Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr6
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: 56482370
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1659275 characters in sequence are not A, C, G, or T
File 128 of 172
Found at i:42687748 original size:20 final size:19
Alignment explanation
Indices: 42687712--42687750 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
42687702 TTTCTTTTTT
* *
42687712 TTTCTTTATTCTTTTATTA
1 TTTCTTTATTATATTATTA
42687731 TTTCTTTTATTATATTATTA
1 TTTC-TTTATTATATTATTA
42687751 AGTATTATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.21, C:0.08, G:0.00, T:0.72
Consensus pattern (19 bp):
TTTCTTTATTATATTATTA
Found at i:42691462 original size:27 final size:27
Alignment explanation
Indices: 42691432--42691504 Score: 92
Period size: 27 Copynumber: 2.7 Consensus size: 27
42691422 ATGAAATGCT
*
42691432 CCGAAGAGCCACTATCACTAAGTTGCA
1 CCGAAGTGCCACTATCACTAAGTTGCA
* * *
42691459 CCGAAGTGCCTCTATCACTGATTTGCA
1 CCGAAGTGCCACTATCACTAAGTTGCA
* *
42691486 CCAAAGTGCCACAATCACT
1 CCGAAGTGCCACTATCACT
42691505 TTATGCGTTG
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.30, C:0.32, G:0.16, T:0.22
Consensus pattern (27 bp):
CCGAAGTGCCACTATCACTAAGTTGCA
Found at i:42693026 original size:15 final size:15
Alignment explanation
Indices: 42692989--42693032 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
42692979 ATACTAACAT
*
42692989 TATATAATTAAAATA
1 TATATTATTAAAATA
* *
42693004 TTTA-TATTATAATA
1 TATATTATTAAAATA
42693018 TATATTATTAAAATA
1 TATATTATTAAAATA
42693033 ATAATTAATT
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
14 11 0.48
15 12 0.52
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TATATTATTAAAATA
Found at i:42693036 original size:21 final size:20
Alignment explanation
Indices: 42693012--42693056 Score: 51
Period size: 19 Copynumber: 2.3 Consensus size: 20
42693002 TATTTATATT
42693012 ATAATATATATT-ATTAAAATA
1 ATAATATA-ATTAATT-AAATA
42693033 ATAAT-TAATTAATTAAATA
1 ATAATATAATTAATTAAATA
42693052 A-AATA
1 ATAATA
42693057 AAATATCACC
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
18 3 0.14
19 9 0.41
20 5 0.23
21 5 0.23
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
ATAATATAATTAATTAAATA
Found at i:42693039 original size:12 final size:13
Alignment explanation
Indices: 42692989--42693040 Score: 52
Period size: 13 Copynumber: 3.8 Consensus size: 13
42692979 ATACTAACAT
42692989 TATATAATTAAAA
1 TATATAATTAAAA
*
42693002 TATTTATATTATAATA
1 TATATA-ATTA-AA-A
*
42693018 TATATTATTAAAA
1 TATATAATTAAAA
42693031 TA-ATAATTAA
1 TATATAATTAA
42693041 TTAATTAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
12 7 0.22
13 8 0.25
14 6 0.19
15 6 0.19
16 5 0.16
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
TATATAATTAAAA
Found at i:42693293 original size:29 final size:29
Alignment explanation
Indices: 42693248--42693309 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
42693238 TCCTTTCCAC
**
42693248 CTTTGATTATTTCCACTTTAGTCCTTCAA
1 CTTTGATTATTTCCACTTTAACCCTTCAA
*
42693277 CTTTG-TTAATTTTCACTTTAACCCTTCAA
1 CTTTGATT-ATTTCCACTTTAACCCTTCAA
42693306 CTTT
1 CTTT
42693310 TGAATATTCA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 2 0.07
29 27 0.93
ACGTcount: A:0.21, C:0.24, G:0.05, T:0.50
Consensus pattern (29 bp):
CTTTGATTATTTCCACTTTAACCCTTCAA
Found at i:42694273 original size:17 final size:17
Alignment explanation
Indices: 42694243--42694283 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
42694233 AAAATAATTA
42694243 AATAAATAATTTAAAAT
1 AATAAATAATTTAAAAT
*
42694260 TATAAA-AATATTAAAAT
1 AATAAATAAT-TTAAAAT
42694277 AATAAAT
1 AATAAAT
42694284 TAGTTCAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
16 3 0.15
17 17 0.85
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
AATAAATAATTTAAAAT
Found at i:42694773 original size:19 final size:18
Alignment explanation
Indices: 42694740--42694778 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 18
42694730 GTTTAAATTT
42694740 TAAATTTAAATAACTCAAA
1 TAAATTTAAATAACT-AAA
42694759 TAAA-TTAAATAAACTAAA
1 TAAATTTAAAT-AACTAAA
42694777 TA
1 TA
42694779 TAAAAACTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.31
Consensus pattern (18 bp):
TAAATTTAAATAACTAAA
Found at i:42694931 original size:18 final size:18
Alignment explanation
Indices: 42694894--42694937 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
42694884 CTTTCCCTTC
*
42694894 AAAATTTTTTATCCCC-A
1 AAAATTTTTGATCCCCAA
*
42694911 AAAATTTTTGCTCCCCTAA
1 AAAATTTTTGATCCCC-AA
42694930 AAAATTTT
1 AAAATTTT
42694938 ACTTTCTTGC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 14 0.61
19 9 0.39
ACGTcount: A:0.36, C:0.20, G:0.02, T:0.41
Consensus pattern (18 bp):
AAAATTTTTGATCCCCAA
Found at i:42695983 original size:4 final size:4
Alignment explanation
Indices: 42695974--42696019 Score: 56
Period size: 4 Copynumber: 11.2 Consensus size: 4
42695964 TAAATTACCT
* * *
42695974 TTTC TTTC TTTC GTTC TTTC TTTC TTTC TTTTC TTTT TTTT TTTC T
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC -TTTC TTTC TTTC TTTC T
42696020 GTTTGTTTCC
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
4 33 0.89
5 4 0.11
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (4 bp):
TTTC
Found at i:42696927 original size:104 final size:104
Alignment explanation
Indices: 42696708--42696936 Score: 280
Period size: 104 Copynumber: 2.2 Consensus size: 104
42696698 AATCTTTGCC
* * *
42696708 CTAGATACGAAAATTCAGGATCCTAGAGACAAATGTTTTAGGGAAAACAAAGAGTGTGTGTAATA
1 CTAGATACGAAAA-TCAGGGTCCTAGAGACAAATATTTTAGGGAAAACAAAGAGTGTGTATAATA
42696773 TAGGTTACAAACATTTGAACATTGATCGATGGTCAAGATT
65 TAGGTTACAAACATTTGAACATTGATCGATGGTCAAGATT
* * * * * * * * *
42696813 CAAAAAACGAAAAGCAGGGTCCTGGTGATAAATATTTTAGGGAAAACGAAGAGTTTGTATAATAT
1 CTAGATACGAAAATCAGGGTCCTAGAGACAAATATTTTAGGGAAAACAAAGAGTGTGTATAATAT
* ** * *
42696878 AGGTTACAATCATTTGAATGTTGATCGATGTTCAAAGCTT
66 AGGTTACAAACATTTGAACATTGATCGATGGTC-AAGATT
42696918 -TAGATACGAAAATCAGGGT
1 CTAGATACGAAAATCAGGGT
42696937 TTGAGCAACA
Statistics
Matches: 102, Mismatches: 21, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
104 87 0.85
105 15 0.15
ACGTcount: A:0.39, C:0.11, G:0.22, T:0.28
Consensus pattern (104 bp):
CTAGATACGAAAATCAGGGTCCTAGAGACAAATATTTTAGGGAAAACAAAGAGTGTGTATAATAT
AGGTTACAAACATTTGAACATTGATCGATGGTCAAGATT
Found at i:42705028 original size:16 final size:15
Alignment explanation
Indices: 42705002--42705036 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
42704992 TGATGTGAAT
42705002 AATATAAAATATTAA
1 AATATAAAATATTAA
*
42705017 AATATCAAAATATTAG
1 AATAT-AAAATATTAA
42705033 AATA
1 AATA
42705037 ATAATAATTA
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:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (15 bp):
AATATAAAATATTAA
Found at i:42706634 original size:87 final size:87
Alignment explanation
Indices: 42706433--42706657 Score: 249
Period size: 87 Copynumber: 2.6 Consensus size: 87
42706423 TGATTCTTTA
* * * *
42706433 CTCGGCATGTGATCCCGA-GCTCAACTCATTTCTCGTAATATGAATTGAATCTTTAAAACTAGAC
1 CTCGGTATGTGA-CCCGAGGCTCAACTCATTTCTCGTAATATGAGTTG-ATTTTTAAAACTAGAA
* *
42706497 ATTAAAAATAGAAATTGAAAATAG
64 ATTAAAAACAGAAATTGAAAATAC
* * * * * *
42706521 CTCAGTACGTGAGCCAAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTAAAAC-A-AAAT
1 CTCGGTATGTGACCCGAGGCTCAACTCATTTCTCGTAATATGAGTTGATTTTTAAAACTAGAAA-
* **
42706584 TTGTAAAACAGATTTTGAAAATAC
65 TT-AAAAACAGAAATTGAAAATAC
*
42706608 CTCGGTATGTGACCCGAGGCTCAACTCATTTATCGTAATATGAGTTGATT
1 CTCGGTATGTGACCCGAGGCTCAACTCATTTCTCGTAATATGAGTTGATT
42706658 CTTGAAAAGC
Statistics
Matches: 112, Mismatches: 22, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
85 2 0.02
86 3 0.03
87 72 0.64
88 35 0.31
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Consensus pattern (87 bp):
CTCGGTATGTGACCCGAGGCTCAACTCATTTCTCGTAATATGAGTTGATTTTTAAAACTAGAAAT
TAAAAACAGAAATTGAAAATAC
Found at i:42706935 original size:78 final size:74
Alignment explanation
Indices: 42706583--42707213 Score: 587
Period size: 71 Copynumber: 8.3 Consensus size: 74
42706573 TAAAACAAAA
* ** * * * ** * *
42706583 TTTGTAAAACAGATTTTGAAAATACCTCGGTATGTGACCCGAGGCTCAACTCATTTATCGTAATA
1 TTTGAAAAACAGAAATTGAAAATACCTCAG--CGTGTCCCGAGGCTCAACTCACCTCTCGCAATA
42706648 TGAGTTGA-TT
64 TGAGTTGATTT
* * * *
42706658 CTTGAAAAGCATAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATATG
1 TTTGAAAAACAGAAATTGAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATG
42706723 AGTTGATTT
66 AGTTGATTT
** * * *
42706732 TTTGATGAACAGAAATT-AAAACTACCTCAACGTGTCCTGAGGCTCAACTCACCTCTCGCAACAT
1 TTTGAAAAACAGAAATTGAAAA-TACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATAT
*
42706796 AAGTTGATTTT
65 GAGTTGA-TTT
* *
42706807 TTTGAAAAACAGAAGTTGAAAACACCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATA
1 TTTGAAAAACAGAAATTGAAAATACCTCAGCGTGT--CCCGAGGCTCAACTCACCTCTCGCAATA
42706872 TGAGTTGATTTT
64 TGAGTTGA-TTT
* * *
42706884 TTTGACAAACAGAAATTGAAAAATACCTCAGCGTGTAAGCCAAGGCTCAACTCACCTCTCGCAAT
1 TTTGAAAAACAGAAATTG-AAAATACCTCAGCGTGT--CCCGAGGCTCAACTCACCTCTCGCAAT
42706949 ATGAGTTGATTT
63 ATGAGTTGATTT
* * *
42706961 TTTGAAAAATAGAAATTGAAAACACCTCAGCATGT---GAGGCTCAACTCACCTCTCGCAATATG
1 TTTGAAAAACAGAAATTGAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATG
42707023 AGTTGA-TT
66 AGTTGATTT
* * ** *
42707031 TTTGAAAAACATAAATTGAGCAGAAATTGAAAATACCTCAACGGGTCTTGAAGCTCAACTCACCT
1 TTTG------A-AAA---A-CAGAAATTGAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCT
*
42707096 CTCACAATATGAGTTGATTT
55 CTCGCAATATGAGTTGATTT
** * ** * ** * *
42707116 TTTG---ATGATAAATTGAAAATACCTCAATGTGACTTGAGGTTCAACTCACCTCTCACAATATG
1 TTTGAAAAACAGAAATTGAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATG
42707178 AGTTGATTT
66 AGTTGATTT
42707187 TTTGAATTAAAACAGAAATTGAAAATA
1 TTTG-A--AAAACAGAAATTGAAAATA
42707214 GAAATGGAAA
Statistics
Matches: 468, Mismatches: 60, Indels: 54
0.80 0.10 0.09
Matches are distributed among these distances:
70 6 0.01
71 94 0.20
73 39 0.08
74 58 0.12
75 52 0.11
76 20 0.04
77 89 0.19
78 51 0.11
80 1 0.00
81 21 0.04
84 31 0.07
85 6 0.01
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (74 bp):
TTTGAAAAACAGAAATTGAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATG
AGTTGATTT
Found at i:42707035 original size:224 final size:221
Alignment explanation
Indices: 42706583--42707041 Score: 593
Period size: 224 Copynumber: 2.0 Consensus size: 221
42706573 TAAAACAAAA
* ** * * * ** *
42706583 TTTGTAAAACAGATTTTGAAAATACCTCGGTATGTGACCCGAGGCTCAACTCATTTATCGTAATA
1 TTTGAAAAACAGAAGTTGAAAACACCTCAGCATGTGACCCGAGGCTCAACTCACCTATCGCAATA
* * *
42706648 TGAGTTGATTCTTGAAAAGCATAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTC
