Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr9
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: 48574783
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2023350 characters in sequence are not A, C, G, or T
File 40 of 135
Found at i:15795562 original size:21 final size:22
Alignment explanation
Indices: 15795517--15795570 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 22
15795507 TAAGGGACAA
15795517 TATGC-ATGTATATGATTGACT
1 TATGCTATGTATATGATTGACT
*
15795538 TATGCTATGTTTATG-TTGA-T
1 TATGCTATGTATATGATTGACT
*
15795558 GTATGATATGTAT
1 -TATGCTATGTAT
15795571 TGTCGAAACC
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
20 1 0.04
21 19 0.68
22 8 0.29
ACGTcount: A:0.26, C:0.06, G:0.20, T:0.48
Consensus pattern (22 bp):
TATGCTATGTATATGATTGACT
Found at i:15796267 original size:25 final size:25
Alignment explanation
Indices: 15796210--15796268 Score: 64
Period size: 25 Copynumber: 2.4 Consensus size: 25
15796200 AAATATATAC
* *
15796210 ATATAAATATGAAAATATTCATTAA
1 ATATATATAGGAAAATATTCATTAA
* * * *
15796235 AAAAATATAGGAAAATATTCGTTTA
1 ATATATATAGGAAAATATTCATTAA
15796260 ATATATATA
1 ATATATATA
15796269 TATATATGTG
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.54, C:0.03, G:0.07, T:0.36
Consensus pattern (25 bp):
ATATATATAGGAAAATATTCATTAA
Found at i:15796911 original size:19 final size:19
Alignment explanation
Indices: 15796887--15796977 Score: 148
Period size: 19 Copynumber: 4.8 Consensus size: 19
15796877 AATCATATAT
15796887 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
**
15796906 TCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATA
15796925 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
15796944 TCTATGATTGCATATCATA
1 TCTAAGATTGCATATCATA
15796963 TC-AAGATTGCATATC
1 TCTAAGATTGCATATC
15796978 CTCAAAAATT
Statistics
Matches: 66, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
18 12 0.18
19 54 0.82
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.38
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:15796934 original size:38 final size:38
Alignment explanation
Indices: 15796864--15796977 Score: 149
Period size: 38 Copynumber: 2.9 Consensus size: 38
15796854 AAATTAAATC
*
15796864 TCTAAGATTACAAAATCATATATTCTAAGATTGCATATCATA
1 TCTAAGATTAC-ATATC--ATA-TCTAAGATTGCATATCATA
*
15796906 TCTAAGATTATATATCATATCTAAGATTGCATATCATA
1 TCTAAGATTACATATCATATCTAAGATTGCATATCATA
* *
15796944 TCTATGATTGCATATCATATC-AAGATTGCATATC
1 TCTAAGATTACATATCATATCTAAGATTGCATATC
15796978 CTCAAAAATT
Statistics
Matches: 67, Mismatches: 5, Indels: 5
0.87 0.06 0.06
Matches are distributed among these distances:
37 13 0.19
38 37 0.55
39 3 0.04
41 4 0.06
42 10 0.15
ACGTcount: A:0.39, C:0.15, G:0.09, T:0.38
Consensus pattern (38 bp):
TCTAAGATTACATATCATATCTAAGATTGCATATCATA
Found at i:15798087 original size:92 final size:90
Alignment explanation
Indices: 15797974--15798142 Score: 214
Period size: 92 Copynumber: 1.9 Consensus size: 90
15797964 TTACTGACAG
* * ** * * *
15797974 CTTTTATCTGCAAACCTGTTATGCATTTACAACCTATTGGCAGTGTATTAACCTACAAACATTGG
1 CTTTTATCTGCAAACCTGTTATGCATTCACAA-CTACTGGCAGCATATTAACATAC-AACACTAG
*
15798039 TGGTTTATCCACAACTATTATTGGCAA
64 TGGTTCATCCACAACTATTATTGGCAA
* *
15798066 CTTTTATCTGCAAATCC-GTTATGTATTCACAACTACTGGCAGCATATTAACATGCAACACTAGT
1 CTTTTATCTGCAAA-CCTGTTATGCATTCACAACTACTGGCAGCATATTAACATACAACACTAGT
15798130 GGTTCATCCACAA
65 GGTTCATCCACAA
15798143 ACTGGAGTGT
Statistics
Matches: 66, Mismatches: 10, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
90 19 0.29
91 18 0.27
92 27 0.41
93 2 0.03
ACGTcount: A:0.30, C:0.22, G:0.14, T:0.34
Consensus pattern (90 bp):
CTTTTATCTGCAAACCTGTTATGCATTCACAACTACTGGCAGCATATTAACATACAACACTAGTG
GTTCATCCACAACTATTATTGGCAA
Found at i:15804025 original size:23 final size:24
Alignment explanation
Indices: 15803986--15804048 Score: 67
Period size: 24 Copynumber: 2.6 Consensus size: 24
15803976 TTTCTAGGAA
15803986 ACCAAACAAAAACCCCTC-A-AACAAC
1 ACCAAA-AAAAA-CCCTCGAGAA-AAC
15804011 ACCAAAAAAAACCCTCGAGAAAAC
1 ACCAAAAAAAACCCTCGAGAAAAC
**
15804035 AAAAAAAAAAACCC
1 ACCAAAAAAAACCC
15804049 GAAATTTAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
23 5 0.15
24 21 0.62
25 8 0.24
ACGTcount: A:0.62, C:0.32, G:0.03, T:0.03
Consensus pattern (24 bp):
ACCAAAAAAAACCCTCGAGAAAAC
Found at i:15805910 original size:17 final size:17
Alignment explanation
Indices: 15805888--15805922 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
15805878 CTTCTGAAAA
15805888 GCTAAAAATTGCAGCTT
1 GCTAAAAATTGCAGCTT
*
15805905 GCTAAAAATTTCAGCTT
1 GCTAAAAATTGCAGCTT
15805922 G
1 G
15805923 TTCTTCACAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31
Consensus pattern (17 bp):
GCTAAAAATTGCAGCTT
Found at i:15808962 original size:250 final size:250
Alignment explanation
Indices: 15808521--15809020 Score: 1000
Period size: 250 Copynumber: 2.0 Consensus size: 250
15808511 AGACAAAATT
15808521 AACTCTATTTTATATTAGTTTAGGATATTAGTCTATTAATAAACGTAAAAGAAGAAGAAGCAATT
1 AACTCTATTTTATATTAGTTTAGGATATTAGTCTATTAATAAACGTAAAAGAAGAAGAAGCAATT
15808586 GTCTTCTTCTGTTGTCCTACTACGTTTTCTTTTGTTACTTAAACAGATTCTTTACAATTATTATA
66 GTCTTCTTCTGTTGTCCTACTACGTTTTCTTTTGTTACTTAAACAGATTCTTTACAATTATTATA
15808651 TATAAATAATTTTTTTCAATTTATTCAAAAAAATTATATATACATCATTTTGTATGTACATTATT
131 TATAAATAATTTTTTTCAATTTATTCAAAAAAATTATATATACATCATTTTGTATGTACATTATT
15808716 ATATTTTAAAAATATATGTAGGACAAATTTGAAATAATTTTACTTTCAATTAAAG
196 ATATTTTAAAAATATATGTAGGACAAATTTGAAATAATTTTACTTTCAATTAAAG
15808771 AACTCTATTTTATATTAGTTTAGGATATTAGTCTATTAATAAACGTAAAAGAAGAAGAAGCAATT
1 AACTCTATTTTATATTAGTTTAGGATATTAGTCTATTAATAAACGTAAAAGAAGAAGAAGCAATT
15808836 GTCTTCTTCTGTTGTCCTACTACGTTTTCTTTTGTTACTTAAACAGATTCTTTACAATTATTATA
66 GTCTTCTTCTGTTGTCCTACTACGTTTTCTTTTGTTACTTAAACAGATTCTTTACAATTATTATA
15808901 TATAAATAATTTTTTTCAATTTATTCAAAAAAATTATATATACATCATTTTGTATGTACATTATT
131 TATAAATAATTTTTTTCAATTTATTCAAAAAAATTATATATACATCATTTTGTATGTACATTATT
15808966 ATATTTTAAAAATATATGTAGGACAAATTTGAAATAATTTTACTTTCAATTAAAG
196 ATATTTTAAAAATATATGTAGGACAAATTTGAAATAATTTTACTTTCAATTAAAG
15809021 TATAAATTAA
Statistics
Matches: 250, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
250 250 1.00
ACGTcount: A:0.37, C:0.10, G:0.09, T:0.44
Consensus pattern (250 bp):
AACTCTATTTTATATTAGTTTAGGATATTAGTCTATTAATAAACGTAAAAGAAGAAGAAGCAATT
GTCTTCTTCTGTTGTCCTACTACGTTTTCTTTTGTTACTTAAACAGATTCTTTACAATTATTATA
TATAAATAATTTTTTTCAATTTATTCAAAAAAATTATATATACATCATTTTGTATGTACATTATT
ATATTTTAAAAATATATGTAGGACAAATTTGAAATAATTTTACTTTCAATTAAAG
Found at i:15813112 original size:29 final size:29
Alignment explanation
Indices: 15813069--15813177 Score: 98
Period size: 29 Copynumber: 3.8 Consensus size: 29
15813059 CCTTTACTGG
* *
15813069 GATTTCCACAGAGGCCTTCCTTTGATAAA
1 GATTGCCACAAAGGCCTTCCTTTGATAAA
* *
15813098 GATTGCCACAAAGGCGTTTCC-TTG-TAGA
1 GATTGCCACAAAGGC-CTTCCTTTGATAAA
* * *
15813126 GATTTGCCACAAAGGCATT-CTTTAACAAA
1 GA-TTGCCACAAAGGCCTTCCTTTGATAAA
* *
15813155 GGTTGCCACAAAGGCCTACCTTT
1 GATTGCCACAAAGGCCTTCCTTT
15813178 CCAAAGTTTT
Statistics
Matches: 64, Mismatches: 11, Indels: 10
0.75 0.13 0.12
Matches are distributed among these distances:
27 1 0.02
28 23 0.36
29 36 0.56
30 4 0.06
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.28
Consensus pattern (29 bp):
GATTGCCACAAAGGCCTTCCTTTGATAAA
Found at i:15813182 original size:28 final size:29
Alignment explanation
Indices: 15813129--15813206 Score: 79
Period size: 28 Copynumber: 2.7 Consensus size: 29
15813119 TTGTAGAGAT
*
15813129 TTGCCACAAAGGCATTCTTTAACAAAG-G
1 TTGCCACAAAGGCATCCTTTAACAAAGTG
* * *
15813157 TTGCCACAAAGGCCTACCTTT-CCAAAGTT
1 TTGCCACAAAGGCAT-CCTTTAACAAAGTG
* *
15813186 TTGCCACAAAAGCATCTTTTA
1 TTGCCACAAAGGCATCCTTTA
15813207 CATTCAATAC
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
28 23 0.57
29 17 0.43
ACGTcount: A:0.32, C:0.26, G:0.14, T:0.28
Consensus pattern (29 bp):
TTGCCACAAAGGCATCCTTTAACAAAGTG
Found at i:15813448 original size:61 final size:60
Alignment explanation
Indices: 15813159--15813449 Score: 230
Period size: 61 Copynumber: 4.8 Consensus size: 60
15813149 AACAAAGGTT
* * * * * * * *
15813159 GCCACAAAGGCCTACCTTTCCAAAGTTTTGCCACAAAAG-CATCTTTTACAT-TCAATACTA
1 GCCACAAAGGCTTTCCTGTCCAGAGTTTTGCCA-AAAAGTTATCCTTTACATCT-AGTACTC
** * * * *
15813219 GCCACAAACACTTTCCTGTCCAGAGATTTACTG-C-AGAAGTTGTTCTTTACATCCAGTACTC
1 GCCACAAAGGCTTTCCTGTCCAGAG-TTT--TGCCAAAAAGTTATCCTTTACATCTAGTACTC
* * * *
15813280 ACCACAAAGGTTTTCCTATCCAGAGTTTTGCCAAAAAAGTTTTCCTTTACATCTAGTACTC
1 GCCACAAAGGCTTTCCTGTCCAGAGTTTTGCC-AAAAAGTTATCCTTTACATCTAGTACTC
* * * * * * *
15813341 GCCACAAAGGCTTTCATGTCCAAAGTTTTACCACAAAGGTTGTCCTTTACATCTAATACTT
1 GCCACAAAGGCTTTCCTGTCCAGAGTTTTGCCA-AAAAGTTATCCTTTACATCTAGTACTC
* * *
15813402 GCCACAAAGGCTTTCCTGTCTAGAGTTTTGCCATAAAGCCTATCCTTT
1 GCCACAAAGGCTTTCCTGTCCAGAGTTTTGCCAAAAAG-TTATCCTTT
15813450 TTTGAGTGTT
Statistics
Matches: 180, Mismatches: 41, Indels: 19
0.75 0.17 0.08
Matches are distributed among these distances:
58 2 0.01
59 1 0.01
60 30 0.17
61 144 0.80
62 1 0.01
63 2 0.01
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.32
Consensus pattern (60 bp):
GCCACAAAGGCTTTCCTGTCCAGAGTTTTGCCAAAAAGTTATCCTTTACATCTAGTACTC
Found at i:15813448 original size:122 final size:121
Alignment explanation
Indices: 15813157--15813449 Score: 295
Period size: 122 Copynumber: 2.4 Consensus size: 121
15813147 TTAACAAAGG
* * * * *
15813157 TTGCCACAAAGGCCTACCTTTCCAAAGTTTTGCCACAAAAGC-ATCTTTTACATTCAATACTAGC
1 TTGCCACAAAGGCTTTCCTATCCAGAGTTTTGCCA-AAAAGCTATCCTTTACATTCAATACTAGC
* * ** * *
15813221 CACAAACACTTTCCTGTCCAGAGATTTACTGCAGAAGTTGTTCTTTACATCCAGTAC
65 CACAAACACTTTCATGTCCAAAGATTTACCACAGAAGTTGTCCTTTACATCCAATAC
** * * * * *
15813278 TCACCACAAAGGTTTTCCTATCCAGAGTTTTGCCAAAAAAGTTTTCCTTTACA-TCTAGTACTCG
1 TTGCCACAAAGGCTTTCCTATCCAGAGTTTTGCC-AAAAAGCTATCCTTTACATTC-AATACTAG
** * *
15813342 CCACAAAGGCTTTCATGTCCAAAGTTTTACCACA-AAGGTTGTCCTTTACATCTAATAC
64 CCACAAACACTTTCATGTCCAAAGATTTACCACAGAA-GTTGTCCTTTACATCCAATAC
* * *
15813400 TTGCCACAAAGGCTTTCCTGTCTAGAGTTTTGCCATAAAGCCTATCCTTT
1 TTGCCACAAAGGCTTTCCTATCCAGAGTTTTGCCAAAAAG-CTATCCTTT
15813450 TTTGAGTGTT
Statistics
Matches: 137, Mismatches: 30, Indels: 9
0.78 0.17 0.05
Matches are distributed among these distances:
121 41 0.30
122 96 0.70
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.32
Consensus pattern (121 bp):
TTGCCACAAAGGCTTTCCTATCCAGAGTTTTGCCAAAAAGCTATCCTTTACATTCAATACTAGCC
ACAAACACTTTCATGTCCAAAGATTTACCACAGAAGTTGTCCTTTACATCCAATAC
Found at i:15820260 original size:15 final size:15
Alignment explanation
Indices: 15820240--15820270 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
15820230 TAAATATGTG
15820240 TATAATTGTGGATAC
1 TATAATTGTGGATAC
