAAG
* *
39051426 TAACATCTCATAAAT-TAATATAACTATTCAAG
1 TAATATCTCATAAATAT-ATATAATTATTCAAG
39051458 TAATAT
1 TAATAT
39051464 TATTTAAATA
Statistics
Matches: 61, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
31 5 0.08
32 56 0.92
ACGTcount: A:0.46, C:0.12, G:0.04, T:0.38
Consensus pattern (32 bp):
TAATATCTCATAAATATATATAATTATTCAAG
Found at i:39051472 original size:32 final size:31
Alignment explanation
Indices: 39051362--39051482 Score: 122
Period size: 32 Copynumber: 3.8 Consensus size: 31
39051352 TTTTTCTGAA
*
39051362 TAATCATCTA-TAAATAGACATAATTATTCAAG
1 TAAT-ATCTATTAAATA-ATATAATTATTCAAG
*
39051394 TAATATCTCTTAAATATATATAATTATTCAAG
1 TAATATCTATTAAATA-ATATAATTATTCAAG
* *
39051426 TAACATCTCA-TAAATTAATATAACTATTCAAG
1 TAATATCT-ATTAAA-TAATATAATTATTCAAG
39051458 TAATAT-TATTTAAATAATTATAATT
1 TAATATCTA-TTAAATAA-TATAATT
39051483 CTTTATTAAA
Statistics
Matches: 75, Mismatches: 8, Indels: 12
0.79 0.08 0.13
Matches are distributed among these distances:
30 1 0.01
31 8 0.11
32 64 0.85
33 2 0.03
ACGTcount: A:0.46, C:0.10, G:0.03, T:0.40
Consensus pattern (31 bp):
TAATATCTATTAAATAATATAATTATTCAAG
Found at i:39063360 original size:12 final size:12
Alignment explanation
Indices: 39063343--39063368 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
39063333 GTAATGGAAC
39063343 AAAAAAAAAAAG
1 AAAAAAAAAAAG
39063355 AAAAAAAAAAAG
1 AAAAAAAAAAAG
39063367 AA
1 AA
39063369 GATTATCATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAAG
Found at i:39064253 original size:21 final size:21
Alignment explanation
Indices: 39064208--39064253 Score: 62
Period size: 19 Copynumber: 2.3 Consensus size: 21
39064198 TATTTTTTTA
39064208 TATT-TTAAATATTAAGATTT
1 TATTGTTAAATATTAAGATTT
39064228 T-TTGTTAAA-ATTAAGATATT
1 TATTGTTAAATATTAAGAT-TT
39064248 TATTGT
1 TATTGT
39064254 CAACAATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
19 10 0.43
20 9 0.39
21 4 0.17
ACGTcount: A:0.37, C:0.00, G:0.09, T:0.54
Consensus pattern (21 bp):
TATTGTTAAATATTAAGATTT
Found at i:39072669 original size:133 final size:134
Alignment explanation
Indices: 39072430--39072690 Score: 382
Period size: 133 Copynumber: 2.0 Consensus size: 134
39072420 GTTGAAACAC
* * * * *
39072430 GTTTATCCTTCTATTTAAATGTTAGGATGGGTTATGGGTAATTCTAAGCTTTGTATCAACTTAAA
1 GTTTATCCTCCTATTTAAAGGTTAGGATGAGCTATGAGTAATTCTAAGCTTTGTATCAACTTAAA
* *
39072495 AACTTTCATATACTTTCACAATTGAATTAGGCGTAGCGTCCAAATTCCATTCATCGATAAAAACT
66 AACTTTCAAATACTTTCACAATTGAATTAGGCGTAACGTCCAAATTCCATTCATCGATAAAAACT
39072560 TTTA
131 TTTA
* * * *
39072564 GTTTATCCTCCTATTTAAAGGTTGGGATGAGCTATGAGTAGTTCTAAG-TATTG-ATTAACTTAG
1 GTTTATCCTCCTATTTAAAGGTTAGGATGAGCTATGAGTAATTCTAAGCT-TTGTATCAACTTAA
* *
39072627 AAACTTTCAAATACTTTCACAATTGAATTAGGTGTAACGTCCAAATTCCATTTATCGATAAAAA
65 AAACTTTCAAATACTTTCACAATTGAATTAGGCGTAACGTCCAAATTCCATTCATCGATAAAAA
39072691 TTCTAAAAGA
Statistics
Matches: 113, Mismatches: 13, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
133 69 0.61
134 44 0.39
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.38
Consensus pattern (134 bp):
GTTTATCCTCCTATTTAAAGGTTAGGATGAGCTATGAGTAATTCTAAGCTTTGTATCAACTTAAA
AACTTTCAAATACTTTCACAATTGAATTAGGCGTAACGTCCAAATTCCATTCATCGATAAAAACT
TTTA
Found at i:39083371 original size:2 final size:2
Alignment explanation
Indices: 39083364--39083388 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
39083354 AATTAATAAG
39083364 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
39083389 ATAGAGTAAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:39085157 original size:17 final size:19
Alignment explanation
Indices: 39085137--39085171 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
39085127 CATCATCTAG
39085137 TACCA-TCAAA-AATCTTT
1 TACCATTCAAACAATCTTT
39085154 TACCATTCAAACAATCTT
1 TACCATTCAAACAATCTT
39085172 GCAAAACTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 5 0.31
19 6 0.38
ACGTcount: A:0.40, C:0.26, G:0.00, T:0.34
Consensus pattern (19 bp):
TACCATTCAAACAATCTTT
Found at i:39094405 original size:29 final size:30
Alignment explanation
Indices: 39094378--39094442 Score: 78
Period size: 30 Copynumber: 2.1 Consensus size: 30
39094368 TCTATACATG
39094378 AATTTTGATTTT-TTACAATTGTACACATTA
1 AATTTTGATTTTATT-CAATTGTACACATTA
* *
39094408 AATTTTTATTTTAATTCAATTGTACATATTTA
1 AATTTTGATTTT-ATTCAATTGTACACA-TTA
39094440 AAT
1 AAT
39094443 AAATGAATAC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
30 11 0.37
31 11 0.37
32 8 0.27
ACGTcount: A:0.35, C:0.08, G:0.05, T:0.52
Consensus pattern (30 bp):
AATTTTGATTTTATTCAATTGTACACATTA
Found at i:39098418 original size:17 final size:19
Alignment explanation
Indices: 39098398--39098432 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
39098388 CATCATCTAG
39098398 TACCA-TCAAA-AATCTTT
1 TACCATTCAAACAATCTTT
39098415 TACCATTCAAACAATCTT
1 TACCATTCAAACAATCTT
39098433 GCAAAACTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 5 0.31
19 6 0.38
ACGTcount: A:0.40, C:0.26, G:0.00, T:0.34
Consensus pattern (19 bp):
TACCATTCAAACAATCTTT
Found at i:39099826 original size:21 final size:19
Alignment explanation
Indices: 39099794--39099863 Score: 74
Period size: 18 Copynumber: 3.7 Consensus size: 19
39099784 GATAAAATAA
39099794 TAATAAA-ATAATTTAAAC
1 TAATAAATATAATTTAAAC
*
39099812 TAATCAAAATTTAATTTAAAC
1 TAAT--AAATATAATTTAAAC
*
39099833 AAATAAATATAATTT-AAC
1 TAATAAATATAATTTAAAC
*
39099851 TAAAAAAT-TAATT
1 TAATAAATATAATT
39099864 CTCAAATTTG
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
17 5 0.11
18 13 0.30
19 10 0.23
20 3 0.07
21 13 0.30
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.36
Consensus pattern (19 bp):
TAATAAATATAATTTAAAC
Found at i:39100825 original size:15 final size:14
Alignment explanation
Indices: 39100801--39100836 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
39100791 TAATCTTTCA
39100801 AAAAATATTATAAT
1 AAAAATATTATAAT
39100815 AAAAATCATTATAAT
1 AAAAAT-ATTATAAT
*
39100830 TAAAATA
1 AAAAATA
39100837 ATTTCAGAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (14 bp):
AAAAATATTATAAT
Found at i:39104276 original size:31 final size:31
Alignment explanation
Indices: 39104232--39104316 Score: 143
Period size: 31 Copynumber: 2.7 Consensus size: 31
39104222 ACTCAACTTT
39104232 GAAAATGTGACAAAACAGTCATTAATGTTATC
1 GAAAA-GTGACAAAACAGTCATTAATGTTATC
* *
39104264 GAAAAGTAACAAAACAGTCACTAATGTTATC
1 GAAAAGTGACAAAACAGTCATTAATGTTATC
39104295 GAAAAGTGACAAAACAGTCATT
1 GAAAAGTGACAAAACAGTCATT
39104317 GAAATTAGAT
