Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D05
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: 63323194
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1953226 characters in sequence are not A, C, G, or T
File 160 of 199
Found at i:52636795 original size:13 final size:13
Alignment explanation
Indices: 52636777--52636840 Score: 67
Period size: 13 Copynumber: 4.9 Consensus size: 13
52636767 AGTTCTTCAA
52636777 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
52636790 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
* *
52636803 TG-ATATGAAAAAG
1 TGCTTTTG-AAAAG
**
52636816 TGCTTTTGAGGAG
1 TGCTTTTGAAAAG
*
52636829 TGCTGTTGAAAA
1 TGCTTTTGAAAA
52636841 ATTTGAGTGT
Statistics
Matches: 40, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
12 3 0.08
13 34 0.85
14 3 0.08
ACGTcount: A:0.33, C:0.06, G:0.27, T:0.34
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:52639494 original size:3 final size:3
Alignment explanation
Indices: 52639486--52639530 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
52639476 ATGTATAGGT
52639486 ATA ATA ATA 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 ATA ATA ATA
52639531 GTAAACTTGA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:52641043 original size:50 final size:50
Alignment explanation
Indices: 52640963--52641534 Score: 378
Period size: 50 Copynumber: 11.4 Consensus size: 50
52640953 GGATTAATTT
* * * * * * *
52640963 CTTCAATTTGTTCAACTGCAATGTCGGGGAAACCAGATCCGCCATCGTAG
1 CTTCAATCTGTTCCATTGCACTGTCAGGGAAACAAGATCCGCCGTCGTAG
** * ** * *
52641013 CTTCAATCTGTTCCACCGCACCGTCAGGGAAGTAAGATCCGCCGTTGTGG
1 CTTCAATCTGTTCCATTGCACTGTCAGGGAAACAAGATCCGCCGTCGTAG
* ** * * *
52641063 CTTCAATCTTTTAAATTGCAATGTCAGGAAAACTAGATCCGCCGTCGTAG
1 CTTCAATCTGTTCCATTGCACTGTCAGGGAAACAAGATCCGCCGTCGTAG
* * ** * * *
52641113 CTTCAATCTATTCCATTGCACTG-CTAAGGAAGTAAGATCCACCGTTGTGG
1 CTTCAATCTGTTCCATTGCACTGTC-AGGGAAACAAGATCCGCCGTCGTAG
* ** * * * * * *
52641163 CTTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCCGTCGGCATAG
1 CTTCAATCTGTTCCATTGCACTGTCAGGGAAACAAGATCCGCCGTCGTAG
* * * ** * * * *
52641213 CTTCAATCTGTTCCACTACACTG-CTAAGGAAGTAAGATCCACCATTGTGG
1 CTTCAATCTGTTCCATTGCACTGTC-AGGGAAACAAGATCCGCCGTCGTAG
* ** * * * *
52641263 CTTCAATCTTTTTGATTGCAATATCAGGGAAACCAGATCCGCCATCGTAG
1 CTTCAATCTGTTCCATTGCACTGTCAGGGAAACAAGATCCGCCGTCGTAG
* * ** * *
52641313 CTTCAATCTGTTCCACTGCACTG-CTAAGGAAGTAAGATCCGCCGTTGTGG
1 CTTCAATCTGTTCCATTGCACTGTC-AGGGAAACAAGATCCGCCGTCGTAG
* ** * * * *
52641363 CTTCAATCTTTTTGATTGCAATATCAGGGAAACCACATCCGCCGTCGTAG
1 CTTCAATCTGTTCCATTGCACTGTCAGGGAAACAAGATCCGCCGTCGTAG
* * ** * *
52641413 CTTCAATCTGTTCCACTGCACTG-CTAAGGAAGTAAGATCCGCCGTTGTGG
1 CTTCAATCTGTTCCATTGCACTGTC-AGGGAAACAAGATCCGCCGTCGTAG
* ** * * *
52641463 CTTCAATCTTTTTGATTGCAATATCAGGGAAACCAGATCCGCCGTCGTAG
1 CTTCAATCTGTTCCATTGCACTGTCAGGGAAACAAGATCCGCCGTCGTAG
*
52641513 CTTCAATCTGTTCCACTGCACT
1 CTTCAATCTGTTCCATTGCACT
52641535 ACTAAGGAAG
Statistics
Matches: 374, Mismatches: 140, Indels: 16
0.71 0.26 0.03
Matches are distributed among these distances:
49 4 0.01
50 366 0.98
51 4 0.01
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.29
Consensus pattern (50 bp):
CTTCAATCTGTTCCATTGCACTGTCAGGGAAACAAGATCCGCCGTCGTAG
Found at i:52641144 original size:100 final size:100
Alignment explanation
Indices: 52640979--52641551 Score: 905
Period size: 100 Copynumber: 5.7 Consensus size: 100
52640969 TTTGTTCAAC
* * * * * *
52640979 TGCAATGTCGGGGAAACCAGATCCGCCATCGTAGCTTCAATCTGTTCCACCGCACCG-TCAGGGA
1 TGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCT-AAGGA
**
52641043 AGTAAGATCCGCCGTTGTGGCTTCAATCTTTTAAAT
65 AGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTGAT
* * * * *
52641079 TGCAATGTCAGGAAAACTAGATCCGCCGTCGTAGCTTCAATCTATTCCATTGCACTGCTAAGGAA
1 TGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAA
* *
52641144 GTAAGATCCACCGTTGTGGCTTCAATCTTTTTAAT
66 GTAAGATCCGCCGTTGTGGCTTCAATCTTTTTGAT
* * * *
52641179 TGCAATATCAGGGAAACCAGATCCGTCGGCATAGCTTCAATCTGTTCCACTACACTGCTAAGGAA
1 TGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAA
* *
52641244 GTAAGATCCACCATTGTGGCTTCAATCTTTTTGAT
66 GTAAGATCCGCCGTTGTGGCTTCAATCTTTTTGAT
*
52641279 TGCAATATCAGGGAAACCAGATCCGCCATCGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAA
1 TGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAA
52641344 GTAAGATCCGCCGTTGTGGCTTCAATCTTTTTGAT
66 GTAAGATCCGCCGTTGTGGCTTCAATCTTTTTGAT
*
52641379 TGCAATATCAGGGAAACCACATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAA
1 TGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAA
52641444 GTAAGATCCGCCGTTGTGGCTTCAATCTTTTTGAT
66 GTAAGATCCGCCGTTGTGGCTTCAATCTTTTTGAT
*
52641479 TGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTACTAAGGAA
1 TGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAA
52641544 GTTAAGAT
66 G-TAAGAT
52641552 TACTGGCTTC
Statistics
Matches: 438, Mismatches: 33, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
100 431 0.98
101 7 0.02
ACGTcount: A:0.26, C:0.25, G:0.21, T:0.28
Consensus pattern (100 bp):
TGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAA
GTAAGATCCGCCGTTGTGGCTTCAATCTTTTTGAT
Found at i:52641907 original size:89 final size:89
Alignment explanation
Indices: 52641739--52642017 Score: 409
Period size: 89 Copynumber: 3.1 Consensus size: 89
52641729 TACCATCTTC
* * *
52641739 GATCTACTTCAAGCCAATACATGAAGACAAGATCTGCTTTTTCCTTCGATCTACTTCGCCACCAG
1 GATCTACTTCACGCCAGTACATGAAGACAAGATCTGC--TTT-CTTCGATCTGCTTCGCCACCAG
52641804 TATGGGAAGGCAAGATCTGTTATCTCT
63 TATGGGAAGGCAAGATCTGTTATCTCT
*
52641831 GATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTCGATCTGTTTCGCCACCAGTAT
1 GATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTCGATCTGCTTCGCCACCAGTAT
* * *
52641896 GGGAAGACAAGATCTATTATCTTT
66 GGGAAGGCAAGATCTGTTATCTCT
* * *
52641920 GATCTACTTCACACCAGTACATGAAGACAAGCTCTGCTTTCTTTGATCTGCTTCGCCACCAGTAT
1 GATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTCGATCTGCTTCGCCACCAGTAT
52641985 GGGAAGGCAAGATCTGTATAT-TC-
66 GGGAAGGCAAGATCTGT-TATCTCT
*
52642008 GATCCACTTC
1 GATCTACTTC
52642018 GCTACCAATA
Statistics
Matches: 171, Mismatches: 15, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
88 9 0.05
89 121 0.71
90 6 0.04
92 35 0.20
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.30
Consensus pattern (89 bp):
GATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTCGATCTGCTTCGCCACCAGTAT
GGGAAGGCAAGATCTGTTATCTCT
Found at i:52642019 original size:133 final size:134
Alignment explanation
Indices: 52641882--52642137 Score: 406
Period size: 133 Copynumber: 1.9 Consensus size: 134
52641872 TTCGATCTGT
* * *
52641882 TTCGCCACCAGTATGGGAAGACAAGATCTATTATCTTTGATCTACTTCACACCAGTACATGAAGA
1 TTCGCCACCAATATAGGAAGACAAGATCTAGTATCTTTGATCTACTTCACACCAGTACATGAAGA
* * *
52641947 CAAGCTCTGCTTTCTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCT-GTATATTCGAT
66 CAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGGCAAGATCTAGTATATTCGAT
52642011 CCAC
131 CCAC
* * * *
52642015 TTCGCTACCAATATAGGAAGACAGGATCTGGTATCTTTGATCTACTTCACGCCAGTACATGAAGA
1 TTCGCCACCAATATAGGAAGACAAGATCTAGTATCTTTGATCTACTTCACACCAGTACATGAAGA
*
52642080 CAAGATCTGTTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGGCAAGATCTAGTAT
66 CAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGGCAAGATCTAGTAT
52642138 CTCTGATCTA
Statistics
Matches: 111, Mismatches: 11, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
133 107 0.96
134 4 0.04
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (134 bp):
TTCGCCACCAATATAGGAAGACAAGATCTAGTATCTTTGATCTACTTCACACCAGTACATGAAGA
CAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGGCAAGATCTAGTATATTCGAT
CCAC
Found at i:52642035 original size:89 final size:88
Alignment explanation
Indices: 52641736--52642106 Score: 388
Period size: 89 Copynumber: 4.1 Consensus size: 88
52641726 ATCTACCATC
52641736 TTCGATCTACTTCA-AGCCAATACATGAAGACAAGATCTGCTTTTTCCTTCGATCTACTTCGCCA
1 TTCGATCTACTTCACA-CCAATACATGAAGACAAGATCTGC--TTT-CTTCGATCTACTTCGCCA
52641800 CCAGTATGGGAAGGCAAGATCTGT-TA
62 CCAGTATGGGAAGGCAAGATCTGTATA
* * **
52641826 TCTCTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTCGATCTGTTTCGCCACC
1 T-TC-GATCTACTTCACACCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACC
* * *
52641891 AGTATGGGAAGACAAGATCTATTATC
64 AGTATGGGAAGGCAAGATCT-GTATA
* * * * *
52641917 TTTGATCTACTTCACACCAGTACATGAAGACAAGCTCTGCTTTCTTTGATCTGCTTCGCCACCAG
1 TTCGATCTACTTCACACCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAG
52641982 TATGGGAAGGCAAGATCTGTATA
66 TATGGGAAGGCAAGATCTGTATA
* * * * * * * * * *
52642005 TTCGATCCACTTCGCTACCAATATAGGAAGACAGGATCTGGTATCTTTGATCTACTTC-ACGCCA
1 TTCGATCTACTTCAC-ACCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCA
*** * * *
52642069 GTACATGAAGACAAGATCTGTTTTC
65 GTATGGGAAGGCAAGATCTG-TATA
52642094 TTCGATCTACTTC
1 TTCGATCTACTTC
52642107 GCCACCAGTA
Statistics
Matches: 239, Mismatches: 35, Indels: 15
0.83 0.12 0.05
Matches are distributed among these distances:
88 35 0.15
89 160 0.67
90 6 0.03
91 4 0.02
92 34 0.14
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.31
Consensus pattern (88 bp):
TTCGATCTACTTCACACCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAG
TATGGGAAGGCAAGATCTGTATA
Found at i:52642107 original size:89 final size:89
Alignment explanation
Indices: 52641898--52642365 Score: 449
Period size: 89 Copynumber: 5.2 Consensus size: 89
52641888 ACCAGTATGG
* * * *** * * *
52641898 GAAGACAAGATCTATTATCTTTGATCTACTTC-ACACCAGTACATGAAGACAAGCTCT-GCTTTC
1 GAAGACAAGATCTGTTATCTTCGATCTACTTCGCCACCAGTATGGGAAGGCAAGATCTAG-TATC
* * * ***
52641961 TTTGATCTGCTTCGCCACCAGTATGG
65 TTTGATCTACTTC-ACGCCAGTACAT
* * * * * * * * *
52641987 GAAGGCAAGATCTG-TATATTCGATCCACTTCGCTACCAATATAGGAAGACAGGATCTGGTATCT
1 GAAGACAAGATCTGTTATCTTCGATCTACTTCGCCACCAGTATGGGAAGGCAAGATCTAGTATCT
52642051 TTGATCTACTTCACGCCAGTACAT
66 TTGATCTACTTCACGCCAGTACAT
*
52642075 GAAGACAAGATCTGTTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGGCAAGATCTAGTATCT
1 GAAGACAAGATCTGTTATCTTCGATCTACTTCGCCACCAGTATGGGAAGGCAAGATCTAGTATCT
*
52642140 CTGATCTACTTCACGCCAGTACAT
66 TTGATCTACTTCACGCCAGTACAT
* * *
52642164 GAAGACAATATCTGCTTTTTCCTTCGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTAGTA
1 GAAGACAAGATCTG--TTAT-CTTCGATCTACTTCGCCACCAGTATGGGAAGGCAAGATCTAGTA
* *
52642229 TCTCTGATCTACTTTACGCCAGTACAT
63 TCTTTGATCTACTTCACGCCAGTACAT
* * * * * * *
52642256 AAAGACAAGATTTGCTCTCTTTGATCTATTTCGCCACCAGTATGGGAAGGCAAGATCT-GCATCT
1 GAAGACAAGATCTGTTATCTTCGATCTACTTCGCCACCAGTATGGGAAGGCAAGATCTAGTATCT
* * * * * *
52642320 TTGATCCACTTCGCTACCAGCATAG
66 TTGATCTACTTCAC-GCCAGTACAT
*
52642345 GAAGACAGGATCTGTTATCTT
1 GAAGACAAGATCTGTTATCTT
52642366 TCAACCTGGT
Statistics
Matches: 317, Mismatches: 55, Indels: 14
0.82 0.14 0.04
Matches are distributed among these distances:
88 49 0.15
89 181 0.57
90 3 0.01
91 4 0.01
92 80 0.25
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (89 bp):
GAAGACAAGATCTGTTATCTTCGATCTACTTCGCCACCAGTATGGGAAGGCAAGATCTAGTATCT
TTGATCTACTTCACGCCAGTACAT
Found at i:52642169 original size:222 final size:225
Alignment explanation
Indices: 52641783--52642229 Score: 702
Period size: 222 Copynumber: 2.0 Consensus size: 225
52641773 TGCTTTTTCC
* * * * *
52641783 TTCGATCTACTTCGCCACCAGTATGGGAAGGCAAGATCTGTTATCTCTGATCTACTTCACGCCAG
1 TTCGATCCACTTCGCCACCAATATAGGAAGACAAGATCTGGTATCTCTGATCTACTTCACGCCAG
** *
52641848 TACATGAAGACAAGATCTGCTTTCTTCGATCTGTTTCGCCACCAGTATGGGAAGACAAGATCTAT
66 TACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTAG
* * *
52641913 TATCTTTGATCTACTTCACACCAGTACATGAAGACAAGCTCTGC-TTT-CTTTGATCTGCTTCGC
131 TATCTCTGATCTACTTCACACCAGTACATGAAGACAAGATCTGCTTTTCCTTCGATCTGCTTCGC
52641976 CACCAGTATGGGAAGGCAAGATCT-GTATA
196 CACCAGTATGGGAAGGCAAGATCTAGTATA
* * *
52642005 TTCGATCCACTTCGCTACCAATATAGGAAGACAGGATCTGGTATCTTTGATCTACTTCACGCCAG
1 TTCGATCCACTTCGCCACCAATATAGGAAGACAAGATCTGGTATCTCTGATCTACTTCACGCCAG
* *
52642070 TACATGAAGACAAGATCTGTTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGGCAAGATCTAG
66 TACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTAG
* *
52642135 TATCTCTGATCTACTTCACGCCAGTACATGAAGACAATATCTGCTTTTTCCTTCGATCTGCTTCG
131 TATCTCTGATCTACTTCACACCAGTACATGAAGACAAGATCTGC-TTTTCCTTCGATCTGCTTCG
52642200 CCACCAGTATGGGAAGGCAAGATCTAGTAT
195 CCACCAGTATGGGAAGGCAAGATCTAGTAT
52642230 CTCTGATCTA
Statistics
Matches: 203, Mismatches: 18, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
222 157 0.77
224 3 0.01
225 39 0.19
226 4 0.02
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.30
Consensus pattern (225 bp):
TTCGATCCACTTCGCCACCAATATAGGAAGACAAGATCTGGTATCTCTGATCTACTTCACGCCAG
TACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTAG
TATCTCTGATCTACTTCACACCAGTACATGAAGACAAGATCTGCTTTTCCTTCGATCTGCTTCGC
CACCAGTATGGGAAGGCAAGATCTAGTATA
Found at i:52642177 original size:133 final size:133
Alignment explanation
Indices: 52641897--52642177 Score: 386
Period size: 133 Copynumber: 2.1 Consensus size: 133
52641887 CACCAGTATG
** *
52641897 GGAAGACAAGATCTATTATCTTTGATCTACTTCACACCAGTACATGAAGACAAGCTCTGCTTTCT
1 GGAAGACAAGATCTGGTATCTTTGATCTACTTCACACCAGTACATGAAGACAAGATCTGCTTTCT
* * *
52641962 TTGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGTATATTCGATCCACTTCGCTACCAAT
66 TCGATCTACTTCGCCACCAGTATGGGAAGGCAAGATCTGTATATTCGATCCACTTCACTACCAAT
*
52642027 ATA
131 ACA
* * *
52642030 GGAAGACAGGATCTGGTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTCT
1 GGAAGACAAGATCTGGTATCTTTGATCTACTTCACACCAGTACATGAAGACAAGATCTGCTTTCT
* * *
52642095 TCGATCTACTTCGCCACCAGTATGGGAAGGCAAGATCTAGTAT-CTCTGATCTACTTCAC-GCCA
66 TCGATCTACTTCGCCACCAGTATGGGAAGGCAAGATCT-GTATATTC-GATCCACTTCACTACCA
*
52642158 GTACA
129 ATACA
* *
52642163 TGAAGACAATATCTG
1 GGAAGACAAGATCTG
52642178 CTTTTTCCTT
Statistics
Matches: 129, Mismatches: 17, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
133 115 0.89
134 14 0.11
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.29
Consensus pattern (133 bp):
GGAAGACAAGATCTGGTATCTTTGATCTACTTCACACCAGTACATGAAGACAAGATCTGCTTTCT
TCGATCTACTTCGCCACCAGTATGGGAAGGCAAGATCTGTATATTCGATCCACTTCACTACCAAT
ACA
Found at i:52642250 original size:181 final size:180
Alignment explanation
Indices: 52642005--52642331 Score: 474
Period size: 181 Copynumber: 1.8 Consensus size: 180
52641995 GATCTGTATA
* * * *