66 TGAGTTGATTCTTGAAAAGCAGAAATTGAAAATACCTCAGCGTGACCCAAGGCTCAACTCACCTC
** *
42706713 TCGCAATATGAGTTGATTTTTTGATGAACAGAAATTAAAACTACCTCAACGTGTCCTGAGGCTCA
131 TCGCAATATGAGTTGATTTTTTGAAAAACAGAAATTAAAACTACCTCAACATG--CTGAGGCTCA
42706778 ACTCACCTCTCGCAACATAAGTTGATTTT
194 ACTCACCTCTCGCAACATAAGTTGA-TTT
* *
42706807 TTTGAAAAACAGAAGTTGAAAACACCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATA
1 TTTGAAAAACAGAAGTTGAAAACACCTCAGCATGTGACCCGAGGCTCAACTCACCTATCGCAATA
* *
42706872 TGAGTTGATTTTTTTGACAAA-CAGAAATTGAAAAATACCTCAGCGTGTAAGCCAAGGCTCAACT
66 TGAGTTGA--TTCTTGA-AAAGCAGAAATTG-AAAATACCTCAGCGTG--ACCCAAGGCTCAACT
* *
42706936 CACCTCTCGCAATATGAGTTGATTTTTTGAAAAATAGAAATTGAAAAC-ACCTCAGCATG-TGAG
125 CACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAGAAATT-AAAACTACCTCAACATGCTGAG
* *
42706999 GCTCAACTCACCTCTCGCAATATGAGTTGA-TT
189 GCTCAACTCACCTCTCGCAACATAAGTTGATTT
42707031 TTTGAAAAACA
1 TTTGAAAAACA
42707042 TAAATTGAGC
Statistics
Matches: 205, Mismatches: 23, Indels: 14
0.85 0.10 0.06
Matches are distributed among these distances:
224 75 0.37
226 46 0.22
227 19 0.09
229 60 0.29
230 5 0.02
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (221 bp):
TTTGAAAAACAGAAGTTGAAAACACCTCAGCATGTGACCCGAGGCTCAACTCACCTATCGCAATA
TGAGTTGATTCTTGAAAAGCAGAAATTGAAAATACCTCAGCGTGACCCAAGGCTCAACTCACCTC
TCGCAATATGAGTTGATTTTTTGAAAAACAGAAATTAAAACTACCTCAACATGCTGAGGCTCAAC
TCACCTCTCGCAACATAAGTTGATTT
Found at i:42707087 original size:155 final size:154
Alignment explanation
Indices: 42706537--42707282 Score: 519
Period size: 155 Copynumber: 4.8 Consensus size: 154
42706527 ACGTGAGCCA
* **
42706537 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTT--AAAACAAAATTTGTAAAACAGATTTT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAAAA-TTG----ACAGAAATT
* * * ** * ** * * *
42706600 GAAAATACCTCGGTATGTGACCCGAGGCTCAACTCATTTATCGTAATATGAGTTGA--TTCTTGA
61 GAAAATACCTC--AACGTGTCTTGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGA
** * * * *
42706663 AAAGCATAAATTGAAAATACCTCAGCGTGCCCCG
124 AAAATAGAAATTGAAAACACCTCAGCATG---TG
42706697 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTG---------A-TGAACAGAAATT-AA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAAACAAAATTG-ACAGAAATTGAA
* * * *
42706751 AACTACCTCAACGTGTCCTGAGGCTCAACTCACCTCTCGCAACATAAGTTGATTTTTTTGAAAAA
64 AA-TACCTCAACGTGTCTTGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAA
* * *
42706816 CAGAAGTTGAAAACACCTCAGCGTGTGACCCG
128 TAGAAATTGAAAACACCTCAGCATGT-----G
***
42706848 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT--TTGAC--AA---ACAGAAATTGAAAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAAAATTGACAGAAATTG-AAA
* **
42706906 ATACCTCAGCGTGT-AAGCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTGAAAA
65 ATACCTCAACGTGTCTTG--AA-GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAA
42706969 ATAGAAATTGAAAACACCTCAGCATGTG
127 ATAGAAATTGAAAACACCTCAGCATGTG
42706997 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACATAAATTGAGCAGAAATTGAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACA-AAATTGA-CAGAAATTGAA
* * **
42707062 AATACCTCAACGGGTCTTGAAGCTCAACTCACCTCTCACAATATGAGTTGA-TTTTTTG-ATGAT
64 AATACCTCAACGTGTCTTGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAAT
* *
42707125 --AAATTGAAAATACCTCAATGTGACT-TG
129 AGAAATTGAAAACACCTC-A-G-CA-TGTG
* * *
42707152 AGGTTCAACTCACCTCTCACAATATGAGTTGATTTTTTGAATTAAAACAGAAATTGAAAATAGAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTG-A--AAAACA-AAATTG---ACAGAA
* * * * * *
42707217 ATGGAAAACACCTC-A-GCGTCTTGAGGTTCAACTCACCTCTCGCAATATGAGCTGATTTTTTTG
58 ATTGAAAATACCTCAACGTGTCTTGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTG
42707280 AAA
123 AAA
42707283 CACATAAATT
Statistics
Matches: 490, Mismatches: 52, Indels: 87
0.78 0.08 0.14
Matches are distributed among these distances:
147 33 0.07
148 4 0.01
149 83 0.17
150 5 0.01
151 35 0.07
152 27 0.06
153 13 0.03
154 47 0.10
155 98 0.20
156 9 0.02
157 17 0.03
158 10 0.02
159 47 0.10
160 39 0.08
161 22 0.04
162 1 0.00
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (154 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAAAATTGACAGAAATTGAAAA
TACCTCAACGTGTCTTGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAATAG
AAATTGAAAACACCTCAGCATGTG
Found at i:42707178 original size:226 final size:221
Alignment explanation
Indices: 42706615--42707211 Score: 593
Period size: 229 Copynumber: 2.6 Consensus size: 221
42706605 TACCTCGGTA
* ** * ** *
42706615 TGTGACCCGAGGCTCAACTCATTTATCGTAATATGAGTTGA--TTCTTGAAAAGCATAAATTGAA
1 TGTGACCCGAAGCTCAACTCACCTCTCACAATATGAGTTGATTTTTTTG-AAA-CATAAATTGAA
* * **
42706678 AATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGATGAACA
64 AATACCTCAGTGTG-ACCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACA
*
42706743 GAAATT-AAAACTACCTCAACGTGTCCTGAGGCTCAACTCACCTCTCGCAACATAAGTTGATTTT
128 GAAATTGAAAACTACCTCAACATG--CTGAGGCTCAACTCACCTCTCGCAACATAAGTTGA-TTT
*
42706807 TTTGAAAAACAGAAGTTGAAAACACCTCAGCG
190 TTTGAAAAACAGAAGTTGAAAACACCTCAACG
* * *
42706839 TGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGACAAACAGAAATTGAA
1 TGTGACCCGAAGCTCAACTCACCTCTCACAATATGAGTTGATTTTTTTG--AAACATAAATTG-A
* *
42706904 AAATACCTCAGCGTGTAAGCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAA
63 AAATACCTCA--GTGTGA-CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAA
* * * *
42706969 ATAGAAATTGAAAAC-ACCTCAGCATG-TGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TT
125 ACAGAAATTGAAAACTACCTCAACATGCTGAGGCTCAACTCACCTCTCGCAACATAAGTTGATTT
*
42707031 TTTGAAAAACATAAATTGAGCAGAAATTGAAAATACCTCAACG
190 TTTGAAAAAC----A--GA--AG---TTGAAAACACCTCAACG
* ** **
42707074 -G-GTCTTGAAGCTCAACTCACCTCTCACAATATGAGTTGA-TTTTTTG-ATGATAAATTGAAAA
1 TGTGACCCGAAGCTCAACTCACCTCTCACAATATGAGTTGATTTTTTTGAAACATAAATTGAAAA
* * * *
42707135 TACCTCAATGTGACTTGAGGTTCAACTCACCTCTCACAATATGAGTTGATTTTTTGAATTAAAAC
66 TACCTCAGTGTGAC-CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTG-A--AAAAC
42707200 AGAAATTGAAAA
127 AGAAATTGAAAA
42707212 TAGAAATGGA
Statistics
Matches: 315, Mismatches: 35, Indels: 41
0.81 0.09 0.10
Matches are distributed among these distances:
224 49 0.16
225 1 0.00
226 86 0.27
227 15 0.05
228 12 0.04
229 87 0.28
230 7 0.02
232 9 0.03
233 33 0.10
234 1 0.00
235 15 0.05
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.29
Consensus pattern (221 bp):
TGTGACCCGAAGCTCAACTCACCTCTCACAATATGAGTTGATTTTTTTGAAACATAAATTGAAAA
TACCTCAGTGTGACCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAGAA
ATTGAAAACTACCTCAACATGCTGAGGCTCAACTCACCTCTCGCAACATAAGTTGATTTTTTGAA
AAACAGAAGTTGAAAACACCTCAACG
Found at i:42707504 original size:77 final size:77
Alignment explanation
Indices: 42707307--42707691 Score: 376
Period size: 77 Copynumber: 4.9 Consensus size: 77
42707297 AAAAAGAAAT
* ** * *
42707307 TAAAAATAGAATTTGAAAGGACCTC-GACGTGTGGCCCGAGACTCAACTCACCTCTCGCAATATG
1 TAAAAATAAAATTTGAAAATACCTCAG-CGTGT--CCTGAGGCTCAACTCACCTCTCGCAATATG
*
42707371 AGTTGATTCTTTT-A
63 AGTTGATTTTTTTGA
** * * *
42707385 -AAAAGCAAAAATTGAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCACAATATGAGT
1 TAAAAATAAAATTTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGT
42707449 TGATTTTTTTGA
66 TGATTTTTTTGA
* *
42707461 TAAAAATAGAATTTGAAAATATCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGT
1 TAAAAATAAAATTTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGT
42707526 TGA--TTTTTGA
66 TGATTTTTTTGA
* * * * *
42707536 CAAACA-AAAA-TTGAAATTACCTCAGC--GTCTTGAGGCTCAACTCACTTCTCGCAATATGAGT
1 TAAAAATAAAATTTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGT
42707597 TGATTTTTTTTTTGAAACA
66 TGA---TTTTTTTG----A
* * * *
42707616 TAAATTAAAAAAAAATTT-AAAATACCTCAACGTGTCTTGAGGCTCAACTCACATCTCGCAATAT
1 T--A--AAAATAAAATTTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATAT
42707680 GAGTTGATTTTT
62 GAGTTGATTTTT
42707692 GAAAAACAGA
Statistics
Matches: 259, Mismatches: 28, Indels: 34
0.81 0.09 0.11
Matches are distributed among these distances:
71 36 0.14
73 14 0.05
74 3 0.01
75 51 0.20
76 7 0.03
77 83 0.32
78 1 0.00
80 1 0.00
82 1 0.00
84 8 0.03
85 15 0.06
86 2 0.01
87 37 0.14
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.31
Consensus pattern (77 bp):
TAAAAATAAAATTTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGT
TGATTTTTTTGA
Found at i:42707736 original size:13 final size:13
Alignment explanation
Indices: 42707693--42707736 Score: 61
Period size: 13 Copynumber: 3.4 Consensus size: 13
42707683 TTGATTTTTG
42707693 AAAAACAGAAATT
1 AAAAACAGAAATT
*
42707706 AAAAGCAGAAATT
1 AAAAACAGAAATT
* *
42707719 GAAAACAAAAATT
1 AAAAACAGAAATT
42707732 AAAAA
1 AAAAA
42707737 TACCTCGGCG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.70, C:0.07, G:0.09, T:0.14
Consensus pattern (13 bp):
AAAAACAGAAATT
Found at i:42707835 original size:13 final size:13
Alignment explanation
Indices: 42707792--42707835 Score: 61
Period size: 13 Copynumber: 3.4 Consensus size: 13
42707782 TTGATTTTTG
42707792 AAAAACAGAAATT
1 AAAAACAGAAATT
*
42707805 AAAAGCAGAAATT
1 AAAAACAGAAATT
* *
42707818 GAAAACAAAAATT
1 AAAAACAGAAATT
42707831 AAAAA
1 AAAAA
42707836 TACCTCGGCG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.70, C:0.07, G:0.09, T:0.14
Consensus pattern (13 bp):
AAAAACAGAAATT
Found at i:42707903 original size:99 final size:99
Alignment explanation
Indices: 42707617--42707894 Score: 470
Period size: 99 Copynumber: 2.8 Consensus size: 99
42707607 TTTGAAACAT
* * ** * * * *
42707617 AAATT-AAAAAAAAATTTAAAA-TACCTCAACGTGTCTTGAGGCTCAACTCACATCTCGCAATAT
1 AAATTGAAAACAAAAATTAAAAATACCTCGGCGTGCCCTGAGGCTCAGCTCACCTCTCGCAATAT
42707680 GAGTTGATTTTTGAAAAACAGAAATTAAAAGCAG
66 GAGTTGATTTTTGAAAAACAGAAATTAAAAGCAG
42707714 AAATTGAAAACAAAAATTAAAAATACCTCGGCGTGCCCTGAGGCTCAGCTCACCTCTCGCAATAT
1 AAATTGAAAACAAAAATTAAAAATACCTCGGCGTGCCCTGAGGCTCAGCTCACCTCTCGCAATAT
42707779 GAGTTGATTTTTGAAAAACAGAAATTAAAAGCAG
66 GAGTTGATTTTTGAAAAACAGAAATTAAAAGCAG
42707813 AAATTGAAAACAAAAATTAAAAATACCTCGGCGTGCCCTGAGGCTCAGCTCACCTCTCGCAATAT
1 AAATTGAAAACAAAAATTAAAAATACCTCGGCGTGCCCTGAGGCTCAGCTCACCTCTCGCAATAT
42707878 GAGTTGATTTTTGAAAA
66 GAGTTGATTTTTGAAAA
42707895 GTATAAATTG
Statistics
Matches: 171, Mismatches: 8, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
97 5 0.03
98 14 0.08
99 152 0.89
ACGTcount: A:0.41, C:0.18, G:0.16, T:0.25
Consensus pattern (99 bp):
AAATTGAAAACAAAAATTAAAAATACCTCGGCGTGCCCTGAGGCTCAGCTCACCTCTCGCAATAT
GAGTTGATTTTTGAAAAACAGAAATTAAAAGCAG
Found at i:42707948 original size:73 final size:74
Alignment explanation
Indices: 42707816--42707982 Score: 239
Period size: 73 Copynumber: 2.3 Consensus size: 74
42707806 AAAGCAGAAA
* * * *
42707816 TTGAAAA-CAAAAATTAAAAATACCTCGGCGTGCCCTGAGGCTCAGCTCACCTCTCGCAATATGA