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
31 44 0.90
32 5 0.10
ACGTcount: A:0.47, C:0.14, G:0.15, T:0.24
Consensus pattern (31 bp):
GAAAAGTGACAAAACAGTCATTAATGTTATC
Found at i:39104710 original size:47 final size:46
Alignment explanation
Indices: 39104659--39104823 Score: 136
Period size: 47 Copynumber: 3.5 Consensus size: 46
39104649 ATTAATTGTG
* * *
39104659 ATTTTTTATTTAAGGTT-TATTCGATTTTGATTTGGATTTTGATTTTC
1 ATTTTTGATTTAGGGTTAT-TTCAATTTTGA-TTGGATTTTGATTTTC
*
39104706 ATTTTTGATTTAGGGTTATTTCAATTTTGATTGGATTTTGATTGCTAC
1 ATTTTTGATTTAGGGTTATTTCAATTTTGATTGGATTTTGATT--TTC
** * ** * *
39104754 TATTTGAGATTTAGGGTTATTTAAATTTTTG-TTTTATTTTTTATTTAC
1 -ATTTTTGATTTAGGGTTATTTCAA-TTTTGATTGGA-TTTTGATTTTC
*
39104802 ATATTTTGGTTTAGGGTTATTT
1 AT-TTTTGATTTAGGGTTATTT
39104824 TGATTAACGT
Statistics
Matches: 98, Mismatches: 13, Indels: 13
0.79 0.10 0.10
Matches are distributed among these distances:
46 13 0.13
47 27 0.28
48 22 0.22
49 24 0.24
50 12 0.12
ACGTcount: A:0.21, C:0.04, G:0.16, T:0.59
Consensus pattern (46 bp):
ATTTTTGATTTAGGGTTATTTCAATTTTGATTGGATTTTGATTTTC
Found at i:39104807 original size:49 final size:48
Alignment explanation
Indices: 39104682--39104823 Score: 134
Period size: 49 Copynumber: 3.0 Consensus size: 48
39104672 GGTTTATTCG
* * *
39104682 ATTTTGATTTGGATTTTGATT-TTC-ATTTTTGATTTAGGGTTATTTCA
1 ATTTTGA-TTGGATTTTGATTCTACTATTTTGGATTTAGGGTTATTTAA
39104729 ATTTTGATTGGATTTTGATTGCTACTA-TTTGAGATTTAGGGTTATTTAA
1 ATTTTGATTGGATTTTGATT-CTACTATTTTG-GATTTAGGGTTATTTAA
** *
39104778 ATTTTTG-TTTTATTTTTTATT-TACATATTTTGG-TTTAGGGTTATTT
1 A-TTTTGATTGGA-TTTTGATTCTAC-TATTTTGGATTTAGGGTTATTT
39104824 TGATTAACGT
Statistics
Matches: 81, Mismatches: 6, Indels: 15
0.79 0.06 0.15
Matches are distributed among these distances:
46 13 0.16
47 7 0.09
48 21 0.26
49 24 0.30
50 16 0.20
ACGTcount: A:0.20, C:0.04, G:0.17, T:0.59
Consensus pattern (48 bp):
ATTTTGATTGGATTTTGATTCTACTATTTTGGATTTAGGGTTATTTAA
Found at i:39104821 original size:24 final size:23
Alignment explanation
Indices: 39104763--39104823 Score: 59
Period size: 24 Copynumber: 2.6 Consensus size: 23
39104753 CTATTTGAGA
*
39104763 TTTAGGGTTATTTAAATTTTTGT
1 TTTAGGGTTATTTAAATTTTTGG
*** *
39104786 TTTATTTTTTATTTACATATTTTGG
1 TTTA-GGGTTATTTAAAT-TTTTGG
39104811 TTTAGGGTTATTT
1 TTTAGGGTTATTT
39104824 TGATTAACGT
Statistics
Matches: 28, Mismatches: 8, Indels: 3
0.72 0.21 0.08
Matches are distributed among these distances:
23 4 0.14
24 15 0.54
25 9 0.32
ACGTcount: A:0.20, C:0.02, G:0.15, T:0.64
Consensus pattern (23 bp):
TTTAGGGTTATTTAAATTTTTGG
Found at i:39110844 original size:18 final size:19
Alignment explanation
Indices: 39110823--39110864 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
39110813 CTTAAAGTCT
*
39110823 TTAAAAACTACAAA-ATTA
1 TTAAAAACTAAAAACATTA
39110841 TTAAAAACTAAAAACATTA
1 TTAAAAACTAAAAACATTA
39110860 -TAAAA
1 TTAAAA
39110865 TTAAAAAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 18 0.82
19 4 0.18
ACGTcount: A:0.64, C:0.10, G:0.00, T:0.26
Consensus pattern (19 bp):
TTAAAAACTAAAAACATTA
Found at i:39110869 original size:17 final size:16
Alignment explanation
Indices: 39110823--39110871 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
39110813 CTTAAAGTCT
*
39110823 TTAAAAACTACAAAATTA
1 TTAAAAACTA-AAAA-CA
39110841 TTAAAAACTAAAAACA
1 TTAAAAACTAAAAACA
*
39110857 TTATAAAATTAAAAA
1 TTA-AAAACTAAAAA
39110872 AACAATATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 4 0.14
17 14 0.50
18 10 0.36
ACGTcount: A:0.65, C:0.08, G:0.00, T:0.27
Consensus pattern (16 bp):
TTAAAAACTAAAAACA
Found at i:39110872 original size:19 final size:21
Alignment explanation
Indices: 39110850--39110899 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
39110840 ATTAAAAACT
39110850 AAAAACATTAT-AAAAT-TAA
1 AAAAACATTATAAAAATATAA
*
39110869 AAAAACAATATAAAAATATAA
1 AAAAACATTATAAAAATATAA
*
39110890 AAAAATATTA
1 AAAAACATTA
39110900 GAAATGTAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 10 0.38
20 5 0.19
21 11 0.42
ACGTcount: A:0.72, C:0.04, G:0.00, T:0.24
Consensus pattern (21 bp):
AAAAACATTATAAAAATATAA
Found at i:39110884 original size:20 final size:20
Alignment explanation
Indices: 39110850--39110894 Score: 65
Period size: 19 Copynumber: 2.2 Consensus size: 20
39110840 ATTAAAAACT
*
39110850 AAAAACATTATAAAAT-TAA
1 AAAAACAATATAAAATATAA
39110869 AAAAACAATATAAAAATATAA
1 AAAAACAATAT-AAAATATAA
39110890 AAAAA
1 AAAAA
39110895 TATTAGAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 10 0.43
20 5 0.22
21 8 0.35
ACGTcount: A:0.76, C:0.04, G:0.00, T:0.20
Consensus pattern (20 bp):
AAAAACAATATAAAATATAA
Found at i:39112108 original size:16 final size:15
Alignment explanation
Indices: 39112068--39112109 Score: 54
Period size: 14 Copynumber: 2.9 Consensus size: 15
39112058 GAAAATTTAA
39112068 TAAAAATAAATAAAT
1 TAAAAATAAATAAAT
39112083 T-AAAAT--ATAAAT
1 TAAAAATAAATAAAT
39112095 GTAAAAATAAATAAA
1 -TAAAAATAAATAAA
39112110 AGAAGAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
12 6 0.26
13 1 0.04
14 10 0.43
15 1 0.04
16 5 0.22
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.26
Consensus pattern (15 bp):
TAAAAATAAATAAAT
Found at i:39112120 original size:28 final size:28
Alignment explanation
Indices: 39112068--39112121 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
39112058 GAAAATTTAA
**
39112068 TAAAAATAAATAAATTAAAATATAAATG
1 TAAAAATAAATAAAAGAAAATATAAATG
39112096 TAAAAATAAATAAAAGAAGAA-ATAAA
1 TAAAAATAAATAAAAGAA-AATATAAA
39112122 AAAATTGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 21 0.91
29 2 0.09
ACGTcount: A:0.72, C:0.00, G:0.06, T:0.22
Consensus pattern (28 bp):
TAAAAATAAATAAAAGAAAATATAAATG
Found at i:39120629 original size:20 final size:21
Alignment explanation
Indices: 39120594--39120634 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
39120584 GACCATCTAA
* *
39120594 ATAATAATCCATTAAGGAAAT
1 ATAATAATCAATTAAGCAAAT
39120615 ATAAT-ATCAATTAAGCAAAT
1 ATAATAATCAATTAAGCAAAT
39120635 TTCCATGGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.54, C:0.10, G:0.07, T:0.29
Consensus pattern (21 bp):
ATAATAATCAATTAAGCAAAT
Found at i:39121847 original size:9 final size:9
Alignment explanation
Indices: 39121833--39121871 Score: 55
Period size: 9 Copynumber: 4.4 Consensus size: 9
39121823 CTTTATACTT
39121833 TTTTAATAA
1 TTTTAATAA
39121842 TTTTAATAA
1 TTTTAATAA
39121851 TTCTT-A-AA
1 TT-TTAATAA
39121859 TTTTAATAA
1 TTTTAATAA
39121868 TTTT
1 TTTT
39121872 TATATTTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