52642005 TTCGATCCACTTCGCTACCAATATAGGAAGACAGGATCTGGTATCTTTGATCTACTTCACGCCAG
1 TTCGATCCACTTCGCCACCAATATAGGAAGACAAGATCTAGTATCTCTGATCTACTTCACGCCAG
* * *
52642070 TACATGAAGACAAGATCTGTTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGGCAAGATCTAG
66 TACATAAAGACAAGATCTGCTCTCTTCGATCTACTTCGCCACCAGTATGGGAAGGCAAGATCT-G
* *
52642135 TATCTCTGATCTACTTCACGCCAGTACATGAAGACAATATCTGCTTTTTCC
130 CATCTCTGATCCACTTCACGCCAGTACATGAAGACAATATCTGCTTTTTCC
** * * * *
52642186 TTCGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTAGTATCTCTGATCTACTTTACGCCAG
1 TTCGATCCACTTCGCCACCAATATAGGAAGACAAGATCTAGTATCTCTGATCTACTTCACGCCAG
* * *
52642251 TACATAAAGACAAGATTTGCTCTCTTTGATCTATTTCGCCACCAGTATGGGAAGGCAAGATCTGC
66 TACATAAAGACAAGATCTGCTCTCTTCGATCTACTTCGCCACCAGTATGGGAAGGCAAGATCTGC
*
52642316 ATCTTTGATCCACTTC
131 ATCTCTGATCCACTTC
52642332 GCTACCAGCA
Statistics
Matches: 127, Mismatches: 19, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
180 15 0.12
181 112 0.88
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.31
Consensus pattern (180 bp):
TTCGATCCACTTCGCCACCAATATAGGAAGACAAGATCTAGTATCTCTGATCTACTTCACGCCAG
TACATAAAGACAAGATCTGCTCTCTTCGATCTACTTCGCCACCAGTATGGGAAGGCAAGATCTGC
ATCTCTGATCCACTTCACGCCAGTACATGAAGACAATATCTGCTTTTTCC
Found at i:52642308 original size:314 final size:313
Alignment explanation
Indices: 52641733--52642366 Score: 1004
Period size: 314 Copynumber: 2.0 Consensus size: 313
52641723 AAAATCTACC
*
52641733 ATCTTCGATCTACTTCAAGCCAATACATGAAGACAAGATCTGCTTTTTCCTTCGATCTACTTCGC
1 ATCTTTGATCTACTTCAAGCCAATACATGAAGACAAGATCTGC-TTTTCCTTCGATCTACTTCGC
52641798 CACCAGTATGGGAAGGCAAGATCTGTTATCTCTGATCTACTTCACGCCAGTACATGAAGACAAGA
65 CACCAGTATGGGAAGGCAAGATCTGTTATCTCTGATCTACTTCACGCCAGTACATGAAGACAAGA
* * *
52641863 TCTGCTTTCTTCGATCTGTTTCGCCACCAGTATGGGAAGACAAGATCTATTATCTTTGATCTACT
130 TCTGCTTTCTTCGATCTGCTTCGCCACCAGTATGGGAAGACAAGATCTAGTATCTCTGATCTACT
* * * *
52641928 TCACACCAGTACATGAAGACAAGCTCTGCTTTCTTTGATCTGCTTCGCCACCAGTATGGGAAGGC
195 TCACACCAGTACATAAAGACAAGATCTGCTCTCTTTGATCTACTTCGCCACCAGTATGGGAAGGC
* *
52641993 AAGATCTGTATATTCGATCCACTTCGCTACCAATATAGGAAGACAGGATCTGGT
260 AAGATCTGCATATTCGATCCACTTCGCTACCAACATAGGAAGACAGGATCTGGT
* *
52642047 ATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTG-TTTT-CTTCGATCTACTTCGCC
1 ATCTTTGATCTACTTCAAGCCAATACATGAAGACAAGATCTGCTTTTCCTTCGATCTACTTCGCC
*
52642110 ACCAGTATGGGAAGGCAAGATCTAG-TATCTCTGATCTACTTCACGCCAGTACATGAAGACAATA
66 ACCAGTATGGGAAGGCAAGATCT-GTTATCTCTGATCTACTTCACGCCAGTACATGAAGACAAGA
*
52642174 TCTGCTTTTTCCTTCGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTAGTATCTCTGATCT
130 TCTGC--TTT-CTTCGATCTGCTTCGCCACCAGTATGGGAAGACAAGATCTAGTATCTCTGATCT
* * * *
52642239 ACTTTACGCCAGTACATAAAGACAAGATTTGCTCTCTTTGATCTATTTCGCCACCAGTATGGGAA
192 ACTTCACACCAGTACATAAAGACAAGATCTGCTCTCTTTGATCTACTTCGCCACCAGTATGGGAA
* * * *
52642304 GGCAAGATCTGCATCTTTGATCCACTTCGCTACCAGCATAGGAAGACAGGATCTGTT
257 GGCAAGATCTGCATATTCGATCCACTTCGCTACCAACATAGGAAGACAGGATCTGGT
52642361 ATCTTT
1 ATCTTT
52642367 CAACCTGGTC
Statistics
Matches: 294, Mismatches: 22, Indels: 8
0.91 0.07 0.02
Matches are distributed among these distances:
311 83 0.28
312 5 0.02
313 3 0.01
314 203 0.69
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.30
Consensus pattern (313 bp):
ATCTTTGATCTACTTCAAGCCAATACATGAAGACAAGATCTGCTTTTCCTTCGATCTACTTCGCC
ACCAGTATGGGAAGGCAAGATCTGTTATCTCTGATCTACTTCACGCCAGTACATGAAGACAAGAT
CTGCTTTCTTCGATCTGCTTCGCCACCAGTATGGGAAGACAAGATCTAGTATCTCTGATCTACTT
CACACCAGTACATAAAGACAAGATCTGCTCTCTTTGATCTACTTCGCCACCAGTATGGGAAGGCA
AGATCTGCATATTCGATCCACTTCGCTACCAACATAGGAAGACAGGATCTGGT
Found at i:52642321 original size:44 final size:44
Alignment explanation
Indices: 52641786--52642366 Score: 434
Period size: 44 Copynumber: 13.0 Consensus size: 44
52641776 TTTTTCCTTC
* * *
52641786 GATCTACTTCGCCACCAGTATGGGAAGGCAAGATCTGTTATCTCT
1 GATCTACTTCGCCACCAGTATAGGAAGACAAGATCTG-TATCTTT
* * * * * *
52641831 GATCTACTTC-ACGCCAGTACATGAAGACAAGATCTGCTTTCTTC
1 GATCTACTTCGCCACCAGTATAGGAAGACAAGATCTG-TATCTTT
** * *
52641875 GATCTGTTTCGCCACCAGTATGGGAAGACAAGATCTATTATCTTT
1 GATCTACTTCGCCACCAGTATAGGAAGACAAGATCT-GTATCTTT
* * * * *
52641920 GATCTACTTC-ACACCAGTACATGAAGACAAGCTCTGCTTTCTTT
1 GATCTACTTCGCCACCAGTATAGGAAGACAAGATCTG-TATCTTT
* * * * *
52641964 GATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGTATATTC
1 GATCTACTTCGCCACCAGTATAGGAAGACAAGATCTGTATCTTT
* * * *
52642008 GATCCACTTCGCTACCAATATAGGAAGACAGGATCTGGTATCTTT
1 GATCTACTTCGCCACCAGTATAGGAAGACAAGATCT-GTATCTTT
* * * * * *
52642053 GATCTACTTC-ACGCCAGTACATGAAGACAAGATCTGTTTTCTTC
1 GATCTACTTCGCCACCAGTATAGGAAGACAAGATCTG-TATCTTT
* * *
52642097 GATCTACTTCGCCACCAGTATGGGAAGGCAAGATCTAGTATCTCT
1 GATCTACTTCGCCACCAGTATAGGAAGACAAGATCT-GTATCTTT
* * * * * * *
52642142 GATCTACTTC-ACGCCAGTACATGAAGACAATATCTGCTTTTTCCTTC
1 GATCTACTTCGCCACCAGTATAGGAAGACAAGATCTG---TAT-CTTT
* * * *
52642189 GATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTAGTATCTCT
1 GATCTACTTCGCCACCAGTATAGGAAGACAAGATCT-GTATCTTT
** * * ** * *
52642234 GATCTACTT-TACGCCAGTACATAAAGACAAGATTTGCTCTCTTT
1 GATCTACTTCGCCACCAGTATAGGAAGACAAGATCTG-TATCTTT
* * * *
52642278 GATCTATTTCGCCACCAGTATGGGAAGGCAAGATCTGCATCTTT
1 GATCTACTTCGCCACCAGTATAGGAAGACAAGATCTGTATCTTT
* * * *
52642322 GATCCACTTCGCTACCAGCATAGGAAGACAGGATCTGTTATCTTT
1 GATCTACTTCGCCACCAGTATAGGAAGACAAGATCTG-TATCTTT
52642367 CAACCTGGTC
Statistics
Matches: 399, Mismatches: 120, Indels: 34
0.72 0.22 0.06
Matches are distributed among these distances:
43 3 0.01
44 216 0.54
45 145 0.36
46 5 0.01
47 11 0.03
48 18 0.05
49 1 0.00
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (44 bp):
GATCTACTTCGCCACCAGTATAGGAAGACAAGATCTGTATCTTT
Found at i:52642366 original size:89 final size:89
Alignment explanation
Indices: 52641786--52642366 Score: 445
Period size: 89 Copynumber: 6.5 Consensus size: 89
52641776 TTTTTCCTTC
* * * * *
52641786 GATCTACTTCGCCACCAGTATGGGAAGGCAAGATCTGTTATCTCTGATCTACTTC-ACGCCAGTA
1 GATCTACTTCG-CACCAGTATAGGAAGACAAGATCTGTTATCTTTGATCTACTTCGCCACCAGTA
* * * *
52641850 CATGAAGACAAGATCT-GCTTTCTTC
65 TAGGAAGACAAGATCTAGC-ATCTTT
** * * *
52641875 GATCTGTTTCGCCACCAGTATGGGAAGACAAGATCTATTATCTTTGATCTACTTC-ACACCAGTA
1 GATCTACTTCG-CACCAGTATAGGAAGACAAGATCTGTTATCTTTGATCTACTTCGCCACCAGTA
* * * *
52641939 CATGAAGACAAGCTCT-GCTTTCTTT
65 TAGGAAGACAAGATCTAGC-ATCTTT
* * * * * * * *
52641964 GATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTG-TATATTCGATCCACTTCGCTACCAATA
1 GATCTACTTCG-CACCAGTATAGGAAGACAAGATCTGTTATCTTTGATCTACTTCGCCACCAGTA
* * *
52642028 TAGGAAGACAGGATCTGGTATCTTT
65 TAGGAAGACAAGATCTAGCATCTTT
* * * * * *
52642053 GATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTCTTCGATCTACTTCGCCACCAGTAT
1 GATCTACTTCGCACCAGTATAGGAAGACAAGATCTGTTATCTTTGATCTACTTCGCCACCAGTAT
* * * *
52642118 GGGAAGGCAAGATCTAGTATCTCT
66 AGGAAGACAAGATCTAGCATCTTT
* * * * * * * *
52642142 GATCTACTTCACGCCAGTACATGAAGACAATATCTGCTTTTTCCTTCGATCTGCTTCGCCACCAG
1 GATCTACTTCGCACCAGTATAGGAAGACAAGATCTG--TTAT-CTTTGATCTACTTCGCCACCAG
* * * *
52642207 TATGGGAAGGCAAGATCTAGTATCTCT
63 TATAGGAAGACAAGATCTAGCATCTTT
** * * ** * * * *
52642234 GATCTACTTTACGCCAGTACATAAAGACAAGATTTGCTCTCTTTGATCTATTTCGCCACCAGTAT
1 GATCTACTTCGCACCAGTATAGGAAGACAAGATCTGTTATCTTTGATCTACTTCGCCACCAGTAT
* *
52642299 GGGAAGGCAAGATCT-GCATCTTT
66 AGGAAGACAAGATCTAGCATCTTT
* * *
52642322 GATCCACTTCGCTACCAGCATAGGAAGACAGGATCTGTTATCTTT
1 GATCTACTTCGC-ACCAGTATAGGAAGACAAGATCTGTTATCTTT
52642367 CAACCTGGTC
Statistics
Matches: 420, Mismatches: 65, Indels: 14
0.84 0.13 0.03
Matches are distributed among these distances:
88 49 0.12
89 284 0.68
90 3 0.01
91 4 0.01
92 80 0.19
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (89 bp):
GATCTACTTCGCACCAGTATAGGAAGACAAGATCTGTTATCTTTGATCTACTTCGCCACCAGTAT
AGGAAGACAAGATCTAGCATCTTT
Found at i:52648695 original size:3 final size:3
Alignment explanation
Indices: 52648687--52648741 Score: 110
Period size: 3 Copynumber: 18.3 Consensus size: 3
52648677 ATGTATAGGT
52648687 ATA ATA ATA ATA 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 ATA ATA ATA ATA
52648735 ATA ATA A
1 ATA ATA A
52648742 AAGTAAATAG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:52652633 original size:16 final size:16
Alignment explanation
Indices: 52652609--52652650 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
52652599 TTTGGTTCGC
* *
52652609 TGTATTGGATTAGAGG
1 TGTAATGGAATAGAGG
52652625 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
52652641 TGTAATGGAA
1 TGTAATGGAA
52652651 AAGCTGTGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.36, T:0.31
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:52652916 original size:18 final size:17
Alignment explanation
Indices: 52652895--52652929 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
52652885 TTATTATTAA
*
52652895 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
52652913 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
52652930 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:52653068 original size:154 final size:156
Alignment explanation
Indices: 52652782--52653079 Score: 546
Period size: 154 Copynumber: 1.9 Consensus size: 156
52652772 TAGAATACCC
52652782 TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTA-TA
*
52652847 TTATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
65 TTATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
52652912 TATATAATTTAATAAAATTCTTAATAA
130 TATATAATTTAATAAAATTCTTAATAA
* *
52652939 TTAGCATAAATTTGTTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTA-A-
1 TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATAT
52653002 TATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAAT
66 TATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAAT
52653067 ATATAATTTAATA
131 ATATAATTTAATA
52653080 TGAATTACTC
Statistics
Matches: 138, Mismatches: 3, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
154 77 0.56
155 1 0.01
157 60 0.43
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.47
Consensus pattern (156 bp):
TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATAT
TATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAAT
ATATAATTTAATAAAATTCTTAATAA
Found at i:52653077 original size:14 final size:15
Alignment explanation
Indices: 52653038--52653171 Score: 77
Period size: 15 Copynumber: 8.9 Consensus size: 15
52653028 TTTAAACATA
*
52653038 ATTATTATTAAATAT
1 ATTATAATTAAATAT
52653053 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
52653067 A-TATAATTTAATAT
1 ATTATAATTAAATAT
*
52653081 GAATTACTCAAATCATAATAT
1 --ATTA-T--AATTA-AATAT
* *
52653102 ATGATACTGTAAA-AT
1 ATTATAAT-TAAATAT
52653117 A-TA-AATTAACATA-
1 ATTATAATTAA-ATAT
*
52653130 ATTATTATTAAATAT
1 ATTATAATTAAATAT
52653145 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
52653159 A-TATAATTTAATA
1 ATTATAATTAAATA
52653172 AAATTCTTAA
Statistics
Matches: 92, Mismatches: 12, Indels: 31
0.68 0.09 0.23
Matches are distributed among these distances:
12 3 0.03
13 22 0.24
14 16 0.17
15 30 0.33
16 5 0.05
17 3 0.03
18 2 0.02
19 3 0.03
20 3 0.03
21 5 0.05
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:52653220 original size:120 final size:117
Alignment explanation
Indices: 52653078--52653294 Score: 330
Period size: 120 Copynumber: 1.8 Consensus size: 117
52653068 TATAATTTAA
* * *
52653078 TATGAATTACTCAAATCATAATATATGATACTGTAAAATATAAATT-AACATAATTATTATTAAA
1 TATGAATTACTCAAATCATAATATATGATACTATAAAAGA-AAATTCAA-ATAATTAATATTAAA
52653142 TAT-ATTATAATTAAAATATATAATTTAATAAAATTCTTAATAAATAAAATTCTTC
64 TATGATT-TAATT-AAATATATAATTTAATAAAATTCTTAATAAATAAAATTCTTC
*
52653197 TATGAATTTACTCAAATCATAATATATGATACTATAAAAGAAATTTCAAATAATTAATATTAAAT
1 TATGAA-TTACTCAAATCATAATATATGATACTATAAAAGAAAATTCAAATAATTAATATTAAAT
*
52653262 ATGATTTAATTAAATATATGATTTAATAAAATT
65 ATGATTTAATTAAATATATAATTTAATAAAATT
52653295 TAAAATTATT
Statistics
Matches: 90, Mismatches: 5, Indels: 7
0.88 0.05 0.07
Matches are distributed among these distances:
118 21 0.23
119 32 0.36
120 37 0.41
ACGTcount: A:0.50, C:0.06, G:0.04, T:0.40
Consensus pattern (117 bp):
TATGAATTACTCAAATCATAATATATGATACTATAAAAGAAAATTCAAATAATTAATATTAAATA
TGATTTAATTAAATATATAATTTAATAAAATTCTTAATAAATAAAATTCTTC
Found at i:52653275 original size:15 final size:15
Alignment explanation
Indices: 52653255--52653293 Score: 51
Period size: 17 Copynumber: 2.5 Consensus size: 15
52653245 AATAATTAAT
52653255 ATTAAATATGATTTA
1 ATTAAATATGATTTA
52653270 ATTAAATATATGATTTA
1 ATT-AA-ATATGATTTA
*
52653287 ATAAAAT
1 ATTAAAT
52653294 TTAAAATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 5 0.24
16 4 0.19
17 12 0.57
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (15 bp):
ATTAAATATGATTTA
Found at i:52653280 original size:17 final size:17
Alignment explanation
Indices: 52653260--52653293 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
52653250 TTAATATTAA
*
52653260 ATATGATTTAATTAAAT
1 ATATGATTTAATAAAAT
52653277 ATATGATTTAATAAAAT
1 ATATGATTTAATAAAAT
52653294 TTAAAATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (17 bp):
ATATGATTTAATAAAAT
Found at i:52653436 original size:93 final size:92
Alignment explanation
Indices: 52653326--52653520 Score: 286
Period size: 93 Copynumber: 2.1 Consensus size: 92
52653316 GATTATAGTT
* * *
52653326 TATGAATTTGTATAATTTAAAATAA-TAATTATTACATATAATT-TAATAATAATATATAATTTC
1 TATGAATTTATACAATTTAAAATAATTAA-TATTAAATATAATTAT-ATAATAATATATAATTTC
* *
52653389 ATAAAATTCTTGATAATAAAAATTTTCTTA
64 ATAAAATTCTTAATAAT-AAAATGTTCTTA
* *
52653419 TATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTATATAGTGATATATAATTTCAT
1 TATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTATATAATAATATATAATTTCAT
52653484 AAAATTCTTAATAATAAAATGTTCTTA
66 AAAATTCTTAATAATAAAATGTTCTTA
52653511 TATGAATTTA
1 TATGAATTTA
52653521 CTAAAATCAA
Statistics
Matches: 93, Mismatches: 7, Indels: 5
0.89 0.07 0.05
Matches are distributed among these distances:
92 21 0.23
93 68 0.73
94 4 0.04
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (92 bp):
TATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTATATAATAATATATAATTTCAT
AAAATTCTTAATAATAAAATGTTCTTA
Found at i:52654932 original size:11 final size:11
Alignment explanation
Indices: 52654918--52654944 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
52654908 AAAAATCAAT
52654918 ACAAAAGTTTC
1 ACAAAAGTTTC
52654929 ACAAAAGTTTC
1 ACAAAAGTTTC
52654940 ACAAA