1 TTGAAAAGCATAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGA
*
42707880 GTTGA-TTT
66 GTTAATTTT
* * * *
42707888 TTGAAAAGTATAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTTGCAATATGA
1 TTGAAAAGCATAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGA
42707953 GTTAATTTT
66 GTTAATTTT
42707962 TTGAAAAGCATAAATTGAAAA
1 TTGAAAAGCATAAATTGAAAA
42707983 AACGGAAATT
Statistics
Matches: 82, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
72 7 0.09
73 53 0.65
74 22 0.27
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (74 bp):
TTGAAAAGCATAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGA
GTTAATTTT
Found at i:42708074 original size:91 final size:89
Alignment explanation
Indices: 42707899--42708075 Score: 250
Period size: 91 Copynumber: 2.0 Consensus size: 89
42707889 TGAAAAGTAT
* * *
42707899 AAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTTGCAATATGAGTTAATTTTTT
1 AAATTGAAAATACCTCAGCGTGTCCTGAGGCCCAACTCACCTCTCGCAATATGAGTTAATTTTTT
* *
42707964 GAAAAGCATAAATTGAAAAAACGG
66 GAAAAGCAGAAATTAAAAAAACGG
*
42707988 AAATTGAAAATACCTCAGCGTGTGACCTGAGGCCCAACTCACCTCTCGCAATATGAGTTGATTTT
1 AAATTGAAAATACCTCAGCGTGT--CCTGAGGCCCAACTCACCTCTCGCAATATGAGTT-AATTT
42708053 TTTG-AAAGACAGAAA-TAAAAAAA
63 TTTGAAAAG-CAGAAATTAAAAAAA
42708076 TCAAAATACC
Statistics
Matches: 78, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
89 22 0.28
91 43 0.55
92 13 0.17
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.27
Consensus pattern (89 bp):
AAATTGAAAATACCTCAGCGTGTCCTGAGGCCCAACTCACCTCTCGCAATATGAGTTAATTTTTT
GAAAAGCAGAAATTAAAAAAACGG
Found at i:42720038 original size:16 final size:15
Alignment explanation
Indices: 42720012--42720046 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
42720002 TGATGTGAAT
42720012 AATATAAAATATTAA
1 AATATAAAATATTAA
*
42720027 AATATCAAAATATTAG
1 AATAT-AAAATATTAA
42720043 AATA
1 AATA
42720047 ATAATAATTA
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:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (15 bp):
AATATAAAATATTAA
Found at i:42720218 original size:20 final size:20
Alignment explanation
Indices: 42720161--42720220 Score: 59
Period size: 23 Copynumber: 2.9 Consensus size: 20
42720151 AATACTACAT
42720161 AAATATGTACAT-ATATAAA
1 AAATATGTACATAATATAAA
** *
42720180 AAATAAATACGTGATAATATTAA
1 AAATATGTAC---ATAATATAAA
42720203 AAATATGTACATAATATA
1 AAATATGTACATAATATA
42720221 GTGTAAAAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 7
0.70 0.14 0.16
Matches are distributed among these distances:
19 8 0.26
20 7 0.23
22 2 0.06
23 14 0.45
ACGTcount: A:0.57, C:0.05, G:0.07, T:0.32
Consensus pattern (20 bp):
AAATATGTACATAATATAAA
Found at i:42720259 original size:22 final size:23
Alignment explanation
Indices: 42720198--42720268 Score: 81
Period size: 25 Copynumber: 3.0 Consensus size: 23
42720188 ACGTGATAAT
*
42720198 ATTAAAAATATGTACATAATATA
1 ATTAAAAATATATACATAATATA
* *
42720221 GTGTAAAAAATACATACATAATATA
1 AT-T-AAAAATATATACATAATATA
*
42720246 ATT-AAAATATATACATAAGATA
1 ATTAAAAATATATACATAATATA
42720268 A
1 A
42720269 CATGTAAAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
22 18 0.45
23 1 0.03
24 2 0.05
25 19 0.47
ACGTcount: A:0.58, C:0.06, G:0.06, T:0.31
Consensus pattern (23 bp):
ATTAAAAATATATACATAATATA
Found at i:42720329 original size:25 final size:25
Alignment explanation
Indices: 42720295--42720418 Score: 84
Period size: 25 Copynumber: 5.2 Consensus size: 25
42720285 ATATAAATAA
42720295 ATAATATAGTATTAA-AGATATATAC
1 ATAATATAGTA-TAATAGATATATAC
* *
42720320 ATAAAATAGTATAATATATATATAC
1 ATAATATAGTATAATAGATATATAC
* * *
42720345 GTAATATAGAAT-TTAGA-ATATAC
1 ATAATATAGTATAATAGATATATAC
* * *
42720368 CTAATATA-T-TAAAAGA-ATATAT
1 ATAATATAGTATAATAGATATATAC
* * *
42720390 ATAATATAATATTA-AGAAATATA-
1 ATAATATAGTATAATAGATATATAC
42720413 ATAATA
1 ATAATA
42720419 ACAAAAAAAG
Statistics
Matches: 80, Mismatches: 14, Indels: 12
0.75 0.13 0.11
Matches are distributed among these distances:
21 1 0.01
22 15 0.19
23 23 0.29
24 13 0.16
25 28 0.35
ACGTcount: A:0.55, C:0.03, G:0.06, T:0.35
Consensus pattern (25 bp):
ATAATATAGTATAATAGATATATAC
Found at i:42720938 original size:30 final size:30
Alignment explanation
Indices: 42720897--42720995 Score: 153
Period size: 30 Copynumber: 3.3 Consensus size: 30
42720887 GAGGTATAAG
*
42720897 TGGTGGTGGAGCAAGTGTGGCTAGTAGAGT
1 TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
* *
42720927 AGGTAGTGGAGCAAGTGTGGCTAGTGGAGT
1 TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
* *
42720957 TGATGGTGGAGCAAGTGTGGTTAGTGGAGT
1 TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
42720987 TGGTGGTGG
1 TGGTGGTGG
42720996 CAAATGCTAG
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 61 1.00
ACGTcount: A:0.19, C:0.05, G:0.48, T:0.27
Consensus pattern (30 bp):
TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
Found at i:42720953 original size:18 final size:18
Alignment explanation
Indices: 42720902--42720955 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
42720892 ATAAGTGGTG
42720902 GTGGAGCAAGTGTGGCTA
1 GTGGAGCAAGTGTGGCTA
*
42720920 GT--AG--AGT-AGG-TA
1 GTGGAGCAAGTGTGGCTA
42720932 GTGGAGCAAGTGTGGCTA
1 GTGGAGCAAGTGTGGCTA
42720950 GTGGAG
1 GTGGAG
42720956 TTGATGGTGG
Statistics
Matches: 28, Mismatches: 2, Indels: 12
0.67 0.05 0.29
Matches are distributed among these distances:
12 4 0.14
13 2 0.07
14 5 0.18
16 5 0.18
17 2 0.07
18 10 0.36
ACGTcount: A:0.24, C:0.07, G:0.46, T:0.22
Consensus pattern (18 bp):
GTGGAGCAAGTGTGGCTA
Found at i:42721805 original size:17 final size:15
Alignment explanation
Indices: 42721765--42721797 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
42721755 TCATTTCGCT
42721765 TTTATATTGTTATTA
1 TTTATATTGTTATTA
42721780 TTT-TATTGTTATTA
1 TTTATATTGTTATTA
42721794 TTTA
1 TTTA
42721798 GATATTGTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 14 0.82
15 3 0.18
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.70
Consensus pattern (15 bp):
TTTATATTGTTATTA
Found at i:42725009 original size:22 final size:23
Alignment explanation
Indices: 42724951--42725010 Score: 70
Period size: 22 Copynumber: 2.6 Consensus size: 23
42724941 TTCTGTAATT
*
42724951 TAAAAAA-AATATTATTTTTACA
1 TAAAAAATAAAATTATTTTTACA
*
42724973 TAATAAAAATTAAATTATTTTTA-A
1 T-A-AAAAATAAAATTATTTTTACA
42724997 TAAAAAATAAAATT
1 TAAAAAATAAAATT
42725011 TTGGATATAC
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
22 12 0.38
23 2 0.06
24 7 0.22
25 11 0.34
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (23 bp):
TAAAAAATAAAATTATTTTTACA
Found at i:42727324 original size:29 final size:31
Alignment explanation
Indices: 42727292--42727356 Score: 98
Period size: 29 Copynumber: 2.2 Consensus size: 31
42727282 AATCTATATA
*
42727292 TTTATAATTTTTAAGGGA-T-AAATTAAATT
1 TTTATAATTTTTAAGGGACTAAAAATAAATT
*
42727321 TTTATTATTTTTAAGGGACTAAAAATAAATT
1 TTTATAATTTTTAAGGGACTAAAAATAAATT
42727352 TTTAT
1 TTTAT
42727357 TTTTACTAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 17 0.53
30 1 0.03
31 14 0.44
ACGTcount: A:0.40, C:0.02, G:0.09, T:0.49
Consensus pattern (31 bp):
TTTATAATTTTTAAGGGACTAAAAATAAATT
Found at i:42731093 original size:20 final size:20
Alignment explanation
Indices: 42731068--42731107 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
42731058 AGGTGAGTTG
42731068 AATCCAAATAGAATATCATA
1 AATCCAAATAGAATATCATA
42731088 AATCCAAATAGAATATCATA
1 AATCCAAATAGAATATCATA
42731108 CTTAAATTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.55, C:0.15, G:0.05, T:0.25
Consensus pattern (20 bp):
AATCCAAATAGAATATCATA
Found at i:42733055 original size:16 final size:16
Alignment explanation
Indices: 42733034--42733072 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
42733024 CAAAATAAAT
*
42733034 TAAACTTGAAATGATC
1 TAAACTCGAAATGATC
* *
42733050 TGAACTCGAATTGATC
1 TAAACTCGAAATGATC
42733066 TAAACTC
1 TAAACTC
42733073 AAAACAACTC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.31
Consensus pattern (16 bp):
TAAACTCGAAATGATC
Found at i:42734367 original size:12 final size:12
Alignment explanation
Indices: 42734335--42734373 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
42734325 AGAACAGCAA
* *
42734335 TTTCAATTGTTG
1 TTTCAATTTTTT
42734347 TTTCAATTTTTT
1 TTTCAATTTTTT
42734359 TTTCAATTTTTT
1 TTTCAATTTTTT
42734371 TTT
1 TTT
42734374 ATTTAGGTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.15, C:0.08, G:0.05, T:0.72
Consensus pattern (12 bp):
TTTCAATTTTTT
Found at i:42734519 original size:19 final size:19
Alignment explanation
Indices: 42734495--42734556 Score: 83
Period size: 19 Copynumber: 3.3 Consensus size: 19
42734485 GAGTACTTTA
42734495 TTATTTATTTACGTTCAAT
1 TTATTTATTTACGTTCAAT
* *
42734514 TTATTT-TTTCCAGTTTAA-
1 TTATTTATTTAC-GTTCAAT
42734532 TTATTTATTTACGTTCAAT
1 TTATTTATTTACGTTCAAT
42734551 TTATTT
1 TTATTT
42734557 TTTCCAATTT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
18 15 0.42
19 21 0.58
ACGTcount: A:0.24, C:0.10, G:0.05, T:0.61
Consensus pattern (19 bp):
TTATTTATTTACGTTCAAT
Found at i:42734537 original size:18 final size:19
Alignment explanation
Indices: 42734511--42734567 Score: 64
Period size: 18 Copynumber: 3.1 Consensus size: 19
42734501 ATTTACGTTC
42734511 AATTTATTTTTTCCAGTTT
1 AATTTATTTTTTCCAGTTT
* *
42734530 AA-TTATTTATTTAC-GTTC
1 AATTTATTT-TTTCCAGTTT
*
42734548 AATTTATTTTTTCCAATTT
1 AATTTATTTTTTCCAGTTT
42734567 A
1 A
42734568 TCTTAACGAG
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
18 15 0.50
19 15 0.50
ACGTcount: A:0.26, C:0.11, G:0.04, T:0.60
Consensus pattern (19 bp):
AATTTATTTTTTCCAGTTT
Found at i:42734544 original size:37 final size:37
Alignment explanation
Indices: 42734494--42734567 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
42734484 TGAGTACTTT
*
42734494 ATTATTTATTTACGTTCAATTTATTTTTTCCAGTTTA
1 ATTATTTATTTACGTTCAATTTATTTTTTCCAATTTA
42734531 ATTATTTATTTACGTTCAATTTATTTTTTCCAATTTA
1 ATTATTTATTTACGTTCAATTTATTTTTTCCAATTTA
42734568 TCTTAACGAG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.26, C:0.11, G:0.04, T:0.59
Consensus pattern (37 bp):
ATTATTTATTTACGTTCAATTTATTTTTTCCAATTTA
Found at i:42735957 original size:26 final size:26
Alignment explanation
Indices: 42735903--42735959 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
42735893 TTTTTATTTT
*
42735903 TATTTTTTAAAATATTTAAAATATTA
1 TATTTTTTAAAATATTTAAAATATCA
*
42735929 TATTTTTTAATAT-TATTAAACATA-CA
1 TATTTTTTAAAATAT-TTAAA-ATATCA
42735955 TATTT
1 TATTT
42735960 AATTATTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
25 1 0.04
26 23 0.85
27 3 0.11
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (26 bp):
TATTTTTTAAAATATTTAAAATATCA