7 2 0.07
8 5 0.19
9 18 0.67
10 2 0.07
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (9 bp):
TTTTAATAA
Found at i:39121862 original size:17 final size:17
Alignment explanation
Indices: 39121840--39121879 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
39121830 CTTTTTTAAT
39121840 AATTTTAATAATTCTTA
1 AATTTTAATAATTCTTA
*
39121857 AATTTTAATAATTTTTA
1 AATTTTAATAATTCTTA
*
39121874 TATTTT
1 AATTTT
39121880 TTTGAATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (17 bp):
AATTTTAATAATTCTTA
Found at i:39123145 original size:2 final size:2
Alignment explanation
Indices: 39123138--39123165 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
39123128 TGCATTAATA
39123138 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
39123166 GGCGTTAAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39124287 original size:29 final size:30
Alignment explanation
Indices: 39124255--39124311 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
39124245 TGATTTAATC
*
39124255 TGCAATTGTACACATGAAATTTT-ATTTTG
1 TGCAATTGTACACATAAAATTTTGATTTTG
* *
39124284 TGCAATTTTATACATAAAATTTTGATTT
1 TGCAATTGTACACATAAAATTTTGATTT
39124312 GATTCAATTC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 20 0.83
30 4 0.17
ACGTcount: A:0.33, C:0.09, G:0.11, T:0.47
Consensus pattern (30 bp):
TGCAATTGTACACATAAAATTTTGATTTTG
Found at i:39124599 original size:3 final size:3
Alignment explanation
Indices: 39124591--39124626 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
39124581 AATAGGACGC
39124591 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
39124627 TTGTAATTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:39127586 original size:164 final size:160
Alignment explanation
Indices: 39127311--39127606 Score: 461
Period size: 164 Copynumber: 1.8 Consensus size: 160
39127301 TTAACGTGGA
* * * *
39127311 AAATATGTTATCGTATGTGTAATGTTATATCAATTTGTCAGTTTCACATGTTACTAAAAATCTAG
1 AAATATATTATCGTATGTGTAATGTTATATCAACTTGTCAATTTCACATGTTACTAAAAATCTAA
39127376 TTCATGGATTAGCGACGATCATTTGCATGAAGATTGAAAGTTTGAAATTCAAATTGCATAGGGAT
66 TTCATGGATTAGCGACGATCATTTGCATGAAGATTGAAAGTTTGAAATTCAAATTGCATAGGGAT
39127441 TTAGGATTATTCAATTGGAGAATATGGAGT
131 TTAGGATTATTCAATTGGAGAATATGGAGT
* *
39127471 AAATATATTATCGTATGTGTAATGTTATATCAGCTTGTTAATTTCACATGTTACTCATTAAAAAT
1 AAATATATTATCGTATGTGTAATGTTATATCAACTTGTCAATTTCACATGTTA--C--TAAAAAT
*
39127536 CTAATT-AGTGGATTAGCGACTG-TCATTTGCATGAAGATTGAAATTTTGAAATTCAAATTGCAT
62 CTAATTCA-TGGATTAGCGAC-GATCATTTGCATGAAGATTGAAAGTTTGAAATTCAAATTGCAT
39127599 AGGGATTT
125 AGGGATTT
39127607 CTATTATCGT
Statistics
Matches: 123, Mismatches: 7, Indels: 8
0.89 0.05 0.06
Matches are distributed among these distances:
160 48 0.39
162 1 0.01
163 1 0.01
164 72 0.59
165 1 0.01
ACGTcount: A:0.34, C:0.10, G:0.18, T:0.38
Consensus pattern (160 bp):
AAATATATTATCGTATGTGTAATGTTATATCAACTTGTCAATTTCACATGTTACTAAAAATCTAA
TTCATGGATTAGCGACGATCATTTGCATGAAGATTGAAAGTTTGAAATTCAAATTGCATAGGGAT
TTAGGATTATTCAATTGGAGAATATGGAGT
Found at i:39127713 original size:132 final size:132
Alignment explanation
Indices: 39127476--39127738 Score: 384
Period size: 132 Copynumber: 2.0 Consensus size: 132
39127466 GGAGTAAATA
* * *
39127476 TATTATCGTATGTGTAATGTTATATCAGCTTGTTAATTTCACATGTTACTCATTAAAAATCTAAT
1 TATTATCGTATGTGTAATGTTATATCAACTTGTTAATTTCACATGTTACACACTAAAAATCTAAT
* * * * * **
39127541 TAGTGGATTAGCGACTGTCATTTGCATGAAGATTGAAATTTTGAAATTCAAATTGCATAGGGATT
66 TAATGGATTAACGACTGTCATTTGCATGAAGATGGAAATTTTAAAATGCAAAAAGCATAGGGATT
39127606 TC
131 TC
* *
39127608 TATTATCGTATGTGTAATGTTATATCAACTTGTTGATTTCACATGTTACACACTAAAAATCTAGT
1 TATTATCGTATGTGTAATGTTATATCAACTTGTTAATTTCACATGTTACACACTAAAAATCTAAT
* *
39127673 TAATGGATTAACGA-TCGTCATTTGTATGAAGATGGAAATTTTAAAATGCAAAAAGCTTAGGGAT
66 TAATGGATTAACGACT-GTCATTTGCATGAAGATGGAAATTTTAAAATGCAAAAAGCATAGGGAT
39127737 TT
130 TT
39127739 AGGATGATTC
Statistics
Matches: 116, Mismatches: 14, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
131 1 0.01
132 115 0.99
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.39
Consensus pattern (132 bp):
TATTATCGTATGTGTAATGTTATATCAACTTGTTAATTTCACATGTTACACACTAAAAATCTAAT
TAATGGATTAACGACTGTCATTTGCATGAAGATGGAAATTTTAAAATGCAAAAAGCATAGGGATT
TC
Found at i:39127855 original size:296 final size:292
Alignment explanation
Indices: 39127318--39127897 Score: 851
Period size: 296 Copynumber: 2.0 Consensus size: 292
39127308 GGAAAATATG
* *
39127318 TTATCGTATGTGTAATGTTATATCAATTTGTCAGTTTCACATGTTACTAAAAATCTAGTTCATGG
1 TTATCGTATGTGTAATGTTATATCAACTTGTCAGTTTCACATGTTACTAAAAATCTAGTTAATGG
* * * * **
39127383 ATTAGCGACGATCATTTGCATGAAGATTGAAAGTTTGAAATTCAAATTGCATAGGGATTTAGGAT
66 ATTAACGACGATCATTTGCATGAAGATGGAAAGTTTAAAATGCAAAAAGCATAGGGATTTAGGAT
* * *
39127448 TATTCAATTGGAGAATATGGAGTAAATATATTATCGTATGTGTAATGTTATATCAGCTTGTTAAT
131 GATTCAATTGGAGAATATGGACTAAATATATTATCGTATGTGTAATGTTATATCACCTTGTTAAT
* *
39127513 TTCACATGTTACTCATTAAAAATCTAATTAGTGGATTAGCGACTGTCATTTGCATGAAGATTGAA
196 TTCACATGTTACTCACTAAAAATCTAATTAATGGATTAGCGACTGTCATTTGCATGAAGATTGAA
* *
39127578 ATTTTGAAATTCAAATTGCATAGGGATTTCTA
261 AATTTAAAATTCAAATTGCATAGGGATTTCTA
*
39127610 TTATCGTATGTGTAATGTTATATCAACTTGT-TGATTTCACATGTTACACACTAAAAATCTAGTT
1 TTATCGTATGTGTAATGTTATATCAACTTGTCAG-TTTCACATGTT----ACTAAAAATCTAGTT
* * *
39127674 AATGGATTAACGATCG-TCATTTGTATGAAGATGGAAATTTTAAAATGCAAAAAGCTTAGGGATT
61 AATGGATTAACGA-CGATCATTTGCATGAAGATGGAAAGTTTAAAATGCAAAAAGCATAGGGATT
* * *
39127738 TAGGATGATTCAATTGGAGAGTATGGACTAAATCTATTATCGTGTGTGTAATGTGT-TATCACCT
125 TAGGATGATTCAATTGGAGAATATGGACTAAATATATTATCGTATGTGTAATGT-TATATCACCT
* * *
39127802 TGTTAATTTCACATGTTACTCACTAAAAATTTAGTTAATGGATTAGTGACTGTCATTTGCATGAA
189 TGTTAATTTCACATGTTACTCACTAAAAATCTAATTAATGGATTAGCGACTGTCATTTGCATGAA
39127867 GATTGAAAATTTAAAATTCAAATTGCATAGG
254 GATTGAAAATTTAAAATTCAAATTGCATAGG
39127898 AATCTAGAAT
Statistics
Matches: 256, Mismatches: 25, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
291 1 0.00
292 41 0.16
296 211 0.82
297 3 0.01
ACGTcount: A:0.34, C:0.11, G:0.18, T:0.38
Consensus pattern (292 bp):
TTATCGTATGTGTAATGTTATATCAACTTGTCAGTTTCACATGTTACTAAAAATCTAGTTAATGG
ATTAACGACGATCATTTGCATGAAGATGGAAAGTTTAAAATGCAAAAAGCATAGGGATTTAGGAT
GATTCAATTGGAGAATATGGACTAAATATATTATCGTATGTGTAATGTTATATCACCTTGTTAAT
TTCACATGTTACTCACTAAAAATCTAATTAATGGATTAGCGACTGTCATTTGCATGAAGATTGAA
AATTTAAAATTCAAATTGCATAGGGATTTCTA
Found at i:39127882 original size:164 final size:164
Alignment explanation
Indices: 39127606--39127938 Score: 445