1 ACAAA
52654945 CTAATTTCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.52, C:0.19, G:0.07, T:0.22
Consensus pattern (11 bp):
ACAAAAGTTTC
Found at i:52657207 original size:15 final size:15
Alignment explanation
Indices: 52657187--52657217 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
52657177 ATATTATGTA
52657187 TAATTGAGGTAAAAT
1 TAATTGAGGTAAAAT
52657202 TAATTGAGGTAAAAT
1 TAATTGAGGTAAAAT
52657217 T
1 T
52657218 TGAAGGTTGG
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:0.45, C:0.00, G:0.19, T:0.35
Consensus pattern (15 bp):
TAATTGAGGTAAAAT
Found at i:52679551 original size:44 final size:44
Alignment explanation
Indices: 52679501--52679969 Score: 449
Period size: 44 Copynumber: 10.5 Consensus size: 44
52679491 GTCACCGTAC
***
52679501 CAAATCTTATCTCCCTAAAGTTGCAGTGGATTGGATTGAAGCTA
1 CAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGCTA
* * * *
52679545 CAAATCTTATCTTCCTAAAGTTGCAGTGGAGTAGATTAAAGCCA
1 CAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGCTA
* * *
52679589 CAAAT-TTCATCTCCCTGAAGTTACAGTGGAGCAGATTGAAGCCA
1 CAAATCTT-ATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGCTA
* * * * *
52679633 CAAATCTTATCTCCCTGAAGTTGCAGTGAAGCAGATTAAAACCA
1 CAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGCTA
* **
52679677 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATAAAAGCTA
1 CAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGCTA
* * * *
52679721 CAAATCTTATCTCCCTAAAGTTACAGCGGAGCAGATTGAGGATA
1 CAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGCTA
* * * * *
52679765 TCGAATCGTATCTCCCTAGAGTTACAGTGGAACAGATTGAAGCTA
1 -CAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGCTA
* * *
52679810 CAAATCTTATCTCCCTAAATTTGTAGTGGAGCAGATTGAAGCGA
1 CAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGCTA
* * * * * * *
52679854 CAAATCATATAC-CTCTGAAGTTACAGTGG-GTCGGATTAAATCTA
1 CAAATCTTAT-CTCCCTAAAGTTGCAGTGGAG-CAGATTGAAGCTA
* *
52679898 CCATAGCGAGTTTTATCTCCCTCAAGTTGCAGTGGAGCAGATTGAAGCTA
1 -CA-A---A-TCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGCTA
* * *
52679948 CGAATCTCATCTCCCTGAAGTT
1 CAAATCTTATCTCCCTAAAGTT
52679970 TTAGTGGGTT
Statistics
Matches: 350, Mismatches: 62, Indels: 26
0.80 0.14 0.06
Matches are distributed among these distances:
43 3 0.01
44 270 0.77
45 43 0.12
46 1 0.00
48 1 0.00
49 3 0.01
50 28 0.08
51 1 0.00
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.28
Consensus pattern (44 bp):
CAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGCTA
Found at i:52683559 original size:40 final size:40
Alignment explanation
Indices: 52683491--52683620 Score: 197
Period size: 40 Copynumber: 3.2 Consensus size: 40
52683481 AGCGGCACTT
*
52683491 TTAGCGGCGTTTGGAGCAAAAGCGCCGCTAAAGAGTGAGCA
1 TTAGCGGCGTTT-AAGCAAAAGCGCCGCTAAAGAGTGAGCA
*
52683532 TTAGCGGCGTTTAAGTAAAAGCGCCGCTAAAGAGTGAGCA
1 TTAGCGGCGTTTAAGCAAAAGCGCCGCTAAAGAGTGAGCA
* * *
52683572 TTAGTGGCGTTTAAGGAAAAGCGCCGCTAAAGAGTGAGCG
1 TTAGCGGCGTTTAAGCAAAAGCGCCGCTAAAGAGTGAGCA
*
52683612 TTAGTGGCG
1 TTAGCGGCG
52683621 GTTATAAAAA
Statistics
Matches: 84, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
40 72 0.86
41 12 0.14
ACGTcount: A:0.29, C:0.17, G:0.34, T:0.20
Consensus pattern (40 bp):
TTAGCGGCGTTTAAGCAAAAGCGCCGCTAAAGAGTGAGCA
Found at i:52683831 original size:112 final size:111
Alignment explanation
Indices: 52683571--52684501 Score: 1511
Period size: 112 Copynumber: 8.3 Consensus size: 111
52683561 AAGAGTGAGC
*** * * ** *
52683571 ATTAGTGGCGTTTAAGGAAAAGCGCCGCTAAAGAGTGAGCGTTAGTGGCGGTTATAAAAAACGCC
1 ATTAGTGGCGTTT-ATTTAAAGCGCCGCTAAAGAGTGAACATTAGCAGCGTTTATAAAAAACGCC
52683636 GCAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTTGGGGGGGGA
65 GCAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTT-GGGGGGGA
* * *
52683684 CTTAGTGGTGTTTATTGTAAAGCGCCGCTAAAGAGTGAACATTAGCAGCGTTTATAAAAAATGCC
1 ATTAGTGGCGTTTATT-TAAAGCGCCGCTAAAGAGTGAACATTAGCAGCGTTTATAAAAAACGCC
*
52683749 ACAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTTGGGGGGGA
65 GCAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTTGGGGGGGA
52683796 ATTAGTGGCGTTTATTTCAAAGCGCCGCTAAAGAGTGAACATTAGCAGCGTTTATAAAAAACGCC
1 ATTAGTGGCGTTTATTT-AAAGCGCCGCTAAAGAGTGAACATTAGCAGCGTTTATAAAAAACGCC
* *
52683861 GCAAATAATACACCCAAACGGTGCCGTTTTGTGGCCTTTGCGGGGGA
65 GCAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTTGGGGGGGA
* *
52683908 ATTAGTGGCGTTTATTGTAAAGCGCCACTAAAGAGTGAACATTAGCAGCGTTTATAAAAAATGCC
1 ATTAGTGGCGTTTATT-TAAAGCGCCGCTAAAGAGTGAACATTAGCAGCGTTTATAAAAAACGCC
*
52683973 GCAAATAATACACCCAGACAGTGCCGTTTTGTGGCCTTTGGGGGGGA
65 GCAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTTGGGGGGGA
52684020 ATTAGTGGCGTTTATTTCAAAGCGCCGCTAAAGAGTGAACATTAGCAGCGTTTATAAAAAACGCC
1 ATTAGTGGCGTTTATTT-AAAGCGCCGCTAAAGAGTGAACATTAGCAGCGTTTATAAAAAACGCC
* * *
52684085 GCAAATAATACACCCAAACGGTGTCGTTTTGTGGCATTTGGGGGGGA
65 GCAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTTGGGGGGGA
*
52684132 ATTAGTGGCGTTTATTGAAAAGCGCCGCTAAAGAGTGAACATTAGCAGCGTTTATAAAAAACGCC
1 ATTAGTGGCGTTTATT-TAAAGCGCCGCTAAAGAGTGAACATTAGCAGCGTTTATAAAAAACGCC
52684197 GCAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTTGGGGGGGA
65 GCAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTTGGGGGGGA
*
52684244 ATTAGTGGCGTTTATTTCAAAGCGCCGCTAAAGAGTGAACATTAGCAGCCTTTATAAAAAACGCC
1 ATTAGTGGCGTTTATTT-AAAGCGCCGCTAAAGAGTGAACATTAGCAGCGTTTATAAAAAACGCC
*
52684309 GCAAATAATACACCCAAACGGTGCCGTTTTGTGGCCTTTGGGGGGGGGA
65 GCAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTT--GGGGGGGA
52684358 ATTAGTGGCGTTTATTGTAAAGCGCCGCTAAAGAGTGAACATTAGCAGCGTTTATAAAAAACGCC
1 ATTAGTGGCGTTTATT-TAAAGCGCCGCTAAAGAGTGAACATTAGCAGCGTTTATAAAAAACGCC
**
52684423 GCAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTTTTCGGGGGA
65 GCAAATAATACACCCAGACGGTGCCGTTTTGTGGCC-TTTGGGGGGGA
*
52684471 CTTAGTGGCGTTTATTGTAAAGCGCCGCTAA
1 ATTAGTGGCGTTTATT-TAAAGCGCCGCTAA
52684502 TCTAGGTGTT
Statistics
Matches: 767, Mismatches: 41, Indels: 20
0.93 0.05 0.02
Matches are distributed among these distances:
111 2 0.00
112 529 0.69
113 127 0.17
114 105 0.14
115 4 0.01
ACGTcount: A:0.29, C:0.19, G:0.27, T:0.25
Consensus pattern (111 bp):
ATTAGTGGCGTTTATTTAAAGCGCCGCTAAAGAGTGAACATTAGCAGCGTTTATAAAAAACGCCG
CAAATAATACACCCAGACGGTGCCGTTTTGTGGCCTTTGGGGGGGA
Found at i:52686350 original size:84 final size:84
Alignment explanation
Indices: 52686209--52686405 Score: 313
Period size: 84 Copynumber: 2.3 Consensus size: 84
52686199 TAAACTTTTG
** * * *
52686209 GTGGCGTTTTTAGGAAAACGCCACAAATAATGCAATTCCAGACCACGAAAACGGTGTCGTTTCTG
1 GTGGCGTTTTTACAAAAACGCCACAAAAAATACAATTCCAAACCACGAAAACGGTGTCGTTTCTG
52686274 TTCACAGCTGTAAGATTTA
66 TTCACAGCTGTAAGATTTA
*
52686293 GTGGCGTTTTTATAAAAACGCCACAAAAAATACAATTCCAAACCACGAAAACGGTGTCGTTTCTG
1 GTGGCGTTTTTACAAAAACGCCACAAAAAATACAATTCCAAACCACGAAAACGGTGTCGTTTCTG
*
52686358 TTCACAGCTGTAATATTTA
66 TTCACAGCTGTAAGATTTA
*
52686377 GTGGCGTTTTTACCAAAAATGCCACAAAA
1 GTGGCGTTTTTA-CAAAAACGCCACAAAA
52686406 CGGTGTTAAT
Statistics
Matches: 104, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
84 90 0.87
85 14 0.13
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.27
Consensus pattern (84 bp):
GTGGCGTTTTTACAAAAACGCCACAAAAAATACAATTCCAAACCACGAAAACGGTGTCGTTTCTG
TTCACAGCTGTAAGATTTA
Found at i:52687629 original size:11 final size:11
Alignment explanation
Indices: 52687609--52687648 Score: 73
Period size: 11 Copynumber: 3.7 Consensus size: 11
52687599 GAATATCTCA
52687609 AACT-ATGGGT
1 AACTAATGGGT
52687619 AACTAATGGGT
1 AACTAATGGGT
52687630 AACTAATGGGT
1 AACTAATGGGT
52687641 AACTAATG
1 AACTAATG
52687649 TATTATCATC
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
10 4 0.14
11 25 0.86
ACGTcount: A:0.38, C:0.10, G:0.25, T:0.28
Consensus pattern (11 bp):
AACTAATGGGT
Found at i:52689012 original size:17 final size:17
Alignment explanation
Indices: 52688990--52689261 Score: 174
Period size: 17 Copynumber: 14.6 Consensus size: 17
52688980 GTTAAATTTA
52688990 TTACTAAAATACATTAC
1 TTACTAAAATACATTAC
*
52689007 TTACTAAAATAAATTAC
1 TTACTAAAATACATTAC
*
52689024 TTACTAAAATTTGTTTAAATTTA-
1 TTACTAAAA------TACA-TTAC
52689047 TTACTAAAATACATTAC
1 TTACTAAAATACATTAC
52689064 TTACTAAAATACATTAC
1 TTACTAAAATACATTAC
* *
52689081 TTACATAAATTTGTTTAAATTTA-
1 TTAC-TAAA-----ATACA-TTAC
*
52689104 TTTCTAAAATACATTAC
1 TTACTAAAATACATTAC
*
52689121 TTACTAAAATAAATTAC
1 TTACTAAAATACATTAC
*
52689138 TTACTAAAATTTGTTTAAATTTA-
1 TTACTAAAA------TACA-TTAC
*
52689161 TAACTAAAATACATTAC
1 TTACTAAAATACATTAC
*
52689178 TTAGTAAAATACATTAC
1 TTACTAAAATACATTAC
*
52689195 TTACTAAAATTTGTTTAAATTTA-
1 TTACTAAAA------TACA-TTAC
52689218 TTACTAAAATACATTAC
1 TTACTAAAATACATTAC
52689235 TTACTAAAATACATTAC
1 TTACTAAAATACATTAC
52689252 TTACTAAAAT
1 TTACTAAAAT
52689262 TTGTTTAAAT
Statistics
Matches: 207, Mismatches: 16, Indels: 64
0.72 0.06 0.22
Matches are distributed among these distances:
16 12 0.06
17 132 0.64
18 4 0.02
22 4 0.02
23 43 0.21
24 12 0.06
ACGTcount: A:0.45, C:0.12, G:0.02, T:0.41
Consensus pattern (17 bp):
TTACTAAAATACATTAC
Found at i:52689069 original size:57 final size:57
Alignment explanation
Indices: 52688981--52689305 Score: 544
Period size: 57 Copynumber: 5.6 Consensus size: 57
52688971 CGATTGAATG
*
52688981 TTAAATTTATTACTAAAATACATTACTTACTAAAATAAATTACTTACTAAAATTTGT
1 TTAAATTTATTACTAAAATACATTACTTACTAAAATACATTACTTACTAAAATTTGT
52689038 TTAAATTTATTACTAAAATACATTACTTACTAAAATACATTACTTAC-ATAAATTTGT
1 TTAAATTTATTACTAAAATACATTACTTACTAAAATACATTACTTACTA-AAATTTGT
* *
52689095 TTAAATTTATTTCTAAAATACATTACTTACTAAAATAAATTACTTACTAAAATTTGT
1 TTAAATTTATTACTAAAATACATTACTTACTAAAATACATTACTTACTAAAATTTGT
* *
52689152 TTAAATTTATAACTAAAATACATTACTTAGTAAAATACATTACTTACTAAAATTTGT
1 TTAAATTTATTACTAAAATACATTACTTACTAAAATACATTACTTACTAAAATTTGT
52689209 TTAAATTTATTACTAAAATACATTACTTACTAAAATACATTACTTACTAAAATTTGT
1 TTAAATTTATTACTAAAATACATTACTTACTAAAATACATTACTTACTAAAATTTGT
*
52689266 TTAAATTTATTAATTACTTAAATACATTACTTACTAAAAT
1 TTAAA--T-TT-ATTACTAAAATACATTACTTACTAAAAT
52689306 TTGTTTAAAT
Statistics
Matches: 252, Mismatches: 10, Indels: 8
0.93 0.04 0.03
Matches are distributed among these distances:
56 1 0.00
57 220 0.87
58 1 0.00
59 1 0.00
60 2 0.01
61 27 0.11
ACGTcount: A:0.45, C:0.11, G:0.02, T:0.42
Consensus pattern (57 bp):
TTAAATTTATTACTAAAATACATTACTTACTAAAATACATTACTTACTAAAATTTGT
Found at i:52689289 original size:44 final size:44
Alignment explanation
Indices: 52689230--52689321 Score: 166
Period size: 44 Copynumber: 2.1 Consensus size: 44
52689220 ACTAAAATAC
*
52689230 ATTACTTACTAAAATACATTACTTACTAAAATTTGTTTAAATTT
1 ATTAATTACTAAAATACATTACTTACTAAAATTTGTTTAAATTT
*
52689274 ATTAATTACTTAAATACATTACTTACTAAAATTTGTTTAAATTT
1 ATTAATTACTAAAATACATTACTTACTAAAATTTGTTTAAATTT
52689318 ATTA
1 ATTA
52689322 CTTAAATATG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.41, C:0.10, G:0.02, T:0.47
Consensus pattern (44 bp):
ATTAATTACTAAAATACATTACTTACTAAAATTTGTTTAAATTT
Found at i:52689296 original size:13 final size:13
Alignment explanation
Indices: 52689278--52689359 Score: 69
Period size: 13 Copynumber: 6.3 Consensus size: 13
52689268 AAATTTATTA
*
52689278 ATTACTTAAATAC
1 ATTACTTAAATAT
*
52689291 ATTACTTACTAAAAT
1 ATTACTTA--AATAT
** *
52689306 -TTGTTTAAATTT
1 ATTACTTAAATAT
52689318 ATTACTTAAATAT
1 ATTACTTAAATAT
* *
52689331 GTTACTTAAATTT
1 ATTACTTAAATAT
52689344 ATTACTTAAATA-
1 ATTACTTAAATAT
52689356 ATTA
1 ATTA
52689360 TAAATAAGAT
Statistics
Matches: 53, Mismatches: 13, Indels: 7
0.73 0.18 0.10
Matches are distributed among these distances:
12 7 0.13
13 38 0.72
14 5 0.09
15 3 0.06
ACGTcount: A:0.41, C:0.09, G:0.02, T:0.48
Consensus pattern (13 bp):
ATTACTTAAATAT
Found at i:52689588 original size:71 final size:72
Alignment explanation
Indices: 52689501--52689790 Score: 541
Period size: 71 Copynumber: 4.1 Consensus size: 72
52689491 TAAAATAAAA
52689501 TATAAAAAATATGTGGAATATTAAAATTGACTATTAAAATAAAATGTTATTTTATTAAATATTAT
1 TATAAAAAATATGTGGAATATTAAAATTGACTATTAAAATAAAATGTTATTTTATTAAATATTAT
52689566 TAATAAT
66 TAATAAT
*
52689573 TATAAAAAA-ATGTGGAATATTAAAATTGACTATTAAAATAAAATGATATTTTATTAAATATTAT
1 TATAAAAAATATGTGGAATATTAAAATTGACTATTAAAATAAAATGTTATTTTATTAAATATTAT
52689637 TAATAAT
66 TAATAAT
52689644 TATAAAAAATATGTGGAATATTAAAATTGACTATTAAAATAAAATGTTATTTTATTAAATATTAT
1 TATAAAAAATATGTGGAATATTAAAATTGACTATTAAAATAAAATGTTATTTTATTAAATATTAT
52689709 TAATAAT
66 TAATAAT
52689716 TATAAAAAAATATGTGGAATATTAAAATTGACTATTAAAAT-AAAT-TTATTTTATTAAATATTA
1 TAT-AAAAAATATGTGGAATATTAAAATTGACTATTAAAATAAAATGTTATTTTATTAAATATTA
52689779 TTAATAAT
65 TTAATAAT
52689787 TATA
1 TATA
52689791 TTATAATTTA
Statistics
Matches: 214, Mismatches: 2, Indels: 6
0.96 0.01 0.03
Matches are distributed among these distances:
70 1 0.00
71 99 0.46
72 77 0.36
73 37 0.17
ACGTcount: A:0.51, C:0.01, G:0.07, T:0.41
Consensus pattern (72 bp):
TATAAAAAATATGTGGAATATTAAAATTGACTATTAAAATAAAATGTTATTTTATTAAATATTAT
TAATAAT
Found at i:52689638 original size:31 final size:31
Alignment explanation
Indices: 52689603--52689711 Score: 83
Period size: 31 Copynumber: 3.2 Consensus size: 31
52689593 TAAAATTGAC
52689603 TATTAAAATAAAATGATATTTTATTAAATAT
1 TATTAAAATAAAATGATATTTTATTAAATAT
** * *
52689634 TATTAATAATTATAAAAAATATGTGGAATATTAAAATTGAC
1 TATTAA-AA-TA-AAATGATAT-T---TTATT-AAA-T-AT
*
52689675 TATTAAAATAAAATGTTATTTTATTAAATAT
1 TATTAAAATAAAATGATATTTTATTAAATAT
52689706 TATTAA
1 TATTAA
52689712 TAATTATAAA
Statistics
Matches: 59, Mismatches: 9, Indels: 20
0.67 0.10 0.23
Matches are distributed among these distances:
31 13 0.22
32 3 0.05
33 5 0.08
34 11 0.19
35 1 0.02
37 1 0.02
38 10 0.17
39 5 0.08
40 3 0.05
41 7 0.12
ACGTcount: A:0.50, C:0.01, G:0.06, T:0.43
Consensus pattern (31 bp):
TATTAAAATAAAATGATATTTTATTAAATAT
Found at i:52689656 original size:143 final size:143
Alignment explanation
Indices: 52689501--52689790 Score: 539
Period size: 143 Copynumber: 2.0 Consensus size: 143
52689491 TAAAATAAAA
52689501 TATAAAAAATATGTGGAATATTAAAATTGACTATTAAAATAAAATGTTATTTTATTAAATATTAT
1 TATAAAAAATATGTGGAATATTAAAATTGACTATTAAAATAAAATGTTATTTTATTAAATATTAT
52689566 TAATAATTAT-AAAAAA-ATGTGGAATATTAAAATTGACTATTAAAATAAAATGATATTTTATTA
66 TAATAATTATAAAAAAATATGTGGAATATTAAAATTGACTATTAAAAT-AAAT-ATATTTTATTA
52689629 AATATTATTAATAAT
129 AATATTATTAATAAT
52689644 TATAAAAAATATGTGGAATATTAAAATTGACTATTAAAATAAAATGTTATTTTATTAAATATTAT