15820255 TATAATTGTGGATAC
1 TATAATTGTGGATAC
15820270 T
1 T
15820271 TTTTCCTTGT
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:0.32, C:0.06, G:0.19, T:0.42
Consensus pattern (15 bp):
TATAATTGTGGATAC
Found at i:15821746 original size:24 final size:26
Alignment explanation
Indices: 15821685--15821754 Score: 81
Period size: 27 Copynumber: 2.7 Consensus size: 26
15821675 ATATAGAGTA
* *
15821685 CGCCTCAAAGGCAATTCTTTCACAGTT
1 CGCCACAAAGGCTATTCTTTCACAG-T
*
15821712 CACCACAAAGGCTATTCTTTCA-A-T
1 CGCCACAAAGGCTATTCTTTCACAGT
*
15821736 CGCCACAAAGGCTACTCTT
1 CGCCACAAAGGCTATTCTT
15821755 AGCAGTCAAG
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
24 18 0.47
26 1 0.03
27 19 0.50
ACGTcount: A:0.29, C:0.31, G:0.13, T:0.27
Consensus pattern (26 bp):
CGCCACAAAGGCTATTCTTTCACAGT
Found at i:15824033 original size:27 final size:28
Alignment explanation
Indices: 15823977--15824036 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
15823967 TGCACCATTA
* *
15823977 AGGC-TTTCCTTTTATGAATTTCCATAG
1 AGGCTTTTCATTTTATGAATTGCCATAG
15824004 AGGCTTTTCATTTTA-GATATTGCCAT-G
1 AGGCTTTTCATTTTATGA-ATTGCCATAG
15824031 AGGCTT
1 AGGCTT
15824037 CCTTTATCCA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 13 0.45
28 16 0.55
ACGTcount: A:0.22, C:0.17, G:0.18, T:0.43
Consensus pattern (28 bp):
AGGCTTTTCATTTTATGAATTGCCATAG
Found at i:15824100 original size:30 final size:29
Alignment explanation
Indices: 15824066--15824183 Score: 130
Period size: 30 Copynumber: 3.9 Consensus size: 29
15824056 CAAAGGCTTT
* *
15824066 CTTTATAGAGTTTCGCCATAAACACTTTTC
1 CTTTACAGAGTTT-GCCATAAAGACTTTTC
* *
15824096 CTTTAAAGAGGTTTGCCACAAA-AGCTTTTC
1 CTTTACAGA-GTTTGCCATAAAGA-CTTTTC
* *
15824126 CTTTACAGAGTCTTGCCATAAAGGCTTTTT
1 CTTTACAGAGT-TTGCCATAAAGACTTTTC
15824156 CTTTACAGAGATTTGCCATAAAGACTTT
1 CTTTACAGAG-TTTGCCATAAAGACTTT
15824184 CATTTTCTGG
Statistics
Matches: 76, Mismatches: 7, Indels: 10
0.82 0.08 0.11
Matches are distributed among these distances:
29 3 0.04
30 68 0.89
31 5 0.07
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.37
Consensus pattern (29 bp):
CTTTACAGAGTTTGCCATAAAGACTTTTC
Found at i:15824154 original size:60 final size:58
Alignment explanation
Indices: 15824053--15824173 Score: 145
Period size: 60 Copynumber: 2.1 Consensus size: 58
15824043 TCCAAGGTCA
* * *
15824053 CCACAAAGGCTTTCTTTATAGAGTTTCGCCATAAACACTTTTCCTTTAAAGAGGTTTG
1 CCACAAAAGCTTTCTTTACAGAGTTTCGCCATAAACACTTTTCCTTTAAAGAGATTTG
** * *
15824111 CCACAAAAGCTTTTCCTTTACAGAGTCTT-GCCATAAAGGCTTTTTCTTTACAGAGATTTG
1 CCACAAAAGC-TTT-CTTTACAGAGT-TTCGCCATAAACACTTTTCCTTTAAAGAGATTTG
15824171 CCA
1 CCA
15824174 TAAAGACTTT
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
58 9 0.17
59 3 0.06
60 39 0.74
61 2 0.04
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.36
Consensus pattern (58 bp):
CCACAAAAGCTTTCTTTACAGAGTTTCGCCATAAACACTTTTCCTTTAAAGAGATTTG
Found at i:15829409 original size:41 final size:41
Alignment explanation
Indices: 15829352--15829461 Score: 175
Period size: 41 Copynumber: 2.7 Consensus size: 41
15829342 CATTGTATGT
*
15829352 AAGGGGTTGCTAAGTGCAGATTCCCCGAATCACTGATCAAA
1 AAGGGGTTGCTAAGTGCAGATTCCCCGAATCACTAATCAAA
* *
15829393 AAGGGGTTGCTAAGTGCAGATTTCCTGAATCACTAATCAAA
1 AAGGGGTTGCTAAGTGCAGATTCCCCGAATCACTAATCAAA
* *
15829434 AAGGGGTTACTAAGTGTAGATTCCCCGA
1 AAGGGGTTGCTAAGTGCAGATTCCCCGA
15829462 GAGGTTGCTA
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 62 1.00
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.25
Consensus pattern (41 bp):
AAGGGGTTGCTAAGTGCAGATTCCCCGAATCACTAATCAAA
Found at i:15835623 original size:47 final size:46
Alignment explanation
Indices: 15835507--15835629 Score: 129
Period size: 47 Copynumber: 2.6 Consensus size: 46
15835497 GTATATATAA
* ** *
15835507 ATATATTTTTTATGCATGAAAATGAATTAATTTATAGCTGAATGTAT
1 ATATATTTATTATGCATG-AAATGAATTAAACTATAGCCGAATGTAT
* * * *
15835554 ATGTAATTATTATGCAGAGAAATGAATTAAACTATGGCCGAATGTAT
1 ATATATTTATTATGCA-TGAAATGAATTAAACTATAGCCGAATGTAT
* *
15835601 ATATATTTGTTATGCATTGAAATAAATTA
1 ATATATTTATTATGCA-TGAAATGAATTA
15835630 TTTGAAATTA
Statistics
Matches: 61, Mismatches: 14, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
47 60 0.98
48 1 0.02
ACGTcount: A:0.40, C:0.06, G:0.15, T:0.40
Consensus pattern (46 bp):
ATATATTTATTATGCATGAAATGAATTAAACTATAGCCGAATGTAT
Found at i:15835707 original size:49 final size:49
Alignment explanation
Indices: 15835651--15835788 Score: 181
Period size: 47 Copynumber: 2.9 Consensus size: 49
15835641 ATAGGTTATG
* *
15835651 GCCGAATGTATATATATATTTGTTATACATTGAAATGAATTAATCTATA
1 GCCGAATGTATATATATATTTGTTATGCATTGAAATGAATTAAACTATA
* * * ** *
15835700 GCTGAATGTATATGTA-A-TCGTTATGCAAAGAAATGAATTAAACTATG
1 GCCGAATGTATATATATATTTGTTATGCATTGAAATGAATTAAACTATA
*
15835747 GCCGAATGTATATATATATTTGTTATGCATTGAAATAAATTA
1 GCCGAATGTATATATATATTTGTTATGCATTGAAATGAATTA
15835789 TTTGAAGTTA
Statistics
Matches: 73, Mismatches: 14, Indels: 4
0.80 0.15 0.04
Matches are distributed among these distances:
47 38 0.52
48 2 0.03
49 33 0.45
ACGTcount: A:0.39, C:0.08, G:0.15, T:0.38
Consensus pattern (49 bp):
GCCGAATGTATATATATATTTGTTATGCATTGAAATGAATTAAACTATA
Found at i:15835724 original size:157 final size:158
Alignment explanation
Indices: 15835502--15835824 Score: 508
Period size: 157 Copynumber: 2.1 Consensus size: 158
15835492 CAAATGTATA
* * * * *
15835502 TATAAATATATTTTTTATGCATGAAAATGAATTAATTTATAGCTGAATGTATATGTAATTATTAT
1 TATATATATATTTGTTATACATGAAAATGAATTAATCTATAGCTGAATGTATATGTAATCATTAT
*
15835567 GCAGAGAAATGAATTAAACTATGGCCGAATG-TATATATATTTGTTATGCATTGAAATAAATTAT
66 GCAAAGAAATGAATTAAACTATGGCCGAATGATATATATATTTGTTATGCATTGAAATAAATTAT
* *
15835631 TTGAAATTACATAGGTTATGGCCGAATG
131 TTGAAATTACATAAGCTATGGCCGAATG
*
15835659 TATATATATATTTGTTATACATTG-AAATGAATTAATCTATAGCTGAATGTATATGTAATCGTTA
1 TATATATATATTTGTTATACA-TGAAAATGAATTAATCTATAGCTGAATGTATATGTAATCATTA
15835723 TGCAAAGAAATGAATTAAACTATGGCCGAATGTATATATATATTTGTTATGCATTGAAATAAATT
65 TGCAAAGAAATGAATTAAACTATGGCCGAATG-ATATATATATTTGTTATGCATTGAAATAAATT
* *
15835788 ATTTGAAGTTACATAAGCTATGGCTGAATG
129 ATTTGAAATTACATAAGCTATGGCCGAATG
15835818 TA-ATATA
1 TATATATA
15835825 GTGAATTGTT
Statistics
Matches: 152, Mismatches: 11, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
157 86 0.57
158 7 0.05
159 59 0.39
ACGTcount: A:0.39, C:0.07, G:0.15, T:0.39
Consensus pattern (158 bp):
TATATATATATTTGTTATACATGAAAATGAATTAATCTATAGCTGAATGTATATGTAATCATTAT
GCAAAGAAATGAATTAAACTATGGCCGAATGATATATATATTTGTTATGCATTGAAATAAATTAT
TTGAAATTACATAAGCTATGGCCGAATG
Found at i:15835949 original size:41 final size:41
Alignment explanation
Indices: 15835892--15836037 Score: 213
Period size: 41 Copynumber: 3.6 Consensus size: 41
15835882 TTTTGTAAGT
*
15835892 TTGGGCTTTATGCCTAGCAGGCTTTGTGCCGGTGAAATGTA
1 TTGGGCTTTATGCCTAGCAGGCTCTGTGCCGGTGAAATGTA
*
15835933 TTGGGCTTTATGCCTAGCAGGCTCTGTGCCTGTGAAATGTA
1 TTGGGCTTTATGCCTAGCAGGCTCTGTGCCGGTGAAATGTA
** *
15835974 TCAGGCTTTATGCCTAGCAAGCTCTGTGCCGGTGAAATGT-
1 TTGGGCTTTATGCCTAGCAGGCTCTGTGCCGGTGAAATGTA
* *
15836014 TTCGGGCTTTGTGTCTAGCAGGCT
1 TT-GGGCTTTATGCCTAGCAGGCT
15836038 TTATGTCGGT
Statistics
Matches: 93, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
40 1 0.01
41 92 0.99
ACGTcount: A:0.16, C:0.20, G:0.30, T:0.34
Consensus pattern (41 bp):
TTGGGCTTTATGCCTAGCAGGCTCTGTGCCGGTGAAATGTA
Found at i:15836062 original size:82 final size:82
Alignment explanation
Indices: 15835895--15836067 Score: 204
Period size: 82 Copynumber: 2.1 Consensus size: 82
15835885 TGTAAGTTTG
* * *
15835895 GGCTTTATGCCTAGCAGGCTTTGTGCCGGTGAAATGTATTGGGCTTTATGCCTAGCAGGCTCTGT
1 GGCTTTATGCCTAGCAAGCTCTGTGCCGGTGAAATGTATTGGGCTTTATGCCTAGCAGGCTCTAT
* * *
15835960 GCCTGTGAAATGTATCA
66 GCCGGTGAAATATATAA
* * *
15835977 GGCTTTATGCCTAGCAAGCTCTGTGCCGGTGAAATGT-TTCGGGCTTTGTGTCTAGCAGGCTTTA
1 GGCTTTATGCCTAGCAAGCTCTGTGCCGGTGAAATGTATT-GGGCTTTATGCCTAGCAGGCTCTA
* ***
15836041 TGTCGGTGTTTTATATAA
65 TGCCGGTGAAATATATAA
*
15836059 GGCTCTATG
1 GGCTTTATG
15836068 TTTAACAAGT
Statistics
Matches: 76, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
81 2 0.03
82 74 0.97
ACGTcount: A:0.17, C:0.18, G:0.29, T:0.35
Consensus pattern (82 bp):
GGCTTTATGCCTAGCAAGCTCTGTGCCGGTGAAATGTATTGGGCTTTATGCCTAGCAGGCTCTAT
GCCGGTGAAATATATAA
Found at i:15841185 original size:27 final size:27
Alignment explanation
Indices: 15841100--15841190 Score: 94
Period size: 27 Copynumber: 3.4 Consensus size: 27
15841090 AATACACCAA
*
15841100 AAAGG-TAGTTCTTTCAGAGTTCACCAC
1 AAAGGCTA-TTCTTTCAGAGTTCGCCAC
* * * *
15841127 AAAGACTGTTCTTTTAGAGTTTGCCAC
1 AAAGGCTATTCTTTCAGAGTTCGCCAC
* * *
15841154 AAAGGTTATTCTTTCAAAGTTCGCCAT
1 AAAGGCTATTCTTTCAGAGTTCGCCAC
15841181 AAAGGCTATT
1 AAAGGCTATT
15841191 ATTAATAGTC
Statistics
Matches: 50, Mismatches: 13, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
27 49 0.98
28 1 0.02
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.34
Consensus pattern (27 bp):
AAAGGCTATTCTTTCAGAGTTCGCCAC
Found at i:15842042 original size:3 final size:3
Alignment explanation
Indices: 15842034--15842070 Score: 65
Period size: 3 Copynumber: 12.0 Consensus size: 3
15842024 ACCACTTGAG
15842034 GAA GAA GAA GAA GAA GAA GAA GAA GAA GGAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA -GAA GAA GAA
15842071 TCCTTTTCAG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 30 0.91
4 3 0.09
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:15850184 original size:31 final size:31
Alignment explanation
Indices: 15850126--15850194 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
15850116 TATGTTAAAT
*
15850126 AATTATTAAATTATTTAAAAAAATTTATTCA
1 AATTATTAAATTATTCAAAAAAATTTATTCA
* * ** *
15850157 AGTTATTAAATTATTCGAAAATTTTTATTTA
1 AATTATTAAATTATTCAAAAAAATTTATTCA
15850188 AATTATT
1 AATTATT
15850195 GATTTATTTT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.49
Consensus pattern (31 bp):
AATTATTAAATTATTCAAAAAAATTTATTCA
Found at i:15850871 original size:27 final size:27
Alignment explanation
Indices: 15850841--15850902 Score: 97
Period size: 27 Copynumber: 2.3 Consensus size: 27
15850831 GCCACTGATA
15850841 GGCGGCACCAAAGGTGCCATTCCCATG
1 GGCGGCACCAAAGGTGCCATTCCCATG
***
15850868 GGCGGCACCGGTGGTGCCATTCCCATG
1 GGCGGCACCAAAGGTGCCATTCCCATG
15850895 GGCGGCAC
1 GGCGGCAC
15850903 TGCTCTTATA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.16, C:0.34, G:0.35, T:0.15
Consensus pattern (27 bp):
GGCGGCACCAAAGGTGCCATTCCCATG
Found at i:15850981 original size:18 final size:18
Alignment explanation
Indices: 15850958--15850992 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
15850948 AAGGAGAGGG
*
15850958 AAAGAAGAAGAAAGAAAT
1 AAAGAAAAAGAAAGAAAT
*
15850976 AAAGAAAAAGAAGGAAA
1 AAAGAAAAAGAAAGAAA