Period size: 164 Copynumber: 2.0 Consensus size: 164
39127596 CATAGGGATT
*
39127606 TCTATTATCGTATGTGTAATGTTATATCAACTTGTTGATTTCACATGTTACACACTAAAAATCTA
1 TCTATTATCGTATGTGTAATGTTATATCAACTTGTTAATTTCACATGTTACACACTAAAAATCTA
* * * *
39127671 GTTAATGGATTAACGATCGTCATTTGTATGAAGATGGAAATTTTAAAATGCAAAAAGCTTAGGGA
66 GTTAATGGATTAACGATCGTCATTTGCATGAAGATGGAAAATTTAAAATGCAAAAAGCATAGGAA
* * * * *
39127736 TTTAGGATGATTCAATTGGAGAGTATGGACTAAA
131 TCTAGAATGATTCAATCGGAGAATATGGACGAAA
* * * *
39127770 TCTATTATCGTGTGTGTAATGTGT-TATCACCTTGTTAATTTCACATGTTACTCACTAAAAATTT
1 TCTATTATCGTATGTGTAATGT-TATATCAACTTGTTAATTTCACATGTTACACACTAAAAATCT
** * * **
39127834 AGTTAATGGATTAGTGA-CTGTCATTTGCATGAAGATTGAAAATTTAAAATTCAAATTGCATAGG
65 AGTTAATGGATTAACGATC-GTCATTTGCATGAAGATGGAAAATTTAAAATGCAAAAAGCATAGG
*
39127898 AATCTAGAATGATTCAATCGGATAATATGGACGAAA
129 AATCTAGAATGATTCAATCGGAGAATATGGACGAAA
39127934 TCTAT
1 TCTAT
39127939 AGCTATACAC
Statistics
Matches: 146, Mismatches: 21, Indels: 4
0.85 0.12 0.02
Matches are distributed among these distances:
163 1 0.01
164 144 0.99
165 1 0.01
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.36
Consensus pattern (164 bp):
TCTATTATCGTATGTGTAATGTTATATCAACTTGTTAATTTCACATGTTACACACTAAAAATCTA
GTTAATGGATTAACGATCGTCATTTGCATGAAGATGGAAAATTTAAAATGCAAAAAGCATAGGAA
TCTAGAATGATTCAATCGGAGAATATGGACGAAA
Found at i:39128063 original size:31 final size:31
Alignment explanation
Indices: 39128026--39128086 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
39128016 GATTTGAAAT
*
39128026 ATATAAAGATTAAAATTAAT-AAATTCAAAAA
1 ATATAAAGACTAAAATTAATCAAATT-AAAAA
*
39128057 ATATAAATACTAAAATTAATCAAATTAAAA
1 ATATAAAGACTAAAATTAATCAAATTAAAA
39128087 CACAAGGACT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 22 0.81
32 5 0.19
ACGTcount: A:0.64, C:0.05, G:0.02, T:0.30
Consensus pattern (31 bp):
ATATAAAGACTAAAATTAATCAAATTAAAAA
Found at i:39132031 original size:22 final size:21
Alignment explanation
Indices: 39131974--39132034 Score: 58
Period size: 20 Copynumber: 2.9 Consensus size: 21
39131964 TCTATCCATA
39131974 ATTAAATTTAAA-TAATAAA-A-
1 ATTAAA-TTAAATTAA-AAATAT
39131994 ATTAAATTAAATTAAAAATAT
1 ATTAAATTAAATTAAAAATAT
39132015 ATTAATATT-AATATAAAAAT
1 ATTAA-ATTAAAT-TAAAAAT
39132035 GCATTTCTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
19 8 0.22
20 10 0.28
21 8 0.22
22 10 0.28
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
ATTAAATTAAATTAAAAATAT
Found at i:39133120 original size:149 final size:149
Alignment explanation
Indices: 39132845--39133125 Score: 337
Period size: 149 Copynumber: 1.9 Consensus size: 149
39132835 TTGAATTTTT
* * * * * * *
39132845 AAAAAATAAGTGGTAAATTTTTATTTGGGTAGTTCATATCATAAATGCGTGAGCATTAATTTTAA
1 AAAAAACAAGTGGTAAACTTTTATTTCGGTAGTTCATACCATAAATACATGAGCATTAACTTTAA
** * * * * * * *
39132910 TTAGTAGTTGTCAATTGAGTTTTAATTCGGTTGATATTAGTATTAGTGTCAATGTACGAGGACGG
66 TTAACAATTGTCAATTGAATCTTAATTCGATTGACATGAGTATTAATGTCAATGTACGAGGACGG
39132975 GAGTTCAAATATGATTCTG
131 GAGTTCAAATATGATTCTG
* * * *
39132994 AAAAAACAAGTGGTAAGCTTTTATTTCGGTAGTTCTTACCATAAGTACATGAGTATTAACTTTAA
1 AAAAAACAAGTGGTAAACTTTTATTTCGGTAGTTCATACCATAAATACATGAGCATTAACTTTAA
* * * * *
39133059 TTAACAATTGTCGATTGAATCTTAGTTCGATTGGCATGGGTATTAATGTCAATGTAGGAGGACGG
66 TTAACAATTGTCAATTGAATCTTAATTCGATTGACATGAGTATTAATGTCAATGTACGAGGACGG
39133124 GA
131 GA
39133126 TTCGAGAGTG
Statistics
Matches: 107, Mismatches: 25, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
149 107 1.00
ACGTcount: A:0.32, C:0.09, G:0.22, T:0.37
Consensus pattern (149 bp):
AAAAAACAAGTGGTAAACTTTTATTTCGGTAGTTCATACCATAAATACATGAGCATTAACTTTAA
TTAACAATTGTCAATTGAATCTTAATTCGATTGACATGAGTATTAATGTCAATGTACGAGGACGG
GAGTTCAAATATGATTCTG
Found at i:39134255 original size:24 final size:24
Alignment explanation
Indices: 39134192--39134261 Score: 77
Period size: 24 Copynumber: 2.9 Consensus size: 24
39134182 AATTAATTTG
**
39134192 TATATTTTTATAATAATAAAAAAA
1 TATATTTTTATAATTTTAAAAAAA
* * * *
39134216 TATAATTTTATTATTTTAATAAAT
1 TATATTTTTATAATTTTAAAAAAA
*
39134240 TATATTTTTATAATTTTTAAAA
1 TATATTTTTATAATTTTAAAAA
39134262 GATTAAATCA
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (24 bp):
TATATTTTTATAATTTTAAAAAAA
Found at i:39137000 original size:41 final size:41
Alignment explanation
Indices: 39136941--39137177 Score: 271
Period size: 41 Copynumber: 5.8 Consensus size: 41
39136931 AAACGCTGCA
* *
39136941 AAAGGT-AGAGCAATAGCGGCGCTTATGGGAAAGCGCCGCT
1 AAAGGTCAGAGCAATAGCGACGCTTATGGGAAAGTGCCGCT
* * * **
39136981 AAAGGTCAGAACAATAGCGGCGCTTATGTGAAAGTGTTGCT
1 AAAGGTCAGAGCAATAGCGACGCTTATGGGAAAGTGCCGCT
* * *
39137022 CAAGGTCA-ACGCAATAGCGATGCTTATGGGCAAGTGCCGCT
1 AAAGGTCAGA-GCAATAGCGACGCTTATGGGAAAGTGCCGCT
* * *
39137063 AAAGGTCAGAGCAATAGCGGCGCTTATGTGAAAGTGTCGCT
1 AAAGGTCAGAGCAATAGCGACGCTTATGGGAAAGTGCCGCT
* * * *
39137104 CAAGGTCAGAGCAATAGCAACGCTTATGGGCAAGCGCCGCT
1 AAAGGTCAGAGCAATAGCGACGCTTATGGGAAAGTGCCGCT
* * *
39137145 AAAGGTCAGAGCATTAGCGACACTTATGTGAAA
1 AAAGGTCAGAGCAATAGCGACGCTTATGGGAAA
39137178 AACACCTCTA
Statistics
Matches: 162, Mismatches: 32, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
40 7 0.04
41 154 0.95
42 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.30, T:0.19
Consensus pattern (41 bp):
AAAGGTCAGAGCAATAGCGACGCTTATGGGAAAGTGCCGCT
Found at i:39137048 original size:82 final size:82
Alignment explanation
Indices: 39136942--39137177 Score: 359
Period size: 82 Copynumber: 2.9 Consensus size: 82
39136932 AACGCTGCAA
* * *
39136942 AAGGT-AGAGCAATAGCGGCGCTTATGGGAAAGCGCCGCTAAAGGTCAGAACAATAGCGGCGCTT
1 AAGGTCAGAGCAATAGCGACGCTTATGGGCAAGCGCCGCTAAAGGTCAGAGCAATAGCGGCGCTT
*
39137006 ATGTGAAAGTGTTGCTC
66 ATGTGAAAGTGTCGCTC
* *
39137023 AAGGTCA-ACGCAATAGCGATGCTTATGGGCAAGTGCCGCTAAAGGTCAGAGCAATAGCGGCGCT
1 AAGGTCAGA-GCAATAGCGACGCTTATGGGCAAGCGCCGCTAAAGGTCAGAGCAATAGCGGCGCT
39137087 TATGTGAAAGTGTCGCTC
65 TATGTGAAAGTGTCGCTC
* * * *
39137105 AAGGTCAGAGCAATAGCAACGCTTATGGGCAAGCGCCGCTAAAGGTCAGAGCATTAGCGACACTT
1 AAGGTCAGAGCAATAGCGACGCTTATGGGCAAGCGCCGCTAAAGGTCAGAGCAATAGCGGCGCTT
39137170 ATGTGAAA
66 ATGTGAAA
39137178 AACACCTCTA
Statistics
Matches: 140, Mismatches: 12, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
81 6 0.04
82 133 0.95
83 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.30, T:0.19
Consensus pattern (82 bp):
AAGGTCAGAGCAATAGCGACGCTTATGGGCAAGCGCCGCTAAAGGTCAGAGCAATAGCGGCGCTT
ATGTGAAAGTGTCGCTC
Found at i:39138509 original size:15 final size:15
Alignment explanation
Indices: 39138489--39138517 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