1 TATAAAAAATATGTGGAATATTAAAATTGACTATTAAAATAAAATGTTATTTTATTAAATATTAT
*
52689709 TAATAATTATAAAAAAATATGTGGAATATTAAAATTGACTATTAAAATAAATTTATTTTATTAAA
66 TAATAATTATAAAAAAATATGTGGAATATTAAAATTGACTATTAAAATAAATATATTTTATTAAA
52689774 TATTATTAATAAT
131 TATTATTAATAAT
52689787 TATA
1 TATA
52689791 TTATAATTTA
Statistics
Matches: 144, Mismatches: 1, Indels: 4
0.97 0.01 0.03
Matches are distributed among these distances:
143 104 0.72
144 10 0.07
145 30 0.21
ACGTcount: A:0.51, C:0.01, G:0.07, T:0.41
Consensus pattern (143 bp):
TATAAAAAATATGTGGAATATTAAAATTGACTATTAAAATAAAATGTTATTTTATTAAATATTAT
TAATAATTATAAAAAAATATGTGGAATATTAAAATTGACTATTAAAATAAATATATTTTATTAAA
TATTATTAATAAT
Found at i:52689820 original size:19 final size:20
Alignment explanation
Indices: 52689784--52689825 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
52689774 TATTATTAAT
52689784 AATTATATTATAATTTATTA
1 AATTATATTATAATTTATTA
*
52689804 AATTATA-TATTATTTATTA
1 AATTATATTATAATTTATTA
52689823 AAT
1 AAT
52689826 AATACATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
AATTATATTATAATTTATTA
Found at i:52689866 original size:18 final size:18
Alignment explanation
Indices: 52689843--52689921 Score: 78
Period size: 18 Copynumber: 4.4 Consensus size: 18
52689833 AATAACTTAC
52689843 AACTTACATAATACATTT
1 AACTTACATAATACATTT
52689861 AACTTACATAACTTACA--T
1 AACTTACATAA--TACATTT
*
52689879 AA--TACATAATA-ACTTAC
1 AACTTACATAATACA-TT-T
52689896 AACTTACATAATACATTT
1 AACTTACATAATACATTT
52689914 AACTTACA
1 AACTTACA
52689922 ACTTACATAA
Statistics
Matches: 50, Mismatches: 2, Indels: 18
0.71 0.03 0.26
Matches are distributed among these distances:
13 1 0.02
14 2 0.04
16 7 0.14
17 2 0.04
18 22 0.44
19 11 0.22
20 5 0.10
ACGTcount: A:0.47, C:0.19, G:0.00, T:0.34
Consensus pattern (18 bp):
AACTTACATAATACATTT
Found at i:52689906 original size:26 final size:25
Alignment explanation
Indices: 52689824--52690180 Score: 549
Period size: 26 Copynumber: 14.1 Consensus size: 25
52689814 TATTTATTAA
52689824 ATAATACATAATAACTTACAACTTAC
1 ATAATACAT-ATAACTTACAACTTAC
*
52689850 ATAATACATTTAACTTACATAACTTAC
1 ATAATACATATAACTTAC--AACTTAC
52689877 ATAATACATAATAACTTACAACTTAC
1 ATAATACAT-ATAACTTACAACTTAC
*
52689903 ATAATACATTTAACTTACAACTTAC
1 ATAATACATATAACTTACAACTTAC
*
52689928 ATAATACATTTAACTTACAACTTAC
1 ATAATACATATAACTTACAACTTAC
*
52689953 ACAATACATAATAACTTACAACTTAC
1 ATAATACAT-ATAACTTACAACTTAC
52689979 ATAATACATAATAACTTACAACTTAC
1 ATAATACAT-ATAACTTACAACTTAC
* *
52690005 ACAATACATTTAACTTACAACTTAC
1 ATAATACATATAACTTACAACTTAC
52690030 ATAATACATAATAACTTACAACTTAC
1 ATAATACAT-ATAACTTACAACTTAC
52690056 ATAATACAT-TAACTTACAACTTAC
1 ATAATACATATAACTTACAACTTAC
52690080 ATAATACAT-TAACTTACAACTTAC
1 ATAATACATATAACTTACAACTTAC
52690104 ATAATACAT-TAACTTACAACTTAC
1 ATAATACATATAACTTACAACTTAC
* *
52690128 ACAATACATTTAACTTACAACTTAC
1 ATAATACATATAACTTACAACTTAC
52690153 ATAATACATAATAACTTACAACTTAC
1 ATAATACAT-ATAACTTACAACTTAC
52690179 AT
1 AT
52690181 TTAACTTACA
Statistics
Matches: 311, Mismatches: 13, Indels: 14
0.92 0.04 0.04
Matches are distributed among these distances:
24 71 0.23
25 102 0.33
26 114 0.37
27 16 0.05
28 8 0.03
ACGTcount: A:0.47, C:0.20, G:0.00, T:0.32
Consensus pattern (25 bp):
ATAATACATATAACTTACAACTTAC
Found at i:52689968 original size:51 final size:51
Alignment explanation
Indices: 52689824--52690180 Score: 573
Period size: 51 Copynumber: 7.0 Consensus size: 51
52689814 TATTTATTAA
52689824 ATAATACATAATAACTTACAACTTACATAATACATTTAACTTACATAACTTAC
1 ATAATACATAATAACTTACAACTTACATAATACATTTAACTTAC--AACTTAC
52689877 ATAATACATAATAACTTACAACTTACATAATACATTTAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTACATAATACATTTAACTTACAACTTAC
* * *
52689928 ATAATACAT-TTAACTTACAACTTACACAATACATAATAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTACATAATACAT-TTAACTTACAACTTAC
*
52689979 ATAATACATAATAACTTACAACTTACACAATACATTTAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTACATAATACATTTAACTTACAACTTAC
52690030 ATAATACATAATAACTTACAACTTACATAATACA-TTAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTACATAATACATTTAACTTACAACTTAC
52690080 ATAATACAT--TAACTTACAACTTACATAATACA-TTAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTACATAATACATTTAACTTACAACTTAC
* * *
52690128 ACAATACAT-TTAACTTACAACTTACATAATACATAATAACTTACAACTTAC
1 ATAATACATAATAACTTACAACTTACATAATACAT-TTAACTTACAACTTAC
52690179 AT
1 AT
52690181 TTAACTTACA
Statistics
Matches: 290, Mismatches: 9, Indels: 12
0.93 0.03 0.04
Matches are distributed among these distances:
48 47 0.16
49 23 0.08
50 48 0.17
51 104 0.36
52 24 0.08
53 44 0.15
ACGTcount: A:0.47, C:0.20, G:0.00, T:0.32
Consensus pattern (51 bp):
ATAATACATAATAACTTACAACTTACATAATACATTTAACTTACAACTTAC
Found at i:52690144 original size:18 final size:18
Alignment explanation
Indices: 52690121--52690208 Score: 61
Period size: 18 Copynumber: 4.4 Consensus size: 18
52690111 ATTAACTTAC
52690121 AACTTACACAATACATTT
1 AACTTACACAATACATTT
*
52690139 AACTTACAACTTACATAATACATAAT
1 AACTT---AC--AC--AATACAT-TT
*
52690165 AACTTACA-ACTTACATTT
1 AACTTACACA-ATACATTT
*
52690183 AACTTACATAATACATTT
1 AACTTACACAATACATTT
52690201 AACTTACA
1 AACTTACA
52690209 TAACTTACAT
Statistics
Matches: 56, Mismatches: 4, Indels: 20
0.70 0.05 0.25
Matches are distributed among these distances:
18 30 0.54
19 6 0.11
21 3 0.05
23 4 0.07
25 7 0.12
26 6 0.11
ACGTcount: A:0.45, C:0.20, G:0.00, T:0.34
Consensus pattern (18 bp):
AACTTACACAATACATTT
Found at i:52690188 original size:11 final size:10
Alignment explanation
Indices: 52690172--52690225 Score: 55
Period size: 9 Copynumber: 5.7 Consensus size: 10
52690162 AATAACTTAC
52690172 AACTTACATTT
1 AACTTACA-TT
52690183 AACTTACA-T
1 AACTTACATT
52690192 AA--TACATTT
1 AACTTACA-TT
52690201 AACTTACA-T
1 AACTTACATT
52690210 AACTTACA-T
1 AACTTACATT
52690219 AACTTAC
1 AACTTAC
52690226 CATTGTAATT
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
7 4 0.10
9 23 0.59
11 12 0.31
ACGTcount: A:0.43, C:0.20, G:0.00, T:0.37
Consensus pattern (10 bp):
AACTTACATT
Found at i:52690209 original size:18 final size:18
Alignment explanation
Indices: 52690146--52690211 Score: 89
Period size: 18 Copynumber: 3.6 Consensus size: 18
52690136 TTTAACTTAC
*
52690146 AACTTACATAATACATAAT
1 AACTTACATAATACAT-TT
*
52690165 AACTTACA-ACTTACATTT
1 AACTTACATA-ATACATTT
52690183 AACTTACATAATACATTT
1 AACTTACATAATACATTT
52690201 AACTTACATAA
1 AACTTACATAA
52690212 CTTACATAAC
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
18 28 0.67
19 14 0.33
ACGTcount: A:0.47, C:0.18, G:0.00, T:0.35
Consensus pattern (18 bp):
AACTTACATAATACATTT
Found at i:52695697 original size:21 final size:21
Alignment explanation
Indices: 52695671--52695741 Score: 88
Period size: 21 Copynumber: 3.4 Consensus size: 21
52695661 CTACAACTTA
* *
52695671 AAGCAGAGGCGGAAGCGAGGG
1 AAGCAGAGGCTGCAGCGAGGG
*
52695692 AAGCAGCGGCTGCAGCGAGGG
1 AAGCAGAGGCTGCAGCGAGGG
* * *
52695713 AAGCGGAGGTTGCAGCGAGAG
1 AAGCAGAGGCTGCAGCGAGGG
52695734 AAGCAGAG
1 AAGCAGAG
52695742 CAGAGCAAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.31, C:0.17, G:0.48, T:0.04
Consensus pattern (21 bp):
AAGCAGAGGCTGCAGCGAGGG
Found at i:52696117 original size:42 final size:42
Alignment explanation
Indices: 52696071--52696270 Score: 231
Period size: 42 Copynumber: 4.8 Consensus size: 42
52696061 GTATAAAAGC
* *
52696071 GCCACTAAAGAACATGTTCTTTTGTGGCGTTTGTAAAAAAAT
1 GCCACTAAAGAACATGTTCTTTAGCGGCGTTTGTAAAAAAAT
*
52696113 GCCACTAAAGAACATGTTCTTTAGCGGCGCTTGTAAAAAAAT
1 GCCACTAAAGAACATGTTCTTTAGCGGCGTTTGTAAAAAAAT
* * * *
52696155 GCCGCTAAAGAACACGTTCTTTAGAGGCGCTTAG-AAAAAAAT
1 GCCACTAAAGAACATGTTCTTTAGCGGCG-TTTGTAAAAAAAT
* * * **** **
52696197 GCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTCCTTAAGC
1 GCCACTAAAGAACATGTTCTTTAGCGGCGTTTGTAAAAAAAT
*
52696239 GCCGCTAAAGAACATGTTCTTTAGCGGCGTTT
1 GCCACTAAAGAACATGTTCTTTAGCGGCGTTT
52696271 TTTTCTAAGC
Statistics
Matches: 136, Mismatches: 20, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
41 2 0.01
42 132 0.97
43 2 0.01
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (42 bp):
GCCACTAAAGAACATGTTCTTTAGCGGCGTTTGTAAAAAAAT
Found at i:52696271 original size:42 final size:42
Alignment explanation
Indices: 52696197--52696398 Score: 282
Period size: 42 Copynumber: 4.8 Consensus size: 42
52696187 AGAAAAAAAT
* *
52696197 GCCGCTAAAGAACATGATCTTTAGCGGCG-TTTTTCCTTAAGC
1 GCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTC-TAAGC
*
52696239 GCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTTCTAAGC
1 GCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAGC
** * *
52696281 GCCGCTAAAGAATGTGGTCTTTAACGGCATTTTTTTAC-AAGC
1 GCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTT-CTAAGC
*
52696323 GCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAGT
1 GCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAGC
* *
52696365 GCTGCTAAAGAACATGGTCTTTAGCAGCGTTTTT
1 GCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTT
52696399 GTTTGTAAAC
Statistics
Matches: 143, Mismatches: 14, Indels: 6
0.88 0.09 0.04
Matches are distributed among these distances:
41 1 0.01
42 135 0.94
43 7 0.05
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.34
Consensus pattern (42 bp):
GCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAGC
Found at i:52696302 original size:126 final size:126
Alignment explanation
Indices: 52696117--52696398 Score: 289
Period size: 126 Copynumber: 2.2 Consensus size: 126
52696107 AAAAATGCCA
* * * *
52696117 CTAAAGAACATGTTCTTTAGCGGCGCTTGTAAAAAAATGCCGCTAAAGAACACGTTCTTTAGA-G
1 CTAAAGAACATGTTCTTTAGCGGCGTTTTTAAAAAAACGCCGCTAAAGAACACGGTCTTTA-ACG
* *
52696181 GCGCTTAGAAAAAAATGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTC-CTTAAGCGCCG
65 GCACTTAGAAAAAAACGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTCTC-TAAGCGCCG
**** * ***
52696243 CTAAAGAACATGTTCTTTAGCGGCGTTTTTTTCTAAGCGCCGCTAAAGAATGTGGTCTTTAACGG
1 CTAAAGAACATGTTCTTTAGCGGCGTTTTTAAAAAAACGCCGCTAAAGAACACGGTCTTTAACGG
* **** * * * * * *
52696308 CATTTTTTTACAAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAGTGCTG
66 CACTTAGAAAAAAACGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTCTCTAAGCGCCG
* *
52696369 CTAAAGAACATGGTCTTTAGCAGCGTTTTT
1 CTAAAGAACATGTTCTTTAGCGGCGTTTTT
52696399 GTTTGTAAAC
Statistics
Matches: 127, Mismatches: 27, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
125 1 0.01
126 125 0.98
127 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.32
Consensus pattern (126 bp):
CTAAAGAACATGTTCTTTAGCGGCGTTTTTAAAAAAACGCCGCTAAAGAACACGGTCTTTAACGG
CACTTAGAAAAAAACGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTCTCTAAGCGCCG
Found at i:52696876 original size:20 final size:19
Alignment explanation
Indices: 52696851--52696901 Score: 61
Period size: 17 Copynumber: 2.7 Consensus size: 19
52696841 AGCAATGAAT
*
52696851 CTGTTCACCAAGAGATATAA
1 CTGTTCA-CAAGAGATACAA
52696871 CTGTTCA-AA-AGATACAA
1 CTGTTCACAAGAGATACAA
52696888 CTGTTCATCAAGAG
1 CTGTTCA-CAAGAG
52696902 TCAGAACTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 14 0.52
18 2 0.07
19 2 0.07
20 9 0.33
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.25
Consensus pattern (19 bp):
CTGTTCACAAGAGATACAA
Found at i:52697275 original size:31 final size:29
Alignment explanation
Indices: 52697203--52697276 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 29
52697193 ACCTTAGGTT
*
52697203 ACATTTTAGTCACTTATGTTTGAAATGTT
1 ACATTTTAGTCACTTATGTTTGAAATGTA
* ***
52697232 ACATTTTTGTCACTTATGTTATCGTGTTGTA
1 ACATTTTAGTCACTTATGTT-T-GAAATGTA
52697263 ACATTTTAGTCACT
1 ACATTTTAGTCACT
52697277 GAGCTATTAA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
29 19 0.51
30 1 0.03
31 17 0.46
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
ACATTTTAGTCACTTATGTTTGAAATGTA
Found at i:52700305 original size:15 final size:15
Alignment explanation
Indices: 52700282--52700314 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
52700272 TTTTTATGCC
52700282 ATTGATGTATTTATT
1 ATTGATGTATTTATT
*
52700297 ATTGTTGTATTTATT
1 ATTGATGTATTTATT
52700312 ATT
1 ATT
52700315 ATAGCATTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.12, T:0.64
Consensus pattern (15 bp):
ATTGATGTATTTATT
Found at i:52712452 original size:84 final size:86
Alignment explanation
Indices: 52712216--52713271 Score: 526
Period size: 84 Copynumber: 12.3 Consensus size: 86
52712206 TCTCATCTAG
* * *
52712216 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGC-AAGTCTTATC-CTCTTGAAGTTG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TTAG-CATCTAA-TCTTATCTCTC-TGAAGTTG
* *
52712279 CAGT-GAGGCAGACTGAAGATGGCA-A-A
62 CAGTGGA-GCAGA-TTAA-A-AGCATAGA
* *** *
52712305 TCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAGCCGATAATCCTATCTC-CTTGAAGTTGC
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT--AGCATCTAATCTTATCTCTC-TGAAGTTGC
* *
52712369 AGTGGAGCAGATTAAAAACACAGA
63 AGTGGAGCAGATTAAAAGCATAGA
** * *
52712393 TCTTATCTCTTTGAAGTTGCAG-AGAGCAGA-TCGCATCTAATCTTATCTCTCTGAAGTTGCAGT
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAGCATCTAATCTTATCTCTCTGAAGTTGCAGT
52712456 GGAGCAGATT-AAAGCTGATA-A
66 GGAGCAGATTAAAAGC--ATAGA
* ** ** *
52712477 T-TCTAT-TCCCTGAAGTTGTAGTGGAGTGGATTAAAATC-AGATCTTATCTCTCTGAATTTGCA
1 TCT-TATCTCCCTGAAGTTGCAGTGGAGCAGATTAGCATCTA-ATCTTATCTCTCTGAAGTTGCA
* *** *
52712539 G-AGAGCAGA-TCGCATC-TAG-
64 GTGGAGCAGATTAAAAGCATAGA
* * * * *
52712558 TCTTATCTCCTTGAAGTTGTAGTGGAGCAGACTAAGTAAGC-AAGTCTTATC-CTTCTGAAGTTG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TTAG-CATCTAA-TCTTATCTC-TCTGAAGTTG
* * * *
52712621 CAGT-GAGGCAGACTGAAGATGGA-AAA
62 CAGTGGA-GCAGA-TTAA-AAGCATAGA
* *** * * *
52712647 TCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCCTAT-TCGCTAAAGTTGCA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT--AGCATCTAATCTTATCTCTCTGAAGTTGCA
* *
52712711 GTGGAGCAGATTAAAAACACAGA
64 GTGGAGCAGATTAAAAGCATAGA
* ** * * * *
52712734 TCTTATCTCTCTGAAGTTATAG-AGAGCAGA-TCGCATCTAATCTTATCTCCCTAAAGTTGCAGT
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAGCATCTAATCTTATCTCTCTGAAGTTGCAGT
52712797 GGAGCAGATT-AAAGCCGATA-A
66 GGAGCAGATTAAAAG-C-ATAGA
* * * **
52712818 TCCTATCTCCCTGAAGTTGTAGTGGA-CTGGATTAAAATC-AGATCTTATCTCTCTGAAGTTGCA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGC-AGATTAGCATCTA-ATCTTATCTCTCTGAAGTTGCA
* * * * *
52712881 G-AGAGCATA-TCACATC-TAG-