Found at i:42736008 original size:22 final size:22
Alignment explanation
Indices: 42735983--42736024 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
42735973 TGGTCATATA
42735983 ATAAATTATTAATATAATAAAT
1 ATAAATTATTAATATAATAAAT
* * *
42736005 ATAATTTATTATTTTAATAA
1 ATAAATTATTAATATAATAA
42736025 TTTATTTAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
ATAAATTATTAATATAATAAAT
Found at i:42736062 original size:13 final size:14
Alignment explanation
Indices: 42736046--42736087 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
42736036 TTTCAATTTT
42736046 ATTTTAATAATA-A
1 ATTTTAATAATATA
*
42736059 ATTTTAAAAATAATA
1 ATTTTAATAAT-ATA
42736074 ATTTTAAATAATAT
1 ATTTT-AATAATAT
42736088 TATTCACATG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 10 0.42
14 1 0.04
15 8 0.33
16 5 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATTTTAATAATATA
Found at i:42736072 original size:16 final size:16
Alignment explanation
Indices: 42736050--42736086 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
42736040 AATTTTATTT
42736050 TAATAATAAATTTTAAA
1 TAATAAT-AATTTTAAA
42736067 -AATAATAATTTTAAA
1 TAATAATAATTTTAAA
42736082 TAATA
1 TAATA
42736087 TTATTCACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATAATAATTTTAAA
Found at i:42736139 original size:15 final size:15
Alignment explanation
Indices: 42736119--42736175 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
42736109 ATTCAATATT
42736119 AATATTTTAATAATA
1 AATATTTTAATAATA
*
42736134 AATATTTATTACAATTATA
1 AATA-TT-TT--AATAATA
*
42736153 AATATATTAATAATA
1 AATATTTTAATAATA
*
42736168 AATGTTTT
1 AATATTTT
42736176 GTAGTATAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
15 16 0.48
16 2 0.06
17 4 0.12
18 1 0.03
19 10 0.30
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:42739259 original size:15 final size:15
Alignment explanation
Indices: 42739234--42739270 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
42739224 TGGTTTTTTC
42739234 ATTTTTA-TTGAAAT
1 ATTTTTATTTGAAAT
*
42739248 ATTTTTATTTGATAT
1 ATTTTTATTTGAAAT
42739263 ATTTTTAT
1 ATTTTTAT
42739271 ACATGAGTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 7 0.33
15 14 0.67
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (15 bp):
ATTTTTATTTGAAAT
Found at i:42740834 original size:19 final size:20
Alignment explanation
Indices: 42740810--42740854 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
42740800 TTCTTGTCTG
42740810 AATTTTGT-T-TTAAAGACTT
1 AATTTTGTATGTTAAA-ACTT
42740829 AATTTT-TATGTTAAAACTT
1 AATTTTGTATGTTAAAACTT
42740848 AATTTTG
1 AATTTTG
42740855 GCGTCTAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
18 1 0.04
19 17 0.74
20 5 0.22
ACGTcount: A:0.33, C:0.04, G:0.09, T:0.53
Consensus pattern (20 bp):
AATTTTGTATGTTAAAACTT
Found at i:42741442 original size:37 final size:37
Alignment explanation
Indices: 42741401--42741476 Score: 134
Period size: 37 Copynumber: 2.1 Consensus size: 37
42741391 ATCGGGTATG
*
42741401 AATTTTGATCTTTCAAATATGTGAATAAATCTAGAGA
1 AATTTTAATCTTTCAAATATGTGAATAAATCTAGAGA
*
42741438 AATTTTAATTTTTCAAATATGTGAATAAATCTAGAGA
1 AATTTTAATCTTTCAAATATGTGAATAAATCTAGAGA
42741475 AA
1 AA
42741477 ATTAATCATA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.43, C:0.07, G:0.12, T:0.38
Consensus pattern (37 bp):
AATTTTAATCTTTCAAATATGTGAATAAATCTAGAGA
Found at i:42744353 original size:25 final size:24
Alignment explanation
Indices: 42744319--42744392 Score: 94
Period size: 24 Copynumber: 3.0 Consensus size: 24
42744309 GGTTTCTTGA
*
42744319 TTTTTTTTTGGGGTTAGGTTTTTC
1 TTTTTTTTTTGGGTTAGGTTTTTC
42744343 TTTTTTTTTTGGGTTAGGTTTTTTC
1 TTTTTTTTTTGGGTTAGG-TTTTTC
**
42744368 TTTCTTTTTTTTTAGTTAGGTTTTT
1 -TT-TTTTTTTTGGGTTAGGTTTTT
42744393 TTTGGGAGGG
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
24 17 0.39
25 6 0.14
26 7 0.16
27 14 0.32
ACGTcount: A:0.05, C:0.04, G:0.19, T:0.72
Consensus pattern (24 bp):
TTTTTTTTTTGGGTTAGGTTTTTC
Found at i:42744393 original size:27 final size:25
Alignment explanation
Indices: 42744319--42744393 Score: 89
Period size: 27 Copynumber: 3.0 Consensus size: 25
42744309 GGTTTCTTGA
* *
42744319 TTTTTTTTTGGGGTTAGG-TTTTTC
1 TTTTTTTTTTGAGTTAGGTTTTTTC
*
42744343 TTTTTTTTTTGGGTTAGGTTTTTTC
1 TTTTTTTTTTGAGTTAGGTTTTTTC
*
42744368 TTTCTTTTTTTTTAGTTAGGTTTTTT
1 -TT-TTTTTTTTGAGTTAGGTTTTTT
42744394 TTGGGAGGGC
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
24 17 0.38
25 6 0.13
26 2 0.04
27 20 0.44
ACGTcount: A:0.05, C:0.04, G:0.19, T:0.72
Consensus pattern (25 bp):
TTTTTTTTTTGAGTTAGGTTTTTTC
Found at i:42748319 original size:14 final size:16
Alignment explanation
Indices: 42748302--42748333 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
42748292 CCCAAAAAAA
42748302 TTATAA-TTA-AAATC
1 TTATAATTTACAAATC
42748316 TTATAATTTACAAATC
1 TTATAATTTACAAATC
42748332 TT
1 TT
42748334 TTCTTTAGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.38
15 3 0.19
16 7 0.44
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (16 bp):
TTATAATTTACAAATC
Found at i:42750762 original size:17 final size:17
Alignment explanation
Indices: 42750740--42750775 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
42750730 TTGAAAACCG
42750740 TGCTAGATAAATACACA
1 TGCTAGATAAATACACA
*
42750757 TGCTAGATAAATACCCA
1 TGCTAGATAAATACACA
42750774 TG
1 TG
42750776 TTCAAGACTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.42, C:0.19, G:0.14, T:0.25
Consensus pattern (17 bp):
TGCTAGATAAATACACA
Found at i:42752669 original size:21 final size:20
Alignment explanation
Indices: 42752643--42752681 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
42752633 AATATATATA
*
42752643 TATTAAAATATATGTAAAAAT
1 TATTAAAAT-TATATAAAAAT
42752664 TATTAAAATTATATAAAA
1 TATTAAAATTATATAAAA
42752682 TACTCTAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (20 bp):
TATTAAAATTATATAAAAAT
Found at i:42762505 original size:18 final size:19
Alignment explanation
Indices: 42762484--42762528 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
42762474 ATTGATTTTT
42762484 TTAATTAAATAAATT-T-AA
1 TTAATTAAA-AAATTCTAAA
*
42762502 TTAATT-GAAAATTCTAAA
1 TTAATTAAAAAATTCTAAA
42762520 TTAATTAAA
1 TTAATTAAA
42762529 GGAAAATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
16 5 0.23
17 2 0.09
18 14 0.64
19 1 0.05
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (19 bp):
TTAATTAAAAAATTCTAAA
Found at i:42762533 original size:22 final size:23
Alignment explanation
Indices: 42762493--42762535 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
42762483 TTTAATTAAA
**
42762493 TAAATTTAATTAATTGAAAATTC
1 TAAATTTAATTAAAGGAAAATTC
42762516 TAAA-TTAATTAAAGGAAAAT
1 TAAATTTAATTAAAGGAAAAT
42762536 ATTAATTTGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.53, C:0.02, G:0.07, T:0.37
Consensus pattern (23 bp):
TAAATTTAATTAAAGGAAAATTC
Found at i:42763944 original size:16 final size:17
Alignment explanation
Indices: 42763914--42763949 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 17
42763904 AACCGGTCTG
42763914 ATTAAAAAATTATTAAAA
1 ATTAAAAAA-TATTAAAA
42763932 ATTAAAAAA-ATTAAAA
1 ATTAAAAAATATTAAAA
42763948 AT
1 AT
42763950 CTGGTTCAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 9 0.50
18 9 0.50
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
ATTAAAAAATATTAAAA
Found at i:42764307 original size:36 final size:36
Alignment explanation
Indices: 42764260--42764329 Score: 122
Period size: 36 Copynumber: 1.9 Consensus size: 36
42764250 ATTCATATTT
*
42764260 AAGCTCTTTCTATATAGTAAGGATAAAAATATAGTG
1 AAGCTCTTTCTATATAATAAGGATAAAAATATAGTG
*
42764296 AAGCTCTTTCTATATAATGAGGATAAAAATATAG
1 AAGCTCTTTCTATATAATAAGGATAAAAATATAG
42764330 CGAAACGAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.43, C:0.09, G:0.16, T:0.33
Consensus pattern (36 bp):
AAGCTCTTTCTATATAATAAGGATAAAAATATAGTG
Found at i:42768408 original size:9 final size:9
Alignment explanation
Indices: 42768394--42768425 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
42768384 CAACGCTTTT
42768394 TTGCATTCA
1 TTGCATTCA
42768403 TTGCATTCA
1 TTGCATTCA
42768412 TTGCATTCA
1 TTGCATTCA
42768421 -TGCAT
1 TTGCAT
42768426 CGGCATTGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 5 0.22
9 18 0.78
ACGTcount: A:0.22, C:0.22, G:0.12, T:0.44
Consensus pattern (9 bp):
TTGCATTCA
Found at i:42776174 original size:44 final size:43
Alignment explanation
Indices: 42776126--42776257 Score: 124
Period size: 44 Copynumber: 3.0 Consensus size: 43
42776116 GGGAATAGAT
*
42776126 TGAAGGCAACTAGCTTTAACCCCCTAAGCAGTAGGGTAACAAGC
1 TGAAGACAA-TAGCTTTAACCCCCTAAGCAGTAGGGTAACAAGC
* * * * * *
42776170 TGAAGTTC-ATAGATCTTATCACCCTAAGCAGTAGGGAAAC-AGA
1 TGAAG-ACAATAGCT-TTAACCCCCTAAGCAGTAGGGTAACAAGC
* *
42776213 TCGAAAATAATGAGCTTTAACCCCCTAAGCAGTAGGGTAACAAGC
1 T-GAAGACAAT-AGCTTTAACCCCCTAAGCAGTAGGGTAACAAGC
42776258 CAAATTTACA
Statistics
Matches: 68, Mismatches: 14, Indels: 11
0.73 0.15 0.12
Matches are distributed among these distances:
43 7 0.10
44 55 0.81
45 6 0.09
ACGTcount: A:0.36, C:0.22, G:0.21, T:0.20
Consensus pattern (43 bp):
TGAAGACAATAGCTTTAACCCCCTAAGCAGTAGGGTAACAAGC
Found at i:42776290 original size:43 final size:42
Alignment explanation
Indices: 42776141--42776295 Score: 150
Period size: 44 Copynumber: 3.6 Consensus size: 42
42776131 GCAACTAGCT
* * *
42776141 TTAACCCCCTAAGCAGTAGGGTAACAAGCTGAAGTTCATAGATC
1 TTAACCCCCTAAGCAGTAGGGTAACAAGC-GAAATTTA-AGACC
* * * * * *
42776185 TTATCACCCTAAGCAGTAGGGAAACAGATCGAAA-ATAATGAGCT
1 TTAACCCCCTAAGCAGTAGGGTAACA-AGCGAAATTTAA-GA-CC
*
42776229 TTAACCCCCTAAGCAGTAGGGTAACAAGCCAAATTTACAGACC
1 TTAACCCCCTAAGCAGTAGGGTAACAAGCGAAATTTA-AGACC
*
42776272 TTAACCCCCTAAGTAGTAGGGTAA
1 TTAACCCCCTAAGCAGTAGGGTAA
42776296 TAGGCTGAAA
Statistics
Matches: 89, Mismatches: 17, Indels: 11
0.76 0.15 0.09
Matches are distributed among these distances:
42 1 0.01
43 32 0.36
44 53 0.60
45 3 0.03
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.21
Consensus pattern (42 bp):
TTAACCCCCTAAGCAGTAGGGTAACAAGCGAAATTTAAGACC
Found at i:42776457 original size:44 final size:43
Alignment explanation
Indices: 42776409--42776563 Score: 143
Period size: 44 Copynumber: 3.5 Consensus size: 43
42776399 TACAAATCTT
*
42776409 ACCCCCTAAGCAGTAGGGAAACAGATCGAAGGCAACGAGCTTTA
1 ACCCCCTAAGCAGTAGGGAAACAGATCGAAGACAA-GAGCTTTA
* * * *
42776453 ACCCCCTAAGCAGTAGGGTAACA-AGCTGAAGTTCATAGATC-TTA
1 ACCCCCTAAGCAGTAGGGAAACAGATC-GAAG-ACA-AGAGCTTTA
* * * * *
42776497 TCACCCTAGGCAGTAAGGAAACAGATCGAAGATAATGAGCTTTA
1 ACCCCCTAAGCAGTAGGGAAACAGATCGAAGACAA-GAGCTTTA
* *
42776541 ACCCCCTAAGCAATAGGGTAACA
1 ACCCCCTAAGCAGTAGGGAAACA
42776564 AGCCAAATTT
Statistics
Matches: 86, Mismatches: 19, Indels: 12
0.74 0.16 0.10