39138479 TACTTTCTAC
39138489 TAATTAATATTTTTG
1 TAATTAATATTTTTG
39138504 TAATTAATATTTTT
1 TAATTAATATTTTT
39138518 CCTACTATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (15 bp):
TAATTAATATTTTTG
Found at i:39139513 original size:42 final size:42
Alignment explanation
Indices: 39139466--39139605 Score: 174
Period size: 42 Copynumber: 3.3 Consensus size: 42
39139456 AATCTATTAA
* *
39139466 CTTTAGCGGCGTTTGTGGGTAAAAGCTGCTAAAGACTATGTT
1 CTTTAGCGGCGTTTGTGGGTAAACGCTGCTAAAGACCATGTT
* * * * * *
39139508 CTTTAGCGACGTTTATGGGGAAGCGCCGCTAAAGACCATATT
1 CTTTAGCGGCGTTTGTGGGTAAACGCTGCTAAAGACCATGTT
* *
39139550 CTTTAACGGCGTTTGT-AGTAAAGCGCTGCTAAAGACCATGTT
1 CTTTAGCGGCGTTTGTGGGTAAA-CGCTGCTAAAGACCATGTT
39139592 CTTTAGCGGCGTTT
1 CTTTAGCGGCGTTT
39139606 TTCCTCATAA
Statistics
Matches: 80, Mismatches: 17, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
41 3 0.04
42 77 0.96
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.31
Consensus pattern (42 bp):
CTTTAGCGGCGTTTGTGGGTAAACGCTGCTAAAGACCATGTT
Found at i:39141301 original size:15 final size:14
Alignment explanation
Indices: 39141277--39141307 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
39141267 GTGGACATGG
39141277 AAGTTTTAGGTTAT
1 AAGTTTTAGGTTAT
39141291 AAGTATTTAGGTTAT
1 AAGT-TTTAGGTTAT
39141306 AA
1 AA
39141308 TTTGATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.35, C:0.00, G:0.19, T:0.45
Consensus pattern (14 bp):
AAGTTTTAGGTTAT
Found at i:39144117 original size:56 final size:53
Alignment explanation
Indices: 39143943--39144110 Score: 203
Period size: 56 Copynumber: 3.1 Consensus size: 53
39143933 CGAGAATTTG
* *
39143943 AAAAAAAA-TTGGTGTTGGCCATTGTATAGTCGACACCCCTTTTTATCTGACA
1 AAAAAAAATTTGGTGTTGGCCATTGTATGGTCGACACCCTTTTTTATCTGACA
* ** *
39143995 AAAAAAAATCTGGTGTTCACCATTGTATGGTCAACACTCCCTTTTTTATCTGACA
1 AAAAAAAATTTGGTGTTGGCCATTGTATGGTCGACA--CCCTTTTTTATCTGACA
* * * *
39144050 GAAAAAAAATTTGGTGTTGGTCATTGCATGGTCGACACCTTTTTTTAATCTGATA
1 -AAAAAAAATTTGGTGTTGGCCATTGTATGGTCGACACCCTTTTTT-ATCTGACA
39144105 AAAAAA
1 AAAAAA
39144111 TTAATTTTTT
Statistics
Matches: 97, Mismatches: 14, Indels: 8
0.82 0.12 0.07
Matches are distributed among these distances:
52 8 0.08
53 22 0.23
54 14 0.14
55 23 0.24
56 30 0.31
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Consensus pattern (53 bp):
AAAAAAAATTTGGTGTTGGCCATTGTATGGTCGACACCCTTTTTTATCTGACA
Found at i:39144248 original size:59 final size:57
Alignment explanation
Indices: 39144118--39144250 Score: 133
Period size: 59 Copynumber: 2.3 Consensus size: 57
39144108 AAATTAATTT
* * *
39144118 TTTTTGTCAGATAAAAAATTCAATTTTTTGGTGTTGGTAATGCCATGGTCGACACCCC
1 TTTTT-TCAGATAAAAAAATCAACTTTTTGGTGTTGGTAATGCCATGGCCGACACCCC
* * * * * *
39144176 TATTTATCTGATAAAAAAATCAAACTTTTTGGTGTTTGTCATTG-CATGGCCGATATCTCC
1 T-TTTTTCAGATAAAAAAATC-AACTTTTTGGTGTTGGT-AATGCCATGGCCGACA-CCCC
39144236 TTTTTTCAGATAAAA
1 TTTTTTCAGATAAAA
39144251 TTTTTTTAAA
Statistics
Matches: 60, Mismatches: 11, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
58 14 0.23
59 39 0.65
60 7 0.12
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.40
Consensus pattern (57 bp):
TTTTTTCAGATAAAAAAATCAACTTTTTGGTGTTGGTAATGCCATGGCCGACACCCC
Found at i:39144503 original size:23 final size:24
Alignment explanation
Indices: 39144459--39144505 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
39144449 TTTTATTTTA
* *
39144459 AAATTGTAAGTAAGAAATTAAGAT
1 AAATTGTAAGAAAAAAATTAAGAT
39144483 AAATTGTAA-AAAAAAATTAAGAT
1 AAATTGTAAGAAAAAAATTAAGAT
39144506 GATAAACCCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 12 0.57
24 9 0.43
ACGTcount: A:0.60, C:0.00, G:0.13, T:0.28
Consensus pattern (24 bp):
AAATTGTAAGAAAAAAATTAAGAT
Found at i:39145042 original size:30 final size:30
Alignment explanation
Indices: 39145008--39145099 Score: 87
Period size: 30 Copynumber: 3.1 Consensus size: 30
39144998 TTCGTTTACT
* *
39145008 TTTTAAGTTTAATTTAAAATTTTGTT-TTTA
1 TTTTAAATTTAATTTAAAATTTT-TTGTATA
* **
39145038 TTTTAAATTTATTTTCTAATTTTTTGTATA
1 TTTTAAATTTAATTTAAAATTTTTTGTATA
* ** *
39145068 TTTTAATTTTAATTTTTAATTTCTTGTATA
1 TTTTAAATTTAATTTAAAATTTTTTGTATA
39145098 TT
1 TT
39145100 CTAATTATTA
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
29 2 0.04
30 50 0.96
ACGTcount: A:0.27, C:0.02, G:0.04, T:0.66
Consensus pattern (30 bp):
TTTTAAATTTAATTTAAAATTTTTTGTATA
Found at i:39145105 original size:30 final size:31
Alignment explanation
Indices: 39145048--39145115 Score: 93
Period size: 30 Copynumber: 2.2 Consensus size: 31
39145038 TTTTAAATTT
* *
39145048 ATTTTCTAATTTTTTGTATATTTTAATT-TTA
1 ATTTT-TAATTTCTTGTATATTCTAATTATTA
39145079 ATTTTTAATTTCTTGTATATTCTAATTATTA
1 ATTTTTAATTTCTTGTATATTCTAATTATTA
*
39145110 TTTTTT
1 ATTTTT
39145116 GAAAATTTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
30 20 0.61
31 13 0.39
ACGTcount: A:0.25, C:0.04, G:0.03, T:0.68
Consensus pattern (31 bp):
ATTTTTAATTTCTTGTATATTCTAATTATTA
Found at i:39145733 original size:31 final size:31
Alignment explanation
Indices: 39145690--39145803 Score: 131
Period size: 31 Copynumber: 3.6 Consensus size: 31
39145680 GCCCCTTCAT
*
39145690 ATGACAGTATATAATTCAACTCCGGCAATAC
1 ATGACAGCATATAATTCAACTCCGGCAATAC
* * * **
39145721 ATGACAGCATATAGTTCAAC-CCTGAAATTTG
1 ATGACAGCATATAATTCAACTCCGGCAA-TAC
*
39145752 ATTGACAGTATATAATTCAACTCCGGCAATAC
1 A-TGACAGCATATAATTCAACTCCGGCAATAC
*
39145784 ATGACAGCATATAGTTCAAC
1 ATGACAGCATATAATTCAAC
39145804 CCTGAAATTT
Statistics
Matches: 66, Mismatches: 14, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
30 5 0.08
31 37 0.56
32 19 0.29
33 5 0.08
ACGTcount: A:0.38, C:0.21, G:0.14, T:0.27
Consensus pattern (31 bp):
ATGACAGCATATAATTCAACTCCGGCAATAC
Found at i:39145765 original size:32 final size:32
Alignment explanation
Indices: 39145722--39145818 Score: 117
Period size: 32 Copynumber: 3.1 Consensus size: 32
39145712 CGGCAATACA
39145722 TGACAGCATATAGTTCAACCCTGAAATTTGAT
1 TGACAGCATATAGTTCAACCCTGAAATTTGAT
* * * * **
39145754 TGACAGTATATAATTCAACTCCGGCAA-TACA-
1 TGACAGCATATAGTTCAAC-CCTGAAATTTGAT
39145785 TGACAGCATATAGTTCAACCCTGAAATTTGAT
1 TGACAGCATATAGTTCAACCCTGAAATTTGAT
39145817 TG
1 TG
39145819 TACACTTCAC
Statistics
Matches: 50, Mismatches: 12, Indels: 6
0.74 0.18 0.09
Matches are distributed among these distances:
30 5 0.10
31 19 0.38
32 21 0.42
33 5 0.10
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.30
Consensus pattern (32 bp):
TGACAGCATATAGTTCAACCCTGAAATTTGAT