15850993 GAAAACGAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.74, C:0.00, G:0.23, T:0.03
Consensus pattern (18 bp):
AAAGAAAAAGAAAGAAAT
Found at i:15851028 original size:44 final size:44
Alignment explanation
Indices: 15850960--15851075 Score: 171
Period size: 44 Copynumber: 2.6 Consensus size: 44
15850950 GGAGAGGGAA
15850960 AGAAGAAGAAAGAAATAAAGAAAAAGAAGGAAAGAAAACGAAAGG
1 AGAAGAAGAAA-AAATAAAGAAAAAGAAGGAAAGAAAACGAAAGG
* * *
15851005 AGAAGAAGAAAAAATAATGAAAAATAAGGAAAGAAAAGGAAAGG
1 AGAAGAAGAAAAAATAAAGAAAAAGAAGGAAAGAAAACGAAAGG
* *
15851049 AGAAG-AGAAAAAAAAAAGAAGAAGAAG
1 AGAAGAAGAAAAAATAAAGAAAAAGAAG
15851076 AGGGGAGGAA
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
43 18 0.28
44 35 0.55
45 11 0.17
ACGTcount: A:0.70, C:0.01, G:0.26, T:0.03
Consensus pattern (44 bp):
AGAAGAAGAAAAAATAAAGAAAAAGAAGGAAAGAAAACGAAAGG
Found at i:15851047 original size:10 final size:11
Alignment explanation
Indices: 15850956--15851047 Score: 50
Period size: 10 Copynumber: 8.5 Consensus size: 11
15850946 AGAAGGAGAG
*
15850956 GGAAAGAAGAA
1 GGAAAGAATAA
15850967 -GAAAGAAATAA
1 GGAAAG-AATAA
* *
15850978 AGAAA-AAGAA
1 GGAAAGAATAA
15850988 GGAAAGAA-AA
1 GGAAAGAATAA
* * *
15850998 CGAAAGGAGAA
1 GGAAAGAATAA
*
15851009 GAAGAAAAAATAA
1 G--GAAAGAATAA
*
15851022 TGAAA-AATAA
1 GGAAAGAATAA
15851032 GGAAAGAA-AA
1 GGAAAGAATAA
15851042 GGAAAG
1 GGAAAG
15851048 GAGAAGAGAA
Statistics
Matches: 63, Mismatches: 11, Indels: 15
0.71 0.12 0.17
Matches are distributed among these distances:
10 38 0.60
11 14 0.22
12 4 0.06
13 7 0.11
ACGTcount: A:0.68, C:0.01, G:0.26, T:0.04
Consensus pattern (11 bp):
GGAAAGAATAA
Found at i:15852030 original size:226 final size:225
Alignment explanation
Indices: 15851637--15852089 Score: 809
Period size: 226 Copynumber: 2.0 Consensus size: 225
15851627 GTACTGAAAT
15851637 AATATAAAATAATAAAATACGAAAATAAAATTATTTTATTGAAAGTAATAAAATTCGGGAAAATA
1 AATATAAAATAATAAAATACGAAAATAAAATTATTTTATTGAAAGTAATAAAATTCGGGAAAATA
* *
15851702 ATATGAGCAAATAGCGTGAATAAGGGTTTTTTTACACTAAATTAATTTAAAAAACACACTAAATT
66 ATACGAGCAAATAGCGGGAATAAGGGTTTTTTTACACTAAATTAATTTAAAAAACACACTAAATT
15851767 AATAAATTTATAAAATTAGAAATTATGAAATTTTTTAAAGTAATAAAATGCGGAGAAAAAAATAC
131 AATAAATTTATAAAATTAGAAATTATGAAATTTTTTAAAGTAATAAAATGCGGAGAAAAAAATAC
*
15851832 GAAGAAATGGCCGATGTAAGAGTGTTTTAC
196 GAAGAAATGGCCGAGGTAAGAGTGTTTTAC
*
15851862 AATATAAAATAATAAAATACGAAAATAAAAATTTTTTTATTGAAAGTAATAAAATTCGGGAAAAT
1 AATATAAAATAATAAAATACGAAAAT-AAAATTATTTTATTGAAAGTAATAAAATTCGGGAAAAT
* * * *
15851927 AATACGAGCAAATGGCGGGAATAAGGGTTTTTTTTACACTAAATTAATTTTAAAAATACACTTAA
65 AATACGAGCAAATAGCGGGAATAAGGG-TTTTTTTACACTAAATTAATTTAAAAAACACACTAAA
15851992 TTAATAAATTTATAAAATTAGAAATTATG-AATTTTTTAAAGTAATAAAATGCGGAGAAAAAAAT
129 TTAATAAATTTATAAAATTAGAAATTATGAAATTTTTTAAAGTAATAAAATGCGGAGAAAAAAAT
15852056 ACGAAGAAATGGCCGAGGTAAGAGTGTTTTAC
194 ACGAAGAAATGGCCGAGGTAAGAGTGTTTTAC
15852088 AA
1 AA
15852090 AATTTTTTAA
Statistics
Matches: 218, Mismatches: 8, Indels: 3
0.95 0.03 0.01
Matches are distributed among these distances:
225 26 0.12
226 129 0.59
227 63 0.29
ACGTcount: A:0.49, C:0.06, G:0.14, T:0.30
Consensus pattern (225 bp):
AATATAAAATAATAAAATACGAAAATAAAATTATTTTATTGAAAGTAATAAAATTCGGGAAAATA
ATACGAGCAAATAGCGGGAATAAGGGTTTTTTTACACTAAATTAATTTAAAAAACACACTAAATT
AATAAATTTATAAAATTAGAAATTATGAAATTTTTTAAAGTAATAAAATGCGGAGAAAAAAATAC
GAAGAAATGGCCGAGGTAAGAGTGTTTTAC
Found at i:15852378 original size:287 final size:287
Alignment explanation
Indices: 15851862--15852425 Score: 997
Period size: 287 Copynumber: 2.0 Consensus size: 287
15851852 AGTGTTTTAC
* * *
15851862 AATATAAAATAATAAAATACGAAAATAAAAATTTTTTTATTGAAAGTAATAAAATTCGGGAAAAT
1 AATATAAAATAAAAAAATACGAAAATAAAAATTATTTTATTGAAAGTAATAAAATTCGAGAAAAT
* * *
15851927 AATACGAGCAAATGGCGGGAATAAGGGTTTTTTTTACACTAAATTAATTTTAAAAATACACTTAA
66 AATACGAGCAAATGGCGGGAATAAGGGTTTTTTTTACACTAAATTAATTTAAAAAACACACTAAA
15851992 TTAATAAATTTATAAAATTAGAAATTATGAATTTTTTAAAGTAATAAAATGCGGAGAAAAAAATA
131 TTAATAAATTTATAAAATTAGAAATTATGAATTTTTTAAAGTAATAAAATGCGGAGAAAAAAATA
* *
15852057 CGAAGAAATGGCCGAGGTAAGAGTGTTTTACAAAATTTTTTAAAAATTCAGAAATAATTAATACA
196 CAAAGAAATGGCCGAGGTAAAAGTGTTTTACAAAATTTTTTAAAAATTCAGAAATAATTAATACA
15852122 AATATTTGAAACAAAATATACTGAAAT
261 AATATTTGAAACAAAATATACTGAAAT
*
15852149 AATATAAAATAAAAAAATACGAAAAT-AAAATTATTTTATTGAAAGTAATAAAATTTGAGAAAAT
1 AATATAAAATAAAAAAATACGAAAATAAAAATTATTTTATTGAAAGTAATAAAATTCGAGAAAAT
* *
15852213 AATACGAGCAAATGGCTGGAATAAGGATTTTTTTTTACACTAAATTAATTTAAAAAACACACTAA
66 AATACGAGCAAATGGCGGGAATAAGG-GTTTTTTTTACACTAAATTAATTTAAAAAACACACTAA
15852278 ATTAATAAATTTATAAAATTAGAAATTATGAAATTTTTTAAAGTAATAAAATGCGGAG-AAAAAA
130 ATTAATAAATTTATAAAATTAGAAATTATG-AATTTTTTAAAGTAATAAAATGCGGAGAAAAAAA
15852342 TACAAAGAAATGGCCGAGGTAAAAGTGTTTTACAAAATTTTTTAAAAATTCAGAAATAATTAATA
194 TACAAAGAAATGGCCGAGGTAAAAGTGTTTTACAAAATTTTTTAAAAATTCAGAAATAATTAATA
15852407 CAAATATTTGAAACAAAAT
259 CAAATATTTGAAACAAAAT
15852426 NNNNNNNNNN
Statistics
Matches: 264, Mismatches: 11, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
286 60 0.23
287 177 0.67
288 27 0.10
ACGTcount: A:0.51, C:0.06, G:0.12, T:0.31
Consensus pattern (287 bp):
AATATAAAATAAAAAAATACGAAAATAAAAATTATTTTATTGAAAGTAATAAAATTCGAGAAAAT
AATACGAGCAAATGGCGGGAATAAGGGTTTTTTTTACACTAAATTAATTTAAAAAACACACTAAA
TTAATAAATTTATAAAATTAGAAATTATGAATTTTTTAAAGTAATAAAATGCGGAGAAAAAAATA
CAAAGAAATGGCCGAGGTAAAAGTGTTTTACAAAATTTTTTAAAAATTCAGAAATAATTAATACA
AATATTTGAAACAAAATATACTGAAAT
Found at i:15855412 original size:18 final size:18
Alignment explanation
Indices: 15855389--15855433 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
15855379 ATCCCAATGA
15855389 TCGCCACCACCTTCTTCT
1 TCGCCACCACCTTCTTCT
*
15855407 TCGCCACCATCTTCTTCT
1 TCGCCACCACCTTCTTCT
*
15855425 TCACCACCA
1 TCGCCACCA
15855434 ACCATATCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.16, C:0.49, G:0.04, T:0.31
Consensus pattern (18 bp):
TCGCCACCACCTTCTTCT
Found at i:15856464 original size:27 final size:27
Alignment explanation
Indices: 15856425--15856486 Score: 106
Period size: 27 Copynumber: 2.3 Consensus size: 27
15856415 AACACGACTA
15856425 GTGCCGCCAATGGGAATGGCACCTTCG
1 GTGCCGCCAATGGGAATGGCACCTTCG
* *
15856452 GTGCCGCCCATGGGAATGGCACCTTTG
1 GTGCCGCCAATGGGAATGGCACCTTCG
15856479 GTGCCGCC
1 GTGCCGCC
15856487 TATCAGTTAG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.15, C:0.32, G:0.34, T:0.19
Consensus pattern (27 bp):
GTGCCGCCAATGGGAATGGCACCTTCG
Found at i:15859221 original size:16 final size:16
Alignment explanation
Indices: 15859200--15859241 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
15859190 AATAATTTGA
*
15859200 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
15859216 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
15859232 TAGTTTTAAT
1 TAATTTTAAT
15859242 TTTATCAAAA
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:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:15859492 original size:27 final size:27
Alignment explanation
Indices: 15859420--15859481 Score: 115
Period size: 27 Copynumber: 2.3 Consensus size: 27
15859410 GGTCTAGTAA
*
15859420 TGGCGCCTCTCTATAAGGCACCTTCAT
1 TGGCGCCTCTCTATGAGGCACCTTCAT
15859447 TGGCGCCTCTCTATGAGGCACCTTCAT
1 TGGCGCCTCTCTATGAGGCACCTTCAT
15859474 TGGCGCCT
1 TGGCGCCT
15859482 ACCTGATAGG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.15, C:0.34, G:0.23, T:0.29
Consensus pattern (27 bp):
TGGCGCCTCTCTATGAGGCACCTTCAT
Found at i:15859557 original size:12 final size:12
Alignment explanation
Indices: 15859542--15859573 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
15859532 CCGTATTTTT
15859542 TTAAAAAAATTA
1 TTAAAAAAATTA
15859554 TTAAAAAAA-TA
1 TTAAAAAAATTA
15859565 -TAAAAAAAT
1 TTAAAAAAAT
15859574 ATTTTATTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
10 8 0.42
11 2 0.11
12 9 0.47
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (12 bp):
TTAAAAAAATTA
Found at i:15863314 original size:15 final size:16
Alignment explanation
Indices: 15863290--15863319 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
15863280 ATCATTTTAT
15863290 TTTTTCTTTTTAACTC
1 TTTTTCTTTTTAACTC
15863306 TTTTT-TTTTTAACT
1 TTTTTCTTTTTAACT
15863320 TTTGGAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTTTCTTTTTAACTC
Found at i:15869762 original size:43 final size:43
Alignment explanation
Indices: 15869714--15869892 Score: 261
Period size: 43 Copynumber: 4.2 Consensus size: 43
15869704 TTTTTAAAAT
* * *
15869714 AAACGCCGCTATAGATCATGATCTTTAGCGGCGCTT-TTCTCAC
1 AAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTCTAC-CAC
*
15869757 AAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTCTACTAC
1 AAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTCTACCAC
*
15869800 AAACGCCGCTAAAGATCATGACCTTTAACGGCGCTTCTACCAC
1 AAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTCTACCAC
* * * *
15869843 AAACGTCGCTAAAGAACATGACCTTTAGCGACGCTTATACCAC
1 AAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTCTACCAC
15869886 AAACGCC
1 AAACGCC
15869893 ACTATAAAGA
Statistics
Matches: 123, Mismatches: 12, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
43 121 0.98
44 2 0.02
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.23
Consensus pattern (43 bp):
AAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTCTACCAC
Found at i:15873219 original size:22 final size:22
Alignment explanation
Indices: 15873163--15873228 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 22
15873153 GTATGTTTGT
* * *
15873163 AAAGTTGGGGGTTTCAAGGGGG
1 AAAGTTGGGGATTTTAGGGGGG
* * *
15873185 AAAATTAGAGATTTTAGGGGGG
1 AAAGTTGGGGATTTTAGGGGGG
*
15873207 AAAGTTGGGGA-TTTCGGGGGG
1 AAAGTTGGGGATTTTAGGGGGG
15873228 A
1 A
15873229 GGGATTTTAT
Statistics
Matches: 34, Mismatches: 10, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
21 10 0.29
22 24 0.71
ACGTcount: A:0.27, C:0.03, G:0.45, T:0.24
Consensus pattern (22 bp):
AAAGTTGGGGATTTTAGGGGGG
Found at i:15874675 original size:41 final size:41
Alignment explanation
Indices: 15874616--15874894 Score: 324
Period size: 41 Copynumber: 6.8 Consensus size: 41
15874606 AAATATTTTT
*
15874616 GCGGCGCTTTTTCAAAAACGCCGCTAAAGCCCAGAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGCCCTGAGCATTA
* ** * *
15874657 GCGGCGCTTCTTGGAAAACGCTGCTAAAGCCCCGAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGCCCTGAGCATTA
* * *
15874698 GCGGCGCTTCTTAAAAAACGCCGCTAAAGCCCCGAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGCCCTGAGCATTA
* * * **
15874739 GTGGCGCTTTTCCAAAAACACCGCTAAAGATCTGAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGCCCTGAGCATTA
* * **
15874780 GCGGCACTTTTTCAAAAACGCCACTAAAGATCTGAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGCCCTGAGCATTA
* * * **