64 GTGGAGCAGATTAAAAGCATAGA
* * *
52712900 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGC-AAGTCTTATC-CTCCTGAAGTTG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TTAG-CATCTAA-TCTTATCTCT-CTGAAGTTG
* * * * *
52712963 CAGT-GAGATAGACTGAAGATGGA-AAA
62 CAGTGGAG-CAGA-TTAA-AAGCATAGA
*** * * *
52712989 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCTCTCTAAAGTTACA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT--AGCATCTAATCTTATCTCTCTGAAGTTGCA
* * *
52713054 GTGGAGCGGATTAAAATCACAGA
64 GTGGAGCAGATTAAAAGCATAGA
* ** * * * * * *
52713077 TCTTATTTATCTGAAGTTGCAG-AGAGCAGA-TCGCATCTAATATCATCTCCCTGAAGCTGCAGT
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAGCATCTAATCTTATCTCTCTGAAGTTGCAGT
52713140 GGAGCAGATT-AAAGTCGATA-A
66 GGAGCAGATTAAAAG-C-ATAGA
* * * * ** *
52713161 TCCTATCTCCCTGAAGTTACAGTAGAGCGGATTAAAACCTTAGATCTTATCTCTCTGAAGTTGCA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAGCATC-TA-ATCTTATCTCTCTGAAGTTGCA
* * *** *
52713226 G-AGAGCATA-TCGCATC-TAG-
64 GTGGAGCAGATTAAAAGCATAGA
52713245 TCTTATCTCCCTGAAGTTGCAGTGGAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAG
52713272 TAGACCCCAG
Statistics
Matches: 739, Mismatches: 158, Indels: 145
0.71 0.15 0.14
Matches are distributed among these distances:
81 6 0.01
82 50 0.07
83 44 0.06
84 230 0.31
85 61 0.08
86 43 0.06
87 51 0.07
88 88 0.12
89 146 0.20
90 20 0.03
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (86 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAGCATCTAATCTTATCTCTCTGAAGTTGCAGT
GGAGCAGATTAAAAGCATAGA
Found at i:52712564 original size:125 final size:127
Alignment explanation
Indices: 52712219--52712588 Score: 439
Period size: 125 Copynumber: 2.9 Consensus size: 127
52712209 CATCTAGTCT
* *
52712219 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCA-AG-TCTTATC-CTCTTGAAGTTGCA
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAA--AAACACAGATCTTATCTCTC-TGAAGTTGCA
* * *
52712281 GTGAGGCAGA-CTGAAGATGGCAAATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAGCCG
63 GAGA-GCAGATC-G--CAT--CTAATCTTATCT-CCTGAAGTTGTAGTGGAGCAGATTAAAGCCG
52712345 ATAATCC
121 ATAATCC
* *
52712352 TATCTCCTTGAAGTTGCAGTGGAGCAGATTAAAAACACAGATCTTATCTCTTTGAAGTTGCAGAG
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAAACACAGATCTTATCTCTCTGAAGTTGCAGAG
* * *
52712417 AGCAGATCGCATCTAATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAGCTGATAATTC
66 AGCAGATCGCATCTAATCTTATCTC-CTGAAGTTGTAGTGGAGCAGATTAAAGCCGATAATCC
* ** * *
52712480 TAT-TCCCTGAAGTTGTAGTGGAGTGGATT-AAAA-TCAGATCTTATCTCTCTGAATTTGCAGAG
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAAACACAGATCTTATCTCTCTGAAGTTGCAGAG
*
52712542 AGCAGATCGCATCTAGTCTTATCTCCTTGAAGTTGTAGTGGAGCAGA
66 AGCAGATCGCATCTAATCTTATCTCC-TGAAGTTGTAGTGGAGCAGA
52712589 CTAAGTAAGC
Statistics
Matches: 212, Mismatches: 19, Indels: 20
0.84 0.08 0.08
Matches are distributed among these distances:
124 1 0.00
125 69 0.33
126 4 0.02
127 23 0.11
128 48 0.23
130 2 0.01
131 4 0.02
132 8 0.04
133 51 0.24
134 2 0.01
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.30
Consensus pattern (127 bp):
TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAAACACAGATCTTATCTCTCTGAAGTTGCAGAG
AGCAGATCGCATCTAATCTTATCTCCTGAAGTTGTAGTGGAGCAGATTAAAGCCGATAATCC
Found at i:52712834 original size:342 final size:342
Alignment explanation
Indices: 52712203--52713276 Score: 1740
Period size: 342 Copynumber: 3.1 Consensus size: 342
52712193 AGCAGATTGA
*
52712203 AGATCTCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATCC
1 AGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATCC
* *
52712268 -TCTTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTTGTAGTGGAG
66 TTC-TGAAGTTGCAGTGAGGCAGACTGAAGATGGAAAATCTTATCTCCCTGAAGTTGCAGTGGAG
*
52712332 CAGATTAAAGCCGATAATCCTATCTCCTTGAAGTTGCAGTGGAGCAGATTAAAAACACAGATCTT
130 CAGATTAAAGCCGATAATCCTATCTCC-TAAAGTTGCAGTGGAGCAGATTAAAAACACAGATCTT
* *
52712397 ATCTCTTTGAAGTTGCAGAGAGCAGATCGCATCTAATCTTATCTCTCTGAAGTTGCAGTGGAGCA
194 ATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCTAATCTTATCTCCCTGAAGTTGCAGTGGAGCA
* *
52712462 GATTAAAGCTGATAATTCTAT-TCCCTGAAGTTGTAGTGGAGTGGATTAAAATCAGATCTTATCT
259 GATTAAAGCCGATAATCCTATCTCCCTGAAGTTGTAGTGGAGTGGATTAAAATCAGATCTTATCT
*
52712526 CTCTGAATTTGCAGAGAGC
324 CTCTGAAGTTGCAGAGAGC
* *
52712545 AGATCGCATCTAGTCTTATCTCCTTGAAGTTGTAGTGGAGCAGACTAAGTAAGCAAGTCTTATCC
1 AGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATCC
*
52712610 TTCTGAAGTTGCAGTGAGGCAGACTGAAGATGGAAAATCTTATCTCCTTGAAGTTGCAGTGGAGC
66 TTCTGAAGTTGCAGTGAGGCAGACTGAAGATGGAAAATCTTATCTCCCTGAAGTTGCAGTGGAGC
52712675 AGATTAAAGCCGATAATCCTAT-TCGCTAAAGTTGCAGTGGAGCAGATTAAAAACACAGATCTTA
131 AGATTAAAGCCGATAATCCTATCTC-CTAAAGTTGCAGTGGAGCAGATTAAAAACACAGATCTTA
** *
52712739 TCTCTCTGAAGTTATAGAGAGCAGATCGCATCTAATCTTATCTCCCTAAAGTTGCAGTGGAGCAG
195 TCTCTCTGAAGTTGCAGAGAGCAGATCGCATCTAATCTTATCTCCCTGAAGTTGCAGTGGAGCAG
*
52712804 ATTAAAGCCGATAATCCTATCTCCCTGAAGTTGTAGTGGACTGGATTAAAATCAGATCTTATCTC
260 ATTAAAGCCGATAATCCTATCTCCCTGAAGTTGTAGTGGAGTGGATTAAAATCAGATCTTATCTC
52712869 TCTGAAGTTGCAGAGAGC
325 TCTGAAGTTGCAGAGAGC
* *
52712887 ATATCACATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATCC
1 AGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATCC
* **
52712952 TCCTGAAGTTGCAGTGAGATAGACTGAAGATGGAAAATCTTATCTCCCTGAAGTTGCAGTGGAGC
66 TTCTGAAGTTGCAGTGAGGCAGACTGAAGATGGAAAATCTTATCTCCCTGAAGTTGCAGTGGAGC
* * *
52713017 AGATTAAAGCCGATAATCCTATCTCTCTAAAGTTACAGTGGAGCGGATTAAAATCACAGATCTTA
131 AGATTAAAGCCGATAATCCTATCTC-CTAAAGTTGCAGTGGAGCAGATTAAAAACACAGATCTTA
* * * * *
52713082 TTTATCTGAAGTTGCAGAGAGCAGATCGCATCTAATATCATCTCCCTGAAGCTGCAGTGGAGCAG
195 TCTCTCTGAAGTTGCAGAGAGCAGATCGCATCTAATCTTATCTCCCTGAAGTTGCAGTGGAGCAG
* ** * * *
52713147 ATTAAAGTCGATAATCCTATCTCCCTGAAGTTACAGTAGAGCGGATTAAAACCTTAGATCTTATC
260 ATTAAAGCCGATAATCCTATCTCCCTGAAGTTGTAGTGGAGTGGATTAAAA--TCAGATCTTATC
52713212 TCTCTGAAGTTGCAGAGAGC
323 TCTCTGAAGTTGCAGAGAGC
* *
52713232 ATATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGTAGAC
1 AGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGAC
52713277 CCCAGAAATA
Statistics
Matches: 681, Mismatches: 45, Indels: 9
0.93 0.06 0.01
Matches are distributed among these distances:
341 117 0.17
342 348 0.51
343 142 0.21
345 74 0.11
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (342 bp):
AGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATCC
TTCTGAAGTTGCAGTGAGGCAGACTGAAGATGGAAAATCTTATCTCCCTGAAGTTGCAGTGGAGC
AGATTAAAGCCGATAATCCTATCTCCTAAAGTTGCAGTGGAGCAGATTAAAAACACAGATCTTAT
CTCTCTGAAGTTGCAGAGAGCAGATCGCATCTAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA
TTAAAGCCGATAATCCTATCTCCCTGAAGTTGTAGTGGAGTGGATTAAAATCAGATCTTATCTCT
CTGAAGTTGCAGAGAGC
Found at i:52712910 original size:126 final size:127
Alignment explanation
Indices: 52712645--52712930 Score: 425
Period size: 126 Copynumber: 2.3 Consensus size: 127
52712635 GAAGATGGAA
* *
52712645 AATCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATTCGCTAAAGTTGC
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATTCCCTAAAGTTGC
* *
52712710 AGTGGAGCAGATTAAAAACACAGATCTTATCTCTCTGAAGTTATAGAGAGCAGATCGCATCT
66 AGTGGAGCAGATTAAAAACACAGATCTTATCTCTCTGAAGTTACAGAGAGCAGATCACATCT
* *
52712772 AATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCTCCCTGAAGTTG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCCTAT-TCCCTAAAGTTG
* * * * *
52712837 TAGTGGA-CTGGATT-AAAA-TCAGATCTTATCTCTCTGAAGTTGCAGAGAGCATATCACATCT
65 CAGTGGAGC-AGATTAAAAACACAGATCTTATCTCTCTGAAGTTACAGAGAGCAGATCACATCT
*
52712898 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA
52712931 CTAAGTAAGC
Statistics
Matches: 144, Mismatches: 13, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
126 69 0.48
127 55 0.38
128 20 0.14
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (127 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATTCCCTAAAGTTGC
AGTGGAGCAGATTAAAAACACAGATCTTATCTCTCTGAAGTTACAGAGAGCAGATCACATCT
Found at i:52713160 original size:128 final size:128
Alignment explanation
Indices: 52712993--52713271 Score: 432
Period size: 128 Copynumber: 2.2 Consensus size: 128
52712983 GGAAAATCTT
* *
52712993 ATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCTCTCTAAAGTTACAGTGG
1 ATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCTCCCTAAAGTTACAGTAG
* *
52713058 AGCGGATTAAAATCACAGATCTTATTTATCTGAAGTTGCAGAGAGCAGATCGCATCTAATATC
66 AGCGGATTAAAACCACAGATCTTATCTATCTGAAGTTGCAGAGAGCAGATCGCATCTAATATC
* * *
52713121 ATCTCCCTGAAGCTGCAGTGGAGCAGATTAAAGTCGATAATCCTATCTCCCTGAAGTTACAGTAG
1 ATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCTCCCTAAAGTTACAGTAG
** * * * * *
52713186 AGCGGATTAAAACCTTAGATCTTATCTCTCTGAAGTTGCAGAGAGCATATCGCATCTAGTCTT
66 AGCGGATTAAAACCACAGATCTTATCTATCTGAAGTTGCAGAGAGCAGATCGCATCTAATATC
52713249 ATCTCCCTGAAGTTGCAGTGGAG
1 ATCTCCCTGAAGTTGCAGTGGAG
52713272 TAGACCCCAG
Statistics
Matches: 136, Mismatches: 15, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
128 136 1.00
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (128 bp):
ATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCTCCCTAAAGTTACAGTAG
AGCGGATTAAAACCACAGATCTTATCTATCTGAAGTTGCAGAGAGCAGATCGCATCTAATATC
Found at i:52713171 original size:44 final size:43
Alignment explanation
Indices: 52712216--52713271 Score: 596
Period size: 44 Copynumber: 24.6 Consensus size: 43
52712206 TCTCATCTAG
* * *
52712216 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT-AAGTAAGCAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTCA-TAA
* * *
52712259 GTCTTATC-CTCTTGAAGTTGCAGT-GAGGCAGACTGAAGATGGCA-AA
1 -TCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGA-TTAA-A-GTCATAA
* *
52712305 TCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAGCCGATAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTC-ATAA
* * ** *
52712349 TCCTATCTCCTTGAAGTTGCAGTGGAGCAGATTAAAAACACAGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTCATA-A
** * ***
52712393 TCTTATCTCTTTGAAGTTGCAG-AGAGCAGATCGCA-TC-TAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTCATAA
* *
52712433 TCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAGCTGATAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG-TCATAA
* ** * *
52712477 T-TCTAT-TCCCTGAAGTTGTAGTGGAGTGGATTAAAATCA-GA
1 TCT-TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTCATAA
* * * *** *
52712518 TCTTATCTCTCTGAATTTGCAG-AGAGCAGATCGCA-TC-TAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTCATAA
* * * * *
52712558 TCTTATCTCCTTGAAGTTGTAGTGGAGCAGACT-AAGTAAGCAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTCA-TAA
* * * * *
52712601 GTCTTATC-CTTCTGAAGTTGCAGT-GAGGCAGACTGAAGATGGAAAA
1 -TCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGATTAAAG-T-CATAA
* *
52712647 TCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTC-ATAA
* * * ** *
52712691 TCCTAT-TCGCTAAAGTTGCAGTGGAGCAGATTAAAAACACAGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTCATA-A
* ** * ***
52712734 TCTTATCTCTCTGAAGTTATAG-AGAGCAGATCGCA-TC-TAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTCATAA
* *
52712774 TCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCCGATAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTC-ATAA
* * * * *
52712818 TCCTATCTCCCTGAAGTTGTAGTGGA-CTGGATTAAAATCA-GA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGC-AGATTAAAGTCATAA
* * * * * *
52712860 TCTTATCTCTCTGAAGTTGCAG-AGAGCATATCACA-TC-TAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTCATAA
* * *
52712900 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT-AAGTAAGCAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTCA-TAA
* * * * *
52712943 GTCTTATC-CTCCTGAAGTTGCAGT-GAGATAGACTGAAGATGGAAAA
1 -TCTTATCTC-CCTGAAGTTGCAGTGGAG-CAGATTAAAG-T-CATAA
*
52712989 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTC-ATAA
* * * * * * *
52713033 TCCTATCTCTCTAAAGTTACAGTGGAGCGGATTAAAATCACAGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTCATA-A
* ** * ***
52713077 TCTTATTTATCTGAAGTTGCAG-AGAGCAGATCGCA-TC-TAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTCATAA
* * *
52713117 TATCATCTCCCTGAAGCTGCAGTGGAGCAGATTAAAGTCGATAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTC-ATAA
* * * * ** *
52713161 TCCTATCTCCCTGAAGTTACAGTAGAGCGGATTAAAACCTTAGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTCATA-A
* * * *** *
52713205 TCTTATCTCTCTGAAGTTGCAG-AGAGCATATCGCA-TC-TAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTCATAA
52713245 TCTTATCTCCCTGAAGTTGCAGTGGAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAG
52713272 TAGACCCCAG
Statistics
Matches: 768, Mismatches: 183, Indels: 125
0.71 0.17 0.12
Matches are distributed among these distances:
40 124 0.16
41 68 0.09
42 48 0.06
43 116 0.15
44 302 0.39
45 86 0.11
46 19 0.02
47 3 0.00
48 2 0.00
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (43 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTCATAA
Found at i:52719256 original size:23 final size:21
Alignment explanation
Indices: 52719230--52719285 Score: 69
Period size: 23 Copynumber: 2.6 Consensus size: 21
52719220 TAAAAAATAT
52719230 ATTAACTAAAATTTTATATAAAA
1 ATTAA-TAAAATTTTA-ATAAAA
*
52719253 ATTAAATAAAATTTTAATTAAA
1 ATT-AATAAAATTTTAATAAAA
52719275 A-TAATAAAATT
1 ATTAATAAAATT
52719286 AAAGGTTTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
20 9 0.29
21 1 0.03
22 6 0.19
23 13 0.42
24 2 0.06
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (21 bp):
ATTAATAAAATTTTAATAAAA
Found at i:52722497 original size:22 final size:22
Alignment explanation
Indices: 52722456--52722498 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
52722446 ACAGCAGAAC
* **
52722456 AGGTTTTTAGCGGCGGTTTTTT
1 AGGTCTTTAGCGGCACTTTTTT
52722478 AGGTCTTTAGCGGCACTTTTT
1 AGGTCTTTAGCGGCACTTTTT
52722499 AACGCCACTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.12, C:0.14, G:0.28, T:0.47
Consensus pattern (22 bp):
AGGTCTTTAGCGGCACTTTTTT
Found at i:52722689 original size:83 final size:84
Alignment explanation
Indices: 52722575--52722914 Score: 524
Period size: 83 Copynumber: 4.1 Consensus size: 84
52722565 GCTAACTATT
*
52722575 GCGGCGCTTACATAAAGAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAAAAAAACGC
1 GCGGCGCTTACA-AAA-AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAAAAAAATGC
* *
52722640 CGCTGAAGATCATGTTTTTTA
64 CGCTAAAGATCATGTTCTTTA
* *