Found at i:39145790 original size:63 final size:63
Alignment explanation
Indices: 39145691--39145818 Score: 256
Period size: 63 Copynumber: 2.0 Consensus size: 63
39145681 CCCCTTCATA
39145691 TGACAGTATATAATTCAACTCCGGCAATACATGACAGCATATAGTTCAACCCTGAAATTTGAT
1 TGACAGTATATAATTCAACTCCGGCAATACATGACAGCATATAGTTCAACCCTGAAATTTGAT
39145754 TGACAGTATATAATTCAACTCCGGCAATACATGACAGCATATAGTTCAACCCTGAAATTTGAT
1 TGACAGTATATAATTCAACTCCGGCAATACATGACAGCATATAGTTCAACCCTGAAATTTGAT
39145817 TG
1 TG
39145819 TACACTTCAC
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 65 1.00
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.29
Consensus pattern (63 bp):
TGACAGTATATAATTCAACTCCGGCAATACATGACAGCATATAGTTCAACCCTGAAATTTGAT
Found at i:39146180 original size:60 final size:59
Alignment explanation
Indices: 39145991--39146185 Score: 175
Period size: 59 Copynumber: 3.3 Consensus size: 59
39145981 ATTGCCTGGA
* * * * * *
39145991 CAACACAAAAAAA-TTGA-TTTTTATCAGAAAAAAAGAGAGTGTC-AGCCATGGGATGGC
1 CAACACAAAAAAATTTAATTTTTTATCAGACAAAAAGAGGGTATCGA-CCATGGCATCGC
* * * * * * *
39146048 CAACATAAAAAAAAATTAAATTTTTTATCTGACAAAAAGGGGGTGTCGACCATGGCATGGT
1 CAAC--ACAAAAAAATTTAATTTTTTATCAGACAAAAAGAGGGTATCGACCATGGCATCGC
* *
39146109 CAACACCAAAAAATTTAATTTTTTATTCAGATAAAAA-AGGGTATCGACCAT-GCAATCGC
1 CAACACAAAAAAATTTAATTTTTTA-TCAGACAAAAAGAGGGTATCGACCATGGC-ATCGC
39146168 CAACACAAAAAAATTTAA
1 CAACACAAAAAAATTTAA
39146186 AAAAAATTTA
Statistics
Matches: 112, Mismatches: 19, Indels: 12
0.78 0.13 0.08
Matches are distributed among these distances:
57 4 0.04
58 2 0.02
59 58 0.52
60 11 0.10
61 36 0.32
62 1 0.01
ACGTcount: A:0.45, C:0.15, G:0.16, T:0.24
Consensus pattern (59 bp):
CAACACAAAAAAATTTAATTTTTTATCAGACAAAAAGAGGGTATCGACCATGGCATCGC
Found at i:39147912 original size:11 final size:11
Alignment explanation
Indices: 39147896--39147920 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
39147886 GTAAAATTAA
39147896 ATATTATAATG
1 ATATTATAATG
39147907 ATATTATAATG
1 ATATTATAATG
39147918 ATA
1 ATA
39147921 CTTCACTCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (11 bp):
ATATTATAATG
Found at i:39151571 original size:15 final size:15
Alignment explanation
Indices: 39151551--39151581 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
39151541 CTCAAACCTA
*
39151551 AAATGATCAGAATCC
1 AAATGATCAAAATCC
39151566 AAATGATCAAAATCC
1 AAATGATCAAAATCC
39151581 A
1 A
39151582 TCATCATCTA
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:0.52, C:0.19, G:0.10, T:0.19
Consensus pattern (15 bp):
AAATGATCAAAATCC
Found at i:39155055 original size:28 final size:27
Alignment explanation
Indices: 39155013--39155073 Score: 104
Period size: 28 Copynumber: 2.2 Consensus size: 27
39155003 AAGTTGACAA
*
39155013 TTAAGTGTTATTTGTGTATGGTATTAG
1 TTAAGTGTTAATTGTGTATGGTATTAG
39155040 TTTAAGTGTTAATTGTGTATGGTATTAG
1 -TTAAGTGTTAATTGTGTATGGTATTAG
39155068 TTAAGT
1 TTAAGT
39155074 TTTTTAAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 6 0.19
28 26 0.81
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.51
Consensus pattern (27 bp):
TTAAGTGTTAATTGTGTATGGTATTAG
Found at i:39155986 original size:11 final size:11
Alignment explanation
Indices: 39155957--39155990 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
39155947 TTTGATTAGT
39155957 TTTATTAAATAA
1 TTTATTAAA-AA
*
39155969 GTTATTAAAAA
1 TTTATTAAAAA
39155980 TTTATTAAAAA
1 TTTATTAAAAA
39155991 ATTCGATTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 12 0.60
12 8 0.40
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (11 bp):
TTTATTAAAAA
Found at i:39160972 original size:3 final size:3
Alignment explanation
Indices: 39160964--39161007 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
39160954 AATGACGTGG
*
39160964 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA CGA AGA AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
39161008 CCTACAGTCA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.64, C:0.02, G:0.34, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:39161076 original size:7 final size:7
Alignment explanation
Indices: 39161042--39161078 Score: 56
Period size: 7 Copynumber: 5.3 Consensus size: 7
39161032 CCTGCTAGGA
*
39161042 TTAGATA
1 TTAGATT
*
39161049 TTAGATA
1 TTAGATT
39161056 TTAGATT
1 TTAGATT
39161063 TTAGATT
1 TTAGATT
39161070 TTAGATT
1 TTAGATT
39161077 TT
1 TT
39161079 TATTCTTCAG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.32, C:0.00, G:0.14, T:0.54
Consensus pattern (7 bp):
TTAGATT
Found at i:39161984 original size:30 final size:31
Alignment explanation
Indices: 39161915--39161985 Score: 85
Period size: 31 Copynumber: 2.3 Consensus size: 31
39161905 AAACTGTTAA
* *
39161915 TTAGTGATTGTTTTGTTACTTTTCGATAATG
1 TTAGTGACTGTTTTGTCACTTTTCGATAATG
39161946 TTAGTGACTGTTTTGTCACATTTTC-A-AA-G
1 TTAGTGACTGTTTTGTCAC-TTTTCGATAATG
39161975 TTCAGTGACTG
1 TT-AGTGACTG
39161986 AAATGTAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
29 3 0.08
30 10 0.28
31 18 0.50
32 5 0.14
ACGTcount: A:0.21, C:0.11, G:0.20, T:0.48
Consensus pattern (31 bp):
TTAGTGACTGTTTTGTCACTTTTCGATAATG
Found at i:39166482 original size:17 final size:17
Alignment explanation
Indices: 39166460--39166492 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
39166450 CTTTTTACAA
*
39166460 AATTAATTTTAAAAAAC
1 AATTAATTATAAAAAAC
39166477 AATTAATTATAAAAAA
1 AATTAATTATAAAAAA
39166493 TGAGTGAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (17 bp):
AATTAATTATAAAAAAC
Found at i:39176023 original size:27 final size:27
Alignment explanation
Indices: 39175993--39176055 Score: 101
Period size: 27 Copynumber: 2.3 Consensus size: 27
39175983 CAAGCCTTAT
39175993 TCCAGGCTCTACAACTC-TGAGCTTTTC
1 TCCAGGCTCTACAAC-CATGAGCTTTTC
*
39176020 TCCAGGCACTACAACCATGAGCTTTTC
1 TCCAGGCTCTACAACCATGAGCTTTTC
39176047 TCCAGGCTC
1 TCCAGGCTC
39176056 CACAGCTGGG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
26 1 0.03
27 32 0.97
ACGTcount: A:0.21, C:0.35, G:0.16, T:0.29
Consensus pattern (27 bp):
TCCAGGCTCTACAACCATGAGCTTTTC
Found at i:39179738 original size:53 final size:53
Alignment explanation
Indices: 39179681--39179804 Score: 169
Period size: 53 Copynumber: 2.3 Consensus size: 53
39179671 TCACATTTTC
* *
39179681 TTAGTAAATTTAGTC-CATGCATTTTTATAGCTTTGTATATCTTAATCCAATCA
1 TTAGTAAATTTAATCAC-TGCATTTTTATAGCTTTGTAAATCTTAATCCAATCA
* * * *
39179734 TTAGTGAATTTAATCACTTCATTTTTATAGGTTTGTAAATCTTAATCCAATTA
1 TTAGTAAATTTAATCACTGCATTTTTATAGCTTTGTAAATCTTAATCCAATCA
*
39179787 TTAGTAACTTTAATCACT