15874821 GCGGCGCATTTTCAAAAACACAGCTAAAGATCTGAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGCCCTGAGCATTA
* *
15874862 GCGACGCTTTTTTTAAAAACGCCGCTAAAGCCC
1 GCGGCGC-TTTTTCAAAAACGCCGCTAAAGCCC
15874895 CGTGGGCTTA
Statistics
Matches: 204, Mismatches: 33, Indels: 1
0.86 0.14 0.00
Matches are distributed among these distances:
41 185 0.91
42 19 0.09
ACGTcount: A:0.30, C:0.27, G:0.21, T:0.22
Consensus pattern (41 bp):
GCGGCGCTTTTTCAAAAACGCCGCTAAAGCCCTGAGCATTA
Found at i:15875501 original size:26 final size:29
Alignment explanation
Indices: 15875453--15875511 Score: 70
Period size: 30 Copynumber: 2.1 Consensus size: 29
15875443 TTTAATTTTT
* *
15875453 TAAAAAAATATTTAATGATATTTTATTAAA
1 TAAAAAAATATTTAA-GATATTTCACTAAA
15875483 TAAAAAAATATTT-A-A-ATTTCACTAAA
1 TAAAAAAATATTTAAGATATTTCACTAAA
15875509 TAA
1 TAA
15875512 TTCTATTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 12 0.44
27 1 0.04
29 1 0.04
30 13 0.48
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.39
Consensus pattern (29 bp):
TAAAAAAATATTTAAGATATTTCACTAAA
Found at i:15875661 original size:128 final size:129
Alignment explanation
Indices: 15875517--15875780 Score: 505
Period size: 128 Copynumber: 2.1 Consensus size: 129
15875507 AATAATTCTA
15875517 TTATATTAATATATTATAGTTTTTTTAATTTAATTTTTTTTA-AACCATACGAAATTTTGAGAAA
1 TTATATTAATATATTATAGTTTTTTTAATTTAATTTTTTTTATAA-CATACGAAATTTTGAGAAA
15875581 TAAACAGATATAGTGCAGGCAATAACTTTACCCCTTTTGAGATGATGCATTATTAAAAACC-ATG
65 TAAACAGATATAGTGCAGGCAATAACTTTACCCCTTTTGAGATGATGCATTATTAAAAACCTATG
15875645 TTATATTAATATATTATAGTTTTTTTAATTTAATTTTTTTTATAACATACGAAATTTTGAGAAAT
1 TTATATTAATATATTATAGTTTTTTTAATTTAATTTTTTTTATAACATACGAAATTTTGAGAAAT
15875710 AAACAGATATAGTGCAGGCAATAACTTTACCCCTTTTGAGATGATGCATTATTAAAAACCTATG
66 AAACAGATATAGTGCAGGCAATAACTTTACCCCTTTTGAGATGATGCATTATTAAAAACCTATG
15875774 TTATATT
1 TTATATT
15875781 TGGCCTATAT
Statistics
Matches: 134, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
128 122 0.91
129 12 0.09
ACGTcount: A:0.37, C:0.10, G:0.11, T:0.42
Consensus pattern (129 bp):
TTATATTAATATATTATAGTTTTTTTAATTTAATTTTTTTTATAACATACGAAATTTTGAGAAAT
AAACAGATATAGTGCAGGCAATAACTTTACCCCTTTTGAGATGATGCATTATTAAAAACCTATG
Found at i:15880375 original size:22 final size:21
Alignment explanation
Indices: 15880327--15880375 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
15880317 AACTAAATCC
** *
15880327 TTTCTCTCAATTTTTCTCTAA
1 TTTCTCTCAATTCCTCTCAAA
15880348 TATTCTCTCAAATTCCTCTCAAA
1 T-TTCTCTC-AATTCCTCTCAAA
15880371 TTTCT
1 TTTCT
15880376 ATTTAAAAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 1 0.04
22 11 0.48
23 11 0.48
ACGTcount: A:0.22, C:0.27, G:0.00, T:0.51
Consensus pattern (21 bp):
TTTCTCTCAATTCCTCTCAAA
Found at i:15882200 original size:18 final size:18
Alignment explanation
Indices: 15882177--15882220 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
15882167 ATGCCAGGTG
* *
15882177 TGTATCCTAGCCCTTTTA
1 TGTATCCTAACCCTTATA
15882195 TGTATCCTAACCCTTATA
1 TGTATCCTAACCCTTATA
*
15882213 TGTTTCCT
1 TGTATCCT
15882221 TTTTCTAGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.18, C:0.27, G:0.09, T:0.45
Consensus pattern (18 bp):
TGTATCCTAACCCTTATA
Found at i:15882703 original size:49 final size:49
Alignment explanation
Indices: 15882641--15882860 Score: 386
Period size: 49 Copynumber: 4.5 Consensus size: 49
15882631 GTTTATATTA
15882641 ATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTG
1 ATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTG
*
15882690 ATGTAATCAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTG
1 ATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTG
*
15882739 ATGTAATCAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTG
1 ATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTG
* *
15882788 ATGTAATAAAATACAAAATAGTTTATTTTGAATAGTTTGATATTATTTC
1 ATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTG
* *
15882837 ATTTAATAAAATATAAAATAGTTT
1 ATGTAATAAAATACAAAATAGTTT
15882861 TGAATAAAGT
Statistics
Matches: 165, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 165 1.00
ACGTcount: A:0.41, C:0.03, G:0.10, T:0.46
Consensus pattern (49 bp):
ATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTG
Found at i:15886151 original size:125 final size:125
Alignment explanation
Indices: 15885899--15886280 Score: 595
Period size: 125 Copynumber: 3.1 Consensus size: 125
15885889 CCCAAACATG
* * * *
15885899 CTACTATAGCAAAAACGCGTCCACGTGGGAGCGATTTCAGAAATTCTTCTAATAAAGCATTCTGC
1 CTACTGTAGCAAAAACGCGTCCACGTGGGAGCGATTTCAAAAATTCTTCTGATAAAGCATCCTGC
* * *
15885964 TTGAAGC-ATTTTTATACTATTTGTTCAGAAACGTCAACTCGAAATTATTTTTTTAGGAC
66 TTGAAGCGATTTTTATACTATTTGCTCAGAAAAGTCAACTCGAAATTATTTTTTCAGGAC
* * * *
15886023 CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCAATTTCAAAAATTCTTCTGATAAAGGATCCTGG
1 CTACTGTAGCAAAAACGCGTCCACGTGGGAGCGATTTCAAAAATTCTTCTGATAAAGCATCCTGC
* *
15886088 TTCAAGCGATTTTTATACTATTTGCTCAGAAATGTCAACTCGAAATTATTTTTTCAGGAC
66 TTGAAGCGATTTTTATACTATTTGCTCAGAAAAGTCAACTCGAAATTATTTTTTCAGGAC
* *
15886148 CTACTGTAGCAAAAAAGCGTCCACGTGGGAGCGATTTCAAAAATTCTTCTGATAAAGCATCTTGC
1 CTACTGTAGCAAAAACGCGTCCACGTGGGAGCGATTTCAAAAATTCTTCTGATAAAGCATCCTGC
* * *
15886213 TTGAAGCGGTTTTTATACTATTTGCTCAGAAAAGTCAACTCAAAATTATTTTTTCAGAAC
66 TTGAAGCGATTTTTATACTATTTGCTCAGAAAAGTCAACTCGAAATTATTTTTTCAGGAC
15886273 CTACTGTA
1 CTACTGTA
15886281 ATAGGCCTAA
Statistics
Matches: 234, Mismatches: 23, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
124 63 0.27
125 171 0.73
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (125 bp):
CTACTGTAGCAAAAACGCGTCCACGTGGGAGCGATTTCAAAAATTCTTCTGATAAAGCATCCTGC
TTGAAGCGATTTTTATACTATTTGCTCAGAAAAGTCAACTCGAAATTATTTTTTCAGGAC
Found at i:15887768 original size:21 final size:22
Alignment explanation
Indices: 15887726--15887768 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 22
15887716 TATACATTGA
*
15887726 TGTTTTAAATCCATAAGGTATTT
1 TGTTTTAAAT-CATAAGATATTT
*
15887749 TGTTTTAAAT-ATAATATATT
1 TGTTTTAAATCATAAGATATT
15887769 ATTATTTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 8 0.44
23 10 0.56
ACGTcount: A:0.35, C:0.05, G:0.09, T:0.51
Consensus pattern (22 bp):
TGTTTTAAATCATAAGATATTT
Found at i:15889483 original size:9 final size:9
Alignment explanation
Indices: 15889466--15889511 Score: 58
Period size: 9 Copynumber: 5.2 Consensus size: 9
15889456 TTTTTTCTCT
15889466 AAAACCCTA
1 AAAACCCTA
*
15889475 AAAATCCT-
1 AAAACCCTA
15889483 AAAACCCTA
1 AAAACCCTA
*
15889492 AAAATCCTA
1 AAAACCCTA
*
15889501 AAACCCCTA
1 AAAACCCTA
15889510 AA
1 AA
15889512 CCTTAAATCC
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
8 7 0.23
9 24 0.77
ACGTcount: A:0.54, C:0.30, G:0.00, T:0.15
Consensus pattern (9 bp):
AAAACCCTA
Found at i:15889486 original size:17 final size:17
Alignment explanation
Indices: 15889464--15889511 Score: 87
Period size: 17 Copynumber: 2.8 Consensus size: 17
15889454 AATTTTTTCT
15889464 CTAAAACCCTAAAAATC
1 CTAAAACCCTAAAAATC
15889481 CTAAAACCCTAAAAATC
1 CTAAAACCCTAAAAATC
15889498 CTAAAACCCCTAAA
1 CTAAAA-CCCTAAA
15889512 CCTTAAATCC
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
17 23 0.77
18 7 0.23
ACGTcount: A:0.52, C:0.31, G:0.00, T:0.17
Consensus pattern (17 bp):
CTAAAACCCTAAAAATC
Found at i:15894889 original size:3 final size:3
Alignment explanation
Indices: 15894881--15894916 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
15894871 TAATTTCTCA
15894881 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
15894917 TGAAATTAGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:15897863 original size:21 final size:23
Alignment explanation
Indices: 15897822--15897865 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 23
15897812 TTATATTAAA
*
15897822 TTATATTAAAAGATTTTTTATTT
1 TTATATTAAAAGATATTTTATTT
15897845 TTATATT-AAA-ATATTTTATTT
1 TTATATTAAAAGATATTTTATTT
15897866 ACTGCATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 10 0.50
22 3 0.15
23 7 0.35
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (23 bp):
TTATATTAAAAGATATTTTATTT
Found at i:15904485 original size:68 final size:69
Alignment explanation
Indices: 15904358--15904488 Score: 201
Period size: 68 Copynumber: 1.9 Consensus size: 69
15904348 TAAACTTAAT
* * * *
15904358 CACTTTAATATTAAATTAATATAATATGTATCAAGATAAATATTAAATTAAATTTAATATTAAGA
1 CACTTTAATATTAAATTAATAAAATATCTATCAAGATAAATACTAAATTAAATTAAATATTAAGA
15904423 TAAC
66 TAAC
* *
15904427 CACTTTAATATTAAATTAATAAAATA-CTATTAAGATAAGTACTAAATTAAATTAAATATTAA
1 CACTTTAATATTAAATTAATAAAATATCTATCAAGATAAATACTAAATTAAATTAAATATTAA
15904489 ACTATTAAAA
Statistics
Matches: 56, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
68 31 0.55
69 25 0.45
ACGTcount: A:0.52, C:0.06, G:0.04, T:0.38
Consensus pattern (69 bp):
CACTTTAATATTAAATTAATAAAATATCTATCAAGATAAATACTAAATTAAATTAAATATTAAGA
TAAC
Found at i:15913967 original size:27 final size:28
Alignment explanation
Indices: 15913935--15913997 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 28
15913925 ATTTGATATA
*
15913935 AATATAAAT-TATATAATTATTATTTA-
1 AATATAAATAAATATAATTATTATTTAT
*
15913961 ACATATATAATAAATATAATTATTTTTTAT
1 A-ATATA-AATAAATATAATTATTATTTAT
15913991 AATATAA
1 AATATAA
15913998 TATATTTGGG
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
26 1 0.03
27 5 0.16
28 4 0.13
29 20 0.65
30 1 0.03
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (28 bp):
AATATAAATAAATATAATTATTATTTAT
Found at i:15915986 original size:31 final size:30
Alignment explanation
Indices: 15915929--15915996 Score: 75
Period size: 31 Copynumber: 2.3 Consensus size: 30
15915919 GATGTAGCAC
*
15915929 CTGTA-TTTTAAATTGATTAATATTAGTCA
1 CTGTACTTTTAAATTGATCAATATTAGTCA
* * * *
15915958 TTGTACTTTTCAAATTGGTCAATTTTAGTCC
1 CTGTACTTTT-AAATTGATCAATATTAGTCA
15915989 CTGTACTT
1 CTGTACTT
15915997 CTTGAATTAT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
29 4 0.13
30 4 0.13
31 23 0.74
ACGTcount: A:0.26, C:0.13, G:0.12, T:0.49
Consensus pattern (30 bp):
CTGTACTTTTAAATTGATCAATATTAGTCA
Found at i:15928335 original size:15 final size:15
Alignment explanation
Indices: 15928315--15928348 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
15928305 TGGAGAAAAT
15928315 AAACCTAAATGTATG
1 AAACCTAAATGTATG
15928330 AAACCTAAATGTATG
1 AAACCTAAATGTATG
15928345 AAAC
1 AAAC
15928349 GTACAAACCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.50, C:0.15, G:0.12, T:0.24
Consensus pattern (15 bp):
AAACCTAAATGTATG
Found at i:15929894 original size:12 final size:12
Alignment explanation
Indices: 15929872--15929901 Score: 51
Period size: 12 Copynumber: 2.4 Consensus size: 12
15929862 ATCAAATATT
15929872 AGAACAATAAAGA
1 AGAA-AATAAAGA
15929885 AGAAAATAAAGA
1 AGAAAATAAAGA
15929897 AGAAA