Matches are distributed among these distances:
42 1 0.01
43 6 0.07
44 71 0.83
45 7 0.08
46 1 0.01
ACGTcount: A:0.37, C:0.23, G:0.22, T:0.18
Consensus pattern (43 bp):
ACCCCCTAAGCAGTAGGGAAACAGATCGAAGACAAGAGCTTTA
Found at i:42776510 original size:88 final size:87
Alignment explanation
Indices: 42776404--42776566 Score: 254
Period size: 88 Copynumber: 1.9 Consensus size: 87
42776394 AGATTTACAA
* * * *
42776404 ATCTTACCCCCTAAGCAGTAGGGAAACAGATCGAAGGCAACGAGCTTTAACCCCCTAAGCAGTAG
1 ATCTTACACCCTAAGCAGTAAGGAAACAGATCGAAGACAACGAGCTTTAACCCCCTAAGCAATAG
42776469 GGTAACAAGCTGAAGTTCATAG
66 GGTAACAAGCTGAAGTTCATAG
* * *
42776491 ATCTTATCACCCTAGGCAGTAAGGAAACAGATCGAAGATAATGAGCTTTAACCCCCTAAGCAATA
1 ATCTTA-CACCCTAAGCAGTAAGGAAACAGATCGAAGACAACGAGCTTTAACCCCCTAAGCAATA
42776556 GGGTAACAAGC
65 GGGTAACAAGC
42776567 CAAATTTATA
Statistics
Matches: 68, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
87 6 0.09
88 62 0.91
ACGTcount: A:0.36, C:0.23, G:0.21, T:0.19
Consensus pattern (87 bp):
ATCTTACACCCTAAGCAGTAAGGAAACAGATCGAAGACAACGAGCTTTAACCCCCTAAGCAATAG
GGTAACAAGCTGAAGTTCATAG
Found at i:42776671 original size:309 final size:309
Alignment explanation
Indices: 42776095--42776792 Score: 1164
Period size: 309 Copynumber: 2.3 Consensus size: 309
42776085 GAATTCACAG
* * * * * *
42776095 ATCTTAACCCATAAGCAGTAGGGGAATAGATTGAAGGCAACTAGCTTTAACCCCCTAAGCAGTAG
1 ATCTTACCCCCTAAGCAGTAGGGAAACAGATCGAAGGCAACGAGCTTTAACCCCCTAAGCAGTAG
*
42776160 GGTAACAAGCTGAAGTTCATAGATCTTATCACCCTAAGCAGTAGGGAAACAGATCGAAAATAATG
66 GGTAACAAGCTGAAGTTCATAGATCTTATCACCCTAAGCAGTAAGGAAACAGATCGAAAATAATG
*
42776225 AGCTTTAACCCCCTAAGCAGTAGGGTAACAAGCCAAATTTACAGACCTTAACCCCCTAAGTAGTA
131 AGCTTTAACCCCCTAAGCAATAGGGTAACAAGCCAAATTTACAGACCTTAACCCCCTAAGTAGTA
* *
42776290 GGGTAATAGGCTGAAAATTACAGATCTTGTCTCCTTGAAGTTGCAGTGGAACAGATCGAATTCAG
196 GGGTAATAGGCTGAAAATTACAGATCTTGTCTCCCTGAAGTTGCAGTGGAACAGATCGAATCCAG
*
42776355 TGAATCTTGTCTTCCTGAAGTTGCAGTGAAGCAGATTGAAGATTTACAA
261 CGAATCTTGTCTTCCTGAAGTTGCAGTGAAGCAGATTGAAGATTTACAA
42776404 ATCTTACCCCCTAAGCAGTAGGGAAACAGATCGAAGGCAACGAGCTTTAACCCCCTAAGCAGTAG
1 ATCTTACCCCCTAAGCAGTAGGGAAACAGATCGAAGGCAACGAGCTTTAACCCCCTAAGCAGTAG
* *
42776469 GGTAACAAGCTGAAGTTCATAGATCTTATCACCCTAGGCAGTAAGGAAACAGATCGAAGATAATG
66 GGTAACAAGCTGAAGTTCATAGATCTTATCACCCTAAGCAGTAAGGAAACAGATCGAAAATAATG
*
42776534 AGCTTTAACCCCCTAAGCAATAGGGTAACAAGCCAAATTTATAGACCTTAACCCCCTAAGTAGTA
131 AGCTTTAACCCCCTAAGCAATAGGGTAACAAGCCAAATTTACAGACCTTAACCCCCTAAGTAGTA
* *
42776599 GGGTAATAGGTTGAAAATTACAGATTTTGTCTCCCTGAAGTTGCAGTGGAACAGATCGAATCCAG
196 GGGTAATAGGCTGAAAATTACAGATCTTGTCTCCCTGAAGTTGCAGTGGAACAGATCGAATCCAG
42776664 CGAATCTTGTCTTCCTGAAGTTGCAGTGAAGCAGATTGAAGATTTACAA
261 CGAATCTTGTCTTCCTGAAGTTGCAGTGAAGCAGATTGAAGATTTACAA
* * * * * *
42776713 ATCTTATCACCCTAAGCAGTAGGGAAACAGATC-AAAGAAGATGGGCCTTAACCCCCTAAGCAGT
1 ATCTTA-CCCCCTAAGCAGTAGGGAAACAGATCGAAGGCA-ACGAGCTTTAACCCCCTAAGCAGT
*
42776777 AGGGTAACAGGCTGAA
64 AGGGTAACAAGCTGAA
42776793 AATCACAGAT
Statistics
Matches: 364, Mismatches: 23, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
309 303 0.83
310 61 0.17
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.23
Consensus pattern (309 bp):
ATCTTACCCCCTAAGCAGTAGGGAAACAGATCGAAGGCAACGAGCTTTAACCCCCTAAGCAGTAG
GGTAACAAGCTGAAGTTCATAGATCTTATCACCCTAAGCAGTAAGGAAACAGATCGAAAATAATG
AGCTTTAACCCCCTAAGCAATAGGGTAACAAGCCAAATTTACAGACCTTAACCCCCTAAGTAGTA
GGGTAATAGGCTGAAAATTACAGATCTTGTCTCCCTGAAGTTGCAGTGGAACAGATCGAATCCAG
CGAATCTTGTCTTCCTGAAGTTGCAGTGAAGCAGATTGAAGATTTACAA
Found at i:42779287 original size:21 final size:21
Alignment explanation
Indices: 42779263--42779304 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
42779253 ATCATTTTCG
*
42779263 TTATCATTGTCAT-TTTTATTT
1 TTAT-ATTGCCATGTTTTATTT
*
42779284 TTATTTTGCCATGTTTTATTT
1 TTATATTGCCATGTTTTATTT
42779305 ATTTTTTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.17, C:0.10, G:0.07, T:0.67
Consensus pattern (21 bp):
TTATATTGCCATGTTTTATTT
Found at i:42781129 original size:38 final size:38
Alignment explanation
Indices: 42781064--42781155 Score: 123
Period size: 38 Copynumber: 2.4 Consensus size: 38
42781054 CTAAAAATAA
* * *
42781064 TAGACATGCTTAA-ATGTATTCAATTCAATAGTAGCAG
1 TAGACATGCTTAACATGTAATCAATTCAACAGTAACAG
*
42781101 TAGACATGCTTAACATGTAATCAGTTCAACAGTAACAG
1 TAGACATGCTTAACATGTAATCAATTCAACAGTAACAG
* *
42781139 TAGGCATGCTGAACATG
1 TAGACATGCTTAACATG
42781156 CAATTGATAA
Statistics
Matches: 48, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
37 13 0.27
38 35 0.73
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.28
Consensus pattern (38 bp):
TAGACATGCTTAACATGTAATCAATTCAACAGTAACAG
Found at i:42782020 original size:18 final size:18
Alignment explanation
Indices: 42781997--42782036 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
42781987 GGATGATTTG
*
42781997 ATTAGGGAAAGCAAAATA
1 ATTAGGGAAAGAAAAATA
42782015 ATTAGGGAAAGAAAAATA
1 ATTAGGGAAAGAAAAATA
42782033 ATTA
1 ATTA
42782037 TCCACAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.57, C:0.03, G:0.20, T:0.20
Consensus pattern (18 bp):
ATTAGGGAAAGAAAAATA
Found at i:42786897 original size:6 final size:6
Alignment explanation
Indices: 42786886--42786917 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
42786876 ATCCAGAGAG
*
42786886 AAATAA AAATAA AAATCA AAATAA AAATAA AA
1 AAATAA AAATAA AAATAA AAATAA AAATAA AA
42786918 CTAATAATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.81, C:0.03, G:0.00, T:0.16
Consensus pattern (6 bp):
AAATAA
Found at i:42799862 original size:23 final size:23
Alignment explanation
Indices: 42799835--42799905 Score: 73
Period size: 23 Copynumber: 3.3 Consensus size: 23
42799825 AATAGTATGT
42799835 ATTTGTATCATAAAAATATCTTA
1 ATTTGTATCATAAAAATATCTTA
*
42799858 ATTTGTA--AT-GAAAT-T-TTA
1 ATTTGTATCATAAAAATATCTTA
42799876 ATTTGT-TACATAAAAATATCTTA
1 ATTTGTAT-CATAAAAATATCTTA
*
42799899 ATGTGTA
1 ATTTGTA
42799906 ATAATAAGTG
Statistics
Matches: 38, Mismatches: 3, Indels: 13
0.70 0.06 0.24
Matches are distributed among these distances:
18 9 0.24
19 1 0.03
20 6 0.16
21 6 0.16
22 1 0.03
23 15 0.39
ACGTcount: A:0.41, C:0.06, G:0.08, T:0.45
Consensus pattern (23 bp):
ATTTGTATCATAAAAATATCTTA
Found at i:42801078 original size:2 final size:2
Alignment explanation
Indices: 42801071--42801101 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
42801061 TATGTTACTT
42801071 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
42801102 TTGATTAGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:42801873 original size:23 final size:25
Alignment explanation
Indices: 42801828--42801873 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
42801818 AAATTAAAAT
**
42801828 ATATTTTTATATTATTTTTAATTTA
1 ATATTTTTATATTATTTAAAATTTA
42801853 ATATTTTTAT-TTA-TTAAAATT
1 ATATTTTTATATTATTTAAAATT
42801874 ATATATATAG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 6 0.32
24 3 0.16
25 10 0.53
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (25 bp):
ATATTTTTATATTATTTAAAATTTA
Found at i:42801879 original size:23 final size:25
Alignment explanation
Indices: 42801826--42801879 Score: 60
Period size: 23 Copynumber: 2.2 Consensus size: 25
42801816 AAAAATTAAA
**
42801826 ATATATTTTTATATTATTTTTAATT
1 ATATATTTTTATATTATTTAAAATT
42801851 -TAATATTTTTAT-TTA-TTAAAATT
1 AT-ATATTTTTATATTATTTAAAATT
42801874 ATATAT
1 ATATAT
42801880 ATAGTCATCT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
23 10 0.40
24 5 0.20
25 10 0.40
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (25 bp):
ATATATTTTTATATTATTTAAAATT
Found at i:42802909 original size:15 final size:15
Alignment explanation
Indices: 42802889--42802920 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
42802879 ATTTTTTTAC
42802889 ACAATACTTAGAACT
1 ACAATACTTAGAACT
42802904 ACAATACTTAGAACT
1 ACAATACTTAGAACT
42802919 AC
1 AC
42802921 GCATAGCCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.47, C:0.22, G:0.06, T:0.25
Consensus pattern (15 bp):
ACAATACTTAGAACT
Found at i:42808168 original size:9 final size:9
Alignment explanation
Indices: 42808154--42808179 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
42808144 TTGTGTGTTC
42808154 TTTATTTTT
1 TTTATTTTT
42808163 TTTATTTTT
1 TTTATTTTT
42808172 TTTATTTT
1 TTTATTTT
42808180 CACAGAGTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (9 bp):
TTTATTTTT
Found at i:42815516 original size:29 final size:30
Alignment explanation
Indices: 42815475--42815531 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
42815465 GTAATTTGTG
42815475 AAAATCAAAAC-AAATTAAAATTTCATGTCT
1 AAAATCAAAACAAAATTAAAATTT-ATGTCT
*
42815505 AAAATC-ACACAAAATTAAAATTTATGT
1 AAAATCAAAACAAAATTAAAATTTATGT
42815532 ATGACATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 7 0.28
30 18 0.72
ACGTcount: A:0.54, C:0.12, G:0.04, T:0.30
Consensus pattern (30 bp):
AAAATCAAAACAAAATTAAAATTTATGTCT
Found at i:42818928 original size:31 final size:31
Alignment explanation
Indices: 42818893--42818953 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
42818883 AAATGATCAT
*
42818893 TAAATTATTCGAAAGTTTTCATTTAAGTCAC
1 TAAATTATTCAAAAGTTTTCATTTAAGTCAC
*
42818924 TAAATTATTCAAAAGTTTTTATTTAAGTCA
1 TAAATTATTCAAAAGTTTTCATTTAAGTCA
42818954 TTGAACTGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.38, C:0.10, G:0.08, T:0.44
Consensus pattern (31 bp):
TAAATTATTCAAAAGTTTTCATTTAAGTCAC
Found at i:42820780 original size:29 final size:29
Alignment explanation
Indices: 42820738--42820798 Score: 113
Period size: 29 Copynumber: 2.1 Consensus size: 29
42820728 TACAATGTAG
*
42820738 ATTTGTTTACGGATCGAGTTATTTGTTTA
1 ATTTGTTTACGGATCGAGTTATTTATTTA
42820767 ATTTGTTTACGGATCGAGTTATTTATTTA
1 ATTTGTTTACGGATCGAGTTATTTATTTA
42820796 ATT
1 ATT
42820799 CGTGAAATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.23, C:0.07, G:0.18, T:0.52
Consensus pattern (29 bp):
ATTTGTTTACGGATCGAGTTATTTATTTA
Found at i:42824616 original size:235 final size:235
Alignment explanation
Indices: 42824185--42824888 Score: 883
Period size: 235 Copynumber: 2.9 Consensus size: 235
42824175 CACCAATTGA
* ** * *
42824185 TAGATCAGAAATAAACCAATAGCTTATTACCAGACA-AAAATATGCAGAAAGACGTTCAGTAACT
1 TAGATCATAAATAAATAAATAGCTTATTACCAGACATAAAATATCCAGAAAGACATTCAGTAACT
* * * * **
42824249 TGAACACCTCAAAATATTATATTTCATTGTTCAACTTCATTCACTTTCACAATCAAATAAATGGG
66 TCAACACCTTAAAAGATCATATCCCATTGTTC--C-T--TT-ACTTTCACAATCAAATAAATGGG
* * *
42824314 AAAGATGTAAATTTTTTTCCTATGTTCTTCCGACTATTCGTTTTTCTTTTTAAGTAACCCTATCC
125 -AAGATGTAAA-TTTTTTCCTATGTTGTTTCGACTATTCATTTTTCTTTTTAAGT-ACCCTATCC
*
42824379 AACACATTTTCGAAGGAGATATGATCCTCTAACAAAGAGCACCTACCGG
187 AACACATTTTCAAAGGAGATATGATCCTCTAACAAAGAGCACCTACCGG
* * * * *
42824428 TAGATCATAAATAAATGAATAGCTTATTACCAGCCATTAAATATTCAGAAAGA-ATTCAATAACT