52722661 GCGGCGCTTA-AAAAAAACGCCGCTAAAGATAATGTTCTTTAGCGGCGCTTAGAAAAAAA-GCCC
1 GCGGCGCTTACAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAAAAAAATGCCG
52722724 CTAAAGATCATGTTCTTTA
66 CTAAAGATCATGTTCTTTA
* * * *
52722743 GCGGCGCTT-TAAAAAAACGCCCCTAAAGATCATGTTCTTTAGCAGCACTTAGAAAAAAATGCCG
1 GCGGCGCTTACAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAAAAAAATGCCG
52722807 CTAAAGATCATGTTCTTTA
66 CTAAAGATCATGTTCTTTA
** *
52722826 GCGGCGCTTAGGAAAAAATGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAAAAAAATGCCG
1 GCGGCGCTTACAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAAAAAAATGCCG
*
52722891 CTAAAGCTCATGTTCTTTA
66 CTAAAGATCATGTTCTTTA
52722910 GCGGC
1 GCGGC
52722915 CTTTTGGAAG
Statistics
Matches: 235, Mismatches: 16, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
82 74 0.31
83 75 0.32
84 75 0.32
85 1 0.00
86 10 0.04
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.25
Consensus pattern (84 bp):
GCGGCGCTTACAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAAAAAAATGCCG
CTAAAGATCATGTTCTTTA
Found at i:52722690 original size:41 final size:42
Alignment explanation
Indices: 52722575--52723004 Score: 532
Period size: 42 Copynumber: 10.2 Consensus size: 42
52722565 GCTAACTATT
*
52722575 GCGGCGCTTACATAAAGAAACGCCGCTAAAGATCATGTTCTTTA
1 GCGGCGCTTAGA-AAA-AAACGCCGCTAAAGATCATGTTCTTTA
* *
52722619 GCGGCGCTTAGAAAAAAACGCCGCTGAAGATCATGTTTTTTA
1 GCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTTCTTTA
*
52722661 GCGGCGCTTA-AAAAAAACGCCGCTAAAGATAATGTTCTTTA
1 GCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTTCTTTA
*
52722702 GCGGCGCTTAGAAAAAAA-GCCCCTAAAGATCATGTTCTTTA
1 GCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTTCTTTA
* *
52722743 GCGGCGCTT-TAAAAAAACGCCCCTAAAGATCATGTTCTTTA
1 GCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTTCTTTA
* * *
52722784 GCAGCACTTAGAAAAAAATGCCGCTAAAGATCATGTTCTTTA
1 GCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTTCTTTA
* *
52722826 GCGGCGCTTAGGAAAAAATGCCGCTAAAGATCATGTTCTTTA
1 GCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTTCTTTA
* *
52722868 GCGGCGCTTAGAAAAAAATGCCGCTAAAGCTCATGTTCTTTA
1 GCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTTCTTTA
* * * * *
52722910 GCGGC-CTTTTGGAAGAAAACGCCTCTAAA-AGTAATGTTCTATA
1 GCGGCGC--TTAGAAAAAAACGCCGCTAAAGA-TCATGTTCTTTA
* ****
52722953 GCCGCGCTTCTTCAAAAACGCCGCTAAA-AGT-AGTGTTCTTTA
1 GCGGCGCTTAGAAAAAAACGCCGCTAAAGA-TCA-TGTTCTTTA
52722995 GCGGCGCTTA
1 GCGGCGCTTA
52723005 TTTCACAAAC
Statistics
Matches: 342, Mismatches: 36, Indels: 18
0.86 0.09 0.05
Matches are distributed among these distances:
40 7 0.02
41 100 0.29
42 189 0.55
43 34 0.10
44 12 0.04
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (42 bp):
GCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTTCTTTA
Found at i:52723460 original size:21 final size:21
Alignment explanation
Indices: 52723436--52723504 Score: 93
Period size: 21 Copynumber: 3.3 Consensus size: 21
52723426 GCTTCTATTG
*
52723436 CTGCTTCTCTCGCTGCGGCCT
1 CTGCTTCTCTCGCTGCAGCCT
* *
52723457 CTGCTTCTCTTGCTGTAGCCT
1 CTGCTTCTCTCGCTGCAGCCT
* *
52723478 CTGCTTCCCTCGCTGCCGCCT
1 CTGCTTCTCTCGCTGCAGCCT
52723499 CTGCTT
1 CTGCTT
52723505 TAAGTTGCTG
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.01, C:0.42, G:0.20, T:0.36
Consensus pattern (21 bp):
CTGCTTCTCTCGCTGCAGCCT
Found at i:52729043 original size:9 final size:9
Alignment explanation
Indices: 52729008--52729149 Score: 182
Period size: 9 Copynumber: 16.0 Consensus size: 9
52728998 TTAAACAATA
52729008 ATGTAAGTT
1 ATGTAAGTT
*
52729017 A-GGAAGGTT
1 ATGTAA-GTT
52729026 ATGT-A-TT
1 ATGTAAGTT
52729033 ATGTAAGTT
1 ATGTAAGTT
52729042 ATGTAAGTT
1 ATGTAAGTT
52729051 ATGTAAGTT
1 ATGTAAGTT
52729060 ATGTAAGTT
1 ATGTAAGTT
* *
52729069 ATTTAATTT
1 ATGTAAGTT
52729078 ATGTAAGTT
1 ATGTAAGTT
*
52729087 ATGTAAGAT
1 ATGTAAGTT
*
52729096 ATGTAAGAT
1 ATGTAAGTT
52729105 ATGTAAGTT
1 ATGTAAGTT
* *
52729114 ATTTAATTT
1 ATGTAAGTT
52729123 ATGTAAGTT
1 ATGTAAGTT
*
52729132 ATGTAAGCT
1 ATGTAAGTT
52729141 ATGTAAGTT
1 ATGTAAGTT
52729150 TATATAAAAA
Statistics
Matches: 115, Mismatches: 14, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
7 6 0.05
8 4 0.03
9 104 0.90
10 1 0.01
ACGTcount: A:0.35, C:0.01, G:0.20, T:0.44
Consensus pattern (9 bp):
ATGTAAGTT
Found at i:52729090 original size:45 final size:45
Alignment explanation
Indices: 52729031--52729149 Score: 211
Period size: 45 Copynumber: 2.6 Consensus size: 45
52729021 AGGTTATGTA
*
52729031 TTATGTAAGTTATGTAAGTTATGTAAGTTATGTAAGTTATTTAAT
1 TTATGTAAGTTATGTAAGATATGTAAGTTATGTAAGTTATTTAAT
*
52729076 TTATGTAAGTTATGTAAGATATGTAAGATATGTAAGTTATTTAAT
1 TTATGTAAGTTATGTAAGATATGTAAGTTATGTAAGTTATTTAAT
*
52729121 TTATGTAAGTTATGTAAGCTATGTAAGTT
1 TTATGTAAGTTATGTAAGATATGTAAGTT
52729150 TATATAAAAA
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 70 1.00
ACGTcount: A:0.34, C:0.01, G:0.18, T:0.46
Consensus pattern (45 bp):
TTATGTAAGTTATGTAAGATATGTAAGTTATGTAAGTTATTTAAT
Found at i:52729189 original size:39 final size:39
Alignment explanation
Indices: 52729126--52729227 Score: 150
Period size: 39 Copynumber: 2.6 Consensus size: 39
52729116 TTAATTTATG
*
52729126 TAAGTTATGTAAGCTATGTAAGTTTATATAAAAAAAAATTA
1 TAAGTTATGT-A-TTATGTAAGTTTATATAAAAAAAAATTA
* **
52729167 TAAGTTATGTATTATGTAAGTTTATATTAAAAAATTTTA
1 TAAGTTATGTATTATGTAAGTTTATATAAAAAAAAATTA
52729206 TAAGTTATGTATTATGTAAGTT
1 TAAGTTATGTATTATGTAAGTT
52729228 AAAAGTAATG
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
39 46 0.81
40 1 0.02
41 10 0.18
ACGTcount: A:0.42, C:0.01, G:0.13, T:0.44
Consensus pattern (39 bp):
TAAGTTATGTATTATGTAAGTTTATATAAAAAAAAATTA
Found at i:52729233 original size:23 final size:23
Alignment explanation
Indices: 52729207--52729250 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
52729197 AAAATTTTAT
*
52729207 AAGTTATGTATTATGTAAGTTAA
1 AAGTAATGTATTATGTAAGTTAA
52729230 AAGTAATGTATTATGTAAGTT
1 AAGTAATGTATTATGTAAGTT
52729251 TACATATATG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.18, T:0.43
Consensus pattern (23 bp):
AAGTAATGTATTATGTAAGTTAA
Found at i:52729250 original size:39 final size:39
Alignment explanation
Indices: 52729121--52729235 Score: 106
Period size: 39 Copynumber: 2.9 Consensus size: 39
52729111 GTTATTTAAT
* * * *
52729121 TTATGTAAGTTATGTAAGCTATGTAAGTTTATA-TAAAAAA
1 TTATATAAGTTATGT-A-TTATGTAAGTTAAAAGTAAAAAA
** * * *
52729161 AAATTATAAGTTATGTATTATGTAAGTTTATATTAAAAAA
1 TTA-TATAAGTTATGTATTATGTAAGTTAAAAGTAAAAAA
*
52729201 TTTTATAAGTTATGTATTATGTAAGTTAAAAGTAA
1 TTATATAAGTTATGTATTATGTAAGTTAAAAGTAA
52729236 TGTATTATGT
Statistics
Matches: 63, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
39 43 0.68
40 9 0.14
41 11 0.17
ACGTcount: A:0.43, C:0.01, G:0.13, T:0.43
Consensus pattern (39 bp):
TTATATAAGTTATGTATTATGTAAGTTAAAAGTAAAAAA
Found at i:52729336 original size:27 final size:27
Alignment explanation
Indices: 52729294--52729369 Score: 127
Period size: 27 Copynumber: 2.9 Consensus size: 27
52729284 GTAATAATTT
*
52729294 TAAGT-AACATACTTAAATTTTACATA
1 TAAGTAAACTTACTTAAATTTTACATA
52729320 TAAGTAAACTTACTTAAATTTTACATA
1 TAAGTAAACTTACTTAAATTTTACATA
*
52729347 TAAGTAAACTTGCTTAAATTTTA
1 TAAGTAAACTTACTTAAATTTTA
52729370 GTAAGTAATA
Statistics
Matches: 47, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
26 5 0.11
27 42 0.89
ACGTcount: A:0.43, C:0.11, G:0.05, T:0.41
Consensus pattern (27 bp):
TAAGTAAACTTACTTAAATTTTACATA
Found at i:52729355 original size:90 final size:89
Alignment explanation
Indices: 52729249--52729595 Score: 559
Period size: 90 Copynumber: 4.0 Consensus size: 89
52729239 ATTATGTAAG
* *
52729249 TTTACATATATGTAAACTTGCTTAAATTTTAGTAAGTAATAATTTTAAGTAACATACTTAAATTT
1 TTTACATATAAGTAAACTTACTTAAATTTTAGTAAGTAAT-ATTTTAAGTAACATACTTAAATTT
52729314 TACATATAAGTAAACTTACTTAAAT
65 TACATATAAGTAAACTTACTTAAAT
*
52729339 TTTACATATAAGTAAACTTGCTTAAATTTTAGTAAGTAATAATTTTAAGTAACATACTTAAATTT
1 TTTACATATAAGTAAACTTACTTAAATTTTAGTAAGTAAT-ATTTTAAGTAACATACTTAAATTT
52729404 TACATATAAGTAAACTTACTTAAAT
65 TACATATAAGTAAACTTACTTAAAT
*
52729429 TTTACATATAAGTAAACTTACTTAAATTTTAGTAAGTAATGTATTTAAGTAACATACTTAAATTT
1 TTTACATATAAGTAAACTTACTTAAATTTTAGTAAGTAATAT-TTTAAGTAACATACTTAAATTT
*
52729494 TAGATATAAGTAAACTTACTTAAAT
65 TACATATAAGTAAACTTACTTAAAT
52729519 TTTACATATAAGTAAACTTACTTAAATTTTAGTAAG--------TAA-TAACATACTTAAATTTT
1 TTTACATATAAGTAAACTTACTTAAATTTTAGTAAGTAATATTTTAAGTAACATACTTAAATTTT
52729575 ACATATAAGTAAACTTACTTA
66 ACATATAAGTAAACTTACTTA
52729596 TGTAAGTTAT
Statistics
Matches: 251, Mismatches: 5, Indels: 12
0.94 0.02 0.04
Matches are distributed among these distances:
80 37 0.15
81 3 0.01
89 1 0.00
90 210 0.84
ACGTcount: A:0.43, C:0.09, G:0.07, T:0.41
Consensus pattern (89 bp):
TTTACATATAAGTAAACTTACTTAAATTTTAGTAAGTAATATTTTAAGTAACATACTTAAATTTT
ACATATAAGTAAACTTACTTAAAT
Found at i:52729426 original size:27 final size:27
Alignment explanation
Indices: 52729384--52729459 Score: 136
Period size: 27 Copynumber: 2.9 Consensus size: 27
52729374 GTAATAATTT
*
52729384 TAAGT-AACATACTTAAATTTTACATA
1 TAAGTAAACTTACTTAAATTTTACATA
52729410 TAAGTAAACTTACTTAAATTTTACATA
1 TAAGTAAACTTACTTAAATTTTACATA
52729437 TAAGTAAACTTACTTAAATTTTA
1 TAAGTAAACTTACTTAAATTTTA
52729460 GTAAGTAATG
Statistics
Matches: 48, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
26 5 0.10
27 43 0.90
ACGTcount: A:0.45, C:0.11, G:0.04, T:0.41
Consensus pattern (27 bp):
TAAGTAAACTTACTTAAATTTTACATA
Found at i:52729516 original size:27 final size:27
Alignment explanation
Indices: 52729474--52729595 Score: 162
Period size: 27 Copynumber: 4.6 Consensus size: 27
52729464 GTAATGTATT
* *
52729474 TAAGT-AACATACTTAAATTTTAGATA
1 TAAGTAAACTTACTTAAATTTTACATA
52729500 TAAGTAAACTTACTTAAATTTTACATA
1 TAAGTAAACTTACTTAAATTTTACATA
*
52729527 TAAGTAAACTTACTTAAATTTT--A-G
1 TAAGTAAACTTACTTAAATTTTACATA
*
52729551 TAAGTAATAACATACTTAAATTTTACATA
1 TAAGT-A-AACTTACTTAAATTTTACATA
52729580 TAAGTAAACTTACTTA
1 TAAGTAAACTTACTTA
52729596 TGTAAGTTAT
Statistics
Matches: 84, Mismatches: 6, Indels: 11
0.83 0.06 0.11
Matches are distributed among these distances:
24 5 0.06
25 2 0.02
26 20 0.24
27 50 0.60
28 2 0.02
29 5 0.06
ACGTcount: A:0.45, C:0.10, G:0.06, T:0.39
Consensus pattern (27 bp):
TAAGTAAACTTACTTAAATTTTACATA
Found at i:52729569 original size:53 final size:54
Alignment explanation
Indices: 52729474--52729595 Score: 180
Period size: 53 Copynumber: 2.3 Consensus size: 54
52729464 GTAATGTATT
* *
52729474 TAAGT-AACATACTTAAATTTTAGATATAAGTAAACTTACTTAAATTTTACATA
1 TAAGTAAACTTACTTAAATTTTAGATATAAGTAAACATACTTAAATTTTACATA
52729527 TAAGTAAACTTACTTAAATTTTAG---TAAGTAATAACATACTTAAATTTTACATA
1 TAAGTAAACTTACTTAAATTTTAGATATAAGT-A-AACATACTTAAATTTTACATA
52729580 TAAGTAAACTTACTTA
1 TAAGTAAACTTACTTA
52729596 TGTAAGTTAT
Statistics
Matches: 64, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
51 5 0.08
52 1 0.02
53 41 0.64
54 17 0.27
ACGTcount: A:0.45, C:0.10, G:0.06, T:0.39
Consensus pattern (54 bp):
TAAGTAAACTTACTTAAATTTTAGATATAAGTAAACATACTTAAATTTTACATA
Found at i:52729623 original size:13 final size:13
Alignment explanation
Indices: 52729607--52729658 Score: 52
Period size: 13 Copynumber: 4.0 Consensus size: 13
52729597 GTAAGTTATG
*
52729607 TAAGTAATGTATT
1 TAAGTAATATATT
*
52729620 TAAGTAACATATT
1 TAAGTAATATATT
* *
52729633 TGAGTAATAAATT
1 TAAGTAATATATT
52729646 TAA-TATATATATT
1 TAAGTA-ATATATT
52729659 AGTAATAAGT
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
12 2 0.06
13 29 0.94
ACGTcount: A:0.44, C:0.02, G:0.10, T:0.44
Consensus pattern (13 bp):
TAAGTAATATATT
Found at i:52731295 original size:10 final size:11
Alignment explanation
Indices: 52731280--52731308 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
52731270 TCAACATTAA
52731280 ATTAAAAA-AT
1 ATTAAAAAGAT
52731290 ATTAAAAAGAT
1 ATTAAAAAGAT
52731301 ATTAAAAA
1 ATTAAAAA
52731309 TTTATTTTGC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 8 0.44
11 10 0.56
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (11 bp):
ATTAAAAAGAT
Found at i:52731762 original size:19 final size:19
Alignment explanation
Indices: 52731738--52731779 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
52731728 GGTCGGGTTT
*
52731738 GGGGAGCTGTTAGGGATTA
1 GGGGAGATGTTAGGGATTA
* *
52731757 GGGGAGATTTTAGGGATTT
1 GGGGAGATGTTAGGGATTA
52731776 GGGG
1 GGGG
52731780 GGAGAAAGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.19, C:0.02, G:0.50, T:0.29
Consensus pattern (19 bp):
GGGGAGATGTTAGGGATTA
Found at i:52732359 original size:74 final size:74
Alignment explanation
Indices: 52732281--52732509 Score: 209
Period size: 74 Copynumber: 3.1 Consensus size: 74
52732271 TCAAGCTTGT
52732281 GGCGTTTCCAAACAAACGCCACTAATACCATTGACAAAACGACAACATTTCGATAAACATAAATA
1 GGCGTTTCCAAACAAACGCCACTAATACCATTGACAAAACGACAACATTTCGATAAACATAAATA
52732346 CAAATTTGC
66 CAAATTTGC
*** * * *** * ***
52732355 GGCGTTT-CATGTAAAGCGCCACTAA-A-TATAAGATC-AAACGATGTCGTTTC-CCCAACATTG
1 GGCGTTTCCAAACAAA-CGCCACTAATACCAT-TGA-CAAAACGACAACATTTCGATAAACA-T-
* ** *
52732415 AACT-CAAGCTTGT
61 AAATACAAATTTGC
*
52732428 GGCGTTTCCAAACAAACGCCACTAATACCATTGACAAAACGACAACATTTTGATAAACATAAATA
1 GGCGTTTCCAAACAAACGCCACTAATACCATTGACAAAACGACAACATTTCGATAAACATAAATA
*
52732493 CAATTTTGC
66 CAAATTTGC
52732502 GGCGTTTC
1 GGCGTTTC
52732510 ATGTAAAGCG
Statistics
Matches: 111, Mismatches: 33, Indels: 22
0.67 0.20 0.13
Matches are distributed among these distances:
72 6 0.05
73 46 0.41
74 53 0.48
75 6 0.05
ACGTcount: A:0.38, C:0.24, G:0.14, T:0.25
Consensus pattern (74 bp):
GGCGTTTCCAAACAAACGCCACTAATACCATTGACAAAACGACAACATTTCGATAAACATAAATA
CAAATTTGC
Found at i:52732375 original size:147 final size:147
Alignment explanation
Indices: 52732220--52732599 Score: 697
Period size: 147 Copynumber: 2.6 Consensus size: 147
52732210 CATTTTAAGC
*
52732220 AAAGCGCCACTAAATATAAGATCAAACGATGTCATTTCCCCAACATTTAACTCAAGCTTGTGGCG
1 AAAGCGCCACTAAATATAAGATCAAACGATGTCGTTTCCCCAACATTTAACTCAAGCTTGTGGCG
52732285 TTTCCAAACAAACGCCACTAATACCATTGACAAAACGACAACATTTCGATAAACATAAATACAAA
66 TTTCCAAACAAACGCCACTAATACCATTGACAAAACGACAACATTTCGATAAACATAAATACAAA
52732350 TTTGCGGCGTTTCATGT
131 TTTGCGGCGTTTCATGT
*
52732367 AAAGCGCCACTAAATATAAGATCAAACGATGTCGTTTCCCCAACATTGAACTCAAGCTTGTGGCG
1 AAAGCGCCACTAAATATAAGATCAAACGATGTCGTTTCCCCAACATTTAACTCAAGCTTGTGGCG
* *