1 AGAAA
15929902 GATGGAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 13 0.76
13 4 0.24
ACGTcount: A:0.73, C:0.03, G:0.17, T:0.07
Consensus pattern (12 bp):
AGAAAATAAAGA
Found at i:15931060 original size:21 final size:22
Alignment explanation
Indices: 15931036--15931084 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 22
15931026 CACAATGACC
15931036 ACATGCCAAAGT-CACATTCAA
1 ACATGCCAAAGTGCACATTCAA
* * **
15931057 ACATACCAAATTGGTCATTCAA
1 ACATGCCAAAGTGCACATTCAA
15931079 ACATGC
1 ACATGC
15931085 ATTAACCCCT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.41, C:0.27, G:0.10, T:0.22
Consensus pattern (22 bp):
ACATGCCAAAGTGCACATTCAA
Found at i:15932265 original size:20 final size:20
Alignment explanation
Indices: 15932242--15932288 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
15932232 ATAGAGACAT
* * *
15932242 CGAAGTGTATACAGGGGCAC
1 CGAAGTGCAAACAAGGGCAC
15932262 CGAAGTGCAAACAAGGGCAC
1 CGAAGTGCAAACAAGGGCAC
15932282 CGAAGTG
1 CGAAGTG
15932289 AAAATCCCGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.34, C:0.21, G:0.34, T:0.11
Consensus pattern (20 bp):
CGAAGTGCAAACAAGGGCAC
Found at i:15941864 original size:23 final size:23
Alignment explanation
Indices: 15941819--15941864 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
15941809 TTATTAATAT
* *
15941819 TGTTTGTGAACATGTTCGTTTAA
1 TGTTCGTGAACATGTTCGATTAA
*
15941842 TGTTCGTGAACATGTTTGATTAA
1 TGTTCGTGAACATGTTCGATTAA
15941865 GTTAAATGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.09, G:0.22, T:0.46
Consensus pattern (23 bp):
TGTTCGTGAACATGTTCGATTAA
Found at i:15945228 original size:17 final size:17
Alignment explanation
Indices: 15945203--15945236 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
15945193 CTCCACTCAA
*
15945203 TTAAGCAAGATCTACTC
1 TTAAACAAGATCTACTC
*
15945220 TTAAACAAGGTCTACTC
1 TTAAACAAGATCTACTC
15945237 AACCACCGAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.35, C:0.24, G:0.12, T:0.29
Consensus pattern (17 bp):
TTAAACAAGATCTACTC
Found at i:15952265 original size:72 final size:74
Alignment explanation
Indices: 15952129--15952266 Score: 235
Period size: 72 Copynumber: 1.9 Consensus size: 74
15952119 GGCATCCATG
15952129 TGTATGCCAAGTTAGCAATTAATTAATTTTTTTAAAAATTAAAAAATATATTTTTATAAACTTTA
1 TGTATGCCAAGTTAGCAATTAATTAATTTTTTTAAAAATTAAAAAATATATTTTTATAAACTTTA
15952194 TTATTAAAA
66 TTATTAAAA
* * *
15952203 TGTATGCCACGTTAGCAATTAATTAA-TTTTTT-AAAATTACAAATTATATTTTTATAAACTTTA
1 TGTATGCCAAGTTAGCAATTAATTAATTTTTTTAAAAATTAAAAAATATATTTTTATAAACTTTA
15952266 T
66 T
15952267 ACTTTTTAAT
Statistics
Matches: 61, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
72 30 0.49
73 6 0.10
74 25 0.41
ACGTcount: A:0.41, C:0.07, G:0.06, T:0.46
Consensus pattern (74 bp):
TGTATGCCAAGTTAGCAATTAATTAATTTTTTTAAAAATTAAAAAATATATTTTTATAAACTTTA
TTATTAAAA
Found at i:15954077 original size:114 final size:114
Alignment explanation
Indices: 15953918--15954125 Score: 271
Period size: 114 Copynumber: 1.8 Consensus size: 114
15953908 ATTAGCAGCT
* * **
15953918 CTTTATCATAAGCACCGCAAAACTATTAAGAAAACGTAGCTGTTTTTCA-TTTATTTTTTCTAGA
1 CTTTATCAGAAGCACCGCAAAACTATTAAGAAAACGTAGCTGTTTTT-AGTTTAGTTTTTAGAGA
* *
15953982 CGTTAGTGGCGATTTTC-AGAAAACGCCGCAGTAGCGAAGCTTTAGTGGCG
65 CGTTAATGGCGATTGTCTA-AAAACGCCGCAGTAGCGAAGCTTTAGTGGCG
* *
15954032 CTTTATCAGAAGCGCCGCAAAACTGTTAAGAAAACG-A-CGTCGTTTTTAGTTTAGTTTTTAGAG
1 CTTTATCAGAAGCACCGCAAAACTATTAAGAAAACGTAGC-T-GTTTTTAGTTTAGTTTTTAGAG
*
15954095 ACGTTAATGGCGCTTGTCTAAAAACGCCGCA
64 ACGTTAATGGCGATTGTCTAAAAACGCCGCA
15954126 AAATATAGGA
Statistics
Matches: 81, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
112 1 0.01
113 3 0.04
114 76 0.94
115 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.31
Consensus pattern (114 bp):
CTTTATCAGAAGCACCGCAAAACTATTAAGAAAACGTAGCTGTTTTTAGTTTAGTTTTTAGAGAC
GTTAATGGCGATTGTCTAAAAACGCCGCAGTAGCGAAGCTTTAGTGGCG
Found at i:15954769 original size:21 final size:21
Alignment explanation
Indices: 15954743--15954788 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
15954733 TGTTCTTTAA
15954743 TTTA-GGGTTTAAGGGATATGG
1 TTTAGGGGTTT-AGGGATATGG
*
15954764 TTTAGGGGTTTATGGATATGG
1 TTTAGGGGTTTAGGGATATGG
15954785 TTTA
1 TTTA
15954789 AGGATTGGGG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 17 0.74
22 6 0.26
ACGTcount: A:0.22, C:0.00, G:0.35, T:0.43
Consensus pattern (21 bp):
TTTAGGGGTTTAGGGATATGG
Found at i:15954808 original size:7 final size:7
Alignment explanation
Indices: 15954796--15954847 Score: 52
Period size: 7 Copynumber: 7.4 Consensus size: 7
15954786 TTAAGGATTG
15954796 GGGTTAA
1 GGGTTAA
15954803 GGGTTAA
1 GGGTTAA
*
15954810 GGGTTTAG
1 GGG-TTAA
15954818 GGGTTAA
1 GGGTTAA
* *
15954825 GTGCT-A
1 GGGTTAA
15954831 GGGTTAA
1 GGGTTAA
*
15954838 GGGTTTA
1 GGGTTAA
15954845 GGG
1 GGG
15954848 GTTTATAGTT
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
6 4 0.11
7 26 0.72
8 6 0.17
ACGTcount: A:0.21, C:0.02, G:0.46, T:0.31
Consensus pattern (7 bp):
GGGTTAA
Found at i:15955041 original size:21 final size:22
Alignment explanation
Indices: 15955015--15955061 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
15955005 TATGGATTAT
*
15955015 GGTTTAAGGGTT-GGGGTTAAG
1 GGTTTAAGGGTTAAGGGTTAAG
* *
15955036 GGTTTATGGGTTAAGGGTTATG
1 GGTTTAAGGGTTAAGGGTTAAG
15955058 GGTT
1 GGTT
15955062 AGGGGTTTAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.17, C:0.00, G:0.45, T:0.38
Consensus pattern (22 bp):
GGTTTAAGGGTTAAGGGTTAAG
Found at i:15955043 original size:28 final size:29
Alignment explanation
Indices: 15955011--15955076 Score: 89
Period size: 29 Copynumber: 2.3 Consensus size: 29
15955001 GGCTTATGGA
*
15955011 TTATGGTTTAAGGGTT-GGGGTTAAGGGT
1 TTATGGGTTAAGGGTTAGGGGTTAAGGGT
* *
15955039 TTATGGGTTAAGGGTTATGGGTTAGGGGT
1 TTATGGGTTAAGGGTTAGGGGTTAAGGGT
*
15955068 TTAGGGGTT
1 TTATGGGTT
15955077 TATAGTTAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
28 15 0.45
29 18 0.55
ACGTcount: A:0.17, C:0.00, G:0.44, T:0.39
Consensus pattern (29 bp):
TTATGGGTTAAGGGTTAGGGGTTAAGGGT
Found at i:15955058 original size:14 final size:14
Alignment explanation
Indices: 15955011--15955068 Score: 73
Period size: 14 Copynumber: 4.1 Consensus size: 14
15955001 GGCTTATGGA
*
15955011 TTATGGTTTAAGGG
1 TTATGGGTTAAGGG
*
15955025 TT-GGGGTTAAGGG
1 TTATGGGTTAAGGG
15955038 TTTATGGGTTAAGGG
1 -TTATGGGTTAAGGG
*
15955053 TTATGGGTTAGGGG
1 TTATGGGTTAAGGG
15955067 TT
1 TT
15955069 TAGGGGTTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
13 9 0.24
14 19 0.50
15 10 0.26
ACGTcount: A:0.17, C:0.00, G:0.43, T:0.40
Consensus pattern (14 bp):
TTATGGGTTAAGGG
Found at i:15955078 original size:8 final size:7
Alignment explanation
Indices: 15954977--15955073 Score: 52
Period size: 7 Copynumber: 13.7 Consensus size: 7
15954967 TCTACGATTC
*
15954977 AAGGTTT
1 AAGGGTT
*
15954984 AAGGGAT
1 AAGGGTT
*
15954991 ATGGGTT
1 AAGGGTT
*
15954998 AGAGGCTT
1 A-AGGGTT
* *
15955006 ATGGATT
1 AAGGGTT
* *
15955013 ATGGTTT
1 AAGGGTT
15955020 AAGGGTT
1 AAGGGTT
*
15955027 -GGGGTT
1 AAGGGTT
15955033 AAGGGTTT
1 AAGGG-TT
*
15955041 ATGGGTT
1 AAGGGTT
15955048 AAGGGTT
1 AAGGGTT
*
15955055 ATGGGTT
1 AAGGGTT
*
15955062 AGGGGTT
1 AAGGGTT
*
15955069 TAGGG
1 AAGGG
15955074 GTTTATAGTT
Statistics
Matches: 68, Mismatches: 19, Indels: 6
0.73 0.20 0.06
Matches are distributed among these distances:
6 5 0.07
7 52 0.76
8 11 0.16
ACGTcount: A:0.22, C:0.01, G:0.42, T:0.35
Consensus pattern (7 bp):
AAGGGTT
Found at i:15956943 original size:27 final size:29
Alignment explanation
Indices: 15956889--15956944 Score: 71
Period size: 30 Copynumber: 2.0 Consensus size: 29
15956879 ATTTAATTTA
* *
15956889 TATTAAGTTGATTGTTACTTTATCAATTAT
1 TATTAAGTTGATTGTTA-GTGATCAATTAT
15956919 TATTAAGTTGATTGTT-GTGAT-AATTA
1 TATTAAGTTGATTGTTAGTGATCAATTA
15956945 AAATTGATAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 5 0.21
28 3 0.12
30 16 0.67
ACGTcount: A:0.30, C:0.04, G:0.14, T:0.52
Consensus pattern (29 bp):
TATTAAGTTGATTGTTAGTGATCAATTAT
Found at i:15960292 original size:41 final size:40
Alignment explanation
Indices: 15960236--15960525 Score: 307
Period size: 41 Copynumber: 7.0 Consensus size: 40
15960226 TTGAGATAAA
*
15960236 AAGCACCGCTAAAGAACATGATCTTTAGCGGCGTCTTTTTT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGT-TTTTTT
* * **
15960277 AAGCGCCGTTAAAGAACATTA-CTTTTCA-CGGCGTTTGTGATAA
1 AAGCGCCGCTAAAGAACATGATC-TTT-AGCGGCGTTT-T--TTT
*
15960320 AAGCGCCGCTAAAGGACATGATCTTTAGCGGCGTTTTTCGTT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTT--TT
*
15960362 AAGCGCCGCTAAAGAACATGATCTTTAGCTGCGTCTTTTTT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGT-TTTTTT
* * * *
15960403 AGGCGCCGCTAAAGAACATTA-CTTTTAGCGGCGTTTGTGATA
1 AAGCGCCGCTAAAGAACATGATC-TTTAGCGGCGTTT-T-TTT
*
15960445 ATAGCGCCGCTAAAGAACATGATTTTTAGCGGCGTTTTTTCT
1 A-AGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTT-T
* *
15960487 AAGCGCCGCTAAAGAACATGACCTTTAGCGGCATTTTTT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTT
15960526 CTGTAAACGC
Statistics
Matches: 208, Mismatches: 25, Indels: 32
0.78 0.09 0.12
Matches are distributed among these distances:
40 7 0.03
41 96 0.46
42 39 0.19
43 65 0.31
44 1 0.00
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.31
Consensus pattern (40 bp):
AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTT
Found at i:15960416 original size:126 final size:125
Alignment explanation
Indices: 15960236--15960518 Score: 453
Period size: 126 Copynumber: 2.3 Consensus size: 125
15960226 TTGAGATAAA
* *
15960236 AAGCACCGCTAAAGAACATGATCTTTAGCGGCGTCTTTTTTAAGCGCCGTTAAAGAACATTACTT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTCTTTTTTAAGCGCCGCTAAAGAACATTACTT
*
15960301 TTCA-CGGCGTTTGTGATAAAAGCGCCGCTAAAGGACATGATCTTTAGCGGCG-TTTTTCGTT
66 TT-AGCGGCGTTTGTGATAAAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTC--T
* *
15960362 AAGCGCCGCTAAAGAACATGATCTTTAGCTGCGTCTTTTTTAGGCGCCGCTAAAGAACATTACTT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTCTTTTTTAAGCGCCGCTAAAGAACATTACTT
* *
15960427 TTAGCGGCGTTTGTGATAATAGCGCCGCTAAAGAACATGATTTTTAGCGGCGTTTTTTCT
66 TTAGCGGCGTTTGTGATAAAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTCT
*
15960487 AAGCGCCGCTAAAGAACATGACCTTTAGCGGC
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGC
15960519 ATTTTTTCTG
Statistics
Matches: 146, Mismatches: 9, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
125 32 0.22
126 108 0.74
127 6 0.04
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.30
Consensus pattern (125 bp):
AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTCTTTTTTAAGCGCCGCTAAAGAACATTACTT
TTAGCGGCGTTTGTGATAAAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTCT
Found at i:15960473 original size:84 final size:83
Alignment explanation
Indices: 15960236--15960518 Score: 276
Period size: 84 Copynumber: 3.4 Consensus size: 83
15960226 TTGAGATAAA
* * * * *
15960236 AAGCACCGCTAAAGAACATGA-TCTTTAGCGGCGTCTT-T-TTTAAGCGCCGTTAAAGAACATTA
1 AAGCGCCGCTAAAGAACATGACT-TTTAGCGGCGT-TTGTCGTAAAGCGCCGCTAAAGAACATGA
* **
15960298 -CTTTTCA-CGGCGTTTGTGATAA
64 TC-TTT-AGCGGCGTTT-T-TTCT
* * *
15960320 AAGCGCCGCTAAAGGACATGA-TCTTTAGCGGCGTTTTTCGTTAAGCGCCGCTAAAGAACATGAT
1 AAGCGCCGCTAAAGAACATGACT-TTTAGCGGCGTTTGTCGTAAAGCGCCGCTAAAGAACATGAT
*
15960384 CTTTAGCTGCGTCTTTTT-T
65 CTTTAGCGGCGT-TTTTTCT
* *
15960403 AGGCGCCGCTAAAGAACATTACTTTTAGCGGCGTTTGT-GATAATAGCGCCGCTAAAGAACATGA
1 AAGCGCCGCTAAAGAACATGACTTTTAGCGGCGTTTGTCG-TAA-AGCGCCGCTAAAGAACATGA
*
15960467 TTTTTAGCGGCGTTTTTTCT
64 TCTTTAGCGGCGTTTTTTCT
*
15960487 AAGCGCCGCTAAAGAACATGACCTTTAGCGGC
1 AAGCGCCGCTAAAGAACATGACTTTTAGCGGC
15960519 ATTTTTTCTG
Statistics
Matches: 172, Mismatches: 18, Indels: 18
0.83 0.09 0.09
Matches are distributed among these distances:
82 1 0.01
83 41 0.24
84 97 0.56
85 30 0.17
86 3 0.02
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.30
Consensus pattern (83 bp):
AAGCGCCGCTAAAGAACATGACTTTTAGCGGCGTTTGTCGTAAAGCGCCGCTAAAGAACATGATC
TTTAGCGGCGTTTTTTCT
Found at i:15962204 original size:31 final size:31
Alignment explanation
Indices: 15962166--15962231 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
15962156 AACAATCTAA
*
15962166 TGACTTAAATAAAAACTTAT-GAATAGTTAAG
1 TGACTTAAATAAAAACTT-TCAAATAGTTAAG
* *
15962197 TGACTTAAATGAAAACTTTCAAATAGTTTAG
1 TGACTTAAATAAAAACTTTCAAATAGTTAAG
15962228 TGAC
1 TGAC
15962232 CTAATTGTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 1 0.03
31 30 0.97
ACGTcount: A:0.44, C:0.09, G:0.14, T:0.33
Consensus pattern (31 bp):
TGACTTAAATAAAAACTTTCAAATAGTTAAG
Found at i:15977472 original size:37 final size:38
Alignment explanation
Indices: 15977398--15977473 Score: 136
Period size: 38 Copynumber: 2.0 Consensus size: 38
15977388 AACAAGAGTC
15977398 ATTATCCTCCTTGGTTAAATGGGAAAAAAATTCCTTTT
1 ATTATCCTCCTTGGTTAAATGGGAAAAAAATTCCTTTT
*
15977436 ATTATTCTCCTTGGTTAAATGGGAAAAAAA-TCCTTTT
1 ATTATCCTCCTTGGTTAAATGGGAAAAAAATTCCTTTT
15977473 A
1 A
15977474 GCCCTCCCAA
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
37 8 0.22
38 29 0.78
ACGTcount: A:0.33, C:0.14, G:0.13, T:0.39
Consensus pattern (38 bp):
ATTATCCTCCTTGGTTAAATGGGAAAAAAATTCCTTTT
Found at i:15984445 original size:26 final size:26
Alignment explanation
Indices: 15984415--15984475 Score: 113
Period size: 26 Copynumber: 2.3 Consensus size: 26
15984405 GAAATTTCCA
*
15984415 TTATTTTTCCCCTTCCATTTCTTTCT
1 TTATTTTACCCCTTCCATTTCTTTCT
15984441 TTATTTTACCCCTTCCATTTCTTTCT
1 TTATTTTACCCCTTCCATTTCTTTCT
15984467 TTATTTTAC
1 TTATTTTAC
15984476 AATTGATTTG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.11, C:0.28, G:0.00, T:0.61
Consensus pattern (26 bp):
TTATTTTACCCCTTCCATTTCTTTCT
Found at i:15984883 original size:22 final size:25
Alignment explanation
Indices: 15984852--15984897 Score: 71
Period size: 22 Copynumber: 2.0 Consensus size: 25
15984842 TGAAATTGCT
15984852 TGATGTCGAAAAA-TA-AGAGAAAA
1 TGATGTCGAAAAATTATAGAGAAAA
15984875 TGAT-TCGAAAAATTATAGAGAAA
1 TGATGTCGAAAAATTATAGAGAAA
15984898 GGAAATAAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 8 0.38
23 6 0.29
24 7 0.33
ACGTcount: A:0.54, C:0.04, G:0.20, T:0.22
Consensus pattern (25 bp):
TGATGTCGAAAAATTATAGAGAAAA
Found at i:15989155 original size:45 final size:45
Alignment explanation
Indices: 15989104--15989485 Score: 539
Period size: 45 Copynumber: 8.5 Consensus size: 45
15989094 GATCAAGACA
* *
15989104 AGTAAGACCATAGCTGAAAGATGCTATGGCATCATTATTCAAATG
1 AGTAAGACCATAGCTGAAAGACGCTATGGCATCATTATTCAGATG
* * * * *
15989149 AGTAAGACTAGAGCTGAAAGACGTTATGACATCATTATTCAGACG
1 AGTAAGACCATAGCTGAAAGACGCTATGGCATCATTATTCAGATG
* * * * *
15989194 AGGAAGACCATAGCTGAAAGACGTTATGACATCATTTTTCAGACG
1 AGTAAGACCATAGCTGAAAGACGCTATGGCATCATTATTCAGATG
* *
15989239 AGTAAGACCATAGCTGAAAGACGTTATGGCATCATTATTTAGATG
1 AGTAAGACCATAGCTGAAAGACGCTATGGCATCATTATTCAGATG
* * * **
15989284 AGTAAGACCATAGCTGAAAGACACTATGGCATTATTATTCAAACA
1 AGTAAGACCATAGCTGAAAGACGCTATGGCATCATTATTCAGATG
* *
15989329 AGTAAGACCATAGCTGAAAGACGCTATGGCATCATGATTCAGATA
1 AGTAAGACCATAGCTGAAAGACGCTATGGCATCATTATTCAGATG
*
15989374 AGTAAGACCATAGCTGAAAGACGTTATGGCATCATTATTCAGATG
1 AGTAAGACCATAGCTGAAAGACGCTATGGCATCATTATTCAGATG
* *
15989419 AGTAAGACCATAGCTGAAAGACGCTATGGAATCATGATTCAGATG
1 AGTAAGACCATAGCTGAAAGACGCTATGGCATCATTATTCAGATG
*
15989464 AGTAAGACCATAGTTGAAAGAC
1 AGTAAGACCATAGCTGAAAGAC
15989486 ATTATAGCAT
Statistics
Matches: 302, Mismatches: 35, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 302 1.00
ACGTcount: A:0.38, C:0.16, G:0.21, T:0.25
Consensus pattern (45 bp):
AGTAAGACCATAGCTGAAAGACGCTATGGCATCATTATTCAGATG
Found at i:15989528 original size:90 final size:89
Alignment explanation
Indices: 15989104--15989543 Score: 479
Period size: 90 Copynumber: 4.9 Consensus size: 89
15989094 GATCAAGACA
*** * * *
15989104 AGTAAGACCATAGCTGAAAGATGCTATGGCATCATTATTCAAATGAGTAAGACTAGAGCTGAAAG
1 AGTAAGACCATAGCTGAAAGACATTATGGCATCA-TATTAAAATGAGTAAGACCATAGCTGAAAG
* * * *
15989169 ACGTTATGACATCATTATTCAGACG
65 ACGCTATGGCATCATGATTCAGATG
* * * * * * *
15989194 AGGAAGACCATAGCTGAAAGACGTTATGACATCATTTTTCAGACGAGTAAGACCATAGCTGAAAG
1 AGTAAGACCATAGCTGAAAGACATTATGGCATCA-TATTAAAATGAGTAAGACCATAGCTGAAAG
* * *
15989259 ACGTTATGGCATCATTATTTAGATG
65 ACGCTATGGCATCATGATTCAGATG
* * * **
15989284 AGTAAGACCATAGCTGAAAGACACTATGGCATTATTATTCAAACAAGTAAGACCATAGCTGAAAG
1 AGTAAGACCATAGCTGAAAGACATTATGGCATCA-TATTAAAATGAGTAAGACCATAGCTGAAAG
*
15989349 ACGCTATGGCATCATGATTCAGATA
65 ACGCTATGGCATCATGATTCAGATG
* * *
15989374 AGTAAGACCATAGCTGAAAGACGTTATGGCATCATTATTCAGATGAGTAAGACCATAGCTGAAAG
1 AGTAAGACCATAGCTGAAAGACATTATGGCATCA-TATTAAAATGAGTAAGACCATAGCTGAAAG
*
15989439 ACGCTATGGAATCATGATTCAGATG
65 ACGCTATGGCATCATGATTCAGATG
* * *
15989464 AGTAAGACCATAGTTGAAAGACATTATAGCATCCA-ATTGAAAATGAATAAGACCATAG-TGGAA
1 AGTAAGACCATAGCTGAAAGACATTATGGCAT-CATATT-AAAATGAGTAAGACCATAGCT-GAA
* * *
15989527 AGGCACTGTGGCATCAT
63 AGACGCTATGGCATCAT
15989544 ATCGGAAAGT
Statistics
Matches: 305, Mismatches: 42, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
89 4 0.01
90 299 0.98
91 2 0.01
ACGTcount: A:0.38, C:0.16, G:0.21, T:0.25
Consensus pattern (89 bp):
AGTAAGACCATAGCTGAAAGACATTATGGCATCATATTAAAATGAGTAAGACCATAGCTGAAAGA
CGCTATGGCATCATGATTCAGATG
Found at i:15989587 original size:46 final size:44
Alignment explanation
Indices: 15989466--15989668 Score: 201
Period size: 46 Copynumber: 4.5 Consensus size: 44
15989456 TTCAGATGAG
* * * * *
15989466 TAAGACCATAGTTGAAAGACATTATAGCATCCAATTGAAAATGAA
1 TAAGACCATGGTTGAAAGACACTATGGCAT-CAATGGAAAGTGAA
* * * *
15989511 TAAGACCATAGTGGAAAGGCACTGTGGCATCATATCGGAAAGTGAA
1 TAAGACCATGGTTGAAAGACACTATGGCATCA-AT-GGAAAGTGAA
* * *
15989557 TAAGACCATGGTTGAAATACACTATTGCATCATATCAGAAAGTGAA
1 TAAGACCATGGTTGAAAGACACTATGGCATCA-AT-GGAAAGTGAA
* * *
15989603 TAAGACCATGGTTGAAAGGCATTATGGCATCAAGTGGAGAA-TAAA
1 TAAGACCATGGTTGAAAGACACTATGGCATCAA-TGGA-AAGTGAA
15989648 TAAGACCATGGTTGAAAGACA
1 TAAGACCATGGTTGAAAGACA
15989669 ACATGACATC
Statistics
Matches: 133, Mismatches: 21, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
44 2 0.02
45 53 0.40
46 78 0.59
ACGTcount: A:0.41, C:0.14, G:0.22, T:0.23
Consensus pattern (44 bp):
TAAGACCATGGTTGAAAGACACTATGGCATCAATGGAAAGTGAA
Found at i:15989587 original size:91 final size:91
Alignment explanation
Indices: 15989466--15989668 Score: 243
Period size: 91 Copynumber: 2.2 Consensus size: 91
15989456 TTCAGATGAG
* * *
15989466 TAAGACCATAGTTGAAAGACATTATAGCATCCA-AT-TGAAAATGAATAAGACCATAGTGGAAAG
1 TAAGACCATGGTTGAAAGACACTATAGCAT-CATATCAGAAAATGAATAAGACCATAGTGGAAAG
* *
15989529 GCACTGTGGCATCATA-TCGGA-AAGTGAA
65 GCACTATGGCATCA-AGT-GGAGAA-TAAA
* * * * *
15989557 TAAGACCATGGTTGAAATACACTATTGCATCATATCAGAAAGTGAATAAGACCATGGTTGAAAGG
1 TAAGACCATGGTTGAAAGACACTATAGCATCATATCAGAAAATGAATAAGACCATAGTGGAAAGG
*
15989622 CATTATGGCATCAAGTGGAGAATAAA
66 CACTATGGCATCAAGTGGAGAATAAA
15989648 TAAGACCATGGTTGAAAGACA
1 TAAGACCATGGTTGAAAGACA
15989669 ACATGACATC
Statistics
Matches: 96, Mismatches: 12, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
90 2 0.02
91 55 0.57
92 39 0.41
ACGTcount: A:0.41, C:0.14, G:0.22, T:0.23
Consensus pattern (91 bp):
TAAGACCATGGTTGAAAGACACTATAGCATCATATCAGAAAATGAATAAGACCATAGTGGAAAGG
CACTATGGCATCAAGTGGAGAATAAA
Found at i:15991121 original size:7 final size:8
Alignment explanation
Indices: 15991093--15991122 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
15991083 TTTCCCAAGT
15991093 TTTTTCGAA
1 TTTTT-GAA
15991102 TTTTTGAA
1 TTTTTGAA
15991110 TTTTTGAA
1 TTTTTGAA
15991118 TTTTT
1 TTTTT
15991123 TCCTTGGTCC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 16 0.76
9 5 0.24
ACGTcount: A:0.20, C:0.03, G:0.10, T:0.67
Consensus pattern (8 bp):
TTTTTGAA
Found at i:15994397 original size:20 final size:20
Alignment explanation
Indices: 15994372--15994439 Score: 75
Period size: 20 Copynumber: 3.4 Consensus size: 20
15994362 GTGCATATTC
15994372 GTGCTCTTATTAGCACTACG
1 GTGCTCTTATTAGCACTACG
* *
15994392 GTGCTCTTAATAGCACATTC-
1 GTGCTCTTATTAGCAC-TACG
* *
15994412 GTGCTCATGTTAGCACTACG
1 GTGCTCTTATTAGCACTACG
*
15994432 ATGCTCTT
1 GTGCTCTT
15994440 GAAAGCACAT
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
19 2 0.05
20 34 0.89
21 2 0.05
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.35
Consensus pattern (20 bp):
GTGCTCTTATTAGCACTACG
Found at i:15994425 original size:40 final size:40
Alignment explanation
Indices: 15994368--15994466 Score: 128
Period size: 40 Copynumber: 2.5 Consensus size: 40
15994358 CTGAGTGCAT
* * *
15994368 ATTCGTGCTCTTATTAGCACTACGGTGCTCTT-AATAGCAC
1 ATTCGTGCTCATGTTAGCACTACGATGCTCTTGAA-AGCAC
15994408 ATTCGTGCTCATGTTAGCACTACGATGCTCTTGAAAGCAC
1 ATTCGTGCTCATGTTAGCACTACGATGCTCTTGAAAGCAC
* * *
15994448 ATTCATGCTCCTGATAGCA
1 ATTCGTGCTCATGTTAGCA
15994467 TATTTATGCT
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
40 50 0.96
41 2 0.04
ACGTcount: A:0.24, C:0.25, G:0.18, T:0.32
Consensus pattern (40 bp):
ATTCGTGCTCATGTTAGCACTACGATGCTCTTGAAAGCAC
Found at i:15994446 original size:20 final size:19
Alignment explanation
Indices: 15994383--15994447 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
15994373 TGCTCTTATT
15994383 AGCACTACGGTGCTCTT-AA
1 AGCACTAC-GTGCTCTTGAA
* * **
15994402 TAGCACATTCGTGCTCATGTT
1 -AGCAC-TACGTGCTCTTGAA
15994423 AGCACTACGATGCTCTTGAA
1 AGCACTACG-TGCTCTTGAA
15994443 AGCAC
1 AGCAC
15994448 ATTCATGCTC
Statistics
Matches: 34, Mismatches: 8, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
19 3 0.09