1 TAGATCATAAATAAATAAATAGCTTATTACCAGACATAAAATATCCAGAAAGACATTCAGTAACT
*
42824492 TCAACACCTTAATAGATCATATCCCATTGTTCCTTTACTTTCACAATCAAATAAATGGGAAGATG
66 TCAACACCTTAAAAGATCATATCCCATTGTTCCTTTACTTTCACAATCAAATAAATGGGAAGATG
* *
42824557 TAACTTTTTTCCTCTGTTGTTTCGACTATTCATTTTTCTTTTTAAGTATCCCTATCCAACACATT
131 TAAATTTTTTCCTATGTTGTTTCGACTATTCATTTTTCTTTTTAAGTA-CCCTATCCAACACATT
* * * *
42824622 TCCAAAGGAGATAAGATCCTCTAACAAAGGGCACCTATCGG
195 TTCAAAGGAGATATGATCCTCTAACAAAGAGCACCTACCGG
* ** * *
42824663 TAGATCATAAATAAATAAAAAAATTATTACCAAACATCAAATATCCAGAAAGACATTCAGTAACT
1 TAGATCATAAATAAATAAATAGCTTATTACCAGACATAAAATATCCAGAAAGACATTCAGTAACT
* * * * * * *
42824728 TCAACGCCTTAACAGATCATATCCTATTGTTCATTAACTTTCACAATCAAATAAATGAGAAGATA
66 TCAACACCTTAAAAGATCATATCCCATTGTTCCTTTACTTTCACAATCAAATAAATGGGAAGATG
*
42824793 TAAATATTTTTCCTATGTTG-TTCGGACTATTCATTTTTTTTCTTTTTAAGTACCCTTATACAAC
131 TAAAT-TTTTTCCTATGTTGTTTC-GACTATTCA---TTTTTCTTTTTAAGTACCC-TATCCAAC
42824857 ACATTTTCAAAGGAGATATGATCCTCTAACAA
190 ACATTTTCAAAGGAGATATGATCCTCTAACAA
42824889 CCTTCCACAT
Statistics
Matches: 406, Mismatches: 46, Indels: 21
0.86 0.10 0.04
Matches are distributed among these distances:
234 1 0.00
235 136 0.33
236 84 0.21
237 45 0.11
238 2 0.00
239 3 0.01
240 54 0.13
241 1 0.00
243 66 0.16
244 14 0.03
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.34
Consensus pattern (235 bp):
TAGATCATAAATAAATAAATAGCTTATTACCAGACATAAAATATCCAGAAAGACATTCAGTAACT
TCAACACCTTAAAAGATCATATCCCATTGTTCCTTTACTTTCACAATCAAATAAATGGGAAGATG
TAAATTTTTTCCTATGTTGTTTCGACTATTCATTTTTCTTTTTAAGTACCCTATCCAACACATTT
TCAAAGGAGATATGATCCTCTAACAAAGAGCACCTACCGG
Found at i:42825038 original size:63 final size:62
Alignment explanation
Indices: 42824952--42825077 Score: 164
Period size: 63 Copynumber: 2.0 Consensus size: 62
42824942 TGACACTTAG
* * *
42824952 ACTCAAATACGCGAAGAGAACATAAATGTATCAA-CCATTTATACCTATAGGCGACACGCACAC
1 ACTCAAATAAGCAAAAAGAACATAAATGTATCAACCCA--TATACCTATAGGCGACACGCACAC
* * *
42825015 ACTCAAATAAGCAAAAAGAACATAGATGTATCAACTCCATATATCTATAGGCGACACTCACAC
1 ACTCAAATAAGCAAAAAGAACATAAATGTATCAAC-CCATATACCTATAGGCGACACGCACAC
42825078 TCAAATCCGA
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
63 52 0.95
65 3 0.05
ACGTcount: A:0.43, C:0.25, G:0.13, T:0.20
Consensus pattern (62 bp):
ACTCAAATAAGCAAAAAGAACATAAATGTATCAACCCATATACCTATAGGCGACACGCACAC
Found at i:42826961 original size:21 final size:21
Alignment explanation
Indices: 42826935--42826988 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
42826925 AGGCCTTAAT
* *
42826935 AAATAACAAAGTTATAAGCCC
1 AAATAACAAAGATACAAGCCC
* *
42826956 AAATAATAAAAATACAAGCCC
1 AAATAACAAAGATACAAGCCC
42826977 AAA-ATACAAAGA
1 AAATA-ACAAAGA
42826989 AAACCCTAGG
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
20 1 0.04
21 25 0.96
ACGTcount: A:0.61, C:0.17, G:0.07, T:0.15
Consensus pattern (21 bp):
AAATAACAAAGATACAAGCCC
Found at i:42836615 original size:81 final size:81
Alignment explanation
Indices: 42836480--42836724 Score: 472
Period size: 81 Copynumber: 3.0 Consensus size: 81
42836470 TACTCGCGTG
42836480 TTCAAATCAGTCCCCTCCTCCTTTATTTATTCTAAAATTCGCCTCTAAAATTTCGTTTTCAACCC
1 TTCAAATCAGTCCCCTCCTCCTTTATTTATTCTAAAATTCGCCTCTAAAATTTCGTTTTCAACCC
42836545 AATTTTGTCCTTTTTT
66 AATTTTGTCCTTTTTT
42836561 TTCAAATCAGTCCCCTCCTCCTTTATTTATTCTAAAATTCGCCTCTAAAATTTCGTTTTCAACCC
1 TTCAAATCAGTCCCCTCCTCCTTTATTTATTCTAAAATTCGCCTCTAAAATTTCGTTTTCAACCC
42836626 AATTTTGTCCTTTTTT
66 AATTTTGTCCTTTTTT
*
42836642 TTCAAATCAGTCCCCTCCTCCTTTATTTATTCTAAAATTCGCCTCTAAAATTCCGTTTTCAACCC
1 TTCAAATCAGTCCCCTCCTCCTTTATTTATTCTAAAATTCGCCTCTAAAATTTCGTTTTCAACCC
*
42836707 AATTTCGTCCTTTTTT
66 AATTTTGTCCTTTTTT
42836723 TT
1 TT
42836725 ACTCTTTTCT
Statistics
Matches: 162, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
81 162 1.00
ACGTcount: A:0.22, C:0.28, G:0.05, T:0.45
Consensus pattern (81 bp):
TTCAAATCAGTCCCCTCCTCCTTTATTTATTCTAAAATTCGCCTCTAAAATTTCGTTTTCAACCC
AATTTTGTCCTTTTTT
Found at i:42837051 original size:12 final size:12
Alignment explanation
Indices: 42837036--42837061 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
42837026 ACATTTTCTA
42837036 ATACATATATAT
1 ATACATATATAT
42837048 ATACATATATAT
1 ATACATATATAT
42837060 AT
1 AT
42837062 TATGTACATA
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:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (12 bp):
ATACATATATAT
Found at i:42837240 original size:3 final size:3
Alignment explanation
Indices: 42837232--42837363 Score: 67
Period size: 3 Copynumber: 44.3 Consensus size: 3
42837222 AATTTCACGT
* * *
42837232 TTA TTA TTA TTA CTA -TA TTA TCA TTG TTA TTA TTA TT- TTCCA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT--A TTA
* * * * * * *
42837277 TTA TTA ATA CTA ATA TTAA TT- TTC CTA TTA TTA CTA TTA TTA GTA
1 TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * **
42837322 TCA -TA GGTA TTA -TA TTA TTA TTA TCG TTA TTA TTA TTA TTA T
1 TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
42837364 GGTCTTTTAT
Statistics
Matches: 97, Mismatches: 23, Indels: 18
0.70 0.17 0.13
Matches are distributed among these distances:
2 9 0.09
3 81 0.84
4 5 0.05
5 2 0.02
ACGTcount: A:0.32, C:0.08, G:0.04, T:0.57
Consensus pattern (3 bp):
TTA
Found at i:42837376 original size:18 final size:20
Alignment explanation
Indices: 42837329--42837378 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
42837319 GTATCATAGG
*
42837329 TATTATATTATTATTATCGT
1 TATTATATTATTATGATCGT
*
42837349 TATTATTATTATTATGGTC-T
1 TATTA-TATTATTATGATCGT
42837369 T-TTATATTAT
1 TATTATATTAT
42837379 CCTTTTATCA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 6 0.22
19 3 0.11
20 7 0.26
21 11 0.41
ACGTcount: A:0.28, C:0.04, G:0.06, T:0.62
Consensus pattern (20 bp):
TATTATATTATTATGATCGT
Found at i:42837470 original size:4 final size:4
Alignment explanation
Indices: 42837461--42837493 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
42837451 CTATGTTTTA
42837461 TATT TATT TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT TATT TATT T
42837494 GCTTATTTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:42845547 original size:46 final size:46
Alignment explanation
Indices: 42845497--42845672 Score: 207
Period size: 46 Copynumber: 3.8 Consensus size: 46
42845487 TGGTTGAGCA
42845497 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
42845543 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
42845588 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
42845636 CCCGAGCTCATTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
42845673 GCGGGTTACA
Statistics
Matches: 110, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 62 0.56
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:42845653 original size:93 final size:93
Alignment explanation
Indices: 42845494--42845665 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
42845484 GGATGGTTGA
* * *
42845494 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCATTGAGT
42845559 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
42845587 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCATTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCATTGAGT
42845652 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
42845666 CTTATGGGCG
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCATTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:42849439 original size:12 final size:12
Alignment explanation
Indices: 42849422--42849446 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
42849412 GGTGTTCATT
42849422 CGGTTAACCGAC
1 CGGTTAACCGAC
42849434 CGGTTAACCGAC
1 CGGTTAACCGAC
42849446 C
1 C
42849447 CGAAATAGCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.36, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTTAACCGAC
Found at i:42849616 original size:9 final size:9
Alignment explanation
Indices: 42849602--42849662 Score: 68
Period size: 9 Copynumber: 6.8 Consensus size: 9
42849592 TAAGTATAAA
42849602 AATTAACCG
1 AATTAACCG
42849611 AATTAACCG
1 AATTAACCG
* *
42849620 ATTTAACCT
1 AATTAACCG
* *
42849629 ATTTAAACG
1 AATTAACCG
* *
42849638 ATTTAACTG
1 AATTAACCG
42849647 AATTAACCG
1 AATTAACCG
42849656 AATTAAC
1 AATTAAC
42849663 AAAAAAAAAG
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 44 1.00
ACGTcount: A:0.43, C:0.18, G:0.08, T:0.31
Consensus pattern (9 bp):
AATTAACCG
Found at i:42856910 original size:87 final size:86
Alignment explanation
Indices: 42856814--42857290 Score: 286
Period size: 87 Copynumber: 5.4 Consensus size: 86
42856804 AGCCTTATCT
* *
42856814 CCCTAAGCAGTAGGGTAACAGGCTGAGTTTACAGATCTTATCACCCTAAGTAGTAGGGAAACAGA
1 CCCTAAGCAGTAGGGTAACAGGCTGAATTTACAGATCTTA-CACCCTAAGCAGTAGGGAAACAGA
*
42856879 TCAAAGACGATGGGCCTTAAAC
65 TCAAAGATGATGGGCCTTAAAC
* * * *
42856901 CCCTAAGCAGTAGGGTAACAGGCTGAATTTACAGATCTTAACCCCCTAAGCAGTAGGGCAGCAGG
1 CCCTAAGCAGTAGGGTAACAGGCTGAATTTACAGATCTT-ACACCCTAAGCAGTAGGGAAACAGA
** * * ** *
42856966 TTGAAGATTATAGATCTT-ATC
65 TCAAAGATGATGGGCCTTAAAC
* * ** ** ** * *
42856987 TCCCTAAGCAGTAGTGGAGTTGATCA-AC-G-ATGCATGGGCCTTAAACCCCTAAGCAGTAGGGT
1 -CCCTAAGCAGTA--GG-G-T-AACAGGCTGAATTTACAGATCTTACA-CCCTAAGCAGTAGGGA
* * * * ** ** *
42857049 AACAG-GCTGAA-TTTACAGATCTTAACC
59 AACAGATC-AAAGATGATGGGCCTTAAAC
* * * * * * ***
42857076 CCCTAAGCAGTAGGGCAGCAGGTTGAAGATTATAGATCTTATCTCCCTAAGCAGTAGTGG-AGTT
1 CCCTAAGCAGTAGGGTAACAGGCTGAA-TTTACAGATCTTA-CACCCTAAGCAGTAG-GGAAACA
*
42857140 GATCAACGATGCATGGGCCTTAAAC
63 GATCAAAGATG-ATGGGCCTTAAAC
** * * *
42857165 CCCTAAGCAGTAGGGTAACAGGCTGAATTGGCAGATCTTAAACCCCTAAGTAGTAGGGAAATAGA
1 CCCTAAGCAGTAGGGTAACAGGCTGAATTTACAGATCTTACA-CCCTAAGCAGTAGGGAAACAGA
*
42857230 TCGAAGATGATGGGCCTT-AAC
65 TCAAAGATGATGGGCCTTAAAC
* *
42857251 CCCTCAAGCAGTAGGGTAACAGGCTGGAAATTACAAATCT
1 CCCT-AAGCAGTAGGGTAACAGGCT-GAATTTACAGATCT
42857291 ATTCTCTTTG
Statistics
Matches: 293, Mismatches: 74, Indels: 45
0.71 0.18 0.11
Matches are distributed among these distances:
83 3 0.01
85 2 0.01
86 12 0.04
87 134 0.46
88 70 0.24
89 65 0.22
90 2 0.01
91 2 0.01
92 3 0.01
ACGTcount: A:0.32, C:0.21, G:0.25, T:0.23
Consensus pattern (86 bp):
CCCTAAGCAGTAGGGTAACAGGCTGAATTTACAGATCTTACACCCTAAGCAGTAGGGAAACAGAT
CAAAGATGATGGGCCTTAAAC
Found at i:42857213 original size:43 final size:43
Alignment explanation
Indices: 42856814--42857222 Score: 179
Period size: 43 Copynumber: 9.3 Consensus size: 43
42856804 AGCCTTATCT
* * *
42856814 CCCTAAGCAGTAGGGTAACAGGCTGAGTTTACAGATCTT-ATC
1 CCCTAAGCAGTAGGGTAACAGGCTGAATTGACAGATCTTAAAC
* * * * *
42856856 ACCCTAAGTAGTAGGGAAACA-GATCAA-AGAC-GATGGGCCTTAAAC
1 -CCCTAAGCAGTAGGGTAACAGGCTGAATTGACAGAT----CTTAAAC
* *
42856901 CCCTAAGCAGTAGGGTAACAGGCTGAATTTACAGATCTTAACC