1 TTAGTAAATTTAATCACT
39179805 CTTGTTAGTT
Statistics
Matches: 62, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
53 61 0.98
54 1 0.02
ACGTcount: A:0.31, C:0.14, G:0.09, T:0.46
Consensus pattern (53 bp):
TTAGTAAATTTAATCACTGCATTTTTATAGCTTTGTAAATCTTAATCCAATCA
Found at i:39181965 original size:30 final size:30
Alignment explanation
Indices: 39181931--39181987 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
39181921 GCGAACCCAA
39181931 CACGTGCGAA-CTCATATAAGCGAATTGCAC
1 CACGTGCGAACCT-ATATAAGCGAATTGCAC
39181961 CACGTGCGAACCTATATAAGCGAATTG
1 CACGTGCGAACCTATATAAGCGAATTG
39181988 TACAGGCCGC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
30 24 0.92
31 2 0.08
ACGTcount: A:0.33, C:0.25, G:0.21, T:0.21
Consensus pattern (30 bp):
CACGTGCGAACCTATATAAGCGAATTGCAC
Found at i:39182601 original size:2 final size:2
Alignment explanation
Indices: 39182594--39182625 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
39182584 ACTTCCCATG
39182594 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
39182626 CTAATTATTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:39197592 original size:28 final size:28
Alignment explanation
Indices: 39197552--39197608 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
39197542 GAATCCCAGC
39197552 AGCCACATTTGTTGATCCATTTTAGGGA
1 AGCCACATTTGTTGATCCATTTTAGGGA
39197580 AGCCACATTTGTTGATCCATTTTAGGGA
1 AGCCACATTTGTTGATCCATTTTAGGGA
39197608 A
1 A
39197609 TGGACTGAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.35
Consensus pattern (28 bp):
AGCCACATTTGTTGATCCATTTTAGGGA
Found at i:39203452 original size:42 final size:42
Alignment explanation
Indices: 39203377--39203460 Score: 116
Period size: 42 Copynumber: 2.0 Consensus size: 42
39203367 CAAATATTTT
* *
39203377 TAAACCCAAATATAATTTCATTCTTCAAAAACACTCTTAAAC
1 TAAACCCAAATATAATTTCATTCCTCAAAAACACTCATAAAC
* *
39203419 TAAATCCAAATATAATTTTATTCCT-AAATAACACTCATAAAC
1 TAAACCCAAATATAATTTCATTCCTCAAA-AACACTCATAAAC
39203461 AACTCCTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
41 3 0.08
42 34 0.92
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.32
Consensus pattern (42 bp):
TAAACCCAAATATAATTTCATTCCTCAAAAACACTCATAAAC
Found at i:39205501 original size:15 final size:18
Alignment explanation
Indices: 39205481--39205523 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 18
39205471 TTTTATTATA
39205481 AATTTAAA-ATA-T-AAT
1 AATTTAAATATACTAAAT
39205496 AATTTAAATATACTAAAT
1 AATTTAAATATACTAAAT
39205514 ATATTTAAAT
1 A-ATTTAAAT
39205524 TTATCATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
15 8 0.33
16 3 0.12
17 1 0.04
18 4 0.17
19 8 0.33
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (18 bp):
AATTTAAATATACTAAAT
Found at i:39205521 original size:19 final size:16
Alignment explanation
Indices: 39205481--39205533 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 16
39205471 TTTTATTATA
39205481 AATTTAAA-ATATAAT
1 AATTTAAATATATAAT
39205496 AATTTAAATATACTAAAT
1 AATTTAAATATA-T-AAT
* *
39205514 ATATTTAAATTTATCAT
1 A-ATTTAAATATATAAT
39205531 AAT
1 AAT
39205534 ATTATGGATT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
15 8 0.25
16 5 0.16
17 4 0.12
18 5 0.16
19 10 0.31
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (16 bp):
AATTTAAATATATAAT
Found at i:39208345 original size:19 final size:19
Alignment explanation
Indices: 39208321--39208363 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
39208311 TCAATTTACA
39208321 AATAAT-ATATATGAATTGT
1 AATAATCATA-ATGAATTGT
*
39208340 AATAATCATAATTAATTGT
1 AATAATCATAATGAATTGT
*
39208359 TATAA
1 AATAA
39208364 AGTATCGAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 18 0.86
20 3 0.14
ACGTcount: A:0.49, C:0.02, G:0.07, T:0.42
Consensus pattern (19 bp):
AATAATCATAATGAATTGT
Found at i:39210891 original size:10 final size:9
Alignment explanation
Indices: 39210878--39210902 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
39210868 GATTTTTAAA
39210878 TTTTTTATT
1 TTTTTTATT
39210887 TTTTTTATT
1 TTTTTTATT
39210896 TTTTTTA
1 TTTTTTA
39210903 AAATTATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (9 bp):
TTTTTTATT
Found at i:39212581 original size:25 final size:25
Alignment explanation
Indices: 39212553--39212615 Score: 69
Period size: 24 Copynumber: 2.6 Consensus size: 25
39212543 ATATCTTAAA
*
39212553 ATAATTAGAATTTAA-TTGAAAAAAG
1 ATAA-TAGAATTTAAGTGGAAAAAAG
*
39212578 ATAATATAATTTAAGTGGAAAAAAG
1 ATAATAGAATTTAAGTGGAAAAAAG
39212603 -TAGA-AGAATTTAA
1 ATA-ATAGAATTTAA
39212616 CTGAAGGCAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
24 19 0.58
25 14 0.42
ACGTcount: A:0.56, C:0.00, G:0.14, T:0.30
Consensus pattern (25 bp):
ATAATAGAATTTAAGTGGAAAAAAG
Found at i:39215068 original size:18 final size:17
Alignment explanation
Indices: 39215035--39215068 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
39215025 CAATTATGCT
*
39215035 ATTCTTGTTCGTTAAAA
1 ATTCTTGTTCGGTAAAA
39215052 ATTCTTGTTTCGGTAAA
1 ATTCTTG-TTCGGTAAA
39215069 TGATTCTATC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.26, C:0.12, G:0.15, T:0.47
Consensus pattern (17 bp):
ATTCTTGTTCGGTAAAA
Found at i:39218558 original size:16 final size:16
Alignment explanation
Indices: 39218537--39218569 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
39218527 TTGCAAATAC
*
39218537 AATTCATAATTAAACA
1 AATTCATAAATAAACA
39218553 AATTCATAAATAAACA
1 AATTCATAAATAAACA
39218569 A
1 A
39218570 GTAAAAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.61, C:0.12, G:0.00, T:0.27
Consensus pattern (16 bp):
AATTCATAAATAAACA
Found at i:39224215 original size:18 final size:18
Alignment explanation
Indices: 39224192--39224234 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
39224182 TAATAGGTTT
39224192 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
*
39224210 TTAATTAAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
39224228 TTAATTA
1 TTAATTA
39224235 CACCTTGAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:39226719 original size:31 final size:30
Alignment explanation
Indices: 39226684--39226743 Score: 102
Period size: 31 Copynumber: 2.0 Consensus size: 30
39226674 ATAAATCATA
39226684 AAAACTCTTGAATAGTTCAATGACTTAAATG
1 AAAACTCTTGAATAGTTCAATGAC-TAAATG
*
39226715 AAAACTTTTGAATAGTTCAATGACTAAAT
1 AAAACTCTTGAATAGTTCAATGACTAAAT
39226744 TGTAATTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 5 0.18
31 23 0.82
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.33
Consensus pattern (30 bp):