52732432 TTTCCAAACAAACGCCACTAATACCATTGACAAAACGACAACATTTTGATAAACATAAATACAAT
66 TTTCCAAACAAACGCCACTAATACCATTGACAAAACGACAACATTTCGATAAACATAAATACAAA
52732497 TTTGCGGCGTTTCATGT
131 TTTGCGGCGTTTCATGT
* * *
52732514 AAAGCGCCACTAAATATAAGATCAAACAATGTTGTTTCCCCAACATTTAACTCAAGCTTGTGGCA
1 AAAGCGCCACTAAATATAAGATCAAACGATGTCGTTTCCCCAACATTTAACTCAAGCTTGTGGCG
52732579 TTTCCAAACAAACGCCACTAA
66 TTTCCAAACAAACGCCACTAA
52732600 AATAAAACAT
Statistics
Matches: 225, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
147 225 1.00
ACGTcount: A:0.38, C:0.24, G:0.13, T:0.25
Consensus pattern (147 bp):
AAAGCGCCACTAAATATAAGATCAAACGATGTCGTTTCCCCAACATTTAACTCAAGCTTGTGGCG
TTTCCAAACAAACGCCACTAATACCATTGACAAAACGACAACATTTCGATAAACATAAATACAAA
TTTGCGGCGTTTCATGT
Found at i:52733375 original size:23 final size:24
Alignment explanation
Indices: 52733347--52733405 Score: 61
Period size: 23 Copynumber: 2.5 Consensus size: 24
52733337 GTACTAAACA
52733347 TTAAACCTTAAACCC-TAAACCC-C
1 TTAAACC-TAAACCCTTAAACCCTC
*
52733370 TTAAA-CTATAGCCCTTAAACCCTC
1 TTAAACCTA-AACCCTTAAACCCTC
52733394 TTAAACCCTAAA
1 TTAAA-CCTAAA
52733406 ATTTTTTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
21 2 0.07
22 5 0.17
23 12 0.41
24 6 0.21
25 1 0.03
26 3 0.10
ACGTcount: A:0.39, C:0.34, G:0.02, T:0.25
Consensus pattern (24 bp):
TTAAACCTAAACCCTTAAACCCTC
Found at i:52733842 original size:72 final size:74
Alignment explanation
Indices: 52733689--52733846 Score: 171
Period size: 72 Copynumber: 2.2 Consensus size: 74
52733679 AAATAATTAT
* *
52733689 TTTGCGGCGCTTATCAATAAACACCGCTAAATCACCCAAATACTAAGTAAAACGATCGCATTGGG
1 TTTGCGGCGCTTATCAATAAACACCGCTAAAACACCCAAATACTAAGTAAAACGATCGCATTCGG
52733754 CTTATGTTA
66 CTTATGTTA
* * * * * * * *
52733763 TTGGCGGCGCTTATCCA-AAACGCCGTTAAAAC-CCCGAATACTCAG-AGAACGAT-GTCGTTCG
1 TTTGCGGCGCTTATCAATAAACACCGCTAAAACACCCAAATACTAAGTAAAACGATCG-CATTCG
*
52733824 GCTTATATTTA
65 GCTTAT-GTTA
52733835 TTTGCGGCGCTT
1 TTTGCGGCGCTT
52733847 TCGTAGAAAC
Statistics
Matches: 70, Mismatches: 12, Indels: 6
0.80 0.14 0.07
Matches are distributed among these distances:
70 1 0.01
71 17 0.24
72 25 0.36
73 12 0.17
74 15 0.21
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.28
Consensus pattern (74 bp):
TTTGCGGCGCTTATCAATAAACACCGCTAAAACACCCAAATACTAAGTAAAACGATCGCATTCGG
CTTATGTTA
Found at i:52733998 original size:73 final size:70
Alignment explanation
Indices: 52733911--52734048 Score: 170
Period size: 73 Copynumber: 1.9 Consensus size: 70
52733901 GCTAGATTAT
* * *
52733911 CGAATGCTCAGAAAACAACGTCGTTGGTCTTAGGTTTGTTTGCGGCGATTTATCA-AAAACGCCG
1 CGAATGCCCAGAAAACAACGTCGTTGGGCTGAGG--T-TTTGCGGCGATTTAT-AGAAAACGCCG
52733975 CTAAATCCC
62 CTAAATCCC
* * * *
52733984 CGAATGCCCTGAAAACGACGTCGTTGGGCTGAGGTTTTGCGGCGCTTTATAGAAATCGCCGCTAA
1 CGAATGCCCAGAAAACAACGTCGTTGGGCTGAGGTTTTGCGGCGATTTATAGAAAACGCCGCTAA
52734049 TGCTTTTTCT
Statistics
Matches: 57, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
69 1 0.02
70 26 0.46
71 1 0.02
73 29 0.51
ACGTcount: A:0.25, C:0.23, G:0.25, T:0.26
Consensus pattern (70 bp):
CGAATGCCCAGAAAACAACGTCGTTGGGCTGAGGTTTTGCGGCGATTTATAGAAAACGCCGCTAA
ATCCC
Found at i:52744634 original size:32 final size:32
Alignment explanation
Indices: 52744580--52744655 Score: 91
Period size: 32 Copynumber: 2.4 Consensus size: 32
52744570 CATTATAAAT
* * *
52744580 TTATAAATTCATTACTTGAATTTAATAACTTA
1 TTATTAATTAATTAATTGAATTTAATAACTTA
* *
52744612 TTATTAATTAATTAATTTAATTTGATAACTTA
1 TTATTAATTAATTAATTGAATTTAATAACTTA
*
52744644 -TATTGATTAATT
1 TTATTAATTAATT
52744656 GAACTTGTTA
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
31 11 0.29
32 27 0.71
ACGTcount: A:0.39, C:0.05, G:0.04, T:0.51
Consensus pattern (32 bp):
TTATTAATTAATTAATTGAATTTAATAACTTA
Found at i:52748018 original size:42 final size:36
Alignment explanation
Indices: 52747970--52748053 Score: 96
Period size: 36 Copynumber: 2.2 Consensus size: 36
52747960 TTTTTTCATT
52747970 ATTTTTCCTTTTTCTCTCATTTTCATTTTGACCTTGATTTTG
1 ATTTTTCCTTTTTCT-TC-TTTTCATTTT----TTGATTTTG
* *
52748012 ATTTTTCTTTTTTCTTCTTTTTATTTTTTGATTTTG
1 ATTTTTCCTTTTTCTTCTTTTCATTTTTTGATTTTG
52748048 ATTTTT
1 ATTTTT
52748054 GATTTTTTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
36 15 0.38
40 9 0.22
41 2 0.05
42 14 0.35
ACGTcount: A:0.11, C:0.13, G:0.06, T:0.70
Consensus pattern (36 bp):
ATTTTTCCTTTTTCTTCTTTTCATTTTTTGATTTTG
Found at i:52748041 original size:30 final size:30
Alignment explanation
Indices: 52748007--52748070 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
52747997 TTGACCTTGA
** **
52748007 TTTTGATTTTTCTTTTTTCTTCTTTTTATT
1 TTTTGATTTTGATTTTTGATTCTTTTTATT
*
52748037 TTTTGATTTTGATTTTTGATTTTTTTTATT
1 TTTTGATTTTGATTTTTGATTCTTTTTATT
52748067 TTTT
1 TTTT
52748071 TTTGGGCTCA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.09, C:0.05, G:0.06, T:0.80
Consensus pattern (30 bp):
TTTTGATTTTGATTTTTGATTCTTTTTATT
Found at i:52748060 original size:36 final size:35
Alignment explanation
Indices: 52748003--52748073 Score: 97
Period size: 36 Copynumber: 2.0 Consensus size: 35
52747993 CATTTTGACC
* *
52748003 TTGATTTTGATTTTTCTTTTTTCTTCTTTTTATTTT
1 TTGATTTTGATTTTTCATTTTTCTTATTTTT-TTTT
* *
52748039 TTGATTTTGATTTTTGATTTTTTTTATTTTTTTTT
1 TTGATTTTGATTTTTCATTTTTCTTATTTTTTTTT
52748074 GGGCTCATAG
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
35 4 0.13
36 27 0.87
ACGTcount: A:0.10, C:0.04, G:0.07, T:0.79
Consensus pattern (35 bp):
TTGATTTTGATTTTTCATTTTTCTTATTTTTTTTT
Found at i:52756079 original size:24 final size:23
Alignment explanation
Indices: 52756047--52756093 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
52756037 GTGCAATCTT
52756047 AGATATGATATATGCAATCTTAGA
1 AGATATGAT-TATGCAATCTTAGA
* * *
52756071 AGATGTGATTTTGTAATCTTAGA
1 AGATATGATTATGCAATCTTAGA
52756094 GATTTAATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.36, C:0.06, G:0.19, T:0.38
Consensus pattern (23 bp):
AGATATGATTATGCAATCTTAGA
Found at i:52756570 original size:16 final size:15
Alignment explanation
Indices: 52756549--52756583 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
52756539 TCTTGTATCA
52756549 TTATTATTATTATTAT
1 TTATTATTATTATT-T
*
52756565 TTATTATTTTTATTT
1 TTATTATTATTATTT
52756580 TTAT
1 TTAT
52756584 ATTCATGCGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (15 bp):
TTATTATTATTATTT
Found at i:52756652 original size:23 final size:23
Alignment explanation
Indices: 52756615--52756658 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
52756605 TTATGTAATA
*
52756615 TATATATATAGTATACGTATGCT
1 TATATATATAGTATACATATGCT
**
52756638 TATATATATCTTATACATATG
1 TATATATATAGTATACATATG
52756659 TTTTTATTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.36, C:0.09, G:0.09, T:0.45
Consensus pattern (23 bp):
TATATATATAGTATACATATGCT
Found at i:52760892 original size:24 final size:23
Alignment explanation
Indices: 52760790--52760896 Score: 76
Period size: 24 Copynumber: 4.4 Consensus size: 23
52760780 AAATTTATTG
52760790 TATATTATTATTTTAATTTTATA
1 TATATTATTATTTTAATTTTATA
*
52760813 TGTATTATT-TTTCTAAGCTTTTCATGCA
1 TATATTATTATTT-TAA--TTTT-AT--A
* *
52760841 T-TATT-TTTTTTTAAAATTTATTA
1 TATATTATTATTTT-AATTTTA-TA
*
52760864 AATATTATTATTTTAATTTTCATA
1 TATATTATTATTTTAATTTT-ATA
52760888 TATATTATT
1 TATATTATT
52760897 TCATATGTTT
Statistics
Matches: 66, Mismatches: 6, Indels: 23
0.69 0.06 0.24
Matches are distributed among these distances:
22 3 0.05
23 12 0.18
24 20 0.30
25 15 0.23
26 5 0.08
27 9 0.14
28 2 0.03
ACGTcount: A:0.31, C:0.05, G:0.03, T:0.62
Consensus pattern (23 bp):
TATATTATTATTTTAATTTTATA
Found at i:52763256 original size:12 final size:10
Alignment explanation
Indices: 52763230--52763268 Score: 51
Period size: 10 Copynumber: 3.7 Consensus size: 10
52763220 TGAACATGAC
52763230 TAATTTTAAT
1 TAATTTTAAT
52763240 TAATTTTATAGT
1 TAATTTTA-A-T
*
52763252 TAATTTTGAT
1 TAATTTTAAT
52763262 TAATTTT
1 TAATTTT
52763269 GACTATTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
10 16 0.62
11 2 0.08
12 8 0.31
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (10 bp):
TAATTTTAAT
Found at i:52771729 original size:12 final size:12
Alignment explanation
Indices: 52771712--52771737 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
52771702 GAAAATAGAC
52771712 TTTTAGCGGCAT
1 TTTTAGCGGCAT
52771724 TTTTAGCGGCAT
1 TTTTAGCGGCAT
52771736 TT
1 TT
52771738 AGACCAAAAA
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:0.15, C:0.15, G:0.23, T:0.46
Consensus pattern (12 bp):
TTTTAGCGGCAT
Found at i:52772045 original size:114 final size:114
Alignment explanation
Indices: 52771844--52772335 Score: 542
Period size: 113 Copynumber: 4.3 Consensus size: 114
52771834 CAAAAGATCA
* * * * * * *
52771844 GCATTAGCAGTGTTTATG-AGAGAAACGCCGCAATAGTTCAAGCATTAGCGGCGCTTTTCCAAAA
1 GCATTAGCGGTGCTTATGCA-A-AAACGCCGCTATAGGTCGAGAATTAGCGGCGCTTTTCTAAAA
* *
52771908 ACGCCG-TAAAAATGTTAATCAAAACGCATCGTTCTATCTTGAGCCTAGTG
64 ACGCCGCAAAAAATGTTAATCAAAACGCATCGTTCTATCTTGAGCTTAGTG
* * * * *
52771958 GCATTAGTGGTGCTTATGCAAAAACACCGTTATAGGTCGAGCATTAGCGGCGCTTTTCTAAAAAT
1 GCATTAGCGGTGCTTATGCAAAAACGCCGCTATAGGTCGAGAATTAGCGGCGCTTTTCTAAAAAC
* *
52772023 GCCGCAAAAAATGTTAATCAAAATGCATTGTTCTATCTTGAGCTTAGTG
66 GCCGCAAAAAATGTTAATCAAAACGCATCGTTCTATCTTGAGCTTAGTG
* * * * * * *
52772072 GAATTAGCGACT-TTTATGC-AAAATGCCGCTATAGGTCAAGAATTAGTGGCGGTTTTCTAAAAA
1 GCATTAGCG-GTGCTTATGCAAAAACGCCGCTATAGGTCGAGAATTAGCGGCGCTTTTCTAAAAA
* * * * *
52772135 TGCCGCAAAAAATGTTAATCAAAGCACATTGTTCTATCTTGAGCTTAATG
65 CGCCGCAAAAAATGTTAATCAAAACGCATCGTTCTATCTTGAGCTTAGTG
* * *
52772185 GCATTAGCGGTGGTGCTTATGCAAAAACGCCACTATAGATCGAGAATTAGCGGCGCTTTTATAAA
1 GCATTAGC---GGTGCTTATGCAAAAACGCCGCTATAGGTCGAGAATTAGCGGCGCTTTTCTAAA
** * * *
52772250 AACATCGCAAAAAATGTTGATCAAAACGCACCCTTCTATCTTGAGCTTAGTG
63 AACGCCGCAAAAAATGTTAATCAAAACGCATCGTTCTATCTTGAGCTTAGTG
* * * *
52772302 GTATTAGCGGCGCTTATGCAAAAGCGCTGCTATA
1 GCATTAGCGGTGCTTATGCAAAAACGCCGCTATA
52772336 TATATGTCGA
Statistics
Matches: 316, Mismatches: 54, Indels: 16
0.82 0.14 0.04
Matches are distributed among these distances:
113 131 0.41
114 91 0.29
115 3 0.01
116 7 0.02
117 84 0.27
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (114 bp):
GCATTAGCGGTGCTTATGCAAAAACGCCGCTATAGGTCGAGAATTAGCGGCGCTTTTCTAAAAAC
GCCGCAAAAAATGTTAATCAAAACGCATCGTTCTATCTTGAGCTTAGTG
Found at i:52772321 original size:230 final size:226
Alignment explanation
Indices: 52771870--52772324 Score: 595
Period size: 230 Copynumber: 2.0 Consensus size: 226
52771860 TGAGAGAAAC
* * * *
52771870 GCCGCAATAGTTCAAGCATTAGCGGCGCTTTTCCAAAAACGCCGTAAAAATGTTAATCAAAACGC
1 GCCGCAATAGGTCAAGAATTAGCGGCGCTTTTCCAAAAACGCCGAAAAAATGTTAATCAAAACAC
* ** * *
52771935 ATCGTTCTATCTTGAGCCTAGTGGCATTAGTGGTGCTTATGCAAAAACACCGTTATAGGTCGAGC
66 ATCGTTCTATCTTGAGCCTAATGGCATTAGTGGTGCTTATGCAAAAACACCACTATAGATCGAGA
* ** * ***
52772000 ATTAGCGGCGCTTTTCTAAAAATGCCGCAAAAAATGTTAATCAAAATGCATTGTTCTATCTTGAG
131 ATTAGCGGCGCTTTTATAAAAACACCGCAAAAAATGTTAATCAAAACGCACCCTTCTATCTTGAG
**
52772065 CTTAGTGGAATTAGCGACTTTTATGCAAAAT
196 CTTAGTGGAATTAGCGACGCTTATGCAAAAT
* * * * * *
52772096 GCCGCTATAGGTCAAGAATTAGTGGCGGTTTTCTAAAAATGCCGCAAAAAATGTTAATCAAAGCA
1 GCCGCAATAGGTCAAGAATTAGCGGCGCTTTTCCAAAAACGCCG-AAAAAATGTTAATCAAAACA
* * *
52772161 CATTGTTCTATCTTGAGCTTAATGGCATTAGCGGTGGTGCTTATGCAAAAACGCCACTATAGATC
65 CATCGTTCTATCTTGAGCCTAATGGCATTA---GTGGTGCTTATGCAAAAACACCACTATAGATC
* *
52772226 GAGAATTAGCGGCGCTTTTATAAAAACATCGCAAAAAATGTTGATCAAAACGCACCCTTCTATCT
127 GAGAATTAGCGGCGCTTTTATAAAAACACCGCAAAAAATGTTAATCAAAACGCACCCTTCTATCT
* *
52772291 TGAGCTTAGTGGTATTAGCGGCGCTTATGCAAAA
192 TGAGCTTAGTGGAATTAGCGACGCTTATGCAAAA
52772325 GCGCTGCTAT
Statistics
Matches: 194, Mismatches: 31, Indels: 4
0.85 0.14 0.02
Matches are distributed among these distances:
226 37 0.19
227 44 0.23
230 113 0.58
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.29
Consensus pattern (226 bp):
GCCGCAATAGGTCAAGAATTAGCGGCGCTTTTCCAAAAACGCCGAAAAAATGTTAATCAAAACAC
ATCGTTCTATCTTGAGCCTAATGGCATTAGTGGTGCTTATGCAAAAACACCACTATAGATCGAGA
ATTAGCGGCGCTTTTATAAAAACACCGCAAAAAATGTTAATCAAAACGCACCCTTCTATCTTGAG
CTTAGTGGAATTAGCGACGCTTATGCAAAAT
Found at i:52772585 original size:27 final size:27
Alignment explanation
Indices: 52772535--52772591 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
52772525 TGTTTATTAT
* *
52772535 TTTGGGTTAAGGGTTTATGTTTTAGAG
1 TTTGGGTTAAGGGTTTAAGGTTTAGAG
*
52772562 TTTGGGTT-AGGAGTTTAAGGTTTAGGG
1 TTTGGGTTAAGG-GTTTAAGGTTTAGAG
52772589 TTT
1 TTT
52772592 AAGGTTTAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 3 0.12
27 23 0.88
ACGTcount: A:0.18, C:0.00, G:0.35, T:0.47
Consensus pattern (27 bp):
TTTGGGTTAAGGGTTTAAGGTTTAGAG
Found at i:52772598 original size:14 final size:15
Alignment explanation
Indices: 52772568--52772599 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
52772558 AGAGTTTGGG
52772568 TTAGGAGTTTAAGGT
1 TTAGGAGTTTAAGGT
52772583 TTAGG-GTTTAAGGT
1 TTAGGAGTTTAAGGT
52772597 TTA
1 TTA
52772600 AGGATACTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.25, C:0.00, G:0.31, T:0.44
Consensus pattern (15 bp):
TTAGGAGTTTAAGGT
Found at i:52772779 original size:14 final size:14
Alignment explanation
Indices: 52772748--52772833 Score: 77
Period size: 14 Copynumber: 6.1 Consensus size: 14
52772738 TTCCTAAAGA
*
52772748 TATGGTTTA-GGAT
1 TATGGTTTAGGGTT
52772761 TATGGTTTAGGGTT
1 TATGGTTTAGGGTT
*
52772775 TATGGTTTAGAGTT
1 TATGGTTTAGGGTT
*
52772789 TAGGGTTT-GGGTTT
1 TATGGTTTAGGG-TT
** * *
52772803 TATAATTTAAGATT
1 TATGGTTTAGGGTT
52772817 TATGGTTTAAGGGTT
1 TATGGTTT-AGGGTT
52772832 TA
1 TA
52772834 GAGAATATTG
Statistics
Matches: 56, Mismatches: 13, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
13 11 0.20
14 38 0.68
15 7 0.12
ACGTcount: A:0.22, C:0.00, G:0.29, T:0.49
Consensus pattern (14 bp):
TATGGTTTAGGGTT
Found at i:52772800 original size:27 final size:27
Alignment explanation
Indices: 52772748--52772802 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
52772738 TTCCTAAAGA
*
52772748 TATGGTTTAGGATTATGGTTTAGGGTT
1 TATGGTTTAGGATTAGGGTTTAGGGTT
*
52772775 TATGGTTTAGAGTTTAGGGTTT-GGGTT
1 TATGGTTTAG-GATTAGGGTTTAGGGTT
52772802 T
1 T
52772803 TATAATTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 16 0.64
28 9 0.36
ACGTcount: A:0.16, C:0.00, G:0.35, T:0.49
Consensus pattern (27 bp):
TATGGTTTAGGATTAGGGTTTAGGGTT
Found at i:52772802 original size:6 final size:7
Alignment explanation