1 CCCTAAGCAGTAGGGTAACAGGCTGAATTGACAGATCTTAAAC
* * * * *
42856944 CCCTAAGCAGTAGGGCAGCAGGTTGAAGATT-ATAGATCTT-ATC
1 CCCTAAGCAGTAGGGTAACAGGCTG-A-ATTGACAGATCTTAAAC
* * **
42856987 TCCCTAAGCAGTAGTGGAGTTGATCA-AC-G-A-TG-CATGGGCCTTAAAC
1 -CCCTAAGCAGTA--GG-G-T-AACAGGCTGAATTGACA--GATCTTAAAC
* *
42857033 CCCTAAGCAGTAGGGTAACAGGCTGAATTTACAGATCTTAACC
1 CCCTAAGCAGTAGGGTAACAGGCTGAATTGACAGATCTTAAAC
* * * * *
42857076 CCCTAAGCAGTAGGGCAGCAGGTTGAAGATT-ATAGATCTT-ATC
1 CCCTAAGCAGTAGGGTAACAGGCTG-A-ATTGACAGATCTTAAAC
* * **
42857119 TCCCTAAGCAGTAGTGGAGTTGATCA-AC-G-A-TG-CATGGGCCTTAAAC
1 -CCCTAAGCAGTA--GG-G-T-AACAGGCTGAATTGACA--GATCTTAAAC
*
42857165 CCCTAAGCAGTAGGGTAACAGGCTGAATTGGCAGATCTTAAAC
1 CCCTAAGCAGTAGGGTAACAGGCTGAATTGACAGATCTTAAAC
*
42857208 CCCTAAGTAGTAGGG
1 CCCTAAGCAGTAGGG
42857223 AAATAGATCG
Statistics
Matches: 272, Mismatches: 52, Indels: 84
0.67 0.13 0.21
Matches are distributed among these distances:
40 9 0.03
41 6 0.02
42 7 0.03
43 111 0.41
44 68 0.25
45 48 0.18
46 10 0.04
47 7 0.03
49 6 0.02
ACGTcount: A:0.31, C:0.21, G:0.25, T:0.23
Consensus pattern (43 bp):
CCCTAAGCAGTAGGGTAACAGGCTGAATTGACAGATCTTAAAC
Found at i:42857264 original size:132 final size:132
Alignment explanation
Indices: 42856814--42857222 Score: 644
Period size: 132 Copynumber: 3.1 Consensus size: 132
42856804 AGCCTTATCT
* * * * * * * ***
42856814 CCCTAAGCAGTAGGGTAACAGGCTG-AGTTTACAGATCTTATCACCCTAAGTAGTAG-GGAAACA
1 CCCTAAGCAGTAGGGCAGCAGGTTGAAGATTATAGATCTTATCTCCCTAAGCAGTAGTGG-AGTT
* *
42856877 GATCAAAGACG-ATGGGCCTTAAACCCCTAAGCAGTAGGGTAACAGGCTGAATTTACAGATCTTA
65 GATCAACGATGCATGGGCCTTAAACCCCTAAGCAGTAGGGTAACAGGCTGAATTTACAGATCTTA
42856941 ACC
130 ACC
42856944 CCCTAAGCAGTAGGGCAGCAGGTTGAAGATTATAGATCTTATCTCCCTAAGCAGTAGTGGAGTTG
1 CCCTAAGCAGTAGGGCAGCAGGTTGAAGATTATAGATCTTATCTCCCTAAGCAGTAGTGGAGTTG
42857009 ATCAACGATGCATGGGCCTTAAACCCCTAAGCAGTAGGGTAACAGGCTGAATTTACAGATCTTAA
66 ATCAACGATGCATGGGCCTTAAACCCCTAAGCAGTAGGGTAACAGGCTGAATTTACAGATCTTAA
42857074 CC
131 CC
42857076 CCCTAAGCAGTAGGGCAGCAGGTTGAAGATTATAGATCTTATCTCCCTAAGCAGTAGTGGAGTTG
1 CCCTAAGCAGTAGGGCAGCAGGTTGAAGATTATAGATCTTATCTCCCTAAGCAGTAGTGGAGTTG
**
42857141 ATCAACGATGCATGGGCCTTAAACCCCTAAGCAGTAGGGTAACAGGCTGAATTGGCAGATCTTAA
66 ATCAACGATGCATGGGCCTTAAACCCCTAAGCAGTAGGGTAACAGGCTGAATTTACAGATCTTAA
*
42857206 AC
131 CC
*
42857208 CCCTAAGTAGTAGGG
1 CCCTAAGCAGTAGGG
42857223 AAATAGATCG
Statistics
Matches: 260, Mismatches: 16, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
130 22 0.08
131 37 0.14
132 201 0.77
ACGTcount: A:0.31, C:0.21, G:0.25, T:0.23
Consensus pattern (132 bp):
CCCTAAGCAGTAGGGCAGCAGGTTGAAGATTATAGATCTTATCTCCCTAAGCAGTAGTGGAGTTG
ATCAACGATGCATGGGCCTTAAACCCCTAAGCAGTAGGGTAACAGGCTGAATTTACAGATCTTAA
CC
Found at i:42858179 original size:17 final size:17
Alignment explanation
Indices: 42858150--42858192 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
42858140 GTCTTATTAA
*
42858150 AAATAACATACATATATT
1 AAATAA-ATACATAAATT
42858168 AAATAAATACATAAATT
1 AAATAAATACATAAATT
*
42858185 AAAAAAAT
1 AAATAAAT
42858193 GAGAGAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 17 0.74
18 6 0.26
ACGTcount: A:0.65, C:0.07, G:0.00, T:0.28
Consensus pattern (17 bp):
AAATAAATACATAAATT
Found at i:42859271 original size:3 final size:3
Alignment explanation
Indices: 42859263--42859406 Score: 100
Period size: 3 Copynumber: 48.3 Consensus size: 3
42859253 AATTTCACGT
* * *
42859263 TTA TTA TTA TTA CTA -TA TTA TCA TTG TTA TTA TTA TT- TTCCA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT--A TTA
* * * * * *
42859308 TTA TTA ATA CTA ATA TTAA TT- TTC TTA TTA TTA CTA TTA TTA GTA
1 TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * **
42859353 TCA -TA GGTA TTA -TA TTA TTA TTA TTA TTA TTA TTA TTA TCG TTA
1 TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
42859397 TTA TTA TTA T
1 TTA TTA TTA T
42859407 GGTCTTTTAT
Statistics
Matches: 111, Mismatches: 21, Indels: 18
0.74 0.14 0.12
Matches are distributed among these distances:
2 9 0.08
3 95 0.86
4 5 0.05
5 2 0.02
ACGTcount: A:0.32, C:0.06, G:0.03, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:42864447 original size:30 final size:30
Alignment explanation
Indices: 42864413--42864474 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
42864403 GTACTCTAAA
42864413 TCTCCGAAATTCATATCAAGTCCAAAAAGG
1 TCTCCGAAATTCATATCAAGTCCAAAAAGG
*
42864443 TCTCCGAAATTCATATCAAGTCCAAAAGGG
1 TCTCCGAAATTCATATCAAGTCCAAAAAGG
42864473 TC
1 TC
42864475 CTCTAGAAGT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.37, C:0.24, G:0.15, T:0.24
Consensus pattern (30 bp):
TCTCCGAAATTCATATCAAGTCCAAAAAGG
Found at i:42865266 original size:44 final size:44
Alignment explanation
Indices: 42865164--42865273 Score: 116
Period size: 44 Copynumber: 2.5 Consensus size: 44
42865154 TGGTGATTCT
* * * *
42865164 TATCTCCCTGAAGTTGTAGTGGAGCAAATTGAAGCCACTAATCT
1 TATCTCCCTGAAGTTGAAGTGGAGCAAATTAAAGCCACAAATCC
* * *
42865208 TATCTCCCTAAAGTT-AAGGTGGAGCAGATTAAAGCGACAAATCC
1 TATCTCCCTGAAGTTGAA-GTGGAGCAAATTAAAGCCACAAATCC
*
42865252 TATAC-CCCTGAAGTTGCAGTGG
1 TAT-CTCCCTGAAGTTGAAGTGG
42865274 GACGAATTGA
Statistics
Matches: 54, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
43 1 0.02
44 51 0.94
45 2 0.04
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (44 bp):
TATCTCCCTGAAGTTGAAGTGGAGCAAATTAAAGCCACAAATCC
Found at i:42865398 original size:137 final size:137
Alignment explanation
Indices: 42865161--42865410 Score: 308
Period size: 137 Copynumber: 1.8 Consensus size: 137
42865151 TATTGGTGAT
* * * *
42865161 TCTTATCTCCCTGAAGTTGTAGTGGAGCAAATTGAAGCCACTAATCTTATCTCCCTAAAGTTAAG
1 TCTTATCTCCCTGAAGTTGTAGTGGAGAAAATTAAAGCCACAAATCTTATCTCCCTAAAGTGAAG
* *
42865226 GTGGAGCAGATTAAAGCGACAAATCCTATACCCCTGAAGTTGCAGTGGGACGAATTGAGGTCACC
66 GTGGAGCAGATTAAAGAGACAAATCCTATACCCCTGAAATTGCAGTGGGACGAATTGAGGTCACC
42865291 GTGACAA
131 GTGACAA
* * * *
42865298 TCTTATTTCCCTGAAGTTGTAGTGGA-AAAGATTAAAGTCACAAATTTTATCTCCCTAAAGTGCA
1 TCTTATCTCCCTGAAGTTGTAGTGGAGAAA-ATTAAAGCCACAAATCTTATCTCCCTAAAGTGAA
* * * * **
42865362 -GTGGAG-AGGATTGAAGATAGCGAATCTTATTTCCCTGAAATTGCAGTGG
65 GGTGGAGCA-GATTAAAGAGA-CAAATCCTATACCCCTGAAATTGCAGTGG
42865411 AATAAATTAA
Statistics
Matches: 94, Mismatches: 16, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
135 1 0.01
136 16 0.17
137 77 0.82
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.28
Consensus pattern (137 bp):
TCTTATCTCCCTGAAGTTGTAGTGGAGAAAATTAAAGCCACAAATCTTATCTCCCTAAAGTGAAG
GTGGAGCAGATTAAAGAGACAAATCCTATACCCCTGAAATTGCAGTGGGACGAATTGAGGTCACC
GTGACAA
Found at i:42865551 original size:44 final size:44
Alignment explanation
Indices: 42865483--42865642 Score: 151
Period size: 44 Copynumber: 3.6 Consensus size: 44
42865473 TTTACCATGG
* * * * **
42865483 CAAATCTTAT-TTCTCTGTAGTTGCAGTGGAGTATATTGAAGCCA
1 CAAATCTTATCTCCT-TGAAGTTGCAGTGGAGAAAATTGAAGAAA
* * **
42865527 CAAACCTTATCTCCTTGAAGTTGCAGTGGAGAAAATTGAATATG
1 CAAATCTTATCTCCTTGAAGTTGCAGTGGAGAAAATTGAAGAAA
* * * *
42865571 CAAATCTTATCTCCTTGAAATTGCAGTAGAGCAGATTGAAGATAA
1 CAAATCTTATCTCCTTGAAGTTGCAGTGGAGAAAATTGAAGA-AA
* *
42865616 CAAATCTTATCTCCCTAAAGTTGCAGT
1 CAAATCTTATCTCCTTGAAGTTGCAGT
42865643 AGGGCAGATT
Statistics
Matches: 94, Mismatches: 20, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
44 67 0.71
45 27 0.29
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Consensus pattern (44 bp):
CAAATCTTATCTCCTTGAAGTTGCAGTGGAGAAAATTGAAGAAA
Found at i:42865640 original size:45 final size:44
Alignment explanation
Indices: 42865501--42865657 Score: 163
Period size: 44 Copynumber: 3.5 Consensus size: 44
42865491 ATTTCTCTGT
* * * ** * *
42865501 AGTTGCAGTGGAGTATATTGAAGCCACAAACCTTATCTCCTTGA
1 AGTTGCAGTAGAGCAGATTGAAGATACAAATCTTATCTCCTTAA
* * * * *
42865545 AGTTGCAGTGGAGAAAATTGAATATGCAAATCTTATCTCCTTGAA
1 AGTTGCAGTAGAGCAGATTGAAGATACAAATCTTATCTCCTT-AA
*
42865590 A-TTGCAGTAGAGCAGATTGAAGATAACAAATCTTATCTCCCTAA
1 AGTTGCAGTAGAGCAGATTGAAGAT-ACAAATCTTATCTCCTTAA
*
42865634 AGTTGCAGTAGGGCAGATTGAAGA
1 AGTTGCAGTAGAGCAGATTGAAGA
42865658 ACATGGTTGC
Statistics
Matches: 95, Mismatches: 15, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
44 57 0.60
45 38 0.40
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.28
Consensus pattern (44 bp):
AGTTGCAGTAGAGCAGATTGAAGATACAAATCTTATCTCCTTAA
Found at i:42865863 original size:21 final size:21
Alignment explanation
Indices: 42865812--42865856 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
42865802 GGGCCTTAAT
*
42865812 AAATAACAAAATTACAGACCC
1 AAATAACAAAAATACAGACCC
42865833 AAATAACAAAAATACA-AGCCC
1 AAATAACAAAAATACAGA-CCC
42865854 AAA
1 AAA
42865857 ATACAAAGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 1 0.05
21 21 0.95
ACGTcount: A:0.62, C:0.22, G:0.04, T:0.11
Consensus pattern (21 bp):
AAATAACAAAAATACAGACCC
Found at i:42870815 original size:16 final size:17
Alignment explanation
Indices: 42870794--42870826 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
42870784 CACATTGAAG
42870794 TGTTTT-TTGAAAACCT
1 TGTTTTATTGAAAACCT
42870810 TGTTTTCATTGAAAACC
1 TGTTTT-ATTGAAAACC
42870827 CTTCTTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.27, C:0.15, G:0.12, T:0.45
Consensus pattern (17 bp):
TGTTTTATTGAAAACCT
Found at i:42872167 original size:29 final size:29
Alignment explanation
Indices: 42872093--42872184 Score: 123
Period size: 29 Copynumber: 3.2 Consensus size: 29
42872083 AAGTTTACAT
* *
42872093 ACATGCATATGGCCCACTAGGCCCAAATC
1 ACATTCATATGGCCCATTAGGCCCAAATC
*
42872122 ACATTCATATGGTCCATTAGGCCCAAATC
1 ACATTCATATGGCCCATTAGGCCCAAATC
** *
42872151 ACATTCATATGGCCCATCCGGCCCGAATC
1 ACATTCATATGGCCCATTAGGCCCAAATC
42872180 A-ATTC
1 ACATTC
42872185 CAAGCCATGT
Statistics
Matches: 56, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
28 4 0.07
29 52 0.93
ACGTcount: A:0.29, C:0.33, G:0.15, T:0.23
Consensus pattern (29 bp):
ACATTCATATGGCCCATTAGGCCCAAATC
Found at i:42874910 original size:42 final size:42
Alignment explanation
Indices: 42874851--42874935 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
42874841 CTACAAGAAA
42874851 CACAATGAAATCTGGTCCAAAATATTTGACCTTTTTAATCCT
1 CACAATGAAATCTGGTCCAAAATATTTGACCTTTTTAATCCT
42874893 CACAATGAAATCTGGTCCAAAATATTTGACCTTTTTAATCCT
1 CACAATGAAATCTGGTCCAAAATATTTGACCTTTTTAATCCT
42874935 C
1 C
42874936 TTACTTCTTC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.33, C:0.22, G:0.09, T:0.35
Consensus pattern (42 bp):
CACAATGAAATCTGGTCCAAAATATTTGACCTTTTTAATCCT
Found at i:42876105 original size:60 final size:61
Alignment explanation
Indices: 42876008--42876125 Score: 211
Period size: 60 Copynumber: 2.0 Consensus size: 61
42875998 CTTTCCCTAA
* *
42876008 AAAAATTCCTCCCTTAGTCAAAATAAACTTATTTGCCTCAAAAACAAGTTTGAAACCATAC