20 29 0.85
21 2 0.06
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.28
Consensus pattern (19 bp):
AGCACTACGTGCTCTTGAA
Found at i:15994455 original size:20 final size:20
Alignment explanation
Indices: 15994393--15994480 Score: 63
Period size: 20 Copynumber: 4.4 Consensus size: 20
15994383 AGCACTACGG
*
15994393 TGCTCTT-AATAGCACATTCG
1 TGCTCTTGAA-AGCACATTCA
* ** *
15994413 TGCTCATGTTAGCAC-TACGA
1 TGCTCTTGAAAGCACATTC-A
15994433 TGCTCTTGAAAGCACATTCA
1 TGCTCTTGAAAGCACATTCA
* * * *
15994453 TGCTCCTGATAGCATATTTA
1 TGCTCTTGAAAGCACATTCA
15994473 TGCTCTTG
1 TGCTCTTG
15994481 TTTGTTTTAC
Statistics
Matches: 51, Mismatches: 14, Indels: 6
0.72 0.20 0.08
Matches are distributed among these distances:
19 2 0.04
20 47 0.92
21 2 0.04
ACGTcount: A:0.24, C:0.24, G:0.17, T:0.35
Consensus pattern (20 bp):
TGCTCTTGAAAGCACATTCA
Found at i:15995601 original size:4 final size:4
Alignment explanation
Indices: 15995592--15995625 Score: 68
Period size: 4 Copynumber: 8.5 Consensus size: 4
15995582 AACATATTTC
15995592 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
15995626 TCATATCTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTAT
Found at i:15996558 original size:25 final size:25
Alignment explanation
Indices: 15996530--15996660 Score: 102
Period size: 25 Copynumber: 5.2 Consensus size: 25
15996520 TTGGCCACTA
**
15996530 AGGCTTCCCAAATAATAAGTTACAT
1 AGGCTTCCCAAATAATAAGCCACAT
*** * * *
15996555 AGGCTTTTTAAATAACAAGGCACAA
1 AGGCTTCCCAAATAATAAGCCACAT
*
15996580 AGGCTTCCCAAATAATACGCCACAT
1 AGGCTTCCCAAATAATAAGCCACAT
** * *
15996605 AGGCTTTTCAAACAACT-AGCCACAA
1 AGGCTTCCCAAATAA-TAAGCCACAT
* *
15996630 AGGCTTTCCAAATAATATGCCACAT
1 AGGCTTCCCAAATAATAAGCCACAT
*
15996655 AAGCTT
1 AGGCTT
15996661 TCTAGATAGC
Statistics
Matches: 80, Mismatches: 24, Indels: 4
0.74 0.22 0.04
Matches are distributed among these distances:
24 1 0.01
25 78 0.98
26 1 0.01
ACGTcount: A:0.39, C:0.24, G:0.13, T:0.24
Consensus pattern (25 bp):
AGGCTTCCCAAATAATAAGCCACAT
Found at i:15996591 original size:50 final size:50
Alignment explanation
Indices: 15996523--15996661 Score: 179
Period size: 50 Copynumber: 2.8 Consensus size: 50
15996513 AGATAACTTG
* ** * *
15996523 GCCACTAAGGCTTCCCAAATAATAAGTTACATAGGCTTTTTAAATAACAA
1 GCCACAAAGGCTTCCCAAATAATAAGCCACATAGGCTTTTCAAACAACAA
* * *
15996573 GGCACAAAGGCTTCCCAAATAATACGCCACATAGGCTTTTCAAACAACTA
1 GCCACAAAGGCTTCCCAAATAATAAGCCACATAGGCTTTTCAAACAACAA
* * *
15996623 GCCACAAAGGCTTTCCAAATAATATGCCACATAAGCTTT
1 GCCACAAAGGCTTCCCAAATAATAAGCCACATAGGCTTT
15996662 CTAGATAGCC
Statistics
Matches: 77, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
50 77 1.00
ACGTcount: A:0.38, C:0.24, G:0.13, T:0.24
Consensus pattern (50 bp):
GCCACAAAGGCTTCCCAAATAATAAGCCACATAGGCTTTTCAAACAACAA
Found at i:15996681 original size:21 final size:22
Alignment explanation
Indices: 15996575--15996681 Score: 58
Period size: 25 Copynumber: 4.5 Consensus size: 22
15996565 AATAACAAGG
*
15996575 CACAAAGGCTTCCCAAATAATACGC
1 CACAAAGGCTTTCC--ATAATA-GC
* * *
15996600 CACATAGGCTTTTCAAACAACTAGC
1 CACAAAGGC-TTTC-CATAA-TAGC
15996625 CACAAAGGCTTTCCAAATAATATGC
1 CACAAAGGCTTTCC--ATAATA-GC
15996650 CACATAA-GCTTT-C-TAGATAGC
1 CACA-AAGGCTTTCCATA-ATAGC
15996671 CACAAAGGCTT
1 CACAAAGGCTT
15996682 ATTTGGTTTT
Statistics
Matches: 66, Mismatches: 7, Indels: 22
0.69 0.07 0.23
Matches are distributed among these distances:
20 2 0.03
21 12 0.18
22 3 0.05
24 7 0.11
25 35 0.53
26 7 0.11
ACGTcount: A:0.37, C:0.27, G:0.13, T:0.22
Consensus pattern (22 bp):
CACAAAGGCTTTCCATAATAGC
Found at i:16001692 original size:26 final size:27
Alignment explanation
Indices: 16001640--16001696 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
16001630 AAAGGTTGCT
*
16001640 AAATGACCAAAATACCCTCGGAGGGTA
1 AAATGACCAAAATACCCTCAGAGGGTA
*
16001667 AAATGACCAAAATACCCTTAGA-GGTA
1 AAATGACCAAAATACCCTCAGAGGGTA
16001693 AAAT
1 AAAT
16001697 TATCGTTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
26 8 0.29
27 20 0.71
ACGTcount: A:0.46, C:0.19, G:0.18, T:0.18
Consensus pattern (27 bp):
AAATGACCAAAATACCCTCAGAGGGTA
Found at i:16006031 original size:20 final size:20
Alignment explanation
Indices: 16006006--16006044 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
16005996 TGGAAAAACC
16006006 ACTCTTCCGTTAACCACTCA
1 ACTCTTCCGTTAACCACTCA
16006026 ACTCTTCCGTTAACCACTC
1 ACTCTTCCGTTAACCACTC
16006045 TCACATCCGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.23, C:0.41, G:0.05, T:0.31
Consensus pattern (20 bp):
ACTCTTCCGTTAACCACTCA
Found at i:16026504 original size:42 final size:41
Alignment explanation
Indices: 16026374--16026597 Score: 168
Period size: 42 Copynumber: 5.3 Consensus size: 41
16026364 ATTCAACACT
* *
16026374 TAGCAACCACC-TTAAATTCAGTGATACG-GAGAATCAGCACA
1 TAGCAACC-CCTTTATATTCAGTTATACGAG-GAATCAGCACA
* * * *** *
16026415 TAGTAACCCCTTTCACAATCAAAGATACG-GTAGAATCAGCACT
1 TAGCAACCCCTTT-ATATTCAGTTATACGAG--GAATCAGCACA
*
16026458 TAGCAGCCACCTTTATATTCAGTTATACGAGGAATCAGCACA
1 TAGCAACC-CCTTTATATTCAGTTATACGAGGAATCAGCACA
* * ** *
16026500 TAGCAACCCCTTTCACAATCAAATATACGATGGAATCAACAC-
1 TAGCAACCCCTTT-ATATTCAGTTATACGA-GGAATCAGCACA
* * *
16026542 TAAGCAACCACCTTTATATTCAGTGATAAGGGGAATCAGCACA
1 T-AGCAACC-CCTTTATATTCAGTTATACGAGGAATCAGCACA
16026585 TAGCAACCCCTTT
1 TAGCAACCCCTTT
16026598 CAAAATCAAA
Statistics
Matches: 145, Mismatches: 28, Indels: 20
0.75 0.15 0.10
Matches are distributed among these distances:
40 2 0.01
41 19 0.13
42 59 0.41
43 54 0.37
44 11 0.08
ACGTcount: A:0.37, C:0.25, G:0.15, T:0.23
Consensus pattern (41 bp):
TAGCAACCCCTTTATATTCAGTTATACGAGGAATCAGCACA
Found at i:16026512 original size:85 final size:84
Alignment explanation
Indices: 16026370--16026633 Score: 370
Period size: 85 Copynumber: 3.1 Consensus size: 84
16026360 GTGGATTCAA
* *
16026370 CACTTAGCAACCACC-TTAAATTCAGTGATACGGAGAATCAGCACATAGTAACCCCTTTCACAAT
1 CACTTAGCAACCACCTTTATATTCAGTGATACGG-GAATCAGCACATAGCAACCCCTTTCACAAT
*
16026434 CAAAGATACGGTAGAATCAG
65 CAAATATACGGTAGAATCAG
* *
16026454 CACTTAGCAGCCACCTTTATATTCAGTTATACGAGGAATCAGCACATAGCAACCCCTTTCACAAT
1 CACTTAGCAACCACCTTTATATTCAGTGATACG-GGAATCAGCACATAGCAACCCCTTTCACAAT
* * *
16026519 CAAATATACGATGGAATCAA
65 CAAATATACGGTAGAATCAG
* * *
16026539 CACTAAGCAACCACCTTTATATTCAGTGATAAGGGGAATCAGCACATAGCAACCCCTTTCAAAAT
1 CACTTAGCAACCACCTTTATATTCAGTGAT-ACGGGAATCAGCACATAGCAACCCCTTTCACAAT
*
16026604 CAAATATACAGTCA-AATCAG
65 CAAATATACGGT-AGAATCAG
16026624 CACTTAGCAA
1 CACTTAGCAA
16026634 GCCCTTGGGG
Statistics
Matches: 158, Mismatches: 18, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
84 14 0.09
85 141 0.89
86 3 0.02
ACGTcount: A:0.38, C:0.25, G:0.14, T:0.23
Consensus pattern (84 bp):
CACTTAGCAACCACCTTTATATTCAGTGATACGGGAATCAGCACATAGCAACCCCTTTCACAATC
AAATATACGGTAGAATCAG
Found at i:16026632 original size:43 final size:42
Alignment explanation
Indices: 16026404--16026639 Score: 171
Period size: 43 Copynumber: 5.5 Consensus size: 42
16026394 GTGATACGGA
* * *
16026404 GAATCAGCACATAGTAACCCCTTTCACAATCAAAGATACGGT
1 GAATCAGCACATAGCAACCCCTTTCACAATCAAATATACAGT
* * * * **
16026446 AGAATCAGCACTTAGCAGCCACCTTT-ATATTCAGTTATACGAG-
1 -GAATCAGCACATAGCAACC-CCTTTCACAATCAAATATAC-AGT
16026489 GAATCAGCACATAGCAACCCCTTTCACAATCAAATATAC-GAT
1 GAATCAGCACATAGCAACCCCTTTCACAATCAAATATACAG-T
* * * * *
16026531 GGAATCAACAC-TAAGCAACCACCTTT-ATATTC-AGTGATA-AGGG
1 -GAATCAGCACAT-AGCAACC-CCTTTCACAATCAAAT-ATACA-GT
*
16026574 GAATCAGCACATAGCAACCCCTTTCAAAATCAAATATACAGT
1 GAATCAGCACATAGCAACCCCTTTCACAATCAAATATACAGT
* * *
16026616 CAAATCAGCACTTAGCAAGCCCTT
1 -GAATCAGCACATAGCAACCCCTT
16026640 GGGGAATCTG
Statistics
Matches: 149, Mismatches: 28, Indels: 32
0.71 0.13 0.15
Matches are distributed among these distances:
40 1 0.01
41 10 0.07
42 54 0.36
43 72 0.48
44 12 0.08
ACGTcount: A:0.38, C:0.26, G:0.14, T:0.23
Consensus pattern (42 bp):
GAATCAGCACATAGCAACCCCTTTCACAATCAAATATACAGT
Found at i:16029984 original size:42 final size:42
Alignment explanation
Indices: 16029904--16029985 Score: 112
Period size: 42 Copynumber: 2.0 Consensus size: 42
16029894 CGTTTTCTCT
* **
16029904 ATGCCATAGTCCAACTATGGTCTTACACATGTTTACATATTG
1 ATGCCATAGCCCAACTATGGTCTTACACATGTGCACATATTG
*
16029946 ATGCCATAGCCCAGCTATGGTCTTACACA-GTAGCACATAT
1 ATGCCATAGCCCAACTATGGTCTTACACATGT-GCACATAT
16029986 CACACCAATG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
41 2 0.06
42 33 0.94
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.30
Consensus pattern (42 bp):
ATGCCATAGCCCAACTATGGTCTTACACATGTGCACATATTG
Found at i:16032611 original size:43 final size:43
Alignment explanation
Indices: 16032484--16032624 Score: 137
Period size: 43 Copynumber: 3.3 Consensus size: 43
16032474 ATCCGTTACT
* *
16032484 CGGTGGATTCAGCACTTAGCAACCA-CATTAAATTCAGTGATA
1 CGGTGGAATCAGCACTTAGCAACCACCTTTAAATTCAGTGATA
** * * **
16032526 CGG-GGAATCAGCACACAGCAACC-CCTTTCACAGTCAAAGATA
1 CGGTGGAATCAGCACTTAGCAACCACCTTT-AAATTCAGTGATA
* * *
16032568 CGGTGGAATCAACAGTTATCAACCACCTTTAAATTCAGTGATA
1 CGGTGGAATCAGCACTTAGCAACCACCTTTAAATTCAGTGATA
*
16032611 CGG-AGAATCAGCAC
1 CGGTGGAATCAGCAC
16032625 ACCTTTAGTA
Statistics
Matches: 75, Mismatches: 20, Indels: 8
0.73 0.19 0.08
Matches are distributed among these distances:
41 20 0.27
42 23 0.31
43 27 0.36
44 5 0.07
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.21
Consensus pattern (43 bp):
CGGTGGAATCAGCACTTAGCAACCACCTTTAAATTCAGTGATA
Found at i:16033059 original size:30 final size:30
Alignment explanation
Indices: 16033011--16033069 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 30
16033001 TCCTTAACTC
*
16033011 AAACTTTTGAAAAATTACAATTTTGCCCCT
1 AAACTTTTGAAAAATTACAATTTTACCCCT
* * * *
16033041 AAACTTTTGCATATTTACACTTTTACCCC
1 AAACTTTTGAAAAATTACAATTTTACCCC
16033070 AAAGCTCGGA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.32, C:0.24, G:0.05, T:0.39
Consensus pattern (30 bp):
AAACTTTTGAAAAATTACAATTTTACCCCT
Found at i:16040125 original size:13 final size:13
Alignment explanation
Indices: 16040107--16040133 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
16040097 ATATGGGTAC
16040107 CCCTGTGTTGTGA
1 CCCTGTGTTGTGA
16040120 CCCTGTGTTGTGA
1 CCCTGTGTTGTGA
16040133 C
1 C
16040134 ACACAACTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.07, C:0.26, G:0.30, T:0.37
Consensus pattern (13 bp):
CCCTGTGTTGTGA
Found at i:16041225 original size:12 final size:12
Alignment explanation
Indices: 16041208--16041234 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
16041198 CACACGCCCG
16041208 TGTGCTAGGCCA
1 TGTGCTAGGCCA
16041220 TGTGCTAGGCCA
1 TGTGCTAGGCCA
16041232 TGT
1 TGT
16041235 AACTCACTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.15, C:0.22, G:0.33, T:0.30
Consensus pattern (12 bp):