AAAACTCTTGAATAGTTCAATGACTAAATG
Found at i:39228341 original size:29 final size:28
Alignment explanation
Indices: 39228285--39228352 Score: 84
Period size: 29 Copynumber: 2.4 Consensus size: 28
39228275 TCTATTTTGA
* *
39228285 TTATTTAATTAAAAAATTTTCATTTTAG
1 TTATTTAATTAAAAAATTATCAATTTAG
39228313 TTATTTAATTAAAAAGAGTTAT-AATTTAG
1 TTATTTAATTAAAAA-A-TTATCAATTTAG
*
39228342 TTATTCAATTA
1 TTATTTAATTA
39228353 TTTAAAAGTT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
28 15 0.43
29 17 0.49
30 3 0.09
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (28 bp):
TTATTTAATTAAAAAATTATCAATTTAG
Found at i:39231213 original size:21 final size:21
Alignment explanation
Indices: 39231187--39231228 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
39231177 TATTTAAATA
39231187 AAATTATT-AATATTTATTTAT
1 AAATTATTGAATATTT-TTTAT
*
39231208 AAATTATTGATTATTTTTTAT
1 AAATTATTGAATATTTTTTAT
39231229 TTAATGATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (21 bp):
AAATTATTGAATATTTTTTAT
Found at i:39232993 original size:10 final size:10
Alignment explanation
Indices: 39232978--39233054 Score: 53
Period size: 9 Copynumber: 8.3 Consensus size: 10
39232968 TTTAAAACAT
39232978 ATTTTTAATA
1 ATTTTTAATA
39232988 ATTTTT-ATA
1 ATTTTTAATA
* *
39232997 CTATTTAA-A
1 ATTTTTAATA
39233006 ATAATTTTAATA
1 AT--TTTTAATA
*
39233018 CTTTTT--T-
1 ATTTTTAATA
39233025 ATTTTTAAT-
1 ATTTTTAATA
39233034 ATTTTTAA-A
1 ATTTTTAATA
39233043 ATTTTTAA-A
1 ATTTTTAATA
39233052 ATT
1 ATT
39233055 AAAAATAATT
Statistics
Matches: 54, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
7 5 0.09
8 1 0.02
9 30 0.56
10 11 0.20
11 5 0.09
12 2 0.04
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (10 bp):
ATTTTTAATA
Found at i:39233001 original size:21 final size:21
Alignment explanation
Indices: 39232968--39233025 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
39232958 ATTAGAAACA
*
39232968 TTTAAAACATATTTTTAATAAT
1 TTTAATAC-TATTTTTAATAAT
* **
39232990 TTTTATACTATTTAAAATAAT
1 TTTAATACTATTTTTAATAAT
39233011 TTTAATACT-TTTTTA
1 TTTAATACTATTTTTA
39233026 TTTTTAATAT
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
20 4 0.14
21 19 0.66
22 6 0.21
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (21 bp):
TTTAATACTATTTTTAATAAT
Found at i:39233366 original size:24 final size:24
Alignment explanation
Indices: 39233334--39233382 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 24
39233324 TAAATGGATG
*
39233334 TTTAACCTTTCATC-TCCATTAACT
1 TTTAACCTTCCATCTTCC-TTAACT
39233358 TTTAACCTTCCATCTTCCTTAACT
1 TTTAACCTTCCATCTTCCTTAACT
39233382 T
1 T
39233383 GCCTTGACTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 20 0.87
25 3 0.13
ACGTcount: A:0.22, C:0.31, G:0.00, T:0.47
Consensus pattern (24 bp):
TTTAACCTTCCATCTTCCTTAACT
Found at i:39238642 original size:29 final size:29
Alignment explanation
Indices: 39238609--39238780 Score: 148
Period size: 29 Copynumber: 5.8 Consensus size: 29
39238599 AAAACATGTA
* *
39238609 GTTTAGGGTTTAAATGGTAATTTTTAGAT
1 GTTTAGGGGTAAAATGGTAATTTTTAGAT
*
39238638 GTTTAGGGGTAAAATGGTAATTTTTGGAT
1 GTTTAGGGGTAAAATGGTAATTTTTAGAT
* *
39238667 ATTTAGGGGTAAAATGGTAATTTTTGGAAAAT
1 GTTTAGGGGTAAAATGGTAATTTTT---AGAT
* * *
39238699 -TTTAGGGTTAAAATGGTAATTTTAAAAT
1 GTTTAGGGGTAAAATGGTAATTTTTAGAT
** * * * *
39238727 GTTCGGGGGTAGAATAGTAATTTTAGAGAA
1 GTTTAGGGGTAAAATGGTAATTTT-TAGAT
* **
39238757 GTTTAGGGGAAAAATCATAATTTT
1 GTTTAGGGGTAAAATGGTAATTTT
39238781 AGAGAAGTTT
Statistics
Matches: 116, Mismatches: 22, Indels: 9
0.79 0.15 0.06
Matches are distributed among these distances:
28 4 0.03
29 68 0.59
30 20 0.17
31 22 0.19
32 2 0.02
ACGTcount: A:0.34, C:0.01, G:0.26, T:0.40
Consensus pattern (29 bp):
GTTTAGGGGTAAAATGGTAATTTTTAGAT
Found at i:39238718 original size:89 final size:89
Alignment explanation
Indices: 39238608--39238810 Score: 223
Period size: 89 Copynumber: 2.3 Consensus size: 89
39238598 AAAAACATGT
* * * * *
39238608 AGTTTAGGGTTTAAATGGTAATTTTTAGATGTTTAGGGGTAAAATGGTAATTTTTG-GATA-TTT
1 AGTTTAGGGTTAAAATGGTAATTTTTAAATGTTCAGGGGTAAAATAGTAATTTTAGAGA-AGTTT
* ** *
39238671 AGGGGTAAAATGGTAATTTTTGGAAA
65 AGGGGAAAAATCATAA-TTTTAGAAA
* * * *
39238697 ATTTTAGGGTTAAAATGGTAATTTTAAAATGTTCGGGGGTAGAATAGTAATTTTAGAGAAGTTTA
1 AGTTTAGGGTTAAAATGGTAATTTTTAAATGTTCAGGGGTAAAATAGTAATTTTAGAGAAGTTTA
*
39238762 GGGGAAAAATCATAATTTTAGAGA
66 GGGGAAAAATCATAATTTTAGAAA
**
39238786 AGTTTAGTTTTAAAAT-GTAATTTTT
1 AGTTTAGGGTTAAAATGGTAATTTTT
39238811 TTAACAAAAC
Statistics
Matches: 94, Mismatches: 18, Indels: 5
0.80 0.15 0.04
Matches are distributed among these distances:
88 8 0.09
89 68 0.72
90 18 0.19
ACGTcount: A:0.34, C:0.01, G:0.24, T:0.40
Consensus pattern (89 bp):
AGTTTAGGGTTAAAATGGTAATTTTTAAATGTTCAGGGGTAAAATAGTAATTTTAGAGAAGTTTA
GGGGAAAAATCATAATTTTAGAAA
Found at i:39240569 original size:40 final size:40
Alignment explanation
Indices: 39240514--39240626 Score: 192
Period size: 39 Copynumber: 2.9 Consensus size: 40
39240504 ATTAAGTTGT
39240514 GGTGAATACATTCAAGCTTCGGCTTAGCAGGCTACGAGCC
1 GGTGAATACATTCAAGCTTCGGCTTAGCAGGCTACGAGCC
39240554 GGTGAATACATTCAAGCTTCGGCTTAGCA-GCTACGAGCC
1 GGTGAATACATTCAAGCTTCGGCTTAGCAGGCTACGAGCC
* * *
39240593 GGTGAATACAATCAAGCTTTGGTTTAGCAGGCTA
1 GGTGAATACATTCAAGCTTCGGCTTAGCAGGCTA
39240627 TAAGCCTGTG
Statistics
Matches: 69, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
39 36 0.52
40 33 0.48
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
GGTGAATACATTCAAGCTTCGGCTTAGCAGGCTACGAGCC
Found at i:39243200 original size:17 final size:19
Alignment explanation
Indices: 39243160--39243194 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
39243150 AAAGTTTTAC
39243160 AAGATTGTTTGAATGGTAA
1 AAGATTGTTTGAATGGTAA
39243179 AAGATT-TTTG-ATGGTA
1 AAGATTGTTTGAATGGTA
39243195 CTAGATGATG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 4 0.25
19 6 0.38
ACGTcount: A:0.34, C:0.00, G:0.26, T:0.40
Consensus pattern (19 bp):
AAGATTGTTTGAATGGTAA
Found at i:39245404 original size:30 final size:27
Alignment explanation
Indices: 39245350--39245407 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 27
39245340 GTATATATGG
*
39245350 AATTTTCTCTCTATTTCTATTTTAAAA
1 AATTTTCTCTCTATTTCTAATTTAAAA
*
39245377 AATTATTCTCTCTATTTTTAGAATTTAAAA
1 AATT-TTCTCTCTATTTCT--AATTTAAAA
39245407 A
1 A
39245408 TATATATTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 4 0.15
28 13 0.50
30 9 0.35
ACGTcount: A:0.34, C:0.12, G:0.02, T:0.52
Consensus pattern (27 bp):
AATTTTCTCTCTATTTCTAATTTAAAA
Done.