1 AAAAATTCCTCCCTTAGTAAAAATAAACTTATCTGCCTCAAAAACAAGTTTGAAACCATAC
42876069 AAAAATTCCTCCCTTAG-AAAAATAAACTTATCTGCCTCAAAAACAAGTTTGAAACCA
1 AAAAATTCCTCCCTTAGTAAAAATAAACTTATCTGCCTCAAAAACAAGTTTGAAACCA
42876126 AACTTATTTA
Statistics
Matches: 55, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
60 38 0.69
61 17 0.31
ACGTcount: A:0.44, C:0.23, G:0.07, T:0.26
Consensus pattern (61 bp):
AAAAATTCCTCCCTTAGTAAAAATAAACTTATCTGCCTCAAAAACAAGTTTGAAACCATAC
Found at i:42877768 original size:18 final size:18
Alignment explanation
Indices: 42877734--42877768 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
42877724 AAATAAACAC
**
42877734 ATAATTATTCATTTAATT
1 ATAATTATTCAAATAATT
42877752 ATAATTATTCAAATAAT
1 ATAATTATTCAAATAAT
42877769 ATTATTTAAA
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:0.46, C:0.06, G:0.00, T:0.49
Consensus pattern (18 bp):
ATAATTATTCAAATAATT
Found at i:42880945 original size:26 final size:25
Alignment explanation
Indices: 42880916--42880965 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
42880906 GATTAGAGTT
* *
42880916 TATATATAATATAAAGTTAATTATTA
1 TATAAATAAT-TAAAATTAATTATTA
*
42880942 TATAAATAATTAAAATTTATTATT
1 TATAAATAATTAAAATTAATTATT
42880966 TAAAACAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 12 0.57
26 9 0.43
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (25 bp):
TATAAATAATTAAAATTAATTATTA
Found at i:42885447 original size:20 final size:21
Alignment explanation
Indices: 42885408--42885447 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
42885398 TAATTTTTTT
*
42885408 TATCATTGAATATTATCAGTGC
1 TATCATTG-ATATAATCAGTGC
42885430 TATCATTG-TATAATCAGT
1 TATCATTGATATAATCAGT
42885448 TGCAACTCAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
22 8 0.47
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.42
Consensus pattern (21 bp):
TATCATTGATATAATCAGTGC
Found at i:42885618 original size:17 final size:18
Alignment explanation
Indices: 42885585--42885620 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
42885575 TTTCATTTTC
*
42885585 TTTTAAAAATATTTTTAT
1 TTTTAAAAATATATTTAT
42885603 TTTTAAAAATA-ATTTAT
1 TTTTAAAAATATATTTAT
42885620 T
1 T
42885621 CAATTGAACC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TTTTAAAAATATATTTAT
Found at i:42888328 original size:30 final size:30
Alignment explanation
Indices: 42888286--42888349 Score: 71
Period size: 30 Copynumber: 2.1 Consensus size: 30
42888276 ATGCGATTAA
42888286 AAATAAGATATAT-AAT-ATGATAATTAAATT
1 AAATAAGATATATCAATAAT-ATAATT-AATT
*
42888316 AAATAA-ACTATATCTATAATATAATTAATT
1 AAATAAGA-TATATCAATAATATAATTAATT
42888346 AAAT
1 AAAT
42888350 TAAGTTAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
29 1 0.03
30 19 0.63
31 8 0.27
32 2 0.07
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (30 bp):
AAATAAGATATATCAATAATATAATTAATT
Found at i:42888918 original size:21 final size:21
Alignment explanation
Indices: 42888894--42888934 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
42888884 TTAATATTTA
42888894 AAATT-TTAAAAATTATTAAAT
1 AAATTATT-AAAATTATTAAAT
*
42888915 AAATTATTAACATTATTAAA
1 AAATTATTAAAATTATTAAA
42888935 AAGTATAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (21 bp):
AAATTATTAAAATTATTAAAT
Found at i:42888942 original size:26 final size:24
Alignment explanation
Indices: 42888913--42888960 Score: 60
Period size: 26 Copynumber: 1.9 Consensus size: 24
42888903 AAATTATTAA
42888913 ATAAATTATTAACATTATTAAAAAGT
1 ATAAATTATTAAC-TT-TTAAAAAGT
* *
42888939 ATAATTTTTTAACTTTTAAAAA
1 ATAAATTATTAACTTTTAAAAA
42888961 AATTAATTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 7 0.35
25 2 0.10
26 11 0.55
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (24 bp):
ATAAATTATTAACTTTTAAAAAGT
Found at i:42891566 original size:28 final size:29
Alignment explanation
Indices: 42891535--42891600 Score: 73
Period size: 28 Copynumber: 2.3 Consensus size: 29
42891525 AATCATAGTT
*
42891535 AAAATTAATTAAAAATAGAAA-TTAGTGG-
1 AAAATTAA-TAAAAATAAAAATTTAGTGGA
* *
42891563 AAAATTCAATAAAATTAAAAATTTATTGGA
1 AAAATT-AATAAAAATAAAAATTTAGTGGA
42891593 AAAATTAA
1 AAAATTAA
42891601 GTACATAAAG
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
28 16 0.50
29 10 0.31
30 6 0.19
ACGTcount: A:0.59, C:0.02, G:0.09, T:0.30
Consensus pattern (29 bp):
AAAATTAATAAAAATAAAAATTTAGTGGA
Found at i:42907830 original size:28 final size:28
Alignment explanation
Indices: 42907790--42907844 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
42907780 AATAAAACTA
42907790 ATGGTACACTAAATCCCTTAACTATCTC
1 ATGGTACACTAAATCCCTTAACTATCTC
42907818 ATGGTACACTAAATCCCTTAACTATCT
1 ATGGTACACTAAATCCCTTAACTATCT
42907845 TCCCAATCCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.33, C:0.27, G:0.07, T:0.33
Consensus pattern (28 bp):
ATGGTACACTAAATCCCTTAACTATCTC
Found at i:42909033 original size:102 final size:102
Alignment explanation
Indices: 42908854--42909057 Score: 354
Period size: 102 Copynumber: 2.0 Consensus size: 102
42908844 CTTGGCAGCT
*
42908854 CATCCAACATAATCATGAGCGAAGGGATTATCTTAGGTAATTTCGAATCAATACAATCACCAATA
1 CATCCAACATAATCATGAGCGAAGGGATTATCTTAGGTAATTTCAAATCAATACAATCACCAATA
42908919 TAATATTCCCTAAGATATATGATATTCCATAATGAGA
66 TAATATTCCCTAAGATATATGATATTCCATAATGAGA
* * *
42908956 CATCCAGCATAATCATGATCGAAGGGATTATCTTGGGTAATTTCAAATCAATACAATCACCAATA
1 CATCCAACATAATCATGAGCGAAGGGATTATCTTAGGTAATTTCAAATCAATACAATCACCAATA
* *
42909021 TAATATTTCCTAAGATATATGATATTTCATAATGAGA
66 TAATATTCCCTAAGATATATGATATTCCATAATGAGA
42909058 TAGATGTCAG
Statistics
Matches: 96, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
102 96 1.00
ACGTcount: A:0.40, C:0.17, G:0.13, T:0.31
Consensus pattern (102 bp):
CATCCAACATAATCATGAGCGAAGGGATTATCTTAGGTAATTTCAAATCAATACAATCACCAATA
TAATATTCCCTAAGATATATGATATTCCATAATGAGA
Found at i:42910293 original size:61 final size:62
Alignment explanation
Indices: 42910211--42910330 Score: 163
Period size: 61 Copynumber: 2.0 Consensus size: 62
42910201 GTGGGAACAA
* ** * *
42910211 AGGACTTGGATAACGGTAGGTTTAATATTTAC-TTTGGCC-TTCAAAGGAGGAATTGGATGGG
1 AGGACTTGCATAAAAGTAGGTTTAATATTTACATTAGGCCTTTAAAAGGA-GAATTGGATGGG
*
42910272 AGGACTTGCATAAAAGTAGGTTTAATATTTACATTAGGCCTTTAAAATGAGAATTGGAT
1 AGGACTTGCATAAAAGTAGGTTTAATATTTACATTAGGCCTTTAAAAGGAGAATTGGAT
42910331 AAGGGTAGGT
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
61 29 0.57
62 15 0.29
63 7 0.14
ACGTcount: A:0.33, C:0.09, G:0.26, T:0.33
Consensus pattern (62 bp):
AGGACTTGCATAAAAGTAGGTTTAATATTTACATTAGGCCTTTAAAAGGAGAATTGGATGGG
Found at i:42911305 original size:31 final size:31
Alignment explanation
Indices: 42911267--42911330 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
42911257 TCTATTTCTA
*
42911267 TTCCATTTCCACAAGTAAACATGGATTCTTT
1 TTCCATTTCCACAAGTAAACATAGATTCTTT
*
42911298 TTCCATTTCCACAAGTAAGCATAGATTCTTT
1 TTCCATTTCCACAAGTAAACATAGATTCTTT
42911329 TT
1 TT
42911331 AACATTAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.28, C:0.22, G:0.09, T:0.41
Consensus pattern (31 bp):
TTCCATTTCCACAAGTAAACATAGATTCTTT
Found at i:42911406 original size:35 final size:35
Alignment explanation
Indices: 42911342--42911410 Score: 93
Period size: 35 Copynumber: 2.0 Consensus size: 35
42911332 ACATTAAATT
* *
42911342 ATTTATTTTATTATTAGTACATGATTCATGATTTA
1 ATTTATTTTATTATGAGTACATGACTCATGATTTA
***
42911377 ATTTATTTTATTATGAGTTTTTGACTCATGATTT
1 ATTTATTTTATTATGAGTACATGACTCATGATTT
42911411 TGATGCTTGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.28, C:0.06, G:0.10, T:0.57
Consensus pattern (35 bp):
ATTTATTTTATTATGAGTACATGACTCATGATTTA
Found at i:42914434 original size:9 final size:9
Alignment explanation
Indices: 42914420--42914478 Score: 75
Period size: 9 Copynumber: 6.6 Consensus size: 9
42914410 ATAAGTATAA
42914420 AATTAACCG
1 AATTAACCG
*
42914429 AATTAACCA
1 AATTAACCG
*
42914438 AATTAATCG
1 AATTAACCG
42914447 AATTAACCG
1 AATTAACCG
*
42914456 AATT-ACCTA
1 AATTAACC-G
42914465 AATTAACCG
1 AATTAACCG
42914474 AATTA
1 AATTA
42914479 TTTGTATAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
8 3 0.07
9 36 0.86
10 3 0.07
ACGTcount: A:0.47, C:0.19, G:0.07, T:0.27
Consensus pattern (9 bp):
AATTAACCG
Found at i:42914450 original size:27 final size:27
Alignment explanation
Indices: 42914420--42914478 Score: 93
Period size: 27 Copynumber: 2.2 Consensus size: 27
42914410 ATAAGTATAA
*
42914420 AATTAACCGAATTAACC-AAATTAATCG
1 AATTAACCGAATT-ACCTAAATTAACCG
42914447 AATTAACCGAATTACCTAAATTAACCG
1 AATTAACCGAATTACCTAAATTAACCG
42914474 AATTA
1 AATTA
42914479 TTTGTATAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
26 3 0.10
27 27 0.90
ACGTcount: A:0.47, C:0.19, G:0.07, T:0.27
Consensus pattern (27 bp):
AATTAACCGAATTACCTAAATTAACCG
Found at i:42914512 original size:5 final size:6
Alignment explanation
Indices: 42914497--42914543 Score: 67
Period size: 6 Copynumber: 7.5 Consensus size: 6
42914487 AAATTATATT
*
42914497 TTTTTA TTTTTA TTTTTA TTTTTA GTTTTAGA TTTTTA TTTTTA TTT
1 TTTTTA TTTTTA TTTTTA TTTTTA -TTTT-TA TTTTTA TTTTTA TTT
42914544 ATTAAATTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
6 28 0.76
7 8 0.22
8 1 0.03
ACGTcount: A:0.17, C:0.00, G:0.04, T:0.79
Consensus pattern (6 bp):
TTTTTA
Found at i:42914518 original size:20 final size:20
Alignment explanation
Indices: 42914497--42914543 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
42914487 AAATTATATT
42914497 TTTTTATTTTT--ATTTTTA
1 TTTTTATTTTTAGATTTTTA
*
42914515 TTTTTAGTTTTAGATTTTTA
1 TTTTTATTTTTAGATTTTTA
42914535 TTTTTATTT
1 TTTTTATTT
42914544 ATTAAATTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 10 0.40
20 15 0.60
ACGTcount: A:0.17, C:0.00, G:0.04, T:0.79
Consensus pattern (20 bp):
TTTTTATTTTTAGATTTTTA
Found at i:42917454 original size:37 final size:37
Alignment explanation
Indices: 42917429--42917509 Score: 96
Period size: 35 Copynumber: 2.2 Consensus size: 37
42917419 AACTTAAACT
*
42917429 TAAAAATATAAAAATAAAATATTTTAATATAATTTAATA
1 TAAAAATA-AAAAA-AAAATATTTTAATATAATTAAATA
* *
42917468 TAAAAATAAAAAAAAAATA--TTAAAATAATTATAT-
1 TAAAAATAAAAAAAAAATATTTTAATATAATTAAATA
42917502 TAAAAATA
1 TAAAAATA
42917510 TTATTAAATT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
34 8 0.21
35 12 0.31
37 6 0.15
38 5 0.13
39 8 0.21
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (37 bp):
TAAAAATAAAAAAAAAATATTTTAATATAATTAAATA
Found at i:42917541 original size:16 final size:17
Alignment explanation
Indices: 42917510--42917542 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
42917500 ATTAAAAATA
42917510 TTATTAAATTATTTTTT
1 TTATTAAATTATTTTTT
*
42917527 TTATTAATTTATTTTT
1 TTATTAAATTATTTTT
42917543 AATAACAATC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (17 bp):
TTATTAAATTATTTTTT
Done.