TGTGCTAGGCCA
Found at i:16042126 original size:20 final size:21
Alignment explanation
Indices: 16042087--16042126 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
16042077 TACATCAATT
*
16042087 AGATCATGCATTCTTTCCATA
1 AGATCATGCATTCATTCCATA
*
16042108 AGATCATGC-TTGATTCCAT
1 AGATCATGCATTCATTCCAT
16042127 TTGAATACTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.28, C:0.23, G:0.12, T:0.38
Consensus pattern (21 bp):
AGATCATGCATTCATTCCATA
Found at i:16045334 original size:14 final size:14
Alignment explanation
Indices: 16045315--16045341 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
16045305 TCAAATGACA
16045315 TAGGTATTTATGAG
1 TAGGTATTTATGAG
16045329 TAGGTATTTATGA
1 TAGGTATTTATGA
16045342 TTGATGAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.00, G:0.26, T:0.44
Consensus pattern (14 bp):
TAGGTATTTATGAG
Found at i:16055717 original size:103 final size:103
Alignment explanation
Indices: 16055539--16055907 Score: 488
Period size: 103 Copynumber: 3.6 Consensus size: 103
16055529 TAACCGTTAT
* * ** * ** *
16055539 CGGTGGATTCTGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCTTGGGG
1 CGGTGGAATCAGCACTTAGCAACCACCAATGGGTAGGGGAATCAGCACTTAGCAACCCCTCGGGG
* * * *
16055604 GAATCAGCACTTAGCAACCCCC-TTCACAATTCAGATG
66 GAATCAGCACTTAGCAACCCCCTTTCACATTTAAAATA
* * * *
16055641 CGGTGGAACCATCACTTAGCAACCACCAAATGGGTTGGGGAGTCAGCACTTAGCAACCCCTCGGG
1 CGGTGGAATCAGCACTTAGCAACCACC-AATGGGTAGGGGAATCAGCACTTAGCAACCCCTCGGG
16055706 GGAATCAGCACTTAGCAACCCCCTTTCACATTTAAAATA
65 GGAATCAGCACTTAGCAACCCCCTTTCACATTTAAAATA
* *
16055745 CGGTGGAATCAGCACTTAGCAACCACCAATAGGTAGGGGAATCAGCACTTAGCAACCCCTCGGGA
1 CGGTGGAATCAGCACTTAGCAACCACCAATGGGTAGGGGAATCAGCACTTAGCAACCCCTCGGGG
16055810 GAATCAGCACTTAGCAACCCCCTTTCACATTTAAAATA
66 GAATCAGCACTTAGCAACCCCCTTTCACATTTAAAATA
* * ** * * **
16055848 TGGTGGGATCAGCACTTAGCAACCACCAATGAATAGGGAAATTAGCACACAGCAACCCCT
1 CGGTGGAATCAGCACTTAGCAACCACCAATGGGTAGGGGAATCAGCACTTAGCAACCCCT
16055908 TTATATGCAA
Statistics
Matches: 235, Mismatches: 30, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
102 23 0.10
103 176 0.75
104 36 0.15
ACGTcount: A:0.31, C:0.29, G:0.21, T:0.19
Consensus pattern (103 bp):
CGGTGGAATCAGCACTTAGCAACCACCAATGGGTAGGGGAATCAGCACTTAGCAACCCCTCGGGG
GAATCAGCACTTAGCAACCCCCTTTCACATTTAAAATA
Found at i:16063814 original size:50 final size:51
Alignment explanation
Indices: 16063754--16063872 Score: 125
Period size: 50 Copynumber: 2.4 Consensus size: 51
16063744 GGACACACCA
* * * * * *
16063754 CAGCTTGTATGAGATTACCGATTTGCAACTCTTGAGAGCTTACCAATTC-T
1 CAGCTCGTATGACATTACAGATTTACAACTCGTGAGAGCATACCAATTCAT
* * * *
16063804 CAGCTCGTATGACCTTACAGATTTACAGCTCGTGAGAGCATATCGATTCAT
1 CAGCTCGTATGACATTACAGATTTACAACTCGTGAGAGCATACCAATTCAT
*
16063855 -AGCTCGTATGACCTTACA
1 CAGCTCGTATGACATTACA
16063873 TGTACAGGAA
Statistics
Matches: 58, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
50 57 0.98
51 1 0.02
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (51 bp):
CAGCTCGTATGACATTACAGATTTACAACTCGTGAGAGCATACCAATTCAT
Found at i:16063820 original size:25 final size:25
Alignment explanation
Indices: 16063792--16063871 Score: 60
Period size: 25 Copynumber: 3.2 Consensus size: 25
16063782 CTCTTGAGAG
16063792 CTTACCAATTCTCAGCTCGTATGAC
1 CTTACCAATTCTCAGCTCGTATGAC
*
16063817 CTTA-CAGATT-TACAGCTCGTGA-GAG
1 CTTACCA-ATTCT-CAGCTCGT-ATGAC
* * *
16063842 CATATCGATTCAT-AGCTCGTATGAC
1 CTTACCAATTC-TCAGCTCGTATGAC
16063867 CTTAC
1 CTTAC
16063872 ATGTACAGGA
Statistics
Matches: 42, Mismatches: 6, Indels: 14
0.68 0.10 0.23
Matches are distributed among these distances:
24 4 0.10
25 35 0.83
26 2 0.05
27 1 0.02
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.31
Consensus pattern (25 bp):
CTTACCAATTCTCAGCTCGTATGAC
Found at i:16074068 original size:18 final size:19
Alignment explanation
Indices: 16074033--16074069 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
16074023 TATAGTAGAA
16074033 GAGAAAGTAAATAATTTAG
1 GAGAAAGTAAATAATTTAG
*
16074052 GAGAAATTAAA-AATTTAG
1 GAGAAAGTAAATAATTTAG
16074070 ATTTAAATAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.54, C:0.00, G:0.19, T:0.27
Consensus pattern (19 bp):
GAGAAAGTAAATAATTTAG
Found at i:16074151 original size:27 final size:27
Alignment explanation
Indices: 16074107--16074158 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
16074097 TAACTAGTGT
* *
16074107 TAATAATAAATTAGATCAGGTTATAAA
1 TAATAATAAATTAAATCAGGATATAAA
16074134 TAATAAT-AATATAAATCAGGATATA
1 TAATAATAAAT-TAAATCAGGATATA
16074159 GATTTAGGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 3 0.14
27 19 0.86
ACGTcount: A:0.54, C:0.04, G:0.10, T:0.33
Consensus pattern (27 bp):
TAATAATAAATTAAATCAGGATATAAA
Found at i:16075641 original size:22 final size:22
Alignment explanation
Indices: 16075601--16075642 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
16075591 TTTACATTAA
16075601 TTTTCTCTTTAGTTTTTTCTAC
1 TTTTCTCTTTAGTTTTTTCTAC
*
16075623 TTTTC-CTTTATTTTCTTTCT
1 TTTTCTCTTTAGTTT-TTTCT
16075643 TCGTCCTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.07, C:0.19, G:0.02, T:0.71
Consensus pattern (22 bp):
TTTTCTCTTTAGTTTTTTCTAC
Found at i:16075981 original size:19 final size:21
Alignment explanation
Indices: 16075945--16075983 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
16075935 TTCTATTTTA
*
16075945 AATTATTTTATTATATTTATG
1 AATTATTTTAATATATTTATG
16075966 AATT-TTTTAATA-ATTTAT
1 AATTATTTTAATATATTTAT
16075984 TTGATCGAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 7 0.41
21 4 0.24
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (21 bp):
AATTATTTTAATATATTTATG
Found at i:16077673 original size:14 final size:15
Alignment explanation
Indices: 16077642--16077674 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
16077632 AAATTTTAAG
16077642 AAAAATGAATATTGT
1 AAAAATGAATATTGT
*
16077657 AAAAATGGATATT-T
1 AAAAATGAATATTGT
16077671 AAAA
1 AAAA
16077675 CAATTCTTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.58, C:0.00, G:0.12, T:0.30
Consensus pattern (15 bp):
AAAAATGAATATTGT
Found at i:16077766 original size:18 final size:18
Alignment explanation
Indices: 16077728--16077771 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
16077718 TAGTTCACTC
16077728 TTACTTTATTTTTTTAGTT
1 TTACTTTA-TTTTTTAGTT
16077747 TTACTTTA-TTTTTAGTTT
1 TTACTTTATTTTTTAG-TT
16077765 TTACTTT
1 TTACTTT
16077772 TACAATTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.29
18 9 0.38
19 8 0.33
ACGTcount: A:0.16, C:0.07, G:0.05, T:0.73
Consensus pattern (18 bp):
TTACTTTATTTTTTAGTT
Found at i:16077773 original size:19 final size:18
Alignment explanation
Indices: 16077728--16077773 Score: 58
Period size: 17 Copynumber: 2.5 Consensus size: 18
16077718 TAGTTCACTC
*
16077728 TTACTTTATTTTTTTAGTT
1 TTACTTT-TATTTTTAGTT
16077747 TTAC-TTTATTTTTAGTTT
1 TTACTTTTATTTTTAG-TT
16077765 TTACTTTTA
1 TTACTTTTA
16077774 CAATTTATAG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 8 0.33
18 8 0.33
19 8 0.33
ACGTcount: A:0.17, C:0.07, G:0.04, T:0.72
Consensus pattern (18 bp):
TTACTTTTATTTTTAGTT
Found at i:16081907 original size:9 final size:9
Alignment explanation
Indices: 16081893--16081917 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
16081883 AATTTTCACA
16081893 TCTAACTGC
1 TCTAACTGC
16081902 TCTAACTGC
1 TCTAACTGC
16081911 TCTAACT
1 TCTAACT
16081918 CAAAGTTGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.24, C:0.32, G:0.08, T:0.36
Consensus pattern (9 bp):
TCTAACTGC
Found at i:16090603 original size:19 final size:19
Alignment explanation
Indices: 16090579--16090634 Score: 103
Period size: 19 Copynumber: 2.9 Consensus size: 19
16090569 AATCATATCT
16090579 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
16090598 TCTAAGATTACATATCATA
1 TCTAAGATTGCATATCATA
16090617 TCTAAGATTGCATATCAT
1 TCTAAGATTGCATATCAT
16090635 TGAAGATTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 35 1.00
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.38
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:16090628 original size:38 final size:40
Alignment explanation
Indices: 16090556--16090634 Score: 117
Period size: 38 Copynumber: 2.0 Consensus size: 40
16090546 AAATTAAATC
16090556 TCTAAGATTACAAAATCATATCTTCTAAGATTGCATATCATA
1 TCTAAGATTACAAAATCATA--TTCTAAGATTGCATATCATA
*
16090598 TCTAAGATTAC-ATATCATA-TCTAAGATTGCATATCAT
1 TCTAAGATTACAAAATCATATTCTAAGATTGCATATCAT
16090635 TGAAGATTAT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
38 18 0.50
41 7 0.19
42 11 0.31
ACGTcount: A:0.39, C:0.16, G:0.08, T:0.37
Consensus pattern (40 bp):
TCTAAGATTACAAAATCATATTCTAAGATTGCATATCATA
Found at i:16090641 original size:36 final size:36
Alignment explanation
Indices: 16090572--16090643 Score: 103
Period size: 38 Copynumber: 2.0 Consensus size: 36
16090562 ATTACAAAAT
*
16090572 CATATCTTCTAAGATTGCATATCATATCTAAGATTA
1 CATATCTTCTAAGATTGCATATCATATCGAAGATTA
16090608 CATATCATATCTAAGATTGCATATCAT-T-GAAGATTA
1 CATATC-T-TCTAAGATTGCATATCATATCGAAGATTA
16090644 TGTTTCCATA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
36 13 0.39
37 2 0.06
38 18 0.55
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.38
Consensus pattern (36 bp):
CATATCTTCTAAGATTGCATATCATATCGAAGATTA
Found at i:16094070 original size:3 final size:3
Alignment explanation
Indices: 16094062--16094119 Score: 116
Period size: 3 Copynumber: 19.3 Consensus size: 3
16094052 ATTTGTATTT
16094062 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
16094110 ATA ATA ATA A
1 ATA ATA ATA A
16094120 AGTAAACAAA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:16097600 original size:16 final size:15
Alignment explanation
Indices: 16097581--16097610 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
16097571 TTATATATAT
16097581 TTTACTTTATTTATTA
1 TTTACTTT-TTTATTA
16097597 TTTACTTTTTTATT
1 TTTACTTTTTTATT
16097611 TACTTTACCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.73
Consensus pattern (15 bp):
TTTACTTTTTTATTA
Found at i:16102587 original size:2 final size:2
Alignment explanation
Indices: 16102580--16102627 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
16102570 AAAACTGAAA
16102580 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
16102622 AC AC AC
1 AC AC AC
16102628 TTTTAGTTGC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:16103315 original size:5 final size:5
Alignment explanation
Indices: 16103305--16103336 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
16103295 TTGCCACTTA
16103305 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT AT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT AT
16103337 AAATATTGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
ATTAT
Done.