Indices: 52772751--52772802 Score: 54
Period size: 7 Copynumber: 7.7 Consensus size: 7
52772741 CTAAAGATAT
52772751 GGTTTA-
1 GGTTTAG
* *
52772757 GGATTAT
1 GGTTTAG
52772764 GGTTTAG
1 GGTTTAG
*
52772771 GGTTTAT
1 GGTTTAG
52772778 GGTTTAG
1 GGTTTAG
*
52772785 AGTTTAG
1 GGTTTAG
52772792 GGTTT-G
1 GGTTTAG
52772798 GGTTT
1 GGTTT
52772803 TATAATTTAA
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
6 11 0.29
7 27 0.71
ACGTcount: A:0.15, C:0.00, G:0.37, T:0.48
Consensus pattern (7 bp):
GGTTTAG
Found at i:52773009 original size:15 final size:15
Alignment explanation
Indices: 52772989--52773018 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
52772979 GATCATTTAG
*
52772989 AATATAAATCTAAAT
1 AATATAAATATAAAT
52773004 AATATAAATATAAAT
1 AATATAAATATAAAT
52773019 TATTATTTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.33
Consensus pattern (15 bp):
AATATAAATATAAAT
Found at i:52773271 original size:21 final size:20
Alignment explanation
Indices: 52773231--52773268 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
52773221 AATATATTGA
52773231 TGTATTTATTTTTTAAAATG
1 TGTATTTATTTTTTAAAATG
52773251 TGTATTTATTTTTTAAAA
1 TGTATTTATTTTTTAAAA
52773269 ATGCATTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.61
Consensus pattern (20 bp):
TGTATTTATTTTTTAAAATG
Found at i:52773946 original size:17 final size:19
Alignment explanation
Indices: 52773925--52773969 Score: 58
Period size: 17 Copynumber: 2.5 Consensus size: 19
52773915 AAATTTTCCC
* *
52773925 CATTTCCCCCAATTCC-AA
1 CATTTCCCCAAATCCCTAA
52773943 -ATTTCCCCAAATCCCTAA
1 CATTTCCCCAAATCCCTAA
52773961 CATTTCCCC
1 CATTTCCCC
52773970 TAACCCTTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 13 0.57
18 2 0.09
19 8 0.35
ACGTcount: A:0.27, C:0.44, G:0.00, T:0.29
Consensus pattern (19 bp):
CATTTCCCCAAATCCCTAA
Found at i:52775239 original size:27 final size:26
Alignment explanation
Indices: 52775209--52775260 Score: 61
Period size: 27 Copynumber: 2.0 Consensus size: 26
52775199 ATTTGAGCTT
*
52775209 GTTA-ATTTGCAATAATTTGTATTTAAA
1 GTTATATTTGAAAT-ATTT-TATTTAAA
*
52775236 GTTATATTTTAAATATTTTATTTAA
1 GTTATATTTGAAATATTTTATTTAA
52775261 TTTTAATGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
26 7 0.32
27 8 0.36
28 7 0.32
ACGTcount: A:0.37, C:0.02, G:0.08, T:0.54
Consensus pattern (26 bp):
GTTATATTTGAAATATTTTATTTAAA
Found at i:52775359 original size:9 final size:9
Alignment explanation
Indices: 52775341--52775420 Score: 79
Period size: 9 Copynumber: 8.6 Consensus size: 9
52775331 GTTCAAATTT
52775341 CATAACTTA
1 CATAACTTA
*
52775350 CATAAATTA
1 CATAACTTA
52775359 CATAACTTA
1 CATAACTTA
*
52775368 CATAATTTAAA
1 CATAACTT--A
* * *
52775379 GATCAAATTT
1 CAT-AACTTA
52775389 CATAACTTA
1 CATAACTTA
*
52775398 CATAATTTA
1 CATAACTTA
52775407 CATAACTTA
1 CATAACTTA
52775416 CATAA
1 CATAA
52775421 TTTAGAGATC
Statistics
Matches: 57, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
9 48 0.84
10 2 0.04
11 3 0.05
12 4 0.07
ACGTcount: A:0.47, C:0.16, G:0.01, T:0.35
Consensus pattern (9 bp):
CATAACTTA
Found at i:52775375 original size:48 final size:48
Alignment explanation
Indices: 52775318--52775443 Score: 225
Period size: 48 Copynumber: 2.6 Consensus size: 48
52775308 TCAAATTTAC
*
52775318 TACATAATTTAAAGTTCAAATTTCATAACTTACATAAATTACATAACT
1 TACATAATTTAAAGATCAAATTTCATAACTTACATAAATTACATAACT
*
52775366 TACATAATTTAAAGATCAAATTTCATAACTTACATAATTTACATAACT
1 TACATAATTTAAAGATCAAATTTCATAACTTACATAAATTACATAACT
*
52775414 TACATAATTTAGAGATCAAATTTCATAACT
1 TACATAATTTAAAGATCAAATTTCATAACT
52775444 ATTTATGAAC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 75 1.00
ACGTcount: A:0.45, C:0.14, G:0.03, T:0.37
Consensus pattern (48 bp):
TACATAATTTAAAGATCAAATTTCATAACTTACATAAATTACATAACT
Found at i:52775421 original size:18 final size:18
Alignment explanation
Indices: 52775336--52775424 Score: 104
Period size: 18 Copynumber: 5.3 Consensus size: 18
52775326 TTAAAGTTCA
52775336 AATTT-CATAACTTACAT
1 AATTTACATAACTTACAT
*
52775353 AAATTACATAACTTACAT
1 AATTTACATAACTTACAT
52775371 AATTTA-A-AGA--T-CA-
1 AATTTACATA-ACTTACAT
52775384 AATTT-CATAACTTACAT
1 AATTTACATAACTTACAT
52775401 AATTTACATAACTTACAT
1 AATTTACATAACTTACAT
52775419 AATTTA
1 AATTTA
52775425 GAGATCAAAT
Statistics
Matches: 61, Mismatches: 2, Indels: 17
0.76 0.03 0.21
Matches are distributed among these distances:
13 7 0.11
14 3 0.05
15 2 0.03
16 3 0.05
17 11 0.18
18 35 0.57
ACGTcount: A:0.46, C:0.15, G:0.01, T:0.38
Consensus pattern (18 bp):
AATTTACATAACTTACAT
Found at i:52775476 original size:17 final size:19
Alignment explanation
Indices: 52775454--52775493 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
52775444 ATTTATGAAC
*
52775454 GAAGATA-TTACG-ATTAT
1 GAAGATATTTAAGAATTAT
52775471 GAAGATATTTAAGAATTAT
1 GAAGATATTTAAGAATTAT
52775490 GAAG
1 GAAG
52775494 TAGTAAGATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 7 0.35
18 4 0.20
19 9 0.45
ACGTcount: A:0.45, C:0.03, G:0.20, T:0.33
Consensus pattern (19 bp):
GAAGATATTTAAGAATTAT
Found at i:52775490 original size:19 final size:17
Alignment explanation
Indices: 52775454--52775503 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
52775444 ATTTATGAAC
*
52775454 GAAGATATTACGATTAT
1 GAAGATATTAAGATTAT
52775471 GAAGATATTTAAGAATTAT
1 GAAGATA-TTAAG-ATTAT
*
52775490 GAAG-TAGTAAGATT
1 GAAGATATTAAGATT
52775504 TTACGATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
16 3 0.10
17 11 0.38
18 6 0.21
19 9 0.31
ACGTcount: A:0.44, C:0.02, G:0.20, T:0.34
Consensus pattern (17 bp):
GAAGATATTAAGATTAT
Found at i:52776792 original size:13 final size:14
Alignment explanation
Indices: 52776776--52776804 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
52776766 TTGTAAATAT
52776776 TTATAAT-GTTTAA
1 TTATAATGGTTTAA
52776789 TTATAATGGTTTAA
1 TTATAATGGTTTAA
52776803 TT
1 TT
52776805 CTTCGTTAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.55
Consensus pattern (14 bp):
TTATAATGGTTTAA
Found at i:52777592 original size:43 final size:43
Alignment explanation
Indices: 52777545--52777742 Score: 124
Period size: 43 Copynumber: 4.6 Consensus size: 43
52777535 GACCACAAAC
52777545 TATAGCGGCGTTTTCAAAAAAAGCGTCGC-AAAGTGCCATGACT
1 TATAGCGGCGTTTTCAAAAAAAGCG-CGCTAAAGTGCCATGACT
* * * *
52777588 TATAGCGGCGCTTT-ATAAAAAAGTGCTGCTAAAGAT--CTTGAAT
1 TATAGCGGCGTTTTCA-AAAAAAGCGC-GCTAAAG-TGCCATGACT
* * * * * *
52777631 TTTCGCGGCGTTTTCTACAAAAGCGCCGCTAAAG-GCAATTACT
1 TATAGCGGCGTTTTCAAAAAAAGCG-CGCTAAAGTGCCATGACT
** *
52777674 TATAGCGGCGTTTT-ATAAATTAGCGCAGCTAAAG-GCCAAGACCT
1 TATAGCGGCGTTTTCA-AAAAAAGCGC-GCTAAAGTGCCATGA-CT
* * *
52777718 T-TAGCGGCATTTTCTATAAAAGCGC
1 TATAGCGGCGTTTTCAAAAAAAGCGC
52777743 CACTAAAAGT
Statistics
Matches: 115, Mismatches: 28, Indels: 24
0.69 0.17 0.14
Matches are distributed among these distances:
42 3 0.03
43 103 0.90
44 8 0.07
45 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (43 bp):
TATAGCGGCGTTTTCAAAAAAAGCGCGCTAAAGTGCCATGACT
Found at i:52777619 original size:86 final size:86
Alignment explanation
Indices: 52777518--52777749 Score: 207
Period size: 86 Copynumber: 2.7 Consensus size: 86
52777508 GCGTTTGTAA
* *
52777518 AAAAAAGCGCCGCTAAAGACCACAAACTATAGCGGCGTTTTCAAAAAAAGCGTCGC-AAAGTGCC
1 AAAAAAGCGCCGCTAAAGACCACAAACTATAGCGGCGTTTTCAAAAAAAGCGCCGCTAAAG-GCA
52777582 ATGACTTATAGCGGCGCTTTAT
65 ATGACTTATAGCGGCGCTTTAT
* * * *** * * * * *
52777604 AAAAAAGTGCTGCTAAAGATCTTGAATTTTCGCGGCGTTTTCTACAAAAGCGCCGCTAAAGGCAA
1 AAAAAAGCGCCGCTAAAGACCACAAACTATAGCGGCGTTTTCAAAAAAAGCGCCGCTAAAGGCAA
* *
52777669 TTACTTATAGCGGCGTTTTAT
66 TGACTTATAGCGGCGCTTTAT
** * * * * * * * *
52777690 AAATTAGCGCAGCTAAAGGCCA-AGACCTTTAGCGGCATTTTCTATAAAAGCGCCACTAAA
1 AAAAAAGCGCCGCTAAAGACCACA-AACTATAGCGGCGTTTTCAAAAAAAGCGCCGCTAAA
52777750 AGTCATGATC
Statistics
Matches: 115, Mismatches: 29, Indels: 4
0.78 0.20 0.03
Matches are distributed among these distances:
86 111 0.97
87 4 0.03
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.24
Consensus pattern (86 bp):
AAAAAAGCGCCGCTAAAGACCACAAACTATAGCGGCGTTTTCAAAAAAAGCGCCGCTAAAGGCAA
TGACTTATAGCGGCGCTTTAT
Found at i:52778295 original size:32 final size:32
Alignment explanation
Indices: 52778247--52778312 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 32
52778237 AATAAAATAT
*
52778247 TTAAAATATATATTTTTA-TAATTAAATTTAAA
1 TTAAAAAATATATTTTTATTAATTAAA-TTAAA
* *
52778279 TTAAAAAATATTTTTTTATTATTTAAATTAAA
1 TTAAAAAATATATTTTTATTAATTAAATTAAA
52778311 TT
1 TT
52778313 TGAATCTAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
32 23 0.77
33 7 0.23
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (32 bp):
TTAAAAAATATATTTTTATTAATTAAATTAAA
Found at i:52780000 original size:28 final size:28
Alignment explanation
Indices: 52779923--52780004 Score: 94
Period size: 28 Copynumber: 3.0 Consensus size: 28
52779913 CATGGGATTC
* * *
52779923 ATTTGCTCACACAAGTTGTAATATTCAA
1 ATTTGCTCACACAAGCTGTGATATTTAA
* * * *
52779951 ATTTTCTCTCA-GAGCTGTGATATTTGA
1 ATTTGCTCACACAAGCTGTGATATTTAA
52779978 ATTTGCTCACACAAGCTGTGATATTTA
1 ATTTGCTCACACAAGCTGTGATATTTA
52780005 GGCCACTCAC
Statistics
Matches: 42, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
27 20 0.48
28 22 0.52
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.39
Consensus pattern (28 bp):
ATTTGCTCACACAAGCTGTGATATTTAA
Found at i:52781218 original size:6 final size:6
Alignment explanation
Indices: 52781207--52781232 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
52781197 TTATTTTCAT
52781207 ATTTTA ATTTTA ATTTTA ATTTTA AT
1 ATTTTA ATTTTA ATTTTA ATTTTA AT
52781233 ATAATTTCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (6 bp):
ATTTTA
Found at i:52804415 original size:24 final size:24
Alignment explanation
Indices: 52804383--52804429 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
52804373 AACTCATGCA
52804383 CTTTGTAACACC-CATTGCTCGATC
1 CTTTGTAAC-CCTCATTGCTCGATC
52804407 CTTTGTAACCCTCATTGCTCGAT
1 CTTTGTAACCCTCATTGCTCGAT
52804430 TCAATTGCCA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 2 0.09
24 20 0.91
ACGTcount: A:0.19, C:0.32, G:0.13, T:0.36
Consensus pattern (24 bp):
CTTTGTAACCCTCATTGCTCGATC
Found at i:52813988 original size:131 final size:131
Alignment explanation
Indices: 52813753--52814012 Score: 364
Period size: 131 Copynumber: 2.0 Consensus size: 131
52813743 AAGAGTAAGA
* *
52813753 AATGACATGTAGCATTGATTATTTGCAATTGTTGACCGTCTAAGAAAAAGATGTAATATGGCTCT
1 AATGACATGTAGCATGGATTATTTGCAATTGTTGACCGTCTAAGAAAAAGATGTAATATGGCTAT
* * *
52813818 TTTCGTTAGGGCGATTACAGTCGTTTTACTCTCGACTGTCTGTGGCCCAGTCCCTCTCTTAGTCG
66 TTTCGCTAGGGCAATTACAGTCGTTTTACTCTAGACTGTCTGTGGCCCAGTCCCTCTCTTAGTCG
52813883 T
131 T
* *
52813884 AATGACATGTAGCATGGCTTATTTGCAATTGTTGACGGTCTAAGAAAAAGATGTAATATGGCTAT
1 AATGACATGTAGCATGGATTATTTGCAATTGTTGACCGTCTAAGAAAAAGATGTAATATGGCTAT
* * * **
52813949 ATTT-GCTAGGGCAATTA-TGCTCTTTTTACTGTTAG-CTGTCTGTGGCCCAGTTTCTCTCTTAG
66 -TTTCGCTAGGGCAATTACAG-TCGTTTTACT-CTAGACTGTCTGTGGCCCAGTCCCTCTCTTAG
52814011 TC
128 TC
52814013 ATTATGTGAT
Statistics
Matches: 114, Mismatches: 12, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
130 1 0.01
131 108 0.95
132 5 0.04
ACGTcount: A:0.23, C:0.18, G:0.22, T:0.37
Consensus pattern (131 bp):
AATGACATGTAGCATGGATTATTTGCAATTGTTGACCGTCTAAGAAAAAGATGTAATATGGCTAT
TTTCGCTAGGGCAATTACAGTCGTTTTACTCTAGACTGTCTGTGGCCCAGTCCCTCTCTTAGTCG
T
Found at i:52823807 original size:14 final size:16
Alignment explanation
Indices: 52823782--52823817 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
52823772 TTTAATTTTC
52823782 AAAATTTCAAAAAA-A
1 AAAATTTCAAAAAATA
52823797 AAAATTT-AAAAAATA
1 AAAATTTCAAAAAATA
52823812 AAAATT
1 AAAATT
52823818 GCATTTTGAC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 6 0.30
15 14 0.70
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (16 bp):
AAAATTTCAAAAAATA
Found at i:52823876 original size:30 final size:30
Alignment explanation
Indices: 52823813--52823883 Score: 90
Period size: 30 Copynumber: 2.4 Consensus size: 30
52823803 TAAAAAATAA
* *
52823813 AAATTGCATTTTGACCCCTAAACTTTTCCT
1 AAATTTCATTTAGACCCCTAAACTTTTCCT
* *
52823843 AAATTTCATTTAGACCCTTAAAC-TTTCATT
1 AAATTTCATTTAGACCCCTAAACTTTTC-CT
52823873 AAATTTCATTT
1 AAATTTCATTT
52823884 TAATCCTAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
29 4 0.11
30 32 0.89
ACGTcount: A:0.31, C:0.21, G:0.04, T:0.44
Consensus pattern (30 bp):
AAATTTCATTTAGACCCCTAAACTTTTCCT
Found at i:52824274 original size:18 final size:18
Alignment explanation
Indices: 52824251--52824288 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
52824241 ACCATCACCT
*
52824251 AAAACACCCCCACAATCA
1 AAAACACCCACACAATCA
52824269 AAAACACCCACACAATCA
1 AAAACACCCACACAATCA
52824287 AA
1 AA
52824289 TAAAATAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.55, C:0.39, G:0.00, T:0.05
Consensus pattern (18 bp):
AAAACACCCACACAATCA
Found at i:52824476 original size:16 final size:16
Alignment explanation
Indices: 52824455--52824486 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
52824445 GAGATTTTTG
*
52824455 AAAAAAACAAAGCAAA
1 AAAAAAACAAAACAAA
52824471 AAAAAAACAAAACAAA
1 AAAAAAACAAAACAAA
52824487 GCAGAAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.84, C:0.12, G:0.03, T:0.00
Consensus pattern (16 bp):
AAAAAAACAAAACAAA
Found at i:52824503 original size:21 final size:21
Alignment explanation
Indices: 52824455--52824512 Score: 73
Period size: 21 Copynumber: 2.7 Consensus size: 21
52824445 GAGATTTTTG
52824455 AAAAAAACAAAGCA-AAAAAA
1 AAAAAAACAAAGCAGAAAAAA
52824475 AAACAAAACAAAGCAGAAAAAA
1 AAA-AAAACAAAGCAGAAAAAA
* *
52824497 ATAAAAATAGAAGCAG
1 AAAAAAACA-AAGCAG
52824513 GCCACAGCCA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.09
21 16 0.48
22 14 0.42
ACGTcount: A:0.76, C:0.10, G:0.10, T:0.03
Consensus pattern (21 bp):
AAAAAAACAAAGCAGAAAAAA
Found at i:52825190 original size:17 final size:17
Alignment explanation
Indices: 52825147--52825194 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
52825137 AAAGAAAAAT
52825147 CGTGTTTCAAAAATTTTCA
1 CGTGTTTC-AAAA-TTTCA
52825166 --TGTCTTCAAAATTTCA
1 CGTGT-TTCAAAATTTCA
52825182 CGTGTTTCAAAAT
1 CGTGTTTCAAAAT
52825195 AATAATAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
16 5 0.19
17 15 0.58
18 6 0.23
ACGTcount: A:0.31, C:0.17, G:0.10, T:0.42
Consensus pattern (17 bp):
CGTGTTTCAAAATTTCA
Done.